Psyllid ID: psy12152

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130---
Protein Sequence
MVFHGVYLLYSRNPRYLGRTYIGYTVDPDRRIKQHNKGKDFGGAHKTSNRGPWDMVLIVYGFPNDISALRFEWAWQHPKMSRRLQHVARKKSKETTYTYCLRLLHIMLQTAPWQRLPLTVQWLKPEYQQVLTE
Secondary Structure (PSIPRED)
ccEEEEEEEEEccccccccEEEEEEccHHHHHHHHHccccccccccccccccEEEEEEEEccccHHHHHHHHHHHccccccHHHHHHHHHcccccHHHHHHHHHHHHHccccccccccEEEEEcHHHHHHHHc
Secondary Structure Prediction (SSPRO)
ccEEEEEEEEcccccccccEEEEcccccHHHHHHccccccccccEEccccccEEEEEEEEccccHHHHHHHHHHHHcccHHHHHHHHHHHccccccHHHHHHHHHHHHccccHccccEEEEEEcHHHHHHHcc
Coil and Loop (DISEMBL)
MVFHGVYLlysrnprylgrtyigytvdpdrrikqhnkgkdfggahktsnrgpwDMVLIVYgfpndisaLRFEWAWQHPKMSRRLQHVARKKSKETTYTYCLRLLHIMLqtapwqrlpltvqwlkpeyqQVLTE
Flexible Loop (DISEMBL)
MVFHGVYLLysrnprylGRTYigytvdpdrrikqhnkgkdfggahktsnrgpWDMVLIVYGFPNDISALRFEWAWQHPKMSRRLQHVARKKSKETTYTYCLRLLHIMLQTAPWQRLPLTVQWLKPEYQQVLTE
Low Complexity Region (SEG)
MVFHGVYLLYSRNPRYLGRTYIGYTVDPDRRIKQHNKGKDFGGAHKTSNRGPWDMVLIVYGFPNDISALRFEWAWQHPKMSRRLQHVARKKSKETTYTYCLRLLHIMLQTAPWQRLPLTVQWLKPEYQQVLTE
Disordered region (IsUnstruct)
*VFHGVYLLYSRNPRYLGRTYIGYTVDPDR*******************RGPWDMVLIVYGFPNDISALRFEWAWQHPKMSRRLQHVARKKSKETTYTYCLRLLHIMLQTAPWQRLPLTVQWLKPEY******
Disordered Region (DISOPRED)
MVFHGVYLLYSRNPRYLGRTYIGYTVDPDRRIKQHNKGKDFGGAHKTSNRGPWDMVLIVYGFPNDISALRFEWAWQHPKM*********************RLLHIMLQTAPWQRLPLTVQWLKPEYQQVLTE
Disordered Region (DISEMBL)
MVFHGVYLLYSRNPRYLGRTYIGYTVDPDRRIKQHNKGKDFGGAHKTSNRGPWDMVLIVYGFPNDISALRFEWAWQHPKMSRRLQHVARKKSKETTYTYCLRLLHIMLQTAPWQRLPLTVQWLKPEYQQVLTE
Disordered Region (DISPRO)
MVFHGVYLLYSRNPRYLGRTYIGYTVDPDRRIKQHNKGKDFGGAHKTSNRGPWDMVLIVYGFPNDISALRFEWAWQHPKMSRRLQHVARKKSKETTYTYCLRLLHIMLQTAPWQRLPLTVQWLKPEYQQVLTE
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MVFHGVYLLYSRNPRYLGRTYIGYTVDPDRRIKQHNKGKDFGGAHKTSNRGPWDMVLIVYGFPNDISALRFEWAWQHPKMSRRLQHVARKKSKETTYTYCLRLLHIMLQTAPWQRLPLTVQWLKPEYQQVLTE
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	133	2.2.26 [Sep-21-2011]
Q0IH86	282	Structure-specific endonu	N/A	N/A	0.954	0.450	0.653	6e-46
Q5TXB2	273	Structure-specific endonu	yes	N/A	0.954	0.465	0.613	9e-44
Q5PQP5	271	Structure-specific endonu	yes	N/A	0.977	0.479	0.584	2e-43
Q32PI0	267	Structure-specific endonu	yes	N/A	0.984	0.490	0.580	1e-42
Q8BX32	270	Structure-specific endonu	yes	N/A	0.977	0.481	0.569	1e-42
A7STV9	270	Structure-specific endonu	N/A	N/A	0.947	0.466	0.614	3e-42
Q9BQ83	275	Structure-specific endonu	yes	N/A	0.977	0.472	0.569	3e-41
B5DXG8	291	Structure-specific endonu	yes	N/A	0.969	0.443	0.559	1e-39
B4JGW7	286	Structure-specific endonu	N/A	N/A	0.954	0.444	0.560	1e-39
A8PV03	333	Structure-specific endonu	N/A	N/A	0.947	0.378	0.589	2e-39

>sp|Q0IH86|SLX1_XENLA Structure-specific endonuclease subunit slx1 OS=Xenopus laevis GN=slx1a PE=2 SV=1

 Score =  182 bits (462), Expect = 6e-46,   Method: Compositional matrix adjust.
 Identities = 83/127 (65%), Positives = 105/127 (82%)

Query: 3   FHGVYLLYSRNPRYLGRTYIGYTVDPDRRIKQHNKGKDFGGAHKTSNRGPWDMVLIVYGF 62
           F+GVYLL+  NP+Y GR YIG+TV+P+RRI+QHN GK  GGA KTS RGPWDMVLIV+GF
Sbjct: 8   FYGVYLLFCTNPKYKGRIYIGFTVNPERRIQQHNGGKHKGGAWKTSGRGPWDMVLIVHGF 67

Query: 63  PNDISALRFEWAWQHPKMSRRLQHVARKKSKETTYTYCLRLLHIMLQTAPWQRLPLTVQW 122
           PNDI+ALRFEWAWQHP +SRRL HV RK  K++++ + L +L  ML+ APW RLPLT++W
Sbjct: 68  PNDIAALRFEWAWQHPHVSRRLTHVPRKTKKQSSFDFHLLVLCHMLRVAPWNRLPLTLRW 127

Query: 123 LKPEYQQ 129
           L+ EY++
Sbjct: 128 LRQEYRR 134

Catalytic subunit of the slx1-slx4 structure-specific endonuclease that resolves DNA secondary structures generated during DNA repair and recombination. Has endonuclease activity towards branched DNA substrates, introducing single-strand cuts in duplex DNA close to junctions with ss-DNA.
Xenopus laevis (taxid: 8355)
EC: 3EC: .EC: 6EC: .EC: 1EC: .EC: -

>sp|Q5TXB2|SLX1_ANOGA Structure-specific endonuclease subunit SLX1 homolog OS=Anopheles gambiae GN=AGAP002259 PE=3 SV=3

 Score =  175 bits (443), Expect = 9e-44,   Method: Compositional matrix adjust.
 Identities = 81/132 (61%), Positives = 103/132 (78%), Gaps = 5/132 (3%)

Query: 3   FHGVYLLYSR--NPRYLGRTYIGYTVDPDRRIKQHNKGKDFGGAHKTSNRGPWDMVLIVY 60
           F+GVYLL S+  NP++ GRTYIGYTVDP+RRIKQHN+G+D GGA +TSNRGPW MVLIV+
Sbjct: 10  FYGVYLLVSKSPNPKFAGRTYIGYTVDPNRRIKQHNRGEDAGGARRTSNRGPWTMVLIVH 69

Query: 61  GFPNDISALRFEWAWQHPKMSRRLQ---HVARKKSKETTYTYCLRLLHIMLQTAPWQRLP 117
           GFPN+ISALRFEWAWQ P++SRRL+    + +K  KE+ + Y  R+L  ML+  PW RLP
Sbjct: 70  GFPNNISALRFEWAWQQPRVSRRLKQMPELQKKLRKESNFEYNFRILTEMLRMGPWNRLP 129

Query: 118 LTVQWLKPEYQQ 129
           L V+W   E+ +
Sbjct: 130 LVVRWFADEFHR 141

Catalytic subunit of a heterodimeric structure-specific endonuclease that resolves DNA secondary structures generated during DNA repair and recombination. Has endonuclease activity towards branched DNA substrates, introducing single-strand cuts in duplex DNA close to junctions with ss-DNA.

Anopheles gambiae (taxid: 7165)

EC: 3

EC: .

EC: 6

EC: .

EC: 1

EC: .

EC: -

>sp|Q5PQP5|SLX1_RAT Structure-specific endonuclease subunit SLX1 OS=Rattus norvegicus GN=Slx1b PE=2 SV=1

 Score =  173 bits (439), Expect = 2e-43,   Method: Compositional matrix adjust.
 Identities = 76/130 (58%), Positives = 102/130 (78%)

Query: 3   FHGVYLLYSRNPRYLGRTYIGYTVDPDRRIKQHNKGKDFGGAHKTSNRGPWDMVLIVYGF 62
           F GVYLLY +NPR+ GR Y+G+TV+P RR++QHN G+  GGA +TS RGPWDMVLI++GF
Sbjct: 10  FFGVYLLYCQNPRHRGRVYVGFTVNPARRVRQHNAGRKKGGAWRTSGRGPWDMVLILHGF 69

Query: 63  PNDISALRFEWAWQHPKMSRRLQHVARKKSKETTYTYCLRLLHIMLQTAPWQRLPLTVQW 122
           P+ ++ALRFEWAWQHP+ SRRL HV  +   E ++T+ LR+L  ML+  PW RLPLTV+W
Sbjct: 70  PSAVAALRFEWAWQHPQASRRLTHVGPRLRSEASFTFHLRVLAHMLRVPPWVRLPLTVRW 129

Query: 123 LKPEYQQVLT 132
           L+P+++  L 
Sbjct: 130 LRPDFRHELC 139

Catalytic subunit of the SLX1-SLX4 structure-specific endonuclease that resolves DNA secondary structures generated during DNA repair and recombination. Has endonuclease activity towards branched DNA substrates, introducing single-strand cuts in duplex DNA close to junctions with ss-DNA. Has a preference for 5'-flap structures, and promotes symmetrical cleavage of static and migrating Holliday junctions (HJs). Resolves HJs by generating two pairs of ligatable, nicked duplex products.

Rattus norvegicus (taxid: 10116)

EC: 3

EC: .

EC: 6

EC: .

EC: 1

EC: .

EC: -

>sp|Q32PI0|SLX1_BOVIN Structure-specific endonuclease subunit SLX1 OS=Bos taurus GN=SLX1A PE=2 SV=1

 Score =  171 bits (433), Expect = 1e-42,   Method: Compositional matrix adjust.
 Identities = 76/131 (58%), Positives = 101/131 (77%)

Query: 2   VFHGVYLLYSRNPRYLGRTYIGYTVDPDRRIKQHNKGKDFGGAHKTSNRGPWDMVLIVYG 61
            F GVYLLY  NPR+ GR Y+G+TV+P RR++QHN G+  GGA +TS RGPW+MVLIV+G
Sbjct: 5   CFFGVYLLYCLNPRHRGRVYVGFTVNPARRVQQHNGGRKKGGAWRTSGRGPWEMVLIVHG 64

Query: 62  FPNDISALRFEWAWQHPKMSRRLQHVARKKSKETTYTYCLRLLHIMLQTAPWQRLPLTVQ 121
           FP+ ++ALRFEWAWQHP+ SRRL HV R+   E T+ + LR+L  ML+  PW RLPLT++
Sbjct: 65  FPSAVAALRFEWAWQHPQASRRLTHVGRRLRGEATFAFHLRVLAHMLRAPPWVRLPLTLR 124

Query: 122 WLKPEYQQVLT 132
           WL+ +++Q L 
Sbjct: 125 WLRADFRQDLC 135

Catalytic subunit of the SLX1-SLX4 structure-specific endonuclease that resolves DNA secondary structures generated during DNA repair and recombination. Has endonuclease activity towards branched DNA substrates, introducing single-strand cuts in duplex DNA close to junctions with ss-DNA. Has a preference for 5'-flap structures, and promotes symmetrical cleavage of static and migrating Holliday junctions (HJs). Resolves HJs by generating two pairs of ligatable, nicked duplex products.

Bos taurus (taxid: 9913)

EC: 3

EC: .

EC: 6

EC: .

EC: 1

EC: .

EC: -

>sp|Q8BX32|SLX1_MOUSE Structure-specific endonuclease subunit SLX1 OS=Mus musculus GN=Slx1b PE=2 SV=1

 Score =  171 bits (433), Expect = 1e-42,   Method: Compositional matrix adjust.
 Identities = 74/130 (56%), Positives = 100/130 (76%)

Query: 3   FHGVYLLYSRNPRYLGRTYIGYTVDPDRRIKQHNKGKDFGGAHKTSNRGPWDMVLIVYGF 62
           F GVYLLY +NPR+ GR Y+G+TV+P RR++QHN G+  GGA +TS RGPWDMVLI++GF
Sbjct: 10  FFGVYLLYCQNPRHRGRVYVGFTVNPARRVRQHNAGRKKGGAWRTSGRGPWDMVLIIHGF 69

Query: 63  PNDISALRFEWAWQHPKMSRRLQHVARKKSKETTYTYCLRLLHIMLQTAPWQRLPLTVQW 122
           P+ ++ALRFEWAWQHP+ SRRL HV  +   E  + + LR+L  ML+  PW RLPLT++W
Sbjct: 70  PSAVAALRFEWAWQHPQASRRLTHVGPRLRSEAAFAFHLRVLAHMLRVPPWVRLPLTLRW 129

Query: 123 LKPEYQQVLT 132
           L+P+++  L 
Sbjct: 130 LRPDFRHELC 139

Catalytic subunit of the SLX1-SLX4 structure-specific endonuclease that resolves DNA secondary structures generated during DNA repair and recombination. Has endonuclease activity towards branched DNA substrates, introducing single-strand cuts in duplex DNA close to junctions with ss-DNA. Has a preference for 5'-flap structures, and promotes symmetrical cleavage of static and migrating Holliday junctions (HJs). Resolves HJs by generating two pairs of ligatable, nicked duplex products.

Mus musculus (taxid: 10090)

EC: 3

EC: .

EC: 6

EC: .

EC: 1

EC: .

EC: -

>sp|A7STV9|SLX1_NEMVE Structure-specific endonuclease subunit SLX1 homolog OS=Nematostella vectensis GN=v1g174298 PE=3 SV=1

 Score =  169 bits (429), Expect = 3e-42,   Method: Compositional matrix adjust.
 Identities = 78/127 (61%), Positives = 98/127 (77%), Gaps = 1/127 (0%)

Query: 3   FHGVYLLYSRNPRYLGRTYIGYTVDPDRRIKQHNKGKDFGGAHKTSNRGPWDMVLIVYGF 62
           FHGVYLLY  NP++ G TYIGYTV+P+RRIKQHN G D GGA+KTS + PW+M+LIV+GF
Sbjct: 10  FHGVYLLYCVNPKFKGHTYIGYTVNPNRRIKQHNGGVDKGGAYKTSRKKPWNMILIVHGF 69

Query: 63  PNDISALRFEWAWQHPKMSRRLQHVA-RKKSKETTYTYCLRLLHIMLQTAPWQRLPLTVQ 121
           PNDI AL+FEWAWQ P +SRRL+  A +KK +E    YC R+L  +L+  PW RLPL ++
Sbjct: 70  PNDIIALQFEWAWQKPTVSRRLKSAATKKKPRERPVQYCFRILSELLRVGPWNRLPLHIR 129

Query: 122 WLKPEYQ 128
           WL  EY+
Sbjct: 130 WLMREYE 136

Catalytic subunit of a heterodimeric structure-specific endonuclease that resolves DNA secondary structures generated during DNA repair and recombination. Has endonuclease activity towards branched DNA substrates, introducing single-strand cuts in duplex DNA close to junctions with ss-DNA.

Nematostella vectensis (taxid: 45351)

EC: 3

EC: .

EC: 6

EC: .

EC: 1

EC: .

EC: -

>sp|Q9BQ83|SLX1_HUMAN Structure-specific endonuclease subunit SLX1 OS=Homo sapiens GN=SLX1A PE=1 SV=1

 Score =  166 bits (421), Expect = 3e-41,   Method: Compositional matrix adjust.
 Identities = 74/130 (56%), Positives = 98/130 (75%)

Query: 3   FHGVYLLYSRNPRYLGRTYIGYTVDPDRRIKQHNKGKDFGGAHKTSNRGPWDMVLIVYGF 62
           F GVYLLY  NPRY GR Y+G+TV+  RR++QHN G+  GGA +TS RGPW+MVL+V+GF
Sbjct: 13  FFGVYLLYCLNPRYRGRVYVGFTVNTARRVQQHNGGRKKGGAWRTSGRGPWEMVLVVHGF 72

Query: 63  PNDISALRFEWAWQHPKMSRRLQHVARKKSKETTYTYCLRLLHIMLQTAPWQRLPLTVQW 122
           P+ ++ALRFEWAWQHP  SRRL HV  +   ET + + LR+L  ML+  PW RLPLT++W
Sbjct: 73  PSSVAALRFEWAWQHPHASRRLAHVGPRLRGETAFAFHLRVLAHMLRAPPWARLPLTLRW 132

Query: 123 LKPEYQQVLT 132
           ++P+ +Q L 
Sbjct: 133 VRPDLRQDLC 142

Catalytic subunit of the SLX1-SLX4 structure-specific endonuclease that resolves DNA secondary structures generated during DNA repair and recombination. Has endonuclease activity towards branched DNA substrates, introducing single-strand cuts in duplex DNA close to junctions with ss-DNA. Has a preference for 5'-flap structures, and promotes symmetrical cleavage of static and migrating Holliday junctions (HJs). Resolves HJs by generating two pairs of ligatable, nicked duplex products.

Homo sapiens (taxid: 9606)

EC: 3

EC: .

EC: 6

EC: .

EC: 1

EC: .

EC: -

>sp|B5DXG8|SLX1_DROPS Structure-specific endonuclease subunit SLX1 homolog OS=Drosophila pseudoobscura pseudoobscura GN=slx1 PE=3 SV=1

 Score =  161 bits (407), Expect = 1e-39,   Method: Compositional matrix adjust.
 Identities = 75/134 (55%), Positives = 100/134 (74%), Gaps = 5/134 (3%)

Query: 3   FHGVYLLYSR--NPRYLGRTYIGYTVDPDRRIKQHNKGKDFGGAHKTSNRGPWDMVLIVY 60
           F+GVYLL S+  + RY  + Y+G+TV+P RRIKQHN+G DFGGA KTS +GPW MV+IV+
Sbjct: 16  FYGVYLLCSQSLDSRYRAKCYVGFTVNPKRRIKQHNRGCDFGGAKKTSKKGPWQMVMIVH 75

Query: 61  GFPNDISALRFEWAWQHPKMSRRLQ---HVARKKSKETTYTYCLRLLHIMLQTAPWQRLP 117
           GFPN+ISAL+FEWAWQ P +S RL+    + RKK KET + Y  R+L+ ML   PW RL 
Sbjct: 76  GFPNNISALQFEWAWQQPTLSTRLKIFPDLKRKKPKETHFDYNFRILNRMLSVGPWHRLA 135

Query: 118 LTVQWLKPEYQQVL 131
           LT++WL+ +Y++  
Sbjct: 136 LTIRWLETDYERAF 149

Catalytic subunit of a heterodimeric structure-specific endonuclease that resolves DNA secondary structures generated during DNA repair and recombination. Has endonuclease activity towards branched DNA substrates, introducing single-strand cuts in duplex DNA close to junctions with ss-DNA.

Drosophila pseudoobscura pseudoobscura (taxid: 46245)

EC: 3

EC: .

EC: 6

EC: .

EC: 1

EC: .

EC: -

>sp|B4JGW7|SLX1_DROGR Structure-specific endonuclease subunit SLX1 homolog OS=Drosophila grimshawi GN=slx1 PE=3 SV=1

 Score =  160 bits (406), Expect = 1e-39,   Method: Compositional matrix adjust.
 Identities = 74/132 (56%), Positives = 101/132 (76%), Gaps = 5/132 (3%)

Query: 3   FHGVYLLYSR--NPRYLGRTYIGYTVDPDRRIKQHNKGKDFGGAHKTSNRGPWDMVLIVY 60
           F+GVYLL S+  + RY G+ Y+G+TV+P RRI QHN+G DFGGAHKTS +GPW MV+IV+
Sbjct: 17  FYGVYLLCSQSLDARYRGKCYVGFTVNPKRRIGQHNRGCDFGGAHKTSRKGPWQMVMIVH 76

Query: 61  GFPNDISALRFEWAWQHPKMSRRLQ---HVARKKSKETTYTYCLRLLHIMLQTAPWQRLP 117
           GFPN+I+AL+FEWAWQ P +S RL+    + RK+ +ET + Y  R+++ ML   PW RLP
Sbjct: 77  GFPNNIAALQFEWAWQQPALSTRLKCYPELRRKQPRETHFDYNFRIVNRMLGIGPWHRLP 136

Query: 118 LTVQWLKPEYQQ 129
           LTV+WL+ E ++
Sbjct: 137 LTVRWLESECER 148

Catalytic subunit of a heterodimeric structure-specific endonuclease that resolves DNA secondary structures generated during DNA repair and recombination. Has endonuclease activity towards branched DNA substrates, introducing single-strand cuts in duplex DNA close to junctions with ss-DNA.

Drosophila grimshawi (taxid: 7222)

EC: 3

EC: .

EC: 6

EC: .

EC: 1

EC: .

EC: -

>sp|A8PV03|SLX1_BRUMA Structure-specific endonuclease subunit SLX1 homolog OS=Brugia malayi GN=Bm1_35165 PE=3 SV=1

 Score =  160 bits (406), Expect = 2e-39,   Method: Compositional matrix adjust.
 Identities = 76/129 (58%), Positives = 99/129 (76%), Gaps = 3/129 (2%)

Query: 3   FHGVYLLYSRNP-RYL-GRTYIGYTVDPDRRIKQHNKGKDFGGAHKTSNRGPWDMVLIVY 60
           F GVY L SR+P RY   R YIGYTV+P+RRI+QHN GK+FGGA KT +RGPWDMV I++
Sbjct: 69  FFGVYCLLSRSPNRYFKNRCYIGYTVNPNRRIRQHNAGKEFGGAKKTDHRGPWDMVCIIH 128

Query: 61  GFPNDISALRFEWAWQHPKMSRRLQHVA-RKKSKETTYTYCLRLLHIMLQTAPWQRLPLT 119
           GFPN +SALRFEWAWQ+P+ SRRL+ +  +K++ ET + + LR+   ML + PW+RL LT
Sbjct: 129 GFPNSVSALRFEWAWQNPEKSRRLRLLNLKKRTSETAFGFRLRIACHMLNSDPWRRLSLT 188

Query: 120 VQWLKPEYQ 128
            +WL PE +
Sbjct: 189 FRWLLPELE 197

Catalytic subunit of a heterodimeric structure-specific endonuclease that resolves DNA secondary structures generated during DNA repair and recombination. Has endonuclease activity towards branched DNA substrates, introducing single-strand cuts in duplex DNA close to junctions with ss-DNA.

Brugia malayi (taxid: 6279)

EC: 3

EC: .

EC: 6

EC: .

EC: 1

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	133
156554325	269	PREDICTED: structure-specific endonuclea	0.939	0.464	0.712	3e-49
307205095	270	GIY-YIG domain-containing protein 1 [Har	0.954	0.470	0.669	1e-46
91084301	241	PREDICTED: similar to GIY-YIG domain con	1.0	0.551	0.646	1e-46
291231787	274	PREDICTED: GIY-YIG domain-containing pro	0.947	0.459	0.650	4e-46
307183277	264	GIY-YIG domain-containing protein 1 [Cam	0.954	0.481	0.661	1e-45
332372746	252	unknown [Dendroctonus ponderosae]	0.924	0.488	0.674	1e-45
198434798	310	PREDICTED: similar to GIY-YIG domain con	0.977	0.419	0.630	1e-44
327280622	270	PREDICTED: structure-specific endonuclea	0.954	0.470	0.677	1e-44
321464388	260	hypothetical protein DAPPUDRAFT_306753 [	0.947	0.484	0.637	3e-44
147901424	282	structure-specific endonuclease subunit	0.954	0.450	0.653	4e-44

>gi|156554325|ref|XP_001602968.1| PREDICTED: structure-specific endonuclease subunit slx1-like [Nasonia vitripennis]

 Score =  199 bits (506), Expect = 3e-49,   Method: Compositional matrix adjust.
 Identities = 89/125 (71%), Positives = 104/125 (83%)

Query: 3   FHGVYLLYSRNPRYLGRTYIGYTVDPDRRIKQHNKGKDFGGAHKTSNRGPWDMVLIVYGF 62
           F GVYLLY +N +Y GRTYIGYTVDP RRIKQHN GKDFGGA +TSNRGPW+MVLIV+GF
Sbjct: 11  FFGVYLLYCKNVKYKGRTYIGYTVDPKRRIKQHNAGKDFGGAWRTSNRGPWEMVLIVHGF 70

Query: 63  PNDISALRFEWAWQHPKMSRRLQHVARKKSKETTYTYCLRLLHIMLQTAPWQRLPLTVQW 122
           PN  SALRFEWAWQHP++SRRL+HV RKKS++ ++ YCL +L  ML   PW RLPLTV+W
Sbjct: 71  PNSTSALRFEWAWQHPELSRRLRHVPRKKSRQKSFDYCLTVLSAMLHVGPWSRLPLTVRW 130

Query: 123 LKPEY 127
           L  E+
Sbjct: 131 LDDEF 135

Source: Nasonia vitripennis

Species: Nasonia vitripennis

Genus: Nasonia

Family: Pteromalidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|307205095|gb|EFN83566.1| GIY-YIG domain-containing protein 1 [Harpegnathos saltator]

 Score =  191 bits (484), Expect = 1e-46,   Method: Compositional matrix adjust.
 Identities = 85/127 (66%), Positives = 101/127 (79%)

Query: 3   FHGVYLLYSRNPRYLGRTYIGYTVDPDRRIKQHNKGKDFGGAHKTSNRGPWDMVLIVYGF 62
           F GVYLLY  NP+Y GRTYIGYTVDP RRIKQHN GK +GGA KTSNRGPWDMVLIV+GF
Sbjct: 11  FFGVYLLYCINPKYKGRTYIGYTVDPKRRIKQHNAGKKYGGAWKTSNRGPWDMVLIVHGF 70

Query: 63  PNDISALRFEWAWQHPKMSRRLQHVARKKSKETTYTYCLRLLHIMLQTAPWQRLPLTVQW 122
           PN  SALRFEWAWQHP +SRRL+H+ +KKS +  + +CL +L  ML+  PW  LPLT++W
Sbjct: 71  PNSTSALRFEWAWQHPHVSRRLKHIPKKKSSQKAFEFCLTVLSEMLKVGPWCCLPLTIRW 130

Query: 123 LKPEYQQ 129
           L  E+ +
Sbjct: 131 LDYEFSK 137

Source: Harpegnathos saltator

Species: Harpegnathos saltator

Genus: Harpegnathos

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|91084301|ref|XP_971859.1| PREDICTED: similar to GIY-YIG domain containing 2 [Tribolium castaneum] gi|270008803|gb|EFA05251.1| hypothetical protein TcasGA2_TC015403 [Tribolium castaneum]

 Score =  190 bits (483), Expect = 1e-46,   Method: Compositional matrix adjust.
 Identities = 86/133 (64%), Positives = 107/133 (80%)

Query: 1   MVFHGVYLLYSRNPRYLGRTYIGYTVDPDRRIKQHNKGKDFGGAHKTSNRGPWDMVLIVY 60
           M F GVYLLY  NP+Y GR YIGYTVDP+RRIKQHN+GK  GGA KTS +GPW MVLI++
Sbjct: 1   MHFFGVYLLYCTNPKYRGRVYIGYTVDPNRRIKQHNRGKQHGGAWKTSQKGPWSMVLIIH 60

Query: 61  GFPNDISALRFEWAWQHPKMSRRLQHVARKKSKETTYTYCLRLLHIMLQTAPWQRLPLTV 120
           GFPN+ISALRFEWAWQHP +SRRL HV++K +KE  Y + +R+L  MLQ  PW+RLPLT+
Sbjct: 61  GFPNNISALRFEWAWQHPHVSRRLAHVSKKNTKEKVYDFTIRVLSEMLQVGPWKRLPLTI 120

Query: 121 QWLKPEYQQVLTE 133
           +WL  E+++ L +
Sbjct: 121 RWLNDEFRRDLEK 133

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|291231787|ref|XP_002735844.1| PREDICTED: GIY-YIG domain-containing protein, putative-like [Saccoglossus kowalevskii]

 Score =  189 bits (479), Expect = 4e-46,   Method: Compositional matrix adjust.
 Identities = 82/126 (65%), Positives = 100/126 (79%)

Query: 3   FHGVYLLYSRNPRYLGRTYIGYTVDPDRRIKQHNKGKDFGGAHKTSNRGPWDMVLIVYGF 62
           F G YLLY  NP+Y GRTYIGYTVDP RRI QHNKG  FGGA +TS +GPW+MVLI++GF
Sbjct: 8   FFGCYLLYCTNPKYKGRTYIGYTVDPRRRITQHNKGSKFGGACRTSGKGPWEMVLIIHGF 67

Query: 63  PNDISALRFEWAWQHPKMSRRLQHVARKKSKETTYTYCLRLLHIMLQTAPWQRLPLTVQW 122
           PN+ISALRFEWAWQHPK SRRL H+  K+ KE  + +C R+L  ML+  PW RLPLT++W
Sbjct: 68  PNNISALRFEWAWQHPKRSRRLCHLTGKQKKENQFQFCFRILSNMLRVGPWNRLPLTIRW 127

Query: 123 LKPEYQ 128
           LK +++
Sbjct: 128 LKQDFK 133

Source: Saccoglossus kowalevskii

Species: Saccoglossus kowalevskii

Genus: Saccoglossus

Family: Harrimaniidae

Class: Enteropneusta

Phylum: Hemichordata

Superkingdom: Eukaryota

>gi|307183277|gb|EFN70146.1| GIY-YIG domain-containing protein 1 [Camponotus floridanus]

 Score =  187 bits (475), Expect = 1e-45,   Method: Compositional matrix adjust.
 Identities = 84/127 (66%), Positives = 100/127 (78%)

Query: 3   FHGVYLLYSRNPRYLGRTYIGYTVDPDRRIKQHNKGKDFGGAHKTSNRGPWDMVLIVYGF 62
           F GVYLLY  NP+Y GRTYIGYTVDP RRIKQHN GK  GGA KTS +GPW+M+LIVYGF
Sbjct: 12  FFGVYLLYCTNPKYRGRTYIGYTVDPRRRIKQHNAGKKHGGAWKTSQKGPWNMILIVYGF 71

Query: 63  PNDISALRFEWAWQHPKMSRRLQHVARKKSKETTYTYCLRLLHIMLQTAPWQRLPLTVQW 122
           PN  SALRFEWAWQHP  SRRL+H+ +KKS +T + +CL +L  ML+  PW RLPLT++W
Sbjct: 72  PNSTSALRFEWAWQHPHESRRLKHIPKKKSTQTKFDFCLIILSEMLKVGPWHRLPLTLRW 131

Query: 123 LKPEYQQ 129
           L  E+ +
Sbjct: 132 LDYEFSK 138

Source: Camponotus floridanus

Species: Camponotus floridanus

Genus: Camponotus

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|332372746|gb|AEE61515.1| unknown [Dendroctonus ponderosae]

 Score =  187 bits (475), Expect = 1e-45,   Method: Compositional matrix adjust.
 Identities = 83/123 (67%), Positives = 102/123 (82%)

Query: 2   VFHGVYLLYSRNPRYLGRTYIGYTVDPDRRIKQHNKGKDFGGAHKTSNRGPWDMVLIVYG 61
            FHGVYLLY  NP+YLGR YIGYTVDP+RRI +HNKGK +GGA++TS RGPW MVLIV+G
Sbjct: 4   AFHGVYLLYCENPKYLGRCYIGYTVDPNRRIVKHNKGKQYGGAYRTSQRGPWTMVLIVHG 63

Query: 62  FPNDISALRFEWAWQHPKMSRRLQHVARKKSKETTYTYCLRLLHIMLQTAPWQRLPLTVQ 121
           F ++ISAL+FEWAWQH + SRRLQHV +KKS+E ++ + L +L  MLQ  PWQRLPLT++
Sbjct: 64  FLDEISALKFEWAWQHSQKSRRLQHVGKKKSREKSFDFYLTVLGQMLQVGPWQRLPLTIR 123

Query: 122 WLK 124
           WL 
Sbjct: 124 WLN 126

Source: Dendroctonus ponderosae

Species: Dendroctonus ponderosae

Genus: Dendroctonus

Family: Curculionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|198434798|ref|XP_002127269.1| PREDICTED: similar to GIY-YIG domain containing 2 [Ciona intestinalis]

 Score =  184 bits (466), Expect = 1e-44,   Method: Compositional matrix adjust.
 Identities = 82/130 (63%), Positives = 102/130 (78%)

Query: 3   FHGVYLLYSRNPRYLGRTYIGYTVDPDRRIKQHNKGKDFGGAHKTSNRGPWDMVLIVYGF 62
           F G YLLYSRN +Y GRTYIG+TV+P+RRI QHN G   GGA++TS RGPWDM +IV+GF
Sbjct: 8   FFGCYLLYSRNSKYKGRTYIGFTVNPERRISQHNAGASKGGAYRTSGRGPWDMTMIVHGF 67

Query: 63  PNDISALRFEWAWQHPKMSRRLQHVARKKSKETTYTYCLRLLHIMLQTAPWQRLPLTVQW 122
           P+DI+ALRFEWAWQ+PK SRRL+H+  K  KE+ + Y +R++  ML   PW++LPLTVQW
Sbjct: 68  PSDIAALRFEWAWQNPKRSRRLKHITCKTRKESMFQYRIRIMSNMLTQTPWKKLPLTVQW 127

Query: 123 LKPEYQQVLT 132
           LK EY   LT
Sbjct: 128 LKQEYAVDLT 137

Source: Ciona intestinalis

Species: Ciona intestinalis

Genus: Ciona

Family: Cionidae

Order: Enterogona

Class: Ascidiacea

Phylum: Chordata

Superkingdom: Eukaryota

>gi|327280622|ref|XP_003225051.1| PREDICTED: structure-specific endonuclease subunit slx1-like [Anolis carolinensis]

 Score =  184 bits (466), Expect = 1e-44,   Method: Compositional matrix adjust.
 Identities = 86/127 (67%), Positives = 102/127 (80%)

Query: 3   FHGVYLLYSRNPRYLGRTYIGYTVDPDRRIKQHNKGKDFGGAHKTSNRGPWDMVLIVYGF 62
           F GVYLLY  NPRY GR YIG+TV+P+RRI QHN GK  GGA KTS RGPWDMVLIV+GF
Sbjct: 8   FFGVYLLYCTNPRYHGRIYIGFTVNPERRIIQHNAGKRRGGAWKTSGRGPWDMVLIVHGF 67

Query: 63  PNDISALRFEWAWQHPKMSRRLQHVARKKSKETTYTYCLRLLHIMLQTAPWQRLPLTVQW 122
           P+D++ALRFEWAWQHP  SRRL HV R+ S+E  + + LR+L  ML+TAPW RLPLT++W
Sbjct: 68  PSDVAALRFEWAWQHPHSSRRLNHVTRRTSRERQFDFHLRVLAHMLRTAPWCRLPLTIRW 127

Query: 123 LKPEYQQ 129
           LK EY +
Sbjct: 128 LKQEYAR 134

Source: Anolis carolinensis

Species: Anolis carolinensis

Genus: Anolis

Family: Iguanidae

Order: Squamata

Phylum: Chordata

Superkingdom: Eukaryota

>gi|321464388|gb|EFX75396.1| hypothetical protein DAPPUDRAFT_306753 [Daphnia pulex]

 Score =  183 bits (464), Expect = 3e-44,   Method: Compositional matrix adjust.
 Identities = 81/127 (63%), Positives = 106/127 (83%), Gaps = 1/127 (0%)

Query: 3   FHGVYLLYSRNPRYLGRTYIGYTVDPDRRIKQHNKGKDFGGAHKTSNRGPWDMVLIVYGF 62
           F+GVYLL+  NP+YLGRTYIGYTV+P+RRI+QHNKG   GGA+KTSN+GPW+M LI++GF
Sbjct: 9   FYGVYLLFCENPKYLGRTYIGYTVNPNRRIQQHNKGVRSGGAYKTSNKGPWEMCLIIHGF 68

Query: 63  PNDISALRFEWAWQHPKMSRRLQH-VARKKSKETTYTYCLRLLHIMLQTAPWQRLPLTVQ 121
           PNDIS LRFEWAWQHP+ SRRL+  + RK++KE ++ + +R+L  ML+  PW RL LT+Q
Sbjct: 69  PNDISGLRFEWAWQHPEKSRRLRKLIERKRTKENSFQHKIRILSHMLRIGPWNRLALTIQ 128

Query: 122 WLKPEYQ 128
           WL P+Y+
Sbjct: 129 WLVPKYR 135

Source: Daphnia pulex

Species: Daphnia pulex

Genus: Daphnia

Family: Daphniidae

Order: Diplostraca

Class: Branchiopoda

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|147901424|ref|NP_001090376.1| structure-specific endonuclease subunit slx1 [Xenopus laevis] gi|123911486|sp|Q0IH86.1|SLX1_XENLA RecName: Full=Structure-specific endonuclease subunit slx1; AltName: Full=GIY-YIG domain-containing protein 1 gi|114108307|gb|AAI23265.1| Giyd1 protein [Xenopus laevis]

 Score =  182 bits (462), Expect = 4e-44,   Method: Compositional matrix adjust.
 Identities = 83/127 (65%), Positives = 105/127 (82%)

Query: 3   FHGVYLLYSRNPRYLGRTYIGYTVDPDRRIKQHNKGKDFGGAHKTSNRGPWDMVLIVYGF 62
           F+GVYLL+  NP+Y GR YIG+TV+P+RRI+QHN GK  GGA KTS RGPWDMVLIV+GF
Sbjct: 8   FYGVYLLFCTNPKYKGRIYIGFTVNPERRIQQHNGGKHKGGAWKTSGRGPWDMVLIVHGF 67

Query: 63  PNDISALRFEWAWQHPKMSRRLQHVARKKSKETTYTYCLRLLHIMLQTAPWQRLPLTVQW 122
           PNDI+ALRFEWAWQHP +SRRL HV RK  K++++ + L +L  ML+ APW RLPLT++W
Sbjct: 68  PNDIAALRFEWAWQHPHVSRRLTHVPRKTKKQSSFDFHLLVLCHMLRVAPWNRLPLTLRW 127

Query: 123 LKPEYQQ 129
           L+ EY++
Sbjct: 128 LRQEYRR 134

Source: Xenopus laevis

Species: Xenopus laevis

Genus: Xenopus

Family: Pipidae

Order: Anura

Class: Amphibia

Phylum: Chordata

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	133
RGD|1311568	271	Slx1b "SLX1 structure-specific	0.969	0.476	0.589	5.2e-42
MGI|MGI:1915220	270	Slx1b "SLX1 structure-specific	0.969	0.477	0.573	2.8e-41
UNIPROTKB|Q32PI0	267	SLX1A "Structure-specific endo	0.969	0.483	0.589	4.6e-41
UNIPROTKB|Q9BQ83	275	SLX1A "Structure-specific endo	0.969	0.469	0.573	4.2e-40
FB|FBgn0037263	297	slx1 "nuclease slx1" [Drosophi	0.954	0.427	0.560	2.4e-37
WB|WBGene00018909	443	slx-1 [Caenorhabditis elegans	0.909	0.273	0.532	6e-32
TAIR|locus:2065775	368	AT2G30350 [Arabidopsis thalian	0.932	0.336	0.448	1.9e-26
POMBASE|SPAP27G11.15	271	slx1 "structure-specific endon	0.902	0.442	0.429	3.8e-23
CGD|CAL0003774	286	orf19.972 [Candida albicans (t	0.962	0.447	0.388	1.7e-18
ASPGD|ASPL0000015291	409	AN8212 [Emericella nidulans (t	0.571	0.185	0.506	3.5e-17

RGD|1311568 Slx1b "SLX1 structure-specific endonuclease subunit homolog B (S. cerevisiae)" [Rattus norvegicus (taxid:10116)]

 Score = 445 (161.7 bits), Expect = 5.2e-42, P = 5.2e-42
 Identities = 76/129 (58%), Positives = 102/129 (79%)

Query:     3 FHGVYLLYSRNPRYLGRTYIGYTVDPDRRIKQHNKGKDFGGAHKTSNRGPWDMVLIVYGF 62
             F GVYLLY +NPR+ GR Y+G+TV+P RR++QHN G+  GGA +TS RGPWDMVLI++GF
Sbjct:    10 FFGVYLLYCQNPRHRGRVYVGFTVNPARRVRQHNAGRKKGGAWRTSGRGPWDMVLILHGF 69

Query:    63 PNDISALRFEWAWQHPKMSRRLQHVARKKSKETTYTYCLRLLHIMLQTAPWQRLPLTVQW 122
             P+ ++ALRFEWAWQHP+ SRRL HV  +   E ++T+ LR+L  ML+  PW RLPLTV+W
Sbjct:    70 PSAVAALRFEWAWQHPQASRRLTHVGPRLRSEASFTFHLRVLAHMLRVPPWVRLPLTVRW 129

Query:   123 LKPEYQQVL 131
             L+P+++  L
Sbjct:   130 LRPDFRHEL 138

GO:0000724 "double-strand break repair via homologous recombination" evidence=ISO

GO:0004519 "endonuclease activity" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0006281 "DNA repair" evidence=IEA;ISO

GO:0006310 "DNA recombination" evidence=IEA

GO:0008821 "crossover junction endodeoxyribonuclease activity" evidence=ISO

GO:0010792 "DNA double-strand break processing involved in repair via single-strand annealing" evidence=ISO

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

GO:0033557 "Slx1-Slx4 complex" evidence=ISO

GO:0046872 "metal ion binding" evidence=IEA

MGI|MGI:1915220 Slx1b "SLX1 structure-specific endonuclease subunit homolog B (S. cerevisiae)" [Mus musculus (taxid:10090)]

 Score = 438 (159.2 bits), Expect = 2.8e-41, P = 2.8e-41
 Identities = 74/129 (57%), Positives = 100/129 (77%)

Query:     3 FHGVYLLYSRNPRYLGRTYIGYTVDPDRRIKQHNKGKDFGGAHKTSNRGPWDMVLIVYGF 62
             F GVYLLY +NPR+ GR Y+G+TV+P RR++QHN G+  GGA +TS RGPWDMVLI++GF
Sbjct:    10 FFGVYLLYCQNPRHRGRVYVGFTVNPARRVRQHNAGRKKGGAWRTSGRGPWDMVLIIHGF 69

Query:    63 PNDISALRFEWAWQHPKMSRRLQHVARKKSKETTYTYCLRLLHIMLQTAPWQRLPLTVQW 122
             P+ ++ALRFEWAWQHP+ SRRL HV  +   E  + + LR+L  ML+  PW RLPLT++W
Sbjct:    70 PSAVAALRFEWAWQHPQASRRLTHVGPRLRSEAAFAFHLRVLAHMLRVPPWVRLPLTLRW 129

Query:   123 LKPEYQQVL 131
             L+P+++  L
Sbjct:   130 LRPDFRHEL 138

GO:0000724 "double-strand break repair via homologous recombination" evidence=ISO

GO:0004518 "nuclease activity" evidence=IEA

GO:0004519 "endonuclease activity" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0006281 "DNA repair" evidence=ISO

GO:0006310 "DNA recombination" evidence=IEA

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

GO:0008821 "crossover junction endodeoxyribonuclease activity" evidence=ISO

GO:0010792 "DNA double-strand break processing involved in repair via single-strand annealing" evidence=ISO

GO:0016787 "hydrolase activity" evidence=IEA

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

GO:0033557 "Slx1-Slx4 complex" evidence=ISO

GO:0046872 "metal ion binding" evidence=IEA

UNIPROTKB|Q32PI0 SLX1A "Structure-specific endonuclease subunit SLX1" [Bos taurus (taxid:9913)]

 Score = 436 (158.5 bits), Expect = 4.6e-41, P = 4.6e-41
 Identities = 76/129 (58%), Positives = 101/129 (78%)

Query:     3 FHGVYLLYSRNPRYLGRTYIGYTVDPDRRIKQHNKGKDFGGAHKTSNRGPWDMVLIVYGF 62
             F GVYLLY  NPR+ GR Y+G+TV+P RR++QHN G+  GGA +TS RGPW+MVLIV+GF
Sbjct:     6 FFGVYLLYCLNPRHRGRVYVGFTVNPARRVQQHNGGRKKGGAWRTSGRGPWEMVLIVHGF 65

Query:    63 PNDISALRFEWAWQHPKMSRRLQHVARKKSKETTYTYCLRLLHIMLQTAPWQRLPLTVQW 122
             P+ ++ALRFEWAWQHP+ SRRL HV R+   E T+ + LR+L  ML+  PW RLPLT++W
Sbjct:    66 PSAVAALRFEWAWQHPQASRRLTHVGRRLRGEATFAFHLRVLAHMLRAPPWVRLPLTLRW 125

Query:   123 LKPEYQQVL 131
             L+ +++Q L
Sbjct:   126 LRADFRQDL 134

GO:0005634 "nucleus" evidence=IEA

GO:0046872 "metal ion binding" evidence=IEA

GO:0006310 "DNA recombination" evidence=IEA

GO:0006281 "DNA repair" evidence=IEA

GO:0004519 "endonuclease activity" evidence=IEA

UNIPROTKB|Q9BQ83 SLX1A "Structure-specific endonuclease subunit SLX1" [Homo sapiens (taxid:9606)]

 Score = 427 (155.4 bits), Expect = 4.2e-40, P = 4.2e-40
 Identities = 74/129 (57%), Positives = 98/129 (75%)

Query:     3 FHGVYLLYSRNPRYLGRTYIGYTVDPDRRIKQHNKGKDFGGAHKTSNRGPWDMVLIVYGF 62
             F GVYLLY  NPRY GR Y+G+TV+  RR++QHN G+  GGA +TS RGPW+MVL+V+GF
Sbjct:    13 FFGVYLLYCLNPRYRGRVYVGFTVNTARRVQQHNGGRKKGGAWRTSGRGPWEMVLVVHGF 72

Query:    63 PNDISALRFEWAWQHPKMSRRLQHVARKKSKETTYTYCLRLLHIMLQTAPWQRLPLTVQW 122
             P+ ++ALRFEWAWQHP  SRRL HV  +   ET + + LR+L  ML+  PW RLPLT++W
Sbjct:    73 PSSVAALRFEWAWQHPHASRRLAHVGPRLRGETAFAFHLRVLAHMLRAPPWARLPLTLRW 132

Query:   123 LKPEYQQVL 131
             ++P+ +Q L
Sbjct:   133 VRPDLRQDL 141

GO:0046872 "metal ion binding" evidence=IEA

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

GO:0008821 "crossover junction endodeoxyribonuclease activity" evidence=IDA

GO:0010792 "DNA double-strand break processing involved in repair via single-strand annealing" evidence=IMP

GO:0006281 "DNA repair" evidence=IMP

GO:0005515 "protein binding" evidence=IPI

GO:0033557 "Slx1-Slx4 complex" evidence=IDA

GO:0000724 "double-strand break repair via homologous recombination" evidence=IMP

FB|FBgn0037263 slx1 "nuclease slx1" [Drosophila melanogaster (taxid:7227)]

 Score = 401 (146.2 bits), Expect = 2.4e-37, P = 2.4e-37
 Identities = 74/132 (56%), Positives = 98/132 (74%)

Query:     3 FHGVYLLYSRN--PRYLGRTYIGYTVDPDRRIKQHNKGKDFGGAHKTSNRGPWDMVLIVY 60
             F+GVYLL S++  PRY G+ Y+G+TV+P RRI+QHN G DFGGA KTS +GPW MV+IV+
Sbjct:    23 FYGVYLLCSQSLDPRYRGKCYVGFTVNPKRRIRQHNLGCDFGGARKTSRKGPWLMVMIVH 82

Query:    61 GFPNDISALRFEWAWQHPKMSRRLQ---HVARKKSKETTYTYCLRLLHIMLQTAPWQRLP 117
             GFPN+  AL+FEWAWQ P +S RL+    + RK  +ET + Y  R+L  ML   PW RLP
Sbjct:    83 GFPNNTVALQFEWAWQQPSLSTRLKMYPELKRKLPRETFFDYNFRILSNMLGVGPWNRLP 142

Query:   118 LTVQWLKPEYQQ 129
             LTV+WL+ +Y++
Sbjct:   143 LTVRWLETDYER 154

GO:0033557 "Slx1-Slx4 complex" evidence=ISS

GO:0004520 "endodeoxyribonuclease activity" evidence=ISS

GO:0005515 "protein binding" evidence=IPI

GO:0007095 "mitotic G2 DNA damage checkpoint" evidence=IMP

WB|WBGene00018909 slx-1 [Caenorhabditis elegans (taxid:6239)]

 Score = 350 (128.3 bits), Expect = 6.0e-32, P = 6.0e-32
 Identities = 66/124 (53%), Positives = 89/124 (71%)

Query:     3 FHGVYLLYSRNPR--YLGRTYIGYTVDPDRRIKQHNKGKDFGGAHKTSNRGPWDMVLIVY 60
             F+GVY L SR+ R  Y  R YIGYTVDP+RRI QHN G+D GGA KT +RGPWDMV +V+
Sbjct:   172 FYGVYCLISRSDRPCYKNRCYIGYTVDPNRRIMQHNGGRDKGGAKKTDSRGPWDMVCVVH 231

Query:    61 GFPNDISALRFEWAWQHPKMSRRLQHVA-RKKSKETTYTYCLRLLHIMLQTAPWQRLPLT 119
             GFPN ++AL FEWAWQ+P +S+ L+    RK+ KET + + LR+   ++ ++ + R  LT
Sbjct:   232 GFPNHVAALHFEWAWQNPLVSKSLKEKQLRKERKETPFAFQLRIACELMNSSAFCRFALT 291

Query:   120 VQWL 123
              +WL
Sbjct:   292 FRWL 295

GO:0008270 "zinc ion binding" evidence=IEA

GO:0009792 "embryo development ending in birth or egg hatching" evidence=IMP

GO:0040007 "growth" evidence=IMP

GO:0002119 "nematode larval development" evidence=IMP

TAIR|locus:2065775 AT2G30350 [Arabidopsis thaliana (taxid:3702)]

 Score = 298 (110.0 bits), Expect = 1.9e-26, P = 1.9e-26
 Identities = 56/125 (44%), Positives = 80/125 (64%)

Query:     3 FHGVYLLYSRNPRYLGRTYIGYTVDPDRRIKQHNKGKDFGGAHKTSNRGPWDMVLIVYGF 62
             F   YLL S +PR+ G+TYIG+TV+P RRI+QHN G+   GA +T  + PW+MVL +YGF
Sbjct:    27 FFACYLLTSLSPRHKGQTYIGFTVNPRRRIRQHN-GEITSGAWRTKKKRPWEMVLCIYGF 85

Query:    63 PNDISALRFEWAWQHPKMSRRLQHVARKKSKETTYTYCLRLLHIMLQTAPWQRLPLTVQW 122
             P ++SAL+FEWAWQHP+ S  ++  A      +     ++L++ ML    W  L LTV +
Sbjct:    86 PTNVSALQFEWAWQHPRESVAVREAAAAFKSFSGVASKIKLVYTMLNLPAWNSLNLTVNY 145

Query:   123 LKPEY 127
                +Y
Sbjct:   146 FSSKY 150

GO:0004518 "nuclease activity" evidence=IEA;ISS

GO:0005622 "intracellular" evidence=IEA;ISS

GO:0005634 "nucleus" evidence=ISM

GO:0006281 "DNA repair" evidence=IEA;ISS

POMBASE|SPAP27G11.15 slx1 "structure-specific endonuclease catalytic subunit" [Schizosaccharomyces pombe (taxid:4896)]

 Score = 267 (99.0 bits), Expect = 3.8e-23, P = 3.8e-23
 Identities = 52/121 (42%), Positives = 74/121 (61%)

Query:     3 FHGVYLLYSRNPRYLGRTYIGYTVDPDRRIKQHNKGKDFGGAHKTSNRGPWDMVLIVYGF 62
             F+  YLL S   +  G  YIG T DP RR++QHN G+  GGA KT +  PW +  +VYGF
Sbjct:     6 FYCCYLLKSNRTQSSGAVYIGSTPDPPRRLRQHN-GEIVGGASKTKHGRPWSISCLVYGF 64

Query:    63 PNDISALRFEWAWQHPKMSRRLQHVARKKSKETTYTYCLRLLHIMLQTAPWQRLPLTVQW 122
             PN +SAL+FEW WQ+  +SR  +    +  K+ T  YCL+ L  ++ +  W+R PL + +
Sbjct:    65 PNKVSALKFEWNWQNLGISRYTKDCDFRSKKQKTIMYCLKGLKHLVDSDTWRRWPLNITF 124

Query:   123 L 123
             L
Sbjct:   125 L 125

GO:0000724 "double-strand break repair via homologous recombination" evidence=IGI

GO:0005515 "protein binding" evidence=IPI

GO:0016894 "endonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 3'-phosphomonoesters" evidence=IDA

GO:0030874 "nucleolar chromatin" evidence=IDA

GO:0030875 "rDNA protrusion" evidence=NAS

GO:0033557 "Slx1-Slx4 complex" evidence=IDA

GO:0034065 "replication fork processing at rDNA locus" evidence=TAS

GO:0043007 "maintenance of rDNA" evidence=IMP

GO:0045458 "recombination within rDNA repeats" evidence=IDA

GO:0046872 "metal ion binding" evidence=IEA

CGD|CAL0003774 orf19.972 [Candida albicans (taxid:5476)]

 Score = 223 (83.6 bits), Expect = 1.7e-18, P = 1.7e-18
 Identities = 52/134 (38%), Positives = 77/134 (57%)

Query:     3 FHGVYLLYS-RNPRYLGRTYIGYTVDPDRRIKQHNKGKDFGGAHKTSNRG--PWDMVLIV 59
             F+GVY+L S   PR    TYIG T DP RR++QHN     GGA++T   G  PW+MV++V
Sbjct:    16 FYGVYILKSIPKPR---STYIGSTPDPKRRLRQHNGDLKVGGAYRTKKDGSRPWNMVVLV 72

Query:    60 YGFPNDISALRFEWAWQHPKMSRRLQHVARKKSKETTYTYCLRLLHIMLQTAPWQRLPLT 119
             YGFP+ I+AL+FE + QH   +R + + AR  S     +   +L +I L T  + ++ L 
Sbjct:    73 YGFPSRIAALQFEHSLQHAYQTRHIDNDARITSSSRQSSIHSKLANIRLLTTSFDKMSLK 132

Query:   120 VQWLKPEYQQVLTE 133
             +     E  ++  E
Sbjct:   133 IAIFDEEVYRMWIE 146

GO:0033557 "Slx1-Slx4 complex" evidence=IEA

GO:0006261 "DNA-dependent DNA replication" evidence=IEA

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

ASPGD|ASPL0000015291 AN8212 [Emericella nidulans (taxid:162425)]

 Score = 198 (74.8 bits), Expect = 3.5e-17, Sum P(2) = 3.5e-17
 Identities = 40/79 (50%), Positives = 53/79 (67%)

Query:    21 YIGYTVDPDRRIKQHNKGKDFGGAHKTSN--RGPWDMVLIVYGFPNDISALRFEWAWQHP 78
             YIG T DP RR+ QHN G   GGA +T++  R PW+MV++V GF + I+AL+FEWAWQHP
Sbjct:    11 YIGSTPDPARRLAQHN-GLCKGGARRTADEKRRPWEMVMVVEGFMSKIAALQFEWAWQHP 69

Query:    79 KMSRRLQHVARKKSKETTY 97
               +R L   A  K +  T+
Sbjct:    70 AATRHLTADAPSKEQSKTH 88

GO:0006281 "DNA repair" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

GO:0033557 "Slx1-Slx4 complex" evidence=IEA

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

GO:0006261 "DNA-dependent DNA replication" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
P91351	SLX1_CAEEL	3, ., 6, ., 1, ., -	0.5322	0.9097	0.2731	yes	N/A
Q5PQP5	SLX1_RAT	3, ., 6, ., 1, ., -	0.5846	0.9774	0.4797	yes	N/A
Q5TXB2	SLX1_ANOGA	3, ., 6, ., 1, ., -	0.6136	0.9548	0.4652	yes	N/A
Q5AU18	SLX1_EMENI	3, ., 6, ., 1, ., -	0.5063	0.5714	0.1858	yes	N/A
Q32PI0	SLX1_BOVIN	3, ., 6, ., 1, ., -	0.5801	0.9849	0.4906	yes	N/A
B5DXG8	SLX1_DROPS	3, ., 6, ., 1, ., -	0.5597	0.9699	0.4432	yes	N/A
Q9BQ83	SLX1_HUMAN	3, ., 6, ., 1, ., -	0.5692	0.9774	0.4727	yes	N/A
Q8BX32	SLX1_MOUSE	3, ., 6, ., 1, ., -	0.5692	0.9774	0.4814	yes	N/A
Q9VN41	SLX1_DROME	3, ., 6, ., 1, ., -	0.5441	0.9849	0.4410	yes	N/A

EC Number Prediction by EFICAz Software

Prediction Level	EC number	Confidence of Prediction
3rd Layer	3.6.1	0.691

---

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	133
cd10455	76	cd10455, GIY-YIG_SLX1, Catalytic GIY-YIG domain of	5e-46
cd10449	67	cd10449, GIY-YIG_SLX1_like, Catalytic GIY-YIG doma	1e-17
pfam01541	76	pfam01541, GIY-YIG, GIY-YIG catalytic domain	1e-09
cd10456	68	cd10456, GIY-YIG_UPF0213, The GIY-YIG domain of un	3e-09
COG2827	95	COG2827, COG2827, Predicted endonuclease containin	8e-08
PRK00329	86	PRK00329, PRK00329, GIY-YIG nuclease superfamily p	1e-07
smart00465	84	smart00465, GIYc, GIY-YIG type nucleases (URI doma	2e-07
cd10447	80	cd10447, GIY-YIG_unchar_2, GIY-YIG domain of uncha	4e-04
cd00719	69	cd00719, GIY-YIG_SF, GIY-YIG nuclease domain super	5e-04

>gnl|CDD|198402 cd10455, GIY-YIG_SLX1, Catalytic GIY-YIG domain of yeast structure-specific endonuclease subunit SLX1 and its eukaryotic homologs

 Score =  143 bits (363), Expect = 5e-46
 Identities = 51/76 (67%), Positives = 65/76 (85%), Gaps = 1/76 (1%)

Query: 3  FHGVYLLYSRNPRYLGRTYIGYTVDPDRRIKQHNKGKDFGGAHKTSNRGPWDMVLIVYGF 62
          F+GVYLL S NP+Y GRTYIG+TV+P RR++QHN G+  GGA KTS + PW+MVLIV+GF
Sbjct: 1  FYGVYLLRSLNPKYKGRTYIGFTVNPPRRLRQHN-GELKGGAKKTSRKRPWEMVLIVHGF 59

Query: 63 PNDISALRFEWAWQHP 78
          P+ ++AL+FEWAWQHP
Sbjct: 60 PSKVAALQFEWAWQHP 75

Structure-specific endonuclease subunit SLX1 is a highly conserved protein from yeast to human, with an N-terminal GIY-YIG endonuclease domain and a C-terminal PHD-type zinc finger postulated to mediate protein-protein or protein-DNA interaction. SLX1 forms active heterodimeric complexes with its SLX4 partner, which has additional roles in the DNA damage response that are distinct from the function of the heterodimeric SLX1-SLX4 nuclease. In yeast, the SLX1-SLX4 complex functions as a 5' flap endonuclease that maintains ribosomal DNA copy number, where SLX1 and SLX4 are shown to be catalytic and regulatory subunits, respectively. This endonuclease introduces single-strand cuts in duplex DNA on the 3' side of junctions with single-strand DNA. In addition to 5' flap endonuclease activity, human SLX1-SLX4 complex has been identified as a Holliday junction resolvase that promotes symmetrical cleavage of static and migrating Holliday junctions. SLX1 also associates with MUS81, EME1, C20orf94, PLK1, and ERCC1. Some eukaryotic SLX1 homologs lack the zinc finger domain, but possess intrinsically unstructured extensions of unknown function. These unstructured segments might be involved in interactions with other proteins. Length = 76

>gnl|CDD|198396 cd10449, GIY-YIG_SLX1_like, Catalytic GIY-YIG domain of yeast structure-specific endonuclease subunit SLX1 and its homologs

 Score = 71.1 bits (175), Expect = 1e-17
 Identities = 30/74 (40%), Positives = 40/74 (54%), Gaps = 8/74 (10%)

Query: 6  VYLLYSRNPRYLGRTYIGYTVDPDRRIKQHNKGKDFGGAHKTSNRGPWDMVLIVYGFPND 65
          VY+LYS     L R YIGYT D +RR++QHN GK    +  TS   PW++V     F + 
Sbjct: 2  VYILYSE---KLDRYYIGYTSDLERRLEQHNSGK----SKFTSKYRPWELVYSEA-FESK 53

Query: 66 ISALRFEWAWQHPK 79
            AL+ E   +  K
Sbjct: 54 SEALKREKYLKSGK 67

Structure-specific endonuclease subunit SLX1 is a highly conserved protein from yeast to human, with an N-terminal GIY-YIG endonuclease domain and a C-terminal PHD-type zinc finger postulated to mediate protein-protein or protein-DNA interaction. SLX1 forms active heterodimeric complexes with its SLX4 partner, which has additional roles in the DNA damage response that are distinct from the function of the heterodimeric SLX1-SLX4 nuclease. In yeast, the SLX1-SLX4 complex functions as a 5' flap endonuclease that maintains ribosomal DNA copy number, where SLX1 and SLX4 are shown to be catalytic and regulatory subunits, respectively. This endonuclease introduces single-strand cuts in duplex DNA on the 3' side of junctions with single-strand DNA. In addition to 5' flap endonuclease activity, human SLX1-SLX4 complex has been identified as a Holliday junction resolvase that promotes symmetrical cleavage of static and migrating Holliday junctions. SLX1 also associates with MUS81, EME1, C20orf94, PLK1, and ERCC1. Some eukaryotic SLX1 homologs lack the zinc finger domain, but possess intrinsically unstructured extensions of unknown function. These unstructured segments might be involved in interactions with other proteins. Length = 67

>gnl|CDD|216559 pfam01541, GIY-YIG, GIY-YIG catalytic domain

 Score = 50.8 bits (122), Expect = 1e-09
 Identities = 20/74 (27%), Positives = 30/74 (40%), Gaps = 9/74 (12%)

Query: 3  FHGVYLLYSRNPRYLGRTYIGYTVDPDRRIKQHNKGKDFGGAHKTSNRGPWDMVLIVYGF 62
            GVY++ +++ + L   Y+G T +  RR+KQH  GK          R      LI+   
Sbjct: 1  KPGVYIITNKDNKVL---YVGSTKNLKRRLKQHFSGKG-----AKKTRNKKPFELIILEE 52

Query: 63 PNDIS-ALRFEWAW 75
                AL  E   
Sbjct: 53 FPTKEEALELEKYL 66

This domain called GIY-YIG is found in the amino terminal region of excinuclease abc subunit c (uvrC), bacteriophage T4 endonucleases segA, segB, segC, segD and segE; it is also found in putative endonucleases encoded by group I introns of fungi and phage. The structure of I-TevI a GIY-YIG endonuclease, reveals a novel alpha/beta-fold with a central three-stranded antiparallel beta-sheet flanked by three helices. The most conserved and putative catalytic residues are located on a shallow, concave surface and include a metal coordination site. Length = 76

>gnl|CDD|198403 cd10456, GIY-YIG_UPF0213, The GIY-YIG domain of uncharacterized protein family UPF0213 related to structure-specific endonuclease SLX1

 Score = 49.3 bits (119), Expect = 3e-09
 Identities = 26/71 (36%), Positives = 35/71 (49%), Gaps = 12/71 (16%)

Query: 6  VYLLYSRNPRYLGRTYIGYTVDPDRRIKQHNKGKDFGGAHKTSNRGPWDMVLIVY--GFP 63
          VY+L   +    G  Y G T D +RR+ +HN GK   GA  T  R P   V +VY   F 
Sbjct: 3  VYILRCAD----GSLYTGITTDLERRLAEHNSGK---GAKYTRGRRP---VKLVYSEEFD 52

Query: 64 NDISALRFEWA 74
          +   AL+ E+ 
Sbjct: 53 DRSEALKREYR 63

This family contains a group of uncharacterized proteins found mainly in bacteria and several in dsDNA viruses. Although their function roles have not been recognized, these proteins show significant sequence similarities with the N-terminal GIY-YIG endonuclease domain of structure-specific endonuclease subunit SLX1, which binds another structure-specific endonuclease subunit SLX4 to form an active heterodimeric SLX1-SLX4 complex. This complex functions as a 5' flap endonuclease in yeast, and has also been identified as a Holliday junction resolvase in human. Length = 68

>gnl|CDD|225383 COG2827, COG2827, Predicted endonuclease containing a URI domain [DNA replication, recombination, and repair]

 Score = 46.6 bits (111), Expect = 8e-08
 Identities = 25/71 (35%), Positives = 32/71 (45%), Gaps = 8/71 (11%)

Query: 4  HGVYLLYSRNPRYLGRTYIGYTVDPDRRIKQHNKGKDFGGAHKTSNRGPWDMVLIVYGFP 63
            VY+L   +    G  Y G T D +RR+ +HN GK   GA  T   GP  +V     F 
Sbjct: 5  WYVYILRCAD----GTLYTGVTTDLERRLAEHNSGK---GAKYTRRYGPVRLV-WYEEFD 56

Query: 64 NDISALRFEWA 74
          +   ALR E  
Sbjct: 57 DKSEALRREKR 67

Length = 95

>gnl|CDD|178979 PRK00329, PRK00329, GIY-YIG nuclease superfamily protein; Validated

 Score = 46.1 bits (110), Expect = 1e-07
 Identities = 27/88 (30%), Positives = 39/88 (44%), Gaps = 10/88 (11%)

Query: 4  HGVYLLYSRNPRYLGRTYIGYTVDPDRRIKQHNKGKDFGGAHKTSNRGPWDMVLI-VYGF 62
            +YLL   +    G  Y G T D +RR  QH  GK   GA  T  R P  + L+ V   
Sbjct: 7  WFLYLLRCAD----GSLYTGITTDVERRFAQHQSGK---GAKYTRGRPP--LTLVFVEPV 57

Query: 63 PNDISALRFEWAWQHPKMSRRLQHVARK 90
           +   ALR E+ ++     ++ + VA  
Sbjct: 58 GDRSEALRAEYRFKQLTKKQKERLVAEG 85

Length = 86

>gnl|CDD|214677 smart00465, GIYc, GIY-YIG type nucleases (URI domain)

 Score = 45.1 bits (107), Expect = 2e-07
 Identities = 16/71 (22%), Positives = 26/71 (36%), Gaps = 10/71 (14%)

Query: 4  HGVYLLYSRNPRYLGRTYIGYTVDPDRRIKQHNKGKDFGGAHKTSNRGPWDMVLIVYGFP 63
           GVY + ++    L   Y+G   +   R+K+H  G           R   D +L   G  
Sbjct: 2  PGVYYITNKKNGKL---YVGKAKNLRNRLKRHFSGSR-------KGRLLIDALLKYGGNF 51

Query: 64 NDISALRFEWA 74
            I    F+ +
Sbjct: 52 EFIILESFDES 62

Length = 84

>gnl|CDD|198394 cd10447, GIY-YIG_unchar_2, GIY-YIG domain of uncharacterized hypothetical protein found in bacteria and archaea

 Score = 36.4 bits (85), Expect = 4e-04
 Identities = 15/38 (39%), Positives = 20/38 (52%), Gaps = 1/38 (2%)

Query: 5  GVYLLYSRNP-RYLGRTYIGYTVDPDRRIKQHNKGKDF 41
          GVY L+  +        YIG   +  +R+KQH K KDF
Sbjct: 1  GVYFLFGEDDEGGKPTVYIGEAENVLKRLKQHLKDKDF 38

The family includes a group of uncharacterized hypothetical proteins, mainly found in bacteria and a few found in archaea, with a GIY-YIG domain that shows statistically significant similarity to the N-terminal catalytic domains of GIY-YIG family of intron-encoded homing endonuclease I-TevI and catalytic GIY-YIG domain of nucleotide excision repair endonuclease UvrC. Length = 80

>gnl|CDD|198380 cd00719, GIY-YIG_SF, GIY-YIG nuclease domain superfamily

 Score = 36.2 bits (84), Expect = 5e-04
 Identities = 16/72 (22%), Positives = 27/72 (37%), Gaps = 9/72 (12%)

Query: 5  GVYLLYSRNPRYLGRTYIGYTVDPDRRIKQHNKGKDFGGAHKTSNRGPWDMVLIVYGFPN 64
          GVY+LY  +   +   Y+G T +   RIK+H + +          +G     ++      
Sbjct: 1  GVYVLYDEDNGLI---YVGQTKNLRNRIKEHLRKQRSD-----WTKGLKPFEILYLEVAP 52

Query: 65 -DISALRFEWAW 75
             S L    A 
Sbjct: 53 EAESELLDLEAA 64

The GIY-YIG nuclease domain superfamily includes a large and diverse group of proteins involved in many cellular processes, such as class I homing GIY-YIG family endonucleases, prokaryotic nucleotide excision repair proteins UvrC and Cho, type II restriction enzymes, the endonuclease/reverse transcriptase of eukaryotic retrotransposable elements, and a family of eukaryotic enzymes that repair stalled replication forks. All of these members contain a conserved GIY-YIG nuclease domain that may serve as a scaffold for the coordination of a divalent metal ion required for catalysis of the phosphodiester bond cleavage. By combining with different specificity, targeting, or other domains, the GIY-YIG nucleases may perform different functions. Length = 69

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	133
KOG3005|consensus	276		100.0
COG2827	95	Predicted endonuclease containing a URI domain [DN	99.97
PRK00329	86	GIY-YIG nuclease superfamily protein; Validated	99.97
PF01541	80	GIY-YIG: GIY-YIG catalytic domain; InterPro: IPR00	99.32
smart00465	84	GIYc GIY-YIG type nucleases (URI domain).	98.5
PF10544	100	T5orf172: T5orf172 domain; InterPro: IPR018306 Thi	97.7
TIGR01453	214	grpIintron_endo group I intron endonuclease. This	97.62
PRK10545	286	nucleotide excision repair endonuclease; Provision	93.88
PHA02598	138	denA endonuclease II; Provisional	93.27
PRK12306	519	uvrC excinuclease ABC subunit C; Reviewed	92.45
PRK00558	598	uvrC excinuclease ABC subunit C; Validated	91.59
PRK14667	567	uvrC excinuclease ABC subunit C; Provisional	91.28
PRK07883	557	hypothetical protein; Validated	91.22
TIGR00194	574	uvrC excinuclease ABC, C subunit. This family cons	91.16
PRK14671	621	uvrC excinuclease ABC subunit C; Provisional	90.93
PRK14669	624	uvrC excinuclease ABC subunit C; Provisional	90.76
PRK14668	577	uvrC excinuclease ABC subunit C; Provisional	90.65
PRK14666	694	uvrC excinuclease ABC subunit C; Provisional	90.44
PRK14672	691	uvrC excinuclease ABC subunit C; Provisional	88.82
PF13455	83	MUG113: Meiotically up-regulated gene 113	85.79
COG0322	581	UvrC Nuclease subunit of the excinuclease complex	84.0

>KOG3005|consensus

Probab=100.00  E-value=2.9e-34  Score=232.18  Aligned_cols=129  Identities=52%  Similarity=0.971  Sum_probs=123.9

Q ss_pred             CceEEEEeeeCCCCCCCcEEEEEeCCHHHHHHHHhcCCCCCCccccccCCCeEEEEEEEccCCHHHHHHHHHHHcCCchh
Q psy12152          2 VFHGVYLLYSRNPRYLGRTYIGYTVDPDRRIKQHNKGKDFGGAHKTSNRGPWDMVLIVYGFPNDISALRFEWAWQHPKMS   81 (133)
Q Consensus         2 ~~~~vYIL~s~~~~~~~~~YiG~T~dl~rRl~qHn~g~~~gGa~~T~~~~pw~lv~~~e~f~sk~~Al~~E~~iK~~~~s   81 (133)
                      +||+||+|.|.+|+++|++|||+|.||.|||+||| |.++|||+.|++.+||+||+.+.+||++..||+|||+||++.-+
T Consensus         7 ~Fy~cYlL~s~sp~~r~~~yigst~nP~rRlRqhN-g~~~gga~kt~~~~PWeMv~iV~GFPn~vsALqFEwAWQ~p~~S   85 (276)
T KOG3005|consen    7 GFYCCYLLTSLSPRYKGRTYIGSTVNPSRRLRQHN-GEIKGGAWKTKKRRPWEMVMIVHGFPNKVSALQFEWAWQHPLIS   85 (276)
T ss_pred             ceEEEEEEeecCcCcCCceEEeeeCCCchhHHhhC-CcccCcccccCCCCCceEEEEeccCCccchhcchhhhccCcchh
Confidence            58999999999999999999999999999999999 58899999999999999999999999999999999999999999


Q ss_pred             hHHHHHhhhcC---CCccHHHHHHHHHHhhcCCCCCCcCcEEEecChhhhhhc
Q psy12152         82 RRLQHVARKKS---KETTYTYCLRLLHIMLQTAPWQRLPLTVQWLKPEYQQVL  131 (133)
Q Consensus        82 rk~~~i~~~~~---~~~~~~~~l~~~~~~l~~~~w~~~~l~v~~~~~~~~~~~  131 (133)
                      +.++.+...+.   +++.+.+.|+++.+|++.++|.++||++.|+++.++..|
T Consensus        86 ~~~k~~~~~~k~~~~et~F~~~Lr~l~~~~~~~aw~R~pl~~~wl~~~~~~~f  138 (276)
T KOG3005|consen   86 RYLKEKDTRLKSKSIETDFMYRLRILNHVLRSGAWARSPLTIRWLETDLETPF  138 (276)
T ss_pred             hhhhhhhhhhhhhhhhhHHHHHHHHHHhhhcCCchhcCCccchhcchhhcCCc
Confidence            99999886665   889999999999999999999999999999999999888

>COG2827 Predicted endonuclease containing a URI domain [DNA replication, recombination, and repair]

Probab=99.97  E-value=2.3e-31  Score=187.03  Aligned_cols=90  Identities=32%  Similarity=0.469  Sum_probs=83.6

Q ss_pred             CCceEEEEeeeCCCCCCCcEEEEEeCCHHHHHHHHhcCCCCCCccccccCCCeEEEEEEEccCCHHHHHHHHHHHcCCch
Q psy12152          1 MVFHGVYLLYSRNPRYLGRTYIGYTVDPDRRIKQHNKGKDFGGAHKTSNRGPWDMVLIVYGFPNDISALRFEWAWQHPKM   80 (133)
Q Consensus         1 M~~~~vYIL~s~~~~~~~~~YiG~T~dl~rRl~qHn~g~~~gGa~~T~~~~pw~lv~~~e~f~sk~~Al~~E~~iK~~~~   80 (133)
                      |+.|+||||.|.|    |++|||+|+|+.+|+.|||+|+   ||+||++++|..|| |++.|+|+++||++|+.+|+|+|
T Consensus         2 ~~~~~vYil~c~d----gtlY~GvT~D~~rR~~~H~~Gk---gakyT~~~~~~~Lv-~~e~~~~~~~A~~~E~~iK~~~R   73 (95)
T COG2827           2 ANNWYVYILRCAD----GTLYTGVTTDLERRLAEHNSGK---GAKYTRRYGPVRLV-WYEEFDDKSEALRREKRIKKLTR   73 (95)
T ss_pred             CcceEEEEEEeCC----CCEEEEecCCHHHHHHHHhccc---ccchhccCCceEEE-EEeecCCHHHHHHHHHHHHHHhH
Confidence            3568999999999    9999999999999999999998   99999999999999 99999999999999999999999


Q ss_pred             hhHHHHHhhhcCCCccHHHHHHHHHHhhcCCCCCCcC
Q psy12152         81 SRRLQHVARKKSKETTYTYCLRLLHIMLQTAPWQRLP  117 (133)
Q Consensus        81 srk~~~i~~~~~~~~~~~~~l~~~~~~l~~~~w~~~~  117 (133)
                      ++|                 +++|+++  +|.|.++.
T Consensus        74 ~~K-----------------~~LIe~~--~~~~~~l~   91 (95)
T COG2827          74 KQK-----------------ERLIEEA--NPEWKDLS   91 (95)
T ss_pred             HHH-----------------HHHHhcc--Cchhhhhh
Confidence            999                 7777777  77877764

>PRK00329 GIY-YIG nuclease superfamily protein; Validated

Probab=99.97  E-value=1.1e-30  Score=180.75  Aligned_cols=81  Identities=35%  Similarity=0.483  Sum_probs=76.3

Q ss_pred             CCceEEEEeeeCCCCCCCcEEEEEeCCHHHHHHHHhcCCCCCCccccccCCCeEEEEEEEccCCHHHHHHHHHHHcCCch
Q psy12152          1 MVFHGVYLLYSRNPRYLGRTYIGYTVDPDRRIKQHNKGKDFGGAHKTSNRGPWDMVLIVYGFPNDISALRFEWAWQHPKM   80 (133)
Q Consensus         1 M~~~~vYIL~s~~~~~~~~~YiG~T~dl~rRl~qHn~g~~~gGa~~T~~~~pw~lv~~~e~f~sk~~Al~~E~~iK~~~~   80 (133)
                      |.+||||||.|.+    |++|||+|+||.+||.|||+|.   ||+||++++||.|| |++.|+|+++|+++|++||+|++
T Consensus         4 ~~~~~vYil~~~~----~~~Y~G~T~dl~~Rl~qH~~g~---ga~~tr~~~p~~Lv-~~e~~~~~~~A~~~E~~lK~~~r   75 (86)
T PRK00329          4 MKPWFLYLLRCAD----GSLYTGITTDVERRFAQHQSGK---GAKYTRGRPPLTLV-FVEPVGDRSEALRAEYRFKQLTK   75 (86)
T ss_pred             CCceEEEEEEcCC----CCEEEEEcCCHHHHHHHHHcCC---CCCCccCCCceEEE-EEEECCCHHHHHHHHHHHhcCCH
Confidence            4679999999988    8999999999999999999987   89999999999999 89999999999999999999999


Q ss_pred             hhHHHHHhh
Q psy12152         81 SRRLQHVAR   89 (133)
Q Consensus        81 srk~~~i~~   89 (133)
                      .+|++.|..
T Consensus        76 ~~K~~li~~   84 (86)
T PRK00329         76 KQKERLVAE   84 (86)
T ss_pred             HHHHHHHhc
Confidence            999887754

>PF01541 GIY-YIG: GIY-YIG catalytic domain; InterPro: IPR000305 During the process of Escherichia coli nucleotide excision repair, DNA damage recognition and processing are achieved by the action of the uvrA, uvrB, and uvrC gene products []

Probab=99.32  E-value=8.6e-12  Score=81.83  Aligned_cols=68  Identities=24%  Similarity=0.492  Sum_probs=56.6

Q ss_pred             ceEEEEeeeCCCCCCCcEEEEEeCCHHHHHHHHhcCCCCCCcccccc----CCCeEEEEEEEccCCHHHHHHHHHHHcC
Q psy12152          3 FHGVYLLYSRNPRYLGRTYIGYTVDPDRRIKQHNKGKDFGGAHKTSN----RGPWDMVLIVYGFPNDISALRFEWAWQH   77 (133)
Q Consensus         3 ~~~vYIL~s~~~~~~~~~YiG~T~dl~rRl~qHn~g~~~gGa~~T~~----~~pw~lv~~~e~f~sk~~Al~~E~~iK~   77 (133)
                      +++||+|.|.+   .+.+|||.|.|+.+|+.+|..+.   ++..+..    ..+++++ +++.+.+..+|+..|..|..
T Consensus         1 k~gIY~i~~~~---~~~~YIG~t~nl~~R~~~H~~~~---~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~E~~~i~   72 (80)
T PF01541_consen    1 KYGIYIIYNKD---NKKIYIGSTKNLKKRLNEHFSGN---KSKKKKQKKYGWDNFEFI-IIEEFNTKSEALKLEQYLIK   72 (80)
T ss_dssp             -EEEEEEEETT---TEEEEEEEESSHHHHHHHHHHHC---THCSHCHHHHHSSCEEEE-EEEEESSHHHHHHHHHHHHH
T ss_pred             CcEEEEEEECC---CCEEEEEEECCHHHHHHHHhcCC---CCCcchhhhcccccEEEE-eeEEeCCHHHHHHHHHHHHH
Confidence            47899999988   46799999999999999998765   3334442    6789999 89999999999999998765

The UvrC proteins contain 4 conserved regions: a central region which interacts with UvrB (Uvr domain), a Helix hairpin Helix (HhH) domain important for 5 prime incision of damage DNA and the homology regions 1 and 2 of unknown function. UvrC homology region 2 is specific for UvrC proteins, whereas UvrC homology region 1 is also shared by few other nucleases. It is found in the amino terminal region of excinuclease abc subunit c (uvrC), Bacteriophage T4 endonucleases segA, segB, segC, segD and segE; it is also found in putative endonucleases encoded by group I introns of fungi and phage.; GO: 0004518 nuclease activity, 0006281 DNA repair, 0005622 intracellular; PDB: 1YWL_A 1YD6_D 1YD5_A 1YD1_A 1YCZ_A 1YD0_A 1YD3_A 1YD4_A 1YD2_A 1LN0_A ....

>smart00465 GIYc GIY-YIG type nucleases (URI domain)

Probab=98.50  E-value=5.8e-07  Score=58.77  Aligned_cols=67  Identities=25%  Similarity=0.461  Sum_probs=43.0

Q ss_pred             eEEEEeeeCCCCCCCcEEEEEeCCHHHHHHHHhcCCCCCCccccc---cCC-CeEEEEEEEccCCHHHHHHHHHHHcC
Q psy12152          4 HGVYLLYSRNPRYLGRTYIGYTVDPDRRIKQHNKGKDFGGAHKTS---NRG-PWDMVLIVYGFPNDISALRFEWAWQH   77 (133)
Q Consensus         4 ~~vYIL~s~~~~~~~~~YiG~T~dl~rRl~qHn~g~~~gGa~~T~---~~~-pw~lv~~~e~f~sk~~Al~~E~~iK~   77 (133)
                      .+||++.+.+   .+.+|||.|.|+.+|+.+|..+..+ +.....   .++ ..+.. ..+.+. .. |...|..+.+
T Consensus         2 ~gvY~i~~~~---~~~~YVG~t~nl~~R~~~h~~~~~~-~~~~~~~~~~~~~~f~~~-~~~~~~-~~-~~~~E~~~i~   72 (84)
T smart00465        2 PGVYYITNKK---NGKLYVGKAKNLRNRLKRHFSGSRK-GRLLIDALLKYGGNFEFI-ILESFD-ES-ALELEKYLIK   72 (84)
T ss_pred             CEEEEEEECC---CCEEEEEEccCHHHHHHHHHhCCCC-ChHHHHHHHHhcCCeEEE-EeecCh-Hh-HHHHHHHHHH
Confidence            4799999965   5999999999999999999976531 122222   122 23333 233322 22 8888887654

>PF10544 T5orf172: T5orf172 domain; InterPro: IPR018306 This entry represents a DNA-binding domain found in bacteriophage T5, ORF172 []

Probab=97.70  E-value=0.00015  Score=49.11  Aligned_cols=64  Identities=23%  Similarity=0.362  Sum_probs=44.8

Q ss_pred             EEEEeeeCCCCCCCc--EEEEEeCCHHHHHHHHhcCCCCCCccccccCCCeEEEEEEEccCCHHHHHHHHHHHcCC
Q psy12152          5 GVYLLYSRNPRYLGR--TYIGYTVDPDRRIKQHNKGKDFGGAHKTSNRGPWDMVLIVYGFPNDISALRFEWAWQHP   78 (133)
Q Consensus         5 ~vYIL~s~~~~~~~~--~YiG~T~dl~rRl~qHn~g~~~gGa~~T~~~~pw~lv~~~e~f~sk~~Al~~E~~iK~~   78 (133)
                      ||||+.+..-  .+.  +=||.|+||.+|+++++..       .+....+++++ +...+.....|-..|..++..
T Consensus         2 yiYi~~~~~~--~~~~~~KIG~T~~~~~Rl~~~~~~-------~~~~~~~~~~~-~~~~~~~~~~~~~~E~~ih~~   67 (100)
T PF10544_consen    2 YIYILTSPSN--PGYNIYKIGYTTNPERRLRELNRN-------STGSPFDFEVI-YEFESVPVPDARKVERLIHRE   67 (100)
T ss_pred             EEEEEEecCC--CCceeEEEeeECCHHHHHHHhhcc-------ccCCCCceeEE-EEEEEEecCCHHHHHHHHHHH
Confidence            7999977541  244  8899999999999999942       23334567776 444555555677778887763

The domain is related to the Bro-N and KilA-N domains that are widespread in large-DNA viruses infecting bacteria and eukaryotes [].

>TIGR01453 grpIintron_endo group I intron endonuclease

Probab=97.62  E-value=0.00026  Score=55.86  Aligned_cols=68  Identities=24%  Similarity=0.366  Sum_probs=45.9

Q ss_pred             eEEEEeeeCCCCCCCcEEEEEeCCHHHHHHHHhcCCCCCCcc-cc----ccCC--CeEEEEEEEccCCHHHHHHHHHHHc
Q psy12152          4 HGVYLLYSRNPRYLGRTYIGYTVDPDRRIKQHNKGKDFGGAH-KT----SNRG--PWDMVLIVYGFPNDISALRFEWAWQ   76 (133)
Q Consensus         4 ~~vYIL~s~~~~~~~~~YiG~T~dl~rRl~qHn~g~~~gGa~-~T----~~~~--pw~lv~~~e~f~sk~~Al~~E~~iK   76 (133)
                      -+||++.|..   .|.+|||.|.|+.+|+.+|...... |.. ..    ..++  -+++. +.+.+.+..+...+|..|-
T Consensus         2 ~GIY~i~n~~---ngk~YIGss~nl~~R~~~h~~~~~~-~~~~~l~~ai~kyG~~nF~~~-ile~~~~~~~l~~lE~~~I   76 (214)
T TIGR01453         2 SGIYKITNNI---NGKIYVGSSVNLEKRLKEHLKLLKK-GNRIKLQKALNKYGWSNFSFE-ILEYYCNKDDLIERETYYI   76 (214)
T ss_pred             CEEEEEEECC---CCcEEEEeccCHHHHHHHHHHHHhc-CChHHHHHHHHHhChHheEEE-EEEEeCCHHHHHHHHHHHH
Confidence            4799999965   4999999999999999999754222 222 11    1233  35555 3454456777778887654

This model represents one subfamily of endonucleases containing the endo/excinuclease amino terminal domain, Pfam:PF01541 at its amino end. A distinct subfamily includes excinuclease abc subunit c (uvrC). Members of pfam01541 are often termed GIY-YIG endonucleases after conserved motifs near the amino end. This subfamily in this model is found in open reading frames of group I introns in both phage and mitochondria. The closely related endonucleases of phage T4: segA, segB, segC, segD and segE, score below the trusted cutoff for the family.

>PRK10545 nucleotide excision repair endonuclease; Provisional

Probab=93.88  E-value=0.1  Score=43.38  Aligned_cols=61  Identities=25%  Similarity=0.263  Sum_probs=42.9

Q ss_pred             eEEEEeeeCCCCCCC-c-EEEEEeCCHHHHHHHHhcCCCCCCccccccCCCeEEEEEEEccCCHHHHHHHHHH
Q psy12152          4 HGVYLLYSRNPRYLG-R-TYIGYTVDPDRRIKQHNKGKDFGGAHKTSNRGPWDMVLIVYGFPNDISALRFEWA   74 (133)
Q Consensus         4 ~~vYIL~s~~~~~~~-~-~YiG~T~dl~rRl~qHn~g~~~gGa~~T~~~~pw~lv~~~e~f~sk~~Al~~E~~   74 (133)
                      -+||+....+    | . +|||=+.|+.+|+.+|=.+. + -+...+  .-..+-  +....+--+|+-.|..
T Consensus        35 PGVYlf~d~~----g~~~LYVGKAknLR~RV~syF~~~-k-~~~m~~--~i~~Ie--~i~T~sEleALLLE~~   97 (286)
T PRK10545         35 PGVYLFHGES----DTMPLYIGKSVNIRSRVLSHLRTP-D-EAAMLR--QSRRIS--WICTAGEIGALLLEAR   97 (286)
T ss_pred             CeEEEEEcCC----CCEEEEEechHhHHHHHHHHcCcH-H-HHHHHH--hcceEE--EEEeCCHHHHHHHHHH
Confidence            4799999887    5 4 89999999999999997432 1 111111  222233  4577889999999966

>PHA02598 denA endonuclease II; Provisional

Probab=93.27  E-value=0.13  Score=38.67  Aligned_cols=32  Identities=25%  Similarity=0.371  Sum_probs=27.4

Q ss_pred             eEEEEeeeCCCCCCCcEEEEEeCCHHHHHHHHhcCC
Q psy12152          4 HGVYLLYSRNPRYLGRTYIGYTVDPDRRIKQHNKGK   39 (133)
Q Consensus         4 ~~vYIL~s~~~~~~~~~YiG~T~dl~rRl~qHn~g~   39 (133)
                      .+||++...+    ..+|||-+.|+..|+.++-++.
T Consensus        34 n~VY~~~~~~----~viYVGKAknLkkRv~sYf~~~   65 (138)
T PHA02598         34 NVIYAIAVDD----ELVYIGKTKNLRKRIDYYRNSK   65 (138)
T ss_pred             eEEEEEEeCC----eEEEEeehhhHHHHHHHHhCcc
Confidence            5899999544    7999999999999999997653

>PRK12306 uvrC excinuclease ABC subunit C; Reviewed

Probab=92.45  E-value=0.24  Score=44.22  Aligned_cols=67  Identities=22%  Similarity=0.286  Sum_probs=47.7

Q ss_pred             eEEEEeeeCCCCCCCcEEEEEeCCHHHHHHHHhcCCCCCCcccccc--CCCeEEEEEEEccCCHHHHHHHHHH-HcC
Q psy12152          4 HGVYLLYSRNPRYLGRTYIGYTVDPDRRIKQHNKGKDFGGAHKTSN--RGPWDMVLIVYGFPNDISALRFEWA-WQH   77 (133)
Q Consensus         4 ~~vYIL~s~~~~~~~~~YiG~T~dl~rRl~qHn~g~~~gGa~~T~~--~~pw~lv~~~e~f~sk~~Al~~E~~-iK~   77 (133)
                      -+||++...+   ...+|||=+.|+.+|+.+|=++... . ..|..  ..-..+-  +....|..+|+-.|.. ||+
T Consensus        11 PGVYl~~d~~---g~vIYVGKAknLr~RV~sYF~~~~~-~-~K~~~lv~~i~~ie--~ivt~sE~eALlLE~~LIK~   80 (519)
T PRK12306         11 PGCYLYKDEE---GTIIYVGKAKNLKKRVSSYFQKKDH-D-PKTQSLVKAIRDIE--FIVTDNEVEALLLENTLIKK   80 (519)
T ss_pred             CeEEEEECCC---CCEEEeccchhHHHHHHHhCCCCCC-C-hHHHHHHHHhcEEE--EEEeCCHHHHHHHHHHHHHH
Confidence            4899999987   4699999999999999999755311 1 23322  2233343  3467899999999977 444

>PRK00558 uvrC excinuclease ABC subunit C; Validated

Probab=91.59  E-value=0.31  Score=44.12  Aligned_cols=67  Identities=19%  Similarity=0.168  Sum_probs=47.0

Q ss_pred             eEEEEeeeCCCCCCCcEEEEEeCCHHHHHHHHhcCCCCCCcccccc--CCCeEEEEEEEccCCHHHHHHHHHH-HcC
Q psy12152          4 HGVYLLYSRNPRYLGRTYIGYTVDPDRRIKQHNKGKDFGGAHKTSN--RGPWDMVLIVYGFPNDISALRFEWA-WQH   77 (133)
Q Consensus         4 ~~vYIL~s~~~~~~~~~YiG~T~dl~rRl~qHn~g~~~gGa~~T~~--~~pw~lv~~~e~f~sk~~Al~~E~~-iK~   77 (133)
                      -+||++...+   ...+|||=+.|+.+|+.+|=++...  ...|..  ..-..+-  +....|..+|+-.|.. ||+
T Consensus        15 PGVY~~~d~~---g~viYVGKAknLr~Rv~sYF~~~~~--~~k~~~lv~~i~~ie--~i~t~sE~eALlLE~~LIK~   84 (598)
T PRK00558         15 PGVYRMKDAN---GTVIYVGKAKNLKNRVRSYFRKSHD--SPKTRAMVSEIADIE--YIVTRSETEALLLENNLIKK   84 (598)
T ss_pred             CeEEEEECCC---CCEEEecCchhHHHHHHhhCCCCCc--ChHHHHHHHhcCeEE--EEEeCCHHHHHHHHHHHHHH
Confidence            5899999977   4699999999999999999654311  123332  1223333  3467789999999977 444

>PRK14667 uvrC excinuclease ABC subunit C; Provisional

Probab=91.28  E-value=0.36  Score=43.58  Aligned_cols=66  Identities=26%  Similarity=0.274  Sum_probs=46.0

Q ss_pred             eEEEEeeeCCCCCCCcEEEEEeCCHHHHHHHHhcCCCCCCcccccc--CCCeEEEEEEEccCCHHHHHHHHHH-HcC
Q psy12152          4 HGVYLLYSRNPRYLGRTYIGYTVDPDRRIKQHNKGKDFGGAHKTSN--RGPWDMVLIVYGFPNDISALRFEWA-WQH   77 (133)
Q Consensus         4 ~~vYIL~s~~~~~~~~~YiG~T~dl~rRl~qHn~g~~~gGa~~T~~--~~pw~lv~~~e~f~sk~~Al~~E~~-iK~   77 (133)
                      -+||+.. .+   ...+|||=+.|+.+|+.+|=++... + ..|..  ..-..+-  +....|..+|+-.|.. ||+
T Consensus        17 PGVYl~~-~~---g~viYVGKAknLr~RV~sYF~~~~~-~-~K~~~lv~~i~~ie--~i~t~sE~EALlLE~~LIK~   85 (567)
T PRK14667         17 PGVYLFK-KK---KRYIYIGKAKNIKNRLLQHYKQSET-D-PKERAIFSESSSLE--WIITRNEYEALVLEIDLIQQ   85 (567)
T ss_pred             CeEEEEe-cC---CeEEEeeCcHhHHHHHHHHcCCCCC-C-hHHHHHHHhhCeEE--EEEeCCHHHHHHHHHHHHHH
Confidence            4799999 66   3589999999999999999754311 1 23332  1223333  3467899999999977 454

>PRK07883 hypothetical protein; Validated

Probab=91.22  E-value=0.49  Score=42.45  Aligned_cols=67  Identities=16%  Similarity=0.131  Sum_probs=47.1

Q ss_pred             eEEEEeeeCCCCCCCcEEEEEeCCHHHHHHHHhcCCCCCCcccccc--CCCeEEEEEEEccCCHHHHHHHHHH-HcC
Q psy12152          4 HGVYLLYSRNPRYLGRTYIGYTVDPDRRIKQHNKGKDFGGAHKTSN--RGPWDMVLIVYGFPNDISALRFEWA-WQH   77 (133)
Q Consensus         4 ~~vYIL~s~~~~~~~~~YiG~T~dl~rRl~qHn~g~~~gGa~~T~~--~~pw~lv~~~e~f~sk~~Al~~E~~-iK~   77 (133)
                      -+||++...+   ...+|||-+.|+.+|+.+|=.+... . ..|..  ..-..+-  +....|..+|+-.|.. ||+
T Consensus       218 PGVY~~~d~~---g~viYVGKAknLr~Rv~sYF~~~~~-~-~k~~~lv~~i~~ie--~i~t~sE~eAllLE~~lIk~  287 (557)
T PRK07883        218 PGVYLFRGPS---GEVLYVGTAVNLRRRVRSYFTAAET-R-GRMREMVALAERVD--HVECAHALEAEVRELRLIAA  287 (557)
T ss_pred             ceEEEEECCC---CcEEEeehhhhHHHHHHHHcCCCCC-C-chHHHHHhhhceEE--EEEeCCHHHHHHHHHHHHHH
Confidence            4799999987   4699999999999999999654211 1 12332  1223333  3467899999999985 554

>TIGR00194 uvrC excinuclease ABC, C subunit

Probab=91.16  E-value=0.37  Score=43.59  Aligned_cols=66  Identities=23%  Similarity=0.262  Sum_probs=46.7

Q ss_pred             eEEEEeeeCCCCCCCcEEEEEeCCHHHHHHHHhcCCCCCCcccccc--CCCeEEEEEEEccCCHHHHHHHHHH-HcC
Q psy12152          4 HGVYLLYSRNPRYLGRTYIGYTVDPDRRIKQHNKGKDFGGAHKTSN--RGPWDMVLIVYGFPNDISALRFEWA-WQH   77 (133)
Q Consensus         4 ~~vYIL~s~~~~~~~~~YiG~T~dl~rRl~qHn~g~~~gGa~~T~~--~~pw~lv~~~e~f~sk~~Al~~E~~-iK~   77 (133)
                      -+||++.+.+   ...+|||-+.|+.+|+.+|=.+..   ...|..  ..-..+-  +....|..+|+-.|.. ||+
T Consensus        12 PGVYl~~d~~---g~viYVGKAknLr~Rv~sYF~~~~---~~K~~~mv~~i~~ie--~ivt~sE~eALlLE~~lIK~   80 (574)
T TIGR00194        12 PGCYLMKDRN---GQVLYVGKAKNLKKRVSSYFRENN---SAKTQALVKQIADIE--YILTKNENEALILEANLIKQ   80 (574)
T ss_pred             CeEEEEECCC---CCEEEEecHHHHHHHHHHhcCCCC---CchHHHHHHhcCeEE--EEEeCCHHHHHHHHHHHHHH
Confidence            4799999987   469999999999999999975431   123432  1223333  3467789999999977 444

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

>PRK14671 uvrC excinuclease ABC subunit C; Provisional

Probab=90.93  E-value=0.47  Score=43.25  Aligned_cols=68  Identities=19%  Similarity=0.148  Sum_probs=47.1

Q ss_pred             eEEEEeeeCCCCCCCcEEEEEeCCHHHHHHHHhcCCCCCCcccccc--CCCeEEEEEEEccCCHHHHHHHHHH-HcC
Q psy12152          4 HGVYLLYSRNPRYLGRTYIGYTVDPDRRIKQHNKGKDFGGAHKTSN--RGPWDMVLIVYGFPNDISALRFEWA-WQH   77 (133)
Q Consensus         4 ~~vYIL~s~~~~~~~~~YiG~T~dl~rRl~qHn~g~~~gGa~~T~~--~~pw~lv~~~e~f~sk~~Al~~E~~-iK~   77 (133)
                      -+||++...+   ...+|||=+.|+.+|+.+|=.+... ....|..  ..-..+-  +....|..+|+-.|.. ||+
T Consensus        23 PGVYl~~d~~---g~viYVGKAknLr~RV~sYF~~~~~-~~~K~~~lv~~i~~ie--~i~t~sE~EALlLE~~LIk~   93 (621)
T PRK14671         23 PGVYQFKNAA---GRVIYVGKAKNLRNRVRSYFRNSRQ-LSGKTLVLVGHIADLE--VIITSSEVEALILENNLIKE   93 (621)
T ss_pred             CeEEEEECCC---CCEEEeecchhHHHHHHHHcCCCCC-CChHHHHHHHhhceEE--EEEeCCHHHHHHHHHHHHHH
Confidence            4799999987   4699999999999999999653210 0112322  2234444  3466899999999977 444

>PRK14669 uvrC excinuclease ABC subunit C; Provisional

Probab=90.76  E-value=0.5  Score=43.18  Aligned_cols=68  Identities=24%  Similarity=0.277  Sum_probs=47.2

Q ss_pred             eEEEEeeeCCCCCCCcEEEEEeCCHHHHHHHHhcCCCCCCcccccc--CCCeEEEEEEEccCCHHHHHHHHHH-HcC
Q psy12152          4 HGVYLLYSRNPRYLGRTYIGYTVDPDRRIKQHNKGKDFGGAHKTSN--RGPWDMVLIVYGFPNDISALRFEWA-WQH   77 (133)
Q Consensus         4 ~~vYIL~s~~~~~~~~~YiG~T~dl~rRl~qHn~g~~~gGa~~T~~--~~pw~lv~~~e~f~sk~~Al~~E~~-iK~   77 (133)
                      -+||++...+   ...+|||=+.|+.+|+.+|=.+... ....|..  ..-.++-  +....|..||+-.|.. ||+
T Consensus        14 PGVYl~~d~~---g~viYVGKAknLr~RV~sYF~~~~~-~~~K~~~lv~~i~~ie--~i~t~sE~EALlLE~~LIk~   84 (624)
T PRK14669         14 PGVYLYKNAG---GEVIYVGKAKNLRSRVRSYFSEDKL-GNIKTGSLIREAVDID--YILVDNEKEALALENNLIKQ   84 (624)
T ss_pred             CeEEEEECCC---CCEEEeeCchhHHHHHHHHhccCcc-CChHHHHHHHhhceEE--EEEeCCHHHHHHHHHHHHhh
Confidence            4899999887   3689999999999999999653210 0123332  2233443  3478899999999977 444

>PRK14668 uvrC excinuclease ABC subunit C; Provisional

Probab=90.65  E-value=0.4  Score=43.39  Aligned_cols=64  Identities=19%  Similarity=0.222  Sum_probs=45.3

Q ss_pred             eEEEEeeeCCCCCCCcEEEEEeCCHHHHHHHHhcCCCCCCcccccc--CCCeEEEEEEEccCCHHHHHHHHHH-HcC
Q psy12152          4 HGVYLLYSRNPRYLGRTYIGYTVDPDRRIKQHNKGKDFGGAHKTSN--RGPWDMVLIVYGFPNDISALRFEWA-WQH   77 (133)
Q Consensus         4 ~~vYIL~s~~~~~~~~~YiG~T~dl~rRl~qHn~g~~~gGa~~T~~--~~pw~lv~~~e~f~sk~~Al~~E~~-iK~   77 (133)
                      -+||+... +   ...+|||=+.|+.+|+.+|-.+.   + ..|..  ..-..+-  +....|..+|+-.|.. ||+
T Consensus        17 PGVYl~~d-~---g~viYVGKAknLr~RV~sYF~~~---~-~k~~~lv~~i~~ie--~i~t~sE~eALlLE~~LIK~   83 (577)
T PRK14668         17 PGVYQFVA-G---GTVLYVGKAVDLRDRVRSYADPR---S-ERIRRMVERADDID--FAVTDTETQALLLEANLIKR   83 (577)
T ss_pred             CEEEEEcC-C---CeEEEeeCcHhHHHHHHHHcCCC---C-hHHHHHHHhhCeEE--EEEeCCHHHHHHHHHHHHHH
Confidence            47999986 4   26999999999999999997532   1 13332  2233333  3467899999999977 454

>PRK14666 uvrC excinuclease ABC subunit C; Provisional

Probab=90.44  E-value=0.53  Score=43.59  Aligned_cols=68  Identities=21%  Similarity=0.179  Sum_probs=47.8

Q ss_pred             eEEEEeeeCCCCCCCcEEEEEeCCHHHHHHHHhcCCCCCCcccccc--CCCeEEEEEEEccCCHHHHHHHHHH-HcC
Q psy12152          4 HGVYLLYSRNPRYLGRTYIGYTVDPDRRIKQHNKGKDFGGAHKTSN--RGPWDMVLIVYGFPNDISALRFEWA-WQH   77 (133)
Q Consensus         4 ~~vYIL~s~~~~~~~~~YiG~T~dl~rRl~qHn~g~~~gGa~~T~~--~~pw~lv~~~e~f~sk~~Al~~E~~-iK~   77 (133)
                      -+||++...+   ...+|||=+.|+.+|+.+|=++... -...|..  ..-..+-  +....|..+|+-.|.. ||+
T Consensus        13 PGVYlfkD~~---G~VIYVGKAKNLR~RV~SYF~~~~~-~~~K~~~Lv~~i~~Ie--~ivT~sE~EALLLE~~LIK~   83 (694)
T PRK14666         13 PGVYLYKDEA---GRIIYVGKARHLRRRVASYFRDVSA-LTPKTVAMLRHAVTID--TLSTTTEKEALLLEASLIKK   83 (694)
T ss_pred             CeEEEEECCC---CCEEEeeCcHhHHHHHHHHcCCCCC-CChHHHHHHHhcCeeE--EEEeCCHHHHHHHHHHHHHH
Confidence            4799999987   4699999999999999999754210 0122322  2334443  4578899999999977 554

>PRK14672 uvrC excinuclease ABC subunit C; Provisional

Probab=88.82  E-value=0.95  Score=41.95  Aligned_cols=66  Identities=18%  Similarity=0.156  Sum_probs=47.1

Q ss_pred             eEEEEeeeCCCCCCCcEEEEEeCCHHHHHHHHhcCCCCCCcccccc--CCCeEEEEEEEccCCHHHHHHHHHH-HcC
Q psy12152          4 HGVYLLYSRNPRYLGRTYIGYTVDPDRRIKQHNKGKDFGGAHKTSN--RGPWDMVLIVYGFPNDISALRFEWA-WQH   77 (133)
Q Consensus         4 ~~vYIL~s~~~~~~~~~YiG~T~dl~rRl~qHn~g~~~gGa~~T~~--~~pw~lv~~~e~f~sk~~Al~~E~~-iK~   77 (133)
                      -+||++...+   ...+|||=+.|+.+|+.+|=.+..   ...|+.  ..-..+-  +....|..+|+-.|.. ||+
T Consensus        22 PGVYlfkd~~---G~VLYVGKAKNLR~RV~SYF~~~~---~~K~~~Lv~~i~~Ie--~ivT~sE~EALLLE~~LIK~   90 (691)
T PRK14672         22 SGVYLWKDVH---GVVIYVGKAKSLRTRLTSYFRCRH---DPKTRVLMSRAAALE--YLQTQHEYEALLLENTLIKK   90 (691)
T ss_pred             CeEEEEECCC---CCEEEeeCcHHHHHHHHHHcCCCC---CchHHHHHHhhCcEE--EEEeCCHHHHHHHHHHHHHH
Confidence            4799999987   358999999999999999975421   123332  2334444  3477899999999977 444

>PF13455 MUG113: Meiotically up-regulated gene 113

Probab=85.79  E-value=0.48  Score=32.34  Aligned_cols=16  Identities=38%  Similarity=0.686  Sum_probs=14.9

Q ss_pred             EEEeCCHHHHHHHHhc
Q psy12152         22 IGYTVDPDRRIKQHNK   37 (133)
Q Consensus        22 iG~T~dl~rRl~qHn~   37 (133)
                      ||.|+||.+|+.|.+.
T Consensus         3 IGrt~nv~rRl~qW~~   18 (83)
T PF13455_consen    3 IGRTTNVERRLNQWSR   18 (83)
T ss_pred             ccccCCHHHHHHHHHH
Confidence            8999999999999874

>COG0322 UvrC Nuclease subunit of the excinuclease complex [DNA replication, recombination, and repair]

Probab=84.00  E-value=2.1  Score=38.94  Aligned_cols=64  Identities=23%  Similarity=0.261  Sum_probs=46.7

Q ss_pred             eEEEEeeeCCCCCCCcEEEEEeCCHHHHHHHHhcCCCCCCcccccc--CCCeEEEEEEEccCCHHHHHHHHHHH
Q psy12152          4 HGVYLLYSRNPRYLGRTYIGYTVDPDRRIKQHNKGKDFGGAHKTSN--RGPWDMVLIVYGFPNDISALRFEWAW   75 (133)
Q Consensus         4 ~~vYIL~s~~~~~~~~~YiG~T~dl~rRl~qHn~g~~~gGa~~T~~--~~pw~lv~~~e~f~sk~~Al~~E~~i   75 (133)
                      -+||+....+   ...+|||=..|+.+|+.++-.|..   ...|..  ...-.+-  +-...+-.|||-.|..+
T Consensus        16 PGvY~~~d~~---g~VlYVGKAknLr~Rv~sYF~~~~---~~kt~~lv~~i~~iE--~ivt~~E~EALlLE~nL   81 (581)
T COG0322          16 PGVYLMKDEN---GTVLYVGKAKNLRKRVSSYFRGRL---DPKTAALVENIADIE--YIVTDTETEALLLENNL   81 (581)
T ss_pred             CeeEEEECCC---CCEEEEeehhhHHHHHHHhhcCCC---cHHHHHHHHhhccee--EEEeCCHHHHHHHHHhH
Confidence            4799999988   579999999999999999976652   223332  2333333  22567899999999874

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	133
1zg2_A	107	Solution Nmr Structure Of The Upf0213 Protein Bh004		5e-08

>pdb|1ZG2|A Chain A, Solution Nmr Structure Of The Upf0213 Protein Bh0048 From Bacillus Halodurans. Northeast Structural Genomics Target Bhr2 Length = 107

Iteration: 1
 Score = 53.1 bits (126), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 34/87 (39%), Positives = 49/87 (56%), Gaps = 8/87 (9%)
Query: 4  HGVYLLYSRNPRYLGRTYIGYTVDPDRRIKQHNKGKDFGGAHKTSNRGPWDMVLIVYGFP 63
          H VY+L  ++    G  Y GYT D DRRIK+H  GK   GA  T  RGP+ +V   + FP
Sbjct: 8  HYVYILECKD----GSWYTGYTTDVDRRIKKHASGK---GAKYTRGRGPFRLV-ATWAFP 59
Query: 64 NDISALRFEWAWQHPKMSRRLQHVARK 90
          +   A+R+E+  +H    ++ Q V+ K
Sbjct: 60 SKEEAMRWEYEVKHLSRRKKEQLVSLK 86

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	133
1zg2_A	107	Hypothetical UPF0213 protein BH0048; BHR2, structu	3e-12
1ywl_A	96	Hypothetical UPF0213 protein EF2693; alpha and bet	1e-10

>1zg2_A Hypothetical UPF0213 protein BH0048; BHR2, structure, autostructure, northeast structural genomics consortium, PSI; NMR {Bacillus halodurans} Length = 107

 Score = 57.7 bits (140), Expect = 3e-12
 Identities = 32/78 (41%), Positives = 45/78 (57%), Gaps = 10/78 (12%)

Query: 6  VYLLYSRNPRYLGRTYIGYTVDPDRRIKQHNKGKDFGGAHKTSNRGPWDMVLIVYGFPND 65
          VY+L  ++    G  Y GYT D DRRIK+H  GK   GA  T  RGP+ +V   + FP+ 
Sbjct: 10 VYILECKD----GSWYTGYTTDVDRRIKKHASGK---GAKYTRGRGPFRLVA-TWAFPSK 61

Query: 66 ISALRFEWAWQHPKMSRR 83
            A+R+E+  +   +SRR
Sbjct: 62 EEAMRWEYEVK--HLSRR 77

>1ywl_A Hypothetical UPF0213 protein EF2693; alpha and beta, structural genomics, northeast structural genomics consortium (NESG); NMR {Enterococcus faecalis} Length = 96

 Score = 53.4 bits (129), Expect = 1e-10
 Identities = 25/98 (25%), Positives = 46/98 (46%), Gaps = 14/98 (14%)

Query: 6  VYLLYSRNPRYLGRTYIGYTVDPDRRIKQHNKGKDFGGAH--KTSNRGPWDMVLIVYGFP 63
           Y+L  ++    G  Y GYT +P+RR+ +HN G    GA   + + R P  M+     F 
Sbjct: 9  FYVLLCQD----GSFYGGYTTEPERRLTEHNSGT---GAKYTRLAKRRPVIMIH-TEKFE 60

Query: 64 NDISALRFEWAWQHPKMSRR--LQHVARKKSKETTYTY 99
              A + E A++  K++R+   Q++     +   + +
Sbjct: 61 TRSEATKAEAAFK--KLTRKQKEQYLKTFHLEHHHHHH 96

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	133
1zg2_A	107	Hypothetical UPF0213 protein BH0048; BHR2, structu	99.98
1ywl_A	96	Hypothetical UPF0213 protein EF2693; alpha and bet	99.97
1mk0_A	97	Intron-associated endonuclease 1; alpha/beta fold,	97.76
1yd6_A	99	UVRC; DNA binding protein; 2.00A {Bacillus caldote	97.28
1yd0_A	96	Uvrabc system protein C; DNA binding protein; 1.50	97.05
2wsh_A	143	Endonuclease II; GIY-YIG, hydrolase; 1.90A {Entero	91.19

>1zg2_A Hypothetical UPF0213 protein BH0048; BHR2, structure, autostructure, northeast structural genomics consortium, PSI; NMR {Bacillus halodurans}

Probab=99.98  E-value=2.3e-33  Score=200.27  Aligned_cols=95  Identities=36%  Similarity=0.653  Sum_probs=83.6

Q ss_pred             CceEEEEeeeCCCCCCCcEEEEEeCCHHHHHHHHhcCCCCCCccccccCCCeEEEEEEEccCCHHHHHHHHHHHcCCchh
Q psy12152          2 VFHGVYLLYSRNPRYLGRTYIGYTVDPDRRIKQHNKGKDFGGAHKTSNRGPWDMVLIVYGFPNDISALRFEWAWQHPKMS   81 (133)
Q Consensus         2 ~~~~vYIL~s~~~~~~~~~YiG~T~dl~rRl~qHn~g~~~gGa~~T~~~~pw~lv~~~e~f~sk~~Al~~E~~iK~~~~s   81 (133)
                      .+||||||.|.+    |++|||+|+||.+||+|||+|.   ||+||++++||+|| |+|.|+|+++|+++|++||+|+|+
T Consensus         6 ~~~~VYIL~~~~----g~lY~G~T~dl~rRl~qH~~g~---ga~~T~~~~p~~LV-y~e~f~~~~~Al~rE~~iK~~~R~   77 (107)
T 1zg2_A            6 MNHYVYILECKD----GSWYTGYTTDVDRRIKKHASGK---GAKYTRGRGPFRLV-ATWAFPSKEEAMRWEYEVKHLSRR   77 (107)
T ss_dssp             CCEEEEEEECTT----SCEEEEEECCHHHHHHHHHHHT---TCCSCCCCSSCEEE-EEEEESCHHHHHHHHHHHHHSCHH
T ss_pred             CceEEEEEEcCC----CCEEEEEECCHHHHHHHHHccC---CCCccccCCCCEEE-EEEecCCHHHHHHHHHHHhcCCHH
Confidence            358999999977    9999999999999999999986   89999999999999 899999999999999999999999


Q ss_pred             hHHHHHhhhcCCCccHHHHHHHHHHhhcCCCCCCcCcEEEec
Q psy12152         82 RRLQHVARKKSKETTYTYCLRLLHIMLQTAPWQRLPLTVQWL  123 (133)
Q Consensus        82 rk~~~i~~~~~~~~~~~~~l~~~~~~l~~~~w~~~~l~v~~~  123 (133)
                      +|                 +++|...  +|.|.+|.-.+..+
T Consensus        78 ~K-----------------~~LI~~~--n~~~~dL~~~~~~~  100 (107)
T 1zg2_A           78 KK-----------------EQLVSLK--GGPYENTTKLSTTL  100 (107)
T ss_dssp             HH-----------------HHHHHHT--TCHHHHCCCTTCC-
T ss_pred             HH-----------------HHHHHhc--CCchHHHHHHHHHH
Confidence            99                 6666666  77777766554433

>1ywl_A Hypothetical UPF0213 protein EF2693; alpha and beta, structural genomics, northeast structural genomics consortium (NESG); NMR {Enterococcus faecalis}

Probab=99.97  E-value=5.4e-32  Score=189.90  Aligned_cols=80  Identities=31%  Similarity=0.476  Sum_probs=74.7

Q ss_pred             CceEEEEeeeCCCCCCCcEEEEEeCCHHHHHHHHhcCCCCCCccccc--cCCCeEEEEEEEccCCHHHHHHHHHHHcCCc
Q psy12152          2 VFHGVYLLYSRNPRYLGRTYIGYTVDPDRRIKQHNKGKDFGGAHKTS--NRGPWDMVLIVYGFPNDISALRFEWAWQHPK   79 (133)
Q Consensus         2 ~~~~vYIL~s~~~~~~~~~YiG~T~dl~rRl~qHn~g~~~gGa~~T~--~~~pw~lv~~~e~f~sk~~Al~~E~~iK~~~   79 (133)
                      .+||||||.|.+    |++|||+|+||.+||.|||+|.   ||+||+  +++||+|| |+|.|+|+++|+++|++||+|+
T Consensus         5 ~~~~vYIL~~~~----g~lY~G~T~dl~rRl~qHn~g~---ga~~T~~~~~~p~~LV-y~e~f~~~~~Al~rE~~iK~~~   76 (96)
T 1ywl_A            5 KSHYFYVLLCQD----GSFYGGYTTEPERRLTEHNSGT---GAKYTRLAKRRPVIMI-HTEKFETRSEATKAEAAFKKLT   76 (96)
T ss_dssp             SSEEEEEEECTT----CCCEEEEESCHHHHHHHHHHHH---SCSSCSSCCSSCCEEE-EEEEESSHHHHHHHHHHHHHSC
T ss_pred             CceEEEEEEcCC----CCEEEEEeCCHHHHHHHHHcCC---CCCcccccCCCCeEEE-EEEecCCHHHHHHHHHHHHcCC
Confidence            468999999977    9999999999999999999986   899999  99999999 8999999999999999999999


Q ss_pred             hhhHHHHHhh
Q psy12152         80 MSRRLQHVAR   89 (133)
Q Consensus        80 ~srk~~~i~~   89 (133)
                      |++|++.|..
T Consensus        77 R~~K~~LI~~   86 (96)
T 1ywl_A           77 RKQKEQYLKT   86 (96)
T ss_dssp             HHHHHHHHHH
T ss_pred             HHHHHHHHhc
Confidence            9999776643

>1mk0_A Intron-associated endonuclease 1; alpha/beta fold, catalytic domain, DNA-binding surface, hydrolase; HET: CIT; 1.60A {Enterobacteria phage T4} SCOP: d.226.1.1 PDB: 1ln0_A

Probab=97.76  E-value=4.3e-05  Score=52.18  Aligned_cols=70  Identities=21%  Similarity=0.330  Sum_probs=47.5

Q ss_pred             CCceEEEEeeeCCCCCCCcEEEEEeCCHHHHHHHHhc----CCCCCCccccc----cC-CCeEEEEEEEccCC-HHHHHH
Q psy12152          1 MVFHGVYLLYSRNPRYLGRTYIGYTVDPDRRIKQHNK----GKDFGGAHKTS----NR-GPWDMVLIVYGFPN-DISALR   70 (133)
Q Consensus         1 M~~~~vYIL~s~~~~~~~~~YiG~T~dl~rRl~qHn~----g~~~gGa~~T~----~~-~pw~lv~~~e~f~s-k~~Al~   70 (133)
                      |.+ +||.+.|..   .|.+|||.|.|+..|+.+|..    |..  +.+.-.    .+ .-..+. +.|.++. ..+...
T Consensus         1 mk~-GIY~I~n~~---ngk~YIGst~~l~~R~~~~~~~l~~g~~--~n~~L~~a~~kyG~~F~~~-iLe~~~~~~~el~~   73 (97)
T 1mk0_A            1 MKS-GIYQIKNTL---NNKVYVGSAKDFEKRWKRHFKDLEKGCH--SSIKLQRSFNKHGNVFECS-ILEEIPYEKDLIIE   73 (97)
T ss_dssp             CCC-EEEEEEETT---TCCEEEEEESSHHHHHHHHHHHHHHTCC--SCHHHHHHHHHHSSCEEEE-EEEECCCCHHHHHH
T ss_pred             Cce-EEEEEEECC---CCCEEEEecCCHHHHHHHHHHHHHcCCC--CCHHHHHHHHhcCcceEEE-EeeECCCCHHHHHH
Confidence            554 799999986   599999999999999999953    321  111111    11 235555 4666774 678888


Q ss_pred             HHHHHcC
Q psy12152         71 FEWAWQH   77 (133)
Q Consensus        71 ~E~~iK~   77 (133)
                      +|..|..
T Consensus        74 ~E~~~i~   80 (97)
T 1mk0_A           74 RANFWIK   80 (97)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            8887654

>1yd6_A UVRC; DNA binding protein; 2.00A {Bacillus caldotenax}

Probab=97.28  E-value=0.00038  Score=48.17  Aligned_cols=63  Identities=21%  Similarity=0.245  Sum_probs=45.0

Q ss_pred             eEEEEeeeCCCCCCCcEEEEEeCCHHHHHHHHhcCCCCCCcccccc--CCCeEEEEEEEccCCHHHHHHHHHH
Q psy12152          4 HGVYLLYSRNPRYLGRTYIGYTVDPDRRIKQHNKGKDFGGAHKTSN--RGPWDMVLIVYGFPNDISALRFEWA   74 (133)
Q Consensus         4 ~~vYIL~s~~~~~~~~~YiG~T~dl~rRl~qHn~g~~~gGa~~T~~--~~pw~lv~~~e~f~sk~~Al~~E~~   74 (133)
                      -+||++...+   ...+|||-+.|+.+|+.+|-.+. .  ...++.  ..-..+-  +....|..+|+-.|..
T Consensus        16 pGVY~~~d~~---g~vlYVGKAknLr~Rv~syf~~~-~--~~k~~~m~~~~~~i~--~~~t~sE~eAlllE~~   80 (99)
T 1yd6_A           16 PGCYLMKDKH---GTVIYVGKAKSLKERVRSYFTGT-H--DGKTQRLVEEIADFE--YIVTSSNAEALILEMN   80 (99)
T ss_dssp             CEEEEEECSS---CCEEEEEEESCHHHHHHGGGSSC-C--CHHHHHHHHHCSEEE--EEECSSHHHHHHHHHH
T ss_pred             CeEEEEEcCC---CCEEEEecCcCHHHHHHHHcccC-C--ChHHHHHHHheeEEE--EEEECCHHHHHHHHHH
Confidence            5899999987   46899999999999999997553 1  112221  1122333  3467899999999976

>1yd0_A Uvrabc system protein C; DNA binding protein; 1.50A {Thermotoga maritima} PDB: 1ycz_A 1yd1_A 1yd4_A 1yd3_A 1yd2_A 1yd5_A

Probab=97.05  E-value=0.00067  Score=46.71  Aligned_cols=61  Identities=18%  Similarity=0.182  Sum_probs=43.7

Q ss_pred             eEEEEeeeCCCCCCCcEEEEEeCCHHHHHHHHhcCCCCCCcccccc--CCCeEEEEEEEccCCHHHHHHHHHH
Q psy12152          4 HGVYLLYSRNPRYLGRTYIGYTVDPDRRIKQHNKGKDFGGAHKTSN--RGPWDMVLIVYGFPNDISALRFEWA   74 (133)
Q Consensus         4 ~~vYIL~s~~~~~~~~~YiG~T~dl~rRl~qHn~g~~~gGa~~T~~--~~pw~lv~~~e~f~sk~~Al~~E~~   74 (133)
                      -+||++.. +   ...+|||-+.|+.+|+.+|-.+.    ...++.  ..-..+-  +....|..+|+-.|..
T Consensus        16 pGVY~~~d-~---g~vlYVGKAknLr~Rv~syf~~~----~~k~~~~~~~~~~i~--~~~t~sE~eAlllE~~   78 (96)
T 1yd0_A           16 PGVYIFKN-K---GVPIYIGKAKRLSNRLRSYLNPQ----TEKVFRIGEEADELE--TIVVMNEREAFILEAN   78 (96)
T ss_dssp             CEEEEEEE-T---TEEEEEEEESSHHHHHHGGGSCS----SHHHHHHHHHCSEEE--EEECSSHHHHHHHHHH
T ss_pred             CeEEEEEC-C---CeEEEEecCcCHHHHHHHHccCC----CHHHHHHHHhccEEE--EEEECCHHHHHHHHHH
Confidence            58999999 6   35899999999999999997653    112221  1122333  3467899999999976

>2wsh_A Endonuclease II; GIY-YIG, hydrolase; 1.90A {Enterobacteria phage T4}

Probab=91.19  E-value=0.25  Score=36.23  Aligned_cols=28  Identities=25%  Similarity=0.358  Sum_probs=24.6

Q ss_pred             EEEEeeeCCCCCCCcEEEEEeCCHHHHHHHHh
Q psy12152          5 GVYLLYSRNPRYLGRTYIGYTVDPDRRIKQHN   36 (133)
Q Consensus         5 ~vYIL~s~~~~~~~~~YiG~T~dl~rRl~qHn   36 (133)
                      +||+....+    ..+|||-+.||.+|+++.-
T Consensus        42 GVY~~~~~g----~ViYVGKAknLkkRv~sYf   69 (143)
T 2wsh_A           42 VIYAIAIND----ELVYIGKTKNLRKRINYYR   69 (143)
T ss_dssp             EEEEEEETT----EEEEEEEESCHHHHHHHHH
T ss_pred             eEEEEEcCC----eEEEEEecccHhHHHHHhc
Confidence            599999744    7999999999999999984

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

No hit with e-value below 0.005

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	133
d1mk0a_	97	Homing endonuclease I-TevI {Bacteriophage T4 [TaxI	98.17

>d1mk0a_ d.226.1.1 (A:) Homing endonuclease I-TevI {Bacteriophage T4 [TaxId: 10665]}

class: Alpha and beta proteins (a+b)
fold: GIY-YIG endonuclease
superfamily: GIY-YIG endonuclease
family: GIY-YIG endonuclease
domain: Homing endonuclease I-TevI
species: Bacteriophage T4 [TaxId: 10665]

Probab=98.17  E-value=2e-06  Score=56.66  Aligned_cols=70  Identities=21%  Similarity=0.357  Sum_probs=45.6

Q ss_pred             CCceEEEEeeeCCCCCCCcEEEEEeCCHHHHHHHHhcCCCCC--Ccccc-c---cC-CCeEEEEEEEccC-CHHHHHHHH
Q psy12152          1 MVFHGVYLLYSRNPRYLGRTYIGYTVDPDRRIKQHNKGKDFG--GAHKT-S---NR-GPWDMVLIVYGFP-NDISALRFE   72 (133)
Q Consensus         1 M~~~~vYIL~s~~~~~~~~~YiG~T~dl~rRl~qHn~g~~~g--Ga~~T-~---~~-~pw~lv~~~e~f~-sk~~Al~~E   72 (133)
                      |+ -+||++.+..   .|.+|||.|.|+.+|+.+|......+  ..... +   .+ .-+.+. ..+.++ ++.++..+|
T Consensus         1 mk-sGIY~i~n~~---ngk~YIG~t~nl~~R~~~h~~~~~~~~~~~~~l~~~~~k~g~~F~~~-ile~~~~~~~~l~~~E   75 (97)
T d1mk0a_           1 MK-SGIYQIKNTL---NNKVYVGSAKDFEKRWKRHFKDLEKGCHSSIKLQRSFNKHGNVFECS-ILEEIPYEKDLIIERA   75 (97)
T ss_dssp             CC-CEEEEEEETT---TCCEEEEEESSHHHHHHHHHHHHHHTCCSCHHHHHHHHHHSSCEEEE-EEEECCCCHHHHHHHH
T ss_pred             CC-CEEEEEEECC---CCeEEEEEeCcHHHHHHHHHHHhhccCCccHHHHHHHHhccCcEEEE-EEEEcCCCHHHHHHHH
Confidence            54 3799999977   68999999999999999995321000  00011 0   11 235555 455554 577888988


Q ss_pred             HHH
Q psy12152         73 WAW   75 (133)
Q Consensus        73 ~~i   75 (133)
                      ..|
T Consensus        76 ~~~   78 (97)
T d1mk0a_          76 NFW   78 (97)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            775