Citrus Sinensis ID: 026681

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-----
Protein Sequence
MKTLEPVYSLGVDETDSSLPPKERRFAVLLSALLSSLTKDKVADGALQRLLQNGLHTAEAIDKADEATIKDLIYPVAFYTRKACNMKKIAKICLTKYDGDIPSSLDELLALPGIGPKMANMVMTLGWFNVQGICVDTHVHRICNRLGWVTQPGTKQKTSSPEQTREALQRWLPKEEWVRINPLLVGFGQTICTPLRPRCGMCTVSEYCPSAFKESSTSSSKSKKSESSSLRKLER
Secondary Structure (PSIPRED)
cccccccccccccccccccccccccHHHHHHHHHHccccHHHHHHHHHHHHHcccccHHHHHHccHHHHHHHcccccccHHHHHHHHHHHHHHHHHccccccccHHHHHccccccHHHHHHHHHHcccccccEEccccHHHHHHHHccccccccccccccHHHHHHHHHHHccHHHHHHHccHHHHccccccccccccccccccccccccccccccccccccccccccHHHHHcc
Secondary Structure Prediction (SSPRO)
ccHHHHHcccccHHHcccccccccHHHHHHHHHHHHHccHHHHHHHHHHHHHHHcccHHHHHcccHHHHHHHHHcHHHHHHHHHHHHHHHHHHHHHHcccccccHHHHHHcccccHHHHHHHHHHHHccccccEEccHHHHHHHHHccccccccccccccHHHHHHHHHHHccHHHHHHHHHHHHHHHHHHcccccccccccccHHHHHHHHccccccccccccccccccHHccc
Coil and Loop (DISEMBL)
mktlepvyslgvdetdsslppkERRFAVLLSALLSSLTKDKVADGALQRLLQNGLHTAEAIDKADEATIKDLIYPVAFYTRKACNMKKIAKICLtkydgdipssLDELlalpgigpkMANMVMTLGWFNVQGICVDTHVHRICnrlgwvtqpgtkqktsspeQTREALQRWlpkeewvrinpllvgfgqtictplrprcgmctvseycpsafkesstssskskksesSSLRKLER
Flexible Loop (DISEMBL)
mktlepvyslgvdetdsslppkERRFAVLLSALLSSLTKDKVADGALQRLLQNGLHTAEAIDKADEATIKDLIYPVAFYTRKACNMKKIAKICLTKYDGDIPSSLDELLALPGIGPKMANMVMTLGWFNVQGICVDTHVHRICNRlgwvtqpgtkqktsspeqtREALQRWLPKEEWVRINPLLVGFGQTICTPLRPRCGMCTVSEYCPSafkesstssskskksessslrkler
Low Complexity Region (SEG)
MKTLEPVYSLGVDETDSSLPPKERRFAVllsallsslTKDKVADGALQRLLQNGLHTAEAIDKADEATIKDLIYPVAFYTRKACNMKKIAKICLTKYDGDIPSSLDELLALPGIGPKMANMVMTLGWFNVQGICVDTHVHRICNRLGWVTQPGTKQKTSSPEQTREALQRWLPKEEWVRINPLLVGFGQTICTPLRPRCGMCTVSEYCPSAFkesstssskskksesssLRKLER
Disordered region (IsUnstruct)
*************************FAVLLSALLSSLTKDKVADGALQRLLQNGLHTAEAIDKADEATIKDLIYPVAFYTRKACNMKKIAKICLTKYDGDIPSSLDELLALPGIGPKMANMVMTLGWFNVQGICVDTHVHRICNRLGWVT*****************LQRWLPKEEWVRINPLLVGFGQTICTPLRPRCGMCTVSEYCP**************************
Disordered Region (DISOPRED)
*KTLEPVYSLGVDETDSSLPPKERRFAVLLSALLSSLTKDKVADGALQRLLQNGLHTAEAIDKADEATIKDLIYPVAFYTRKACNMKKIAKICLTKYDGDIPSSLDELLALPGIGPKMANMVMTLGWFNVQGICVDTHVHRICNRLGWVTQPGTKQKTSSPEQTREALQRWLPKEEWVRINPLLVGFGQTICTPLRPRCGMCTVSEYC***************************
Disordered Region (DISEMBL)
MKTLEPVYSLGVDETDSSLPPKERRFAVLLSALLSSLTKDKVADGALQRLLQNGLHTAEAIDKADEATIKDLIYPVAFYTRKACNMKKIAKICLTKYDGDIPSSLDELLALPGIGPKMANMVMTLGWFNVQGICVDTHVHRICNRLGWVTQ****************LQRWLPKEEWVRINPLLVGFGQTICTPLRPRCGMCTVSEYCP**************************
Disordered Region (DISPRO)
MKTLEPVYSLGVDETDSSLPPKERRFAVLLSALLSSLTKDKVADGALQRLLQNGLHTAEAIDKADEATIKDLIYPVAFYTRKACNMKKIAKICLTKYDGDIPSSLDELLALPGIGPKMANMVMTLGWFNVQGICVDTHVHRICNRLGWVTQPGTKQKTSSPEQTREALQRWLPKEEWVRINPLLVGFGQTICTPLRPRCGMCTVSEYCPSAFKES********************
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MKTLEPVYSLGVDETDSSLPPKERRFAVLLSALLSSLTKDKVADGALQRLLQNGLHTAEAIDKADEATIKDLIYPVAFYTRKACNMKKIAKICLTKYDGDIPSSLDELLALPGIGPKMANMVMTLGWFNVQGICVDTHVHRICNRLGWVTQPGTKQKTSSPEQTREALQRWLPKEEWVRINPLLVGFGQTICTPLRPRCGMCTVSEYCPSAFKESSTSSSKSKKSESSSLRKLER
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	235	2.2.26 [Sep-21-2011]
Q2KID2	305	Endonuclease III-like pro	yes	no	0.851	0.655	0.531	4e-57
P78549	312	Endonuclease III-like pro	yes	no	0.851	0.641	0.536	9e-57
O35980	300	Endonuclease III-like pro	yes	no	0.851	0.666	0.512	3e-55
P54137	298	Probable endonuclease III	no	no	0.897	0.708	0.473	2e-49
Q09907	355	Endonuclease III homolog	yes	no	0.880	0.583	0.454	7e-46
Q8SRB8	238	Endonuclease III homolog	yes	no	0.846	0.836	0.420	4e-39
Q08214	380	DNA base excision repair	yes	no	0.868	0.536	0.396	6e-37
P31378	399	Mitochondrial DNA base ex	no	no	0.719	0.423	0.419	1e-34
Q9WYK0	213	Endonuclease III OS=Therm	yes	no	0.740	0.816	0.420	6e-34
Q58030	344	Putative endonuclease MJ0	yes	no	0.740	0.505	0.456	3e-30

>sp|Q2KID2|NTHL1_BOVIN Endonuclease III-like protein 1 OS=Bos taurus GN=NTHL1 PE=2 SV=1

 Score =  221 bits (562), Expect = 4e-57,   Method: Compositional matrix adjust.
 Identities = 110/207 (53%), Positives = 139/207 (67%), Gaps = 7/207 (3%)

Query: 6   PVYSLGVDET-DSSLPPKERRFAVLLSALLSSLTKDKVADGALQRLLQNGLHTAEAIDKA 64
           PV  LG +   D S  PK RR+ VLLS +LSS TKD+V  GA+QRL   GL T ++I + 
Sbjct: 102 PVDQLGAEHCFDPSASPKVRRYQVLLSLMLSSQTKDQVTAGAMQRLRARGL-TVDSILQT 160

Query: 65  DEATIKDLIYPVAFYTRKACNMKKIAKICLTKYDGDIPSSLDELLALPGIGPKMANMVMT 124
           D++T+  LIYPV F+  K   +K+ + I   +YDGDIP+S+ EL+ALPG+GPKMA++ M 
Sbjct: 161 DDSTLGALIYPVGFWRSKVKYIKQTSAILQQRYDGDIPASVAELVALPGVGPKMAHLAMA 220

Query: 125 LGWFNVQGICVDTHVHRICNRLGWVTQPGTKQKTSSPEQTREALQRWLPKEEWVRINPLL 184
           + W  V GI VDTHVHRI NRL W     TK+ T SPE+TR AL+ WLP+E W  IN LL
Sbjct: 221 VAWGTVSGIAVDTHVHRIANRLRW-----TKKATKSPEETRRALEEWLPRELWSEINGLL 275

Query: 185 VGFGQTICTPLRPRCGMCTVSEYCPSA 211
           VGFGQ  C P+RPRC  C     CP+A
Sbjct: 276 VGFGQQTCLPIRPRCQACLNRALCPAA 302

Has both an apurinic and/or apyrimidinic endonuclease activity and a DNA N-glycosylase activity. Incises damaged DNA at cytosines, thymines and guanines. Acts on a damaged strand, 5' from the damaged site. Required for the repair of both oxidative DNA damage and spontaneous mutagenic lesions.
Bos taurus (taxid: 9913)
EC: 4EC: .EC: 2EC: .EC: 9EC: 9EC: .EC: 1EC: 8

>sp|P78549|NTHL1_HUMAN Endonuclease III-like protein 1 OS=Homo sapiens GN=NTHL1 PE=1 SV=2

 Score =  219 bits (559), Expect = 9e-57,   Method: Compositional matrix adjust.
 Identities = 111/207 (53%), Positives = 138/207 (66%), Gaps = 7/207 (3%)

Query: 6   PVYSLGVDE-TDSSLPPKERRFAVLLSALLSSLTKDKVADGALQRLLQNGLHTAEAIDKA 64
           PV  LG +   DSS PPK RR+ VLLS +LSS TKD+V  GA+QRL   GL T ++I + 
Sbjct: 109 PVDHLGTEHCYDSSAPPKVRRYQVLLSLMLSSQTKDQVTAGAMQRLRARGL-TVDSILQT 167

Query: 65  DEATIKDLIYPVAFYTRKACNMKKIAKICLTKYDGDIPSSLDELLALPGIGPKMANMVMT 124
           D+AT+  LIYPV F+  K   +K+ + I    Y GDIP+S+ EL+ALPG+GPKMA++ M 
Sbjct: 168 DDATLGKLIYPVGFWRSKVKYIKQTSAILQQHYGGDIPASVAELVALPGVGPKMAHLAMA 227

Query: 125 LGWFNVQGICVDTHVHRICNRLGWVTQPGTKQKTSSPEQTREALQRWLPKEEWVRINPLL 184
           + W  V GI VDTHVHRI NRL W     TK+ T SPE+TR AL+ WLP+E W  IN LL
Sbjct: 228 VAWGTVSGIAVDTHVHRIANRLRW-----TKKATKSPEETRAALEEWLPRELWHEINGLL 282

Query: 185 VGFGQTICTPLRPRCGMCTVSEYCPSA 211
           VGFGQ  C P+ PRC  C     CP+A
Sbjct: 283 VGFGQQTCLPVHPRCHACLNQALCPAA 309

Has both an apurinic and/or apyrimidinic endonuclease activity and a DNA N-glycosylase activity. Incises damaged DNA at cytosines, thymines and guanines. Acts on a damaged strand, 5' from the damaged site. Required for the repair of both oxidative DNA damage and spontaneous mutagenic lesions.

Homo sapiens (taxid: 9606)

EC: 4

EC: .

EC: 2

EC: .

EC: 9

EC: 9

EC: .

EC: 1

EC: 8

>sp|O35980|NTHL1_MOUSE Endonuclease III-like protein 1 OS=Mus musculus GN=Nthl1 PE=2 SV=1

 Score =  215 bits (547), Expect = 3e-55,   Method: Compositional matrix adjust.
 Identities = 106/207 (51%), Positives = 138/207 (66%), Gaps = 7/207 (3%)

Query: 6   PVYSLGVDE-TDSSLPPKERRFAVLLSALLSSLTKDKVADGALQRLLQNGLHTAEAIDKA 64
           PV  LG +   D+S PPK RR+ VLLS +LSS TKD+V  GA+QRL   GL T E+I + 
Sbjct: 97  PVDQLGAEHCYDASAPPKVRRYQVLLSLMLSSQTKDQVTAGAMQRLRARGL-TVESILQT 155

Query: 65  DEATIKDLIYPVAFYTRKACNMKKIAKICLTKYDGDIPSSLDELLALPGIGPKMANMVMT 124
           D+ T+  LIYPV F+  K   +K+   I   +Y+GDIP+S+ EL+ALPG+GPKMA++ M 
Sbjct: 156 DDDTLGRLIYPVGFWRNKVKYIKQTTAILQQRYEGDIPASVAELVALPGVGPKMAHLAMA 215

Query: 125 LGWFNVQGICVDTHVHRICNRLGWVTQPGTKQKTSSPEQTREALQRWLPKEEWVRINPLL 184
           + W  + GI VDTHVHRI NRL W     TK+ T +PE+TR+ L+ WLP+  W  +N LL
Sbjct: 216 VAWGTISGIAVDTHVHRIANRLRW-----TKKMTKTPEETRKNLEEWLPRVLWSEVNGLL 270

Query: 185 VGFGQTICTPLRPRCGMCTVSEYCPSA 211
           VGFGQ IC P+ PRC  C     CP+A
Sbjct: 271 VGFGQQICLPVHPRCQACLNKALCPAA 297

Has both an apurinic and/or apyrimidinic endonuclease activity and a DNA N-glycosylase activity. Incises damaged DNA at cytosines, thymines and guanines. Acts on a damaged strand, 5' from the damaged site. Required for the repair of both oxidative DNA damage and spontaneous mutagenic lesions.

Mus musculus (taxid: 10090)

EC: 4

EC: .

EC: 2

EC: .

EC: 9

EC: 9

EC: .

EC: 1

EC: 8

>sp|P54137|NTH1_CAEEL Probable endonuclease III homolog OS=Caenorhabditis elegans GN=nth-1 PE=1 SV=2

 Score =  196 bits (497), Expect = 2e-49,   Method: Compositional matrix adjust.
 Identities = 109/230 (47%), Positives = 143/230 (62%), Gaps = 19/230 (8%)

Query: 4   LEPVYSLGVDE-TDSSLPPKERRFAVLLSALLSSLTKDKVADGALQRLLQNGLHTAEAID 62
           + PV ++G  +  D    P   RF VL++ +LSS T+D+V   A++RL  +GL    +I 
Sbjct: 45  IAPVDTMGCHKLADPLAAPPVHRFQVLVALMLSSQTRDEVNAAAMKRLKDHGL----SIG 100

Query: 63  KADEATIKDL---IYPVAFYTRKACNMKKIAKICLTKYDGDIPSSLDELLALPGIGPKMA 119
           K  E  + DL   + PV FY RKA  ++K AKI    + GDIP SLD L ALPG+GPKMA
Sbjct: 101 KILEFKVPDLETILCPVGFYKRKAVYLQKTAKILKDDFSGDIPDSLDGLCALPGVGPKMA 160

Query: 120 NMVMTLGWFNVQGICVDTHVHRICNRLGWVTQPGTKQKTSSPEQTREALQRWLPKEEWVR 179
           N+VM + W    GI VDTHVHRI NRLGW+       KTS+PE+T++AL+  LPK EW  
Sbjct: 161 NLVMQIAWGECVGIAVDTHVHRISNRLGWI-------KTSTPEKTQKALEILLPKSEWQP 213

Query: 180 INPLLVGFGQTICTPLRPRCGMCTVSEYCPSAFKESSTSSSKSKKSESSS 229
           IN LLVGFGQ  C P+RP+CG C     CPS    S+  + KS+  E+S+
Sbjct: 214 INHLLVGFGQMQCQPVRPKCGTCLCRFTCPS----STAKNVKSETEETST 259

Has both an apurinic and/or apyrimidinic endonuclease activity and a DNA N-glycosylase activity. Primarily excises oxidized pyrimidine bases.

Caenorhabditis elegans (taxid: 6239)

EC: 4

EC: .

EC: 2

EC: .

EC: 9

EC: 9

EC: .

EC: 1

EC: 8

>sp|Q09907|NTH1_SCHPO Endonuclease III homolog OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=nth1 PE=1 SV=1

 Score =  183 bits (465), Expect = 7e-46,   Method: Compositional matrix adjust.
 Identities = 100/220 (45%), Positives = 127/220 (57%), Gaps = 13/220 (5%)

Query: 2   KTLEPVYSLGVDETDSSLPPKERRFAVLLSALLSSLTKDKVADGALQRL---LQNGLHTA 58
           K + PV   G         PK+ RF  L++ +LSS TKD V    ++ L   L  GL   
Sbjct: 25  KVVAPVDVQGCHTLGERNDPKKFRFQTLVALMLSSQTKDIVLGPTMRNLKEKLAGGL-CL 83

Query: 59  EAIDKADEATIKDLIYPVAFYTRKACNMKKIAKICLTKYDGDIPSSLDELLALPGIGPKM 118
           E I   DE ++  LI  V F+ RK   +K++A+I   K+ GDIP ++++L+ LPG+GPKM
Sbjct: 84  EDIQNIDEVSLNKLIEKVGFHNRKTIYLKQMARILSEKFQGDIPDTVEDLMTLPGVGPKM 143

Query: 119 ANMVMTLGWFNVQGICVDTHVHRICNRLGWVTQPGTKQKTSSPEQTREALQRWLPKEEWV 178
             + M++ W    GI VD HVHRICN L W         T + EQTR ALQ WLPKE W 
Sbjct: 144 GYLCMSIAWNKTVGIGVDVHVHRICNLLHWCN-------TKTEEQTRAALQSWLPKELWF 196

Query: 179 RINPLLVGFGQTICTPLRPRCGMCTVSE--YCPSAFKESS 216
            +N  LVGFGQTIC P   RC MCT+S    CPSAFKE S
Sbjct: 197 ELNHTLVGFGQTICLPRGRRCDMCTLSSKGLCPSAFKEKS 236

Has both an apurinic and/or apyrimidinic endonuclease activity and a DNA N-glycosylase activity. Possesses glycosylase activity on different types of DNA substrates with pyrimidines damage. It can release both urea and thymine glycol from double-stranded polymers.

Schizosaccharomyces pombe (strain 972 / ATCC 24843) (taxid: 284812)

EC: 4

EC: .

EC: 2

EC: .

EC: 9

EC: 9

EC: .

EC: 1

EC: 8

>sp|Q8SRB8|NTH1_ENCCU Endonuclease III homolog OS=Encephalitozoon cuniculi (strain GB-M1) GN=NTH1 PE=1 SV=1

 Score =  161 bits (407), Expect = 4e-39,   Method: Compositional matrix adjust.
 Identities = 93/221 (42%), Positives = 124/221 (56%), Gaps = 22/221 (9%)

Query: 4   LEPVYSLGVDETDSSLPPKERRFAVLLSALLSSLTKDKVADGALQRLLQ----------- 52
           + PV ++G   T S    +ERRF +L+S LLSS TKD+V   A+ RL +           
Sbjct: 27  VSPVDTMGCSITPSCRTEEERRFHILVSLLLSSQTKDEVTYEAMARLRKLLPESAATDGE 86

Query: 53  -NGLHTAEAIDKADEATIKDLIYPVAFYTRKACNMKKIAKICLTKYDGDIPSSLDELLAL 111
             G  T E +  +D   I + I  V F+ RKA N+KKIA+I   K    +P  + +L++L
Sbjct: 87  ARGGLTIERVANSDVKHINECIKKVGFHNRKAANLKKIAEILREK---GLPREMKDLISL 143

Query: 112 PGIGPKMANMVMTLGWFNVQGICVDTHVHRICNRLGWVTQPGTKQKTSSPEQTREALQRW 171
           PGIG KMA + M+       GI VDTHVHRI NR+G V       +T   E TR  L+R 
Sbjct: 144 PGIGNKMALLYMSHACNRTVGISVDTHVHRISNRIGLV-------RTRDVESTRRELERV 196

Query: 172 LPKEEWVRINPLLVGFGQTICTPLRPRCGMCTVSEYCPSAF 212
           +P++EW  IN +LVGFGQTIC   RPRC  C +   CPS+ 
Sbjct: 197 VPRKEWKTINNILVGFGQTICVAKRPRCEECCIRGRCPSSL 237

Has both an apurinic and/or apyrimidinic endonuclease activity and a DNA N-glycosylase activity. Possesses glycosylase activity on different types of DNA substrates with pyrimidines damage. It can release both urea and thymine glycol from double-stranded polymers.

Encephalitozoon cuniculi (strain GB-M1) (taxid: 284813)

EC: 4

EC: .

EC: 2

EC: .

EC: 9

EC: 9

EC: .

EC: 1

EC: 8

>sp|Q08214|NTG2_YEAST DNA base excision repair N-glycosylase 2 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=NTG2 PE=1 SV=1

 Score =  154 bits (388), Expect = 6e-37,   Method: Compositional matrix adjust.
 Identities = 86/217 (39%), Positives = 119/217 (54%), Gaps = 13/217 (5%)

Query: 19  LPPKERRFAVLLSALLSSLTKD-KVADGALQ--RLLQNGLHTAEAID-----KADEATIK 70
           + PK  R   L+  +LS+ T+D ++A  AL       N L  AE I      K DE  + 
Sbjct: 142 VDPKNFRLQFLIGTMLSAQTRDERMAQAALNITEYCLNTLKIAEGITLDGLLKIDEPVLA 201

Query: 71  DLIYPVAFYTRKACNMKKIAKICLTKYDGDIPSSLDELLALPGIGPKMANMVMTLGWFNV 130
           +LI  V+FYTRKA  +K+ A++ +  +D DIP  ++ +L+LPG+GPKM  + +  GW  +
Sbjct: 202 NLIRCVSFYTRKANFIKRTAQLLVDNFDSDIPYDIEGILSLPGVGPKMGYLTLQKGWGLI 261

Query: 131 QGICVDTHVHRICNRLGWVTQPGTKQKTSSPEQTREALQRWLPKEEWVRINPLLVGFGQT 190
            GICVD HVHR+C    WV       K  + E TR+ LQ WLP   W  IN +LVGFGQ 
Sbjct: 262 AGICVDVHVHRLCKMWNWVDPI----KCKTAEHTRKELQVWLPHSLWYEINTVLVGFGQL 317

Query: 191 ICTPLRPRCGMCTVSEYCPSAFKESSTSSSKSKKSES 227
           IC     RC +C  ++ C +A  E    SSK  + E 
Sbjct: 318 ICMARGKRCDLCLANDVC-NARNEKLIESSKFHQLED 353

Excision repair N-glycosylase involved in the repair of DNA base damage in the nucleus. NTG2 can use dihydrothymine (poor substrate), urea, and uracil glycol are substrates.

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (taxid: 559292)

>sp|P31378|NTG1_YEAST Mitochondrial DNA base excision repair N-glycosylase 1 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=NTG1 PE=1 SV=1

 Score =  146 bits (369), Expect = 1e-34,   Method: Compositional matrix adjust.
 Identities = 76/181 (41%), Positives = 109/181 (60%), Gaps = 12/181 (6%)

Query: 19  LPPKERRFAVLLSALLSSLTKDKVADGALQRLLQ---NGLH-----TAEAIDKADEATIK 70
           + P++ R  VLL  +LSS TKD+V   A+  +++   + LH     T EA+ + +E  + 
Sbjct: 137 ISPRDYRLQVLLGVMLSSQTKDEVTAMAMLNIMRYCIDELHSEEGMTLEAVLQINETKLD 196

Query: 71  DLIYPVAFYTRKACNMKKIAKICLTKYDGDIPSSLDELLALPGIGPKMANMVMTLGWFNV 130
           +LI+ V F+TRKA  +    KI   ++  D+P++++ELL LPG+GPKMA + +   W  +
Sbjct: 197 ELIHSVGFHTRKAKYILSTCKILQDQFSSDVPATINELLGLPGVGPKMAYLTLQKAWGKI 256

Query: 131 QGICVDTHVHRICNRLGWVTQPGTKQKTSSPEQTREALQRWLPKEEWVRINPLLVGFGQT 190
           +GICVD HV R+     WV      QK  +P+QTR  LQ WLPK  W  IN LLVGFGQ 
Sbjct: 257 EGICVDVHVDRLTKLWKWV----DAQKCKTPDQTRTQLQNWLPKGLWTEINGLLVGFGQI 312

Query: 191 I 191
           I
Sbjct: 313 I 313

Excision repair N-glycosylase involved in the repair of DNA base damage in the mitochondria. NTG1 can use dihydrothymine, urea, and uracil glycol are substrates.

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (taxid: 559292)

>sp|Q9WYK0|END3_THEMA Endonuclease III OS=Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099) GN=nth PE=3 SV=1

 Score =  144 bits (362), Expect = 6e-34,   Method: Compositional matrix adjust.
 Identities = 77/183 (42%), Positives = 111/183 (60%), Gaps = 9/183 (4%)

Query: 26  FAVLLSALLSSLTKDKVADGALQRLLQNGLHTAEAIDKADEATIKDLIYPVAFYTRKACN 85
           F VL+S +LS  T+D+  + A ++L +    T + + KA    + DLI     Y +KA  
Sbjct: 23  FRVLISTVLSQRTRDENTEKASKKLFE-VYRTPQELAKAKPEDLYDLIKESGMYRQKAER 81

Query: 86  MKKIAKICLTKYDGDIPSSLDELLALPGIGPKMANMVMTLGWFNVQGICVDTHVHRICNR 145
           + +I++I + KY G +P SL+ELL LPG+G K AN+V+ +G F    + VDTHVHRI NR
Sbjct: 82  IVEISRILVEKYGGRVPDSLEELLKLPGVGRKTANIVLWVG-FKKPALAVDTHVHRISNR 140

Query: 146 LGWVTQPGTKQKTSSPEQTREALQRWLPKEEWVRINPLLVGFGQTICTPLRPRCGMCTVS 205
           LGWV       KT +PE+T EAL++ LP++ W  IN  +V FG+ IC P  P C  C + 
Sbjct: 141 LGWV-------KTRTPEETEEALKKLLPEDLWGPINGSMVEFGRRICKPQNPLCEECFLK 193

Query: 206 EYC 208
            +C
Sbjct: 194 NHC 196

Has both an apurinic and/or apyrimidinic endonuclease activity and a DNA N-glycosylase activity. Incises damaged DNA at cytosines, thymines and guanines. Acts on a damaged strand, 5' from the damaged site.

Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099) (taxid: 243274)

EC: 4

EC: .

EC: 2

EC: .

EC: 9

EC: 9

EC: .

EC: 1

EC: 8

>sp|Q58030|Y613_METJA Putative endonuclease MJ0613 OS=Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440) GN=MJ0613 PE=3 SV=2

 Score =  131 bits (330), Expect = 3e-30,   Method: Compositional matrix adjust.
 Identities = 85/186 (45%), Positives = 116/186 (62%), Gaps = 12/186 (6%)

Query: 26  FAVLLSALLSSLTKDKVADGALQRLLQNGLHTAEAIDKADEATIKDLIYPVAFYTRKACN 85
           F VL+S ++S+ TKD+V +   ++L +  +   + +   DE  + DLIYP  FY  KA N
Sbjct: 27  FKVLISTIISARTKDEVTEEVSKKLFKE-IKDVDDLLNIDEEKLADLIYPAGFYKNKAKN 85

Query: 86  MKKIAKICLTKYDGDIPSSLDELLALPGIGPKMANMVMTLGWFNVQGICVDTHVHRICNR 145
           +KK+AKI    Y+G +P SL+ELL LPG+G K AN+V+TL  FN  GICVDTHVHRICNR
Sbjct: 86  LKKLAKILKENYNGKVPDSLEELLKLPGVGRKTANLVITLA-FNKDGICVDTHVHRICNR 144

Query: 146 LGWVTQPGTKQKTSSPEQTREALQRWLPKEEWVRINPLLVGFGQTICTPLRPRCGMC--T 203
              V        T +PE+T   L++ LPK+ W  IN LLV FG+ IC+  + +C  C   
Sbjct: 145 WEIVD-------TETPEETEFELRKKLPKKYWKVINNLLVVFGREICSS-KSKCDKCFKE 196

Query: 204 VSEYCP 209
           + E CP
Sbjct: 197 IKEKCP 202

Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440) (taxid: 243232)

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	235
255587056	357	endonuclease III, putative [Ricinus comm	0.961	0.633	0.738	2e-96
356541151	354	PREDICTED: endonuclease III-like protein	0.893	0.593	0.761	3e-93
21537257	379	putative endonuclease [Arabidopsis thali	0.893	0.554	0.747	5e-92
11181952	354	endonuclease III homologue [Arabidopsis	0.893	0.593	0.747	7e-92
145330326	377	endonuclease III [Arabidopsis thaliana]	0.893	0.557	0.742	8e-92
18402669	379	endonuclease III [Arabidopsis thaliana]	0.893	0.554	0.742	8e-92
359478121	355	PREDICTED: endonuclease III-like protein	0.931	0.616	0.771	9e-91
297826589	354	predicted protein [Arabidopsis lyrata su	0.893	0.593	0.733	1e-90
297743769	379	unnamed protein product [Vitis vinifera]	0.931	0.577	0.761	4e-89
297843388	384	hypothetical protein ARALYDRAFT_470604 [	0.914	0.559	0.705	1e-88

>gi|255587056|ref|XP_002534117.1| endonuclease III, putative [Ricinus communis] gi|223525829|gb|EEF28268.1| endonuclease III, putative [Ricinus communis]

 Score =  357 bits (917), Expect = 2e-96,   Method: Compositional matrix adjust.
 Identities = 167/226 (73%), Positives = 196/226 (86%)

Query: 6   PVYSLGVDETDSSLPPKERRFAVLLSALLSSLTKDKVADGALQRLLQNGLHTAEAIDKAD 65
           PV ++G ++  S LP KERRFAVL+S+L+SS TKD V  GA+QRL QN L TA+AIDKAD
Sbjct: 132 PVDTMGCEKAGSFLPSKERRFAVLVSSLMSSQTKDHVTHGAVQRLHQNSLLTADAIDKAD 191

Query: 66  EATIKDLIYPVAFYTRKACNMKKIAKICLTKYDGDIPSSLDELLALPGIGPKMANMVMTL 125
           E TIKDLIYPV FYTRKA N+KKIAKICL KYDGDIP SL++LL+LPGIGPKMA++VM +
Sbjct: 192 ETTIKDLIYPVGFYTRKASNLKKIAKICLMKYDGDIPRSLEDLLSLPGIGPKMAHLVMNV 251

Query: 126 GWFNVQGICVDTHVHRICNRLGWVTQPGTKQKTSSPEQTREALQRWLPKEEWVRINPLLV 185
            W +VQGICVDTHVHRICNRLGWV++PGT+QKTS+PE+TR ALQ WLPKEEWV INPLLV
Sbjct: 252 AWDDVQGICVDTHVHRICNRLGWVSRPGTEQKTSNPEETRVALQLWLPKEEWVPINPLLV 311

Query: 186 GFGQTICTPLRPRCGMCTVSEYCPSAFKESSTSSSKSKKSESSSLR 231
           GFGQTICTPLRPRCGMC+++E+CPSAFKE+S+ +SK KKS  S  R
Sbjct: 312 GFGQTICTPLRPRCGMCSITEFCPSAFKETSSPASKMKKSGLSRKR 357

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356541151|ref|XP_003539044.1| PREDICTED: endonuclease III-like protein 1-like [Glycine max]

 Score =  347 bits (890), Expect = 3e-93,   Method: Compositional matrix adjust.
 Identities = 160/210 (76%), Positives = 184/210 (87%)

Query: 6   PVYSLGVDETDSSLPPKERRFAVLLSALLSSLTKDKVADGALQRLLQNGLHTAEAIDKAD 65
           PV ++G ++   +LPPKERRFAVL+S+LLSS TKD V  GA+QRLLQN L TA+AI+ AD
Sbjct: 126 PVDTMGCEKAGETLPPKERRFAVLVSSLLSSQTKDPVTHGAIQRLLQNDLLTADAINDAD 185

Query: 66  EATIKDLIYPVAFYTRKACNMKKIAKICLTKYDGDIPSSLDELLALPGIGPKMANMVMTL 125
           E TIK LIYPV FYTRKA N+KKIA ICL KYDGDIPSS+++LL LPGIGPKMA++VM +
Sbjct: 186 EETIKKLIYPVGFYTRKASNLKKIANICLMKYDGDIPSSIEQLLLLPGIGPKMAHLVMNV 245

Query: 126 GWFNVQGICVDTHVHRICNRLGWVTQPGTKQKTSSPEQTREALQRWLPKEEWVRINPLLV 185
           GW NVQGICVDTHVHRICNRLGWV++ GTKQKTS+PE+TRE LQRWLPKEEWV INPLLV
Sbjct: 246 GWNNVQGICVDTHVHRICNRLGWVSRLGTKQKTSTPEETREELQRWLPKEEWVPINPLLV 305

Query: 186 GFGQTICTPLRPRCGMCTVSEYCPSAFKES 215
           GFGQTICTPLRPRCG C++SE CPSAFKE+
Sbjct: 306 GFGQTICTPLRPRCGECSISELCPSAFKET 335

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|21537257|gb|AAM61598.1| putative endonuclease [Arabidopsis thaliana]

 Score =  342 bits (878), Expect = 5e-92,   Method: Compositional matrix adjust.
 Identities = 157/210 (74%), Positives = 183/210 (87%)

Query: 6   PVYSLGVDETDSSLPPKERRFAVLLSALLSSLTKDKVADGALQRLLQNGLHTAEAIDKAD 65
           PV S+G D+  S LPP ERRFAVLL ALLSS TKD+V + A+ RL QNGL T EA+DKAD
Sbjct: 154 PVDSMGCDKAGSFLPPTERRFAVLLGALLSSQTKDQVNNAAIHRLHQNGLLTPEAVDKAD 213

Query: 66  EATIKDLIYPVAFYTRKACNMKKIAKICLTKYDGDIPSSLDELLALPGIGPKMANMVMTL 125
           E+TIK+LIYPV FYTRKA  MKKIA+ICL KYDGDIPSSLD+LL+LPGIGPKMA++++ +
Sbjct: 214 ESTIKELIYPVGFYTRKATYMKKIARICLVKYDGDIPSSLDDLLSLPGIGPKMAHLILHI 273

Query: 126 GWFNVQGICVDTHVHRICNRLGWVTQPGTKQKTSSPEQTREALQRWLPKEEWVRINPLLV 185
            W +VQGICVDTHVHRICNRLGWV++PGTKQKT+SPE+TR ALQ+WLPKEEWV INPLLV
Sbjct: 274 AWNDVQGICVDTHVHRICNRLGWVSRPGTKQKTTSPEETRVALQQWLPKEEWVAINPLLV 333

Query: 186 GFGQTICTPLRPRCGMCTVSEYCPSAFKES 215
           GFGQ ICTPLRPRC  C+VS+ CP+AFKE+
Sbjct: 334 GFGQMICTPLRPRCEACSVSKLCPAAFKET 363

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|11181952|emb|CAC16135.1| endonuclease III homologue [Arabidopsis thaliana]

 Score =  342 bits (877), Expect = 7e-92,   Method: Compositional matrix adjust.
 Identities = 157/210 (74%), Positives = 183/210 (87%)

Query: 6   PVYSLGVDETDSSLPPKERRFAVLLSALLSSLTKDKVADGALQRLLQNGLHTAEAIDKAD 65
           PV S+G D+  S LPP ERRFAVLL ALLSS TKD+V + A+ RL QNGL T EA+DKAD
Sbjct: 129 PVDSMGCDKAGSFLPPTERRFAVLLGALLSSQTKDQVNNAAIHRLHQNGLLTPEAVDKAD 188

Query: 66  EATIKDLIYPVAFYTRKACNMKKIAKICLTKYDGDIPSSLDELLALPGIGPKMANMVMTL 125
           E+TIK+LIYPV FYTRKA  MKKIA+ICL KYDGDIPSSLD+LL+LPGIGPKMA++++ +
Sbjct: 189 ESTIKELIYPVGFYTRKATYMKKIARICLVKYDGDIPSSLDDLLSLPGIGPKMAHLILHI 248

Query: 126 GWFNVQGICVDTHVHRICNRLGWVTQPGTKQKTSSPEQTREALQRWLPKEEWVRINPLLV 185
            W +VQGICVDTHVHRICNRLGWV++PGTKQKT+SPE+TR ALQ+WLPKEEWV INPLLV
Sbjct: 249 AWNDVQGICVDTHVHRICNRLGWVSRPGTKQKTTSPEETRVALQQWLPKEEWVAINPLLV 308

Query: 186 GFGQTICTPLRPRCGMCTVSEYCPSAFKES 215
           GFGQ ICTPLRPRC  C+VS+ CP+AFKE+
Sbjct: 309 GFGQMICTPLRPRCEACSVSKLCPAAFKET 338

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|145330326|ref|NP_001077988.1| endonuclease III [Arabidopsis thaliana] gi|17380754|gb|AAL36207.1| putative endonuclease [Arabidopsis thaliana] gi|20259623|gb|AAM14168.1| putative endonuclease [Arabidopsis thaliana] gi|330253456|gb|AEC08550.1| endonuclease III [Arabidopsis thaliana]

 Score =  342 bits (877), Expect = 8e-92,   Method: Compositional matrix adjust.
 Identities = 156/210 (74%), Positives = 183/210 (87%)

Query: 6   PVYSLGVDETDSSLPPKERRFAVLLSALLSSLTKDKVADGALQRLLQNGLHTAEAIDKAD 65
           PV S+G D+  S LPP ERRFAVLL ALLSS TKD+V + A+ RL QNGL T EA+DKAD
Sbjct: 152 PVDSMGCDKAGSFLPPTERRFAVLLGALLSSQTKDQVNNAAIHRLHQNGLLTPEAVDKAD 211

Query: 66  EATIKDLIYPVAFYTRKACNMKKIAKICLTKYDGDIPSSLDELLALPGIGPKMANMVMTL 125
           E+TIK+LIYPV FYTRKA  MKKIA+ICL KYDGDIPSSLD+LL+LPGIGPKMA++++ +
Sbjct: 212 ESTIKELIYPVGFYTRKATYMKKIARICLVKYDGDIPSSLDDLLSLPGIGPKMAHLILHI 271

Query: 126 GWFNVQGICVDTHVHRICNRLGWVTQPGTKQKTSSPEQTREALQRWLPKEEWVRINPLLV 185
            W +VQGICVDTHVHRICNRLGWV++PGTKQKT+SPE+TR ALQ+WLPKEEWV INPLLV
Sbjct: 272 AWNDVQGICVDTHVHRICNRLGWVSRPGTKQKTTSPEETRVALQQWLPKEEWVAINPLLV 331

Query: 186 GFGQTICTPLRPRCGMCTVSEYCPSAFKES 215
           GFGQ ICTP+RPRC  C+VS+ CP+AFKE+
Sbjct: 332 GFGQMICTPIRPRCEACSVSKLCPAAFKET 361

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|18402669|ref|NP_565725.1| endonuclease III [Arabidopsis thaliana] gi|20198157|gb|AAD26474.2| putative endonuclease [Arabidopsis thaliana] gi|330253455|gb|AEC08549.1| endonuclease III [Arabidopsis thaliana]

 Score =  342 bits (877), Expect = 8e-92,   Method: Compositional matrix adjust.
 Identities = 156/210 (74%), Positives = 183/210 (87%)

Query: 6   PVYSLGVDETDSSLPPKERRFAVLLSALLSSLTKDKVADGALQRLLQNGLHTAEAIDKAD 65
           PV S+G D+  S LPP ERRFAVLL ALLSS TKD+V + A+ RL QNGL T EA+DKAD
Sbjct: 154 PVDSMGCDKAGSFLPPTERRFAVLLGALLSSQTKDQVNNAAIHRLHQNGLLTPEAVDKAD 213

Query: 66  EATIKDLIYPVAFYTRKACNMKKIAKICLTKYDGDIPSSLDELLALPGIGPKMANMVMTL 125
           E+TIK+LIYPV FYTRKA  MKKIA+ICL KYDGDIPSSLD+LL+LPGIGPKMA++++ +
Sbjct: 214 ESTIKELIYPVGFYTRKATYMKKIARICLVKYDGDIPSSLDDLLSLPGIGPKMAHLILHI 273

Query: 126 GWFNVQGICVDTHVHRICNRLGWVTQPGTKQKTSSPEQTREALQRWLPKEEWVRINPLLV 185
            W +VQGICVDTHVHRICNRLGWV++PGTKQKT+SPE+TR ALQ+WLPKEEWV INPLLV
Sbjct: 274 AWNDVQGICVDTHVHRICNRLGWVSRPGTKQKTTSPEETRVALQQWLPKEEWVAINPLLV 333

Query: 186 GFGQTICTPLRPRCGMCTVSEYCPSAFKES 215
           GFGQ ICTP+RPRC  C+VS+ CP+AFKE+
Sbjct: 334 GFGQMICTPIRPRCEACSVSKLCPAAFKET 363

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359478121|ref|XP_002264475.2| PREDICTED: endonuclease III-like protein 1-like [Vitis vinifera]

 Score =  338 bits (868), Expect = 9e-91,   Method: Compositional matrix adjust.
 Identities = 169/219 (77%), Positives = 192/219 (87%)

Query: 6   PVYSLGVDETDSSLPPKERRFAVLLSALLSSLTKDKVADGALQRLLQNGLHTAEAIDKAD 65
           PV S+G ++  SSLPP+ERRFAVL+S+LLSS TKD V  GA+QRLLQNGL  A+AIDKAD
Sbjct: 130 PVDSMGCEKAGSSLPPRERRFAVLVSSLLSSQTKDNVTHGAIQRLLQNGLLVADAIDKAD 189

Query: 66  EATIKDLIYPVAFYTRKACNMKKIAKICLTKYDGDIPSSLDELLALPGIGPKMANMVMTL 125
           EAT+K LIYPV FY+RKA N+KKIAKICL KYDGDIPSSL+ELL LPGIGPKMA++VM +
Sbjct: 190 EATVKSLIYPVGFYSRKAGNLKKIAKICLMKYDGDIPSSLEELLLLPGIGPKMAHLVMNV 249

Query: 126 GWFNVQGICVDTHVHRICNRLGWVTQPGTKQKTSSPEQTREALQRWLPKEEWVRINPLLV 185
            W NVQGICVDTHVHRICNRLGWV++ GTKQKTS PE+TRE+LQ WLPKEEWV INPLLV
Sbjct: 250 AWNNVQGICVDTHVHRICNRLGWVSRRGTKQKTSLPEETRESLQLWLPKEEWVPINPLLV 309

Query: 186 GFGQTICTPLRPRCGMCTVSEYCPSAFKESSTSSSKSKK 224
           GFGQTICTPLRPRCG+C VS+ CPSAFKE+ + SSK KK
Sbjct: 310 GFGQTICTPLRPRCGVCGVSDLCPSAFKEAQSPSSKMKK 348

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297826589|ref|XP_002881177.1| predicted protein [Arabidopsis lyrata subsp. lyrata] gi|297327016|gb|EFH57436.1| predicted protein [Arabidopsis lyrata subsp. lyrata]

 Score =  338 bits (867), Expect = 1e-90,   Method: Compositional matrix adjust.
 Identities = 154/210 (73%), Positives = 183/210 (87%)

Query: 6   PVYSLGVDETDSSLPPKERRFAVLLSALLSSLTKDKVADGALQRLLQNGLHTAEAIDKAD 65
           PV S+G D+  S LPP ERRFAVLL ALLSS TKD+V + A+ RL QN L T EA+DKAD
Sbjct: 129 PVDSMGCDKAGSFLPPTERRFAVLLGALLSSQTKDQVNNAAIHRLHQNSLLTPEAVDKAD 188

Query: 66  EATIKDLIYPVAFYTRKACNMKKIAKICLTKYDGDIPSSLDELLALPGIGPKMANMVMTL 125
           E+TI++LIYPV FYTRKA  MKKIA+ICL KY+GDIPSSLD+LL+LPGIGPKMA++++ +
Sbjct: 189 ESTIRELIYPVGFYTRKATYMKKIARICLVKYNGDIPSSLDDLLSLPGIGPKMAHLILHI 248

Query: 126 GWFNVQGICVDTHVHRICNRLGWVTQPGTKQKTSSPEQTREALQRWLPKEEWVRINPLLV 185
            W +VQGICVDTHVHRICNRLGWV++PGTKQKT+SPE+TR ALQ+WLPKEEWV INPLLV
Sbjct: 249 AWNDVQGICVDTHVHRICNRLGWVSRPGTKQKTTSPEETRVALQQWLPKEEWVAINPLLV 308

Query: 186 GFGQTICTPLRPRCGMCTVSEYCPSAFKES 215
           GFGQTICTPLRPRC  C+V++ CP+AFKE+
Sbjct: 309 GFGQTICTPLRPRCEACSVTKLCPAAFKET 338

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297743769|emb|CBI36652.3| unnamed protein product [Vitis vinifera]

 Score =  333 bits (854), Expect = 4e-89,   Method: Compositional matrix adjust.
 Identities = 169/222 (76%), Positives = 192/222 (86%), Gaps = 3/222 (1%)

Query: 6   PVYSLGVDETDSSLPPKERRFAVLLSALLSSLTKDKVADG---ALQRLLQNGLHTAEAID 62
           PV S+G ++  SSLPP+ERRFAVL+S+LLSS TKD V  G   A+QRLLQNGL  A+AID
Sbjct: 151 PVDSMGCEKAGSSLPPRERRFAVLVSSLLSSQTKDNVTHGNAGAIQRLLQNGLLVADAID 210

Query: 63  KADEATIKDLIYPVAFYTRKACNMKKIAKICLTKYDGDIPSSLDELLALPGIGPKMANMV 122
           KADEAT+K LIYPV FY+RKA N+KKIAKICL KYDGDIPSSL+ELL LPGIGPKMA++V
Sbjct: 211 KADEATVKSLIYPVGFYSRKAGNLKKIAKICLMKYDGDIPSSLEELLLLPGIGPKMAHLV 270

Query: 123 MTLGWFNVQGICVDTHVHRICNRLGWVTQPGTKQKTSSPEQTREALQRWLPKEEWVRINP 182
           M + W NVQGICVDTHVHRICNRLGWV++ GTKQKTS PE+TRE+LQ WLPKEEWV INP
Sbjct: 271 MNVAWNNVQGICVDTHVHRICNRLGWVSRRGTKQKTSLPEETRESLQLWLPKEEWVPINP 330

Query: 183 LLVGFGQTICTPLRPRCGMCTVSEYCPSAFKESSTSSSKSKK 224
           LLVGFGQTICTPLRPRCG+C VS+ CPSAFKE+ + SSK KK
Sbjct: 331 LLVGFGQTICTPLRPRCGVCGVSDLCPSAFKEAQSPSSKMKK 372

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297843388|ref|XP_002889575.1| hypothetical protein ARALYDRAFT_470604 [Arabidopsis lyrata subsp. lyrata] gi|297335417|gb|EFH65834.1| hypothetical protein ARALYDRAFT_470604 [Arabidopsis lyrata subsp. lyrata]

 Score =  332 bits (850), Expect = 1e-88,   Method: Compositional matrix adjust.
 Identities = 153/217 (70%), Positives = 183/217 (84%), Gaps = 2/217 (0%)

Query: 1   MKTLE--PVYSLGVDETDSSLPPKERRFAVLLSALLSSLTKDKVADGALQRLLQNGLHTA 58
           MK+ E  P  ++  D T S LPPKERRF VL+  LLSS TK+ +   A++RL QNGL T 
Sbjct: 152 MKSSEEAPANAVECDRTGSFLPPKERRFYVLIGTLLSSQTKEHITGAAVERLHQNGLLTP 211

Query: 59  EAIDKADEATIKDLIYPVAFYTRKACNMKKIAKICLTKYDGDIPSSLDELLALPGIGPKM 118
           EAIDKADE+TIK+LIYPV FYTRKA N+KK+AKICL KYDGDIP +L+ELL+LPG+GPK+
Sbjct: 212 EAIDKADESTIKELIYPVGFYTRKATNVKKVAKICLMKYDGDIPRTLEELLSLPGVGPKI 271

Query: 119 ANMVMTLGWFNVQGICVDTHVHRICNRLGWVTQPGTKQKTSSPEQTREALQRWLPKEEWV 178
           A++V+ + W +VQGICVDTHVHRICNRLGWV++PGTKQKT SPE+TR ALQ+WLPKEEWV
Sbjct: 272 AHLVLHVAWNDVQGICVDTHVHRICNRLGWVSKPGTKQKTLSPEETRVALQQWLPKEEWV 331

Query: 179 RINPLLVGFGQTICTPLRPRCGMCTVSEYCPSAFKES 215
            IN LLVGFGQTICTPLRPRCG C+++E CPSAFKE+
Sbjct: 332 AINFLLVGFGQTICTPLRPRCGTCSITELCPSAFKET 368

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	235
TAIR|locus:2061345	379	ATNTH1 [Arabidopsis thaliana (	0.880	0.546	0.710	6e-80
TAIR|locus:2198738	386	NTH2 "endonuclease III 2" [Ara	0.902	0.549	0.677	2.7e-77
UNIPROTKB|E2QX23	312	NTHL1 "Uncharacterized protein	0.851	0.641	0.507	4.6e-50
UNIPROTKB|Q2KID2	305	NTHL1 "Endonuclease III-like p	0.851	0.655	0.502	1.5e-49
UNIPROTKB|P78549	312	NTHL1 "Endonuclease III-like p	0.851	0.641	0.507	2e-49
UNIPROTKB|F1RFB3	313	NTHL1 "Uncharacterized protein	0.851	0.638	0.495	2.3e-48
MGI|MGI:1313275	300	Nthl1 "nth (endonuclease III)-	0.851	0.666	0.483	2.3e-48
RGD|1309289	300	Nthl1 "nth (endonuclease III)-	0.851	0.666	0.487	1.6e-47
UNIPROTKB|F1NQP6	251	NTHL1 "Uncharacterized protein	0.851	0.796	0.473	4.2e-47
DICTYBASE|DDB_G0277247	349	apnB "putative endonuclease II	0.851	0.573	0.454	5.4e-47

TAIR|locus:2061345 ATNTH1 [Arabidopsis thaliana (taxid:3702)]

 Score = 803 (287.7 bits), Expect = 6.0e-80, P = 6.0e-80
 Identities = 147/207 (71%), Positives = 173/207 (83%)

Query:     6 PVYSLGVDETDSSLPPKERRFAVXXXXXXXXXTKDKVADGALQRLLQNGLHTAEAIDKAD 65
             PV S+G D+  S LPP ERRFAV         TKD+V + A+ RL QNGL T EA+DKAD
Sbjct:   154 PVDSMGCDKAGSFLPPTERRFAVLLGALLSSQTKDQVNNAAIHRLHQNGLLTPEAVDKAD 213

Query:    66 EATIKDLIYPVAFYTRKACNMKKIAKICLTKYDGDIPSSLDELLALPGIGPKMANMVMTL 125
             E+TIK+LIYPV FYTRKA  MKKIA+ICL KYDGDIPSSLD+LL+LPGIGPKMA++++ +
Sbjct:   214 ESTIKELIYPVGFYTRKATYMKKIARICLVKYDGDIPSSLDDLLSLPGIGPKMAHLILHI 273

Query:   126 GWFNVQGICVDTHVHRICNRLGWVTQPGTKQKTSSPEQTREALQRWLPKEEWVRINPLLV 185
              W +VQGICVDTHVHRICNRLGWV++PGTKQKT+SPE+TR ALQ+WLPKEEWV INPLLV
Sbjct:   274 AWNDVQGICVDTHVHRICNRLGWVSRPGTKQKTTSPEETRVALQQWLPKEEWVAINPLLV 333

Query:   186 GFGQTICTPLRPRCGMCTVSEYCPSAF 212
             GFGQ ICTP+RPRC  C+VS+ CP+AF
Sbjct:   334 GFGQMICTPIRPRCEACSVSKLCPAAF 360

GO:0003677 "DNA binding" evidence=IEA

GO:0003824 "catalytic activity" evidence=IEA

GO:0004519 "endonuclease activity" evidence=IEA

GO:0005634 "nucleus" evidence=ISM

GO:0005739 "mitochondrion" evidence=ISM

GO:0006281 "DNA repair" evidence=IEA

GO:0006284 "base-excision repair" evidence=IEA;ISS;IDA

GO:0051539 "4 iron, 4 sulfur cluster binding" evidence=IEA

GO:0019104 "DNA N-glycosylase activity" evidence=IDA

GO:0042644 "chloroplast nucleoid" evidence=IDA

TAIR|locus:2198738 NTH2 "endonuclease III 2" [Arabidopsis thaliana (taxid:3702)]

 Score = 778 (278.9 bits), Expect = 2.7e-77, P = 2.7e-77
 Identities = 145/214 (67%), Positives = 173/214 (80%)

Query:     1 MKTLE--PVYSLGVDETDSSLPPKERRFAVXXXXXXXXXTKDKVADGALQRLLQNGLHTA 58
             MK  E  PV ++  D T S LPPKERRF V         TK+ +   A++RL QNGL T 
Sbjct:   154 MKPSEEAPVNAVECDRTGSFLPPKERRFYVLIGTLLSSQTKEHITGAAVERLHQNGLLTP 213

Query:    59 EAIDKADEATIKDLIYPVAFYTRKACNMKKIAKICLTKYDGDIPSSLDELLALPGIGPKM 118
             EAIDKADE+TIK+LIYPV FYTRKA N+KK+AKICL +YDGDIP +L+ELL+LPG+GPK+
Sbjct:   214 EAIDKADESTIKELIYPVGFYTRKATNVKKVAKICLMEYDGDIPRTLEELLSLPGVGPKI 273

Query:   119 ANMVMTLGWFNVQGICVDTHVHRICNRLGWVTQPGTKQKTSSPEQTREALQRWLPKEEWV 178
             A++V+ + W +VQGICVDTHVHRICNRLGWV++PGTKQKTSSPE+TR ALQ+WLPK EWV
Sbjct:   274 AHLVLHVAWNDVQGICVDTHVHRICNRLGWVSKPGTKQKTSSPEETRVALQQWLPKGEWV 333

Query:   179 RINPLLVGFGQTICTPLRPRCGMCTVSEYCPSAF 212
              IN LLVGFGQTICTPLRP CG C+++E CPSAF
Sbjct:   334 AINFLLVGFGQTICTPLRPHCGTCSITEICPSAF 367

GO:0003677 "DNA binding" evidence=IEA

GO:0003824 "catalytic activity" evidence=IEA

GO:0004519 "endonuclease activity" evidence=IEA

GO:0005634 "nucleus" evidence=ISM

GO:0005739 "mitochondrion" evidence=ISM

GO:0006281 "DNA repair" evidence=IEA

GO:0006284 "base-excision repair" evidence=IEA;ISS;IDA

GO:0051539 "4 iron, 4 sulfur cluster binding" evidence=IEA

GO:0019104 "DNA N-glycosylase activity" evidence=IDA

GO:0042644 "chloroplast nucleoid" evidence=IDA

UNIPROTKB|E2QX23 NTHL1 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 521 (188.5 bits), Expect = 4.6e-50, P = 4.6e-50
 Identities = 105/207 (50%), Positives = 135/207 (65%)

Query:     6 PVYSLGVDET-DSSLPPKERRFAVXXXXXXXXXTKDKVADGALQRLLQNGLHTAEAIDKA 64
             PV  LGV+   D S PPK +R+ V         TKD+V  GA+QRL  +GL T ++I + 
Sbjct:   109 PVDWLGVEHCHDPSAPPKVQRYQVLLSLMLSSQTKDQVTAGAMQRLRAHGL-TVDSILQT 167

Query:    65 DEATIKDLIYPVAFYTRKACNMKKIAKICLTKYDGDIPSSLDELLALPGIGPKMANMVMT 124
             D+AT+  LIYPV F+  K   +K+ + I   +Y GDIP+S+ EL+ALPG+GPKMA++ M 
Sbjct:   168 DDATLGSLIYPVGFWRSKVKYIKQTSAILQQRYGGDIPASVAELVALPGVGPKMAHLAMA 227

Query:   125 LGWFNVQGICVDTHVHRICNRLGWVTQPGTKQKTSSPEQTREALQRWLPKEEWVRINPLL 184
             + W  V GI VDTHVHRI NRL W     T+  T+SPE+TR AL+ WLP+E W  IN LL
Sbjct:   228 VAWGTVSGIAVDTHVHRIANRLRW-----TRTTTTSPEKTRAALEEWLPRELWGEINGLL 282

Query:   185 VGFGQTICTPLRPRCGMCTVSEYCPSA 211
             VGFGQ  C P+RPRCG C     CP+A
Sbjct:   283 VGFGQQTCLPVRPRCGACLNRSLCPAA 309

GO:0019104 "DNA N-glycosylase activity" evidence=IEA

GO:0006296 "nucleotide-excision repair, DNA incision, 5'-to lesion" evidence=IEA

GO:0006285 "base-excision repair, AP site formation" evidence=IEA

GO:0005739 "mitochondrion" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0003906 "DNA-(apurinic or apyrimidinic site) lyase activity" evidence=IEA

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

GO:0051539 "4 iron, 4 sulfur cluster binding" evidence=IEA

GO:0004519 "endonuclease activity" evidence=IEA

UNIPROTKB|Q2KID2 NTHL1 "Endonuclease III-like protein 1" [Bos taurus (taxid:9913)]

 Score = 516 (186.7 bits), Expect = 1.5e-49, P = 1.5e-49
 Identities = 104/207 (50%), Positives = 132/207 (63%)

Query:     6 PVYSLGVDET-DSSLPPKERRFAVXXXXXXXXXTKDKVADGALQRLLQNGLHTAEAIDKA 64
             PV  LG +   D S  PK RR+ V         TKD+V  GA+QRL   GL T ++I + 
Sbjct:   102 PVDQLGAEHCFDPSASPKVRRYQVLLSLMLSSQTKDQVTAGAMQRLRARGL-TVDSILQT 160

Query:    65 DEATIKDLIYPVAFYTRKACNMKKIAKICLTKYDGDIPSSLDELLALPGIGPKMANMVMT 124
             D++T+  LIYPV F+  K   +K+ + I   +YDGDIP+S+ EL+ALPG+GPKMA++ M 
Sbjct:   161 DDSTLGALIYPVGFWRSKVKYIKQTSAILQQRYDGDIPASVAELVALPGVGPKMAHLAMA 220

Query:   125 LGWFNVQGICVDTHVHRICNRLGWVTQPGTKQKTSSPEQTREALQRWLPKEEWVRINPLL 184
             + W  V GI VDTHVHRI NRL W     TK+ T SPE+TR AL+ WLP+E W  IN LL
Sbjct:   221 VAWGTVSGIAVDTHVHRIANRLRW-----TKKATKSPEETRRALEEWLPRELWSEINGLL 275

Query:   185 VGFGQTICTPLRPRCGMCTVSEYCPSA 211
             VGFGQ  C P+RPRC  C     CP+A
Sbjct:   276 VGFGQQTCLPIRPRCQACLNRALCPAA 302

GO:0005739 "mitochondrion" evidence=IEA

GO:0019104 "DNA N-glycosylase activity" evidence=IEA

GO:0006296 "nucleotide-excision repair, DNA incision, 5'-to lesion" evidence=IEA

GO:0006285 "base-excision repair, AP site formation" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

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

GO:0003906 "DNA-(apurinic or apyrimidinic site) lyase activity" evidence=IEA

GO:0051539 "4 iron, 4 sulfur cluster binding" evidence=IEA

GO:0046872 "metal ion binding" evidence=IEA

GO:0004519 "endonuclease activity" evidence=IEA

UNIPROTKB|P78549 NTHL1 "Endonuclease III-like protein 1" [Homo sapiens (taxid:9606)]

 Score = 515 (186.3 bits), Expect = 2.0e-49, P = 2.0e-49
 Identities = 105/207 (50%), Positives = 131/207 (63%)

Query:     6 PVYSLGVDET-DSSLPPKERRFAVXXXXXXXXXTKDKVADGALQRLLQNGLHTAEAIDKA 64
             PV  LG +   DSS PPK RR+ V         TKD+V  GA+QRL   GL T ++I + 
Sbjct:   109 PVDHLGTEHCYDSSAPPKVRRYQVLLSLMLSSQTKDQVTAGAMQRLRARGL-TVDSILQT 167

Query:    65 DEATIKDLIYPVAFYTRKACNMKKIAKICLTKYDGDIPSSLDELLALPGIGPKMANMVMT 124
             D+AT+  LIYPV F+  K   +K+ + I    Y GDIP+S+ EL+ALPG+GPKMA++ M 
Sbjct:   168 DDATLGKLIYPVGFWRSKVKYIKQTSAILQQHYGGDIPASVAELVALPGVGPKMAHLAMA 227

Query:   125 LGWFNVQGICVDTHVHRICNRLGWVTQPGTKQKTSSPEQTREALQRWLPKEEWVRINPLL 184
             + W  V GI VDTHVHRI NRL W     TK+ T SPE+TR AL+ WLP+E W  IN LL
Sbjct:   228 VAWGTVSGIAVDTHVHRIANRLRW-----TKKATKSPEETRAALEEWLPRELWHEINGLL 282

Query:   185 VGFGQTICTPLRPRCGMCTVSEYCPSA 211
             VGFGQ  C P+ PRC  C     CP+A
Sbjct:   283 VGFGQQTCLPVHPRCHACLNQALCPAA 309

GO:0004519 "endonuclease activity" evidence=IEA

GO:0046872 "metal ion binding" evidence=IEA

GO:0051539 "4 iron, 4 sulfur cluster binding" evidence=IEA

GO:0005739 "mitochondrion" evidence=IEA

GO:0006296 "nucleotide-excision repair, DNA incision, 5'-to lesion" evidence=IDA

GO:0003906 "DNA-(apurinic or apyrimidinic site) lyase activity" evidence=IDA

GO:0019104 "DNA N-glycosylase activity" evidence=IDA

GO:0005634 "nucleus" evidence=IDA

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

GO:0006285 "base-excision repair, AP site formation" evidence=IDA;TAS

GO:0005515 "protein binding" evidence=IPI

GO:0005654 "nucleoplasm" evidence=TAS

GO:0006281 "DNA repair" evidence=TAS

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

GO:0045008 "depyrimidination" evidence=TAS

UNIPROTKB|F1RFB3 NTHL1 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 505 (182.8 bits), Expect = 2.3e-48, P = 2.3e-48
 Identities = 103/208 (49%), Positives = 133/208 (63%)

Query:     6 PVYSLGVDET-DSSLPPKE-RRFAVXXXXXXXXXTKDKVADGALQRLLQNGLHTAEAIDK 63
             PV  LG +   D S PPK+ RR+ V         TKD+V  GA+QRL  +GL T ++I +
Sbjct:   109 PVDQLGAEHCYDPSAPPKQVRRYQVLLSLMLSSQTKDQVTAGAMQRLRAHGL-TVDSILQ 167

Query:    64 ADEATIKDLIYPVAFYTRKACNMKKIAKICLTKYDGDIPSSLDELLALPGIGPKMANMVM 123
              D++T+  LIYPV F+  K   +K+ + I   +Y GDIP+S+ EL+ALPG+GPKMA++ M
Sbjct:   168 MDDSTLGTLIYPVGFWRSKVKYIKQTSAILQQRYGGDIPASVPELVALPGVGPKMAHLAM 227

Query:   124 TLGWFNVQGICVDTHVHRICNRLGWVTQPGTKQKTSSPEQTREALQRWLPKEEWVRINPL 183
              + W  V GI VDTHVHRI  RL W     TK+ T SPE+TR AL+ WLP+E W  IN L
Sbjct:   228 AVAWGTVSGIAVDTHVHRIAGRLKW-----TKKATKSPEKTRTALEEWLPRELWSEINGL 282

Query:   184 LVGFGQTICTPLRPRCGMCTVSEYCPSA 211
             LVGFGQ  C P+RPRC  C     CP+A
Sbjct:   283 LVGFGQQTCLPVRPRCQACLNRALCPAA 310

GO:0019104 "DNA N-glycosylase activity" evidence=IEA

GO:0006296 "nucleotide-excision repair, DNA incision, 5'-to lesion" evidence=IEA

GO:0006285 "base-excision repair, AP site formation" evidence=IEA

GO:0005739 "mitochondrion" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0003906 "DNA-(apurinic or apyrimidinic site) lyase activity" evidence=IEA

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

GO:0051539 "4 iron, 4 sulfur cluster binding" evidence=IEA

GO:0004519 "endonuclease activity" evidence=IEA

MGI|MGI:1313275 Nthl1 "nth (endonuclease III)-like 1 (E.coli)" [Mus musculus (taxid:10090)]

 Score = 505 (182.8 bits), Expect = 2.3e-48, P = 2.3e-48
 Identities = 100/207 (48%), Positives = 131/207 (63%)

Query:     6 PVYSLGVDET-DSSLPPKERRFAVXXXXXXXXXTKDKVADGALQRLLQNGLHTAEAIDKA 64
             PV  LG +   D+S PPK RR+ V         TKD+V  GA+QRL   GL T E+I + 
Sbjct:    97 PVDQLGAEHCYDASAPPKVRRYQVLLSLMLSSQTKDQVTAGAMQRLRARGL-TVESILQT 155

Query:    65 DEATIKDLIYPVAFYTRKACNMKKIAKICLTKYDGDIPSSLDELLALPGIGPKMANMVMT 124
             D+ T+  LIYPV F+  K   +K+   I   +Y+GDIP+S+ EL+ALPG+GPKMA++ M 
Sbjct:   156 DDDTLGRLIYPVGFWRNKVKYIKQTTAILQQRYEGDIPASVAELVALPGVGPKMAHLAMA 215

Query:   125 LGWFNVQGICVDTHVHRICNRLGWVTQPGTKQKTSSPEQTREALQRWLPKEEWVRINPLL 184
             + W  + GI VDTHVHRI NRL W     TK+ T +PE+TR+ L+ WLP+  W  +N LL
Sbjct:   216 VAWGTISGIAVDTHVHRIANRLRW-----TKKMTKTPEETRKNLEEWLPRVLWSEVNGLL 270

Query:   185 VGFGQTICTPLRPRCGMCTVSEYCPSA 211
             VGFGQ IC P+ PRC  C     CP+A
Sbjct:   271 VGFGQQICLPVHPRCQACLNKALCPAA 297

GO:0003677 "DNA binding" evidence=IEA

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

GO:0003824 "catalytic activity" evidence=IEA

GO:0003906 "DNA-(apurinic or apyrimidinic site) lyase activity" evidence=ISO;IDA

GO:0004519 "endonuclease activity" evidence=IEA

GO:0005634 "nucleus" evidence=ISO;IDA

GO:0005739 "mitochondrion" evidence=IDA

GO:0006281 "DNA repair" evidence=TAS

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

GO:0006285 "base-excision repair, AP site formation" evidence=ISO

GO:0006296 "nucleotide-excision repair, DNA incision, 5'-to lesion" evidence=ISO;IDA

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

GO:0008152 "metabolic process" evidence=IEA

GO:0016787 "hydrolase activity" evidence=IEA

GO:0016798 "hydrolase activity, acting on glycosyl bonds" evidence=IEA

GO:0016829 "lyase activity" evidence=IEA

GO:0019104 "DNA N-glycosylase activity" evidence=ISO;IDA

GO:0046872 "metal ion binding" evidence=IEA

GO:0051536 "iron-sulfur cluster binding" evidence=IEA

GO:0051539 "4 iron, 4 sulfur cluster binding" evidence=IEA

RGD|1309289 Nthl1 "nth (endonuclease III)-like 1 (E.coli)" [Rattus norvegicus (taxid:10116)]

 Score = 497 (180.0 bits), Expect = 1.6e-47, P = 1.6e-47
 Identities = 101/207 (48%), Positives = 129/207 (62%)

Query:     6 PVYSLGVDET-DSSLPPKERRFAVXXXXXXXXXTKDKVADGALQRLLQNGLHTAEAIDKA 64
             PV  LG ++  D + PPK RR+ V         TKD+V  GA+QRL   GL T E+I + 
Sbjct:    97 PVDQLGAEQCYDITAPPKVRRYQVLLSLMLSSQTKDQVTAGAMQRLRARGL-TVESILQT 155

Query:    65 DEATIKDLIYPVAFYTRKACNMKKIAKICLTKYDGDIPSSLDELLALPGIGPKMANMVMT 124
             D+  +  LIYPV F+  K   +K+   I   +Y+GDIP+S+ EL+ALPG+GPKMA++ M 
Sbjct:   156 DDDLLGRLIYPVGFWRSKVKFIKQTTAILQQRYEGDIPASVAELVALPGVGPKMAHLAMA 215

Query:   125 LGWFNVQGICVDTHVHRICNRLGWVTQPGTKQKTSSPEQTREALQRWLPKEEWVRINPLL 184
             + W  V GI VDTHVHRI NRL W     TK+ T SPE+TR  L+ WLP+  W  IN LL
Sbjct:   216 VAWGTVSGIAVDTHVHRIANRLKW-----TKKMTKSPEETRRNLEEWLPRVLWSEINGLL 270

Query:   185 VGFGQTICTPLRPRCGMCTVSEYCPSA 211
             VGFGQ IC P+ PRC  C     CP+A
Sbjct:   271 VGFGQQICLPVHPRCQACLNKALCPAA 297

GO:0003690 "double-stranded DNA binding" evidence=IEA;ISO

GO:0003906 "DNA-(apurinic or apyrimidinic site) lyase activity" evidence=IEA;ISO

GO:0004519 "endonuclease activity" evidence=IEA

GO:0005634 "nucleus" evidence=IEA;ISO

GO:0005739 "mitochondrion" evidence=IEA;ISO

GO:0006285 "base-excision repair, AP site formation" evidence=IEA;ISO

GO:0006296 "nucleotide-excision repair, DNA incision, 5'-to lesion" evidence=IEA;ISO

GO:0019104 "DNA N-glycosylase activity" evidence=IEA;ISO

GO:0051539 "4 iron, 4 sulfur cluster binding" evidence=IEA

UNIPROTKB|F1NQP6 NTHL1 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 493 (178.6 bits), Expect = 4.2e-47, P = 4.2e-47
 Identities = 98/207 (47%), Positives = 132/207 (63%)

Query:     6 PVYSLGVDET-DSSLPPKERRFAVXXXXXXXXXTKDKVADGALQRLLQNGLHTAEAIDKA 64
             PV  +GVD+  D+S PP+  R+ V         TKD+V   A+ RL Q GL T ++I + 
Sbjct:    48 PVDEMGVDKCYDTSAPPQVMRYQVLLSLMLSSQTKDQVTSAAMLRLRQRGL-TVDSILQM 106

Query:    65 DEATIKDLIYPVAFYTRKACNMKKIAKICLTKYDGDIPSSLDELLALPGIGPKMANMVMT 124
             D+AT+  +IYPV F+  K   +K+   I   KY GDIP +++EL+ LPG+GPKMA++ M 
Sbjct:   107 DDATLGQIIYPVGFWRNKVKYIKQTTAILKQKYGGDIPGTVEELVKLPGVGPKMAHLAMN 166

Query:   125 LGWFNVQGICVDTHVHRICNRLGWVTQPGTKQKTSSPEQTREALQRWLPKEEWVRINPLL 184
             + W +V GI VDTHVHRI NRL WV     K++T  PE+TR AL+ WLP++ W  IN LL
Sbjct:   167 IAWNSVSGIAVDTHVHRITNRLKWV-----KKETRYPEETRVALEDWLPRDLWREINWLL 221

Query:   185 VGFGQTICTPLRPRCGMCTVSEYCPSA 211
             VGFGQ  C P+ PRC  C   + CP+A
Sbjct:   222 VGFGQQTCLPVNPRCKECLNQDICPTA 248

GO:0004519 "endonuclease activity" evidence=IEA

GO:0051539 "4 iron, 4 sulfur cluster binding" evidence=IEA

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

GO:0003906 "DNA-(apurinic or apyrimidinic site) lyase activity" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0005739 "mitochondrion" evidence=IEA

GO:0006285 "base-excision repair, AP site formation" evidence=IEA

GO:0006296 "nucleotide-excision repair, DNA incision, 5'-to lesion" evidence=IEA

GO:0019104 "DNA N-glycosylase activity" evidence=IEA

DICTYBASE|DDB_G0277247 apnB "putative endonuclease III" [Dictyostelium discoideum (taxid:44689)]

 Score = 492 (178.3 bits), Expect = 5.4e-47, P = 5.4e-47
 Identities = 95/209 (45%), Positives = 130/209 (62%)

Query:     2 KTLEPVYSLGVDE-TDSSLPPKERRFAVXXXXXXXXXTKDKVADGALQRLLQNGLHTAEA 60
             + L PV +LG +     ++ P E+RF +         TKD +   A+ RL + GL T + 
Sbjct:   130 ENLAPVDTLGAESFNQDNIEPIEKRFHILVGCLLSSQTKDAITHAAVVRLKEYGL-TVDK 188

Query:    61 IDKADEATIKDLIYPVAFYTRKACNMKKIAKICLTKYDGDIPSSLDELLALPGIGPKMAN 120
             +   D   ++ L+YPV FY RKA  +KKIA+I   KY+GDIP +  E+  LPGIGPKM N
Sbjct:   189 MLTIDTNELETLLYPVGFYKRKAIYLKKIAEILKNKYNGDIPPTFKEIEQLPGIGPKMTN 248

Query:   121 MVMTLGWFNVQGICVDTHVHRICNRLGWVTQPGTKQKTSSPEQTREALQRWLPKEEWVRI 180
             +++ + W  V+GI VD H+HRI NRLGWV       KT +PE+T + L+ WLPKE W  +
Sbjct:   249 LIVQIAWGRVEGIAVDVHMHRISNRLGWV-------KTKTPEETMKDLESWLPKENWATV 301

Query:   181 NPLLVGFGQTICTPLRPRCGMCTVSEYCP 209
             N LLVGFGQTIC+P+ P+C  C V+  CP
Sbjct:   302 NHLLVGFGQTICSPVNPKCSNCLVNNLCP 330

GO:0051539 "4 iron, 4 sulfur cluster binding" evidence=IEA

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

GO:0006281 "DNA repair" evidence=IEA

GO:0004519 "endonuclease activity" evidence=IEA

GO:0003824 "catalytic activity" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q2KID2	NTHL1_BOVIN	4, ., 2, ., 9, 9, ., 1, 8	0.5314	0.8510	0.6557	yes	no
Q8SRB8	NTH1_ENCCU	4, ., 2, ., 9, 9, ., 1, 8	0.4208	0.8468	0.8361	yes	no
P78549	NTHL1_HUMAN	4, ., 2, ., 9, 9, ., 1, 8	0.5362	0.8510	0.6410	yes	no
O35980	NTHL1_MOUSE	4, ., 2, ., 9, 9, ., 1, 8	0.5120	0.8510	0.6666	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

Prediction Level	EC number	Confidence of Prediction
3rd Layer	4.2.99	0.766
4th Layer	4.2.99.18	0.824

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	235
COG0177	211	COG0177, Nth, Predicted EndoIII-related endonuclea	3e-74
cd00056	158	cd00056, ENDO3c, endonuclease III; includes endonu	5e-50
smart00478	149	smart00478, ENDO3c, endonuclease III	2e-45
TIGR01083	191	TIGR01083, nth, endonuclease III	3e-45
pfam00730	144	pfam00730, HhH-GPD, HhH-GPD superfamily base excis	2e-35
PRK10702	211	PRK10702, PRK10702, endonuclease III; Provisional	8e-24
COG1194	342	COG1194, MutY, A/G-specific DNA glycosylase [DNA r	1e-21
TIGR01084	275	TIGR01084, mutY, A/G-specific adenine glycosylase	3e-17
PRK13910	289	PRK13910, PRK13910, DNA glycosylase MutY; Provisio	6e-15
COG2231	215	COG2231, COG2231, Uncharacterized protein related	2e-11
PRK10880	350	PRK10880, PRK10880, adenine DNA glycosylase; Provi	2e-09
pfam00633	30	pfam00633, HHH, Helix-hairpin-helix motif	1e-07
TIGR00588	310	TIGR00588, ogg, 8-oxoguanine DNA-glycosylase (ogg)	8e-05
smart00525	21	smart00525, FES, iron-sulpphur binding domain in D	1e-04

>gnl|CDD|223255 COG0177, Nth, Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]

 Score =  223 bits (572), Expect = 3e-74
 Identities = 74/190 (38%), Positives = 115/190 (60%), Gaps = 9/190 (4%)

Query: 25  RFAVLLSALLSSLTKDKVADGALQRLLQNGLHTAEAIDKADEATIKDLIYPVAFYTRKAC 84
            F +L++ +LS+ T D+V + A   L +    T E +  ADE  +++LI  +  Y  KA 
Sbjct: 29  PFELLVAVILSAQTTDEVVNKATPALFKR-YPTPEDLLNADEEELEELIKSIGLYRNKAK 87

Query: 85  NMKKIAKICLTKYDGDIPSSLDELLALPGIGPKMANMVMTLGWFNVQGICVDTHVHRICN 144
           N+K++A+I L K+ G++P + +ELL+LPG+G K AN+V++   F +  I VDTHVHR+ N
Sbjct: 88  NIKELARILLEKFGGEVPDTREELLSLPGVGRKTANVVLSFA-FGIPAIAVDTHVHRVSN 146

Query: 145 RLGWVTQPGTKQKTSSPEQTREALQRWLPKEEWVRINPLLVGFGQTICTPLRPRCGMCTV 204
           RLG V          +PE+  EAL + +PKE W  ++  L+  G+ IC   +PRC  C +
Sbjct: 147 RLGLV-------PGKTPEEVEEALMKLIPKELWTDLHHWLILHGRYICKARKPRCEECPL 199

Query: 205 SEYCPSAFKE 214
           ++ CPSA K 
Sbjct: 200 ADLCPSAGKT 209

Length = 211

>gnl|CDD|238013 cd00056, ENDO3c, endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases

 Score =  160 bits (407), Expect = 5e-50
 Identities = 60/166 (36%), Positives = 89/166 (53%), Gaps = 11/166 (6%)

Query: 26  FAVLLSALLSSLTKDKVADGALQRLLQNGLHTAEAIDKADEATIKDLIYPVAFYTRKACN 85
           F VL+S +LS  T DK  + A +RL +    T EA+  ADE  +++LI  + +  RKA  
Sbjct: 1   FEVLVSEILSQQTTDKAVNKAYERLFERYGPTPEALAAADEEELRELIRSLGYR-RKAKY 59

Query: 86  MKKIAKICLTKYDGDI---PSSLDELLALPGIGPKMANMVMTLGWFNVQGICVDTHVHRI 142
           +K++A+  +  + G +   P + +ELLALPG+G K AN+V+           VDTHV R+
Sbjct: 60  LKELARAIVEGFGGLVLDDPDAREELLALPGVGRKTANVVLLFA-LGPDAFPVDTHVRRV 118

Query: 143 CNRLGWVTQPGTKQKTSSPEQTREALQRWLPKEEWVRINPLLVGFG 188
             RLG +       K  +PE+  E L+  LPK  W   N  L+  G
Sbjct: 119 LKRLGLIP------KKKTPEELEELLEELLPKPYWGEANQALMDLG 158

Length = 158

>gnl|CDD|214684 smart00478, ENDO3c, endonuclease III

 Score =  148 bits (375), Expect = 2e-45
 Identities = 62/157 (39%), Positives = 93/157 (59%), Gaps = 8/157 (5%)

Query: 34  LSSLTKDKVADGALQRLLQNGLHTAEAIDKADEATIKDLIYPVAFYTRKACNMKKIAKIC 93
           LS  T D+  + A +RL +    T E +  ADE  +++LI  + FY RKA  + ++A+I 
Sbjct: 1   LSQQTTDERVNKATERLFEKFP-TPEDLAAADEEELEELIRGLGFYRRKARYLIELARIL 59

Query: 94  LTKYDGDIPSSLDELLALPGIGPKMANMVMTLGWFNVQGICVDTHVHRICNRLGWVTQPG 153
           + +Y G++P   +ELL LPG+G K AN V++        I VDTHV RI  RLG V    
Sbjct: 60  VEEYGGEVPDDREELLKLPGVGRKTANAVLSFAL-GKPFIPVDTHVLRIAKRLGLV---- 114

Query: 154 TKQKTSSPEQTREALQRWLPKEEWVRINPLLVGFGQT 190
              K S+PE+  + L++ LP+E+W  +N LL+ FG+T
Sbjct: 115 --DKKSTPEEVEKLLEKLLPEEDWRELNLLLIDFGRT 149

includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases. Length = 149

>gnl|CDD|130155 TIGR01083, nth, endonuclease III

 Score =  149 bits (378), Expect = 3e-45
 Identities = 55/174 (31%), Positives = 98/174 (56%), Gaps = 9/174 (5%)

Query: 26  FAVLLSALLSSLTKDKVADGALQRLLQNGLHTAEAIDKADEATIKDLIYPVAFYTRKACN 85
           F +L++ +LS+   DK  + A ++L +    T +A+ +A    +++ I  +  Y  KA N
Sbjct: 27  FELLVATILSAQATDKSVNKATKKLFEV-YPTPQALAQAGLEELEEYIKSIGLYRNKAKN 85

Query: 86  MKKIAKICLTKYDGDIPSSLDELLALPGIGPKMANMVMTLGWFNVQGICVDTHVHRICNR 145
           +  + +I + +Y G++P   +EL+ LPG+G K AN+V+ +  F +  I VDTHV R+ NR
Sbjct: 86  IIALCRILVERYGGEVPEDREELVKLPGVGRKTANVVLNVA-FGIPAIAVDTHVFRVSNR 144

Query: 146 LGWVTQPGTKQKTSSPEQTREALQRWLPKEEWVRINPLLVGFGQTICTPLRPRC 199
           LG      +K K   P++  E L + +P+E W +++  L+  G+  C   +P C
Sbjct: 145 LGL-----SKGKD--PDKVEEELLKLIPREFWTKLHHWLILHGRYTCKARKPLC 191

This equivalog model identifes nth members of the pfam00730 superfamily (HhH-GPD: Helix-hairpin-helix and Gly/Pro rich loop followed by a conserved aspartate). The major members of the superfamily are nth and mutY [DNA metabolism, DNA replication, recombination, and repair]. Length = 191

>gnl|CDD|216088 pfam00730, HhH-GPD, HhH-GPD superfamily base excision DNA repair protein

 Score =  122 bits (308), Expect = 2e-35
 Identities = 51/150 (34%), Positives = 76/150 (50%), Gaps = 11/150 (7%)

Query: 30  LSALLSSLTKDKVADGALQRLLQ-NGLHTAEAIDKADEATIKDLIYPVAFYTRKACNMKK 88
           +SA+LS  T DK A+   +RL +  G  T E + +ADE  +++LI  + FY RKA  +K+
Sbjct: 1   VSAILSQQTSDKAANKITKRLFERYGFPTPEDLAEADEEELRELIKGLGFYRRKAKYIKE 60

Query: 89  IAKICLTKYDGDIPSSLDE---LLALPGIGPKMANMVMTLGW-FNVQGICVDTHVHRICN 144
           +A+I +  Y G +P  L+E   LLALPG+G   A  V+            VDTHV R+  
Sbjct: 61  LARILVEGYLGLVPLDLEELEALLALPGVGRWTAEAVLLFALGRPDVFPAVDTHVRRVAK 120

Query: 145 RLGWVTQPGTKQKTSSPEQTREALQRWLPK 174
           RLG +            ++    L+   P 
Sbjct: 121 RLGLI------DTKPPKKEVERELEELWPP 144

This family contains a diverse range of structurally related DNA repair proteins. The superfamily is called the HhH-GPD family after its hallmark Helix-hairpin-helix and Gly/Pro rich loop followed by a conserved aspartate. This includes endonuclease III, EC:4.2.99.18 and MutY an A/G-specific adenine glycosylase, both have a C terminal 4Fe-4S cluster. The family also includes 8-oxoguanine DNA glycosylases. The methyl-CPG binding protein MBD4 also contains a related domain that is a thymine DNA glycosylase. The family also includes DNA-3-methyladenine glycosylase II EC:3.2.2.21 and other members of the AlkA family. Length = 144

>gnl|CDD|182661 PRK10702, PRK10702, endonuclease III; Provisional

 Score = 94.3 bits (234), Expect = 8e-24
 Identities = 62/191 (32%), Positives = 96/191 (50%), Gaps = 15/191 (7%)

Query: 26  FAVLLSALLSSLTKDKVADGALQRLLQNGLHTAEAIDKADEATIKDLIYPVAFYTRKACN 85
           F +L++ LLS+   D   + A  +L     +T  A+ +     +K  I  +  Y  KA N
Sbjct: 30  FELLIAVLLSAQATDVSVNKATAKLYPVA-NTPAAMLELGVEGVKTYIKTIGLYNSKAEN 88

Query: 86  MKKIAKICLTKYDGDIPSSLDELLALPGIGPKMANMVM--TLGWFNVQGICVDTHVHRIC 143
           + K  +I L +++G++P     L ALPG+G K AN+V+    GW     I VDTH+ R+C
Sbjct: 89  VIKTCRILLEQHNGEVPEDRAALEALPGVGRKTANVVLNTAFGW---PTIAVDTHIFRVC 145

Query: 144 NRLGWVTQPGTKQKTSSPEQTREALQRWLPKEEWVRINPLLVGFGQTICTPLRPRCGMCT 203
           NR  +   PG      + EQ  E L + +P E  V  +  L+  G+  C   +PRCG C 
Sbjct: 146 NRTQFA--PG-----KNVEQVEEKLLKVVPAEFKVDCHHWLILHGRYTCIARKPRCGSCI 198

Query: 204 VSEYCPSAFKE 214
           + + C   +KE
Sbjct: 199 IEDLC--EYKE 207

Length = 211

>gnl|CDD|224115 COG1194, MutY, A/G-specific DNA glycosylase [DNA replication, recombination, and repair]

 Score = 91.3 bits (227), Expect = 1e-21
 Identities = 46/178 (25%), Positives = 86/178 (48%), Gaps = 6/178 (3%)

Query: 57  TAEAIDKADEATIKDLIYPVAFYTRKACNMKKIAKICLTKYDGDIPSSLDELLALPGIGP 116
           T +A+  A E  +      + +Y+R A N+ K A+  + ++ G+ P   +EL ALPG+GP
Sbjct: 65  TIKALAAAPEDEVLKAWEGLGYYSR-ARNLHKAAQEVVERHGGEFPDDEEELAALPGVGP 123

Query: 117 KMANMVMTLGWFNVQGICVDTHVHRICNRLGWVTQPGTKQKTSSPEQTREALQRWLPKEE 176
             A  +++   FN     +D +V R+ +RL      G   K  + ++  E  ++ L  + 
Sbjct: 124 YTAGAILSFA-FNQPEPVLDGNVKRVLSRL--FAISGDIGKPKTKKELWELAEQLLTPDR 180

Query: 177 WVR-INPLLVGFGQTICTPLRPRCGMCTVSEYCPSAFKESSTSSSKSKKSESSSLRKL 233
                N  ++  G TICT  +P+C +C + + C +A++  +      KK +    R+ 
Sbjct: 181 RPGDFNQAMMDLGATICTAKKPKCSLCPLRDNC-AAYRNGTPEKYPVKKPKKKLPRRF 237

Length = 342

>gnl|CDD|130156 TIGR01084, mutY, A/G-specific adenine glycosylase

 Score = 78.2 bits (193), Expect = 3e-17
 Identities = 44/168 (26%), Positives = 82/168 (48%), Gaps = 5/168 (2%)

Query: 57  TAEAIDKADEATIKDLIYPVAFYTRKACNMKKIAKICLTKYDGDIPSSLDELLALPGIGP 116
           T +A+  A +  +  L   + +Y R A N+ K A+  + ++ G+ P   ++L ALPG+G 
Sbjct: 57  TVQALANAPQDEVLKLWEGLGYYAR-ARNLHKAAQEVVEEFGGEFPQDFEDLAALPGVGR 115

Query: 117 KMANMVMTLGWFNVQGICVDTHVHRICNRLGWVTQPGTKQKTSSPEQTREALQRWLPKEE 176
             A  +++    N     +D +V R+ +RL  V     K+K  +  +     +  LPK +
Sbjct: 116 YTAGAILSFA-LNKPYPILDGNVKRVLSRLFAVEGWPGKKKVEN--RLWTLAESLLPKAD 172

Query: 177 WVRINPLLVGFGQTICTPLRPRCGMCTVSEYCPSAFKESSTSSSKSKK 224
               N  L+  G  ICT  +P+C +C + ++C  A+++ +      KK
Sbjct: 173 PEAFNQALMDLGAMICTRKKPKCDLCPLQDFC-LAYQQGTWEEYPVKK 219

This equivalog model identifies mutY members of the pfam00730 superfamily (HhH-GPD: Helix-hairpin-helix and Gly/Pro rich loop followed by a conserved aspartate). The major members of the superfamily are nth and mutY [DNA metabolism, DNA replication, recombination, and repair]. Length = 275

>gnl|CDD|172427 PRK13910, PRK13910, DNA glycosylase MutY; Provisional

 Score = 72.0 bits (176), Expect = 6e-15
 Identities = 42/134 (31%), Positives = 66/134 (49%), Gaps = 16/134 (11%)

Query: 79  YTRKACNMKKIAKICLTKYDGDIPSSLDELLALPGIGPKMANMVMTLGWFNVQGICVDTH 138
           Y  +A N+KK A+IC+ ++   +P+    LL LPGIG   AN ++  G F  +  CVD +
Sbjct: 45  YYSRAKNLKKSAEICVKEHHSQLPNDYQSLLKLPGIGAYTANAILCFG-FREKSACVDAN 103

Query: 139 VHRICNRLGWVTQPGTKQKTSSPEQTREALQR----WLPKEEWVRINPLLVGFGQTICTP 194
           + R+  RL  +           P    + LQ     +L   E    N  L+  G  IC+P
Sbjct: 104 IKRVLLRLFGL----------DPNIHAKDLQIKANDFLNLNESFNHNQALIDLGALICSP 153

Query: 195 LRPRCGMCTVSEYC 208
            +P+C +C ++ YC
Sbjct: 154 -KPKCAICPLNPYC 166

Length = 289

>gnl|CDD|225140 COG2231, COG2231, Uncharacterized protein related to Endonuclease III [DNA replication, recombination, and repair]

 Score = 61.2 bits (149), Expect = 2e-11
 Identities = 48/194 (24%), Positives = 88/194 (45%), Gaps = 15/194 (7%)

Query: 21  PKERRFAVLLSALLSSLTKDKVADGALQRLLQNGLHTAEAIDKADEATIKDLIYPVAFYT 80
           P + +  +++ A+L+  T  K  + AL+ L   G+   + I K DE  + +LI P  FY 
Sbjct: 26  PADNKDEIIIGAILTQNTSWKNVEKALENLKNEGILNLKKILKLDEEELAELIRPSGFYN 85

Query: 81  RKACNMKKIAKICL---TKYDGDIPSSL-DELLALPGIGPKMANMVMTLGWFNVQGICVD 136
           +KA  +K ++K         +      L +ELL++ GIG + A+  + L   +     VD
Sbjct: 86  QKAKRLKALSKNLAKFFINLESFKSEVLREELLSIKGIGKETAD-SILLYALDRPVFVVD 144

Query: 137 THVHRICNRLGWVTQPGTKQKTSSPEQTREALQRWLPKEEWVRIN--PLLVGFGQTICTP 194
            +  R+ +RLG +       +    ++ +E  +  LP+   +      L+V   +  C  
Sbjct: 145 KYTRRLLSRLGGI-------EEKKYDEIKELFEENLPENLRLYQEFHALIVEHAKHFCKK 197

Query: 195 LRPRCGMCTVSEYC 208
            +P C  C + E C
Sbjct: 198 -KPLCEKCPLKEKC 210

Length = 215

>gnl|CDD|182805 PRK10880, PRK10880, adenine DNA glycosylase; Provisional

 Score = 56.3 bits (136), Expect = 2e-09
 Identities = 43/151 (28%), Positives = 70/151 (46%), Gaps = 13/151 (8%)

Query: 78  FYTRKACNMKKIAKICLTKYDGDIPSSLDELLALPGIGPKMANMVMTLGWFNVQGICVDT 137
           +Y R A N+ K A+   T + G+ P + +E+ ALPG+G   A  +++L       I +D 
Sbjct: 82  YYAR-ARNLHKAAQQVATLHGGEFPETFEEVAALPGVGRSTAGAILSLSLGKHFPI-LDG 139

Query: 138 HVHRICNRL----GWVTQPGTKQKTSSPEQTREALQRWLPKEEWVRINPLLVGFGQTICT 193
           +V R+  R     GW   PG K+  +   Q  E +    P     R N  ++  G  +CT
Sbjct: 140 NVKRVLARCYAVSGW---PGKKEVENRLWQLSEQVT---PAVGVERFNQAMMDLGAMVCT 193

Query: 194 PLRPRCGMCTVSEYCPSAFKESSTSSSKSKK 224
             +P+C +C +   C  A+   S +    KK
Sbjct: 194 RSKPKCELCPLQNGC-IAYANHSWALYPGKK 223

Length = 350

>gnl|CDD|109681 pfam00633, HHH, Helix-hairpin-helix motif

 Score = 46.2 bits (111), Expect = 1e-07
 Identities = 15/28 (53%), Positives = 21/28 (75%)

Query: 96  KYDGDIPSSLDELLALPGIGPKMANMVM 123
             +G IP+S +ELLALPG+GPK A  ++
Sbjct: 1   SLEGLIPASREELLALPGVGPKTAEAIL 28

The helix-hairpin-helix DNA-binding motif is found to be duplicated in the central domain of RuvA. The HhH domain of DisA, a bacterial checkpoint control protein, is a DNA-binding domain. Length = 30

>gnl|CDD|211589 TIGR00588, ogg, 8-oxoguanine DNA-glycosylase (ogg)

 Score = 42.6 bits (100), Expect = 8e-05
 Identities = 24/71 (33%), Positives = 33/71 (46%), Gaps = 4/71 (5%)

Query: 108 LLALPGIGPKMANMVMTLGWFNVQGICVDTHVHRICNRL-GWVTQPGTKQKTSSPEQTRE 166
           L  LPG+GPK+A+ +  +G    Q + VD HV RI NR   W   P T +        R+
Sbjct: 222 LCELPGVGPKVADCICLMGLDKPQAVPVDVHVWRIANRDYPW--HPKTSRAKGPSPFARK 279

Query: 167 ALQRWLPKEEW 177
            L     +  W
Sbjct: 280 ELGN-FFRSLW 289

All proteins in this family for which functions are known are 8-oxo-guanaine DNA glycosylases that function in base excision repair. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). This family is distantly realted to the Nth-MutY superfamily [DNA metabolism, DNA replication, recombination, and repair]. Length = 310

>gnl|CDD|197771 smart00525, FES, iron-sulpphur binding domain in DNA-(apurinic or apyrimidinic site) lyase (subfamily of ENDO3)

 Score = 37.5 bits (88), Expect = 1e-04
 Identities = 9/21 (42%), Positives = 13/21 (61%)

Query: 191 ICTPLRPRCGMCTVSEYCPSA 211
           ICT  +PRC  C + + CP+ 
Sbjct: 1   ICTARKPRCDECPLKDLCPAY 21

Length = 21

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	235
COG0177	211	Nth Predicted EndoIII-related endonuclease [DNA re	100.0
KOG1921	286	consensus Endonuclease III [Replication, recombina	100.0
PRK10702	211	endonuclease III; Provisional	100.0
TIGR01084	275	mutY A/G-specific adenine glycosylase. This equiva	100.0
PRK10880	350	adenine DNA glycosylase; Provisional	100.0
COG1194	342	MutY A/G-specific DNA glycosylase [DNA replication	100.0
TIGR01083	191	nth endonuclease III. This equivalog model identif	100.0
PRK13910	289	DNA glycosylase MutY; Provisional	100.0
PRK13913	218	3-methyladenine DNA glycosylase; Provisional	100.0
COG2231	215	Uncharacterized protein related to Endonuclease II	100.0
KOG2457	555	consensus A/G-specific adenine DNA glycosylase [Re	100.0
smart00478	149	ENDO3c endonuclease III. includes endonuclease III	100.0
cd00056	158	ENDO3c endonuclease III; includes endonuclease III	100.0
PRK01229	208	N-glycosylase/DNA lyase; Provisional	99.97
TIGR00588	310	ogg 8-oxoguanine DNA-glycosylase (ogg). All protei	99.95
COG0122	285	AlkA 3-methyladenine DNA glycosylase/8-oxoguanine	99.94
PRK10308	283	3-methyl-adenine DNA glycosylase II; Provisional	99.93
TIGR03252	177	uncharacterized HhH-GPD family protein. This model	99.92
KOG2875	323	consensus 8-oxoguanine DNA glycosylase [Replicatio	99.86
KOG1918	254	consensus 3-methyladenine DNA glycosidase [Replica	99.86
PF00730	108	HhH-GPD: HhH-GPD superfamily base excision DNA rep	99.83
COG1059	210	Thermostable 8-oxoguanine DNA glycosylase [DNA rep	99.27
PF00633	30	HHH: Helix-hairpin-helix motif; InterPro: IPR00044	98.71
PF10576	17	EndIII_4Fe-2S: Iron-sulfur binding domain of endon	98.26
smart00525	26	FES FES domain. iron-sulpphur binding domain in DN	97.65
PF09674	232	DUF2400: Protein of unknown function (DUF2400); In	96.8
PF03352	179	Adenine_glyco: Methyladenine glycosylase; InterPro	96.53
smart00278	26	HhH1 Helix-hairpin-helix DNA-binding motif class 1	96.0
TIGR02757	229	conserved hypothetical protein TIGR02757. Members	95.63
PRK10353	187	3-methyl-adenine DNA glycosylase I; Provisional	95.52
PF14716	68	HHH_8: Helix-hairpin-helix domain; PDB: 2W9M_A 1HU	95.51
PRK13901	196	ruvA Holliday junction DNA helicase RuvA; Provisio	95.5
PF12826	64	HHH_2: Helix-hairpin-helix motif; PDB: 1X2I_B 1DGS	95.2
COG2818	188	Tag 3-methyladenine DNA glycosylase [DNA replicati	95.15
TIGR00624	179	tag DNA-3-methyladenine glycosylase I. This family	94.87
PRK14601	183	ruvA Holliday junction DNA helicase RuvA; Provisio	94.42
PRK14606	188	ruvA Holliday junction DNA helicase RuvA; Provisio	93.97
PF14520	60	HHH_5: Helix-hairpin-helix domain; PDB: 3AUO_B 3AU	93.88
PRK14602	203	ruvA Holliday junction DNA helicase RuvA; Provisio	93.52
COG0632	201	RuvA Holliday junction resolvasome, DNA-binding su	93.47
PRK14604	195	ruvA Holliday junction DNA helicase RuvA; Provisio	93.42
TIGR00084	191	ruvA Holliday junction DNA helicase, RuvA subunit.	93.25
PRK14605	194	ruvA Holliday junction DNA helicase RuvA; Provisio	93.19
PRK14603	197	ruvA Holliday junction DNA helicase RuvA; Provisio	93.07
PRK14600	186	ruvA Holliday junction DNA helicase RuvA; Provisio	92.12
TIGR00426	69	competence protein ComEA helix-hairpin-helix repea	91.98
PRK02515	132	psbU photosystem II complex extrinsic protein prec	91.93
PRK14973	936	DNA topoisomerase I; Provisional	91.91
PF02371	87	Transposase_20: Transposase IS116/IS110/IS902 fami	91.82
COG0353	198	RecR Recombinational DNA repair protein (RecF path	91.16
cd00141	307	NT_POLXc Nucleotidyltransferase (NT) domain of fam	91.11
smart00483	334	POLXc DNA polymerase X family. includes vertebrate	90.87
PF14229	122	DUF4332: Domain of unknown function (DUF4332)	90.86
PRK13844	200	recombination protein RecR; Provisional	90.78
PRK00076	196	recR recombination protein RecR; Reviewed	90.5
PRK00116	192	ruvA Holliday junction DNA helicase RuvA; Reviewed	90.45
TIGR00615	195	recR recombination protein RecR. This family is ba	90.3
TIGR00608	218	radc DNA repair protein radc. This family is based	90.12
PF14520	60	HHH_5: Helix-hairpin-helix domain; PDB: 3AUO_B 3AU	90.05
TIGR00575	652	dnlj DNA ligase, NAD-dependent. The member of this	89.78
PRK00116	192	ruvA Holliday junction DNA helicase RuvA; Reviewed	89.71
PF12836	65	HHH_3: Helix-hairpin-helix motif; PDB: 2EDU_A 2OCE	88.26
PRK07956	665	ligA NAD-dependent DNA ligase LigA; Validated	87.92
TIGR01954	50	nusA_Cterm_rpt transcription termination factor Nu	87.68
PRK08097	562	ligB NAD-dependent DNA ligase LigB; Reviewed	87.46
PRK14350	669	ligA NAD-dependent DNA ligase LigA; Provisional	87.31
PRK08609	570	hypothetical protein; Provisional	87.19
PRK00024	224	hypothetical protein; Reviewed	86.48
PF11731	93	Cdd1: Pathogenicity locus; InterPro: IPR021725 Cdd	86.42
smart00483	334	POLXc DNA polymerase X family. includes vertebrate	86.4
COG1555	149	ComEA DNA uptake protein and related DNA-binding p	85.88
COG1555	149	ComEA DNA uptake protein and related DNA-binding p	85.62
PRK14351	689	ligA NAD-dependent DNA ligase LigA; Provisional	84.86
TIGR01259	120	comE comEA protein. This model describes the ComEA	84.77
PF09171	246	DUF1886: Domain of unknown function (DUF1886); Int	84.66
PRK07945	335	hypothetical protein; Provisional	84.58
TIGR00084	191	ruvA Holliday junction DNA helicase, RuvA subunit.	84.42
PRK14605	194	ruvA Holliday junction DNA helicase RuvA; Provisio	84.0
PF11798	32	IMS_HHH: IMS family HHH motif; InterPro: IPR024728	83.96
COG1796	326	POL4 DNA polymerase IV (family X) [DNA replication	83.83
PF10391	52	DNA_pol_lambd_f: Fingers domain of DNA polymerase	83.72
TIGR01259	120	comE comEA protein. This model describes the ComEA	83.62
PRK13901	196	ruvA Holliday junction DNA helicase RuvA; Provisio	83.37
PRK14601	183	ruvA Holliday junction DNA helicase RuvA; Provisio	82.97
PRK14603	197	ruvA Holliday junction DNA helicase RuvA; Provisio	82.75
COG1415	373	Uncharacterized conserved protein [Function unknow	82.42
PRK00024	224	hypothetical protein; Reviewed	82.23
smart00279	36	HhH2 Helix-hairpin-helix class 2 (Pol1 family) mot	81.85
PRK14606	188	ruvA Holliday junction DNA helicase RuvA; Provisio	81.62
cd00141	307	NT_POLXc Nucleotidyltransferase (NT) domain of fam	81.58

>COG0177 Nth Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]

Probab=100.00  E-value=1.7e-57  Score=377.12  Aligned_cols=183  Identities=40%  Similarity=0.728  Sum_probs=177.9

Q ss_pred             CChHHHHHHHHHhccccHHHHHHHHHHHHHcCCCCHHHHhcCCHHHHHHhhccCCChHHHHHHHHHHHHHHHHhcCCCCh
Q 026681           23 ERRFAVLLSALLSSLTKDKVADGALQRLLQNGLHTAEAIDKADEATIKDLIYPVAFYTRKACNMKKIAKICLTKYDGDIP  102 (235)
Q Consensus        23 ~~~f~~lv~~iLsqqt~~~~~~~~~~~l~~~~~pt~~~la~a~~e~l~~~l~~~G~~~~Ka~~l~~~a~~i~~~~~g~~~  102 (235)
                      .|||++||++||||||+++++.+++.+|++ .++||++++++++++|+++|+..|||++||++|+++++.|+++|+|++|
T Consensus        27 ~~pf~lLva~iLSaqttD~~vn~at~~Lf~-~~~t~e~l~~a~~~~l~~~I~~iGlyr~KAk~I~~~~~~l~e~~~g~vP  105 (211)
T COG0177          27 KDPFELLVAVILSAQTTDEVVNKATPALFK-RYPTPEDLLNADEEELEELIKSIGLYRNKAKNIKELARILLEKFGGEVP  105 (211)
T ss_pred             CCcHHHHHHHHHhccCchHHHHHHHHHHHH-HcCCHHHHHcCCHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHHcCCCCC
Confidence            799999999999999999999999999999 5999999999999999999999999999999999999999999999999


Q ss_pred             hhHHHHHcCCCCcHHHHHHHHHHhcCCcceeecchHHHHHHHHhcCcCCCCCCCCCCCHHHHHHHHHHhCCcccHHHHHH
Q 026681          103 SSLDELLALPGIGPKMANMVMTLGWFNVQGICVDTHVHRICNRLGWVTQPGTKQKTSSPEQTREALQRWLPKEEWVRINP  182 (235)
Q Consensus       103 ~~~~~L~~l~GIG~~tA~~il~~~~~~~~~~pvDt~v~Rv~~Rlg~~~~~~~~~~~~~~~~~~~~l~~~~p~~~~~~~~~  182 (235)
                      +++++|++|||||+|||++||+++||.+ +|+|||||+||++|+||++       +.++++++..+++++|.+.|..+|.
T Consensus       106 ~~~~eL~~LPGVGrKTAnvVL~~a~g~p-~i~VDTHV~Rvs~R~gl~~-------~~~p~~ve~~L~~~iP~~~~~~~h~  177 (211)
T COG0177         106 DTREELLSLPGVGRKTANVVLSFAFGIP-AIAVDTHVHRVSNRLGLVP-------GKTPEEVEEALMKLIPKELWTDLHH  177 (211)
T ss_pred             chHHHHHhCCCcchHHHHHHHHhhcCCC-cccccchHHHHHHHhCCCC-------CCCHHHHHHHHHHHCCHHHHHHHHH
Confidence            9999999999999999999999999996 9999999999999999986       5789999999999999999999999


Q ss_pred             HHHHHHhhhcCCCCCCCCCCcccccCcccccC
Q 026681          183 LLVGFGQTICTPLRPRCGMCTVSEYCPSAFKE  214 (235)
Q Consensus       183 ~l~~~G~~iC~~~~P~C~~Cpl~~~C~~~~~~  214 (235)
                      +|+.|||.+|++++|+|+.||+++.|+++.+.
T Consensus       178 ~lI~~GR~iC~ar~P~C~~C~l~~~C~~~~~~  209 (211)
T COG0177         178 WLILHGRYICKARKPRCEECPLADLCPSAGKT  209 (211)
T ss_pred             HHHHhhhhhccCCCCCcCcccchhhCchhccc
Confidence            99999999999999999999999999987654

>KOG1921 consensus Endonuclease III [Replication, recombination and repair]

Probab=100.00  E-value=4.6e-54  Score=356.58  Aligned_cols=223  Identities=58%  Similarity=0.992  Sum_probs=208.8

Q ss_pred             CCCCCCccccCCCCCC-CCCCCCChHHHHHHHHHhccccHHHHHHHHHHHHHcCCCCHHHHhcCCHHHHHHhhccCCChH
Q 026681            2 KTLEPVYSLGVDETDS-SLPPKERRFAVLLSALLSSLTKDKVADGALQRLLQNGLHTAEAIDKADEATIKDLIYPVAFYT   80 (235)
Q Consensus         2 ~~~~~~~~~g~~~~~~-~~p~~~~~f~~lv~~iLsqqt~~~~~~~~~~~l~~~~~pt~~~la~a~~e~l~~~l~~~G~~~   80 (235)
                      +..||||.|||+..+. ..++.+..|++||+.+||.||.+++...++.+|.+++..|+++|.++++..|.++|.++|||.
T Consensus        54 k~~APVD~mGc~~~~~~~~~pk~~RfqvLv~lmLSSQTKDevt~~Am~rL~~~~gLT~e~v~~~de~~l~~LI~~VgFy~  133 (286)
T KOG1921|consen   54 KIVAPVDTMGCSRIPSLKADPKERRFQVLVGLMLSSQTKDEVTAAAMLRLKEYGGLTLEAVLKIDEPTLNELIYPVGFYT  133 (286)
T ss_pred             cccCCccccccccCccccCChhhHhHHHHHHHHHhcchHHHHHHHHHHHHHHhcCCCHHHHhccChHhHHhhhhhccchH
Confidence            3789999999999998 788889999999999999999999999999999998779999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHhcCCCChhhHHHHHcCCCCcHHHHHHHHHHhcCCcceeecchHHHHHHHHhcCcCCCCCCCCCCC
Q 026681           81 RKACNMKKIAKICLTKYDGDIPSSLDELLALPGIGPKMANMVMTLGWFNVQGICVDTHVHRICNRLGWVTQPGTKQKTSS  160 (235)
Q Consensus        81 ~Ka~~l~~~a~~i~~~~~g~~~~~~~~L~~l~GIG~~tA~~il~~~~~~~~~~pvDt~v~Rv~~Rlg~~~~~~~~~~~~~  160 (235)
                      +||.||+.+|+.+.++|+||+|++.++|++|||||||.|..+|..+||....|.||+||+|+++||||++.     +.++
T Consensus       134 rKA~ylkkta~IL~d~f~gDIP~~v~dLlsLPGVGPKMa~L~m~~AWn~i~GI~VDtHVHRi~nrlgWv~~-----ktks  208 (286)
T KOG1921|consen  134 RKAKYLKKTAKILQDKFDGDIPDTVEDLLSLPGVGPKMAHLTMQVAWNKIVGICVDTHVHRICNRLGWVDT-----KTKS  208 (286)
T ss_pred             HHHHHHHHHHHHHHHHhCCCCchhHHHHhcCCCCchHHHHHHHHHHhccceeEEeehHHHHHHHHhccccc-----ccCC
Confidence            99999999999999999999999999999999999999999999999999999999999999999999973     4678


Q ss_pred             HHHHHHHHHHhCCcccHHHHHHHHHHHHhhhcCCCCCCCCCCcc-cccCcccccCCCCCCCCCccccchh
Q 026681          161 PEQTREALQRWLPKEEWVRINPLLVGFGQTICTPLRPRCGMCTV-SEYCPSAFKESSTSSSKSKKSESSS  229 (235)
Q Consensus       161 ~~~~~~~l~~~~p~~~~~~~~~~l~~~G~~iC~~~~P~C~~Cpl-~~~C~~~~~~~~~~~~k~~~~~~~~  229 (235)
                      +|+++.+|+.|+|.+.|.++|..|+.||+.||+|++|+|+.|-+ ++.|++.++..+....+.++++..+
T Consensus       209 pE~TR~aLq~wLPk~lW~eIN~lLVGFGQ~iC~p~~prC~~C~~~~~~Cpss~~~~~~~~~~~~~~~~~k  278 (286)
T KOG1921|consen  209 PEQTRVALQQWLPKSLWVEINHLLVGFGQTICTPRRPRCGLCLLSRDLCPSSFKEASSLTKELKKSIMVK  278 (286)
T ss_pred             HHHHHHHHHHhCcHHHHhhhhceeecccceeeecCCCCccccccCcccCchhhhhccchhHHHHhhhhhc
Confidence            99999999999999999999999999999999999999999999 6999998877666656555554443

>PRK10702 endonuclease III; Provisional

Probab=100.00  E-value=3.1e-52  Score=349.51  Aligned_cols=184  Identities=31%  Similarity=0.497  Sum_probs=175.4

Q ss_pred             CCChHHHHHHHHHhccccHHHHHHHHHHHHHcCCCCHHHHhcCCHHHHHHhhccCCChHHHHHHHHHHHHHHHHhcCCCC
Q 026681           22 KERRFAVLLSALLSSLTKDKVADGALQRLLQNGLHTAEAIDKADEATIKDLIYPVAFYTRKACNMKKIAKICLTKYDGDI  101 (235)
Q Consensus        22 ~~~~f~~lv~~iLsqqt~~~~~~~~~~~l~~~~~pt~~~la~a~~e~l~~~l~~~G~~~~Ka~~l~~~a~~i~~~~~g~~  101 (235)
                      .++||++||++||||||++.++.+++.+|+. .||||++|++++.++|+++|+++|||++||++|+++|+.+.++|+|++
T Consensus        26 ~~~p~e~lvs~iLsq~t~~~~v~~~~~~L~~-~~pt~e~l~~a~~~~l~~~i~~~G~y~~kA~~l~~~a~~i~~~~~~~~  104 (211)
T PRK10702         26 FSSPFELLIAVLLSAQATDVSVNKATAKLYP-VANTPAAMLELGVEGVKTYIKTIGLYNSKAENVIKTCRILLEQHNGEV  104 (211)
T ss_pred             CCChHHHHHHHHHHhhcCHHHHHHHHHHHHH-HcCCHHHHHCCCHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHcCCCC
Confidence            5799999999999999999999999999998 699999999999999999999999999999999999999999999999


Q ss_pred             hhhHHHHHcCCCCcHHHHHHHHHHhcCCcceeecchHHHHHHHHhcCcCCCCCCCCCCCHHHHHHHHHHhCCcccHHHHH
Q 026681          102 PSSLDELLALPGIGPKMANMVMTLGWFNVQGICVDTHVHRICNRLGWVTQPGTKQKTSSPEQTREALQRWLPKEEWVRIN  181 (235)
Q Consensus       102 ~~~~~~L~~l~GIG~~tA~~il~~~~~~~~~~pvDt~v~Rv~~Rlg~~~~~~~~~~~~~~~~~~~~l~~~~p~~~~~~~~  181 (235)
                      |+++++|++|||||+|||++||+|+|++ ++||||+||+||++|+|+..       ..++++++..++..+|.+.|.++|
T Consensus       105 p~~~~~Ll~lpGVG~ktA~~ill~a~~~-~~~~VDt~v~Rv~~r~g~~~-------~~~~~~~~~~l~~~lp~~~~~~~~  176 (211)
T PRK10702        105 PEDRAALEALPGVGRKTANVVLNTAFGW-PTIAVDTHIFRVCNRTQFAP-------GKNVEQVEEKLLKVVPAEFKVDCH  176 (211)
T ss_pred             CchHHHHhcCCcccHHHHHHHHHHHcCC-CcccccchHHHHHHHhCCCC-------CCCHHHHHHHHHHhCCchHHHHHH
Confidence            9999999999999999999999999998 68999999999999999864       357889999999999999999999


Q ss_pred             HHHHHHHhhhcCCCCCCCCCCcccccCcccccC
Q 026681          182 PLLVGFGQTICTPLRPRCGMCTVSEYCPSAFKE  214 (235)
Q Consensus       182 ~~l~~~G~~iC~~~~P~C~~Cpl~~~C~~~~~~  214 (235)
                      .+||+||+.+|++++|+|+.|||++.|+++.+.
T Consensus       177 ~~li~~Gr~~C~~~~P~C~~Cpl~~~C~~~~~~  209 (211)
T PRK10702        177 HWLILHGRYTCIARKPRCGSCIIEDLCEYKEKV  209 (211)
T ss_pred             HHHHHHhHHHcCCCCCCCCCCcChhhcCccccc
Confidence            999999999999999999999999999976543

>TIGR01084 mutY A/G-specific adenine glycosylase

Probab=100.00  E-value=1e-50  Score=352.38  Aligned_cols=207  Identities=23%  Similarity=0.407  Sum_probs=180.7

Q ss_pred             CCCC-CCCCC--CChHHHHHHHHHhccccHHHHHHHHHHHHHcCCCCHHHHhcCCHHHHHHhhccCCChHHHHHHHHHHH
Q 026681           14 ETDS-SLPPK--ERRFAVLLSALLSSLTKDKVADGALQRLLQNGLHTAEAIDKADEATIKDLIYPVAFYTRKACNMKKIA   90 (235)
Q Consensus        14 ~~~~-~~p~~--~~~f~~lv~~iLsqqt~~~~~~~~~~~l~~~~~pt~~~la~a~~e~l~~~l~~~G~~~~Ka~~l~~~a   90 (235)
                      ++++ ++||+  .|||++||++||+|||++++|.+++.+|.+ .||||++|+++++++|.++|+++||| +||++|+++|
T Consensus        12 ~~~r~~lpWr~~~dpy~vlvseIL~QQT~v~~v~~~~~rl~~-~fpt~~~La~a~~eeL~~~~~~lG~y-~RAr~L~~~A   89 (275)
T TIGR01084        12 KYGRKTLPWRQNKTPYRVWLSEVMLQQTQVATVIPYFERFLE-RFPTVQALANAPQDEVLKLWEGLGYY-ARARNLHKAA   89 (275)
T ss_pred             HhCCCCCCCCCCCCHHHHHHHHHHHhhccHHHHHHHHHHHHH-hCCCHHHHHCcCHHHHHHHHHHCCcH-HHHHHHHHHH
Confidence            5676 89997  589999999999999999999999999999 59999999999999999999999999 5799999999


Q ss_pred             HHHHHhcCCCChhhHHHHHcCCCCcHHHHHHHHHHhcCCcceeecchHHHHHHHHhcCcCCCCCCCCCCCHHHHHHHHHH
Q 026681           91 KICLTKYDGDIPSSLDELLALPGIGPKMANMVMTLGWFNVQGICVDTHVHRICNRLGWVTQPGTKQKTSSPEQTREALQR  170 (235)
Q Consensus        91 ~~i~~~~~g~~~~~~~~L~~l~GIG~~tA~~il~~~~~~~~~~pvDt~v~Rv~~Rlg~~~~~~~~~~~~~~~~~~~~l~~  170 (235)
                      +.|.++|+|.+|+++++|++|||||+|||++|++|+|+++ .++||+||+||+.|+++++...+  .....+.++..++.
T Consensus        90 ~~i~~~~~g~~p~~~~~L~~LpGIG~~TA~~Il~~a~~~~-~~~vD~~v~RVl~Rl~~~~~~~~--~~~~~~~l~~~~~~  166 (275)
T TIGR01084        90 QEVVEEFGGEFPQDFEDLAALPGVGRYTAGAILSFALNKP-YPILDGNVKRVLSRLFAVEGWPG--KKKVENRLWTLAES  166 (275)
T ss_pred             HHHHHHcCCCCcHHHHHHHhCCCCCHHHHHHHHHHHCCCC-CCcchHhHHHHHHHHccCcCCCC--HHHHHHHHHHHHHH
Confidence            9999999999999999999999999999999999999985 56799999999999987653211  11122334455899


Q ss_pred             hCCcccHHHHHHHHHHHHhhhcCCCCCCCCCCcccccCcccccC--CCCCCCCCccc
Q 026681          171 WLPKEEWVRINPLLVGFGQTICTPLRPRCGMCTVSEYCPSAFKE--SSTSSSKSKKS  225 (235)
Q Consensus       171 ~~p~~~~~~~~~~l~~~G~~iC~~~~P~C~~Cpl~~~C~~~~~~--~~~~~~k~~~~  225 (235)
                      ++|.+.+..+|++||+||+.||++++|+|+.|||++.|.++...  ..+|.+++|++
T Consensus       167 ~lp~~~~~~~n~alm~lG~~vC~~~~P~C~~Cpl~~~C~~~~~~~~~~~p~~~~~~~  223 (275)
T TIGR01084       167 LLPKADPEAFNQALMDLGAMICTRKKPKCDLCPLQDFCLAYQQGTWEEYPVKKPKAA  223 (275)
T ss_pred             HCChhhHHHHHHHHHHHhHHHcCCCCCCCCCCCChhhCHHHHcCCHhhcCCCCCCCC
Confidence            99999999999999999999999999999999999999987653  46666554443

This equivalog model identifies mutY members of the pfam00730 superfamily (HhH-GPD: Helix-hairpin-helix and Gly/Pro rich loop followed by a conserved aspartate). The major members of the superfamily are nth and mutY.

>PRK10880 adenine DNA glycosylase; Provisional

Probab=100.00  E-value=9.1e-51  Score=362.28  Aligned_cols=207  Identities=21%  Similarity=0.345  Sum_probs=179.3

Q ss_pred             CCCC-CCCCC--CChHHHHHHHHHhccccHHHHHHHHHHHHHcCCCCHHHHhcCCHHHHHHhhccCCChHHHHHHHHHHH
Q 026681           14 ETDS-SLPPK--ERRFAVLLSALLSSLTKDKVADGALQRLLQNGLHTAEAIDKADEATIKDLIYPVAFYTRKACNMKKIA   90 (235)
Q Consensus        14 ~~~~-~~p~~--~~~f~~lv~~iLsqqt~~~~~~~~~~~l~~~~~pt~~~la~a~~e~l~~~l~~~G~~~~Ka~~l~~~a   90 (235)
                      ++++ ++||+  .|||++||++||+|||++++|.+++.+|++ .|||+++|+++++++|.++|+++|||+ ||++|+++|
T Consensus        16 ~~~r~~lpWr~~~dpy~ilVseILlQQT~v~~v~~~~~rl~~-~fPt~~~La~a~~eel~~~~~glGyy~-RAr~L~~~A   93 (350)
T PRK10880         16 KYGRKTLPWQIDKTPYKVWLSEVMLQQTQVATVIPYFERFMA-RFPTVTDLANAPLDEVLHLWTGLGYYA-RARNLHKAA   93 (350)
T ss_pred             HcCCCCCCCCCCCCHHHHHHHHHHHhhccHHHHHHHHHHHHH-HCcCHHHHHCcCHHHHHHHHHcCChHH-HHHHHHHHH
Confidence            5675 78998  489999999999999999999999999999 599999999999999999999999996 899999999


Q ss_pred             HHHHHhcCCCChhhHHHHHcCCCCcHHHHHHHHHHhcCCcceeecchHHHHHHHHhcCcCCCCCCCCCCCHHHHHHHHHH
Q 026681           91 KICLTKYDGDIPSSLDELLALPGIGPKMANMVMTLGWFNVQGICVDTHVHRICNRLGWVTQPGTKQKTSSPEQTREALQR  170 (235)
Q Consensus        91 ~~i~~~~~g~~~~~~~~L~~l~GIG~~tA~~il~~~~~~~~~~pvDt~v~Rv~~Rlg~~~~~~~~~~~~~~~~~~~~l~~  170 (235)
                      +.++++|+|.+|+++++|++|||||+|||++||+|+|++ +.++||+||+||+.|++.+....+  .....+.+++.++.
T Consensus        94 ~~i~~~~~g~~p~~~~~L~~LpGIG~~TA~aIl~~af~~-~~~iVD~nV~RV~~Rl~~i~~~~~--~~~~~~~l~~~~~~  170 (350)
T PRK10880         94 QQVATLHGGEFPETFEEVAALPGVGRSTAGAILSLSLGK-HFPILDGNVKRVLARCYAVSGWPG--KKEVENRLWQLSEQ  170 (350)
T ss_pred             HHHHHHhCCCchhhHHHHhcCCCccHHHHHHHHHHHCCC-CeecccHHHHHHHHHHhcccCCCC--hHHHHHHHHHHHHH
Confidence            999999999999999999999999999999999999998 466689999999999876642111  11122234455678


Q ss_pred             hCCcccHHHHHHHHHHHHhhhcCCCCCCCCCCcccccCcccccC--CCCCCCCCccc
Q 026681          171 WLPKEEWVRINPLLVGFGQTICTPLRPRCGMCTVSEYCPSAFKE--SSTSSSKSKKS  225 (235)
Q Consensus       171 ~~p~~~~~~~~~~l~~~G~~iC~~~~P~C~~Cpl~~~C~~~~~~--~~~~~~k~~~~  225 (235)
                      ++|.+.++++|++||+||+.||++++|+|+.|||++.|.++...  ...|.+++|++
T Consensus       171 l~p~~~~~~~nqalm~lGa~vC~p~~P~C~~Cpl~~~C~~~~~~~~~~~P~k~~k~~  227 (350)
T PRK10880        171 VTPAVGVERFNQAMMDLGAMVCTRSKPKCELCPLQNGCIAYANHSWALYPGKKPKQT  227 (350)
T ss_pred             hCChhHHHHHHHHHHHhhHHhccCCCCCCCCCccHhhhHHHHcCCHhhCCCCCCCCC
Confidence            89999999999999999999999999999999999999987654  35665544443

>COG1194 MutY A/G-specific DNA glycosylase [DNA replication, recombination, and repair]

Probab=100.00  E-value=8.2e-47  Score=330.84  Aligned_cols=210  Identities=24%  Similarity=0.416  Sum_probs=183.7

Q ss_pred             CCCCCCCCCCC--ChHHHHHHHHHhccccHHHHHHHHHHHHHcCCCCHHHHhcCCHHHHHHhhccCCChHHHHHHHHHHH
Q 026681           13 DETDSSLPPKE--RRFAVLLSALLSSLTKDKVADGALQRLLQNGLHTAEAIDKADEATIKDLIYPVAFYTRKACNMKKIA   90 (235)
Q Consensus        13 ~~~~~~~p~~~--~~f~~lv~~iLsqqt~~~~~~~~~~~l~~~~~pt~~~la~a~~e~l~~~l~~~G~~~~Ka~~l~~~a   90 (235)
                      +++++++||++  +||.+|||+||+|||++++|.+++.++.+ .|||+++||.|+.+++..+|.++|||.| |++|+++|
T Consensus        20 ~~~~R~LPWR~~~~PY~VwvSEiMLQQT~v~~Vi~yy~~fl~-rfPti~~LA~A~~~evl~~W~gLGYysR-ArnL~~~A   97 (342)
T COG1194          20 DKNGRDLPWRETKDPYRVWVSEIMLQQTQVATVIPYYERFLE-RFPTIKALAAAPEDEVLKAWEGLGYYSR-ARNLHKAA   97 (342)
T ss_pred             HHhCCcCCCCCCCCcceehhHHHHhhhccHhhhhhhHHHHHH-hCCCHHHHhcCCHHHHHHHHHhcChHHH-HHHHHHHH
Confidence            46788999996  68999999999999999999999999999 5999999999999999999999998765 99999999


Q ss_pred             HHHHHhcCCCChhhHHHHHcCCCCcHHHHHHHHHHhcCCcceeecchHHHHHHHHhcCcCCCCCCCCCCCHHHHHHHHHH
Q 026681           91 KICLTKYDGDIPSSLDELLALPGIGPKMANMVMTLGWFNVQGICVDTHVHRICNRLGWVTQPGTKQKTSSPEQTREALQR  170 (235)
Q Consensus        91 ~~i~~~~~g~~~~~~~~L~~l~GIG~~tA~~il~~~~~~~~~~pvDt~v~Rv~~Rlg~~~~~~~~~~~~~~~~~~~~l~~  170 (235)
                      +.++++|+|.+|++.+.|.+|||||+|||.+|++|+|+++ ...||+||.||+.|+..+..+.  .+..+...++..++.
T Consensus        98 ~~v~~~~~G~~P~~~~~l~~LpGiG~yTa~Ail~~a~~~~-~~~lDgNV~RVl~R~f~i~~~~--~~~~~~~~~~~~~~~  174 (342)
T COG1194          98 QEVVERHGGEFPDDEEELAALPGVGPYTAGAILSFAFNQP-EPVLDGNVKRVLSRLFAISGDI--GKPKTKKELWELAEQ  174 (342)
T ss_pred             HHHHHHcCCCCCCCHHHHHhCCCCcHHHHHHHHHHHhCCC-Cceeecchheeehhhhcccccc--cccchhHHHHHHHHH
Confidence            9999999999999999999999999999999999999985 4459999999999998776432  223456678888888


Q ss_pred             hCCcc-cHHHHHHHHHHHHhhhcCCCCCCCCCCcccccCcccccCC--CCCCCCCccccc
Q 026681          171 WLPKE-EWVRINPLLVGFGQTICTPLRPRCGMCTVSEYCPSAFKES--STSSSKSKKSES  227 (235)
Q Consensus       171 ~~p~~-~~~~~~~~l~~~G~~iC~~~~P~C~~Cpl~~~C~~~~~~~--~~~~~k~~~~~~  227 (235)
                      +++++ ...+||++||++|+.||++.+|+|+.|||++.|..+....  .+|.++.|++.+
T Consensus       175 ll~p~~~~~~fnqammdlGA~ICt~~~P~C~~CPl~~~c~a~~~g~~~~~P~k~~k~~~~  234 (342)
T COG1194         175 LLTPDRRPGDFNQAMMDLGATICTAKKPKCSLCPLRDNCAAYRNGTPEKYPVKKPKKKLP  234 (342)
T ss_pred             hcCCCCChHHHHHHHHHhhhHhhcCCCCCCCcCcchHHHHHHHcCCcccCCCcCcccccc
Confidence            55544 4999999999999999999999999999999999776543  566555444444

>TIGR01083 nth endonuclease III

Probab=100.00  E-value=1.8e-45  Score=305.02  Aligned_cols=169  Identities=31%  Similarity=0.613  Sum_probs=162.1

Q ss_pred             CCChHHHHHHHHHhccccHHHHHHHHHHHHHcCCCCHHHHhcCCHHHHHHhhccCCChHHHHHHHHHHHHHHHHhcCCCC
Q 026681           22 KERRFAVLLSALLSSLTKDKVADGALQRLLQNGLHTAEAIDKADEATIKDLIYPVAFYTRKACNMKKIAKICLTKYDGDI  101 (235)
Q Consensus        22 ~~~~f~~lv~~iLsqqt~~~~~~~~~~~l~~~~~pt~~~la~a~~e~l~~~l~~~G~~~~Ka~~l~~~a~~i~~~~~g~~  101 (235)
                      .+|||++||++||||||+++++.+++.+|++ .||||++|+++++++|+++|+++||+++||++|+++|+++.++|+|++
T Consensus        23 ~~dpf~~Li~~ILsqqt~~~~~~~~~~~l~~-~~pt~~~l~~~~~~~L~~~ir~~G~~~~Ka~~i~~~a~~i~~~~~~~~  101 (191)
T TIGR01083        23 YNNPFELLVATILSAQATDKSVNKATKKLFE-VYPTPQALAQAGLEELEEYIKSIGLYRNKAKNIIALCRILVERYGGEV  101 (191)
T ss_pred             CCCHHHHHHHHHHHhhCcHHHHHHHHHHHHH-HCCCHHHHHcCCHHHHHHHHHhcCChHHHHHHHHHHHHHHHHHcCCCC
Confidence            4799999999999999999999999999999 699999999999999999999999999999999999999999999999


Q ss_pred             hhhHHHHHcCCCCcHHHHHHHHHHhcCCcceeecchHHHHHHHHhcCcCCCCCCCCCCCHHHHHHHHHHhCCcccHHHHH
Q 026681          102 PSSLDELLALPGIGPKMANMVMTLGWFNVQGICVDTHVHRICNRLGWVTQPGTKQKTSSPEQTREALQRWLPKEEWVRIN  181 (235)
Q Consensus       102 ~~~~~~L~~l~GIG~~tA~~il~~~~~~~~~~pvDt~v~Rv~~Rlg~~~~~~~~~~~~~~~~~~~~l~~~~p~~~~~~~~  181 (235)
                      |+.++.|++|||||+|||++||+|+++++ .||||+|++|++.|+|+..       ..+++++++.++.++|.+.|.++|
T Consensus       102 ~~~~~~L~~l~GIG~ktA~~ill~~~~~~-~~~vD~~v~Ri~~r~g~~~-------~~~~~~~~~~l~~~~p~~~~~~~h  173 (191)
T TIGR01083       102 PEDREELVKLPGVGRKTANVVLNVAFGIP-AIAVDTHVFRVSNRLGLSK-------GKDPDKVEEELLKLIPREFWTKLH  173 (191)
T ss_pred             chHHHHHHhCCCCcHHHHHHHHHHHcCCC-ccccchhHHHHHHHcCCCC-------CCCHHHHHHHHHHHCCchhHHHHH
Confidence            99999999999999999999999999985 6999999999999999874       346899999999999999999999


Q ss_pred             HHHHHHHhhhcCCCCCCC
Q 026681          182 PLLVGFGQTICTPLRPRC  199 (235)
Q Consensus       182 ~~l~~~G~~iC~~~~P~C  199 (235)
                      ++|++||+.+|++++|+|
T Consensus       174 ~~li~~G~~~C~~~~P~C  191 (191)
T TIGR01083       174 HWLILHGRYTCKARKPLC  191 (191)
T ss_pred             HHHHHHhHHhcCCCCCCC
Confidence            999999999999999999

This equivalog model identifes nth members of the pfam00730 superfamily (HhH-GPD: Helix-hairpin-helix and Gly/Pro rich loop followed by a conserved aspartate). The major members of the superfamily are nth and mutY.

>PRK13910 DNA glycosylase MutY; Provisional

Probab=100.00  E-value=5.7e-45  Score=317.49  Aligned_cols=175  Identities=25%  Similarity=0.490  Sum_probs=157.9

Q ss_pred             HhccccHHHHHH-HHHHHHHcCCCCHHHHhcCCHHHHHHhhccCCChHHHHHHHHHHHHHHHHhcCCCChhhHHHHHcCC
Q 026681           34 LSSLTKDKVADG-ALQRLLQNGLHTAEAIDKADEATIKDLIYPVAFYTRKACNMKKIAKICLTKYDGDIPSSLDELLALP  112 (235)
Q Consensus        34 Lsqqt~~~~~~~-~~~~l~~~~~pt~~~la~a~~e~l~~~l~~~G~~~~Ka~~l~~~a~~i~~~~~g~~~~~~~~L~~l~  112 (235)
                      |+|||+++++.. ++.+|++ .|||+++|+++++++|.++|+++|||+ ||++|+++|+.+.++|+|.+|.++++|++||
T Consensus         1 mlQQT~v~~v~~~yy~rf~~-~fPt~e~La~a~~~el~~~~~glGyy~-RAr~L~~~A~~i~~~~~g~~P~~~~~L~~Lp   78 (289)
T PRK13910          1 MSQQTQINTVVERFYSPFLE-AFPTLKDLANAPLEEVLLLWRGLGYYS-RAKNLKKSAEICVKEHHSQLPNDYQSLLKLP   78 (289)
T ss_pred             CCCCCcHHHhHHHHHHHHHH-HCCCHHHHHCCCHHHHHHHHHcCCcHH-HHHHHHHHHHHHHHHhCCCCChhHHHHHhCC
Confidence            689999999975 9999999 599999999999999999999999995 7999999999999999999999999999999


Q ss_pred             CCcHHHHHHHHHHhcCCcceeecchHHHHHHHHhcCcCCCCCCCCCCCHHHHHHHHHHhCCcccHHHHHHHHHHHHhhhc
Q 026681          113 GIGPKMANMVMTLGWFNVQGICVDTHVHRICNRLGWVTQPGTKQKTSSPEQTREALQRWLPKEEWVRINPLLVGFGQTIC  192 (235)
Q Consensus       113 GIG~~tA~~il~~~~~~~~~~pvDt~v~Rv~~Rlg~~~~~~~~~~~~~~~~~~~~l~~~~p~~~~~~~~~~l~~~G~~iC  192 (235)
                      |||+|||++||+|+|++ ++++||+||+||+.|++++..      ..+.++++...+.++|...+..+|++||+||+.||
T Consensus        79 GIG~kTA~aIl~~af~~-~~~~VD~nV~RVl~Rl~g~~~------~~~~~~l~~~~~~~l~~~~~~~~nqaLm~~Ga~iC  151 (289)
T PRK13910         79 GIGAYTANAILCFGFRE-KSACVDANIKRVLLRLFGLDP------NIHAKDLQIKANDFLNLNESFNHNQALIDLGALIC  151 (289)
T ss_pred             CCCHHHHHHHHHHHCCC-CcCcccHHHHHHHHHHhcCCC------CccHHHHHHHHHHhCCccchHHHHHHHHHHhHHHc
Confidence            99999999999999998 478999999999999854432      23456677778889999999999999999999999


Q ss_pred             CCCCCCCCCCcccccCcccccCCCCC
Q 026681          193 TPLRPRCGMCTVSEYCPSAFKESSTS  218 (235)
Q Consensus       193 ~~~~P~C~~Cpl~~~C~~~~~~~~~~  218 (235)
                      ++ +|+|+.|||++.|.++......+
T Consensus       152 ~~-~P~C~~CPl~~~C~~~~~~~~~~  176 (289)
T PRK13910        152 SP-KPKCAICPLNPYCLGKNNPEKHT  176 (289)
T ss_pred             CC-CCCCCCCcChhhhhhhhcCCccc
Confidence            99 79999999999999876544443

>PRK13913 3-methyladenine DNA glycosylase; Provisional

Probab=100.00  E-value=4.6e-39  Score=269.89  Aligned_cols=172  Identities=17%  Similarity=0.235  Sum_probs=152.7

Q ss_pred             CCCCCCCC-CCChHHHHHHHHHhccccHHHHHHHHHHHHHc------CCCCHHHHhcCCHHHHHHhhccCCChHHHHHHH
Q 026681           14 ETDSSLPP-KERRFAVLLSALLSSLTKDKVADGALQRLLQN------GLHTAEAIDKADEATIKDLIYPVAFYTRKACNM   86 (235)
Q Consensus        14 ~~~~~~p~-~~~~f~~lv~~iLsqqt~~~~~~~~~~~l~~~------~~pt~~~la~a~~e~l~~~l~~~G~~~~Ka~~l   86 (235)
                      +.+...|| +.+||++||++||+|||+++++.+++.+|.+.      ++|||++|++++.++|+++|++.||+++||++|
T Consensus        18 ~~~~~~WWp~~~~fevLV~aILsQqT~~~~v~~a~~~L~~~~~~~~~~~~t~e~L~~a~~eeL~~~Irp~Gf~~~KA~~L   97 (218)
T PRK13913         18 KNAPAWWWPNALKFEALLGAVLTQNTKFEAVEKSLENLKNAFILENDDEINLKKIAYIEFSKLAECVRPSGFYNQKAKRL   97 (218)
T ss_pred             hcCCCCCCcCcCHHHHHHHHHHHhhhhHHHHHHHHHHHHHhcccccccCCCHHHHHcCCHHHHHHHHHhcCCHHHHHHHH
Confidence            33444455 58999999999999999999999999999874      367999999999999999999999999999999


Q ss_pred             HHHHHHHHHhcCC----CChhhHHHHHcCCCCcHHHHHHHHHHhcCCcceeecchHHHHHHHHhcCcCCCCCCCCCCCHH
Q 026681           87 KKIAKICLTKYDG----DIPSSLDELLALPGIGPKMANMVMTLGWFNVQGICVDTHVHRICNRLGWVTQPGTKQKTSSPE  162 (235)
Q Consensus        87 ~~~a~~i~~~~~g----~~~~~~~~L~~l~GIG~~tA~~il~~~~~~~~~~pvDt~v~Rv~~Rlg~~~~~~~~~~~~~~~  162 (235)
                      +++|+.+.++|++    ..++++++|+++||||+|||++||+|++++ ++|+||+|++||++|+|+..        .+++
T Consensus        98 k~la~~i~~~~g~~~~~~~~~~re~Ll~l~GIG~kTAd~iLlya~~r-p~fvVDty~~Rv~~RlG~~~--------~~y~  168 (218)
T PRK13913         98 IDLSENILKDFGSFENFKQEVTREWLLDQKGIGKESADAILCYVCAK-EVMVVDKYSYLFLKKLGIEI--------EDYD  168 (218)
T ss_pred             HHHHHHHHHHcCCchhccCchHHHHHHcCCCccHHHHHHHHHHHcCC-CccccchhHHHHHHHcCCCC--------CCHH
Confidence            9999999999876    256789999999999999999999999998 58999999999999999963        3689


Q ss_pred             HHHHHHHHhC-----------Cc-----ccHHHHHHHHHHHHhhhcCC
Q 026681          163 QTREALQRWL-----------PK-----EEWVRINPLLVGFGQTICTP  194 (235)
Q Consensus       163 ~~~~~l~~~~-----------p~-----~~~~~~~~~l~~~G~~iC~~  194 (235)
                      +++..++..+           |.     ..|.+||..|++||+..|.-
T Consensus       169 ~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~Halive~~k~~~~~  216 (218)
T PRK13913        169 ELQHFFEKGVQENLNSALALYENTISLAQLYARFHGKIVEFSKQKLEL  216 (218)
T ss_pred             HHHHHHHHhhhhhhhhhhccccccchHHHHHHHHHHHHHHHHHHhhhc
Confidence            9999998876           21     24899999999999999964

>COG2231 Uncharacterized protein related to Endonuclease III [DNA replication, recombination, and repair]

Probab=100.00  E-value=7.9e-36  Score=243.05  Aligned_cols=186  Identities=25%  Similarity=0.415  Sum_probs=166.7

Q ss_pred             CCCCCCChHHHHHHHHHhccccHHHHHHHHHHHHHcCCCCHHHHhcCCHHHHHHhhccCCChHHHHHHHHHHHHHHHHhc
Q 026681           18 SLPPKERRFAVLLSALLSSLTKDKVADGALQRLLQNGLHTAEAIDKADEATIKDLIYPVAFYTRKACNMKKIAKICLTKY   97 (235)
Q Consensus        18 ~~p~~~~~f~~lv~~iLsqqt~~~~~~~~~~~l~~~~~pt~~~la~a~~e~l~~~l~~~G~~~~Ka~~l~~~a~~i~~~~   97 (235)
                      +.|+..+.+|+++++||.|+|+|++|.+++++|...+..++++|...+.++|.++|++.|||++||.+|+.+...+...|
T Consensus        23 ~WWp~~~~~EiiigAILtQNT~WknvekAlenLk~~~~~~l~~I~~~~~~~L~elIrpsGFYnqKa~rLk~l~k~l~~~~  102 (215)
T COG2231          23 GWWPADNKDEIIIGAILTQNTSWKNVEKALENLKNEGILNLKKILKLDEEELAELIRPSGFYNQKAKRLKALSKNLAKFF  102 (215)
T ss_pred             cCCCCCCchhHHHHHHHhccccHHHHHHHHHHHHHcccCCHHHHhcCCHHHHHHHHhccchHHHHHHHHHHHHHHHHHHh
Confidence            46667788999999999999999999999999999888899999999999999999999999999999988887777654


Q ss_pred             CC---CChh-hHHHHHcCCCCcHHHHHHHHHHhcCCcceeecchHHHHHHHHhcCcCCCCCCCCCCCHHHHHHHHHHhCC
Q 026681           98 DG---DIPS-SLDELLALPGIGPKMANMVMTLGWFNVQGICVDTHVHRICNRLGWVTQPGTKQKTSSPEQTREALQRWLP  173 (235)
Q Consensus        98 ~g---~~~~-~~~~L~~l~GIG~~tA~~il~~~~~~~~~~pvDt~v~Rv~~Rlg~~~~~~~~~~~~~~~~~~~~l~~~~p  173 (235)
                      .+   .-+. .+++|++++|||+.|||+||++++++ ++|+||.+..|++.|+|.+.       ..+++++++.++..+|
T Consensus       103 ~~~~~~~~~~~R~~LL~iKGIG~ETaDsILlYa~~r-p~FVvD~Yt~R~l~rlg~i~-------~k~ydeik~~fe~~l~  174 (215)
T COG2231         103 INLESFKSEVLREELLSIKGIGKETADSILLYALDR-PVFVVDKYTRRLLSRLGGIE-------EKKYDEIKELFEENLP  174 (215)
T ss_pred             hhhhccchHHHHHHHHccCCcchhhHHHHHHHHhcC-cccchhHHHHHHHHHhcccc-------cccHHHHHHHHHhcch
Confidence            32   2222 59999999999999999999999988 69999999999999999986       3479999999999888


Q ss_pred             ccc--HHHHHHHHHHHHhhhcCCCCCCCCCCcccccCcccc
Q 026681          174 KEE--WVRINPLLVGFGQTICTPLRPRCGMCTVSEYCPSAF  212 (235)
Q Consensus       174 ~~~--~~~~~~~l~~~G~~iC~~~~P~C~~Cpl~~~C~~~~  212 (235)
                      .+.  |.++|..++.||+.+|+. +|.|+.|||...|.++.
T Consensus       175 ~~~~lyqe~HAlIv~~~K~f~~k-~~~~~~cpL~~~~~~~~  214 (215)
T COG2231         175 ENLRLYQEFHALIVEHAKHFCKK-KPLCEKCPLKEKCKKYR  214 (215)
T ss_pred             hHHHHHHHHHHHHHHHHHHHccC-CcCCCCchHHHHHhhcc
Confidence            764  899999999999999998 59999999999998653

>KOG2457 consensus A/G-specific adenine DNA glycosylase [Replication, recombination and repair]

Probab=100.00  E-value=2.3e-36  Score=264.96  Aligned_cols=195  Identities=24%  Similarity=0.394  Sum_probs=176.4

Q ss_pred             CCCCCCCCCCCC-----------hHHHHHHHHHhccccHHHHHHHHHHHHHcCCCCHHHHhcCCH-HHHHHhhccCCChH
Q 026681           13 DETDSSLPPKER-----------RFAVLLSALLSSLTKDKVADGALQRLLQNGLHTAEAIDKADE-ATIKDLIYPVAFYT   80 (235)
Q Consensus        13 ~~~~~~~p~~~~-----------~f~~lv~~iLsqqt~~~~~~~~~~~l~~~~~pt~~~la~a~~-e~l~~~l~~~G~~~   80 (235)
                      +.+.+++||+..           .|+++|++||+|||+++.|.++|.++++ .+||..+++.|+. +++.++|.++|||+
T Consensus       102 D~~KRdLPWR~r~sEde~DwerRaYeVwVSEiMLQQTrV~TV~~YYt~WMq-kwPTl~dla~Asl~~eVn~lWaGlGyY~  180 (555)
T KOG2457|consen  102 DVNKRDLPWRNRRSEDEKDWERRAYEVWVSEIMLQQTRVQTVMKYYTRWMQ-KWPTLYDLAQASLEKEVNELWAGLGYYR  180 (555)
T ss_pred             hhhcccCccccCCccchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-hCchHHHHHHHHHHHHHHHHHhhhhHHH
Confidence            456778888743           5999999999999999999999999999 6999999999999 79999999999997


Q ss_pred             HHHHHHHHHHHHHHHhcCCCChhhHHHHHc-CCCCcHHHHHHHHHHhcCCcceeecchHHHHHHHHhcCcCCCCCCCCCC
Q 026681           81 RKACNMKKIAKICLTKYDGDIPSSLDELLA-LPGIGPKMANMVMTLGWFNVQGICVDTHVHRICNRLGWVTQPGTKQKTS  159 (235)
Q Consensus        81 ~Ka~~l~~~a~~i~~~~~g~~~~~~~~L~~-l~GIG~~tA~~il~~~~~~~~~~pvDt~v~Rv~~Rlg~~~~~~~~~~~~  159 (235)
                      + +++|.+.|+.+++.++|.+|.+-+.|++ +||||+|||.+|++++|+++..+ ||.||.|++.|.--+..+  ..+++
T Consensus       181 R-~rrL~ega~~vv~~~~ge~Prta~~l~kgvpGVG~YTAGAiaSIAf~q~tGi-VDGNVirvlsRalAIhsD--cSkgk  256 (555)
T KOG2457|consen  181 R-ARRLLEGAKMVVAGTEGEFPRTASSLMKGVPGVGQYTAGAIASIAFNQVTGI-VDGNVIRVLSRALAIHSD--CSKGK  256 (555)
T ss_pred             H-HHHHHHHHHHHHHhCCCCCCChHHHHHhhCCCCCccchhhhhhhhhcCcccc-cccchHHHhHHhHhhcCC--cchhh
Confidence            6 9999999999999999999999999998 99999999999999999997665 999999999998766643  33455


Q ss_pred             CHHHHHHHHHHhCCcccHHHHHHHHHHHHhhhcCCCCCCCCCCcccccCcccc
Q 026681          160 SPEQTREALQRWLPKEEWVRINPLLVGFGQTICTPLRPRCGMCTVSEYCPSAF  212 (235)
Q Consensus       160 ~~~~~~~~l~~~~p~~~~~~~~~~l~~~G~~iC~~~~P~C~~Cpl~~~C~~~~  212 (235)
                      --..++..+..++.+..+++||+++|++|+.+|+|.+|.|+.||+...|+.+.
T Consensus       257 ~~q~~wkLA~qLVDP~RPGDFNQalMELGAt~CTpq~P~CS~CPvss~CrA~q  309 (555)
T KOG2457|consen  257 FFQSSWKLAAQLVDPSRPGDFNQALMELGATLCTPQKPSCSSCPVSSQCRAFQ  309 (555)
T ss_pred             HHHHHHHHHHHhcCCCCCCcHHHHHHHhcCeeccCCCCCcCCCCcHHHHHHHh
Confidence            55677888899999999999999999999999999999999999999999764

>smart00478 ENDO3c endonuclease III

Probab=100.00  E-value=3.7e-33  Score=222.30  Aligned_cols=148  Identities=42%  Similarity=0.721  Sum_probs=140.9

Q ss_pred             HhccccHHHHHHHHHHHHHcCCCCHHHHhcCCHHHHHHhhccCCChHHHHHHHHHHHHHHHHhcCCCChhhHHHHHcCCC
Q 026681           34 LSSLTKDKVADGALQRLLQNGLHTAEAIDKADEATIKDLIYPVAFYTRKACNMKKIAKICLTKYDGDIPSSLDELLALPG  113 (235)
Q Consensus        34 Lsqqt~~~~~~~~~~~l~~~~~pt~~~la~a~~e~l~~~l~~~G~~~~Ka~~l~~~a~~i~~~~~g~~~~~~~~L~~l~G  113 (235)
                      |+|||+++++..++.+|.+ .||||++|+++++++|.++|+++||+++||++|+++++.+.+.+++++|+.++.|++|||
T Consensus         1 l~qq~~~~~a~~~~~~l~~-~~~~~~~l~~~~~~eL~~~l~~~g~~~~ka~~i~~~a~~~~~~~~~~~~~~~~~L~~l~G   79 (149)
T smart00478        1 LSQQTSDEAVNKATERLFE-KFPTPEDLAAADEEELEELIRPLGFYRRKAKYLIELARILVEEYGGEVPDDREELLKLPG   79 (149)
T ss_pred             CCCcccHHHHHHHHHHHHH-HCCCHHHHHCCCHHHHHHHHHHcCChHHHHHHHHHHHHHHHHHHCCCccHHHHHHHcCCC
Confidence            6899999999999999999 599999999999999999999999999999999999999999999999999999999999


Q ss_pred             CcHHHHHHHHHHhcCCcceeecchHHHHHHHHhcCcCCCCCCCCCCCHHHHHHHHHHhCCcccHHHHHHHHHHHHh
Q 026681          114 IGPKMANMVMTLGWFNVQGICVDTHVHRICNRLGWVTQPGTKQKTSSPEQTREALQRWLPKEEWVRINPLLVGFGQ  189 (235)
Q Consensus       114 IG~~tA~~il~~~~~~~~~~pvDt~v~Rv~~Rlg~~~~~~~~~~~~~~~~~~~~l~~~~p~~~~~~~~~~l~~~G~  189 (235)
                      ||+|||++|++|++++ +.+|+|+|+.|++.|+|+.+.      ..++++++..++.++|.+.|..+|++++++|+
T Consensus        80 IG~~tA~~~l~~~~~~-~~~~~D~~v~r~~~rl~~~~~------~~~~~~~~~~~~~~~p~~~~~~~~~~~l~~g~  148 (149)
T smart00478       80 VGRKTANAVLSFALGK-PFIPVDTHVLRIAKRLGLVDK------KSTPEEVEKLLEKLLPKEDWRELNLLLIDFGR  148 (149)
T ss_pred             CcHHHHHHHHHHHCCC-CCCccchHHHHHHHHhCCCCC------CCCHHHHHHHHHHHCCHHHHHHHHHHHHHHcC
Confidence            9999999999999998 789999999999999998862      45789999999999999899999999999997

includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases

>cd00056 ENDO3c endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases

Probab=100.00  E-value=8.9e-33  Score=222.07  Aligned_cols=154  Identities=39%  Similarity=0.645  Sum_probs=144.4

Q ss_pred             HHHHHHHHHhccccHHHHHHHHHHHHHcCC-CCHHHHhcCCHHHHHHhhccCCChHHHHHHHHHHHHHHHHhcCCCC---
Q 026681           26 FAVLLSALLSSLTKDKVADGALQRLLQNGL-HTAEAIDKADEATIKDLIYPVAFYTRKACNMKKIAKICLTKYDGDI---  101 (235)
Q Consensus        26 f~~lv~~iLsqqt~~~~~~~~~~~l~~~~~-pt~~~la~a~~e~l~~~l~~~G~~~~Ka~~l~~~a~~i~~~~~g~~---  101 (235)
                      |++|+++||+|||+++++..++.+|.+. | |||++|+.+++++|++++.+.| +++||++|+++++.+.+.+++..   
T Consensus         1 ~e~Li~~il~q~~s~~~a~~~~~~l~~~-~gpt~~~l~~~~~~~l~~~~~~~G-~~~kA~~i~~~a~~~~~~~~~~~~~~   78 (158)
T cd00056           1 FEVLVSEILSQQTTDKAVNKAYERLFER-YGPTPEALAAADEEELRELIRSLG-YRRKAKYLKELARAIVEGFGGLVLDD   78 (158)
T ss_pred             CHHHHHHHHHhcccHHHHHHHHHHHHHH-hCCCHHHHHCCCHHHHHHHHHhcC-hHHHHHHHHHHHHHHHHHcCCccCCC
Confidence            7899999999999999999999999994 8 9999999999999999999999 78899999999999999988866   


Q ss_pred             hhhHHHHHcCCCCcHHHHHHHHHHhcCCcceeecchHHHHHHHHhcCcCCCCCCCCCCCHHHHHHHHHHhCCcccHHHHH
Q 026681          102 PSSLDELLALPGIGPKMANMVMTLGWFNVQGICVDTHVHRICNRLGWVTQPGTKQKTSSPEQTREALQRWLPKEEWVRIN  181 (235)
Q Consensus       102 ~~~~~~L~~l~GIG~~tA~~il~~~~~~~~~~pvDt~v~Rv~~Rlg~~~~~~~~~~~~~~~~~~~~l~~~~p~~~~~~~~  181 (235)
                      ++.++.|++|||||+|||+++++|+++ .++||+|+|+.|++.|+|+++.      ..+++++++.++.+.|...+..+|
T Consensus        79 ~~~~~~L~~l~GIG~~tA~~~l~~~~~-~~~~pvD~~v~r~~~~~~~~~~------~~~~~~~~~~~~~~~~~~~~~~~~  151 (158)
T cd00056          79 PDAREELLALPGVGRKTANVVLLFALG-PDAFPVDTHVRRVLKRLGLIPK------KKTPEELEELLEELLPKPYWGEAN  151 (158)
T ss_pred             cccHHHHHcCCCCCHHHHHHHHHHHCC-CCCCccchhHHHHHHHhCCCCC------CCCHHHHHHHHHHHCCHHHHHHHH
Confidence            889999999999999999999999999 6899999999999999998642      568899999999999977889999


Q ss_pred             HHHHHHH
Q 026681          182 PLLVGFG  188 (235)
Q Consensus       182 ~~l~~~G  188 (235)
                      +.|++||
T Consensus       152 ~~l~~~g  158 (158)
T cd00056         152 QALMDLG  158 (158)
T ss_pred             HHHHHcC
Confidence            9999987

>PRK01229 N-glycosylase/DNA lyase; Provisional

Probab=99.97  E-value=5.9e-30  Score=213.12  Aligned_cols=157  Identities=17%  Similarity=0.169  Sum_probs=131.5

Q ss_pred             CCChHHHHHHHHHhccccHHHHHHHHHHHHHcCCCCHHHHhcCCHHHHHHhhccCC--ChHHHHHHHHHHHHH---HHHh
Q 026681           22 KERRFAVLLSALLSSLTKDKVADGALQRLLQNGLHTAEAIDKADEATIKDLIYPVA--FYTRKACNMKKIAKI---CLTK   96 (235)
Q Consensus        22 ~~~~f~~lv~~iLsqqt~~~~~~~~~~~l~~~~~pt~~~la~a~~e~l~~~l~~~G--~~~~Ka~~l~~~a~~---i~~~   96 (235)
                      .++||+.||++||||||++.++.+++.+|.      ++.+ .++.++|+++|++.|  ||++||++|+++++.   +.+.
T Consensus        34 ~~~~f~~Lv~~ILsqnT~~~~v~~a~~~L~------~~~l-~~~~eeL~~~Ir~~Gygf~~~KAk~I~~~~~~~~~l~~~  106 (208)
T PRK01229         34 EEDLFSELSFCILTANSSAEGGIKAQKEIG------DGFL-YLSEEELEEKLKEVGHRFYNKRAEYIVEARKLYGKLKEI  106 (208)
T ss_pred             cCChHHHHHHHHhcCcCcHHHHHHHHHhcC------HHHc-CCCHHHHHHHHHHhhcccHHHHHHHHHHHHHHHHHHHHH
Confidence            578999999999999999999999999884      3455 899999999999995  999999999999987   6566


Q ss_pred             c--CCCChhhHHHHH-cCCCCcHHHHHHHHHHhcCCcceeecchHHHHHHHHhcCcCCCCCCCCCCCHHHHHHHHHHhCC
Q 026681           97 Y--DGDIPSSLDELL-ALPGIGPKMANMVMTLGWFNVQGICVDTHVHRICNRLGWVTQPGTKQKTSSPEQTREALQRWLP  173 (235)
Q Consensus        97 ~--~g~~~~~~~~L~-~l~GIG~~tA~~il~~~~~~~~~~pvDt~v~Rv~~Rlg~~~~~~~~~~~~~~~~~~~~l~~~~p  173 (235)
                      +  +++.|+++++|+ ++||||+|||++||.....+ ++|+||+|++|++.|+|+++.........+|.+++..+.++.+
T Consensus       107 ~~~~~~~~~~R~~Ll~~lpGIG~KTAd~vL~~~~~~-~~~iVDtHv~Ri~~RlG~~~~~~~~lt~~~y~~~E~~l~~~~~  185 (208)
T PRK01229        107 IKADKDQFEAREFLVKNIKGIGYKEASHFLRNVGYE-DLAILDRHILRFLKRYGLIEEIPKTLSKKRYLEIEEILREIAE  185 (208)
T ss_pred             HhccCCchHHHHHHHHcCCCCcHHHHHHHHHHccCC-CeeeeeHHHHHHHHHhCCCcccccccCcCCHHHHHHHHHHHHH
Confidence            5  889999999999 99999999999999654444 6899999999999999998753223345789999999988887


Q ss_pred             ccc--HHHHHHHHHH
Q 026681          174 KEE--WVRINPLLVG  186 (235)
Q Consensus       174 ~~~--~~~~~~~l~~  186 (235)
                      .-.  .+.+.+.|+.
T Consensus       186 ~~~~~~~~Ldl~~w~  200 (208)
T PRK01229        186 ELGISLGELDLYIWY  200 (208)
T ss_pred             HcCCCHHHHHHHHHH
Confidence            544  3444455544

>TIGR00588 ogg 8-oxoguanine DNA-glycosylase (ogg)

Probab=99.95  E-value=5.6e-27  Score=207.46  Aligned_cols=155  Identities=21%  Similarity=0.267  Sum_probs=125.0

Q ss_pred             CCCCCCCCCCChHHHHHHHHHhccccHHHHHHHHHHHHHc--------------CCCCHHHHhcCCHHHHHHhhccCCCh
Q 026681           14 ETDSSLPPKERRFAVLLSALLSSLTKDKVADGALQRLLQN--------------GLHTAEAIDKADEATIKDLIYPVAFY   79 (235)
Q Consensus        14 ~~~~~~p~~~~~f~~lv~~iLsqqt~~~~~~~~~~~l~~~--------------~~pt~~~la~a~~e~l~~~l~~~G~~   79 (235)
                      -.|.++|.. ||||++|++|+|||+++.++.+++.+|.+.              .||||++|+.++.++   .|+.+||.
T Consensus       109 ~~GlRi~~~-d~fE~lv~~IlsQq~si~~a~~~~~rL~~~~G~~~~~~~g~~~~~FPtp~~La~~~~e~---~Lr~~G~g  184 (310)
T TIGR00588       109 FQGVRLLRQ-DPFECLISFICSSNNNIARITRMVERLCQAFGPRLITLDGVTYHGFPSLHALTGPEAEA---HLRKLGLG  184 (310)
T ss_pred             CCCCCCCCC-CHHHHHHHHHHhCCCCHHHHHHHHHHHHHHhCCCcccCCCcccccCCCHHHHhCCChHH---HHHHcCCH
Confidence            345677765 999999999999999999999999999762              389999999876542   34455884


Q ss_pred             HHHHHHHHHHHHHHHHhcCCC----------ChhhHHHHHcCCCCcHHHHHHHHHHhcCCcceeecchHHHHHHHHhcCc
Q 026681           80 TRKACNMKKIAKICLTKYDGD----------IPSSLDELLALPGIGPKMANMVMTLGWFNVQGICVDTHVHRICNRLGWV  149 (235)
Q Consensus        80 ~~Ka~~l~~~a~~i~~~~~g~----------~~~~~~~L~~l~GIG~~tA~~il~~~~~~~~~~pvDt~v~Rv~~Rlg~~  149 (235)
                       .||++|+++|+++.+.+++.          .++.+++|++|||||+|||++|++|+++++++||+|+||+|++.|++..
T Consensus       185 -~Ra~~I~~~A~~i~~~~~~~~~l~~l~~~~~~~~~~~L~~l~GIG~~tAd~vll~~l~~~d~~PvD~~v~r~~~r~y~~  263 (310)
T TIGR00588       185 -YRARYIRETARALLEEQGGRAWLQQIRGASYEDAREALCELPGVGPKVADCICLMGLDKPQAVPVDVHVWRIANRDYPW  263 (310)
T ss_pred             -HHHHHHHHHHHHHHhccCCchhHHhhccCChHHHHHHHHhCCCccHHHHHHHHHHhCCCCCceeecHHHHHHHHHHhcc
Confidence             36999999999999977654          5678999999999999999999999999999999999999999998654


Q ss_pred             CCCCCC---CCCCCHHHHHHHHHHhCC
Q 026681          150 TQPGTK---QKTSSPEQTREALQRWLP  173 (235)
Q Consensus       150 ~~~~~~---~~~~~~~~~~~~l~~~~p  173 (235)
                      ......   ....+++++++...+.++
T Consensus       264 ~~~~~~~~~~~~~~~~~i~~~~~~~~g  290 (310)
T TIGR00588       264 HPKTSRAKGPSPFARKELGNFFRSLWG  290 (310)
T ss_pred             cccccccccCChhHHHHHHHHHHHHhc
Confidence            321111   234567777777776555

All proteins in this family for which functions are known are 8-oxo-guanaine DNA glycosylases that function in base excision repair. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). This family is distantly realted to the Nth-MutY superfamily.

>COG0122 AlkA 3-methyladenine DNA glycosylase/8-oxoguanine DNA glycosylase [DNA replication, recombination, and repair]

Probab=99.94  E-value=2.2e-25  Score=194.73  Aligned_cols=162  Identities=24%  Similarity=0.304  Sum_probs=135.0

Q ss_pred             CCCCCCCCCChHHHHHHHHHhccccHHHHHHHHHHHHHc-C--------CCCHHHHhcCCHHHHHHhhccCCChHHHHHH
Q 026681           15 TDSSLPPKERRFAVLLSALLSSLTKDKVADGALQRLLQN-G--------LHTAEAIDKADEATIKDLIYPVAFYTRKACN   85 (235)
Q Consensus        15 ~~~~~p~~~~~f~~lv~~iLsqqt~~~~~~~~~~~l~~~-~--------~pt~~~la~a~~e~l~~~l~~~G~~~~Ka~~   85 (235)
                      .|...|...+||+.||++|++||.|.+.+.+++++|.+. +        ||||++|+.++++.+.++    |++.+|++|
T Consensus        95 ~g~~~~~~~d~fe~lv~aI~~QqvS~~~A~~i~~rl~~~~g~~~~~~~~fptpe~l~~~~~~~l~~~----g~s~~Ka~y  170 (285)
T COG0122          95 PGLRLPLAPDPFEALVRAILSQQVSVAAAAKIWARLVSLYGNALEIYHSFPTPEQLAAADEEALRRC----GLSGRKAEY  170 (285)
T ss_pred             cCcccCCCCCHHHHHHHHHHHhHhhHHHHHHHHHHHHHHhCCccccccCCCCHHHHHhcCHHHHHHh----CCcHHHHHH
Confidence            345567789999999999999999999999999999885 4        899999999999998876    999999999


Q ss_pred             HHHHHHHHHHhc-------CCCChhhHHHHHcCCCCcHHHHHHHHHHhcCCcceee-cchHHHHHHHHhcCcCCCCCCCC
Q 026681           86 MKKIAKICLTKY-------DGDIPSSLDELLALPGIGPKMANMVMTLGWFNVQGIC-VDTHVHRICNRLGWVTQPGTKQK  157 (235)
Q Consensus        86 l~~~a~~i~~~~-------~g~~~~~~~~L~~l~GIG~~tA~~il~~~~~~~~~~p-vDt~v~Rv~~Rlg~~~~~~~~~~  157 (235)
                      |+++|+++.+..       +.+..++++.|++|+|||+|||++||+|+++++++|| .|.++++.+++++..+      +
T Consensus       171 i~~~A~~~~~g~~~~~~l~~~~~e~a~e~L~~i~GIG~WTAe~~llf~lgr~dvfP~~D~~lr~~~~~~~~~~------~  244 (285)
T COG0122         171 IISLARAAAEGELDLSELKPLSDEEAIEELTALKGIGPWTAEMFLLFGLGRPDVFPADDLGLRRAIKKLYRLP------T  244 (285)
T ss_pred             HHHHHHHHHcCCccHHHhccCCHHHHHHHHHcCCCcCHHHHHHHHHHcCCCCCCCChHHHHHHHHHHHHhcCC------C
Confidence            999999998731       1123357999999999999999999999999999999 5677777788887322      2


Q ss_pred             CCCHHHHHHHHHHhCCcccHHHHHHHHHH
Q 026681          158 TSSPEQTREALQRWLPKEEWVRINPLLVG  186 (235)
Q Consensus       158 ~~~~~~~~~~l~~~~p~~~~~~~~~~l~~  186 (235)
                      ..+...++...+.|-|...+..++.|-..
T Consensus       245 ~~~~~~~~~~~e~w~p~rs~A~~yLw~~~  273 (285)
T COG0122         245 RPTEKEVRELAERWGPYRSYAALYLWRYA  273 (285)
T ss_pred             CchHHHHHHHHhcccCHHHHHHHHHHHhh
Confidence            33445577888999999888888876543

>PRK10308 3-methyl-adenine DNA glycosylase II; Provisional

Probab=99.93  E-value=7.4e-25  Score=191.50  Aligned_cols=154  Identities=23%  Similarity=0.321  Sum_probs=132.3

Q ss_pred             CCCCCCCCCCCChHHHHHHHHHhccccHHHHHHHHHHHHHc------------CCCCHHHHhcCCHHHHHHhhccCCChH
Q 026681           13 DETDSSLPPKERRFAVLLSALLSSLTKDKVADGALQRLLQN------------GLHTAEAIDKADEATIKDLIYPVAFYT   80 (235)
Q Consensus        13 ~~~~~~~p~~~~~f~~lv~~iLsqqt~~~~~~~~~~~l~~~------------~~pt~~~la~a~~e~l~~~l~~~G~~~   80 (235)
                      ...|.++|...|+||.+|++|++||.+...+.....+|.+.            .||||++|++++.++|.++    |++.
T Consensus       101 ~~~GlR~p~~~d~fE~lv~aIigQqisv~~a~~~~~rlv~~~G~~l~~~~~~~~FPtpe~La~~~~~eL~~~----Gl~~  176 (283)
T PRK10308        101 ARPGLRLPGSVDAFEQGVRAILGQLVSVAMAAKLTAKVAQLYGERLDDFPEYVCFPTPERLAAADPQALKAL----GMPL  176 (283)
T ss_pred             hCCCCcCCCCCCHHHHHHHHHHHhHHHHHHHHHHHHHHHHHhCccccCCCCccCCCCHHHHHcCCHHHHHHC----CCCH
Confidence            45677889899999999999999999999999999998763            3799999999999998765    9999


Q ss_pred             HHHHHHHHHHHHHHHh-cC----CCChhhHHHHHcCCCCcHHHHHHHHHHhcCCccee-ecchHHHHHHHHhcCcCCCCC
Q 026681           81 RKACNMKKIAKICLTK-YD----GDIPSSLDELLALPGIGPKMANMVMTLGWFNVQGI-CVDTHVHRICNRLGWVTQPGT  154 (235)
Q Consensus        81 ~Ka~~l~~~a~~i~~~-~~----g~~~~~~~~L~~l~GIG~~tA~~il~~~~~~~~~~-pvDt~v~Rv~~Rlg~~~~~~~  154 (235)
                      +|+++|+++|+++.+. ..    .+..+.++.|++|||||+|||++|++|+++++++| +.|.+++|.+   +       
T Consensus       177 ~Ra~~L~~lA~~i~~g~l~l~~~~~~~~~~~~L~~LpGIGpwTA~~vllr~lg~~D~fp~~D~~l~~~~---~-------  246 (283)
T PRK10308        177 KRAEALIHLANAALEGTLPLTIPGDVEQAMKTLQTFPGIGRWTANYFALRGWQAKDVFLPDDYLIKQRF---P-------  246 (283)
T ss_pred             HHHHHHHHHHHHHHcCCCCccccCCHHHHHHHHhcCCCcCHHHHHHHHHHhCCCCCCCCcccHHHHHhc---c-------
Confidence            9999999999999871 11    12234689999999999999999999999999999 6899888743   1       


Q ss_pred             CCCCCCHHHHHHHHHHhCCcccHHHHHHH
Q 026681          155 KQKTSSPEQTREALQRWLPKEEWVRINPL  183 (235)
Q Consensus       155 ~~~~~~~~~~~~~l~~~~p~~~~~~~~~~  183 (235)
                         ..++++++...+.|-|.+.|..+|.|
T Consensus       247 ---~~~~~~~~~~a~~w~P~rsya~~~LW  272 (283)
T PRK10308        247 ---GMTPAQIRRYAERWKPWRSYALLHIW  272 (283)
T ss_pred             ---cCCHHHHHHHHHhcCCHHHHHHHHHH
Confidence               23578899999999999999999876

>TIGR03252 uncharacterized HhH-GPD family protein

Probab=99.92  E-value=1.1e-24  Score=176.11  Aligned_cols=107  Identities=28%  Similarity=0.350  Sum_probs=97.5

Q ss_pred             CCChHHHHHHHHHhccccHHHHHHHHHHHHH-cCCCCHHHHhcCCHHHHHHhhccC----CChHHHHHHHHHHHHHHHHh
Q 026681           22 KERRFAVLLSALLSSLTKDKVADGALQRLLQ-NGLHTAEAIDKADEATIKDLIYPV----AFYTRKACNMKKIAKICLTK   96 (235)
Q Consensus        22 ~~~~f~~lv~~iLsqqt~~~~~~~~~~~l~~-~~~pt~~~la~a~~e~l~~~l~~~----G~~~~Ka~~l~~~a~~i~~~   96 (235)
                      .++||++||++||||||++++|.+++.+|+. .+.+||++|++++.++|+++|++.    |||++||++|+++++.|+++
T Consensus        15 ~~~pFelLVa~ILSQqTtd~nv~kA~~~L~~~~g~~tp~~La~a~~eeL~~lI~~~pal~Gfy~~KAk~Lk~~a~~iie~   94 (177)
T TIGR03252        15 SSDPFALLTGMLLDQQVPMERAFAGPHKIARRMGSLDAEDIAKYDPQAFVALFSERPAVHRFPGSMAKRVQALAQYVVDT   94 (177)
T ss_pred             cCChHHHHHHHHHhccCcHHHHHHHHHHHHHHhCCCCHHHHHcCCHHHHHHHHhcCccccCchHHHHHHHHHHHHHHHHH
Confidence            4689999999999999999999999999975 344899999999999999999765    99999999999999999999


Q ss_pred             cCCCC--------hhh---HHHHHcCCCCcHHHHHHHHHHhcC
Q 026681           97 YDGDI--------PSS---LDELLALPGIGPKMANMVMTLGWF  128 (235)
Q Consensus        97 ~~g~~--------~~~---~~~L~~l~GIG~~tA~~il~~~~~  128 (235)
                      |+|++        |++   +++|++|||||+|||++||.+.-.
T Consensus        95 y~G~v~~L~~~~~p~t~~lre~Ll~LpGVG~KTAnvVL~~l~~  137 (177)
T TIGR03252        95 YDGDATAVWTEGDPDGKELLRRLKALPGFGKQKAKIFLALLGK  137 (177)
T ss_pred             hCCChhhhhcccCCCcHHHHHHHHcCCCCCHHHHHHHHHHHHH
Confidence            99987        654   789999999999999999997543

This model describes a small, well-conserved bacterial protein family. Its sequence largely consists of a domain, HhH-GPD, found in a variety of related base excision DNA repair enzymes (see pfam00730).

>KOG2875 consensus 8-oxoguanine DNA glycosylase [Replication, recombination and repair]

Probab=99.86  E-value=2.9e-21  Score=163.84  Aligned_cols=145  Identities=21%  Similarity=0.307  Sum_probs=115.3

Q ss_pred             CCChHHHHHHHHHhccccHHHHHHHHHHHHHc--------------CCCCHHHHhcCCHHHHHHhhccCCChHHHHHHHH
Q 026681           22 KERRFAVLLSALLSSLTKDKVADGALQRLLQN--------------GLHTAEAIDKADEATIKDLIYPVAFYTRKACNMK   87 (235)
Q Consensus        22 ~~~~f~~lv~~iLsqqt~~~~~~~~~~~l~~~--------------~~pt~~~la~a~~e~l~~~l~~~G~~~~Ka~~l~   87 (235)
                      +++|+|.|++.|+|+|.+.+++..+.++|...              +|||.++++.   +++++-||.+||..| |+||.
T Consensus       114 rQdP~E~lfSFiCSSNNNIaRIT~Mve~fc~~fG~~i~~~dg~~~h~FPsl~~L~g---~~~Ea~LR~~gfGYR-AkYI~  189 (323)
T KOG2875|consen  114 RQDPIECLFSFICSSNNNIARITGMVERFCQAFGPRIIQLDGVDYHGFPSLQALAG---PEVEAELRKLGFGYR-AKYIS  189 (323)
T ss_pred             hcCcHHHHHHHHhcCCCcHHHHHHHHHHHHHhhCcceEeecCcccccCccHHHhcC---cHhHHHHHHcCcchh-HHHHH
Confidence            68999999999999999999999999988763              7999999985   455555666677554 99999


Q ss_pred             HHHHHHHHhcCC----------CChhhHHHHHcCCCCcHHHHHHHHHHhcCCcceeecchHHHHHHHHhcCcCCCCCC-C
Q 026681           88 KIAKICLTKYDG----------DIPSSLDELLALPGIGPKMANMVMTLGWFNVQGICVDTHVHRICNRLGWVTQPGTK-Q  156 (235)
Q Consensus        88 ~~a~~i~~~~~g----------~~~~~~~~L~~l~GIG~~tA~~il~~~~~~~~~~pvDt~v~Rv~~Rlg~~~~~~~~-~  156 (235)
                      ..|++|.++++|          .++++++.|+.+||||+|+||||++++++...++|||+|+.|+++-....+..+.+ .
T Consensus       190 ~ta~~l~~~~g~~~wLqsl~~~~yeear~~L~~lpGVG~KVADCI~Lm~l~~~~~VPVDvHi~ria~~y~l~~~~g~k~l  269 (323)
T KOG2875|consen  190 ATARALQEKQGGLAWLQSLRKSSYEEAREALCSLPGVGPKVADCICLMSLDKLSAVPVDVHIWRIAQDYILPGLSGAKEL  269 (323)
T ss_pred             HHHHHHHHhcccchHHHHHhcccHHHHHHHHhcCCCCcchHhhhhhhhhcCCCCcccchhhHHHHhhcccCCCccccccC
Confidence            999999999887          24578999999999999999999999999999999999999999943111111211 2


Q ss_pred             CCCCHHHHHHHHHH
Q 026681          157 KTSSPEQTREALQR  170 (235)
Q Consensus       157 ~~~~~~~~~~~l~~  170 (235)
                      +...+.++...+..
T Consensus       270 ~~ki~~ev~~~f~~  283 (323)
T KOG2875|consen  270 TPKINGEVSNFFRS  283 (323)
T ss_pred             CcchhHHHHHHHHH
Confidence            33445556555543

>KOG1918 consensus 3-methyladenine DNA glycosidase [Replication, recombination and repair]

Probab=99.86  E-value=3.8e-21  Score=158.06  Aligned_cols=159  Identities=18%  Similarity=0.243  Sum_probs=128.9

Q ss_pred             CCCCCCCCChHHHHHHHHHhccccHHHHHHHHHHHHHc-----CCCCHHHHhcCCHHHHHHhhccCCChHHHHHHHHHHH
Q 026681           16 DSSLPPKERRFAVLLSALLSSLTKDKVADGALQRLLQN-----GLHTAEAIDKADEATIKDLIYPVAFYTRKACNMKKIA   90 (235)
Q Consensus        16 ~~~~p~~~~~f~~lv~~iLsqqt~~~~~~~~~~~l~~~-----~~pt~~~la~a~~e~l~~~l~~~G~~~~Ka~~l~~~a   90 (235)
                      +..+-..+.||+.|+++|+|||.+.+.+..++++|...     .||+|+.+..++.++|.++    ||+.+|+.||+.+|
T Consensus        66 p~~~~~~q~Pf~~LiraIlsQQLs~kAansI~~Rfvsl~~g~~~~~~pe~i~~~~~~~lrkc----G~S~rK~~yLh~lA  141 (254)
T KOG1918|consen   66 PLTFKETQTPFERLIRAILSQQLSGKAANSIYNRFVSLCGGAEKFPTPEFIDPLDCEELRKC----GFSKRKASYLHSLA  141 (254)
T ss_pred             CCCcccccCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCcCCCCchhcCcCCHHHHHHh----CcchhhHHHHHHHH
Confidence            34455578999999999999999999999999999874     5899999999999999888    99999999999999


Q ss_pred             HHHHHhcCCCCh-----------hhHHHHHcCCCCcHHHHHHHHHHhcCCcceeecchH-HHHHHHHhcCcCCCCCCCCC
Q 026681           91 KICLTKYDGDIP-----------SSLDELLALPGIGPKMANMVMTLGWFNVQGICVDTH-VHRICNRLGWVTQPGTKQKT  158 (235)
Q Consensus        91 ~~i~~~~~g~~~-----------~~~~~L~~l~GIG~~tA~~il~~~~~~~~~~pvDt~-v~Rv~~Rlg~~~~~~~~~~~  158 (235)
                      ++..+.   -+|           +..+.|..++|||+||+.++|.|+++++|++|+|.- +++-++.+....+      .
T Consensus       142 ~~~~ng---~I~s~~~i~~mseEeL~~~LT~VKGIg~Wtv~MflIfsL~R~DVmp~dDlgir~g~k~l~gl~~------~  212 (254)
T KOG1918|consen  142 EAYTNG---YIPSKSGIEKMSEEELIERLTNVKGIGRWTVEMFLIFSLHRPDVMPADDLGIRNGVKKLLGLKP------L  212 (254)
T ss_pred             HHHhcC---CCCchHHHhhcCHHHHHHHHHhccCccceeeeeeeeeccCCCcccCchhhhHHHHHHHHhCCCC------C
Confidence            998873   244           356788999999999999999999999999998655 4555666655432      3


Q ss_pred             CCHHHHHHHHHHhCCcccHH-HHHHHHHHH
Q 026681          159 SSPEQTREALQRWLPKEEWV-RINPLLVGF  187 (235)
Q Consensus       159 ~~~~~~~~~l~~~~p~~~~~-~~~~~l~~~  187 (235)
                      ..+.+++...+.|-|.+... .+.|-+++.
T Consensus       213 p~~~evekl~e~~kpyRtvaawYlWki~~~  242 (254)
T KOG1918|consen  213 PLPKEVEKLCEKCKPYRTVAAWYLWKIIKL  242 (254)
T ss_pred             CchHHHHHHhhhccchHHHHHHHHHhhhhh
Confidence            45778888888888876533 334444443

>PF00730 HhH-GPD: HhH-GPD superfamily base excision DNA repair protein This entry corresponds to Endonuclease III This entry corresponds to Alkylbase DNA glycosidase; InterPro: IPR003265 Endonuclease III (4

Probab=99.83  E-value=7.6e-20  Score=137.82  Aligned_cols=105  Identities=34%  Similarity=0.480  Sum_probs=92.0

Q ss_pred             HHHHHhccccHHHHHHHHHHHHHc-CCCCHHHHhcCCHHHHHHhhccCCChHHHHHHHHHHHHHHHHhcCCCChhhHHHH
Q 026681           30 LSALLSSLTKDKVADGALQRLLQN-GLHTAEAIDKADEATIKDLIYPVAFYTRKACNMKKIAKICLTKYDGDIPSSLDEL  108 (235)
Q Consensus        30 v~~iLsqqt~~~~~~~~~~~l~~~-~~pt~~~la~a~~e~l~~~l~~~G~~~~Ka~~l~~~a~~i~~~~~g~~~~~~~~L  108 (235)
                      |++||+|||+++++.+++.+|.+. +||||++|+++++++|+++|+++||+++||++|+++|+.+.              
T Consensus         1 V~~Il~qq~s~~~a~~~~~~l~~~~g~pt~~~l~~~~~~el~~~i~~~G~~~~ka~~i~~~a~~~~--------------   66 (108)
T PF00730_consen    1 VRAILSQQTSIKAARKIYRRLFERYGFPTPEALAEASEEELRELIRPLGFSRRKAKYIIELARAIL--------------   66 (108)
T ss_dssp             HHHHHCTTS-HHHHHHHHHHHHHHHSCSSHHHHHCSHHHHHHHHHTTSTSHHHHHHHHHHHHHHHH--------------
T ss_pred             CeeeecCcCcHHHHHHHHHHHHHHhcCCCHHHHHhCCHHHHHHHhhccCCCHHHHHHHHHHHHHhh--------------
Confidence            689999999999999999999996 57999999999999999999999999999999999999987              


Q ss_pred             HcCCCCcHHHHHHHHHHhcCCcc-eeecchHHHHHHHHhcCcCCCCCCCCCCCHHHHHHHHHHhCC
Q 026681          109 LALPGIGPKMANMVMTLGWFNVQ-GICVDTHVHRICNRLGWVTQPGTKQKTSSPEQTREALQRWLP  173 (235)
Q Consensus       109 ~~l~GIG~~tA~~il~~~~~~~~-~~pvDt~v~Rv~~Rlg~~~~~~~~~~~~~~~~~~~~l~~~~p  173 (235)
                                         ++++ ++|+|+|+.|++.|+++++.      ..+++++++.++++.|
T Consensus        67 -------------------~~~d~~~~~D~~v~r~~~r~~~~~~------~~~~~~~~~~~~e~~~  107 (108)
T PF00730_consen   67 -------------------GRPDPFPPVDTHVRRVLQRLGGIPE------KKTKEETEKKLEELWP  107 (108)
T ss_dssp             -------------------C-SSSS-TTSHHHHHHHHHHTSSSS------STTHHHHHHHHHHHGT
T ss_pred             -------------------hcccceecCcHHHHHHHHHHcCCCC------CCCHHHHHHHHHhhCc
Confidence                               4444 78999999999999999863      3678899988866654

2.99.18 from EC) is a DNA repair enzyme which removes a number of damaged pyrimidines from DNA via its glycosylase activity and also cleaves the phosphodiester backbone at apurinic / apyrimidinic sites via a beta-elimination mechanism [, ]. The structurally related DNA glycosylase MutY recognises and excises the mutational intermediate 8-oxoguanine-adenine mispair []. The 3-D structures of Escherichia coli endonuclease III [] and catalytic domain of MutY [] have been determined. The structures contain two all-alpha domains: a sequence-continuous, six-helix domain (residues 22-132) and a Greek-key, four-helix domain formed by one N-terminal and three C-terminal helices (residues 1-21 and 133-211) together with the [Fe4S4] cluster. The cluster is bound entirely within the C-terminal loop by four cysteine residues with a ligation pattern Cys-(Xaa)6-Cys-(Xaa)2-Cys-(Xaa)5-Cys which is distinct from all other known Fe4S4 proteins. This structural motif is referred to as a [Fe4S4] cluster loop (FCL) []. Two DNA-binding motifs have been proposed, one at either end of the interdomain groove: the helix-hairpin-helix (HhH) and FCL motifs (see IPR003651 from INTERPRO). The primary role of the iron-sulphur cluster appears to involve positioning conserved basic residues for interaction with the DNA phosphate backbone by forming the loop of the FCL motif [, ]. The HhH-GPD domain gets its name from its hallmark helix-hairpin-helix and Gly/Pro rich loop followed by a conserved aspartate. This domain is found in a diverse range of structurally related DNA repair proteins that include: endonuclease III, 4.2.99.18 from EC and DNA glycosylase MutY, an A/G-specific adenine glycosylase. Both of these enzymes have a C-terminal iron-sulphur cluster loop (FCL). The methyl-CPG binding protein (MBD4) also contain a related domain that is a thymine DNA glycosylase. The family also includes DNA-3-methyladenine glycosylase II 3.2.2.21 from EC, 8-oxoguanine DNA glycosylases and other members of the AlkA family.; GO: 0006284 base-excision repair; PDB: 3F0Z_A 3I0X_A 3F10_A 3I0W_A 3S6I_D 3N5N_Y 1PU7_A 1PU8_B 1PU6_B 1NGN_A ....

>COG1059 Thermostable 8-oxoguanine DNA glycosylase [DNA replication, recombination, and repair]

Probab=99.27  E-value=3.8e-11  Score=97.21  Aligned_cols=140  Identities=19%  Similarity=0.212  Sum_probs=105.6

Q ss_pred             CChHHHHHHHHHhccccHHHHHHHHHHHHHcCCCCHHHHhcCCHHHHHHhhccCC--ChHHHHHHHHHHHHHHHHh----
Q 026681           23 ERRFAVLLSALLSSLTKDKVADGALQRLLQNGLHTAEAIDKADEATIKDLIYPVA--FYTRKACNMKKIAKICLTK----   96 (235)
Q Consensus        23 ~~~f~~lv~~iLsqqt~~~~~~~~~~~l~~~~~pt~~~la~a~~e~l~~~l~~~G--~~~~Ka~~l~~~a~~i~~~----   96 (235)
                      .+.|.-|..+||.+|++...+.++.+.|-+ +|..      ++.|||++.|+..|  ||+.||+||.++-+.+-+-    
T Consensus        37 e~lf~ELsFCILTANsSA~~~~~~q~~lG~-gfly------~~~eEL~e~Lk~~g~Rf~n~raeyIVeaR~~~~~lk~~v  109 (210)
T COG1059          37 EDLFKELSFCILTANSSATMGLRAQNELGD-GFLY------LSEEELREKLKEVGYRFYNVRAEYIVEAREKFDDLKIIV  109 (210)
T ss_pred             HHHHHHHHHHhccccchHHHHHHHHHHhcc-cccc------CCHHHHHHHHHHhcchhcccchHHHHHHHHHHHHHHHHH
Confidence            467999999999999999999999999886 6654      68899999999875  7899999999876654210    


Q ss_pred             cCCCChh-hHHHHH-cCCCCcHHHHHHHH-HHhcCCcceeecchHHHHHHHHhcCcCCCCCCCCCCCHHHHHHHHHHh
Q 026681           97 YDGDIPS-SLDELL-ALPGIGPKMANMVM-TLGWFNVQGICVDTHVHRICNRLGWVTQPGTKQKTSSPEQTREALQRW  171 (235)
Q Consensus        97 ~~g~~~~-~~~~L~-~l~GIG~~tA~~il-~~~~~~~~~~pvDt~v~Rv~~Rlg~~~~~~~~~~~~~~~~~~~~l~~~  171 (235)
                      -..+.+. +++.|. .++|||-|-|..+| +.++.  +...+|.|+.|.+.|.|.+...+.....+.|-++++.+..+
T Consensus       110 ~~~~~~~vaRE~Lv~nikGiGyKEASHFLRNVG~~--D~AIlDrHIlr~l~r~g~i~e~~kt~t~K~YLe~E~ilr~i  185 (210)
T COG1059         110 KADENEKVARELLVENIKGIGYKEASHFLRNVGFE--DLAILDRHILRWLVRYGLIDENPKTLTRKLYLEIEEILRSI  185 (210)
T ss_pred             hcCcchHHHHHHHHHHcccccHHHHHHHHHhcChh--HHHHHHHHHHHHHHHhcccccCcccccHHHHHHHHHHHHHH
Confidence            0122233 788888 89999999999999 45553  45569999999999999987543333333444555555444

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

Probab=98.71  E-value=3.1e-09  Score=61.59  Aligned_cols=29  Identities=55%  Similarity=1.052  Sum_probs=25.2

Q ss_pred             cCCCChhhHHHHHcCCCCcHHHHHHHHHH
Q 026681           97 YDGDIPSSLDELLALPGIGPKMANMVMTL  125 (235)
Q Consensus        97 ~~g~~~~~~~~L~~l~GIG~~tA~~il~~  125 (235)
                      |+|.+|.++++|+++||||+|||+.|+.|
T Consensus         2 ~~g~~pas~eeL~~lpGIG~~tA~~I~~~   30 (30)
T PF00633_consen    2 LDGLIPASIEELMKLPGIGPKTANAILSF   30 (30)
T ss_dssp             HHHHHTSSHHHHHTSTT-SHHHHHHHHHH
T ss_pred             CCCcCCCCHHHHHhCCCcCHHHHHHHHhC
Confidence            45678899999999999999999999976

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

>PF10576 EndIII_4Fe-2S: Iron-sulfur binding domain of endonuclease III; InterPro: IPR003651 Endonuclease III (4

Probab=98.26  E-value=2.4e-07  Score=46.39  Aligned_cols=17  Identities=41%  Similarity=1.376  Sum_probs=11.6

Q ss_pred             cCCCCCCCCCCcccccC
Q 026681          192 CTPLRPRCGMCTVSEYC  208 (235)
Q Consensus       192 C~~~~P~C~~Cpl~~~C  208 (235)
                      |++++|+|+.|||+++|
T Consensus         1 Ctar~P~C~~Cpl~~~C   17 (17)
T PF10576_consen    1 CTARKPKCEECPLADYC   17 (17)
T ss_dssp             S-SSS--GGG-TTGGG-
T ss_pred             CcCCCCccccCCCcccC
Confidence            89999999999999998

2.99.18 from EC) is a DNA repair enzyme which removes a number of damaged pyrimidines from DNA via its glycosylase activity and also cleaves the phosphodiester backbone at apurinic / apyrimidinic sites via a beta-elimination mechanism [, ]. The structurally related DNA glycosylase MutY recognises and excises the mutational intermediate 8-oxoguanine-adenine mispair []. The 3-D structures of Escherichia coli endonuclease III [] and catalytic domain of MutY [] have been determined. The structures contain two all-alpha domains: a sequence-continuous, six-helix domain (residues 22-132) and a Greek-key, four-helix domain formed by one N-terminal and three C-terminal helices (residues 1-21 and 133-211) together with the [Fe4S4] cluster. The cluster is bound entirely within the C-terminal loop by four cysteine residues with a ligation pattern Cys-(Xaa)6-Cys-(Xaa)2-Cys-(Xaa)5-Cys which is distinct from all other known Fe4S4 proteins. This structural motif is referred to as a [Fe4S4] cluster loop (FCL) []. Two DNA-binding motifs have been proposed, one at either end of the interdomain groove: the helix-hairpin-helix (HhH) and FCL motifs. The primary role of the iron-sulphur cluster appears to involve positioning conserved basic residues for interaction with the DNA phosphate backbone by forming the loop of the FCL motif [, ]. The iron-sulphur cluster loop (FCL) is also found in DNA-(apurinic or apyrimidinic site) lyase, a subfamily of endonuclease III. The enzyme has both apurinic and apyrimidinic endonuclease activity and a DNA N-glycosylase activity. It cuts damaged DNA at cytosines, thymines and guanines, and acts on the damaged strand 5' of the damaged site. The enzyme binds a 4Fe-4S cluster which is not important for the catalytic activity, but is probably involved in the alignment of the enzyme along the DNA strand.; GO: 0004519 endonuclease activity, 0051539 4 iron, 4 sulfur cluster binding; PDB: 1VRL_A 1RRQ_A 3G0Q_A 3FSQ_A 1RRS_A 3FSP_A 2ABK_A 1KG7_A 1KG2_A 1MUN_A ....

>smart00525 FES FES domain

Probab=97.65  E-value=1.5e-05  Score=44.44  Aligned_cols=21  Identities=43%  Similarity=1.187  Sum_probs=19.3

Q ss_pred             hcCCCCCCCCCCcccccCccc
Q 026681          191 ICTPLRPRCGMCTVSEYCPSA  211 (235)
Q Consensus       191 iC~~~~P~C~~Cpl~~~C~~~  211 (235)
                      +|++++|+|+.||+++.|.++
T Consensus         1 vC~ar~P~C~~Cpl~~~C~~~   21 (26)
T smart00525        1 ICTARKPRCDECPLKDLCPAY   21 (26)
T ss_pred             CccCCCCCCCCCcCHHHhhhh
Confidence            699999999999999999864

iron-sulpphur binding domain in DNA-(apurinic or apyrimidinic site) lyase (subfamily of ENDO3)

>PF09674 DUF2400: Protein of unknown function (DUF2400); InterPro: IPR014127 Members of this uncharacterised protein family are found sporadically, so far only among spirochetes, epsilon and delta proteobacteria, and Bacteroides

Probab=96.80  E-value=0.041  Score=47.02  Aligned_cols=161  Identities=22%  Similarity=0.239  Sum_probs=88.9

Q ss_pred             hHHHHHHHHHhccccHHHHHHHHHHHHHcCCCCHH-HHhcCCHHHHHHhhccCC--ChH-HHHHHHHHHHHHHHHhcCC-
Q 026681           25 RFAVLLSALLSSLTKDKVADGALQRLLQNGLHTAE-AIDKADEATIKDLIYPVA--FYT-RKACNMKKIAKICLTKYDG-   99 (235)
Q Consensus        25 ~f~~lv~~iLsqqt~~~~~~~~~~~l~~~~~pt~~-~la~a~~e~l~~~l~~~G--~~~-~Ka~~l~~~a~~i~~~~~g-   99 (235)
                      -.-.+|+++|+-. +.++..+..+.|++.--++|. -|...+.+++.+.+.+.-  |++ .-...+....+.+.++|++ 
T Consensus        16 Ei~afiaA~lAyG-~~~~I~~~~~~ll~~~~~~P~~~v~~~~~~~~~~~~~~~~yRf~~~~D~~~~~~~l~~i~~~~gsL   94 (232)
T PF09674_consen   16 EIAAFIAALLAYG-NRKQIIKKLERLLDLMGPSPYDFVLSGDEKDDRKDLEGFFYRFQNGEDMYAFFIALKRIYQEYGSL   94 (232)
T ss_pred             HHHHHHHHHHHcc-CHHHHHHHHHHHHHHhCCCHHHHHHcCCHhhhHHHccCCCcCCCCHHHHHHHHHHHHHHHHccCCH
Confidence            4667888888766 667777777777664234554 355666666766666432  221 1233344444444455432 


Q ss_pred             ------------CChh----hHHHHHcC------------------CCCcHHHHHHHHHHhcCCcc--------------
Q 026681          100 ------------DIPS----SLDELLAL------------------PGIGPKMANMVMTLGWFNVQ--------------  131 (235)
Q Consensus       100 ------------~~~~----~~~~L~~l------------------~GIG~~tA~~il~~~~~~~~--------------  131 (235)
                                  ++-+    ..+.+.++                  +|-.-|--+++|-..-.+..              
T Consensus        95 e~~f~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~l~~p~~~SacKR~~MFLRWMVR~d~~VD~GlW~~i~ps~  174 (232)
T PF09674_consen   95 EEAFAKGYNKSEDVLEAICAFIEEFFELPHSSRGYKHLFGLLPPPEKGSACKRLNMFLRWMVRKDSPVDFGLWSSIDPSD  174 (232)
T ss_pred             HHHHHhhccCCCCHHHHHHHHHHHHHHhhcccccccccccccCCCCCCcHHHHHHHHHHhhccCCCCCCCcCCCCCCHHH
Confidence                        1111    12223331                  12222444556533222211              


Q ss_pred             -eeecchHHHHHHHHhcCcCCCCCCCCCCCHHHHHHHHHHhCCcccHHHHHHHHHHHHh
Q 026681          132 -GICVDTHVHRICNRLGWVTQPGTKQKTSSPEQTREALQRWLPKEEWVRINPLLVGFGQ  189 (235)
Q Consensus       132 -~~pvDt~v~Rv~~Rlg~~~~~~~~~~~~~~~~~~~~l~~~~p~~~~~~~~~~l~~~G~  189 (235)
                       .+|+||||.|++.+||++.....  .-++..++-+.+.++.| +++..+..+|..+|.
T Consensus       175 LiiPLDtHv~~var~LGL~~rk~~--d~k~A~elT~~lr~~~p-~DPvKYDFAL~~~Gi  230 (232)
T PF09674_consen  175 LIIPLDTHVFRVARKLGLLKRKSA--DWKAARELTEALREFDP-DDPVKYDFALFRLGI  230 (232)
T ss_pred             ccccchHhHHHHHHHcCCccCCCc--cHHHHHHHHHHHHhcCC-CCCcchhhhcccCCc
Confidence             47999999999999999864211  12244556666777776 566666777777664

The function is unknown and its gene neighbourhoods show little conservation.

>PF03352 Adenine_glyco: Methyladenine glycosylase; InterPro: IPR005019 This family of methyladenine glycosylases includes DNA-3-methyladenine glycosylase I (3

Probab=96.53  E-value=0.039  Score=45.26  Aligned_cols=100  Identities=17%  Similarity=0.204  Sum_probs=69.0

Q ss_pred             hHHHHHHHHHhccccHHHHHHHHHHHHHcCC--CCHHHHhcCCHHHHHHhhccCCC--hHHHHHHHHHHHHHHHH---hc
Q 026681           25 RFAVLLSALLSSLTKDKVADGALQRLLQNGL--HTAEAIDKADEATIKDLIYPVAF--YTRKACNMKKIAKICLT---KY   97 (235)
Q Consensus        25 ~f~~lv~~iLsqqt~~~~~~~~~~~l~~~~~--pt~~~la~a~~e~l~~~l~~~G~--~~~Ka~~l~~~a~~i~~---~~   97 (235)
                      -||.|+-+++..--++..+.+-...+.+. |  .+|+.+|..+++++++++..-|.  +++|.+.+++=|+++.+   +|
T Consensus        26 LFe~L~Le~fQaGLsW~~Il~Kr~~~r~a-F~~Fd~~~vA~~~e~~ie~l~~d~~iIRnr~KI~Avi~NA~~~l~i~~e~  104 (179)
T PF03352_consen   26 LFEMLTLEGFQAGLSWSTILKKREAFREA-FAGFDPEKVAKMDEEDIERLMQDPGIIRNRRKIRAVINNARAILKIQEEF  104 (179)
T ss_dssp             HHHHHHHHHHTTTS-HHHHHHTHHHHHHH-TGGGHHHHHHT--HHHHHHHTTSTTSS--HHHHHHHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHhhCCHHHHHHHHHHHHHH-HHCCCHHHHHcCCHHHHHHHhcCcchhhhHHHHHHHHHHHHHHHHHHHhc
Confidence            49999999999999999999988888874 5  57999999999999999998887  56777777777777653   33


Q ss_pred             CC----------------------CChh-------hHHHHHc--CCCCcHHHHHHHHHH
Q 026681           98 DG----------------------DIPS-------SLDELLA--LPGIGPKMANMVMTL  125 (235)
Q Consensus        98 ~g----------------------~~~~-------~~~~L~~--l~GIG~~tA~~il~~  125 (235)
                      |+                      ++|.       .-+.|.+  ++-|||.|+.++|.-
T Consensus       105 gsF~~ylw~f~~~~~i~~~~~~~~~~p~~t~~s~~isk~lkk~GF~FvGpt~vysflqA  163 (179)
T PF03352_consen  105 GSFSDYLWSFVNGKPIVNHWRSPEDVPASTPLSEAISKDLKKRGFKFVGPTTVYSFLQA  163 (179)
T ss_dssp             S-HHHHHHHCTTTS-EE---SSGGGS-S--HHHHHHHHHHHHTT--S--HHHHHHHHHH
T ss_pred             CCHHHHHHhcCCCcCccccccccccCcCccHHHHHHHHHHHhCcceeECHHHHHHHHHH
Confidence            32                      1111       2244553  677888888888765

2.2.20 from EC) which acts as a base excision repair enzyme by severing the glycosylic bond of numerous damaged bases. The enzyme is constitutively expressed and is specific for the alkylated 3-methyladenine DNA.; GO: 0008725 DNA-3-methyladenine glycosylase I activity, 0006284 base-excision repair; PDB: 2OFI_A 2OFK_A 2JG6_A 4AIA_E 4AI5_C 4AI4_A 1LMZ_A 1P7M_A 1NKU_A.

>smart00278 HhH1 Helix-hairpin-helix DNA-binding motif class 1

Probab=96.00  E-value=0.0055  Score=33.97  Aligned_cols=20  Identities=50%  Similarity=0.894  Sum_probs=17.6

Q ss_pred             HHHcCCCCcHHHHHHHHHHh
Q 026681          107 ELLALPGIGPKMANMVMTLG  126 (235)
Q Consensus       107 ~L~~l~GIG~~tA~~il~~~  126 (235)
                      .|.++||||+++|..++.+.
T Consensus         2 ~L~~i~GiG~k~A~~il~~~   21 (26)
T smart00278        2 ELLKVPGIGPKTAEKILEAX   21 (26)
T ss_pred             hhhhCCCCCHHHHHHHHHhc
Confidence            58899999999999998754

>TIGR02757 conserved hypothetical protein TIGR02757

Probab=95.63  E-value=0.0053  Score=52.24  Aligned_cols=55  Identities=27%  Similarity=0.379  Sum_probs=37.2

Q ss_pred             eeecchHHHHHHHHhcCcCCCCCCCCCCCHHHHHHHHHHhCCcccHHHHHHHHHHHHh
Q 026681          132 GICVDTHVHRICNRLGWVTQPGTKQKTSSPEQTREALQRWLPKEEWVRINPLLVGFGQ  189 (235)
Q Consensus       132 ~~pvDt~v~Rv~~Rlg~~~~~~~~~~~~~~~~~~~~l~~~~p~~~~~~~~~~l~~~G~  189 (235)
                      .+|+|||+.||+.+||++......  -++..++-+.+.++.| +++..+..+|..+|.
T Consensus       173 iiPLDtH~~rvar~LgL~~Rk~~d--~kaa~ElT~~Lr~~dp-~DPvKYDFAL~~lGi  227 (229)
T TIGR02757       173 ILPLDTHVFRIAKKLKLLKRKSYD--LKAAIEITEALRELNP-EDPIKYDFALFRLGQ  227 (229)
T ss_pred             eeechHhHHHHHHHhCCcccCchh--HHHHHHHHHHHHhcCC-CCCcchhhhcccCCc
Confidence            579999999999999998642111  1233445555666666 566667777777774

Members of this uncharacterized protein family are found sporadically, so far only among spirochetes, epsilon and delta proteobacteria, and Bacteroides. The function is unknown and its gene neighborhoods show little conservation.

>PRK10353 3-methyl-adenine DNA glycosylase I; Provisional

Probab=95.52  E-value=0.4  Score=39.64  Aligned_cols=70  Identities=9%  Similarity=-0.037  Sum_probs=57.5

Q ss_pred             hHHHHHHHHHhccccHHHHHHHHHHHHHc-CCCCHHHHhcCCHHHHHHhhccCCCh--HHHHHHHHHHHHHHH
Q 026681           25 RFAVLLSALLSSLTKDKVADGALQRLLQN-GLHTAEAIDKADEATIKDLIYPVAFY--TRKACNMKKIAKICL   94 (235)
Q Consensus        25 ~f~~lv~~iLsqqt~~~~~~~~~~~l~~~-~~pt~~~la~a~~e~l~~~l~~~G~~--~~Ka~~l~~~a~~i~   94 (235)
                      -||.|+=+.+..-.++..+.+-...+.+. .-.+|+.+|..+++++++++..-|.-  ++|.+.+++=|+++.
T Consensus        31 LFE~L~Le~~QAGLSW~tIL~Kre~fr~aF~~Fd~~~VA~~~e~die~Ll~d~~IIRnr~KI~Avi~NA~~~l  103 (187)
T PRK10353         31 LFEMICLEGQQAGLSWITVLKKRENYRACFHQFDPVKVAAMQEEDVERLVQDAGIIRHRGKIQAIIGNARAYL  103 (187)
T ss_pred             HHHHHHHHHhcccccHHHHHHHHHHHHHHHcCCCHHHHhCCCHHHHHHHhcCchhHHhHHHHHHHHHHHHHHH
Confidence            49999999999999999999988888774 23689999999999999999988874  456666666555554

>PF14716 HHH_8: Helix-hairpin-helix domain; PDB: 2W9M_A 1HUZ_A 1HUO_A 2BPG_B 2BPF_A 1DK3_A 1BPE_A 1BNO_A 1BNP_A 1DK2_A

Probab=95.51  E-value=0.066  Score=36.68  Aligned_cols=57  Identities=23%  Similarity=0.233  Sum_probs=36.6

Q ss_pred             HHHHhhccCCChHHHHHHHHHHHHHHHHhcCCCChhhHHHHHcCCCCcHHHHHHHHHH
Q 026681           68 TIKDLIYPVAFYTRKACNMKKIAKICLTKYDGDIPSSLDELLALPGIGPKMANMVMTL  125 (235)
Q Consensus        68 ~l~~~l~~~G~~~~Ka~~l~~~a~~i~~~~~g~~~~~~~~L~~l~GIG~~tA~~il~~  125 (235)
                      ++.+...-.|=..-|+..-.+++..|.. +...+.+..+.+.+|||||+.+|..|--|
T Consensus        10 ~la~~~~~~~~~~~r~~aY~~Aa~~i~~-l~~~i~~~~~~~~~l~gIG~~ia~kI~E~   66 (68)
T PF14716_consen   10 ELADLYELQGGDPFRARAYRRAAAAIKA-LPYPITSGEEDLKKLPGIGKSIAKKIDEI   66 (68)
T ss_dssp             HHHHHHHHTSTSHHHHHHHHHHHHHHHH-SSS-HHSHHHHHCTSTTTTHHHHHHHHHH
T ss_pred             HHHHHHHHhhCCcHHHHHHHHHHHHHHh-CCHhHhhHHHHHhhCCCCCHHHHHHHHHH
Confidence            3333333333234467888888888655 55555554224999999999999988644

...

>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional

Probab=95.50  E-value=0.074  Score=44.29  Aligned_cols=64  Identities=17%  Similarity=0.158  Sum_probs=42.9

Q ss_pred             CCCCHHHHhcCCHHHHHHhhccCCChHHHHHHHH------HHHHHHHHhcCCCChhhHHHHHcCCCCcHHHHHHHHHHhc
Q 026681           54 GLHTAEAIDKADEATIKDLIYPVAFYTRKACNMK------KIAKICLTKYDGDIPSSLDELLALPGIGPKMANMVMTLGW  127 (235)
Q Consensus        54 ~~pt~~~la~a~~e~l~~~l~~~G~~~~Ka~~l~------~~a~~i~~~~~g~~~~~~~~L~~l~GIG~~tA~~il~~~~  127 (235)
                      ||.|.++.     +-++.++.--|-..+.|-.|.      ++.++|..       .+.+.|.++||||+|||.-+..---
T Consensus        61 GF~t~~Er-----~lF~~LisVsGIGPK~ALaILs~~~~~el~~aI~~-------~D~~~L~~vpGIGkKtAeRIIlELk  128 (196)
T PRK13901         61 GFLNSSER-----EVFEELIGVDGIGPRAALRVLSGIKYNEFRDAIDR-------EDIELISKVKGIGNKMAGKIFLKLR  128 (196)
T ss_pred             CCCCHHHH-----HHHHHHhCcCCcCHHHHHHHHcCCCHHHHHHHHHh-------CCHHHHhhCCCCCHHHHHHHHHHHH
Confidence            78887663     444455544455455566665      45555544       4678999999999999999986544


Q ss_pred             CC
Q 026681          128 FN  129 (235)
Q Consensus       128 ~~  129 (235)
                      ++
T Consensus       129 dK  130 (196)
T PRK13901        129 GK  130 (196)
T ss_pred             Hh
Confidence            33

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

Probab=95.20  E-value=0.034  Score=37.74  Aligned_cols=35  Identities=37%  Similarity=0.738  Sum_probs=23.6

Q ss_pred             HHHHHHhcCCCCh----hhHHHHHcCCCCcHHHHHHHHHH
Q 026681           90 AKICLTKYDGDIP----SSLDELLALPGIGPKMANMVMTL  125 (235)
Q Consensus        90 a~~i~~~~~g~~~----~~~~~L~~l~GIG~~tA~~il~~  125 (235)
                      |+.+.+.|+ +++    .+.++|.+++|||+.+|..|..|
T Consensus        16 ak~L~~~f~-sl~~l~~a~~e~L~~i~gIG~~~A~si~~f   54 (64)
T PF12826_consen   16 AKLLAKHFG-SLEALMNASVEELSAIPGIGPKIAQSIYEF   54 (64)
T ss_dssp             HHHHHHCCS-CHHHHCC--HHHHCTSTT--HHHHHHHHHH
T ss_pred             HHHHHHHcC-CHHHHHHcCHHHHhccCCcCHHHHHHHHHH
Confidence            444555554 443    46899999999999999999877

>COG2818 Tag 3-methyladenine DNA glycosylase [DNA replication, recombination, and repair]

Probab=95.15  E-value=0.45  Score=39.14  Aligned_cols=101  Identities=14%  Similarity=0.159  Sum_probs=73.5

Q ss_pred             ChHHHHHHHHHhccccHHHHHHHHHHHHHcCC--CCHHHHhcCCHHHHHHhhccCCChH--HHHHHHHHHHHHHH---Hh
Q 026681           24 RRFAVLLSALLSSLTKDKVADGALQRLLQNGL--HTAEAIDKADEATIKDLIYPVAFYT--RKACNMKKIAKICL---TK   96 (235)
Q Consensus        24 ~~f~~lv~~iLsqqt~~~~~~~~~~~l~~~~~--pt~~~la~a~~e~l~~~l~~~G~~~--~Ka~~l~~~a~~i~---~~   96 (235)
                      .-||.|+-++...-.++..+.+-.+++.+. |  .+|+.+|..++++++.++...|.-+  .|.+.++.=|+++.   ++
T Consensus        31 ~LFE~l~Le~fQAGLSW~tVL~KRe~frea-F~~Fd~~kVA~~~~~dverLl~d~gIIR~r~KI~A~i~NA~~~l~l~~e  109 (188)
T COG2818          31 RLFELLCLEGFQAGLSWLTVLKKREAFREA-FHGFDPEKVAAMTEEDVERLLADAGIIRNRGKIKATINNARAVLELQKE  109 (188)
T ss_pred             HHHHHHHHHHHhccchHHHHHHhHHHHHHH-HhcCCHHHHHcCCHHHHHHHHhCcchhhhHHHHHHHHHHHHHHHHHHHH
Confidence            359999999999999999999988888773 3  5899999999999999999988754  44555555555543   34


Q ss_pred             cCC----------------------CChh-------hHHHHHc--CCCCcHHHHHHHHHH
Q 026681           97 YDG----------------------DIPS-------SLDELLA--LPGIGPKMANMVMTL  125 (235)
Q Consensus        97 ~~g----------------------~~~~-------~~~~L~~--l~GIG~~tA~~il~~  125 (235)
                      ||+                      ++|.       .-+.|.+  ++-|||.|+..+|.-
T Consensus       110 ~Gsf~~flWsf~~~~~~~~~~~~~~~~pa~t~~S~~mskaLKkrGf~fvGpTt~yafmqA  169 (188)
T COG2818         110 FGSFSEFLWSFVGGKPSRNQVNDGSEVPASTELSDAMSKALKKRGFKFVGPTTVYAFMQA  169 (188)
T ss_pred             cCCHHHHHHHhcCCCcccccccchhhccccchhHHHHHHHHHHccCeecCcHHHHHHHHH
Confidence            432                      1111       1244553  677888888877765

>TIGR00624 tag DNA-3-methyladenine glycosylase I

Probab=94.87  E-value=0.86  Score=37.39  Aligned_cols=71  Identities=8%  Similarity=-0.041  Sum_probs=57.2

Q ss_pred             hHHHHHHHHHhccccHHHHHHHHHHHHHc-CCCCHHHHhcCCHHHHHHhhccCCChH--HHHHHHHHHHHHHHH
Q 026681           25 RFAVLLSALLSSLTKDKVADGALQRLLQN-GLHTAEAIDKADEATIKDLIYPVAFYT--RKACNMKKIAKICLT   95 (235)
Q Consensus        25 ~f~~lv~~iLsqqt~~~~~~~~~~~l~~~-~~pt~~~la~a~~e~l~~~l~~~G~~~--~Ka~~l~~~a~~i~~   95 (235)
                      -||.|+-+++..-.++..+.+-...+.+. .-.+|+.+|..+++++++++..-|.-+  .|.+.+++=|+++.+
T Consensus        30 LFE~L~Le~fQAGLSW~tIL~Kr~~fr~aF~~Fd~~~VA~~~e~~ie~L~~d~~IIRnr~KI~Avi~NA~~~l~  103 (179)
T TIGR00624        30 LFERMSLEGFQAGLSWITVLRKRENYRRAFSGFDIVKVARMTDADVERLLQDDGIIRNRGKIEATIANARAALQ  103 (179)
T ss_pred             HHHHHHHHHHhCcCCHHHHHHhHHHHHHHHcCCCHHHHhCCCHHHHHHHhcCccchhhHHHHHHHHHHHHHHHH
Confidence            59999999999999999999988888764 236899999999999999999888754  445556655665543

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

>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional

Probab=94.42  E-value=0.22  Score=41.02  Aligned_cols=64  Identities=19%  Similarity=0.145  Sum_probs=39.8

Q ss_pred             CCCCHHHHhcCCHHHHHHhhccCCChHHHHHHHH------HHHHHHHHhcCCCChhhHHHHHcCCCCcHHHHHHHHHHhc
Q 026681           54 GLHTAEAIDKADEATIKDLIYPVAFYTRKACNMK------KIAKICLTKYDGDIPSSLDELLALPGIGPKMANMVMTLGW  127 (235)
Q Consensus        54 ~~pt~~~la~a~~e~l~~~l~~~G~~~~Ka~~l~------~~a~~i~~~~~g~~~~~~~~L~~l~GIG~~tA~~il~~~~  127 (235)
                      ||.|.++-     +-++.++.--|-..+.|-.|.      ++..+|..       .+.+.|.++||||+|||.-+..---
T Consensus        62 GF~~~~Er-----~lF~~Li~VsGIGpK~Al~ILs~~~~~el~~aI~~-------~D~~~L~~vpGIGkKtAeRIilELk  129 (183)
T PRK14601         62 GFLDKDEQ-----KMFEMLLKVNGIGANTAMAVCSSLDVNSFYKALSL-------GDESVLKKVPGIGPKSAKRIIAELS  129 (183)
T ss_pred             CCCCHHHH-----HHHHHHhccCCccHHHHHHHHcCCCHHHHHHHHHh-------CCHHHHhhCCCCCHHHHHHHHHHHH
Confidence            78776662     344444443444444455443      23334333       4678999999999999999986544


Q ss_pred             CC
Q 026681          128 FN  129 (235)
Q Consensus       128 ~~  129 (235)
                      ++
T Consensus       130 dK  131 (183)
T PRK14601        130 DA  131 (183)
T ss_pred             HH
Confidence            43

>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional

Probab=93.97  E-value=0.31  Score=40.35  Aligned_cols=63  Identities=16%  Similarity=0.169  Sum_probs=38.8

Q ss_pred             CCCCHHHHhcCCHHHHHHhhccCCChHHHHHHHH------HHHHHHHHhcCCCChhhHHHHHcCCCCcHHHHHHHHHHhc
Q 026681           54 GLHTAEAIDKADEATIKDLIYPVAFYTRKACNMK------KIAKICLTKYDGDIPSSLDELLALPGIGPKMANMVMTLGW  127 (235)
Q Consensus        54 ~~pt~~~la~a~~e~l~~~l~~~G~~~~Ka~~l~------~~a~~i~~~~~g~~~~~~~~L~~l~GIG~~tA~~il~~~~  127 (235)
                      ||.|.++-     +-++.++.--|-..+.|-.|.      ++.++|..       .+.+.|.++||||+|||.-+..---
T Consensus        62 GF~~~~Er-----~lF~~Li~V~GIGpK~AL~iLs~~~~~el~~aI~~-------~D~~~L~~vpGIGkKtAerIilELk  129 (188)
T PRK14606         62 GFSNERKK-----ELFLSLTKVSRLGPKTALKIISNEDAETLVTMIAS-------QDVEGLSKLPGISKKTAERIVMELK  129 (188)
T ss_pred             CCCCHHHH-----HHHHHHhccCCccHHHHHHHHcCCCHHHHHHHHHh-------CCHHHHhhCCCCCHHHHHHHHHHHH
Confidence            67776652     333444443344444455543      23444433       4678999999999999999985543


Q ss_pred             C
Q 026681          128 F  128 (235)
Q Consensus       128 ~  128 (235)
                      +
T Consensus       130 d  130 (188)
T PRK14606        130 D  130 (188)
T ss_pred             H
Confidence            3

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

Probab=93.88  E-value=0.18  Score=33.45  Aligned_cols=41  Identities=20%  Similarity=0.338  Sum_probs=22.0

Q ss_pred             HHHHHHcCCCCHHHHhcCCHHHHHHhhccCCChHHHHHHHHHHH
Q 026681           47 LQRLLQNGLHTAEAIDKADEATIKDLIYPVAFYTRKACNMKKIA   90 (235)
Q Consensus        47 ~~~l~~~~~pt~~~la~a~~e~l~~~l~~~G~~~~Ka~~l~~~a   90 (235)
                      ..+|.+.+|.|+++|+.++.++|.++ .  |+...+|+.|.+.+
T Consensus        18 a~~L~~~G~~t~~~l~~a~~~~L~~i-~--Gig~~~a~~i~~~~   58 (60)
T PF14520_consen   18 AEKLYEAGIKTLEDLANADPEELAEI-P--GIGEKTAEKIIEAA   58 (60)
T ss_dssp             HHHHHHTTCSSHHHHHTSHHHHHHTS-T--TSSHHHHHHHHHHH
T ss_pred             HHHHHhcCCCcHHHHHcCCHHHHhcC-C--CCCHHHHHHHHHHH
Confidence            34455545666666666666655443 2  44444555555443

...

>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional

Probab=93.52  E-value=0.39  Score=40.18  Aligned_cols=62  Identities=19%  Similarity=0.188  Sum_probs=38.3

Q ss_pred             CCCCHHHHhcCCHHHHHHhhccCCChHHHHHHHHH------HHHHHHHhcCCCChhhHHHHHcCCCCcHHHHHHHHHHhc
Q 026681           54 GLHTAEAIDKADEATIKDLIYPVAFYTRKACNMKK------IAKICLTKYDGDIPSSLDELLALPGIGPKMANMVMTLGW  127 (235)
Q Consensus        54 ~~pt~~~la~a~~e~l~~~l~~~G~~~~Ka~~l~~------~a~~i~~~~~g~~~~~~~~L~~l~GIG~~tA~~il~~~~  127 (235)
                      ||.|.++-     +-++.++.--|...+.|-.|..      ++++|.+       .+.+.|.++||||+|||+-+..---
T Consensus        63 GF~~~~Er-----~lF~~Li~V~GIGpK~Al~iLs~~~~~~l~~aI~~-------~D~~~L~~ipGIGkKtAerIilELk  130 (203)
T PRK14602         63 GFATWDER-----QTFIVLISISKVGAKTALAILSQFRPDDLRRLVAE-------EDVAALTRVSGIGKKTAQHIFLELK  130 (203)
T ss_pred             CCCCHHHH-----HHHHHHhCCCCcCHHHHHHHHhhCCHHHHHHHHHh-------CCHHHHhcCCCcCHHHHHHHHHHHH
Confidence            67776652     3344444434444445555543      2333332       4678999999999999999985433

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

Probab=93.47  E-value=0.38  Score=40.20  Aligned_cols=64  Identities=22%  Similarity=0.222  Sum_probs=39.1

Q ss_pred             CCCCHHHHhcCCHHHHHHhhccCCChHHHHHHHH------HHHHHHHHhcCCCChhhHHHHHcCCCCcHHHHHHHHHHhc
Q 026681           54 GLHTAEAIDKADEATIKDLIYPVAFYTRKACNMK------KIAKICLTKYDGDIPSSLDELLALPGIGPKMANMVMTLGW  127 (235)
Q Consensus        54 ~~pt~~~la~a~~e~l~~~l~~~G~~~~Ka~~l~------~~a~~i~~~~~g~~~~~~~~L~~l~GIG~~tA~~il~~~~  127 (235)
                      ||.|.++     .+-+..+++--|-..+-|-.|.      +++++|..       ++.+.|.++||||+|||+-++.---
T Consensus        62 GF~~~~E-----R~lF~~LisVnGIGpK~ALaiLs~~~~~~l~~aI~~-------~d~~~L~k~PGIGkKtAerivleLk  129 (201)
T COG0632          62 GFLTEEE-----RELFRLLISVNGIGPKLALAILSNLDPEELAQAIAN-------EDVKALSKIPGIGKKTAERIVLELK  129 (201)
T ss_pred             CCCCHHH-----HHHHHHHHccCCccHHHHHHHHcCCCHHHHHHHHHh-------cChHhhhcCCCCCHHHHHHHHHHHh
Confidence            6887665     3445555554444433333332      22333332       4678999999999999999986543


Q ss_pred             CC
Q 026681          128 FN  129 (235)
Q Consensus       128 ~~  129 (235)
                      ++
T Consensus       130 ~K  131 (201)
T COG0632         130 GK  131 (201)
T ss_pred             hh
Confidence            33

>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional

Probab=93.42  E-value=0.41  Score=39.80  Aligned_cols=63  Identities=21%  Similarity=0.161  Sum_probs=38.8

Q ss_pred             CCCCHHHHhcCCHHHHHHhhccCCChHHHHHHHHH------HHHHHHHhcCCCChhhHHHHHcCCCCcHHHHHHHHHHhc
Q 026681           54 GLHTAEAIDKADEATIKDLIYPVAFYTRKACNMKK------IAKICLTKYDGDIPSSLDELLALPGIGPKMANMVMTLGW  127 (235)
Q Consensus        54 ~~pt~~~la~a~~e~l~~~l~~~G~~~~Ka~~l~~------~a~~i~~~~~g~~~~~~~~L~~l~GIG~~tA~~il~~~~  127 (235)
                      ||.|.++-     +-+..++.--|...+.|-.|..      +..+|.+       .+.+.|.++||||+|||+-+..---
T Consensus        62 GF~~~~Er-----~lF~~Li~V~GIGpK~Al~iLs~~~~~el~~aI~~-------~D~~~L~kvpGIGkKtAerIilELk  129 (195)
T PRK14604         62 GFSTPAQR-----QLFELLIGVSGVGPKAALNLLSSGTPDELQLAIAG-------GDVARLARVPGIGKKTAERIVLELK  129 (195)
T ss_pred             CCCCHHHH-----HHHHHHhCcCCcCHHHHHHHHcCCCHHHHHHHHHh-------CCHHHHhhCCCCCHHHHHHHHHHHH
Confidence            67776552     3344444434444455555543      2333332       4678999999999999999985543


Q ss_pred             C
Q 026681          128 F  128 (235)
Q Consensus       128 ~  128 (235)
                      +
T Consensus       130 ~  130 (195)
T PRK14604        130 G  130 (195)
T ss_pred             H
Confidence            3

>TIGR00084 ruvA Holliday junction DNA helicase, RuvA subunit

Probab=93.25  E-value=0.28  Score=40.65  Aligned_cols=64  Identities=20%  Similarity=0.252  Sum_probs=39.6

Q ss_pred             CCCCHHHHhcCCHHHHHHhhccCCChHHHHHHHHHHH--HHHHHhcCCCChhhHHHHHcCCCCcHHHHHHHHHH
Q 026681           54 GLHTAEAIDKADEATIKDLIYPVAFYTRKACNMKKIA--KICLTKYDGDIPSSLDELLALPGIGPKMANMVMTL  125 (235)
Q Consensus        54 ~~pt~~~la~a~~e~l~~~l~~~G~~~~Ka~~l~~~a--~~i~~~~~g~~~~~~~~L~~l~GIG~~tA~~il~~  125 (235)
                      ||.|.++     .+-+..++.--|...++|..|....  ..+.+   --...+...|.++||||+|||.-|+.-
T Consensus        61 GF~~~~E-----r~lF~~L~~V~GIGpK~Al~iL~~~~~~el~~---aI~~~d~~~L~~ipGiGkKtAerIile  126 (191)
T TIGR00084        61 GFNTLEE-----RELFKELIKVNGVGPKLALAILSNMSPEEFVY---AIETEEVKALVKIPGVGKKTAERLLLE  126 (191)
T ss_pred             CCCCHHH-----HHHHHHHhCCCCCCHHHHHHHHhcCCHHHHHH---HHHhCCHHHHHhCCCCCHHHHHHHHHH
Confidence            7888766     3455556655566566676664321  11111   001135678999999999999999843

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

>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional

Probab=93.19  E-value=0.46  Score=39.47  Aligned_cols=59  Identities=24%  Similarity=0.346  Sum_probs=37.3

Q ss_pred             CCCCHHHHhcCCHHHHHHhhccCCChHHHHHHHHHH------HHHHHHhcCCCChhhHHHHHcCCCCcHHHHHHHHH
Q 026681           54 GLHTAEAIDKADEATIKDLIYPVAFYTRKACNMKKI------AKICLTKYDGDIPSSLDELLALPGIGPKMANMVMT  124 (235)
Q Consensus        54 ~~pt~~~la~a~~e~l~~~l~~~G~~~~Ka~~l~~~------a~~i~~~~~g~~~~~~~~L~~l~GIG~~tA~~il~  124 (235)
                      ||.|.++-     +-+..++.--|.....|..|.+.      ..+|.       .++.+.|.++||||+|||.-+..
T Consensus        62 GF~~~~Er-----~lF~~Li~V~GIGpK~Al~ILs~~~~~~l~~aI~-------~~D~~~L~~vpGIGkKtAerIil  126 (194)
T PRK14605         62 GFATTEEL-----SLFETLIDVSGIGPKLGLAMLSAMNAEALASAII-------SGNAELLSTIPGIGKKTASRIVL  126 (194)
T ss_pred             CCCCHHHH-----HHHHHHhCCCCCCHHHHHHHHHhCCHHHHHHHHH-------hCCHHHHHhCCCCCHHHHHHHHH
Confidence            67776652     34444544444445556666553      22222       24678899999999999999663

>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional

Probab=93.07  E-value=0.51  Score=39.32  Aligned_cols=61  Identities=16%  Similarity=0.199  Sum_probs=37.1

Q ss_pred             CCCCHHHHhcCCHHHHHHhhccCCChHHHHHHHHH------HHHHHHHhcCCCChhhHHHHHcCCCCcHHHHHHHHHHh
Q 026681           54 GLHTAEAIDKADEATIKDLIYPVAFYTRKACNMKK------IAKICLTKYDGDIPSSLDELLALPGIGPKMANMVMTLG  126 (235)
Q Consensus        54 ~~pt~~~la~a~~e~l~~~l~~~G~~~~Ka~~l~~------~a~~i~~~~~g~~~~~~~~L~~l~GIG~~tA~~il~~~  126 (235)
                      ||.|.++-     +-+..++.--|...+.|-.|..      +.++|..       .+.+.|.++||||+|||.-+..--
T Consensus        61 GF~~~~Er-----~lF~~L~~V~GIGpK~AL~iLs~~~~~~l~~aI~~-------~D~~~L~kvpGIGkKtAerIilEL  127 (197)
T PRK14603         61 GFPDEDSL-----ELFELLLGVSGVGPKLALALLSALPPALLARALLE-------GDARLLTSASGVGKKLAERIALEL  127 (197)
T ss_pred             CcCCHHHH-----HHHHHHhCcCCcCHHHHHHHHcCCCHHHHHHHHHh-------CCHHHHhhCCCCCHHHHHHHHHHH
Confidence            67775552     3333444333444444554433      3344333       467899999999999999998543

>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional

Probab=92.12  E-value=0.33  Score=40.10  Aligned_cols=61  Identities=18%  Similarity=0.227  Sum_probs=37.5

Q ss_pred             CCCCHHHHhcCCHHHHHHhhccCCChHHHHHHHHH------HHHHHHHhcCCCChhhHHHHHcCCCCcHHHHHHHHHHhc
Q 026681           54 GLHTAEAIDKADEATIKDLIYPVAFYTRKACNMKK------IAKICLTKYDGDIPSSLDELLALPGIGPKMANMVMTLGW  127 (235)
Q Consensus        54 ~~pt~~~la~a~~e~l~~~l~~~G~~~~Ka~~l~~------~a~~i~~~~~g~~~~~~~~L~~l~GIG~~tA~~il~~~~  127 (235)
                      ||.|.++-     +-++.++.--|-..+.|-.|..      +.++|.+       .+.+.| ++||||+|||+-++.---
T Consensus        62 GF~~~~Er-----~lF~~LisV~GIGpK~Al~iLs~~~~~~l~~aI~~-------~D~~~L-~vpGIGkKtAerIilELk  128 (186)
T PRK14600         62 GFLNREEQ-----DCLRMLVKVSGVNYKTAMSILSKLTPEQLFSAIVN-------EDKAAL-KVNGIGEKLINRIITELQ  128 (186)
T ss_pred             CCCCHHHH-----HHHHHHhCcCCcCHHHHHHHHccCCHHHHHHHHHc-------CCHhhe-ECCCCcHHHHHHHHHHHH
Confidence            68776662     4444444444444445555543      3334333       356888 999999999999985433

>TIGR00426 competence protein ComEA helix-hairpin-helix repeat region

Probab=91.98  E-value=0.67  Score=31.53  Aligned_cols=58  Identities=21%  Similarity=0.460  Sum_probs=38.2

Q ss_pred             HHhcCCHHHHHHhhccCCChHHHHHHHHHHHHHHHHhcCCCChhhHHHHHcCCCCcHHHHHHHHHH
Q 026681           60 AIDKADEATIKDLIYPVAFYTRKACNMKKIAKICLTKYDGDIPSSLDELLALPGIGPKMANMVMTL  125 (235)
Q Consensus        60 ~la~a~~e~l~~~l~~~G~~~~Ka~~l~~~a~~i~~~~~g~~~~~~~~L~~l~GIG~~tA~~il~~  125 (235)
                      .|-.++.++|..++.++|.  .+|+.|.+--.    .+ |.+ ...++|..++|||.++++-++.+
T Consensus         9 nvNta~~~~L~~~ipgig~--~~a~~Il~~R~----~~-g~~-~s~~dL~~v~gi~~~~~~~i~~~   66 (69)
T TIGR00426         9 NINTATAEELQRAMNGVGL--KKAEAIVSYRE----EY-GPF-KTVEDLKQVPGIGNSLVEKNLAV   66 (69)
T ss_pred             ECcCCCHHHHHhHCCCCCH--HHHHHHHHHHH----Hc-CCc-CCHHHHHcCCCCCHHHHHHHHhh
Confidence            4445788888887676665  33433332211    12 223 37899999999999999988765

Members of the subfamily recognized by this model include competence protein ComEA and closely related proteins from a number of species that exhibit competence for transformation by exongenous DNA, including Streptococcus pneumoniae, Bacillus subtilis, Neisseria meningitidis, and Haemophilus influenzae. This model represents a region of two tandem copies of a helix-hairpin-helix domain (pfam00633), each about 30 residues in length. Limited sequence similarity can be found among some members of this family N-terminal to the region covered by this model.

>PRK02515 psbU photosystem II complex extrinsic protein precursor U; Provisional

Probab=91.93  E-value=0.42  Score=37.09  Aligned_cols=58  Identities=14%  Similarity=0.340  Sum_probs=39.8

Q ss_pred             CCCHHHHhcCCHHHHHHhhccCCChHHHHHHHHHHHHHHHHhcCCCChhhHHHHHcCCCCcHHHHHHHHHH
Q 026681           55 LHTAEAIDKADEATIKDLIYPVAFYTRKACNMKKIAKICLTKYDGDIPSSLDELLALPGIGPKMANMVMTL  125 (235)
Q Consensus        55 ~pt~~~la~a~~e~l~~~l~~~G~~~~Ka~~l~~~a~~i~~~~~g~~~~~~~~L~~l~GIG~~tA~~il~~  125 (235)
                      +...=+|-.++.+++..+ .  |++..+|+.|..         +|.+ ...++|.++||||+++.+.+--+
T Consensus        49 ~~~kIdiN~A~~~el~~l-p--GigP~~A~~IV~---------nGpf-~sveDL~~V~GIgekqk~~l~k~  106 (132)
T PRK02515         49 FGEKIDLNNSSVRAFRQF-P--GMYPTLAGKIVK---------NAPY-DSVEDVLNLPGLSERQKELLEAN  106 (132)
T ss_pred             cCCcccCCccCHHHHHHC-C--CCCHHHHHHHHH---------CCCC-CCHHHHHcCCCCCHHHHHHHHHh
Confidence            344555667788887763 4  666777777762         2444 56888899999999887766544

>PRK14973 DNA topoisomerase I; Provisional

Probab=91.91  E-value=0.58  Score=47.77  Aligned_cols=99  Identities=15%  Similarity=0.226  Sum_probs=63.3

Q ss_pred             HHHHHHHcCCCCHHHHhcCCHHHHHHhhccCCChHHHHHHHHHHHH-HHHHh-c----CCCChhhHHHHHcCCCCcHHHH
Q 026681           46 ALQRLLQNGLHTAEAIDKADEATIKDLIYPVAFYTRKACNMKKIAK-ICLTK-Y----DGDIPSSLDELLALPGIGPKMA  119 (235)
Q Consensus        46 ~~~~l~~~~~pt~~~la~a~~e~l~~~l~~~G~~~~Ka~~l~~~a~-~i~~~-~----~g~~~~~~~~L~~l~GIG~~tA  119 (235)
                      ..+.+.+.||-++++++.+++++|...   .|+....+..+...|. .+... .    ...+...+.+|++++|||++|+
T Consensus       814 ~~~~~~~~G~~~~~d~~~a~p~~La~~---~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~el~~vkg~ge~t~  890 (936)
T PRK14973        814 SLKKYQEAGFDTPEDFCSVHPAYLALK---TGISPETICRHAKLVCEKLGRPVPEKISKAAFERGRAELLSVPGLGETTL  890 (936)
T ss_pred             HHHHHHHhcCCCHHHHHhcCHHHHhcC---CCCChhhHHHHHHHHHHHhcCCCchhhhhhhhcccchhhhhccCCCHHHH
Confidence            445556669999999999999998776   5887655666655444 33221 0    0112234456999999999999


Q ss_pred             HHHHHHhcCCcceeecchHHHHHHHHhcC
Q 026681          120 NMVMTLGWFNVQGICVDTHVHRICNRLGW  148 (235)
Q Consensus       120 ~~il~~~~~~~~~~pvDt~v~Rv~~Rlg~  148 (235)
                      +..-.-+.-..+.+..+ ...+++.+-|+
T Consensus       891 ~~l~~ag~~~~e~l~~~-d~~~la~~~~i  918 (936)
T PRK14973        891 EKLYLAGVYDGDLLVSA-DPKKLAKVTGI  918 (936)
T ss_pred             HHHHHcCCCCHHHhccC-CHHHHhhhcCC
Confidence            77666555443333222 45566666655

>PF02371 Transposase_20: Transposase IS116/IS110/IS902 family; InterPro: IPR003346 Transposases are needed for efficient transposition of the insertion sequence or transposon DNA

Probab=91.82  E-value=0.13  Score=36.83  Aligned_cols=41  Identities=20%  Similarity=0.330  Sum_probs=29.2

Q ss_pred             HHHHcCCCCcHHHHHHHHHHhcCCcceeecchHHHHHHHHhcCcC
Q 026681          106 DELLALPGIGPKMANMVMTLGWFNVQGICVDTHVHRICNRLGWVT  150 (235)
Q Consensus       106 ~~L~~l~GIG~~tA~~il~~~~~~~~~~pvDt~v~Rv~~Rlg~~~  150 (235)
                      +.|+++||||+-||..++... ++...|+-..+   +...+|+.+
T Consensus         2 ~~l~sipGig~~~a~~llaei-gd~~rF~~~~~---l~~~~Gl~P   42 (87)
T PF02371_consen    2 ELLTSIPGIGPITAATLLAEI-GDISRFKSAKQ---LASYAGLAP   42 (87)
T ss_pred             chhcCCCCccHHHHHHHHHHH-cCchhcccchh---hhhcccccc
Confidence            468899999999999998876 45456644444   555566654

This family includes transposases for IS116, IS110 and IS902. It is often found with the transposase IS111A/IS1328/IS1533 family (see IPR002525 from INTERPRO) [, ]. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated

>COG0353 RecR Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]

Probab=91.16  E-value=0.15  Score=42.15  Aligned_cols=30  Identities=33%  Similarity=0.424  Sum_probs=24.4

Q ss_pred             CChhhHHHHHcCCCCcHHHHHHHHHHhcCC
Q 026681          100 DIPSSLDELLALPGIGPKMANMVMTLGWFN  129 (235)
Q Consensus       100 ~~~~~~~~L~~l~GIG~~tA~~il~~~~~~  129 (235)
                      .+....+.|.+|||||+|+|.=+..+-+.+
T Consensus         6 ~i~~LI~~l~kLPGvG~KsA~R~AfhLL~~   35 (198)
T COG0353           6 PIEKLIDALKKLPGVGPKSAQRLAFHLLQR   35 (198)
T ss_pred             HHHHHHHHHhhCCCCChhHHHHHHHHHHcc
Confidence            345678899999999999999887776654

>cd00141 NT_POLXc Nucleotidyltransferase (NT) domain of family X DNA Polymerases

Probab=91.11  E-value=0.82  Score=40.67  Aligned_cols=49  Identities=29%  Similarity=0.489  Sum_probs=33.8

Q ss_pred             hccCCChHHHHHHHHHHHHH----HHHhcCCCChhhHHHHHcCCCCcHHHHHHHH
Q 026681           73 IYPVAFYTRKACNMKKIAKI----CLTKYDGDIPSSLDELLALPGIGPKMANMVM  123 (235)
Q Consensus        73 l~~~G~~~~Ka~~l~~~a~~----i~~~~~g~~~~~~~~L~~l~GIG~~tA~~il  123 (235)
                      |.++|  ..-|..|.++.+.    ..++...+.|....+|+++|||||++|..+-
T Consensus        50 ipgiG--~~ia~kI~E~~~tG~~~~le~l~~~~~~~l~~l~~i~GiGpk~a~~l~  102 (307)
T cd00141          50 LPGIG--KKIAEKIEEILETGKLRKLEELREDVPPGLLLLLRVPGVGPKTARKLY  102 (307)
T ss_pred             CCCcc--HHHHHHHHHHHHcCCHHHHHHHhccchHHHHHHHcCCCCCHHHHHHHH
Confidence            34444  4456677666543    2233334578888999999999999998776

X family polymerases fill in short gaps during DNA repair. They are relatively inaccurate enzymes and play roles in base excision repair, in non-homologous end joining (NHEJ) which acts mainly to repair damage due to ionizing radiation, and in V(D)J recombination. This family includes eukaryotic Pol beta, Pol lambda, Pol mu, and terminal deoxyribonucleotidyl transferase (TdT). Pol beta and Pol lambda are primarily DNA template-dependent polymerases. TdT is a DNA template-independent polymerase. Pol mu has both template dependent and template independent activities. This subgroup belongs to the Pol beta-like NT superfamily. In the majority of enzymes in this superfamily, two carboxylates, Dx[D/E], together with a third more distal carboxylate, coordinate two divalent metal cations involved in a two-metal ion mechanism of nucleotide addition. These three carboxylate residues are fairly well conserved in this

>smart00483 POLXc DNA polymerase X family

Probab=90.87  E-value=0.95  Score=40.76  Aligned_cols=50  Identities=18%  Similarity=0.282  Sum_probs=34.3

Q ss_pred             hccCCChHHHHHHHHHHHHH-----HHHhcCCCChhhHHHHHcCCCCcHHHHHHHHH
Q 026681           73 IYPVAFYTRKACNMKKIAKI-----CLTKYDGDIPSSLDELLALPGIGPKMANMVMT  124 (235)
Q Consensus        73 l~~~G~~~~Ka~~l~~~a~~-----i~~~~~g~~~~~~~~L~~l~GIG~~tA~~il~  124 (235)
                      |.++|  ..=|..|.++.+.     +.+.....+|....+|+++|||||++|..+-.
T Consensus        53 lpgIG--~~ia~kI~Eil~tG~~~~~~e~l~~~~p~~l~~l~~i~GiGpk~a~~l~~  107 (334)
T smart00483       53 LPGIG--DKIKKKIEEIIETGKSSKVLEILNDEVYKSLKLFTNVFGVGPKTAAKWYR  107 (334)
T ss_pred             CCCcc--HHHHHHHHHHHHhCcHHHHHHHhcCcHHHHHHHHHccCCcCHHHHHHHHH
Confidence            35455  3345666666443     23334456788899999999999999987755

includes vertebrate polymerase beta and terminal deoxynucleotidyltransferases

>PF14229 DUF4332: Domain of unknown function (DUF4332)

Probab=90.86  E-value=1.6  Score=33.37  Aligned_cols=84  Identities=23%  Similarity=0.428  Sum_probs=55.7

Q ss_pred             HHHHHHcCCCCHHHHhcCCHHHHHH--hhccCCChHHHHHHHHHHHHHHHHhcCCCChhhHHHHHcCCCCcHHHHHHHHH
Q 026681           47 LQRLLQNGLHTAEAIDKADEATIKD--LIYPVAFYTRKACNMKKIAKICLTKYDGDIPSSLDELLALPGIGPKMANMVMT  124 (235)
Q Consensus        47 ~~~l~~~~~pt~~~la~a~~e~l~~--~l~~~G~~~~Ka~~l~~~a~~i~~~~~g~~~~~~~~L~~l~GIG~~tA~~il~  124 (235)
                      ..+|.+.|..|+++|.+.+......  +....|...+   +|.+..             .+..|..+||||+..|..++.
T Consensus         8 ~~~L~~~GI~t~~~Ll~~~~~~~~r~~La~~~~i~~~---~l~~w~-------------~~AdL~ri~gi~~~~a~LL~~   71 (122)
T PF14229_consen    8 AAKLKAAGIKTTGDLLEAGDTPLGRKALAKKLGISER---NLLKWV-------------NQADLMRIPGIGPQYAELLEH   71 (122)
T ss_pred             HHHHHHcCCCcHHHHHHcCCCHHHHHHHHHhcCCCHH---HHHHHH-------------hHHHhhhcCCCCHHHHHHHHH
Confidence            4556666889999999988877766  6666676533   333322             245677899999999998887


Q ss_pred             HhcCCcceeecchHHHHHHHHhc
Q 026681          125 LGWFNVQGICVDTHVHRICNRLG  147 (235)
Q Consensus       125 ~~~~~~~~~pvDt~v~Rv~~Rlg  147 (235)
                      -+..-...+ ...+..++..+++
T Consensus        72 AGv~Tv~~L-A~~~p~~L~~~l~   93 (122)
T PF14229_consen   72 AGVDTVEEL-AQRNPQNLHQKLG   93 (122)
T ss_pred             hCcCcHHHH-HhCCHHHHHHHHH
Confidence            776543322 4455555555543

>PRK13844 recombination protein RecR; Provisional

Probab=90.78  E-value=0.17  Score=42.19  Aligned_cols=29  Identities=24%  Similarity=0.289  Sum_probs=24.1

Q ss_pred             ChhhHHHHHcCCCCcHHHHHHHHHHhcCC
Q 026681          101 IPSSLDELLALPGIGPKMANMVMTLGWFN  129 (235)
Q Consensus       101 ~~~~~~~L~~l~GIG~~tA~~il~~~~~~  129 (235)
                      +....+.|.+|||||+|+|.-+..+-+..
T Consensus        10 ~~~LI~~l~~LPGIG~KsA~Rla~~lL~~   38 (200)
T PRK13844         10 ISAVIESLRKLPTIGKKSSQRLALYLLDK   38 (200)
T ss_pred             HHHHHHHHHHCCCCCHHHHHHHHHHHHcC
Confidence            44667889999999999999888877754

>PRK00076 recR recombination protein RecR; Reviewed

Probab=90.50  E-value=0.25  Score=41.12  Aligned_cols=29  Identities=34%  Similarity=0.433  Sum_probs=24.3

Q ss_pred             ChhhHHHHHcCCCCcHHHHHHHHHHhcCC
Q 026681          101 IPSSLDELLALPGIGPKMANMVMTLGWFN  129 (235)
Q Consensus       101 ~~~~~~~L~~l~GIG~~tA~~il~~~~~~  129 (235)
                      +.+..+.|.+|||||+|+|.=+..+-+..
T Consensus         6 ~~~Li~~l~~LPGIG~KsA~Rla~~ll~~   34 (196)
T PRK00076          6 IEKLIEALRKLPGIGPKSAQRLAFHLLQR   34 (196)
T ss_pred             HHHHHHHHHHCCCCCHHHHHHHHHHHHcC
Confidence            44667889999999999999888887754

>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed

Probab=90.45  E-value=0.93  Score=37.52  Aligned_cols=20  Identities=35%  Similarity=0.561  Sum_probs=12.7

Q ss_pred             HHHHcCCCCcHHHHHHHHHH
Q 026681          106 DELLALPGIGPKMANMVMTL  125 (235)
Q Consensus       106 ~~L~~l~GIG~~tA~~il~~  125 (235)
                      +.|.++||||+++|+.|+..
T Consensus       108 ~~L~~v~Gig~k~A~~I~~~  127 (192)
T PRK00116        108 KALTKVPGIGKKTAERIVLE  127 (192)
T ss_pred             HHHHhCCCCCHHHHHHHHHH
Confidence            45666777777777666533

>TIGR00615 recR recombination protein RecR

Probab=90.30  E-value=0.27  Score=40.84  Aligned_cols=29  Identities=34%  Similarity=0.439  Sum_probs=23.9

Q ss_pred             ChhhHHHHHcCCCCcHHHHHHHHHHhcCC
Q 026681          101 IPSSLDELLALPGIGPKMANMVMTLGWFN  129 (235)
Q Consensus       101 ~~~~~~~L~~l~GIG~~tA~~il~~~~~~  129 (235)
                      +.+..+.|.+|||||+|+|.-+..+-+..
T Consensus         6 ~~~Li~~l~~LPGIG~KsA~RlA~~ll~~   34 (195)
T TIGR00615         6 ISKLIESLKKLPGIGPKSAQRLAFHLLKR   34 (195)
T ss_pred             HHHHHHHHHHCCCCCHHHHHHHHHHHHcC
Confidence            44667889999999999999888777654

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

>TIGR00608 radc DNA repair protein radc

Probab=90.12  E-value=0.53  Score=39.87  Aligned_cols=57  Identities=18%  Similarity=0.264  Sum_probs=40.8

Q ss_pred             CCHHHHHHhhccCCChHHHHH-HHHHHHHHHHHhcC--CCCh----hhHHHHHcCCCCcHHHHHHHH
Q 026681           64 ADEATIKDLIYPVAFYTRKAC-NMKKIAKICLTKYD--GDIP----SSLDELLALPGIGPKMANMVM  123 (235)
Q Consensus        64 a~~e~l~~~l~~~G~~~~Ka~-~l~~~a~~i~~~~~--g~~~----~~~~~L~~l~GIG~~tA~~il  123 (235)
                      .+..||.++|=..|..   -+ ...++|+.+.++|.  |.+.    ...++|++++|||+..|..++
T Consensus        14 Lsd~ELLailL~~g~~---~~~~~~~lA~~ll~~f~~~g~l~~l~~a~~~eL~~i~GiG~aka~~l~   77 (218)
T TIGR00608        14 LSDYELLAIILRTGTP---KGLDVLSLSKRLLDVFGRQDSLGHLLSAPPEELSSVPGIGEAKAIQLK   77 (218)
T ss_pred             CCHHHHHHHHHhCCCC---CCCCHHHHHHHHHHHhcccCCHHHHHhCCHHHHHhCcCCcHHHHHHHH
Confidence            4566777765455553   34 67789999999883  4554    367899999999997776554

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

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

Probab=90.05  E-value=0.36  Score=32.00  Aligned_cols=26  Identities=42%  Similarity=0.749  Sum_probs=19.1

Q ss_pred             hHHHHHcCCCCcHHHHHHHHHHhcCC
Q 026681          104 SLDELLALPGIGPKMANMVMTLGWFN  129 (235)
Q Consensus       104 ~~~~L~~l~GIG~~tA~~il~~~~~~  129 (235)
                      ....|.++||||+++|..+...++.-
T Consensus         3 ~~~~L~~I~Gig~~~a~~L~~~G~~t   28 (60)
T PF14520_consen    3 VFDDLLSIPGIGPKRAEKLYEAGIKT   28 (60)
T ss_dssp             HHHHHHTSTTCHHHHHHHHHHTTCSS
T ss_pred             HHHhhccCCCCCHHHHHHHHhcCCCc
Confidence            35678888888888888777766553

...

>TIGR00575 dnlj DNA ligase, NAD-dependent

Probab=89.78  E-value=2.2  Score=41.96  Aligned_cols=77  Identities=22%  Similarity=0.461  Sum_probs=50.9

Q ss_pred             HHHHHHHHcCC-CCHHHHhcCCHHHHHHhhccCCChHHHHHHHHHHHHHH-------------------------HHhcC
Q 026681           45 GALQRLLQNGL-HTAEAIDKADEATIKDLIYPVAFYTRKACNMKKIAKIC-------------------------LTKYD   98 (235)
Q Consensus        45 ~~~~~l~~~~~-pt~~~la~a~~e~l~~~l~~~G~~~~Ka~~l~~~a~~i-------------------------~~~~~   98 (235)
                      +.+..|++.++ -++++|..+..++|.++ .  ||....+..|.+..+.-                         .+.| 
T Consensus       443 k~i~~L~~~g~I~~~~Dl~~L~~~~L~~L-~--GfG~Ksa~nIl~~Ie~sk~~~l~r~L~aLgIpgVG~~~ak~L~~~f-  518 (652)
T TIGR00575       443 KVIEQLFEKKLVRSVADLYALKKEDLLEL-E--GFGEKSAQNLLNAIEKSKEKPLARLLFALGIRHVGEVTAKNLAKHF-  518 (652)
T ss_pred             HHHHHHHHcCCcCCHHHHHhcCHHHHhhc-c--CccHHHHHHHHHHHHHhccCcHHHHHhhccCCCcCHHHHHHHHHHh-
Confidence            34566666544 58999999998887765 3  66666677776655431                         1222 


Q ss_pred             CCChh----hHHHHHcCCCCcHHHHHHHHHH
Q 026681           99 GDIPS----SLDELLALPGIGPKMANMVMTL  125 (235)
Q Consensus        99 g~~~~----~~~~L~~l~GIG~~tA~~il~~  125 (235)
                      +++..    +.++|.+++|||+++|..|..|
T Consensus       519 ~sl~~l~~As~eeL~~i~GIG~~~A~~I~~f  549 (652)
T TIGR00575       519 GTLDKLKAASLEELLSVEGVGPKVAESIVNF  549 (652)
T ss_pred             CCHHHHHhCCHHHHhcCCCcCHHHHHHHHHH
Confidence            22322    3567888999999999988877

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

>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed

Probab=89.71  E-value=0.56  Score=38.82  Aligned_cols=20  Identities=30%  Similarity=0.750  Sum_probs=17.5

Q ss_pred             HHHHHcCCCCcHHHHHHHHH
Q 026681          105 LDELLALPGIGPKMANMVMT  124 (235)
Q Consensus       105 ~~~L~~l~GIG~~tA~~il~  124 (235)
                      ...|.++|||||++|..++.
T Consensus        72 f~~L~~i~GIGpk~A~~il~   91 (192)
T PRK00116         72 FRLLISVSGVGPKLALAILS   91 (192)
T ss_pred             HHHHhcCCCCCHHHHHHHHH
Confidence            56788999999999998875

>PF12836 HHH_3: Helix-hairpin-helix motif; PDB: 2EDU_A 2OCE_A 3BZK_A 3BZC_A 2DUY_A

Probab=88.26  E-value=0.56  Score=31.69  Aligned_cols=22  Identities=55%  Similarity=0.875  Sum_probs=17.5

Q ss_pred             hHHHHHcCCCCcHHHHHHHHHH
Q 026681          104 SLDELLALPGIGPKMANMVMTL  125 (235)
Q Consensus       104 ~~~~L~~l~GIG~~tA~~il~~  125 (235)
                      +.++|.++||||++.|..|+.+
T Consensus        12 s~~eL~~lpgi~~~~A~~Iv~~   33 (65)
T PF12836_consen   12 SAEELQALPGIGPKQAKAIVEY   33 (65)
T ss_dssp             -HHHHHTSTT--HHHHHHHHHH
T ss_pred             CHHHHHHcCCCCHHHHHHHHHH
Confidence            5789999999999999999976

>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated

Probab=87.92  E-value=3.3  Score=40.88  Aligned_cols=76  Identities=21%  Similarity=0.395  Sum_probs=50.0

Q ss_pred             HHHHHHHcC-CCCHHHHhcCCHHHHHHhhccCCChHHHHHHHHHHHHH-------------------------HHHhcCC
Q 026681           46 ALQRLLQNG-LHTAEAIDKADEATIKDLIYPVAFYTRKACNMKKIAKI-------------------------CLTKYDG   99 (235)
Q Consensus        46 ~~~~l~~~~-~pt~~~la~a~~e~l~~~l~~~G~~~~Ka~~l~~~a~~-------------------------i~~~~~g   99 (235)
                      .+..|.+.+ ..++++|..+..++|.++ .  ||...++..|.+..+.                         +...| +
T Consensus       457 ~i~~L~~~g~I~~i~DL~~L~~~~L~~l-~--gfG~Ksa~~ll~~Ie~sk~~~l~R~l~algi~~IG~~~ak~L~~~f-~  532 (665)
T PRK07956        457 IIEQLFEKGLIHDPADLFKLTAEDLLGL-E--GFGEKSAQNLLDAIEKSKETSLARFLYALGIRHVGEKAAKALARHF-G  532 (665)
T ss_pred             HHHHHHHcCCCCCHHHHHhcCHHHHhcC-c--CcchHHHHHHHHHHHHhhcCCHHHhhHhhhccCcCHHHHHHHHHHc-C
Confidence            445566543 468999998888877665 2  6666666666544332                         22222 2


Q ss_pred             CCh----hhHHHHHcCCCCcHHHHHHHHHH
Q 026681          100 DIP----SSLDELLALPGIGPKMANMVMTL  125 (235)
Q Consensus       100 ~~~----~~~~~L~~l~GIG~~tA~~il~~  125 (235)
                      ++.    .+.++|.+++|||+++|..|..|
T Consensus       533 sl~~l~~As~eeL~~i~GIG~~~A~sI~~f  562 (665)
T PRK07956        533 SLEALRAASEEELAAVEGVGEVVAQSIVEF  562 (665)
T ss_pred             CHHHHHhCCHHHHhccCCcCHHHHHHHHHH
Confidence            222    24578999999999999999877

>TIGR01954 nusA_Cterm_rpt transcription termination factor NusA, C-terminal duplication

Probab=87.68  E-value=2.7  Score=26.25  Aligned_cols=44  Identities=18%  Similarity=0.206  Sum_probs=35.8

Q ss_pred             HHHHHHHcCCCCHHHHhcCCHHHHHHhhccCCChHHHHHHHHHHHHH
Q 026681           46 ALQRLLQNGLHTAEAIDKADEATIKDLIYPVAFYTRKACNMKKIAKI   92 (235)
Q Consensus        46 ~~~~l~~~~~pt~~~la~a~~e~l~~~l~~~G~~~~Ka~~l~~~a~~   92 (235)
                      ....|...||-|.++++.+++++|.++   -|+...++..|+..++.
T Consensus         5 ~~~~L~~~G~~s~e~la~~~~~eL~~i---~g~~~e~a~~ii~~a~~   48 (50)
T TIGR01954         5 IAQLLVEEGFTTVEDLAYVPIDELLSI---EGFDEETAKELINRARN   48 (50)
T ss_pred             HHHHHHHcCCCCHHHHHccCHHHHhcC---CCCCHHHHHHHHHHHHH
Confidence            456677779999999999999999886   47777788888777663

NusA is a bacterial transcription termination factor. It is named for its interaction with phage lambda protein N, as part of the N utilization substance. Some members of the NusA family have a long C-terminal extension. This model represents an acidic 50-residue region found in two copies toward the C-terminus of most Proteobacterial NusA proteins, spaced about 26 residues apart. Analogous C-terminal extensions in some other bacterial lineages lack apparent homology but appear similarly acidic.

>PRK08097 ligB NAD-dependent DNA ligase LigB; Reviewed

Probab=87.46  E-value=4.3  Score=39.16  Aligned_cols=78  Identities=17%  Similarity=0.180  Sum_probs=53.2

Q ss_pred             HHHHHHHHHcCC-CCHHHHhcCCHHHHHHhhccCCChHHHHHHHHHHHHHHHH----------------------hcCCC
Q 026681           44 DGALQRLLQNGL-HTAEAIDKADEATIKDLIYPVAFYTRKACNMKKIAKICLT----------------------KYDGD  100 (235)
Q Consensus        44 ~~~~~~l~~~~~-pt~~~la~a~~e~l~~~l~~~G~~~~Ka~~l~~~a~~i~~----------------------~~~g~  100 (235)
                      .+.+..|++.++ -++.+|..+..++|.++   -||...++..|.+..+.-.+                      .| ++
T Consensus       435 e~~i~~L~~~G~i~~~~Diy~L~~~~l~~l---~gfgeks~~nll~aIe~sk~~~l~r~l~aLGI~~vG~~~ak~~~-~~  510 (562)
T PRK08097        435 EGTWRALHQTGLFEHLFSWLALTPEQLANT---PGIGKARAEQLWHQFNLARQQPFSRWLKALGIPLPQAALNALDD-RS  510 (562)
T ss_pred             HHHHHHHHHcCCcCCHHHHhcCCHHHHhcC---cCccHHHHHHHHHHHHHHcCCCHHHHHHHcCCccHHHHHHHHhc-CC
Confidence            345666777665 68999999998877665   36766677776555433110                      11 22


Q ss_pred             Ch----hhHHHHHcCCCCcHHHHHHHHHH
Q 026681          101 IP----SSLDELLALPGIGPKMANMVMTL  125 (235)
Q Consensus       101 ~~----~~~~~L~~l~GIG~~tA~~il~~  125 (235)
                      +.    .+.++|.+++|||+.+|+.|..|
T Consensus       511 i~~l~~a~~e~l~~i~gIG~~~a~si~~~  539 (562)
T PRK08097        511 WQQLLSRSEQQWQQLPGIGEGRARQLIAF  539 (562)
T ss_pred             HHHHHcCCHHHHhcCCCchHHHHHHHHHH
Confidence            22    24578999999999999999888

>PRK14350 ligA NAD-dependent DNA ligase LigA; Provisional

Probab=87.31  E-value=3.7  Score=40.49  Aligned_cols=79  Identities=18%  Similarity=0.292  Sum_probs=50.4

Q ss_pred             HHHHHHHHHcCC-CCHHHHhcCCHHHHHHhhccCCChHHHHHHHHHHHHH-------------------------HH-Hh
Q 026681           44 DGALQRLLQNGL-HTAEAIDKADEATIKDLIYPVAFYTRKACNMKKIAKI-------------------------CL-TK   96 (235)
Q Consensus        44 ~~~~~~l~~~~~-pt~~~la~a~~e~l~~~l~~~G~~~~Ka~~l~~~a~~-------------------------i~-~~   96 (235)
                      ...+..|++.++ -++.+|..+..++|.++   =||...++..|.+..+.                         +. ..
T Consensus       446 ~~~i~~L~~~G~i~~~~Dly~L~~~~l~~l---~g~geksa~nl~~~Ie~sk~~~l~r~l~ALGI~~vG~~~ak~La~~~  522 (669)
T PRK14350        446 DKTIEFLFEKKFISSEIDLYTFNFDRLINL---KGFKDKRINNLKRSIEASKKRPFSKLLLSMGIKDLGENTILLLINNN  522 (669)
T ss_pred             HHHHHHHHHcCCcCCHHHHhhCCHHHHhhc---cCccHHHHHHHHHHHHHHhCCCHHHHHHHcCCCchhHHHHHHHHHHh
Confidence            345677777654 46888888887776655   26666666665443322                         22 12


Q ss_pred             cCCCCh----------hhHHHHHcCCCCcHHHHHHHHHHh
Q 026681           97 YDGDIP----------SSLDELLALPGIGPKMANMVMTLG  126 (235)
Q Consensus        97 ~~g~~~----------~~~~~L~~l~GIG~~tA~~il~~~  126 (235)
                      | +.+.          .+.++|++++|||+.+|..+..|-
T Consensus       523 f-~~~~~l~~~~~~~~~~~e~l~~i~giG~~~a~si~~ff  561 (669)
T PRK14350        523 L-NSFDKISTLCQDREFALSKLLKIKGIGEKIALNIIEAF  561 (669)
T ss_pred             h-CCHHHHHhhhhccCCCHHHHhhCCCccHHHHHHHHHHH
Confidence            2 1222          244679999999999999998883

>PRK08609 hypothetical protein; Provisional

Probab=87.19  E-value=1.6  Score=42.27  Aligned_cols=49  Identities=22%  Similarity=0.383  Sum_probs=32.1

Q ss_pred             hccCCChHHHHHHHHHHHHH----HHHhcCCCChhhHHHHHcCCCCcHHHHHHHH
Q 026681           73 IYPVAFYTRKACNMKKIAKI----CLTKYDGDIPSSLDELLALPGIGPKMANMVM  123 (235)
Q Consensus        73 l~~~G~~~~Ka~~l~~~a~~----i~~~~~g~~~~~~~~L~~l~GIG~~tA~~il  123 (235)
                      |.++|  ..=|..|.++.+.    ..++...++|....+|+++|||||++|..+-
T Consensus        53 ipgIG--~~ia~kI~Eil~tG~~~~le~l~~~~p~~~~~l~~i~GiGpk~a~~l~  105 (570)
T PRK08609         53 LKGIG--KGTAEVIQEYRETGESSVLQELKKEVPEGLLPLLKLPGLGGKKIAKLY  105 (570)
T ss_pred             CCCcC--HHHHHHHHHHHHhCChHHHHHHHhhCcHHHHHHhcCCCCCHHHHHHHH
Confidence            34444  3445666666543    1233334677788899999999999997654

>PRK00024 hypothetical protein; Reviewed

Probab=86.48  E-value=1.1  Score=38.08  Aligned_cols=56  Identities=21%  Similarity=0.393  Sum_probs=40.1

Q ss_pred             CCHHHHHHhhccCCChHHHHHHHHHHHHHHHHhcCCCCh----hhHHHHHcCCCCcHHHHHHHH
Q 026681           64 ADEATIKDLIYPVAFYTRKACNMKKIAKICLTKYDGDIP----SSLDELLALPGIGPKMANMVM  123 (235)
Q Consensus        64 a~~e~l~~~l~~~G~~~~Ka~~l~~~a~~i~~~~~g~~~----~~~~~L~~l~GIG~~tA~~il  123 (235)
                      .+..||.+++=..|..   -+....+|+.+.++|++ +.    ...++|.+++|||+..|..++
T Consensus        24 Lsd~ELLa~lL~~g~~---~~~~~~LA~~LL~~fgs-L~~l~~as~~eL~~i~GIG~akA~~L~   83 (224)
T PRK00024         24 LSDAELLAILLRTGTK---GKSVLDLARELLQRFGS-LRGLLDASLEELQSIKGIGPAKAAQLK   83 (224)
T ss_pred             CCHHHHHHHHHcCCCC---CCCHHHHHHHHHHHcCC-HHHHHhCCHHHHhhccCccHHHHHHHH
Confidence            4566777765455553   34667889999988863 43    357899999999999886554

>PF11731 Cdd1: Pathogenicity locus; InterPro: IPR021725 Cdd1 is expressed as part of the pathogenicity locus operon in several different orders of bacteria []

Probab=86.42  E-value=0.76  Score=33.61  Aligned_cols=27  Identities=30%  Similarity=0.452  Sum_probs=22.7

Q ss_pred             hhHHHHHcCCCCcHHHHHHHHHHhcCC
Q 026681          103 SSLDELLALPGIGPKMANMVMTLGWFN  129 (235)
Q Consensus       103 ~~~~~L~~l~GIG~~tA~~il~~~~~~  129 (235)
                      +....|..|||||+.+|.-+...++..
T Consensus         9 ~~~~~L~~iP~IG~a~a~DL~~LGi~s   35 (93)
T PF11731_consen    9 AGLSDLTDIPNIGKATAEDLRLLGIRS   35 (93)
T ss_pred             HHHHHHhcCCCccHHHHHHHHHcCCCC
Confidence            356789999999999999888877754

Many members of the family are annotated as being putative mitomycin resistance proteins but this could not be confirmed.

>smart00483 POLXc DNA polymerase X family

Probab=86.40  E-value=1.9  Score=38.85  Aligned_cols=48  Identities=27%  Similarity=0.393  Sum_probs=33.5

Q ss_pred             CCChHHHHHHHHHHHHHHHHhcCCCChhhHHHHHcCCCCcHHHHHHHHHH
Q 026681           76 VAFYTRKACNMKKIAKICLTKYDGDIPSSLDELLALPGIGPKMANMVMTL  125 (235)
Q Consensus        76 ~G~~~~Ka~~l~~~a~~i~~~~~g~~~~~~~~L~~l~GIG~~tA~~il~~  125 (235)
                      .|=...|..+..++|..|.. +..++.+ .+.|.+|||||+.+|+.|--+
T Consensus        20 ~gen~~k~~ay~~Aa~~i~~-l~~~i~~-~~~l~~lpgIG~~ia~kI~Ei   67 (334)
T smart00483       20 FGENKRKCSYFRKAASVLKS-LPFPINS-MKDLKGLPGIGDKIKKKIEEI   67 (334)
T ss_pred             hcccHHHHHHHHHHHHHHHh-CCCCCCC-HHHHhcCCCccHHHHHHHHHH
Confidence            34334467777777777543 4455543 468999999999999988743

includes vertebrate polymerase beta and terminal deoxynucleotidyltransferases

>COG1555 ComEA DNA uptake protein and related DNA-binding proteins [DNA replication, recombination, and repair]

Probab=85.88  E-value=0.73  Score=36.66  Aligned_cols=23  Identities=52%  Similarity=0.830  Sum_probs=20.8

Q ss_pred             hHHHHHcCCCCcHHHHHHHHHHh
Q 026681          104 SLDELLALPGIGPKMANMVMTLG  126 (235)
Q Consensus       104 ~~~~L~~l~GIG~~tA~~il~~~  126 (235)
                      +.++|..|||||++.|..|..+-
T Consensus        95 s~eeL~~lpgIG~~kA~aIi~yR  117 (149)
T COG1555          95 SAEELQALPGIGPKKAQAIIDYR  117 (149)
T ss_pred             CHHHHHHCCCCCHHHHHHHHHHH
Confidence            57889999999999999999874

>COG1555 ComEA DNA uptake protein and related DNA-binding proteins [DNA replication, recombination, and repair]

Probab=85.62  E-value=1.9  Score=34.28  Aligned_cols=55  Identities=24%  Similarity=0.340  Sum_probs=38.2

Q ss_pred             HhcCCHHHHHHhhccCCChHHHHHHHHHHHHHHHHhcCCCChhhHHHHHcCCCCcHHHHHHHHH
Q 026681           61 IDKADEATIKDLIYPVAFYTRKACNMKKIAKICLTKYDGDIPSSLDELLALPGIGPKMANMVMT  124 (235)
Q Consensus        61 la~a~~e~l~~~l~~~G~~~~Ka~~l~~~a~~i~~~~~g~~~~~~~~L~~l~GIG~~tA~~il~  124 (235)
                      |-.|+.++| +.|.++|-  .||+.|.+--    +++ | .-...+.|...+|||+++.+-...
T Consensus        91 iNtAs~eeL-~~lpgIG~--~kA~aIi~yR----e~~-G-~f~sv~dL~~v~GiG~~~~ekl~~  145 (149)
T COG1555          91 INTASAEEL-QALPGIGP--KKAQAIIDYR----EEN-G-PFKSVDDLAKVKGIGPKTLEKLKD  145 (149)
T ss_pred             ccccCHHHH-HHCCCCCH--HHHHHHHHHH----HHc-C-CCCcHHHHHhccCCCHHHHHHHHh
Confidence            445788888 66677775  4676665532    333 3 336789999999999999876543

>PRK14351 ligA NAD-dependent DNA ligase LigA; Provisional

Probab=84.86  E-value=5.7  Score=39.35  Aligned_cols=77  Identities=18%  Similarity=0.301  Sum_probs=48.8

Q ss_pred             HHHHHHHHcCC-CCHHHHhcCCHHHHHHhhccCCChHHHHHHHHHHHHH-------------------------HHHhcC
Q 026681           45 GALQRLLQNGL-HTAEAIDKADEATIKDLIYPVAFYTRKACNMKKIAKI-------------------------CLTKYD   98 (235)
Q Consensus        45 ~~~~~l~~~~~-pt~~~la~a~~e~l~~~l~~~G~~~~Ka~~l~~~a~~-------------------------i~~~~~   98 (235)
                      +.+..|.+.++ -++.+|..+..++|.++ .  ||...++..|.+..+.                         +...| 
T Consensus       473 k~i~~L~~~g~V~~~~Dl~~L~~~~L~~l-~--g~g~Ksa~~Ll~~Ie~sk~~~l~r~l~ALgIpgIG~~~ak~L~~~F-  548 (689)
T PRK14351        473 ERVQQLVDAGLVESLADLYDLTVADLAEL-E--GWGETSAENLLAELEASREPPLADFLVALGIPEVGPTTARNLAREF-  548 (689)
T ss_pred             HHHHHHHHcCCCCCHHHHHHcCHHHHhcC-c--CcchhHHHHHHHHHHHHccCCHHHHHHHcCCCCcCHHHHHHHHHHh-
Confidence            34566666554 58999999988876554 2  5655556655443222                         22233 


Q ss_pred             CCCh----hhHHHHHcCCCCcHHHHHHHHHH
Q 026681           99 GDIP----SSLDELLALPGIGPKMANMVMTL  125 (235)
Q Consensus        99 g~~~----~~~~~L~~l~GIG~~tA~~il~~  125 (235)
                      +++.    .+.++|.+++|||+++|..|..|
T Consensus       549 ~si~~L~~As~eeL~~i~GIG~k~A~sI~~f  579 (689)
T PRK14351        549 GTFEAIMDADEEALRAVDDVGPTVAEEIREF  579 (689)
T ss_pred             CCHHHHHhCCHHHHhccCCcCHHHHHHHHHH
Confidence            2232    24567888999999999888777

>TIGR01259 comE comEA protein

Probab=84.77  E-value=0.96  Score=34.58  Aligned_cols=22  Identities=55%  Similarity=0.907  Sum_probs=20.3

Q ss_pred             hHHHHHcCCCCcHHHHHHHHHH
Q 026681          104 SLDELLALPGIGPKMANMVMTL  125 (235)
Q Consensus       104 ~~~~L~~l~GIG~~tA~~il~~  125 (235)
                      +.++|.++||||++.|..|+.+
T Consensus        66 ~~~eL~~lpGIG~~~A~~Ii~~   87 (120)
T TIGR01259        66 SLEELQALPGIGPAKAKAIIEY   87 (120)
T ss_pred             CHHHHhcCCCCCHHHHHHHHHH
Confidence            5789999999999999999877

This model describes the ComEA protein in bacteria. The com E locus is obligatory for bacterial cell competence - the process of internalizing the exogenous added DNA. Lesions in the loci has been variously described for the appearance of competence-related pheonotypes and impairment of competence, suggesting their intimate functional role in bacterial transformation.

>PF09171 DUF1886: Domain of unknown function (DUF1886); InterPro: IPR015254 This entry represents a set of known and suspected archaeal N-glycosylase/DNA lyases

Probab=84.66  E-value=0.59  Score=40.25  Aligned_cols=156  Identities=16%  Similarity=0.175  Sum_probs=79.2

Q ss_pred             HHHHhccccHHHHHHHHHHHHHcCCC--CHHHHhcCCHHHHHHhhccC----CChHHHHHHHHHHHHHHHH--------h
Q 026681           31 SALLSSLTKDKVADGALQRLLQNGLH--TAEAIDKADEATIKDLIYPV----AFYTRKACNMKKIAKICLT--------K   96 (235)
Q Consensus        31 ~~iLsqqt~~~~~~~~~~~l~~~~~p--t~~~la~a~~e~l~~~l~~~----G~~~~Ka~~l~~~a~~i~~--------~   96 (235)
                      .++.|-|-+..- ...|..|.+. |.  +++++    .+++.+.+...    -+.+.|.++|.++...+..        .
T Consensus        45 NaLvSYqLs~kG-Ee~W~~Fs~y-fs~~~~~~~----~~~~~~FL~~s~~n~r~~~~KikRl~k~~~~~~~l~l~~~~~~  118 (246)
T PF09171_consen   45 NALVSYQLSGKG-EEYWWEFSEY-FSKRPIEDI----CEAFIEFLSNSKYNRRLLEQKIKRLRKFCPFLENLSLQDNPLY  118 (246)
T ss_dssp             HHHT-SS-TT-H-HHHHHHHHHH-HCTS--SSH----HHHHHHHCCC-TTS-TTHHHHHHHHHHHCCHHHTT-HHHHHHH
T ss_pred             HHHHHHhcCCch-HHHHHHHHHH-HhcCCchhH----HHHHHHHHhhCcchHHHHHHHHHHHHHHHHHHHHhhhhhhhhh
Confidence            456677766543 4566666553 22  12222    46666777643    2456888898888655322        2


Q ss_pred             cCCCChhhHHHHHcCCCCcH---HHHHHHH------HHhcCCc------ceeecchHHHHHHHHhcCcCCCCCCCCCCCH
Q 026681           97 YDGDIPSSLDELLALPGIGP---KMANMVM------TLGWFNV------QGICVDTHVHRICNRLGWVTQPGTKQKTSSP  161 (235)
Q Consensus        97 ~~g~~~~~~~~L~~l~GIG~---~tA~~il------~~~~~~~------~~~pvDt~v~Rv~~Rlg~~~~~~~~~~~~~~  161 (235)
                      | .++...++.|...-|-.+   .++-++-      ..++|..      -.+|||.|+.++..+.|+++...... ..+.
T Consensus       119 y-~~l~~l~~~La~~L~~~~~~KTiVFAvKM~~Ya~r~~~g~~~~~p~~IpIPvD~Rva~~T~~sGi~~~~~~~~-~~~~  196 (246)
T PF09171_consen  119 Y-EDLEELWRELAKILNSKPESKTIVFAVKMFGYACRIAFGEFRPYPEEIPIPVDYRVAKLTKRSGIIECEREEM-MRTR  196 (246)
T ss_dssp             H-CTHHHHHHHHHHHHTS-TTSHHHHHHHHHHHHHHHHHCTS-----TTS-----HHHHHHHHCTTS-SS-HHHH-HCTC
T ss_pred             h-hhHHHHHHHHHHHhCCCCccchhhHHHHHHHHHHHHhcCCCCCCcccCCCCccHHHHHHHHHhccccccHHhh-hccH
Confidence            3 677777777777555443   2233333      3343441      14699999999999999976321100 0222


Q ss_pred             HHHHHHHHHhCCcc--cHHHHHHHHH-HHHhhhcCC
Q 026681          162 EQTREALQRWLPKE--EWVRINPLLV-GFGQTICTP  194 (235)
Q Consensus       162 ~~~~~~l~~~~p~~--~~~~~~~~l~-~~G~~iC~~  194 (235)
                      +.++..+....-..  .+-.++..|+ -+|+.....
T Consensus       197 ~~v~~~W~~Va~~sgIpplhLDs~lW~l~G~~~~~~  232 (246)
T PF09171_consen  197 EEVQKAWREVAKESGIPPLHLDSLLWPLLGRARDVK  232 (246)
T ss_dssp             CHHHHHHHHHHHHHT--HHHHHHHHHHHHCCHHCCT
T ss_pred             HHHHHHHHHHHhhcCCCchhhhhHHHHhcccchhhh
Confidence            33444433221111  2456677888 889887654

These DNA repair enzymes are part of the base excision repair (BER) pathway; they protect from oxidative damage by removing the major product of DNA oxidation, 8-oxoguanine (GO), from single- and double-stranded DNA substrates [].Cleavage of the N-glycosidic bond between the aberrant base and the sugar-phosphate backbone generates an apurinic (AP) site. Subsequently, the phosphodiester bond 3' from the AP site is cleaved by an elimination reaction, leaving a 3'-terminal unsaturated sugar and a product with a terminal 5'-phosphate. The protein contains two alpha-helical subdomains, with the 8-oxoguanine binding site located in a cleft at their interface. A helix-hairpin-helix (HhH) structural motif and a Gly/Pro-rich sequence followed by a conserved Asp (HhH-GPD motif) are present [].; GO: 0003906 DNA-(apurinic or apyrimidinic site) lyase activity, 0016799 hydrolase activity, hydrolyzing N-glycosyl compounds; PDB: 1XQP_A 1XQO_A 1XG7_A.

>PRK07945 hypothetical protein; Provisional

Probab=84.58  E-value=1.9  Score=38.81  Aligned_cols=58  Identities=24%  Similarity=0.328  Sum_probs=37.3

Q ss_pred             HHHHHhhccCCChHHHHHHHHHHHHHHHHhcCCC-ChhhHH--HHHcCCCCcHHHHHHHHHH
Q 026681           67 ATIKDLIYPVAFYTRKACNMKKIAKICLTKYDGD-IPSSLD--ELLALPGIGPKMANMVMTL  125 (235)
Q Consensus        67 e~l~~~l~~~G~~~~Ka~~l~~~a~~i~~~~~g~-~~~~~~--~L~~l~GIG~~tA~~il~~  125 (235)
                      +++..+|.-.|=..-|++.-+++|+.|.. .+.+ +.+..+  .|.+|||||+-+|..|.-+
T Consensus         8 ~~~a~lle~~~~n~frv~ayr~aa~~~~~-~~~~~~~~~~~~g~l~~~~giG~~~a~~i~e~   68 (335)
T PRK07945          8 RRIAFLLERARADTYRVRAFRRAADVVEA-LDAAERARRARAGSLTSLPGIGPKTAKVIAQA   68 (335)
T ss_pred             HHHHHHHHHcCCChhhHHHHHHHHHHHHh-cChhHHHHHHhcCCcccCCCcCHHHHHHHHHH
Confidence            34444444445444477888888888644 3333 333222  5889999999999988754

>TIGR00084 ruvA Holliday junction DNA helicase, RuvA subunit

Probab=84.42  E-value=0.91  Score=37.60  Aligned_cols=23  Identities=30%  Similarity=0.645  Sum_probs=19.4

Q ss_pred             hhHHHHHcCCCCcHHHHHHHHHH
Q 026681          103 SSLDELLALPGIGPKMANMVMTL  125 (235)
Q Consensus       103 ~~~~~L~~l~GIG~~tA~~il~~  125 (235)
                      +.+..|++++||||++|-.+|..
T Consensus        69 ~lF~~L~~V~GIGpK~Al~iL~~   91 (191)
T TIGR00084        69 ELFKELIKVNGVGPKLALAILSN   91 (191)
T ss_pred             HHHHHHhCCCCCCHHHHHHHHhc
Confidence            35688999999999999888653

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

>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional

Probab=84.00  E-value=0.99  Score=37.49  Aligned_cols=23  Identities=30%  Similarity=0.663  Sum_probs=20.0

Q ss_pred             hhHHHHHcCCCCcHHHHHHHHHH
Q 026681          103 SSLDELLALPGIGPKMANMVMTL  125 (235)
Q Consensus       103 ~~~~~L~~l~GIG~~tA~~il~~  125 (235)
                      +.++.|.+++||||++|-.|+..
T Consensus        70 ~lF~~Li~V~GIGpK~Al~ILs~   92 (194)
T PRK14605         70 SLFETLIDVSGIGPKLGLAMLSA   92 (194)
T ss_pred             HHHHHHhCCCCCCHHHHHHHHHh
Confidence            35688999999999999999874

>PF11798 IMS_HHH: IMS family HHH motif; InterPro: IPR024728 This helix-hairpin-helix motif is found in proteins belonging to the type-Y family of DNA polymerases []

Probab=83.96  E-value=0.75  Score=26.66  Aligned_cols=15  Identities=33%  Similarity=0.445  Sum_probs=11.4

Q ss_pred             HHcCCCCcHHHHHHH
Q 026681          108 LLALPGIGPKMANMV  122 (235)
Q Consensus       108 L~~l~GIG~~tA~~i  122 (235)
                      +.+++|||++|+.-+
T Consensus        13 i~~~~GIG~kt~~kL   27 (32)
T PF11798_consen   13 IRKFWGIGKKTAKKL   27 (32)
T ss_dssp             GGGSTTS-HHHHHHH
T ss_pred             HHhhCCccHHHHHHH
Confidence            457899999999764

This type of polymerases are thought to be involved in UV protection and mutation [, ]. ; PDB: 3PZP_B 2OH2_B 2W7O_B 3IN5_B 1T94_A 2W7P_B 2W8K_A 2AGQ_A 1RYR_A 3RAX_A ....

>COG1796 POL4 DNA polymerase IV (family X) [DNA replication, recombination, and repair]

Probab=83.83  E-value=2.1  Score=38.18  Aligned_cols=56  Identities=23%  Similarity=0.240  Sum_probs=39.0

Q ss_pred             HHHhhccCCChHHHHHHHHHHHHHHHHhcCCCChhhHHH--HHcCCCCcHHHHHHHHHH
Q 026681           69 IKDLIYPVAFYTRKACNMKKIAKICLTKYDGDIPSSLDE--LLALPGIGPKMANMVMTL  125 (235)
Q Consensus        69 l~~~l~~~G~~~~Ka~~l~~~a~~i~~~~~g~~~~~~~~--L~~l~GIG~~tA~~il~~  125 (235)
                      +...+.-.|=..-|+..-+.+|+.+. .-+-+++...+.  ++.|||||+.+|+.|.-+
T Consensus        15 iA~~me~~Gen~fk~~aYr~Aa~sle-~~~e~~~ei~e~~~~t~l~gIGk~ia~~I~e~   72 (326)
T COG1796          15 IADYMELEGENPFKIRAYRKAAQSLE-NLTEDLEEIEERGRLTELPGIGKGIAEKISEY   72 (326)
T ss_pred             HHHHHHhcCCCccchHHHHHHHHhhh-hcccchHHHHhhcccCCCCCccHHHHHHHHHH
Confidence            33333333433346777777788754 345678887777  999999999999999854

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

Probab=83.72  E-value=1.2  Score=28.91  Aligned_cols=22  Identities=27%  Similarity=0.380  Sum_probs=16.4

Q ss_pred             HHHHcCCCCcHHHHHHHHHHhc
Q 026681          106 DELLALPGIGPKMANMVMTLGW  127 (235)
Q Consensus       106 ~~L~~l~GIG~~tA~~il~~~~  127 (235)
                      +.++.+.|||+.||.-....++
T Consensus         2 ~~f~~I~GVG~~tA~~w~~~G~   23 (52)
T PF10391_consen    2 KLFTGIWGVGPKTARKWYAKGI   23 (52)
T ss_dssp             HHHHTSTT--HHHHHHHHHTT-
T ss_pred             cchhhcccccHHHHHHHHHhCC
Confidence            5788999999999998887665

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

>TIGR01259 comE comEA protein

Probab=83.62  E-value=2.8  Score=32.00  Aligned_cols=61  Identities=23%  Similarity=0.303  Sum_probs=40.5

Q ss_pred             CCHHHHhcCCHHHHHHhhccCCChHHHHHHHHHHHHHHHHhcCCCChhhHHHHHcCCCCcHHHHHHHHHH
Q 026681           56 HTAEAIDKADEATIKDLIYPVAFYTRKACNMKKIAKICLTKYDGDIPSSLDELLALPGIGPKMANMVMTL  125 (235)
Q Consensus        56 pt~~~la~a~~e~l~~~l~~~G~~~~Ka~~l~~~a~~i~~~~~g~~~~~~~~L~~l~GIG~~tA~~il~~  125 (235)
                      ..+-.|-.++.++|..+ .++|  ..+|+.|.+--..     .|.+ ...++|..++|||+++++-+..+
T Consensus        57 ~~~iniNtA~~~eL~~l-pGIG--~~~A~~Ii~~R~~-----~g~f-~s~eeL~~V~GIg~k~~~~i~~~  117 (120)
T TIGR01259        57 LAAVNINAASLEELQAL-PGIG--PAKAKAIIEYREE-----NGAF-KSVDDLTKVSGIGEKSLEKLKDY  117 (120)
T ss_pred             CCCEeCCcCCHHHHhcC-CCCC--HHHHHHHHHHHHh-----cCCc-CCHHHHHcCCCCCHHHHHHHHhc
Confidence            34555667888888764 4444  4566666543222     1333 56899999999999999887654

This model describes the ComEA protein in bacteria. The com E locus is obligatory for bacterial cell competence - the process of internalizing the exogenous added DNA. Lesions in the loci has been variously described for the appearance of competence-related pheonotypes and impairment of competence, suggesting their intimate functional role in bacterial transformation.

>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional

Probab=83.37  E-value=0.98  Score=37.63  Aligned_cols=23  Identities=35%  Similarity=0.634  Sum_probs=19.7

Q ss_pred             hhHHHHHcCCCCcHHHHHHHHHH
Q 026681          103 SSLDELLALPGIGPKMANMVMTL  125 (235)
Q Consensus       103 ~~~~~L~~l~GIG~~tA~~il~~  125 (235)
                      +.++.|.++.||||++|=.||+.
T Consensus        69 ~lF~~LisVsGIGPK~ALaILs~   91 (196)
T PRK13901         69 EVFEELIGVDGIGPRAALRVLSG   91 (196)
T ss_pred             HHHHHHhCcCCcCHHHHHHHHcC
Confidence            35788999999999999999853

>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional

Probab=82.97  E-value=0.99  Score=37.19  Aligned_cols=23  Identities=30%  Similarity=0.421  Sum_probs=19.7

Q ss_pred             hhHHHHHcCCCCcHHHHHHHHHH
Q 026681          103 SSLDELLALPGIGPKMANMVMTL  125 (235)
Q Consensus       103 ~~~~~L~~l~GIG~~tA~~il~~  125 (235)
                      +.++.|.++.|||||+|=.+|+.
T Consensus        70 ~lF~~Li~VsGIGpK~Al~ILs~   92 (183)
T PRK14601         70 KMFEMLLKVNGIGANTAMAVCSS   92 (183)
T ss_pred             HHHHHHhccCCccHHHHHHHHcC
Confidence            35788999999999999988854

>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional

Probab=82.75  E-value=0.99  Score=37.60  Aligned_cols=23  Identities=30%  Similarity=0.641  Sum_probs=19.8

Q ss_pred             hhHHHHHcCCCCcHHHHHHHHHH
Q 026681          103 SSLDELLALPGIGPKMANMVMTL  125 (235)
Q Consensus       103 ~~~~~L~~l~GIG~~tA~~il~~  125 (235)
                      +.++.|+++.||||++|=.+|..
T Consensus        69 ~lF~~L~~V~GIGpK~AL~iLs~   91 (197)
T PRK14603         69 ELFELLLGVSGVGPKLALALLSA   91 (197)
T ss_pred             HHHHHHhCcCCcCHHHHHHHHcC
Confidence            35678999999999999999873

>COG1415 Uncharacterized conserved protein [Function unknown]

Probab=82.42  E-value=3.3  Score=37.31  Aligned_cols=70  Identities=20%  Similarity=0.278  Sum_probs=47.8

Q ss_pred             hhhHHHHHcCCCCcHHHHHHHHHH---hcCCcceeecchHHHHHHHHhcCcCCCCCCCCCCCHHHHHHHHHHhCCc
Q 026681          102 PSSLDELLALPGIGPKMANMVMTL---GWFNVQGICVDTHVHRICNRLGWVTQPGTKQKTSSPEQTREALQRWLPK  174 (235)
Q Consensus       102 ~~~~~~L~~l~GIG~~tA~~il~~---~~~~~~~~pvDt~v~Rv~~Rlg~~~~~~~~~~~~~~~~~~~~l~~~~p~  174 (235)
                      |.++++|+-.|||||.|+-++.+.   .+|.+..+ -|--  +.+.-+|+-+.-..+....+|+++-+++++.+..
T Consensus       274 p~Df~elLl~~GiGpstvRALalVAEvIyg~~~s~-rDP~--~yafA~GGKDgvP~pV~~~~yde~I~~l~~~ve~  346 (373)
T COG1415         274 PDDFEELLLVPGIGPSTVRALALVAEVIYGEPPSF-RDPV--KYAFAVGGKDGVPFPVNRKTYDELIEFLEELVEK  346 (373)
T ss_pred             cccHHHHHhccCCCHHHHHHHHHHHHHHhCCCCCc-CCch--hhhhhhcCCCCCCCCcchhhHHHHHHHHHHHHHh
Confidence            568899999999999999887765   45544333 1211  2666677655444555677888888888777654

>PRK00024 hypothetical protein; Reviewed

Probab=82.23  E-value=4.7  Score=34.23  Aligned_cols=62  Identities=24%  Similarity=0.268  Sum_probs=48.0

Q ss_pred             HHHHHHHHhccccHHHHHHHHHHHHHcCCCCHHHHhcCCHHHHHHhhccCCChHHHHHHHHHHHHH
Q 026681           27 AVLLSALLSSLTKDKVADGALQRLLQNGLHTAEAIDKADEATIKDLIYPVAFYTRKACNMKKIAKI   92 (235)
Q Consensus        27 ~~lv~~iLsqqt~~~~~~~~~~~l~~~~~pt~~~la~a~~e~l~~~l~~~G~~~~Ka~~l~~~a~~   92 (235)
                      ..|++.+|..-+....+....++|.+ .|.+...+..++.++|.++ .++|  ..||..|..+.+.
T Consensus        27 ~ELLa~lL~~g~~~~~~~~LA~~LL~-~fgsL~~l~~as~~eL~~i-~GIG--~akA~~L~a~~El   88 (224)
T PRK00024         27 AELLAILLRTGTKGKSVLDLARELLQ-RFGSLRGLLDASLEELQSI-KGIG--PAKAAQLKAALEL   88 (224)
T ss_pred             HHHHHHHHcCCCCCCCHHHHHHHHHH-HcCCHHHHHhCCHHHHhhc-cCcc--HHHHHHHHHHHHH
Confidence            34778888888888888889999998 4999999999999999875 5555  4567666544433

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

Probab=81.85  E-value=1.2  Score=26.56  Aligned_cols=16  Identities=38%  Similarity=0.609  Sum_probs=12.9

Q ss_pred             HcCCCCcHHHHHHHHH
Q 026681          109 LALPGIGPKMANMVMT  124 (235)
Q Consensus       109 ~~l~GIG~~tA~~il~  124 (235)
                      -.+||||+++|.-++.
T Consensus        19 ~Gv~giG~ktA~~ll~   34 (36)
T smart00279       19 PGVKGIGPKTALKLLR   34 (36)
T ss_pred             CCCCcccHHHHHHHHH
Confidence            3689999999987663

>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional

Probab=81.62  E-value=1.1  Score=37.00  Aligned_cols=23  Identities=22%  Similarity=0.313  Sum_probs=19.5

Q ss_pred             hhHHHHHcCCCCcHHHHHHHHHH
Q 026681          103 SSLDELLALPGIGPKMANMVMTL  125 (235)
Q Consensus       103 ~~~~~L~~l~GIG~~tA~~il~~  125 (235)
                      +.++.|.++.||||++|=.+|..
T Consensus        70 ~lF~~Li~V~GIGpK~AL~iLs~   92 (188)
T PRK14606         70 ELFLSLTKVSRLGPKTALKIISN   92 (188)
T ss_pred             HHHHHHhccCCccHHHHHHHHcC
Confidence            35688999999999999998853

>cd00141 NT_POLXc Nucleotidyltransferase (NT) domain of family X DNA Polymerases

Probab=81.58  E-value=3.2  Score=36.88  Aligned_cols=42  Identities=31%  Similarity=0.449  Sum_probs=30.7

Q ss_pred             HHHHHHHHHHHHHHhcCCCChhhHHHHHcCCCCcHHHHHHHHHH
Q 026681           82 KACNMKKIAKICLTKYDGDIPSSLDELLALPGIGPKMANMVMTL  125 (235)
Q Consensus        82 Ka~~l~~~a~~i~~~~~g~~~~~~~~L~~l~GIG~~tA~~il~~  125 (235)
                      |++.-..+|..|.. +.-++. ..+++.+|||||+.+|+.|--+
T Consensus        23 r~~aY~~Aa~~l~~-l~~~i~-~~~~~~~ipgiG~~ia~kI~E~   64 (307)
T cd00141          23 RVRAYRKAARALES-LPEPIE-SLEEAKKLPGIGKKIAEKIEEI   64 (307)
T ss_pred             hHHHHHHHHHHHHh-CCcccC-CHHHhcCCCCccHHHHHHHHHH
Confidence            67777777777644 444443 3567899999999999998755

X family polymerases fill in short gaps during DNA repair. They are relatively inaccurate enzymes and play roles in base excision repair, in non-homologous end joining (NHEJ) which acts mainly to repair damage due to ionizing radiation, and in V(D)J recombination. This family includes eukaryotic Pol beta, Pol lambda, Pol mu, and terminal deoxyribonucleotidyl transferase (TdT). Pol beta and Pol lambda are primarily DNA template-dependent polymerases. TdT is a DNA template-independent polymerase. Pol mu has both template dependent and template independent activities. This subgroup belongs to the Pol beta-like NT superfamily. In the majority of enzymes in this superfamily, two carboxylates, Dx[D/E], together with a third more distal carboxylate, coordinate two divalent metal cations involved in a two-metal ion mechanism of nucleotide addition. These three carboxylate residues are fairly well conserved in this

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	235
1orn_A	226	Structure Of A Trapped Endonuclease Iii-Dna Covalen		4e-19
1p59_A	226	Structure Of A Non-Covalent Endonuclease Iii-Dna Co		7e-19
2abk_A	211	Refinement Of The Native Structure Of Endonuclease		5e-18
3fsp_A	369	Muty Adenine Glycosylase Bound To A Transition Stat		1e-13
3g0q_A	352	Crystal Structure Of Muty Bound To Its Inhibitor Dn		2e-13
1rrs_A	369	Muty Adenine Glycosylase In Complex With Dna Contai		5e-13
1rrq_A	369	Muty Adenine Glycosylase In Complex With Dna Contai		6e-13
1kea_A	221	Structure Of A Thermostable Thymine-Dna Glycosylase		3e-09
1kg5_A	225	Crystal Structure Of The K142q Mutant Of E.Coli Mut		1e-08
1kg7_A	225	Crystal Structure Of The E161a Mutant Of E.coli Mut		2e-08
1kg6_A	225	Crystal Structure Of The K142r Mutant Of E.Coli Mut		2e-08
1wef_A	225	Catalytic Domain Of Muty From Escherichia Coli K20a		2e-08
1muy_A	225	Catalytic Domain Of Muty From Escherichia Coli Leng		2e-08
1kg4_A	225	Crystal Structure Of The K142a Mutant Of E. Coli Mu		2e-08
1mud_A	225	Catalytic Domain Of Muty From Escherichia Coli, D13		8e-08
1kqj_A	225	Crystal Structure Of A Mutant Of Muty Catalytic Dom		3e-07
3n5n_X	287	Crystal Structure Analysis Of The Catalytic Domain		1e-05

>pdb|1ORN|A Chain A, Structure Of A Trapped Endonuclease Iii-Dna Covalent Intermediate: Estranged-Guanine Complex Length = 226

Iteration: 1
 Score = 91.7 bits (226), Expect = 4e-19,   Method: Compositional matrix adjust.
 Identities = 47/136 (34%), Positives = 75/136 (55%), Gaps = 7/136 (5%)
Query: 73  IYPVAFYTRKACNMKKIAKICLTKYDGDIPSSLDELLALPGIGPKMANMVMTLGWFNVQG 132
           I  +  Y  KA N++K+  + + KY+G++P   DEL+ LPG+G K AN+V+++  F V  
Sbjct: 80  IRSIGLYRNKARNIQKLCAMLIDKYNGEVPRDRDELMKLPGVGRKTANVVVSVA-FGVPA 138
Query: 133 ICVDTHVHRICNRLGWVTQPGTKQKTSSPEQTREALQRWLPKEEWVRINPLLVGFGQTIC 192
           I VDTHV R+  RLG+       +   S  +  + L + +PKEEW   +  ++ FG+  C
Sbjct: 139 IAVDTHVERVSKRLGFC------RWDDSVLEVEKTLMKIIPKEEWSITHHRMIFFGRYHC 192
Query: 193 TPLRPRCGMCTVSEYC 208
               P+C  C +   C
Sbjct: 193 KAQSPQCPSCPLLHLC 208

>pdb|1P59|A Chain A, Structure Of A Non-Covalent Endonuclease Iii-Dna Complex Length = 226

Iteration: 1
 Score = 90.5 bits (223), Expect = 7e-19,   Method: Compositional matrix adjust.
 Identities = 47/136 (34%), Positives = 74/136 (54%), Gaps = 7/136 (5%)
Query: 73  IYPVAFYTRKACNMKKIAKICLTKYDGDIPSSLDELLALPGIGPKMANMVMTLGWFNVQG 132
           I  +  Y  KA N++K+  + + KY+G++P   DEL+ LPG+G K AN+V++   F V  
Sbjct: 80  IRSIGLYRNKARNIQKLCAMLIDKYNGEVPRDRDELMKLPGVGRKTANVVVSTA-FGVPA 138
Query: 133 ICVDTHVHRICNRLGWVTQPGTKQKTSSPEQTREALQRWLPKEEWVRINPLLVGFGQTIC 192
           I VDTHV R+  RLG+       +   S  +  + L + +PKEEW   +  ++ FG+  C
Sbjct: 139 IAVDTHVERVSKRLGFC------RWDDSVLEVEKTLMKIIPKEEWSITHHRMIFFGRYHC 192
Query: 193 TPLRPRCGMCTVSEYC 208
               P+C  C +   C
Sbjct: 193 KAQSPQCPSCPLLHLC 208

>pdb|2ABK|A Chain A, Refinement Of The Native Structure Of Endonuclease Iii To A Resolution Of 1.85 Angstrom Length = 211

Iteration: 1
 Score = 87.8 bits (216), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 50/142 (35%), Positives = 74/142 (52%), Gaps = 12/142 (8%)
Query: 69  IKDLIYPVAFYTRKACNMKKIAKICLTKYDGDIPSSLDELLALPGIGPKMANMVMT--LG 126
           +K  I  +  Y  KA N+ K  +I L +++G++P     L ALPG+G K AN+V+    G
Sbjct: 72  VKTYIKTIGLYNSKAENIIKTCRILLEQHNGEVPEDRAALEALPGVGRKTANVVLNTAFG 131
Query: 127 WFNVQGICVDTHVHRICNRLGWVTQPGTKQKTSSPEQTREALQRWLPKEEWVRINPLLVG 186
           W     I VDTH+ R+CNR  +   PG      + EQ  E L + +P E  V  +  L+ 
Sbjct: 132 W---PTIAVDTHIFRVCNRTQFA--PG-----KNVEQVEEKLLKVVPAEFKVDCHHWLIL 181
Query: 187 FGQTICTPLRPRCGMCTVSEYC 208
            G+  C   +PRCG C + + C
Sbjct: 182 HGRYTCIARKPRCGSCIIEDLC 203

>pdb|3FSP|A Chain A, Muty Adenine Glycosylase Bound To A Transition State Analog (1n) Paired With Dg In Duplexed Dna Length = 369

Iteration: 1
 Score = 72.8 bits (177), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 47/152 (30%), Positives = 72/152 (47%), Gaps = 4/152 (2%)
Query: 57  TAEAIDKADEATIKDLIYPVAFYTRKACNMKKIAKICLTKYDGDIPSSLDELLALPGIGP 116
           T EA+  ADE  +      + +Y+R   N+    K   T+Y G +P   DE   L G+GP
Sbjct: 70  TLEALADADEDEVLKAWEGLGYYSR-VRNLHAAVKEVKTRYGGKVPDDPDEFSRLKGVGP 128
Query: 117 KMANMVMTLGWFNVQGICVDTHVHRICNRLGWVTQPGTKQKTSSPEQTREALQRWLPKEE 176
                V++L  + V    VD +V R+ +RL  VT      K S+ ++  + ++  +  E 
Sbjct: 129 YTVGAVLSLA-YGVPEPAVDGNVMRVLSRLFLVTD--DIAKPSTRKRFEQIVREIMAYEN 185
Query: 177 WVRINPLLVGFGQTICTPLRPRCGMCTVSEYC 208
               N  L+  G  +CTP RP C +C V  YC
Sbjct: 186 PGAFNEALIELGALVCTPRRPSCLLCPVQAYC 217

>pdb|3G0Q|A Chain A, Crystal Structure Of Muty Bound To Its Inhibitor Dna Length = 352

Iteration: 1
 Score = 72.4 bits (176), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 47/152 (30%), Positives = 72/152 (47%), Gaps = 4/152 (2%)
Query: 57  TAEAIDKADEATIKDLIYPVAFYTRKACNMKKIAKICLTKYDGDIPSSLDELLALPGIGP 116
           T EA+  ADE  +      + +Y+R   N+    K   T+Y G +P   DE   L G+GP
Sbjct: 59  TLEALADADEDEVLKAWEGLGYYSR-VRNLHAAVKEVKTRYGGKVPDDPDEFSRLKGVGP 117
Query: 117 KMANMVMTLGWFNVQGICVDTHVHRICNRLGWVTQPGTKQKTSSPEQTREALQRWLPKEE 176
                V++L  + V    VD +V R+ +RL  VT      K S+ ++  + ++  +  E 
Sbjct: 118 YTVGAVLSLA-YGVPEPAVDGNVMRVLSRLFLVTD--DIAKCSTRKRFEQIVREIMAYEN 174
Query: 177 WVRINPLLVGFGQTICTPLRPRCGMCTVSEYC 208
               N  L+  G  +CTP RP C +C V  YC
Sbjct: 175 PGAFNEALIELGALVCTPRRPSCLLCPVQAYC 206

>pdb|1RRS|A Chain A, Muty Adenine Glycosylase In Complex With Dna Containing An Abasic Site Length = 369

Iteration: 1
 Score = 71.2 bits (173), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 46/152 (30%), Positives = 72/152 (47%), Gaps = 4/152 (2%)
Query: 57  TAEAIDKADEATIKDLIYPVAFYTRKACNMKKIAKICLTKYDGDIPSSLDELLALPGIGP 116
           T EA+  ADE  +      + +Y+R   N+    K   T+Y G +P   DE   L G+GP
Sbjct: 70  TLEALADADEDEVLKAWEGLGYYSR-VRNLHAAVKEVKTRYGGKVPDDPDEFSRLKGVGP 128
Query: 117 KMANMVMTLGWFNVQGICVDTHVHRICNRLGWVTQPGTKQKTSSPEQTREALQRWLPKEE 176
                V++L  + V    V+ +V R+ +RL  VT      K S+ ++  + ++  +  E 
Sbjct: 129 YTVGAVLSLA-YGVPEPAVNGNVMRVLSRLFLVTD--DIAKPSTRKRFEQIVREIMAYEN 185
Query: 177 WVRINPLLVGFGQTICTPLRPRCGMCTVSEYC 208
               N  L+  G  +CTP RP C +C V  YC
Sbjct: 186 PGAFNEALIELGALVCTPRRPSCLLCPVQAYC 217

>pdb|1RRQ|A Chain A, Muty Adenine Glycosylase In Complex With Dna Containing An A:oxog Pair Length = 369

Iteration: 1
 Score = 70.9 bits (172), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 46/152 (30%), Positives = 72/152 (47%), Gaps = 4/152 (2%)
Query: 57  TAEAIDKADEATIKDLIYPVAFYTRKACNMKKIAKICLTKYDGDIPSSLDELLALPGIGP 116
           T EA+  ADE  +      + +Y+R   N+    K   T+Y G +P   DE   L G+GP
Sbjct: 70  TLEALADADEDEVLKAWEGLGYYSR-VRNLHAAVKEVKTRYGGKVPDDPDEFSRLKGVGP 128
Query: 117 KMANMVMTLGWFNVQGICVDTHVHRICNRLGWVTQPGTKQKTSSPEQTREALQRWLPKEE 176
                V++L  + V    V+ +V R+ +RL  VT      K S+ ++  + ++  +  E 
Sbjct: 129 YTVGAVLSLA-YGVPEPAVNGNVMRVLSRLFLVTD--DIAKCSTRKRFEQIVREIMAYEN 185
Query: 177 WVRINPLLVGFGQTICTPLRPRCGMCTVSEYC 208
               N  L+  G  +CTP RP C +C V  YC
Sbjct: 186 PGAFNEALIELGALVCTPRRPSCLLCPVQAYC 217

>pdb|1KEA|A Chain A, Structure Of A Thermostable Thymine-Dna Glycosylase Length = 221

Iteration: 1
 Score = 58.5 bits (140), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 39/150 (26%), Positives = 67/150 (44%), Gaps = 4/150 (2%)
Query: 59  EAIDKADEATIKDLIYPVAFYTRKACNMKKIAKICLTKYDGDIPSSLDELLALPGIGPKM 118
           E I K  ++ I   I  +    ++A  +K++A++ +  Y G +P +   +L LPG+G   
Sbjct: 68  EDILKTPKSEIAKDIKEIGLSNQRAEQLKELARVVINDYGGRVPRNRKAILDLPGVGKYT 127
Query: 119 ANMVMTLGWFNVQGICVDTHVHRICNRLGWVTQPGTKQKTSSPEQTREALQRWLPKEEWV 178
              VM L  F  +   VD +  R+ NR    +         +  +  E L   +P  +  
Sbjct: 128 CAAVMCLA-FGKKAAMVDANFVRVINRYFGGSYENLNYNHKALWELAETL---VPGGKCR 183
Query: 179 RINPLLVGFGQTICTPLRPRCGMCTVSEYC 208
             N  L+ F   IC P +P+C  C +S+ C
Sbjct: 184 DFNLGLMDFSAIICAPRKPKCEKCGMSKLC 213

>pdb|1KG5|A Chain A, Crystal Structure Of The K142q Mutant Of E.Coli Muty (Core Fragment) Length = 225

Iteration: 1
 Score = 56.2 bits (134), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 38/137 (27%), Positives = 62/137 (45%), Gaps = 11/137 (8%)
Query: 79  YTRKACNMKKIAKICLTKYDGDIPSSLDELLALPGIGPKMANMVMTLGWFNVQGICVDTH 138
           Y  +A N+ K A+   T + G  P + +E+ ALPG+G   A  +++L         +D +
Sbjct: 82  YYARARNLHKAAQQVATLHGGKFPETFEEVAALPGVGRSTAGAILSLS-LGKHFPILDGN 140
Query: 139 VHRICNRL----GWVTQPGTKQKTSSPEQTREALQRWLPKEEWVRINPLLVGFGQTICTP 194
           V R+  R     GW   PG K+  +      E +    P     R N  ++  G  ICT 
Sbjct: 141 VQRVLARCYAVSGW---PGKKEVENKLWSLSEQVT---PAVGVERFNQAMMDLGAMICTR 194
Query: 195 LRPRCGMCTVSEYCPSA 211
            +P+C +C +   C +A
Sbjct: 195 SKPKCSLCPLQNGCIAA 211

>pdb|1KG7|A Chain A, Crystal Structure Of The E161a Mutant Of E.coli Muty (core Fragment) Length = 225

Iteration: 1
 Score = 56.2 bits (134), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 38/137 (27%), Positives = 62/137 (45%), Gaps = 11/137 (8%)
Query: 79  YTRKACNMKKIAKICLTKYDGDIPSSLDELLALPGIGPKMANMVMTLGWFNVQGICVDTH 138
           Y  +A N+ K A+   T + G  P + +E+ ALPG+G   A  +++L         +D +
Sbjct: 82  YYARARNLHKAAQQVATLHGGKFPETFEEVAALPGVGRSTAGAILSLS-LGKHFPILDGN 140
Query: 139 VHRICNRL----GWVTQPGTKQKTSSPEQTREALQRWLPKEEWVRINPLLVGFGQTICTP 194
           V R+  R     GW   PG K+  +      E +    P     R N  ++  G  ICT 
Sbjct: 141 VKRVLARCYAVSGW---PGKKEVANKLWSLSEQVT---PAVGVERFNQAMMDLGAMICTR 194
Query: 195 LRPRCGMCTVSEYCPSA 211
            +P+C +C +   C +A
Sbjct: 195 SKPKCSLCPLQNGCIAA 211

>pdb|1KG6|A Chain A, Crystal Structure Of The K142r Mutant Of E.Coli Muty (Core Fragment) Length = 225

Iteration: 1
 Score = 55.8 bits (133), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 38/137 (27%), Positives = 62/137 (45%), Gaps = 11/137 (8%)
Query: 79  YTRKACNMKKIAKICLTKYDGDIPSSLDELLALPGIGPKMANMVMTLGWFNVQGICVDTH 138
           Y  +A N+ K A+   T + G  P + +E+ ALPG+G   A  +++L         +D +
Sbjct: 82  YYARARNLHKAAQQVATLHGGKFPETFEEVAALPGVGRSTAGAILSLS-LGKHFPILDGN 140
Query: 139 VHRICNRL----GWVTQPGTKQKTSSPEQTREALQRWLPKEEWVRINPLLVGFGQTICTP 194
           V R+  R     GW   PG K+  +      E +    P     R N  ++  G  ICT 
Sbjct: 141 VRRVLARCYAVSGW---PGKKEVENKLWSLSEQVT---PAVGVERFNQAMMDLGAMICTR 194
Query: 195 LRPRCGMCTVSEYCPSA 211
            +P+C +C +   C +A
Sbjct: 195 SKPKCSLCPLQNGCIAA 211

>pdb|1WEF|A Chain A, Catalytic Domain Of Muty From Escherichia Coli K20a Mutant Length = 225

Iteration: 1
 Score = 55.8 bits (133), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 38/137 (27%), Positives = 62/137 (45%), Gaps = 11/137 (8%)
Query: 79  YTRKACNMKKIAKICLTKYDGDIPSSLDELLALPGIGPKMANMVMTLGWFNVQGICVDTH 138
           Y  +A N+ K A+   T + G  P + +E+ ALPG+G   A  +++L         +D +
Sbjct: 82  YYARARNLHKAAQQVATLHGGKFPETFEEVAALPGVGRSTAGAILSLS-LGKHFPILDGN 140
Query: 139 VHRICNRL----GWVTQPGTKQKTSSPEQTREALQRWLPKEEWVRINPLLVGFGQTICTP 194
           V R+  R     GW   PG K+  +      E +    P     R N  ++  G  ICT 
Sbjct: 141 VKRVLARCYAVSGW---PGKKEVENKLWSLSEQVT---PAVGVERFNQAMMDLGAMICTR 194
Query: 195 LRPRCGMCTVSEYCPSA 211
            +P+C +C +   C +A
Sbjct: 195 SKPKCSLCPLQNGCIAA 211

>pdb|1MUY|A Chain A, Catalytic Domain Of Muty From Escherichia Coli Length = 225

Iteration: 1
 Score = 55.5 bits (132), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 38/137 (27%), Positives = 62/137 (45%), Gaps = 11/137 (8%)
Query: 79  YTRKACNMKKIAKICLTKYDGDIPSSLDELLALPGIGPKMANMVMTLGWFNVQGICVDTH 138
           Y  +A N+ K A+   T + G  P + +E+ ALPG+G   A  +++L         +D +
Sbjct: 82  YYARARNLHKAAQQVATLHGGKFPETFEEVAALPGVGRSTAGAILSLS-LGKHFPILDGN 140
Query: 139 VHRICNRL----GWVTQPGTKQKTSSPEQTREALQRWLPKEEWVRINPLLVGFGQTICTP 194
           V R+  R     GW   PG K+  +      E +    P     R N  ++  G  ICT 
Sbjct: 141 VKRVLARCYAVSGW---PGKKEVENKLWSLSEQVT---PAVGVERFNQAMMDLGAMICTR 194
Query: 195 LRPRCGMCTVSEYCPSA 211
            +P+C +C +   C +A
Sbjct: 195 SKPKCSLCPLQNGCIAA 211

>pdb|1KG4|A Chain A, Crystal Structure Of The K142a Mutant Of E. Coli Muty (Core Fragment) Length = 225

Iteration: 1
 Score = 55.5 bits (132), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 38/137 (27%), Positives = 62/137 (45%), Gaps = 11/137 (8%)
Query: 79  YTRKACNMKKIAKICLTKYDGDIPSSLDELLALPGIGPKMANMVMTLGWFNVQGICVDTH 138
           Y  +A N+ K A+   T + G  P + +E+ ALPG+G   A  +++L         +D +
Sbjct: 82  YYARARNLHKAAQQVATLHGGKFPETFEEVAALPGVGRSTAGAILSLS-LGKHFPILDGN 140
Query: 139 VHRICNRL----GWVTQPGTKQKTSSPEQTREALQRWLPKEEWVRINPLLVGFGQTICTP 194
           V R+  R     GW   PG K+  +      E +    P     R N  ++  G  ICT 
Sbjct: 141 VARVLARCYAVSGW---PGKKEVENKLWSLSEQVT---PAVGVERFNQAMMDLGAMICTR 194
Query: 195 LRPRCGMCTVSEYCPSA 211
            +P+C +C +   C +A
Sbjct: 195 SKPKCSLCPLQNGCIAA 211

>pdb|1MUD|A Chain A, Catalytic Domain Of Muty From Escherichia Coli, D138n Mutant Complexed To Adenine Length = 225

Iteration: 1
 Score = 53.9 bits (128), Expect = 8e-08,   Method: Compositional matrix adjust.
 Identities = 37/137 (27%), Positives = 62/137 (45%), Gaps = 11/137 (8%)
Query: 79  YTRKACNMKKIAKICLTKYDGDIPSSLDELLALPGIGPKMANMVMTLGWFNVQGICVDTH 138
           Y  +A N+ K A+   T + G  P + +E+ ALPG+G   A  +++L         ++ +
Sbjct: 82  YYARARNLHKAAQQVATLHGGKFPETFEEVAALPGVGRSTAGAILSLS-LGKHFPILNGN 140
Query: 139 VHRICNRL----GWVTQPGTKQKTSSPEQTREALQRWLPKEEWVRINPLLVGFGQTICTP 194
           V R+  R     GW   PG K+  +      E +    P     R N  ++  G  ICT 
Sbjct: 141 VKRVLARCYAVSGW---PGKKEVENKLWSLSEQVT---PAVGVERFNQAMMDLGAMICTR 194
Query: 195 LRPRCGMCTVSEYCPSA 211
            +P+C +C +   C +A
Sbjct: 195 SKPKCSLCPLQNGCIAA 211

>pdb|1KQJ|A Chain A, Crystal Structure Of A Mutant Of Muty Catalytic Domain Length = 225

Iteration: 1
 Score = 51.6 bits (122), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 37/137 (27%), Positives = 61/137 (44%), Gaps = 11/137 (8%)
Query: 79  YTRKACNMKKIAKICLTKYDGDIPSSLDELLALPGIGPKMANMVMTLGWFNVQGICVDTH 138
           Y  +A N+ K A+   T + G  P + +E+ ALPG+G   A  +++L         +D +
Sbjct: 82  YYARARNLHKAAQQVATLHGGKFPETFEEVAALPGVGRSTAGAILSLS-LGKHFPILDGN 140
Query: 139 VHRICNRL----GWVTQPGTKQKTSSPEQTREALQRWLPKEEWVRINPLLVGFGQTICTP 194
           V R+  R     GW   PG K+  +      E +    P     R N  ++  G  ICT 
Sbjct: 141 VKRVLARCYAVSGW---PGKKEVENKLWSLSEQVT---PAVGVERFNQAMMDLGAMICTR 194
Query: 195 LRPRCGMCTVSEYCPSA 211
            +P+  +C +   C +A
Sbjct: 195 SKPKHSLCPLQNGCIAA 211

>pdb|3N5N|X Chain X, Crystal Structure Analysis Of The Catalytic Domain And Interdomain Connector Of Human Muty Homologue Length = 287

Iteration: 1
 Score = 46.6 bits (109), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 37/159 (23%), Positives = 68/159 (42%), Gaps = 17/159 (10%)
Query: 57  TAEAIDKADEATIKDLIYPVAFYTRKACNMKKIAKICLTKYDGDIPSSLDELLAL-PGIG 115
           T + +  A    +  L   + +Y+R    +++ A+  + +  G +P + + L  L PG+G
Sbjct: 80  TLQDLASASLEEVNQLWAGLGYYSRGR-RLQEGARKVVEELGGHMPRTAETLQQLLPGVG 138
Query: 116 PKMANMVMTLGWFNVQGICVDTHVHRICNRLGWVTQPGTKQKTSSPEQTREALQRWLPKE 175
              A  + ++ +    G+ VD +V R+  R+        +   + P  T  + Q W   +
Sbjct: 139 RYTAGAIASIAFGQATGV-VDGNVARVLCRV--------RAIGADPSSTLVSQQLWGLAQ 189
Query: 176 EWVR------INPLLVGFGQTICTPLRPRCGMCTVSEYC 208
           + V        N   +  G T+CTP RP C  C V   C
Sbjct: 190 QLVDPARPGDFNQAAMELGATVCTPQRPLCSQCPVESLC 228

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	235
1pu6_A	218	3-methyladenine DNA glycosylase; helix-hairpin-hel	6e-46
1orn_A	226	Endonuclease III; DNA repair, DNA glycosylase, [4F	4e-45
2abk_A	211	Endonuclease III; DNA-repair, DNA glycosylase; 1.8	3e-44
3fhg_A	207	Mjogg, N-glycosylase/DNA lyase, DNA-(apurinic; hel	7e-28
1kea_A	221	Possible G-T mismatches repair enzyme; DNA repair,	2e-22
3n0u_A	219	Probable N-glycosylase/DNA lyase; structural genom	9e-21
1kg2_A	225	A/G-specific adenine glycosylase; DNA repair, hydr	2e-19
3fsp_A	369	A/G-specific adenine glycosylase; protein-DNA comp	8e-19
3n5n_X	287	A/G-specific adenine DNA glycosylase; alpha-helice	5e-17
3fhf_A	214	Mjogg, N-glycosylase/DNA lyase, DNA-(apurinic; hel	9e-13
4e9f_A	161	Methyl-CPG-binding domain protein 4; HHH DNA glyco	8e-11
3i0w_A	290	8-oxoguanine-DNA-glycosylase; OGG, cacogg, DNA, 8-	6e-09
2xhi_A	360	N-glycosylase/DNA lyase; lyase-DNA complex, lyase/	7e-09
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	4e-05
2jhn_A	295	ALKA, 3-methyladenine DNA-glycosylase; DNA repair,	3e-04

>1pu6_A 3-methyladenine DNA glycosylase; helix-hairpin-helix, base excision repair, hydrolase; HET: KCX; 1.64A {Helicobacter pylori} SCOP: a.96.1.5 PDB: 1pu7_A* 1pu8_A* Length = 218

 Score =  151 bits (383), Expect = 6e-46
 Identities = 33/220 (15%), Positives = 80/220 (36%), Gaps = 36/220 (16%)

Query: 2   KTLEPVYSLGVDETDSSLP-PKERRFAVLLSALLSSLTKDKVADGALQRL------LQNG 54
           + L+ + SL + +   +   P   +F  LL A+L+  TK +    +L+ L        + 
Sbjct: 6   EILKALKSLDLLKNAPAWWWPNALKFEALLGAVLTQNTKFEAVLKSLENLKNAFILENDD 65

Query: 55  LHTAEAIDKADEATIKDLIYPVAFYTRKACNMKKIAKICLTKYDG----DIPSSLDELLA 110
               + I   + + + + + P  FY +KA  +  ++   L  +          + + LL 
Sbjct: 66  EINLKKIAYIEFSKLAECVRPSGFYNQKAKRLIDLSGNILKDFQSFENFKQEVTREWLLD 125

Query: 111 LPGIGPKMANMVMTLGWFNVQGICVDTHVHRICNRLGWVTQPGTKQKTSSPEQTREALQR 170
             GIG + A+ ++       + + VD + +    +LG   +          ++ +   ++
Sbjct: 126 QKGIGKESADAILCYA-CAKEVMVVDKYSYLFLKKLGIEIE--------DYDELQHFFEK 176

Query: 171 WLPKEE----------------WVRINPLLVGFGQTICTP 194
            + +                  + R +  +V F +     
Sbjct: 177 GVQENLNSALALYENTISLAQLYARFHGKIVEFSKQKLEL 216

>1orn_A Endonuclease III; DNA repair, DNA glycosylase, [4Fe-4S] cluster, iron-sulfur cluster, hydrolase/DNA complex; HET: PED; 1.70A {Geobacillus stearothermophilus} SCOP: a.96.1.1 PDB: 1orp_A* 1p59_A* Length = 226

 Score =  149 bits (378), Expect = 4e-45
 Identities = 50/170 (29%), Positives = 80/170 (47%), Gaps = 7/170 (4%)

Query: 57  TAEAIDKADEATIKDLIYPVAFYTRKACNMKKIAKICLTKYDGDIPSSLDELLALPGIGP 116
           T           ++  I  +  Y  KA N++K+  + + KY+G++P   DEL+ LPG+G 
Sbjct: 64  TPHDYIAVPLEELEQDIRSIGLYRNKARNIQKLCAMLIDKYNGEVPRDRDELMKLPGVGR 123

Query: 117 KMANMVMTLGWFNVQGICVDTHVHRICNRLGWVTQPGTKQKTSSPEQTREALQRWLPKEE 176
           K AN+V++   F V  I VDTHV R+  RLG+           S  +  + L + +PKEE
Sbjct: 124 KTANVVVS-VAFGVPAIAVDTHVERVSKRLGFCRW------DDSVLEVEKTLMKIIPKEE 176

Query: 177 WVRINPLLVGFGQTICTPLRPRCGMCTVSEYCPSAFKESSTSSSKSKKSE 226
           W   +  ++ FG+  C    P+C  C +   C    K       K+   +
Sbjct: 177 WSITHHRMIFFGRYHCKAQSPQCPSCPLLHLCREGKKRMRKREEKAANQK 226

>2abk_A Endonuclease III; DNA-repair, DNA glycosylase; 1.85A {Escherichia coli} SCOP: a.96.1.1 Length = 211

 Score =  146 bits (371), Expect = 3e-44
 Identities = 51/157 (32%), Positives = 76/157 (48%), Gaps = 8/157 (5%)

Query: 57  TAEAIDKADEATIKDLIYPVAFYTRKACNMKKIAKICLTKYDGDIPSSLDELLALPGIGP 116
           T  A+ +     +K  I  +  Y  KA N+ K  +I L +++G++P     L ALPG+G 
Sbjct: 60  TPAAMLELGVEGVKTYIKTIGLYNSKAENIIKTCRILLEQHNGEVPEDRAALEALPGVGR 119

Query: 117 KMANMVMTLGWFNVQGICVDTHVHRICNRLGWVTQPGTKQKTSSPEQTREALQRWLPKEE 176
           K AN+V+    F    I VDTH+ R+CNR  +        K    EQ  E L + +P E 
Sbjct: 120 KTANVVLNT-AFGWPTIAVDTHIFRVCNRTQF-----APGKN--VEQVEEKLLKVVPAEF 171

Query: 177 WVRINPLLVGFGQTICTPLRPRCGMCTVSEYCPSAFK 213
            V  +  L+  G+  C   +PRCG C + + C    K
Sbjct: 172 KVDCHHWLILHGRYTCIARKPRCGSCIIEDLCEYKEK 208

>3fhg_A Mjogg, N-glycosylase/DNA lyase, DNA-(apurinic; helix-hairpin-helix, 8-oxoguanine, 8-OXOG, DNA damage, DNA repair, glycosidase, hydrolase; 1.90A {Sulfolobus solfataricus} Length = 207

 Score =  104 bits (260), Expect = 7e-28
 Identities = 34/185 (18%), Positives = 62/185 (33%), Gaps = 33/185 (17%)

Query: 21  PKERRFAVLLSALLSSLTKDKVADGALQRLLQNGLHTAEAIDKADEATIKDLIYPV--AF 78
            +E  F  L   LL++ +    A  AL  L Q           A+E  I++++      F
Sbjct: 29  NEEVWFRELTLCLLTANSSFISAYQALNCLGQKIY-------YANEEEIRNILKSCKYRF 81

Query: 79  YTRKACNMKKIAKICLTKYDGDIPSSLDE--------LLALPGIGPKMANMVMTLGWFNV 130
           Y  KA  +    +    +   +I    DE        LL + GIG + A+  +       
Sbjct: 82  YNLKAKYIIMAREKVYGRLKEEIKPLADEDQQLARERLLNIKGIGMQEASHFL-RNVGYF 140

Query: 131 QGICVDTHVHRICNRLGWVTQPGTKQKTSSPEQTREALQRWLPKEEWVRINPLLVGFGQT 190
               +D H+     R+G + +   KQ +               K  ++    +L      
Sbjct: 141 DLAIIDRHIIDFMRRIGAIGETNVKQLS---------------KSLYISFENILKSIASN 185

Query: 191 ICTPL 195
           +   +
Sbjct: 186 LNMSV 190

>1kea_A Possible G-T mismatches repair enzyme; DNA repair, DNA glycosylase, DNA mismatch, methylation; 2.00A {Methanothermobacter thermautotrophicusorganism_taxid} SCOP: a.96.1.2 Length = 221

 Score = 90.7 bits (226), Expect = 2e-22
 Identities = 36/139 (25%), Positives = 64/139 (46%), Gaps = 5/139 (3%)

Query: 79  YTRKACNMKKIAKICLTKYDGDIPSSLDELLALPGIGPKMANMVMTLGWFNVQGICVDTH 138
             ++A  +K++A++ +  Y G +P +   +L LPG+G      VM L  F  +   VD +
Sbjct: 88  SNQRAEQLKELARVVINDYGGRVPRNRKAILDLPGVGKYTCAAVMCLA-FGKKAAMVDAN 146

Query: 139 VHRICNRLGWVTQPGTKQKTSSPEQTREALQRWLPKEEWVRINPLLVGFGQTICTPLRPR 198
             R+ NR    +           +   E  +  +P  +    N  L+ F   IC P +P+
Sbjct: 147 FVRVINRYFGGSYENLNYNH---KALWELAETLVPGGKCRDFNLGLMDFSAIICAPRKPK 203

Query: 199 CGMCTVSEYCPSAFKESST 217
           C  C +S+ C S +++ ST
Sbjct: 204 CEKCGMSKLC-SYYEKCST 221

>3n0u_A Probable N-glycosylase/DNA lyase; structural genomics, ISFI, DNA repair, 8-oxoguanine, base EX repair, PSI-2, protein structure initiative; 1.50A {Thermotoga maritima} Length = 219

 Score = 85.9 bits (212), Expect = 9e-21
 Identities = 25/181 (13%), Positives = 58/181 (32%), Gaps = 30/181 (16%)

Query: 21  PKERRFAVLLSALLSSLTKDKVADGALQRLLQNGLHTAEAIDKADEATIKDLIYPV--AF 78
            +E  F  L   +L++    +    A + + +                + + +  V   +
Sbjct: 46  TEEDLFCELSFCVLTANWSAEGGIRAQKEIGKG-------FVHLPLEELAEKLREVGHRY 98

Query: 79  YTRKACNMKKIAKIC---LTKYDGDIPSSLDELLA-LPGIGPKMANMVMTLGWFNVQGIC 134
             ++A  + +  K+         GD   S + L+    GIG K A+  +           
Sbjct: 99  PQKRAEFIVENRKLLGKLKNLVKGDPFQSREFLVRNAKGIGWKEASHFL-RNTGVEDLAI 157

Query: 135 VDTHVHRICNRLGWVTQPGTKQKTSSPEQTREALQRWLPKEEWVRINPLLVGFGQTICTP 194
           +D HV R+  R G + +                + +   K+ ++ +  +L    +     
Sbjct: 158 LDKHVLRLMKRHGLIQE----------------IPKGWSKKRYLYVEEILRKVAEAFGES 201

Query: 195 L 195
            
Sbjct: 202 P 202

>1kg2_A A/G-specific adenine glycosylase; DNA repair, hydrolase; 1.20A {Escherichia coli} SCOP: a.96.1.2 PDB: 1kg3_A 1muy_A 1kg6_A 1kg5_A 1mun_A 1mud_A 1kg4_A 1weg_A 1wei_A* 1wef_A* 1kg7_A 1kqj_A Length = 225

 Score = 82.2 bits (204), Expect = 2e-19
 Identities = 38/153 (24%), Positives = 65/153 (42%), Gaps = 15/153 (9%)

Query: 78  FYTRKACNMKKIAKICLTKYDGDIPSSLDELLALPGIGPKMANMVMTLGWFNVQGICVDT 137
           +Y R A N+ K A+   T + G  P + +E+ ALPG+G   A  +++L         +D 
Sbjct: 82  YYAR-ARNLHKAAQQVATLHGGKFPETFEEVAALPGVGRSTAGAILSLS-LGKHFPILDG 139

Query: 138 HVHRICNRL----GWVTQPGTKQKTSSPEQTREALQRWLPKEEWVRINPLLVGFGQTICT 193
           +V R+  R     GW  +   +       +     ++  P     R N  ++  G  ICT
Sbjct: 140 NVKRVLARCYAVSGWPGKKEVEN------KLWSLSEQVTPAVGVERFNQAMMDLGAMICT 193

Query: 194 PLRPRCGMCTVSEYCPSAFKESSTSS--SKSKK 224
             +P+C +C +   C  A   +S +    K  K
Sbjct: 194 RSKPKCSLCPLQNGC-IAAANNSWALYPGKKPK 225

>3fsp_A A/G-specific adenine glycosylase; protein-DNA complex, DNA glycosylase, transition state analog, DNA repair; HET: NRI; 2.20A {Geobacillus stearothermophilus} PDB: 3fsq_A* 1rrs_A* 1vrl_A* 1rrq_A* 3g0q_A* Length = 369

 Score = 82.8 bits (205), Expect = 8e-19
 Identities = 45/152 (29%), Positives = 68/152 (44%), Gaps = 15/152 (9%)

Query: 79  YTRKACNMKKIAKICLTKYDGDIPSSLDELLALPGIGPKMANMVMTLGWFNVQGICVDTH 138
           Y+R   N+    K   T+Y G +P   DE   L G+GP     V++L  + V    VD +
Sbjct: 92  YSR-VRNLHAAVKEVKTRYGGKVPDDPDEFSRLKGVGPYTVGAVLSLA-YGVPEPAVDGN 149

Query: 139 VHRICNRL----GWVTQPGTKQKTSSPEQTREALQRWLPKEEWVRINPLLVGFGQTICTP 194
           V R+ +RL      + +P T++      +  + ++  +  E     N  L+  G  +CTP
Sbjct: 150 VMRVLSRLFLVTDDIAKPSTRK------RFEQIVREIMAYENPGAFNEALIELGALVCTP 203

Query: 195 LRPRCGMCTVSEYCPSAFKESSTSS--SKSKK 224
            RP C +C V  YC  AF E        K KK
Sbjct: 204 RRPSCLLCPVQAYC-QAFAEGVAEELPVKMKK 234

>3n5n_X A/G-specific adenine DNA glycosylase; alpha-helices, helix-hairpin-helix motif, iron-sulfur cluste hydrolase; 2.30A {Homo sapiens} Length = 287

 Score = 76.9 bits (190), Expect = 5e-17
 Identities = 34/155 (21%), Positives = 58/155 (37%), Gaps = 16/155 (10%)

Query: 79  YTRKACNMKKIAKICLTKYDGDIPSSLDELLA-LPGIGPKMANMVMTLGWFNVQGICVDT 137
           Y+R    +++ A+  + +  G +P + + L   LPG+G   A  + ++  F      VD 
Sbjct: 102 YSR-GRRLQEGARKVVEELGGHMPRTAETLQQLLPGVGRYTAGAIASIA-FGQATGVVDG 159

Query: 138 HVHRICNRL----GWVTQPGTKQKTSSPEQTREALQRWLPKEEWVRINPLLVGFGQTICT 193
           +V R+  R+       +     Q      Q     Q+ +        N   +  G T+CT
Sbjct: 160 NVARVLCRVRAIGADPSSTLVSQ------QLWGLAQQLVDPARPGDFNQAAMELGATVCT 213

Query: 194 PLRPRCGMCTVSEYCPSAFKESSTSS--SKSKKSE 226
           P RP C  C V   C  A +        +    S 
Sbjct: 214 PQRPLCSQCPVESLC-RARQRVEQEQLLASGSLSG 247

>3fhf_A Mjogg, N-glycosylase/DNA lyase, DNA-(apurinic; helix-hairpin-helix, 8-oxoguanine, 8-OXOG, DNA damage, DNA repair, glycosidase; 2.00A {Methanocaldococcus jannaschii} PDB: 3knt_A* Length = 214

 Score = 64.3 bits (156), Expect = 9e-13
 Identities = 22/154 (14%), Positives = 51/154 (33%), Gaps = 18/154 (11%)

Query: 21  PKERRFAVLLSALLSSLTKDKVADGALQRLLQNGLHTAEAIDKADEATIKDLIYPVA--F 78
             E  F  L   +L++    +      + +    L             +++ +  +   F
Sbjct: 40  SNEEWFKELCFCILTANFTAEGGIRIQKEIGDGFL-------TLPREELEEKLKNLGHRF 92

Query: 79  YTRKACNMKKIAKICLTKYDGDIPSSLDE-----LLALPGIGPKMANMVMTLGWFNVQGI 133
           Y ++A  +    +    K   +   +        +  + GIG K A+  +    ++   I
Sbjct: 93  YRKRAEYIVLARRFKNIKDIVESFENEKVAREFLVRNIKGIGYKEASHFLRNVGYDDVAI 152

Query: 134 CVDTHVHRICNRLGWVTQPGTKQKTSSPEQTREA 167
            +D H+ R      ++ +     KT S  +  E 
Sbjct: 153 -IDRHILRELYENNYIDE---IPKTLSRRKYLEI 182

>4e9f_A Methyl-CPG-binding domain protein 4; HHH DNA glycosylase family, hydrolase-DNA complex; HET: DNA 3DR; 1.79A {Homo sapiens} PDB: 4e9e_A* 4e9g_A* 4e9h_A* 4ea5_A* 4dk9_A* 1ngn_A 4ea4_A* 4ew4_A* 4evv_A* 4ew0_A* 3iho_A Length = 161

 Score = 57.9 bits (140), Expect = 8e-11
 Identities = 19/91 (20%), Positives = 38/91 (41%), Gaps = 8/91 (8%)

Query: 26  FAVLLSALLSSLTKDKVADGALQRLLQNGLHTAEAIDKADEATIKDLIYPVAFYTRKACN 85
           + +L++ +  + T  K+A   L + L+    +AE    AD   + +L+ P+  Y  +A  
Sbjct: 32  WKLLIATIFLNRTSGKMAIPVLWKFLEK-YPSAEVARTADWRDVSELLKPLGLYDLRAKT 90

Query: 86  MKKIAKICLTKYDGDIPSSLDELLALPGIGP 116
           + K +          +       + L GIG 
Sbjct: 91  IVKFSD-------EYLTKQWKYPIELHGIGK 114

>3i0w_A 8-oxoguanine-DNA-glycosylase; OGG, cacogg, DNA, 8-OXOG, 8OXOG, glycosylase, cytosine, hydrolase,lyase/DNA complex; HET: 8OG; 1.73A {Clostridium acetobutylicum} PDB: 3i0x_A* 3f10_A* 3f0z_A Length = 290

 Score = 54.2 bits (130), Expect = 6e-09
 Identities = 22/176 (12%), Positives = 56/176 (31%), Gaps = 35/176 (19%)

Query: 20  PPKERRFAVLLSALLSSLTKDKVADGALQRLLQN-------------GLHTAEAIDKADE 66
             ++  F +LLS ++S+  +  +    +  + +                 T + + +  E
Sbjct: 110 ILRQDPFEILLSFIISANNRIPMIKKCINNISEKAGKKLEYKGKIYYAFPTVDKLHEFTE 169

Query: 67  ATIKDLIYPVAFYTRKACNMKKIAKICLTK-------YDGDIPSSLDELLALPGIGPKMA 119
              ++          +A  +K                   +     +EL    G+GP++A
Sbjct: 170 KDFEECTAG-----FRAKYLKDTVDRIYNGELNLEYIKSLNDNECHEELKKFMGVGPQVA 224

Query: 120 NMVM--TLGWFNVQGICVDTHVHRICNRLGWVTQPGTKQKTSSPEQTREALQRWLP 173
           + +M  ++  ++     VDT V +    L            S  +      +++  
Sbjct: 225 DCIMLFSMQKYSA--FPVDTWVKKAMMSLYVAP------DVSLKKIRDFGREKFGS 272

>2xhi_A N-glycosylase/DNA lyase; lyase-DNA complex, lyase/DNA complex, separation-OF-function helix-hairpin-helix, DNA repair; HET: 8OG; 1.55A {Homo sapiens} PDB: 1ko9_A 1lwy_A* 1hu0_A* 1lwv_A* 1lww_A* 2noe_A* 2noh_A* 2nol_A* 1n3c_A* 1fn7_A* 2noz_A* 1yqk_A 1yqr_A* 1yql_A* 1yqm_A* 2noi_A 1ebm_A* 1m3q_A* 1m3h_A* 1n39_A* ... Length = 360

 Score = 54.4 bits (130), Expect = 7e-09
 Identities = 31/174 (17%), Positives = 57/174 (32%), Gaps = 26/174 (14%)

Query: 26  FAVLLSALLSSLTKDKVADGALQRLLQ---NGLHTAEAIDKADEATIKDL-------IYP 75
              L S + SS        G ++RL Q     L   + +      +++ L          
Sbjct: 153 IECLFSFICSSNNNIARITGMVERLCQAFGPRLIQLDDVTYHGFPSLQALAGPEVEAHLR 212

Query: 76  VAFYTRKACNMKKIAKICLTKYDG----------DIPSSLDELLALPGIGPKMANMV--M 123
                 +A  +   A+  L +  G              +   L  LPG+G  +A+ +  M
Sbjct: 213 KLGLGYRARYVSASARAILEEQGGLAWLQQLRESSYEEAHKALCILPGVGTCVADKICLM 272

Query: 124 TLGWFNVQGICVDTHVHRICNRLGWVTQPGTKQKTSSPEQTREALQRWLPKEEW 177
            L       + V+ H+  I  R        ++ K  SP+  +E    +  +  W
Sbjct: 273 ALDKPQA--VPVNVHMWHIAQRDYSWHPTTSQAKGPSPQTNKELGNFF--RSLW 322

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 43.3 bits (101), Expect = 4e-05
 Identities = 34/234 (14%), Positives = 73/234 (31%), Gaps = 64/234 (27%)

Query: 35  SSLTKDKVADGALQRLLQNGLHTAEAIDKADEATIKDLIYPV-AFYTRKACNMKKIAKIC 93
           + +  D      +Q  +   +     ++  +  + + ++  +     +   N        
Sbjct: 164 TWVALDVCLSYKVQCKMDFKIFW---LNLKNCNSPETVLEMLQKLLYQIDPNWTS----- 215

Query: 94  LTKYDGDIPSSLDE-----------------LLALPGI-GPKMANMVMTLGWFNVQGIC- 134
            + +  +I   +                   LL L  +   K  N       FN+   C 
Sbjct: 216 RSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLNVQNAKAWNA------FNLS--CK 267

Query: 135 --VDTHVHRICNRLGWVTQP----GTKQKTSSPEQTREALQRW-------LPKEEWVRIN 181
             + T   ++ + L   T           T +P++ +  L ++       LP+E  +  N
Sbjct: 268 ILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPREV-LTTN 326

Query: 182 PLLVG-FGQTICTPLRPRCGMCTVSEYCPSAFKESSTSSSKSKKSESSSLRKLE 234
           P  +    ++I      R G+ T  +     +K  +    K      SSL  LE
Sbjct: 327 PRRLSIIAESI------RDGLAT-WDN----WKHVNC--DKLTTIIESSLNVLE 367

>2jhn_A ALKA, 3-methyladenine DNA-glycosylase; DNA repair, N1-methyladenine, N3-methylcytosine, hyperthermophiles, hydrolase; HET: MBO MES; 1.8A {Archaeoglobus fulgidus} PDB: 2jhj_A Length = 295

 Score = 39.8 bits (93), Expect = 3e-04
 Identities = 27/123 (21%), Positives = 47/123 (38%), Gaps = 19/123 (15%)

Query: 57  TAEAIDKADEATIKDLIYPVAFYTRKACNMKKIAKICLTKY--DGDIPSSLDELLALPGI 114
           T EAI KA    +++         RKA  + +IAK    +   +     + + L +  GI
Sbjct: 163 TQEAILKAGVEGLRECGLS----RRKAELIVEIAKEENLEELKEWGEEEAYEYLTSFKGI 218

Query: 115 GPKMANMVMTLGW----FNVQGICVDTHVHRICNRLGWVTQPGTKQKTSSPEQTREALQR 170
           G   A +V+++      F       D  V R  +RL         +  S+ +    A +R
Sbjct: 219 GRWTAELVLSIALGKNVFPAD----DLGVRRAVSRLY-----FNGEIQSAEKVREIARER 269

Query: 171 WLP 173
           +  
Sbjct: 270 FGR 272

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	235
1orn_A	226	Endonuclease III; DNA repair, DNA glycosylase, [4F	100.0
2abk_A	211	Endonuclease III; DNA-repair, DNA glycosylase; 1.8	100.0
1kg2_A	225	A/G-specific adenine glycosylase; DNA repair, hydr	100.0
1kea_A	221	Possible G-T mismatches repair enzyme; DNA repair,	100.0
3n5n_X	287	A/G-specific adenine DNA glycosylase; alpha-helice	100.0
3fsp_A	369	A/G-specific adenine glycosylase; protein-DNA comp	100.0
1pu6_A	218	3-methyladenine DNA glycosylase; helix-hairpin-hel	100.0
3fhf_A	214	Mjogg, N-glycosylase/DNA lyase, DNA-(apurinic; hel	100.0
4b21_A	232	Probable DNA-3-methyladenine glycosylase 2; hydrol	100.0
2h56_A	233	DNA-3-methyladenine glycosidase; 10174367, EC 3.2.	99.98
4e9f_A	161	Methyl-CPG-binding domain protein 4; HHH DNA glyco	99.97
3fhg_A	207	Mjogg, N-glycosylase/DNA lyase, DNA-(apurinic; hel	99.97
3n0u_A	219	Probable N-glycosylase/DNA lyase; structural genom	99.97
2yg9_A	225	DNA-3-methyladenine glycosidase II, putative; hydr	99.97
3s6i_A	228	DNA-3-methyladenine glycosylase 1; DNA glycosylase	99.97
3i0w_A	290	8-oxoguanine-DNA-glycosylase; OGG, cacogg, DNA, 8-	99.97
1mpg_A	282	ALKA, 3-methyladenine DNA glycosylase II; DNA repa	99.96
2xhi_A	360	N-glycosylase/DNA lyase; lyase-DNA complex, lyase/	99.96
2jhn_A	295	ALKA, 3-methyladenine DNA-glycosylase; DNA repair,	99.95
2ofk_A	183	3-methyladenine DNA glycosylase I, constitutive; D	96.16
2jg6_A	186	DNA-3-methyladenine glycosidase; 3-methyladenine-D	96.09
1wcn_A	70	Transcription elongation protein NUSA; RNA-binding	94.04
4glx_A	586	DNA ligase; inhibitor, ligase-ligase inhibitor-DNA	92.95
1u9l_A	70	Transcription elongation protein NUSA; escherichia	92.47
3vdp_A	212	Recombination protein RECR; zinc finger, DNA repai	92.17
1x2i_A	75	HEF helicase/nuclease; alpha helix, helix-hairpin-	91.38
2fmp_A	335	DNA polymerase beta; nucleotidyl transferase, tran	91.37
1vdd_A	228	Recombination protein RECR; helix-hairpin-helix, z	91.19
2fmp_A	335	DNA polymerase beta; nucleotidyl transferase, tran	90.61
2ztd_A	212	Holliday junction ATP-dependent DNA helicase RUVA;	90.09
2duy_A	75	Competence protein comea-related protein; helix-ha	89.58
4gfj_A	685	Topoisomerase V; helix-hairpin-helix, DNA repair e	89.51
2ihm_A	360	POL MU, DNA polymerase MU; helix-turn-helix, trans	89.4
1z00_A	89	DNA excision repair protein ERCC-1; helix-hairpin-	89.28
1kft_A	78	UVRC, excinuclease ABC subunit C; helix-hairpin-he	89.04
1ixr_A	191	Holliday junction DNA helicase RUVA; heterooligome	88.9
2bcq_A	335	DNA polymerase lambda; misalignment, extrahelical,	88.63
2ihm_A	360	POL MU, DNA polymerase MU; helix-turn-helix, trans	88.6
2bcq_A	335	DNA polymerase lambda; misalignment, extrahelical,	88.49
1jms_A	381	Terminal deoxynucleotidyltransferase; polymerase;	88.39
2a1j_B	91	DNA excision repair protein ERCC-1; XPF, xeroderma	88.3
1cuk_A	203	RUVA protein; DNA repair, SOS response, DNA-bindin	88.3
2a1j_A	63	DNA repair endonuclease XPF; XPF, xeroderma pigmen	87.23
1b22_A	114	DNA repair protein RAD51; DNA binding, riken struc	86.6
1dgs_A	667	DNA ligase; AMP complex, NAD+-dependent; HET: DNA	86.56
2owo_A	671	DNA ligase; protein-DNA complex, ligase-DNA comple	86.49
1z00_B	84	DNA repair endonuclease XPF; helix-hairpin-helix,	86.25
2edu_A	98	Kinesin-like protein KIF22; kinesin-like DNA bindi	86.14
2ztd_A	212	Holliday junction ATP-dependent DNA helicase RUVA;	84.57
1ixr_A	191	Holliday junction DNA helicase RUVA; heterooligome	84.05
2a1j_A	63	DNA repair endonuclease XPF; XPF, xeroderma pigmen	83.77
2i5h_A	205	Hypothetical protein AF1531; PFAM:DUF655, PSI-2, s	83.15
1s5l_U	134	Photosystem II 12 kDa extrinsic protein; photosynt	82.85
2edu_A	98	Kinesin-like protein KIF22; kinesin-like DNA bindi	82.71
1s5l_U	134	Photosystem II 12 kDa extrinsic protein; photosynt	82.13
1jms_A	381	Terminal deoxynucleotidyltransferase; polymerase;	81.37
2kp7_A	87	Crossover junction endonuclease MUS81; helix-hairp	80.76
1cuk_A	203	RUVA protein; DNA repair, SOS response, DNA-bindin	80.39
3arc_U	97	Photosystem II 12 kDa extrinsic protein; PSII, mem	80.23

>1orn_A Endonuclease III; DNA repair, DNA glycosylase, [4Fe-4S] cluster, iron-sulfur cluster, hydrolase/DNA complex; HET: PED; 1.70A {Geobacillus stearothermophilus} SCOP: a.96.1.1 PDB: 1orp_A* 1p59_A*

Probab=100.00  E-value=3.7e-51  Score=346.04  Aligned_cols=185  Identities=29%  Similarity=0.563  Sum_probs=176.3

Q ss_pred             CCChHHHHHHHHHhccccHHHHHHHHHHHHHcCCCCHHHHhcCCHHHHHHhhccCCChHHHHHHHHHHHHHHHHhcCCCC
Q 026681           22 KERRFAVLLSALLSSLTKDKVADGALQRLLQNGLHTAEAIDKADEATIKDLIYPVAFYTRKACNMKKIAKICLTKYDGDI  101 (235)
Q Consensus        22 ~~~~f~~lv~~iLsqqt~~~~~~~~~~~l~~~~~pt~~~la~a~~e~l~~~l~~~G~~~~Ka~~l~~~a~~i~~~~~g~~  101 (235)
                      .+|||++||++||+|||++++|..++.+|+. .||||++|+++++++|+++|+++||+++||++|+++|+.+.++|+|++
T Consensus        30 ~~~pfe~Lv~~IlsQqts~~~v~~~~~~l~~-~fpt~~~la~a~~~~l~~~i~~~G~~~~KA~~l~~~a~~i~~~~~g~~  108 (226)
T 1orn_A           30 HRNPFELLIAVVLSAQCTDALVNKVTKRLFE-KYRTPHDYIAVPLEELEQDIRSIGLYRNKARNIQKLCAMLIDKYNGEV  108 (226)
T ss_dssp             CSSHHHHHHHHHHHTTSCHHHHHHHHHHHHH-HCCSHHHHHSSCHHHHHHHTGGGSSHHHHHHHHHHHHHHHHHHSTTSC
T ss_pred             CCCHHHHHHHHHHhCCCcHHHHHHHHHHHHH-HCCCHHHHHcCCHHHHHHHHHHcCChHHHHHHHHHHHHHHHHHhCCCc
Confidence            4799999999999999999999999999999 599999999999999999999999999999999999999999999999


Q ss_pred             hhhHHHHHcCCCCcHHHHHHHHHHhcCCcceeecchHHHHHHHHhcCcCCCCCCCCCCCHHHHHHHHHHhCCcccHHHHH
Q 026681          102 PSSLDELLALPGIGPKMANMVMTLGWFNVQGICVDTHVHRICNRLGWVTQPGTKQKTSSPEQTREALQRWLPKEEWVRIN  181 (235)
Q Consensus       102 ~~~~~~L~~l~GIG~~tA~~il~~~~~~~~~~pvDt~v~Rv~~Rlg~~~~~~~~~~~~~~~~~~~~l~~~~p~~~~~~~~  181 (235)
                      |+++++|++|||||+|||++|++|+|++ ++||||+|+.|++.|+|+++.      ..++++++..++.++|.+.|..+|
T Consensus       109 p~~~~~L~~lpGIG~~TA~~il~~a~g~-~~~~vD~~v~Rv~~rlg~~~~------~~~~~~~~~~l~~~~p~~~~~~~~  181 (226)
T 1orn_A          109 PRDRDELMKLPGVGRKTANVVVSVAFGV-PAIAVDTHVERVSKRLGFCRW------DDSVLEVEKTLMKIIPKEEWSITH  181 (226)
T ss_dssp             CSCHHHHTTSTTCCHHHHHHHHHHHHCC-CCCCCCHHHHHHHHHHTSSCT------TCCHHHHHHHHHHHSCGGGHHHHH
T ss_pred             HHHHHHHHHCCCccHHHHHHHHHHHCCC-ceeeeCHHHHHHHHHhCCCCC------CCCHHHHHHHHHHhcChhhHHHHH
Confidence            9999999999999999999999999998 499999999999999998752      467899999999999999999999


Q ss_pred             HHHHHHHhhhcCCCCCCCCCCcccccCcccccC
Q 026681          182 PLLVGFGQTICTPLRPRCGMCTVSEYCPSAFKE  214 (235)
Q Consensus       182 ~~l~~~G~~iC~~~~P~C~~Cpl~~~C~~~~~~  214 (235)
                      ++|++||+.+|++++|+|+.|||++.|+++.+.
T Consensus       182 ~~lv~~G~~~C~~~~P~C~~Cpl~~~C~~~~~~  214 (226)
T 1orn_A          182 HRMIFFGRYHCKAQSPQCPSCPLLHLCREGKKR  214 (226)
T ss_dssp             HHHHHHHHHTSCSSCCCGGGCTTGGGCHHHHHH
T ss_pred             HHHHHHHHHHcCCCCCCCCCCCChhhhhhHhhc
Confidence            999999999999999999999999999987553

>2abk_A Endonuclease III; DNA-repair, DNA glycosylase; 1.85A {Escherichia coli} SCOP: a.96.1.1

Probab=100.00  E-value=6.2e-51  Score=341.51  Aligned_cols=181  Identities=31%  Similarity=0.508  Sum_probs=173.7

Q ss_pred             CCChHHHHHHHHHhccccHHHHHHHHHHHHHcCCCCHHHHhcCCHHHHHHhhccCCChHHHHHHHHHHHHHHHHhcCCCC
Q 026681           22 KERRFAVLLSALLSSLTKDKVADGALQRLLQNGLHTAEAIDKADEATIKDLIYPVAFYTRKACNMKKIAKICLTKYDGDI  101 (235)
Q Consensus        22 ~~~~f~~lv~~iLsqqt~~~~~~~~~~~l~~~~~pt~~~la~a~~e~l~~~l~~~G~~~~Ka~~l~~~a~~i~~~~~g~~  101 (235)
                      .+|||++||++||||||++++|..++.+|+. .||||++|+++++++|+++|+++|||++||++|+++|+.+.++|+|++
T Consensus        26 ~~~pfe~lv~~Il~qqts~~~v~~~~~~l~~-~fpt~~~la~a~~~~l~~~i~~~G~~~~KA~~l~~~a~~~~~~~~g~~  104 (211)
T 2abk_A           26 FSSPFELLIAVLLSAQATDVSVNKATAKLYP-VANTPAAMLELGVEGVKTYIKTIGLYNSKAENIIKTCRILLEQHNGEV  104 (211)
T ss_dssp             CSSHHHHHHHHHHTTTSCHHHHHHHHHHHTT-TCCSHHHHHHHHHHHHHHHHTTSTTHHHHHHHHHHHHHHHHHHTTTSC
T ss_pred             CCCHHHHHHHHHHhCCCCHHHHHHHHHHHHH-HCCCHHHHHCCCHHHHHHHHHHcCCChHHHHHHHHHHHHHHHHcCCCc
Confidence            5799999999999999999999999999998 599999999999999999999999999999999999999999999999


Q ss_pred             hhhHHHHHcCCCCcHHHHHHHHHHhcCCcceeecchHHHHHHHHhcCcCCCCCCCCCCCHHHHHHHHHHhCCcccHHHHH
Q 026681          102 PSSLDELLALPGIGPKMANMVMTLGWFNVQGICVDTHVHRICNRLGWVTQPGTKQKTSSPEQTREALQRWLPKEEWVRIN  181 (235)
Q Consensus       102 ~~~~~~L~~l~GIG~~tA~~il~~~~~~~~~~pvDt~v~Rv~~Rlg~~~~~~~~~~~~~~~~~~~~l~~~~p~~~~~~~~  181 (235)
                      |+++++|++|||||+|||++|++|+++++ +||||+|+.|++.|+|+..       ..++++++..+++|+|.+.|..+|
T Consensus       105 ~~~~~~L~~l~GIG~~tA~~il~~~~~~~-~~~vD~~v~Rv~~rlgl~~-------~~~~~~~~~~~~~~~p~~~~~~~~  176 (211)
T 2abk_A          105 PEDRAALEALPGVGRKTANVVLNTAFGWP-TIAVDTHIFRVCNRTQFAP-------GKNVEQVEEKLLKVVPAEFKVDCH  176 (211)
T ss_dssp             CSCHHHHHHSTTCCHHHHHHHHHHHHCCC-CCCCCHHHHHHHHHHCSSC-------CSSHHHHHHHHHHHSCGGGTTTHH
T ss_pred             hHHHHHHHhCCCCChHHHHHHHHHHCCCC-cCCcCHHHHHHHHHhCCCC-------CCCHHHHHHHHHHhcChhhHHHHH
Confidence            99999999999999999999999999986 9999999999999999753       357899999999999999999999


Q ss_pred             HHHHHHHhhhcCCCCCCCCCCcccccCccc
Q 026681          182 PLLVGFGQTICTPLRPRCGMCTVSEYCPSA  211 (235)
Q Consensus       182 ~~l~~~G~~iC~~~~P~C~~Cpl~~~C~~~  211 (235)
                      ++|++||+.+|++++|+|+.|||++.|+++
T Consensus       177 ~~l~~~G~~~C~~~~P~C~~Cpl~~~C~~~  206 (211)
T 2abk_A          177 HWLILHGRYTCIARKPRCGSCIIEDLCEYK  206 (211)
T ss_dssp             HHHHHHHHHTSCSSSCCGGGCTTGGGCCCT
T ss_pred             HHHHHHHHHHCCCCCCCCCCCCChhhCCCc
Confidence            999999999999999999999999999975

>1kg2_A A/G-specific adenine glycosylase; DNA repair, hydrolase; 1.20A {Escherichia coli} SCOP: a.96.1.2 PDB: 1kg3_A 1muy_A 1kg6_A 1kg5_A 1mun_A 1mud_A 1kg4_A 1weg_A 1wei_A* 1wef_A* 1kg7_A 1kqj_A

Probab=100.00  E-value=5.9e-51  Score=344.73  Aligned_cols=192  Identities=23%  Similarity=0.358  Sum_probs=173.9

Q ss_pred             CCCCC--CChHHHHHHHHHhccccHHHHHHHHHHHHHcCCCCHHHHhcCCHHHHHHhhccCCChHHHHHHHHHHHHHHHH
Q 026681           18 SLPPK--ERRFAVLLSALLSSLTKDKVADGALQRLLQNGLHTAEAIDKADEATIKDLIYPVAFYTRKACNMKKIAKICLT   95 (235)
Q Consensus        18 ~~p~~--~~~f~~lv~~iLsqqt~~~~~~~~~~~l~~~~~pt~~~la~a~~e~l~~~l~~~G~~~~Ka~~l~~~a~~i~~   95 (235)
                      ++||.  +|||++||++||||||++++|.+++.+|+. .||||++|+++++++|+++|+++||+ +||++|+++|+.+.+
T Consensus        21 ~l~w~~~~~pfe~lv~~IlsQqt~~~~v~~~~~~l~~-~~pt~~~la~~~~~~l~~~i~~~G~~-~kA~~l~~~a~~i~~   98 (225)
T 1kg2_A           21 TLPWQIDKTPYKVWLSEVMLQQTQVATVIPYFERFMA-RFPTVTDLANAPLDEVLHLWTGLGYY-ARARNLHKAAQQVAT   98 (225)
T ss_dssp             CSGGGSSCCHHHHHHHHHHHTSSCHHHHHHHHHHHHH-HCSSHHHHHHSCHHHHHHHHTTSCCT-HHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCHHHHHHHHHHHCcCCHHHHHHHHHHHHH-HCCCHHHHHCCCHHHHHHHHHhCChH-HHHHHHHHHHHHHHH
Confidence            46664  799999999999999999999999999998 59999999999999999999999999 589999999999999


Q ss_pred             hcCCCChhhHHHHHcCCCCcHHHHHHHHHHhcCCcceeecchHHHHHHHHhcCcCCCCCCCCCCCHHHHHHHHHHhCCcc
Q 026681           96 KYDGDIPSSLDELLALPGIGPKMANMVMTLGWFNVQGICVDTHVHRICNRLGWVTQPGTKQKTSSPEQTREALQRWLPKE  175 (235)
Q Consensus        96 ~~~g~~~~~~~~L~~l~GIG~~tA~~il~~~~~~~~~~pvDt~v~Rv~~Rlg~~~~~~~~~~~~~~~~~~~~l~~~~p~~  175 (235)
                      +|+|++|+++++|++|||||+|||++||+|+|+++ .|+||+||+|++.|+++++...+  ...+++++++.++.|+|.+
T Consensus        99 ~~~g~~p~~~~~L~~lpGIG~~TA~~il~~a~~~~-~~~vD~~v~Rv~~rl~~~~~~~~--~~~~~~~l~~~~~~~~p~~  175 (225)
T 1kg2_A           99 LHGGKFPETFEEVAALPGVGRSTAGAILSLSLGKH-FPILDGNVKRVLARCYAVSGWPG--KKEVENKLWSLSEQVTPAV  175 (225)
T ss_dssp             HSTTSCCCSHHHHHTSTTCCHHHHHHHHHHHHCCS-CCCCCHHHHHHHHHHHTCCSCTT--SHHHHHHHHHHHHHHCCST
T ss_pred             HhCCCchHHHHHHhcCCCCcHHHHHHHHHHhCCCC-cceeCHHHHHHHHHHcCCCCCCC--ccchHHHHHHHHHHHCCcc
Confidence            99999999999999999999999999999999986 67899999999999977653111  1224566777788899999


Q ss_pred             cHHHHHHHHHHHHhhhcCCCCCCCCCCcccccCcccccC
Q 026681          176 EWVRINPLLVGFGQTICTPLRPRCGMCTVSEYCPSAFKE  214 (235)
Q Consensus       176 ~~~~~~~~l~~~G~~iC~~~~P~C~~Cpl~~~C~~~~~~  214 (235)
                      .|..+|++||+||+.+|++++|+|+.|||++.|+++...
T Consensus       176 ~~~~~~~~lv~~G~~~C~~~~P~C~~Cpl~~~C~~~~~~  214 (225)
T 1kg2_A          176 GVERFNQAMMDLGAMICTRSKPKCSLCPLQNGCIAAANN  214 (225)
T ss_dssp             THHHHHHHHHHHHHHTSCSSSCCGGGCTTTTTCHHHHHT
T ss_pred             cHHHHHHHHHHHHHHHcCCCCCCCCCCCChhhCHHHHcC
Confidence            999999999999999999999999999999999987654

>1kea_A Possible G-T mismatches repair enzyme; DNA repair, DNA glycosylase, DNA mismatch, methylation; 2.00A {Methanothermobacter thermautotrophicusorganism_taxid} SCOP: a.96.1.2

Probab=100.00  E-value=1.3e-50  Score=341.71  Aligned_cols=192  Identities=22%  Similarity=0.404  Sum_probs=175.2

Q ss_pred             CCCCCCCC--CChHHHHHHHHHhccccHHHHHHHHHHHHHcCCCCHHHHhcCCHHHHHHhhccCCChHHHHHHHHHHHHH
Q 026681           15 TDSSLPPK--ERRFAVLLSALLSSLTKDKVADGALQRLLQNGLHTAEAIDKADEATIKDLIYPVAFYTRKACNMKKIAKI   92 (235)
Q Consensus        15 ~~~~~p~~--~~~f~~lv~~iLsqqt~~~~~~~~~~~l~~~~~pt~~~la~a~~e~l~~~l~~~G~~~~Ka~~l~~~a~~   92 (235)
                      +++.+||.  +|||++||++||||||++++|.+++.+|++ .||||++|+++++++|+++|+++||+++||++|+++|+.
T Consensus        23 ~~~~~pw~~~~~pfe~lv~~IlsQqts~~~~~~~~~~l~~-~fptp~~la~a~~e~l~~~i~~~G~~~~KA~~l~~~a~~  101 (221)
T 1kea_A           23 DRRDFPWRHTRDPYVILITEILLRRTTAGHVKKIYDKFFV-KYKCFEDILKTPKSEIAKDIKEIGLSNQRAEQLKELARV  101 (221)
T ss_dssp             SCCCCGGGGCCCHHHHHHHHHHTTTSCHHHHHHHHHHHHH-HCCSHHHHHHSCHHHHHHHTGGGSCHHHHHHHHHHHHHH
T ss_pred             hhhhCcCCCCCCHHHHHHHHHHHccCCHHHHHHHHHHHHH-HCCCHHHHHCCCHHHHHHHHHHCCCCHHHHHHHHHHHHH
Confidence            45567775  689999999999999999999999999999 499999999999999999999999999999999999999


Q ss_pred             HHHhcCCCChhhHHHHHcCCCCcHHHHHHHHHHhcCCcceeecchHHHHHHHHh-cCcCCCCCCCCCCCHHHHHHHHHHh
Q 026681           93 CLTKYDGDIPSSLDELLALPGIGPKMANMVMTLGWFNVQGICVDTHVHRICNRL-GWVTQPGTKQKTSSPEQTREALQRW  171 (235)
Q Consensus        93 i~~~~~g~~~~~~~~L~~l~GIG~~tA~~il~~~~~~~~~~pvDt~v~Rv~~Rl-g~~~~~~~~~~~~~~~~~~~~l~~~  171 (235)
                      +.++|+|++|+++++|++|||||+|||++|++|++++ ++||||+|++|++.|+ |+...+ +   ....++++..++.|
T Consensus       102 i~~~~~g~~p~~~~~L~~lpGIG~~TA~~il~~~~~~-~~~~vD~~v~Rv~~rl~gl~~~~-~---~~~~~~l~~~ae~~  176 (221)
T 1kea_A          102 VINDYGGRVPRNRKAILDLPGVGKYTCAAVMCLAFGK-KAAMVDANFVRVINRYFGGSYEN-L---NYNHKALWELAETL  176 (221)
T ss_dssp             HHHHHTTSCCSCHHHHHTSTTCCHHHHHHHHHHTTCC-CCCCCCHHHHHHHHHHHCGGGTT-C---CTTSHHHHHHHHHH
T ss_pred             HHHHhCCCchHHHHHHHhCCCCcHHHHHHHHHHhcCC-CcceecHHHHHHHHHHhCCCCCC-C---cHHHHHHHHHHHHh
Confidence            9999999999999999999999999999999999998 4899999999999999 765421 1   11135677888999


Q ss_pred             CCcccHHHHHHHHHHHHhhhcCCCCCCCCCCcccccCcccc
Q 026681          172 LPKEEWVRINPLLVGFGQTICTPLRPRCGMCTVSEYCPSAF  212 (235)
Q Consensus       172 ~p~~~~~~~~~~l~~~G~~iC~~~~P~C~~Cpl~~~C~~~~  212 (235)
                      +|.+.|..+|++||+||+.||++++|+|+.|||++.|+++.
T Consensus       177 ~P~~~~~~~~~~lv~~G~~~C~~~~P~C~~Cpl~~~C~~~~  217 (221)
T 1kea_A          177 VPGGKCRDFNLGLMDFSAIICAPRKPKCEKCGMSKLCSYYE  217 (221)
T ss_dssp             SCTTCHHHHHHHHHHHHHHTSCSSSCCGGGCTTTTTCHHHH
T ss_pred             CChhhHHHHHHHHHHHHHHHcCCCCCCCCCCCChhhchhhh
Confidence            99999999999999999999999999999999999999753

>3n5n_X A/G-specific adenine DNA glycosylase; alpha-helices, helix-hairpin-helix motif, iron-sulfur cluste hydrolase; 2.30A {Homo sapiens}

Probab=100.00  E-value=3.6e-51  Score=355.64  Aligned_cols=191  Identities=21%  Similarity=0.362  Sum_probs=174.5

Q ss_pred             CCCCCCCCCC----------ChHHHHHHHHHhccccHHHHHHHHHHHHHcCCCCHHHHhcCCHHHHHHhhccCCChHHHH
Q 026681           14 ETDSSLPPKE----------RRFAVLLSALLSSLTKDKVADGALQRLLQNGLHTAEAIDKADEATIKDLIYPVAFYTRKA   83 (235)
Q Consensus        14 ~~~~~~p~~~----------~~f~~lv~~iLsqqt~~~~~~~~~~~l~~~~~pt~~~la~a~~e~l~~~l~~~G~~~~Ka   83 (235)
                      ++++++||+.          |||++||++||+|||++++|..++.+|++ .||||++|++++.++|+++|+++|||+ ||
T Consensus        28 ~~~R~lPWR~~~~~~~d~~~dpfe~LVs~ILsQQts~~~v~~~~~rL~~-~fptpe~La~a~~eel~~~ir~lG~~~-KA  105 (287)
T 3n5n_X           28 QEKRDLPWRRRAEDEMDLDRRAYAVWVSEVMLQQTQVATVINYYTGWMQ-KWPTLQDLASASLEEVNQLWAGLGYYS-RG  105 (287)
T ss_dssp             HHCCCCHHHHHHHHCCSHHHHHHHHHHHHHHHHTSCHHHHHHHHHHHHH-HCCSHHHHHTSCHHHHHHHHTTSSCHH-HH
T ss_pred             HcCCCCCCcCcCccccCCCCCHHHHHHHHHHhCCCcHHHHHHHHHHHHH-HCCCHHHHHcCCHHHHHHHHHHcCCHH-HH
Confidence            4678999986          58999999999999999999999999999 599999999999999999999999997 89


Q ss_pred             HHHHHHHHHHHHhcCCCChhhHHHHHc-CCCCcHHHHHHHHHHhcCCcceeecchHHHHHHHHhcCcCCCCCCCCCCCHH
Q 026681           84 CNMKKIAKICLTKYDGDIPSSLDELLA-LPGIGPKMANMVMTLGWFNVQGICVDTHVHRICNRLGWVTQPGTKQKTSSPE  162 (235)
Q Consensus        84 ~~l~~~a~~i~~~~~g~~~~~~~~L~~-l~GIG~~tA~~il~~~~~~~~~~pvDt~v~Rv~~Rlg~~~~~~~~~~~~~~~  162 (235)
                      ++|+++|+.++++|+|++|+++++|++ |||||+|||++||+|+|+++ +|+||+||+||+.|+|+++..      .++.
T Consensus       106 ~~L~~~A~~i~~~~~g~~p~~~~~Ll~~LpGIG~kTA~~iL~~a~g~p-~~~VDt~V~Rv~~Rlg~i~~~------~~~~  178 (287)
T 3n5n_X          106 RRLQEGARKVVEELGGHMPRTAETLQQLLPGVGRYTAGAIASIAFGQA-TGVVDGNVARVLCRVRAIGAD------PSST  178 (287)
T ss_dssp             HHHHHHHHHHHHHSTTCCCSSHHHHHHHSTTCCHHHHHHHHHHHSCCC-CCCCCHHHHHHHHHHTTCCSC------TTSH
T ss_pred             HHHHHHHHHHHHHhCCCCcHHHHHHHHHcCCCCHHHHHHHHHHhcCCC-CccccHHHHHHHHHhCCCCCC------CChH
Confidence            999999999999999999999999999 99999999999999999985 789999999999999998632      2223


Q ss_pred             HHH----HHHHHhCCcccHHHHHHHHHHHHhhhcCCCCCCCCCCcccccCccccc
Q 026681          163 QTR----EALQRWLPKEEWVRINPLLVGFGQTICTPLRPRCGMCTVSEYCPSAFK  213 (235)
Q Consensus       163 ~~~----~~l~~~~p~~~~~~~~~~l~~~G~~iC~~~~P~C~~Cpl~~~C~~~~~  213 (235)
                      +++    ..++.++|.+.|.+||++||+||+.||++++|+|+.|||++.|+++.+
T Consensus       179 ~~~~~l~~~a~~~lp~~~~~~~h~~L~~~Gr~iC~~r~P~C~~Cpl~~~C~~~~~  233 (287)
T 3n5n_X          179 LVSQQLWGLAQQLVDPARPGDFNQAAMELGATVCTPQRPLCSQCPVESLCRARQR  233 (287)
T ss_dssp             HHHHHHHHHHHHHSCSSCHHHHHHHHHHHHHHTSCSSSCCTTSCTTGGGCHHHHH
T ss_pred             HHHHHHHHHHHHhCCHHHHHHHHHHHHHHhHHHcCCCCCCCCCCCChhhhHHHHh
Confidence            333    334778999999999999999999999999999999999999998754

>3fsp_A A/G-specific adenine glycosylase; protein-DNA complex, DNA glycosylase, transition state analog, DNA repair; HET: NRI; 2.20A {Geobacillus stearothermophilus} PDB: 3fsq_A* 1rrs_A* 1vrl_A* 1rrq_A* 3g0q_A*

Probab=100.00  E-value=5.7e-50  Score=361.17  Aligned_cols=206  Identities=25%  Similarity=0.410  Sum_probs=186.2

Q ss_pred             CCCCCCCC--CChHHHHHHHHHhccccHHHHHHHHHHHHHcCCCCHHHHhcCCHHHHHHhhccCCChHHHHHHHHHHHHH
Q 026681           15 TDSSLPPK--ERRFAVLLSALLSSLTKDKVADGALQRLLQNGLHTAEAIDKADEATIKDLIYPVAFYTRKACNMKKIAKI   92 (235)
Q Consensus        15 ~~~~~p~~--~~~f~~lv~~iLsqqt~~~~~~~~~~~l~~~~~pt~~~la~a~~e~l~~~l~~~G~~~~Ka~~l~~~a~~   92 (235)
                      +++++||+  +|||++||++||+|||++++|.+++.+|++ .||||++|+++++++|.++|+++|||+ ||++|+++|+.
T Consensus        27 ~~r~lpw~~~~~p~~~lv~~il~qqt~~~~~~~~~~~l~~-~~pt~~~la~a~~~~l~~~i~~~G~~~-ra~~l~~~a~~  104 (369)
T 3fsp_A           27 ERRDLPWRKDRDPYKVWVSEVMLQQTRVETVIPYFEQFID-RFPTLEALADADEDEVLKAWEGLGYYS-RVRNLHAAVKE  104 (369)
T ss_dssp             HCCCCGGGSCCCHHHHHHHHHHTTTSCHHHHHHHHHHHHH-HCCSHHHHHTSCHHHHHHTTTTSSCTH-HHHHHHHHHHH
T ss_pred             hCCCCCCCCCCChHHHHHHHHHhccCcHHHHHHHHHHHHH-HCCCHHHHHCCCHHHHHHHHHhcChHH-HHHHHHHHHHH
Confidence            45678886  689999999999999999999999999999 599999999999999999999999997 89999999999


Q ss_pred             HHHhcCCCChhhHHHHHcCCCCcHHHHHHHHHHhcCCcceeecchHHHHHHHHhcCcCCCCCCCCCCCHHHHHHHHHHhC
Q 026681           93 CLTKYDGDIPSSLDELLALPGIGPKMANMVMTLGWFNVQGICVDTHVHRICNRLGWVTQPGTKQKTSSPEQTREALQRWL  172 (235)
Q Consensus        93 i~~~~~g~~~~~~~~L~~l~GIG~~tA~~il~~~~~~~~~~pvDt~v~Rv~~Rlg~~~~~~~~~~~~~~~~~~~~l~~~~  172 (235)
                      +.++|+|++|+++++|++|||||+|||++||+|+|+++ +++||+||+|++.|+|+++.+.+  ...++++++..++.++
T Consensus       105 ~~~~~~g~~p~~~~~L~~l~GIG~~tA~~il~~~~~~~-~~~vD~~v~Rv~~rl~~~~~~~~--~~~~~~~~~~~~~~~~  181 (369)
T 3fsp_A          105 VKTRYGGKVPDDPDEFSRLKGVGPYTVGAVLSLAYGVP-EPAVDGNVMRVLSRLFLVTDDIA--KPSTRKRFEQIVREIM  181 (369)
T ss_dssp             HHHHHTTCCCCSHHHHHTSTTCCHHHHHHHHHHHHCCC-CCCCCHHHHHHHHHHTTCCSCTT--SHHHHHHHHHHHHHHC
T ss_pred             HHHHcCCCChhHHHHHhcCCCcCHHHHHHHHHHHCCCC-cccccHHHHHHHHHHcCcccCcc--ccchHHHHHHHHHHhC
Confidence            99999999999999999999999999999999999984 88999999999999998764211  2345778888999999


Q ss_pred             CcccHHHHHHHHHHHHhhhcCCCCCCCCCCcccccCcccccC--CCCCCCCCccc
Q 026681          173 PKEEWVRINPLLVGFGQTICTPLRPRCGMCTVSEYCPSAFKE--SSTSSSKSKKS  225 (235)
Q Consensus       173 p~~~~~~~~~~l~~~G~~iC~~~~P~C~~Cpl~~~C~~~~~~--~~~~~~k~~~~  225 (235)
                      |.+.|..+|++||+||+.||++++|+|+.|||++.|.++...  ..+|.+++|++
T Consensus       182 p~~~~~~~~~~l~~~G~~~C~~~~P~C~~Cpl~~~C~~~~~~~~~~~PvK~~kk~  236 (369)
T 3fsp_A          182 AYENPGAFNEALIELGALVCTPRRPSCLLCPVQAYCQAFAEGVAEELPVKMKKTA  236 (369)
T ss_dssp             CSSSHHHHHHHHHHHHHHTSCSSSCCTTTCTTGGGCHHHHHTCGGGCSCCCCCCC
T ss_pred             ChhhHHHHHHHHHHHHHHhcCCCCCCCCCCCChhhhHHHhcCCcccCCccccccC
Confidence            999999999999999999999999999999999999987653  56665554444

>1pu6_A 3-methyladenine DNA glycosylase; helix-hairpin-helix, base excision repair, hydrolase; HET: KCX; 1.64A {Helicobacter pylori} SCOP: a.96.1.5 PDB: 1pu7_A* 1pu8_A*

Probab=100.00  E-value=1.6e-38  Score=267.31  Aligned_cols=167  Identities=18%  Similarity=0.238  Sum_probs=151.9

Q ss_pred             CCCCCCC-CCChHHHHHHHHHhccccHHHHHHHHHHHHHcCCCC------HHHHhcCCHHHHHHhhccCCChHHHHHHHH
Q 026681           15 TDSSLPP-KERRFAVLLSALLSSLTKDKVADGALQRLLQNGLHT------AEAIDKADEATIKDLIYPVAFYTRKACNMK   87 (235)
Q Consensus        15 ~~~~~p~-~~~~f~~lv~~iLsqqt~~~~~~~~~~~l~~~~~pt------~~~la~a~~e~l~~~l~~~G~~~~Ka~~l~   87 (235)
                      ++..++| .+|||++||++||||||+++++.+++.+|++.+|||      |++|+++++++|+++|+++||+++||++|+
T Consensus        19 ~~~~~~~~~~dpfe~Lv~~ILsQqts~~~v~~~~~~L~~~~~pt~~~~~t~~~la~~~~e~L~~~ir~~G~~~~KA~~L~   98 (218)
T 1pu6_A           19 NAPAWWWPNALKFEALLGAVLTQNTKFEAVLKSLENLKNAFILENDDEINLKKIAYIEFSKLAECVRPSGFYNQKAKRLI   98 (218)
T ss_dssp             TSCTTSSTTTTSHHHHHHHHHTTTSCHHHHHHHHHHHHHTTSSCSCHHHHHHHHHHSCHHHHHHHTGGGSCHHHHHHHHH
T ss_pred             cCCCcCCCCCCHHHHHHHHHHcCCCCHHHHHHHHHHHHHccCCCccccccHHHHHhCCHHHHHHHHHHCCCcHHHHHHHH
Confidence            3333333 489999999999999999999999999999955999      999999999999999999999999999999


Q ss_pred             HHHHHHHHhcCC----CChhhHHHHHcCCCCcHHHHHHHHHHhcCCcceeecchHHHHHHHHhcCcCCCCCCCCCCCHHH
Q 026681           88 KIAKICLTKYDG----DIPSSLDELLALPGIGPKMANMVMTLGWFNVQGICVDTHVHRICNRLGWVTQPGTKQKTSSPEQ  163 (235)
Q Consensus        88 ~~a~~i~~~~~g----~~~~~~~~L~~l~GIG~~tA~~il~~~~~~~~~~pvDt~v~Rv~~Rlg~~~~~~~~~~~~~~~~  163 (235)
                      ++|+.+.++|+|    +.|+++++|++|||||+|||++|++|+++++ +||||+|++|++.|+|+.        ..++++
T Consensus        99 ~~a~~i~~~~~~l~~~~~~~~~~~L~~lpGIG~kTA~~il~~a~~~~-~~~vD~~v~Ri~~rlg~~--------~~~~~~  169 (218)
T 1pu6_A           99 DLSGNILKDFQSFENFKQEVTREWLLDQKGIGKESADAILCYACAKE-VMVVDKYSYLFLKKLGIE--------IEDYDE  169 (218)
T ss_dssp             HHHHHHHHHHSSHHHHHHHCCHHHHHTSTTCCHHHHHHHHHHTTCCS-CCCCCHHHHHHHHHTTCC--------CCSHHH
T ss_pred             HHHHHHHHhcCChhhccchHHHHHHHcCCCcCHHHHHHHHHHHCCCC-ccccCHHHHHHHHHcCCC--------CCCHHH
Confidence            999999999988    7889999999999999999999999999984 999999999999999875        257899


Q ss_pred             HHHHHHH----hCC------------cccHHHHHHHHHHHHhh
Q 026681          164 TREALQR----WLP------------KEEWVRINPLLVGFGQT  190 (235)
Q Consensus       164 ~~~~l~~----~~p------------~~~~~~~~~~l~~~G~~  190 (235)
                      ++..++.    ++|            .+.|.++|..|+.||+.
T Consensus       170 ~~~~l~~~~p~~lp~~~~~~~~~~~~~~~~~~~h~liv~~Gk~  212 (218)
T 1pu6_A          170 LQHFFEKGVQENLNSALALYENTISLAQLYARFHGKIVEFSKQ  212 (218)
T ss_dssp             HHHHHHHHHHTTHHHHHHTTTTCSCHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHhhhhcCcchhhhcccccchHHHHHHHHHHHHHHhhh
Confidence            9999988    676            34599999999999997

>3fhf_A Mjogg, N-glycosylase/DNA lyase, DNA-(apurinic; helix-hairpin-helix, 8-oxoguanine, 8-OXOG, DNA damage, DNA repair, glycosidase; 2.00A {Methanocaldococcus jannaschii} PDB: 3knt_A*

Probab=100.00  E-value=5.1e-33  Score=232.41  Aligned_cols=148  Identities=14%  Similarity=0.212  Sum_probs=133.7

Q ss_pred             CCChHHHHHHHHHhccccHHHHHHHHHHHHHcCCCCHHHHhcCCHHHHHHhhccCC--ChHHHHHHHHHHHH--HHHHhc
Q 026681           22 KERRFAVLLSALLSSLTKDKVADGALQRLLQNGLHTAEAIDKADEATIKDLIYPVA--FYTRKACNMKKIAK--ICLTKY   97 (235)
Q Consensus        22 ~~~~f~~lv~~iLsqqt~~~~~~~~~~~l~~~~~pt~~~la~a~~e~l~~~l~~~G--~~~~Ka~~l~~~a~--~i~~~~   97 (235)
                      .++||++||++||||||+++++.+++.+|.       +.|+.+++++|+++|+++|  ||++||++|+++++  .+.+.+
T Consensus        41 ~~~~fe~Lv~~ILsqqt~~~~v~~a~~~L~-------~~l~~~~~eeL~~~Ir~~G~rf~~~KA~~I~~~a~~~~l~~~~  113 (214)
T 3fhf_A           41 NEEWFKELCFCILTANFTAEGGIRIQKEIG-------DGFLTLPREELEEKLKNLGHRFYRKRAEYIVLARRFKNIKDIV  113 (214)
T ss_dssp             HHHHHHHHHHHHHHTTSCHHHHHHHHHHHT-------THHHHSCHHHHHHHHHHTTCTTHHHHHHHHHHHGGGCCHHHHH
T ss_pred             CCChHHHHHHHHHcCCCCHHHHHHHHHHHH-------HHHHCCCHHHHHHHHHHHhhHHHHHHHHHHHHHHHhhHHHHHh
Confidence            468999999999999999999999999995       6799999999999999999  99999999999999  888888


Q ss_pred             CC--CChhhHHHHH-cCCCCcHHHHHHHHHHhcCCcceee-cchHHHHHHHHhcCcCCCCCCCCCCCHHHHHHHHHHhCC
Q 026681           98 DG--DIPSSLDELL-ALPGIGPKMANMVMTLGWFNVQGIC-VDTHVHRICNRLGWVTQPGTKQKTSSPEQTREALQRWLP  173 (235)
Q Consensus        98 ~g--~~~~~~~~L~-~l~GIG~~tA~~il~~~~~~~~~~p-vDt~v~Rv~~Rlg~~~~~~~~~~~~~~~~~~~~l~~~~p  173 (235)
                      ++  ++|+++++|+ +|||||+|||++||+++ +. +.+| ||+|++|+++|+|+++..        +        +.+|
T Consensus       114 ~~~~~~~~~re~Ll~~LpGVG~KTA~~vL~~~-g~-~~~~vVDthv~Ri~~RlG~~~~~--------~--------k~lt  175 (214)
T 3fhf_A          114 ESFENEKVAREFLVRNIKGIGYKEASHFLRNV-GY-DDVAIIDRHILRELYENNYIDEI--------P--------KTLS  175 (214)
T ss_dssp             HHSSSHHHHHHHHHHHSTTCCHHHHHHHHHHT-TC-CSCCCCCHHHHHHHHHTTSSSSC--------C--------SSCC
T ss_pred             cccCCcHHHHHHHHHhCCCCCHHHHHHHHHHc-CC-CCcccCcHHHHHHHHHcCCCCCC--------C--------CcCC
Confidence            77  7899999999 99999999999999998 56 5677 999999999999998631        1        3356


Q ss_pred             cccHHHHHHHHHHHHhhhcCC
Q 026681          174 KEEWVRINPLLVGFGQTICTP  194 (235)
Q Consensus       174 ~~~~~~~~~~l~~~G~~iC~~  194 (235)
                      ...|.++|..|+.||+.+|.+
T Consensus       176 ~~~y~e~~~~l~~~g~~~g~~  196 (214)
T 3fhf_A          176 RRKYLEIENILRDIGEEVNLK  196 (214)
T ss_dssp             HHHHHHHHHHHHHHHHHTTCC
T ss_pred             HHHHHHHHHHHHHHHHHHCCC
Confidence            678999999999999999976

>4b21_A Probable DNA-3-methyladenine glycosylase 2; hydrolase-DNA complex, helix-hairpin-helix; HET: BGC 3DR; 1.45A {Schizosaccharomyces pombe} PDB: 4b22_A* 4b23_A* 4b24_A*

Probab=100.00  E-value=6e-32  Score=228.95  Aligned_cols=154  Identities=14%  Similarity=0.203  Sum_probs=135.5

Q ss_pred             CCCCC--CCChHHHHHHHHHhccccHHHHHHHHHHHHHc-C----CCCHHHHhcCCHHHHHHhhccCCChHHHHHHHHHH
Q 026681           17 SSLPP--KERRFAVLLSALLSSLTKDKVADGALQRLLQN-G----LHTAEAIDKADEATIKDLIYPVAFYTRKACNMKKI   89 (235)
Q Consensus        17 ~~~p~--~~~~f~~lv~~iLsqqt~~~~~~~~~~~l~~~-~----~pt~~~la~a~~e~l~~~l~~~G~~~~Ka~~l~~~   89 (235)
                      ..+|+  .+|||++||++||+|||+++++..++.+|.+. +    ||||++|+++++++|.    .+||+.+||++|+++
T Consensus        50 ~rl~~~~~~dpfe~Lv~~Il~Qq~s~~~a~~~~~rL~~~~G~~~~fPtpe~la~~~~e~Lr----~~Gl~~~Ka~~l~~~  125 (232)
T 4b21_A           50 CTLTPHPEHAPYEGIIRAITSQKLSDAATNSIINKFCTQCSDNDEFPTPKQIMETDVETLH----ECGFSKLKSQEIHIV  125 (232)
T ss_dssp             CCCCCCTTSCHHHHHHHHHHTTTCCHHHHHHHHHHHHHHHCSSSSCCCHHHHHTSCHHHHH----TTTCCHHHHHHHHHH
T ss_pred             CCCCCCCCCCHHHHHHHHHHhCcCcHHHHHHHHHHHHHHhCCCCCCCCHHHHHcCCHHHHH----HcCCcHHHHHHHHHH
Confidence            34554  46999999999999999999999999999984 3    9999999999999864    569999999999999


Q ss_pred             HHHHHHhcCCCCh-----------hhHHHHHcCCCCcHHHHHHHHHHhcCCcceeec-chHHHHHHHHhcCcCCCCCCCC
Q 026681           90 AKICLTKYDGDIP-----------SSLDELLALPGIGPKMANMVMTLGWFNVQGICV-DTHVHRICNRLGWVTQPGTKQK  157 (235)
Q Consensus        90 a~~i~~~~~g~~~-----------~~~~~L~~l~GIG~~tA~~il~~~~~~~~~~pv-Dt~v~Rv~~Rlg~~~~~~~~~~  157 (235)
                      |+++.+   |.+|           +.+++|++|||||+|||++|++|+++++++||| |+||+|++.|++..+.      
T Consensus       126 A~~~~~---g~~p~l~~l~~~~~~~~~~~L~~l~GIG~~TA~~ill~alg~pd~fpv~D~~v~r~~~rl~~~~~------  196 (232)
T 4b21_A          126 AEAALN---KQIPSKSEIEKMSEEELMESLSKIKGVKRWTIEMYSIFTLGRLDIMPADDSTLKNEAKEFFGLSS------  196 (232)
T ss_dssp             HHHHHT---TCSCCHHHHHHSCHHHHHHHHTTSTTCCHHHHHHHHHHTSCCSSCCCTTCHHHHHHHHHHTTCSS------
T ss_pred             HHHHHh---CCCCCHHHHHcCCHHHHHHHHHhCCCcCHHHHHHHHHHhCCCCCeeeCccHHHHHHHHHHhCCCC------
Confidence            999987   5443           578999999999999999999999999999999 9999999999977642      


Q ss_pred             CCCHHHHHHHHHHhCCcccHHHHHHH
Q 026681          158 TSSPEQTREALQRWLPKEEWVRINPL  183 (235)
Q Consensus       158 ~~~~~~~~~~l~~~~p~~~~~~~~~~  183 (235)
                      ..+++++++..+.|-|...|..++.|
T Consensus       197 ~~~~~~~~~~~e~w~P~rs~A~~yLw  222 (232)
T 4b21_A          197 KPQTEEVEKLTKPCKPYRTIAAWYLW  222 (232)
T ss_dssp             CCCHHHHHHHTGGGTTCHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHccCHHHHHHHHHH
Confidence            45788899999999999888777765

>2h56_A DNA-3-methyladenine glycosidase; 10174367, EC 3.2.2.-, struc genomics, PSI-2, protein structure initiative, joint center structural genomics; 2.55A {Bacillus halodurans}

Probab=99.98  E-value=2.7e-32  Score=231.48  Aligned_cols=163  Identities=16%  Similarity=0.158  Sum_probs=142.6

Q ss_pred             CCCCChHHHHHHHHHhccccHHHHHHHHHHHHHc---CCCCHHHHhcCCHHHHHHhhccCCChHHHHHHHHHHHHHHHHh
Q 026681           20 PPKERRFAVLLSALLSSLTKDKVADGALQRLLQN---GLHTAEAIDKADEATIKDLIYPVAFYTRKACNMKKIAKICLTK   96 (235)
Q Consensus        20 p~~~~~f~~lv~~iLsqqt~~~~~~~~~~~l~~~---~~pt~~~la~a~~e~l~~~l~~~G~~~~Ka~~l~~~a~~i~~~   96 (235)
                      +..+|||++||++||+|||+++++..++.+|++.   .||||++|+++++++|    +++||+++||++|+++|+.+.+.
T Consensus        46 ~~~~dpfe~Lv~~IlsQqts~~~a~~~~~rL~~~~G~~fPtp~~la~~~~e~L----r~~G~~~~KA~~I~~~A~~i~~~  121 (233)
T 2h56_A           46 PTKPNPFQSLVSSIVEQQLSIKAASAIYGRVEQLVGGALEKPEQLYRVSDEAL----RQAGVSKRKIEYIRHVCEHVESG  121 (233)
T ss_dssp             ECCSCHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHTSCCCCTHHHHTSCHHHH----HHTTCCHHHHHHHHHHHHHHHTT
T ss_pred             CCCCCHHHHHHHHHHcCCCCHHHHHHHHHHHHHHhCCCCCCHHHHHcCCHHHH----HHcCCCHHHHHHHHHHHHHHHhC
Confidence            3568999999999999999999999999999985   2679999999999998    55699999999999999999886


Q ss_pred             c-CCC-C---h--hhHHHHHcCCCCcHHHHHHHHHHhcCCcceeecchHHHHHHHHhcCcCCCCCCCCCCCHHHHHHHHH
Q 026681           97 Y-DGD-I---P--SSLDELLALPGIGPKMANMVMTLGWFNVQGICVDTHVHRICNRLGWVTQPGTKQKTSSPEQTREALQ  169 (235)
Q Consensus        97 ~-~g~-~---~--~~~~~L~~l~GIG~~tA~~il~~~~~~~~~~pvDt~v~Rv~~Rlg~~~~~~~~~~~~~~~~~~~~l~  169 (235)
                      + +++ +   |  +++++|++|||||+|||++||+|+++++++||||+|+.|++.|+++...     ...++++++..++
T Consensus       122 ~~~~~~l~~~p~~~~~~~L~~lpGIG~kTA~~ill~alg~pd~~pvdd~~~r~~~~~~~~~~-----~~~~~~~~~~~~e  196 (233)
T 2h56_A          122 RLDFTELEGAEATTVIEKLTAIKGIGQWTAEMFMMFSLGRLDVLSVGDVGLQRGAKWLYGNG-----EGDGKKLLIYHGK  196 (233)
T ss_dssp             SSCHHHHTTSCHHHHHHHHHTSTTCCHHHHHHHHHHTTCCSCCCCTTCHHHHHHHHHHHSSS-----CSCHHHHHHHHHG
T ss_pred             CCCHHHHhcCCHHHHHHHHHhCCCcCHHHHHHHHHHhCCCCCeeeCchHHHHHHHHHhccCC-----CCCCHHHHHHHHH
Confidence            5 332 2   5  7899999999999999999999999998899999999999999876432     2457889999999


Q ss_pred             HhCCcccHHHHHHHHHHHHhhh
Q 026681          170 RWLPKEEWVRINPLLVGFGQTI  191 (235)
Q Consensus       170 ~~~p~~~~~~~~~~l~~~G~~i  191 (235)
                      .|.|...|..+|.|.++.+..-
T Consensus       197 ~~~P~~~~a~~~lw~~~~~~~~  218 (233)
T 2h56_A          197 AWAPYETVACLYLWKAAGTFAE  218 (233)
T ss_dssp             GGTTCHHHHHHHHHHHHTHHHH
T ss_pred             HcCcHHHHHHHHHHhccccccc
Confidence            9999999999998888877654

>4e9f_A Methyl-CPG-binding domain protein 4; HHH DNA glycosylase family, hydrolase-DNA complex; HET: DNA 3DR; 1.79A {Homo sapiens} PDB: 4e9e_A* 4e9g_A* 4e9h_A* 4ea5_A* 4dk9_A* 1ngn_A 4ea4_A* 4ew4_A* 4evv_A* 4ew0_A* 3iho_A

Probab=99.97  E-value=7.1e-32  Score=216.21  Aligned_cols=118  Identities=19%  Similarity=0.210  Sum_probs=110.3

Q ss_pred             CChHHHHHHHHHhccccHHHHHHHHHHHHHcCCCCHHHHhcCCHHHHHHhhccCCChHHHHHHHHHHHHHHHHhcCCCCh
Q 026681           23 ERRFAVLLSALLSSLTKDKVADGALQRLLQNGLHTAEAIDKADEATIKDLIYPVAFYTRKACNMKKIAKICLTKYDGDIP  102 (235)
Q Consensus        23 ~~~f~~lv~~iLsqqt~~~~~~~~~~~l~~~~~pt~~~la~a~~e~l~~~l~~~G~~~~Ka~~l~~~a~~i~~~~~g~~~  102 (235)
                      +|||++||++||||||++++|.+++.+|++ .||||++|++++.++|.++|+++|||++||++|+++++.+       +|
T Consensus        29 ~dP~~vLVs~ILsqQT~~~~v~~~~~~l~~-~~pt~~~la~a~~~el~~~i~~lG~y~~KAk~i~~~a~~~-------vp  100 (161)
T 4e9f_A           29 HDPWKLLIATIFLNRTSGKMAIPVLWKFLE-KYPSAEVARTADWRDVSELLKPLGLYDLRAKTIVKFSDEY-------LT  100 (161)
T ss_dssp             TSHHHHHHHHHHTTTSCHHHHHHHHHHHHH-HSCSHHHHTTSCHHHHHHHHGGGSCHHHHHHHHHHHHHHH-------HH
T ss_pred             CChHHHHHHHHHHhhCcHHHHHHHHHHHHH-HCCCHHHHhccChHhHHhHhhhcCCHHHHHHHHHHHhCCc-------CC
Confidence            699999999999999999999999999999 5999999999999999999999999999999999998754       56


Q ss_pred             hhHHHHHcCCCCcHHHHHHHHHHhcCC-cceeecchHHHHHHHHhcC
Q 026681          103 SSLDELLALPGIGPKMANMVMTLGWFN-VQGICVDTHVHRICNRLGW  148 (235)
Q Consensus       103 ~~~~~L~~l~GIG~~tA~~il~~~~~~-~~~~pvDt~v~Rv~~Rlg~  148 (235)
                      +++++|++|||||+|||++|++|++|+ ..++|+|.++.|++.++..
T Consensus       101 ~~~~~L~~LpGVG~yTAdav~~F~~~e~~~V~p~D~~l~r~l~wl~~  147 (161)
T 4e9f_A          101 KQWKYPIELHGIGKYGNDSYRIFCVNEWKQVHPEDHKLNKYHDWLWE  147 (161)
T ss_dssp             SCCSSGGGSTTCCHHHHHHHHHHTSSCGGGCCCCSHHHHHHHHHHHH
T ss_pred             CChhhhhcCCCchHHHHHHHHHHHCCCCCCCCCCcHHHHHHHHHHHc
Confidence            778899999999999999999999996 4688999999999999843

>3fhg_A Mjogg, N-glycosylase/DNA lyase, DNA-(apurinic; helix-hairpin-helix, 8-oxoguanine, 8-OXOG, DNA damage, DNA repair, glycosidase, hydrolase; 1.90A {Sulfolobus solfataricus}

Probab=99.97  E-value=2.2e-31  Score=222.05  Aligned_cols=148  Identities=21%  Similarity=0.277  Sum_probs=126.9

Q ss_pred             CChHHHHHHHHHhccccHHHHHHHHHHHHHcCCCCHHHHhcCCHHHHHHhhccCC--ChHHHHHHHHHHHHHHH------
Q 026681           23 ERRFAVLLSALLSSLTKDKVADGALQRLLQNGLHTAEAIDKADEATIKDLIYPVA--FYTRKACNMKKIAKICL------   94 (235)
Q Consensus        23 ~~~f~~lv~~iLsqqt~~~~~~~~~~~l~~~~~pt~~~la~a~~e~l~~~l~~~G--~~~~Ka~~l~~~a~~i~------   94 (235)
                      +|||+.||++||||||++++|.+++.+|       ++.|+.+++++|+++|+++|  ||++||++|+++|+++.      
T Consensus        31 ~~~fe~Lv~~ILsqqts~~~~~~~~~~L-------~~~l~~~~~e~l~~~ir~~G~g~~~~KA~~l~~~a~~~~~~~~~~  103 (207)
T 3fhg_A           31 EVWFRELTLCLLTANSSFISAYQALNCL-------GQKIYYANEEEIRNILKSCKYRFYNLKAKYIIMAREKVYGRLKEE  103 (207)
T ss_dssp             HHHHHHHHHHHHHTTSCHHHHHHHHHHH-------GGGGGTCCHHHHHHHHHHTTCTTHHHHHHHHHHHHHHHTTTHHHH
T ss_pred             CCHHHHHHHHHHcCCCCHHHHHHHHHHH-------HHHHHcCCHHHHHHHHHHhccCcHHHHHHHHHHHHHHHHHHhhhh
Confidence            5899999999999999999999999998       47899999999999999665  99999999999999653      


Q ss_pred             -HhcCCCCh-hhHHHHHcCCCCcHHHHHHHHHH-hcCCcceeecchHHHHHHHHhcCcCCCCCCCCCCCHHHHHHHHHHh
Q 026681           95 -TKYDGDIP-SSLDELLALPGIGPKMANMVMTL-GWFNVQGICVDTHVHRICNRLGWVTQPGTKQKTSSPEQTREALQRW  171 (235)
Q Consensus        95 -~~~~g~~~-~~~~~L~~l~GIG~~tA~~il~~-~~~~~~~~pvDt~v~Rv~~Rlg~~~~~~~~~~~~~~~~~~~~l~~~  171 (235)
                       +.++|..| +++++|++|||||+|||++||+| ++  .++||||+|++|++.|+|+++..               +...
T Consensus       104 l~~~~~~~~~~~~~~L~~lpGIG~kTA~~il~~~~~--~~~~~vD~~v~Ri~~rlg~~~~~---------------~~k~  166 (207)
T 3fhg_A          104 IKPLADEDQQLARERLLNIKGIGMQEASHFLRNVGY--FDLAIIDRHIIDFMRRIGAIGET---------------NVKQ  166 (207)
T ss_dssp             HHHHHHHCHHHHHHHHTTSTTCCHHHHHHHHHHTTC--CSSCCCCHHHHHHHHHTTSSCCC---------------CCSC
T ss_pred             HHHHhCCCHHHHHHHHHcCCCcCHHHHHHHHHHhCC--CCcceecHHHHHHHHHcCCCCcc---------------cccc
Confidence             34445566 78999999999999999999998 55  47899999999999999997531               1123


Q ss_pred             CCcccHHHHHHHHHHHHhhhcCC
Q 026681          172 LPKEEWVRINPLLVGFGQTICTP  194 (235)
Q Consensus       172 ~p~~~~~~~~~~l~~~G~~iC~~  194 (235)
                      ++...|.++|..|+.||+.+|.+
T Consensus       167 ~~~k~y~~~~~~l~~~~~~~~~~  189 (207)
T 3fhg_A          167 LSKSLYISFENILKSIASNLNMS  189 (207)
T ss_dssp             CCHHHHHHHHHHHHHHHHHTTSC
T ss_pred             CCHHHHHHHHHHHHHHHHHhCCC
Confidence            45667889999999999998864

>3n0u_A Probable N-glycosylase/DNA lyase; structural genomics, ISFI, DNA repair, 8-oxoguanine, base EX repair, PSI-2, protein structure initiative; 1.50A {Thermotoga maritima}

Probab=99.97  E-value=3e-31  Score=222.58  Aligned_cols=143  Identities=17%  Similarity=0.109  Sum_probs=123.0

Q ss_pred             CCChHHHHHHHHHhccccHHHHHHHHHHHHHcCCCCHHHHhcCCHHHHHHhhccCC--ChHHHHHHHHHHHHHH---HHh
Q 026681           22 KERRFAVLLSALLSSLTKDKVADGALQRLLQNGLHTAEAIDKADEATIKDLIYPVA--FYTRKACNMKKIAKIC---LTK   96 (235)
Q Consensus        22 ~~~~f~~lv~~iLsqqt~~~~~~~~~~~l~~~~~pt~~~la~a~~e~l~~~l~~~G--~~~~Ka~~l~~~a~~i---~~~   96 (235)
                      .++||+.||++||||||+++++.+++.+|       |+.|+.+++++|+++|+++|  |+++||++|+++|+.+   .+.
T Consensus        47 ~~~~fe~Lv~~ILsqqts~~~~~~a~~~L-------p~~l~~~~~eeL~~~Ir~~G~Rf~~~KA~~I~~~a~~ig~l~~~  119 (219)
T 3n0u_A           47 EEDLFCELSFCVLTANWSAEGGIRAQKEI-------GKGFVHLPLEELAEKLREVGHRYPQKRAEFIVENRKLLGKLKNL  119 (219)
T ss_dssp             HHHHHHHHHHHHHTTTSCHHHHHHHHHHH-------TTHHHHCCHHHHHHHHHHTTCSSHHHHHHHHHHHGGGTTTHHHH
T ss_pred             CCCHHHHHHHHHHhCCCCHHHHHHHHHHH-------HHHHHcCCHHHHHHHHHHhcchHHHHHHHHHHHHHHHHHHHHHH
Confidence            46899999999999999999999999988       67899999999999999999  9999999999999975   666


Q ss_pred             cCCCChhhHHHHH-cCCCCcHHHHHHHHHHhcCCcceeecchHHHHHHHHhcCcCCCCCCCCCCCHHHHHHHHHHhC
Q 026681           97 YDGDIPSSLDELL-ALPGIGPKMANMVMTLGWFNVQGICVDTHVHRICNRLGWVTQPGTKQKTSSPEQTREALQRWL  172 (235)
Q Consensus        97 ~~g~~~~~~~~L~-~l~GIG~~tA~~il~~~~~~~~~~pvDt~v~Rv~~Rlg~~~~~~~~~~~~~~~~~~~~l~~~~  172 (235)
                      +++++|+++++|+ ++||||+|||++||++ ++..++||||+|++|++.|+|+++.........++.++++.+..+.
T Consensus       120 ~~~~~~~~r~~L~~~l~GVG~kTA~~vL~~-~g~~~~~~VDthv~Ri~~rlg~~~~~~k~~t~k~y~~ie~~~~~~a  195 (219)
T 3n0u_A          120 VKGDPFQSREFLVRNAKGIGWKEASHFLRN-TGVEDLAILDKHVLRLMKRHGLIQEIPKGWSKKRYLYVEEILRKVA  195 (219)
T ss_dssp             HHSCHHHHHHHHHHHSTTCCHHHHHHHHHT-TTCCSCCCCCHHHHHHHHHTTSCSSCCSSCCHHHHHHHHHHHHHHH
T ss_pred             hcCCcHHHHHHHHHhCCCCCHHHHHHHHHH-cCCCCeeeecHHHHHHHHHcCCCCcCcCcCCHHHHHHHHHHHHHHH
Confidence            7899999999999 9999999999999999 7776799999999999999999865222222244555666655543

>2yg9_A DNA-3-methyladenine glycosidase II, putative; hydrolase, DNA repair; 1.95A {Deinococcus radiodurans} PDB: 2yg8_A

Probab=99.97  E-value=3.5e-30  Score=217.38  Aligned_cols=148  Identities=20%  Similarity=0.208  Sum_probs=128.3

Q ss_pred             CCCCCChHHHHHHHHHhccccHHHHHHHHHHHHHcCC--CCHHHHhcCCHHHHHHhhccCCChHHHHHHHHHHHHHHHHh
Q 026681           19 LPPKERRFAVLLSALLSSLTKDKVADGALQRLLQNGL--HTAEAIDKADEATIKDLIYPVAFYTRKACNMKKIAKICLTK   96 (235)
Q Consensus        19 ~p~~~~~f~~lv~~iLsqqt~~~~~~~~~~~l~~~~~--pt~~~la~a~~e~l~~~l~~~G~~~~Ka~~l~~~a~~i~~~   96 (235)
                      .+..+|||+.||++||+|||+++++..++.+|.+. |  |||++|+++++++|.    ++||+++||++|+++|+.+.+.
T Consensus        55 ~~~~~dpfe~Lv~~IlsQq~s~~~a~~~~~rL~~~-~G~ptp~~la~~~~e~Lr----~~G~~~~KA~~i~~lA~~~~~g  129 (225)
T 2yg9_A           55 LAPTPDPFGRLVRSVAGQQLSVKAAQAIYGRLEGL-PGGVVPAALLKVSGDDLR----GVGLSWAKVRTVQAAAAAAVSG  129 (225)
T ss_dssp             CCCCSCHHHHHHHHHHHTTSCHHHHHHHHHHHHTS-TTCSCHHHHTTSCHHHHH----HTTCCHHHHHHHHHHHHHHHTT
T ss_pred             CCCCCCHHHHHHHHHHhCcChHHHHHHHHHHHHHH-hCcCCHHHHHcCCHHHHH----HCCCcHHHHHHHHHHHHHHHhC
Confidence            45578999999999999999999999999999994 7  999999999999874    5599999999999999999872


Q ss_pred             cC-------CCChhhHHHHHcCCCCcHHHHHHHHHHhcCCcceeec-chHHHHHHHHhcCcCCCCCCCCCCCHHHHHHHH
Q 026681           97 YD-------GDIPSSLDELLALPGIGPKMANMVMTLGWFNVQGICV-DTHVHRICNRLGWVTQPGTKQKTSSPEQTREAL  168 (235)
Q Consensus        97 ~~-------g~~~~~~~~L~~l~GIG~~tA~~il~~~~~~~~~~pv-Dt~v~Rv~~Rlg~~~~~~~~~~~~~~~~~~~~l  168 (235)
                      ..       .+.++.+++|++|||||+|||++|++|+++++++||| |+|++|++.|++  + +         +++++..
T Consensus       130 ~~~l~~l~~~~~~e~~~~L~~l~GIG~~TA~~ill~~lg~~d~fpv~D~~v~r~~~~l~--~-~---------~~~~~~~  197 (225)
T 2yg9_A          130 QIDFAHLSGQPDELVIAELVQLPGIGRWTAEMFLLFALARPDVFSSGDLALRQGVERLY--P-G---------EDWRDVT  197 (225)
T ss_dssp             SSCGGGCTTSCHHHHHHHHHTSTTCCHHHHHHHHHHTSCCSCCCCTTCHHHHHHHHHHS--T-T---------SCHHHHH
T ss_pred             CcCHHHHhcCCHHHHHHHHHcCCCCCHHHHHHHHHHhCCCCCeeeCccHHHHHHHHHhC--C-H---------HHHHHHH
Confidence            10       0122459999999999999999999999999889999 999999999998  1 1         2366778


Q ss_pred             HHhCCcccHHHHHHH
Q 026681          169 QRWLPKEEWVRINPL  183 (235)
Q Consensus       169 ~~~~p~~~~~~~~~~  183 (235)
                      +.|.|...|..+|.|
T Consensus       198 e~~~P~r~~a~~~Lw  212 (225)
T 2yg9_A          198 ARWAPYRSLASRYLW  212 (225)
T ss_dssp             HHHTTCHHHHHHHHH
T ss_pred             HHcCCHHHHHHHHHH
Confidence            999999998888866

>3s6i_A DNA-3-methyladenine glycosylase 1; DNA glycosylase, DNA repair, helix-hairpin-helix (HHH), ABAS tetrahydrofuran (THF); HET: 3DR; 2.28A {Schizosaccharomyces pombe}

Probab=99.97  E-value=1.3e-29  Score=214.23  Aligned_cols=153  Identities=18%  Similarity=0.215  Sum_probs=132.2

Q ss_pred             CCCC--CC-ChHHHHHHHHHhccccHHHHHHHHHHHHHc-----CCCCHHHHhcCCHHHHHHhhccCCChHHHHHHHHHH
Q 026681           18 SLPP--KE-RRFAVLLSALLSSLTKDKVADGALQRLLQN-----GLHTAEAIDKADEATIKDLIYPVAFYTRKACNMKKI   89 (235)
Q Consensus        18 ~~p~--~~-~~f~~lv~~iLsqqt~~~~~~~~~~~l~~~-----~~pt~~~la~a~~e~l~~~l~~~G~~~~Ka~~l~~~   89 (235)
                      .+++  .+ |||+.||++||+|||+++++..++.+| +.     .||||++|+.++.++|..    +||+++||++|+++
T Consensus        40 r~~~~~~~~d~fe~Lv~~Il~Qq~s~~~a~~~~~rL-~~~Gg~~~fPtp~~la~~~~e~Lr~----~G~~~rKa~~i~~~  114 (228)
T 3s6i_A           40 RPNRSMEKKEPYEELIRAVASQQLHSKAANAIFNRF-KSISNNGQFPTPEEIRDMDFEIMRA----CGFSARKIDSLKSI  114 (228)
T ss_dssp             CCCCTTTTSCHHHHHHHHHHHSSSCHHHHHHHHHHH-HTSSGGGSCCCHHHHHHSCHHHHHH----HTCCHHHHHHHHHH
T ss_pred             CCCCCCCcCCHHHHHHHHHHhCcCCHHHHHHHHHHH-HHhcCCCCCCCHHHHHcCCHHHHHH----cCCCHHHHHHHHHH
Confidence            4444  34 999999999999999999999999999 63     269999999999999755    49999999999999


Q ss_pred             HHHHHHhcCCCCh-----------hhHHHHHcCCCCcHHHHHHHHHHhcCCcceeecc-hHHHHHHHHhcCcCCCCCCCC
Q 026681           90 AKICLTKYDGDIP-----------SSLDELLALPGIGPKMANMVMTLGWFNVQGICVD-THVHRICNRLGWVTQPGTKQK  157 (235)
Q Consensus        90 a~~i~~~~~g~~~-----------~~~~~L~~l~GIG~~tA~~il~~~~~~~~~~pvD-t~v~Rv~~Rlg~~~~~~~~~~  157 (235)
                      |+.+.+   |.+|           +.++.|++|||||+|||++||+|+++++++|||| .|++|++.+++..+.      
T Consensus       115 A~~~~~---g~~p~~~~l~~~~~~e~~~~L~~l~GIG~~TA~~ill~~lg~pd~fpvdD~~v~r~~~~~~~~~~------  185 (228)
T 3s6i_A          115 AEATIS---GLIPTKEEAERLSNEELIERLTQIKGIGRWTVEMLLIFSLNRDDVMPADDLSIRNGYRYLHRLPK------  185 (228)
T ss_dssp             HHHHHH---TSSCCHHHHTTSCHHHHHHHHTTSTTCCHHHHHHHHHHTSCCSSCCCTTCHHHHHHHHHHTTCSS------
T ss_pred             HHHHHc---CCCCChHHHhcCCHHHHHHHHHhCCCcCHHHHHHHHHHhCCCCCEEecccHHHHHHHHHHhCCCC------
Confidence            999986   6664           3489999999999999999999999999899996 578999999876542      


Q ss_pred             CCCHHHHHHHHHHhCCcccHHHHHHHH
Q 026681          158 TSSPEQTREALQRWLPKEEWVRINPLL  184 (235)
Q Consensus       158 ~~~~~~~~~~l~~~~p~~~~~~~~~~l  184 (235)
                      ..+++++++..+.|-|...|..+|.|-
T Consensus       186 ~~~~~~~~~~~e~w~P~r~~A~~yLw~  212 (228)
T 3s6i_A          186 IPTKMYVLKHSEICAPFRTAAAWYLWK  212 (228)
T ss_dssp             CCCHHHHHHHHGGGTTCHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHhCCHHHHHHHHHHH
Confidence            457888999999999998888877653

>3i0w_A 8-oxoguanine-DNA-glycosylase; OGG, cacogg, DNA, 8-OXOG, 8OXOG, glycosylase, cytosine, hydrolase,lyase/DNA complex; HET: 8OG; 1.73A {Clostridium acetobutylicum} PDB: 3i0x_A* 3f10_A* 3f0z_A

Probab=99.97  E-value=1.3e-29  Score=221.35  Aligned_cols=161  Identities=16%  Similarity=0.197  Sum_probs=137.0

Q ss_pred             CCCCCCCCCChHHHHHHHHHhccccHHHHHHHHHHHHHc-------------CCCCHHHHhcCCHHHHHHhhccCCChHH
Q 026681           15 TDSSLPPKERRFAVLLSALLSSLTKDKVADGALQRLLQN-------------GLHTAEAIDKADEATIKDLIYPVAFYTR   81 (235)
Q Consensus        15 ~~~~~p~~~~~f~~lv~~iLsqqt~~~~~~~~~~~l~~~-------------~~pt~~~la~a~~e~l~~~l~~~G~~~~   81 (235)
                      .|.++| ++||||.||++||+||++++++.+++.+|.+.             .||||++|+.+++++|.++  ++||   
T Consensus       106 ~glR~~-~~dpfE~Lv~~IlsQq~s~~~a~~~~~rL~~~~G~~~~~~g~~~~~fPtpe~la~~~~e~L~~~--g~g~---  179 (290)
T 3i0w_A          106 EGIRIL-RQDPFEILLSFIISANNRIPMIKKCINNISEKAGKKLEYKGKIYYAFPTVDKLHEFTEKDFEEC--TAGF---  179 (290)
T ss_dssp             TTCCCC-CCCHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHSCEEEETTEEEECCCCHHHHTTCCHHHHHHT--TCGG---
T ss_pred             CCCCCC-CCCHHHHHHHHHHhCcccHHHHHHHHHHHHHHhCCCcccCCcccccCCcHHHHHCCCHHHHHHc--CCch---
Confidence            345665 49999999999999999999999999999873             3899999999999999884  4554   


Q ss_pred             HHHHHHHHHHHHHHhcC-------CCChhhHHHHHcCCCCcHHHHHHHHHHhcCCcceeecchHHHHHHHHhcCcCCCCC
Q 026681           82 KACNMKKIAKICLTKYD-------GDIPSSLDELLALPGIGPKMANMVMTLGWFNVQGICVDTHVHRICNRLGWVTQPGT  154 (235)
Q Consensus        82 Ka~~l~~~a~~i~~~~~-------g~~~~~~~~L~~l~GIG~~tA~~il~~~~~~~~~~pvDt~v~Rv~~Rlg~~~~~~~  154 (235)
                      ||++|+++|+.+.+.+.       .+.+++++.|++|||||+|||++|++|+++++++||||+||+|++.|+|+.+    
T Consensus       180 Ra~~I~~~A~~i~~g~~~l~~l~~~~~~~~~~~L~~lpGIG~~TA~~ill~~lg~pd~fpvD~~v~r~~~rl~~~~----  255 (290)
T 3i0w_A          180 RAKYLKDTVDRIYNGELNLEYIKSLNDNECHEELKKFMGVGPQVADCIMLFSMQKYSAFPVDTWVKKAMMSLYVAP----  255 (290)
T ss_dssp             GHHHHHHHHHHHHTTSSCHHHHHHSCHHHHHHHHTTSTTCCHHHHHHHHHHHHCCTTCCCCCHHHHHHHHHHTSCT----
T ss_pred             HHHHHHHHHHHHHhCCCCHHHHhcCCHHHHHHHHHhCCCcCHHHHHHHHHHhCCCCCcceecHHHHHHHHHhcCCC----
Confidence            79999999999987431       3567899999999999999999999999999889999999999999999864    


Q ss_pred             CCCCCCHHHHHHHH-HHhCCcccHHHHHHHHHHHHhh
Q 026681          155 KQKTSSPEQTREAL-QRWLPKEEWVRINPLLVGFGQT  190 (235)
Q Consensus       155 ~~~~~~~~~~~~~l-~~~~p~~~~~~~~~~l~~~G~~  190 (235)
                         ..+++++++.+ +.|-|  ..+..++.|+.+|+.
T Consensus       256 ---~~~~~~i~~~~~~~~~p--~~~~A~~~Lw~~~R~  287 (290)
T 3i0w_A          256 ---DVSLKKIRDFGREKFGS--LSGFAQQYLFYYARE  287 (290)
T ss_dssp             ---TCCHHHHHHHHHHHHGG--GHHHHHHHHHHHHHH
T ss_pred             ---CCCHHHHHHHHHhhcch--HHHHHHHHHHHhhhh
Confidence               35788898887 66665  455566777888875

>1mpg_A ALKA, 3-methyladenine DNA glycosylase II; DNA repair, base excision, methylation, ALK hydrolase; 1.80A {Escherichia coli} SCOP: a.96.1.3 d.129.1.2 PDB: 1diz_A 1pvs_A* 3cvs_A* 3cvt_A* 3cw7_A* 3cwa_A* 3cws_A* 3cwt_A* 3cwu_A* 3d4v_A* 3ogd_A* 3oh9_A* 3oh6_A*

Probab=99.96  E-value=3.4e-28  Score=211.67  Aligned_cols=155  Identities=21%  Similarity=0.295  Sum_probs=135.1

Q ss_pred             CCCCCCCCCChHHHHHHHHHhccccHHHHHHHHHHHHH------------cCCCCHHHHhcCCHHHHHHhhccCCChHHH
Q 026681           15 TDSSLPPKERRFAVLLSALLSSLTKDKVADGALQRLLQ------------NGLHTAEAIDKADEATIKDLIYPVAFYTRK   82 (235)
Q Consensus        15 ~~~~~p~~~~~f~~lv~~iLsqqt~~~~~~~~~~~l~~------------~~~pt~~~la~a~~e~l~~~l~~~G~~~~K   82 (235)
                      .|.+++...||||+||++||+|||+++++.+++.+|.+            +.||||++|+++++++|    +++||+++|
T Consensus       103 ~glR~~~~~d~fe~lv~~Il~Qq~s~~~a~~~~~rL~~~~G~~~~~~~~~~~fPtp~~la~~~~~~L----r~~G~~~~r  178 (282)
T 1mpg_A          103 PGLRLPGCVDAFEQGVRAILGQLVSVAMAAKLTARVAQLYGERLDDFPEYICFPTPQRLAAADPQAL----KALGMPLKR  178 (282)
T ss_dssp             TTCCCCCCSCHHHHHHHHHHTTTSCHHHHHHHHHHHHHHHCCBCSSCTTCBCCCCHHHHHTCCHHHH----HHTTSCHHH
T ss_pred             CCCcCCCCCCHHHHHHHHHHhCcccHHHHHHHHHHHHHHhCCCCCCCCCcccCCCHHHHHcCCHHHH----HHcCCCHHH
Confidence            45566767999999999999999999999999999974            24899999999999998    455999999


Q ss_pred             HHHHHHHHHHHHHh-cCCCC----hhhHHHHHcCCCCcHHHHHHHHHHhcCCcceeecchHHHHHHHHhcCcCCCCCCCC
Q 026681           83 ACNMKKIAKICLTK-YDGDI----PSSLDELLALPGIGPKMANMVMTLGWFNVQGICVDTHVHRICNRLGWVTQPGTKQK  157 (235)
Q Consensus        83 a~~l~~~a~~i~~~-~~g~~----~~~~~~L~~l~GIG~~tA~~il~~~~~~~~~~pvDt~v~Rv~~Rlg~~~~~~~~~~  157 (235)
                      |++|+++|+.+.+. ++++.    ++.+++|++|||||+|||++|++|+++++++||+|+|+.|  ++++          
T Consensus       179 a~~i~~~A~~~~~~~~~~~~~~~~~~~~~~L~~lpGIG~~TA~~ill~~lg~~d~~pvdd~~~r--~~l~----------  246 (282)
T 1mpg_A          179 AEALIHLANAALEGTLPMTIPGDVEQAMKTLQTFPGIGRWTANYFALRGWQAKDVFLPDDYLIK--QRFP----------  246 (282)
T ss_dssp             HHHHHHHHHHHHHTCSCSSCCSCHHHHHHHHTTSTTCCHHHHHHHHHHHSCCSSCCCTTCHHHH--HHST----------
T ss_pred             HHHHHHHHHHHHcCCCCccccCCHHHHHHHHhcCCCcCHHHHHHHHHHhCCCCCcCccccHHHH--HHhc----------
Confidence            99999999999985 55543    4579999999999999999999999999889999999877  5552          


Q ss_pred             CCCHHHHHHHHHHhCCcccHHHHHHHHH
Q 026681          158 TSSPEQTREALQRWLPKEEWVRINPLLV  185 (235)
Q Consensus       158 ~~~~~~~~~~l~~~~p~~~~~~~~~~l~  185 (235)
                      ..+++++++.++.|.|.+.|..+|.|..
T Consensus       247 ~~~~~~~~~~~~~~~P~r~~a~~~lw~~  274 (282)
T 1mpg_A          247 GMTPAQIRRYAERWKPWRSYALLHIWYT  274 (282)
T ss_dssp             TCCHHHHHHHHGGGTTCHHHHHHHHHTC
T ss_pred             cCCHHHHHHHHHHcCCHHHHHHHHHHHh
Confidence            3568899999999999999999998754

>2xhi_A N-glycosylase/DNA lyase; lyase-DNA complex, lyase/DNA complex, separation-OF-function helix-hairpin-helix, DNA repair; HET: 8OG; 1.55A {Homo sapiens} PDB: 1ko9_A 1lwy_A* 1hu0_A* 1lwv_A* 1lww_A* 2noe_A* 2noh_A* 2nol_A* 1n3c_A* 1fn7_A* 2noz_A* 1yqk_A 1yqr_A* 1yql_A* 1yqm_A* 2noi_A 1ebm_A* 1m3q_A* 1m3h_A* 1n39_A* ...

Probab=99.96  E-value=3e-28  Score=218.26  Aligned_cols=165  Identities=20%  Similarity=0.299  Sum_probs=129.4

Q ss_pred             CCCCCCCChHHHHHHHHHhccccHHHHHHHHHHHHHc--------------CCCCHHHHhcCCHHHHHHhhccCCChHHH
Q 026681           17 SSLPPKERRFAVLLSALLSSLTKDKVADGALQRLLQN--------------GLHTAEAIDKADEATIKDLIYPVAFYTRK   82 (235)
Q Consensus        17 ~~~p~~~~~f~~lv~~iLsqqt~~~~~~~~~~~l~~~--------------~~pt~~~la~a~~e~l~~~l~~~G~~~~K   82 (235)
                      .+++ .+||||+||++||+|||+++++..++.+|++.              .||||++|+.++.+   +.|+.+||. .|
T Consensus       145 lR~~-~~dpfE~LV~~ILsQq~s~~~a~~~~~rL~~~~G~~~~~~~g~~~~~fPtpe~La~~~~e---e~Lr~~Gl~-~R  219 (360)
T 2xhi_A          145 VRLL-RQDPIECLFSFICSSNNNIARITGMVERLCQAFGPRLIQLDDVTYHGFPSLQALAGPEVE---AHLRKLGLG-YR  219 (360)
T ss_dssp             CCCC-CCCHHHHHHHHHTTTTSCHHHHHHHHHHHHHHHSCEEEEETTEEEECCCCHHHHTSTTHH---HHHHHTTCT-TH
T ss_pred             CCCC-CCCHHHHHHHHHHhCcCcHHHHHHHHHHHHHHhCCCcccCCCcccccCCCHHHHHcCCHH---HHHHHcCCc-HH
Confidence            3444 48999999999999999999999999999883              48999999999764   234556884 68


Q ss_pred             HHHHHHHHHHHHHhcCCC--------Ch--hhHHHHHcCCCCcHHHHHHHHHHhcCCcceeecchHHHHHHHHh-cCcCC
Q 026681           83 ACNMKKIAKICLTKYDGD--------IP--SSLDELLALPGIGPKMANMVMTLGWFNVQGICVDTHVHRICNRL-GWVTQ  151 (235)
Q Consensus        83 a~~l~~~a~~i~~~~~g~--------~~--~~~~~L~~l~GIG~~tA~~il~~~~~~~~~~pvDt~v~Rv~~Rl-g~~~~  151 (235)
                      |++|+++|+.+.+.|+|+        +|  +++++|++|||||+|||++|++|+++++++||||+||.|++.|+ |+...
T Consensus       220 A~~I~~~A~~i~~~~~G~~~L~~l~~~~~~~~~~~L~~LpGIGp~TA~~ill~alg~pd~fpvDthV~Ri~~r~~gl~~~  299 (360)
T 2xhi_A          220 ARYVSASARAILEEQGGLAWLQQLRESSYEEAHKALCILPGVGTCVADKICLMALDKPQAVPVNVHMWHIAQRDYSWHPT  299 (360)
T ss_dssp             HHHHHHHHHHHHHTTCTHHHHHGGGTSCHHHHHHHHTTSTTCCHHHHHHHHHHHSCCTTCCCCSHHHHHHHHHHHCCCCS
T ss_pred             HHHHHHHHHHHHhccCCccCHHHHhcCCHHHHHHHHHhCCCCCHHHHHHHHHHhCCCCCEEEecHHHHHHHHHHhCcccc
Confidence            999999999999988775        44  78999999999999999999999999988999999999999996 76542


Q ss_pred             CCCCCCCCCH---HHHHH-HHHHhCCcccHHHHHHHHHHH
Q 026681          152 PGTKQKTSSP---EQTRE-ALQRWLPKEEWVRINPLLVGF  187 (235)
Q Consensus       152 ~~~~~~~~~~---~~~~~-~l~~~~p~~~~~~~~~~l~~~  187 (235)
                      .. ..+..+.   +++++ ..+.|-|...|..++.|-.++
T Consensus       300 ~~-~~k~~~~~~~~~l~~~~~e~w~p~~~~a~~yLw~~~~  338 (360)
T 2xhi_A          300 TS-QAKGPSPQTNKELGNFFRSLWGPYAGWAQAVLFSADL  338 (360)
T ss_dssp             SC-SCSSCCHHHHHHHHHHHHHHHCTTHHHHHHHHHHHHH
T ss_pred             cc-cccCCChHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence            11 0011222   22222 356677777777777665443

>2jhn_A ALKA, 3-methyladenine DNA-glycosylase; DNA repair, N1-methyladenine, N3-methylcytosine, hyperthermophiles, hydrolase; HET: MBO MES; 1.8A {Archaeoglobus fulgidus} PDB: 2jhj_A

Probab=99.95  E-value=9.3e-28  Score=210.14  Aligned_cols=158  Identities=20%  Similarity=0.172  Sum_probs=131.1

Q ss_pred             CCCCCC--CCChHHHHHHHHHhccccHHHHHHHHHHHHHc-C------------CCCHHHHhcCCHHHHHHhhccCCChH
Q 026681           16 DSSLPP--KERRFAVLLSALLSSLTKDKVADGALQRLLQN-G------------LHTAEAIDKADEATIKDLIYPVAFYT   80 (235)
Q Consensus        16 ~~~~p~--~~~~f~~lv~~iLsqqt~~~~~~~~~~~l~~~-~------------~pt~~~la~a~~e~l~~~l~~~G~~~   80 (235)
                      |..++.  .+||||.||++||+|||+++++.+++.+|.+. +            ||||++|+++++++|    +++||+.
T Consensus       107 glr~~~~~~~d~fe~lv~~Il~Qq~s~~~a~~~~~rL~~~~G~~~~~~g~~~~~fPtp~~la~~~~~~L----r~~G~~~  182 (295)
T 2jhn_A          107 GFGRAGLMSMSVFEGIAKAIIQQQISFVVAEKLAAKIVGRFGDEVEWNGLKFYGFPTQEAILKAGVEGL----RECGLSR  182 (295)
T ss_dssp             TCCSCCCSCSSHHHHHHHHHHTTTSCHHHHHHHHHHHHHHHSCEEEETTEEEECCCCHHHHHHHHHHHH----HHTTCCH
T ss_pred             CCCCCCCCCCCHHHHHHHHHHcCcccHHHHHHHHHHHHHHhCCCCCCCCCccccCCCHHHHHcCCHHHH----HHcCCCH
Confidence            445665  68999999999999999999999999999884 2            899999999999887    4559999


Q ss_pred             HHHHHHHHHHHHHHHhcCC--CCh--hhHHHHHcCCCCcHHHHHHHHHHhcCCcceeecc-hHHHHHHHHhcCcCCCCCC
Q 026681           81 RKACNMKKIAKICLTKYDG--DIP--SSLDELLALPGIGPKMANMVMTLGWFNVQGICVD-THVHRICNRLGWVTQPGTK  155 (235)
Q Consensus        81 ~Ka~~l~~~a~~i~~~~~g--~~~--~~~~~L~~l~GIG~~tA~~il~~~~~~~~~~pvD-t~v~Rv~~Rlg~~~~~~~~  155 (235)
                      +||++|+++|+.  .++++  .+|  +.++.|++|||||+|||++|++|+++ +++|||| .|++|++.|++....    
T Consensus       183 rKa~~i~~~A~~--g~l~~l~~~~~~e~~~~L~~lpGIG~~TA~~ill~~lg-~d~fpvdD~~~rr~~~~~~g~~~----  255 (295)
T 2jhn_A          183 RKAELIVEIAKE--ENLEELKEWGEEEAYEYLTSFKGIGRWTAELVLSIALG-KNVFPADDLGVRRAVSRLYFNGE----  255 (295)
T ss_dssp             HHHHHHHHHHTC--SSGGGGGGSCHHHHHHHHHTSTTCCHHHHHHHHHHTTC-CCCCCTTCHHHHHHHHHHHSTTC----
T ss_pred             HHHHHHHHHHHC--CCHhhhhcCCHHHHHHHHhcCCCcCHHHHHHHHHHccC-CCcccchHHHHHHHHHHHhcCCC----
Confidence            999999999998  33332  233  36899999999999999999999999 8999995 555669999843321    


Q ss_pred             CCCCCHHHHHHHHHHhCCcccHHHHHHHHH
Q 026681          156 QKTSSPEQTREALQRWLPKEEWVRINPLLV  185 (235)
Q Consensus       156 ~~~~~~~~~~~~l~~~~p~~~~~~~~~~l~  185 (235)
                       +..+++++++..+.|.|...|..+|.|..
T Consensus       256 -~~~~~~~~~~~~e~~~p~r~~a~~~Lw~~  284 (295)
T 2jhn_A          256 -IQSAEKVREIARERFGRFARDILFYLFLY  284 (295)
T ss_dssp             -CCCHHHHHHHHHHHTGGGHHHHHHHHHHH
T ss_pred             -CCCCHHHHHHHHHhcccHHHHHHHHHHHh
Confidence             13578889999999999999988887754

>2ofk_A 3-methyladenine DNA glycosylase I, constitutive; DNA repair, base excision, helix-hairpin-helix, hydrolase; HET: PGE; 1.50A {Salmonella typhi} PDB: 2ofi_A* 1lmz_A 1nku_A 1p7m_A*

Probab=96.16  E-value=0.087  Score=42.17  Aligned_cols=100  Identities=12%  Similarity=0.061  Sum_probs=77.7

Q ss_pred             hHHHHHHHHHhccccHHHHHHHHHHHHHcCC--CCHHHHhcCCHHHHHHhhccCCC--hHHHHHHHHHHHHHHHH---hc
Q 026681           25 RFAVLLSALLSSLTKDKVADGALQRLLQNGL--HTAEAIDKADEATIKDLIYPVAF--YTRKACNMKKIAKICLT---KY   97 (235)
Q Consensus        25 ~f~~lv~~iLsqqt~~~~~~~~~~~l~~~~~--pt~~~la~a~~e~l~~~l~~~G~--~~~Ka~~l~~~a~~i~~---~~   97 (235)
                      -||.|+-+.+..-.++..+.+-...+.+. |  .+|+.+|..+++++++++..-|.  ++.|.+.+++=|+++.+   +|
T Consensus        31 LFE~L~Le~fQAGLSW~tIL~KRe~fr~A-F~~Fd~~~VA~~~e~~ve~Ll~d~~IIRnr~KI~A~i~NA~~~l~i~~e~  109 (183)
T 2ofk_A           31 LFEMICLEGQQAGLSWITVLKKRENYRAC-FHQFDPIRIAAMQEEDVERLLQNTGIIRHRGKIQAIISNARAWLAMEQNG  109 (183)
T ss_dssp             HHHHHHHHHHTTTSCHHHHHHTHHHHHHH-TGGGCHHHHHTCCHHHHHHHTTCTTSCCCHHHHHHHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHhccCCHHHHHHhHHHHHHH-HcCCCHHHHcCCCHHHHHHHhcCCcchhhHHHHHHHHHHHHHHHHHHHhc
Confidence            49999999999999999999988888874 4  58999999999999999998887  45677777777777553   44


Q ss_pred             CC----------------------CChh-------hHHHHHc--CCCCcHHHHHHHHHH
Q 026681           98 DG----------------------DIPS-------SLDELLA--LPGIGPKMANMVMTL  125 (235)
Q Consensus        98 ~g----------------------~~~~-------~~~~L~~--l~GIG~~tA~~il~~  125 (235)
                      |+                      ++|.       .-+.|.+  ++-|||.|+.++|.-
T Consensus       110 Gsf~~ylW~fv~~~pi~~~~~~~~~vp~~t~~S~~lsk~LKkrGfkFvGpT~~yafmQA  168 (183)
T 2ofk_A          110 ESFADFVWSFVDGQPQITQAASLDKIPTSTPASDALAKALKKRGFKFVGTTICYSFMQA  168 (183)
T ss_dssp             CCHHHHHHHTTTTSCEECCCSSGGGSCSCCHHHHHHHHHHHHTTCCSCCHHHHHHHHHH
T ss_pred             CCHHHHHhhcCCCCCccCCccchhhccCCCHHHHHHHHHHHhCCCeecChHHHHHHHHH
Confidence            32                      1110       2355664  888999999888765

>2jg6_A DNA-3-methyladenine glycosidase; 3-methyladenine-DNA-glycosylase-I, hydrolase; 1.70A {Staphylococcus aureus} PDB: 4aia_A* 4ai5_A* 4ai4_A

Probab=96.09  E-value=0.095  Score=42.02  Aligned_cols=100  Identities=13%  Similarity=0.047  Sum_probs=78.0

Q ss_pred             hHHHHHHHHHhccccHHHHHHHHHHHHHcCC--CCHHHHhcCCHHHHHHhhccCCC--hHHHHHHHHHHHHHHH---Hhc
Q 026681           25 RFAVLLSALLSSLTKDKVADGALQRLLQNGL--HTAEAIDKADEATIKDLIYPVAF--YTRKACNMKKIAKICL---TKY   97 (235)
Q Consensus        25 ~f~~lv~~iLsqqt~~~~~~~~~~~l~~~~~--pt~~~la~a~~e~l~~~l~~~G~--~~~Ka~~l~~~a~~i~---~~~   97 (235)
                      -||.|+-+.+..-.++..+.+-...+.+. |  .+|+.||..+++++++++..-|.  ++.|.+.+++=|+++.   ++|
T Consensus        31 LFE~L~LEgfQAGLSW~tIL~KRe~fR~A-F~~FD~~~VA~~~e~dve~Ll~d~gIIRnr~KI~A~i~NA~~~l~i~~e~  109 (186)
T 2jg6_A           31 LFKLLALESQHAGLSWLTILKKKEAYEEA-FYDFEPEKVAQMTAQDIDRLMTFPNIVHHRKKLEAIVNQAQGYLKIEQAY  109 (186)
T ss_dssp             HHHHHHHHHTCTTSCHHHHHHHHHHHHHH-TGGGCHHHHTTCCHHHHHHHTTCTTSCCCHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhccCCHHHHHHhHHHHHHH-HcCCCHHHHhCCCHHHHHHHhcCccchhhHHHHHHHHHHHHHHHHHHHhc
Confidence            49999999999999999999998888874 4  58999999999999999998887  4567777777676654   344


Q ss_pred             CC----------------------CCh-------hhHHHHHc--CCCCcHHHHHHHHHH
Q 026681           98 DG----------------------DIP-------SSLDELLA--LPGIGPKMANMVMTL  125 (235)
Q Consensus        98 ~g----------------------~~~-------~~~~~L~~--l~GIG~~tA~~il~~  125 (235)
                      |+                      ++|       ..-+.|.+  ++-|||.|+.++|.-
T Consensus       110 gsf~~ylW~fv~~~p~~~~~~~~~~vp~~t~~S~~lsKdLKkrGFkFvGpt~~YafmQA  168 (186)
T 2jg6_A          110 GSFSKFLWSYVNGKPKDLQYEHASDRITVDDTATQLSKDLKQYGFKFLGPVTVFSFLEA  168 (186)
T ss_dssp             SCHHHHHHGGGTTSCEECCCCSGGGCCSCCHHHHHHHHHHHTTTCCSCCHHHHHHHHHH
T ss_pred             CCHHHHHHhcCCCCCccCCccchhhcCCCCHHHHHHHHHHHHCCCeeechHHHHHHHHH
Confidence            32                      122       12355665  889999999998865

>1wcn_A Transcription elongation protein NUSA; RNA-binding protein, escherichia coli NUSA, transcription regulation, regulation of RNA binding; NMR {Escherichia coli} PDB: 2jzb_B

Probab=94.04  E-value=0.12  Score=34.83  Aligned_cols=45  Identities=18%  Similarity=0.189  Sum_probs=39.5

Q ss_pred             HHHHHHHHcCCCCHHHHhcCCHHHHHHhhccCCChHHHHHHHHHHHHH
Q 026681           45 GALQRLLQNGLHTAEAIDKADEATIKDLIYPVAFYTRKACNMKKIAKI   92 (235)
Q Consensus        45 ~~~~~l~~~~~pt~~~la~a~~e~l~~~l~~~G~~~~Ka~~l~~~a~~   92 (235)
                      ....+|.+.++-|.++|+.++.++|.++.   |++..||..|+..|+.
T Consensus        18 ~~~~kL~e~Gi~TvedlA~~~~~eL~~i~---gise~kA~~ii~aAr~   62 (70)
T 1wcn_A           18 DLAFKLAARGVCTLEDLAEQGIDDLADIE---GLTDEKAGALIMAARN   62 (70)
T ss_dssp             HHHHHHHTTTCCSHHHHHTSCHHHHHTSS---SCCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHcCCCcHHHHHcCCHHHHHHcc---CCCHHHHHHHHHHHHH
Confidence            34577888899999999999999998864   9999999999999987

>4glx_A DNA ligase; inhibitor, ligase-ligase inhibitor-DNA complex; HET: DNA 0XS; 1.90A {Escherichia coli}

Probab=92.95  E-value=0.23  Score=46.70  Aligned_cols=92  Identities=18%  Similarity=0.324  Sum_probs=62.6

Q ss_pred             HHHHHHHHHHcCC-CCHHHHhcCCHHHHHHhhccCCChHHHHHHHHHHHHH-------------------------HHHh
Q 026681           43 ADGALQRLLQNGL-HTAEAIDKADEATIKDLIYPVAFYTRKACNMKKIAKI-------------------------CLTK   96 (235)
Q Consensus        43 ~~~~~~~l~~~~~-pt~~~la~a~~e~l~~~l~~~G~~~~Ka~~l~~~a~~-------------------------i~~~   96 (235)
                      ....+..|++.++ -++.+|..++.++|..+   =||....|..|.+.-+.                         +.+.
T Consensus       455 G~~~i~~L~~~g~i~~~~Dly~L~~~~L~~l---~g~geKsa~nL~~aIe~sk~~~l~r~l~aLGI~~vG~~~a~~La~~  531 (586)
T 4glx_A          455 GDKIIDQLVEKEYVHTPADLFKLTAGKLTGL---ERMGPKSAQNVVNALEKAKETTFARFLYALGIREVGEATAAGLAAY  531 (586)
T ss_dssp             CHHHHHHHHHTTCCSSGGGGGTCCHHHHHTS---TTCCHHHHHHHHHHHHHHTBCCHHHHHHHTTCTTCCHHHHHHHHHH
T ss_pred             CHHHHHHHHhcCCCCCHHHHhCCCHHHHhcc---cCccHHHHHHHHHHHHHHcCCCHHHHHHHcCCCchhHHHHHHHHHH
Confidence            4556777887765 68999999998887654   37777777777654333                         2222


Q ss_pred             cCCCCh----hhHHHHHcCCCCcHHHHHHHHHHhcCCcceeecchHHHHHHHHh
Q 026681           97 YDGDIP----SSLDELLALPGIGPKMANMVMTLGWFNVQGICVDTHVHRICNRL  146 (235)
Q Consensus        97 ~~g~~~----~~~~~L~~l~GIG~~tA~~il~~~~~~~~~~pvDt~v~Rv~~Rl  146 (235)
                      | +++.    .+.++|.+++|||+.+|..|..| |.       |.+...++.+|
T Consensus       532 f-~sl~~l~~a~~e~l~~i~giG~~~A~si~~f-f~-------~~~n~~~i~~L  576 (586)
T 4glx_A          532 F-GTLEALEAASIEELQKVPDVGIVVASHVHNF-FA-------EESNRNVISEL  576 (586)
T ss_dssp             H-CSHHHHHHCCHHHHTTSTTCCHHHHHHHHHH-HH-------SHHHHHHHHHH
T ss_pred             c-CCHHHHHccCHHHHhcCCCccHHHHHHHHHH-Hc-------CHHHHHHHHHH
Confidence            2 2332    24688999999999999999887 22       33555666665

>1u9l_A Transcription elongation protein NUSA; escherichia coli NUSA, phage lambda protein N, regulation of RNA binding, transcription antitermination, X-RAY crystallography; 1.90A {Escherichia coli} SCOP: a.60.4.2 PDB: 1wcl_A

Probab=92.47  E-value=0.35  Score=32.49  Aligned_cols=48  Identities=15%  Similarity=0.180  Sum_probs=40.7

Q ss_pred             HHHHHHHcCCCCHHHHhcCCHHHHHHhhccCCChHHHHHHHHHHHHHHHHh
Q 026681           46 ALQRLLQNGLHTAEAIDKADEATIKDLIYPVAFYTRKACNMKKIAKICLTK   96 (235)
Q Consensus        46 ~~~~l~~~~~pt~~~la~a~~e~l~~~l~~~G~~~~Ka~~l~~~a~~i~~~   96 (235)
                      ....|.+.||-|.++|+.++.++|.++   -||...|+.-|++-|+.++..
T Consensus        18 ~a~~L~~~Gf~tve~vA~~~~~eL~~I---~G~dE~~a~~l~~~A~~~l~~   65 (70)
T 1u9l_A           18 FATVLVEEGFSTLEELAYVPMKELLEI---EGLDEPTVEALRERAKNALAT   65 (70)
T ss_dssp             HHHHHHHTTCCCHHHHHHSCHHHHTTS---TTCCHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHcCcCcHHHHHcCCHHHHhhc---cCCCHHHHHHHHHHHHHHHHH
Confidence            456777789999999999999998665   499999999999999887653

>3vdp_A Recombination protein RECR; zinc finger, DNA repair, DNA binding; 2.45A {Thermoanaerobacter tengcongensis} PDB: 3vdu_A 3ve5_D

Probab=92.17  E-value=0.067  Score=43.73  Aligned_cols=29  Identities=34%  Similarity=0.480  Sum_probs=23.9

Q ss_pred             ChhhHHHHHcCCCCcHHHHHHHHHHhcCC
Q 026681          101 IPSSLDELLALPGIGPKMANMVMTLGWFN  129 (235)
Q Consensus       101 ~~~~~~~L~~l~GIG~~tA~~il~~~~~~  129 (235)
                      +.+..+.|.+|||||+|+|.=+..+.+..
T Consensus        21 l~~LI~~l~~LPGIG~KsA~RlA~hLL~~   49 (212)
T 3vdp_A           21 VAKLIEELSKLPGIGPKTAQRLAFFIINM   49 (212)
T ss_dssp             HHHHHHHHHTSTTCCHHHHHHHHHHHTTS
T ss_pred             HHHHHHHHHHCCCCCHHHHHHHHHHHHcC
Confidence            45677889999999999999887776654

>1x2i_A HEF helicase/nuclease; alpha helix, helix-hairpin-helix DNA binding domain, homodimer, hydrolase; 1.45A {Pyrococcus furiosus} SCOP: a.60.2.5

Probab=91.38  E-value=0.26  Score=32.74  Aligned_cols=23  Identities=35%  Similarity=0.538  Sum_probs=19.7

Q ss_pred             hHHHHHcCCCCcHHHHHHHHHHh
Q 026681          104 SLDELLALPGIGPKMANMVMTLG  126 (235)
Q Consensus       104 ~~~~L~~l~GIG~~tA~~il~~~  126 (235)
                      ..+.|.+++|||+++|..+..+.
T Consensus        44 ~~~~L~~i~Gig~~~a~~i~~~~   66 (75)
T 1x2i_A           44 SVAELMKVEGIGEKIAKEIRRVI   66 (75)
T ss_dssp             CHHHHTTSTTCCHHHHHHHHHHH
T ss_pred             CHHHHhcCCCCCHHHHHHHHHHH
Confidence            56889999999999999887663

>2fmp_A DNA polymerase beta; nucleotidyl transferase, transferase/DNA complex; HET: DNA DOC DCT; 1.65A {Homo sapiens} SCOP: a.60.6.1 a.60.12.1 d.218.1.2 PDB: 1bpx_A* 1bpz_A* 1mq2_A* 1mq3_A* 1bpy_A* 1tva_A* 1zjm_A* 1zjn_A* 1zqa_A* 1zqb_A* 1zqc_A* 1zqd_A* 1zqe_A* 1zqf_A* 1zqg_A* 1zqh_A* 1zqi_A* 1zqj_A* 1zqk_A* 1zql_A* ...

Probab=91.37  E-value=0.3  Score=42.68  Aligned_cols=51  Identities=27%  Similarity=0.303  Sum_probs=32.9

Q ss_pred             hccCCChHHHHHHHHHHHHH----HHHhcCCCC-hhhHHHHHcCCCCcHHHHHHHHHH
Q 026681           73 IYPVAFYTRKACNMKKIAKI----CLTKYDGDI-PSSLDELLALPGIGPKMANMVMTL  125 (235)
Q Consensus        73 l~~~G~~~~Ka~~l~~~a~~----i~~~~~g~~-~~~~~~L~~l~GIG~~tA~~il~~  125 (235)
                      |.++|  ...|..|.++.+.    -.++...+. |.....|+++||||+++|..+-.-
T Consensus        62 LpGIG--~~~A~kI~E~l~tG~~~~le~l~~~~~~~~l~~l~~V~GiGpk~a~~l~~~  117 (335)
T 2fmp_A           62 LPGVG--TKIAEKIDEFLATGKLRKLEKIRQDDTSSSINFLTRVSGIGPSAARKFVDE  117 (335)
T ss_dssp             STTCC--HHHHHHHHHHHHHSSCHHHHHHHHCHHHHHHHHHTTSTTCCHHHHHHHHHT
T ss_pred             CCCCc--HHHHHHHHHHHHhCCcHHHHHHHcccchhHHHHHhCCCCCCHHHHHHHHHc
Confidence            45555  4557777776543    011111233 677899999999999999987543

>1vdd_A Recombination protein RECR; helix-hairpin-helix, zinc finger, toprim, walker B ATP binding motif; 2.50A {Deinococcus radiodurans} SCOP: e.49.1.1 PDB: 2v1c_A

Probab=91.19  E-value=0.1  Score=43.12  Aligned_cols=29  Identities=38%  Similarity=0.473  Sum_probs=23.8

Q ss_pred             ChhhHHHHHcCCCCcHHHHHHHHHHhcCC
Q 026681          101 IPSSLDELLALPGIGPKMANMVMTLGWFN  129 (235)
Q Consensus       101 ~~~~~~~L~~l~GIG~~tA~~il~~~~~~  129 (235)
                      +.+..+.|.+|||||+|||.=+..+.+..
T Consensus         7 l~~LI~~l~~LPGIG~KSA~RlA~hLL~~   35 (228)
T 1vdd_A            7 LVSLIRELSRLPGIGPKSAQRLAFHLFEQ   35 (228)
T ss_dssp             HHHHHHHHHTSTTCCHHHHHHHHHHHSSS
T ss_pred             HHHHHHHHhHCCCCCHHHHHHHHHHHHcC
Confidence            44678899999999999998877776654

>2fmp_A DNA polymerase beta; nucleotidyl transferase, transferase/DNA complex; HET: DNA DOC DCT; 1.65A {Homo sapiens} SCOP: a.60.6.1 a.60.12.1 d.218.1.2 PDB: 1bpx_A* 1bpz_A* 1mq2_A* 1mq3_A* 1bpy_A* 1tva_A* 1zjm_A* 1zjn_A* 1zqa_A* 1zqb_A* 1zqc_A* 1zqd_A* 1zqe_A* 1zqf_A* 1zqg_A* 1zqh_A* 1zqi_A* 1zqj_A* 1zqk_A* 1zql_A* ...

Probab=90.61  E-value=0.57  Score=40.91  Aligned_cols=56  Identities=27%  Similarity=0.331  Sum_probs=38.3

Q ss_pred             HHHHhhccCCChHHHHHHHHHHHHHHHHhcCCCChhhHHHHHcCCCCcHHHHHHHHHH
Q 026681           68 TIKDLIYPVAFYTRKACNMKKIAKICLTKYDGDIPSSLDELLALPGIGPKMANMVMTL  125 (235)
Q Consensus        68 ~l~~~l~~~G~~~~Ka~~l~~~a~~i~~~~~g~~~~~~~~L~~l~GIG~~tA~~il~~  125 (235)
                      ++..++...|=..-|+..-+++|..|. .+..++.+ ..+|.+|||||+++|+.|.-+
T Consensus        21 ~ia~l~e~~~~~~~rv~AYr~Aa~~l~-~l~~~i~~-~~~l~~LpGIG~~~A~kI~E~   76 (335)
T 2fmp_A           21 ELANFEKNVSQAIHKYNAYRKAASVIA-KYPHKIKS-GAEAKKLPGVGTKIAEKIDEF   76 (335)
T ss_dssp             HHHHHHHHTTCCHHHHHHHHHHHHHHH-HCSSCCCC-HHHHHTSTTCCHHHHHHHHHH
T ss_pred             HHHHHHHhcCCCcHHHHHHHHHHHHHH-hCCccccC-HHHHhcCCCCcHHHHHHHHHH
Confidence            344444433434446777888888864 45555544 456999999999999999865

>2ztd_A Holliday junction ATP-dependent DNA helicase RUVA; recombination, branch migration, DNA BIND oligomerization, acidic PIN; 2.40A {Mycobacterium tuberculosis} PDB: 2ztc_A 2zte_A 2h5x_A 1bvs_A

Probab=90.09  E-value=0.18  Score=41.28  Aligned_cols=27  Identities=22%  Similarity=0.262  Sum_probs=22.1

Q ss_pred             hhHHHHHcCCCCcHHHHHHHHHHhcCC
Q 026681          103 SSLDELLALPGIGPKMANMVMTLGWFN  129 (235)
Q Consensus       103 ~~~~~L~~l~GIG~~tA~~il~~~~~~  129 (235)
                      .+.+.|.++||||+|||+-|..---++
T Consensus       120 ~d~~~L~~vpGIG~KtA~rIi~elk~k  146 (212)
T 2ztd_A          120 GNVAALTRVPGIGKRGAERMVLELRDK  146 (212)
T ss_dssp             TCHHHHHTSTTCCHHHHHHHHHHHTTT
T ss_pred             CCHHHHhhCCCCCHHHHHHHHHHHHHh
Confidence            567899999999999999987654443

>2duy_A Competence protein comea-related protein; helix-hairpin-helix, structural genomics, NPPSFA; 1.75A {Thermus thermophilus} SCOP: a.60.2.7

Probab=89.58  E-value=0.2  Score=33.75  Aligned_cols=22  Identities=55%  Similarity=0.915  Sum_probs=19.6

Q ss_pred             hHHHHHcCCCCcHHHHHHHHHH
Q 026681          104 SLDELLALPGIGPKMANMVMTL  125 (235)
Q Consensus       104 ~~~~L~~l~GIG~~tA~~il~~  125 (235)
                      ..+.|.++||||+++|..|+..
T Consensus        25 ~~~~L~~ipGIG~~~A~~Il~~   46 (75)
T 2duy_A           25 SLEELMALPGIGPVLARRIVEG   46 (75)
T ss_dssp             CHHHHTTSTTCCHHHHHHHHHT
T ss_pred             CHHHHHhCCCCCHHHHHHHHHH
Confidence            5678999999999999999875

>4gfj_A Topoisomerase V; helix-hairpin-helix, DNA repair enzyme, DNA B isomerase; 2.91A {Methanopyrus kandleri AV19}

Probab=89.51  E-value=0.34  Score=43.72  Aligned_cols=69  Identities=23%  Similarity=0.453  Sum_probs=34.3

Q ss_pred             HHHcCCCCHHHHhcCCHHHHHHhhccCCChHHHHHHHHHHHHH------------HHHhcCCC------Ch---------
Q 026681           50 LLQNGLHTAEAIDKADEATIKDLIYPVAFYTRKACNMKKIAKI------------CLTKYDGD------IP---------  102 (235)
Q Consensus        50 l~~~~~pt~~~la~a~~e~l~~~l~~~G~~~~Ka~~l~~~a~~------------i~~~~~g~------~~---------  102 (235)
                      |.. .|.+..++..++.++|.++    ||+.++...|+.+-+.            +.++|+.-      +|         
T Consensus       534 lkr-~ygs~savr~~pv~elrel----g~sd~~ia~ikgip~~~~~~~~~e~a~~l~er~~~~~~~~~~~~~~~l~~~g~  608 (685)
T 4gfj_A          534 LKR-KYGSASAVRRLPVEELREL----GFSDDEIAEIKGIPKKLREAFDLETAAELYERYGSLKEIGRRLSYDDLLELGA  608 (685)
T ss_dssp             HHH-HSSCHHHHHHSCHHHHHTT----SCCHHHHHHHHTCCHHHHHHSCHHHHHHHHHHHSSSTGGGGSCGGGCCSSSCC
T ss_pred             HHH-hhccHHHHHhccHHHHHHc----CCchhhHHHhcCCcHHHHhhcCHHHHHHHHHHhccHHHHhhcCCHHHHhccCC
Confidence            444 5899999999999998776    9999998888765443            44555421      11         


Q ss_pred             ----------hhHHHHHcCCCCcHHHHHHHH
Q 026681          103 ----------SSLDELLALPGIGPKMANMVM  123 (235)
Q Consensus       103 ----------~~~~~L~~l~GIG~~tA~~il  123 (235)
                                ..++.|+.++||||+.|+-++
T Consensus       609 ~~~~~~eik~p~~k~ll~~~gv~p~la~r~~  639 (685)
T 4gfj_A          609 TPKAAAEIKGPEFKFLLNIEGVGPKLAERIL  639 (685)
T ss_dssp             GGGC---------------------------
T ss_pred             CHHHHHHhcChhHHHhhcccCCCHHHHHHHH
Confidence                      146778899999999988665

>2ihm_A POL MU, DNA polymerase MU; helix-turn-helix, transferase/DNA complex; HET: DNA D3T; 2.40A {Mus musculus}

Probab=89.40  E-value=0.48  Score=41.84  Aligned_cols=47  Identities=17%  Similarity=0.238  Sum_probs=34.2

Q ss_pred             CCChHHHHHHHHHHHHHHHHhcCCCChhhHHHHHcCCCCcHHHHHHHHHH
Q 026681           76 VAFYTRKACNMKKIAKICLTKYDGDIPSSLDELLALPGIGPKMANMVMTL  125 (235)
Q Consensus        76 ~G~~~~Ka~~l~~~a~~i~~~~~g~~~~~~~~L~~l~GIG~~tA~~il~~  125 (235)
                      .| ..-|+..-+++|..|.. +..++.+. ++|.+|||||+++|+.|.-+
T Consensus        34 ~g-~~~r~~AYr~Aa~~l~~-l~~~i~~~-~~l~~lpGIG~~~A~kI~E~   80 (360)
T 2ihm_A           34 EA-NEGRLLSFSRAASVLKS-LPCPVASL-SQLHGLPYFGEHSTRVIQEL   80 (360)
T ss_dssp             TT-CHHHHHHHHHHHHHHHH-CSSCCCSG-GGGTTCTTCCHHHHHHHHHH
T ss_pred             cC-CcHHHHHHHHHHHHHHh-CCcccCCH-HHHhcCCCCCHHHHHHHHHH
Confidence            35 44567777888888654 55555443 34999999999999999865

>1z00_A DNA excision repair protein ERCC-1; helix-hairpin-helix, hydrolase; HET: DNA; NMR {Homo sapiens} SCOP: a.60.2.5

Probab=89.28  E-value=0.37  Score=33.47  Aligned_cols=23  Identities=30%  Similarity=0.560  Sum_probs=20.1

Q ss_pred             hHHHHHcCCCCcHHHHHHHHHHh
Q 026681          104 SLDELLALPGIGPKMANMVMTLG  126 (235)
Q Consensus       104 ~~~~L~~l~GIG~~tA~~il~~~  126 (235)
                      ..++|.++||||+++|..+..+-
T Consensus        49 ~~~eL~~i~GIG~~~a~~I~~~l   71 (89)
T 1z00_A           49 SREDLALCPGLGPQKARRLFDVL   71 (89)
T ss_dssp             CHHHHHTSTTCCHHHHHHHHHHH
T ss_pred             CHHHHHhCCCCCHHHHHHHHHHH
Confidence            56889999999999999998764

>1kft_A UVRC, excinuclease ABC subunit C; helix-hairpin-helix, HHH domain, DNA-binding domain, DNA binding protein; NMR {Escherichia coli} SCOP: a.60.2.3

Probab=89.04  E-value=0.32  Score=32.95  Aligned_cols=22  Identities=27%  Similarity=0.522  Sum_probs=19.2

Q ss_pred             hHHHHHcCCCCcHHHHHHHHHH
Q 026681          104 SLDELLALPGIGPKMANMVMTL  125 (235)
Q Consensus       104 ~~~~L~~l~GIG~~tA~~il~~  125 (235)
                      ..++|.++||||+++|..+..+
T Consensus        54 ~~eeL~~i~GIG~~~a~~I~~~   75 (78)
T 1kft_A           54 SVEEIAKVPGISQGLAEKIFWS   75 (78)
T ss_dssp             CHHHHTTSSSTTSHHHHHHHHH
T ss_pred             CHHHHHHCCCCCHHHHHHHHHH
Confidence            5788999999999999988765

>1ixr_A Holliday junction DNA helicase RUVA; heterooligomeric complex, octameric RUVA, AAA-ATPase domain, complex with nucleotide, hydrolase; HET: ANP; 3.30A {Thermus thermophilus} SCOP: a.60.2.1 b.40.4.2

Probab=88.90  E-value=0.25  Score=39.76  Aligned_cols=27  Identities=15%  Similarity=0.102  Sum_probs=22.0

Q ss_pred             hhHHHHHcCCCCcHHHHHHHHHHhcCC
Q 026681          103 SSLDELLALPGIGPKMANMVMTLGWFN  129 (235)
Q Consensus       103 ~~~~~L~~l~GIG~~tA~~il~~~~~~  129 (235)
                      .+.+.|.++||||+++|.-|...--++
T Consensus       104 ~d~~~L~~vpGIG~K~A~rI~~~lk~k  130 (191)
T 1ixr_A          104 GDARLLTSASGVGRRLAERIALELKGK  130 (191)
T ss_dssp             TCHHHHTTSTTCCHHHHHHHHHHHTTT
T ss_pred             CCHHHHHhCCCCCHHHHHHHHHHHHHh
Confidence            567899999999999999997654333

>2bcq_A DNA polymerase lambda; misalignment, extrahelical, mutagenesis, mutation, deletion, streisinger, slippage, transferase, lyase/DNA complex; HET: DNA; 1.65A {Homo sapiens} SCOP: a.60.6.1 a.60.12.1 d.218.1.2 PDB: 1xsl_A* 2bcr_A* 2bcs_A* 2bcu_A* 2bcv_A* 2gws_A* 3c5g_A* 3c5f_A* 2pfn_A* 1xsp_A* 1xsn_A* 2pfo_A* 2pfp_A* 2pfq_A* 3hw8_A* 3hwt_A* 1rzt_A* 3hx0_A* 3mdc_A* 3mda_A* ...

Probab=88.63  E-value=0.54  Score=41.07  Aligned_cols=50  Identities=24%  Similarity=0.273  Sum_probs=30.2

Q ss_pred             hccCCChHHHHHHHHHHHHH----HHHhcCCCChhhHHHHHcCCCCcHHHHHHHHHH
Q 026681           73 IYPVAFYTRKACNMKKIAKI----CLTKYDGDIPSSLDELLALPGIGPKMANMVMTL  125 (235)
Q Consensus        73 l~~~G~~~~Ka~~l~~~a~~----i~~~~~g~~~~~~~~L~~l~GIG~~tA~~il~~  125 (235)
                      |.++|  ...|..|.++.+.    -+++....+| ..+.|+++||||++||..+-.-
T Consensus        62 lpGIG--~~~A~kI~E~l~tG~~~~le~l~~~~p-~l~ll~~v~GiG~k~a~~l~~~  115 (335)
T 2bcq_A           62 IPGIG--KRMAEKIIEILESGHLRKLDHISESVP-VLELFSNIWGAGTKTAQMWYQQ  115 (335)
T ss_dssp             STTCC--HHHHHHHHHHHHSSSCGGGGGCCTTHH-HHHHHHTSTTCCHHHHHHHHHT
T ss_pred             CCCcc--HHHHHHHHHHHHcCCchHHHHHhhhhH-HHHHHhcCCCcCHHHHHHHHHc
Confidence            45555  4556677666442    0112223344 5566779999999999977543

>2ihm_A POL MU, DNA polymerase MU; helix-turn-helix, transferase/DNA complex; HET: DNA D3T; 2.40A {Mus musculus}

Probab=88.60  E-value=0.34  Score=42.76  Aligned_cols=50  Identities=10%  Similarity=0.071  Sum_probs=31.6

Q ss_pred             ccCCChHHHHHHHHHHHHH----HHHhcC-CCChhhHHHHHcCCCCcHHHHHHHHHH
Q 026681           74 YPVAFYTRKACNMKKIAKI----CLTKYD-GDIPSSLDELLALPGIGPKMANMVMTL  125 (235)
Q Consensus        74 ~~~G~~~~Ka~~l~~~a~~----i~~~~~-g~~~~~~~~L~~l~GIG~~tA~~il~~  125 (235)
                      .++|  ...|..|.++.+.    -+++.. ...|.....|+++||||++||..+-.-
T Consensus        67 pGIG--~~~A~kI~E~l~tG~~~~le~L~~d~~~~~l~~l~~I~GvG~kta~~l~~~  121 (360)
T 2ihm_A           67 PYFG--EHSTRVIQELLEHGTCEEVKQVRCSERYQTMKLFTQVFGVGVKTANRWYQE  121 (360)
T ss_dssp             TTCC--HHHHHHHHHHHHHSCCHHHHHHHHSHHHHHHHHHHTSTTCCHHHHHHHHHT
T ss_pred             CCCC--HHHHHHHHHHHHcCChHHHHHHhcccchHHHHHHhCCCCCCHHHHHHHHHc
Confidence            4444  4557777666543    011111 245567789999999999999987443

>2bcq_A DNA polymerase lambda; misalignment, extrahelical, mutagenesis, mutation, deletion, streisinger, slippage, transferase, lyase/DNA complex; HET: DNA; 1.65A {Homo sapiens} SCOP: a.60.6.1 a.60.12.1 d.218.1.2 PDB: 1xsl_A* 2bcr_A* 2bcs_A* 2bcu_A* 2bcv_A* 2gws_A* 3c5g_A* 3c5f_A* 2pfn_A* 1xsp_A* 1xsn_A* 2pfo_A* 2pfp_A* 2pfq_A* 3hw8_A* 3hwt_A* 1rzt_A* 3hx0_A* 3mdc_A* 3mda_A* ...

Probab=88.49  E-value=0.91  Score=39.61  Aligned_cols=43  Identities=23%  Similarity=0.447  Sum_probs=32.6

Q ss_pred             HHHHHHHHHHHHHHHhcCCCChhhHHHHHcCCCCcHHHHHHHHHH
Q 026681           81 RKACNMKKIAKICLTKYDGDIPSSLDELLALPGIGPKMANMVMTL  125 (235)
Q Consensus        81 ~Ka~~l~~~a~~i~~~~~g~~~~~~~~L~~l~GIG~~tA~~il~~  125 (235)
                      -|+..-.++|..|.. +..++.+ .++|.+|||||+++|+.|.-+
T Consensus        34 ~r~~AYr~Aa~~l~~-l~~~i~~-~~~l~~lpGIG~~~A~kI~E~   76 (335)
T 2bcq_A           34 WRALGYAKAINALKS-FHKPVTS-YQEACSIPGIGKRMAEKIIEI   76 (335)
T ss_dssp             HHHHHHHHHHHHHHS-CCSCCCC-HHHHHTSTTCCHHHHHHHHHH
T ss_pred             HhHHHHHHHHHHHHh-CCccccC-HHHHhcCCCccHHHHHHHHHH
Confidence            467777888888643 5555544 456999999999999999866

>1jms_A Terminal deoxynucleotidyltransferase; polymerase; 2.36A {Mus musculus} SCOP: a.60.6.1 a.60.12.1 d.218.1.2 PDB: 1kdh_A* 1kej_A*

Probab=88.39  E-value=0.57  Score=41.70  Aligned_cols=52  Identities=10%  Similarity=0.090  Sum_probs=36.4

Q ss_pred             HhhccCCChHHHHHHHHHHHHHHHHhcCCCChhhHHHHHcCCCCcHHHHHHHHHH
Q 026681           71 DLIYPVAFYTRKACNMKKIAKICLTKYDGDIPSSLDELLALPGIGPKMANMVMTL  125 (235)
Q Consensus        71 ~~l~~~G~~~~Ka~~l~~~a~~i~~~~~g~~~~~~~~L~~l~GIG~~tA~~il~~  125 (235)
                      +++.-.| ..-|+..-+++|..|. .+..++.+. +.|.+|||||+.+|+.|.-+
T Consensus        48 ~~~e~~g-~~~rv~AYr~Aa~~l~-~l~~~i~~~-~~l~~lpGIG~~ia~kI~E~   99 (381)
T 1jms_A           48 ENDELRE-NEGSCLAFMRASSVLK-SLPFPITSM-KDTEGIPCLGDKVKSIIEGI   99 (381)
T ss_dssp             HHHHHTT-CHHHHHHHHHHHHHHH-TCSSCCCSG-GGGTTCSSCCHHHHHHHHHH
T ss_pred             HHHHhhC-CcHHHHHHHHHHHHHH-hCCccccCH-HHHhcCCCCcHHHHHHHHHH
Confidence            3333345 4557888888888864 455555443 34999999999999999865

>2a1j_B DNA excision repair protein ERCC-1; XPF, xeroderma pigmentosum, DNA repair, endonuclease, helix-hairpin-helix, DNA binding protein; HET: DNA; 2.70A {Homo sapiens} SCOP: a.60.2.5

Probab=88.30  E-value=0.46  Score=33.15  Aligned_cols=23  Identities=30%  Similarity=0.560  Sum_probs=20.0

Q ss_pred             hHHHHHcCCCCcHHHHHHHHHHh
Q 026681          104 SLDELLALPGIGPKMANMVMTLG  126 (235)
Q Consensus       104 ~~~~L~~l~GIG~~tA~~il~~~  126 (235)
                      ..++|.+++|||+++|..+..+.
T Consensus        62 s~~eL~~i~GIG~~~a~~I~~~l   84 (91)
T 2a1j_B           62 SREDLALCPGLGPQKARRLFDVL   84 (91)
T ss_dssp             CHHHHHTSSSCCSHHHHHHHHHH
T ss_pred             CHHHHHhCCCCCHHHHHHHHHHH
Confidence            56889999999999999988764

>1cuk_A RUVA protein; DNA repair, SOS response, DNA-binding, DNA recombination; 1.90A {Escherichia coli} SCOP: a.5.1.1 a.60.2.1 b.40.4.2 PDB: 1hjp_A 1bdx_A* 1c7y_A 1d8l_A

Probab=88.30  E-value=0.31  Score=39.56  Aligned_cols=23  Identities=35%  Similarity=0.603  Sum_probs=20.3

Q ss_pred             hhHHHHHcCCCCcHHHHHHHHHH
Q 026681          103 SSLDELLALPGIGPKMANMVMTL  125 (235)
Q Consensus       103 ~~~~~L~~l~GIG~~tA~~il~~  125 (235)
                      .+.+.|.++||||+|+|.-|...
T Consensus       105 ~d~~~L~~vpGIG~K~A~rI~~e  127 (203)
T 1cuk_A          105 EEVGALVKLPGIGKKTAERLIVE  127 (203)
T ss_dssp             TCHHHHHTSTTCCHHHHHHHHHH
T ss_pred             CCHHHHhhCCCCCHHHHHHHHHH
Confidence            56789999999999999998754

>2a1j_A DNA repair endonuclease XPF; XPF, xeroderma pigmentosum, DNA repair, endonuclease, helix-hairpin-helix, DNA binding protein; HET: DNA; 2.70A {Homo sapiens} SCOP: a.60.2.5 PDB: 2kn7_A*

Probab=87.23  E-value=0.39  Score=31.36  Aligned_cols=24  Identities=33%  Similarity=0.415  Sum_probs=18.9

Q ss_pred             HHHHHcCCCCcHHHHHHHHHHhcCC
Q 026681          105 LDELLALPGIGPKMANMVMTLGWFN  129 (235)
Q Consensus       105 ~~~L~~l~GIG~~tA~~il~~~~~~  129 (235)
                      ...|.++||||++.+..+|.. |+.
T Consensus         3 ~s~L~~IpGIG~kr~~~LL~~-Fgs   26 (63)
T 2a1j_A            3 QDFLLKMPGVNAKNCRSLMHH-VKN   26 (63)
T ss_dssp             CHHHHTSTTCCHHHHHHHHHH-CSS
T ss_pred             HhHHHcCCCCCHHHHHHHHHH-cCC
Confidence            357889999999999888754 443

>1b22_A DNA repair protein RAD51; DNA binding, riken structural genomics/proteomics initiative, RSGI, structural genomics, DNA binding protein; HET: DNA; NMR {Homo sapiens} SCOP: a.60.4.1

Probab=86.60  E-value=0.45  Score=35.08  Aligned_cols=47  Identities=21%  Similarity=0.275  Sum_probs=38.6

Q ss_pred             HHHHHHHHcCCCCHHHHhcCCHHHHHHhhccCCChHHHHHHHHHHHHHHH
Q 026681           45 GALQRLLQNGLHTAEAIDKADEATIKDLIYPVAFYTRKACNMKKIAKICL   94 (235)
Q Consensus        45 ~~~~~l~~~~~pt~~~la~a~~e~l~~~l~~~G~~~~Ka~~l~~~a~~i~   94 (235)
                      ...++|.+.||-|.++|+.++.++|.++   -|++..||..|++.|+.+.
T Consensus        36 ~~i~kL~eAG~~Tve~va~a~~~eL~~i---~GIse~ka~kIi~aA~kl~   82 (114)
T 1b22_A           36 NDVKKLEEAGFHTVEAVAYAPKKELINI---KGISEAKADKILAEAAKLV   82 (114)
T ss_dssp             HHHHHHHTTCCSSGGGBTSSBHHHHHTT---TTCSTTHHHHHHHHHHHHS
T ss_pred             HHHHHHHHcCcCcHHHHHhCCHHHHHHc---cCCCHHHHHHHHHHHHHHc
Confidence            3467788889999999999999988765   4888889999999988764

>1dgs_A DNA ligase; AMP complex, NAD+-dependent; HET: DNA AMP; 2.90A {Thermus filiformis} SCOP: a.60.2.2 b.40.4.6 d.142.2.2 PDB: 1v9p_A*

Probab=86.56  E-value=0.72  Score=44.01  Aligned_cols=76  Identities=17%  Similarity=0.328  Sum_probs=49.4

Q ss_pred             HHHHHHHcC-CCCHHHHhcCCHHHHHHhhccCCChHHHHHHHHHHH-------------------------HHHHHhcCC
Q 026681           46 ALQRLLQNG-LHTAEAIDKADEATIKDLIYPVAFYTRKACNMKKIA-------------------------KICLTKYDG   99 (235)
Q Consensus        46 ~~~~l~~~~-~pt~~~la~a~~e~l~~~l~~~G~~~~Ka~~l~~~a-------------------------~~i~~~~~g   99 (235)
                      .+..|.+.+ .-++.+|..+..++|.++ .  ||...++..|.+..                         +.+.+.|+ 
T Consensus       453 ~i~~L~~~g~I~~~~DL~~L~~e~L~~l-~--g~G~Ksa~nLl~aIe~sk~~~l~R~L~alGI~~VG~~~Ak~La~~Fg-  528 (667)
T 1dgs_A          453 LIERLLEKGLVRDVADLYHLRKEDLLGL-E--RMGEKSAQNLLRQIEESKHRGLERLLYALGLPGVGEVLARNLARRFG-  528 (667)
T ss_dssp             HHHHHHHTTSCSSGGGGGGGCCHHHHTT-S--SCCSTTHHHHHHHHHHGGGCCHHHHHHHTTCSSCCHHHHHHHHHTTS-
T ss_pred             HHHHHHHcCCCCCHHHHHhcCHHHHhcc-c--ccchhhHHHHHHHHHHHhcCcHHHhhHhhccCCccHHHHHHHHHHcC-
Confidence            445555543 368889988887777654 3  55555566665442                         22233332 


Q ss_pred             CCh----hhHHHHHcCCCCcHHHHHHHHHH
Q 026681          100 DIP----SSLDELLALPGIGPKMANMVMTL  125 (235)
Q Consensus       100 ~~~----~~~~~L~~l~GIG~~tA~~il~~  125 (235)
                      ++.    .+.++|.+++|||+++|+.|..|
T Consensus       529 sl~~l~~As~eeL~~I~GIG~~~A~sI~~f  558 (667)
T 1dgs_A          529 TMDRLLEASLEELIEVEEVGELTARAILET  558 (667)
T ss_dssp             BHHHHTTCCHHHHHTSTTCCHHHHHHHHHH
T ss_pred             CHHHHHhCCHHHHHhccCcCHHHHHHHHHH
Confidence            222    35688999999999999999877

>2owo_A DNA ligase; protein-DNA complex, ligase-DNA complex; HET: DNA OMC AMP; 2.30A {Escherichia coli}

Probab=86.49  E-value=2.1  Score=40.80  Aligned_cols=77  Identities=18%  Similarity=0.294  Sum_probs=51.4

Q ss_pred             HHHHHHHHcCC-CCHHHHhcCCHHHHHHhhccCCChHHHHHHHHHHHHH-------------------------HHHhcC
Q 026681           45 GALQRLLQNGL-HTAEAIDKADEATIKDLIYPVAFYTRKACNMKKIAKI-------------------------CLTKYD   98 (235)
Q Consensus        45 ~~~~~l~~~~~-pt~~~la~a~~e~l~~~l~~~G~~~~Ka~~l~~~a~~-------------------------i~~~~~   98 (235)
                      +.+..|.+.++ -++.+|..+..++|..+   -||....+..|.+..+.                         +.+.|+
T Consensus       457 k~i~~L~~~g~I~~~aDL~~L~~~~L~~l---~gfG~Ksa~nLl~aIe~sk~~~l~R~L~algi~~VG~~~Ak~La~~Fg  533 (671)
T 2owo_A          457 KIIDQLVEKEYVHTPADLFKLTAGKLTGL---ERMGPKSAQNVVNALEKAKETTFARFLYALGIREVGEATAAGLAAYFG  533 (671)
T ss_dssp             HHHHHHHHTTCCSSGGGGGTCCHHHHHTS---TTCCHHHHHHHHHHHHHHTBCCHHHHHHHTTCTTCCHHHHHHHHHHHC
T ss_pred             HHHHHHHHcCCCCCHHHHHhhCHHHhhcc---cccchhHHHHHHHHHHHHhcCChhheehhhcccCccHHHHHHHHHHcC
Confidence            34555666543 68999999988877654   36766667777665322                         122221


Q ss_pred             CCCh----hhHHHHHcCCCCcHHHHHHHHHH
Q 026681           99 GDIP----SSLDELLALPGIGPKMANMVMTL  125 (235)
Q Consensus        99 g~~~----~~~~~L~~l~GIG~~tA~~il~~  125 (235)
                       ++.    .+.++|.+++|||+++|..|..|
T Consensus       534 -sl~~l~~As~eeL~~i~GIG~~~A~sI~~f  563 (671)
T 2owo_A          534 -TLEALEAASIEELQKVPDVGIVVASHVHNF  563 (671)
T ss_dssp             -SHHHHHTCCHHHHTTSTTCCHHHHHHHHHH
T ss_pred             -CHHHHHhCCHHHHhhcCCCCHHHHHHHHHH
Confidence             222    24688999999999999999877

>1z00_B DNA repair endonuclease XPF; helix-hairpin-helix, hydrolase; HET: DNA; NMR {Homo sapiens} SCOP: a.60.2.5 PDB: 2aq0_A*

Probab=86.25  E-value=0.63  Score=32.31  Aligned_cols=23  Identities=30%  Similarity=0.475  Sum_probs=19.6

Q ss_pred             hhHHHHHcCCCCcHHHHHHHHHH
Q 026681          103 SSLDELLALPGIGPKMANMVMTL  125 (235)
Q Consensus       103 ~~~~~L~~l~GIG~~tA~~il~~  125 (235)
                      .....|.+|||||++....+|..
T Consensus        15 ~~~s~L~~IpGIG~kr~~~LL~~   37 (84)
T 1z00_B           15 GPQDFLLKMPGVNAKNCRSLMHH   37 (84)
T ss_dssp             HHHHHHHTCSSCCHHHHHHHHHH
T ss_pred             cHHHHHHhCCCCCHHHHHHHHHH
Confidence            45678999999999999888754

>2edu_A Kinesin-like protein KIF22; kinesin-like DNA binding domain, helix turn helix motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.60.2.7

Probab=86.14  E-value=2  Score=30.27  Aligned_cols=60  Identities=13%  Similarity=0.284  Sum_probs=38.6

Q ss_pred             HHHHhcCCHHHHHHhhccCCChHHHHHHHHHHHHHHHHhcCCCChhhHHHHHcCCCCcHHHHHHHHHHh
Q 026681           58 AEAIDKADEATIKDLIYPVAFYTRKACNMKKIAKICLTKYDGDIPSSLDELLALPGIGPKMANMVMTLG  126 (235)
Q Consensus        58 ~~~la~a~~e~l~~~l~~~G~~~~Ka~~l~~~a~~i~~~~~g~~~~~~~~L~~l~GIG~~tA~~il~~~  126 (235)
                      +-+|..++.++|.. |.++|  ...|+.|.+.-..     .|.+ ...++|..++|||+++++.+...+
T Consensus        31 ~i~iN~a~~~~L~~-ipGIG--~~~A~~Il~~r~~-----~g~f-~s~edL~~v~Gig~k~~~~l~~~g   90 (98)
T 2edu_A           31 LDLLNEGSARDLRS-LQRIG--PKKAQLIVGWREL-----HGPF-SQVEDLERVEGITGKQMESFLKAN   90 (98)
T ss_dssp             HHHHHHSCHHHHHH-STTCC--HHHHHHHHHHHHH-----HCCC-SSGGGGGGSTTCCHHHHHHHHHHH
T ss_pred             CeehhhCCHHHHHH-CCCCC--HHHHHHHHHHHHh-----cCCc-CCHHHHHhCCCCCHHHHHHHHHCc
Confidence            34566677777765 45555  3456666554221     1444 456668999999999999887654

>2ztd_A Holliday junction ATP-dependent DNA helicase RUVA; recombination, branch migration, DNA BIND oligomerization, acidic PIN; 2.40A {Mycobacterium tuberculosis} PDB: 2ztc_A 2zte_A 2h5x_A 1bvs_A

Probab=84.57  E-value=0.63  Score=38.06  Aligned_cols=22  Identities=27%  Similarity=0.626  Sum_probs=19.1

Q ss_pred             hHHHHHcCCCCcHHHHHHHHHH
Q 026681          104 SLDELLALPGIGPKMANMVMTL  125 (235)
Q Consensus       104 ~~~~L~~l~GIG~~tA~~il~~  125 (235)
                      .+..|.+++||||++|..|+..
T Consensus        86 lf~~L~sv~GIGpk~A~~Ils~  107 (212)
T 2ztd_A           86 LFLTLLSVSGVGPRLAMAALAV  107 (212)
T ss_dssp             HHHHHHTSTTCCHHHHHHHHHH
T ss_pred             HHHHhcCcCCcCHHHHHHHHHh
Confidence            4677999999999999999864

>1ixr_A Holliday junction DNA helicase RUVA; heterooligomeric complex, octameric RUVA, AAA-ATPase domain, complex with nucleotide, hydrolase; HET: ANP; 3.30A {Thermus thermophilus} SCOP: a.60.2.1 b.40.4.2

Probab=84.05  E-value=0.74  Score=36.99  Aligned_cols=22  Identities=32%  Similarity=0.658  Sum_probs=18.7

Q ss_pred             hHHHHHcCCCCcHHHHHHHHHH
Q 026681          104 SLDELLALPGIGPKMANMVMTL  125 (235)
Q Consensus       104 ~~~~L~~l~GIG~~tA~~il~~  125 (235)
                      ....|.+++||||++|..+|..
T Consensus        70 ~f~~L~~v~GIGpk~A~~iL~~   91 (191)
T 1ixr_A           70 LFELLLSVSGVGPKVALALLSA   91 (191)
T ss_dssp             HHHHHHSSSCCCHHHHHHHHHH
T ss_pred             HHHHHhcCCCcCHHHHHHHHHh
Confidence            3457889999999999999865

>2a1j_A DNA repair endonuclease XPF; XPF, xeroderma pigmentosum, DNA repair, endonuclease, helix-hairpin-helix, DNA binding protein; HET: DNA; 2.70A {Homo sapiens} SCOP: a.60.2.5 PDB: 2kn7_A*

Probab=83.77  E-value=2.2  Score=27.62  Aligned_cols=38  Identities=5%  Similarity=0.217  Sum_probs=28.9

Q ss_pred             HHHHHHcCCCCHHHHhcCCHHHHHHhhccCCChHHH-HHHHHHHH
Q 026681           47 LQRLLQNGLHTAEAIDKADEATIKDLIYPVAFYTRK-ACNMKKIA   90 (235)
Q Consensus        47 ~~~l~~~~~pt~~~la~a~~e~l~~~l~~~G~~~~K-a~~l~~~a   90 (235)
                      ...|..+ |.|.++|.+|+.|||.+++   |  ... |+.|.+..
T Consensus        17 ~~~LL~~-Fgs~~~i~~As~eeL~~vi---g--~~~~A~~I~~~l   55 (63)
T 2a1j_A           17 CRSLMHH-VKNIAELAALSQDELTSIL---G--NAANAKQLYDFI   55 (63)
T ss_dssp             HHHHHHH-CSSHHHHHTCCHHHHHHHH---S--CHHHHHHHHHHH
T ss_pred             HHHHHHH-cCCHHHHHHCCHHHHHHHc---C--chHHHHHHHHHH
Confidence            4566674 9999999999999999994   5  234 77776543

>2i5h_A Hypothetical protein AF1531; PFAM:DUF655, PSI-2, structural genomics, protein structure initiative; 1.74A {Archaeoglobus fulgidus} SCOP: e.71.1.1

Probab=83.15  E-value=0.32  Score=39.42  Aligned_cols=45  Identities=22%  Similarity=0.333  Sum_probs=30.2

Q ss_pred             CChhhHHHHHcCCCCcHHHHHHHHHHhcCCcceeecchHHHHHHHHhcCc
Q 026681          100 DIPSSLDELLALPGIGPKMANMVMTLGWFNVQGICVDTHVHRICNRLGWV  149 (235)
Q Consensus       100 ~~~~~~~~L~~l~GIG~~tA~~il~~~~~~~~~~pvDt~v~Rv~~Rlg~~  149 (235)
                      .+..+.++|..|||||+++|..|+.+=-..  .|   +.+--+..|++++
T Consensus       126 pITA~~~eL~~LpGIG~k~A~~IIeyRe~G--~F---~s~eDL~~RV~GI  170 (205)
T 2i5h_A          126 SITTRMHQLELLPGVGKKMMWAIIEERKKR--PF---ESFEDIAQRVKGI  170 (205)
T ss_dssp             CBCSSSBGGGGSTTCCHHHHHHHHHHHHHS--CC---CSHHHHHHHSTTC
T ss_pred             CccCCHHHHhcCCCcCHHHHHHHHHHHhcC--CC---CCHHHHHHhcCCC
Confidence            455577889999999999999999763211  22   1233455677654

>1s5l_U Photosystem II 12 kDa extrinsic protein; photosynthesis, oxygen-evolving, tetra- manganese, membrane; HET: CL1 PHO HEM PL9 LMT BCR; 3.50A {Thermosynechococcus elongatus}

Probab=82.85  E-value=0.42  Score=36.16  Aligned_cols=52  Identities=13%  Similarity=0.307  Sum_probs=34.6

Q ss_pred             HhcCCHHHHHHhhccCCChHHHHHHHHHHHHHHHHhcCCCChhhHHHHHcCCCCcHHHHHHHHHH
Q 026681           61 IDKADEATIKDLIYPVAFYTRKACNMKKIAKICLTKYDGDIPSSLDELLALPGIGPKMANMVMTL  125 (235)
Q Consensus        61 la~a~~e~l~~~l~~~G~~~~Ka~~l~~~a~~i~~~~~g~~~~~~~~L~~l~GIG~~tA~~il~~  125 (235)
                      |-.|+.++|.. +  -|++..||+.|.       +  +|.+ ...++|++++|||+++.+.+--+
T Consensus        57 iNtA~~~eL~~-L--pGiGp~~A~~II-------~--~GpF-~svedL~~V~GIg~k~~e~l~~~  108 (134)
T 1s5l_U           57 LNNTNIAAFIQ-Y--RGLYPTLAKLIV-------K--NAPY-ESVEDVLNIPGLTERQKQILREN  108 (134)
T ss_dssp             TTTSCGGGGGG-S--TTCTHHHHHHHH-------H--TCCC-SSGGGGGGCTTCCHHHHHHHHHH
T ss_pred             CcccCHHHHHH-C--CCCCHHHHHHHH-------H--cCCC-CCHHHHHhCCCCCHHHHHHHHHh
Confidence            44566666655 2  377777887776       2  2444 45788889999999887766543

>2edu_A Kinesin-like protein KIF22; kinesin-like DNA binding domain, helix turn helix motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.60.2.7

Probab=82.71  E-value=0.82  Score=32.37  Aligned_cols=22  Identities=36%  Similarity=0.575  Sum_probs=19.6

Q ss_pred             hHHHHHcCCCCcHHHHHHHHHH
Q 026681          104 SLDELLALPGIGPKMANMVMTL  125 (235)
Q Consensus       104 ~~~~L~~l~GIG~~tA~~il~~  125 (235)
                      ..+.|.++||||+++|..|+..
T Consensus        38 ~~~~L~~ipGIG~~~A~~Il~~   59 (98)
T 2edu_A           38 SARDLRSLQRIGPKKAQLIVGW   59 (98)
T ss_dssp             CHHHHHHSTTCCHHHHHHHHHH
T ss_pred             CHHHHHHCCCCCHHHHHHHHHH
Confidence            4678999999999999999976

>1s5l_U Photosystem II 12 kDa extrinsic protein; photosynthesis, oxygen-evolving, tetra- manganese, membrane; HET: CL1 PHO HEM PL9 LMT BCR; 3.50A {Thermosynechococcus elongatus}

Probab=82.13  E-value=0.4  Score=36.29  Aligned_cols=21  Identities=14%  Similarity=0.537  Sum_probs=19.1

Q ss_pred             hHHHHHcCCCCcHHHHHHHHH
Q 026681          104 SLDELLALPGIGPKMANMVMT  124 (235)
Q Consensus       104 ~~~~L~~l~GIG~~tA~~il~  124 (235)
                      +.++|.+||||||+.|..|..
T Consensus        61 ~~~eL~~LpGiGp~~A~~II~   81 (134)
T 1s5l_U           61 NIAAFIQYRGLYPTLAKLIVK   81 (134)
T ss_dssp             CGGGGGGSTTCTHHHHHHHHH
T ss_pred             CHHHHHHCCCCCHHHHHHHHH
Confidence            578899999999999999984

>1jms_A Terminal deoxynucleotidyltransferase; polymerase; 2.36A {Mus musculus} SCOP: a.60.6.1 a.60.12.1 d.218.1.2 PDB: 1kdh_A* 1kej_A*

Probab=81.37  E-value=1.1  Score=39.86  Aligned_cols=50  Identities=12%  Similarity=0.048  Sum_probs=31.4

Q ss_pred             ccCCChHHHHHHHHHHHHH----HHHhcC-CCChhhHHHHHcCCCCcHHHHHHHHHH
Q 026681           74 YPVAFYTRKACNMKKIAKI----CLTKYD-GDIPSSLDELLALPGIGPKMANMVMTL  125 (235)
Q Consensus        74 ~~~G~~~~Ka~~l~~~a~~----i~~~~~-g~~~~~~~~L~~l~GIG~~tA~~il~~  125 (235)
                      .++|  ..-|..|.++.+.    -.++.. ...|.....|++++|||+++|..+-.-
T Consensus        86 pGIG--~~ia~kI~E~l~tG~~~~le~l~~d~~~~~l~~l~~I~GvGpk~a~~ly~~  140 (381)
T 1jms_A           86 PCLG--DKVKSIIEGIIEDGESSEAKAVLNDERYKSFKLFTSVFGVGLKTAEKWFRM  140 (381)
T ss_dssp             SSCC--HHHHHHHHHHHHHSSCHHHHHHHHCHHHHHHHHHHTSTTCCHHHHHHHHHT
T ss_pred             CCCc--HHHHHHHHHHHHcCCcHHHHHHhcCcchhHHHHHHccCCCCHHHHHHHHHc
Confidence            4444  4456666666543    111111 245667789999999999999987443

>2kp7_A Crossover junction endonuclease MUS81; helix-hairpin-helix, tumour suppressor, DNA damage, DNA recombination, DNA repair, hydrolase, magnesium; NMR {Mus musculus}

Probab=80.76  E-value=2.5  Score=29.45  Aligned_cols=40  Identities=18%  Similarity=0.163  Sum_probs=27.8

Q ss_pred             HHHHHHHHHHHHHhcCCCChhhHHHHHcCCCCcHHHHHHHHH
Q 026681           83 ACNMKKIAKICLTKYDGDIPSSLDELLALPGIGPKMANMVMT  124 (235)
Q Consensus        83 a~~l~~~a~~i~~~~~g~~~~~~~~L~~l~GIG~~tA~~il~  124 (235)
                      +.....++..+.. |...+ ..-+++..|+|||++++..+--
T Consensus        37 ~~~Y~KA~~sLk~-~P~~i-~s~~e~~~L~giG~ki~~~L~e   76 (87)
T 2kp7_A           37 RFVFQKALRSLQR-YPLPL-RSGKEAKILQHFGDRLCRMLDE   76 (87)
T ss_dssp             HHHHHHHHHHHHH-CCSCC-CSHHHHHTCTTTCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHh-CCCCC-CCHHHHHHhhcccHHHHHHHHH
Confidence            4556666666543 44444 3567889999999999987753

>1cuk_A RUVA protein; DNA repair, SOS response, DNA-binding, DNA recombination; 1.90A {Escherichia coli} SCOP: a.5.1.1 a.60.2.1 b.40.4.2 PDB: 1hjp_A 1bdx_A* 1c7y_A 1d8l_A

Probab=80.39  E-value=1.1  Score=36.34  Aligned_cols=21  Identities=33%  Similarity=0.665  Sum_probs=18.1

Q ss_pred             HHHHHcCCCCcHHHHHHHHHH
Q 026681          105 LDELLALPGIGPKMANMVMTL  125 (235)
Q Consensus       105 ~~~L~~l~GIG~~tA~~il~~  125 (235)
                      .+.|.+++||||++|..+|..
T Consensus        72 f~~L~~V~GIGpk~A~~iL~~   92 (203)
T 1cuk_A           72 FKELIKTNGVGPKLALAILSG   92 (203)
T ss_dssp             HHHHHHSSSCCHHHHHHHHHH
T ss_pred             HHHHhcCCCcCHHHHHHHHhh
Confidence            457889999999999999874

>3arc_U Photosystem II 12 kDa extrinsic protein; PSII, membrane-protein complex, transmembrane alpha-helix, E transport, photosynthesis; HET: OEX CLA PHO BCR PL9 SQD LMG UNL LMT HTG DGD LHG HEM; 1.90A {Thermosynechococcus vulcanus} PDB: 3bz1_U* 2axt_U* 3bz2_U* 3kzi_U* 3prq_U* 3prr_U* 3a0b_U* 3a0h_U*

Probab=80.23  E-value=0.42  Score=34.21  Aligned_cols=21  Identities=14%  Similarity=0.537  Sum_probs=19.2

Q ss_pred             hHHHHHcCCCCcHHHHHHHHH
Q 026681          104 SLDELLALPGIGPKMANMVMT  124 (235)
Q Consensus       104 ~~~~L~~l~GIG~~tA~~il~  124 (235)
                      +.++|..+||||++.|..|..
T Consensus        24 s~~eL~~lpGIG~~~A~~IV~   44 (97)
T 3arc_U           24 NIAAFIQYRGLYPTLAKLIVK   44 (97)
T ss_dssp             CGGGGGGSTTCTTHHHHHHHH
T ss_pred             CHHHHhHCCCCCHHHHHHHHH
Confidence            568899999999999999988

---

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	235
d1pu6a_	217	a.96.1.5 (A:) 3-Methyladenine DNA glycosylase III	3e-29
d1orna_	214	a.96.1.1 (A:) Endonuclease III {Escherichia coli [	2e-25
d2abka_	211	a.96.1.1 (A:) Endonuclease III {Escherichia coli [	5e-23
d1kg2a_	224	a.96.1.2 (A:) Catalytic domain of MutY {Escherichi	1e-21
d1keaa_	217	a.96.1.2 (A:) Thymine-DNA glycosylase {Archaeon Me	2e-21
d1rrqa1	221	a.96.1.2 (A:9-229) Catalytic domain of MutY {Bacil	6e-21
d2noha1	190	a.96.1.3 (A:136-325) 8-oxoguanine glycosylase {Hum	3e-20
d1ngna_	144	a.96.1.2 (A:) Mismatch-specific thymine glycosylas	3e-11

>d1pu6a_ a.96.1.5 (A:) 3-Methyladenine DNA glycosylase III (MagIII) {Helicobacter pylori [TaxId: 210]} Length = 217

class: All alpha proteins
fold: DNA-glycosylase
superfamily: DNA-glycosylase
family: 3-Methyladenine DNA glycosylase III (MagIII)
domain: 3-Methyladenine DNA glycosylase III (MagIII)
species: Helicobacter pylori [TaxId: 210]

 Score =  107 bits (267), Expect = 3e-29
 Identities = 30/200 (15%), Positives = 72/200 (36%), Gaps = 35/200 (17%)

Query: 21  PKERRFAVLLSALLSSLTKDKVADGALQRLLQNGLH------TAEAIDKADEATIKDLIY 74
           P   +F  LL A+L+  TK +    +L+ L    +         + I   + + + + + 
Sbjct: 25  PNALKFEALLGAVLTQNTKFEAVLKSLENLKNAFILENDDEINLKKIAYIEFSKLAECVR 84

Query: 75  PVAFYTRKACNMKKIAKICLTKYD----GDIPSSLDELLALPGIGPKMANMVMTLGWFNV 130
           P  FY +KA  +  ++   L  +          + + LL   GIG + A+ ++       
Sbjct: 85  PSGFYNQKAKRLIDLSGNILKDFQSFENFKQEVTREWLLDQKGIGKESADAIL-CYACAK 143

Query: 131 QGICVDTHVHRICNRLGWVTQPGTKQKTSSPEQTREALQRWLPK---------------- 174
           + + VD + +    +LG   +          ++ +   ++ + +                
Sbjct: 144 EVMVVDKYSYLFLKKLGIEIE--------DYDELQHFFEKGVQENLNSALALYENTISLA 195

Query: 175 EEWVRINPLLVGFGQTICTP 194
           + + R +  +V F +     
Sbjct: 196 QLYARFHGKIVEFSKQKLEL 215

>d1orna_ a.96.1.1 (A:) Endonuclease III {Escherichia coli [TaxId: 562]} Length = 214

class: All alpha proteins
fold: DNA-glycosylase
superfamily: DNA-glycosylase
family: Endonuclease III
domain: Endonuclease III
species: Escherichia coli [TaxId: 562]

 Score = 96.9 bits (240), Expect = 2e-25
 Identities = 54/188 (28%), Positives = 94/188 (50%), Gaps = 8/188 (4%)

Query: 26  FAVLLSALLSSLTKDKVADGALQRLLQNGLHTAEAIDKADEATIKDLIYPVAFYTRKACN 85
           F +L++ +LS+   D + +   +RL +    T           ++  I  +  Y  KA N
Sbjct: 31  FELLIAVVLSAQCTDALVNKVTKRLFEKY-RTPHDYIAVPLEELEQDIRSIGLYRNKARN 89

Query: 86  MKKIAKICLTKYDGDIPSSLDELLALPGIGPKMANMVMTLGWFNVQGICVDTHVHRICNR 145
           ++K+  + + KY+G++P   DEL+ LPG+G K AN+V+++ +     I VDTHV R+  R
Sbjct: 90  IQKLCAMLIDKYNGEVPRDRDELMKLPGVGRKTANVVVSVAFGV-PAIAVDTHVERVSKR 148

Query: 146 LGWVTQPGTKQKTSSPEQTREALQRWLPKEEWVRINPLLVGFGQTICTPLRPRCGMCTVS 205
           LG+       +   S  +  + L + +PKEEW   +  ++ FG+  C    P+C  C + 
Sbjct: 149 LGF------CRWDDSVLEVEKTLMKIIPKEEWSITHHRMIFFGRYHCKAQSPQCPSCPLL 202

Query: 206 EYCPSAFK 213
             C    K
Sbjct: 203 HLCREGKK 210

>d2abka_ a.96.1.1 (A:) Endonuclease III {Escherichia coli [TaxId: 562]} Length = 211

class: All alpha proteins
fold: DNA-glycosylase
superfamily: DNA-glycosylase
family: Endonuclease III
domain: Endonuclease III
species: Escherichia coli [TaxId: 562]

 Score = 90.4 bits (223), Expect = 5e-23
 Identities = 57/188 (30%), Positives = 91/188 (48%), Gaps = 9/188 (4%)

Query: 26  FAVLLSALLSSLTKDKVADGALQRLLQNGLHTAEAIDKADEATIKDLIYPVAFYTRKACN 85
           F +L++ LLS+   D   + A  +L     +T  A+ +     +K  I  +  Y  KA N
Sbjct: 30  FELLIAVLLSAQATDVSVNKATAKLYPVA-NTPAAMLELGVEGVKTYIKTIGLYNSKAEN 88

Query: 86  MKKIAKICLTKYDGDIPSSLDELLALPGIGPKMANMVMTLGWFNVQGICVDTHVHRICNR 145
           + K  +I L +++G++P     L ALPG+G K AN+V+   +     I VDTH+ R+CNR
Sbjct: 89  IIKTCRILLEQHNGEVPEDRAALEALPGVGRKTANVVLNTAFGW-PTIAVDTHIFRVCNR 147

Query: 146 LGWVTQPGTKQKTSSPEQTREALQRWLPKEEWVRINPLLVGFGQTICTPLRPRCGMCTVS 205
             +           + EQ  E L + +P E  V  +  L+  G+  C   +PRCG C + 
Sbjct: 148 TQFA-------PGKNVEQVEEKLLKVVPAEFKVDCHHWLILHGRYTCIARKPRCGSCIIE 200

Query: 206 EYCPSAFK 213
           + C    K
Sbjct: 201 DLCEYKEK 208

>d1kg2a_ a.96.1.2 (A:) Catalytic domain of MutY {Escherichia coli [TaxId: 562]} Length = 224

class: All alpha proteins
fold: DNA-glycosylase
superfamily: DNA-glycosylase
family: Mismatch glycosylase
domain: Catalytic domain of MutY
species: Escherichia coli [TaxId: 562]

 Score = 87.4 bits (215), Expect = 1e-21
 Identities = 48/209 (22%), Positives = 88/209 (42%), Gaps = 8/209 (3%)

Query: 18  SLPPKERR--FAVLLSALLSSLTKDKVADGALQRLLQNGLHTAEAIDKADEATIKDLIYP 75
           +LP +  +  + V LS ++   T+        +R +     T   +  A    +  L   
Sbjct: 21  TLPWQIDKTPYKVWLSEVMLQQTQVATVIPYFERFMARF-PTVTDLANAPLDEVLHLWTG 79

Query: 76  VAFYTRKACNMKKIAKICLTKYDGDIPSSLDELLALPGIGPKMANMVMTLGWFNVQGICV 135
           + +Y R   N+ K A+   T + G  P + +E+ ALPG+G   A  +++L       I +
Sbjct: 80  LGYYARA-RNLHKAAQQVATLHGGKFPETFEEVAALPGVGRSTAGAILSLSLGKHFPI-L 137

Query: 136 DTHVHRICNRLGWVTQPGTKQKTSSPEQTREALQRWLPKEEWVRINPLLVGFGQTICTPL 195
           D +V R+  R   V+    K++     +     ++  P     R N  ++  G  ICT  
Sbjct: 138 DGNVKRVLARCYAVSGWPGKKEV--ENKLWSLSEQVTPAVGVERFNQAMMDLGAMICTRS 195

Query: 196 RPRCGMCTVSEYCPSAFKESSTSSSKSKK 224
           +P+C +C +   C  A   +S +    KK
Sbjct: 196 KPKCSLCPLQNGCI-AAANNSWALYPGKK 223

>d1keaa_ a.96.1.2 (A:) Thymine-DNA glycosylase {Archaeon Methanobacterium thermoformicicum [TaxId: 145262]} Length = 217

class: All alpha proteins
fold: DNA-glycosylase
superfamily: DNA-glycosylase
family: Mismatch glycosylase
domain: Thymine-DNA glycosylase
species: Archaeon Methanobacterium thermoformicicum [TaxId: 145262]

 Score = 86.6 bits (213), Expect = 2e-21
 Identities = 42/195 (21%), Positives = 79/195 (40%), Gaps = 7/195 (3%)

Query: 18  SLPPKERR--FAVLLSALLSSLTKDKVADGALQRLLQNGLHTAEAIDKADEATIKDLIYP 75
             P +  R  + +L++ +L   T          +         E I K  ++ I   I  
Sbjct: 24  DFPWRHTRDPYVILITEILLRRTTAGHVKKIYDKFFVKY-KCFEDILKTPKSEIAKDIKE 82

Query: 76  VAFYTRKACNMKKIAKICLTKYDGDIPSSLDELLALPGIGPKMANMVMTLGWFNVQGICV 135
           +    ++A  +K++A++ +  Y G +P +   +L LPG+G      VM L +   +   V
Sbjct: 83  IGLSNQRAEQLKELARVVINDYGGRVPRNRKAILDLPGVGKYTCAAVMCLAF-GKKAAMV 141

Query: 136 DTHVHRICNRLGWVTQPGTKQKTSSPEQTREALQRWLPKEEWVRINPLLVGFGQTICTPL 195
           D +  R+ NR    +         + +   E  +  +P  +    N  L+ F   IC P 
Sbjct: 142 DANFVRVINRYFGGSYENLNY---NHKALWELAETLVPGGKCRDFNLGLMDFSAIICAPR 198

Query: 196 RPRCGMCTVSEYCPS 210
           +P+C  C +S+ C  
Sbjct: 199 KPKCEKCGMSKLCSY 213

>d1rrqa1 a.96.1.2 (A:9-229) Catalytic domain of MutY {Bacillus stearothermophilus [TaxId: 1422]} Length = 221

class: All alpha proteins
fold: DNA-glycosylase
superfamily: DNA-glycosylase
family: Mismatch glycosylase
domain: Catalytic domain of MutY
species: Bacillus stearothermophilus [TaxId: 1422]

 Score = 85.4 bits (210), Expect = 6e-21
 Identities = 44/195 (22%), Positives = 81/195 (41%), Gaps = 7/195 (3%)

Query: 18  SLPPKERR--FAVLLSALLSSLTKDKVADGALQRLLQNGLHTAEAIDKADEATIKDLIYP 75
            LP ++ R  + V +S ++   T+ +      ++ +          D  ++  +K     
Sbjct: 19  DLPWRKDRDPYKVWVSEVMLQQTRVETVIPYFEQFIDRFPTLEALADADEDEVLKAWEGL 78

Query: 76  VAFYTRKACNMKKIAKICLTKYDGDIPSSLDELLALPGIGPKMANMVMTLGWFNVQGICV 135
             +   +  +     K   T+Y G +P   DE   L G+GP     V+    + V    V
Sbjct: 79  GYYSRVRNLHAAV--KEVKTRYGGKVPDDPDEFSRLKGVGPYTVGAVL-SLAYGVPEPAV 135

Query: 136 DTHVHRICNRLGWVTQPGTKQKTSSPEQTREALQRWLPKEEWVRINPLLVGFGQTICTPL 195
           + +V R+ +RL  VT      K S+ ++  + ++  +  E     N  L+  G  +CTP 
Sbjct: 136 NGNVMRVLSRLFLVTDD--IAKCSTRKRFEQIVREIMAYENPGAFNEALIELGALVCTPR 193

Query: 196 RPRCGMCTVSEYCPS 210
           RP C +C V  YC +
Sbjct: 194 RPSCLLCPVQAYCQA 208

>d2noha1 a.96.1.3 (A:136-325) 8-oxoguanine glycosylase {Human (Homo sapiens) [TaxId: 9606]} Length = 190

class: All alpha proteins
fold: DNA-glycosylase
superfamily: DNA-glycosylase
family: DNA repair glycosylase, 2 C-terminal domains
domain: 8-oxoguanine glycosylase
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 82.5 bits (203), Expect = 3e-20
 Identities = 31/190 (16%), Positives = 62/190 (32%), Gaps = 34/190 (17%)

Query: 26  FAVLLSALLSSLTKDKVADGALQRLLQ--------------NGLHTAEAIDKADEATIKD 71
              L S + SS        G ++RL Q              +G  + +A+   +      
Sbjct: 3   IECLFSFICSSNNNIARITGMVERLCQAFGPRLIQLDDVTYHGFPSLQALAGPEVEAHLR 62

Query: 72  LIYPVAFYTRKACNMKKIAKICLTKY----------DGDIPSSLDELLALPGIGPKMANM 121
            +        +A  +   A+  L +           +     +   L  LPG+G ++A+ 
Sbjct: 63  KLG----LGYRARYVSASARAILEEQGGLAWLQQLRESSYEEAHKALCILPGVGTQVADC 118

Query: 122 VMTLGWFNVQGICVDTHVHRICNRLGWVTQPGTKQKTSSPEQTREALQRWLPKEEWVRIN 181
           +  +     Q + VD H+  I  R        ++ K  SP+  +E    +  +  W    
Sbjct: 119 ICLMALDKPQAVPVDVHMWHIAQRDYSWHPTTSQAKGPSPQTNKELGNFF--RSLWGP-- 174

Query: 182 PLLVGFGQTI 191
               G+   +
Sbjct: 175 --YAGWAAAV 182

>d1ngna_ a.96.1.2 (A:) Mismatch-specific thymine glycosylase domain of the methyl-GpG binding protein mbd4 {Mouse (Mus musculus) [TaxId: 10090]} Length = 144

class: All alpha proteins
fold: DNA-glycosylase
superfamily: DNA-glycosylase
family: Mismatch glycosylase
domain: Mismatch-specific thymine glycosylase domain of the methyl-GpG binding protein mbd4
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 57.4 bits (138), Expect = 3e-11
 Identities = 23/122 (18%), Positives = 46/122 (37%), Gaps = 9/122 (7%)

Query: 26  FAVLLSALLSSLTKDKVADGALQRLLQNGLHTAEAIDKADEATIKDLIYPVAFYTRKACN 85
           + +L++ +  + T  K+A   L   L+      E    AD   + +L+ P+  Y  +A  
Sbjct: 21  WKLLIATIFLNRTSGKMAIPVLWEFLEKYPSA-EVARAADWRDVSELLKPLGLYDLRAKT 79

Query: 86  MKKIAKICLTKYDGDIPSSLDELLALPGIGPKMANMVMTLGWFNVQGICV-DTHVHRICN 144
           + K +   LTK            + L GIG    +          + +   D  +++  +
Sbjct: 80  IIKFSDEYLTKQ-------WRYPIELHGIGKYGNDSYRIFCVNEWKQVHPEDHKLNKYHD 132

Query: 145 RL 146
            L
Sbjct: 133 WL 134

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	235
d1keaa_	217	Thymine-DNA glycosylase {Archaeon Methanobacterium	100.0
d1orna_	214	Endonuclease III {Escherichia coli [TaxId: 562]}	100.0
d2abka_	211	Endonuclease III {Escherichia coli [TaxId: 562]}	100.0
d1rrqa1	221	Catalytic domain of MutY {Bacillus stearothermophi	100.0
d1kg2a_	224	Catalytic domain of MutY {Escherichia coli [TaxId:	100.0
d1pu6a_	217	3-Methyladenine DNA glycosylase III (MagIII) {Heli	100.0
d2noha1	190	8-oxoguanine glycosylase {Human (Homo sapiens) [Ta	99.97
d1mpga1	183	3-Methyladenine DNA glycosylase II (gene alkA or a	99.96
d1ngna_	144	Mismatch-specific thymine glycosylase domain of th	99.96
d2i1qa1	60	DNA repair protein Rad51, N-terminal domain {Archa	96.17
d1nkua_	187	3-Methyladenine DNA glycosylase I (Tag) {Escherich	96.08
d1szpa1	64	DNA repair protein Rad51, N-terminal domain {Baker	95.66
d2fmpa1	82	DNA polymerase beta, N-terminal (8 kD)-domain {Hum	95.57
d1pzna1	61	DNA repair protein Rad51, N-terminal domain {Archa	95.56
d1ixra1	73	DNA helicase RuvA subunit, middle domain {Thermus	95.49
d1cuka2	78	DNA helicase RuvA subunit, middle domain {Escheric	95.15
d1bvsa2	71	DNA helicase RuvA subunit, middle domain {Mycobact	95.05
d2bcqa1	76	DNA polymerase lambda {Human (Homo sapiens) [TaxId	94.58
d1x2ia1	68	ATP-dependent RNA helicase PF2015 {Pyrococcus furi	94.46
d1kfta_	56	Excinuclease UvrC C-terminal domain {Escherichia c	94.36
d1dgsa1	181	NAD+-dependent DNA ligase, domain 3 {Thermus filif	94.18
d1b22a_	70	DNA repair protein Rad51, N-terminal domain {Human	93.91
d2bgwa1	70	DNA repair endonuclease XPF {Aeropyrum pernix [Tax	92.32
d2a1ja1	62	DNA repair endonuclease XPF {Human (Homo sapiens)	92.13
d1jmsa1	95	Terminal deoxynucleotidyl transferase {Mouse (Mus	92.03
d1bvsa2	71	DNA helicase RuvA subunit, middle domain {Mycobact	91.89
d1vdda_	199	Recombination protein RecR {Deinococcus radioduran	91.71
d1ixra1	73	DNA helicase RuvA subunit, middle domain {Thermus	91.04
d2a1ja1	62	DNA repair endonuclease XPF {Human (Homo sapiens)	90.92
d1cuka2	78	DNA helicase RuvA subunit, middle domain {Escheric	90.9
d2a1jb1	78	DNA excision repair protein ERCC-1 {Human (Homo sa	90.8
d2duya1	65	Uncharacterized protein TTHA1967 {Thermus thermoph	89.89
d1pzna1	61	DNA repair protein Rad51, N-terminal domain {Archa	89.1
d3bzka1	90	Transcriptional accessory factor Tex {Pseudomonas	89.01
d1jmsa3	60	Terminal deoxynucleotidyl transferase {Mouse (Mus	88.96
d2fmpa2	57	DNA polymerase beta {Human (Homo sapiens) [TaxId:	88.3
d2bgwa1	70	DNA repair endonuclease XPF {Aeropyrum pernix [Tax	87.35
d2i1qa1	60	DNA repair protein Rad51, N-terminal domain {Archa	86.74
d2edua1	91	KIF22, C-terminal domain {Human (Homo sapiens) [Ta	86.71
d2bcqa2	57	DNA polymerase lambda {Human (Homo sapiens) [TaxId	85.53
d1kfta_	56	Excinuclease UvrC C-terminal domain {Escherichia c	85.31
d2edua1	91	KIF22, C-terminal domain {Human (Homo sapiens) [Ta	84.77
d1wuda1	77	HRDC domain from RecQ helicase {Escherichia coli [	83.71
d2axtu1	98	Photosystem II 12 kDa extrinsic protein PsbU {Ther	83.39
d3bzka1	90	Transcriptional accessory factor Tex {Pseudomonas	82.8
d2a1jb1	78	DNA excision repair protein ERCC-1 {Human (Homo sa	81.35

>d1keaa_ a.96.1.2 (A:) Thymine-DNA glycosylase {Archaeon Methanobacterium thermoformicicum [TaxId: 145262]}

class: All alpha proteins
fold: DNA-glycosylase
superfamily: DNA-glycosylase
family: Mismatch glycosylase
domain: Thymine-DNA glycosylase
species: Archaeon Methanobacterium thermoformicicum [TaxId: 145262]

Probab=100.00  E-value=9.6e-55  Score=363.86  Aligned_cols=195  Identities=22%  Similarity=0.379  Sum_probs=180.9

Q ss_pred             CCCCCCCCC--CChHHHHHHHHHhccccHHHHHHHHHHHHHcCCCCHHHHhcCCHHHHHHhhccCCChHHHHHHHHHHHH
Q 026681           14 ETDSSLPPK--ERRFAVLLSALLSSLTKDKVADGALQRLLQNGLHTAEAIDKADEATIKDLIYPVAFYTRKACNMKKIAK   91 (235)
Q Consensus        14 ~~~~~~p~~--~~~f~~lv~~iLsqqt~~~~~~~~~~~l~~~~~pt~~~la~a~~e~l~~~l~~~G~~~~Ka~~l~~~a~   91 (235)
                      .+.+++||+  .|||++||++||||||++++|.+++.+|++ .||||++|+++++++|+++|+++|||++||++|+++|+
T Consensus        20 ~~~r~lpWr~~~dp~~vLv~~iLsqqT~~~~v~~~~~~l~~-~~pt~~~la~a~~~~l~~~i~~~G~~~~KA~~l~~~a~   98 (217)
T d1keaa_          20 TDRRDFPWRHTRDPYVILITEILLRRTTAGHVKKIYDKFFV-KYKCFEDILKTPKSEIAKDIKEIGLSNQRAEQLKELAR   98 (217)
T ss_dssp             HSCCCCGGGGCCCHHHHHHHHHHTTTSCHHHHHHHHHHHHH-HCCSHHHHHHSCHHHHHHHTGGGSCHHHHHHHHHHHHH
T ss_pred             HcCCCCCCCCCCCHHHHHHHHHHHccCcHHHHHHHHHHHHH-hcccHHHHHHhhHHHHHHHHHHHHhhhHHHHHHHHHHH
Confidence            367899997  689999999999999999999999999999 59999999999999999999999999999999999999


Q ss_pred             HHHHhcCCCChhhHHHHHcCCCCcHHHHHHHHHHhcCCcceeecchHHHHHHHHhcCcCCCCCCCCCCCHHHHHHHHHHh
Q 026681           92 ICLTKYDGDIPSSLDELLALPGIGPKMANMVMTLGWFNVQGICVDTHVHRICNRLGWVTQPGTKQKTSSPEQTREALQRW  171 (235)
Q Consensus        92 ~i~~~~~g~~~~~~~~L~~l~GIG~~tA~~il~~~~~~~~~~pvDt~v~Rv~~Rlg~~~~~~~~~~~~~~~~~~~~l~~~  171 (235)
                      .|+++|+|.+|.++++|++|||||+|||++||+|+|++ ++++||+|+.||+.|++++..+.   ...+.+.+++.++.+
T Consensus        99 ~i~~~~~g~~p~~~~~L~~LpGVG~kTA~~il~~~~~~-~~~~vD~~v~Rv~~R~~~~~~~~---~~~~~~~l~~~~~~~  174 (217)
T d1keaa_          99 VVINDYGGRVPRNRKAILDLPGVGKYTCAAVMCLAFGK-KAAMVDANFVRVINRYFGGSYEN---LNYNHKALWELAETL  174 (217)
T ss_dssp             HHHHHHTTSCCSCHHHHHTSTTCCHHHHHHHHHHTTCC-CCCCCCHHHHHHHHHHHCGGGTT---CCTTSHHHHHHHHHH
T ss_pred             HHHhhccCCcchhhHHHHHHHhhhhhhhHHHHHHhcCC-cccccccchhhhhhhccccCccc---cchHHHHHHHHHHHc
Confidence            99999999999999999999999999999999999998 58899999999999998765321   134456788889999


Q ss_pred             CCcccHHHHHHHHHHHHhhhcCCCCCCCCCCcccccCccccc
Q 026681          172 LPKEEWVRINPLLVGFGQTICTPLRPRCGMCTVSEYCPSAFK  213 (235)
Q Consensus       172 ~p~~~~~~~~~~l~~~G~~iC~~~~P~C~~Cpl~~~C~~~~~  213 (235)
                      +|.+.|.++|++||+||+.||++++|+|+.|||++.|+||.+
T Consensus       175 ~p~~~~~~~~~~l~~~G~~iC~~~~P~C~~Cpl~~~C~~y~k  216 (217)
T d1keaa_         175 VPGGKCRDFNLGLMDFSAIICAPRKPKCEKCGMSKLCSYYEK  216 (217)
T ss_dssp             SCTTCHHHHHHHHHHHHHHTSCSSSCCGGGCTTTTTCHHHHT
T ss_pred             CCcccHHHHHHHHHHHHHHhcCCCCCCCCCCCCcccCcCccC
Confidence            999999999999999999999999999999999999999864

>d1orna_ a.96.1.1 (A:) Endonuclease III {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA-glycosylase
superfamily: DNA-glycosylase
family: Endonuclease III
domain: Endonuclease III
species: Escherichia coli [TaxId: 562]

Probab=100.00  E-value=8.9e-54  Score=357.38  Aligned_cols=190  Identities=29%  Similarity=0.555  Sum_probs=179.4

Q ss_pred             CCCCCCCCCChHHHHHHHHHhccccHHHHHHHHHHHHHcCCCCHHHHhcCCHHHHHHhhccCCChHHHHHHHHHHHHHHH
Q 026681           15 TDSSLPPKERRFAVLLSALLSSLTKDKVADGALQRLLQNGLHTAEAIDKADEATIKDLIYPVAFYTRKACNMKKIAKICL   94 (235)
Q Consensus        15 ~~~~~p~~~~~f~~lv~~iLsqqt~~~~~~~~~~~l~~~~~pt~~~la~a~~e~l~~~l~~~G~~~~Ka~~l~~~a~~i~   94 (235)
                      ....++|+ |||++||++||||||++++|.+++.+|++ .|||+++++.++.+++.+.|+++|||++||++|+++|+.|+
T Consensus        21 ~~~~l~~~-dp~~vLVs~iLsqqT~~~~v~~~~~~l~~-~~pt~~~la~~~~~e~~~~i~~~g~y~~ka~~l~~~a~~i~   98 (214)
T d1orna_          21 AHCELVHR-NPFELLIAVVLSAQCTDALVNKVTKRLFE-KYRTPHDYIAVPLEELEQDIRSIGLYRNKARNIQKLCAMLI   98 (214)
T ss_dssp             CCCCSCCS-SHHHHHHHHHHHTTSCHHHHHHHHHHHHH-HCCSHHHHHSSCHHHHHHHTGGGSSHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCC-CHHHHHHHHHHHhcChHHHHHHHHhhhhc-ccCchhhhhhccHHHhhhhhhhhhhhhHHHHHHHHHhhhHH
Confidence            34567875 99999999999999999999999999999 59999999999999999999999999999999999999999


Q ss_pred             HhcCCCChhhHHHHHcCCCCcHHHHHHHHHHhcCCcceeecchHHHHHHHHhcCcCCCCCCCCCCCHHHHHHHHHHhCCc
Q 026681           95 TKYDGDIPSSLDELLALPGIGPKMANMVMTLGWFNVQGICVDTHVHRICNRLGWVTQPGTKQKTSSPEQTREALQRWLPK  174 (235)
Q Consensus        95 ~~~~g~~~~~~~~L~~l~GIG~~tA~~il~~~~~~~~~~pvDt~v~Rv~~Rlg~~~~~~~~~~~~~~~~~~~~l~~~~p~  174 (235)
                      ++|+|++|.++++|++|||||+|||++||+|+|++ ++|+||+||+||+.|+|+++.      ..++..++..+++++|.
T Consensus        99 ~~~~g~vp~~~~~L~~LpGVG~kTA~~il~~a~~~-~~~~VDtnv~RV~~Rlg~~~~------~~~~~~~~~~l~~~~p~  171 (214)
T d1orna_          99 DKYNGEVPRDRDELMKLPGVGRKTANVVVSVAFGV-PAIAVDTHVERVSKRLGFCRW------DDSVLEVEKTLMKIIPK  171 (214)
T ss_dssp             HHSTTSCCSCHHHHTTSTTCCHHHHHHHHHHHHCC-CCCCCCHHHHHHHHHHTSSCT------TCCHHHHHHHHHHHSCG
T ss_pred             HHhCCCCCCCHHHHHhCcCcccchHHHHHHHHhcC-CcccccchHHHHHHHHHHhhc------ccchhhhhhhhhhcCcc
Confidence            99999999999999999999999999999999998 589999999999999999863      34678899999999999


Q ss_pred             ccHHHHHHHHHHHHhhhcCCCCCCCCCCcccccCccccc
Q 026681          175 EEWVRINPLLVGFGQTICTPLRPRCGMCTVSEYCPSAFK  213 (235)
Q Consensus       175 ~~~~~~~~~l~~~G~~iC~~~~P~C~~Cpl~~~C~~~~~  213 (235)
                      +.|.++|++||+||+.||++++|+|+.|||++.|++|.+
T Consensus       172 ~~~~~~~~~l~~~G~~iC~~~~P~C~~Cpl~~~C~~~~k  210 (214)
T d1orna_         172 EEWSITHHRMIFFGRYHCKAQSPQCPSCPLLHLCREGKK  210 (214)
T ss_dssp             GGHHHHHHHHHHHHHHTSCSSCCCGGGCTTGGGCHHHHH
T ss_pred             ccHHHHHHHHHHHHHHHCcCCCCCCCCCCCcccChhhcc
Confidence            999999999999999999999999999999999998754

>d2abka_ a.96.1.1 (A:) Endonuclease III {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA-glycosylase
superfamily: DNA-glycosylase
family: Endonuclease III
domain: Endonuclease III
species: Escherichia coli [TaxId: 562]

Probab=100.00  E-value=9.1e-54  Score=356.50  Aligned_cols=184  Identities=31%  Similarity=0.498  Sum_probs=176.0

Q ss_pred             CCChHHHHHHHHHhccccHHHHHHHHHHHHHcCCCCHHHHhcCCHHHHHHhhccCCChHHHHHHHHHHHHHHHHhcCCCC
Q 026681           22 KERRFAVLLSALLSSLTKDKVADGALQRLLQNGLHTAEAIDKADEATIKDLIYPVAFYTRKACNMKKIAKICLTKYDGDI  101 (235)
Q Consensus        22 ~~~~f~~lv~~iLsqqt~~~~~~~~~~~l~~~~~pt~~~la~a~~e~l~~~l~~~G~~~~Ka~~l~~~a~~i~~~~~g~~  101 (235)
                      ..|||++||++||||||++++|.+++.+|++ .|||+++++.++.++|+++|+++|||++||++|+++|+.+.++|+|.+
T Consensus        26 ~~~p~~vli~~iLsqqT~~~~v~~~~~~l~~-~~~t~~~la~a~~~~l~~~i~~~G~y~~Ka~~l~~~a~~i~~~~~g~~  104 (211)
T d2abka_          26 FSSPFELLIAVLLSAQATDVSVNKATAKLYP-VANTPAAMLELGVEGVKTYIKTIGLYNSKAENIIKTCRILLEQHNGEV  104 (211)
T ss_dssp             CSSHHHHHHHHHHTTTSCHHHHHHHHHHHTT-TCCSHHHHHHHHHHHHHHHHTTSTTHHHHHHHHHHHHHHHHHHTTTSC
T ss_pred             CCCHHHHHHHHHHhccchHHHHHHHHHHHHH-hccChHHHHhhhHhHhHHHHHHhhhhhhHHHHHHHHHHHHHHHhcCch
Confidence            3689999999999999999999999999999 599999999999999999999999999999999999999999999999


Q ss_pred             hhhHHHHHcCCCCcHHHHHHHHHHhcCCcceeecchHHHHHHHHhcCcCCCCCCCCCCCHHHHHHHHHHhCCcccHHHHH
Q 026681          102 PSSLDELLALPGIGPKMANMVMTLGWFNVQGICVDTHVHRICNRLGWVTQPGTKQKTSSPEQTREALQRWLPKEEWVRIN  181 (235)
Q Consensus       102 ~~~~~~L~~l~GIG~~tA~~il~~~~~~~~~~pvDt~v~Rv~~Rlg~~~~~~~~~~~~~~~~~~~~l~~~~p~~~~~~~~  181 (235)
                      |+++++|++|||||+|||++||+|+|++ ++|+||+||+||+.|+|+++       ..++++++..+..++|.+.|.++|
T Consensus       105 p~~~~~L~~LpGVG~~TA~~Il~~a~~~-p~~~vD~nv~Rv~~R~g~~~-------~~~~~~~~~~~~~~~p~~~~~~~~  176 (211)
T d2abka_         105 PEDRAALEALPGVGRKTANVVLNTAFGW-PTIAVDTHIFRVCNRTQFAP-------GKNVEQVEEKLLKVVPAEFKVDCH  176 (211)
T ss_dssp             CSCHHHHHHSTTCCHHHHHHHHHHHHCC-CCCCCCHHHHHHHHHHCSSC-------CSSHHHHHHHHHHHSCGGGTTTHH
T ss_pred             hHHHHHHHHHHhhchHHHHHHHHHHhcC-ccccccHHHHHHHHHhccCc-------cchhhHHHHHHhhcCccccHHHHH
Confidence            9999999999999999999999999998 58999999999999999975       457889999999999999999999


Q ss_pred             HHHHHHHhhhcCCCCCCCCCCcccccCcccccC
Q 026681          182 PLLVGFGQTICTPLRPRCGMCTVSEYCPSAFKE  214 (235)
Q Consensus       182 ~~l~~~G~~iC~~~~P~C~~Cpl~~~C~~~~~~  214 (235)
                      ++||+||+.||++++|+|+.|||++.|+|+.+.
T Consensus       177 ~~l~~~G~~vC~~~~P~C~~Cpl~~~C~~~~k~  209 (211)
T d2abka_         177 HWLILHGRYTCIARKPRCGSCIIEDLCEYKEKV  209 (211)
T ss_dssp             HHHHHHHHHTSCSSSCCGGGCTTGGGCCCTTCS
T ss_pred             HHHHHHhhhhccCCCCCCCCCCCcccCCCcCcC
Confidence            999999999999999999999999999987653

>d1rrqa1 a.96.1.2 (A:9-229) Catalytic domain of MutY {Bacillus stearothermophilus [TaxId: 1422]}

class: All alpha proteins
fold: DNA-glycosylase
superfamily: DNA-glycosylase
family: Mismatch glycosylase
domain: Catalytic domain of MutY
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=100.00  E-value=2.2e-52  Score=350.51  Aligned_cols=197  Identities=25%  Similarity=0.422  Sum_probs=179.2

Q ss_pred             CCCCCCCC--CChHHHHHHHHHhccccHHHHHHHHHHHHHcCCCCHHHHhcCCHHHHHHhhccCCChHHHHHHHHHHHHH
Q 026681           15 TDSSLPPK--ERRFAVLLSALLSSLTKDKVADGALQRLLQNGLHTAEAIDKADEATIKDLIYPVAFYTRKACNMKKIAKI   92 (235)
Q Consensus        15 ~~~~~p~~--~~~f~~lv~~iLsqqt~~~~~~~~~~~l~~~~~pt~~~la~a~~e~l~~~l~~~G~~~~Ka~~l~~~a~~   92 (235)
                      +.+++||+  .|||++||++||||||++++|.+++.+|++ .|||+++|+.+++++|+++|+++|||+ |+.++++.+..
T Consensus        16 ~~r~lpWr~~~dp~~vLV~~iLsqqT~~~~v~~~~~~L~~-~~~t~~~la~a~~~~l~~~i~~~G~~~-ra~~l~~~~~~   93 (221)
T d1rrqa1          16 ERRDLPWRKDRDPYKVWVSEVMLQQTRVETVIPYFEQFID-RFPTLEALADADEDEVLKAWEGLGYYS-RVRNLHAAVKE   93 (221)
T ss_dssp             HCCCCGGGSCCCHHHHHHHHHHHTTSCHHHHHHHHHHHHH-HSCSHHHHHHSCHHHHHHHHTTSSCTH-HHHHHHHHHHH
T ss_pred             cCCCCCCCCCCCHHHHHHHHHHHhhCcHHHHHHHHHHHHH-hcchHHHHHhhcHHHHHhhhccchhhh-hhHHHHHHHHH
Confidence            46789876  589999999999999999999999999999 599999999999999999999999996 48888889999


Q ss_pred             HHHhcCCCChhhHHHHHcCCCCcHHHHHHHHHHhcCCcceeecchHHHHHHHHhcCcCCCCCCCCCCCHHHHHHHHHHhC
Q 026681           93 CLTKYDGDIPSSLDELLALPGIGPKMANMVMTLGWFNVQGICVDTHVHRICNRLGWVTQPGTKQKTSSPEQTREALQRWL  172 (235)
Q Consensus        93 i~~~~~g~~~~~~~~L~~l~GIG~~tA~~il~~~~~~~~~~pvDt~v~Rv~~Rlg~~~~~~~~~~~~~~~~~~~~l~~~~  172 (235)
                      ++++|+|++|.++++|++|||||+|||++||+|+||+ ++|+||+||.||++|+|++....  .+..+.+.++..+..++
T Consensus        94 ~~~~~~G~vp~~~~~Ll~LpGIG~kTA~~il~~a~~~-p~~~VDt~v~Rv~~Rl~~~~~~~--~~~~~~~~~~~~~~~~~  170 (221)
T d1rrqa1          94 VKTRYGGKVPDDPDEFSRLKGVGPYTVGAVLSLAYGV-PEPAVNGNVMRVLSRLFLVTDDI--AKCSTRKRFEQIVREIM  170 (221)
T ss_dssp             HHHHHTTCCCCSHHHHHTSTTCCHHHHHHHHHHHTCC-CCCCCCHHHHHHHHHHTTCCSCT--TSTTHHHHHHHHHHHHC
T ss_pred             HhhhcCCCCchHHHHHHHHHHhhhHHHHHHHHHHhcC-cccccCccHHHHHHHhhccCCCc--hhhhHHHHHHHhhhhhh
Confidence            9999999999999999999999999999999999998 57899999999999999886422  12345667788888999


Q ss_pred             CcccHHHHHHHHHHHHhhhcCCCCCCCCCCcccccCcccccCCC
Q 026681          173 PKEEWVRINPLLVGFGQTICTPLRPRCGMCTVSEYCPSAFKESS  216 (235)
Q Consensus       173 p~~~~~~~~~~l~~~G~~iC~~~~P~C~~Cpl~~~C~~~~~~~~  216 (235)
                      |.+.|.++|++||+||+.||++++|+|+.|||++.|+||.+...
T Consensus       171 ~~~~~~~~~~~l~~~G~~iC~~~~P~C~~Cpl~~~C~~~~~~~~  214 (221)
T d1rrqa1         171 AYENPGAFNEALIELGALVCTPRRPSCLLCPVQAYCQAFAEGVA  214 (221)
T ss_dssp             CTTCHHHHHHHHHHHHHHTSCSSSCCGGGCTTGGGCHHHHTTCT
T ss_pred             hcccchHHHHHHHHHHHHHcCCCCCCCCCCcChhhCHHhhcCCc
Confidence            99999999999999999999999999999999999998866543

>d1kg2a_ a.96.1.2 (A:) Catalytic domain of MutY {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA-glycosylase
superfamily: DNA-glycosylase
family: Mismatch glycosylase
domain: Catalytic domain of MutY
species: Escherichia coli [TaxId: 562]

Probab=100.00  E-value=2.6e-52  Score=350.80  Aligned_cols=194  Identities=23%  Similarity=0.366  Sum_probs=174.3

Q ss_pred             CCCCCC--CChHHHHHHHHHhccccHHHHHHHHHHHHHcCCCCHHHHhcCCHHHHHHhhccCCChHHHHHHHHHHHHHHH
Q 026681           17 SSLPPK--ERRFAVLLSALLSSLTKDKVADGALQRLLQNGLHTAEAIDKADEATIKDLIYPVAFYTRKACNMKKIAKICL   94 (235)
Q Consensus        17 ~~~p~~--~~~f~~lv~~iLsqqt~~~~~~~~~~~l~~~~~pt~~~la~a~~e~l~~~l~~~G~~~~Ka~~l~~~a~~i~   94 (235)
                      +++||+  .|||++||++||||||++++|..++.+|++ .||||++|++++.++|+++|+++|||+ |+++|+++++.++
T Consensus        20 ~~lPWr~~~~p~~vlvs~iLsqqT~~~~v~~~~~~l~~-~~pt~~~la~a~~~~l~~~i~~~g~~~-ka~~l~~~~~~i~   97 (224)
T d1kg2a_          20 KTLPWQIDKTPYKVWLSEVMLQQTQVATVIPYFERFMA-RFPTVTDLANAPLDEVLHLWTGLGYYA-RARNLHKAAQQVA   97 (224)
T ss_dssp             CCSGGGSSCCHHHHHHHHHHHTSSCHHHHHHHHHHHHH-HCSSHHHHHHSCHHHHHHHHTTSCCTH-HHHHHHHHHHHHH
T ss_pred             CCCCCCCCCChHHHHHHHHHHhcCcHHHHHHHHHHHHH-HhccHHHHHHhhHHHHHhHhhhhhHHH-HHHHHHHhhhhhh
Confidence            368885  789999999999999999999999999999 599999999999999999999999996 6899999999999


Q ss_pred             HhcCCCChhhHHHHHcCCCCcHHHHHHHHHHhcCCcceeecchHHHHHHHHhcCcCCCCCCCCCCCHHHHHHHHHHhCCc
Q 026681           95 TKYDGDIPSSLDELLALPGIGPKMANMVMTLGWFNVQGICVDTHVHRICNRLGWVTQPGTKQKTSSPEQTREALQRWLPK  174 (235)
Q Consensus        95 ~~~~g~~~~~~~~L~~l~GIG~~tA~~il~~~~~~~~~~pvDt~v~Rv~~Rlg~~~~~~~~~~~~~~~~~~~~l~~~~p~  174 (235)
                      ++|+|++|+++++|++|||||+|||++||+|++++ ++++||+||.||+.|+|++....+  .......++..++.++|.
T Consensus        98 ~~~~g~vp~~~~~L~~LpGVG~kTA~~il~~a~~~-~~~~vD~~v~Rv~~Rl~~~~~~~~--~~~~~~~l~~~~~~~lp~  174 (224)
T d1kg2a_          98 TLHGGKFPETFEEVAALPGVGRSTAGAILSLSLGK-HFPILDGNVKRVLARCYAVSGWPG--KKEVENKLWSLSEQVTPA  174 (224)
T ss_dssp             HHSTTSCCCSHHHHHTSTTCCHHHHHHHHHHHHCC-SCCCCCHHHHHHHHHHHTCCSCTT--SHHHHHHHHHHHHHHCCS
T ss_pred             hhccCCcchHHHHHHHHHhhhhhhhHHHHHHhhhc-ccccccchHHHHHHHhccccCCcc--chHHHHHHHHHhhccCcc
Confidence            99999999999999999999999999999999998 588999999999999988753211  112233455566788999


Q ss_pred             ccHHHHHHHHHHHHhhhcCCCCCCCCCCcccccCcccccCC
Q 026681          175 EEWVRINPLLVGFGQTICTPLRPRCGMCTVSEYCPSAFKES  215 (235)
Q Consensus       175 ~~~~~~~~~l~~~G~~iC~~~~P~C~~Cpl~~~C~~~~~~~  215 (235)
                      ..|..+|++||+||+.||++++|+|+.|||++.|.+|.+..
T Consensus       175 ~~~~~~~~~l~~~G~~iC~~~~P~C~~Cpl~~~C~~~~~~~  215 (224)
T d1kg2a_         175 VGVERFNQAMMDLGAMICTRSKPKCSLCPLQNGCIAAANNS  215 (224)
T ss_dssp             TTHHHHHHHHHHHHHHTSCSSSCCGGGCTTTTTCHHHHHTC
T ss_pred             hhhhHHHHHHHHHhHHHccCCCCCCCCCcChhhChHhhcCC
Confidence            99999999999999999999999999999999999886653

>d1pu6a_ a.96.1.5 (A:) 3-Methyladenine DNA glycosylase III (MagIII) {Helicobacter pylori [TaxId: 210]}

class: All alpha proteins
fold: DNA-glycosylase
superfamily: DNA-glycosylase
family: 3-Methyladenine DNA glycosylase III (MagIII)
domain: 3-Methyladenine DNA glycosylase III (MagIII)
species: Helicobacter pylori [TaxId: 210]

Probab=100.00  E-value=3.5e-42  Score=287.22  Aligned_cols=166  Identities=18%  Similarity=0.261  Sum_probs=150.5

Q ss_pred             CCCChHHHHHHHHHhccccHHHHHHHHHHHHHc------CCCCHHHHhcCCHHHHHHhhccCCChHHHHHHHHHHHHHHH
Q 026681           21 PKERRFAVLLSALLSSLTKDKVADGALQRLLQN------GLHTAEAIDKADEATIKDLIYPVAFYTRKACNMKKIAKICL   94 (235)
Q Consensus        21 ~~~~~f~~lv~~iLsqqt~~~~~~~~~~~l~~~------~~pt~~~la~a~~e~l~~~l~~~G~~~~Ka~~l~~~a~~i~   94 (235)
                      +.++|||+||++||+|||++++|.+++++|...      +||||++|+++++++|+++|+++|||++||++|+++|+.+.
T Consensus        25 ~~~~pfe~lv~aIL~Qqts~~~a~~a~~~L~~~~~~~~~~~~t~~~la~a~~eel~~~ir~~G~~~~KA~~i~~~a~~i~  104 (217)
T d1pu6a_          25 PNALKFEALLGAVLTQNTKFEAVLKSLENLKNAFILENDDEINLKKIAYIEFSKLAECVRPSGFYNQKAKRLIDLSGNIL  104 (217)
T ss_dssp             TTTTSHHHHHHHHHTTTSCHHHHHHHHHHHHHTTSSCSCHHHHHHHHHHSCHHHHHHHTGGGSCHHHHHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHhhccccCCCHHHHHCCCHHHHHHHHHHCCCcHHHHHHHHHHHHHHH
Confidence            468999999999999999999999999999874      35899999999999999999999999999999999999999


Q ss_pred             HhcCC----CChhhHHHHHcCCCCcHHHHHHHHHHhcCCcceeecchHHHHHHHHhcCcCCCCCCCCCCCHHHHHHHHHH
Q 026681           95 TKYDG----DIPSSLDELLALPGIGPKMANMVMTLGWFNVQGICVDTHVHRICNRLGWVTQPGTKQKTSSPEQTREALQR  170 (235)
Q Consensus        95 ~~~~g----~~~~~~~~L~~l~GIG~~tA~~il~~~~~~~~~~pvDt~v~Rv~~Rlg~~~~~~~~~~~~~~~~~~~~l~~  170 (235)
                      ++|++    +.|+++++|++|||||+|||++||+|++++ ++||||+||+|+++|+|+..        .++++++..+++
T Consensus       105 ~~~~~~~~~~~~~~~~~L~~lpGIG~kTA~~vl~~~~~~-~~~~vD~hv~Rv~~Rlg~~~--------~~~~~~~~~~~~  175 (217)
T d1pu6a_         105 KDFQSFENFKQEVTREWLLDQKGIGKESADAILCYACAK-EVMVVDKYSYLFLKKLGIEI--------EDYDELQHFFEK  175 (217)
T ss_dssp             HHHSSHHHHHHHCCHHHHHTSTTCCHHHHHHHHHHTTCC-SCCCCCHHHHHHHHHTTCCC--------CSHHHHHHHHHH
T ss_pred             HhhhhcccCCcHHHHHHHHHHhhhhhHHHHHHHHHHcCC-eeeecChHHHHHHHHhCCCC--------CCHHHHHHHHHH
Confidence            99876    578899999999999999999999999998 68999999999999999964        357888888777


Q ss_pred             hCCcc----------------cHHHHHHHHHHHHhhhcCCC
Q 026681          171 WLPKE----------------EWVRINPLLVGFGQTICTPL  195 (235)
Q Consensus       171 ~~p~~----------------~~~~~~~~l~~~G~~iC~~~  195 (235)
                      .+|.+                .|.+||..|++||+.+|+++
T Consensus       176 ~l~~~~~~~~~~~~~~~~~~~~~~~~H~llv~~Gk~~C~ak  216 (217)
T d1pu6a_         176 GVQENLNSALALYENTISLAQLYARFHGKIVEFSKQKLELK  216 (217)
T ss_dssp             HHHTTHHHHHHTTTTCSCHHHHHHHHHHHHHHHHHHHHHTC
T ss_pred             HhHHHHHHHHHHhcccchHHHHHHHHHHHHHHHhHHHCCCC
Confidence            66643                25789999999999999975

>d2noha1 a.96.1.3 (A:136-325) 8-oxoguanine glycosylase {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA-glycosylase
superfamily: DNA-glycosylase
family: DNA repair glycosylase, 2 C-terminal domains
domain: 8-oxoguanine glycosylase
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.97  E-value=1.9e-29  Score=205.79  Aligned_cols=152  Identities=21%  Similarity=0.291  Sum_probs=120.7

Q ss_pred             ChHHHHHHHHHhccccHHHHHHHHHHHHHc--------------CCCCHHHHhcCCHHHHHHhhccCCChHHHHHHHHHH
Q 026681           24 RRFAVLLSALLSSLTKDKVADGALQRLLQN--------------GLHTAEAIDKADEATIKDLIYPVAFYTRKACNMKKI   89 (235)
Q Consensus        24 ~~f~~lv~~iLsqqt~~~~~~~~~~~l~~~--------------~~pt~~~la~a~~e~l~~~l~~~G~~~~Ka~~l~~~   89 (235)
                      ||||+||++|+|||+++.++.+++++|.+.              .||||++|++++.+++...   .|+. .||++|+++
T Consensus         1 DPfe~lv~~IisQq~s~~~~~~~~~~L~~~~G~~~~~~~~~~~~~FP~~~~la~~~~e~~l~~---~~~~-~ra~~i~~~   76 (190)
T d2noha1           1 DPIECLFSFICSSNNNIARITGMVERLCQAFGPRLIQLDDVTYHGFPSLQALAGPEVEAHLRK---LGLG-YRARYVSAS   76 (190)
T ss_dssp             CHHHHHHHHHTTTTSCHHHHHHHHHHHHHHHSCEEEEETTEEEECCCCHHHHHSTTHHHHHHH---TTCT-THHHHHHHH
T ss_pred             ChHHHHHHHHHHcccCHHHHHHHHHHHHHHHCCCccccCcchhhccCCHHHHHHcchHHHHHh---cchH-HHHHHHHHH
Confidence            799999999999999999999999999774              4899999999999876554   3543 379999999


Q ss_pred             HHHHHHhcCC----------CChhhHHHHHcCCCCcHHHHHHHHHHhcCCcceeecchHHHHHHHHhcCcCCCCCCCCCC
Q 026681           90 AKICLTKYDG----------DIPSSLDELLALPGIGPKMANMVMTLGWFNVQGICVDTHVHRICNRLGWVTQPGTKQKTS  159 (235)
Q Consensus        90 a~~i~~~~~g----------~~~~~~~~L~~l~GIG~~tA~~il~~~~~~~~~~pvDt~v~Rv~~Rlg~~~~~~~~~~~~  159 (235)
                      |+.+.+.+++          +.++.+++|++|||||+|||++|++|+++++++||||+||+|++.|++.........+..
T Consensus        77 a~~i~~~~~~~~~l~~l~~~~~~~~~~~L~~l~GIG~wTA~~il~~~~~~~d~fpvD~~v~R~~~r~~~~~~~~~~~k~~  156 (190)
T d2noha1          77 ARAILEEQGGLAWLQQLRESSYEEAHKALCILPGVGTQVADCICLMALDKPQAVPVDVHMWHIAQRDYSWHPTTSQAKGP  156 (190)
T ss_dssp             HHHHHHTSCSHHHHHHTTTSCHHHHHHHHTTSTTCCHHHHHHHHHHHSCCTTCCCCCHHHHHHHHHHHCCCCSSSSCSSS
T ss_pred             HHHHHHhcccccCHHHhcCCCcHHHHHHHHHcCCchHHHHHHHHHHHcCCCCeEeecHHHHHHHHHHhcccCcchhhccc
Confidence            9999987655          346789999999999999999999999999999999999999999986655433333333


Q ss_pred             CH---HHHHHHH-HHhCCcccHHH
Q 026681          160 SP---EQTREAL-QRWLPKEEWVR  179 (235)
Q Consensus       160 ~~---~~~~~~l-~~~~p~~~~~~  179 (235)
                      ++   .++.+.+ +.|-|...|..
T Consensus       157 ~~~~~~~~~~~~~~~~g~y~g~a~  180 (190)
T d2noha1         157 SPQTNKELGNFFRSLWGPYAGWAA  180 (190)
T ss_dssp             CHHHHHHHHHHHHHHHCTTHHHHH
T ss_pred             cHHHHHHHHHHHHHHhcchhhHHH
Confidence            33   2333333 44555544433

>d1mpga1 a.96.1.3 (A:100-282) 3-Methyladenine DNA glycosylase II (gene alkA or aidA) {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA-glycosylase
superfamily: DNA-glycosylase
family: DNA repair glycosylase, 2 C-terminal domains
domain: 3-Methyladenine DNA glycosylase II (gene alkA or aidA)
species: Escherichia coli [TaxId: 562]

Probab=99.96  E-value=8.4e-29  Score=200.81  Aligned_cols=154  Identities=23%  Similarity=0.321  Sum_probs=133.6

Q ss_pred             CCCCCCCCCCCChHHHHHHHHHhccccHHHHHHHHHHHHHc------------CCCCHHHHhcCCHHHHHHhhccCCChH
Q 026681           13 DETDSSLPPKERRFAVLLSALLSSLTKDKVADGALQRLLQN------------GLHTAEAIDKADEATIKDLIYPVAFYT   80 (235)
Q Consensus        13 ~~~~~~~p~~~~~f~~lv~~iLsqqt~~~~~~~~~~~l~~~------------~~pt~~~la~a~~e~l~~~l~~~G~~~   80 (235)
                      ...|.++|...||||.||.+|++||++.+++..++++|.+.            .||||++|+++++++|..+    |++.
T Consensus         2 ~~pGlRi~~~~dpfe~Lv~~Ii~Qqis~~aA~~i~~rl~~~~g~~~~~~~~~~~FPtp~~l~~~~~~~lr~~----Gls~   77 (183)
T d1mpga1           2 ARPGLRLPGCVDAFEQGVRAILGQLVSVAMAAKLTARVAQLYGERLDDFPEYICFPTPQRLAAADPQALKAL----GMPL   77 (183)
T ss_dssp             TCTTCCCCCCSCHHHHHHHHHHTTTSCHHHHHHHHHHHHHHHCCBCSSCTTCBCCCCHHHHHTCCHHHHHHT----TSCH
T ss_pred             cCCCCcCCCCCCHHHHHHHHHHhchhhHHHHHHHHHHHHHHhCccccccccccCCCcHHHHHcCCHHHHHHc----CCcH
Confidence            35678899888999999999999999999999999999763            4899999999999998766    9999


Q ss_pred             HHHHHHHHHHHHHHHh-----cCCCChhhHHHHHcCCCCcHHHHHHHHHHhcCCcceeec-chHHHHHHHHhcCcCCCCC
Q 026681           81 RKACNMKKIAKICLTK-----YDGDIPSSLDELLALPGIGPKMANMVMTLGWFNVQGICV-DTHVHRICNRLGWVTQPGT  154 (235)
Q Consensus        81 ~Ka~~l~~~a~~i~~~-----~~g~~~~~~~~L~~l~GIG~~tA~~il~~~~~~~~~~pv-Dt~v~Rv~~Rlg~~~~~~~  154 (235)
                      +|+++|+++|+.+.+.     ..++.++.++.|+++||||+|||++|++|+++++++||+ |.+++|.+.          
T Consensus        78 ~Ka~~i~~~a~~~~~g~l~~~~~~~~~e~~~~L~~l~GIGpwTAd~illf~lg~~dvfP~~D~~lr~~~~----------  147 (183)
T d1mpga1          78 KRAEALIHLANAALEGTLPMTIPGDVEQAMKTLQTFPGIGRWTANYFALRGWQAKDVFLPDDYLIKQRFP----------  147 (183)
T ss_dssp             HHHHHHHHHHHHHHHTCSCSSCCSCHHHHHHHHTTSTTCCHHHHHHHHHHHSCCSSCCCTTCHHHHHHST----------
T ss_pred             HHHHHHHHHHHHHHcCchhhhccccHHHHHHHHHHhhcccHHHHHHHHHhhCCCCCccccchHHHHHHhh----------
Confidence            9999999999999873     123455789999999999999999999999999999999 888876542          


Q ss_pred             CCCCCCHHHHHHHHHHhCCcccHHHHHHH
Q 026681          155 KQKTSSPEQTREALQRWLPKEEWVRINPL  183 (235)
Q Consensus       155 ~~~~~~~~~~~~~l~~~~p~~~~~~~~~~  183 (235)
                         ..+++++++..+.|-|+..|..+|.|
T Consensus       148 ---~l~~~~~~~~~~~~~Pyrs~a~~yLW  173 (183)
T d1mpga1         148 ---GMTPAQIRRYAERWKPWRSYALLHIW  173 (183)
T ss_dssp             ---TCCHHHHHHHHGGGTTCHHHHHHHHH
T ss_pred             ---hCCHHHHHHHHHhccCHHHHHHHHHH
Confidence               23567899999999998888887764

>d1ngna_ a.96.1.2 (A:) Mismatch-specific thymine glycosylase domain of the methyl-GpG binding protein mbd4 {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: DNA-glycosylase
superfamily: DNA-glycosylase
family: Mismatch glycosylase
domain: Mismatch-specific thymine glycosylase domain of the methyl-GpG binding protein mbd4
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.96  E-value=1.2e-29  Score=198.23  Aligned_cols=117  Identities=20%  Similarity=0.219  Sum_probs=105.4

Q ss_pred             CCChHHHHHHHHHhccccHHHHHHHHHHHHHcCCCCHHHHhcCCHHHHHHhhccCCChHHHHHHHHHHHHHHHHhcCCCC
Q 026681           22 KERRFAVLLSALLSSLTKDKVADGALQRLLQNGLHTAEAIDKADEATIKDLIYPVAFYTRKACNMKKIAKICLTKYDGDI  101 (235)
Q Consensus        22 ~~~~f~~lv~~iLsqqt~~~~~~~~~~~l~~~~~pt~~~la~a~~e~l~~~l~~~G~~~~Ka~~l~~~a~~i~~~~~g~~  101 (235)
                      .+|||++||++||||||++++|.+++.+|++ .||||++|++++.++|+++|+++|||++||++|+++++.++.      
T Consensus        17 ~~dPf~~LV~~ILsqqT~~~~v~~v~~~L~~-~~pt~e~la~a~~~el~~~Ir~~G~~~~KAk~I~~~a~~~ip------   89 (144)
T d1ngna_          17 FHDPWKLLIATIFLNRTSGKMAIPVLWEFLE-KYPSAEVARAADWRDVSELLKPLGLYDLRAKTIIKFSDEYLT------   89 (144)
T ss_dssp             TTSHHHHHHHHHHHTTSCHHHHHHHHHHHHH-HSCSHHHHHHSCHHHHHHHTGGGSCHHHHHHHHHHHHHHHHH------
T ss_pred             cCCHHHHHHHHHHHccCCHHHHHHHHHHHHH-hCCchhhhhccCHHHHHHHHHhhhhHHHHHHHHHHHHhhHhh------
Confidence            3789999999999999999999999999999 599999999999999999999999999999999999998864      


Q ss_pred             hhhHHHHHcCCCCcHHHHHHHHHHhcCCcc-eeecchHHHHHHHHh
Q 026681          102 PSSLDELLALPGIGPKMANMVMTLGWFNVQ-GICVDTHVHRICNRL  146 (235)
Q Consensus       102 ~~~~~~L~~l~GIG~~tA~~il~~~~~~~~-~~pvDt~v~Rv~~Rl  146 (235)
                       +..++|++|||||+|||+++++|++++.+ ++|.|.+++|.+.++
T Consensus        90 -~~~~~l~~LpGVG~~tad~~~if~~~~~~~v~~~D~~l~r~~~~~  134 (144)
T d1ngna_          90 -KQWRYPIELHGIGKYGNDSYRIFCVNEWKQVHPEDHKLNKYHDWL  134 (144)
T ss_dssp             -SCCSSGGGSTTCCHHHHHHHHHHTSSCGGGCCCCSHHHHHHHHHH
T ss_pred             -hhhhhHHhcCCccHHHHHHHHHHHcCCCCCCCCCChHHHHHHHHH
Confidence             45678999999999999999999999854 456677777776664

>d2i1qa1 a.60.4.1 (A:5-64) DNA repair protein Rad51, N-terminal domain {Archaeon Methanococcus voltae [TaxId: 2188]}

class: All alpha proteins
fold: SAM domain-like
superfamily: Rad51 N-terminal domain-like
family: DNA repair protein Rad51, N-terminal domain
domain: DNA repair protein Rad51, N-terminal domain
species: Archaeon Methanococcus voltae [TaxId: 2188]

Probab=96.17  E-value=0.0049  Score=38.81  Aligned_cols=47  Identities=17%  Similarity=0.172  Sum_probs=38.8

Q ss_pred             HHHHHHHcCCCCHHHHhcCCHHHHHHhhccCCChHHHHHHHHHHHHHHHH
Q 026681           46 ALQRLLQNGLHTAEAIDKADEATIKDLIYPVAFYTRKACNMKKIAKICLT   95 (235)
Q Consensus        46 ~~~~l~~~~~pt~~~la~a~~e~l~~~l~~~G~~~~Ka~~l~~~a~~i~~   95 (235)
                      ..++|.+++|.|.++|+.+++++|.++   -|+...+|+.|.+.|+.+.+
T Consensus        11 ~a~~L~~~G~~tv~~l~~a~~eeL~~i---~Gi~~~~A~~i~~~ar~~~d   57 (60)
T d2i1qa1          11 TAEKLVEAGYIDFMKIATATVGELTDI---EGISEKAAAKMIMGARDLCD   57 (60)
T ss_dssp             HHHHHHHHTCCSHHHHHTCCHHHHHTS---TTCCHHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHccCCCHHHHHhCCHHHHHHC---CCCCHHHHHHHHHHHHHHcC
Confidence            456777768999999999999999774   38888899999988887643

>d1nkua_ a.96.1.4 (A:) 3-Methyladenine DNA glycosylase I (Tag) {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA-glycosylase
superfamily: DNA-glycosylase
family: 3-Methyladenine DNA glycosylase I (Tag)
domain: 3-Methyladenine DNA glycosylase I (Tag)
species: Escherichia coli [TaxId: 562]

Probab=96.08  E-value=0.094  Score=40.23  Aligned_cols=102  Identities=11%  Similarity=0.032  Sum_probs=78.9

Q ss_pred             hHHHHHHHHHhccccHHHHHHHHHHHHHc-CCCCHHHHhcCCHHHHHHhhccCCC--hHHHHHHHHHHHHHHHH---hcC
Q 026681           25 RFAVLLSALLSSLTKDKVADGALQRLLQN-GLHTAEAIDKADEATIKDLIYPVAF--YTRKACNMKKIAKICLT---KYD   98 (235)
Q Consensus        25 ~f~~lv~~iLsqqt~~~~~~~~~~~l~~~-~~pt~~~la~a~~e~l~~~l~~~G~--~~~Ka~~l~~~a~~i~~---~~~   98 (235)
                      -||.|+-+++..-.++..+.+-...+.+. ...+|+.||..+++++++++..-|.  +++|.+.+++=|+++.+   ++|
T Consensus        31 LFE~L~Le~fQaGLsW~~IL~Kr~~fr~aF~~Fd~~~vA~~~e~~ie~Ll~d~~IIRNr~KI~Avi~NAr~~l~i~~e~g  110 (187)
T d1nkua_          31 LFEMICLEGQQAGLSWITVLKKRENYRACFHQFDPVKVAAMQEEDVERLVQDAGIIRHRGKIQAIIGNARAYLQMEQNGE  110 (187)
T ss_dssp             HHHHHHHHHHHTTSCHHHHHHHHHHHHHHHTTTCHHHHHTCCHHHHHHHHTCCSSCCCHHHHHHHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHhccCCHHHHHHHHHHHHHHHhCCCHHHHHcCCHHHHHHHhccCCeeechHHHHHHHHHHHHHHHHHHhcC
Confidence            49999999999999999999988888764 2469999999999999999998776  56788888777777554   443


Q ss_pred             C----------------------CChh-------hHHHHHc--CCCCcHHHHHHHHHHh
Q 026681           99 G----------------------DIPS-------SLDELLA--LPGIGPKMANMVMTLG  126 (235)
Q Consensus        99 g----------------------~~~~-------~~~~L~~--l~GIG~~tA~~il~~~  126 (235)
                      +                      ++|.       .-+.|.+  ++=|||.|..++|...
T Consensus       111 sf~~~lw~f~~~~p~~~~~~~~~~ip~~t~~s~~lsk~LKk~GfkFvGpt~~ysfmqa~  169 (187)
T d1nkua_         111 PFADFVWSFVNHQPQMTQATTLSEIPTSTPASDALSKALKKRGFKFVGTTICYSFMQAC  169 (187)
T ss_dssp             CHHHHHHHHTTTCCEECCCSSGGGSCSCCHHHHHHHHHHHHHTCCCCCHHHHHHHHHHH
T ss_pred             CHHHHHHhcCCCCCcCCCccCHHHhhcCCHHHHHHHHHHHhcCCeecChHHHHHHHHHc
Confidence            2                      1121       2345553  8889999998888653

>d1szpa1 a.60.4.1 (A:81-144) DNA repair protein Rad51, N-terminal domain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All alpha proteins
fold: SAM domain-like
superfamily: Rad51 N-terminal domain-like
family: DNA repair protein Rad51, N-terminal domain
domain: DNA repair protein Rad51, N-terminal domain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=95.66  E-value=0.0067  Score=38.74  Aligned_cols=46  Identities=26%  Similarity=0.330  Sum_probs=40.4

Q ss_pred             HHHHHHHcCCCCHHHHhcCCHHHHHHhhccCCChHHHHHHHHHHHHHHH
Q 026681           46 ALQRLLQNGLHTAEAIDKADEATIKDLIYPVAFYTRKACNMKKIAKICL   94 (235)
Q Consensus        46 ~~~~l~~~~~pt~~~la~a~~e~l~~~l~~~G~~~~Ka~~l~~~a~~i~   94 (235)
                      ..++|.+.||.|.++|+.++.++|.++   -||...+|..|++.|+.++
T Consensus        15 ~~~kL~~aG~~Tve~ia~~t~~~L~~i---~Gi~e~~a~KIi~~A~k~~   60 (64)
T d1szpa1          15 DVKKLRESGLHTAEAVAYAPRKDLLEI---KGISEAKADKLLNEAARLV   60 (64)
T ss_dssp             HHHHHHTTSCCSHHHHHHSCSHHHHTS---TTCCHHHHHHHHHHHHHHS
T ss_pred             HHHHHHHcCCCcHHHHHhCCHHHHHHc---CCCCHHHHHHHHHHHHHHc
Confidence            467788889999999999999998776   4999999999999999864

>d2fmpa1 a.60.6.1 (A:10-91) DNA polymerase beta, N-terminal (8 kD)-domain {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: SAM domain-like
superfamily: DNA polymerase beta, N-terminal domain-like
family: DNA polymerase beta, N-terminal domain-like
domain: DNA polymerase beta, N-terminal (8 kD)-domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.57  E-value=0.023  Score=37.86  Aligned_cols=57  Identities=26%  Similarity=0.329  Sum_probs=40.5

Q ss_pred             HHHHHhhccCCChHHHHHHHHHHHHHHHHhcCCCChhhHHHHHcCCCCcHHHHHHHHHH
Q 026681           67 ATIKDLIYPVAFYTRKACNMKKIAKICLTKYDGDIPSSLDELLALPGIGPKMANMVMTL  125 (235)
Q Consensus        67 e~l~~~l~~~G~~~~Ka~~l~~~a~~i~~~~~g~~~~~~~~L~~l~GIG~~tA~~il~~  125 (235)
                      +++.++.+..|-..-|++.-..++..|. .+..++. +.+.|.++||||+.+|..|.-|
T Consensus        11 ~ela~l~~~~~~~~fr~~AY~~Aa~~i~-~l~~~i~-~~~~l~~i~GIGk~ia~kI~E~   67 (82)
T d2fmpa1          11 TELANFEKNVSQAIHKYNAYRKAASVIA-KYPHKIK-SGAEAKKLPGVGTKIAEKIDEF   67 (82)
T ss_dssp             HHHHHHHHHTTCCHHHHHHHHHHHHHHH-HCSSCCC-CHHHHHTSTTCCHHHHHHHHHH
T ss_pred             HHHHHHHHHhCcChHHHHHHHHHHHHHH-hCCcccC-CHHHHhcCCCccHHHHHHHHHH
Confidence            3445555544533347888888888875 4555553 5788999999999999988765

>d1pzna1 a.60.4.1 (A:35-95) DNA repair protein Rad51, N-terminal domain {Archaeon Pyrococcus furiosus [TaxId: 2261]}

class: All alpha proteins
fold: SAM domain-like
superfamily: Rad51 N-terminal domain-like
family: DNA repair protein Rad51, N-terminal domain
domain: DNA repair protein Rad51, N-terminal domain
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=95.56  E-value=0.014  Score=36.67  Aligned_cols=46  Identities=22%  Similarity=0.268  Sum_probs=37.9

Q ss_pred             HHHHHHHcCCCCHHHHhcCCHHHHHHhhccCCChHHHHHHHHHHHHHHH
Q 026681           46 ALQRLLQNGLHTAEAIDKADEATIKDLIYPVAFYTRKACNMKKIAKICL   94 (235)
Q Consensus        46 ~~~~l~~~~~pt~~~la~a~~e~l~~~l~~~G~~~~Ka~~l~~~a~~i~   94 (235)
                      ..++|.+.+|.|.++|+.+++++|.++ .  |+...+|..|.+.|+.+.
T Consensus        13 ~a~~L~~~g~~sv~~l~~a~~~eL~~i-~--Gi~~~~A~~i~~~ar~~~   58 (61)
T d1pzna1          13 TAEKLREAGYDTLEAIAVASPIELKEV-A--GISEGTALKIIQAARKAA   58 (61)
T ss_dssp             HHHHHHTTTCCSHHHHHTCCHHHHHHH-H--CCCHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHhcCCCHHHHHhCCHHHHHHC-C--CCCHHHHHHHHHHHHHHc
Confidence            346777767899999999999999885 3  777888999998888754

>d1ixra1 a.60.2.1 (A:63-135) DNA helicase RuvA subunit, middle domain {Thermus thermophilus [TaxId: 274]}

class: All alpha proteins
fold: SAM domain-like
superfamily: RuvA domain 2-like
family: DNA helicase RuvA subunit, middle domain
domain: DNA helicase RuvA subunit, middle domain
species: Thermus thermophilus [TaxId: 274]

Probab=95.49  E-value=0.02  Score=37.39  Aligned_cols=26  Identities=15%  Similarity=0.096  Sum_probs=21.1

Q ss_pred             hhHHHHHcCCCCcHHHHHHHHHHhcC
Q 026681          103 SSLDELLALPGIGPKMANMVMTLGWF  128 (235)
Q Consensus       103 ~~~~~L~~l~GIG~~tA~~il~~~~~  128 (235)
                      .+.+.|.++||||+|||+-+..---+
T Consensus        42 ~D~~~L~~vpGIG~KtA~rIi~eLk~   67 (73)
T d1ixra1          42 GDARLLTSASGVGRRLAERIALELKG   67 (73)
T ss_dssp             TCHHHHTTSTTCCHHHHHHHHHHHTT
T ss_pred             cCHHHhhcCCCCCHHHHHHHHHHHHh
Confidence            46789999999999999988755433

>d1cuka2 a.60.2.1 (A:65-142) DNA helicase RuvA subunit, middle domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: SAM domain-like
superfamily: RuvA domain 2-like
family: DNA helicase RuvA subunit, middle domain
domain: DNA helicase RuvA subunit, middle domain
species: Escherichia coli [TaxId: 562]

Probab=95.15  E-value=0.028  Score=37.15  Aligned_cols=25  Identities=32%  Similarity=0.462  Sum_probs=20.8

Q ss_pred             hhHHHHHcCCCCcHHHHHHHHHHhc
Q 026681          103 SSLDELLALPGIGPKMANMVMTLGW  127 (235)
Q Consensus       103 ~~~~~L~~l~GIG~~tA~~il~~~~  127 (235)
                      .+.+.|.++||||+|||+-+..---
T Consensus        41 ~D~~~L~~vpGIG~KtA~rIi~eLk   65 (78)
T d1cuka2          41 EEVGALVKLPGIGKKTAERLIVEMK   65 (78)
T ss_dssp             TCHHHHHTSTTCCHHHHHHHHHHHH
T ss_pred             cCHHHhhcCCCCCHHHHHHHHHHHH
Confidence            4678999999999999998875433

>d1bvsa2 a.60.2.1 (A:64-134) DNA helicase RuvA subunit, middle domain {Mycobacterium leprae [TaxId: 1769]}

class: All alpha proteins
fold: SAM domain-like
superfamily: RuvA domain 2-like
family: DNA helicase RuvA subunit, middle domain
domain: DNA helicase RuvA subunit, middle domain
species: Mycobacterium leprae [TaxId: 1769]

Probab=95.05  E-value=0.036  Score=35.90  Aligned_cols=23  Identities=30%  Similarity=0.488  Sum_probs=19.8

Q ss_pred             hhHHHHHcCCCCcHHHHHHHHHH
Q 026681          103 SSLDELLALPGIGPKMANMVMTL  125 (235)
Q Consensus       103 ~~~~~L~~l~GIG~~tA~~il~~  125 (235)
                      .+.+.|.++||||+|||+-+..-
T Consensus        41 ~D~~~L~~vpGIG~KtA~rIi~e   63 (71)
T d1bvsa2          41 SDVASLTRVPGIGRRGAERIVLE   63 (71)
T ss_dssp             TCHHHHHTSTTCCHHHHHHHHHH
T ss_pred             CCHHHhhcCCCCCHHHHHHHHHH
Confidence            56789999999999999988654

>d2bcqa1 a.60.6.1 (A:252-327) DNA polymerase lambda {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: SAM domain-like
superfamily: DNA polymerase beta, N-terminal domain-like
family: DNA polymerase beta, N-terminal domain-like
domain: DNA polymerase lambda
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.58  E-value=0.054  Score=35.27  Aligned_cols=44  Identities=23%  Similarity=0.427  Sum_probs=33.0

Q ss_pred             HHHHHHHHHHHHHHHHhcCCCChhhHHHHHcCCCCcHHHHHHHHHH
Q 026681           80 TRKACNMKKIAKICLTKYDGDIPSSLDELLALPGIGPKMANMVMTL  125 (235)
Q Consensus        80 ~~Ka~~l~~~a~~i~~~~~g~~~~~~~~L~~l~GIG~~tA~~il~~  125 (235)
                      .-|++.-..++..|. .+..++. +.++|.++||||+.+++.|.-+
T Consensus        22 ~fr~~AY~~A~~~l~-~l~~~i~-~~~~l~~lpGiG~~i~~kI~Ei   65 (76)
T d2bcqa1          22 KWRALGYAKAINALK-SFHKPVT-SYQEACSIPGIGKRMAEKIIEI   65 (76)
T ss_dssp             HHHHHHHHHHHHHHH-SCCSCCC-CHHHHHTSTTCCHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHH-hCCcccC-CHHHHhcCCCccHHHHHHHHHH
Confidence            346777778777764 4555554 4578999999999999988755

>d1x2ia1 a.60.2.5 (A:2-69) ATP-dependent RNA helicase PF2015 {Pyrococcus furiosus [TaxId: 2261]}

class: All alpha proteins
fold: SAM domain-like
superfamily: RuvA domain 2-like
family: Hef domain-like
domain: ATP-dependent RNA helicase PF2015
species: Pyrococcus furiosus [TaxId: 2261]

Probab=94.46  E-value=0.022  Score=36.55  Aligned_cols=23  Identities=35%  Similarity=0.619  Sum_probs=20.4

Q ss_pred             hhHHHHHcCCCCcHHHHHHHHHH
Q 026681          103 SSLDELLALPGIGPKMANMVMTL  125 (235)
Q Consensus       103 ~~~~~L~~l~GIG~~tA~~il~~  125 (235)
                      .+.++|.+++|||+++|+.|..+
T Consensus        39 As~eeL~~i~GIG~~~A~~I~~~   61 (68)
T d1x2ia1          39 ASVAELMKVEGIGEKIAKEIRRV   61 (68)
T ss_dssp             CCHHHHTTSTTCCHHHHHHHHHH
T ss_pred             hHHHHHHhCCCcCHHHHHHHHHH
Confidence            36789999999999999999766

>d1kfta_ a.60.2.3 (A:) Excinuclease UvrC C-terminal domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: SAM domain-like
superfamily: RuvA domain 2-like
family: Excinuclease UvrC C-terminal domain
domain: Excinuclease UvrC C-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=94.36  E-value=0.016  Score=35.78  Aligned_cols=22  Identities=27%  Similarity=0.522  Sum_probs=19.7

Q ss_pred             hHHHHHcCCCCcHHHHHHHHHH
Q 026681          104 SLDELLALPGIGPKMANMVMTL  125 (235)
Q Consensus       104 ~~~~L~~l~GIG~~tA~~il~~  125 (235)
                      ..++|.+++|||+++|..|..+
T Consensus        32 s~eeL~~v~GIg~~~A~~I~~~   53 (56)
T d1kfta_          32 SVEEIAKVPGISQGLAEKIFWS   53 (56)
T ss_dssp             CHHHHTTSSSTTSHHHHHHHHH
T ss_pred             hHHHHHhcCCCCHHHHHHHHHH
Confidence            5789999999999999988765

>d1dgsa1 a.60.2.2 (A:401-581) NAD+-dependent DNA ligase, domain 3 {Thermus filiformis [TaxId: 276]}

class: All alpha proteins
fold: SAM domain-like
superfamily: RuvA domain 2-like
family: NAD+-dependent DNA ligase, domain 3
domain: NAD+-dependent DNA ligase, domain 3
species: Thermus filiformis [TaxId: 276]

Probab=94.18  E-value=0.036  Score=42.41  Aligned_cols=79  Identities=19%  Similarity=0.355  Sum_probs=52.0

Q ss_pred             HHHHHHHHHHcCC-CCHHHHhcCCHHHHHHhhccCCChHHHHHHHHHHHHH-------------------------HHHh
Q 026681           43 ADGALQRLLQNGL-HTAEAIDKADEATIKDLIYPVAFYTRKACNMKKIAKI-------------------------CLTK   96 (235)
Q Consensus        43 ~~~~~~~l~~~~~-pt~~~la~a~~e~l~~~l~~~G~~~~Ka~~l~~~a~~-------------------------i~~~   96 (235)
                      ....+..|++.++ -++.+|.....++|..+ .  ||...++..|.+..+.                         +.+.
T Consensus        50 G~~~i~~L~~~g~i~~~~Dly~L~~~~l~~l-~--~~g~ksa~nl~~~Ie~sk~~~l~r~l~aLGI~~vG~~~Ak~La~~  126 (181)
T d1dgsa1          50 GEKLIERLLEKGLVRDVADLYHLRKEDLLGL-E--RMGEKSAQNLLRQIEESKHRGLERLLYALGLPGVGEVLARNLARR  126 (181)
T ss_dssp             CHHHHHHHHHTTSCSSGGGGGGGCCHHHHTT-S--SCCSTTHHHHHHHHHHGGGCCHHHHHHHTTCSSCCHHHHHHHHHT
T ss_pred             HHHHHHHHhhcCCcchhhhhhhhhhHHHhcc-c--ccchHHHHHHHHHHHhhcchhHHHHHHHHHhhhhhHHHHHHHHHH
Confidence            3445677777664 67888888888887665 2  5555555555443322                         2333


Q ss_pred             cCCCCh----hhHHHHHcCCCCcHHHHHHHHHH
Q 026681           97 YDGDIP----SSLDELLALPGIGPKMANMVMTL  125 (235)
Q Consensus        97 ~~g~~~----~~~~~L~~l~GIG~~tA~~il~~  125 (235)
                      | ++++    .+.++|.+++|||+++|..|..|
T Consensus       127 f-~sl~~l~~as~eeL~~I~GIG~~~A~si~~f  158 (181)
T d1dgsa1         127 F-GTMDRLLEASLEELIEVEEVGELTARAILET  158 (181)
T ss_dssp             T-SBHHHHTTCCHHHHHTSTTCCHHHHHHHHHH
T ss_pred             h-hhhhhhhhhHHHHHhhcCCcCHHHHHHHHHH
Confidence            3 2232    35789999999999999998877

>d1b22a_ a.60.4.1 (A:) DNA repair protein Rad51, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: SAM domain-like
superfamily: Rad51 N-terminal domain-like
family: DNA repair protein Rad51, N-terminal domain
domain: DNA repair protein Rad51, N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=93.91  E-value=0.015  Score=37.66  Aligned_cols=46  Identities=22%  Similarity=0.278  Sum_probs=39.5

Q ss_pred             HHHHHHHcCCCCHHHHhcCCHHHHHHhhccCCChHHHHHHHHHHHHHHH
Q 026681           46 ALQRLLQNGLHTAEAIDKADEATIKDLIYPVAFYTRKACNMKKIAKICL   94 (235)
Q Consensus        46 ~~~~l~~~~~pt~~~la~a~~e~l~~~l~~~G~~~~Ka~~l~~~a~~i~   94 (235)
                      ..++|.+.+|.|.++|+.++.++|.++   -||...+|..|++.|+.++
T Consensus        22 ~i~kL~~aG~~Tv~~i~~at~~~L~~i---~G~~e~~A~KIi~~a~k~~   67 (70)
T d1b22a_          22 DVKKLEEAGFHTVEAVAYAPKKELINI---KGISEAKADKILAEAAKLV   67 (70)
T ss_dssp             HHHHHHTTCCSSGGGBTSSBHHHHHTT---TTCSTTHHHHHHHHHHHHS
T ss_pred             HHHHHHHcCcchHHHHHhCCHHHHHHc---CCCCHHHHHHHHHHHHHHc
Confidence            356777789999999999999998776   4999999999999998865

>d2bgwa1 a.60.2.5 (A:160-229) DNA repair endonuclease XPF {Aeropyrum pernix [TaxId: 56636]}

class: All alpha proteins
fold: SAM domain-like
superfamily: RuvA domain 2-like
family: Hef domain-like
domain: DNA repair endonuclease XPF
species: Aeropyrum pernix [TaxId: 56636]

Probab=92.32  E-value=0.068  Score=34.17  Aligned_cols=23  Identities=30%  Similarity=0.439  Sum_probs=20.2

Q ss_pred             hhHHHHHcCCCCcHHHHHHHHHH
Q 026681          103 SSLDELLALPGIGPKMANMVMTL  125 (235)
Q Consensus       103 ~~~~~L~~l~GIG~~tA~~il~~  125 (235)
                      .+.++|.+++|||+++|..|..|
T Consensus        42 As~eeL~~v~GIG~~~A~~I~~~   64 (70)
T d2bgwa1          42 ASKAEISKVEGIGEKRAEEIKKI   64 (70)
T ss_dssp             CCHHHHHHSTTCCHHHHHHHHHH
T ss_pred             cCHHHHHcCCCCCHHHHHHHHHH
Confidence            35799999999999999998766

>d2a1ja1 a.60.2.5 (A:837-898) DNA repair endonuclease XPF {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: SAM domain-like
superfamily: RuvA domain 2-like
family: Hef domain-like
domain: DNA repair endonuclease XPF
species: Human (Homo sapiens) [TaxId: 9606]

Probab=92.13  E-value=0.2  Score=31.01  Aligned_cols=39  Identities=5%  Similarity=0.188  Sum_probs=30.4

Q ss_pred             HHHHHHcCCCCHHHHhcCCHHHHHHhhccCCChHHHHHHHHHHH
Q 026681           47 LQRLLQNGLHTAEAIDKADEATIKDLIYPVAFYTRKACNMKKIA   90 (235)
Q Consensus        47 ~~~l~~~~~pt~~~la~a~~e~l~~~l~~~G~~~~Ka~~l~~~a   90 (235)
                      .+.|.. .|.|.++|.+|+.++|.++.   | ....|+.|.+..
T Consensus        16 ~~~Ll~-~f~Si~~l~~As~~eL~~v~---G-~~~~A~~i~~f~   54 (62)
T d2a1ja1          16 CRSLMH-HVKNIAELAALSQDELTSIL---G-NAANAKQLYDFI   54 (62)
T ss_dssp             HHHHHH-HCSSHHHHHTCCHHHHHHHH---S-CHHHHHHHHHHH
T ss_pred             HHHHHH-HhccHHHHHhCCHHHHHHCc---C-cHHHHHHHHHHH
Confidence            456666 49999999999999999995   5 555677777654

>d1jmsa1 a.60.6.1 (A:148-242) Terminal deoxynucleotidyl transferase {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: SAM domain-like
superfamily: DNA polymerase beta, N-terminal domain-like
family: DNA polymerase beta, N-terminal domain-like
domain: Terminal deoxynucleotidyl transferase
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=92.03  E-value=0.13  Score=34.97  Aligned_cols=43  Identities=12%  Similarity=0.238  Sum_probs=32.1

Q ss_pred             HHHHHHHHHHHHHHHhcCCCChhhHHHHHcCCCCcHHHHHHHHHH
Q 026681           81 RKACNMKKIAKICLTKYDGDIPSSLDELLALPGIGPKMANMVMTL  125 (235)
Q Consensus        81 ~Ka~~l~~~a~~i~~~~~g~~~~~~~~L~~l~GIG~~tA~~il~~  125 (235)
                      -|+..-..++..|. .+..++. +.++|.++||||+.+++-|.-|
T Consensus        39 fr~~AY~rAa~~i~-~l~~~i~-~~~~l~~i~GIGk~i~~kI~Ei   81 (95)
T d1jmsa1          39 GSCLAFMRASSVLK-SLPFPIT-SMKDTEGIPCLGDKVKSIIEGI   81 (95)
T ss_dssp             HHHHHHHHHHHHHH-TCSSCCC-SGGGGTTCSSCCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHH-hCCcccC-CHHHHHhccchhHHHHHHHHHH
Confidence            36777777787764 4566665 3467999999999999988654

>d1bvsa2 a.60.2.1 (A:64-134) DNA helicase RuvA subunit, middle domain {Mycobacterium leprae [TaxId: 1769]}

class: All alpha proteins
fold: SAM domain-like
superfamily: RuvA domain 2-like
family: DNA helicase RuvA subunit, middle domain
domain: DNA helicase RuvA subunit, middle domain
species: Mycobacterium leprae [TaxId: 1769]

Probab=91.89  E-value=0.059  Score=34.84  Aligned_cols=46  Identities=15%  Similarity=0.234  Sum_probs=28.5

Q ss_pred             hhHHHHHcCCCCcHHHHHHHHHH-hcCCcceeecchHHHHHHHHhcCc
Q 026681          103 SSLDELLALPGIGPKMANMVMTL-GWFNVQGICVDTHVHRICNRLGWV  149 (235)
Q Consensus       103 ~~~~~L~~l~GIG~~tA~~il~~-~~~~~~~~pvDt~v~Rv~~Rlg~~  149 (235)
                      +.++.|.+++||||++|-.+|+. ..... .-.+..+=...+.++-++
T Consensus         6 ~~F~~Li~V~GIGpK~Al~iLs~~~~~~l-~~aI~~~D~~~L~~vpGI   52 (71)
T d1bvsa2           6 DLFLALLSVSGVGPRLAMATLAVHDAAAL-RQALADSDVASLTRVPGI   52 (71)
T ss_dssp             HHHHHHHTSSSCCHHHHHHHHHHSCHHHH-HHHTTTTCHHHHHTSTTC
T ss_pred             HHHHHHhccCCcCHHHHHHHHHhCCHHHH-HHHHHcCCHHHhhcCCCC
Confidence            35688999999999999999854 43321 112333333455566444

>d1vdda_ e.49.1.1 (A:) Recombination protein RecR {Deinococcus radiodurans [TaxId: 1299]}

class: Multi-domain proteins (alpha and beta)
fold: Recombination protein RecR
superfamily: Recombination protein RecR
family: Recombination protein RecR
domain: Recombination protein RecR
species: Deinococcus radiodurans [TaxId: 1299]

Probab=91.71  E-value=0.035  Score=43.15  Aligned_cols=29  Identities=38%  Similarity=0.473  Sum_probs=24.0

Q ss_pred             ChhhHHHHHcCCCCcHHHHHHHHHHhcCC
Q 026681          101 IPSSLDELLALPGIGPKMANMVMTLGWFN  129 (235)
Q Consensus       101 ~~~~~~~L~~l~GIG~~tA~~il~~~~~~  129 (235)
                      +.+..+.|.+|||||+++|.=+..+-+..
T Consensus         7 i~~LI~~l~kLPGIG~KsA~Rla~~LL~~   35 (199)
T d1vdda_           7 LVSLIRELSRLPGIGPKSAQRLAFHLFEQ   35 (199)
T ss_dssp             HHHHHHHHHTSTTCCHHHHHHHHHHHSSS
T ss_pred             HHHHHHHHHHCCCCCHHHHHHHHHHHHcC
Confidence            34567889999999999999888887765

>d1ixra1 a.60.2.1 (A:63-135) DNA helicase RuvA subunit, middle domain {Thermus thermophilus [TaxId: 274]}

class: All alpha proteins
fold: SAM domain-like
superfamily: RuvA domain 2-like
family: DNA helicase RuvA subunit, middle domain
domain: DNA helicase RuvA subunit, middle domain
species: Thermus thermophilus [TaxId: 274]

Probab=91.04  E-value=0.083  Score=34.28  Aligned_cols=23  Identities=30%  Similarity=0.645  Sum_probs=19.7

Q ss_pred             hhHHHHHcCCCCcHHHHHHHHHH
Q 026681          103 SSLDELLALPGIGPKMANMVMTL  125 (235)
Q Consensus       103 ~~~~~L~~l~GIG~~tA~~il~~  125 (235)
                      +.++.|.++.||||++|-.+|+.
T Consensus         7 ~lF~~Li~V~GIGpk~Al~iLs~   29 (73)
T d1ixra1           7 ALFELLLSVSGVGPKVALALLSA   29 (73)
T ss_dssp             HHHHHHHSSSCCCHHHHHHHHHH
T ss_pred             HHHHHHhccCCcCHHHHHHHHHH
Confidence            35678999999999999999853

>d2a1ja1 a.60.2.5 (A:837-898) DNA repair endonuclease XPF {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: SAM domain-like
superfamily: RuvA domain 2-like
family: Hef domain-like
domain: DNA repair endonuclease XPF
species: Human (Homo sapiens) [TaxId: 9606]

Probab=90.92  E-value=0.075  Score=33.16  Aligned_cols=23  Identities=35%  Similarity=0.456  Sum_probs=18.7

Q ss_pred             HHHHcCCCCcHHHHHHHHHHhcCC
Q 026681          106 DELLALPGIGPKMANMVMTLGWFN  129 (235)
Q Consensus       106 ~~L~~l~GIG~~tA~~il~~~~~~  129 (235)
                      +.|.+|||||++++..++.. |+-
T Consensus         3 d~L~~iPGIg~~~~~~Ll~~-f~S   25 (62)
T d2a1ja1           3 DFLLKMPGVNAKNCRSLMHH-VKN   25 (62)
T ss_dssp             HHHHTSTTCCHHHHHHHHHH-CSS
T ss_pred             hHHhcCCCCCHHHHHHHHHH-hcc
Confidence            56899999999999988753 443

>d1cuka2 a.60.2.1 (A:65-142) DNA helicase RuvA subunit, middle domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: SAM domain-like
superfamily: RuvA domain 2-like
family: DNA helicase RuvA subunit, middle domain
domain: DNA helicase RuvA subunit, middle domain
species: Escherichia coli [TaxId: 562]

Probab=90.90  E-value=0.075  Score=34.95  Aligned_cols=23  Identities=30%  Similarity=0.599  Sum_probs=19.8

Q ss_pred             hhHHHHHcCCCCcHHHHHHHHHH
Q 026681          103 SSLDELLALPGIGPKMANMVMTL  125 (235)
Q Consensus       103 ~~~~~L~~l~GIG~~tA~~il~~  125 (235)
                      +.++.|.+++||||++|-.+|..
T Consensus         6 ~~F~~Li~V~GIGpK~Al~iLs~   28 (78)
T d1cuka2           6 TLFKELIKTNGVGPKLALAILSG   28 (78)
T ss_dssp             HHHHHHHHSSSCCHHHHHHHHHH
T ss_pred             HHHHHHHccCCccHHHHHHHHHh
Confidence            35688999999999999999853

>d2a1jb1 a.60.2.5 (B:219-296) DNA excision repair protein ERCC-1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: SAM domain-like
superfamily: RuvA domain 2-like
family: Hef domain-like
domain: DNA excision repair protein ERCC-1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=90.80  E-value=0.11  Score=33.82  Aligned_cols=23  Identities=30%  Similarity=0.560  Sum_probs=20.4

Q ss_pred             hHHHHHcCCCCcHHHHHHHHHHh
Q 026681          104 SLDELLALPGIGPKMANMVMTLG  126 (235)
Q Consensus       104 ~~~~L~~l~GIG~~tA~~il~~~  126 (235)
                      ..++|.+++|||++.|..+..|-
T Consensus        49 ~~eeL~~i~GiG~~~A~~i~~~f   71 (78)
T d2a1jb1          49 SREDLALCPGLGPQKARRLFDVL   71 (78)
T ss_dssp             CHHHHHTSSSCCSHHHHHHHHHH
T ss_pred             hHHHHHHhhhhhHHHHHHHHHHH
Confidence            57899999999999999998773

>d2duya1 a.60.2.7 (A:11-75) Uncharacterized protein TTHA1967 {Thermus thermophilus [TaxId: 274]}

class: All alpha proteins
fold: SAM domain-like
superfamily: RuvA domain 2-like
family: ComEA-like
domain: Uncharacterized protein TTHA1967
species: Thermus thermophilus [TaxId: 274]

Probab=89.89  E-value=0.088  Score=33.24  Aligned_cols=22  Identities=55%  Similarity=0.915  Sum_probs=20.0

Q ss_pred             hHHHHHcCCCCcHHHHHHHHHH
Q 026681          104 SLDELLALPGIGPKMANMVMTL  125 (235)
Q Consensus       104 ~~~~L~~l~GIG~~tA~~il~~  125 (235)
                      +.++|.++||||+++|..|..+
T Consensus        15 ~~~eL~~lpgig~~~A~~Iv~~   36 (65)
T d2duya1          15 SLEELMALPGIGPVLARRIVEG   36 (65)
T ss_dssp             CHHHHTTSTTCCHHHHHHHHHT
T ss_pred             CHHHHHHCCCCCHHHHHHHHHc
Confidence            5789999999999999999876

>d1pzna1 a.60.4.1 (A:35-95) DNA repair protein Rad51, N-terminal domain {Archaeon Pyrococcus furiosus [TaxId: 2261]}

class: All alpha proteins
fold: SAM domain-like
superfamily: Rad51 N-terminal domain-like
family: DNA repair protein Rad51, N-terminal domain
domain: DNA repair protein Rad51, N-terminal domain
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=89.10  E-value=0.13  Score=31.89  Aligned_cols=23  Identities=26%  Similarity=0.225  Sum_probs=18.9

Q ss_pred             hHHHHHcCCCCcHHHHHHHHHHh
Q 026681          104 SLDELLALPGIGPKMANMVMTLG  126 (235)
Q Consensus       104 ~~~~L~~l~GIG~~tA~~il~~~  126 (235)
                      +.++|.+++|||.++|+-|...+
T Consensus        32 ~~~eL~~i~Gi~~~~A~~i~~~a   54 (61)
T d1pzna1          32 SPIELKEVAGISEGTALKIIQAA   54 (61)
T ss_dssp             CHHHHHHHHCCCHHHHHHHHHHH
T ss_pred             CHHHHHHCCCCCHHHHHHHHHHH
Confidence            56889999999999999887654

>d3bzka1 a.60.2.6 (A:474-563) Transcriptional accessory factor Tex {Pseudomonas aeruginosa [TaxId: 287]}

class: All alpha proteins
fold: SAM domain-like
superfamily: RuvA domain 2-like
family: Tex HhH-containing domain-like
domain: Transcriptional accessory factor Tex
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=89.01  E-value=0.26  Score=33.02  Aligned_cols=22  Identities=18%  Similarity=0.315  Sum_probs=15.7

Q ss_pred             hHHHHHcCCCCcHHHHHHHHHH
Q 026681          104 SLDELLALPGIGPKMANMVMTL  125 (235)
Q Consensus       104 ~~~~L~~l~GIG~~tA~~il~~  125 (235)
                      +.++|.++||||+.+|..|..+
T Consensus        33 s~~~L~~lpGig~~~A~~Iv~~   54 (90)
T d3bzka1          33 SAALLARISGLNSTLAQNIVAH   54 (90)
T ss_dssp             CHHHHTTSTTCCHHHHHHHHHH
T ss_pred             CHHHHhHCCCCCHHHHHHHHHH
Confidence            4667777777777777777654

>d1jmsa3 a.60.12.1 (A:243-302) Terminal deoxynucleotidyl transferase {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: SAM domain-like
superfamily: PsbU/PolX domain-like
family: DNA polymerase beta-like, second domain
domain: Terminal deoxynucleotidyl transferase
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=88.96  E-value=0.15  Score=31.64  Aligned_cols=25  Identities=24%  Similarity=0.429  Sum_probs=20.5

Q ss_pred             hhHHHHHcCCCCcHHHHHHHHHHhc
Q 026681          103 SSLDELLALPGIGPKMANMVMTLGW  127 (235)
Q Consensus       103 ~~~~~L~~l~GIG~~tA~~il~~~~  127 (235)
                      ..++.|+++.||||++|.-+..-++
T Consensus         5 ~~l~~f~~I~GvGp~~A~~l~~~Gi   29 (60)
T d1jmsa3           5 KSFKLFTSVFGVGLKTAEKWFRMGF   29 (60)
T ss_dssp             HHHHHHHTSTTCCHHHHHHHHHTTC
T ss_pred             HHHHHHhccccccHHHHHHHHHhCC
Confidence            3578899999999999988866554

>d2fmpa2 a.60.12.1 (A:92-148) DNA polymerase beta {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: SAM domain-like
superfamily: PsbU/PolX domain-like
family: DNA polymerase beta-like, second domain
domain: DNA polymerase beta
species: Human (Homo sapiens) [TaxId: 9606]

Probab=88.30  E-value=0.17  Score=31.14  Aligned_cols=25  Identities=36%  Similarity=0.521  Sum_probs=20.7

Q ss_pred             hhHHHHHcCCCCcHHHHHHHHHHhc
Q 026681          103 SSLDELLALPGIGPKMANMVMTLGW  127 (235)
Q Consensus       103 ~~~~~L~~l~GIG~~tA~~il~~~~  127 (235)
                      .+.+.|+++.||||.+|.-+..-++
T Consensus         4 ~~l~~l~~I~GvGp~~A~~l~~~Gi   28 (57)
T d2fmpa2           4 SSINFLTRVSGIGPSAARKFVDEGI   28 (57)
T ss_dssp             HHHHHHTTSTTCCHHHHHHHHHTTC
T ss_pred             hHHHHHhccccccHHHHHHHHHhCC
Confidence            4578899999999999998865544

>d2bgwa1 a.60.2.5 (A:160-229) DNA repair endonuclease XPF {Aeropyrum pernix [TaxId: 56636]}

class: All alpha proteins
fold: SAM domain-like
superfamily: RuvA domain 2-like
family: Hef domain-like
domain: DNA repair endonuclease XPF
species: Aeropyrum pernix [TaxId: 56636]

Probab=87.35  E-value=0.55  Score=29.59  Aligned_cols=41  Identities=24%  Similarity=0.327  Sum_probs=31.3

Q ss_pred             HHHHHHHcCCCCHHHHhcCCHHHHHHhhccCCChHHHHHHHHHHH
Q 026681           46 ALQRLLQNGLHTAEAIDKADEATIKDLIYPVAFYTRKACNMKKIA   90 (235)
Q Consensus        46 ~~~~l~~~~~pt~~~la~a~~e~l~~~l~~~G~~~~Ka~~l~~~a   90 (235)
                      ..++|..+ |.|.+.|..++.++|.++ .  |+...+|+.|++..
T Consensus        25 ~a~~L~~~-F~s~~~l~~As~eeL~~v-~--GIG~~~A~~I~~~~   65 (70)
T d2bgwa1          25 TAERILER-FGSLERFFTASKAEISKV-E--GIGEKRAEEIKKIL   65 (70)
T ss_dssp             HHHHHHHH-HSSHHHHTTCCHHHHHHS-T--TCCHHHHHHHHHHH
T ss_pred             HHHHHHHH-hCCHHHHHHcCHHHHHcC-C--CCCHHHHHHHHHHH
Confidence            34566664 899999999999999886 3  55567788887654

>d2i1qa1 a.60.4.1 (A:5-64) DNA repair protein Rad51, N-terminal domain {Archaeon Methanococcus voltae [TaxId: 2188]}

class: All alpha proteins
fold: SAM domain-like
superfamily: Rad51 N-terminal domain-like
family: DNA repair protein Rad51, N-terminal domain
domain: DNA repair protein Rad51, N-terminal domain
species: Archaeon Methanococcus voltae [TaxId: 2188]

Probab=86.74  E-value=0.59  Score=28.61  Aligned_cols=23  Identities=26%  Similarity=0.372  Sum_probs=19.4

Q ss_pred             hhHHHHHcCCCCcHHHHHHHHHH
Q 026681          103 SSLDELLALPGIGPKMANMVMTL  125 (235)
Q Consensus       103 ~~~~~L~~l~GIG~~tA~~il~~  125 (235)
                      .+.++|.+++|||+++|.-|...
T Consensus        29 a~~eeL~~i~Gi~~~~A~~i~~~   51 (60)
T d2i1qa1          29 ATVGELTDIEGISEKAAAKMIMG   51 (60)
T ss_dssp             CCHHHHHTSTTCCHHHHHHHHHH
T ss_pred             CCHHHHHHCCCCCHHHHHHHHHH
Confidence            35788999999999999988654

>d2edua1 a.60.2.7 (A:8-98) KIF22, C-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: SAM domain-like
superfamily: RuvA domain 2-like
family: ComEA-like
domain: KIF22, C-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=86.71  E-value=0.2  Score=33.70  Aligned_cols=23  Identities=35%  Similarity=0.556  Sum_probs=20.0

Q ss_pred             hhHHHHHcCCCCcHHHHHHHHHH
Q 026681          103 SSLDELLALPGIGPKMANMVMTL  125 (235)
Q Consensus       103 ~~~~~L~~l~GIG~~tA~~il~~  125 (235)
                      .+.++|.++||||+++|..|..+
T Consensus        30 As~~eL~~lpgig~~~A~~II~y   52 (91)
T d2edua1          30 GSARDLRSLQRIGPKKAQLIVGW   52 (91)
T ss_dssp             SCHHHHHHSTTCCHHHHHHHHHH
T ss_pred             CCHHHHhhCCCCCHHHHHHHHHH
Confidence            35788999999999999999865

>d2bcqa2 a.60.12.1 (A:329-385) DNA polymerase lambda {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: SAM domain-like
superfamily: PsbU/PolX domain-like
family: DNA polymerase beta-like, second domain
domain: DNA polymerase lambda
species: Human (Homo sapiens) [TaxId: 9606]

Probab=85.53  E-value=0.32  Score=29.75  Aligned_cols=25  Identities=28%  Similarity=0.388  Sum_probs=20.2

Q ss_pred             hhHHHHHcCCCCcHHHHHHHHHHhc
Q 026681          103 SSLDELLALPGIGPKMANMVMTLGW  127 (235)
Q Consensus       103 ~~~~~L~~l~GIG~~tA~~il~~~~  127 (235)
                      ...+.++++.||||++|.-+..-++
T Consensus         5 ~~l~~ft~I~GvGp~~A~~l~~~Gi   29 (57)
T d2bcqa2           5 PVLELFSNIWGAGTKTAQMWYQQGF   29 (57)
T ss_dssp             HHHHHHHTSTTCCHHHHHHHHHTTC
T ss_pred             HHHHHHhccccccHHHHHHHHHhCC
Confidence            4577899999999999997765544

>d1kfta_ a.60.2.3 (A:) Excinuclease UvrC C-terminal domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: SAM domain-like
superfamily: RuvA domain 2-like
family: Excinuclease UvrC C-terminal domain
domain: Excinuclease UvrC C-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=85.31  E-value=0.32  Score=29.49  Aligned_cols=39  Identities=15%  Similarity=0.052  Sum_probs=29.9

Q ss_pred             HHHHHHcCCCCHHHHhcCCHHHHHHhhccCCChHHHHHHHHHH
Q 026681           47 LQRLLQNGLHTAEAIDKADEATIKDLIYPVAFYTRKACNMKKI   89 (235)
Q Consensus        47 ~~~l~~~~~pt~~~la~a~~e~l~~~l~~~G~~~~Ka~~l~~~   89 (235)
                      .+.|.++ |.|.+.|.+|+.++|.++ .  |....+|+.|.+.
T Consensus        15 a~~L~~~-F~s~~~i~~As~eeL~~v-~--GIg~~~A~~I~~~   53 (56)
T d1kfta_          15 RQMLLKY-MGGLQGLRNASVEEIAKV-P--GISQGLAEKIFWS   53 (56)
T ss_dssp             HHHHHHH-HSCHHHHHHCCHHHHTTS-S--STTSHHHHHHHHH
T ss_pred             HHHHHHH-hCCHHHHHHhhHHHHHhc-C--CCCHHHHHHHHHH
Confidence            4667774 999999999999999776 4  4445677777654

>d2edua1 a.60.2.7 (A:8-98) KIF22, C-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: SAM domain-like
superfamily: RuvA domain 2-like
family: ComEA-like
domain: KIF22, C-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=84.77  E-value=1  Score=30.02  Aligned_cols=55  Identities=16%  Similarity=0.281  Sum_probs=37.4

Q ss_pred             HhcCCHHHHHHhhccCCChHHHHHHHHHHHHHHHHhcCCCChhhHHHHHcCCCCcHHHHHHHHH
Q 026681           61 IDKADEATIKDLIYPVAFYTRKACNMKKIAKICLTKYDGDIPSSLDELLALPGIGPKMANMVMT  124 (235)
Q Consensus        61 la~a~~e~l~~~l~~~G~~~~Ka~~l~~~a~~i~~~~~g~~~~~~~~L~~l~GIG~~tA~~il~  124 (235)
                      |-.++.++|..+ .++|.  .+|+.|.+.=..    + |.+ ...++|..++|||+++.+-+.-
T Consensus        27 iNtAs~~eL~~l-pgig~--~~A~~II~yR~~----~-G~f-~sledL~~V~Gi~~k~~eki~k   81 (91)
T d2edua1          27 LNEGSARDLRSL-QRIGP--KKAQLIVGWREL----H-GPF-SQVEDLERVEGITGKQMESFLK   81 (91)
T ss_dssp             HHHSCHHHHHHS-TTCCH--HHHHHHHHHHHH----H-CCC-SSGGGGGGSTTCCHHHHHHHHH
T ss_pred             cccCCHHHHhhC-CCCCH--HHHHHHHHHHHH----c-CCC-CCHHHHhcCCCCCHHHHHHHHH
Confidence            455788888664 54554  567777664333    2 444 3467799999999999987763

>d1wuda1 a.60.8.1 (A:530-606) HRDC domain from RecQ helicase {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: SAM domain-like
superfamily: HRDC-like
family: HRDC domain from helicases
domain: HRDC domain from RecQ helicase
species: Escherichia coli [TaxId: 562]

Probab=83.71  E-value=0.59  Score=30.05  Aligned_cols=30  Identities=20%  Similarity=0.461  Sum_probs=23.5

Q ss_pred             HHHHHHHHHHHhcCCCChhhHHHHHcCCCCcHHHHHHH
Q 026681           85 NMKKIAKICLTKYDGDIPSSLDELLALPGIGPKMANMV  122 (235)
Q Consensus        85 ~l~~~a~~i~~~~~g~~~~~~~~L~~l~GIG~~tA~~i  122 (235)
                      .|.++|+.        .|.+.++|.+++|||++.++-+
T Consensus        33 ~L~~ia~~--------~P~s~~~L~~I~G~g~~k~~~y   62 (77)
T d1wuda1          33 TLIEMAEQ--------MPITASEMLSVNGVGMRKLERF   62 (77)
T ss_dssp             HHHHHHHH--------CCCSHHHHHTSTTCCHHHHHHH
T ss_pred             HHHHHHHH--------CCCCHHHHhCCCCCCHHHHHHH
Confidence            45555554        5899999999999999987654

>d2axtu1 a.60.12.2 (U:37-134) Photosystem II 12 kDa extrinsic protein PsbU {Thermosynechococcus elongatus [TaxId: 146786]}

class: All alpha proteins
fold: SAM domain-like
superfamily: PsbU/PolX domain-like
family: PsbU-like
domain: Photosystem II 12 kDa extrinsic protein PsbU
species: Thermosynechococcus elongatus [TaxId: 146786]

Probab=83.39  E-value=0.15  Score=34.92  Aligned_cols=22  Identities=14%  Similarity=0.535  Sum_probs=19.5

Q ss_pred             hhHHHHHcCCCCcHHHHHHHHH
Q 026681          103 SSLDELLALPGIGPKMANMVMT  124 (235)
Q Consensus       103 ~~~~~L~~l~GIG~~tA~~il~  124 (235)
                      .+.++|.+|||||+.+|..|..
T Consensus        24 As~~eL~~lpGIg~~~A~~Iv~   45 (98)
T d2axtu1          24 TNIAAFIQYRGLYPTLAKLIVK   45 (98)
T ss_dssp             SCGGGGTTSTTCTHHHHHHHHH
T ss_pred             ccHHHHHHhhhhcHHHHHHHHH
Confidence            3578899999999999999985

>d3bzka1 a.60.2.6 (A:474-563) Transcriptional accessory factor Tex {Pseudomonas aeruginosa [TaxId: 287]}

class: All alpha proteins
fold: SAM domain-like
superfamily: RuvA domain 2-like
family: Tex HhH-containing domain-like
domain: Transcriptional accessory factor Tex
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=82.80  E-value=0.45  Score=31.77  Aligned_cols=55  Identities=18%  Similarity=0.226  Sum_probs=37.1

Q ss_pred             hcCCHHHHHHhhccCCChHHHHHHHHHHHHHHHHhcCCCChhhHHHHHcCCCCcHHHHHHHHHH
Q 026681           62 DKADEATIKDLIYPVAFYTRKACNMKKIAKICLTKYDGDIPSSLDELLALPGIGPKMANMVMTL  125 (235)
Q Consensus        62 a~a~~e~l~~~l~~~G~~~~Ka~~l~~~a~~i~~~~~g~~~~~~~~L~~l~GIG~~tA~~il~~  125 (235)
                      -.|+.++|..+   -|+..++|+.|.+.=+.    . |.+ ..++.|..++|||+++-+-+.-|
T Consensus        30 N~As~~~L~~l---pGig~~~A~~Iv~~R~~----~-G~f-~s~edL~~v~gi~~k~~e~i~~~   84 (90)
T d3bzka1          30 NTASAALLARI---SGLNSTLAQNIVAHRDA----N-GAF-RTRDELKKVSRLGEKTFEQAAGF   84 (90)
T ss_dssp             TTCCHHHHTTS---TTCCHHHHHHHHHHHHH----H-CSC-SSSGGGGGSTTCCHHHHHHHHTT
T ss_pred             hhCCHHHHhHC---CCCCHHHHHHHHHHHHH----c-CCC-CCHHHHhhCCCCCHHHHHHhcCC
Confidence            34666666443   26667788887764332    2 555 45788999999999998766433

>d2a1jb1 a.60.2.5 (B:219-296) DNA excision repair protein ERCC-1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: SAM domain-like
superfamily: RuvA domain 2-like
family: Hef domain-like
domain: DNA excision repair protein ERCC-1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=81.35  E-value=0.95  Score=29.06  Aligned_cols=39  Identities=18%  Similarity=0.163  Sum_probs=29.4

Q ss_pred             HHHHHcCCCCHHHHhcCCHHHHHHhhccCCChHHHHHHHHHHH
Q 026681           48 QRLLQNGLHTAEAIDKADEATIKDLIYPVAFYTRKACNMKKIA   90 (235)
Q Consensus        48 ~~l~~~~~pt~~~la~a~~e~l~~~l~~~G~~~~Ka~~l~~~a   90 (235)
                      ..|.++ |.|.++|..++.++|.++ .++|  ..+|+.|.+..
T Consensus        33 ~~L~~~-F~s~~~i~~A~~eeL~~i-~GiG--~~~A~~i~~~f   71 (78)
T d2a1jb1          33 QTLLTT-FGSLEQLIAASREDLALC-PGLG--PQKARRLFDVL   71 (78)
T ss_dssp             HHHHHH-HSSHHHHHSCCHHHHHTS-SSCC--SHHHHHHHHHH
T ss_pred             HHHHHH-hCCcHHHHhhhHHHHHHh-hhhh--HHHHHHHHHHH
Confidence            455564 899999999999999765 5455  46788887654