Citrus Sinensis ID: 027752

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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-------22
Protein Sequence
MQLEFECSNVNKWKEALASYEACVESLNKPNLISLDDYYRKELPSLIHQRNPNPHINTTELSKLVRWKLTRGKWRPRLLVFVSSLDDSSVKSASEKAFKSLPDLTKAVSELTVLKGVGPATASAVLAAYAPDLAPFMSDEAMGAALGHSKDYSLKQYLLFADKLQAKAKELVSEENCFTPFDVERALWSSAIGLKLKASKSNQDSEIKTTKNSKRKRKH
Secondary Structure (PSIPRED)
cccccccccHHHHHHHHHHHHHHHHHcccccHHHHHHHHHHHccHHHHHccccccccHHHHHHHHHHHHHcccccccHHHHHHHccHHHHHHHHHHHHHHcccHHHHHHHHHccccccHHHHHHHHHHHcccccccccHHHHHHHHcccccccHHHHHHHHHHHHHHHHHHHcccccccHHHHHHHHHHHHHHcccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
cccccccccHHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHcHHHHHHccccccccHHHHHHHHHHHHHcccccHHHHHHHHHccHHHHHHHHHHHHHHcccHHHHHHHHHHHccccHHHHHHHHHHcccccccccHHHHHHHcccccccccHHHHHHHHHHHHHHHHHHHHccccccHHHHHHHHHHHHHHHHHccccccccccccccccccccccc
Coil and Loop (DISEMBL)
MQLEFECSNVNKWKEALASYEACVEslnkpnlislddyyrkelpslihqrnpnphintteLSKLVRWKLTRGKWRPRLLVFVSSlddssvksASEKAFKSLPDLTKAVSELTVLKGVGPATASAVLAAyapdlapfmsdeamgaalghskdysLKQYLLFADKLQAKAKELVseencftpfDVERALWSSAIGLKlkasksnqdseikttknskrkrkh
Flexible Loop (DISEMBL)
MQLEFECSNVNKWKEALASYEACVESLNKPNLISLDDYYRKELPslihqrnpnphinttelSKLVRWKLTRGKWRPRLLVFvsslddssvksasekafkslpdlTKAVSELTVLKGVGPATASAVLAAYAPDLAPFMSDEAMGAALGHSKDYSLKQYLLFADKLQAKAKELVSEENCFTPFDVERALWSSAIGLklkasksnqdseikttknskrkrkh
Low Complexity Region (SEG)
MQLEFECSNVNKWKEALASYEACVESLNKPNLISLDDYYRKELPSLIHQRNPNPHINTTELSKLVRWKLTRGKWRPRllvfvsslddssvksasEKAFKSLPDLTKAVSELTVLKGVGPATASAVLAAYAPDLAPFMSDEAMGAALGHSKDYSLKQYLLFADKLQAKAKELVSEENCFTPFDVERALWSSAIGLKLKASKSNQDSEIKTTKNSKRKRKH
Disordered region (IsUnstruct)
*****ECSNVNKWKEALASYEACVESLNKPNLISLDDYYRKELPSLIHQRNPNPHINTTELSKLVRWKLTRGKWRPRLLVFVSSL******************LTKAVSELTVLKGVGPATASAVLAAYAPDLAPFMSDEAMGAALGHSKDYSLKQYLLFADKLQAKAKELVSEENCFTPFDVERALWSSAIGLK************************
Disordered Region (DISOPRED)
*******SNVNKWKEALASYEAC********LISLDDYYRKELPSLIHQRNPNPHINTTELSKLVRWKLTRGKWRPRLLVFV*SLD*SSVKSASEKAFKSLPDLTKAVSELTVLKGVGPATASAVLAAYAPDLAPFMSDEAMGAALGHSKDYSLKQYLLFADKLQAKAKELVSEENCFTPFDVERALWSSAI***************************
Disordered Region (DISEMBL)
********NVNKWKEALASYEACVESLNKPNLISLDDYYRKELPSLIHQRNPNPHINTTELSKLVRWKLTRGKWRPRLLVFVSSL************FKSLPDLTKAVSELTVLKGVGPATASAVLAAYAPDLAPFMSDEAMGAALGHSKDYSLKQYLLFADKLQAKAKELVSEENCFTPFDVERALWSSAIGLKLK**********************
Disordered Region (DISPRO)
***EFECSNVNKWKEALASYEACVESLNKPNLISLDDYYRKELPSLIHQRNPNPHINTTELSKLVRWKLTRGKWRPRLLVFVSSLDDSSVKSASEKAFKSLPDLTKAVSELTVLKGVGPATASAVLAAYAPDLAPFMSDEAMGAALGHSKDYSLKQYLLFADKLQAKAKELVSEENCFTPFDVERALWSSAIGLKLK**********************
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
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Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MQLEFECSNVNKWKEALASYEACVESLNKPNLISLDDYYRKELPSLIHQRNPNPHINTTELSKLVRWKLTRGKWRPRLLVFVSSLDDSSVKSASEKAFKSLPDLTKAVSELTVLKGVGPATASAVLAAYAPDLAPFMSDEAMGAALGHSKDYSLKQYLLFADKLQAKAKELVSEENCFTPFDVERALWSSAIGLKLKASKSNQDSEIKTTKNSKRKRKH
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

No hits with e-value below 0.001 by BLAST

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	219
224067158	218	predicted protein [Populus trichocarpa]	0.990	0.995	0.715	1e-84
225458920	213	PREDICTED: uncharacterized protein LOC10	0.972	1.0	0.695	3e-82
449447089	220	PREDICTED: uncharacterized protein LOC10	0.986	0.981	0.699	4e-81
255537954	217	conserved hypothetical protein [Ricinus	0.931	0.940	0.710	2e-77
356552290	220	PREDICTED: uncharacterized protein LOC10	0.986	0.981	0.656	9e-77
297829776	209	hypothetical protein ARALYDRAFT_478581 [	0.954	1.0	0.677	1e-76
15795142	292	unnamed protein product [Arabidopsis tha	0.958	0.719	0.674	7e-71
18399536	209	DNA binding protein [Arabidopsis thalian	0.922	0.966	0.702	1e-70
294463602	225	unknown [Picea sitchensis]	0.986	0.96	0.569	4e-65
326532330	209	predicted protein [Hordeum vulgare subsp	0.936	0.980	0.586	2e-64

>gi|224067158|ref|XP_002302384.1| predicted protein [Populus trichocarpa] gi|222844110|gb|EEE81657.1| predicted protein [Populus trichocarpa]

 Score =  318 bits (814), Expect = 1e-84,   Method: Compositional matrix adjust.
 Identities = 156/218 (71%), Positives = 187/218 (85%), Gaps = 1/218 (0%)

Query: 3   LEFECSNVNKWKEALASYEACVESLNKPNLISLDDYYRKELPSLIHQRNPNPHINTTELS 62
           +EF  S+V+ WK +L++Y A ++SLNKPNL+SLDD+YR ELPSLIHQRNP+PHI T ELS
Sbjct: 1   MEFGSSDVSLWKNSLSAYPARIQSLNKPNLVSLDDFYRIELPSLIHQRNPDPHITTPELS 60

Query: 63  KLVRWKLTRGKWRPRLLVFVSSLDDSSVKSASEKAFKSLPDLTKAVSELTVLKGVGPATA 122
           KL++WKL+RGKWRPRLL FVSSLD+S VKSAS+KAF+SLPD++KAVS LTVLKGVGPATA
Sbjct: 61  KLMQWKLSRGKWRPRLLDFVSSLDESHVKSASQKAFESLPDVSKAVSALTVLKGVGPATA 120

Query: 123 SAVLAAYAPDLAPFMSDEAMGAALGHSKDYSLKQYLLFADKLQAKAKELVSEENCFTPFD 182
           SAVLAAYAPD+APFMSDEAM A LG+SKDY+LKQYLLF DKLQ K+KEL S  + FTP D
Sbjct: 121 SAVLAAYAPDVAPFMSDEAMEAVLGNSKDYTLKQYLLFVDKLQTKSKELSSVRDIFTPSD 180

Query: 183 VERALWSSAIGLKLKASKSNQDS-EIKTTKNSKRKRKH 219
           +ERALWSSA+G KL A +S+ DS +  T ++ KRKRK 
Sbjct: 181 IERALWSSAVGAKLLALQSDPDSKKANTARDIKRKRKR 218

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225458920|ref|XP_002285490.1| PREDICTED: uncharacterized protein LOC100259164 [Vitis vinifera]

 Score =  310 bits (793), Expect = 3e-82,   Method: Compositional matrix adjust.
 Identities = 151/217 (69%), Positives = 185/217 (85%), Gaps = 4/217 (1%)

Query: 3   LEFECSNVNKWKEALASYEACVESLNKPNLISLDDYYRKELPSLIHQRNPNPHINTTELS 62
           ++F+C N + WKEAL+SY A + SLNKP L+SLDD+Y  +LP+LI QRNPNP+I T+ELS
Sbjct: 1   MDFQCLNRSVWKEALSSYSARIVSLNKPQLVSLDDFYCNQLPALIRQRNPNPYITTSELS 60

Query: 63  KLVRWKLTRGKWRPRLLVFVSSLDDSSVKSASEKAFKSLPDLTKAVSELTVLKGVGPATA 122
           KL++WKLTRGKWRPRLL FVSSLD++ VKSAS+KAF+SLPD++KA+SELTVLKGVGPATA
Sbjct: 61  KLMQWKLTRGKWRPRLLDFVSSLDEALVKSASQKAFQSLPDISKAISELTVLKGVGPATA 120

Query: 123 SAVLAAYAPDLAPFMSDEAMGAALGHSKDYSLKQYLLFADKLQAKAKELVSEENCFTPFD 182
           SA+LAAYAPD+APFMSDEAM AALG+SKDY+LKQYL+FADKLQ KA+EL  E + +TP D
Sbjct: 121 SALLAAYAPDVAPFMSDEAMVAALGNSKDYTLKQYLVFADKLQNKARELSVEGDSYTPSD 180

Query: 183 VERALWSSAIGLKLKASKSNQDSEIKTTKNSKRKRKH 219
           VERALWSSA+G KL  S  N + ++    N+KRKRK 
Sbjct: 181 VERALWSSAVGTKLLDSLPNSEPKV----NTKRKRKQ 213

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449447089|ref|XP_004141302.1| PREDICTED: uncharacterized protein LOC101204707 [Cucumis sativus] gi|449509259|ref|XP_004163537.1| PREDICTED: uncharacterized LOC101204707 [Cucumis sativus]

 Score =  306 bits (783), Expect = 4e-81,   Method: Compositional matrix adjust.
 Identities = 151/216 (69%), Positives = 179/216 (82%)

Query: 3   LEFECSNVNKWKEALASYEACVESLNKPNLISLDDYYRKELPSLIHQRNPNPHINTTELS 62
           +EF  S+   W+EAL++Y + +E+L KPNL+SLDD+YR ELP ++H+RNP+P+I T+ELS
Sbjct: 2   MEFSISDPTLWREALSTYSSQIEALGKPNLVSLDDFYRNELPLILHKRNPSPYITTSELS 61

Query: 63  KLVRWKLTRGKWRPRLLVFVSSLDDSSVKSASEKAFKSLPDLTKAVSELTVLKGVGPATA 122
           KL++WKLTRGKWRPRLL FVSSLD+S VK AS+KAF+ LPD++KAVSELT LKGVGPATA
Sbjct: 62  KLMQWKLTRGKWRPRLLDFVSSLDESLVKLASQKAFQCLPDISKAVSELTPLKGVGPATA 121

Query: 123 SAVLAAYAPDLAPFMSDEAMGAALGHSKDYSLKQYLLFADKLQAKAKELVSEENCFTPFD 182
           SAVLAAYAPD+APFMSDEAM AALG+SKDYSLKQYLLFA+KL+ KAKEL  E   FTP D
Sbjct: 122 SAVLAAYAPDVAPFMSDEAMEAALGNSKDYSLKQYLLFANKLEQKAKELSLEGEIFTPSD 181

Query: 183 VERALWSSAIGLKLKASKSNQDSEIKTTKNSKRKRK 218
           VERALWS AIG KLK SKS  D        +KRKRK
Sbjct: 182 VERALWSRAIGEKLKGSKSQLDPNNGGKTGTKRKRK 217

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255537954|ref|XP_002510042.1| conserved hypothetical protein [Ricinus communis] gi|223550743|gb|EEF52229.1| conserved hypothetical protein [Ricinus communis]

 Score =  294 bits (752), Expect = 2e-77,   Method: Compositional matrix adjust.
 Identities = 145/204 (71%), Positives = 172/204 (84%)

Query: 3   LEFECSNVNKWKEALASYEACVESLNKPNLISLDDYYRKELPSLIHQRNPNPHINTTELS 62
           ++F  S+++ WKEALA Y A +ESL K NLISLD++YR +LPSLI +RNPNP+I T ELS
Sbjct: 1   MDFRSSDISLWKEALADYPARIESLKKSNLISLDEFYRIQLPSLIQKRNPNPYITTPELS 60

Query: 63  KLVRWKLTRGKWRPRLLVFVSSLDDSSVKSASEKAFKSLPDLTKAVSELTVLKGVGPATA 122
           KL++WKL+RGKWRPRLL +VSSLD+  VKSAS+KAF+SLPD++KAV+ELTVLKGVGPATA
Sbjct: 61  KLMQWKLSRGKWRPRLLDYVSSLDEEIVKSASQKAFQSLPDVSKAVTELTVLKGVGPATA 120

Query: 123 SAVLAAYAPDLAPFMSDEAMGAALGHSKDYSLKQYLLFADKLQAKAKELVSEENCFTPFD 182
           SAVLAAYAPD+APFMSDEAM AALG SKDY+LKQYL F DKLQ KAKEL S E+ FTP D
Sbjct: 121 SAVLAAYAPDVAPFMSDEAMEAALGSSKDYTLKQYLSFVDKLQTKAKELSSNEDSFTPSD 180

Query: 183 VERALWSSAIGLKLKASKSNQDSE 206
           VE ALWS A+  K  ASK + DS+
Sbjct: 181 VETALWSYAVRAKSLASKEDLDSK 204

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356552290|ref|XP_003544501.1| PREDICTED: uncharacterized protein LOC100803511 isoform 1 [Glycine max]

 Score =  291 bits (746), Expect = 9e-77,   Method: Compositional matrix adjust.
 Identities = 145/221 (65%), Positives = 180/221 (81%), Gaps = 5/221 (2%)

Query: 3   LEFECSNVNKWKEALASYEACVESL----NKPNLISLDDYYRKELPSLIHQRNPNPHINT 58
           ++  CS+ + WKEAL+ Y + +++L    NKP+L+SLDD+Y  +LP L+HQRNPNP I T
Sbjct: 1   MDLGCSDASVWKEALSLYPSRIQTLSVKKNKPDLVSLDDFYCNQLPLLLHQRNPNPFITT 60

Query: 59  TELSKLVRWKLTRGKWRPRLLVFVSSLDDSSVKSASEKAFKSLPDLTKAVSELTVLKGVG 118
            ELS L++WKLTRGKWRPRLL FVSSLDD+ VKSAS+KAF+SLPD++KAVSELTVLKGVG
Sbjct: 61  PELSTLMQWKLTRGKWRPRLLDFVSSLDDAVVKSASQKAFQSLPDVSKAVSELTVLKGVG 120

Query: 119 PATASAVLAAYAPDLAPFMSDEAMGAALGHSKDYSLKQYLLFADKLQAKAKELVSEENCF 178
           PATASAVLA +AP L PFMSDEAM AALG SKDYSLKQY+ F DKLQ KA+EL SE + F
Sbjct: 121 PATASAVLATFAPHLTPFMSDEAMEAALGSSKDYSLKQYIKFVDKLQRKAEELSSEGDSF 180

Query: 179 TPFDVERALWSSAIGLKLKASKSNQDSEIKTTKNSKRKRKH 219
           TP DVERALWS A+G +    +++QD + K +++SKRKRK+
Sbjct: 181 TPSDVERALWSFAVG-QSSGPQADQDPKTKPSRSSKRKRKN 220

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297829776|ref|XP_002882770.1| hypothetical protein ARALYDRAFT_478581 [Arabidopsis lyrata subsp. lyrata] gi|297328610|gb|EFH59029.1| hypothetical protein ARALYDRAFT_478581 [Arabidopsis lyrata subsp. lyrata]

 Score =  291 bits (745), Expect = 1e-76,   Method: Compositional matrix adjust.
 Identities = 147/217 (67%), Positives = 178/217 (82%), Gaps = 8/217 (3%)

Query: 1   MQLEFECSNVNKWKEALASYEACVESLNKPNLISLDDYYRKELPSLIHQRNPNPHINTTE 60
           M+L+F+CS+V  WKEAL+SYE+ +ESLNKP+L+SLD +YR +LPSL+H R+P+P++ T+E
Sbjct: 1   MELDFKCSDVGVWKEALSSYESRIESLNKPDLVSLDQFYRVKLPSLLHDRDPDPYLTTSE 60

Query: 61  LSKLVRWKLTRGKWRPRLLVFVSSLDDSSVKSASEKAFKSLPDLTKAVSELTVLKGVGPA 120
           LS+L++WKL+RGKWRPRLL FVSSL+DS VKSASEKAFKSLPD++KAV ELTVLKGVGPA
Sbjct: 61  LSQLMKWKLSRGKWRPRLLDFVSSLEDSVVKSASEKAFKSLPDISKAVKELTVLKGVGPA 120

Query: 121 TASAVLAAYAPDLAPFMSDEAMGAALGHSKDYSLKQYLLFADKLQAKAKELVSEENCFTP 180
           TASAVLAAYAPD+APFMSDEAM  ALG+SKDYSLKQYLLF  KLQ KAKEL  +     P
Sbjct: 121 TASAVLAAYAPDIAPFMSDEAMEVALGNSKDYSLKQYLLFVTKLQDKAKELKLKGEWDGP 180

Query: 181 FDVERALWSSAIGLKLKASKSNQDSEIKTTKNSKRKR 217
            DVERALWS  +      +KS  D   K++   KRKR
Sbjct: 181 SDVERALWSCTV-----RAKSQPD---KSSSGKKRKR 209

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|15795142|dbj|BAB03130.1| unnamed protein product [Arabidopsis thaliana]

 Score =  272 bits (696), Expect = 7e-71,   Method: Compositional matrix adjust.
 Identities = 147/218 (67%), Positives = 175/218 (80%), Gaps = 8/218 (3%)

Query: 1   MQLEFECSNVNKWKEALASYEACVESLNKPNLISLDDYYRKELPSLIHQRNPNPHINTTE 60
           M+LEF+CS+V  WKEAL+SY++ +ESLNKP L+SLD +YR +LP L+H R+PNP++ T+E
Sbjct: 1   MELEFKCSDVGVWKEALSSYDSRIESLNKPELVSLDQFYRIKLPCLLHDRDPNPYLTTSE 60

Query: 61  LSKLVRWKLTRGKWRPRLLVFVSSLDDSSVKSASEKAFKSLPDLTKAVSELTVLKGVGPA 120
           LS+L++WKL+RGKWRPRLL FVSSLDDS VKSASEKAFKSLPD++KAV ELTVLKGVG A
Sbjct: 61  LSQLMKWKLSRGKWRPRLLDFVSSLDDSVVKSASEKAFKSLPDISKAVKELTVLKGVGAA 120

Query: 121 TASAVLAAYAPDLAPFMSDEAMGAALGHSKDYSLKQYLLFADKLQAKAKELVSEENCFTP 180
           TASAVLAAYAPD+APFMSDEAM  ALG+SKDYSLKQYLLFA KLQ KAKEL  +     P
Sbjct: 121 TASAVLAAYAPDIAPFMSDEAMEVALGNSKDYSLKQYLLFATKLQDKAKELKLKGEWDGP 180

Query: 181 FDVERALWSSAIGLKLKASKSNQDSEIKTTKNSKRKRK 218
            D+ERALWS  +  K +  KS        +   KRKRK
Sbjct: 181 SDIERALWSCTVRAKSQPEKS--------SSGKKRKRK 210

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|18399536|ref|NP_566413.1| DNA binding protein [Arabidopsis thaliana] gi|12322054|gb|AAG51077.1|AC069472_17 unknown protein; 19524-20560 [Arabidopsis thaliana] gi|21592729|gb|AAM64678.1| unknown [Arabidopsis thaliana] gi|332641646|gb|AEE75167.1| DNA binding protein [Arabidopsis thaliana]

 Score =  271 bits (693), Expect = 1e-70,   Method: Compositional matrix adjust.
 Identities = 142/202 (70%), Positives = 170/202 (84%)

Query: 1   MQLEFECSNVNKWKEALASYEACVESLNKPNLISLDDYYRKELPSLIHQRNPNPHINTTE 60
           M+LEF+CS+V  WKEAL+SY++ +ESLNKP L+SLD +YR +LP L+H R+PNP++ T+E
Sbjct: 1   MELEFKCSDVGVWKEALSSYDSRIESLNKPELVSLDQFYRIKLPCLLHDRDPNPYLTTSE 60

Query: 61  LSKLVRWKLTRGKWRPRLLVFVSSLDDSSVKSASEKAFKSLPDLTKAVSELTVLKGVGPA 120
           LS+L++WKL+RGKWRPRLL FVSSLDDS VKSASEKAFKSLPD++KAV ELTVLKGVG A
Sbjct: 61  LSQLMKWKLSRGKWRPRLLDFVSSLDDSVVKSASEKAFKSLPDISKAVKELTVLKGVGAA 120

Query: 121 TASAVLAAYAPDLAPFMSDEAMGAALGHSKDYSLKQYLLFADKLQAKAKELVSEENCFTP 180
           TASAVLAAYAPD+APFMSDEAM  ALG+SKDYSLKQYLLFA KLQ KAKEL  +     P
Sbjct: 121 TASAVLAAYAPDIAPFMSDEAMEVALGNSKDYSLKQYLLFATKLQDKAKELKLKGEWDGP 180

Query: 181 FDVERALWSSAIGLKLKASKSN 202
            D+ERALWS  +  K +  KS+
Sbjct: 181 SDIERALWSCTVRAKSQPEKSS 202

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|294463602|gb|ADE77329.1| unknown [Picea sitchensis]

 Score =  253 bits (646), Expect = 4e-65,   Method: Compositional matrix adjust.
 Identities = 127/223 (56%), Positives = 160/223 (71%), Gaps = 7/223 (3%)

Query: 3   LEFECSNVNKWKEALASYEACVESLNKPNLISLDDYYRKELPSLIHQRNPNPHINTTELS 62
           ++F CS+   W++AL+SY+  +ESLN P L  LD  YR ELP  +H R P  HI   EL+
Sbjct: 1   MDFGCSDPGAWRDALSSYDKHMESLNNPKLAELDKLYRTELPRSLHSRTPTAHITKNELN 60

Query: 63  KLVRWKLTRGKWRPRLLVFVSSLDDSSVKSASEKAFKSLPDLTKAVSELTVLKGVGPATA 122
           K++ WKLTRGKWRPRLL FVSSLD++SVK+AS+KAF +LPDL +AV+ L+ LKGVGPATA
Sbjct: 61  KVMEWKLTRGKWRPRLLSFVSSLDETSVKTASQKAFAALPDLKEAVNALSTLKGVGPATA 120

Query: 123 SAVLAAYAPDLAPFMSDEAMGAALGHSKDYSLKQYLLFADKLQAKAKELVS-------EE 175
           SAVLAA+ P +APFMSDEAM AALG SK+Y+LKQYL+FA+KLQ KAKEL S       + 
Sbjct: 121 SAVLAAFDPHIAPFMSDEAMVAALGSSKEYTLKQYLVFAEKLQNKAKELNSKGQVKEGDN 180

Query: 176 NCFTPFDVERALWSSAIGLKLKASKSNQDSEIKTTKNSKRKRK 218
             FT  D+ERALWS+A G K      +        +N +RKR+
Sbjct: 181 GFFTASDIERALWSAAAGAKNVVDMPDGKGRTNLKENGQRKRR 223

Source: Picea sitchensis

Species: Picea sitchensis

Genus: Picea

Family: Pinaceae

Order: Coniferales

Class: Coniferopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|326532330|dbj|BAK05094.1| predicted protein [Hordeum vulgare subsp. vulgare]

 Score =  250 bits (639), Expect = 2e-64,   Method: Compositional matrix adjust.
 Identities = 126/215 (58%), Positives = 161/215 (74%), Gaps = 10/215 (4%)

Query: 3   LEFECSNVNKWKEALASYEACVESLNKPNLISLDDYYRKELPSLIHQRNPNPHINTTELS 62
           ++F   +   W+ AL +Y+  + +L+KP+L+  D +YR +LP L+H+R+P+P++   EL 
Sbjct: 5   VDFASGDGEAWRAALGAYDRRLAALDKPDLLDADSFYRHDLPLLLHRRDPDPYLAKPELV 64

Query: 63  KLVRWKLTRGKWRPRLLVFVSSLDDSSVKSASEKAFKSLPDLTKAVSELTVLKGVGPATA 122
           +L++WKL+RGKWRPRL+ FV SLDD  V+SAS KAF +LPDL+KA++ELTVLKGVGPATA
Sbjct: 65  QLMQWKLSRGKWRPRLMDFVKSLDDKVVESASRKAFAALPDLSKAITELTVLKGVGPATA 124

Query: 123 SAVLAAYAPDLAPFMSDEAMGAALGHSKDYSLKQYLLFADKLQAKAKELVSEENCFTPFD 182
           SAVLAAYAPD+APFMSDEAM AALG+ K+Y+LKQYL FA+KLQ KA+EL      FTP D
Sbjct: 125 SAVLAAYAPDVAPFMSDEAMVAALGNVKEYTLKQYLAFAEKLQDKAEELSVGGESFTPSD 184

Query: 183 VERALWSSAIGLKLKASKSNQDSEIKTTKNSKRKR 217
           VERALWSSAI     ASK       K     KRKR
Sbjct: 185 VERALWSSAI-----ASKPP-----KAPAGGKRKR 209

Source: Hordeum vulgare subsp. vulgare

Species: Hordeum vulgare

Genus: Hordeum

Family: Poaceae

Order: Poales

Class: Liliopsida

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	219
TAIR|locus:2082224	209	AT3G12210 [Arabidopsis thalian	0.949	0.995	0.615	1.8e-64
UNIPROTKB|F1RG53	232	LOC100524737 "Uncharacterized	0.863	0.814	0.410	2.3e-30
ZFIN|ZDB-GENE-050320-25	238	zgc:112496 "zgc:112496" [Danio	0.968	0.890	0.370	1.3e-27
FB|FBgn0030328	550	Amun "Amun" [Drosophila melano	0.735	0.292	0.413	3.8e-24
ASPGD|ASPL0000059149	312	AN10183 [Emericella nidulans (	0.726	0.509	0.263	6.6e-08

TAIR|locus:2082224 AT3G12210 [Arabidopsis thaliana (taxid:3702)]

 Score = 657 (236.3 bits), Expect = 1.8e-64, P = 1.8e-64
 Identities = 128/208 (61%), Positives = 157/208 (75%)

Query:     1 MQLEFECSNVNKWKEALASYEACVESLNKPNLISLDDYYRKELPSLIHQRNPNPHINTTE 60
             M+LEF+CS+V  WKEAL+SY++ +ESLNKP L+SLD +YR +LP L+H R+PNP++ T+E
Sbjct:     1 MELEFKCSDVGVWKEALSSYDSRIESLNKPELVSLDQFYRIKLPCLLHDRDPNPYLTTSE 60

Query:    61 LSKLVRWKLTRGKWRPRXXXXXXXXXXXXXXXXXEKAFKSLPDLTKAVSELTVLKGVGPA 120
             LS+L++WKL+RGKWRPR                 EKAFKSLPD++KAV ELTVLKGVG A
Sbjct:    61 LSQLMKWKLSRGKWRPRLLDFVSSLDDSVVKSASEKAFKSLPDISKAVKELTVLKGVGAA 120

Query:   121 TASAVLAAYAPDLAPFMSDEAMGAALGHSKDYSLKQYLLFADKLQAKAKELVSEENCFTP 180
             TASAVLAAYAPD+APFMSDEAM  ALG+SKDYSLKQYLLFA KLQ KAKEL  +     P
Sbjct:   121 TASAVLAAYAPDIAPFMSDEAMEVALGNSKDYSLKQYLLFATKLQDKAKELKLKGEWDGP 180

Query:   181 FDVERALWSSAIGLKLKASKSNQDSEIK 208
              D+ERALWS  +  K +  KS+   + K
Sbjct:   181 SDIERALWSCTVRAKSQPEKSSSGKKRK 208

GO:0003677 "DNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISM

GO:0006281 "DNA repair" evidence=IEA

UNIPROTKB|F1RG53 LOC100524737 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 335 (123.0 bits), Expect = 2.3e-30, P = 2.3e-30
 Identities = 80/195 (41%), Positives = 109/195 (55%)

Query:     7 CSNVNKWKEALASYEACVESLNKPN--LISLDDYYRKELPSLIHQRNPNPHINTTELSKL 64
             C + + W   L  +   + +   P   L +LD +YR+ LP+ I  R    H+   EL +L
Sbjct:    10 CEDPSLWAAVLGRHGEVLRARAGPQGRLEALDRWYREALPAAIEGREEK-HVTREELGQL 68

Query:    65 VRWKLTRGKWRPRXXXXXXXXXXXXXXXXXEKAFKSLPDLTKAVSELTVLKGVGPATASA 124
             + WKL RG++RPR                   AF  LPD+  AV+EL  L+GVGPATASA
Sbjct:    69 LAWKLARGRFRPRLHQLVSANAPELVVQHSAAAFPLLPDMHAAVTELRALRGVGPATASA 128

Query:   125 VLAAYAPDLAPFMSDEAMGAALG-HSKDYSLKQYLLFADKLQAKAKELV--SEENCFTPF 181
             VLAA AP++A FMS+EA+ A  G  +  Y+LK YLL+  ++Q +A  L   S    +TP 
Sbjct:   129 VLAAGAPEVAAFMSEEAVAAVPGLPALQYTLKHYLLYLSRVQERATALSHGSASGLWTPH 188

Query:   182 DVERALWSSAIGLKL 196
              VE ALW+ AIG KL
Sbjct:   189 RVETALWTWAIGQKL 203

GO:0006281 "DNA repair" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

ZFIN|ZDB-GENE-050320-25 zgc:112496 "zgc:112496" [Danio rerio (taxid:7955)]

 Score = 309 (113.8 bits), Expect = 1.3e-27, P = 1.3e-27
 Identities = 83/224 (37%), Positives = 114/224 (50%)

Query:     5 FECSNVNKWKEALASYEACVE--SLNKPN----LISLDDYYRKELPSLIHQRNPNPHINT 58
             F C +   WK     Y   VE  S  K      L+ LD +++++LP+ I  R P   +  
Sbjct:     4 FTCEDPAVWKAVHNKYWTVVEAKSAGKRKTSGKLLQLDKWFQEDLPAAITAR-PERFLTH 62

Query:    59 TELSKLVRWKLTRGKWRPRXXXXXXXXXXXXXXXXXEKAFKSLPDLTKAVSELTVLKGVG 118
              EL K++ WKLT+GK+RPR                  KAF  LPD+  A+ EL  LKGVG
Sbjct:    63 AELVKIMEWKLTKGKFRPRLQQLIGSNNEEAVQSSSSKAFSLLPDVQAAIKELCKLKGVG 122

Query:   119 PATASAVLAAYAPDLAPFMSDEAMGA-ALGHSKDYSLKQYLLFADKLQAKAKEL--VSEE 175
              ATASAVL A APD   FM+DEA+ + A     +Y+ K Y L+  K+  K  EL  V  +
Sbjct:   123 SATASAVLVAGAPDKVAFMADEAVESIAELRPVEYTDKHYALYLQKMLWKTSELNKVDAQ 182

Query:   176 NCFTPFDVERALWSSAIGLKLKASKSNQDSEIKTTKNSK-RKRK 218
               +TP  VE+ LW+  +  +++ S   Q   +K   N K  KRK
Sbjct:   183 QDWTPHRVEQCLWTWTVANQIQPSLL-QGVSLKDATNQKPEKRK 225

GO:0003677 "DNA binding" evidence=IEA

GO:0006281 "DNA repair" evidence=IEA

FB|FBgn0030328 Amun "Amun" [Drosophila melanogaster (taxid:7227)]

 Score = 283 (104.7 bits), Expect = 3.8e-24, P = 3.8e-24
 Identities = 69/167 (41%), Positives = 95/167 (56%)

Query:    29 KPN-LISLDDYYRKELPSLIHQRNPNPHINTTELSKLVRWKLTRGKWRPRXXXXXXXXXX 87
             KP  LI LD +Y+ ELP LI  R  + H+   EL + ++WK +RGK+ P+          
Sbjct:    40 KPQELIRLDQWYQNELPKLIKARGKDAHMVYDELVQSMKWKQSRGKFYPQLSYLVKVNTP 99

Query:    88 XXXXXXXEKAFKSLPDLTKAVSELTVLKGVGPATASAVLAAYAPDLAPFMSDEAMGAALG 147
                    +KAF+ LP+L +A++ L+ LKGVG   ASA+LAA APD APFM+DE + A   
Sbjct:   100 RAVIQETKKAFRKLPNLEQAITALSNLKGVGTTMASALLAAAAPDSAPFMADECLMAIPE 159

Query:   148 -HSKDYSLKQYLLFADKLQAKAKELVSEENCFTPF----DVERALWS 189
                 DY+ K+YL F + +QA  + L +E    TP      VE ALWS
Sbjct:   160 IEGIDYTTKEYLNFVNHIQATVERLNAEVGGDTPHWSPHRVELALWS 206

GO:0035220 "wing disc development" evidence=IGI

GO:0048749 "compound eye development" evidence=IGI

GO:0005634 "nucleus" evidence=IDA

GO:0022416 "chaeta development" evidence=IMP

ASPGD|ASPL0000059149 AN10183 [Emericella nidulans (taxid:162425)]

 Score = 139 (54.0 bits), Expect = 6.6e-08, P = 6.6e-08
 Identities = 48/182 (26%), Positives = 80/182 (43%)

Query:    48 HQRNPNPHINTTELSKLVRWKLTRGKWRPRXXXXXXXXXXXXXXXXXEKAFKSLPD---- 103
             ++R    H++  EL +L+ WKL  G +RP                    AF SLP     
Sbjct:   102 NERGSGGHLSREELVQLMEWKLKHGVYRPTLLGMIRQNQEKIISDTTASAFSSLPGSVEG 161

Query:   104 ------LTKAVSELTV-LKGVGPATASAVLAAYAPDLAPFMSDEA-MGAALGHSKDYSLK 155
                   +  A+  LT  L+GVGPATAS +L+   P++ PF SD+  +    G     S  
Sbjct:   162 KDGFEAIENALLTLTTPLRGVGPATASLILSVACPEMIPFYSDDVYLWVCAGVYPSSS-- 219

Query:   156 QYLLFADKLQAKAKELVSEENCFTPFDVE--RALWSSAIGLKLKASKSNQDSEIKTTKNS 213
                 F+ K   K+KE+    +    ++V   R LW    GL+ + ++   + +  + K+ 
Sbjct:   220 ----FSSK---KSKEVKPNGDPNVKYNVAEYRRLWERVEGLRARLNEEADEGKRVSCKDI 272

Query:   214 KR 215
             ++
Sbjct:   273 EK 274


Parameters:
  V=100
  filter=SEG
  E=0.001

  ctxfactor=1.00

  Query                        -----  As Used  -----    -----  Computed  ----
  Frame  MatID Matrix name     Lambda    K       H      Lambda    K       H
   +0      0   BLOSUM62        0.313   0.127   0.368    same    same    same
               Q=9,R=2         0.244   0.0300  0.180     n/a     n/a     n/a

  Query
  Frame  MatID  Length  Eff.Length     E     S W   T  X   E2     S2
   +0      0      219       202   0.00090  111 3  11 23  0.39    33
                                                     31  0.46    35


Statistics:

  Database:  /share/blast/go-seqdb.fasta
   Title:  go_20130330-seqdb.fasta
   Posted:  5:47:42 AM PDT Apr 1, 2013
   Created:  5:47:42 AM PDT Apr 1, 2013
   Format:  XDF-1
   # of letters in database:  169,044,731
   # of sequences in database:  368,745
   # of database sequences satisfying E:  5
  No. of states in DFA:  611 (65 KB)
  Total size of DFA:  176 KB (2102 KB)
  Time to generate neighborhood:  0.00u 0.00s 0.00t   Elapsed:  00:00:00
  No. of threads or processors used:  24
  Search cpu time:  17.03u 0.10s 17.13t   Elapsed:  00:00:00
  Total cpu time:  17.03u 0.10s 17.13t   Elapsed:  00:00:00
  Start:  Sat May 11 07:56:56 2013   End:  Sat May 11 07:56:56 2013

GO:0008150 "biological_process" evidence=ND

GO:0003674 "molecular_function" evidence=ND

GO:0005575 "cellular_component" evidence=ND

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

No confident hit for EC number transfering in SWISSPROT detected by BLAST

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input: estExt_fgenesh4_pg.C_LG_II1044 hypothetical protein (219 aa) (Populus trichocarpa)

Predicted Functional Partners:

Sorry, there are no predicted associations at the current settings.

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	219
PF00633	30	HHH: Helix-hairpin-helix motif; InterPro: IPR00044	97.56
PRK01229	208	N-glycosylase/DNA lyase; Provisional	96.86
COG0177	211	Nth Predicted EndoIII-related endonuclease [DNA re	96.8
TIGR01084	275	mutY A/G-specific adenine glycosylase. This equiva	96.2
cd00056	158	ENDO3c endonuclease III; includes endonuclease III	95.99
PRK10702	211	endonuclease III; Provisional	94.99
PRK10880	350	adenine DNA glycosylase; Provisional	94.7
smart00478	149	ENDO3c endonuclease III. includes endonuclease III	94.66
PF02371	87	Transposase_20: Transposase IS116/IS110/IS902 fami	94.62
PRK13910	289	DNA glycosylase MutY; Provisional	94.43
COG1194	342	MutY A/G-specific DNA glycosylase [DNA replication	94.42
COG0122	285	AlkA 3-methyladenine DNA glycosylase/8-oxoguanine	94.1
TIGR01083	191	nth endonuclease III. This equivalog model identif	94.08
TIGR00588	310	ogg 8-oxoguanine DNA-glycosylase (ogg). All protei	93.7
TIGR03252	177	uncharacterized HhH-GPD family protein. This model	93.6
PRK02515	132	psbU photosystem II complex extrinsic protein prec	93.43
PRK13913	218	3-methyladenine DNA glycosylase; Provisional	93.26
PRK10308	283	3-methyl-adenine DNA glycosylase II; Provisional	93.07
smart00278	26	HhH1 Helix-hairpin-helix DNA-binding motif class 1	91.74
PF11731	93	Cdd1: Pathogenicity locus; InterPro: IPR021725 Cdd	89.85
PF10391	52	DNA_pol_lambd_f: Fingers domain of DNA polymerase	87.51
TIGR01259	120	comE comEA protein. This model describes the ComEA	87.42
PF14716	68	HHH_8: Helix-hairpin-helix domain; PDB: 2W9M_A 1HU	85.71
PRK14605	194	ruvA Holliday junction DNA helicase RuvA; Provisio	84.95
KOG1921	286	consensus Endonuclease III [Replication, recombina	83.82
KOG2875	323	consensus 8-oxoguanine DNA glycosylase [Replicatio	81.64
PRK00116	192	ruvA Holliday junction DNA helicase RuvA; Reviewed	81.35
PF14520	60	HHH_5: Helix-hairpin-helix domain; PDB: 3AUO_B 3AU	80.95
TIGR00084	191	ruvA Holliday junction DNA helicase, RuvA subunit.	80.84
PRK13901	196	ruvA Holliday junction DNA helicase RuvA; Provisio	80.78
COG2003	224	RadC DNA repair proteins [DNA replication, recombi	80.41
PRK14600	186	ruvA Holliday junction DNA helicase RuvA; Provisio	80.16

>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=97.56  E-value=6.3e-05  Score=46.69  Aligned_cols=24  Identities=42%  Similarity=0.700  Sum_probs=20.1

Q ss_pred             HHHHHHhhccCCCChHHHHHHHHh
Q 027752          105 TKAVSELTVLKGVGPATASAVLAA  128 (219)
Q Consensus       105 ~~al~~L~~LkGVGPATASaiLa~  128 (219)
                      .+.++.|++|+||||.||.+|++.
T Consensus         7 pas~eeL~~lpGIG~~tA~~I~~~   30 (30)
T PF00633_consen    7 PASIEELMKLPGIGPKTANAILSF   30 (30)
T ss_dssp             TSSHHHHHTSTT-SHHHHHHHHHH
T ss_pred             CCCHHHHHhCCCcCHHHHHHHHhC
Confidence            346889999999999999999973

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 ....

>PRK01229 N-glycosylase/DNA lyase; Provisional

Probab=96.86  E-value=0.0042  Score=54.28  Aligned_cols=81  Identities=26%  Similarity=0.257  Sum_probs=59.2

Q ss_pred             cHHHHHHHhh-ccCCCChHHHHHHHH-hhCCCCCCcccHHHHHHh---cCC----CCCCCHHHHHHHHHHHHHHHHHhhc
Q 027752          103 DLTKAVSELT-VLKGVGPATASAVLA-AYAPDLAPFMSDEAMGAA---LGH----SKDYSLKQYLLFADKLQAKAKELVS  173 (219)
Q Consensus       103 d~~~al~~L~-~LkGVGPATASaiLa-~~~P~~~pFfsDEa~~~~---~g~----~~kYt~keY~~~~~~l~~~~~~L~~  173 (219)
                      ++..+.+.|. +||||||=|||.||. +..  ...|.-|.-..-+   .|-    +..-|.+.|.+.-..+.+.+..+  
T Consensus       112 ~~~~~R~~Ll~~lpGIG~KTAd~vL~~~~~--~~~~iVDtHv~Ri~~RlG~~~~~~~~lt~~~y~~~E~~l~~~~~~~--  187 (208)
T PRK01229        112 DQFEAREFLVKNIKGIGYKEASHFLRNVGY--EDLAILDRHILRFLKRYGLIEEIPKTLSKKRYLEIEEILREIAEEL--  187 (208)
T ss_pred             CchHHHHHHHHcCCCCcHHHHHHHHHHccC--CCeeeeeHHHHHHHHHhCCCcccccccCcCCHHHHHHHHHHHHHHc--
Confidence            5678899999 999999999999994 444  2123345433322   351    22456689999999999999887  


Q ss_pred             cCCCCCHHHHHHHHHHH
Q 027752          174 EENCFTPFDVERALWSS  190 (219)
Q Consensus       174 ~~~~~t~~~VEkalw~~  190 (219)
                         .+.+..+.-++|-.
T Consensus       188 ---~~~~~~Ldl~~w~~  201 (208)
T PRK01229        188 ---GISLGELDLYIWYK  201 (208)
T ss_pred             ---CCCHHHHHHHHHHH
Confidence               47899999999964

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

Probab=96.80  E-value=0.0051  Score=53.98  Aligned_cols=71  Identities=21%  Similarity=0.228  Sum_probs=45.9

Q ss_pred             CHHHHHHHHHHHhhcCCCCcchHHHhhhCCHHHHHHHHHHH-H------h------hC-----ccHHHHHHHhhccCCCC
Q 027752           57 NTTELSKLVRWKLTRGKWRPRLLVFVSSLDDSSVKSASEKA-F------K------SL-----PDLTKAVSELTVLKGVG  118 (219)
Q Consensus        57 tkdEL~~LveWKL~rGkfRP~L~~lV~sN~~~~V~~~t~~A-f------~------~l-----~d~~~al~~L~~LkGVG  118 (219)
                      |.|+.+.-+.=+|-.  .-|+...+...+.+ .+++.++.. |      +      ++     .++...++.|.+|+|||
T Consensus        42 ttD~~vn~at~~Lf~--~~~t~e~l~~a~~~-~l~~~I~~iGlyr~KAk~I~~~~~~l~e~~~g~vP~~~~eL~~LPGVG  118 (211)
T COG0177          42 TTDEVVNKATPALFK--RYPTPEDLLNADEE-ELEELIKSIGLYRNKAKNIKELARILLEKFGGEVPDTREELLSLPGVG  118 (211)
T ss_pred             CchHHHHHHHHHHHH--HcCCHHHHHcCCHH-HHHHHHHhcCCcHHHHHHHHHHHHHHHHHcCCCCCchHHHHHhCCCcc
Confidence            467777766666542  23455666665544 444443322 2      0      11     14567899999999999


Q ss_pred             hHHHHHHHHhhC
Q 027752          119 PATASAVLAAYA  130 (219)
Q Consensus       119 PATASaiLa~~~  130 (219)
                      +=||..||+...
T Consensus       119 rKTAnvVL~~a~  130 (211)
T COG0177         119 RKTANVVLSFAF  130 (211)
T ss_pred             hHHHHHHHHhhc
Confidence            999999999854

>TIGR01084 mutY A/G-specific adenine glycosylase

Probab=96.20  E-value=0.042  Score=49.75  Aligned_cols=36  Identities=31%  Similarity=0.405  Sum_probs=27.9

Q ss_pred             HHHHHHHhhccCCCChHHHHHHHHhhCCCCCCcccHH
Q 027752          104 LTKAVSELTVLKGVGPATASAVLAAYAPDLAPFMSDE  140 (219)
Q Consensus       104 ~~~al~~L~~LkGVGPATASaiLa~~~P~~~pFfsDE  140 (219)
                      +...++.|++|+||||-||++||+...-...|+ -|-
T Consensus       100 ~p~~~~~L~~LpGIG~~TA~~Il~~a~~~~~~~-vD~  135 (275)
T TIGR01084       100 FPQDFEDLAALPGVGRYTAGAILSFALNKPYPI-LDG  135 (275)
T ss_pred             CcHHHHHHHhCCCCCHHHHHHHHHHHCCCCCCc-chH
Confidence            345689999999999999999999865444454 444

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.

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

Probab=95.99  E-value=0.037  Score=44.71  Aligned_cols=37  Identities=41%  Similarity=0.484  Sum_probs=28.4

Q ss_pred             HHHHHHhhccCCCChHHHHHHHHhhC-CCCCCcccHHHHH
Q 027752          105 TKAVSELTVLKGVGPATASAVLAAYA-PDLAPFMSDEAMG  143 (219)
Q Consensus       105 ~~al~~L~~LkGVGPATASaiLa~~~-P~~~pFfsDEa~~  143 (219)
                      ..+.+.|++||||||-||+.||.... ++.+|.  |-...
T Consensus        79 ~~~~~~L~~l~GIG~~tA~~~l~~~~~~~~~pv--D~~v~  116 (158)
T cd00056          79 PDAREELLALPGVGRKTANVVLLFALGPDAFPV--DTHVR  116 (158)
T ss_pred             cccHHHHHcCCCCCHHHHHHHHHHHCCCCCCcc--chhHH
Confidence            67899999999999999999998743 444554  55443

>PRK10702 endonuclease III; Provisional

Probab=94.99  E-value=0.042  Score=47.81  Aligned_cols=28  Identities=32%  Similarity=0.383  Sum_probs=24.5

Q ss_pred             HHHHHHHhhccCCCChHHHHHHHHhhCC
Q 027752          104 LTKAVSELTVLKGVGPATASAVLAAYAP  131 (219)
Q Consensus       104 ~~~al~~L~~LkGVGPATASaiLa~~~P  131 (219)
                      +..+++.|.+|+||||-||.+||....-
T Consensus       104 ~p~~~~~Ll~lpGVG~ktA~~ill~a~~  131 (211)
T PRK10702        104 VPEDRAALEALPGVGRKTANVVLNTAFG  131 (211)
T ss_pred             CCchHHHHhcCCcccHHHHHHHHHHHcC
Confidence            4568999999999999999999998654

>PRK10880 adenine DNA glycosylase; Provisional

Probab=94.70  E-value=0.051  Score=50.93  Aligned_cols=29  Identities=31%  Similarity=0.472  Sum_probs=25.1

Q ss_pred             HHHHHHHhhccCCCChHHHHHHHHhhCCC
Q 027752          104 LTKAVSELTVLKGVGPATASAVLAAYAPD  132 (219)
Q Consensus       104 ~~~al~~L~~LkGVGPATASaiLa~~~P~  132 (219)
                      +...++.|.+||||||-||++||+...-.
T Consensus       104 ~p~~~~~L~~LpGIG~~TA~aIl~~af~~  132 (350)
T PRK10880        104 FPETFEEVAALPGVGRSTAGAILSLSLGK  132 (350)
T ss_pred             chhhHHHHhcCCCccHHHHHHHHHHHCCC
Confidence            45678999999999999999999987654

>smart00478 ENDO3c endonuclease III

Probab=94.66  E-value=0.21  Score=39.97  Aligned_cols=29  Identities=38%  Similarity=0.386  Sum_probs=24.7

Q ss_pred             HHHHHHHhhccCCCChHHHHHHHHhhCCC
Q 027752          104 LTKAVSELTVLKGVGPATASAVLAAYAPD  132 (219)
Q Consensus       104 ~~~al~~L~~LkGVGPATASaiLa~~~P~  132 (219)
                      +...++.|++|+||||-||++||...--.
T Consensus        67 ~~~~~~~L~~l~GIG~~tA~~~l~~~~~~   95 (149)
T smart00478       67 VPDDREELLKLPGVGRKTANAVLSFALGK   95 (149)
T ss_pred             ccHHHHHHHcCCCCcHHHHHHHHHHHCCC
Confidence            44678899999999999999999987554

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

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

Probab=94.62  E-value=0.03  Score=41.80  Aligned_cols=37  Identities=32%  Similarity=0.497  Sum_probs=30.2

Q ss_pred             HHhhccCCCChHHHHHHHHhh-CCCCCCcccHHHHHHhcC
Q 027752          109 SELTVLKGVGPATASAVLAAY-APDLAPFMSDEAMGAALG  147 (219)
Q Consensus       109 ~~L~~LkGVGPATASaiLa~~-~P~~~pFfsDEa~~~~~g  147 (219)
                      +.|+.++||||-||..||+.. +|+  -|=+...+...+|
T Consensus         2 ~~l~sipGig~~~a~~llaeigd~~--rF~~~~~l~~~~G   39 (87)
T PF02371_consen    2 ELLTSIPGIGPITAATLLAEIGDIS--RFKSAKQLASYAG   39 (87)
T ss_pred             chhcCCCCccHHHHHHHHHHHcCch--hcccchhhhhccc
Confidence            468899999999999999986 443  4667888887777

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

>PRK13910 DNA glycosylase MutY; Provisional

Probab=94.43  E-value=0.14  Score=46.79  Aligned_cols=30  Identities=27%  Similarity=0.300  Sum_probs=24.7

Q ss_pred             HHHHHhhccCCCChHHHHHHHHhhCCCCCC
Q 027752          106 KAVSELTVLKGVGPATASAVLAAYAPDLAP  135 (219)
Q Consensus       106 ~al~~L~~LkGVGPATASaiLa~~~P~~~p  135 (219)
                      ...+.|.+|+||||-||.+||+...-..++
T Consensus        69 ~~~~~L~~LpGIG~kTA~aIl~~af~~~~~   98 (289)
T PRK13910         69 NDYQSLLKLPGIGAYTANAILCFGFREKSA   98 (289)
T ss_pred             hhHHHHHhCCCCCHHHHHHHHHHHCCCCcC
Confidence            358999999999999999999986543333

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

Probab=94.42  E-value=0.055  Score=50.69  Aligned_cols=36  Identities=33%  Similarity=0.450  Sum_probs=29.1

Q ss_pred             HHHhhccCCCChHHHHHHHHhhCCCCCCcccHHHHH
Q 027752          108 VSELTVLKGVGPATASAVLAAYAPDLAPFMSDEAMG  143 (219)
Q Consensus       108 l~~L~~LkGVGPATASaiLa~~~P~~~pFfsDEa~~  143 (219)
                      .+.|.+|+||||-||+||||...-...|+.+--+..
T Consensus       112 ~~~l~~LpGiG~yTa~Ail~~a~~~~~~~lDgNV~R  147 (342)
T COG1194         112 EEELAALPGVGPYTAGAILSFAFNQPEPVLDGNVKR  147 (342)
T ss_pred             HHHHHhCCCCcHHHHHHHHHHHhCCCCceeecchhe
Confidence            456667999999999999999887777877755554

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

Probab=94.10  E-value=0.12  Score=47.13  Aligned_cols=72  Identities=28%  Similarity=0.270  Sum_probs=51.4

Q ss_pred             CCCHHHHHHHHHHHhh-cCCCCcchHHHhhhCCHHHHHHHHHHHHhhCc--------cHHHHHHHhhccCCCChHHHHHH
Q 027752           55 HINTTELSKLVRWKLT-RGKWRPRLLVFVSSLDDSSVKSASEKAFKSLP--------DLTKAVSELTVLKGVGPATASAV  125 (219)
Q Consensus        55 ~ltkdEL~~LveWKL~-rGkfRP~L~~lV~sN~~~~V~~~t~~Af~~l~--------d~~~al~~L~~LkGVGPATASai  125 (219)
                      +.|-++|..+=++-|. -|..+..         .+.+..+++...+-.+        +...+++.|+.||||||=||-.+
T Consensus       144 fptpe~l~~~~~~~l~~~g~s~~K---------a~yi~~~A~~~~~g~~~~~~l~~~~~e~a~e~L~~i~GIG~WTAe~~  214 (285)
T COG0122         144 FPTPEQLAAADEEALRRCGLSGRK---------AEYIISLARAAAEGELDLSELKPLSDEEAIEELTALKGIGPWTAEMF  214 (285)
T ss_pred             CCCHHHHHhcCHHHHHHhCCcHHH---------HHHHHHHHHHHHcCCccHHHhccCCHHHHHHHHHcCCCcCHHHHHHH
Confidence            6788888888888776 4555442         3455566655554321        46779999999999999999999


Q ss_pred             HHh--hCCCCCC
Q 027752          126 LAA--YAPDLAP  135 (219)
Q Consensus       126 La~--~~P~~~p  135 (219)
                      |-.  ..|+.+|
T Consensus       215 llf~lgr~dvfP  226 (285)
T COG0122         215 LLFGLGRPDVFP  226 (285)
T ss_pred             HHHcCCCCCCCC
Confidence            976  4566544

>TIGR01083 nth endonuclease III

Probab=94.08  E-value=0.14  Score=43.35  Aligned_cols=27  Identities=37%  Similarity=0.423  Sum_probs=23.5

Q ss_pred             HHHHHHHhhccCCCChHHHHHHHHhhC
Q 027752          104 LTKAVSELTVLKGVGPATASAVLAAYA  130 (219)
Q Consensus       104 ~~~al~~L~~LkGVGPATASaiLa~~~  130 (219)
                      +..+++.|++|+||||=||.+||....
T Consensus       101 ~~~~~~~L~~l~GIG~ktA~~ill~~~  127 (191)
T TIGR01083       101 VPEDREELVKLPGVGRKTANVVLNVAF  127 (191)
T ss_pred             CchHHHHHHhCCCCcHHHHHHHHHHHc
Confidence            345788999999999999999998764

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.

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

Probab=93.70  E-value=0.061  Score=49.27  Aligned_cols=37  Identities=30%  Similarity=0.426  Sum_probs=29.7

Q ss_pred             HHHHHHHhhccCCCChHHHHHHHHhh--CCCCCCcccHHHH
Q 027752          104 LTKAVSELTVLKGVGPATASAVLAAY--APDLAPFMSDEAM  142 (219)
Q Consensus       104 ~~~al~~L~~LkGVGPATASaiLa~~--~P~~~pFfsDEa~  142 (219)
                      ...+++.|++||||||=||.+||...  .|+.+|.  |-..
T Consensus       215 ~~~~~~~L~~l~GIG~~tAd~vll~~l~~~d~~Pv--D~~v  253 (310)
T TIGR00588       215 YEDAREALCELPGVGPKVADCICLMGLDKPQAVPV--DVHV  253 (310)
T ss_pred             hHHHHHHHHhCCCccHHHHHHHHHHhCCCCCceee--cHHH
Confidence            56789999999999999999999774  5666663  6544

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.

>TIGR03252 uncharacterized HhH-GPD family protein

Probab=93.60  E-value=0.059  Score=46.21  Aligned_cols=44  Identities=30%  Similarity=0.373  Sum_probs=32.4

Q ss_pred             ccHHHHHHHhhccCCCChHHHHHHHHhhCCCCCCcccHHHHHHhcC
Q 027752          102 PDLTKAVSELTVLKGVGPATASAVLAAYAPDLAPFMSDEAMGAALG  147 (219)
Q Consensus       102 ~d~~~al~~L~~LkGVGPATASaiLa~~~P~~~pFfsDEa~~~~~g  147 (219)
                      |+-...++.|.+|+||||-||..||+...-+.  -.-||-|....|
T Consensus       108 p~t~~lre~Ll~LpGVG~KTAnvVL~~l~~~~--~~~~~~~~~~~~  151 (177)
T TIGR03252       108 PDGKELLRRLKALPGFGKQKAKIFLALLGKQL--GVTPEGWREAAG  151 (177)
T ss_pred             CCcHHHHHHHHcCCCCCHHHHHHHHHHHHHHh--CCCCcchHHhcc
Confidence            44455689999999999999999999765432  234677765544

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).

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

Probab=93.43  E-value=0.083  Score=43.42  Aligned_cols=39  Identities=23%  Similarity=0.303  Sum_probs=32.4

Q ss_pred             HHHHHHhhccCCCChHHHHHHHHhhCCCCCCcccHHHHHHhcCC
Q 027752          105 TKAVSELTVLKGVGPATASAVLAAYAPDLAPFMSDEAMGAALGH  148 (219)
Q Consensus       105 ~~al~~L~~LkGVGPATASaiLa~~~P~~~pFfsDEa~~~~~g~  148 (219)
                      .+....|..|+||||++|..|.     .+.||-|=|-...+.|-
T Consensus        57 ~A~~~el~~lpGigP~~A~~IV-----~nGpf~sveDL~~V~GI   95 (132)
T PRK02515         57 NSSVRAFRQFPGMYPTLAGKIV-----KNAPYDSVEDVLNLPGL   95 (132)
T ss_pred             ccCHHHHHHCCCCCHHHHHHHH-----HCCCCCCHHHHHcCCCC
Confidence            3456778999999999999999     36799998888878773

>PRK13913 3-methyladenine DNA glycosylase; Provisional

Probab=93.26  E-value=0.24  Score=43.60  Aligned_cols=39  Identities=21%  Similarity=0.130  Sum_probs=27.8

Q ss_pred             HHHHHhhccCCCChHHHHHHHHhhCCCCCCcccHHHHHHh
Q 027752          106 KAVSELTVLKGVGPATASAVLAAYAPDLAPFMSDEAMGAA  145 (219)
Q Consensus       106 ~al~~L~~LkGVGPATASaiLa~~~P~~~pFfsDEa~~~~  145 (219)
                      ...+.|.+|+||||=||.+||....- +..|..|--..-+
T Consensus       118 ~~re~Ll~l~GIG~kTAd~iLlya~~-rp~fvVDty~~Rv  156 (218)
T PRK13913        118 VTREWLLDQKGIGKESADAILCYVCA-KEVMVVDKYSYLF  156 (218)
T ss_pred             hHHHHHHcCCCccHHHHHHHHHHHcC-CCccccchhHHHH
Confidence            46688999999999999999987543 3234445544434

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

Probab=93.07  E-value=0.11  Score=47.15  Aligned_cols=33  Identities=27%  Similarity=0.323  Sum_probs=27.8

Q ss_pred             cHHHHHHHhhccCCCChHHHHHHHHh--hCCCCCC
Q 027752          103 DLTKAVSELTVLKGVGPATASAVLAA--YAPDLAP  135 (219)
Q Consensus       103 d~~~al~~L~~LkGVGPATASaiLa~--~~P~~~p  135 (219)
                      +..++++.|+.||||||-||..||-.  ..|+.+|
T Consensus       201 ~~~~~~~~L~~LpGIGpwTA~~vllr~lg~~D~fp  235 (283)
T PRK10308        201 DVEQAMKTLQTFPGIGRWTANYFALRGWQAKDVFL  235 (283)
T ss_pred             CHHHHHHHHhcCCCcCHHHHHHHHHHhCCCCCCCC
Confidence            56778999999999999999999865  5777655

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

Probab=91.74  E-value=0.14  Score=30.19  Aligned_cols=19  Identities=47%  Similarity=0.763  Sum_probs=16.9

Q ss_pred             HhhccCCCChHHHHHHHHh
Q 027752          110 ELTVLKGVGPATASAVLAA  128 (219)
Q Consensus       110 ~L~~LkGVGPATASaiLa~  128 (219)
                      .|+.++|||+.+|..|+..
T Consensus         2 ~L~~i~GiG~k~A~~il~~   20 (26)
T smart00278        2 ELLKVPGIGPKTAEKILEA   20 (26)
T ss_pred             hhhhCCCCCHHHHHHHHHh
Confidence            4789999999999999974

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

Probab=89.85  E-value=0.23  Score=38.48  Aligned_cols=26  Identities=27%  Similarity=0.261  Sum_probs=22.1

Q ss_pred             HHHHHHHhhccCCCChHHHHHHHHhh
Q 027752          104 LTKAVSELTVLKGVGPATASAVLAAY  129 (219)
Q Consensus       104 ~~~al~~L~~LkGVGPATASaiLa~~  129 (219)
                      ..+.+..|+.|+|||||||-=+..++
T Consensus         7 ~~~~~~~L~~iP~IG~a~a~DL~~LG   32 (93)
T PF11731_consen    7 KRAGLSDLTDIPNIGKATAEDLRLLG   32 (93)
T ss_pred             HHHHHHHHhcCCCccHHHHHHHHHcC
Confidence            34578899999999999999887764

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

>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=87.51  E-value=0.38  Score=33.27  Aligned_cols=22  Identities=36%  Similarity=0.351  Sum_probs=17.1

Q ss_pred             HHHhhccCCCChHHHHHHHHhh
Q 027752          108 VSELTVLKGVGPATASAVLAAY  129 (219)
Q Consensus       108 l~~L~~LkGVGPATASaiLa~~  129 (219)
                      |+.++.+-||||+||.-..+..
T Consensus         1 l~~f~~I~GVG~~tA~~w~~~G   22 (52)
T PF10391_consen    1 LKLFTGIWGVGPKTARKWYAKG   22 (52)
T ss_dssp             HHHHHTSTT--HHHHHHHHHTT
T ss_pred             CcchhhcccccHHHHHHHHHhC
Confidence            5789999999999999888764

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=87.42  E-value=0.61  Score=37.16  Aligned_cols=42  Identities=29%  Similarity=0.487  Sum_probs=33.4

Q ss_pred             HHHHHHhhccCCCChHHHHHHHHhhCCCCCCcccHHHHHHhcC
Q 027752          105 TKAVSELTVLKGVGPATASAVLAAYAPDLAPFMSDEAMGAALG  147 (219)
Q Consensus       105 ~~al~~L~~LkGVGPATASaiLa~~~P~~~pFfsDEa~~~~~g  147 (219)
                      .+....|..|+||||.+|..|+.-.. .+.+|-|-|-+.-+.|
T Consensus        64 tA~~~eL~~lpGIG~~~A~~Ii~~R~-~~g~f~s~eeL~~V~G  105 (120)
T TIGR01259        64 AASLEELQALPGIGPAKAKAIIEYRE-ENGAFKSVDDLTKVSG  105 (120)
T ss_pred             cCCHHHHhcCCCCCHHHHHHHHHHHH-hcCCcCCHHHHHcCCC
Confidence            34577899999999999999999754 3568888777766665

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.

>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=85.71  E-value=1.2  Score=31.68  Aligned_cols=31  Identities=32%  Similarity=0.415  Sum_probs=22.1

Q ss_pred             HHhhCccHHHHHHH-hhccCCCChHHHHHHHH
Q 027752           97 AFKSLPDLTKAVSE-LTVLKGVGPATASAVLA  127 (219)
Q Consensus        97 Af~~l~d~~~al~~-L~~LkGVGPATASaiLa  127 (219)
                      +...+|..-..++. +..|+|||+.+|.-|--
T Consensus        34 ~i~~l~~~i~~~~~~~~~l~gIG~~ia~kI~E   65 (68)
T PF14716_consen   34 AIKALPYPITSGEEDLKKLPGIGKSIAKKIDE   65 (68)
T ss_dssp             HHHHSSS-HHSHHHHHCTSTTTTHHHHHHHHH
T ss_pred             HHHhCCHhHhhHHHHHhhCCCCCHHHHHHHHH
Confidence            34556654445565 99999999999998743

...

>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional

Probab=84.95  E-value=0.66  Score=39.94  Aligned_cols=31  Identities=23%  Similarity=0.362  Sum_probs=27.0

Q ss_pred             cHHHHHHHhhccCCCChHHHHHHHHhhCCCC
Q 027752          103 DLTKAVSELTVLKGVGPATASAVLAAYAPDL  133 (219)
Q Consensus       103 d~~~al~~L~~LkGVGPATASaiLa~~~P~~  133 (219)
                      +.+.-+..|.+..||||-||-+||+.+.|+.
T Consensus        67 ~Er~lF~~Li~V~GIGpK~Al~ILs~~~~~~   97 (194)
T PRK14605         67 EELSLFETLIDVSGIGPKLGLAMLSAMNAEA   97 (194)
T ss_pred             HHHHHHHHHhCCCCCCHHHHHHHHHhCCHHH
Confidence            4577889999999999999999999877754

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

Probab=83.82  E-value=1.7  Score=39.55  Aligned_cols=31  Identities=29%  Similarity=0.470  Sum_probs=27.7

Q ss_pred             cHHHHHHHhhccCCCChHHHHHHHHhhCCCC
Q 027752          103 DLTKAVSELTVLKGVGPATASAVLAAYAPDL  133 (219)
Q Consensus       103 d~~~al~~L~~LkGVGPATASaiLa~~~P~~  133 (219)
                      |+-..++.|..|+||||-+|=+.|+++.-..
T Consensus       153 DIP~~v~dLlsLPGVGPKMa~L~m~~AWn~i  183 (286)
T KOG1921|consen  153 DIPDTVEDLLSLPGVGPKMAHLTMQVAWNKI  183 (286)
T ss_pred             CCchhHHHHhcCCCCchHHHHHHHHHHhccc
Confidence            7888999999999999999999999976544

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

Probab=81.64  E-value=2.3  Score=39.39  Aligned_cols=61  Identities=18%  Similarity=0.175  Sum_probs=38.3

Q ss_pred             HHHHHHHhhccCCCChHHHHHHHHh--hCCCCCCcccHHHHH-----HhcC-CCC-CCCHHHHHHHHHHHH
Q 027752          104 LTKAVSELTVLKGVGPATASAVLAA--YAPDLAPFMSDEAMG-----AALG-HSK-DYSLKQYLLFADKLQ  165 (219)
Q Consensus       104 ~~~al~~L~~LkGVGPATASaiLa~--~~P~~~pFfsDEa~~-----~~~g-~~~-kYt~keY~~~~~~l~  165 (219)
                      ...|.++||.|+||||-.|-+|+-.  .-+..+|+ +--+|.     +++| ... .-+.+-|.++-...+
T Consensus       213 yeear~~L~~lpGVG~KVADCI~Lm~l~~~~~VPV-DvHi~ria~~y~l~~~~g~k~l~~ki~~ev~~~f~  282 (323)
T KOG2875|consen  213 YEEAREALCSLPGVGPKVADCICLMSLDKLSAVPV-DVHIWRIAQDYILPGLSGAKELTPKINGEVSNFFR  282 (323)
T ss_pred             HHHHHHHHhcCCCCcchHhhhhhhhhcCCCCcccc-hhhHHHHhhcccCCCccccccCCcchhHHHHHHHH
Confidence            4569999999999999999988754  34445562 222332     3344 122 367777777553333

>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed

Probab=81.35  E-value=1.4  Score=37.66  Aligned_cols=28  Identities=32%  Similarity=0.489  Sum_probs=23.1

Q ss_pred             HHHHHHHhhccCCCChHHHHHHHHhhCC
Q 027752          104 LTKAVSELTVLKGVGPATASAVLAAYAP  131 (219)
Q Consensus       104 ~~~al~~L~~LkGVGPATASaiLa~~~P  131 (219)
                      .+.....|..++||||.||-.||+.+.+
T Consensus        68 ek~~f~~L~~i~GIGpk~A~~il~~fg~   95 (192)
T PRK00116         68 ERELFRLLISVSGVGPKLALAILSGLSP   95 (192)
T ss_pred             HHHHHHHHhcCCCCCHHHHHHHHHhCCH
Confidence            3445778999999999999999987654

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

Probab=80.95  E-value=1.6  Score=30.17  Aligned_cols=23  Identities=26%  Similarity=0.479  Sum_probs=20.2

Q ss_pred             HHHHhhccCCCChHHHHHHHHhh
Q 027752          107 AVSELTVLKGVGPATASAVLAAY  129 (219)
Q Consensus       107 al~~L~~LkGVGPATASaiLa~~  129 (219)
                      ....|..++||||.+|..+....
T Consensus         3 ~~~~L~~I~Gig~~~a~~L~~~G   25 (60)
T PF14520_consen    3 VFDDLLSIPGIGPKRAEKLYEAG   25 (60)
T ss_dssp             HHHHHHTSTTCHHHHHHHHHHTT
T ss_pred             HHHhhccCCCCCHHHHHHHHhcC
Confidence            45778899999999999999984

...

>TIGR00084 ruvA Holliday junction DNA helicase, RuvA subunit

Probab=80.84  E-value=1.1  Score=38.40  Aligned_cols=30  Identities=33%  Similarity=0.579  Sum_probs=25.0

Q ss_pred             cHHHHHHHhhccCCCChHHHHHHHHhhCCC
Q 027752          103 DLTKAVSELTVLKGVGPATASAVLAAYAPD  132 (219)
Q Consensus       103 d~~~al~~L~~LkGVGPATASaiLa~~~P~  132 (219)
                      +.+.-+..|...+||||-||-+||+...|+
T Consensus        66 ~Er~lF~~L~~V~GIGpK~Al~iL~~~~~~   95 (191)
T TIGR00084        66 EERELFKELIKVNGVGPKLALAILSNMSPE   95 (191)
T ss_pred             HHHHHHHHHhCCCCCCHHHHHHHHhcCCHH
Confidence            456778889999999999999999987663

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.

>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional

Probab=80.78  E-value=1.1  Score=39.05  Aligned_cols=31  Identities=26%  Similarity=0.355  Sum_probs=26.7

Q ss_pred             cHHHHHHHhhccCCCChHHHHHHHHhhCCCC
Q 027752          103 DLTKAVSELTVLKGVGPATASAVLAAYAPDL  133 (219)
Q Consensus       103 d~~~al~~L~~LkGVGPATASaiLa~~~P~~  133 (219)
                      +.+.-+..|....||||-||-+||+...|+.
T Consensus        66 ~Er~lF~~LisVsGIGPK~ALaILs~~~~~e   96 (196)
T PRK13901         66 SEREVFEELIGVDGIGPRAALRVLSGIKYNE   96 (196)
T ss_pred             HHHHHHHHHhCcCCcCHHHHHHHHcCCCHHH
Confidence            4567888999999999999999999988754

>COG2003 RadC DNA repair proteins [DNA replication, recombination, and repair]

Probab=80.41  E-value=3.3  Score=36.91  Aligned_cols=153  Identities=21%  Similarity=0.261  Sum_probs=84.9

Q ss_pred             hhhHHHhhhhhHhhccCCCCCCCHHHHHHHHHHHhhcCCCCcchHHHhhhCCHHHHHHHHHHHHhhC---ccHH-HHHHH
Q 027752           35 LDDYYRKELPSLIHQRNPNPHINTTELSKLVRWKLTRGKWRPRLLVFVSSLDDSSVKSASEKAFKSL---PDLT-KAVSE  110 (219)
Q Consensus        35 LD~w~~~elp~~~~~r~~~~~ltkdEL~~LveWKL~rGkfRP~L~~lV~sN~~~~V~~~t~~Af~~l---~d~~-~al~~  110 (219)
                      +.+|...+.|.-=--+.....|+-.||..|+   |+.|.-+-            .|...++.-.+.+   ..+. +.++.
T Consensus         3 i~~~~~~~rPRErll~~G~~~Lsd~ELLail---LrtG~~~~------------~~~~la~~lL~~fg~L~~l~~a~~~e   67 (224)
T COG2003           3 IKDNPENERPRERLLKLGAEALSDAELLAIL---LRTGTKGE------------SVLDLAKELLQEFGSLAELLKASVEE   67 (224)
T ss_pred             ccccccccchHHHHHHhChhhcchHHHHHHH---HhcCCCCC------------CHHHHHHHHHHHcccHHHHHhCCHHH
Confidence            4456665555321111223589999977776   56665332            5666776665543   3444 45999


Q ss_pred             hhccCCCChHHHHHHHHhhCCCCCCcccHHHHHHhcCCCCCC-CHHHHHHHHH-HHHHHHHH------hhccC-------
Q 027752          111 LTVLKGVGPATASAVLAAYAPDLAPFMSDEAMGAALGHSKDY-SLKQYLLFAD-KLQAKAKE------LVSEE-------  175 (219)
Q Consensus       111 L~~LkGVGPATASaiLa~~~P~~~pFfsDEa~~~~~g~~~kY-t~keY~~~~~-~l~~~~~~------L~~~~-------  175 (219)
                      ||.++|||+|-|.-+.++..      ++-+.+..-.-.+... |.....+|+. .|...-++      |++++       
T Consensus        68 l~~v~GiG~aka~~l~a~~E------l~~R~~~~~~~~~~~i~sp~~~~~~l~~~l~~~~~E~f~vL~Ld~qnrlI~~e~  141 (224)
T COG2003          68 LSSVKGIGLAKAIQIKAAIE------LGKRILAERLREGVVITSPEAVAEYLRAELGGEEREHFVVLYLDSQNRLIATET  141 (224)
T ss_pred             HhhCCCccHHHHHHHHHHHH------HHHHHHHHHhccCCccCCHHHHHHHHHHHhhhhHHHHHHHHHhcCcCceeccee
Confidence            99999999999999998842      2222222111111111 2222333322 22222111      12111       


Q ss_pred             --------CCCCHHHH-HHHHHHHHhhhhhcccCCCCccchh
Q 027752          176 --------NCFTPFDV-ERALWSSAIGLKLKASKSNQDSEIK  208 (219)
Q Consensus       176 --------~~~t~~~V-Ekalw~~~v~~k~~~~~~~~~~~~~  208 (219)
                              ..+-|++| .+|+...+.+=.+.---|+|+|..+
T Consensus       142 lf~GTi~~s~V~PREI~k~Al~~nAaavIlaHNHPSGd~~PS  183 (224)
T COG2003         142 LFIGTLNVSEVHPREIFKEALKYNAAAVILAHNHPSGDPTPS  183 (224)
T ss_pred             EEeeecccceecHHHHHHHHHHhcchhhheeccCCCCCCCcC
Confidence                    25678876 6777777766666666778877766

>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional

Probab=80.16  E-value=1.1  Score=38.44  Aligned_cols=31  Identities=23%  Similarity=0.359  Sum_probs=26.8

Q ss_pred             cHHHHHHHhhccCCCChHHHHHHHHhhCCCC
Q 027752          103 DLTKAVSELTVLKGVGPATASAVLAAYAPDL  133 (219)
Q Consensus       103 d~~~al~~L~~LkGVGPATASaiLa~~~P~~  133 (219)
                      +.+.-+..|.+..||||-||-+||+...|+.
T Consensus        67 ~Er~lF~~LisV~GIGpK~Al~iLs~~~~~~   97 (186)
T PRK14600         67 EEQDCLRMLVKVSGVNYKTAMSILSKLTPEQ   97 (186)
T ss_pred             HHHHHHHHHhCcCCcCHHHHHHHHccCCHHH
Confidence            4567788999999999999999999887754

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	219
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	1e-05
4f9i_A	1026	Proline dehydrogenase/delta-1-pyrroline-5-carboxy	2e-04

>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 = 44.5 bits (104), Expect = 1e-05
 Identities = 39/194 (20%), Positives = 55/194 (28%), Gaps = 64/194 (32%)

Query: 19  SYEACVESLNK------PNLISLDDYYRKELPSLIHQRNPNPHINT--TELSKLVRWKLT 70
           S E  +E L K      PN  S  D          H  N    I++   EL +L++ K  
Sbjct: 194 SPETVLEMLQKLLYQIDPNWTSRSD----------HSSNIKLRIHSIQAELRRLLKSKP- 242

Query: 71  RGKWRPR-LLVFVSSLDDSSVKSASE-KAF----KSLPDLTKAVSELTVLKGVGPATASA 124
                   LLV    L +  V++A    AF    K L   T+       L        S 
Sbjct: 243 ----YENCLLV----LLN--VQNAKAWNAFNLSCKILL-TTRFKQVTDFLSAATTTHISL 291

Query: 125 VLAAYAPDLAPFMSDEAMGAALGHSKDYSLKQYLLFADKLQAKAKELVSEENCFT-PFDV 183
                         DE                  L    L  + ++L   E   T P  +
Sbjct: 292 D-----HHSMTLTPDEVKS---------------LLLKYLDCRPQDL-PREVLTTNPRRL 330

Query: 184 ERALWSSAIGLKLK 197
                 S I   ++
Sbjct: 331 ------SIIAESIR 338

>4f9i_A Proline dehydrogenase/delta-1-pyrroline-5-carboxy dehydrogenase; proline utilization A, PUTA, flavoenzyme, structural genomic biology; HET: FAD MES; 2.20A {Geobacter sulfurreducens} Length = 1026

 Score = 40.8 bits (96), Expect = 2e-04
 Identities = 15/128 (11%), Positives = 38/128 (29%), Gaps = 9/128 (7%)

Query: 41  KELPSLIHQRNPNPHINTTELSKLVRWKLTRGKWRPRLLVFVSSL----DDSSVKSASEK 96
           KE    I    P+       + K + W +   +++ ++  FV           +     +
Sbjct: 37  KEFFGSISGEKPSLFNKGAWMGKAMDWSMQNEQFKIQMFRFVDVFPSLTTSKLLTEHIRE 96

Query: 97  AFKSLPDLTKAVSELTVLKGVG-----PATASAVLAAYAPDLAPFMSDEAMGAALGHSKD 151
            F +  D+   +S    + G+            + +        F+  E    A+ + + 
Sbjct: 97  YFGNEQDMPAFMSTGAKVAGMLGSFGGAVLNKVLTSNIEEMARQFIVGETTKEAVKNLEK 156

Query: 152 YSLKQYLL 159
                +  
Sbjct: 157 LRKDGFAA 164

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	219
3fhg_A	207	Mjogg, N-glycosylase/DNA lyase, DNA-(apurinic; hel	97.96
3fhf_A	214	Mjogg, N-glycosylase/DNA lyase, DNA-(apurinic; hel	97.87
3n0u_A	219	Probable N-glycosylase/DNA lyase; structural genom	97.7
2xhi_A	360	N-glycosylase/DNA lyase; lyase-DNA complex, lyase/	96.28
3s6i_A	228	DNA-3-methyladenine glycosylase 1; DNA glycosylase	96.09
4e9f_A	161	Methyl-CPG-binding domain protein 4; HHH DNA glyco	95.86
3i0w_A	290	8-oxoguanine-DNA-glycosylase; OGG, cacogg, DNA, 8-	95.7
2h56_A	233	DNA-3-methyladenine glycosidase; 10174367, EC 3.2.	95.67
4b21_A	232	Probable DNA-3-methyladenine glycosylase 2; hydrol	95.52
1mpg_A	282	ALKA, 3-methyladenine DNA glycosylase II; DNA repa	94.92
2yg9_A	225	DNA-3-methyladenine glycosidase II, putative; hydr	94.9
3n5n_X	287	A/G-specific adenine DNA glycosylase; alpha-helice	94.82
1pu6_A	218	3-methyladenine DNA glycosylase; helix-hairpin-hel	94.26
1kea_A	221	Possible G-T mismatches repair enzyme; DNA repair,	94.06
2abk_A	211	Endonuclease III; DNA-repair, DNA glycosylase; 1.8	94.01
2jhn_A	295	ALKA, 3-methyladenine DNA-glycosylase; DNA repair,	93.68
1orn_A	226	Endonuclease III; DNA repair, DNA glycosylase, [4F	93.22
1kg2_A	225	A/G-specific adenine glycosylase; DNA repair, hydr	93.02
3fsp_A	369	A/G-specific adenine glycosylase; protein-DNA comp	92.4
3arc_U	97	Photosystem II 12 kDa extrinsic protein; PSII, mem	91.72
1s5l_U	134	Photosystem II 12 kDa extrinsic protein; photosynt	91.51
2duy_A	75	Competence protein comea-related protein; helix-ha	88.67
2a1j_B	91	DNA excision repair protein ERCC-1; XPF, xeroderma	87.72
2i5h_A	205	Hypothetical protein AF1531; PFAM:DUF655, PSI-2, s	87.66
1x2i_A	75	HEF helicase/nuclease; alpha helix, helix-hairpin-	86.69
2ztd_A	212	Holliday junction ATP-dependent DNA helicase RUVA;	83.49
2edu_A	98	Kinesin-like protein KIF22; kinesin-like DNA bindi	81.3
1kft_A	78	UVRC, excinuclease ABC subunit C; helix-hairpin-he	81.21
1ixr_A	191	Holliday junction DNA helicase RUVA; heterooligome	80.48

>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=97.96  E-value=7.7e-05  Score=62.92  Aligned_cols=85  Identities=22%  Similarity=0.277  Sum_probs=64.7

Q ss_pred             cHHHHHHHhhccCCCChHHHHHHHHh-hCCCCCCcccHHHHHHh--cC---C--CCCCCHHHHHHHHHHHHHHHHHhhcc
Q 027752          103 DLTKAVSELTVLKGVGPATASAVLAA-YAPDLAPFMSDEAMGAA--LG---H--SKDYSLKQYLLFADKLQAKAKELVSE  174 (219)
Q Consensus       103 d~~~al~~L~~LkGVGPATASaiLa~-~~P~~~pFfsDEa~~~~--~g---~--~~kYt~keY~~~~~~l~~~~~~L~~~  174 (219)
                      +...+++.|++||||||-||++||.. ..++ ++..++-+...+  .|   .  +..-+.++|.++-..++..++.+   
T Consensus       111 ~~~~~~~~L~~lpGIG~kTA~~il~~~~~~~-~~~vD~~v~Ri~~rlg~~~~~~~k~~~~k~y~~~~~~l~~~~~~~---  186 (207)
T 3fhg_A          111 DQQLARERLLNIKGIGMQEASHFLRNVGYFD-LAIIDRHIIDFMRRIGAIGETNVKQLSKSLYISFENILKSIASNL---  186 (207)
T ss_dssp             CHHHHHHHHTTSTTCCHHHHHHHHHHTTCCS-SCCCCHHHHHHHHHTTSSCCCCCSCCCHHHHHHHHHHHHHHHHHT---
T ss_pred             CHHHHHHHHHcCCCcCHHHHHHHHHHhCCCC-cceecHHHHHHHHHcCCCCccccccCCHHHHHHHHHHHHHHHHHh---
Confidence            34578999999999999999999995 5543 233444444432  23   1  34678999999999999998887   


Q ss_pred             CCCCCHHHHHHHHHHHHhh
Q 027752          175 ENCFTPFDVERALWSSAIG  193 (219)
Q Consensus       175 ~~~~t~~~VEkalw~~~v~  193 (219)
                        .+++..++.++|...-+
T Consensus       187 --~~~~~~lDl~lw~~~~g  203 (207)
T 3fhg_A          187 --NMSVGILDLFIWYKETN  203 (207)
T ss_dssp             --TSCHHHHHHHHHHHHHS
T ss_pred             --CCCHHHHHHHHHHHHhC
Confidence              48899999999987543

>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=97.87  E-value=0.00021  Score=61.11  Aligned_cols=89  Identities=20%  Similarity=0.255  Sum_probs=66.2

Q ss_pred             HhhCccHHHHHHHhh-ccCCCChHHHHHHHHhhCCCCCCcc-cHH-HHHHh--cC----CCCCCCHHHHHHHHHHHHHHH
Q 027752           98 FKSLPDLTKAVSELT-VLKGVGPATASAVLAAYAPDLAPFM-SDE-AMGAA--LG----HSKDYSLKQYLLFADKLQAKA  168 (219)
Q Consensus        98 f~~l~d~~~al~~L~-~LkGVGPATASaiLa~~~P~~~pFf-sDE-a~~~~--~g----~~~kYt~keY~~~~~~l~~~~  168 (219)
                      |..+.++..+++.|. +||||||-||++||....  ..+|+ -|- +...+  .|    .+...|.+.|.++-..++..+
T Consensus       113 ~~~~~~~~~~re~Ll~~LpGVG~KTA~~vL~~~g--~~~~~vVDthv~Ri~~RlG~~~~~~k~lt~~~y~e~~~~l~~~g  190 (214)
T 3fhf_A          113 VESFENEKVAREFLVRNIKGIGYKEASHFLRNVG--YDDVAIIDRHILRELYENNYIDEIPKTLSRRKYLEIENILRDIG  190 (214)
T ss_dssp             HHHSSSHHHHHHHHHHHSTTCCHHHHHHHHHHTT--CCSCCCCCHHHHHHHHHTTSSSSCCSSCCHHHHHHHHHHHHHHH
T ss_pred             hcccCCcHHHHHHHHHhCCCCCHHHHHHHHHHcC--CCCcccCcHHHHHHHHHcCCCCCCCCcCCHHHHHHHHHHHHHHH
Confidence            333346788999999 999999999999998642  22444 454 33322  34    235678899999999999999


Q ss_pred             HHhhccCCCCCHHHHHHHHHHHHhh
Q 027752          169 KELVSEENCFTPFDVERALWSSAIG  193 (219)
Q Consensus       169 ~~L~~~~~~~t~~~VEkalw~~~v~  193 (219)
                      +.+     .+++..+...+|...-+
T Consensus       191 ~~~-----g~~~g~lDl~lW~~~tg  210 (214)
T 3fhf_A          191 EEV-----NLKLSELDLYIWYLRTG  210 (214)
T ss_dssp             HHT-----TCCHHHHHHHHHHHHHS
T ss_pred             HHH-----CCCHHHHHHHHHHHHhC
Confidence            888     47899999999987543

>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=97.70  E-value=0.00034  Score=59.92  Aligned_cols=84  Identities=26%  Similarity=0.290  Sum_probs=64.5

Q ss_pred             cHHHHHHHhh-ccCCCChHHHHHHHHh-hCCCCCCcccHHHHHHh--cC----CCCCCCHHHHHHHHHHHHHHHHHhhcc
Q 027752          103 DLTKAVSELT-VLKGVGPATASAVLAA-YAPDLAPFMSDEAMGAA--LG----HSKDYSLKQYLLFADKLQAKAKELVSE  174 (219)
Q Consensus       103 d~~~al~~L~-~LkGVGPATASaiLa~-~~P~~~pFfsDEa~~~~--~g----~~~kYt~keY~~~~~~l~~~~~~L~~~  174 (219)
                      ++..+++.|+ .|+||||-||++||.. ..++.+| .++-+...+  .|    .+..-|-+.|.++-+.+++.+.++   
T Consensus       123 ~~~~~r~~L~~~l~GVG~kTA~~vL~~~g~~~~~~-VDthv~Ri~~rlg~~~~~~k~~t~k~y~~ie~~~~~~a~~~---  198 (219)
T 3n0u_A          123 DPFQSREFLVRNAKGIGWKEASHFLRNTGVEDLAI-LDKHVLRLMKRHGLIQEIPKGWSKKRYLYVEEILRKVAEAF---  198 (219)
T ss_dssp             CHHHHHHHHHHHSTTCCHHHHHHHHHTTTCCSCCC-CCHHHHHHHHHTTSCSSCCSSCCHHHHHHHHHHHHHHHHHH---
T ss_pred             CcHHHHHHHHHhCCCCCHHHHHHHHHHcCCCCeee-ecHHHHHHHHHcCCCCcCcCcCCHHHHHHHHHHHHHHHHHH---
Confidence            5678999999 9999999999999975 3433333 444455432  23    244678899999999999999888   


Q ss_pred             CCCCCHHHHHHHHHHHHh
Q 027752          175 ENCFTPFDVERALWSSAI  192 (219)
Q Consensus       175 ~~~~t~~~VEkalw~~~v  192 (219)
                        .+++..+...+|...-
T Consensus       199 --g~~~~~ldl~lW~~~~  214 (219)
T 3n0u_A          199 --GESPGKFDLYLWYLVK  214 (219)
T ss_dssp             --TCCHHHHHHHHHHHHH
T ss_pred             --CCCHHHHHHHHHHHHh
Confidence              4889999999998743

>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=96.28  E-value=0.042  Score=50.00  Aligned_cols=61  Identities=18%  Similarity=0.207  Sum_probs=40.8

Q ss_pred             cHHHHHHHhhccCCCChHHHHHHHHh--hCCCCCCcccHHHHH---HhcCC--C----CCCCHHHHHHHHHHH
Q 027752          103 DLTKAVSELTVLKGVGPATASAVLAA--YAPDLAPFMSDEAMG---AALGH--S----KDYSLKQYLLFADKL  164 (219)
Q Consensus       103 d~~~al~~L~~LkGVGPATASaiLa~--~~P~~~pFfsDEa~~---~~~g~--~----~kYt~keY~~~~~~l  164 (219)
                      +...+++.|++|+||||-||.+||..  ..|+.+|+ +--+..   ...|-  .    ...+.+.|.++.+.+
T Consensus       247 ~~~~~~~~L~~LpGIGp~TA~~ill~alg~pd~fpv-DthV~Ri~~r~~gl~~~~~~~k~~~~~~~~~l~~~~  318 (360)
T 2xhi_A          247 SYEEAHKALCILPGVGTCVADKICLMALDKPQAVPV-NVHMWHIAQRDYSWHPTTSQAKGPSPQTNKELGNFF  318 (360)
T ss_dssp             CHHHHHHHHTTSTTCCHHHHHHHHHHHSCCTTCCCC-SHHHHHHHHHHHCCCCSSCSCSSCCHHHHHHHHHHH
T ss_pred             CHHHHHHHHHhCCCCCHHHHHHHHHHhCCCCCEEEe-cHHHHHHHHHHhCcccccccccCCChHHHHHHHHHH
Confidence            34589999999999999999999986  46777775 323322   22341  1    123467787765555

>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=96.09  E-value=0.012  Score=50.21  Aligned_cols=55  Identities=22%  Similarity=0.147  Sum_probs=35.8

Q ss_pred             HHHHHHHhhccCCCChHHHHHHHHh--hCCCCCCcccHH----HHHHhcCCCCCCCHHHHHH
Q 027752          104 LTKAVSELTVLKGVGPATASAVLAA--YAPDLAPFMSDE----AMGAALGHSKDYSLKQYLL  159 (219)
Q Consensus       104 ~~~al~~L~~LkGVGPATASaiLa~--~~P~~~pFfsDE----a~~~~~g~~~kYt~keY~~  159 (219)
                      ...+++.|+.|+||||-||.+||..  ..|+.+|+ +|=    ++..+.|.+..-+.++..+
T Consensus       134 ~~e~~~~L~~l~GIG~~TA~~ill~~lg~pd~fpv-dD~~v~r~~~~~~~~~~~~~~~~~~~  194 (228)
T 3s6i_A          134 NEELIERLTQIKGIGRWTVEMLLIFSLNRDDVMPA-DDLSIRNGYRYLHRLPKIPTKMYVLK  194 (228)
T ss_dssp             HHHHHHHHTTSTTCCHHHHHHHHHHTSCCSSCCCT-TCHHHHHHHHHHTTCSSCCCHHHHHH
T ss_pred             HHHHHHHHHhCCCcCHHHHHHHHHHhCCCCCEEec-ccHHHHHHHHHHhCCCCCCCHHHHHH
Confidence            4568999999999999999999976  46665553 333    3334445333335554443

>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=95.86  E-value=0.0043  Score=50.73  Aligned_cols=73  Identities=18%  Similarity=0.140  Sum_probs=45.9

Q ss_pred             CHHHHHHHHHHHhhcCCCCcchHHHhhhCCHHHHHHHHHHH-H------hhCc----cHHHHHHHhhccCCCChHHHHHH
Q 027752           57 NTTELSKLVRWKLTRGKWRPRLLVFVSSLDDSSVKSASEKA-F------KSLP----DLTKAVSELTVLKGVGPATASAV  125 (219)
Q Consensus        57 tkdEL~~LveWKL~rGkfRP~L~~lV~sN~~~~V~~~t~~A-f------~~l~----d~~~al~~L~~LkGVGPATASai  125 (219)
                      |.++-+.-+-.+|.. + -|+...+.+.+ +++|++..+-. |      .+..    .+....+.|.+|+||||-||.+|
T Consensus        44 T~~~~v~~~~~~l~~-~-~pt~~~la~a~-~~el~~~i~~lG~y~~KAk~i~~~a~~~vp~~~~~L~~LpGVG~yTAdav  120 (161)
T 4e9f_A           44 TSGKMAIPVLWKFLE-K-YPSAEVARTAD-WRDVSELLKPLGLYDLRAKTIVKFSDEYLTKQWKYPIELHGIGKYGNDSY  120 (161)
T ss_dssp             SCHHHHHHHHHHHHH-H-SCSHHHHTTSC-HHHHHHHHGGGSCHHHHHHHHHHHHHHHHHSCCSSGGGSTTCCHHHHHHH
T ss_pred             CcHHHHHHHHHHHHH-H-CCCHHHHhccC-hHhHHhHhhhcCCHHHHHHHHHHHhCCcCCCChhhhhcCCCchHHHHHHH
Confidence            567777777777653 2 37777766555 45555443321 1      1100    13335678899999999999999


Q ss_pred             HHhhCCC
Q 027752          126 LAAYAPD  132 (219)
Q Consensus       126 La~~~P~  132 (219)
                      +++..-+
T Consensus       121 ~~F~~~e  127 (161)
T 4e9f_A          121 RIFCVNE  127 (161)
T ss_dssp             HHHTSSC
T ss_pred             HHHHCCC
Confidence            9986543

>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=95.70  E-value=0.0069  Score=53.46  Aligned_cols=38  Identities=24%  Similarity=0.327  Sum_probs=31.4

Q ss_pred             cHHHHHHHhhccCCCChHHHHHHHHh--hCCCCCCcccHHHH
Q 027752          103 DLTKAVSELTVLKGVGPATASAVLAA--YAPDLAPFMSDEAM  142 (219)
Q Consensus       103 d~~~al~~L~~LkGVGPATASaiLa~--~~P~~~pFfsDEa~  142 (219)
                      +...+++.|++||||||-||..||..  ..|+.+|.  |-..
T Consensus       205 ~~~~~~~~L~~lpGIG~~TA~~ill~~lg~pd~fpv--D~~v  244 (290)
T 3i0w_A          205 NDNECHEELKKFMGVGPQVADCIMLFSMQKYSAFPV--DTWV  244 (290)
T ss_dssp             CHHHHHHHHTTSTTCCHHHHHHHHHHHHCCTTCCCC--CHHH
T ss_pred             CHHHHHHHHHhCCCcCHHHHHHHHHHhCCCCCccee--cHHH
Confidence            46789999999999999999999965  57888886  5443

>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=95.67  E-value=0.019  Score=49.04  Aligned_cols=37  Identities=27%  Similarity=0.412  Sum_probs=28.8

Q ss_pred             HHHHHHhhccCCCChHHHHHHHHhh--CCCCCCcccHHHH
Q 027752          105 TKAVSELTVLKGVGPATASAVLAAY--APDLAPFMSDEAM  142 (219)
Q Consensus       105 ~~al~~L~~LkGVGPATASaiLa~~--~P~~~pFfsDEa~  142 (219)
                      ..+++.|++||||||-||.+||...  .|+.+| .+|=.+
T Consensus       134 ~~~~~~L~~lpGIG~kTA~~ill~alg~pd~~p-vdd~~~  172 (233)
T 2h56_A          134 TTVIEKLTAIKGIGQWTAEMFMMFSLGRLDVLS-VGDVGL  172 (233)
T ss_dssp             HHHHHHHHTSTTCCHHHHHHHHHHTTCCSCCCC-TTCHHH
T ss_pred             HHHHHHHHhCCCcCHHHHHHHHHHhCCCCCeee-CchHHH
Confidence            4789999999999999999999864  566555 344443

>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=95.52  E-value=0.034  Score=47.65  Aligned_cols=33  Identities=21%  Similarity=0.159  Sum_probs=27.2

Q ss_pred             HHHHHHHhhccCCCChHHHHHHHHhh--CCCCCCc
Q 027752          104 LTKAVSELTVLKGVGPATASAVLAAY--APDLAPF  136 (219)
Q Consensus       104 ~~~al~~L~~LkGVGPATASaiLa~~--~P~~~pF  136 (219)
                      ...+++.|+.||||||-||.+||...  .|+.+|+
T Consensus       145 ~~~~~~~L~~l~GIG~~TA~~ill~alg~pd~fpv  179 (232)
T 4b21_A          145 EEELMESLSKIKGVKRWTIEMYSIFTLGRLDIMPA  179 (232)
T ss_dssp             HHHHHHHHTTSTTCCHHHHHHHHHHTSCCSSCCCT
T ss_pred             HHHHHHHHHhCCCcCHHHHHHHHHHhCCCCCeeeC
Confidence            34789999999999999999999874  5666563

>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=94.92  E-value=0.045  Score=47.71  Aligned_cols=44  Identities=23%  Similarity=0.224  Sum_probs=33.1

Q ss_pred             cHHHHHHHhhccCCCChHHHHHHHHhh--CCCCCCcccHHHHHHhcC
Q 027752          103 DLTKAVSELTVLKGVGPATASAVLAAY--APDLAPFMSDEAMGAALG  147 (219)
Q Consensus       103 d~~~al~~L~~LkGVGPATASaiLa~~--~P~~~pFfsDEa~~~~~g  147 (219)
                      +...+++.|++|+||||-||.+||...  .|+.+| .+|-.+.-..+
T Consensus       201 ~~~~~~~~L~~lpGIG~~TA~~ill~~lg~~d~~p-vdd~~~r~~l~  246 (282)
T 1mpg_A          201 DVEQAMKTLQTFPGIGRWTANYFALRGWQAKDVFL-PDDYLIKQRFP  246 (282)
T ss_dssp             CHHHHHHHHTTSTTCCHHHHHHHHHHHSCCSSCCC-TTCHHHHHHST
T ss_pred             CHHHHHHHHhcCCCcCHHHHHHHHHHhCCCCCcCc-cccHHHHHHhc
Confidence            667899999999999999999999864  565544 45555554443

>2yg9_A DNA-3-methyladenine glycosidase II, putative; hydrolase, DNA repair; 1.95A {Deinococcus radiodurans} PDB: 2yg8_A

Probab=94.90  E-value=0.021  Score=48.59  Aligned_cols=33  Identities=30%  Similarity=0.336  Sum_probs=27.3

Q ss_pred             cHHHHHHHhhccCCCChHHHHHHHHhh--CCCCCC
Q 027752          103 DLTKAVSELTVLKGVGPATASAVLAAY--APDLAP  135 (219)
Q Consensus       103 d~~~al~~L~~LkGVGPATASaiLa~~--~P~~~p  135 (219)
                      +...+++.|+.|+||||=||.+||...  .|+.+|
T Consensus       140 ~~~e~~~~L~~l~GIG~~TA~~ill~~lg~~d~fp  174 (225)
T 2yg9_A          140 PDELVIAELVQLPGIGRWTAEMFLLFALARPDVFS  174 (225)
T ss_dssp             CHHHHHHHHHTSTTCCHHHHHHHHHHTSCCSCCCC
T ss_pred             CHHHHHHHHHcCCCCCHHHHHHHHHHhCCCCCeee
Confidence            456789999999999999999999874  566555

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

Probab=94.82  E-value=0.071  Score=47.30  Aligned_cols=35  Identities=26%  Similarity=0.234  Sum_probs=25.4

Q ss_pred             HHHHhhc-cCCCChHHHHHHHHhhCCCCCCcccHHHH
Q 027752          107 AVSELTV-LKGVGPATASAVLAAYAPDLAPFMSDEAM  142 (219)
Q Consensus       107 al~~L~~-LkGVGPATASaiLa~~~P~~~pFfsDEa~  142 (219)
                      .++.|.+ |+||||-||.+||....-.. .|..|--.
T Consensus       126 ~~~~Ll~~LpGIG~kTA~~iL~~a~g~p-~~~VDt~V  161 (287)
T 3n5n_X          126 TAETLQQLLPGVGRYTAGAIASIAFGQA-TGVVDGNV  161 (287)
T ss_dssp             SHHHHHHHSTTCCHHHHHHHHHHHSCCC-CCCCCHHH
T ss_pred             HHHHHHHHcCCCCHHHHHHHHHHhcCCC-CccccHHH
Confidence            5788887 99999999999999864332 23445433

>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=94.26  E-value=0.032  Score=47.12  Aligned_cols=27  Identities=26%  Similarity=0.233  Sum_probs=23.2

Q ss_pred             HHHHHHHhhccCCCChHHHHHHHHhhC
Q 027752          104 LTKAVSELTVLKGVGPATASAVLAAYA  130 (219)
Q Consensus       104 ~~~al~~L~~LkGVGPATASaiLa~~~  130 (219)
                      ...+++.|++||||||-||++||....
T Consensus       116 ~~~~~~~L~~lpGIG~kTA~~il~~a~  142 (218)
T 1pu6_A          116 QEVTREWLLDQKGIGKESADAILCYAC  142 (218)
T ss_dssp             HHCCHHHHHTSTTCCHHHHHHHHHHTT
T ss_pred             chHHHHHHHcCCCcCHHHHHHHHHHHC
Confidence            445788899999999999999999753

>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=94.06  E-value=0.054  Score=45.71  Aligned_cols=25  Identities=28%  Similarity=0.319  Sum_probs=21.9

Q ss_pred             HHHHHhhccCCCChHHHHHHHHhhC
Q 027752          106 KAVSELTVLKGVGPATASAVLAAYA  130 (219)
Q Consensus       106 ~al~~L~~LkGVGPATASaiLa~~~  130 (219)
                      .+++.|++||||||-||.+||....
T Consensus       112 ~~~~~L~~lpGIG~~TA~~il~~~~  136 (221)
T 1kea_A          112 RNRKAILDLPGVGKYTCAAVMCLAF  136 (221)
T ss_dssp             SCHHHHHTSTTCCHHHHHHHHHHTT
T ss_pred             HHHHHHHhCCCCcHHHHHHHHHHhc
Confidence            4578899999999999999999753

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

Probab=94.01  E-value=0.12  Score=43.15  Aligned_cols=24  Identities=38%  Similarity=0.475  Sum_probs=21.5

Q ss_pred             HHHHHhhccCCCChHHHHHHHHhh
Q 027752          106 KAVSELTVLKGVGPATASAVLAAY  129 (219)
Q Consensus       106 ~al~~L~~LkGVGPATASaiLa~~  129 (219)
                      .+++.|++|+||||-||.+||...
T Consensus       106 ~~~~~L~~l~GIG~~tA~~il~~~  129 (211)
T 2abk_A          106 EDRAALEALPGVGRKTANVVLNTA  129 (211)
T ss_dssp             SCHHHHHHSTTCCHHHHHHHHHHH
T ss_pred             HHHHHHHhCCCCChHHHHHHHHHH
Confidence            467889999999999999999974

>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=93.68  E-value=0.051  Score=47.79  Aligned_cols=37  Identities=32%  Similarity=0.405  Sum_probs=28.3

Q ss_pred             HHHHHHhhccCCCChHHHHHHHHhh-CCCCCCcccHHHH
Q 027752          105 TKAVSELTVLKGVGPATASAVLAAY-APDLAPFMSDEAM  142 (219)
Q Consensus       105 ~~al~~L~~LkGVGPATASaiLa~~-~P~~~pFfsDEa~  142 (219)
                      ..+++.|++|+||||-||.+||... .|+.+| .+|=.+
T Consensus       206 ~e~~~~L~~lpGIG~~TA~~ill~~lg~d~fp-vdD~~~  243 (295)
T 2jhn_A          206 EEAYEYLTSFKGIGRWTAELVLSIALGKNVFP-ADDLGV  243 (295)
T ss_dssp             HHHHHHHHTSTTCCHHHHHHHHHHTTCCCCCC-TTCHHH
T ss_pred             HHHHHHHhcCCCcCHHHHHHHHHHccCCCccc-chHHHH
Confidence            6789999999999999999999852 366555 334433

>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=93.22  E-value=0.08  Score=44.92  Aligned_cols=36  Identities=28%  Similarity=0.377  Sum_probs=26.9

Q ss_pred             HHHHHhhccCCCChHHHHHHHHhh--CCCCCCcccHHHHH
Q 027752          106 KAVSELTVLKGVGPATASAVLAAY--APDLAPFMSDEAMG  143 (219)
Q Consensus       106 ~al~~L~~LkGVGPATASaiLa~~--~P~~~pFfsDEa~~  143 (219)
                      .+++.|++|+||||-||.+||...  .| .+| .++-+..
T Consensus       110 ~~~~~L~~lpGIG~~TA~~il~~a~g~~-~~~-vD~~v~R  147 (226)
T 1orn_A          110 RDRDELMKLPGVGRKTANVVVSVAFGVP-AIA-VDTHVER  147 (226)
T ss_dssp             SCHHHHTTSTTCCHHHHHHHHHHHHCCC-CCC-CCHHHHH
T ss_pred             HHHHHHHHCCCccHHHHHHHHHHHCCCc-eee-eCHHHHH
Confidence            468899999999999999999874  44 333 4554544

>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=93.02  E-value=0.088  Score=44.43  Aligned_cols=24  Identities=38%  Similarity=0.573  Sum_probs=21.5

Q ss_pred             HHHHHhhccCCCChHHHHHHHHhh
Q 027752          106 KAVSELTVLKGVGPATASAVLAAY  129 (219)
Q Consensus       106 ~al~~L~~LkGVGPATASaiLa~~  129 (219)
                      .+++.|++|+||||-||.+||...
T Consensus       106 ~~~~~L~~lpGIG~~TA~~il~~a  129 (225)
T 1kg2_A          106 ETFEEVAALPGVGRSTAGAILSLS  129 (225)
T ss_dssp             CSHHHHHTSTTCCHHHHHHHHHHH
T ss_pred             HHHHHHhcCCCCcHHHHHHHHHHh
Confidence            367899999999999999999875

>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=92.40  E-value=0.11  Score=46.75  Aligned_cols=38  Identities=34%  Similarity=0.409  Sum_probs=27.4

Q ss_pred             HHHHHhhccCCCChHHHHHHHHhhCCCCCCcccHHHHH
Q 027752          106 KAVSELTVLKGVGPATASAVLAAYAPDLAPFMSDEAMG  143 (219)
Q Consensus       106 ~al~~L~~LkGVGPATASaiLa~~~P~~~pFfsDEa~~  143 (219)
                      .+++.|++|+||||-||.+||+...-..++..+.-+..
T Consensus       115 ~~~~~L~~l~GIG~~tA~~il~~~~~~~~~~vD~~v~R  152 (369)
T 3fsp_A          115 DDPDEFSRLKGVGPYTVGAVLSLAYGVPEPAVDGNVMR  152 (369)
T ss_dssp             CSHHHHHTSTTCCHHHHHHHHHHHHCCCCCCCCHHHHH
T ss_pred             hHHHHHhcCCCcCHHHHHHHHHHHCCCCcccccHHHHH
Confidence            46888999999999999999998643333434443433

>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=91.72  E-value=0.045  Score=41.37  Aligned_cols=37  Identities=22%  Similarity=0.333  Sum_probs=30.4

Q ss_pred             HHHHHhhccCCCChHHHHHHHHhhCCCCCCcccHHHHHHhcC
Q 027752          106 KAVSELTVLKGVGPATASAVLAAYAPDLAPFMSDEAMGAALG  147 (219)
Q Consensus       106 ~al~~L~~LkGVGPATASaiLa~~~P~~~pFfsDEa~~~~~g  147 (219)
                      +..+.|+.|+||||++|..|+.     +-||-|-|-+.-+.|
T Consensus        23 As~~eL~~lpGIG~~~A~~IV~-----~GpF~s~edL~~V~G   59 (97)
T 3arc_U           23 TNIAAFIQYRGLYPTLAKLIVK-----NAPYESVEDVLNIPG   59 (97)
T ss_dssp             SCGGGGGGSTTCTTHHHHHHHH-----HCCCSSGGGGGGCTT
T ss_pred             CCHHHHhHCCCCCHHHHHHHHH-----cCCCCCHHHHHhccC
Confidence            4567899999999999999999     358888777766655

>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=91.51  E-value=0.048  Score=43.74  Aligned_cols=38  Identities=21%  Similarity=0.315  Sum_probs=30.5

Q ss_pred             HHHHHhhccCCCChHHHHHHHHhhCCCCCCcccHHHHHHhcCC
Q 027752          106 KAVSELTVLKGVGPATASAVLAAYAPDLAPFMSDEAMGAALGH  148 (219)
Q Consensus       106 ~al~~L~~LkGVGPATASaiLa~~~P~~~pFfsDEa~~~~~g~  148 (219)
                      +..+.|+.|+||||++|.+|.     ++.||-|=|=..-+.|-
T Consensus        60 A~~~eL~~LpGiGp~~A~~II-----~~GpF~svedL~~V~GI   97 (134)
T 1s5l_U           60 TNIAAFIQYRGLYPTLAKLIV-----KNAPYESVEDVLNIPGL   97 (134)
T ss_dssp             SCGGGGGGSTTCTHHHHHHHH-----HTCCCSSGGGGGGCTTC
T ss_pred             cCHHHHHHCCCCCHHHHHHHH-----HcCCCCCHHHHHhCCCC
Confidence            457789999999999999999     35688887666667663

>2duy_A Competence protein comea-related protein; helix-hairpin-helix, structural genomics, NPPSFA; 1.75A {Thermus thermophilus} SCOP: a.60.2.7

Probab=88.67  E-value=0.24  Score=34.60  Aligned_cols=36  Identities=28%  Similarity=0.522  Sum_probs=26.5

Q ss_pred             HHHHhhccCCCChHHHHHHHHhhCCCCCCcccHHHHHHhcC
Q 027752          107 AVSELTVLKGVGPATASAVLAAYAPDLAPFMSDEAMGAALG  147 (219)
Q Consensus       107 al~~L~~LkGVGPATASaiLa~~~P~~~pFfsDEa~~~~~g  147 (219)
                      ....|..++||||.+|..|+...     +|-+-+-+..+.|
T Consensus        25 ~~~~L~~ipGIG~~~A~~Il~~r-----~~~s~~eL~~v~G   60 (75)
T 2duy_A           25 SLEELMALPGIGPVLARRIVEGR-----PYARVEDLLKVKG   60 (75)
T ss_dssp             CHHHHTTSTTCCHHHHHHHHHTC-----CCSSGGGGGGSTT
T ss_pred             CHHHHHhCCCCCHHHHHHHHHHc-----ccCCHHHHHhCCC
Confidence            45678899999999999999964     5555554444544

>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=87.72  E-value=0.96  Score=32.63  Aligned_cols=42  Identities=19%  Similarity=0.309  Sum_probs=27.9

Q ss_pred             hhCCHHHHHHHHHHHHhhCccHHHHHHHhhccCCCChHHHHHHHHhh
Q 027752           83 SSLDDSSVKSASEKAFKSLPDLTKAVSELTVLKGVGPATASAVLAAY  129 (219)
Q Consensus        83 ~sN~~~~V~~~t~~Af~~l~d~~~al~~L~~LkGVGPATASaiLa~~  129 (219)
                      ++++++.+..-...-+     ....+..|+.++||||.+|-.||..+
T Consensus        11 ~~~~~~~~~~~~~~~~-----~~~~~~~L~~IpgIG~~~A~~Ll~~f   52 (91)
T 2a1j_B           11 SQDPADLLMEKLEQDF-----VSRVTECLTTVKSVNKTDSQTLLTTF   52 (91)
T ss_dssp             --CCSHHHHHHHHHHH-----HHHHHHHHTTSTTCCHHHHHHHHHHH
T ss_pred             ccCCHHHHhhhccCCH-----HHHHHHHHHcCCCCCHHHHHHHHHHC
Confidence            4566666665544433     33456678889999999999888864

>2i5h_A Hypothetical protein AF1531; PFAM:DUF655, PSI-2, structural genomics, protein structure initiative; 1.74A {Archaeoglobus fulgidus} SCOP: e.71.1.1

Probab=87.66  E-value=0.13  Score=43.90  Aligned_cols=63  Identities=22%  Similarity=0.328  Sum_probs=41.4

Q ss_pred             hHHHhhhCCHHHHHHHHHHHHhhCccHHHHHHHhhccCCCChHHHHHHHHhhCCCCCCcccHHHHHH-hcC
Q 027752           78 LLVFVSSLDDSSVKSASEKAFKSLPDLTKAVSELTVLKGVGPATASAVLAAYAPDLAPFMSDEAMGA-ALG  147 (219)
Q Consensus        78 L~~lV~sN~~~~V~~~t~~Af~~l~d~~~al~~L~~LkGVGPATASaiLa~~~P~~~pFfsDEa~~~-~~g  147 (219)
                      +.+.|..|....|. .    |+....+.+.+..|..|+||||++|-+|+.--.-  -||-|=|-+.- +.|
T Consensus       106 v~~iV~~~E~~fv~-f----~n~a~pITA~~~eL~~LpGIG~k~A~~IIeyRe~--G~F~s~eDL~~RV~G  169 (205)
T 2i5h_A          106 IEHIIKQDEKKYVD-F----FNKADSITTRMHQLELLPGVGKKMMWAIIEERKK--RPFESFEDIAQRVKG  169 (205)
T ss_dssp             HHHHHHTTHHHHHH-H----HC--CCBCSSSBGGGGSTTCCHHHHHHHHHHHHH--SCCCSHHHHHHHSTT
T ss_pred             HHHHHHhchhhhhh-h----ccccCCccCCHHHHhcCCCcCHHHHHHHHHHHhc--CCCCCHHHHHHhcCC
Confidence            34555555444443 2    3333334667778999999999999999997543  59999665543 655

>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=86.69  E-value=0.46  Score=32.40  Aligned_cols=23  Identities=26%  Similarity=0.442  Sum_probs=19.3

Q ss_pred             HHHhhccCCCChHHHHHHHHhhC
Q 027752          108 VSELTVLKGVGPATASAVLAAYA  130 (219)
Q Consensus       108 l~~L~~LkGVGPATASaiLa~~~  130 (219)
                      .+.|+.++||||.+|..|.+...
T Consensus        45 ~~~L~~i~Gig~~~a~~i~~~~~   67 (75)
T 1x2i_A           45 VAELMKVEGIGEKIAKEIRRVIT   67 (75)
T ss_dssp             HHHHTTSTTCCHHHHHHHHHHHH
T ss_pred             HHHHhcCCCCCHHHHHHHHHHHh
Confidence            56788999999999999988764

>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=83.49  E-value=0.49  Score=40.22  Aligned_cols=29  Identities=31%  Similarity=0.331  Sum_probs=21.4

Q ss_pred             HHHHHHHhhccCCCChHHHHHHHHhhCCC
Q 027752          104 LTKAVSELTVLKGVGPATASAVLAAYAPD  132 (219)
Q Consensus       104 ~~~al~~L~~LkGVGPATASaiLa~~~P~  132 (219)
                      .+.-+..|..++||||.||-+||+.+.|+
T Consensus        83 Er~lf~~L~sv~GIGpk~A~~Ils~~~~~  111 (212)
T 2ztd_A           83 TRDLFLTLLSVSGVGPRLAMAALAVHDAP  111 (212)
T ss_dssp             HHHHHHHHHTSTTCCHHHHHHHHHHSCHH
T ss_pred             HHHHHHHhcCcCCcCHHHHHHHHHhCCHH
Confidence            44455667778888888888888876664

>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=81.30  E-value=0.45  Score=35.00  Aligned_cols=49  Identities=24%  Similarity=0.350  Sum_probs=32.0

Q ss_pred             HHHHhhccCCCChHHHHHHHHhhCCCCCCcccHHHHHHhcCCCCCCCHHHHHHH
Q 027752          107 AVSELTVLKGVGPATASAVLAAYAPDLAPFMSDEAMGAALGHSKDYSLKQYLLF  160 (219)
Q Consensus       107 al~~L~~LkGVGPATASaiLa~~~P~~~pFfsDEa~~~~~g~~~kYt~keY~~~  160 (219)
                      ....|..++||||.+|..|+...... -+|-+-+-+..+.|    .+.+-+..+
T Consensus        38 ~~~~L~~ipGIG~~~A~~Il~~r~~~-g~f~s~edL~~v~G----ig~k~~~~l   86 (98)
T 2edu_A           38 SARDLRSLQRIGPKKAQLIVGWRELH-GPFSQVEDLERVEG----ITGKQMESF   86 (98)
T ss_dssp             CHHHHHHSTTCCHHHHHHHHHHHHHH-CCCSSGGGGGGSTT----CCHHHHHHH
T ss_pred             CHHHHHHCCCCCHHHHHHHHHHHHhc-CCcCCHHHHHhCCC----CCHHHHHHH
Confidence            35578899999999999999986432 26655444444444    344444444

>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=81.21  E-value=1.3  Score=30.98  Aligned_cols=22  Identities=18%  Similarity=0.365  Sum_probs=15.0

Q ss_pred             HHHhhccCCCChHHHHHHHHhh
Q 027752          108 VSELTVLKGVGPATASAVLAAY  129 (219)
Q Consensus       108 l~~L~~LkGVGPATASaiLa~~  129 (219)
                      .+.|++++||||.+|..|.+..
T Consensus        55 ~eeL~~i~GIG~~~a~~I~~~~   76 (78)
T 1kft_A           55 VEEIAKVPGISQGLAEKIFWSL   76 (78)
T ss_dssp             HHHHTTSSSTTSHHHHHHHHHH
T ss_pred             HHHHHHCCCCCHHHHHHHHHHH
Confidence            4566777777777777776653

>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=80.48  E-value=0.93  Score=37.75  Aligned_cols=27  Identities=37%  Similarity=0.518  Sum_probs=21.9

Q ss_pred             HHHHHHhhccCCCChHHHHHHHHhhCC
Q 027752          105 TKAVSELTVLKGVGPATASAVLAAYAP  131 (219)
Q Consensus       105 ~~al~~L~~LkGVGPATASaiLa~~~P  131 (219)
                      +.-+..|..++||||.||-+||+.+.|
T Consensus        68 k~~f~~L~~v~GIGpk~A~~iL~~f~~   94 (191)
T 1ixr_A           68 LALFELLLSVSGVGPKVALALLSALPP   94 (191)
T ss_dssp             HHHHHHHHSSSCCCHHHHHHHHHHSCH
T ss_pred             HHHHHHHhcCCCcCHHHHHHHHHhCCh
Confidence            445567888999999999999998665

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

No hit with e-value below 0.005

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	219
d2noha1	190	8-oxoguanine glycosylase {Human (Homo sapiens) [Ta	96.94
d1keaa_	217	Thymine-DNA glycosylase {Archaeon Methanobacterium	96.33
d1rrqa1	221	Catalytic domain of MutY {Bacillus stearothermophi	96.3
d1orna_	214	Endonuclease III {Escherichia coli [TaxId: 562]}	96.26
d1kg2a_	224	Catalytic domain of MutY {Escherichia coli [TaxId:	96.02
d2abka_	211	Endonuclease III {Escherichia coli [TaxId: 562]}	95.88
d1mpga1	183	3-Methyladenine DNA glycosylase II (gene alkA or a	95.62
d1pu6a_	217	3-Methyladenine DNA glycosylase III (MagIII) {Heli	94.22
d2fmpa2	57	DNA polymerase beta {Human (Homo sapiens) [TaxId:	93.9
d1ngna_	144	Mismatch-specific thymine glycosylase domain of th	93.15
d1cuka2	78	DNA helicase RuvA subunit, middle domain {Escheric	91.42
d1pzna1	61	DNA repair protein Rad51, N-terminal domain {Archa	90.92
d1ixra1	73	DNA helicase RuvA subunit, middle domain {Thermus	90.88
d2axtu1	98	Photosystem II 12 kDa extrinsic protein PsbU {Ther	90.8
d1bvsa2	71	DNA helicase RuvA subunit, middle domain {Mycobact	90.72
d2a1jb1	78	DNA excision repair protein ERCC-1 {Human (Homo sa	90.4
d1jmsa3	60	Terminal deoxynucleotidyl transferase {Mouse (Mus	90.23
d2bcqa2	57	DNA polymerase lambda {Human (Homo sapiens) [TaxId	88.94
d2i1qa1	60	DNA repair protein Rad51, N-terminal domain {Archa	88.14
d2bgwa1	70	DNA repair endonuclease XPF {Aeropyrum pernix [Tax	87.89
d1cuka2	78	DNA helicase RuvA subunit, middle domain {Escheric	87.14
d1ixra1	73	DNA helicase RuvA subunit, middle domain {Thermus	86.57
d1bvsa2	71	DNA helicase RuvA subunit, middle domain {Mycobact	83.8
d2a1ja1	62	DNA repair endonuclease XPF {Human (Homo sapiens)	83.68
d2a1jb1	78	DNA excision repair protein ERCC-1 {Human (Homo sa	83.38
d1kfta_	56	Excinuclease UvrC C-terminal domain {Escherichia c	83.14
d1kfta_	56	Excinuclease UvrC C-terminal domain {Escherichia c	82.95
d2fmpa1	82	DNA polymerase beta, N-terminal (8 kD)-domain {Hum	81.19
d2duya1	65	Uncharacterized protein TTHA1967 {Thermus thermoph	80.92
d2bgwa1	70	DNA repair endonuclease XPF {Aeropyrum pernix [Tax	80.46

>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=96.94  E-value=0.0012  Score=52.63  Aligned_cols=63  Identities=19%  Similarity=0.235  Sum_probs=43.3

Q ss_pred             cHHHHHHHhhccCCCChHHHHHHHHh--hCCCCCCcccHHHHHHh---cC------CCCCCCHHHHHHHHHHHHH
Q 027752          103 DLTKAVSELTVLKGVGPATASAVLAA--YAPDLAPFMSDEAMGAA---LG------HSKDYSLKQYLLFADKLQA  166 (219)
Q Consensus       103 d~~~al~~L~~LkGVGPATASaiLa~--~~P~~~pFfsDEa~~~~---~g------~~~kYt~keY~~~~~~l~~  166 (219)
                      +...+++.|++||||||-||.+||..  ..|+.+|. +.-+...+   .|      ...+-+.+.|.++.+..++
T Consensus        97 ~~~~~~~~L~~l~GIG~wTA~~il~~~~~~~d~fpv-D~~v~R~~~r~~~~~~~~~~~k~~~~~~~~~~~~~~~~  170 (190)
T d2noha1          97 SYEEAHKALCILPGVGTQVADCICLMALDKPQAVPV-DVHMWHIAQRDYSWHPTTSQAKGPSPQTNKELGNFFRS  170 (190)
T ss_dssp             CHHHHHHHHTTSTTCCHHHHHHHHHHHSCCTTCCCC-CHHHHHHHHHHHCCCCSSSSCSSSCHHHHHHHHHHHHH
T ss_pred             CcHHHHHHHHHcCCchHHHHHHHHHHHcCCCCeEee-cHHHHHHHHHHhcccCcchhhccccHHHHHHHHHHHHH
Confidence            45789999999999999999998886  46777785 55554433   23      1224466777765544433

>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=96.33  E-value=0.0021  Score=52.54  Aligned_cols=84  Identities=15%  Similarity=0.133  Sum_probs=53.1

Q ss_pred             CHHHHHHHHHHHhhcCCCCcchHHHhhhCCHHHHHHHHHHH-H------hh------Cc-----cHHHHHHHhhccCCCC
Q 027752           57 NTTELSKLVRWKLTRGKWRPRLLVFVSSLDDSSVKSASEKA-F------KS------LP-----DLTKAVSELTVLKGVG  118 (219)
Q Consensus        57 tkdEL~~LveWKL~rGkfRP~L~~lV~sN~~~~V~~~t~~A-f------~~------l~-----d~~~al~~L~~LkGVG  118 (219)
                      |.++.+.-+--+|. .+| |+...+.+.+ +++|+++.+-+ |      .+      +-     .+....+.|.+|+|||
T Consensus        46 T~~~~v~~~~~~l~-~~~-pt~~~la~a~-~~~l~~~i~~~G~~~~KA~~l~~~a~~i~~~~~g~~p~~~~~L~~LpGVG  122 (217)
T d1keaa_          46 TTAGHVKKIYDKFF-VKY-KCFEDILKTP-KSEIAKDIKEIGLSNQRAEQLKELARVVINDYGGRVPRNRKAILDLPGVG  122 (217)
T ss_dssp             SCHHHHHHHHHHHH-HHC-CSHHHHHHSC-HHHHHHHTGGGSCHHHHHHHHHHHHHHHHHHHTTSCCSCHHHHHTSTTCC
T ss_pred             CcHHHHHHHHHHHH-Hhc-ccHHHHHHhh-HHHHHHHHHHHHhhhHHHHHHHHHHHHHHhhccCCcchhhHHHHHHHhhh
Confidence            57777777766664 234 7877777775 55566443221 1      10      00     1233578899999999


Q ss_pred             hHHHHHHHHhhCCCCCCcccHHHHH
Q 027752          119 PATASAVLAAYAPDLAPFMSDEAMG  143 (219)
Q Consensus       119 PATASaiLa~~~P~~~pFfsDEa~~  143 (219)
                      |-||++||+...-..++..++-+..
T Consensus       123 ~kTA~~il~~~~~~~~~~vD~~v~R  147 (217)
T d1keaa_         123 KYTCAAVMCLAFGKKAAMVDANFVR  147 (217)
T ss_dssp             HHHHHHHHHHTTCCCCCCCCHHHHH
T ss_pred             hhhhHHHHHHhcCCcccccccchhh
Confidence            9999999999765444445555544

>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=96.30  E-value=0.0023  Score=52.21  Aligned_cols=38  Identities=34%  Similarity=0.413  Sum_probs=28.1

Q ss_pred             HHHHHhhccCCCChHHHHHHHHhhCCCCCCcccHHHHH
Q 027752          106 KAVSELTVLKGVGPATASAVLAAYAPDLAPFMSDEAMG  143 (219)
Q Consensus       106 ~al~~L~~LkGVGPATASaiLa~~~P~~~pFfsDEa~~  143 (219)
                      ...+.|.+|+||||-||++||+...-..++..+.-+..
T Consensus       104 ~~~~~Ll~LpGIG~kTA~~il~~a~~~p~~~VDt~v~R  141 (221)
T d1rrqa1         104 DDPDEFSRLKGVGPYTVGAVLSLAYGVPEPAVNGNVMR  141 (221)
T ss_dssp             CSHHHHHTSTTCCHHHHHHHHHHHTCCCCCCCCHHHHH
T ss_pred             hHHHHHHHHHHhhhHHHHHHHHHHhcCcccccCccHHH
Confidence            35678999999999999999999765444444444443

>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=96.26  E-value=0.0059  Score=49.47  Aligned_cols=25  Identities=36%  Similarity=0.380  Sum_probs=21.9

Q ss_pred             HHHHhhccCCCChHHHHHHHHhhCC
Q 027752          107 AVSELTVLKGVGPATASAVLAAYAP  131 (219)
Q Consensus       107 al~~L~~LkGVGPATASaiLa~~~P  131 (219)
                      ..+.|.+|+||||-||++||+...-
T Consensus       108 ~~~~L~~LpGVG~kTA~~il~~a~~  132 (214)
T d1orna_         108 DRDELMKLPGVGRKTANVVVSVAFG  132 (214)
T ss_dssp             CHHHHTTSTTCCHHHHHHHHHHHHC
T ss_pred             CHHHHHhCcCcccchHHHHHHHHhc
Confidence            4678999999999999999998654

>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=96.02  E-value=0.0033  Score=51.35  Aligned_cols=72  Identities=15%  Similarity=0.145  Sum_probs=44.0

Q ss_pred             CHHHHHHHHHHHhhcCCCCcchHHHhhhCCHHHHHHHHHHHH------h------hC-----ccHHHHHHHhhccCCCCh
Q 027752           57 NTTELSKLVRWKLTRGKWRPRLLVFVSSLDDSSVKSASEKAF------K------SL-----PDLTKAVSELTVLKGVGP  119 (219)
Q Consensus        57 tkdEL~~LveWKL~rGkfRP~L~~lV~sN~~~~V~~~t~~Af------~------~l-----~d~~~al~~L~~LkGVGP  119 (219)
                      |+++-+.-+-=+|- .+| |+...+.+.+ +++|+++.+-+.      +      .+     .++....+.|.+|+||||
T Consensus        43 T~~~~v~~~~~~l~-~~~-pt~~~la~a~-~~~l~~~i~~~g~~~ka~~l~~~~~~i~~~~~g~vp~~~~~L~~LpGVG~  119 (224)
T d1kg2a_          43 TQVATVIPYFERFM-ARF-PTVTDLANAP-LDEVLHLWTGLGYYARARNLHKAAQQVATLHGGKFPETFEEVAALPGVGR  119 (224)
T ss_dssp             SCHHHHHHHHHHHH-HHC-SSHHHHHHSC-HHHHHHHHTTSCCTHHHHHHHHHHHHHHHHSTTSCCCSHHHHHTSTTCCH
T ss_pred             CcHHHHHHHHHHHH-HHh-ccHHHHHHhh-HHHHHhHhhhhhHHHHHHHHHHhhhhhhhhccCCcchHHHHHHHHHhhhh
Confidence            45666555433342 223 7777777775 556665543321      0      00     012334678999999999


Q ss_pred             HHHHHHHHhhCC
Q 027752          120 ATASAVLAAYAP  131 (219)
Q Consensus       120 ATASaiLa~~~P  131 (219)
                      -||.+||+...-
T Consensus       120 kTA~~il~~a~~  131 (224)
T d1kg2a_         120 STAGAILSLSLG  131 (224)
T ss_dssp             HHHHHHHHHHHC
T ss_pred             hhhHHHHHHhhh
Confidence            999999998653

>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=95.88  E-value=0.0076  Score=48.81  Aligned_cols=83  Identities=18%  Similarity=0.066  Sum_probs=47.9

Q ss_pred             CHHHHHHHHHHHhhcCCCCcchHHHhhhCCHHHHHHHHHH-HH------hh------Cc-----cHHHHHHHhhccCCCC
Q 027752           57 NTTELSKLVRWKLTRGKWRPRLLVFVSSLDDSSVKSASEK-AF------KS------LP-----DLTKAVSELTVLKGVG  118 (219)
Q Consensus        57 tkdEL~~LveWKL~rGkfRP~L~~lV~sN~~~~V~~~t~~-Af------~~------l~-----d~~~al~~L~~LkGVG  118 (219)
                      |+++-+.-+-=+| ..+| |+...+.+.+ .++|+++.+- +|      .+      +.     .+....+.|..|+|||
T Consensus        42 T~~~~v~~~~~~l-~~~~-~t~~~la~a~-~~~l~~~i~~~G~y~~Ka~~l~~~a~~i~~~~~g~~p~~~~~L~~LpGVG  118 (211)
T d2abka_          42 ATDVSVNKATAKL-YPVA-NTPAAMLELG-VEGVKTYIKTIGLYNSKAENIIKTCRILLEQHNGEVPEDRAALEALPGVG  118 (211)
T ss_dssp             SCHHHHHHHHHHH-TTTC-CSHHHHHHHH-HHHHHHHHTTSTTHHHHHHHHHHHHHHHHHHTTTSCCSCHHHHHHSTTCC
T ss_pred             chHHHHHHHHHHH-HHhc-cChHHHHhhh-HhHhHHHHHHhhhhhhHHHHHHHHHHHHHHHhcCchhHHHHHHHHHHhhc
Confidence            4566665444444 3444 8888887775 4445443321 11      10      00     1223567788999999


Q ss_pred             hHHHHHHHHhhCCCCCCcccHHHH
Q 027752          119 PATASAVLAAYAPDLAPFMSDEAM  142 (219)
Q Consensus       119 PATASaiLa~~~P~~~pFfsDEa~  142 (219)
                      |-||++||+......++..+--+.
T Consensus       119 ~~TA~~Il~~a~~~p~~~vD~nv~  142 (211)
T d2abka_         119 RKTANVVLNTAFGWPTIAVDTHIF  142 (211)
T ss_dssp             HHHHHHHHHHHHCCCCCCCCHHHH
T ss_pred             hHHHHHHHHHHhcCccccccHHHH
Confidence            999999999876544333333333

>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=95.62  E-value=0.0042  Score=49.25  Aligned_cols=40  Identities=25%  Similarity=0.269  Sum_probs=31.3

Q ss_pred             cHHHHHHHhhccCCCChHHHHHHHHh--hCCCCCCcccHHHHH
Q 027752          103 DLTKAVSELTVLKGVGPATASAVLAA--YAPDLAPFMSDEAMG  143 (219)
Q Consensus       103 d~~~al~~L~~LkGVGPATASaiLa~--~~P~~~pFfsDEa~~  143 (219)
                      +...+++.|+.|+||||=||..||-.  ..|+.+| ..|=.+.
T Consensus       102 ~~~e~~~~L~~l~GIGpwTAd~illf~lg~~dvfP-~~D~~lr  143 (183)
T d1mpga1         102 DVEQAMKTLQTFPGIGRWTANYFALRGWQAKDVFL-PDDYLIK  143 (183)
T ss_dssp             CHHHHHHHHTTSTTCCHHHHHHHHHHHSCCSSCCC-TTCHHHH
T ss_pred             cHHHHHHHHHHhhcccHHHHHHHHHhhCCCCCccc-cchHHHH
Confidence            57789999999999999999999865  5687766 3343333

>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=94.22  E-value=0.031  Score=45.32  Aligned_cols=39  Identities=21%  Similarity=0.134  Sum_probs=28.1

Q ss_pred             HHHHHHHhhccCCCChHHHHHHHHhhCCCCCCcccHHHHH
Q 027752          104 LTKAVSELTVLKGVGPATASAVLAAYAPDLAPFMSDEAMG  143 (219)
Q Consensus       104 ~~~al~~L~~LkGVGPATASaiLa~~~P~~~pFfsDEa~~  143 (219)
                      ...+.+.|+.||||||=||++||....-.. .|.-|.-..
T Consensus       115 ~~~~~~~L~~lpGIG~kTA~~vl~~~~~~~-~~~vD~hv~  153 (217)
T d1pu6a_         115 QEVTREWLLDQKGIGKESADAILCYACAKE-VMVVDKYSY  153 (217)
T ss_dssp             HHCCHHHHHTSTTCCHHHHHHHHHHTTCCS-CCCCCHHHH
T ss_pred             cHHHHHHHHHHhhhhhHHHHHHHHHHcCCe-eeecChHHH
Confidence            456788999999999999999998854322 333455443

>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=93.90  E-value=0.014  Score=38.64  Aligned_cols=25  Identities=24%  Similarity=0.493  Sum_probs=22.0

Q ss_pred             HHHHHHHhhccCCCChHHHHHHHHh
Q 027752          104 LTKAVSELTVLKGVGPATASAVLAA  128 (219)
Q Consensus       104 ~~~al~~L~~LkGVGPATASaiLa~  128 (219)
                      -..+|+.|+++-||||+||.-+..-
T Consensus         2 ~~~~l~~l~~I~GvGp~~A~~l~~~   26 (57)
T d2fmpa2           2 TSSSINFLTRVSGIGPSAARKFVDE   26 (57)
T ss_dssp             HHHHHHHHTTSTTCCHHHHHHHHHT
T ss_pred             cchHHHHHhccccccHHHHHHHHHh
Confidence            4578999999999999999988765

>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=93.15  E-value=0.025  Score=43.19  Aligned_cols=72  Identities=15%  Similarity=0.143  Sum_probs=42.5

Q ss_pred             CHHHHHHHHHHHhhcCCCCcchHHHhhhCCHHHHHHHHHHH-H-----hhCccHH-----HHHHHhhccCCCChHHHHHH
Q 027752           57 NTTELSKLVRWKLTRGKWRPRLLVFVSSLDDSSVKSASEKA-F-----KSLPDLT-----KAVSELTVLKGVGPATASAV  125 (219)
Q Consensus        57 tkdEL~~LveWKL~rGkfRP~L~~lV~sN~~~~V~~~t~~A-f-----~~l~d~~-----~al~~L~~LkGVGPATASai  125 (219)
                      |.++-+.-+-.+|-. + -|+...+.+.+ .++++++.+.+ |     +.+.++.     ...+.|++|+||||-||.++
T Consensus        33 T~~~~v~~v~~~L~~-~-~pt~e~la~a~-~~el~~~Ir~~G~~~~KAk~I~~~a~~~ip~~~~~l~~LpGVG~~tad~~  109 (144)
T d1ngna_          33 TSGKMAIPVLWEFLE-K-YPSAEVARAAD-WRDVSELLKPLGLYDLRAKTIIKFSDEYLTKQWRYPIELHGIGKYGNDSY  109 (144)
T ss_dssp             SCHHHHHHHHHHHHH-H-SCSHHHHHHSC-HHHHHHHTGGGSCHHHHHHHHHHHHHHHHHSCCSSGGGSTTCCHHHHHHH
T ss_pred             CCHHHHHHHHHHHHH-h-CCchhhhhccC-HHHHHHHHHhhhhHHHHHHHHHHHHhhHhhhhhhhHHhcCCccHHHHHHH
Confidence            567777777777743 1 36666665544 44555444322 1     0111111     23445889999999999998


Q ss_pred             HHhhCC
Q 027752          126 LAAYAP  131 (219)
Q Consensus       126 La~~~P  131 (219)
                      +.+..-
T Consensus       110 ~if~~~  115 (144)
T d1ngna_         110 RIFCVN  115 (144)
T ss_dssp             HHHTSS
T ss_pred             HHHHcC
Confidence            887543

>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=91.42  E-value=0.039  Score=38.49  Aligned_cols=29  Identities=31%  Similarity=0.425  Sum_probs=24.6

Q ss_pred             HHHHHHHhhccCCCChHHHHHHHHhhCCC
Q 027752          104 LTKAVSELTVLKGVGPATASAVLAAYAPD  132 (219)
Q Consensus       104 ~~~al~~L~~LkGVGPATASaiLa~~~P~  132 (219)
                      .+.-+..|....||||-||=+||+.+.|+
T Consensus         4 Er~~F~~Li~V~GIGpK~Al~iLs~~~~~   32 (78)
T d1cuka2           4 ERTLFKELIKTNGVGPKLALAILSGMSAQ   32 (78)
T ss_dssp             HHHHHHHHHHSSSCCHHHHHHHHHHSCHH
T ss_pred             HHHHHHHHHccCCccHHHHHHHHHhCCHH
Confidence            34567889999999999999999987764

>d1pzna1 a.60.4.1 (A:35-95) DNA repair protein Rad51, N-terminal domain {Archaeon Pyrococcus furiosus [TaxId: 2261]}

class: All alpha proteins
fold: SAM domain-like
superfamily: Rad51 N-terminal domain-like
family: DNA repair protein Rad51, N-terminal domain
domain: DNA repair protein Rad51, N-terminal domain
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=90.92  E-value=0.052  Score=35.61  Aligned_cols=39  Identities=28%  Similarity=0.292  Sum_probs=26.5

Q ss_pred             HhhccCCCChHHHHHHHHhhCC--CCCCcccHHHHHHhcCC
Q 027752          110 ELTVLKGVGPATASAVLAAYAP--DLAPFMSDEAMGAALGH  148 (219)
Q Consensus       110 ~L~~LkGVGPATASaiLa~~~P--~~~pFfsDEa~~~~~g~  148 (219)
                      .|.+++||||+||..++..+..  +.+...+-+-...+.|-
T Consensus         2 ~L~~i~GIG~~~a~~L~~~g~~sv~~l~~a~~~eL~~i~Gi   42 (61)
T d1pzna1           2 SIEDLPGVGPATAEKLREAGYDTLEAIAVASPIELKEVAGI   42 (61)
T ss_dssp             CSSCCTTCCHHHHHHHHTTTCCSHHHHHTCCHHHHHHHHCC
T ss_pred             ccccCCCCCHHHHHHHHHhcCCCHHHHHhCCHHHHHHCCCC
Confidence            3778999999999999986533  22444455555556663

>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=90.88  E-value=0.068  Score=36.83  Aligned_cols=29  Identities=34%  Similarity=0.445  Sum_probs=24.3

Q ss_pred             HHHHHHHhhccCCCChHHHHHHHHhhCCC
Q 027752          104 LTKAVSELTVLKGVGPATASAVLAAYAPD  132 (219)
Q Consensus       104 ~~~al~~L~~LkGVGPATASaiLa~~~P~  132 (219)
                      .+.-+..|....||||-||-+||+.++|+
T Consensus         5 Er~lF~~Li~V~GIGpk~Al~iLs~~~~~   33 (73)
T d1ixra1           5 NLALFELLLSVSGVGPKVALALLSALPPR   33 (73)
T ss_dssp             HHHHHHHHHSSSCCCHHHHHHHHHHSCHH
T ss_pred             HHHHHHHHhccCCcCHHHHHHHHHHccHH
Confidence            34567889999999999999999987663

>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=90.80  E-value=0.029  Score=40.89  Aligned_cols=38  Identities=21%  Similarity=0.308  Sum_probs=31.2

Q ss_pred             HHHHHhhccCCCChHHHHHHHHhhCCCCCCcccHHHHHHhcCC
Q 027752          106 KAVSELTVLKGVGPATASAVLAAYAPDLAPFMSDEAMGAALGH  148 (219)
Q Consensus       106 ~al~~L~~LkGVGPATASaiLa~~~P~~~pFfsDEa~~~~~g~  148 (219)
                      +....|+.|+||||++|-.|+.     +-||-|-|=+..+.|-
T Consensus        24 As~~eL~~lpGIg~~~A~~Iv~-----~gpf~s~edL~~V~GI   61 (98)
T d2axtu1          24 TNIAAFIQYRGLYPTLAKLIVK-----NAPYESVEDVLNIPGL   61 (98)
T ss_dssp             SCGGGGTTSTTCTHHHHHHHHH-----SCCCSSGGGGGGCTTC
T ss_pred             ccHHHHHHhhhhcHHHHHHHHH-----cCCcCCHHHHhhCCCC
Confidence            4567899999999999999995     3589997777777763

>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=90.72  E-value=0.073  Score=36.46  Aligned_cols=29  Identities=31%  Similarity=0.316  Sum_probs=24.5

Q ss_pred             HHHHHHHhhccCCCChHHHHHHHHhhCCC
Q 027752          104 LTKAVSELTVLKGVGPATASAVLAAYAPD  132 (219)
Q Consensus       104 ~~~al~~L~~LkGVGPATASaiLa~~~P~  132 (219)
                      .+.-+..|....||||-||-+||+.+.|+
T Consensus         4 Er~~F~~Li~V~GIGpK~Al~iLs~~~~~   32 (71)
T d1bvsa2           4 NRDLFLALLSVSGVGPRLAMATLAVHDAA   32 (71)
T ss_dssp             HHHHHHHHHTSSSCCHHHHHHHHHHSCHH
T ss_pred             HHHHHHHHhccCCcCHHHHHHHHHhCCHH
Confidence            34567789999999999999999987764

>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=90.40  E-value=0.22  Score=33.83  Aligned_cols=24  Identities=21%  Similarity=0.364  Sum_probs=16.9

Q ss_pred             HHHHHHhhccCCCChHHHHHHHHh
Q 027752          105 TKAVSELTVLKGVGPATASAVLAA  128 (219)
Q Consensus       105 ~~al~~L~~LkGVGPATASaiLa~  128 (219)
                      ..-+..|+.++|||+.+|-.|+.-
T Consensus        15 ~~~~~~L~~I~gIg~~~a~~L~~~   38 (78)
T d2a1jb1          15 SRVTECLTTVKSVNKTDSQTLLTT   38 (78)
T ss_dssp             HHHHHHHTTSTTCCHHHHHHHHHH
T ss_pred             HHHHHHhcCCCCcCHHHHHHHHHH
Confidence            345667777777777777777765

>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=90.23  E-value=0.067  Score=35.54  Aligned_cols=25  Identities=28%  Similarity=0.195  Sum_probs=21.8

Q ss_pred             HHHHHHhhccCCCChHHHHHHHHhh
Q 027752          105 TKAVSELTVLKGVGPATASAVLAAY  129 (219)
Q Consensus       105 ~~al~~L~~LkGVGPATASaiLa~~  129 (219)
                      ..+|..|+++-||||.||.-+..-.
T Consensus         4 ~~~l~~f~~I~GvGp~~A~~l~~~G   28 (60)
T d1jmsa3           4 YKSFKLFTSVFGVGLKTAEKWFRMG   28 (60)
T ss_dssp             HHHHHHHHTSTTCCHHHHHHHHHTT
T ss_pred             hHHHHHHhccccccHHHHHHHHHhC
Confidence            4689999999999999998887653

>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=88.94  E-value=0.097  Score=34.45  Aligned_cols=24  Identities=17%  Similarity=0.192  Sum_probs=20.7

Q ss_pred             HHHHHHhhccCCCChHHHHHHHHh
Q 027752          105 TKAVSELTVLKGVGPATASAVLAA  128 (219)
Q Consensus       105 ~~al~~L~~LkGVGPATASaiLa~  128 (219)
                      ..+|+.||.+-||||.||.-+...
T Consensus         4 ~~~l~~ft~I~GvGp~~A~~l~~~   27 (57)
T d2bcqa2           4 VPVLELFSNIWGAGTKTAQMWYQQ   27 (57)
T ss_dssp             HHHHHHHHTSTTCCHHHHHHHHHT
T ss_pred             hHHHHHHhccccccHHHHHHHHHh
Confidence            468999999999999999877654

>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=88.14  E-value=0.11  Score=34.00  Aligned_cols=19  Identities=53%  Similarity=0.684  Sum_probs=17.1

Q ss_pred             hhccCCCChHHHHHHHHhh
Q 027752          111 LTVLKGVGPATASAVLAAY  129 (219)
Q Consensus       111 L~~LkGVGPATASaiLa~~  129 (219)
                      |+.++||||++|..++...
T Consensus         1 L~~IpGIG~~~a~~L~~~G   19 (60)
T d2i1qa1           1 LTDLPGVGPSTAEKLVEAG   19 (60)
T ss_dssp             CTTSTTCCHHHHHHHHHHT
T ss_pred             CCCCCCCCHHHHHHHHHcc
Confidence            6789999999999999873

>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=87.89  E-value=0.15  Score=33.98  Aligned_cols=40  Identities=20%  Similarity=0.285  Sum_probs=26.4

Q ss_pred             HHHhhccCCCChHHHHHHHHhhCC-CCCCcccHHHHHHhcC
Q 027752          108 VSELTVLKGVGPATASAVLAAYAP-DLAPFMSDEAMGAALG  147 (219)
Q Consensus       108 l~~L~~LkGVGPATASaiLa~~~P-~~~pFfsDEa~~~~~g  147 (219)
                      +-+|+.++||||.||-.|+.-+.- +.+.--|.|-+..+.|
T Consensus        12 ~~~L~~IpgIG~~~a~~L~~~F~s~~~l~~As~eeL~~v~G   52 (70)
T d2bgwa1          12 LYILQSFPGIGRRTAERILERFGSLERFFTASKAEISKVEG   52 (70)
T ss_dssp             HHHHHTSTTCCHHHHHHHHHHHSSHHHHTTCCHHHHHHSTT
T ss_pred             HHHHcCCCCcCHHHHHHHHHHhCCHHHHHHcCHHHHHcCCC
Confidence            567889999999999999996431 1111223455555555

>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=87.14  E-value=0.27  Score=34.02  Aligned_cols=41  Identities=27%  Similarity=0.457  Sum_probs=27.4

Q ss_pred             HHHhhhCCHHHHHHHHHHHHhhCccHHHHHHHhhccCCCChHHHHHHHHh
Q 027752           79 LVFVSSLDDSSVKSASEKAFKSLPDLTKAVSELTVLKGVGPATASAVLAA  128 (219)
Q Consensus        79 ~~lV~sN~~~~V~~~t~~Af~~l~d~~~al~~L~~LkGVGPATASaiLa~  128 (219)
                      +..+++.+++.+.++...     .|    .+.|+.++|||+-||.-|+.-
T Consensus        23 l~iLs~~~~~~l~~aI~~-----~D----~~~L~~vpGIG~KtA~rIi~e   63 (78)
T d1cuka2          23 LAILSGMSAQQFVNAVER-----EE----VGALVKLPGIGKKTAERLIVE   63 (78)
T ss_dssp             HHHHHHSCHHHHHHHHHT-----TC----HHHHHTSTTCCHHHHHHHHHH
T ss_pred             HHHHHhCCHHHHHHHHHc-----cC----HHHhhcCCCCCHHHHHHHHHH
Confidence            445555555555544432     12    457999999999999998764

>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=86.57  E-value=0.48  Score=32.30  Aligned_cols=42  Identities=24%  Similarity=0.237  Sum_probs=27.4

Q ss_pred             HHHhhhCCHHHHHHHHHHHHhhCccHHHHHHHhhccCCCChHHHHHHHHhh
Q 027752           79 LVFVSSLDDSSVKSASEKAFKSLPDLTKAVSELTVLKGVGPATASAVLAAY  129 (219)
Q Consensus        79 ~~lV~sN~~~~V~~~t~~Af~~l~d~~~al~~L~~LkGVGPATASaiLa~~  129 (219)
                      +.++++.+.+.+.++....         =.+.|++++|||+-||--|+.-.
T Consensus        24 l~iLs~~~~~~l~~aI~~~---------D~~~L~~vpGIG~KtA~rIi~eL   65 (73)
T d1ixra1          24 LALLSALPPRLLARALLEG---------DARLLTSASGVGRRLAERIALEL   65 (73)
T ss_dssp             HHHHHHSCHHHHHHHHHTT---------CHHHHTTSTTCCHHHHHHHHHHH
T ss_pred             HHHHHHccHHHHHHHHHhc---------CHHHhhcCCCCCHHHHHHHHHHH
Confidence            4445555555554444321         24579999999999998887544

>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=83.80  E-value=0.29  Score=33.25  Aligned_cols=20  Identities=30%  Similarity=0.498  Sum_probs=17.3

Q ss_pred             HHHhhccCCCChHHHHHHHH
Q 027752          108 VSELTVLKGVGPATASAVLA  127 (219)
Q Consensus       108 l~~L~~LkGVGPATASaiLa  127 (219)
                      ...|++++||||-||.-|+.
T Consensus        43 ~~~L~~vpGIG~KtA~rIi~   62 (71)
T d1bvsa2          43 VASLTRVPGIGRRGAERIVL   62 (71)
T ss_dssp             HHHHHTSTTCCHHHHHHHHH
T ss_pred             HHHhhcCCCCCHHHHHHHHH
Confidence            45799999999999988764

>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=83.68  E-value=0.3  Score=31.69  Aligned_cols=39  Identities=15%  Similarity=0.222  Sum_probs=26.7

Q ss_pred             HHhhccCCCChHHHHHHHHhhC-CCCCCcccHHHHHHhcC
Q 027752          109 SELTVLKGVGPATASAVLAAYA-PDLAPFMSDEAMGAALG  147 (219)
Q Consensus       109 ~~L~~LkGVGPATASaiLa~~~-P~~~pFfsDEa~~~~~g  147 (219)
                      +.|..++||||.++-.|+.-+- -+.+.-.|-|-...+.|
T Consensus         3 d~L~~iPGIg~~~~~~Ll~~f~Si~~l~~As~~eL~~v~G   42 (62)
T d2a1ja1           3 DFLLKMPGVNAKNCRSLMHHVKNIAELAALSQDELTSILG   42 (62)
T ss_dssp             HHHHTSTTCCHHHHHHHHHHCSSHHHHHTCCHHHHHHHHS
T ss_pred             hHHhcCCCCCHHHHHHHHHHhccHHHHHhCCHHHHHHCcC
Confidence            4688999999999999997431 11234455555555666

>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=83.38  E-value=0.35  Score=32.72  Aligned_cols=37  Identities=30%  Similarity=0.591  Sum_probs=27.0

Q ss_pred             HhhCccHH-HHHHHhhccCCCChHHHHHHHHhhCCCCCCcc
Q 027752           98 FKSLPDLT-KAVSELTVLKGVGPATASAVLAAYAPDLAPFM  137 (219)
Q Consensus        98 f~~l~d~~-~al~~L~~LkGVGPATASaiLa~~~P~~~pFf  137 (219)
                      |..+.++. +..+.|.+++|||+..|..|..+..-   ||+
T Consensus        39 F~s~~~i~~A~~eeL~~i~GiG~~~A~~i~~~f~~---pf~   76 (78)
T d2a1jb1          39 FGSLEQLIAASREDLALCPGLGPQKARRLFDVLHE---PFL   76 (78)
T ss_dssp             HSSHHHHHSCCHHHHHTSSSCCSHHHHHHHHHHHS---CSC
T ss_pred             hCCcHHHHhhhHHHHHHhhhhhHHHHHHHHHHHcC---ccc
Confidence            54444433 34778999999999999999998643   554

>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=83.14  E-value=0.42  Score=30.56  Aligned_cols=31  Identities=19%  Similarity=0.372  Sum_probs=19.8

Q ss_pred             HhhCccHHH-HHHHhhccCCCChHHHHHHHHh
Q 027752           98 FKSLPDLTK-AVSELTVLKGVGPATASAVLAA  128 (219)
Q Consensus        98 f~~l~d~~~-al~~L~~LkGVGPATASaiLa~  128 (219)
                      |..+.++.. ..+.|.+++||||.+|..|...
T Consensus        22 F~s~~~i~~As~eeL~~v~GIg~~~A~~I~~~   53 (56)
T d1kfta_          22 MGGLQGLRNASVEEIAKVPGISQGLAEKIFWS   53 (56)
T ss_dssp             HSCHHHHHHCCHHHHTTSSSTTSHHHHHHHHH
T ss_pred             hCCHHHHHHhhHHHHHhcCCCCHHHHHHHHHH
Confidence            544444433 4677778888888888777643

>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=82.95  E-value=0.2  Score=32.20  Aligned_cols=20  Identities=30%  Similarity=0.561  Sum_probs=17.5

Q ss_pred             HhhccCCCChHHHHHHHHhh
Q 027752          110 ELTVLKGVGPATASAVLAAY  129 (219)
Q Consensus       110 ~L~~LkGVGPATASaiLa~~  129 (219)
                      .|..++||||.||-.|+.-+
T Consensus         3 ~L~~I~gVG~~~a~~L~~~F   22 (56)
T d1kfta_           3 SLETIEGVGPKRRQMLLKYM   22 (56)
T ss_dssp             GGGGCTTCSSSHHHHHHHHH
T ss_pred             CcccCCCccHHHHHHHHHHh
Confidence            47889999999999999864

>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=81.19  E-value=0.28  Score=33.72  Aligned_cols=32  Identities=25%  Similarity=0.283  Sum_probs=23.3

Q ss_pred             HhhCccHHHHHHHhhccCCCChHHHHHHHHhh
Q 027752           98 FKSLPDLTKAVSELTVLKGVGPATASAVLAAY  129 (219)
Q Consensus        98 f~~l~d~~~al~~L~~LkGVGPATASaiLa~~  129 (219)
                      +..++..-...+.|++++|||+.+|+-|--..
T Consensus        37 i~~l~~~i~~~~~l~~i~GIGk~ia~kI~E~~   68 (82)
T d2fmpa1          37 IAKYPHKIKSGAEAKKLPGVGTKIAEKIDEFL   68 (82)
T ss_dssp             HHHCSSCCCCHHHHHTSTTCCHHHHHHHHHHH
T ss_pred             HHhCCcccCCHHHHhcCCCccHHHHHHHHHHH
Confidence            44555322356789999999999999887654

>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=80.92  E-value=0.43  Score=31.42  Aligned_cols=37  Identities=27%  Similarity=0.504  Sum_probs=27.9

Q ss_pred             HHHHHhhccCCCChHHHHHHHHhhCCCCCCcccHHHHHHhcC
Q 027752          106 KAVSELTVLKGVGPATASAVLAAYAPDLAPFMSDEAMGAALG  147 (219)
Q Consensus       106 ~al~~L~~LkGVGPATASaiLa~~~P~~~pFfsDEa~~~~~g  147 (219)
                      +..+.|..|+|||+.+|..|+..-     +|-|-|=+.-+.|
T Consensus        14 A~~~eL~~lpgig~~~A~~Iv~~R-----~f~s~edL~~v~g   50 (65)
T d2duya1          14 ASLEELMALPGIGPVLARRIVEGR-----PYARVEDLLKVKG   50 (65)
T ss_dssp             CCHHHHTTSTTCCHHHHHHHHHTC-----CCSSGGGGGGSTT
T ss_pred             CCHHHHHHCCCCCHHHHHHHHHcC-----CCCCHHHHHhCCC
Confidence            346789999999999999999863     4777655554544

>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=80.46  E-value=0.4  Score=31.71  Aligned_cols=43  Identities=19%  Similarity=0.337  Sum_probs=28.5

Q ss_pred             HHHHHHHHHHHHhhCccHHH-HHHHhhccCCCChHHHHHHHHhhC
Q 027752           87 DSSVKSASEKAFKSLPDLTK-AVSELTVLKGVGPATASAVLAAYA  130 (219)
Q Consensus        87 ~~~V~~~t~~Af~~l~d~~~-al~~L~~LkGVGPATASaiLa~~~  130 (219)
                      +...+...+. |..+.++.. ..+.|++++|||+.+|-.|.....
T Consensus        23 ~~~a~~L~~~-F~s~~~l~~As~eeL~~v~GIG~~~A~~I~~~~~   66 (70)
T d2bgwa1          23 RRTAERILER-FGSLERFFTASKAEISKVEGIGEKRAEEIKKILM   66 (70)
T ss_dssp             HHHHHHHHHH-HSSHHHHTTCCHHHHHHSTTCCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHH-hCCHHHHHHcCHHHHHcCCCCCHHHHHHHHHHHh
Confidence            3333343333 554444433 478999999999999999987753