Citrus Sinensis ID: 029726

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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-------19
Protein Sequence
MELEFECSNVNKWKEALASYEARVESLNKPNLISLDDYYRKELPSLIHQRNPNPHINTTELSKLVRWKLTRGKWRPRLLDFVSSLDDSSVKSASEKAFKSLPDLTKAVSELTVLKGVGPATASAVLAAYAPGVAPFMSDEAMGAALGHSKDYSLRQYLLFADKLQAKAKFLKKIASHHSMWKGHCGVLP
Secondary Structure (PSIPRED)
cccccccccHHHHHHHHHHHHHHHHccccccHHHHHHHHHHHccHHHHcccccccccHHHHHHHHHHHHHccccccHHHHHHHcccHHHHHHHHHHHHHHcccHHHHHHHHHccccccHHHHHHHHHHHcccccccccHHHHHHHccccccccHHHHHHHHHHHHHHHHHHHccccccccccccccccc
Secondary Structure Prediction (SSPRO)
cccEcccccHHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHHHHHHHHccccccccHHHHHHHHHHHHHcccccHHHHHHHHHccHHHHHHHHHHHHHHcccHHHHHHHHHHHccccHHHHHHHHHHccccccccccHHHHHHcccccccccHHHHHHHHHHHHHHHHHHHHcccccccccccccccc
Coil and Loop (DISEMBL)
melefecsNVNKWKEALASYEARVEslnkpnlislddyyrkelpslihqrnpnphintteLSKLVRWKLtrgkwrprlLDFVSSLDDSSVKSASEKAFKSLPDLTKAVSELTVLKGVGPATASAVLAAyapgvapfmsdeamgaalghskdySLRQYLLFADKLQAKAKFLKKIASHHsmwkghcgvlp
Flexible Loop (DISEMBL)
melefecsnvnKWKEALASYEARVESLNKPNLISLDDYYRKELPslihqrnpnphinttelsKLVRWKLTRGKWRPRLLDFVSSLDDSSVKsasekafkslpdlTKAVSELTVLKGVGPATASAVLAAYAPGVAPFMSDEAMGAALGHSKDYSLRQYLLFADKLQAKAKFLKKIAShhsmwkghcgvlp
Low Complexity Region (SEG)
MELEFECSNVNKWKEALASYEARVESLNKPNLISLDDYYRKELPSLIHQRNPNPHINTTELSKLVRWKLTRGKWRPRlldfvsslddssvksasEKAFKSLPDLTKAVSELTVLKGVGPATASAVLAAYAPGVAPFMSDEAMGAALGHSKDYSLRQYLLFADKLQAKAKFLKKIASHHSMWKGHCGVLP
Disordered region (IsUnstruct)
*******SNVNKWKEALASYEARVESLNKPNLISLDDYYRKELPSLIHQRNPNPHINTTELSKLVRWKLTRGKWRPRLLDFVS********************LTKAVSELTVLKGVGPATASAVLAAYAPGVAPFMSDEAMGAALGHSKDYSLRQYLLFADKLQAKAKFLKKIASHHSMWKGHCGV**
Disordered Region (DISOPRED)
********NVNKWKEALASYEA*********LISLDDYYRKELPSLIHQRNPNPHINTTELSKLVRWKLTRGKWRPRL**********SVKSASEKAFKSLPDLTKAVSELTVLKGVGPATASAVLAAYAPGVAPFMSDEAMGAALGHSKDYSLRQYLLFADKLQAKA************WKGHC*VL*
Disordered Region (DISEMBL)
********NVNKWKEALASYEARVESLNKPNLISLDDYYRKELPSLIHQRNPNPHINTTELSKLVRWKLTRGKWRPRLLDFVSS*************FKSLPDLTKAVSELTVLKGVGPATASAVLAAYAPGVAPFMSDEAMGAALGHSKDYSLRQYLLFADKLQAKAKFLKKIASHHSMWKGHCGVLP
Disordered Region (DISPRO)
*ELEFECSNVNKWKEALASYEARVESLNKPNLISLDDYYRKELPSLIHQRNPNPHINTTELSKLVRWKLTRGKWRPRLLDFVSSLDDSSVKSASEKAFKSLPDLTKAVSELTVLKGVGPATASAVLAAYAPGVAPFMSDEAMGAALGHSKDYSLRQYLLFADKLQAKAKFLKKIA**HSMWKGHCGVLP
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MELEFECSNVNKWKEALASYEARVESLNKPNLISLDDYYRKELPSLIHQRNPNPHINTTELSKLVRWKLTRGKWRPRLLDFVSSLDDSSVKSASEKAFKSLPDLTKAVSELTVLKGVGPATASAVLAAYAPGVAPFMSDEAMGAALGHSKDYSLRQYLLFADKLQAKAKFLKKIASHHSMWKGHCGVLP
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	189
297829776	209	hypothetical protein ARALYDRAFT_478581 [	0.910	0.822	0.761	4e-72
224067158	218	predicted protein [Populus trichocarpa]	0.973	0.844	0.691	2e-71
225458920	213	PREDICTED: uncharacterized protein LOC10	0.894	0.793	0.751	3e-70
255537954	217	conserved hypothetical protein [Ricinus	0.894	0.778	0.745	3e-68
449447089	220	PREDICTED: uncharacterized protein LOC10	0.894	0.768	0.727	5e-67
15795142	292	unnamed protein product [Arabidopsis tha	0.910	0.589	0.767	1e-66
18399536	209	DNA binding protein [Arabidopsis thalian	0.910	0.822	0.767	1e-66
356552292	190	PREDICTED: uncharacterized protein LOC10	0.894	0.889	0.693	6e-64
356552290	220	PREDICTED: uncharacterized protein LOC10	0.894	0.768	0.693	1e-63
294463602	225	unknown [Picea sitchensis]	0.894	0.751	0.639	4e-57

>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 =  276 bits (705), Expect = 4e-72,   Method: Compositional matrix adjust.
 Identities = 131/172 (76%), Positives = 157/172 (91%)

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

Query: 61  LSKLVRWKLTRGKWRPRLLDFVSSLDDSSVKSASEKAFKSLPDLTKAVSELTVLKGVGPA 120
           LS+L++WKL+RGKWRPRLLDFVSSL+DS VKSASEKAFKSLPD++KAV ELTVLKGVGPA
Sbjct: 61  LSQLMKWKLSRGKWRPRLLDFVSSLEDSVVKSASEKAFKSLPDISKAVKELTVLKGVGPA 120

Query: 121 TASAVLAAYAPGVAPFMSDEAMGAALGHSKDYSLRQYLLFADKLQAKAKFLK 172
           TASAVLAAYAP +APFMSDEAM  ALG+SKDYSL+QYLLF  KLQ KAK LK
Sbjct: 121 TASAVLAAYAPDIAPFMSDEAMEVALGNSKDYSLKQYLLFVTKLQDKAKELK 172

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  273 bits (698), Expect = 2e-71,   Method: Compositional matrix adjust.
 Identities = 132/191 (69%), Positives = 158/191 (82%), Gaps = 7/191 (3%)

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

Query: 63  KLVRWKLTRGKWRPRLLDFVSSLDDSSVKSASEKAFKSLPDLTKAVSELTVLKGVGPATA 122
           KL++WKL+RGKWRPRLLDFVSSLD+S VKSAS+KAF+SLPD++KAVS LTVLKGVGPATA
Sbjct: 61  KLMQWKLSRGKWRPRLLDFVSSLDESHVKSASQKAFESLPDVSKAVSALTVLKGVGPATA 120

Query: 123 SAVLAAYAPGVAPFMSDEAMGAALGHSKDYSLRQYLLFADKLQAKAKFLKKIAS------ 176
           SAVLAAYAP VAPFMSDEAM A LG+SKDY+L+QYLLF DKLQ K+K L  +        
Sbjct: 121 SAVLAAYAPDVAPFMSDEAMEAVLGNSKDYTLKQYLLFVDKLQTKSKELSSVRDIFTPSD 180

Query: 177 -HHSMWKGHCG 186
              ++W    G
Sbjct: 181 IERALWSSAVG 191

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 =  270 bits (689), Expect = 3e-70,   Method: Compositional matrix adjust.
 Identities = 127/169 (75%), Positives = 154/169 (91%)

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

Query: 63  KLVRWKLTRGKWRPRLLDFVSSLDDSSVKSASEKAFKSLPDLTKAVSELTVLKGVGPATA 122
           KL++WKLTRGKWRPRLLDFVSSLD++ VKSAS+KAF+SLPD++KA+SELTVLKGVGPATA
Sbjct: 61  KLMQWKLTRGKWRPRLLDFVSSLDEALVKSASQKAFQSLPDISKAISELTVLKGVGPATA 120

Query: 123 SAVLAAYAPGVAPFMSDEAMGAALGHSKDYSLRQYLLFADKLQAKAKFL 171
           SA+LAAYAP VAPFMSDEAM AALG+SKDY+L+QYL+FADKLQ KA+ L
Sbjct: 121 SALLAAYAPDVAPFMSDEAMVAALGNSKDYTLKQYLVFADKLQNKAREL 169

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

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 =  263 bits (671), Expect = 3e-68,   Method: Compositional matrix adjust.
 Identities = 126/169 (74%), Positives = 149/169 (88%)

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

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

Query: 123 SAVLAAYAPGVAPFMSDEAMGAALGHSKDYSLRQYLLFADKLQAKAKFL 171
           SAVLAAYAP VAPFMSDEAM AALG SKDY+L+QYL F DKLQ KAK L
Sbjct: 121 SAVLAAYAPDVAPFMSDEAMEAALGSSKDYTLKQYLSFVDKLQTKAKEL 169

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

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 =  259 bits (661), Expect = 5e-67,   Method: Compositional matrix adjust.
 Identities = 123/169 (72%), Positives = 151/169 (89%)

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

Query: 63  KLVRWKLTRGKWRPRLLDFVSSLDDSSVKSASEKAFKSLPDLTKAVSELTVLKGVGPATA 122
           KL++WKLTRGKWRPRLLDFVSSLD+S VK AS+KAF+ LPD++KAVSELT LKGVGPATA
Sbjct: 62  KLMQWKLTRGKWRPRLLDFVSSLDESLVKLASQKAFQCLPDISKAVSELTPLKGVGPATA 121

Query: 123 SAVLAAYAPGVAPFMSDEAMGAALGHSKDYSLRQYLLFADKLQAKAKFL 171
           SAVLAAYAP VAPFMSDEAM AALG+SKDYSL+QYLLFA+KL+ KAK L
Sbjct: 122 SAVLAAYAPDVAPFMSDEAMEAALGNSKDYSLKQYLLFANKLEQKAKEL 170

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  258 bits (658), Expect = 1e-66,   Method: Compositional matrix adjust.
 Identities = 132/172 (76%), Positives = 155/172 (90%)

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

Query: 61  LSKLVRWKLTRGKWRPRLLDFVSSLDDSSVKSASEKAFKSLPDLTKAVSELTVLKGVGPA 120
           LS+L++WKL+RGKWRPRLLDFVSSLDDS VKSASEKAFKSLPD++KAV ELTVLKGVG A
Sbjct: 61  LSQLMKWKLSRGKWRPRLLDFVSSLDDSVVKSASEKAFKSLPDISKAVKELTVLKGVGAA 120

Query: 121 TASAVLAAYAPGVAPFMSDEAMGAALGHSKDYSLRQYLLFADKLQAKAKFLK 172
           TASAVLAAYAP +APFMSDEAM  ALG+SKDYSL+QYLLFA KLQ KAK LK
Sbjct: 121 TASAVLAAYAPDIAPFMSDEAMEVALGNSKDYSLKQYLLFATKLQDKAKELK 172

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 =  258 bits (658), Expect = 1e-66,   Method: Compositional matrix adjust.
 Identities = 132/172 (76%), Positives = 155/172 (90%)

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

Query: 61  LSKLVRWKLTRGKWRPRLLDFVSSLDDSSVKSASEKAFKSLPDLTKAVSELTVLKGVGPA 120
           LS+L++WKL+RGKWRPRLLDFVSSLDDS VKSASEKAFKSLPD++KAV ELTVLKGVG A
Sbjct: 61  LSQLMKWKLSRGKWRPRLLDFVSSLDDSVVKSASEKAFKSLPDISKAVKELTVLKGVGAA 120

Query: 121 TASAVLAAYAPGVAPFMSDEAMGAALGHSKDYSLRQYLLFADKLQAKAKFLK 172
           TASAVLAAYAP +APFMSDEAM  ALG+SKDYSL+QYLLFA KLQ KAK LK
Sbjct: 121 TASAVLAAYAPDIAPFMSDEAMEVALGNSKDYSLKQYLLFATKLQDKAKELK 172

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356552292|ref|XP_003544502.1| PREDICTED: uncharacterized protein LOC100803511 isoform 2 [Glycine max]

 Score =  248 bits (634), Expect = 6e-64,   Method: Compositional matrix adjust.
 Identities = 120/173 (69%), Positives = 146/173 (84%), Gaps = 4/173 (2%)

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

Query: 59  TELSKLVRWKLTRGKWRPRLLDFVSSLDDSSVKSASEKAFKSLPDLTKAVSELTVLKGVG 118
            ELS L++WKLTRGKWRPRLLDFVSSLDD+ VKSAS+KAF+SLPD++KAVSELTVLKGVG
Sbjct: 61  PELSTLMQWKLTRGKWRPRLLDFVSSLDDAVVKSASQKAFQSLPDVSKAVSELTVLKGVG 120

Query: 119 PATASAVLAAYAPGVAPFMSDEAMGAALGHSKDYSLRQYLLFADKLQAKAKFL 171
           PATASAVLA +AP + PFMSDEAM AALG SKDYSL+QY+ F DKLQ KA+ L
Sbjct: 121 PATASAVLATFAPHLTPFMSDEAMEAALGSSKDYSLKQYIKFVDKLQRKAEVL 173

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  248 bits (632), Expect = 1e-63,   Method: Compositional matrix adjust.
 Identities = 120/173 (69%), Positives = 146/173 (84%), Gaps = 4/173 (2%)

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

Query: 59  TELSKLVRWKLTRGKWRPRLLDFVSSLDDSSVKSASEKAFKSLPDLTKAVSELTVLKGVG 118
            ELS L++WKLTRGKWRPRLLDFVSSLDD+ VKSAS+KAF+SLPD++KAVSELTVLKGVG
Sbjct: 61  PELSTLMQWKLTRGKWRPRLLDFVSSLDDAVVKSASQKAFQSLPDVSKAVSELTVLKGVG 120

Query: 119 PATASAVLAAYAPGVAPFMSDEAMGAALGHSKDYSLRQYLLFADKLQAKAKFL 171
           PATASAVLA +AP + PFMSDEAM AALG SKDYSL+QY+ F DKLQ KA+ L
Sbjct: 121 PATASAVLATFAPHLTPFMSDEAMEAALGSSKDYSLKQYIKFVDKLQRKAEEL 173

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  226 bits (575), Expect = 4e-57,   Method: Compositional matrix adjust.
 Identities = 108/169 (63%), Positives = 135/169 (79%)

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

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

Query: 123 SAVLAAYAPGVAPFMSDEAMGAALGHSKDYSLRQYLLFADKLQAKAKFL 171
           SAVLAA+ P +APFMSDEAM AALG SK+Y+L+QYL+FA+KLQ KAK L
Sbjct: 121 SAVLAAFDPHIAPFMSDEAMVAALGSSKEYTLKQYLVFAEKLQNKAKEL 169

Source: Picea sitchensis

Species: Picea sitchensis

Genus: Picea

Family: Pinaceae

Order: Coniferales

Class: Coniferopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

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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	189
TAIR|locus:2082224	209	AT3G12210 [Arabidopsis thalian	0.910	0.822	0.674	3.5e-59
UNIPROTKB|F1RG53	232	LOC100524737 "Uncharacterized	0.931	0.758	0.386	8.4e-26
ZFIN|ZDB-GENE-050320-25	238	zgc:112496 "zgc:112496" [Danio	0.941	0.747	0.358	1e-22
FB|FBgn0030328	550	Amun "Amun" [Drosophila melano	0.825	0.283	0.377	2.6e-21
ASPGD|ASPL0000059149	312	AN10183 [Emericella nidulans (	0.703	0.426	0.268	6.5e-08

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

 Score = 607 (218.7 bits), Expect = 3.5e-59, P = 3.5e-59
 Identities = 116/172 (67%), Positives = 139/172 (80%)

Query:     1 MELEFECSNVNKWKEALASYEARVESLNKPNLISLDDYYRKELPSLIHQRNPNPHINTTE 60
             MELEF+CS+V  WKEAL+SY++R+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 TASAVLAAYAPGVAPFMSDEAMGAALGHSKDYSLRQYLLFADKLQAKAKFLK 172
             TASAVLAAYAP +APFMSDEAM  ALG+SKDYSL+QYLLFA KLQ KAK LK
Sbjct:   121 TASAVLAAYAPDIAPFMSDEAMEVALGNSKDYSLKQYLLFATKLQDKAKELK 172

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 = 292 (107.8 bits), Expect = 8.4e-26, P = 8.4e-26
 Identities = 70/181 (38%), Positives = 97/181 (53%)

Query:     7 CSNVNKWKEALASYEARVESLNKPN--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 VLAAYAPGVAPFMSDEAMGAALG-HSKDYSLRQYLLFADKLQAKAKFLKKIASHHSMWKG 183
             VLAA AP VA FMS+EA+ A  G  +  Y+L+ YLL+  ++Q +A  L    S   +W  
Sbjct:   129 VLAAGAPEVAAFMSEEAVAAVPGLPALQYTLKHYLLYLSRVQERATALSH-GSASGLWTP 187

Query:   184 H 184
             H
Sbjct:   188 H 188

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 = 263 (97.6 bits), Expect = 1.0e-22, P = 1.0e-22
 Identities = 67/187 (35%), Positives = 94/187 (50%)

Query:     5 FECSNVNKWKEALASY----EARVESLNKPN--LISLDDYYRKELPSLIHQRNPNPHINT 58
             F C +   WK     Y    EA+     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 PATASAVLAAYAPGVAPFMSDEAMGA-ALGHSKDYSLRQYLLFADKLQAKAKFLKKIASH 177
              ATASAVL A AP    FM+DEA+ + A     +Y+ + Y L+  K+  K   L K+ + 
Sbjct:   123 SATASAVLVAGAPDKVAFMADEAVESIAELRPVEYTDKHYALYLQKMLWKTSELNKVDAQ 182

Query:   178 HSMWKGH 184
                W  H
Sbjct:   183 QD-WTPH 188

GO:0003677 "DNA binding" evidence=IEA

GO:0006281 "DNA repair" evidence=IEA

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

 Score = 257 (95.5 bits), Expect = 2.6e-21, P = 2.6e-21
 Identities = 60/159 (37%), Positives = 88/159 (55%)

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

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

Query:   148 -HSKDYSLRQYLLFADKLQAKAKFLK-KIASHHSMWKGH 184
                 DY+ ++YL F + +QA  + L  ++      W  H
Sbjct:   160 IEGIDYTTKEYLNFVNHIQATVERLNAEVGGDTPHWSPH 198

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 = 129 (50.5 bits), Expect = 6.5e-08, P = 6.5e-08
 Identities = 40/149 (26%), Positives = 64/149 (42%)

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

Query:   104 ------LTKAVSELTV-LKGVGPATASAVLAAYAPGVAPFMSDEA---MGAALGHSKDYS 153
                   +  A+  LT  L+GVGPATAS +L+   P + PF SD+    + A +  S  +S
Sbjct:   162 KDGFEAIENALLTLTTPLRGVGPATASLILSVACPEMIPFYSDDVYLWVCAGVYPSSSFS 221

Query:   154 LRQYLLFADKLQAKAKFLKKIASHHSMWK 182
              ++            K+   +A +  +W+
Sbjct:   222 SKKSKEVKPNGDPNVKY--NVAEYRRLWE 248


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        0.316   0.131   0.393    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      189       172   0.00093  108 3  11 22  0.42    32
                                                     31  0.48    34


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:  603 (64 KB)
  Total size of DFA:  163 KB (2095 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:  15.74u 0.11s 15.85t   Elapsed:  00:00:00
  Total cpu time:  15.74u 0.11s 15.85t   Elapsed:  00:00:00
  Start:  Mon May 20 23:39:04 2013   End:  Mon May 20 23:39:04 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: fgenesh2_kg.3__1282__AT3G12210.2 annotation not avaliable (209 aa) (Arabidopsis lyrata)

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	189
PF00633	30	HHH: Helix-hairpin-helix motif; InterPro: IPR00044	97.7
PRK01229	208	N-glycosylase/DNA lyase; Provisional	96.75
cd00056	158	ENDO3c endonuclease III; includes endonuclease III	96.57
COG0177	211	Nth Predicted EndoIII-related endonuclease [DNA re	96.24
TIGR01084	275	mutY A/G-specific adenine glycosylase. This equiva	96.02
PRK10702	211	endonuclease III; Provisional	95.47
smart00478	149	ENDO3c endonuclease III. includes endonuclease III	95.47
COG0122	285	AlkA 3-methyladenine DNA glycosylase/8-oxoguanine	95.4
TIGR01083	191	nth endonuclease III. This equivalog model identif	95.25
PRK10880	350	adenine DNA glycosylase; Provisional	94.97
TIGR00588	310	ogg 8-oxoguanine DNA-glycosylase (ogg). All protei	94.81
PF02371	87	Transposase_20: Transposase IS116/IS110/IS902 fami	94.7
PRK02515	132	psbU photosystem II complex extrinsic protein prec	94.68
PRK13913	218	3-methyladenine DNA glycosylase; Provisional	94.62
PRK13910	289	DNA glycosylase MutY; Provisional	94.6
TIGR03252	177	uncharacterized HhH-GPD family protein. This model	94.48
PRK10308	283	3-methyl-adenine DNA glycosylase II; Provisional	94.38
COG1194	342	MutY A/G-specific DNA glycosylase [DNA replication	94.26
smart00278	26	HhH1 Helix-hairpin-helix DNA-binding motif class 1	92.64
PF11731	93	Cdd1: Pathogenicity locus; InterPro: IPR021725 Cdd	91.12
PF10391	52	DNA_pol_lambd_f: Fingers domain of DNA polymerase	89.47
PF14716	68	HHH_8: Helix-hairpin-helix domain; PDB: 2W9M_A 1HU	87.81
PRK14605	194	ruvA Holliday junction DNA helicase RuvA; Provisio	87.48
TIGR01259	120	comE comEA protein. This model describes the ComEA	86.85
KOG1921	286	consensus Endonuclease III [Replication, recombina	86.59
PF12826	64	HHH_2: Helix-hairpin-helix motif; PDB: 1X2I_B 1DGS	85.62
COG2231	215	Uncharacterized protein related to Endonuclease II	85.33
PRK00116	192	ruvA Holliday junction DNA helicase RuvA; Reviewed	84.87
PRK14600	186	ruvA Holliday junction DNA helicase RuvA; Provisio	84.47
PF14520	60	HHH_5: Helix-hairpin-helix domain; PDB: 3AUO_B 3AU	84.45
PRK13901	196	ruvA Holliday junction DNA helicase RuvA; Provisio	84.39
TIGR00084	191	ruvA Holliday junction DNA helicase, RuvA subunit.	84.36
TIGR00608	218	radc DNA repair protein radc. This family is based	82.86
PRK14601	183	ruvA Holliday junction DNA helicase RuvA; Provisio	82.5
PRK00024	224	hypothetical protein; Reviewed	81.82
PRK13901	196	ruvA Holliday junction DNA helicase RuvA; Provisio	81.34
PF14520	60	HHH_5: Helix-hairpin-helix domain; PDB: 3AUO_B 3AU	80.15

>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=97.70  E-value=3.1e-05  Score=47.29  Aligned_cols=24  Identities=42%  Similarity=0.700  Sum_probs=20.2

Q ss_pred             HHHHHHhhcccCcChHHHHHHHHh
Q 029726          105 TKAVSELTVLKGVGPATASAVLAA  128 (189)
Q Consensus       105 ~~al~~Lt~LkGVGPATASaiLa~  128 (189)
                      .+.++.|++|+||||.||.+|++.
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            456889999999999999999974

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=96.75  E-value=0.009  Score=51.12  Aligned_cols=72  Identities=26%  Similarity=0.209  Sum_probs=52.8

Q ss_pred             cHHHHHHHhh-cccCcChHHHHHHH-HhhcCCCCCcccHHHHHHhh---C--C--CCCCCHHHHHHHHHHHHHHHHHHhh
Q 029726          103 DLTKAVSELT-VLKGVGPATASAVL-AAYAPGVAPFMSDEAMGAAL---G--H--SKDYSLRQYLLFADKLQAKAKFLKK  173 (189)
Q Consensus       103 d~~~al~~Lt-~LkGVGPATASaiL-a~~~P~~~pFfsDEa~~~~~---g--~--~~kYt~keY~~~~~~~~~~~~~L~~  173 (189)
                      ++..+.+.|. +||||||=|||.|| .+..  ..-|.-|--..-++   |  .  +..-|.+.|.+.-..+++.++.+|.
T Consensus       112 ~~~~~R~~Ll~~lpGIG~KTAd~vL~~~~~--~~~~iVDtHv~Ri~~RlG~~~~~~~~lt~~~y~~~E~~l~~~~~~~~~  189 (208)
T PRK01229        112 DQFEAREFLVKNIKGIGYKEASHFLRNVGY--EDLAILDRHILRFLKRYGLIEEIPKTLSKKRYLEIEEILREIAEELGI  189 (208)
T ss_pred             CchHHHHHHHHcCCCCcHHHHHHHHHHccC--CCeeeeeHHHHHHHHHhCCCcccccccCcCCHHHHHHHHHHHHHHcCC
Confidence            5678899999 99999999999999 4544  21344666544332   4  1  2245669999999999999999887


Q ss_pred             hcc
Q 029726          174 IAS  176 (189)
Q Consensus       174 ~~~  176 (189)
                      ..+
T Consensus       190 ~~~  192 (208)
T PRK01229        190 SLG  192 (208)
T ss_pred             CHH
Confidence            653

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

Probab=96.57  E-value=0.012  Score=46.31  Aligned_cols=40  Identities=38%  Similarity=0.449  Sum_probs=30.1

Q ss_pred             HHHHHHhhcccCcChHHHHHHHHhhc-CCCCCcccHHHHHHhh
Q 029726          105 TKAVSELTVLKGVGPATASAVLAAYA-PGVAPFMSDEAMGAAL  146 (189)
Q Consensus       105 ~~al~~Lt~LkGVGPATASaiLa~~~-P~~~pFfsDEa~~~~~  146 (189)
                      ..+.+.|++||||||-||+.+|.... ++.+|.  |-...-++
T Consensus        79 ~~~~~~L~~l~GIG~~tA~~~l~~~~~~~~~pv--D~~v~r~~  119 (158)
T cd00056          79 PDAREELLALPGVGRKTANVVLLFALGPDAFPV--DTHVRRVL  119 (158)
T ss_pred             cccHHHHHcCCCCCHHHHHHHHHHHCCCCCCcc--chhHHHHH
Confidence            67899999999999999999998753 444443  66554433

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

Probab=96.24  E-value=0.0059  Score=52.49  Aligned_cols=72  Identities=24%  Similarity=0.235  Sum_probs=45.7

Q ss_pred             CHHHHHHHHHHHhhCCCCCcchhhHhhhCCHHHHHHHHHHHH------------hhC-----ccHHHHHHHhhcccCcCh
Q 029726           57 NTTELSKLVRWKLTRGKWRPRLLDFVSSLDDSSVKSASEKAF------------KSL-----PDLTKAVSELTVLKGVGP  119 (189)
Q Consensus        57 tkdEL~~LveWKL~rGkfRP~L~~lv~sN~~~~V~~~t~~Af------------~~l-----~d~~~al~~Lt~LkGVGP  119 (189)
                      |.|+.++-+-=+|-  +..|+...+...+.++..+-+-.-+|            +++     .++...++.|.+|+|||+
T Consensus        42 ttD~~vn~at~~Lf--~~~~t~e~l~~a~~~~l~~~I~~iGlyr~KAk~I~~~~~~l~e~~~g~vP~~~~eL~~LPGVGr  119 (211)
T COG0177          42 TTDEVVNKATPALF--KRYPTPEDLLNADEEELEELIKSIGLYRNKAKNIKELARILLEKFGGEVPDTREELLSLPGVGR  119 (211)
T ss_pred             CchHHHHHHHHHHH--HHcCCHHHHHcCCHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHHcCCCCCchHHHHHhCCCcch
Confidence            46777766665554  23456666655554443333222222            011     156778999999999999


Q ss_pred             HHHHHHHHhhc
Q 029726          120 ATASAVLAAYA  130 (189)
Q Consensus       120 ATASaiLa~~~  130 (189)
                      -||..+|+...
T Consensus       120 KTAnvVL~~a~  130 (211)
T COG0177         120 KTANVVLSFAF  130 (211)
T ss_pred             HHHHHHHHhhc
Confidence            99999999854

>TIGR01084 mutY A/G-specific adenine glycosylase

Probab=96.02  E-value=0.034  Score=49.22  Aligned_cols=38  Identities=29%  Similarity=0.385  Sum_probs=29.0

Q ss_pred             HHHHHHHhhcccCcChHHHHHHHHhhcCCCCCcccHHHH
Q 029726          104 LTKAVSELTVLKGVGPATASAVLAAYAPGVAPFMSDEAM  142 (189)
Q Consensus       104 ~~~al~~Lt~LkGVGPATASaiLa~~~P~~~pFfsDEa~  142 (189)
                      +...++.|++|+||||-||++||+...-...|+ -|--.
T Consensus       100 ~p~~~~~L~~LpGIG~~TA~~Il~~a~~~~~~~-vD~~v  137 (275)
T TIGR01084       100 FPQDFEDLAALPGVGRYTAGAILSFALNKPYPI-LDGNV  137 (275)
T ss_pred             CcHHHHHHHhCCCCCHHHHHHHHHHHCCCCCCc-chHhH
Confidence            345789999999999999999999865443454 55544

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.

>PRK10702 endonuclease III; Provisional

Probab=95.47  E-value=0.023  Score=48.36  Aligned_cols=39  Identities=26%  Similarity=0.249  Sum_probs=29.1

Q ss_pred             HHHHHHHhhcccCcChHHHHHHHHhhcCCCCCcccHHHHH
Q 029726          104 LTKAVSELTVLKGVGPATASAVLAAYAPGVAPFMSDEAMG  143 (189)
Q Consensus       104 ~~~al~~Lt~LkGVGPATASaiLa~~~P~~~pFfsDEa~~  143 (189)
                      +..+.+.|.+|+||||-||.+||....-. ..|.-|--..
T Consensus       104 ~p~~~~~Ll~lpGVG~ktA~~ill~a~~~-~~~~VDt~v~  142 (211)
T PRK10702        104 VPEDRAALEALPGVGRKTANVVLNTAFGW-PTIAVDTHIF  142 (211)
T ss_pred             CCchHHHHhcCCcccHHHHHHHHHHHcCC-CcccccchHH
Confidence            45688999999999999999999986543 2344554333

>smart00478 ENDO3c endonuclease III

Probab=95.47  E-value=0.1  Score=40.82  Aligned_cols=39  Identities=31%  Similarity=0.293  Sum_probs=28.6

Q ss_pred             cHHHHHHHhhcccCcChHHHHHHHHhhcCCCCCcccHHHH
Q 029726          103 DLTKAVSELTVLKGVGPATASAVLAAYAPGVAPFMSDEAM  142 (189)
Q Consensus       103 d~~~al~~Lt~LkGVGPATASaiLa~~~P~~~pFfsDEa~  142 (189)
                      ++....+.|++|+||||-||+++|...--. .-|..|--.
T Consensus        66 ~~~~~~~~L~~l~GIG~~tA~~~l~~~~~~-~~~~~D~~v  104 (149)
T smart00478       66 EVPDDREELLKLPGVGRKTANAVLSFALGK-PFIPVDTHV  104 (149)
T ss_pred             CccHHHHHHHcCCCCcHHHHHHHHHHHCCC-CCCccchHH
Confidence            344678899999999999999999986554 233444433

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

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

Probab=95.40  E-value=0.035  Score=49.33  Aligned_cols=72  Identities=28%  Similarity=0.256  Sum_probs=52.5

Q ss_pred             CCCHHHHHHHHHHHhh-CCCCCcchhhHhhhCCHHHHHHHHHHHHhhCc--------cHHHHHHHhhcccCcChHHHHHH
Q 029726           55 HINTTELSKLVRWKLT-RGKWRPRLLDFVSSLDDSSVKSASEKAFKSLP--------DLTKAVSELTVLKGVGPATASAV  125 (189)
Q Consensus        55 ~ltkdEL~~LveWKL~-rGkfRP~L~~lv~sN~~~~V~~~t~~Af~~l~--------d~~~al~~Lt~LkGVGPATASai  125 (189)
                      +.|-++|..+=++-|+ -|..+.+         .+.++.+++...+-.+        +...+++.|++||||||=||-.+
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            6788888888888876 5665553         3455556655554322        46779999999999999999999


Q ss_pred             HHh--hcCCCCC
Q 029726          126 LAA--YAPGVAP  135 (189)
Q Consensus       126 La~--~~P~~~p  135 (189)
                      |-.  ..|+.+|
T Consensus       215 llf~lgr~dvfP  226 (285)
T COG0122         215 LLFGLGRPDVFP  226 (285)
T ss_pred             HHHcCCCCCCCC
Confidence            876  4677655

>TIGR01083 nth endonuclease III

Probab=95.25  E-value=0.062  Score=44.49  Aligned_cols=41  Identities=27%  Similarity=0.210  Sum_probs=29.4

Q ss_pred             HHHHHHHhhcccCcChHHHHHHHHhhcCCCCCcccHHHHHHh
Q 029726          104 LTKAVSELTVLKGVGPATASAVLAAYAPGVAPFMSDEAMGAA  145 (189)
Q Consensus       104 ~~~al~~Lt~LkGVGPATASaiLa~~~P~~~pFfsDEa~~~~  145 (189)
                      +..+.+.|++|+||||=||.+||....-.. -|.-|--..-+
T Consensus       101 ~~~~~~~L~~l~GIG~ktA~~ill~~~~~~-~~~vD~~v~Ri  141 (191)
T TIGR01083       101 VPEDREELVKLPGVGRKTANVVLNVAFGIP-AIAVDTHVFRV  141 (191)
T ss_pred             CchHHHHHHhCCCCcHHHHHHHHHHHcCCC-ccccchhHHHH
Confidence            445788999999999999999998864322 24555544433

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.

>PRK10880 adenine DNA glycosylase; Provisional

Probab=94.97  E-value=0.039  Score=50.55  Aligned_cols=29  Identities=31%  Similarity=0.454  Sum_probs=25.2

Q ss_pred             HHHHHHHhhcccCcChHHHHHHHHhhcCC
Q 029726          104 LTKAVSELTVLKGVGPATASAVLAAYAPG  132 (189)
Q Consensus       104 ~~~al~~Lt~LkGVGPATASaiLa~~~P~  132 (189)
                      +....+.|.+|+||||-||++||+...-.
T Consensus       104 ~p~~~~~L~~LpGIG~~TA~aIl~~af~~  132 (350)
T PRK10880        104 FPETFEEVAALPGVGRSTAGAILSLSLGK  132 (350)
T ss_pred             chhhHHHHhcCCCccHHHHHHHHHHHCCC
Confidence            45678999999999999999999987644

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

Probab=94.81  E-value=0.026  Score=50.46  Aligned_cols=39  Identities=28%  Similarity=0.360  Sum_probs=31.0

Q ss_pred             cHHHHHHHhhcccCcChHHHHHHHHhh--cCCCCCcccHHHHH
Q 029726          103 DLTKAVSELTVLKGVGPATASAVLAAY--APGVAPFMSDEAMG  143 (189)
Q Consensus       103 d~~~al~~Lt~LkGVGPATASaiLa~~--~P~~~pFfsDEa~~  143 (189)
                      +...+.+.|++||||||=||.+||...  .|+.+|  .|-...
T Consensus       214 ~~~~~~~~L~~l~GIG~~tAd~vll~~l~~~d~~P--vD~~v~  254 (310)
T TIGR00588       214 SYEDAREALCELPGVGPKVADCICLMGLDKPQAVP--VDVHVW  254 (310)
T ss_pred             ChHHHHHHHHhCCCccHHHHHHHHHHhCCCCCcee--ecHHHH
Confidence            356789999999999999999999774  566666  375553

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.

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

Probab=94.70  E-value=0.027  Score=41.15  Aligned_cols=37  Identities=32%  Similarity=0.496  Sum_probs=30.0

Q ss_pred             HHhhcccCcChHHHHHHHHhh-cCCCCCcccHHHHHHhhC
Q 029726          109 SELTVLKGVGPATASAVLAAY-APGVAPFMSDEAMGAALG  147 (189)
Q Consensus       109 ~~Lt~LkGVGPATASaiLa~~-~P~~~pFfsDEa~~~~~g  147 (189)
                      +.|+.++||||-||..||+.. +++  -|=+...+...+|
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  4667888887776

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

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

Probab=94.68  E-value=0.016  Score=46.66  Aligned_cols=37  Identities=24%  Similarity=0.325  Sum_probs=32.1

Q ss_pred             HHHHHhhcccCcChHHHHHHHHhhcCCCCCcccHHHHHHhhC
Q 029726          106 KAVSELTVLKGVGPATASAVLAAYAPGVAPFMSDEAMGAALG  147 (189)
Q Consensus       106 ~al~~Lt~LkGVGPATASaiLa~~~P~~~pFfsDEa~~~~~g  147 (189)
                      +.++.|..|+||||++|..|.     .+.||-|=|-...+.|
T Consensus        58 A~~~el~~lpGigP~~A~~IV-----~nGpf~sveDL~~V~G   94 (132)
T PRK02515         58 SSVRAFRQFPGMYPTLAGKIV-----KNAPYDSVEDVLNLPG   94 (132)
T ss_pred             cCHHHHHHCCCCCHHHHHHHH-----HCCCCCCHHHHHcCCC
Confidence            456789999999999999999     3679999998888887

>PRK13913 3-methyladenine DNA glycosylase; Provisional

Probab=94.62  E-value=0.094  Score=45.15  Aligned_cols=40  Identities=23%  Similarity=0.163  Sum_probs=29.0

Q ss_pred             HHHHHhhcccCcChHHHHHHHHhhcCCCCCcccHHHHHHhh
Q 029726          106 KAVSELTVLKGVGPATASAVLAAYAPGVAPFMSDEAMGAAL  146 (189)
Q Consensus       106 ~al~~Lt~LkGVGPATASaiLa~~~P~~~pFfsDEa~~~~~  146 (189)
                      ...+.|.+|+||||=||.+||....- ..-|..|--..-++
T Consensus       118 ~~re~Ll~l~GIG~kTAd~iLlya~~-rp~fvVDty~~Rv~  157 (218)
T PRK13913        118 VTREWLLDQKGIGKESADAILCYVCA-KEVMVVDKYSYLFL  157 (218)
T ss_pred             hHHHHHHcCCCccHHHHHHHHHHHcC-CCccccchhHHHHH
Confidence            45688999999999999999987543 32456666554443

>PRK13910 DNA glycosylase MutY; Provisional

Probab=94.60  E-value=0.051  Score=48.54  Aligned_cols=34  Identities=26%  Similarity=0.262  Sum_probs=26.5

Q ss_pred             HHHHHhhcccCcChHHHHHHHHhhcCCCCCcccHH
Q 029726          106 KAVSELTVLKGVGPATASAVLAAYAPGVAPFMSDE  140 (189)
Q Consensus       106 ~al~~Lt~LkGVGPATASaiLa~~~P~~~pFfsDE  140 (189)
                      ...+.|.+|+||||-||.+||+...-..++ .-|-
T Consensus        69 ~~~~~L~~LpGIG~kTA~aIl~~af~~~~~-~VD~  102 (289)
T PRK13910         69 NDYQSLLKLPGIGAYTANAILCFGFREKSA-CVDA  102 (289)
T ss_pred             hhHHHHHhCCCCCHHHHHHHHHHHCCCCcC-cccH
Confidence            458999999999999999999986544333 4444

>TIGR03252 uncharacterized HhH-GPD family protein

Probab=94.48  E-value=0.031  Score=46.95  Aligned_cols=44  Identities=27%  Similarity=0.342  Sum_probs=32.7

Q ss_pred             ccHHHHHHHhhcccCcChHHHHHHHHhhcCCCCCcccHHHHHHhhC
Q 029726          102 PDLTKAVSELTVLKGVGPATASAVLAAYAPGVAPFMSDEAMGAALG  147 (189)
Q Consensus       102 ~d~~~al~~Lt~LkGVGPATASaiLa~~~P~~~pFfsDEa~~~~~g  147 (189)
                      |+-....+.|.+|+||||-||..||+...-+-  -.-||-|....|
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            45556689999999999999999999765431  145677766554

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).

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

Probab=94.38  E-value=0.046  Score=48.43  Aligned_cols=36  Identities=28%  Similarity=0.294  Sum_probs=29.4

Q ss_pred             cHHHHHHHhhcccCcChHHHHHHHHh--hcCCCCCcccH
Q 029726          103 DLTKAVSELTVLKGVGPATASAVLAA--YAPGVAPFMSD  139 (189)
Q Consensus       103 d~~~al~~Lt~LkGVGPATASaiLa~--~~P~~~pFfsD  139 (189)
                      +...+++.|++||||||-||..||-.  ..|+.+| -.|
T Consensus       201 ~~~~~~~~L~~LpGIGpwTA~~vllr~lg~~D~fp-~~D  238 (283)
T PRK10308        201 DVEQAMKTLQTFPGIGRWTANYFALRGWQAKDVFL-PDD  238 (283)
T ss_pred             CHHHHHHHHhcCCCcCHHHHHHHHHHhCCCCCCCC-ccc
Confidence            56778999999999999999999865  5787655 444

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

Probab=94.26  E-value=0.058  Score=49.51  Aligned_cols=56  Identities=25%  Similarity=0.335  Sum_probs=38.3

Q ss_pred             HHHhhcccCcChHHHHHHHHhhcCCCCCcccHHHHHH---hhC----CCCCCCHHHHHHHHHH
Q 029726          108 VSELTVLKGVGPATASAVLAAYAPGVAPFMSDEAMGA---ALG----HSKDYSLRQYLLFADK  163 (189)
Q Consensus       108 l~~Lt~LkGVGPATASaiLa~~~P~~~pFfsDEa~~~---~~g----~~~kYt~keY~~~~~~  163 (189)
                      .+.|.+|+||||-||+||||...-...|+..--+...   +.+    .+.+=+-+++..+.+.
T Consensus       112 ~~~l~~LpGiG~yTa~Ail~~a~~~~~~~lDgNV~RVl~R~f~i~~~~~~~~~~~~~~~~~~~  174 (342)
T COG1194         112 EEELAALPGVGPYTAGAILSFAFNQPEPVLDGNVKRVLSRLFAISGDIGKPKTKKELWELAEQ  174 (342)
T ss_pred             HHHHHhCCCCcHHHHHHHHHHHhCCCCceeecchheeehhhhcccccccccchhHHHHHHHHH
Confidence            4567779999999999999998777778766655542   222    1223456666666655

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

Probab=92.64  E-value=0.091  Score=30.42  Aligned_cols=19  Identities=47%  Similarity=0.763  Sum_probs=16.9

Q ss_pred             HhhcccCcChHHHHHHHHh
Q 029726          110 ELTVLKGVGPATASAVLAA  128 (189)
Q Consensus       110 ~Lt~LkGVGPATASaiLa~  128 (189)
                      .|++++|||+.+|..|+..
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=91.12  E-value=0.15  Score=38.73  Aligned_cols=26  Identities=27%  Similarity=0.261  Sum_probs=22.2

Q ss_pred             HHHHHHHhhcccCcChHHHHHHHHhh
Q 029726          104 LTKAVSELTVLKGVGPATASAVLAAY  129 (189)
Q Consensus       104 ~~~al~~Lt~LkGVGPATASaiLa~~  129 (189)
                      ..+.+..|+.|+|||||||-=+..++
T Consensus         7 ~~~~~~~L~~iP~IG~a~a~DL~~LG   32 (93)
T PF11731_consen    7 KRAGLSDLTDIPNIGKATAEDLRLLG   32 (93)
T ss_pred             HHHHHHHHhcCCCccHHHHHHHHHcC
Confidence            34578899999999999999888774

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=89.47  E-value=0.24  Score=33.69  Aligned_cols=22  Identities=36%  Similarity=0.351  Sum_probs=17.3

Q ss_pred             HHHhhcccCcChHHHHHHHHhh
Q 029726          108 VSELTVLKGVGPATASAVLAAY  129 (189)
Q Consensus       108 l~~Lt~LkGVGPATASaiLa~~  129 (189)
                      |+.++++-||||.||.-..+..
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 ....

>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=87.81  E-value=0.78  Score=32.01  Aligned_cols=31  Identities=32%  Similarity=0.415  Sum_probs=22.5

Q ss_pred             HHhhCccHHHHHHH-hhcccCcChHHHHHHHH
Q 029726           97 AFKSLPDLTKAVSE-LTVLKGVGPATASAVLA  127 (189)
Q Consensus        97 Af~~l~d~~~al~~-Lt~LkGVGPATASaiLa  127 (189)
                      +.+.+|..-..++. +.+|+|||+.+|.-|--
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            34556755555575 99999999999988743

...

>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional

Probab=87.48  E-value=0.39  Score=40.40  Aligned_cols=30  Identities=23%  Similarity=0.348  Sum_probs=25.1

Q ss_pred             cHHHHHHHhhcccCcChHHHHHHHHhhcCC
Q 029726          103 DLTKAVSELTVLKGVGPATASAVLAAYAPG  132 (189)
Q Consensus       103 d~~~al~~Lt~LkGVGPATASaiLa~~~P~  132 (189)
                      +-+.-+..|.+..||||-||-+||+.+.|+
T Consensus        67 ~Er~lF~~Li~V~GIGpK~Al~ILs~~~~~   96 (194)
T PRK14605         67 EELSLFETLIDVSGIGPKLGLAMLSAMNAE   96 (194)
T ss_pred             HHHHHHHHHhCCCCCCHHHHHHHHHhCCHH
Confidence            346678889999999999999999987764

>TIGR01259 comE comEA protein

Probab=86.85  E-value=0.77  Score=35.75  Aligned_cols=42  Identities=29%  Similarity=0.468  Sum_probs=33.7

Q ss_pred             HHHHHHhhcccCcChHHHHHHHHhhcCCCCCcccHHHHHHhhC
Q 029726          105 TKAVSELTVLKGVGPATASAVLAAYAPGVAPFMSDEAMGAALG  147 (189)
Q Consensus       105 ~~al~~Lt~LkGVGPATASaiLa~~~P~~~pFfsDEa~~~~~g  147 (189)
                      .+..+.|..|+||||.+|..|+.-..- ..||-|-|-+..+.|
T Consensus        64 tA~~~eL~~lpGIG~~~A~~Ii~~R~~-~g~f~s~eeL~~V~G  105 (120)
T TIGR01259        64 AASLEELQALPGIGPAKAKAIIEYREE-NGAFKSVDDLTKVSG  105 (120)
T ss_pred             cCCHHHHhcCCCCCHHHHHHHHHHHHh-cCCcCCHHHHHcCCC
Confidence            345678999999999999999998653 558888777776765

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.

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

Probab=86.59  E-value=1.1  Score=40.12  Aligned_cols=29  Identities=31%  Similarity=0.464  Sum_probs=26.4

Q ss_pred             cHHHHHHHhhcccCcChHHHHHHHHhhcC
Q 029726          103 DLTKAVSELTVLKGVGPATASAVLAAYAP  131 (189)
Q Consensus       103 d~~~al~~Lt~LkGVGPATASaiLa~~~P  131 (189)
                      |+-..++.|..|+||||-+|=+.|++.--
T Consensus       153 DIP~~v~dLlsLPGVGPKMa~L~m~~AWn  181 (286)
T KOG1921|consen  153 DIPDTVEDLLSLPGVGPKMAHLTMQVAWN  181 (286)
T ss_pred             CCchhHHHHhcCCCCchHHHHHHHHHHhc
Confidence            78889999999999999999999998543

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

Probab=85.62  E-value=2  Score=29.77  Aligned_cols=24  Identities=29%  Similarity=0.670  Sum_probs=17.7

Q ss_pred             HHHHHhhcccCcChHHHHHHHHhh
Q 029726          106 KAVSELTVLKGVGPATASAVLAAY  129 (189)
Q Consensus       106 ~al~~Lt~LkGVGPATASaiLa~~  129 (189)
                      +..+.|++++||||.+|..|....
T Consensus        32 a~~e~L~~i~gIG~~~A~si~~ff   55 (64)
T PF12826_consen   32 ASVEELSAIPGIGPKIAQSIYEFF   55 (64)
T ss_dssp             --HHHHCTSTT--HHHHHHHHHHH
T ss_pred             cCHHHHhccCCcCHHHHHHHHHHH
Confidence            357889999999999999998764

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

Probab=85.33  E-value=3.2  Score=36.04  Aligned_cols=68  Identities=22%  Similarity=0.278  Sum_probs=42.8

Q ss_pred             HHHHhhcccCcChHHHHHHHHhhcCCCCCcccHHHHHHhh---C-CCC-CCC-HHHHH--------HHHHHHHHHHHHHh
Q 029726          107 AVSELTVLKGVGPATASAVLAAYAPGVAPFMSDEAMGAAL---G-HSK-DYS-LRQYL--------LFADKLQAKAKFLK  172 (189)
Q Consensus       107 al~~Lt~LkGVGPATASaiLa~~~P~~~pFfsDEa~~~~~---g-~~~-kYt-~keY~--------~~~~~~~~~~~~L~  172 (189)
                      .-+.|-++||||+=||=+||--.. +..-|.-|..-.-+.   | ... +|+ +|+..        .+++..+++..+.+
T Consensus       113 ~R~~LL~iKGIG~ETaDsILlYa~-~rp~FVvD~Yt~R~l~rlg~i~~k~ydeik~~fe~~l~~~~~lyqe~HAlIv~~~  191 (215)
T COG2231         113 LREELLSIKGIGKETADSILLYAL-DRPVFVVDKYTRRLLSRLGGIEEKKYDEIKELFEENLPENLRLYQEFHALIVEHA  191 (215)
T ss_pred             HHHHHHccCCcchhhHHHHHHHHh-cCcccchhHHHHHHHHHhcccccccHHHHHHHHHhcchhHHHHHHHHHHHHHHHH
Confidence            357788999999999999987643 344677776554433   3 222 575 33332        24556666666666


Q ss_pred             hhc
Q 029726          173 KIA  175 (189)
Q Consensus       173 ~~~  175 (189)
                      +..
T Consensus       192 K~f  194 (215)
T COG2231         192 KHF  194 (215)
T ss_pred             HHH
Confidence            654

>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed

Probab=84.87  E-value=0.82  Score=38.17  Aligned_cols=27  Identities=33%  Similarity=0.541  Sum_probs=21.0

Q ss_pred             HHHHHHhhcccCcChHHHHHHHHhhcC
Q 029726          105 TKAVSELTVLKGVGPATASAVLAAYAP  131 (189)
Q Consensus       105 ~~al~~Lt~LkGVGPATASaiLa~~~P  131 (189)
                      +.....|..++||||.||-.||+.+.+
T Consensus        69 k~~f~~L~~i~GIGpk~A~~il~~fg~   95 (192)
T PRK00116         69 RELFRLLISVSGVGPKLALAILSGLSP   95 (192)
T ss_pred             HHHHHHHhcCCCCCHHHHHHHHHhCCH
Confidence            344678888999999999999887554

>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional

Probab=84.47  E-value=0.6  Score=39.21  Aligned_cols=30  Identities=23%  Similarity=0.350  Sum_probs=23.2

Q ss_pred             cHHHHHHHhhcccCcChHHHHHHHHhhcCC
Q 029726          103 DLTKAVSELTVLKGVGPATASAVLAAYAPG  132 (189)
Q Consensus       103 d~~~al~~Lt~LkGVGPATASaiLa~~~P~  132 (189)
                      +-+.-+..|.+..||||-||-+||+...|+
T Consensus        67 ~Er~lF~~LisV~GIGpK~Al~iLs~~~~~   96 (186)
T PRK14600         67 EEQDCLRMLVKVSGVNYKTAMSILSKLTPE   96 (186)
T ss_pred             HHHHHHHHHhCcCCcCHHHHHHHHccCCHH
Confidence            345567788888888888888888887664

>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=84.45  E-value=1  Score=30.52  Aligned_cols=23  Identities=26%  Similarity=0.479  Sum_probs=20.3

Q ss_pred             HHHHhhcccCcChHHHHHHHHhh
Q 029726          107 AVSELTVLKGVGPATASAVLAAY  129 (189)
Q Consensus       107 al~~Lt~LkGVGPATASaiLa~~  129 (189)
                      ....|..++||||.+|..|....
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

...

>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional

Probab=84.39  E-value=0.62  Score=39.67  Aligned_cols=29  Identities=28%  Similarity=0.385  Sum_probs=20.3

Q ss_pred             HHHHHHHhhcccCcChHHHHHHHHhhcCC
Q 029726          104 LTKAVSELTVLKGVGPATASAVLAAYAPG  132 (189)
Q Consensus       104 ~~~al~~Lt~LkGVGPATASaiLa~~~P~  132 (189)
                      -+.-+..|.+..||||-||-+|||...|+
T Consensus        67 Er~lF~~LisVsGIGPK~ALaILs~~~~~   95 (196)
T PRK13901         67 EREVFEELIGVDGIGPRAALRVLSGIKYN   95 (196)
T ss_pred             HHHHHHHHhCcCCcCHHHHHHHHcCCCHH
Confidence            34556677777777777777777776664

>TIGR00084 ruvA Holliday junction DNA helicase, RuvA subunit

Probab=84.36  E-value=0.66  Score=38.94  Aligned_cols=28  Identities=36%  Similarity=0.557  Sum_probs=21.6

Q ss_pred             HHHHHHHhhcccCcChHHHHHHHHhhcC
Q 029726          104 LTKAVSELTVLKGVGPATASAVLAAYAP  131 (189)
Q Consensus       104 ~~~al~~Lt~LkGVGPATASaiLa~~~P  131 (189)
                      -+.-+..|.+++||||-||-+||+...|
T Consensus        67 Er~lF~~L~~V~GIGpK~Al~iL~~~~~   94 (191)
T TIGR00084        67 ERELFKELIKVNGVGPKLALAILSNMSP   94 (191)
T ss_pred             HHHHHHHHhCCCCCCHHHHHHHHhcCCH
Confidence            4556777888888888888888887655

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.

>TIGR00608 radc DNA repair protein radc

Probab=82.86  E-value=1.7  Score=37.28  Aligned_cols=61  Identities=30%  Similarity=0.385  Sum_probs=39.3

Q ss_pred             CCCCHHHHHHHHHHHhhCCCCCcchhhHhhhCCHHHHHHHHHHHHhh------CccH-HHHHHHhhcccCcChHHHHHHH
Q 029726           54 PHINTTELSKLVRWKLTRGKWRPRLLDFVSSLDDSSVKSASEKAFKS------LPDL-TKAVSELTVLKGVGPATASAVL  126 (189)
Q Consensus        54 ~~ltkdEL~~LveWKL~rGkfRP~L~~lv~sN~~~~V~~~t~~Af~~------l~d~-~~al~~Lt~LkGVGPATASaiL  126 (189)
                      ..|+-.||..++   |.-|.-|-        +   .|...+++-++.      +.++ ....+.|++++|||||.|..|+
T Consensus        12 ~~Lsd~ELLail---L~~g~~~~--------~---~~~~lA~~ll~~f~~~g~l~~l~~a~~~eL~~i~GiG~aka~~l~   77 (218)
T TIGR00608        12 EALSDYELLAII---LRTGTPKG--------L---DVLSLSKRLLDVFGRQDSLGHLLSAPPEELSSVPGIGEAKAIQLK   77 (218)
T ss_pred             ccCCHHHHHHHH---HhCCCCCC--------C---CHHHHHHHHHHHhcccCCHHHHHhCCHHHHHhCcCCcHHHHHHHH
Confidence            578888866554   45554332        0   334444433332      3333 3357889999999999999999


Q ss_pred             Hh
Q 029726          127 AA  128 (189)
Q Consensus       127 a~  128 (189)
                      ++
T Consensus        78 a~   79 (218)
T TIGR00608        78 AA   79 (218)
T ss_pred             HH
Confidence            98

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

>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional

Probab=82.50  E-value=0.82  Score=38.40  Aligned_cols=29  Identities=28%  Similarity=0.303  Sum_probs=20.6

Q ss_pred             HHHHHHHhhcccCcChHHHHHHHHhhcCC
Q 029726          104 LTKAVSELTVLKGVGPATASAVLAAYAPG  132 (189)
Q Consensus       104 ~~~al~~Lt~LkGVGPATASaiLa~~~P~  132 (189)
                      -+.-+..|.+..||||-||-+|||...|+
T Consensus        68 Er~lF~~Li~VsGIGpK~Al~ILs~~~~~   96 (183)
T PRK14601         68 EQKMFEMLLKVNGIGANTAMAVCSSLDVN   96 (183)
T ss_pred             HHHHHHHHhccCCccHHHHHHHHcCCCHH
Confidence            34556777777777777777777776664

>PRK00024 hypothetical protein; Reviewed

Probab=81.82  E-value=2.3  Score=36.54  Aligned_cols=60  Identities=28%  Similarity=0.449  Sum_probs=40.2

Q ss_pred             CCCCHHHHHHHHHHHhhCCCCCcchhhHhhhCCHHHHHHHHHHHHhhCccH----HHHHHHhhcccCcChHHHHHHHHh
Q 029726           54 PHINTTELSKLVRWKLTRGKWRPRLLDFVSSLDDSSVKSASEKAFKSLPDL----TKAVSELTVLKGVGPATASAVLAA  128 (189)
Q Consensus        54 ~~ltkdEL~~LveWKL~rGkfRP~L~~lv~sN~~~~V~~~t~~Af~~l~d~----~~al~~Lt~LkGVGPATASaiLa~  128 (189)
                      ..|+-.||..++   |..|..|.            .|....++-++...++    ....+.|++++||||+.|..|+++
T Consensus        22 ~~Lsd~ELLa~l---L~~g~~~~------------~~~~LA~~LL~~fgsL~~l~~as~~eL~~i~GIG~akA~~L~a~   85 (224)
T PRK00024         22 AALSDAELLAIL---LRTGTKGK------------SVLDLARELLQRFGSLRGLLDASLEELQSIKGIGPAKAAQLKAA   85 (224)
T ss_pred             ccCCHHHHHHHH---HcCCCCCC------------CHHHHHHHHHHHcCCHHHHHhCCHHHHhhccCccHHHHHHHHHH
Confidence            578888865543   56665443            4555555544433332    234678999999999999999887

>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional

Probab=81.34  E-value=6  Score=33.70  Aligned_cols=111  Identities=14%  Similarity=0.192  Sum_probs=64.2

Q ss_pred             CCCCHHHHHHHHHHHhhCCCCCc-chhhHhhhCCHHHHHHHHHHHHhhCccHHHHHHHhhcccCcChHHHHHHHHhhcC-
Q 029726           54 PHINTTELSKLVRWKLTRGKWRP-RLLDFVSSLDDSSVKSASEKAFKSLPDLTKAVSELTVLKGVGPATASAVLAAYAP-  131 (189)
Q Consensus        54 ~~ltkdEL~~LveWKL~rGkfRP-~L~~lv~sN~~~~V~~~t~~Af~~l~d~~~al~~Lt~LkGVGPATASaiLa~~~P-  131 (189)
                      ++.|++|..-...-.--.| -=| .-+..++..+++.+.+++..         .=.+.||+++|||+-||.=|.-=... 
T Consensus        61 GF~t~~Er~lF~~LisVsG-IGPK~ALaILs~~~~~el~~aI~~---------~D~~~L~~vpGIGkKtAeRIIlELkdK  130 (196)
T PRK13901         61 GFLNSSEREVFEELIGVDG-IGPRAALRVLSGIKYNEFRDAIDR---------EDIELISKVKGIGNKMAGKIFLKLRGK  130 (196)
T ss_pred             CCCCHHHHHHHHHHhCcCC-cCHHHHHHHHcCCCHHHHHHHHHh---------CCHHHHhhCCCCCHHHHHHHHHHHHHh
Confidence            5788888655444433333 233 34556666677666655533         23568999999999999977632111 


Q ss_pred             -------CCCCcccHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHhhhcc
Q 029726          132 -------GVAPFMSDEAMGAALGHSKDYSLRQYLLFADKLQAKAKFLKKIAS  176 (189)
Q Consensus       132 -------~~~pFfsDEa~~~~~g~~~kYt~keY~~~~~~~~~~~~~L~~~~~  176 (189)
                             ...+-..+|+..++..  ..|+-++=...+..+.-.-..|+-+++
T Consensus       131 l~~~~~~~~~~~~~~ea~~AL~~--LGy~~~ea~~al~~v~~~~~~~~~~~~  180 (196)
T PRK13901        131 LVKNDELESSLFKFKELEQSIVN--MGFDRKLVNSAIKEIMLLDEFLNLKDS  180 (196)
T ss_pred             hccccccccCcccHHHHHHHHHH--cCCCHHHHHHHHHHHhcchhhhhhhhh
Confidence                   1111113677777653  557666666666555444455555443

>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=80.15  E-value=0.95  Score=30.62  Aligned_cols=41  Identities=29%  Similarity=0.458  Sum_probs=26.0

Q ss_pred             HHHHHHHHHHHhhCccHHH-HHHHhhcccCcChHHHHHHHHh
Q 029726           88 SSVKSASEKAFKSLPDLTK-AVSELTVLKGVGPATASAVLAA  128 (189)
Q Consensus        88 ~~V~~~t~~Af~~l~d~~~-al~~Lt~LkGVGPATASaiLa~  128 (189)
                      ..++.....+|..+.|+.. ..+.|++++|||+.+|.-|...
T Consensus        16 ~~a~~L~~~G~~t~~~l~~a~~~~L~~i~Gig~~~a~~i~~~   57 (60)
T PF14520_consen   16 KRAEKLYEAGIKTLEDLANADPEELAEIPGIGEKTAEKIIEA   57 (60)
T ss_dssp             HHHHHHHHTTCSSHHHHHTSHHHHHHTSTTSSHHHHHHHHHH
T ss_pred             HHHHHHHhcCCCcHHHHHcCCHHHHhcCCCCCHHHHHHHHHH
Confidence            3334443444443333322 4577999999999999988764

...

---

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

No hit with e-value below 0.005

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	189
3fhf_A	214	Mjogg, N-glycosylase/DNA lyase, DNA-(apurinic; hel	97.59
3n0u_A	219	Probable N-glycosylase/DNA lyase; structural genom	97.57
3fhg_A	207	Mjogg, N-glycosylase/DNA lyase, DNA-(apurinic; hel	97.57
3s6i_A	228	DNA-3-methyladenine glycosylase 1; DNA glycosylase	96.61
2h56_A	233	DNA-3-methyladenine glycosidase; 10174367, EC 3.2.	96.21
3i0w_A	290	8-oxoguanine-DNA-glycosylase; OGG, cacogg, DNA, 8-	96.13
2xhi_A	360	N-glycosylase/DNA lyase; lyase-DNA complex, lyase/	95.96
4e9f_A	161	Methyl-CPG-binding domain protein 4; HHH DNA glyco	95.95
2yg9_A	225	DNA-3-methyladenine glycosidase II, putative; hydr	95.82
4b21_A	232	Probable DNA-3-methyladenine glycosylase 2; hydrol	95.77
2jhn_A	295	ALKA, 3-methyladenine DNA-glycosylase; DNA repair,	95.72
1mpg_A	282	ALKA, 3-methyladenine DNA glycosylase II; DNA repa	95.7
1pu6_A	218	3-methyladenine DNA glycosylase; helix-hairpin-hel	95.43
1kg2_A	225	A/G-specific adenine glycosylase; DNA repair, hydr	95.13
2abk_A	211	Endonuclease III; DNA-repair, DNA glycosylase; 1.8	94.91
1orn_A	226	Endonuclease III; DNA repair, DNA glycosylase, [4F	94.53
1kea_A	221	Possible G-T mismatches repair enzyme; DNA repair,	94.47
3fsp_A	369	A/G-specific adenine glycosylase; protein-DNA comp	93.96
3n5n_X	287	A/G-specific adenine DNA glycosylase; alpha-helice	92.75
1s5l_U	134	Photosystem II 12 kDa extrinsic protein; photosynt	92.13
3arc_U	97	Photosystem II 12 kDa extrinsic protein; PSII, mem	91.77
2duy_A	75	Competence protein comea-related protein; helix-ha	90.29
2i5h_A	205	Hypothetical protein AF1531; PFAM:DUF655, PSI-2, s	90.2
1x2i_A	75	HEF helicase/nuclease; alpha helix, helix-hairpin-	88.98
2a1j_B	91	DNA excision repair protein ERCC-1; XPF, xeroderma	88.94
1kft_A	78	UVRC, excinuclease ABC subunit C; helix-hairpin-he	87.63
2ztd_A	212	Holliday junction ATP-dependent DNA helicase RUVA;	86.7
2edu_A	98	Kinesin-like protein KIF22; kinesin-like DNA bindi	84.93
1ixr_A	191	Holliday junction DNA helicase RUVA; heterooligome	84.47
1cuk_A	203	RUVA protein; DNA repair, SOS response, DNA-bindin	82.19
1z00_A	89	DNA excision repair protein ERCC-1; helix-hairpin-	81.39
1x2i_A	75	HEF helicase/nuclease; alpha helix, helix-hairpin-	81.03
2a1j_A	63	DNA repair endonuclease XPF; XPF, xeroderma pigmen	80.98
3u5c_S	146	40S ribosomal protein S18-A, 40S ribosomal protein	80.4
1z00_A	89	DNA excision repair protein ERCC-1; helix-hairpin-	80.27

>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=97.59  E-value=0.00031  Score=58.74  Aligned_cols=76  Identities=22%  Similarity=0.194  Sum_probs=57.1

Q ss_pred             HhhCccHHHHHHHhh-cccCcChHHHHHHHHhhcCCCCCcc-cHHHHHHhh---C----CCCCCCHHHHHHHHHHHHHHH
Q 029726           98 FKSLPDLTKAVSELT-VLKGVGPATASAVLAAYAPGVAPFM-SDEAMGAAL---G----HSKDYSLRQYLLFADKLQAKA  168 (189)
Q Consensus        98 f~~l~d~~~al~~Lt-~LkGVGPATASaiLa~~~P~~~pFf-sDEa~~~~~---g----~~~kYt~keY~~~~~~~~~~~  168 (189)
                      |..+.++..+.+.|. +|+||||-||++||....  ..+|+ -|--..-++   |    .+...|-+.|.++-..++..+
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            444457888999999 999999999999998642  23555 666544332   4    235678999999999999999


Q ss_pred             HHHhhhc
Q 029726          169 KFLKKIA  175 (189)
Q Consensus       169 ~~L~~~~  175 (189)
                      ++++...
T Consensus       191 ~~~g~~~  197 (214)
T 3fhf_A          191 EEVNLKL  197 (214)
T ss_dssp             HHTTCCH
T ss_pred             HHHCCCH
Confidence            9988754

>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=97.57  E-value=0.00024  Score=59.54  Aligned_cols=72  Identities=22%  Similarity=0.245  Sum_probs=54.0

Q ss_pred             cHHHHHHHhh-cccCcChHHHHHHHHh-hcCCCCCcccHHHHHHh--hC----CCCCCCHHHHHHHHHHHHHHHHHHhhh
Q 029726          103 DLTKAVSELT-VLKGVGPATASAVLAA-YAPGVAPFMSDEAMGAA--LG----HSKDYSLRQYLLFADKLQAKAKFLKKI  174 (189)
Q Consensus       103 d~~~al~~Lt-~LkGVGPATASaiLa~-~~P~~~pFfsDEa~~~~--~g----~~~kYt~keY~~~~~~~~~~~~~L~~~  174 (189)
                      ++..+.+.|+ +|+||||-||++||.. ..++.+| .++-+...+  .|    .+..-|-+.|.++-+.+++.++++|..
T Consensus       123 ~~~~~r~~L~~~l~GVG~kTA~~vL~~~g~~~~~~-VDthv~Ri~~rlg~~~~~~k~~t~k~y~~ie~~~~~~a~~~g~~  201 (219)
T 3n0u_A          123 DPFQSREFLVRNAKGIGWKEASHFLRNTGVEDLAI-LDKHVLRLMKRHGLIQEIPKGWSKKRYLYVEEILRKVAEAFGES  201 (219)
T ss_dssp             CHHHHHHHHHHHSTTCCHHHHHHHHHTTTCCSCCC-CCHHHHHHHHHTTSCSSCCSSCCHHHHHHHHHHHHHHHHHHTCC
T ss_pred             CcHHHHHHHHHhCCCCCHHHHHHHHHHcCCCCeee-ecHHHHHHHHHcCCCCcCcCcCCHHHHHHHHHHHHHHHHHHCCC
Confidence            6778999999 9999999999999985 3433333 344444422  23    244778999999999999999998875


Q ss_pred             c
Q 029726          175 A  175 (189)
Q Consensus       175 ~  175 (189)
                      .
T Consensus       202 ~  202 (219)
T 3n0u_A          202 P  202 (219)
T ss_dssp             H
T ss_pred             H
Confidence            4

>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=97.57  E-value=0.00034  Score=57.49  Aligned_cols=72  Identities=24%  Similarity=0.242  Sum_probs=52.6

Q ss_pred             cHHHHHHHhhcccCcChHHHHHHHHh-hcCCCCCcccHHHHHHh--hC--C---CCCCCHHHHHHHHHHHHHHHHHHhhh
Q 029726          103 DLTKAVSELTVLKGVGPATASAVLAA-YAPGVAPFMSDEAMGAA--LG--H---SKDYSLRQYLLFADKLQAKAKFLKKI  174 (189)
Q Consensus       103 d~~~al~~Lt~LkGVGPATASaiLa~-~~P~~~pFfsDEa~~~~--~g--~---~~kYt~keY~~~~~~~~~~~~~L~~~  174 (189)
                      +...+.+.|++||||||-||++||.. ..++ ++...+-+...+  .|  .   +..-|.++|.++-..++..++.++..
T Consensus       111 ~~~~~~~~L~~lpGIG~kTA~~il~~~~~~~-~~~vD~~v~Ri~~rlg~~~~~~~k~~~~k~y~~~~~~l~~~~~~~~~~  189 (207)
T 3fhg_A          111 DQQLARERLLNIKGIGMQEASHFLRNVGYFD-LAIIDRHIIDFMRRIGAIGETNVKQLSKSLYISFENILKSIASNLNMS  189 (207)
T ss_dssp             CHHHHHHHHTTSTTCCHHHHHHHHHHTTCCS-SCCCCHHHHHHHHHTTSSCCCCCSCCCHHHHHHHHHHHHHHHHHTTSC
T ss_pred             CHHHHHHHHHcCCCcCHHHHHHHHHHhCCCC-cceecHHHHHHHHHcCCCCccccccCCHHHHHHHHHHHHHHHHHhCCC
Confidence            45578999999999999999999996 5543 222333344322  23  1   24678999999999999999988765


Q ss_pred             c
Q 029726          175 A  175 (189)
Q Consensus       175 ~  175 (189)
                      .
T Consensus       190 ~  190 (207)
T 3fhg_A          190 V  190 (207)
T ss_dssp             H
T ss_pred             H
Confidence            3

>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=96.61  E-value=0.0033  Score=52.47  Aligned_cols=38  Identities=26%  Similarity=0.363  Sum_probs=29.3

Q ss_pred             HHHHHHHhhcccCcChHHHHHHHHh--hcCCCCCcccHHHH
Q 029726          104 LTKAVSELTVLKGVGPATASAVLAA--YAPGVAPFMSDEAM  142 (189)
Q Consensus       104 ~~~al~~Lt~LkGVGPATASaiLa~--~~P~~~pFfsDEa~  142 (189)
                      ...+++.|++|+||||-||.+||..  ..|+.+| ..|=.+
T Consensus       134 ~~e~~~~L~~l~GIG~~TA~~ill~~lg~pd~fp-vdD~~v  173 (228)
T 3s6i_A          134 NEELIERLTQIKGIGRWTVEMLLIFSLNRDDVMP-ADDLSI  173 (228)
T ss_dssp             HHHHHHHHTTSTTCCHHHHHHHHHHTSCCSSCCC-TTCHHH
T ss_pred             HHHHHHHHHhCCCcCHHHHHHHHHHhCCCCCEEe-cccHHH
Confidence            4668999999999999999999976  4676656 344333

>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=96.21  E-value=0.008  Score=50.15  Aligned_cols=38  Identities=26%  Similarity=0.366  Sum_probs=29.4

Q ss_pred             HHHHHHhhcccCcChHHHHHHHHhh--cCCCCCcccHHHHH
Q 029726          105 TKAVSELTVLKGVGPATASAVLAAY--APGVAPFMSDEAMG  143 (189)
Q Consensus       105 ~~al~~Lt~LkGVGPATASaiLa~~--~P~~~pFfsDEa~~  143 (189)
                      ..+++.|++|+||||-||++||...  .|+.+| ..|=.+.
T Consensus       134 ~~~~~~L~~lpGIG~kTA~~ill~alg~pd~~p-vdd~~~r  173 (233)
T 2h56_A          134 TTVIEKLTAIKGIGQWTAEMFMMFSLGRLDVLS-VGDVGLQ  173 (233)
T ss_dssp             HHHHHHHHTSTTCCHHHHHHHHHHTTCCSCCCC-TTCHHHH
T ss_pred             HHHHHHHHhCCCcCHHHHHHHHHHhCCCCCeee-CchHHHH
Confidence            4789999999999999999999874  666655 4444443

>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=96.13  E-value=0.0034  Score=54.09  Aligned_cols=41  Identities=24%  Similarity=0.320  Sum_probs=33.1

Q ss_pred             cHHHHHHHhhcccCcChHHHHHHHHh--hcCCCCCcccHHHHHHh
Q 029726          103 DLTKAVSELTVLKGVGPATASAVLAA--YAPGVAPFMSDEAMGAA  145 (189)
Q Consensus       103 d~~~al~~Lt~LkGVGPATASaiLa~--~~P~~~pFfsDEa~~~~  145 (189)
                      +...+.+.|++||||||-||..||..  ..|+.+|.  |-...-+
T Consensus       205 ~~~~~~~~L~~lpGIG~~TA~~ill~~lg~pd~fpv--D~~v~r~  247 (290)
T 3i0w_A          205 NDNECHEELKKFMGVGPQVADCIMLFSMQKYSAFPV--DTWVKKA  247 (290)
T ss_dssp             CHHHHHHHHTTSTTCCHHHHHHHHHHHHCCTTCCCC--CHHHHHH
T ss_pred             CHHHHHHHHHhCCCcCHHHHHHHHHHhCCCCCccee--cHHHHHH
Confidence            46789999999999999999999965  57888885  6655433

>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=95.96  E-value=0.049  Score=48.43  Aligned_cols=34  Identities=26%  Similarity=0.421  Sum_probs=28.8

Q ss_pred             cHHHHHHHhhcccCcChHHHHHHHHh--hcCCCCCc
Q 029726          103 DLTKAVSELTVLKGVGPATASAVLAA--YAPGVAPF  136 (189)
Q Consensus       103 d~~~al~~Lt~LkGVGPATASaiLa~--~~P~~~pF  136 (189)
                      +...+++.|++|+||||-||.+||..  ..|+.+|.
T Consensus       247 ~~~~~~~~L~~LpGIGp~TA~~ill~alg~pd~fpv  282 (360)
T 2xhi_A          247 SYEEAHKALCILPGVGTCVADKICLMALDKPQAVPV  282 (360)
T ss_dssp             CHHHHHHHHTTSTTCCHHHHHHHHHHHSCCTTCCCC
T ss_pred             CHHHHHHHHHhCCCCCHHHHHHHHHHhCCCCCEEEe
Confidence            35589999999999999999999986  47777674

>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=95.95  E-value=0.0038  Score=49.92  Aligned_cols=73  Identities=16%  Similarity=0.072  Sum_probs=45.3

Q ss_pred             CHHHHHHHHHHHhhCCCCCcchhhHhhhCCHHHHHHHHH-------HHHhhCc----cHHHHHHHhhcccCcChHHHHHH
Q 029726           57 NTTELSKLVRWKLTRGKWRPRLLDFVSSLDDSSVKSASE-------KAFKSLP----DLTKAVSELTVLKGVGPATASAV  125 (189)
Q Consensus        57 tkdEL~~LveWKL~rGkfRP~L~~lv~sN~~~~V~~~t~-------~Af~~l~----d~~~al~~Lt~LkGVGPATASai  125 (189)
                      |+++-+.-+-.+|-.  .-|+...|.+.+ ++.|++..+       +|-.+..    .+....+.|.+|+||||-||.+|
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--KYPSAEVARTAD-WRDVSELLKPLGLYDLRAKTIVKFSDEYLTKQWKYPIELHGIGKYGNDSY  120 (161)
T ss_dssp             SCHHHHHHHHHHHHH--HSCSHHHHTTSC-HHHHHHHHGGGSCHHHHHHHHHHHHHHHHHSCCSSGGGSTTCCHHHHHHH
T ss_pred             CcHHHHHHHHHHHHH--HCCCHHHHhccC-hHhHHhHhhhcCCHHHHHHHHHHHhCCcCCCChhhhhcCCCchHHHHHHH
Confidence            567777666666652  347877776554 444544432       1111100    13334577999999999999999


Q ss_pred             HHhhcCC
Q 029726          126 LAAYAPG  132 (189)
Q Consensus       126 La~~~P~  132 (189)
                      +++..-+
T Consensus       121 ~~F~~~e  127 (161)
T 4e9f_A          121 RIFCVNE  127 (161)
T ss_dssp             HHHTSSC
T ss_pred             HHHHCCC
Confidence            9986543

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

Probab=95.82  E-value=0.016  Score=48.19  Aligned_cols=39  Identities=31%  Similarity=0.311  Sum_probs=30.0

Q ss_pred             cHHHHHHHhhcccCcChHHHHHHHHhh--cCCCCCcccHHHH
Q 029726          103 DLTKAVSELTVLKGVGPATASAVLAAY--APGVAPFMSDEAM  142 (189)
Q Consensus       103 d~~~al~~Lt~LkGVGPATASaiLa~~--~P~~~pFfsDEa~  142 (189)
                      +...+++.|++|+||||-||.+||...  .|+.+| ..|-..
T Consensus       140 ~~~e~~~~L~~l~GIG~~TA~~ill~~lg~~d~fp-v~D~~v  180 (225)
T 2yg9_A          140 PDELVIAELVQLPGIGRWTAEMFLLFALARPDVFS-SGDLAL  180 (225)
T ss_dssp             CHHHHHHHHHTSTTCCHHHHHHHHHHTSCCSCCCC-TTCHHH
T ss_pred             CHHHHHHHHHcCCCCCHHHHHHHHHHhCCCCCeee-CccHHH
Confidence            456789999999999999999999874  566655 335443

>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=95.77  E-value=0.0072  Score=50.67  Aligned_cols=38  Identities=18%  Similarity=0.191  Sum_probs=29.6

Q ss_pred             HHHHHHHhhcccCcChHHHHHHHHhh--cCCCCCcccHHHH
Q 029726          104 LTKAVSELTVLKGVGPATASAVLAAY--APGVAPFMSDEAM  142 (189)
Q Consensus       104 ~~~al~~Lt~LkGVGPATASaiLa~~--~P~~~pFfsDEa~  142 (189)
                      ...+++.|++||||||-||.+||...  .|+.+| ..|-..
T Consensus       145 ~~~~~~~L~~l~GIG~~TA~~ill~alg~pd~fp-v~D~~v  184 (232)
T 4b21_A          145 EEELMESLSKIKGVKRWTIEMYSIFTLGRLDIMP-ADDSTL  184 (232)
T ss_dssp             HHHHHHHHTTSTTCCHHHHHHHHHHTSCCSSCCC-TTCHHH
T ss_pred             HHHHHHHHHhCCCcCHHHHHHHHHHhCCCCCeee-CccHHH
Confidence            34689999999999999999999874  576656 335444

>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=95.72  E-value=0.031  Score=47.99  Aligned_cols=38  Identities=34%  Similarity=0.384  Sum_probs=29.2

Q ss_pred             HHHHHHhhcccCcChHHHHHHHHhh-cCCCCCcccHHHHH
Q 029726          105 TKAVSELTVLKGVGPATASAVLAAY-APGVAPFMSDEAMG  143 (189)
Q Consensus       105 ~~al~~Lt~LkGVGPATASaiLa~~-~P~~~pFfsDEa~~  143 (189)
                      ..+++.|++|+||||-||.+||... .|+.+| ..|=.+.
T Consensus       206 ~e~~~~L~~lpGIG~~TA~~ill~~lg~d~fp-vdD~~~r  244 (295)
T 2jhn_A          206 EEAYEYLTSFKGIGRWTAELVLSIALGKNVFP-ADDLGVR  244 (295)
T ss_dssp             HHHHHHHHTSTTCCHHHHHHHHHHTTCCCCCC-TTCHHHH
T ss_pred             HHHHHHHhcCCCcCHHHHHHHHHHccCCCccc-chHHHHH
Confidence            6789999999999999999999862 376655 4454443

>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=95.70  E-value=0.019  Score=48.96  Aligned_cols=43  Identities=23%  Similarity=0.219  Sum_probs=33.2

Q ss_pred             cHHHHHHHhhcccCcChHHHHHHHHhh--cCCCCCcccHHHHHHhh
Q 029726          103 DLTKAVSELTVLKGVGPATASAVLAAY--APGVAPFMSDEAMGAAL  146 (189)
Q Consensus       103 d~~~al~~Lt~LkGVGPATASaiLa~~--~P~~~pFfsDEa~~~~~  146 (189)
                      +...+++.|++|+||||-||.+||...  .|+.+| ..|-.+....
T Consensus       201 ~~~~~~~~L~~lpGIG~~TA~~ill~~lg~~d~~p-vdd~~~r~~l  245 (282)
T 1mpg_A          201 DVEQAMKTLQTFPGIGRWTANYFALRGWQAKDVFL-PDDYLIKQRF  245 (282)
T ss_dssp             CHHHHHHHHTTSTTCCHHHHHHHHHHHSCCSSCCC-TTCHHHHHHS
T ss_pred             CHHHHHHHHhcCCCcCHHHHHHHHHHhCCCCCcCc-cccHHHHHHh
Confidence            677899999999999999999999864  566544 4565555444

>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=95.43  E-value=0.015  Score=48.07  Aligned_cols=38  Identities=21%  Similarity=0.166  Sum_probs=27.4

Q ss_pred             HHHHHHHhhcccCcChHHHHHHHHhhcCCCCCcccHHHH
Q 029726          104 LTKAVSELTVLKGVGPATASAVLAAYAPGVAPFMSDEAM  142 (189)
Q Consensus       104 ~~~al~~Lt~LkGVGPATASaiLa~~~P~~~pFfsDEa~  142 (189)
                      ...+++.|++||||||-||++||....-.. .|-.|--.
T Consensus       116 ~~~~~~~L~~lpGIG~kTA~~il~~a~~~~-~~~vD~~v  153 (218)
T 1pu6_A          116 QEVTREWLLDQKGIGKESADAILCYACAKE-VMVVDKYS  153 (218)
T ss_dssp             HHCCHHHHHTSTTCCHHHHHHHHHHTTCCS-CCCCCHHH
T ss_pred             chHHHHHHHcCCCcCHHHHHHHHHHHCCCC-ccccCHHH
Confidence            455788899999999999999999753222 33445443

>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=95.13  E-value=0.011  Score=48.94  Aligned_cols=37  Identities=27%  Similarity=0.292  Sum_probs=27.0

Q ss_pred             HHHHHhhcccCcChHHHHHHHHhhcCCCCCcccHHHHH
Q 029726          106 KAVSELTVLKGVGPATASAVLAAYAPGVAPFMSDEAMG  143 (189)
Q Consensus       106 ~al~~Lt~LkGVGPATASaiLa~~~P~~~pFfsDEa~~  143 (189)
                      .+++.|++|+||||-||.+||....-.. -|..|--..
T Consensus       106 ~~~~~L~~lpGIG~~TA~~il~~a~~~~-~~~vD~~v~  142 (225)
T 1kg2_A          106 ETFEEVAALPGVGRSTAGAILSLSLGKH-FPILDGNVK  142 (225)
T ss_dssp             CSHHHHHTSTTCCHHHHHHHHHHHHCCS-CCCCCHHHH
T ss_pred             HHHHHHhcCCCCcHHHHHHHHHHhCCCC-cceeCHHHH
Confidence            4678999999999999999998753222 245665443

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

Probab=94.91  E-value=0.024  Score=46.30  Aligned_cols=25  Identities=36%  Similarity=0.457  Sum_probs=22.0

Q ss_pred             HHHHHHhhcccCcChHHHHHHHHhh
Q 029726          105 TKAVSELTVLKGVGPATASAVLAAY  129 (189)
Q Consensus       105 ~~al~~Lt~LkGVGPATASaiLa~~  129 (189)
                      ..+++.|++|+||||-||.+||...
T Consensus       105 ~~~~~~L~~l~GIG~~tA~~il~~~  129 (211)
T 2abk_A          105 PEDRAALEALPGVGRKTANVVLNTA  129 (211)
T ss_dssp             CSCHHHHHHSTTCCHHHHHHHHHHH
T ss_pred             hHHHHHHHhCCCCChHHHHHHHHHH
Confidence            3467889999999999999999974

>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=94.53  E-value=0.034  Score=46.10  Aligned_cols=25  Identities=36%  Similarity=0.469  Sum_probs=21.9

Q ss_pred             HHHHHHhhcccCcChHHHHHHHHhh
Q 029726          105 TKAVSELTVLKGVGPATASAVLAAY  129 (189)
Q Consensus       105 ~~al~~Lt~LkGVGPATASaiLa~~  129 (189)
                      ..+++.|++|+||||-||.+||...
T Consensus       109 p~~~~~L~~lpGIG~~TA~~il~~a  133 (226)
T 1orn_A          109 PRDRDELMKLPGVGRKTANVVVSVA  133 (226)
T ss_dssp             CSCHHHHTTSTTCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHCCCccHHHHHHHHHHH
Confidence            3467899999999999999999874

>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=94.47  E-value=0.04  Score=45.41  Aligned_cols=35  Identities=26%  Similarity=0.241  Sum_probs=25.7

Q ss_pred             HHHHHhhcccCcChHHHHHHHHhhcCCCCCcccHHH
Q 029726          106 KAVSELTVLKGVGPATASAVLAAYAPGVAPFMSDEA  141 (189)
Q Consensus       106 ~al~~Lt~LkGVGPATASaiLa~~~P~~~pFfsDEa  141 (189)
                      .+++.|.+|+||||-||.+||....-.. .|-.|--
T Consensus       112 ~~~~~L~~lpGIG~~TA~~il~~~~~~~-~~~vD~~  146 (221)
T 1kea_A          112 RNRKAILDLPGVGKYTCAAVMCLAFGKK-AAMVDAN  146 (221)
T ss_dssp             SCHHHHHTSTTCCHHHHHHHHHHTTCCC-CCCCCHH
T ss_pred             HHHHHHHhCCCCcHHHHHHHHHHhcCCC-cceecHH
Confidence            4578899999999999999999753322 2344543

>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=93.96  E-value=0.14  Score=44.80  Aligned_cols=37  Identities=35%  Similarity=0.416  Sum_probs=27.1

Q ss_pred             HHHHHHhhcccCcChHHHHHHHHhhcCCCCCcccHHHH
Q 029726          105 TKAVSELTVLKGVGPATASAVLAAYAPGVAPFMSDEAM  142 (189)
Q Consensus       105 ~~al~~Lt~LkGVGPATASaiLa~~~P~~~pFfsDEa~  142 (189)
                      ..+++.|.+|+||||-||.+||+...-..++ .-|--.
T Consensus       114 p~~~~~L~~l~GIG~~tA~~il~~~~~~~~~-~vD~~v  150 (369)
T 3fsp_A          114 PDDPDEFSRLKGVGPYTVGAVLSLAYGVPEP-AVDGNV  150 (369)
T ss_dssp             CCSHHHHHTSTTCCHHHHHHHHHHHHCCCCC-CCCHHH
T ss_pred             hhHHHHHhcCCCcCHHHHHHHHHHHCCCCcc-cccHHH
Confidence            3467889999999999999999986433333 444433

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

Probab=92.75  E-value=0.11  Score=45.08  Aligned_cols=36  Identities=25%  Similarity=0.227  Sum_probs=26.7

Q ss_pred             HHHHhhc-ccCcChHHHHHHHHhhcCCCCCcccHHHHH
Q 029726          107 AVSELTV-LKGVGPATASAVLAAYAPGVAPFMSDEAMG  143 (189)
Q Consensus       107 al~~Lt~-LkGVGPATASaiLa~~~P~~~pFfsDEa~~  143 (189)
                      .++.|.+ |+||||-||.+||....-.. .|..|--..
T Consensus       126 ~~~~Ll~~LpGIG~kTA~~iL~~a~g~p-~~~VDt~V~  162 (287)
T 3n5n_X          126 TAETLQQLLPGVGRYTAGAIASIAFGQA-TGVVDGNVA  162 (287)
T ss_dssp             SHHHHHHHSTTCCHHHHHHHHHHHSCCC-CCCCCHHHH
T ss_pred             HHHHHHHHcCCCCHHHHHHHHHHhcCCC-CccccHHHH
Confidence            5788887 99999999999999864332 345565443

>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=92.13  E-value=0.033  Score=43.84  Aligned_cols=37  Identities=22%  Similarity=0.340  Sum_probs=30.3

Q ss_pred             HHHHHhhcccCcChHHHHHHHHhhcCCCCCcccHHHHHHhhC
Q 029726          106 KAVSELTVLKGVGPATASAVLAAYAPGVAPFMSDEAMGAALG  147 (189)
Q Consensus       106 ~al~~Lt~LkGVGPATASaiLa~~~P~~~pFfsDEa~~~~~g  147 (189)
                      +..+.|++|+||||++|.+|..     +.||-|=|=+.-+.|
T Consensus        60 A~~~eL~~LpGiGp~~A~~II~-----~GpF~svedL~~V~G   96 (134)
T 1s5l_U           60 TNIAAFIQYRGLYPTLAKLIVK-----NAPYESVEDVLNIPG   96 (134)
T ss_dssp             SCGGGGGGSTTCTHHHHHHHHH-----TCCCSSGGGGGGCTT
T ss_pred             cCHHHHHHCCCCCHHHHHHHHH-----cCCCCCHHHHHhCCC
Confidence            3467899999999999999993     558888777776776

>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=91.77  E-value=0.039  Score=40.88  Aligned_cols=37  Identities=22%  Similarity=0.340  Sum_probs=30.0

Q ss_pred             HHHHHhhcccCcChHHHHHHHHhhcCCCCCcccHHHHHHhhC
Q 029726          106 KAVSELTVLKGVGPATASAVLAAYAPGVAPFMSDEAMGAALG  147 (189)
Q Consensus       106 ~al~~Lt~LkGVGPATASaiLa~~~P~~~pFfsDEa~~~~~g  147 (189)
                      +..+.|+.|+||||++|..|+.     .-||-|-|-+.-+.|
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            3467899999999999999999     348888777766655

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

Probab=90.29  E-value=0.13  Score=35.13  Aligned_cols=36  Identities=28%  Similarity=0.522  Sum_probs=26.8

Q ss_pred             HHHHhhcccCcChHHHHHHHHhhcCCCCCcccHHHHHHhhC
Q 029726          107 AVSELTVLKGVGPATASAVLAAYAPGVAPFMSDEAMGAALG  147 (189)
Q Consensus       107 al~~Lt~LkGVGPATASaiLa~~~P~~~pFfsDEa~~~~~g  147 (189)
                      ....|..++||||.+|..|+...     +|-+-+-+..+.|
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     5555555554544

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

Probab=90.20  E-value=0.059  Score=45.14  Aligned_cols=63  Identities=22%  Similarity=0.341  Sum_probs=41.7

Q ss_pred             hhhHhhhCCHHHHHHHHHHHHhhCccHHHHHHHhhcccCcChHHHHHHHHhhcCCCCCcccHHHHHH-hhC
Q 029726           78 LLDFVSSLDDSSVKSASEKAFKSLPDLTKAVSELTVLKGVGPATASAVLAAYAPGVAPFMSDEAMGA-ALG  147 (189)
Q Consensus        78 L~~lv~sN~~~~V~~~t~~Af~~l~d~~~al~~Lt~LkGVGPATASaiLa~~~P~~~pFfsDEa~~~-~~g  147 (189)
                      +.+.|+.|....|. .    |+....+.+.+..|..|+||||++|-+|+.--.-  -||-|=|-+.- +.|
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            34445555544443 2    3322334667788999999999999999998653  59999666643 665

>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=88.98  E-value=0.27  Score=32.78  Aligned_cols=23  Identities=26%  Similarity=0.442  Sum_probs=19.6

Q ss_pred             HHHhhcccCcChHHHHHHHHhhc
Q 029726          108 VSELTVLKGVGPATASAVLAAYA  130 (189)
Q Consensus       108 l~~Lt~LkGVGPATASaiLa~~~  130 (189)
                      .+.|++++||||.+|..|.+...
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            56788999999999999988864

>2a1j_B DNA excision repair protein ERCC-1; XPF, xeroderma pigmentosum, DNA repair, endonuclease, helix-hairpin-helix, DNA binding protein; HET: DNA; 2.70A {Homo sapiens} SCOP: a.60.2.5

Probab=88.94  E-value=0.73  Score=32.52  Aligned_cols=42  Identities=19%  Similarity=0.309  Sum_probs=27.0

Q ss_pred             hhCCHHHHHHHHHHHHhhCccHHHHHHHhhcccCcChHHHHHHHHhh
Q 029726           83 SSLDDSSVKSASEKAFKSLPDLTKAVSELTVLKGVGPATASAVLAAY  129 (189)
Q Consensus        83 ~sN~~~~V~~~t~~Af~~l~d~~~al~~Lt~LkGVGPATASaiLa~~  129 (189)
                      +.++++.+..-.+.-+     ....+..|+.++||||.||-.||..+
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            3456666655544433     33456678888889988888888764

>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=87.63  E-value=0.41  Score=32.86  Aligned_cols=22  Identities=18%  Similarity=0.365  Sum_probs=15.5

Q ss_pred             HHHhhcccCcChHHHHHHHHhh
Q 029726          108 VSELTVLKGVGPATASAVLAAY  129 (189)
Q Consensus       108 l~~Lt~LkGVGPATASaiLa~~  129 (189)
                      .+.|++++||||.+|..|.+..
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            4567777777777777776654

>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=86.70  E-value=0.28  Score=40.87  Aligned_cols=20  Identities=25%  Similarity=0.418  Sum_probs=10.2

Q ss_pred             HHhhcccCcChHHHHHHHHh
Q 029726          109 SELTVLKGVGPATASAVLAA  128 (189)
Q Consensus       109 ~~Lt~LkGVGPATASaiLa~  128 (189)
                      +.|++++|||+-||--|..-
T Consensus       123 ~~L~~vpGIG~KtA~rIi~e  142 (212)
T 2ztd_A          123 AALTRVPGIGKRGAERMVLE  142 (212)
T ss_dssp             HHHHTSTTCCHHHHHHHHHH
T ss_pred             HHHhhCCCCCHHHHHHHHHH
Confidence            44555555555555544433

>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=84.93  E-value=0.23  Score=35.77  Aligned_cols=49  Identities=22%  Similarity=0.319  Sum_probs=32.3

Q ss_pred             HHHhhcccCcChHHHHHHHHhhcCCCCCcccHHHHHHhhCCCCCCCHHHHHHHH
Q 029726          108 VSELTVLKGVGPATASAVLAAYAPGVAPFMSDEAMGAALGHSKDYSLRQYLLFA  161 (189)
Q Consensus       108 l~~Lt~LkGVGPATASaiLa~~~P~~~pFfsDEa~~~~~g~~~kYt~keY~~~~  161 (189)
                      ...|..++||||.+|..|+...... -+|-+-+-+..+.|    .+.+-+..++
T Consensus        39 ~~~L~~ipGIG~~~A~~Il~~r~~~-g~f~s~edL~~v~G----ig~k~~~~l~   87 (98)
T 2edu_A           39 ARDLRSLQRIGPKKAQLIVGWRELH-GPFSQVEDLERVEG----ITGKQMESFL   87 (98)
T ss_dssp             HHHHHHSTTCCHHHHHHHHHHHHHH-CCCSSGGGGGGSTT----CCHHHHHHHH
T ss_pred             HHHHHHCCCCCHHHHHHHHHHHHhc-CCcCCHHHHHhCCC----CCHHHHHHHH
Confidence            5678899999999999999986432 26655444554544    3444444443

>1ixr_A Holliday junction DNA helicase RUVA; heterooligomeric complex, octameric RUVA, AAA-ATPase domain, complex with nucleotide, hydrolase; HET: ANP; 3.30A {Thermus thermophilus} SCOP: a.60.2.1 b.40.4.2

Probab=84.47  E-value=0.52  Score=38.44  Aligned_cols=24  Identities=42%  Similarity=0.623  Sum_probs=13.5

Q ss_pred             HHHhhcccCcChHHHHHHHHhhcC
Q 029726          108 VSELTVLKGVGPATASAVLAAYAP  131 (189)
Q Consensus       108 l~~Lt~LkGVGPATASaiLa~~~P  131 (189)
                      +..|.+++||||.||-+||+.+.|
T Consensus        71 f~~L~~v~GIGpk~A~~iL~~f~~   94 (191)
T 1ixr_A           71 FELLLSVSGVGPKVALALLSALPP   94 (191)
T ss_dssp             HHHHHSSSCCCHHHHHHHHHHSCH
T ss_pred             HHHHhcCCCcCHHHHHHHHHhCCh
Confidence            344555666666666666665443

>1cuk_A RUVA protein; DNA repair, SOS response, DNA-binding, DNA recombination; 1.90A {Escherichia coli} SCOP: a.5.1.1 a.60.2.1 b.40.4.2 PDB: 1hjp_A 1bdx_A* 1c7y_A 1d8l_A

Probab=82.19  E-value=0.71  Score=37.94  Aligned_cols=27  Identities=33%  Similarity=0.480  Sum_probs=21.1

Q ss_pred             HHHHHHhhcccCcChHHHHHHHHhhcC
Q 029726          105 TKAVSELTVLKGVGPATASAVLAAYAP  131 (189)
Q Consensus       105 ~~al~~Lt~LkGVGPATASaiLa~~~P  131 (189)
                      +.-+..|.+++||||.+|-+||+.+.|
T Consensus        69 k~~f~~L~~V~GIGpk~A~~iL~~f~~   95 (203)
T 1cuk_A           69 RTLFKELIKTNGVGPKLALAILSGMSA   95 (203)
T ss_dssp             HHHHHHHHHSSSCCHHHHHHHHHHSCH
T ss_pred             HHHHHHHhcCCCcCHHHHHHHHhhCCh
Confidence            344567888999999999999998655

>1z00_A DNA excision repair protein ERCC-1; helix-hairpin-helix, hydrolase; HET: DNA; NMR {Homo sapiens} SCOP: a.60.2.5

Probab=81.39  E-value=1.3  Score=30.94  Aligned_cols=25  Identities=20%  Similarity=0.417  Sum_probs=20.3

Q ss_pred             HHHHHHhhcccCcChHHHHHHHHhh
Q 029726          105 TKAVSELTVLKGVGPATASAVLAAY  129 (189)
Q Consensus       105 ~~al~~Lt~LkGVGPATASaiLa~~  129 (189)
                      ...+..|+.++||||.+|-.|+..+
T Consensus        15 ~~~~~~L~~IpgIG~~~A~~Ll~~f   39 (89)
T 1z00_A           15 SRVTECLTTVKSVNKTDSQTLLTTF   39 (89)
T ss_dssp             HHHHHHHTTSSSCCHHHHHHHHHHT
T ss_pred             HHHHHHHHcCCCCCHHHHHHHHHHC
Confidence            3456678899999999999999874

>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=81.03  E-value=1.4  Score=29.13  Aligned_cols=25  Identities=16%  Similarity=0.145  Sum_probs=20.8

Q ss_pred             HHHHHHhhcccCcChHHHHHHHHhh
Q 029726          105 TKAVSELTVLKGVGPATASAVLAAY  129 (189)
Q Consensus       105 ~~al~~Lt~LkGVGPATASaiLa~~  129 (189)
                      ......|+.++||||.+|..|+..+
T Consensus        10 ~~~~~~L~~i~giG~~~a~~Ll~~f   34 (75)
T 1x2i_A           10 ERQRLIVEGLPHVSATLARRLLKHF   34 (75)
T ss_dssp             HHHHHHHTTSTTCCHHHHHHHHHHH
T ss_pred             HHHHHHHcCCCCCCHHHHHHHHHHc
Confidence            3345678999999999999999864

>2a1j_A DNA repair endonuclease XPF; XPF, xeroderma pigmentosum, DNA repair, endonuclease, helix-hairpin-helix, DNA binding protein; HET: DNA; 2.70A {Homo sapiens} SCOP: a.60.2.5 PDB: 2kn7_A*

Probab=80.98  E-value=0.53  Score=31.62  Aligned_cols=40  Identities=15%  Similarity=0.218  Sum_probs=26.0

Q ss_pred             HHHhhcccCcChHHHHHHHHhhc-CCCCCcccHHHHHHhhC
Q 029726          108 VSELTVLKGVGPATASAVLAAYA-PGVAPFMSDEAMGAALG  147 (189)
Q Consensus       108 l~~Lt~LkGVGPATASaiLa~~~-P~~~pFfsDEa~~~~~g  147 (189)
                      ...|..++||||.+.-.||.-+. -+.+.=.|-|-+..+.|
T Consensus         3 ~s~L~~IpGIG~kr~~~LL~~Fgs~~~i~~As~eeL~~vig   43 (63)
T 2a1j_A            3 QDFLLKMPGVNAKNCRSLMHHVKNIAELAALSQDELTSILG   43 (63)
T ss_dssp             CHHHHTSTTCCHHHHHHHHHHCSSHHHHHTCCHHHHHHHHS
T ss_pred             HhHHHcCCCCCHHHHHHHHHHcCCHHHHHHCCHHHHHHHcC
Confidence            46788999999999999998632 12223344444444444

>3u5c_S 40S ribosomal protein S18-A, 40S ribosomal protein S17-A; translation, ribosome, ribosomal, ribosomal R ribosomal protein, eukaryotic ribosome, RNA-protein C; 3.00A {Saccharomyces cerevisiae} PDB: 3izb_M 3o30_L 3o2z_L 3u5g_S 1s1h_M 3jyv_M* 2zkq_m

Probab=80.40  E-value=2.4  Score=33.51  Aligned_cols=49  Identities=24%  Similarity=0.302  Sum_probs=35.0

Q ss_pred             HHHHHhhcccCcChHHHHHHHHhh--cCC-CCCcccHHHHHHh---hCCCCCCCH
Q 029726          106 KAVSELTVLKGVGPATASAVLAAY--APG-VAPFMSDEAMGAA---LGHSKDYSL  154 (189)
Q Consensus       106 ~al~~Lt~LkGVGPATASaiLa~~--~P~-~~pFfsDEa~~~~---~g~~~kYt~  154 (189)
                      ...-+||.++|||+.||-.|+...  +|+ .+=-.+||-...+   ...+.+|.+
T Consensus        27 ~v~~ALt~I~GIG~~~A~~I~~~~gid~~~r~g~Lt~~ei~~l~~~i~~~~~~~i   81 (146)
T 3u5c_S           27 KIVYALTTIKGVGRRYSNLVCKKADVDLHKRAGELTQEELERIVQIMQNPTHYKI   81 (146)
T ss_dssp             CTTTTGGGSTTCCHHHHHHHHHHHTCCTTSCSSSCCHHHHHHHHHHHTCTTTTTC
T ss_pred             chHhhHhhhcCCCHHHHHHHHHHcCCCCCceeccCCHHHHHHHHHHHHhhcccCc
Confidence            344568999999999999999985  554 5566788766543   345556654

>1z00_A DNA excision repair protein ERCC-1; helix-hairpin-helix, hydrolase; HET: DNA; NMR {Homo sapiens} SCOP: a.60.2.5

Probab=80.27  E-value=1.1  Score=31.22  Aligned_cols=23  Identities=22%  Similarity=0.466  Sum_probs=20.5

Q ss_pred             HHHhhcccCcChHHHHHHHHhhc
Q 029726          108 VSELTVLKGVGPATASAVLAAYA  130 (189)
Q Consensus       108 l~~Lt~LkGVGPATASaiLa~~~  130 (189)
                      .+.|++++|||+.+|..|.+...
T Consensus        50 ~~eL~~i~GIG~~~a~~I~~~l~   72 (89)
T 1z00_A           50 REDLALCPGLGPQKARRLFDVLH   72 (89)
T ss_dssp             HHHHHTSTTCCHHHHHHHHHHHH
T ss_pred             HHHHHhCCCCCHHHHHHHHHHHH
Confidence            56789999999999999999864

---

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	189
d2noha1	190	8-oxoguanine glycosylase {Human (Homo sapiens) [Ta	97.13
d1keaa_	217	Thymine-DNA glycosylase {Archaeon Methanobacterium	96.56
d1rrqa1	221	Catalytic domain of MutY {Bacillus stearothermophi	96.36
d1orna_	214	Endonuclease III {Escherichia coli [TaxId: 562]}	96.29
d1mpga1	183	3-Methyladenine DNA glycosylase II (gene alkA or a	96.14
d1kg2a_	224	Catalytic domain of MutY {Escherichia coli [TaxId:	96.13
d2abka_	211	Endonuclease III {Escherichia coli [TaxId: 562]}	95.77
d1pu6a_	217	3-Methyladenine DNA glycosylase III (MagIII) {Heli	95.01
d1ngna_	144	Mismatch-specific thymine glycosylase domain of th	94.69
d2fmpa2	57	DNA polymerase beta {Human (Homo sapiens) [TaxId:	94.46
d1cuka2	78	DNA helicase RuvA subunit, middle domain {Escheric	92.61
d1ixra1	73	DNA helicase RuvA subunit, middle domain {Thermus	92.15
d1pzna1	61	DNA repair protein Rad51, N-terminal domain {Archa	92.04
d1bvsa2	71	DNA helicase RuvA subunit, middle domain {Mycobact	91.77
d1jmsa3	60	Terminal deoxynucleotidyl transferase {Mouse (Mus	91.7
d2a1jb1	78	DNA excision repair protein ERCC-1 {Human (Homo sa	91.41
d2axtu1	98	Photosystem II 12 kDa extrinsic protein PsbU {Ther	90.85
d2bcqa2	57	DNA polymerase lambda {Human (Homo sapiens) [TaxId	90.68
d2i1qa1	60	DNA repair protein Rad51, N-terminal domain {Archa	89.18
d2a1jb1	78	DNA excision repair protein ERCC-1 {Human (Homo sa	89.0
d2bgwa1	70	DNA repair endonuclease XPF {Aeropyrum pernix [Tax	88.6
d1kfta_	56	Excinuclease UvrC C-terminal domain {Escherichia c	87.23
d2bgwa1	70	DNA repair endonuclease XPF {Aeropyrum pernix [Tax	86.3
d1kfta_	56	Excinuclease UvrC C-terminal domain {Escherichia c	85.79
d1bvsa2	71	DNA helicase RuvA subunit, middle domain {Mycobact	85.78
d2a1ja1	62	DNA repair endonuclease XPF {Human (Homo sapiens)	85.59
d1cuka2	78	DNA helicase RuvA subunit, middle domain {Escheric	84.23
d2fmpa1	82	DNA polymerase beta, N-terminal (8 kD)-domain {Hum	84.08
d2duya1	65	Uncharacterized protein TTHA1967 {Thermus thermoph	83.74
d1x2ia1	68	ATP-dependent RNA helicase PF2015 {Pyrococcus furi	82.52
d2i1qa1	60	DNA repair protein Rad51, N-terminal domain {Archa	82.39
d1ixra1	73	DNA helicase RuvA subunit, middle domain {Thermus	82.34
d2bcqa1	76	DNA polymerase lambda {Human (Homo sapiens) [TaxId	82.19
d1x2ia1	68	ATP-dependent RNA helicase PF2015 {Pyrococcus furi	80.65
d2uubm1	125	Ribosomal protein S13 {Thermus thermophilus [TaxId	80.03

>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=97.13  E-value=0.00071  Score=52.63  Aligned_cols=63  Identities=19%  Similarity=0.232  Sum_probs=42.6

Q ss_pred             cHHHHHHHhhcccCcChHHHHHHHHh--hcCCCCCcccHHHHHHh---hC------CCCCCCHHHHHHHHHHHHH
Q 029726          103 DLTKAVSELTVLKGVGPATASAVLAA--YAPGVAPFMSDEAMGAA---LG------HSKDYSLRQYLLFADKLQA  166 (189)
Q Consensus       103 d~~~al~~Lt~LkGVGPATASaiLa~--~~P~~~pFfsDEa~~~~---~g------~~~kYt~keY~~~~~~~~~  166 (189)
                      +...+++.|++||||||-||.+||..  ..|+.+|. ..-+...+   .|      ...+-+.+.|.++.+..++
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            46779999999999999999998886  46777774 33333322   23      1234566777666555443

>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=96.56  E-value=0.0031  Score=50.26  Aligned_cols=84  Identities=18%  Similarity=0.158  Sum_probs=51.4

Q ss_pred             CHHHHHHHHHHHhhCCCCCcchhhHhhhCCHHHHHHHHH-------HHHhh------C-----ccHHHHHHHhhcccCcC
Q 029726           57 NTTELSKLVRWKLTRGKWRPRLLDFVSSLDDSSVKSASE-------KAFKS------L-----PDLTKAVSELTVLKGVG  118 (189)
Q Consensus        57 tkdEL~~LveWKL~rGkfRP~L~~lv~sN~~~~V~~~t~-------~Af~~------l-----~d~~~al~~Lt~LkGVG  118 (189)
                      |+++-+.-+-=+|. -+| |+...+.+.+ ++.|+++.+       +|-.+      +     ..+....+.|.+|+|||
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            56777766666663 223 7888887765 455554432       22110      0     02333578899999999


Q ss_pred             hHHHHHHHHhhcCCCCCcccHHHHH
Q 029726          119 PATASAVLAAYAPGVAPFMSDEAMG  143 (189)
Q Consensus       119 PATASaiLa~~~P~~~pFfsDEa~~  143 (189)
                      |-||++||+...-..++...+-+..
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            9999999999765443334444443

>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=96.36  E-value=0.0021  Score=51.19  Aligned_cols=36  Identities=31%  Similarity=0.298  Sum_probs=27.2

Q ss_pred             HHHHHhhcccCcChHHHHHHHHhhcCCCCCcccHHHH
Q 029726          106 KAVSELTVLKGVGPATASAVLAAYAPGVAPFMSDEAM  142 (189)
Q Consensus       106 ~al~~Lt~LkGVGPATASaiLa~~~P~~~pFfsDEa~  142 (189)
                      ...+.|.+|+||||-||++||++..-..+ |.-|--.
T Consensus       104 ~~~~~Ll~LpGIG~kTA~~il~~a~~~p~-~~VDt~v  139 (221)
T d1rrqa1         104 DDPDEFSRLKGVGPYTVGAVLSLAYGVPE-PAVNGNV  139 (221)
T ss_dssp             CSHHHHHTSTTCCHHHHHHHHHHHTCCCC-CCCCHHH
T ss_pred             hHHHHHHHHHHhhhHHHHHHHHHHhcCcc-cccCccH
Confidence            34678999999999999999999765443 3445433

>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=96.29  E-value=0.0061  Score=48.20  Aligned_cols=33  Identities=30%  Similarity=0.279  Sum_probs=24.9

Q ss_pred             HHHHhhcccCcChHHHHHHHHhhcCCCCCcccHH
Q 029726          107 AVSELTVLKGVGPATASAVLAAYAPGVAPFMSDE  140 (189)
Q Consensus       107 al~~Lt~LkGVGPATASaiLa~~~P~~~pFfsDE  140 (189)
                      ..+.|.+|+||||-||++||++..-.. .|.-|-
T Consensus       108 ~~~~L~~LpGVG~kTA~~il~~a~~~~-~~~VDt  140 (214)
T d1orna_         108 DRDELMKLPGVGRKTANVVVSVAFGVP-AIAVDT  140 (214)
T ss_dssp             CHHHHTTSTTCCHHHHHHHHHHHHCCC-CCCCCH
T ss_pred             CHHHHHhCcCcccchHHHHHHHHhcCC-cccccc
Confidence            467799999999999999999965433 333444

>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=96.14  E-value=0.0018  Score=50.23  Aligned_cols=40  Identities=25%  Similarity=0.244  Sum_probs=32.0

Q ss_pred             cHHHHHHHhhcccCcChHHHHHHHHh--hcCCCCCcccHHHHH
Q 029726          103 DLTKAVSELTVLKGVGPATASAVLAA--YAPGVAPFMSDEAMG  143 (189)
Q Consensus       103 d~~~al~~Lt~LkGVGPATASaiLa~--~~P~~~pFfsDEa~~  143 (189)
                      +...+++.|++||||||=||.+||-.  ..|+.+| ..|=.+.
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            67789999999999999999999866  5788777 4454443

>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=96.13  E-value=0.0028  Score=50.48  Aligned_cols=72  Identities=17%  Similarity=0.199  Sum_probs=43.3

Q ss_pred             CHHHHHHHHHHHhhCCCCCcchhhHhhhCCHHHHHHHHHHH-H-----------hhC-----ccHHHHHHHhhcccCcCh
Q 029726           57 NTTELSKLVRWKLTRGKWRPRLLDFVSSLDDSSVKSASEKA-F-----------KSL-----PDLTKAVSELTVLKGVGP  119 (189)
Q Consensus        57 tkdEL~~LveWKL~rGkfRP~L~~lv~sN~~~~V~~~t~~A-f-----------~~l-----~d~~~al~~Lt~LkGVGP  119 (189)
                      |+++-+.-+-=+|- .+ -|+...+.+.+ .+.++++.+-+ |           +.+     .++....+.|.+|+||||
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-AR-FPTVTDLANAP-LDEVLHLWTGLGYYARARNLHKAAQQVATLHGGKFPETFEEVAALPGVGR  119 (224)
T ss_dssp             SCHHHHHHHHHHHH-HH-CSSHHHHHHSC-HHHHHHHHTTSCCTHHHHHHHHHHHHHHHHSTTSCCCSHHHHHTSTTCCH
T ss_pred             CcHHHHHHHHHHHH-HH-hccHHHHHHhh-HHHHHhHhhhhhHHHHHHHHHHhhhhhhhhccCCcchHHHHHHHHHhhhh
Confidence            45665554433332 12 37887887775 45666554322 1           000     022334677999999999


Q ss_pred             HHHHHHHHhhcC
Q 029726          120 ATASAVLAAYAP  131 (189)
Q Consensus       120 ATASaiLa~~~P  131 (189)
                      -||++||+...-
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=95.77  E-value=0.011  Score=46.82  Aligned_cols=82  Identities=20%  Similarity=0.093  Sum_probs=46.8

Q ss_pred             CHHHHHHHHHHHhhCCCCCcchhhHhhhCCHHHHHHHHH-HHH------hh------C-----ccHHHHHHHhhcccCcC
Q 029726           57 NTTELSKLVRWKLTRGKWRPRLLDFVSSLDDSSVKSASE-KAF------KS------L-----PDLTKAVSELTVLKGVG  118 (189)
Q Consensus        57 tkdEL~~LveWKL~rGkfRP~L~~lv~sN~~~~V~~~t~-~Af------~~------l-----~d~~~al~~Lt~LkGVG  118 (189)
                      |+++-+.-+-=+| .-+| |+...+.+.+ .+.|+++.+ -+|      .+      +     ..+....+.|.+|+|||
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            4556554443344 2344 8888887764 444444332 111      10      0     01233467788999999


Q ss_pred             hHHHHHHHHhhcCCCCCcccHHHH
Q 029726          119 PATASAVLAAYAPGVAPFMSDEAM  142 (189)
Q Consensus       119 PATASaiLa~~~P~~~pFfsDEa~  142 (189)
                      |-||++||+...... -|.-|--.
T Consensus       119 ~~TA~~Il~~a~~~p-~~~vD~nv  141 (211)
T d2abka_         119 RKTANVVLNTAFGWP-TIAVDTHI  141 (211)
T ss_dssp             HHHHHHHHHHHHCCC-CCCCCHHH
T ss_pred             hHHHHHHHHHHhcCc-cccccHHH
Confidence            999999999876543 34445433

>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=95.01  E-value=0.013  Score=46.60  Aligned_cols=41  Identities=20%  Similarity=0.109  Sum_probs=30.0

Q ss_pred             HHHHHHHhhcccCcChHHHHHHHHhhcCCCCCcccHHHHHHh
Q 029726          104 LTKAVSELTVLKGVGPATASAVLAAYAPGVAPFMSDEAMGAA  145 (189)
Q Consensus       104 ~~~al~~Lt~LkGVGPATASaiLa~~~P~~~pFfsDEa~~~~  145 (189)
                      ...+.+.|++|+||||-||++||....-. .-|.-|--..-+
T Consensus       115 ~~~~~~~L~~lpGIG~kTA~~vl~~~~~~-~~~~vD~hv~Rv  155 (217)
T d1pu6a_         115 QEVTREWLLDQKGIGKESADAILCYACAK-EVMVVDKYSYLF  155 (217)
T ss_dssp             HHCCHHHHHTSTTCCHHHHHHHHHHTTCC-SCCCCCHHHHHH
T ss_pred             cHHHHHHHHHHhhhhhHHHHHHHHHHcCC-eeeecChHHHHH
Confidence            45578899999999999999999985433 234456655433

>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=94.69  E-value=0.028  Score=41.94  Aligned_cols=72  Identities=11%  Similarity=0.071  Sum_probs=41.9

Q ss_pred             CHHHHHHHHHHHhhCCCCCcchhhHhhhCCHHHHHHHHHHH-H-----hhCccHHH-----HHHHhhcccCcChHHHHHH
Q 029726           57 NTTELSKLVRWKLTRGKWRPRLLDFVSSLDDSSVKSASEKA-F-----KSLPDLTK-----AVSELTVLKGVGPATASAV  125 (189)
Q Consensus        57 tkdEL~~LveWKL~rGkfRP~L~~lv~sN~~~~V~~~t~~A-f-----~~l~d~~~-----al~~Lt~LkGVGPATASai  125 (189)
                      |.++-+.-+-.+|-.  .-|+.-.+.+.+ .+.++++.+.+ |     +.+-++.+     ..+.|++|+||||-||.++
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--KYPSAEVARAAD-WRDVSELLKPLGLYDLRAKTIIKFSDEYLTKQWRYPIELHGIGKYGNDSY  109 (144)
T ss_dssp             SCHHHHHHHHHHHHH--HSCSHHHHHHSC-HHHHHHHTGGGSCHHHHHHHHHHHHHHHHHSCCSSGGGSTTCCHHHHHHH
T ss_pred             CCHHHHHHHHHHHHH--hCCchhhhhccC-HHHHHHHHHhhhhHHHHHHHHHHHHhhHhhhhhhhHHhcCCccHHHHHHH
Confidence            466666666677642  236766665444 44444443321 2     11112222     2355889999999999999


Q ss_pred             HHhhcC
Q 029726          126 LAAYAP  131 (189)
Q Consensus       126 La~~~P  131 (189)
                      +.+..-
T Consensus       110 ~if~~~  115 (144)
T d1ngna_         110 RIFCVN  115 (144)
T ss_dssp             HHHTSS
T ss_pred             HHHHcC
Confidence            887543

>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=94.46  E-value=0.009  Score=38.96  Aligned_cols=26  Identities=23%  Similarity=0.423  Sum_probs=22.4

Q ss_pred             HHHHHHHhhcccCcChHHHHHHHHhh
Q 029726          104 LTKAVSELTVLKGVGPATASAVLAAY  129 (189)
Q Consensus       104 ~~~al~~Lt~LkGVGPATASaiLa~~  129 (189)
                      -..+|+.|+++-||||+||.-+..-.
T Consensus         2 ~~~~l~~l~~I~GvGp~~A~~l~~~G   27 (57)
T d2fmpa2           2 TSSSINFLTRVSGIGPSAARKFVDEG   27 (57)
T ss_dssp             HHHHHHHHTTSTTCCHHHHHHHHHTT
T ss_pred             cchHHHHHhccccccHHHHHHHHHhC
Confidence            45789999999999999999887653

>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=92.61  E-value=0.024  Score=38.87  Aligned_cols=28  Identities=32%  Similarity=0.451  Sum_probs=23.9

Q ss_pred             HHHHHHhhcccCcChHHHHHHHHhhcCC
Q 029726          105 TKAVSELTVLKGVGPATASAVLAAYAPG  132 (189)
Q Consensus       105 ~~al~~Lt~LkGVGPATASaiLa~~~P~  132 (189)
                      +.-+..|.+..||||-||=+||+.++|+
T Consensus         5 r~~F~~Li~V~GIGpK~Al~iLs~~~~~   32 (78)
T d1cuka2           5 RTLFKELIKTNGVGPKLALAILSGMSAQ   32 (78)
T ss_dssp             HHHHHHHHHSSSCCHHHHHHHHHHSCHH
T ss_pred             HHHHHHHHccCCccHHHHHHHHHhCCHH
Confidence            4456789999999999999999987763

>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=92.15  E-value=0.031  Score=37.91  Aligned_cols=28  Identities=36%  Similarity=0.488  Sum_probs=23.6

Q ss_pred             HHHHHHhhcccCcChHHHHHHHHhhcCC
Q 029726          105 TKAVSELTVLKGVGPATASAVLAAYAPG  132 (189)
Q Consensus       105 ~~al~~Lt~LkGVGPATASaiLa~~~P~  132 (189)
                      +.-+..|.+..||||-||-+||+.++|+
T Consensus         6 r~lF~~Li~V~GIGpk~Al~iLs~~~~~   33 (73)
T d1ixra1           6 LALFELLLSVSGVGPKVALALLSALPPR   33 (73)
T ss_dssp             HHHHHHHHSSSCCCHHHHHHHHHHSCHH
T ss_pred             HHHHHHHhccCCcCHHHHHHHHHHccHH
Confidence            4456788999999999999999987663

>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=92.04  E-value=0.032  Score=35.93  Aligned_cols=38  Identities=29%  Similarity=0.300  Sum_probs=26.3

Q ss_pred             HhhcccCcChHHHHHHHHhhcC--CCCCcccHHHHHHhhC
Q 029726          110 ELTVLKGVGPATASAVLAAYAP--GVAPFMSDEAMGAALG  147 (189)
Q Consensus       110 ~Lt~LkGVGPATASaiLa~~~P--~~~pFfsDEa~~~~~g  147 (189)
                      .|.+++||||+||..|+..+..  +.+-..+-+-...+.|
T Consensus         2 ~L~~i~GIG~~~a~~L~~~g~~sv~~l~~a~~~eL~~i~G   41 (61)
T d1pzna1           2 SIEDLPGVGPATAEKLREAGYDTLEAIAVASPIELKEVAG   41 (61)
T ss_dssp             CSSCCTTCCHHHHHHHHTTTCCSHHHHHTCCHHHHHHHHC
T ss_pred             ccccCCCCCHHHHHHHHHhcCCCHHHHHhCCHHHHHHCCC
Confidence            3678999999999999986533  3334455555556666

>d1bvsa2 a.60.2.1 (A:64-134) DNA helicase RuvA subunit, middle domain {Mycobacterium leprae [TaxId: 1769]}

class: All alpha proteins
fold: SAM domain-like
superfamily: RuvA domain 2-like
family: DNA helicase RuvA subunit, middle domain
domain: DNA helicase RuvA subunit, middle domain
species: Mycobacterium leprae [TaxId: 1769]

Probab=91.77  E-value=0.048  Score=36.70  Aligned_cols=28  Identities=32%  Similarity=0.373  Sum_probs=23.8

Q ss_pred             HHHHHHhhcccCcChHHHHHHHHhhcCC
Q 029726          105 TKAVSELTVLKGVGPATASAVLAAYAPG  132 (189)
Q Consensus       105 ~~al~~Lt~LkGVGPATASaiLa~~~P~  132 (189)
                      +.-+..|.+..||||-||-+||+.++|+
T Consensus         5 r~~F~~Li~V~GIGpK~Al~iLs~~~~~   32 (71)
T d1bvsa2           5 RDLFLALLSVSGVGPRLAMATLAVHDAA   32 (71)
T ss_dssp             HHHHHHHHTSSSCCHHHHHHHHHHSCHH
T ss_pred             HHHHHHHhccCCcCHHHHHHHHHhCCHH
Confidence            4456788999999999999999997764

>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=91.70  E-value=0.039  Score=36.05  Aligned_cols=25  Identities=28%  Similarity=0.195  Sum_probs=21.9

Q ss_pred             HHHHHHhhcccCcChHHHHHHHHhh
Q 029726          105 TKAVSELTVLKGVGPATASAVLAAY  129 (189)
Q Consensus       105 ~~al~~Lt~LkGVGPATASaiLa~~  129 (189)
                      -++|+.|+++-||||.||.-+..-+
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            4689999999999999998887764

>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=91.41  E-value=0.15  Score=34.02  Aligned_cols=25  Identities=20%  Similarity=0.417  Sum_probs=16.4

Q ss_pred             HHHHHHhhcccCcChHHHHHHHHhh
Q 029726          105 TKAVSELTVLKGVGPATASAVLAAY  129 (189)
Q Consensus       105 ~~al~~Lt~LkGVGPATASaiLa~~  129 (189)
                      +.-+..|+.++|||+.+|-.|+.-+
T Consensus        15 ~~~~~~L~~I~gIg~~~a~~L~~~F   39 (78)
T d2a1jb1          15 SRVTECLTTVKSVNKTDSQTLLTTF   39 (78)
T ss_dssp             HHHHHHHTTSTTCCHHHHHHHHHHH
T ss_pred             HHHHHHhcCCCCcCHHHHHHHHHHh
Confidence            3456666677777777777776653

>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=90.85  E-value=0.024  Score=40.55  Aligned_cols=37  Identities=22%  Similarity=0.340  Sum_probs=31.2

Q ss_pred             HHHHHhhcccCcChHHHHHHHHhhcCCCCCcccHHHHHHhhC
Q 029726          106 KAVSELTVLKGVGPATASAVLAAYAPGVAPFMSDEAMGAALG  147 (189)
Q Consensus       106 ~al~~Lt~LkGVGPATASaiLa~~~P~~~pFfsDEa~~~~~g  147 (189)
                      +..+.|+.|+||||++|-.|..     .-||-|-|=+..+.|
T Consensus        24 As~~eL~~lpGIg~~~A~~Iv~-----~gpf~s~edL~~V~G   60 (98)
T d2axtu1          24 TNIAAFIQYRGLYPTLAKLIVK-----NAPYESVEDVLNIPG   60 (98)
T ss_dssp             SCGGGGTTSTTCTHHHHHHHHH-----SCCCSSGGGGGGCTT
T ss_pred             ccHHHHHHhhhhcHHHHHHHHH-----cCCcCCHHHHhhCCC
Confidence            3567899999999999999995     348999888887877

>d2bcqa2 a.60.12.1 (A:329-385) DNA polymerase lambda {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: SAM domain-like
superfamily: PsbU/PolX domain-like
family: DNA polymerase beta-like, second domain
domain: DNA polymerase lambda
species: Human (Homo sapiens) [TaxId: 9606]

Probab=90.68  E-value=0.057  Score=34.96  Aligned_cols=24  Identities=17%  Similarity=0.192  Sum_probs=20.7

Q ss_pred             HHHHHHhhcccCcChHHHHHHHHh
Q 029726          105 TKAVSELTVLKGVGPATASAVLAA  128 (189)
Q Consensus       105 ~~al~~Lt~LkGVGPATASaiLa~  128 (189)
                      .++|+.+|++-||||.||.-+...
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=89.18  E-value=0.076  Score=34.05  Aligned_cols=19  Identities=53%  Similarity=0.684  Sum_probs=17.0

Q ss_pred             hhcccCcChHHHHHHHHhh
Q 029726          111 LTVLKGVGPATASAVLAAY  129 (189)
Q Consensus       111 Lt~LkGVGPATASaiLa~~  129 (189)
                      |+.++||||++|..++..+
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

>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=89.00  E-value=0.12  Score=34.49  Aligned_cols=47  Identities=23%  Similarity=0.475  Sum_probs=31.5

Q ss_pred             HHHHHHHHHHHHhhCccHHH-HHHHhhcccCcChHHHHHHHHhhcCCCCCcc
Q 029726           87 DSSVKSASEKAFKSLPDLTK-AVSELTVLKGVGPATASAVLAAYAPGVAPFM  137 (189)
Q Consensus        87 ~~~V~~~t~~Af~~l~d~~~-al~~Lt~LkGVGPATASaiLa~~~P~~~pFf  137 (189)
                      +...+...+. |..+.++.. ..+.|.+++|||+..|..|..+..-   ||+
T Consensus        29 ~~~a~~L~~~-F~s~~~i~~A~~eeL~~i~GiG~~~A~~i~~~f~~---pf~   76 (78)
T d2a1jb1          29 KTDSQTLLTT-FGSLEQLIAASREDLALCPGLGPQKARRLFDVLHE---PFL   76 (78)
T ss_dssp             HHHHHHHHHH-HSSHHHHHSCCHHHHHTSSSCCSHHHHHHHHHHHS---CSC
T ss_pred             HHHHHHHHHH-hCCcHHHHhhhHHHHHHhhhhhHHHHHHHHHHHcC---ccc
Confidence            3344444433 554444433 3788999999999999999998643   664

>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=88.60  E-value=0.12  Score=33.68  Aligned_cols=40  Identities=20%  Similarity=0.257  Sum_probs=27.0

Q ss_pred             HHHhhcccCcChHHHHHHHHhhcC-CCCCcccHHHHHHhhC
Q 029726          108 VSELTVLKGVGPATASAVLAAYAP-GVAPFMSDEAMGAALG  147 (189)
Q Consensus       108 l~~Lt~LkGVGPATASaiLa~~~P-~~~pFfsDEa~~~~~g  147 (189)
                      +-+|+.++||||.||-.|+.-+.- +.+---|.|-+..+.|
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            567889999999999999997532 1212224555555655

>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=87.23  E-value=0.19  Score=31.67  Aligned_cols=31  Identities=19%  Similarity=0.372  Sum_probs=19.5

Q ss_pred             HhhCccHHH-HHHHhhcccCcChHHHHHHHHh
Q 029726           98 FKSLPDLTK-AVSELTVLKGVGPATASAVLAA  128 (189)
Q Consensus        98 f~~l~d~~~-al~~Lt~LkGVGPATASaiLa~  128 (189)
                      |..+.++.. ..+.|.+++||||.+|..|...
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 4667777777777777776543

>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=86.30  E-value=0.17  Score=32.97  Aligned_cols=43  Identities=19%  Similarity=0.337  Sum_probs=29.1

Q ss_pred             HHHHHHHHHHHHhhCccHHH-HHHHhhcccCcChHHHHHHHHhhc
Q 029726           87 DSSVKSASEKAFKSLPDLTK-AVSELTVLKGVGPATASAVLAAYA  130 (189)
Q Consensus        87 ~~~V~~~t~~Af~~l~d~~~-al~~Lt~LkGVGPATASaiLa~~~  130 (189)
                      +...+...+. |..+.++.. ..+.|++++|||+.+|-.|.....
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            3444444433 554444433 378999999999999999988753

>d1kfta_ a.60.2.3 (A:) Excinuclease UvrC C-terminal domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: SAM domain-like
superfamily: RuvA domain 2-like
family: Excinuclease UvrC C-terminal domain
domain: Excinuclease UvrC C-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=85.79  E-value=0.12  Score=32.59  Aligned_cols=20  Identities=30%  Similarity=0.561  Sum_probs=17.6

Q ss_pred             HhhcccCcChHHHHHHHHhh
Q 029726          110 ELTVLKGVGPATASAVLAAY  129 (189)
Q Consensus       110 ~Lt~LkGVGPATASaiLa~~  129 (189)
                      .|..++||||.||-.|+.-+
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            47889999999999999875

>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=85.78  E-value=0.21  Score=33.42  Aligned_cols=20  Identities=30%  Similarity=0.498  Sum_probs=17.1

Q ss_pred             HHHhhcccCcChHHHHHHHH
Q 029726          108 VSELTVLKGVGPATASAVLA  127 (189)
Q Consensus       108 l~~Lt~LkGVGPATASaiLa  127 (189)
                      ...|++++||||-||.-|+.
T Consensus        43 ~~~L~~vpGIG~KtA~rIi~   62 (71)
T d1bvsa2          43 VASLTRVPGIGRRGAERIVL   62 (71)
T ss_dssp             HHHHHTSTTCCHHHHHHHHH
T ss_pred             HHHhhcCCCCCHHHHHHHHH
Confidence            46799999999999987764

>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=85.59  E-value=0.22  Score=31.77  Aligned_cols=39  Identities=15%  Similarity=0.237  Sum_probs=27.8

Q ss_pred             HHhhcccCcChHHHHHHHHhhc-CCCCCcccHHHHHHhhC
Q 029726          109 SELTVLKGVGPATASAVLAAYA-PGVAPFMSDEAMGAALG  147 (189)
Q Consensus       109 ~~Lt~LkGVGPATASaiLa~~~-P~~~pFfsDEa~~~~~g  147 (189)
                      +.|..++||||.++-.|+.-+- -+.+.-.|-|-+..+.|
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            4688999999999999997532 12334456666666776

>d1cuka2 a.60.2.1 (A:65-142) DNA helicase RuvA subunit, middle domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: SAM domain-like
superfamily: RuvA domain 2-like
family: DNA helicase RuvA subunit, middle domain
domain: DNA helicase RuvA subunit, middle domain
species: Escherichia coli [TaxId: 562]

Probab=84.23  E-value=0.26  Score=33.40  Aligned_cols=21  Identities=33%  Similarity=0.540  Sum_probs=18.0

Q ss_pred             HHHhhcccCcChHHHHHHHHh
Q 029726          108 VSELTVLKGVGPATASAVLAA  128 (189)
Q Consensus       108 l~~Lt~LkGVGPATASaiLa~  128 (189)
                      .+.|++++|||+-||.-|..=
T Consensus        43 ~~~L~~vpGIG~KtA~rIi~e   63 (78)
T d1cuka2          43 VGALVKLPGIGKKTAERLIVE   63 (78)
T ss_dssp             HHHHHTSTTCCHHHHHHHHHH
T ss_pred             HHHhhcCCCCCHHHHHHHHHH
Confidence            467999999999999988754

>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=84.08  E-value=0.18  Score=33.98  Aligned_cols=33  Identities=24%  Similarity=0.275  Sum_probs=24.1

Q ss_pred             HHhhCccHHHHHHHhhcccCcChHHHHHHHHhh
Q 029726           97 AFKSLPDLTKAVSELTVLKGVGPATASAVLAAY  129 (189)
Q Consensus        97 Af~~l~d~~~al~~Lt~LkGVGPATASaiLa~~  129 (189)
                      +...+|..-...+.+++++|||+.+|+-|--..
T Consensus        36 ~i~~l~~~i~~~~~l~~i~GIGk~ia~kI~E~~   68 (82)
T d2fmpa1          36 VIAKYPHKIKSGAEAKKLPGVGTKIAEKIDEFL   68 (82)
T ss_dssp             HHHHCSSCCCCHHHHHTSTTCCHHHHHHHHHHH
T ss_pred             HHHhCCcccCCHHHHhcCCCccHHHHHHHHHHH
Confidence            345566322356789999999999999887654

>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=83.74  E-value=0.25  Score=31.96  Aligned_cols=36  Identities=28%  Similarity=0.522  Sum_probs=28.1

Q ss_pred             HHHHhhcccCcChHHHHHHHHhhcCCCCCcccHHHHHHhhC
Q 029726          107 AVSELTVLKGVGPATASAVLAAYAPGVAPFMSDEAMGAALG  147 (189)
Q Consensus       107 al~~Lt~LkGVGPATASaiLa~~~P~~~pFfsDEa~~~~~g  147 (189)
                      ..+.|..|+|||+.+|..|+..-     ||-|-|=+.-+.|
T Consensus        15 ~~~eL~~lpgig~~~A~~Iv~~R-----~f~s~edL~~v~g   50 (65)
T d2duya1          15 SLEELMALPGIGPVLARRIVEGR-----PYARVEDLLKVKG   50 (65)
T ss_dssp             CHHHHTTSTTCCHHHHHHHHHTC-----CCSSGGGGGGSTT
T ss_pred             CHHHHHHCCCCCHHHHHHHHHcC-----CCCCHHHHHhCCC
Confidence            46789999999999999999873     4777665555554

>d1x2ia1 a.60.2.5 (A:2-69) ATP-dependent RNA helicase PF2015 {Pyrococcus furiosus [TaxId: 2261]}

class: All alpha proteins
fold: SAM domain-like
superfamily: RuvA domain 2-like
family: Hef domain-like
domain: ATP-dependent RNA helicase PF2015
species: Pyrococcus furiosus [TaxId: 2261]

Probab=82.52  E-value=0.58  Score=30.18  Aligned_cols=43  Identities=19%  Similarity=0.315  Sum_probs=25.0

Q ss_pred             HHHHHHHHHHHHhhCccHHH-HHHHhhcccCcChHHHHHHHHhhc
Q 029726           87 DSSVKSASEKAFKSLPDLTK-AVSELTVLKGVGPATASAVLAAYA  130 (189)
Q Consensus        87 ~~~V~~~t~~Af~~l~d~~~-al~~Lt~LkGVGPATASaiLa~~~  130 (189)
                      +...+...+. |..+.++.. ..+.|.++.||||.+|-.|.....
T Consensus        20 ~~~a~~L~~~-f~s~~~i~~As~eeL~~i~GIG~~~A~~I~~~~~   63 (68)
T d1x2ia1          20 ATLARRLLKH-FGSVERVFTASVAELMKVEGIGEKIAKEIRRVIT   63 (68)
T ss_dssp             HHHHHHHHHH-HCSHHHHHHCCHHHHTTSTTCCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHH-cCCHHHHHHhHHHHHHhCCCcCHHHHHHHHHHHh
Confidence            3333343333 544444333 467777788888888877776643

>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=82.39  E-value=0.25  Score=31.43  Aligned_cols=42  Identities=19%  Similarity=0.364  Sum_probs=31.0

Q ss_pred             HHHHHHHHHHHHhhCccHHH-HHHHhhcccCcChHHHHHHHHh
Q 029726           87 DSSVKSASEKAFKSLPDLTK-AVSELTVLKGVGPATASAVLAA  128 (189)
Q Consensus        87 ~~~V~~~t~~Af~~l~d~~~-al~~Lt~LkGVGPATASaiLa~  128 (189)
                      +..+++.....|..+.++.. ..+.|++++|||+.+|.-|...
T Consensus         9 ~~~a~~L~~~G~~tv~~l~~a~~eeL~~i~Gi~~~~A~~i~~~   51 (60)
T d2i1qa1           9 PSTAEKLVEAGYIDFMKIATATVGELTDIEGISEKAAAKMIMG   51 (60)
T ss_dssp             HHHHHHHHHHTCCSHHHHHTCCHHHHHTSTTCCHHHHHHHHHH
T ss_pred             HHHHHHHHHccCCCHHHHHhCCHHHHHHCCCCCHHHHHHHHHH
Confidence            45556666666766555533 4788999999999999998765

>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=82.34  E-value=0.58  Score=31.25  Aligned_cols=22  Identities=27%  Similarity=0.274  Sum_probs=18.1

Q ss_pred             HHHhhcccCcChHHHHHHHHhh
Q 029726          108 VSELTVLKGVGPATASAVLAAY  129 (189)
Q Consensus       108 l~~Lt~LkGVGPATASaiLa~~  129 (189)
                      .+.|++++|||+-||--|..=.
T Consensus        44 ~~~L~~vpGIG~KtA~rIi~eL   65 (73)
T d1ixra1          44 ARLLTSASGVGRRLAERIALEL   65 (73)
T ss_dssp             HHHHTTSTTCCHHHHHHHHHHH
T ss_pred             HHHhhcCCCCCHHHHHHHHHHH
Confidence            4679999999999998876543

>d2bcqa1 a.60.6.1 (A:252-327) DNA polymerase lambda {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: SAM domain-like
superfamily: DNA polymerase beta, N-terminal domain-like
family: DNA polymerase beta, N-terminal domain-like
domain: DNA polymerase lambda
species: Human (Homo sapiens) [TaxId: 9606]

Probab=82.19  E-value=0.24  Score=32.72  Aligned_cols=35  Identities=20%  Similarity=0.330  Sum_probs=24.8

Q ss_pred             HHhhCccHHHHHHHhhcccCcChHHHHHHHHhhcC
Q 029726           97 AFKSLPDLTKAVSELTVLKGVGPATASAVLAAYAP  131 (189)
Q Consensus        97 Af~~l~d~~~al~~Lt~LkGVGPATASaiLa~~~P  131 (189)
                      +.+.+|..-..++.|.+|+|||+.+|+-|--...-
T Consensus        34 ~l~~l~~~i~~~~~l~~lpGiG~~i~~kI~Eil~t   68 (76)
T d2bcqa1          34 ALKSFHKPVTSYQEACSIPGIGKRMAEKIIEILES   68 (76)
T ss_dssp             HHHSCCSCCCCHHHHHTSTTCCHHHHHHHHHHHHS
T ss_pred             HHHhCCcccCCHHHHhcCCCccHHHHHHHHHHHHh
Confidence            34556632234567899999999999998776543

>d1x2ia1 a.60.2.5 (A:2-69) ATP-dependent RNA helicase PF2015 {Pyrococcus furiosus [TaxId: 2261]}

class: All alpha proteins
fold: SAM domain-like
superfamily: RuvA domain 2-like
family: Hef domain-like
domain: ATP-dependent RNA helicase PF2015
species: Pyrococcus furiosus [TaxId: 2261]

Probab=80.65  E-value=0.6  Score=30.13  Aligned_cols=40  Identities=15%  Similarity=0.000  Sum_probs=26.1

Q ss_pred             HHHhhcccCcChHHHHHHHHhhc-CCCCCcccHHHHHHhhC
Q 029726          108 VSELTVLKGVGPATASAVLAAYA-PGVAPFMSDEAMGAALG  147 (189)
Q Consensus       108 l~~Lt~LkGVGPATASaiLa~~~-P~~~pFfsDEa~~~~~g  147 (189)
                      .-.|..++||||.||-.|+.-+. .+.+..-+.|-+..+.|
T Consensus         9 ~~~L~~I~gIG~~~a~~L~~~f~s~~~i~~As~eeL~~i~G   49 (68)
T d1x2ia1           9 RLIVEGLPHVSATLARRLLKHFGSVERVFTASVAELMKVEG   49 (68)
T ss_dssp             HHHHTTSTTCCHHHHHHHHHHHCSHHHHHHCCHHHHTTSTT
T ss_pred             HHHHcCCCCcCHHHHHHHHHHcCCHHHHHHhHHHHHHhCCC
Confidence            34688999999999999998753 22222224555555554

>d2uubm1 a.156.1.1 (M:2-126) Ribosomal protein S13 {Thermus thermophilus [TaxId: 274]}

class: All alpha proteins
fold: S13-like H2TH domain
superfamily: S13-like H2TH domain
family: Ribosomal protein S13
domain: Ribosomal protein S13
species: Thermus thermophilus [TaxId: 274]

Probab=80.03  E-value=0.76  Score=33.25  Aligned_cols=39  Identities=21%  Similarity=0.248  Sum_probs=30.9

Q ss_pred             HHHHhhcccCcChHHHHHHHHhh--cCC-CCCcccHHHHHHh
Q 029726          107 AVSELTVLKGVGPATASAVLAAY--APG-VAPFMSDEAMGAA  145 (189)
Q Consensus       107 al~~Lt~LkGVGPATASaiLa~~--~P~-~~pFfsDEa~~~~  145 (189)
                      -.-.|+.++|||+.+|-.|+...  +|+ .+-.++||=+..+
T Consensus        14 v~~ALt~I~GIG~~~A~~Ic~~lgId~~~k~~~Lt~~qi~~I   55 (125)
T d2uubm1          14 VDVALTYIYGIGKARAKEALEKTGINPATRVKDLTEAEVVRL   55 (125)
T ss_dssp             HHHHHTTSTTCCHHHHHHHHHTTTCCTTSBGGGCCHHHHHHH
T ss_pred             EEEeeeeeeCcCHHHHHHHHHHcCCCcccccccccHHHHHHH
Confidence            44568999999999999999984  676 4677888876544