Citrus Sinensis ID: 030389

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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-------18
Protein Sequence
MQLEFECSNVNKWKEALASYEACVESLNKPNLISLDDYYRKELPSLIHQRNPNPHINTTELSKLVRWKLTRGKWRPRLLVFVSSLDDSSVKSASEKAFKSLPDLTKAVSELTVLKGVGPATASAVLAAYAPDLAPFMSDEVCFCSFSFKFTLLYSLFIYFYLTFVNGMEGYGGSTWPL
Secondary Structure (PSIPRED)
cccccccccHHHHHHHHHHHHHHHHHcccccHHHHHHHHHHHccHHHHHccccccccHHHHHHHHHHHHHccccccHHHHHHHHccHHHHHHHHHHHHHHcccHHHHHHHHHHHccccHHHHHHHHHHHcccccccccHHHHHHHccccccccccHHHHHHHHHHHHHHHcccccccc
Secondary Structure Prediction (SSPRO)
cccEcccccHHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHHHHHHHHccccccccHHHHHHHHHHHHHcccccHHHHHHHHcccHHHHHHHHHHHHHHcccHHHHHHHHHHHccccHHHHHHHHHHcccccccccccHEEEccccccccccccHHHHHHHHHHHHHHHcccccccc
Coil and Loop (DISEMBL)
MQLEFECSNVNKWKEALASYEACVEslnkpnlislddyyrkelpslihqrnpnphintteLSKLVRWKLTRGKWRPRLLVFVSSlddssvksASEKAFKSLPDLTKAVSELTVLKGVGPATASAVLAAyapdlapfmsdevcfcsfsfkfTLLYSLFIYFYLTFVNgmegyggstwpl
Flexible Loop (DISEMBL)
MQLEFECSNVNKWKEALASYEACVESLNKPNLISLDDYYRKELPslihqrnpnphinttelSKLVRWKLTRGKWRPRLLVFvsslddssvksasekafkslpdlTKAVSELTVLKGVGPATASAVLAAYAPDLAPFMSDEVCFCSFSFKFTLLYSLFIYFYLTFVNGMEGYGGSTWPL
Low Complexity Region (SEG)
MQLEFECSNVNKWKEALASYEACVESLNKPNLISLDDYYRKELPSLIHQRNPNPHINTTELSKLVRWKLTRGKWRPRllvfvsslddssvksasEKAFKSLPDLTKAVSELTVLKGVGPATASAVLAAYAPDLAPFMSDEVCFCSFSFKFTLLYSLFIYFYLTFVNGMEGYGGSTWPL
Disordered region (IsUnstruct)
*****ECSNVNKWKEALASYEACVESLNKPNLISLDDYYRKELPSLIHQRNPNPHINTTELSKLVRWKLTRGKWRPRLLVFVSSL******************LTKAVSELTVLKGVGPATASAVLAAYAPDLAPFMSDEVCFCSFSFKFTLLYSLFIYFYLTFVNGMEGYG******
Disordered Region (DISOPRED)
*********VNKWKEALASYEACV*******LISLDDYYRKELPSLIHQRNPNPHINTTELSKLVRWKLTRGKWRPRLLVFV**LD**SVKSASEKAFKSLPDLTKAVSELTVLKGVGPATASAVLAAYAPDLAPFMSDEVCFCSFSFKFTLLYSLFIYFYLTFVNGMEGYG******
Disordered Region (DISEMBL)
********NVNKWKEALASYEACVESLNKPNLISLDDYYRKELPSLIHQRNPNPHINTTELSKLVRWKLTRGKWRPRLLVFVSSL************FKSLPDLTKAVSELTVLKGVGPATASAVLAAYAPDLAPFMSDEVCFCSFSFKFTLLYSLFIYFYLTFVNGMEGYGGSTWPL
Disordered Region (DISPRO)
*QLEFECSNVNKWKEALASYEACVESLNKPNLISLDDYYRKELPSLIHQRNPNPHINTTELSKLVRWKLTRGKWRPRLLVFVSSLDDSSVKSASEKAFKSLPDLTKAVSELTVLKGVGPATASAVLAAYAPDLAPFMSDEVCFCSFSFKFTLLYSLFIYFYLTFVNGMEGYGGS****
Transmembrane Helix (TMHMM)
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Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHHHHHHooooooooooooo
Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHHHoooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MQLEFECSNVNKWKEALASYEACVESLNKPNLISLDDYYRKELPSLIHQRNPNPHINTTELSKLVRWKLTRGKWRPRLLVFVSSLDDSSVKSASEKAFKSLPDLTKAVSELTVLKGVGPATASAVLAAYAPDLAPFMSDEVCFCSFSFKFTLLYSLFIYFYLTFVNGMEGYGGSTWPL
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	178
297829776	209	hypothetical protein ARALYDRAFT_478581 [	0.926	0.789	0.662	3e-57
224067158	218	predicted protein [Populus trichocarpa]	0.904	0.738	0.668	5e-57
225458920	213	PREDICTED: uncharacterized protein LOC10	0.910	0.760	0.635	4e-55
255537954	217	conserved hypothetical protein [Ricinus	0.904	0.741	0.639	1e-54
449447089	220	PREDICTED: uncharacterized protein LOC10	0.915	0.740	0.634	8e-53
15795142	292	unnamed protein product [Arabidopsis tha	0.792	0.482	0.744	3e-51
18399536	209	DNA binding protein [Arabidopsis thalian	0.792	0.674	0.744	6e-51
30682101	155	DNA binding protein [Arabidopsis thalian	0.786	0.903	0.75	1e-50
356552290	220	PREDICTED: uncharacterized protein LOC10	0.915	0.740	0.602	2e-49
356552292	190	PREDICTED: uncharacterized protein LOC10	0.775	0.726	0.683	2e-49

>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 =  226 bits (576), Expect = 3e-57,   Method: Compositional matrix adjust.
 Identities = 112/169 (66%), Positives = 140/169 (82%), Gaps = 4/169 (2%)

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

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

Query: 121 TASAVLAAYAPDLAPFMSDEVCFCSFSFKFTLLYSLFIYFYLTFVNGME 169
           TASAVLAAYAPD+APFMSDE    +        YSL    YL FV  ++
Sbjct: 121 TASAVLAAYAPDIAPFMSDEAMEVALGNSKD--YSL--KQYLLFVTKLQ 165

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 =  225 bits (574), Expect = 5e-57,   Method: Compositional matrix adjust.
 Identities = 113/169 (66%), Positives = 137/169 (81%), Gaps = 8/169 (4%)

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

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

Query: 123 SAVLAAYAPDLAPFMSDEV--CFCSFSFKFTLLYSLFIYFYLTFVNGME 169
           SAVLAAYAPD+APFMSDE        S  +TL        YL FV+ ++
Sbjct: 121 SAVLAAYAPDVAPFMSDEAMEAVLGNSKDYTLKQ------YLLFVDKLQ 163

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 =  219 bits (557), Expect = 4e-55,   Method: Compositional matrix adjust.
 Identities = 108/170 (63%), Positives = 136/170 (80%), Gaps = 8/170 (4%)

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

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

Query: 123 SAVLAAYAPDLAPFMSDEVCFCSF--SFKFTLLYSLFIYFYLTFVNGMEG 170
           SA+LAAYAPD+APFMSDE    +   S  +TL        YL F + ++ 
Sbjct: 121 SALLAAYAPDVAPFMSDEAMVAALGNSKDYTLKQ------YLVFADKLQN 164

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 =  217 bits (553), Expect = 1e-54,   Method: Compositional matrix adjust.
 Identities = 108/169 (63%), Positives = 136/169 (80%), Gaps = 8/169 (4%)

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

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

Query: 123 SAVLAAYAPDLAPFMSDEVCFCSF--SFKFTLLYSLFIYFYLTFVNGME 169
           SAVLAAYAPD+APFMSDE    +   S  +TL        YL+FV+ ++
Sbjct: 121 SAVLAAYAPDVAPFMSDEAMEAALGSSKDYTLKQ------YLSFVDKLQ 163

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 =  211 bits (538), Expect = 8e-53,   Method: Compositional matrix adjust.
 Identities = 106/167 (63%), Positives = 132/167 (79%), Gaps = 4/167 (2%)

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

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

Query: 123 SAVLAAYAPDLAPFMSDEVCFCSFSFKFTLLYSLFIYFYLTFVNGME 169
           SAVLAAYAPD+APFMSDE    +        YSL    YL F N +E
Sbjct: 122 SAVLAAYAPDVAPFMSDEAMEAALGNSKD--YSL--KQYLLFANKLE 164

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 =  206 bits (524), Expect = 3e-51,   Method: Compositional matrix adjust.
 Identities = 105/141 (74%), Positives = 127/141 (90%)

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

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

Query: 121 TASAVLAAYAPDLAPFMSDEV 141
           TASAVLAAYAPD+APFMSDE 
Sbjct: 121 TASAVLAAYAPDIAPFMSDEA 141

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 =  205 bits (522), Expect = 6e-51,   Method: Compositional matrix adjust.
 Identities = 105/141 (74%), Positives = 127/141 (90%)

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

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

Query: 121 TASAVLAAYAPDLAPFMSDEV 141
           TASAVLAAYAPD+APFMSDE 
Sbjct: 121 TASAVLAAYAPDIAPFMSDEA 141

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|30682101|ref|NP_850569.1| DNA binding protein [Arabidopsis thaliana] gi|13878009|gb|AAK44082.1|AF370267_1 unknown protein [Arabidopsis thaliana] gi|17104615|gb|AAL34196.1| unknown protein [Arabidopsis thaliana] gi|332641647|gb|AEE75168.1| DNA binding protein [Arabidopsis thaliana]

 Score =  204 bits (519), Expect = 1e-50,   Method: Compositional matrix adjust.
 Identities = 105/140 (75%), Positives = 127/140 (90%)

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

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

Query: 121 TASAVLAAYAPDLAPFMSDE 140
           TASAVLAAYAPD+APFMSDE
Sbjct: 121 TASAVLAAYAPDIAPFMSDE 140

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  200 bits (509), Expect = 2e-49,   Method: Compositional matrix adjust.
 Identities = 103/171 (60%), Positives = 131/171 (76%), Gaps = 8/171 (4%)

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

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

Query: 119 PATASAVLAAYAPDLAPFMSDEVCFCSFSFKFTLLYSLFIYFYLTFVNGME 169
           PATASAVLA +AP L PFMSDE    +     +  YSL    Y+ FV+ ++
Sbjct: 121 PATASAVLATFAPHLTPFMSDEAMEAALG--SSKDYSL--KQYIKFVDKLQ 167

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  200 bits (508), Expect = 2e-49,   Method: Compositional matrix adjust.
 Identities = 97/142 (68%), Positives = 119/142 (83%), Gaps = 4/142 (2%)

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

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

Query: 119 PATASAVLAAYAPDLAPFMSDE 140
           PATASAVLA +AP L PFMSDE
Sbjct: 121 PATASAVLATFAPHLTPFMSDE 142

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

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	178
TAIR|locus:2082224	209	AT3G12210 [Arabidopsis thalian	0.786	0.669	0.642	1.8e-46
UNIPROTKB|F1RG53	232	LOC100524737 "Uncharacterized	0.747	0.573	0.404	2.1e-20
ZFIN|ZDB-GENE-050320-25	238	zgc:112496 "zgc:112496" [Danio	0.758	0.567	0.408	3.5e-20
FB|FBgn0030328	550	Amun "Amun" [Drosophila melano	0.775	0.250	0.401	6.4e-19
ASPGD|ASPL0000059149	312	AN10183 [Emericella nidulans (	0.528	0.301	0.333	8.5e-09

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

 Score = 487 (176.5 bits), Expect = 1.8e-46, P = 1.8e-46
 Identities = 90/140 (64%), Positives = 112/140 (80%)

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

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

Query:   121 TASAVLAAYAPDLAPFMSDE 140
             TASAVLAAYAPD+APFMSDE
Sbjct:   121 TASAVLAAYAPDIAPFMSDE 140

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 = 241 (89.9 bits), Expect = 2.1e-20, P = 2.1e-20
 Identities = 55/136 (40%), Positives = 75/136 (55%)

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

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

Query:   125 VLAAYAPDLAPFMSDE 140
             VLAA AP++A FMS+E
Sbjct:   129 VLAAGAPEVAAFMSEE 144

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 = 239 (89.2 bits), Expect = 3.5e-20, P = 3.5e-20
 Identities = 58/142 (40%), Positives = 74/142 (52%)

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

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

Query:   119 PATASAVLAAYAPDLAPFMSDE 140
              ATASAVL A APD   FM+DE
Sbjct:   123 SATASAVLVAGAPDKVAFMADE 144

GO:0003677 "DNA binding" evidence=IEA

GO:0006281 "DNA repair" evidence=IEA

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

 Score = 235 (87.8 bits), Expect = 6.4e-19, P = 6.4e-19
 Identities = 57/142 (40%), Positives = 81/142 (57%)

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

Query:    88 XXXXXXXEKAFKSLPDLTKAVSELTVLKGVGPATASAVLAAYAPDLAPFMSDEVCFCSFS 147
                    +KAF+ LP+L +A++ L+ LKGVG   ASA+LAA APD APFM+DE C  +  
Sbjct:   100 RAVIQETKKAFRKLPNLEQAITALSNLKGVGTTMASALLAAAAPDSAPFMADE-CLMAIP 158

Query:   148 FKFTLLYSLFIYFYLTFVNGME 169
                 + Y+     YL FVN ++
Sbjct:   159 EIEGIDYTT--KEYLNFVNHIQ 178

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 = 137 (53.3 bits), Expect = 8.5e-09, P = 8.5e-09
 Identities = 35/105 (33%), Positives = 50/105 (47%)

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

Query:   104 ------LTKAVSELTV-LKGVGPATASAVLAAYAPDLAPFMSDEV 141
                   +  A+  LT  L+GVGPATAS +L+   P++ PF SD+V
Sbjct:   162 KDGFEAIENALLTLTTPLRGVGPATASLILSVACPEMIPFYSDDV 206


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        0.320   0.135   0.422    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      178       161   0.00074  107 3  11 22  0.36    32
                                                     30  0.44    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:  611 (65 KB)
  Total size of DFA:  166 KB (2097 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:  13.69u 0.10s 13.79t   Elapsed:  00:00:01
  Total cpu time:  13.69u 0.10s 13.79t   Elapsed:  00:00:01
  Start:  Fri May 10 23:08:31 2013   End:  Fri May 10 23:08:32 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

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	178
PF00633	30	HHH: Helix-hairpin-helix motif; InterPro: IPR00044	97.68
COG0177	211	Nth Predicted EndoIII-related endonuclease [DNA re	96.26
cd00056	158	ENDO3c endonuclease III; includes endonuclease III	96.25
smart00478	149	ENDO3c endonuclease III. includes endonuclease III	95.91
TIGR01084	275	mutY A/G-specific adenine glycosylase. This equiva	95.87
COG0122	285	AlkA 3-methyladenine DNA glycosylase/8-oxoguanine	95.49
PRK10702	211	endonuclease III; Provisional	95.34
PRK10880	350	adenine DNA glycosylase; Provisional	95.21
TIGR01083	191	nth endonuclease III. This equivalog model identif	95.04
TIGR00588	310	ogg 8-oxoguanine DNA-glycosylase (ogg). All protei	94.94
PRK02515	132	psbU photosystem II complex extrinsic protein prec	94.81
PRK13910	289	DNA glycosylase MutY; Provisional	94.79
COG1194	342	MutY A/G-specific DNA glycosylase [DNA replication	94.58
PRK10308	283	3-methyl-adenine DNA glycosylase II; Provisional	94.57
TIGR03252	177	uncharacterized HhH-GPD family protein. This model	94.45
PRK01229	208	N-glycosylase/DNA lyase; Provisional	94.21
PF02371	87	Transposase_20: Transposase IS116/IS110/IS902 fami	93.29
PRK13913	218	3-methyladenine DNA glycosylase; Provisional	92.8
TIGR01259	120	comE comEA protein. This model describes the ComEA	92.77
smart00278	26	HhH1 Helix-hairpin-helix DNA-binding motif class 1	92.62
PF11731	93	Cdd1: Pathogenicity locus; InterPro: IPR021725 Cdd	91.01
PF10391	52	DNA_pol_lambd_f: Fingers domain of DNA polymerase	89.2
PF14716	68	HHH_8: Helix-hairpin-helix domain; PDB: 2W9M_A 1HU	88.91
PF14520	60	HHH_5: Helix-hairpin-helix domain; PDB: 3AUO_B 3AU	87.69
PRK13901	196	ruvA Holliday junction DNA helicase RuvA; Provisio	87.4
PRK14605	194	ruvA Holliday junction DNA helicase RuvA; Provisio	87.22
KOG1921	286	consensus Endonuclease III [Replication, recombina	86.23
PRK14601	183	ruvA Holliday junction DNA helicase RuvA; Provisio	86.03
PRK00116	192	ruvA Holliday junction DNA helicase RuvA; Reviewed	85.03
PRK14600	186	ruvA Holliday junction DNA helicase RuvA; Provisio	84.19
TIGR00084	191	ruvA Holliday junction DNA helicase, RuvA subunit.	84.1
PRK14606	188	ruvA Holliday junction DNA helicase RuvA; Provisio	83.98
TIGR00426	69	competence protein ComEA helix-hairpin-helix repea	83.6
TIGR00608	218	radc DNA repair protein radc. This family is based	83.35
PRK14603	197	ruvA Holliday junction DNA helicase RuvA; Provisio	83.19
PRK14602	203	ruvA Holliday junction DNA helicase RuvA; Provisio	82.91
COG1555	149	ComEA DNA uptake protein and related DNA-binding p	82.01
PRK00024	224	hypothetical protein; Reviewed	81.68
PF12826	64	HHH_2: Helix-hairpin-helix motif; PDB: 1X2I_B 1DGS	81.38
PF14520	60	HHH_5: Helix-hairpin-helix domain; PDB: 3AUO_B 3AU	80.76
KOG2875	323	consensus 8-oxoguanine DNA glycosylase [Replicatio	80.62

>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=97.68  E-value=3.4e-05  Score=46.99  Aligned_cols=25  Identities=40%  Similarity=0.709  Sum_probs=20.6

Q ss_pred             HHHHHHHhhcccCcchHHHHHHHhh
Q 030389          104 LTKAVSELTVLKGVGPATASAVLAA  128 (178)
Q Consensus       104 ~~~al~~L~~LkGVGPATASaiLa~  128 (178)
                      +.+.++.|++|+||||.||.+|++.
T Consensus         6 ~pas~eeL~~lpGIG~~tA~~I~~~   30 (30)
T PF00633_consen    6 IPASIEELMKLPGIGPKTANAILSF   30 (30)
T ss_dssp             HTSSHHHHHTSTT-SHHHHHHHHHH
T ss_pred             CCCCHHHHHhCCCcCHHHHHHHHhC
Confidence            3456899999999999999999973

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 ....

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

Probab=96.26  E-value=0.0054  Score=52.36  Aligned_cols=71  Identities=20%  Similarity=0.203  Sum_probs=45.3

Q ss_pred             CHHHHHHHHHHHhhCCCCCchhHHHhhhCCHHHHHHHHHH-HH------------hh-----CccHHHHHHHhhcccCcc
Q 030389           57 NTTELSKLVRWKLTRGKWRPRLLVFVSSLDDSSVKSASEK-AF------------KS-----LPDLTKAVSELTVLKGVG  118 (178)
Q Consensus        57 tkdEL~~LveWKL~rGkfRP~L~~lv~sN~~~~V~~~t~~-Af------------~~-----l~d~~~al~~L~~LkGVG  118 (178)
                      |.|+.+.-+-=+|-.  .-|+...+...+.+ .+++.++. +|            ++     -.++..+++.|.+|+|||
T Consensus        42 ttD~~vn~at~~Lf~--~~~t~e~l~~a~~~-~l~~~I~~iGlyr~KAk~I~~~~~~l~e~~~g~vP~~~~eL~~LPGVG  118 (211)
T COG0177          42 TTDEVVNKATPALFK--RYPTPEDLLNADEE-ELEELIKSIGLYRNKAKNIKELARILLEKFGGEVPDTREELLSLPGVG  118 (211)
T ss_pred             CchHHHHHHHHHHHH--HcCCHHHHHcCCHH-HHHHHHHhcCCcHHHHHHHHHHHHHHHHHcCCCCCchHHHHHhCCCcc
Confidence            467777666655542  33455666555544 34433332 22            01     115678899999999999


Q ss_pred             hHHHHHHHhhhC
Q 030389          119 PATASAVLAAYA  130 (178)
Q Consensus       119 PATASaiLa~~~  130 (178)
                      +-||..+|+...
T Consensus       119 rKTAnvVL~~a~  130 (211)
T COG0177         119 RKTANVVLSFAF  130 (211)
T ss_pred             hHHHHHHHHhhc
Confidence            999999999853

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

Probab=96.25  E-value=0.0084  Score=46.77  Aligned_cols=39  Identities=38%  Similarity=0.389  Sum_probs=29.9

Q ss_pred             HHHHHHhhcccCcchHHHHHHHhhhC-CCCCCccchhHHhhh
Q 030389          105 TKAVSELTVLKGVGPATASAVLAAYA-PDLAPFMSDEVCFCS  145 (178)
Q Consensus       105 ~~al~~L~~LkGVGPATASaiLa~~~-P~~~pFfSDEa~~~~  145 (178)
                      ..+.+.|++||||||-||+.+|.... ++.+|-  |-...-+
T Consensus        79 ~~~~~~L~~l~GIG~~tA~~~l~~~~~~~~~pv--D~~v~r~  118 (158)
T cd00056          79 PDAREELLALPGVGRKTANVVLLFALGPDAFPV--DTHVRRV  118 (158)
T ss_pred             cccHHHHHcCCCCCHHHHHHHHHHHCCCCCCcc--chhHHHH
Confidence            67899999999999999999998753 333444  6665543

>smart00478 ENDO3c endonuclease III

Probab=95.91  E-value=0.017  Score=44.78  Aligned_cols=36  Identities=36%  Similarity=0.496  Sum_probs=28.2

Q ss_pred             cHHHHHHHhhcccCcchHHHHHHHhhhCCCCCCccchh
Q 030389          103 DLTKAVSELTVLKGVGPATASAVLAAYAPDLAPFMSDE  140 (178)
Q Consensus       103 d~~~al~~L~~LkGVGPATASaiLa~~~P~~~pFfSDE  140 (178)
                      ++....+.|++|+||||-||+.+|...--.  +++..+
T Consensus        66 ~~~~~~~~L~~l~GIG~~tA~~~l~~~~~~--~~~~~D  101 (149)
T smart00478       66 EVPDDREELLKLPGVGRKTANAVLSFALGK--PFIPVD  101 (149)
T ss_pred             CccHHHHHHHcCCCCcHHHHHHHHHHHCCC--CCCccc
Confidence            345678999999999999999999987554  555544

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

>TIGR01084 mutY A/G-specific adenine glycosylase

Probab=95.87  E-value=0.018  Score=50.46  Aligned_cols=40  Identities=28%  Similarity=0.301  Sum_probs=30.0

Q ss_pred             HHHHHHHhhcccCcchHHHHHHHhhhCCCCCCccchhHHhh
Q 030389          104 LTKAVSELTVLKGVGPATASAVLAAYAPDLAPFMSDEVCFC  144 (178)
Q Consensus       104 ~~~al~~L~~LkGVGPATASaiLa~~~P~~~pFfSDEa~~~  144 (178)
                      +...++.|++|+||||-||++||+...-...|+ -|--+.-
T Consensus       100 ~p~~~~~L~~LpGIG~~TA~~Il~~a~~~~~~~-vD~~v~R  139 (275)
T TIGR01084       100 FPQDFEDLAALPGVGRYTAGAILSFALNKPYPI-LDGNVKR  139 (275)
T ss_pred             CcHHHHHHHhCCCCCHHHHHHHHHHHCCCCCCc-chHhHHH
Confidence            345789999999999999999999865433444 5655443

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.

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

Probab=95.49  E-value=0.032  Score=49.16  Aligned_cols=72  Identities=28%  Similarity=0.270  Sum_probs=51.2

Q ss_pred             CCCHHHHHHHHHHHhh-CCCCCchhHHHhhhCCHHHHHHHHHHHHhhCc--------cHHHHHHHhhcccCcchHHHHHH
Q 030389           55 HINTTELSKLVRWKLT-RGKWRPRLLVFVSSLDDSSVKSASEKAFKSLP--------DLTKAVSELTVLKGVGPATASAV  125 (178)
Q Consensus        55 ~ltkdEL~~LveWKL~-rGkfRP~L~~lv~sN~~~~V~~~t~~Af~~l~--------d~~~al~~L~~LkGVGPATASai  125 (178)
                      +.|-++|..+=++-|+ -|..+.+         .+.+..+++...+-.+        +...+++.|++||||||=||-.+
T Consensus       144 fptpe~l~~~~~~~l~~~g~s~~K---------a~yi~~~A~~~~~g~~~~~~l~~~~~e~a~e~L~~i~GIG~WTAe~~  214 (285)
T COG0122         144 FPTPEQLAAADEEALRRCGLSGRK---------AEYIISLARAAAEGELDLSELKPLSDEEAIEELTALKGIGPWTAEMF  214 (285)
T ss_pred             CCCHHHHHhcCHHHHHHhCCcHHH---------HHHHHHHHHHHHcCCccHHHhccCCHHHHHHHHHcCCCcCHHHHHHH
Confidence            6788888888888776 4555443         3455556655544321        46789999999999999999999


Q ss_pred             Hhh--hCCCCCC
Q 030389          126 LAA--YAPDLAP  135 (178)
Q Consensus       126 La~--~~P~~~p  135 (178)
                      |-.  ..|+.+|
T Consensus       215 llf~lgr~dvfP  226 (285)
T COG0122         215 LLFGLGRPDVFP  226 (285)
T ss_pred             HHHcCCCCCCCC
Confidence            876  4565533

>PRK10702 endonuclease III; Provisional

Probab=95.34  E-value=0.023  Score=47.90  Aligned_cols=28  Identities=32%  Similarity=0.383  Sum_probs=24.5

Q ss_pred             HHHHHHHhhcccCcchHHHHHHHhhhCC
Q 030389          104 LTKAVSELTVLKGVGPATASAVLAAYAP  131 (178)
Q Consensus       104 ~~~al~~L~~LkGVGPATASaiLa~~~P  131 (178)
                      +..+.+.|.+|+||||-||.+||....-
T Consensus       104 ~p~~~~~Ll~lpGVG~ktA~~ill~a~~  131 (211)
T PRK10702        104 VPEDRAALEALPGVGRKTANVVLNTAFG  131 (211)
T ss_pred             CCchHHHHhcCCcccHHHHHHHHHHHcC
Confidence            5568999999999999999999988643

>PRK10880 adenine DNA glycosylase; Provisional

Probab=95.21  E-value=0.02  Score=51.97  Aligned_cols=38  Identities=29%  Similarity=0.362  Sum_probs=29.2

Q ss_pred             HHHHHHHhhcccCcchHHHHHHHhhhCCCCCCccc-hhHHh
Q 030389          104 LTKAVSELTVLKGVGPATASAVLAAYAPDLAPFMS-DEVCF  143 (178)
Q Consensus       104 ~~~al~~L~~LkGVGPATASaiLa~~~P~~~pFfS-DEa~~  143 (178)
                      +....+.|.+|+||||-||++||+...-.  ||+- |=-..
T Consensus       104 ~p~~~~~L~~LpGIG~~TA~aIl~~af~~--~~~iVD~nV~  142 (350)
T PRK10880        104 FPETFEEVAALPGVGRSTAGAILSLSLGK--HFPILDGNVK  142 (350)
T ss_pred             chhhHHHHhcCCCccHHHHHHHHHHHCCC--CeecccHHHH
Confidence            45778999999999999999999987643  4554 54433

>TIGR01083 nth endonuclease III

Probab=95.04  E-value=0.045  Score=44.85  Aligned_cols=39  Identities=31%  Similarity=0.307  Sum_probs=28.2

Q ss_pred             HHHHHHHhhcccCcchHHHHHHHhhhCCCCCCccchhHHh
Q 030389          104 LTKAVSELTVLKGVGPATASAVLAAYAPDLAPFMSDEVCF  143 (178)
Q Consensus       104 ~~~al~~L~~LkGVGPATASaiLa~~~P~~~pFfSDEa~~  143 (178)
                      +..+.+.|++|+||||-||.+||....-.. -|.-|--+.
T Consensus       101 ~~~~~~~L~~l~GIG~ktA~~ill~~~~~~-~~~vD~~v~  139 (191)
T TIGR01083       101 VPEDREELVKLPGVGRKTANVVLNVAFGIP-AIAVDTHVF  139 (191)
T ss_pred             CchHHHHHHhCCCCcHHHHHHHHHHHcCCC-ccccchhHH
Confidence            456789999999999999999998864322 244454443

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

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

Probab=94.94  E-value=0.024  Score=50.29  Aligned_cols=40  Identities=28%  Similarity=0.388  Sum_probs=31.8

Q ss_pred             cHHHHHHHhhcccCcchHHHHHHHhh--hCCCCCCccchhHHhh
Q 030389          103 DLTKAVSELTVLKGVGPATASAVLAA--YAPDLAPFMSDEVCFC  144 (178)
Q Consensus       103 d~~~al~~L~~LkGVGPATASaiLa~--~~P~~~pFfSDEa~~~  144 (178)
                      +...+.+.|++||||||-||..||..  ..|+.+|  .|-.+.-
T Consensus       214 ~~~~~~~~L~~l~GIG~~tAd~vll~~l~~~d~~P--vD~~v~r  255 (310)
T TIGR00588       214 SYEDAREALCELPGVGPKVADCICLMGLDKPQAVP--VDVHVWR  255 (310)
T ss_pred             ChHHHHHHHHhCCCccHHHHHHHHHHhCCCCCcee--ecHHHHH
Confidence            36678999999999999999999976  4566666  3866554

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.

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

Probab=94.81  E-value=0.028  Score=45.11  Aligned_cols=41  Identities=20%  Similarity=0.225  Sum_probs=33.6

Q ss_pred             HHHHHHhhcccCcchHHHHHHHhhhCCCCCCccchhHHhhhhcCcc
Q 030389          105 TKAVSELTVLKGVGPATASAVLAAYAPDLAPFMSDEVCFCSFSFKF  150 (178)
Q Consensus       105 ~~al~~L~~LkGVGPATASaiLa~~~P~~~pFfSDEa~~~~~~~~~  150 (178)
                      .+.++.|..|+||||++|..|.     ++.||-|=|-+..++|+.+
T Consensus        57 ~A~~~el~~lpGigP~~A~~IV-----~nGpf~sveDL~~V~GIge   97 (132)
T PRK02515         57 NSSVRAFRQFPGMYPTLAGKIV-----KNAPYDSVEDVLNLPGLSE   97 (132)
T ss_pred             ccCHHHHHHCCCCCHHHHHHHH-----HCCCCCCHHHHHcCCCCCH
Confidence            3457789999999999999999     3679999776777888764

>PRK13910 DNA glycosylase MutY; Provisional

Probab=94.79  E-value=0.029  Score=49.70  Aligned_cols=37  Identities=24%  Similarity=0.187  Sum_probs=27.5

Q ss_pred             HHHHHhhcccCcchHHHHHHHhhhCCCCCCccchhHHh
Q 030389          106 KAVSELTVLKGVGPATASAVLAAYAPDLAPFMSDEVCF  143 (178)
Q Consensus       106 ~al~~L~~LkGVGPATASaiLa~~~P~~~pFfSDEa~~  143 (178)
                      ...+.|.+|+||||-||.+||+...-..+ |.-|-=+.
T Consensus        69 ~~~~~L~~LpGIG~kTA~aIl~~af~~~~-~~VD~nV~  105 (289)
T PRK13910         69 NDYQSLLKLPGIGAYTANAILCFGFREKS-ACVDANIK  105 (289)
T ss_pred             hhHHHHHhCCCCCHHHHHHHHHHHCCCCc-CcccHHHH
Confidence            46899999999999999999998654322 23454433

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

Probab=94.58  E-value=0.048  Score=49.75  Aligned_cols=33  Identities=36%  Similarity=0.514  Sum_probs=25.3

Q ss_pred             HHHhhcccCcchHHHHHHHhhhCCCCCCccchh
Q 030389          108 VSELTVLKGVGPATASAVLAAYAPDLAPFMSDE  140 (178)
Q Consensus       108 l~~L~~LkGVGPATASaiLa~~~P~~~pFfSDE  140 (178)
                      .+.|.+|+||||-||+||||...-...|+..=-
T Consensus       112 ~~~l~~LpGiG~yTa~Ail~~a~~~~~~~lDgN  144 (342)
T COG1194         112 EEELAALPGVGPYTAGAILSFAFNQPEPVLDGN  144 (342)
T ss_pred             HHHHHhCCCCcHHHHHHHHHHHhCCCCceeecc
Confidence            456677999999999999999766555655433

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

Probab=94.57  E-value=0.04  Score=48.38  Aligned_cols=33  Identities=27%  Similarity=0.323  Sum_probs=27.5

Q ss_pred             cHHHHHHHhhcccCcchHHHHHHHhh--hCCCCCC
Q 030389          103 DLTKAVSELTVLKGVGPATASAVLAA--YAPDLAP  135 (178)
Q Consensus       103 d~~~al~~L~~LkGVGPATASaiLa~--~~P~~~p  135 (178)
                      +...+++.|++||||||-||..||-.  ..|+..|
T Consensus       201 ~~~~~~~~L~~LpGIGpwTA~~vllr~lg~~D~fp  235 (283)
T PRK10308        201 DVEQAMKTLQTFPGIGRWTANYFALRGWQAKDVFL  235 (283)
T ss_pred             CHHHHHHHHhcCCCcCHHHHHHHHHHhCCCCCCCC
Confidence            56778999999999999999999865  5776544

>TIGR03252 uncharacterized HhH-GPD family protein

Probab=94.45  E-value=0.032  Score=46.57  Aligned_cols=41  Identities=27%  Similarity=0.264  Sum_probs=29.2

Q ss_pred             ccHHHHHHHhhcccCcchHHHHHHHhhhCCCCCCccchhHHhh
Q 030389          102 PDLTKAVSELTVLKGVGPATASAVLAAYAPDLAPFMSDEVCFC  144 (178)
Q Consensus       102 ~d~~~al~~L~~LkGVGPATASaiLa~~~P~~~pFfSDEa~~~  144 (178)
                      |+-....+.|.+|+||||-||..+|+...-+.  -.-||-|.-
T Consensus       108 p~t~~lre~Ll~LpGVG~KTAnvVL~~l~~~~--~~~~~~~~~  148 (177)
T TIGR03252       108 PDGKELLRRLKALPGFGKQKAKIFLALLGKQL--GVTPEGWRE  148 (177)
T ss_pred             CCcHHHHHHHHcCCCCCHHHHHHHHHHHHHHh--CCCCcchHH
Confidence            44556689999999999999999999753321  123555554

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).

>PRK01229 N-glycosylase/DNA lyase; Provisional

Probab=94.21  E-value=0.12  Score=43.94  Aligned_cols=28  Identities=32%  Similarity=0.249  Sum_probs=24.1

Q ss_pred             cHHHHHHHhh-cccCcchHHHHHHH-hhhC
Q 030389          103 DLTKAVSELT-VLKGVGPATASAVL-AAYA  130 (178)
Q Consensus       103 d~~~al~~L~-~LkGVGPATASaiL-a~~~  130 (178)
                      ++..+.+.|. +||||||=||+.|| .+..
T Consensus       112 ~~~~~R~~Ll~~lpGIG~KTAd~vL~~~~~  141 (208)
T PRK01229        112 DQFEAREFLVKNIKGIGYKEASHFLRNVGY  141 (208)
T ss_pred             CchHHHHHHHHcCCCCcHHHHHHHHHHccC
Confidence            5678899999 99999999999999 4543

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

Probab=93.29  E-value=0.072  Score=38.52  Aligned_cols=40  Identities=30%  Similarity=0.415  Sum_probs=30.6

Q ss_pred             HHhhcccCcchHHHHHHHhhhCCCCCCccchhHHhhhhcCc
Q 030389          109 SELTVLKGVGPATASAVLAAYAPDLAPFMSDEVCFCSFSFK  149 (178)
Q Consensus       109 ~~L~~LkGVGPATASaiLa~~~P~~~pFfSDEa~~~~~~~~  149 (178)
                      +.|+.++||||-||..||+.. .+.--|=+...+....|+-
T Consensus         2 ~~l~sipGig~~~a~~llaei-gd~~rF~~~~~l~~~~Gl~   41 (87)
T PF02371_consen    2 ELLTSIPGIGPITAATLLAEI-GDISRFKSAKQLASYAGLA   41 (87)
T ss_pred             chhcCCCCccHHHHHHHHHHH-cCchhcccchhhhhccccc
Confidence            468899999999999999986 2223477888888765543

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

>PRK13913 3-methyladenine DNA glycosylase; Provisional

Probab=92.80  E-value=0.21  Score=42.73  Aligned_cols=37  Identities=22%  Similarity=0.273  Sum_probs=27.1

Q ss_pred             HHHHHhhcccCcchHHHHHHHhhhCCCCCCccchhHHh
Q 030389          106 KAVSELTVLKGVGPATASAVLAAYAPDLAPFMSDEVCF  143 (178)
Q Consensus       106 ~al~~L~~LkGVGPATASaiLa~~~P~~~pFfSDEa~~  143 (178)
                      ...+.|.+|+||||=||.+||....- +.-|--|-=..
T Consensus       118 ~~re~Ll~l~GIG~kTAd~iLlya~~-rp~fvVDty~~  154 (218)
T PRK13913        118 VTREWLLDQKGIGKESADAILCYVCA-KEVMVVDKYSY  154 (218)
T ss_pred             hHHHHHHcCCCccHHHHHHHHHHHcC-CCccccchhHH
Confidence            46688999999999999999987543 32355555444

>TIGR01259 comE comEA protein

Probab=92.77  E-value=0.1  Score=40.42  Aligned_cols=46  Identities=24%  Similarity=0.261  Sum_probs=37.2

Q ss_pred             HHHHHHhhcccCcchHHHHHHHhhhCCCCCCccchhHHhhhhcCccc
Q 030389          105 TKAVSELTVLKGVGPATASAVLAAYAPDLAPFMSDEVCFCSFSFKFT  151 (178)
Q Consensus       105 ~~al~~L~~LkGVGPATASaiLa~~~P~~~pFfSDEa~~~~~~~~~~  151 (178)
                      .+..+.|..|+||||.+|..|+.-..- ..||-|-|-+..++|+.++
T Consensus        64 tA~~~eL~~lpGIG~~~A~~Ii~~R~~-~g~f~s~eeL~~V~GIg~k  109 (120)
T TIGR01259        64 AASLEELQALPGIGPAKAKAIIEYREE-NGAFKSVDDLTKVSGIGEK  109 (120)
T ss_pred             cCCHHHHhcCCCCCHHHHHHHHHHHHh-cCCcCCHHHHHcCCCCCHH
Confidence            345778999999999999999998653 5689897777778887543

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.

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

Probab=92.62  E-value=0.079  Score=30.57  Aligned_cols=19  Identities=47%  Similarity=0.763  Sum_probs=16.9

Q ss_pred             HhhcccCcchHHHHHHHhh
Q 030389          110 ELTVLKGVGPATASAVLAA  128 (178)
Q Consensus       110 ~L~~LkGVGPATASaiLa~  128 (178)
                      .|++++|||+.+|..|+..
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=91.01  E-value=0.16  Score=38.43  Aligned_cols=26  Identities=27%  Similarity=0.261  Sum_probs=22.2

Q ss_pred             HHHHHHHhhcccCcchHHHHHHHhhh
Q 030389          104 LTKAVSELTVLKGVGPATASAVLAAY  129 (178)
Q Consensus       104 ~~~al~~L~~LkGVGPATASaiLa~~  129 (178)
                      ..+.+..|+.|+|||||||-=+..++
T Consensus         7 ~~~~~~~L~~iP~IG~a~a~DL~~LG   32 (93)
T PF11731_consen    7 KRAGLSDLTDIPNIGKATAEDLRLLG   32 (93)
T ss_pred             HHHHHHHHhcCCCccHHHHHHHHHcC
Confidence            35678899999999999999887774

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=89.20  E-value=0.26  Score=33.34  Aligned_cols=23  Identities=35%  Similarity=0.325  Sum_probs=17.6

Q ss_pred             HHHhhcccCcchHHHHHHHhhhC
Q 030389          108 VSELTVLKGVGPATASAVLAAYA  130 (178)
Q Consensus       108 l~~L~~LkGVGPATASaiLa~~~  130 (178)
                      |+.+++.-||||+||.-..+.+.
T Consensus         1 l~~f~~I~GVG~~tA~~w~~~G~   23 (52)
T PF10391_consen    1 LKLFTGIWGVGPKTARKWYAKGI   23 (52)
T ss_dssp             HHHHHTSTT--HHHHHHHHHTT-
T ss_pred             CcchhhcccccHHHHHHHHHhCC
Confidence            57899999999999999888653

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=88.91  E-value=0.61  Score=32.33  Aligned_cols=32  Identities=31%  Similarity=0.398  Sum_probs=23.2

Q ss_pred             HHHhhCccHHHHHHH-hhcccCcchHHHHHHHh
Q 030389           96 KAFKSLPDLTKAVSE-LTVLKGVGPATASAVLA  127 (178)
Q Consensus        96 ~Af~~l~d~~~al~~-L~~LkGVGPATASaiLa  127 (178)
                      .+.+.+|..-..++. +.+|+|||+.+|.-|--
T Consensus        33 ~~i~~l~~~i~~~~~~~~~l~gIG~~ia~kI~E   65 (68)
T PF14716_consen   33 AAIKALPYPITSGEEDLKKLPGIGKSIAKKIDE   65 (68)
T ss_dssp             HHHHHSSS-HHSHHHHHCTSTTTTHHHHHHHHH
T ss_pred             HHHHhCCHhHhhHHHHHhhCCCCCHHHHHHHHH
Confidence            345567755555675 99999999999988743

...

>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=87.69  E-value=0.28  Score=33.06  Aligned_cols=23  Identities=26%  Similarity=0.479  Sum_probs=19.2

Q ss_pred             HHHHhhcccCcchHHHHHHHhhh
Q 030389          107 AVSELTVLKGVGPATASAVLAAY  129 (178)
Q Consensus       107 al~~L~~LkGVGPATASaiLa~~  129 (178)
                      ....|..++||||.+|..+....
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            45678889999999999998884

...

>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional

Probab=87.40  E-value=0.27  Score=41.61  Aligned_cols=28  Identities=29%  Similarity=0.453  Sum_probs=14.8

Q ss_pred             HHHHHHhhcccCcchHHHHHHHhhhCCC
Q 030389          105 TKAVSELTVLKGVGPATASAVLAAYAPD  132 (178)
Q Consensus       105 ~~al~~L~~LkGVGPATASaiLa~~~P~  132 (178)
                      +.-+..|....||||-||-+|||...|+
T Consensus        68 r~lF~~LisVsGIGPK~ALaILs~~~~~   95 (196)
T PRK13901         68 REVFEELIGVDGIGPRAALRVLSGIKYN   95 (196)
T ss_pred             HHHHHHHhCcCCcCHHHHHHHHcCCCHH
Confidence            3445555555555555555555554443

>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional

Probab=87.22  E-value=0.42  Score=39.89  Aligned_cols=31  Identities=23%  Similarity=0.362  Sum_probs=24.8

Q ss_pred             cHHHHHHHhhcccCcchHHHHHHHhhhCCCC
Q 030389          103 DLTKAVSELTVLKGVGPATASAVLAAYAPDL  133 (178)
Q Consensus       103 d~~~al~~L~~LkGVGPATASaiLa~~~P~~  133 (178)
                      +-+.-+..|.+..||||-||-+||+...|+.
T Consensus        67 ~Er~lF~~Li~V~GIGpK~Al~ILs~~~~~~   97 (194)
T PRK14605         67 EELSLFETLIDVSGIGPKLGLAMLSAMNAEA   97 (194)
T ss_pred             HHHHHHHHHhCCCCCCHHHHHHHHHhCCHHH
Confidence            4566788888899999999999998877754

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

Probab=86.23  E-value=1.2  Score=39.76  Aligned_cols=28  Identities=32%  Similarity=0.491  Sum_probs=25.9

Q ss_pred             cHHHHHHHhhcccCcchHHHHHHHhhhC
Q 030389          103 DLTKAVSELTVLKGVGPATASAVLAAYA  130 (178)
Q Consensus       103 d~~~al~~L~~LkGVGPATASaiLa~~~  130 (178)
                      |+-..++.|..|+||||-+|=+.|+++-
T Consensus       153 DIP~~v~dLlsLPGVGPKMa~L~m~~AW  180 (286)
T KOG1921|consen  153 DIPDTVEDLLSLPGVGPKMAHLTMQVAW  180 (286)
T ss_pred             CCchhHHHHhcCCCCchHHHHHHHHHHh
Confidence            7889999999999999999999999853

>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional

Probab=86.03  E-value=0.35  Score=40.33  Aligned_cols=19  Identities=37%  Similarity=0.686  Sum_probs=11.2

Q ss_pred             HHhhcccCcchHHHHHHHh
Q 030389          109 SELTVLKGVGPATASAVLA  127 (178)
Q Consensus       109 ~~L~~LkGVGPATASaiLa  127 (178)
                      +.|++++|||+-||.=|+-
T Consensus       108 ~~L~~vpGIGkKtAeRIil  126 (183)
T PRK14601        108 SVLKKVPGIGPKSAKRIIA  126 (183)
T ss_pred             HHHhhCCCCCHHHHHHHHH
Confidence            4566666666666665543

>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed

Probab=85.03  E-value=0.7  Score=38.27  Aligned_cols=27  Identities=33%  Similarity=0.541  Sum_probs=20.2

Q ss_pred             HHHHHHhhcccCcchHHHHHHHhhhCC
Q 030389          105 TKAVSELTVLKGVGPATASAVLAAYAP  131 (178)
Q Consensus       105 ~~al~~L~~LkGVGPATASaiLa~~~P  131 (178)
                      +.....|..++||||.||-.||+.+.+
T Consensus        69 k~~f~~L~~i~GIGpk~A~~il~~fg~   95 (192)
T PRK00116         69 RELFRLLISVSGVGPKLALAILSGLSP   95 (192)
T ss_pred             HHHHHHHhcCCCCCHHHHHHHHHhCCH
Confidence            344667788888888888888887654

>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional

Probab=84.19  E-value=0.65  Score=38.74  Aligned_cols=30  Identities=23%  Similarity=0.389  Sum_probs=22.1

Q ss_pred             cHHHHHHHhhcccCcchHHHHHHHhhhCCC
Q 030389          103 DLTKAVSELTVLKGVGPATASAVLAAYAPD  132 (178)
Q Consensus       103 d~~~al~~L~~LkGVGPATASaiLa~~~P~  132 (178)
                      +-+.-+..|.+..||||-||-+||+...|+
T Consensus        67 ~Er~lF~~LisV~GIGpK~Al~iLs~~~~~   96 (186)
T PRK14600         67 EEQDCLRMLVKVSGVNYKTAMSILSKLTPE   96 (186)
T ss_pred             HHHHHHHHHhCcCCcCHHHHHHHHccCCHH
Confidence            345567777788888888888888876664

>TIGR00084 ruvA Holliday junction DNA helicase, RuvA subunit

Probab=84.10  E-value=0.71  Score=38.47  Aligned_cols=29  Identities=34%  Similarity=0.568  Sum_probs=21.5

Q ss_pred             cHHHHHHHhhcccCcchHHHHHHHhhhCC
Q 030389          103 DLTKAVSELTVLKGVGPATASAVLAAYAP  131 (178)
Q Consensus       103 d~~~al~~L~~LkGVGPATASaiLa~~~P  131 (178)
                      +-+.-+..|...+||||-||-+||+...|
T Consensus        66 ~Er~lF~~L~~V~GIGpK~Al~iL~~~~~   94 (191)
T TIGR00084        66 EERELFKELIKVNGVGPKLALAILSNMSP   94 (191)
T ss_pred             HHHHHHHHHhCCCCCCHHHHHHHHhcCCH
Confidence            34566777778888888888888877666

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.

>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional

Probab=83.98  E-value=0.49  Score=39.47  Aligned_cols=42  Identities=19%  Similarity=0.213  Sum_probs=23.2

Q ss_pred             HHHhhcccCcchHHHHHHHhhhCCCC----CC--ccchhHHhhhhcCc
Q 030389          108 VSELTVLKGVGPATASAVLAAYAPDL----AP--FMSDEVCFCSFSFK  149 (178)
Q Consensus       108 l~~L~~LkGVGPATASaiLa~~~P~~----~p--FfSDEa~~~~~~~~  149 (178)
                      .+.||+++|||+-||.-|.-=.-...    .+  -..||+..++.+++
T Consensus       107 ~~~L~~vpGIGkKtAerIilELkdK~~~~~~~~~~~~~e~~~AL~~LG  154 (188)
T PRK14606        107 VEGLSKLPGISKKTAERIVMELKDEFESAGIKDMRIYHESLEALVSLG  154 (188)
T ss_pred             HHHHhhCCCCCHHHHHHHHHHHHHhhccccCCCcccHHHHHHHHHHcC
Confidence            45677778888888876654322211    10  12266777665554

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

Probab=83.60  E-value=1.6  Score=29.99  Aligned_cols=41  Identities=24%  Similarity=0.256  Sum_probs=31.7

Q ss_pred             HHHhhc-ccCcchHHHHHHHhhhCCCCCCccchhHHhhhhcCc
Q 030389          108 VSELTV-LKGVGPATASAVLAAYAPDLAPFMSDEVCFCSFSFK  149 (178)
Q Consensus       108 l~~L~~-LkGVGPATASaiLa~~~P~~~pFfSDEa~~~~~~~~  149 (178)
                      .+.|.. ++|||+.+|.+|+.-... ..+|-+-+.+..++|+.
T Consensus        15 ~~~L~~~ipgig~~~a~~Il~~R~~-~g~~~s~~dL~~v~gi~   56 (69)
T TIGR00426        15 AEELQRAMNGVGLKKAEAIVSYREE-YGPFKTVEDLKQVPGIG   56 (69)
T ss_pred             HHHHHhHCCCCCHHHHHHHHHHHHH-cCCcCCHHHHHcCCCCC
Confidence            446777 999999999999998643 33777867777777764

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

>TIGR00608 radc DNA repair protein radc

Probab=83.35  E-value=1.3  Score=37.78  Aligned_cols=61  Identities=31%  Similarity=0.402  Sum_probs=39.4

Q ss_pred             CCCCHHHHHHHHHHHhhCCCCCchhHHHhhhCCHHHHHHHHHHHHh------hCccH-HHHHHHhhcccCcchHHHHHHH
Q 030389           54 PHINTTELSKLVRWKLTRGKWRPRLLVFVSSLDDSSVKSASEKAFK------SLPDL-TKAVSELTVLKGVGPATASAVL  126 (178)
Q Consensus        54 ~~ltkdEL~~LveWKL~rGkfRP~L~~lv~sN~~~~V~~~t~~Af~------~l~d~-~~al~~L~~LkGVGPATASaiL  126 (178)
                      ..|+-.||..++   |..|.-|-        +   .|.+.+++-++      .+.++ .+..+.|++.+|||||.|..|+
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            578888966654   46665442        0   23333333332      23333 3458899999999999999999


Q ss_pred             hh
Q 030389          127 AA  128 (178)
Q Consensus       127 a~  128 (178)
                      ++
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).

>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional

Probab=83.19  E-value=0.55  Score=39.41  Aligned_cols=46  Identities=28%  Similarity=0.309  Sum_probs=27.5

Q ss_pred             HHHHHHHhhcccCcchHHHHHHHhhhCCCC---CCccchhHHhh-hhcCc
Q 030389          104 LTKAVSELTVLKGVGPATASAVLAAYAPDL---APFMSDEVCFC-SFSFK  149 (178)
Q Consensus       104 ~~~al~~L~~LkGVGPATASaiLa~~~P~~---~pFfSDEa~~~-~~~~~  149 (178)
                      -+.-+..|....||||-||-+||+...|+.   +.--.|..... +||++
T Consensus        67 Er~lF~~L~~V~GIGpK~AL~iLs~~~~~~l~~aI~~~D~~~L~kvpGIG  116 (197)
T PRK14603         67 SLELFELLLGVSGVGPKLALALLSALPPALLARALLEGDARLLTSASGVG  116 (197)
T ss_pred             HHHHHHHHhCcCCcCHHHHHHHHcCCCHHHHHHHHHhCCHHHHhhCCCCC
Confidence            345566777777777777777777766643   22333444443 56654

>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional

Probab=82.91  E-value=0.63  Score=39.16  Aligned_cols=29  Identities=31%  Similarity=0.456  Sum_probs=19.7

Q ss_pred             HHHHHHHhhcccCcchHHHHHHHhhhCCC
Q 030389          104 LTKAVSELTVLKGVGPATASAVLAAYAPD  132 (178)
Q Consensus       104 ~~~al~~L~~LkGVGPATASaiLa~~~P~  132 (178)
                      -+.-+..|.+..||||-||-+||+...|+
T Consensus        69 Er~lF~~Li~V~GIGpK~Al~iLs~~~~~   97 (203)
T PRK14602         69 ERQTFIVLISISKVGAKTALAILSQFRPD   97 (203)
T ss_pred             HHHHHHHHhCCCCcCHHHHHHHHhhCCHH
Confidence            34556667777777777777777766664

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

Probab=82.01  E-value=1.2  Score=35.91  Aligned_cols=46  Identities=26%  Similarity=0.290  Sum_probs=35.4

Q ss_pred             HHHHHHhhcccCcchHHHHHHHhhhCCCCCCccchhHHhhhhcCccc
Q 030389          105 TKAVSELTVLKGVGPATASAVLAAYAPDLAPFMSDEVCFCSFSFKFT  151 (178)
Q Consensus       105 ~~al~~L~~LkGVGPATASaiLa~~~P~~~pFfSDEa~~~~~~~~~~  151 (178)
                      .+..+.|..|+||||+.|-+|.+-..- ..||=|=|=..-++|+.+.
T Consensus        93 tAs~eeL~~lpgIG~~kA~aIi~yRe~-~G~f~sv~dL~~v~GiG~~  138 (149)
T COG1555          93 TASAEELQALPGIGPKKAQAIIDYREE-NGPFKSVDDLAKVKGIGPK  138 (149)
T ss_pred             ccCHHHHHHCCCCCHHHHHHHHHHHHH-cCCCCcHHHHHhccCCCHH
Confidence            455778899999999999999998644 4488885656667777653

>PRK00024 hypothetical protein; Reviewed

Probab=81.68  E-value=2.4  Score=36.07  Aligned_cols=60  Identities=28%  Similarity=0.447  Sum_probs=39.8

Q ss_pred             CCCCHHHHHHHHHHHhhCCCCCchhHHHhhhCCHHHHHHHHHHHHhhCc---cH-HHHHHHhhcccCcchHHHHHHHhh
Q 030389           54 PHINTTELSKLVRWKLTRGKWRPRLLVFVSSLDDSSVKSASEKAFKSLP---DL-TKAVSELTVLKGVGPATASAVLAA  128 (178)
Q Consensus        54 ~~ltkdEL~~LveWKL~rGkfRP~L~~lv~sN~~~~V~~~t~~Af~~l~---d~-~~al~~L~~LkGVGPATASaiLa~  128 (178)
                      ..|+-.||..++   |..|..|.            .|...+++-++...   ++ .+..+.|++++|||||.|..|+++
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            44444444443333   22 335778999999999999999887

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

Probab=81.38  E-value=1.4  Score=30.40  Aligned_cols=24  Identities=29%  Similarity=0.670  Sum_probs=17.5

Q ss_pred             HHHHHhhcccCcchHHHHHHHhhh
Q 030389          106 KAVSELTVLKGVGPATASAVLAAY  129 (178)
Q Consensus       106 ~al~~L~~LkGVGPATASaiLa~~  129 (178)
                      +..+.|++++||||.+|..|....
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            467899999999999999988753

>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=80.76  E-value=0.88  Score=30.57  Aligned_cols=22  Identities=32%  Similarity=0.531  Sum_probs=18.8

Q ss_pred             HHHHhhcccCcchHHHHHHHhh
Q 030389          107 AVSELTVLKGVGPATASAVLAA  128 (178)
Q Consensus       107 al~~L~~LkGVGPATASaiLa~  128 (178)
                      ..+.|++++||||.+|.-|...
T Consensus        36 ~~~~L~~i~Gig~~~a~~i~~~   57 (60)
T PF14520_consen   36 DPEELAEIPGIGEKTAEKIIEA   57 (60)
T ss_dssp             HHHHHHTSTTSSHHHHHHHHHH
T ss_pred             CHHHHhcCCCCCHHHHHHHHHH
Confidence            4678999999999999988764

...

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

Probab=80.62  E-value=2.6  Score=38.17  Aligned_cols=32  Identities=28%  Similarity=0.376  Sum_probs=24.5

Q ss_pred             HHHHHHHhhcccCcchHHHHHHHhh--hCCCCCC
Q 030389          104 LTKAVSELTVLKGVGPATASAVLAA--YAPDLAP  135 (178)
Q Consensus       104 ~~~al~~L~~LkGVGPATASaiLa~--~~P~~~p  135 (178)
                      ..+|-++||.|+||||-.|-.|+-.  +-+..+|
T Consensus       213 yeear~~L~~lpGVG~KVADCI~Lm~l~~~~~VP  246 (323)
T KOG2875|consen  213 YEEAREALCSLPGVGPKVADCICLMSLDKLSAVP  246 (323)
T ss_pred             HHHHHHHHhcCCCCcchHhhhhhhhhcCCCCccc
Confidence            4669999999999999999987644  3444444

---

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	178
3fhg_A	207	Mjogg, N-glycosylase/DNA lyase, DNA-(apurinic; hel	96.96
3fhf_A	214	Mjogg, N-glycosylase/DNA lyase, DNA-(apurinic; hel	96.8
3n0u_A	219	Probable N-glycosylase/DNA lyase; structural genom	96.27
3i0w_A	290	8-oxoguanine-DNA-glycosylase; OGG, cacogg, DNA, 8-	96.22
2h56_A	233	DNA-3-methyladenine glycosidase; 10174367, EC 3.2.	96.22
3s6i_A	228	DNA-3-methyladenine glycosylase 1; DNA glycosylase	96.16
4e9f_A	161	Methyl-CPG-binding domain protein 4; HHH DNA glyco	96.05
2yg9_A	225	DNA-3-methyladenine glycosidase II, putative; hydr	95.84
4b21_A	232	Probable DNA-3-methyladenine glycosylase 2; hydrol	95.81
1mpg_A	282	ALKA, 3-methyladenine DNA glycosylase II; DNA repa	95.77
1pu6_A	218	3-methyladenine DNA glycosylase; helix-hairpin-hel	95.19
2xhi_A	360	N-glycosylase/DNA lyase; lyase-DNA complex, lyase/	95.05
1kg2_A	225	A/G-specific adenine glycosylase; DNA repair, hydr	94.88
3arc_U	97	Photosystem II 12 kDa extrinsic protein; PSII, mem	94.8
2jhn_A	295	ALKA, 3-methyladenine DNA-glycosylase; DNA repair,	94.75
2abk_A	211	Endonuclease III; DNA-repair, DNA glycosylase; 1.8	94.66
2duy_A	75	Competence protein comea-related protein; helix-ha	94.39
1orn_A	226	Endonuclease III; DNA repair, DNA glycosylase, [4F	94.31
1kea_A	221	Possible G-T mismatches repair enzyme; DNA repair,	94.15
1s5l_U	134	Photosystem II 12 kDa extrinsic protein; photosynt	93.81
2edu_A	98	Kinesin-like protein KIF22; kinesin-like DNA bindi	93.68
2i5h_A	205	Hypothetical protein AF1531; PFAM:DUF655, PSI-2, s	93.36
3fsp_A	369	A/G-specific adenine glycosylase; protein-DNA comp	92.79
3n5n_X	287	A/G-specific adenine DNA glycosylase; alpha-helice	92.24
2a1j_B	91	DNA excision repair protein ERCC-1; XPF, xeroderma	91.52
2ztd_A	212	Holliday junction ATP-dependent DNA helicase RUVA;	90.06
1x2i_A	75	HEF helicase/nuclease; alpha helix, helix-hairpin-	90.03
1kft_A	78	UVRC, excinuclease ABC subunit C; helix-hairpin-he	87.35
1kft_A	78	UVRC, excinuclease ABC subunit C; helix-hairpin-he	85.31
1ixr_A	191	Holliday junction DNA helicase RUVA; heterooligome	84.0
2bcq_A	335	DNA polymerase lambda; misalignment, extrahelical,	83.72
1cuk_A	203	RUVA protein; DNA repair, SOS response, DNA-bindin	81.54
2w9m_A	578	Polymerase X; SAXS, DNA repair, DNA polymerase, DN	81.45
2a1j_A	63	DNA repair endonuclease XPF; XPF, xeroderma pigmen	81.34
1z00_A	89	DNA excision repair protein ERCC-1; helix-hairpin-	81.08
1z00_A	89	DNA excision repair protein ERCC-1; helix-hairpin-	80.95
1x2i_A	75	HEF helicase/nuclease; alpha helix, helix-hairpin-	80.1
3r8n_M	114	30S ribosomal protein S13; protein biosynthesis, R	80.03

>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=96.96  E-value=0.0011  Score=53.96  Aligned_cols=70  Identities=21%  Similarity=0.165  Sum_probs=44.5

Q ss_pred             cHHHHHHHhhcccCcchHHHHHHHhh-hCCCCCCccchhHHh-hh--hcCccc-ccchhhHHHHHHHHhhhhccCCC
Q 030389          103 DLTKAVSELTVLKGVGPATASAVLAA-YAPDLAPFMSDEVCF-CS--FSFKFT-LLYSLFIYFYLTFVNGMEGYGGS  174 (178)
Q Consensus       103 d~~~al~~L~~LkGVGPATASaiLa~-~~P~~~pFfSDEa~~-~~--~~~~~~-l~ys~~~y~y~~~~~~i~~~g~~  174 (178)
                      +...+.+.|++||||||-||++||.. ..++ ++ --|--.. .+  .|+.+. +.=+...-.|..+-+.++.+|+.
T Consensus       111 ~~~~~~~~L~~lpGIG~kTA~~il~~~~~~~-~~-~vD~~v~Ri~~rlg~~~~~~~k~~~~k~y~~~~~~l~~~~~~  185 (207)
T 3fhg_A          111 DQQLARERLLNIKGIGMQEASHFLRNVGYFD-LA-IIDRHIIDFMRRIGAIGETNVKQLSKSLYISFENILKSIASN  185 (207)
T ss_dssp             CHHHHHHHHTTSTTCCHHHHHHHHHHTTCCS-SC-CCCHHHHHHHHHTTSSCCCCCSCCCHHHHHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHcCCCcCHHHHHHHHHHhCCCC-cc-eecHHHHHHHHHcCCCCccccccCCHHHHHHHHHHHHHHHHH
Confidence            45689999999999999999999995 5532 22 2344333 32  243222 11122334688888888877754

>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=96.80  E-value=0.003  Score=52.29  Aligned_cols=74  Identities=20%  Similarity=0.152  Sum_probs=47.5

Q ss_pred             HhhCccHHHHHHHhh-cccCcchHHHHHHHhhhCCCCCCcc-chhHHhhh---hcCcccccchhhHHHHHHHHhhhhccC
Q 030389           98 FKSLPDLTKAVSELT-VLKGVGPATASAVLAAYAPDLAPFM-SDEVCFCS---FSFKFTLLYSLFIYFYLTFVNGMEGYG  172 (178)
Q Consensus        98 f~~l~d~~~al~~L~-~LkGVGPATASaiLa~~~P~~~pFf-SDEa~~~~---~~~~~~l~ys~~~y~y~~~~~~i~~~g  172 (178)
                      |..+.++..+.+.|. +|+||||-||+.||....  ..+|+ -|-=..-+   .|+.+...-+++...|..+-..|+.+|
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  23565 66654432   343322111222346777777777666


Q ss_pred             C
Q 030389          173 G  173 (178)
Q Consensus       173 ~  173 (178)
                      .
T Consensus       191 ~  191 (214)
T 3fhf_A          191 E  191 (214)
T ss_dssp             H
T ss_pred             H
Confidence            3

>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=96.27  E-value=0.0067  Score=50.24  Aligned_cols=69  Identities=20%  Similarity=0.071  Sum_probs=41.1

Q ss_pred             cHHHHHHHhh-cccCcchHHHHHHHhh-hCCCCCCccchhHHhhh--hcCcccccchhhHHHHHHHHhhhhccC
Q 030389          103 DLTKAVSELT-VLKGVGPATASAVLAA-YAPDLAPFMSDEVCFCS--FSFKFTLLYSLFIYFYLTFVNGMEGYG  172 (178)
Q Consensus       103 d~~~al~~L~-~LkGVGPATASaiLa~-~~P~~~pFfSDEa~~~~--~~~~~~l~ys~~~y~y~~~~~~i~~~g  172 (178)
                      ++..+.+.|+ +|+||||-||+.||.. ..++.+| ..+=+.+.+  .|+.+.+.-+.....|...-+.++.|+
T Consensus       123 ~~~~~r~~L~~~l~GVG~kTA~~vL~~~g~~~~~~-VDthv~Ri~~rlg~~~~~~k~~t~k~y~~ie~~~~~~a  195 (219)
T 3n0u_A          123 DPFQSREFLVRNAKGIGWKEASHFLRNTGVEDLAI-LDKHVLRLMKRHGLIQEIPKGWSKKRYLYVEEILRKVA  195 (219)
T ss_dssp             CHHHHHHHHHHHSTTCCHHHHHHHHHTTTCCSCCC-CCHHHHHHHHHTTSCSSCCSSCCHHHHHHHHHHHHHHH
T ss_pred             CcHHHHHHHHHhCCCCCHHHHHHHHHHcCCCCeee-ecHHHHHHHHHcCCCCcCcCcCCHHHHHHHHHHHHHHH
Confidence            6788999999 9999999999999975 3332323 233344432  343322211222345666655555543

>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=96.22  E-value=0.0031  Score=53.83  Aligned_cols=42  Identities=21%  Similarity=0.264  Sum_probs=34.2

Q ss_pred             cHHHHHHHhhcccCcchHHHHHHHhh--hCCCCCCccchhHHhhhh
Q 030389          103 DLTKAVSELTVLKGVGPATASAVLAA--YAPDLAPFMSDEVCFCSF  146 (178)
Q Consensus       103 d~~~al~~L~~LkGVGPATASaiLa~--~~P~~~pFfSDEa~~~~~  146 (178)
                      +...+.+.|++||||||-||..||..  ..|+.+|.  |=...-+.
T Consensus       205 ~~~~~~~~L~~lpGIG~~TA~~ill~~lg~pd~fpv--D~~v~r~~  248 (290)
T 3i0w_A          205 NDNECHEELKKFMGVGPQVADCIMLFSMQKYSAFPV--DTWVKKAM  248 (290)
T ss_dssp             CHHHHHHHHTTSTTCCHHHHHHHHHHHHCCTTCCCC--CHHHHHHH
T ss_pred             CHHHHHHHHHhCCCcCHHHHHHHHHHhCCCCCccee--cHHHHHHH
Confidence            56789999999999999999999865  67887786  76665543

>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=96.22  E-value=0.008  Score=49.69  Aligned_cols=31  Identities=29%  Similarity=0.404  Sum_probs=25.6

Q ss_pred             HHHHHHhhcccCcchHHHHHHHhhh--CCCCCC
Q 030389          105 TKAVSELTVLKGVGPATASAVLAAY--APDLAP  135 (178)
Q Consensus       105 ~~al~~L~~LkGVGPATASaiLa~~--~P~~~p  135 (178)
                      ..+++.|++|+||||-||.+||...  .|+.+|
T Consensus       134 ~~~~~~L~~lpGIG~kTA~~ill~alg~pd~~p  166 (233)
T 2h56_A          134 TTVIEKLTAIKGIGQWTAEMFMMFSLGRLDVLS  166 (233)
T ss_dssp             HHHHHHHHTSTTCCHHHHHHHHHHTTCCSCCCC
T ss_pred             HHHHHHHHhCCCcCHHHHHHHHHHhCCCCCeee
Confidence            4789999999999999999999874  554433

>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=96.16  E-value=0.0033  Score=52.02  Aligned_cols=33  Identities=27%  Similarity=0.399  Sum_probs=26.4

Q ss_pred             cHHHHHHHhhcccCcchHHHHHHHhh--hCCCCCC
Q 030389          103 DLTKAVSELTVLKGVGPATASAVLAA--YAPDLAP  135 (178)
Q Consensus       103 d~~~al~~L~~LkGVGPATASaiLa~--~~P~~~p  135 (178)
                      +...+++.|++|+||||-||..||..  ..|+.+|
T Consensus       133 ~~~e~~~~L~~l~GIG~~TA~~ill~~lg~pd~fp  167 (228)
T 3s6i_A          133 SNEELIERLTQIKGIGRWTVEMLLIFSLNRDDVMP  167 (228)
T ss_dssp             CHHHHHHHHTTSTTCCHHHHHHHHHHTSCCSSCCC
T ss_pred             CHHHHHHHHHhCCCcCHHHHHHHHHHhCCCCCEEe
Confidence            34678999999999999999999976  4555433

>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=96.05  E-value=0.0033  Score=49.91  Aligned_cols=72  Identities=17%  Similarity=0.107  Sum_probs=44.6

Q ss_pred             CHHHHHHHHHHHhhCCCCCchhHHHhhhCCHHHHHHHHHH-HH------hhC----ccHHHHHHHhhcccCcchHHHHHH
Q 030389           57 NTTELSKLVRWKLTRGKWRPRLLVFVSSLDDSSVKSASEK-AF------KSL----PDLTKAVSELTVLKGVGPATASAV  125 (178)
Q Consensus        57 tkdEL~~LveWKL~rGkfRP~L~~lv~sN~~~~V~~~t~~-Af------~~l----~d~~~al~~L~~LkGVGPATASai  125 (178)
                      |+++-+.-+-.+|-.  .-|+...+.+.+ +++|++..+- +|      .+.    ..+....+.|.+|+||||-||.+|
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            566666666666652  237877776655 4445443321 11      100    023445678899999999999999


Q ss_pred             HhhhCC
Q 030389          126 LAAYAP  131 (178)
Q Consensus       126 La~~~P  131 (178)
                      +++..-
T Consensus       121 ~~F~~~  126 (161)
T 4e9f_A          121 RIFCVN  126 (161)
T ss_dssp             HHHTSS
T ss_pred             HHHHCC
Confidence            998543

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

Probab=95.84  E-value=0.015  Score=47.80  Aligned_cols=33  Identities=30%  Similarity=0.336  Sum_probs=26.9

Q ss_pred             cHHHHHHHhhcccCcchHHHHHHHhhh--CCCCCC
Q 030389          103 DLTKAVSELTVLKGVGPATASAVLAAY--APDLAP  135 (178)
Q Consensus       103 d~~~al~~L~~LkGVGPATASaiLa~~--~P~~~p  135 (178)
                      +...+++.|++|+||||-||..||...  .|+.+|
T Consensus       140 ~~~e~~~~L~~l~GIG~~TA~~ill~~lg~~d~fp  174 (225)
T 2yg9_A          140 PDELVIAELVQLPGIGRWTAEMFLLFALARPDVFS  174 (225)
T ss_dssp             CHHHHHHHHHTSTTCCHHHHHHHHHHTSCCSCCCC
T ss_pred             CHHHHHHHHHcCCCCCHHHHHHHHHHhCCCCCeee
Confidence            456789999999999999999999874  555434

>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=95.81  E-value=0.0067  Score=50.38  Aligned_cols=32  Identities=22%  Similarity=0.187  Sum_probs=26.1

Q ss_pred             HHHHHHHhhcccCcchHHHHHHHhhh--CCCCCC
Q 030389          104 LTKAVSELTVLKGVGPATASAVLAAY--APDLAP  135 (178)
Q Consensus       104 ~~~al~~L~~LkGVGPATASaiLa~~--~P~~~p  135 (178)
                      ...+++.|++||||||-||..||...  .|+.+|
T Consensus       145 ~~~~~~~L~~l~GIG~~TA~~ill~alg~pd~fp  178 (232)
T 4b21_A          145 EEELMESLSKIKGVKRWTIEMYSIFTLGRLDIMP  178 (232)
T ss_dssp             HHHHHHHHTTSTTCCHHHHHHHHHHTSCCSSCCC
T ss_pred             HHHHHHHHHhCCCcCHHHHHHHHHHhCCCCCeee
Confidence            44789999999999999999999874  555434

>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=95.77  E-value=0.017  Score=48.71  Aligned_cols=31  Identities=29%  Similarity=0.368  Sum_probs=26.6

Q ss_pred             cHHHHHHHhhcccCcchHHHHHHHhhh--CCCC
Q 030389          103 DLTKAVSELTVLKGVGPATASAVLAAY--APDL  133 (178)
Q Consensus       103 d~~~al~~L~~LkGVGPATASaiLa~~--~P~~  133 (178)
                      +...+++.|++|+||||-||..||...  .|+.
T Consensus       201 ~~~~~~~~L~~lpGIG~~TA~~ill~~lg~~d~  233 (282)
T 1mpg_A          201 DVEQAMKTLQTFPGIGRWTANYFALRGWQAKDV  233 (282)
T ss_dssp             CHHHHHHHHTTSTTCCHHHHHHHHHHHSCCSSC
T ss_pred             CHHHHHHHHhcCCCcCHHHHHHHHHHhCCCCCc
Confidence            677899999999999999999999874  4543

>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=95.19  E-value=0.016  Score=47.45  Aligned_cols=40  Identities=20%  Similarity=0.232  Sum_probs=28.4

Q ss_pred             cHHHHHHHhhcccCcchHHHHHHHhhhCCCCCCccchhHHh
Q 030389          103 DLTKAVSELTVLKGVGPATASAVLAAYAPDLAPFMSDEVCF  143 (178)
Q Consensus       103 d~~~al~~L~~LkGVGPATASaiLa~~~P~~~pFfSDEa~~  143 (178)
                      +...+.+.|++||||||-||.+||....-.. .|--|--..
T Consensus       115 ~~~~~~~~L~~lpGIG~kTA~~il~~a~~~~-~~~vD~~v~  154 (218)
T 1pu6_A          115 KQEVTREWLLDQKGIGKESADAILCYACAKE-VMVVDKYSY  154 (218)
T ss_dssp             HHHCCHHHHHTSTTCCHHHHHHHHHHTTCCS-CCCCCHHHH
T ss_pred             cchHHHHHHHcCCCcCHHHHHHHHHHHCCCC-ccccCHHHH
Confidence            3456788999999999999999999753322 334454433

>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=95.05  E-value=0.039  Score=48.62  Aligned_cols=34  Identities=26%  Similarity=0.427  Sum_probs=28.7

Q ss_pred             cHHHHHHHhhcccCcchHHHHHHHhh--hCCCCCCc
Q 030389          103 DLTKAVSELTVLKGVGPATASAVLAA--YAPDLAPF  136 (178)
Q Consensus       103 d~~~al~~L~~LkGVGPATASaiLa~--~~P~~~pF  136 (178)
                      +...+++.|++|+||||-||..||..  ..|+.+|.
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            35689999999999999999999986  56766665

>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=94.88  E-value=0.014  Score=47.81  Aligned_cols=38  Identities=26%  Similarity=0.230  Sum_probs=27.3

Q ss_pred             HHHHHhhcccCcchHHHHHHHhhhCCCCCCccchhHHhh
Q 030389          106 KAVSELTVLKGVGPATASAVLAAYAPDLAPFMSDEVCFC  144 (178)
Q Consensus       106 ~al~~L~~LkGVGPATASaiLa~~~P~~~pFfSDEa~~~  144 (178)
                      .+++.|++|+||||-||.+||....-.. -|.-|--..-
T Consensus       106 ~~~~~L~~lpGIG~~TA~~il~~a~~~~-~~~vD~~v~R  143 (225)
T 1kg2_A          106 ETFEEVAALPGVGRSTAGAILSLSLGKH-FPILDGNVKR  143 (225)
T ss_dssp             CSHHHHHTSTTCCHHHHHHHHHHHHCCS-CCCCCHHHHH
T ss_pred             HHHHHHhcCCCCcHHHHHHHHHHhCCCC-cceeCHHHHH
Confidence            4688999999999999999998743222 2346654443

>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=94.80  E-value=0.011  Score=43.62  Aligned_cols=42  Identities=17%  Similarity=0.218  Sum_probs=34.4

Q ss_pred             HHHHHHhhcccCcchHHHHHHHhhhCCCCCCccchhHHhhhhcCccc
Q 030389          105 TKAVSELTVLKGVGPATASAVLAAYAPDLAPFMSDEVCFCSFSFKFT  151 (178)
Q Consensus       105 ~~al~~L~~LkGVGPATASaiLa~~~P~~~pFfSDEa~~~~~~~~~~  151 (178)
                      .+..+.|+.|+||||++|..|+.     .-||-|=|-+.-++|+.++
T Consensus        22 tAs~~eL~~lpGIG~~~A~~IV~-----~GpF~s~edL~~V~Gig~~   63 (97)
T 3arc_U           22 NTNIAAFIQYRGLYPTLAKLIVK-----NAPYESVEDVLNIPGLTER   63 (97)
T ss_dssp             TSCGGGGGGSTTCTTHHHHHHHH-----HCCCSSGGGGGGCTTCCHH
T ss_pred             cCCHHHHhHCCCCCHHHHHHHHH-----cCCCCCHHHHHhccCCCHH
Confidence            34567899999999999999999     3599997777778887643

>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=94.75  E-value=0.023  Score=48.35  Aligned_cols=30  Identities=33%  Similarity=0.367  Sum_probs=24.9

Q ss_pred             HHHHHHHhhcccCcchHHHHHHHhhh-CCCC
Q 030389          104 LTKAVSELTVLKGVGPATASAVLAAY-APDL  133 (178)
Q Consensus       104 ~~~al~~L~~LkGVGPATASaiLa~~-~P~~  133 (178)
                      ...+.+.|++|+||||-||..||... .|+.
T Consensus       205 ~~e~~~~L~~lpGIG~~TA~~ill~~lg~d~  235 (295)
T 2jhn_A          205 EEEAYEYLTSFKGIGRWTAELVLSIALGKNV  235 (295)
T ss_dssp             HHHHHHHHHTSTTCCHHHHHHHHHHTTCCCC
T ss_pred             HHHHHHHHhcCCCcCHHHHHHHHHHccCCCc
Confidence            36789999999999999999999862 2544

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

Probab=94.66  E-value=0.017  Score=46.78  Aligned_cols=25  Identities=36%  Similarity=0.457  Sum_probs=22.0

Q ss_pred             HHHHHHhhcccCcchHHHHHHHhhh
Q 030389          105 TKAVSELTVLKGVGPATASAVLAAY  129 (178)
Q Consensus       105 ~~al~~L~~LkGVGPATASaiLa~~  129 (178)
                      ..+++.|++|+||||-||.+||...
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            3567889999999999999999974

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

Probab=94.39  E-value=0.028  Score=38.32  Aligned_cols=39  Identities=23%  Similarity=0.352  Sum_probs=31.9

Q ss_pred             HHHHhhcccCcchHHHHHHHhhhCCCCCCccchhHHhhhhcCcc
Q 030389          107 AVSELTVLKGVGPATASAVLAAYAPDLAPFMSDEVCFCSFSFKF  150 (178)
Q Consensus       107 al~~L~~LkGVGPATASaiLa~~~P~~~pFfSDEa~~~~~~~~~  150 (178)
                      ....|..++||||.+|..|+.-.     +|-+-|-+..++|+.+
T Consensus        25 ~~~~L~~ipGIG~~~A~~Il~~r-----~~~s~~eL~~v~Gig~   63 (75)
T 2duy_A           25 SLEELMALPGIGPVLARRIVEGR-----PYARVEDLLKVKGIGP   63 (75)
T ss_dssp             CHHHHTTSTTCCHHHHHHHHHTC-----CCSSGGGGGGSTTCCH
T ss_pred             CHHHHHhCCCCCHHHHHHHHHHc-----ccCCHHHHHhCCCCCH
Confidence            45678899999999999999964     7878777777888754

>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=94.31  E-value=0.022  Score=46.80  Aligned_cols=25  Identities=36%  Similarity=0.469  Sum_probs=22.0

Q ss_pred             HHHHHHhhcccCcchHHHHHHHhhh
Q 030389          105 TKAVSELTVLKGVGPATASAVLAAY  129 (178)
Q Consensus       105 ~~al~~L~~LkGVGPATASaiLa~~  129 (178)
                      ..+++.|++|+||||-||.+||...
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            3468899999999999999999874

>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=94.15  E-value=0.024  Score=46.28  Aligned_cols=37  Identities=24%  Similarity=0.215  Sum_probs=26.8

Q ss_pred             HHHHHhhcccCcchHHHHHHHhhhCCCCCCccchhHHh
Q 030389          106 KAVSELTVLKGVGPATASAVLAAYAPDLAPFMSDEVCF  143 (178)
Q Consensus       106 ~al~~L~~LkGVGPATASaiLa~~~P~~~pFfSDEa~~  143 (178)
                      .+++.|++|+||||-||.+||....-.. -|--|--..
T Consensus       112 ~~~~~L~~lpGIG~~TA~~il~~~~~~~-~~~vD~~v~  148 (221)
T 1kea_A          112 RNRKAILDLPGVGKYTCAAVMCLAFGKK-AAMVDANFV  148 (221)
T ss_dssp             SCHHHHHTSTTCCHHHHHHHHHHTTCCC-CCCCCHHHH
T ss_pred             HHHHHHHhCCCCcHHHHHHHHHHhcCCC-cceecHHHH
Confidence            4678899999999999999999753322 234454443

>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=93.81  E-value=0.024  Score=44.45  Aligned_cols=41  Identities=17%  Similarity=0.233  Sum_probs=32.4

Q ss_pred             HHHHHHhhcccCcchHHHHHHHhhhCCCCCCccchhHHhhhhcCcc
Q 030389          105 TKAVSELTVLKGVGPATASAVLAAYAPDLAPFMSDEVCFCSFSFKF  150 (178)
Q Consensus       105 ~~al~~L~~LkGVGPATASaiLa~~~P~~~pFfSDEa~~~~~~~~~  150 (178)
                      .+..+.|++|+||||++|.+|.     ++.||=|=|=+.-++|+.+
T Consensus        59 tA~~~eL~~LpGiGp~~A~~II-----~~GpF~svedL~~V~GIg~   99 (134)
T 1s5l_U           59 NTNIAAFIQYRGLYPTLAKLIV-----KNAPYESVEDVLNIPGLTE   99 (134)
T ss_dssp             TSCGGGGGGSTTCTHHHHHHHH-----HTCCCSSGGGGGGCTTCCH
T ss_pred             ccCHHHHHHCCCCCHHHHHHHH-----HcCCCCCHHHHHhCCCCCH
Confidence            3457789999999999999999     3568999555556888764

>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=93.68  E-value=0.058  Score=38.73  Aligned_cols=42  Identities=19%  Similarity=0.157  Sum_probs=32.4

Q ss_pred             HHHhhcccCcchHHHHHHHhhhCCCCCCccchhHHhhhhcCcc
Q 030389          108 VSELTVLKGVGPATASAVLAAYAPDLAPFMSDEVCFCSFSFKF  150 (178)
Q Consensus       108 l~~L~~LkGVGPATASaiLa~~~P~~~pFfSDEa~~~~~~~~~  150 (178)
                      ...|..++||||.+|..|+..... .-+|-+=|-+..++|+.+
T Consensus        39 ~~~L~~ipGIG~~~A~~Il~~r~~-~g~f~s~edL~~v~Gig~   80 (98)
T 2edu_A           39 ARDLRSLQRIGPKKAQLIVGWREL-HGPFSQVEDLERVEGITG   80 (98)
T ss_dssp             HHHHHHSTTCCHHHHHHHHHHHHH-HCCCSSGGGGGGSTTCCH
T ss_pred             HHHHHHCCCCCHHHHHHHHHHHHh-cCCcCCHHHHHhCCCCCH
Confidence            567889999999999999998643 237877666777888654

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

Probab=93.36  E-value=0.017  Score=48.19  Aligned_cols=65  Identities=18%  Similarity=0.301  Sum_probs=42.9

Q ss_pred             hHHHhhhCCHHHHHHHHHHHHhhCccHHHHHHHhhcccCcchHHHHHHHhhhCCCCCCccc-hhHHhhhhcCc
Q 030389           78 LLVFVSSLDDSSVKSASEKAFKSLPDLTKAVSELTVLKGVGPATASAVLAAYAPDLAPFMS-DEVCFCSFSFK  149 (178)
Q Consensus        78 L~~lv~sN~~~~V~~~t~~Af~~l~d~~~al~~L~~LkGVGPATASaiLa~~~P~~~pFfS-DEa~~~~~~~~  149 (178)
                      +.+.|+.|....|. .    |+....+.+.+..|..|+||||++|-+|+.--.-  -||-| ||...-+.|++
T Consensus       106 v~~iV~~~E~~fv~-f----~n~a~pITA~~~eL~~LpGIG~k~A~~IIeyRe~--G~F~s~eDL~~RV~GIg  171 (205)
T 2i5h_A          106 IEHIIKQDEKKYVD-F----FNKADSITTRMHQLELLPGVGKKMMWAIIEERKK--RPFESFEDIAQRVKGIQ  171 (205)
T ss_dssp             HHHHHHTTHHHHHH-H----HC--CCBCSSSBGGGGSTTCCHHHHHHHHHHHHH--SCCCSHHHHHHHSTTCC
T ss_pred             HHHHHHhchhhhhh-h----ccccCCccCCHHHHhcCCCcCHHHHHHHHHHHhc--CCCCCHHHHHHhcCCCC
Confidence            33445555444443 1    3322334667888999999999999999998654  59999 55545577743

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

Probab=92.79  E-value=0.19  Score=43.52  Aligned_cols=38  Identities=32%  Similarity=0.283  Sum_probs=27.4

Q ss_pred             HHHHHHhhcccCcchHHHHHHHhhhCCCCCCccchhHHh
Q 030389          105 TKAVSELTVLKGVGPATASAVLAAYAPDLAPFMSDEVCF  143 (178)
Q Consensus       105 ~~al~~L~~LkGVGPATASaiLa~~~P~~~pFfSDEa~~  143 (178)
                      ..+++.|++|+||||-||.+||+...-.. -|.-|--..
T Consensus       114 p~~~~~L~~l~GIG~~tA~~il~~~~~~~-~~~vD~~v~  151 (369)
T 3fsp_A          114 PDDPDEFSRLKGVGPYTVGAVLSLAYGVP-EPAVDGNVM  151 (369)
T ss_dssp             CCSHHHHHTSTTCCHHHHHHHHHHHHCCC-CCCCCHHHH
T ss_pred             hhHHHHHhcCCCcCHHHHHHHHHHHCCCC-cccccHHHH
Confidence            34788999999999999999999854332 234454433

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

Probab=92.24  E-value=0.084  Score=45.40  Aligned_cols=37  Identities=24%  Similarity=0.150  Sum_probs=27.5

Q ss_pred             HHHHhhc-ccCcchHHHHHHHhhhCCCCCCccchhHHhh
Q 030389          107 AVSELTV-LKGVGPATASAVLAAYAPDLAPFMSDEVCFC  144 (178)
Q Consensus       107 al~~L~~-LkGVGPATASaiLa~~~P~~~pFfSDEa~~~  144 (178)
                      .++.|.+ |+||||-||.+||....-.. .|.-|--..-
T Consensus       126 ~~~~Ll~~LpGIG~kTA~~iL~~a~g~p-~~~VDt~V~R  163 (287)
T 3n5n_X          126 TAETLQQLLPGVGRYTAGAIASIAFGQA-TGVVDGNVAR  163 (287)
T ss_dssp             SHHHHHHHSTTCCHHHHHHHHHHHSCCC-CCCCCHHHHH
T ss_pred             HHHHHHHHcCCCCHHHHHHHHHHhcCCC-CccccHHHHH
Confidence            5788887 99999999999999864332 3456665543

>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=91.52  E-value=0.23  Score=34.88  Aligned_cols=63  Identities=16%  Similarity=0.120  Sum_probs=38.0

Q ss_pred             hhCCHHHHHHHHHHHHhhCccHHHHHHHhhcccCcchHHHHHHHhhhC-CCCCCccchhHHhhhhcCcc
Q 030389           83 SSLDDSSVKSASEKAFKSLPDLTKAVSELTVLKGVGPATASAVLAAYA-PDLAPFMSDEVCFCSFSFKF  150 (178)
Q Consensus        83 ~sN~~~~V~~~t~~Af~~l~d~~~al~~L~~LkGVGPATASaiLa~~~-P~~~pFfSDEa~~~~~~~~~  150 (178)
                      +.++++.++.-.+.-+     ....+..|+.++||||.||-.|+..+. .+.+--.+-|.+..++|+..
T Consensus        11 ~~~~~~~~~~~~~~~~-----~~~~~~~L~~IpgIG~~~A~~Ll~~fgs~~~l~~as~~eL~~i~GIG~   74 (91)
T 2a1j_B           11 SQDPADLLMEKLEQDF-----VSRVTECLTTVKSVNKTDSQTLLTTFGSLEQLIAASREDLALCPGLGP   74 (91)
T ss_dssp             --CCSHHHHHHHHHHH-----HHHHHHHHTTSTTCCHHHHHHHHHHHSSHHHHHSCCHHHHHTSSSCCS
T ss_pred             ccCCHHHHhhhccCCH-----HHHHHHHHHcCCCCCHHHHHHHHHHCCCHHHHHhCCHHHHHhCCCCCH
Confidence            4566666665544433     344677888999999999999998653 22222223344555677654

>2ztd_A Holliday junction ATP-dependent DNA helicase RUVA; recombination, branch migration, DNA BIND oligomerization, acidic PIN; 2.40A {Mycobacterium tuberculosis} PDB: 2ztc_A 2zte_A 2h5x_A 1bvs_A

Probab=90.06  E-value=0.084  Score=43.69  Aligned_cols=29  Identities=31%  Similarity=0.331  Sum_probs=20.0

Q ss_pred             HHHHHHHhhcccCcchHHHHHHHhhhCCC
Q 030389          104 LTKAVSELTVLKGVGPATASAVLAAYAPD  132 (178)
Q Consensus       104 ~~~al~~L~~LkGVGPATASaiLa~~~P~  132 (178)
                      .+.-...|..++||||.||-+||+...|+
T Consensus        83 Er~lf~~L~sv~GIGpk~A~~Ils~~~~~  111 (212)
T 2ztd_A           83 TRDLFLTLLSVSGVGPRLAMAALAVHDAP  111 (212)
T ss_dssp             HHHHHHHHHTSTTCCHHHHHHHHHHSCHH
T ss_pred             HHHHHHHhcCcCCcCHHHHHHHHHhCCHH
Confidence            34445557777888888888888776664

>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=90.03  E-value=0.19  Score=33.27  Aligned_cols=22  Identities=27%  Similarity=0.452  Sum_probs=15.8

Q ss_pred             HHHhhcccCcchHHHHHHHhhh
Q 030389          108 VSELTVLKGVGPATASAVLAAY  129 (178)
Q Consensus       108 l~~L~~LkGVGPATASaiLa~~  129 (178)
                      .+.|++++||||.+|..|.+..
T Consensus        45 ~~~L~~i~Gig~~~a~~i~~~~   66 (75)
T 1x2i_A           45 VAELMKVEGIGEKIAKEIRRVI   66 (75)
T ss_dssp             HHHHTTSTTCCHHHHHHHHHHH
T ss_pred             HHHHhcCCCCCHHHHHHHHHHH
Confidence            4567777777777777777765

>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=87.35  E-value=0.39  Score=32.67  Aligned_cols=18  Identities=33%  Similarity=0.623  Sum_probs=10.1

Q ss_pred             hhcccCcchHHHHHHHhh
Q 030389          111 LTVLKGVGPATASAVLAA  128 (178)
Q Consensus       111 L~~LkGVGPATASaiLa~  128 (178)
                      |..++||||.||-.|+..
T Consensus        26 L~~I~gIG~~~A~~Ll~~   43 (78)
T 1kft_A           26 LETIEGVGPKRRQMLLKY   43 (78)
T ss_dssp             GGGCTTCSSSHHHHHHHH
T ss_pred             HhcCCCCCHHHHHHHHHH
Confidence            445555555555555554

>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=85.31  E-value=0.19  Score=34.27  Aligned_cols=47  Identities=13%  Similarity=0.237  Sum_probs=31.5

Q ss_pred             hhhCCHHHHHHHHHHHHhhCccHHH-HHHHhhcccCcchHHHHHHHhhh
Q 030389           82 VSSLDDSSVKSASEKAFKSLPDLTK-AVSELTVLKGVGPATASAVLAAY  129 (178)
Q Consensus        82 v~sN~~~~V~~~t~~Af~~l~d~~~-al~~L~~LkGVGPATASaiLa~~  129 (178)
                      |..-.+...+++.+ .|..+.++.. ..+.|++++||||.+|..|.+..
T Consensus        29 I~gIG~~~A~~Ll~-~fgsl~~l~~a~~eeL~~i~GIG~~~a~~I~~~~   76 (78)
T 1kft_A           29 IEGVGPKRRQMLLK-YMGGLQGLRNASVEEIAKVPGISQGLAEKIFWSL   76 (78)
T ss_dssp             CTTCSSSHHHHHHH-HHSCHHHHHHCCHHHHTTSSSTTSHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHH-HcCCHHHHHHCCHHHHHHCCCCCHHHHHHHHHHH
Confidence            44444555555553 3654434433 37789999999999999998765

>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=84.00  E-value=0.57  Score=37.90  Aligned_cols=26  Identities=38%  Similarity=0.554  Sum_probs=16.8

Q ss_pred             HHHHHhhcccCcchHHHHHHHhhhCC
Q 030389          106 KAVSELTVLKGVGPATASAVLAAYAP  131 (178)
Q Consensus       106 ~al~~L~~LkGVGPATASaiLa~~~P  131 (178)
                      ..+..|..++||||.||-+||+.+.+
T Consensus        69 ~~f~~L~~v~GIGpk~A~~iL~~f~~   94 (191)
T 1ixr_A           69 ALFELLLSVSGVGPKVALALLSALPP   94 (191)
T ss_dssp             HHHHHHHSSSCCCHHHHHHHHHHSCH
T ss_pred             HHHHHHhcCCCcCHHHHHHHHHhCCh
Confidence            33445666777777777777776555

>2bcq_A DNA polymerase lambda; misalignment, extrahelical, mutagenesis, mutation, deletion, streisinger, slippage, transferase, lyase/DNA complex; HET: DNA; 1.65A {Homo sapiens} SCOP: a.60.6.1 a.60.12.1 d.218.1.2 PDB: 1xsl_A* 2bcr_A* 2bcs_A* 2bcu_A* 2bcv_A* 2gws_A* 3c5g_A* 3c5f_A* 2pfn_A* 1xsp_A* 1xsn_A* 2pfo_A* 2pfp_A* 2pfq_A* 3hw8_A* 3hwt_A* 1rzt_A* 3hx0_A* 3mdc_A* 3mda_A* ...

Probab=83.72  E-value=0.53  Score=40.89  Aligned_cols=54  Identities=13%  Similarity=0.122  Sum_probs=32.9

Q ss_pred             HhhCccHHHHHHHhhcccCcchHHHHHHHhhhCCCCCCcc--------chhHHhhhhcCccc
Q 030389           98 FKSLPDLTKAVSELTVLKGVGPATASAVLAAYAPDLAPFM--------SDEVCFCSFSFKFT  151 (178)
Q Consensus        98 f~~l~d~~~al~~L~~LkGVGPATASaiLa~~~P~~~pFf--------SDEa~~~~~~~~~~  151 (178)
                      ++.+|..-..+..|++|+|||+.||..|--...-......        .=+.|..|+|++++
T Consensus        46 l~~l~~~i~~~~~l~~lpGIG~~~A~kI~E~l~tG~~~~le~l~~~~p~l~ll~~v~GiG~k  107 (335)
T 2bcq_A           46 LKSFHKPVTSYQEACSIPGIGKRMAEKIIEILESGHLRKLDHISESVPVLELFSNIWGAGTK  107 (335)
T ss_dssp             HHSCCSCCCCHHHHHTSTTCCHHHHHHHHHHHHSSSCGGGGGCCTTHHHHHHHHTSTTCCHH
T ss_pred             HHhCCccccCHHHHhcCCCccHHHHHHHHHHHHcCCchHHHHHhhhhHHHHHHhcCCCcCHH
Confidence            4455533334556899999999999999877432221111        22345567887653

>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=81.54  E-value=0.78  Score=37.36  Aligned_cols=47  Identities=21%  Similarity=0.100  Sum_probs=29.9

Q ss_pred             HHHHHHHhhcccCcchHHHHHHHhhhCCCC---CCcc-chhHHhhhhcCcc
Q 030389          104 LTKAVSELTVLKGVGPATASAVLAAYAPDL---APFM-SDEVCFCSFSFKF  150 (178)
Q Consensus       104 ~~~al~~L~~LkGVGPATASaiLa~~~P~~---~pFf-SDEa~~~~~~~~~  150 (178)
                      -+.-+..|..++||||.+|-+||+.+.|+.   ...- +-|....+||+..
T Consensus        68 ek~~f~~L~~V~GIGpk~A~~iL~~f~~~~l~~aI~~~d~~~L~~vpGIG~  118 (203)
T 1cuk_A           68 ERTLFKELIKTNGVGPKLALAILSGMSAQQFVNAVEREEVGALVKLPGIGK  118 (203)
T ss_dssp             HHHHHHHHHHSSSCCHHHHHHHHHHSCHHHHHHHHHTTCHHHHHTSTTCCH
T ss_pred             HHHHHHHHhcCCCcCHHHHHHHHhhCChHHHHHHHHhCCHHHHhhCCCCCH
Confidence            344556788899999999999999876632   1112 2233444777654

>2w9m_A Polymerase X; SAXS, DNA repair, DNA polymerase, DNA replication; 2.46A {Deinococcus radiodurans}

Probab=81.45  E-value=0.91  Score=41.85  Aligned_cols=24  Identities=21%  Similarity=0.432  Sum_probs=21.8

Q ss_pred             HHHHHHhhcccCcchHHHHHHHhh
Q 030389          105 TKAVSELTVLKGVGPATASAVLAA  128 (178)
Q Consensus       105 ~~al~~L~~LkGVGPATASaiLa~  128 (178)
                      ...+..|+++.||||.||-.|++.
T Consensus        93 ~~~~~~L~~v~GVGpk~A~~i~~~  116 (578)
T 2w9m_A           93 PPGLLDLLGVRGLGPKKIRSLWLA  116 (578)
T ss_dssp             CHHHHHHTTSTTCCHHHHHHHHHT
T ss_pred             HHHHHHHhCCCCcCHHHHHHHHHc
Confidence            458889999999999999999986

>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=81.34  E-value=0.51  Score=31.49  Aligned_cols=41  Identities=10%  Similarity=0.060  Sum_probs=28.4

Q ss_pred             HHHHhhcccCcchHHHHHHHhhhC-CCCCCccchhHHhhhhc
Q 030389          107 AVSELTVLKGVGPATASAVLAAYA-PDLAPFMSDEVCFCSFS  147 (178)
Q Consensus       107 al~~L~~LkGVGPATASaiLa~~~-P~~~pFfSDEa~~~~~~  147 (178)
                      +...|..++||||.+.-.+|.-+. -+.+.=.|-|-+..+.|
T Consensus         2 ~~s~L~~IpGIG~kr~~~LL~~Fgs~~~i~~As~eeL~~vig   43 (63)
T 2a1j_A            2 PQDFLLKMPGVNAKNCRSLMHHVKNIAELAALSQDELTSILG   43 (63)
T ss_dssp             CCHHHHTSTTCCHHHHHHHHHHCSSHHHHHTCCHHHHHHHHS
T ss_pred             HHhHHHcCCCCCHHHHHHHHHHcCCHHHHHHCCHHHHHHHcC
Confidence            346788999999999999998632 22344456555555555

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

Probab=81.08  E-value=1.3  Score=30.70  Aligned_cols=46  Identities=15%  Similarity=0.129  Sum_probs=29.8

Q ss_pred             HHHHHHhhcccCcchHHHHHHHhhhCC-CCCCccchhHHhhhhcCcc
Q 030389          105 TKAVSELTVLKGVGPATASAVLAAYAP-DLAPFMSDEVCFCSFSFKF  150 (178)
Q Consensus       105 ~~al~~L~~LkGVGPATASaiLa~~~P-~~~pFfSDEa~~~~~~~~~  150 (178)
                      ...+..|+.++||||.+|-.|+..+.. +.+--.+-|.+..++|+.+
T Consensus        15 ~~~~~~L~~IpgIG~~~A~~Ll~~fgsl~~l~~a~~~eL~~i~GIG~   61 (89)
T 1z00_A           15 SRVTECLTTVKSVNKTDSQTLLTTFGSLEQLIAASREDLALCPGLGP   61 (89)
T ss_dssp             HHHHHHHTTSSSCCHHHHHHHHHHTCBHHHHHHCCHHHHHTSTTCCH
T ss_pred             HHHHHHHHcCCCCCHHHHHHHHHHCCCHHHHHhCCHHHHHhCCCCCH
Confidence            345667889999999999999987532 1122223445555777653

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

Probab=80.95  E-value=0.83  Score=31.68  Aligned_cols=24  Identities=21%  Similarity=0.462  Sum_probs=20.8

Q ss_pred             HHHHhhcccCcchHHHHHHHhhhC
Q 030389          107 AVSELTVLKGVGPATASAVLAAYA  130 (178)
Q Consensus       107 al~~L~~LkGVGPATASaiLa~~~  130 (178)
                      ..+.|++++|||+.+|..|.+...
T Consensus        49 ~~~eL~~i~GIG~~~a~~I~~~l~   72 (89)
T 1z00_A           49 SREDLALCPGLGPQKARRLFDVLH   72 (89)
T ss_dssp             CHHHHHTSTTCCHHHHHHHHHHHH
T ss_pred             CHHHHHhCCCCCHHHHHHHHHHHH
Confidence            356799999999999999999863

>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=80.10  E-value=1.5  Score=28.74  Aligned_cols=46  Identities=11%  Similarity=-0.057  Sum_probs=29.4

Q ss_pred             HHHHHHhhcccCcchHHHHHHHhhhCC-CCCCccchhHHhhhhcCcc
Q 030389          105 TKAVSELTVLKGVGPATASAVLAAYAP-DLAPFMSDEVCFCSFSFKF  150 (178)
Q Consensus       105 ~~al~~L~~LkGVGPATASaiLa~~~P-~~~pFfSDEa~~~~~~~~~  150 (178)
                      ......|+.++||||.+|..|+..+.. +.+---+-|.+..++|+.+
T Consensus        10 ~~~~~~L~~i~giG~~~a~~Ll~~fgs~~~l~~a~~~~L~~i~Gig~   56 (75)
T 1x2i_A           10 ERQRLIVEGLPHVSATLARRLLKHFGSVERVFTASVAELMKVEGIGE   56 (75)
T ss_dssp             HHHHHHHTTSTTCCHHHHHHHHHHHCSHHHHHHCCHHHHTTSTTCCH
T ss_pred             HHHHHHHcCCCCCCHHHHHHHHHHcCCHHHHHhCCHHHHhcCCCCCH
Confidence            344567899999999999999986522 1111123344555677653

---

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	178
d2noha1	190	8-oxoguanine glycosylase {Human (Homo sapiens) [Ta	96.67
d1mpga1	183	3-Methyladenine DNA glycosylase II (gene alkA or a	96.2
d1keaa_	217	Thymine-DNA glycosylase {Archaeon Methanobacterium	96.18
d1rrqa1	221	Catalytic domain of MutY {Bacillus stearothermophi	96.08
d1kg2a_	224	Catalytic domain of MutY {Escherichia coli [TaxId:	95.98
d1orna_	214	Endonuclease III {Escherichia coli [TaxId: 562]}	95.97
d2abka_	211	Endonuclease III {Escherichia coli [TaxId: 562]}	95.54
d1pu6a_	217	3-Methyladenine DNA glycosylase III (MagIII) {Heli	95.35
d1ngna_	144	Mismatch-specific thymine glycosylase domain of th	94.69
d2axtu1	98	Photosystem II 12 kDa extrinsic protein PsbU {Ther	94.42
d2fmpa2	57	DNA polymerase beta {Human (Homo sapiens) [TaxId:	94.41
d2a1jb1	78	DNA excision repair protein ERCC-1 {Human (Homo sa	93.44
d1bvsa2	71	DNA helicase RuvA subunit, middle domain {Mycobact	93.37
d1pzna1	61	DNA repair protein Rad51, N-terminal domain {Archa	93.07
d1cuka2	78	DNA helicase RuvA subunit, middle domain {Escheric	92.65
d2bgwa1	70	DNA repair endonuclease XPF {Aeropyrum pernix [Tax	92.41
d1ixra1	73	DNA helicase RuvA subunit, middle domain {Thermus	91.9
d1kfta_	56	Excinuclease UvrC C-terminal domain {Escherichia c	91.75
d1jmsa3	60	Terminal deoxynucleotidyl transferase {Mouse (Mus	91.74
d2duya1	65	Uncharacterized protein TTHA1967 {Thermus thermoph	91.48
d2bcqa2	57	DNA polymerase lambda {Human (Homo sapiens) [TaxId	90.64
d2edua1	91	KIF22, C-terminal domain {Human (Homo sapiens) [Ta	90.34
d2i1qa1	60	DNA repair protein Rad51, N-terminal domain {Archa	89.21
d1ixra1	73	DNA helicase RuvA subunit, middle domain {Thermus	88.27
d1cuka2	78	DNA helicase RuvA subunit, middle domain {Escheric	88.19
d2a1jb1	78	DNA excision repair protein ERCC-1 {Human (Homo sa	88.19
d1kfta_	56	Excinuclease UvrC C-terminal domain {Escherichia c	86.82
d1x2ia1	68	ATP-dependent RNA helicase PF2015 {Pyrococcus furi	86.82
d2bgwa1	70	DNA repair endonuclease XPF {Aeropyrum pernix [Tax	86.51
d1bvsa2	71	DNA helicase RuvA subunit, middle domain {Mycobact	86.0
d2fmpa1	82	DNA polymerase beta, N-terminal (8 kD)-domain {Hum	85.77
d2a1ja1	62	DNA repair endonuclease XPF {Human (Homo sapiens)	85.23
d2bcqa1	76	DNA polymerase lambda {Human (Homo sapiens) [TaxId	84.16
d3bzka1	90	Transcriptional accessory factor Tex {Pseudomonas	83.89
d1x2ia1	68	ATP-dependent RNA helicase PF2015 {Pyrococcus furi	83.44
d2i1qa1	60	DNA repair protein Rad51, N-terminal domain {Archa	82.32
d2uubm1	125	Ribosomal protein S13 {Thermus thermophilus [TaxId	81.66
d2gy9m1	114	Ribosomal protein S13 {Escherichia coli [TaxId: 56	80.7

>d2noha1 a.96.1.3 (A:136-325) 8-oxoguanine glycosylase {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA-glycosylase
superfamily: DNA-glycosylase
family: DNA repair glycosylase, 2 C-terminal domains
domain: 8-oxoguanine glycosylase
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.67  E-value=0.00063  Score=52.38  Aligned_cols=39  Identities=26%  Similarity=0.404  Sum_probs=31.3

Q ss_pred             cHHHHHHHhhcccCcchHHHHHHHhh--hCCCCCCccchhHHh
Q 030389          103 DLTKAVSELTVLKGVGPATASAVLAA--YAPDLAPFMSDEVCF  143 (178)
Q Consensus       103 d~~~al~~L~~LkGVGPATASaiLa~--~~P~~~pFfSDEa~~  143 (178)
                      +...+++.|++||||||-||..||..  ..|+.+|.  |--..
T Consensus        97 ~~~~~~~~L~~l~GIG~wTA~~il~~~~~~~d~fpv--D~~v~  137 (190)
T d2noha1          97 SYEEAHKALCILPGVGTQVADCICLMALDKPQAVPV--DVHMW  137 (190)
T ss_dssp             CHHHHHHHHTTSTTCCHHHHHHHHHHHSCCTTCCCC--CHHHH
T ss_pred             CcHHHHHHHHHcCCchHHHHHHHHHHHcCCCCeEee--cHHHH
Confidence            56789999999999999999998876  56777774  54443

>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=96.20  E-value=0.0016  Score=50.06  Aligned_cols=34  Identities=26%  Similarity=0.276  Sum_probs=28.5

Q ss_pred             cHHHHHHHhhcccCcchHHHHHHHhh--hCCCCCCc
Q 030389          103 DLTKAVSELTVLKGVGPATASAVLAA--YAPDLAPF  136 (178)
Q Consensus       103 d~~~al~~L~~LkGVGPATASaiLa~--~~P~~~pF  136 (178)
                      +...+++.|++||||||=||..||-.  ..|+.+|.
T Consensus       102 ~~~e~~~~L~~l~GIGpwTAd~illf~lg~~dvfP~  137 (183)
T d1mpga1         102 DVEQAMKTLQTFPGIGRWTANYFALRGWQAKDVFLP  137 (183)
T ss_dssp             CHHHHHHHHTTSTTCCHHHHHHHHHHHSCCSSCCCT
T ss_pred             cHHHHHHHHHHhhcccHHHHHHHHHhhCCCCCcccc
Confidence            67889999999999999999999865  56766553

>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=96.18  E-value=0.0027  Score=50.13  Aligned_cols=83  Identities=18%  Similarity=0.125  Sum_probs=51.1

Q ss_pred             CHHHHHHHHHHHhhCCCCCchhHHHhhhCCHHHHHHHHH-------HHHhh------C-----ccHHHHHHHhhcccCcc
Q 030389           57 NTTELSKLVRWKLTRGKWRPRLLVFVSSLDDSSVKSASE-------KAFKS------L-----PDLTKAVSELTVLKGVG  118 (178)
Q Consensus        57 tkdEL~~LveWKL~rGkfRP~L~~lv~sN~~~~V~~~t~-------~Af~~------l-----~d~~~al~~L~~LkGVG  118 (178)
                      |+++.+.-+-=+|. -+| |+...+.+.+ +++|+++.+       +|-.+      +     ..+....+.|.+|+|||
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            56776666666663 234 7888877775 455554432       12110      0     02334578899999999


Q ss_pred             hHHHHHHHhhhCCCCCCccchhHHh
Q 030389          119 PATASAVLAAYAPDLAPFMSDEVCF  143 (178)
Q Consensus       119 PATASaiLa~~~P~~~pFfSDEa~~  143 (178)
                      |-||++||+...-.. .|.-|--..
T Consensus       123 ~kTA~~il~~~~~~~-~~~vD~~v~  146 (217)
T d1keaa_         123 KYTCAAVMCLAFGKK-AAMVDANFV  146 (217)
T ss_dssp             HHHHHHHHHHTTCCC-CCCCCHHHH
T ss_pred             hhhhHHHHHHhcCCc-ccccccchh
Confidence            999999999965544 444554443

>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=96.08  E-value=0.0033  Score=49.51  Aligned_cols=38  Identities=29%  Similarity=0.266  Sum_probs=28.2

Q ss_pred             HHHHHHhhcccCcchHHHHHHHhhhCCCCCCccchhHHh
Q 030389          105 TKAVSELTVLKGVGPATASAVLAAYAPDLAPFMSDEVCF  143 (178)
Q Consensus       105 ~~al~~L~~LkGVGPATASaiLa~~~P~~~pFfSDEa~~  143 (178)
                      ....+.|.+|+||||-||++||+...-..+ |.-|-=..
T Consensus       103 p~~~~~Ll~LpGIG~kTA~~il~~a~~~p~-~~VDt~v~  140 (221)
T d1rrqa1         103 PDDPDEFSRLKGVGPYTVGAVLSLAYGVPE-PAVNGNVM  140 (221)
T ss_dssp             CCSHHHHHTSTTCCHHHHHHHHHHHTCCCC-CCCCHHHH
T ss_pred             chHHHHHHHHHHhhhHHHHHHHHHHhcCcc-cccCccHH
Confidence            345778999999999999999999765433 44455444

>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=95.98  E-value=0.002  Score=50.91  Aligned_cols=71  Identities=15%  Similarity=0.206  Sum_probs=42.9

Q ss_pred             CHHHHHHHHHHHhhCCCCCchhHHHhhhCCHHHHHHHHHHH-H-----------hhC-----ccHHHHHHHhhcccCcch
Q 030389           57 NTTELSKLVRWKLTRGKWRPRLLVFVSSLDDSSVKSASEKA-F-----------KSL-----PDLTKAVSELTVLKGVGP  119 (178)
Q Consensus        57 tkdEL~~LveWKL~rGkfRP~L~~lv~sN~~~~V~~~t~~A-f-----------~~l-----~d~~~al~~L~~LkGVGP  119 (178)
                      |++|-+.-+-=+|- .+| |+...+.+.+ .+.++++.+-+ |           +.+     .++....+.|.+|+||||
T Consensus        43 T~~~~v~~~~~~l~-~~~-pt~~~la~a~-~~~l~~~i~~~g~~~ka~~l~~~~~~i~~~~~g~vp~~~~~L~~LpGVG~  119 (224)
T d1kg2a_          43 TQVATVIPYFERFM-ARF-PTVTDLANAP-LDEVLHLWTGLGYYARARNLHKAAQQVATLHGGKFPETFEEVAALPGVGR  119 (224)
T ss_dssp             SCHHHHHHHHHHHH-HHC-SSHHHHHHSC-HHHHHHHHTTSCCTHHHHHHHHHHHHHHHHSTTSCCCSHHHHHTSTTCCH
T ss_pred             CcHHHHHHHHHHHH-HHh-ccHHHHHHhh-HHHHHhHhhhhhHHHHHHHHHHhhhhhhhhccCCcchHHHHHHHHHhhhh
Confidence            45555544433332 123 7888877775 45666554322 1           000     023345678999999999


Q ss_pred             HHHHHHHhhhC
Q 030389          120 ATASAVLAAYA  130 (178)
Q Consensus       120 ATASaiLa~~~  130 (178)
                      -||.+||+...
T Consensus       120 kTA~~il~~a~  130 (224)
T d1kg2a_         120 STAGAILSLSL  130 (224)
T ss_dssp             HHHHHHHHHHH
T ss_pred             hhhHHHHHHhh
Confidence            99999999864

>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=95.97  E-value=0.0021  Score=50.57  Aligned_cols=36  Identities=28%  Similarity=0.268  Sum_probs=25.9

Q ss_pred             HHHHhhcccCcchHHHHHHHhhhCCCCCCccchhHHh
Q 030389          107 AVSELTVLKGVGPATASAVLAAYAPDLAPFMSDEVCF  143 (178)
Q Consensus       107 al~~L~~LkGVGPATASaiLa~~~P~~~pFfSDEa~~  143 (178)
                      ..+.|.+|+||||-||++||+...- ..-|.-|-=..
T Consensus       108 ~~~~L~~LpGVG~kTA~~il~~a~~-~~~~~VDtnv~  143 (214)
T d1orna_         108 DRDELMKLPGVGRKTANVVVSVAFG-VPAIAVDTHVE  143 (214)
T ss_dssp             CHHHHTTSTTCCHHHHHHHHHHHHC-CCCCCCCHHHH
T ss_pred             CHHHHHhCcCcccchHHHHHHHHhc-CCcccccchHH
Confidence            4678999999999999999998643 22333454333

>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=95.54  E-value=0.003  Score=49.68  Aligned_cols=72  Identities=21%  Similarity=0.115  Sum_probs=42.2

Q ss_pred             CHHHHHHHHHHHhhCCCCCchhHHHhhhCCHHHHHHHHHH-HH------h------hCc-----cHHHHHHHhhcccCcc
Q 030389           57 NTTELSKLVRWKLTRGKWRPRLLVFVSSLDDSSVKSASEK-AF------K------SLP-----DLTKAVSELTVLKGVG  118 (178)
Q Consensus        57 tkdEL~~LveWKL~rGkfRP~L~~lv~sN~~~~V~~~t~~-Af------~------~l~-----d~~~al~~L~~LkGVG  118 (178)
                      |+++-+.-+-=+| .-+| |+...+.+.+ .++|+++.+- +|      .      .+-     .+....+.|.+|+|||
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            3455554443344 2344 8888887764 4444443221 11      0      000     1234567788999999


Q ss_pred             hHHHHHHHhhhCC
Q 030389          119 PATASAVLAAYAP  131 (178)
Q Consensus       119 PATASaiLa~~~P  131 (178)
                      |-||++||+....
T Consensus       119 ~~TA~~Il~~a~~  131 (211)
T d2abka_         119 RKTANVVLNTAFG  131 (211)
T ss_dssp             HHHHHHHHHHHHC
T ss_pred             hHHHHHHHHHHhc
Confidence            9999999998654

>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=95.35  E-value=0.0077  Score=47.54  Aligned_cols=40  Identities=20%  Similarity=0.238  Sum_probs=29.5

Q ss_pred             HHHHHHHhhcccCcchHHHHHHHhhhCCCCCCccchhHHhh
Q 030389          104 LTKAVSELTVLKGVGPATASAVLAAYAPDLAPFMSDEVCFC  144 (178)
Q Consensus       104 ~~~al~~L~~LkGVGPATASaiLa~~~P~~~pFfSDEa~~~  144 (178)
                      +..+.+.|++|+||||-||++||....-. .-|.-|--..-
T Consensus       115 ~~~~~~~L~~lpGIG~kTA~~vl~~~~~~-~~~~vD~hv~R  154 (217)
T d1pu6a_         115 QEVTREWLLDQKGIGKESADAILCYACAK-EVMVVDKYSYL  154 (217)
T ss_dssp             HHCCHHHHHTSTTCCHHHHHHHHHHTTCC-SCCCCCHHHHH
T ss_pred             cHHHHHHHHHHhhhhhHHHHHHHHHHcCC-eeeecChHHHH
Confidence            45678899999999999999999885432 23444665543

>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=0.0089  Score=44.39  Aligned_cols=72  Identities=15%  Similarity=0.117  Sum_probs=41.5

Q ss_pred             CHHHHHHHHHHHhhCCCCCchhHHHhhhCCHHHHHHHHHHH-H-----hhCccH-----HHHHHHhhcccCcchHHHHHH
Q 030389           57 NTTELSKLVRWKLTRGKWRPRLLVFVSSLDDSSVKSASEKA-F-----KSLPDL-----TKAVSELTVLKGVGPATASAV  125 (178)
Q Consensus        57 tkdEL~~LveWKL~rGkfRP~L~~lv~sN~~~~V~~~t~~A-f-----~~l~d~-----~~al~~L~~LkGVGPATASai  125 (178)
                      |.++-+.-+-.+|-.  .-|+..++.+.+ .+.++++.+.+ |     +.+.++     ....+.|++|+||||-||.++
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            456666666666632  236766665444 44444443222 1     111122     223456889999999999999


Q ss_pred             HhhhCC
Q 030389          126 LAAYAP  131 (178)
Q Consensus       126 La~~~P  131 (178)
                      +.+..-
T Consensus       110 ~if~~~  115 (144)
T d1ngna_         110 RIFCVN  115 (144)
T ss_dssp             HHHTSS
T ss_pred             HHHHcC
Confidence            887543

>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=94.42  E-value=0.0095  Score=42.53  Aligned_cols=42  Identities=17%  Similarity=0.218  Sum_probs=34.2

Q ss_pred             HHHHHHhhcccCcchHHHHHHHhhhCCCCCCccchhHHhhhhcCccc
Q 030389          105 TKAVSELTVLKGVGPATASAVLAAYAPDLAPFMSDEVCFCSFSFKFT  151 (178)
Q Consensus       105 ~~al~~L~~LkGVGPATASaiLa~~~P~~~pFfSDEa~~~~~~~~~~  151 (178)
                      .+..+.|+.|+||||++|-.|..     .-||-|=|=+..+.|+.++
T Consensus        23 ~As~~eL~~lpGIg~~~A~~Iv~-----~gpf~s~edL~~V~GIg~~   64 (98)
T d2axtu1          23 NTNIAAFIQYRGLYPTLAKLIVK-----NAPYESVEDVLNIPGLTER   64 (98)
T ss_dssp             SSCGGGGTTSTTCTHHHHHHHHH-----SCCCSSGGGGGGCTTCCTT
T ss_pred             cccHHHHHHhhhhcHHHHHHHHH-----cCCcCCHHHHhhCCCCCHH
Confidence            34577899999999999999994     3499997777778887653

>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=94.41  E-value=0.0095  Score=38.69  Aligned_cols=26  Identities=23%  Similarity=0.423  Sum_probs=22.8

Q ss_pred             HHHHHHHhhcccCcchHHHHHHHhhh
Q 030389          104 LTKAVSELTVLKGVGPATASAVLAAY  129 (178)
Q Consensus       104 ~~~al~~L~~LkGVGPATASaiLa~~  129 (178)
                      -..+|+.|+++-||||+||.-+..-+
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            45789999999999999999987664

>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=93.44  E-value=0.016  Score=38.75  Aligned_cols=48  Identities=15%  Similarity=0.136  Sum_probs=31.5

Q ss_pred             HHHHHHHhhcccCcchHHHHHHHhhhCC-CCCCccchhHHhhhhcCccc
Q 030389          104 LTKAVSELTVLKGVGPATASAVLAAYAP-DLAPFMSDEVCFCSFSFKFT  151 (178)
Q Consensus       104 ~~~al~~L~~LkGVGPATASaiLa~~~P-~~~pFfSDEa~~~~~~~~~~  151 (178)
                      .+.-+..|+.++|||+.+|-.|+.-+.- +.+-=-+-|-+..++|++..
T Consensus        14 ~~~~~~~L~~I~gIg~~~a~~L~~~F~s~~~i~~A~~eeL~~i~GiG~~   62 (78)
T d2a1jb1          14 VSRVTECLTTVKSVNKTDSQTLLTTFGSLEQLIAASREDLALCPGLGPQ   62 (78)
T ss_dssp             HHHHHHHHTTSTTCCHHHHHHHHHHHSSHHHHHSCCHHHHHTSSSCCSH
T ss_pred             HHHHHHHhcCCCCcCHHHHHHHHHHhCCcHHHHhhhHHHHHHhhhhhHH
Confidence            3467788999999999999999886432 11111234455667777653

>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=93.37  E-value=0.015  Score=39.18  Aligned_cols=46  Identities=26%  Similarity=0.126  Sum_probs=32.3

Q ss_pred             HHHHHHhhcccCcchHHHHHHHhhhCCCC---CCccchhHH-hhhhcCcc
Q 030389          105 TKAVSELTVLKGVGPATASAVLAAYAPDL---APFMSDEVC-FCSFSFKF  150 (178)
Q Consensus       105 ~~al~~L~~LkGVGPATASaiLa~~~P~~---~pFfSDEa~-~~~~~~~~  150 (178)
                      +.-+..|....||||-||-+||+.+.|+.   +.--.|... ..+||+++
T Consensus         5 r~~F~~Li~V~GIGpK~Al~iLs~~~~~~l~~aI~~~D~~~L~~vpGIG~   54 (71)
T d1bvsa2           5 RDLFLALLSVSGVGPRLAMATLAVHDAAALRQALADSDVASLTRVPGIGR   54 (71)
T ss_dssp             HHHHHHHHTSSSCCHHHHHHHHHHSCHHHHHHHTTTTCHHHHHTSTTCCH
T ss_pred             HHHHHHHhccCCcCHHHHHHHHHhCCHHHHHHHHHcCCHHHhhcCCCCCH
Confidence            45677899999999999999999987753   233334333 34777653

>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=93.07  E-value=0.019  Score=36.89  Aligned_cols=40  Identities=25%  Similarity=0.148  Sum_probs=28.9

Q ss_pred             HhhcccCcchHHHHHHHhhhCC--CCCCccchhHHhhhhcCc
Q 030389          110 ELTVLKGVGPATASAVLAAYAP--DLAPFMSDEVCFCSFSFK  149 (178)
Q Consensus       110 ~L~~LkGVGPATASaiLa~~~P--~~~pFfSDEa~~~~~~~~  149 (178)
                      .|.+++||||+||..++..+..  +.+-..+-|-...++|+.
T Consensus         2 ~L~~i~GIG~~~a~~L~~~g~~sv~~l~~a~~~eL~~i~Gi~   43 (61)
T d1pzna1           2 SIEDLPGVGPATAEKLREAGYDTLEAIAVASPIELKEVAGIS   43 (61)
T ss_dssp             CSSCCTTCCHHHHHHHHTTTCCSHHHHHTCCHHHHHHHHCCC
T ss_pred             ccccCCCCCHHHHHHHHHhcCCCHHHHHhCCHHHHHHCCCCC
Confidence            3778999999999999987533  334555555566688865

>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=92.65  E-value=0.024  Score=38.69  Aligned_cols=46  Identities=22%  Similarity=0.159  Sum_probs=32.7

Q ss_pred             HHHHHHhhcccCcchHHHHHHHhhhCCCC---CCccchhHHh-hhhcCcc
Q 030389          105 TKAVSELTVLKGVGPATASAVLAAYAPDL---APFMSDEVCF-CSFSFKF  150 (178)
Q Consensus       105 ~~al~~L~~LkGVGPATASaiLa~~~P~~---~pFfSDEa~~-~~~~~~~  150 (178)
                      +.-++.|....||||-||=+||+.+.|+.   +..-.|.... .+||++.
T Consensus         5 r~~F~~Li~V~GIGpK~Al~iLs~~~~~~l~~aI~~~D~~~L~~vpGIG~   54 (78)
T d1cuka2           5 RTLFKELIKTNGVGPKLALAILSGMSAQQFVNAVEREEVGALVKLPGIGK   54 (78)
T ss_dssp             HHHHHHHHHSSSCCHHHHHHHHHHSCHHHHHHHHHTTCHHHHHTSTTCCH
T ss_pred             HHHHHHHHccCCccHHHHHHHHHhCCHHHHHHHHHccCHHHhhcCCCCCH
Confidence            45678899999999999999999987754   2233344443 3677654

>d2bgwa1 a.60.2.5 (A:160-229) DNA repair endonuclease XPF {Aeropyrum pernix [TaxId: 56636]}

class: All alpha proteins
fold: SAM domain-like
superfamily: RuvA domain 2-like
family: Hef domain-like
domain: DNA repair endonuclease XPF
species: Aeropyrum pernix [TaxId: 56636]

Probab=92.41  E-value=0.028  Score=36.74  Aligned_cols=44  Identities=16%  Similarity=0.083  Sum_probs=30.4

Q ss_pred             HHHhhcccCcchHHHHHHHhhhCC-CCCCccchhHHhhhhcCccc
Q 030389          108 VSELTVLKGVGPATASAVLAAYAP-DLAPFMSDEVCFCSFSFKFT  151 (178)
Q Consensus       108 l~~L~~LkGVGPATASaiLa~~~P-~~~pFfSDEa~~~~~~~~~~  151 (178)
                      +-+|+.++||||.||-.|+.-+.- +.+---|.|-+..++|+.+.
T Consensus        12 ~~~L~~IpgIG~~~a~~L~~~F~s~~~l~~As~eeL~~v~GIG~~   56 (70)
T d2bgwa1          12 LYILQSFPGIGRRTAERILERFGSLERFFTASKAEISKVEGIGEK   56 (70)
T ss_dssp             HHHHHTSTTCCHHHHHHHHHHHSSHHHHTTCCHHHHHHSTTCCHH
T ss_pred             HHHHcCCCCcCHHHHHHHHHHhCCHHHHHHcCHHHHHcCCCCCHH
Confidence            556889999999999999987532 22222256667778887643

>d1ixra1 a.60.2.1 (A:63-135) DNA helicase RuvA subunit, middle domain {Thermus thermophilus [TaxId: 274]}

class: All alpha proteins
fold: SAM domain-like
superfamily: RuvA domain 2-like
family: DNA helicase RuvA subunit, middle domain
domain: DNA helicase RuvA subunit, middle domain
species: Thermus thermophilus [TaxId: 274]

Probab=91.90  E-value=0.045  Score=36.89  Aligned_cols=46  Identities=28%  Similarity=0.320  Sum_probs=31.8

Q ss_pred             HHHHHHhhcccCcchHHHHHHHhhhCCCC---CCccchhHHh-hhhcCcc
Q 030389          105 TKAVSELTVLKGVGPATASAVLAAYAPDL---APFMSDEVCF-CSFSFKF  150 (178)
Q Consensus       105 ~~al~~L~~LkGVGPATASaiLa~~~P~~---~pFfSDEa~~-~~~~~~~  150 (178)
                      +.-+..|....||||-||-+||+..+|+.   +..-.|.... .+||+++
T Consensus         6 r~lF~~Li~V~GIGpk~Al~iLs~~~~~~l~~aI~~~D~~~L~~vpGIG~   55 (73)
T d1ixra1           6 LALFELLLSVSGVGPKVALALLSALPPRLLARALLEGDARLLTSASGVGR   55 (73)
T ss_dssp             HHHHHHHHSSSCCCHHHHHHHHHHSCHHHHHHHHHTTCHHHHTTSTTCCH
T ss_pred             HHHHHHHhccCCcCHHHHHHHHHHccHHHHHHHHHhcCHHHhhcCCCCCH
Confidence            45678899999999999999999877743   2222344333 3666553

>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=91.75  E-value=0.025  Score=35.87  Aligned_cols=40  Identities=23%  Similarity=0.190  Sum_probs=23.3

Q ss_pred             hhcccCcchHHHHHHHhhhCCCCCCcc--chhHHhhhhcCccc
Q 030389          111 LTVLKGVGPATASAVLAAYAPDLAPFM--SDEVCFCSFSFKFT  151 (178)
Q Consensus       111 L~~LkGVGPATASaiLa~~~P~~~pFf--SDEa~~~~~~~~~~  151 (178)
                      |..++||||.||-.|+.-+.- .--.+  |.|-+..++|+.+.
T Consensus         4 L~~I~gVG~~~a~~L~~~F~s-~~~i~~As~eeL~~v~GIg~~   45 (56)
T d1kfta_           4 LETIEGVGPKRRQMLLKYMGG-LQGLRNASVEEIAKVPGISQG   45 (56)
T ss_dssp             GGGCTTCSSSHHHHHHHHHSC-HHHHHHCCHHHHTTSSSTTSH
T ss_pred             cccCCCccHHHHHHHHHHhCC-HHHHHHhhHHHHHhcCCCCHH
Confidence            567777777777777766422 21222  45555556666543

>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=91.74  E-value=0.039  Score=35.89  Aligned_cols=25  Identities=28%  Similarity=0.195  Sum_probs=22.2

Q ss_pred             HHHHHHhhcccCcchHHHHHHHhhh
Q 030389          105 TKAVSELTVLKGVGPATASAVLAAY  129 (178)
Q Consensus       105 ~~al~~L~~LkGVGPATASaiLa~~  129 (178)
                      .++|+.|+++-||||.||.-+..-+
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            4689999999999999999887764

>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=91.48  E-value=0.075  Score=34.47  Aligned_cols=40  Identities=23%  Similarity=0.340  Sum_probs=32.3

Q ss_pred             HHHHHhhcccCcchHHHHHHHhhhCCCCCCccchhHHhhhhcCcc
Q 030389          106 KAVSELTVLKGVGPATASAVLAAYAPDLAPFMSDEVCFCSFSFKF  150 (178)
Q Consensus       106 ~al~~L~~LkGVGPATASaiLa~~~P~~~pFfSDEa~~~~~~~~~  150 (178)
                      +..+.|..|+|||+.+|..|+...     ||-|=|-+.-+.|+..
T Consensus        14 A~~~eL~~lpgig~~~A~~Iv~~R-----~f~s~edL~~v~gi~~   53 (65)
T d2duya1          14 ASLEELMALPGIGPVLARRIVEGR-----PYARVEDLLKVKGIGP   53 (65)
T ss_dssp             CCHHHHTTSTTCCHHHHHHHHHTC-----CCSSGGGGGGSTTCCH
T ss_pred             CCHHHHHHCCCCCHHHHHHHHHcC-----CCCCHHHHHhCCCCCH
Confidence            346789999999999999999874     5888777777777643

>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=90.64  E-value=0.059  Score=34.77  Aligned_cols=25  Identities=16%  Similarity=0.131  Sum_probs=21.4

Q ss_pred             HHHHHHhhcccCcchHHHHHHHhhh
Q 030389          105 TKAVSELTVLKGVGPATASAVLAAY  129 (178)
Q Consensus       105 ~~al~~L~~LkGVGPATASaiLa~~  129 (178)
                      .++|+.+|++-||||.||.-+...+
T Consensus         4 ~~~l~~ft~I~GvGp~~A~~l~~~G   28 (57)
T d2bcqa2           4 VPVLELFSNIWGAGTKTAQMWYQQG   28 (57)
T ss_dssp             HHHHHHHHTSTTCCHHHHHHHHHTT
T ss_pred             hHHHHHHhccccccHHHHHHHHHhC
Confidence            4689999999999999999776653

>d2edua1 a.60.2.7 (A:8-98) KIF22, C-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: SAM domain-like
superfamily: RuvA domain 2-like
family: ComEA-like
domain: KIF22, C-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=90.34  E-value=0.15  Score=35.12  Aligned_cols=46  Identities=17%  Similarity=0.144  Sum_probs=35.6

Q ss_pred             HHHHHHhhcccCcchHHHHHHHhhhCCCCCCccchhHHhhhhcCccc
Q 030389          105 TKAVSELTVLKGVGPATASAVLAAYAPDLAPFMSDEVCFCSFSFKFT  151 (178)
Q Consensus       105 ~~al~~L~~LkGVGPATASaiLa~~~P~~~pFfSDEa~~~~~~~~~~  151 (178)
                      .+..+.|..|+||||.+|..|+.--.- .-||-|=|-+.-++|+.++
T Consensus        29 tAs~~eL~~lpgig~~~A~~II~yR~~-~G~f~sledL~~V~Gi~~k   74 (91)
T d2edua1          29 EGSARDLRSLQRIGPKKAQLIVGWREL-HGPFSQVEDLERVEGITGK   74 (91)
T ss_dssp             HSCHHHHHHSTTCCHHHHHHHHHHHHH-HCCCSSGGGGGGSTTCCHH
T ss_pred             cCCHHHHhhCCCCCHHHHHHHHHHHHH-cCCCCCHHHHhcCCCCCHH
Confidence            446888999999999999999998543 4589885555668887543

>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=89.21  E-value=0.078  Score=33.82  Aligned_cols=40  Identities=28%  Similarity=0.121  Sum_probs=26.2

Q ss_pred             hhcccCcchHHHHHHHhhhCCC--CCCccchhHHhhhhcCcc
Q 030389          111 LTVLKGVGPATASAVLAAYAPD--LAPFMSDEVCFCSFSFKF  150 (178)
Q Consensus       111 L~~LkGVGPATASaiLa~~~P~--~~pFfSDEa~~~~~~~~~  150 (178)
                      |++++||||++|..++..+.-.  .+-..+=|-...++|+..
T Consensus         1 L~~IpGIG~~~a~~L~~~G~~tv~~l~~a~~eeL~~i~Gi~~   42 (60)
T d2i1qa1           1 LTDLPGVGPSTAEKLVEAGYIDFMKIATATVGELTDIEGISE   42 (60)
T ss_dssp             CTTSTTCCHHHHHHHHHHTCCSHHHHHTCCHHHHHTSTTCCH
T ss_pred             CCCCCCCCHHHHHHHHHccCCCHHHHHhCCHHHHHHCCCCCH
Confidence            6789999999999999874322  233333344444677643

>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=88.27  E-value=0.33  Score=32.43  Aligned_cols=22  Identities=27%  Similarity=0.274  Sum_probs=18.2

Q ss_pred             HHHhhcccCcchHHHHHHHhhh
Q 030389          108 VSELTVLKGVGPATASAVLAAY  129 (178)
Q Consensus       108 l~~L~~LkGVGPATASaiLa~~  129 (178)
                      .+.|++++|||+-||--|..=.
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

>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=88.19  E-value=0.2  Score=33.86  Aligned_cols=21  Identities=33%  Similarity=0.540  Sum_probs=18.1

Q ss_pred             HHHhhcccCcchHHHHHHHhh
Q 030389          108 VSELTVLKGVGPATASAVLAA  128 (178)
Q Consensus       108 l~~L~~LkGVGPATASaiLa~  128 (178)
                      .+.|++++|||+-||.-|..=
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

>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=88.19  E-value=0.13  Score=34.07  Aligned_cols=47  Identities=23%  Similarity=0.475  Sum_probs=31.6

Q ss_pred             HHHHHHHHHHHHhhCccHHH-HHHHhhcccCcchHHHHHHHhhhCCCCCCcc
Q 030389           87 DSSVKSASEKAFKSLPDLTK-AVSELTVLKGVGPATASAVLAAYAPDLAPFM  137 (178)
Q Consensus        87 ~~~V~~~t~~Af~~l~d~~~-al~~L~~LkGVGPATASaiLa~~~P~~~pFf  137 (178)
                      +...+...+. |..+.++.. ..+.|.+++|||+..|..|..+..-   ||+
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            3444444433 554444433 4788999999999999999998633   564

>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=86.82  E-value=0.16  Score=31.82  Aligned_cols=39  Identities=15%  Similarity=0.243  Sum_probs=27.6

Q ss_pred             HHHHHHHHHHhhCccHHH-HHHHhhcccCcchHHHHHHHhh
Q 030389           89 SVKSASEKAFKSLPDLTK-AVSELTVLKGVGPATASAVLAA  128 (178)
Q Consensus        89 ~V~~~t~~Af~~l~d~~~-al~~L~~LkGVGPATASaiLa~  128 (178)
                      ..+...+. |..+.++.. ..+.|.+++||||.+|..|...
T Consensus        14 ~a~~L~~~-F~s~~~i~~As~eeL~~v~GIg~~~A~~I~~~   53 (56)
T d1kfta_          14 RRQMLLKY-MGGLQGLRNASVEEIAKVPGISQGLAEKIFWS   53 (56)
T ss_dssp             HHHHHHHH-HSCHHHHHHCCHHHHTTSSSTTSHHHHHHHHH
T ss_pred             HHHHHHHH-hCCHHHHHHhhHHHHHhcCCCCHHHHHHHHHH
Confidence            33344433 665555544 5889999999999999988754

>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=86.82  E-value=0.13  Score=33.34  Aligned_cols=42  Identities=12%  Similarity=-0.084  Sum_probs=26.0

Q ss_pred             HHhhcccCcchHHHHHHHhhhC-CCCCCccchhHHhhhhcCcc
Q 030389          109 SELTVLKGVGPATASAVLAAYA-PDLAPFMSDEVCFCSFSFKF  150 (178)
Q Consensus       109 ~~L~~LkGVGPATASaiLa~~~-P~~~pFfSDEa~~~~~~~~~  150 (178)
                      -.|..++||||.||-.|+.-+. .+.+.--+.|-+..++|+.+
T Consensus        10 ~~L~~I~gIG~~~a~~L~~~f~s~~~i~~As~eeL~~i~GIG~   52 (68)
T d1x2ia1          10 LIVEGLPHVSATLARRLLKHFGSVERVFTASVAELMKVEGIGE   52 (68)
T ss_dssp             HHHTTSTTCCHHHHHHHHHHHCSHHHHHHCCHHHHTTSTTCCH
T ss_pred             HHHcCCCCcCHHHHHHHHHHcCCHHHHHHhHHHHHHhCCCcCH
Confidence            3566788888888887777643 22222335666666777654

>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=86.51  E-value=0.15  Score=33.01  Aligned_cols=42  Identities=19%  Similarity=0.351  Sum_probs=29.1

Q ss_pred             HHHHHHHHHHHHhhCccHHH-HHHHhhcccCcchHHHHHHHhhh
Q 030389           87 DSSVKSASEKAFKSLPDLTK-AVSELTVLKGVGPATASAVLAAY  129 (178)
Q Consensus        87 ~~~V~~~t~~Af~~l~d~~~-al~~L~~LkGVGPATASaiLa~~  129 (178)
                      +...+...+. |..+.++.. ..+.|++++|||+.+|-.|....
T Consensus        23 ~~~a~~L~~~-F~s~~~l~~As~eeL~~v~GIG~~~A~~I~~~~   65 (70)
T d2bgwa1          23 RRTAERILER-FGSLERFFTASKAEISKVEGIGEKRAEEIKKIL   65 (70)
T ss_dssp             HHHHHHHHHH-HSSHHHHTTCCHHHHHHSTTCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHH-hCCHHHHHHcCHHHHHcCCCCCHHHHHHHHHHH
Confidence            4444444433 654444433 47899999999999999998775

>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=86.00  E-value=0.2  Score=33.31  Aligned_cols=20  Identities=30%  Similarity=0.498  Sum_probs=17.1

Q ss_pred             HHHhhcccCcchHHHHHHHh
Q 030389          108 VSELTVLKGVGPATASAVLA  127 (178)
Q Consensus       108 l~~L~~LkGVGPATASaiLa  127 (178)
                      .+.|++++||||-||.-|+.
T Consensus        43 ~~~L~~vpGIG~KtA~rIi~   62 (71)
T d1bvsa2          43 VASLTRVPGIGRRGAERIVL   62 (71)
T ss_dssp             HHHHHTSTTCCHHHHHHHHH
T ss_pred             HHHhhcCCCCCHHHHHHHHH
Confidence            56799999999999987764

>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=85.77  E-value=0.14  Score=34.33  Aligned_cols=34  Identities=24%  Similarity=0.268  Sum_probs=24.3

Q ss_pred             HHHhhCccHHHHHHHhhcccCcchHHHHHHHhhh
Q 030389           96 KAFKSLPDLTKAVSELTVLKGVGPATASAVLAAY  129 (178)
Q Consensus        96 ~Af~~l~d~~~al~~L~~LkGVGPATASaiLa~~  129 (178)
                      .+.+.++..-...+.+++++|||+.+|+-|--..
T Consensus        35 ~~i~~l~~~i~~~~~l~~i~GIGk~ia~kI~E~~   68 (82)
T d2fmpa1          35 SVIAKYPHKIKSGAEAKKLPGVGTKIAEKIDEFL   68 (82)
T ss_dssp             HHHHHCSSCCCCHHHHHTSTTCCHHHHHHHHHHH
T ss_pred             HHHHhCCcccCCHHHHhcCCCccHHHHHHHHHHH
Confidence            3345566433456789999999999999876543

>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=85.23  E-value=0.23  Score=31.39  Aligned_cols=39  Identities=10%  Similarity=0.088  Sum_probs=29.1

Q ss_pred             HHhhcccCcchHHHHHHHhhhCC-CCCCccchhHHhhhhc
Q 030389          109 SELTVLKGVGPATASAVLAAYAP-DLAPFMSDEVCFCSFS  147 (178)
Q Consensus       109 ~~L~~LkGVGPATASaiLa~~~P-~~~pFfSDEa~~~~~~  147 (178)
                      +.|..++||||+++-.|+.-+-- +.+.-.|-|-+..++|
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            56889999999999999975322 2355667677777787

>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=84.16  E-value=0.18  Score=33.12  Aligned_cols=33  Identities=21%  Similarity=0.346  Sum_probs=23.9

Q ss_pred             HHhhCccHHHHHHHhhcccCcchHHHHHHHhhh
Q 030389           97 AFKSLPDLTKAVSELTVLKGVGPATASAVLAAY  129 (178)
Q Consensus        97 Af~~l~d~~~al~~L~~LkGVGPATASaiLa~~  129 (178)
                      +.+.+|..-..++.|.+|+|||+.+|+-|--..
T Consensus        34 ~l~~l~~~i~~~~~l~~lpGiG~~i~~kI~Eil   66 (76)
T d2bcqa1          34 ALKSFHKPVTSYQEACSIPGIGKRMAEKIIEIL   66 (76)
T ss_dssp             HHHSCCSCCCCHHHHHTSTTCCHHHHHHHHHHH
T ss_pred             HHHhCCcccCCHHHHhcCCCccHHHHHHHHHHH
Confidence            345566333345678999999999999887654

>d3bzka1 a.60.2.6 (A:474-563) Transcriptional accessory factor Tex {Pseudomonas aeruginosa [TaxId: 287]}

class: All alpha proteins
fold: SAM domain-like
superfamily: RuvA domain 2-like
family: Tex HhH-containing domain-like
domain: Transcriptional accessory factor Tex
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=83.89  E-value=0.19  Score=34.35  Aligned_cols=44  Identities=11%  Similarity=0.083  Sum_probs=34.5

Q ss_pred             HHHHHhhcccCcchHHHHHHHhhhCCCCCCccchhHHhhhhcCcc
Q 030389          106 KAVSELTVLKGVGPATASAVLAAYAPDLAPFMSDEVCFCSFSFKF  150 (178)
Q Consensus       106 ~al~~L~~LkGVGPATASaiLa~~~P~~~pFfSDEa~~~~~~~~~  150 (178)
                      +..+.|..++||||.+|..|+....- .-||-|=|-+.-++|+.+
T Consensus        32 As~~~L~~lpGig~~~A~~Iv~~R~~-~G~f~s~edL~~v~gi~~   75 (90)
T d3bzka1          32 ASAALLARISGLNSTLAQNIVAHRDA-NGAFRTRDELKKVSRLGE   75 (90)
T ss_dssp             CCHHHHTTSTTCCHHHHHHHHHHHHH-HCSCSSSGGGGGSTTCCH
T ss_pred             CCHHHHhHCCCCCHHHHHHHHHHHHH-cCCCCCHHHHhhCCCCCH
Confidence            35678999999999999999997532 358888777777777643

>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=83.44  E-value=0.41  Score=30.78  Aligned_cols=45  Identities=18%  Similarity=0.318  Sum_probs=31.4

Q ss_pred             CCHHHHHHHHHHHHhhCccHHH-HHHHhhcccCcchHHHHHHHhhhC
Q 030389           85 LDDSSVKSASEKAFKSLPDLTK-AVSELTVLKGVGPATASAVLAAYA  130 (178)
Q Consensus        85 N~~~~V~~~t~~Af~~l~d~~~-al~~L~~LkGVGPATASaiLa~~~  130 (178)
                      -.+...+...+. |..+.++.. ..+.|.++.||||.+|-.|.....
T Consensus        18 IG~~~a~~L~~~-f~s~~~i~~As~eeL~~i~GIG~~~A~~I~~~~~   63 (68)
T d1x2ia1          18 VSATLARRLLKH-FGSVERVFTASVAELMKVEGIGEKIAKEIRRVIT   63 (68)
T ss_dssp             CCHHHHHHHHHH-HCSHHHHHHCCHHHHTTSTTCCHHHHHHHHHHHH
T ss_pred             cCHHHHHHHHHH-cCCHHHHHHhHHHHHHhCCCcCHHHHHHHHHHHh
Confidence            344444554444 665544443 588999999999999999987753

>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=82.32  E-value=0.26  Score=31.22  Aligned_cols=42  Identities=19%  Similarity=0.360  Sum_probs=30.9

Q ss_pred             HHHHHHHHHHHHhhCccHH-HHHHHhhcccCcchHHHHHHHhh
Q 030389           87 DSSVKSASEKAFKSLPDLT-KAVSELTVLKGVGPATASAVLAA  128 (178)
Q Consensus        87 ~~~V~~~t~~Af~~l~d~~-~al~~L~~LkGVGPATASaiLa~  128 (178)
                      +..+++.....|..+.++. +..+.|++++|+|+.+|.-|...
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            4455666655676555554 35888999999999999988765

>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=81.66  E-value=0.57  Score=33.71  Aligned_cols=41  Identities=20%  Similarity=0.237  Sum_probs=32.1

Q ss_pred             HHHHHHhhcccCcchHHHHHHHhhh--CCCC-CCccchhHHhhh
Q 030389          105 TKAVSELTVLKGVGPATASAVLAAY--APDL-APFMSDEVCFCS  145 (178)
Q Consensus       105 ~~al~~L~~LkGVGPATASaiLa~~--~P~~-~pFfSDEa~~~~  145 (178)
                      +.-.-.|+.++|||+.+|-.|+...  +|+. +-.++||=+..+
T Consensus        12 K~v~~ALt~I~GIG~~~A~~Ic~~lgId~~~k~~~Lt~~qi~~I   55 (125)
T d2uubm1          12 KRVDVALTYIYGIGKARAKEALEKTGINPATRVKDLTEAEVVRL   55 (125)
T ss_dssp             SBHHHHHTTSTTCCHHHHHHHHHTTTCCTTSBGGGCCHHHHHHH
T ss_pred             CEEEEeeeeeeCcCHHHHHHHHHHcCCCcccccccccHHHHHHH
Confidence            3345578999999999999999984  6765 778888877653

>d2gy9m1 a.156.1.1 (M:1-114) Ribosomal protein S13 {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: S13-like H2TH domain
superfamily: S13-like H2TH domain
family: Ribosomal protein S13
domain: Ribosomal protein S13
species: Escherichia coli [TaxId: 562]

Probab=80.70  E-value=0.54  Score=33.31  Aligned_cols=44  Identities=36%  Similarity=0.397  Sum_probs=33.5

Q ss_pred             ccHHHHHHHhhcccCcchHHHHHHHhhh--CCCC-CCccchhHHhhh
Q 030389          102 PDLTKAVSELTVLKGVGPATASAVLAAY--APDL-APFMSDEVCFCS  145 (178)
Q Consensus       102 ~d~~~al~~L~~LkGVGPATASaiLa~~--~P~~-~pFfSDEa~~~~  145 (178)
                      |+-+...-+|+.++|||+.+|-.|+...  +|+. +=.++||-+..+
T Consensus         9 p~~K~v~~ALt~I~GIG~~~A~~Ic~~lgid~~~kv~~Lt~~qi~~l   55 (114)
T d2gy9m1           9 PDHKHAVIALTSIYGVGKTRSKAILAAAGIAEDVKISELSEGQIDTL   55 (114)
T ss_dssp             CCSSBHHHHHTTSSSCCHHHHHHHHHHHTCCTTSBTTSCCHHHHHHH
T ss_pred             CCCCEEEEEeeeeeCcCHHHHHHHHHHcCCCcccccCcccHHHHHHH
Confidence            3334455678999999999999999984  5654 677888877764