Citrus Sinensis ID: 029905

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-----
Protein Sequence
MQLEFECSNVNKWKEALASYEACVESLNKPNLISLDDYYRKELPSLIHQRNPNPHINTTELSKLVRWKLTRGKWRPRLLVFVSSLDDSSVKSASEKAFKSLPDLTKAVSELTVLKGVGPATASAVLAAYAPDLAPFMSDEAMGAALGHSKDYSLKQYLLFADKLQAKAKVSDIFFFLNICVYFSS
Secondary Structure (PSIPRED)
cccccccccHHHHHHHHHHHHHHHHHcccccHHHHHHHHHHHccHHHHHccccccccHHHHHHHHHHHHHccccccHHHHHHHHccHHHHHHHHHHHHHHcccHHHHHHHHHHcccccHHHHHHHHHHHcccccccccHHHHHHHccccccccHHHHHHHHHHHHHHHHHcccHHHHcEEEEccc
Secondary Structure Prediction (SSPRO)
cccccccccHHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHHHHHHHHccccccccHHHHHHHHHHHHHcccccHHHHHHHHHccHHHHHHHHHHHHHHcccHHHHHHHHHHHccccHHHHHHHHHHccccccccccHHHHHHcccccccccHHHHHHHHHHHHHHHcHHHHHEEEEEEEEEcc
Coil and Loop (DISEMBL)
MQLEFECSNVNKWKEALASYEACVEslnkpnlislddyyrkelpslihqrnpnphintteLSKLVRWKLTRGKWRPRLLVFVSSlddssvksASEKAFKSLPDLTKAVSELTVLKGVGPATASAVLAAyapdlapfmsdeamgaalghskdysLKQYLLFADKLQAKAKVSDIFFFLNICVYFSS
Flexible Loop (DISEMBL)
MQLEFECSNVNKWKEALASYEACVESLNKPNLISLDDYYRKELPslihqrnpnphinttelSKLVRWKLTRGKWRPRLLVFvsslddssvksasekafkslpdlTKAVSELTVLKGVGPATASAVLAAYAPDLAPFMSDEAMGAALGHSKDYSLKQYLLFADKLQAKAKVSDIFFFLNICVYFSS
Low Complexity Region (SEG)
MQLEFECSNVNKWKEALASYEACVESLNKPNLISLDDYYRKELPSLIHQRNPNPHINTTELSKLVRWKLTRGKWRPRllvfvsslddssvksasEKAFKSLPDLTKAVSELTVLKGVGPATASAVLAAYAPDLAPFMSDEAMGAALGHSKDYSLKQYLLFADKLQAKAKVSDIFFFLNICVYFSS
Disordered region (IsUnstruct)
*****ECSNVNKWKEALASYEACVESLNKPNLISLDDYYRKELPSLIHQRNPNPHINTTELSKLVRWKLTRGKWRPRLLVFVSSL******************LTKAVSELTVLKGVGPATASAVLAAYAPDLAPFMSDEAMGAALGHSKDYSLKQYLLFADKLQAKAKVSDIFFFLNICVYF**
Disordered Region (DISOPRED)
*********VNKWKEALASYEAC********LISLDDYYRKELPSLI*******HINTTELSKLVRWKLTRGKWRPRLL*FV**LD*SSVKSASEKAFKSLPDLTKAVSELTVLKGVGPATASAVLAAYAPDLAPFMSDEAMGAALGHSKDYSLKQYLLFADKLQAKAKVSDIFFFLNICVYFSS
Disordered Region (DISEMBL)
********NVNKWKEALASYEACVESLNKPNLISLDDYYRKELPSLIHQRNPNPHINTTELSKLVRWKLTRGKWRPRLLVFVSSL************FKSLPDLTKAVSELTVLKGVGPATASAVLAAYAPDLAPFMSDEAMGAALGHSKDYSLKQYLLFADKLQAKAKVSDIFFFLNICVYFSS
Disordered Region (DISPRO)
***EFECSNVNKWKEALASYEACVESLNKPNLISLDDYYRKELPSLIHQRNPNPHINTTELSKLVRWKLTRGKWRPRLLVFVSSLDDSSVKSASEKAFKSLPDLTKAVSELTVLKGVGPATASAVLAAYAPDLAPFMSDEAMGAALGHSKDYSLKQYLLFADKLQAKAKVSDIFFFLNICVYFSS
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHo
Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MQLEFECSNVNKWKEALASYEACVESLNKPNLISLDDYYRKELPSLIHQRNPNPHINTTELSKLVRWKLTRGKWRPRLLVFVSSLDDSSVKSASEKAFKSLPDLTKAVSELTVLKGVGPATASAVLAAYAPDLAPFMSDEAMGAALGHSKDYSLKQYLLFADKLQAKAKVSDIFFFLNICVYFSS
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	185
224067158	218	predicted protein [Populus trichocarpa]	0.929	0.788	0.75	1e-70
297829776	209	hypothetical protein ARALYDRAFT_478581 [	0.913	0.808	0.757	6e-70
225458920	213	PREDICTED: uncharacterized protein LOC10	0.902	0.784	0.748	2e-68
255537954	217	conserved hypothetical protein [Ricinus	0.902	0.769	0.742	1e-66
449447089	220	PREDICTED: uncharacterized protein LOC10	0.902	0.759	0.730	3e-66
15795142	292	unnamed protein product [Arabidopsis tha	0.913	0.578	0.763	1e-64
18399536	209	DNA binding protein [Arabidopsis thalian	0.913	0.808	0.763	2e-64
356552292	190	PREDICTED: uncharacterized protein LOC10	0.908	0.884	0.697	2e-62
356552290	220	PREDICTED: uncharacterized protein LOC10	0.902	0.759	0.695	5e-62
294463602	225	unknown [Picea sitchensis]	0.902	0.742	0.646	3e-57

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

 Score =  271 bits (692), Expect = 1e-70,   Method: Compositional matrix adjust.
 Identities = 132/176 (75%), Positives = 155/176 (88%), Gaps = 4/176 (2%)

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 SAVLAAYAPDLAPFMSDEAMGAALGHSKDYSLKQYLLFADKLQAKAK----VSDIF 174
           SAVLAAYAPD+APFMSDEAM A LG+SKDY+LKQYLLF DKLQ K+K    V DIF
Sbjct: 121 SAVLAAYAPDVAPFMSDEAMEAVLGNSKDYTLKQYLLFVDKLQTKSKELSSVRDIF 176

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  268 bits (686), Expect = 6e-70,   Method: Compositional matrix adjust.
 Identities = 128/169 (75%), Positives = 154/169 (91%)

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 TASAVLAAYAPDLAPFMSDEAMGAALGHSKDYSLKQYLLFADKLQAKAK 169
           TASAVLAAYAPD+APFMSDEAM  ALG+SKDYSLKQYLLF  KLQ KAK
Sbjct: 121 TASAVLAAYAPDIAPFMSDEAMEVALGNSKDYSLKQYLLFVTKLQDKAK 169

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  263 bits (673), Expect = 2e-68,   Method: Compositional matrix adjust.
 Identities = 125/167 (74%), Positives = 152/167 (91%)

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 SAVLAAYAPDLAPFMSDEAMGAALGHSKDYSLKQYLLFADKLQAKAK 169
           SA+LAAYAPD+APFMSDEAM AALG+SKDY+LKQYL+FADKLQ KA+
Sbjct: 121 SALLAAYAPDVAPFMSDEAMVAALGNSKDYTLKQYLVFADKLQNKAR 167

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 =  258 bits (658), Expect = 1e-66,   Method: Compositional matrix adjust.
 Identities = 124/167 (74%), Positives = 147/167 (88%)

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 SAVLAAYAPDLAPFMSDEAMGAALGHSKDYSLKQYLLFADKLQAKAK 169
           SAVLAAYAPD+APFMSDEAM AALG SKDY+LKQYL F DKLQ KAK
Sbjct: 121 SAVLAAYAPDVAPFMSDEAMEAALGSSKDYTLKQYLSFVDKLQTKAK 167

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 =  256 bits (653), Expect = 3e-66,   Method: Compositional matrix adjust.
 Identities = 122/167 (73%), Positives = 149/167 (89%)

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 SAVLAAYAPDLAPFMSDEAMGAALGHSKDYSLKQYLLFADKLQAKAK 169
           SAVLAAYAPD+APFMSDEAM AALG+SKDYSLKQYLLFA+KL+ KAK
Sbjct: 122 SAVLAAYAPDVAPFMSDEAMEAALGNSKDYSLKQYLLFANKLEQKAK 168

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 =  251 bits (640), Expect = 1e-64,   Method: Compositional matrix adjust.
 Identities = 129/169 (76%), Positives = 152/169 (89%)

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 TASAVLAAYAPDLAPFMSDEAMGAALGHSKDYSLKQYLLFADKLQAKAK 169
           TASAVLAAYAPD+APFMSDEAM  ALG+SKDYSLKQYLLFA KLQ KAK
Sbjct: 121 TASAVLAAYAPDIAPFMSDEAMEVALGNSKDYSLKQYLLFATKLQDKAK 169

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 =  250 bits (638), Expect = 2e-64,   Method: Compositional matrix adjust.
 Identities = 129/169 (76%), Positives = 152/169 (89%)

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 TASAVLAAYAPDLAPFMSDEAMGAALGHSKDYSLKQYLLFADKLQAKAK 169
           TASAVLAAYAPD+APFMSDEAM  ALG+SKDYSLKQYLLFA KLQ KAK
Sbjct: 121 TASAVLAAYAPDIAPFMSDEAMEVALGNSKDYSLKQYLLFATKLQDKAK 169

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  244 bits (622), Expect = 2e-62,   Method: Compositional matrix adjust.
 Identities = 120/172 (69%), Positives = 144/172 (83%), Gaps = 4/172 (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 PATASAVLAAYAPDLAPFMSDEAMGAALGHSKDYSLKQYLLFADKLQAKAKV 170
           PATASAVLA +AP L PFMSDEAM AALG SKDYSLKQY+ F DKLQ KA+V
Sbjct: 121 PATASAVLATFAPHLTPFMSDEAMEAALGSSKDYSLKQYIKFVDKLQRKAEV 172

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  242 bits (618), Expect = 5e-62,   Method: Compositional matrix adjust.
 Identities = 119/171 (69%), Positives = 143/171 (83%), Gaps = 4/171 (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 PATASAVLAAYAPDLAPFMSDEAMGAALGHSKDYSLKQYLLFADKLQAKAK 169
           PATASAVLA +AP L PFMSDEAM AALG SKDYSLKQY+ F DKLQ KA+
Sbjct: 121 PATASAVLATFAPHLTPFMSDEAMEAALGSSKDYSLKQYIKFVDKLQRKAE 171

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  226 bits (576), Expect = 3e-57,   Method: Compositional matrix adjust.
 Identities = 108/167 (64%), Positives = 134/167 (80%)

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

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

Query: 123 SAVLAAYAPDLAPFMSDEAMGAALGHSKDYSLKQYLLFADKLQAKAK 169
           SAVLAA+ P +APFMSDEAM AALG SK+Y+LKQYL+FA+KLQ KAK
Sbjct: 121 SAVLAAFDPHIAPFMSDEAMVAALGSSKEYTLKQYLVFAEKLQNKAK 167

Source: Picea sitchensis

Species: Picea sitchensis

Genus: Picea

Family: Pinaceae

Order: Coniferales

Class: Coniferopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

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Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	185
TAIR|locus:2082224	209	AT3G12210 [Arabidopsis thalian	0.913	0.808	0.674	2.5e-58
UNIPROTKB|F1RG53	232	LOC100524737 "Uncharacterized	0.870	0.693	0.4	2.2e-25
ZFIN|ZDB-GENE-050320-25	238	zgc:112496 "zgc:112496" [Danio	0.859	0.668	0.389	3.4e-22
FB|FBgn0030328	550	Amun "Amun" [Drosophila melano	0.745	0.250	0.421	1.2e-21
ASPGD|ASPL0000059149	312	AN10183 [Emericella nidulans (	0.502	0.298	0.326	2.3e-08

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

 Score = 599 (215.9 bits), Expect = 2.5e-58, P = 2.5e-58
 Identities = 114/169 (67%), Positives = 137/169 (81%)

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 TASAVLAAYAPDLAPFMSDEAMGAALGHSKDYSLKQYLLFADKLQAKAK 169
             TASAVLAAYAPD+APFMSDEAM  ALG+SKDYSLKQYLLFA KLQ KAK
Sbjct:   121 TASAVLAAYAPDIAPFMSDEAMEVALGNSKDYSLKQYLLFATKLQDKAK 169

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 = 288 (106.4 bits), Expect = 2.2e-25, P = 2.2e-25
 Identities = 66/165 (40%), Positives = 93/165 (56%)

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

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

Query:   125 VLAAYAPDLAPFMSDEAMGAALG-HSKDYSLKQYLLFADKLQAKA 168
             VLAA AP++A FMS+EA+ A  G  +  Y+LK YLL+  ++Q +A
Sbjct:   129 VLAAGAPEVAAFMSEEAVAAVPGLPALQYTLKHYLLYLSRVQERA 173

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 = 258 (95.9 bits), Expect = 3.4e-22, P = 3.4e-22
 Identities = 65/167 (38%), Positives = 87/167 (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 PATASAVLAAYAPDLAPFMSDEAMGA-ALGHSKDYSLKQYLLFADKL 164
              ATASAVL A APD   FM+DEA+ + A     +Y+ K Y L+  K+
Sbjct:   123 SATASAVLVAGAPDKVAFMADEAVESIAELRPVEYTDKHYALYLQKM 169

GO:0003677 "DNA binding" evidence=IEA

GO:0006281 "DNA repair" evidence=IEA

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

 Score = 260 (96.6 bits), Expect = 1.2e-21, P = 1.2e-21
 Identities = 59/140 (42%), Positives = 83/140 (59%)

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

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

Query:   148 -HSKDYSLKQYLLFADKLQA 166
                 DY+ K+YL F + +QA
Sbjct:   160 IEGIDYTTKEYLNFVNHIQA 179

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 = 133 (51.9 bits), Expect = 2.3e-08, P = 2.3e-08
 Identities = 34/104 (32%), Positives = 49/104 (47%)

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

Query:   104 ------LTKAVSELTV-LKGVGPATASAVLAAYAPDLAPFMSDE 140
                   +  A+  LT  L+GVGPATAS +L+   P++ PF SD+
Sbjct:   162 KDGFEAIENALLTLTTPLRGVGPATASLILSVACPEMIPFYSDD 205


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        0.318   0.132   0.391    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      185       168   0.00079  108 3  11 22  0.39    32
                                                     31  0.46    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:  602 (64 KB)
  Total size of DFA:  158 KB (2093 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:  14.37u 0.14s 14.51t   Elapsed:  00:00:01
  Total cpu time:  14.37u 0.14s 14.51t   Elapsed:  00:00:01
  Start:  Fri May 10 00:07:45 2013   End:  Fri May 10 00:07:46 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	185
PF00633	30	HHH: Helix-hairpin-helix motif; InterPro: IPR00044	97.68
PRK01229	208	N-glycosylase/DNA lyase; Provisional	96.99
cd00056	158	ENDO3c endonuclease III; includes endonuclease III	96.49
COG0177	211	Nth Predicted EndoIII-related endonuclease [DNA re	96.33
TIGR01084	275	mutY A/G-specific adenine glycosylase. This equiva	95.95
COG0122	285	AlkA 3-methyladenine DNA glycosylase/8-oxoguanine	95.73
PRK10702	211	endonuclease III; Provisional	95.38
smart00478	149	ENDO3c endonuclease III. includes endonuclease III	95.26
PF02371	87	Transposase_20: Transposase IS116/IS110/IS902 fami	95.11
TIGR00588	310	ogg 8-oxoguanine DNA-glycosylase (ogg). All protei	94.91
TIGR01083	191	nth endonuclease III. This equivalog model identif	94.9
PRK10880	350	adenine DNA glycosylase; Provisional	94.89
PRK13913	218	3-methyladenine DNA glycosylase; Provisional	94.81
PRK02515	132	psbU photosystem II complex extrinsic protein prec	94.77
PRK13910	289	DNA glycosylase MutY; Provisional	94.54
TIGR03252	177	uncharacterized HhH-GPD family protein. This model	94.53
PRK10308	283	3-methyl-adenine DNA glycosylase II; Provisional	94.47
COG1194	342	MutY A/G-specific DNA glycosylase [DNA replication	94.29
smart00278	26	HhH1 Helix-hairpin-helix DNA-binding motif class 1	92.68
PF11731	93	Cdd1: Pathogenicity locus; InterPro: IPR021725 Cdd	91.33
PF10391	52	DNA_pol_lambd_f: Fingers domain of DNA polymerase	89.53
PF14716	68	HHH_8: Helix-hairpin-helix domain; PDB: 2W9M_A 1HU	88.76
PRK14605	194	ruvA Holliday junction DNA helicase RuvA; Provisio	87.59
TIGR01259	120	comE comEA protein. This model describes the ComEA	87.22
KOG1921	286	consensus Endonuclease III [Replication, recombina	85.99
PRK00116	192	ruvA Holliday junction DNA helicase RuvA; Reviewed	85.52
PF12826	64	HHH_2: Helix-hairpin-helix motif; PDB: 1X2I_B 1DGS	85.25
TIGR00084	191	ruvA Holliday junction DNA helicase, RuvA subunit.	84.7
PRK13901	196	ruvA Holliday junction DNA helicase RuvA; Provisio	84.67
PRK14600	186	ruvA Holliday junction DNA helicase RuvA; Provisio	84.55
PRK00024	224	hypothetical protein; Reviewed	84.53
PF14520	60	HHH_5: Helix-hairpin-helix domain; PDB: 3AUO_B 3AU	84.44
PRK14601	183	ruvA Holliday junction DNA helicase RuvA; Provisio	82.73
TIGR00608	218	radc DNA repair protein radc. This family is based	82.43
PF14520	60	HHH_5: Helix-hairpin-helix domain; PDB: 3AUO_B 3AU	81.52
PRK14601	183	ruvA Holliday junction DNA helicase RuvA; Provisio	81.34
PRK14606	188	ruvA Holliday junction DNA helicase RuvA; Provisio	80.57
COG2003	224	RadC DNA repair proteins [DNA replication, recombi	80.51

>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=3.5e-05  Score=46.97  Aligned_cols=24  Identities=42%  Similarity=0.700  Sum_probs=20.1

Q ss_pred             HHHHHHhhcccCcChHHHHHHHhh
Q 029905          105 TKAVSELTVLKGVGPATASAVLAA  128 (185)
Q Consensus       105 ~~al~~L~~LkGVGPATASaiLa~  128 (185)
                      .+.++.|.+|+||||.||.+|++.
T Consensus         7 pas~eeL~~lpGIG~~tA~~I~~~   30 (30)
T PF00633_consen    7 PASIEELMKLPGIGPKTANAILSF   30 (30)
T ss_dssp             TSSHHHHHTSTT-SHHHHHHHHHH
T ss_pred             CCCHHHHHhCCCcCHHHHHHHHhC
Confidence            446889999999999999999973

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

>PRK01229 N-glycosylase/DNA lyase; Provisional

Probab=96.99  E-value=0.0048  Score=52.62  Aligned_cols=72  Identities=28%  Similarity=0.206  Sum_probs=53.0

Q ss_pred             cHHHHHHHhh-cccCcChHHHHHHH-hhhCCCCCCcccHHHHHhhh---C--C--CCCCCHHHHHHHHHHHHHHHHhhCc
Q 029905          103 DLTKAVSELT-VLKGVGPATASAVL-AAYAPDLAPFMSDEAMGAAL---G--H--SKDYSLKQYLLFADKLQAKAKVSDI  173 (185)
Q Consensus       103 dv~~al~~L~-~LkGVGPATASaiL-a~~~P~~~pFfSDEa~~~~~---g--~--~ikYt~keY~~~~~~l~~~a~~L~~  173 (185)
                      ++..+.+.|. +||||||=||+.|| .+..  ..-|.-|--..-++   |  .  +..-|.+.|.+.-..+.+.++.+|+
T Consensus       112 ~~~~~R~~Ll~~lpGIG~KTAd~vL~~~~~--~~~~iVDtHv~Ri~~RlG~~~~~~~~lt~~~y~~~E~~l~~~~~~~~~  189 (208)
T PRK01229        112 DQFEAREFLVKNIKGIGYKEASHFLRNVGY--EDLAILDRHILRFLKRYGLIEEIPKTLSKKRYLEIEEILREIAEELGI  189 (208)
T ss_pred             CchHHHHHHHHcCCCCcHHHHHHHHHHccC--CCeeeeeHHHHHHHHHhCCCcccccccCcCCHHHHHHHHHHHHHHcCC
Confidence            5678899999 99999999999999 4544  21344666444333   4  1  2245669999999999999999998


Q ss_pred             hhh
Q 029905          174 FFF  176 (185)
Q Consensus       174 ~~~  176 (185)
                      ...
T Consensus       190 ~~~  192 (208)
T PRK01229        190 SLG  192 (208)
T ss_pred             CHH
Confidence            653

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

Probab=96.49  E-value=0.019  Score=45.13  Aligned_cols=57  Identities=32%  Similarity=0.380  Sum_probs=36.9

Q ss_pred             HHHHHHhhcccCcChHHHHHHHhhhC-CCCCCcccHHHHHhhh---C-CCCCCCHHHHHHHHHH
Q 029905          105 TKAVSELTVLKGVGPATASAVLAAYA-PDLAPFMSDEAMGAAL---G-HSKDYSLKQYLLFADK  163 (185)
Q Consensus       105 ~~al~~L~~LkGVGPATASaiLa~~~-P~~~pFfSDEa~~~~~---g-~~ikYt~keY~~~~~~  163 (185)
                      ..+.+.|++||||||-||+.+|.... ++.+|.  |-...-++   | .+.+-|-++..+..+.
T Consensus        79 ~~~~~~L~~l~GIG~~tA~~~l~~~~~~~~~pv--D~~v~r~~~~~~~~~~~~~~~~~~~~~~~  140 (158)
T cd00056          79 PDAREELLALPGVGRKTANVVLLFALGPDAFPV--DTHVRRVLKRLGLIPKKKTPEELEELLEE  140 (158)
T ss_pred             cccHHHHHcCCCCCHHHHHHHHHHHCCCCCCcc--chhHHHHHHHhCCCCCCCCHHHHHHHHHH
Confidence            67899999999999999999998743 444454  66554343   2 2333344444444433

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

Probab=96.33  E-value=0.0046  Score=53.02  Aligned_cols=71  Identities=23%  Similarity=0.245  Sum_probs=46.4

Q ss_pred             CHHHHHHHHHHHhhCCCCCchhhhHhhhCCHHHHHHHHHH-HH------------hhC-----ccHHHHHHHhhcccCcC
Q 029905           57 NTTELSKLVRWKLTRGKWRPRLLVFVSSLDDSSVKSASEK-AF------------KSL-----PDLTKAVSELTVLKGVG  118 (185)
Q Consensus        57 tkdEL~~LveWKL~rGkfRP~L~~lV~sN~~~~V~~~t~~-Af------------~~l-----~dv~~al~~L~~LkGVG  118 (185)
                      |.|+.+.-+.=+|-  +..|+...+...+.+ .+++.++. +|            +++     .++...++.|.+|+|||
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 TTDEVVNKATPALF--KRYPTPEDLLNADEE-ELEELIKSIGLYRNKAKNIKELARILLEKFGGEVPDTREELLSLPGVG  118 (211)
T ss_pred             CchHHHHHHHHHHH--HHcCCHHHHHcCCHH-HHHHHHHhcCCcHHHHHHHHHHHHHHHHHcCCCCCchHHHHHhCCCcc
Confidence            46777766665554  234566666655544 44444432 22            011     15677899999999999


Q ss_pred             hHHHHHHHhhhC
Q 029905          119 PATASAVLAAYA  130 (185)
Q Consensus       119 PATASaiLa~~~  130 (185)
                      +-||..+|+...
T Consensus       119 rKTAnvVL~~a~  130 (211)
T COG0177         119 RKTANVVLSFAF  130 (211)
T ss_pred             hHHHHHHHHhhc
Confidence            999999999854

>TIGR01084 mutY A/G-specific adenine glycosylase

Probab=95.95  E-value=0.033  Score=49.13  Aligned_cols=38  Identities=29%  Similarity=0.395  Sum_probs=28.9

Q ss_pred             HHHHHHHhhcccCcChHHHHHHHhhhCCCCCCcccHHHH
Q 029905          104 LTKAVSELTVLKGVGPATASAVLAAYAPDLAPFMSDEAM  142 (185)
Q Consensus       104 v~~al~~L~~LkGVGPATASaiLa~~~P~~~pFfSDEa~  142 (185)
                      +...++.|++|+||||-||++||+...-...|+ -|--.
T Consensus       100 ~p~~~~~L~~LpGIG~~TA~~Il~~a~~~~~~~-vD~~v  137 (275)
T TIGR01084       100 FPQDFEDLAALPGVGRYTAGAILSFALNKPYPI-LDGNV  137 (275)
T ss_pred             CcHHHHHHHhCCCCCHHHHHHHHHHHCCCCCCc-chHhH
Confidence            345689999999999999999999865433454 55544

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

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

Probab=95.73  E-value=0.035  Score=49.17  Aligned_cols=72  Identities=28%  Similarity=0.270  Sum_probs=52.9

Q ss_pred             CCCHHHHHHHHHHHhh-CCCCCchhhhHhhhCCHHHHHHHHHHHHhhCc--------cHHHHHHHhhcccCcChHHHHHH
Q 029905           55 HINTTELSKLVRWKLT-RGKWRPRLLVFVSSLDDSSVKSASEKAFKSLP--------DLTKAVSELTVLKGVGPATASAV  125 (185)
Q Consensus        55 ~ltkdEL~~LveWKL~-rGkfRP~L~~lV~sN~~~~V~~~t~~Af~~l~--------dv~~al~~L~~LkGVGPATASai  125 (185)
                      +.|-++|..+=++-|+ -|..+.+         .+.+.++++...+-.+        +...+++.|++||||||=||-.+
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            6888888888888886 5665553         3445555555554322        46779999999999999999999


Q ss_pred             Hhh--hCCCCCC
Q 029905          126 LAA--YAPDLAP  135 (185)
Q Consensus       126 La~--~~P~~~p  135 (185)
                      |-.  ..|+.+|
T Consensus       215 llf~lgr~dvfP  226 (285)
T COG0122         215 LLFGLGRPDVFP  226 (285)
T ss_pred             HHHcCCCCCCCC
Confidence            876  4676655

>PRK10702 endonuclease III; Provisional

Probab=95.38  E-value=0.022  Score=48.32  Aligned_cols=38  Identities=26%  Similarity=0.290  Sum_probs=28.4

Q ss_pred             HHHHHHHhhcccCcChHHHHHHHhhhCCCCCCcccHHHH
Q 029905          104 LTKAVSELTVLKGVGPATASAVLAAYAPDLAPFMSDEAM  142 (185)
Q Consensus       104 v~~al~~L~~LkGVGPATASaiLa~~~P~~~pFfSDEa~  142 (185)
                      +..+.+.|.+|+||||-||.+||....-. ..|--|--.
T Consensus       104 ~p~~~~~Ll~lpGVG~ktA~~ill~a~~~-~~~~VDt~v  141 (211)
T PRK10702        104 VPEDRAALEALPGVGRKTANVVLNTAFGW-PTIAVDTHI  141 (211)
T ss_pred             CCchHHHHhcCCcccHHHHHHHHHHHcCC-CcccccchH
Confidence            45689999999999999999999986532 234445433

>smart00478 ENDO3c endonuclease III

Probab=95.26  E-value=0.13  Score=40.07  Aligned_cols=39  Identities=31%  Similarity=0.307  Sum_probs=28.3

Q ss_pred             cHHHHHHHhhcccCcChHHHHHHHhhhCCCCCCcccHHHH
Q 029905          103 DLTKAVSELTVLKGVGPATASAVLAAYAPDLAPFMSDEAM  142 (185)
Q Consensus       103 dv~~al~~L~~LkGVGPATASaiLa~~~P~~~pFfSDEa~  142 (185)
                      ++....+.|++||||||-||+++|...--. .-|-.|--.
T Consensus        66 ~~~~~~~~L~~l~GIG~~tA~~~l~~~~~~-~~~~~D~~v  104 (149)
T smart00478       66 EVPDDREELLKLPGVGRKTANAVLSFALGK-PFIPVDTHV  104 (149)
T ss_pred             CccHHHHHHHcCCCCcHHHHHHHHHHHCCC-CCCccchHH
Confidence            344678899999999999999999986544 223444433

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

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

Probab=95.11  E-value=0.018  Score=41.90  Aligned_cols=37  Identities=32%  Similarity=0.497  Sum_probs=30.0

Q ss_pred             HHhhcccCcChHHHHHHHhhh-CCCCCCcccHHHHHhhhC
Q 029905          109 SELTVLKGVGPATASAVLAAY-APDLAPFMSDEAMGAALG  147 (185)
Q Consensus       109 ~~L~~LkGVGPATASaiLa~~-~P~~~pFfSDEa~~~~~g  147 (185)
                      +.|+.++||||-||..||+.. +|+  -|=+...+...+|
T Consensus         2 ~~l~sipGig~~~a~~llaeigd~~--rF~~~~~l~~~~G   39 (87)
T PF02371_consen    2 ELLTSIPGIGPITAATLLAEIGDIS--RFKSAKQLASYAG   39 (87)
T ss_pred             chhcCCCCccHHHHHHHHHHHcCch--hcccchhhhhccc
Confidence            468899999999999999986 443  4667888887776

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

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

Probab=94.91  E-value=0.024  Score=50.54  Aligned_cols=39  Identities=28%  Similarity=0.376  Sum_probs=31.1

Q ss_pred             cHHHHHHHhhcccCcChHHHHHHHhh--hCCCCCCcccHHHHH
Q 029905          103 DLTKAVSELTVLKGVGPATASAVLAA--YAPDLAPFMSDEAMG  143 (185)
Q Consensus       103 dv~~al~~L~~LkGVGPATASaiLa~--~~P~~~pFfSDEa~~  143 (185)
                      +...+.+.|++||||||-||.+||..  ..|+.+|  .|-...
T Consensus       214 ~~~~~~~~L~~l~GIG~~tAd~vll~~l~~~d~~P--vD~~v~  254 (310)
T TIGR00588       214 SYEDAREALCELPGVGPKVADCICLMGLDKPQAVP--VDVHVW  254 (310)
T ss_pred             ChHHHHHHHHhCCCccHHHHHHHHHHhCCCCCcee--ecHHHH
Confidence            35678999999999999999999976  4566667  376553

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.

>TIGR01083 nth endonuclease III

Probab=94.90  E-value=0.08  Score=43.65  Aligned_cols=39  Identities=28%  Similarity=0.227  Sum_probs=28.4

Q ss_pred             HHHHHHHhhcccCcChHHHHHHHhhhCCCCCCcccHHHHH
Q 029905          104 LTKAVSELTVLKGVGPATASAVLAAYAPDLAPFMSDEAMG  143 (185)
Q Consensus       104 v~~al~~L~~LkGVGPATASaiLa~~~P~~~pFfSDEa~~  143 (185)
                      +..+.+.|++||||||-||.+||....-.. -|.-|--..
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            445788999999999999999998764321 245555443

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

>PRK10880 adenine DNA glycosylase; Provisional

Probab=94.89  E-value=0.041  Score=50.23  Aligned_cols=29  Identities=31%  Similarity=0.472  Sum_probs=25.1

Q ss_pred             HHHHHHHhhcccCcChHHHHHHHhhhCCC
Q 029905          104 LTKAVSELTVLKGVGPATASAVLAAYAPD  132 (185)
Q Consensus       104 v~~al~~L~~LkGVGPATASaiLa~~~P~  132 (185)
                      +....+.|.+||||||-||++||+...-.
T Consensus       104 ~p~~~~~L~~LpGIG~~TA~aIl~~af~~  132 (350)
T PRK10880        104 FPETFEEVAALPGVGRSTAGAILSLSLGK  132 (350)
T ss_pred             chhhHHHHhcCCCccHHHHHHHHHHHCCC
Confidence            45678999999999999999999987643

>PRK13913 3-methyladenine DNA glycosylase; Provisional

Probab=94.81  E-value=0.11  Score=44.58  Aligned_cols=39  Identities=21%  Similarity=0.130  Sum_probs=28.1

Q ss_pred             HHHHHhhcccCcChHHHHHHHhhhCCCCCCcccHHHHHhh
Q 029905          106 KAVSELTVLKGVGPATASAVLAAYAPDLAPFMSDEAMGAA  145 (185)
Q Consensus       106 ~al~~L~~LkGVGPATASaiLa~~~P~~~pFfSDEa~~~~  145 (185)
                      ...+.|.+||||||=||.+||....- +.-|..|.-..-+
T Consensus       118 ~~re~Ll~l~GIG~kTAd~iLlya~~-rp~fvVDty~~Rv  156 (218)
T PRK13913        118 VTREWLLDQKGIGKESADAILCYVCA-KEVMVVDKYSYLF  156 (218)
T ss_pred             hHHHHHHcCCCccHHHHHHHHHHHcC-CCccccchhHHHH
Confidence            45688999999999999999987542 3245556544433

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

Probab=94.77  E-value=0.017  Score=46.38  Aligned_cols=37  Identities=24%  Similarity=0.332  Sum_probs=32.3

Q ss_pred             HHHHHhhcccCcChHHHHHHHhhhCCCCCCcccHHHHHhhhC
Q 029905          106 KAVSELTVLKGVGPATASAVLAAYAPDLAPFMSDEAMGAALG  147 (185)
Q Consensus       106 ~al~~L~~LkGVGPATASaiLa~~~P~~~pFfSDEa~~~~~g  147 (185)
                      +..+.|..|+||||++|..|.     .+.||-|=|-...+.|
T Consensus        58 A~~~el~~lpGigP~~A~~IV-----~nGpf~sveDL~~V~G   94 (132)
T PRK02515         58 SSVRAFRQFPGMYPTLAGKIV-----KNAPYDSVEDVLNLPG   94 (132)
T ss_pred             cCHHHHHHCCCCCHHHHHHHH-----HCCCCCCHHHHHcCCC
Confidence            447789999999999999999     3679999998888887

>PRK13910 DNA glycosylase MutY; Provisional

Probab=94.54  E-value=0.054  Score=48.25  Aligned_cols=34  Identities=26%  Similarity=0.293  Sum_probs=26.3

Q ss_pred             HHHHHhhcccCcChHHHHHHHhhhCCCCCCcccHH
Q 029905          106 KAVSELTVLKGVGPATASAVLAAYAPDLAPFMSDE  140 (185)
Q Consensus       106 ~al~~L~~LkGVGPATASaiLa~~~P~~~pFfSDE  140 (185)
                      ...+.|.+|+||||-||.+||+...-..++ .-|-
T Consensus        69 ~~~~~L~~LpGIG~kTA~aIl~~af~~~~~-~VD~  102 (289)
T PRK13910         69 NDYQSLLKLPGIGAYTANAILCFGFREKSA-CVDA  102 (289)
T ss_pred             hhHHHHHhCCCCCHHHHHHHHHHHCCCCcC-cccH
Confidence            358999999999999999999986543333 4444

>TIGR03252 uncharacterized HhH-GPD family protein

Probab=94.53  E-value=0.03  Score=46.90  Aligned_cols=44  Identities=30%  Similarity=0.373  Sum_probs=32.7

Q ss_pred             ccHHHHHHHhhcccCcChHHHHHHHhhhCCCCCCcccHHHHHhhhC
Q 029905          102 PDLTKAVSELTVLKGVGPATASAVLAAYAPDLAPFMSDEAMGAALG  147 (185)
Q Consensus       102 ~dv~~al~~L~~LkGVGPATASaiLa~~~P~~~pFfSDEa~~~~~g  147 (185)
                      |+-....+.|.+|+||||-||..+|+...-+.  -.-||-|....|
T Consensus       108 p~t~~lre~Ll~LpGVG~KTAnvVL~~l~~~~--~~~~~~~~~~~~  151 (177)
T TIGR03252       108 PDGKELLRRLKALPGFGKQKAKIFLALLGKQL--GVTPEGWREAAG  151 (177)
T ss_pred             CCcHHHHHHHHcCCCCCHHHHHHHHHHHHHHh--CCCCcchHHhcc
Confidence            45556689999999999999999999755432  245677765554

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

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

Probab=94.47  E-value=0.043  Score=48.41  Aligned_cols=36  Identities=28%  Similarity=0.322  Sum_probs=29.4

Q ss_pred             cHHHHHHHhhcccCcChHHHHHHHhh--hCCCCCCcccH
Q 029905          103 DLTKAVSELTVLKGVGPATASAVLAA--YAPDLAPFMSD  139 (185)
Q Consensus       103 dv~~al~~L~~LkGVGPATASaiLa~--~~P~~~pFfSD  139 (185)
                      +...+++.|++||||||-||..||-.  ..|+..| -.|
T Consensus       201 ~~~~~~~~L~~LpGIGpwTA~~vllr~lg~~D~fp-~~D  238 (283)
T PRK10308        201 DVEQAMKTLQTFPGIGRWTANYFALRGWQAKDVFL-PDD  238 (283)
T ss_pred             CHHHHHHHHhcCCCcCHHHHHHHHHHhCCCCCCCC-ccc
Confidence            56778999999999999999999865  5787755 444

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

Probab=94.29  E-value=0.057  Score=49.42  Aligned_cols=56  Identities=27%  Similarity=0.346  Sum_probs=37.5

Q ss_pred             HHHhhcccCcChHHHHHHHhhhCCCCCCcccHHHHHhh---hC----CCCCCCHHHHHHHHHH
Q 029905          108 VSELTVLKGVGPATASAVLAAYAPDLAPFMSDEAMGAA---LG----HSKDYSLKQYLLFADK  163 (185)
Q Consensus       108 l~~L~~LkGVGPATASaiLa~~~P~~~pFfSDEa~~~~---~g----~~ikYt~keY~~~~~~  163 (185)
                      .+.|.+|+||||-||+||||...-...|+..--+...+   .+    .+.+=+-+++.++++.
T Consensus       112 ~~~l~~LpGiG~yTa~Ail~~a~~~~~~~lDgNV~RVl~R~f~i~~~~~~~~~~~~~~~~~~~  174 (342)
T COG1194         112 EEELAALPGVGPYTAGAILSFAFNQPEPVLDGNVKRVLSRLFAISGDIGKPKTKKELWELAEQ  174 (342)
T ss_pred             HHHHHhCCCCcHHHHHHHHHHHhCCCCceeecchheeehhhhcccccccccchhHHHHHHHHH
Confidence            45666799999999999999987766787666555422   22    1223455666655554

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

Probab=92.68  E-value=0.09  Score=30.38  Aligned_cols=19  Identities=47%  Similarity=0.763  Sum_probs=16.9

Q ss_pred             HhhcccCcChHHHHHHHhh
Q 029905          110 ELTVLKGVGPATASAVLAA  128 (185)
Q Consensus       110 ~L~~LkGVGPATASaiLa~  128 (185)
                      .|.+++|||+.+|..|+..
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=91.33  E-value=0.15  Score=38.77  Aligned_cols=26  Identities=27%  Similarity=0.261  Sum_probs=22.1

Q ss_pred             HHHHHHHhhcccCcChHHHHHHHhhh
Q 029905          104 LTKAVSELTVLKGVGPATASAVLAAY  129 (185)
Q Consensus       104 v~~al~~L~~LkGVGPATASaiLa~~  129 (185)
                      ..+.+..|+.|+|||||||-=+..++
T Consensus         7 ~~~~~~~L~~iP~IG~a~a~DL~~LG   32 (93)
T PF11731_consen    7 KRAGLSDLTDIPNIGKATAEDLRLLG   32 (93)
T ss_pred             HHHHHHHHhcCCCccHHHHHHHHHcC
Confidence            34578999999999999999887774

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=89.53  E-value=0.24  Score=33.59  Aligned_cols=22  Identities=36%  Similarity=0.351  Sum_probs=17.2

Q ss_pred             HHHhhcccCcChHHHHHHHhhh
Q 029905          108 VSELTVLKGVGPATASAVLAAY  129 (185)
Q Consensus       108 l~~L~~LkGVGPATASaiLa~~  129 (185)
                      |+.+++.-||||+||.-..+.+
T Consensus         1 l~~f~~I~GVG~~tA~~w~~~G   22 (52)
T PF10391_consen    1 LKLFTGIWGVGPKTARKWYAKG   22 (52)
T ss_dssp             HHHHHTSTT--HHHHHHHHHTT
T ss_pred             CcchhhcccccHHHHHHHHHhC
Confidence            5789999999999999888764

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

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

Probab=88.76  E-value=0.64  Score=32.37  Aligned_cols=32  Identities=31%  Similarity=0.398  Sum_probs=23.1

Q ss_pred             HHHhhCccHHHHHHH-hhcccCcChHHHHHHHh
Q 029905           96 KAFKSLPDLTKAVSE-LTVLKGVGPATASAVLA  127 (185)
Q Consensus        96 ~Af~~l~dv~~al~~-L~~LkGVGPATASaiLa  127 (185)
                      .+.+.+|..-..++. +.+|+|||+.+|.-|--
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            334567755555675 99999999999987743

...

>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional

Probab=87.59  E-value=0.39  Score=40.28  Aligned_cols=31  Identities=23%  Similarity=0.362  Sum_probs=25.3

Q ss_pred             cHHHHHHHhhcccCcChHHHHHHHhhhCCCC
Q 029905          103 DLTKAVSELTVLKGVGPATASAVLAAYAPDL  133 (185)
Q Consensus       103 dv~~al~~L~~LkGVGPATASaiLa~~~P~~  133 (185)
                      +-+.-...|.+.+||||-||-+||+.+.|+.
T Consensus        67 ~Er~lF~~Li~V~GIGpK~Al~ILs~~~~~~   97 (194)
T PRK14605         67 EELSLFETLIDVSGIGPKLGLAMLSAMNAEA   97 (194)
T ss_pred             HHHHHHHHHhCCCCCCHHHHHHHHHhCCHHH
Confidence            3566788899999999999999999877643

>TIGR01259 comE comEA protein

Probab=87.22  E-value=0.73  Score=35.78  Aligned_cols=42  Identities=29%  Similarity=0.462  Sum_probs=33.9

Q ss_pred             HHHHHHhhcccCcChHHHHHHHhhhCCCCCCcccHHHHHhhhC
Q 029905          105 TKAVSELTVLKGVGPATASAVLAAYAPDLAPFMSDEAMGAALG  147 (185)
Q Consensus       105 ~~al~~L~~LkGVGPATASaiLa~~~P~~~pFfSDEa~~~~~g  147 (185)
                      .+..+.|..|+||||.+|..|+.-..- +.||-|-|-+..+.|
T Consensus        64 tA~~~eL~~lpGIG~~~A~~Ii~~R~~-~g~f~s~eeL~~V~G  105 (120)
T TIGR01259        64 AASLEELQALPGIGPAKAKAIIEYREE-NGAFKSVDDLTKVSG  105 (120)
T ss_pred             cCCHHHHhcCCCCCHHHHHHHHHHHHh-cCCcCCHHHHHcCCC
Confidence            345678999999999999999998653 568888777777766

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

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

Probab=85.99  E-value=1.2  Score=39.71  Aligned_cols=29  Identities=31%  Similarity=0.464  Sum_probs=26.4

Q ss_pred             cHHHHHHHhhcccCcChHHHHHHHhhhCC
Q 029905          103 DLTKAVSELTVLKGVGPATASAVLAAYAP  131 (185)
Q Consensus       103 dv~~al~~L~~LkGVGPATASaiLa~~~P  131 (185)
                      |+...++.|..|+||||-+|=+.|++.--
T Consensus       153 DIP~~v~dLlsLPGVGPKMa~L~m~~AWn  181 (286)
T KOG1921|consen  153 DIPDTVEDLLSLPGVGPKMAHLTMQVAWN  181 (286)
T ss_pred             CCchhHHHHhcCCCCchHHHHHHHHHHhc
Confidence            78889999999999999999999998543

>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed

Probab=85.52  E-value=0.64  Score=38.69  Aligned_cols=26  Identities=35%  Similarity=0.565  Sum_probs=19.9

Q ss_pred             HHHHHhhcccCcChHHHHHHHhhhCC
Q 029905          106 KAVSELTVLKGVGPATASAVLAAYAP  131 (185)
Q Consensus       106 ~al~~L~~LkGVGPATASaiLa~~~P  131 (185)
                      .....|..++||||.||-.||+.+.+
T Consensus        70 ~~f~~L~~i~GIGpk~A~~il~~fg~   95 (192)
T PRK00116         70 ELFRLLISVSGVGPKLALAILSGLSP   95 (192)
T ss_pred             HHHHHHhcCCCCCHHHHHHHHHhCCH
Confidence            34667888888888888888887554

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

Probab=85.25  E-value=2.1  Score=29.51  Aligned_cols=24  Identities=29%  Similarity=0.670  Sum_probs=17.7

Q ss_pred             HHHHHhhcccCcChHHHHHHHhhh
Q 029905          106 KAVSELTVLKGVGPATASAVLAAY  129 (185)
Q Consensus       106 ~al~~L~~LkGVGPATASaiLa~~  129 (185)
                      +..+.|++++||||.+|..|....
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            357899999999999999998764

>TIGR00084 ruvA Holliday junction DNA helicase, RuvA subunit

Probab=84.70  E-value=0.64  Score=38.90  Aligned_cols=28  Identities=36%  Similarity=0.557  Sum_probs=19.8

Q ss_pred             HHHHHHHhhcccCcChHHHHHHHhhhCC
Q 029905          104 LTKAVSELTVLKGVGPATASAVLAAYAP  131 (185)
Q Consensus       104 v~~al~~L~~LkGVGPATASaiLa~~~P  131 (185)
                      -+.-...|...+||||-||-+||+...|
T Consensus        67 Er~lF~~L~~V~GIGpK~Al~iL~~~~~   94 (191)
T TIGR00084        67 ERELFKELIKVNGVGPKLALAILSNMSP   94 (191)
T ss_pred             HHHHHHHHhCCCCCCHHHHHHHHhcCCH
Confidence            4556677777777777777777777555

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

>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional

Probab=84.67  E-value=0.61  Score=39.59  Aligned_cols=29  Identities=28%  Similarity=0.406  Sum_probs=20.8

Q ss_pred             HHHHHHHhhcccCcChHHHHHHHhhhCCC
Q 029905          104 LTKAVSELTVLKGVGPATASAVLAAYAPD  132 (185)
Q Consensus       104 v~~al~~L~~LkGVGPATASaiLa~~~P~  132 (185)
                      -+.-...|.+..||||-||-+|||...|+
T Consensus        67 Er~lF~~LisVsGIGPK~ALaILs~~~~~   95 (196)
T PRK13901         67 EREVFEELIGVDGIGPRAALRVLSGIKYN   95 (196)
T ss_pred             HHHHHHHHhCcCCcCHHHHHHHHcCCCHH
Confidence            45566777777778888877777776664

>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional

Probab=84.55  E-value=0.61  Score=39.05  Aligned_cols=29  Identities=24%  Similarity=0.371  Sum_probs=21.6

Q ss_pred             HHHHHHHhhcccCcChHHHHHHHhhhCCC
Q 029905          104 LTKAVSELTVLKGVGPATASAVLAAYAPD  132 (185)
Q Consensus       104 v~~al~~L~~LkGVGPATASaiLa~~~P~  132 (185)
                      -+.-...|.+..||||-||-+||+...|+
T Consensus        68 Er~lF~~LisV~GIGpK~Al~iLs~~~~~   96 (186)
T PRK14600         68 EQDCLRMLVKVSGVNYKTAMSILSKLTPE   96 (186)
T ss_pred             HHHHHHHHhCcCCcCHHHHHHHHccCCHH
Confidence            45567777888888888888888876664

>PRK00024 hypothetical protein; Reviewed

Probab=84.53  E-value=5.1  Score=34.27  Aligned_cols=60  Identities=28%  Similarity=0.449  Sum_probs=40.0

Q ss_pred             CCCCHHHHHHHHHHHhhCCCCCchhhhHhhhCCHHHHHHHHHHHHhhCcc---H-HHHHHHhhcccCcChHHHHHHHhh
Q 029905           54 PHINTTELSKLVRWKLTRGKWRPRLLVFVSSLDDSSVKSASEKAFKSLPD---L-TKAVSELTVLKGVGPATASAVLAA  128 (185)
Q Consensus        54 ~~ltkdEL~~LveWKL~rGkfRP~L~~lV~sN~~~~V~~~t~~Af~~l~d---v-~~al~~L~~LkGVGPATASaiLa~  128 (185)
                      ..|+-.||..++   |..|..|.            .|....++-++...+   + ....+.|++++|||||.|..|+++
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            444555544443332   2 234678999999999999999887

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

Probab=84.44  E-value=1  Score=30.39  Aligned_cols=23  Identities=26%  Similarity=0.479  Sum_probs=20.3

Q ss_pred             HHHHhhcccCcChHHHHHHHhhh
Q 029905          107 AVSELTVLKGVGPATASAVLAAY  129 (185)
Q Consensus       107 al~~L~~LkGVGPATASaiLa~~  129 (185)
                      ....|..++||||.+|..+....
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            46788899999999999999984

...

>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional

Probab=82.73  E-value=0.81  Score=38.30  Aligned_cols=29  Identities=28%  Similarity=0.323  Sum_probs=19.0

Q ss_pred             HHHHHHHhhcccCcChHHHHHHHhhhCCC
Q 029905          104 LTKAVSELTVLKGVGPATASAVLAAYAPD  132 (185)
Q Consensus       104 v~~al~~L~~LkGVGPATASaiLa~~~P~  132 (185)
                      -+.-+..|.+..||||-||-+|||...|+
T Consensus        68 Er~lF~~Li~VsGIGpK~Al~ILs~~~~~   96 (183)
T PRK14601         68 EQKMFEMLLKVNGIGANTAMAVCSSLDVN   96 (183)
T ss_pred             HHHHHHHHhccCCccHHHHHHHHcCCCHH
Confidence            34456666677777777777777766553

>TIGR00608 radc DNA repair protein radc

Probab=82.43  E-value=1.4  Score=37.67  Aligned_cols=61  Identities=28%  Similarity=0.351  Sum_probs=39.3

Q ss_pred             CCCCHHHHHHHHHHHhhCCCCCchhhhHhhhCCHHHHHHHHHHHHhh------CccH-HHHHHHhhcccCcChHHHHHHH
Q 029905           54 PHINTTELSKLVRWKLTRGKWRPRLLVFVSSLDDSSVKSASEKAFKS------LPDL-TKAVSELTVLKGVGPATASAVL  126 (185)
Q Consensus        54 ~~ltkdEL~~LveWKL~rGkfRP~L~~lV~sN~~~~V~~~t~~Af~~------l~dv-~~al~~L~~LkGVGPATASaiL  126 (185)
                      ..|+-.||..++   |..|.-|..           .|.+.+++-++.      +.++ ....+.|++.+|||||.|..|+
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---LRTGTPKGL-----------DVLSLSKRLLDVFGRQDSLGHLLSAPPEELSSVPGIGEAKAIQLK   77 (218)
T ss_pred             ccCCHHHHHHHH---HhCCCCCCC-----------CHHHHHHHHHHHhcccCCHHHHHhCCHHHHHhCcCCcHHHHHHHH
Confidence            578888966554   566653320           233444433332      3333 3357889999999999999999


Q ss_pred             hh
Q 029905          127 AA  128 (185)
Q Consensus       127 a~  128 (185)
                      ++
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).

>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=81.52  E-value=0.91  Score=30.63  Aligned_cols=41  Identities=29%  Similarity=0.458  Sum_probs=26.1

Q ss_pred             HHHHHHHHHHHhhCccHHH-HHHHhhcccCcChHHHHHHHhh
Q 029905           88 SSVKSASEKAFKSLPDLTK-AVSELTVLKGVGPATASAVLAA  128 (185)
Q Consensus        88 ~~V~~~t~~Af~~l~dv~~-al~~L~~LkGVGPATASaiLa~  128 (185)
                      ..++.....+|..+.|+.. ..+.|.+++||||.+|.-|...
T Consensus        16 ~~a~~L~~~G~~t~~~l~~a~~~~L~~i~Gig~~~a~~i~~~   57 (60)
T PF14520_consen   16 KRAEKLYEAGIKTLEDLANADPEELAEIPGIGEKTAEKIIEA   57 (60)
T ss_dssp             HHHHHHHHTTCSSHHHHHTSHHHHHHTSTTSSHHHHHHHHHH
T ss_pred             HHHHHHHhcCCCcHHHHHcCCHHHHhcCCCCCHHHHHHHHHH
Confidence            3334444444443333322 4678999999999999988764

...

>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional

Probab=81.34  E-value=2.1  Score=35.80  Aligned_cols=98  Identities=19%  Similarity=0.233  Sum_probs=60.1

Q ss_pred             CCCCHHHHHHHHHHHhhCCCCCc-hhhhHhhhCCHHHHHHHHHHHHhhCccHHHHHHHhhcccCcChHHHHHHHhhhCC-
Q 029905           54 PHINTTELSKLVRWKLTRGKWRP-RLLVFVSSLDDSSVKSASEKAFKSLPDLTKAVSELTVLKGVGPATASAVLAAYAP-  131 (185)
Q Consensus        54 ~~ltkdEL~~LveWKL~rGkfRP-~L~~lV~sN~~~~V~~~t~~Af~~l~dv~~al~~L~~LkGVGPATASaiLa~~~P-  131 (185)
                      .+.|++|..-...-.--.| -=| .-+..++..+++.+.++....         =.+.|++++|||+-||.=|+-=.-. 
T Consensus        62 GF~~~~Er~lF~~Li~VsG-IGpK~Al~ILs~~~~~el~~aI~~~---------D~~~L~~vpGIGkKtAeRIilELkdK  131 (183)
T PRK14601         62 GFLDKDEQKMFEMLLKVNG-IGANTAMAVCSSLDVNSFYKALSLG---------DESVLKKVPGIGPKSAKRIIAELSDA  131 (183)
T ss_pred             CCCCHHHHHHHHHHhccCC-ccHHHHHHHHcCCCHHHHHHHHHhC---------CHHHHhhCCCCCHHHHHHHHHHHHHH
Confidence            4788888655444433333 334 345566667777776665542         2678999999999999987632111 


Q ss_pred             -----CCCCcccHHHHHhhhCCCCCCCHHHHHHHHHHH
Q 029905          132 -----DLAPFMSDEAMGAALGHSKDYSLKQYLLFADKL  164 (185)
Q Consensus       132 -----~~~pFfSDEa~~~~~g~~ikYt~keY~~~~~~l  164 (185)
                           ...+ -.+|+..++.+  ..|+.++=...+..+
T Consensus       132 ~~~~~~~~~-~~~ea~~AL~~--LGy~~~ea~~a~~~~  166 (183)
T PRK14601        132 KTKLENVSD-DKSEALAALLT--LGFKQEKIIKVLASC  166 (183)
T ss_pred             hhccCCCCc-cHHHHHHHHHH--cCCCHHHHHHHHHhc
Confidence                 1111 13678877763  567777766665554

>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional

Probab=80.57  E-value=2.3  Score=35.59  Aligned_cols=99  Identities=17%  Similarity=0.161  Sum_probs=60.3

Q ss_pred             CCCCHHHHHHHHHHHhhCCCCCc-hhhhHhhhCCHHHHHHHHHHHHhhCccHHHHHHHhhcccCcChHHHHHHHhhhCCC
Q 029905           54 PHINTTELSKLVRWKLTRGKWRP-RLLVFVSSLDDSSVKSASEKAFKSLPDLTKAVSELTVLKGVGPATASAVLAAYAPD  132 (185)
Q Consensus        54 ~~ltkdEL~~LveWKL~rGkfRP-~L~~lV~sN~~~~V~~~t~~Af~~l~dv~~al~~L~~LkGVGPATASaiLa~~~P~  132 (185)
                      .+.|++|..-.-.-.--.| -=| +-+.+++..+++.+.+++...         =.+.||+++|||+-||.-|.-=.-..
T Consensus        62 GF~~~~Er~lF~~Li~V~G-IGpK~AL~iLs~~~~~el~~aI~~~---------D~~~L~~vpGIGkKtAerIilELkdK  131 (188)
T PRK14606         62 GFSNERKKELFLSLTKVSR-LGPKTALKIISNEDAETLVTMIASQ---------DVEGLSKLPGISKKTAERIVMELKDE  131 (188)
T ss_pred             CCCCHHHHHHHHHHhccCC-ccHHHHHHHHcCCCHHHHHHHHHhC---------CHHHHhhCCCCCHHHHHHHHHHHHHh
Confidence            4788888655444433333 234 345666666777776665542         26789999999999999876321110


Q ss_pred             ----CC--CcccHHHHHhhhCCCCCCCHHHHHHHHHHH
Q 029905          133 ----LA--PFMSDEAMGAALGHSKDYSLKQYLLFADKL  164 (185)
Q Consensus       133 ----~~--pFfSDEa~~~~~g~~ikYt~keY~~~~~~l  164 (185)
                          ..  .-..+|+..++.  ...|+-++=..-+.++
T Consensus       132 ~~~~~~~~~~~~~e~~~AL~--~LGy~~~ea~~av~~~  167 (188)
T PRK14606        132 FESAGIKDMRIYHESLEALV--SLGYPEKQAREAVKHV  167 (188)
T ss_pred             hccccCCCcccHHHHHHHHH--HcCCCHHHHHHHHHHH
Confidence                00  012377887776  3567777766555554

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

Probab=80.51  E-value=3.3  Score=36.04  Aligned_cols=79  Identities=27%  Similarity=0.375  Sum_probs=51.9

Q ss_pred             hhhhHHhhhchh-hhccCCCCCCCHHHHHHHHHHHhhCCCCCchhhhHhhhCCHHHHHHHHHHHHhhC---ccHHH-HHH
Q 029905           35 LDDYYRKELPSL-IHQRNPNPHINTTELSKLVRWKLTRGKWRPRLLVFVSSLDDSSVKSASEKAFKSL---PDLTK-AVS  109 (185)
Q Consensus        35 LD~w~~~~lp~~-~~~r~~~~~ltkdEL~~LveWKL~rGkfRP~L~~lV~sN~~~~V~~~t~~Af~~l---~dv~~-al~  109 (185)
                      +.+|...+.|.- +...+ ...|+-.||.-|+   |+.|..+-            .|...++.-++.+   .++.. .++
T Consensus         3 i~~~~~~~rPRErll~~G-~~~Lsd~ELLail---LrtG~~~~------------~~~~la~~lL~~fg~L~~l~~a~~~   66 (224)
T COG2003           3 IKDNPENERPRERLLKLG-AEALSDAELLAIL---LRTGTKGE------------SVLDLAKELLQEFGSLAELLKASVE   66 (224)
T ss_pred             ccccccccchHHHHHHhC-hhhcchHHHHHHH---HhcCCCCC------------CHHHHHHHHHHHcccHHHHHhCCHH
Confidence            345555555531 11122 3589999976665   67776433            5666666665533   34444 499


Q ss_pred             HhhcccCcChHHHHHHHhhh
Q 029905          110 ELTVLKGVGPATASAVLAAY  129 (185)
Q Consensus       110 ~L~~LkGVGPATASaiLa~~  129 (185)
                      .||.++|||+|-|.=+.++.
T Consensus        67 el~~v~GiG~aka~~l~a~~   86 (224)
T COG2003          67 ELSSVKGIGLAKAIQIKAAI   86 (224)
T ss_pred             HHhhCCCccHHHHHHHHHHH
Confidence            99999999999999988873

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	185
4f9i_A	1026	Proline dehydrogenase/delta-1-pyrroline-5-carboxy	2e-04

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

 Score = 40.4 bits (95), Expect = 2e-04
 Identities = 15/128 (11%), Positives = 38/128 (29%), Gaps = 9/128 (7%)

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

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

Query: 152 YSLKQYLL 159
                +  
Sbjct: 157 LRKDGFAA 164

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	185
3fhf_A	214	Mjogg, N-glycosylase/DNA lyase, DNA-(apurinic; hel	97.75
3n0u_A	219	Probable N-glycosylase/DNA lyase; structural genom	97.74
3fhg_A	207	Mjogg, N-glycosylase/DNA lyase, DNA-(apurinic; hel	97.72
3s6i_A	228	DNA-3-methyladenine glycosylase 1; DNA glycosylase	96.46
2h56_A	233	DNA-3-methyladenine glycosidase; 10174367, EC 3.2.	96.21
4e9f_A	161	Methyl-CPG-binding domain protein 4; HHH DNA glyco	96.03
2xhi_A	360	N-glycosylase/DNA lyase; lyase-DNA complex, lyase/	95.95
3i0w_A	290	8-oxoguanine-DNA-glycosylase; OGG, cacogg, DNA, 8-	95.94
2yg9_A	225	DNA-3-methyladenine glycosidase II, putative; hydr	95.8
4b21_A	232	Probable DNA-3-methyladenine glycosylase 2; hydrol	95.79
2jhn_A	295	ALKA, 3-methyladenine DNA-glycosylase; DNA repair,	95.77
1mpg_A	282	ALKA, 3-methyladenine DNA glycosylase II; DNA repa	95.69
1pu6_A	218	3-methyladenine DNA glycosylase; helix-hairpin-hel	94.82
1kg2_A	225	A/G-specific adenine glycosylase; DNA repair, hydr	94.74
2abk_A	211	Endonuclease III; DNA-repair, DNA glycosylase; 1.8	94.68
1kea_A	221	Possible G-T mismatches repair enzyme; DNA repair,	94.31
1orn_A	226	Endonuclease III; DNA repair, DNA glycosylase, [4F	94.23
3fsp_A	369	A/G-specific adenine glycosylase; protein-DNA comp	93.68
1s5l_U	134	Photosystem II 12 kDa extrinsic protein; photosynt	93.42
3arc_U	97	Photosystem II 12 kDa extrinsic protein; PSII, mem	93.0
3n5n_X	287	A/G-specific adenine DNA glycosylase; alpha-helice	92.43
2duy_A	75	Competence protein comea-related protein; helix-ha	91.59
2i5h_A	205	Hypothetical protein AF1531; PFAM:DUF655, PSI-2, s	89.87
2a1j_B	91	DNA excision repair protein ERCC-1; XPF, xeroderma	89.2
1x2i_A	75	HEF helicase/nuclease; alpha helix, helix-hairpin-	88.84
2edu_A	98	Kinesin-like protein KIF22; kinesin-like DNA bindi	87.3
1kft_A	78	UVRC, excinuclease ABC subunit C; helix-hairpin-he	87.08
2ztd_A	212	Holliday junction ATP-dependent DNA helicase RUVA;	86.61
1ixr_A	191	Holliday junction DNA helicase RUVA; heterooligome	84.49
1cuk_A	203	RUVA protein; DNA repair, SOS response, DNA-bindin	81.92
2a1j_A	63	DNA repair endonuclease XPF; XPF, xeroderma pigmen	81.86
3u5c_S	146	40S ribosomal protein S18-A, 40S ribosomal protein	81.71
1z00_A	89	DNA excision repair protein ERCC-1; helix-hairpin-	81.49
1x2i_A	75	HEF helicase/nuclease; alpha helix, helix-hairpin-	80.92
1z00_A	89	DNA excision repair protein ERCC-1; helix-hairpin-	80.57

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

Probab=97.75  E-value=0.00018  Score=59.98  Aligned_cols=76  Identities=21%  Similarity=0.223  Sum_probs=57.7

Q ss_pred             HhhCccHHHHHHHhh-cccCcChHHHHHHHhhhCCCCCCcc-cHHHHHhhh---C----CCCCCCHHHHHHHHHHHHHHH
Q 029905           98 FKSLPDLTKAVSELT-VLKGVGPATASAVLAAYAPDLAPFM-SDEAMGAAL---G----HSKDYSLKQYLLFADKLQAKA  168 (185)
Q Consensus        98 f~~l~dv~~al~~L~-~LkGVGPATASaiLa~~~P~~~pFf-SDEa~~~~~---g----~~ikYt~keY~~~~~~l~~~a  168 (185)
                      |..+.++..+.+.|. +||||||-||+.||....  ..+|+ -|--..-++   |    .+...|.+.|.++-..++..+
T Consensus       113 ~~~~~~~~~~re~Ll~~LpGVG~KTA~~vL~~~g--~~~~~vVDthv~Ri~~RlG~~~~~~k~lt~~~y~e~~~~l~~~g  190 (214)
T 3fhf_A          113 VESFENEKVAREFLVRNIKGIGYKEASHFLRNVG--YDDVAIIDRHILRELYENNYIDEIPKTLSRRKYLEIENILRDIG  190 (214)
T ss_dssp             HHHSSSHHHHHHHHHHHSTTCCHHHHHHHHHHTT--CCSCCCCCHHHHHHHHHTTSSSSCCSSCCHHHHHHHHHHHHHHH
T ss_pred             hcccCCcHHHHHHHHHhCCCCCHHHHHHHHHHcC--CCCcccCcHHHHHHHHHcCCCCCCCCcCCHHHHHHHHHHHHHHH
Confidence            444457888999999 999999999999998642  23555 666444332   4    245678999999999999999


Q ss_pred             HhhCchh
Q 029905          169 KVSDIFF  175 (185)
Q Consensus       169 ~~L~~~~  175 (185)
                      +++|+..
T Consensus       191 ~~~g~~~  197 (214)
T 3fhf_A          191 EEVNLKL  197 (214)
T ss_dssp             HHTTCCH
T ss_pred             HHHCCCH
Confidence            9998764

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

Probab=97.74  E-value=9.7e-05  Score=61.73  Aligned_cols=72  Identities=26%  Similarity=0.232  Sum_probs=54.8

Q ss_pred             cHHHHHHHhh-cccCcChHHHHHHHhh-hCCCCCCcccHHHHHhh--hC----CCCCCCHHHHHHHHHHHHHHHHhhCch
Q 029905          103 DLTKAVSELT-VLKGVGPATASAVLAA-YAPDLAPFMSDEAMGAA--LG----HSKDYSLKQYLLFADKLQAKAKVSDIF  174 (185)
Q Consensus       103 dv~~al~~L~-~LkGVGPATASaiLa~-~~P~~~pFfSDEa~~~~--~g----~~ikYt~keY~~~~~~l~~~a~~L~~~  174 (185)
                      ++..+.+.|+ +|+||||-||+.||.. ..++.+| .++-+...+  .|    .+..-|-+.|.++-+.+++.++++|+.
T Consensus       123 ~~~~~r~~L~~~l~GVG~kTA~~vL~~~g~~~~~~-VDthv~Ri~~rlg~~~~~~k~~t~k~y~~ie~~~~~~a~~~g~~  201 (219)
T 3n0u_A          123 DPFQSREFLVRNAKGIGWKEASHFLRNTGVEDLAI-LDKHVLRLMKRHGLIQEIPKGWSKKRYLYVEEILRKVAEAFGES  201 (219)
T ss_dssp             CHHHHHHHHHHHSTTCCHHHHHHHHHTTTCCSCCC-CCHHHHHHHHHTTSCSSCCSSCCHHHHHHHHHHHHHHHHHHTCC
T ss_pred             CcHHHHHHHHHhCCCCCHHHHHHHHHHcCCCCeee-ecHHHHHHHHHcCCCCcCcCcCCHHHHHHHHHHHHHHHHHHCCC
Confidence            6788999999 9999999999999985 3433333 344444422  23    245778999999999999999999986


Q ss_pred             h
Q 029905          175 F  175 (185)
Q Consensus       175 ~  175 (185)
                      .
T Consensus       202 ~  202 (219)
T 3n0u_A          202 P  202 (219)
T ss_dssp             H
T ss_pred             H
Confidence            5

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

Probab=97.72  E-value=0.00016  Score=59.26  Aligned_cols=73  Identities=25%  Similarity=0.265  Sum_probs=53.9

Q ss_pred             cHHHHHHHhhcccCcChHHHHHHHhh-hCCCCCCcccHHHHHhh--hC---C--CCCCCHHHHHHHHHHHHHHHHhhCch
Q 029905          103 DLTKAVSELTVLKGVGPATASAVLAA-YAPDLAPFMSDEAMGAA--LG---H--SKDYSLKQYLLFADKLQAKAKVSDIF  174 (185)
Q Consensus       103 dv~~al~~L~~LkGVGPATASaiLa~-~~P~~~pFfSDEa~~~~--~g---~--~ikYt~keY~~~~~~l~~~a~~L~~~  174 (185)
                      +...+.+.|++||||||-||++||.. ..++. +...+-+...+  .|   .  +..-|.++|.++...++..++.+|+.
T Consensus       111 ~~~~~~~~L~~lpGIG~kTA~~il~~~~~~~~-~~vD~~v~Ri~~rlg~~~~~~~k~~~~k~y~~~~~~l~~~~~~~~~~  189 (207)
T 3fhg_A          111 DQQLARERLLNIKGIGMQEASHFLRNVGYFDL-AIIDRHIIDFMRRIGAIGETNVKQLSKSLYISFENILKSIASNLNMS  189 (207)
T ss_dssp             CHHHHHHHHTTSTTCCHHHHHHHHHHTTCCSS-CCCCHHHHHHHHHTTSSCCCCCSCCCHHHHHHHHHHHHHHHHHTTSC
T ss_pred             CHHHHHHHHHcCCCcCHHHHHHHHHHhCCCCc-ceecHHHHHHHHHcCCCCccccccCCHHHHHHHHHHHHHHHHHhCCC
Confidence            45678999999999999999999995 55432 22333344322  23   2  35679999999999999999998876


Q ss_pred             hh
Q 029905          175 FF  176 (185)
Q Consensus       175 ~~  176 (185)
                      ..
T Consensus       190 ~~  191 (207)
T 3fhg_A          190 VG  191 (207)
T ss_dssp             HH
T ss_pred             HH
Confidence            43

>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=96.46  E-value=0.0044  Score=51.53  Aligned_cols=56  Identities=21%  Similarity=0.173  Sum_probs=36.3

Q ss_pred             HHHHHHHhhcccCcChHHHHHHHhh--hCCCCCCcccHHHH----HhhhCCCCCCCHHHHHHH
Q 029905          104 LTKAVSELTVLKGVGPATASAVLAA--YAPDLAPFMSDEAM----GAALGHSKDYSLKQYLLF  160 (185)
Q Consensus       104 v~~al~~L~~LkGVGPATASaiLa~--~~P~~~pFfSDEa~----~~~~g~~ikYt~keY~~~  160 (185)
                      ...+++.|++|+||||-||..||..  ..|+.+| ..|=.+    ..+.|.+..=+.++...+
T Consensus       134 ~~e~~~~L~~l~GIG~~TA~~ill~~lg~pd~fp-vdD~~v~r~~~~~~~~~~~~~~~~~~~~  195 (228)
T 3s6i_A          134 NEELIERLTQIKGIGRWTVEMLLIFSLNRDDVMP-ADDLSIRNGYRYLHRLPKIPTKMYVLKH  195 (228)
T ss_dssp             HHHHHHHHTTSTTCCHHHHHHHHHHTSCCSSCCC-TTCHHHHHHHHHHTTCSSCCCHHHHHHH
T ss_pred             HHHHHHHHHhCCCcCHHHHHHHHHHhCCCCCEEe-cccHHHHHHHHHHhCCCCCCCHHHHHHH
Confidence            4667999999999999999999976  5676655 334333    233343333344554443

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

Probab=96.21  E-value=0.0084  Score=49.88  Aligned_cols=37  Identities=27%  Similarity=0.393  Sum_probs=28.9

Q ss_pred             HHHHHHhhcccCcChHHHHHHHhh--hCCCCCCcccHHHH
Q 029905          105 TKAVSELTVLKGVGPATASAVLAA--YAPDLAPFMSDEAM  142 (185)
Q Consensus       105 ~~al~~L~~LkGVGPATASaiLa~--~~P~~~pFfSDEa~  142 (185)
                      ..+++.|++||||||-||.+||..  ..|+.+| ..|=..
T Consensus       134 ~~~~~~L~~lpGIG~kTA~~ill~alg~pd~~p-vdd~~~  172 (233)
T 2h56_A          134 TTVIEKLTAIKGIGQWTAEMFMMFSLGRLDVLS-VGDVGL  172 (233)
T ss_dssp             HHHHHHHHTSTTCCHHHHHHHHHHTTCCSCCCC-TTCHHH
T ss_pred             HHHHHHHHhCCCcCHHHHHHHHHHhCCCCCeee-CchHHH
Confidence            478999999999999999999986  4666655 344444

>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=96.03  E-value=0.0037  Score=49.85  Aligned_cols=72  Identities=17%  Similarity=0.107  Sum_probs=46.0

Q ss_pred             CHHHHHHHHHHHhhCCCCCchhhhHhhhCCHHHHHHHHHH-HH------hhC----ccHHHHHHHhhcccCcChHHHHHH
Q 029905           57 NTTELSKLVRWKLTRGKWRPRLLVFVSSLDDSSVKSASEK-AF------KSL----PDLTKAVSELTVLKGVGPATASAV  125 (185)
Q Consensus        57 tkdEL~~LveWKL~rGkfRP~L~~lV~sN~~~~V~~~t~~-Af------~~l----~dv~~al~~L~~LkGVGPATASai  125 (185)
                      |+++-+.-+-.+|-.  .-|+...+.+.+ ++.|++..+- +|      .+.    ..+....+.|.+|+||||-||.+|
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            567777766666653  348877776655 4455554331 11      110    013345678899999999999999


Q ss_pred             HhhhCC
Q 029905          126 LAAYAP  131 (185)
Q Consensus       126 La~~~P  131 (185)
                      +++..-
T Consensus       121 ~~F~~~  126 (161)
T 4e9f_A          121 RIFCVN  126 (161)
T ss_dssp             HHHTSS
T ss_pred             HHHHCC
Confidence            998654

>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=95.95  E-value=0.05  Score=48.20  Aligned_cols=60  Identities=18%  Similarity=0.219  Sum_probs=40.7

Q ss_pred             cHHHHHHHhhcccCcChHHHHHHHhh--hCCCCCCcccHHH-HH---hhhC--CC----CCCCHHHHHHHHHHH
Q 029905          103 DLTKAVSELTVLKGVGPATASAVLAA--YAPDLAPFMSDEA-MG---AALG--HS----KDYSLKQYLLFADKL  164 (185)
Q Consensus       103 dv~~al~~L~~LkGVGPATASaiLa~--~~P~~~pFfSDEa-~~---~~~g--~~----ikYt~keY~~~~~~l  164 (185)
                      +...+++.|++|+||||-||..||..  ..|+.+|.  |-- ..   ...|  ..    ...+.+.|.++.+.+
T Consensus       247 ~~~~~~~~L~~LpGIGp~TA~~ill~alg~pd~fpv--DthV~Ri~~r~~gl~~~~~~~k~~~~~~~~~l~~~~  318 (360)
T 2xhi_A          247 SYEEAHKALCILPGVGTCVADKICLMALDKPQAVPV--NVHMWHIAQRDYSWHPTTSQAKGPSPQTNKELGNFF  318 (360)
T ss_dssp             CHHHHHHHHTTSTTCCHHHHHHHHHHHSCCTTCCCC--SHHHHHHHHHHHCCCCSSCSCSSCCHHHHHHHHHHH
T ss_pred             CHHHHHHHHHhCCCCCHHHHHHHHHHhCCCCCEEEe--cHHHHHHHHHHhCcccccccccCCChHHHHHHHHHH
Confidence            35689999999999999999999986  57777675  532 22   1224  11    223467787766555

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

Probab=95.94  E-value=0.0049  Score=52.93  Aligned_cols=41  Identities=24%  Similarity=0.310  Sum_probs=33.2

Q ss_pred             cHHHHHHHhhcccCcChHHHHHHHhh--hCCCCCCcccHHHHHhh
Q 029905          103 DLTKAVSELTVLKGVGPATASAVLAA--YAPDLAPFMSDEAMGAA  145 (185)
Q Consensus       103 dv~~al~~L~~LkGVGPATASaiLa~--~~P~~~pFfSDEa~~~~  145 (185)
                      +...+.+.|++||||||-||..||..  ..|+.+|.  |-...-+
T Consensus       205 ~~~~~~~~L~~lpGIG~~TA~~ill~~lg~pd~fpv--D~~v~r~  247 (290)
T 3i0w_A          205 NDNECHEELKKFMGVGPQVADCIMLFSMQKYSAFPV--DTWVKKA  247 (290)
T ss_dssp             CHHHHHHHHTTSTTCCHHHHHHHHHHHHCCTTCCCC--CHHHHHH
T ss_pred             CHHHHHHHHHhCCCcCHHHHHHHHHHhCCCCCccee--cHHHHHH
Confidence            46789999999999999999999965  67888886  7655433

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

Probab=95.80  E-value=0.017  Score=47.86  Aligned_cols=39  Identities=31%  Similarity=0.336  Sum_probs=29.8

Q ss_pred             cHHHHHHHhhcccCcChHHHHHHHhh--hCCCCCCcccHHHH
Q 029905          103 DLTKAVSELTVLKGVGPATASAVLAA--YAPDLAPFMSDEAM  142 (185)
Q Consensus       103 dv~~al~~L~~LkGVGPATASaiLa~--~~P~~~pFfSDEa~  142 (185)
                      +...+++.|++||||||-||..||..  ..|+.+| ..|-..
T Consensus       140 ~~~e~~~~L~~l~GIG~~TA~~ill~~lg~~d~fp-v~D~~v  180 (225)
T 2yg9_A          140 PDELVIAELVQLPGIGRWTAEMFLLFALARPDVFS-SGDLAL  180 (225)
T ss_dssp             CHHHHHHHHHTSTTCCHHHHHHHHHHTSCCSCCCC-TTCHHH
T ss_pred             CHHHHHHHHHcCCCCCHHHHHHHHHHhCCCCCeee-CccHHH
Confidence            45678999999999999999999987  4566655 334433

>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=95.79  E-value=0.0071  Score=50.54  Aligned_cols=38  Identities=21%  Similarity=0.211  Sum_probs=29.4

Q ss_pred             HHHHHHHhhcccCcChHHHHHHHhh--hCCCCCCcccHHHH
Q 029905          104 LTKAVSELTVLKGVGPATASAVLAA--YAPDLAPFMSDEAM  142 (185)
Q Consensus       104 v~~al~~L~~LkGVGPATASaiLa~--~~P~~~pFfSDEa~  142 (185)
                      ...+++.|++||||||-||.+||..  ..|+.+| ..|-..
T Consensus       145 ~~~~~~~L~~l~GIG~~TA~~ill~alg~pd~fp-v~D~~v  184 (232)
T 4b21_A          145 EEELMESLSKIKGVKRWTIEMYSIFTLGRLDIMP-ADDSTL  184 (232)
T ss_dssp             HHHHHHHHTTSTTCCHHHHHHHHHHTSCCSSCCC-TTCHHH
T ss_pred             HHHHHHHHHhCCCcCHHHHHHHHHHhCCCCCeee-CccHHH
Confidence            3478999999999999999999987  4676656 335444

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

Probab=95.77  E-value=0.03  Score=47.93  Aligned_cols=38  Identities=32%  Similarity=0.405  Sum_probs=29.1

Q ss_pred             HHHHHHhhcccCcChHHHHHHHhh-hCCCCCCcccHHHHH
Q 029905          105 TKAVSELTVLKGVGPATASAVLAA-YAPDLAPFMSDEAMG  143 (185)
Q Consensus       105 ~~al~~L~~LkGVGPATASaiLa~-~~P~~~pFfSDEa~~  143 (185)
                      ..+.+.|++||||||-||..||.. ..|+.+| ..|=.+.
T Consensus       206 ~e~~~~L~~lpGIG~~TA~~ill~~lg~d~fp-vdD~~~r  244 (295)
T 2jhn_A          206 EEAYEYLTSFKGIGRWTAELVLSIALGKNVFP-ADDLGVR  244 (295)
T ss_dssp             HHHHHHHHTSTTCCHHHHHHHHHHTTCCCCCC-TTCHHHH
T ss_pred             HHHHHHHhcCCCcCHHHHHHHHHHccCCCccc-chHHHHH
Confidence            678999999999999999999985 2276655 3444443

>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=95.69  E-value=0.019  Score=48.73  Aligned_cols=43  Identities=23%  Similarity=0.260  Sum_probs=32.9

Q ss_pred             cHHHHHHHhhcccCcChHHHHHHHhh--hCCCCCCcccHHHHHhhh
Q 029905          103 DLTKAVSELTVLKGVGPATASAVLAA--YAPDLAPFMSDEAMGAAL  146 (185)
Q Consensus       103 dv~~al~~L~~LkGVGPATASaiLa~--~~P~~~pFfSDEa~~~~~  146 (185)
                      +...+++.|++||||||-||..||..  ..|+.+| ..|-.+....
T Consensus       201 ~~~~~~~~L~~lpGIG~~TA~~ill~~lg~~d~~p-vdd~~~r~~l  245 (282)
T 1mpg_A          201 DVEQAMKTLQTFPGIGRWTANYFALRGWQAKDVFL-PDDYLIKQRF  245 (282)
T ss_dssp             CHHHHHHHHTTSTTCCHHHHHHHHHHHSCCSSCCC-TTCHHHHHHS
T ss_pred             CHHHHHHHHhcCCCcCHHHHHHHHHHhCCCCCcCc-cccHHHHHHh
Confidence            67789999999999999999999986  4565544 4555555444

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

Probab=94.82  E-value=0.011  Score=48.65  Aligned_cols=27  Identities=26%  Similarity=0.233  Sum_probs=23.3

Q ss_pred             HHHHHHHhhcccCcChHHHHHHHhhhC
Q 029905          104 LTKAVSELTVLKGVGPATASAVLAAYA  130 (185)
Q Consensus       104 v~~al~~L~~LkGVGPATASaiLa~~~  130 (185)
                      ...+.+.|++||||||-||.+||....
T Consensus       116 ~~~~~~~L~~lpGIG~kTA~~il~~a~  142 (218)
T 1pu6_A          116 QEVTREWLLDQKGIGKESADAILCYAC  142 (218)
T ss_dssp             HHCCHHHHHTSTTCCHHHHHHHHHHTT
T ss_pred             chHHHHHHHcCCCcCHHHHHHHHHHHC
Confidence            455788999999999999999999743

>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=94.74  E-value=0.015  Score=47.82  Aligned_cols=37  Identities=27%  Similarity=0.307  Sum_probs=26.7

Q ss_pred             HHHHHhhcccCcChHHHHHHHhhhCCCCCCcccHHHHH
Q 029905          106 KAVSELTVLKGVGPATASAVLAAYAPDLAPFMSDEAMG  143 (185)
Q Consensus       106 ~al~~L~~LkGVGPATASaiLa~~~P~~~pFfSDEa~~  143 (185)
                      .+++.|.+|+||||-||.+||....-.. -|..|--..
T Consensus       106 ~~~~~L~~lpGIG~~TA~~il~~a~~~~-~~~vD~~v~  142 (225)
T 1kg2_A          106 ETFEEVAALPGVGRSTAGAILSLSLGKH-FPILDGNVK  142 (225)
T ss_dssp             CSHHHHHTSTTCCHHHHHHHHHHHHCCS-CCCCCHHHH
T ss_pred             HHHHHHhcCCCCcHHHHHHHHHHhCCCC-cceeCHHHH
Confidence            3688999999999999999998743222 234665443

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

Probab=94.68  E-value=0.028  Score=45.72  Aligned_cols=25  Identities=36%  Similarity=0.457  Sum_probs=21.9

Q ss_pred             HHHHHHhhcccCcChHHHHHHHhhh
Q 029905          105 TKAVSELTVLKGVGPATASAVLAAY  129 (185)
Q Consensus       105 ~~al~~L~~LkGVGPATASaiLa~~  129 (185)
                      ..+++.|++||||||-||.+||...
T Consensus       105 ~~~~~~L~~l~GIG~~tA~~il~~~  129 (211)
T 2abk_A          105 PEDRAALEALPGVGRKTANVVLNTA  129 (211)
T ss_dssp             CSCHHHHHHSTTCCHHHHHHHHHHH
T ss_pred             hHHHHHHHhCCCCChHHHHHHHHHH
Confidence            3467889999999999999999974

>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=94.31  E-value=0.045  Score=44.93  Aligned_cols=25  Identities=28%  Similarity=0.319  Sum_probs=21.9

Q ss_pred             HHHHHhhcccCcChHHHHHHHhhhC
Q 029905          106 KAVSELTVLKGVGPATASAVLAAYA  130 (185)
Q Consensus       106 ~al~~L~~LkGVGPATASaiLa~~~  130 (185)
                      .+++.|.+|+||||-||.+||...-
T Consensus       112 ~~~~~L~~lpGIG~~TA~~il~~~~  136 (221)
T 1kea_A          112 RNRKAILDLPGVGKYTCAAVMCLAF  136 (221)
T ss_dssp             SCHHHHHTSTTCCHHHHHHHHHHTT
T ss_pred             HHHHHHHhCCCCcHHHHHHHHHHhc
Confidence            4578899999999999999999753

>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=94.23  E-value=0.042  Score=45.43  Aligned_cols=24  Identities=38%  Similarity=0.487  Sum_probs=21.5

Q ss_pred             HHHHHhhcccCcChHHHHHHHhhh
Q 029905          106 KAVSELTVLKGVGPATASAVLAAY  129 (185)
Q Consensus       106 ~al~~L~~LkGVGPATASaiLa~~  129 (185)
                      .+++.|.+|+||||-||.+||...
T Consensus       110 ~~~~~L~~lpGIG~~TA~~il~~a  133 (226)
T 1orn_A          110 RDRDELMKLPGVGRKTANVVVSVA  133 (226)
T ss_dssp             SCHHHHTTSTTCCHHHHHHHHHHH
T ss_pred             HHHHHHHHCCCccHHHHHHHHHHH
Confidence            468899999999999999999873

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

Probab=93.68  E-value=0.17  Score=44.18  Aligned_cols=36  Identities=36%  Similarity=0.425  Sum_probs=26.4

Q ss_pred             HHHHHhhcccCcChHHHHHHHhhhCCCCCCcccHHHH
Q 029905          106 KAVSELTVLKGVGPATASAVLAAYAPDLAPFMSDEAM  142 (185)
Q Consensus       106 ~al~~L~~LkGVGPATASaiLa~~~P~~~pFfSDEa~  142 (185)
                      .+++.|.+|+||||-||.+||+...-..++ .-|--.
T Consensus       115 ~~~~~L~~l~GIG~~tA~~il~~~~~~~~~-~vD~~v  150 (369)
T 3fsp_A          115 DDPDEFSRLKGVGPYTVGAVLSLAYGVPEP-AVDGNV  150 (369)
T ss_dssp             CSHHHHHTSTTCCHHHHHHHHHHHHCCCCC-CCCHHH
T ss_pred             hHHHHHhcCCCcCHHHHHHHHHHHCCCCcc-cccHHH
Confidence            468889999999999999999985433233 444433

>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=93.42  E-value=0.025  Score=44.45  Aligned_cols=37  Identities=22%  Similarity=0.341  Sum_probs=31.3

Q ss_pred             HHHHHhhcccCcChHHHHHHHhhhCCCCCCcccHHHHHhhhC
Q 029905          106 KAVSELTVLKGVGPATASAVLAAYAPDLAPFMSDEAMGAALG  147 (185)
Q Consensus       106 ~al~~L~~LkGVGPATASaiLa~~~P~~~pFfSDEa~~~~~g  147 (185)
                      +..+.|++|+||||++|.+|.     ++.||-|=|=+.-+.|
T Consensus        60 A~~~eL~~LpGiGp~~A~~II-----~~GpF~svedL~~V~G   96 (134)
T 1s5l_U           60 TNIAAFIQYRGLYPTLAKLIV-----KNAPYESVEDVLNIPG   96 (134)
T ss_dssp             SCGGGGGGSTTCTHHHHHHHH-----HTCCCSSGGGGGGCTT
T ss_pred             cCHHHHHHCCCCCHHHHHHHH-----HcCCCCCHHHHHhCCC
Confidence            347789999999999999999     3568988888877877

>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=93.00  E-value=0.036  Score=40.98  Aligned_cols=37  Identities=22%  Similarity=0.333  Sum_probs=31.1

Q ss_pred             HHHHHhhcccCcChHHHHHHHhhhCCCCCCcccHHHHHhhhC
Q 029905          106 KAVSELTVLKGVGPATASAVLAAYAPDLAPFMSDEAMGAALG  147 (185)
Q Consensus       106 ~al~~L~~LkGVGPATASaiLa~~~P~~~pFfSDEa~~~~~g  147 (185)
                      +..+.|+.|+||||++|..|..     +-||-|-|-+.-+.|
T Consensus        23 As~~eL~~lpGIG~~~A~~IV~-----~GpF~s~edL~~V~G   59 (97)
T 3arc_U           23 TNIAAFIQYRGLYPTLAKLIVK-----NAPYESVEDVLNIPG   59 (97)
T ss_dssp             SCGGGGGGSTTCTTHHHHHHHH-----HCCCSSGGGGGGCTT
T ss_pred             CCHHHHhHCCCCCHHHHHHHHH-----cCCCCCHHHHHhccC
Confidence            3467899999999999999999     348888888777766

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

Probab=92.43  E-value=0.12  Score=44.57  Aligned_cols=36  Identities=25%  Similarity=0.232  Sum_probs=26.5

Q ss_pred             HHHHhhc-ccCcChHHHHHHHhhhCCCCCCcccHHHHH
Q 029905          107 AVSELTV-LKGVGPATASAVLAAYAPDLAPFMSDEAMG  143 (185)
Q Consensus       107 al~~L~~-LkGVGPATASaiLa~~~P~~~pFfSDEa~~  143 (185)
                      .++.|.+ |+||||-||.+||....-.. .|..|--..
T Consensus       126 ~~~~Ll~~LpGIG~kTA~~iL~~a~g~p-~~~VDt~V~  162 (287)
T 3n5n_X          126 TAETLQQLLPGVGRYTAGAIASIAFGQA-TGVVDGNVA  162 (287)
T ss_dssp             SHHHHHHHSTTCCHHHHHHHHHHHSCCC-CCCCCHHHH
T ss_pred             HHHHHHHHcCCCCHHHHHHHHHHhcCCC-CccccHHHH
Confidence            5788887 99999999999999854322 344565443

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

Probab=91.59  E-value=0.13  Score=35.11  Aligned_cols=36  Identities=28%  Similarity=0.522  Sum_probs=28.0

Q ss_pred             HHHHhhcccCcChHHHHHHHhhhCCCCCCcccHHHHHhhhC
Q 029905          107 AVSELTVLKGVGPATASAVLAAYAPDLAPFMSDEAMGAALG  147 (185)
Q Consensus       107 al~~L~~LkGVGPATASaiLa~~~P~~~pFfSDEa~~~~~g  147 (185)
                      ....|..++||||.+|..|+.-.     +|-+-+-+..+.|
T Consensus        25 ~~~~L~~ipGIG~~~A~~Il~~r-----~~~s~~eL~~v~G   60 (75)
T 2duy_A           25 SLEELMALPGIGPVLARRIVEGR-----PYARVEDLLKVKG   60 (75)
T ss_dssp             CHHHHTTSTTCCHHHHHHHHHTC-----CCSSGGGGGGSTT
T ss_pred             CHHHHHhCCCCCHHHHHHHHHHc-----ccCCHHHHHhCCC
Confidence            35678899999999999999964     6666666665655

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

Probab=89.87  E-value=0.065  Score=44.74  Aligned_cols=63  Identities=22%  Similarity=0.328  Sum_probs=41.3

Q ss_pred             hhhHhhhCCHHHHHHHHHHHHhhCccHHHHHHHhhcccCcChHHHHHHHhhhCCCCCCcccHHHHHh-hhC
Q 029905           78 LLVFVSSLDDSSVKSASEKAFKSLPDLTKAVSELTVLKGVGPATASAVLAAYAPDLAPFMSDEAMGA-ALG  147 (185)
Q Consensus        78 L~~lV~sN~~~~V~~~t~~Af~~l~dv~~al~~L~~LkGVGPATASaiLa~~~P~~~pFfSDEa~~~-~~g  147 (185)
                      +.+.|+.|....|. .    |+....+.+.+..|..|+||||++|-+|+.--.-  -||-|=|-+.- +.|
T Consensus       106 v~~iV~~~E~~fv~-f----~n~a~pITA~~~eL~~LpGIG~k~A~~IIeyRe~--G~F~s~eDL~~RV~G  169 (205)
T 2i5h_A          106 IEHIIKQDEKKYVD-F----FNKADSITTRMHQLELLPGVGKKMMWAIIEERKK--RPFESFEDIAQRVKG  169 (205)
T ss_dssp             HHHHHHTTHHHHHH-H----HC--CCBCSSSBGGGGSTTCCHHHHHHHHHHHHH--SCCCSHHHHHHHSTT
T ss_pred             HHHHHHhchhhhhh-h----ccccCCccCCHHHHhcCCCcCHHHHHHHHHHHhc--CCCCCHHHHHHhcCC
Confidence            34445555444443 2    3322334666788999999999999999998653  59999666643 665

>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=89.20  E-value=0.65  Score=32.67  Aligned_cols=42  Identities=19%  Similarity=0.309  Sum_probs=26.3

Q ss_pred             hhCCHHHHHHHHHHHHhhCccHHHHHHHhhcccCcChHHHHHHHhhh
Q 029905           83 SSLDDSSVKSASEKAFKSLPDLTKAVSELTVLKGVGPATASAVLAAY  129 (185)
Q Consensus        83 ~sN~~~~V~~~t~~Af~~l~dv~~al~~L~~LkGVGPATASaiLa~~  129 (185)
                      +.++++.++.-.+.-+     ....+..|+.++||||.||-.|+..+
T Consensus        11 ~~~~~~~~~~~~~~~~-----~~~~~~~L~~IpgIG~~~A~~Ll~~f   52 (91)
T 2a1j_B           11 SQDPADLLMEKLEQDF-----VSRVTECLTTVKSVNKTDSQTLLTTF   52 (91)
T ss_dssp             --CCSHHHHHHHHHHH-----HHHHHHHHTTSTTCCHHHHHHHHHHH
T ss_pred             ccCCHHHHhhhccCCH-----HHHHHHHHHcCCCCCHHHHHHHHHHC
Confidence            3455665555544433     33456677788888888888888764

>1x2i_A HEF helicase/nuclease; alpha helix, helix-hairpin-helix DNA binding domain, homodimer, hydrolase; 1.45A {Pyrococcus furiosus} SCOP: a.60.2.5

Probab=88.84  E-value=0.28  Score=32.62  Aligned_cols=23  Identities=26%  Similarity=0.442  Sum_probs=19.6

Q ss_pred             HHHhhcccCcChHHHHHHHhhhC
Q 029905          108 VSELTVLKGVGPATASAVLAAYA  130 (185)
Q Consensus       108 l~~L~~LkGVGPATASaiLa~~~  130 (185)
                      .+.|++++||||.+|..|.+...
T Consensus        45 ~~~L~~i~Gig~~~a~~i~~~~~   67 (75)
T 1x2i_A           45 VAELMKVEGIGEKIAKEIRRVIT   67 (75)
T ss_dssp             HHHHTTSTTCCHHHHHHHHHHHH
T ss_pred             HHHHhcCCCCCHHHHHHHHHHHh
Confidence            56788999999999999988764

>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=87.30  E-value=0.21  Score=35.90  Aligned_cols=39  Identities=23%  Similarity=0.394  Sum_probs=29.0

Q ss_pred             HHHhhcccCcChHHHHHHHhhhCCCCCCcccHHHHHhhhC
Q 029905          108 VSELTVLKGVGPATASAVLAAYAPDLAPFMSDEAMGAALG  147 (185)
Q Consensus       108 l~~L~~LkGVGPATASaiLa~~~P~~~pFfSDEa~~~~~g  147 (185)
                      ...|..++||||.+|..|+...... -+|-+-+-+..+.|
T Consensus        39 ~~~L~~ipGIG~~~A~~Il~~r~~~-g~f~s~edL~~v~G   77 (98)
T 2edu_A           39 ARDLRSLQRIGPKKAQLIVGWRELH-GPFSQVEDLERVEG   77 (98)
T ss_dssp             HHHHHHSTTCCHHHHHHHHHHHHHH-CCCSSGGGGGGSTT
T ss_pred             HHHHHHCCCCCHHHHHHHHHHHHhc-CCcCCHHHHHhCCC
Confidence            5578899999999999999986432 26765555655655

>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=87.08  E-value=0.45  Score=32.55  Aligned_cols=22  Identities=18%  Similarity=0.365  Sum_probs=15.8

Q ss_pred             HHHhhcccCcChHHHHHHHhhh
Q 029905          108 VSELTVLKGVGPATASAVLAAY  129 (185)
Q Consensus       108 l~~L~~LkGVGPATASaiLa~~  129 (185)
                      .+.|++++||||.+|..|.+..
T Consensus        55 ~eeL~~i~GIG~~~a~~I~~~~   76 (78)
T 1kft_A           55 VEEIAKVPGISQGLAEKIFWSL   76 (78)
T ss_dssp             HHHHTTSSSTTSHHHHHHHHHH
T ss_pred             HHHHHHCCCCCHHHHHHHHHHH
Confidence            5567777778877777776654

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

Probab=86.61  E-value=0.29  Score=40.65  Aligned_cols=22  Identities=23%  Similarity=0.371  Sum_probs=12.4

Q ss_pred             HHhhcccCcChHHHHHHHhhhC
Q 029905          109 SELTVLKGVGPATASAVLAAYA  130 (185)
Q Consensus       109 ~~L~~LkGVGPATASaiLa~~~  130 (185)
                      +.|++++||||-||--|..-+.
T Consensus       123 ~~L~~vpGIG~KtA~rIi~elk  144 (212)
T 2ztd_A          123 AALTRVPGIGKRGAERMVLELR  144 (212)
T ss_dssp             HHHHTSTTCCHHHHHHHHHHHT
T ss_pred             HHHhhCCCCCHHHHHHHHHHHH
Confidence            4556666666666665554443

>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=84.49  E-value=0.53  Score=38.26  Aligned_cols=20  Identities=45%  Similarity=0.610  Sum_probs=9.9

Q ss_pred             HhhcccCcChHHHHHHHhhh
Q 029905          110 ELTVLKGVGPATASAVLAAY  129 (185)
Q Consensus       110 ~L~~LkGVGPATASaiLa~~  129 (185)
                      .|.+++||||.||-+||+.+
T Consensus        73 ~L~~v~GIGpk~A~~iL~~f   92 (191)
T 1ixr_A           73 LLLSVSGVGPKVALALLSAL   92 (191)
T ss_dssp             HHHSSSCCCHHHHHHHHHHS
T ss_pred             HHhcCCCcCHHHHHHHHHhC
Confidence            34445555555555555443

>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=81.92  E-value=0.73  Score=37.73  Aligned_cols=27  Identities=33%  Similarity=0.480  Sum_probs=19.4

Q ss_pred             HHHHHHhhcccCcChHHHHHHHhhhCC
Q 029905          105 TKAVSELTVLKGVGPATASAVLAAYAP  131 (185)
Q Consensus       105 ~~al~~L~~LkGVGPATASaiLa~~~P  131 (185)
                      +.-+..|.+++||||.||-+||+.+.|
T Consensus        69 k~~f~~L~~V~GIGpk~A~~iL~~f~~   95 (203)
T 1cuk_A           69 RTLFKELIKTNGVGPKLALAILSGMSA   95 (203)
T ss_dssp             HHHHHHHHHSSSCCHHHHHHHHHHSCH
T ss_pred             HHHHHHHhcCCCcCHHHHHHHHhhCCh
Confidence            334556777888888888888887555

>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=81.86  E-value=0.48  Score=31.74  Aligned_cols=40  Identities=15%  Similarity=0.204  Sum_probs=25.8

Q ss_pred             HHHhhcccCcChHHHHHHHhhhC-CCCCCcccHHHHHhhhC
Q 029905          108 VSELTVLKGVGPATASAVLAAYA-PDLAPFMSDEAMGAALG  147 (185)
Q Consensus       108 l~~L~~LkGVGPATASaiLa~~~-P~~~pFfSDEa~~~~~g  147 (185)
                      ...|..++||||.+.-.+|.-+. -+.+.=.|-|-+..+.|
T Consensus         3 ~s~L~~IpGIG~kr~~~LL~~Fgs~~~i~~As~eeL~~vig   43 (63)
T 2a1j_A            3 QDFLLKMPGVNAKNCRSLMHHVKNIAELAALSQDELTSILG   43 (63)
T ss_dssp             CHHHHTSTTCCHHHHHHHHHHCSSHHHHHTCCHHHHHHHHS
T ss_pred             HhHHHcCCCCCHHHHHHHHHHcCCHHHHHHCCHHHHHHHcC
Confidence            46788999999999999998532 11223344444444444

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

Probab=81.71  E-value=2.5  Score=33.27  Aligned_cols=50  Identities=24%  Similarity=0.303  Sum_probs=35.3

Q ss_pred             HHHHHHhhcccCcChHHHHHHHhhh--CCCC-CCcccHHHHHhh---hCCCCCCCH
Q 029905          105 TKAVSELTVLKGVGPATASAVLAAY--APDL-APFMSDEAMGAA---LGHSKDYSL  154 (185)
Q Consensus       105 ~~al~~L~~LkGVGPATASaiLa~~--~P~~-~pFfSDEa~~~~---~g~~ikYt~  154 (185)
                      +...-+||.++|||+.||-.|+...  +|+. +=-.+||-...+   ...+.+|.+
T Consensus        26 k~v~~ALt~I~GIG~~~A~~I~~~~gid~~~r~g~Lt~~ei~~l~~~i~~~~~~~i   81 (146)
T 3u5c_S           26 IKIVYALTTIKGVGRRYSNLVCKKADVDLHKRAGELTQEELERIVQIMQNPTHYKI   81 (146)
T ss_dssp             SCTTTTGGGSTTCCHHHHHHHHHHHTCCTTSCSSSCCHHHHHHHHHHHTCTTTTTC
T ss_pred             cchHhhHhhhcCCCHHHHHHHHHHcCCCCCceeccCCHHHHHHHHHHHHhhcccCc
Confidence            3445578999999999999999984  5643 666788766533   345556654

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

Probab=81.49  E-value=1.2  Score=30.97  Aligned_cols=24  Identities=21%  Similarity=0.414  Sum_probs=19.4

Q ss_pred             HHHHHhhcccCcChHHHHHHHhhh
Q 029905          106 KAVSELTVLKGVGPATASAVLAAY  129 (185)
Q Consensus       106 ~al~~L~~LkGVGPATASaiLa~~  129 (185)
                      .....|..++||||.||-.|+..+
T Consensus        16 ~~~~~L~~IpgIG~~~A~~Ll~~f   39 (89)
T 1z00_A           16 RVTECLTTVKSVNKTDSQTLLTTF   39 (89)
T ss_dssp             HHHHHHTTSSSCCHHHHHHHHHHT
T ss_pred             HHHHHHHcCCCCCHHHHHHHHHHC
Confidence            346678889999999999998864

>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=80.92  E-value=1.4  Score=29.09  Aligned_cols=25  Identities=16%  Similarity=0.145  Sum_probs=20.8

Q ss_pred             HHHHHHhhcccCcChHHHHHHHhhh
Q 029905          105 TKAVSELTVLKGVGPATASAVLAAY  129 (185)
Q Consensus       105 ~~al~~L~~LkGVGPATASaiLa~~  129 (185)
                      ......|+.++||||.+|..|+..+
T Consensus        10 ~~~~~~L~~i~giG~~~a~~Ll~~f   34 (75)
T 1x2i_A           10 ERQRLIVEGLPHVSATLARRLLKHF   34 (75)
T ss_dssp             HHHHHHHTTSTTCCHHHHHHHHHHH
T ss_pred             HHHHHHHcCCCCCCHHHHHHHHHHc
Confidence            3345678999999999999999864

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

Probab=80.57  E-value=0.81  Score=31.90  Aligned_cols=23  Identities=22%  Similarity=0.466  Sum_probs=20.5

Q ss_pred             HHHhhcccCcChHHHHHHHhhhC
Q 029905          108 VSELTVLKGVGPATASAVLAAYA  130 (185)
Q Consensus       108 l~~L~~LkGVGPATASaiLa~~~  130 (185)
                      .+.|++++|||+.+|..|.+...
T Consensus        50 ~~eL~~i~GIG~~~a~~I~~~l~   72 (89)
T 1z00_A           50 REDLALCPGLGPQKARRLFDVLH   72 (89)
T ss_dssp             HHHHHTSTTCCHHHHHHHHHHHH
T ss_pred             HHHHHhCCCCCHHHHHHHHHHHH
Confidence            56789999999999999999864

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

No hit with e-value below 0.005

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	185
d2noha1	190	8-oxoguanine glycosylase {Human (Homo sapiens) [Ta	97.15
d1keaa_	217	Thymine-DNA glycosylase {Archaeon Methanobacterium	96.55
d1rrqa1	221	Catalytic domain of MutY {Bacillus stearothermophi	96.29
d1orna_	214	Endonuclease III {Escherichia coli [TaxId: 562]}	96.27
d1mpga1	183	3-Methyladenine DNA glycosylase II (gene alkA or a	96.17
d1kg2a_	224	Catalytic domain of MutY {Escherichia coli [TaxId:	96.04
d2abka_	211	Endonuclease III {Escherichia coli [TaxId: 562]}	95.76
d1pu6a_	217	3-Methyladenine DNA glycosylase III (MagIII) {Heli	94.95
d2fmpa2	57	DNA polymerase beta {Human (Homo sapiens) [TaxId:	94.52
d1ngna_	144	Mismatch-specific thymine glycosylase domain of th	94.34
d1cuka2	78	DNA helicase RuvA subunit, middle domain {Escheric	92.54
d2axtu1	98	Photosystem II 12 kDa extrinsic protein PsbU {Ther	92.51
d1pzna1	61	DNA repair protein Rad51, N-terminal domain {Archa	92.15
d1ixra1	73	DNA helicase RuvA subunit, middle domain {Thermus	92.07
d1jmsa3	60	Terminal deoxynucleotidyl transferase {Mouse (Mus	91.94
d1bvsa2	71	DNA helicase RuvA subunit, middle domain {Mycobact	91.94
d2a1jb1	78	DNA excision repair protein ERCC-1 {Human (Homo sa	91.56
d2bcqa2	57	DNA polymerase lambda {Human (Homo sapiens) [TaxId	90.76
d1cuka2	78	DNA helicase RuvA subunit, middle domain {Escheric	90.44
d1ixra1	73	DNA helicase RuvA subunit, middle domain {Thermus	89.95
d2i1qa1	60	DNA repair protein Rad51, N-terminal domain {Archa	89.63
d2bgwa1	70	DNA repair endonuclease XPF {Aeropyrum pernix [Tax	88.7
d2a1jb1	78	DNA excision repair protein ERCC-1 {Human (Homo sa	88.12
d1kfta_	56	Excinuclease UvrC C-terminal domain {Escherichia c	86.44
d1bvsa2	71	DNA helicase RuvA subunit, middle domain {Mycobact	86.2
d2duya1	65	Uncharacterized protein TTHA1967 {Thermus thermoph	86.02
d1kfta_	56	Excinuclease UvrC C-terminal domain {Escherichia c	85.96
d2a1ja1	62	DNA repair endonuclease XPF {Human (Homo sapiens)	85.89
d2bgwa1	70	DNA repair endonuclease XPF {Aeropyrum pernix [Tax	85.73
d2fmpa1	82	DNA polymerase beta, N-terminal (8 kD)-domain {Hum	85.28
d2bcqa1	76	DNA polymerase lambda {Human (Homo sapiens) [TaxId	83.62
d2i1qa1	60	DNA repair protein Rad51, N-terminal domain {Archa	83.02
d1x2ia1	68	ATP-dependent RNA helicase PF2015 {Pyrococcus furi	82.12
d1x2ia1	68	ATP-dependent RNA helicase PF2015 {Pyrococcus furi	80.6

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

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

Probab=97.15  E-value=0.00084  Score=52.01  Aligned_cols=63  Identities=19%  Similarity=0.235  Sum_probs=43.1

Q ss_pred             cHHHHHHHhhcccCcChHHHHHHHhh--hCCCCCCcccHHHHHhh---hC------CCCCCCHHHHHHHHHHHHH
Q 029905          103 DLTKAVSELTVLKGVGPATASAVLAA--YAPDLAPFMSDEAMGAA---LG------HSKDYSLKQYLLFADKLQA  166 (185)
Q Consensus       103 dv~~al~~L~~LkGVGPATASaiLa~--~~P~~~pFfSDEa~~~~---~g------~~ikYt~keY~~~~~~l~~  166 (185)
                      +...+++.|++||||||-||..||..  ..|+.+|. ..-+...+   .|      ...+-+.+.|.++.+..++
T Consensus        97 ~~~~~~~~L~~l~GIG~wTA~~il~~~~~~~d~fpv-D~~v~R~~~r~~~~~~~~~~~k~~~~~~~~~~~~~~~~  170 (190)
T d2noha1          97 SYEEAHKALCILPGVGTQVADCICLMALDKPQAVPV-DVHMWHIAQRDYSWHPTTSQAKGPSPQTNKELGNFFRS  170 (190)
T ss_dssp             CHHHHHHHHTTSTTCCHHHHHHHHHHHSCCTTCCCC-CHHHHHHHHHHHCCCCSSSSCSSSCHHHHHHHHHHHHH
T ss_pred             CcHHHHHHHHHcCCchHHHHHHHHHHHcCCCCeEee-cHHHHHHHHHHhcccCcchhhccccHHHHHHHHHHHHH
Confidence            56788999999999999999998876  57777774 33333322   23      1234567777666655544

>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=96.55  E-value=0.0032  Score=49.99  Aligned_cols=84  Identities=17%  Similarity=0.133  Sum_probs=51.9

Q ss_pred             CHHHHHHHHHHHhhCCCCCchhhhHhhhCCHHHHHHHHH-------HHHh------hCc-----cHHHHHHHhhcccCcC
Q 029905           57 NTTELSKLVRWKLTRGKWRPRLLVFVSSLDDSSVKSASE-------KAFK------SLP-----DLTKAVSELTVLKGVG  118 (185)
Q Consensus        57 tkdEL~~LveWKL~rGkfRP~L~~lV~sN~~~~V~~~t~-------~Af~------~l~-----dv~~al~~L~~LkGVG  118 (185)
                      |+++-+.-+--+|. .+| |+...+.+.+ +++|+++.+       +|-.      .+-     .+....+.|.+|+|||
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            57777766666663 223 7888887775 555665433       2211      000     2333578899999999


Q ss_pred             hHHHHHHHhhhCCCCCCcccHHHHH
Q 029905          119 PATASAVLAAYAPDLAPFMSDEAMG  143 (185)
Q Consensus       119 PATASaiLa~~~P~~~pFfSDEa~~  143 (185)
                      |-||++||+...-..++...+-+..
T Consensus       123 ~kTA~~il~~~~~~~~~~vD~~v~R  147 (217)
T d1keaa_         123 KYTCAAVMCLAFGKKAAMVDANFVR  147 (217)
T ss_dssp             HHHHHHHHHHTTCCCCCCCCHHHHH
T ss_pred             hhhhHHHHHHhcCCcccccccchhh
Confidence            9999999999654443334444443

>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=96.29  E-value=0.0024  Score=50.69  Aligned_cols=37  Identities=30%  Similarity=0.290  Sum_probs=27.5

Q ss_pred             HHHHHHhhcccCcChHHHHHHHhhhCCCCCCcccHHHH
Q 029905          105 TKAVSELTVLKGVGPATASAVLAAYAPDLAPFMSDEAM  142 (185)
Q Consensus       105 ~~al~~L~~LkGVGPATASaiLa~~~P~~~pFfSDEa~  142 (185)
                      ....+.|.+|+||||-||++||+...-..+ |.-|--.
T Consensus       103 p~~~~~Ll~LpGIG~kTA~~il~~a~~~p~-~~VDt~v  139 (221)
T d1rrqa1         103 PDDPDEFSRLKGVGPYTVGAVLSLAYGVPE-PAVNGNV  139 (221)
T ss_dssp             CCSHHHHHTSTTCCHHHHHHHHHHHTCCCC-CCCCHHH
T ss_pred             chHHHHHHHHHHhhhHHHHHHHHHHhcCcc-cccCccH
Confidence            335678999999999999999999765443 3444433

>d1orna_ a.96.1.1 (A:) Endonuclease III {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA-glycosylase
superfamily: DNA-glycosylase
family: Endonuclease III
domain: Endonuclease III
species: Escherichia coli [TaxId: 562]

Probab=96.27  E-value=0.0061  Score=48.04  Aligned_cols=25  Identities=36%  Similarity=0.380  Sum_probs=21.8

Q ss_pred             HHHHhhcccCcChHHHHHHHhhhCC
Q 029905          107 AVSELTVLKGVGPATASAVLAAYAP  131 (185)
Q Consensus       107 al~~L~~LkGVGPATASaiLa~~~P  131 (185)
                      ..+.|.+|+||||-||++||+...-
T Consensus       108 ~~~~L~~LpGVG~kTA~~il~~a~~  132 (214)
T d1orna_         108 DRDELMKLPGVGRKTANVVVSVAFG  132 (214)
T ss_dssp             CHHHHTTSTTCCHHHHHHHHHHHHC
T ss_pred             CHHHHHhCcCcccchHHHHHHHHhc
Confidence            4678999999999999999998643

>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=96.17  E-value=0.0017  Score=50.21  Aligned_cols=40  Identities=25%  Similarity=0.269  Sum_probs=32.0

Q ss_pred             cHHHHHHHhhcccCcChHHHHHHHhh--hCCCCCCcccHHHHH
Q 029905          103 DLTKAVSELTVLKGVGPATASAVLAA--YAPDLAPFMSDEAMG  143 (185)
Q Consensus       103 dv~~al~~L~~LkGVGPATASaiLa~--~~P~~~pFfSDEa~~  143 (185)
                      +...+++.|++||||||=||..||-.  ..|+.+| ..|=...
T Consensus       102 ~~~e~~~~L~~l~GIGpwTAd~illf~lg~~dvfP-~~D~~lr  143 (183)
T d1mpga1         102 DVEQAMKTLQTFPGIGRWTANYFALRGWQAKDVFL-PDDYLIK  143 (183)
T ss_dssp             CHHHHHHHHTTSTTCCHHHHHHHHHHHSCCSSCCC-TTCHHHH
T ss_pred             cHHHHHHHHHHhhcccHHHHHHHHHhhCCCCCccc-cchHHHH
Confidence            67789999999999999999999865  5788777 3454443

>d1kg2a_ a.96.1.2 (A:) Catalytic domain of MutY {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA-glycosylase
superfamily: DNA-glycosylase
family: Mismatch glycosylase
domain: Catalytic domain of MutY
species: Escherichia coli [TaxId: 562]

Probab=96.04  E-value=0.0032  Score=50.00  Aligned_cols=72  Identities=15%  Similarity=0.164  Sum_probs=43.9

Q ss_pred             CHHHHHHHHHHHhhCCCCCchhhhHhhhCCHHHHHHHHHHH-H-----------hhC-----ccHHHHHHHhhcccCcCh
Q 029905           57 NTTELSKLVRWKLTRGKWRPRLLVFVSSLDDSSVKSASEKA-F-----------KSL-----PDLTKAVSELTVLKGVGP  119 (185)
Q Consensus        57 tkdEL~~LveWKL~rGkfRP~L~~lV~sN~~~~V~~~t~~A-f-----------~~l-----~dv~~al~~L~~LkGVGP  119 (185)
                      |++|-+.-+-=+|- .+ -|+...+.+.+ ++.++++.+-+ |           +.+     .++....+.|.+|+||||
T Consensus        43 T~~~~v~~~~~~l~-~~-~pt~~~la~a~-~~~l~~~i~~~g~~~ka~~l~~~~~~i~~~~~g~vp~~~~~L~~LpGVG~  119 (224)
T d1kg2a_          43 TQVATVIPYFERFM-AR-FPTVTDLANAP-LDEVLHLWTGLGYYARARNLHKAAQQVATLHGGKFPETFEEVAALPGVGR  119 (224)
T ss_dssp             SCHHHHHHHHHHHH-HH-CSSHHHHHHSC-HHHHHHHHTTSCCTHHHHHHHHHHHHHHHHSTTSCCCSHHHHHTSTTCCH
T ss_pred             CcHHHHHHHHHHHH-HH-hccHHHHHHhh-HHHHHhHhhhhhHHHHHHHHHHhhhhhhhhccCCcchHHHHHHHHHhhhh
Confidence            45665554433332 12 37888887775 55666655432 1           000     023334678999999999


Q ss_pred             HHHHHHHhhhCC
Q 029905          120 ATASAVLAAYAP  131 (185)
Q Consensus       120 ATASaiLa~~~P  131 (185)
                      -||.+||+...-
T Consensus       120 kTA~~il~~a~~  131 (224)
T d1kg2a_         120 STAGAILSLSLG  131 (224)
T ss_dssp             HHHHHHHHHHHC
T ss_pred             hhhHHHHHHhhh
Confidence            999999998653

>d2abka_ a.96.1.1 (A:) Endonuclease III {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA-glycosylase
superfamily: DNA-glycosylase
family: Endonuclease III
domain: Endonuclease III
species: Escherichia coli [TaxId: 562]

Probab=95.76  E-value=0.011  Score=46.53  Aligned_cols=82  Identities=22%  Similarity=0.090  Sum_probs=47.2

Q ss_pred             CHHHHHHHHHHHhhCCCCCchhhhHhhhCCHHHHHHHHH-------HHHh------hCc-----cHHHHHHHhhcccCcC
Q 029905           57 NTTELSKLVRWKLTRGKWRPRLLVFVSSLDDSSVKSASE-------KAFK------SLP-----DLTKAVSELTVLKGVG  118 (185)
Q Consensus        57 tkdEL~~LveWKL~rGkfRP~L~~lV~sN~~~~V~~~t~-------~Af~------~l~-----dv~~al~~L~~LkGVG  118 (185)
                      |+++-+.-+-=+| ..+| |+...+.+.+ .+.|+++.+       +|-.      .+-     .+....+.|.+|+|||
T Consensus        42 T~~~~v~~~~~~l-~~~~-~t~~~la~a~-~~~l~~~i~~~G~y~~Ka~~l~~~a~~i~~~~~g~~p~~~~~L~~LpGVG  118 (211)
T d2abka_          42 ATDVSVNKATAKL-YPVA-NTPAAMLELG-VEGVKTYIKTIGLYNSKAENIIKTCRILLEQHNGEVPEDRAALEALPGVG  118 (211)
T ss_dssp             SCHHHHHHHHHHH-TTTC-CSHHHHHHHH-HHHHHHHHTTSTTHHHHHHHHHHHHHHHHHHTTTSCCSCHHHHHHSTTCC
T ss_pred             chHHHHHHHHHHH-HHhc-cChHHHHhhh-HhHhHHHHHHhhhhhhHHHHHHHHHHHHHHHhcCchhHHHHHHHHHHhhc
Confidence            4556554443344 2344 8888887774 444554432       1110      000     1233467788999999


Q ss_pred             hHHHHHHHhhhCCCCCCcccHHHH
Q 029905          119 PATASAVLAAYAPDLAPFMSDEAM  142 (185)
Q Consensus       119 PATASaiLa~~~P~~~pFfSDEa~  142 (185)
                      |-||++||+...... -|.-|--.
T Consensus       119 ~~TA~~Il~~a~~~p-~~~vD~nv  141 (211)
T d2abka_         119 RKTANVVLNTAFGWP-TIAVDTHI  141 (211)
T ss_dssp             HHHHHHHHHHHHCCC-CCCCCHHH
T ss_pred             hHHHHHHHHHHhcCc-cccccHHH
Confidence            999999999865443 33445433

>d1pu6a_ a.96.1.5 (A:) 3-Methyladenine DNA glycosylase III (MagIII) {Helicobacter pylori [TaxId: 210]}

class: All alpha proteins
fold: DNA-glycosylase
superfamily: DNA-glycosylase
family: 3-Methyladenine DNA glycosylase III (MagIII)
domain: 3-Methyladenine DNA glycosylase III (MagIII)
species: Helicobacter pylori [TaxId: 210]

Probab=94.95  E-value=0.0096  Score=47.23  Aligned_cols=41  Identities=20%  Similarity=0.122  Sum_probs=29.7

Q ss_pred             HHHHHHHhhcccCcChHHHHHHHhhhCCCCCCcccHHHHHhh
Q 029905          104 LTKAVSELTVLKGVGPATASAVLAAYAPDLAPFMSDEAMGAA  145 (185)
Q Consensus       104 v~~al~~L~~LkGVGPATASaiLa~~~P~~~pFfSDEa~~~~  145 (185)
                      +..+.+.|++||||||-||++||....-. .-|.-|--..-+
T Consensus       115 ~~~~~~~L~~lpGIG~kTA~~vl~~~~~~-~~~~vD~hv~Rv  155 (217)
T d1pu6a_         115 QEVTREWLLDQKGIGKESADAILCYACAK-EVMVVDKYSYLF  155 (217)
T ss_dssp             HHCCHHHHHTSTTCCHHHHHHHHHHTTCC-SCCCCCHHHHHH
T ss_pred             cHHHHHHHHHHhhhhhHHHHHHHHHHcCC-eeeecChHHHHH
Confidence            45678899999999999999999885432 234456655433

>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=94.52  E-value=0.0088  Score=38.92  Aligned_cols=25  Identities=24%  Similarity=0.493  Sum_probs=22.0

Q ss_pred             HHHHHHHhhcccCcChHHHHHHHhh
Q 029905          104 LTKAVSELTVLKGVGPATASAVLAA  128 (185)
Q Consensus       104 v~~al~~L~~LkGVGPATASaiLa~  128 (185)
                      -..+|+.|+++-||||+||.-+..-
T Consensus         2 ~~~~l~~l~~I~GvGp~~A~~l~~~   26 (57)
T d2fmpa2           2 TSSSINFLTRVSGIGPSAARKFVDE   26 (57)
T ss_dssp             HHHHHHHHTTSTTCCHHHHHHHHHT
T ss_pred             cchHHHHHhccccccHHHHHHHHHh
Confidence            4578999999999999999988665

>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=94.34  E-value=0.012  Score=43.96  Aligned_cols=72  Identities=14%  Similarity=0.112  Sum_probs=42.6

Q ss_pred             CHHHHHHHHHHHhhCCCCCchhhhHhhhCCHHHHHHHHHHH-H-----hhCccHH-----HHHHHhhcccCcChHHHHHH
Q 029905           57 NTTELSKLVRWKLTRGKWRPRLLVFVSSLDDSSVKSASEKA-F-----KSLPDLT-----KAVSELTVLKGVGPATASAV  125 (185)
Q Consensus        57 tkdEL~~LveWKL~rGkfRP~L~~lV~sN~~~~V~~~t~~A-f-----~~l~dv~-----~al~~L~~LkGVGPATASai  125 (185)
                      |.++-+.-+-.+|-.  .-|+...+.+.+ .+.+++..+.+ |     +.+-++.     ...+.|++|+||||-||.++
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            566767677777642  237766665544 44455444322 2     1111222     23456889999999999998


Q ss_pred             HhhhCC
Q 029905          126 LAAYAP  131 (185)
Q Consensus       126 La~~~P  131 (185)
                      +.+..-
T Consensus       110 ~if~~~  115 (144)
T d1ngna_         110 RIFCVN  115 (144)
T ss_dssp             HHHTSS
T ss_pred             HHHHcC
Confidence            887443

>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=92.54  E-value=0.025  Score=38.70  Aligned_cols=28  Identities=32%  Similarity=0.474  Sum_probs=23.8

Q ss_pred             HHHHHHhhcccCcChHHHHHHHhhhCCC
Q 029905          105 TKAVSELTVLKGVGPATASAVLAAYAPD  132 (185)
Q Consensus       105 ~~al~~L~~LkGVGPATASaiLa~~~P~  132 (185)
                      +.-...|.+..||||-||=+||+.+.|+
T Consensus         5 r~~F~~Li~V~GIGpK~Al~iLs~~~~~   32 (78)
T d1cuka2           5 RTLFKELIKTNGVGPKLALAILSGMSAQ   32 (78)
T ss_dssp             HHHHHHHHHSSSCCHHHHHHHHHHSCHH
T ss_pred             HHHHHHHHccCCccHHHHHHHHHhCCHH
Confidence            4457789999999999999999987763

>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=92.51  E-value=0.018  Score=41.10  Aligned_cols=37  Identities=22%  Similarity=0.333  Sum_probs=31.8

Q ss_pred             HHHHHhhcccCcChHHHHHHHhhhCCCCCCcccHHHHHhhhC
Q 029905          106 KAVSELTVLKGVGPATASAVLAAYAPDLAPFMSDEAMGAALG  147 (185)
Q Consensus       106 ~al~~L~~LkGVGPATASaiLa~~~P~~~pFfSDEa~~~~~g  147 (185)
                      +..+.|..|+||||++|-.|..     +-||-|-|=+..+.|
T Consensus        24 As~~eL~~lpGIg~~~A~~Iv~-----~gpf~s~edL~~V~G   60 (98)
T d2axtu1          24 TNIAAFIQYRGLYPTLAKLIVK-----NAPYESVEDVLNIPG   60 (98)
T ss_dssp             SCGGGGTTSTTCTHHHHHHHHH-----SCCCSSGGGGGGCTT
T ss_pred             ccHHHHHHhhhhcHHHHHHHHH-----cCCcCCHHHHhhCCC
Confidence            4577899999999999999994     358999998888887

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

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

Probab=92.15  E-value=0.026  Score=36.34  Aligned_cols=38  Identities=29%  Similarity=0.319  Sum_probs=27.2

Q ss_pred             HhhcccCcChHHHHHHHhhhCC--CCCCcccHHHHHhhhC
Q 029905          110 ELTVLKGVGPATASAVLAAYAP--DLAPFMSDEAMGAALG  147 (185)
Q Consensus       110 ~L~~LkGVGPATASaiLa~~~P--~~~pFfSDEa~~~~~g  147 (185)
                      .|.+++||||+||..++..+..  +.+-..+-+-...+.|
T Consensus         2 ~L~~i~GIG~~~a~~L~~~g~~sv~~l~~a~~~eL~~i~G   41 (61)
T d1pzna1           2 SIEDLPGVGPATAEKLREAGYDTLEAIAVASPIELKEVAG   41 (61)
T ss_dssp             CSSCCTTCCHHHHHHHHTTTCCSHHHHHTCCHHHHHHHHC
T ss_pred             ccccCCCCCHHHHHHHHHhcCCCHHHHHhCCHHHHHHCCC
Confidence            4778999999999999987533  2344455555566776

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

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

Probab=92.07  E-value=0.033  Score=37.69  Aligned_cols=28  Identities=36%  Similarity=0.496  Sum_probs=23.5

Q ss_pred             HHHHHHhhcccCcChHHHHHHHhhhCCC
Q 029905          105 TKAVSELTVLKGVGPATASAVLAAYAPD  132 (185)
Q Consensus       105 ~~al~~L~~LkGVGPATASaiLa~~~P~  132 (185)
                      +.-...|.+..||||-||-+||+.++|+
T Consensus         6 r~lF~~Li~V~GIGpk~Al~iLs~~~~~   33 (73)
T d1ixra1           6 LALFELLLSVSGVGPKVALALLSALPPR   33 (73)
T ss_dssp             HHHHHHHHSSSCCCHHHHHHHHHHSCHH
T ss_pred             HHHHHHHhccCCcCHHHHHHHHHHccHH
Confidence            4457788999999999999999987763

>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=91.94  E-value=0.036  Score=36.12  Aligned_cols=25  Identities=28%  Similarity=0.195  Sum_probs=21.8

Q ss_pred             HHHHHHhhcccCcChHHHHHHHhhh
Q 029905          105 TKAVSELTVLKGVGPATASAVLAAY  129 (185)
Q Consensus       105 ~~al~~L~~LkGVGPATASaiLa~~  129 (185)
                      .++|+.|+++-||||.||.-+..-+
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            4689999999999999998887664

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

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

Probab=91.94  E-value=0.035  Score=37.31  Aligned_cols=28  Identities=32%  Similarity=0.363  Sum_probs=23.6

Q ss_pred             HHHHHHhhcccCcChHHHHHHHhhhCCC
Q 029905          105 TKAVSELTVLKGVGPATASAVLAAYAPD  132 (185)
Q Consensus       105 ~~al~~L~~LkGVGPATASaiLa~~~P~  132 (185)
                      +.-...|....||||-||-+||+.++|+
T Consensus         5 r~~F~~Li~V~GIGpK~Al~iLs~~~~~   32 (71)
T d1bvsa2           5 RDLFLALLSVSGVGPRLAMATLAVHDAA   32 (71)
T ss_dssp             HHHHHHHHTSSSCCHHHHHHHHHHSCHH
T ss_pred             HHHHHHHhccCCcCHHHHHHHHHhCCHH
Confidence            4456788999999999999999997764

>d2a1jb1 a.60.2.5 (B:219-296) DNA excision repair protein ERCC-1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: SAM domain-like
superfamily: RuvA domain 2-like
family: Hef domain-like
domain: DNA excision repair protein ERCC-1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=91.56  E-value=0.14  Score=34.01  Aligned_cols=24  Identities=21%  Similarity=0.364  Sum_probs=15.9

Q ss_pred             HHHHHHhhcccCcChHHHHHHHhh
Q 029905          105 TKAVSELTVLKGVGPATASAVLAA  128 (185)
Q Consensus       105 ~~al~~L~~LkGVGPATASaiLa~  128 (185)
                      +.-+..|+.++||||.+|-.++.-
T Consensus        15 ~~~~~~L~~I~gIg~~~a~~L~~~   38 (78)
T d2a1jb1          15 SRVTECLTTVKSVNKTDSQTLLTT   38 (78)
T ss_dssp             HHHHHHHTTSTTCCHHHHHHHHHH
T ss_pred             HHHHHHhcCCCCcCHHHHHHHHHH
Confidence            345666667777777777776665

>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=90.76  E-value=0.057  Score=34.88  Aligned_cols=24  Identities=17%  Similarity=0.192  Sum_probs=20.6

Q ss_pred             HHHHHHhhcccCcChHHHHHHHhh
Q 029905          105 TKAVSELTVLKGVGPATASAVLAA  128 (185)
Q Consensus       105 ~~al~~L~~LkGVGPATASaiLa~  128 (185)
                      .++|+.+|++-||||.||.-+...
T Consensus         4 ~~~l~~ft~I~GvGp~~A~~l~~~   27 (57)
T d2bcqa2           4 VPVLELFSNIWGAGTKTAQMWYQQ   27 (57)
T ss_dssp             HHHHHHHHTSTTCCHHHHHHHHHT
T ss_pred             hHHHHHHhccccccHHHHHHHHHh
Confidence            468999999999999999877654

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

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

Probab=90.44  E-value=0.12  Score=35.13  Aligned_cols=21  Identities=33%  Similarity=0.540  Sum_probs=18.1

Q ss_pred             HHHhhcccCcChHHHHHHHhh
Q 029905          108 VSELTVLKGVGPATASAVLAA  128 (185)
Q Consensus       108 l~~L~~LkGVGPATASaiLa~  128 (185)
                      .+.|++++|||+-||.-|..=
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            567999999999999988754

>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=89.95  E-value=0.23  Score=33.26  Aligned_cols=22  Identities=27%  Similarity=0.274  Sum_probs=18.3

Q ss_pred             HHHhhcccCcChHHHHHHHhhh
Q 029905          108 VSELTVLKGVGPATASAVLAAY  129 (185)
Q Consensus       108 l~~L~~LkGVGPATASaiLa~~  129 (185)
                      .+.|++++||||-||--|..=.
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            5679999999999998876543

>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=89.63  E-value=0.07  Score=34.14  Aligned_cols=19  Identities=53%  Similarity=0.684  Sum_probs=17.0

Q ss_pred             hhcccCcChHHHHHHHhhh
Q 029905          111 LTVLKGVGPATASAVLAAY  129 (185)
Q Consensus       111 L~~LkGVGPATASaiLa~~  129 (185)
                      |++++||||++|..++..+
T Consensus         1 L~~IpGIG~~~a~~L~~~G   19 (60)
T d2i1qa1           1 LTDLPGVGPSTAEKLVEAG   19 (60)
T ss_dssp             CTTSTTCCHHHHHHHHHHT
T ss_pred             CCCCCCCCHHHHHHHHHcc
Confidence            6789999999999999873

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

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

Probab=88.70  E-value=0.12  Score=33.59  Aligned_cols=40  Identities=20%  Similarity=0.285  Sum_probs=26.8

Q ss_pred             HHHhhcccCcChHHHHHHHhhhCC-CCCCcccHHHHHhhhC
Q 029905          108 VSELTVLKGVGPATASAVLAAYAP-DLAPFMSDEAMGAALG  147 (185)
Q Consensus       108 l~~L~~LkGVGPATASaiLa~~~P-~~~pFfSDEa~~~~~g  147 (185)
                      +-+|+.++||||.||-.|+.-+.- +.+---|.|-+..+.|
T Consensus        12 ~~~L~~IpgIG~~~a~~L~~~F~s~~~l~~As~eeL~~v~G   52 (70)
T d2bgwa1          12 LYILQSFPGIGRRTAERILERFGSLERFFTASKAEISKVEG   52 (70)
T ss_dssp             HHHHHTSTTCCHHHHHHHHHHHSSHHHHTTCCHHHHHHSTT
T ss_pred             HHHHcCCCCcCHHHHHHHHHHhCCHHHHHHcCHHHHHcCCC
Confidence            557889999999999999987531 1111224455555655

>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=88.12  E-value=0.14  Score=33.97  Aligned_cols=47  Identities=23%  Similarity=0.475  Sum_probs=31.1

Q ss_pred             HHHHHHHHHHHHhhCccHHH-HHHHhhcccCcChHHHHHHHhhhCCCCCCcc
Q 029905           87 DSSVKSASEKAFKSLPDLTK-AVSELTVLKGVGPATASAVLAAYAPDLAPFM  137 (185)
Q Consensus        87 ~~~V~~~t~~Af~~l~dv~~-al~~L~~LkGVGPATASaiLa~~~P~~~pFf  137 (185)
                      +...+...+. |..+.++.. ..+.|.+++|||+..|..|..+..-   ||+
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            3334443333 554444433 3778999999999999999998643   554

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

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

Probab=86.44  E-value=0.19  Score=31.56  Aligned_cols=30  Identities=20%  Similarity=0.372  Sum_probs=19.1

Q ss_pred             HhhCccHHH-HHHHhhcccCcChHHHHHHHh
Q 029905           98 FKSLPDLTK-AVSELTVLKGVGPATASAVLA  127 (185)
Q Consensus        98 f~~l~dv~~-al~~L~~LkGVGPATASaiLa  127 (185)
                      |..+.++.. ..+.|.+++||||.+|..|..
T Consensus        22 F~s~~~i~~As~eeL~~v~GIg~~~A~~I~~   52 (56)
T d1kfta_          22 MGGLQGLRNASVEEIAKVPGISQGLAEKIFW   52 (56)
T ss_dssp             HSCHHHHHHCCHHHHTTSSSTTSHHHHHHHH
T ss_pred             hCCHHHHHHhhHHHHHhcCCCCHHHHHHHHH
Confidence            544444433 466777778888877777654

>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=86.20  E-value=0.2  Score=33.46  Aligned_cols=20  Identities=30%  Similarity=0.498  Sum_probs=17.2

Q ss_pred             HHHhhcccCcChHHHHHHHh
Q 029905          108 VSELTVLKGVGPATASAVLA  127 (185)
Q Consensus       108 l~~L~~LkGVGPATASaiLa  127 (185)
                      .+.|++++||||-||.-|..
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

>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=86.02  E-value=0.26  Score=31.81  Aligned_cols=36  Identities=28%  Similarity=0.522  Sum_probs=29.0

Q ss_pred             HHHHhhcccCcChHHHHHHHhhhCCCCCCcccHHHHHhhhC
Q 029905          107 AVSELTVLKGVGPATASAVLAAYAPDLAPFMSDEAMGAALG  147 (185)
Q Consensus       107 al~~L~~LkGVGPATASaiLa~~~P~~~pFfSDEa~~~~~g  147 (185)
                      ..+.|..|+|||+.+|..|+..-     ||-|-|=+.-+.|
T Consensus        15 ~~~eL~~lpgig~~~A~~Iv~~R-----~f~s~edL~~v~g   50 (65)
T d2duya1          15 SLEELMALPGIGPVLARRIVEGR-----PYARVEDLLKVKG   50 (65)
T ss_dssp             CHHHHTTSTTCCHHHHHHHHHTC-----CCSSGGGGGGSTT
T ss_pred             CHHHHHHCCCCCHHHHHHHHHcC-----CCCCHHHHHhCCC
Confidence            46789999999999999999873     5777776666655

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

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

Probab=85.96  E-value=0.12  Score=32.64  Aligned_cols=20  Identities=30%  Similarity=0.561  Sum_probs=17.6

Q ss_pred             HhhcccCcChHHHHHHHhhh
Q 029905          110 ELTVLKGVGPATASAVLAAY  129 (185)
Q Consensus       110 ~L~~LkGVGPATASaiLa~~  129 (185)
                      .|..++||||.||-.|+.-+
T Consensus         3 ~L~~I~gVG~~~a~~L~~~F   22 (56)
T d1kfta_           3 SLETIEGVGPKRRQMLLKYM   22 (56)
T ss_dssp             GGGGCTTCSSSHHHHHHHHH
T ss_pred             CcccCCCccHHHHHHHHHHh
Confidence            47789999999999999874

>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=85.89  E-value=0.21  Score=31.76  Aligned_cols=39  Identities=15%  Similarity=0.237  Sum_probs=27.6

Q ss_pred             HHhhcccCcChHHHHHHHhhhCC-CCCCcccHHHHHhhhC
Q 029905          109 SELTVLKGVGPATASAVLAAYAP-DLAPFMSDEAMGAALG  147 (185)
Q Consensus       109 ~~L~~LkGVGPATASaiLa~~~P-~~~pFfSDEa~~~~~g  147 (185)
                      +.|..++||||+++-.|+.-+-- +...-.|-|-+..+.|
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            46889999999999999975321 2234456666666676

>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=85.73  E-value=0.18  Score=32.73  Aligned_cols=42  Identities=19%  Similarity=0.351  Sum_probs=28.3

Q ss_pred             HHHHHHHHHHHHhhCccHHH-HHHHhhcccCcChHHHHHHHhhh
Q 029905           87 DSSVKSASEKAFKSLPDLTK-AVSELTVLKGVGPATASAVLAAY  129 (185)
Q Consensus        87 ~~~V~~~t~~Af~~l~dv~~-al~~L~~LkGVGPATASaiLa~~  129 (185)
                      +...+...+. |..+.++.. ..+.|++++|||+.+|-.|....
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            3334444333 554444433 47899999999999999998775

>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=85.28  E-value=0.15  Score=34.29  Aligned_cols=33  Identities=24%  Similarity=0.275  Sum_probs=24.0

Q ss_pred             HHhhCccHHHHHHHhhcccCcChHHHHHHHhhh
Q 029905           97 AFKSLPDLTKAVSELTVLKGVGPATASAVLAAY  129 (185)
Q Consensus        97 Af~~l~dv~~al~~L~~LkGVGPATASaiLa~~  129 (185)
                      +...+|..-...+.+++++|||+.+|+-|--..
T Consensus        36 ~i~~l~~~i~~~~~l~~i~GIGk~ia~kI~E~~   68 (82)
T d2fmpa1          36 VIAKYPHKIKSGAEAKKLPGVGTKIAEKIDEFL   68 (82)
T ss_dssp             HHHHCSSCCCCHHHHHTSTTCCHHHHHHHHHHH
T ss_pred             HHHhCCcccCCHHHHhcCCCccHHHHHHHHHHH
Confidence            345566433356789999999999999886553

>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=83.62  E-value=0.19  Score=33.05  Aligned_cols=34  Identities=21%  Similarity=0.336  Sum_probs=24.3

Q ss_pred             HHhhCccHHHHHHHhhcccCcChHHHHHHHhhhC
Q 029905           97 AFKSLPDLTKAVSELTVLKGVGPATASAVLAAYA  130 (185)
Q Consensus        97 Af~~l~dv~~al~~L~~LkGVGPATASaiLa~~~  130 (185)
                      +.+.+|..-..++.|.+|+|||+.+|+-|--...
T Consensus        34 ~l~~l~~~i~~~~~l~~lpGiG~~i~~kI~Eil~   67 (76)
T d2bcqa1          34 ALKSFHKPVTSYQEACSIPGIGKRMAEKIIEILE   67 (76)
T ss_dssp             HHHSCCSCCCCHHHHHTSTTCCHHHHHHHHHHHH
T ss_pred             HHHhCCcccCCHHHHhcCCCccHHHHHHHHHHHH
Confidence            3455663333456789999999999998876643

>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=83.02  E-value=0.26  Score=31.27  Aligned_cols=42  Identities=19%  Similarity=0.364  Sum_probs=31.3

Q ss_pred             HHHHHHHHHHHHhhCccHHH-HHHHhhcccCcChHHHHHHHhh
Q 029905           87 DSSVKSASEKAFKSLPDLTK-AVSELTVLKGVGPATASAVLAA  128 (185)
Q Consensus        87 ~~~V~~~t~~Af~~l~dv~~-al~~L~~LkGVGPATASaiLa~  128 (185)
                      +..+++.....|..+.++.. ..+.|++++|+|+.+|.-|...
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            45566666666766655543 4888999999999999998765

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

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

Probab=82.12  E-value=0.6  Score=30.02  Aligned_cols=43  Identities=19%  Similarity=0.315  Sum_probs=24.6

Q ss_pred             HHHHHHHHHHHHhhCccHHH-HHHHhhcccCcChHHHHHHHhhhC
Q 029905           87 DSSVKSASEKAFKSLPDLTK-AVSELTVLKGVGPATASAVLAAYA  130 (185)
Q Consensus        87 ~~~V~~~t~~Af~~l~dv~~-al~~L~~LkGVGPATASaiLa~~~  130 (185)
                      +...+...+. |..+.++.. ..+.|.++.||||.+|-.|.....
T Consensus        20 ~~~a~~L~~~-f~s~~~i~~As~eeL~~i~GIG~~~A~~I~~~~~   63 (68)
T d1x2ia1          20 ATLARRLLKH-FGSVERVFTASVAELMKVEGIGEKIAKEIRRVIT   63 (68)
T ss_dssp             HHHHHHHHHH-HCSHHHHHHCCHHHHTTSTTCCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHH-cCCHHHHHHhHHHHHHhCCCcCHHHHHHHHHHHh
Confidence            3333333333 544444333 466777788888888877776643

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

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

Probab=80.60  E-value=0.61  Score=29.98  Aligned_cols=40  Identities=15%  Similarity=0.027  Sum_probs=26.7

Q ss_pred             HHHhhcccCcChHHHHHHHhhhC-CCCCCcccHHHHHhhhC
Q 029905          108 VSELTVLKGVGPATASAVLAAYA-PDLAPFMSDEAMGAALG  147 (185)
Q Consensus       108 l~~L~~LkGVGPATASaiLa~~~-P~~~pFfSDEa~~~~~g  147 (185)
                      .-.|..++||||.||-.|+.-+. .+.+.--+.|-+..+.|
T Consensus         9 ~~~L~~I~gIG~~~a~~L~~~f~s~~~i~~As~eeL~~i~G   49 (68)
T d1x2ia1           9 RLIVEGLPHVSATLARRLLKHFGSVERVFTASVAELMKVEG   49 (68)
T ss_dssp             HHHHTTSTTCCHHHHHHHHHHHCSHHHHHHCCHHHHTTSTT
T ss_pred             HHHHcCCCCcCHHHHHHHHHHcCCHHHHHHhHHHHHHhCCC
Confidence            34688999999999999998753 22222225555555655