Citrus Sinensis ID: 035374

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60------
Protein Sequence
MASFGMEDFARKYGELKPSQFVDVISLVGDKADNIPGVEGIGDVRAVQLITKFGMLVFNVECFSEM
Secondary Structure (PSIPRED)
cccccHHHHHHHHccccccHHHHHHHHHccccccccccccccHHHHHHHHHHHccHHHHHHHHccc
Secondary Structure Prediction (SSPRO)
cccccHHHHHHHHccccHHHHHHHHHHHccccccccccccccHHHHHHHHHHHccHHHHHHHHccc
Coil and Loop (DISEMBL)
MASFGMEDFARkygelkpsqFVDVISLvgdkadnipgvegigdvRAVQLITKFGMLVFNVECFSEM
Flexible Loop (DISEMBL)
MASFGMEDFArkygelkpsQFVDVISLVGDKADNIPGVEGIGDVRAVQLITKFGMLVFNVECFSEM
Low Complexity Region (SEG)
MASFGMEDFARKYGELKPSQFVDVISLVGDKADNIPGVEGIGDVRAVQLITKFGMLVFNVECFSEM
Disordered region (IsUnstruct)
************YGELKPSQFVDVISLVGDKADNIPGVEGIGDVRAVQLITKFGMLVFNVECF***
Disordered Region (DISOPRED)
*ASFGMEDFARKYGELKPSQFVDVISLVGDKADNIPGVEGIGDVRAVQLITKFGMLVFNVECFS**
Disordered Region (DISEMBL)
MASFGMEDFARKYGELKPSQFVDVISLVGDKADNIPGVEGIGDVRAVQLITKFGMLVFNVECFSEM
Disordered Region (DISPRO)
*ASFGMEDFARKYGELKPSQFVDVISLVGDKADNIPGVEGIGDVRAVQLITKFGMLVFNVECFSEM
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhoooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
oooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiii
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MASFGMEDFARKYGELKPSQFVDVISLVGDKADNIPGVEGIGDVRAVQLITKFGMLVFNVECFSEM
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	66	2.2.26 [Sep-21-2011]
P52026	876	DNA polymerase I OS=Geoba	N/A	no	0.833	0.062	0.5	3e-08
Q04957	877	DNA polymerase I OS=Bacil	N/A	no	0.742	0.055	0.54	1e-07
P80194	834	DNA polymerase I, thermos	N/A	no	0.681	0.053	0.543	2e-07
P52028	834	DNA polymerase I, thermos	yes	no	0.666	0.052	0.533	6e-07
Q9KAV6	303	5'-3' exonuclease OS=Baci	yes	no	0.742	0.161	0.46	7e-07
P30313	831	DNA polymerase I, thermos	no	no	0.666	0.052	0.555	1e-06
O08307	942	DNA polymerase I OS=Chlor	yes	no	0.803	0.056	0.415	4e-06
O67550	289	5'-3' exonuclease OS=Aqui	yes	no	0.757	0.173	0.411	4e-06
O52225	833	DNA polymerase I, thermos	N/A	no	0.712	0.056	0.458	5e-06
P19821	832	DNA polymerase I, thermos	N/A	no	0.666	0.052	0.488	1e-05

>sp|P52026|DPO1_GEOSE DNA polymerase I OS=Geobacillus stearothermophilus GN=polA PE=1 SV=2

 Score = 57.4 bits (137), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 28/56 (50%), Positives = 38/56 (67%), Gaps = 1/56 (1%)

Query: 1   MASFGMEDFARKYGELKPSQFVDVISLVGDKADNIPGVEGIGDVRAVQLITKFGML 56
           + S+  E    KYG L P Q VD+  L+GDK+DNIPGV GIG+  AV+L+ +FG +
Sbjct: 157 IESYTPETVVEKYG-LTPEQIVDLKGLMGDKSDNIPGVPGIGEKTAVKLLKQFGTV 211

In addition to polymerase activity, this DNA polymerase exhibits 5' to 3' exonuclease activity.
Geobacillus stearothermophilus (taxid: 1422)
EC: 2EC: .EC: 7EC: .EC: 7EC: .EC: 7

>sp|Q04957|DPO1_BACCA DNA polymerase I OS=Bacillus caldotenax GN=polA PE=1 SV=1

 Score = 55.1 bits (131), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 27/50 (54%), Positives = 35/50 (70%), Gaps = 1/50 (2%)

Query: 7   EDFARKYGELKPSQFVDVISLVGDKADNIPGVEGIGDVRAVQLITKFGML 56
           E    KYG L P Q VD+  L+GDK+DNIPGV GIG+  AV+L+ +FG +
Sbjct: 163 EAVREKYG-LTPEQIVDLKGLMGDKSDNIPGVPGIGEKTAVKLLRQFGTV 211

In addition to polymerase activity, this DNA polymerase exhibits 3' to 5' and 5' to 3' exonuclease activity.

Bacillus caldotenax (taxid: 1395)

EC: 2

EC: .

EC: 7

EC: .

EC: 7

EC: .

EC: 7

>sp|P80194|DPO1_THECA DNA polymerase I, thermostable OS=Thermus caldophilus GN=polA PE=1 SV=2

 Score = 54.3 bits (129), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 25/46 (54%), Positives = 37/46 (80%), Gaps = 1/46 (2%)

Query: 11  RKYGELKPSQFVDVISLVGDKADNIPGVEGIGDVRAVQLITKFGML 56
           +KYG LKP Q+VD  +LVGD +DN+PGV+GIG+  A++L+ ++G L
Sbjct: 171 QKYG-LKPEQWVDFRALVGDPSDNLPGVKGIGEKTALKLLKEWGSL 215

Has 5'-to-3' exonuclease activity and no 3'-to-5' exonuclease activity.

Thermus caldophilus (taxid: 272)

EC: 2

EC: .

EC: 7

EC: .

EC: 7

EC: .

EC: 7

>sp|P52028|DPO1T_THET8 DNA polymerase I, thermostable OS=Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) GN=polA PE=3 SV=2

 Score = 52.8 bits (125), Expect = 6e-07,   Method: Composition-based stats.
 Identities = 24/45 (53%), Positives = 36/45 (80%), Gaps = 1/45 (2%)

Query: 12  KYGELKPSQFVDVISLVGDKADNIPGVEGIGDVRAVQLITKFGML 56
           KYG L+P Q+VD  +LVGD +DN+PGV+GIG+  A++L+ ++G L
Sbjct: 172 KYG-LRPEQWVDFRALVGDPSDNLPGVKGIGEKTALKLLKEWGSL 215

Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (taxid: 300852)

EC: 2

EC: .

EC: 7

EC: .

EC: 7

EC: .

EC: 7

>sp|Q9KAV6|EX53_BACHD 5'-3' exonuclease OS=Bacillus halodurans (strain ATCC BAA-125 / DSM 18197 / FERM 7344 / JCM 9153 / C-125) GN=BH2180 PE=3 SV=1

 Score = 52.8 bits (125), Expect = 7e-07,   Method: Composition-based stats.
 Identities = 23/50 (46%), Positives = 36/50 (72%), Gaps = 1/50 (2%)

Query: 7   EDFARKYGELKPSQFVDVISLVGDKADNIPGVEGIGDVRAVQLITKFGML 56
           E+F   Y  + P+Q+VDV +L+GDK+DNIPG  G+G+  A+ LI ++G +
Sbjct: 171 ENFRNDY-NISPAQWVDVKALLGDKSDNIPGCPGVGEKSALPLIQQYGTI 219

5'-3' exonuclease acting preferentially on double-stranded DNA.

Bacillus halodurans (strain ATCC BAA-125 / DSM 18197 / FERM 7344 / JCM 9153 / C-125) (taxid: 272558)

EC: 3

EC: .

EC: 1

EC: .

EC: 1

EC: 1

EC: .

EC: -

>sp|P30313|DPO1F_THETH DNA polymerase I, thermostable OS=Thermus thermophilus GN=polA PE=1 SV=1

 Score = 51.6 bits (122), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 25/45 (55%), Positives = 34/45 (75%), Gaps = 1/45 (2%)

Query: 12  KYGELKPSQFVDVISLVGDKADNIPGVEGIGDVRAVQLITKFGML 56
           KYG L+P Q+VD  +L GD +DNIPGV+GIG+  A +LI ++G L
Sbjct: 170 KYG-LRPEQWVDYRALAGDPSDNIPGVKGIGEKTAQRLIREWGSL 213

Thermus thermophilus (taxid: 274)

EC: 2

EC: .

EC: 7

EC: .

EC: 7

EC: .

EC: 7

>sp|O08307|DPO1_CHLAA DNA polymerase I OS=Chloroflexus aurantiacus (strain ATCC 29366 / DSM 635 / J-10-fl) GN=polA PE=3 SV=1

 Score = 50.1 bits (118), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 22/53 (41%), Positives = 33/53 (62%)

Query: 4   FGMEDFARKYGELKPSQFVDVISLVGDKADNIPGVEGIGDVRAVQLITKFGML 56
           + +E   ++Y  L+P Q  D+  L GD +DNIPGV GIG+  A+ L+ +F  L
Sbjct: 164 YDLEQVRKRYDGLEPDQLADLRGLKGDTSDNIPGVRGIGEKGAIALLKQFRSL 216

In addition to polymerase activity, this DNA polymerase exhibits 3' to 5' and 5' to 3' exonuclease activity.

Chloroflexus aurantiacus (strain ATCC 29366 / DSM 635 / J-10-fl) (taxid: 324602)

EC: 2

EC: .

EC: 7

EC: .

EC: 7

EC: .

EC: 7

>sp|O67550|EX53_AQUAE 5'-3' exonuclease OS=Aquifex aeolicus (strain VF5) GN=aq_1628 PE=3 SV=1

 Score = 50.1 bits (118), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 21/51 (41%), Positives = 35/51 (68%), Gaps = 1/51 (1%)

Query: 4   FGMEDFARKYGELKPSQFVDVISLVGDKADNIPGVEGIGDVRAVQLITKFG 54
           F  E   +K+G ++P +  D ++LVGDK DN+PG+EG+G   A+ ++ K+G
Sbjct: 155 FTKERVIKKFG-VEPQKIPDYLALVGDKVDNVPGIEGVGPKTAINILKKYG 204

5'-3' exonuclease acting preferentially on double-stranded DNA.

Aquifex aeolicus (strain VF5) (taxid: 224324)

EC: 3

EC: .

EC: 1

EC: .

EC: 1

EC: 1

EC: .

EC: -

>sp|O52225|DPO1_THEFI DNA polymerase I, thermostable OS=Thermus filiformis GN=polA PE=1 SV=1

 Score = 49.7 bits (117), Expect = 5e-06,   Method: Composition-based stats.
 Identities = 22/48 (45%), Positives = 35/48 (72%), Gaps = 1/48 (2%)

Query: 7   EDFARKYGELKPSQFVDVISLVGDKADNIPGVEGIGDVRAVQLITKFG 54
           +D   KYG + P ++VD  +L GD++DNIPGV GIG+  A++L+ ++G
Sbjct: 165 KDVQEKYG-VPPERWVDFRALTGDRSDNIPGVAGIGEKTALRLLAEWG 211

Has 5'-to-3' exonuclease activity and no 3'-to-5' exonuclease activity.

Thermus filiformis (taxid: 276)

EC: 2

EC: .

EC: 7

EC: .

EC: 7

EC: .

EC: 7

>sp|P19821|DPO1_THEAQ DNA polymerase I, thermostable OS=Thermus aquaticus GN=polA PE=1 SV=1

 Score = 48.5 bits (114), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 22/45 (48%), Positives = 34/45 (75%), Gaps = 1/45 (2%)

Query: 12  KYGELKPSQFVDVISLVGDKADNIPGVEGIGDVRAVQLITKFGML 56
           KYG L+P Q+ D  +L GD++DN+PGV+GIG+  A +L+ ++G L
Sbjct: 171 KYG-LRPDQWADYRALTGDESDNLPGVKGIGEKTARKLLEEWGSL 214

Thermus aquaticus (taxid: 271)

EC: 2

EC: .

EC: 7

EC: .

EC: 7

EC: .

EC: 7

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	66
359478321	441	PREDICTED: DNA polymerase I-like [Vitis	1.0	0.149	0.727	2e-21
242036411	421	hypothetical protein SORBIDRAFT_01g04187	0.848	0.133	0.767	8e-19
108706960	416	5'-3' exonuclease, N-terminal resolvase-	0.848	0.134	0.767	1e-18
255579458	246	DNA polymerase I, putative [Ricinus comm	0.939	0.252	0.741	1e-18
218192373	421	hypothetical protein OsI_10602 [Oryza sa	0.848	0.133	0.767	1e-18
115451687	421	Os03g0227300 [Oryza sativa Japonica Grou	0.848	0.133	0.767	1e-18
24421685	443	Unknown protein [Oryza sativa Japonica G	0.848	0.126	0.767	1e-18
194696700	422	unknown [Zea mays] gi|195654367|gb|ACG46	0.848	0.132	0.75	3e-18
449453197	461	PREDICTED: DNA polymerase I-like [Cucumi	0.848	0.121	0.767	3e-18
42565846	425	5'-3' exonuclease-like protein [Arabidop	0.848	0.131	0.714	4e-18

>gi|359478321|ref|XP_002275974.2| PREDICTED: DNA polymerase I-like [Vitis vinifera] gi|296084279|emb|CBI24667.3| unnamed protein product [Vitis vinifera]

 Score =  106 bits (264), Expect = 2e-21,   Method: Composition-based stats.
 Identities = 48/66 (72%), Positives = 57/66 (86%)

Query: 1   MASFGMEDFARKYGELKPSQFVDVISLVGDKADNIPGVEGIGDVRAVQLITKFGMLVFNV 60
           M SFGMEDFA++YG L+PSQFVDVISLVGDK+DNIPGVEGIG+V AVQLITKFG L   +
Sbjct: 290 MTSFGMEDFAKRYGNLEPSQFVDVISLVGDKSDNIPGVEGIGNVHAVQLITKFGTLENLL 349

Query: 61  ECFSEM 66
           +C  ++
Sbjct: 350 QCVDQV 355

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|242036411|ref|XP_002465600.1| hypothetical protein SORBIDRAFT_01g041870 [Sorghum bicolor] gi|241919454|gb|EER92598.1| hypothetical protein SORBIDRAFT_01g041870 [Sorghum bicolor]

 Score = 97.8 bits (242), Expect = 8e-19,   Method: Composition-based stats.
 Identities = 43/56 (76%), Positives = 50/56 (89%)

Query: 1   MASFGMEDFARKYGELKPSQFVDVISLVGDKADNIPGVEGIGDVRAVQLITKFGML 56
           M SFG+EDF ++YG LKPSQFVDV++L GDKADNIPGVEGIGD+ AV+LITKFG L
Sbjct: 272 MVSFGVEDFVKRYGALKPSQFVDVVALSGDKADNIPGVEGIGDINAVKLITKFGSL 327

Source: Sorghum bicolor

Species: Sorghum bicolor

Genus: Sorghum

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|108706960|gb|ABF94755.1| 5'-3' exonuclease, N-terminal resolvase-like domain containing protein, expressed [Oryza sativa Japonica Group]

 Score = 97.4 bits (241), Expect = 1e-18,   Method: Composition-based stats.
 Identities = 43/56 (76%), Positives = 50/56 (89%)

Query: 1   MASFGMEDFARKYGELKPSQFVDVISLVGDKADNIPGVEGIGDVRAVQLITKFGML 56
           M SFG+EDF ++YG LKPSQFVDV++L GDKADNIPGVEGIGD+ AV+LITKFG L
Sbjct: 266 MVSFGVEDFVKRYGALKPSQFVDVVALSGDKADNIPGVEGIGDINAVKLITKFGSL 321

Source: Oryza sativa Japonica Group

Species: Oryza sativa

Genus: Oryza

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255579458|ref|XP_002530572.1| DNA polymerase I, putative [Ricinus communis] gi|223529871|gb|EEF31802.1| DNA polymerase I, putative [Ricinus communis]

 Score = 97.4 bits (241), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 46/62 (74%), Positives = 54/62 (87%)

Query: 1   MASFGMEDFARKYGELKPSQFVDVISLVGDKADNIPGVEGIGDVRAVQLITKFGMLVFNV 60
           M SFGMEDFA+ YGEL+PSQFVDV++L+GDK+DNIPGVEGIG V AV+LITKFG L   +
Sbjct: 95  MVSFGMEDFAKLYGELRPSQFVDVMALMGDKSDNIPGVEGIGTVYAVELITKFGTLENLL 154

Query: 61  EC 62
           EC
Sbjct: 155 EC 156

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|218192373|gb|EEC74800.1| hypothetical protein OsI_10602 [Oryza sativa Indica Group]

 Score = 97.1 bits (240), Expect = 1e-18,   Method: Composition-based stats.
 Identities = 43/56 (76%), Positives = 50/56 (89%)

Query: 1   MASFGMEDFARKYGELKPSQFVDVISLVGDKADNIPGVEGIGDVRAVQLITKFGML 56
           M SFG+EDF ++YG LKPSQFVDV++L GDKADNIPGVEGIGD+ AV+LITKFG L
Sbjct: 271 MVSFGVEDFVKRYGALKPSQFVDVVALSGDKADNIPGVEGIGDINAVKLITKFGSL 326

Source: Oryza sativa Indica Group

Species: Oryza sativa

Genus: Oryza

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|115451687|ref|NP_001049444.1| Os03g0227300 [Oryza sativa Japonica Group] gi|108706959|gb|ABF94754.1| 5'-3' exonuclease, N-terminal resolvase-like domain containing protein, expressed [Oryza sativa Japonica Group] gi|113547915|dbj|BAF11358.1| Os03g0227300 [Oryza sativa Japonica Group] gi|215704203|dbj|BAG93043.1| unnamed protein product [Oryza sativa Japonica Group] gi|222624502|gb|EEE58634.1| hypothetical protein OsJ_10000 [Oryza sativa Japonica Group]

 Score = 97.1 bits (240), Expect = 1e-18,   Method: Composition-based stats.
 Identities = 43/56 (76%), Positives = 50/56 (89%)

Query: 1   MASFGMEDFARKYGELKPSQFVDVISLVGDKADNIPGVEGIGDVRAVQLITKFGML 56
           M SFG+EDF ++YG LKPSQFVDV++L GDKADNIPGVEGIGD+ AV+LITKFG L
Sbjct: 271 MVSFGVEDFVKRYGALKPSQFVDVVALSGDKADNIPGVEGIGDINAVKLITKFGSL 326

Source: Oryza sativa Japonica Group

Species: Oryza sativa

Genus: Oryza

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|24421685|gb|AAN60992.1| Unknown protein [Oryza sativa Japonica Group]

 Score = 96.7 bits (239), Expect = 1e-18,   Method: Composition-based stats.
 Identities = 43/56 (76%), Positives = 50/56 (89%)

Query: 1   MASFGMEDFARKYGELKPSQFVDVISLVGDKADNIPGVEGIGDVRAVQLITKFGML 56
           M SFG+EDF ++YG LKPSQFVDV++L GDKADNIPGVEGIGD+ AV+LITKFG L
Sbjct: 293 MVSFGVEDFVKRYGALKPSQFVDVVALSGDKADNIPGVEGIGDINAVKLITKFGSL 348

Source: Oryza sativa Japonica Group

Species: Oryza sativa

Genus: Oryza

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|194696700|gb|ACF82434.1| unknown [Zea mays] gi|195654367|gb|ACG46651.1| DNA polymerase I [Zea mays] gi|413956435|gb|AFW89084.1| DNA polymerase I [Zea mays]

 Score = 95.9 bits (237), Expect = 3e-18,   Method: Composition-based stats.
 Identities = 42/56 (75%), Positives = 50/56 (89%)

Query: 1   MASFGMEDFARKYGELKPSQFVDVISLVGDKADNIPGVEGIGDVRAVQLITKFGML 56
           M SFG+EDF ++YG LKPSQFVDV++L GDKADNIPGVEGIGD+ AV+LI+KFG L
Sbjct: 272 MVSFGVEDFVKRYGPLKPSQFVDVVALSGDKADNIPGVEGIGDINAVKLISKFGSL 327

Source: Zea mays

Species: Zea mays

Genus: Zea

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449453197|ref|XP_004144345.1| PREDICTED: DNA polymerase I-like [Cucumis sativus]

 Score = 95.9 bits (237), Expect = 3e-18,   Method: Composition-based stats.
 Identities = 43/56 (76%), Positives = 51/56 (91%)

Query: 1   MASFGMEDFARKYGELKPSQFVDVISLVGDKADNIPGVEGIGDVRAVQLITKFGML 56
           M SFG+EDFA K+G L+PSQFVDV+SLVGDK+DNIPGV+GIG+V AVQLIT+FG L
Sbjct: 310 MVSFGLEDFADKFGVLEPSQFVDVMSLVGDKSDNIPGVDGIGNVNAVQLITRFGTL 365

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|42565846|ref|NP_190773.2| 5'-3' exonuclease-like protein [Arabidopsis thaliana] gi|145362483|ref|NP_974414.2| 5'-3' exonuclease-like protein [Arabidopsis thaliana] gi|109946597|gb|ABG48477.1| At3g52050 [Arabidopsis thaliana] gi|332645358|gb|AEE78879.1| 5'-3' exonuclease-like protein [Arabidopsis thaliana] gi|332645359|gb|AEE78880.1| 5'-3' exonuclease-like protein [Arabidopsis thaliana]

 Score = 95.5 bits (236), Expect = 4e-18,   Method: Composition-based stats.
 Identities = 40/56 (71%), Positives = 52/56 (92%)

Query: 1   MASFGMEDFARKYGELKPSQFVDVISLVGDKADNIPGVEGIGDVRAVQLITKFGML 56
           MASFGMEDFA+K+G L+P+QFVD+I+L GDK+DNIPGV+GIG+V AV+LI++FG L
Sbjct: 273 MASFGMEDFAKKFGNLEPAQFVDIIALAGDKSDNIPGVDGIGNVHAVELISRFGTL 328

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

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	66
TAIR|locus:2083775	448	AT3G52050 [Arabidopsis thalian	0.848	0.125	0.714	7.5e-18
TIGR_CMR|BA_4831	877	BA_4831 "DNA polymerase I" [Ba	0.712	0.053	0.479	1.1e-06
TIGR_CMR|GSU_0541	891	GSU_0541 "DNA polymerase I" [G	0.772	0.057	0.442	1.2e-06
TIGR_CMR|SO_4669	922	SO_4669 "DNA polymerase I" [Sh	0.742	0.053	0.46	1.2e-06
UNIPROTKB|Q3ABL3	831	polA "DNA polymerase" [Carboxy	0.621	0.049	0.595	2.8e-06
TIGR_CMR|CHY_1650	831	CHY_1650 "DNA polymerase I" [C	0.621	0.049	0.595	2.8e-06
TIGR_CMR|NSE_0675	829	NSE_0675 "DNA polymerase I" [N	0.772	0.061	0.461	3.6e-06
TIGR_CMR|CJE_0383	879	CJE_0383 "DNA polymerase type	0.666	0.050	0.511	1.7e-05
DICTYBASE|DDB_G0267464	1369	polA "mitochondrial DNA polyme	0.818	0.039	0.436	1.7e-05
TIGR_CMR|ECH_0080	944	ECH_0080 "DNA polymerase I" [E	0.742	0.051	0.44	1.9e-05

TAIR|locus:2083775 AT3G52050 [Arabidopsis thaliana (taxid:3702)]

 Score = 223 (83.6 bits), Expect = 7.5e-18, P = 7.5e-18
 Identities = 40/56 (71%), Positives = 52/56 (92%)

Query:     1 MASFGMEDFARKYGELKPSQFVDVISLVGDKADNIPGVEGIGDVRAVQLITKFGML 56
             MASFGMEDFA+K+G L+P+QFVD+I+L GDK+DNIPGV+GIG+V AV+LI++FG L
Sbjct:   296 MASFGMEDFAKKFGNLEPAQFVDIIALAGDKSDNIPGVDGIGNVHAVELISRFGTL 351

GO:0003677 "DNA binding" evidence=IEA

GO:0003824 "catalytic activity" evidence=IEA;ISS

GO:0005634 "nucleus" evidence=ISM

GO:0008409 "5'-3' exonuclease activity" evidence=IEA

TIGR_CMR|BA_4831 BA_4831 "DNA polymerase I" [Bacillus anthracis str. Ames (taxid:198094)]

 Score = 124 (48.7 bits), Expect = 1.1e-06, P = 1.1e-06
 Identities = 23/48 (47%), Positives = 34/48 (70%)

Query:     7 EDFARKYGELKPSQFVDVISLVGDKADNIPGVEGIGDVRAVQLITKFG 54
             E    KY  L P Q +D+  L+GD++DNIPGV G+G+  A++L+T+FG
Sbjct:   163 EALFEKYS-LSPKQIIDMKGLMGDQSDNIPGVPGVGEKTAIKLLTQFG 209

GO:0003887 "DNA-directed DNA polymerase activity" evidence=ISS

GO:0006260 "DNA replication" evidence=ISS

TIGR_CMR|GSU_0541 GSU_0541 "DNA polymerase I" [Geobacter sulfurreducens PCA (taxid:243231)]

 Score = 124 (48.7 bits), Expect = 1.2e-06, P = 1.2e-06
 Identities = 23/52 (44%), Positives = 35/52 (67%)

Query:     5 GMEDFARKYGELKPSQFVDVISLVGDKADNIPGVEGIGDVRAVQLITKFGML 56
             G+ +   ++G + P Q +D++ L GD +DNIPGV GIG+  A +LI +FG L
Sbjct:   158 GIPEVVERFG-VGPGQVIDILGLAGDTSDNIPGVPGIGEKTATKLIQEFGSL 208

GO:0003887 "DNA-directed DNA polymerase activity" evidence=ISS

GO:0006260 "DNA replication" evidence=ISS

GO:0006308 "DNA catabolic process" evidence=ISS

GO:0008409 "5'-3' exonuclease activity" evidence=ISS

TIGR_CMR|SO_4669 SO_4669 "DNA polymerase I" [Shewanella oneidensis MR-1 (taxid:211586)]

 Score = 124 (48.7 bits), Expect = 1.2e-06, P = 1.2e-06
 Identities = 23/50 (46%), Positives = 36/50 (72%)

Query:     5 GMEDFARKYGELKPSQFVDVISLVGDKADNIPGVEGIGDVRAVQLITKFG 54
             G E+ A KYG + P + +D ++L+GDKADNIPG+ G+G+  A+ ++T  G
Sbjct:   161 GPEEVAAKYG-VGPDRIIDFLALMGDKADNIPGLPGVGEKTALAMLTGAG 209

GO:0003887 "DNA-directed DNA polymerase activity" evidence=ISS

GO:0006260 "DNA replication" evidence=ISS

UNIPROTKB|Q3ABL3 polA "DNA polymerase" [Carboxydothermus hydrogenoformans Z-2901 (taxid:246194)]

 Score = 120 (47.3 bits), Expect = 2.8e-06, P = 2.8e-06
 Identities = 25/42 (59%), Positives = 30/42 (71%)

Query:    13 YGELKPSQFVDVISLVGDKADNIPGVEGIGDVRAVQLITKFG 54
             YG LKP Q VDV  L+GD +DNIPGV GIG+  A+ LI  +G
Sbjct:   168 YG-LKPKQLVDVKGLMGDPSDNIPGVPGIGEKTALDLIKTYG 208

GO:0003887 "DNA-directed DNA polymerase activity" evidence=ISS

TIGR_CMR|CHY_1650 CHY_1650 "DNA polymerase I" [Carboxydothermus hydrogenoformans Z-2901 (taxid:246194)]

 Score = 120 (47.3 bits), Expect = 2.8e-06, P = 2.8e-06
 Identities = 25/42 (59%), Positives = 30/42 (71%)

Query:    13 YGELKPSQFVDVISLVGDKADNIPGVEGIGDVRAVQLITKFG 54
             YG LKP Q VDV  L+GD +DNIPGV GIG+  A+ LI  +G
Sbjct:   168 YG-LKPKQLVDVKGLMGDPSDNIPGVPGIGEKTALDLIKTYG 208

GO:0003887 "DNA-directed DNA polymerase activity" evidence=ISS

GO:0006260 "DNA replication" evidence=ISS

TIGR_CMR|NSE_0675 NSE_0675 "DNA polymerase I" [Neorickettsia sennetsu str. Miyayama (taxid:222891)]

 Score = 119 (46.9 bits), Expect = 3.6e-06, P = 3.6e-06
 Identities = 24/52 (46%), Positives = 33/52 (63%)

Query:     5 GMEDFARKYGELKPSQFVDVISLVGDKADNIPGVEGIGDVRAVQLITKFGML 56
             G+ +   K+G   P+Q  D +SLVGD +DNIPGV GIG   A +L+  FG +
Sbjct:   155 GVNEVKEKFGVF-PTQMTDFLSLVGDTSDNIPGVPGIGVKTAAKLLNTFGAI 205

GO:0003887 "DNA-directed DNA polymerase activity" evidence=ISS

GO:0006260 "DNA replication" evidence=ISS

TIGR_CMR|CJE_0383 CJE_0383 "DNA polymerase type I" [Campylobacter jejuni RM1221 (taxid:195099)]

 Score = 113 (44.8 bits), Expect = 1.7e-05, P = 1.7e-05
 Identities = 23/45 (51%), Positives = 32/45 (71%)

Query:    12 KYGELKPSQFVDVISLVGDKADNIPGVEGIGDVRAVQLITKFGML 56
             KYG +KP+Q  D ++L GD +DNIPGV+GIG   A  L+ +FG +
Sbjct:   164 KYG-VKPNQIRDFLALCGDSSDNIPGVKGIGAKGAKTLLDEFGSI 207

GO:0003887 "DNA-directed DNA polymerase activity" evidence=ISS

GO:0006260 "DNA replication" evidence=ISS

GO:0009360 "DNA polymerase III complex" evidence=ISS

DICTYBASE|DDB_G0267464 polA "mitochondrial DNA polymerase A" [Dictyostelium discoideum (taxid:44689)]

 Score = 115 (45.5 bits), Expect = 1.7e-05, P = 1.7e-05
 Identities = 24/55 (43%), Positives = 35/55 (63%)

Query:    12 KYGELKPSQFVDVISLVGDKADNIPGVEGIGDVRAVQLITKFGMLVFNVECFSEM 66
             K+G  +P++FV   SL+GDK DNIPG+  IG+  A  +I KFG L   +E   ++
Sbjct:   456 KFG-FEPNKFVTFQSLIGDKVDNIPGIPRIGEKTATDIIKKFGNLNSIIENIDQL 509

GO:0008409 "5'-3' exonuclease activity" evidence=IEA

GO:0008408 "3'-5' exonuclease activity" evidence=IEA

GO:0006260 "DNA replication" evidence=IEA

GO:0006139 "nucleobase-containing compound metabolic process" evidence=IEA

GO:0005622 "intracellular" evidence=IEA

GO:0003887 "DNA-directed DNA polymerase activity" evidence=IEA

GO:0003824 "catalytic activity" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

TIGR_CMR|ECH_0080 ECH_0080 "DNA polymerase I" [Ehrlichia chaffeensis str. Arkansas (taxid:205920)]

 Score = 113 (44.8 bits), Expect = 1.9e-05, P = 1.9e-05
 Identities = 22/50 (44%), Positives = 32/50 (64%)

Query:     7 EDFARKYGELKPSQFVDVISLVGDKADNIPGVEGIGDVRAVQLITKFGML 56
             ED   K+G +  +Q +D +SL GD +DN+PG+ GIG   A +L+  FG L
Sbjct:   159 EDVQSKFG-ISSNQLLDFLSLTGDASDNVPGIPGIGVKTAAKLLNDFGSL 207

GO:0003887 "DNA-directed DNA polymerase activity" evidence=ISS

GO:0006260 "DNA replication" evidence=ISS

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input:
	GSVIVG00034655001	SubName- Full=Chromosome chr5 scaffold_72, whole genome shotgun sequence; (394 aa)
		(Vitis vinifera)
Predicted Functional Partners:
	GSVIVG00032487001	SubName- Full=Chromosome chr4 scaffold_6, whole genome shotgun sequence; (436 aa)		•					•		0.902
	GSVIVG00027855001	SubName- Full=Chromosome chr19 scaffold_4, whole genome shotgun sequence; (897 aa)		•							0.439
	GSVIVG00015405001	RecName- Full=Delta-aminolevulinic acid dehydratase; EC=4.2.1.24; (430 aa)	•								0.439

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	66
smart00475	259	smart00475, 53EXOc, 5'-3' exonuclease	2e-18
cd09898	73	cd09898, H3TH_53EXO, H3TH domain of the 5'-3' exon	2e-17
PRK05755	880	PRK05755, PRK05755, DNA polymerase I; Provisional	4e-16
COG0258	310	COG0258, Exo, 5'-3' exonuclease (including N-termi	6e-16
pfam01367	100	pfam01367, 5_3_exonuc, 5'-3' exonuclease, C-termin	6e-14
TIGR00593	887	TIGR00593, pola, DNA polymerase I	8e-14
PRK14976	281	PRK14976, PRK14976, 5'-3' exonuclease; Provisional	6e-13
smart00279	36	smart00279, HhH2, Helix-hairpin-helix class 2 (Pol	9e-11
PRK09482	256	PRK09482, PRK09482, flap endonuclease-like protein	9e-11
cd00080	71	cd00080, H3TH_StructSpec-5'-nucleases, H3TH domain	4e-07
cd09899	74	cd09899, H3TH_T4-like, H3TH domain of bacteriophag	4e-05
cd09907	70	cd09907, H3TH_FEN1-Euk, H3TH domain of Flap Endonu	0.001
PRK03980	292	PRK03980, PRK03980, flap endonuclease-1; Provision	0.001

>gnl|CDD|214682 smart00475, 53EXOc, 5'-3' exonuclease

 Score = 74.9 bits (185), Expect = 2e-18
 Identities = 25/56 (44%), Positives = 35/56 (62%), Gaps = 1/56 (1%)

Query: 1   MASFGMEDFARKYGELKPSQFVDVISLVGDKADNIPGVEGIGDVRAVQLITKFGML 56
              +  E+   KYG L P Q +D  +L+GD +DNIPGV GIG+  A +L+ +FG L
Sbjct: 155 FELYTPENVIEKYG-LTPEQIIDYKALMGDSSDNIPGVPGIGEKTAAKLLKEFGSL 209

Length = 259

>gnl|CDD|188618 cd09898, H3TH_53EXO, H3TH domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs

 Score = 68.2 bits (168), Expect = 2e-17
 Identities = 19/37 (51%), Positives = 27/37 (72%)

Query: 18 PSQFVDVISLVGDKADNIPGVEGIGDVRAVQLITKFG 54
          P Q +D ++LVGD +DNIPGV GIG   A +L+ ++G
Sbjct: 1  PEQIIDYLALVGDSSDNIPGVPGIGPKTAAKLLQEYG 37

H3TH (helix-3-turn-helix) domains of the 5'-3' exonuclease (53EXO) of mutli-domain DNA polymerase I and single domain protein homologs are included in this family. Taq DNA polymerase I contains a polymerase domain for synthesizing a new DNA strand and a 53EXO domain for cleaving RNA primers or damaged DNA strands. Taq's 53EXO recognizes and endonucleolytically cleaves a structure-specific DNA substrate that has a bifurcated downstream duplex and an upstream template-primer duplex that overlaps the downstream duplex by 1 bp. The 53EXO cleaves the unpaired 5'-arm of the overlap flap DNA substrate. 5'-3' exonucleases are members of the structure-specific, 5' nuclease family that catalyzes hydrolysis of DNA duplex-containing nucleic acid structures during DNA replication, repair, and recombination. These nucleases contain a PIN (PilT N terminus) domain with a helical arch/clamp region/I domain (not included here) and inserted within the PIN domain is an atypical helix-hairpin-helix-2 (HhH2)-like region. This atypical HhH2 region, the H3TH domain, has an extended loop with at least three turns between the first two helices, and only three of the four helices appear to be conserved. Both the H3TH domain and the helical arch/clamp region are involved in DNA binding. Studies suggest that a glycine-rich loop in the H3TH domain contacts the phosphate backbone of the template strand in the downstream DNA duplex. The nucleases within this family have a carboxylate rich active site that is involved in binding essential divalent metal ion cofactors (i. e., Mg2+ or Mn2+ or Zn2+) required for nuclease activity. The first metal binding site is composed entirely of Asp/Glu residues from the PIN domain, whereas, the second metal binding site is composed generally of two Asp residues from the PIN domain and two Asp residues from the H3TH domain. Together with the helical arch and network of amino acids interacting with metal binding ions, the H3TH region defines a positively charged active-site DNA-binding groove in structure-specific 5' nucleases. Length = 73

>gnl|CDD|235591 PRK05755, PRK05755, DNA polymerase I; Provisional

 Score = 70.1 bits (173), Expect = 4e-16
 Identities = 22/51 (43%), Positives = 34/51 (66%), Gaps = 1/51 (1%)

Query: 4   FGMEDFARKYGELKPSQFVDVISLVGDKADNIPGVEGIGDVRAVQLITKFG 54
              E+   KYG + P Q +D ++L+GD +DNIPGV GIG+  A +L+ ++G
Sbjct: 159 LDPEEVVEKYG-VTPEQIIDYLALMGDSSDNIPGVPGIGEKTAAKLLQEYG 208

Length = 880

>gnl|CDD|223336 COG0258, Exo, 5'-3' exonuclease (including N-terminal domain of PolI) [DNA replication, recombination, and repair]

 Score = 68.9 bits (169), Expect = 6e-16
 Identities = 23/53 (43%), Positives = 36/53 (67%)

Query: 4   FGMEDFARKYGELKPSQFVDVISLVGDKADNIPGVEGIGDVRAVQLITKFGML 56
             +E+   K+  L P Q +D+ +LVGD +DNIPGV+GIG   A++L+ ++G L
Sbjct: 169 LDLEEVEEKFKGLTPEQLIDLKALVGDSSDNIPGVKGIGPKTALKLLQEYGSL 221

Length = 310

>gnl|CDD|216458 pfam01367, 5_3_exonuc, 5'-3' exonuclease, C-terminal SAM fold

 Score = 59.9 bits (146), Expect = 6e-14
 Identities = 21/41 (51%), Positives = 29/41 (70%)

Query: 16 LKPSQFVDVISLVGDKADNIPGVEGIGDVRAVQLITKFGML 56
          L P Q +D  +LVGD +DNIPGV GIG+  A +L+ ++G L
Sbjct: 1  LTPEQIIDYKALVGDSSDNIPGVPGIGEKTAAKLLKEYGSL 41

Length = 100

>gnl|CDD|233038 TIGR00593, pola, DNA polymerase I

 Score = 63.5 bits (155), Expect = 8e-14
 Identities = 26/53 (49%), Positives = 35/53 (66%), Gaps = 1/53 (1%)

Query: 4   FGMEDFARKYGELKPSQFVDVISLVGDKADNIPGVEGIGDVRAVQLITKFGML 56
              E    KYG + P Q VD+ +LVGD +DNIPGV+GIG+  A +L+ +FG L
Sbjct: 157 ITPEYVVEKYG-VTPDQLVDLKALVGDSSDNIPGVKGIGEKTAAKLLQEFGSL 208

All proteins in this family for which functions are known are DNA polymerases Many also have an exonuclease motif. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University) [DNA metabolism, DNA replication, recombination, and repair]. Length = 887

>gnl|CDD|237877 PRK14976, PRK14976, 5'-3' exonuclease; Provisional

 Score = 60.3 bits (147), Expect = 6e-13
 Identities = 22/50 (44%), Positives = 33/50 (66%), Gaps = 1/50 (2%)

Query: 7   EDFARKYGELKPSQFVDVISLVGDKADNIPGVEGIGDVRAVQLITKFGML 56
            +F   YG ++P Q +D   LVGD +DNI GV+GIG   A++L+ K+G +
Sbjct: 166 NNFFELYG-IEPKQIIDYKGLVGDSSDNIKGVKGIGPKTAIKLLNKYGNI 214

Length = 281

>gnl|CDD|197623 smart00279, HhH2, Helix-hairpin-helix class 2 (Pol1 family) motifs

 Score = 50.5 bits (122), Expect = 9e-11
 Identities = 20/36 (55%), Positives = 27/36 (75%)

Query: 18 PSQFVDVISLVGDKADNIPGVEGIGDVRAVQLITKF 53
          P QF+D   LVGD +DNIPGV+GIG   A++L+ +F
Sbjct: 1  PEQFIDYAILVGDYSDNIPGVKGIGPKTALKLLREF 36

Length = 36

>gnl|CDD|181896 PRK09482, PRK09482, flap endonuclease-like protein; Provisional

 Score = 54.1 bits (131), Expect = 9e-11
 Identities = 17/51 (33%), Positives = 26/51 (50%), Gaps = 1/51 (1%)

Query: 6   MEDFARKYGELKPSQFVDVISLVGDKADNIPGVEGIGDVRAVQLITKFGML 56
                +++G ++P Q  D   L G  +  IPGV GIG   A +L+ +F  L
Sbjct: 156 APFIEQEFG-VEPQQLPDYWGLAGISSSKIPGVAGIGPKSAAELLNQFRSL 205

Length = 256

>gnl|CDD|188616 cd00080, H3TH_StructSpec-5'-nucleases, H3TH domains of structure-specific 5' nucleases (or flap endonuclease-1-like) involved in DNA replication, repair, and recombination

 Score = 42.0 bits (99), Expect = 4e-07
 Identities = 20/38 (52%), Positives = 26/38 (68%), Gaps = 2/38 (5%)

Query: 20 QFVDVISLVG-DKADNIPGVEGIGDVRAVQLITKFGML 56
          QF+D+ +LVG D +DN PGV GIG   A +L  K+G L
Sbjct: 2  QFIDLCALVGCDYSDN-PGVPGIGPKTAAKLALKYGSL 38

The 5' nucleases of this superfamily are capable of both 5'-3' exonucleolytic activity and cleaving bifurcated or branched DNA, in an endonucleolytic, structure-specific manner, and are involved in DNA replication, repair, and recombination. The superfamily includes the H3TH (helix-3-turn-helix) domains of Flap Endonuclease-1 (FEN1), Exonuclease-1 (EXO1), Mkt1, Gap Endonuclease 1 (GEN1) and Xeroderma pigmentosum complementation group G (XPG) nuclease. Also included are the H3TH domains of the 5'-3' exonucleases of DNA polymerase I and single domain protein homologs, as well as, the bacteriophage T4 RNase H, T5-5'nuclease, and other homologs. These nucleases contain a PIN (PilT N terminus) domain with a helical arch/clamp region/I domain (not included here) and inserted within the C-terminal region of the PIN domain is an atypical helix-hairpin-helix-2 (HhH2)-like region. This atypical HhH2 region, the H3TH domain, has an extended loop with at least three turns between the first two helices, and only three of the four helices appear to be conserved. Both the H3TH domain and the helical arch/clamp region are involved in DNA binding. Studies suggest that a glycine-rich loop in the H3TH domain contacts the phosphate backbone of the template strand in the downstream DNA duplex. Typically, the nucleases within this superfamily have a carboxylate rich active site that is involved in binding essential divalent metal ion cofactors (i. e., Mg2+, Mn2+, Zn2+, or Co2+) required for nuclease activity. The first metal binding site is composed entirely of Asp/Glu residues from the PIN domain, whereas, the second metal binding site is composed generally of two Asp residues from the PIN domain and one or two Asp residues from the H3TH domain. Together with the helical arch and network of amino acids interacting with metal binding ions, the H3TH region defines a positively charged active-site DNA-binding groove in structure-specific 5' nucleases. Length = 71

>gnl|CDD|188619 cd09899, H3TH_T4-like, H3TH domain of bacteriophage T3, T4 RNase H, T5-5' nucleases, and homologs

 Score = 37.1 bits (86), Expect = 4e-05
 Identities = 16/37 (43%), Positives = 22/37 (59%)

Query: 18 PSQFVDVISLVGDKADNIPGVEGIGDVRAVQLITKFG 54
          P  ++   +L GD  DNI GV GIG  RA +L+ + G
Sbjct: 2  PEAYLSAKALAGDTKDNIAGVPGIGTGRATKLLEEIG 38

H3TH (helix-3-turn-helix) domains of bacteriophage T5-5'nuclease (5'-3' exonuclease or T5FEN), bacteriophage T4 RNase H (T4FEN), bacteriophage T3 (T3 phage exodeoxyribonuclease) and other similar 5' nucleases are included in this family. The T5-5'nuclease is a 5'-3' exodeoxyribonuclease that also exhibits endonucleolytic activity on flap structures (branched duplex DNA containing a free single-stranded 5'end). T4 RNase H, which removes the RNA primers that initiate lagging strand fragments, has 5'- 3' exonuclease activity on DNA/DNA and RNA/DNA duplexes and has endonuclease activity on flap or forked DNA structures. Bacteriophage T3 is believed to function in the removal of DNA-linked RNA primers and is essential for phage DNA replication and also necessary for host DNA degradation and phage genetic recombination. These nucleases are members of the structure-specific, 5' nuclease family that catalyzes hydrolysis of DNA duplex-containing nucleic acid structures during DNA replication, repair, and recombination. They contain a PIN (PilT N terminus) domain with a helical arch/clamp region/I domain (not included here) and inserted within the PIN domain is an atypical helix-hairpin-helix-2 (HhH2)-like region. This atypical HhH2 region, the H3TH domain, has an extended loop with at least three turns between the first two helices, and only three of the four helices appear to be conserved. Both the H3TH domain and the helical arch/clamp region are involved in DNA binding. Studies suggest that a glycine-rich loop in the H3TH domain contacts the phosphate backbone of the template strand in the downstream DNA duplex. The nucleases within this family have a carboxylate rich active site that is involved in binding essential divalent metal ion cofactors required for nuclease activity. The first metal binding site (MBS-1) is composed entirely of Asp/Glu residues from the PIN domain, whereas, the second metal binding site (MBS-2) is composed generally of two Asp residues from the PIN domain and two Asp residues from the H3TH domain. In the T5-5'nuclease, structure-specific endonuclease activity requires binding of a single metal ion in the high-affinity, MBS-1, whereas exonuclease activity requires both, the high-affinity, MBS-1 and the low-affinity, MBS-2 to be occupied by a divalent cofactor. The T5-5'nuclease is reported to be able to bind several metal ions including, Mg2+, Mn2+, Zn2+ and Co2+, as co-factors. Together with the helical arch and network of amino acids interacting with metal binding ions, the H3TH region defines a positively charged active-site DNA-binding groove in structure-specific 5' nucleases. Length = 74

>gnl|CDD|188627 cd09907, H3TH_FEN1-Euk, H3TH domain of Flap Endonuclease-1, a structure-specific, divalent-metal-ion dependent, 5' nuclease: Eukaryotic homologs

 Score = 33.3 bits (77), Expect = 0.001
 Identities = 13/36 (36%), Positives = 20/36 (55%), Gaps = 2/36 (5%)

Query: 19 SQFVDVISLVGDKADNIPGVEGIGDVRAVQLITKFG 54
           QF+D+  L+G   D    ++GIG   A++LI K  
Sbjct: 1  EQFIDLCILLG--CDYCESIKGIGPKTALKLIKKHK 34

Members of this subgroup include the H3TH (helix-3-turn-helix) domains of eukaryotic Flap endonuclease-1 (FEN1), 5' nucleases. FEN1 is involved in multiple DNA metabolic pathways, including DNA replication processes (5' flap DNA endonuclease activity and double stranded DNA 5'-exonuclease activity) and DNA repair processes (long-patch base excision repair) in eukaryotes and archaea. Interaction between FEN1 and PCNA (Proliferating cell nuclear antigen) is an essential prerequisite to FEN1's DNA replication functionality and stimulates FEN1 nuclease activity by 10-50 fold. These nucleases contain a PIN (PilT N terminus) domain with a helical arch/clamp region/I domain (not included here) and inserted within the PIN domain is an atypical helix-hairpin-helix-2 (HhH2)-like region. This atypical HhH2 region, the H3TH domain, has an extended loop with at least three turns between the first two helices, and only three of the four helices appear to be conserved. Both the H3TH domain and the helical arch/clamp region are involved in DNA binding. Studies suggest that a glycine-rich loop in the H3TH domain contacts the phosphate backbone of the template strand in the downstream DNA duplex. The nucleases within this subfamily have a carboxylate rich active site that is involved in binding essential divalent metal ion cofactors (Mg2+ or Mn2+) required for nuclease activity. The first metal binding site is composed entirely of Asp/Glu residues from the PIN domain, whereas, the second metal binding site is composed generally of two Asp residues from the PIN domain and one Asp residue from the H3TH domain. Together with the helical arch and network of amino acids interacting with metal binding ions, the H3TH region defines a positively charged active-site DNA-binding groove in structure-specific 5' nucleases. Also, FEN1 has a C-terminal extension containing residues forming the consensus PIP-box - Qxx(M/L/I)xxF(Y/F) which serves to anchor FEN1 to PCNA. Length = 70

>gnl|CDD|235185 PRK03980, PRK03980, flap endonuclease-1; Provisional

 Score = 34.4 bits (80), Expect = 0.001
 Identities = 17/37 (45%), Positives = 23/37 (62%), Gaps = 2/37 (5%)

Query: 20  QFVDVISLVGDKADNIPGVEGIGDVRAVQLITKFGML 56
           Q +D+  LVG   D  PG++GIG   A++LI K G L
Sbjct: 178 QLIDIAILVG--TDYNPGIKGIGPKTALKLIKKHGDL 212

Length = 292

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	66
PRK09482	256	flap endonuclease-like protein; Provisional	99.91
smart00475	259	53EXOc 5'-3' exonuclease.	99.91
PRK14976	281	5'-3' exonuclease; Provisional	99.9
cd00008	240	53EXOc 5'-3' exonuclease; T5 type 5'-3' exonucleas	99.89
cd00080	75	HhH2_motif Helix-hairpin-helix class 2 (Pol1 famil	99.89
PF01367	101	5_3_exonuc: 5'-3' exonuclease, C-terminal SAM fold	99.89
TIGR00593	887	pola DNA polymerase I. This family is based on the	99.87
PRK05755	880	DNA polymerase I; Provisional	99.85
COG0258	310	Exo 5'-3' exonuclease (including N-terminal domain	99.84
smart00279	36	HhH2 Helix-hairpin-helix class 2 (Pol1 family) mot	99.79
PTZ00217	393	flap endonuclease-1; Provisional	99.77
PRK03980	292	flap endonuclease-1; Provisional	99.76
TIGR03674	338	fen_arch flap structure-specific endonuclease. End	99.74
cd00128	316	XPG Xeroderma pigmentosum G N- and I-regions (XPGN	99.73
PHA00439	286	exonuclease	99.54
TIGR00600	1034	rad2 DNA excision repair protein (rad2). All prote	99.39
KOG2519	449	consensus 5'-3' exonuclease [Replication, recombin	99.25
PHA02567	304	rnh RnaseH; Provisional	98.63
KOG2518	556	consensus 5'-3' exonuclease [Replication, recombin	98.54
KOG2520	815	consensus 5'-3' exonuclease [Replication, recombin	98.35
PF12826	64	HHH_2: Helix-hairpin-helix motif; PDB: 1X2I_B 1DGS	98.19
PRK14667	567	uvrC excinuclease ABC subunit C; Provisional	97.73
TIGR00194	574	uvrC excinuclease ABC, C subunit. This family cons	97.69
PRK14670	574	uvrC excinuclease ABC subunit C; Provisional	97.64
PRK14669	624	uvrC excinuclease ABC subunit C; Provisional	97.61
PRK14672	691	uvrC excinuclease ABC subunit C; Provisional	97.39
PF14520	60	HHH_5: Helix-hairpin-helix domain; PDB: 3AUO_B 3AU	97.34
PRK14671	621	uvrC excinuclease ABC subunit C; Provisional	97.24
TIGR00084	191	ruvA Holliday junction DNA helicase, RuvA subunit.	97.14
PRK00558	598	uvrC excinuclease ABC subunit C; Validated	97.1
PRK14668	577	uvrC excinuclease ABC subunit C; Provisional	97.1
PRK12766	232	50S ribosomal protein L32e; Provisional	97.1
PF00633	30	HHH: Helix-hairpin-helix motif; InterPro: IPR00044	97.1
COG0322	581	UvrC Nuclease subunit of the excinuclease complex	97.08
PRK00116	192	ruvA Holliday junction DNA helicase RuvA; Reviewed	97.03
PRK14666	694	uvrC excinuclease ABC subunit C; Provisional	96.98
PRK14601	183	ruvA Holliday junction DNA helicase RuvA; Provisio	96.97
PF10391	52	DNA_pol_lambd_f: Fingers domain of DNA polymerase	96.94
PRK14605	194	ruvA Holliday junction DNA helicase RuvA; Provisio	96.89
PRK14602	203	ruvA Holliday junction DNA helicase RuvA; Provisio	96.89
PRK14600	186	ruvA Holliday junction DNA helicase RuvA; Provisio	96.86
PRK13901	196	ruvA Holliday junction DNA helicase RuvA; Provisio	96.74
PRK14602	203	ruvA Holliday junction DNA helicase RuvA; Provisio	96.74
smart00278	26	HhH1 Helix-hairpin-helix DNA-binding motif class 1	96.68
PRK14601	183	ruvA Holliday junction DNA helicase RuvA; Provisio	96.67
PRK13901	196	ruvA Holliday junction DNA helicase RuvA; Provisio	96.64
PRK14604	195	ruvA Holliday junction DNA helicase RuvA; Provisio	96.63
PRK14604	195	ruvA Holliday junction DNA helicase RuvA; Provisio	96.58
PRK14606	188	ruvA Holliday junction DNA helicase RuvA; Provisio	96.57
PRK14606	188	ruvA Holliday junction DNA helicase RuvA; Provisio	96.56
PRK14600	186	ruvA Holliday junction DNA helicase RuvA; Provisio	96.55
PRK14603	197	ruvA Holliday junction DNA helicase RuvA; Provisio	96.55
PRK14603	197	ruvA Holliday junction DNA helicase RuvA; Provisio	96.54
PF00867	94	XPG_I: XPG I-region; InterPro: IPR006086 This entr	96.46
TIGR00575	652	dnlj DNA ligase, NAD-dependent. The member of this	96.39
COG1948	254	MUS81 ERCC4-type nuclease [DNA replication, recomb	96.29
PRK14351	689	ligA NAD-dependent DNA ligase LigA; Provisional	96.22
PRK13482	352	DNA integrity scanning protein DisA; Provisional	96.07
COG0632	201	RuvA Holliday junction resolvasome, DNA-binding su	96.04
PF02371	87	Transposase_20: Transposase IS116/IS110/IS902 fami	95.99
TIGR01259	120	comE comEA protein. This model describes the ComEA	95.91
TIGR00084	191	ruvA Holliday junction DNA helicase, RuvA subunit.	95.9
TIGR00596	814	rad1 DNA repair protein (rad1). This family is bas	95.82
PRK07956	665	ligA NAD-dependent DNA ligase LigA; Validated	95.66
PRK13766	773	Hef nuclease; Provisional	95.64
COG0632	201	RuvA Holliday junction resolvasome, DNA-binding su	95.55
PRK14605	194	ruvA Holliday junction DNA helicase RuvA; Provisio	95.42
PRK02515	132	psbU photosystem II complex extrinsic protein prec	95.41
smart00483	334	POLXc DNA polymerase X family. includes vertebrate	95.1
PF12826	64	HHH_2: Helix-hairpin-helix motif; PDB: 1X2I_B 1DGS	94.9
PF11798	32	IMS_HHH: IMS family HHH motif; InterPro: IPR024728	94.84
PRK08609	570	hypothetical protein; Provisional	94.61
cd00141	307	NT_POLXc Nucleotidyltransferase (NT) domain of fam	94.57
PF14520	60	HHH_5: Helix-hairpin-helix domain; PDB: 3AUO_B 3AU	94.26
COG0272	667	Lig NAD-dependent DNA ligase (contains BRCT domain	94.2
COG1555	149	ComEA DNA uptake protein and related DNA-binding p	94.14
TIGR00426	69	competence protein ComEA helix-hairpin-helix repea	94.1
PRK00254	720	ski2-like helicase; Provisional	93.6
TIGR02236	310	recomb_radA DNA repair and recombination protein R	93.49
TIGR01448	720	recD_rel helicase, putative, RecD/TraA family. Thi	93.23
COG0177	211	Nth Predicted EndoIII-related endonuclease [DNA re	92.68
KOG2841	254	consensus Structure-specific endonuclease ERCC1-XP	92.38
PRK00116	192	ruvA Holliday junction DNA helicase RuvA; Reviewed	90.92
COG0353	198	RecR Recombinational DNA repair protein (RecF path	90.88
TIGR03252	177	uncharacterized HhH-GPD family protein. This model	90.43
PRK00076	196	recR recombination protein RecR; Reviewed	90.33
TIGR00615	195	recR recombination protein RecR. This family is ba	90.31
PRK13844	200	recombination protein RecR; Provisional	89.65
PRK14350	669	ligA NAD-dependent DNA ligase LigA; Provisional	89.5
PF13052	57	DUF3913: Protein of unknown function (DUF3913)	89.17
PRK04301	317	radA DNA repair and recombination protein RadA; Va	88.89
PF14716	68	HHH_8: Helix-hairpin-helix domain; PDB: 2W9M_A 1HU	88.86
PF04919	181	DUF655: Protein of unknown function (DUF655); Inte	88.32
PRK10702	211	endonuclease III; Provisional	87.99
KOG2841	254	consensus Structure-specific endonuclease ERCC1-XP	87.98
PF11731	93	Cdd1: Pathogenicity locus; InterPro: IPR021725 Cdd	87.9
PRK13910	289	DNA glycosylase MutY; Provisional	87.79
PRK01229	208	N-glycosylase/DNA lyase; Provisional	87.76
cd00056	158	ENDO3c endonuclease III; includes endonuclease III	86.94
PRK13482	352	DNA integrity scanning protein DisA; Provisional	86.67
PRK13913	218	3-methyladenine DNA glycosylase; Provisional	86.24
PF00416	107	Ribosomal_S13: Ribosomal protein S13/S18; InterPro	85.87
TIGR01084	275	mutY A/G-specific adenine glycosylase. This equiva	85.76
PF12836	65	HHH_3: Helix-hairpin-helix motif; PDB: 2EDU_A 2OCE	85.69
COG1491	202	Predicted RNA-binding protein [Translation, riboso	84.87
PF14579	90	HHH_6: Helix-hairpin-helix motif; PDB: 2HPM_A 2HPI	84.79
smart00478	149	ENDO3c endonuclease III. includes endonuclease III	84.62
PF14490	94	HHH_4: Helix-hairpin-helix containing domain; PDB:	84.08
TIGR01083	191	nth endonuclease III. This equivalog model identif	83.97
PRK10880	350	adenine DNA glycosylase; Provisional	83.52
PRK10736	374	hypothetical protein; Provisional	83.37
PF14229	122	DUF4332: Domain of unknown function (DUF4332)	82.45
PTZ00134	154	40S ribosomal protein S18; Provisional	82.21
KOG1921	286	consensus Endonuclease III [Replication, recombina	80.63
COG1194	342	MutY A/G-specific DNA glycosylase [DNA replication	80.13

>PRK09482 flap endonuclease-like protein; Provisional

Probab=99.91  E-value=8.5e-25  Score=151.82  Aligned_cols=62  Identities=29%  Similarity=0.479  Sum_probs=59.4

Q ss_pred             eeCHHHHHHHhCCCChhHHHHHHHhhCCCCCCCCCCCCccHHHHHHHHHHhCCHHHHHhhhcc
Q 035374            3 SFGMEDFARKYGELKPSQFVDVISLVGDKADNIPGVEGIGDVRAVQLITKFGMLVFNVECFSE   65 (66)
Q Consensus         3 ~~~~~~v~~~~g~i~p~q~~d~~~L~Gd~~D~i~gi~GiG~K~A~~Ll~~fgsl~~i~~~~~~   65 (66)
                      .++.++|.++|| ++|+|++||++|+||+|||||||||||||||.+||++|||+++|++++++
T Consensus       153 ~~~~~~v~~~~G-v~P~q~~D~~aL~GD~sDnIpGVpGIG~KtA~~LL~~~gsle~i~~~~~~  214 (256)
T PRK09482        153 WLDAPFIEQEFG-VEPQQLPDYWGLAGISSSKIPGVAGIGPKSAAELLNQFRSLENIYESLDA  214 (256)
T ss_pred             cCCHHHHHHHhC-CCHHHHHHHHHHhCCCccCCCCCCCcChHHHHHHHHHhCCHHHHHHhHHH
Confidence            479999999998 99999999999999999999999999999999999999999999998765

>smart00475 53EXOc 5'-3' exonuclease

Probab=99.91  E-value=1.8e-24  Score=149.69  Aligned_cols=62  Identities=42%  Similarity=0.739  Sum_probs=59.6

Q ss_pred             eeCHHHHHHHhCCCChhHHHHHHHhhCCCCCCCCCCCCccHHHHHHHHHHhCCHHHHHhhhcc
Q 035374            3 SFGMEDFARKYGELKPSQFVDVISLVGDKADNIPGVEGIGDVRAVQLITKFGMLVFNVECFSE   65 (66)
Q Consensus         3 ~~~~~~v~~~~g~i~p~q~~d~~~L~Gd~~D~i~gi~GiG~K~A~~Ll~~fgsl~~i~~~~~~   65 (66)
                      .++.++|.++|| ++|+||+||++|+||+|||||||||||||||.+||++|||++++++++++
T Consensus       157 ~~~~~~v~~~~G-v~p~q~~d~~aL~GD~sDnipGV~GIG~KtA~~Ll~~ygsle~i~~~~~~  218 (259)
T smart00475      157 LYTPENVIEKYG-LTPEQIIDYKALMGDSSDNIPGVPGIGEKTAAKLLKEFGSLENILENLDK  218 (259)
T ss_pred             EEcHHHHHHHhC-cCHHHHHHHHHHhCCcccCCCCCCCCCHHHHHHHHHHhCCHHHHHHHHHH
Confidence            589999999998 99999999999999999999999999999999999999999999998765

>PRK14976 5'-3' exonuclease; Provisional

Probab=99.90  E-value=3.2e-24  Score=149.87  Aligned_cols=63  Identities=37%  Similarity=0.644  Sum_probs=59.8

Q ss_pred             ceeCHHHHHHHhCCCChhHHHHHHHhhCCCCCCCCCCCCccHHHHHHHHHHhCCHHHHHhhhcc
Q 035374            2 ASFGMEDFARKYGELKPSQFVDVISLVGDKADNIPGVEGIGDVRAVQLITKFGMLVFNVECFSE   65 (66)
Q Consensus         2 ~~~~~~~v~~~~g~i~p~q~~d~~~L~Gd~~D~i~gi~GiG~K~A~~Ll~~fgsl~~i~~~~~~   65 (66)
                      ..++++.|.++|| ++|+||+|+++|+||+|||||||||||||||.+||++|||++++++++++
T Consensus       161 ~~~~~~~v~~~~g-v~p~q~~d~~aL~GD~sDnipGVpGIG~KtA~~LL~~~gsle~i~~~~~~  223 (281)
T PRK14976        161 FILNTNNFFELYG-IEPKQIIDYKGLVGDSSDNIKGVKGIGPKTAIKLLNKYGNIENIYENIDK  223 (281)
T ss_pred             EEEcHHHHHHHhC-cCHHHHHHHHHHhCCccCCCCCCCcccHHHHHHHHHHcCCHHHHHHhHHH
Confidence            3589999999998 99999999999999999999999999999999999999999999988765

>cd00008 53EXOc 5'-3' exonuclease; T5 type 5'-3' exonuclease domains may co-occur with DNA polymerase I (Pol I) domains, or be part of Pol I containing complexes

Probab=99.89  E-value=1.8e-23  Score=142.74  Aligned_cols=62  Identities=39%  Similarity=0.686  Sum_probs=59.1

Q ss_pred             eeCHHHHHHHhCCCChhHHHHHHHhhCCCCCCCCCCCCccHHHHHHHHHHhCCHHHHHhhhcc
Q 035374            3 SFGMEDFARKYGELKPSQFVDVISLVGDKADNIPGVEGIGDVRAVQLITKFGMLVFNVECFSE   65 (66)
Q Consensus         3 ~~~~~~v~~~~g~i~p~q~~d~~~L~Gd~~D~i~gi~GiG~K~A~~Ll~~fgsl~~i~~~~~~   65 (66)
                      .++.+.|.++|| ++|+||+|+++|+||+|||+|||||||||||.+||++|||++++++++++
T Consensus       154 ~i~~~~v~~~~g-~~p~q~~d~~~L~GD~sDnipGv~GiG~ktA~~Ll~~~gsle~i~~~~~~  215 (240)
T cd00008         154 LVTEENVIEKYG-VTPAQIIDYKALMGDSSDNIPGVPGIGEKTAAKLLKEYGSLEGILENLDK  215 (240)
T ss_pred             EEeHHHHHHHhC-cCHHHHHHHHHHcCCcccCCCCCCccCHHHHHHHHHHhCCHHHHHHhHHH
Confidence            578999999998 99999999999999999999999999999999999999999999988764

They digest dsDNA and ssDNA, releasing mono-,di- and tri-nucleotides, as well as oligonucleotides, and have also been reported to possess RNase H activity. Also called 5' nuclease family, involved in structure-specific cleavage of flaps formed by Pol I activity (similar to mammalian flap endonuclease I, FEN-1). A single nucleic acid strand may be threaded through the 5' nuclease enzyme before cleavage occurs. The domain binds two divalent metal ions which are necessary for activity.

>cd00080 HhH2_motif Helix-hairpin-helix class 2 (Pol1 family) motif

Probab=99.89  E-value=1e-23  Score=123.14  Aligned_cols=52  Identities=50%  Similarity=0.845  Sum_probs=49.5

Q ss_pred             HhCCCChhHHHHHHHhhCCCCCCCCCCCCccHHHHHHHHHHhCCHHHHHhhhc
Q 035374           12 KYGELKPSQFVDVISLVGDKADNIPGVEGIGDVRAVQLITKFGMLVFNVECFS   64 (66)
Q Consensus        12 ~~g~i~p~q~~d~~~L~Gd~~D~i~gi~GiG~K~A~~Ll~~fgsl~~i~~~~~   64 (66)
                      +|| ++|+||+|+|+|+||++||+|||||||+|+|.+||++|+++++++++++
T Consensus         2 ~~g-~~~~q~~d~~~L~GD~~D~i~gv~giG~k~A~~ll~~~~~~~~~~~~~~   53 (75)
T cd00080           2 KLG-LTPEQFIDLAILVGDKSDNIPGVPGIGPKTALKLLKEYGSLENLLENLD   53 (75)
T ss_pred             CCC-cCHHHHHHHHHHcCCccccCCCCCcccHHHHHHHHHHhCCHHHHHHHHH
Confidence            577 9999999999999999999999999999999999999999999998764

HhH2 domains are found in Rad2 family of prokaryotic and eukaryotic replication and repair nucleases, i.e., DNA polymerase I, Taq DNA polymerase, DNA repair protein Rad2 endonuclease, flap endonuclease, exonuclease I and IX, 5'-3' exonuclease and also bacteriophage Rnase H. These nucleases degrade RNA-DNA or DNA-DNA duplexes, or both and play essential roles in DNA duplication, repair, and recombination.

>PF01367 5_3_exonuc: 5'-3' exonuclease, C-terminal SAM fold; InterPro: IPR020045 This entry represents the C-terminal domain of 5' to 3' exonucleases

Probab=99.89  E-value=1.3e-25  Score=138.22  Aligned_cols=51  Identities=41%  Similarity=0.697  Sum_probs=42.2

Q ss_pred             CChhHHHHHHHhhCCCCCCCCCCCCccHHHHHHHHHHhCCHHHHHhhhccC
Q 035374           16 LKPSQFVDVISLVGDKADNIPGVEGIGDVRAVQLITKFGMLVFNVECFSEM   66 (66)
Q Consensus        16 i~p~q~~d~~~L~Gd~~D~i~gi~GiG~K~A~~Ll~~fgsl~~i~~~~~~~   66 (66)
                      ++|+|++||++|+||+|||||||||||||||.+||++|||+++|+++++++
T Consensus         1 V~P~q~~D~~aL~GD~sDNIPGV~GIG~KtA~~LL~~ygsle~i~~~~~~~   51 (101)
T PF01367_consen    1 VPPEQIADYKALVGDSSDNIPGVPGIGPKTAAKLLQEYGSLENILANLDEI   51 (101)
T ss_dssp             --GHHHHHHCCCC-CCCCTB---TTSTCHCCCCCHHHHTSCHCCCCC-SSS
T ss_pred             CCHHHHHHHHHHcCCcccCCCCCCCCCHHHHHHHHHHcCCHHHHHHhHHhc
Confidence            589999999999999999999999999999999999999999999887753

The 5'-3' exonucleases are conserved in organisms as diverse as bacteriophage and mammals. It adopts a SAM fold consisting of 4-5 helices packed into a bundle of two orthogonally packed alpha-hairpins. This domain is involved in interactions with DNA and proteins. 5' to 3' exonucleases that contain this domain include: Bacteriophage T4 RNase H, which has sequence similarity to the RAD2 family of eukaryotic proteins []. 5' to 3' exonuclease domain of DNA polymerase Taq, which is homologous to Escherichia coli DNA polymerase I (pol I) [, ]. Bacteriophage T5 5'-exonuclease, which are structure-specific endonucleases []. Flap endonuclease-1 (Fen-1 nuclease), a structure specific nuclease that is an essential enzyme for eukaryotic DNA replication and repair []. ; GO: 0003677 DNA binding, 0003824 catalytic activity; PDB: 1TAQ_A 1BGX_T 1TAU_A 1XO1_B 1EXN_A 1UT8_A 1UT5_B.

>TIGR00593 pola DNA polymerase I

Probab=99.87  E-value=2e-22  Score=157.13  Aligned_cols=63  Identities=43%  Similarity=0.727  Sum_probs=60.1

Q ss_pred             eeCHHHHHHHhCCCChhHHHHHHHhhCCCCCCCCCCCCccHHHHHHHHHHhCCHHHHHhhhccC
Q 035374            3 SFGMEDFARKYGELKPSQFVDVISLVGDKADNIPGVEGIGDVRAVQLITKFGMLVFNVECFSEM   66 (66)
Q Consensus         3 ~~~~~~v~~~~g~i~p~q~~d~~~L~Gd~~D~i~gi~GiG~K~A~~Ll~~fgsl~~i~~~~~~~   66 (66)
                      .++.++|.++|| ++|+||+||++|+||+|||||||||||||||.+||++|||+++|+++++++
T Consensus       156 ~~~~~~v~~~~G-v~p~q~~D~~aL~GD~sDnIpGVpGIG~KtA~kLL~~ygsle~i~~~~~~i  218 (887)
T TIGR00593       156 EITPEYVVEKYG-VTPDQLVDLKALVGDSSDNIPGVKGIGEKTAAKLLQEFGSLENIYENLDQI  218 (887)
T ss_pred             EEcHHHHHHHhC-CCHHHHHHHHHHcCCcccCCCCCCCcCHHHHHHHHHHcCCHHHHHHHHHHh
Confidence            589999999998 999999999999999999999999999999999999999999999988753

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

>PRK05755 DNA polymerase I; Provisional

Probab=99.85  E-value=1.7e-21  Score=150.95  Aligned_cols=62  Identities=40%  Similarity=0.737  Sum_probs=59.4

Q ss_pred             eeCHHHHHHHhCCCChhHHHHHHHhhCCCCCCCCCCCCccHHHHHHHHHHhCCHHHHHhhhcc
Q 035374            3 SFGMEDFARKYGELKPSQFVDVISLVGDKADNIPGVEGIGDVRAVQLITKFGMLVFNVECFSE   65 (66)
Q Consensus         3 ~~~~~~v~~~~g~i~p~q~~d~~~L~Gd~~D~i~gi~GiG~K~A~~Ll~~fgsl~~i~~~~~~   65 (66)
                      .++.+.|.++|| ++|+||+|+++|+||+|||||||||||||||.+||++|||+++|++++++
T Consensus       158 ~~~~~~v~~~~g-~~p~q~~d~~~L~GD~sDnipGv~GiG~ktA~~Ll~~~gsle~i~~~~~~  219 (880)
T PRK05755        158 ELDPEEVVEKYG-VTPEQIIDYLALMGDSSDNIPGVPGIGEKTAAKLLQEYGSLEGLYENLDE  219 (880)
T ss_pred             EEcHHHHHHHHC-cCHHHHHHHHHHhCCccCCCCCCCCccHHHHHHHHHHcCCHHHHHHhHHH
Confidence            588999999998 99999999999999999999999999999999999999999999988764

>COG0258 Exo 5'-3' exonuclease (including N-terminal domain of PolI) [DNA replication, recombination, and repair]

Probab=99.84  E-value=6.9e-21  Score=133.37  Aligned_cols=61  Identities=39%  Similarity=0.712  Sum_probs=57.3

Q ss_pred             eCHHHHHHHhCCCChhHHHHHHHhhCCCCCCCCCCCCccHHHHHHHHHHhCCHHHHHhhhc
Q 035374            4 FGMEDFARKYGELKPSQFVDVISLVGDKADNIPGVEGIGDVRAVQLITKFGMLVFNVECFS   64 (66)
Q Consensus         4 ~~~~~v~~~~g~i~p~q~~d~~~L~Gd~~D~i~gi~GiG~K~A~~Ll~~fgsl~~i~~~~~   64 (66)
                      ++.+.+.++|.+++|+|++|+++|+||+|||+|||||||||||.+||++||+++.++++++
T Consensus       169 ~~~~~~~e~~~g~~p~qliD~~~L~Gd~sDnipGV~GIG~ktA~~Ll~~~gs~e~i~~~~~  229 (310)
T COG0258         169 LDLEEVEEKFKGLTPEQLIDLKALVGDSSDNIPGVKGIGPKTALKLLQEYGSLEGLYENLD  229 (310)
T ss_pred             CCHHHHHHHHcCCCHHHHHHHHHHhCCcccCCCCCCCcCHHHHHHHHHHhCCHHHHHHhhh
Confidence            6889999999339999999999999999999999999999999999999999999998764

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

Probab=99.79  E-value=1.3e-19  Score=93.61  Aligned_cols=36  Identities=53%  Similarity=0.932  Sum_probs=35.0

Q ss_pred             hhHHHHHHHhhCCCCCCCCCCCCccHHHHHHHHHHh
Q 035374           18 PSQFVDVISLVGDKADNIPGVEGIGDVRAVQLITKF   53 (66)
Q Consensus        18 p~q~~d~~~L~Gd~~D~i~gi~GiG~K~A~~Ll~~f   53 (66)
                      |+||+|+++|+||.+||+|||||||+|+|.+||++|
T Consensus         1 p~q~~~~~~L~GD~~dni~Gv~giG~ktA~~ll~~~   36 (36)
T smart00279        1 PEQLIDYAILVGDYSDNIPGVKGIGPKTALKLLREF   36 (36)
T ss_pred             CHHHHHHHHHhCcCCCCCCCCCcccHHHHHHHHHhC
Confidence            689999999999999999999999999999999987

>PTZ00217 flap endonuclease-1; Provisional

Probab=99.77  E-value=8.4e-19  Score=127.36  Aligned_cols=60  Identities=27%  Similarity=0.442  Sum_probs=56.6

Q ss_pred             eeCHHHHHHHhCCCChhHHHHHHHhhCCCCCCCCCCCCccHHHHHHHHHHhCCHHHHHhhhcc
Q 035374            3 SFGMEDFARKYGELKPSQFVDVISLVGDKADNIPGVEGIGDVRAVQLITKFGMLVFNVECFSE   65 (66)
Q Consensus         3 ~~~~~~v~~~~g~i~p~q~~d~~~L~Gd~~D~i~gi~GiG~K~A~~Ll~~fgsl~~i~~~~~~   65 (66)
                      .++.+.+++.+| ++|+||+|+|+|+|  +||+|||||||||||.+||++|+|+++++++++.
T Consensus       208 ~~~~~~v~~~~g-l~~~q~id~~iL~G--~Dy~pgi~GIG~ktA~~Li~~~gsle~il~~~~~  267 (393)
T PTZ00217        208 EINLSTVLEELG-LSMDQFIDLCILCG--CDYCDTIKGIGPKTAYKLIKKYKSIEEILEHLDK  267 (393)
T ss_pred             EEEHHHHHHHhC-CCHHHHHHHHHHhC--CCCCCCCCCccHHHHHHHHHHcCCHHHHHHHHHh
Confidence            588999999998 99999999999999  6999999999999999999999999999987653

>PRK03980 flap endonuclease-1; Provisional

Probab=99.76  E-value=1.2e-18  Score=122.51  Aligned_cols=58  Identities=34%  Similarity=0.554  Sum_probs=54.9

Q ss_pred             eeCHHHHHHHhCCCChhHHHHHHHhhCCCCCCCCCCCCccHHHHHHHHHHhCCHHHHHhhh
Q 035374            3 SFGMEDFARKYGELKPSQFVDVISLVGDKADNIPGVEGIGDVRAVQLITKFGMLVFNVECF   63 (66)
Q Consensus         3 ~~~~~~v~~~~g~i~p~q~~d~~~L~Gd~~D~i~gi~GiG~K~A~~Ll~~fgsl~~i~~~~   63 (66)
                      .++.+.+++++| ++|+||+|+|+|+|  +||+|||||||||||.+|+++|+|+++++++.
T Consensus       162 ~~~~~~vl~~lg-l~~~q~id~~iL~G--~Dy~~GI~GIG~ktA~kLi~~~~sle~i~~~~  219 (292)
T PRK03980        162 LIELEEVLKELG-ITREQLIDIAILVG--TDYNPGIKGIGPKTALKLIKKHGDLEKVLEER  219 (292)
T ss_pred             eeeHHHHHHHhC-CCHHHHHHHHHhcC--CCCCCCCCCccHHHHHHHHHHCCCHHHHHHhc
Confidence            588999999998 99999999999999  69999999999999999999999999999753

>TIGR03674 fen_arch flap structure-specific endonuclease

Probab=99.74  E-value=4.2e-18  Score=121.39  Aligned_cols=59  Identities=31%  Similarity=0.478  Sum_probs=54.4

Q ss_pred             eeCHHHHHHHhCCCChhHHHHHHHhhCCCCCCCCCCCCccHHHHHHHHHHhCCHHHHHhhhc
Q 035374            3 SFGMEDFARKYGELKPSQFVDVISLVGDKADNIPGVEGIGDVRAVQLITKFGMLVFNVECFS   64 (66)
Q Consensus         3 ~~~~~~v~~~~g~i~p~q~~d~~~L~Gd~~D~i~gi~GiG~K~A~~Ll~~fgsl~~i~~~~~   64 (66)
                      .++.+++++++| ++|+||+|+|+|+||  |+.|||||||||||.+|+++|+|+++++++++
T Consensus       209 ~~~~~~v~~~lg-l~~~q~id~~iL~G~--dyn~Gv~GIG~ktA~kli~~~gsie~il~~~~  267 (338)
T TIGR03674       209 LIELEEVLSELG-ITREQLIDIAILVGT--DYNEGVKGIGPKTALKLIKEHGDLEKVLKARG  267 (338)
T ss_pred             eeeHHHHHHHhC-CCHHHHHHHHHhcCC--CCCCCCCCccHHHHHHHHHHcCCHHHHHHhhc
Confidence            378999999998 999999999999998  44499999999999999999999999998754

Endonuclease that cleaves the 5'-overhanging flap structure that is generated by displacement synthesis when DNA polymerase encounters the 5'-end of a downstream Okazaki fragment. Has 5'-endo-/exonuclease and 5'-pseudo-Y-endonuclease activities. Cleaves the junction between single and double-stranded regions of flap DNA

>cd00128 XPG Xeroderma pigmentosum G N- and I-regions (XPGN, XPGI); contains the HhH2 motif; domain in nucleases

Probab=99.73  E-value=9.7e-18  Score=117.34  Aligned_cols=59  Identities=31%  Similarity=0.613  Sum_probs=54.4

Q ss_pred             ceeCHHHHHHHhCCCChhHHHHHHHhhCCCCCCCCCCCCccHHHHHHHHHHhCCHHHHHhhh
Q 035374            2 ASFGMEDFARKYGELKPSQFVDVISLVGDKADNIPGVEGIGDVRAVQLITKFGMLVFNVECF   63 (66)
Q Consensus         2 ~~~~~~~v~~~~g~i~p~q~~d~~~L~Gd~~D~i~gi~GiG~K~A~~Ll~~fgsl~~i~~~~   63 (66)
                      ..++.+.+.+++| ++|+||+|+|+|+|  +||+|||||||+|||.+|+++|+|++++++++
T Consensus       195 ~~~~~~~~~~~lg-l~~~q~id~~~L~G--~Dy~~gv~giG~k~A~~li~~~~~~~~~~~~l  253 (316)
T cd00128         195 EEIDLEKILKELG-LTREKLIDLAILLG--CDYTEGIPGIGPVTALKLIKKYGDIEKDIERL  253 (316)
T ss_pred             EEEEHHHHHHHcC-CCHHHHHHHHHhcC--CCCCCCCCCccHHHHHHHHHHcCChHHHHHHH
Confidence            3588999999998 99999999999999  69999999999999999999999988877654

XPG is a eukaryotic enzyme that functions in nucleotide-excision repair and transcription-coupled repair of oxidative DNA damage. Functionally/structurally related to FEN-1; divalent metal ion-dependent exo- and endonuclease, and bacterial and bacteriophage 5'3' exonucleases.

>PHA00439 exonuclease

Probab=99.54  E-value=4.2e-15  Score=104.96  Aligned_cols=45  Identities=18%  Similarity=0.324  Sum_probs=41.3

Q ss_pred             ChhHHHHHHHhhCCCCCCCCCCCCccHHHHHHHHHH---hCCHHHHHhh
Q 035374           17 KPSQFVDVISLVGDKADNIPGVEGIGDVRAVQLITK---FGMLVFNVEC   62 (66)
Q Consensus        17 ~p~q~~d~~~L~Gd~~D~i~gi~GiG~K~A~~Ll~~---fgsl~~i~~~   62 (66)
                      .|+||+|+++|+||+||||||||||| |||.+||++   |..+++.+++
T Consensus       172 ~p~~~~d~~AL~GDsSDNIPGVpGIG-KTA~kLL~~~~~~~~~~~~~~s  219 (286)
T PHA00439        172 TADRWHLFQTIKGDSTDGYSGIPGWG-DTAEAFLENPYIFEQVEKVLKS  219 (286)
T ss_pred             cHHHHHhhhhcccccccCCCCCCCcC-HHHHHHHhCccccchhhHHhhc
Confidence            58999999999999999999999999 999999999   7777777755

>TIGR00600 rad2 DNA excision repair protein (rad2)

Probab=99.39  E-value=6.8e-13  Score=105.53  Aligned_cols=55  Identities=22%  Similarity=0.448  Sum_probs=50.5

Q ss_pred             eeCHHHHHHHhCCCChhHHHHHHHhhCCCCCCCCCCCCccHHHHHHHHHHhC--CHHHHH
Q 035374            3 SFGMEDFARKYGELKPSQFVDVISLVGDKADNIPGVEGIGDVRAVQLITKFG--MLVFNV   60 (66)
Q Consensus         3 ~~~~~~v~~~~g~i~p~q~~d~~~L~Gd~~D~i~gi~GiG~K~A~~Ll~~fg--sl~~i~   60 (66)
                      +|+.+++++.+| ++++||+++|+|+|  +||.+||||||||+|.+||++|+  +++.++
T Consensus       839 ~~~~~~i~~~lg-lt~~qli~laiL~G--~DY~~GI~GIGpktAl~li~~~~~~~le~L~  895 (1034)
T TIGR00600       839 YYQYVDIHNQLG-LDRNKLINLAYLLG--SDYTEGIPTVGPVSAMEILNEFPGDGLEPLL  895 (1034)
T ss_pred             EeeHHHHHHHhC-CCHHHHHHHHHeeC--CCCCCCCCcccHHHHHHHHHHcCCCCHHHHH
Confidence            578899999998 99999999999999  59999999999999999999999  466655

All proteins in this family for which functions are known are flap endonucleases that generate the 3' incision next to DNA damage as part of nucleotide excision repair. This family is related to many other flap endonuclease families including the fen1 family. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).

>KOG2519 consensus 5'-3' exonuclease [Replication, recombination and repair]

Probab=99.25  E-value=1.3e-11  Score=91.54  Aligned_cols=57  Identities=30%  Similarity=0.534  Sum_probs=54.6

Q ss_pred             ceeCHHHHHHHhCCCChhHHHHHHHhhCCCCCCCCCCCCccHHHHHHHHHHhCCHHHHHh
Q 035374            2 ASFGMEDFARKYGELKPSQFVDVISLVGDKADNIPGVEGIGDVRAVQLITKFGMLVFNVE   61 (66)
Q Consensus         2 ~~~~~~~v~~~~g~i~p~q~~d~~~L~Gd~~D~i~gi~GiG~K~A~~Ll~~fgsl~~i~~   61 (66)
                      .+|+.+.+++.++ ++.++|+|+|+|+|+  ||.++|.|||+++|.+|+++|++++++++
T Consensus       201 ~e~~~~~il~~l~-l~~~~fidL~lLlGC--DYc~~I~Gig~~~al~lir~~~~i~~ile  257 (449)
T KOG2519|consen  201 SEYDMSRILEGLG-LSRESFIDLCLLLGC--DYCPTIRGIGPKKALKLIRQHGDIENILE  257 (449)
T ss_pred             EEeeHHHHHHHhc-ccHHHHHHHHHHhcC--cccccccccChHHHHHHHHHhcCHHHHhh
Confidence            5789999999999 999999999999995  99999999999999999999999999987

>PHA02567 rnh RnaseH; Provisional

Probab=98.63  E-value=3.5e-08  Score=70.55  Aligned_cols=35  Identities=23%  Similarity=0.349  Sum_probs=31.7

Q ss_pred             eCHHHHHHHhCCCChhHHHHHHHhhCCCCCCCCCCCC
Q 035374            4 FGMEDFARKYGELKPSQFVDVISLVGDKADNIPGVEG   40 (66)
Q Consensus         4 ~~~~~v~~~~g~i~p~q~~d~~~L~Gd~~D~i~gi~G   40 (66)
                      ++.++|.++||  .|+|++||++|+||+||||||||-
T Consensus       173 ~~~~~V~~k~G--~P~q~iD~kaL~GDsSDNIPGVp~  207 (304)
T PHA02567        173 MQKKWVKPKYG--SPEKDLMTKIIKGDKKDGVASIKV  207 (304)
T ss_pred             CCHHHHHHHhC--CHHHHHHHHHhCCcccCCcCCCCC
Confidence            46688999998  499999999999999999999975

>KOG2518 consensus 5'-3' exonuclease [Replication, recombination and repair]

Probab=98.54  E-value=1.3e-07  Score=71.69  Aligned_cols=44  Identities=20%  Similarity=0.317  Sum_probs=40.8

Q ss_pred             CChhHHHHHHHhhCCCCCCCCCCCCccHHHHHHHHHHhCCHHHHHh
Q 035374           16 LKPSQFVDVISLVGDKADNIPGVEGIGDVRAVQLITKFGMLVFNVE   61 (66)
Q Consensus        16 i~p~q~~d~~~L~Gd~~D~i~gi~GiG~K~A~~Ll~~fgsl~~i~~   61 (66)
                      ++-++|.++|+|.||  ||++||||||-+||.+++.+|.+.+.++.
T Consensus       210 ~~~ekfr~mciLSGC--DYl~slpGvGl~tA~k~l~k~~~~d~vi~  253 (556)
T KOG2518|consen  210 FTEEKFRRMCILSGC--DYLSSLPGVGLATAHKLLSKYNTPDRVII  253 (556)
T ss_pred             cCHHHHHHHHHhcCC--cccccCccccHHHHHHHHHhcCcHHHHHH
Confidence            568899999999995  99999999999999999999999998763

>KOG2520 consensus 5'-3' exonuclease [Replication, recombination and repair]

Probab=98.35  E-value=1e-06  Score=69.52  Aligned_cols=50  Identities=26%  Similarity=0.674  Sum_probs=47.5

Q ss_pred             ceeCHHHHHHHhCCCChhHHHHHHHhhCCCCCCCCCCCCccHHHHHHHHHHhC
Q 035374            2 ASFGMEDFARKYGELKPSQFVDVISLVGDKADNIPGVEGIGDVRAVQLITKFG   54 (66)
Q Consensus         2 ~~~~~~~v~~~~g~i~p~q~~d~~~L~Gd~~D~i~gi~GiG~K~A~~Ll~~fg   54 (66)
                      ..|..+.+.++|+ +++..+|.++.|+|  +||..||+||||++|..+|.+|+
T Consensus       532 e~y~~~di~kel~-l~R~~lI~lA~LlG--sDYt~Gl~giGpV~AlEil~Efp  581 (815)
T KOG2520|consen  532 EKYQLDDIEKELG-LDRPNLISLAQLLG--SDYTEGLKGIGPVSALEILAEFP  581 (815)
T ss_pred             eeeehHHHHHHHc-cCchhhHHHHHhcc--cccccCCCcccchHHHHHHHHcC
Confidence            3578899999998 99999999999999  69999999999999999999999

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

Probab=98.19  E-value=9.4e-07  Score=49.87  Aligned_cols=25  Identities=32%  Similarity=0.545  Sum_probs=21.6

Q ss_pred             CCCCccHHHHHHHHHHhCCHHHHHh
Q 035374           37 GVEGIGDVRAVQLITKFGMLVFNVE   61 (66)
Q Consensus        37 gi~GiG~K~A~~Ll~~fgsl~~i~~   61 (66)
                      ||||||+++|..|.++|+|++++.+
T Consensus         7 GI~~VG~~~ak~L~~~f~sl~~l~~   31 (64)
T PF12826_consen    7 GIPGVGEKTAKLLAKHFGSLEALMN   31 (64)
T ss_dssp             TSTT--HHHHHHHHHCCSCHHHHCC
T ss_pred             CCCCccHHHHHHHHHHcCCHHHHHH
Confidence            7899999999999999999999875

>PRK14667 uvrC excinuclease ABC subunit C; Provisional

Probab=97.73  E-value=2.2e-05  Score=60.01  Aligned_cols=29  Identities=21%  Similarity=0.359  Sum_probs=25.8

Q ss_pred             CCCCCCCccHHHHHHHHHHhCCHHHHHhh
Q 035374           34 NIPGVEGIGDVRAVQLITKFGMLVFNVEC   62 (66)
Q Consensus        34 ~i~gi~GiG~K~A~~Ll~~fgsl~~i~~~   62 (66)
                      -+.+||||||||..+||++|||+++|.++
T Consensus       515 ~Ld~I~GiG~kr~~~Ll~~Fgs~~~ik~A  543 (567)
T PRK14667        515 ILDKIKGIGEVKKEIIYRNFKTLYDFLKA  543 (567)
T ss_pred             ccccCCCCCHHHHHHHHHHhCCHHHHHhC
Confidence            45567999999999999999999999864

>TIGR00194 uvrC excinuclease ABC, C subunit

Probab=97.69  E-value=3.2e-05  Score=59.08  Aligned_cols=30  Identities=23%  Similarity=0.354  Sum_probs=26.1

Q ss_pred             CCCCCCCccHHHHHHHHHHhCCHHHHHhhh
Q 035374           34 NIPGVEGIGDVRAVQLITKFGMLVFNVECF   63 (66)
Q Consensus        34 ~i~gi~GiG~K~A~~Ll~~fgsl~~i~~~~   63 (66)
                      -+.+||||||||..+||++|||+++|.++.
T Consensus       542 ~Ld~I~GIG~kr~~~LL~~Fgs~~~i~~As  571 (574)
T TIGR00194       542 PLLKIPGVGEKRVQKLLKYFGSLKGIKKAS  571 (574)
T ss_pred             HHhcCCCCCHHHHHHHHHHcCCHHHHHhCC
Confidence            345669999999999999999999998753

This family consists of the DNA repair enzyme UvrC, an ABC excinuclease subunit which interacts with the UvrA/UvrB complex to excise UV-damaged nucleotide segments.

>PRK14670 uvrC excinuclease ABC subunit C; Provisional

Probab=97.64  E-value=4.3e-05  Score=58.48  Aligned_cols=30  Identities=20%  Similarity=0.310  Sum_probs=26.7

Q ss_pred             CCCCCCCCccHHHHHHHHHHhCCHHHHHhh
Q 035374           33 DNIPGVEGIGDVRAVQLITKFGMLVFNVEC   62 (66)
Q Consensus        33 D~i~gi~GiG~K~A~~Ll~~fgsl~~i~~~   62 (66)
                      .-+..||||||||..+||+.|||+++|.++
T Consensus       514 s~L~~I~GiG~kr~~~LL~~Fgs~~~I~~A  543 (574)
T PRK14670        514 LNYTKIKGIGEKKAKKILKSLGTYKDILLL  543 (574)
T ss_pred             cccccCCCCCHHHHHHHHHHhCCHHHHHhC
Confidence            356778999999999999999999999864

>PRK14669 uvrC excinuclease ABC subunit C; Provisional

Probab=97.61  E-value=4.3e-05  Score=59.00  Aligned_cols=29  Identities=21%  Similarity=0.373  Sum_probs=25.9

Q ss_pred             CCCCCCCccHHHHHHHHHHhCCHHHHHhh
Q 035374           34 NIPGVEGIGDVRAVQLITKFGMLVFNVEC   62 (66)
Q Consensus        34 ~i~gi~GiG~K~A~~Ll~~fgsl~~i~~~   62 (66)
                      -+.+||||||||+.+||++|||+++|.++
T Consensus       553 ~L~~IpGIG~kr~~~LL~~FgSi~~I~~A  581 (624)
T PRK14669        553 ELLEIPGVGAKTVQRLLKHFGSLERVRAA  581 (624)
T ss_pred             HHhcCCCCCHHHHHHHHHHcCCHHHHHhC
Confidence            45677999999999999999999999864

>PRK14672 uvrC excinuclease ABC subunit C; Provisional

Probab=97.39  E-value=0.00016  Score=56.61  Aligned_cols=29  Identities=24%  Similarity=0.393  Sum_probs=25.5

Q ss_pred             CCCCCCCccHHHHHHHHHHhCCHHHHHhh
Q 035374           34 NIPGVEGIGDVRAVQLITKFGMLVFNVEC   62 (66)
Q Consensus        34 ~i~gi~GiG~K~A~~Ll~~fgsl~~i~~~   62 (66)
                      -+..|||||+||+.+||+.|||+++|.++
T Consensus       609 ~L~~IpGiG~kr~~~LL~~FgS~~~i~~A  637 (691)
T PRK14672        609 SFERLPHVGKVRAHRLLAHFGSFRSLQSA  637 (691)
T ss_pred             ccccCCCCCHHHHHHHHHHhcCHHHHHhC
Confidence            34566999999999999999999999864

>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=97.34  E-value=0.00023  Score=39.22  Aligned_cols=27  Identities=26%  Similarity=0.253  Sum_probs=24.0

Q ss_pred             CCCCCccHHHHHHHHHH-hCCHHHHHhh
Q 035374           36 PGVEGIGDVRAVQLITK-FGMLVFNVEC   62 (66)
Q Consensus        36 ~gi~GiG~K~A~~Ll~~-fgsl~~i~~~   62 (66)
                      ..||||||++|.+|... |.|++++...
T Consensus         8 ~~I~Gig~~~a~~L~~~G~~t~~~l~~a   35 (60)
T PF14520_consen    8 LSIPGIGPKRAEKLYEAGIKTLEDLANA   35 (60)
T ss_dssp             HTSTTCHHHHHHHHHHTTCSSHHHHHTS
T ss_pred             ccCCCCCHHHHHHHHhcCCCcHHHHHcC
Confidence            46799999999999999 9999999753

...

>PRK14671 uvrC excinuclease ABC subunit C; Provisional

Probab=97.24  E-value=0.00027  Score=54.51  Aligned_cols=29  Identities=24%  Similarity=0.492  Sum_probs=25.5

Q ss_pred             CCCCCCCccHHHHHHHHHHhCCHHHHHhh
Q 035374           34 NIPGVEGIGDVRAVQLITKFGMLVFNVEC   62 (66)
Q Consensus        34 ~i~gi~GiG~K~A~~Ll~~fgsl~~i~~~   62 (66)
                      -+.+|||||+|+|..|++.|||++++.++
T Consensus       570 ~L~~I~GIG~k~a~~Ll~~Fgs~~~i~~A  598 (621)
T PRK14671        570 ELTDIAGIGEKTAEKLLEHFGSVEKVAKA  598 (621)
T ss_pred             hhhcCCCcCHHHHHHHHHHcCCHHHHHhC
Confidence            45678999999999999999999998753

>TIGR00084 ruvA Holliday junction DNA helicase, RuvA subunit

Probab=97.14  E-value=0.00097  Score=44.68  Aligned_cols=43  Identities=16%  Similarity=0.102  Sum_probs=25.7

Q ss_pred             HHHhCCCChhHHHHHHHhhCCCCCCCCCCCCccHHHHHHHHHHhCCHHHHHh
Q 035374           10 ARKYGELKPSQFVDVISLVGDKADNIPGVEGIGDVRAVQLITKFGMLVFNVE   61 (66)
Q Consensus        10 ~~~~g~i~p~q~~d~~~L~Gd~~D~i~gi~GiG~K~A~~Ll~~fgsl~~i~~   61 (66)
                      ..-||+.+++.---|..|++        |+|||||+|..+|..+ +++++.+
T Consensus        57 ~~LyGF~~~~Er~lF~~L~~--------V~GIGpK~Al~iL~~~-~~~el~~   99 (191)
T TIGR00084        57 ELLFGFNTLEERELFKELIK--------VNGVGPKLALAILSNM-SPEEFVY   99 (191)
T ss_pred             ceeeCCCCHHHHHHHHHHhC--------CCCCCHHHHHHHHhcC-CHHHHHH
Confidence            34566566666555565543        4677777777777665 4555544

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.

>PRK00558 uvrC excinuclease ABC subunit C; Validated

Probab=97.10  E-value=0.00038  Score=53.41  Aligned_cols=29  Identities=31%  Similarity=0.470  Sum_probs=25.8

Q ss_pred             CCCCCCCccHHHHHHHHHHhCCHHHHHhh
Q 035374           34 NIPGVEGIGDVRAVQLITKFGMLVFNVEC   62 (66)
Q Consensus        34 ~i~gi~GiG~K~A~~Ll~~fgsl~~i~~~   62 (66)
                      -+.+|||||++++.+|++.|||++++.++
T Consensus       544 ~L~~IpGIG~k~~k~Ll~~FgS~~~i~~A  572 (598)
T PRK00558        544 ALDDIPGIGPKRRKALLKHFGSLKAIKEA  572 (598)
T ss_pred             hHhhCCCcCHHHHHHHHHHcCCHHHHHhC
Confidence            45678999999999999999999999864

>PRK14668 uvrC excinuclease ABC subunit C; Provisional

Probab=97.10  E-value=0.00039  Score=53.31  Aligned_cols=30  Identities=23%  Similarity=0.354  Sum_probs=26.8

Q ss_pred             CCCCCCCCccHHHHHHHHHHhCCHHHHHhh
Q 035374           33 DNIPGVEGIGDVRAVQLITKFGMLVFNVEC   62 (66)
Q Consensus        33 D~i~gi~GiG~K~A~~Ll~~fgsl~~i~~~   62 (66)
                      .-+..|||||++++.+||++|||+++|.++
T Consensus       525 ~~L~~IpGIG~kr~~~LL~~FGS~~~I~~A  554 (577)
T PRK14668        525 TVLDDVPGVGPETRKRLLRRFGSVEGVREA  554 (577)
T ss_pred             hHHhcCCCCCHHHHHHHHHHcCCHHHHHhC
Confidence            456778999999999999999999999864

>PRK12766 50S ribosomal protein L32e; Provisional

Probab=97.10  E-value=0.00057  Score=47.59  Aligned_cols=29  Identities=17%  Similarity=0.252  Sum_probs=25.7

Q ss_pred             CCCCCCCccHHHHHHHHHH-hCCHHHHHhh
Q 035374           34 NIPGVEGIGDVRAVQLITK-FGMLVFNVEC   62 (66)
Q Consensus        34 ~i~gi~GiG~K~A~~Ll~~-fgsl~~i~~~   62 (66)
                      .+..|||||++++.+|++. |+|+++|..+
T Consensus         4 ~L~~IpGIG~krakkLl~~GF~Sve~Ik~A   33 (232)
T PRK12766          4 ELEDISGVGPSKAEALREAGFESVEDVRAA   33 (232)
T ss_pred             ccccCCCcCHHHHHHHHHcCCCCHHHHHhC
Confidence            4667899999999999999 9999999754

>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=97.10  E-value=0.00014  Score=35.90  Aligned_cols=20  Identities=20%  Similarity=0.419  Sum_probs=14.8

Q ss_pred             CCCCCCCCCccHHHHHHHHH
Q 035374           32 ADNIPGVEGIGDVRAVQLIT   51 (66)
Q Consensus        32 ~D~i~gi~GiG~K~A~~Ll~   51 (66)
                      .+.+..+||||+|+|..++.
T Consensus        10 ~eeL~~lpGIG~~tA~~I~~   29 (30)
T PF00633_consen   10 IEELMKLPGIGPKTANAILS   29 (30)
T ss_dssp             HHHHHTSTT-SHHHHHHHHH
T ss_pred             HHHHHhCCCcCHHHHHHHHh
Confidence            34455789999999998874

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 ....

>COG0322 UvrC Nuclease subunit of the excinuclease complex [DNA replication, recombination, and repair]

Probab=97.08  E-value=0.00061  Score=52.42  Aligned_cols=48  Identities=19%  Similarity=0.277  Sum_probs=34.2

Q ss_pred             HhCCCChhHHHHHHHhhCCCCCCCCCCCCccHHHHHHHHHHhCCHHHHHhhh
Q 035374           12 KYGELKPSQFVDVISLVGDKADNIPGVEGIGDVRAVQLITKFGMLVFNVECF   63 (66)
Q Consensus        12 ~~g~i~p~q~~d~~~L~Gd~~D~i~gi~GiG~K~A~~Ll~~fgsl~~i~~~~   63 (66)
                      +|. ++-..=.--+...-.+.|   .||||||||..+||+.|||+++|.++.
T Consensus       513 rfA-i~~hR~~R~k~~~~s~Ld---~I~GiG~~r~~~LL~~Fgs~~~i~~As  560 (581)
T COG0322         513 RFA-ITYHRKKRSKAMLQSSLD---DIPGIGPKRRKALLKHFGSLKGIKSAS  560 (581)
T ss_pred             HHH-HHHHHHHhhhhhhcCccc---cCCCcCHHHHHHHHHHhhCHHHHHhcC
Confidence            344 444444445565554444   559999999999999999999998643

>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed

Probab=97.03  E-value=0.0006  Score=45.45  Aligned_cols=25  Identities=16%  Similarity=0.294  Sum_probs=20.3

Q ss_pred             CCCCccHHHHHHHHHHhCC---HHHHHh
Q 035374           37 GVEGIGDVRAVQLITKFGM---LVFNVE   61 (66)
Q Consensus        37 gi~GiG~K~A~~Ll~~fgs---l~~i~~   61 (66)
                      .|||||||+|.++++.|++   .+.+.+
T Consensus        77 ~i~GIGpk~A~~il~~fg~~~l~~~i~~  104 (192)
T PRK00116         77 SVSGVGPKLALAILSGLSPEELVQAIAN  104 (192)
T ss_pred             cCCCCCHHHHHHHHHhCCHHHHHHHHHh
Confidence            3699999999999999987   444443

>PRK14666 uvrC excinuclease ABC subunit C; Provisional

Probab=96.98  E-value=0.00054  Score=53.71  Aligned_cols=29  Identities=34%  Similarity=0.464  Sum_probs=26.0

Q ss_pred             CCCCCCCccHHHHHHHHHHhCCHHHHHhh
Q 035374           34 NIPGVEGIGDVRAVQLITKFGMLVFNVEC   62 (66)
Q Consensus        34 ~i~gi~GiG~K~A~~Ll~~fgsl~~i~~~   62 (66)
                      .+..|||||+|++.+|+++|||++++.++
T Consensus       638 ~L~~IPGIGpkr~k~LL~~FGSle~I~~A  666 (694)
T PRK14666        638 ELQRVEGIGPATARLLWERFGSLQAMAAA  666 (694)
T ss_pred             HHhhCCCCCHHHHHHHHHHhCCHHHHHhc
Confidence            45677999999999999999999999864

>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional

Probab=96.97  E-value=0.0012  Score=44.30  Aligned_cols=42  Identities=24%  Similarity=0.332  Sum_probs=26.9

Q ss_pred             HHHHhCCCChhHHHHHHHhhCCCCCCCCCCCCccHHHHHHHHHH
Q 035374            9 FARKYGELKPSQFVDVISLVGDKADNIPGVEGIGDVRAVQLITK   52 (66)
Q Consensus         9 v~~~~g~i~p~q~~d~~~L~Gd~~D~i~gi~GiG~K~A~~Ll~~   52 (66)
                      -+.-...++|+++... +..|| ...+..+||||+|||.+++-+
T Consensus        86 Al~ILs~~~~~el~~a-I~~~D-~~~L~~vpGIGkKtAeRIilE  127 (183)
T PRK14601         86 AMAVCSSLDVNSFYKA-LSLGD-ESVLKKVPGIGPKSAKRIIAE  127 (183)
T ss_pred             HHHHHcCCCHHHHHHH-HHhCC-HHHHhhCCCCCHHHHHHHHHH
Confidence            3344444677777742 33455 457778888888888888754

>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=96.94  E-value=0.0014  Score=35.95  Aligned_cols=26  Identities=23%  Similarity=0.216  Sum_probs=19.2

Q ss_pred             CCCCCccHHHHHHHHHH-hCCHHHHHh
Q 035374           36 PGVEGIGDVRAVQLITK-FGMLVFNVE   61 (66)
Q Consensus        36 ~gi~GiG~K~A~~Ll~~-fgsl~~i~~   61 (66)
                      .+|.||||+||.++..+ |.|++++..
T Consensus         5 ~~I~GVG~~tA~~w~~~G~rtl~Dl~~   31 (52)
T PF10391_consen    5 TGIWGVGPKTARKWYAKGIRTLEDLRK   31 (52)
T ss_dssp             HTSTT--HHHHHHHHHTT--SHHHHHH
T ss_pred             hhcccccHHHHHHHHHhCCCCHHHHhh
Confidence            36799999999999998 789999865

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 ....

>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional

Probab=96.89  E-value=0.0025  Score=42.80  Aligned_cols=44  Identities=14%  Similarity=0.191  Sum_probs=30.5

Q ss_pred             HHHHhCCCChhHHHHHHHhhCCCCCCCCCCCCccHHHHHHHHHHhCCHHHHHh
Q 035374            9 FARKYGELKPSQFVDVISLVGDKADNIPGVEGIGDVRAVQLITKFGMLVFNVE   61 (66)
Q Consensus         9 v~~~~g~i~p~q~~d~~~L~Gd~~D~i~gi~GiG~K~A~~Ll~~fgsl~~i~~   61 (66)
                      -..-||+.+++.---|..|++        |+|||||+|..+|..|+ .+++.+
T Consensus        57 ~~~LyGF~~~~Er~lF~~Li~--------V~GIGpK~Al~ILs~~~-~~~l~~  100 (194)
T PRK14605         57 ALSLFGFATTEELSLFETLID--------VSGIGPKLGLAMLSAMN-AEALAS  100 (194)
T ss_pred             CceeeCCCCHHHHHHHHHHhC--------CCCCCHHHHHHHHHhCC-HHHHHH
Confidence            345577777777777777754        58888888888888874 445433

>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional

Probab=96.89  E-value=0.0024  Score=43.18  Aligned_cols=41  Identities=15%  Similarity=0.173  Sum_probs=20.0

Q ss_pred             HHhCCCChhHHHHHHHhhCCCCCCCCCCCCccHHHHHHHHHHhCCHHHHH
Q 035374           11 RKYGELKPSQFVDVISLVGDKADNIPGVEGIGDVRAVQLITKFGMLVFNV   60 (66)
Q Consensus        11 ~~~g~i~p~q~~d~~~L~Gd~~D~i~gi~GiG~K~A~~Ll~~fgsl~~i~   60 (66)
                      .-||+.+.++-.-|..|++        |.|||||+|..+|..+ +.+++.
T Consensus        60 ~LyGF~~~~Er~lF~~Li~--------V~GIGpK~Al~iLs~~-~~~~l~  100 (203)
T PRK14602         60 ELFGFATWDERQTFIVLIS--------ISKVGAKTALAILSQF-RPDDLR  100 (203)
T ss_pred             eeeCCCCHHHHHHHHHHhC--------CCCcCHHHHHHHHhhC-CHHHHH
Confidence            3355445554444444433        3555555555555554 333333

>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional

Probab=96.86  E-value=0.0021  Score=43.06  Aligned_cols=34  Identities=35%  Similarity=0.546  Sum_probs=15.5

Q ss_pred             CChhHHHHHHHhhCCCCCCCCCCCCccHHHHHHHHHH
Q 035374           16 LKPSQFVDVISLVGDKADNIPGVEGIGDVRAVQLITK   52 (66)
Q Consensus        16 i~p~q~~d~~~L~Gd~~D~i~gi~GiG~K~A~~Ll~~   52 (66)
                      ++|+++.+.-+ -||. ..+ .+||||+|+|.+++-+
T Consensus        93 ~~~~~l~~aI~-~~D~-~~L-~vpGIGkKtAerIilE  126 (186)
T PRK14600         93 LTPEQLFSAIV-NEDK-AAL-KVNGIGEKLINRIITE  126 (186)
T ss_pred             CCHHHHHHHHH-cCCH-hhe-ECCCCcHHHHHHHHHH
Confidence            34444443222 3442 344 5555555555555544

>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional

Probab=96.74  E-value=0.0022  Score=43.50  Aligned_cols=40  Identities=30%  Similarity=0.361  Sum_probs=24.8

Q ss_pred             HHhCCCChhHHHHHHHhhCCCCCCCCCCCCccHHHHHHHHHH
Q 035374           11 RKYGELKPSQFVDVISLVGDKADNIPGVEGIGDVRAVQLITK   52 (66)
Q Consensus        11 ~~~g~i~p~q~~d~~~L~Gd~~D~i~gi~GiG~K~A~~Ll~~   52 (66)
                      .-...++|+++... +.-|| ...+..+||||+|||.+++-+
T Consensus        87 aILs~~~~~el~~a-I~~~D-~~~L~~vpGIGkKtAeRIIlE  126 (196)
T PRK13901         87 RVLSGIKYNEFRDA-IDRED-IELISKVKGIGNKMAGKIFLK  126 (196)
T ss_pred             HHHcCCCHHHHHHH-HHhCC-HHHHhhCCCCCHHHHHHHHHH
Confidence            33433567777643 23455 446677788888888877754

>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional

Probab=96.74  E-value=0.0018  Score=43.81  Aligned_cols=43  Identities=16%  Similarity=0.308  Sum_probs=30.9

Q ss_pred             HHHHhCCCChhHHHHHHHhhCCCCCCCCCCCCccHHHHHHHHHHh
Q 035374            9 FARKYGELKPSQFVDVISLVGDKADNIPGVEGIGDVRAVQLITKF   53 (66)
Q Consensus         9 v~~~~g~i~p~q~~d~~~L~Gd~~D~i~gi~GiG~K~A~~Ll~~f   53 (66)
                      -+.-...++|+++... +.-|| ...+..+||||+|||.+++-+.
T Consensus        87 Al~iLs~~~~~~l~~a-I~~~D-~~~L~~ipGIGkKtAerIilEL  129 (203)
T PRK14602         87 ALAILSQFRPDDLRRL-VAEED-VAALTRVSGIGKKTAQHIFLEL  129 (203)
T ss_pred             HHHHHhhCCHHHHHHH-HHhCC-HHHHhcCCCcCHHHHHHHHHHH
Confidence            3344444688888842 33555 6688999999999999998654

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

Probab=96.68  E-value=0.0014  Score=30.88  Aligned_cols=18  Identities=28%  Similarity=0.445  Sum_probs=15.6

Q ss_pred             CCCCCCccHHHHHHHHHH
Q 035374           35 IPGVEGIGDVRAVQLITK   52 (66)
Q Consensus        35 i~gi~GiG~K~A~~Ll~~   52 (66)
                      +..|||||+|+|.++++.
T Consensus         3 L~~i~GiG~k~A~~il~~   20 (26)
T smart00278        3 LLKVPGIGPKTAEKILEA   20 (26)
T ss_pred             hhhCCCCCHHHHHHHHHh
Confidence            457899999999999974

>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional

Probab=96.67  E-value=0.0035  Score=41.98  Aligned_cols=48  Identities=23%  Similarity=0.252  Sum_probs=37.0

Q ss_pred             HHHHHHhCCCChhHHHHHHHhhCCCCCCCCCCCCccHHHHHHHHHHhCCHHHHHhhh
Q 035374            7 EDFARKYGELKPSQFVDVISLVGDKADNIPGVEGIGDVRAVQLITKFGMLVFNVECF   63 (66)
Q Consensus         7 ~~v~~~~g~i~p~q~~d~~~L~Gd~~D~i~gi~GiG~K~A~~Ll~~fgsl~~i~~~~   63 (66)
                      |+-..-||+.+++.---|..|++        |.|||||+|..+|..+ +++++.++.
T Consensus        55 Ed~~~LyGF~~~~Er~lF~~Li~--------VsGIGpK~Al~ILs~~-~~~el~~aI  102 (183)
T PRK14601         55 EDSNKLYGFLDKDEQKMFEMLLK--------VNGIGANTAMAVCSSL-DVNSFYKAL  102 (183)
T ss_pred             cCCceeeCCCCHHHHHHHHHHhc--------cCCccHHHHHHHHcCC-CHHHHHHHH
Confidence            33445688888888888888754        5899999999999996 677776543

>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional

Probab=96.64  E-value=0.0038  Score=42.37  Aligned_cols=48  Identities=25%  Similarity=0.330  Sum_probs=36.8

Q ss_pred             HHHHHHhCCCChhHHHHHHHhhCCCCCCCCCCCCccHHHHHHHHHHhCCHHHHHhhh
Q 035374            7 EDFARKYGELKPSQFVDVISLVGDKADNIPGVEGIGDVRAVQLITKFGMLVFNVECF   63 (66)
Q Consensus         7 ~~v~~~~g~i~p~q~~d~~~L~Gd~~D~i~gi~GiG~K~A~~Ll~~fgsl~~i~~~~   63 (66)
                      |+-..-||+.+.+.---|..|++        |.|||||+|..+|..+ +++++.++.
T Consensus        54 ED~~~LYGF~t~~Er~lF~~Lis--------VsGIGPK~ALaILs~~-~~~el~~aI  101 (196)
T PRK13901         54 EDELKLFGFLNSSEREVFEELIG--------VDGIGPRAALRVLSGI-KYNEFRDAI  101 (196)
T ss_pred             cCCceeeCCCCHHHHHHHHHHhC--------cCCcCHHHHHHHHcCC-CHHHHHHHH
Confidence            33446688888888888888764        5899999999999997 666666543

>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional

Probab=96.63  E-value=0.0037  Score=42.11  Aligned_cols=19  Identities=26%  Similarity=0.508  Sum_probs=9.8

Q ss_pred             CCCCCCCccHHHHHHHHHH
Q 035374           34 NIPGVEGIGDVRAVQLITK   52 (66)
Q Consensus        34 ~i~gi~GiG~K~A~~Ll~~   52 (66)
                      .+..+||||+|||.+++-+
T Consensus       109 ~L~kvpGIGkKtAerIilE  127 (195)
T PRK14604        109 RLARVPGIGKKTAERIVLE  127 (195)
T ss_pred             HHhhCCCCCHHHHHHHHHH
Confidence            4445555555555555544

>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional

Probab=96.58  E-value=0.0029  Score=42.68  Aligned_cols=48  Identities=27%  Similarity=0.225  Sum_probs=36.6

Q ss_pred             HHHHHHhCCCChhHHHHHHHhhCCCCCCCCCCCCccHHHHHHHHHHhCCHHHHHhhh
Q 035374            7 EDFARKYGELKPSQFVDVISLVGDKADNIPGVEGIGDVRAVQLITKFGMLVFNVECF   63 (66)
Q Consensus         7 ~~v~~~~g~i~p~q~~d~~~L~Gd~~D~i~gi~GiG~K~A~~Ll~~fgsl~~i~~~~   63 (66)
                      |+-..-||+.+.+.---|..|++        |.|||||+|..+|..+ +++++.+++
T Consensus        55 Ed~~~LyGF~~~~Er~lF~~Li~--------V~GIGpK~Al~iLs~~-~~~el~~aI  102 (195)
T PRK14604         55 EDALTLYGFSTPAQRQLFELLIG--------VSGVGPKAALNLLSSG-TPDELQLAI  102 (195)
T ss_pred             cCCceeeCCCCHHHHHHHHHHhC--------cCCcCHHHHHHHHcCC-CHHHHHHHH
Confidence            34445688788887777777754        5899999999999986 677776544

>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional

Probab=96.57  E-value=0.0044  Score=41.56  Aligned_cols=35  Identities=14%  Similarity=0.284  Sum_probs=17.1

Q ss_pred             CChhHHHHHHHhhCCCCCCCCCCCCccHHHHHHHHHH
Q 035374           16 LKPSQFVDVISLVGDKADNIPGVEGIGDVRAVQLITK   52 (66)
Q Consensus        16 i~p~q~~d~~~L~Gd~~D~i~gi~GiG~K~A~~Ll~~   52 (66)
                      ++|+++.+. +..|| ...+..+||||+|||.+++-+
T Consensus        93 ~~~~el~~a-I~~~D-~~~L~~vpGIGkKtAerIilE  127 (188)
T PRK14606         93 EDAETLVTM-IASQD-VEGLSKLPGISKKTAERIVME  127 (188)
T ss_pred             CCHHHHHHH-HHhCC-HHHHhhCCCCCHHHHHHHHHH
Confidence            455555432 22343 334555555555555555544

>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional

Probab=96.56  E-value=0.003  Score=42.33  Aligned_cols=48  Identities=21%  Similarity=0.136  Sum_probs=36.8

Q ss_pred             HHHHHHhCCCChhHHHHHHHhhCCCCCCCCCCCCccHHHHHHHHHHhCCHHHHHhhh
Q 035374            7 EDFARKYGELKPSQFVDVISLVGDKADNIPGVEGIGDVRAVQLITKFGMLVFNVECF   63 (66)
Q Consensus         7 ~~v~~~~g~i~p~q~~d~~~L~Gd~~D~i~gi~GiG~K~A~~Ll~~fgsl~~i~~~~   63 (66)
                      |+-..-||+.+.++---|..|++        |.|||||+|..+|..+ +++++.+++
T Consensus        55 Ed~~~LyGF~~~~Er~lF~~Li~--------V~GIGpK~AL~iLs~~-~~~el~~aI  102 (188)
T PRK14606         55 QDGITLYGFSNERKKELFLSLTK--------VSRLGPKTALKIISNE-DAETLVTMI  102 (188)
T ss_pred             cCCceeeCCCCHHHHHHHHHHhc--------cCCccHHHHHHHHcCC-CHHHHHHHH
Confidence            34456688778888877888754        5899999999999986 677776543

>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional

Probab=96.55  E-value=0.0051  Score=41.21  Aligned_cols=49  Identities=18%  Similarity=0.220  Sum_probs=38.1

Q ss_pred             HHHHHHHhCCCChhHHHHHHHhhCCCCCCCCCCCCccHHHHHHHHHHhCCHHHHHhhh
Q 035374            6 MEDFARKYGELKPSQFVDVISLVGDKADNIPGVEGIGDVRAVQLITKFGMLVFNVECF   63 (66)
Q Consensus         6 ~~~v~~~~g~i~p~q~~d~~~L~Gd~~D~i~gi~GiG~K~A~~Ll~~fgsl~~i~~~~   63 (66)
                      .|+-..-||+.+++.---|..|++        |.|||||+|..+|..+ +++++.+++
T Consensus        54 rEd~~~LyGF~~~~Er~lF~~Lis--------V~GIGpK~Al~iLs~~-~~~~l~~aI  102 (186)
T PRK14600         54 RDNVTQLYGFLNREEQDCLRMLVK--------VSGVNYKTAMSILSKL-TPEQLFSAI  102 (186)
T ss_pred             ecCCceeeCCCCHHHHHHHHHHhC--------cCCcCHHHHHHHHccC-CHHHHHHHH
Confidence            344556789888888888888754        5899999999999997 677776544

>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional

Probab=96.55  E-value=0.0045  Score=41.74  Aligned_cols=36  Identities=25%  Similarity=0.420  Sum_probs=18.1

Q ss_pred             CChhHHHHHHHhhCCCCCCCCCCCCccHHHHHHHHHHh
Q 035374           16 LKPSQFVDVISLVGDKADNIPGVEGIGDVRAVQLITKF   53 (66)
Q Consensus        16 i~p~q~~d~~~L~Gd~~D~i~gi~GiG~K~A~~Ll~~f   53 (66)
                      ++|+++... +.-|| ...+..+||||+|+|.+++-+.
T Consensus        92 ~~~~~l~~a-I~~~D-~~~L~kvpGIGkKtAerIilEL  127 (197)
T PRK14603         92 LPPALLARA-LLEGD-ARLLTSASGVGKKLAERIALEL  127 (197)
T ss_pred             CCHHHHHHH-HHhCC-HHHHhhCCCCCHHHHHHHHHHH
Confidence            455555532 22344 3345555666666666665443

>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional

Probab=96.54  E-value=0.0031  Score=42.51  Aligned_cols=48  Identities=23%  Similarity=0.292  Sum_probs=35.8

Q ss_pred             HHHHHHhCCCChhHHHHHHHhhCCCCCCCCCCCCccHHHHHHHHHHhCCHHHHHhhh
Q 035374            7 EDFARKYGELKPSQFVDVISLVGDKADNIPGVEGIGDVRAVQLITKFGMLVFNVECF   63 (66)
Q Consensus         7 ~~v~~~~g~i~p~q~~d~~~L~Gd~~D~i~gi~GiG~K~A~~Ll~~fgsl~~i~~~~   63 (66)
                      |+-..-||+.+.+.-.-|..|++        |.|||||+|..+|..+ +++++.+++
T Consensus        54 Ed~~~LyGF~~~~Er~lF~~L~~--------V~GIGpK~AL~iLs~~-~~~~l~~aI  101 (197)
T PRK14603         54 EDALSLYGFPDEDSLELFELLLG--------VSGVGPKLALALLSAL-PPALLARAL  101 (197)
T ss_pred             cCCceeeCcCCHHHHHHHHHHhC--------cCCcCHHHHHHHHcCC-CHHHHHHHH
Confidence            33445688777777777777754        5899999999999996 677776543

>PF00867 XPG_I: XPG I-region; InterPro: IPR006086 This entry represents endonucleases that cleave the 5'-overhanging flap structure that is generated by displacement synthesis when DNA polymerase encounters the 5'-end of a downstream Okazaki fragment

Probab=96.46  E-value=0.0029  Score=37.61  Aligned_cols=28  Identities=29%  Similarity=0.570  Sum_probs=25.5

Q ss_pred             ceeCHHHHHHHhCCCChhHHHHHHHhhCC
Q 035374            2 ASFGMEDFARKYGELKPSQFVDVISLVGD   30 (66)
Q Consensus         2 ~~~~~~~v~~~~g~i~p~q~~d~~~L~Gd   30 (66)
                      ..++.+.+.+.++ ++++||+++++|+|+
T Consensus        66 ~~~~~~~i~~~l~-l~~~~fi~~~iL~G~   93 (94)
T PF00867_consen   66 EVIDLDDILKELG-LTREQFIDLCILCGC   93 (94)
T ss_dssp             EEEEHHHHHHHHT-TSHHHHHHHHHHHHE
T ss_pred             EEEEHHHHHHHcC-CCHHHHHHHheecCC
Confidence            3678899999998 999999999999995

Has 5'-endo-/exonuclease and 5'-pseudo-Y-endonuclease activities. Cleaves the junction between single and double-stranded regions of flap DNA. The endonuclease binds 2 magnesium ions per subunit. which probably participate in the reaction catalyzed by the enzyme. May bind an additional third magnesium ion after substrate binding.; GO: 0004518 nuclease activity, 0006281 DNA repair; PDB: 1UL1_Z 3Q8K_A 3Q8M_A 3Q8L_A 2IZO_A 1A77_A 1A76_A 3QEA_Z 3QE9_Y 3QEB_Z ....

>TIGR00575 dnlj DNA ligase, NAD-dependent

Probab=96.39  E-value=0.003  Score=49.00  Aligned_cols=26  Identities=31%  Similarity=0.465  Sum_probs=23.8

Q ss_pred             CCCCccHHHHHHHHHHhCCHHHHHhh
Q 035374           37 GVEGIGDVRAVQLITKFGMLVFNVEC   62 (66)
Q Consensus        37 gi~GiG~K~A~~Ll~~fgsl~~i~~~   62 (66)
                      ||||||+++|..|+++|+|++++.++
T Consensus       502 gIpgVG~~~ak~L~~~f~sl~~l~~A  527 (652)
T TIGR00575       502 GIRHVGEVTAKNLAKHFGTLDKLKAA  527 (652)
T ss_pred             cCCCcCHHHHHHHHHHhCCHHHHHhC
Confidence            67999999999999999999998754

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

>COG1948 MUS81 ERCC4-type nuclease [DNA replication, recombination, and repair]

Probab=96.29  E-value=0.0044  Score=43.69  Aligned_cols=27  Identities=30%  Similarity=0.431  Sum_probs=24.3

Q ss_pred             CCCCCccHHHHHHHHHHhCCHHHHHhh
Q 035374           36 PGVEGIGDVRAVQLITKFGMLVFNVEC   62 (66)
Q Consensus        36 ~gi~GiG~K~A~~Ll~~fgsl~~i~~~   62 (66)
                      .++||||++.|..|+++|||+++++.+
T Consensus       185 ~s~pgig~~~a~~ll~~fgS~~~~~ta  211 (254)
T COG1948         185 ESIPGIGPKLAERLLKKFGSVEDVLTA  211 (254)
T ss_pred             HcCCCccHHHHHHHHHHhcCHHHHhhc
Confidence            456899999999999999999999865

>PRK14351 ligA NAD-dependent DNA ligase LigA; Provisional

Probab=96.22  E-value=0.0049  Score=48.28  Aligned_cols=26  Identities=23%  Similarity=0.454  Sum_probs=23.7

Q ss_pred             CCCCccHHHHHHHHHHhCCHHHHHhh
Q 035374           37 GVEGIGDVRAVQLITKFGMLVFNVEC   62 (66)
Q Consensus        37 gi~GiG~K~A~~Ll~~fgsl~~i~~~   62 (66)
                      ||||||+++|.+|++.|+|++++.++
T Consensus       532 gIpgIG~~~ak~L~~~F~si~~L~~A  557 (689)
T PRK14351        532 GIPEVGPTTARNLAREFGTFEAIMDA  557 (689)
T ss_pred             CCCCcCHHHHHHHHHHhCCHHHHHhC
Confidence            57999999999999999999998753

>PRK13482 DNA integrity scanning protein DisA; Provisional

Probab=96.07  E-value=0.017  Score=42.43  Aligned_cols=58  Identities=19%  Similarity=0.319  Sum_probs=43.4

Q ss_pred             CHHHHHHHhCCCChhHHHHHH---HhhCCCC-----CC---------CCCCCCccHHHHHHHHHHhCCHHHHHhh
Q 035374            5 GMEDFARKYGELKPSQFVDVI---SLVGDKA-----DN---------IPGVEGIGDVRAVQLITKFGMLVFNVEC   62 (66)
Q Consensus         5 ~~~~v~~~~g~i~p~q~~d~~---~L~Gd~~-----D~---------i~gi~GiG~K~A~~Ll~~fgsl~~i~~~   62 (66)
                      +.+++.+++..++.+++.|..   .++|=+.     |.         +..||+++++.|.+|+++|||+.+++++
T Consensus       242 ~~~~~~~~l~~l~~~~lld~~~ia~~lGy~~~~~~ld~~v~prGyRiLs~IPrl~k~iAk~Ll~~FGSL~~Il~A  316 (352)
T PRK13482        242 DPEEILEELQELSSEELLDLSAIARLLGYPGGSEALDTPVSPRGYRLLSKIPRLPSAVIENLVEHFGSLQGLLAA  316 (352)
T ss_pred             CHHHHHHHHHhCCHHHhcCHHHHHHHhCCCCCCcccccccCCcHHHHHhcCCCCCHHHHHHHHHHcCCHHHHHcC
Confidence            356777777778888887764   4566211     11         2357999999999999999999999864

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

Probab=96.04  E-value=0.017  Score=39.39  Aligned_cols=47  Identities=23%  Similarity=0.198  Sum_probs=24.1

Q ss_pred             HHHHHHHhCCCChhHHHHHHHhhCCCCCCCCCCCCccHHHHHHHHHHhCCHHHHHh
Q 035374            6 MEDFARKYGELKPSQFVDVISLVGDKADNIPGVEGIGDVRAVQLITKFGMLVFNVE   61 (66)
Q Consensus         6 ~~~v~~~~g~i~p~q~~d~~~L~Gd~~D~i~gi~GiG~K~A~~Ll~~fgsl~~i~~   61 (66)
                      .|+...-||+.+.+.=..|..|..        |.|||||+|..+|..+ +++++.+
T Consensus        54 REd~~~LyGF~~~~ER~lF~~Lis--------VnGIGpK~ALaiLs~~-~~~~l~~  100 (201)
T COG0632          54 REDAHLLYGFLTEEERELFRLLIS--------VNGIGPKLALAILSNL-DPEELAQ  100 (201)
T ss_pred             hhhHHHHcCCCCHHHHHHHHHHHc--------cCCccHHHHHHHHcCC-CHHHHHH
Confidence            344455566545544444444433        3466666666666553 4444443

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

Probab=95.99  E-value=0.0062  Score=35.69  Aligned_cols=27  Identities=22%  Similarity=0.394  Sum_probs=23.0

Q ss_pred             CCCCCCCccHHHHHHHHHHhCCHHHHH
Q 035374           34 NIPGVEGIGDVRAVQLITKFGMLVFNV   60 (66)
Q Consensus        34 ~i~gi~GiG~K~A~~Ll~~fgsl~~i~   60 (66)
                      -+..|||||+.+|..|+.+.++++.+-
T Consensus         3 ~l~sipGig~~~a~~llaeigd~~rF~   29 (87)
T PF02371_consen    3 LLTSIPGIGPITAATLLAEIGDISRFK   29 (87)
T ss_pred             hhcCCCCccHHHHHHHHHHHcCchhcc
Confidence            356889999999999999999887653

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

>TIGR01259 comE comEA protein

Probab=95.91  E-value=0.0081  Score=37.51  Aligned_cols=26  Identities=19%  Similarity=0.188  Sum_probs=20.8

Q ss_pred             CCCCCCccHHHHHHHHHHh------CCHHHHH
Q 035374           35 IPGVEGIGDVRAVQLITKF------GMLVFNV   60 (66)
Q Consensus        35 i~gi~GiG~K~A~~Ll~~f------gsl~~i~   60 (66)
                      +..+||||+++|.++++.+      .|++++.
T Consensus        70 L~~lpGIG~~~A~~Ii~~R~~~g~f~s~eeL~  101 (120)
T TIGR01259        70 LQALPGIGPAKAKAIIEYREENGAFKSVDDLT  101 (120)
T ss_pred             HhcCCCCCHHHHHHHHHHHHhcCCcCCHHHHH
Confidence            4567999999999999984      6677664

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.

>TIGR00084 ruvA Holliday junction DNA helicase, RuvA subunit

Probab=95.90  E-value=0.013  Score=39.19  Aligned_cols=47  Identities=19%  Similarity=0.350  Sum_probs=32.6

Q ss_pred             eCHHHHHHHhCCCChhHHHHHHHhhCCCCCCCCCCCCccHHHHHHHHHH
Q 035374            4 FGMEDFARKYGELKPSQFVDVISLVGDKADNIPGVEGIGDVRAVQLITK   52 (66)
Q Consensus         4 ~~~~~v~~~~g~i~p~q~~d~~~L~Gd~~D~i~gi~GiG~K~A~~Ll~~   52 (66)
                      +++.....-.+..+++++.+... -+| ...+..+||||+|||.+++-+
T Consensus        80 IGpK~Al~iL~~~~~~el~~aI~-~~d-~~~L~~ipGiGkKtAerIile  126 (191)
T TIGR00084        80 VGPKLALAILSNMSPEEFVYAIE-TEE-VKALVKIPGVGKKTAERLLLE  126 (191)
T ss_pred             CCHHHHHHHHhcCCHHHHHHHHH-hCC-HHHHHhCCCCCHHHHHHHHHH
Confidence            34444555566467888874332 466 447889999999999999854

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.

>TIGR00596 rad1 DNA repair protein (rad1)

Probab=95.82  E-value=0.0076  Score=48.02  Aligned_cols=29  Identities=10%  Similarity=-0.020  Sum_probs=25.5

Q ss_pred             CCCCCCCccHHHHHHHHHHhCCHHHHHhh
Q 035374           34 NIPGVEGIGDVRAVQLITKFGMLVFNVEC   62 (66)
Q Consensus        34 ~i~gi~GiG~K~A~~Ll~~fgsl~~i~~~   62 (66)
                      ++-++||||++.|..||++|+|++++.++
T Consensus       758 ~L~~lPgI~~~~a~~ll~~f~si~~l~~a  786 (814)
T TIGR00596       758 FLLKLPGVTKKNYRNLRKKVKSIRELAKL  786 (814)
T ss_pred             HHHHCCCCCHHHHHHHHHHcCCHHHHHhC
Confidence            34568999999999999999999999863

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

>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated

Probab=95.66  E-value=0.01  Score=46.27  Aligned_cols=26  Identities=27%  Similarity=0.391  Sum_probs=23.7

Q ss_pred             CCCCccHHHHHHHHHHhCCHHHHHhh
Q 035374           37 GVEGIGDVRAVQLITKFGMLVFNVEC   62 (66)
Q Consensus        37 gi~GiG~K~A~~Ll~~fgsl~~i~~~   62 (66)
                      ||||||+++|..|+++|+|++++.++
T Consensus       515 gi~~IG~~~ak~L~~~f~sl~~l~~A  540 (665)
T PRK07956        515 GIRHVGEKAAKALARHFGSLEALRAA  540 (665)
T ss_pred             hccCcCHHHHHHHHHHcCCHHHHHhC
Confidence            68999999999999999999998753

>PRK13766 Hef nuclease; Provisional

Probab=95.64  E-value=0.012  Score=45.37  Aligned_cols=28  Identities=21%  Similarity=0.389  Sum_probs=24.7

Q ss_pred             CCCCCCccHHHHHHHHHHhCCHHHHHhh
Q 035374           35 IPGVEGIGDVRAVQLITKFGMLVFNVEC   62 (66)
Q Consensus        35 i~gi~GiG~K~A~~Ll~~fgsl~~i~~~   62 (66)
                      +.++||||+++|.+|+++|||+++++++
T Consensus       717 L~~ipgig~~~a~~Ll~~fgs~~~i~~a  744 (773)
T PRK13766        717 VESLPDVGPVLARNLLEHFGSVEAVMTA  744 (773)
T ss_pred             HhcCCCCCHHHHHHHHHHcCCHHHHHhC
Confidence            4567999999999999999999998753

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

Probab=95.55  E-value=0.027  Score=38.37  Aligned_cols=44  Identities=18%  Similarity=0.369  Sum_probs=31.6

Q ss_pred             HHHHhCCCChhHHHHHHHhhCCCCCCCCCCCCccHHHHHHHHHHhC
Q 035374            9 FARKYGELKPSQFVDVISLVGDKADNIPGVEGIGDVRAVQLITKFG   54 (66)
Q Consensus         9 v~~~~g~i~p~q~~d~~~L~Gd~~D~i~gi~GiG~K~A~~Ll~~fg   54 (66)
                      -+.-...++++.+.+.-+ .+| ...+-.+||||+|+|.+++-+-.
T Consensus        86 ALaiLs~~~~~~l~~aI~-~~d-~~~L~k~PGIGkKtAerivleLk  129 (201)
T COG0632          86 ALAILSNLDPEELAQAIA-NED-VKALSKIPGIGKKTAERIVLELK  129 (201)
T ss_pred             HHHHHcCCCHHHHHHHHH-hcC-hHhhhcCCCCCHHHHHHHHHHHh
Confidence            334444467888885433 555 55889999999999999987643

>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional

Probab=95.42  E-value=0.017  Score=38.72  Aligned_cols=35  Identities=17%  Similarity=0.446  Sum_probs=25.1

Q ss_pred             CChhHHHHHHHhhCCCCCCCCCCCCccHHHHHHHHHH
Q 035374           16 LKPSQFVDVISLVGDKADNIPGVEGIGDVRAVQLITK   52 (66)
Q Consensus        16 i~p~q~~d~~~L~Gd~~D~i~gi~GiG~K~A~~Ll~~   52 (66)
                      ++|++|+.. +..+| ...+..|||||+|||.+++-+
T Consensus        93 ~~~~~l~~a-I~~~D-~~~L~~vpGIGkKtAerIilE  127 (194)
T PRK14605         93 MNAEALASA-IISGN-AELLSTIPGIGKKTASRIVLE  127 (194)
T ss_pred             CCHHHHHHH-HHhCC-HHHHHhCCCCCHHHHHHHHHH
Confidence            567777642 22566 447889999999999996543

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

Probab=95.41  E-value=0.016  Score=37.41  Aligned_cols=26  Identities=8%  Similarity=0.092  Sum_probs=22.3

Q ss_pred             CCCCCccHHHHHHHHHH--hCCHHHHHh
Q 035374           36 PGVEGIGDVRAVQLITK--FGMLVFNVE   61 (66)
Q Consensus        36 ~gi~GiG~K~A~~Ll~~--fgsl~~i~~   61 (66)
                      ..+|||||++|.++++.  |.|+|++++
T Consensus        64 ~~lpGigP~~A~~IV~nGpf~sveDL~~   91 (132)
T PRK02515         64 RQFPGMYPTLAGKIVKNAPYDSVEDVLN   91 (132)
T ss_pred             HHCCCCCHHHHHHHHHCCCCCCHHHHHc
Confidence            45799999999999984  889998874

>smart00483 POLXc DNA polymerase X family

Probab=95.10  E-value=0.024  Score=40.64  Aligned_cols=29  Identities=21%  Similarity=0.109  Sum_probs=22.8

Q ss_pred             CCCCCCccHHHHHHHHHH-hCCHHHHHhhh
Q 035374           35 IPGVEGIGDVRAVQLITK-FGMLVFNVECF   63 (66)
Q Consensus        35 i~gi~GiG~K~A~~Ll~~-fgsl~~i~~~~   63 (66)
                      +-.|||||||||.+|.+. +.|++++.++.
T Consensus        91 l~~i~GiGpk~a~~l~~lGi~tl~eL~~a~  120 (334)
T smart00483       91 FTNVFGVGPKTAAKWYRKGIRTLEELKKNK  120 (334)
T ss_pred             HHccCCcCHHHHHHHHHhCCCCHHHHHhcc
Confidence            346799999999999993 24889887654

includes vertebrate polymerase beta and terminal deoxynucleotidyltransferases

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

Probab=94.90  E-value=0.004  Score=34.88  Aligned_cols=33  Identities=18%  Similarity=0.252  Sum_probs=21.9

Q ss_pred             HhhCCCCCCCCCCCCccHHHHHHHHHHhCCHHH
Q 035374           26 SLVGDKADNIPGVEGIGDVRAVQLITKFGMLVF   58 (66)
Q Consensus        26 ~L~Gd~~D~i~gi~GiG~K~A~~Ll~~fgsl~~   58 (66)
                      .+.--+.+.+..||||||++|..+.+-|.+.++
T Consensus        28 ~l~~a~~e~L~~i~gIG~~~A~si~~ff~~~~n   60 (64)
T PF12826_consen   28 ALMNASVEELSAIPGIGPKIAQSIYEFFQDPEN   60 (64)
T ss_dssp             HHCC--HHHHCTSTT--HHHHHHHHHHHH-HHH
T ss_pred             HHHHcCHHHHhccCCcCHHHHHHHHHHHCCHHh
Confidence            344444566788999999999999999877654

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

Probab=94.84  E-value=0.019  Score=28.34  Aligned_cols=16  Identities=38%  Similarity=0.395  Sum_probs=12.7

Q ss_pred             CCCCCCCccHHHHHHH
Q 035374           34 NIPGVEGIGDVRAVQL   49 (66)
Q Consensus        34 ~i~gi~GiG~K~A~~L   49 (66)
                      .+..++|||+|++.+|
T Consensus        12 pi~~~~GIG~kt~~kL   27 (32)
T PF11798_consen   12 PIRKFWGIGKKTAKKL   27 (32)
T ss_dssp             BGGGSTTS-HHHHHHH
T ss_pred             CHHhhCCccHHHHHHH
Confidence            4667899999999985

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

>PRK08609 hypothetical protein; Provisional

Probab=94.61  E-value=0.041  Score=42.08  Aligned_cols=28  Identities=14%  Similarity=0.096  Sum_probs=22.8

Q ss_pred             CCCCCccHHHHHHHHHHh--CCHHHHHhhh
Q 035374           36 PGVEGIGDVRAVQLITKF--GMLVFNVECF   63 (66)
Q Consensus        36 ~gi~GiG~K~A~~Ll~~f--gsl~~i~~~~   63 (66)
                      -.|||||||+|.+|.++.  .|++++.+++
T Consensus        91 ~~i~GiGpk~a~~l~~~lGi~tl~~L~~a~  120 (570)
T PRK08609         91 LKLPGLGGKKIAKLYKELGVVDKESLKEAC  120 (570)
T ss_pred             hcCCCCCHHHHHHHHHHhCCCCHHHHHHHH
Confidence            468999999999999865  5888887654

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

Probab=94.57  E-value=0.043  Score=38.90  Aligned_cols=27  Identities=22%  Similarity=0.126  Sum_probs=21.5

Q ss_pred             CCCCCccHHHHHHHHHH-hCCHHHHHhh
Q 035374           36 PGVEGIGDVRAVQLITK-FGMLVFNVEC   62 (66)
Q Consensus        36 ~gi~GiG~K~A~~Ll~~-fgsl~~i~~~   62 (66)
                      -+|||||||+|.+|... +.|++++..+
T Consensus        88 ~~i~GiGpk~a~~l~~lGi~sl~dL~~a  115 (307)
T cd00141          88 LRVPGVGPKTARKLYELGIRTLEDLRKA  115 (307)
T ss_pred             HcCCCCCHHHHHHHHHcCCCCHHHHHHH
Confidence            36899999999999932 5588888765

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

>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=94.26  E-value=0.016  Score=31.72  Aligned_cols=22  Identities=23%  Similarity=0.498  Sum_probs=18.4

Q ss_pred             CCCCCCCCCccHHHHHHHHHHh
Q 035374           32 ADNIPGVEGIGDVRAVQLITKF   53 (66)
Q Consensus        32 ~D~i~gi~GiG~K~A~~Ll~~f   53 (66)
                      .+.+..|||||+++|.+|+...
T Consensus        37 ~~~L~~i~Gig~~~a~~i~~~~   58 (60)
T PF14520_consen   37 PEELAEIPGIGEKTAEKIIEAA   58 (60)
T ss_dssp             HHHHHTSTTSSHHHHHHHHHHH
T ss_pred             HHHHhcCCCCCHHHHHHHHHHH
Confidence            3567788999999999999864

...

>COG0272 Lig NAD-dependent DNA ligase (contains BRCT domain type II) [DNA replication, recombination, and repair]

Probab=94.20  E-value=0.035  Score=43.66  Aligned_cols=27  Identities=26%  Similarity=0.436  Sum_probs=24.7

Q ss_pred             CCCCCccHHHHHHHHHHhCCHHHHHhh
Q 035374           36 PGVEGIGDVRAVQLITKFGMLVFNVEC   62 (66)
Q Consensus        36 ~gi~GiG~K~A~~Ll~~fgsl~~i~~~   62 (66)
                      -|||.||+++|..|-+.|+|+++++++
T Consensus       514 LGIr~VG~~~Ak~La~~f~sl~~l~~a  540 (667)
T COG0272         514 LGIRHVGETTAKSLARHFGTLEALLAA  540 (667)
T ss_pred             cCCchhhHHHHHHHHHHhhhHHHHHhc
Confidence            478999999999999999999999864

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

Probab=94.14  E-value=0.053  Score=35.14  Aligned_cols=25  Identities=24%  Similarity=0.295  Sum_probs=19.2

Q ss_pred             CCCCCccHHHHHHHHH------HhCCHHHHH
Q 035374           36 PGVEGIGDVRAVQLIT------KFGMLVFNV   60 (66)
Q Consensus        36 ~gi~GiG~K~A~~Ll~------~fgsl~~i~   60 (66)
                      ..+||||+|+|.+++.      .|.|++++.
T Consensus       100 ~~lpgIG~~kA~aIi~yRe~~G~f~sv~dL~  130 (149)
T COG1555         100 QALPGIGPKKAQAIIDYREENGPFKSVDDLA  130 (149)
T ss_pred             HHCCCCCHHHHHHHHHHHHHcCCCCcHHHHH
Confidence            4568999999999887      356777765

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

Probab=94.10  E-value=0.078  Score=29.57  Aligned_cols=15  Identities=20%  Similarity=0.477  Sum_probs=11.8

Q ss_pred             CCCccHHHHHHHHHH
Q 035374           38 VEGIGDVRAVQLITK   52 (66)
Q Consensus        38 i~GiG~K~A~~Ll~~   52 (66)
                      +||||+++|.++++.
T Consensus        22 ipgig~~~a~~Il~~   36 (69)
T TIGR00426        22 MNGVGLKKAEAIVSY   36 (69)
T ss_pred             CCCCCHHHHHHHHHH
Confidence            577888888888877

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

>PRK00254 ski2-like helicase; Provisional

Probab=93.60  E-value=0.057  Score=41.81  Aligned_cols=29  Identities=24%  Similarity=0.209  Sum_probs=25.8

Q ss_pred             CCCCCCCccHHHHHHHHHH-hCCHHHHHhh
Q 035374           34 NIPGVEGIGDVRAVQLITK-FGMLVFNVEC   62 (66)
Q Consensus        34 ~i~gi~GiG~K~A~~Ll~~-fgsl~~i~~~   62 (66)
                      .+..|||+|+++|.+|++. |+|++++.++
T Consensus       646 ~L~~ipgig~~~~~~l~~~g~~s~~~i~~a  675 (720)
T PRK00254        646 ELMRLPMIGRKRARALYNAGFRSIEDIVNA  675 (720)
T ss_pred             hhhcCCCCCHHHHHHHHHccCCCHHHHHhC
Confidence            4558899999999999999 9999999764

>TIGR02236 recomb_radA DNA repair and recombination protein RadA

Probab=93.49  E-value=0.089  Score=36.57  Aligned_cols=26  Identities=15%  Similarity=0.224  Sum_probs=23.6

Q ss_pred             CCCCCccHHHHHHHHHH-hCCHHHHHh
Q 035374           36 PGVEGIGDVRAVQLITK-FGMLVFNVE   61 (66)
Q Consensus        36 ~gi~GiG~K~A~~Ll~~-fgsl~~i~~   61 (66)
                      ..+||||++++.+|.+. |.|++++..
T Consensus         2 ~~i~gig~~~~~~L~~~Gi~ti~dl~~   28 (310)
T TIGR02236         2 EDLPGVGPATAEKLREAGYDTFEAIAV   28 (310)
T ss_pred             cccCCCCHHHHHHHHHcCCCCHHHHHc
Confidence            46799999999999999 999999875

This family consists exclusively of archaeal RadA protein, a homolog of bacterial RecA (TIGR02012), eukaryotic RAD51 (TIGR02239), and archaeal RadB (TIGR02237). This protein is involved in DNA repair and recombination. The member from Pyrococcus horikoshii contains an intein.

>TIGR01448 recD_rel helicase, putative, RecD/TraA family

Probab=93.23  E-value=0.079  Score=41.53  Aligned_cols=37  Identities=19%  Similarity=0.377  Sum_probs=25.2

Q ss_pred             ChhHHHHHHHhhCCCCCCCCCCCCccHHHHHHHHHHhCC--HHHHHh
Q 035374           17 KPSQFVDVISLVGDKADNIPGVEGIGDVRAVQLITKFGM--LVFNVE   61 (66)
Q Consensus        17 ~p~q~~d~~~L~Gd~~D~i~gi~GiG~K~A~~Ll~~fgs--l~~i~~   61 (66)
                      +.+.++.|..     |..   +||||||+|.++++.||.  ++.+.+
T Consensus        76 ~~~~i~~yL~-----s~~---~~GIG~~~A~~iv~~fg~~~~~~i~~  114 (720)
T TIGR01448        76 SKEGIVAYLS-----SRS---IKGVGKKLAQRIVKTFGEAAFDVLDD  114 (720)
T ss_pred             CHHHHHHHHh-----cCC---CCCcCHHHHHHHHHHhCHhHHHHHHh
Confidence            3456666644     223   589999999999999984  444443

This model describes a family similar to RecD, the exodeoxyribonuclease V alpha chain of TIGR01447. Members of this family, however, are not found in a context of RecB and RecC and are longer by about 200 amino acids at the amino end. Chlamydia muridarum has both a member of this family and a RecD.

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

Probab=92.68  E-value=0.24  Score=34.03  Aligned_cols=20  Identities=25%  Similarity=0.519  Sum_probs=16.2

Q ss_pred             CCCCCccHHHHHHHHHH-hCC
Q 035374           36 PGVEGIGDVRAVQLITK-FGM   55 (66)
Q Consensus        36 ~gi~GiG~K~A~~Ll~~-fgs   55 (66)
                      ..+||||+|||.-.|.. ||-
T Consensus       112 ~~LPGVGrKTAnvVL~~a~g~  132 (211)
T COG0177         112 LSLPGVGRKTANVVLSFAFGI  132 (211)
T ss_pred             HhCCCcchHHHHHHHHhhcCC
Confidence            45699999999998887 553

>KOG2841 consensus Structure-specific endonuclease ERCC1-XPF, ERCC1 component [Replication, recombination and repair]

Probab=92.38  E-value=0.1  Score=36.82  Aligned_cols=29  Identities=24%  Similarity=0.357  Sum_probs=25.7

Q ss_pred             CCCCCCccHHHHHHHHHHhCCHHHHHhhh
Q 035374           35 IPGVEGIGDVRAVQLITKFGMLVFNVECF   63 (66)
Q Consensus        35 i~gi~GiG~K~A~~Ll~~fgsl~~i~~~~   63 (66)
                      +..||||+..-|..||.+|||++++..+.
T Consensus       197 Lt~i~~VnKtda~~LL~~FgsLq~~~~AS  225 (254)
T KOG2841|consen  197 LTTIPGVNKTDAQLLLQKFGSLQQISNAS  225 (254)
T ss_pred             HHhCCCCCcccHHHHHHhcccHHHHHhcC
Confidence            55689999999999999999999998643

>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed

Probab=90.92  E-value=0.31  Score=32.45  Aligned_cols=23  Identities=22%  Similarity=0.384  Sum_probs=19.4

Q ss_pred             CCCCCCCCccHHHHHHHHHHhCC
Q 035374           33 DNIPGVEGIGDVRAVQLITKFGM   55 (66)
Q Consensus        33 D~i~gi~GiG~K~A~~Ll~~fgs   55 (66)
                      ..+..+||||+|+|.+++.++..
T Consensus       108 ~~L~~v~Gig~k~A~~I~~~l~~  130 (192)
T PRK00116        108 KALTKVPGIGKKTAERIVLELKD  130 (192)
T ss_pred             HHHHhCCCCCHHHHHHHHHHHHH
Confidence            35778999999999999988753

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

Probab=90.88  E-value=0.07  Score=36.52  Aligned_cols=17  Identities=24%  Similarity=0.421  Sum_probs=13.6

Q ss_pred             CCCCCCCccHHHHHHHH
Q 035374           34 NIPGVEGIGDVRAVQLI   50 (66)
Q Consensus        34 ~i~gi~GiG~K~A~~Ll   50 (66)
                      .+..+||||||+|.++-
T Consensus        13 ~l~kLPGvG~KsA~R~A   29 (198)
T COG0353          13 ALKKLPGVGPKSAQRLA   29 (198)
T ss_pred             HHhhCCCCChhHHHHHH
Confidence            45667999999998863

>TIGR03252 uncharacterized HhH-GPD family protein

Probab=90.43  E-value=0.16  Score=34.07  Aligned_cols=22  Identities=18%  Similarity=0.448  Sum_probs=18.4

Q ss_pred             CCCCCCCccHHHHHHHHHHhCC
Q 035374           34 NIPGVEGIGDVRAVQLITKFGM   55 (66)
Q Consensus        34 ~i~gi~GiG~K~A~~Ll~~fgs   55 (66)
                      .+-.+||||+|||--+|..+++
T Consensus       116 ~Ll~LpGVG~KTAnvVL~~l~~  137 (177)
T TIGR03252       116 RLKALPGFGKQKAKIFLALLGK  137 (177)
T ss_pred             HHHcCCCCCHHHHHHHHHHHHH
Confidence            4678899999999998887664

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).

>PRK00076 recR recombination protein RecR; Reviewed

Probab=90.33  E-value=0.18  Score=34.33  Aligned_cols=18  Identities=28%  Similarity=0.385  Sum_probs=14.4

Q ss_pred             CCCCCCccHHHHHHHHHH
Q 035374           35 IPGVEGIGDVRAVQLITK   52 (66)
Q Consensus        35 i~gi~GiG~K~A~~Ll~~   52 (66)
                      +..+||||+|+|.++--.
T Consensus        13 l~~LPGIG~KsA~Rla~~   30 (196)
T PRK00076         13 LRKLPGIGPKSAQRLAFH   30 (196)
T ss_pred             HHHCCCCCHHHHHHHHHH
Confidence            456799999999987544

>TIGR00615 recR recombination protein RecR

Probab=90.31  E-value=0.18  Score=34.32  Aligned_cols=18  Identities=28%  Similarity=0.396  Sum_probs=14.3

Q ss_pred             CCCCCCCccHHHHHHHHH
Q 035374           34 NIPGVEGIGDVRAVQLIT   51 (66)
Q Consensus        34 ~i~gi~GiG~K~A~~Ll~   51 (66)
                      .+..+||||+|+|.++--
T Consensus        12 ~l~~LPGIG~KsA~RlA~   29 (195)
T TIGR00615        12 SLKKLPGIGPKSAQRLAF   29 (195)
T ss_pred             HHHHCCCCCHHHHHHHHH
Confidence            355679999999998843

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

>PRK13844 recombination protein RecR; Provisional

Probab=89.65  E-value=0.22  Score=34.05  Aligned_cols=19  Identities=16%  Similarity=0.212  Sum_probs=14.9

Q ss_pred             CCCCCCCccHHHHHHHHHH
Q 035374           34 NIPGVEGIGDVRAVQLITK   52 (66)
Q Consensus        34 ~i~gi~GiG~K~A~~Ll~~   52 (66)
                      .+..+||||+|+|.++--.
T Consensus        16 ~l~~LPGIG~KsA~Rla~~   34 (200)
T PRK13844         16 SLRKLPTIGKKSSQRLALY   34 (200)
T ss_pred             HHHHCCCCCHHHHHHHHHH
Confidence            3556799999999987544

>PRK14350 ligA NAD-dependent DNA ligase LigA; Provisional

Probab=89.50  E-value=0.39  Score=37.81  Aligned_cols=25  Identities=16%  Similarity=0.299  Sum_probs=22.3

Q ss_pred             CCCCccHHHHHHHH-HHhCCHHHHHh
Q 035374           37 GVEGIGDVRAVQLI-TKFGMLVFNVE   61 (66)
Q Consensus        37 gi~GiG~K~A~~Ll-~~fgsl~~i~~   61 (66)
                      |||+||+++|..|. +.|++++++.+
T Consensus       506 GI~~vG~~~ak~La~~~f~~~~~l~~  531 (669)
T PRK14350        506 GIKDLGENTILLLINNNLNSFDKIST  531 (669)
T ss_pred             CCCchhHHHHHHHHHHhhCCHHHHHh
Confidence            57999999999999 89999998864

>PF13052 DUF3913: Protein of unknown function (DUF3913)

Probab=89.17  E-value=0.21  Score=27.50  Aligned_cols=29  Identities=24%  Similarity=0.444  Sum_probs=20.9

Q ss_pred             hhCCCCCCCCCCCCccHHHHHHHHHHhCCHHH
Q 035374           27 LVGDKADNIPGVEGIGDVRAVQLITKFGMLVF   58 (66)
Q Consensus        27 L~Gd~~D~i~gi~GiG~K~A~~Ll~~fgsl~~   58 (66)
                      |+|- +||+|.||.||+|.  ++|+.-.++.+
T Consensus        14 llgi-wdnvptiprigekv--eilktirtvtd   42 (57)
T PF13052_consen   14 LLGI-WDNVPTIPRIGEKV--EILKTIRTVTD   42 (57)
T ss_pred             hhhh-hccCCCccccchhh--hHHhhhheeee
Confidence            4564 89999999999985  45665555443

>PRK04301 radA DNA repair and recombination protein RadA; Validated

Probab=88.89  E-value=0.36  Score=33.84  Aligned_cols=28  Identities=14%  Similarity=0.265  Sum_probs=24.4

Q ss_pred             CCCCCCCccHHHHHHHHHH-hCCHHHHHh
Q 035374           34 NIPGVEGIGDVRAVQLITK-FGMLVFNVE   61 (66)
Q Consensus        34 ~i~gi~GiG~K~A~~Ll~~-fgsl~~i~~   61 (66)
                      .+..+||||+++|.+|.+. |.|++++.+
T Consensus         7 ~l~~l~gIg~~~a~~L~~~Gi~t~~dl~~   35 (317)
T PRK04301          7 DLEDLPGVGPATAEKLREAGYDTVEAIAV   35 (317)
T ss_pred             cHhhcCCCCHHHHHHHHHcCCCCHHHHHc
Confidence            4567899999999999999 899999865

>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=88.86  E-value=0.36  Score=26.97  Aligned_cols=15  Identities=27%  Similarity=0.483  Sum_probs=13.4

Q ss_pred             CCCCCCccHHHHHHH
Q 035374           35 IPGVEGIGDVRAVQL   49 (66)
Q Consensus        35 i~gi~GiG~K~A~~L   49 (66)
                      +.++||||+++|.++
T Consensus        49 ~~~l~gIG~~ia~kI   63 (68)
T PF14716_consen   49 LKKLPGIGKSIAKKI   63 (68)
T ss_dssp             HCTSTTTTHHHHHHH
T ss_pred             HhhCCCCCHHHHHHH
Confidence            578899999999887

...

>PF04919 DUF655: Protein of unknown function (DUF655); InterPro: IPR007003 This family includes several uncharacterised archaeal proteins

Probab=88.32  E-value=0.63  Score=31.49  Aligned_cols=45  Identities=18%  Similarity=0.214  Sum_probs=25.9

Q ss_pred             ChhHHHHHHHhhCCCCCCC---CCCCCccHHHHHHHHHH-----hCCHHHHHh
Q 035374           17 KPSQFVDVISLVGDKADNI---PGVEGIGDVRAVQLITK-----FGMLVFNVE   61 (66)
Q Consensus        17 ~p~q~~d~~~L~Gd~~D~i---~gi~GiG~K~A~~Ll~~-----fgsl~~i~~   61 (66)
                      +.+.|++|---+|-.+..+   .=+||||.|+.+++|.+     |.|.++|-+
T Consensus        97 ~E~~FV~FfN~A~PIt~RlH~LeLLPGIGKK~m~~ILeERkkkpFeSFeDi~~  149 (181)
T PF04919_consen   97 NEERFVDFFNEAQPITLRLHSLELLPGIGKKTMWKILEERKKKPFESFEDIEE  149 (181)
T ss_dssp             THHHHHHHH-----B-SSSBGGGGSTT--HHHHHHHHHHHHHS---SHHHHHH
T ss_pred             ChHHHHHHhhcCCCChHHHHHHhhcccccHHHHHHHHHHHccCCCCCHHHHHH
Confidence            5678899887777433332   23699999999999975     888887754

; PDB: 2I5H_A.

>PRK10702 endonuclease III; Provisional

Probab=87.99  E-value=0.83  Score=30.95  Aligned_cols=19  Identities=16%  Similarity=0.384  Sum_probs=14.8

Q ss_pred             CCCCCCCccHHHHHHHHHH
Q 035374           34 NIPGVEGIGDVRAVQLITK   52 (66)
Q Consensus        34 ~i~gi~GiG~K~A~~Ll~~   52 (66)
                      .+-.+||||+|||--++--
T Consensus       110 ~Ll~lpGVG~ktA~~ill~  128 (211)
T PRK10702        110 ALEALPGVGRKTANVVLNT  128 (211)
T ss_pred             HHhcCCcccHHHHHHHHHH
Confidence            3446899999999887643

>KOG2841 consensus Structure-specific endonuclease ERCC1-XPF, ERCC1 component [Replication, recombination and repair]

Probab=87.98  E-value=0.54  Score=33.30  Aligned_cols=42  Identities=14%  Similarity=0.302  Sum_probs=30.6

Q ss_pred             CHHHHHHHhCCCChhHHHHHHHhhCCCCCCCCCCCCccHHHHHHHHHHhC
Q 035374            5 GMEDFARKYGELKPSQFVDVISLVGDKADNIPGVEGIGDVRAVQLITKFG   54 (66)
Q Consensus         5 ~~~~v~~~~g~i~p~q~~d~~~L~Gd~~D~i~gi~GiG~K~A~~Ll~~fg   54 (66)
                      |...++.+||  +      ++.+.+-+...+..+||+||..|.+|.+-|.
T Consensus       207 da~~LL~~Fg--s------Lq~~~~AS~~ele~~~G~G~~kak~l~~~l~  248 (254)
T KOG2841|consen  207 DAQLLLQKFG--S------LQQISNASEGELEQCPGLGPAKAKRLHKFLH  248 (254)
T ss_pred             cHHHHHHhcc--c------HHHHHhcCHhHHHhCcCcCHHHHHHHHHHHh
Confidence            4445556665  3      4455566667789999999999999988764

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

Probab=87.90  E-value=0.58  Score=28.48  Aligned_cols=26  Identities=15%  Similarity=0.051  Sum_probs=20.1

Q ss_pred             CCCCCCccHHHHHHHHHH-hCCHHHHH
Q 035374           35 IPGVEGIGDVRAVQLITK-FGMLVFNV   60 (66)
Q Consensus        35 i~gi~GiG~K~A~~Ll~~-fgsl~~i~   60 (66)
                      +..|||||+++|..|..= +.|++++.
T Consensus        14 L~~iP~IG~a~a~DL~~LGi~s~~~L~   40 (93)
T PF11731_consen   14 LTDIPNIGKATAEDLRLLGIRSPADLK   40 (93)
T ss_pred             HhcCCCccHHHHHHHHHcCCCCHHHHh
Confidence            456799999999999864 55676664

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

>PRK13910 DNA glycosylase MutY; Provisional

Probab=87.79  E-value=1  Score=32.03  Aligned_cols=19  Identities=21%  Similarity=0.408  Sum_probs=15.3

Q ss_pred             CCCCCCCCccHHHHHHHHH
Q 035374           33 DNIPGVEGIGDVRAVQLIT   51 (66)
Q Consensus        33 D~i~gi~GiG~K~A~~Ll~   51 (66)
                      +.+-.+||||+|||-.++.
T Consensus        72 ~~L~~LpGIG~kTA~aIl~   90 (289)
T PRK13910         72 QSLLKLPGIGAYTANAILC   90 (289)
T ss_pred             HHHHhCCCCCHHHHHHHHH
Confidence            3455679999999998876

>PRK01229 N-glycosylase/DNA lyase; Provisional

Probab=87.76  E-value=0.45  Score=32.51  Aligned_cols=18  Identities=28%  Similarity=0.602  Sum_probs=15.0

Q ss_pred             CCCCccHHHHHHHHHHhC
Q 035374           37 GVEGIGDVRAVQLITKFG   54 (66)
Q Consensus        37 gi~GiG~K~A~~Ll~~fg   54 (66)
                      .+||||+|||--+|...+
T Consensus       123 ~lpGIG~KTAd~vL~~~~  140 (208)
T PRK01229        123 NIKGIGYKEASHFLRNVG  140 (208)
T ss_pred             cCCCCcHHHHHHHHHHcc
Confidence            789999999999995433

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

Probab=86.94  E-value=0.48  Score=29.68  Aligned_cols=18  Identities=17%  Similarity=0.281  Sum_probs=14.9

Q ss_pred             CCCCCCccHHHHHHHHHH
Q 035374           35 IPGVEGIGDVRAVQLITK   52 (66)
Q Consensus        35 i~gi~GiG~K~A~~Ll~~   52 (66)
                      +..+||||+|+|.-++.-
T Consensus        85 L~~l~GIG~~tA~~~l~~  102 (158)
T cd00056          85 LLALPGVGRKTANVVLLF  102 (158)
T ss_pred             HHcCCCCCHHHHHHHHHH
Confidence            358899999999987764

>PRK13482 DNA integrity scanning protein DisA; Provisional

Probab=86.67  E-value=0.4  Score=35.29  Aligned_cols=35  Identities=31%  Similarity=0.676  Sum_probs=26.6

Q ss_pred             HHHHHHhCCCChhHHHHHHHhhCCCCCCCCCCCCccHHHHHHH
Q 035374            7 EDFARKYGELKPSQFVDVISLVGDKADNIPGVEGIGDVRAVQL   49 (66)
Q Consensus         7 ~~v~~~~g~i~p~q~~d~~~L~Gd~~D~i~gi~GiG~K~A~~L   49 (66)
                      +++.++||        .++.++.-+.+.+..|+|||+++|..+
T Consensus       301 k~Ll~~FG--------SL~~Il~As~eeL~~VeGIGe~rA~~I  335 (352)
T PRK13482        301 ENLVEHFG--------SLQGLLAASIEDLDEVEGIGEVRARAI  335 (352)
T ss_pred             HHHHHHcC--------CHHHHHcCCHHHHhhCCCcCHHHHHHH
Confidence            45566666        556667766778889999999999984

>PRK13913 3-methyladenine DNA glycosylase; Provisional

Probab=86.24  E-value=0.53  Score=32.33  Aligned_cols=17  Identities=24%  Similarity=0.399  Sum_probs=14.6

Q ss_pred             CCCCCCccHHHHHHHHH
Q 035374           35 IPGVEGIGDVRAVQLIT   51 (66)
Q Consensus        35 i~gi~GiG~K~A~~Ll~   51 (66)
                      +-.+||||++||--+|-
T Consensus       123 Ll~l~GIG~kTAd~iLl  139 (218)
T PRK13913        123 LLDQKGIGKESADAILC  139 (218)
T ss_pred             HHcCCCccHHHHHHHHH
Confidence            55789999999988775

>PF00416 Ribosomal_S13: Ribosomal protein S13/S18; InterPro: IPR001892 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms

Probab=85.87  E-value=0.72  Score=28.09  Aligned_cols=19  Identities=37%  Similarity=0.597  Sum_probs=16.7

Q ss_pred             CCCCCccHHHHHHHHHHhC
Q 035374           36 PGVEGIGDVRAVQLITKFG   54 (66)
Q Consensus        36 ~gi~GiG~K~A~~Ll~~fg   54 (66)
                      ..|.|||+++|..+.++.|
T Consensus        18 t~IyGIG~~~A~~Ic~~lg   36 (107)
T PF00416_consen   18 TKIYGIGRRKAKQICKKLG   36 (107)
T ss_dssp             TTSTTBCHHHHHHHHHHTT
T ss_pred             hhhhccCHHHHHHHHHHcC
Confidence            4579999999999999875

The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein S13 is one of the proteins from the small ribosomal subunit. In Escherichia coli, S13 is known to be involved in binding fMet-tRNA and, hence, in the initiation of translation. It is a basic protein of 115 to 177 amino-acid residues that contains thee helices and a beta-hairpin in the core of the protein, forming a helix-two turns-helix (H2TH) motif, and a non-globular C-terminal extension. This family of ribosomal proteins is present in prokaryotes, eukaryotes and archaea [, ].; GO: 0003723 RNA binding, 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3BBN_M 2QBB_M 3I1M_M 3OFP_M 3OFX_M 3OFO_M 1VS5_M 3OAQ_M 2QAL_M 3J18_M ....

>TIGR01084 mutY A/G-specific adenine glycosylase

Probab=85.76  E-value=1.6  Score=30.70  Aligned_cols=18  Identities=17%  Similarity=0.516  Sum_probs=14.3

Q ss_pred             CCCCCCCccHHHHHHHHH
Q 035374           34 NIPGVEGIGDVRAVQLIT   51 (66)
Q Consensus        34 ~i~gi~GiG~K~A~~Ll~   51 (66)
                      .+-.+||||+|||.-++.
T Consensus       106 ~L~~LpGIG~~TA~~Il~  123 (275)
T TIGR01084       106 DLAALPGVGRYTAGAILS  123 (275)
T ss_pred             HHHhCCCCCHHHHHHHHH
Confidence            445679999999987665

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.

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

Probab=85.69  E-value=1.5  Score=24.18  Aligned_cols=15  Identities=27%  Similarity=0.412  Sum_probs=5.9

Q ss_pred             CCCCCCCccHHHHHH
Q 035374           34 NIPGVEGIGDVRAVQ   48 (66)
Q Consensus        34 ~i~gi~GiG~K~A~~   48 (66)
                      .+..|+|||+++..+
T Consensus        45 dL~~v~gi~~~~~~~   59 (65)
T PF12836_consen   45 DLKEVPGIGPKTYEK   59 (65)
T ss_dssp             GGGGSTT--HHHHHH
T ss_pred             HHhhCCCCCHHHHHH
Confidence            334445555554443

>COG1491 Predicted RNA-binding protein [Translation, ribosomal structure and biogenesis]

Probab=84.87  E-value=1.2  Score=30.66  Aligned_cols=44  Identities=16%  Similarity=0.177  Sum_probs=28.5

Q ss_pred             hhHHHHHHHhhCCCCC---CCCCCCCccHHHHHHHHHH-----hCCHHHHHh
Q 035374           18 PSQFVDVISLVGDKAD---NIPGVEGIGDVRAVQLITK-----FGMLVFNVE   61 (66)
Q Consensus        18 p~q~~d~~~L~Gd~~D---~i~gi~GiG~K~A~~Ll~~-----fgsl~~i~~   61 (66)
                      .+.|++|.-=++-.+-   .+.=+||||.|+.+.+|.+     |.|.+++.+
T Consensus       112 E~rFV~fFN~A~PIt~RLH~LELLpGiGkK~m~~ILeERkkkpFeSFeDi~~  163 (202)
T COG1491         112 EDRFVKFFNEAEPITLRLHQLELLPGIGKKTMWAILEERKKKPFESFEDIKE  163 (202)
T ss_pred             hhHHHHHhcccCcchHHHHHHHhcccccHHHHHHHHHHHhcCCCcCHHHHHH
Confidence            3456665544442211   1234699999999999975     788887754

>PF14579 HHH_6: Helix-hairpin-helix motif; PDB: 2HPM_A 2HPI_A 3E0D_A 3F2C_A 3F2B_A 3F2D_A 2HQA_A 2HNH_A

Probab=84.79  E-value=1.3  Score=25.88  Aligned_cols=28  Identities=18%  Similarity=0.399  Sum_probs=21.1

Q ss_pred             CCCCCCccHHHHHHHHHH-----hCCHHHHHhh
Q 035374           35 IPGVEGIGDVRAVQLITK-----FGMLVFNVEC   62 (66)
Q Consensus        35 i~gi~GiG~K~A~~Ll~~-----fgsl~~i~~~   62 (66)
                      +..|+|||++.|.+++++     |.|+++++..
T Consensus        29 l~~Ikglg~~~a~~I~~~R~~g~f~s~~df~~R   61 (90)
T PF14579_consen   29 LSAIKGLGEEVAEKIVEERENGPFKSLEDFIQR   61 (90)
T ss_dssp             GGGSTTS-HHHHHHHHHHHHCSS-SSHHHHHHH
T ss_pred             HhhcCCCCHHHHHHHHHhHhcCCCCCHHHHHHH
Confidence            457899999999999964     6788887754

>smart00478 ENDO3c endonuclease III

Probab=84.62  E-value=0.75  Score=28.59  Aligned_cols=19  Identities=16%  Similarity=0.326  Sum_probs=14.4

Q ss_pred             CCCCCCCccHHHHHHHHHH
Q 035374           34 NIPGVEGIGDVRAVQLITK   52 (66)
Q Consensus        34 ~i~gi~GiG~K~A~~Ll~~   52 (66)
                      .+..+||||+|+|.-++..
T Consensus        73 ~L~~l~GIG~~tA~~~l~~   91 (149)
T smart00478       73 ELLKLPGVGRKTANAVLSF   91 (149)
T ss_pred             HHHcCCCCcHHHHHHHHHH
Confidence            3457899999999766544

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

>PF14490 HHH_4: Helix-hairpin-helix containing domain; PDB: 3GPL_A 3E1S_A 3GP8_A

Probab=84.08  E-value=5.6  Score=23.37  Aligned_cols=46  Identities=28%  Similarity=0.486  Sum_probs=30.0

Q ss_pred             HHHHHhCCCChhHHHHHHHhhC---------CCCCCCCCCCCccHHHHHHHHHHhC
Q 035374            8 DFARKYGELKPSQFVDVISLVG---------DKADNIPGVEGIGDVRAVQLITKFG   54 (66)
Q Consensus         8 ~v~~~~g~i~p~q~~d~~~L~G---------d~~D~i~gi~GiG~K~A~~Ll~~fg   54 (66)
                      .++.+|| +++..-.-+...-|         ++..-+..|+|||-|+|-++-+++|
T Consensus        13 ~~L~~~g-l~~~~a~kl~~~yg~~ai~~l~~nPY~L~~~i~gi~F~~aD~iA~~~g   67 (94)
T PF14490_consen   13 AFLQEYG-LSPKLAMKLYKKYGDDAIEILKENPYRLIEDIDGIGFKTADKIALKLG   67 (94)
T ss_dssp             HHHHHTT---HHHHHHHHHHH-TTHHHHHHH-STCCCB-SSSSBHHHHHHHHHTTT
T ss_pred             HHHHHcC-CCHHHHHHHHHHHhHHHHHHHHHChHHHHHHccCCCHHHHHHHHHHcC
Confidence            4567777 88776555544444         5555555689999999999999986

>TIGR01083 nth endonuclease III

Probab=83.97  E-value=0.74  Score=30.29  Aligned_cols=19  Identities=16%  Similarity=0.323  Sum_probs=15.4

Q ss_pred             CCCCCCCccHHHHHHHHHH
Q 035374           34 NIPGVEGIGDVRAVQLITK   52 (66)
Q Consensus        34 ~i~gi~GiG~K~A~~Ll~~   52 (66)
                      .+..+||||+|+|.-++..
T Consensus       107 ~L~~l~GIG~ktA~~ill~  125 (191)
T TIGR01083       107 ELVKLPGVGRKTANVVLNV  125 (191)
T ss_pred             HHHhCCCCcHHHHHHHHHH
Confidence            4558899999999887754

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=83.52  E-value=2.2  Score=31.18  Aligned_cols=22  Identities=18%  Similarity=0.581  Sum_probs=16.5

Q ss_pred             CCCCCCCCccHHHHHHHHH-HhC
Q 035374           33 DNIPGVEGIGDVRAVQLIT-KFG   54 (66)
Q Consensus        33 D~i~gi~GiG~K~A~~Ll~-~fg   54 (66)
                      +.+-.+||||+|||-.++. .|+
T Consensus       109 ~~L~~LpGIG~~TA~aIl~~af~  131 (350)
T PRK10880        109 EEVAALPGVGRSTAGAILSLSLG  131 (350)
T ss_pred             HHHhcCCCccHHHHHHHHHHHCC
Confidence            3455679999999998876 344

>PRK10736 hypothetical protein; Provisional

Probab=83.37  E-value=1.1  Score=33.13  Aligned_cols=22  Identities=9%  Similarity=0.054  Sum_probs=19.6

Q ss_pred             CCCCccHHHHHHHHHHhCCHHH
Q 035374           37 GVEGIGDVRAVQLITKFGMLVF   58 (66)
Q Consensus        37 gi~GiG~K~A~~Ll~~fgsl~~   58 (66)
                      .+||||+++..+|++.|++.++
T Consensus        12 ~~~giG~~~~~~L~~~~~~~~~   33 (374)
T PRK10736         12 SVSSLYGDKMVRIAHRLLAQSQ   33 (374)
T ss_pred             hCCCCCHHHHHHHHHHhcChhh
Confidence            3599999999999999999874

>PF14229 DUF4332: Domain of unknown function (DUF4332)

Probab=82.45  E-value=4.9  Score=24.94  Aligned_cols=47  Identities=19%  Similarity=0.215  Sum_probs=36.8

Q ss_pred             HHHHHhCCCChhHHHHHHHhhCCCCCCCCCCCCccHHHHHHHHHH-hCCHHHHH
Q 035374            8 DFARKYGELKPSQFVDVISLVGDKADNIPGVEGIGDVRAVQLITK-FGMLVFNV   60 (66)
Q Consensus         8 ~v~~~~g~i~p~q~~d~~~L~Gd~~D~i~gi~GiG~K~A~~Ll~~-fgsl~~i~   60 (66)
                      ...++.+ ++...+..+..+.    |- -.|||||+..|.-|++. +.|++++-
T Consensus        34 ~La~~~~-i~~~~l~~w~~~A----dL-~ri~gi~~~~a~LL~~AGv~Tv~~LA   81 (122)
T PF14229_consen   34 ALAKKLG-ISERNLLKWVNQA----DL-MRIPGIGPQYAELLEHAGVDTVEELA   81 (122)
T ss_pred             HHHHhcC-CCHHHHHHHHhHH----Hh-hhcCCCCHHHHHHHHHhCcCcHHHHH
Confidence            4667777 9999999887763    33 37899999999988887 56777764

>PTZ00134 40S ribosomal protein S18; Provisional

Probab=82.21  E-value=2.1  Score=28.17  Aligned_cols=36  Identities=22%  Similarity=0.477  Sum_probs=28.2

Q ss_pred             hHHHHHHHhhCCCCCC-------CCCCCCccHHHHHHHHHHhC
Q 035374           19 SQFVDVISLVGDKADN-------IPGVEGIGDVRAVQLITKFG   54 (66)
Q Consensus        19 ~q~~d~~~L~Gd~~D~-------i~gi~GiG~K~A~~Ll~~fg   54 (66)
                      ++|-.+.-++|...|+       +..|.|||..+|..++++.|
T Consensus         9 ~~~~~mvrI~~~~l~~~K~v~~aLt~I~GIG~~~A~~I~~~lg   51 (154)
T PTZ00134          9 DDFQHILRILNTNVDGKRKVPYALTAIKGIGRRFAYLVCKKAG   51 (154)
T ss_pred             hhhhhhhhccCccCCCCCEEEEeecccccccHHHHHHHHHHcC
Confidence            5777777788865544       34579999999999999975

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

Probab=80.63  E-value=2.7  Score=30.20  Aligned_cols=17  Identities=18%  Similarity=0.196  Sum_probs=14.4

Q ss_pred             CCCCCccHHHHHHHHHH
Q 035374           36 PGVEGIGDVRAVQLITK   52 (66)
Q Consensus        36 ~gi~GiG~K~A~~Ll~~   52 (66)
                      -++||||||-|.-.|+.
T Consensus       162 lsLPGVGPKMa~L~m~~  178 (286)
T KOG1921|consen  162 LSLPGVGPKMAHLTMQV  178 (286)
T ss_pred             hcCCCCchHHHHHHHHH
Confidence            36799999999988875

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

Probab=80.13  E-value=3  Score=30.72  Aligned_cols=35  Identities=14%  Similarity=0.302  Sum_probs=26.2

Q ss_pred             HHHHHHhCCCChhHHHHHHHhhCCCCCCCCCCCCccHHHHHHHHHH
Q 035374            7 EDFARKYGELKPSQFVDVISLVGDKADNIPGVEGIGDVRAVQLITK   52 (66)
Q Consensus         7 ~~v~~~~g~i~p~q~~d~~~L~Gd~~D~i~gi~GiG~K~A~~Ll~~   52 (66)
                      ..+.++|+|.-|+..-+++.           +||||+-||..++.-
T Consensus        98 ~~v~~~~~G~~P~~~~~l~~-----------LpGiG~yTa~Ail~~  132 (342)
T COG1194          98 QEVVERHGGEFPDDEEELAA-----------LPGVGPYTAGAILSF  132 (342)
T ss_pred             HHHHHHcCCCCCCCHHHHHh-----------CCCCcHHHHHHHHHH
Confidence            45667777777777666654           489999999998864

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	66
1taq_A	832	Structure Of Taq Dna Polymerase Length = 832		8e-07
1bgx_T	832	Taq Polymerase In Complex With Tp7, An Inhibitory F		8e-07
1ut5_A	291	Divalent Metal Ions (Manganese) Bound To T5 5'-Exon		6e-04
1xo1_A	291	T5 5'-Exonuclease Mutant K83a Length = 291		6e-04
1exn_A	290	T5 5'-Exonuclease Length = 290		8e-04

>pdb|1TAQ|A Chain A, Structure Of Taq Dna Polymerase Length = 832

Iteration: 1
 Score = 48.5 bits (114), Expect = 8e-07,   Method: Composition-based stats.
 Identities = 22/45 (48%), Positives = 34/45 (75%), Gaps = 1/45 (2%)
Query: 12  KYGELKPSQFVDVISLVGDKADNIPGVEGIGDVRAVQLITKFGML 56
           KYG L+P Q+ D  +L GD++DN+PGV+GIG+  A +L+ ++G L
Sbjct: 171 KYG-LRPDQWADYRALTGDESDNLPGVKGIGEKTARKLLEEWGSL 214

>pdb|1BGX|T Chain T, Taq Polymerase In Complex With Tp7, An Inhibitory Fab Length = 832

Iteration: 1
 Score = 48.5 bits (114), Expect = 8e-07,   Method: Composition-based stats.
 Identities = 22/45 (48%), Positives = 34/45 (75%), Gaps = 1/45 (2%)
Query: 12  KYGELKPSQFVDVISLVGDKADNIPGVEGIGDVRAVQLITKFGML 56
           KYG L+P Q+ D  +L GD++DN+PGV+GIG+  A +L+ ++G L
Sbjct: 171 KYG-LRPDQWADYRALTGDESDNLPGVKGIGEKTARKLLEEWGSL 214

>pdb|1UT5|A Chain A, Divalent Metal Ions (Manganese) Bound To T5 5'-Exonuclease Length = 291

Iteration: 1
 Score = 39.3 bits (90), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 17/35 (48%), Positives = 24/35 (68%)
Query: 20  QFVDVISLVGDKADNIPGVEGIGDVRAVQLITKFG 54
           QF+ + +++GD  DNI GVEGIG  R   +I +FG
Sbjct: 191 QFISLKAIMGDLGDNIRGVEGIGAKRGYNIIREFG 225

>pdb|1XO1|A Chain A, T5 5'-Exonuclease Mutant K83a Length = 291

Iteration: 1
 Score = 39.3 bits (90), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 17/35 (48%), Positives = 24/35 (68%)
Query: 20  QFVDVISLVGDKADNIPGVEGIGDVRAVQLITKFG 54
           QF+ + +++GD  DNI GVEGIG  R   +I +FG
Sbjct: 191 QFISLKAIMGDLGDNIRGVEGIGAKRGYNIIREFG 225

>pdb|1EXN|A Chain A, T5 5'-Exonuclease Length = 290

Iteration: 1
 Score = 38.9 bits (89), Expect = 8e-04,   Method: Composition-based stats.
 Identities = 17/35 (48%), Positives = 23/35 (65%)
Query: 20  QFVDVISLVGDKADNIPGVEGIGDVRAVQLITKFG 54
           QF+ + ++ GD  DNI GVEGIG  R   +I +FG
Sbjct: 190 QFISLKAIXGDLGDNIRGVEGIGAKRGYNIIREFG 224

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	66
1bgx_T	832	TAQ DNA polymerase; DNA polymerase, FAB, PCR, inhi	2e-16
1exn_A	290	5'-exonuclease, 5'-nuclease; hydrolase; 2.50A {Ent	1e-15

>1bgx_T TAQ DNA polymerase; DNA polymerase, FAB, PCR, inhibition, helix-coil dynamics, inhibitor design, complex (polymerase/inhibitor); 2.30A {Thermus aquaticus} SCOP: a.60.7.1 c.120.1.2 c.55.3.5 e.8.1.1 PDB: 1cmw_A 1tau_A* 1taq_A* Length = 832

 Score = 69.9 bits (172), Expect = 2e-16
 Identities = 21/51 (41%), Positives = 33/51 (64%), Gaps = 1/51 (1%)

Query: 4   FGMEDFARKYGELKPSQFVDVISLVGDKADNIPGVEGIGDVRAVQLITKFG 54
                   KYG L+P Q+ D  +L GD++DN+PGV+GIG+  A +L+ ++G
Sbjct: 163 ITPAWLWEKYG-LRPDQWADYRALTGDESDNLPGVKGIGEKTARKLLEEWG 212

>1exn_A 5'-exonuclease, 5'-nuclease; hydrolase; 2.50A {Enterobacteria phage T5} SCOP: a.60.7.1 c.120.1.2 PDB: 1ut5_A 1ut8_A 1xo1_A Length = 290

 Score = 67.3 bits (165), Expect = 1e-15
 Identities = 18/54 (33%), Positives = 28/54 (51%)

Query: 1   MASFGMEDFARKYGELKPSQFVDVISLVGDKADNIPGVEGIGDVRAVQLITKFG 54
              + + D    +      QF+ + +++GD  DNI GVEGIG  R   +I +FG
Sbjct: 171 RREYHLRDMYEHHNVDDVEQFISLKAIMGDLGDNIRGVEGIGAKRGYNIIREFG 224

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	66
1exn_A	290	5'-exonuclease, 5'-nuclease; hydrolase; 2.50A {Ent	99.9
1rxw_A	336	Flap structure-specific endonuclease; helical clam	99.82
2izo_A	346	FEN1, flap structure-specific endonuclease; hydrol	99.8
3q8k_A	341	Flap endonuclease 1; helix-3 turn-helix, hydrophob	99.79
3ory_A	363	Flap endonuclease 1; hydrolase; 2.00A {Desulfuroco	99.79
1b43_A	340	Protein (FEN-1); nuclease, DNA repair, DNA replica	99.78
1bgx_T	832	TAQ DNA polymerase; DNA polymerase, FAB, PCR, inhi	99.77
1a76_A	326	Flap endonuclease-1 protein; 5'-3' EXO/endo nuclea	99.77
1ul1_X	379	Flap endonuclease-1; protein complex, DNA-binding	99.72
3qe9_Y	352	Exonuclease 1; exonuclease, hydrolase-DNA complex;	99.65
3h7i_A	305	Ribonuclease H, RNAse H; BPT4 RNAse H, 5'-3' exonu	99.35
2a1j_A	63	DNA repair endonuclease XPF; XPF, xeroderma pigmen	98.48
1z00_B	84	DNA repair endonuclease XPF; helix-hairpin-helix,	98.31
1kft_A	78	UVRC, excinuclease ABC subunit C; helix-hairpin-he	98.06
1x2i_A	75	HEF helicase/nuclease; alpha helix, helix-hairpin-	98.0
1z00_A	89	DNA excision repair protein ERCC-1; helix-hairpin-	97.95
2nrt_A	220	Uvrabc system protein C; UVRC, endonuclease, RNAse	97.91
2a1j_B	91	DNA excision repair protein ERCC-1; XPF, xeroderma	97.9
3c65_A	226	Uvrabc system protein C; UVRC, endonuclease, nucle	97.57
2bgw_A	219	XPF endonuclease; hydrolase, structure specific en	97.37
1ixr_A	191	Holliday junction DNA helicase RUVA; heterooligome	97.17
4gfj_A	685	Topoisomerase V; helix-hairpin-helix, DNA repair e	97.03
1cuk_A	203	RUVA protein; DNA repair, SOS response, DNA-bindin	96.99
2owo_A	671	DNA ligase; protein-DNA complex, ligase-DNA comple	96.27
1vq8_Y	241	50S ribosomal protein L32E; ribosome 50S, protein-	96.23
3sgi_A	615	DNA ligase; HET: DNA AMP; 3.50A {Mycobacterium tub	96.19
1s5l_U	134	Photosystem II 12 kDa extrinsic protein; photosynt	96.11
3c1y_A	377	DNA integrity scanning protein DISA; DNA damage, D	95.93
1dgs_A	667	DNA ligase; AMP complex, NAD+-dependent; HET: DNA	95.85
2i5h_A	205	Hypothetical protein AF1531; PFAM:DUF655, PSI-2, s	95.79
2w9m_A	578	Polymerase X; SAXS, DNA repair, DNA polymerase, DN	95.63
2ztd_A	212	Holliday junction ATP-dependent DNA helicase RUVA;	95.56
3arc_U	97	Photosystem II 12 kDa extrinsic protein; PSII, mem	95.35
2duy_A	75	Competence protein comea-related protein; helix-ha	95.27
1ixr_A	191	Holliday junction DNA helicase RUVA; heterooligome	95.22
2bcq_A	335	DNA polymerase lambda; misalignment, extrahelical,	95.13
2fmp_A	335	DNA polymerase beta; nucleotidyl transferase, tran	95.07
2ziu_A	311	MUS81 protein; helix-hairpin-helix, alternative sp	94.91
2ztd_A	212	Holliday junction ATP-dependent DNA helicase RUVA;	94.87
3b0x_A	575	DNA polymerase beta family (X family); structural	94.81
4glx_A	586	DNA ligase; inhibitor, ligase-ligase inhibitor-DNA	94.77
2ihm_A	360	POL MU, DNA polymerase MU; helix-turn-helix, trans	94.57
3maj_A	382	DNA processing chain A; MCSG, PSI-2, structural ge	94.56
1jms_A	381	Terminal deoxynucleotidyltransferase; polymerase;	94.51
1cuk_A	203	RUVA protein; DNA repair, SOS response, DNA-bindin	93.91
1x2i_A	75	HEF helicase/nuclease; alpha helix, helix-hairpin-	93.09
1kft_A	78	UVRC, excinuclease ABC subunit C; helix-hairpin-he	92.38
2edu_A	98	Kinesin-like protein KIF22; kinesin-like DNA bindi	92.35
1z00_A	89	DNA excision repair protein ERCC-1; helix-hairpin-	92.34
3b0x_A	575	DNA polymerase beta family (X family); structural	91.69
3vdp_A	212	Recombination protein RECR; zinc finger, DNA repai	91.17
3c1y_A	377	DNA integrity scanning protein DISA; DNA damage, D	90.58
2zix_A	307	Crossover junction endonuclease MUS81; helix-hairp	90.4
2a1j_B	91	DNA excision repair protein ERCC-1; XPF, xeroderma	90.23
2csb_A	519	Topoisomerase V, TOP61; topoisomerase IB, helix-tu	90.07
1vdd_A	228	Recombination protein RECR; helix-hairpin-helix, z	90.06
3fhg_A	207	Mjogg, N-glycosylase/DNA lyase, DNA-(apurinic; hel	89.33
3n0u_A	219	Probable N-glycosylase/DNA lyase; structural genom	88.47
1pu6_A	218	3-methyladenine DNA glycosylase; helix-hairpin-hel	87.82
3fhf_A	214	Mjogg, N-glycosylase/DNA lyase, DNA-(apurinic; hel	87.44
1ci4_A	89	Protein (barrier-TO-autointegration factor (BAF) )	86.95
1vq8_Y	241	50S ribosomal protein L32E; ribosome 50S, protein-	86.88
1kea_A	221	Possible G-T mismatches repair enzyme; DNA repair,	86.57
2w9m_A	578	Polymerase X; SAXS, DNA repair, DNA polymerase, DN	86.4
2h56_A	233	DNA-3-methyladenine glycosidase; 10174367, EC 3.2.	86.37
1kg2_A	225	A/G-specific adenine glycosylase; DNA repair, hydr	86.34
2bgw_A	219	XPF endonuclease; hydrolase, structure specific en	86.25
4e9f_A	161	Methyl-CPG-binding domain protein 4; HHH DNA glyco	85.49
1orn_A	226	Endonuclease III; DNA repair, DNA glycosylase, [4F	84.73
2abk_A	211	Endonuclease III; DNA-repair, DNA glycosylase; 1.8	84.53
4b21_A	232	Probable DNA-3-methyladenine glycosylase 2; hydrol	84.35
2yg9_A	225	DNA-3-methyladenine glycosidase II, putative; hydr	84.32
3s6i_A	228	DNA-3-methyladenine glycosylase 1; DNA glycosylase	84.31
4glx_A	586	DNA ligase; inhibitor, ligase-ligase inhibitor-DNA	84.1
3i0w_A	290	8-oxoguanine-DNA-glycosylase; OGG, cacogg, DNA, 8-	83.63
1mpg_A	282	ALKA, 3-methyladenine DNA glycosylase II; DNA repa	83.27
3n5n_X	287	A/G-specific adenine DNA glycosylase; alpha-helice	82.51
2jhn_A	295	ALKA, 3-methyladenine DNA-glycosylase; DNA repair,	82.46
2dla_A	222	397AA long hypothetical protein; helix bundle, twi	82.25

>1exn_A 5'-exonuclease, 5'-nuclease; hydrolase; 2.50A {Enterobacteria phage T5} SCOP: a.60.7.1 c.120.1.2 PDB: 1ut5_A 1ut8_A 1xo1_A

Probab=99.90  E-value=1.2e-24  Score=151.84  Aligned_cols=64  Identities=28%  Similarity=0.527  Sum_probs=60.8

Q ss_pred             ceeCHHHHHHHhCCCCh-hHHHHHHHhhCCCCCCCCCCCCccHHHHHHHHHHhCCHHHHHhhhccC
Q 035374            2 ASFGMEDFARKYGELKP-SQFVDVISLVGDKADNIPGVEGIGDVRAVQLITKFGMLVFNVECFSEM   66 (66)
Q Consensus         2 ~~~~~~~v~~~~g~i~p-~q~~d~~~L~Gd~~D~i~gi~GiG~K~A~~Ll~~fgsl~~i~~~~~~~   66 (66)
                      ..++++.|.++|| ++| +||+|+++|+||+|||+|||||||||||.+||++|||+++++++++++
T Consensus       172 ~~~~~~~v~ek~G-v~p~~q~iD~~~L~GD~sDniPGVpGIG~KTA~kLL~~~gsle~i~~~~~~~  236 (290)
T 1exn_A          172 REYHLRDMYEHHN-VDDVEQFISLKAIMGDLGDNIRGVEGIGAKRGYNIIREFGNVLDIIDQLPLP  236 (290)
T ss_dssp             EEECGGGHHHHHS-SSSHHHHHHHHHHHCBGGGTBCCCTTCCHHHHHHHHHHHCSHHHHHHHCSCS
T ss_pred             EEEcHHHHHHHcC-CCHHHHHHHHHHhcCCCcCCCCCCCcCCHhHHHHHHHHcCCHHHHHHHHHHh
Confidence            3688999999998 999 999999999999999999999999999999999999999999988764

>1rxw_A Flap structure-specific endonuclease; helical clamp, helix-3 turn-helix, hydrophobic wedge, 3' FLA site, hydrolase-DNA complex; 2.00A {Archaeoglobus fulgidus} SCOP: a.60.7.1 c.120.1.2 PDB: 1rxv_A

Probab=99.82  E-value=1.4e-20  Score=131.74  Aligned_cols=59  Identities=27%  Similarity=0.502  Sum_probs=56.6

Q ss_pred             eeCHHHHHHHhCCCChhHHHHHHHhhCCCCCCCCCCCCccHHHHHHHHHHhCCHHHHHhhhc
Q 035374            3 SFGMEDFARKYGELKPSQFVDVISLVGDKADNIPGVEGIGDVRAVQLITKFGMLVFNVECFS   64 (66)
Q Consensus         3 ~~~~~~v~~~~g~i~p~q~~d~~~L~Gd~~D~i~gi~GiG~K~A~~Ll~~fgsl~~i~~~~~   64 (66)
                      .|+.+.+.++|| ++|+||+|+++|+|  |||+|||||||+|||.+||++|||+++++++++
T Consensus       208 ~~~~~~v~~~~g-l~~~q~id~~~L~G--sD~ipGv~GiG~KtA~kLl~~~gsle~i~~~~~  266 (336)
T 1rxw_A          208 IIILESNLKRLG-LTREQLIDIAILVG--TDYNEGVKGVGVKKALNYIKTYGDIFRALKALK  266 (336)
T ss_dssp             EEEHHHHHHHHT-CCHHHHHHHHHHHC--BTTBCCCTTCCHHHHHHHHHHHSSHHHHHHHHT
T ss_pred             EeEHHHHHHHcC-CCHHHHHHHHhhcC--CCCCCCCCCcCHHHHHHHHHHcCCHHHHHHhCC
Confidence            488999999998 99999999999999  799999999999999999999999999998875

>2izo_A FEN1, flap structure-specific endonuclease; hydrolase, DNA repair, DNA-binding, endonuclease, metal-BIND excision repair, DNA replication, PCNA; HET: DNA; 2.9A {Sulfolobus solfataricus}

Probab=99.80  E-value=6.5e-20  Score=129.01  Aligned_cols=60  Identities=32%  Similarity=0.525  Sum_probs=49.6

Q ss_pred             eeCHHHHHHHhCCCChhHHHHHHHhhCCCCCCCC-CCCCccHHHHHHHHHHhCCHHHHHhhhcc
Q 035374            3 SFGMEDFARKYGELKPSQFVDVISLVGDKADNIP-GVEGIGDVRAVQLITKFGMLVFNVECFSE   65 (66)
Q Consensus         3 ~~~~~~v~~~~g~i~p~q~~d~~~L~Gd~~D~i~-gi~GiG~K~A~~Ll~~fgsl~~i~~~~~~   65 (66)
                      .|+.+++.++|| ++|+||+|+|+|+|  +||+| ||||||+|||.+||++|||++++++++++
T Consensus       206 ~~~~~~v~~~~g-l~~~q~id~~~L~G--~D~~p~Gv~GIG~KtA~kLi~~~gsle~i~~~~~~  266 (346)
T 2izo_A          206 LIETEILLKKLG-ITREQLIDIGILIG--TDYNPDGIRGIGPERALKIIKKYGKIEKAMEYGEI  266 (346)
T ss_dssp             EEEHHHHHHHHT-CCHHHHHHHHHHHC--CSSSTTCSTTCCHHHHHHHHHHSSCC---------
T ss_pred             EEEHHHHHHHcC-CCHHHHHHHHHHcC--CCCCCCCCCCcCHHHHHHHHHHcCCHHHHHHHHHh
Confidence            488999999998 99999999999999  79999 99999999999999999999999988764

>3q8k_A Flap endonuclease 1; helix-3 turn-helix, hydrophobic wedge, 3' flap binding site, hydrolase-DNA complex, DNA repair, replication; HET: DNA; 2.20A {Homo sapiens} PDB: 3q8l_A* 3q8m_A*

Probab=99.79  E-value=1.2e-19  Score=128.27  Aligned_cols=61  Identities=33%  Similarity=0.496  Sum_probs=56.8

Q ss_pred             ceeCHHHHHHHhCCCChhHHHHHHHhhCCCCCCCCCCCCccHHHHHHHHHHhCCHHHHHhhhcc
Q 035374            2 ASFGMEDFARKYGELKPSQFVDVISLVGDKADNIPGVEGIGDVRAVQLITKFGMLVFNVECFSE   65 (66)
Q Consensus         2 ~~~~~~~v~~~~g~i~p~q~~d~~~L~Gd~~D~i~gi~GiG~K~A~~Ll~~fgsl~~i~~~~~~   65 (66)
                      ..++.+++.++|| ++|+||+|+++|+|  +|+.|||||||||||.+||++|||++++++++++
T Consensus       204 ~~~~~~~v~~~~g-l~~~q~id~~~L~G--~D~~~gipGiG~KtA~kll~~~gsle~i~~~~~~  264 (341)
T 3q8k_A          204 QEFHLSRILQELG-LNQEQFVDLCILLG--SDYCESIRGIGPKRAVDLIQKHKSIEEIVRRLDP  264 (341)
T ss_dssp             EEEEHHHHHHHHT-CCHHHHHHHHHHHC--CSSSCCCTTCCHHHHHHHHHHHCSHHHHHHHSCT
T ss_pred             EEEcHHHHHHHhC-CCHHHHHHHHHhcC--CCCCCCCCCccHHHHHHHHHHcCCHHHHHHHHHh
Confidence            3588999999998 99999999999999  5888999999999999999999999999998764

>3ory_A Flap endonuclease 1; hydrolase; 2.00A {Desulfurococcus amylolyticus}

Probab=99.79  E-value=5.8e-20  Score=130.85  Aligned_cols=59  Identities=25%  Similarity=0.452  Sum_probs=56.6

Q ss_pred             eeCHHHHHHHhCCCChhHHHHHHHhhCCCCCCCC-CCCCccHHHHHHHHHHhCCHHHHHhhhc
Q 035374            3 SFGMEDFARKYGELKPSQFVDVISLVGDKADNIP-GVEGIGDVRAVQLITKFGMLVFNVECFS   64 (66)
Q Consensus         3 ~~~~~~v~~~~g~i~p~q~~d~~~L~Gd~~D~i~-gi~GiG~K~A~~Ll~~fgsl~~i~~~~~   64 (66)
                      .|+.+.+.++|| ++|+||+|+++|+|  |||+| ||||||+|||.+||++|||+++++++++
T Consensus       223 ~~~~~~v~~~~g-l~~~q~id~~~L~G--sDy~p~GVpGIG~KtA~kLl~~~gsle~il~~~~  282 (363)
T 3ory_A          223 LIELDKLLVQLG-ITLENLIDIGILLG--TDYNPDGFEGIGPKKALQLVKAYGGIEKIPKPIL  282 (363)
T ss_dssp             EEEHHHHHHHHT-CCHHHHHHHHHHHC--BTTBTTCSTTCCHHHHHHHHHHHTSSTTSCGGGC
T ss_pred             EEcHHHHHHHhC-cCHHHHHHHHHHhC--CCCCCCCCCCcCHHHHHHHHHHcCCHHHHHHhcc
Confidence            589999999998 99999999999999  79999 9999999999999999999999998876

>1b43_A Protein (FEN-1); nuclease, DNA repair, DNA replication, transferase; 2.00A {Pyrococcus furiosus} SCOP: a.60.7.1 c.120.1.2 PDB: 1mc8_A

Probab=99.78  E-value=1.7e-19  Score=126.31  Aligned_cols=60  Identities=22%  Similarity=0.387  Sum_probs=56.9

Q ss_pred             eeCHHHHHHHhCCCChhHHHHHHHhhCCCCCCCC-CCCCccHHHHHHHHHHhCCHHHHHhhhcc
Q 035374            3 SFGMEDFARKYGELKPSQFVDVISLVGDKADNIP-GVEGIGDVRAVQLITKFGMLVFNVECFSE   65 (66)
Q Consensus         3 ~~~~~~v~~~~g~i~p~q~~d~~~L~Gd~~D~i~-gi~GiG~K~A~~Ll~~fgsl~~i~~~~~~   65 (66)
                      .|+.+.+.+++| ++|+||+|+++|+|  +||+| ||||||+|||.+|+++|||+++++++.++
T Consensus       209 ~~~~~~v~~~~g-l~~~q~id~~~L~G--~Dy~p~gv~GiG~ktA~kli~~~gsle~il~~~~~  269 (340)
T 1b43_A          209 LIILEEVLKELK-LTREKLIELAILVG--TDYNPGGIKGIGLKKALEIVRHSKDPLAKFQKQSD  269 (340)
T ss_dssp             EEEHHHHHHHHT-CCHHHHHHHHHHHC--CTTSTTCSTTCCHHHHHHHHHTCSSGGGGTGGGCS
T ss_pred             EEEHHHHHHHhC-CCHHHHHHHHHhcC--CCCCCCCCCCccHHHHHHHHHHcCCHHHHHcCCCC
Confidence            489999999998 99999999999999  79999 99999999999999999999999988665

>1bgx_T TAQ DNA polymerase; DNA polymerase, FAB, PCR, inhibition, helix-coil dynamics, inhibitor design, complex (polymerase/inhibitor); 2.30A {Thermus aquaticus} SCOP: a.60.7.1 c.120.1.2 c.55.3.5 e.8.1.1 PDB: 1cmw_A 1tau_A* 1taq_A*

Probab=99.77  E-value=2e-21  Score=149.41  Aligned_cols=63  Identities=35%  Similarity=0.625  Sum_probs=59.4

Q ss_pred             eeCHHHHHHHhCCCChhHHHHHHHhhCCCCCCCCCCCCccHHHHHHHHHHhCCHHHHHhhhccC
Q 035374            3 SFGMEDFARKYGELKPSQFVDVISLVGDKADNIPGVEGIGDVRAVQLITKFGMLVFNVECFSEM   66 (66)
Q Consensus         3 ~~~~~~v~~~~g~i~p~q~~d~~~L~Gd~~D~i~gi~GiG~K~A~~Ll~~fgsl~~i~~~~~~~   66 (66)
                      .|+.++|.++|| ++|+||+|+++|+||+|||+|||||||||||.+||++|||+++++++++++
T Consensus       162 ~~~~~~v~~~~g-v~p~q~id~~~L~GD~sDnipGVpGIG~KtA~kLl~~~gsle~i~~~~~~~  224 (832)
T 1bgx_T          162 LITPAWLWEKYG-LRPDQWADYRALTGDESDNLPGVKGIGEKTARKLLEEWGSLEALLKNLDRL  224 (832)
T ss_dssp             CBCSTTHHHHTC-CCGGGTTTTTTSSCCSSSCCCCCCCSSSCTTTTTGGGTTSSCSSSSSCCCC
T ss_pred             EEcHHHHHHHHC-cCHHHHHHHHHhcCCccccCCCCCCcCchHHHHHHHHCCCHHHHHHHHHHh
Confidence            478899999998 999999999999999999999999999999999999999999999887753

>1a76_A Flap endonuclease-1 protein; 5'-3' EXO/endo nuclease, DNA replication, RTH, RAD27, DNA repair; 2.00A {Methanocaldococcus jannaschii} SCOP: a.60.7.1 c.120.1.2 PDB: 1a77_A

Probab=99.77  E-value=5.2e-19  Score=123.31  Aligned_cols=60  Identities=22%  Similarity=0.377  Sum_probs=56.3

Q ss_pred             ceeCHHHHHHHhCCCChhHHHHHHHhhCCCCCCCC-CCCCccHHHHHHHHHHhCCHHHHH-hhhcc
Q 035374            2 ASFGMEDFARKYGELKPSQFVDVISLVGDKADNIP-GVEGIGDVRAVQLITKFGMLVFNV-ECFSE   65 (66)
Q Consensus         2 ~~~~~~~v~~~~g~i~p~q~~d~~~L~Gd~~D~i~-gi~GiG~K~A~~Ll~~fgsl~~i~-~~~~~   65 (66)
                      ..|+.+++.++|| ++|+||+|+++|+|  +||+| ||||||||||.+|+++ ||+++++ +++++
T Consensus       196 ~~~~~~~v~~~~g-l~~~q~id~~~L~G--sD~~p~GvpGiG~ktA~kli~~-gsle~i~~~~~~~  257 (326)
T 1a76_A          196 ELIELNEVLEDLR-ISLDDLIDIAIFMG--TDYNPGGVKGIGFKRAYELVRS-GVAKDVLKKEVEY  257 (326)
T ss_dssp             EEEEHHHHHHHHT-CCHHHHHHHHHHHC--CTTSTTTTTTCCHHHHHHHHHH-TCHHHHHHHHSTT
T ss_pred             EEEEHHHHHHHcC-CCHHHHHHHHHHcC--CCCCCCCCCCcCHHHHHHHHHc-CCHHHHHHHHHhH
Confidence            3689999999998 99999999999999  79999 9999999999999999 9999999 87753

>1ul1_X Flap endonuclease-1; protein complex, DNA-binding protein, flap DNA, flap endonuclease, sliding clamp, DNA clamp; 2.90A {Homo sapiens} SCOP: a.60.7.1 c.120.1.2

Probab=99.72  E-value=8.1e-18  Score=119.73  Aligned_cols=60  Identities=33%  Similarity=0.505  Sum_probs=54.5

Q ss_pred             eeCHHHHHHHhCCCChhHHHHHHHhhCCCCCCCCCCCCccHHHHHHHHHHhCCHHHHHhhhcc
Q 035374            3 SFGMEDFARKYGELKPSQFVDVISLVGDKADNIPGVEGIGDVRAVQLITKFGMLVFNVECFSE   65 (66)
Q Consensus         3 ~~~~~~v~~~~g~i~p~q~~d~~~L~Gd~~D~i~gi~GiG~K~A~~Ll~~fgsl~~i~~~~~~   65 (66)
                      .|+.+++.++|| ++|+||+|+++|+|  +|+.++|||||+|||.+||++|+|++++++++++
T Consensus       205 ~~~~~~v~~~~g-l~~~q~id~~~L~G--~D~~d~IpGIG~KtA~kLl~~~gsle~i~~~~~~  264 (379)
T 1ul1_X          205 EFHLSRILQELG-LNQEQFVDLCILLG--SDYCESIRGIGPKRAVDLIQKHKSIEEIVRRLDP  264 (379)
T ss_dssp             EEEHHHHHHHHT-CCHHHHHHHHHHHH--CSSSCCCTTCCHHHHHHHHHHSSSHHHHHTTCCC
T ss_pred             EEeHHHHHHHhC-CCHHHHHHHHHHhC--CCcCCCCCCcCHHHHHHHHHHcCCHHHHHHHHHh
Confidence            588999999998 99999999999999  3555667999999999999999999999998764

>3qe9_Y Exonuclease 1; exonuclease, hydrolase-DNA complex; HET: DNA; 2.51A {Homo sapiens} PDB: 3qeb_Z* 3qea_Z*

Probab=99.65  E-value=1.3e-16  Score=113.19  Aligned_cols=59  Identities=19%  Similarity=0.315  Sum_probs=50.4

Q ss_pred             eCHHHH--HHHhC-CCChhHHHHHHHhhCCCCCCCCCCCCccHHHHHHHHHHh--CCHHHHHhhhc
Q 035374            4 FGMEDF--ARKYG-ELKPSQFVDVISLVGDKADNIPGVEGIGDVRAVQLITKF--GMLVFNVECFS   64 (66)
Q Consensus         4 ~~~~~v--~~~~g-~i~p~q~~d~~~L~Gd~~D~i~gi~GiG~K~A~~Ll~~f--gsl~~i~~~~~   64 (66)
                      ++.+.+  .+++| +++|+||+|+++|+|  +||+|||||||+|||.+||++|  +|+++++++++
T Consensus       195 ~~~~~~~~~~~~g~~l~~~q~id~~~L~G--~D~~pgv~GiG~ktA~kli~~~~~~~l~~il~~~~  258 (352)
T 3qe9_Y          195 IDQARLGMCRQLGDVFTEEKFRYMCILSG--CDYLSSLRGIGLAKACKVLRLANNPDIVKVIKKIG  258 (352)
T ss_dssp             EEGGGGTTCCTTCSSCCHHHHHHHHHHHC--CSSSCCCTTCCHHHHHHHHHHCCCSCHHHHHTTHH
T ss_pred             EeHHHHHHHHHhCCCCCHHHHHHHHHhcC--CCCCCCCCCeeHHHHHHHHHHhCCCCHHHHHHHHH
Confidence            444443  46664 389999999999999  7999999999999999999999  68999998764

>3h7i_A Ribonuclease H, RNAse H; BPT4 RNAse H, 5'-3' exonuclease, hydrolase, endonuclease; 1.50A {Enterobacteria phage T4} PDB: 2ihn_A 3h8w_A 3h8j_A 1tfr_A 3h8s_A

Probab=99.35  E-value=4.2e-14  Score=99.62  Aligned_cols=38  Identities=26%  Similarity=0.145  Sum_probs=34.8

Q ss_pred             CHHHHHHHhCCCChhHHHHHHHhhCCCCCCCCCCCCccHH
Q 035374            5 GMEDFARKYGELKPSQFVDVISLVGDKADNIPGVEGIGDV   44 (66)
Q Consensus         5 ~~~~v~~~~g~i~p~q~~d~~~L~Gd~~D~i~gi~GiG~K   44 (66)
                      +.+.|.++|| + |+|++|+++|+||+|||||||||||++
T Consensus       174 ~~~~V~ek~G-v-P~q~iD~~aL~GDsSDNIPGVpGIG~~  211 (305)
T 3h7i_A          174 HKKWVKIKSG-S-AEIDCMTKILKGDKKDNVASVKVRSDF  211 (305)
T ss_dssp             TTEEECSSCS-C-HHHHHHHHHHHCBGGGTBCCTTSCTTH
T ss_pred             CHHHHHHHhC-C-HHHHhhHHheeCccccCCCCCCcCCcc
Confidence            3466788998 8 999999999999999999999999997

>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=98.48  E-value=9.1e-08  Score=53.15  Aligned_cols=28  Identities=7%  Similarity=0.071  Sum_probs=25.0

Q ss_pred             CCCCCCccHHHHHHHHHHhCCHHHHHhh
Q 035374           35 IPGVEGIGDVRAVQLITKFGMLVFNVEC   62 (66)
Q Consensus        35 i~gi~GiG~K~A~~Ll~~fgsl~~i~~~   62 (66)
                      +..|||||||++..||++|||++++.++
T Consensus         6 L~~IpGIG~kr~~~LL~~Fgs~~~i~~A   33 (63)
T 2a1j_A            6 LLKMPGVNAKNCRSLMHHVKNIAELAAL   33 (63)
T ss_dssp             HHTSTTCCHHHHHHHHHHCSSHHHHHTC
T ss_pred             HHcCCCCCHHHHHHHHHHcCCHHHHHHC
Confidence            4567999999999999999999999863

>1z00_B DNA repair endonuclease XPF; helix-hairpin-helix, hydrolase; HET: DNA; NMR {Homo sapiens} SCOP: a.60.2.5 PDB: 2aq0_A*

Probab=98.31  E-value=4.9e-07  Score=53.01  Aligned_cols=27  Identities=7%  Similarity=0.039  Sum_probs=24.3

Q ss_pred             CCCCCccHHHHHHHHHHhCCHHHHHhh
Q 035374           36 PGVEGIGDVRAVQLITKFGMLVFNVEC   62 (66)
Q Consensus        36 ~gi~GiG~K~A~~Ll~~fgsl~~i~~~   62 (66)
                      ..|||||||++..||++|+|+++|.++
T Consensus        21 ~~IpGIG~kr~~~LL~~FgSl~~i~~A   47 (84)
T 1z00_B           21 LKMPGVNAKNCRSLMHHVKNIAELAAL   47 (84)
T ss_dssp             HTCSSCCHHHHHHHHHHSSCHHHHHHS
T ss_pred             HhCCCCCHHHHHHHHHHcCCHHHHHHC
Confidence            357999999999999999999999864

>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=98.06  E-value=1.6e-06  Score=49.07  Aligned_cols=30  Identities=23%  Similarity=0.313  Sum_probs=26.2

Q ss_pred             CCCCCCCCccHHHHHHHHHHhCCHHHHHhh
Q 035374           33 DNIPGVEGIGDVRAVQLITKFGMLVFNVEC   62 (66)
Q Consensus        33 D~i~gi~GiG~K~A~~Ll~~fgsl~~i~~~   62 (66)
                      ..+.+|||||+++|.+|+++|++++++.++
T Consensus        24 ~~L~~I~gIG~~~A~~Ll~~fgsl~~l~~a   53 (78)
T 1kft_A           24 SSLETIEGVGPKRRQMLLKYMGGLQGLRNA   53 (78)
T ss_dssp             CGGGGCTTCSSSHHHHHHHHHSCHHHHHHC
T ss_pred             HHHhcCCCCCHHHHHHHHHHcCCHHHHHHC
Confidence            346689999999999999999999988764

>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=98.00  E-value=4.6e-06  Score=46.01  Aligned_cols=27  Identities=19%  Similarity=0.293  Sum_probs=23.9

Q ss_pred             CCCCCccHHHHHHHHHHhCCHHHHHhh
Q 035374           36 PGVEGIGDVRAVQLITKFGMLVFNVEC   62 (66)
Q Consensus        36 ~gi~GiG~K~A~~Ll~~fgsl~~i~~~   62 (66)
                      .+|||||+++|.+|++.|+|++++.++
T Consensus        17 ~~i~giG~~~a~~Ll~~fgs~~~l~~a   43 (75)
T 1x2i_A           17 EGLPHVSATLARRLLKHFGSVERVFTA   43 (75)
T ss_dssp             TTSTTCCHHHHHHHHHHHCSHHHHHHC
T ss_pred             cCCCCCCHHHHHHHHHHcCCHHHHHhC
Confidence            357999999999999999999998753

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

Probab=97.95  E-value=7.1e-06  Score=47.32  Aligned_cols=28  Identities=21%  Similarity=0.380  Sum_probs=24.6

Q ss_pred             CCCCCCccHHHHHHHHHHhCCHHHHHhh
Q 035374           35 IPGVEGIGDVRAVQLITKFGMLVFNVEC   62 (66)
Q Consensus        35 i~gi~GiG~K~A~~Ll~~fgsl~~i~~~   62 (66)
                      +.+|||||+++|.+|++.|+|++++.++
T Consensus        21 L~~IpgIG~~~A~~Ll~~fgsl~~l~~a   48 (89)
T 1z00_A           21 LTTVKSVNKTDSQTLLTTFGSLEQLIAA   48 (89)
T ss_dssp             HTTSSSCCHHHHHHHHHHTCBHHHHHHC
T ss_pred             HHcCCCCCHHHHHHHHHHCCCHHHHHhC
Confidence            4567999999999999999999988753

>2nrt_A Uvrabc system protein C; UVRC, endonuclease, RNAse H, helix hairpin helix, NER, hydrolase; 1.50A {Thermotoga maritima} PDB: 2nrv_A 2nrw_A 2nrx_A 2nrz_A

Probab=97.91  E-value=5.3e-06  Score=56.06  Aligned_cols=28  Identities=36%  Similarity=0.533  Sum_probs=25.2

Q ss_pred             CCCCCCccHHHHHHHHHHhCCHHHHHhh
Q 035374           35 IPGVEGIGDVRAVQLITKFGMLVFNVEC   62 (66)
Q Consensus        35 i~gi~GiG~K~A~~Ll~~fgsl~~i~~~   62 (66)
                      +.||||||+|+|.+|++.|||++++.++
T Consensus       170 LdgIpGIG~k~ak~Ll~~FgSl~~i~~A  197 (220)
T 2nrt_A          170 LDNVPGIGPIRKKKLIEHFGSLENIRSA  197 (220)
T ss_dssp             HTTSTTCCHHHHHHHHHHHCSHHHHHTS
T ss_pred             ccCCCCcCHHHHHHHHHHcCCHHHHHhC
Confidence            4678999999999999999999999864

>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=97.90  E-value=8.6e-06  Score=47.29  Aligned_cols=28  Identities=21%  Similarity=0.380  Sum_probs=24.3

Q ss_pred             CCCCCCccHHHHHHHHHHhCCHHHHHhh
Q 035374           35 IPGVEGIGDVRAVQLITKFGMLVFNVEC   62 (66)
Q Consensus        35 i~gi~GiG~K~A~~Ll~~fgsl~~i~~~   62 (66)
                      +.+|||||+++|.+|++.|+++++++++
T Consensus        34 L~~IpgIG~~~A~~Ll~~fgs~~~l~~a   61 (91)
T 2a1j_B           34 LTTVKSVNKTDSQTLLTTFGSLEQLIAA   61 (91)
T ss_dssp             HTTSTTCCHHHHHHHHHHHSSHHHHHSC
T ss_pred             HHcCCCCCHHHHHHHHHHCCCHHHHHhC
Confidence            3467999999999999999999988753

>3c65_A Uvrabc system protein C; UVRC, endonuclease, nucleotide excision repair, DNA repair, RNAse H, cytoplasm, DNA damage, DNA excision; 1.90A {Bacillus stearothermophilus}

Probab=97.57  E-value=1e-05  Score=54.75  Aligned_cols=29  Identities=24%  Similarity=0.423  Sum_probs=0.0

Q ss_pred             CCCCCCCccHHHHHHHHHHhCCHHHHHhh
Q 035374           34 NIPGVEGIGDVRAVQLITKFGMLVFNVEC   62 (66)
Q Consensus        34 ~i~gi~GiG~K~A~~Ll~~fgsl~~i~~~   62 (66)
                      -+.+|||||+++|.+|++.|||++++.++
T Consensus       174 ~L~~IpGIG~k~ak~Ll~~FGSl~~i~~A  202 (226)
T 3c65_A          174 VLDDIPGVGEKRKKALLNYFGSVKKMKEA  202 (226)
T ss_dssp             -----------------------------
T ss_pred             cccccCCCCHHHHHHHHHHhCCHHHHHhC
Confidence            46788999999999999999999998754

>2bgw_A XPF endonuclease; hydrolase, structure specific endonuclease, nucleotide excision repair; 2.8A {Aeropyrum pernix} SCOP: a.60.2.5 c.52.1.20 PDB: 2bhn_A

Probab=97.37  E-value=9.7e-05  Score=48.30  Aligned_cols=27  Identities=26%  Similarity=0.411  Sum_probs=24.0

Q ss_pred             CCCCCccHHHHHHHHHHhCCHHHHHhh
Q 035374           36 PGVEGIGDVRAVQLITKFGMLVFNVEC   62 (66)
Q Consensus        36 ~gi~GiG~K~A~~Ll~~fgsl~~i~~~   62 (66)
                      .+|||||+++|..|+++|+|+++++++
T Consensus       165 ~~i~gVg~~~a~~Ll~~fgs~~~l~~a  191 (219)
T 2bgw_A          165 QSFPGIGRRTAERILERFGSLERFFTA  191 (219)
T ss_dssp             HTSTTCCHHHHHHHHHHHSSHHHHTTC
T ss_pred             hcCCCCCHHHHHHHHHHcCCHHHHHhC
Confidence            367999999999999999999998753

>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=97.17  E-value=0.00023  Score=46.82  Aligned_cols=24  Identities=25%  Similarity=0.311  Sum_probs=20.6

Q ss_pred             CCCccHHHHHHHHHHhCC---HHHHHh
Q 035374           38 VEGIGDVRAVQLITKFGM---LVFNVE   61 (66)
Q Consensus        38 i~GiG~K~A~~Ll~~fgs---l~~i~~   61 (66)
                      |||||||+|.+||+.|++   .+.|.+
T Consensus        77 v~GIGpk~A~~iL~~f~~~~l~~aI~~  103 (191)
T 1ixr_A           77 VSGVGPKVALALLSALPPRLLARALLE  103 (191)
T ss_dssp             SSCCCHHHHHHHHHHSCHHHHHHHHHT
T ss_pred             CCCcCHHHHHHHHHhCChHHHHHHHHh
Confidence            699999999999999998   555553

>4gfj_A Topoisomerase V; helix-hairpin-helix, DNA repair enzyme, DNA B isomerase; 2.91A {Methanopyrus kandleri AV19}

Probab=97.03  E-value=0.00038  Score=52.17  Aligned_cols=26  Identities=31%  Similarity=0.424  Sum_probs=24.0

Q ss_pred             CCCCccHHHHHHHHHHhCCHHHHHhh
Q 035374           37 GVEGIGDVRAVQLITKFGMLVFNVEC   62 (66)
Q Consensus        37 gi~GiG~K~A~~Ll~~fgsl~~i~~~   62 (66)
                      .||||||++|..||++|||++.+..+
T Consensus       472 AIaGIGp~tAeRLLEkFGSVe~Vm~A  497 (685)
T 4gfj_A          472 SIRGIDRERAERLLKKYGGYSKVREA  497 (685)
T ss_dssp             TSTTCCHHHHHHHHHHHTSHHHHHHS
T ss_pred             ccCCCCHHHHHHHHHHhcCHHHHHhC
Confidence            47999999999999999999999864

>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=96.99  E-value=0.0004  Score=45.94  Aligned_cols=24  Identities=13%  Similarity=0.245  Sum_probs=20.9

Q ss_pred             CCCccHHHHHHHHHHhCC---HHHHHh
Q 035374           38 VEGIGDVRAVQLITKFGM---LVFNVE   61 (66)
Q Consensus        38 i~GiG~K~A~~Ll~~fgs---l~~i~~   61 (66)
                      |+|||||+|.+||+.|++   .+.|.+
T Consensus        78 V~GIGpk~A~~iL~~f~~~~l~~aI~~  104 (203)
T 1cuk_A           78 TNGVGPKLALAILSGMSAQQFVNAVER  104 (203)
T ss_dssp             SSSCCHHHHHHHHHHSCHHHHHHHHHT
T ss_pred             CCCcCHHHHHHHHhhCChHHHHHHHHh
Confidence            699999999999999998   666653

>2owo_A DNA ligase; protein-DNA complex, ligase-DNA complex; HET: DNA OMC AMP; 2.30A {Escherichia coli}

Probab=96.27  E-value=0.0025  Score=48.66  Aligned_cols=26  Identities=27%  Similarity=0.427  Sum_probs=23.8

Q ss_pred             CCCCccHHHHHHHHHHhCCHHHHHhh
Q 035374           37 GVEGIGDVRAVQLITKFGMLVFNVEC   62 (66)
Q Consensus        37 gi~GiG~K~A~~Ll~~fgsl~~i~~~   62 (66)
                      ||||||+++|..|++.|+|++++.++
T Consensus       516 gi~~VG~~~Ak~La~~Fgsl~~l~~A  541 (671)
T 2owo_A          516 GIREVGEATAAGLAAYFGTLEALEAA  541 (671)
T ss_dssp             TCTTCCHHHHHHHHHHHCSHHHHHTC
T ss_pred             cccCccHHHHHHHHHHcCCHHHHHhC
Confidence            67999999999999999999998754

>1vq8_Y 50S ribosomal protein L32E; ribosome 50S, protein-protein complex, RNA-RNA complex, PROT complex, peptidyl transferase reaction; HET: 1MA OMU OMG UR3 PSU SPS; 2.20A {Haloarcula marismortui} SCOP: c.9.2.1 PDB: 1vq4_Y* 1vq5_Y* 1vq6_Y* 1vq7_Y* 1s72_Y* 1vq9_Y* 1vqk_Y* 1vql_Y* 1vqm_Y* 1vqn_Y* 1vqo_Y* 1vqp_Y* 1yhq_Y* 1yi2_Y* 1yij_Y* 1yit_Y* 1yj9_Y* 1yjn_Y* 1yjw_Y* 2otj_Y* ...

Probab=96.23  E-value=0.00075  Score=45.81  Aligned_cols=28  Identities=18%  Similarity=0.258  Sum_probs=0.0

Q ss_pred             CCCCCCCccHHHHHHHHHH-hCCHHHHHh
Q 035374           34 NIPGVEGIGDVRAVQLITK-FGMLVFNVE   61 (66)
Q Consensus        34 ~i~gi~GiG~K~A~~Ll~~-fgsl~~i~~   61 (66)
                      .+..|||||||+|.+|++. |+|++++.+
T Consensus        16 ~L~~IpGIGpk~a~~Ll~~gf~sve~L~~   44 (241)
T 1vq8_Y           16 ELTDISGVGPSKAESLREAGFESVEDVRG   44 (241)
T ss_dssp             -----------------------------
T ss_pred             HHhcCCCCCHHHHHHHHHcCCCCHHHHHh
Confidence            5667899999999999998 999998863

>3sgi_A DNA ligase; HET: DNA AMP; 3.50A {Mycobacterium tuberculosis}

Probab=96.19  E-value=0.0008  Score=50.99  Aligned_cols=27  Identities=26%  Similarity=0.304  Sum_probs=0.0

Q ss_pred             CCCCCccHHHHHHHHHHhCCHHHHHhh
Q 035374           36 PGVEGIGDVRAVQLITKFGMLVFNVEC   62 (66)
Q Consensus        36 ~gi~GiG~K~A~~Ll~~fgsl~~i~~~   62 (66)
                      -||||||+++|..|++.|+|++++.++
T Consensus       532 LGIp~VG~~~ak~La~~Fgsle~L~~A  558 (615)
T 3sgi_A          532 LSIRHVGPTAARALATEFGSLDAIAAA  558 (615)
T ss_dssp             ---------------------------
T ss_pred             cCCCCCCHHHHHHHHHHcCCHHHHHhC
Confidence            378999999999999999999998764

>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=96.11  E-value=0.0015  Score=41.25  Aligned_cols=27  Identities=7%  Similarity=0.050  Sum_probs=22.7

Q ss_pred             CCCCCCccHHHHHHHHHH--hCCHHHHHh
Q 035374           35 IPGVEGIGDVRAVQLITK--FGMLVFNVE   61 (66)
Q Consensus        35 i~gi~GiG~K~A~~Ll~~--fgsl~~i~~   61 (66)
                      +..+|||||++|.++++.  |.|+|++++
T Consensus        65 L~~LpGiGp~~A~~II~~GpF~svedL~~   93 (134)
T 1s5l_U           65 FIQYRGLYPTLAKLIVKNAPYESVEDVLN   93 (134)
T ss_dssp             GGGSTTCTHHHHHHHHHTCCCSSGGGGGG
T ss_pred             HHHCCCCCHHHHHHHHHcCCCCCHHHHHh
Confidence            456899999999999986  888888764

>3c1y_A DNA integrity scanning protein DISA; DNA damage, DNA repair, DNA-binding, DNA binding protein; HET: DNA 2BA; 2.10A {Thermotoga maritima} PDB: 3c1z_A* 3c21_A* 3c23_A*

Probab=95.93  E-value=0.0041  Score=44.84  Aligned_cols=26  Identities=15%  Similarity=0.020  Sum_probs=24.1

Q ss_pred             CCCCccHHHHHHHHHHhCCHHHHHhh
Q 035374           37 GVEGIGDVRAVQLITKFGMLVFNVEC   62 (66)
Q Consensus        37 gi~GiG~K~A~~Ll~~fgsl~~i~~~   62 (66)
                      .||+||++.|.+|+.+|||+++++++
T Consensus       319 ~IPrl~~~iae~Lv~~FGsLq~Il~A  344 (377)
T 3c1y_A          319 TVARIPLSIGYNVVRMFKTLDQISKA  344 (377)
T ss_dssp             HTSCCCHHHHHHHHHHHCSHHHHTTC
T ss_pred             hCCCCCHHHHHHHHHHhCCHHHHHhC
Confidence            38999999999999999999999864

>1dgs_A DNA ligase; AMP complex, NAD+-dependent; HET: DNA AMP; 2.90A {Thermus filiformis} SCOP: a.60.2.2 b.40.4.6 d.142.2.2 PDB: 1v9p_A*

Probab=95.85  E-value=0.0042  Score=47.38  Aligned_cols=26  Identities=35%  Similarity=0.609  Sum_probs=23.5

Q ss_pred             CCCCccHHHHHHHHHHhCCHHHHHhh
Q 035374           37 GVEGIGDVRAVQLITKFGMLVFNVEC   62 (66)
Q Consensus        37 gi~GiG~K~A~~Ll~~fgsl~~i~~~   62 (66)
                      ||||||+++|..|++.|+|++++.++
T Consensus       511 GI~~VG~~~Ak~La~~Fgsl~~l~~A  536 (667)
T 1dgs_A          511 GLPGVGEVLARNLARRFGTMDRLLEA  536 (667)
T ss_dssp             TCSSCCHHHHHHHHHTTSBHHHHTTC
T ss_pred             ccCCccHHHHHHHHHHcCCHHHHHhC
Confidence            67999999999999999999998653

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

Probab=95.79  E-value=0.018  Score=38.61  Aligned_cols=46  Identities=13%  Similarity=0.243  Sum_probs=32.9

Q ss_pred             CChhHHHHHHHhhCC---CCCCCCCCCCccHHHHHHHHHH-----hCCHHHHHh
Q 035374           16 LKPSQFVDVISLVGD---KADNIPGVEGIGDVRAVQLITK-----FGMLVFNVE   61 (66)
Q Consensus        16 i~p~q~~d~~~L~Gd---~~D~i~gi~GiG~K~A~~Ll~~-----fgsl~~i~~   61 (66)
                      -..++|++|..-.+.   +..-+..+||||+++|.+++..     |.|++++.+
T Consensus       112 ~~E~~fv~f~n~a~pITA~~~eL~~LpGIG~k~A~~IIeyRe~G~F~s~eDL~~  165 (205)
T 2i5h_A          112 QDEKKYVDFFNKADSITTRMHQLELLPGVGKKMMWAIIEERKKRPFESFEDIAQ  165 (205)
T ss_dssp             TTHHHHHHHHC--CCBCSSSBGGGGSTTCCHHHHHHHHHHHHHSCCCSHHHHHH
T ss_pred             hchhhhhhhccccCCccCCHHHHhcCCCcCHHHHHHHHHHHhcCCCCCHHHHHH
Confidence            356777777554432   2345668999999999999975     889988854

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

Probab=95.63  E-value=0.0071  Score=44.76  Aligned_cols=27  Identities=26%  Similarity=0.249  Sum_probs=23.5

Q ss_pred             CCCCCccHHHHHHHHHH-hCCHHHHHhh
Q 035374           36 PGVEGIGDVRAVQLITK-FGMLVFNVEC   62 (66)
Q Consensus        36 ~gi~GiG~K~A~~Ll~~-fgsl~~i~~~   62 (66)
                      -+|+|||||+|.+|+++ |.|++++.++
T Consensus       100 ~~v~GVGpk~A~~i~~~G~~s~edL~~a  127 (578)
T 2w9m_A          100 LGVRGLGPKKIRSLWLAGIDSLERLREA  127 (578)
T ss_dssp             TTSTTCCHHHHHHHHHTTCCSHHHHHHH
T ss_pred             hCCCCcCHHHHHHHHHcCCCCHHHHHHH
Confidence            46799999999999998 6799988765

>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=95.56  E-value=0.007  Score=40.38  Aligned_cols=18  Identities=22%  Similarity=0.346  Sum_probs=16.8

Q ss_pred             CCCccHHHHHHHHHHhCC
Q 035374           38 VEGIGDVRAVQLITKFGM   55 (66)
Q Consensus        38 i~GiG~K~A~~Ll~~fgs   55 (66)
                      |+|||||+|..+|..|+.
T Consensus        93 v~GIGpk~A~~Ils~~~~  110 (212)
T 2ztd_A           93 VSGVGPRLAMAALAVHDA  110 (212)
T ss_dssp             STTCCHHHHHHHHHHSCH
T ss_pred             cCCcCHHHHHHHHHhCCH
Confidence            699999999999999976

>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=95.35  E-value=0.0043  Score=36.96  Aligned_cols=27  Identities=7%  Similarity=0.036  Sum_probs=21.2

Q ss_pred             CCCCCCCccHHHHHHHHHH--hCCHHHHH
Q 035374           34 NIPGVEGIGDVRAVQLITK--FGMLVFNV   60 (66)
Q Consensus        34 ~i~gi~GiG~K~A~~Ll~~--fgsl~~i~   60 (66)
                      -+..+||||+++|.++++.  |.|++++.
T Consensus        27 eL~~lpGIG~~~A~~IV~~GpF~s~edL~   55 (97)
T 3arc_U           27 AFIQYRGLYPTLAKLIVKNAPYESVEDVL   55 (97)
T ss_dssp             GGGGSTTCTTHHHHHHHHHCCCSSGGGGG
T ss_pred             HHhHCCCCCHHHHHHHHHcCCCCCHHHHH
Confidence            4567899999999999985  66777654

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

Probab=95.27  E-value=0.0075  Score=33.34  Aligned_cols=25  Identities=20%  Similarity=0.195  Sum_probs=19.1

Q ss_pred             CCCCCCccHHHHHHHHHHh--CCHHHH
Q 035374           35 IPGVEGIGDVRAVQLITKF--GMLVFN   59 (66)
Q Consensus        35 i~gi~GiG~K~A~~Ll~~f--gsl~~i   59 (66)
                      +..+||||+++|.++++.+  .+++++
T Consensus        29 L~~ipGIG~~~A~~Il~~r~~~s~~eL   55 (75)
T 2duy_A           29 LMALPGIGPVLARRIVEGRPYARVEDL   55 (75)
T ss_dssp             HTTSTTCCHHHHHHHHHTCCCSSGGGG
T ss_pred             HHhCCCCCHHHHHHHHHHcccCCHHHH
Confidence            3467999999999999974  455544

>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=95.22  E-value=0.016  Score=37.87  Aligned_cols=23  Identities=17%  Similarity=0.281  Sum_probs=20.0

Q ss_pred             CCCCCCCCCccHHHHHHHHHHhC
Q 035374           32 ADNIPGVEGIGDVRAVQLITKFG   54 (66)
Q Consensus        32 ~D~i~gi~GiG~K~A~~Ll~~fg   54 (66)
                      .+.+..|||||+|+|.+++..+.
T Consensus       106 ~~~L~~vpGIG~K~A~rI~~~lk  128 (191)
T 1ixr_A          106 ARLLTSASGVGRRLAERIALELK  128 (191)
T ss_dssp             HHHHTTSTTCCHHHHHHHHHHHT
T ss_pred             HHHHHhCCCCCHHHHHHHHHHHH
Confidence            55778999999999999998874

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

Probab=95.13  E-value=0.016  Score=40.59  Aligned_cols=27  Identities=19%  Similarity=0.068  Sum_probs=22.6

Q ss_pred             CCCCCccHHHHHHHHHH-hCCHHHHHhh
Q 035374           36 PGVEGIGDVRAVQLITK-FGMLVFNVEC   62 (66)
Q Consensus        36 ~gi~GiG~K~A~~Ll~~-fgsl~~i~~~   62 (66)
                      ..|||||||+|.+|.++ +.|++++.++
T Consensus        99 ~~v~GiG~k~a~~l~~~Gi~tledL~~a  126 (335)
T 2bcq_A           99 SNIWGAGTKTAQMWYQQGFRSLEDIRSQ  126 (335)
T ss_dssp             HTSTTCCHHHHHHHHHTTCCSHHHHHHH
T ss_pred             hcCCCcCHHHHHHHHHcCCCCHHHHHHH
Confidence            37899999999999988 4589888764

>2fmp_A DNA polymerase beta; nucleotidyl transferase, transferase/DNA complex; HET: DNA DOC DCT; 1.65A {Homo sapiens} SCOP: a.60.6.1 a.60.12.1 d.218.1.2 PDB: 1bpx_A* 1bpz_A* 1mq2_A* 1mq3_A* 1bpy_A* 1tva_A* 1zjm_A* 1zjn_A* 1zqa_A* 1zqb_A* 1zqc_A* 1zqd_A* 1zqe_A* 1zqf_A* 1zqg_A* 1zqh_A* 1zqi_A* 1zqj_A* 1zqk_A* 1zql_A* ...

Probab=95.07  E-value=0.018  Score=40.21  Aligned_cols=28  Identities=21%  Similarity=0.239  Sum_probs=23.3

Q ss_pred             CCCCCCccHHHHHHHHHH-hCCHHHHHhh
Q 035374           35 IPGVEGIGDVRAVQLITK-FGMLVFNVEC   62 (66)
Q Consensus        35 i~gi~GiG~K~A~~Ll~~-fgsl~~i~~~   62 (66)
                      +-.|||||||+|.+|.++ +.|++++.++
T Consensus       100 l~~V~GiGpk~a~~l~~~Gi~tledL~~a  128 (335)
T 2fmp_A          100 LTRVSGIGPSAARKFVDEGIKTLEDLRKN  128 (335)
T ss_dssp             HTTSTTCCHHHHHHHHHTTCCSHHHHHTC
T ss_pred             HhCCCCCCHHHHHHHHHcCCCCHHHHHHh
Confidence            456799999999999998 4589988764

>2ziu_A MUS81 protein; helix-hairpin-helix, alternative splicing, DNA damage, DNA recombination, DNA repair, hydrolase, magnesium; 2.70A {Danio rerio} PDB: 2ziv_A 2ziw_A

Probab=94.91  E-value=0.017  Score=39.32  Aligned_cols=30  Identities=7%  Similarity=0.330  Sum_probs=26.3

Q ss_pred             CCCCCCccHHHHHHHHHHhCCHHHHHhhhc
Q 035374           35 IPGVEGIGDVRAVQLITKFGMLVFNVECFS   64 (66)
Q Consensus        35 i~gi~GiG~K~A~~Ll~~fgsl~~i~~~~~   64 (66)
                      +-.||||+++.|..++++|+|+..++++.+
T Consensus       239 L~~IpGVs~~~A~~I~~~ypTp~~L~~Ay~  268 (311)
T 2ziu_A          239 LMQISGVSGDKAAAVLEHYSTVSSLLQAYD  268 (311)
T ss_dssp             HTTBTTCCHHHHHHHHHHCSSHHHHHHHHH
T ss_pred             HHhccCCCHHHHHHHHHHCCCHHHHHHHHH
Confidence            456899999999999999999999887653

>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=94.87  E-value=0.012  Score=39.17  Aligned_cols=37  Identities=16%  Similarity=0.293  Sum_probs=25.8

Q ss_pred             ChhHHHHHHHhhCCCCCCCCCCCCccHHHHHHHHHHhCC
Q 035374           17 KPSQFVDVISLVGDKADNIPGVEGIGDVRAVQLITKFGM   55 (66)
Q Consensus        17 ~p~q~~d~~~L~Gd~~D~i~gi~GiG~K~A~~Ll~~fgs   55 (66)
                      +++.+.. .++-+| ...+..|||||+|+|.+++.++.+
T Consensus       109 ~~~~l~~-aI~~~d-~~~L~~vpGIG~KtA~rIi~elk~  145 (212)
T 2ztd_A          109 DAPALRQ-VLADGN-VAALTRVPGIGKRGAERMVLELRD  145 (212)
T ss_dssp             CHHHHHH-HHHTTC-HHHHHTSTTCCHHHHHHHHHHHTT
T ss_pred             CHHHHHH-HHHhCC-HHHHhhCCCCCHHHHHHHHHHHHH
Confidence            3555542 244555 446778999999999999988743

>3b0x_A DNA polymerase beta family (X family); structural genomics, riken structural genomics/proteomics in RSGI, polxc, PHP, DRP lyase; HET: DNA DGT; 1.36A {Thermus thermophilus} PDB: 3au2_A* 3au6_A* 3auo_A* 3b0y_A*

Probab=94.81  E-value=0.018  Score=42.46  Aligned_cols=27  Identities=22%  Similarity=0.163  Sum_probs=22.6

Q ss_pred             CCCCccHHHHHHHHHH--hCCHHHHHhhh
Q 035374           37 GVEGIGDVRAVQLITK--FGMLVFNVECF   63 (66)
Q Consensus        37 gi~GiG~K~A~~Ll~~--fgsl~~i~~~~   63 (66)
                      +|+|||||+|.+++.+  +.|++++.++.
T Consensus        97 ~v~GvGpk~A~~~~~~lg~~~~~~l~~a~  125 (575)
T 3b0x_A           97 EVPGVGPKTARLLYEGLGIDSLEKLKAAL  125 (575)
T ss_dssp             TSTTTCHHHHHHHHHTSCCCSHHHHHHHH
T ss_pred             cCCCcCHHHHHHHHHhcCCCCHHHHHHHH
Confidence            5699999999999997  57898887643

>4glx_A DNA ligase; inhibitor, ligase-ligase inhibitor-DNA complex; HET: DNA 0XS; 1.90A {Escherichia coli}

Probab=94.77  E-value=0.02  Score=43.07  Aligned_cols=26  Identities=27%  Similarity=0.427  Sum_probs=23.5

Q ss_pred             CCCCccHHHHHHHHHHhCCHHHHHhh
Q 035374           37 GVEGIGDVRAVQLITKFGMLVFNVEC   62 (66)
Q Consensus        37 gi~GiG~K~A~~Ll~~fgsl~~i~~~   62 (66)
                      |||+||+++|..|.+.|+|++++.++
T Consensus       516 GI~~vG~~~a~~La~~f~sl~~l~~a  541 (586)
T 4glx_A          516 GIREVGEATAAGLAAYFGTLEALEAA  541 (586)
T ss_dssp             TCTTCCHHHHHHHHHHHCSHHHHHHC
T ss_pred             CCCchhHHHHHHHHHHcCCHHHHHcc
Confidence            67999999999999999999998753

>2ihm_A POL MU, DNA polymerase MU; helix-turn-helix, transferase/DNA complex; HET: DNA D3T; 2.40A {Mus musculus}

Probab=94.57  E-value=0.026  Score=39.79  Aligned_cols=25  Identities=20%  Similarity=0.058  Sum_probs=21.2

Q ss_pred             CCCCCccHHHHHHHHHH-hCCHHHHH
Q 035374           36 PGVEGIGDVRAVQLITK-FGMLVFNV   60 (66)
Q Consensus        36 ~gi~GiG~K~A~~Ll~~-fgsl~~i~   60 (66)
                      -.|||||||||.+|.++ +.|++++.
T Consensus       105 ~~I~GvG~kta~~l~~~Gi~tledL~  130 (360)
T 2ihm_A          105 TQVFGVGVKTANRWYQEGLRTLDELR  130 (360)
T ss_dssp             HTSTTCCHHHHHHHHHTTCCSHHHHH
T ss_pred             hCCCCCCHHHHHHHHHcCCCCHHHHH
Confidence            36799999999999988 44888876

>3maj_A DNA processing chain A; MCSG, PSI-2, structural genomics, protein structure initiati midwest center for structural genomics; HET: DNA; 2.05A {Rhodopseudomonas palustris}

Probab=94.56  E-value=0.048  Score=39.21  Aligned_cols=40  Identities=28%  Similarity=0.379  Sum_probs=31.3

Q ss_pred             CChhHHHHHHHhhCCCCCCCCCCCCccHHHHHHHHHHhCCHHHHHhhh
Q 035374           16 LKPSQFVDVISLVGDKADNIPGVEGIGDVRAVQLITKFGMLVFNVECF   63 (66)
Q Consensus        16 i~p~q~~d~~~L~Gd~~D~i~gi~GiG~K~A~~Ll~~fgsl~~i~~~~   63 (66)
                      ++.++...+..|.-        +||+|+++..+|+++||+.+++++++
T Consensus        17 m~~~e~~~wL~L~~--------~~gvG~~~~~~Ll~~fgs~~~~~~a~   56 (382)
T 3maj_A           17 LTEAQRIDWMRLIR--------AENVGPRTFRSLINHFGSARAALERL   56 (382)
T ss_dssp             SCHHHHHHHHHHHT--------STTCCHHHHHHHHHHHSSHHHHHHHH
T ss_pred             CCHHHHHHHHHHHc--------CCCCCHHHHHHHHHHcCCHHHHHHcC
Confidence            45556666666643        48999999999999999999888653

>1jms_A Terminal deoxynucleotidyltransferase; polymerase; 2.36A {Mus musculus} SCOP: a.60.6.1 a.60.12.1 d.218.1.2 PDB: 1kdh_A* 1kej_A*

Probab=94.51  E-value=0.027  Score=40.14  Aligned_cols=25  Identities=24%  Similarity=0.162  Sum_probs=21.3

Q ss_pred             CCCCccHHHHHHHHHH-hCCHHHHHh
Q 035374           37 GVEGIGDVRAVQLITK-FGMLVFNVE   61 (66)
Q Consensus        37 gi~GiG~K~A~~Ll~~-fgsl~~i~~   61 (66)
                      .|||||||||.+|.++ +.|++++.+
T Consensus       125 ~I~GvGpk~a~~ly~~Gi~tledL~~  150 (381)
T 1jms_A          125 SVFGVGLKTAEKWFRMGFRTLSKIQS  150 (381)
T ss_dssp             TSTTCCHHHHHHHHHTTCCSHHHHHH
T ss_pred             ccCCCCHHHHHHHHHcCCCcHHHHHh
Confidence            6799999999999998 448888874

>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=93.91  E-value=0.027  Score=37.07  Aligned_cols=34  Identities=26%  Similarity=0.436  Sum_probs=23.9

Q ss_pred             hhHHHHHHHhhCCCCCCCCCCCCccHHHHHHHHHHh
Q 035374           18 PSQFVDVISLVGDKADNIPGVEGIGDVRAVQLITKF   53 (66)
Q Consensus        18 p~q~~d~~~L~Gd~~D~i~gi~GiG~K~A~~Ll~~f   53 (66)
                      ++++.  .++.-.+.+.+..|||||+|+|.+++.++
T Consensus        95 ~~~l~--~aI~~~d~~~L~~vpGIG~K~A~rI~~el  128 (203)
T 1cuk_A           95 AQQFV--NAVEREEVGALVKLPGIGKKTAERLIVEM  128 (203)
T ss_dssp             HHHHH--HHHHTTCHHHHHTSTTCCHHHHHHHHHHH
T ss_pred             hHHHH--HHHHhCCHHHHhhCCCCCHHHHHHHHHHH
Confidence            44444  23333335567889999999999999876

>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=93.09  E-value=0.015  Score=31.44  Aligned_cols=23  Identities=26%  Similarity=0.343  Sum_probs=18.9

Q ss_pred             CCCCCCCCCccHHHHHHHHHHhC
Q 035374           32 ADNIPGVEGIGDVRAVQLITKFG   54 (66)
Q Consensus        32 ~D~i~gi~GiG~K~A~~Ll~~fg   54 (66)
                      .+.+..|||||+++|..+...|.
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            44567789999999999988764

>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=92.38  E-value=0.026  Score=31.33  Aligned_cols=41  Identities=15%  Similarity=0.167  Sum_probs=26.8

Q ss_pred             HHHHHHHhCCCChhHHHHHHHhhCCCCCCCCCCCCccHHHHHHHHHHhC
Q 035374            6 MEDFARKYGELKPSQFVDVISLVGDKADNIPGVEGIGDVRAVQLITKFG   54 (66)
Q Consensus         6 ~~~v~~~~g~i~p~q~~d~~~L~Gd~~D~i~gi~GiG~K~A~~Ll~~fg   54 (66)
                      ...+.+.|+  +.+.+.      -.+.+.+..|||||+++|..++..|.
T Consensus        37 A~~Ll~~fg--sl~~l~------~a~~eeL~~i~GIG~~~a~~I~~~~~   77 (78)
T 1kft_A           37 RQMLLKYMG--GLQGLR------NASVEEIAKVPGISQGLAEKIFWSLK   77 (78)
T ss_dssp             HHHHHHHHS--CHHHHH------HCCHHHHTTSSSTTSHHHHHHHHHHT
T ss_pred             HHHHHHHcC--CHHHHH------HCCHHHHHHCCCCCHHHHHHHHHHHh
Confidence            345566666  333322      22345567789999999999988764

>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=92.35  E-value=0.079  Score=30.63  Aligned_cols=20  Identities=15%  Similarity=0.257  Sum_probs=17.2

Q ss_pred             CCCCCCCccHHHHHHHHHHh
Q 035374           34 NIPGVEGIGDVRAVQLITKF   53 (66)
Q Consensus        34 ~i~gi~GiG~K~A~~Ll~~f   53 (66)
                      -+..|||||+++|.++++.+
T Consensus        41 ~L~~ipGIG~~~A~~Il~~r   60 (98)
T 2edu_A           41 DLRSLQRIGPKKAQLIVGWR   60 (98)
T ss_dssp             HHHHSTTCCHHHHHHHHHHH
T ss_pred             HHHHCCCCCHHHHHHHHHHH
Confidence            35678999999999999876

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

Probab=92.34  E-value=0.033  Score=31.53  Aligned_cols=23  Identities=17%  Similarity=0.361  Sum_probs=18.7

Q ss_pred             CCCCCCCCCccHHHHHHHHHHhC
Q 035374           32 ADNIPGVEGIGDVRAVQLITKFG   54 (66)
Q Consensus        32 ~D~i~gi~GiG~K~A~~Ll~~fg   54 (66)
                      .+.+..|||||+++|.+++..|.
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            34566789999999999998774

>3b0x_A DNA polymerase beta family (X family); structural genomics, riken structural genomics/proteomics in RSGI, polxc, PHP, DRP lyase; HET: DNA DGT; 1.36A {Thermus thermophilus} PDB: 3au2_A* 3au6_A* 3auo_A* 3b0y_A*

Probab=91.69  E-value=0.21  Score=36.81  Aligned_cols=41  Identities=17%  Similarity=0.235  Sum_probs=26.9

Q ss_pred             HHhCCCChhHHHHHHHhhCCCCCCCCCCCCccHHHHHHHHHHhCCH
Q 035374           11 RKYGELKPSQFVDVISLVGDKADNIPGVEGIGDVRAVQLITKFGML   56 (66)
Q Consensus        11 ~~~g~i~p~q~~d~~~L~Gd~~D~i~gi~GiG~K~A~~Ll~~fgsl   56 (66)
                      ..+|..+++++... +..||    +..+||||+|+|.+++......
T Consensus       111 ~~lg~~~~~~l~~a-~~~~~----l~~~~GiG~k~a~~i~~~l~~~  151 (575)
T 3b0x_A          111 EGLGIDSLEKLKAA-LDRGD----LTRLKGFGPKRAERIREGLALA  151 (575)
T ss_dssp             HTSCCCSHHHHHHH-HHHTG----GGGSTTCCHHHHHHHHHHHHHH
T ss_pred             HhcCCCCHHHHHHH-HHcCC----cccCCCCCccHHHHHHHHHHHH
Confidence            33343577777643 23454    6789999999999996554433

>3vdp_A Recombination protein RECR; zinc finger, DNA repair, DNA binding; 2.45A {Thermoanaerobacter tengcongensis} PDB: 3vdu_A 3ve5_D

Probab=91.17  E-value=0.088  Score=35.34  Aligned_cols=18  Identities=28%  Similarity=0.337  Sum_probs=14.1

Q ss_pred             CCCCCCccHHHHHHHHHH
Q 035374           35 IPGVEGIGDVRAVQLITK   52 (66)
Q Consensus        35 i~gi~GiG~K~A~~Ll~~   52 (66)
                      +..+||||+|+|.++--.
T Consensus        28 l~~LPGIG~KsA~RlA~h   45 (212)
T 3vdp_A           28 LSKLPGIGPKTAQRLAFF   45 (212)
T ss_dssp             HHTSTTCCHHHHHHHHHH
T ss_pred             HHHCCCCCHHHHHHHHHH
Confidence            445799999999987543

>3c1y_A DNA integrity scanning protein DISA; DNA damage, DNA repair, DNA-binding, DNA binding protein; HET: DNA 2BA; 2.10A {Thermotoga maritima} PDB: 3c1z_A* 3c21_A* 3c23_A*

Probab=90.58  E-value=0.11  Score=37.51  Aligned_cols=39  Identities=21%  Similarity=0.338  Sum_probs=29.3

Q ss_pred             HHHHHHHhCCCChhHHHHHHHhhCCCCCCCCCCCCccHHHHHHHHHH
Q 035374            6 MEDFARKYGELKPSQFVDVISLVGDKADNIPGVEGIGDVRAVQLITK   52 (66)
Q Consensus         6 ~~~v~~~~g~i~p~q~~d~~~L~Gd~~D~i~gi~GiG~K~A~~Ll~~   52 (66)
                      .++++++||        .++.++--+.+.+..|+|||+++|..+-+-
T Consensus       328 ae~Lv~~FG--------sLq~Il~AS~eEL~~VeGIGe~rAr~Ireg  366 (377)
T 3c1y_A          328 GYNVVRMFK--------TLDQISKASVEDLKKVEGIGEKRARAISES  366 (377)
T ss_dssp             HHHHHHHHC--------SHHHHTTCCHHHHTTSTTCCHHHHHHHHHH
T ss_pred             HHHHHHHhC--------CHHHHHhCCHHHHHhccCccHHHHHHHHHH
Confidence            356667776        456667767778889999999999987543

>2zix_A Crossover junction endonuclease MUS81; helix-hairpin-helix, DNA damage, DNA recombination, DNA repair, hydrolase, magnesium, metal-binding, nucleus; 3.50A {Homo sapiens}

Probab=90.40  E-value=0.024  Score=38.72  Aligned_cols=31  Identities=13%  Similarity=0.343  Sum_probs=27.3

Q ss_pred             CCCCCCCccHHHHHHHHHHhCCHHHHHhhhc
Q 035374           34 NIPGVEGIGDVRAVQLITKFGMLVFNVECFS   64 (66)
Q Consensus        34 ~i~gi~GiG~K~A~~Ll~~fgsl~~i~~~~~   64 (66)
                      -+..||||++++|..++++|.|+..++++.+
T Consensus       234 ~L~~I~GVs~~~A~~I~~~ypTp~~L~~Ay~  264 (307)
T 2zix_A          234 QLMQVRGVSGEKAAALVDRYSTPASLLAAYD  264 (307)
T ss_dssp             TTTCSTTCCSTTTTTSSSSSCSHHHHHHHHH
T ss_pred             HHHhccCCCHHHHHHHHHHcCCHHHHHHHHH
Confidence            3668899999999999999999999887654

>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=90.23  E-value=0.053  Score=30.91  Aligned_cols=23  Identities=17%  Similarity=0.361  Sum_probs=18.8

Q ss_pred             CCCCCCCCCccHHHHHHHHHHhC
Q 035374           32 ADNIPGVEGIGDVRAVQLITKFG   54 (66)
Q Consensus        32 ~D~i~gi~GiG~K~A~~Ll~~fg   54 (66)
                      .+.+..|||||+++|.+++..|.
T Consensus        63 ~~eL~~i~GIG~~~a~~I~~~l~   85 (91)
T 2a1j_B           63 REDLALCPGLGPQKARRLFDVLH   85 (91)
T ss_dssp             HHHHHTSSSCCSHHHHHHHHHHH
T ss_pred             HHHHHhCCCCCHHHHHHHHHHHh
Confidence            44566789999999999988763

>2csb_A Topoisomerase V, TOP61; topoisomerase IB, helix-turn-helix, helix-H helix, HHH motif, three helix bundle, methanopyrus kandleri isomerase; 2.30A {Methanopyrus kandleri} SCOP: a.60.2.4 a.60.2.4 a.60.2.4 a.60.2.4 a.267.1.1 PDB: 2csd_A

Probab=90.07  E-value=0.26  Score=35.35  Aligned_cols=23  Identities=30%  Similarity=0.403  Sum_probs=21.2

Q ss_pred             CCccHHHHHHHHHHhCCHHHHHh
Q 035374           39 EGIGDVRAVQLITKFGMLVFNVE   61 (66)
Q Consensus        39 ~GiG~K~A~~Ll~~fgsl~~i~~   61 (66)
                      .|+|.|||..||+.||+.+.+.+
T Consensus       417 egvgrktaerllrafgnpervkq  439 (519)
T 2csb_A          417 EGVGRKTAERLLRAFGNPERVKQ  439 (519)
T ss_dssp             TTCCHHHHHHHHHHHSSHHHHHH
T ss_pred             cccchhHHHHHHHHhCCHHHHHH
Confidence            79999999999999999998764

>1vdd_A Recombination protein RECR; helix-hairpin-helix, zinc finger, toprim, walker B ATP binding motif; 2.50A {Deinococcus radiodurans} SCOP: e.49.1.1 PDB: 2v1c_A

Probab=90.06  E-value=0.13  Score=34.95  Aligned_cols=18  Identities=28%  Similarity=0.410  Sum_probs=14.0

Q ss_pred             CCCCCCccHHHHHHHHHH
Q 035374           35 IPGVEGIGDVRAVQLITK   52 (66)
Q Consensus        35 i~gi~GiG~K~A~~Ll~~   52 (66)
                      +..+||||+|+|.++--.
T Consensus        14 l~~LPGIG~KSA~RlA~h   31 (228)
T 1vdd_A           14 LSRLPGIGPKSAQRLAFH   31 (228)
T ss_dssp             HHTSTTCCHHHHHHHHHH
T ss_pred             HhHCCCCCHHHHHHHHHH
Confidence            345699999999988543

>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=89.33  E-value=0.23  Score=32.18  Aligned_cols=20  Identities=25%  Similarity=0.551  Sum_probs=16.1

Q ss_pred             CCCCCCccHHHHHHHHHHhC
Q 035374           35 IPGVEGIGDVRAVQLITKFG   54 (66)
Q Consensus        35 i~gi~GiG~K~A~~Ll~~fg   54 (66)
                      +-.+||||+|||.-++..++
T Consensus       119 L~~lpGIG~kTA~~il~~~~  138 (207)
T 3fhg_A          119 LLNIKGIGMQEASHFLRNVG  138 (207)
T ss_dssp             HTTSTTCCHHHHHHHHHHTT
T ss_pred             HHcCCCcCHHHHHHHHHHhC
Confidence            45789999999999887533

>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=88.47  E-value=0.23  Score=32.87  Aligned_cols=19  Identities=26%  Similarity=0.464  Sum_probs=16.1

Q ss_pred             CCCCccHHHHHHHHHHhCC
Q 035374           37 GVEGIGDVRAVQLITKFGM   55 (66)
Q Consensus        37 gi~GiG~K~A~~Ll~~fgs   55 (66)
                      .+||||+|||--+|..++-
T Consensus       134 ~l~GVG~kTA~~vL~~~g~  152 (219)
T 3n0u_A          134 NAKGIGWKEASHFLRNTGV  152 (219)
T ss_dssp             HSTTCCHHHHHHHHHTTTC
T ss_pred             hCCCCCHHHHHHHHHHcCC
Confidence            7799999999998876654

>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=87.82  E-value=0.26  Score=32.23  Aligned_cols=18  Identities=22%  Similarity=0.339  Sum_probs=15.3

Q ss_pred             CCCCCCccHHHHHHHHHH
Q 035374           35 IPGVEGIGDVRAVQLITK   52 (66)
Q Consensus        35 i~gi~GiG~K~A~~Ll~~   52 (66)
                      +-.+||||+|||.-++..
T Consensus       123 L~~lpGIG~kTA~~il~~  140 (218)
T 1pu6_A          123 LLDQKGIGKESADAILCY  140 (218)
T ss_dssp             HHTSTTCCHHHHHHHHHH
T ss_pred             HHcCCCcCHHHHHHHHHH
Confidence            567899999999988764

>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=87.44  E-value=0.34  Score=31.98  Aligned_cols=18  Identities=28%  Similarity=0.602  Sum_probs=15.0

Q ss_pred             CCCCccHHHHHHHHHHhC
Q 035374           37 GVEGIGDVRAVQLITKFG   54 (66)
Q Consensus        37 gi~GiG~K~A~~Ll~~fg   54 (66)
                      .+||||+|||--+|...+
T Consensus       129 ~LpGVG~KTA~~vL~~~g  146 (214)
T 3fhf_A          129 NIKGIGYKEASHFLRNVG  146 (214)
T ss_dssp             HSTTCCHHHHHHHHHHTT
T ss_pred             hCCCCCHHHHHHHHHHcC
Confidence            679999999998887543

>1ci4_A Protein (barrier-TO-autointegration factor (BAF) ); DNA binding protein, retroviral integration, preintegration complex; 1.90A {Homo sapiens} SCOP: a.60.5.1 PDB: 1qck_A 2bzf_A 2ezx_A 2ezy_A 2ezz_A 2odg_A

Probab=86.95  E-value=0.67  Score=27.29  Aligned_cols=30  Identities=23%  Similarity=0.453  Sum_probs=20.8

Q ss_pred             hhCCCCCCCCCCCCccHHHHHHHHHH-hCCHHH
Q 035374           27 LVGDKADNIPGVEGIGDVRAVQLITK-FGMLVF   58 (66)
Q Consensus        27 L~Gd~~D~i~gi~GiG~K~A~~Ll~~-fgsl~~   58 (66)
                      =+|+  ..+.-||||||+.+.+|-.+ |.....
T Consensus        14 Pmge--K~V~evpGIG~~~~~~L~~~Gf~kAy~   44 (89)
T 1ci4_A           14 PMGE--KPVGSLAGIGEVLGKKLEERGFDKAYV   44 (89)
T ss_dssp             CCTT--CCGGGSTTCCHHHHHHHHHTTCCSHHH
T ss_pred             CCCC--CCcccCCCcCHHHHHHHHHcCccHHHH
Confidence            4565  44678999999999888765 333333

>1vq8_Y 50S ribosomal protein L32E; ribosome 50S, protein-protein complex, RNA-RNA complex, PROT complex, peptidyl transferase reaction; HET: 1MA OMU OMG UR3 PSU SPS; 2.20A {Haloarcula marismortui} SCOP: c.9.2.1 PDB: 1vq4_Y* 1vq5_Y* 1vq6_Y* 1vq7_Y* 1s72_Y* 1vq9_Y* 1vqk_Y* 1vql_Y* 1vqm_Y* 1vqn_Y* 1vqo_Y* 1vqp_Y* 1yhq_Y* 1yi2_Y* 1yij_Y* 1yit_Y* 1yj9_Y* 1yjn_Y* 1yjw_Y* 2otj_Y* ...

Probab=86.88  E-value=0.12  Score=34.82  Aligned_cols=36  Identities=28%  Similarity=0.469  Sum_probs=0.0

Q ss_pred             HHHHHHhhCCCCCCCCCCCCccHHHHHHHHHHhCCH
Q 035374           21 FVDVISLVGDKADNIPGVEGIGDVRAVQLITKFGML   56 (66)
Q Consensus        21 ~~d~~~L~Gd~~D~i~gi~GiG~K~A~~Ll~~fgsl   56 (66)
                      |-++..|...+.+.+-.+||||+|+|.+++..+..+
T Consensus        36 f~sve~L~~a~~~eL~~v~GIG~ktAe~I~~~l~~~   71 (241)
T 1vq8_Y           36 FESVEDVRGADQSALADVSGIGNALAARIKADVGGL   71 (241)
T ss_dssp             ------------------------------------
T ss_pred             CCCHHHHHhCCHHHHHhccCCCHHHHHHHHHHHHHH
Confidence            334455555556778899999999999998877544

>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=86.57  E-value=0.34  Score=31.64  Aligned_cols=18  Identities=17%  Similarity=0.385  Sum_probs=14.7

Q ss_pred             CCCCCCccHHHHHHHHHH
Q 035374           35 IPGVEGIGDVRAVQLITK   52 (66)
Q Consensus        35 i~gi~GiG~K~A~~Ll~~   52 (66)
                      +-.+||||+|||.-++..
T Consensus       117 L~~lpGIG~~TA~~il~~  134 (221)
T 1kea_A          117 ILDLPGVGKYTCAAVMCL  134 (221)
T ss_dssp             HHTSTTCCHHHHHHHHHH
T ss_pred             HHhCCCCcHHHHHHHHHH
Confidence            346899999999988764

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

Probab=86.40  E-value=1.5  Score=32.37  Aligned_cols=33  Identities=18%  Similarity=0.383  Sum_probs=22.7

Q ss_pred             CCCChhHHHHHHHhhCCCCCCCCCCCCccHHHHHHHHH
Q 035374           14 GELKPSQFVDVISLVGDKADNIPGVEGIGDVRAVQLIT   51 (66)
Q Consensus        14 g~i~p~q~~d~~~L~Gd~~D~i~gi~GiG~K~A~~Ll~   51 (66)
                      |..+++++.... -.|    .+..+||||+|||.+++.
T Consensus       117 G~~s~edL~~a~-~~~----~L~~~~GiG~Ktaq~I~~  149 (578)
T 2w9m_A          117 GIDSLERLREAA-ESG----ELAGLKGFGAKSAATILE  149 (578)
T ss_dssp             TCCSHHHHHHHH-HHT----TTTTSTTCCHHHHHHHHH
T ss_pred             CCCCHHHHHHHH-hhC----ccccCCCCCHHHHHHHHH
Confidence            435667666422 233    677889999999999943

>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=86.37  E-value=0.35  Score=31.91  Aligned_cols=19  Identities=26%  Similarity=0.476  Sum_probs=15.4

Q ss_pred             CCCCccHHHHHHHHHH-hCC
Q 035374           37 GVEGIGDVRAVQLITK-FGM   55 (66)
Q Consensus        37 gi~GiG~K~A~~Ll~~-fgs   55 (66)
                      .+||||+|||.-++.. |+-
T Consensus       142 ~lpGIG~kTA~~ill~alg~  161 (233)
T 2h56_A          142 AIKGIGQWTAEMFMMFSLGR  161 (233)
T ss_dssp             TSTTCCHHHHHHHHHHTTCC
T ss_pred             hCCCcCHHHHHHHHHHhCCC
Confidence            7899999999988765 443

>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=86.34  E-value=0.36  Score=31.58  Aligned_cols=18  Identities=17%  Similarity=0.444  Sum_probs=14.5

Q ss_pred             CCCCCCccHHHHHHHHHH
Q 035374           35 IPGVEGIGDVRAVQLITK   52 (66)
Q Consensus        35 i~gi~GiG~K~A~~Ll~~   52 (66)
                      +-.+||||+|||.-++..
T Consensus       111 L~~lpGIG~~TA~~il~~  128 (225)
T 1kg2_A          111 VAALPGVGRSTAGAILSL  128 (225)
T ss_dssp             HHTSTTCCHHHHHHHHHH
T ss_pred             HhcCCCCcHHHHHHHHHH
Confidence            346899999999887764

>2bgw_A XPF endonuclease; hydrolase, structure specific endonuclease, nucleotide excision repair; 2.8A {Aeropyrum pernix} SCOP: a.60.2.5 c.52.1.20 PDB: 2bhn_A

Probab=86.25  E-value=0.099  Score=33.81  Aligned_cols=23  Identities=35%  Similarity=0.476  Sum_probs=18.7

Q ss_pred             CCCCCCCCCccHHHHHHHHHHhC
Q 035374           32 ADNIPGVEGIGDVRAVQLITKFG   54 (66)
Q Consensus        32 ~D~i~gi~GiG~K~A~~Ll~~fg   54 (66)
                      .+.+..+||||+++|.++...|.
T Consensus       193 ~e~L~~v~GiG~~~a~~i~~~~~  215 (219)
T 2bgw_A          193 KAEISKVEGIGEKRAEEIKKILM  215 (219)
T ss_dssp             HHHHHHSTTCCHHHHHHHHHHHH
T ss_pred             HHHHhhCCCCCHHHHHHHHHHHh
Confidence            34566789999999999988764

>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=85.49  E-value=0.5  Score=29.91  Aligned_cols=26  Identities=12%  Similarity=0.056  Sum_probs=20.3

Q ss_pred             HhhCCCCCCCCCCCCccHHHHHHHHH
Q 035374           26 SLVGDKADNIPGVEGIGDVRAVQLIT   51 (66)
Q Consensus        26 ~L~Gd~~D~i~gi~GiG~K~A~~Ll~   51 (66)
                      ..+-+..+.+..+||||++||-.++-
T Consensus        97 ~~vp~~~~~L~~LpGVG~yTAdav~~  122 (161)
T 4e9f_A           97 EYLTKQWKYPIELHGIGKYGNDSYRI  122 (161)
T ss_dssp             HHHHSCCSSGGGSTTCCHHHHHHHHH
T ss_pred             CcCCCChhhhhcCCCchHHHHHHHHH
Confidence            34556678889999999999977554

>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=84.73  E-value=0.47  Score=31.15  Aligned_cols=18  Identities=17%  Similarity=0.337  Sum_probs=14.9

Q ss_pred             CCCCCCccHHHHHHHHHH
Q 035374           35 IPGVEGIGDVRAVQLITK   52 (66)
Q Consensus        35 i~gi~GiG~K~A~~Ll~~   52 (66)
                      +-.+||||+|||.-++..
T Consensus       115 L~~lpGIG~~TA~~il~~  132 (226)
T 1orn_A          115 LMKLPGVGRKTANVVVSV  132 (226)
T ss_dssp             HTTSTTCCHHHHHHHHHH
T ss_pred             HHHCCCccHHHHHHHHHH
Confidence            457899999999888764

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

Probab=84.53  E-value=0.46  Score=30.67  Aligned_cols=18  Identities=17%  Similarity=0.410  Sum_probs=14.5

Q ss_pred             CCCCCCccHHHHHHHHHH
Q 035374           35 IPGVEGIGDVRAVQLITK   52 (66)
Q Consensus        35 i~gi~GiG~K~A~~Ll~~   52 (66)
                      +-.+||||+|||.-++..
T Consensus       111 L~~l~GIG~~tA~~il~~  128 (211)
T 2abk_A          111 LEALPGVGRKTANVVLNT  128 (211)
T ss_dssp             HHHSTTCCHHHHHHHHHH
T ss_pred             HHhCCCCChHHHHHHHHH
Confidence            346899999999887764

>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=84.35  E-value=0.5  Score=31.33  Aligned_cols=18  Identities=6%  Similarity=0.049  Sum_probs=15.1

Q ss_pred             CCCCCCccHHHHHHHHHH
Q 035374           35 IPGVEGIGDVRAVQLITK   52 (66)
Q Consensus        35 i~gi~GiG~K~A~~Ll~~   52 (66)
                      +-.+||||+|||.-++-.
T Consensus       152 L~~l~GIG~~TA~~ill~  169 (232)
T 4b21_A          152 LSKIKGVKRWTIEMYSIF  169 (232)
T ss_dssp             HTTSTTCCHHHHHHHHHH
T ss_pred             HHhCCCcCHHHHHHHHHH
Confidence            567899999999987764

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

Probab=84.32  E-value=0.5  Score=31.04  Aligned_cols=18  Identities=22%  Similarity=0.281  Sum_probs=14.7

Q ss_pred             CCCCCCccHHHHHHHHHH
Q 035374           35 IPGVEGIGDVRAVQLITK   52 (66)
Q Consensus        35 i~gi~GiG~K~A~~Ll~~   52 (66)
                      +-.+||||+|||.-++-.
T Consensus       148 L~~l~GIG~~TA~~ill~  165 (225)
T 2yg9_A          148 LVQLPGIGRWTAEMFLLF  165 (225)
T ss_dssp             HHTSTTCCHHHHHHHHHH
T ss_pred             HHcCCCCCHHHHHHHHHH
Confidence            347899999999987764

>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=84.31  E-value=0.5  Score=31.14  Aligned_cols=22  Identities=18%  Similarity=0.326  Sum_probs=17.0

Q ss_pred             CCCCCCCccHHHHHHHHHH-hCC
Q 035374           34 NIPGVEGIGDVRAVQLITK-FGM   55 (66)
Q Consensus        34 ~i~gi~GiG~K~A~~Ll~~-fgs   55 (66)
                      .+-.+||||++||.-++-. |+-
T Consensus       140 ~L~~l~GIG~~TA~~ill~~lg~  162 (228)
T 3s6i_A          140 RLTQIKGIGRWTVEMLLIFSLNR  162 (228)
T ss_dssp             HHTTSTTCCHHHHHHHHHHTSCC
T ss_pred             HHHhCCCcCHHHHHHHHHHhCCC
Confidence            4568899999999987754 443

>4glx_A DNA ligase; inhibitor, ligase-ligase inhibitor-DNA complex; HET: DNA 0XS; 1.90A {Escherichia coli}

Probab=84.10  E-value=0.5  Score=35.53  Aligned_cols=35  Identities=17%  Similarity=0.176  Sum_probs=27.0

Q ss_pred             HHHHhhCCCCCCCCCCCCccHHHHHHHHHHhCCHH
Q 035374           23 DVISLVGDKADNIPGVEGIGDVRAVQLITKFGMLV   57 (66)
Q Consensus        23 d~~~L~Gd~~D~i~gi~GiG~K~A~~Ll~~fgsl~   57 (66)
                      ++..|..-+.+.+..|+|||+++|..+..-|...+
T Consensus       534 sl~~l~~a~~e~l~~i~giG~~~A~si~~ff~~~~  568 (586)
T 4glx_A          534 TLEALEAASIEELQKVPDVGIVVASHVHNFFAEES  568 (586)
T ss_dssp             SHHHHHHCCHHHHTTSTTCCHHHHHHHHHHHHSHH
T ss_pred             CHHHHHccCHHHHhcCCCccHHHHHHHHHHHcCHH
Confidence            34455554556778899999999999999998754

>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=83.63  E-value=0.55  Score=31.97  Aligned_cols=21  Identities=14%  Similarity=0.134  Sum_probs=16.5

Q ss_pred             CCCCCCccHHHHHHHHHH-hCC
Q 035374           35 IPGVEGIGDVRAVQLITK-FGM   55 (66)
Q Consensus        35 i~gi~GiG~K~A~~Ll~~-fgs   55 (66)
                      +..+||||||||.-++-. ++-
T Consensus       213 L~~lpGIG~~TA~~ill~~lg~  234 (290)
T 3i0w_A          213 LKKFMGVGPQVADCIMLFSMQK  234 (290)
T ss_dssp             HTTSTTCCHHHHHHHHHHHHCC
T ss_pred             HHhCCCcCHHHHHHHHHHhCCC
Confidence            557899999999987754 444

>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=83.27  E-value=0.58  Score=31.48  Aligned_cols=18  Identities=22%  Similarity=0.303  Sum_probs=14.9

Q ss_pred             CCCCCCccHHHHHHHHHH
Q 035374           35 IPGVEGIGDVRAVQLITK   52 (66)
Q Consensus        35 i~gi~GiG~K~A~~Ll~~   52 (66)
                      +-.+||||+|||.-++..
T Consensus       209 L~~lpGIG~~TA~~ill~  226 (282)
T 1mpg_A          209 LQTFPGIGRWTANYFALR  226 (282)
T ss_dssp             HTTSTTCCHHHHHHHHHH
T ss_pred             HhcCCCcCHHHHHHHHHH
Confidence            458899999999887764

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

Probab=82.51  E-value=1.3  Score=30.43  Aligned_cols=15  Identities=20%  Similarity=0.364  Sum_probs=13.1

Q ss_pred             CCCccHHHHHHHHHH
Q 035374           38 VEGIGDVRAVQLITK   52 (66)
Q Consensus        38 i~GiG~K~A~~Ll~~   52 (66)
                      +||||+|||.-++.-
T Consensus       134 LpGIG~kTA~~iL~~  148 (287)
T 3n5n_X          134 LPGVGRYTAGAIASI  148 (287)
T ss_dssp             STTCCHHHHHHHHHH
T ss_pred             cCCCCHHHHHHHHHH
Confidence            899999999987764

>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=82.46  E-value=0.65  Score=31.53  Aligned_cols=18  Identities=22%  Similarity=0.401  Sum_probs=15.0

Q ss_pred             CCCCCCccHHHHHHHHHH
Q 035374           35 IPGVEGIGDVRAVQLITK   52 (66)
Q Consensus        35 i~gi~GiG~K~A~~Ll~~   52 (66)
                      +-.+||||+|||.-++..
T Consensus       212 L~~lpGIG~~TA~~ill~  229 (295)
T 2jhn_A          212 LTSFKGIGRWTAELVLSI  229 (295)
T ss_dssp             HHTSTTCCHHHHHHHHHH
T ss_pred             HhcCCCcCHHHHHHHHHH
Confidence            447899999999988765

>2dla_A 397AA long hypothetical protein; helix bundle, twisted beta-sheet, replication; 2.90A {Pyrococcus horikoshii}

Probab=82.25  E-value=0.65  Score=31.18  Aligned_cols=21  Identities=19%  Similarity=0.325  Sum_probs=18.3

Q ss_pred             HHHHHHHHHhCCHHHHHhhhc
Q 035374           44 VRAVQLITKFGMLVFNVECFS   64 (66)
Q Consensus        44 K~A~~Ll~~fgsl~~i~~~~~   64 (66)
                      ++|.+|++.|||+.++++.+.
T Consensus        10 ~~Ak~LlkeFG~in~fLe~IP   30 (222)
T 2dla_A           10 EKAKELLKGFGSINDFMDAIP   30 (222)
T ss_dssp             HHHHHHTTTTSSHHHHHHHGG
T ss_pred             HHHHHHHHHhccHHHHHHHcc
Confidence            689999999999999987653

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

ID	Length	Definition	E-value
Query	66
d1cmwa1	116	a.60.7.1 (A:174-289) 5' to 3' exonuclease domain o	8e-09
d1xo1a1	105	a.60.7.1 (A:186-290) T5 5'-exonuclease {Bacterioph	4e-08
d1ul1x1	140	a.60.7.1 (X:218-357) Flap endonuclease-1 (Fen-1 nu	1e-07
d1a77a1	108	a.60.7.1 (A:209-316) Flap endonuclease-1 (Fen-1 nu	5e-07
d1rxwa1	105	a.60.7.1 (A:220-324) Flap endonuclease-1 (Fen-1 nu	5e-07
d1b43a1	120	a.60.7.1 (A:220-339) Flap endonuclease-1 (Fen-1 nu	5e-04

>d1cmwa1 a.60.7.1 (A:174-289) 5' to 3' exonuclease domain of DNA polymerase Taq {Thermus aquaticus [TaxId: 271]} Length = 116

class: All alpha proteins
fold: SAM domain-like
superfamily: 5' to 3' exonuclease, C-terminal subdomain
family: 5' to 3' exonuclease, C-terminal subdomain
domain: 5' to 3' exonuclease domain of DNA polymerase Taq
species: Thermus aquaticus [TaxId: 271]

 Score = 45.6 bits (107), Expect = 8e-09
 Identities = 19/51 (37%), Positives = 34/51 (66%)

Query: 16 LKPSQFVDVISLVGDKADNIPGVEGIGDVRAVQLITKFGMLVFNVECFSEM 66
          L+P Q+ D  +L GD++DN+PGV+GIG+  A +L+ ++G L   ++    +
Sbjct: 1  LRPDQWADYRALTGDESDNLPGVKGIGEKTARKLLEEWGSLEALLKNLDRL 51

>d1xo1a1 a.60.7.1 (A:186-290) T5 5'-exonuclease {Bacteriophage T5 [TaxId: 10726]} Length = 105

class: All alpha proteins
fold: SAM domain-like
superfamily: 5' to 3' exonuclease, C-terminal subdomain
family: 5' to 3' exonuclease, C-terminal subdomain
domain: T5 5'-exonuclease
species: Bacteriophage T5 [TaxId: 10726]

 Score = 43.8 bits (103), Expect = 4e-08
 Identities = 17/37 (45%), Positives = 24/37 (64%)

Query: 18 PSQFVDVISLVGDKADNIPGVEGIGDVRAVQLITKFG 54
            QF+ + +++GD  DNI GVEGIG  R   +I +FG
Sbjct: 4  VEQFISLKAIMGDLGDNIRGVEGIGAKRGYNIIREFG 40

>d1ul1x1 a.60.7.1 (X:218-357) Flap endonuclease-1 (Fen-1 nuclease) {Human (Homo sapiens) [TaxId: 9606]} Length = 140

class: All alpha proteins
fold: SAM domain-like
superfamily: 5' to 3' exonuclease, C-terminal subdomain
family: 5' to 3' exonuclease, C-terminal subdomain
domain: Flap endonuclease-1 (Fen-1 nuclease)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 43.1 bits (101), Expect = 1e-07
 Identities = 17/41 (41%), Positives = 22/41 (53%), Gaps = 2/41 (4%)

Query: 16 LKPSQFVDVISLVGDKADNIPGVEGIGDVRAVQLITKFGML 56
          L   QFVD+  L+G  +D    + GIG  RAV LI K   +
Sbjct: 1  LNQEQFVDLCILLG--SDYCESIRGIGPKRAVDLIQKHKSI 39

>d1a77a1 a.60.7.1 (A:209-316) Flap endonuclease-1 (Fen-1 nuclease) {Archaeon Methanococcus jannaschii [TaxId: 2190]} Length = 108

class: All alpha proteins
fold: SAM domain-like
superfamily: 5' to 3' exonuclease, C-terminal subdomain
family: 5' to 3' exonuclease, C-terminal subdomain
domain: Flap endonuclease-1 (Fen-1 nuclease)
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

 Score = 41.0 bits (96), Expect = 5e-07
 Identities = 11/51 (21%), Positives = 19/51 (37%), Gaps = 1/51 (1%)

Query: 16 LKPSQFVDVISLVGDKADNIPGVEGIGDVRAVQLITKFGMLVFNVECFSEM 66
          +     +D+   +G    N  GV+GIG  RA +L+          +     
Sbjct: 1  ISLDDLIDIAIFMGT-DYNPGGVKGIGFKRAYELVRSGVAKDVLKKEVEYY 50

>d1rxwa1 a.60.7.1 (A:220-324) Flap endonuclease-1 (Fen-1 nuclease) {Archaeon Archaeoglobus fulgidus [TaxId: 2234]} Length = 105

class: All alpha proteins
fold: SAM domain-like
superfamily: 5' to 3' exonuclease, C-terminal subdomain
family: 5' to 3' exonuclease, C-terminal subdomain
domain: Flap endonuclease-1 (Fen-1 nuclease)
species: Archaeon Archaeoglobus fulgidus [TaxId: 2234]

 Score = 40.7 bits (95), Expect = 5e-07
 Identities = 14/39 (35%), Positives = 21/39 (53%), Gaps = 2/39 (5%)

Query: 16 LKPSQFVDVISLVGDKADNIPGVEGIGDVRAVQLITKFG 54
          L   Q +D+  LVG   D   GV+G+G  +A+  I  +G
Sbjct: 1  LTREQLIDIAILVG--TDYNEGVKGVGVKKALNYIKTYG 37

>d1b43a1 a.60.7.1 (A:220-339) Flap endonuclease-1 (Fen-1 nuclease) {Archaeon Pyrococcus furiosus [TaxId: 2261]} Length = 120

class: All alpha proteins
fold: SAM domain-like
superfamily: 5' to 3' exonuclease, C-terminal subdomain
family: 5' to 3' exonuclease, C-terminal subdomain
domain: Flap endonuclease-1 (Fen-1 nuclease)
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

 Score = 32.9 bits (75), Expect = 5e-04
 Identities = 10/46 (21%), Positives = 23/46 (50%), Gaps = 1/46 (2%)

Query: 16 LKPSQFVDVISLVGDKADNIPGVEGIGDVRAVQLITKFGMLVFNVE 61
          L   + +++  LVG    N  G++GIG  +A++++      +   +
Sbjct: 1  LTREKLIELAILVG-TDYNPGGIKGIGLKKALEIVRHSKDPLAKFQ 45

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	66
d1xo1a1	105	T5 5'-exonuclease {Bacteriophage T5 [TaxId: 10726]	99.89
d1cmwa1	116	5' to 3' exonuclease domain of DNA polymerase Taq	99.87
d1rxwa1	105	Flap endonuclease-1 (Fen-1 nuclease) {Archaeon Arc	99.87
d1ul1x1	140	Flap endonuclease-1 (Fen-1 nuclease) {Human (Homo	99.85
d1a77a1	108	Flap endonuclease-1 (Fen-1 nuclease) {Archaeon Met	99.83
d1b43a1	120	Flap endonuclease-1 (Fen-1 nuclease) {Archaeon Pyr	99.67
d1kfta_	56	Excinuclease UvrC C-terminal domain {Escherichia c	98.54
d2a1ja1	62	DNA repair endonuclease XPF {Human (Homo sapiens)	98.44
d1x2ia1	68	ATP-dependent RNA helicase PF2015 {Pyrococcus furi	98.38
d2bgwa1	70	DNA repair endonuclease XPF {Aeropyrum pernix [Tax	98.34
d2i1qa1	60	DNA repair protein Rad51, N-terminal domain {Archa	98.11
d2a1jb1	78	DNA excision repair protein ERCC-1 {Human (Homo sa	98.04
d1pzna1	61	DNA repair protein Rad51, N-terminal domain {Archa	97.96
d1bvsa2	71	DNA helicase RuvA subunit, middle domain {Mycobact	97.24
d1ixra1	73	DNA helicase RuvA subunit, middle domain {Thermus	97.22
d1dgsa1	181	NAD+-dependent DNA ligase, domain 3 {Thermus filif	97.19
d2fmpa2	57	DNA polymerase beta {Human (Homo sapiens) [TaxId:	97.19
d1jmsa3	60	Terminal deoxynucleotidyl transferase {Mouse (Mus	97.17
d1ixra1	73	DNA helicase RuvA subunit, middle domain {Thermus	97.17
d2bcqa2	57	DNA polymerase lambda {Human (Homo sapiens) [TaxId	97.13
d1cuka2	78	DNA helicase RuvA subunit, middle domain {Escheric	97.11
d1tfra1	123	T4 RNase H {Bacteriophage T4 [TaxId: 10665]}	97.06
d1bvsa2	71	DNA helicase RuvA subunit, middle domain {Mycobact	97.01
d1cuka2	78	DNA helicase RuvA subunit, middle domain {Escheric	96.93
d2csba3	55	Topoisomerase V {Methanopyrus kandleri [TaxId: 232	96.76
d2axtu1	98	Photosystem II 12 kDa extrinsic protein PsbU {Ther	95.86
d1kfta_	56	Excinuclease UvrC C-terminal domain {Escherichia c	95.85
d1x2ia1	68	ATP-dependent RNA helicase PF2015 {Pyrococcus furi	95.01
d2duya1	65	Uncharacterized protein TTHA1967 {Thermus thermoph	94.27
d2bgwa1	70	DNA repair endonuclease XPF {Aeropyrum pernix [Tax	94.27
d1keaa_	217	Thymine-DNA glycosylase {Archaeon Methanobacterium	94.13
d2abka_	211	Endonuclease III {Escherichia coli [TaxId: 562]}	93.89
d2p6ra2	198	Hel308 helicase {Archaeoglobus fulgidus [TaxId: 22	93.87
d2a1jb1	78	DNA excision repair protein ERCC-1 {Human (Homo sa	93.57
d2csba4	55	Topoisomerase V {Methanopyrus kandleri [TaxId: 232	93.18
d1dgsa1	181	NAD+-dependent DNA ligase, domain 3 {Thermus filif	93.09
d1orna_	214	Endonuclease III {Escherichia coli [TaxId: 562]}	92.81
d2i5ha1	180	Hypothetical protein AF1531 {Archaeoglobus fulgidu	92.53
d1szpa1	64	DNA repair protein Rad51, N-terminal domain {Baker	92.12
d1gm5a2	180	RecG "wedge" domain {Thermotoga maritima [TaxId: 2	91.04
d1vdda_	199	Recombination protein RecR {Deinococcus radioduran	90.77
d3bzka1	90	Transcriptional accessory factor Tex {Pseudomonas	90.6
d1kg2a_	224	Catalytic domain of MutY {Escherichia coli [TaxId:	90.44
d1rrqa1	221	Catalytic domain of MutY {Bacillus stearothermophi	90.08
d2i1qa1	60	DNA repair protein Rad51, N-terminal domain {Archa	89.99
d2edua1	91	KIF22, C-terminal domain {Human (Homo sapiens) [Ta	89.42
d2noha1	190	8-oxoguanine glycosylase {Human (Homo sapiens) [Ta	88.6
d1pu6a_	217	3-Methyladenine DNA glycosylase III (MagIII) {Heli	88.1
d1jmsa1	95	Terminal deoxynucleotidyl transferase {Mouse (Mus	87.96
d2bcqa1	76	DNA polymerase lambda {Human (Homo sapiens) [TaxId	86.73
d2edua1	91	KIF22, C-terminal domain {Human (Homo sapiens) [Ta	86.47
d1szpa1	64	DNA repair protein Rad51, N-terminal domain {Baker	85.84
d2fmpa1	82	DNA polymerase beta, N-terminal (8 kD)-domain {Hum	84.65
d1mpga1	183	3-Methyladenine DNA glycosylase II (gene alkA or a	84.24
d1jiha2	389	DNA polymerase eta {Baker's yeast (Saccharomyces c	83.85
d1ngna_	144	Mismatch-specific thymine glycosylase domain of th	83.83
d1im4a_	209	DinB homolog (DBH) {Archaeon Sulfolobus solfataric	82.98

>d1xo1a1 a.60.7.1 (A:186-290) T5 5'-exonuclease {Bacteriophage T5 [TaxId: 10726]}

class: All alpha proteins
fold: SAM domain-like
superfamily: 5' to 3' exonuclease, C-terminal subdomain
family: 5' to 3' exonuclease, C-terminal subdomain
domain: T5 5'-exonuclease
species: Bacteriophage T5 [TaxId: 10726]

Probab=99.89  E-value=6.3e-24  Score=128.47  Aligned_cols=49  Identities=35%  Similarity=0.618  Sum_probs=46.8

Q ss_pred             ChhHHHHHHHhhCCCCCCCCCCCCccHHHHHHHHHHhCCHHHHHhhhcc
Q 035374           17 KPSQFVDVISLVGDKADNIPGVEGIGDVRAVQLITKFGMLVFNVECFSE   65 (66)
Q Consensus        17 ~p~q~~d~~~L~Gd~~D~i~gi~GiG~K~A~~Ll~~fgsl~~i~~~~~~   65 (66)
                      .|+||+||++|+||+|||||||||||+|||.+|+++|+|+++++++++.
T Consensus         3 ~~eq~~d~~aL~GD~sDnipGV~GiG~KtA~kli~~~gsle~i~~~~~~   51 (105)
T d1xo1a1           3 DVEQFISLKAIMGDLGDNIRGVEGIGAKRGYNIIREFGNVLDIIDQLPL   51 (105)
T ss_dssp             SHHHHHHHHHHHCBGGGTBCCCTTCCHHHHHHHHHHHCSHHHHHHHCSC
T ss_pred             cHHHHHHHHHHhCCcccCCcCcCCcCHHHHHHHHHHcchhHHHHHhHHH
Confidence            6899999999999999999999999999999999999999999988764

>d1cmwa1 a.60.7.1 (A:174-289) 5' to 3' exonuclease domain of DNA polymerase Taq {Thermus aquaticus [TaxId: 271]}

class: All alpha proteins
fold: SAM domain-like
superfamily: 5' to 3' exonuclease, C-terminal subdomain
family: 5' to 3' exonuclease, C-terminal subdomain
domain: 5' to 3' exonuclease domain of DNA polymerase Taq
species: Thermus aquaticus [TaxId: 271]

Probab=99.87  E-value=7.3e-25  Score=132.75  Aligned_cols=50  Identities=38%  Similarity=0.725  Sum_probs=47.7

Q ss_pred             CChhHHHHHHHhhCCCCCCCCCCCCccHHHHHHHHHHhCCHHHHHhhhcc
Q 035374           16 LKPSQFVDVISLVGDKADNIPGVEGIGDVRAVQLITKFGMLVFNVECFSE   65 (66)
Q Consensus        16 i~p~q~~d~~~L~Gd~~D~i~gi~GiG~K~A~~Ll~~fgsl~~i~~~~~~   65 (66)
                      +.|+||+||++|+||+|||||||||||+|||.+|+++|+|++++++++++
T Consensus         1 ~~P~~~~~~~~l~GD~sDnipGv~GiG~KtA~kll~~~gsle~i~~~~~~   50 (116)
T d1cmwa1           1 LRPDQWADYRALTGDESDNLPGVKGIGEKTARKLLEEWGSLEALLKNLDR   50 (116)
T ss_dssp             CCGGGHHHHHHTTCCSSSCCCCCCCSTTCTTTTTGGGGGTTCSSSSSCCC
T ss_pred             CCHHHHHHHHHHhCccccCcccccccCchhHHHHHHhcchHHHHHHHHhh
Confidence            58999999999999999999999999999999999999999999987765

>d1rxwa1 a.60.7.1 (A:220-324) Flap endonuclease-1 (Fen-1 nuclease) {Archaeon Archaeoglobus fulgidus [TaxId: 2234]}

class: All alpha proteins
fold: SAM domain-like
superfamily: 5' to 3' exonuclease, C-terminal subdomain
family: 5' to 3' exonuclease, C-terminal subdomain
domain: Flap endonuclease-1 (Fen-1 nuclease)
species: Archaeon Archaeoglobus fulgidus [TaxId: 2234]

Probab=99.87  E-value=4.9e-23  Score=124.00  Aligned_cols=48  Identities=29%  Similarity=0.539  Sum_probs=45.5

Q ss_pred             CChhHHHHHHHhhCCCCCCCCCCCCccHHHHHHHHHHhCCHHHHHhhhcc
Q 035374           16 LKPSQFVDVISLVGDKADNIPGVEGIGDVRAVQLITKFGMLVFNVECFSE   65 (66)
Q Consensus        16 i~p~q~~d~~~L~Gd~~D~i~gi~GiG~K~A~~Ll~~fgsl~~i~~~~~~   65 (66)
                      +||+||+|+|+|+|  |||+|||||||||||.+||++|+|+++++++++.
T Consensus         1 lt~eq~iD~~~L~G--sDn~pGV~GIG~ktA~kli~~~gsle~i~~~~~~   48 (105)
T d1rxwa1           1 LTREQLIDIAILVG--TDYNEGVKGVGVKKALNYIKTYGDIFRALKALKV   48 (105)
T ss_dssp             CCHHHHHHHHHHHC--BTTBCCCTTCCHHHHHHHHHHHSSHHHHHHHHTC
T ss_pred             CCHHHHHHHHHHhC--CCCCCCCCCcCHHHHHHHHHHhCCHHHHHHHHHh
Confidence            68999999999999  8999999999999999999999999999987753

>d1ul1x1 a.60.7.1 (X:218-357) Flap endonuclease-1 (Fen-1 nuclease) {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: SAM domain-like
superfamily: 5' to 3' exonuclease, C-terminal subdomain
family: 5' to 3' exonuclease, C-terminal subdomain
domain: Flap endonuclease-1 (Fen-1 nuclease)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.85  E-value=3.7e-22  Score=123.91  Aligned_cols=48  Identities=38%  Similarity=0.509  Sum_probs=45.6

Q ss_pred             CChhHHHHHHHhhCCCCCCCCCCCCccHHHHHHHHHHhCCHHHHHhhhcc
Q 035374           16 LKPSQFVDVISLVGDKADNIPGVEGIGDVRAVQLITKFGMLVFNVECFSE   65 (66)
Q Consensus        16 i~p~q~~d~~~L~Gd~~D~i~gi~GiG~K~A~~Ll~~fgsl~~i~~~~~~   65 (66)
                      ++++||+|+|+|+|  |||+|||||||+|||.+||++|+|+++|+++++.
T Consensus         1 l~~~q~id~~~L~G--sD~~pgv~gIG~ktA~kli~~~~~le~i~~~~~~   48 (140)
T d1ul1x1           1 LNQEQFVDLCILLG--SDYCESIRGIGPKRAVDLIQKHKSIEEIVRRLDP   48 (140)
T ss_dssp             CCHHHHHHHHHHHH--CSSSCCCTTCCHHHHHHHHHHSSSHHHHHTTCCC
T ss_pred             CCHHHHHHHHHHhC--CCCCCCCCCccHHHHHHHHHHhCCHHHHHHHHHH
Confidence            68999999999999  7999999999999999999999999999998764

>d1a77a1 a.60.7.1 (A:209-316) Flap endonuclease-1 (Fen-1 nuclease) {Archaeon Methanococcus jannaschii [TaxId: 2190]}

class: All alpha proteins
fold: SAM domain-like
superfamily: 5' to 3' exonuclease, C-terminal subdomain
family: 5' to 3' exonuclease, C-terminal subdomain
domain: Flap endonuclease-1 (Fen-1 nuclease)
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

Probab=99.83  E-value=1.4e-21  Score=117.76  Aligned_cols=48  Identities=23%  Similarity=0.249  Sum_probs=43.9

Q ss_pred             CChhHHHHHHHhhCCCCCCCCCCCCccHHHHHHHHHHhCCHHHHHhhhc
Q 035374           16 LKPSQFVDVISLVGDKADNIPGVEGIGDVRAVQLITKFGMLVFNVECFS   64 (66)
Q Consensus        16 i~p~q~~d~~~L~Gd~~D~i~gi~GiG~K~A~~Ll~~fgsl~~i~~~~~   64 (66)
                      +||+||+|+|+|+|+ +||+|||||||||||.+|+++|+|++.++++.+
T Consensus         1 lt~~q~IDl~iL~G~-dyn~pGV~GIGpktA~klIk~~g~ie~l~~~~~   48 (108)
T d1a77a1           1 ISLDDLIDIAIFMGT-DYNPGGVKGIGFKRAYELVRSGVAKDVLKKEVE   48 (108)
T ss_dssp             CCHHHHHHHHHHHCC-TTSTTCSTTCCHHHHHHHHHTTCHHHHHHHHCT
T ss_pred             CCHHHHHHHHHHhCC-cCCCCCCCCcCHHHHHHHHHHcCCHHHHHHhhh
Confidence            689999999999995 567799999999999999999999999998654

>d1b43a1 a.60.7.1 (A:220-339) Flap endonuclease-1 (Fen-1 nuclease) {Archaeon Pyrococcus furiosus [TaxId: 2261]}

class: All alpha proteins
fold: SAM domain-like
superfamily: 5' to 3' exonuclease, C-terminal subdomain
family: 5' to 3' exonuclease, C-terminal subdomain
domain: Flap endonuclease-1 (Fen-1 nuclease)
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=99.67  E-value=1.4e-17  Score=102.08  Aligned_cols=45  Identities=22%  Similarity=0.392  Sum_probs=40.7

Q ss_pred             CChhHHHHHHHhhCCCCCCC-CCCCCccHHHHHHHHHHhCCHHHHHhh
Q 035374           16 LKPSQFVDVISLVGDKADNI-PGVEGIGDVRAVQLITKFGMLVFNVEC   62 (66)
Q Consensus        16 i~p~q~~d~~~L~Gd~~D~i-~gi~GiG~K~A~~Ll~~fgsl~~i~~~   62 (66)
                      +|++||+|+|+|+|  |||. +||||||||||.+|+++|+++++++..
T Consensus         1 lt~eqfIdl~iL~G--~DY~~~gI~GIGpktAlklikk~~~~~~~~~~   46 (120)
T d1b43a1           1 LTREKLIELAILVG--TDYNPGGIKGIGLKKALEIVRHSKDPLAKFQK   46 (120)
T ss_dssp             CCHHHHHHHHHHHC--CTTSTTCSTTCCHHHHHHHHHTCSSGGGGTGG
T ss_pred             CCHHHHHHHHHHhC--CCCCcccCCCcCHHHHHHHHHHhCCHHHHHHh
Confidence            68999999999999  5887 699999999999999999999877654

>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=98.54  E-value=1.1e-08  Score=54.58  Aligned_cols=29  Identities=24%  Similarity=0.318  Sum_probs=26.0

Q ss_pred             CCCCCCCccHHHHHHHHHHhCCHHHHHhh
Q 035374           34 NIPGVEGIGDVRAVQLITKFGMLVFNVEC   62 (66)
Q Consensus        34 ~i~gi~GiG~K~A~~Ll~~fgsl~~i~~~   62 (66)
                      .+.+||||||++|.+|+++|+|++++.++
T Consensus         3 ~L~~I~gVG~~~a~~L~~~F~s~~~i~~A   31 (56)
T d1kfta_           3 SLETIEGVGPKRRQMLLKYMGGLQGLRNA   31 (56)
T ss_dssp             GGGGCTTCSSSHHHHHHHHHSCHHHHHHC
T ss_pred             CcccCCCccHHHHHHHHHHhCCHHHHHHh
Confidence            35678999999999999999999999863

>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=98.44  E-value=2.3e-08  Score=54.07  Aligned_cols=30  Identities=10%  Similarity=0.084  Sum_probs=26.3

Q ss_pred             CCCCCCCCccHHHHHHHHHHhCCHHHHHhh
Q 035374           33 DNIPGVEGIGDVRAVQLITKFGMLVFNVEC   62 (66)
Q Consensus        33 D~i~gi~GiG~K~A~~Ll~~fgsl~~i~~~   62 (66)
                      |-+.+|||||+|++..|+++|+|++++.++
T Consensus         3 d~L~~iPGIg~~~~~~Ll~~f~Si~~l~~A   32 (62)
T d2a1ja1           3 DFLLKMPGVNAKNCRSLMHHVKNIAELAAL   32 (62)
T ss_dssp             HHHHTSTTCCHHHHHHHHHHCSSHHHHHTC
T ss_pred             hHHhcCCCCCHHHHHHHHHHhccHHHHHhC
Confidence            445678999999999999999999999863

>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=98.38  E-value=1.1e-07  Score=52.21  Aligned_cols=27  Identities=19%  Similarity=0.293  Sum_probs=24.7

Q ss_pred             CCCCCccHHHHHHHHHHhCCHHHHHhh
Q 035374           36 PGVEGIGDVRAVQLITKFGMLVFNVEC   62 (66)
Q Consensus        36 ~gi~GiG~K~A~~Ll~~fgsl~~i~~~   62 (66)
                      .||||||+++|.+|+++|+|+++++++
T Consensus        13 ~~I~gIG~~~a~~L~~~f~s~~~i~~A   39 (68)
T d1x2ia1          13 EGLPHVSATLARRLLKHFGSVERVFTA   39 (68)
T ss_dssp             TTSTTCCHHHHHHHHHHHCSHHHHHHC
T ss_pred             cCCCCcCHHHHHHHHHHcCCHHHHHHh
Confidence            478999999999999999999999864

>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=98.34  E-value=1.4e-07  Score=51.73  Aligned_cols=27  Identities=26%  Similarity=0.411  Sum_probs=24.1

Q ss_pred             CCCCCccHHHHHHHHHHhCCHHHHHhh
Q 035374           36 PGVEGIGDVRAVQLITKFGMLVFNVEC   62 (66)
Q Consensus        36 ~gi~GiG~K~A~~Ll~~fgsl~~i~~~   62 (66)
                      .+|||||+++|.+|+++|+|++++.++
T Consensus        16 ~~IpgIG~~~a~~L~~~F~s~~~l~~A   42 (70)
T d2bgwa1          16 QSFPGIGRRTAERILERFGSLERFFTA   42 (70)
T ss_dssp             HTSTTCCHHHHHHHHHHHSSHHHHTTC
T ss_pred             cCCCCcCHHHHHHHHHHhCCHHHHHHc
Confidence            356999999999999999999999863

>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=98.11  E-value=1.3e-06  Score=46.78  Aligned_cols=27  Identities=15%  Similarity=0.250  Sum_probs=24.1

Q ss_pred             CCCCCccHHHHHHHHHH-hCCHHHHHhh
Q 035374           36 PGVEGIGDVRAVQLITK-FGMLVFNVEC   62 (66)
Q Consensus        36 ~gi~GiG~K~A~~Ll~~-fgsl~~i~~~   62 (66)
                      ..||||||++|.+|++. |+|++++.++
T Consensus         2 ~~IpGIG~~~a~~L~~~G~~tv~~l~~a   29 (60)
T d2i1qa1           2 TDLPGVGPSTAEKLVEAGYIDFMKIATA   29 (60)
T ss_dssp             TTSTTCCHHHHHHHHHHTCCSHHHHHTC
T ss_pred             CCCCCCCHHHHHHHHHccCCCHHHHHhC
Confidence            46799999999999998 9999999853

>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=98.04  E-value=1.6e-06  Score=48.29  Aligned_cols=28  Identities=21%  Similarity=0.380  Sum_probs=24.8

Q ss_pred             CCCCCCccHHHHHHHHHHhCCHHHHHhh
Q 035374           35 IPGVEGIGDVRAVQLITKFGMLVFNVEC   62 (66)
Q Consensus        35 i~gi~GiG~K~A~~Ll~~fgsl~~i~~~   62 (66)
                      +.+|||||+++|..|+++|+|+++++++
T Consensus        21 L~~I~gIg~~~a~~L~~~F~s~~~i~~A   48 (78)
T d2a1jb1          21 LTTVKSVNKTDSQTLLTTFGSLEQLIAA   48 (78)
T ss_dssp             HTTSTTCCHHHHHHHHHHHSSHHHHHSC
T ss_pred             hcCCCCcCHHHHHHHHHHhCCcHHHHhh
Confidence            3467999999999999999999999863

>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=97.96  E-value=2.4e-06  Score=45.74  Aligned_cols=28  Identities=21%  Similarity=0.285  Sum_probs=24.2

Q ss_pred             CCCCCCccHHHHHHHHHH-hCCHHHHHhh
Q 035374           35 IPGVEGIGDVRAVQLITK-FGMLVFNVEC   62 (66)
Q Consensus        35 i~gi~GiG~K~A~~Ll~~-fgsl~~i~~~   62 (66)
                      +..||||||++|.+|++. |+|++++.++
T Consensus         3 L~~i~GIG~~~a~~L~~~g~~sv~~l~~a   31 (61)
T d1pzna1           3 IEDLPGVGPATAEKLREAGYDTLEAIAVA   31 (61)
T ss_dssp             SSCCTTCCHHHHHHHHTTTCCSHHHHHTC
T ss_pred             cccCCCCCHHHHHHHHHhcCCCHHHHHhC
Confidence            456799999999999986 7999999853

>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=97.24  E-value=0.00016  Score=39.88  Aligned_cols=26  Identities=15%  Similarity=0.160  Sum_probs=21.4

Q ss_pred             CCCCccHHHHHHHHHHhCCHHHHHhhh
Q 035374           37 GVEGIGDVRAVQLITKFGMLVFNVECF   63 (66)
Q Consensus        37 gi~GiG~K~A~~Ll~~fgsl~~i~~~~   63 (66)
                      +|+|||||+|..+|..| +++++.++.
T Consensus        13 ~V~GIGpK~Al~iLs~~-~~~~l~~aI   38 (71)
T d1bvsa2          13 SVSGVGPRLAMATLAVH-DAAALRQAL   38 (71)
T ss_dssp             TSSSCCHHHHHHHHHHS-CHHHHHHHT
T ss_pred             ccCCcCHHHHHHHHHhC-CHHHHHHHH
Confidence            46899999999999998 677776544

>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=97.22  E-value=9.7e-05  Score=41.00  Aligned_cols=36  Identities=25%  Similarity=0.389  Sum_probs=19.7

Q ss_pred             CChhHHHHHHHhhCCCCCCCCCCCCccHHHHHHHHHHh
Q 035374           16 LKPSQFVDVISLVGDKADNIPGVEGIGDVRAVQLITKF   53 (66)
Q Consensus        16 i~p~q~~d~~~L~Gd~~D~i~gi~GiG~K~A~~Ll~~f   53 (66)
                      ++++++.. .+.-+| ...+..|||||+|+|.+++-+.
T Consensus        30 ~~~~~l~~-aI~~~D-~~~L~~vpGIG~KtA~rIi~eL   65 (73)
T d1ixra1          30 LPPRLLAR-ALLEGD-ARLLTSASGVGRRLAERIALEL   65 (73)
T ss_dssp             SCHHHHHH-HHHTTC-HHHHTTSTTCCHHHHHHHHHHH
T ss_pred             ccHHHHHH-HHHhcC-HHHhhcCCCCCHHHHHHHHHHH
Confidence            34555553 122333 4456666777777777766554

>d1dgsa1 a.60.2.2 (A:401-581) NAD+-dependent DNA ligase, domain 3 {Thermus filiformis [TaxId: 276]}

class: All alpha proteins
fold: SAM domain-like
superfamily: RuvA domain 2-like
family: NAD+-dependent DNA ligase, domain 3
domain: NAD+-dependent DNA ligase, domain 3
species: Thermus filiformis [TaxId: 276]

Probab=97.19  E-value=8.8e-05  Score=46.66  Aligned_cols=26  Identities=35%  Similarity=0.609  Sum_probs=23.6

Q ss_pred             CCCCccHHHHHHHHHHhCCHHHHHhh
Q 035374           37 GVEGIGDVRAVQLITKFGMLVFNVEC   62 (66)
Q Consensus        37 gi~GiG~K~A~~Ll~~fgsl~~i~~~   62 (66)
                      |||+||+++|..|.++|+|++++.++
T Consensus       111 GI~~vG~~~Ak~La~~f~sl~~l~~a  136 (181)
T d1dgsa1         111 GLPGVGEVLARNLARRFGTMDRLLEA  136 (181)
T ss_dssp             TCSSCCHHHHHHHHHTTSBHHHHTTC
T ss_pred             HhhhhhHHHHHHHHHHhhhhhhhhhh
Confidence            57999999999999999999998753

>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=97.19  E-value=0.00018  Score=38.16  Aligned_cols=27  Identities=22%  Similarity=0.213  Sum_probs=22.7

Q ss_pred             CCCCCccHHHHHHHHHH-hCCHHHHHhh
Q 035374           36 PGVEGIGDVRAVQLITK-FGMLVFNVEC   62 (66)
Q Consensus        36 ~gi~GiG~K~A~~Ll~~-fgsl~~i~~~   62 (66)
                      .+|.||||++|.+|+++ +.|++++.+.
T Consensus        10 ~~I~GvGp~~A~~l~~~Gi~ti~dLr~~   37 (57)
T d2fmpa2          10 TRVSGIGPSAARKFVDEGIKTLEDLRKN   37 (57)
T ss_dssp             TTSTTCCHHHHHHHHHTTCCSHHHHHTC
T ss_pred             hccccccHHHHHHHHHhCCCCHHHHHhh
Confidence            46799999999999998 5689988653

>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=97.17  E-value=0.00016  Score=38.73  Aligned_cols=26  Identities=23%  Similarity=0.115  Sum_probs=22.7

Q ss_pred             CCCCccHHHHHHHHHH-hCCHHHHHhh
Q 035374           37 GVEGIGDVRAVQLITK-FGMLVFNVEC   62 (66)
Q Consensus        37 gi~GiG~K~A~~Ll~~-fgsl~~i~~~   62 (66)
                      +|.||||++|.+++++ +.|++++.++
T Consensus        12 ~I~GvGp~~A~~l~~~Gi~ti~dL~~~   38 (60)
T d1jmsa3          12 SVFGVGLKTAEKWFRMGFRTLSKIQSD   38 (60)
T ss_dssp             TSTTCCHHHHHHHHHTTCCSHHHHHHC
T ss_pred             ccccccHHHHHHHHHhCCCCHHHHHhc
Confidence            5799999999999999 6799998754

>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=97.17  E-value=0.00019  Score=39.76  Aligned_cols=26  Identities=19%  Similarity=0.333  Sum_probs=20.8

Q ss_pred             CCCCccHHHHHHHHHHhCCHHHHHhhh
Q 035374           37 GVEGIGDVRAVQLITKFGMLVFNVECF   63 (66)
Q Consensus        37 gi~GiG~K~A~~Ll~~fgsl~~i~~~~   63 (66)
                      +|.|||||+|..+|..|+ .+++.+++
T Consensus        14 ~V~GIGpk~Al~iLs~~~-~~~l~~aI   39 (73)
T d1ixra1          14 SVSGVGPKVALALLSALP-PRLLARAL   39 (73)
T ss_dssp             SSSCCCHHHHHHHHHHSC-HHHHHHHH
T ss_pred             ccCCcCHHHHHHHHHHcc-HHHHHHHH
Confidence            468999999999999874 66676543

>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=97.13  E-value=0.00019  Score=38.11  Aligned_cols=27  Identities=19%  Similarity=0.068  Sum_probs=23.0

Q ss_pred             CCCCCccHHHHHHHHHH-hCCHHHHHhh
Q 035374           36 PGVEGIGDVRAVQLITK-FGMLVFNVEC   62 (66)
Q Consensus        36 ~gi~GiG~K~A~~Ll~~-fgsl~~i~~~   62 (66)
                      .+|-||||++|.+|+++ +.|++++.+.
T Consensus        11 t~I~GvGp~~A~~l~~~Gi~ti~dLr~~   38 (57)
T d2bcqa2          11 SNIWGAGTKTAQMWYQQGFRSLEDIRSQ   38 (57)
T ss_dssp             HTSTTCCHHHHHHHHHTTCCSHHHHHHH
T ss_pred             hccccccHHHHHHHHHhCCCCHHHHHhc
Confidence            35789999999999999 5799998764

>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=97.11  E-value=9.1e-05  Score=41.53  Aligned_cols=36  Identities=25%  Similarity=0.414  Sum_probs=24.2

Q ss_pred             CChhHHHHHHHhhCCCCCCCCCCCCccHHHHHHHHHHh
Q 035374           16 LKPSQFVDVISLVGDKADNIPGVEGIGDVRAVQLITKF   53 (66)
Q Consensus        16 i~p~q~~d~~~L~Gd~~D~i~gi~GiG~K~A~~Ll~~f   53 (66)
                      ++|+++.+. +.-+| .+.+..|||||+|+|.+++-+.
T Consensus        29 ~~~~~l~~a-I~~~D-~~~L~~vpGIG~KtA~rIi~eL   64 (78)
T d1cuka2          29 MSAQQFVNA-VEREE-VGALVKLPGIGKKTAERLIVEM   64 (78)
T ss_dssp             SCHHHHHHH-HHTTC-HHHHHTSTTCCHHHHHHHHHHH
T ss_pred             CCHHHHHHH-HHccC-HHHhhcCCCCCHHHHHHHHHHH
Confidence            467777642 22444 5567788888888888887653

>d1tfra1 a.60.7.1 (A:183-305) T4 RNase H {Bacteriophage T4 [TaxId: 10665]}

class: All alpha proteins
fold: SAM domain-like
superfamily: 5' to 3' exonuclease, C-terminal subdomain
family: 5' to 3' exonuclease, C-terminal subdomain
domain: T4 RNase H
species: Bacteriophage T4 [TaxId: 10665]

Probab=97.06  E-value=0.00012  Score=44.04  Aligned_cols=35  Identities=20%  Similarity=0.172  Sum_probs=31.5

Q ss_pred             ChhHHHHHHHhhCCCCCCCCCC----------------CCccHHHHHHHHH
Q 035374           17 KPSQFVDVISLVGDKADNIPGV----------------EGIGDVRAVQLIT   51 (66)
Q Consensus        17 ~p~q~~d~~~L~Gd~~D~i~gi----------------~GiG~K~A~~Ll~   51 (66)
                      +|+...-.+++.||+||+||.|                |.++.|++.++..
T Consensus         2 ~p~~~L~~KIikGD~sDgIPnils~dd~~~t~veg~Rqk~~~kk~~~~~~~   52 (123)
T d1tfra1           2 SAEIDCMTKILKGDKKDNVASVKVRSDFWFTRVEGERTPSMKTSIVEAIAN   52 (123)
T ss_dssp             HHHHHHHHHHHHEEGGGTEECTTSCTTHHHHCCTTCCCCCCCHHHHHHHHH
T ss_pred             CHHHHHHHHHHcCCCcCCcCccccCCccceeccccccccchhHHHHHHHHc
Confidence            5888888999999999999999                7799999998875

>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=97.01  E-value=0.00011  Score=40.52  Aligned_cols=37  Identities=16%  Similarity=0.267  Sum_probs=26.6

Q ss_pred             CChhHHHHHHHhhCCCCCCCCCCCCccHHHHHHHHHHhC
Q 035374           16 LKPSQFVDVISLVGDKADNIPGVEGIGDVRAVQLITKFG   54 (66)
Q Consensus        16 i~p~q~~d~~~L~Gd~~D~i~gi~GiG~K~A~~Ll~~fg   54 (66)
                      ++++++.+. +.-+| ...+..|||||+|||.+++-+..
T Consensus        29 ~~~~~l~~a-I~~~D-~~~L~~vpGIG~KtA~rIi~eLk   65 (71)
T d1bvsa2          29 HDAAALRQA-LADSD-VASLTRVPGIGRRGAERIVLELA   65 (71)
T ss_dssp             SCHHHHHHH-TTTTC-HHHHHTSTTCCHHHHHHHHHHSS
T ss_pred             CCHHHHHHH-HHcCC-HHHhhcCCCCCHHHHHHHHHHHH
Confidence            467777642 23444 45678999999999999987753

>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=96.93  E-value=0.00031  Score=39.24  Aligned_cols=26  Identities=15%  Similarity=0.235  Sum_probs=20.8

Q ss_pred             CCCCccHHHHHHHHHHhCCHHHHHhhh
Q 035374           37 GVEGIGDVRAVQLITKFGMLVFNVECF   63 (66)
Q Consensus        37 gi~GiG~K~A~~Ll~~fgsl~~i~~~~   63 (66)
                      +|+|||||+|..+|..| +.+++.+++
T Consensus        13 ~V~GIGpK~Al~iLs~~-~~~~l~~aI   38 (78)
T d1cuka2          13 KTNGVGPKLALAILSGM-SAQQFVNAV   38 (78)
T ss_dssp             HSSSCCHHHHHHHHHHS-CHHHHHHHH
T ss_pred             ccCCccHHHHHHHHHhC-CHHHHHHHH
Confidence            46899999999999998 566666543

>d2csba3 a.60.2.4 (A:410-464) Topoisomerase V {Methanopyrus kandleri [TaxId: 2320]}

class: All alpha proteins
fold: SAM domain-like
superfamily: RuvA domain 2-like
family: Topoisomerase V repeat domain
domain: Topoisomerase V
species: Methanopyrus kandleri [TaxId: 2320]

Probab=96.76  E-value=0.00078  Score=34.76  Aligned_cols=23  Identities=30%  Similarity=0.403  Sum_probs=21.2

Q ss_pred             CCccHHHHHHHHHHhCCHHHHHh
Q 035374           39 EGIGDVRAVQLITKFGMLVFNVE   61 (66)
Q Consensus        39 ~GiG~K~A~~Ll~~fgsl~~i~~   61 (66)
                      .|+|.|+|..||+.||+.+.+.+
T Consensus         8 egvgrktaerllrafgnpervkq   30 (55)
T d2csba3           8 EGVGRKTAERLLRAFGNPERVKQ   30 (55)
T ss_dssp             TTCCHHHHHHHHHHHSSHHHHHH
T ss_pred             ccccHhHHHHHHHHhCCHHHHHH
Confidence            79999999999999999998764

>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=95.86  E-value=0.0011  Score=38.34  Aligned_cols=28  Identities=7%  Similarity=0.031  Sum_probs=21.0

Q ss_pred             CCCCCCCCccHHHHHHHHHH--hCCHHHHH
Q 035374           33 DNIPGVEGIGDVRAVQLITK--FGMLVFNV   60 (66)
Q Consensus        33 D~i~gi~GiG~K~A~~Ll~~--fgsl~~i~   60 (66)
                      ..+..+|||||++|.++++.  |.|+++++
T Consensus        27 ~eL~~lpGIg~~~A~~Iv~~gpf~s~edL~   56 (98)
T d2axtu1          27 AAFIQYRGLYPTLAKLIVKNAPYESVEDVL   56 (98)
T ss_dssp             GGGTTSTTCTHHHHHHHHHSCCCSSGGGGG
T ss_pred             HHHHHhhhhcHHHHHHHHHcCCcCCHHHHh
Confidence            34567899999999999964  45566554

>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=95.85  E-value=0.00072  Score=35.16  Aligned_cols=42  Identities=14%  Similarity=0.153  Sum_probs=29.3

Q ss_pred             HHHHHHHhCCCChhHHHHHHHhhCCCCCCCCCCCCccHHHHHHHHHHhCC
Q 035374            6 MEDFARKYGELKPSQFVDVISLVGDKADNIPGVEGIGDVRAVQLITKFGM   55 (66)
Q Consensus         6 ~~~v~~~~g~i~p~q~~d~~~L~Gd~~D~i~gi~GiG~K~A~~Ll~~fgs   55 (66)
                      .+.+.++|+  +.+.+.      --+.+.+..|||||+++|.++.+.|.+
T Consensus        15 a~~L~~~F~--s~~~i~------~As~eeL~~v~GIg~~~A~~I~~~l~N   56 (56)
T d1kfta_          15 RQMLLKYMG--GLQGLR------NASVEEIAKVPGISQGLAEKIFWSLKH   56 (56)
T ss_dssp             HHHHHHHHS--CHHHHH------HCCHHHHTTSSSTTSHHHHHHHHHHTC
T ss_pred             HHHHHHHhC--CHHHHH------HhhHHHHHhcCCCCHHHHHHHHHHHcC
Confidence            356667776  444433      223456778899999999999988754

>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=95.01  E-value=0.0017  Score=34.66  Aligned_cols=42  Identities=17%  Similarity=0.304  Sum_probs=29.4

Q ss_pred             HHHHHHHhCCCChhHHHHHHHhhCCCCCCCCCCCCccHHHHHHHHHHhCC
Q 035374            6 MEDFARKYGELKPSQFVDVISLVGDKADNIPGVEGIGDVRAVQLITKFGM   55 (66)
Q Consensus         6 ~~~v~~~~g~i~p~q~~d~~~L~Gd~~D~i~gi~GiG~K~A~~Ll~~fgs   55 (66)
                      ...+.++|+  +.+++..      -+.+.+..|+|||+++|..+.+.|.+
T Consensus        23 a~~L~~~f~--s~~~i~~------As~eeL~~i~GIG~~~A~~I~~~~~~   64 (68)
T d1x2ia1          23 ARRLLKHFG--SVERVFT------ASVAELMKVEGIGEKIAKEIRRVITA   64 (68)
T ss_dssp             HHHHHHHHC--SHHHHHH------CCHHHHTTSTTCCHHHHHHHHHHHHS
T ss_pred             HHHHHHHcC--CHHHHHH------hHHHHHHhCCCcCHHHHHHHHHHHhc
Confidence            355667776  5555542      23356678899999999999887754

>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=94.27  E-value=0.0064  Score=32.20  Aligned_cols=27  Identities=19%  Similarity=0.316  Sum_probs=20.5

Q ss_pred             CCCCCCCccHHHHHHHHHH--hCCHHHHH
Q 035374           34 NIPGVEGIGDVRAVQLITK--FGMLVFNV   60 (66)
Q Consensus        34 ~i~gi~GiG~K~A~~Ll~~--fgsl~~i~   60 (66)
                      .+..+||||+++|.++++.  |.|++++.
T Consensus        18 eL~~lpgig~~~A~~Iv~~R~f~s~edL~   46 (65)
T d2duya1          18 ELMALPGIGPVLARRIVEGRPYARVEDLL   46 (65)
T ss_dssp             HHTTSTTCCHHHHHHHHHTCCCSSGGGGG
T ss_pred             HHHHCCCCCHHHHHHHHHcCCCCCHHHHH
Confidence            3456799999999999974  66666654

>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=94.27  E-value=0.0025  Score=34.03  Aligned_cols=32  Identities=25%  Similarity=0.334  Sum_probs=24.0

Q ss_pred             HHHhhCCCCCCCCCCCCccHHHHHHHHHHhCC
Q 035374           24 VISLVGDKADNIPGVEGIGDVRAVQLITKFGM   55 (66)
Q Consensus        24 ~~~L~Gd~~D~i~gi~GiG~K~A~~Ll~~fgs   55 (66)
                      +..++.-+.+.+..|+|||+++|..+.+-|.+
T Consensus        36 ~~~l~~As~eeL~~v~GIG~~~A~~I~~~~~~   67 (70)
T d2bgwa1          36 LERFFTASKAEISKVEGIGEKRAEEIKKILMT   67 (70)
T ss_dssp             HHHHTTCCHHHHHHSTTCCHHHHHHHHHHHHS
T ss_pred             HHHHHHcCHHHHHcCCCCCHHHHHHHHHHHhC
Confidence            44555545566778999999999999887643

>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=94.13  E-value=0.021  Score=36.02  Aligned_cols=35  Identities=17%  Similarity=0.296  Sum_probs=23.5

Q ss_pred             HHHHHHhCCCChhHHHHHHHhhCCCCCCCCCCCCccHHHHHHHHHH
Q 035374            7 EDFARKYGELKPSQFVDVISLVGDKADNIPGVEGIGDVRAVQLITK   52 (66)
Q Consensus         7 ~~v~~~~g~i~p~q~~d~~~L~Gd~~D~i~gi~GiG~K~A~~Ll~~   52 (66)
                      +.+.++|+|..|+..-+           +..+||||+|||..+|.-
T Consensus        98 ~~i~~~~~g~~p~~~~~-----------L~~LpGVG~kTA~~il~~  132 (217)
T d1keaa_          98 RVVINDYGGRVPRNRKA-----------ILDLPGVGKYTCAAVMCL  132 (217)
T ss_dssp             HHHHHHHTTSCCSCHHH-----------HHTSTTCCHHHHHHHHHH
T ss_pred             HHHHhhccCCcchhhHH-----------HHHHHhhhhhhhHHHHHH
Confidence            34556666555554332           345699999999998875

>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=93.89  E-value=0.028  Score=35.27  Aligned_cols=35  Identities=11%  Similarity=0.158  Sum_probs=24.5

Q ss_pred             HHHHHHhCCCChhHHHHHHHhhCCCCCCCCCCCCccHHHHHHHHHH
Q 035374            7 EDFARKYGELKPSQFVDVISLVGDKADNIPGVEGIGDVRAVQLITK   52 (66)
Q Consensus         7 ~~v~~~~g~i~p~q~~d~~~L~Gd~~D~i~gi~GiG~K~A~~Ll~~   52 (66)
                      +.+.++|+|..|+..-++.           ++||||++||..++.-
T Consensus        94 ~~i~~~~~g~~p~~~~~L~-----------~LpGVG~~TA~~Il~~  128 (211)
T d2abka_          94 RILLEQHNGEVPEDRAALE-----------ALPGVGRKTANVVLNT  128 (211)
T ss_dssp             HHHHHHTTTSCCSCHHHHH-----------HSTTCCHHHHHHHHHH
T ss_pred             HHHHHHhcCchhHHHHHHH-----------HHHhhchHHHHHHHHH
Confidence            3456677766666655443           4699999999888763

>d2p6ra2 a.289.1.2 (A:489-686) Hel308 helicase {Archaeoglobus fulgidus [TaxId: 2234]}

class: All alpha proteins
fold: Sec63 N-terminal domain-like
superfamily: Sec63 N-terminal domain-like
family: Achaeal helicase C-terminal domain
domain: Hel308 helicase
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=93.87  E-value=0.016  Score=36.58  Aligned_cols=28  Identities=25%  Similarity=0.118  Sum_probs=23.0

Q ss_pred             CCCCCccHHHHHHHHHH-hCCHHHHHhhh
Q 035374           36 PGVEGIGDVRAVQLITK-FGMLVFNVECF   63 (66)
Q Consensus        36 ~gi~GiG~K~A~~Ll~~-fgsl~~i~~~~   63 (66)
                      -.|||||++||.+|.+. +.|++++.++.
T Consensus       147 ~~i~gvgr~rAr~L~~~Gi~t~~dl~~a~  175 (198)
T d2p6ra2         147 VRIRHIGRVRARKLYNAGIRNAEDIVRHR  175 (198)
T ss_dssp             HTSTTCCHHHHHHHHTTTCCSHHHHHHTH
T ss_pred             hcCCCCCHHHHHHHHHcCCCCHHHHHHcc
Confidence            36899999999999976 56899887654

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

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

Probab=93.57  E-value=0.01  Score=32.14  Aligned_cols=40  Identities=15%  Similarity=0.372  Sum_probs=28.0

Q ss_pred             HHHHHHhCCCChhHHHHHHHhhCCCCCCCCCCCCccHHHHHHHHHHhC
Q 035374            7 EDFARKYGELKPSQFVDVISLVGDKADNIPGVEGIGDVRAVQLITKFG   54 (66)
Q Consensus         7 ~~v~~~~g~i~p~q~~d~~~L~Gd~~D~i~gi~GiG~K~A~~Ll~~fg   54 (66)
                      ..+.++|+  +.+      .+.--+.+.+..|||||++.|..+.+-|.
T Consensus        33 ~~L~~~F~--s~~------~i~~A~~eeL~~i~GiG~~~A~~i~~~f~   72 (78)
T d2a1jb1          33 QTLLTTFG--SLE------QLIAASREDLALCPGLGPQKARRLFDVLH   72 (78)
T ss_dssp             HHHHHHHS--SHH------HHHSCCHHHHHTSSSCCSHHHHHHHHHHH
T ss_pred             HHHHHHhC--CcH------HHHhhhHHHHHHhhhhhHHHHHHHHHHHc
Confidence            45556665  333      34344456778899999999999988774

>d2csba4 a.60.2.4 (A:465-519) Topoisomerase V {Methanopyrus kandleri [TaxId: 2320]}

class: All alpha proteins
fold: SAM domain-like
superfamily: RuvA domain 2-like
family: Topoisomerase V repeat domain
domain: Topoisomerase V
species: Methanopyrus kandleri [TaxId: 2320]

Probab=93.18  E-value=0.055  Score=27.48  Aligned_cols=25  Identities=32%  Similarity=0.434  Sum_probs=22.3

Q ss_pred             CCCCccHHHHHHHHHHhCCHHHHHh
Q 035374           37 GVEGIGDVRAVQLITKFGMLVFNVE   61 (66)
Q Consensus        37 gi~GiG~K~A~~Ll~~fgsl~~i~~   61 (66)
                      +|.||-..+|..||++||...++.+
T Consensus         8 sirgidreraerllkkyggyskvre   32 (55)
T d2csba4           8 SIRGIDRERAERLLKKYGGYSKVRE   32 (55)
T ss_dssp             TSTTCCHHHHHHHHHHHTSHHHHHT
T ss_pred             eeecccHHHHHHHHHHhcChhHHHH
Confidence            5799999999999999999887764

>d1dgsa1 a.60.2.2 (A:401-581) NAD+-dependent DNA ligase, domain 3 {Thermus filiformis [TaxId: 276]}

class: All alpha proteins
fold: SAM domain-like
superfamily: RuvA domain 2-like
family: NAD+-dependent DNA ligase, domain 3
domain: NAD+-dependent DNA ligase, domain 3
species: Thermus filiformis [TaxId: 276]

Probab=93.09  E-value=0.0073  Score=37.51  Aligned_cols=41  Identities=15%  Similarity=0.181  Sum_probs=29.8

Q ss_pred             HHHHhhCCCCCCCCCCCCccHHHHHHHHHHhCCHH--HHHhhh
Q 035374           23 DVISLVGDKADNIPGVEGIGDVRAVQLITKFGMLV--FNVECF   63 (66)
Q Consensus        23 d~~~L~Gd~~D~i~gi~GiG~K~A~~Ll~~fgsl~--~i~~~~   63 (66)
                      ++..|.--+.+.+..|+||||++|..+..-|.+.+  ++++.+
T Consensus       129 sl~~l~~as~eeL~~I~GIG~~~A~si~~ff~~~~n~~~i~~L  171 (181)
T d1dgsa1         129 TMDRLLEASLEELIEVEEVGELTARAILETLKDPAFRDLVRRL  171 (181)
T ss_dssp             BHHHHTTCCHHHHHTSTTCCHHHHHHHHHHHHCHHHHHHHHHH
T ss_pred             hhhhhhhhHHHHHhhcCCcCHHHHHHHHHHHCCHHHHHHHHHH
Confidence            34445555556677899999999999999998765  344443

>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=92.81  E-value=0.04  Score=34.43  Aligned_cols=18  Identities=17%  Similarity=0.337  Sum_probs=15.0

Q ss_pred             CCCCCCccHHHHHHHHHH
Q 035374           35 IPGVEGIGDVRAVQLITK   52 (66)
Q Consensus        35 i~gi~GiG~K~A~~Ll~~   52 (66)
                      +-.+||||+|||..++.-
T Consensus       112 L~~LpGVG~kTA~~il~~  129 (214)
T d1orna_         112 LMKLPGVGRKTANVVVSV  129 (214)
T ss_dssp             HTTSTTCCHHHHHHHHHH
T ss_pred             HHhCcCcccchHHHHHHH
Confidence            556899999999988754

>d2i5ha1 e.71.1.1 (A:16-195) Hypothetical protein AF1531 {Archaeoglobus fulgidus [TaxId: 2234]}

class: Multi-domain proteins (alpha and beta)
fold: AF1531-like
superfamily: AF1531-like
family: AF1531-like
domain: Hypothetical protein AF1531
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=92.53  E-value=0.047  Score=34.30  Aligned_cols=46  Identities=13%  Similarity=0.212  Sum_probs=32.8

Q ss_pred             CChhHHHHHHHhhCCCCCC---CCCCCCccHHHHHHHHHH-----hCCHHHHHh
Q 035374           16 LKPSQFVDVISLVGDKADN---IPGVEGIGDVRAVQLITK-----FGMLVFNVE   61 (66)
Q Consensus        16 i~p~q~~d~~~L~Gd~~D~---i~gi~GiG~K~A~~Ll~~-----fgsl~~i~~   61 (66)
                      -+++.|++|---+|--+-.   +.=+||||+|+|++++.+     |.|.+++-+
T Consensus        95 ~ne~~FV~FfN~A~pit~klH~leLLPGIGkk~~~~iveeR~~~~f~sf~dl~~  148 (180)
T d2i5ha1          95 QDEKKYVDFFNKADSITTRMHQLELLPGVGKKMMWAIIEERKKRPFESFEDIAQ  148 (180)
T ss_dssp             TTHHHHHHHHC--CCBCSSSBGGGGSTTCCHHHHHHHHHHHHHSCCCSHHHHHH
T ss_pred             hChhhheeeeecCCccchhhHHHHhcccccHHHHHHHHHHHccCCCCCHHHHHH
Confidence            4678899988888833322   234799999999999975     788887753

>d1szpa1 a.60.4.1 (A:81-144) DNA repair protein Rad51, N-terminal domain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All alpha proteins
fold: SAM domain-like
superfamily: Rad51 N-terminal domain-like
family: DNA repair protein Rad51, N-terminal domain
domain: DNA repair protein Rad51, N-terminal domain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=92.12  E-value=0.051  Score=28.55  Aligned_cols=24  Identities=17%  Similarity=0.029  Sum_probs=21.3

Q ss_pred             CCCccHHHHHHHHHH-hCCHHHHHh
Q 035374           38 VEGIGDVRAVQLITK-FGMLVFNVE   61 (66)
Q Consensus        38 i~GiG~K~A~~Ll~~-fgsl~~i~~   61 (66)
                      ++||||+++.+|-.. |.|++++..
T Consensus         8 ~~Gig~~~~~kL~~aG~~Tve~ia~   32 (64)
T d1szpa1           8 VNGITMADVKKLRESGLHTAEAVAY   32 (64)
T ss_dssp             CTTCCHHHHHHHHTTSCCSHHHHHH
T ss_pred             HCCCCHHHHHHHHHcCCCcHHHHHh
Confidence            589999999999988 889999874

>d1gm5a2 b.40.4.9 (A:106-285) RecG "wedge" domain {Thermotoga maritima [TaxId: 2336]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: RecG "wedge" domain
domain: RecG "wedge" domain
species: Thermotoga maritima [TaxId: 2336]

Probab=91.04  E-value=0.069  Score=31.98  Aligned_cols=27  Identities=30%  Similarity=0.374  Sum_probs=19.1

Q ss_pred             CCCCCCCCccHHHHHHHHHHhC--CHHHHH
Q 035374           33 DNIPGVEGIGDVRAVQLITKFG--MLVFNV   60 (66)
Q Consensus        33 D~i~gi~GiG~K~A~~Ll~~fg--sl~~i~   60 (66)
                      +.+..++|||||+|..|= +.|  ++.+++
T Consensus        10 ~~i~~lkGvGpk~~~~L~-klgI~ti~DLL   38 (180)
T d1gm5a2          10 TDIQYAKGVGPNRKKKLK-KLGIETLRDLL   38 (180)
T ss_dssp             CCSSSSSSCCHHHHHHHH-TTTCCSSGGGT
T ss_pred             CChhhcCCcCHHHHHHHH-HhCCCcHHHHH
Confidence            467788999999998874 443  444444

>d1vdda_ e.49.1.1 (A:) Recombination protein RecR {Deinococcus radiodurans [TaxId: 1299]}

class: Multi-domain proteins (alpha and beta)
fold: Recombination protein RecR
superfamily: Recombination protein RecR
family: Recombination protein RecR
domain: Recombination protein RecR
species: Deinococcus radiodurans [TaxId: 1299]

Probab=90.77  E-value=0.048  Score=34.54  Aligned_cols=18  Identities=28%  Similarity=0.410  Sum_probs=14.5

Q ss_pred             CCCCCCccHHHHHHHHHH
Q 035374           35 IPGVEGIGDVRAVQLITK   52 (66)
Q Consensus        35 i~gi~GiG~K~A~~Ll~~   52 (66)
                      +..+||||+|+|.++.-.
T Consensus        14 l~kLPGIG~KsA~Rla~~   31 (199)
T d1vdda_          14 LSRLPGIGPKSAQRLAFH   31 (199)
T ss_dssp             HHTSTTCCHHHHHHHHHH
T ss_pred             HHHCCCCCHHHHHHHHHH
Confidence            445799999999998654

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

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

Probab=90.60  E-value=0.059  Score=29.87  Aligned_cols=20  Identities=10%  Similarity=0.317  Sum_probs=16.5

Q ss_pred             CCCCCCCCccHHHHHHHHHH
Q 035374           33 DNIPGVEGIGDVRAVQLITK   52 (66)
Q Consensus        33 D~i~gi~GiG~K~A~~Ll~~   52 (66)
                      +-+..+|||||++|.++++.
T Consensus        35 ~~L~~lpGig~~~A~~Iv~~   54 (90)
T d3bzka1          35 ALLARISGLNSTLAQNIVAH   54 (90)
T ss_dssp             HHHTTSTTCCHHHHHHHHHH
T ss_pred             HHHhHCCCCCHHHHHHHHHH
Confidence            34677899999999999863

>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=90.44  E-value=0.11  Score=32.52  Aligned_cols=18  Identities=17%  Similarity=0.444  Sum_probs=14.9

Q ss_pred             CCCCCCccHHHHHHHHHH
Q 035374           35 IPGVEGIGDVRAVQLITK   52 (66)
Q Consensus        35 i~gi~GiG~K~A~~Ll~~   52 (66)
                      +-.+||||+|||..+|.-
T Consensus       111 L~~LpGVG~kTA~~il~~  128 (224)
T d1kg2a_         111 VAALPGVGRSTAGAILSL  128 (224)
T ss_dssp             HHTSTTCCHHHHHHHHHH
T ss_pred             HHHHHhhhhhhhHHHHHH
Confidence            456799999999988864

>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=90.08  E-value=0.074  Score=33.25  Aligned_cols=18  Identities=11%  Similarity=0.340  Sum_probs=15.0

Q ss_pred             CCCCCCccHHHHHHHHHH
Q 035374           35 IPGVEGIGDVRAVQLITK   52 (66)
Q Consensus        35 i~gi~GiG~K~A~~Ll~~   52 (66)
                      +-.+||||+|||..+|.-
T Consensus       109 Ll~LpGIG~kTA~~il~~  126 (221)
T d1rrqa1         109 FSRLKGVGPYTVGAVLSL  126 (221)
T ss_dssp             HHTSTTCCHHHHHHHHHH
T ss_pred             HHHHHHhhhHHHHHHHHH
Confidence            447899999999988854

>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=89.99  E-value=0.047  Score=28.14  Aligned_cols=29  Identities=17%  Similarity=0.343  Sum_probs=21.2

Q ss_pred             HhhCCCCCCCCCCCCccHHHHHHHHHHhC
Q 035374           26 SLVGDKADNIPGVEGIGDVRAVQLITKFG   54 (66)
Q Consensus        26 ~L~Gd~~D~i~gi~GiG~K~A~~Ll~~fg   54 (66)
                      .+.--+.+.+..|||||+++|.++++.+.
T Consensus        25 ~l~~a~~eeL~~i~Gi~~~~A~~i~~~ar   53 (60)
T d2i1qa1          25 KIATATVGELTDIEGISEKAAAKMIMGAR   53 (60)
T ss_dssp             HHHTCCHHHHHTSTTCCHHHHHHHHHHHH
T ss_pred             HHHhCCHHHHHHCCCCCHHHHHHHHHHHH
Confidence            33343345567789999999999988754

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

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

Probab=89.42  E-value=0.26  Score=27.27  Aligned_cols=33  Identities=21%  Similarity=0.340  Sum_probs=18.6

Q ss_pred             HHHHHHHhhC--CCCCCCCCCCCccHHHHHHHHHH
Q 035374           20 QFVDVISLVG--DKADNIPGVEGIGDVRAVQLITK   52 (66)
Q Consensus        20 q~~d~~~L~G--d~~D~i~gi~GiG~K~A~~Ll~~   52 (66)
                      .++.+.-..|  .+.+.+..|+|||+++..++.+.
T Consensus        48 ~II~yR~~~G~f~sledL~~V~Gi~~k~~eki~k~   82 (91)
T d2edua1          48 LIVGWRELHGPFSQVEDLERVEGITGKQMESFLKA   82 (91)
T ss_dssp             HHHHHHHHHCCCSSGGGGGGSTTCCHHHHHHHHHH
T ss_pred             HHHHHHHHcCCCCCHHHHhcCCCCCHHHHHHHHHc
Confidence            4555555555  33444556666666666666654

>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=88.60  E-value=0.1  Score=31.66  Aligned_cols=23  Identities=13%  Similarity=0.050  Sum_probs=17.0

Q ss_pred             CCCCCCccHHHHHHHHH-HhCCHH
Q 035374           35 IPGVEGIGDVRAVQLIT-KFGMLV   57 (66)
Q Consensus        35 i~gi~GiG~K~A~~Ll~-~fgsl~   57 (66)
                      +-.+|||||+||.-++- .++..+
T Consensus       105 L~~l~GIG~wTA~~il~~~~~~~d  128 (190)
T d2noha1         105 LCILPGVGTQVADCICLMALDKPQ  128 (190)
T ss_dssp             HTTSTTCCHHHHHHHHHHHSCCTT
T ss_pred             HHHcCCchHHHHHHHHHHHcCCCC
Confidence            55789999999998654 455543

>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=88.10  E-value=0.12  Score=32.49  Aligned_cols=18  Identities=22%  Similarity=0.339  Sum_probs=15.0

Q ss_pred             CCCCCCccHHHHHHHHHH
Q 035374           35 IPGVEGIGDVRAVQLITK   52 (66)
Q Consensus        35 i~gi~GiG~K~A~~Ll~~   52 (66)
                      +-.+||||+|||.-++.-
T Consensus       122 L~~lpGIG~kTA~~vl~~  139 (217)
T d1pu6a_         122 LLDQKGIGKESADAILCY  139 (217)
T ss_dssp             HHTSTTCCHHHHHHHHHH
T ss_pred             HHHHhhhhhHHHHHHHHH
Confidence            557899999999988754

>d1jmsa1 a.60.6.1 (A:148-242) Terminal deoxynucleotidyl transferase {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: SAM domain-like
superfamily: DNA polymerase beta, N-terminal domain-like
family: DNA polymerase beta, N-terminal domain-like
domain: Terminal deoxynucleotidyl transferase
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=87.96  E-value=0.12  Score=28.68  Aligned_cols=18  Identities=17%  Similarity=0.298  Sum_probs=14.7

Q ss_pred             CCCCCCCCccHHHHHHHH
Q 035374           33 DNIPGVEGIGDVRAVQLI   50 (66)
Q Consensus        33 D~i~gi~GiG~K~A~~Ll   50 (66)
                      +.+.+|||||++.|.++-
T Consensus        62 ~~l~~i~GIGk~i~~kI~   79 (95)
T d1jmsa1          62 KDTEGIPCLGDKVKSIIE   79 (95)
T ss_dssp             GGGTTCSSCCHHHHHHHH
T ss_pred             HHHHhccchhHHHHHHHH
Confidence            567889999999987653

>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=86.73  E-value=0.16  Score=26.83  Aligned_cols=17  Identities=29%  Similarity=0.448  Sum_probs=13.7

Q ss_pred             CCCCCCCccHHHHHHHH
Q 035374           34 NIPGVEGIGDVRAVQLI   50 (66)
Q Consensus        34 ~i~gi~GiG~K~A~~Ll   50 (66)
                      .+.++||||++.|.++-
T Consensus        47 ~l~~lpGiG~~i~~kI~   63 (76)
T d2bcqa1          47 EACSIPGIGKRMAEKII   63 (76)
T ss_dssp             HHHTSTTCCHHHHHHHH
T ss_pred             HHhcCCCccHHHHHHHH
Confidence            35678999999988764

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

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

Probab=86.47  E-value=0.19  Score=27.87  Aligned_cols=28  Identities=14%  Similarity=0.216  Sum_probs=20.8

Q ss_pred             CCCCCCCCccHHHHHHHHH------HhCCHHHHH
Q 035374           33 DNIPGVEGIGDVRAVQLIT------KFGMLVFNV   60 (66)
Q Consensus        33 D~i~gi~GiG~K~A~~Ll~------~fgsl~~i~   60 (66)
                      +-+..+||||+++|.++++      .|.+++++.
T Consensus        33 ~eL~~lpgig~~~A~~II~yR~~~G~f~sledL~   66 (91)
T d2edua1          33 RDLRSLQRIGPKKAQLIVGWRELHGPFSQVEDLE   66 (91)
T ss_dssp             HHHHHSTTCCHHHHHHHHHHHHHHCCCSSGGGGG
T ss_pred             HHHhhCCCCCHHHHHHHHHHHHHcCCCCCHHHHh
Confidence            4455679999999999994      456666553

>d1szpa1 a.60.4.1 (A:81-144) DNA repair protein Rad51, N-terminal domain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All alpha proteins
fold: SAM domain-like
superfamily: Rad51 N-terminal domain-like
family: DNA repair protein Rad51, N-terminal domain
domain: DNA repair protein Rad51, N-terminal domain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=85.84  E-value=0.24  Score=25.75  Aligned_cols=22  Identities=18%  Similarity=0.478  Sum_probs=18.3

Q ss_pred             CCCCCCCCCCccHHHHHHHHHH
Q 035374           31 KADNIPGVEGIGDVRAVQLITK   52 (66)
Q Consensus        31 ~~D~i~gi~GiG~K~A~~Ll~~   52 (66)
                      +.+.+-.|+|+|+++|.++++.
T Consensus        34 t~~~L~~i~Gi~e~~a~KIi~~   55 (64)
T d1szpa1          34 PRKDLLEIKGISEAKADKLLNE   55 (64)
T ss_dssp             CSHHHHTSTTCCHHHHHHHHHH
T ss_pred             CHHHHHHcCCCCHHHHHHHHHH
Confidence            3456778899999999999986

>d2fmpa1 a.60.6.1 (A:10-91) DNA polymerase beta, N-terminal (8 kD)-domain {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: SAM domain-like
superfamily: DNA polymerase beta, N-terminal domain-like
family: DNA polymerase beta, N-terminal domain-like
domain: DNA polymerase beta, N-terminal (8 kD)-domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=84.65  E-value=0.23  Score=26.71  Aligned_cols=25  Identities=20%  Similarity=0.190  Sum_probs=17.0

Q ss_pred             CCCCCCCccHHHHHHHHH--HhCCHHH
Q 035374           34 NIPGVEGIGDVRAVQLIT--KFGMLVF   58 (66)
Q Consensus        34 ~i~gi~GiG~K~A~~Ll~--~fgsl~~   58 (66)
                      .+.+|||||++.|.++-.  +-|++..
T Consensus        49 ~l~~i~GIGk~ia~kI~E~~~TG~~~~   75 (82)
T d2fmpa1          49 EAKKLPGVGTKIAEKIDEFLATGKLRK   75 (82)
T ss_dssp             HHHTSTTCCHHHHHHHHHHHHHSSCHH
T ss_pred             HHhcCCCccHHHHHHHHHHHHhCChHH
Confidence            456889999999987633  2255443

>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=84.24  E-value=0.25  Score=29.93  Aligned_cols=22  Identities=18%  Similarity=0.228  Sum_probs=15.9

Q ss_pred             CCCCCCCccHHHHHHHHH-HhCC
Q 035374           34 NIPGVEGIGDVRAVQLIT-KFGM   55 (66)
Q Consensus        34 ~i~gi~GiG~K~A~~Ll~-~fgs   55 (66)
                      .+-.+|||||+||.-++- .++.
T Consensus       109 ~L~~l~GIGpwTAd~illf~lg~  131 (183)
T d1mpga1         109 TLQTFPGIGRWTANYFALRGWQA  131 (183)
T ss_dssp             HHTTSTTCCHHHHHHHHHHHSCC
T ss_pred             HHHHhhcccHHHHHHHHHhhCCC
Confidence            356789999999998553 3443

>d1jiha2 e.8.1.7 (A:1-389) DNA polymerase eta {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Multi-domain proteins (alpha and beta)
fold: DNA/RNA polymerases
superfamily: DNA/RNA polymerases
family: Lesion bypass DNA polymerase (Y-family), catalytic domain
domain: DNA polymerase eta
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=83.85  E-value=0.31  Score=32.98  Aligned_cols=21  Identities=24%  Similarity=0.314  Sum_probs=18.3

Q ss_pred             CCCCCCCccHHHHHHHHHHhC
Q 035374           34 NIPGVEGIGDVRAVQLITKFG   54 (66)
Q Consensus        34 ~i~gi~GiG~K~A~~Ll~~fg   54 (66)
                      .+..|||||.|++.+|.+.++
T Consensus       301 pi~ki~GIG~k~~kkL~~~lg  321 (389)
T d1jiha2         301 EITSFWTLGGVLGKELIDVLD  321 (389)
T ss_dssp             CGGGSGGGSSHHHHHHHHHTT
T ss_pred             ChhhcCCCCHHHHHHHHHHhC
Confidence            467889999999999998874

>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=83.83  E-value=0.32  Score=28.54  Aligned_cols=24  Identities=13%  Similarity=0.055  Sum_probs=18.8

Q ss_pred             hhCCCCCCCCCCCCccHHHHHHHH
Q 035374           27 LVGDKADNIPGVEGIGDVRAVQLI   50 (66)
Q Consensus        27 L~Gd~~D~i~gi~GiG~K~A~~Ll   50 (66)
                      ++-+..+.+-.+||||+++|..++
T Consensus        87 ~ip~~~~~l~~LpGVG~~tad~~~  110 (144)
T d1ngna_          87 YLTKQWRYPIELHGIGKYGNDSYR  110 (144)
T ss_dssp             HHHSCCSSGGGSTTCCHHHHHHHH
T ss_pred             HhhhhhhhHHhcCCccHHHHHHHH
Confidence            445567888899999999987653

>d1im4a_ e.8.1.7 (A:) DinB homolog (DBH) {Archaeon Sulfolobus solfataricus [TaxId: 2287]}

class: Multi-domain proteins (alpha and beta)
fold: DNA/RNA polymerases
superfamily: DNA/RNA polymerases
family: Lesion bypass DNA polymerase (Y-family), catalytic domain
domain: DinB homolog (DBH)
species: Archaeon Sulfolobus solfataricus [TaxId: 2287]

Probab=82.98  E-value=0.6  Score=28.66  Aligned_cols=33  Identities=30%  Similarity=0.596  Sum_probs=22.0

Q ss_pred             CChhHHHHHHHhhCCCCCCCCCCCCccHHHHHHHHHHhC
Q 035374           16 LKPSQFVDVISLVGDKADNIPGVEGIGDVRAVQLITKFG   54 (66)
Q Consensus        16 i~p~q~~d~~~L~Gd~~D~i~gi~GiG~K~A~~Ll~~fg   54 (66)
                      ++|+...++..-     -.+..+||||++++.+| +++|
T Consensus       171 i~~~~~~~~L~~-----lpi~~i~GIG~~~~~~L-~~~G  203 (209)
T d1im4a_         171 IRPTEVQDFLNE-----LDIDEIPGIGSVLARRL-NELG  203 (209)
T ss_dssp             CCGGGHHHHHHT-----CBGGGSTTCCHHHHHHH-HHTT
T ss_pred             ECHHHHHHHHhC-----CCceeeCCchHHHHHHH-HHcC
Confidence            556665554332     24667899999999887 5554