Citrus Sinensis ID: 033363

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-
Protein Sequence
MAQIYSIRLKEIAILLKAGRVISDLFTLCPDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQEYLGESWTHVTQLHGVGKYAADAFAIFCTGKWDRVRPTDHMLNYYWEFLVSTKGNL
Secondary Structure (PSIPRED)
ccHHHHHHHHHHHHHHHHHHHHHHHHHHcccHHHHHcccHHHHHHHHHcccccHHHHHHHHHHHHHHHcccccccccccccccccccHHEEEEEccccccccccHHHHHHHHHHHHHcccc
Secondary Structure Prediction (SSPRO)
ccEEEEEEHHHHHHHHHHHHHHHHHHHHcccHHHHHHccHHHHHHHcHHHccHHHHHHHHHHHHHHHHHcccccHHHcccccHHHHHHHHHHccccHHHcccccHHHHHHHHHHHHHcccc
Coil and Loop (DISEMBL)
MAQIYSIRLKEIAILLKAGRVISDLftlcpdaktateVDAEEIEKIISTLGLQKKRAPMIKRFSQEYLGESWTHVTQLHGVGKYAADAFAIFCtgkwdrvrptdhMLNYYWEFLVSTKGNL
Flexible Loop (DISEMBL)
MAQIYSIRLKEIAILLKAGRVISDLFTLCPDAktatevdaeEIEKIIstlglqkkraPMIKRFSQEYLGESWTHVTQLHGVGKYAADAFAIFCTGKWDRVRPTDHMLNYYWEFLVSTKGNL
Low Complexity Region (SEG)
MAQIYSIRLKEIAILLKAGRVISDLFTLCPDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQEYLGESWTHVTQLHGVGKYAADAFAIFCTGKWDRVRPTDHMLNYYWEFLVSTKGNL
Disordered region (IsUnstruct)
***IYSIRLKEIAILLKAGRVISDLFTLCPDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQEYLGESWTHVTQLHGVGKYAADAFAIFCTGKWDRVRPTDHMLNYYWEFLVS*****
Disordered Region (DISOPRED)
**QIYSIRLKEIAILLKAGRVISDLFTLCPDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQEYLGESWTHVTQLHGVGKYAADAFAIFCTGKWDRVRPTDHMLNYYWEFLVSTK***
Disordered Region (DISEMBL)
MAQIYSIRLKEIAILLKAGRVISDLFTLCPDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQEYLGESWTHVTQLHGVGKYAADAFAIFCTGKWDRVRPTDHMLNYYWEFLVSTKGNL
Disordered Region (DISPRO)
MAQIYSIRLKEIAILLKAGRVISDLFTLCPDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQEYLGESWTHVTQLHGVGKYAADAFAIFCTGKWDRVRPTDHMLNYYWEFLVSTK***
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MAQIYSIRLKEIAILLKAGRVISDLFTLCPDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQEYLGESWTHVTQLHGVGKYAADAFAIFCTGKWDRVRPTDHMLNYYWEFLVSTKGNL
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	121	2.2.26 [Sep-21-2011]
Q9Z2D7	554	Methyl-CpG-binding domain	yes	no	0.702	0.153	0.411	5e-16
O95243	580	Methyl-CpG-binding domain	yes	no	0.702	0.146	0.411	1e-15

>sp|Q9Z2D7|MBD4_MOUSE Methyl-CpG-binding domain protein 4 OS=Mus musculus GN=Mbd4 PE=1 SV=1

 Score = 83.2 bits (204), Expect = 5e-16,   Method: Composition-based stats.
 Identities = 35/85 (41%), Positives = 52/85 (61%)

Query: 30  PDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQEYLGESWTHVTQLHGVGKYAADAF 89
           P A+ A   D  ++ +++  LGL   RA  I +FS EYL + W +  +LHG+GKY  D++
Sbjct: 460 PSAEVARAADWRDVSELLKPLGLYDLRAKTIIKFSDEYLTKQWRYPIELHGIGKYGNDSY 519

Query: 90  AIFCTGKWDRVRPTDHMLNYYWEFL 114
            IFC  +W +V P DH LN Y ++L
Sbjct: 520 RIFCVNEWKQVHPEDHKLNKYHDWL 544

Mismatch-specific DNA N-glycosylase involved in DNA repair. Has thymine glycosylase activity and is specific for G:T mismatches within methylated and unmethylated CpG sites. Can also remove uracil or 5-fluorouracil in G:U mismatches. Has no lyase activity. Was first identified as methyl-CpG-binding protein.
Mus musculus (taxid: 10090)
EC: 3EC: .EC: 2EC: .EC: 2EC: .EC: -

>sp|O95243|MBD4_HUMAN Methyl-CpG-binding domain protein 4 OS=Homo sapiens GN=MBD4 PE=1 SV=1

 Score = 81.6 bits (200), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 35/85 (41%), Positives = 52/85 (61%)

Query: 30  PDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQEYLGESWTHVTQLHGVGKYAADAF 89
           P A+ A   D  ++ +++  LGL   RA  I +FS EYL + W +  +LHG+GKY  D++
Sbjct: 486 PSAEVARTADWRDVSELLKPLGLYDLRAKTIVKFSDEYLTKQWKYPIELHGIGKYGNDSY 545

Query: 90  AIFCTGKWDRVRPTDHMLNYYWEFL 114
            IFC  +W +V P DH LN Y ++L
Sbjct: 546 RIFCVNEWKQVHPEDHKLNKYHDWL 570

Mismatch-specific DNA N-glycosylase involved in DNA repair. Has thymine glycosylase activity and is specific for G:T mismatches within methylated and unmethylated CpG sites. Can also remove uracil or 5-fluorouracil in G:U mismatches. Has no lyase activity. Was first identified as methyl-CpG-binding protein.

Homo sapiens (taxid: 9606)

EC: 3

EC: .

EC: 2

EC: .

EC: 2

EC: .

EC: -

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	121
255546672	608	conserved hypothetical protein [Ricinus	0.776	0.154	0.819	9e-42
297829352	435	hypothetical protein ARALYDRAFT_896965 [	0.776	0.216	0.797	5e-41
356551311	1505	PREDICTED: uncharacterized protein LOC10	0.842	0.067	0.725	7e-40
296085641	599	unnamed protein product [Vitis vinifera]	0.818	0.165	0.747	1e-39
224118080	107	predicted protein [Populus trichocarpa]	0.876	0.990	0.698	1e-39
147837937	635	hypothetical protein VITISV_044254 [Viti	0.842	0.160	0.737	2e-39
225469167	536	PREDICTED: uncharacterized protein LOC10	0.818	0.184	0.747	2e-39
42572315	445	methyl-CpG-binding domain protein 4 [Ara	0.776	0.211	0.776	3e-39
6648205	419	hypothetical protein [Arabidopsis thalia	0.776	0.224	0.776	3e-39
27754344	407	unknown protein [Arabidopsis thaliana]	0.776	0.230	0.776	4e-39

>gi|255546672|ref|XP_002514395.1| conserved hypothetical protein [Ricinus communis] gi|223546492|gb|EEF47991.1| conserved hypothetical protein [Ricinus communis]

 Score =  174 bits (440), Expect = 9e-42,   Method: Compositional matrix adjust.
 Identities = 77/94 (81%), Positives = 82/94 (87%)

Query: 21  VISDLFTLCPDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQEYLGESWTHVTQLHG 80
           VISD FTLCPDAK ATE   EEIEKII  LGLQKKRA MI+R SQEYL + WTHVTQLHG
Sbjct: 508 VISDFFTLCPDAKAATEAKTEEIEKIIVPLGLQKKRAVMIQRLSQEYLADDWTHVTQLHG 567

Query: 81  VGKYAADAFAIFCTGKWDRVRPTDHMLNYYWEFL 114
           VGKYAADA+AIFCTGKWD+VRP DHMLNYYW+FL
Sbjct: 568 VGKYAADAYAIFCTGKWDQVRPKDHMLNYYWDFL 601

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297829352|ref|XP_002882558.1| hypothetical protein ARALYDRAFT_896965 [Arabidopsis lyrata subsp. lyrata] gi|297328398|gb|EFH58817.1| hypothetical protein ARALYDRAFT_896965 [Arabidopsis lyrata subsp. lyrata]

 Score =  171 bits (433), Expect = 5e-41,   Method: Composition-based stats.
 Identities = 75/94 (79%), Positives = 81/94 (86%)

Query: 21  VISDLFTLCPDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQEYLGESWTHVTQLHG 80
           VI DLF LCPDAKTATEV+  EIE +I  LGLQKKRA MI+RFS EYL ESWTHVTQLHG
Sbjct: 336 VIEDLFALCPDAKTATEVEEREIESLIKPLGLQKKRARMIQRFSLEYLQESWTHVTQLHG 395

Query: 81  VGKYAADAFAIFCTGKWDRVRPTDHMLNYYWEFL 114
           +GKYAADA+AIFC G WDRV+P DHMLNYYWEFL
Sbjct: 396 IGKYAADAYAIFCNGNWDRVKPDDHMLNYYWEFL 429

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356551311|ref|XP_003544020.1| PREDICTED: uncharacterized protein LOC100793802 [Glycine max]

 Score =  167 bits (423), Expect = 7e-40,   Method: Composition-based stats.
 Identities = 74/102 (72%), Positives = 83/102 (81%)

Query: 20   RVISDLFTLCPDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQEYLGESWTHVTQLH 79
            +V+S+ F LCPDAK+ T+V  EEIEK I TLG Q KRA M++R S+EYL ESWTHVTQLH
Sbjct: 1404 KVVSNFFKLCPDAKSCTQVTREEIEKTIKTLGFQHKRAEMLQRLSEEYLDESWTHVTQLH 1463

Query: 80   GVGKYAADAFAIFCTGKWDRVRPTDHMLNYYWEFLVSTKGNL 121
            GVGKYAADA+AIF TG WDRV PTDHMLNYYWEFL S K  L
Sbjct: 1464 GVGKYAADAYAIFVTGMWDRVTPTDHMLNYYWEFLHSIKHEL 1505

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|296085641|emb|CBI29440.3| unnamed protein product [Vitis vinifera]

 Score =  166 bits (421), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 74/99 (74%), Positives = 85/99 (85%)

Query: 16  LKAGRVISDLFTLCPDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQEYLGESWTHV 75
           L+A RVISDLFTLCPDAKTAT+V  E IEK+I TLGLQKKRA MI+RFS+EYL +SWTHV
Sbjct: 489 LQASRVISDLFTLCPDAKTATDVPTEMIEKVIETLGLQKKRAAMIQRFSREYLDDSWTHV 548

Query: 76  TQLHGVGKYAADAFAIFCTGKWDRVRPTDHMLNYYWEFL 114
           TQLHG+GKYAADA+AIFC+G W  V P DHML  YW++L
Sbjct: 549 TQLHGIGKYAADAYAIFCSGDWGLVVPNDHMLVKYWKYL 587

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224118080|ref|XP_002317727.1| predicted protein [Populus trichocarpa] gi|222858400|gb|EEE95947.1| predicted protein [Populus trichocarpa]

 Score =  166 bits (421), Expect = 1e-39,   Method: Compositional matrix adjust.
 Identities = 74/106 (69%), Positives = 89/106 (83%)

Query: 16  LKAGRVISDLFTLCPDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQEYLGESWTHV 75
           ++A RV++DLFTLCPDAK AT V  EEIE+ I +LGLQK+RA M++R S++YL E WTHV
Sbjct: 1   MQAERVVADLFTLCPDAKAATGVATEEIERAIKSLGLQKRRAKMVQRLSEDYLEEDWTHV 60

Query: 76  TQLHGVGKYAADAFAIFCTGKWDRVRPTDHMLNYYWEFLVSTKGNL 121
           TQL GVGKYAADA+AIFCTGKW++VRP DHMLN YWE+L STK  L
Sbjct: 61  TQLPGVGKYAADAYAIFCTGKWEQVRPNDHMLNRYWEYLCSTKNAL 106

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147837937|emb|CAN67143.1| hypothetical protein VITISV_044254 [Vitis vinifera]

 Score =  166 bits (419), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 76/103 (73%), Positives = 87/103 (84%), Gaps = 1/103 (0%)

Query: 12  IAILLKAGRVISDLFTLCPDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQEYLGES 71
           + ILL A RVISDLFTLCPDAKTAT+V  E IEK+I TLGLQKKRA MI+RFS+EYL +S
Sbjct: 522 VGILL-ASRVISDLFTLCPDAKTATDVPTEMIEKVIETLGLQKKRAAMIQRFSREYLDDS 580

Query: 72  WTHVTQLHGVGKYAADAFAIFCTGKWDRVRPTDHMLNYYWEFL 114
           WTHVTQLHG+GKYAADA+AIFC+G W  V P DHML  YW++L
Sbjct: 581 WTHVTQLHGIGKYAADAYAIFCSGDWGLVVPNDHMLVKYWKYL 623

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225469167|ref|XP_002271845.1| PREDICTED: uncharacterized protein LOC100244192 [Vitis vinifera]

 Score =  166 bits (419), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 74/99 (74%), Positives = 85/99 (85%)

Query: 16  LKAGRVISDLFTLCPDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQEYLGESWTHV 75
           L+A RVISDLFTLCPDAKTAT+V  E IEK+I TLGLQKKRA MI+RFS+EYL +SWTHV
Sbjct: 426 LQASRVISDLFTLCPDAKTATDVPTEMIEKVIETLGLQKKRAAMIQRFSREYLDDSWTHV 485

Query: 76  TQLHGVGKYAADAFAIFCTGKWDRVRPTDHMLNYYWEFL 114
           TQLHG+GKYAADA+AIFC+G W  V P DHML  YW++L
Sbjct: 486 TQLHGIGKYAADAYAIFCSGDWGLVVPNDHMLVKYWKYL 524

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|42572315|ref|NP_974253.1| methyl-CpG-binding domain protein 4 [Arabidopsis thaliana] gi|114050633|gb|ABI49466.1| At3g07930 [Arabidopsis thaliana] gi|332641100|gb|AEE74621.1| methyl-CpG-binding domain protein 4 [Arabidopsis thaliana]

 Score =  165 bits (418), Expect = 3e-39,   Method: Composition-based stats.
 Identities = 73/94 (77%), Positives = 79/94 (84%)

Query: 21  VISDLFTLCPDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQEYLGESWTHVTQLHG 80
           VISDLF LC DAKTATEV  EEIE +I  LGLQKKR  MI+R S EYL ESWTHVTQLHG
Sbjct: 346 VISDLFGLCTDAKTATEVKEEEIENLIKPLGLQKKRTKMIQRLSLEYLQESWTHVTQLHG 405

Query: 81  VGKYAADAFAIFCTGKWDRVRPTDHMLNYYWEFL 114
           VGKYAADA+AIFC G WDRV+P DHMLNYYW++L
Sbjct: 406 VGKYAADAYAIFCNGNWDRVKPNDHMLNYYWDYL 439

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|6648205|gb|AAF21203.1|AC013483_27 hypothetical protein [Arabidopsis thaliana]

 Score =  165 bits (418), Expect = 3e-39,   Method: Composition-based stats.
 Identities = 73/94 (77%), Positives = 79/94 (84%)

Query: 21  VISDLFTLCPDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQEYLGESWTHVTQLHG 80
           VISDLF LC DAKTATEV  EEIE +I  LGLQKKR  MI+R S EYL ESWTHVTQLHG
Sbjct: 320 VISDLFGLCTDAKTATEVKEEEIENLIKPLGLQKKRTKMIQRLSLEYLQESWTHVTQLHG 379

Query: 81  VGKYAADAFAIFCTGKWDRVRPTDHMLNYYWEFL 114
           VGKYAADA+AIFC G WDRV+P DHMLNYYW++L
Sbjct: 380 VGKYAADAYAIFCNGNWDRVKPNDHMLNYYWDYL 413

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|27754344|gb|AAO22623.1| unknown protein [Arabidopsis thaliana]

 Score =  165 bits (417), Expect = 4e-39,   Method: Composition-based stats.
 Identities = 73/94 (77%), Positives = 79/94 (84%)

Query: 21  VISDLFTLCPDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQEYLGESWTHVTQLHG 80
           VISDLF LC DAKTATEV  EEIE +I  LGLQKKR  MI+R S EYL ESWTHVTQLHG
Sbjct: 308 VISDLFGLCTDAKTATEVKEEEIENLIKPLGLQKKRTKMIQRLSLEYLQESWTHVTQLHG 367

Query: 81  VGKYAADAFAIFCTGKWDRVRPTDHMLNYYWEFL 114
           VGKYAADA+AIFC G WDRV+P DHMLNYYW++L
Sbjct: 368 VGKYAADAYAIFCNGNWDRVKPNDHMLNYYWDYL 401

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	121
TAIR|locus:2077357	445	AT3G07930 [Arabidopsis thalian	0.776	0.211	0.776	6.3e-37
UNIPROTKB|O95243	580	MBD4 "Methyl-CpG-binding domai	0.702	0.146	0.411	1.3e-16
UNIPROTKB|Q2MD36	262	MBD4 "Methyl-CpG-binding domai	0.702	0.324	0.411	2.3e-16
UNIPROTKB|E1BVB1	108	MBD4 "Uncharacterized protein"	0.702	0.787	0.411	7.7e-16
UNIPROTKB|F1P366	199	MBD4 "Uncharacterized protein"	0.702	0.427	0.411	7.7e-16
MGI|MGI:1333850	554	Mbd4 "methyl-CpG binding domai	0.702	0.153	0.411	2.4e-15
UNIPROTKB|E2RL50	570	MBD4 "Uncharacterized protein"	0.702	0.149	0.411	3.3e-15
UNIPROTKB|F1MUX1	554	MBD4 "Uncharacterized protein"	0.702	0.153	0.411	4e-15
UNIPROTKB|E9PEE4	572	MBD4 "Methyl-CpG-binding domai	0.611	0.129	0.405	3.3e-13
RGD|1585874	530	Mbd4 "methyl-CpG binding domai	0.537	0.122	0.461	1.3e-11

TAIR|locus:2077357 AT3G07930 [Arabidopsis thaliana (taxid:3702)]

 Score = 397 (144.8 bits), Expect = 6.3e-37, P = 6.3e-37
 Identities = 73/94 (77%), Positives = 79/94 (84%)

Query:    21 VISDLFTLCPDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQEYLGESWTHVTQLHG 80
             VISDLF LC DAKTATEV  EEIE +I  LGLQKKR  MI+R S EYL ESWTHVTQLHG
Sbjct:   346 VISDLFGLCTDAKTATEVKEEEIENLIKPLGLQKKRTKMIQRLSLEYLQESWTHVTQLHG 405

Query:    81 VGKYAADAFAIFCTGKWDRVRPTDHMLNYYWEFL 114
             VGKYAADA+AIFC G WDRV+P DHMLNYYW++L
Sbjct:   406 VGKYAADAYAIFCNGNWDRVKPNDHMLNYYWDYL 439

GO:0003824 "catalytic activity" evidence=IEA

GO:0005634 "nucleus" evidence=ISM

GO:0006281 "DNA repair" evidence=IEA

GO:0006284 "base-excision repair" evidence=IEA;ISS

GO:0006306 "DNA methylation" evidence=RCA

UNIPROTKB|O95243 MBD4 "Methyl-CpG-binding domain protein 4" [Homo sapiens (taxid:9606)]

 Score = 203 (76.5 bits), Expect = 1.3e-16, Sum P(2) = 1.3e-16
 Identities = 35/85 (41%), Positives = 52/85 (61%)

Query:    30 PDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQEYLGESWTHVTQLHGVGKYAADAF 89
             P A+ A   D  ++ +++  LGL   RA  I +FS EYL + W +  +LHG+GKY  D++
Sbjct:   486 PSAEVARTADWRDVSELLKPLGLYDLRAKTIVKFSDEYLTKQWKYPIELHGIGKYGNDSY 545

Query:    90 AIFCTGKWDRVRPTDHMLNYYWEFL 114
              IFC  +W +V P DH LN Y ++L
Sbjct:   546 RIFCVNEWKQVHPEDHKLNKYHDWL 570

GO:0000785 "chromatin" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0008630 "intrinsic apoptotic signaling pathway in response to DNA damage" evidence=IEA

GO:0009314 "response to radiation" evidence=IEA

GO:0031572 "G2 DNA damage checkpoint" evidence=IEA

GO:0004520 "endodeoxyribonuclease activity" evidence=TAS

GO:0008263 "pyrimidine-specific mismatch base pair DNA N-glycosylase activity" evidence=IDA

GO:0003696 "satellite DNA binding" evidence=TAS

GO:0005654 "nucleoplasm" evidence=TAS

GO:0006281 "DNA repair" evidence=TAS

GO:0006284 "base-excision repair" evidence=TAS

GO:0006285 "base-excision repair, AP site formation" evidence=TAS

GO:0045008 "depyrimidination" evidence=TAS

GO:0005515 "protein binding" evidence=IPI

GO:0005634 "nucleus" evidence=IDA

GO:0005730 "nucleolus" evidence=IDA

UNIPROTKB|Q2MD36 MBD4 "Methyl-CpG-binding domain protein 4" [Homo sapiens (taxid:9606)]

 Score = 203 (76.5 bits), Expect = 2.3e-16, P = 2.3e-16
 Identities = 35/85 (41%), Positives = 52/85 (61%)

Query:    30 PDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQEYLGESWTHVTQLHGVGKYAADAF 89
             P A+ A   D  ++ +++  LGL   RA  I +FS EYL + W +  +LHG+GKY  D++
Sbjct:   168 PSAEVARTADWRDVSELLKPLGLYDLRAKTIVKFSDEYLTKQWKYPIELHGIGKYGNDSY 227

Query:    90 AIFCTGKWDRVRPTDHMLNYYWEFL 114
              IFC  +W +V P DH LN Y ++L
Sbjct:   228 RIFCVNEWKQVHPEDHKLNKYHDWL 252

GO:0003824 "catalytic activity" evidence=IEA

GO:0006284 "base-excision repair" evidence=IEA

UNIPROTKB|E1BVB1 MBD4 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 198 (74.8 bits), Expect = 7.7e-16, P = 7.7e-16
 Identities = 35/85 (41%), Positives = 51/85 (60%)

Query:    30 PDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQEYLGESWTHVTQLHGVGKYAADAF 89
             P  + A   D +E+ +++  LGL   RA  I +FS EYL + W +  +LHG+GKY  D++
Sbjct:    14 PSPEVARTADWKEMSELLRPLGLYALRAKTIIKFSDEYLNKQWKYPIELHGIGKYGNDSY 73

Query:    90 AIFCTGKWDRVRPTDHMLNYYWEFL 114
              IFC  +W  V+P DH LN Y  +L
Sbjct:    74 RIFCVNEWKEVQPQDHKLNIYHAWL 98

GO:0006284 "base-excision repair" evidence=IEA

GO:0000785 "chromatin" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0008263 "pyrimidine-specific mismatch base pair DNA N-glycosylase activity" evidence=IEA

GO:0008630 "intrinsic apoptotic signaling pathway in response to DNA damage" evidence=IEA

GO:0009314 "response to radiation" evidence=IEA

GO:0031572 "G2 DNA damage checkpoint" evidence=IEA

UNIPROTKB|F1P366 MBD4 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 198 (74.8 bits), Expect = 7.7e-16, P = 7.7e-16
 Identities = 35/85 (41%), Positives = 51/85 (60%)

Query:    30 PDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQEYLGESWTHVTQLHGVGKYAADAF 89
             P  + A   D +E+ +++  LGL   RA  I +FS EYL + W +  +LHG+GKY  D++
Sbjct:   105 PSPEVARTADWKEMSELLRPLGLYALRAKTIIKFSDEYLNKQWKYPIELHGIGKYGNDSY 164

Query:    90 AIFCTGKWDRVRPTDHMLNYYWEFL 114
              IFC  +W  V+P DH LN Y  +L
Sbjct:   165 RIFCVNEWKEVQPQDHKLNIYHAWL 189

GO:0006284 "base-excision repair" evidence=IEA

GO:0000785 "chromatin" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0008263 "pyrimidine-specific mismatch base pair DNA N-glycosylase activity" evidence=IEA

GO:0008630 "intrinsic apoptotic signaling pathway in response to DNA damage" evidence=IEA

GO:0009314 "response to radiation" evidence=IEA

GO:0031572 "G2 DNA damage checkpoint" evidence=IEA

MGI|MGI:1333850 Mbd4 "methyl-CpG binding domain protein 4" [Mus musculus (taxid:10090)]

 Score = 202 (76.2 bits), Expect = 2.4e-15, P = 2.4e-15
 Identities = 35/85 (41%), Positives = 52/85 (61%)

Query:    30 PDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQEYLGESWTHVTQLHGVGKYAADAF 89
             P A+ A   D  ++ +++  LGL   RA  I +FS EYL + W +  +LHG+GKY  D++
Sbjct:   460 PSAEVARAADWRDVSELLKPLGLYDLRAKTIIKFSDEYLTKQWRYPIELHGIGKYGNDSY 519

Query:    90 AIFCTGKWDRVRPTDHMLNYYWEFL 114
              IFC  +W +V P DH LN Y ++L
Sbjct:   520 RIFCVNEWKQVHPEDHKLNKYHDWL 544

GO:0000785 "chromatin" evidence=IDA

GO:0003677 "DNA binding" evidence=IDA

GO:0003824 "catalytic activity" evidence=IEA

GO:0005634 "nucleus" evidence=IDA

GO:0005737 "cytoplasm" evidence=IDA

GO:0006281 "DNA repair" evidence=IEA

GO:0006284 "base-excision repair" evidence=IEA

GO:0006306 "DNA methylation" evidence=TAS

GO:0006974 "response to DNA damage stimulus" evidence=IMP

GO:0008152 "metabolic process" evidence=ISO

GO:0008263 "pyrimidine-specific mismatch base pair DNA N-glycosylase activity" evidence=ISO

GO:0008630 "intrinsic apoptotic signaling pathway in response to DNA damage" evidence=IMP

GO:0009314 "response to radiation" evidence=IMP

GO:0016787 "hydrolase activity" evidence=IEA

GO:0031572 "G2 DNA damage checkpoint" evidence=IMP

UNIPROTKB|E2RL50 MBD4 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 201 (75.8 bits), Expect = 3.3e-15, P = 3.3e-15
 Identities = 35/85 (41%), Positives = 52/85 (61%)

Query:    30 PDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQEYLGESWTHVTQLHGVGKYAADAF 89
             P A+ A   D  ++ +++  LGL   RA  I +FS EYL + W +  +LHG+GKY  D++
Sbjct:   476 PSAEVARTADWRDVSELLKPLGLYDLRAKTIIKFSDEYLTKQWRYPIELHGIGKYGNDSY 535

Query:    90 AIFCTGKWDRVRPTDHMLNYYWEFL 114
              IFC  +W +V P DH LN Y ++L
Sbjct:   536 RIFCINEWKQVHPEDHKLNKYHDWL 560

GO:0006284 "base-excision repair" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0003824 "catalytic activity" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

UNIPROTKB|F1MUX1 MBD4 "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 200 (75.5 bits), Expect = 4.0e-15, P = 4.0e-15
 Identities = 35/85 (41%), Positives = 51/85 (60%)

Query:    30 PDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQEYLGESWTHVTQLHGVGKYAADAF 89
             P A+ A   D  ++ + +  LGL   RA  I +FS EYL + W +  +LHG+GKY  D++
Sbjct:   460 PSAEAARTADWRDVSEFLKPLGLYDLRAKTIIKFSDEYLTKQWKYPIELHGIGKYGNDSY 519

Query:    90 AIFCTGKWDRVRPTDHMLNYYWEFL 114
              IFC  +W +V P DH LN Y ++L
Sbjct:   520 RIFCVNEWKQVHPEDHKLNKYHDWL 544

GO:0031572 "G2 DNA damage checkpoint" evidence=IEA

GO:0009314 "response to radiation" evidence=IEA

GO:0008630 "intrinsic apoptotic signaling pathway in response to DNA damage" evidence=IEA

GO:0008263 "pyrimidine-specific mismatch base pair DNA N-glycosylase activity" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

GO:0000785 "chromatin" evidence=IEA

GO:0006284 "base-excision repair" evidence=IEA

UNIPROTKB|E9PEE4 MBD4 "Methyl-CpG-binding domain protein 4" [Homo sapiens (taxid:9606)]

 Score = 171 (65.3 bits), Expect = 3.3e-13, Sum P(2) = 3.3e-13
 Identities = 30/74 (40%), Positives = 45/74 (60%)

Query:    30 PDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQEYLGESWTHVTQLHGVGKYAADAF 89
             P A+ A   D  ++ +++  LGL   RA  I +FS EYL + W +  +LHG+GKY  D++
Sbjct:   486 PSAEVARTADWRDVSELLKPLGLYDLRAKTIVKFSDEYLTKQWKYPIELHGIGKYGNDSY 545

Query:    90 AIFCTGKWDRVRPT 103
              IFC  +W +VR T
Sbjct:   546 RIFCVNEWKQVRLT 559

GO:0003677 "DNA binding" evidence=IEA

GO:0003824 "catalytic activity" evidence=IEA

GO:0006284 "base-excision repair" evidence=IEA

GO:0005634 "nucleus" evidence=IDA

GO:0005730 "nucleolus" evidence=IDA

RGD|1585874 Mbd4 "methyl-CpG binding domain protein 4" [Rattus norvegicus (taxid:10116)]

 Score = 167 (63.8 bits), Expect = 1.3e-11, P = 1.3e-11
 Identities = 30/65 (46%), Positives = 41/65 (63%)

Query:    50 LGLQKKRAPMIKRFSQEYLGESWTHVTQLHGVGKYAADAFAIFCTGKWDRVRPTDHMLNY 109
             L L   RA  I +FS EYL + W +  +LHG+GKY  D++ IFC  +W +V P DH LN 
Sbjct:   456 LELYDLRAKTIIKFSDEYLTKPWRYPIELHGIGKYGNDSYRIFCVNEWKQVHPEDHKLNK 515

Query:   110 YWEFL 114
             Y ++L
Sbjct:   516 YHDWL 520


Parameters:
  V=100
  filter=SEG
  E=0.001

  ctxfactor=1.00

  Query                        -----  As Used  -----    -----  Computed  ----
  Frame  MatID Matrix name     Lambda    K       H      Lambda    K       H
   +0      0   BLOSUM62        0.322   0.136   0.412    same    same    same
               Q=9,R=2         0.244   0.0300  0.180     n/a     n/a     n/a

  Query
  Frame  MatID  Length  Eff.Length     E     S W   T  X   E2     S2
   +0      0      121       121   0.00091  102 3  11 22  0.46    30
                                                     29  0.49    32


Statistics:

  Database:  /share/blast/go-seqdb.fasta
   Title:  go_20130330-seqdb.fasta
   Posted:  5:47:42 AM PDT Apr 1, 2013
   Created:  5:47:42 AM PDT Apr 1, 2013
   Format:  XDF-1
   # of letters in database:  169,044,731
   # of sequences in database:  368,745
   # of database sequences satisfying E:  10
  No. of states in DFA:  602 (64 KB)
  Total size of DFA:  139 KB (2085 KB)
  Time to generate neighborhood:  0.00u 0.00s 0.00t   Elapsed:  00:00:00
  No. of threads or processors used:  24
  Search cpu time:  12.94u 0.11s 13.05t   Elapsed:  00:00:00
  Total cpu time:  12.94u 0.11s 13.05t   Elapsed:  00:00:00
  Start:  Sat May 11 00:33:18 2013   End:  Sat May 11 00:33:18 2013

GO:0000785 "chromatin" evidence=ISO

GO:0003674 "molecular_function" evidence=ND

GO:0003677 "DNA binding" evidence=IEA;ISO

GO:0003824 "catalytic activity" evidence=IEA

GO:0005575 "cellular_component" evidence=ND

GO:0005634 "nucleus" evidence=IEA;ISO

GO:0005737 "cytoplasm" evidence=ISO

GO:0006281 "DNA repair" evidence=IEA

GO:0006974 "response to DNA damage stimulus" evidence=ISO

GO:0008150 "biological_process" evidence=ND

GO:0008263 "pyrimidine-specific mismatch base pair DNA N-glycosylase activity" evidence=ISO

GO:0008630 "intrinsic apoptotic signaling pathway in response to DNA damage" evidence=ISO

GO:0009314 "response to radiation" evidence=ISO

GO:0031572 "G2 DNA damage checkpoint" evidence=ISO

GO:0005730 "nucleolus" evidence=ISO

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	121
pfam00730	144	pfam00730, HhH-GPD, HhH-GPD superfamily base excis	2e-13
smart00478	149	smart00478, ENDO3c, endonuclease III	3e-04
cd00056	158	cd00056, ENDO3c, endonuclease III; includes endonu	0.002
COG0177	211	COG0177, Nth, Predicted EndoIII-related endonuclea	0.002

>gnl|CDD|216088 pfam00730, HhH-GPD, HhH-GPD superfamily base excision DNA repair protein

 Score = 61.6 bits (150), Expect = 2e-13
 Identities = 28/115 (24%), Positives = 48/115 (41%), Gaps = 14/115 (12%)

Query: 18  AGRVISDLFTLC--PDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQEYLGESWTHV 75
           A ++   LF     P  +   E D EE+ ++I  LG  +++A  IK  ++  +      V
Sbjct: 14  ANKITKRLFERYGFPTPEDLAEADEEELRELIKGLGFYRRKAKYIKELARILVEGYLGLV 73

Query: 76  ----------TQLHGVGKYAADAFAIFCTGKWDRVRPTDHMLNYYWE--FLVSTK 118
                       L GVG++ A+A  +F  G+ D     D  +    +   L+ TK
Sbjct: 74  PLDLEELEALLALPGVGRWTAEAVLLFALGRPDVFPAVDTHVRRVAKRLGLIDTK 128

This family contains a diverse range of structurally related DNA repair proteins. The superfamily is called the HhH-GPD family after its hallmark Helix-hairpin-helix and Gly/Pro rich loop followed by a conserved aspartate. This includes endonuclease III, EC:4.2.99.18 and MutY an A/G-specific adenine glycosylase, both have a C terminal 4Fe-4S cluster. The family also includes 8-oxoguanine DNA glycosylases. The methyl-CPG binding protein MBD4 also contains a related domain that is a thymine DNA glycosylase. The family also includes DNA-3-methyladenine glycosylase II EC:3.2.2.21 and other members of the AlkA family. Length = 144

>gnl|CDD|214684 smart00478, ENDO3c, endonuclease III

 Score = 38.0 bits (89), Expect = 3e-04
 Identities = 24/86 (27%), Positives = 39/86 (45%), Gaps = 7/86 (8%)

Query: 18 AGRVISDLFTLCPDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQ----EYLGE--- 70
            +    LF   P  +     D EE+E++I  LG  +++A  +   ++    EY GE   
Sbjct: 10 VNKATERLFEKFPTPEDLAAADEEELEELIRGLGFYRRKARYLIELARILVEEYGGEVPD 69

Query: 71 SWTHVTQLHGVGKYAADAFAIFCTGK 96
              + +L GVG+  A+A   F  GK
Sbjct: 70 DREELLKLPGVGRKTANAVLSFALGK 95

includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases. Length = 149

>gnl|CDD|238013 cd00056, ENDO3c, endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases

 Score = 35.3 bits (82), Expect = 0.002
 Identities = 17/77 (22%), Positives = 33/77 (42%), Gaps = 11/77 (14%)

Query: 30  PDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQ----EYLGESWTH------VTQLH 79
           P  +     D EE+ ++I +LG  +++A  +K  ++     + G           +  L 
Sbjct: 31  PTPEALAAADEEELRELIRSLGY-RRKAKYLKELARAIVEGFGGLVLDDPDAREELLALP 89

Query: 80  GVGKYAADAFAIFCTGK 96
           GVG+  A+   +F  G 
Sbjct: 90  GVGRKTANVVLLFALGP 106

Length = 158

>gnl|CDD|223255 COG0177, Nth, Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]

 Score = 35.6 bits (83), Expect = 0.002
 Identities = 21/74 (28%), Positives = 35/74 (47%), Gaps = 15/74 (20%)

Query: 25  LFTLCPDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQ----EYLGESWTHV----- 75
           LF   P  +     D EE+E++I ++GL + +A  IK  ++    ++ GE    V     
Sbjct: 54  LFKRYPTPEDLLNADEEELEELIKSIGLYRNKAKNIKELARILLEKFGGE----VPDTRE 109

Query: 76  --TQLHGVGKYAAD 87
               L GVG+  A+
Sbjct: 110 ELLSLPGVGRKTAN 123

Length = 211

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	121
COG0177	211	Nth Predicted EndoIII-related endonuclease [DNA re	99.97
PRK10702	211	endonuclease III; Provisional	99.96
PRK13913	218	3-methyladenine DNA glycosylase; Provisional	99.95
TIGR01083	191	nth endonuclease III. This equivalog model identif	99.95
PRK10880	350	adenine DNA glycosylase; Provisional	99.94
TIGR01084	275	mutY A/G-specific adenine glycosylase. This equiva	99.94
PRK13910	289	DNA glycosylase MutY; Provisional	99.93
smart00478	149	ENDO3c endonuclease III. includes endonuclease III	99.93
cd00056	158	ENDO3c endonuclease III; includes endonuclease III	99.92
COG1194	342	MutY A/G-specific DNA glycosylase [DNA replication	99.88
COG0122	285	AlkA 3-methyladenine DNA glycosylase/8-oxoguanine	99.88
PRK10308	283	3-methyl-adenine DNA glycosylase II; Provisional	99.86
TIGR00588	310	ogg 8-oxoguanine DNA-glycosylase (ogg). All protei	99.85
TIGR03252	177	uncharacterized HhH-GPD family protein. This model	99.83
PRK01229	208	N-glycosylase/DNA lyase; Provisional	99.81
COG2231	215	Uncharacterized protein related to Endonuclease II	99.81
KOG1921	286	consensus Endonuclease III [Replication, recombina	99.8
KOG1918	254	consensus 3-methyladenine DNA glycosidase [Replica	99.74
PF00730	108	HhH-GPD: HhH-GPD superfamily base excision DNA rep	99.67
KOG2457	555	consensus A/G-specific adenine DNA glycosylase [Re	99.61
KOG2875	323	consensus 8-oxoguanine DNA glycosylase [Replicatio	99.57
PF00633	30	HHH: Helix-hairpin-helix motif; InterPro: IPR00044	98.67
COG1059	210	Thermostable 8-oxoguanine DNA glycosylase [DNA rep	97.43
PF14716	68	HHH_8: Helix-hairpin-helix domain; PDB: 2W9M_A 1HU	97.03
smart00278	26	HhH1 Helix-hairpin-helix DNA-binding motif class 1	96.95
PRK13901	196	ruvA Holliday junction DNA helicase RuvA; Provisio	96.91
PF12826	64	HHH_2: Helix-hairpin-helix motif; PDB: 1X2I_B 1DGS	96.91
PRK14606	188	ruvA Holliday junction DNA helicase RuvA; Provisio	96.51
PRK14601	183	ruvA Holliday junction DNA helicase RuvA; Provisio	96.51
PRK14602	203	ruvA Holliday junction DNA helicase RuvA; Provisio	96.41
PRK14603	197	ruvA Holliday junction DNA helicase RuvA; Provisio	96.34
COG0632	201	RuvA Holliday junction resolvasome, DNA-binding su	96.33
PRK14604	195	ruvA Holliday junction DNA helicase RuvA; Provisio	96.31
PRK14605	194	ruvA Holliday junction DNA helicase RuvA; Provisio	96.2
TIGR00084	191	ruvA Holliday junction DNA helicase, RuvA subunit.	95.96
PRK14600	186	ruvA Holliday junction DNA helicase RuvA; Provisio	95.9
PF14520	60	HHH_5: Helix-hairpin-helix domain; PDB: 3AUO_B 3AU	95.83
PF02371	87	Transposase_20: Transposase IS116/IS110/IS902 fami	95.75
PRK02515	132	psbU photosystem II complex extrinsic protein prec	95.75
PRK00116	192	ruvA Holliday junction DNA helicase RuvA; Reviewed	95.58
TIGR00426	69	competence protein ComEA helix-hairpin-helix repea	95.3
PF12836	65	HHH_3: Helix-hairpin-helix motif; PDB: 2EDU_A 2OCE	95.13
PF14520	60	HHH_5: Helix-hairpin-helix domain; PDB: 3AUO_B 3AU	94.62
TIGR00615	195	recR recombination protein RecR. This family is ba	94.27
PRK00076	196	recR recombination protein RecR; Reviewed	94.2
PRK14973	936	DNA topoisomerase I; Provisional	94.18
PF14490	94	HHH_4: Helix-hairpin-helix containing domain; PDB:	94.16
PRK13844	200	recombination protein RecR; Provisional	94.12
TIGR01259	120	comE comEA protein. This model describes the ComEA	94.11
smart00483	334	POLXc DNA polymerase X family. includes vertebrate	94.09
COG0353	198	RecR Recombinational DNA repair protein (RecF path	93.94
PF11731	93	Cdd1: Pathogenicity locus; InterPro: IPR021725 Cdd	93.76
cd00141	307	NT_POLXc Nucleotidyltransferase (NT) domain of fam	93.66
KOG2841	254	consensus Structure-specific endonuclease ERCC1-XP	93.52
PF12836	65	HHH_3: Helix-hairpin-helix motif; PDB: 2EDU_A 2OCE	93.45
PRK07956	665	ligA NAD-dependent DNA ligase LigA; Validated	93.42
PF11798	32	IMS_HHH: IMS family HHH motif; InterPro: IPR024728	93.36
TIGR00575	652	dnlj DNA ligase, NAD-dependent. The member of this	93.35
PRK07945	335	hypothetical protein; Provisional	93.12
COG1555	149	ComEA DNA uptake protein and related DNA-binding p	92.65
PRK08097	562	ligB NAD-dependent DNA ligase LigB; Reviewed	92.61
PF05559	319	DUF763: Protein of unknown function (DUF763); Inte	92.56
COG1555	149	ComEA DNA uptake protein and related DNA-binding p	92.55
TIGR01259	120	comE comEA protein. This model describes the ComEA	92.36
PF10391	52	DNA_pol_lambd_f: Fingers domain of DNA polymerase	92.05
PRK14350	669	ligA NAD-dependent DNA ligase LigA; Provisional	91.98
COG0272	667	Lig NAD-dependent DNA ligase (contains BRCT domain	91.45
PRK13482	352	DNA integrity scanning protein DisA; Provisional	91.06
TIGR00084	191	ruvA Holliday junction DNA helicase, RuvA subunit.	90.95
PRK00116	192	ruvA Holliday junction DNA helicase RuvA; Reviewed	90.79
PRK08609	570	hypothetical protein; Provisional	90.72
PF03352	179	Adenine_glyco: Methyladenine glycosylase; InterPro	90.45
PF14229	122	DUF4332: Domain of unknown function (DUF4332)	90.24
PRK14605	194	ruvA Holliday junction DNA helicase RuvA; Provisio	89.99
smart00279	36	HhH2 Helix-hairpin-helix class 2 (Pol1 family) mot	89.99
PRK00024	224	hypothetical protein; Reviewed	89.96
PRK12766	232	50S ribosomal protein L32e; Provisional	89.57
PF12826	64	HHH_2: Helix-hairpin-helix motif; PDB: 1X2I_B 1DGS	89.45
smart00483	334	POLXc DNA polymerase X family. includes vertebrate	89.01
cd00141	307	NT_POLXc Nucleotidyltransferase (NT) domain of fam	88.57
PRK02515	132	psbU photosystem II complex extrinsic protein prec	88.48
PRK00024	224	hypothetical protein; Reviewed	88.28
cd00080	75	HhH2_motif Helix-hairpin-helix class 2 (Pol1 famil	87.4
PRK14351	689	ligA NAD-dependent DNA ligase LigA; Provisional	87.31
KOG2534	353	consensus DNA polymerase IV (family X) [Replicatio	87.15
COG1796	326	POL4 DNA polymerase IV (family X) [DNA replication	86.88
PF03118	66	RNA_pol_A_CTD: Bacterial RNA polymerase, alpha cha	85.98
TIGR00426	69	competence protein ComEA helix-hairpin-helix repea	85.74
PRK00254	720	ski2-like helicase; Provisional	84.63
PRK13901	196	ruvA Holliday junction DNA helicase RuvA; Provisio	83.85
TIGR00608	218	radc DNA repair protein radc. This family is based	83.8
PRK14600	186	ruvA Holliday junction DNA helicase RuvA; Provisio	83.7
PRK14601	183	ruvA Holliday junction DNA helicase RuvA; Provisio	83.47
PRK14606	188	ruvA Holliday junction DNA helicase RuvA; Provisio	82.74
PRK14603	197	ruvA Holliday junction DNA helicase RuvA; Provisio	82.51
PRK14602	203	ruvA Holliday junction DNA helicase RuvA; Provisio	82.51
PRK09482	256	flap endonuclease-like protein; Provisional	82.4
PF09597	57	IGR: IGR protein motif; InterPro: IPR019083 This e	81.86
PRK12766	232	50S ribosomal protein L32e; Provisional	81.78
PRK14604	195	ruvA Holliday junction DNA helicase RuvA; Provisio	81.53
PRK14351	689	ligA NAD-dependent DNA ligase LigA; Provisional	81.52
TIGR01954	50	nusA_Cterm_rpt transcription termination factor Nu	81.42
TIGR01448	720	recD_rel helicase, putative, RecD/TraA family. Thi	80.65

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

Probab=99.97  E-value=4.9e-30  Score=193.11  Aligned_cols=103  Identities=22%  Similarity=0.345  Sum_probs=95.3

Q ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHHhCCCHHHHhcCCHHHHHHHHhhcCChhHHHHHHHHHHHHHHH-------hhHHHh
Q 033363            3 QIYSIRLKEIAILLKAGRVISDLFTLCPDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQEYLG-------ESWTHV   75 (121)
Q Consensus         3 ~~~si~~~~~~~~~~v~~v~~~l~~~~pt~~~la~a~~~eL~~~i~~~Gl~~~Ka~~i~~~a~~i~~-------~~~~~L   75 (121)
                      .+.++.+|+++||+.|++++.+||++||||++++++++++|++.|+++|||++||++|+++|+++++       +++++|
T Consensus        32 lLva~iLSaqttD~~vn~at~~Lf~~~~t~e~l~~a~~~~l~~~I~~iGlyr~KAk~I~~~~~~l~e~~~g~vP~~~~eL  111 (211)
T COG0177          32 LLVAVILSAQTTDEVVNKATPALFKRYPTPEDLLNADEEELEELIKSIGLYRNKAKNIKELARILLEKFGGEVPDTREEL  111 (211)
T ss_pred             HHHHHHHhccCchHHHHHHHHHHHHHcCCHHHHHcCCHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHHcCCCCCchHHHH
Confidence            3567788888999999999999999999999999999999999999999999999999999999999       489999


Q ss_pred             ccCCCCcHHHHHHHHHHhcCCCCccCcchHHH
Q 033363           76 TQLHGVGKYAADAFAIFCTGKWDRVRPTDHML  107 (121)
Q Consensus        76 ~~lpGIG~~tA~~vl~f~~~~~~~v~p~D~~l  107 (121)
                      .+|||||+|||++||.++||.|  .+|+|+++
T Consensus       112 ~~LPGVGrKTAnvVL~~a~g~p--~i~VDTHV  141 (211)
T COG0177         112 LSLPGVGRKTANVVLSFAFGIP--AIAVDTHV  141 (211)
T ss_pred             HhCCCcchHHHHHHHHhhcCCC--cccccchH
Confidence            9999999999999999999998  56666544

>PRK10702 endonuclease III; Provisional

Probab=99.96  E-value=1.2e-28  Score=185.80  Aligned_cols=110  Identities=17%  Similarity=0.207  Sum_probs=100.4

Q ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHHhCCCHHHHhcCCHHHHHHHHhhcCChhHHHHHHHHHHHHHHH-------hhHHHh
Q 033363            3 QIYSIRLKEIAILLKAGRVISDLFTLCPDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQEYLG-------ESWTHV   75 (121)
Q Consensus         3 ~~~si~~~~~~~~~~v~~v~~~l~~~~pt~~~la~a~~~eL~~~i~~~Gl~~~Ka~~i~~~a~~i~~-------~~~~~L   75 (121)
                      ++.|..+++.+++.+|++++.+|+.+||||++|+++++++|+++|+++||+++||++|+++|+.+.+       +++++|
T Consensus        32 ~lvs~iLsq~t~~~~v~~~~~~L~~~~pt~e~l~~a~~~~l~~~i~~~G~y~~kA~~l~~~a~~i~~~~~~~~p~~~~~L  111 (211)
T PRK10702         32 LLIAVLLSAQATDVSVNKATAKLYPVANTPAAMLELGVEGVKTYIKTIGLYNSKAENVIKTCRILLEQHNGEVPEDRAAL  111 (211)
T ss_pred             HHHHHHHHhhcCHHHHHHHHHHHHHHcCCHHHHHCCCHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHcCCCCCchHHHH
Confidence            4556666666778889999999999999999999999999999999999999999999999999987       489999


Q ss_pred             ccCCCCcHHHHHHHHHHhcCCCCccCcchHHHHHHHHHH
Q 033363           76 TQLHGVGKYAADAFAIFCTGKWDRVRPTDHMLNYYWEFL  114 (121)
Q Consensus        76 ~~lpGIG~~tA~~vl~f~~~~~~~v~p~D~~l~~~~~wl  114 (121)
                      ++|||||+|||++|++|+||++  .+|+|.+++|....+
T Consensus       112 l~lpGVG~ktA~~ill~a~~~~--~~~VDt~v~Rv~~r~  148 (211)
T PRK10702        112 EALPGVGRKTANVVLNTAFGWP--TIAVDTHIFRVCNRT  148 (211)
T ss_pred             hcCCcccHHHHHHHHHHHcCCC--cccccchHHHHHHHh
Confidence            9999999999999999999996  799999998887665

>PRK13913 3-methyladenine DNA glycosylase; Provisional

Probab=99.95  E-value=2.3e-27  Score=179.67  Aligned_cols=109  Identities=16%  Similarity=0.202  Sum_probs=97.2

Q ss_pred             hHHHHHHHHHHHHHHHHHHHHHHH-------hCCCHHHHhcCCHHHHHHHHhhcCChhHHHHHHHHHHHHHHH-------
Q 033363            4 IYSIRLKEIAILLKAGRVISDLFT-------LCPDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQEYLG-------   69 (121)
Q Consensus         4 ~~si~~~~~~~~~~v~~v~~~l~~-------~~pt~~~la~a~~~eL~~~i~~~Gl~~~Ka~~i~~~a~~i~~-------   69 (121)
                      +.+..++|.|+.++|++++.+|++       +||||++|++++.++|+++|+|+||+++||++|+++|+.+.+       
T Consensus        34 LV~aILsQqT~~~~v~~a~~~L~~~~~~~~~~~~t~e~L~~a~~eeL~~~Irp~Gf~~~KA~~Lk~la~~i~~~~g~~~~  113 (218)
T PRK13913         34 LLGAVLTQNTKFEAVEKSLENLKNAFILENDDEINLKKIAYIEFSKLAECVRPSGFYNQKAKRLIDLSENILKDFGSFEN  113 (218)
T ss_pred             HHHHHHHhhhhHHHHHHHHHHHHHhcccccccCCCHHHHHcCCHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHcCCchh
Confidence            455566666888899999999987       467999999999999999999999999999999999999976       


Q ss_pred             ----hhHHHhccCCCCcHHHHHHHHHHhcCCCCccCcchHHHHHHHHHH
Q 033363           70 ----ESWTHVTQLHGVGKYAADAFAIFCTGKWDRVRPTDHMLNYYWEFL  114 (121)
Q Consensus        70 ----~~~~~L~~lpGIG~~tA~~vl~f~~~~~~~v~p~D~~l~~~~~wl  114 (121)
                          ..+++|+++||||+||||+||+|++++|  +||+|.+++|..+.+
T Consensus       114 ~~~~~~re~Ll~l~GIG~kTAd~iLlya~~rp--~fvVDty~~Rv~~Rl  160 (218)
T PRK13913        114 FKQEVTREWLLDQKGIGKESADAILCYVCAKE--VMVVDKYSYLFLKKL  160 (218)
T ss_pred             ccCchHHHHHHcCCCccHHHHHHHHHHHcCCC--ccccchhHHHHHHHc
Confidence                2678999999999999999999999997  799999888776554

>TIGR01083 nth endonuclease III

Probab=99.95  E-value=5.5e-27  Score=173.89  Aligned_cols=109  Identities=20%  Similarity=0.260  Sum_probs=97.5

Q ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHhCCCHHHHhcCCHHHHHHHHhhcCChhHHHHHHHHHHHHHHH-------hhHHHhc
Q 033363            4 IYSIRLKEIAILLKAGRVISDLFTLCPDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQEYLG-------ESWTHVT   76 (121)
Q Consensus         4 ~~si~~~~~~~~~~v~~v~~~l~~~~pt~~~la~a~~~eL~~~i~~~Gl~~~Ka~~i~~~a~~i~~-------~~~~~L~   76 (121)
                      +.+..+++.++.+++.+++.+|++.||||++|+++++++|+++|+++||+++||++|+++|+.+.+       +.+++|+
T Consensus        30 Li~~ILsqqt~~~~~~~~~~~l~~~~pt~~~l~~~~~~~L~~~ir~~G~~~~Ka~~i~~~a~~i~~~~~~~~~~~~~~L~  109 (191)
T TIGR01083        30 LVATILSAQATDKSVNKATKKLFEVYPTPQALAQAGLEELEEYIKSIGLYRNKAKNIIALCRILVERYGGEVPEDREELV  109 (191)
T ss_pred             HHHHHHHhhCcHHHHHHHHHHHHHHCCCHHHHHcCCHHHHHHHHHhcCChHHHHHHHHHHHHHHHHHcCCCCchHHHHHH
Confidence            345555566667788999999999999999999999999999999999999999999999999986       4789999


Q ss_pred             cCCCCcHHHHHHHHHHhcCCCCccCcchHHHHHHHHHH
Q 033363           77 QLHGVGKYAADAFAIFCTGKWDRVRPTDHMLNYYWEFL  114 (121)
Q Consensus        77 ~lpGIG~~tA~~vl~f~~~~~~~v~p~D~~l~~~~~wl  114 (121)
                      +|||||+|||+++++|++++|  .+|+|.++.|.+.++
T Consensus       110 ~l~GIG~ktA~~ill~~~~~~--~~~vD~~v~Ri~~r~  145 (191)
T TIGR01083       110 KLPGVGRKTANVVLNVAFGIP--AIAVDTHVFRVSNRL  145 (191)
T ss_pred             hCCCCcHHHHHHHHHHHcCCC--ccccchhHHHHHHHc
Confidence            999999999999999999997  488888888887665

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=99.94  E-value=3.3e-26  Score=183.54  Aligned_cols=112  Identities=19%  Similarity=0.245  Sum_probs=100.2

Q ss_pred             hHHHHHHHHH----HHHHHHHHHHHHHHhCCCHHHHhcCCHHHHHHHHhhcCChhHHHHHHHHHHHHHHH-------hhH
Q 033363            4 IYSIRLKEIA----ILLKAGRVISDLFTLCPDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQEYLG-------ESW   72 (121)
Q Consensus         4 ~~si~~~~~~----~~~~v~~v~~~l~~~~pt~~~la~a~~~eL~~~i~~~Gl~~~Ka~~i~~~a~~i~~-------~~~   72 (121)
                      -|.|++++|+    +.++|.++|.+|+++|||+++|+++++++|.++|+++|||+ ||++|+++|+.+.+       .++
T Consensus        30 py~ilVseILlQQT~v~~v~~~~~rl~~~fPt~~~La~a~~eel~~~~~glGyy~-RAr~L~~~A~~i~~~~~g~~p~~~  108 (350)
T PRK10880         30 PYKVWLSEVMLQQTQVATVIPYFERFMARFPTVTDLANAPLDEVLHLWTGLGYYA-RARNLHKAAQQVATLHGGEFPETF  108 (350)
T ss_pred             HHHHHHHHHHHhhccHHHHHHHHHHHHHHCcCHHHHHCcCHHHHHHHHHcCChHH-HHHHHHHHHHHHHHHhCCCchhhH
Confidence            3677777775    45788999999999999999999999999999999999995 99999999999976       478


Q ss_pred             HHhccCCCCcHHHHHHHHHHhcCCCCccCcchHHHHHHHHHHHHhh
Q 033363           73 THVTQLHGVGKYAADAFAIFCTGKWDRVRPTDHMLNYYWEFLVSTK  118 (121)
Q Consensus        73 ~~L~~lpGIG~~tA~~vl~f~~~~~~~v~p~D~~l~~~~~wl~~~~  118 (121)
                      ++|++|||||+|||++|++|+||++  ++++|.+++|.++.+..-.
T Consensus       109 ~~L~~LpGIG~~TA~aIl~~af~~~--~~iVD~nV~RV~~Rl~~i~  152 (350)
T PRK10880        109 EEVAALPGVGRSTAGAILSLSLGKH--FPILDGNVKRVLARCYAVS  152 (350)
T ss_pred             HHHhcCCCccHHHHHHHHHHHCCCC--eecccHHHHHHHHHHhccc
Confidence            9999999999999999999999996  7889999999888775433

>TIGR01084 mutY A/G-specific adenine glycosylase

Probab=99.94  E-value=1e-25  Score=175.75  Aligned_cols=111  Identities=21%  Similarity=0.307  Sum_probs=98.6

Q ss_pred             HHHHHHHH----HHHHHHHHHHHHHHHhCCCHHHHhcCCHHHHHHHHhhcCChhHHHHHHHHHHHHHHH-------hhHH
Q 033363            5 YSIRLKEI----AILLKAGRVISDLFTLCPDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQEYLG-------ESWT   73 (121)
Q Consensus         5 ~si~~~~~----~~~~~v~~v~~~l~~~~pt~~~la~a~~~eL~~~i~~~Gl~~~Ka~~i~~~a~~i~~-------~~~~   73 (121)
                      |.+++++|    ++.++|.++|.+|+++||||++|+++++++|.++|+++||+ +||++|+++|+.+.+       .+++
T Consensus        27 y~vlvseIL~QQT~v~~v~~~~~rl~~~fpt~~~La~a~~eeL~~~~~~lG~y-~RAr~L~~~A~~i~~~~~g~~p~~~~  105 (275)
T TIGR01084        27 YRVWLSEVMLQQTQVATVIPYFERFLERFPTVQALANAPQDEVLKLWEGLGYY-ARARNLHKAAQEVVEEFGGEFPQDFE  105 (275)
T ss_pred             HHHHHHHHHHhhccHHHHHHHHHHHHHhCCCHHHHHCcCHHHHHHHHHHCCcH-HHHHHHHHHHHHHHHHcCCCCcHHHH
Confidence            55555555    45678899999999999999999999999999999999999 699999999999987       4789


Q ss_pred             HhccCCCCcHHHHHHHHHHhcCCCCccCcchHHHHHHHHHHHHhh
Q 033363           74 HVTQLHGVGKYAADAFAIFCTGKWDRVRPTDHMLNYYWEFLVSTK  118 (121)
Q Consensus        74 ~L~~lpGIG~~tA~~vl~f~~~~~~~v~p~D~~l~~~~~wl~~~~  118 (121)
                      +|++|||||+|||++|++|+||++  .+++|.+++|.++.+....
T Consensus       106 ~L~~LpGIG~~TA~~Il~~a~~~~--~~~vD~~v~RVl~Rl~~~~  148 (275)
T TIGR01084       106 DLAALPGVGRYTAGAILSFALNKP--YPILDGNVKRVLSRLFAVE  148 (275)
T ss_pred             HHHhCCCCCHHHHHHHHHHHCCCC--CCcchHhHHHHHHHHccCc
Confidence            999999999999999999999998  5779999999988876543

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.

>PRK13910 DNA glycosylase MutY; Provisional

Probab=99.93  E-value=1.2e-25  Score=176.31  Aligned_cols=102  Identities=20%  Similarity=0.227  Sum_probs=91.8

Q ss_pred             HHHHHHHH-HHHHHHHHhCCCHHHHhcCCHHHHHHHHhhcCChhHHHHHHHHHHHHHHH-------hhHHHhccCCCCcH
Q 033363           12 IAILLKAG-RVISDLFTLCPDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQEYLG-------ESWTHVTQLHGVGK   83 (121)
Q Consensus        12 ~~~~~~v~-~v~~~l~~~~pt~~~la~a~~~eL~~~i~~~Gl~~~Ka~~i~~~a~~i~~-------~~~~~L~~lpGIG~   83 (121)
                      +|+.++|. ++|.+|+++|||+++|++++++||+++|+++||| +||++|+++|+.+.+       .++++|++|||||+
T Consensus         4 QT~v~~v~~~yy~rf~~~fPt~e~La~a~~~el~~~~~glGyy-~RAr~L~~~A~~i~~~~~g~~P~~~~~L~~LpGIG~   82 (289)
T PRK13910          4 QTQINTVVERFYSPFLEAFPTLKDLANAPLEEVLLLWRGLGYY-SRAKNLKKSAEICVKEHHSQLPNDYQSLLKLPGIGA   82 (289)
T ss_pred             CCcHHHhHHHHHHHHHHHCCCHHHHHCCCHHHHHHHHHcCCcH-HHHHHHHHHHHHHHHHhCCCCChhHHHHHhCCCCCH
Confidence            44555675 4999999999999999999999999999999999 599999999999987       37999999999999


Q ss_pred             HHHHHHHHHhcCCCCccCcchHHHHHHHHHHHH
Q 033363           84 YAADAFAIFCTGKWDRVRPTDHMLNYYWEFLVS  116 (121)
Q Consensus        84 ~tA~~vl~f~~~~~~~v~p~D~~l~~~~~wl~~  116 (121)
                      |||++|++|+||++  ++|+|.+++|.++.+.+
T Consensus        83 kTA~aIl~~af~~~--~~~VD~nV~RVl~Rl~g  113 (289)
T PRK13910         83 YTANAILCFGFREK--SACVDANIKRVLLRLFG  113 (289)
T ss_pred             HHHHHHHHHHCCCC--cCcccHHHHHHHHHHhc
Confidence            99999999999997  67999999988877643

>smart00478 ENDO3c endonuclease III

Probab=99.93  E-value=4.3e-25  Score=156.83  Aligned_cols=104  Identities=22%  Similarity=0.331  Sum_probs=94.6

Q ss_pred             HHHHHHHHHHHHHHHHHhCCCHHHHhcCCHHHHHHHHhhcCChhHHHHHHHHHHHHHHH-------hhHHHhccCCCCcH
Q 033363           11 EIAILLKAGRVISDLFTLCPDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQEYLG-------ESWTHVTQLHGVGK   83 (121)
Q Consensus        11 ~~~~~~~v~~v~~~l~~~~pt~~~la~a~~~eL~~~i~~~Gl~~~Ka~~i~~~a~~i~~-------~~~~~L~~lpGIG~   83 (121)
                      +.++.+++.+++.+|.+.||||++++++++++|.++|+++||+++|+++|+++|+.+.+       +.+++|++|||||+
T Consensus         3 qq~~~~~a~~~~~~l~~~~~~~~~l~~~~~~eL~~~l~~~g~~~~ka~~i~~~a~~~~~~~~~~~~~~~~~L~~l~GIG~   82 (149)
T smart00478        3 QQTSDEAVNKATERLFEKFPTPEDLAAADEEELEELIRPLGFYRRKAKYLIELARILVEEYGGEVPDDREELLKLPGVGR   82 (149)
T ss_pred             CcccHHHHHHHHHHHHHHCCCHHHHHCCCHHHHHHHHHHcCChHHHHHHHHHHHHHHHHHHCCCccHHHHHHHcCCCCcH
Confidence            34445688899999999999999999999999999999999999999999999999887       37899999999999


Q ss_pred             HHHHHHHHHhcCCCCccCcchHHHHHHHHHHHH
Q 033363           84 YAADAFAIFCTGKWDRVRPTDHMLNYYWEFLVS  116 (121)
Q Consensus        84 ~tA~~vl~f~~~~~~~v~p~D~~l~~~~~wl~~  116 (121)
                      |||+++++|++++  .++|+|.++.|..+++..
T Consensus        83 ~tA~~~l~~~~~~--~~~~~D~~v~r~~~rl~~  113 (149)
T smart00478       83 KTANAVLSFALGK--PFIPVDTHVLRIAKRLGL  113 (149)
T ss_pred             HHHHHHHHHHCCC--CCCccchHHHHHHHHhCC
Confidence            9999999999999  389999999998887653

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

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

Probab=99.92  E-value=3.5e-24  Score=153.28  Aligned_cols=111  Identities=22%  Similarity=0.344  Sum_probs=100.0

Q ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHHhC-CCHHHHhcCCHHHHHHHHhhcCChhHHHHHHHHHHHHHHH----------hh
Q 033363            3 QIYSIRLKEIAILLKAGRVISDLFTLC-PDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQEYLG----------ES   71 (121)
Q Consensus         3 ~~~si~~~~~~~~~~v~~v~~~l~~~~-pt~~~la~a~~~eL~~~i~~~Gl~~~Ka~~i~~~a~~i~~----------~~   71 (121)
                      ++.+..++++++.+++..++.+|.+.| |||++|+++++++|.+++.++| +++||++|+++|+.+.+          +.
T Consensus         3 ~Li~~il~q~~s~~~a~~~~~~l~~~~gpt~~~l~~~~~~~l~~~~~~~G-~~~kA~~i~~~a~~~~~~~~~~~~~~~~~   81 (158)
T cd00056           3 VLVSEILSQQTTDKAVNKAYERLFERYGPTPEALAAADEEELRELIRSLG-YRRKAKYLKELARAIVEGFGGLVLDDPDA   81 (158)
T ss_pred             HHHHHHHHhcccHHHHHHHHHHHHHHhCCCHHHHHCCCHHHHHHHHHhcC-hHHHHHHHHHHHHHHHHHcCCccCCCccc
Confidence            456666677777778999999999999 9999999999999999999999 78999999999999986          36


Q ss_pred             HHHhccCCCCcHHHHHHHHHHhcCCCCccCcchHHHHHHHHHHHH
Q 033363           72 WTHVTQLHGVGKYAADAFAIFCTGKWDRVRPTDHMLNYYWEFLVS  116 (121)
Q Consensus        72 ~~~L~~lpGIG~~tA~~vl~f~~~~~~~v~p~D~~l~~~~~wl~~  116 (121)
                      +++|+++||||||||+++++|+++ ++ ++|.|.+++|..+++..
T Consensus        82 ~~~L~~l~GIG~~tA~~~l~~~~~-~~-~~pvD~~v~r~~~~~~~  124 (158)
T cd00056          82 REELLALPGVGRKTANVVLLFALG-PD-AFPVDTHVRRVLKRLGL  124 (158)
T ss_pred             HHHHHcCCCCCHHHHHHHHHHHCC-CC-CCccchhHHHHHHHhCC
Confidence            789999999999999999999999 55 88889999999988764

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

Probab=99.88  E-value=1e-22  Score=162.04  Aligned_cols=113  Identities=21%  Similarity=0.263  Sum_probs=103.6

Q ss_pred             hHHHHHHHHHH----HHHHHHHHHHHHHhCCCHHHHhcCCHHHHHHHHhhcCChhHHHHHHHHHHHHHHH-------hhH
Q 033363            4 IYSIRLKEIAI----LLKAGRVISDLFTLCPDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQEYLG-------ESW   72 (121)
Q Consensus         4 ~~si~~~~~~~----~~~v~~v~~~l~~~~pt~~~la~a~~~eL~~~i~~~Gl~~~Ka~~i~~~a~~i~~-------~~~   72 (121)
                      -|.|++|||+.    -++|.++|.+|.++|||+++||+|+.+|+.+++.++|+| +||++|+++|+.+.+       ++.
T Consensus        34 PY~VwvSEiMLQQT~v~~Vi~yy~~fl~rfPti~~LA~A~~~evl~~W~gLGYy-sRArnL~~~A~~v~~~~~G~~P~~~  112 (342)
T COG1194          34 PYRVWVSEIMLQQTQVATVIPYYERFLERFPTIKALAAAPEDEVLKAWEGLGYY-SRARNLHKAAQEVVERHGGEFPDDE  112 (342)
T ss_pred             cceehhHHHHhhhccHhhhhhhHHHHHHhCCCHHHHhcCCHHHHHHHHHhcChH-HHHHHHHHHHHHHHHHcCCCCCCCH
Confidence            58899999975    356888999999999999999999999999999999987 899999999999998       489


Q ss_pred             HHhccCCCCcHHHHHHHHHHhcCCCCccCcchHHHHHHHHHHHHhhc
Q 033363           73 THVTQLHGVGKYAADAFAIFCTGKWDRVRPTDHMLNYYWEFLVSTKG  119 (121)
Q Consensus        73 ~~L~~lpGIG~~tA~~vl~f~~~~~~~v~p~D~~l~~~~~wl~~~~~  119 (121)
                      ++|.+|||||+|||.+|++|++|++  .+..|.+++|.++.++.-++
T Consensus       113 ~~l~~LpGiG~yTa~Ail~~a~~~~--~~~lDgNV~RVl~R~f~i~~  157 (342)
T COG1194         113 EELAALPGVGPYTAGAILSFAFNQP--EPVLDGNVKRVLSRLFAISG  157 (342)
T ss_pred             HHHHhCCCCcHHHHHHHHHHHhCCC--Cceeecchheeehhhhcccc
Confidence            9999999999999999999999997  78899999999888776554

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

Probab=99.88  E-value=4.3e-22  Score=156.08  Aligned_cols=109  Identities=21%  Similarity=0.318  Sum_probs=92.2

Q ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHHh----------CCCHHHHhcCCHHHHHHHHhhcCChhHHHHHHHHHHHHHHHh--
Q 033363            3 QIYSIRLKEIAILLKAGRVISDLFTL----------CPDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQEYLGE--   70 (121)
Q Consensus         3 ~~~si~~~~~~~~~~v~~v~~~l~~~----------~pt~~~la~a~~~eL~~~i~~~Gl~~~Ka~~i~~~a~~i~~~--   70 (121)
                      |+-|..++|+...+.+.+++.+|...          ||||++|++++++.    ++.+|++.+|+++|+++|+.+.++  
T Consensus       108 ~lv~aI~~QqvS~~~A~~i~~rl~~~~g~~~~~~~~fptpe~l~~~~~~~----l~~~g~s~~Ka~yi~~~A~~~~~g~~  183 (285)
T COG0122         108 ALVRAILSQQVSVAAAAKIWARLVSLYGNALEIYHSFPTPEQLAAADEEA----LRRCGLSGRKAEYIISLARAAAEGEL  183 (285)
T ss_pred             HHHHHHHHhHhhHHHHHHHHHHHHHHhCCccccccCCCCHHHHHhcCHHH----HHHhCCcHHHHHHHHHHHHHHHcCCc
Confidence            45555566655555667777777642          89999999999998    568999999999999999999983  


Q ss_pred             ------------hHHHhccCCCCcHHHHHHHHHHhcCCCCccCcchHHHHHHHHHHH
Q 033363           71 ------------SWTHVTQLHGVGKYAADAFAIFCTGKWDRVRPTDHMLNYYWEFLV  115 (121)
Q Consensus        71 ------------~~~~L~~lpGIG~~tA~~vl~f~~~~~~~v~p~D~~l~~~~~wl~  115 (121)
                                  .+++|++|||||||||+|+++|++|++|.++++|+.+++..+|++
T Consensus       184 ~~~~l~~~~~e~a~e~L~~i~GIG~WTAe~~llf~lgr~dvfP~~D~~lr~~~~~~~  240 (285)
T COG0122         184 DLSELKPLSDEEAIEELTALKGIGPWTAEMFLLFGLGRPDVFPADDLGLRRAIKKLY  240 (285)
T ss_pred             cHHHhccCCHHHHHHHHHcCCCcCHHHHHHHHHHcCCCCCCCChHHHHHHHHHHHHh
Confidence                        589999999999999999999999999844559999999999987

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

Probab=99.86  E-value=3e-21  Score=151.11  Aligned_cols=81  Identities=20%  Similarity=0.356  Sum_probs=73.5

Q ss_pred             HhCCCHHHHhcCCHHHHHHHHhhcCChhHHHHHHHHHHHHHHHh------------hHHHhccCCCCcHHHHHHHHHHhc
Q 033363           27 TLCPDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQEYLGE------------SWTHVTQLHGVGKYAADAFAIFCT   94 (121)
Q Consensus        27 ~~~pt~~~la~a~~~eL~~~i~~~Gl~~~Ka~~i~~~a~~i~~~------------~~~~L~~lpGIG~~tA~~vl~f~~   94 (121)
                      ..||||++|+++++++    |+++|++++|+++|+++|+.+.++            .+++|++|||||||||++|++|++
T Consensus       153 ~~FPtpe~La~~~~~e----L~~~Gl~~~Ra~~L~~lA~~i~~g~l~l~~~~~~~~~~~~L~~LpGIGpwTA~~vllr~l  228 (283)
T PRK10308        153 VCFPTPERLAAADPQA----LKALGMPLKRAEALIHLANAALEGTLPLTIPGDVEQAMKTLQTFPGIGRWTANYFALRGW  228 (283)
T ss_pred             cCCCCHHHHHcCCHHH----HHHCCCCHHHHHHHHHHHHHHHcCCCCccccCCHHHHHHHHhcCCCcCHHHHHHHHHHhC
Confidence            4689999999999999    567999999999999999999872            478999999999999999999999


Q ss_pred             CCCCccCcchHHHHHHH
Q 033363           95 GKWDRVRPTDHMLNYYW  111 (121)
Q Consensus        95 ~~~~~v~p~D~~l~~~~  111 (121)
                      |++|.++|+|.++++.+
T Consensus       229 g~~D~fp~~D~~l~~~~  245 (283)
T PRK10308        229 QAKDVFLPDDYLIKQRF  245 (283)
T ss_pred             CCCCCCCcccHHHHHhc
Confidence            99996678999998754

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

Probab=99.85  E-value=5.9e-21  Score=151.08  Aligned_cols=108  Identities=22%  Similarity=0.227  Sum_probs=86.0

Q ss_pred             hHHHHHHHHHHHHHHHHHHHHHH---------------HhCCCHHHHhcCCHHHHHHHHhhcCChhHHHHHHHHHHHHHH
Q 033363            4 IYSIRLKEIAILLKAGRVISDLF---------------TLCPDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQEYL   68 (121)
Q Consensus         4 ~~si~~~~~~~~~~v~~v~~~l~---------------~~~pt~~~la~a~~~eL~~~i~~~Gl~~~Ka~~i~~~a~~i~   68 (121)
                      +.+..+++.+..+++.++..+|.               ..||||++|++++.++   .|+++||+ .||++|+++|+.+.
T Consensus       123 lv~~IlsQq~si~~a~~~~~rL~~~~G~~~~~~~g~~~~~FPtp~~La~~~~e~---~Lr~~G~g-~Ra~~I~~~A~~i~  198 (310)
T TIGR00588       123 LISFICSSNNNIARITRMVERLCQAFGPRLITLDGVTYHGFPSLHALTGPEAEA---HLRKLGLG-YRARYIRETARALL  198 (310)
T ss_pred             HHHHHHhCCCCHHHHHHHHHHHHHHhCCCcccCCCcccccCCCHHHHhCCChHH---HHHHcCCH-HHHHHHHHHHHHHH
Confidence            34444444444456667777774               3599999999976553   48899995 68999999999998


Q ss_pred             Hh-----------------hHHHhccCCCCcHHHHHHHHHHhcCCCCccCcchHHHHHHHHHHHH
Q 033363           69 GE-----------------SWTHVTQLHGVGKYAADAFAIFCTGKWDRVRPTDHMLNYYWEFLVS  116 (121)
Q Consensus        69 ~~-----------------~~~~L~~lpGIG~~tA~~vl~f~~~~~~~v~p~D~~l~~~~~wl~~  116 (121)
                      ++                 .+++|++|||||||||+||++|+++++| ++|.|.+++|....++.
T Consensus       199 ~~~~~~~~l~~l~~~~~~~~~~~L~~l~GIG~~tAd~vll~~l~~~d-~~PvD~~v~r~~~r~y~  262 (310)
T TIGR00588       199 EEQGGRAWLQQIRGASYEDAREALCELPGVGPKVADCICLMGLDKPQ-AVPVDVHVWRIANRDYP  262 (310)
T ss_pred             hccCCchhHHhhccCChHHHHHHHHhCCCccHHHHHHHHHHhCCCCC-ceeecHHHHHHHHHHhc
Confidence            72                 4689999999999999999999999997 78889999988877764

All proteins in this family for which functions are known are 8-oxo-guanaine DNA glycosylases that function in base excision repair. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). This family is distantly realted to the Nth-MutY superfamily.

>TIGR03252 uncharacterized HhH-GPD family protein

Probab=99.83  E-value=3.5e-20  Score=136.39  Aligned_cols=93  Identities=15%  Similarity=0.150  Sum_probs=81.2

Q ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHhC--CCHHHHhcCCHHHHHHHHhhc----CChhHHHHHHHHHHHHHHHh-------
Q 033363            4 IYSIRLKEIAILLKAGRVISDLFTLC--PDAKTATEVDAEEIEKIISTL----GLQKKRAPMIKRFSQEYLGE-------   70 (121)
Q Consensus         4 ~~si~~~~~~~~~~v~~v~~~l~~~~--pt~~~la~a~~~eL~~~i~~~----Gl~~~Ka~~i~~~a~~i~~~-------   70 (121)
                      +.+..+++.+++++|++++.+|++++  +||++|++++.++|+++|++.    ||+++||++|+++|+.+.++       
T Consensus        22 LVa~ILSQqTtd~nv~kA~~~L~~~~g~~tp~~La~a~~eeL~~lI~~~pal~Gfy~~KAk~Lk~~a~~iie~y~G~v~~  101 (177)
T TIGR03252        22 LTGMLLDQQVPMERAFAGPHKIARRMGSLDAEDIAKYDPQAFVALFSERPAVHRFPGSMAKRVQALAQYVVDTYDGDATA  101 (177)
T ss_pred             HHHHHHhccCcHHHHHHHHHHHHHHhCCCCHHHHHcCCHHHHHHHHhcCccccCchHHHHHHHHHHHHHHHHHhCCChhh
Confidence            55666677777789999999998765  799999999999999999876    99999999999999999861       


Q ss_pred             --------h---HHHhccCCCCcHHHHHHHHHHhcCC
Q 033363           71 --------S---WTHVTQLHGVGKYAADAFAIFCTGK   96 (121)
Q Consensus        71 --------~---~~~L~~lpGIG~~tA~~vl~f~~~~   96 (121)
                              +   +++|++||||||||||+||.+.-.+
T Consensus       102 L~~~~~p~t~~lre~Ll~LpGVG~KTAnvVL~~l~~~  138 (177)
T TIGR03252       102 VWTEGDPDGKELLRRLKALPGFGKQKAKIFLALLGKQ  138 (177)
T ss_pred             hhcccCCCcHHHHHHHHcCCCCCHHHHHHHHHHHHHH
Confidence                    1   5799999999999999999977654

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

>PRK01229 N-glycosylase/DNA lyase; Provisional

Probab=99.81  E-value=1.9e-19  Score=135.67  Aligned_cols=101  Identities=15%  Similarity=0.101  Sum_probs=80.5

Q ss_pred             chhHHHHHHHHHHHHHHHHHHHHHHHhCCCHHHHhcCCHHHHHHHHhhcC--ChhHHHHHHHHHHHH---HHH-------
Q 033363            2 AQIYSIRLKEIAILLKAGRVISDLFTLCPDAKTATEVDAEEIEKIISTLG--LQKKRAPMIKRFSQE---YLG-------   69 (121)
Q Consensus         2 ~~~~si~~~~~~~~~~v~~v~~~l~~~~pt~~~la~a~~~eL~~~i~~~G--l~~~Ka~~i~~~a~~---i~~-------   69 (121)
                      +||+|+    .++++++++++.+|.     ++.+ +++.++|+++|+++|  |+++||++|+++++.   +.+       
T Consensus        43 ~~ILsq----nT~~~~v~~a~~~L~-----~~~l-~~~~eeL~~~Ir~~Gygf~~~KAk~I~~~~~~~~~l~~~~~~~~~  112 (208)
T PRK01229         43 FCILTA----NSSAEGGIKAQKEIG-----DGFL-YLSEEELEEKLKEVGHRFYNKRAEYIVEARKLYGKLKEIIKADKD  112 (208)
T ss_pred             HHHhcC----cCcHHHHHHHHHhcC-----HHHc-CCCHHHHHHHHHHhhcccHHHHHHHHHHHHHHHHHHHHHHhccCC
Confidence            345554    445557778888883     5667 999999999999995  999999999999986   221       


Q ss_pred             --hhHHHhc-cCCCCcHHHHHHHHHHhcCCCCccCcchHHHHHHHHHH
Q 033363           70 --ESWTHVT-QLHGVGKYAADAFAIFCTGKWDRVRPTDHMLNYYWEFL  114 (121)
Q Consensus        70 --~~~~~L~-~lpGIG~~tA~~vl~f~~~~~~~v~p~D~~l~~~~~wl  114 (121)
                        +.+++|+ ++||||+|||+++|..+..++  ++|+|.++.|+...+
T Consensus       113 ~~~~R~~Ll~~lpGIG~KTAd~vL~~~~~~~--~~iVDtHv~Ri~~Rl  158 (208)
T PRK01229        113 QFEAREFLVKNIKGIGYKEASHFLRNVGYED--LAILDRHILRFLKRY  158 (208)
T ss_pred             chHHHHHHHHcCCCCcHHHHHHHHHHccCCC--eeeeeHHHHHHHHHh
Confidence              4789999 999999999999997555443  899998888876554

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

Probab=99.81  E-value=6e-19  Score=131.93  Aligned_cols=110  Identities=17%  Similarity=0.221  Sum_probs=93.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhC-CCHHHHhcCCHHHHHHHHhhcCChhHHHHHHHHHHHHHHH-----------hhH
Q 033363            5 YSIRLKEIAILLKAGRVISDLFTLC-PDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQEYLG-----------ESW   72 (121)
Q Consensus         5 ~si~~~~~~~~~~v~~v~~~l~~~~-pt~~~la~a~~~eL~~~i~~~Gl~~~Ka~~i~~~a~~i~~-----------~~~   72 (121)
                      .+..+.|-|.=++|+++..++.... -+++++.+.|.++|+++|||.|||++||++|+.+++.+..           ..+
T Consensus        35 igAILtQNT~WknvekAlenLk~~~~~~l~~I~~~~~~~L~elIrpsGFYnqKa~rLk~l~k~l~~~~~~~~~~~~~~~R  114 (215)
T COG2231          35 IGAILTQNTSWKNVEKALENLKNEGILNLKKILKLDEEELAELIRPSGFYNQKAKRLKALSKNLAKFFINLESFKSEVLR  114 (215)
T ss_pred             HHHHHhccccHHHHHHHHHHHHHcccCCHHHHhcCCHHHHHHHHhccchHHHHHHHHHHHHHHHHHHhhhhhccchHHHH
Confidence            3344444444578999999998765 4799999999999999999999999999999777776665           248


Q ss_pred             HHhccCCCCcHHHHHHHHHHhcCCCCccCcchHHHHHHHHHHHH
Q 033363           73 THVTQLHGVGKYAADAFAIFCTGKWDRVRPTDHMLNYYWEFLVS  116 (121)
Q Consensus        73 ~~L~~lpGIG~~tA~~vl~f~~~~~~~v~p~D~~l~~~~~wl~~  116 (121)
                      ++|++++|||+.|||++|+|++++|  +||+|..-+|.+..+-.
T Consensus       115 ~~LL~iKGIG~ETaDsILlYa~~rp--~FVvD~Yt~R~l~rlg~  156 (215)
T COG2231         115 EELLSIKGIGKETADSILLYALDRP--VFVVDKYTRRLLSRLGG  156 (215)
T ss_pred             HHHHccCCcchhhHHHHHHHHhcCc--ccchhHHHHHHHHHhcc
Confidence            9999999999999999999999997  89999999998876543

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

Probab=99.80  E-value=5e-19  Score=135.45  Aligned_cols=113  Identities=12%  Similarity=0.145  Sum_probs=97.9

Q ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHhC-CCHHHHhcCCHHHHHHHHhhcCChhHHHHHHHHHHHHHHH-------hhHHHh
Q 033363            4 IYSIRLKEIAILLKAGRVISDLFTLC-PDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQEYLG-------ESWTHV   75 (121)
Q Consensus         4 ~~si~~~~~~~~~~v~~v~~~l~~~~-pt~~~la~a~~~eL~~~i~~~Gl~~~Ka~~i~~~a~~i~~-------~~~~~L   75 (121)
                      +.++.++-++.++....+..+|.+.. -|++++.++|+.+|.++|.++|||++||+||+++|+++.+       .++++|
T Consensus        82 Lv~lmLSSQTKDevt~~Am~rL~~~~gLT~e~v~~~de~~l~~LI~~VgFy~rKA~ylkkta~IL~d~f~gDIP~~v~dL  161 (286)
T KOG1921|consen   82 LVGLMLSSQTKDEVTAAAMLRLKEYGGLTLEAVLKIDEPTLNELIYPVGFYTRKAKYLKKTAKILQDKFDGDIPDTVEDL  161 (286)
T ss_pred             HHHHHHhcchHHHHHHHHHHHHHHhcCCCHHHHhccChHhHHhhhhhccchHHHHHHHHHHHHHHHHHhCCCCchhHHHH
Confidence            44556666666666678889999887 7999999999999999999999999999999999999998       389999


Q ss_pred             ccCCCCcHHHHHHHHHHhcCCCCccCcchHH--HHHHHHHHHH
Q 033363           76 TQLHGVGKYAADAFAIFCTGKWDRVRPTDHM--LNYYWEFLVS  116 (121)
Q Consensus        76 ~~lpGIG~~tA~~vl~f~~~~~~~v~p~D~~--l~~~~~wl~~  116 (121)
                      ++|||||||+|..+|..++|+--++.+|.|.  +++.++|+..
T Consensus       162 lsLPGVGPKMa~L~m~~AWn~i~GI~VDtHVHRi~nrlgWv~~  204 (286)
T KOG1921|consen  162 LSLPGVGPKMAHLTMQVAWNKIVGICVDTHVHRICNRLGWVDT  204 (286)
T ss_pred             hcCCCCchHHHHHHHHHHhccceeEEeehHHHHHHHHhccccc
Confidence            9999999999999999999998777777754  4577888753

>KOG1918 consensus 3-methyladenine DNA glycosidase [Replication, recombination and repair]

Probab=99.74  E-value=4.3e-18  Score=128.57  Aligned_cols=107  Identities=19%  Similarity=0.335  Sum_probs=90.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHH------hCCCHHHHhcCCHHHHHHHHhhcCChhHHHHHHHHHHHHHHHh----------
Q 033363            7 IRLKEIAILLKAGRVISDLFT------LCPDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQEYLGE----------   70 (121)
Q Consensus         7 i~~~~~~~~~~v~~v~~~l~~------~~pt~~~la~a~~~eL~~~i~~~Gl~~~Ka~~i~~~a~~i~~~----------   70 (121)
                      |..||++ .++++.+|.+|..      .||+|+.+..++.++    |+.|||+.+|+.+|+.+|+.+.++          
T Consensus        83 IlsQQLs-~kAansI~~Rfvsl~~g~~~~~~pe~i~~~~~~~----lrkcG~S~rK~~yLh~lA~~~~ng~I~s~~~i~~  157 (254)
T KOG1918|consen   83 ILSQQLS-GKAANSIYNRFVSLCGGAEKFPTPEFIDPLDCEE----LRKCGFSKRKASYLHSLAEAYTNGYIPSKSGIEK  157 (254)
T ss_pred             HHHHHHH-HHHHHHHHHHHHHHhCCCcCCCCchhcCcCCHHH----HHHhCcchhhHHHHHHHHHHHhcCCCCchHHHhh
Confidence            3333333 4478899999984      589999999999999    788999999999999999999872          


Q ss_pred             -----hHHHhccCCCCcHHHHHHHHHHhcCCCCccCcchHHHHHHHHHHHHhh
Q 033363           71 -----SWTHVTQLHGVGKYAADAFAIFCTGKWDRVRPTDHMLNYYWEFLVSTK  118 (121)
Q Consensus        71 -----~~~~L~~lpGIG~~tA~~vl~f~~~~~~~v~p~D~~l~~~~~wl~~~~  118 (121)
                           .++.|+.++|||+||+.++++|+++|+|..+|+|..+++-++.+++.+
T Consensus       158 mseEeL~~~LT~VKGIg~Wtv~MflIfsL~R~DVmp~dDlgir~g~k~l~gl~  210 (254)
T KOG1918|consen  158 MSEEELIERLTNVKGIGRWTVEMFLIFSLHRPDVMPADDLGIRNGVKKLLGLK  210 (254)
T ss_pred             cCHHHHHHHHHhccCccceeeeeeeeeccCCCcccCchhhhHHHHHHHHhCCC
Confidence                 467899999999999999999999999966778899988877776543

>PF00730 HhH-GPD: HhH-GPD superfamily base excision DNA repair protein This entry corresponds to Endonuclease III This entry corresponds to Alkylbase DNA glycosidase; InterPro: IPR003265 Endonuclease III (4

Probab=99.67  E-value=2.7e-16  Score=105.98  Aligned_cols=85  Identities=22%  Similarity=0.375  Sum_probs=72.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHh--CCCHHHHhcCCHHHHHHHHhhcCChhHHHHHHHHHHHHHHHhhHHHhccCCCCcHHHH
Q 033363            9 LKEIAILLKAGRVISDLFTL--CPDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQEYLGESWTHVTQLHGVGKYAA   86 (121)
Q Consensus         9 ~~~~~~~~~v~~v~~~l~~~--~pt~~~la~a~~~eL~~~i~~~Gl~~~Ka~~i~~~a~~i~~~~~~~L~~lpGIG~~tA   86 (121)
                      ++++++.+++.+++.+|++.  ||||++|+++++++|.++|+++||+++||++|+++|+.+.                  
T Consensus         5 l~qq~s~~~a~~~~~~l~~~~g~pt~~~l~~~~~~el~~~i~~~G~~~~ka~~i~~~a~~~~------------------   66 (108)
T PF00730_consen    5 LSQQTSIKAARKIYRRLFERYGFPTPEALAEASEEELRELIRPLGFSRRKAKYIIELARAIL------------------   66 (108)
T ss_dssp             HCTTS-HHHHHHHHHHHHHHHSCSSHHHHHCSHHHHHHHHHTTSTSHHHHHHHHHHHHHHHH------------------
T ss_pred             ecCcCcHHHHHHHHHHHHHHhcCCCHHHHHhCCHHHHHHHhhccCCCHHHHHHHHHHHHHhh------------------
Confidence            34444556788999999998  5999999999999999999999999999999999999996                  


Q ss_pred             HHHHHHhcCCCCccCcchHHHHHHHHHHHHhhc
Q 033363           87 DAFAIFCTGKWDRVRPTDHMLNYYWEFLVSTKG  119 (121)
Q Consensus        87 ~~vl~f~~~~~~~v~p~D~~l~~~~~wl~~~~~  119 (121)
                              |++|.++|+|.+++|.+.|+...+.
T Consensus        67 --------~~~d~~~~~D~~v~r~~~r~~~~~~   91 (108)
T PF00730_consen   67 --------GRPDPFPPVDTHVRRVLQRLGGIPE   91 (108)
T ss_dssp             --------C-SSSS-TTSHHHHHHHHHHTSSSS
T ss_pred             --------hcccceecCcHHHHHHHHHHcCCCC
Confidence                    8887799999999999999876554

2.99.18 from EC) is a DNA repair enzyme which removes a number of damaged pyrimidines from DNA via its glycosylase activity and also cleaves the phosphodiester backbone at apurinic / apyrimidinic sites via a beta-elimination mechanism [, ]. The structurally related DNA glycosylase MutY recognises and excises the mutational intermediate 8-oxoguanine-adenine mispair []. The 3-D structures of Escherichia coli endonuclease III [] and catalytic domain of MutY [] have been determined. The structures contain two all-alpha domains: a sequence-continuous, six-helix domain (residues 22-132) and a Greek-key, four-helix domain formed by one N-terminal and three C-terminal helices (residues 1-21 and 133-211) together with the [Fe4S4] cluster. The cluster is bound entirely within the C-terminal loop by four cysteine residues with a ligation pattern Cys-(Xaa)6-Cys-(Xaa)2-Cys-(Xaa)5-Cys which is distinct from all other known Fe4S4 proteins. This structural motif is referred to as a [Fe4S4] cluster loop (FCL) []. Two DNA-binding motifs have been proposed, one at either end of the interdomain groove: the helix-hairpin-helix (HhH) and FCL motifs (see IPR003651 from INTERPRO). The primary role of the iron-sulphur cluster appears to involve positioning conserved basic residues for interaction with the DNA phosphate backbone by forming the loop of the FCL motif [, ]. The HhH-GPD domain gets its name from its hallmark helix-hairpin-helix and Gly/Pro rich loop followed by a conserved aspartate. This domain is found in a diverse range of structurally related DNA repair proteins that include: endonuclease III, 4.2.99.18 from EC and DNA glycosylase MutY, an A/G-specific adenine glycosylase. Both of these enzymes have a C-terminal iron-sulphur cluster loop (FCL). The methyl-CPG binding protein (MBD4) also contain a related domain that is a thymine DNA glycosylase. The family also includes DNA-3-methyladenine glycosylase II 3.2.2.21 from EC, 8-oxoguanine DNA glycosylases and other members of the AlkA family.; GO: 0006284 base-excision repair; PDB: 3F0Z_A 3I0X_A 3F10_A 3I0W_A 3S6I_D 3N5N_Y 1PU7_A 1PU8_B 1PU6_B 1NGN_A ....

>KOG2457 consensus A/G-specific adenine DNA glycosylase [Replication, recombination and repair]

Probab=99.61  E-value=4.3e-15  Score=120.30  Aligned_cols=107  Identities=16%  Similarity=0.228  Sum_probs=93.3

Q ss_pred             hhHHHHHHHHHHH----HHHHHHHHHHHHhCCCHHHHhcCCH-HHHHHHHhhcCChhHHHHHHHHHHHHHHH-------h
Q 033363            3 QIYSIRLKEIAIL----LKAGRVISDLFTLCPDAKTATEVDA-EEIEKIISTLGLQKKRAPMIKRFSQEYLG-------E   70 (121)
Q Consensus         3 ~~~si~~~~~~~~----~~v~~v~~~l~~~~pt~~~la~a~~-~eL~~~i~~~Gl~~~Ka~~i~~~a~~i~~-------~   70 (121)
                      -.|.++++||+..    ..|.+.|.+.++++||..+++.|+. +|+.+++.++||| +|+++|.+-|+++++       +
T Consensus       124 RaYeVwVSEiMLQQTrV~TV~~YYt~WMqkwPTl~dla~Asl~~eVn~lWaGlGyY-~R~rrL~ega~~vv~~~~ge~Pr  202 (555)
T KOG2457|consen  124 RAYEVWVSEIMLQQTRVQTVMKYYTRWMQKWPTLYDLAQASLEKEVNELWAGLGYY-RRARRLLEGAKMVVAGTEGEFPR  202 (555)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCchHHHHHHHHHHHHHHHHHhhhhHH-HHHHHHHHHHHHHHHhCCCCCCC
Confidence            3699999999863    3467789999999999999999998 8899999999999 899999999999998       3


Q ss_pred             hHHHhcc-CCCCcHHHHHHHHHHhcCCCCccCcchHHHHHHHH
Q 033363           71 SWTHVTQ-LHGVGKYAADAFAIFCTGKWDRVRPTDHMLNYYWE  112 (121)
Q Consensus        71 ~~~~L~~-lpGIG~~tA~~vl~f~~~~~~~v~p~D~~l~~~~~  112 (121)
                      +-+.|.+ +||||+|||.+|+..+||.+  --.+|.++-|.+.
T Consensus       203 ta~~l~kgvpGVG~YTAGAiaSIAf~q~--tGiVDGNVirvls  243 (555)
T KOG2457|consen  203 TASSLMKGVPGVGQYTAGAIASIAFNQV--TGIVDGNVIRVLS  243 (555)
T ss_pred             hHHHHHhhCCCCCccchhhhhhhhhcCc--ccccccchHHHhH
Confidence            5677877 99999999999999999997  4667777766654

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

Probab=99.57  E-value=3.8e-15  Score=116.03  Aligned_cols=87  Identities=22%  Similarity=0.264  Sum_probs=73.1

Q ss_pred             HhCCCHHHHhcCCHHHHHHHHhhcCChhHHHHHHHHHHHHHHH-----------------hhHHHhccCCCCcHHHHHHH
Q 033363           27 TLCPDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQEYLG-----------------ESWTHVTQLHGVGKYAADAF   89 (121)
Q Consensus        27 ~~~pt~~~la~a~~~eL~~~i~~~Gl~~~Ka~~i~~~a~~i~~-----------------~~~~~L~~lpGIG~~tA~~v   89 (121)
                      +.|||.+.++.   .+++.-+|.+||. .|||||...|+.+.+                 +.++.|+.+||||+|+||||
T Consensus       159 h~FPsl~~L~g---~~~Ea~LR~~gfG-YRAkYI~~ta~~l~~~~g~~~wLqsl~~~~yeear~~L~~lpGVG~KVADCI  234 (323)
T KOG2875|consen  159 HGFPSLQALAG---PEVEAELRKLGFG-YRAKYISATARALQEKQGGLAWLQSLRKSSYEEAREALCSLPGVGPKVADCI  234 (323)
T ss_pred             ccCccHHHhcC---cHhHHHHHHcCcc-hhHHHHHHHHHHHHHhcccchHHHHHhcccHHHHHHHHhcCCCCcchHhhhh
Confidence            56999999986   5677779999998 999999999999998                 26889999999999999999


Q ss_pred             HHHhcCCCCccCcchHHHHHHHH--HHHHhh
Q 033363           90 AIFCTGKWDRVRPTDHMLNYYWE--FLVSTK  118 (121)
Q Consensus        90 l~f~~~~~~~v~p~D~~l~~~~~--wl~~~~  118 (121)
                      ++++++.. .+.|+|.++-+...  |+.+..
T Consensus       235 ~Lm~l~~~-~~VPVDvHi~ria~~y~l~~~~  264 (323)
T KOG2875|consen  235 CLMSLDKL-SAVPVDVHIWRIAQDYILPGLS  264 (323)
T ss_pred             hhhhcCCC-CcccchhhHHHHhhcccCCCcc
Confidence            99999998 47777777655543  544443

>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=98.67  E-value=1.9e-08  Score=54.04  Aligned_cols=24  Identities=29%  Similarity=0.430  Sum_probs=20.8

Q ss_pred             HhhHHHhccCCCCcHHHHHHHHHH
Q 033363           69 GESWTHVTQLHGVGKYAADAFAIF   92 (121)
Q Consensus        69 ~~~~~~L~~lpGIG~~tA~~vl~f   92 (121)
                      ..++++|.++||||||||++|+.|
T Consensus         7 pas~eeL~~lpGIG~~tA~~I~~~   30 (30)
T PF00633_consen    7 PASIEELMKLPGIGPKTANAILSF   30 (30)
T ss_dssp             TSSHHHHHTSTT-SHHHHHHHHHH
T ss_pred             CCCHHHHHhCCCcCHHHHHHHHhC
Confidence            357899999999999999999976

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 ....

>COG1059 Thermostable 8-oxoguanine DNA glycosylase [DNA replication, recombination, and repair]

Probab=97.43  E-value=0.00078  Score=50.52  Aligned_cols=58  Identities=16%  Similarity=0.250  Sum_probs=48.1

Q ss_pred             HHHhcCCHHHHHHHHhhc--CChhHHHHHHHHHHHHHHH-----------h-hHHHhc-cCCCCcHHHHHHHH
Q 033363           33 KTATEVDAEEIEKIISTL--GLQKKRAPMIKRFSQEYLG-----------E-SWTHVT-QLHGVGKYAADAFA   90 (121)
Q Consensus        33 ~~la~a~~~eL~~~i~~~--Gl~~~Ka~~i~~~a~~i~~-----------~-~~~~L~-~lpGIG~~tA~~vl   90 (121)
                      +.+..++.+||.+.++.+  .|++.||++|.+.=+.+-+           . .++.|. .++|+|-|-|.-+|
T Consensus        66 ~gfly~~~eEL~e~Lk~~g~Rf~n~raeyIVeaR~~~~~lk~~v~~~~~~~vaRE~Lv~nikGiGyKEASHFL  138 (210)
T COG1059          66 DGFLYLSEEELREKLKEVGYRFYNVRAEYIVEAREKFDDLKIIVKADENEKVARELLVENIKGIGYKEASHFL  138 (210)
T ss_pred             cccccCCHHHHHHHHHHhcchhcccchHHHHHHHHHHHHHHHHHhcCcchHHHHHHHHHHcccccHHHHHHHH
Confidence            456677899999999999  5899999999997666533           1 567777 99999999999887

>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=97.03  E-value=0.0063  Score=37.89  Aligned_cols=52  Identities=23%  Similarity=0.262  Sum_probs=38.7

Q ss_pred             HHHHHHHhhcCChhHHHHHHHHHHHHHHH-----hhHHH-hccCCCCcHHHHHHHHHH
Q 033363           41 EEIEKIISTLGLQKKRAPMIKRFSQEYLG-----ESWTH-VTQLHGVGKYAADAFAIF   92 (121)
Q Consensus        41 ~eL~~~i~~~Gl~~~Ka~~i~~~a~~i~~-----~~~~~-L~~lpGIG~~tA~~vl~f   92 (121)
                      +++.+...-.|=...|+..-.+.+..+..     .+.++ +.+|||||+.++.-|--|
T Consensus         9 ~~la~~~~~~~~~~~r~~aY~~Aa~~i~~l~~~i~~~~~~~~~l~gIG~~ia~kI~E~   66 (68)
T PF14716_consen    9 EELADLYELQGGDPFRARAYRRAAAAIKALPYPITSGEEDLKKLPGIGKSIAKKIDEI   66 (68)
T ss_dssp             HHHHHHHHHTSTSHHHHHHHHHHHHHHHHSSS-HHSHHHHHCTSTTTTHHHHHHHHHH
T ss_pred             HHHHHHHHHhhCCcHHHHHHHHHHHHHHhCCHhHhhHHHHHhhCCCCCHHHHHHHHHH
Confidence            44555555554446889999999988877     35566 999999999999987543

...

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

Probab=96.95  E-value=0.00059  Score=34.97  Aligned_cols=21  Identities=14%  Similarity=0.208  Sum_probs=18.1

Q ss_pred             HhccCCCCcHHHHHHHHHHhc
Q 033363           74 HVTQLHGVGKYAADAFAIFCT   94 (121)
Q Consensus        74 ~L~~lpGIG~~tA~~vl~f~~   94 (121)
                      .|.++||||+++|+.++.+..
T Consensus         2 ~L~~i~GiG~k~A~~il~~~~   22 (26)
T smart00278        2 ELLKVPGIGPKTAEKILEAXX   22 (26)
T ss_pred             hhhhCCCCCHHHHHHHHHhcc
Confidence            588999999999999987543

>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional

Probab=96.91  E-value=0.0029  Score=47.59  Aligned_cols=53  Identities=21%  Similarity=0.323  Sum_probs=42.0

Q ss_pred             HHHHhhcCChhHHHHHHH------HHHHHHHHhhHHHhccCCCCcHHHHHHHHHHhcCC
Q 033363           44 EKIISTLGLQKKRAPMIK------RFSQEYLGESWTHVTQLHGVGKYAADAFAIFCTGK   96 (121)
Q Consensus        44 ~~~i~~~Gl~~~Ka~~i~------~~a~~i~~~~~~~L~~lpGIG~~tA~~vl~f~~~~   96 (121)
                      +.+++--|...+.|-.|.      +++++|.+++.+.|.++||||+|||+=+.+---++
T Consensus        72 ~~LisVsGIGPK~ALaILs~~~~~el~~aI~~~D~~~L~~vpGIGkKtAeRIIlELkdK  130 (196)
T PRK13901         72 EELIGVDGIGPRAALRVLSGIKYNEFRDAIDREDIELISKVKGIGNKMAGKIFLKLRGK  130 (196)
T ss_pred             HHHhCcCCcCHHHHHHHHcCCCHHHHHHHHHhCCHHHHhhCCCCCHHHHHHHHHHHHHh
Confidence            344555677777787777      67888888999999999999999999888654444

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

Probab=96.91  E-value=0.0012  Score=40.82  Aligned_cols=24  Identities=21%  Similarity=0.338  Sum_probs=17.4

Q ss_pred             hHHHhccCCCCcHHHHHHHHHHhc
Q 033363           71 SWTHVTQLHGVGKYAADAFAIFCT   94 (121)
Q Consensus        71 ~~~~L~~lpGIG~~tA~~vl~f~~   94 (121)
                      +.++|.++||||+.+|+.+..|--
T Consensus        33 ~~e~L~~i~gIG~~~A~si~~ff~   56 (64)
T PF12826_consen   33 SVEELSAIPGIGPKIAQSIYEFFQ   56 (64)
T ss_dssp             -HHHHCTSTT--HHHHHHHHHHHH
T ss_pred             CHHHHhccCCcCHHHHHHHHHHHC
Confidence            456789999999999999987643

>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional

Probab=96.51  E-value=0.0032  Score=46.92  Aligned_cols=50  Identities=16%  Similarity=0.145  Sum_probs=36.7

Q ss_pred             HhhcCChhHHHHHHH------HHHHHHHHhhHHHhccCCCCcHHHHHHHHHHhcCC
Q 033363           47 ISTLGLQKKRAPMIK------RFSQEYLGESWTHVTQLHGVGKYAADAFAIFCTGK   96 (121)
Q Consensus        47 i~~~Gl~~~Ka~~i~------~~a~~i~~~~~~~L~~lpGIG~~tA~~vl~f~~~~   96 (121)
                      ++--|...+.|-.|.      +++++|.+++.+.|+++||||+|||+-+.+---++
T Consensus        76 i~V~GIGpK~AL~iLs~~~~~el~~aI~~~D~~~L~~vpGIGkKtAerIilELkdK  131 (188)
T PRK14606         76 TKVSRLGPKTALKIISNEDAETLVTMIASQDVEGLSKLPGISKKTAERIVMELKDE  131 (188)
T ss_pred             hccCCccHHHHHHHHcCCCHHHHHHHHHhCCHHHHhhCCCCCHHHHHHHHHHHHHh
Confidence            333455555555554      46777778999999999999999999988554444

>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional

Probab=96.51  E-value=0.0033  Score=46.76  Aligned_cols=51  Identities=12%  Similarity=0.146  Sum_probs=37.2

Q ss_pred             HHhhcCChhHHHHHHH------HHHHHHHHhhHHHhccCCCCcHHHHHHHHHHhcCC
Q 033363           46 IISTLGLQKKRAPMIK------RFSQEYLGESWTHVTQLHGVGKYAADAFAIFCTGK   96 (121)
Q Consensus        46 ~i~~~Gl~~~Ka~~i~------~~a~~i~~~~~~~L~~lpGIG~~tA~~vl~f~~~~   96 (121)
                      +++--|...+.|-.|.      ++.++|.+++.+.|.++||||+|||+=+.+---++
T Consensus        75 Li~VsGIGpK~Al~ILs~~~~~el~~aI~~~D~~~L~~vpGIGkKtAeRIilELkdK  131 (183)
T PRK14601         75 LLKVNGIGANTAMAVCSSLDVNSFYKALSLGDESVLKKVPGIGPKSAKRIIAELSDA  131 (183)
T ss_pred             HhccCCccHHHHHHHHcCCCHHHHHHHHHhCCHHHHhhCCCCCHHHHHHHHHHHHHH
Confidence            3444555555555444      46777777999999999999999999988655444

>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional

Probab=96.41  E-value=0.0041  Score=46.85  Aligned_cols=50  Identities=24%  Similarity=0.195  Sum_probs=35.7

Q ss_pred             HhhcCChhHHHHHHHH------HHHHHHHhhHHHhccCCCCcHHHHHHHHHHhcCC
Q 033363           47 ISTLGLQKKRAPMIKR------FSQEYLGESWTHVTQLHGVGKYAADAFAIFCTGK   96 (121)
Q Consensus        47 i~~~Gl~~~Ka~~i~~------~a~~i~~~~~~~L~~lpGIG~~tA~~vl~f~~~~   96 (121)
                      +.--|...+.|-.|..      ++++|.+++.+.|.++||||+|||+-+..---++
T Consensus        77 i~V~GIGpK~Al~iLs~~~~~~l~~aI~~~D~~~L~~ipGIGkKtAerIilELkdK  132 (203)
T PRK14602         77 ISISKVGAKTALAILSQFRPDDLRRLVAEEDVAALTRVSGIGKKTAQHIFLELKYK  132 (203)
T ss_pred             hCCCCcCHHHHHHHHhhCCHHHHHHHHHhCCHHHHhcCCCcCHHHHHHHHHHHHHh
Confidence            3444555555555543      4567777899999999999999999988544333

>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional

Probab=96.34  E-value=0.0047  Score=46.36  Aligned_cols=43  Identities=26%  Similarity=0.248  Sum_probs=32.3

Q ss_pred             cCChhHHHHHHH------HHHHHHHHhhHHHhccCCCCcHHHHHHHHHH
Q 033363           50 LGLQKKRAPMIK------RFSQEYLGESWTHVTQLHGVGKYAADAFAIF   92 (121)
Q Consensus        50 ~Gl~~~Ka~~i~------~~a~~i~~~~~~~L~~lpGIG~~tA~~vl~f   92 (121)
                      -|...+.|-.|.      +++++|.+++.+.|.++||||+|||+-+..-
T Consensus        78 ~GIGpK~AL~iLs~~~~~~l~~aI~~~D~~~L~kvpGIGkKtAerIilE  126 (197)
T PRK14603         78 SGVGPKLALALLSALPPALLARALLEGDARLLTSASGVGKKLAERIALE  126 (197)
T ss_pred             CCcCHHHHHHHHcCCCHHHHHHHHHhCCHHHHhhCCCCCHHHHHHHHHH
Confidence            445544554443      4677777799999999999999999988743

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

Probab=96.33  E-value=0.0046  Score=46.66  Aligned_cols=54  Identities=26%  Similarity=0.371  Sum_probs=37.6

Q ss_pred             HHHHhhcCChhHHHHHH------HHHHHHHHHhhHHHhccCCCCcHHHHHHHHHHhcCCC
Q 033363           44 EKIISTLGLQKKRAPMI------KRFSQEYLGESWTHVTQLHGVGKYAADAFAIFCTGKW   97 (121)
Q Consensus        44 ~~~i~~~Gl~~~Ka~~i------~~~a~~i~~~~~~~L~~lpGIG~~tA~~vl~f~~~~~   97 (121)
                      ..+|+--|...+=|-.|      -+++++|..++.+.|.++||||+|||+-+++---++.
T Consensus        73 ~~LisVnGIGpK~ALaiLs~~~~~~l~~aI~~~d~~~L~k~PGIGkKtAerivleLk~K~  132 (201)
T COG0632          73 RLLISVNGIGPKLALAILSNLDPEELAQAIANEDVKALSKIPGIGKKTAERIVLELKGKL  132 (201)
T ss_pred             HHHHccCCccHHHHHHHHcCCCHHHHHHHHHhcChHhhhcCCCCCHHHHHHHHHHHhhhh
Confidence            33444455554334333      3457777778999999999999999999887655543

>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional

Probab=96.31  E-value=0.005  Score=46.15  Aligned_cols=50  Identities=22%  Similarity=0.333  Sum_probs=35.9

Q ss_pred             HhhcCChhHHHHHHH------HHHHHHHHhhHHHhccCCCCcHHHHHHHHHHhcCC
Q 033363           47 ISTLGLQKKRAPMIK------RFSQEYLGESWTHVTQLHGVGKYAADAFAIFCTGK   96 (121)
Q Consensus        47 i~~~Gl~~~Ka~~i~------~~a~~i~~~~~~~L~~lpGIG~~tA~~vl~f~~~~   96 (121)
                      ++--|...+.|-.|.      +++++|.+++.+.|.++||||+|||+=+..---++
T Consensus        76 i~V~GIGpK~Al~iLs~~~~~el~~aI~~~D~~~L~kvpGIGkKtAerIilELk~K  131 (195)
T PRK14604         76 IGVSGVGPKAALNLLSSGTPDELQLAIAGGDVARLARVPGIGKKTAERIVLELKGK  131 (195)
T ss_pred             hCcCCcCHHHHHHHHcCCCHHHHHHHHHhCCHHHHhhCCCCCHHHHHHHHHHHHHH
Confidence            333455555555544      45667777899999999999999999888654444

>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional

Probab=96.20  E-value=0.014  Score=43.57  Aligned_cols=46  Identities=15%  Similarity=0.281  Sum_probs=35.4

Q ss_pred             HHHhhcCChhHHHHHHHH------HHHHHHHhhHHHhccCCCCcHHHHHHHH
Q 033363           45 KIISTLGLQKKRAPMIKR------FSQEYLGESWTHVTQLHGVGKYAADAFA   90 (121)
Q Consensus        45 ~~i~~~Gl~~~Ka~~i~~------~a~~i~~~~~~~L~~lpGIG~~tA~~vl   90 (121)
                      .+++--|.....|..|.+      +++.+.+++.+.|.++||||+|||+-+.
T Consensus        74 ~Li~V~GIGpK~Al~ILs~~~~~~l~~aI~~~D~~~L~~vpGIGkKtAerIi  125 (194)
T PRK14605         74 TLIDVSGIGPKLGLAMLSAMNAEALASAIISGNAELLSTIPGIGKKTASRIV  125 (194)
T ss_pred             HHhCCCCCCHHHHHHHHHhCCHHHHHHHHHhCCHHHHHhCCCCCHHHHHHHH
Confidence            334445667677777766      3666777899999999999999999954

>TIGR00084 ruvA Holliday junction DNA helicase, RuvA subunit

Probab=95.96  E-value=0.024  Score=42.27  Aligned_cols=51  Identities=24%  Similarity=0.273  Sum_probs=36.3

Q ss_pred             HHHHhhcCChhHHHHHHHH------HHHHHHHhhHHHhccCCCCcHHHHHHHHHHhc
Q 033363           44 EKIISTLGLQKKRAPMIKR------FSQEYLGESWTHVTQLHGVGKYAADAFAIFCT   94 (121)
Q Consensus        44 ~~~i~~~Gl~~~Ka~~i~~------~a~~i~~~~~~~L~~lpGIG~~tA~~vl~f~~   94 (121)
                      ..+++--|...++|..|..      +.+++.+++.+.|.++||||+|||+-+++---
T Consensus        72 ~~L~~V~GIGpK~Al~iL~~~~~~el~~aI~~~d~~~L~~ipGiGkKtAerIileLk  128 (191)
T TIGR00084        72 KELIKVNGVGPKLALAILSNMSPEEFVYAIETEEVKALVKIPGVGKKTAERLLLELK  128 (191)
T ss_pred             HHHhCCCCCCHHHHHHHHhcCCHHHHHHHHHhCCHHHHHhCCCCCHHHHHHHHHHHH
Confidence            3344555677677776654      34455557889999999999999999984433

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.

>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional

Probab=95.90  E-value=0.0081  Score=44.72  Aligned_cols=49  Identities=16%  Similarity=0.200  Sum_probs=34.4

Q ss_pred             HhhcCChhHHHHHHH------HHHHHHHHhhHHHhccCCCCcHHHHHHHHHHhcCC
Q 033363           47 ISTLGLQKKRAPMIK------RFSQEYLGESWTHVTQLHGVGKYAADAFAIFCTGK   96 (121)
Q Consensus        47 i~~~Gl~~~Ka~~i~------~~a~~i~~~~~~~L~~lpGIG~~tA~~vl~f~~~~   96 (121)
                      ++--|...+.|-.|.      ++.++|.+++.+.| ++||||+|||+-+.+---++
T Consensus        76 isV~GIGpK~Al~iLs~~~~~~l~~aI~~~D~~~L-~vpGIGkKtAerIilELk~K  130 (186)
T PRK14600         76 VKVSGVNYKTAMSILSKLTPEQLFSAIVNEDKAAL-KVNGIGEKLINRIITELQYK  130 (186)
T ss_pred             hCcCCcCHHHHHHHHccCCHHHHHHHHHcCCHhhe-ECCCCcHHHHHHHHHHHHHH
Confidence            344455555555444      35667777899999 99999999999988544443

>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=95.83  E-value=0.068  Score=32.21  Aligned_cols=21  Identities=14%  Similarity=0.316  Sum_probs=13.7

Q ss_pred             hHHHhccCCCCcHHHHHHHHH
Q 033363           71 SWTHVTQLHGVGKYAADAFAI   91 (121)
Q Consensus        71 ~~~~L~~lpGIG~~tA~~vl~   91 (121)
                      +.++|.++||||+++|+-+..
T Consensus        36 ~~~~L~~i~Gig~~~a~~i~~   56 (60)
T PF14520_consen   36 DPEELAEIPGIGEKTAEKIIE   56 (60)
T ss_dssp             HHHHHHTSTTSSHHHHHHHHH
T ss_pred             CHHHHhcCCCCCHHHHHHHHH
Confidence            445677777777777766553

...

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

Probab=95.75  E-value=0.0081  Score=39.04  Aligned_cols=40  Identities=18%  Similarity=0.204  Sum_probs=32.6

Q ss_pred             HHhccCCCCcHHHHHHHHHHhcCCCCccCcchHHHHHHHHHH
Q 033363           73 THVTQLHGVGKYAADAFAIFCTGKWDRVRPTDHMLNYYWEFL  114 (121)
Q Consensus        73 ~~L~~lpGIG~~tA~~vl~f~~~~~~~v~p~D~~l~~~~~wl  114 (121)
                      +.|+++||||+-||..++... +.++ -|+....+..|.++-
T Consensus         2 ~~l~sipGig~~~a~~llaei-gd~~-rF~~~~~l~~~~Gl~   41 (87)
T PF02371_consen    2 ELLTSIPGIGPITAATLLAEI-GDIS-RFKSAKQLASYAGLA   41 (87)
T ss_pred             chhcCCCCccHHHHHHHHHHH-cCch-hcccchhhhhccccc
Confidence            458999999999999999877 6653 688888888886653

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

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

Probab=95.75  E-value=0.023  Score=40.21  Aligned_cols=65  Identities=12%  Similarity=0.089  Sum_probs=47.9

Q ss_pred             HHHHHHHHHHhCCCHHHHhcCCHHHHHHHHhhcCChhHHHHHHHHHHHHHHH---hhHHHhccCCCCcHHHHHHHHHH
Q 033363           18 AGRVISDLFTLCPDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQEYLG---ESWTHVTQLHGVGKYAADAFAIF   92 (121)
Q Consensus        18 v~~v~~~l~~~~pt~~~la~a~~~eL~~~i~~~Gl~~~Ka~~i~~~a~~i~~---~~~~~L~~lpGIG~~tA~~vl~f   92 (121)
                      +|++=.++- .+...=++-.++.+++++ +  =|++..+|+.|.+      .   .+.++|..+||||+++.+.+--+
T Consensus        39 ~N~~d~kl~-~~~~kIdiN~A~~~el~~-l--pGigP~~A~~IV~------nGpf~sveDL~~V~GIgekqk~~l~k~  106 (132)
T PRK02515         39 QNVADAKLG-EFGEKIDLNNSSVRAFRQ-F--PGMYPTLAGKIVK------NAPYDSVEDVLNLPGLSERQKELLEAN  106 (132)
T ss_pred             cChhhHHHH-hcCCcccCCccCHHHHHH-C--CCCCHHHHHHHHH------CCCCCCHHHHHcCCCCCHHHHHHHHHh
Confidence            344445555 566677788888888776 3  4777889988872      3   48899999999999988776654

>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed

Probab=95.58  E-value=0.032  Score=41.46  Aligned_cols=50  Identities=26%  Similarity=0.237  Sum_probs=36.3

Q ss_pred             HhhcCChhHHHHHHHHH------HHHHHHhhHHHhccCCCCcHHHHHHHHHHhcCC
Q 033363           47 ISTLGLQKKRAPMIKRF------SQEYLGESWTHVTQLHGVGKYAADAFAIFCTGK   96 (121)
Q Consensus        47 i~~~Gl~~~Ka~~i~~~------a~~i~~~~~~~L~~lpGIG~~tA~~vl~f~~~~   96 (121)
                      +.-=|....+|+.|.+.      .+.+.+++.++|.++||||+++|+.+...--+.
T Consensus        76 ~~i~GIGpk~A~~il~~fg~~~l~~~i~~~d~~~L~~v~Gig~k~A~~I~~~l~~~  131 (192)
T PRK00116         76 ISVSGVGPKLALAILSGLSPEELVQAIANGDVKALTKVPGIGKKTAERIVLELKDK  131 (192)
T ss_pred             hcCCCCCHHHHHHHHHhCCHHHHHHHHHhCCHHHHHhCCCCCHHHHHHHHHHHHHH
Confidence            33456667788877664      233555788999999999999999998654443

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

Probab=95.30  E-value=0.027  Score=34.90  Aligned_cols=58  Identities=21%  Similarity=0.334  Sum_probs=39.2

Q ss_pred             HHHhcCCHHHHHHHHhhcCChhHHHHHHHHHHHHHH-HhhHHHhccCCCCcHHHHHHHHHH
Q 033363           33 KTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQEYL-GESWTHVTQLHGVGKYAADAFAIF   92 (121)
Q Consensus        33 ~~la~a~~~eL~~~i~~~Gl~~~Ka~~i~~~a~~i~-~~~~~~L~~lpGIG~~tA~~vl~f   92 (121)
                      =++-.++.++|..++.  |+...+++.|.+-=...- -.+.++|.++||||+++++-+.-+
T Consensus         8 invNta~~~~L~~~ip--gig~~~a~~Il~~R~~~g~~~s~~dL~~v~gi~~~~~~~i~~~   66 (69)
T TIGR00426         8 VNINTATAEELQRAMN--GVGLKKAEAIVSYREEYGPFKTVEDLKQVPGIGNSLVEKNLAV   66 (69)
T ss_pred             eECcCCCHHHHHhHCC--CCCHHHHHHHHHHHHHcCCcCCHHHHHcCCCCCHHHHHHHHhh
Confidence            3455678888776554  455456666655422110 047899999999999999988765

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.

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

Probab=95.13  E-value=0.032  Score=34.39  Aligned_cols=51  Identities=22%  Similarity=0.378  Sum_probs=31.3

Q ss_pred             HhcCCHHHHHHHHhhc-CChhHHHHHHHHHHHHHHH-hhHHHhccCCCCcHHHHHHH
Q 033363           35 ATEVDAEEIEKIISTL-GLQKKRAPMIKRFSQEYLG-ESWTHVTQLHGVGKYAADAF   89 (121)
Q Consensus        35 la~a~~~eL~~~i~~~-Gl~~~Ka~~i~~~a~~i~~-~~~~~L~~lpGIG~~tA~~v   89 (121)
                      +-.|+.+||    ..+ |++...|+.|.+.=+..-. .+.++|..++|||+.+.+-+
T Consensus         8 iN~as~~eL----~~lpgi~~~~A~~Iv~~R~~~G~f~s~~dL~~v~gi~~~~~~~l   60 (65)
T PF12836_consen    8 INTASAEEL----QALPGIGPKQAKAIVEYREKNGPFKSLEDLKEVPGIGPKTYEKL   60 (65)
T ss_dssp             TTTS-HHHH----HTSTT--HHHHHHHHHHHHHH-S-SSGGGGGGSTT--HHHHHHH
T ss_pred             CccCCHHHH----HHcCCCCHHHHHHHHHHHHhCcCCCCHHHHhhCCCCCHHHHHHH
Confidence            345677774    344 8888888888765444311 47889999999999987754

>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=94.62  E-value=0.096  Score=31.54  Aligned_cols=42  Identities=21%  Similarity=0.303  Sum_probs=33.3

Q ss_pred             HHHHHHHh-CCCHHHHhcCCHHHHHHHHhhcCChhHHHHHHHHHHH
Q 033363           21 VISDLFTL-CPDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQ   65 (121)
Q Consensus        21 v~~~l~~~-~pt~~~la~a~~~eL~~~i~~~Gl~~~Ka~~i~~~a~   65 (121)
                      ...+|.+. |.|+++++.+++++|.++   -|+...+++.|++-++
T Consensus        17 ~a~~L~~~G~~t~~~l~~a~~~~L~~i---~Gig~~~a~~i~~~~~   59 (60)
T PF14520_consen   17 RAEKLYEAGIKTLEDLANADPEELAEI---PGIGEKTAEKIIEAAR   59 (60)
T ss_dssp             HHHHHHHTTCSSHHHHHTSHHHHHHTS---TTSSHHHHHHHHHHHH
T ss_pred             HHHHHHhcCCCcHHHHHcCCHHHHhcC---CCCCHHHHHHHHHHHh
Confidence            34456666 999999999999997653   5888899999988765

...

>TIGR00615 recR recombination protein RecR

Probab=94.27  E-value=0.054  Score=40.74  Aligned_cols=29  Identities=17%  Similarity=0.232  Sum_probs=24.9

Q ss_pred             HhhHHHhccCCCCcHHHHHHHHHHhcCCC
Q 033363           69 GESWTHVTQLHGVGKYAADAFAIFCTGKW   97 (121)
Q Consensus        69 ~~~~~~L~~lpGIG~~tA~~vl~f~~~~~   97 (121)
                      ++..+.|.+|||||+|+|.=+..+-+..+
T Consensus         7 ~~Li~~l~~LPGIG~KsA~RlA~~ll~~~   35 (195)
T TIGR00615         7 SKLIESLKKLPGIGPKSAQRLAFHLLKRD   35 (195)
T ss_pred             HHHHHHHHHCCCCCHHHHHHHHHHHHcCC
Confidence            45678899999999999999998888764

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

>PRK00076 recR recombination protein RecR; Reviewed

Probab=94.20  E-value=0.055  Score=40.71  Aligned_cols=29  Identities=17%  Similarity=0.209  Sum_probs=24.9

Q ss_pred             HhhHHHhccCCCCcHHHHHHHHHHhcCCC
Q 033363           69 GESWTHVTQLHGVGKYAADAFAIFCTGKW   97 (121)
Q Consensus        69 ~~~~~~L~~lpGIG~~tA~~vl~f~~~~~   97 (121)
                      ++..+.|.+|||||+|+|.=+..+-+.++
T Consensus         7 ~~Li~~l~~LPGIG~KsA~Rla~~ll~~~   35 (196)
T PRK00076          7 EKLIEALRKLPGIGPKSAQRLAFHLLQRD   35 (196)
T ss_pred             HHHHHHHHHCCCCCHHHHHHHHHHHHcCC
Confidence            45678899999999999999998888764

>PRK14973 DNA topoisomerase I; Provisional

Probab=94.18  E-value=0.25  Score=44.92  Aligned_cols=88  Identities=8%  Similarity=0.046  Sum_probs=59.8

Q ss_pred             HhCCCHHHHhcCCHHHHHHHHhhcCChhHHHHHHHHHHH-HHHH------------hhHHHhccCCCCcHHHHHHHHHHh
Q 033363           27 TLCPDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQ-EYLG------------ESWTHVTQLHGVGKYAADAFAIFC   93 (121)
Q Consensus        27 ~~~pt~~~la~a~~~eL~~~i~~~Gl~~~Ka~~i~~~a~-~i~~------------~~~~~L~~lpGIG~~tA~~vl~f~   93 (121)
                      ..|-++++++.+++++|..   --|++..-...+...+. ....            ....+|.+++|||++|.+-.-.-+
T Consensus       821 ~G~~~~~d~~~a~p~~La~---~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~el~~vkg~ge~t~~~l~~ag  897 (936)
T PRK14973        821 AGFDTPEDFCSVHPAYLAL---KTGISPETICRHAKLVCEKLGRPVPEKISKAAFERGRAELLSVPGLGETTLEKLYLAG  897 (936)
T ss_pred             hcCCCHHHHHhcCHHHHhc---CCCCChhhHHHHHHHHHHHhcCCCchhhhhhhhcccchhhhhccCCCHHHHHHHHHcC
Confidence            4588999999999999864   47898767666655554 3332            245669999999999997766655


Q ss_pred             cCCCCccCcch------------HHHHHHHHHHHHh
Q 033363           94 TGKWDRVRPTD------------HMLNYYWEFLVST  117 (121)
Q Consensus        94 ~~~~~~v~p~D------------~~l~~~~~wl~~~  117 (121)
                      .-.++.+.-.|            ..+|.+.+|+.-.
T Consensus       898 ~~~~e~l~~~d~~~la~~~~i~~k~~~~~~~~~~~~  933 (936)
T PRK14973        898 VYDGDLLVSADPKKLAKVTGIDEKKLRNLQAYAKKV  933 (936)
T ss_pred             CCCHHHhccCCHHHHhhhcCCCHHHHHHHHHHHhhh
Confidence            54433232223            3567777776543

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

Probab=94.16  E-value=0.35  Score=31.78  Aligned_cols=61  Identities=21%  Similarity=0.329  Sum_probs=36.2

Q ss_pred             HHHHHHHHhhcCChhHHHHHHHHHHH-----HHHHhhHHHhccCCCCcHHHHHHHHHHhcCCCCccCcchH
Q 033363           40 AEEIEKIISTLGLQKKRAPMIKRFSQ-----EYLGESWTHVTQLHGVGKYAADAFAIFCTGKWDRVRPTDH  105 (121)
Q Consensus        40 ~~eL~~~i~~~Gl~~~Ka~~i~~~a~-----~i~~~~~~~L~~lpGIG~~tA~~vl~f~~~~~~~v~p~D~  105 (121)
                      ..++...|.+.|++...+..|.+.-.     .+.++...-+..++|||-++||.+... +|    +.++|.
T Consensus         8 ~~~~~~~L~~~gl~~~~a~kl~~~yg~~ai~~l~~nPY~L~~~i~gi~F~~aD~iA~~-~g----~~~~d~   73 (94)
T PF14490_consen    8 LRELMAFLQEYGLSPKLAMKLYKKYGDDAIEILKENPYRLIEDIDGIGFKTADKIALK-LG----IEPDDP   73 (94)
T ss_dssp             -HHHHHHHHHTT--HHHHHHHHHHH-TTHHHHHHH-STCCCB-SSSSBHHHHHHHHHT-TT------TT-H
T ss_pred             HHHHHHHHHHcCCCHHHHHHHHHHHhHHHHHHHHHChHHHHHHccCCCHHHHHHHHHH-cC----CCCCCH
Confidence            45666678899999888887776522     222233333444999999999999874 44    566664

>PRK13844 recombination protein RecR; Provisional

Probab=94.12  E-value=0.059  Score=40.69  Aligned_cols=29  Identities=17%  Similarity=0.289  Sum_probs=25.1

Q ss_pred             HhhHHHhccCCCCcHHHHHHHHHHhcCCC
Q 033363           69 GESWTHVTQLHGVGKYAADAFAIFCTGKW   97 (121)
Q Consensus        69 ~~~~~~L~~lpGIG~~tA~~vl~f~~~~~   97 (121)
                      ++..+.|.+|||||+|+|.=+..+-+..+
T Consensus        11 ~~LI~~l~~LPGIG~KsA~Rla~~lL~~~   39 (200)
T PRK13844         11 SAVIESLRKLPTIGKKSSQRLALYLLDKS   39 (200)
T ss_pred             HHHHHHHHHCCCCCHHHHHHHHHHHHcCC
Confidence            45678899999999999999998888764

>TIGR01259 comE comEA protein

Probab=94.11  E-value=0.073  Score=36.81  Aligned_cols=58  Identities=19%  Similarity=0.311  Sum_probs=39.5

Q ss_pred             HHHHhcCCHHHHHHHHhhcCChhHHHHHHHHHHHHHH-HhhHHHhccCCCCcHHHHHHHHHH
Q 033363           32 AKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQEYL-GESWTHVTQLHGVGKYAADAFAIF   92 (121)
Q Consensus        32 ~~~la~a~~~eL~~~i~~~Gl~~~Ka~~i~~~a~~i~-~~~~~~L~~lpGIG~~tA~~vl~f   92 (121)
                      +-++-.|+.++|+.+   -|+...+|+.|.+-=+.-- -.++++|..+||||+++++-+.-|
T Consensus        59 ~iniNtA~~~eL~~l---pGIG~~~A~~Ii~~R~~~g~f~s~eeL~~V~GIg~k~~~~i~~~  117 (120)
T TIGR01259        59 AVNINAASLEELQAL---PGIGPAKAKAIIEYREENGAFKSVDDLTKVSGIGEKSLEKLKDY  117 (120)
T ss_pred             CEeCCcCCHHHHhcC---CCCCHHHHHHHHHHHHhcCCcCCHHHHHcCCCCCHHHHHHHHhc
Confidence            445667777777653   4666678877766543210 147889999999999998877644

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.

>smart00483 POLXc DNA polymerase X family

Probab=94.09  E-value=0.17  Score=40.65  Aligned_cols=52  Identities=12%  Similarity=0.218  Sum_probs=37.7

Q ss_pred             HHHHHHhhcCChhHHHHHHHHHHHHHHH-----hhHHHhccCCCCcHHHHHHHHHHh
Q 033363           42 EIEKIISTLGLQKKRAPMIKRFSQEYLG-----ESWTHVTQLHGVGKYAADAFAIFC   93 (121)
Q Consensus        42 eL~~~i~~~Gl~~~Ka~~i~~~a~~i~~-----~~~~~L~~lpGIG~~tA~~vl~f~   93 (121)
                      ++.+++.-.|=...|.++..++|..+..     .+.++|.+|||||+.+|+-|--+.
T Consensus        12 ~la~l~el~gen~~k~~ay~~Aa~~i~~l~~~i~~~~~l~~lpgIG~~ia~kI~Eil   68 (334)
T smart00483       12 ILAENYEVFGENKRKCSYFRKAASVLKSLPFPINSMKDLKGLPGIGDKIKKKIEEII   68 (334)
T ss_pred             HHHHHHHHhcccHHHHHHHHHHHHHHHhCCCCCCCHHHHhcCCCccHHHHHHHHHHH
Confidence            3444444455555677888888887765     466789999999999999887553

includes vertebrate polymerase beta and terminal deoxynucleotidyltransferases

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

Probab=93.94  E-value=0.06  Score=40.56  Aligned_cols=29  Identities=21%  Similarity=0.217  Sum_probs=24.5

Q ss_pred             HhhHHHhccCCCCcHHHHHHHHHHhcCCC
Q 033363           69 GESWTHVTQLHGVGKYAADAFAIFCTGKW   97 (121)
Q Consensus        69 ~~~~~~L~~lpGIG~~tA~~vl~f~~~~~   97 (121)
                      ++.++.|.+|||||+|+|.=+..+-+.+.
T Consensus         8 ~~LI~~l~kLPGvG~KsA~R~AfhLL~~~   36 (198)
T COG0353           8 EKLIDALKKLPGVGPKSAQRLAFHLLQRD   36 (198)
T ss_pred             HHHHHHHhhCCCCChhHHHHHHHHHHccC
Confidence            45678899999999999999888877663

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

Probab=93.76  E-value=0.065  Score=35.80  Aligned_cols=31  Identities=13%  Similarity=0.259  Sum_probs=25.7

Q ss_pred             hhHHHhccCCCCcHHHHHHHHHHhcCCCCcc
Q 033363           70 ESWTHVTQLHGVGKYAADAFAIFCTGKWDRV  100 (121)
Q Consensus        70 ~~~~~L~~lpGIG~~tA~~vl~f~~~~~~~v  100 (121)
                      +...+|+.|||||+.+|.-+...++..++.+
T Consensus         9 ~~~~~L~~iP~IG~a~a~DL~~LGi~s~~~L   39 (93)
T PF11731_consen    9 AGLSDLTDIPNIGKATAEDLRLLGIRSPADL   39 (93)
T ss_pred             HHHHHHhcCCCccHHHHHHHHHcCCCCHHHH
Confidence            4577899999999999999998888765433

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

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

Probab=93.66  E-value=0.2  Score=39.72  Aligned_cols=44  Identities=23%  Similarity=0.234  Sum_probs=28.0

Q ss_pred             CChhHHHHHHHHHHHH--HHH---------hhHHHhccCCCCcHHHHHHHHHHhcCC
Q 033363           51 GLQKKRAPMIKRFSQE--YLG---------ESWTHVTQLHGVGKYAADAFAIFCTGK   96 (121)
Q Consensus        51 Gl~~~Ka~~i~~~a~~--i~~---------~~~~~L~~lpGIG~~tA~~vl~f~~~~   96 (121)
                      |....-++.|.++.+.  +..         ..+.+|+++|||||++|..+-  .+|-
T Consensus        52 giG~~ia~kI~E~~~tG~~~~le~l~~~~~~~l~~l~~i~GiGpk~a~~l~--~lGi  106 (307)
T cd00141          52 GIGKKIAEKIEEILETGKLRKLEELREDVPPGLLLLLRVPGVGPKTARKLY--ELGI  106 (307)
T ss_pred             CccHHHHHHHHHHHHcCCHHHHHHHhccchHHHHHHHcCCCCCHHHHHHHH--HcCC
Confidence            6665556666555442  000         145688899999999998776  4443

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

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

Probab=93.52  E-value=0.13  Score=39.91  Aligned_cols=42  Identities=17%  Similarity=0.260  Sum_probs=35.3

Q ss_pred             HHHHHHhCCCHHHHhcCCHHHHHHHHhhcCChhHHHHHHHHHHHH
Q 033363           22 ISDLFTLCPDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQE   66 (121)
Q Consensus        22 ~~~l~~~~pt~~~la~a~~~eL~~~i~~~Gl~~~Ka~~i~~~a~~   66 (121)
                      ...|...|+|.+.+.+|+.+||+++   -|+..+||+.|++..++
T Consensus       208 a~~LL~~FgsLq~~~~AS~~ele~~---~G~G~~kak~l~~~l~~  249 (254)
T KOG2841|consen  208 AQLLLQKFGSLQQISNASEGELEQC---PGLGPAKAKRLHKFLHQ  249 (254)
T ss_pred             HHHHHHhcccHHHHHhcCHhHHHhC---cCcCHHHHHHHHHHHhc
Confidence            3467788999999999999998876   68888999999887654

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

Probab=93.45  E-value=0.086  Score=32.39  Aligned_cols=23  Identities=26%  Similarity=0.341  Sum_probs=18.3

Q ss_pred             hHHHhccCCCCcHHHHHHHHHHh
Q 033363           71 SWTHVTQLHGVGKYAADAFAIFC   93 (121)
Q Consensus        71 ~~~~L~~lpGIG~~tA~~vl~f~   93 (121)
                      +.++|.++||||++.|+.+..+=
T Consensus        12 s~~eL~~lpgi~~~~A~~Iv~~R   34 (65)
T PF12836_consen   12 SAEELQALPGIGPKQAKAIVEYR   34 (65)
T ss_dssp             -HHHHHTSTT--HHHHHHHHHHH
T ss_pred             CHHHHHHcCCCCHHHHHHHHHHH
Confidence            67899999999999999998875

>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated

Probab=93.42  E-value=0.53  Score=41.35  Aligned_cols=69  Identities=22%  Similarity=0.282  Sum_probs=45.3

Q ss_pred             HHHHHHh--CCCHHHHhcCCHHHHHHHHhhcCChhHHHHHHHHHHHHHHH------------------------------
Q 033363           22 ISDLFTL--CPDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQEYLG------------------------------   69 (121)
Q Consensus        22 ~~~l~~~--~pt~~~la~a~~~eL~~~i~~~Gl~~~Ka~~i~~~a~~i~~------------------------------   69 (121)
                      ...|++.  -.++++|.++..++|.++   =||...+++.|.+.-+...+                              
T Consensus       458 i~~L~~~g~I~~i~DL~~L~~~~L~~l---~gfG~Ksa~~ll~~Ie~sk~~~l~R~l~algi~~IG~~~ak~L~~~f~sl  534 (665)
T PRK07956        458 IEQLFEKGLIHDPADLFKLTAEDLLGL---EGFGEKSAQNLLDAIEKSKETSLARFLYALGIRHVGEKAAKALARHFGSL  534 (665)
T ss_pred             HHHHHHcCCCCCHHHHHhcCHHHHhcC---cCcchHHHHHHHHHHHHhhcCCHHHhhHhhhccCcCHHHHHHHHHHcCCH
Confidence            3445543  358888888887775442   26776677666554443322                              


Q ss_pred             -----hhHHHhccCCCCcHHHHHHHHHHh
Q 033363           70 -----ESWTHVTQLHGVGKYAADAFAIFC   93 (121)
Q Consensus        70 -----~~~~~L~~lpGIG~~tA~~vl~f~   93 (121)
                           .+.++|.+++|||+++|..+..|-
T Consensus       535 ~~l~~As~eeL~~i~GIG~~~A~sI~~ff  563 (665)
T PRK07956        535 EALRAASEEELAAVEGVGEVVAQSIVEFF  563 (665)
T ss_pred             HHHHhCCHHHHhccCCcCHHHHHHHHHHH
Confidence                 145788889999999998887664

>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=93.36  E-value=0.06  Score=28.86  Aligned_cols=16  Identities=25%  Similarity=0.563  Sum_probs=12.7

Q ss_pred             HhccCCCCcHHHHHHH
Q 033363           74 HVTQLHGVGKYAADAF   89 (121)
Q Consensus        74 ~L~~lpGIG~~tA~~v   89 (121)
                      .+.++||||++|+.-+
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            5789999999999764

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 ....

>TIGR00575 dnlj DNA ligase, NAD-dependent

Probab=93.35  E-value=0.53  Score=41.25  Aligned_cols=69  Identities=19%  Similarity=0.257  Sum_probs=42.8

Q ss_pred             HHHHHHhC--CCHHHHhcCCHHHHHHHHhhcCChhHHHHHHHHHHHHHHH------------------------------
Q 033363           22 ISDLFTLC--PDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQEYLG------------------------------   69 (121)
Q Consensus        22 ~~~l~~~~--pt~~~la~a~~~eL~~~i~~~Gl~~~Ka~~i~~~a~~i~~------------------------------   69 (121)
                      ...|++..  -++.+|..++.++|.++   =||....++.|.+..+....                              
T Consensus       445 i~~L~~~g~I~~~~Dl~~L~~~~L~~L---~GfG~Ksa~nIl~~Ie~sk~~~l~r~L~aLgIpgVG~~~ak~L~~~f~sl  521 (652)
T TIGR00575       445 IEQLFEKKLVRSVADLYALKKEDLLEL---EGFGEKSAQNLLNAIEKSKEKPLARLLFALGIRHVGEVTAKNLAKHFGTL  521 (652)
T ss_pred             HHHHHHcCCcCCHHHHHhcCHHHHhhc---cCccHHHHHHHHHHHHHhccCcHHHHHhhccCCCcCHHHHHHHHHHhCCH
Confidence            34455432  47888888887775542   26666677766665554332                              


Q ss_pred             -----hhHHHhccCCCCcHHHHHHHHHHh
Q 033363           70 -----ESWTHVTQLHGVGKYAADAFAIFC   93 (121)
Q Consensus        70 -----~~~~~L~~lpGIG~~tA~~vl~f~   93 (121)
                           .+.++|.++||||+++|..+..|-
T Consensus       522 ~~l~~As~eeL~~i~GIG~~~A~~I~~ff  550 (652)
T TIGR00575       522 DKLKAASLEELLSVEGVGPKVAESIVNFF  550 (652)
T ss_pred             HHHHhCCHHHHhcCCCcCHHHHHHHHHHH
Confidence                 134567777777777777776653

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.

>PRK07945 hypothetical protein; Provisional

Probab=93.12  E-value=0.31  Score=39.18  Aligned_cols=54  Identities=17%  Similarity=0.179  Sum_probs=38.8

Q ss_pred             HHHHHHHhhcCChhHHHHHHHHHHHHHHHh--h-HH------HhccCCCCcHHHHHHHHHHhc
Q 033363           41 EEIEKIISTLGLQKKRAPMIKRFSQEYLGE--S-WT------HVTQLHGVGKYAADAFAIFCT   94 (121)
Q Consensus        41 ~eL~~~i~~~Gl~~~Ka~~i~~~a~~i~~~--~-~~------~L~~lpGIG~~tA~~vl~f~~   94 (121)
                      +++..++.--|=..-|.+.-++.|+.+..-  . .+      +|.+|||||+-||..+.-+.-
T Consensus         8 ~~~a~lle~~~~n~frv~ayr~aa~~~~~~~~~~~~~~~~~g~l~~~~giG~~~a~~i~e~~~   70 (335)
T PRK07945          8 RRIAFLLERARADTYRVRAFRRAADVVEALDAAERARRARAGSLTSLPGIGPKTAKVIAQALA   70 (335)
T ss_pred             HHHHHHHHHcCCChhhHHHHHHHHHHHHhcChhHHHHHHhcCCcccCCCcCHHHHHHHHHHHh
Confidence            344445555565566888888888887762  1 11      689999999999999887754

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

Probab=92.65  E-value=0.21  Score=35.85  Aligned_cols=53  Identities=19%  Similarity=0.333  Sum_probs=30.5

Q ss_pred             HhcCCHHHHHHHHhhcCChhHHHHHHHHHHHHHHH-hhHHHhccCCCCcHHHHHHHH
Q 033363           35 ATEVDAEEIEKIISTLGLQKKRAPMIKRFSQEYLG-ESWTHVTQLHGVGKYAADAFA   90 (121)
Q Consensus        35 la~a~~~eL~~~i~~~Gl~~~Ka~~i~~~a~~i~~-~~~~~L~~lpGIG~~tA~~vl   90 (121)
                      +-.|+.+|| +.|..+  ...||+.|++--+.--. .++++|...+|||+++-+-..
T Consensus        91 iNtAs~eeL-~~lpgI--G~~kA~aIi~yRe~~G~f~sv~dL~~v~GiG~~~~ekl~  144 (149)
T COG1555          91 INTASAEEL-QALPGI--GPKKAQAIIDYREENGPFKSVDDLAKVKGIGPKTLEKLK  144 (149)
T ss_pred             ccccCHHHH-HHCCCC--CHHHHHHHHHHHHHcCCCCcHHHHHhccCCCHHHHHHHH
Confidence            445566666 334433  44577666553332211 367788888888888776544

>PRK08097 ligB NAD-dependent DNA ligase LigB; Reviewed

Probab=92.61  E-value=0.78  Score=39.63  Aligned_cols=71  Identities=18%  Similarity=0.127  Sum_probs=47.1

Q ss_pred             HHHHHHHh--CCCHHHHhcCCHHHHHHHHhhcCChhHHHHHHHHHHHHHHH-----------------------------
Q 033363           21 VISDLFTL--CPDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQEYLG-----------------------------   69 (121)
Q Consensus        21 v~~~l~~~--~pt~~~la~a~~~eL~~~i~~~Gl~~~Ka~~i~~~a~~i~~-----------------------------   69 (121)
                      ....|++.  ..++.+|..++.++|.++   =||...+++.|.+.-+.-.+                             
T Consensus       437 ~i~~L~~~G~i~~~~Diy~L~~~~l~~l---~gfgeks~~nll~aIe~sk~~~l~r~l~aLGI~~vG~~~ak~~~~~i~~  513 (562)
T PRK08097        437 TWRALHQTGLFEHLFSWLALTPEQLANT---PGIGKARAEQLWHQFNLARQQPFSRWLKALGIPLPQAALNALDDRSWQQ  513 (562)
T ss_pred             HHHHHHHcCCcCCHHHHhcCCHHHHhcC---cCccHHHHHHHHHHHHHHcCCCHHHHHHHcCCccHHHHHHHHhcCCHHH
Confidence            34455543  367888888887765442   26666666666554332222                             


Q ss_pred             ---hhHHHhccCCCCcHHHHHHHHHHhc
Q 033363           70 ---ESWTHVTQLHGVGKYAADAFAIFCT   94 (121)
Q Consensus        70 ---~~~~~L~~lpGIG~~tA~~vl~f~~   94 (121)
                         .+.++|.+++|||+.+|+++..|--
T Consensus       514 l~~a~~e~l~~i~gIG~~~a~si~~~f~  541 (562)
T PRK08097        514 LLSRSEQQWQQLPGIGEGRARQLIAFLQ  541 (562)
T ss_pred             HHcCCHHHHhcCCCchHHHHHHHHHHHc
Confidence               1457899999999999999987744

>PF05559 DUF763: Protein of unknown function (DUF763); InterPro: IPR008482 This family consists of several uncharacterised bacterial and archaeal proteins of unknown function

Probab=92.56  E-value=0.46  Score=38.28  Aligned_cols=40  Identities=15%  Similarity=0.215  Sum_probs=29.9

Q ss_pred             HHHHHHHHHHHH---hhHHHhccCCCCcHHHHHHHHHHh---cCCC
Q 033363           58 PMIKRFSQEYLG---ESWTHVTQLHGVGKYAADAFAIFC---TGKW   97 (121)
Q Consensus        58 ~~i~~~a~~i~~---~~~~~L~~lpGIG~~tA~~vl~f~---~~~~   97 (121)
                      +.+.++.+.+.+   ++.++|+.+|||||+|..++.+.+   +|.|
T Consensus       251 ~~~~~~l~~~~e~~p~~feeLL~~~GvGp~TlRALaLvaelIyg~p  296 (319)
T PF05559_consen  251 RRLWKVLEKAYERQPSDFEELLLIKGVGPSTLRALALVAELIYGVP  296 (319)
T ss_pred             HHHHHHHHHHhhCCccCHHHHHhcCCCCHHHHHHHHHHHHHHcCCC
Confidence            344455555555   689999999999999999988876   4554

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

Probab=92.55  E-value=0.11  Score=37.27  Aligned_cols=24  Identities=25%  Similarity=0.300  Sum_probs=21.6

Q ss_pred             hHHHhccCCCCcHHHHHHHHHHhc
Q 033363           71 SWTHVTQLHGVGKYAADAFAIFCT   94 (121)
Q Consensus        71 ~~~~L~~lpGIG~~tA~~vl~f~~   94 (121)
                      +.++|..|||||++.|..|..+--
T Consensus        95 s~eeL~~lpgIG~~kA~aIi~yRe  118 (149)
T COG1555          95 SAEELQALPGIGPKKAQAIIDYRE  118 (149)
T ss_pred             CHHHHHHCCCCCHHHHHHHHHHHH
Confidence            678999999999999999998763

>TIGR01259 comE comEA protein

Probab=92.36  E-value=0.14  Score=35.43  Aligned_cols=23  Identities=26%  Similarity=0.365  Sum_probs=21.0

Q ss_pred             hHHHhccCCCCcHHHHHHHHHHh
Q 033363           71 SWTHVTQLHGVGKYAADAFAIFC   93 (121)
Q Consensus        71 ~~~~L~~lpGIG~~tA~~vl~f~   93 (121)
                      +.++|.++||||++.|..++.+-
T Consensus        66 ~~~eL~~lpGIG~~~A~~Ii~~R   88 (120)
T TIGR01259        66 SLEELQALPGIGPAKAKAIIEYR   88 (120)
T ss_pred             CHHHHhcCCCCCHHHHHHHHHHH
Confidence            67899999999999999999874

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.

>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=92.05  E-value=0.14  Score=30.51  Aligned_cols=24  Identities=21%  Similarity=0.155  Sum_probs=17.0

Q ss_pred             HHHhccCCCCcHHHHHHHHHHhcC
Q 033363           72 WTHVTQLHGVGKYAADAFAIFCTG   95 (121)
Q Consensus        72 ~~~L~~lpGIG~~tA~~vl~f~~~   95 (121)
                      ++.++.+.||||.||.-....++.
T Consensus         1 l~~f~~I~GVG~~tA~~w~~~G~r   24 (52)
T PF10391_consen    1 LKLFTGIWGVGPKTARKWYAKGIR   24 (52)
T ss_dssp             HHHHHTSTT--HHHHHHHHHTT--
T ss_pred             CcchhhcccccHHHHHHHHHhCCC
Confidence            367899999999999998876654

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 ....

>PRK14350 ligA NAD-dependent DNA ligase LigA; Provisional

Probab=91.98  E-value=0.35  Score=42.50  Aligned_cols=24  Identities=13%  Similarity=0.217  Sum_probs=20.3

Q ss_pred             hHHHhccCCCCcHHHHHHHHHHhc
Q 033363           71 SWTHVTQLHGVGKYAADAFAIFCT   94 (121)
Q Consensus        71 ~~~~L~~lpGIG~~tA~~vl~f~~   94 (121)
                      +.++|.+++|||+.+|+.+..|--
T Consensus       539 ~~e~l~~i~giG~~~a~si~~ff~  562 (669)
T PRK14350        539 ALSKLLKIKGIGEKIALNIIEAFN  562 (669)
T ss_pred             CHHHHhhCCCccHHHHHHHHHHHc
Confidence            556899999999999999987653

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

Probab=91.45  E-value=0.45  Score=41.81  Aligned_cols=24  Identities=21%  Similarity=0.369  Sum_probs=20.8

Q ss_pred             hHHHhccCCCCcHHHHHHHHHHhc
Q 033363           71 SWTHVTQLHGVGKYAADAFAIFCT   94 (121)
Q Consensus        71 ~~~~L~~lpGIG~~tA~~vl~f~~   94 (121)
                      +.++|.++||||+.+|..+.-|--
T Consensus       541 ~~e~l~~i~giG~~vA~si~~ff~  564 (667)
T COG0272         541 SEEELASIPGIGEVVARSIIEFFA  564 (667)
T ss_pred             CHHHHhhccchhHHHHHHHHHHHc
Confidence            678999999999999999987644

>PRK13482 DNA integrity scanning protein DisA; Provisional

Probab=91.06  E-value=0.75  Score=37.58  Aligned_cols=48  Identities=17%  Similarity=0.250  Sum_probs=38.7

Q ss_pred             HHHHHHHHhCCCHHHHhcCCHHHHHHHHhhcCChhHHHHHHHHHHHHHHHh
Q 033363           20 RVISDLFTLCPDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQEYLGE   70 (121)
Q Consensus        20 ~v~~~l~~~~pt~~~la~a~~~eL~~~i~~~Gl~~~Ka~~i~~~a~~i~~~   70 (121)
                      ++..++.++|.|.+.+.+|+.++|.++ .  |+...||+.|++.++.+.+.
T Consensus       298 ~iAk~Ll~~FGSL~~Il~As~eeL~~V-e--GIGe~rA~~I~e~l~Rl~e~  345 (352)
T PRK13482        298 AVIENLVEHFGSLQGLLAASIEDLDEV-E--GIGEVRARAIREGLSRLAEQ  345 (352)
T ss_pred             HHHHHHHHHcCCHHHHHcCCHHHHhhC-C--CcCHHHHHHHHHHHHHHHHH
Confidence            667788899999999999999997653 3  56678899999988887664

>TIGR00084 ruvA Holliday junction DNA helicase, RuvA subunit

Probab=90.95  E-value=0.2  Score=37.38  Aligned_cols=22  Identities=27%  Similarity=0.347  Sum_probs=18.5

Q ss_pred             hhHHHhccCCCCcHHHHHHHHH
Q 033363           70 ESWTHVTQLHGVGKYAADAFAI   91 (121)
Q Consensus        70 ~~~~~L~~lpGIG~~tA~~vl~   91 (121)
                      +....|.++||||||+|-.++.
T Consensus        69 ~lF~~L~~V~GIGpK~Al~iL~   90 (191)
T TIGR00084        69 ELFKELIKVNGVGPKLALAILS   90 (191)
T ss_pred             HHHHHHhCCCCCCHHHHHHHHh
Confidence            3467899999999999988854

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.

>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed

Probab=90.79  E-value=0.2  Score=37.19  Aligned_cols=31  Identities=23%  Similarity=0.288  Sum_probs=23.3

Q ss_pred             cCChhHHHHHHHHHHHHHHHhhHHHhccCCCCcHHHHHHHHH
Q 033363           50 LGLQKKRAPMIKRFSQEYLGESWTHVTQLHGVGKYAADAFAI   91 (121)
Q Consensus        50 ~Gl~~~Ka~~i~~~a~~i~~~~~~~L~~lpGIG~~tA~~vl~   91 (121)
                      .||.+.+.+.+           ...|.++|||||++|..++.
T Consensus        61 ~gF~~~~ek~~-----------f~~L~~i~GIGpk~A~~il~   91 (192)
T PRK00116         61 YGFLTKEEREL-----------FRLLISVSGVGPKLALAILS   91 (192)
T ss_pred             cCcCCHHHHHH-----------HHHHhcCCCCCHHHHHHHHH
Confidence            67775544433           44689999999999998875

>PRK08609 hypothetical protein; Provisional

Probab=90.72  E-value=0.74  Score=39.63  Aligned_cols=20  Identities=15%  Similarity=0.200  Sum_probs=16.7

Q ss_pred             hHHHhccCCCCcHHHHHHHH
Q 033363           71 SWTHVTQLHGVGKYAADAFA   90 (121)
Q Consensus        71 ~~~~L~~lpGIG~~tA~~vl   90 (121)
                      ...+|+++|||||+||..+-
T Consensus        86 ~~~~l~~i~GiGpk~a~~l~  105 (570)
T PRK08609         86 GLLPLLKLPGLGGKKIAKLY  105 (570)
T ss_pred             HHHHHhcCCCCCHHHHHHHH
Confidence            56789999999999996665

>PF03352 Adenine_glyco: Methyladenine glycosylase; InterPro: IPR005019 This family of methyladenine glycosylases includes DNA-3-methyladenine glycosylase I (3

Probab=90.45  E-value=2.3  Score=31.52  Aligned_cols=52  Identities=13%  Similarity=0.280  Sum_probs=37.7

Q ss_pred             HHHHHHHHHHhCC--CHHHHhcCCHHHHHHHHhhcCC--hhHHHHHHHHHHHHHHH
Q 033363           18 AGRVISDLFTLCP--DAKTATEVDAEEIEKIISTLGL--QKKRAPMIKRFSQEYLG   69 (121)
Q Consensus        18 v~~v~~~l~~~~p--t~~~la~a~~~eL~~~i~~~Gl--~~~Ka~~i~~~a~~i~~   69 (121)
                      +.+=.+.|.+.|-  +|+.++..++++++++++.-|+  .+.|.+.++.=|+.+.+
T Consensus        44 Il~Kr~~~r~aF~~Fd~~~vA~~~e~~ie~l~~d~~iIRnr~KI~Avi~NA~~~l~   99 (179)
T PF03352_consen   44 ILKKREAFREAFAGFDPEKVAKMDEEDIERLMQDPGIIRNRRKIRAVINNARAILK   99 (179)
T ss_dssp             HHHTHHHHHHHTGGGHHHHHHT--HHHHHHHTTSTTSS--HHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHCCCHHHHHcCCHHHHHHHhcCcchhhhHHHHHHHHHHHHHHHH
Confidence            3344455556665  6899999999999999998888  66777778877887776

2.2.20 from EC) which acts as a base excision repair enzyme by severing the glycosylic bond of numerous damaged bases. The enzyme is constitutively expressed and is specific for the alkylated 3-methyladenine DNA.; GO: 0008725 DNA-3-methyladenine glycosylase I activity, 0006284 base-excision repair; PDB: 2OFI_A 2OFK_A 2JG6_A 4AIA_E 4AI5_C 4AI4_A 1LMZ_A 1P7M_A 1NKU_A.

>PF14229 DUF4332: Domain of unknown function (DUF4332)

Probab=90.24  E-value=1  Score=31.05  Aligned_cols=58  Identities=10%  Similarity=0.171  Sum_probs=42.4

Q ss_pred             CCCHHHHhcCCHHHHHH--HHhhcCChhHHHHHHHHHHHHHHHhhHHHhccCCCCcHHHHHHHHHHhcC
Q 033363           29 CPDAKTATEVDAEEIEK--IISTLGLQKKRAPMIKRFSQEYLGESWTHVTQLHGVGKYAADAFAIFCTG   95 (121)
Q Consensus        29 ~pt~~~la~a~~~eL~~--~i~~~Gl~~~Ka~~i~~~a~~i~~~~~~~L~~lpGIG~~tA~~vl~f~~~   95 (121)
                      .-|+++|.+.+.+...+  +.+..|...+.-..+.         .+.+|..+||||+..|..+.--+..
T Consensus        16 I~t~~~Ll~~~~~~~~r~~La~~~~i~~~~l~~w~---------~~AdL~ri~gi~~~~a~LL~~AGv~   75 (122)
T PF14229_consen   16 IKTTGDLLEAGDTPLGRKALAKKLGISERNLLKWV---------NQADLMRIPGIGPQYAELLEHAGVD   75 (122)
T ss_pred             CCcHHHHHHcCCCHHHHHHHHHhcCCCHHHHHHHH---------hHHHhhhcCCCCHHHHHHHHHhCcC
Confidence            35888888888887776  6777888743333332         3457889999999999888876664

>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional

Probab=89.99  E-value=0.28  Score=36.65  Aligned_cols=22  Identities=14%  Similarity=0.228  Sum_probs=19.4

Q ss_pred             hhHHHhccCCCCcHHHHHHHHH
Q 033363           70 ESWTHVTQLHGVGKYAADAFAI   91 (121)
Q Consensus        70 ~~~~~L~~lpGIG~~tA~~vl~   91 (121)
                      +....|.+++||||++|-.++.
T Consensus        70 ~lF~~Li~V~GIGpK~Al~ILs   91 (194)
T PRK14605         70 SLFETLIDVSGIGPKLGLAMLS   91 (194)
T ss_pred             HHHHHHhCCCCCCHHHHHHHHH
Confidence            3467899999999999999987

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

Probab=89.99  E-value=0.25  Score=27.20  Aligned_cols=17  Identities=18%  Similarity=0.370  Sum_probs=13.9

Q ss_pred             HhccCCCCcHHHHHHHH
Q 033363           74 HVTQLHGVGKYAADAFA   90 (121)
Q Consensus        74 ~L~~lpGIG~~tA~~vl   90 (121)
                      -+..+||||++||--++
T Consensus        17 ni~Gv~giG~ktA~~ll   33 (36)
T smart00279       17 NIPGVKGIGPKTALKLL   33 (36)
T ss_pred             CCCCCCcccHHHHHHHH
Confidence            35689999999998665

>PRK00024 hypothetical protein; Reviewed

Probab=89.96  E-value=0.46  Score=36.23  Aligned_cols=51  Identities=18%  Similarity=0.324  Sum_probs=34.2

Q ss_pred             cCCHHHHHHHHhhcCChhHHHHHHHHHHHHHHH----------hhHHHhccCCCCcHHHHHHHH
Q 033363           37 EVDAEEIEKIISTLGLQKKRAPMIKRFSQEYLG----------ESWTHVTQLHGVGKYAADAFA   90 (121)
Q Consensus        37 ~a~~~eL~~~i~~~Gl~~~Ka~~i~~~a~~i~~----------~~~~~L~~lpGIG~~tA~~vl   90 (121)
                      ..+..||.+++=..|..   .+..+.+|+.+.+          -+.++|.+++|||+..|..++
T Consensus        23 ~Lsd~ELLa~lL~~g~~---~~~~~~LA~~LL~~fgsL~~l~~as~~eL~~i~GIG~akA~~L~   83 (224)
T PRK00024         23 ALSDAELLAILLRTGTK---GKSVLDLARELLQRFGSLRGLLDASLEELQSIKGIGPAKAAQLK   83 (224)
T ss_pred             cCCHHHHHHHHHcCCCC---CCCHHHHHHHHHHHcCCHHHHHhCCHHHHhhccCccHHHHHHHH
Confidence            34566777666444543   3455666776665          267899999999999885543

>PRK12766 50S ribosomal protein L32e; Provisional

Probab=89.57  E-value=0.77  Score=35.46  Aligned_cols=40  Identities=18%  Similarity=0.160  Sum_probs=24.9

Q ss_pred             HHHHHh-CCCHHHHhcCCHHHHHHHHhhcCChhHHHHHHHHHHH
Q 033363           23 SDLFTL-CPDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQ   65 (121)
Q Consensus        23 ~~l~~~-~pt~~~la~a~~~eL~~~i~~~Gl~~~Ka~~i~~~a~   65 (121)
                      ..|++. |.|.++|..|+.++|.++   -|++..+|+.|++...
T Consensus        17 kkLl~~GF~Sve~Ik~AS~eEL~~V---~GIg~k~AekI~e~l~   57 (232)
T PRK12766         17 EALREAGFESVEDVRAADQSELAEV---DGIGNALAARIKADVG   57 (232)
T ss_pred             HHHHHcCCCCHHHHHhCCHHHHHHc---cCCCHHHHHHHHHHhc
Confidence            345555 777777777777775432   3666666666666554

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

Probab=89.45  E-value=1.5  Score=26.79  Aligned_cols=43  Identities=23%  Similarity=0.207  Sum_probs=29.5

Q ss_pred             HHHHHHHHhCCCHHHHhcCCHHHHHHHHhhcCChhHHHHHHHHHHH
Q 033363           20 RVISDLFTLCPDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQ   65 (121)
Q Consensus        20 ~v~~~l~~~~pt~~~la~a~~~eL~~~i~~~Gl~~~Ka~~i~~~a~   65 (121)
                      ..-..|.+.|+|.+.+.+++.++|.++   =|+....|+.|.+.-+
T Consensus        14 ~~ak~L~~~f~sl~~l~~a~~e~L~~i---~gIG~~~A~si~~ff~   56 (64)
T PF12826_consen   14 KTAKLLAKHFGSLEALMNASVEELSAI---PGIGPKIAQSIYEFFQ   56 (64)
T ss_dssp             HHHHHHHHCCSCHHHHCC--HHHHCTS---TT--HHHHHHHHHHHH
T ss_pred             HHHHHHHHHcCCHHHHHHcCHHHHhcc---CCcCHHHHHHHHHHHC
Confidence            345678899999999999999996542   3677778888876544

>smart00483 POLXc DNA polymerase X family

Probab=89.01  E-value=0.55  Score=37.76  Aligned_cols=21  Identities=29%  Similarity=0.317  Sum_probs=18.3

Q ss_pred             hHHHhccCCCCcHHHHHHHHH
Q 033363           71 SWTHVTQLHGVGKYAADAFAI   91 (121)
Q Consensus        71 ~~~~L~~lpGIG~~tA~~vl~   91 (121)
                      .+.+|+++|||||+||..+--
T Consensus        87 ~l~~l~~i~GiGpk~a~~l~~  107 (334)
T smart00483       87 SLKLFTNVFGVGPKTAAKWYR  107 (334)
T ss_pred             HHHHHHccCCcCHHHHHHHHH
Confidence            578999999999999977754

includes vertebrate polymerase beta and terminal deoxynucleotidyltransferases

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

Probab=88.57  E-value=0.64  Score=36.91  Aligned_cols=53  Identities=21%  Similarity=0.311  Sum_probs=38.9

Q ss_pred             HHHHHHhhcCChhHHHHHHHHHHHHHHH-----hhHHHhccCCCCcHHHHHHHHHHhc
Q 033363           42 EIEKIISTLGLQKKRAPMIKRFSQEYLG-----ESWTHVTQLHGVGKYAADAFAIFCT   94 (121)
Q Consensus        42 eL~~~i~~~Gl~~~Ka~~i~~~a~~i~~-----~~~~~L~~lpGIG~~tA~~vl~f~~   94 (121)
                      ++..++.--|=-..|++.-.++|..+..     .+.+++.++||||+.+|+.|--+.-
T Consensus         9 ~ia~~~e~~~~~~~r~~aY~~Aa~~l~~l~~~i~~~~~~~~ipgiG~~ia~kI~E~~~   66 (307)
T cd00141           9 ELADLLELLGGNPFRVRAYRKAARALESLPEPIESLEEAKKLPGIGKKIAEKIEEILE   66 (307)
T ss_pred             HHHHHHHhccCCcchHHHHHHHHHHHHhCCcccCCHHHhcCCCCccHHHHHHHHHHHH
Confidence            3444444444334688888888888776     7778999999999999999877654

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

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

Probab=88.48  E-value=0.39  Score=34.02  Aligned_cols=21  Identities=19%  Similarity=0.061  Sum_probs=19.2

Q ss_pred             hHHHhccCCCCcHHHHHHHHH
Q 033363           71 SWTHVTQLHGVGKYAADAFAI   91 (121)
Q Consensus        71 ~~~~L~~lpGIG~~tA~~vl~   91 (121)
                      +.++|.++|||||..|..|..
T Consensus        59 ~~~el~~lpGigP~~A~~IV~   79 (132)
T PRK02515         59 SVRAFRQFPGMYPTLAGKIVK   79 (132)
T ss_pred             CHHHHHHCCCCCHHHHHHHHH
Confidence            678999999999999999984

>PRK00024 hypothetical protein; Reviewed

Probab=88.28  E-value=0.76  Score=35.02  Aligned_cols=49  Identities=14%  Similarity=0.137  Sum_probs=37.5

Q ss_pred             HHHHHHHHHHHHHhCCCHHHHhcCCHHHHHHHHhhcCChhHHHHHHHHHHHH
Q 033363           15 LLKAGRVISDLFTLCPDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQE   66 (121)
Q Consensus        15 ~~~v~~v~~~l~~~~pt~~~la~a~~~eL~~~i~~~Gl~~~Ka~~i~~~a~~   66 (121)
                      +..|.+...+++++|++...+.+++++||.+ +  -|+...||..|..+.+.
T Consensus        40 ~~~~~~LA~~LL~~fgsL~~l~~as~~eL~~-i--~GIG~akA~~L~a~~El   88 (224)
T PRK00024         40 GKSVLDLARELLQRFGSLRGLLDASLEELQS-I--KGIGPAKAAQLKAALEL   88 (224)
T ss_pred             CCCHHHHHHHHHHHcCCHHHHHhCCHHHHhh-c--cCccHHHHHHHHHHHHH
Confidence            3457788999999999999999999999765 3  46666788766554443

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

Probab=87.40  E-value=0.35  Score=30.62  Aligned_cols=25  Identities=16%  Similarity=0.183  Sum_probs=19.5

Q ss_pred             hHHHhccCCCCcHHHHHHHHHHhcCC
Q 033363           71 SWTHVTQLHGVGKYAADAFAIFCTGK   96 (121)
Q Consensus        71 ~~~~L~~lpGIG~~tA~~vl~f~~~~   96 (121)
                      .-+.+..+||||++||.-++. -++.
T Consensus        20 ~~D~i~gv~giG~k~A~~ll~-~~~~   44 (75)
T cd00080          20 KSDNIPGVPGIGPKTALKLLK-EYGS   44 (75)
T ss_pred             ccccCCCCCcccHHHHHHHHH-HhCC
Confidence            456688999999999998885 3443

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.

>PRK14351 ligA NAD-dependent DNA ligase LigA; Provisional

Probab=87.31  E-value=0.82  Score=40.39  Aligned_cols=69  Identities=10%  Similarity=0.112  Sum_probs=39.8

Q ss_pred             HHHHHHHhC--CCHHHHhcCCHHHHHHHHhhcCChhHHHHHHHHHHHHHHH-----------------------------
Q 033363           21 VISDLFTLC--PDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQEYLG-----------------------------   69 (121)
Q Consensus        21 v~~~l~~~~--pt~~~la~a~~~eL~~~i~~~Gl~~~Ka~~i~~~a~~i~~-----------------------------   69 (121)
                      ....|++..  -++.+|..+..++|.++   -||...+++.|.+--+.-.+                             
T Consensus       474 ~i~~L~~~g~V~~~~Dl~~L~~~~L~~l---~g~g~Ksa~~Ll~~Ie~sk~~~l~r~l~ALgIpgIG~~~ak~L~~~F~s  550 (689)
T PRK14351        474 RVQQLVDAGLVESLADLYDLTVADLAEL---EGWGETSAENLLAELEASREPPLADFLVALGIPEVGPTTARNLAREFGT  550 (689)
T ss_pred             HHHHHHHcCCCCCHHHHHHcCHHHHhcC---cCcchhHHHHHHHHHHHHccCCHHHHHHHcCCCCcCHHHHHHHHHHhCC
Confidence            344455432  47777777777664432   25555555554443332221                             


Q ss_pred             ------hhHHHhccCCCCcHHHHHHHHHH
Q 033363           70 ------ESWTHVTQLHGVGKYAADAFAIF   92 (121)
Q Consensus        70 ------~~~~~L~~lpGIG~~tA~~vl~f   92 (121)
                            .+.++|.+++|||+++|+.+..|
T Consensus       551 i~~L~~As~eeL~~i~GIG~k~A~sI~~f  579 (689)
T PRK14351        551 FEAIMDADEEALRAVDDVGPTVAEEIREF  579 (689)
T ss_pred             HHHHHhCCHHHHhccCCcCHHHHHHHHHH
Confidence                  14567778888888888777665

>KOG2534 consensus DNA polymerase IV (family X) [Replication, recombination and repair]

Probab=87.15  E-value=1.1  Score=36.30  Aligned_cols=41  Identities=20%  Similarity=0.222  Sum_probs=31.1

Q ss_pred             hHHHHHHHHHHHHHHH-----hhHHHhccCCCCcHHHHHHHHHHhc
Q 033363           54 KKRAPMIKRFSQEYLG-----ESWTHVTQLHGVGKYAADAFAIFCT   94 (121)
Q Consensus        54 ~~Ka~~i~~~a~~i~~-----~~~~~L~~lpGIG~~tA~~vl~f~~   94 (121)
                      .-|+..-..++..+..     .+.+++.+|||||+++|..|--|.-
T Consensus        32 ~~r~~~y~~Aasvlk~~p~~I~S~~ea~~lP~iG~kia~ki~Eile   77 (353)
T KOG2534|consen   32 EDRARAYRRAASVLKSLPFPITSGEEAEKLPGIGPKIAEKIQEILE   77 (353)
T ss_pred             HHHHHHHHHHHHHHHhCCCCcccHHHhcCCCCCCHHHHHHHHHHHH
Confidence            3566666666666655     4789999999999999999876653

>COG1796 POL4 DNA polymerase IV (family X) [DNA replication, recombination, and repair]

Probab=86.88  E-value=2.3  Score=34.38  Aligned_cols=53  Identities=19%  Similarity=0.217  Sum_probs=38.1

Q ss_pred             HHHHHHHhhcCChhHHHHHHHHHHHHHHHh------hHH--HhccCCCCcHHHHHHHHHHh
Q 033363           41 EEIEKIISTLGLQKKRAPMIKRFSQEYLGE------SWT--HVTQLHGVGKYAADAFAIFC   93 (121)
Q Consensus        41 ~eL~~~i~~~Gl~~~Ka~~i~~~a~~i~~~------~~~--~L~~lpGIG~~tA~~vl~f~   93 (121)
                      +++...+.-.|=..-|++.-++.|+.+.+.      ..+  .+++|||||+-+|+.+.-|-
T Consensus        13 e~iA~~me~~Gen~fk~~aYr~Aa~sle~~~e~~~ei~e~~~~t~l~gIGk~ia~~I~e~l   73 (326)
T COG1796          13 ERIADYMELEGENPFKIRAYRKAAQSLENLTEDLEEIEERGRLTELPGIGKGIAEKISEYL   73 (326)
T ss_pred             HHHHHHHHhcCCCccchHHHHHHHHhhhhcccchHHHHhhcccCCCCCccHHHHHHHHHHH
Confidence            445555555666557888888888887761      222  38899999999999987665

>PF03118 RNA_pol_A_CTD: Bacterial RNA polymerase, alpha chain C terminal domain; InterPro: IPR011260 The core of the bacterial RNA polymerase (RNAP) consists of four subunits, two alpha, a beta and a beta', which are conserved from bacteria to mammals

Probab=85.98  E-value=1.3  Score=27.44  Aligned_cols=43  Identities=21%  Similarity=0.244  Sum_probs=27.5

Q ss_pred             HhhcCChhHHHHHHHHHHH-----HHHHhhHHHhccCCCCcHHHHHHHH
Q 033363           47 ISTLGLQKKRAPMIKRFSQ-----EYLGESWTHVTQLHGVGKYAADAFA   90 (121)
Q Consensus        47 i~~~Gl~~~Ka~~i~~~a~-----~i~~~~~~~L~~lpGIG~~tA~~vl   90 (121)
                      |..+||+ .|+.+...-+.     .++.-+.++|.++||+|+++.+-+.
T Consensus        14 I~~L~LS-~Ra~n~L~~~~I~tv~dL~~~s~~~L~~i~n~G~ksl~EI~   61 (66)
T PF03118_consen   14 IEDLGLS-VRAYNCLKRAGIHTVGDLVKYSEEDLLKIKNFGKKSLEEIK   61 (66)
T ss_dssp             GGGSTSB-HHHHHHHHCTT--BHHHHHCS-HHHHHTSTTSHHHHHHHHH
T ss_pred             HHHhCCC-HHHHHHHHHhCCcCHHHHHhCCHHHHHhCCCCCHhHHHHHH
Confidence            5568898 55544433222     1222367899999999999988664

The alpha subunit (RpoA) initiates RNAP assembly by dimerising to form a platform on which the beta subunits can interact. The alpha subunit consists of a N-terminal domain (NTD) and a C-terminal domain (CTD), connected by a short linker. The NTD is essential for RNAP assembly, while the CTD is necessary for transcription regulation, interacting with transcription factors and promoter upstream elements. In Escherichia coli, the catabolite activator protein (CAP or CRP) was shown to exert its effect through its interactions with the CTD, where CAP binding to CTD promotes RNAP binding to promoter DNA, thereby stimulating transcription initiation at class I CAP-dependent promoters. At class II CAP-dependent promoters, the interaction of CAP with CTD is one of multiple interactions involved in activation []. The CTD has a compact structure of four helices and two long arms enclosing its hydrophobic core, making its folding topology distinct from most other binding proteins. The upstream promoter element-binding site is formed from helices 1 and 4 [].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3N97_B 1XS9_D 3K4G_A 3N4M_B 1COO_A 1LB2_E 3IYD_A 1Z3E_B 3GFK_B 3IHQ_B ....

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

Probab=85.74  E-value=0.92  Score=27.85  Aligned_cols=22  Identities=23%  Similarity=0.447  Sum_probs=19.5

Q ss_pred             hHHHhcc-CCCCcHHHHHHHHHH
Q 033363           71 SWTHVTQ-LHGVGKYAADAFAIF   92 (121)
Q Consensus        71 ~~~~L~~-lpGIG~~tA~~vl~f   92 (121)
                      ..++|.. +||||+.+|..++.+
T Consensus        14 ~~~~L~~~ipgig~~~a~~Il~~   36 (69)
T TIGR00426        14 TAEELQRAMNGVGLKKAEAIVSY   36 (69)
T ss_pred             CHHHHHhHCCCCCHHHHHHHHHH
Confidence            4568888 999999999999987

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=84.63  E-value=3.1  Score=36.50  Aligned_cols=43  Identities=12%  Similarity=0.189  Sum_probs=28.5

Q ss_pred             cCChhHHHHHHHHH----HHHHHHhhHHHhccCCCCcHHHHHHHHHH
Q 033363           50 LGLQKKRAPMIKRF----SQEYLGESWTHVTQLHGVGKYAADAFAIF   92 (121)
Q Consensus        50 ~Gl~~~Ka~~i~~~----a~~i~~~~~~~L~~lpGIG~~tA~~vl~f   92 (121)
                      -|+.+.|++.+.+.    -..+.+.+.++|.++||||+++|..+..+
T Consensus       651 pgig~~~~~~l~~~g~~s~~~i~~a~~~el~~~~gi~~~~a~~i~~~  697 (720)
T PRK00254        651 PMIGRKRARALYNAGFRSIEDIVNAKPSELLKVEGIGAKIVEGIFKH  697 (720)
T ss_pred             CCCCHHHHHHHHHccCCCHHHHHhCCHHHHhcCCCCCHHHHHHHHHH
Confidence            36666666666655    22333346777888888888888887665

>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional

Probab=83.85  E-value=0.88  Score=34.23  Aligned_cols=22  Identities=23%  Similarity=0.306  Sum_probs=19.0

Q ss_pred             hhHHHhccCCCCcHHHHHHHHH
Q 033363           70 ESWTHVTQLHGVGKYAADAFAI   91 (121)
Q Consensus        70 ~~~~~L~~lpGIG~~tA~~vl~   91 (121)
                      +..+.|.++.|||||+|=.+|.
T Consensus        69 ~lF~~LisVsGIGPK~ALaILs   90 (196)
T PRK13901         69 EVFEELIGVDGIGPRAALRVLS   90 (196)
T ss_pred             HHHHHHhCcCCcCHHHHHHHHc
Confidence            3467899999999999988884

>TIGR00608 radc DNA repair protein radc

Probab=83.80  E-value=2  Score=32.68  Aligned_cols=47  Identities=13%  Similarity=0.164  Sum_probs=36.5

Q ss_pred             HHHHHHHHHHHhC---CCHHHHhcCCHHHHHHHHhhcCChhHHHHHHHHHHHH
Q 033363           17 KAGRVISDLFTLC---PDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQE   66 (121)
Q Consensus        17 ~v~~v~~~l~~~~---pt~~~la~a~~~eL~~~i~~~Gl~~~Ka~~i~~~a~~   66 (121)
                      .+.+...+++++|   ++...+.+++++||.+ ++  |....||..|..+.+.
T Consensus        33 ~~~~lA~~ll~~f~~~g~l~~l~~a~~~eL~~-i~--GiG~aka~~l~a~~El   82 (218)
T TIGR00608        33 DVLSLSKRLLDVFGRQDSLGHLLSAPPEELSS-VP--GIGEAKAIQLKAAVEL   82 (218)
T ss_pred             CHHHHHHHHHHHhcccCCHHHHHhCCHHHHHh-Cc--CCcHHHHHHHHHHHHH
Confidence            5778888999998   8999999999999876 34  5555688777655443

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

>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional

Probab=83.70  E-value=0.88  Score=33.85  Aligned_cols=22  Identities=14%  Similarity=0.166  Sum_probs=19.0

Q ss_pred             hhHHHhccCCCCcHHHHHHHHH
Q 033363           70 ESWTHVTQLHGVGKYAADAFAI   91 (121)
Q Consensus        70 ~~~~~L~~lpGIG~~tA~~vl~   91 (121)
                      +..+.|.++.|||||+|=.+|.
T Consensus        70 ~lF~~LisV~GIGpK~Al~iLs   91 (186)
T PRK14600         70 DCLRMLVKVSGVNYKTAMSILS   91 (186)
T ss_pred             HHHHHHhCcCCcCHHHHHHHHc
Confidence            3467899999999999988886

>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional

Probab=83.47  E-value=0.92  Score=33.70  Aligned_cols=22  Identities=18%  Similarity=0.345  Sum_probs=18.9

Q ss_pred             hhHHHhccCCCCcHHHHHHHHH
Q 033363           70 ESWTHVTQLHGVGKYAADAFAI   91 (121)
Q Consensus        70 ~~~~~L~~lpGIG~~tA~~vl~   91 (121)
                      +..+.|.++.|||||+|=.+|.
T Consensus        70 ~lF~~Li~VsGIGpK~Al~ILs   91 (183)
T PRK14601         70 KMFEMLLKVNGIGANTAMAVCS   91 (183)
T ss_pred             HHHHHHhccCCccHHHHHHHHc
Confidence            3567899999999999988885

>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional

Probab=82.74  E-value=1.1  Score=33.37  Aligned_cols=21  Identities=14%  Similarity=0.146  Sum_probs=18.3

Q ss_pred             hHHHhccCCCCcHHHHHHHHH
Q 033363           71 SWTHVTQLHGVGKYAADAFAI   91 (121)
Q Consensus        71 ~~~~L~~lpGIG~~tA~~vl~   91 (121)
                      ..+.|.++.|||||+|=.+|.
T Consensus        71 lF~~Li~V~GIGpK~AL~iLs   91 (188)
T PRK14606         71 LFLSLTKVSRLGPKTALKIIS   91 (188)
T ss_pred             HHHHHhccCCccHHHHHHHHc
Confidence            467899999999999988884

>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional

Probab=82.51  E-value=1.1  Score=33.55  Aligned_cols=21  Identities=24%  Similarity=0.210  Sum_probs=18.6

Q ss_pred             hHHHhccCCCCcHHHHHHHHH
Q 033363           71 SWTHVTQLHGVGKYAADAFAI   91 (121)
Q Consensus        71 ~~~~L~~lpGIG~~tA~~vl~   91 (121)
                      ....|.++.|||||+|=.+|.
T Consensus        70 lF~~L~~V~GIGpK~AL~iLs   90 (197)
T PRK14603         70 LFELLLGVSGVGPKLALALLS   90 (197)
T ss_pred             HHHHHhCcCCcCHHHHHHHHc
Confidence            467899999999999988886

>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional

Probab=82.51  E-value=1.2  Score=33.53  Aligned_cols=21  Identities=19%  Similarity=0.197  Sum_probs=18.6

Q ss_pred             hHHHhccCCCCcHHHHHHHHH
Q 033363           71 SWTHVTQLHGVGKYAADAFAI   91 (121)
Q Consensus        71 ~~~~L~~lpGIG~~tA~~vl~   91 (121)
                      ....|.++.|||||+|=.+|.
T Consensus        72 lF~~Li~V~GIGpK~Al~iLs   92 (203)
T PRK14602         72 TFIVLISISKVGAKTALAILS   92 (203)
T ss_pred             HHHHHhCCCCcCHHHHHHHHh
Confidence            466799999999999998886

>PRK09482 flap endonuclease-like protein; Provisional

Probab=82.40  E-value=1.5  Score=34.20  Aligned_cols=30  Identities=17%  Similarity=0.173  Sum_probs=22.1

Q ss_pred             HHHHhhHHHhccCCCCcHHHHHHHHHHhcCC
Q 033363           66 EYLGESWTHVTQLHGVGKYAADAFAIFCTGK   96 (121)
Q Consensus        66 ~i~~~~~~~L~~lpGIG~~tA~~vl~f~~~~   96 (121)
                      .+..++-+-+..+||||||||.-++. -+|-
T Consensus       175 aL~GD~sDnIpGVpGIG~KtA~~LL~-~~gs  204 (256)
T PRK09482        175 GLAGISSSKIPGVAGIGPKSAAELLN-QFRS  204 (256)
T ss_pred             HHhCCCccCCCCCCCcChHHHHHHHH-HhCC
Confidence            34445667789999999999988775 3443

>PF09597 IGR: IGR protein motif; InterPro: IPR019083 This entry is found in fungal and plant proteins and contains a conserved IGR motif

Probab=81.86  E-value=4.5  Score=24.59  Aligned_cols=43  Identities=12%  Similarity=0.224  Sum_probs=33.6

Q ss_pred             HHHHHHhCCC-HHHHhcCCHHHHHHHHhhcCChhHHHHHHHHHHHHHH
Q 033363           22 ISDLFTLCPD-AKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQEYL   68 (121)
Q Consensus        22 ~~~l~~~~pt-~~~la~a~~~eL~~~i~~~Gl~~~Ka~~i~~~a~~i~   68 (121)
                      ......+|++ |+++..++-.+    ++..|..-+--+||....+.+.
T Consensus        12 ~~~~~~kf~~~w~~lf~~~s~~----LK~~GIp~r~RryiL~~~ek~r   55 (57)
T PF09597_consen   12 CEEHAEKFESDWEKLFTTSSKQ----LKELGIPVRQRRYILRWREKYR   55 (57)
T ss_pred             HHHHHHHHHHHHHHHHhcCHHH----HHHCCCCHHHHHHHHHHHHHHh
Confidence            3455567888 99999999988    6778998777788887776653

Its function is unknown.

>PRK12766 50S ribosomal protein L32e; Provisional

Probab=81.78  E-value=3.4  Score=31.92  Aligned_cols=47  Identities=13%  Similarity=0.244  Sum_probs=37.1

Q ss_pred             cCChhHHHHHHHHH----HHHHHHhhHHHhccCCCCcHHHHHHHHHHhcCCC
Q 033363           50 LGLQKKRAPMIKRF----SQEYLGESWTHVTQLHGVGKYAADAFAIFCTGKW   97 (121)
Q Consensus        50 ~Gl~~~Ka~~i~~~----a~~i~~~~~~~L~~lpGIG~~tA~~vl~f~~~~~   97 (121)
                      -|....+++.|.+.    .+.+...+.++|.++||||+.+|..+..+ ++.+
T Consensus         9 pGIG~krakkLl~~GF~Sve~Ik~AS~eEL~~V~GIg~k~AekI~e~-l~~~   59 (232)
T PRK12766          9 SGVGPSKAEALREAGFESVEDVRAADQSELAEVDGIGNALAARIKAD-VGGL   59 (232)
T ss_pred             CCcCHHHHHHHHHcCCCCHHHHHhCCHHHHHHccCCCHHHHHHHHHH-hccc
Confidence            46667788888776    55666678999999999999999999877 4443

>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional

Probab=81.53  E-value=1.3  Score=33.24  Aligned_cols=21  Identities=24%  Similarity=0.235  Sum_probs=18.7

Q ss_pred             hHHHhccCCCCcHHHHHHHHH
Q 033363           71 SWTHVTQLHGVGKYAADAFAI   91 (121)
Q Consensus        71 ~~~~L~~lpGIG~~tA~~vl~   91 (121)
                      ....|.++.|||||+|=.+|.
T Consensus        71 lF~~Li~V~GIGpK~Al~iLs   91 (195)
T PRK14604         71 LFELLIGVSGVGPKAALNLLS   91 (195)
T ss_pred             HHHHHhCcCCcCHHHHHHHHc
Confidence            467899999999999988886

>PRK14351 ligA NAD-dependent DNA ligase LigA; Provisional

Probab=81.52  E-value=7.2  Score=34.60  Aligned_cols=14  Identities=29%  Similarity=0.339  Sum_probs=9.7

Q ss_pred             cCCCCcHHHHHHHH
Q 033363           77 QLHGVGKYAADAFA   90 (121)
Q Consensus        77 ~lpGIG~~tA~~vl   90 (121)
                      .+||||+++|..++
T Consensus       532 gIpgIG~~~ak~L~  545 (689)
T PRK14351        532 GIPEVGPTTARNLA  545 (689)
T ss_pred             CCCCcCHHHHHHHH
Confidence            37777777777655

>TIGR01954 nusA_Cterm_rpt transcription termination factor NusA, C-terminal duplication

Probab=81.42  E-value=4.3  Score=22.84  Aligned_cols=37  Identities=14%  Similarity=0.138  Sum_probs=30.7

Q ss_pred             HhCCCHHHHhcCCHHHHHHHHhhcCChhHHHHHHHHHHHH
Q 033363           27 TLCPDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQE   66 (121)
Q Consensus        27 ~~~pt~~~la~a~~~eL~~~i~~~Gl~~~Ka~~i~~~a~~   66 (121)
                      ..|-|.++++.+++++|.++   -|+...++..|+..++.
T Consensus        12 ~G~~s~e~la~~~~~eL~~i---~g~~~e~a~~ii~~a~~   48 (50)
T TIGR01954        12 EGFTTVEDLAYVPIDELLSI---EGFDEETAKELINRARN   48 (50)
T ss_pred             cCCCCHHHHHccCHHHHhcC---CCCCHHHHHHHHHHHHH
Confidence            35889999999999998764   67888899998887764

NusA is a bacterial transcription termination factor. It is named for its interaction with phage lambda protein N, as part of the N utilization substance. Some members of the NusA family have a long C-terminal extension. This model represents an acidic 50-residue region found in two copies toward the C-terminus of most Proteobacterial NusA proteins, spaced about 26 residues apart. Analogous C-terminal extensions in some other bacterial lineages lack apparent homology but appear similarly acidic.

>TIGR01448 recD_rel helicase, putative, RecD/TraA family

Probab=80.65  E-value=12  Score=33.26  Aligned_cols=60  Identities=20%  Similarity=0.245  Sum_probs=38.4

Q ss_pred             HHHHHHHhhcCChhHHHHHHHH-----HHHHHHHhhHHHhccCCCCcHHHHHHHHHHhcCCCCccCcchH
Q 033363           41 EEIEKIISTLGLQKKRAPMIKR-----FSQEYLGESWTHVTQLHGVGKYAADAFAIFCTGKWDRVRPTDH  105 (121)
Q Consensus        41 ~eL~~~i~~~Gl~~~Ka~~i~~-----~a~~i~~~~~~~L~~lpGIG~~tA~~vl~f~~~~~~~v~p~D~  105 (121)
                      .++...|.+.|++...+..|.+     ..+.+.++...-+.+++|||.++||-+... +|    +.|+|.
T Consensus       144 ~~~~~~L~~~gi~~~~a~ki~~~yg~~~~~~i~~nPY~L~~~i~gigF~~aD~iA~~-~g----~~~~d~  208 (720)
T TIGR01448       144 RRLLAGLQGLGIGIKLAQRIYKFYQADTLDRVEKDPYLLAEDVKGIGFLTADQLAQA-LG----IALNDP  208 (720)
T ss_pred             HHHHHHHHHcCCCHHHHHHHHHHHhHHHHHHHHhCchhhhhhcCCCCHHHHHHHHHH-cC----CCCCCH
Confidence            4444556677777666666655     223333345544557999999999998754 55    456664

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.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	121
1ngn_A	155	Mismatch Repair In Methylated Dna. Structure Of The		9e-17
4ew4_A	146	Mouse Mbd4 Glycosylase Domain In Complex With Dna C		9e-17
4e9e_A	161	Structure Of The Glycosylase Domain Of Mbd4 Length		1e-16
4dk9_A	157	Crystal Structure Of Mbd4 Catalytic Domain Bound To		1e-16
3iho_A	138	The C-Terminal Glycosylase Domain Of Human Mbd4 Len		1e-16
4evv_A	146	Mouse Mbd4 Glycosylase Domain In Complex With A G:t		3e-16
4e9g_A	161	Structure Of The Glycosylase Domain Of Mbd4 Bound T		1e-15
4ea4_A	155	Structure Of The Glycosylase Domain Of Mbd4 Bound T		1e-15
4ea5_A	160	Structure Of The Glycoslyase Domain Of Mbd4 Bound T		1e-15

>pdb|1NGN|A Chain A, Mismatch Repair In Methylated Dna. Structure Of The Mismatch-Specific Thymine Glycosylase Domain Of Methyl-Cpg- Binding Protein Mbd4 Length = 155

Iteration: 1
 Score = 81.6 bits (200), Expect = 9e-17,   Method: Compositional matrix adjust.
 Identities = 36/94 (38%), Positives = 55/94 (58%)
Query: 21  VISDLFTLCPDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQEYLGESWTHVTQLHG 80
           V+ +     P A+ A   D  ++ +++  LGL   RA  I +FS EYL + W +  +LHG
Sbjct: 52  VLWEFLEKYPSAEVARAADWRDVSELLKPLGLYDLRAKTIIKFSDEYLTKQWRYPIELHG 111
Query: 81  VGKYAADAFAIFCTGKWDRVRPTDHMLNYYWEFL 114
           +GKY  D++ IFC  +W +V P DH LN Y ++L
Sbjct: 112 IGKYGNDSYRIFCVNEWKQVHPEDHKLNKYHDWL 145

>pdb|4EW4|A Chain A, Mouse Mbd4 Glycosylase Domain In Complex With Dna Containing A Ribose Sugar Length = 146

Iteration: 1
 Score = 81.6 bits (200), Expect = 9e-17,   Method: Compositional matrix adjust.
 Identities = 37/101 (36%), Positives = 56/101 (55%)
Query: 21  VISDLFTLCPDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQEYLGESWTHVTQLHG 80
           V+ +     P A+ A   D  ++ +++  LGL   RA  I +FS EYL + W +  +LHG
Sbjct: 43  VLWEFLEKYPSAEVARAADWRDVSELLKPLGLYDLRAKTIIKFSDEYLTKQWRYPIELHG 102
Query: 81  VGKYAADAFAIFCTGKWDRVRPTDHMLNYYWEFLVSTKGNL 121
           +GKY  D++ IFC  +W +V P DH LN Y ++L      L
Sbjct: 103 IGKYGNDSYRIFCVNEWKQVHPEDHKLNKYHDWLWENHEKL 143

>pdb|4E9E|A Chain A, Structure Of The Glycosylase Domain Of Mbd4 Length = 161

Iteration: 1
 Score = 81.3 bits (199), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 35/85 (41%), Positives = 52/85 (61%)
Query: 30  PDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQEYLGESWTHVTQLHGVGKYAADAF 89
           P A+ A   D  ++ +++  LGL   RA  I +FS EYL + W +  +LHG+GKY  D++
Sbjct: 61  PSAEVARTADWRDVSELLKPLGLYDLRAKTIVKFSDEYLTKQWKYPIELHGIGKYGNDSY 120
Query: 90  AIFCTGKWDRVRPTDHMLNYYWEFL 114
            IFC  +W +V P DH LN Y ++L
Sbjct: 121 RIFCVNEWKQVHPEDHKLNKYHDWL 145

>pdb|4DK9|A Chain A, Crystal Structure Of Mbd4 Catalytic Domain Bound To Abasic Dna Length = 157

Iteration: 1
 Score = 81.3 bits (199), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 35/85 (41%), Positives = 52/85 (61%)
Query: 30  PDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQEYLGESWTHVTQLHGVGKYAADAF 89
           P A+ A   D  ++ +++  LGL   RA  I +FS EYL + W +  +LHG+GKY  D++
Sbjct: 63  PSAEVARTADWRDVSELLKPLGLYDLRAKTIVKFSDEYLTKQWKYPIELHGIGKYGNDSY 122
Query: 90  AIFCTGKWDRVRPTDHMLNYYWEFL 114
            IFC  +W +V P DH LN Y ++L
Sbjct: 123 RIFCVNEWKQVHPEDHKLNKYHDWL 147

>pdb|3IHO|A Chain A, The C-Terminal Glycosylase Domain Of Human Mbd4 Length = 138

Iteration: 1
 Score = 81.3 bits (199), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 35/85 (41%), Positives = 52/85 (61%)
Query: 30  PDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQEYLGESWTHVTQLHGVGKYAADAF 89
           P A+ A   D  ++ +++  LGL   RA  I +FS EYL + W +  +LHG+GKY  D++
Sbjct: 50  PSAEVARTADWRDVSELLKPLGLYDLRAKTIVKFSDEYLTKQWKYPIELHGIGKYGNDSY 109
Query: 90  AIFCTGKWDRVRPTDHMLNYYWEFL 114
            IFC  +W +V P DH LN Y ++L
Sbjct: 110 RIFCVNEWKQVHPEDHKLNKYHDWL 134

>pdb|4EVV|A Chain A, Mouse Mbd4 Glycosylase Domain In Complex With A G:t Mismatch Length = 146

Iteration: 1
 Score = 80.1 bits (196), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 36/101 (35%), Positives = 56/101 (55%)
Query: 21  VISDLFTLCPDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQEYLGESWTHVTQLHG 80
           V+ +     P A+ A   D  ++ +++  LGL   RA  I +FS EYL + W +  +LHG
Sbjct: 43  VLWEFLEKYPSAEVARAADWRDVSELLKPLGLYDLRAKTIIKFSDEYLTKQWRYPIELHG 102
Query: 81  VGKYAADAFAIFCTGKWDRVRPTDHMLNYYWEFLVSTKGNL 121
           +GKY  D++ IFC  +W +V P +H LN Y ++L      L
Sbjct: 103 IGKYGNDSYRIFCVNEWKQVHPENHKLNKYHDWLWENHEKL 143

>pdb|4E9G|A Chain A, Structure Of The Glycosylase Domain Of Mbd4 Bound To Thymine Containing Dna Length = 161

Iteration: 1
 Score = 78.2 bits (191), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 34/85 (40%), Positives = 51/85 (60%)
Query: 30  PDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQEYLGESWTHVTQLHGVGKYAADAF 89
           P A+ A   D  ++ +++  LGL   RA  I +FS EYL + W +  +LHG+GKY  D++
Sbjct: 61  PSAEVARTADWRDVSELLKPLGLYDLRAKTIVKFSDEYLTKQWKYPIELHGIGKYGNDSY 120
Query: 90  AIFCTGKWDRVRPTDHMLNYYWEFL 114
            IFC  +W +V P  H LN Y ++L
Sbjct: 121 RIFCVNEWKQVHPEAHKLNKYHDWL 145

>pdb|4EA4|A Chain A, Structure Of The Glycosylase Domain Of Mbd4 Bound To 5hmu-Containing Dna Length = 155

Iteration: 1
 Score = 78.2 bits (191), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 34/85 (40%), Positives = 51/85 (60%)
Query: 30  PDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQEYLGESWTHVTQLHGVGKYAADAF 89
           P A+ A   D  ++ +++  LGL   RA  I +FS EYL + W +  +LHG+GKY  D++
Sbjct: 61  PSAEVARTADWRDVSELLKPLGLYDLRAKTIVKFSDEYLTKQWKYPIELHGIGKYGNDSY 120
Query: 90  AIFCTGKWDRVRPTDHMLNYYWEFL 114
            IFC  +W +V P  H LN Y ++L
Sbjct: 121 RIFCVNEWKQVHPEAHKLNKYHDWL 145

>pdb|4EA5|A Chain A, Structure Of The Glycoslyase Domain Of Mbd4 Bound To A 5hmu Containing Dna Length = 160

Iteration: 1
 Score = 78.2 bits (191), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 34/85 (40%), Positives = 51/85 (60%)
Query: 30  PDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQEYLGESWTHVTQLHGVGKYAADAF 89
           P A+ A   D  ++ +++  LGL   RA  I +FS EYL + W +  +LHG+GKY  D++
Sbjct: 61  PSAEVARTADWRDVSELLKPLGLYDLRAKTIVKFSDEYLTKQWKYPIELHGIGKYGNDSY 120
Query: 90  AIFCTGKWDRVRPTDHMLNYYWEFL 114
            IFC  +W +V P  H LN Y ++L
Sbjct: 121 RIFCVNEWKQVHPEAHKLNKYHDWL 145

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	121
4e9f_A	161	Methyl-CPG-binding domain protein 4; HHH DNA glyco	4e-31
1orn_A	226	Endonuclease III; DNA repair, DNA glycosylase, [4F	7e-04

>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 Length = 161

 Score =  107 bits (268), Expect = 4e-31
 Identities = 36/94 (38%), Positives = 54/94 (57%)

Query: 21  VISDLFTLCPDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQEYLGESWTHVTQLHG 80
           V+       P A+ A   D  ++ +++  LGL   RA  I +FS EYL + W +  +LHG
Sbjct: 52  VLWKFLEKYPSAEVARTADWRDVSELLKPLGLYDLRAKTIVKFSDEYLTKQWKYPIELHG 111

Query: 81  VGKYAADAFAIFCTGKWDRVRPTDHMLNYYWEFL 114
           +GKY  D++ IFC  +W +V P DH LN Y ++L
Sbjct: 112 IGKYGNDSYRIFCVNEWKQVHPEDHKLNKYHDWL 145

>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* Length = 226

 Score = 36.4 bits (85), Expect = 7e-04
 Identities = 23/85 (27%), Positives = 37/85 (43%), Gaps = 14/85 (16%)

Query: 12  IAILLKA-------GRVISDLFTLCPDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFS 64
           IA++L A        +V   LF           V  EE+E+ I ++GL + +A  I++  
Sbjct: 38  IAVVLSAQCTDALVNKVTKRLFEKYRTPHDYIAVPLEELEQDIRSIGLYRNKARNIQKLC 97

Query: 65  Q----EYLGE---SWTHVTQLHGVG 82
                +Y GE       + +L GVG
Sbjct: 98  AMLIDKYNGEVPRDRDELMKLPGVG 122

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	121
4e9f_A	161	Methyl-CPG-binding domain protein 4; HHH DNA glyco	100.0
1orn_A	226	Endonuclease III; DNA repair, DNA glycosylase, [4F	99.95
1kea_A	221	Possible G-T mismatches repair enzyme; DNA repair,	99.94
2abk_A	211	Endonuclease III; DNA-repair, DNA glycosylase; 1.8	99.94
1kg2_A	225	A/G-specific adenine glycosylase; DNA repair, hydr	99.94
1pu6_A	218	3-methyladenine DNA glycosylase; helix-hairpin-hel	99.93
3n5n_X	287	A/G-specific adenine DNA glycosylase; alpha-helice	99.93
4b21_A	232	Probable DNA-3-methyladenine glycosylase 2; hydrol	99.93
2h56_A	233	DNA-3-methyladenine glycosidase; 10174367, EC 3.2.	99.92
2yg9_A	225	DNA-3-methyladenine glycosidase II, putative; hydr	99.92
3s6i_A	228	DNA-3-methyladenine glycosylase 1; DNA glycosylase	99.92
3fsp_A	369	A/G-specific adenine glycosylase; protein-DNA comp	99.92
1mpg_A	282	ALKA, 3-methyladenine DNA glycosylase II; DNA repa	99.9
2jhn_A	295	ALKA, 3-methyladenine DNA-glycosylase; DNA repair,	99.88
3i0w_A	290	8-oxoguanine-DNA-glycosylase; OGG, cacogg, DNA, 8-	99.88
3n0u_A	219	Probable N-glycosylase/DNA lyase; structural genom	99.86
3fhf_A	214	Mjogg, N-glycosylase/DNA lyase, DNA-(apurinic; hel	99.86
3fhg_A	207	Mjogg, N-glycosylase/DNA lyase, DNA-(apurinic; hel	99.86
2xhi_A	360	N-glycosylase/DNA lyase; lyase-DNA complex, lyase/	99.86
2ztd_A	212	Holliday junction ATP-dependent DNA helicase RUVA;	96.31
4gfj_A	685	Topoisomerase V; helix-hairpin-helix, DNA repair e	96.22
1ixr_A	191	Holliday junction DNA helicase RUVA; heterooligome	95.98
1z00_A	89	DNA excision repair protein ERCC-1; helix-hairpin-	95.87
1x2i_A	75	HEF helicase/nuclease; alpha helix, helix-hairpin-	95.85
1kft_A	78	UVRC, excinuclease ABC subunit C; helix-hairpin-he	95.81
2fmp_A	335	DNA polymerase beta; nucleotidyl transferase, tran	95.66
2a1j_B	91	DNA excision repair protein ERCC-1; XPF, xeroderma	95.47
4glx_A	586	DNA ligase; inhibitor, ligase-ligase inhibitor-DNA	95.34
1cuk_A	203	RUVA protein; DNA repair, SOS response, DNA-bindin	95.34
2ihm_A	360	POL MU, DNA polymerase MU; helix-turn-helix, trans	95.3
2bcq_A	335	DNA polymerase lambda; misalignment, extrahelical,	95.02
1jms_A	381	Terminal deoxynucleotidyltransferase; polymerase;	94.96
3vdp_A	212	Recombination protein RECR; zinc finger, DNA repai	94.84
2csb_A	519	Topoisomerase V, TOP61; topoisomerase IB, helix-tu	94.82
2a1j_A	63	DNA repair endonuclease XPF; XPF, xeroderma pigmen	94.61
2duy_A	75	Competence protein comea-related protein; helix-ha	94.49
2duy_A	75	Competence protein comea-related protein; helix-ha	94.46
1vdd_A	228	Recombination protein RECR; helix-hairpin-helix, z	94.26
1s5l_U	134	Photosystem II 12 kDa extrinsic protein; photosynt	94.17
2edu_A	98	Kinesin-like protein KIF22; kinesin-like DNA bindi	93.93
2a1j_A	63	DNA repair endonuclease XPF; XPF, xeroderma pigmen	93.42
2owo_A	671	DNA ligase; protein-DNA complex, ligase-DNA comple	92.99
2bgw_A	219	XPF endonuclease; hydrolase, structure specific en	92.79
1z00_B	84	DNA repair endonuclease XPF; helix-hairpin-helix,	92.56
3arc_U	97	Photosystem II 12 kDa extrinsic protein; PSII, mem	92.46
2fmp_A	335	DNA polymerase beta; nucleotidyl transferase, tran	92.45
2kp7_A	87	Crossover junction endonuclease MUS81; helix-hairp	92.22
1s5l_U	134	Photosystem II 12 kDa extrinsic protein; photosynt	92.14
1wcn_A	70	Transcription elongation protein NUSA; RNA-binding	92.01
1z00_B	84	DNA repair endonuclease XPF; helix-hairpin-helix,	91.93
2i5h_A	205	Hypothetical protein AF1531; PFAM:DUF655, PSI-2, s	91.87
3arc_U	97	Photosystem II 12 kDa extrinsic protein; PSII, mem	91.34
1dgs_A	667	DNA ligase; AMP complex, NAD+-dependent; HET: DNA	91.23
2ihm_A	360	POL MU, DNA polymerase MU; helix-turn-helix, trans	91.04
2edu_A	98	Kinesin-like protein KIF22; kinesin-like DNA bindi	90.92
1ixr_A	191	Holliday junction DNA helicase RUVA; heterooligome	90.78
2ztd_A	212	Holliday junction ATP-dependent DNA helicase RUVA;	90.55
3c1y_A	377	DNA integrity scanning protein DISA; DNA damage, D	89.88
3b0x_A	575	DNA polymerase beta family (X family); structural	89.84
2jg6_A	186	DNA-3-methyladenine glycosidase; 3-methyladenine-D	89.78
2w9m_A	578	Polymerase X; SAXS, DNA repair, DNA polymerase, DN	89.28
1cuk_A	203	RUVA protein; DNA repair, SOS response, DNA-bindin	88.98
1z00_A	89	DNA excision repair protein ERCC-1; helix-hairpin-	88.67
1jms_A	381	Terminal deoxynucleotidyltransferase; polymerase;	88.53
3sgi_A	615	DNA ligase; HET: DNA AMP; 3.50A {Mycobacterium tub	88.51
1kft_A	78	UVRC, excinuclease ABC subunit C; helix-hairpin-he	88.2
1x2i_A	75	HEF helicase/nuclease; alpha helix, helix-hairpin-	88.13
2ofk_A	183	3-methyladenine DNA glycosylase I, constitutive; D	87.49
2bcq_A	335	DNA polymerase lambda; misalignment, extrahelical,	87.41
2a1j_B	91	DNA excision repair protein ERCC-1; XPF, xeroderma	86.67
1u9l_A	70	Transcription elongation protein NUSA; escherichia	86.65
1z3e_B	73	DNA-directed RNA polymerase alpha chain; bacterial	85.22
2w9m_A	578	Polymerase X; SAXS, DNA repair, DNA polymerase, DN	83.9
3k4g_A	86	DNA-directed RNA polymerase subunit alpha; bacteri	83.53
4gfj_A	685	Topoisomerase V; helix-hairpin-helix, DNA repair e	82.45
1dgs_A	667	DNA ligase; AMP complex, NAD+-dependent; HET: DNA	82.16
1vq8_Y	241	50S ribosomal protein L32E; ribosome 50S, protein-	82.14
2bgw_A	219	XPF endonuclease; hydrolase, structure specific en	80.94
1b22_A	114	DNA repair protein RAD51; DNA binding, riken struc	80.17
3gfk_B	79	DNA-directed RNA polymerase subunit alpha; protein	80.13

>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=100.00  E-value=2.9e-35  Score=212.89  Aligned_cols=114  Identities=33%  Similarity=0.650  Sum_probs=106.1

Q ss_pred             HHHHHHHH----HHHHHHHHHHHHHHHhCCCHHHHhcCCHHHHHHHHhhcCChhHHHHHHHHHHHHHHHhhHHHhccCCC
Q 033363            5 YSIRLKEI----AILLKAGRVISDLFTLCPDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQEYLGESWTHVTQLHG   80 (121)
Q Consensus         5 ~si~~~~~----~~~~~v~~v~~~l~~~~pt~~~la~a~~~eL~~~i~~~Gl~~~Ka~~i~~~a~~i~~~~~~~L~~lpG   80 (121)
                      |.+.+++|    |++++|++++.+|+++||||++|+++++++|+++|+++|||++||++|+++|+.++.+++++|++|||
T Consensus        32 ~~vLVs~ILsqQT~~~~v~~~~~~l~~~~pt~~~la~a~~~el~~~i~~lG~y~~KAk~i~~~a~~~vp~~~~~L~~LpG  111 (161)
T 4e9f_A           32 WKLLIATIFLNRTSGKMAIPVLWKFLEKYPSAEVARTADWRDVSELLKPLGLYDLRAKTIVKFSDEYLTKQWKYPIELHG  111 (161)
T ss_dssp             HHHHHHHHHTTTSCHHHHHHHHHHHHHHSCSHHHHTTSCHHHHHHHHGGGSCHHHHHHHHHHHHHHHHHSCCSSGGGSTT
T ss_pred             HHHHHHHHHHhhCcHHHHHHHHHHHHHHCCCHHHHhccChHhHHhHhhhcCCHHHHHHHHHHHhCCcCCCChhhhhcCCC
Confidence            45555555    56789999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CcHHHHHHHHHHhcCCCCccCcchHHHHHHHHHHHHhh
Q 033363           81 VGKYAADAFAIFCTGKWDRVRPTDHMLNYYWEFLVSTK  118 (121)
Q Consensus        81 IG~~tA~~vl~f~~~~~~~v~p~D~~l~~~~~wl~~~~  118 (121)
                      ||+||||++++||+|++..|+|+|+++++|++|+++..
T Consensus       112 VG~yTAdav~~F~~~e~~~V~p~D~~l~r~l~wl~~~~  149 (161)
T 4e9f_A          112 IGKYGNDSYRIFCVNEWKQVHPEDHKLNKYHDWLWENH  149 (161)
T ss_dssp             CCHHHHHHHHHHTSSCGGGCCCCSHHHHHHHHHHHHTC
T ss_pred             chHHHHHHHHHHHCCCCCCCCCCcHHHHHHHHHHHcCc
Confidence            99999999999999987779999999999999998764

>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=99.95  E-value=5e-27  Score=177.13  Aligned_cols=107  Identities=20%  Similarity=0.247  Sum_probs=94.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHhCCCHHHHhcCCHHHHHHHHhhcCChhHHHHHHHHHHHHHHH-------hhHHHhccC
Q 033363            6 SIRLKEIAILLKAGRVISDLFTLCPDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQEYLG-------ESWTHVTQL   78 (121)
Q Consensus         6 si~~~~~~~~~~v~~v~~~l~~~~pt~~~la~a~~~eL~~~i~~~Gl~~~Ka~~i~~~a~~i~~-------~~~~~L~~l   78 (121)
                      +..++++++.++|++++.+|++.||||++|+++++++|+++|+++||+++||++|+++|+.+.+       +++++|++|
T Consensus        39 ~~IlsQqts~~~v~~~~~~l~~~fpt~~~la~a~~~~l~~~i~~~G~~~~KA~~l~~~a~~i~~~~~g~~p~~~~~L~~l  118 (226)
T 1orn_A           39 AVVLSAQCTDALVNKVTKRLFEKYRTPHDYIAVPLEELEQDIRSIGLYRNKARNIQKLCAMLIDKYNGEVPRDRDELMKL  118 (226)
T ss_dssp             HHHHHTTSCHHHHHHHHHHHHHHCCSHHHHHSSCHHHHHHHTGGGSSHHHHHHHHHHHHHHHHHHSTTSCCSCHHHHTTS
T ss_pred             HHHHhCCCcHHHHHHHHHHHHHHCCCHHHHHcCCHHHHHHHHHHcCChHHHHHHHHHHHHHHHHHhCCCcHHHHHHHHHC
Confidence            3344444556789999999999999999999999999999999999999999999999999987       378999999


Q ss_pred             CCCcHHHHHHHHHHhcCCCCccCcchHHHHHHHHHH
Q 033363           79 HGVGKYAADAFAIFCTGKWDRVRPTDHMLNYYWEFL  114 (121)
Q Consensus        79 pGIG~~tA~~vl~f~~~~~~~v~p~D~~l~~~~~wl  114 (121)
                      ||||+|||++|++|++|++  ++|+|.++.|...++
T Consensus       119 pGIG~~TA~~il~~a~g~~--~~~vD~~v~Rv~~rl  152 (226)
T 1orn_A          119 PGVGRKTANVVVSVAFGVP--AIAVDTHVERVSKRL  152 (226)
T ss_dssp             TTCCHHHHHHHHHHHHCCC--CCCCCHHHHHHHHHH
T ss_pred             CCccHHHHHHHHHHHCCCc--eeeeCHHHHHHHHHh
Confidence            9999999999999999996  778887777766554

>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=99.94  E-value=6.1e-27  Score=175.96  Aligned_cols=108  Identities=19%  Similarity=0.220  Sum_probs=96.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHhCCCHHHHhcCCHHHHHHHHhhcCChhHHHHHHHHHHHHHHH-------hhHHHhccCC
Q 033363            7 IRLKEIAILLKAGRVISDLFTLCPDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQEYLG-------ESWTHVTQLH   79 (121)
Q Consensus         7 i~~~~~~~~~~v~~v~~~l~~~~pt~~~la~a~~~eL~~~i~~~Gl~~~Ka~~i~~~a~~i~~-------~~~~~L~~lp   79 (121)
                      ..++++++.++|++++.+|++.||||++|+++++++|+++|+++||+++||++|+++|+.+.+       +++++|++||
T Consensus        42 ~IlsQqts~~~~~~~~~~l~~~fptp~~la~a~~e~l~~~i~~~G~~~~KA~~l~~~a~~i~~~~~g~~p~~~~~L~~lp  121 (221)
T 1kea_A           42 EILLRRTTAGHVKKIYDKFFVKYKCFEDILKTPKSEIAKDIKEIGLSNQRAEQLKELARVVINDYGGRVPRNRKAILDLP  121 (221)
T ss_dssp             HHHTTTSCHHHHHHHHHHHHHHCCSHHHHHHSCHHHHHHHTGGGSCHHHHHHHHHHHHHHHHHHHTTSCCSCHHHHHTST
T ss_pred             HHHHccCCHHHHHHHHHHHHHHCCCHHHHHCCCHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHhCCCchHHHHHHHhCC
Confidence            334444456789999999999999999999999999999999999999999999999999987       3689999999


Q ss_pred             CCcHHHHHHHHHHhcCCCCccCcchHHHHHHHHHHHH
Q 033363           80 GVGKYAADAFAIFCTGKWDRVRPTDHMLNYYWEFLVS  116 (121)
Q Consensus        80 GIG~~tA~~vl~f~~~~~~~v~p~D~~l~~~~~wl~~  116 (121)
                      |||+|||++|++|++|++  ++|+|.+++|....+++
T Consensus       122 GIG~~TA~~il~~~~~~~--~~~vD~~v~Rv~~rl~g  156 (221)
T 1kea_A          122 GVGKYTCAAVMCLAFGKK--AAMVDANFVRVINRYFG  156 (221)
T ss_dssp             TCCHHHHHHHHHHTTCCC--CCCCCHHHHHHHHHHHC
T ss_pred             CCcHHHHHHHHHHhcCCC--cceecHHHHHHHHHHhC
Confidence            999999999999999996  68889888888777643

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

Probab=99.94  E-value=3.9e-27  Score=175.77  Aligned_cols=107  Identities=19%  Similarity=0.214  Sum_probs=95.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHhCCCHHHHhcCCHHHHHHHHhhcCChhHHHHHHHHHHHHHHH-------hhHHHhccC
Q 033363            6 SIRLKEIAILLKAGRVISDLFTLCPDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQEYLG-------ESWTHVTQL   78 (121)
Q Consensus         6 si~~~~~~~~~~v~~v~~~l~~~~pt~~~la~a~~~eL~~~i~~~Gl~~~Ka~~i~~~a~~i~~-------~~~~~L~~l   78 (121)
                      +..++++++.++|++++.+|++.||||++|+++++++|+++|+++||+++||++|+++|+.+.+       +++++|++|
T Consensus        35 ~~Il~qqts~~~v~~~~~~l~~~fpt~~~la~a~~~~l~~~i~~~G~~~~KA~~l~~~a~~~~~~~~g~~~~~~~~L~~l  114 (211)
T 2abk_A           35 AVLLSAQATDVSVNKATAKLYPVANTPAAMLELGVEGVKTYIKTIGLYNSKAENIIKTCRILLEQHNGEVPEDRAALEAL  114 (211)
T ss_dssp             HHHHTTTSCHHHHHHHHHHHTTTCCSHHHHHHHHHHHHHHHHTTSTTHHHHHHHHHHHHHHHHHHTTTSCCSCHHHHHHS
T ss_pred             HHHHhCCCCHHHHHHHHHHHHHHCCCHHHHHCCCHHHHHHHHHHcCCChHHHHHHHHHHHHHHHHcCCCchHHHHHHHhC
Confidence            3334444556789999999999999999999999999999999999999999999999999987       368999999


Q ss_pred             CCCcHHHHHHHHHHhcCCCCccCcchHHHHHHHHHH
Q 033363           79 HGVGKYAADAFAIFCTGKWDRVRPTDHMLNYYWEFL  114 (121)
Q Consensus        79 pGIG~~tA~~vl~f~~~~~~~v~p~D~~l~~~~~wl  114 (121)
                      ||||+|||++|++|++|++  ++|+|.+++|...++
T Consensus       115 ~GIG~~tA~~il~~~~~~~--~~~vD~~v~Rv~~rl  148 (211)
T 2abk_A          115 PGVGRKTANVVLNTAFGWP--TIAVDTHIFRVCNRT  148 (211)
T ss_dssp             TTCCHHHHHHHHHHHHCCC--CCCCCHHHHHHHHHH
T ss_pred             CCCChHHHHHHHHHHCCCC--cCCcCHHHHHHHHHh
Confidence            9999999999999999997  788888887776655

>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=99.94  E-value=2.3e-26  Score=173.13  Aligned_cols=106  Identities=17%  Similarity=0.203  Sum_probs=95.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhCCCHHHHhcCCHHHHHHHHhhcCChhHHHHHHHHHHHHHHH-------hhHHHhccCCC
Q 033363            8 RLKEIAILLKAGRVISDLFTLCPDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQEYLG-------ESWTHVTQLHG   80 (121)
Q Consensus         8 ~~~~~~~~~~v~~v~~~l~~~~pt~~~la~a~~~eL~~~i~~~Gl~~~Ka~~i~~~a~~i~~-------~~~~~L~~lpG   80 (121)
                      .++++++.++|.+++.+|++.||||++|+++++++|+++|+++||+ +||++|+++|+.+.+       +++++|++|||
T Consensus        38 IlsQqt~~~~v~~~~~~l~~~~pt~~~la~~~~~~l~~~i~~~G~~-~kA~~l~~~a~~i~~~~~g~~p~~~~~L~~lpG  116 (225)
T 1kg2_A           38 VMLQQTQVATVIPYFERFMARFPTVTDLANAPLDEVLHLWTGLGYY-ARARNLHKAAQQVATLHGGKFPETFEEVAALPG  116 (225)
T ss_dssp             HHHTSSCHHHHHHHHHHHHHHCSSHHHHHHSCHHHHHHHHTTSCCT-HHHHHHHHHHHHHHHHSTTSCCCSHHHHHTSTT
T ss_pred             HHHCcCCHHHHHHHHHHHHHHCCCHHHHHCCCHHHHHHHHHhCChH-HHHHHHHHHHHHHHHHhCCCchHHHHHHhcCCC
Confidence            3333445678999999999999999999999999999999999999 699999999999987       36899999999


Q ss_pred             CcHHHHHHHHHHhcCCCCccCcchHHHHHHHHHHHH
Q 033363           81 VGKYAADAFAIFCTGKWDRVRPTDHMLNYYWEFLVS  116 (121)
Q Consensus        81 IG~~tA~~vl~f~~~~~~~v~p~D~~l~~~~~wl~~  116 (121)
                      ||+|||++|++|++|++  .+|+|.+++|..+.+..
T Consensus       117 IG~~TA~~il~~a~~~~--~~~vD~~v~Rv~~rl~~  150 (225)
T 1kg2_A          117 VGRSTAGAILSLSLGKH--FPILDGNVKRVLARCYA  150 (225)
T ss_dssp             CCHHHHHHHHHHHHCCS--CCCCCHHHHHHHHHHHT
T ss_pred             CcHHHHHHHHHHhCCCC--cceeCHHHHHHHHHHcC
Confidence            99999999999999998  46899999998887754

>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=99.93  E-value=4.3e-26  Score=171.20  Aligned_cols=107  Identities=15%  Similarity=0.184  Sum_probs=93.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHh-CCC------HHHHhcCCHHHHHHHHhhcCChhHHHHHHHHHHHHHHH--------
Q 033363            5 YSIRLKEIAILLKAGRVISDLFTL-CPD------AKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQEYLG--------   69 (121)
Q Consensus         5 ~si~~~~~~~~~~v~~v~~~l~~~-~pt------~~~la~a~~~eL~~~i~~~Gl~~~Ka~~i~~~a~~i~~--------   69 (121)
                      .+..++++++.+++++++.+|+++ |||      |++|+++++++|+++|+++||+++||++|+++|+.+.+        
T Consensus        35 v~~ILsQqts~~~v~~~~~~L~~~~~pt~~~~~t~~~la~~~~e~L~~~ir~~G~~~~KA~~L~~~a~~i~~~~~~l~~~  114 (218)
T 1pu6_A           35 LGAVLTQNTKFEAVLKSLENLKNAFILENDDEINLKKIAYIEFSKLAECVRPSGFYNQKAKRLIDLSGNILKDFQSFENF  114 (218)
T ss_dssp             HHHHHTTTSCHHHHHHHHHHHHHTTSSCSCHHHHHHHHHHSCHHHHHHHTGGGSCHHHHHHHHHHHHHHHHHHHSSHHHH
T ss_pred             HHHHHcCCCCHHHHHHHHHHHHHccCCCccccccHHHHHhCCHHHHHHHHHHCCCcHHHHHHHHHHHHHHHHhcCChhhc
Confidence            344444555667899999999999 999      99999999999999999999999999999999999986        


Q ss_pred             ---hhHHHhccCCCCcHHHHHHHHHHhcCCCCccCcchHHHHHHHHH
Q 033363           70 ---ESWTHVTQLHGVGKYAADAFAIFCTGKWDRVRPTDHMLNYYWEF  113 (121)
Q Consensus        70 ---~~~~~L~~lpGIG~~tA~~vl~f~~~~~~~v~p~D~~l~~~~~w  113 (121)
                         +.+++|++|||||||||++|++|++|++  ++|+|.+++|....
T Consensus       115 ~~~~~~~~L~~lpGIG~kTA~~il~~a~~~~--~~~vD~~v~Ri~~r  159 (218)
T 1pu6_A          115 KQEVTREWLLDQKGIGKESADAILCYACAKE--VMVVDKYSYLFLKK  159 (218)
T ss_dssp             HHHCCHHHHHTSTTCCHHHHHHHHHHTTCCS--CCCCCHHHHHHHHH
T ss_pred             cchHHHHHHHcCCCcCHHHHHHHHHHHCCCC--ccccCHHHHHHHHH
Confidence               2578999999999999999999999996  78888887776544

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

Probab=99.93  E-value=1.4e-25  Score=174.78  Aligned_cols=105  Identities=16%  Similarity=0.192  Sum_probs=94.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhCCCHHHHhcCCHHHHHHHHhhcCChhHHHHHHHHHHHHHHH-------hhHHHhcc-CC
Q 033363            8 RLKEIAILLKAGRVISDLFTLCPDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQEYLG-------ESWTHVTQ-LH   79 (121)
Q Consensus         8 ~~~~~~~~~~v~~v~~~l~~~~pt~~~la~a~~~eL~~~i~~~Gl~~~Ka~~i~~~a~~i~~-------~~~~~L~~-lp   79 (121)
                      .++++++.++|.+++.+|+++||||++|+++++++|+++|+++||++ ||++|+++|+.+.+       .++++|++ ||
T Consensus        57 ILsQQts~~~v~~~~~rL~~~fptpe~La~a~~eel~~~ir~lG~~~-KA~~L~~~A~~i~~~~~g~~p~~~~~Ll~~Lp  135 (287)
T 3n5n_X           57 VMLQQTQVATVINYYTGWMQKWPTLQDLASASLEEVNQLWAGLGYYS-RGRRLQEGARKVVEELGGHMPRTAETLQQLLP  135 (287)
T ss_dssp             HHHHTSCHHHHHHHHHHHHHHCCSHHHHHTSCHHHHHHHHTTSSCHH-HHHHHHHHHHHHHHHSTTCCCSSHHHHHHHST
T ss_pred             HHhCCCcHHHHHHHHHHHHHHCCCHHHHHcCCHHHHHHHHHHcCCHH-HHHHHHHHHHHHHHHhCCCCcHHHHHHHHHcC
Confidence            33344456789999999999999999999999999999999999996 99999999999998       37899999 99


Q ss_pred             CCcHHHHHHHHHHhcCCCCccCcchHHHHHHHHHHH
Q 033363           80 GVGKYAADAFAIFCTGKWDRVRPTDHMLNYYWEFLV  115 (121)
Q Consensus        80 GIG~~tA~~vl~f~~~~~~~v~p~D~~l~~~~~wl~  115 (121)
                      |||+|||++|++|++|++  ++|+|.+++|....+.
T Consensus       136 GIG~kTA~~iL~~a~g~p--~~~VDt~V~Rv~~Rlg  169 (287)
T 3n5n_X          136 GVGRYTAGAIASIAFGQA--TGVVDGNVARVLCRVR  169 (287)
T ss_dssp             TCCHHHHHHHHHHHSCCC--CCCCCHHHHHHHHHHT
T ss_pred             CCCHHHHHHHHHHhcCCC--CccccHHHHHHHHHhC
Confidence            999999999999999997  6789999988877664

>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=99.93  E-value=2.3e-25  Score=168.88  Aligned_cols=109  Identities=20%  Similarity=0.324  Sum_probs=94.1

Q ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHh------CCCHHHHhcCCHHHHHHHHhhcCChhHHHHHHHHHHHHHHH--------
Q 033363            4 IYSIRLKEIAILLKAGRVISDLFTL------CPDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQEYLG--------   69 (121)
Q Consensus         4 ~~si~~~~~~~~~~v~~v~~~l~~~------~pt~~~la~a~~~eL~~~i~~~Gl~~~Ka~~i~~~a~~i~~--------   69 (121)
                      +.+..++|+++.+++++++.+|.+.      ||||++|+++++++    |+++||+++|+++|+++|+.+.+        
T Consensus        64 Lv~~Il~Qq~s~~~a~~~~~rL~~~~G~~~~fPtpe~la~~~~e~----Lr~~Gl~~~Ka~~l~~~A~~~~~g~~p~l~~  139 (232)
T 4b21_A           64 IIRAITSQKLSDAATNSIINKFCTQCSDNDEFPTPKQIMETDVET----LHECGFSKLKSQEIHIVAEAALNKQIPSKSE  139 (232)
T ss_dssp             HHHHHHTTTCCHHHHHHHHHHHHHHHCSSSSCCCHHHHHTSCHHH----HHTTTCCHHHHHHHHHHHHHHHTTCSCCHHH
T ss_pred             HHHHHHhCcCcHHHHHHHHHHHHHHhCCCCCCCCHHHHHcCCHHH----HHHcCCcHHHHHHHHHHHHHHHhCCCCCHHH
Confidence            3344444555567899999999988      99999999999998    68899999999999999999986        


Q ss_pred             -------hhHHHhccCCCCcHHHHHHHHHHhcCCCCccCcc-hHHHHHHHHHHHHh
Q 033363           70 -------ESWTHVTQLHGVGKYAADAFAIFCTGKWDRVRPT-DHMLNYYWEFLVST  117 (121)
Q Consensus        70 -------~~~~~L~~lpGIG~~tA~~vl~f~~~~~~~v~p~-D~~l~~~~~wl~~~  117 (121)
                             +.+++|++|||||||||++|++|++|+|| ++|. |.++++..++++..
T Consensus       140 l~~~~~~~~~~~L~~l~GIG~~TA~~ill~alg~pd-~fpv~D~~v~r~~~rl~~~  194 (232)
T 4b21_A          140 IEKMSEEELMESLSKIKGVKRWTIEMYSIFTLGRLD-IMPADDSTLKNEAKEFFGL  194 (232)
T ss_dssp             HHHSCHHHHHHHHTTSTTCCHHHHHHHHHHTSCCSS-CCCTTCHHHHHHHHHHTTC
T ss_pred             HHcCCHHHHHHHHHhCCCcCHHHHHHHHHHhCCCCC-eeeCccHHHHHHHHHHhCC
Confidence                   25789999999999999999999999997 6555 99999999887653

>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=99.92  E-value=3.8e-25  Score=167.49  Aligned_cols=108  Identities=18%  Similarity=0.281  Sum_probs=92.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHh----CCCHHHHhcCCHHHHHHHHhhcCChhHHHHHHHHHHHHHHH-----------
Q 033363            5 YSIRLKEIAILLKAGRVISDLFTL----CPDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQEYLG-----------   69 (121)
Q Consensus         5 ~si~~~~~~~~~~v~~v~~~l~~~----~pt~~~la~a~~~eL~~~i~~~Gl~~~Ka~~i~~~a~~i~~-----------   69 (121)
                      .+..++|+++.+++.+++.+|+++    ||||++|+++++++    |+++||+++||++|+++|+.+.+           
T Consensus        56 v~~IlsQqts~~~a~~~~~rL~~~~G~~fPtp~~la~~~~e~----Lr~~G~~~~KA~~I~~~A~~i~~~~~~~~~l~~~  131 (233)
T 2h56_A           56 VSSIVEQQLSIKAASAIYGRVEQLVGGALEKPEQLYRVSDEA----LRQAGVSKRKIEYIRHVCEHVESGRLDFTELEGA  131 (233)
T ss_dssp             HHHHHHTTSCHHHHHHHHHHHHHHHTSCCCCTHHHHTSCHHH----HHHTTCCHHHHHHHHHHHHHHHTTSSCHHHHTTS
T ss_pred             HHHHHcCCCCHHHHHHHHHHHHHHhCCCCCCHHHHHcCCHHH----HHHcCCCHHHHHHHHHHHHHHHhCCCCHHHHhcC
Confidence            344444555567889999999987    47999999999998    48999999999999999999875           


Q ss_pred             ---hhHHHhccCCCCcHHHHHHHHHHhcCCCCccCcchHHHHHHHHHHHH
Q 033363           70 ---ESWTHVTQLHGVGKYAADAFAIFCTGKWDRVRPTDHMLNYYWEFLVS  116 (121)
Q Consensus        70 ---~~~~~L~~lpGIG~~tA~~vl~f~~~~~~~v~p~D~~l~~~~~wl~~  116 (121)
                         +.+++|++|||||||||++|++|++|+||.++++|+++|+..+|.+.
T Consensus       132 p~~~~~~~L~~lpGIG~kTA~~ill~alg~pd~~pvdd~~~r~~~~~~~~  181 (233)
T 2h56_A          132 EATTVIEKLTAIKGIGQWTAEMFMMFSLGRLDVLSVGDVGLQRGAKWLYG  181 (233)
T ss_dssp             CHHHHHHHHHTSTTCCHHHHHHHHHHTTCCSCCCCTTCHHHHHHHHHHHS
T ss_pred             CHHHHHHHHHhCCCcCHHHHHHHHHHhCCCCCeeeCchHHHHHHHHHhcc
Confidence               35788999999999999999999999998566678999999888764

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

Probab=99.92  E-value=4e-25  Score=166.71  Aligned_cols=106  Identities=18%  Similarity=0.217  Sum_probs=92.6

Q ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHhC--CCHHHHhcCCHHHHHHHHhhcCChhHHHHHHHHHHHHHHHh-----------
Q 033363            4 IYSIRLKEIAILLKAGRVISDLFTLC--PDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQEYLGE-----------   70 (121)
Q Consensus         4 ~~si~~~~~~~~~~v~~v~~~l~~~~--pt~~~la~a~~~eL~~~i~~~Gl~~~Ka~~i~~~a~~i~~~-----------   70 (121)
                      +.+..++|+++.+++.+++.+|.+.|  |||++|+++++++    |+++||+++|+++|+++|+.+.++           
T Consensus        65 Lv~~IlsQq~s~~~a~~~~~rL~~~~G~ptp~~la~~~~e~----Lr~~G~~~~KA~~i~~lA~~~~~g~~~l~~l~~~~  140 (225)
T 2yg9_A           65 LVRSVAGQQLSVKAAQAIYGRLEGLPGGVVPAALLKVSGDD----LRGVGLSWAKVRTVQAAAAAAVSGQIDFAHLSGQP  140 (225)
T ss_dssp             HHHHHHHTTSCHHHHHHHHHHHHTSTTCSCHHHHTTSCHHH----HHHTTCCHHHHHHHHHHHHHHHTTSSCGGGCTTSC
T ss_pred             HHHHHHhCcChHHHHHHHHHHHHHHhCcCCHHHHHcCCHHH----HHHCCCcHHHHHHHHHHHHHHHhCCcCHHHHhcCC
Confidence            44555555566678999999999999  9999999999998    589999999999999999999762           


Q ss_pred             ---hHHHhccCCCCcHHHHHHHHHHhcCCCCccCcc-hHHHHHHHHHH
Q 033363           71 ---SWTHVTQLHGVGKYAADAFAIFCTGKWDRVRPT-DHMLNYYWEFL  114 (121)
Q Consensus        71 ---~~~~L~~lpGIG~~tA~~vl~f~~~~~~~v~p~-D~~l~~~~~wl  114 (121)
                         .+++|++|||||+|||++|++|++|++| +||. |+++++..+++
T Consensus       141 ~~e~~~~L~~l~GIG~~TA~~ill~~lg~~d-~fpv~D~~v~r~~~~l  187 (225)
T 2yg9_A          141 DELVIAELVQLPGIGRWTAEMFLLFALARPD-VFSSGDLALRQGVERL  187 (225)
T ss_dssp             HHHHHHHHHTSTTCCHHHHHHHHHHTSCCSC-CCCTTCHHHHHHHHHH
T ss_pred             HHHHHHHHHcCCCCCHHHHHHHHHHhCCCCC-eeeCccHHHHHHHHHh
Confidence               3789999999999999999999999997 5555 99999988765

>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=99.92  E-value=6.9e-25  Score=165.76  Aligned_cols=107  Identities=14%  Similarity=0.270  Sum_probs=91.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHh------CCCHHHHhcCCHHHHHHHHhhcCChhHHHHHHHHHHHHHHHh---------
Q 033363            6 SIRLKEIAILLKAGRVISDLFTL------CPDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQEYLGE---------   70 (121)
Q Consensus         6 si~~~~~~~~~~v~~v~~~l~~~------~pt~~~la~a~~~eL~~~i~~~Gl~~~Ka~~i~~~a~~i~~~---------   70 (121)
                      +..++|+++.+++.+++.+| +.      ||||++|+++++++    |+++||+++|+++|+++|+.+.++         
T Consensus        56 ~~Il~Qq~s~~~a~~~~~rL-~~~Gg~~~fPtp~~la~~~~e~----Lr~~G~~~rKa~~i~~~A~~~~~g~~p~~~~l~  130 (228)
T 3s6i_A           56 RAVASQQLHSKAANAIFNRF-KSISNNGQFPTPEEIRDMDFEI----MRACGFSARKIDSLKSIAEATISGLIPTKEEAE  130 (228)
T ss_dssp             HHHHHSSSCHHHHHHHHHHH-HTSSGGGSCCCHHHHHHSCHHH----HHHHTCCHHHHHHHHHHHHHHHHTSSCCHHHHT
T ss_pred             HHHHhCcCCHHHHHHHHHHH-HHhcCCCCCCCHHHHHcCCHHH----HHHcCCCHHHHHHHHHHHHHHHcCCCCChHHHh
Confidence            33444445567889999999 66      49999999999998    589999999999999999999862         


Q ss_pred             ------hHHHhccCCCCcHHHHHHHHHHhcCCCCccCcchHHHHHHHHHHHHh
Q 033363           71 ------SWTHVTQLHGVGKYAADAFAIFCTGKWDRVRPTDHMLNYYWEFLVST  117 (121)
Q Consensus        71 ------~~~~L~~lpGIG~~tA~~vl~f~~~~~~~v~p~D~~l~~~~~wl~~~  117 (121)
                            .+++|++|||||+|||++|++|++|++|.++++|+++++.+++++..
T Consensus       131 ~~~~~e~~~~L~~l~GIG~~TA~~ill~~lg~pd~fpvdD~~v~r~~~~~~~~  183 (228)
T 3s6i_A          131 RLSNEELIERLTQIKGIGRWTVEMLLIFSLNRDDVMPADDLSIRNGYRYLHRL  183 (228)
T ss_dssp             TSCHHHHHHHHTTSTTCCHHHHHHHHHHTSCCSSCCCTTCHHHHHHHHHHTTC
T ss_pred             cCCHHHHHHHHHhCCCcCHHHHHHHHHHhCCCCCEEecccHHHHHHHHHHhCC
Confidence                  37899999999999999999999999985566689999999888654

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

Probab=99.92  E-value=8.6e-25  Score=174.32  Aligned_cols=109  Identities=17%  Similarity=0.210  Sum_probs=96.7

Q ss_pred             HHHHHHHH----HHHHHHHHHHHHHHHhCCCHHHHhcCCHHHHHHHHhhcCChhHHHHHHHHHHHHHHH-------hhHH
Q 033363            5 YSIRLKEI----AILLKAGRVISDLFTLCPDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQEYLG-------ESWT   73 (121)
Q Consensus         5 ~si~~~~~----~~~~~v~~v~~~l~~~~pt~~~la~a~~~eL~~~i~~~Gl~~~Ka~~i~~~a~~i~~-------~~~~   73 (121)
                      |.+.+++|    ++.++|.+++.+|+++||||++|+++++++|+++|+++||++ ||++|+++|+.+.+       ++++
T Consensus        40 ~~~lv~~il~qqt~~~~~~~~~~~l~~~~pt~~~la~a~~~~l~~~i~~~G~~~-ra~~l~~~a~~~~~~~~g~~p~~~~  118 (369)
T 3fsp_A           40 YKVWVSEVMLQQTRVETVIPYFEQFIDRFPTLEALADADEDEVLKAWEGLGYYS-RVRNLHAAVKEVKTRYGGKVPDDPD  118 (369)
T ss_dssp             HHHHHHHHHTTTSCHHHHHHHHHHHHHHCCSHHHHHTSCHHHHHHTTTTSSCTH-HHHHHHHHHHHHHHHHTTCCCCSHH
T ss_pred             HHHHHHHHHhccCcHHHHHHHHHHHHHHCCCHHHHHCCCHHHHHHHHHhcChHH-HHHHHHHHHHHHHHHcCCCChhHHH
Confidence            44444444    446789999999999999999999999999999999999997 99999999999997       3799


Q ss_pred             HhccCCCCcHHHHHHHHHHhcCCCCccCcchHHHHHHHHHHHH
Q 033363           74 HVTQLHGVGKYAADAFAIFCTGKWDRVRPTDHMLNYYWEFLVS  116 (121)
Q Consensus        74 ~L~~lpGIG~~tA~~vl~f~~~~~~~v~p~D~~l~~~~~wl~~  116 (121)
                      +|++|||||+|||++|++|++|++  ++|+|.+++|....+..
T Consensus       119 ~L~~l~GIG~~tA~~il~~~~~~~--~~~vD~~v~Rv~~rl~~  159 (369)
T 3fsp_A          119 EFSRLKGVGPYTVGAVLSLAYGVP--EPAVDGNVMRVLSRLFL  159 (369)
T ss_dssp             HHHTSTTCCHHHHHHHHHHHHCCC--CCCCCHHHHHHHHHHTT
T ss_pred             HHhcCCCcCHHHHHHHHHHHCCCC--cccccHHHHHHHHHHcC
Confidence            999999999999999999999997  78999999888777643

>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=99.90  E-value=6.6e-24  Score=164.22  Aligned_cols=104  Identities=17%  Similarity=0.287  Sum_probs=88.6

Q ss_pred             hHHHHHHHHHHHHHHHHHHHHHH-------------HhCCCHHHHhcCCHHHHHHHHhhcCChhHHHHHHHHHHHHHHHh
Q 033363            4 IYSIRLKEIAILLKAGRVISDLF-------------TLCPDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQEYLGE   70 (121)
Q Consensus         4 ~~si~~~~~~~~~~v~~v~~~l~-------------~~~pt~~~la~a~~~eL~~~i~~~Gl~~~Ka~~i~~~a~~i~~~   70 (121)
                      +.+..++|+++.+++.+++.+|.             ..||||++|+++++++    |+++||+++|+++|+++|+.+.++
T Consensus       117 lv~~Il~Qq~s~~~a~~~~~rL~~~~G~~~~~~~~~~~fPtp~~la~~~~~~----Lr~~G~~~~ra~~i~~~A~~~~~~  192 (282)
T 1mpg_A          117 GVRAILGQLVSVAMAAKLTARVAQLYGERLDDFPEYICFPTPQRLAAADPQA----LKALGMPLKRAEALIHLANAALEG  192 (282)
T ss_dssp             HHHHHHTTTSCHHHHHHHHHHHHHHHCCBCSSCTTCBCCCCHHHHHTCCHHH----HHHTTSCHHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHhCcccHHHHHHHHHHHHHHhCCCCCCCCCcccCCCHHHHHcCCHHH----HHHcCCCHHHHHHHHHHHHHHHcC
Confidence            33444455555678889999996             4589999999999998    589999999999999999999873


Q ss_pred             ------------hHHHhccCCCCcHHHHHHHHHHhcCCCCccCcchHHHHHHH
Q 033363           71 ------------SWTHVTQLHGVGKYAADAFAIFCTGKWDRVRPTDHMLNYYW  111 (121)
Q Consensus        71 ------------~~~~L~~lpGIG~~tA~~vl~f~~~~~~~v~p~D~~l~~~~  111 (121)
                                  .+++|++|||||||||++|++|++|++|.++++|+++++.+
T Consensus       193 ~~~~~~~~~~~~~~~~L~~lpGIG~~TA~~ill~~lg~~d~~pvdd~~~r~~l  245 (282)
T 1mpg_A          193 TLPMTIPGDVEQAMKTLQTFPGIGRWTANYFALRGWQAKDVFLPDDYLIKQRF  245 (282)
T ss_dssp             CSCSSCCSCHHHHHHHHTTSTTCCHHHHHHHHHHHSCCSSCCCTTCHHHHHHS
T ss_pred             CCCccccCCHHHHHHHHhcCCCcCHHHHHHHHHHhCCCCCcCccccHHHHHHh
Confidence                        48999999999999999999999999986667899988654

>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=99.88  E-value=6e-23  Score=159.90  Aligned_cols=107  Identities=15%  Similarity=0.252  Sum_probs=89.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHh--------------CCCHHHHhcCCHHHHHHHHhhcCChhHHHHHHHHHHHH----
Q 033363            5 YSIRLKEIAILLKAGRVISDLFTL--------------CPDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQE----   66 (121)
Q Consensus         5 ~si~~~~~~~~~~v~~v~~~l~~~--------------~pt~~~la~a~~~eL~~~i~~~Gl~~~Ka~~i~~~a~~----   66 (121)
                      .+..++|+++.+++.+++.+|.++              ||||++|+++++++    |+++||+++|+++|+++|+.    
T Consensus       123 v~~Il~Qq~s~~~a~~~~~rL~~~~G~~~~~~g~~~~~fPtp~~la~~~~~~----Lr~~G~~~rKa~~i~~~A~~g~l~  198 (295)
T 2jhn_A          123 AKAIIQQQISFVVAEKLAAKIVGRFGDEVEWNGLKFYGFPTQEAILKAGVEG----LRECGLSRRKAELIVEIAKEENLE  198 (295)
T ss_dssp             HHHHHTTTSCHHHHHHHHHHHHHHHSCEEEETTEEEECCCCHHHHHHHHHHH----HHHTTCCHHHHHHHHHHHTCSSGG
T ss_pred             HHHHHcCcccHHHHHHHHHHHHHHhCCCCCCCCCccccCCCHHHHHcCCHHH----HHHcCCCHHHHHHHHHHHHCCCHh
Confidence            344444445566888999999887              89999999999988    58999999999999999987    


Q ss_pred             -HH----HhhHHHhccCCCCcHHHHHHHHHHhcCCCCccCcchHHHHHHHHHHHH
Q 033363           67 -YL----GESWTHVTQLHGVGKYAADAFAIFCTGKWDRVRPTDHMLNYYWEFLVS  116 (121)
Q Consensus        67 -i~----~~~~~~L~~lpGIG~~tA~~vl~f~~~~~~~v~p~D~~l~~~~~wl~~  116 (121)
                       +.    ++.+++|++|||||||||++|++|++| +|.++++|+++++..+++++
T Consensus       199 ~l~~~~~~e~~~~L~~lpGIG~~TA~~ill~~lg-~d~fpvdD~~~rr~~~~~~g  252 (295)
T 2jhn_A          199 ELKEWGEEEAYEYLTSFKGIGRWTAELVLSIALG-KNVFPADDLGVRRAVSRLYF  252 (295)
T ss_dssp             GGGGSCHHHHHHHHHTSTTCCHHHHHHHHHHTTC-CCCCCTTCHHHHHHHHHHHS
T ss_pred             hhhcCCHHHHHHHHhcCCCcCHHHHHHHHHHccC-CCcccchHHHHHHHHHHHhc
Confidence             11    135899999999999999999999999 98556668999998887754

>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=99.88  E-value=4.1e-22  Score=155.10  Aligned_cols=107  Identities=18%  Similarity=0.235  Sum_probs=89.3

Q ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHh--------------CCCHHHHhcCCHHHHHHHHhhcCChhHHHHHHHHHHHHHHH
Q 033363            4 IYSIRLKEIAILLKAGRVISDLFTL--------------CPDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQEYLG   69 (121)
Q Consensus         4 ~~si~~~~~~~~~~v~~v~~~l~~~--------------~pt~~~la~a~~~eL~~~i~~~Gl~~~Ka~~i~~~a~~i~~   69 (121)
                      +.+..++++++.+++.+++.+|.++              ||||++|+++++++|.+    +|++ .||++|+++|+.+.+
T Consensus       119 Lv~~IlsQq~s~~~a~~~~~rL~~~~G~~~~~~g~~~~~fPtpe~la~~~~e~L~~----~g~g-~Ra~~I~~~A~~i~~  193 (290)
T 3i0w_A          119 LLSFIISANNRIPMIKKCINNISEKAGKKLEYKGKIYYAFPTVDKLHEFTEKDFEE----CTAG-FRAKYLKDTVDRIYN  193 (290)
T ss_dssp             HHHHHHHTTCCHHHHHHHHHHHHHHHSCEEEETTEEEECCCCHHHHTTCCHHHHHH----TTCG-GGHHHHHHHHHHHHT
T ss_pred             HHHHHHhCcccHHHHHHHHHHHHHHhCCCcccCCcccccCCcHHHHHCCCHHHHHH----cCCc-hHHHHHHHHHHHHHh
Confidence            3444455555567888999999764              89999999999999654    6776 499999999999986


Q ss_pred             --------------hhHHHhccCCCCcHHHHHHHHHHhcCCCCccCcchHHHHHHHHHHHH
Q 033363           70 --------------ESWTHVTQLHGVGKYAADAFAIFCTGKWDRVRPTDHMLNYYWEFLVS  116 (121)
Q Consensus        70 --------------~~~~~L~~lpGIG~~tA~~vl~f~~~~~~~v~p~D~~l~~~~~wl~~  116 (121)
                                    +.+++|++|||||||||++|++|++|+|| ++|+|.++++..+++..
T Consensus       194 g~~~l~~l~~~~~~~~~~~L~~lpGIG~~TA~~ill~~lg~pd-~fpvD~~v~r~~~rl~~  253 (290)
T 3i0w_A          194 GELNLEYIKSLNDNECHEELKKFMGVGPQVADCIMLFSMQKYS-AFPVDTWVKKAMMSLYV  253 (290)
T ss_dssp             TSSCHHHHHHSCHHHHHHHHTTSTTCCHHHHHHHHHHHHCCTT-CCCCCHHHHHHHHHHTS
T ss_pred             CCCCHHHHhcCCHHHHHHHHHhCCCcCHHHHHHHHHHhCCCCC-cceecHHHHHHHHHhcC
Confidence                          25789999999999999999999999997 77779999998887653

>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=99.86  E-value=3.2e-22  Score=150.61  Aligned_cols=97  Identities=19%  Similarity=0.137  Sum_probs=82.7

Q ss_pred             HHHHHHHHHHHHHHHHHHhCCCHHHHhcCCHHHHHHHHhhcC--ChhHHHHHHHHHHHHH---HH-------hhHHHhc-
Q 033363           10 KEIAILLKAGRVISDLFTLCPDAKTATEVDAEEIEKIISTLG--LQKKRAPMIKRFSQEY---LG-------ESWTHVT-   76 (121)
Q Consensus        10 ~~~~~~~~v~~v~~~l~~~~pt~~~la~a~~~eL~~~i~~~G--l~~~Ka~~i~~~a~~i---~~-------~~~~~L~-   76 (121)
                      +++++++++++++.+|      |+.++++++++|+++|+++|  |+++||++|+++|+.+   .+       +.+++|+ 
T Consensus        60 sqqts~~~~~~a~~~L------p~~l~~~~~eeL~~~Ir~~G~Rf~~~KA~~I~~~a~~ig~l~~~~~~~~~~~r~~L~~  133 (219)
T 3n0u_A           60 TANWSAEGGIRAQKEI------GKGFVHLPLEELAEKLREVGHRYPQKRAEFIVENRKLLGKLKNLVKGDPFQSREFLVR  133 (219)
T ss_dssp             TTTSCHHHHHHHHHHH------TTHHHHCCHHHHHHHHHHTTCSSHHHHHHHHHHHGGGTTTHHHHHHSCHHHHHHHHHH
T ss_pred             hCCCCHHHHHHHHHHH------HHHHHcCCHHHHHHHHHHhcchHHHHHHHHHHHHHHHHHHHHHHhcCCcHHHHHHHHH
Confidence            3445567889999999      68899999999999999999  9999999999999975   22       5789999 


Q ss_pred             cCCCCcHHHHHHHHHHhcCCCCccCcchHHHHHHHHHH
Q 033363           77 QLHGVGKYAADAFAIFCTGKWDRVRPTDHMLNYYWEFL  114 (121)
Q Consensus        77 ~lpGIG~~tA~~vl~f~~~~~~~v~p~D~~l~~~~~wl  114 (121)
                      ++||||||||++||+| ++.++ ++|+|.++.|....+
T Consensus       134 ~l~GVG~kTA~~vL~~-~g~~~-~~~VDthv~Ri~~rl  169 (219)
T 3n0u_A          134 NAKGIGWKEASHFLRN-TGVED-LAILDKHVLRLMKRH  169 (219)
T ss_dssp             HSTTCCHHHHHHHHHT-TTCCS-CCCCCHHHHHHHHHT
T ss_pred             hCCCCCHHHHHHHHHH-cCCCC-eeeecHHHHHHHHHc
Confidence            9999999999999999 88754 788888887765443

>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=99.86  E-value=7.1e-22  Score=148.29  Aligned_cols=101  Identities=18%  Similarity=0.093  Sum_probs=84.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHhCCCHHHHhcCCHHHHHHHHhhcC--ChhHHHHHHHHHHH--HHHH---------hhH
Q 033363            6 SIRLKEIAILLKAGRVISDLFTLCPDAKTATEVDAEEIEKIISTLG--LQKKRAPMIKRFSQ--EYLG---------ESW   72 (121)
Q Consensus         6 si~~~~~~~~~~v~~v~~~l~~~~pt~~~la~a~~~eL~~~i~~~G--l~~~Ka~~i~~~a~--~i~~---------~~~   72 (121)
                      +..+++++++++|++++.+|+      +.++++++++|+++|+++|  |+++||++|+++|+  .+.+         .++
T Consensus        50 ~~ILsqqt~~~~v~~a~~~L~------~~l~~~~~eeL~~~Ir~~G~rf~~~KA~~I~~~a~~~~l~~~~~~~~~~~~~r  123 (214)
T 3fhf_A           50 FCILTANFTAEGGIRIQKEIG------DGFLTLPREELEEKLKNLGHRFYRKRAEYIVLARRFKNIKDIVESFENEKVAR  123 (214)
T ss_dssp             HHHHHTTSCHHHHHHHHHHHT------THHHHSCHHHHHHHHHHTTCTTHHHHHHHHHHHGGGCCHHHHHHHSSSHHHHH
T ss_pred             HHHHcCCCCHHHHHHHHHHHH------HHHHCCCHHHHHHHHHHHhhHHHHHHHHHHHHHHHhhHHHHHhcccCCcHHHH
Confidence            444445566778899999996      7899999999999999999  99999999999999  5443         368


Q ss_pred             HHhc-cCCCCcHHHHHHHHHHhcCCCCccCcchHHHHHHHHHH
Q 033363           73 THVT-QLHGVGKYAADAFAIFCTGKWDRVRPTDHMLNYYWEFL  114 (121)
Q Consensus        73 ~~L~-~lpGIG~~tA~~vl~f~~~~~~~v~p~D~~l~~~~~wl  114 (121)
                      ++|+ +|||||||||++||+++ +.+ .++++|.++.|....+
T Consensus       124 e~Ll~~LpGVG~KTA~~vL~~~-g~~-~~~vVDthv~Ri~~Rl  164 (214)
T 3fhf_A          124 EFLVRNIKGIGYKEASHFLRNV-GYD-DVAIIDRHILRELYEN  164 (214)
T ss_dssp             HHHHHHSTTCCHHHHHHHHHHT-TCC-SCCCCCHHHHHHHHHT
T ss_pred             HHHHHhCCCCCHHHHHHHHHHc-CCC-CcccCcHHHHHHHHHc
Confidence            8999 99999999999999998 664 4666998888775543

>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=99.86  E-value=1e-21  Score=146.27  Aligned_cols=101  Identities=17%  Similarity=0.215  Sum_probs=82.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHhCCCHHHHhcCCHHHHHHHHhhcC--ChhHHHHHHHHHHHHHHH--------------
Q 033363            6 SIRLKEIAILLKAGRVISDLFTLCPDAKTATEVDAEEIEKIISTLG--LQKKRAPMIKRFSQEYLG--------------   69 (121)
Q Consensus         6 si~~~~~~~~~~v~~v~~~l~~~~pt~~~la~a~~~eL~~~i~~~G--l~~~Ka~~i~~~a~~i~~--------------   69 (121)
                      +..++++++.++|++++.+|      |++++++++++|+++|+++|  |+++||++|+++|+.+.+              
T Consensus        39 ~~ILsqqts~~~~~~~~~~L------~~~l~~~~~e~l~~~ir~~G~g~~~~KA~~l~~~a~~~~~~~~~~l~~~~~~~~  112 (207)
T 3fhg_A           39 LCLLTANSSFISAYQALNCL------GQKIYYANEEEIRNILKSCKYRFYNLKAKYIIMAREKVYGRLKEEIKPLADEDQ  112 (207)
T ss_dssp             HHHHHTTSCHHHHHHHHHHH------GGGGGTCCHHHHHHHHHHTTCTTHHHHHHHHHHHHHHHTTTHHHHHHHHHHHCH
T ss_pred             HHHHcCCCCHHHHHHHHHHH------HHHHHcCCHHHHHHHHHHhccCcHHHHHHHHHHHHHHHHHHhhhhHHHHhCCCH
Confidence            33344445567888999998      58999999999999999887  999999999999994422              


Q ss_pred             -hhHHHhccCCCCcHHHHHHHHHHhcCCCCccCcchHHHHHHHHHH
Q 033363           70 -ESWTHVTQLHGVGKYAADAFAIFCTGKWDRVRPTDHMLNYYWEFL  114 (121)
Q Consensus        70 -~~~~~L~~lpGIG~~tA~~vl~f~~~~~~~v~p~D~~l~~~~~wl  114 (121)
                       +.+++|++|||||||||++|++|+ +.++ ++|+|.+++|....+
T Consensus       113 ~~~~~~L~~lpGIG~kTA~~il~~~-~~~~-~~~vD~~v~Ri~~rl  156 (207)
T 3fhg_A          113 QLARERLLNIKGIGMQEASHFLRNV-GYFD-LAIIDRHIIDFMRRI  156 (207)
T ss_dssp             HHHHHHHTTSTTCCHHHHHHHHHHT-TCCS-SCCCCHHHHHHHHHT
T ss_pred             HHHHHHHHcCCCcCHHHHHHHHHHh-CCCC-cceecHHHHHHHHHc
Confidence             468999999999999999999983 3344 899999888877654

>2xhi_A N-glycosylase/DNA lyase; lyase-DNA complex, lyase/DNA complex, separation-OF-function helix-hairpin-helix, DNA repair; HET: 8OG; 1.55A {Homo sapiens} PDB: 1ko9_A 1lwy_A* 1hu0_A* 1lwv_A* 1lww_A* 2noe_A* 2noh_A* 2nol_A* 1n3c_A* 1fn7_A* 2noz_A* 1yqk_A 1yqr_A* 1yql_A* 1yqm_A* 2noi_A 1ebm_A* 1m3q_A* 1m3h_A* 1n39_A* ...

Probab=99.86  E-value=1.6e-21  Score=155.89  Aligned_cols=105  Identities=18%  Similarity=0.180  Sum_probs=87.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHH---------------hCCCHHHHhcCCHHHHHHHHhhcCChhHHHHHHHHHHHHHHH-
Q 033363            6 SIRLKEIAILLKAGRVISDLFT---------------LCPDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQEYLG-   69 (121)
Q Consensus         6 si~~~~~~~~~~v~~v~~~l~~---------------~~pt~~~la~a~~~eL~~~i~~~Gl~~~Ka~~i~~~a~~i~~-   69 (121)
                      +..++++++.+++.+++.+|.+               .||||++|++++.++   .|+++|| .+||++|+++|+.+.+ 
T Consensus       158 ~~ILsQq~s~~~a~~~~~rL~~~~G~~~~~~~g~~~~~fPtpe~La~~~~ee---~Lr~~Gl-~~RA~~I~~~A~~i~~~  233 (360)
T 2xhi_A          158 SFICSSNNNIARITGMVERLCQAFGPRLIQLDDVTYHGFPSLQALAGPEVEA---HLRKLGL-GYRARYVSASARAILEE  233 (360)
T ss_dssp             HHHTTTTSCHHHHHHHHHHHHHHHSCEEEEETTEEEECCCCHHHHTSTTHHH---HHHHTTC-TTHHHHHHHHHHHHHHT
T ss_pred             HHHHhCcCcHHHHHHHHHHHHHHhCCCcccCCCcccccCCCHHHHHcCCHHH---HHHHcCC-cHHHHHHHHHHHHHHhc
Confidence            4444444556678899999987               589999999997543   4889999 4899999999999865 


Q ss_pred             ----------------hhHHHhccCCCCcHHHHHHHHHHhcCCCCccCcchHHHHHHHHHHH
Q 033363           70 ----------------ESWTHVTQLHGVGKYAADAFAIFCTGKWDRVRPTDHMLNYYWEFLV  115 (121)
Q Consensus        70 ----------------~~~~~L~~lpGIG~~tA~~vl~f~~~~~~~v~p~D~~l~~~~~wl~  115 (121)
                                      +.+++|++|||||||||++|++|++|+|| ++|+|.+++|....++
T Consensus       234 ~~G~~~L~~l~~~~~~~~~~~L~~LpGIGp~TA~~ill~alg~pd-~fpvDthV~Ri~~r~~  294 (360)
T 2xhi_A          234 QGGLAWLQQLRESSYEEAHKALCILPGVGTCVADKICLMALDKPQ-AVPVNVHMWHIAQRDY  294 (360)
T ss_dssp             TCTHHHHHGGGTSCHHHHHHHHTTSTTCCHHHHHHHHHHHSCCTT-CCCCSHHHHHHHHHHH
T ss_pred             cCCccCHHHHhcCCHHHHHHHHHhCCCCCHHHHHHHHHHhCCCCC-EEEecHHHHHHHHHHh
Confidence                            35789999999999999999999999997 8888999988876543

>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=96.31  E-value=0.011  Score=43.78  Aligned_cols=56  Identities=18%  Similarity=0.222  Sum_probs=41.0

Q ss_pred             HHHHH-HHhhcCChhHHHHHHHHH------HHHHHHhhHHHhccCCCCcHHHHHHHHHHhcCC
Q 033363           41 EEIEK-IISTLGLQKKRAPMIKRF------SQEYLGESWTHVTQLHGVGKYAADAFAIFCTGK   96 (121)
Q Consensus        41 ~eL~~-~i~~~Gl~~~Ka~~i~~~------a~~i~~~~~~~L~~lpGIG~~tA~~vl~f~~~~   96 (121)
                      .++.+ +++--|.....|..|.+.      .+.+.+++.+.|.++||||+|||+-+..---++
T Consensus        84 r~lf~~L~sv~GIGpk~A~~Ils~~~~~~l~~aI~~~d~~~L~~vpGIG~KtA~rIi~elk~k  146 (212)
T 2ztd_A           84 RDLFLTLLSVSGVGPRLAMAALAVHDAPALRQVLADGNVAALTRVPGIGKRGAERMVLELRDK  146 (212)
T ss_dssp             HHHHHHHHTSTTCCHHHHHHHHHHSCHHHHHHHHHTTCHHHHHTSTTCCHHHHHHHHHHHTTT
T ss_pred             HHHHHHhcCcCCcCHHHHHHHHHhCCHHHHHHHHHhCCHHHHhhCCCCCHHHHHHHHHHHHHh
Confidence            34444 334456667788888764      555777899999999999999999987655454

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

Probab=96.22  E-value=0.0033  Score=51.67  Aligned_cols=64  Identities=19%  Similarity=0.304  Sum_probs=37.3

Q ss_pred             HHHHHhCCCHHHHhcCCHHHHHHHHhhcCChhHHHHHHHHHHHHHHH---------------------------------
Q 033363           23 SDLFTLCPDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQEYLG---------------------------------   69 (121)
Q Consensus        23 ~~l~~~~pt~~~la~a~~~eL~~~i~~~Gl~~~Ka~~i~~~a~~i~~---------------------------------   69 (121)
                      ..|.++|.+..++..+|.+|    ++.+||+..|...|+.+-+.+.+                                 
T Consensus       532 ~elkr~ygs~savr~~pv~e----lrelg~sd~~ia~ikgip~~~~~~~~~e~a~~l~er~~~~~~~~~~~~~~~l~~~g  607 (685)
T 4gfj_A          532 DELKRKYGSASAVRRLPVEE----LRELGFSDDEIAEIKGIPKKLREAFDLETAAELYERYGSLKEIGRRLSYDDLLELG  607 (685)
T ss_dssp             HHHHHHSSCHHHHHHSCHHH----HHTTSCCHHHHHHHHTCCHHHHHHSCHHHHHHHHHHHSSSTGGGGSCGGGCCSSSC
T ss_pred             HHHHHhhccHHHHHhccHHH----HHHcCCchhhHHHhcCCcHHHHhhcCHHHHHHHHHHhccHHHHhhcCCHHHHhccC
Confidence            46788999999999999999    78899999999999877666554                                 


Q ss_pred             -----------hhHHHhccCCCCcHHHHHHHH
Q 033363           70 -----------ESWTHVTQLHGVGKYAADAFA   90 (121)
Q Consensus        70 -----------~~~~~L~~lpGIG~~tA~~vl   90 (121)
                                 ..++.|+.+.||||+.|+-++
T Consensus       608 ~~~~~~~eik~p~~k~ll~~~gv~p~la~r~~  639 (685)
T 4gfj_A          608 ATPKAAAEIKGPEFKFLLNIEGVGPKLAERIL  639 (685)
T ss_dssp             CGGGC---------------------------
T ss_pred             CCHHHHHHhcChhHHHhhcccCCCHHHHHHHH
Confidence                       157889999999999998765

>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=95.98  E-value=0.021  Score=41.50  Aligned_cols=50  Identities=26%  Similarity=0.288  Sum_probs=38.1

Q ss_pred             HhhcCChhHHHHHHHHH------HHHHHHhhHHHhccCCCCcHHHHHHHHHHhcCC
Q 033363           47 ISTLGLQKKRAPMIKRF------SQEYLGESWTHVTQLHGVGKYAADAFAIFCTGK   96 (121)
Q Consensus        47 i~~~Gl~~~Ka~~i~~~------a~~i~~~~~~~L~~lpGIG~~tA~~vl~f~~~~   96 (121)
                      ++--|....+|+.|.+.      .+.+.+.+.++|.++||||+|||+-+...--++
T Consensus        75 ~~v~GIGpk~A~~iL~~f~~~~l~~aI~~~d~~~L~~vpGIG~K~A~rI~~~lk~k  130 (191)
T 1ixr_A           75 LSVSGVGPKVALALLSALPPRLLARALLEGDARLLTSASGVGRRLAERIALELKGK  130 (191)
T ss_dssp             HSSSCCCHHHHHHHHHHSCHHHHHHHHHTTCHHHHTTSTTCCHHHHHHHHHHHTTT
T ss_pred             hcCCCcCHHHHHHHHHhCChHHHHHHHHhCCHHHHHhCCCCCHHHHHHHHHHHHHh
Confidence            34456667788877754      445667899999999999999999997655454

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

Probab=95.87  E-value=0.02  Score=36.18  Aligned_cols=46  Identities=11%  Similarity=0.109  Sum_probs=31.5

Q ss_pred             CChhHHHHHHHHH---HHHHHHhhHHHhccCCCCcHHHHHHHHHHhcCC
Q 033363           51 GLQKKRAPMIKRF---SQEYLGESWTHVTQLHGVGKYAADAFAIFCTGK   96 (121)
Q Consensus        51 Gl~~~Ka~~i~~~---a~~i~~~~~~~L~~lpGIG~~tA~~vl~f~~~~   96 (121)
                      |.....++.|.+-   .+.+.+.+.++|.++||||+++|..+..+--+.
T Consensus        26 gIG~~~A~~Ll~~fgsl~~l~~a~~~eL~~i~GIG~~~a~~I~~~l~~~   74 (89)
T 1z00_A           26 SVNKTDSQTLLTTFGSLEQLIAASREDLALCPGLGPQKARRLFDVLHEP   74 (89)
T ss_dssp             SCCHHHHHHHHHHTCBHHHHHHCCHHHHHTSTTCCHHHHHHHHHHHHSC
T ss_pred             CCCHHHHHHHHHHCCCHHHHHhCCHHHHHhCCCCCHHHHHHHHHHHHHH
Confidence            3333455555443   234445678899999999999999998876543

>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=95.85  E-value=0.024  Score=34.14  Aligned_cols=45  Identities=13%  Similarity=0.188  Sum_probs=30.7

Q ss_pred             CChhHHHHHHHHH---HHHHHHhhHHHhccCCCCcHHHHHHHHHHhcC
Q 033363           51 GLQKKRAPMIKRF---SQEYLGESWTHVTQLHGVGKYAADAFAIFCTG   95 (121)
Q Consensus        51 Gl~~~Ka~~i~~~---a~~i~~~~~~~L~~lpGIG~~tA~~vl~f~~~   95 (121)
                      |.....|+.|.+-   ...+.+.+.++|.++||||+++|..+..+.-.
T Consensus        21 giG~~~a~~Ll~~fgs~~~l~~a~~~~L~~i~Gig~~~a~~i~~~~~~   68 (75)
T 1x2i_A           21 HVSATLARRLLKHFGSVERVFTASVAELMKVEGIGEKIAKEIRRVITA   68 (75)
T ss_dssp             TCCHHHHHHHHHHHCSHHHHHHCCHHHHTTSTTCCHHHHHHHHHHHHS
T ss_pred             CCCHHHHHHHHHHcCCHHHHHhCCHHHHhcCCCCCHHHHHHHHHHHhC
Confidence            3344456655543   23344457889999999999999998876543

>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=95.81  E-value=0.013  Score=36.23  Aligned_cols=41  Identities=17%  Similarity=0.238  Sum_probs=28.7

Q ss_pred             ChhHHHHHHHHH---HHHHHHhhHHHhccCCCCcHHHHHHHHHH
Q 033363           52 LQKKRAPMIKRF---SQEYLGESWTHVTQLHGVGKYAADAFAIF   92 (121)
Q Consensus        52 l~~~Ka~~i~~~---a~~i~~~~~~~L~~lpGIG~~tA~~vl~f   92 (121)
                      ....+++.|.+-   .+.+.+.+.++|.++||||+++|..+..+
T Consensus        32 IG~~~A~~Ll~~fgsl~~l~~a~~eeL~~i~GIG~~~a~~I~~~   75 (78)
T 1kft_A           32 VGPKRRQMLLKYMGGLQGLRNASVEEIAKVPGISQGLAEKIFWS   75 (78)
T ss_dssp             CSSSHHHHHHHHHSCHHHHHHCCHHHHTTSSSTTSHHHHHHHHH
T ss_pred             CCHHHHHHHHHHcCCHHHHHHCCHHHHHHCCCCCHHHHHHHHHH
Confidence            333456666553   23444567889999999999999988764

>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=95.66  E-value=0.032  Score=43.66  Aligned_cols=54  Identities=15%  Similarity=0.177  Sum_probs=43.9

Q ss_pred             HHHHHHHHhhcCChhHHHHHHHHHHHHHHH-----hhHHHhccCCCCcHHHHHHHHHHh
Q 033363           40 AEEIEKIISTLGLQKKRAPMIKRFSQEYLG-----ESWTHVTQLHGVGKYAADAFAIFC   93 (121)
Q Consensus        40 ~~eL~~~i~~~Gl~~~Ka~~i~~~a~~i~~-----~~~~~L~~lpGIG~~tA~~vl~f~   93 (121)
                      .++|..++.-.|=...|++.-.++|..+..     .+.++|.+|||||+++|+.|.-+.
T Consensus        19 L~~ia~l~e~~~~~~~rv~AYr~Aa~~l~~l~~~i~~~~~l~~LpGIG~~~A~kI~E~l   77 (335)
T 2fmp_A           19 LTELANFEKNVSQAIHKYNAYRKAASVIAKYPHKIKSGAEAKKLPGVGTKIAEKIDEFL   77 (335)
T ss_dssp             HHHHHHHHHHTTCCHHHHHHHHHHHHHHHHCSSCCCCHHHHHTSTTCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHhcCCCcHHHHHHHHHHHHHHhCCccccCHHHHhcCCCCcHHHHHHHHHHH
Confidence            456666666566667899999999999876     467789999999999999998764

>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=95.47  E-value=0.021  Score=36.27  Aligned_cols=45  Identities=11%  Similarity=0.116  Sum_probs=30.6

Q ss_pred             CChhHHHHHHHHH---HHHHHHhhHHHhccCCCCcHHHHHHHHHHhcC
Q 033363           51 GLQKKRAPMIKRF---SQEYLGESWTHVTQLHGVGKYAADAFAIFCTG   95 (121)
Q Consensus        51 Gl~~~Ka~~i~~~---a~~i~~~~~~~L~~lpGIG~~tA~~vl~f~~~   95 (121)
                      |.....++.|.+-   .+.+.+.+.++|.++||||+++|..+..+.-+
T Consensus        39 gIG~~~A~~Ll~~fgs~~~l~~as~~eL~~i~GIG~~~a~~I~~~l~~   86 (91)
T 2a1j_B           39 SVNKTDSQTLLTTFGSLEQLIAASREDLALCPGLGPQKARRLFDVLHE   86 (91)
T ss_dssp             TCCHHHHHHHHHHHSSHHHHHSCCHHHHHTSSSCCSHHHHHHHHHHHS
T ss_pred             CCCHHHHHHHHHHCCCHHHHHhCCHHHHHhCCCCCHHHHHHHHHHHhh
Confidence            4444455555543   23344457889999999999999999876543

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

Probab=95.34  E-value=0.044  Score=46.13  Aligned_cols=71  Identities=14%  Similarity=0.132  Sum_probs=46.9

Q ss_pred             HHHHHHHHhC--CCHHHHhcCCHHHHHHHHhhcCChhHHHHHHHHHHHHHHH----------------------------
Q 033363           20 RVISDLFTLC--PDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQEYLG----------------------------   69 (121)
Q Consensus        20 ~v~~~l~~~~--pt~~~la~a~~~eL~~~i~~~Gl~~~Ka~~i~~~a~~i~~----------------------------   69 (121)
                      ..+..|++..  .++.++..++.++|.++   =||...++..|.+.-+...+                            
T Consensus       457 ~~i~~L~~~g~i~~~~Dly~L~~~~L~~l---~g~geKsa~nL~~aIe~sk~~~l~r~l~aLGI~~vG~~~a~~La~~f~  533 (586)
T 4glx_A          457 KIIDQLVEKEYVHTPADLFKLTAGKLTGL---ERMGPKSAQNVVNALEKAKETTFARFLYALGIREVGEATAAGLAAYFG  533 (586)
T ss_dssp             HHHHHHHHTTCCSSGGGGGTCCHHHHHTS---TTCCHHHHHHHHHHHHHHTBCCHHHHHHHTTCTTCCHHHHHHHHHHHC
T ss_pred             HHHHHHHhcCCCCCHHHHhCCCHHHHhcc---cCccHHHHHHHHHHHHHHcCCCHHHHHHHcCCCchhHHHHHHHHHHcC
Confidence            4455565542  57777877777774332   26666666666554332221                            


Q ss_pred             -------hhHHHhccCCCCcHHHHHHHHHHh
Q 033363           70 -------ESWTHVTQLHGVGKYAADAFAIFC   93 (121)
Q Consensus        70 -------~~~~~L~~lpGIG~~tA~~vl~f~   93 (121)
                             .+.++|.+++|||+.+|+.+..|-
T Consensus       534 sl~~l~~a~~e~l~~i~giG~~~A~si~~ff  564 (586)
T 4glx_A          534 TLEALEAASIEELQKVPDVGIVVASHVHNFF  564 (586)
T ss_dssp             SHHHHHHCCHHHHTTSTTCCHHHHHHHHHHH
T ss_pred             CHHHHHccCHHHHhcCCCccHHHHHHHHHHH
Confidence                   256899999999999999998764

>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=95.34  E-value=0.027  Score=41.32  Aligned_cols=46  Identities=24%  Similarity=0.187  Sum_probs=34.6

Q ss_pred             hhcCChhHHHHHHHHH------HHHHHHhhHHHhccCCCCcHHHHHHHHHHh
Q 033363           48 STLGLQKKRAPMIKRF------SQEYLGESWTHVTQLHGVGKYAADAFAIFC   93 (121)
Q Consensus        48 ~~~Gl~~~Ka~~i~~~------a~~i~~~~~~~L~~lpGIG~~tA~~vl~f~   93 (121)
                      +--|....+|..|.+.      .+.|.+.+.++|.++||||+|||+-+...-
T Consensus        77 ~V~GIGpk~A~~iL~~f~~~~l~~aI~~~d~~~L~~vpGIG~K~A~rI~~el  128 (203)
T 1cuk_A           77 KTNGVGPKLALAILSGMSAQQFVNAVEREEVGALVKLPGIGKKTAERLIVEM  128 (203)
T ss_dssp             HSSSCCHHHHHHHHHHSCHHHHHHHHHTTCHHHHHTSTTCCHHHHHHHHHHH
T ss_pred             cCCCcCHHHHHHHHhhCChHHHHHHHHhCCHHHHhhCCCCCHHHHHHHHHHH
Confidence            3346666677777652      445667899999999999999999987644

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

Probab=95.30  E-value=0.033  Score=44.03  Aligned_cols=54  Identities=11%  Similarity=0.075  Sum_probs=43.1

Q ss_pred             HHHHHHHHhhcCChhHHHHHHHHHHHHHHH-----hhHHHhccCCCCcHHHHHHHHHHhc
Q 033363           40 AEEIEKIISTLGLQKKRAPMIKRFSQEYLG-----ESWTHVTQLHGVGKYAADAFAIFCT   94 (121)
Q Consensus        40 ~~eL~~~i~~~Gl~~~Ka~~i~~~a~~i~~-----~~~~~L~~lpGIG~~tA~~vl~f~~   94 (121)
                      .++|.+++.--| ...|++.-.++|..+..     .+.++|.+|||||+++|+.|.-+.-
T Consensus        24 L~~ia~~~e~~g-~~~r~~AYr~Aa~~l~~l~~~i~~~~~l~~lpGIG~~~A~kI~E~l~   82 (360)
T 2ihm_A           24 LETLAEAAGFEA-NEGRLLSFSRAASVLKSLPCPVASLSQLHGLPYFGEHSTRVIQELLE   82 (360)
T ss_dssp             HHHHHHHHHHTT-CHHHHHHHHHHHHHHHHCSSCCCSGGGGTTCTTCCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcC-CcHHHHHHHHHHHHHHhCCcccCCHHHHhcCCCCCHHHHHHHHHHHH
Confidence            355666666667 67899999999999876     3566799999999999999987643

>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=95.02  E-value=0.06  Score=42.16  Aligned_cols=50  Identities=20%  Similarity=0.201  Sum_probs=31.3

Q ss_pred             HHHHHHhhcCChhHHHHHHHHHHHHHHH-----hhHHHhccCCCCcHHHHHHHHHH
Q 033363           42 EIEKIISTLGLQKKRAPMIKRFSQEYLG-----ESWTHVTQLHGVGKYAADAFAIF   92 (121)
Q Consensus        42 eL~~~i~~~Gl~~~Ka~~i~~~a~~i~~-----~~~~~L~~lpGIG~~tA~~vl~f   92 (121)
                      +|..++.-.|=. .|++.-.++|..+..     .+.++|.+|||||+++|+.|.-+
T Consensus        22 ~ia~~~e~~g~~-~r~~AYr~Aa~~l~~l~~~i~~~~~l~~lpGIG~~~A~kI~E~   76 (335)
T 2bcq_A           22 VLAKAYSVQGDK-WRALGYAKAINALKSFHKPVTSYQEACSIPGIGKRMAEKIIEI   76 (335)
T ss_dssp             HHHHHHHHTTCH-HHHHHHHHHHHHHHSCCSCCCCHHHHHTSTTCCHHHHHHHHHH
T ss_pred             HHHHHHHHcCcc-HhHHHHHHHHHHHHhCCccccCHHHHhcCCCccHHHHHHHHHH
Confidence            344444444443 677777777777665     35556777777777777777655

>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=94.96  E-value=0.044  Score=43.68  Aligned_cols=54  Identities=7%  Similarity=-0.036  Sum_probs=43.7

Q ss_pred             HHHHHHHHhhcCChhHHHHHHHHHHHHHHH-----hhHHHhccCCCCcHHHHHHHHHHhc
Q 033363           40 AEEIEKIISTLGLQKKRAPMIKRFSQEYLG-----ESWTHVTQLHGVGKYAADAFAIFCT   94 (121)
Q Consensus        40 ~~eL~~~i~~~Gl~~~Ka~~i~~~a~~i~~-----~~~~~L~~lpGIG~~tA~~vl~f~~   94 (121)
                      .++|..++.--| ...|++.-.++|..+..     ...++|.+|||||+.+|+.|.-+.-
T Consensus        43 L~~ia~~~e~~g-~~~rv~AYr~Aa~~l~~l~~~i~~~~~l~~lpGIG~~ia~kI~E~l~  101 (381)
T 1jms_A           43 LDILAENDELRE-NEGSCLAFMRASSVLKSLPFPITSMKDTEGIPCLGDKVKSIIEGIIE  101 (381)
T ss_dssp             HHHHHHHHHHTT-CHHHHHHHHHHHHHHHTCSSCCCSGGGGTTCSSCCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhhC-CcHHHHHHHHHHHHHHhCCccccCHHHHhcCCCCcHHHHHHHHHHHH
Confidence            456666666677 67899999999999876     3566799999999999999987643

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

Probab=94.84  E-value=0.025  Score=42.01  Aligned_cols=29  Identities=21%  Similarity=0.316  Sum_probs=24.8

Q ss_pred             HhhHHHhccCCCCcHHHHHHHHHHhcCCC
Q 033363           69 GESWTHVTQLHGVGKYAADAFAIFCTGKW   97 (121)
Q Consensus        69 ~~~~~~L~~lpGIG~~tA~~vl~f~~~~~   97 (121)
                      ++.+++|.+|||||||||.=+..+-+.++
T Consensus        22 ~~LI~~l~~LPGIG~KsA~RlA~hLL~~~   50 (212)
T 3vdp_A           22 AKLIEELSKLPGIGPKTAQRLAFFIINMP   50 (212)
T ss_dssp             HHHHHHHHTSTTCCHHHHHHHHHHHTTSC
T ss_pred             HHHHHHHHHCCCCCHHHHHHHHHHHHcCC
Confidence            35678899999999999999998888764

>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=94.82  E-value=0.12  Score=40.40  Aligned_cols=70  Identities=19%  Similarity=0.215  Sum_probs=51.9

Q ss_pred             HHHHHHHhCCCHHHHhcCCHHHHHHHHhhcCChhHHHHHHHHHHHHHHHhhHHHhccCCCCcHHHHHHHHHHhcCCCC
Q 033363           21 VISDLFTLCPDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQEYLGESWTHVTQLHGVGKYAADAFAIFCTGKWD   98 (121)
Q Consensus        21 v~~~l~~~~pt~~~la~a~~~eL~~~i~~~Gl~~~Ka~~i~~~a~~i~~~~~~~L~~lpGIG~~tA~~vl~f~~~~~~   98 (121)
                      +...+++.|-+...+.+.+.++++.+...-.++..-.+       ..++-...+|++-.|||+|||+-++ .+||.|.
T Consensus       366 aadeliehfesiagilatdleeiermyeegrlseeayr-------aaveiqlaeltkkegvgrktaerll-rafgnpe  435 (519)
T 2csb_A          366 AADELIEHFESIAGILATDLEEIERMYEEGRLSEEAYR-------AAVEIQLAELTKKEGVGRKTAERLL-RAFGNPE  435 (519)
T ss_dssp             HHHHHHHHHSSHHHHHTSCHHHHHHHHHHTSSCHHHHH-------HHHHHHHHHHHTSTTCCHHHHHHHH-HHHSSHH
T ss_pred             hHHHHHHHHHHHHHHHhccHHHHHHHHHcccccHHHHH-------HHHHHHHHHHhhhcccchhHHHHHH-HHhCCHH
Confidence            34566778888999999999999998877777743222       2223356789999999999999765 6888764

>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=94.61  E-value=0.072  Score=31.81  Aligned_cols=39  Identities=18%  Similarity=0.276  Sum_probs=31.3

Q ss_pred             HHHHHHHhCCCHHHHhcCCHHHHHHHHhhcCChhHH-HHHHHHHH
Q 033363           21 VISDLFTLCPDAKTATEVDAEEIEKIISTLGLQKKR-APMIKRFS   64 (121)
Q Consensus        21 v~~~l~~~~pt~~~la~a~~~eL~~~i~~~Gl~~~K-a~~i~~~a   64 (121)
                      -...|++.|.|.+.+.+|+.+||.++   +|  ... |+.|.+..
T Consensus        16 r~~~LL~~Fgs~~~i~~As~eeL~~v---ig--~~~~A~~I~~~l   55 (63)
T 2a1j_A           16 NCRSLMHHVKNIAELAALSQDELTSI---LG--NAANAKQLYDFI   55 (63)
T ss_dssp             HHHHHHHHCSSHHHHHTCCHHHHHHH---HS--CHHHHHHHHHHH
T ss_pred             HHHHHHHHcCCHHHHHHCCHHHHHHH---cC--chHHHHHHHHHH
Confidence            35678899999999999999999887   45  345 88887644

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

Probab=94.49  E-value=0.0029  Score=38.95  Aligned_cols=54  Identities=15%  Similarity=0.131  Sum_probs=37.9

Q ss_pred             HHHHhcCCHHHHHHHHhhcCChhHHHHHHHHHHHHHHHhhHHHhccCCCCcHHHHHHHHH
Q 033363           32 AKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQEYLGESWTHVTQLHGVGKYAADAFAI   91 (121)
Q Consensus        32 ~~~la~a~~~eL~~~i~~~Gl~~~Ka~~i~~~a~~i~~~~~~~L~~lpGIG~~tA~~vl~   91 (121)
                      +-++..++.++|.++   -|+...+|+.|.+.-   ...+.++|.++||+|+++++-+.-
T Consensus        18 ~idiN~a~~~~L~~i---pGIG~~~A~~Il~~r---~~~s~~eL~~v~Gig~k~~~~i~~   71 (75)
T 2duy_A           18 PVSLNEASLEELMAL---PGIGPVLARRIVEGR---PYARVEDLLKVKGIGPATLERLRP   71 (75)
T ss_dssp             SEETTTCCHHHHTTS---TTCCHHHHHHHHHTC---CCSSGGGGGGSTTCCHHHHHHHGG
T ss_pred             ccChhhCCHHHHHhC---CCCCHHHHHHHHHHc---ccCCHHHHHhCCCCCHHHHHHHHH
Confidence            445677777776542   366667777776632   226788999999999999987653

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

Probab=94.46  E-value=0.025  Score=34.60  Aligned_cols=22  Identities=23%  Similarity=0.211  Sum_probs=19.6

Q ss_pred             hHHHhccCCCCcHHHHHHHHHH
Q 033363           71 SWTHVTQLHGVGKYAADAFAIF   92 (121)
Q Consensus        71 ~~~~L~~lpGIG~~tA~~vl~f   92 (121)
                      +.++|.++||||+++|..++.+
T Consensus        25 ~~~~L~~ipGIG~~~A~~Il~~   46 (75)
T 2duy_A           25 SLEELMALPGIGPVLARRIVEG   46 (75)
T ss_dssp             CHHHHTTSTTCCHHHHHHHHHT
T ss_pred             CHHHHHhCCCCCHHHHHHHHHH
Confidence            5678999999999999999874

>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=94.26  E-value=0.039  Score=41.33  Aligned_cols=29  Identities=17%  Similarity=0.181  Sum_probs=25.0

Q ss_pred             HhhHHHhccCCCCcHHHHHHHHHHhcCCC
Q 033363           69 GESWTHVTQLHGVGKYAADAFAIFCTGKW   97 (121)
Q Consensus        69 ~~~~~~L~~lpGIG~~tA~~vl~f~~~~~   97 (121)
                      ++.+++|.+|||||||||.=+..+-+.++
T Consensus         8 ~~LI~~l~~LPGIG~KSA~RlA~hLL~~~   36 (228)
T 1vdd_A            8 VSLIRELSRLPGIGPKSAQRLAFHLFEQP   36 (228)
T ss_dssp             HHHHHHHHTSTTCCHHHHHHHHHHHSSSC
T ss_pred             HHHHHHHhHCCCCCHHHHHHHHHHHHcCC
Confidence            45678999999999999999988888764

>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=94.17  E-value=0.029  Score=38.83  Aligned_cols=48  Identities=17%  Similarity=0.185  Sum_probs=33.9

Q ss_pred             HhcCCHHHHHHHHhhcCChhHHHHHHHHHHHHHHH---hhHHHhccCCCCcHHHHHHHHH
Q 033363           35 ATEVDAEEIEKIISTLGLQKKRAPMIKRFSQEYLG---ESWTHVTQLHGVGKYAADAFAI   91 (121)
Q Consensus        35 la~a~~~eL~~~i~~~Gl~~~Ka~~i~~~a~~i~~---~~~~~L~~lpGIG~~tA~~vl~   91 (121)
                      |-.|+.+++++   ==|++..||+.|++      .   ...++|..+||||+++-+.+--
T Consensus        57 iNtA~~~eL~~---LpGiGp~~A~~II~------~GpF~svedL~~V~GIg~k~~e~l~~  107 (134)
T 1s5l_U           57 LNNTNIAAFIQ---YRGLYPTLAKLIVK------NAPYESVEDVLNIPGLTERQKQILRE  107 (134)
T ss_dssp             TTTSCGGGGGG---STTCTHHHHHHHHH------TCCCSSGGGGGGCTTCCHHHHHHHHH
T ss_pred             CcccCHHHHHH---CCCCCHHHHHHHHH------cCCCCCHHHHHhCCCCCHHHHHHHHH
Confidence            45566666443   23888888888871      2   4788999999999988776643

>2edu_A Kinesin-like protein KIF22; kinesin-like DNA binding domain, helix turn helix motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.60.2.7

Probab=93.93  E-value=0.12  Score=33.11  Aligned_cols=59  Identities=12%  Similarity=0.159  Sum_probs=40.3

Q ss_pred             HHHHhcCCHHHHHHHHhhcCChhHHHHHHHHHHHHHHH-hhHHHhccCCCCcHHHHHHHHHHh
Q 033363           32 AKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQEYLG-ESWTHVTQLHGVGKYAADAFAIFC   93 (121)
Q Consensus        32 ~~~la~a~~~eL~~~i~~~Gl~~~Ka~~i~~~a~~i~~-~~~~~L~~lpGIG~~tA~~vl~f~   93 (121)
                      +-+|..++.++|.. |.  |+....|+.|.+.-+.--. .+.++|..+||||+++++.+...+
T Consensus        31 ~i~iN~a~~~~L~~-ip--GIG~~~A~~Il~~r~~~g~f~s~edL~~v~Gig~k~~~~l~~~g   90 (98)
T 2edu_A           31 LDLLNEGSARDLRS-LQ--RIGPKKAQLIVGWRELHGPFSQVEDLERVEGITGKQMESFLKAN   90 (98)
T ss_dssp             HHHHHHSCHHHHHH-ST--TCCHHHHHHHHHHHHHHCCCSSGGGGGGSTTCCHHHHHHHHHHH
T ss_pred             CeehhhCCHHHHHH-CC--CCCHHHHHHHHHHHHhcCCcCCHHHHHhCCCCCHHHHHHHHHCc
Confidence            45677788887654 34  5556677777765321100 467889999999999999886554

>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=93.42  E-value=0.047  Score=32.64  Aligned_cols=23  Identities=9%  Similarity=0.096  Sum_probs=18.9

Q ss_pred             HHHhccCCCCcHHHHHHHHHHhcC
Q 033363           72 WTHVTQLHGVGKYAADAFAIFCTG   95 (121)
Q Consensus        72 ~~~L~~lpGIG~~tA~~vl~f~~~   95 (121)
                      ...|.++||||++....+|. -||
T Consensus         3 ~s~L~~IpGIG~kr~~~LL~-~Fg   25 (63)
T 2a1j_A            3 QDFLLKMPGVNAKNCRSLMH-HVK   25 (63)
T ss_dssp             CHHHHTSTTCCHHHHHHHHH-HCS
T ss_pred             HhHHHcCCCCCHHHHHHHHH-HcC
Confidence            35789999999999999885 444

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

Probab=92.99  E-value=0.29  Score=41.83  Aligned_cols=69  Identities=14%  Similarity=0.110  Sum_probs=44.7

Q ss_pred             HHHHHHhC--CCHHHHhcCCHHHHHHHHhhcCChhHHHHHHHHHHH---------HHHH---------------------
Q 033363           22 ISDLFTLC--PDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQ---------EYLG---------------------   69 (121)
Q Consensus        22 ~~~l~~~~--pt~~~la~a~~~eL~~~i~~~Gl~~~Ka~~i~~~a~---------~i~~---------------------   69 (121)
                      ...|++..  -++.+|..+..++|.++   =||....++.|.+.-+         .+..                     
T Consensus       459 i~~L~~~g~I~~~aDL~~L~~~~L~~l---~gfG~Ksa~nLl~aIe~sk~~~l~R~L~algi~~VG~~~Ak~La~~Fgsl  535 (671)
T 2owo_A          459 IDQLVEKEYVHTPADLFKLTAGKLTGL---ERMGPKSAQNVVNALEKAKETTFARFLYALGIREVGEATAAGLAAYFGTL  535 (671)
T ss_dssp             HHHHHHTTCCSSGGGGGTCCHHHHHTS---TTCCHHHHHHHHHHHHHHTBCCHHHHHHHTTCTTCCHHHHHHHHHHHCSH
T ss_pred             HHHHHHcCCCCCHHHHHhhCHHHhhcc---cccchhHHHHHHHHHHHHhcCChhheehhhcccCccHHHHHHHHHHcCCH
Confidence            44455442  47778888877765432   3666666777665522         2221                     


Q ss_pred             -----hhHHHhccCCCCcHHHHHHHHHHh
Q 033363           70 -----ESWTHVTQLHGVGKYAADAFAIFC   93 (121)
Q Consensus        70 -----~~~~~L~~lpGIG~~tA~~vl~f~   93 (121)
                           .+.++|.++||||+++|..+..|-
T Consensus       536 ~~l~~As~eeL~~i~GIG~~~A~sI~~ff  564 (671)
T 2owo_A          536 EALEAASIEELQKVPDVGIVVASHVHNFF  564 (671)
T ss_dssp             HHHHTCCHHHHTTSTTCCHHHHHHHHHHH
T ss_pred             HHHHhCCHHHHhhcCCCCHHHHHHHHHHH
Confidence                 146789999999999999888764

>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=92.79  E-value=0.14  Score=37.24  Aligned_cols=43  Identities=16%  Similarity=0.343  Sum_probs=29.8

Q ss_pred             CChhHHHHHHHHHH---HHHHHhhHHHhccCCCCcHHHHHHHHHHh
Q 033363           51 GLQKKRAPMIKRFS---QEYLGESWTHVTQLHGVGKYAADAFAIFC   93 (121)
Q Consensus        51 Gl~~~Ka~~i~~~a---~~i~~~~~~~L~~lpGIG~~tA~~vl~f~   93 (121)
                      |....+|+.|.+--   +.+.+.+.++|.++||||+++|..+..|-
T Consensus       169 gVg~~~a~~Ll~~fgs~~~l~~a~~e~L~~v~GiG~~~a~~i~~~~  214 (219)
T 2bgw_A          169 GIGRRTAERILERFGSLERFFTASKAEISKVEGIGEKRAEEIKKIL  214 (219)
T ss_dssp             TCCHHHHHHHHHHHSSHHHHTTCCHHHHHHSTTCCHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHcCCHHHHHhCCHHHHhhCCCCCHHHHHHHHHHH
Confidence            44456677666542   23334577889999999999999887654

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

Probab=92.56  E-value=0.19  Score=31.85  Aligned_cols=40  Identities=18%  Similarity=0.242  Sum_probs=31.6

Q ss_pred             HHHHHHHhCCCHHHHhcCCHHHHHHHHhhcCChhHHHHHHHHHH
Q 033363           21 VISDLFTLCPDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFS   64 (121)
Q Consensus        21 v~~~l~~~~pt~~~la~a~~~eL~~~i~~~Gl~~~Ka~~i~~~a   64 (121)
                      -...|+..|.|.+.|.+|+.+||.++   +|- ..+|+.|.+..
T Consensus        30 r~~~LL~~FgSl~~i~~AS~eEL~~v---ig~-~~~A~~I~~~l   69 (84)
T 1z00_B           30 NCRSLMHHVKNIAELAALSQDELTSI---LGN-AANAKQLYDFI   69 (84)
T ss_dssp             HHHHHHHHSSCHHHHHHSCHHHHHHH---HSC-HHHHHHHHHHH
T ss_pred             HHHHHHHHcCCHHHHHHCCHHHHHHH---hCc-hHHHHHHHHHH
Confidence            45688899999999999999999988   452 23388887654

>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=92.46  E-value=0.013  Score=38.37  Aligned_cols=55  Identities=15%  Similarity=0.140  Sum_probs=41.0

Q ss_pred             CCCHHHHhcCCHHHHHHHHhhcCChhHHHHHHHHHHHHHHH--hhHHHhccCCCCcHHHHHHHHH
Q 033363           29 CPDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQEYLG--ESWTHVTQLHGVGKYAADAFAI   91 (121)
Q Consensus        29 ~pt~~~la~a~~~eL~~~i~~~Gl~~~Ka~~i~~~a~~i~~--~~~~~L~~lpGIG~~tA~~vl~   91 (121)
                      .+.+-++-.|+.++|+. |  -|+...+|+.|.+     ..  .++++|.+++|||+++.+-+.-
T Consensus        14 ~~~~vdiNtAs~~eL~~-l--pGIG~~~A~~IV~-----~GpF~s~edL~~V~Gig~~~~e~l~~   70 (97)
T 3arc_U           14 YGEKIDLNNTNIAAFIQ-Y--RGLYPTLAKLIVK-----NAPYESVEDVLNIPGLTERQKQILRE   70 (97)
T ss_dssp             GGTSEETTTSCGGGGGG-S--TTCTTHHHHHHHH-----HCCCSSGGGGGGCTTCCHHHHHHHHH
T ss_pred             cCCceeCCcCCHHHHhH-C--CCCCHHHHHHHHH-----cCCCCCHHHHHhccCCCHHHHHHHHH
Confidence            44555677788888654 3  4666678888887     22  4789999999999999888765

>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=92.45  E-value=0.38  Score=37.51  Aligned_cols=41  Identities=29%  Similarity=0.370  Sum_probs=28.1

Q ss_pred             CChhHHHHHHHHHHHH--------HH----HhhHHHhccCCCCcHHHHHHHHH
Q 033363           51 GLQKKRAPMIKRFSQE--------YL----GESWTHVTQLHGVGKYAADAFAI   91 (121)
Q Consensus        51 Gl~~~Ka~~i~~~a~~--------i~----~~~~~~L~~lpGIG~~tA~~vl~   91 (121)
                      |....-|+.|.++.+.        +.    ...+.+|+++|||||+||.-+--
T Consensus        64 GIG~~~A~kI~E~l~tG~~~~le~l~~~~~~~~l~~l~~V~GiGpk~a~~l~~  116 (335)
T 2fmp_A           64 GVGTKIAEKIDEFLATGKLRKLEKIRQDDTSSSINFLTRVSGIGPSAARKFVD  116 (335)
T ss_dssp             TCCHHHHHHHHHHHHHSSCHHHHHHHHCHHHHHHHHHTTSTTCCHHHHHHHHH
T ss_pred             CCcHHHHHHHHHHHHhCCcHHHHHHHcccchhHHHHHhCCCCCCHHHHHHHHH
Confidence            4555666666666431        11    13678999999999999997743

>2kp7_A Crossover junction endonuclease MUS81; helix-hairpin-helix, tumour suppressor, DNA damage, DNA recombination, DNA repair, hydrolase, magnesium; NMR {Mus musculus}

Probab=92.22  E-value=0.18  Score=32.19  Aligned_cols=35  Identities=9%  Similarity=0.036  Sum_probs=27.5

Q ss_pred             HHHHHHHHHHHHHH-----hhHHHhccCCCCcHHHHHHHH
Q 033363           56 RAPMIKRFSQEYLG-----ESWTHVTQLHGVGKYAADAFA   90 (121)
Q Consensus        56 Ka~~i~~~a~~i~~-----~~~~~L~~lpGIG~~tA~~vl   90 (121)
                      ++....++.+.+..     ...+++..|+|||+++++.+-
T Consensus        36 ~~~~Y~KA~~sLk~~P~~i~s~~e~~~L~giG~ki~~~L~   75 (87)
T 2kp7_A           36 TRFVFQKALRSLQRYPLPLRSGKEAKILQHFGDRLCRMLD   75 (87)
T ss_dssp             THHHHHHHHHHHHHCCSCCCSHHHHHTCTTTCHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhCCCCCCCHHHHHHhhcccHHHHHHHH
Confidence            55666677777665     477899999999999998764

>1s5l_U Photosystem II 12 kDa extrinsic protein; photosynthesis, oxygen-evolving, tetra- manganese, membrane; HET: CL1 PHO HEM PL9 LMT BCR; 3.50A {Thermosynechococcus elongatus}

Probab=92.14  E-value=0.088  Score=36.41  Aligned_cols=20  Identities=15%  Similarity=0.089  Sum_probs=18.9

Q ss_pred             hHHHhccCCCCcHHHHHHHH
Q 033363           71 SWTHVTQLHGVGKYAADAFA   90 (121)
Q Consensus        71 ~~~~L~~lpGIG~~tA~~vl   90 (121)
                      +.++|.+||||||+.|..|.
T Consensus        61 ~~~eL~~LpGiGp~~A~~II   80 (134)
T 1s5l_U           61 NIAAFIQYRGLYPTLAKLIV   80 (134)
T ss_dssp             CGGGGGGSTTCTHHHHHHHH
T ss_pred             CHHHHHHCCCCCHHHHHHHH
Confidence            67899999999999999999

>1wcn_A Transcription elongation protein NUSA; RNA-binding protein, escherichia coli NUSA, transcription regulation, regulation of RNA binding; NMR {Escherichia coli} PDB: 2jzb_B

Probab=92.01  E-value=0.16  Score=31.03  Aligned_cols=40  Identities=15%  Similarity=0.179  Sum_probs=33.1

Q ss_pred             HHHH-hCCCHHHHhcCCHHHHHHHHhhcCChhHHHHHHHHHHHH
Q 033363           24 DLFT-LCPDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQE   66 (121)
Q Consensus        24 ~l~~-~~pt~~~la~a~~~eL~~~i~~~Gl~~~Ka~~i~~~a~~   66 (121)
                      +|.+ .|-|.++++.++.++|.++   .|++..|+..|+..|+.
T Consensus        22 kL~e~Gi~TvedlA~~~~~eL~~i---~gise~kA~~ii~aAr~   62 (70)
T 1wcn_A           22 KLAARGVCTLEDLAEQGIDDLADI---EGLTDEKAGALIMAARN   62 (70)
T ss_dssp             HHHTTTCCSHHHHHTSCHHHHHTS---SSCCHHHHHHHHHHHHH
T ss_pred             HHHHcCCCcHHHHHcCCHHHHHHc---cCCCHHHHHHHHHHHHH
Confidence            4443 4789999999999998664   59999999999999886

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

Probab=91.93  E-value=0.094  Score=33.27  Aligned_cols=24  Identities=8%  Similarity=0.098  Sum_probs=19.8

Q ss_pred             hHHHhccCCCCcHHHHHHHHHHhcC
Q 033363           71 SWTHVTQLHGVGKYAADAFAIFCTG   95 (121)
Q Consensus        71 ~~~~L~~lpGIG~~tA~~vl~f~~~   95 (121)
                      ....|.+|||||++....+|. -|+
T Consensus        16 ~~s~L~~IpGIG~kr~~~LL~-~Fg   39 (84)
T 1z00_B           16 PQDFLLKMPGVNAKNCRSLMH-HVK   39 (84)
T ss_dssp             HHHHHHTCSSCCHHHHHHHHH-HSS
T ss_pred             HHHHHHhCCCCCHHHHHHHHH-HcC
Confidence            456799999999999999885 444

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

Probab=91.87  E-value=0.055  Score=39.92  Aligned_cols=23  Identities=26%  Similarity=0.112  Sum_probs=20.2

Q ss_pred             hHHHhccCCCCcHHHHHHHHHHh
Q 033363           71 SWTHVTQLHGVGKYAADAFAIFC   93 (121)
Q Consensus        71 ~~~~L~~lpGIG~~tA~~vl~f~   93 (121)
                      +.++|..|||||+++|..|.-+=
T Consensus       130 ~~~eL~~LpGIG~k~A~~IIeyR  152 (205)
T 2i5h_A          130 RMHQLELLPGVGKKMMWAIIEER  152 (205)
T ss_dssp             SSBGGGGSTTCCHHHHHHHHHHH
T ss_pred             CHHHHhcCCCcCHHHHHHHHHHH
Confidence            56789999999999999998764

>3arc_U Photosystem II 12 kDa extrinsic protein; PSII, membrane-protein complex, transmembrane alpha-helix, E transport, photosynthesis; HET: OEX CLA PHO BCR PL9 SQD LMG UNL LMT HTG DGD LHG HEM; 1.90A {Thermosynechococcus vulcanus} PDB: 3bz1_U* 2axt_U* 3bz2_U* 3kzi_U* 3prq_U* 3prr_U* 3a0b_U* 3a0h_U*

Probab=91.34  E-value=0.065  Score=34.99  Aligned_cols=21  Identities=14%  Similarity=0.052  Sum_probs=19.4

Q ss_pred             hHHHhccCCCCcHHHHHHHHH
Q 033363           71 SWTHVTQLHGVGKYAADAFAI   91 (121)
Q Consensus        71 ~~~~L~~lpGIG~~tA~~vl~   91 (121)
                      +.++|..|||||++.|..|..
T Consensus        24 s~~eL~~lpGIG~~~A~~IV~   44 (97)
T 3arc_U           24 NIAAFIQYRGLYPTLAKLIVK   44 (97)
T ss_dssp             CGGGGGGSTTCTTHHHHHHHH
T ss_pred             CHHHHhHCCCCCHHHHHHHHH
Confidence            568999999999999999997

>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=91.23  E-value=0.17  Score=43.21  Aligned_cols=23  Identities=22%  Similarity=0.231  Sum_probs=19.5

Q ss_pred             hHHHhccCCCCcHHHHHHHHHHh
Q 033363           71 SWTHVTQLHGVGKYAADAFAIFC   93 (121)
Q Consensus        71 ~~~~L~~lpGIG~~tA~~vl~f~   93 (121)
                      +.++|.++||||+++|+.+..|-
T Consensus       537 s~eeL~~I~GIG~~~A~sI~~ff  559 (667)
T 1dgs_A          537 SLEELIEVEEVGELTARAILETL  559 (667)
T ss_dssp             CHHHHHTSTTCCHHHHHHHHHHH
T ss_pred             CHHHHHhccCcCHHHHHHHHHHH
Confidence            56789999999999999998764

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

Probab=91.04  E-value=0.34  Score=38.19  Aligned_cols=21  Identities=29%  Similarity=0.360  Sum_probs=18.0

Q ss_pred             hHHHhccCCCCcHHHHHHHHH
Q 033363           71 SWTHVTQLHGVGKYAADAFAI   91 (121)
Q Consensus        71 ~~~~L~~lpGIG~~tA~~vl~   91 (121)
                      .+.+|+++|||||+||..+--
T Consensus       100 ~l~~l~~I~GvG~kta~~l~~  120 (360)
T 2ihm_A          100 TMKLFTQVFGVGVKTANRWYQ  120 (360)
T ss_dssp             HHHHHHTSTTCCHHHHHHHHH
T ss_pred             HHHHHhCCCCCCHHHHHHHHH
Confidence            567899999999999997743

>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=90.92  E-value=0.15  Score=32.76  Aligned_cols=24  Identities=17%  Similarity=0.151  Sum_probs=20.9

Q ss_pred             hhHHHhccCCCCcHHHHHHHHHHh
Q 033363           70 ESWTHVTQLHGVGKYAADAFAIFC   93 (121)
Q Consensus        70 ~~~~~L~~lpGIG~~tA~~vl~f~   93 (121)
                      .+.++|.++||||+++|..++-+-
T Consensus        37 a~~~~L~~ipGIG~~~A~~Il~~r   60 (98)
T 2edu_A           37 GSARDLRSLQRIGPKKAQLIVGWR   60 (98)
T ss_dssp             SCHHHHHHSTTCCHHHHHHHHHHH
T ss_pred             CCHHHHHHCCCCCHHHHHHHHHHH
Confidence            367789999999999999999864

>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=90.78  E-value=0.16  Score=36.84  Aligned_cols=21  Identities=24%  Similarity=0.246  Sum_probs=18.0

Q ss_pred             HHHhccCCCCcHHHHHHHHHH
Q 033363           72 WTHVTQLHGVGKYAADAFAIF   92 (121)
Q Consensus        72 ~~~L~~lpGIG~~tA~~vl~f   92 (121)
                      ...|.++|||||++|..++..
T Consensus        71 f~~L~~v~GIGpk~A~~iL~~   91 (191)
T 1ixr_A           71 FELLLSVSGVGPKVALALLSA   91 (191)
T ss_dssp             HHHHHSSSCCCHHHHHHHHHH
T ss_pred             HHHHhcCCCcCHHHHHHHHHh
Confidence            346899999999999999863

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

Probab=90.55  E-value=0.15  Score=37.58  Aligned_cols=21  Identities=24%  Similarity=0.203  Sum_probs=18.6

Q ss_pred             hHHHhccCCCCcHHHHHHHHH
Q 033363           71 SWTHVTQLHGVGKYAADAFAI   91 (121)
Q Consensus        71 ~~~~L~~lpGIG~~tA~~vl~   91 (121)
                      ....|.+++||||++|..++.
T Consensus        86 lf~~L~sv~GIGpk~A~~Ils  106 (212)
T 2ztd_A           86 LFLTLLSVSGVGPRLAMAALA  106 (212)
T ss_dssp             HHHHHHTSTTCCHHHHHHHHH
T ss_pred             HHHHhcCcCCcCHHHHHHHHH
Confidence            456799999999999999986

>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=89.88  E-value=0.31  Score=38.99  Aligned_cols=46  Identities=15%  Similarity=0.248  Sum_probs=36.5

Q ss_pred             HHHHHHHHhCCCHHHHhcCCHHHHHHHHhhcCChhHHHHHHHHHHHHHH
Q 033363           20 RVISDLFTLCPDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQEYL   68 (121)
Q Consensus        20 ~v~~~l~~~~pt~~~la~a~~~eL~~~i~~~Gl~~~Ka~~i~~~a~~i~   68 (121)
                      .+..+|.+.|.|.+.+.+|+.+||.++   =|....||+.|++....+.
T Consensus       326 ~iae~Lv~~FGsLq~Il~AS~eEL~~V---eGIGe~rAr~IregL~r~~  371 (377)
T 3c1y_A          326 SIGYNVVRMFKTLDQISKASVEDLKKV---EGIGEKRARAISESISSLK  371 (377)
T ss_dssp             HHHHHHHHHHCSHHHHTTCCHHHHTTS---TTCCHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhCCHHHHHhCCHHHHHhc---cCccHHHHHHHHHHHHHHh
Confidence            456788889999999999999997542   4677789999988877664

>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=89.84  E-value=0.62  Score=38.62  Aligned_cols=49  Identities=16%  Similarity=0.241  Sum_probs=25.5

Q ss_pred             HHHHHHHhhcCChhHHHHHHHHH-----HHHHHH-hhHHHhccCCCCcHHHHHHH
Q 033363           41 EEIEKIISTLGLQKKRAPMIKRF-----SQEYLG-ESWTHVTQLHGVGKYAADAF   89 (121)
Q Consensus        41 ~eL~~~i~~~Gl~~~Ka~~i~~~-----a~~i~~-~~~~~L~~lpGIG~~tA~~v   89 (121)
                      +.+..+++--|....+|..|..-     ...+.. -...+|.++||||+|||.-+
T Consensus        90 ~~~~~l~~v~GvGpk~A~~~~~~lg~~~~~~l~~a~~~~~l~~~~GiG~k~a~~i  144 (575)
T 3b0x_A           90 RGVLEVMEVPGVGPKTARLLYEGLGIDSLEKLKAALDRGDLTRLKGFGPKRAERI  144 (575)
T ss_dssp             HHHHHHHTSTTTCHHHHHHHHHTSCCCSHHHHHHHHHHTGGGGSTTCCHHHHHHH
T ss_pred             HHHHHHhcCCCcCHHHHHHHHHhcCCCCHHHHHHHHHcCCcccCCCCCccHHHHH
Confidence            34445555556666666665431     111111 01123777777777777766

>2jg6_A DNA-3-methyladenine glycosidase; 3-methyladenine-DNA-glycosylase-I, hydrolase; 1.70A {Staphylococcus aureus} PDB: 4aia_A* 4ai5_A* 4ai4_A

Probab=89.78  E-value=4.3  Score=29.29  Aligned_cols=49  Identities=14%  Similarity=0.243  Sum_probs=37.4

Q ss_pred             HHHHHHHhCC--CHHHHhcCCHHHHHHHHhhcCCh--hHHHHHHHHHHHHHHH
Q 033363           21 VISDLFTLCP--DAKTATEVDAEEIEKIISTLGLQ--KKRAPMIKRFSQEYLG   69 (121)
Q Consensus        21 v~~~l~~~~p--t~~~la~a~~~eL~~~i~~~Gl~--~~Ka~~i~~~a~~i~~   69 (121)
                      =.+.|.+.|-  +|+.++..+++++++++..-|.-  +.|.+.+++=|+.+.+
T Consensus        52 KRe~fR~AF~~FD~~~VA~~~e~dve~Ll~d~gIIRnr~KI~A~i~NA~~~l~  104 (186)
T 2jg6_A           52 KKEAYEEAFYDFEPEKVAQMTAQDIDRLMTFPNIVHHRKKLEAIVNQAQGYLK  104 (186)
T ss_dssp             HHHHHHHHTGGGCHHHHTTCCHHHHHHHTTCTTSCCCHHHHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHcCCCHHHHhCCCHHHHHHHhcCccchhhHHHHHHHHHHHHHHHH
Confidence            3444555554  79999999999999999998884  4566777777777775

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

Probab=89.28  E-value=0.4  Score=39.84  Aligned_cols=49  Identities=14%  Similarity=0.168  Sum_probs=24.5

Q ss_pred             HHHHHHHhhcCChhHHHHHHHHH----HHHHHHh-hHHHhccCCCCcHHHHHHH
Q 033363           41 EEIEKIISTLGLQKKRAPMIKRF----SQEYLGE-SWTHVTQLHGVGKYAADAF   89 (121)
Q Consensus        41 ~eL~~~i~~~Gl~~~Ka~~i~~~----a~~i~~~-~~~~L~~lpGIG~~tA~~v   89 (121)
                      +.+.++++=-|....+|+.|.+.    .+.+.+. ....|.++||||+||+.-+
T Consensus        94 ~~~~~L~~v~GVGpk~A~~i~~~G~~s~edL~~a~~~~~L~~~~GiG~Ktaq~I  147 (578)
T 2w9m_A           94 PGLLDLLGVRGLGPKKIRSLWLAGIDSLERLREAAESGELAGLKGFGAKSAATI  147 (578)
T ss_dssp             HHHHHHTTSTTCCHHHHHHHHHTTCCSHHHHHHHHHHTTTTTSTTCCHHHHHHH
T ss_pred             HHHHHHhCCCCcCHHHHHHHHHcCCCCHHHHHHHHhhCccccCCCCCHHHHHHH
Confidence            34444555556666666666542    0000000 1125666777777777666

>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=88.98  E-value=0.24  Score=36.20  Aligned_cols=20  Identities=25%  Similarity=0.305  Sum_probs=17.4

Q ss_pred             HHHhccCCCCcHHHHHHHHH
Q 033363           72 WTHVTQLHGVGKYAADAFAI   91 (121)
Q Consensus        72 ~~~L~~lpGIG~~tA~~vl~   91 (121)
                      ...|.++|||||++|..++.
T Consensus        72 f~~L~~V~GIGpk~A~~iL~   91 (203)
T 1cuk_A           72 FKELIKTNGVGPKLALAILS   91 (203)
T ss_dssp             HHHHHHSSSCCHHHHHHHHH
T ss_pred             HHHHhcCCCcCHHHHHHHHh
Confidence            34688999999999999986

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

Probab=88.67  E-value=1.4  Score=27.38  Aligned_cols=41  Identities=15%  Similarity=0.111  Sum_probs=31.8

Q ss_pred             HHHHHHHhCCCHHHHhcCCHHHHHHHHhhcCChhHHHHHHHHHH
Q 033363           21 VISDLFTLCPDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFS   64 (121)
Q Consensus        21 v~~~l~~~~pt~~~la~a~~~eL~~~i~~~Gl~~~Ka~~i~~~a   64 (121)
                      ...++.+.|.+++++.+++.++|.+   --|+...++..|....
T Consensus        31 ~A~~Ll~~fgsl~~l~~a~~~eL~~---i~GIG~~~a~~I~~~l   71 (89)
T 1z00_A           31 DSQTLLTTFGSLEQLIAASREDLAL---CPGLGPQKARRLFDVL   71 (89)
T ss_dssp             HHHHHHHHTCBHHHHHHCCHHHHHT---STTCCHHHHHHHHHHH
T ss_pred             HHHHHHHHCCCHHHHHhCCHHHHHh---CCCCCHHHHHHHHHHH
Confidence            4567778899999999999998644   2477778888887654

>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=88.53  E-value=0.42  Score=38.01  Aligned_cols=21  Identities=29%  Similarity=0.400  Sum_probs=18.0

Q ss_pred             hHHHhccCCCCcHHHHHHHHH
Q 033363           71 SWTHVTQLHGVGKYAADAFAI   91 (121)
Q Consensus        71 ~~~~L~~lpGIG~~tA~~vl~   91 (121)
                      .+.+|+++|||||+||..+--
T Consensus       119 ~l~~l~~I~GvGpk~a~~ly~  139 (381)
T 1jms_A          119 SFKLFTSVFGVGLKTAEKWFR  139 (381)
T ss_dssp             HHHHHHTSTTCCHHHHHHHHH
T ss_pred             HHHHHHccCCCCHHHHHHHHH
Confidence            567899999999999997743

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

Probab=88.51  E-value=0.086  Score=44.64  Aligned_cols=25  Identities=24%  Similarity=0.271  Sum_probs=0.0

Q ss_pred             hHHHhccCCCCcHHHHHHHHHHhcC
Q 033363           71 SWTHVTQLHGVGKYAADAFAIFCTG   95 (121)
Q Consensus        71 ~~~~L~~lpGIG~~tA~~vl~f~~~   95 (121)
                      +.++|.++||||+++|..+..|--.
T Consensus       559 s~eeL~~I~GIG~~~A~sI~~ff~~  583 (615)
T 3sgi_A          559 STDQLAAVEGVGPTIAAAVTEWFAV  583 (615)
T ss_dssp             -------------------------
T ss_pred             CHHHHhhCCCCCHHHHHHHHHHHcC
Confidence            5688999999999999999876544

>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=88.20  E-value=0.81  Score=27.78  Aligned_cols=39  Identities=21%  Similarity=0.153  Sum_probs=29.8

Q ss_pred             HHHHHHhCCCHHHHhcCCHHHHHHHHhhcCChhHHHHHHHHH
Q 033363           22 ISDLFTLCPDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRF   63 (121)
Q Consensus        22 ~~~l~~~~pt~~~la~a~~~eL~~~i~~~Gl~~~Ka~~i~~~   63 (121)
                      ..++.+.|.+++++.+++.++|.++   -|+...++..|...
T Consensus        37 A~~Ll~~fgsl~~l~~a~~eeL~~i---~GIG~~~a~~I~~~   75 (78)
T 1kft_A           37 RQMLLKYMGGLQGLRNASVEEIAKV---PGISQGLAEKIFWS   75 (78)
T ss_dssp             HHHHHHHHSCHHHHHHCCHHHHTTS---SSTTSHHHHHHHHH
T ss_pred             HHHHHHHcCCHHHHHHCCHHHHHHC---CCCCHHHHHHHHHH
Confidence            4567777899999999999996432   36777888888654

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

Probab=88.13  E-value=1.3  Score=26.07  Aligned_cols=41  Identities=20%  Similarity=0.222  Sum_probs=31.2

Q ss_pred             HHHHHHHhCCCHHHHhcCCHHHHHHHHhhcCChhHHHHHHHHHH
Q 033363           21 VISDLFTLCPDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFS   64 (121)
Q Consensus        21 v~~~l~~~~pt~~~la~a~~~eL~~~i~~~Gl~~~Ka~~i~~~a   64 (121)
                      ...++...|.+++++.+++.++|.+   --|+...++..|....
T Consensus        26 ~a~~Ll~~fgs~~~l~~a~~~~L~~---i~Gig~~~a~~i~~~~   66 (75)
T 1x2i_A           26 LARRLLKHFGSVERVFTASVAELMK---VEGIGEKIAKEIRRVI   66 (75)
T ss_dssp             HHHHHHHHHCSHHHHHHCCHHHHTT---STTCCHHHHHHHHHHH
T ss_pred             HHHHHHHHcCCHHHHHhCCHHHHhc---CCCCCHHHHHHHHHHH
Confidence            4567777889999999999998533   2377778888887654

>2ofk_A 3-methyladenine DNA glycosylase I, constitutive; DNA repair, base excision, helix-hairpin-helix, hydrolase; HET: PGE; 1.50A {Salmonella typhi} PDB: 2ofi_A* 1lmz_A 1nku_A 1p7m_A*

Probab=87.49  E-value=5.7  Score=28.58  Aligned_cols=49  Identities=12%  Similarity=0.259  Sum_probs=37.8

Q ss_pred             HHHHHHHhCC--CHHHHhcCCHHHHHHHHhhcCCh--hHHHHHHHHHHHHHHH
Q 033363           21 VISDLFTLCP--DAKTATEVDAEEIEKIISTLGLQ--KKRAPMIKRFSQEYLG   69 (121)
Q Consensus        21 v~~~l~~~~p--t~~~la~a~~~eL~~~i~~~Gl~--~~Ka~~i~~~a~~i~~   69 (121)
                      =.+.|.+.|-  +|+.++..+++++++++..-|.-  +.|.+.+++=|+.+.+
T Consensus        52 KRe~fr~AF~~Fd~~~VA~~~e~~ve~Ll~d~~IIRnr~KI~A~i~NA~~~l~  104 (183)
T 2ofk_A           52 KRENYRACFHQFDPIRIAAMQEEDVERLLQNTGIIRHRGKIQAIISNARAWLA  104 (183)
T ss_dssp             THHHHHHHTGGGCHHHHHTCCHHHHHHHTTCTTSCCCHHHHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHcCCCHHHHcCCCHHHHHHHhcCCcchhhHHHHHHHHHHHHHHHH
Confidence            3444555554  79999999999999999988884  4577777777887776

>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=87.41  E-value=0.29  Score=38.22  Aligned_cols=40  Identities=20%  Similarity=0.304  Sum_probs=25.0

Q ss_pred             CChhHHHHHHHHHHHH--H--HH------hhHHHhccCCCCcHHHHHHHH
Q 033363           51 GLQKKRAPMIKRFSQE--Y--LG------ESWTHVTQLHGVGKYAADAFA   90 (121)
Q Consensus        51 Gl~~~Ka~~i~~~a~~--i--~~------~~~~~L~~lpGIG~~tA~~vl   90 (121)
                      |.....|+.|.++.+.  +  ++      ..++.|+++|||||+||.-+-
T Consensus        64 GIG~~~A~kI~E~l~tG~~~~le~l~~~~p~l~ll~~v~GiG~k~a~~l~  113 (335)
T 2bcq_A           64 GIGKRMAEKIIEILESGHLRKLDHISESVPVLELFSNIWGAGTKTAQMWY  113 (335)
T ss_dssp             TCCHHHHHHHHHHHHSSSCGGGGGCCTTHHHHHHHHTSTTCCHHHHHHHH
T ss_pred             CccHHHHHHHHHHHHcCCchHHHHHhhhhHHHHHHhcCCCcCHHHHHHHH
Confidence            5555667776665441  0  00      123444799999999999774

>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=86.67  E-value=1.4  Score=27.50  Aligned_cols=41  Identities=15%  Similarity=0.106  Sum_probs=30.9

Q ss_pred             HHHHHHHhCCCHHHHhcCCHHHHHHHHhhcCChhHHHHHHHHHH
Q 033363           21 VISDLFTLCPDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFS   64 (121)
Q Consensus        21 v~~~l~~~~pt~~~la~a~~~eL~~~i~~~Gl~~~Ka~~i~~~a   64 (121)
                      ...++.+.|.+++++.+++.++|.++   -|+...+++.|.+..
T Consensus        44 ~A~~Ll~~fgs~~~l~~as~~eL~~i---~GIG~~~a~~I~~~l   84 (91)
T 2a1j_B           44 DSQTLLTTFGSLEQLIAASREDLALC---PGLGPQKARRLFDVL   84 (91)
T ss_dssp             HHHHHHHHHSSHHHHHSCCHHHHHTS---SSCCSHHHHHHHHHH
T ss_pred             HHHHHHHHCCCHHHHHhCCHHHHHhC---CCCCHHHHHHHHHHH
Confidence            35567778999999999999986542   366667888887653

>1u9l_A Transcription elongation protein NUSA; escherichia coli NUSA, phage lambda protein N, regulation of RNA binding, transcription antitermination, X-RAY crystallography; 1.90A {Escherichia coli} SCOP: a.60.4.2 PDB: 1wcl_A

Probab=86.65  E-value=0.86  Score=27.77  Aligned_cols=40  Identities=13%  Similarity=0.132  Sum_probs=33.4

Q ss_pred             HhCCCHHHHhcCCHHHHHHHHhhcCChhHHHHHHHHHHHHHHH
Q 033363           27 TLCPDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQEYLG   69 (121)
Q Consensus        27 ~~~pt~~~la~a~~~eL~~~i~~~Gl~~~Ka~~i~~~a~~i~~   69 (121)
                      ..|-|.++++-+|.++|.+   --||+..|+.-|++-|+.++.
T Consensus        25 ~Gf~tve~vA~~~~~eL~~---I~G~dE~~a~~l~~~A~~~l~   64 (70)
T 1u9l_A           25 EGFSTLEELAYVPMKELLE---IEGLDEPTVEALRERAKNALA   64 (70)
T ss_dssp             TTCCCHHHHHHSCHHHHTT---STTCCHHHHHHHHHHHHHHHH
T ss_pred             cCcCcHHHHHcCCHHHHhh---ccCCCHHHHHHHHHHHHHHHH
Confidence            3589999999999999644   369999999999999987754

>1z3e_B DNA-directed RNA polymerase alpha chain; bacterial transcription regulation, disulfide stress; 1.50A {Bacillus subtilis} SCOP: a.60.3.1 PDB: 3ihq_B

Probab=85.22  E-value=0.74  Score=28.34  Aligned_cols=44  Identities=16%  Similarity=0.219  Sum_probs=28.9

Q ss_pred             HhhcCChhHHHHHHHHHH-----HHHHHhhHHHhccCCCCcHHHHHHHHH
Q 033363           47 ISTLGLQKKRAPMIKRFS-----QEYLGESWTHVTQLHGVGKYAADAFAI   91 (121)
Q Consensus        47 i~~~Gl~~~Ka~~i~~~a-----~~i~~~~~~~L~~lpGIG~~tA~~vl~   91 (121)
                      |..++|+ .|+.+..+-+     ..++..+.++|.+++|+|+++.+-+.-
T Consensus        11 Ie~L~LS-~Ra~NcLkragI~Tv~dL~~~s~~dLlki~n~G~kSl~EI~~   59 (73)
T 1z3e_B           11 IEELDLS-VRSYNCLKRAGINTVQELANKTEEDMMKVRNLGRKSLEEVKA   59 (73)
T ss_dssp             GGGSCCB-HHHHHHHHHTTCCBHHHHHTSCHHHHHTSTTCCHHHHHHHHH
T ss_pred             HHHhCCC-HHHHHHHHHcCCCcHHHHHcCCHHHHHHcCCCCHHHHHHHHH
Confidence            4557887 5554443322     222234788999999999999887654

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

Probab=83.90  E-value=0.58  Score=38.91  Aligned_cols=22  Identities=9%  Similarity=0.176  Sum_probs=19.5

Q ss_pred             hHHHhccCCCCcHHHHHHHHHH
Q 033363           71 SWTHVTQLHGVGKYAADAFAIF   92 (121)
Q Consensus        71 ~~~~L~~lpGIG~~tA~~vl~f   92 (121)
                      ...+|+++|||||++|..++.-
T Consensus        95 ~~~~L~~v~GVGpk~A~~i~~~  116 (578)
T 2w9m_A           95 GLLDLLGVRGLGPKKIRSLWLA  116 (578)
T ss_dssp             HHHHHTTSTTCCHHHHHHHHHT
T ss_pred             HHHHHhCCCCcCHHHHHHHHHc
Confidence            5678999999999999998864

>3k4g_A DNA-directed RNA polymerase subunit alpha; bacterial transcription regulation, DNA-directed RNA polymer nucleotidyltransferase; HET: MLY; 2.05A {Escherichia coli k-12} SCOP: a.60.3.1 PDB: 3n4m_B* 1lb2_B* 3n97_B* 1xs9_D

Probab=83.53  E-value=1.3  Score=28.16  Aligned_cols=44  Identities=9%  Similarity=0.089  Sum_probs=30.6

Q ss_pred             HhhcCChhHHHHHHHHHHH-----HHHHhhHHHhccCCCCcHHHHHHHHH
Q 033363           47 ISTLGLQKKRAPMIKRFSQ-----EYLGESWTHVTQLHGVGKYAADAFAI   91 (121)
Q Consensus        47 i~~~Gl~~~Ka~~i~~~a~-----~i~~~~~~~L~~lpGIG~~tA~~vl~   91 (121)
                      |..++|+ .|+.+..+-+.     .++..+.++|.+++|+|+++.+-|.-
T Consensus        14 I~~L~LS-vRa~NcLkragI~Tv~dL~~~se~dLlki~n~G~KSl~EI~~   62 (86)
T 3k4g_A           14 VDDLELT-VRSANCLXAEAIHYIGDLVQRTEVELLXTPNLGXXSLTEIXD   62 (86)
T ss_dssp             GGGGCCC-HHHHHHHHHTTCCBHHHHHHSCHHHHHTSTTCCHHHHHHHHH
T ss_pred             HHHhCCC-HHHHHHHHHcCCCcHHHHHhCCHHHHhhccccCcccHHHHHH
Confidence            4457887 56555444333     23335788999999999999998864

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

Probab=82.45  E-value=0.81  Score=37.79  Aligned_cols=42  Identities=17%  Similarity=0.151  Sum_probs=35.4

Q ss_pred             HHHHHHhCCCHHHHhcCCHHHHHHHHhhcCChhHHHHHHHHHHHHH
Q 033363           22 ISDLFTLCPDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQEY   67 (121)
Q Consensus        22 ~~~l~~~~pt~~~la~a~~~eL~~~i~~~Gl~~~Ka~~i~~~a~~i   67 (121)
                      ..+|+++|+|.+.+.+|+++||    +.-|+...|++.|+.+-...
T Consensus       481 AeRLLEkFGSVe~Vm~AteDEL----RedGIGekqarrI~gl~~l~  522 (685)
T 4gfj_A          481 AERLLKKYGGYSKVREAGVEEL----REDGLTDAQIRELKGLKTLE  522 (685)
T ss_dssp             HHHHHHHHTSHHHHHHSCHHHH----HHTTCCHHHHHHHHTCHHHH
T ss_pred             HHHHHHHhcCHHHHHhCCHHHH----HHccccHHHHHHHhhHHHHH
Confidence            4688899999999999999996    44899999999998765443

>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=82.16  E-value=1.3  Score=37.87  Aligned_cols=68  Identities=21%  Similarity=0.179  Sum_probs=47.4

Q ss_pred             HHHHHHHhC--CCHHHHhcCCHHHHHHHHhhcCChhHHHHHHHHHHHHHHHhh-HHHhc--cCCCCcHHHHHHHHH
Q 033363           21 VISDLFTLC--PDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQEYLGES-WTHVT--QLHGVGKYAADAFAI   91 (121)
Q Consensus        21 v~~~l~~~~--pt~~~la~a~~~eL~~~i~~~Gl~~~Ka~~i~~~a~~i~~~~-~~~L~--~lpGIG~~tA~~vl~   91 (121)
                      ....|++..  -++.+|..+..++|.++   =||...+++.|.+.-+...+.. ...|.  .+||||+.+|..++-
T Consensus       453 ~i~~L~~~g~I~~~~DL~~L~~e~L~~l---~g~G~Ksa~nLl~aIe~sk~~~l~R~L~alGI~~VG~~~Ak~La~  525 (667)
T 1dgs_A          453 LIERLLEKGLVRDVADLYHLRKEDLLGL---ERMGEKSAQNLLRQIEESKHRGLERLLYALGLPGVGEVLARNLAR  525 (667)
T ss_dssp             HHHHHHHTTSCSSGGGGGGGCCHHHHTT---SSCCSTTHHHHHHHHHHGGGCCHHHHHHHTTCSSCCHHHHHHHHH
T ss_pred             HHHHHHHcCCCCCHHHHHhcCHHHHhcc---cccchhhHHHHHHHHHHHhcCcHHHhhHhhccCCccHHHHHHHHH
Confidence            344566654  48999999987776543   3787788888877655544434 33343  899999999998764

>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=82.14  E-value=0.27  Score=36.91  Aligned_cols=41  Identities=15%  Similarity=0.255  Sum_probs=0.0

Q ss_pred             cCChhHHHHHHHHHHHHHHH-hhH-----HHhccCCCCcHHHHHHHHHH
Q 033363           50 LGLQKKRAPMIKRFSQEYLG-ESW-----THVTQLHGVGKYAADAFAIF   92 (121)
Q Consensus        50 ~Gl~~~Ka~~i~~~a~~i~~-~~~-----~~L~~lpGIG~~tA~~vl~f   92 (121)
                      -|+...+++.|.+.  -+.. +.+     ++|.++||||+++|+-+...
T Consensus        21 pGIGpk~a~~Ll~~--gf~sve~L~~a~~~eL~~v~GIG~ktAe~I~~~   67 (241)
T 1vq8_Y           21 SGVGPSKAESLREA--GFESVEDVRGADQSALADVSGIGNALAARIKAD   67 (241)
T ss_dssp             -------------------------------------------------
T ss_pred             CCCCHHHHHHHHHc--CCCCHHHHHhCCHHHHHhccCCCHHHHHHHHHH
Confidence            36666788887765  1211 221     46779999999999988653

>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=80.94  E-value=2.4  Score=30.51  Aligned_cols=42  Identities=24%  Similarity=0.298  Sum_probs=33.0

Q ss_pred             HHHHHHHHhCCCHHHHhcCCHHHHHHHHhhcCChhHHHHHHHHHH
Q 033363           20 RVISDLFTLCPDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFS   64 (121)
Q Consensus        20 ~v~~~l~~~~pt~~~la~a~~~eL~~~i~~~Gl~~~Ka~~i~~~a   64 (121)
                      ....++.+.|+|++++.+++.++|.++   -|+...+|+.|.+.-
T Consensus       173 ~~a~~Ll~~fgs~~~l~~a~~e~L~~v---~GiG~~~a~~i~~~~  214 (219)
T 2bgw_A          173 RTAERILERFGSLERFFTASKAEISKV---EGIGEKRAEEIKKIL  214 (219)
T ss_dssp             HHHHHHHHHHSSHHHHTTCCHHHHHHS---TTCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHcCCHHHHHhCCHHHHhhC---CCCCHHHHHHHHHHH
Confidence            445678889999999999999997553   477778888887643

>1b22_A DNA repair protein RAD51; DNA binding, riken structural genomics/proteomics initiative, RSGI, structural genomics, DNA binding protein; HET: DNA; NMR {Homo sapiens} SCOP: a.60.4.1

Probab=80.17  E-value=0.72  Score=30.74  Aligned_cols=41  Identities=12%  Similarity=0.075  Sum_probs=28.9

Q ss_pred             HHHH-hCCCHHHHhcCCHHHHHHHHhhcCChhHHHHHHHHHHHHH
Q 033363           24 DLFT-LCPDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQEY   67 (121)
Q Consensus        24 ~l~~-~~pt~~~la~a~~~eL~~~i~~~Gl~~~Ka~~i~~~a~~i   67 (121)
                      +|.+ .|-|.++++.+++++|.+   --|++..|+..|++.|+.+
T Consensus        40 kL~eAG~~Tve~va~a~~~eL~~---i~GIse~ka~kIi~aA~kl   81 (114)
T 1b22_A           40 KLEEAGFHTVEAVAYAPKKELIN---IKGISEAKADKILAEAAKL   81 (114)
T ss_dssp             HHHTTCCSSGGGBTSSBHHHHHT---TTTCSTTHHHHHHHHHHHH
T ss_pred             HHHHcCcCcHHHHHhCCHHHHHH---ccCCCHHHHHHHHHHHHHH
Confidence            4443 377888888888887644   3577778888888877765

>3gfk_B DNA-directed RNA polymerase subunit alpha; protein-protein complex, cytoplasm, redox-active center, stress response, transcription; 2.30A {Bacillus subtilis} SCOP: a.60.3.1

Probab=80.13  E-value=1.4  Score=27.51  Aligned_cols=44  Identities=11%  Similarity=0.143  Sum_probs=30.2

Q ss_pred             HhhcCChhHHHHHHHHHHHH-----HHHhhHHHhccCCCCcHHHHHHHHH
Q 033363           47 ISTLGLQKKRAPMIKRFSQE-----YLGESWTHVTQLHGVGKYAADAFAI   91 (121)
Q Consensus        47 i~~~Gl~~~Ka~~i~~~a~~-----i~~~~~~~L~~lpGIG~~tA~~vl~   91 (121)
                      |..++|+ .|+.+..+-+.+     ++..+.++|++++|+|+++.+-|.-
T Consensus        18 Ie~L~LS-~Ra~NcLk~agI~Tv~dL~~~se~dLlki~n~G~kSl~EI~~   66 (79)
T 3gfk_B           18 IEELDLS-VRSYNCLKRAGINTVQELANKTEEDMMKVRNLGRKSLEEVKA   66 (79)
T ss_dssp             GGGSCCB-HHHHHHHHHTTCCBHHHHTTCCHHHHTTSTTCHHHHHHHHHH
T ss_pred             HHHhCCC-HHHHHHHHHhCCCCHHHHHhCCHHHHHHcCCCCHhHHHHHHH
Confidence            4567887 566554443321     2224778999999999999987753

---

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	121
d1ngna_	144	a.96.1.2 (A:) Mismatch-specific thymine glycosylas	2e-14

>d1ngna_ a.96.1.2 (A:) Mismatch-specific thymine glycosylase domain of the methyl-GpG binding protein mbd4 {Mouse (Mus musculus) [TaxId: 10090]} Length = 144

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]

 Score = 63.2 bits (153), Expect = 2e-14
 Identities = 36/95 (37%), Positives = 55/95 (57%)

Query: 20  RVISDLFTLCPDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQEYLGESWTHVTQLH 79
            V+ +     P A+ A   D  ++ +++  LGL   RA  I +FS EYL + W +  +LH
Sbjct: 40  PVLWEFLEKYPSAEVARAADWRDVSELLKPLGLYDLRAKTIIKFSDEYLTKQWRYPIELH 99

Query: 80  GVGKYAADAFAIFCTGKWDRVRPTDHMLNYYWEFL 114
           G+GKY  D++ IFC  +W +V P DH LN Y ++L
Sbjct: 100 GIGKYGNDSYRIFCVNEWKQVHPEDHKLNKYHDWL 134

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	121
d1ngna_	144	Mismatch-specific thymine glycosylase domain of th	100.0
d1keaa_	217	Thymine-DNA glycosylase {Archaeon Methanobacterium	99.95
d2abka_	211	Endonuclease III {Escherichia coli [TaxId: 562]}	99.95
d1orna_	214	Endonuclease III {Escherichia coli [TaxId: 562]}	99.94
d1kg2a_	224	Catalytic domain of MutY {Escherichia coli [TaxId:	99.94
d1pu6a_	217	3-Methyladenine DNA glycosylase III (MagIII) {Heli	99.94
d1rrqa1	221	Catalytic domain of MutY {Bacillus stearothermophi	99.93
d1mpga1	183	3-Methyladenine DNA glycosylase II (gene alkA or a	99.89
d2noha1	190	8-oxoguanine glycosylase {Human (Homo sapiens) [Ta	99.88
d1ixra1	73	DNA helicase RuvA subunit, middle domain {Thermus	97.33
d1cuka2	78	DNA helicase RuvA subunit, middle domain {Escheric	97.25
d1bvsa2	71	DNA helicase RuvA subunit, middle domain {Mycobact	97.24
d2fmpa1	82	DNA polymerase beta, N-terminal (8 kD)-domain {Hum	96.92
d2bcqa1	76	DNA polymerase lambda {Human (Homo sapiens) [TaxId	96.89
d1x2ia1	68	ATP-dependent RNA helicase PF2015 {Pyrococcus furi	96.69
d2i1qa1	60	DNA repair protein Rad51, N-terminal domain {Archa	96.57
d1kfta_	56	Excinuclease UvrC C-terminal domain {Escherichia c	96.39
d1pzna1	61	DNA repair protein Rad51, N-terminal domain {Archa	96.13
d2i1qa1	60	DNA repair protein Rad51, N-terminal domain {Archa	95.92
d2a1ja1	62	DNA repair endonuclease XPF {Human (Homo sapiens)	95.9
d1jmsa1	95	Terminal deoxynucleotidyl transferase {Mouse (Mus	95.88
d2bgwa1	70	DNA repair endonuclease XPF {Aeropyrum pernix [Tax	95.76
d1dgsa1	181	NAD+-dependent DNA ligase, domain 3 {Thermus filif	95.75
d1pzna1	61	DNA repair protein Rad51, N-terminal domain {Archa	95.4
d1vdda_	199	Recombination protein RecR {Deinococcus radioduran	94.55
d2bgwa1	70	DNA repair endonuclease XPF {Aeropyrum pernix [Tax	94.41
d2edua1	91	KIF22, C-terminal domain {Human (Homo sapiens) [Ta	94.29
d2a1ja1	62	DNA repair endonuclease XPF {Human (Homo sapiens)	94.29
d1kfta_	56	Excinuclease UvrC C-terminal domain {Escherichia c	94.28
d2a1jb1	78	DNA excision repair protein ERCC-1 {Human (Homo sa	94.21
d1bvsa2	71	DNA helicase RuvA subunit, middle domain {Mycobact	94.1
d3bzka1	90	Transcriptional accessory factor Tex {Pseudomonas	94.09
d1szpa1	64	DNA repair protein Rad51, N-terminal domain {Baker	94.04
d2duya1	65	Uncharacterized protein TTHA1967 {Thermus thermoph	94.04
d1jmsa3	60	Terminal deoxynucleotidyl transferase {Mouse (Mus	93.74
d2a1jb1	78	DNA excision repair protein ERCC-1 {Human (Homo sa	93.59
d2edua1	91	KIF22, C-terminal domain {Human (Homo sapiens) [Ta	93.58
d2fmpa2	57	DNA polymerase beta {Human (Homo sapiens) [TaxId:	93.54
d3bzka1	90	Transcriptional accessory factor Tex {Pseudomonas	93.26
d1ixra1	73	DNA helicase RuvA subunit, middle domain {Thermus	93.15
d1cuka2	78	DNA helicase RuvA subunit, middle domain {Escheric	93.13
d1x2ia1	68	ATP-dependent RNA helicase PF2015 {Pyrococcus furi	92.25
d2axtu1	98	Photosystem II 12 kDa extrinsic protein PsbU {Ther	92.08
d2bcqa2	57	DNA polymerase lambda {Human (Homo sapiens) [TaxId	91.64
d2duya1	65	Uncharacterized protein TTHA1967 {Thermus thermoph	91.29
d1b22a_	70	DNA repair protein Rad51, N-terminal domain {Human	91.26
d1doqa_	69	C-terminal domain of RNA polymerase alpha subunit	91.08
d2csba3	55	Topoisomerase V {Methanopyrus kandleri [TaxId: 232	90.09
d1a77a1	108	Flap endonuclease-1 (Fen-1 nuclease) {Archaeon Met	88.86
d2axtu1	98	Photosystem II 12 kDa extrinsic protein PsbU {Ther	88.54
d1rxwa1	105	Flap endonuclease-1 (Fen-1 nuclease) {Archaeon Arc	87.47
d1szpa1	64	DNA repair protein Rad51, N-terminal domain {Baker	87.07
d1xo1a1	105	T5 5'-exonuclease {Bacteriophage T5 [TaxId: 10726]	85.19
d1z3eb1	67	C-terminal domain of RNA polymerase alpha subunit	83.79
d1ul1x1	140	Flap endonuclease-1 (Fen-1 nuclease) {Human (Homo	83.36
d1nkua_	187	3-Methyladenine DNA glycosylase I (Tag) {Escherich	82.53
d1b43a1	120	Flap endonuclease-1 (Fen-1 nuclease) {Archaeon Pyr	82.49
d2e1fa1	94	Werner syndrome ATP-dependent helicase, WRN {Human	80.9

>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=100.00  E-value=3.4e-35  Score=207.17  Aligned_cols=116  Identities=32%  Similarity=0.605  Sum_probs=107.3

Q ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHhCCCHHHHhcCCHHHHHHHHhhcCChhHHHHHHHHHHHHHHHhhHHHhccCCCCcH
Q 033363            4 IYSIRLKEIAILLKAGRVISDLFTLCPDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQEYLGESWTHVTQLHGVGK   83 (121)
Q Consensus         4 ~~si~~~~~~~~~~v~~v~~~l~~~~pt~~~la~a~~~eL~~~i~~~Gl~~~Ka~~i~~~a~~i~~~~~~~L~~lpGIG~   83 (121)
                      +.+..+++++++++|++++.+|+++||||+++++++.++|+++|+++||+++||++|+++|+.++.++.++|++|||||+
T Consensus        24 LV~~ILsqqT~~~~v~~v~~~L~~~~pt~e~la~a~~~el~~~Ir~~G~~~~KAk~I~~~a~~~ip~~~~~l~~LpGVG~  103 (144)
T d1ngna_          24 LIATIFLNRTSGKMAIPVLWEFLEKYPSAEVARAADWRDVSELLKPLGLYDLRAKTIIKFSDEYLTKQWRYPIELHGIGK  103 (144)
T ss_dssp             HHHHHHHTTSCHHHHHHHHHHHHHHSCSHHHHHHSCHHHHHHHTGGGSCHHHHHHHHHHHHHHHHHSCCSSGGGSTTCCH
T ss_pred             HHHHHHHccCCHHHHHHHHHHHHHhCCchhhhhccCHHHHHHHHHhhhhHHHHHHHHHHHHhhHhhhhhhhHHhcCCccH
Confidence            34555555566789999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHhcCCCCccCcchHHHHHHHHHHHHhhc
Q 033363           84 YAADAFAIFCTGKWDRVRPTDHMLNYYWEFLVSTKG  119 (121)
Q Consensus        84 ~tA~~vl~f~~~~~~~v~p~D~~l~~~~~wl~~~~~  119 (121)
                      |||+++++|++|+.+.++|+||++++|++|+++...
T Consensus       104 ~tad~~~if~~~~~~~v~~~D~~l~r~~~~~~~~~~  139 (144)
T d1ngna_         104 YGNDSYRIFCVNEWKQVHPEDHKLNKYHDWLWENHE  139 (144)
T ss_dssp             HHHHHHHHHTSSCGGGCCCCSHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCCCCCCCCChHHHHHHHHHHcCcc
Confidence            999999999999987799999999999999997653

>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=99.95  E-value=1.6e-28  Score=182.70  Aligned_cols=105  Identities=23%  Similarity=0.309  Sum_probs=92.2

Q ss_pred             HHHHHHHH----HHHHHHHHHHHHHHHhCCCHHHHhcCCHHHHHHHHhhcCChhHHHHHHHHHHHHHHH-------hhHH
Q 033363            5 YSIRLKEI----AILLKAGRVISDLFTLCPDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQEYLG-------ESWT   73 (121)
Q Consensus         5 ~si~~~~~----~~~~~v~~v~~~l~~~~pt~~~la~a~~~eL~~~i~~~Gl~~~Ka~~i~~~a~~i~~-------~~~~   73 (121)
                      |.+.+++|    |++++|++++.+|+++||||+++++++++||+++|+++||+++||++|+++|+.+.+       .+++
T Consensus        34 ~~vLv~~iLsqqT~~~~v~~~~~~l~~~~pt~~~la~a~~~~l~~~i~~~G~~~~KA~~l~~~a~~i~~~~~g~~p~~~~  113 (217)
T d1keaa_          34 YVILITEILLRRTTAGHVKKIYDKFFVKYKCFEDILKTPKSEIAKDIKEIGLSNQRAEQLKELARVVINDYGGRVPRNRK  113 (217)
T ss_dssp             HHHHHHHHHTTTSCHHHHHHHHHHHHHHCCSHHHHHHSCHHHHHHHTGGGSCHHHHHHHHHHHHHHHHHHHTTSCCSCHH
T ss_pred             HHHHHHHHHHccCcHHHHHHHHHHHHHhcccHHHHHHhhHHHHHHHHHHHHhhhHHHHHHHHHHHHHHhhccCCcchhhH
Confidence            44555554    567899999999999999999999999999999999999999999999999999998       3899


Q ss_pred             HhccCCCCcHHHHHHHHHHhcCCCCccCcchHHHHHHH
Q 033363           74 HVTQLHGVGKYAADAFAIFCTGKWDRVRPTDHMLNYYW  111 (121)
Q Consensus        74 ~L~~lpGIG~~tA~~vl~f~~~~~~~v~p~D~~l~~~~  111 (121)
                      +|++|||||+|||++||+|++|++  .+++|.++.|.+
T Consensus       114 ~L~~LpGVG~kTA~~il~~~~~~~--~~~vD~~v~Rv~  149 (217)
T d1keaa_         114 AILDLPGVGKYTCAAVMCLAFGKK--AAMVDANFVRVI  149 (217)
T ss_dssp             HHHTSTTCCHHHHHHHHHHTTCCC--CCCCCHHHHHHH
T ss_pred             HHHHHHhhhhhhhHHHHHHhcCCc--ccccccchhhhh
Confidence            999999999999999999999997  455555554443

>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=99.95  E-value=2.6e-28  Score=180.80  Aligned_cols=109  Identities=17%  Similarity=0.221  Sum_probs=98.9

Q ss_pred             HHHHHHHH----HHHHHHHHHHHHHHHhCCCHHHHhcCCHHHHHHHHhhcCChhHHHHHHHHHHHHHHH-------hhHH
Q 033363            5 YSIRLKEI----AILLKAGRVISDLFTLCPDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQEYLG-------ESWT   73 (121)
Q Consensus         5 ~si~~~~~----~~~~~v~~v~~~l~~~~pt~~~la~a~~~eL~~~i~~~Gl~~~Ka~~i~~~a~~i~~-------~~~~   73 (121)
                      |.+.+++|    |++++|+++|.+|+++||||+++++++.++|+++|+++||+++||++|+++|+.+.+       ++++
T Consensus        30 ~~vli~~iLsqqT~~~~v~~~~~~l~~~~~t~~~la~a~~~~l~~~i~~~G~y~~Ka~~l~~~a~~i~~~~~g~~p~~~~  109 (211)
T d2abka_          30 FELLIAVLLSAQATDVSVNKATAKLYPVANTPAAMLELGVEGVKTYIKTIGLYNSKAENIIKTCRILLEQHNGEVPEDRA  109 (211)
T ss_dssp             HHHHHHHHHTTTSCHHHHHHHHHHHTTTCCSHHHHHHHHHHHHHHHHTTSTTHHHHHHHHHHHHHHHHHHTTTSCCSCHH
T ss_pred             HHHHHHHHHhccchHHHHHHHHHHHHHhccChHHHHhhhHhHhHHHHHHhhhhhhHHHHHHHHHHHHHHHhcCchhHHHH
Confidence            44555555    567899999999999999999999999999999999999999999999999999998       4899


Q ss_pred             HhccCCCCcHHHHHHHHHHhcCCCCccCcchHHHHHHHHHHH
Q 033363           74 HVTQLHGVGKYAADAFAIFCTGKWDRVRPTDHMLNYYWEFLV  115 (121)
Q Consensus        74 ~L~~lpGIG~~tA~~vl~f~~~~~~~v~p~D~~l~~~~~wl~  115 (121)
                      +|++|||||+|||++|++|++|+|  ++|+|.+++|.++.+.
T Consensus       110 ~L~~LpGVG~~TA~~Il~~a~~~p--~~~vD~nv~Rv~~R~g  149 (211)
T d2abka_         110 ALEALPGVGRKTANVVLNTAFGWP--TIAVDTHIFRVCNRTQ  149 (211)
T ss_dssp             HHHHSTTCCHHHHHHHHHHHHCCC--CCCCCHHHHHHHHHHC
T ss_pred             HHHHHHhhchHHHHHHHHHHhcCc--cccccHHHHHHHHHhc
Confidence            999999999999999999999996  8999999998877653

>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=99.94  E-value=3.3e-27  Score=175.00  Aligned_cols=109  Identities=18%  Similarity=0.248  Sum_probs=98.5

Q ss_pred             HHHHHHHH----HHHHHHHHHHHHHHHhCCCHHHHhcCCHHHHHHHHhhcCChhHHHHHHHHHHHHHHH-------hhHH
Q 033363            5 YSIRLKEI----AILLKAGRVISDLFTLCPDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQEYLG-------ESWT   73 (121)
Q Consensus         5 ~si~~~~~----~~~~~v~~v~~~l~~~~pt~~~la~a~~~eL~~~i~~~Gl~~~Ka~~i~~~a~~i~~-------~~~~   73 (121)
                      |.+.+++|    |++++|+++|.+|+++|||++++++++.+++++.|+++||+++||++|+++|+.+.+       .+++
T Consensus        31 ~~vLVs~iLsqqT~~~~v~~~~~~l~~~~pt~~~la~~~~~e~~~~i~~~g~y~~ka~~l~~~a~~i~~~~~g~vp~~~~  110 (214)
T d1orna_          31 FELLIAVVLSAQCTDALVNKVTKRLFEKYRTPHDYIAVPLEELEQDIRSIGLYRNKARNIQKLCAMLIDKYNGEVPRDRD  110 (214)
T ss_dssp             HHHHHHHHHHTTSCHHHHHHHHHHHHHHCCSHHHHHSSCHHHHHHHTGGGSSHHHHHHHHHHHHHHHHHHSTTSCCSCHH
T ss_pred             HHHHHHHHHHhcChHHHHHHHHhhhhcccCchhhhhhccHHHhhhhhhhhhhhhHHHHHHHHHhhhHHHHhCCCCCCCHH
Confidence            45555555    567889999999999999999999999999999999999999999999999999988       3899


Q ss_pred             HhccCCCCcHHHHHHHHHHhcCCCCccCcchHHHHHHHHHHH
Q 033363           74 HVTQLHGVGKYAADAFAIFCTGKWDRVRPTDHMLNYYWEFLV  115 (121)
Q Consensus        74 ~L~~lpGIG~~tA~~vl~f~~~~~~~v~p~D~~l~~~~~wl~  115 (121)
                      +|++|||||+|||++|++|++|++  ++|+|.+++|.+..+.
T Consensus       111 ~L~~LpGVG~kTA~~il~~a~~~~--~~~VDtnv~RV~~Rlg  150 (214)
T d1orna_         111 ELMKLPGVGRKTANVVVSVAFGVP--AIAVDTHVERVSKRLG  150 (214)
T ss_dssp             HHTTSTTCCHHHHHHHHHHHHCCC--CCCCCHHHHHHHHHHT
T ss_pred             HHHhCcCcccchHHHHHHHHhcCC--cccccchHHHHHHHHH
Confidence            999999999999999999999996  7999999988866553

>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=99.94  E-value=8.9e-27  Score=173.59  Aligned_cols=109  Identities=19%  Similarity=0.264  Sum_probs=96.8

Q ss_pred             HHHHHHHH----HHHHHHHHHHHHHHHhCCCHHHHhcCCHHHHHHHHhhcCChhHHHHHHHHHHHHHHH-------hhHH
Q 033363            5 YSIRLKEI----AILLKAGRVISDLFTLCPDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQEYLG-------ESWT   73 (121)
Q Consensus         5 ~si~~~~~----~~~~~v~~v~~~l~~~~pt~~~la~a~~~eL~~~i~~~Gl~~~Ka~~i~~~a~~i~~-------~~~~   73 (121)
                      |.+.+++|    |++++|++++.+|+++||||+++++++.++|+++|+++||+ +|+++|+++++.+.+       .+++
T Consensus        31 ~~vlvs~iLsqqT~~~~v~~~~~~l~~~~pt~~~la~a~~~~l~~~i~~~g~~-~ka~~l~~~~~~i~~~~~g~vp~~~~  109 (224)
T d1kg2a_          31 YKVWLSEVMLQQTQVATVIPYFERFMARFPTVTDLANAPLDEVLHLWTGLGYY-ARARNLHKAAQQVATLHGGKFPETFE  109 (224)
T ss_dssp             HHHHHHHHHHTSSCHHHHHHHHHHHHHHCSSHHHHHHSCHHHHHHHHTTSCCT-HHHHHHHHHHHHHHHHSTTSCCCSHH
T ss_pred             HHHHHHHHHHhcCcHHHHHHHHHHHHHHhccHHHHHHhhHHHHHhHhhhhhHH-HHHHHHHHhhhhhhhhccCCcchHHH
Confidence            44444444    56789999999999999999999999999999999999999 589999999999988       4899


Q ss_pred             HhccCCCCcHHHHHHHHHHhcCCCCccCcchHHHHHHHHHHHH
Q 033363           74 HVTQLHGVGKYAADAFAIFCTGKWDRVRPTDHMLNYYWEFLVS  116 (121)
Q Consensus        74 ~L~~lpGIG~~tA~~vl~f~~~~~~~v~p~D~~l~~~~~wl~~  116 (121)
                      +|++|||||+|||++||+|++|++  ++|+|.++.|.+..+..
T Consensus       110 ~L~~LpGVG~kTA~~il~~a~~~~--~~~vD~~v~Rv~~Rl~~  150 (224)
T d1kg2a_         110 EVAALPGVGRSTAGAILSLSLGKH--FPILDGNVKRVLARCYA  150 (224)
T ss_dssp             HHHTSTTCCHHHHHHHHHHHHCCS--CCCCCHHHHHHHHHHHT
T ss_pred             HHHHHHhhhhhhhHHHHHHhhhcc--cccccchHHHHHHHhcc
Confidence            999999999999999999999997  78899988888766543

>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=99.94  E-value=4.9e-27  Score=174.69  Aligned_cols=109  Identities=16%  Similarity=0.199  Sum_probs=95.4

Q ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHhC-------CCHHHHhcCCHHHHHHHHhhcCChhHHHHHHHHHHHHHHH-------
Q 033363            4 IYSIRLKEIAILLKAGRVISDLFTLC-------PDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQEYLG-------   69 (121)
Q Consensus         4 ~~si~~~~~~~~~~v~~v~~~l~~~~-------pt~~~la~a~~~eL~~~i~~~Gl~~~Ka~~i~~~a~~i~~-------   69 (121)
                      +.|..++|+++.++|.+++.+|..++       |||++|+++++++|+++|+++||+++||++|+++|+.+.+       
T Consensus        33 lv~aIL~Qqts~~~a~~a~~~L~~~~~~~~~~~~t~~~la~a~~eel~~~ir~~G~~~~KA~~i~~~a~~i~~~~~~~~~  112 (217)
T d1pu6a_          33 LLGAVLTQNTKFEAVLKSLENLKNAFILENDDEINLKKIAYIEFSKLAECVRPSGFYNQKAKRLIDLSGNILKDFQSFEN  112 (217)
T ss_dssp             HHHHHHTTTSCHHHHHHHHHHHHHTTSSCSCHHHHHHHHHHSCHHHHHHHTGGGSCHHHHHHHHHHHHHHHHHHHSSHHH
T ss_pred             HHHHHHhcCCCHHHHHHHHHHHHHHHhhccccCCCHHHHHCCCHHHHHHHHHHCCCcHHHHHHHHHHHHHHHHhhhhccc
Confidence            34455555566778999999998764       7999999999999999999999999999999999999976       


Q ss_pred             ----hhHHHhccCCCCcHHHHHHHHHHhcCCCCccCcchHHHHHHHHHH
Q 033363           70 ----ESWTHVTQLHGVGKYAADAFAIFCTGKWDRVRPTDHMLNYYWEFL  114 (121)
Q Consensus        70 ----~~~~~L~~lpGIG~~tA~~vl~f~~~~~~~v~p~D~~l~~~~~wl  114 (121)
                          +.+++|++|||||+|||++|++|+++++  ++|+|.++.|...++
T Consensus       113 ~~~~~~~~~L~~lpGIG~kTA~~vl~~~~~~~--~~~vD~hv~Rv~~Rl  159 (217)
T d1pu6a_         113 FKQEVTREWLLDQKGIGKESADAILCYACAKE--VMVVDKYSYLFLKKL  159 (217)
T ss_dssp             HHHHCCHHHHHTSTTCCHHHHHHHHHHTTCCS--CCCCCHHHHHHHHHT
T ss_pred             CCcHHHHHHHHHHhhhhhHHHHHHHHHHcCCe--eeecChHHHHHHHHh
Confidence                3678999999999999999999999995  788899998887664

>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=99.93  E-value=5.3e-26  Score=169.07  Aligned_cols=108  Identities=16%  Similarity=0.142  Sum_probs=92.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHhCCCHHHHhcCCHHHHHHHHhhcCChhHHHHHHHHHHHHHHH-------hhHHHhccC
Q 033363            6 SIRLKEIAILLKAGRVISDLFTLCPDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQEYLG-------ESWTHVTQL   78 (121)
Q Consensus         6 si~~~~~~~~~~v~~v~~~l~~~~pt~~~la~a~~~eL~~~i~~~Gl~~~Ka~~i~~~a~~i~~-------~~~~~L~~l   78 (121)
                      |..++++|++++|++++.+|+++||||++++++++++|+++|+++||+ +|++++++.++.+.+       .++++|++|
T Consensus        34 ~~iLsqqT~~~~v~~~~~~L~~~~~t~~~la~a~~~~l~~~i~~~G~~-~ra~~l~~~~~~~~~~~~G~vp~~~~~Ll~L  112 (221)
T d1rrqa1          34 SEVMLQQTRVETVIPYFEQFIDRFPTLEALADADEDEVLKAWEGLGYY-SRVRNLHAAVKEVKTRYGGKVPDDPDEFSRL  112 (221)
T ss_dssp             HHHHHTTSCHHHHHHHHHHHHHHSCSHHHHHHSCHHHHHHHHTTSSCT-HHHHHHHHHHHHHHHHHTTCCCCSHHHHHTS
T ss_pred             HHHHHhhCcHHHHHHHHHHHHHhcchHHHHHhhcHHHHHhhhccchhh-hhhHHHHHHHHHHhhhcCCCCchHHHHHHHH
Confidence            333444455789999999999999999999999999999999999999 577888888888877       389999999


Q ss_pred             CCCcHHHHHHHHHHhcCCCCccCcchHHHHHHHHHHHH
Q 033363           79 HGVGKYAADAFAIFCTGKWDRVRPTDHMLNYYWEFLVS  116 (121)
Q Consensus        79 pGIG~~tA~~vl~f~~~~~~~v~p~D~~l~~~~~wl~~  116 (121)
                      ||||+|||++||+|++|++  ++|+|.++.|.+..+..
T Consensus       113 pGIG~kTA~~il~~a~~~p--~~~VDt~v~Rv~~Rl~~  148 (221)
T d1rrqa1         113 KGVGPYTVGAVLSLAYGVP--EPAVNGNVMRVLSRLFL  148 (221)
T ss_dssp             TTCCHHHHHHHHHHHTCCC--CCCCCHHHHHHHHHHTT
T ss_pred             HHhhhHHHHHHHHHHhcCc--ccccCccHHHHHHHhhc
Confidence            9999999999999999997  68888888877665543

>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=99.89  E-value=1.8e-23  Score=151.44  Aligned_cols=106  Identities=17%  Similarity=0.273  Sum_probs=86.9

Q ss_pred             hHHHHHHHHHHHHHHHHHHHHHHH-------------hCCCHHHHhcCCHHHHHHHHhhcCChhHHHHHHHHHHHHHHH-
Q 033363            4 IYSIRLKEIAILLKAGRVISDLFT-------------LCPDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQEYLG-   69 (121)
Q Consensus         4 ~~si~~~~~~~~~~v~~v~~~l~~-------------~~pt~~~la~a~~~eL~~~i~~~Gl~~~Ka~~i~~~a~~i~~-   69 (121)
                      +....++|+...+++..++.+|.+             .||||+.|+++++++    |+.+|++.+|+++|+.+|+.+.+ 
T Consensus        18 Lv~~Ii~Qqis~~aA~~i~~rl~~~~g~~~~~~~~~~~FPtp~~l~~~~~~~----lr~~Gls~~Ka~~i~~~a~~~~~g   93 (183)
T d1mpga1          18 GVRAILGQLVSVAMAAKLTARVAQLYGERLDDFPEYICFPTPQRLAAADPQA----LKALGMPLKRAEALIHLANAALEG   93 (183)
T ss_dssp             HHHHHHTTTSCHHHHHHHHHHHHHHHCCBCSSCTTCBCCCCHHHHHTCCHHH----HHHTTSCHHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHhchhhHHHHHHHHHHHHHHhCccccccccccCCCcHHHHHcCCHHH----HHHcCCcHHHHHHHHHHHHHHHcC
Confidence            334444444444577888888864             489999999999998    68899999999999999999987 


Q ss_pred             -----------hhHHHhccCCCCcHHHHHHHHHHhcCCCCccCcchHHHHHHHHH
Q 033363           70 -----------ESWTHVTQLHGVGKYAADAFAIFCTGKWDRVRPTDHMLNYYWEF  113 (121)
Q Consensus        70 -----------~~~~~L~~lpGIG~~tA~~vl~f~~~~~~~v~p~D~~l~~~~~w  113 (121)
                                 +.++.|+++||||||||+|+++|++|++|.++++|.++++.++.
T Consensus        94 ~l~~~~~~~~~e~~~~L~~l~GIGpwTAd~illf~lg~~dvfP~~D~~lr~~~~~  148 (183)
T d1mpga1          94 TLPMTIPGDVEQAMKTLQTFPGIGRWTANYFALRGWQAKDVFLPDDYLIKQRFPG  148 (183)
T ss_dssp             CSCSSCCSCHHHHHHHHTTSTTCCHHHHHHHHHHHSCCSSCCCTTCHHHHHHSTT
T ss_pred             chhhhccccHHHHHHHHHHhhcccHHHHHHHHHhhCCCCCccccchHHHHHHhhh
Confidence                       35789999999999999999999999998444459999887543

>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=99.88  E-value=8.5e-23  Score=148.22  Aligned_cols=107  Identities=20%  Similarity=0.207  Sum_probs=84.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHH---------------hCCCHHHHhcCCHHHHHHHHhhcCChhHHHHHHHHHHHHHHH
Q 033363            5 YSIRLKEIAILLKAGRVISDLFT---------------LCPDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQEYLG   69 (121)
Q Consensus         5 ~si~~~~~~~~~~v~~v~~~l~~---------------~~pt~~~la~a~~~eL~~~i~~~Gl~~~Ka~~i~~~a~~i~~   69 (121)
                      .+..++|++...++.++..+|.+               .||||++|++++++++   ++.+|+. .|+++|+++|+.+.+
T Consensus         7 v~~IisQq~s~~~~~~~~~~L~~~~G~~~~~~~~~~~~~FP~~~~la~~~~e~~---l~~~~~~-~ra~~i~~~a~~i~~   82 (190)
T d2noha1           7 FSFICSSNNNIARITGMVERLCQAFGPRLIQLDDVTYHGFPSLQALAGPEVEAH---LRKLGLG-YRARYVSASARAILE   82 (190)
T ss_dssp             HHHHTTTTSCHHHHHHHHHHHHHHHSCEEEEETTEEEECCCCHHHHHSTTHHHH---HHHTTCT-THHHHHHHHHHHHHH
T ss_pred             HHHHHHcccCHHHHHHHHHHHHHHHCCCccccCcchhhccCCHHHHHHcchHHH---HHhcchH-HHHHHHHHHHHHHHH
Confidence            33444444444455666666654               3799999999998875   6677875 799999999999886


Q ss_pred             -----------------hhHHHhccCCCCcHHHHHHHHHHhcCCCCccCcchHHHHHHHHHHHH
Q 033363           70 -----------------ESWTHVTQLHGVGKYAADAFAIFCTGKWDRVRPTDHMLNYYWEFLVS  116 (121)
Q Consensus        70 -----------------~~~~~L~~lpGIG~~tA~~vl~f~~~~~~~v~p~D~~l~~~~~wl~~  116 (121)
                                       +.+++|++|||||||||+++++|++|+|| ++|+|.+++|.+..+++
T Consensus        83 ~~~~~~~l~~l~~~~~~~~~~~L~~l~GIG~wTA~~il~~~~~~~d-~fpvD~~v~R~~~r~~~  145 (190)
T d2noha1          83 EQGGLAWLQQLRESSYEEAHKALCILPGVGTQVADCICLMALDKPQ-AVPVDVHMWHIAQRDYS  145 (190)
T ss_dssp             TSCSHHHHHHTTTSCHHHHHHHHTTSTTCCHHHHHHHHHHHSCCTT-CCCCCHHHHHHHHHHHC
T ss_pred             hcccccCHHHhcCCCcHHHHHHHHHcCCchHHHHHHHHHHHcCCCC-eEeecHHHHHHHHHHhc
Confidence                             24688999999999999999999999997 77889999888766554

>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=97.33  E-value=0.00034  Score=42.37  Aligned_cols=50  Identities=24%  Similarity=0.313  Sum_probs=35.5

Q ss_pred             HHhhcCChhHHHHHHHH------HHHHHHHhhHHHhccCCCCcHHHHHHHHHHhcC
Q 033363           46 IISTLGLQKKRAPMIKR------FSQEYLGESWTHVTQLHGVGKYAADAFAIFCTG   95 (121)
Q Consensus        46 ~i~~~Gl~~~Ka~~i~~------~a~~i~~~~~~~L~~lpGIG~~tA~~vl~f~~~   95 (121)
                      +++--|...+.|-.|.+      +.++|.+++.+.|.++||||+|||+-+..---+
T Consensus        12 Li~V~GIGpk~Al~iLs~~~~~~l~~aI~~~D~~~L~~vpGIG~KtA~rIi~eLk~   67 (73)
T d1ixra1          12 LLSVSGVGPKVALALLSALPPRLLARALLEGDARLLTSASGVGRRLAERIALELKG   67 (73)
T ss_dssp             HHSSSCCCHHHHHHHHHHSCHHHHHHHHHTTCHHHHTTSTTCCHHHHHHHHHHHTT
T ss_pred             HhccCCcCHHHHHHHHHHccHHHHHHHHHhcCHHHhhcCCCCCHHHHHHHHHHHHh
Confidence            34444555556655553      366677789999999999999999988754333

>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=97.25  E-value=0.00043  Score=42.39  Aligned_cols=44  Identities=25%  Similarity=0.281  Sum_probs=32.0

Q ss_pred             cCChhHHHHHHH------HHHHHHHHhhHHHhccCCCCcHHHHHHHHHHh
Q 033363           50 LGLQKKRAPMIK------RFSQEYLGESWTHVTQLHGVGKYAADAFAIFC   93 (121)
Q Consensus        50 ~Gl~~~Ka~~i~------~~a~~i~~~~~~~L~~lpGIG~~tA~~vl~f~   93 (121)
                      -|.....|-.|.      ++.+++.+++.+.|.++||||+|||+-+..--
T Consensus        15 ~GIGpK~Al~iLs~~~~~~l~~aI~~~D~~~L~~vpGIG~KtA~rIi~eL   64 (78)
T d1cuka2          15 NGVGPKLALAILSGMSAQQFVNAVEREEVGALVKLPGIGKKTAERLIVEM   64 (78)
T ss_dssp             SSCCHHHHHHHHHHSCHHHHHHHHHTTCHHHHHTSTTCCHHHHHHHHHHH
T ss_pred             CCccHHHHHHHHHhCCHHHHHHHHHccCHHHhhcCCCCCHHHHHHHHHHH
Confidence            444445555554      33566677899999999999999999887543

>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=0.00029  Score=42.48  Aligned_cols=42  Identities=17%  Similarity=0.285  Sum_probs=30.1

Q ss_pred             cCChhHHHHHHHH------HHHHHHHhhHHHhccCCCCcHHHHHHHHH
Q 033363           50 LGLQKKRAPMIKR------FSQEYLGESWTHVTQLHGVGKYAADAFAI   91 (121)
Q Consensus        50 ~Gl~~~Ka~~i~~------~a~~i~~~~~~~L~~lpGIG~~tA~~vl~   91 (121)
                      -|.....|-.|..      +.+++.+++.+.|.++||||+|||+-+.+
T Consensus        15 ~GIGpK~Al~iLs~~~~~~l~~aI~~~D~~~L~~vpGIG~KtA~rIi~   62 (71)
T d1bvsa2          15 SGVGPRLAMATLAVHDAAALRQALADSDVASLTRVPGIGRRGAERIVL   62 (71)
T ss_dssp             SSCCHHHHHHHHHHSCHHHHHHHTTTTCHHHHHTSTTCCHHHHHHHHH
T ss_pred             CCcCHHHHHHHHHhCCHHHHHHHHHcCCHHHhhcCCCCCHHHHHHHHH
Confidence            3455445544442      35556668999999999999999998764

>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=96.92  E-value=0.0021  Score=39.26  Aligned_cols=53  Identities=15%  Similarity=0.188  Sum_probs=42.3

Q ss_pred             HHHHHHHhhcCChhHHHHHHHHHHHHHHH-----hhHHHhccCCCCcHHHHHHHHHHh
Q 033363           41 EEIEKIISTLGLQKKRAPMIKRFSQEYLG-----ESWTHVTQLHGVGKYAADAFAIFC   93 (121)
Q Consensus        41 ~eL~~~i~~~Gl~~~Ka~~i~~~a~~i~~-----~~~~~L~~lpGIG~~tA~~vl~f~   93 (121)
                      +++.++.+..|=...|++.-.+++..+..     .+.++|.++||||+.+++-+.-|.
T Consensus        11 ~ela~l~~~~~~~~fr~~AY~~Aa~~i~~l~~~i~~~~~l~~i~GIGk~ia~kI~E~~   68 (82)
T d2fmpa1          11 TELANFEKNVSQAIHKYNAYRKAASVIAKYPHKIKSGAEAKKLPGVGTKIAEKIDEFL   68 (82)
T ss_dssp             HHHHHHHHHTTCCHHHHHHHHHHHHHHHHCSSCCCCHHHHHTSTTCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHhCcChHHHHHHHHHHHHHHhCCcccCCHHHHhcCCCccHHHHHHHHHHH
Confidence            45666666666545789999999999887     367899999999999999887665

>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=96.89  E-value=0.0018  Score=38.81  Aligned_cols=52  Identities=23%  Similarity=0.249  Sum_probs=40.0

Q ss_pred             HHHHHHHhhcCChhHHHHHHHHHHHHHHH-----hhHHHhccCCCCcHHHHHHHHHHh
Q 033363           41 EEIEKIISTLGLQKKRAPMIKRFSQEYLG-----ESWTHVTQLHGVGKYAADAFAIFC   93 (121)
Q Consensus        41 ~eL~~~i~~~Gl~~~Ka~~i~~~a~~i~~-----~~~~~L~~lpGIG~~tA~~vl~f~   93 (121)
                      ++|.++.+-.| -..|++.-.+++..+..     .+.++|.++||||+.+++-+.-|-
T Consensus        10 ~~la~~~~~~g-d~fr~~AY~~A~~~l~~l~~~i~~~~~l~~lpGiG~~i~~kI~Eil   66 (76)
T d2bcqa1          10 EVLAKAYSVQG-DKWRALGYAKAINALKSFHKPVTSYQEACSIPGIGKRMAEKIIEIL   66 (76)
T ss_dssp             HHHHHHHHHTT-CHHHHHHHHHHHHHHHSCCSCCCCHHHHHTSTTCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHcC-ChHHHHHHHHHHHHHHhCCcccCCHHHHhcCCCccHHHHHHHHHHH
Confidence            44555555556 45789999998888876     467899999999999999887553

>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=96.69  E-value=0.0021  Score=37.79  Aligned_cols=44  Identities=14%  Similarity=0.150  Sum_probs=30.0

Q ss_pred             hhHHHHHHHHHHH---HHHHhhHHHhccCCCCcHHHHHHHHHHhcCC
Q 033363           53 QKKRAPMIKRFSQ---EYLGESWTHVTQLHGVGKYAADAFAIFCTGK   96 (121)
Q Consensus        53 ~~~Ka~~i~~~a~---~i~~~~~~~L~~lpGIG~~tA~~vl~f~~~~   96 (121)
                      ...+|+.|.+--.   .+.+.+.++|.++||||+++|+.+.-|--..
T Consensus        19 G~~~a~~L~~~f~s~~~i~~As~eeL~~i~GIG~~~A~~I~~~~~~~   65 (68)
T d1x2ia1          19 SATLARRLLKHFGSVERVFTASVAELMKVEGIGEKIAKEIRRVITAP   65 (68)
T ss_dssp             CHHHHHHHHHHHCSHHHHHHCCHHHHTTSTTCCHHHHHHHHHHHHSC
T ss_pred             CHHHHHHHHHHcCCHHHHHHhHHHHHHhCCCcCHHHHHHHHHHHhch
Confidence            3345655544432   3333578899999999999999998765443

>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=96.57  E-value=0.0023  Score=36.84  Aligned_cols=44  Identities=14%  Similarity=0.117  Sum_probs=35.0

Q ss_pred             HHHHHHh-CCCHHHHhcCCHHHHHHHHhhcCChhHHHHHHHHHHHHHH
Q 033363           22 ISDLFTL-CPDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQEYL   68 (121)
Q Consensus        22 ~~~l~~~-~pt~~~la~a~~~eL~~~i~~~Gl~~~Ka~~i~~~a~~i~   68 (121)
                      ..+|.+. |.|.++|++++++||.+   --|++..+|+.|++.|+...
T Consensus        12 a~~L~~~G~~tv~~l~~a~~eeL~~---i~Gi~~~~A~~i~~~ar~~~   56 (60)
T d2i1qa1          12 AEKLVEAGYIDFMKIATATVGELTD---IEGISEKAAAKMIMGARDLC   56 (60)
T ss_dssp             HHHHHHHTCCSHHHHHTCCHHHHHT---STTCCHHHHHHHHHHHHHHT
T ss_pred             HHHHHHccCCCHHHHHhCCHHHHHH---CCCCCHHHHHHHHHHHHHHc
Confidence            3466765 99999999999999754   35888899999988887654

>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=96.39  E-value=0.0013  Score=37.48  Aligned_cols=23  Identities=13%  Similarity=0.161  Sum_probs=18.5

Q ss_pred             hhHHHhccCCCCcHHHHHHHHHH
Q 033363           70 ESWTHVTQLHGVGKYAADAFAIF   92 (121)
Q Consensus        70 ~~~~~L~~lpGIG~~tA~~vl~f   92 (121)
                      .+.++|.++||||+++|..+.-+
T Consensus        31 As~eeL~~v~GIg~~~A~~I~~~   53 (56)
T d1kfta_          31 ASVEEIAKVPGISQGLAEKIFWS   53 (56)
T ss_dssp             CCHHHHTTSSSTTSHHHHHHHHH
T ss_pred             hhHHHHHhcCCCCHHHHHHHHHH
Confidence            46778888899999988887655

>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=96.13  E-value=0.0062  Score=34.94  Aligned_cols=43  Identities=12%  Similarity=0.127  Sum_probs=35.1

Q ss_pred             HHHHHh-CCCHHHHhcCCHHHHHHHHhhcCChhHHHHHHHHHHHHHH
Q 033363           23 SDLFTL-CPDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQEYL   68 (121)
Q Consensus        23 ~~l~~~-~pt~~~la~a~~~eL~~~i~~~Gl~~~Ka~~i~~~a~~i~   68 (121)
                      .+|.+. |.|.++|+++++++|.++   -|++..+|+.|.+.|+...
T Consensus        15 ~~L~~~g~~sv~~l~~a~~~eL~~i---~Gi~~~~A~~i~~~ar~~~   58 (61)
T d1pzna1          15 EKLREAGYDTLEAIAVASPIELKEV---AGISEGTALKIIQAARKAA   58 (61)
T ss_dssp             HHHHTTTCCSHHHHHTCCHHHHHHH---HCCCHHHHHHHHHHHHHHC
T ss_pred             HHHHHhcCCCHHHHHhCCHHHHHHC---CCCCHHHHHHHHHHHHHHc
Confidence            466764 799999999999998874   3888899999998887653

>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=95.92  E-value=0.0098  Score=34.01  Aligned_cols=44  Identities=14%  Similarity=0.147  Sum_probs=31.3

Q ss_pred             CChhHHHHHHHHH----HHHHHHhhHHHhccCCCCcHHHHHHHHHHhc
Q 033363           51 GLQKKRAPMIKRF----SQEYLGESWTHVTQLHGVGKYAADAFAIFCT   94 (121)
Q Consensus        51 Gl~~~Ka~~i~~~----a~~i~~~~~~~L~~lpGIG~~tA~~vl~f~~   94 (121)
                      |....+++.|.+.    .+.+...+.++|.++||||+++|+-+...+-
T Consensus         6 GIG~~~a~~L~~~G~~tv~~l~~a~~eeL~~i~Gi~~~~A~~i~~~ar   53 (60)
T d2i1qa1           6 GVGPSTAEKLVEAGYIDFMKIATATVGELTDIEGISEKAAAKMIMGAR   53 (60)
T ss_dssp             TCCHHHHHHHHHHTCCSHHHHHTCCHHHHHTSTTCCHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHccCCCHHHHHhCCHHHHHHCCCCCHHHHHHHHHHHH
Confidence            4444566665554    3445556889999999999999998876554

>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=95.90  E-value=0.017  Score=33.07  Aligned_cols=40  Identities=15%  Similarity=0.262  Sum_probs=32.7

Q ss_pred             HHHHHHHhCCCHHHHhcCCHHHHHHHHhhcCChhHHHHHHHHHH
Q 033363           21 VISDLFTLCPDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFS   64 (121)
Q Consensus        21 v~~~l~~~~pt~~~la~a~~~eL~~~i~~~Gl~~~Ka~~i~~~a   64 (121)
                      -...|.++|.|.++|.+|+.+||+++.   | ....|+.|.+.-
T Consensus        15 ~~~~Ll~~f~Si~~l~~As~~eL~~v~---G-~~~~A~~i~~f~   54 (62)
T d2a1ja1          15 NCRSLMHHVKNIAELAALSQDELTSIL---G-NAANAKQLYDFI   54 (62)
T ss_dssp             HHHHHHHHCSSHHHHHTCCHHHHHHHH---S-CHHHHHHHHHHH
T ss_pred             HHHHHHHHhccHHHHHhCCHHHHHHCc---C-cHHHHHHHHHHH
Confidence            456788899999999999999998874   6 667788887754

>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=95.88  E-value=0.011  Score=36.89  Aligned_cols=51  Identities=8%  Similarity=-0.047  Sum_probs=39.4

Q ss_pred             HHHHHHHhhcCChhHHHHHHHHHHHHHHH-----hhHHHhccCCCCcHHHHHHHHHH
Q 033363           41 EEIEKIISTLGLQKKRAPMIKRFSQEYLG-----ESWTHVTQLHGVGKYAADAFAIF   92 (121)
Q Consensus        41 ~eL~~~i~~~Gl~~~Ka~~i~~~a~~i~~-----~~~~~L~~lpGIG~~tA~~vl~f   92 (121)
                      ++|.++..--|- ..|++.-.+++..+..     .+.+++.++||||+.+++-+.-|
T Consensus        26 ~~la~~~e~~g~-~fr~~AY~rAa~~i~~l~~~i~~~~~l~~i~GIGk~i~~kI~Ei   81 (95)
T d1jmsa1          26 DILAENDELREN-EGSCLAFMRASSVLKSLPFPITSMKDTEGIPCLGDKVKSIIEGI   81 (95)
T ss_dssp             HHHHHHHHHTTC-HHHHHHHHHHHHHHHTCSSCCCSGGGGTTCSSCCHHHHHHHHHH
T ss_pred             HHHHHHHHHcCC-cHHHHHHHHHHHHHHhCCcccCCHHHHHhccchhHHHHHHHHHH
Confidence            455555555564 5799999999998877     36688999999999999887654

>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=95.76  E-value=0.0053  Score=36.06  Aligned_cols=41  Identities=15%  Similarity=0.262  Sum_probs=25.8

Q ss_pred             hhHHHHHHHHHHH---HHHHhhHHHhccCCCCcHHHHHHHHHHh
Q 033363           53 QKKRAPMIKRFSQ---EYLGESWTHVTQLHGVGKYAADAFAIFC   93 (121)
Q Consensus        53 ~~~Ka~~i~~~a~---~i~~~~~~~L~~lpGIG~~tA~~vl~f~   93 (121)
                      ...+|+.|.+--.   .+...+.++|.+++|||+.+|+.+.-|-
T Consensus        22 G~~~a~~L~~~F~s~~~l~~As~eeL~~v~GIG~~~A~~I~~~~   65 (70)
T d2bgwa1          22 GRRTAERILERFGSLERFFTASKAEISKVEGIGEKRAEEIKKIL   65 (70)
T ss_dssp             CHHHHHHHHHHHSSHHHHTTCCHHHHHHSTTCCHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHhCCHHHHHHcCHHHHHcCCCCCHHHHHHHHHHH
Confidence            3345555554322   2222467888888888888888877654

>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=95.75  E-value=0.0018  Score=45.09  Aligned_cols=24  Identities=21%  Similarity=0.223  Sum_probs=20.3

Q ss_pred             hHHHhccCCCCcHHHHHHHHHHhc
Q 033363           71 SWTHVTQLHGVGKYAADAFAIFCT   94 (121)
Q Consensus        71 ~~~~L~~lpGIG~~tA~~vl~f~~   94 (121)
                      +.++|.+++|||+.+|+.+.-|--
T Consensus       137 s~eeL~~I~GIG~~~A~si~~ff~  160 (181)
T d1dgsa1         137 SLEELIEVEEVGELTARAILETLK  160 (181)
T ss_dssp             CHHHHHTSTTCCHHHHHHHHHHHH
T ss_pred             HHHHHhhcCCcCHHHHHHHHHHHC
Confidence            578999999999999999887643

>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=95.40  E-value=0.0055  Score=35.17  Aligned_cols=44  Identities=11%  Similarity=0.067  Sum_probs=30.3

Q ss_pred             CChhHHHHHHHHH----HHHHHHhhHHHhccCCCCcHHHHHHHHHHhc
Q 033363           51 GLQKKRAPMIKRF----SQEYLGESWTHVTQLHGVGKYAADAFAIFCT   94 (121)
Q Consensus        51 Gl~~~Ka~~i~~~----a~~i~~~~~~~L~~lpGIG~~tA~~vl~f~~   94 (121)
                      |....+++.|.+.    .+.+.+.+.++|.++||||+++|+.+...+-
T Consensus         8 GIG~~~a~~L~~~g~~sv~~l~~a~~~eL~~i~Gi~~~~A~~i~~~ar   55 (61)
T d1pzna1           8 GVGPATAEKLREAGYDTLEAIAVASPIELKEVAGISEGTALKIIQAAR   55 (61)
T ss_dssp             TCCHHHHHHHHTTTCCSHHHHHTCCHHHHHHHHCCCHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHhcCCCHHHHHhCCHHHHHHCCCCCHHHHHHHHHHHH
Confidence            4555566655542    3445556788899999999999988876553

>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=94.55  E-value=0.015  Score=41.02  Aligned_cols=29  Identities=17%  Similarity=0.181  Sum_probs=24.9

Q ss_pred             HhhHHHhccCCCCcHHHHHHHHHHhcCCC
Q 033363           69 GESWTHVTQLHGVGKYAADAFAIFCTGKW   97 (121)
Q Consensus        69 ~~~~~~L~~lpGIG~~tA~~vl~f~~~~~   97 (121)
                      ++.++.|.+|||||||+|.=+..+-+..+
T Consensus         8 ~~LI~~l~kLPGIG~KsA~Rla~~LL~~~   36 (199)
T d1vdda_           8 VSLIRELSRLPGIGPKSAQRLAFHLFEQP   36 (199)
T ss_dssp             HHHHHHHHTSTTCCHHHHHHHHHHHSSSC
T ss_pred             HHHHHHHHHCCCCCHHHHHHHHHHHHcCC
Confidence            34577899999999999999998888764

>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=94.41  E-value=0.027  Score=32.78  Aligned_cols=41  Identities=22%  Similarity=0.267  Sum_probs=33.3

Q ss_pred             HHHHHHHhCCCHHHHhcCCHHHHHHHHhhcCChhHHHHHHHHHH
Q 033363           21 VISDLFTLCPDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFS   64 (121)
Q Consensus        21 v~~~l~~~~pt~~~la~a~~~eL~~~i~~~Gl~~~Ka~~i~~~a   64 (121)
                      ...+|.+.|+|.+++.+++.+||.++   =|+...+|+.|++.-
T Consensus        25 ~a~~L~~~F~s~~~l~~As~eeL~~v---~GIG~~~A~~I~~~~   65 (70)
T d2bgwa1          25 TAERILERFGSLERFFTASKAEISKV---EGIGEKRAEEIKKIL   65 (70)
T ss_dssp             HHHHHHHHHSSHHHHTTCCHHHHHHS---TTCCHHHHHHHHHHH
T ss_pred             HHHHHHHHhCCHHHHHHcCHHHHHcC---CCCCHHHHHHHHHHH
Confidence            45577788999999999999997663   477778999998764

>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=94.29  E-value=0.044  Score=33.75  Aligned_cols=55  Identities=13%  Similarity=0.189  Sum_probs=37.5

Q ss_pred             HHhcCCHHHHHHHHhhcCChhHHHHHHHHHHHHHHH-hhHHHhccCCCCcHHHHHHHHH
Q 033363           34 TATEVDAEEIEKIISTLGLQKKRAPMIKRFSQEYLG-ESWTHVTQLHGVGKYAADAFAI   91 (121)
Q Consensus        34 ~la~a~~~eL~~~i~~~Gl~~~Ka~~i~~~a~~i~~-~~~~~L~~lpGIG~~tA~~vl~   91 (121)
                      .|-.++.++|.. +  =|++..+|+.|++.=+..-. .++++|..+||||+++.+-+.-
T Consensus        26 ~iNtAs~~eL~~-l--pgig~~~A~~II~yR~~~G~f~sledL~~V~Gi~~k~~eki~k   81 (91)
T d2edua1          26 LLNEGSARDLRS-L--QRIGPKKAQLIVGWRELHGPFSQVEDLERVEGITGKQMESFLK   81 (91)
T ss_dssp             HHHHSCHHHHHH-S--TTCCHHHHHHHHHHHHHHCCCSSGGGGGGSTTCCHHHHHHHHH
T ss_pred             ccccCCHHHHhh-C--CCCCHHHHHHHHHHHHHcCCCCCHHHHhcCCCCCHHHHHHHHH
Confidence            567777777654 2  36666688777664333111 4788999999999999886653

>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=94.29  E-value=0.012  Score=33.66  Aligned_cols=22  Identities=9%  Similarity=0.141  Sum_probs=18.4

Q ss_pred             HHhccCCCCcHHHHHHHHHHhcC
Q 033363           73 THVTQLHGVGKYAADAFAIFCTG   95 (121)
Q Consensus        73 ~~L~~lpGIG~~tA~~vl~f~~~   95 (121)
                      +-|.++||||++++..++. -|+
T Consensus         3 d~L~~iPGIg~~~~~~Ll~-~f~   24 (62)
T d2a1ja1           3 DFLLKMPGVNAKNCRSLMH-HVK   24 (62)
T ss_dssp             HHHHTSTTCCHHHHHHHHH-HCS
T ss_pred             hHHhcCCCCCHHHHHHHHH-Hhc
Confidence            4689999999999999985 444

>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=94.28  E-value=0.027  Score=31.59  Aligned_cols=39  Identities=21%  Similarity=0.153  Sum_probs=31.6

Q ss_pred             HHHHHHhCCCHHHHhcCCHHHHHHHHhhcCChhHHHHHHHHH
Q 033363           22 ISDLFTLCPDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRF   63 (121)
Q Consensus        22 ~~~l~~~~pt~~~la~a~~~eL~~~i~~~Gl~~~Ka~~i~~~   63 (121)
                      ...|.+.|.|.+++.+|+.+||.++   -|+...+|+.|.+.
T Consensus        15 a~~L~~~F~s~~~i~~As~eeL~~v---~GIg~~~A~~I~~~   53 (56)
T d1kfta_          15 RQMLLKYMGGLQGLRNASVEEIAKV---PGISQGLAEKIFWS   53 (56)
T ss_dssp             HHHHHHHHSCHHHHHHCCHHHHTTS---SSTTSHHHHHHHHH
T ss_pred             HHHHHHHhCCHHHHHHhhHHHHHhc---CCCCHHHHHHHHHH
Confidence            4578889999999999999997542   47777899988764

>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=94.21  E-value=0.033  Score=33.16  Aligned_cols=25  Identities=16%  Similarity=0.097  Sum_probs=19.4

Q ss_pred             hhHHHhccCCCCcHHHHHHHHHHhc
Q 033363           70 ESWTHVTQLHGVGKYAADAFAIFCT   94 (121)
Q Consensus        70 ~~~~~L~~lpGIG~~tA~~vl~f~~   94 (121)
                      .+.++|.++||||+..|..+.-|.-
T Consensus        48 A~~eeL~~i~GiG~~~A~~i~~~f~   72 (78)
T d2a1jb1          48 ASREDLALCPGLGPQKARRLFDVLH   72 (78)
T ss_dssp             CCHHHHHTSSSCCSHHHHHHHHHHH
T ss_pred             hhHHHHHHhhhhhHHHHHHHHHHHc
Confidence            4677888888888888888876653

>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=94.10  E-value=0.017  Score=34.34  Aligned_cols=21  Identities=24%  Similarity=0.197  Sum_probs=18.6

Q ss_pred             hHHHhccCCCCcHHHHHHHHH
Q 033363           71 SWTHVTQLHGVGKYAADAFAI   91 (121)
Q Consensus        71 ~~~~L~~lpGIG~~tA~~vl~   91 (121)
                      -.+.|.+++||||++|-.+|.
T Consensus         7 ~F~~Li~V~GIGpK~Al~iLs   27 (71)
T d1bvsa2           7 LFLALLSVSGVGPRLAMATLA   27 (71)
T ss_dssp             HHHHHHTSSSCCHHHHHHHHH
T ss_pred             HHHHHhccCCcCHHHHHHHHH
Confidence            457899999999999999985

>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=94.09  E-value=0.013  Score=36.11  Aligned_cols=53  Identities=13%  Similarity=0.146  Sum_probs=35.3

Q ss_pred             HhcCCHHHHHHHHhhcCChhHHHHHHHHHHHHHHH-hhHHHhccCCCCcHHHHHHHH
Q 033363           35 ATEVDAEEIEKIISTLGLQKKRAPMIKRFSQEYLG-ESWTHVTQLHGVGKYAADAFA   90 (121)
Q Consensus        35 la~a~~~eL~~~i~~~Gl~~~Ka~~i~~~a~~i~~-~~~~~L~~lpGIG~~tA~~vl   90 (121)
                      +-.|+.++|..   -.|+...+|+.|.+.=+.--. ..+++|.+++|||+++-+-+.
T Consensus        29 iN~As~~~L~~---lpGig~~~A~~Iv~~R~~~G~f~s~edL~~v~gi~~k~~e~i~   82 (90)
T d3bzka1          29 VNTASAALLAR---ISGLNSTLAQNIVAHRDANGAFRTRDELKKVSRLGEKTFEQAA   82 (90)
T ss_dssp             TTTCCHHHHTT---STTCCHHHHHHHHHHHHHHCSCSSSGGGGGSTTCCHHHHHHHH
T ss_pred             hhhCCHHHHhH---CCCCCHHHHHHHHHHHHHcCCCCCHHHHhhCCCCCHHHHHHhc
Confidence            55666676432   248888888888774322101 477899999999999877554

>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=94.04  E-value=0.023  Score=32.95  Aligned_cols=43  Identities=9%  Similarity=0.090  Sum_probs=33.3

Q ss_pred             HHHHH-hCCCHHHHhcCCHHHHHHHHhhcCChhHHHHHHHHHHHHHH
Q 033363           23 SDLFT-LCPDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQEYL   68 (121)
Q Consensus        23 ~~l~~-~~pt~~~la~a~~~eL~~~i~~~Gl~~~Ka~~i~~~a~~i~   68 (121)
                      .+|.+ .|.|.++++.+++++|.+   --||+..||..|++.|+.++
T Consensus        17 ~kL~~aG~~Tve~ia~~t~~~L~~---i~Gi~e~~a~KIi~~A~k~~   60 (64)
T d1szpa1          17 KKLRESGLHTAEAVAYAPRKDLLE---IKGISEAKADKLLNEAARLV   60 (64)
T ss_dssp             HHHHTTSCCSHHHHHHSCSHHHHT---STTCCHHHHHHHHHHHHHHS
T ss_pred             HHHHHcCCCcHHHHHhCCHHHHHH---cCCCCHHHHHHHHHHHHHHc
Confidence            34444 488999999999998754   36888999999999888763

>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=94.04  E-value=0.015  Score=33.71  Aligned_cols=22  Identities=23%  Similarity=0.211  Sum_probs=17.1

Q ss_pred             hHHHhccCCCCcHHHHHHHHHH
Q 033363           71 SWTHVTQLHGVGKYAADAFAIF   92 (121)
Q Consensus        71 ~~~~L~~lpGIG~~tA~~vl~f   92 (121)
                      +.++|.++||||+++|+.+..+
T Consensus        15 ~~~eL~~lpgig~~~A~~Iv~~   36 (65)
T d2duya1          15 SLEELMALPGIGPVLARRIVEG   36 (65)
T ss_dssp             CHHHHTTSTTCCHHHHHHHHHT
T ss_pred             CHHHHHHCCCCCHHHHHHHHHc
Confidence            5677888888888888887754

>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=93.74  E-value=0.019  Score=33.05  Aligned_cols=25  Identities=24%  Similarity=0.317  Sum_probs=20.5

Q ss_pred             hhHHHhccCCCCcHHHHHHHHHHhc
Q 033363           70 ESWTHVTQLHGVGKYAADAFAIFCT   94 (121)
Q Consensus        70 ~~~~~L~~lpGIG~~tA~~vl~f~~   94 (121)
                      ..++.|++++||||.+|.-+..-++
T Consensus         5 ~~l~~f~~I~GvGp~~A~~l~~~Gi   29 (60)
T d1jmsa3           5 KSFKLFTSVFGVGLKTAEKWFRMGF   29 (60)
T ss_dssp             HHHHHHHTSTTCCHHHHHHHHHTTC
T ss_pred             HHHHHHhccccccHHHHHHHHHhCC
Confidence            3578899999999999988865554

>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=93.59  E-value=0.047  Score=32.41  Aligned_cols=41  Identities=15%  Similarity=0.139  Sum_probs=32.7

Q ss_pred             HHHHHHhCCCHHHHhcCCHHHHHHHHhhcCChhHHHHHHHHHHH
Q 033363           22 ISDLFTLCPDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQ   65 (121)
Q Consensus        22 ~~~l~~~~pt~~~la~a~~~eL~~~i~~~Gl~~~Ka~~i~~~a~   65 (121)
                      ...|.+.|.|.+++.+|+.+||.++   =|+...+|+.|++..+
T Consensus        32 a~~L~~~F~s~~~i~~A~~eeL~~i---~GiG~~~A~~i~~~f~   72 (78)
T d2a1jb1          32 SQTLLTTFGSLEQLIAASREDLALC---PGLGPQKARRLFDVLH   72 (78)
T ss_dssp             HHHHHHHHSSHHHHHSCCHHHHHTS---SSCCSHHHHHHHHHHH
T ss_pred             HHHHHHHhCCcHHHHhhhHHHHHHh---hhhhHHHHHHHHHHHc
Confidence            4577788999999999999998653   4666689999987643

>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=93.58  E-value=0.071  Score=32.76  Aligned_cols=27  Identities=15%  Similarity=0.087  Sum_probs=22.8

Q ss_pred             HHHhhHHHhccCCCCcHHHHHHHHHHh
Q 033363           67 YLGESWTHVTQLHGVGKYAADAFAIFC   93 (121)
Q Consensus        67 i~~~~~~~L~~lpGIG~~tA~~vl~f~   93 (121)
                      +-..+.++|.++||||+++|..+..+=
T Consensus        27 iNtAs~~eL~~lpgig~~~A~~II~yR   53 (91)
T d2edua1          27 LNEGSARDLRSLQRIGPKKAQLIVGWR   53 (91)
T ss_dssp             HHHSCHHHHHHSTTCCHHHHHHHHHHH
T ss_pred             cccCCHHHHhhCCCCCHHHHHHHHHHH
Confidence            334688999999999999999998664

>d2fmpa2 a.60.12.1 (A:92-148) DNA polymerase beta {Human (Homo sapiens) [TaxId: 9606]}

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

Probab=93.54  E-value=0.023  Score=32.37  Aligned_cols=25  Identities=28%  Similarity=0.309  Sum_probs=20.6

Q ss_pred             hhHHHhccCCCCcHHHHHHHHHHhc
Q 033363           70 ESWTHVTQLHGVGKYAADAFAIFCT   94 (121)
Q Consensus        70 ~~~~~L~~lpGIG~~tA~~vl~f~~   94 (121)
                      .+++.|+++.||||.+|.-+.--++
T Consensus         4 ~~l~~l~~I~GvGp~~A~~l~~~Gi   28 (57)
T d2fmpa2           4 SSINFLTRVSGIGPSAARKFVDEGI   28 (57)
T ss_dssp             HHHHHHTTSTTCCHHHHHHHHHTTC
T ss_pred             hHHHHHhccccccHHHHHHHHHhCC
Confidence            3578899999999999999865544

>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=93.26  E-value=0.081  Score=32.34  Aligned_cols=23  Identities=13%  Similarity=0.156  Sum_probs=20.7

Q ss_pred             hHHHhccCCCCcHHHHHHHHHHh
Q 033363           71 SWTHVTQLHGVGKYAADAFAIFC   93 (121)
Q Consensus        71 ~~~~L~~lpGIG~~tA~~vl~f~   93 (121)
                      +.++|.++|||||.+|..+..+=
T Consensus        33 s~~~L~~lpGig~~~A~~Iv~~R   55 (90)
T d3bzka1          33 SAALLARISGLNSTLAQNIVAHR   55 (90)
T ss_dssp             CHHHHTTSTTCCHHHHHHHHHHH
T ss_pred             CHHHHhHCCCCCHHHHHHHHHHH
Confidence            67899999999999999988763

>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=93.15  E-value=0.03  Score=33.35  Aligned_cols=21  Identities=24%  Similarity=0.249  Sum_probs=18.6

Q ss_pred             hHHHhccCCCCcHHHHHHHHH
Q 033363           71 SWTHVTQLHGVGKYAADAFAI   91 (121)
Q Consensus        71 ~~~~L~~lpGIG~~tA~~vl~   91 (121)
                      -.+.|.+++||||++|=.+|.
T Consensus         8 lF~~Li~V~GIGpk~Al~iLs   28 (73)
T d1ixra1           8 LFELLLSVSGVGPKVALALLS   28 (73)
T ss_dssp             HHHHHHSSSCCCHHHHHHHHH
T ss_pred             HHHHHhccCCcCHHHHHHHHH
Confidence            457899999999999999985

>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=93.13  E-value=0.026  Score=34.01  Aligned_cols=21  Identities=24%  Similarity=0.257  Sum_probs=18.7

Q ss_pred             hHHHhccCCCCcHHHHHHHHH
Q 033363           71 SWTHVTQLHGVGKYAADAFAI   91 (121)
Q Consensus        71 ~~~~L~~lpGIG~~tA~~vl~   91 (121)
                      ..+.|.+++||||++|=.+|.
T Consensus         7 ~F~~Li~V~GIGpK~Al~iLs   27 (78)
T d1cuka2           7 LFKELIKTNGVGPKLALAILS   27 (78)
T ss_dssp             HHHHHHHSSSCCHHHHHHHHH
T ss_pred             HHHHHHccCCccHHHHHHHHH
Confidence            457899999999999999985

>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=92.25  E-value=0.089  Score=30.36  Aligned_cols=41  Identities=20%  Similarity=0.222  Sum_probs=32.8

Q ss_pred             HHHHHHHhCCCHHHHhcCCHHHHHHHHhhcCChhHHHHHHHHHH
Q 033363           21 VISDLFTLCPDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFS   64 (121)
Q Consensus        21 v~~~l~~~~pt~~~la~a~~~eL~~~i~~~Gl~~~Ka~~i~~~a   64 (121)
                      .-.+|.+.|.|++.+.+++.+||.+   --|+...+|+.|.+.-
T Consensus        22 ~a~~L~~~f~s~~~i~~As~eeL~~---i~GIG~~~A~~I~~~~   62 (68)
T d1x2ia1          22 LARRLLKHFGSVERVFTASVAELMK---VEGIGEKIAKEIRRVI   62 (68)
T ss_dssp             HHHHHHHHHCSHHHHHHCCHHHHTT---STTCCHHHHHHHHHHH
T ss_pred             HHHHHHHHcCCHHHHHHhHHHHHHh---CCCcCHHHHHHHHHHH
Confidence            4456778899999999999999654   2477888999988754

>d2axtu1 a.60.12.2 (U:37-134) Photosystem II 12 kDa extrinsic protein PsbU {Thermosynechococcus elongatus [TaxId: 146786]}

class: All alpha proteins
fold: SAM domain-like
superfamily: PsbU/PolX domain-like
family: PsbU-like
domain: Photosystem II 12 kDa extrinsic protein PsbU
species: Thermosynechococcus elongatus [TaxId: 146786]

Probab=92.08  E-value=0.028  Score=35.35  Aligned_cols=21  Identities=14%  Similarity=0.052  Sum_probs=15.5

Q ss_pred             hHHHhccCCCCcHHHHHHHHH
Q 033363           71 SWTHVTQLHGVGKYAADAFAI   91 (121)
Q Consensus        71 ~~~~L~~lpGIG~~tA~~vl~   91 (121)
                      +.++|.+||||||..|..+.-
T Consensus        25 s~~eL~~lpGIg~~~A~~Iv~   45 (98)
T d2axtu1          25 NIAAFIQYRGLYPTLAKLIVK   45 (98)
T ss_dssp             CGGGGTTSTTCTHHHHHHHHH
T ss_pred             cHHHHHHhhhhcHHHHHHHHH
Confidence            456778888888888877763

>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=91.64  E-value=0.054  Score=30.70  Aligned_cols=23  Identities=13%  Similarity=0.147  Sum_probs=18.7

Q ss_pred             hHHHhccCCCCcHHHHHHHHHHh
Q 033363           71 SWTHVTQLHGVGKYAADAFAIFC   93 (121)
Q Consensus        71 ~~~~L~~lpGIG~~tA~~vl~f~   93 (121)
                      .++.++++.||||++|.-+..-+
T Consensus         6 ~l~~ft~I~GvGp~~A~~l~~~G   28 (57)
T d2bcqa2           6 VLELFSNIWGAGTKTAQMWYQQG   28 (57)
T ss_dssp             HHHHHHTSTTCCHHHHHHHHHTT
T ss_pred             HHHHHhccccccHHHHHHHHHhC
Confidence            46789999999999999765443

>d2duya1 a.60.2.7 (A:11-75) Uncharacterized protein TTHA1967 {Thermus thermophilus [TaxId: 274]}

class: All alpha proteins
fold: SAM domain-like
superfamily: RuvA domain 2-like
family: ComEA-like
domain: Uncharacterized protein TTHA1967
species: Thermus thermophilus [TaxId: 274]

Probab=91.29  E-value=0.03  Score=32.37  Aligned_cols=51  Identities=18%  Similarity=0.229  Sum_probs=36.4

Q ss_pred             HHhcCCHHHHHHHHhhcCChhHHHHHHHHHHHHHHHhhHHHhccCCCCcHHHHHHHH
Q 033363           34 TATEVDAEEIEKIISTLGLQKKRAPMIKRFSQEYLGESWTHVTQLHGVGKYAADAFA   90 (121)
Q Consensus        34 ~la~a~~~eL~~~i~~~Gl~~~Ka~~i~~~a~~i~~~~~~~L~~lpGIG~~tA~~vl   90 (121)
                      ++-.|+.++|..   --|++...|+.|.+.=. +  ...++|.+++|||+++.+-+.
T Consensus        10 diNtA~~~eL~~---lpgig~~~A~~Iv~~R~-f--~s~edL~~v~gi~~~~~~~i~   60 (65)
T d2duya1          10 SLNEASLEELMA---LPGIGPVLARRIVEGRP-Y--ARVEDLLKVKGIGPATLERLR   60 (65)
T ss_dssp             ETTTCCHHHHTT---STTCCHHHHHHHHHTCC-C--SSGGGGGGSTTCCHHHHHHHG
T ss_pred             ccccCCHHHHHH---CCCCCHHHHHHHHHcCC-C--CCHHHHHhCCCCCHHHHHHHH
Confidence            355678887532   24888788887775321 1  578999999999999987653

>d1b22a_ a.60.4.1 (A:) DNA repair protein Rad51, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

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: Human (Homo sapiens) [TaxId: 9606]

Probab=91.26  E-value=0.027  Score=33.23  Aligned_cols=38  Identities=11%  Similarity=0.093  Sum_probs=31.3

Q ss_pred             hCCCHHHHhcCCHHHHHHHHhhcCChhHHHHHHHHHHHHHH
Q 033363           28 LCPDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQEYL   68 (121)
Q Consensus        28 ~~pt~~~la~a~~~eL~~~i~~~Gl~~~Ka~~i~~~a~~i~   68 (121)
                      -|.|.++|+.+++++|.+   --||+..||+.|++.|+.++
T Consensus        30 G~~Tv~~i~~at~~~L~~---i~G~~e~~A~KIi~~a~k~~   67 (70)
T d1b22a_          30 GFHTVEAVAYAPKKELIN---IKGISEAKADKILAEAAKLV   67 (70)
T ss_dssp             CCSSGGGBTSSBHHHHHT---TTTCSTTHHHHHHHHHHHHS
T ss_pred             CcchHHHHHhCCHHHHHH---cCCCCHHHHHHHHHHHHHHc
Confidence            588999999999998754   47888899999999888764

>d1doqa_ a.60.3.1 (A:) C-terminal domain of RNA polymerase alpha subunit {Thermus thermophilus [TaxId: 274]}

class: All alpha proteins
fold: SAM domain-like
superfamily: C-terminal domain of RNA polymerase alpha subunit
family: C-terminal domain of RNA polymerase alpha subunit
domain: C-terminal domain of RNA polymerase alpha subunit
species: Thermus thermophilus [TaxId: 274]

Probab=91.08  E-value=0.17  Score=29.45  Aligned_cols=41  Identities=17%  Similarity=0.312  Sum_probs=26.4

Q ss_pred             hcCChhHHHHHHHHHH-----HHHHHhhHHHhccCCCCcHHHHHHHH
Q 033363           49 TLGLQKKRAPMIKRFS-----QEYLGESWTHVTQLHGVGKYAADAFA   90 (121)
Q Consensus        49 ~~Gl~~~Ka~~i~~~a-----~~i~~~~~~~L~~lpGIG~~tA~~vl   90 (121)
                      .++|+ .|+.+..+-+     ..++.-+.++|.++||+|+++.+-|.
T Consensus        12 ~L~LS-~R~~N~L~~~gI~tv~dL~~~s~~dLl~i~n~G~ksl~EI~   57 (69)
T d1doqa_          12 ELGLS-TRVLHSLKEEGIESVRALLALNLKDLKNIPGIGERSLEEIK   57 (69)
T ss_dssp             HHTCC-HHHHHHHHHTTCCSHHHHHHSCHHHHTTSTTCCHHHHHHHH
T ss_pred             HcCCC-HHHHHHHHHcCCccHHHHHHCCHHHHHhCCCCCHHHHHHHH
Confidence            35676 4544433321     22223478899999999999988765

>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=90.09  E-value=0.057  Score=29.39  Aligned_cols=25  Identities=24%  Similarity=0.380  Sum_probs=20.7

Q ss_pred             HHhccCCCCcHHHHHHHHHHhcCCCC
Q 033363           73 THVTQLHGVGKYAADAFAIFCTGKWD   98 (121)
Q Consensus        73 ~~L~~lpGIG~~tA~~vl~f~~~~~~   98 (121)
                      .+|++-.|||++||+-++ .+||.|.
T Consensus         2 aeltkkegvgrktaerll-rafgnpe   26 (55)
T d2csba3           2 AELTKKEGVGRKTAERLL-RAFGNPE   26 (55)
T ss_dssp             HHHHTSTTCCHHHHHHHH-HHHSSHH
T ss_pred             hhhhhhccccHhHHHHHH-HHhCCHH
Confidence            578889999999999765 7888764

>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=88.86  E-value=0.068  Score=33.47  Aligned_cols=20  Identities=15%  Similarity=0.052  Sum_probs=14.8

Q ss_pred             hccCCCCcHHHHHHHHHHhcC
Q 033363           75 VTQLHGVGKYAADAFAIFCTG   95 (121)
Q Consensus        75 L~~lpGIG~~tA~~vl~f~~~   95 (121)
                      .-.+|||||+||--++ --+|
T Consensus        19 ~pGV~GIGpktA~klI-k~~g   38 (108)
T d1a77a1          19 PGGVKGIGFKRAYELV-RSGV   38 (108)
T ss_dssp             TTCSTTCCHHHHHHHH-HTTC
T ss_pred             CCCCCCcCHHHHHHHH-HHcC
Confidence            3479999999998754 3444

>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=88.54  E-value=0.14  Score=31.94  Aligned_cols=53  Identities=15%  Similarity=0.115  Sum_probs=39.0

Q ss_pred             HHHhcCCHHHHHHHHhhcCChhHHHHHHHHHHHHHHH--hhHHHhccCCCCcHHHHHHHHHHh
Q 033363           33 KTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQEYLG--ESWTHVTQLHGVGKYAADAFAIFC   93 (121)
Q Consensus        33 ~~la~a~~~eL~~~i~~~Gl~~~Ka~~i~~~a~~i~~--~~~~~L~~lpGIG~~tA~~vl~f~   93 (121)
                      =++-.|+.++|.. |  -|++..+|+.|.+     ..  ...++|.+++|||+++.+.+.-+.
T Consensus        19 idlN~As~~eL~~-l--pGIg~~~A~~Iv~-----~gpf~s~edL~~V~GIg~~~~e~lk~yl   73 (98)
T d2axtu1          19 IDLNNTNIAAFIQ-Y--RGLYPTLAKLIVK-----NAPYESVEDVLNIPGLTERQKQILRENL   73 (98)
T ss_dssp             EESSSSCGGGGTT-S--TTCTHHHHHHHHH-----SCCCSSGGGGGGCTTCCTTHHHHHHHHG
T ss_pred             eecccccHHHHHH-h--hhhcHHHHHHHHH-----cCCcCCHHHHhhCCCCCHHHHHHHHHHH
Confidence            3455677777644 2  4777788888863     11  478999999999999999887754

>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=87.47  E-value=0.13  Score=32.02  Aligned_cols=19  Identities=21%  Similarity=0.170  Sum_probs=15.2

Q ss_pred             HHhccCCCCcHHHHHHHHH
Q 033363           73 THVTQLHGVGKYAADAFAI   91 (121)
Q Consensus        73 ~~L~~lpGIG~~tA~~vl~   91 (121)
                      +....+|||||+||--++.
T Consensus        16 Dn~pGV~GIG~ktA~kli~   34 (105)
T d1rxwa1          16 DYNEGVKGVGVKKALNYIK   34 (105)
T ss_dssp             TTBCCCTTCCHHHHHHHHH
T ss_pred             CCCCCCCCcCHHHHHHHHH
Confidence            4466899999999987664

>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=87.07  E-value=0.32  Score=27.71  Aligned_cols=28  Identities=11%  Similarity=0.112  Sum_probs=22.6

Q ss_pred             HHHhhHHHhccCCCCcHHHHHHHHHHhc
Q 033363           67 YLGESWTHVTQLHGVGKYAADAFAIFCT   94 (121)
Q Consensus        67 i~~~~~~~L~~lpGIG~~tA~~vl~f~~   94 (121)
                      +..-+.++|.+++|+|+.+|+-+..-+-
T Consensus        30 ia~~t~~~L~~i~Gi~e~~a~KIi~~A~   57 (64)
T d1szpa1          30 VAYAPRKDLLEIKGISEAKADKLLNEAA   57 (64)
T ss_dssp             HHHSCSHHHHTSTTCCHHHHHHHHHHHH
T ss_pred             HHhCCHHHHHHcCCCCHHHHHHHHHHHH
Confidence            3445788999999999999998876553

>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=85.19  E-value=0.19  Score=31.41  Aligned_cols=22  Identities=9%  Similarity=0.158  Sum_probs=17.8

Q ss_pred             hhHHHhccCCCCcHHHHHHHHH
Q 033363           70 ESWTHVTQLHGVGKYAADAFAI   91 (121)
Q Consensus        70 ~~~~~L~~lpGIG~~tA~~vl~   91 (121)
                      +.-+-+-.+||||+|||.-++.
T Consensus        16 D~sDnipGV~GiG~KtA~kli~   37 (105)
T d1xo1a1          16 DLGDNIRGVEGIGAKRGYNIIR   37 (105)
T ss_dssp             BGGGTBCCCTTCCHHHHHHHHH
T ss_pred             CcccCCcCcCCcCHHHHHHHHH
Confidence            3456688999999999988765

>d1z3eb1 a.60.3.1 (B:245-311) C-terminal domain of RNA polymerase alpha subunit {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: SAM domain-like
superfamily: C-terminal domain of RNA polymerase alpha subunit
family: C-terminal domain of RNA polymerase alpha subunit
domain: C-terminal domain of RNA polymerase alpha subunit
species: Bacillus subtilis [TaxId: 1423]

Probab=83.79  E-value=1.3  Score=25.34  Aligned_cols=43  Identities=14%  Similarity=0.201  Sum_probs=29.2

Q ss_pred             HhhcCChhHHHHHHHHHHH-----HHHHhhHHHhccCCCCcHHHHHHHH
Q 033363           47 ISTLGLQKKRAPMIKRFSQ-----EYLGESWTHVTQLHGVGKYAADAFA   90 (121)
Q Consensus        47 i~~~Gl~~~Ka~~i~~~a~-----~i~~~~~~~L~~lpGIG~~tA~~vl   90 (121)
                      |..++|+ .|+.+..+-+.     .++.-+.++|.++|+.|+++.+=|.
T Consensus         9 I~~L~LS-~R~~N~Lk~~~I~tv~dL~~~s~~dLl~~~nfG~kSl~EIk   56 (67)
T d1z3eb1           9 IEELDLS-VRSYNCLKRAGINTVQELANKTEEDMMKVRNLGRKSLEEVK   56 (67)
T ss_dssp             GGGSCCB-HHHHHHHHHTTCCBHHHHHTSCHHHHHTSTTCCHHHHHHHH
T ss_pred             HHHhcCC-HHHHHHHHHcCCcCHHHHHHCCHHHHHhCCCCchhhHHHHH
Confidence            5568888 56555544322     2223478999999999999987654

>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=83.36  E-value=0.26  Score=31.74  Aligned_cols=19  Identities=16%  Similarity=0.226  Sum_probs=15.7

Q ss_pred             HHhccCCCCcHHHHHHHHH
Q 033363           73 THVTQLHGVGKYAADAFAI   91 (121)
Q Consensus        73 ~~L~~lpGIG~~tA~~vl~   91 (121)
                      +.+-.+||||++||--++.
T Consensus        16 D~~pgv~gIG~ktA~kli~   34 (140)
T d1ul1x1          16 DYCESIRGIGPKRAVDLIQ   34 (140)
T ss_dssp             SSSCCCTTCCHHHHHHHHH
T ss_pred             CCCCCCCCccHHHHHHHHH
Confidence            4567999999999987764

>d1nkua_ a.96.1.4 (A:) 3-Methyladenine DNA glycosylase I (Tag) {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA-glycosylase
superfamily: DNA-glycosylase
family: 3-Methyladenine DNA glycosylase I (Tag)
domain: 3-Methyladenine DNA glycosylase I (Tag)
species: Escherichia coli [TaxId: 562]

Probab=82.53  E-value=5.3  Score=26.99  Aligned_cols=48  Identities=15%  Similarity=0.299  Sum_probs=37.6

Q ss_pred             HHHHHHhC--CCHHHHhcCCHHHHHHHHhhcCC--hhHHHHHHHHHHHHHHH
Q 033363           22 ISDLFTLC--PDAKTATEVDAEEIEKIISTLGL--QKKRAPMIKRFSQEYLG   69 (121)
Q Consensus        22 ~~~l~~~~--pt~~~la~a~~~eL~~~i~~~Gl--~~~Ka~~i~~~a~~i~~   69 (121)
                      .+.|.+.|  -+|+.++..++++|++++..-|+  .+.|.+.++.=|+.+.+
T Consensus        53 r~~fr~aF~~Fd~~~vA~~~e~~ie~Ll~d~~IIRNr~KI~Avi~NAr~~l~  104 (187)
T d1nkua_          53 RENYRACFHQFDPVKVAAMQEEDVERLVQDAGIIRHRGKIQAIIGNARAYLQ  104 (187)
T ss_dssp             HHHHHHHHTTTCHHHHHTCCHHHHHHHHTCCSSCCCHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHhCCCHHHHHcCCHHHHHHHhccCCeeechHHHHHHHHHHHHHHH
Confidence            34444444  48999999999999999998888  55777788888887776

>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=82.49  E-value=0.22  Score=31.76  Aligned_cols=16  Identities=19%  Similarity=0.212  Sum_probs=12.9

Q ss_pred             ccCCCCcHHHHHHHHH
Q 033363           76 TQLHGVGKYAADAFAI   91 (121)
Q Consensus        76 ~~lpGIG~~tA~~vl~   91 (121)
                      ..+|||||+||=-++-
T Consensus        20 ~gI~GIGpktAlklik   35 (120)
T d1b43a1          20 GGIKGIGLKKALEIVR   35 (120)
T ss_dssp             TCSTTCCHHHHHHHHH
T ss_pred             ccCCCcCHHHHHHHHH
Confidence            4799999999976543

>d2e1fa1 a.60.8.1 (A:1142-1235) Werner syndrome ATP-dependent helicase, WRN {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: SAM domain-like
superfamily: HRDC-like
family: HRDC domain from helicases
domain: Werner syndrome ATP-dependent helicase, WRN
species: Human (Homo sapiens) [TaxId: 9606]

Probab=80.90  E-value=0.49  Score=28.74  Aligned_cols=31  Identities=13%  Similarity=0.215  Sum_probs=22.3

Q ss_pred             HHHHHHHHHHHHhhHHHhccCCCCcHHHHHHH
Q 033363           58 PMIKRFSQEYLGESWTHVTQLHGVGKYAADAF   89 (121)
Q Consensus        58 ~~i~~~a~~i~~~~~~~L~~lpGIG~~tA~~v   89 (121)
                      +.|.++|+. .-.+.++|.+++|||++.++-+
T Consensus        41 ~~L~~ia~~-~P~t~~eL~~I~G~g~~k~~ky   71 (94)
T d2e1fa1          41 KILVDMAKM-RPTTVENVKRIDGVSEGKAAML   71 (94)
T ss_dssp             HHHHHHHHH-CCCSHHHHTTSTTCCHHHHHHT
T ss_pred             HHHHHHHHc-CCCCHHHHcCCCCCCHHHHHHH
Confidence            455555553 2258999999999999987643