Citrus Sinensis ID: 035092

Local Sequence Feature Prediction

Prediction and (Method)Result
Residue Number Marker
Protein Sequence ?
Secondary Structure (PSIPRED) ?
Secondary Structure Prediction (SSPRO) ?
Coil and Loop (DISEMBL) ?
Flexible Loop (DISEMBL) ?
Low Complexity Region (SEG) ?
Disordered region (IsUnstruct) ?
Disordered Region (DISOPRED) ?
Disordered Region (DISEMBL) ?
Disordered Region (DISPRO) ?
Transmembrane Helix (TMHMM) ?
Transmembrane Helix (HMMTOP) ?
Transmembrane Helix (MEMSAT) ?
TM Helix, Signal Peptide (MEMSAT_SVM) ?
TM Helix, Signal Peptide (Phobius) ?
Signal Peptide (SignalP HMM Mode) ?
Signal Peptide (SignalP NN Mode) ?
Coiled Coils (COILS) ?
Positional Conservation ?
 
--------10--------20--------30--------40--------50--------60--------70---
MHFYFINAGVEGTGDVCAVQLITKFGSLENLLQCVYQVEEERTRKALITFADQAVLSKNLVIIIAFSSTCYLV
cEEEEEccccccccHHHHHHHHHHHccHHHHHHHHHcccHHHHHHHHHHcHHHHHHHHHHHHHHHcccccccc
cEEEEEccccccccHHHHHHHHHHcccHHHHHHcHHHccHHHHHHHHHHHHHHHHHHHHHHHHHHHcccEEcc
MHFYFInagvegtgdVCAVQLITKFGSLENLLQCVYQVEEERTRKALITFADQAVLSKNLVIIIAFSSTCYLV
MHFYFINAGVEGTGDVCAVQLITKFGSLENLLQCVYQVEEERTRKALITfadqavlskNLVIIIAFSSTCYLV
MHFYFINAGVEGTGDVCAVQLITKFGSLENLLQCVYQVEEERTRKALITFADQAVLSKNLVIIIAFSSTCYLV
**FYFINAGVEGTGDVCAVQLITKFGSLENLLQCVYQVEEERTRKALITFADQAVLSKNLVIIIAFSSTCYL*
MHFYFINAGVEGTGDVCAVQLITKFGSLENLLQCVY************TFADQAVLSKNLVIIIAFSSTCYLV
MHFYFINAGVEGTGDVCAVQLITKFGSLENLLQCVYQVEEERTRKALITFADQAVLSKNLVIIIAFSSTCYLV
MHFYFINAGVEGTGDVCAVQLITKFGSLENLLQCVYQVEEERTRKALITFADQAVLSKNLVIIIAFSSTCYLV
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MHFYFINAGVEGTGDVCAVQLITKFGSLENLLQCVYQVEEERTRKALITFADQAVLSKNLVIIIAFSSTCYLV
no confident homologs detected

Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST ?

Original result of BLAST against SWISS-PROT Database

ID ?Alignment graph ?Length ? Definition ? RBH(Q2H) ? RBH(H2Q) ? Q cover ? H cover ? Identity ? E-value ?
Query73 2.2.26 [Sep-21-2011]
O34996 880 DNA polymerase I OS=Bacil yes no 0.767 0.063 0.375 4e-05
P52026 876 DNA polymerase I OS=Geoba N/A no 0.753 0.062 0.381 9e-05
Q04957 877 DNA polymerase I OS=Bacil N/A no 0.753 0.062 0.363 0.0005
>sp|O34996|DPO1_BACSU DNA polymerase I OS=Bacillus subtilis (strain 168) GN=polA PE=3 SV=1 Back     alignment and function desciption
 Score = 46.6 bits (109), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 21/56 (37%), Positives = 37/56 (66%)

Query: 9   GVEGTGDVCAVQLITKFGSLENLLQCVYQVEEERTRKALITFADQAVLSKNLVIII 64
           GV G G+  A++L+ +F S+E LL+ + +V  ++ ++ L  F DQA++SK L  I+
Sbjct: 194 GVPGVGEKTAIKLLKQFDSVEKLLESIDEVSGKKLKEKLEEFKDQALMSKELATIM 249
In addition to polymerase activity, this DNA polymerase exhibits 3' to 5' and 5' to 3' exonuclease activity.
Bacillus subtilis (strain 168) (taxid: 224308)
EC: 2EC: .EC: 7EC: .EC: 7EC: .EC: 7
>sp|P52026|DPO1_GEOSE DNA polymerase I OS=Geobacillus stearothermophilus GN=polA PE=1 SV=2 Back     alignment and function description
>sp|Q04957|DPO1_BACCA DNA polymerase I OS=Bacillus caldotenax GN=polA PE=1 SV=1 Back     alignment and function description

Close Homologs in the Non-Redundant Database Detected by BLAST ?

Original result of BLAST against Nonredundant Database

GI ?Alignment Graph ?Length ? Definition ? Q cover ? H cover ? Identity ? E-value ?
Query73
147858394 734 hypothetical protein VITISV_010447 [Viti 0.863 0.085 0.682 5e-16
359478321 441 PREDICTED: DNA polymerase I-like [Vitis 0.753 0.124 0.781 6e-16
255579458 246 DNA polymerase I, putative [Ricinus comm 0.753 0.223 0.672 5e-12
357113266 419 PREDICTED: DNA polymerase I-like [Brachy 0.753 0.131 0.636 2e-11
449453197 461 PREDICTED: DNA polymerase I-like [Cucumi 0.753 0.119 0.636 2e-11
226530274 422 DNA polymerase I [Zea mays] gi|195650551 0.753 0.130 0.581 3e-11
218192373 421 hypothetical protein OsI_10602 [Oryza sa 0.753 0.130 0.618 8e-11
108706960 416 5'-3' exonuclease, N-terminal resolvase- 0.753 0.132 0.618 8e-11
115451687 421 Os03g0227300 [Oryza sativa Japonica Grou 0.753 0.130 0.618 8e-11
24421685 443 Unknown protein [Oryza sativa Japonica G 0.753 0.124 0.618 8e-11
>gi|147858394|emb|CAN81408.1| hypothetical protein VITISV_010447 [Vitis vinifera] Back     alignment and taxonomy information
 Score = 88.2 bits (217), Expect = 5e-16,   Method: Composition-based stats.
 Identities = 43/63 (68%), Positives = 51/63 (80%)

Query: 1   MHFYFINAGVEGTGDVCAVQLITKFGSLENLLQCVYQVEEERTRKALITFADQAVLSKNL 60
           +    +  GVEG G+V AVQLITKFG+LENLLQCV QV+EER RKALI+ ADQAVLSKNL
Sbjct: 611 LRIVLLGNGVEGIGNVHAVQLITKFGTLENLLQCVDQVQEERIRKALISGADQAVLSKNL 670

Query: 61  VII 63
            ++
Sbjct: 671 ALL 673

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota
>gi|359478321|ref|XP_002275974.2| PREDICTED: DNA polymerase I-like [Vitis vinifera] gi|296084279|emb|CBI24667.3| unnamed protein product [Vitis vinifera] Back     alignment and taxonomy information
>gi|255579458|ref|XP_002530572.1| DNA polymerase I, putative [Ricinus communis] gi|223529871|gb|EEF31802.1| DNA polymerase I, putative [Ricinus communis] Back     alignment and taxonomy information
>gi|357113266|ref|XP_003558425.1| PREDICTED: DNA polymerase I-like [Brachypodium distachyon] Back     alignment and taxonomy information
>gi|449453197|ref|XP_004144345.1| PREDICTED: DNA polymerase I-like [Cucumis sativus] Back     alignment and taxonomy information
>gi|226530274|ref|NP_001151880.1| DNA polymerase I [Zea mays] gi|195650551|gb|ACG44743.1| DNA polymerase I [Zea mays] Back     alignment and taxonomy information
>gi|218192373|gb|EEC74800.1| hypothetical protein OsI_10602 [Oryza sativa Indica Group] Back     alignment and taxonomy information
>gi|108706960|gb|ABF94755.1| 5'-3' exonuclease, N-terminal resolvase-like domain containing protein, expressed [Oryza sativa Japonica Group] Back     alignment and taxonomy information
>gi|115451687|ref|NP_001049444.1| Os03g0227300 [Oryza sativa Japonica Group] gi|108706959|gb|ABF94754.1| 5'-3' exonuclease, N-terminal resolvase-like domain containing protein, expressed [Oryza sativa Japonica Group] gi|113547915|dbj|BAF11358.1| Os03g0227300 [Oryza sativa Japonica Group] gi|215704203|dbj|BAG93043.1| unnamed protein product [Oryza sativa Japonica Group] gi|222624502|gb|EEE58634.1| hypothetical protein OsJ_10000 [Oryza sativa Japonica Group] Back     alignment and taxonomy information
>gi|24421685|gb|AAN60992.1| Unknown protein [Oryza sativa Japonica Group] Back     alignment and taxonomy information

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST ?

Original result of BLAST against Gene Ontology (AMIGO)

ID ? Alignment graph ? Length ? Definition ? Q cover ? H cover ? Identity ? E-value ?
Query73
TAIR|locus:2083775448 AT3G52050 [Arabidopsis thalian 0.753 0.122 0.527 6.9e-10
TIGR_CMR|ECH_0080 944 ECH_0080 "DNA polymerase I" [E 0.753 0.058 0.4 1.1e-05
TIGR_CMR|APH_0001 853 APH_0001 "DNA polymerase I" [A 0.726 0.062 0.433 2.1e-05
TIGR_CMR|BA_4831 877 BA_4831 "DNA polymerase I" [Ba 0.767 0.063 0.375 0.00012
UNIPROTKB|Q0C2B4 929 polA "DNA polymerase I" [Hypho 0.726 0.057 0.396 0.00044
TAIR|locus:2083775 AT3G52050 [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
 Score = 150 (57.9 bits), Expect = 6.9e-10, P = 6.9e-10
 Identities = 29/55 (52%), Positives = 45/55 (81%)

Query:     9 GVEGTGDVCAVQLITKFGSLENLLQCVYQVEEERTRKALITFADQAVLSKNLVII 63
             GV+G G+V AV+LI++FG+LENLLQ V +++E + +++LI  ADQA+LSK L ++
Sbjct:   332 GVDGIGNVHAVELISRFGTLENLLQSVDEIKEGKIKESLIASADQAILSKKLALL 386
GO:0003677 "DNA binding" evidence=IEA
GO:0003824 "catalytic activity" evidence=IEA;ISS
GO:0005634 "nucleus" evidence=ISM
GO:0008409 "5'-3' exonuclease activity" evidence=IEA
TIGR_CMR|ECH_0080 ECH_0080 "DNA polymerase I" [Ehrlichia chaffeensis str. Arkansas (taxid:205920)] Back     alignment and assigned GO terms
TIGR_CMR|APH_0001 APH_0001 "DNA polymerase I" [Anaplasma phagocytophilum HZ (taxid:212042)] Back     alignment and assigned GO terms
TIGR_CMR|BA_4831 BA_4831 "DNA polymerase I" [Bacillus anthracis str. Ames (taxid:198094)] Back     alignment and assigned GO terms
UNIPROTKB|Q0C2B4 polA "DNA polymerase I" [Hyphomonas neptunium ATCC 15444 (taxid:228405)] Back     alignment and assigned GO terms

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 ?Alignment Graph ?Length ? Definition ? E-value ?
Query73
cd0989873 cd09898, H3TH_53EXO, H3TH domain of the 5'-3' exon 1e-11
PRK05755 880 PRK05755, PRK05755, DNA polymerase I; Provisional 3e-10
smart00475259 smart00475, 53EXOc, 5'-3' exonuclease 7e-10
TIGR00593 887 TIGR00593, pola, DNA polymerase I 3e-08
pfam01367100 pfam01367, 5_3_exonuc, 5'-3' exonuclease, C-termin 8e-08
COG0258310 COG0258, Exo, 5'-3' exonuclease (including N-termi 1e-06
PRK09482256 PRK09482, PRK09482, flap endonuclease-like protein 1e-05
cd0008071 cd00080, H3TH_StructSpec-5'-nucleases, H3TH domain 2e-05
PRK14976281 PRK14976, PRK14976, 5'-3' exonuclease; Provisional 5e-04
>gnl|CDD|188618 cd09898, H3TH_53EXO, H3TH domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs Back     alignment and domain information 
 Score = 53.9 bits (131), Expect = 1e-11
 Identities = 19/55 (34%), Positives = 32/55 (58%), Gaps = 1/55 (1%)

Query: 9  GVEGTGDVCAVQLITKFGSLENLLQCVYQVEEERTRKALITFADQAVLSKNLVII 63
          GV G G   A +L+ ++GSLEN+L  +    + + R+ L    +QA+LS+ L  +
Sbjct: 20 GVPGIGPKTAAKLLQEYGSLENILANL-DELKGKLREKLEENKEQALLSRKLATL 73

H3TH (helix-3-turn-helix) domains of the 5'-3' exonuclease (53EXO) of mutli-domain DNA polymerase I and single domain protein homologs are included in this family. Taq DNA polymerase I contains a polymerase domain for synthesizing a new DNA strand and a 53EXO domain for cleaving RNA primers or damaged DNA strands. Taq's 53EXO recognizes and endonucleolytically cleaves a structure-specific DNA substrate that has a bifurcated downstream duplex and an upstream template-primer duplex that overlaps the downstream duplex by 1 bp. The 53EXO cleaves the unpaired 5'-arm of the overlap flap DNA substrate. 5'-3' exonucleases are members of the structure-specific, 5' nuclease family that catalyzes hydrolysis of DNA duplex-containing nucleic acid structures during DNA replication, repair, and recombination. These nucleases contain a PIN (PilT N terminus) domain with a helical arch/clamp region/I domain (not included here) and inserted within the PIN domain is an atypical helix-hairpin-helix-2 (HhH2)-like region. This atypical HhH2 region, the H3TH domain, has an extended loop with at least three turns between the first two helices, and only three of the four helices appear to be conserved. Both the H3TH domain and the helical arch/clamp region are involved in DNA binding. Studies suggest that a glycine-rich loop in the H3TH domain contacts the phosphate backbone of the template strand in the downstream DNA duplex. The nucleases within this family have a carboxylate rich active site that is involved in binding essential divalent metal ion cofactors (i. e., Mg2+ or Mn2+ or Zn2+) required for nuclease activity. The first metal binding site is composed entirely of Asp/Glu residues from the PIN domain, whereas, the second metal binding site is composed generally of two Asp residues from the PIN domain and two Asp residues from the H3TH domain. Together with the helical arch and network of amino acids interacting with metal binding ions, the H3TH region defines a positively charged active-site DNA-binding groove in structure-specific 5' nucleases. Length = 73
>gnl|CDD|235591 PRK05755, PRK05755, DNA polymerase I; Provisional Back     alignment and domain information
>gnl|CDD|214682 smart00475, 53EXOc, 5'-3' exonuclease Back     alignment and domain information
>gnl|CDD|233038 TIGR00593, pola, DNA polymerase I Back     alignment and domain information
>gnl|CDD|216458 pfam01367, 5_3_exonuc, 5'-3' exonuclease, C-terminal SAM fold Back     alignment and domain information
>gnl|CDD|223336 COG0258, Exo, 5'-3' exonuclease (including N-terminal domain of PolI) [DNA replication, recombination, and repair] Back     alignment and domain information
>gnl|CDD|181896 PRK09482, PRK09482, flap endonuclease-like protein; Provisional Back     alignment and domain information
>gnl|CDD|188616 cd00080, H3TH_StructSpec-5'-nucleases, H3TH domains of structure-specific 5' nucleases (or flap endonuclease-1-like) involved in DNA replication, repair, and recombination Back     alignment and domain information
>gnl|CDD|237877 PRK14976, PRK14976, 5'-3' exonuclease; Provisional Back     alignment and domain information

Conserved Domains Detected by HHsearch ?

Original result of HHsearch against CDD database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query 73
PF01367101 5_3_exonuc: 5'-3' exonuclease, C-terminal SAM fold 99.82
PRK09482256 flap endonuclease-like protein; Provisional 99.81
smart00475259 53EXOc 5'-3' exonuclease. 99.79
PRK14976281 5'-3' exonuclease; Provisional 99.79
TIGR00593 887 pola DNA polymerase I. This family is based on the 99.74
cd00008240 53EXOc 5'-3' exonuclease; T5 type 5'-3' exonucleas 99.7
PRK05755 880 DNA polymerase I; Provisional 99.65
COG0258310 Exo 5'-3' exonuclease (including N-terminal domain 99.55
cd0008075 HhH2_motif Helix-hairpin-helix class 2 (Pol1 famil 99.52
smart0027936 HhH2 Helix-hairpin-helix class 2 (Pol1 family) mot 98.85
PF1282664 HHH_2: Helix-hairpin-helix motif; PDB: 1X2I_B 1DGS 98.84
PTZ00217393 flap endonuclease-1; Provisional 98.67
PRK03980292 flap endonuclease-1; Provisional 98.61
TIGR03674338 fen_arch flap structure-specific endonuclease. End 98.59
cd00128316 XPG Xeroderma pigmentosum G N- and I-regions (XPGN 98.51
PRK14670574 uvrC excinuclease ABC subunit C; Provisional 98.5
PRK14667567 uvrC excinuclease ABC subunit C; Provisional 98.46
PHA00439286 exonuclease 98.44
PRK14669624 uvrC excinuclease ABC subunit C; Provisional 98.35
PF1452060 HHH_5: Helix-hairpin-helix domain; PDB: 3AUO_B 3AU 98.26
PRK14671621 uvrC excinuclease ABC subunit C; Provisional 98.14
PRK14666694 uvrC excinuclease ABC subunit C; Provisional 98.12
PRK14672691 uvrC excinuclease ABC subunit C; Provisional 98.11
COG0322581 UvrC Nuclease subunit of the excinuclease complex 98.06
PRK12766 232 50S ribosomal protein L32e; Provisional 98.02
TIGR00194574 uvrC excinuclease ABC, C subunit. This family cons 98.0
PRK00116192 ruvA Holliday junction DNA helicase RuvA; Reviewed 97.99
PRK00558598 uvrC excinuclease ABC subunit C; Validated 97.94
PRK14668577 uvrC excinuclease ABC subunit C; Provisional 97.85
TIGR00575652 dnlj DNA ligase, NAD-dependent. The member of this 97.83
PRK14351689 ligA NAD-dependent DNA ligase LigA; Provisional 97.76
PRK07956665 ligA NAD-dependent DNA ligase LigA; Validated 97.66
TIGR00084191 ruvA Holliday junction DNA helicase, RuvA subunit. 97.34
PF0063330 HHH: Helix-hairpin-helix motif; InterPro: IPR00044 97.19
COG0272667 Lig NAD-dependent DNA ligase (contains BRCT domain 97.16
TIGR006001034 rad2 DNA excision repair protein (rad2). All prote 97.13
COG1948254 MUS81 ERCC4-type nuclease [DNA replication, recomb 97.11
PRK13766773 Hef nuclease; Provisional 97.07
TIGR00596814 rad1 DNA repair protein (rad1). This family is bas 96.97
PRK14602203 ruvA Holliday junction DNA helicase RuvA; Provisio 96.89
PRK13482352 DNA integrity scanning protein DisA; Provisional 96.86
TIGR01259120 comE comEA protein. This model describes the ComEA 96.85
PRK02515132 psbU photosystem II complex extrinsic protein prec 96.77
PRK14603197 ruvA Holliday junction DNA helicase RuvA; Provisio 96.75
PRK14605194 ruvA Holliday junction DNA helicase RuvA; Provisio 96.75
smart0027826 HhH1 Helix-hairpin-helix DNA-binding motif class 1 96.73
PRK13901196 ruvA Holliday junction DNA helicase RuvA; Provisio 96.71
PRK00254720 ski2-like helicase; Provisional 96.66
PRK14601183 ruvA Holliday junction DNA helicase RuvA; Provisio 96.66
PRK14604195 ruvA Holliday junction DNA helicase RuvA; Provisio 96.65
PRK14600186 ruvA Holliday junction DNA helicase RuvA; Provisio 96.64
KOG2841254 consensus Structure-specific endonuclease ERCC1-XP 96.64
PRK14606188 ruvA Holliday junction DNA helicase RuvA; Provisio 96.56
PRK14350669 ligA NAD-dependent DNA ligase LigA; Provisional 96.52
TIGR0042669 competence protein ComEA helix-hairpin-helix repea 96.51
PF0237187 Transposase_20: Transposase IS116/IS110/IS902 fami 96.06
TIGR01448 720 recD_rel helicase, putative, RecD/TraA family. Thi 96.0
PF1179832 IMS_HHH: IMS family HHH motif; InterPro: IPR024728 95.92
PF1039152 DNA_pol_lambd_f: Fingers domain of DNA polymerase 95.88
KOG2519 449 consensus 5'-3' exonuclease [Replication, recombin 95.83
cd00141 307 NT_POLXc Nucleotidyltransferase (NT) domain of fam 95.73
PRK08609 570 hypothetical protein; Provisional 95.68
TIGR02236 310 recomb_radA DNA repair and recombination protein R 95.64
COG1555149 ComEA DNA uptake protein and related DNA-binding p 95.39
PF1282664 HHH_2: Helix-hairpin-helix motif; PDB: 1X2I_B 1DGS 95.25
PRK08097562 ligB NAD-dependent DNA ligase LigB; Reviewed 95.04
PRK07956 665 ligA NAD-dependent DNA ligase LigA; Validated 94.89
PRK14601183 ruvA Holliday junction DNA helicase RuvA; Provisio 94.8
PRK14600186 ruvA Holliday junction DNA helicase RuvA; Provisio 94.73
PF04919181 DUF655: Protein of unknown function (DUF655); Inte 94.67
COG0632201 RuvA Holliday junction resolvasome, DNA-binding su 94.62
COG1491202 Predicted RNA-binding protein [Translation, riboso 94.61
KOG2518 556 consensus 5'-3' exonuclease [Replication, recombin 94.59
PRK13901196 ruvA Holliday junction DNA helicase RuvA; Provisio 94.53
PRK14604195 ruvA Holliday junction DNA helicase RuvA; Provisio 94.5
PRK14606188 ruvA Holliday junction DNA helicase RuvA; Provisio 94.44
PRK14602203 ruvA Holliday junction DNA helicase RuvA; Provisio 94.44
PF1452060 HHH_5: Helix-hairpin-helix domain; PDB: 3AUO_B 3AU 94.34
PRK14603197 ruvA Holliday junction DNA helicase RuvA; Provisio 94.29
TIGR00575 652 dnlj DNA ligase, NAD-dependent. The member of this 94.28
smart00483 334 POLXc DNA polymerase X family. includes vertebrate 93.92
TIGR00084191 ruvA Holliday junction DNA helicase, RuvA subunit. 93.15
TIGR00615 195 recR recombination protein RecR. This family is ba 92.97
PRK14605194 ruvA Holliday junction DNA helicase RuvA; Provisio 92.94
PRK00076 196 recR recombination protein RecR; Reviewed 92.93
PRK04301 317 radA DNA repair and recombination protein RadA; Va 92.53
PRK13844 200 recombination protein RecR; Provisional 92.35
TIGR03252177 uncharacterized HhH-GPD family protein. This model 91.92
COG0632201 RuvA Holliday junction resolvasome, DNA-binding su 91.83
COG0353 198 RecR Recombinational DNA repair protein (RecF path 91.54
PRK14351 689 ligA NAD-dependent DNA ligase LigA; Provisional 91.47
PF1471668 HHH_8: Helix-hairpin-helix domain; PDB: 2W9M_A 1HU 91.05
PRK00116192 ruvA Holliday junction DNA helicase RuvA; Reviewed 91.03
PRK01229208 N-glycosylase/DNA lyase; Provisional 90.21
PF1457990 HHH_6: Helix-hairpin-helix motif; PDB: 2HPM_A 2HPI 89.98
COG1796 326 POL4 DNA polymerase IV (family X) [DNA replication 89.67
PRK10702211 endonuclease III; Provisional 89.35
COG0177211 Nth Predicted EndoIII-related endonuclease [DNA re 89.22
cd00056158 ENDO3c endonuclease III; includes endonuclease III 89.14
PRK13913218 3-methyladenine DNA glycosylase; Provisional 88.97
KOG2520 815 consensus 5'-3' exonuclease [Replication, recombin 88.91
PF00416107 Ribosomal_S13: Ribosomal protein S13/S18; InterPro 88.36
smart00478149 ENDO3c endonuclease III. includes endonuclease III 88.08
TIGR01083191 nth endonuclease III. This equivalog model identif 87.88
PRK02362737 ski2-like helicase; Provisional 86.87
PF1173193 Cdd1: Pathogenicity locus; InterPro: IPR021725 Cdd 86.49
PRK13910 289 DNA glycosylase MutY; Provisional 85.77
PRK10736 374 hypothetical protein; Provisional 85.49
TIGR01084 275 mutY A/G-specific adenine glycosylase. This equiva 85.02
PRK10880 350 adenine DNA glycosylase; Provisional 83.55
PF14635104 HHH_7: Helix-hairpin-helix motif ; PDB: 3PSI_A 3PS 83.04
PRK08097562 ligB NAD-dependent DNA ligase LigB; Reviewed 82.98
PF1283665 HHH_3: Helix-hairpin-helix motif; PDB: 2EDU_A 2OCE 82.45
PF1305257 DUF3913: Protein of unknown function (DUF3913) 81.73
PF14229122 DUF4332: Domain of unknown function (DUF4332) 81.46
COG1936 180 Predicted nucleotide kinase (related to CMP and AM 81.26
>PF01367 5_3_exonuc: 5'-3' exonuclease, C-terminal SAM fold; InterPro: IPR020045 This entry represents the C-terminal domain of 5' to 3' exonucleases Back     alignment and domain information 
Probab=99.82  E-value=6e-24  Score=135.72  Aligned_cols=65  Identities=29%  Similarity=0.412  Sum_probs=52.1

Q ss_pred             cccCCCCcccHHHHHHHHHHhCCHHHHHHHhhhhhhHHHHHHHHHhHHHHHHHHHhhhHhhcCcc
Q 035092            5 FINAGVEGTGDVCAVQLITKFGSLENLLQCVYQVEEERTRKALITFADQAVLSKNLVIIIAFSST   69 (73)
Q Consensus         5 ~~I~gVpGIG~KtA~~LL~~fgsle~i~~~~~~l~~~k~~~~L~~~~e~a~ls~~L~~L~~~~~~   69 (73)
                      -|||||||||||||.+||++|||+|+|+++++++++++++++|.++.|++++||+|++|++++|-
T Consensus        18 DNIPGV~GIG~KtA~~LL~~ygsle~i~~~~~~~~~~k~~~~l~~~~e~a~ls~~L~tl~~dv~l   82 (101)
T PF01367_consen   18 DNIPGVPGIGPKTAAKLLQEYGSLENILANLDEIKGKKIREKLRENKEQALLSRKLATLKTDVPL   82 (101)
T ss_dssp             CTB---TTSTCHCCCCCHHHHTSCHCCCCC-SSS-TSCCCHHHHTSCCCCCCHHHHH-H-S----
T ss_pred             cCCCCCCCCCHHHHHHHHHHcCCHHHHHHhHHhccccHHHHHHHHHHHHHHHhHHHhhhhcCCCC
Confidence            59999999999999999999999999999999998767899999999999999999999999874

The 5'-3' exonucleases are conserved in organisms as diverse as bacteriophage and mammals. It adopts a SAM fold consisting of 4-5 helices packed into a bundle of two orthogonally packed alpha-hairpins. This domain is involved in interactions with DNA and proteins. 5' to 3' exonucleases that contain this domain include: Bacteriophage T4 RNase H, which has sequence similarity to the RAD2 family of eukaryotic proteins []. 5' to 3' exonuclease domain of DNA polymerase Taq, which is homologous to Escherichia coli DNA polymerase I (pol I) [, ]. Bacteriophage T5 5'-exonuclease, which are structure-specific endonucleases []. Flap endonuclease-1 (Fen-1 nuclease), a structure specific nuclease that is an essential enzyme for eukaryotic DNA replication and repair []. ; GO: 0003677 DNA binding, 0003824 catalytic activity; PDB: 1TAQ_A 1BGX_T 1TAU_A 1XO1_B 1EXN_A 1UT8_A 1UT5_B.
>PRK09482 flap endonuclease-like protein; Provisional Back     alignment and domain information
>smart00475 53EXOc 5'-3' exonuclease Back     alignment and domain information
>PRK14976 5'-3' exonuclease; Provisional Back     alignment and domain information
>TIGR00593 pola DNA polymerase I Back     alignment and domain information
>cd00008 53EXOc 5'-3' exonuclease; T5 type 5'-3' exonuclease domains may co-occur with DNA polymerase I (Pol I) domains, or be part of Pol I containing complexes Back     alignment and domain information
>PRK05755 DNA polymerase I; Provisional Back     alignment and domain information
>COG0258 Exo 5'-3' exonuclease (including N-terminal domain of PolI) [DNA replication, recombination, and repair] Back     alignment and domain information
>cd00080 HhH2_motif Helix-hairpin-helix class 2 (Pol1 family) motif Back     alignment and domain information
>smart00279 HhH2 Helix-hairpin-helix class 2 (Pol1 family) motifs Back     alignment and domain information
>PF12826 HHH_2: Helix-hairpin-helix motif; PDB: 1X2I_B 1DGS_A 1V9P_B Back     alignment and domain information
>PTZ00217 flap endonuclease-1; Provisional Back     alignment and domain information
>PRK03980 flap endonuclease-1; Provisional Back     alignment and domain information
>TIGR03674 fen_arch flap structure-specific endonuclease Back     alignment and domain information
>cd00128 XPG Xeroderma pigmentosum G N- and I-regions (XPGN, XPGI); contains the HhH2 motif; domain in nucleases Back     alignment and domain information
>PRK14670 uvrC excinuclease ABC subunit C; Provisional Back     alignment and domain information
>PRK14667 uvrC excinuclease ABC subunit C; Provisional Back     alignment and domain information
>PHA00439 exonuclease Back     alignment and domain information
>PRK14669 uvrC excinuclease ABC subunit C; Provisional Back     alignment and domain information
>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 Back     alignment and domain information
>PRK14671 uvrC excinuclease ABC subunit C; Provisional Back     alignment and domain information
>PRK14666 uvrC excinuclease ABC subunit C; Provisional Back     alignment and domain information
>PRK14672 uvrC excinuclease ABC subunit C; Provisional Back     alignment and domain information
>COG0322 UvrC Nuclease subunit of the excinuclease complex [DNA replication, recombination, and repair] Back     alignment and domain information
>PRK12766 50S ribosomal protein L32e; Provisional Back     alignment and domain information
>TIGR00194 uvrC excinuclease ABC, C subunit Back     alignment and domain information
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed Back     alignment and domain information
>PRK00558 uvrC excinuclease ABC subunit C; Validated Back     alignment and domain information
>PRK14668 uvrC excinuclease ABC subunit C; Provisional Back     alignment and domain information
>TIGR00575 dnlj DNA ligase, NAD-dependent Back     alignment and domain information
>PRK14351 ligA NAD-dependent DNA ligase LigA; Provisional Back     alignment and domain information
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated Back     alignment and domain information
>TIGR00084 ruvA Holliday junction DNA helicase, RuvA subunit Back     alignment and domain information
>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 [, , ] Back     alignment and domain information
>COG0272 Lig NAD-dependent DNA ligase (contains BRCT domain type II) [DNA replication, recombination, and repair] Back     alignment and domain information
>TIGR00600 rad2 DNA excision repair protein (rad2) Back     alignment and domain information
>COG1948 MUS81 ERCC4-type nuclease [DNA replication, recombination, and repair] Back     alignment and domain information
>PRK13766 Hef nuclease; Provisional Back     alignment and domain information
>TIGR00596 rad1 DNA repair protein (rad1) Back     alignment and domain information
>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional Back     alignment and domain information
>PRK13482 DNA integrity scanning protein DisA; Provisional Back     alignment and domain information
>TIGR01259 comE comEA protein Back     alignment and domain information
>PRK02515 psbU photosystem II complex extrinsic protein precursor U; Provisional Back     alignment and domain information
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional Back     alignment and domain information
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional Back     alignment and domain information
>smart00278 HhH1 Helix-hairpin-helix DNA-binding motif class 1 Back     alignment and domain information
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional Back     alignment and domain information
>PRK00254 ski2-like helicase; Provisional Back     alignment and domain information
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional Back     alignment and domain information
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional Back     alignment and domain information
>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional Back     alignment and domain information
>KOG2841 consensus Structure-specific endonuclease ERCC1-XPF, ERCC1 component [Replication, recombination and repair] Back     alignment and domain information
>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional Back     alignment and domain information
>PRK14350 ligA NAD-dependent DNA ligase LigA; Provisional Back     alignment and domain information
>TIGR00426 competence protein ComEA helix-hairpin-helix repeat region Back     alignment and domain information
>PF02371 Transposase_20: Transposase IS116/IS110/IS902 family; InterPro: IPR003346 Transposases are needed for efficient transposition of the insertion sequence or transposon DNA Back     alignment and domain information
>TIGR01448 recD_rel helicase, putative, RecD/TraA family Back     alignment and domain information
>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 [] Back     alignment and domain information
>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 Back     alignment and domain information
>KOG2519 consensus 5'-3' exonuclease [Replication, recombination and repair] Back     alignment and domain information
>cd00141 NT_POLXc Nucleotidyltransferase (NT) domain of family X DNA Polymerases Back     alignment and domain information
>PRK08609 hypothetical protein; Provisional Back     alignment and domain information
>TIGR02236 recomb_radA DNA repair and recombination protein RadA Back     alignment and domain information
>COG1555 ComEA DNA uptake protein and related DNA-binding proteins [DNA replication, recombination, and repair] Back     alignment and domain information
>PF12826 HHH_2: Helix-hairpin-helix motif; PDB: 1X2I_B 1DGS_A 1V9P_B Back     alignment and domain information
>PRK08097 ligB NAD-dependent DNA ligase LigB; Reviewed Back     alignment and domain information
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated Back     alignment and domain information
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional Back     alignment and domain information
>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional Back     alignment and domain information
>PF04919 DUF655: Protein of unknown function (DUF655); InterPro: IPR007003 This family includes several uncharacterised archaeal proteins Back     alignment and domain information
>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair] Back     alignment and domain information
>COG1491 Predicted RNA-binding protein [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>KOG2518 consensus 5'-3' exonuclease [Replication, recombination and repair] Back     alignment and domain information
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional Back     alignment and domain information
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional Back     alignment and domain information
>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional Back     alignment and domain information
>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional Back     alignment and domain information
>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 Back     alignment and domain information
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional Back     alignment and domain information
>TIGR00575 dnlj DNA ligase, NAD-dependent Back     alignment and domain information
>smart00483 POLXc DNA polymerase X family Back     alignment and domain information
>TIGR00084 ruvA Holliday junction DNA helicase, RuvA subunit Back     alignment and domain information
>TIGR00615 recR recombination protein RecR Back     alignment and domain information
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional Back     alignment and domain information
>PRK00076 recR recombination protein RecR; Reviewed Back     alignment and domain information
>PRK04301 radA DNA repair and recombination protein RadA; Validated Back     alignment and domain information
>PRK13844 recombination protein RecR; Provisional Back     alignment and domain information
>TIGR03252 uncharacterized HhH-GPD family protein Back     alignment and domain information
>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair] Back     alignment and domain information
>COG0353 RecR Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair] Back     alignment and domain information
>PRK14351 ligA NAD-dependent DNA ligase LigA; Provisional Back     alignment and domain information
>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 Back     alignment and domain information
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed Back     alignment and domain information
>PRK01229 N-glycosylase/DNA lyase; Provisional Back     alignment and domain information
>PF14579 HHH_6: Helix-hairpin-helix motif; PDB: 2HPM_A 2HPI_A 3E0D_A 3F2C_A 3F2B_A 3F2D_A 2HQA_A 2HNH_A Back     alignment and domain information
>COG1796 POL4 DNA polymerase IV (family X) [DNA replication, recombination, and repair] Back     alignment and domain information
>PRK10702 endonuclease III; Provisional Back     alignment and domain information
>COG0177 Nth Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair] Back     alignment and domain information
>cd00056 ENDO3c endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases Back     alignment and domain information
>PRK13913 3-methyladenine DNA glycosylase; Provisional Back     alignment and domain information
>KOG2520 consensus 5'-3' exonuclease [Replication, recombination and repair] Back     alignment and domain information
>PF00416 Ribosomal_S13: Ribosomal protein S13/S18; InterPro: IPR001892 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms Back     alignment and domain information
>smart00478 ENDO3c endonuclease III Back     alignment and domain information
>TIGR01083 nth endonuclease III Back     alignment and domain information
>PRK02362 ski2-like helicase; Provisional Back     alignment and domain information
>PF11731 Cdd1: Pathogenicity locus; InterPro: IPR021725 Cdd1 is expressed as part of the pathogenicity locus operon in several different orders of bacteria [] Back     alignment and domain information
>PRK13910 DNA glycosylase MutY; Provisional Back     alignment and domain information
>PRK10736 hypothetical protein; Provisional Back     alignment and domain information
>TIGR01084 mutY A/G-specific adenine glycosylase Back     alignment and domain information
>PRK10880 adenine DNA glycosylase; Provisional Back     alignment and domain information
>PF14635 HHH_7: Helix-hairpin-helix motif ; PDB: 3PSI_A 3PSF_A Back     alignment and domain information
>PRK08097 ligB NAD-dependent DNA ligase LigB; Reviewed Back     alignment and domain information
>PF12836 HHH_3: Helix-hairpin-helix motif; PDB: 2EDU_A 2OCE_A 3BZK_A 3BZC_A 2DUY_A Back     alignment and domain information
>PF13052 DUF3913: Protein of unknown function (DUF3913) Back     alignment and domain information
>PF14229 DUF4332: Domain of unknown function (DUF4332) Back     alignment and domain information
>COG1936 Predicted nucleotide kinase (related to CMP and AMP kinases) [Nucleotide transport and metabolism] Back     alignment and domain information

Homologous Structure Templates

Structure Templates Detected by BLAST ?

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST ?

Original result of RPS-BLAST against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query73
1exn_A290 5'-exonuclease, 5'-nuclease; hydrolase; 2.50A {Ent 3e-10
1bgx_T 832 TAQ DNA polymerase; DNA polymerase, FAB, PCR, inhi 1e-08
>1exn_A 5'-exonuclease, 5'-nuclease; hydrolase; 2.50A {Enterobacteria phage T5} SCOP: a.60.7.1 c.120.1.2 PDB: 1ut5_A 1ut8_A 1xo1_A Length = 290 Back     alignment and structure
 Score = 53.1 bits (128), Expect = 3e-10
 Identities = 11/55 (20%), Positives = 26/55 (47%)

Query: 9   GVEGTGDVCAVQLITKFGSLENLLQCVYQVEEERTRKALITFADQAVLSKNLVII 63
           GVEG G      +I +FG++ +++  +    +++  + L    +    +  LV +
Sbjct: 207 GVEGIGAKRGYNIIREFGNVLDIIDQLPLPGKQKYIQNLNASEELLFRNLILVDL 261
>1bgx_T TAQ DNA polymerase; DNA polymerase, FAB, PCR, inhibition, helix-coil dynamics, inhibitor design, complex (polymerase/inhibitor); 2.30A {Thermus aquaticus} SCOP: a.60.7.1 c.120.1.2 c.55.3.5 e.8.1.1 PDB: 1cmw_A 1tau_A* 1taq_A* Length = 832 Back     alignment and structure

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query73
1exn_A290 5'-exonuclease, 5'-nuclease; hydrolase; 2.50A {Ent 99.79
1bgx_T 832 TAQ DNA polymerase; DNA polymerase, FAB, PCR, inhi 99.4
1rxw_A336 Flap structure-specific endonuclease; helical clam 99.08
3q8k_A341 Flap endonuclease 1; helix-3 turn-helix, hydrophob 99.06
2izo_A346 FEN1, flap structure-specific endonuclease; hydrol 99.05
2a1j_A63 DNA repair endonuclease XPF; XPF, xeroderma pigmen 98.96
1a76_A326 Flap endonuclease-1 protein; 5'-3' EXO/endo nuclea 98.89
3qe9_Y352 Exonuclease 1; exonuclease, hydrolase-DNA complex; 98.82
1z00_B84 DNA repair endonuclease XPF; helix-hairpin-helix, 98.82
1b43_A340 Protein (FEN-1); nuclease, DNA repair, DNA replica 98.81
1ul1_X379 Flap endonuclease-1; protein complex, DNA-binding 98.7
3ory_A363 Flap endonuclease 1; hydrolase; 2.00A {Desulfuroco 98.7
1kft_A78 UVRC, excinuclease ABC subunit C; helix-hairpin-he 98.52
1z00_A89 DNA excision repair protein ERCC-1; helix-hairpin- 98.48
1x2i_A75 HEF helicase/nuclease; alpha helix, helix-hairpin- 98.48
2a1j_B91 DNA excision repair protein ERCC-1; XPF, xeroderma 98.42
2nrt_A220 Uvrabc system protein C; UVRC, endonuclease, RNAse 98.42
3c65_A226 Uvrabc system protein C; UVRC, endonuclease, nucle 98.1
2bgw_A219 XPF endonuclease; hydrolase, structure specific en 98.07
1ixr_A191 Holliday junction DNA helicase RUVA; heterooligome 98.02
1cuk_A203 RUVA protein; DNA repair, SOS response, DNA-bindin 97.98
2owo_A671 DNA ligase; protein-DNA complex, ligase-DNA comple 97.81
1dgs_A667 DNA ligase; AMP complex, NAD+-dependent; HET: DNA 97.65
3sgi_A615 DNA ligase; HET: DNA AMP; 3.50A {Mycobacterium tub 97.61
3c1y_A377 DNA integrity scanning protein DISA; DNA damage, D 97.57
4glx_A586 DNA ligase; inhibitor, ligase-ligase inhibitor-DNA 97.51
1vq8_Y 241 50S ribosomal protein L32E; ribosome 50S, protein- 97.45
4gfj_A 685 Topoisomerase V; helix-hairpin-helix, DNA repair e 97.42
2ztd_A212 Holliday junction ATP-dependent DNA helicase RUVA; 97.23
2w9m_A 578 Polymerase X; SAXS, DNA repair, DNA polymerase, DN 97.09
1s5l_U134 Photosystem II 12 kDa extrinsic protein; photosynt 97.03
2duy_A75 Competence protein comea-related protein; helix-ha 96.76
3b0x_A 575 DNA polymerase beta family (X family); structural 96.62
2edu_A98 Kinesin-like protein KIF22; kinesin-like DNA bindi 96.31
2i5h_A205 Hypothetical protein AF1531; PFAM:DUF655, PSI-2, s 96.17
3arc_U97 Photosystem II 12 kDa extrinsic protein; PSII, mem 95.98
2ziu_A311 MUS81 protein; helix-hairpin-helix, alternative sp 95.84
3h7i_A305 Ribonuclease H, RNAse H; BPT4 RNAse H, 5'-3' exonu 95.5
3maj_A 382 DNA processing chain A; MCSG, PSI-2, structural ge 95.02
2fmp_A 335 DNA polymerase beta; nucleotidyl transferase, tran 94.59
2ztd_A212 Holliday junction ATP-dependent DNA helicase RUVA; 94.18
1ixr_A191 Holliday junction DNA helicase RUVA; heterooligome 93.93
2ihm_A 360 POL MU, DNA polymerase MU; helix-turn-helix, trans 93.48
2bcq_A 335 DNA polymerase lambda; misalignment, extrahelical, 93.35
2owo_A 671 DNA ligase; protein-DNA complex, ligase-DNA comple 93.16
1x2i_A75 HEF helicase/nuclease; alpha helix, helix-hairpin- 92.6
1dgs_A 667 DNA ligase; AMP complex, NAD+-dependent; HET: DNA 92.4
1jms_A 381 Terminal deoxynucleotidyltransferase; polymerase; 92.39
1vdd_A 228 Recombination protein RECR; helix-hairpin-helix, z 92.37
1cuk_A203 RUVA protein; DNA repair, SOS response, DNA-bindin 92.36
2csb_A519 Topoisomerase V, TOP61; topoisomerase IB, helix-tu 91.76
3fhg_A207 Mjogg, N-glycosylase/DNA lyase, DNA-(apurinic; hel 91.74
3n0u_A219 Probable N-glycosylase/DNA lyase; structural genom 91.41
3vdp_A 212 Recombination protein RECR; zinc finger, DNA repai 91.06
1kft_A78 UVRC, excinuclease ABC subunit C; helix-hairpin-he 90.99
1z00_A89 DNA excision repair protein ERCC-1; helix-hairpin- 90.81
3fhf_A214 Mjogg, N-glycosylase/DNA lyase, DNA-(apurinic; hel 90.74
3b0x_A 575 DNA polymerase beta family (X family); structural 89.98
1pu6_A218 3-methyladenine DNA glycosylase; helix-hairpin-hel 89.91
1kea_A221 Possible G-T mismatches repair enzyme; DNA repair, 89.27
4glx_A586 DNA ligase; inhibitor, ligase-ligase inhibitor-DNA 89.06
2h56_A233 DNA-3-methyladenine glycosidase; 10174367, EC 3.2. 88.91
1kg2_A225 A/G-specific adenine glycosylase; DNA repair, hydr 88.83
2a1j_B91 DNA excision repair protein ERCC-1; XPF, xeroderma 88.53
2abk_A211 Endonuclease III; DNA-repair, DNA glycosylase; 1.8 88.47
1orn_A226 Endonuclease III; DNA repair, DNA glycosylase, [4F 87.93
2zix_A307 Crossover junction endonuclease MUS81; helix-hairp 87.68
4b21_A232 Probable DNA-3-methyladenine glycosylase 2; hydrol 86.69
3i0w_A290 8-oxoguanine-DNA-glycosylase; OGG, cacogg, DNA, 8- 86.67
3s6i_A228 DNA-3-methyladenine glycosylase 1; DNA glycosylase 86.65
4e9f_A161 Methyl-CPG-binding domain protein 4; HHH DNA glyco 86.57
2yg9_A225 DNA-3-methyladenine glycosidase II, putative; hydr 86.39
1mpg_A282 ALKA, 3-methyladenine DNA glycosylase II; DNA repa 86.17
2jhn_A295 ALKA, 3-methyladenine DNA-glycosylase; DNA repair, 85.61
2bgw_A219 XPF endonuclease; hydrolase, structure specific en 84.17
3n5n_X287 A/G-specific adenine DNA glycosylase; alpha-helice 84.12
2w9m_A 578 Polymerase X; SAXS, DNA repair, DNA polymerase, DN 83.83
3fsp_A 369 A/G-specific adenine glycosylase; protein-DNA comp 83.43
1ci4_A89 Protein (barrier-TO-autointegration factor (BAF) ) 83.08
2xhi_A360 N-glycosylase/DNA lyase; lyase-DNA complex, lyase/ 82.63
2kp7_A87 Crossover junction endonuclease MUS81; helix-hairp 80.3
>1exn_A 5'-exonuclease, 5'-nuclease; hydrolase; 2.50A {Enterobacteria phage T5} SCOP: a.60.7.1 c.120.1.2 PDB: 1ut5_A 1ut8_A 1xo1_A Back     alignment and structure
Probab=99.79  E-value=7.4e-20  Score=132.61  Aligned_cols=64  Identities=17%  Similarity=0.201  Sum_probs=61.1

Q ss_pred             cccCCCCcccHHHHHHHHHHhCCHHHHHHHhhhh-hhHHHHHHHHHhHHHHHHHHHhhhHhhcCcc
Q 035092            5 FINAGVEGTGDVCAVQLITKFGSLENLLQCVYQV-EEERTRKALITFADQAVLSKNLVIIIAFSST   69 (73)
Q Consensus         5 ~~I~gVpGIG~KtA~~LL~~fgsle~i~~~~~~l-~~~k~~~~L~~~~e~a~ls~~L~~L~~~~~~   69 (73)
                      -|||||||||||||.+||++|||+|+|+++++++ ++ +++++|.++.+++++|++|++|++++|-
T Consensus       203 DniPGVpGIG~KTA~kLL~~~gsle~i~~~~~~~~~~-~~~~~L~~~~~~~~ls~~L~~i~~d~~~  267 (290)
T 1exn_A          203 DNIRGVEGIGAKRGYNIIREFGNVLDIIDQLPLPGKQ-KYIQNLNASEELLFRNLILVDLPTYCVD  267 (290)
T ss_dssp             GTBCCCTTCCHHHHHHHHHHHCSHHHHHHHCSCSCCC-HHHHHHHTCHHHHHHHHHHHCHHHHHHH
T ss_pred             CCCCCCCcCCHhHHHHHHHHcCCHHHHHHHHHHhccH-HHHHHHHHhHHHHHHHHHhceeeeCCCC
Confidence            5899999999999999999999999999999999 77 8999999999999999999999999873
>1bgx_T TAQ DNA polymerase; DNA polymerase, FAB, PCR, inhibition, helix-coil dynamics, inhibitor design, complex (polymerase/inhibitor); 2.30A {Thermus aquaticus} SCOP: a.60.7.1 c.120.1.2 c.55.3.5 e.8.1.1 PDB: 1cmw_A 1tau_A* 1taq_A* Back     alignment and structure
>1rxw_A Flap structure-specific endonuclease; helical clamp, helix-3 turn-helix, hydrophobic wedge, 3' FLA site, hydrolase-DNA complex; 2.00A {Archaeoglobus fulgidus} SCOP: a.60.7.1 c.120.1.2 PDB: 1rxv_A Back     alignment and structure
>3q8k_A Flap endonuclease 1; helix-3 turn-helix, hydrophobic wedge, 3' flap binding site, hydrolase-DNA complex, DNA repair, replication; HET: DNA; 2.20A {Homo sapiens} PDB: 3q8l_A* 3q8m_A* Back     alignment and structure
>2izo_A FEN1, flap structure-specific endonuclease; hydrolase, DNA repair, DNA-binding, endonuclease, metal-BIND excision repair, DNA replication, PCNA; HET: DNA; 2.9A {Sulfolobus solfataricus} Back     alignment and structure
>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* Back     alignment and structure
>1a76_A Flap endonuclease-1 protein; 5'-3' EXO/endo nuclease, DNA replication, RTH, RAD27, DNA repair; 2.00A {Methanocaldococcus jannaschii} SCOP: a.60.7.1 c.120.1.2 PDB: 1a77_A Back     alignment and structure
>3qe9_Y Exonuclease 1; exonuclease, hydrolase-DNA complex; HET: DNA; 2.51A {Homo sapiens} PDB: 3qeb_Z* 3qea_Z* Back     alignment and structure
>1z00_B DNA repair endonuclease XPF; helix-hairpin-helix, hydrolase; HET: DNA; NMR {Homo sapiens} SCOP: a.60.2.5 PDB: 2aq0_A* Back     alignment and structure
>1b43_A Protein (FEN-1); nuclease, DNA repair, DNA replication, transferase; 2.00A {Pyrococcus furiosus} SCOP: a.60.7.1 c.120.1.2 PDB: 1mc8_A Back     alignment and structure
>1ul1_X Flap endonuclease-1; protein complex, DNA-binding protein, flap DNA, flap endonuclease, sliding clamp, DNA clamp; 2.90A {Homo sapiens} SCOP: a.60.7.1 c.120.1.2 Back     alignment and structure
>3ory_A Flap endonuclease 1; hydrolase; 2.00A {Desulfurococcus amylolyticus} Back     alignment and structure
>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 Back     alignment and structure
>1z00_A DNA excision repair protein ERCC-1; helix-hairpin-helix, hydrolase; HET: DNA; NMR {Homo sapiens} SCOP: a.60.2.5 Back     alignment and structure
>1x2i_A HEF helicase/nuclease; alpha helix, helix-hairpin-helix DNA binding domain, homodimer, hydrolase; 1.45A {Pyrococcus furiosus} SCOP: a.60.2.5 Back     alignment and structure
>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 Back     alignment and structure
>2nrt_A Uvrabc system protein C; UVRC, endonuclease, RNAse H, helix hairpin helix, NER, hydrolase; 1.50A {Thermotoga maritima} PDB: 2nrv_A 2nrw_A 2nrx_A 2nrz_A Back     alignment and structure
>3c65_A Uvrabc system protein C; UVRC, endonuclease, nucleotide excision repair, DNA repair, RNAse H, cytoplasm, DNA damage, DNA excision; 1.90A {Bacillus stearothermophilus} Back     alignment and structure
>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 Back     alignment and structure
>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 Back     alignment and structure
>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 Back     alignment and structure
>2owo_A DNA ligase; protein-DNA complex, ligase-DNA complex; HET: DNA OMC AMP; 2.30A {Escherichia coli} Back     alignment and structure
>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* Back     alignment and structure
>3sgi_A DNA ligase; HET: DNA AMP; 3.50A {Mycobacterium tuberculosis} Back     alignment and structure
>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* Back     alignment and structure
>4glx_A DNA ligase; inhibitor, ligase-ligase inhibitor-DNA complex; HET: DNA 0XS; 1.90A {Escherichia coli} Back     alignment and structure
>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* ... Back     alignment and structure
>4gfj_A Topoisomerase V; helix-hairpin-helix, DNA repair enzyme, DNA B isomerase; 2.91A {Methanopyrus kandleri AV19} Back     alignment and structure
>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 Back     alignment and structure
>2w9m_A Polymerase X; SAXS, DNA repair, DNA polymerase, DNA replication; 2.46A {Deinococcus radiodurans} Back     alignment and structure
>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} Back     alignment and structure
>2duy_A Competence protein comea-related protein; helix-hairpin-helix, structural genomics, NPPSFA; 1.75A {Thermus thermophilus} SCOP: a.60.2.7 Back     alignment and structure
>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* Back     alignment and structure
>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 Back     alignment and structure
>2i5h_A Hypothetical protein AF1531; PFAM:DUF655, PSI-2, structural genomics, protein structure initiative; 1.74A {Archaeoglobus fulgidus} SCOP: e.71.1.1 Back     alignment and structure
>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* Back     alignment and structure
>2ziu_A MUS81 protein; helix-hairpin-helix, alternative splicing, DNA damage, DNA recombination, DNA repair, hydrolase, magnesium; 2.70A {Danio rerio} PDB: 2ziv_A 2ziw_A Back     alignment and structure
>3h7i_A Ribonuclease H, RNAse H; BPT4 RNAse H, 5'-3' exonuclease, hydrolase, endonuclease; 1.50A {Enterobacteria phage T4} PDB: 2ihn_A 3h8w_A 3h8j_A 1tfr_A 3h8s_A Back     alignment and structure
>3maj_A DNA processing chain A; MCSG, PSI-2, structural genomics, protein structure initiati midwest center for structural genomics; HET: DNA; 2.05A {Rhodopseudomonas palustris} Back     alignment and structure
>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* ... Back     alignment and structure
>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 Back     alignment and structure
>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 Back     alignment and structure
>2ihm_A POL MU, DNA polymerase MU; helix-turn-helix, transferase/DNA complex; HET: DNA D3T; 2.40A {Mus musculus} Back     alignment and structure
>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* ... Back     alignment and structure
>2owo_A DNA ligase; protein-DNA complex, ligase-DNA complex; HET: DNA OMC AMP; 2.30A {Escherichia coli} Back     alignment and structure
>1x2i_A HEF helicase/nuclease; alpha helix, helix-hairpin-helix DNA binding domain, homodimer, hydrolase; 1.45A {Pyrococcus furiosus} SCOP: a.60.2.5 Back     alignment and structure
>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* Back     alignment and structure
>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* Back     alignment and structure
>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 Back     alignment and structure
>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 Back     alignment and structure
>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 Back     alignment and structure
>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} Back     alignment and structure
>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} Back     alignment and structure
>3vdp_A Recombination protein RECR; zinc finger, DNA repair, DNA binding; 2.45A {Thermoanaerobacter tengcongensis} PDB: 3vdu_A 3ve5_D Back     alignment and structure
>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 Back     alignment and structure
>1z00_A DNA excision repair protein ERCC-1; helix-hairpin-helix, hydrolase; HET: DNA; NMR {Homo sapiens} SCOP: a.60.2.5 Back     alignment and structure
>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* Back     alignment and structure
>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* Back     alignment and structure
>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* Back     alignment and structure
>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 Back     alignment and structure
>4glx_A DNA ligase; inhibitor, ligase-ligase inhibitor-DNA complex; HET: DNA 0XS; 1.90A {Escherichia coli} Back     alignment and structure
>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} Back     alignment and structure
>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 Back     alignment and structure
>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 Back     alignment and structure
>2abk_A Endonuclease III; DNA-repair, DNA glycosylase; 1.85A {Escherichia coli} SCOP: a.96.1.1 Back     alignment and structure
>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* Back     alignment and structure
>2zix_A Crossover junction endonuclease MUS81; helix-hairpin-helix, DNA damage, DNA recombination, DNA repair, hydrolase, magnesium, metal-binding, nucleus; 3.50A {Homo sapiens} Back     alignment and structure
>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* Back     alignment and structure
>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 Back     alignment and structure
>3s6i_A DNA-3-methyladenine glycosylase 1; DNA glycosylase, DNA repair, helix-hairpin-helix (HHH), ABAS tetrahydrofuran (THF); HET: 3DR; 2.28A {Schizosaccharomyces pombe} Back     alignment and structure
>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 Back     alignment and structure
>2yg9_A DNA-3-methyladenine glycosidase II, putative; hydrolase, DNA repair; 1.95A {Deinococcus radiodurans} PDB: 2yg8_A Back     alignment and structure
>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* Back     alignment and structure
>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 Back     alignment and structure
>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 Back     alignment and structure
>3n5n_X A/G-specific adenine DNA glycosylase; alpha-helices, helix-hairpin-helix motif, iron-sulfur cluste hydrolase; 2.30A {Homo sapiens} Back     alignment and structure
>2w9m_A Polymerase X; SAXS, DNA repair, DNA polymerase, DNA replication; 2.46A {Deinococcus radiodurans} Back     alignment and structure
>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* Back     alignment and structure
>1ci4_A Protein (barrier-TO-autointegration factor (BAF) ); DNA binding protein, retroviral integration, preintegration complex; 1.90A {Homo sapiens} SCOP: a.60.5.1 PDB: 1qck_A 2bzf_A 2ezx_A 2ezy_A 2ezz_A 2odg_A Back     alignment and structure
>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* ... Back     alignment and structure
>2kp7_A Crossover junction endonuclease MUS81; helix-hairpin-helix, tumour suppressor, DNA damage, DNA recombination, DNA repair, hydrolase, magnesium; NMR {Mus musculus} Back     alignment and structure

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST ?

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

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query 73
d1ul1x1140 a.60.7.1 (X:218-357) Flap endonuclease-1 (Fen-1 nu 8e-04
>d1ul1x1 a.60.7.1 (X:218-357) Flap endonuclease-1 (Fen-1 nuclease) {Human (Homo sapiens) [TaxId: 9606]} Length = 140 Back     information, alignment and structure

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

 Score = 33.0 bits (75), Expect = 8e-04
 Identities = 13/57 (22%), Positives = 22/57 (38%)

Query: 7  NAGVEGTGDVCAVQLITKFGSLENLLQCVYQVEEERTRKALITFADQAVLSKNLVII 63
             + G G   AV LI K  S+E +++ +   +       L   A Q  L   ++  
Sbjct: 18 CESIRGIGPKRAVDLIQKHKSIEEIVRRLDPNKYPVPENWLHKEAHQLFLEPEVLDP 74

Homologous Domains Detected by HHsearch ?

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

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query73
d1cmwa1116 5' to 3' exonuclease domain of DNA polymerase Taq 99.75
d1xo1a1105 T5 5'-exonuclease {Bacteriophage T5 [TaxId: 10726] 99.75
d1ul1x1140 Flap endonuclease-1 (Fen-1 nuclease) {Human (Homo 99.39
d1rxwa1105 Flap endonuclease-1 (Fen-1 nuclease) {Archaeon Arc 99.37
d1a77a1108 Flap endonuclease-1 (Fen-1 nuclease) {Archaeon Met 99.33
d1kfta_56 Excinuclease UvrC C-terminal domain {Escherichia c 99.06
d1x2ia168 ATP-dependent RNA helicase PF2015 {Pyrococcus furi 98.92
d2a1ja162 DNA repair endonuclease XPF {Human (Homo sapiens) 98.92
d2bgwa170 DNA repair endonuclease XPF {Aeropyrum pernix [Tax 98.9
d1b43a1120 Flap endonuclease-1 (Fen-1 nuclease) {Archaeon Pyr 98.76
d2i1qa160 DNA repair protein Rad51, N-terminal domain {Archa 98.71
d2a1jb178 DNA excision repair protein ERCC-1 {Human (Homo sa 98.66
d1pzna161 DNA repair protein Rad51, N-terminal domain {Archa 98.58
d1dgsa1181 NAD+-dependent DNA ligase, domain 3 {Thermus filif 98.33
d1bvsa271 DNA helicase RuvA subunit, middle domain {Mycobact 97.72
d1ixra173 DNA helicase RuvA subunit, middle domain {Thermus 97.52
d1cuka278 DNA helicase RuvA subunit, middle domain {Escheric 97.41
d1jmsa360 Terminal deoxynucleotidyl transferase {Mouse (Mus 97.26
d2bcqa257 DNA polymerase lambda {Human (Homo sapiens) [TaxId 97.2
d2csba355 Topoisomerase V {Methanopyrus kandleri [TaxId: 232 97.02
d1szpa164 DNA repair protein Rad51, N-terminal domain {Baker 96.8
d1ixra173 DNA helicase RuvA subunit, middle domain {Thermus 96.36
d1bvsa271 DNA helicase RuvA subunit, middle domain {Mycobact 96.34
d2fmpa257 DNA polymerase beta {Human (Homo sapiens) [TaxId: 96.2
d1cuka278 DNA helicase RuvA subunit, middle domain {Escheric 95.97
d2p6ra2198 Hel308 helicase {Archaeoglobus fulgidus [TaxId: 22 95.67
d1kfta_56 Excinuclease UvrC C-terminal domain {Escherichia c 95.45
d2axtu198 Photosystem II 12 kDa extrinsic protein PsbU {Ther 95.37
d2i5ha1180 Hypothetical protein AF1531 {Archaeoglobus fulgidu 95.17
d1x2ia168 ATP-dependent RNA helicase PF2015 {Pyrococcus furi 94.65
d1gm5a2 180 RecG "wedge" domain {Thermotoga maritima [TaxId: 2 94.26
d1dgsa1181 NAD+-dependent DNA ligase, domain 3 {Thermus filif 93.21
d1keaa_217 Thymine-DNA glycosylase {Archaeon Methanobacterium 93.09
d2bgwa170 DNA repair endonuclease XPF {Aeropyrum pernix [Tax 92.87
d1b22a_70 DNA repair protein Rad51, N-terminal domain {Human 92.8
d1orna_214 Endonuclease III {Escherichia coli [TaxId: 562]} 92.19
d1rrqa1221 Catalytic domain of MutY {Bacillus stearothermophi 92.05
d1kg2a_224 Catalytic domain of MutY {Escherichia coli [TaxId: 91.93
d2i1qa160 DNA repair protein Rad51, N-terminal domain {Archa 91.82
d2abka_211 Endonuclease III {Escherichia coli [TaxId: 562]} 91.4
d2a1jb178 DNA excision repair protein ERCC-1 {Human (Homo sa 90.99
d1vdda_ 199 Recombination protein RecR {Deinococcus radioduran 90.89
d2noha1190 8-oxoguanine glycosylase {Human (Homo sapiens) [Ta 90.27
d1pu6a_217 3-Methyladenine DNA glycosylase III (MagIII) {Heli 89.97
d2bcqa176 DNA polymerase lambda {Human (Homo sapiens) [TaxId 89.87
d3bzka190 Transcriptional accessory factor Tex {Pseudomonas 89.55
d1pzna161 DNA repair protein Rad51, N-terminal domain {Archa 89.46
d2csba455 Topoisomerase V {Methanopyrus kandleri [TaxId: 232 89.23
d1jmsa195 Terminal deoxynucleotidyl transferase {Mouse (Mus 89.2
d2duya165 Uncharacterized protein TTHA1967 {Thermus thermoph 88.89
d2fmpa182 DNA polymerase beta, N-terminal (8 kD)-domain {Hum 88.29
d2edua191 KIF22, C-terminal domain {Human (Homo sapiens) [Ta 86.97
d1mpga1183 3-Methyladenine DNA glycosylase II (gene alkA or a 86.41
d1jiha2389 DNA polymerase eta {Baker's yeast (Saccharomyces c 85.55
d1ngna_144 Mismatch-specific thymine glycosylase domain of th 85.21
d1im4a_209 DinB homolog (DBH) {Archaeon Sulfolobus solfataric 84.78
d1szpa164 DNA repair protein Rad51, N-terminal domain {Baker 84.74
d2csba159 Topoisomerase V {Methanopyrus kandleri [TaxId: 232 83.19
>d1cmwa1 a.60.7.1 (A:174-289) 5' to 3' exonuclease domain of DNA polymerase Taq {Thermus aquaticus [TaxId: 271]} Back     information, alignment and structure
class: All alpha proteins
fold: SAM domain-like
superfamily: 5' to 3' exonuclease, C-terminal subdomain
family: 5' to 3' exonuclease, C-terminal subdomain
domain: 5' to 3' exonuclease domain of DNA polymerase Taq
species: Thermus aquaticus [TaxId: 271]

Probab=99.75  E-value=4.1e-22  Score=124.64  Aligned_cols=64  Identities=27%  Similarity=0.353  Sum_probs=60.6

Q ss_pred             cccCCCCcccHHHHHHHHHHhCCHHHHHHHhhhhhhHHHHHHHHHhHHHHHHHHHhhhHhhcCcc
Q 035092            5 FINAGVEGTGDVCAVQLITKFGSLENLLQCVYQVEEERTRKALITFADQAVLSKNLVIIIAFSST   69 (73)
Q Consensus         5 ~~I~gVpGIG~KtA~~LL~~fgsle~i~~~~~~l~~~k~~~~L~~~~e~a~ls~~L~~L~~~~~~   69 (73)
                      -|||||||||||||.+|+++|+|+|+++++.+++++ +++++|.++++.+.+|++|++|++++|.
T Consensus        18 DnipGv~GiG~KtA~kll~~~gsle~i~~~~~~i~~-k~~~~l~~~~e~~~~~~~L~~L~~dv~~   81 (116)
T d1cmwa1          18 DNLPGVKGIGEKTARKLLEEWGSLEALLKNLDRLKP-AIREKILAHMDDLKLSWDLAKVRTDLPL   81 (116)
T ss_dssp             SCCCCCCCSTTCTTTTTGGGGGTTCSSSSSCCCCCT-TTTHHHHTSTTTTTTGGGGGCCCSCCCC
T ss_pred             cCcccccccCchhHHHHHHhcchHHHHHHHHhhhcc-chhhhhHHHHHHHHHHHHHhccCcCCCC
Confidence            599999999999999999999999999999999987 7899999999999999999999998874
>d1xo1a1 a.60.7.1 (A:186-290) T5 5'-exonuclease {Bacteriophage T5 [TaxId: 10726]} Back     information, alignment and structure
>d1ul1x1 a.60.7.1 (X:218-357) Flap endonuclease-1 (Fen-1 nuclease) {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1rxwa1 a.60.7.1 (A:220-324) Flap endonuclease-1 (Fen-1 nuclease) {Archaeon Archaeoglobus fulgidus [TaxId: 2234]} Back     information, alignment and structure
>d1a77a1 a.60.7.1 (A:209-316) Flap endonuclease-1 (Fen-1 nuclease) {Archaeon Methanococcus jannaschii [TaxId: 2190]} Back     information, alignment and structure
>d1kfta_ a.60.2.3 (A:) Excinuclease UvrC C-terminal domain {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1x2ia1 a.60.2.5 (A:2-69) ATP-dependent RNA helicase PF2015 {Pyrococcus furiosus [TaxId: 2261]} Back     information, alignment and structure
>d2a1ja1 a.60.2.5 (A:837-898) DNA repair endonuclease XPF {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d2bgwa1 a.60.2.5 (A:160-229) DNA repair endonuclease XPF {Aeropyrum pernix [TaxId: 56636]} Back     information, alignment and structure
>d1b43a1 a.60.7.1 (A:220-339) Flap endonuclease-1 (Fen-1 nuclease) {Archaeon Pyrococcus furiosus [TaxId: 2261]} Back     information, alignment and structure
>d2i1qa1 a.60.4.1 (A:5-64) DNA repair protein Rad51, N-terminal domain {Archaeon Methanococcus voltae [TaxId: 2188]} Back     information, alignment and structure
>d2a1jb1 a.60.2.5 (B:219-296) DNA excision repair protein ERCC-1 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1pzna1 a.60.4.1 (A:35-95) DNA repair protein Rad51, N-terminal domain {Archaeon Pyrococcus furiosus [TaxId: 2261]} Back     information, alignment and structure
>d1dgsa1 a.60.2.2 (A:401-581) NAD+-dependent DNA ligase, domain 3 {Thermus filiformis [TaxId: 276]} Back     information, alignment and structure
>d1bvsa2 a.60.2.1 (A:64-134) DNA helicase RuvA subunit, middle domain {Mycobacterium leprae [TaxId: 1769]} Back     information, alignment and structure
>d1ixra1 a.60.2.1 (A:63-135) DNA helicase RuvA subunit, middle domain {Thermus thermophilus [TaxId: 274]} Back     information, alignment and structure
>d1cuka2 a.60.2.1 (A:65-142) DNA helicase RuvA subunit, middle domain {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1jmsa3 a.60.12.1 (A:243-302) Terminal deoxynucleotidyl transferase {Mouse (Mus musculus) [TaxId: 10090]} Back     information, alignment and structure
>d2bcqa2 a.60.12.1 (A:329-385) DNA polymerase lambda {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d2csba3 a.60.2.4 (A:410-464) Topoisomerase V {Methanopyrus kandleri [TaxId: 2320]} Back     information, alignment and structure
>d1szpa1 a.60.4.1 (A:81-144) DNA repair protein Rad51, N-terminal domain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Back     information, alignment and structure
>d1ixra1 a.60.2.1 (A:63-135) DNA helicase RuvA subunit, middle domain {Thermus thermophilus [TaxId: 274]} Back     information, alignment and structure
>d1bvsa2 a.60.2.1 (A:64-134) DNA helicase RuvA subunit, middle domain {Mycobacterium leprae [TaxId: 1769]} Back     information, alignment and structure
>d2fmpa2 a.60.12.1 (A:92-148) DNA polymerase beta {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1cuka2 a.60.2.1 (A:65-142) DNA helicase RuvA subunit, middle domain {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d2p6ra2 a.289.1.2 (A:489-686) Hel308 helicase {Archaeoglobus fulgidus [TaxId: 2234]} Back     information, alignment and structure
>d1kfta_ a.60.2.3 (A:) Excinuclease UvrC C-terminal domain {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d2axtu1 a.60.12.2 (U:37-134) Photosystem II 12 kDa extrinsic protein PsbU {Thermosynechococcus elongatus [TaxId: 146786]} Back     information, alignment and structure
>d2i5ha1 e.71.1.1 (A:16-195) Hypothetical protein AF1531 {Archaeoglobus fulgidus [TaxId: 2234]} Back     information, alignment and structure
>d1x2ia1 a.60.2.5 (A:2-69) ATP-dependent RNA helicase PF2015 {Pyrococcus furiosus [TaxId: 2261]} Back     information, alignment and structure
>d1gm5a2 b.40.4.9 (A:106-285) RecG "wedge" domain {Thermotoga maritima [TaxId: 2336]} Back     information, alignment and structure
>d1dgsa1 a.60.2.2 (A:401-581) NAD+-dependent DNA ligase, domain 3 {Thermus filiformis [TaxId: 276]} Back     information, alignment and structure
>d1keaa_ a.96.1.2 (A:) Thymine-DNA glycosylase {Archaeon Methanobacterium thermoformicicum [TaxId: 145262]} Back     information, alignment and structure
>d2bgwa1 a.60.2.5 (A:160-229) DNA repair endonuclease XPF {Aeropyrum pernix [TaxId: 56636]} Back     information, alignment and structure
>d1b22a_ a.60.4.1 (A:) DNA repair protein Rad51, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1orna_ a.96.1.1 (A:) Endonuclease III {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1rrqa1 a.96.1.2 (A:9-229) Catalytic domain of MutY {Bacillus stearothermophilus [TaxId: 1422]} Back     information, alignment and structure
>d1kg2a_ a.96.1.2 (A:) Catalytic domain of MutY {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d2i1qa1 a.60.4.1 (A:5-64) DNA repair protein Rad51, N-terminal domain {Archaeon Methanococcus voltae [TaxId: 2188]} Back     information, alignment and structure
>d2abka_ a.96.1.1 (A:) Endonuclease III {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d2a1jb1 a.60.2.5 (B:219-296) DNA excision repair protein ERCC-1 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1vdda_ e.49.1.1 (A:) Recombination protein RecR {Deinococcus radiodurans [TaxId: 1299]} Back     information, alignment and structure
>d2noha1 a.96.1.3 (A:136-325) 8-oxoguanine glycosylase {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1pu6a_ a.96.1.5 (A:) 3-Methyladenine DNA glycosylase III (MagIII) {Helicobacter pylori [TaxId: 210]} Back     information, alignment and structure
>d2bcqa1 a.60.6.1 (A:252-327) DNA polymerase lambda {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d3bzka1 a.60.2.6 (A:474-563) Transcriptional accessory factor Tex {Pseudomonas aeruginosa [TaxId: 287]} Back     information, alignment and structure
>d1pzna1 a.60.4.1 (A:35-95) DNA repair protein Rad51, N-terminal domain {Archaeon Pyrococcus furiosus [TaxId: 2261]} Back     information, alignment and structure
>d2csba4 a.60.2.4 (A:465-519) Topoisomerase V {Methanopyrus kandleri [TaxId: 2320]} Back     information, alignment and structure
>d1jmsa1 a.60.6.1 (A:148-242) Terminal deoxynucleotidyl transferase {Mouse (Mus musculus) [TaxId: 10090]} Back     information, alignment and structure
>d2duya1 a.60.2.7 (A:11-75) Uncharacterized protein TTHA1967 {Thermus thermophilus [TaxId: 274]} Back     information, alignment and structure
>d2fmpa1 a.60.6.1 (A:10-91) DNA polymerase beta, N-terminal (8 kD)-domain {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d2edua1 a.60.2.7 (A:8-98) KIF22, C-terminal domain {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1mpga1 a.96.1.3 (A:100-282) 3-Methyladenine DNA glycosylase II (gene alkA or aidA) {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1jiha2 e.8.1.7 (A:1-389) DNA polymerase eta {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Back     information, alignment and structure
>d1ngna_ a.96.1.2 (A:) Mismatch-specific thymine glycosylase domain of the methyl-GpG binding protein mbd4 {Mouse (Mus musculus) [TaxId: 10090]} Back     information, alignment and structure
>d1im4a_ e.8.1.7 (A:) DinB homolog (DBH) {Archaeon Sulfolobus solfataricus [TaxId: 2287]} Back     information, alignment and structure
>d1szpa1 a.60.4.1 (A:81-144) DNA repair protein Rad51, N-terminal domain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Back     information, alignment and structure
>d2csba1 a.60.2.4 (A:351-409) Topoisomerase V {Methanopyrus kandleri [TaxId: 2320]} Back     information, alignment and structure