Query gi|254780303|ref|YP_003064716.1| DNA protecting protein DprA [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 77
No_of_seqs 102 out of 154
Neff 3.5
Searched_HMMs 23785
Date Mon May 30 08:18:37 2011
Command /home/congqian_1/programs/hhpred/hhsearch -i 254780303.hhm -d /home/congqian_1/database/pdb/pdb70.hhm
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 3maj_A DNA processing chain A; 99.4 3.5E-13 1.5E-17 94.9 9.0 71 6-76 10-80 (382)
2 1kft_A UVRC, excinuclease ABC 91.5 0.067 2.8E-06 30.9 1.9 38 24-61 26-64 (78)
3 1x2i_A HEF helicase/nuclease; 91.3 0.31 1.3E-05 27.2 5.1 32 24-55 16-47 (75)
4 2a1j_A DNA repair endonuclease 90.8 0.17 7.1E-06 28.6 3.4 37 24-60 6-43 (63)
5 1z00_B DNA repair endonuclease 90.7 0.2 8.3E-06 28.2 3.7 38 23-60 19-57 (84)
6 1exn_A 5'-exonuclease, 5'-nucl 90.1 0.16 6.8E-06 28.7 2.8 39 16-54 189-235 (290)
7 1rxw_A Flap structure-specific 86.9 0.45 1.9E-05 26.2 3.3 44 11-54 218-267 (336)
8 1z00_A DNA excision repair pro 85.5 0.61 2.6E-05 25.5 3.4 33 24-56 21-53 (89)
9 2a1j_B DNA excision repair pro 84.4 0.49 2.1E-05 26.0 2.5 31 26-56 36-66 (91)
10 1ul1_X Flap endonuclease-1; pr 83.1 0.68 2.9E-05 25.2 2.8 42 11-52 215-262 (379)
11 2nrt_A Uvrabc system protein C 82.4 0.76 3.2E-05 24.9 2.9 38 24-61 170-208 (220)
12 2izo_A FEN1, flap structure-sp 81.1 0.59 2.5E-05 25.6 1.9 42 12-54 217-266 (346)
13 3c65_A Uvrabc system protein C 80.4 0.27 1.1E-05 27.4 0.0 38 24-61 175-212 (226)
14 2ziu_A MUS81 protein; helix-ha 68.0 5 0.00021 20.3 3.9 33 21-53 236-268 (311)
15 1b43_A Protein (FEN-1); nuclea 64.6 1.6 6.8E-05 23.1 0.8 41 12-53 220-268 (340)
16 1a76_A Flap endonuclease-1 pro 63.8 4.5 0.00019 20.6 3.0 42 12-53 208-256 (326)
17 2bgw_A XPF endonuclease; hydro 35.4 26 0.0011 16.2 5.2 34 22-55 162-195 (219)
18 2zj8_A DNA helicase, putative 34.3 17 0.0007 17.3 2.0 35 24-58 648-683 (720)
19 2ztd_A Holliday junction ATP-d 30.3 32 0.0013 15.7 4.6 34 12-45 78-111 (212)
20 1bgx_T TAQ DNA polymerase; DNA 28.5 3.2 0.00014 21.4 -2.5 29 27-55 196-224 (832)
21 1cuk_A RUVA protein; DNA repai 24.8 40 0.0017 15.2 5.9 32 12-43 63-94 (203)
22 2csb_A Topoisomerase V, TOP61; 23.8 42 0.0018 15.1 3.2 28 23-50 412-439 (519)
23 1ixr_A Holliday junction DNA h 22.9 44 0.0018 14.9 4.5 33 12-44 62-94 (191)
No 1
>3maj_A DNA processing chain A; MCSG, PSI-2, structural genomics, protein structure initiati midwest center for structural genomics; HET: DNA; 2.05A {Rhodopseudomonas palustris}
Probab=99.44 E-value=3.5e-13 Score=94.87 Aligned_cols=71 Identities=42% Similarity=0.721 Sum_probs=65.6
Q ss_pred CCCCCCCCCHHHHHHHHHHHHCCCCCHHHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHH
Q ss_conf 11248788999999999998658968999999999749999999970999996145588767898997540
Q gi|254780303|r 6 PLKGGVSLTDDQKISWLRLIRSDNISPATCRDMINYFGSAEQALEMIPELAQRGAVYAGKRAFVQKNQQKK 76 (77)
Q Consensus 6 ~~~~~~~ls~~erlawLRL~Rt~~VGp~Tf~~Ll~~fGsA~aAL~aLP~la~rgG~~~~~ri~s~~~Ae~E 76 (77)
+-+.-..|||+|+++||+|.++++|||.|+++|+++|||++++++++|++.++.|..+..++.+.++|++|
T Consensus 10 ~~~~~~~~t~~e~l~wl~L~~~~giG~~~~~~Ll~~fgs~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~ 80 (382)
T 3maj_A 10 SDQGTTVLTEAQRIDWMRLIRAENVGPRTFRSLINHFGSARAALERLPELARRGGAARAGRIPSEDEARRE 80 (382)
T ss_dssp ---CCCCSCHHHHHHHHHHHTSTTCCHHHHHHHHHHHSSHHHHHHHHHHHHHHHTCSSCCCCCCHHHHHHH
T ss_pred CCCCCCCCCHHHHHHHHHHHCCCCCCHHHHHHHHHHHCCHHHHHHCCHHHHHHHHHHHHHCCCCHHHHHHH
T ss_conf 77788889999999999998289964999999999839999999779999987635665427998899999
No 2
>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=91.51 E-value=0.067 Score=30.91 Aligned_cols=38 Identities=16% Similarity=0.260 Sum_probs=29.2
Q ss_pred HHHCCCCCHHHHHHHHHHCCCHHHHHHHHHHH-HHHHCC
Q ss_conf 98658968999999999749999999970999-996145
Q gi|254780303|r 24 LIRSDNISPATCRDMINYFGSAEQALEMIPEL-AQRGAV 61 (77)
Q Consensus 24 L~Rt~~VGp~Tf~~Ll~~fGsA~aAL~aLP~l-a~rgG~ 61 (77)
|---|+|||.+...|+++|||-++...|-++- .+--|.
T Consensus 26 L~~IpGIG~k~ak~Ll~~F~si~~i~~As~eeL~~v~GI 64 (78)
T 1kft_A 26 LETIEGVGPKRRQMLLKYMGGLQGLRNASVEEIAKVPGI 64 (78)
T ss_dssp GGGCTTCSSSHHHHHHHHHSCHHHHHHCCHHHHTTSSST
T ss_pred CCCCCCCCHHHHHHHHHHHCCHHHHHHHCHHHHHCCCCC
T ss_conf 656999329999999999299499988379999807998
No 3
>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=91.30 E-value=0.31 Score=27.16 Aligned_cols=32 Identities=19% Similarity=0.277 Sum_probs=27.4
Q ss_pred HHHCCCCCHHHHHHHHHHCCCHHHHHHHHHHH
Q ss_conf 98658968999999999749999999970999
Q gi|254780303|r 24 LIRSDNISPATCRDMINYFGSAEQALEMIPEL 55 (77)
Q Consensus 24 L~Rt~~VGp~Tf~~Ll~~fGsA~aAL~aLP~l 55 (77)
|---|+|||++...|+++|||....+.|-.+-
T Consensus 16 L~~IpgIG~~~a~~L~~~F~s~~~i~~As~ee 47 (75)
T 1x2i_A 16 VEGLPHVSATLARRLLKHFGSVERVFTASVAE 47 (75)
T ss_dssp HTTSTTCCHHHHHHHHHHHCSHHHHHHCCHHH
T ss_pred HCCCCCCCHHHHHHHHHHHCCHHHHHHHHHHH
T ss_conf 84899942999999999968889899978999
No 4
>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=90.77 E-value=0.17 Score=28.62 Aligned_cols=37 Identities=14% Similarity=0.312 Sum_probs=28.1
Q ss_pred HHHCCCCCHHHHHHHHHHCCCHHHHHHHHH-HHHHHHC
Q ss_conf 986589689999999997499999999709-9999614
Q gi|254780303|r 24 LIRSDNISPATCRDMINYFGSAEQALEMIP-ELAQRGA 60 (77)
Q Consensus 24 L~Rt~~VGp~Tf~~Ll~~fGsA~aAL~aLP-~la~rgG 60 (77)
|..-|+||+.+...|+.+|||-.+...|-. +|..--|
T Consensus 6 L~~IPGIg~~~~~~Ll~~fgSi~~l~~as~eeL~~v~G 43 (63)
T 2a1j_A 6 LLKMPGVNAKNCRSLMHHVKNIAELAALSQDELTSILG 43 (63)
T ss_dssp HHTSTTCCHHHHHHHHHHCSSHHHHHTCCHHHHHHHHS
T ss_pred HHCCCCCCHHHHHHHHHHCCCHHHHHHCCHHHHHHCCC
T ss_conf 85299988999999999867999998799999987869
No 5
>1z00_B DNA repair endonuclease XPF; helix-hairpin-helix, hydrolase; HET: DNA; NMR {Homo sapiens} SCOP: a.60.2.5 PDB: 2aq0_A*
Probab=90.66 E-value=0.2 Score=28.24 Aligned_cols=38 Identities=13% Similarity=0.276 Sum_probs=29.2
Q ss_pred HHHHCCCCCHHHHHHHHHHCCCHHHHHHHHH-HHHHHHC
Q ss_conf 9986589689999999997499999999709-9999614
Q gi|254780303|r 23 RLIRSDNISPATCRDMINYFGSAEQALEMIP-ELAQRGA 60 (77)
Q Consensus 23 RL~Rt~~VGp~Tf~~Ll~~fGsA~aAL~aLP-~la~rgG 60 (77)
=|..-|+|||.+...||.+|||-.+...|-- +|..--|
T Consensus 19 ~L~~iPGIg~k~~~~Ll~~f~sl~~i~~AS~eeL~~v~G 57 (84)
T 1z00_B 19 FLLKMPGVNAKNCRSLMHHVKNIAELAALSQDELTSILG 57 (84)
T ss_dssp HHHTCSSCCHHHHHHHHHHSSCHHHHHHSCHHHHHHHHS
T ss_pred HHHCCCCCCHHHHHHHHHHCCCHHHHHHCCHHHHHHCCC
T ss_conf 998389999999999999966999998599999988759
No 6
>1exn_A 5'-exonuclease, 5'-nuclease; hydrolase; 2.50A {Enterobacteria phage T5} SCOP: a.60.7.1 c.120.1.2 PDB: 1ut5_A 1ut8_A 1xo1_A
Probab=90.12 E-value=0.16 Score=28.75 Aligned_cols=39 Identities=21% Similarity=0.359 Sum_probs=29.8
Q ss_pred HHHHHHHHHHH--------CCCCCHHHHHHHHHHCCCHHHHHHHHHH
Q ss_conf 99999999986--------5896899999999974999999997099
Q gi|254780303|r 16 DQKISWLRLIR--------SDNISPATCRDMINYFGSAEQALEMIPE 54 (77)
Q Consensus 16 ~erlawLRL~R--------t~~VGp~Tf~~Ll~~fGsA~aAL~aLP~ 54 (77)
.+-++++-|.= -++|||.|...||+.|||-+..+++++.
T Consensus 189 ~q~~d~kaL~GD~SDNIpGV~GiG~KtA~kLl~~ygsle~i~~~~~~ 235 (290)
T 1exn_A 189 EQFISLKAIMGDLGDNIRGVEGIGAKRGYNIIREFGNVLDIIDQLPL 235 (290)
T ss_dssp HHHHHHHHHHCBGGGTBCCCTTCCHHHHHHHHHHHCSHHHHHHHCSC
T ss_pred HHHCCEEECCCCCCCCCCCCCCCCHHHHHHHHHHHCCHHHHHHHHHH
T ss_conf 22102120788450179999985899999999873899999987775
No 7
>1rxw_A Flap structure-specific endonuclease; helical clamp, helix-3 turn-helix, hydrophobic wedge, 3' flap binding site, hydrolase/DNA complex; 2.00A {Archaeoglobus fulgidus} SCOP: a.60.7.1 c.120.1.2 PDB: 1rxv_A
Probab=86.90 E-value=0.45 Score=26.22 Aligned_cols=44 Identities=20% Similarity=0.305 Sum_probs=36.0
Q ss_pred CCCCHHHHHHHHHHHHC------CCCCHHHHHHHHHHCCCHHHHHHHHHH
Q ss_conf 78899999999999865------896899999999974999999997099
Q gi|254780303|r 11 VSLTDDQKISWLRLIRS------DNISPATCRDMINYFGSAEQALEMIPE 54 (77)
Q Consensus 11 ~~ls~~erlawLRL~Rt------~~VGp~Tf~~Ll~~fGsA~aAL~aLP~ 54 (77)
..++.++-++..=|.=+ ++|||.|...||+.|||-+..++.+..
T Consensus 218 lgl~~~qfid~~iL~G~Dy~~gv~giG~ktA~kli~~~~~i~~i~~~~~~ 267 (336)
T 1rxw_A 218 LGLTREQLIDIAILVGTDYNEGVKGVGVKKALNYIKTYGDIFRALKALKV 267 (336)
T ss_dssp HTCCHHHHHHHHHHHCBTTBCCCTTCCHHHHHHHHHHHSSHHHHHHHHTC
T ss_pred CCCCHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHCCHHHHHHHHHH
T ss_conf 09999999999986088768999996889999999992999999998763
No 8
>1z00_A DNA excision repair protein ERCC-1; helix-hairpin-helix, hydrolase; HET: DNA; NMR {Homo sapiens} SCOP: a.60.2.5
Probab=85.46 E-value=0.61 Score=25.47 Aligned_cols=33 Identities=21% Similarity=0.314 Sum_probs=27.9
Q ss_pred HHHCCCCCHHHHHHHHHHCCCHHHHHHHHHHHH
Q ss_conf 986589689999999997499999999709999
Q gi|254780303|r 24 LIRSDNISPATCRDMINYFGSAEQALEMIPELA 56 (77)
Q Consensus 24 L~Rt~~VGp~Tf~~Ll~~fGsA~aAL~aLP~la 56 (77)
|-.-++||+.+...|+++|||-++...|-++-.
T Consensus 21 L~~I~gIG~~~a~~L~~~Fgsl~~i~~As~eeL 53 (89)
T 1z00_A 21 LTTVKSVNKTDSQTLLTTFGSLEQLIAASREDL 53 (89)
T ss_dssp HTTSSSCCHHHHHHHHHHTCBHHHHHHCCHHHH
T ss_pred HCCCCCCCHHHHHHHHHHHCCHHHHHHHHHHHH
T ss_conf 758997599999999999488899999878777
No 9
>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=84.40 E-value=0.49 Score=26.00 Aligned_cols=31 Identities=19% Similarity=0.297 Sum_probs=27.0
Q ss_pred HCCCCCHHHHHHHHHHCCCHHHHHHHHHHHH
Q ss_conf 6589689999999997499999999709999
Q gi|254780303|r 26 RSDNISPATCRDMINYFGSAEQALEMIPELA 56 (77)
Q Consensus 26 Rt~~VGp~Tf~~Ll~~fGsA~aAL~aLP~la 56 (77)
--++||+.+...|+++|||-++...|-++-.
T Consensus 36 ~I~gIGk~~A~~L~~~F~Si~~l~~As~eeL 66 (91)
T 2a1j_B 36 TVKSVNKTDSQTLLTTFGSLEQLIAASREDL 66 (91)
T ss_dssp TSTTCCHHHHHHHHHHHSSHHHHHSCCHHHH
T ss_pred CCCCCCHHHHHHHHHHHCCCHHHHHHHHHHH
T ss_conf 6888599999999999588298999899975
No 10
>1ul1_X Flap endonuclease-1; protein complex, DNA-binding protein, flap DNA, flap endonuclease, sliding clamp, DNA clamp; 2.90A {Homo sapiens} SCOP: a.60.7.1 c.120.1.2
Probab=83.10 E-value=0.68 Score=25.18 Aligned_cols=42 Identities=26% Similarity=0.396 Sum_probs=35.1
Q ss_pred CCCCHHHHHHHHHHHHCC------CCCHHHHHHHHHHCCCHHHHHHHH
Q ss_conf 788999999999998658------968999999999749999999970
Q gi|254780303|r 11 VSLTDDQKISWLRLIRSD------NISPATCRDMINYFGSAEQALEMI 52 (77)
Q Consensus 11 ~~ls~~erlawLRL~Rt~------~VGp~Tf~~Ll~~fGsA~aAL~aL 52 (77)
..++.++-++..=|.=++ +|||.|...||..|||-+..++.+
T Consensus 215 ~g~~~~q~id~~~L~G~Dy~~gv~giG~ktA~kli~~~~sle~i~~~~ 262 (379)
T 1ul1_X 215 LGLNQEQFVDLCILLGSDYCESIRGIGPKRAVDLIQKHKSIEEIVRRL 262 (379)
T ss_dssp HTCCHHHHHHHHHHHHCSSSCCCTTCCHHHHHHHHHHSSSHHHHHTTC
T ss_pred CCCCHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHCCCHHHHHHHH
T ss_conf 089999999999971986677678866899999999819999999999
No 11
>2nrt_A Uvrabc system protein C; UVRC, endonuclease, RNAse H, helix hairpin helix, NER, hydrolase; 1.50A {Thermotoga maritima} PDB: 2nrv_A 2nrw_A 2nrx_A 2nrz_A
Probab=82.44 E-value=0.76 Score=24.92 Aligned_cols=38 Identities=26% Similarity=0.271 Sum_probs=30.4
Q ss_pred HHHCCCCCHHHHHHHHHHCCCHHHHHHHHHH-HHHHHCC
Q ss_conf 9865896899999999974999999997099-9996145
Q gi|254780303|r 24 LIRSDNISPATCRDMINYFGSAEQALEMIPE-LAQRGAV 61 (77)
Q Consensus 24 L~Rt~~VGp~Tf~~Ll~~fGsA~aAL~aLP~-la~rgG~ 61 (77)
|---|+|||.+-..||.+|||-++...|-.+ |++-.|.
T Consensus 170 Ld~I~GIG~k~~~~Ll~~Fgs~~~I~~As~eeL~~v~g~ 208 (220)
T 2nrt_A 170 LDNVPGIGPIRKKKLIEHFGSLENIRSASLEEIARVIGS 208 (220)
T ss_dssp HTTSTTCCHHHHHHHHHHHCSHHHHHTSCHHHHHHHHTC
T ss_pred CHHCCCCCHHHHHHHHHHCCCHHHHHHCCHHHHHHCCCC
T ss_conf 100379699999999998189999971899999868695
No 12
>2izo_A FEN1, flap structure-specific endonuclease; hydrolase, DNA repair, DNA-binding, endonuclease, metal-binding, excision repair, DNA replication, PCNA; HET: DNA; 2.9A {Sulfolobus solfataricus}
Probab=81.08 E-value=0.59 Score=25.57 Aligned_cols=42 Identities=24% Similarity=0.367 Sum_probs=31.3
Q ss_pred CCCHHHHHHHHHHH--------HCCCCCHHHHHHHHHHCCCHHHHHHHHHH
Q ss_conf 88999999999998--------65896899999999974999999997099
Q gi|254780303|r 12 SLTDDQKISWLRLI--------RSDNISPATCRDMINYFGSAEQALEMIPE 54 (77)
Q Consensus 12 ~ls~~erlawLRL~--------Rt~~VGp~Tf~~Ll~~fGsA~aAL~aLP~ 54 (77)
.++.++-++. -++ --++|||.|...||..|||-+..++.+-.
T Consensus 217 gi~~~qfid~-~iL~G~dyn~~gv~giG~ktA~kli~~~~sle~i~~~~~~ 266 (346)
T 2izo_A 217 GITREQLIDI-GILIGTDYNPDGIRGIGPERALKIIKKYGKIEKAMEYGEI 266 (346)
T ss_dssp TCCHHHHHHH-HHHHCCSSSTTCSTTCCHHHHHHHHHHSSCC---------
T ss_pred CCCHHHHHHH-HHHCCCCCCCCCCCCCCHHHHHHHHHHHCCHHHHHHHHHH
T ss_conf 9999999999-9845865686668983799999999993999999998998
No 13
>3c65_A Uvrabc system protein C; UVRC, endonuclease, nucleotide excision repair, DNA repair, RNAse H, cytoplasm, DNA damage, DNA excision; 1.90A {Bacillus stearothermophilus}
Probab=80.39 E-value=0.27 Score=27.44 Aligned_cols=38 Identities=26% Similarity=0.384 Sum_probs=30.2
Q ss_pred HHHCCCCCHHHHHHHHHHCCCHHHHHHHHHHHHHHHCC
Q ss_conf 98658968999999999749999999970999996145
Q gi|254780303|r 24 LIRSDNISPATCRDMINYFGSAEQALEMIPELAQRGAV 61 (77)
Q Consensus 24 L~Rt~~VGp~Tf~~Ll~~fGsA~aAL~aLP~la~rgG~ 61 (77)
|-.-|+|||.+-..|+.+|||-++...|-.+=...-|.
T Consensus 175 Ld~I~GIG~~~~~~Ll~~Fgs~~~i~~As~eeL~~vgI 212 (226)
T 3c65_A 175 LDDIPGVGEKRKKALLNYFGSVKKMKEATVEELQRANI 212 (226)
T ss_dssp --------------------------------------
T ss_pred CCCCCCCCHHHHHHHHHHCCCHHHHHHCCHHHHHHCCC
T ss_conf 10268869999999999818999997389999987699
No 14
>2ziu_A MUS81 protein; helix-hairpin-helix, alternative splicing, DNA damage, DNA recombination, DNA repair, hydrolase, magnesium; 2.70A {Danio rerio} PDB: 2ziv_A 2ziw_A
Probab=68.02 E-value=5 Score=20.30 Aligned_cols=33 Identities=9% Similarity=0.193 Sum_probs=29.3
Q ss_pred HHHHHHCCCCCHHHHHHHHHHCCCHHHHHHHHH
Q ss_conf 999986589689999999997499999999709
Q gi|254780303|r 21 WLRLIRSDNISPATCRDMINYFGSAEQALEMIP 53 (77)
Q Consensus 21 wLRL~Rt~~VGp~Tf~~Ll~~fGsA~aAL~aLP 53 (77)
-..|..-|+||+.....++++|+|+..-++|+-
T Consensus 236 ~~~L~qIpGIs~~~A~~I~~~y~T~~~L~~a~~ 268 (311)
T 2ziu_A 236 ARQLMQISGVSGDKAAAVLEHYSTVSSLLQAYD 268 (311)
T ss_dssp HHHHTTBTTCCHHHHHHHHHHCSSHHHHHHHHH
T ss_pred HHHHHHCCCCCHHHHHHHHHHCCCHHHHHHHHH
T ss_conf 999982799999999999997699999999998
No 15
>1b43_A Protein (FEN-1); nuclease, DNA repair, DNA replication, transferase; 2.00A {Pyrococcus furiosus} SCOP: a.60.7.1 c.120.1.2 PDB: 1mc8_A
Probab=64.62 E-value=1.6 Score=23.06 Aligned_cols=41 Identities=12% Similarity=0.169 Sum_probs=28.9
Q ss_pred CCCHHHHHHHHHHH--------HCCCCCHHHHHHHHHHCCCHHHHHHHHH
Q ss_conf 88999999999998--------6589689999999997499999999709
Q gi|254780303|r 12 SLTDDQKISWLRLI--------RSDNISPATCRDMINYFGSAEQALEMIP 53 (77)
Q Consensus 12 ~ls~~erlawLRL~--------Rt~~VGp~Tf~~Ll~~fGsA~aAL~aLP 53 (77)
-++.++-++ +=|+ --++|||.|...||+.|||-+..++...
T Consensus 220 gl~~~q~id-~all~G~dyn~~gi~giG~ktA~~li~~~~~~~~~~~~~~ 268 (340)
T 1b43_A 220 KLTREKLIE-LAILVGTDYNPGGIKGIGLKKALEIVRHSKDPLAKFQKQS 268 (340)
T ss_dssp TCCHHHHHH-HHHHHCCTTSTTCSTTCCHHHHHHHHHTCSSGGGGTGGGC
T ss_pred CCCHHHHHH-HHHHCCCCCCCCCCCCCCHHHHHHHHHHHCCHHHHHHHCC
T ss_conf 999999989-9997187568555798279999999999599999987501
No 16
>1a76_A Flap endonuclease-1 protein; 5'-3' EXO/endo nuclease, DNA replication, RTH, RAD27, DNA repair; 2.00A {Methanocaldococcus jannaschii} SCOP: a.60.7.1 c.120.1.2 PDB: 1a77_A
Probab=63.79 E-value=4.5 Score=20.56 Aligned_cols=42 Identities=7% Similarity=0.032 Sum_probs=28.1
Q ss_pred CCCHHHHHHHHHHH-------HCCCCCHHHHHHHHHHCCCHHHHHHHHH
Q ss_conf 88999999999998-------6589689999999997499999999709
Q gi|254780303|r 12 SLTDDQKISWLRLI-------RSDNISPATCRDMINYFGSAEQALEMIP 53 (77)
Q Consensus 12 ~ls~~erlawLRL~-------Rt~~VGp~Tf~~Ll~~fGsA~aAL~aLP 53 (77)
.++.++-++.-=|. .-++|||.|...||+.|||-+..++.+-
T Consensus 208 ~~~~~q~id~~il~g~d~n~~gi~giG~k~A~~li~~~~s~e~i~~~~~ 256 (326)
T 1a76_A 208 RISLDDLIDIAIFMGTDYNPGGVKGIGFKRAYELVRSGVAKDVLKKEVE 256 (326)
T ss_dssp TCCHHHHHHHHHHHCCTTSTTTTTTCCHHHHHHHHHHTCHHHHHHHHST
T ss_pred CCCHHHHHHHHHEECCCCCCCCCCCCCHHHHHHHHHHCCCHHHHHHHHH
T ss_conf 2587999987802796457889994249999999998499999988653
No 17
>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=35.43 E-value=26 Score=16.23 Aligned_cols=34 Identities=21% Similarity=0.200 Sum_probs=27.8
Q ss_pred HHHHHCCCCCHHHHHHHHHHCCCHHHHHHHHHHH
Q ss_conf 9998658968999999999749999999970999
Q gi|254780303|r 22 LRLIRSDNISPATCRDMINYFGSAEQALEMIPEL 55 (77)
Q Consensus 22 LRL~Rt~~VGp~Tf~~Ll~~fGsA~aAL~aLP~l 55 (77)
--|.--|+||+.+...|+++|||-..-+.|..+-
T Consensus 162 ~~L~~Ipgi~~~~A~~Ll~~f~Sl~~l~~as~~e 195 (219)
T 2bgw_A 162 YILQSFPGIGRRTAERILERFGSLERFFTASKAE 195 (219)
T ss_dssp HHHHTSTTCCHHHHHHHHHHHSSHHHHTTCCHHH
T ss_pred HHHHCCCCCCHHHHHHHHHHCCCHHHHHHCCHHH
T ss_conf 9984079989999999999869999998688999
No 18
>2zj8_A DNA helicase, putative SKI2-type helicase; RECA fold, ATP-binding, hydrolase, nucleotide- binding; 2.00A {Pyrococcus furiosus} PDB: 2zj5_A* 2zj2_A 2zja_A*
Probab=34.33 E-value=17 Score=17.33 Aligned_cols=35 Identities=23% Similarity=0.276 Sum_probs=28.6
Q ss_pred HHHCCCCCHHHHHHHHHH-CCCHHHHHHHHHHHHHH
Q ss_conf 986589689999999997-49999999970999996
Q gi|254780303|r 24 LIRSDNISPATCRDMINY-FGSAEQALEMIPELAQR 58 (77)
Q Consensus 24 L~Rt~~VGp~Tf~~Ll~~-fGsA~aAL~aLP~la~r 58 (77)
|..-|+|||+..+.|+++ |+|..+...+-|+-..+
T Consensus 648 L~~i~~ig~~~ar~L~~~G~~s~~~i~~~~~~~l~~ 683 (720)
T 2zj8_A 648 LMQLPLVGRRRARALYNSGFRSIEDISQARPEELLK 683 (720)
T ss_dssp GTTSTTCCHHHHHHHHTTTCCSHHHHHTCCHHHHHT
T ss_pred CCCCCCCCHHHHHHHHHCCCCCHHHHHCCCHHHHHH
T ss_conf 227899999999999987999999997499889852
No 19
>2ztd_A Holliday junction ATP-dependent DNA helicase RUVA; recombination, branch migration, DNA binding, oligomerization, acidic PIN; 2.40A {Mycobacterium tuberculosis} PDB: 2ztc_A 2zte_A 2h5x_A 1bvs_A
Probab=30.27 E-value=32 Score=15.73 Aligned_cols=34 Identities=9% Similarity=0.180 Sum_probs=27.7
Q ss_pred CCCHHHHHHHHHHHHCCCCCHHHHHHHHHHCCCH
Q ss_conf 8899999999999865896899999999974999
Q gi|254780303|r 12 SLTDDQKISWLRLIRSDNISPATCRDMINYFGSA 45 (77)
Q Consensus 12 ~ls~~erlawLRL~Rt~~VGp~Tf~~Ll~~fGsA 45 (77)
..+..||--+..|+--.+|||.+--.+|..+.-.
T Consensus 78 F~~~~Er~lF~~Li~VsGIGPK~AL~ILs~~~~~ 111 (212)
T 2ztd_A 78 FPDGETRDLFLTLLSVSGVGPRLAMAALAVHDAP 111 (212)
T ss_dssp ESSHHHHHHHHHHHTSTTCCHHHHHHHHHHSCHH
T ss_pred CCCHHHHHHHHHHHHCCCCCHHHHHHHHHCCCHH
T ss_conf 5998999999999834897746787888549999
No 20
>1bgx_T TAQ DNA polymerase; DNA polymerase, FAB, PCR, inhibition, helix-coil dynamics, inhibitor design, complex (polymerase/inhibitor); 2.30A {Thermus aquaticus} SCOP: a.60.7.1 c.120.1.2 c.55.3.5 e.8.1.1 PDB: 1cmw_A 1tau_A* 1taq_A*
Probab=28.55 E-value=3.2 Score=21.35 Aligned_cols=29 Identities=28% Similarity=0.441 Sum_probs=22.5
Q ss_pred CCCCCHHHHHHHHHHCCCHHHHHHHHHHH
Q ss_conf 58968999999999749999999970999
Q gi|254780303|r 27 SDNISPATCRDMINYFGSAEQALEMIPEL 55 (77)
Q Consensus 27 t~~VGp~Tf~~Ll~~fGsA~aAL~aLP~l 55 (77)
-++|||.|...||+.|||-+..++++.++
T Consensus 196 v~giG~ktA~~ll~~~~~~~~i~~~~~~~ 224 (832)
T 1bgx_T 196 VKGIGEKTARKLLEEWGSLEALLKNLDRL 224 (832)
T ss_dssp CCCSSSCTTTTTGGGTTSSCSSSSSCCCC
T ss_pred CCCCCHHHHHHHHHHCCCHHHHHHHHHHC
T ss_conf 66557477999986156078888777640
No 21
>1cuk_A RUVA protein; DNA repair, SOS response, DNA-binding, DNA recombination, helicase; 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=24.75 E-value=40 Score=15.15 Aligned_cols=32 Identities=9% Similarity=0.274 Sum_probs=26.0
Q ss_pred CCCHHHHHHHHHHHHCCCCCHHHHHHHHHHCC
Q ss_conf 88999999999998658968999999999749
Q gi|254780303|r 12 SLTDDQKISWLRLIRSDNISPATCRDMINYFG 43 (77)
Q Consensus 12 ~ls~~erlawLRL~Rt~~VGp~Tf~~Ll~~fG 43 (77)
..+..||--+..|+--.+|||.+--.+|..+.
T Consensus 63 F~~~~Er~lF~~Li~VsGIGPK~AL~ILs~~~ 94 (203)
T 1cuk_A 63 FNNKQERTLFKELIKTNGVGPKLALAILSGMS 94 (203)
T ss_dssp ESSHHHHHHHHHHHHSSSCCHHHHHHHHHHSC
T ss_pred CCCHHHHHHHHHHHCCCCCCHHHHHHHHHCCC
T ss_conf 19469999999985768857566888861279
No 22
>2csb_A Topoisomerase V, TOP61; topoisomerase IB, helix-turn-helix, helix- hairpin-helix, HHH motif, three helix bundle; 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=23.84 E-value=42 Score=15.05 Aligned_cols=28 Identities=18% Similarity=0.457 Sum_probs=23.7
Q ss_pred HHHHCCCCCHHHHHHHHHHCCCHHHHHH
Q ss_conf 9986589689999999997499999999
Q gi|254780303|r 23 RLIRSDNISPATCRDMINYFGSAEQALE 50 (77)
Q Consensus 23 RL~Rt~~VGp~Tf~~Ll~~fGsA~aAL~ 50 (77)
-|-..++||..|..+|+..||.++.+-.
T Consensus 412 eltkkegvgrktaerllrafgnpervkq 439 (519)
T 2csb_A 412 ELTKKEGVGRKTAERLLRAFGNPERVKQ 439 (519)
T ss_dssp HHHTSTTCCHHHHHHHHHHHSSHHHHHH
T ss_pred HHHHHCCCCHHHHHHHHHHHCCHHHHHH
T ss_conf 7765406456579999997099899999
No 23
>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=22.89 E-value=44 Score=14.94 Aligned_cols=33 Identities=6% Similarity=0.153 Sum_probs=25.3
Q ss_pred CCCHHHHHHHHHHHHCCCCCHHHHHHHHHHCCC
Q ss_conf 889999999999986589689999999997499
Q gi|254780303|r 12 SLTDDQKISWLRLIRSDNISPATCRDMINYFGS 44 (77)
Q Consensus 12 ~ls~~erlawLRL~Rt~~VGp~Tf~~Ll~~fGs 44 (77)
..+..||--+..|+--.+|||.+.-.+|..+.-
T Consensus 62 F~~~~Er~lF~~Li~V~GIGpK~Al~ILs~~~~ 94 (191)
T 1ixr_A 62 FPDEENLALFELLLSVSGVGPKVALALLSALPP 94 (191)
T ss_dssp ESSHHHHHHHHHHHSSSCCCHHHHHHHHHHSCH
T ss_pred CCCHHHHHHHHHHHCCCCCCHHHHHHHHHCCCH
T ss_conf 182899999999857688377889888725999
Done!