Query psy10399
Match_columns 442
No_of_seqs 325 out of 1044
Neff 6.3
Searched_HMMs 29240
Date Fri Aug 16 16:53:42 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy10399.a3m -d /work/01045/syshi/HHdatabase/pdb70.hhm -o /work/01045/syshi/hhsearch_pdb/10399hhsearch_pdb -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 3qio_A GAG-POL polyprotein; RN 98.4 1.2E-07 4E-12 84.7 2.9 33 276-308 115-147 (150)
2 2kq2_A Ribonuclease H-related 98.3 5.9E-08 2E-12 86.2 -0.4 31 280-310 109-139 (147)
3 3h08_A RNH (ribonuclease H); R 98.2 1.5E-07 5.1E-12 83.0 -1.2 29 279-307 115-143 (146)
4 3p1g_A Xenotropic murine leuke 98.1 3.3E-07 1.1E-11 83.2 -0.5 31 277-307 120-155 (165)
5 2qkb_A Ribonuclease H1, HS-RNA 98.1 5.7E-07 1.9E-11 80.1 0.6 30 278-307 121-150 (154)
6 1jl1_A Ribonuclease HI; RNAse 98.0 8.9E-07 3E-11 79.1 0.8 30 279-308 114-143 (155)
7 2e4l_A Ribonuclease HI, RNAse 98.0 9.1E-07 3.1E-11 79.3 0.8 30 279-308 116-145 (158)
8 1ril_A Ribonuclease H; hydrola 97.8 2E-06 6.8E-11 77.8 -0.7 30 279-308 119-148 (166)
9 1mu2_A HIV-2 RT; HIV-2 reverse 97.7 1.1E-05 3.7E-10 86.0 3.4 31 276-306 525-555 (555)
10 2lsn_A Reverse transcriptase; 97.7 4E-06 1.4E-10 76.1 -0.8 30 277-306 126-161 (165)
11 2zd1_A Reverse transcriptase/r 97.6 1.8E-05 6.1E-10 84.4 1.8 29 277-305 529-557 (557)
12 3hst_B Protein RV2228C/MT2287; 96.0 0.0021 7.2E-08 55.2 1.5 30 273-306 102-131 (141)
13 3u3g_D Ribonuclease H, RNAse H 95.6 0.0025 8.6E-08 54.3 0.8 27 276-306 109-135 (140)
14 2ehg_A Ribonuclease HI; RNAse 94.9 0.0055 1.9E-07 53.5 0.4 24 280-307 110-133 (149)
No 1
>3qio_A GAG-POL polyprotein; RNAse H, inhibitor, nuclease, transferase, hydrolase- complex; HET: QID; 1.40A {Hiv-1 M} SCOP: c.55.3.1 PDB: 3qin_A* 3hyf_A* 1o1w_A 3lp3_A* 1hrh_A 3k2p_A* 1rdh_A
Probab=98.38 E-value=1.2e-07 Score=84.71 Aligned_cols=33 Identities=30% Similarity=0.526 Sum_probs=29.7
Q ss_pred hccceeEEEeccCCCCCCCChHHHHHhcCCCCC
Q psy10399 276 ACGKEISFMWCPSHCGISGNEAVDVAAKNPSPS 308 (442)
Q Consensus 276 ~~~~~I~l~WIPgH~gI~GNE~AD~lAK~A~~~ 308 (442)
.+...|+|.|||||+|++|||.||++|++|+..
T Consensus 115 ~~~~~v~~~wV~gH~g~~~Ne~AD~LA~~a~~~ 147 (150)
T 3qio_A 115 IKKEKVYLAWVPAHKGIGGNEQVDKLVSAGIRK 147 (150)
T ss_dssp TTCSEEEEEECCTTSCCHHHHHHHHHHHTTTSC
T ss_pred hhcCceEEEEccCcCCChhHHHHHHHHHHHHHH
Confidence 356789999999999999999999999999754
No 2
>2kq2_A Ribonuclease H-related protein; PSI, NESG, protein structure, APO enzyme, structural genomics, protein structure initiative; NMR {Desulfitobacterium hafniense dcb-2} PDB: 2kw4_A
Probab=98.32 E-value=5.9e-08 Score=86.17 Aligned_cols=31 Identities=29% Similarity=0.182 Sum_probs=28.0
Q ss_pred eeEEEeccCCCCCCCChHHHHHhcCCCCCCC
Q psy10399 280 EISFMWCPSHCGISGNEAVDVAAKNPSPSFP 310 (442)
Q Consensus 280 ~I~l~WIPgH~gI~GNE~AD~lAK~A~~~~~ 310 (442)
.|+|.|||||+|++|||.||+|||+|+...+
T Consensus 109 ~v~~~wV~gH~g~~~Ne~AD~LA~~a~~~~~ 139 (147)
T 2kq2_A 109 IYSFEKVKAHSGNEFNDYVDMKAKSALGIRD 139 (147)
T ss_dssp TCCBCCCCCCCCCHHHHHHHHHHHHHHTCCC
T ss_pred CeeEEEecCcCCCcchHHHHHHHHHHHhccc
Confidence 7999999999999999999999999876543
No 3
>3h08_A RNH (ribonuclease H); RNAse H, 3D-structure, endonuclease, hydrolase, magnesium, metal-binding; 1.60A {Chlorobaculum tepidum}
Probab=98.17 E-value=1.5e-07 Score=82.98 Aligned_cols=29 Identities=17% Similarity=0.146 Sum_probs=25.4
Q ss_pred ceeEEEeccCCCCCCCChHHHHHhcCCCC
Q psy10399 279 KEISFMWCPSHCGISGNEAVDVAAKNPSP 307 (442)
Q Consensus 279 ~~I~l~WIPgH~gI~GNE~AD~lAK~A~~ 307 (442)
..|+|.|||||+|++|||.||+|||+|+.
T Consensus 115 ~~v~~~~V~gH~g~~~N~~AD~LA~~a~~ 143 (146)
T 3h08_A 115 HRVTFHKVKGHSDNPYNSRADELARLAIK 143 (146)
T ss_dssp SEEEEEECCC-CCSHHHHHHHHHHHHHHH
T ss_pred CceEEEEcCCcCCcHhHHHHHHHHHHHHH
Confidence 45999999999999999999999998763
No 4
>3p1g_A Xenotropic murine leukemia virus-related virus (X H domain; XMRV, RNAse H, reverse transcriptase, transcription; 1.50A {Xenotropic mulv-related virus} PDB: 3v1q_A 3v1o_A 3v1r_A* 2hb5_A 4e89_A
Probab=98.10 E-value=3.3e-07 Score=83.19 Aligned_cols=31 Identities=32% Similarity=0.538 Sum_probs=28.5
Q ss_pred ccceeEEEeccCCCC-----CCCChHHHHHhcCCCC
Q psy10399 277 CGKEISFMWCPSHCG-----ISGNEAVDVAAKNPSP 307 (442)
Q Consensus 277 ~~~~I~l~WIPgH~g-----I~GNE~AD~lAK~A~~ 307 (442)
.+..|+|.|||||+| ++|||.||++||+|+.
T Consensus 120 ~~~~v~~~wVkgH~g~~~~~~~gNe~AD~LA~~aa~ 155 (165)
T 3p1g_A 120 LPKRLSIIHCPGHQKGNSAEARGNRMADQAAREAAM 155 (165)
T ss_dssp SBSEEEEEECCSSCCSCSHHHHHHHHHHHHHHHHHH
T ss_pred cCCceEEEEecCCCCCCcCcchHHHHHHHHHHHHHh
Confidence 567899999999999 9999999999998864
No 5
>2qkb_A Ribonuclease H1, HS-RNAse HC, RNAse H1; RNA/DNA hybrid; 2.40A {Homo sapiens} PDB: 2qk9_A 2qkk_A*
Probab=98.08 E-value=5.7e-07 Score=80.08 Aligned_cols=30 Identities=37% Similarity=0.663 Sum_probs=27.5
Q ss_pred cceeEEEeccCCCCCCCChHHHHHhcCCCC
Q psy10399 278 GKEISFMWCPSHCGISGNEAVDVAAKNPSP 307 (442)
Q Consensus 278 ~~~I~l~WIPgH~gI~GNE~AD~lAK~A~~ 307 (442)
+..|+|.|||||+|++|||.||+|||+|+.
T Consensus 121 ~~~v~~~~V~~H~g~~~N~~AD~LA~~a~~ 150 (154)
T 2qkb_A 121 GMDIQWMHVPGHSGFIGNEEADRLAREGAK 150 (154)
T ss_dssp TCEEEEEECCTTSSCHHHHHHHHHHHHHHT
T ss_pred CCceEEEEccCCCCCHhHHHHHHHHHHHHH
Confidence 467999999999999999999999998864
No 6
>1jl1_A Ribonuclease HI; RNAse HI, protein stability, thermostability, hydrogen exchange, cooperativity, hydrolase; 1.30A {Escherichia coli} SCOP: c.55.3.1 PDB: 1f21_A 1jxb_A 1g15_A 1rch_A 1rdd_A 1rnh_A* 2rn2_A 1rda_A 1law_A 1rdb_A 1lav_A 3aa4_A 1rbu_A 1gob_A 1rdc_A 1kvc_A 3aa3_A 3aa2_A 3aa5_X 1rbv_A ...
Probab=98.03 E-value=8.9e-07 Score=79.10 Aligned_cols=30 Identities=27% Similarity=0.509 Sum_probs=27.3
Q ss_pred ceeEEEeccCCCCCCCChHHHHHhcCCCCC
Q psy10399 279 KEISFMWCPSHCGISGNEAVDVAAKNPSPS 308 (442)
Q Consensus 279 ~~I~l~WIPgH~gI~GNE~AD~lAK~A~~~ 308 (442)
..|+|.|||||+|++|||.||+|||+|+..
T Consensus 114 ~~v~~~wV~gH~g~~~Ne~AD~LA~~a~~~ 143 (155)
T 1jl1_A 114 HQIKWEWVKGHAGHPENERADELARAAAMN 143 (155)
T ss_dssp CEEEEEECCSSTTCHHHHHHHHHHHHHHHS
T ss_pred CceEEEEcCCCCCCHHHHHHHHHHHHHHhc
Confidence 479999999999999999999999998643
No 7
>2e4l_A Ribonuclease HI, RNAse HI; hydrolase, endoribonuclease; 2.00A {Shewanella oneidensis} PDB: 2zqb_A
Probab=98.02 E-value=9.1e-07 Score=79.34 Aligned_cols=30 Identities=27% Similarity=0.551 Sum_probs=27.5
Q ss_pred ceeEEEeccCCCCCCCChHHHHHhcCCCCC
Q psy10399 279 KEISFMWCPSHCGISGNEAVDVAAKNPSPS 308 (442)
Q Consensus 279 ~~I~l~WIPgH~gI~GNE~AD~lAK~A~~~ 308 (442)
..|+|.|||||+|++|||.||+|||+|+..
T Consensus 116 ~~v~~~wV~gH~g~~~Ne~AD~LAk~a~~~ 145 (158)
T 2e4l_A 116 HQIDWRWVKGHAGHAENERCDQLARAAAEA 145 (158)
T ss_dssp SEEEEEECCTTCCCHHHHHHHHHHHHHHHS
T ss_pred CcEEEEEccCCCCchhHHHHHHHHHHHHHh
Confidence 479999999999999999999999998654
No 8
>1ril_A Ribonuclease H; hydrolase(endoribonuclease); 2.80A {Thermus thermophilus} SCOP: c.55.3.1 PDB: 2rpi_A
Probab=97.82 E-value=2e-06 Score=77.82 Aligned_cols=30 Identities=30% Similarity=0.486 Sum_probs=27.4
Q ss_pred ceeEEEeccCCCCCCCChHHHHHhcCCCCC
Q psy10399 279 KEISFMWCPSHCGISGNEAVDVAAKNPSPS 308 (442)
Q Consensus 279 ~~I~l~WIPgH~gI~GNE~AD~lAK~A~~~ 308 (442)
..|+|.|||||+|++|||.||+|||+|+..
T Consensus 119 ~~v~~~wV~gH~g~~~Ne~AD~LAk~a~~~ 148 (166)
T 1ril_A 119 HRVRFHFVKGHTGHPENERVDREARRQAQS 148 (166)
T ss_dssp SEEECCCCCGGGSCTHHHHHHHHHHHHHTS
T ss_pred CeEEEEEeeCCCCchhHHHHHHHHHHHHHH
Confidence 479999999999999999999999988654
No 9
>1mu2_A HIV-2 RT; HIV-2 reverse transcriptase, AIDS, polymerase, drug design, transferase; 2.35A {Human immunodeficiency virus 2} SCOP: c.55.3.1 e.8.1.2 PDB: 1mu2_B
Probab=97.74 E-value=1.1e-05 Score=86.02 Aligned_cols=31 Identities=32% Similarity=0.534 Sum_probs=28.4
Q ss_pred hccceeEEEeccCCCCCCCChHHHHHhcCCC
Q psy10399 276 ACGKEISFMWCPSHCGISGNEAVDVAAKNPS 306 (442)
Q Consensus 276 ~~~~~I~l~WIPgH~gI~GNE~AD~lAK~A~ 306 (442)
..+..|+|.|||||+|++|||.||++||+|+
T Consensus 525 ~~~~~v~~~wV~~H~g~~~Ne~AD~LA~~a~ 555 (555)
T 1mu2_A 525 IKKEAIYVAWVPAHKGIGGNQEVDHLVSQGI 555 (555)
T ss_dssp HHCSEEEEEECCSSSCCTTHHHHHHHHHTTC
T ss_pred ccCCcEEEEEEECCCCChhHHHHHHHHHhhC
Confidence 4567899999999999999999999999884
No 10
>2lsn_A Reverse transcriptase; RNAse H, viral protein; NMR {Simian foamy virus}
Probab=97.69 E-value=4e-06 Score=76.05 Aligned_cols=30 Identities=23% Similarity=0.203 Sum_probs=25.8
Q ss_pred ccceeEEEeccCCCCC------CCChHHHHHhcCCC
Q psy10399 277 CGKEISFMWCPSHCGI------SGNEAVDVAAKNPS 306 (442)
Q Consensus 277 ~~~~I~l~WIPgH~gI------~GNE~AD~lAK~A~ 306 (442)
....|+|.|||||+|+ +|||.||+||++|+
T Consensus 126 ~~~~v~~~~VkgH~g~~~~~~~~gNe~AD~LA~~gA 161 (165)
T 2lsn_A 126 MKPDITIQHEKGHQPTNTSIHTEGNALADKLATQGS 161 (165)
T ss_dssp HCTTCEEEECCSSSCSSSCHHHHHHHHHHHHHHHHH
T ss_pred CCCCEEEEEEeCCCCccCCCCChHHHHHHHHHHHhh
Confidence 3456999999999996 58999999999875
No 11
>2zd1_A Reverse transcriptase/ribonuclease H; P51/P66, hetero dimer, NNRTI, nonnucleoside inhibitor, AIDS, HIV, rilpivirine, diarylpyrimidine, DAPY, DNA recombination; HET: T27; 1.80A {Human immunodeficiency virus 1} PDB: 3is9_A* 3irx_A* 2ze2_A* 3bgr_A* 3qlh_A* 3klf_A* 3qo9_A* 1dlo_A 1bqm_A 2be2_A* 1s6q_A* 1s6p_A* 1s9g_A* 1suq_A* 2b5j_A* 2b6a_A* 2ban_A* 1s9e_A* 1hni_A* 1hnv_A* ...
Probab=97.56 E-value=1.8e-05 Score=84.44 Aligned_cols=29 Identities=34% Similarity=0.637 Sum_probs=24.2
Q ss_pred ccceeEEEeccCCCCCCCChHHHHHhcCC
Q psy10399 277 CGKEISFMWCPSHCGISGNEAVDVAAKNP 305 (442)
Q Consensus 277 ~~~~I~l~WIPgH~gI~GNE~AD~lAK~A 305 (442)
....|+|.|||||+|++|||.||++||+|
T Consensus 529 ~~~~v~~~wV~~H~g~~~Ne~AD~LA~~a 557 (557)
T 2zd1_A 529 KKEKVYLAWVPAHKGIGGNEQVDKLVSAG 557 (557)
T ss_dssp HCSEEEEEECCSSSCCTTCCGGGGCC---
T ss_pred cCCCEEEEEcCCCCCChhHHHHHHHHhcC
Confidence 35689999999999999999999999986
No 12
>3hst_B Protein RV2228C/MT2287; ribonuclease H1, RV2228C N-terminal domain, fusion protein, maltose binding protein, HYDR; HET: MLR TAR; 2.25A {Mycobacterium tuberculosis}
Probab=95.95 E-value=0.0021 Score=55.15 Aligned_cols=30 Identities=23% Similarity=0.418 Sum_probs=25.0
Q ss_pred hhhhccceeEEEeccCCCCCCCChHHHHHhcCCC
Q psy10399 273 DLVACGKEISFMWCPSHCGISGNEAVDVAAKNPS 306 (442)
Q Consensus 273 ~L~~~~~~I~l~WIPgH~gI~GNE~AD~lAK~A~ 306 (442)
.+..+...|+|.|||+ +|||.||++||+|.
T Consensus 102 ~l~~~~~~v~~~~V~~----~~N~~AD~LA~~a~ 131 (141)
T 3hst_B 102 ALASQFRRINYEWVPR----ARNTYADRLANDAM 131 (141)
T ss_dssp HHHTTSSEEEEEECCG----GGCHHHHHHHHHHH
T ss_pred HHHhcCCeEEEEEcCC----cccHHHHHHHHHHH
Confidence 3445567899999995 99999999999875
No 13
>3u3g_D Ribonuclease H, RNAse H1; hydrolase, cleave the RNA strand of RNA/DNA hybrid; 1.40A {Uncultured organism}
Probab=95.65 E-value=0.0025 Score=54.31 Aligned_cols=27 Identities=15% Similarity=0.187 Sum_probs=22.6
Q ss_pred hccceeEEEeccCCCCCCCChHHHHHhcCCC
Q psy10399 276 ACGKEISFMWCPSHCGISGNEAVDVAAKNPS 306 (442)
Q Consensus 276 ~~~~~I~l~WIPgH~gI~GNE~AD~lAK~A~ 306 (442)
++...|+|.|||+ +|||.||++||+|.
T Consensus 109 ~~~~~v~~~~V~~----~~N~~AD~LA~~a~ 135 (140)
T 3u3g_D 109 ERVPNLVFVHIPR----EKNARADELVNEAI 135 (140)
T ss_dssp HHCTTCEEEECCG----GGGHHHHHHHHHHH
T ss_pred cCCCcEEEEEcCc----hhhHHHHHHHHHHH
Confidence 3335899999994 99999999999874
No 14
>2ehg_A Ribonuclease HI; RNAse HI, hyperthermophilic archaeon, D stranded RNA-dependent RNAse, hydrolase; 1.60A {Sulfolobus tokodaii} PDB: 3aly_A
Probab=94.87 E-value=0.0055 Score=53.45 Aligned_cols=24 Identities=17% Similarity=0.462 Sum_probs=21.2
Q ss_pred eeEEEeccCCCCCCCChHHHHHhcCCCC
Q psy10399 280 EISFMWCPSHCGISGNEAVDVAAKNPSP 307 (442)
Q Consensus 280 ~I~l~WIPgH~gI~GNE~AD~lAK~A~~ 307 (442)
.|+|.|||+ +|||.||++||+|+.
T Consensus 110 ~v~~~~V~~----~~N~~AD~LA~~a~~ 133 (149)
T 2ehg_A 110 NATLIWVPR----EENKEADRLSRVAYE 133 (149)
T ss_dssp TCEEEECCG----GGCHHHHHHHHHHHH
T ss_pred CEEEEEcCC----cccHHHHHHHHHHHH
Confidence 499999999 599999999998753
Done!