Query psy13365
Match_columns 231
No_of_seqs 155 out of 270
Neff 6.8
Searched_HMMs 29240
Date Fri Aug 16 17:38:15 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy13365.a3m -d /work/01045/syshi/HHdatabase/pdb70.hhm -o /work/01045/syshi/hhsearch_pdb/13365hhsearch_pdb -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 2qkb_A Ribonuclease H1, HS-RNA 98.7 3E-09 1E-13 85.0 2.5 27 42-68 121-147 (154)
2 3qio_A GAG-POL polyprotein; RN 98.7 6.2E-09 2.1E-13 83.3 3.5 28 41-68 116-143 (150)
3 3h08_A RNH (ribonuclease H); R 98.7 5.3E-09 1.8E-13 82.6 2.4 47 22-68 63-140 (146)
4 2e4l_A Ribonuclease HI, RNAse 98.6 1.4E-08 4.7E-13 81.6 3.0 27 43-69 116-142 (158)
5 2kq2_A Ribonuclease H-related 98.5 7.9E-09 2.7E-13 82.2 -0.8 46 23-69 71-134 (147)
6 1ril_A Ribonuclease H; hydrola 98.5 2.9E-08 1E-12 80.4 1.8 27 43-69 119-145 (166)
7 1jl1_A Ribonuclease HI; RNAse 98.5 6.6E-08 2.2E-12 77.3 2.8 27 43-69 114-140 (155)
8 3p1g_A Xenotropic murine leuke 98.3 1.4E-07 4.8E-12 76.6 2.2 47 22-68 81-152 (165)
9 1mu2_A HIV-2 RT; HIV-2 reverse 98.2 6.4E-07 2.2E-11 85.1 3.9 47 22-68 490-553 (555)
10 2zd1_A Reverse transcriptase/r 98.2 6.3E-07 2.2E-11 85.2 2.8 47 22-68 493-556 (557)
11 2lsn_A Reverse transcriptase; 98.1 8.4E-07 2.9E-11 72.0 1.4 26 43-68 128-159 (165)
12 3hst_B Protein RV2228C/MT2287; 97.3 8.9E-05 3E-09 57.1 2.2 46 19-68 64-129 (141)
13 3u3g_D Ribonuclease H, RNAse H 97.2 9.2E-05 3.1E-09 56.7 1.5 51 14-68 58-133 (140)
14 2ehg_A Ribonuclease HI; RNAse 96.8 0.00037 1.3E-08 54.5 1.9 44 21-68 68-130 (149)
No 1
>2qkb_A Ribonuclease H1, HS-RNAse HC, RNAse H1; RNA/DNA hybrid; 2.40A {Homo sapiens} PDB: 2qk9_A 2qkk_A*
Probab=98.74 E-value=3e-09 Score=84.98 Aligned_cols=27 Identities=15% Similarity=0.183 Sum_probs=24.8
Q ss_pred CCeEEEEEeccCCCCCcchhHHHHhhh
Q psy13365 42 SQAVHLVSGMVHSALEGKKTFYQVQRH 68 (231)
Q Consensus 42 ~~~V~l~WIPgH~GI~GNE~AD~aak~ 68 (231)
+..|+|.|||||+|++|||.||+||++
T Consensus 121 ~~~v~~~~V~~H~g~~~N~~AD~LA~~ 147 (154)
T 2qkb_A 121 GMDIQWMHVPGHSGFIGNEEADRLARE 147 (154)
T ss_dssp TCEEEEEECCTTSSCHHHHHHHHHHHH
T ss_pred CCceEEEEccCCCCCHhHHHHHHHHHH
Confidence 457999999999999999999999985
No 2
>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=98.71 E-value=6.2e-09 Score=83.26 Aligned_cols=28 Identities=18% Similarity=0.196 Sum_probs=25.7
Q ss_pred CCCeEEEEEeccCCCCCcchhHHHHhhh
Q psy13365 41 KSQAVHLVSGMVHSALEGKKTFYQVQRH 68 (231)
Q Consensus 41 ~~~~V~l~WIPgH~GI~GNE~AD~aak~ 68 (231)
+...|+|.|||||+|++|||.||+||++
T Consensus 116 ~~~~v~~~wV~gH~g~~~Ne~AD~LA~~ 143 (150)
T 3qio_A 116 KKEKVYLAWVPAHKGIGGNEQVDKLVSA 143 (150)
T ss_dssp TCSEEEEEECCTTSCCHHHHHHHHHHHT
T ss_pred hcCceEEEEccCcCCChhHHHHHHHHHH
Confidence 4568999999999999999999999985
No 3
>3h08_A RNH (ribonuclease H); RNAse H, 3D-structure, endonuclease, hydrolase, magnesium, metal-binding; 1.60A {Chlorobaculum tepidum}
Probab=98.68 E-value=5.3e-09 Score=82.63 Aligned_cols=47 Identities=15% Similarity=0.032 Sum_probs=37.3
Q ss_pred ccccccCCchhhHHHHHh-------------h------------------CCCeEEEEEeccCCCCCcchhHHHHhhh
Q psy13365 22 KTLKNHCDSCCDVKILQN-------------E------------------KSQAVHLVSGMVHSALEGKKTFYQVQRH 68 (231)
Q Consensus 22 ~~~~~~~~~~~~~~~~~~-------------~------------------~~~~V~l~WIPgH~GI~GNE~AD~aak~ 68 (231)
..+.+.+||...|+.|.. + +...|+|.|||||+|++|||.||+||++
T Consensus 63 ~~v~I~tDS~~vi~~i~~~w~~~W~~~~w~~~~~~~v~n~~l~~~~~~~~~~~~v~~~~V~gH~g~~~N~~AD~LA~~ 140 (146)
T 3h08_A 63 ARVQLYSDSAYLVNAMNEGWLKRWVKNGWKTAAKKPVENIDLWQEILKLTTLHRVTFHKVKGHSDNPYNSRADELARL 140 (146)
T ss_dssp CEEEEEESCHHHHHHHHSSHHHHHHHTTCC----CCCTTHHHHHHHHHHHHHSEEEEEECCC-CCSHHHHHHHHHHHH
T ss_pred CcEEEEeChHHHHHHHHHHHHHHHHHCCCccCCCCCcCCHHHHHHHHHHHhhCceEEEEcCCcCCcHhHHHHHHHHHH
Confidence 677888888888877765 1 1236999999999999999999999885
No 4
>2e4l_A Ribonuclease HI, RNAse HI; hydrolase, endoribonuclease; 2.00A {Shewanella oneidensis} PDB: 2zqb_A
Probab=98.61 E-value=1.4e-08 Score=81.65 Aligned_cols=27 Identities=11% Similarity=0.021 Sum_probs=24.8
Q ss_pred CeEEEEEeccCCCCCcchhHHHHhhhc
Q psy13365 43 QAVHLVSGMVHSALEGKKTFYQVQRHN 69 (231)
Q Consensus 43 ~~V~l~WIPgH~GI~GNE~AD~aak~~ 69 (231)
..|+|.|||||+|++|||.||+||+++
T Consensus 116 ~~v~~~wV~gH~g~~~Ne~AD~LAk~a 142 (158)
T 2e4l_A 116 HQIDWRWVKGHAGHAENERCDQLARAA 142 (158)
T ss_dssp SEEEEEECCTTCCCHHHHHHHHHHHHH
T ss_pred CcEEEEEccCCCCchhHHHHHHHHHHH
Confidence 479999999999999999999998863
No 5
>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=98.52 E-value=7.9e-09 Score=82.17 Aligned_cols=46 Identities=9% Similarity=-0.101 Sum_probs=34.8
Q ss_pred cccccCCchhhHHHHH------------------hhCCCeEEEEEeccCCCCCcchhHHHHhhhc
Q psy13365 23 TLKNHCDSCCDVKILQ------------------NEKSQAVHLVSGMVHSALEGKKTFYQVQRHN 69 (231)
Q Consensus 23 ~~~~~~~~~~~~~~~~------------------~~~~~~V~l~WIPgH~GI~GNE~AD~aak~~ 69 (231)
.+.+.+||.+.++-+. .-.. .|+|.|||||+|++|||.||+||+++
T Consensus 71 ~v~I~tDS~~i~~w~~~~w~~~~~~~~~~~~l~~~l~~-~v~~~wV~gH~g~~~Ne~AD~LA~~a 134 (147)
T 2kq2_A 71 KIRILHDYAGIAFWATGEWKAKNEFTQAYAKLMNQYRG-IYSFEKVKAHSGNEFNDYVDMKAKSA 134 (147)
T ss_dssp CCCBSSCCSTHHHHTTSSSSCCHHHHHHHHCGGGGGST-TCCBCCCCCCCCCHHHHHHHHHHHHH
T ss_pred eEEEEECcHHHHHHHhCCCccCCcchHHHHHHHHHhcC-CeeEEEecCcCCCcchHHHHHHHHHH
Confidence 6777888865554332 1111 79999999999999999999999863
No 6
>1ril_A Ribonuclease H; hydrolase(endoribonuclease); 2.80A {Thermus thermophilus} SCOP: c.55.3.1 PDB: 2rpi_A
Probab=98.49 E-value=2.9e-08 Score=80.44 Aligned_cols=27 Identities=11% Similarity=0.041 Sum_probs=24.8
Q ss_pred CeEEEEEeccCCCCCcchhHHHHhhhc
Q psy13365 43 QAVHLVSGMVHSALEGKKTFYQVQRHN 69 (231)
Q Consensus 43 ~~V~l~WIPgH~GI~GNE~AD~aak~~ 69 (231)
..|+|.|||||+|++|||.||+||+++
T Consensus 119 ~~v~~~wV~gH~g~~~Ne~AD~LAk~a 145 (166)
T 1ril_A 119 HRVRFHFVKGHTGHPENERVDREARRQ 145 (166)
T ss_dssp SEEECCCCCGGGSCTHHHHHHHHHHHH
T ss_pred CeEEEEEeeCCCCchhHHHHHHHHHHH
Confidence 479999999999999999999998864
No 7
>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=98.45 E-value=6.6e-08 Score=77.35 Aligned_cols=27 Identities=7% Similarity=-0.012 Sum_probs=24.7
Q ss_pred CeEEEEEeccCCCCCcchhHHHHhhhc
Q psy13365 43 QAVHLVSGMVHSALEGKKTFYQVQRHN 69 (231)
Q Consensus 43 ~~V~l~WIPgH~GI~GNE~AD~aak~~ 69 (231)
..|+|.|||||+|++|||.||+||+++
T Consensus 114 ~~v~~~wV~gH~g~~~Ne~AD~LA~~a 140 (155)
T 1jl1_A 114 HQIKWEWVKGHAGHPENERADELARAA 140 (155)
T ss_dssp CEEEEEECCSSTTCHHHHHHHHHHHHH
T ss_pred CceEEEEcCCCCCCHHHHHHHHHHHHH
Confidence 479999999999999999999998853
No 8
>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=98.34 E-value=1.4e-07 Score=76.63 Aligned_cols=47 Identities=17% Similarity=0.112 Sum_probs=36.2
Q ss_pred ccccccCCchhhHHHH-------------------H-hhCCCeEEEEEeccCCC-----CCcchhHHHHhhh
Q psy13365 22 KTLKNHCDSCCDVKIL-------------------Q-NEKSQAVHLVSGMVHSA-----LEGKKTFYQVQRH 68 (231)
Q Consensus 22 ~~~~~~~~~~~~~~~~-------------------~-~~~~~~V~l~WIPgH~G-----I~GNE~AD~aak~ 68 (231)
..+.+.+||...++.| . ..++..|+|.|||||+| ++|||.||++|++
T Consensus 81 ~~v~I~tDS~~vi~~iw~~~~g~~v~n~dl~~~l~~~l~~~~~v~~~wVkgH~g~~~~~~~gNe~AD~LA~~ 152 (165)
T 3p1g_A 81 KKLNVYTDSRYAFATAHVHSEGREIKNKNEILALLKALFLPKRLSIIHCPGHQKGNSAEARGNRMADQAARE 152 (165)
T ss_dssp SEEEEEECCHHHHHHHHSCCCSCCCSSHHHHHHHHHHTTSBSEEEEEECCSSCCSCSHHHHHHHHHHHHHHH
T ss_pred ceEEEEEchHHHHhhhhcccCCCcccCHHHHHHHHHHHhcCCceEEEEecCCCCCCcCcchHHHHHHHHHHH
Confidence 5666777776555443 1 12567899999999999 9999999999885
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=98.20 E-value=6.4e-07 Score=85.10 Aligned_cols=47 Identities=15% Similarity=0.151 Sum_probs=36.5
Q ss_pred ccccccCCchhhHHHHHh-----------------hCCCeEEEEEeccCCCCCcchhHHHHhhh
Q psy13365 22 KTLKNHCDSCCDVKILQN-----------------EKSQAVHLVSGMVHSALEGKKTFYQVQRH 68 (231)
Q Consensus 22 ~~~~~~~~~~~~~~~~~~-----------------~~~~~V~l~WIPgH~GI~GNE~AD~aak~ 68 (231)
..+.+..||...++.++. .++..|++.|||||+|++|||.||+||++
T Consensus 490 ~~v~I~tDS~~v~~~i~~~~~~~~~~l~~~~~~~~~~~~~v~~~wV~~H~g~~~Ne~AD~LA~~ 553 (555)
T 1mu2_A 490 PKVNIIVDSQYVMGIVASQPTESESKIVNQIIEEMIKKEAIYVAWVPAHKGIGGNQEVDHLVSQ 553 (555)
T ss_dssp SEEEEEESCHHHHHHHHTCCSEESCHHHHHHHHHHHHCSEEEEEECCSSSCCTTHHHHHHHHHT
T ss_pred CeEEEEEehHHHHHHHhcccccccHHHHHHHHHHhccCCcEEEEEEECCCCChhHHHHHHHHHh
Confidence 456666777766665542 23467999999999999999999999984
No 10
>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=98.16 E-value=6.3e-07 Score=85.21 Aligned_cols=47 Identities=19% Similarity=0.160 Sum_probs=34.8
Q ss_pred ccccccCCchhhHHHHHh-----------------hCCCeEEEEEeccCCCCCcchhHHHHhhh
Q psy13365 22 KTLKNHCDSCCDVKILQN-----------------EKSQAVHLVSGMVHSALEGKKTFYQVQRH 68 (231)
Q Consensus 22 ~~~~~~~~~~~~~~~~~~-----------------~~~~~V~l~WIPgH~GI~GNE~AD~aak~ 68 (231)
..+.+.+||...++.++. .+...|++.|||||+|++|||.||+||++
T Consensus 493 ~~v~I~tDS~~vi~~i~~~~~~~~~~l~~~~~~~l~~~~~v~~~wV~~H~g~~~Ne~AD~LA~~ 556 (557)
T 2zd1_A 493 LEVNIVTDSQYALGIIQAQPDKSESELVNQIIEQLIKKEKVYLAWVPAHKGIGGNEQVDKLVSA 556 (557)
T ss_dssp SEEEEEECCHHHHHHHTTCCSEESSHHHHHHHHHHHHCSEEEEEECCSSSCCTTCCGGGGCC--
T ss_pred CcEEEEeChHHHHHHHhcCCccCCHHHHHHHHHHHhcCCCEEEEEcCCCCCChhHHHHHHHHhc
Confidence 456667777766666542 12347999999999999999999999984
No 11
>2lsn_A Reverse transcriptase; RNAse H, viral protein; NMR {Simian foamy virus}
Probab=98.07 E-value=8.4e-07 Score=72.04 Aligned_cols=26 Identities=12% Similarity=0.148 Sum_probs=23.2
Q ss_pred CeEEEEEeccCCCC------CcchhHHHHhhh
Q psy13365 43 QAVHLVSGMVHSAL------EGKKTFYQVQRH 68 (231)
Q Consensus 43 ~~V~l~WIPgH~GI------~GNE~AD~aak~ 68 (231)
..|+|.|||||+|+ +|||.||+||++
T Consensus 128 ~~v~~~~VkgH~g~~~~~~~~gNe~AD~LA~~ 159 (165)
T 2lsn_A 128 PDITIQHEKGHQPTNTSIHTEGNALADKLATQ 159 (165)
T ss_dssp TTCEEEECCSSSCSSSCHHHHHHHHHHHHHHH
T ss_pred CCEEEEEEeCCCCccCCCCChHHHHHHHHHHH
Confidence 47999999999995 589999999985
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=97.28 E-value=8.9e-05 Score=57.07 Aligned_cols=46 Identities=7% Similarity=-0.148 Sum_probs=35.3
Q ss_pred CCCccccccCCchhhHHHHHhh--------------------CCCeEEEEEeccCCCCCcchhHHHHhhh
Q psy13365 19 NPWKTLKNHCDSCCDVKILQNE--------------------KSQAVHLVSGMVHSALEGKKTFYQVQRH 68 (231)
Q Consensus 19 ~~~~~~~~~~~~~~~~~~~~~~--------------------~~~~V~l~WIPgH~GI~GNE~AD~aak~ 68 (231)
..++.+.+.+||...|+.++.. +...|+|.|||+ +|||.||+||++
T Consensus 64 ~~~~~v~i~tDS~~vv~~i~~~~~~~~~~l~~~~~~i~~l~~~~~~v~~~~V~~----~~N~~AD~LA~~ 129 (141)
T 3hst_B 64 LGATEAAVLMDSKLVVEQMSGRWKVKHPDLLKLYVQAQALASQFRRINYEWVPR----ARNTYADRLAND 129 (141)
T ss_dssp HTCSEEEEEESCHHHHHHHTTSSCCCSHHHHHHHHHHHHHHTTSSEEEEEECCG----GGCHHHHHHHHH
T ss_pred CCCceEEEEeChHHHHHHHhCCcccCCHHHHHHHHHHHHHHhcCCeEEEEEcCC----cccHHHHHHHHH
Confidence 3456777888887777766531 336899999995 999999999885
No 13
>3u3g_D Ribonuclease H, RNAse H1; hydrolase, cleave the RNA strand of RNA/DNA hybrid; 1.40A {Uncultured organism}
Probab=97.21 E-value=9.2e-05 Score=56.65 Aligned_cols=51 Identities=18% Similarity=0.032 Sum_probs=36.6
Q ss_pred hhhcCCCCc----cccccCCchhhHHHHHh---------------------hCCCeEEEEEeccCCCCCcchhHHHHhhh
Q psy13365 14 DILRGNPWK----TLKNHCDSCCDVKILQN---------------------EKSQAVHLVSGMVHSALEGKKTFYQVQRH 68 (231)
Q Consensus 14 ~~~~~~~~~----~~~~~~~~~~~~~~~~~---------------------~~~~~V~l~WIPgH~GI~GNE~AD~aak~ 68 (231)
..+...+.+ .+.+.+||...|+.++. ++-..|+|.|||+ +|||.||+||++
T Consensus 58 ~~a~~~~~~~~~~~v~i~tDS~~vi~~i~~~~~~~~~~l~~~~~~i~~l~~~~~~~v~~~~V~~----~~N~~AD~LA~~ 133 (140)
T 3u3g_D 58 EDLQMFGDKLVDMEVEVRMDSELIVRQMQGVYKVKEPTLKEKFAKIAHIKMERVPNLVFVHIPR----EKNARADELVNE 133 (140)
T ss_dssp HHHGGGGGGGTTCEEEEEESCHHHHHHHTTSSCCCCGGGHHHHHHHHHHHHHHCTTCEEEECCG----GGGHHHHHHHHH
T ss_pred HHHHHcCCCCCCceEEEEeChHHHHHHhCCCcccCCHHHHHHHHHHHHHhhcCCCcEEEEEcCc----hhhHHHHHHHHH
Confidence 333344555 77788888777776653 1114799999994 999999999885
No 14
>2ehg_A Ribonuclease HI; RNAse HI, hyperthermophilic archaeon, D stranded RNA-dependent RNAse, hydrolase; 1.60A {Sulfolobus tokodaii} PDB: 3aly_A
Probab=96.85 E-value=0.00037 Score=54.50 Aligned_cols=44 Identities=20% Similarity=0.073 Sum_probs=34.3
Q ss_pred CccccccCCchhhHHHHHhh-C--C----------------CeEEEEEeccCCCCCcchhHHHHhhh
Q psy13365 21 WKTLKNHCDSCCDVKILQNE-K--S----------------QAVHLVSGMVHSALEGKKTFYQVQRH 68 (231)
Q Consensus 21 ~~~~~~~~~~~~~~~~~~~~-~--~----------------~~V~l~WIPgH~GI~GNE~AD~aak~ 68 (231)
...+.+.+||...|+.++.. + + ..|+|.|||+ +|||.||+||++
T Consensus 68 ~~~v~i~tDS~~vi~~i~~~w~~~~~~~~~l~~~i~~l~~~~~v~~~~V~~----~~N~~AD~LA~~ 130 (149)
T 2ehg_A 68 ISSPIIKGDSQLVIKQMNGEYKVKAKRIIPLYEKAIELKKKLNATLIWVPR----EENKEADRLSRV 130 (149)
T ss_dssp CCSCEEEESCHHHHHHHTTSSCCCCTTHHHHHHHHHHHHHHHTCEEEECCG----GGCHHHHHHHHH
T ss_pred CCEEEEEeChHHHHHHHhCccccCCHHHHHHHHHHHHHHhcCCEEEEEcCC----cccHHHHHHHHH
Confidence 35778888888888877653 1 0 1499999999 599999999885
Done!