Query psy12036
Match_columns 236
No_of_seqs 221 out of 664
Neff 7.9
Searched_HMMs 29240
Date Fri Aug 16 16:59:21 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy12036.a3m -d /work/01045/syshi/HHdatabase/pdb70.hhm -o /work/01045/syshi/hhsearch_pdb/12036hhsearch_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 1.3E-07 4.4E-12 73.9 4.0 34 64-97 114-147 (150)
2 3h08_A RNH (ribonuclease H); R 98.2 2.5E-07 8.5E-12 71.5 1.6 30 68-97 115-144 (146)
3 2qkb_A Ribonuclease H1, HS-RNA 98.2 6.7E-07 2.3E-11 69.8 3.9 32 67-98 121-152 (154)
4 2kq2_A Ribonuclease H-related 98.2 1.8E-07 6.3E-12 72.6 0.6 31 69-99 109-139 (147)
5 1jl1_A Ribonuclease HI; RNAse 98.2 8.3E-07 2.8E-11 69.4 3.9 33 67-99 113-145 (155)
6 3p1g_A Xenotropic murine leuke 98.2 5.2E-07 1.8E-11 71.5 2.8 35 65-99 119-158 (165)
7 2e4l_A Ribonuclease HI, RNAse 98.2 1.2E-06 4E-11 68.8 3.8 31 67-97 115-145 (158)
8 1ril_A Ribonuclease H; hydrola 98.0 1.8E-06 6.3E-11 68.3 2.6 33 67-99 118-150 (166)
9 2lsn_A Reverse transcriptase; 97.8 5.6E-06 1.9E-10 65.5 2.5 38 59-96 119-162 (165)
10 1mu2_A HIV-2 RT; HIV-2 reverse 97.7 1.6E-05 5.4E-10 74.3 4.0 31 65-95 525-555 (555)
11 2zd1_A Reverse transcriptase/r 97.5 2.6E-05 8.8E-10 72.9 2.1 28 67-94 530-557 (557)
12 3hst_B Protein RV2228C/MT2287; 96.3 0.0035 1.2E-07 47.1 4.0 33 61-97 101-133 (141)
13 3u3g_D Ribonuclease H, RNAse H 96.0 0.0042 1.4E-07 46.5 3.3 28 65-96 109-136 (140)
14 2ehg_A Ribonuclease HI; RNAse 95.4 0.0065 2.2E-07 46.3 2.2 24 69-96 110-133 (149)
15 3alr_A Nanos protein; zinc-fin 42.3 10 0.00034 27.0 1.4 24 178-201 72-97 (106)
16 2fqc_A Conotoxin PL14A; alpha- 27.2 20 0.00067 18.5 0.7 8 159-166 11-18 (26)
17 2ysa_A Retinoblastoma-binding 22.3 39 0.0013 21.0 1.5 18 177-197 7-26 (55)
18 1a6b_B Momulv, zinc finger pro 20.0 62 0.0021 18.6 2.0 21 175-198 8-30 (40)
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=98.43 E-value=1.3e-07 Score=73.85 Aligned_cols=34 Identities=24% Similarity=0.558 Sum_probs=30.5
Q ss_pred hhCCCceEEEEeccCCCCCcchHHHHHHhhhhcc
Q psy12036 64 STNGSQISFMWIPSHSNIALNDKADQLAKNSINS 97 (236)
Q Consensus 64 ~~~~~~v~~~wip~H~gi~gNE~Ad~~Ak~a~~~ 97 (236)
-.+...|.|.|||||+|++|||.||+||++|+..
T Consensus 114 l~~~~~v~~~wV~gH~g~~~Ne~AD~LA~~a~~~ 147 (150)
T 3qio_A 114 LIKKEKVYLAWVPAHKGIGGNEQVDKLVSAGIRK 147 (150)
T ss_dssp HTTCSEEEEEECCTTSCCHHHHHHHHHHHTTTSC
T ss_pred HhhcCceEEEEccCcCCChhHHHHHHHHHHHHHH
Confidence 3467889999999999999999999999998764
No 2
>3h08_A RNH (ribonuclease H); RNAse H, 3D-structure, endonuclease, hydrolase, magnesium, metal-binding; 1.60A {Chlorobaculum tepidum}
Probab=98.24 E-value=2.5e-07 Score=71.55 Aligned_cols=30 Identities=30% Similarity=0.522 Sum_probs=26.4
Q ss_pred CceEEEEeccCCCCCcchHHHHHHhhhhcc
Q psy12036 68 SQISFMWIPSHSNIALNDKADQLAKNSINS 97 (236)
Q Consensus 68 ~~v~~~wip~H~gi~gNE~Ad~~Ak~a~~~ 97 (236)
..|.|.|||||+|++|||.||+||++|+..
T Consensus 115 ~~v~~~~V~gH~g~~~N~~AD~LA~~a~~~ 144 (146)
T 3h08_A 115 HRVTFHKVKGHSDNPYNSRADELARLAIKE 144 (146)
T ss_dssp SEEEEEECCC-CCSHHHHHHHHHHHHHHHH
T ss_pred CceEEEEcCCcCCcHhHHHHHHHHHHHHHh
Confidence 469999999999999999999999998754
No 3
>2qkb_A Ribonuclease H1, HS-RNAse HC, RNAse H1; RNA/DNA hybrid; 2.40A {Homo sapiens} PDB: 2qk9_A 2qkk_A*
Probab=98.23 E-value=6.7e-07 Score=69.80 Aligned_cols=32 Identities=34% Similarity=0.624 Sum_probs=28.9
Q ss_pred CCceEEEEeccCCCCCcchHHHHHHhhhhccC
Q psy12036 67 GSQISFMWIPSHSNIALNDKADQLAKNSINSK 98 (236)
Q Consensus 67 ~~~v~~~wip~H~gi~gNE~Ad~~Ak~a~~~~ 98 (236)
+..|.|.|||+|+|++|||.||+||++|+..+
T Consensus 121 ~~~v~~~~V~~H~g~~~N~~AD~LA~~a~~~~ 152 (154)
T 2qkb_A 121 GMDIQWMHVPGHSGFIGNEEADRLAREGAKQS 152 (154)
T ss_dssp TCEEEEEECCTTSSCHHHHHHHHHHHHHHTCC
T ss_pred CCceEEEEccCCCCCHhHHHHHHHHHHHHHhc
Confidence 56799999999999999999999999998653
No 4
>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=98.23 E-value=1.8e-07 Score=72.62 Aligned_cols=31 Identities=29% Similarity=0.306 Sum_probs=28.7
Q ss_pred ceEEEEeccCCCCCcchHHHHHHhhhhccCc
Q psy12036 69 QISFMWIPSHSNIALNDKADQLAKNSINSKL 99 (236)
Q Consensus 69 ~v~~~wip~H~gi~gNE~Ad~~Ak~a~~~~~ 99 (236)
.|.|.|||||+|++|||.||+||++|+....
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 7999999999999999999999999987654
No 5
>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=98.21 E-value=8.3e-07 Score=69.44 Aligned_cols=33 Identities=27% Similarity=0.516 Sum_probs=30.1
Q ss_pred CCceEEEEeccCCCCCcchHHHHHHhhhhccCc
Q psy12036 67 GSQISFMWIPSHSNIALNDKADQLAKNSINSKL 99 (236)
Q Consensus 67 ~~~v~~~wip~H~gi~gNE~Ad~~Ak~a~~~~~ 99 (236)
...|.|.|||||+|++|||.||+||++|+..+.
T Consensus 113 ~~~v~~~wV~gH~g~~~Ne~AD~LA~~a~~~~~ 145 (155)
T 1jl1_A 113 QHQIKWEWVKGHAGHPENERADELARAAAMNPT 145 (155)
T ss_dssp TCEEEEEECCSSTTCHHHHHHHHHHHHHHHSCC
T ss_pred cCceEEEEcCCCCCCHHHHHHHHHHHHHHhccc
Confidence 468999999999999999999999999987654
No 6
>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=98.21 E-value=5.2e-07 Score=71.52 Aligned_cols=35 Identities=23% Similarity=0.258 Sum_probs=30.8
Q ss_pred hCCCceEEEEeccCCC-----CCcchHHHHHHhhhhccCc
Q psy12036 65 TNGSQISFMWIPSHSN-----IALNDKADQLAKNSINSKL 99 (236)
Q Consensus 65 ~~~~~v~~~wip~H~g-----i~gNE~Ad~~Ak~a~~~~~ 99 (236)
..+..|.|.|||||+| ++|||.||++|++|+..+.
T Consensus 119 ~~~~~v~~~wVkgH~g~~~~~~~gNe~AD~LA~~aa~~~~ 158 (165)
T 3p1g_A 119 FLPKRLSIIHCPGHQKGNSAEARGNRMADQAAREAAMKAV 158 (165)
T ss_dssp TSBSEEEEEECCSSCCSCSHHHHHHHHHHHHHHHHHHHHH
T ss_pred hcCCceEEEEecCCCCCCcCcchHHHHHHHHHHHHHhcCC
Confidence 3678899999999999 9999999999999876543
No 7
>2e4l_A Ribonuclease HI, RNAse HI; hydrolase, endoribonuclease; 2.00A {Shewanella oneidensis} PDB: 2zqb_A
Probab=98.15 E-value=1.2e-06 Score=68.83 Aligned_cols=31 Identities=32% Similarity=0.589 Sum_probs=28.7
Q ss_pred CCceEEEEeccCCCCCcchHHHHHHhhhhcc
Q psy12036 67 GSQISFMWIPSHSNIALNDKADQLAKNSINS 97 (236)
Q Consensus 67 ~~~v~~~wip~H~gi~gNE~Ad~~Ak~a~~~ 97 (236)
+..|.|.|||||+|++|||.||+||++|+..
T Consensus 115 ~~~v~~~wV~gH~g~~~Ne~AD~LAk~a~~~ 145 (158)
T 2e4l_A 115 LHQIDWRWVKGHAGHAENERCDQLARAAAEA 145 (158)
T ss_dssp TSEEEEEECCTTCCCHHHHHHHHHHHHHHHS
T ss_pred cCcEEEEEccCCCCchhHHHHHHHHHHHHHh
Confidence 4689999999999999999999999999875
No 8
>1ril_A Ribonuclease H; hydrolase(endoribonuclease); 2.80A {Thermus thermophilus} SCOP: c.55.3.1 PDB: 2rpi_A
Probab=98.02 E-value=1.8e-06 Score=68.28 Aligned_cols=33 Identities=18% Similarity=0.392 Sum_probs=29.6
Q ss_pred CCceEEEEeccCCCCCcchHHHHHHhhhhccCc
Q psy12036 67 GSQISFMWIPSHSNIALNDKADQLAKNSINSKL 99 (236)
Q Consensus 67 ~~~v~~~wip~H~gi~gNE~Ad~~Ak~a~~~~~ 99 (236)
...|.|.|||||+|.+|||.||+||++|+....
T Consensus 118 ~~~v~~~wV~gH~g~~~Ne~AD~LAk~a~~~~~ 150 (166)
T 1ril_A 118 PHRVRFHFVKGHTGHPENERVDREARRQAQSQA 150 (166)
T ss_dssp TSEEECCCCCGGGSCTHHHHHHHHHHHHHTSSC
T ss_pred cCeEEEEEeeCCCCchhHHHHHHHHHHHHHHhh
Confidence 358999999999999999999999999987643
No 9
>2lsn_A Reverse transcriptase; RNAse H, viral protein; NMR {Simian foamy virus}
Probab=97.85 E-value=5.6e-06 Score=65.52 Aligned_cols=38 Identities=18% Similarity=0.071 Sum_probs=29.6
Q ss_pred HHHHHhhCCCceEEEEeccCCCC------CcchHHHHHHhhhhc
Q psy12036 59 EYYFASTNGSQISFMWIPSHSNI------ALNDKADQLAKNSIN 96 (236)
Q Consensus 59 ~~~~~~~~~~~v~~~wip~H~gi------~gNE~Ad~~Ak~a~~ 96 (236)
++..+......|.|.|||||+|+ +|||.||+||++++.
T Consensus 119 ~l~~~~~~~~~v~~~~VkgH~g~~~~~~~~gNe~AD~LA~~gA~ 162 (165)
T 2lsn_A 119 SIAECLSMKPDITIQHEKGHQPTNTSIHTEGNALADKLATQGSY 162 (165)
T ss_dssp HHHHHHHHCTTCEEEECCSSSCSSSCHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHhCCCCEEEEEEeCCCCccCCCCChHHHHHHHHHHHhhh
Confidence 33333344567999999999996 589999999999874
No 10
>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=1.6e-05 Score=74.28 Aligned_cols=31 Identities=29% Similarity=0.586 Sum_probs=27.9
Q ss_pred hCCCceEEEEeccCCCCCcchHHHHHHhhhh
Q psy12036 65 TNGSQISFMWIPSHSNIALNDKADQLAKNSI 95 (236)
Q Consensus 65 ~~~~~v~~~wip~H~gi~gNE~Ad~~Ak~a~ 95 (236)
..+..|.+.|||||+|++|||.||+||++|+
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 3467899999999999999999999999874
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=97.52 E-value=2.6e-05 Score=72.87 Aligned_cols=28 Identities=25% Similarity=0.647 Sum_probs=23.7
Q ss_pred CCceEEEEeccCCCCCcchHHHHHHhhh
Q psy12036 67 GSQISFMWIPSHSNIALNDKADQLAKNS 94 (236)
Q Consensus 67 ~~~v~~~wip~H~gi~gNE~Ad~~Ak~a 94 (236)
...|.|.|||||+|++|||.||+||++|
T Consensus 530 ~~~v~~~wV~~H~g~~~Ne~AD~LA~~a 557 (557)
T 2zd1_A 530 KEKVYLAWVPAHKGIGGNEQVDKLVSAG 557 (557)
T ss_dssp CSEEEEEECCSSSCCTTCCGGGGCC---
T ss_pred CCCEEEEEcCCCCCChhHHHHHHHHhcC
Confidence 4579999999999999999999999875
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=96.26 E-value=0.0035 Score=47.12 Aligned_cols=33 Identities=27% Similarity=0.543 Sum_probs=26.6
Q ss_pred HHHhhCCCceEEEEeccCCCCCcchHHHHHHhhhhcc
Q psy12036 61 YFASTNGSQISFMWIPSHSNIALNDKADQLAKNSINS 97 (236)
Q Consensus 61 ~~~~~~~~~v~~~wip~H~gi~gNE~Ad~~Ak~a~~~ 97 (236)
..+......|.|.|||+ ++||.||+||++|...
T Consensus 101 ~~l~~~~~~v~~~~V~~----~~N~~AD~LA~~a~~~ 133 (141)
T 3hst_B 101 QALASQFRRINYEWVPR----ARNTYADRLANDAMDA 133 (141)
T ss_dssp HHHHTTSSEEEEEECCG----GGCHHHHHHHHHHHHH
T ss_pred HHHHhcCCeEEEEEcCC----cccHHHHHHHHHHHHH
Confidence 34445568899999996 7999999999988643
No 13
>3u3g_D Ribonuclease H, RNAse H1; hydrolase, cleave the RNA strand of RNA/DNA hybrid; 1.40A {Uncultured organism}
Probab=96.03 E-value=0.0042 Score=46.46 Aligned_cols=28 Identities=29% Similarity=0.537 Sum_probs=23.5
Q ss_pred hCCCceEEEEeccCCCCCcchHHHHHHhhhhc
Q psy12036 65 TNGSQISFMWIPSHSNIALNDKADQLAKNSIN 96 (236)
Q Consensus 65 ~~~~~v~~~wip~H~gi~gNE~Ad~~Ak~a~~ 96 (236)
.+-..|.|.|||. ++||.||+||++|+.
T Consensus 109 ~~~~~v~~~~V~~----~~N~~AD~LA~~a~~ 136 (140)
T 3u3g_D 109 ERVPNLVFVHIPR----EKNARADELVNEAID 136 (140)
T ss_dssp HHCTTCEEEECCG----GGGHHHHHHHHHHHH
T ss_pred cCCCcEEEEEcCc----hhhHHHHHHHHHHHH
Confidence 3335899999995 799999999999864
No 14
>2ehg_A Ribonuclease HI; RNAse HI, hyperthermophilic archaeon, D stranded RNA-dependent RNAse, hydrolase; 1.60A {Sulfolobus tokodaii} PDB: 3aly_A
Probab=95.37 E-value=0.0065 Score=46.35 Aligned_cols=24 Identities=25% Similarity=0.684 Sum_probs=21.4
Q ss_pred ceEEEEeccCCCCCcchHHHHHHhhhhc
Q psy12036 69 QISFMWIPSHSNIALNDKADQLAKNSIN 96 (236)
Q Consensus 69 ~v~~~wip~H~gi~gNE~Ad~~Ak~a~~ 96 (236)
.|.|.|||+| +|+.||+||++|+.
T Consensus 110 ~v~~~~V~~~----~N~~AD~LA~~a~~ 133 (149)
T 2ehg_A 110 NATLIWVPRE----ENKEADRLSRVAYE 133 (149)
T ss_dssp TCEEEECCGG----GCHHHHHHHHHHHH
T ss_pred CEEEEEcCCc----ccHHHHHHHHHHHH
Confidence 4999999994 89999999998864
No 15
>3alr_A Nanos protein; zinc-finger, translational repression, RNA, 3'-UTR, metal BI protein; 2.10A {Danio rerio}
Probab=42.31 E-value=10 Score=26.96 Aligned_cols=24 Identities=25% Similarity=0.281 Sum_probs=20.5
Q ss_pred CCc-ccCCCCCcchhc-cccCchHHH
Q psy12036 178 PIC-TCGFPLTVKHIF-ECNKYKKFR 201 (236)
Q Consensus 178 p~C-~CG~~eTv~HiL-~Cp~~~~~R 201 (236)
-.| .||...+-.|.+ .||......
T Consensus 72 Y~CpiCGATGd~AHT~kYCP~~~~~~ 97 (106)
T 3alr_A 72 YKCPLCGATGAKAHTKRFCPMVDKNY 97 (106)
T ss_dssp CCCTTTCCCGGGCCCGGGCTTCGGGG
T ss_pred ccCCCCCCcCCcccceecCCCCCCcc
Confidence 469 899999999999 999987543
No 16
>2fqc_A Conotoxin PL14A; alpha-helix, disulfide bonds; NMR {Synthetic}
Probab=27.16 E-value=20 Score=18.55 Aligned_cols=8 Identities=25% Similarity=0.177 Sum_probs=4.9
Q ss_pred HhcCcccc
Q psy12036 159 LRIGHTRI 166 (236)
Q Consensus 159 lrTGH~~~ 166 (236)
-|+|||..
T Consensus 11 CR~g~GH~ 18 (26)
T 2fqc_A 11 CRAGIGHK 18 (26)
T ss_dssp HHHTGGGT
T ss_pred HhccCCcc
Confidence 36677655
No 17
>2ysa_A Retinoblastoma-binding protein 6; zinc finger, CCHC, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}
Probab=22.29 E-value=39 Score=20.99 Aligned_cols=18 Identities=33% Similarity=0.814 Sum_probs=13.9
Q ss_pred CCCc-ccCCCCCcchhc-cccCc
Q psy12036 177 HPIC-TCGFPLTVKHIF-ECNKY 197 (236)
Q Consensus 177 ~p~C-~CG~~eTv~HiL-~Cp~~ 197 (236)
.-.| .||.. -|++ .||.-
T Consensus 7 ~~~C~kCGk~---GH~~k~Cp~~ 26 (55)
T 2ysa_A 7 GYTCFRCGKP---GHYIKNCPTN 26 (55)
T ss_dssp SCCCTTTCCT---TSCGGGCSGG
T ss_pred CCccccCCCc---CcccccCCCC
Confidence 4579 89976 3999 99944
No 18
>1a6b_B Momulv, zinc finger protein NCP10; nucleocapsid protein, intercalation, nucleic acid, retrovirus, viral protein/DNA complex; HET: DNA; NMR {Synthetic} SCOP: g.40.1.1
Probab=20.04 E-value=62 Score=18.62 Aligned_cols=21 Identities=24% Similarity=0.415 Sum_probs=16.0
Q ss_pred CCCCCc-ccCCCCCcchhc-cccCch
Q psy12036 175 TPHPIC-TCGFPLTVKHIF-ECNKYK 198 (236)
Q Consensus 175 ~~~p~C-~CG~~eTv~HiL-~Cp~~~ 198 (236)
.+...| .||.. -|+- +||.-.
T Consensus 8 ~~~~~C~~Cgk~---GH~ardCP~~~ 30 (40)
T 1a6b_B 8 LDRDQCAYCKEK---GHWAKDCPKKP 30 (40)
T ss_dssp CCSSSCSSSCCT---TCCTTSCSSSC
T ss_pred CCCCeeeECCCC---CcchhhCcCCc
Confidence 456789 99964 5889 999854
Done!