Query psy17175
Match_columns 285
No_of_seqs 203 out of 244
Neff 4.8
Searched_HMMs 46136
Date Fri Aug 16 23:48:17 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy17175.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/17175hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF00075 RNase_H: RNase H; In 97.1 0.00018 4E-09 57.9 1.2 25 117-142 101-126 (132)
2 PRK08719 ribonuclease H; Revie 97.0 0.00028 6.1E-09 60.5 1.7 23 119-142 118-140 (147)
3 PRK00203 rnhA ribonuclease H; 96.8 0.0006 1.3E-08 57.9 1.6 23 119-142 113-135 (150)
4 PRK06548 ribonuclease H; Provi 96.6 0.00085 1.8E-08 58.7 1.4 23 119-142 113-135 (161)
5 COG0328 RnhA Ribonuclease HI [ 95.6 0.0052 1.1E-07 53.7 1.4 28 114-142 110-138 (154)
6 cd06222 RnaseH RNase H (RNase 95.0 0.015 3.3E-07 44.2 2.1 25 117-142 101-125 (130)
7 KOG3752|consensus 92.2 0.076 1.6E-06 52.3 1.8 25 117-142 334-358 (371)
8 PF13966 zf-RVT: zinc-binding 88.2 0.31 6.7E-06 37.5 1.8 26 225-250 55-83 (86)
9 PF13966 zf-RVT: zinc-binding 34.6 20 0.00044 27.3 1.1 41 71-121 40-85 (86)
10 KOG0466|consensus 27.3 48 0.001 33.1 2.5 15 117-131 120-136 (466)
11 PRK13907 rnhA ribonuclease H; 23.1 46 0.001 26.8 1.3 21 117-142 100-120 (128)
12 PF03563 Bunya_G2: Bunyavirus 22.6 53 0.0012 31.6 1.8 20 11-30 66-85 (285)
13 COG2888 Predicted Zn-ribbon RN 20.6 59 0.0013 24.6 1.3 26 225-250 5-34 (61)
No 1
>PF00075 RNase_H: RNase H; InterPro: IPR002156 The RNase H domain is responsible for hydrolysis of the RNA portion of RNA x DNA hybrids, and this activity requires the presence of divalent cations (Mg2+ or Mn2+) that bind its active site. This domain is a part of a large family of homologous RNase H enzymes of which the RNase HI protein from Escherichia coli is the best characterised []. Secondary structure predictions for the enzymes from E. coli, yeast, human liver and diverse retroviruses (such as Rous sarcoma virus and the Foamy viruses) supported, in every case, the five beta-strands (1 to 5) and four or five alpha-helices (A, B/C, D, E) that have been identified by crystallography in the RNase H domain of Human immunodeficiency virus 1 (HIV-1) reverse transcriptase and in E. coli RNase H []. Reverse transcriptase (RT) is a modular enzyme carrying polymerase and ribonuclease H (RNase H) activities in separable domains. Reverse transcriptase (RT) converts the single-stranded RNA genome of a retrovirus into a double-stranded DNA copy for integration into the host genome. This process requires ribonuclease H as well as RNA- and DNA-directed DNA polymerase activities. Retroviral RNase H is synthesised as part of the POL polyprotein that contains; an aspartyl protease, a reverse transcriptase, RNase H and integrase. POL polyprotein undergoes specific enzymatic cleavage to yield the mature proteins. Bacterial RNase H 3.1.26.4 from EC catalyses endonucleolytic cleavage to 5'-phosphomonoester acting on RNA-DNA hybrids. The 3D structure of the RNase H domain from diverse bacteria and retroviruses has been solved [, , ]. All have four beta strands and four to five alpha helices. The E. coli RNase H1 protein binds a single Mg2+ ion cofactor in the active site of the enzyme. The divalent cation is bound by the carboxyl groups of four acidic residues, Asp-10, Glu-48, Asp-70, and Asp-134 []. The first three acidic residues are highly conserved in all bacterial and retroviral RNase H sequences. ; GO: 0003676 nucleic acid binding, 0004523 ribonuclease H activity; PDB: 3LP3_B 2KW4_A 3P1G_A 1RIL_A 2RPI_A 4EQJ_G 4EP2_B 3OTY_P 3U3G_D 2ZQB_D ....
Probab=97.11 E-value=0.00018 Score=57.89 Aligned_cols=25 Identities=24% Similarity=0.294 Sum_probs=21.4
Q ss_pred cccccceeeeecCCCCc-CcchhHHhh
Q psy17175 117 AALSVRHILFCHQHDNA-AGVESLFLL 142 (285)
Q Consensus 117 ~~~~vr~~~WIPGH~gI-pGNE~AD~~ 142 (285)
....|+ |.|||||+|+ .|||.||++
T Consensus 101 ~~~~v~-~~~V~~H~~~~~~N~~aD~l 126 (132)
T PF00075_consen 101 RGIKVR-FRWVPGHSGVPQGNERADRL 126 (132)
T ss_dssp HSSEEE-EEESSSSSSSHHHHHHHHHH
T ss_pred cceEEe-eeeccCcCCCchhHHHHHHH
Confidence 355675 9999999999 599999987
No 2
>PRK08719 ribonuclease H; Reviewed
Probab=97.04 E-value=0.00028 Score=60.47 Aligned_cols=23 Identities=22% Similarity=0.184 Sum_probs=20.7
Q ss_pred cccceeeeecCCCCcCcchhHHhh
Q psy17175 119 LSVRHILFCHQHDNAAGVESLFLL 142 (285)
Q Consensus 119 ~~vr~~~WIPGH~gIpGNE~AD~~ 142 (285)
..|+ |.|||||+|++|||.||++
T Consensus 118 ~~i~-~~~VkgH~g~~~Ne~aD~l 140 (147)
T PRK08719 118 KYVE-VEKVTAHSGIEGNEAADML 140 (147)
T ss_pred CcEE-EEEecCCCCChhHHHHHHH
Confidence 4575 9999999999999999987
No 3
>PRK00203 rnhA ribonuclease H; Reviewed
Probab=96.78 E-value=0.0006 Score=57.88 Aligned_cols=23 Identities=13% Similarity=0.042 Sum_probs=20.6
Q ss_pred cccceeeeecCCCCcCcchhHHhh
Q psy17175 119 LSVRHILFCHQHDNAAGVESLFLL 142 (285)
Q Consensus 119 ~~vr~~~WIPGH~gIpGNE~AD~~ 142 (285)
..| ++.|||||+|++|||.||++
T Consensus 113 ~~v-~~~wV~~H~~~~~N~~AD~l 135 (150)
T PRK00203 113 HQI-KWHWVKGHAGHPENERCDEL 135 (150)
T ss_pred Cce-EEEEecCCCCCHHHHHHHHH
Confidence 456 49999999999999999987
No 4
>PRK06548 ribonuclease H; Provisional
Probab=96.61 E-value=0.00085 Score=58.73 Aligned_cols=23 Identities=17% Similarity=0.171 Sum_probs=20.8
Q ss_pred cccceeeeecCCCCcCcchhHHhh
Q psy17175 119 LSVRHILFCHQHDNAAGVESLFLL 142 (285)
Q Consensus 119 ~~vr~~~WIPGH~gIpGNE~AD~~ 142 (285)
..|+ |.||+||+|++|||.||++
T Consensus 113 ~~v~-~~wVkgHsg~~gNe~aD~L 135 (161)
T PRK06548 113 RNIR-MSWVNAHTGHPLNEAADSL 135 (161)
T ss_pred CceE-EEEEecCCCCHHHHHHHHH
Confidence 3576 9999999999999999987
No 5
>COG0328 RnhA Ribonuclease HI [DNA replication, recombination, and repair]
Probab=95.64 E-value=0.0052 Score=53.73 Aligned_cols=28 Identities=14% Similarity=-0.052 Sum_probs=22.8
Q ss_pred cccccc-ccceeeeecCCCCcCcchhHHhh
Q psy17175 114 QCGAAL-SVRHILFCHQHDNAAGVESLFLL 142 (285)
Q Consensus 114 ~c~~~~-~vr~~~WIPGH~gIpGNE~AD~~ 142 (285)
++-+.. .| .+.|||||.|.++||.||++
T Consensus 110 ~~~~~~~~v-~~~WVkgH~g~~~NeraD~L 138 (154)
T COG0328 110 ELLKRHELV-FWEWVKGHAGHPENERADQL 138 (154)
T ss_pred HHHhhCCeE-EEEEeeCCCCChHHHHHHHH
Confidence 444555 44 59999999999999999987
No 6
>cd06222 RnaseH RNase H (RNase HI) is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a not sequence-specific manner. One of the important functions of RNase H is to remove Okazaki fragments during DNA replication. RNase H knockout mice lack mitochondrial DNA replication and die as embryos. The retroviral reverse transcriptase contains an RNase H domain that plays an important role in converting a single stranded retroviral genomic RNA into a dsDNA for integration into host chromosomes. RNase H inhibitors have been explored as an anti-HIV drug target because RNase H inactivation inhibits reverse transcription.
Probab=95.01 E-value=0.015 Score=44.18 Aligned_cols=25 Identities=24% Similarity=0.190 Sum_probs=21.4
Q ss_pred cccccceeeeecCCCCcCcchhHHhh
Q psy17175 117 AALSVRHILFCHQHDNAAGVESLFLL 142 (285)
Q Consensus 117 ~~~~vr~~~WIPGH~gIpGNE~AD~~ 142 (285)
....++ +.|||+|+++.+|+.||.+
T Consensus 101 ~~~~~~-i~~v~~h~~~~~n~~ad~l 125 (130)
T cd06222 101 RFHKVR-FEWVPGHSGIEGNERADAL 125 (130)
T ss_pred CCCeEE-EEEcCCCCCCcchHHHHHH
Confidence 345565 9999999999999999987
No 7
>KOG3752|consensus
Probab=92.21 E-value=0.076 Score=52.32 Aligned_cols=25 Identities=20% Similarity=0.139 Sum_probs=21.7
Q ss_pred cccccceeeeecCCCCcCcchhHHhh
Q psy17175 117 AALSVRHILFCHQHDNAAGVESLFLL 142 (285)
Q Consensus 117 ~~~~vr~~~WIPGH~gIpGNE~AD~~ 142 (285)
...+|+ +.|||||.||.|||+||.+
T Consensus 334 ~~~~vq-~~~V~Gh~gi~gne~Ad~l 358 (371)
T KOG3752|consen 334 SNKKVQ-QEYVGGHSGILGNEMADAL 358 (371)
T ss_pred ccCceE-EEEecCcCCcchHHHHHHH
Confidence 456674 9999999999999999986
No 8
>PF13966 zf-RVT: zinc-binding in reverse transcriptase
Probab=88.16 E-value=0.31 Score=37.55 Aligned_cols=26 Identities=27% Similarity=0.698 Sum_probs=21.6
Q ss_pred CCCCCCCc-cCCC-ccccceeec-cccch
Q psy17175 225 TKIDPPLC-QCGA-ALSVRHILF-CHQHV 250 (285)
Q Consensus 225 ~~~~~P~C-~CG~-~~Tv~HIl~-Cp~y~ 250 (285)
+-..++.| .||. .||+.|+|. ||...
T Consensus 55 ~~~~~~~C~~C~~~~Et~~Hlf~~C~~a~ 83 (86)
T PF13966_consen 55 GIQVDPICPLCGNEEETIEHLFFHCPFAR 83 (86)
T ss_pred CCccCCccccCCCccccccceeccCcCcc
Confidence 33577999 9996 899999999 99754
No 9
>PF13966 zf-RVT: zinc-binding in reverse transcriptase
Probab=34.57 E-value=20 Score=27.33 Aligned_cols=41 Identities=29% Similarity=0.630 Sum_probs=27.1
Q ss_pred ccceee-eccccCCC--CCCCCcc-cCC-chhhhhhhhccccCCCCcccccccccc
Q psy17175 71 IGHTRL-THNHLFTK--TDPPLCQ-CGA-ALSVRHILSCHTKIDPPLCQCGAALSV 121 (285)
Q Consensus 71 ight~~-th~~l~~k--~~~p~c~-c~~-~ltv~hi~~~~~~~~~~~~~c~~~~~v 121 (285)
.-|-++ |-.-|..+ ..++.|. |+. .=|+.|++. .||.+-.+
T Consensus 40 ~~~~rL~t~~~l~~r~~~~~~~C~~C~~~~Et~~Hlf~----------~C~~a~~~ 85 (86)
T PF13966_consen 40 ALHNRLPTKDNLQRRGIQVDPICPLCGNEEETIEHLFF----------HCPFAREL 85 (86)
T ss_pred eccccchhhhhhhccCCccCCccccCCCccccccceec----------cCcCcccc
Confidence 344444 33444333 5679996 984 889999998 78776543
No 10
>KOG0466|consensus
Probab=27.27 E-value=48 Score=33.08 Aligned_cols=15 Identities=47% Similarity=0.820 Sum_probs=12.4
Q ss_pred cccccceeee--ecCCC
Q psy17175 117 AALSVRHILF--CHQHD 131 (285)
Q Consensus 117 ~~~~vr~~~W--IPGH~ 131 (285)
++.-|||+-+ +|||.
T Consensus 120 ~~klvRHVSfVDCPGHD 136 (466)
T KOG0466|consen 120 KMKLVRHVSFVDCPGHD 136 (466)
T ss_pred ceEEEEEEEeccCCchH
Confidence 5778999988 69995
No 11
>PRK13907 rnhA ribonuclease H; Provisional
Probab=23.08 E-value=46 Score=26.82 Aligned_cols=21 Identities=10% Similarity=-0.208 Sum_probs=15.7
Q ss_pred cccccceeeeecCCCCcCcchhHHhh
Q psy17175 117 AALSVRHILFCHQHDNAAGVESLFLL 142 (285)
Q Consensus 117 ~~~~vr~~~WIPGH~gIpGNE~AD~~ 142 (285)
.+..++ +.|||+ ++|+.||.+
T Consensus 100 ~f~~~~-~~~v~r----~~N~~Ad~L 120 (128)
T PRK13907 100 SFDLFF-IKWIPS----SQNKVADEL 120 (128)
T ss_pred cCCceE-EEEcCc----hhchhHHHH
Confidence 344553 799998 588999986
No 12
>PF03563 Bunya_G2: Bunyavirus glycoprotein G2; InterPro: IPR005168 Bunyavirus has three genomic segments: small (S), middle-sized (M), and large (L). The S segment encodes the nucleocapsid and a non-structural protein. The M segment codes for two glycoproteins, G1 and G2, and another non-structural protein (NSm). The L segment codes for an RNA polymerase. This entry represents the polyprotein region forming the G2 glycoprotein, which interacts with the IPR005167 from INTERPRO G1 glycoprotein [].
Probab=22.59 E-value=53 Score=31.58 Aligned_cols=20 Identities=35% Similarity=0.478 Sum_probs=18.7
Q ss_pred CCCccCCCceeeeeeecccc
Q psy17175 11 NPIQTDFGPCMLFEVKHSLN 30 (285)
Q Consensus 11 ~~~~~~~~~~~~~~~~~~~~ 30 (285)
||+++..|+=|+|||.+.|+
T Consensus 66 nPi~~~~Gti~Vievd~dl~ 85 (285)
T PF03563_consen 66 NPIKDAGGTINVIEVDNDLM 85 (285)
T ss_pred CCeecCCCcEEEEEECCCce
Confidence 89999999999999998775
No 13
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=20.61 E-value=59 Score=24.59 Aligned_cols=26 Identities=27% Similarity=0.660 Sum_probs=17.3
Q ss_pred CCCCCCCc-cCCCcc-ccceeec--cccch
Q psy17175 225 TKIDPPLC-QCGAAL-SVRHILF--CHQHV 250 (285)
Q Consensus 225 ~~~~~P~C-~CG~~~-Tv~HIl~--Cp~y~ 250 (285)
...++|.| +||..+ -.++-.. ||.-.
T Consensus 5 ~~~~~~~CtSCg~~i~p~e~~v~F~CPnCG 34 (61)
T COG2888 5 EMKDPPVCTSCGREIAPGETAVKFPCPNCG 34 (61)
T ss_pred cccCCceeccCCCEeccCCceeEeeCCCCC
Confidence 34458999 999877 3444443 88753
Done!