Query psy10399
Match_columns 442
No_of_seqs 325 out of 1044
Neff 6.3
Searched_HMMs 46136
Date Fri Aug 16 16:53:22 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy10399.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/10399hhsearch_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 98.2 3.1E-07 6.7E-12 79.9 0.3 31 276-306 100-131 (132)
2 PRK08719 ribonuclease H; Revie 98.2 8.3E-07 1.8E-11 80.4 2.2 30 278-307 117-146 (147)
3 PRK00203 rnhA ribonuclease H; 98.0 1.5E-06 3.3E-11 78.6 0.3 31 278-308 112-142 (150)
4 PRK06548 ribonuclease H; Provi 97.9 3.9E-06 8.4E-11 77.2 0.9 29 279-307 113-141 (161)
5 COG0328 RnhA Ribonuclease HI [ 97.6 2.3E-05 5E-10 71.4 1.4 33 275-307 112-144 (154)
6 cd06222 RnaseH RNase H (RNase 97.4 0.00011 2.4E-09 61.2 3.0 31 275-305 99-129 (130)
7 KOG3752|consensus 96.9 0.00061 1.3E-08 69.6 2.7 31 277-307 334-364 (371)
8 PF02992 Transposase_21: Trans 94.2 0.024 5.2E-07 55.0 1.7 49 105-174 132-182 (226)
9 PF13966 zf-RVT: zinc-binding 88.7 0.27 5.8E-06 40.1 1.9 38 372-409 38-83 (86)
10 PRK13907 rnhA ribonuclease H; 82.9 0.64 1.4E-05 40.4 1.4 28 275-306 98-125 (128)
11 PF13456 RVT_3: Reverse transc 72.0 1.9 4.1E-05 33.9 1.1 31 271-305 54-84 (87)
12 PF06869 DUF1258: Protein of u 68.4 3.7 8E-05 40.6 2.4 42 105-166 180-221 (258)
13 PRK07708 hypothetical protein; 61.1 4.6 9.9E-05 39.1 1.5 27 279-309 183-209 (219)
14 PRK07238 bifunctional RNase H/ 59.3 4.9 0.00011 41.5 1.5 28 274-305 102-129 (372)
15 PF10281 Ish1: Putative stress 23.7 46 0.001 22.9 1.2 27 46-72 7-37 (38)
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=98.20 E-value=3.1e-07 Score=79.93 Aligned_cols=31 Identities=39% Similarity=0.795 Sum_probs=28.5
Q ss_pred hccceeEEEeccCCCCC-CCChHHHHHhcCCC
Q psy10399 276 ACGKEISFMWCPSHCGI-SGNEAVDVAAKNPS 306 (442)
Q Consensus 276 ~~~~~I~l~WIPgH~gI-~GNE~AD~lAK~A~ 306 (442)
..+..|.|.|||||+|+ .|||.||++||+|+
T Consensus 100 ~~~~~v~~~~V~~H~~~~~~N~~aD~lAk~a~ 131 (132)
T PF00075_consen 100 SRGIKVRFRWVPGHSGVPQGNERADRLAKEAA 131 (132)
T ss_dssp HHSSEEEEEESSSSSSSHHHHHHHHHHHHHHH
T ss_pred ccceEEeeeeccCcCCCchhHHHHHHHHHHhc
Confidence 66899999999999999 69999999999764
No 2
>PRK08719 ribonuclease H; Reviewed
Probab=98.16 E-value=8.3e-07 Score=80.39 Aligned_cols=30 Identities=33% Similarity=0.463 Sum_probs=27.2
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 117 ~~~i~~~~VkgH~g~~~Ne~aD~lA~~a~~ 146 (147)
T PRK08719 117 RKYVEVEKVTAHSGIEGNEAADMLAQAAAE 146 (147)
T ss_pred CCcEEEEEecCCCCChhHHHHHHHHHHHhh
Confidence 356999999999999999999999999863
No 3
>PRK00203 rnhA ribonuclease H; Reviewed
Probab=97.99 E-value=1.5e-06 Score=78.56 Aligned_cols=31 Identities=26% Similarity=0.481 Sum_probs=27.9
Q ss_pred cceeEEEeccCCCCCCCChHHHHHhcCCCCC
Q psy10399 278 GKEISFMWCPSHCGISGNEAVDVAAKNPSPS 308 (442)
Q Consensus 278 ~~~I~l~WIPgH~gI~GNE~AD~lAK~A~~~ 308 (442)
...|.|.|||||+|++|||.||++||+|...
T Consensus 112 ~~~v~~~wV~~H~~~~~N~~AD~lA~~a~~~ 142 (150)
T PRK00203 112 RHQIKWHWVKGHAGHPENERCDELARAGAEE 142 (150)
T ss_pred cCceEEEEecCCCCCHHHHHHHHHHHHHHHH
Confidence 3679999999999999999999999988654
No 4
>PRK06548 ribonuclease H; Provisional
Probab=97.87 E-value=3.9e-06 Score=77.21 Aligned_cols=29 Identities=31% Similarity=0.536 Sum_probs=26.4
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 113 ~~v~~~wVkgHsg~~gNe~aD~LA~~aa~ 141 (161)
T PRK06548 113 RNIRMSWVNAHTGHPLNEAADSLARQAAN 141 (161)
T ss_pred CceEEEEEecCCCCHHHHHHHHHHHHHHH
Confidence 36999999999999999999999998763
No 5
>COG0328 RnhA Ribonuclease HI [DNA replication, recombination, and repair]
Probab=97.59 E-value=2.3e-05 Score=71.44 Aligned_cols=33 Identities=21% Similarity=0.385 Sum_probs=28.3
Q ss_pred hhccceeEEEeccCCCCCCCChHHHHHhcCCCC
Q psy10399 275 VACGKEISFMWCPSHCGISGNEAVDVAAKNPSP 307 (442)
Q Consensus 275 ~~~~~~I~l~WIPgH~gI~GNE~AD~lAK~A~~ 307 (442)
..+-..|.+.|||||+|.++||+||++|++|+.
T Consensus 112 ~~~~~~v~~~WVkgH~g~~~NeraD~LA~~~~~ 144 (154)
T COG0328 112 LKRHELVFWEWVKGHAGHPENERADQLAREAAR 144 (154)
T ss_pred HhhCCeEEEEEeeCCCCChHHHHHHHHHHHHHH
Confidence 444447999999999999999999999998754
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=97.39 E-value=0.00011 Score=61.23 Aligned_cols=31 Identities=39% Similarity=0.717 Sum_probs=28.3
Q ss_pred hhccceeEEEeccCCCCCCCChHHHHHhcCC
Q psy10399 275 VACGKEISFMWCPSHCGISGNEAVDVAAKNP 305 (442)
Q Consensus 275 ~~~~~~I~l~WIPgH~gI~GNE~AD~lAK~A 305 (442)
...+..++|.|||+|+|+++|+.||.+||+|
T Consensus 99 ~~~~~~~~i~~v~~h~~~~~n~~ad~la~~~ 129 (130)
T cd06222 99 LKRFHKVRFEWVPGHSGIEGNERADALAKEA 129 (130)
T ss_pred HhCCCeEEEEEcCCCCCCcchHHHHHHHHhh
Confidence 3567889999999999999999999999986
No 7
>KOG3752|consensus
Probab=96.86 E-value=0.00061 Score=69.65 Aligned_cols=31 Identities=32% Similarity=0.482 Sum_probs=28.3
Q ss_pred ccceeEEEeccCCCCCCCChHHHHHhcCCCC
Q psy10399 277 CGKEISFMWCPSHCGISGNEAVDVAAKNPSP 307 (442)
Q Consensus 277 ~~~~I~l~WIPgH~gI~GNE~AD~lAK~A~~ 307 (442)
++..|++.|||||.||.|||.||.+|++++.
T Consensus 334 ~~~~vq~~~V~Gh~gi~gne~Ad~lARkgs~ 364 (371)
T KOG3752|consen 334 SNKKVQQEYVGGHSGILGNEMADALARKGST 364 (371)
T ss_pred ccCceEEEEecCcCCcchHHHHHHHHhhhhh
Confidence 4799999999999999999999999998753
No 8
>PF02992 Transposase_21: Transposase family tnp2; InterPro: IPR004242 This family includes a En/Spm-like transposable element, Tdc1 from carrot []. The function of these proteins is unknown. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=94.16 E-value=0.024 Score=54.96 Aligned_cols=49 Identities=20% Similarity=0.026 Sum_probs=38.3
Q ss_pred ecceeeEEEcCCccchhhhhccCCcccchhhhhhhhhccccccchhhhhhhhhcccceE--ecccceeEeCc
Q psy10399 105 RYPRIKHFICDTPAKGYLLNIKGHTGFSFIVAHAAKLRDSTVKMQEHFIFQILQLQGYL--LNIKGHTGFNF 174 (442)
Q Consensus 105 ~~~~i~~~~~D~pak~~~~~~k~~~g~~~c~~~~~~~~~~~~~C~~~~~~~~~~~~G~~--~~~~~~~~f~~ 174 (442)
+++.+..+|||.||++.+.+.++| |+++|. .|. ..+.+ +.++.+++|..
T Consensus 132 ~ra~l~~~i~D~PA~~~l~G~~~~-G~~~C~-----------~C~---------~~t~~~~L~~~~K~~y~~ 182 (226)
T PF02992_consen 132 LRAALLCTIADYPARRKLSGFSGH-GKYGCP-----------FCM---------DKTESFYLKHGRKTVYMG 182 (226)
T ss_pred EeeeeEEEEecchhccchhhcccc-cCccCC-----------CCc---------chhhhccccccccccccc
Confidence 367777899999999999999875 788999 999 66655 33445677766
No 9
>PF13966 zf-RVT: zinc-binding in reverse transcriptase
Probab=88.69 E-value=0.27 Score=40.09 Aligned_cols=38 Identities=26% Similarity=0.260 Sum_probs=26.2
Q ss_pred hhcccccc-cc--ccccCCCCCCCCc-CC---CCccc-cccCcCcc
Q psy10399 372 MRIGHTRL-TH--SYLFSRSPQPTCR-CP---EFIVQ-KIDTTELT 409 (442)
Q Consensus 372 LRTGH~~l-~h--~~r~~~~dsp~C~-CG---et~~H-L~~Cp~~~ 409 (442)
-|.-|.++ +- +.+.+...++.|. || ||++| |++||...
T Consensus 38 W~~~~~rL~t~~~l~~r~~~~~~~C~~C~~~~Et~~Hlf~~C~~a~ 83 (86)
T PF13966_consen 38 WRALHNRLPTKDNLQRRGIQVDPICPLCGNEEETIEHLFFHCPFAR 83 (86)
T ss_pred eeeccccchhhhhhhccCCccCCccccCCCccccccceeccCcCcc
Confidence 44555565 21 3344556789999 98 39999 99999754
No 10
>PRK13907 rnhA ribonuclease H; Provisional
Probab=82.92 E-value=0.64 Score=40.38 Aligned_cols=28 Identities=25% Similarity=0.339 Sum_probs=22.3
Q ss_pred hhccceeEEEeccCCCCCCCChHHHHHhcCCC
Q psy10399 275 VACGKEISFMWCPSHCGISGNEAVDVAAKNPS 306 (442)
Q Consensus 275 ~~~~~~I~l~WIPgH~gI~GNE~AD~lAK~A~ 306 (442)
..+-..+.|.|||. ++|+.||.+|+.|.
T Consensus 98 ~~~f~~~~~~~v~r----~~N~~Ad~LA~~a~ 125 (128)
T PRK13907 98 IKSFDLFFIKWIPS----SQNKVADELARKAI 125 (128)
T ss_pred HhcCCceEEEEcCc----hhchhHHHHHHHHH
Confidence 44445677899998 59999999999874
No 11
>PF13456 RVT_3: Reverse transcriptase-like; PDB: 3ALY_A 2EHG_A 3HST_B.
Probab=72.04 E-value=1.9 Score=33.94 Aligned_cols=31 Identities=23% Similarity=0.111 Sum_probs=23.5
Q ss_pred hhhhhhccceeEEEeccCCCCCCCChHHHHHhcCC
Q psy10399 271 WLDLVACGKEISFMWCPSHCGISGNEAVDVAAKNP 305 (442)
Q Consensus 271 ~~~L~~~~~~I~l~WIPgH~gI~GNE~AD~lAK~A 305 (442)
+..+...-..+++.||| =++|..||.+||.|
T Consensus 54 i~~~~~~~~~~~~~~i~----r~~N~~A~~LA~~a 84 (87)
T PF13456_consen 54 IRSLLDRFWNVSVSHIP----REQNKVADALAKFA 84 (87)
T ss_dssp HHHHHCCCSCEEEEE------GGGSHHHHHHHHHH
T ss_pred hhhhhccccceEEEEEC----hHHhHHHHHHHHHH
Confidence 44455667889999999 78999999999865
No 12
>PF06869 DUF1258: Protein of unknown function (DUF1258); InterPro: IPR009667 This family represents a conserved region approximately 260 residues long within a number of hypothetical proteins of unknown function that seem to be specific to Caenorhabditis elegans. Note that this family contains a number of conserved cysteine and histidine residues.
Probab=68.37 E-value=3.7 Score=40.56 Aligned_cols=42 Identities=26% Similarity=0.256 Sum_probs=37.3
Q ss_pred ecceeeEEEcCCccchhhhhccCCcccchhhhhhhhhccccccchhhhhhhhhcccceEecc
Q psy10399 105 RYPRIKHFICDTPAKGYLLNIKGHTGFSFIVAHAAKLRDSTVKMQEHFIFQILQLQGYLLNI 166 (442)
Q Consensus 105 ~~~~i~~~~~D~pak~~~~~~k~~~g~~~c~~~~~~~~~~~~~C~~~~~~~~~~~~G~~~~~ 166 (442)
++..|..+++|-|||-.+.++++|++-.+|- .|. -.|.+...
T Consensus 180 ~~~~i~t~~aDqpAkR~~fg~r~H~s~~SC~-----------ycl---------s~~T~~K~ 221 (258)
T PF06869_consen 180 FSCHIVTCSADQPAKRSLFGMRGHSSSGSCF-----------YCL---------SQGTLYKT 221 (258)
T ss_pred EEEEEEEEecCchhhHHhhccccccccccee-----------eEe---------cCcceEec
Confidence 3778888999999999999999999999988 999 88877654
No 13
>PRK07708 hypothetical protein; Validated
Probab=61.12 E-value=4.6 Score=39.10 Aligned_cols=27 Identities=11% Similarity=-0.038 Sum_probs=21.7
Q ss_pred ceeEEEeccCCCCCCCChHHHHHhcCCCCCC
Q psy10399 279 KEISFMWCPSHCGISGNEAVDVAAKNPSPSF 309 (442)
Q Consensus 279 ~~I~l~WIPgH~gI~GNE~AD~lAK~A~~~~ 309 (442)
..+++.|||- .-|+.||++|+.|....
T Consensus 183 l~~~~~~VpR----~~N~~AD~LAk~Al~~~ 209 (219)
T PRK07708 183 LTPVYEPISR----KQNKEADQLATQALEGT 209 (219)
T ss_pred ceEEEEECCc----hhhhHHHHHHHHHHhcC
Confidence 3578899985 56999999999997643
No 14
>PRK07238 bifunctional RNase H/acid phosphatase; Provisional
Probab=59.27 E-value=4.9 Score=41.53 Aligned_cols=28 Identities=21% Similarity=0.425 Sum_probs=22.9
Q ss_pred hhhccceeEEEeccCCCCCCCChHHHHHhcCC
Q psy10399 274 LVACGKEISFMWCPSHCGISGNEAVDVAAKNP 305 (442)
Q Consensus 274 L~~~~~~I~l~WIPgH~gI~GNE~AD~lAK~A 305 (442)
+.++-..+++.|||. ++|+.||.+|+.|
T Consensus 102 l~~~f~~~~i~~v~r----~~N~~AD~LA~~a 129 (372)
T PRK07238 102 LASQFGRVTYTWIPR----ARNAHADRLANEA 129 (372)
T ss_pred HHhcCCceEEEECCc----hhhhHHHHHHHHH
Confidence 344446799999997 7899999999976
No 15
>PF10281 Ish1: Putative stress-responsive nuclear envelope protein; InterPro: IPR018803 This group of proteins, found primarily in fungi, consists of putative stress-responsive nuclear envelope protein Ish1 and homologues [].
Probab=23.71 E-value=46 Score=22.88 Aligned_cols=27 Identities=19% Similarity=0.324 Sum_probs=21.5
Q ss_pred HHhhhhhhccCCCHH----HHHHHHHHhccc
Q psy10399 46 AELTKWTLESRISKN----HVSSLLRSLRPY 72 (442)
Q Consensus 46 ~~L~~Wa~~~ni~~~----a~~~LL~iLk~~ 72 (442)
++|+.|..+|||+.. .-+.||+.+|++
T Consensus 7 ~~L~~wL~~~gi~~~~~~~~rd~Ll~~~k~~ 37 (38)
T PF10281_consen 7 SDLKSWLKSHGIPVPKSAKTRDELLKLAKKN 37 (38)
T ss_pred HHHHHHHHHcCCCCCCCCCCHHHHHHHHHHh
Confidence 678999999998875 577888887764
Done!