Query psy5385
Match_columns 180
No_of_seqs 133 out of 166
Neff 5.4
Searched_HMMs 46136
Date Sat Aug 17 01:14:23 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy5385.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/5385hhsearch_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 98.0 4.8E-06 1.1E-10 62.3 2.7 28 20-47 100-129 (132)
2 PRK08719 ribonuclease H; Revie 97.7 1.5E-05 3.3E-10 63.2 2.3 31 17-48 113-144 (147)
3 PRK00203 rnhA ribonuclease H; 97.7 3.2E-05 6.9E-10 60.9 2.8 26 22-47 112-138 (150)
4 PRK06548 ribonuclease H; Provi 97.4 0.0001 2.2E-09 59.7 2.6 25 23-47 113-138 (161)
5 cd06222 RnaseH RNase H (RNase 96.9 0.00066 1.4E-08 48.1 2.5 30 18-47 98-128 (130)
6 COG0328 RnhA Ribonuclease HI [ 96.6 0.0014 2.9E-08 53.0 2.4 31 17-47 110-141 (154)
7 PF13966 zf-RVT: zinc-binding 94.9 0.013 2.9E-07 41.8 1.5 27 116-142 55-83 (86)
8 PF15322 PMSI1: Protein missin 56.8 5.4 0.00012 35.5 1.1 40 93-147 210-249 (311)
9 PRK13907 rnhA ribonuclease H; 48.3 12 0.00027 27.8 1.8 27 17-47 96-123 (128)
10 PF13456 RVT_3: Reverse transc 44.4 20 0.00044 24.0 2.2 27 17-47 56-83 (87)
11 KOG0466|consensus 38.6 16 0.00034 33.7 1.1 34 112-145 101-139 (466)
12 PF00098 zf-CCHC: Zinc knuckle 37.4 19 0.00041 18.8 0.9 15 122-140 2-18 (18)
13 COG2888 Predicted Zn-ribbon RN 27.3 33 0.00071 23.8 1.0 25 117-141 6-33 (61)
14 PF14169 YdjO: Cold-inducible 27.3 35 0.00075 23.5 1.1 20 116-135 35-56 (59)
15 PF13005 zf-IS66: zinc-finger 25.5 35 0.00075 21.2 0.8 11 119-129 1-12 (47)
16 COG1645 Uncharacterized Zn-fin 22.3 28 0.0006 27.6 -0.1 31 100-142 18-51 (131)
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=97.97 E-value=4.8e-06 Score=62.34 Aligned_cols=28 Identities=14% Similarity=0.042 Sum_probs=25.3
Q ss_pred ccCCceEEEEecccccc-chh-HHHHhhhc
Q psy5385 20 KTQETLRYLHAPSVVLL-TIR-IARRYTIL 47 (180)
Q Consensus 20 ~~~~~V~l~WIP~H~gi-pGN-~ADr~A~~ 47 (180)
..+..|+|.|||||+|+ .|| .||++|+.
T Consensus 100 ~~~~~v~~~~V~~H~~~~~~N~~aD~lAk~ 129 (132)
T PF00075_consen 100 SRGIKVRFRWVPGHSGVPQGNERADRLAKE 129 (132)
T ss_dssp HHSSEEEEEESSSSSSSHHHHHHHHHHHHH
T ss_pred ccceEEeeeeccCcCCCchhHHHHHHHHHH
Confidence 56899999999999999 599 99999964
No 2
>PRK08719 ribonuclease H; Reviewed
Probab=97.75 E-value=1.5e-05 Score=63.19 Aligned_cols=31 Identities=3% Similarity=-0.139 Sum_probs=25.7
Q ss_pred cccccCCceEEEEeccccccchh-HHHHhhhcC
Q psy5385 17 ARPKTQETLRYLHAPSVVLLTIR-IARRYTILS 48 (180)
Q Consensus 17 ~l~~~~~~V~l~WIP~H~gipGN-~ADr~A~~s 48 (180)
++.+ ...|+|.|||||+|++|| .||++|+.+
T Consensus 113 ~l~~-~~~i~~~~VkgH~g~~~Ne~aD~lA~~a 144 (147)
T PRK08719 113 ELRA-RKYVEVEKVTAHSGIEGNEAADMLAQAA 144 (147)
T ss_pred HHhC-CCcEEEEEecCCCCChhHHHHHHHHHHH
Confidence 3444 466999999999999999 999999653
No 3
>PRK00203 rnhA ribonuclease H; Reviewed
Probab=97.66 E-value=3.2e-05 Score=60.88 Aligned_cols=26 Identities=0% Similarity=-0.082 Sum_probs=23.7
Q ss_pred CCceEEEEeccccccchh-HHHHhhhc
Q psy5385 22 QETLRYLHAPSVVLLTIR-IARRYTIL 47 (180)
Q Consensus 22 ~~~V~l~WIP~H~gipGN-~ADr~A~~ 47 (180)
...|.|.|||||+|++|| .||++|+.
T Consensus 112 ~~~v~~~wV~~H~~~~~N~~AD~lA~~ 138 (150)
T PRK00203 112 RHQIKWHWVKGHAGHPENERCDELARA 138 (150)
T ss_pred cCceEEEEecCCCCCHHHHHHHHHHHH
Confidence 478999999999999999 99999864
No 4
>PRK06548 ribonuclease H; Provisional
Probab=97.39 E-value=0.0001 Score=59.67 Aligned_cols=25 Identities=8% Similarity=-0.021 Sum_probs=23.0
Q ss_pred CceEEEEeccccccchh-HHHHhhhc
Q psy5385 23 ETLRYLHAPSVVLLTIR-IARRYTIL 47 (180)
Q Consensus 23 ~~V~l~WIP~H~gipGN-~ADr~A~~ 47 (180)
..|+|.|||||.|++|| .||++|+.
T Consensus 113 ~~v~~~wVkgHsg~~gNe~aD~LA~~ 138 (161)
T PRK06548 113 RNIRMSWVNAHTGHPLNEAADSLARQ 138 (161)
T ss_pred CceEEEEEecCCCCHHHHHHHHHHHH
Confidence 47999999999999999 99999864
No 5
>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=96.92 E-value=0.00066 Score=48.11 Aligned_cols=30 Identities=13% Similarity=-0.015 Sum_probs=26.0
Q ss_pred ccccCCceEEEEeccccccchh-HHHHhhhc
Q psy5385 18 RPKTQETLRYLHAPSVVLLTIR-IARRYTIL 47 (180)
Q Consensus 18 l~~~~~~V~l~WIP~H~gipGN-~ADr~A~~ 47 (180)
+.+....++|.|||+|+|+++| .||.+|+.
T Consensus 98 ~~~~~~~~~i~~v~~h~~~~~n~~ad~la~~ 128 (130)
T cd06222 98 LLKRFHKVRFEWVPGHSGIEGNERADALAKE 128 (130)
T ss_pred HHhCCCeEEEEEcCCCCCCcchHHHHHHHHh
Confidence 3346788999999999999999 99999864
No 6
>COG0328 RnhA Ribonuclease HI [DNA replication, recombination, and repair]
Probab=96.60 E-value=0.0014 Score=53.04 Aligned_cols=31 Identities=10% Similarity=-0.136 Sum_probs=25.9
Q ss_pred cccccCCceEEEEeccccccchh-HHHHhhhc
Q psy5385 17 ARPKTQETLRYLHAPSVVLLTIR-IARRYTIL 47 (180)
Q Consensus 17 ~l~~~~~~V~l~WIP~H~gipGN-~ADr~A~~ 47 (180)
++.++--.|.+.|||||.|.|+| .||++|..
T Consensus 110 ~~~~~~~~v~~~WVkgH~g~~~NeraD~LA~~ 141 (154)
T COG0328 110 ELLKRHELVFWEWVKGHAGHPENERADQLARE 141 (154)
T ss_pred HHHhhCCeEEEEEeeCCCCChHHHHHHHHHHH
Confidence 45445558999999999999999 99998864
No 7
>PF13966 zf-RVT: zinc-binding in reverse transcriptase
Probab=94.95 E-value=0.013 Score=41.83 Aligned_cols=27 Identities=30% Similarity=0.787 Sum_probs=22.6
Q ss_pred CCCCCCCcc-cCCcccchhhh-hcCcccH
Q psy5385 116 TRSPQPTCR-CGDILTTVKHI-LTCPLDI 142 (180)
Q Consensus 116 ~~~d~p~C~-Cg~~~QTv~HI-~eCp~~~ 142 (180)
+...++.|. |+...+|+.|+ ++||...
T Consensus 55 ~~~~~~~C~~C~~~~Et~~Hlf~~C~~a~ 83 (86)
T PF13966_consen 55 GIQVDPICPLCGNEEETIEHLFFHCPFAR 83 (86)
T ss_pred CCccCCccccCCCccccccceeccCcCcc
Confidence 446789999 99866699999 9999754
No 8
>PF15322 PMSI1: Protein missing in infertile sperm 1, putative
Probab=56.82 E-value=5.4 Score=35.53 Aligned_cols=40 Identities=33% Similarity=0.533 Sum_probs=30.5
Q ss_pred chhHhhhhhhcccccccccccccCCCCCCCcccCCcccchhhhhcCcccHHHhhh
Q psy5385 93 RLEEVVLTRMRIGHTRLTHSYLFTRSPQPTCRCGDILTTVKHILTCPLDIQLRSS 147 (180)
Q Consensus 93 R~~~~iL~RLRtGHt~lth~~l~~~~d~p~C~Cg~~~QTv~HI~eCp~~~~~R~~ 147 (180)
|-.--.|+||||.|--+|+ -.|.|+-.. .|||+-......
T Consensus 210 rLRvGALsqLrTehrPCtY---------~~C~Cnr~~------eECPLD~~lc~d 249 (311)
T PF15322_consen 210 RLRVGALSQLRTEHRPCTY---------QQCPCNRER------EECPLDSSLCPD 249 (311)
T ss_pred ceecchhhhhhhccCCccc---------ccCCccccc------ccCCCCCCCCCC
Confidence 3345689999999999986 578888776 788887766654
No 9
>PRK13907 rnhA ribonuclease H; Provisional
Probab=48.34 E-value=12 Score=27.83 Aligned_cols=27 Identities=15% Similarity=0.060 Sum_probs=19.8
Q ss_pred cccccCCceEEEEeccccccchh-HHHHhhhc
Q psy5385 17 ARPKTQETLRYLHAPSVVLLTIR-IARRYTIL 47 (180)
Q Consensus 17 ~l~~~~~~V~l~WIP~H~gipGN-~ADr~A~~ 47 (180)
.+.+.-..+.|.|||. +.| .||.+|+.
T Consensus 96 ~l~~~f~~~~~~~v~r----~~N~~Ad~LA~~ 123 (128)
T PRK13907 96 QYIKSFDLFFIKWIPS----SQNKVADELARK 123 (128)
T ss_pred HHHhcCCceEEEEcCc----hhchhHHHHHHH
Confidence 3344455677899998 589 89998864
No 10
>PF13456 RVT_3: Reverse transcriptase-like; PDB: 3ALY_A 2EHG_A 3HST_B.
Probab=44.35 E-value=20 Score=23.99 Aligned_cols=27 Identities=11% Similarity=0.038 Sum_probs=18.9
Q ss_pred cccccCCceEEEEeccccccchh-HHHHhhhc
Q psy5385 17 ARPKTQETLRYLHAPSVVLLTIR-IARRYTIL 47 (180)
Q Consensus 17 ~l~~~~~~V~l~WIP~H~gipGN-~ADr~A~~ 47 (180)
.+.+.-..+.|.||| =.+| .||.+|+.
T Consensus 56 ~~~~~~~~~~~~~i~----r~~N~~A~~LA~~ 83 (87)
T PF13456_consen 56 SLLDRFWNVSVSHIP----REQNKVADALAKF 83 (87)
T ss_dssp HHHCCCSCEEEEE------GGGSHHHHHHHHH
T ss_pred hhhccccceEEEEEC----hHHhHHHHHHHHH
Confidence 444456779999999 6789 89998864
No 11
>KOG0466|consensus
Probab=38.64 E-value=16 Score=33.65 Aligned_cols=34 Identities=26% Similarity=0.511 Sum_probs=27.4
Q ss_pred ccccCCCCCCCcc-cCCc--ccchhhh--hcCcccHHHh
Q psy5385 112 SYLFTRSPQPTCR-CGDI--LTTVKHI--LTCPLDIQLR 145 (180)
Q Consensus 112 ~~l~~~~d~p~C~-Cg~~--~QTv~HI--~eCp~~~~~R 145 (180)
+|--+++|.|.|+ ||.. .--|.|+ ++||=..-+=
T Consensus 101 s~gS~k~d~~~c~~~g~~~~~klvRHVSfVDCPGHDiLM 139 (466)
T KOG0466|consen 101 SFGSSKEDRPPCDRPGCEGKMKLVRHVSFVDCPGHDILM 139 (466)
T ss_pred ccCCCCCCCCCcccCCCCCceEEEEEEEeccCCchHHHH
Confidence 4666899999999 8865 5578999 9999876554
No 12
>PF00098 zf-CCHC: Zinc knuckle; InterPro: IPR001878 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the CysCysHisCys (CCHC) type zinc finger domains, and have the sequence: C-X2-C-X4-H-X4-C where X can be any amino acid, and number indicates the number of residues. These 18 residues CCHC zinc finger domains are mainly found in the nucleocapsid protein of retroviruses. It is required for viral genome packaging and for early infection process [, , ]. It is also found in eukaryotic proteins involved in RNA binding or single-stranded DNA binding []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding; PDB: 2L44_A 1A1T_A 1WWG_A 1U6P_A 1WWD_A 1WWE_A 1A6B_B 1F6U_A 1MFS_A 1NCP_C ....
Probab=37.38 E-value=19 Score=18.76 Aligned_cols=15 Identities=47% Similarity=1.116 Sum_probs=11.2
Q ss_pred Ccc-cCCcccchhhh-hcCcc
Q psy5385 122 TCR-CGDILTTVKHI-LTCPL 140 (180)
Q Consensus 122 ~C~-Cg~~~QTv~HI-~eCp~ 140 (180)
.|- ||.. -|+ .+||.
T Consensus 2 ~C~~C~~~----GH~~~~Cp~ 18 (18)
T PF00098_consen 2 KCFNCGEP----GHIARDCPK 18 (18)
T ss_dssp BCTTTSCS----SSCGCTSSS
T ss_pred cCcCCCCc----CcccccCcc
Confidence 577 8844 599 99984
No 13
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=27.32 E-value=33 Score=23.82 Aligned_cols=25 Identities=24% Similarity=0.624 Sum_probs=17.7
Q ss_pred CCCCCCcc-cCCcccchhhh--hcCccc
Q psy5385 117 RSPQPTCR-CGDILTTVKHI--LTCPLD 141 (180)
Q Consensus 117 ~~d~p~C~-Cg~~~QTv~HI--~eCp~~ 141 (180)
..++|.|. ||..+.-.++- +.||.-
T Consensus 6 ~~~~~~CtSCg~~i~p~e~~v~F~CPnC 33 (61)
T COG2888 6 MKDPPVCTSCGREIAPGETAVKFPCPNC 33 (61)
T ss_pred ccCCceeccCCCEeccCCceeEeeCCCC
Confidence 34589999 99887444444 888874
No 14
>PF14169 YdjO: Cold-inducible protein YdjO
Probab=27.30 E-value=35 Score=23.50 Aligned_cols=20 Identities=15% Similarity=0.561 Sum_probs=14.6
Q ss_pred CCCCCCCcc-cCCcc-cchhhh
Q psy5385 116 TRSPQPTCR-CGDIL-TTVKHI 135 (180)
Q Consensus 116 ~~~d~p~C~-Cg~~~-QTv~HI 135 (180)
..++.|.|. |+... +.++++
T Consensus 35 s~~~~p~CPlC~s~M~~~~r~L 56 (59)
T PF14169_consen 35 SFEEEPVCPLCKSPMVSGTRML 56 (59)
T ss_pred ccCCCccCCCcCCccccceeec
Confidence 457889999 99876 455544
No 15
>PF13005 zf-IS66: zinc-finger binding domain of transposase IS66 ; InterPro: IPR024474 This entry represents a predicted helix-turn-helix domain from insertion element IS66 transposases [].
Probab=25.50 E-value=35 Score=21.23 Aligned_cols=11 Identities=36% Similarity=0.881 Sum_probs=9.4
Q ss_pred CCCCcc-cCCcc
Q psy5385 119 PQPTCR-CGDIL 129 (180)
Q Consensus 119 d~p~C~-Cg~~~ 129 (180)
|+..|. ||..+
T Consensus 1 e~~~C~~Cg~~l 12 (47)
T PF13005_consen 1 EPRACPDCGGEL 12 (47)
T ss_pred CCCcCCCCCcee
Confidence 578899 99987
No 16
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=22.33 E-value=28 Score=27.61 Aligned_cols=31 Identities=26% Similarity=0.517 Sum_probs=21.6
Q ss_pred hhhcccccccccccccCCCCCCCcc-cCCcccchhhh--hcCcccH
Q psy5385 100 TRMRIGHTRLTHSYLFTRSPQPTCR-CGDILTTVKHI--LTCPLDI 142 (180)
Q Consensus 100 ~RLRtGHt~lth~~l~~~~d~p~C~-Cg~~~QTv~HI--~eCp~~~ 142 (180)
..|+-|++-|.+ .|. ||..+ ++|- +-||.-.
T Consensus 18 ~lLl~GAkML~~----------hCp~Cg~PL--F~KdG~v~CPvC~ 51 (131)
T COG1645 18 ELLLQGAKMLAK----------HCPKCGTPL--FRKDGEVFCPVCG 51 (131)
T ss_pred HHHHhhhHHHHh----------hCcccCCcc--eeeCCeEECCCCC
Confidence 788999999962 477 77776 2233 7777753
Done!