Query psy529
Match_columns 338
No_of_seqs 187 out of 410
Neff 6.0
Searched_HMMs 46136
Date Fri Aug 16 22:47:08 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy529.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/529hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3752|consensus 99.7 1E-17 2.3E-22 162.9 5.0 103 85-193 244-363 (371)
2 PRK08719 ribonuclease H; Revie 99.4 9.4E-14 2E-18 121.1 3.5 96 86-194 40-146 (147)
3 COG0328 RnhA Ribonuclease HI [ 99.4 1.6E-13 3.6E-18 120.3 4.8 113 67-196 23-146 (154)
4 PRK00203 rnhA ribonuclease H; 99.4 7.4E-14 1.6E-18 121.6 2.6 94 92-196 39-143 (150)
5 PRK06548 ribonuclease H; Provi 99.4 2.2E-13 4.8E-18 120.6 2.8 92 93-194 39-141 (161)
6 PF00075 RNase_H: RNase H; In 99.3 5.7E-13 1.2E-17 111.4 2.1 97 85-193 30-131 (132)
7 cd06222 RnaseH RNase H (RNase 99.0 3.9E-10 8.4E-15 90.5 5.1 92 92-192 37-129 (130)
8 PRK13907 rnhA ribonuclease H; 98.1 1.3E-06 2.9E-11 73.4 2.4 90 92-194 37-126 (128)
9 COG3341 Predicted double-stran 98.0 2.1E-06 4.6E-11 78.8 1.3 114 13-134 18-147 (225)
10 PRK07708 hypothetical protein; 97.8 1.7E-05 3.7E-10 73.7 4.6 93 89-195 111-208 (219)
11 PF13456 RVT_3: Reverse transc 97.7 2E-05 4.3E-10 60.7 2.3 84 97-193 2-85 (87)
12 PRK07238 bifunctional RNase H/ 97.5 0.00011 2.4E-09 72.8 4.7 93 88-193 38-130 (372)
13 PF01693 Cauli_VI: Caulimoviru 97.3 2.3E-05 5E-10 54.8 -1.8 28 14-41 14-41 (44)
14 PF13966 zf-RVT: zinc-binding 93.3 0.045 9.7E-07 43.0 1.7 43 256-298 36-83 (86)
15 PF09862 DUF2089: Protein of u 44.7 8.6 0.00019 32.4 0.4 49 279-330 1-52 (113)
16 KOG2456|consensus 24.3 48 0.001 34.1 1.9 105 18-134 262-376 (477)
17 PF00336 DNA_pol_viral_C: DNA 22.8 59 0.0013 30.4 2.1 37 85-134 118-154 (245)
18 PF13917 zf-CCHC_3: Zinc knuck 22.3 68 0.0015 22.3 1.8 18 276-296 4-22 (42)
No 1
>KOG3752|consensus
Probab=99.70 E-value=1e-17 Score=162.91 Aligned_cols=103 Identities=16% Similarity=0.112 Sum_probs=76.3
Q ss_pred ceeeecC-CCCCccchhhhhHHhchhhhhhHhhhcCCCeEEEEeCCccccccc------cccCCccccc---------cc
Q psy529 85 QFSFKSN-SRPSAYKADVLLAELTRLPGKHFLVLHRDTTIQITQNQQIAPQFS------FKSNSRPSAY---------KA 148 (338)
Q Consensus 85 ~~~~kl~-~~~s~~~AE~~A~el~i~~gl~~a~~~~~~~i~I~sDSq~a~~~~------~k~~s~~~~~---------~~ 148 (338)
+.++.+. ...++|.||++| +..||+.|.+....+++|.|||+++++.. |+...+.+.. ++
T Consensus 244 N~s~pv~~g~qtNnrAEl~A----v~~ALkka~~~~~~kv~I~TDS~~~i~~l~~wv~~~k~~~~k~~~~~~~i~~~v~n 319 (371)
T KOG3752|consen 244 NVSGPLAGGRQTNNRAELIA----AIEALKKARSKNINKVVIRTDSEYFINSLTLWVQGWKKNGWKTSNGSDRICAYVKN 319 (371)
T ss_pred cccccCCCCcccccHHHHHH----HHHHHHHHHhcCCCcEEEEechHHHHHHHHHHHhhhccCccccccCCCccceeeec
Confidence 4788887 899999999999 78889999998888999999999998842 5544433221 12
Q ss_pred cCchhhhhccCCCccccccceEEEEeCCCCCC-CchhHhhhhcccc
Q psy529 149 DVLPAELTRLPGKHFLVLHRGTTIHITQNQQI-GNEEVDRGANRDT 193 (338)
Q Consensus 149 ~~~~~~l~~~~~~~~~~~~~i~~~wip~h~~i-gNe~aD~~a~~a~ 193 (338)
.+.-.++.++.+.. ...+|++.||+||.|| |||+||.+|++..
T Consensus 320 ~~~~~e~~~l~q~~--~~~~vq~~~V~Gh~gi~gne~Ad~lARkgs 363 (371)
T KOG3752|consen 320 QDFFNELDELEQEI--SNKKVQQEYVGGHSGILGNEMADALARKGS 363 (371)
T ss_pred chHHHHHHHHHhhh--ccCceEEEEecCcCCcchHHHHHHHHhhhh
Confidence 22222333332211 1267899999999999 9999999999874
No 2
>PRK08719 ribonuclease H; Reviewed
Probab=99.41 E-value=9.4e-14 Score=121.14 Aligned_cols=96 Identities=15% Similarity=0.066 Sum_probs=70.1
Q ss_pred eeeecCCCCCccchhhhhHHhchhhhhhHhhhcCCCeEEEEeCCccccccc------cccCCcc----ccccccCchhhh
Q psy529 86 FSFKSNSRPSAYKADVLLAELTRLPGKHFLVLHRDTTIQITQNQQIAPQFS------FKSNSRP----SAYKADVLPAEL 155 (338)
Q Consensus 86 ~~~kl~~~~s~~~AE~~A~el~i~~gl~~a~~~~~~~i~I~sDSq~a~~~~------~k~~s~~----~~~~~~~~~~~l 155 (338)
.++.+....++..||+.| +..||+.+... ..|+|||+++++.+ |+.+++. ..+.+..+...+
T Consensus 40 ~~~~~~~~~Tnn~aEl~A----~~~aL~~~~~~----~~i~tDS~yvi~~i~~~~~~W~~~~w~~s~g~~v~n~dl~~~i 111 (147)
T PRK08719 40 QSITVNRYTDNAELELLA----LIEALEYARDG----DVIYSDSDYCVRGFNEWLDTWKQKGWRKSDKKPVANRDLWQQV 111 (147)
T ss_pred EEecCCCCccHHHHHHHH----HHHHHHHcCCC----CEEEechHHHHHHHHHHHHHHHhCCcccCCCcccccHHHHHHH
Confidence 445566668999999999 77788877643 37999999998753 5555554 223344444444
Q ss_pred hccCCCccccccceEEEEeCCCCCC-CchhHhhhhccccc
Q psy529 156 TRLPGKHFLVLHRGTTIHITQNQQI-GNEEVDRGANRDTH 194 (338)
Q Consensus 156 ~~~~~~~~~~~~~i~~~wip~h~~i-gNe~aD~~a~~a~~ 194 (338)
..+.. ..+|+|.|||||+|+ |||.||++|++|+.
T Consensus 112 ~~l~~-----~~~i~~~~VkgH~g~~~Ne~aD~lA~~a~~ 146 (147)
T PRK08719 112 DELRA-----RKYVEVEKVTAHSGIEGNEAADMLAQAAAE 146 (147)
T ss_pred HHHhC-----CCcEEEEEecCCCCChhHHHHHHHHHHHhh
Confidence 44332 356999999999999 99999999998853
No 3
>COG0328 RnhA Ribonuclease HI [DNA replication, recombination, and repair]
Probab=99.41 E-value=1.6e-13 Score=120.28 Aligned_cols=113 Identities=17% Similarity=0.097 Sum_probs=87.2
Q ss_pred eEEeccCCccccccCCCCceeeecCCCCCccchhhhhHHhchhhhhhHhhhcCCCeEEEEeCCccccccc------cccC
Q psy529 67 WVLLFDDFHLLPFLHPAPQFSFKSNSRPSAYKADVLLAELTRLPGKHFLVLHRDTTIQITQNQQIAPQFS------FKSN 140 (338)
Q Consensus 67 ~~~~~~~~~~~~~~~~~~~~~~kl~~~~s~~~AE~~A~el~i~~gl~~a~~~~~~~i~I~sDSq~a~~~~------~k~~ 140 (338)
.++.|++.+. +++.... ..|+..||+.| ++.||+.+.+...++|.|+||||++++.+ |+.+
T Consensus 23 ~vl~~~~~~~--------~~s~~~~-~tTNNraEl~A----~i~AL~~l~~~~~~~v~l~tDS~yv~~~i~~w~~~w~~~ 89 (154)
T COG0328 23 AVLRYGDGEK--------ELSGGEG-RTTNNRAELRA----LIEALEALKELGACEVTLYTDSKYVVEGITRWIVKWKKN 89 (154)
T ss_pred EEEEcCCceE--------EEeeeee-cccChHHHHHH----HHHHHHHHHhcCCceEEEEecHHHHHHHHHHHHhhcccc
Confidence 4777777666 2444445 88999999999 88999999998899999999999998853 5555
Q ss_pred Ccc----ccccccCchhhhhccCCCccccccceEEEEeCCCCCC-CchhHhhhhccccccc
Q psy529 141 SRP----SAYKADVLPAELTRLPGKHFLVLHRGTTIHITQNQQI-GNEEVDRGANRDTHTQ 196 (338)
Q Consensus 141 s~~----~~~~~~~~~~~l~~~~~~~~~~~~~i~~~wip~h~~i-gNe~aD~~a~~a~~~~ 196 (338)
++. .++++..++.++.++...+ ..|.+.|||||+|. |||.||++|+.++...
T Consensus 90 ~w~~~~~~pvkn~dl~~~~~~~~~~~----~~v~~~WVkgH~g~~~NeraD~LA~~~~~~~ 146 (154)
T COG0328 90 GWKTADKKPVKNKDLWEELDELLKRH----ELVFWEWVKGHAGHPENERADQLAREAARAA 146 (154)
T ss_pred CccccccCccccHHHHHHHHHHHhhC----CeEEEEEeeCCCCChHHHHHHHHHHHHHHhh
Confidence 554 4556666666665544221 26899999999999 9999999999996543
No 4
>PRK00203 rnhA ribonuclease H; Reviewed
Probab=99.41 E-value=7.4e-14 Score=121.56 Aligned_cols=94 Identities=14% Similarity=0.058 Sum_probs=68.4
Q ss_pred CCCCccchhhhhHHhchhhhhhHhhhcCCCeEEEEeCCccccccc------cccCCccc----cccccCchhhhhccCCC
Q psy529 92 SRPSAYKADVLLAELTRLPGKHFLVLHRDTTIQITQNQQIAPQFS------FKSNSRPS----AYKADVLPAELTRLPGK 161 (338)
Q Consensus 92 ~~~s~~~AE~~A~el~i~~gl~~a~~~~~~~i~I~sDSq~a~~~~------~k~~s~~~----~~~~~~~~~~l~~~~~~ 161 (338)
...++..||+.| ++.||+.+.. ...|.|+|||+++++.+ |+..++.+ .+.+..+...+..+.
T Consensus 39 ~~~TN~~aEL~A----i~~AL~~~~~--~~~v~I~tDS~yvi~~i~~w~~~Wk~~~~~~~~g~~v~n~dl~~~i~~l~-- 110 (150)
T PRK00203 39 ALTTNNRMELMA----AIEALEALKE--PCEVTLYTDSQYVRQGITEWIHGWKKNGWKTADKKPVKNVDLWQRLDAAL-- 110 (150)
T ss_pred CCCcHHHHHHHH----HHHHHHHcCC--CCeEEEEECHHHHHHHHHHHHHHHHHcCCcccCCCccccHHHHHHHHHHh--
Confidence 357889999999 7788886653 46799999999998743 55554443 333443444444332
Q ss_pred ccccccceEEEEeCCCCCC-CchhHhhhhccccccc
Q psy529 162 HFLVLHRGTTIHITQNQQI-GNEEVDRGANRDTHTQ 196 (338)
Q Consensus 162 ~~~~~~~i~~~wip~h~~i-gNe~aD~~a~~a~~~~ 196 (338)
...+|.|.|||||+|+ |||.||++|++|....
T Consensus 111 ---~~~~v~~~wV~~H~~~~~N~~AD~lA~~a~~~~ 143 (150)
T PRK00203 111 ---KRHQIKWHWVKGHAGHPENERCDELARAGAEEA 143 (150)
T ss_pred ---ccCceEEEEecCCCCCHHHHHHHHHHHHHHHHh
Confidence 2257999999999999 9999999999997543
No 5
>PRK06548 ribonuclease H; Provisional
Probab=99.37 E-value=2.2e-13 Score=120.60 Aligned_cols=92 Identities=13% Similarity=0.001 Sum_probs=68.2
Q ss_pred CCCccchhhhhHHhchhhhhhHhhhcCCCeEEEEeCCccccccc------cccCCcc----ccccccCchhhhhccCCCc
Q psy529 93 RPSAYKADVLLAELTRLPGKHFLVLHRDTTIQITQNQQIAPQFS------FKSNSRP----SAYKADVLPAELTRLPGKH 162 (338)
Q Consensus 93 ~~s~~~AE~~A~el~i~~gl~~a~~~~~~~i~I~sDSq~a~~~~------~k~~s~~----~~~~~~~~~~~l~~~~~~~ 162 (338)
..++..||+.| ++.||+.+ ......|.|+|||+||++.+ |+.+++. .++.|..+...|.++..
T Consensus 39 ~~TNnraEl~A----ii~aL~~~-~~~~~~v~I~TDS~yvi~~i~~W~~~Wk~~gWk~s~G~pV~N~dL~~~l~~l~~-- 111 (161)
T PRK06548 39 IATNNIAELTA----VRELLIAT-RHTDRPILILSDSKYVINSLTKWVYSWKMRKWRKADGKPVLNQEIIQEIDSLME-- 111 (161)
T ss_pred CCCHHHHHHHH----HHHHHHhh-hcCCceEEEEeChHHHHHHHHHHHHHHHHCCCcccCCCccccHHHHHHHHHHHh--
Confidence 57899999999 76777643 33345799999999999953 6655554 33445555555544432
Q ss_pred cccccceEEEEeCCCCCC-CchhHhhhhccccc
Q psy529 163 FLVLHRGTTIHITQNQQI-GNEEVDRGANRDTH 194 (338)
Q Consensus 163 ~~~~~~i~~~wip~h~~i-gNe~aD~~a~~a~~ 194 (338)
...|+|.|||||+|+ |||.||+||++|..
T Consensus 112 ---~~~v~~~wVkgHsg~~gNe~aD~LA~~aa~ 141 (161)
T PRK06548 112 ---NRNIRMSWVNAHTGHPLNEAADSLARQAAN 141 (161)
T ss_pred ---cCceEEEEEecCCCCHHHHHHHHHHHHHHH
Confidence 246899999999999 99999999999863
No 6
>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=99.31 E-value=5.7e-13 Score=111.43 Aligned_cols=97 Identities=18% Similarity=0.165 Sum_probs=65.0
Q ss_pred ceeeecCCCCCccchhhhhHHhchhhhhhHhhhcCCCeEEEEeCCccccccccc---cCCccccccccCchhhhhccCCC
Q psy529 85 QFSFKSNSRPSAYKADVLLAELTRLPGKHFLVLHRDTTIQITQNQQIAPQFSFK---SNSRPSAYKADVLPAELTRLPGK 161 (338)
Q Consensus 85 ~~~~kl~~~~s~~~AE~~A~el~i~~gl~~a~~~~~~~i~I~sDSq~a~~~~~k---~~s~~~~~~~~~~~~~l~~~~~~ 161 (338)
..++.++ ..+++.||+.| +..||+ ++ ....|.|+|||+++++..-+ ..++........+..++.++.
T Consensus 30 ~~~~~~~-~~s~~~aEl~A----i~~AL~-~~--~~~~v~I~tDS~~v~~~l~~~~~~~~~~~~~~~~~i~~~i~~~~-- 99 (132)
T PF00075_consen 30 NFSFRLG-GQSNNRAELQA----IIEALK-AL--EHRKVTIYTDSQYVLNALNKWLHGNGWKKTSNGRPIKNEIWELL-- 99 (132)
T ss_dssp EEEEEEE-SECHHHHHHHH----HHHHHH-TH--STSEEEEEES-HHHHHHHHTHHHHTTSBSCTSSSBHTHHHHHHH--
T ss_pred EEEeccc-ccchhhhheeh----HHHHHH-Hh--hcccccccccHHHHHHHHHHhccccccccccccccchhheeecc--
Confidence 3666667 89999999999 777888 55 34899999999999884322 012211111111222222211
Q ss_pred ccccccceEEEEeCCCCCC--CchhHhhhhcccc
Q psy529 162 HFLVLHRGTTIHITQNQQI--GNEEVDRGANRDT 193 (338)
Q Consensus 162 ~~~~~~~i~~~wip~h~~i--gNe~aD~~a~~a~ 193 (338)
.....|.|.|||||+|+ |||.||++||.|.
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 13467899999999999 9999999999874
No 7
>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=99.01 E-value=3.9e-10 Score=90.50 Aligned_cols=92 Identities=16% Similarity=0.091 Sum_probs=64.6
Q ss_pred CCCCccchhhhhHHhchhhhhhHhhhcCCCeEEEEeCCccccccccccCCccccccccCchhhhhccCCCccccccceEE
Q psy529 92 SRPSAYKADVLLAELTRLPGKHFLVLHRDTTIQITQNQQIAPQFSFKSNSRPSAYKADVLPAELTRLPGKHFLVLHRGTT 171 (338)
Q Consensus 92 ~~~s~~~AE~~A~el~i~~gl~~a~~~~~~~i~I~sDSq~a~~~~~k~~s~~~~~~~~~~~~~l~~~~~~~~~~~~~i~~ 171 (338)
...+++.||+.| ++.|++.+......++.|++||+.+++...+..... ..........+..+. .....+.+
T Consensus 37 ~~~s~~~aEl~a----l~~al~~~~~~~~~~i~i~~Ds~~~~~~~~~~~~~~-~~~~~~~~~~i~~~~----~~~~~~~i 107 (130)
T cd06222 37 GNTTNNRAELLA----LIEALELALELGGKKVNIYTDSQYVINALTGWYEGK-PVKNVDLWQRLLALL----KRFHKVRF 107 (130)
T ss_pred CCCcHHHHHHHH----HHHHHHHHHhCCCceEEEEECHHHHHHHhhccccCC-ChhhHHHHHHHHHHH----hCCCeEEE
Confidence 578899999999 888999998888899999999998887643322100 000010111111111 12246899
Q ss_pred EEeCCCCCC-CchhHhhhhccc
Q psy529 172 IHITQNQQI-GNEEVDRGANRD 192 (338)
Q Consensus 172 ~wip~h~~i-gNe~aD~~a~~a 192 (338)
.|||+|+|+ +|+.||.+|+.+
T Consensus 108 ~~v~~h~~~~~n~~ad~la~~~ 129 (130)
T cd06222 108 EWVPGHSGIEGNERADALAKEA 129 (130)
T ss_pred EEcCCCCCCcchHHHHHHHHhh
Confidence 999999999 999999999976
No 8
>PRK13907 rnhA ribonuclease H; Provisional
Probab=98.12 E-value=1.3e-06 Score=73.44 Aligned_cols=90 Identities=13% Similarity=0.024 Sum_probs=60.5
Q ss_pred CCCCccchhhhhHHhchhhhhhHhhhcCCCeEEEEeCCccccccccccCCccccccccCchhhhhccCCCccccccceEE
Q psy529 92 SRPSAYKADVLLAELTRLPGKHFLVLHRDTTIQITQNQQIAPQFSFKSNSRPSAYKADVLPAELTRLPGKHFLVLHRGTT 171 (338)
Q Consensus 92 ~~~s~~~AE~~A~el~i~~gl~~a~~~~~~~i~I~sDSq~a~~~~~k~~s~~~~~~~~~~~~~l~~~~~~~~~~~~~i~~ 171 (338)
...++..||+.| ++.||+.+.......|.|+|||++++....+.. ........+..++..+... -..+.+
T Consensus 37 ~~~tn~~AE~~A----ll~aL~~a~~~g~~~v~i~sDS~~vi~~~~~~~--~~~~~~~~l~~~~~~l~~~----f~~~~~ 106 (128)
T PRK13907 37 GTMSNHEAEYHA----LLAALKYCTEHNYNIVSFRTDSQLVERAVEKEY--AKNKMFAPLLEEALQYIKS----FDLFFI 106 (128)
T ss_pred cccCCcHHHHHH----HHHHHHHHHhCCCCEEEEEechHHHHHHHhHHH--hcChhHHHHHHHHHHHHhc----CCceEE
Confidence 457899999999 899999999888889999999998877543211 1000111122222221111 123577
Q ss_pred EEeCCCCCCCchhHhhhhccccc
Q psy529 172 IHITQNQQIGNEEVDRGANRDTH 194 (338)
Q Consensus 172 ~wip~h~~igNe~aD~~a~~a~~ 194 (338)
.|||.+ +|+.||.+|+.|..
T Consensus 107 ~~v~r~---~N~~Ad~LA~~a~~ 126 (128)
T PRK13907 107 KWIPSS---QNKVADELARKAIL 126 (128)
T ss_pred EEcCch---hchhHHHHHHHHHh
Confidence 999985 89999999998753
No 9
>COG3341 Predicted double-stranded RNA/RNA-DNA hybrid binding protein [General function prediction only]
Probab=97.99 E-value=2.1e-06 Score=78.80 Aligned_cols=114 Identities=17% Similarity=0.176 Sum_probs=65.5
Q ss_pred CCCchhhhcccCCCCCCCcccccccccCCCcccchhhhcccc-cCCCchhhhhcceEEeccCCcccc-----ccCCCC-c
Q psy529 13 PYLGWDRIDATPSCLPGERLDLYTTEAGRPDRRRYVALQPYL-SGLPDSEWLALQWVLLFDDFHLLP-----FLHPAP-Q 85 (338)
Q Consensus 13 ~~~~~~~~~~~~~~~~~~~~~~~~t~~~~~~~~~~~~~~~~~-s~~~~~~~~~~~~~~~~~~~~~~~-----~~~~~~-~ 85 (338)
-|.|||||..||++||||+||.|.+.-+| ..|....... -+.++..-..+-..-+||. .+.+ +.+... +
T Consensus 18 IyktW~Ec~~qVkGy~ga~YKsf~s~EeA---~a~~~g~i~~~tp~~~~e~~i~~~~G~y~~-~p~t~~~k~yr~k~~~~ 93 (225)
T COG3341 18 IYKTWDECEKQVKGYPGAKYKSFKSYEEA---EAYCEGNIESVTPYLDFEYIISWAKGDYDA-KPGTQEFKEYRGKCTIE 93 (225)
T ss_pred eeccHHHHHHHhcCCCcccccccccHHHH---HHHhccCccccCcccchhccceeccCCccc-cCCCcceeEEecccccc
Confidence 48999999999999999999999999888 7777751000 0112222221111111211 1111 111111 0
Q ss_pred ee-eecCCC---CCccchhhhhHHhchhhhhhHhhhcCCCeEEE-E----eCCccccc
Q psy529 86 FS-FKSNSR---PSAYKADVLLAELTRLPGKHFLVLHRDTTIQI-T----QNQQIAPQ 134 (338)
Q Consensus 86 ~~-~kl~~~---~s~~~AE~~A~el~i~~gl~~a~~~~~~~i~I-~----sDSq~a~~ 134 (338)
.+ ++-.+. .++-++|++| ++.|+..++..++.+..| + .|||+...
T Consensus 94 ~~~lt~~~~~~~~~n~s~d~la----~ly~~~~~~~~~nrk~~i~y~~~~~ds~a~~k 147 (225)
T COG3341 94 YSWLTESSEFSIKSNDSGDVLA----KLYGLRYEVPLDNRKSVINYLTPGNDSWAYFK 147 (225)
T ss_pred ceeeeeecccccccCchHHHHH----HhccccccccccCccceeeccCCcchhHHHHH
Confidence 11 111222 3355789999 888899888877776655 6 68876544
No 10
>PRK07708 hypothetical protein; Validated
Probab=97.84 E-value=1.7e-05 Score=73.69 Aligned_cols=93 Identities=10% Similarity=-0.018 Sum_probs=58.7
Q ss_pred ecCCCCCccchhhhhHHhchhhhhhHhhhcCCC--eEEEEeCCccccccc---cccCCccccccccCchhhhhccCCCcc
Q psy529 89 KSNSRPSAYKADVLLAELTRLPGKHFLVLHRDT--TIQITQNQQIAPQFS---FKSNSRPSAYKADVLPAELTRLPGKHF 163 (338)
Q Consensus 89 kl~~~~s~~~AE~~A~el~i~~gl~~a~~~~~~--~i~I~sDSq~a~~~~---~k~~s~~~~~~~~~~~~~l~~~~~~~~ 163 (338)
.++...++..||..| ++.||+.|...... .|.|++|||.++... |++.... ...+. ..+..+... +
T Consensus 111 ~l~~~~TNN~AEy~A----li~aL~~A~e~g~~~~~V~I~~DSqlVi~qi~g~wk~~~~~---l~~y~-~~i~~l~~~-~ 181 (219)
T PRK07708 111 YIEGIYDNNEAEYAA----LYYAMQELEELGVKHEPVTFRGDSQVVLNQLAGEWPCYDEH---LNHWL-DRIEQKLKQ-L 181 (219)
T ss_pred cccccccCcHHHHHH----HHHHHHHHHHcCCCcceEEEEeccHHHHHHhCCCceeCChh---HHHHH-HHHHHHHhh-C
Confidence 455568999999999 88999999887654 489999999887642 3222110 00000 111111100 0
Q ss_pred ccccceEEEEeCCCCCCCchhHhhhhcccccc
Q psy529 164 LVLHRGTTIHITQNQQIGNEEVDRGANRDTHT 195 (338)
Q Consensus 164 ~~~~~i~~~wip~h~~igNe~aD~~a~~a~~~ 195 (338)
..++.+.|||-. -|+.||++|+.|.+.
T Consensus 182 --~l~~~~~~VpR~---~N~~AD~LAk~Al~~ 208 (219)
T PRK07708 182 --KLTPVYEPISRK---QNKEADQLATQALEG 208 (219)
T ss_pred --CceEEEEECCch---hhhHHHHHHHHHHhc
Confidence 123567787533 699999999999764
No 11
>PF13456 RVT_3: Reverse transcriptase-like; PDB: 3ALY_A 2EHG_A 3HST_B.
Probab=97.71 E-value=2e-05 Score=60.69 Aligned_cols=84 Identities=17% Similarity=0.126 Sum_probs=51.8
Q ss_pred cchhhhhHHhchhhhhhHhhhcCCCeEEEEeCCccccccccccCCccccccccCchhhhhccCCCccccccceEEEEeCC
Q psy529 97 YKADVLLAELTRLPGKHFLVLHRDTTIQITQNQQIAPQFSFKSNSRPSAYKADVLPAELTRLPGKHFLVLHRGTTIHITQ 176 (338)
Q Consensus 97 ~~AE~~A~el~i~~gl~~a~~~~~~~i~I~sDSq~a~~~~~k~~s~~~~~~~~~~~~~l~~~~~~~~~~~~~i~~~wip~ 176 (338)
..||+.| ++.|++.+...+-.+|.|.|||+.+++.+-+.......+.. +..++..+... -.++.+.|||-
T Consensus 2 ~~aE~~a----l~~al~~a~~~g~~~i~v~sDs~~vv~~i~~~~~~~~~~~~--~~~~i~~~~~~----~~~~~~~~i~r 71 (87)
T PF13456_consen 2 LEAEALA----LLEALQLAWELGIRKIIVESDSQLVVDAINGRSSSRSELRP--LIQDIRSLLDR----FWNVSVSHIPR 71 (87)
T ss_dssp HHHHHHH----HHHHHHHHHCCT-SCEEEEES-HHHHHHHTTSS---SCCHH--HHHHHHHHHCC----CSCEEEEE--G
T ss_pred cHHHHHH----HHHHHHHHHHCCCCEEEEEecCccccccccccccccccccc--cchhhhhhhcc----ccceEEEEECh
Confidence 4699999 99999999999999999999999887765332111111111 11122222211 14578889863
Q ss_pred CCCCCchhHhhhhcccc
Q psy529 177 NQQIGNEEVDRGANRDT 193 (338)
Q Consensus 177 h~~igNe~aD~~a~~a~ 193 (338)
- +|..||.+||.|.
T Consensus 72 ~---~N~~A~~LA~~a~ 85 (87)
T PF13456_consen 72 E---QNKVADALAKFAL 85 (87)
T ss_dssp G---GSHHHHHHHHHHH
T ss_pred H---HhHHHHHHHHHHh
Confidence 2 8999999999763
No 12
>PRK07238 bifunctional RNase H/acid phosphatase; Provisional
Probab=97.49 E-value=0.00011 Score=72.80 Aligned_cols=93 Identities=14% Similarity=0.019 Sum_probs=62.4
Q ss_pred eecCCCCCccchhhhhHHhchhhhhhHhhhcCCCeEEEEeCCccccccccccCCccccccccCchhhhhccCCCcccccc
Q psy529 88 FKSNSRPSAYKADVLLAELTRLPGKHFLVLHRDTTIQITQNQQIAPQFSFKSNSRPSAYKADVLPAELTRLPGKHFLVLH 167 (338)
Q Consensus 88 ~kl~~~~s~~~AE~~A~el~i~~gl~~a~~~~~~~i~I~sDSq~a~~~~~k~~s~~~~~~~~~~~~~l~~~~~~~~~~~~ 167 (338)
..+. .+++..||..| ++.||+.+.......|.|++||+++++.+.+ .+ ..++..+...+.++.. ....-.
T Consensus 38 ~~~~-~~tnn~AE~~A----ll~gL~~a~~~g~~~v~i~~DS~lvi~~i~~--~~--~~~~~~l~~~~~~i~~-l~~~f~ 107 (372)
T PRK07238 38 EAIG-RATNNVAEYRG----LIAGLEAAAELGATEVEVRMDSKLVVEQMSG--RW--KVKHPDMKPLAAQARE-LASQFG 107 (372)
T ss_pred cccC-CCCchHHHHHH----HHHHHHHHHhCCCCeEEEEeCcHHHHHHhCC--CC--ccCChHHHHHHHHHHH-HHhcCC
Confidence 3344 67788999999 9999999998888899999999988875322 11 0122222222222111 010114
Q ss_pred ceEEEEeCCCCCCCchhHhhhhcccc
Q psy529 168 RGTTIHITQNQQIGNEEVDRGANRDT 193 (338)
Q Consensus 168 ~i~~~wip~h~~igNe~aD~~a~~a~ 193 (338)
.+.+.|||. -+|+.||.+|+.|.
T Consensus 108 ~~~i~~v~r---~~N~~AD~LA~~a~ 130 (372)
T PRK07238 108 RVTYTWIPR---ARNAHADRLANEAM 130 (372)
T ss_pred ceEEEECCc---hhhhHHHHHHHHHH
Confidence 689999996 37999999999984
No 13
>PF01693 Cauli_VI: Caulimovirus viroplasmin; InterPro: IPR011320 This entry represents the N-terminal domain of RNase HI, which has a 3-layer alpha/beta/alpha structure []. This domain is lacking in retroviral and prokaryotic enzymes, but shows a striking structural similarity to the ribosomal protein L9 N-terminal domain, and may function as a regulatory RNA-binding module. However, the topology of this domain differs from structures of known RNA binding domains such as the double-stranded RNA binding domain (dsRBD), the hnRNP K homology (KH) domain and the RNP motif. Eukaryotic RNases HI possess either one or two copies of this small N-terminal domain, in addition to the well-conserved catalytic RNase H domain. RNase HI belongs to the family of ribonuclease H enzymes that recognise RNA:DNA hybrids and degrade the RNA component. ; PDB: 1QHK_A 3BSU_C.
Probab=97.32 E-value=2.3e-05 Score=54.79 Aligned_cols=28 Identities=21% Similarity=0.424 Sum_probs=24.9
Q ss_pred CCchhhhcccCCCCCCCcccccccccCC
Q psy529 14 YLGWDRIDATPSCLPGERLDLYTTEAGR 41 (338)
Q Consensus 14 ~~~~~~~~~~~~~~~~~~~~~~~t~~~~ 41 (338)
|.+|++|..||+++||+.||.|.|+.+|
T Consensus 14 y~~W~~~~~~v~g~~ga~~k~F~t~~eA 41 (44)
T PF01693_consen 14 YTSWAECKKQVSGYPGAIYKSFKTREEA 41 (44)
T ss_dssp ECCHHHHHHHCTT-TT-EEEEESSHHHH
T ss_pred ECCHHHHHHHhCCCCCceECCcCCHHHH
Confidence 7999999999999999999999999887
No 14
>PF13966 zf-RVT: zinc-binding in reverse transcriptase
Probab=93.34 E-value=0.045 Score=43.05 Aligned_cols=43 Identities=26% Similarity=0.366 Sum_probs=29.6
Q ss_pred hhhhcCccccc-cccc--ccCCCCCCCCCCCC-ccchhhh-hhccCcc
Q psy529 256 SRLRIGHTRVT-HSYL--FERTTPPLCSCGEN-LLTVKHL-LDCVHHA 298 (338)
Q Consensus 256 ~RLRTGH~~l~-H~~l--~~~~dsp~C~~Cg~-~eTv~HI-~~Cp~~~ 298 (338)
.-.|.-|.++. ...+ .+...++.|..|+. .||+.|+ ++||...
T Consensus 36 f~W~~~~~rL~t~~~l~~r~~~~~~~C~~C~~~~Et~~Hlf~~C~~a~ 83 (86)
T PF13966_consen 36 FLWRALHNRLPTKDNLQRRGIQVDPICPLCGNEEETIEHLFFHCPFAR 83 (86)
T ss_pred EeeeeccccchhhhhhhccCCccCCccccCCCccccccceeccCcCcc
Confidence 33445555552 1222 35567899999996 8999999 9999864
No 15
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=44.69 E-value=8.6 Score=32.39 Aligned_cols=49 Identities=24% Similarity=0.226 Sum_probs=29.4
Q ss_pred CCCCCCccchhhh--hhccCcccccccCCCCccccccCCCcchhhH-HHHhcCce
Q psy529 279 CSCGENLLTVKHL--LDCVHHAPSNKRKPVQVQFYLLRPYFGQKFK-TCKKSGLL 330 (338)
Q Consensus 279 C~~Cg~~eTv~HI--~~Cp~~~~~R~~l~~~~~l~el~p~~~~~~~-~ik~~~~~ 330 (338)
|+.||....|..+ -.|.. ..+..+.++ -+..|.+.....++ ||+++|=+
T Consensus 1 CPvCg~~l~vt~l~C~~C~t--~i~G~F~l~-~~~~L~~E~~~Fi~~Fi~~rGnl 52 (113)
T PF09862_consen 1 CPVCGGELVVTRLKCPSCGT--EIEGEFELP-WFARLSPEQLEFIKLFIKNRGNL 52 (113)
T ss_pred CCCCCCceEEEEEEcCCCCC--EEEeeeccc-hhhcCCHHHHHHHHHHHHhcCCH
Confidence 8999988766665 45544 234444432 24456666556555 77777643
No 16
>KOG2456|consensus
Probab=24.27 E-value=48 Score=34.08 Aligned_cols=105 Identities=15% Similarity=0.099 Sum_probs=63.1
Q ss_pred hhhcccCCCCCCCcccccccccCCCcccchh---hhcccccCCCchhhhhcceEEeccCCccccccCCCCceeeecCCCC
Q psy529 18 DRIDATPSCLPGERLDLYTTEAGRPDRRRYV---ALQPYLSGLPDSEWLALQWVLLFDDFHLLPFLHPAPQFSFKSNSRP 94 (338)
Q Consensus 18 ~~~~~~~~~~~~~~~~~~~t~~~~~~~~~~~---~~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~kl~~~~ 94 (338)
++|+.+++.|=|..++ +-|+.+|.+ .|| +++++-++. ..+++|......=..-.+++-.-.+...
T Consensus 262 ~alk~~l~eFYG~n~~------eS~d~sRiIn~~hf~-Rl~~ll~~~-----~kv~~Gg~~d~~d~~I~PTIL~DV~~~~ 329 (477)
T KOG2456|consen 262 DALKSTLKEFYGENPK------ESKDLSRIINQRHFQ-RLSALLDET-----GKVAIGGESDESDRYIAPTILLDVPEDS 329 (477)
T ss_pred HHHHHHHHHHhCCCcc------ccccHHHHhhHHHHH-HHHHHhcCC-----CceecCCccchhhcccCCeEEecCCCCC
Confidence 5778888888887766 445555444 344 455544443 2566765555443344566666667777
Q ss_pred CccchhhhhH-----Hhc-hhhhhhHhhhcC-CCeEEEEeCCccccc
Q psy529 95 SAYKADVLLA-----ELT-RLPGKHFLVLHR-DTTIQITQNQQIAPQ 134 (338)
Q Consensus 95 s~~~AE~~A~-----el~-i~~gl~~a~~~~-~~~i~I~sDSq~a~~ 134 (338)
.+-.-|+|+= ... +..+++++.+.. ..-+.|||+|+..++
T Consensus 330 p~M~eEIFGPiLPIi~v~~l~Eai~~In~~eKPLa~Y~Fs~n~~~vk 376 (477)
T KOG2456|consen 330 PVMQEEIFGPILPIITVQSLDEAINFINEREKPLALYIFSNNEKLVK 376 (477)
T ss_pred hhhhhhhccCccceeEhhhHHHHHHHHhcCCCceEEEEecCCHHHHH
Confidence 7777888872 222 445556555443 235789999975554
No 17
>PF00336 DNA_pol_viral_C: DNA polymerase (viral) C-terminal domain; InterPro: IPR001462 This domain is at the C terminus of hepatitis B-type viruses P proteins and represents a functional domain that controls the RNase H activities of the protein. The domain is always associated with IPR000201 from INTERPRO and .; GO: 0004523 ribonuclease H activity
Probab=22.80 E-value=59 Score=30.44 Aligned_cols=37 Identities=14% Similarity=0.084 Sum_probs=25.1
Q ss_pred ceeeecCCCCCccchhhhhHHhchhhhhhHhhhcCCCeEEEEeCCccccc
Q psy529 85 QFSFKSNSRPSAYKADVLLAELTRLPGKHFLVLHRDTTIQITQNQQIAPQ 134 (338)
Q Consensus 85 ~~~~kl~~~~s~~~AE~~A~el~i~~gl~~a~~~~~~~i~I~sDSq~a~~ 134 (338)
++++.++ |.+||++| ++. |....+.++ |.|||.+|+-
T Consensus 118 Tfs~~l~----IhtaELla----aCl----Ar~~~~~r~-l~tDnt~Vls 154 (245)
T PF00336_consen 118 TFSKPLP----IHTAELLA----ACL----ARLMSGARC-LGTDNTVVLS 154 (245)
T ss_pred eeccccc----chHHHHHH----HHH----HHhccCCcE-EeecCcEEEe
Confidence 4555555 99999999 433 333345566 9999987764
No 18
>PF13917 zf-CCHC_3: Zinc knuckle
Probab=22.30 E-value=68 Score=22.29 Aligned_cols=18 Identities=17% Similarity=0.327 Sum_probs=14.9
Q ss_pred CCCCCCCCCccchhhh-hhccC
Q psy529 276 PPLCSCGENLLTVKHL-LDCVH 296 (338)
Q Consensus 276 sp~C~~Cg~~eTv~HI-~~Cp~ 296 (338)
...|.-|+.. -|+ ++||.
T Consensus 4 ~~~CqkC~~~---GH~tyeC~~ 22 (42)
T PF13917_consen 4 RVRCQKCGQK---GHWTYECPN 22 (42)
T ss_pred CCcCcccCCC---CcchhhCCC
Confidence 4578889876 799 99996
Done!