Query psy874
Match_columns 191
No_of_seqs 208 out of 1261
Neff 6.1
Searched_HMMs 46136
Date Fri Aug 16 17:58:35 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy874.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/874hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG0328 RnhA Ribonuclease HI [ 100.0 3E-30 6.5E-35 206.5 10.5 137 5-165 2-145 (154)
2 PRK06548 ribonuclease H; Provi 100.0 2E-29 4.4E-34 203.4 9.7 138 5-178 4-144 (161)
3 PRK08719 ribonuclease H; Revie 99.9 8.9E-27 1.9E-31 185.2 8.9 127 5-158 3-137 (147)
4 KOG3752|consensus 99.9 2.9E-25 6.3E-30 197.2 11.3 141 5-165 211-361 (371)
5 PRK00203 rnhA ribonuclease H; 99.9 1.8E-25 4E-30 177.1 8.9 124 6-158 3-132 (150)
6 PRK13907 rnhA ribonuclease H; 99.8 4.5E-19 9.8E-24 136.1 12.1 79 6-90 1-80 (128)
7 PRK07708 hypothetical protein; 99.7 9.8E-16 2.1E-20 129.2 14.5 85 2-90 69-159 (219)
8 PF00075 RNase_H: RNase H; In 99.7 4.6E-17 1E-21 123.7 5.4 74 5-89 2-75 (132)
9 PRK07238 bifunctional RNase H/ 99.6 4.9E-15 1.1E-19 132.4 12.9 78 6-89 2-83 (372)
10 cd06222 RnaseH RNase H (RNase 99.2 1.7E-10 3.8E-15 83.7 8.9 78 8-90 1-80 (130)
11 KOG1132|consensus 98.6 8.4E-09 1.8E-13 100.5 1.5 78 95-183 634-717 (945)
12 PF13456 RVT_3: Reverse transc 98.0 3.4E-05 7.3E-10 53.9 7.2 40 49-90 1-40 (87)
13 smart00491 HELICc2 helicase su 94.5 0.0065 1.4E-07 47.9 -1.1 73 96-183 59-134 (142)
14 TIGR00604 rad3 DNA repair heli 94.4 0.0097 2.1E-07 57.9 -0.5 74 94-183 592-669 (705)
15 PF13307 Helicase_C_2: Helicas 91.0 0.03 6.6E-07 44.8 -1.9 72 96-183 71-145 (167)
16 smart00492 HELICc3 helicase su 89.6 0.07 1.5E-06 42.0 -1.0 72 96-183 58-133 (141)
17 KOG1133|consensus 85.6 0.3 6.5E-06 48.0 0.5 77 93-183 696-775 (821)
18 COG1199 DinG Rad3-related DNA 77.0 1.2 2.7E-05 42.6 1.4 74 95-184 537-613 (654)
19 PF05380 Peptidase_A17: Pao re 52.5 52 0.0011 25.9 6.1 21 46-66 123-143 (159)
20 PF00336 DNA_pol_viral_C: DNA 48.0 18 0.0004 30.9 2.9 60 6-85 94-154 (245)
21 COG3341 Predicted double-stran 37.2 81 0.0018 27.0 5.1 74 7-85 66-147 (225)
22 KOG3284|consensus 32.7 28 0.0006 29.3 1.6 33 49-85 25-57 (213)
23 KOG0419|consensus 22.6 7 0.00015 31.0 -3.4 38 46-84 28-65 (152)
24 PF10298 WhiA_N: WhiA N-termin 20.9 63 0.0014 22.8 1.5 36 49-85 3-38 (86)
No 1
>COG0328 RnhA Ribonuclease HI [DNA replication, recombination, and repair]
Probab=99.97 E-value=3e-30 Score=206.52 Aligned_cols=137 Identities=24% Similarity=0.301 Sum_probs=109.2
Q ss_pred CcEEEEEeeccCCCCCCCCceEEEEEEcC-CceeEEEeccCCCCChHHHHHHHHHHHHHHhHhcCCcceeEEEEcChHHH
Q psy874 5 NHVVVFTDGACPRNGKVGASAGYGVYFGE-NNPLNVAGKVTGRVTNNNAEIQGAIHALKQAKSANEKVKLKRSYNDTHAQ 83 (191)
Q Consensus 5 ~~i~IYtDGac~~N~~~~~~AG~Gv~~~~-~~~~~~s~~l~g~~TNnrAEL~Avi~AL~~~~~~~~~~~v~~I~TDS~Yv 83 (191)
..++|||||||++||||+ |||+++.. ....+++++. +.+|||+|||+|+|+||+.+++.+. +.++ |+|||+||
T Consensus 2 ~~v~if~DGa~~gNpG~g---G~g~vl~~~~~~~~~s~~~-~~tTNNraEl~A~i~AL~~l~~~~~-~~v~-l~tDS~yv 75 (154)
T COG0328 2 KKVEIFTDGACLGNPGPG---GWGAVLRYGDGEKELSGGE-GRTTNNRAELRALIEALEALKELGA-CEVT-LYTDSKYV 75 (154)
T ss_pred CceEEEecCccCCCCCCc---eEEEEEEcCCceEEEeeee-ecccChHHHHHHHHHHHHHHHhcCC-ceEE-EEecHHHH
Confidence 478999999999999885 99998643 3556688774 4899999999999999999998655 5999 99999999
Q ss_pred Hccccccccccccccccccccccee-ecCCCc--chhHHHHHHHHHHHHHHhhhhcCCCCCCcceEEEeccccccchH--
Q psy874 84 KKVRNVSSVAMRIAQKVDYISHDVI-SVGIPF--PSIQDENVKLKRSYNDTHAQKKGIPFPSIQDEKVKLKRSYNDTH-- 158 (191)
Q Consensus 84 v~~~~~~~~~~~w~~~edW~~ng~~-s~G~PV--~dL~~~~v~l~~~~~d~~~~~~g~~~~~~~~~~v~a~r~~n~~~-- 158 (191)
+++++ . |..+ |++++|. +.+.|| +|||+++.++...+. ....+|...+++++.||++
T Consensus 76 ~~~i~-~-----w~~~--w~~~~w~~~~~~pvkn~dl~~~~~~~~~~~~----------~v~~~WVkgH~g~~~NeraD~ 137 (154)
T COG0328 76 VEGIT-R-----WIVK--WKKNGWKTADKKPVKNKDLWEELDELLKRHE----------LVFWEWVKGHAGHPENERADQ 137 (154)
T ss_pred HHHHH-H-----HHhh--ccccCccccccCccccHHHHHHHHHHHhhCC----------eEEEEEeeCCCCChHHHHHHH
Confidence 99887 3 7666 9999984 789999 999999888765431 1245666666789999966
Q ss_pred -hhhhhhc
Q psy874 159 -AQKKVRN 165 (191)
Q Consensus 159 -~~~~~~~ 165 (191)
|.+++++
T Consensus 138 LA~~~~~~ 145 (154)
T COG0328 138 LAREAARA 145 (154)
T ss_pred HHHHHHHh
Confidence 4444443
No 2
>PRK06548 ribonuclease H; Provisional
Probab=99.96 E-value=2e-29 Score=203.36 Aligned_cols=138 Identities=19% Similarity=0.177 Sum_probs=102.6
Q ss_pred CcEEEEEeeccCCCCCCCCceEEEEEEcCCceeEEEeccCCCCChHHHHHHHHHHHHHHhHhcCCcceeEEEEcChHHHH
Q psy874 5 NHVVVFTDGACPRNGKVGASAGYGVYFGENNPLNVAGKVTGRVTNNNAEIQGAIHALKQAKSANEKVKLKRSYNDTHAQK 84 (191)
Q Consensus 5 ~~i~IYtDGac~~N~~~~~~AG~Gv~~~~~~~~~~s~~l~g~~TNnrAEL~Avi~AL~~~~~~~~~~~v~~I~TDS~Yvv 84 (191)
..++|||||||++||+++ |||+++.... ..+++ .+.+|||+|||+|+++||+.+.... .+++ |+|||+||+
T Consensus 4 ~~~~IytDGa~~gnpg~~---G~g~~~~~~~--~~~g~-~~~~TNnraEl~Aii~aL~~~~~~~--~~v~-I~TDS~yvi 74 (161)
T PRK06548 4 NEIIAATDGSSLANPGPS---GWAWYVDENT--WDSGG-WDIATNNIAELTAVRELLIATRHTD--RPIL-ILSDSKYVI 74 (161)
T ss_pred CEEEEEEeeccCCCCCce---EEEEEEeCCc--EEccC-CCCCCHHHHHHHHHHHHHHhhhcCC--ceEE-EEeChHHHH
Confidence 349999999999999884 9999876433 23444 3468999999999999998776432 3799 999999999
Q ss_pred ccccccccccccccccccccccee-ecCCCc--chhHHHHHHHHHHHHHHhhhhcCCCCCCcceEEEeccccccchHhhh
Q psy874 85 KVRNVSSVAMRIAQKVDYISHDVI-SVGIPF--PSIQDENVKLKRSYNDTHAQKKGIPFPSIQDEKVKLKRSYNDTHAQK 161 (191)
Q Consensus 85 ~~~~~~~~~~~w~~~edW~~ng~~-s~G~PV--~dL~~~~v~l~~~~~d~~~~~~g~~~~~~~~~~v~a~r~~n~~~~~~ 161 (191)
+.++ + |..+ |++|+|+ +.|+|| +|||+++..+.+.. . ..+.|+..+.+...|+.
T Consensus 75 ~~i~---~---W~~~--Wk~~gWk~s~G~pV~N~dL~~~l~~l~~~~--------~---v~~~wVkgHsg~~gNe~---- 131 (161)
T PRK06548 75 NSLT---K---WVYS--WKMRKWRKADGKPVLNQEIIQEIDSLMENR--------N---IRMSWVNAHTGHPLNEA---- 131 (161)
T ss_pred HHHH---H---HHHH--HHHCCCcccCCCccccHHHHHHHHHHHhcC--------c---eEEEEEecCCCCHHHHH----
Confidence 9664 2 8888 9999985 889999 89999887775431 1 14555555667789984
Q ss_pred hhhccchhhHHHHhhcc
Q psy874 162 KVRNVSSVAMRIAQKVD 178 (191)
Q Consensus 162 ~~~~~~~~~~~~~~~~~ 178 (191)
+|.+|+.-|.+..
T Consensus 132 ----aD~LA~~aa~~~~ 144 (161)
T PRK06548 132 ----ADSLARQAANNFS 144 (161)
T ss_pred ----HHHHHHHHHHHhc
Confidence 4445555444443
No 3
>PRK08719 ribonuclease H; Reviewed
Probab=99.94 E-value=8.9e-27 Score=185.17 Aligned_cols=127 Identities=19% Similarity=0.175 Sum_probs=96.7
Q ss_pred CcEEEEEeeccCCCCCCCCceEEEEEEc--CCcee-EEEeccCCCCChHHHHHHHHHHHHHHhHhcCCcceeEEEEcChH
Q psy874 5 NHVVVFTDGACPRNGKVGASAGYGVYFG--ENNPL-NVAGKVTGRVTNNNAEIQGAIHALKQAKSANEKVKLKRSYNDTH 81 (191)
Q Consensus 5 ~~i~IYtDGac~~N~~~~~~AG~Gv~~~--~~~~~-~~s~~l~g~~TNnrAEL~Avi~AL~~~~~~~~~~~v~~I~TDS~ 81 (191)
..++|||||||.+||++.++||||+++. .+... ..+.++.+.+|||+|||+|++.||+.+.+ ..+ |+|||+
T Consensus 3 ~~~~iYtDGs~~~n~~~~~~~G~G~vv~~~~~~~~~~~~~~~~~~~Tnn~aEl~A~~~aL~~~~~-----~~~-i~tDS~ 76 (147)
T PRK08719 3 ASYSIYIDGAAPNNQHGCVRGGIGLVVYDEAGEIVDEQSITVNRYTDNAELELLALIEALEYARD-----GDV-IYSDSD 76 (147)
T ss_pred ceEEEEEecccCCCCCCCCCcEEEEEEEeCCCCeeEEEEecCCCCccHHHHHHHHHHHHHHHcCC-----CCE-EEechH
Confidence 5689999999999998767889999753 23322 34555555689999999999999999876 247 999999
Q ss_pred HHHccccccccccccccccccccccee-ecCCCc--chhHHHHHHHHHHHHHHhhhhcCCCCCCcceEEEec--cccccc
Q psy874 82 AQKKVRNVSSVAMRIAQKVDYISHDVI-SVGIPF--PSIQDENVKLKRSYNDTHAQKKGIPFPSIQDEKVKL--KRSYND 156 (191)
Q Consensus 82 Yvv~~~~~~~~~~~w~~~edW~~ng~~-s~G~PV--~dL~~~~v~l~~~~~d~~~~~~g~~~~~~~~~~v~a--~r~~n~ 156 (191)
||+++++. |..+ |++++|. +.|.|| .|||+.+.+|.++ ..+.|.+|+. +.+.|+
T Consensus 77 yvi~~i~~------~~~~--W~~~~w~~s~g~~v~n~dl~~~i~~l~~~-------------~~i~~~~VkgH~g~~~Ne 135 (147)
T PRK08719 77 YCVRGFNE------WLDT--WKQKGWRKSDKKPVANRDLWQQVDELRAR-------------KYVEVEKVTAHSGIEGNE 135 (147)
T ss_pred HHHHHHHH------HHHH--HHhCCcccCCCcccccHHHHHHHHHHhCC-------------CcEEEEEecCCCCChhHH
Confidence 99997652 7777 9999996 778999 8899976665431 1355566555 457888
Q ss_pred hH
Q psy874 157 TH 158 (191)
Q Consensus 157 ~~ 158 (191)
.+
T Consensus 136 ~a 137 (147)
T PRK08719 136 AA 137 (147)
T ss_pred HH
Confidence 55
No 4
>KOG3752|consensus
Probab=99.92 E-value=2.9e-25 Score=197.23 Aligned_cols=141 Identities=32% Similarity=0.417 Sum_probs=113.9
Q ss_pred CcEEEEEeeccCCCCCCCCceEEEEEEcCCceeEEEeccC-CCCChHHHHHHHHHHHHHHhHhcCCcceeEEEEcChHHH
Q psy874 5 NHVVVFTDGACPRNGKVGASAGYGVYFGENNPLNVAGKVT-GRVTNNNAEIQGAIHALKQAKSANEKVKLKRSYNDTHAQ 83 (191)
Q Consensus 5 ~~i~IYtDGac~~N~~~~~~AG~Gv~~~~~~~~~~s~~l~-g~~TNnrAEL~Avi~AL~~~~~~~~~~~v~~I~TDS~Yv 83 (191)
+.++|||||+|.+|+.++++|||||||+++++.|.++|+. |.+|||||||.|+++||+.+.+.... +|+ |+|||+|+
T Consensus 211 ~~~vvytDGS~~~ng~~~~~AGyGvywg~~~e~N~s~pv~~g~qtNnrAEl~Av~~ALkka~~~~~~-kv~-I~TDS~~~ 288 (371)
T KOG3752|consen 211 EIQVVYTDGSSSGNGRKSSRAGYGVYWGPGHELNVSGPLAGGRQTNNRAELIAAIEALKKARSKNIN-KVV-IRTDSEYF 288 (371)
T ss_pred cceEEEecCccccCCCCCCcceeEEeeCCCCcccccccCCCCcccccHHHHHHHHHHHHHHHhcCCC-cEE-EEechHHH
Confidence 4589999999999999999999999999999999999998 69999999999999999999987665 899 99999999
Q ss_pred Hccccccccccccccccccccccee-ecCCC-----c--chhHHHHHHHHHHHHHHhhhhcCCCCCCcceEEEecccc-c
Q psy874 84 KKVRNVSSVAMRIAQKVDYISHDVI-SVGIP-----F--PSIQDENVKLKRSYNDTHAQKKGIPFPSIQDEKVKLKRS-Y 154 (191)
Q Consensus 84 v~~~~~~~~~~~w~~~edW~~ng~~-s~G~P-----V--~dL~~~~v~l~~~~~d~~~~~~g~~~~~~~~~~v~a~r~-~ 154 (191)
++.++ .|..+ |++++|. +.+.+ | +|...++-+|.+.. ++ ..++|++|+.+.- +
T Consensus 289 i~~l~------~wv~~--~k~~~~k~~~~~~~i~~~v~n~~~~~e~~~l~q~~-------~~---~~vq~~~V~Gh~gi~ 350 (371)
T KOG3752|consen 289 INSLT------LWVQG--WKKNGWKTSNGSDRICAYVKNQDFFNELDELEQEI-------SN---KKVQQEYVGGHSGIL 350 (371)
T ss_pred HHHHH------HHHhh--hccCccccccCCCccceeeecchHHHHHHHHHhhh-------cc---CceEEEEecCcCCcc
Confidence 99776 28888 9999985 66777 6 66666666655544 12 3689999988643 3
Q ss_pred cchHhhhhhhc
Q psy874 155 NDTHAQKKVRN 165 (191)
Q Consensus 155 n~~~~~~~~~~ 165 (191)
+-.-|...+|+
T Consensus 351 gne~Ad~lARk 361 (371)
T KOG3752|consen 351 GNEMADALARK 361 (371)
T ss_pred hHHHHHHHHhh
Confidence 33334444444
No 5
>PRK00203 rnhA ribonuclease H; Reviewed
Probab=99.92 E-value=1.8e-25 Score=177.09 Aligned_cols=124 Identities=21% Similarity=0.262 Sum_probs=95.7
Q ss_pred cEEEEEeeccCCCCCCCCceEEEEEEc-CCceeEEEeccCCCCChHHHHHHHHHHHHHHhHhcCCcceeEEEEcChHHHH
Q psy874 6 HVVVFTDGACPRNGKVGASAGYGVYFG-ENNPLNVAGKVTGRVTNNNAEIQGAIHALKQAKSANEKVKLKRSYNDTHAQK 84 (191)
Q Consensus 6 ~i~IYtDGac~~N~~~~~~AG~Gv~~~-~~~~~~~s~~l~g~~TNnrAEL~Avi~AL~~~~~~~~~~~v~~I~TDS~Yvv 84 (191)
+++|||||||.+||++ +|||+++. .++...+++.. +.+|||+|||+|++.||+.+.+. +.++ |+|||+||+
T Consensus 3 ~v~iytDGs~~~n~~~---~g~g~v~~~~~~~~~~~~~~-~~~TN~~aEL~Ai~~AL~~~~~~---~~v~-I~tDS~yvi 74 (150)
T PRK00203 3 QVEIYTDGACLGNPGP---GGWGAILRYKGHEKELSGGE-ALTTNNRMELMAAIEALEALKEP---CEVT-LYTDSQYVR 74 (150)
T ss_pred eEEEEEEecccCCCCc---eEEEEEEEECCeeEEEecCC-CCCcHHHHHHHHHHHHHHHcCCC---CeEE-EEECHHHHH
Confidence 5899999999999976 59998764 34445566553 47899999999999999988752 4799 999999999
Q ss_pred ccccccccccccccccccccccee-ecCCCc--chhHHHHHHHHHHHHHHhhhhcCCCCCCcceEEEe--ccccccchH
Q psy874 85 KVRNVSSVAMRIAQKVDYISHDVI-SVGIPF--PSIQDENVKLKRSYNDTHAQKKGIPFPSIQDEKVK--LKRSYNDTH 158 (191)
Q Consensus 85 ~~~~~~~~~~~w~~~edW~~ng~~-s~G~PV--~dL~~~~v~l~~~~~d~~~~~~g~~~~~~~~~~v~--a~r~~n~~~ 158 (191)
+.++. |..+ |++++|. +.|.|| +|||+++.++.+. ..+.|.+|+ .++..|+.+
T Consensus 75 ~~i~~------w~~~--Wk~~~~~~~~g~~v~n~dl~~~i~~l~~~-------------~~v~~~wV~~H~~~~~N~~A 132 (150)
T PRK00203 75 QGITE------WIHG--WKKNGWKTADKKPVKNVDLWQRLDAALKR-------------HQIKWHWVKGHAGHPENERC 132 (150)
T ss_pred HHHHH------HHHH--HHHcCCcccCCCccccHHHHHHHHHHhcc-------------CceEEEEecCCCCCHHHHHH
Confidence 97652 7777 9999996 689999 8899987766432 124445544 566788866
No 6
>PRK13907 rnhA ribonuclease H; Provisional
Probab=99.81 E-value=4.5e-19 Score=136.07 Aligned_cols=79 Identities=22% Similarity=0.297 Sum_probs=64.9
Q ss_pred cEEEEEeeccCCCCCCCCceEEEEEEcCC-ceeEEEeccCCCCChHHHHHHHHHHHHHHhHhcCCcceeEEEEcChHHHH
Q psy874 6 HVVVFTDGACPRNGKVGASAGYGVYFGEN-NPLNVAGKVTGRVTNNNAEIQGAIHALKQAKSANEKVKLKRSYNDTHAQK 84 (191)
Q Consensus 6 ~i~IYtDGac~~N~~~~~~AG~Gv~~~~~-~~~~~s~~l~g~~TNnrAEL~Avi~AL~~~~~~~~~~~v~~I~TDS~Yvv 84 (191)
|++|||||||.+||++ +|||+++.+. .....+++ .+..|||+||++|++.||+.+.+.+.. ++. |+|||+||+
T Consensus 1 ~~~iy~DGa~~~~~g~---~G~G~vi~~~~~~~~~~~~-~~~~tn~~AE~~All~aL~~a~~~g~~-~v~-i~sDS~~vi 74 (128)
T PRK13907 1 MIEVYIDGASKGNPGP---SGAGVFIKGVQPAVQLSLP-LGTMSNHEAEYHALLAALKYCTEHNYN-IVS-FRTDSQLVE 74 (128)
T ss_pred CEEEEEeeCCCCCCCc---cEEEEEEEECCeeEEEEec-ccccCCcHHHHHHHHHHHHHHHhCCCC-EEE-EEechHHHH
Confidence 6899999999999987 5999987543 22334444 356899999999999999999998875 899 999999999
Q ss_pred cccccc
Q psy874 85 KVRNVS 90 (191)
Q Consensus 85 ~~~~~~ 90 (191)
+.++..
T Consensus 75 ~~~~~~ 80 (128)
T PRK13907 75 RAVEKE 80 (128)
T ss_pred HHHhHH
Confidence 977653
No 7
>PRK07708 hypothetical protein; Validated
Probab=99.68 E-value=9.8e-16 Score=129.21 Aligned_cols=85 Identities=19% Similarity=0.272 Sum_probs=65.4
Q ss_pred CCCCcEEEEEeeccCCCCCCCCceEEEEEE--cCCc-ee--EEEeccCCCCChHHHHHHHHHHHHHHhHhcCCc-ceeEE
Q psy874 2 DPDNHVVVFTDGACPRNGKVGASAGYGVYF--GENN-PL--NVAGKVTGRVTNNNAEIQGAIHALKQAKSANEK-VKLKR 75 (191)
Q Consensus 2 ~~~~~i~IYtDGac~~N~~~~~~AG~Gv~~--~~~~-~~--~~s~~l~g~~TNnrAEL~Avi~AL~~~~~~~~~-~~v~~ 75 (191)
.+++.+++||||||.+|+++ +|+|+++ ..+. .. ..+..+.+..|||.||+.|++.||+.+.+.|.. .+|.
T Consensus 69 ~ep~~~~vY~DGs~~~n~g~---aG~GvVI~~~~g~~~~~~~~~~~l~~~~TNN~AEy~Ali~aL~~A~e~g~~~~~V~- 144 (219)
T PRK07708 69 EEPHEILVYFDGGFDKETKL---AGLGIVIYYKQGNKRYRIRRNAYIEGIYDNNEAEYAALYYAMQELEELGVKHEPVT- 144 (219)
T ss_pred cCCCcEEEEEeeccCCCCCC---cEEEEEEEECCCCEEEEEEeeccccccccCcHHHHHHHHHHHHHHHHcCCCcceEE-
Confidence 35678999999999999876 5888865 3332 22 222344446899999999999999999998764 2489
Q ss_pred EEcChHHHHcccccc
Q psy874 76 SYNDTHAQKKVRNVS 90 (191)
Q Consensus 76 I~TDS~Yvv~~~~~~ 90 (191)
|++||++|+++++..
T Consensus 145 I~~DSqlVi~qi~g~ 159 (219)
T PRK07708 145 FRGDSQVVLNQLAGE 159 (219)
T ss_pred EEeccHHHHHHhCCC
Confidence 999999999976643
No 8
>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=99.68 E-value=4.6e-17 Score=123.73 Aligned_cols=74 Identities=28% Similarity=0.391 Sum_probs=57.7
Q ss_pred CcEEEEEeeccCCCCCCCCceEEEEEEcCCceeEEEeccCCCCChHHHHHHHHHHHHHHhHhcCCcceeEEEEcChHHHH
Q psy874 5 NHVVVFTDGACPRNGKVGASAGYGVYFGENNPLNVAGKVTGRVTNNNAEIQGAIHALKQAKSANEKVKLKRSYNDTHAQK 84 (191)
Q Consensus 5 ~~i~IYtDGac~~N~~~~~~AG~Gv~~~~~~~~~~s~~l~g~~TNnrAEL~Avi~AL~~~~~~~~~~~v~~I~TDS~Yvv 84 (191)
+.++|||||||..+++. +|+|+++..+ .+.+.++. .+||++|||+|+++||+.+ .. .+++ |+|||+|++
T Consensus 2 ~~~~iytDgS~~~~~~~---~~~g~v~~~~--~~~~~~~~-~~s~~~aEl~Ai~~AL~~~-~~---~~v~-I~tDS~~v~ 70 (132)
T PF00075_consen 2 KAIIIYTDGSCRPNPGK---GGAGYVVWGG--RNFSFRLG-GQSNNRAELQAIIEALKAL-EH---RKVT-IYTDSQYVL 70 (132)
T ss_dssp TSEEEEEEEEECTTTTE---EEEEEEEETT--EEEEEEEE-SECHHHHHHHHHHHHHHTH-ST---SEEE-EEES-HHHH
T ss_pred CcEEEEEeCCccCCCCc---eEEEEEEECC--eEEEeccc-ccchhhhheehHHHHHHHh-hc---cccc-ccccHHHHH
Confidence 56899999999988765 3667665434 36676665 7999999999999999955 32 4899 999999999
Q ss_pred ccccc
Q psy874 85 KVRNV 89 (191)
Q Consensus 85 ~~~~~ 89 (191)
+.++.
T Consensus 71 ~~l~~ 75 (132)
T PF00075_consen 71 NALNK 75 (132)
T ss_dssp HHHHT
T ss_pred HHHHH
Confidence 96543
No 9
>PRK07238 bifunctional RNase H/acid phosphatase; Provisional
Probab=99.62 E-value=4.9e-15 Score=132.41 Aligned_cols=78 Identities=29% Similarity=0.334 Sum_probs=64.1
Q ss_pred cEEEEEeeccCCCCCCCCceEEEEEEcC--Cc-e-eEEEeccCCCCChHHHHHHHHHHHHHHhHhcCCcceeEEEEcChH
Q psy874 6 HVVVFTDGACPRNGKVGASAGYGVYFGE--NN-P-LNVAGKVTGRVTNNNAEIQGAIHALKQAKSANEKVKLKRSYNDTH 81 (191)
Q Consensus 6 ~i~IYtDGac~~N~~~~~~AG~Gv~~~~--~~-~-~~~s~~l~g~~TNnrAEL~Avi~AL~~~~~~~~~~~v~~I~TDS~ 81 (191)
.++|||||||++||++ ||||+++.. +. . ..++..+ +..|||+||+.|++.||+.+.+.+.. +++ |+|||+
T Consensus 2 ~~~i~~DGa~~~n~g~---aG~G~vi~~~~~~~~~~~~~~~~-~~~tnn~AE~~All~gL~~a~~~g~~-~v~-i~~DS~ 75 (372)
T PRK07238 2 KVVVEADGGSRGNPGP---AGYGAVVWDADRGEVLAERAEAI-GRATNNVAEYRGLIAGLEAAAELGAT-EVE-VRMDSK 75 (372)
T ss_pred eEEEEecCCCCCCCCc---eEEEEEEEeCCCCcEEEEeeccc-CCCCchHHHHHHHHHHHHHHHhCCCC-eEE-EEeCcH
Confidence 4789999999999976 599998643 22 2 2445553 47899999999999999999998875 899 999999
Q ss_pred HHHccccc
Q psy874 82 AQKKVRNV 89 (191)
Q Consensus 82 Yvv~~~~~ 89 (191)
||++.++.
T Consensus 76 lvi~~i~~ 83 (372)
T PRK07238 76 LVVEQMSG 83 (372)
T ss_pred HHHHHhCC
Confidence 99998764
No 10
>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=99.17 E-value=1.7e-10 Score=83.74 Aligned_cols=78 Identities=32% Similarity=0.447 Sum_probs=58.7
Q ss_pred EEEEeeccCCCCCCCCceEEEEEEcCC-ceeEEEeccC-CCCChHHHHHHHHHHHHHHhHhcCCcceeEEEEcChHHHHc
Q psy874 8 VVFTDGACPRNGKVGASAGYGVYFGEN-NPLNVAGKVT-GRVTNNNAEIQGAIHALKQAKSANEKVKLKRSYNDTHAQKK 85 (191)
Q Consensus 8 ~IYtDGac~~N~~~~~~AG~Gv~~~~~-~~~~~s~~l~-g~~TNnrAEL~Avi~AL~~~~~~~~~~~v~~I~TDS~Yvv~ 85 (191)
++|||||+..+.+. +|+|+++... .......... ...||+.+|+.|++.||+.+...+.. ++. |+|||+++++
T Consensus 1 ~~~~Dgs~~~~~~~---~g~g~v~~~~~~~~~~~~~~~~~~~s~~~aEl~al~~al~~~~~~~~~-~i~-i~~Ds~~~~~ 75 (130)
T cd06222 1 VIYTDGSCRGNPGP---AGAGVVLRDPGGEVLLSGGLLGGNTTNNRAELLALIEALELALELGGK-KVN-IYTDSQYVIN 75 (130)
T ss_pred CEEecccCCCCCCc---eEEEEEEEeCCCeEEEeccccCCCCcHHHHHHHHHHHHHHHHHhCCCc-eEE-EEECHHHHHH
Confidence 48999999877643 6999987443 2222222211 46899999999999999999876654 899 9999999999
Q ss_pred ccccc
Q psy874 86 VRNVS 90 (191)
Q Consensus 86 ~~~~~ 90 (191)
.++..
T Consensus 76 ~~~~~ 80 (130)
T cd06222 76 ALTGW 80 (130)
T ss_pred Hhhcc
Confidence 77643
No 11
>KOG1132|consensus
Probab=98.64 E-value=8.4e-09 Score=100.51 Aligned_cols=78 Identities=26% Similarity=0.500 Sum_probs=70.3
Q ss_pred cccccccccccc---eeecCCCcchhHHHHHHHHHHHHHHhhhhcC---CCCCCcceEEEeccccccchHhhhhhhccch
Q psy874 95 RIAQKVDYISHD---VISVGIPFPSIQDENVKLKRSYNDTHAQKKG---IPFPSIQDEKVKLKRSYNDTHAQKKVRNVSS 168 (191)
Q Consensus 95 ~w~~~edW~~ng---~~s~G~PV~dL~~~~v~l~~~~~d~~~~~~g---~~~~~~~~~~v~a~r~~n~~~~~~~~~~~~~ 168 (191)
+.+++-|+.+.. ++..|+|+|.+.++.|+|++.|+|++.+.+| ..+++.+||..+++||+|| +
T Consensus 634 KVSEGlDFsD~~~RaVI~tGlPyP~~~D~~V~lK~~y~D~~~~~~g~~s~~lsg~eWY~~qA~RAvNQ-----------A 702 (945)
T KOG1132|consen 634 KVSEGLDFSDDNGRAVIITGLPYPPVMDPRVKLKKQYLDENSSLKGAKSQLLSGQEWYSQQAYRAVNQ-----------A 702 (945)
T ss_pred cccCCCCccccCCceeEEecCCCCCCCCHHHHHHHHhhhhhccccccccccccchHHHHhhHHHHHHH-----------H
Confidence 488999998853 6899999999999999999999999998665 3467899999999999999 9
Q ss_pred hhHHHHhhcccceee
Q psy874 169 VAMRIAQKVDYKLLV 183 (191)
Q Consensus 169 ~~~~~~~~~~~~~~~ 183 (191)
++|+|+||-||++++
T Consensus 703 iGRviRHR~D~Gav~ 717 (945)
T KOG1132|consen 703 IGRVIRHRNDYGAVI 717 (945)
T ss_pred HHHHHhhhcccceee
Confidence 999999999999986
No 12
>PF13456 RVT_3: Reverse transcriptase-like; PDB: 3ALY_A 2EHG_A 3HST_B.
Probab=97.99 E-value=3.4e-05 Score=53.87 Aligned_cols=40 Identities=20% Similarity=0.088 Sum_probs=34.3
Q ss_pred hHHHHHHHHHHHHHHhHhcCCcceeEEEEcChHHHHcccccc
Q psy874 49 NNNAEIQGAIHALKQAKSANEKVKLKRSYNDTHAQKKVRNVS 90 (191)
Q Consensus 49 NnrAEL~Avi~AL~~~~~~~~~~~v~~I~TDS~Yvv~~~~~~ 90 (191)
|..||+.|++.||+.+.+.|.. ++. |+|||+-+++.++..
T Consensus 1 ~~~aE~~al~~al~~a~~~g~~-~i~-v~sDs~~vv~~i~~~ 40 (87)
T PF13456_consen 1 PLEAEALALLEALQLAWELGIR-KII-VESDSQLVVDAINGR 40 (87)
T ss_dssp HHHHHHHHHHHHHHHHHCCT-S-CEE-EEES-HHHHHHHTTS
T ss_pred CcHHHHHHHHHHHHHHHHCCCC-EEE-EEecCcccccccccc
Confidence 5689999999999999999887 999 999999999987654
No 13
>smart00491 HELICc2 helicase superfamily c-terminal domain.
Probab=94.54 E-value=0.0065 Score=47.88 Aligned_cols=73 Identities=27% Similarity=0.448 Sum_probs=55.3
Q ss_pred ccccccccccc---eeecCCCcchhHHHHHHHHHHHHHHhhhhcCCCCCCcceEEEeccccccchHhhhhhhccchhhHH
Q psy874 96 IAQKVDYISHD---VISVGIPFPSIQDENVKLKRSYNDTHAQKKGIPFPSIQDEKVKLKRSYNDTHAQKKVRNVSSVAMR 172 (191)
Q Consensus 96 w~~~edW~~ng---~~s~G~PV~dL~~~~v~l~~~~~d~~~~~~g~~~~~~~~~~v~a~r~~n~~~~~~~~~~~~~~~~~ 172 (191)
.++|.|++.+. ++-.|.|+|..-+..++++..|.+... +. .+...|+..++.+.+|| +++|.
T Consensus 59 ~~EGiD~~g~~~r~vii~glPfp~~~d~~~~~~~~~~~~~~---~~-~~~~~~~~~~a~~~~~Q-----------a~GR~ 123 (142)
T smart00491 59 VSEGIDFPDDLGRAVIIVGIPFPNPDSPILRARLEYLDEKG---GI-RPFDEVYLFDAMRALAQ-----------AIGRA 123 (142)
T ss_pred eecceecCCCccEEEEEEecCCCCCCCHHHHHHHHHHHHhc---CC-CcHHHHHHHHHHHHHHH-----------HhCcc
Confidence 67888888863 567799997666666666766655432 11 23467888899999999 99999
Q ss_pred HHhhcccceee
Q psy874 173 IAQKVDYKLLV 183 (191)
Q Consensus 173 ~~~~~~~~~~~ 183 (191)
|+++-||+.++
T Consensus 124 iR~~~D~g~i~ 134 (142)
T smart00491 124 IRHKNDYGVVV 134 (142)
T ss_pred ccCccceEEEE
Confidence 99999999886
No 14
>TIGR00604 rad3 DNA repair helicase (rad3). All proteins in this family for which funcitons are known are DNA-DNA helicases that funciton in the initiation of transcription and nucleotide excision repair as part of the TFIIH complex. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=94.38 E-value=0.0097 Score=57.89 Aligned_cols=74 Identities=19% Similarity=0.280 Sum_probs=52.5
Q ss_pred ccccccccccccc---eeecCCCcchhHHHHHHHHHHHHHHhhhhcCCCCCCc-ceEEEeccccccchHhhhhhhccchh
Q psy874 94 MRIAQKVDYISHD---VISVGIPFPSIQDENVKLKRSYNDTHAQKKGIPFPSI-QDEKVKLKRSYNDTHAQKKVRNVSSV 169 (191)
Q Consensus 94 ~~w~~~edW~~ng---~~s~G~PV~dL~~~~v~l~~~~~d~~~~~~g~~~~~~-~~~~v~a~r~~n~~~~~~~~~~~~~~ 169 (191)
-+.++|.|+..+. ++-.|.|++..-+..+..+..|-+.. .+ ..+. .||..++.|.+|| ++
T Consensus 592 Gk~sEGIDf~~~~~r~ViivGlPf~~~~~~~~~~~~~~~~~~---~~--~~~~~~~y~~~a~~~v~Q-----------ai 655 (705)
T TIGR00604 592 GKVSEGIDFCDDLGRAVIMVGIPYEYTESRILLARLEFLRDQ---YP--IRENQDFYEFDAMRAVNQ-----------AI 655 (705)
T ss_pred CcccCccccCCCCCcEEEEEccCCCCCCCHHHHHHHHHHHhh---cC--CCccHHHHHHHHHHHHHH-----------Hh
Confidence 3588999999863 55789999443333444443332221 11 1345 8999999999999 99
Q ss_pred hHHHHhhcccceee
Q psy874 170 AMRIAQKVDYKLLV 183 (191)
Q Consensus 170 ~~~~~~~~~~~~~~ 183 (191)
+|.|+++-||++++
T Consensus 656 GR~IR~~~D~G~ii 669 (705)
T TIGR00604 656 GRVIRHKDDYGSIV 669 (705)
T ss_pred CccccCcCceEEEE
Confidence 99999999999987
No 15
>PF13307 Helicase_C_2: Helicase C-terminal domain; PDB: 4A15_A 2VSF_A 3CRV_A 3CRW_1 2VL7_A.
Probab=91.03 E-value=0.03 Score=44.76 Aligned_cols=72 Identities=26% Similarity=0.392 Sum_probs=46.0
Q ss_pred ccccccccccc---eeecCCCcchhHHHHHHHHHHHHHHhhhhcCCCCCCcceEEEeccccccchHhhhhhhccchhhHH
Q psy874 96 IAQKVDYISHD---VISVGIPFPSIQDENVKLKRSYNDTHAQKKGIPFPSIQDEKVKLKRSYNDTHAQKKVRNVSSVAMR 172 (191)
Q Consensus 96 w~~~edW~~ng---~~s~G~PV~dL~~~~v~l~~~~~d~~~~~~g~~~~~~~~~~v~a~r~~n~~~~~~~~~~~~~~~~~ 172 (191)
.++|.|++... ++-.|.|+|.+-+..+..+..|.+... + .+...|+..++-+.++| +++|.
T Consensus 71 ~~EGiD~~~~~~r~vii~glPfp~~~d~~~~~~~~~~~~~~---~--~~~~~~~~~~a~~~l~Q-----------a~GR~ 134 (167)
T PF13307_consen 71 FSEGIDFPGDLLRAVIIVGLPFPPPSDPLVQAKREYLDKQG---K--NPFRDWYLPPAIRKLKQ-----------AIGRL 134 (167)
T ss_dssp CGSSS--ECESEEEEEEES-----TTCHHHHHHHHHHHHCC---T--TCHHHHTHHHHHHHHHH-----------HHHCC
T ss_pred EEEeecCCCchhheeeecCCCCCCCCCHHHHHHHHHHHHHh---c--cchhhHhhHHHHHHHhh-----------hcCcc
Confidence 67887888653 567899997766666777766655532 1 23578888889999999 99999
Q ss_pred HHhhcccceee
Q psy874 173 IAQKVDYKLLV 183 (191)
Q Consensus 173 ~~~~~~~~~~~ 183 (191)
|+++=||+.++
T Consensus 135 iR~~~D~g~i~ 145 (167)
T PF13307_consen 135 IRSEDDYGVII 145 (167)
T ss_dssp --STT-EEEEE
T ss_pred eeccCCcEEEE
Confidence 99999999987
No 16
>smart00492 HELICc3 helicase superfamily c-terminal domain.
Probab=89.58 E-value=0.07 Score=41.98 Aligned_cols=72 Identities=22% Similarity=0.283 Sum_probs=48.8
Q ss_pred ccccccccccc---eeecCCCcchhHHHHHHHHHHHHHHhhhhcCCCCCCcce-EEEeccccccchHhhhhhhccchhhH
Q psy874 96 IAQKVDYISHD---VISVGIPFPSIQDENVKLKRSYNDTHAQKKGIPFPSIQD-EKVKLKRSYNDTHAQKKVRNVSSVAM 171 (191)
Q Consensus 96 w~~~edW~~ng---~~s~G~PV~dL~~~~v~l~~~~~d~~~~~~g~~~~~~~~-~~v~a~r~~n~~~~~~~~~~~~~~~~ 171 (191)
.++|.|++.+. ++-.|.|++..-+..+.++..|.+... +. ++... +..++.|.++| +++|
T Consensus 58 ~~EGiD~~g~~~r~vii~glPfp~~~d~~~~~~~~~~~~~~---~~--~~~~~~~~~~a~~~l~Q-----------a~GR 121 (141)
T smart00492 58 FSEGVDFPGDYLRAVIIDGLPFPYPDSPILKARLELLRDKG---QI--RPFDFVSLPDAMRTLAQ-----------CVGR 121 (141)
T ss_pred eecceecCCCCeeEEEEEecCCCCCCCHHHHHHHHHHHHhC---CC--CchhHHHHHHHHHHHHH-----------HhCc
Confidence 34566677653 457799997666667777766655431 11 22222 23567788899 9999
Q ss_pred HHHhhcccceee
Q psy874 172 RIAQKVDYKLLV 183 (191)
Q Consensus 172 ~~~~~~~~~~~~ 183 (191)
.|+++=||+.++
T Consensus 122 ~iR~~~D~g~i~ 133 (141)
T smart00492 122 LIRGANDYGVVV 133 (141)
T ss_pred cccCcCceEEEE
Confidence 999999999876
No 17
>KOG1133|consensus
Probab=85.55 E-value=0.3 Score=47.96 Aligned_cols=77 Identities=18% Similarity=0.326 Sum_probs=54.9
Q ss_pred ccccccccccccc-c--eeecCCCcchhHHHHHHHHHHHHHHhhhhcCCCCCCcceEEEeccccccchHhhhhhhccchh
Q psy874 93 AMRIAQKVDYISH-D--VISVGIPFPSIQDENVKLKRSYNDTHAQKKGIPFPSIQDEKVKLKRSYNDTHAQKKVRNVSSV 169 (191)
Q Consensus 93 ~~~w~~~edW~~n-g--~~s~G~PV~dL~~~~v~l~~~~~d~~~~~~g~~~~~~~~~~v~a~r~~n~~~~~~~~~~~~~~ 169 (191)
|-+-++|..|.+. | ++-.|-|+|+...-=+..+.+|.+.-. +.|+.+.++|+--..+|.|| |+
T Consensus 696 GGKlSEGINF~D~LgRaVvvVGlPyPN~~s~EL~er~k~l~~k~---~~~gagke~yEnlCMkAVNQ-----------sI 761 (821)
T KOG1133|consen 696 GGKLSEGINFSDDLGRAVVVVGLPYPNIQSVELQERMKHLDGKL---PTPGAGKELYENLCMKAVNQ-----------SI 761 (821)
T ss_pred ccccccccccccccccEEEEeecCCCCCCCHHHHHHHHHhhhcc---CCCCchHHHHHHHHHHHHHH-----------HH
Confidence 3356677667764 3 668899997655533444556655533 33556788887777889999 99
Q ss_pred hHHHHhhcccceee
Q psy874 170 AMRIAQKVDYKLLV 183 (191)
Q Consensus 170 ~~~~~~~~~~~~~~ 183 (191)
+|.|+|.-||-.|+
T Consensus 762 GRAIRH~~DYA~i~ 775 (821)
T KOG1133|consen 762 GRAIRHRKDYASIY 775 (821)
T ss_pred HHHHhhhccceeEE
Confidence 99999999998875
No 18
>COG1199 DinG Rad3-related DNA helicases [Transcription / DNA replication, recombination, and repair]
Probab=76.99 E-value=1.2 Score=42.61 Aligned_cols=74 Identities=22% Similarity=0.254 Sum_probs=53.7
Q ss_pred cccccccccccc---eeecCCCcchhHHHHHHHHHHHHHHhhhhcCCCCCCcceEEEeccccccchHhhhhhhccchhhH
Q psy874 95 RIAQKVDYISHD---VISVGIPFPSIQDENVKLKRSYNDTHAQKKGIPFPSIQDEKVKLKRSYNDTHAQKKVRNVSSVAM 171 (191)
Q Consensus 95 ~w~~~edW~~ng---~~s~G~PV~dL~~~~v~l~~~~~d~~~~~~g~~~~~~~~~~v~a~r~~n~~~~~~~~~~~~~~~~ 171 (191)
+.++|.|++.+. ++-.|.|+|..-+..+..+.++...+. +. +-..|+..++.+.++| +++|
T Consensus 537 sf~EGVD~~g~~l~~vvI~~lPfp~p~dp~~~~r~~~~~~~g---~~--~f~~~~l~~A~~~l~Q-----------avGR 600 (654)
T COG1199 537 SFWEGVDFPGDALRLVVIVGLPFPNPDDPLLKARLEFLKRLG---GD--PFEEFYLPPAVIKLRQ-----------AVGR 600 (654)
T ss_pred cccCcccCCCCCeeEEEEEecCCCCCCCHHHHHHHHHHHHhc---CC--CceEeehHHHHHHHHH-----------hhcc
Confidence 466777777763 457799997666666666666655542 22 2356666678888999 9999
Q ss_pred HHHhhcccceeee
Q psy874 172 RIAQKVDYKLLVS 184 (191)
Q Consensus 172 ~~~~~~~~~~~~~ 184 (191)
-|+.+=||+.+|-
T Consensus 601 lIR~~~D~G~ivl 613 (654)
T COG1199 601 LIRSEDDRGVIVL 613 (654)
T ss_pred ccccCCCceEEEE
Confidence 9999999999873
No 19
>PF05380 Peptidase_A17: Pao retrotransposon peptidase ; InterPro: IPR008042 This signature identifies members of the Pao retrotransposon family.
Probab=52.52 E-value=52 Score=25.91 Aligned_cols=21 Identities=24% Similarity=0.284 Sum_probs=18.0
Q ss_pred CCChHHHHHHHHHHHHHHhHh
Q psy874 46 RVTNNNAEIQGAIHALKQAKS 66 (191)
Q Consensus 46 ~~TNnrAEL~Avi~AL~~~~~ 66 (191)
..|-=|.||+|++.+.+.+..
T Consensus 123 ~~tIPRlEL~a~~l~~~l~~~ 143 (159)
T PF05380_consen 123 TVTIPRLELLAALLGVRLANT 143 (159)
T ss_pred CCcHHHHHHHHHHHHHHHHHH
Confidence 458899999999999998754
No 20
>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=47.97 E-value=18 Score=30.86 Aligned_cols=60 Identities=17% Similarity=0.131 Sum_probs=38.0
Q ss_pred cEEEEEeeccCCCCCCCCceEEEEEEcCCcee-EEEeccCCCCChHHHHHHHHHHHHHHhHhcCCcceeEEEEcChHHHH
Q psy874 6 HVVVFTDGACPRNGKVGASAGYGVYFGENNPL-NVAGKVTGRVTNNNAEIQGAIHALKQAKSANEKVKLKRSYNDTHAQK 84 (191)
Q Consensus 6 ~i~IYtDGac~~N~~~~~~AG~Gv~~~~~~~~-~~s~~l~g~~TNnrAEL~Avi~AL~~~~~~~~~~~v~~I~TDS~Yvv 84 (191)
.-.|++|.. + -|||+.++.+... .++.+ -.-+.+||.|+..|--.+.. -. |-|||.+|+
T Consensus 94 lc~VfaDAT------p---Tgwgi~i~~~~~~~Tfs~~----l~IhtaELlaaClAr~~~~~------r~-l~tDnt~Vl 153 (245)
T PF00336_consen 94 LCQVFADAT------P---TGWGISITGQRMRGTFSKP----LPIHTAELLAACLARLMSGA------RC-LGTDNTVVL 153 (245)
T ss_pred CCceeccCC------C---CcceeeecCceeeeeeccc----ccchHHHHHHHHHHHhccCC------cE-EeecCcEEE
Confidence 345666653 2 2788877654322 23333 34567999999888765543 24 779999988
Q ss_pred c
Q psy874 85 K 85 (191)
Q Consensus 85 ~ 85 (191)
.
T Consensus 154 s 154 (245)
T PF00336_consen 154 S 154 (245)
T ss_pred e
Confidence 6
No 21
>COG3341 Predicted double-stranded RNA/RNA-DNA hybrid binding protein [General function prediction only]
Probab=37.16 E-value=81 Score=27.04 Aligned_cols=74 Identities=15% Similarity=0.262 Sum_probs=44.0
Q ss_pred EEEEEeeccCCCCCCCCceEEEEEEcCC----ceeEEEeccCCCCChHHHHHHHHHHHHHHhHhcCCcceeEEEE----c
Q psy874 7 VVVFTDGACPRNGKVGASAGYGVYFGEN----NPLNVAGKVTGRVTNNNAEIQGAIHALKQAKSANEKVKLKRSY----N 78 (191)
Q Consensus 7 i~IYtDGac~~N~~~~~~AG~Gv~~~~~----~~~~~s~~l~g~~TNnrAEL~Avi~AL~~~~~~~~~~~v~~I~----T 78 (191)
+.-+.+|+....|+.+ +.=++.+.. ..+..+.+ .+..+|+.+|.+|.+.+|+.+...+....++ +| .
T Consensus 66 ~i~~~~G~y~~~p~t~---~~k~yr~k~~~~~~~lt~~~~-~~~~~n~s~d~la~ly~~~~~~~~~nrk~~i-~y~~~~~ 140 (225)
T COG3341 66 IISWAKGDYDAKPGTQ---EFKEYRGKCTIEYSWLTESSE-FSIKSNDSGDVLAKLYGLRYEVPLDNRKSVI-NYLTPGN 140 (225)
T ss_pred cceeccCCccccCCCc---ceeEEeccccccceeeeeecc-cccccCchHHHHHHhccccccccccCcccee-eccCCcc
Confidence 4455566665555432 222333321 22222333 2467999999999999999988765442344 46 6
Q ss_pred ChHHHHc
Q psy874 79 DTHAQKK 85 (191)
Q Consensus 79 DS~Yvv~ 85 (191)
||+-.++
T Consensus 141 ds~a~~k 147 (225)
T COG3341 141 DSWAYFK 147 (225)
T ss_pred hhHHHHH
Confidence 8877765
No 22
>KOG3284|consensus
Probab=32.71 E-value=28 Score=29.34 Aligned_cols=33 Identities=21% Similarity=0.231 Sum_probs=24.0
Q ss_pred hHHHHHHHHHHHHHHhHhcCCcceeEEEEcChHHHHc
Q psy874 49 NNNAEIQGAIHALKQAKSANEKVKLKRSYNDTHAQKK 85 (191)
Q Consensus 49 NnrAEL~Avi~AL~~~~~~~~~~~v~~I~TDS~Yvv~ 85 (191)
-|.+||.||+.||+.+...-.. .. .|+|+|.-.
T Consensus 25 enlseLyaIi~ale~LEKAyir-D~---is~sey~s~ 57 (213)
T KOG3284|consen 25 ENLSELYAIIKALEQLEKAYIR-DC---ISPSEYTSE 57 (213)
T ss_pred HHHHHHHHHHHHHHHHHHHHHH-cc---CCHHHHHHH
Confidence 4779999999999988653111 33 389999754
No 23
>KOG0419|consensus
Probab=22.64 E-value=7 Score=31.04 Aligned_cols=38 Identities=18% Similarity=0.083 Sum_probs=31.5
Q ss_pred CCChHHHHHHHHHHHHHHhHhcCCcceeEEEEcChHHHH
Q psy874 46 RVTNNNAEIQGAIHALKQAKSANEKVKLKRSYNDTHAQK 84 (191)
Q Consensus 46 ~~TNnrAEL~Avi~AL~~~~~~~~~~~v~~I~TDS~Yvv 84 (191)
+..||.||+.|+|.+.+-..-.|-.-+++ |.-+++|--
T Consensus 28 P~~~niM~W~a~I~Gp~~tp~e~gtFkLt-l~FteeYpn 65 (152)
T KOG0419|consen 28 PVENNIMEWNAVIFGPQDTPFEGGTFKLT-LEFTEEYPN 65 (152)
T ss_pred CCccceeeeeeeEEcCCCCCcCCceEEEE-EEcccccCC
Confidence 67899999999999998776655445899 999999964
No 24
>PF10298 WhiA_N: WhiA N-terminal LAGLIDADG-like domain; InterPro: IPR018478 This entry represents the N-terminal domain of sporulation factor WhiA []. This domain is related to the LAGLIDADG homing endonuclease domain while the C-terminal domain of WhiA is predicted to be a DNA binding helix-turn-helix domain [].; PDB: 3HYI_A 3HYJ_D.
Probab=20.94 E-value=63 Score=22.81 Aligned_cols=36 Identities=17% Similarity=0.165 Sum_probs=22.1
Q ss_pred hHHHHHHHHHHHHHHhHhcCCcceeEEEEcChHHHHc
Q psy874 49 NNNAEIQGAIHALKQAKSANEKVKLKRSYNDTHAQKK 85 (191)
Q Consensus 49 NnrAEL~Avi~AL~~~~~~~~~~~v~~I~TDS~Yvv~ 85 (191)
-+.|||.|++.---.+.-.+-...+. |.||+..+.+
T Consensus 3 c~~AELaAlir~~G~l~~~~~~~~l~-~~ten~~vAR 38 (86)
T PF10298_consen 3 CRIAELAALIRFSGSLSISNGRISLE-ISTENAAVAR 38 (86)
T ss_dssp HHHHHHHHHHHHHEEECTTTTEEEE---EES-HHHHH
T ss_pred HHHHHHHHHHHhCCEEEEECCEEEEE-EEeCCHHHHH
Confidence 36899999987665443322223677 8999998865
Done!