Query psy12553
Match_columns 401
No_of_seqs 299 out of 1387
Neff 4.8
Searched_HMMs 46136
Date Fri Aug 16 22:18:02 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy12553.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/12553hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2299|consensus 100.0 6.7E-86 1.4E-90 627.5 18.3 297 11-334 1-300 (301)
2 cd07181 RNaseH_typeII_eukaryot 100.0 8.9E-61 1.9E-65 451.0 19.0 210 43-274 1-216 (216)
3 cd07180 RNaseH_typeII_Archaea_ 100.0 7.8E-56 1.7E-60 413.6 18.5 201 43-273 1-203 (204)
4 PRK14551 rnhB ribonuclease HII 100.0 1.4E-55 3E-60 415.3 18.6 201 41-276 1-203 (212)
5 TIGR00729 ribonuclease H, mamm 100.0 2.3E-55 5E-60 411.2 20.0 202 42-274 1-205 (206)
6 COG0164 RnhB Ribonuclease HII 100.0 1.9E-51 4.1E-56 383.0 18.6 186 41-276 1-190 (199)
7 PRK00015 rnhB ribonuclease HII 100.0 4.5E-51 9.8E-56 380.9 18.8 178 38-270 16-197 (197)
8 cd06266 RNaseH_typeII Ribonucl 100.0 2.4E-51 5.3E-56 379.3 16.4 189 43-271 1-193 (193)
9 PRK14550 rnhB ribonuclease HII 100.0 1.9E-50 4.1E-55 378.7 14.1 193 41-279 1-197 (204)
10 cd07182 RNaseH_typeII_bacteria 100.0 6.1E-50 1.3E-54 368.1 17.1 174 43-270 1-178 (179)
11 cd06590 RNaseH_typeII_bacteria 100.0 4.6E-50 9.9E-55 375.5 16.1 202 43-273 1-207 (208)
12 PRK13926 ribonuclease HII; Pro 100.0 2.1E-49 4.6E-54 372.3 19.7 182 37-275 19-204 (207)
13 PRK13925 rnhB ribonuclease HII 100.0 1.1E-49 2.3E-54 372.1 17.5 186 39-273 7-196 (198)
14 PF01351 RNase_HII: Ribonuclea 100.0 4E-48 8.7E-53 358.9 14.2 195 43-270 1-198 (198)
15 PRK00996 ribonuclease HIII; Pr 100.0 9.3E-44 2E-48 350.8 18.9 205 39-275 86-300 (304)
16 TIGR00716 rnhC ribonuclease HI 100.0 7.2E-39 1.6E-43 313.6 18.2 192 39-264 80-276 (284)
17 COG1039 RnhC Ribonuclease HIII 100.0 1.5E-31 3.4E-36 259.8 13.8 204 39-275 82-295 (297)
18 PRK04342 DNA topoisomerase VI 29.7 27 0.00058 36.3 1.3 17 235-252 220-236 (367)
19 PRK12362 germination protease; 25.7 47 0.001 34.1 2.2 34 82-119 264-297 (318)
20 cd00223 TOPRIM_TopoIIB_SPO TOP 24.4 48 0.001 29.9 1.8 16 235-251 30-45 (160)
21 KOG3495|consensus 24.4 69 0.0015 24.5 2.3 19 204-222 12-30 (50)
22 PF09010 AsiA: Anti-Sigma Fact 22.9 40 0.00087 28.7 0.9 20 202-221 10-29 (91)
23 TIGR01441 GPR GPR endopeptidas 20.5 1.5E+02 0.0032 31.1 4.6 34 82-119 296-329 (358)
No 1
>KOG2299|consensus
Probab=100.00 E-value=6.7e-86 Score=627.47 Aligned_cols=297 Identities=50% Similarity=0.819 Sum_probs=269.8
Q ss_pred ccchhhhhccCCCCceEEecCCCcCCCCCCcEeeeccCCCCCCccceeEEEEEeeCCCChhHhhhcCCCCCCcCCHHHHH
Q psy12553 11 TEVESCIRSNDNSRNLIISSTIPESCKSQPCVLGIDEAGRGPVLGPMVYGTAYCPKDNNEELLKNLGCADSKALTEKKRD 90 (401)
Q Consensus 11 ~~~~~~~~~~~~~~~~~~~s~~p~~~~~~~~viGIDEAGRGpv~GPmVvaav~~p~~~~~~~L~~lGv~DSKkLSe~kRe 90 (401)
|+++++ +++|+..+.++|++|+.|++.||++||||||||||+||||||++|||.+.. ..|..+||+|||+|++.+|+
T Consensus 1 ~~~~sl--~~~~~~~s~~~s~vp~~~~~~PcvlGIDEAGRGPVLGPMVYa~~ycP~~~~-~~l~~lgfaDSK~L~e~kRe 77 (301)
T KOG2299|consen 1 MLPPSL--EKENPSKSIYFSPVPDEQKSEPCVLGIDEAGRGPVLGPMVYAAAYCPLDYL-EDLENLGFADSKTLTEAKRE 77 (301)
T ss_pred CCCccc--cccCcccceeccCCcccccCCceEeeccccCCCCcccceeeEEEeccchhh-hhhhhcCccchhhccHHHHH
Confidence 567777 889999999999999999999999999999999999999999999999998 78999999999999999999
Q ss_pred HHHHHHhhc---cceeeEEEEEEChHhHHHHhHhHhHhhHHHHHHHHHHHHHHHHHHcCCCccEEEEcCCCCccchhhhh
Q psy12553 91 DILDSICKE---NAWLGWMVEIISPNVICNSMLRRQKYSLNEVSHDAAIGLIRKVIAAGVNVREVYVDTVGPPESYKKKL 167 (401)
Q Consensus 91 ~L~~~I~~~---~~~v~~aV~visp~eId~~ml~~~~~NLN~l~~~aai~lI~~~l~~gv~~~~V~VD~~g~p~~Y~~~L 167 (401)
+||+.|++. ...+||++.+|||++|++.|++++++|||+++|++|+.||+.+++.|+++.+|||||+|+|.+||++|
T Consensus 78 ~lf~~i~~d~~~~~~vgwA~~~isP~~IS~~Ml~r~kynLNevshdsam~LI~~v~~~gvnvteiyVDTVGpp~~Yq~kL 157 (301)
T KOG2299|consen 78 ELFNKIKEDEELTSNVGWATDCISPREISASMLRRNKYNLNEVSHDSAMGLIDEVLDQGVNVTEIYVDTVGPPAKYQEKL 157 (301)
T ss_pred HHHHHHhhhhhhhhceeeEeeecCHHHHHHHHHHHhcCCchhhhhHHHHHHHHHHHHhCCceEEEEEecCCChHHHHHHH
Confidence 999999864 24689999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhccCcceEEEeecCCCCCccccccccccCCCccchhhhhhHHHHHHHHHHHhhhhhhhhhhhhcCCCCCCCCCCHHHHH
Q psy12553 168 SEIFPELIITVASKADSTYPVVGAAIASKADSTYPVVGAASICAKVSRDSALKSWTFQEGIQIENNAWGSGYPGDPVTKK 247 (401)
Q Consensus 168 ~~~fp~i~i~v~~KADs~y~v~~~~~~~kgD~~yp~VAAASIvAKVtRD~~m~~~~~~e~l~~~~~~yGsGYPSDp~Tk~ 247 (401)
++.||+++++|..||||+ ||+|||||||||||||+.+++|++.|.+.....+||||||+||+|++
T Consensus 158 ek~FP~~k~tV~kKADSl---------------fpiVS~ASI~AKVtRD~alk~w~~~E~~~~~d~~~GSGYP~DP~T~~ 222 (301)
T KOG2299|consen 158 EKRFPGIKFTVTKKADSL---------------FPIVSAASIVAKVTRDRALKEWQFEEKLSDPDEDLGSGYPSDPETKA 222 (301)
T ss_pred HhhCCCeEEEEeeccccc---------------ccchhhhhhhhhhhhccccceeeeeeecccCCccccCCCCCChhHHH
Confidence 999999999999999999 99999999999999999999999999877778899999999999999
Q ss_pred HHHhcCCCCcccccccccCchhHHHHhhccCceeeeccCCchhhhhccccccccccccccCCCCCCCCcccccccccccc
Q psy12553 248 FLSENIDPVFGFPQLVRFSWSTASKILKEKAVLVEGDEIDDEEEEGENKKTRSIRNFFKPKADENVESPVVEERHAFFKE 327 (401)
Q Consensus 248 ~L~~~i~~~fG~p~~hR~SW~tvk~il~~~~~~v~w~~~~~~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~r~~ff~~ 327 (401)
||+.+++++||||++|||||+|++.+|++++.++.|++++.+. .+....++++||+++...+ + ..|...| +
T Consensus 223 wLk~~v~~VFGfp~lVRfSW~Ta~t~L~~~~~~~~~e~~~~e~---~~~~~~~~T~~~~~~~~s~---~--~~r~~~~-~ 293 (301)
T KOG2299|consen 223 WLKENVDSVFGFPSLVRFSWKTAKTLLEDRSEPLKWEESGFEL---DKTPLLKFTKKFKPNPASR---S--VPRSERF-E 293 (301)
T ss_pred HHHhcccccccCccceeeeHHHHHHHHhcccccceeecccccc---cchHHHHHHHHhcCCCccc---c--cchhHHH-H
Confidence 9999999999999999999999999999999999998764431 1123567899998753222 2 2233355 9
Q ss_pred CCCCCcc
Q psy12553 328 SPYGGSK 334 (401)
Q Consensus 328 r~l~~~~ 334 (401)
|+|+++.
T Consensus 294 r~l~~~~ 300 (301)
T KOG2299|consen 294 RHLENWY 300 (301)
T ss_pred Hhhhhhc
Confidence 9998764
No 2
>cd07181 RNaseH_typeII_eukaryota_like Eukaryotic Ribonuclease HII; putative role in Okazaki fragment removal during replication. Ribonuclease (RNase) HII endonucleolytically hydrolyzes an RNA strand when it is annealed to a complementary DNA strand in the presence of divalent cations, in DNA replication and repair. RNase H is classified into two families, type I (prokaryotic RNase HI, eukaryotic RNase H1 and viral RNase H) and type II (prokaryotic RNase HII and HIII, and eukaryotic RNase H2/HII). The enzyme can be found in bacteria, archaea, and eukaryotes. Most prokaryotic and eukaryotic genomes contain multiple RNase H genes. Despite a lack of evidence for homology from sequence comparisons, type I and type II RNase H share a common fold and similar steric configurations of the four acidic active-site residues, suggesting identical or very similar catalytic mechanisms. Eukaryotic RNase HII is a type II RNase H that is active during replication and is believed to play a role in removal
Probab=100.00 E-value=8.9e-61 Score=451.01 Aligned_cols=210 Identities=64% Similarity=1.085 Sum_probs=188.9
Q ss_pred eeeccCCCCCCccceeEEEEEeeCCCChhHhhhcCCCCCCcCCHHHHHHHHHHHhhccceeeEEEEEEChHhHHHHhHhH
Q psy12553 43 LGIDEAGRGPVLGPMVYGTAYCPKDNNEELLKNLGCADSKALTEKKRDDILDSICKENAWLGWMVEIISPNVICNSMLRR 122 (401)
Q Consensus 43 iGIDEAGRGpv~GPmVvaav~~p~~~~~~~L~~lGv~DSKkLSe~kRe~L~~~I~~~~~~v~~aV~visp~eId~~ml~~ 122 (401)
+|||||||||+|||||||||+++.+.. +.|..+||+|||+||+++|++|++.|++...++.|.+.+++|++||+.|+..
T Consensus 1 iGiDEaGRG~~~GPlvvaav~~~~~~~-~~l~~~gv~DSK~Ls~~~r~~L~~~I~~~~~~~~~~i~~i~~~~id~~~~~~ 79 (216)
T cd07181 1 LGIDEAGRGPVLGPMVYGIAYCPISYE-EDLKKLGFADSKTLTEEKREELFKKIKEKSEALGWATRILSPQYISAKMLAR 79 (216)
T ss_pred CCCcCCCCCCChhhhEEEEEEEchHhh-hhhhhcCCCcCCcCCHHHHHHHHHHHHhccccceEEEEEECHHHHCHHhhhc
Confidence 699999999999999999999998765 5677799999999999999999999995222678999999999999987655
Q ss_pred hHhhHHHHHHHHHHHHHHHHHHcCCCccEEEEcCCCCccchhhhhhhccCcceEEEeecCCCCCccccccccccCCCccc
Q psy12553 123 QKYSLNEVSHDAAIGLIRKVIAAGVNVREVYVDTVGPPESYKKKLSEIFPELIITVASKADSTYPVVGAAIASKADSTYP 202 (401)
Q Consensus 123 ~~~NLN~l~~~aai~lI~~~l~~gv~~~~V~VD~~g~p~~Y~~~L~~~fp~i~i~v~~KADs~y~v~~~~~~~kgD~~yp 202 (401)
..+|||+++|+++++++++++..+.++..|+||+++.+++|.++|+..+|++++++++|||++ ||
T Consensus 80 ~~~nln~~~~~~~~~~i~~~~~~~~~~~~vliD~~~~~~~~~~~L~~~~~~~~~~~~~kaD~~---------------~~ 144 (216)
T cd07181 80 TKYNLNEISHDAAIGLIKSVLDKGVNVTEVYVDTVGPPEKYQAKLKKLFPGIKFTVEKKADSL---------------YP 144 (216)
T ss_pred ccccHHHHHHHHHHHHHHHHHcCCCCCCEEEECCCCChhHHHHhhhhcCCCCceEEeeCcccc---------------cH
Confidence 567999999999999998887767788999999999888999999877777778888999999 99
Q ss_pred hhhhhhHHHHHHHHHHHhhhhhhhhhhhhc------CCCCCCCCCCHHHHHHHHhcCCCCcccccccccCchhHHHHh
Q psy12553 203 VVGAASICAKVSRDSALKSWTFQEGIQIEN------NAWGSGYPGDPVTKKFLSENIDPVFGFPQLVRFSWSTASKIL 274 (401)
Q Consensus 203 ~VAAASIvAKVtRD~~m~~~~~~e~l~~~~------~~yGsGYPSDp~Tk~~L~~~i~~~fG~p~~hR~SW~tvk~il 274 (401)
+||||||||||+||++|+.+. ..+ +++||||||||.|++||++++++.+|+|++||+||+|++++|
T Consensus 145 ~VAAASIvAKV~RD~~m~~l~------~~~~~~~~~~~~gsGYpsd~~t~~~l~~~~~~~~~~~~~~R~sw~t~~~~l 216 (216)
T cd07181 145 IVSAASIVAKVTRDRALKNWQ------FDEYLIDPDGDFGSGYPSDPKTKKWLKKNVDPVFGFPSLVRFSWSTAKKLL 216 (216)
T ss_pred HHHHHHHHHHHHHHHHHHHHH------hhCccccccCCCceECCCHHHHHHHHHhcCCCcCCCCCceEccccchHhcC
Confidence 999999999999999999873 444 467899999999999999999999999999999999999875
No 3
>cd07180 RNaseH_typeII_Archaea_like Archaeal ribonuclease HII. Ribonuclease (RNase) H is classified into two families, type I (prokaryotic RNase HI, eukaryotic RNase H1 and viral RNase H) and type II (prokaryotic RNase HII and HIII, archaeal RNase HII and eukaryotic RNase H2/HII). RNase H endonucleolytically hydrolyzes an RNA strand when it is annealed to a complementary DNA strand in the presence of divalent cations, in DNA replication or repair. Some archaeal RNase HII show broad divalent cation specificity. It is proposed that three of the four acidic residues at the active site are involved in metal binding and the fourth one involved in the catalytic process in archaea. Most archaeal genomes contain multiple RNase H genes. Despite a lack of evidence for homology from sequence comparisons, type I and type II RNase H share a common fold and similar steric configurations of the four acidic active-site residues, suggesting identical or very similar catalytic mechanisms. It appears tha
Probab=100.00 E-value=7.8e-56 Score=413.58 Aligned_cols=201 Identities=39% Similarity=0.579 Sum_probs=179.1
Q ss_pred eeeccCCCCCCccceeEEEEEeeCCCChhHhhhcCCCCCCcCCHHHHHHHHHHHhhccceeeEEEEEEChHhHHHHhHhH
Q psy12553 43 LGIDEAGRGPVLGPMVYGTAYCPKDNNEELLKNLGCADSKALTEKKRDDILDSICKENAWLGWMVEIISPNVICNSMLRR 122 (401)
Q Consensus 43 iGIDEAGRGpv~GPmVvaav~~p~~~~~~~L~~lGv~DSKkLSe~kRe~L~~~I~~~~~~v~~aV~visp~eId~~ml~~ 122 (401)
+|||||||||+|||||||||++|.+.. ..|+.+||+|||+||+++|++|++.|++ ..+.|++.+++|++||+.|
T Consensus 1 iGiDEaGrG~~~GPlvvaav~~~~~~~-~~l~~~gv~DSK~Ls~~~r~~l~~~I~~--~~~~~~i~~i~~~~id~~~--- 74 (204)
T cd07180 1 CGIDEAGRGPVIGPMVVAGVAIDEESL-KKLKSLGVKDSKKLTPKKREELYNEILK--VADDVVIVIVSPEEIDERR--- 74 (204)
T ss_pred CCCCCCCCCCcccceEEEEEEECHHHh-hhHhhcCCCcCCCCCHHHHHHHHHHHHh--cCCeEEEEEECHHHhChhh---
Confidence 699999999999999999999998866 6788999999999999999999999995 4678999999999999875
Q ss_pred hHhhHHHHHHHHHHHHHHHHHHcCCCccEEEEcCC-CCccchhhhhhhcc-CcceEEEeecCCCCCccccccccccCCCc
Q psy12553 123 QKYSLNEVSHDAAIGLIRKVIAAGVNVREVYVDTV-GPPESYKKKLSEIF-PELIITVASKADSTYPVVGAAIASKADST 200 (401)
Q Consensus 123 ~~~NLN~l~~~aai~lI~~~l~~gv~~~~V~VD~~-g~p~~Y~~~L~~~f-p~i~i~v~~KADs~y~v~~~~~~~kgD~~ 200 (401)
...|||.+++.++.++|+++. ..+..|+||++ +.+++|.++|++.+ +..++++++|||++
T Consensus 75 ~~~nln~~~~~~~~~~i~~l~---~~~~~iliD~~~~~~~~~~~~l~~~~~~~~~~~~~~KgD~~--------------- 136 (204)
T cd07180 75 EAHNLNELEAEAFAELINRLS---DKPDIVYVDACDVNEERFAEELRERLNSGVEVIAEHKADAK--------------- 136 (204)
T ss_pred hhcCHHHHHHHHHHHHHHHhh---cCCCEEEEeCCCCCHHHHHHHHHHhcCCCCcEEEEeCCccc---------------
Confidence 257999999999999888764 35788999999 56778998888765 34667788999999
Q ss_pred cchhhhhhHHHHHHHHHHHhhhhhhhhhhhhcCCCCCCCCCCHHHHHHHHhcCCCCcccccccccCchhHHHH
Q psy12553 201 YPVVGAASICAKVSRDSALKSWTFQEGIQIENNAWGSGYPGDPVTKKFLSENIDPVFGFPQLVRFSWSTASKI 273 (401)
Q Consensus 201 yp~VAAASIvAKVtRD~~m~~~~~~e~l~~~~~~yGsGYPSDp~Tk~~L~~~i~~~fG~p~~hR~SW~tvk~i 273 (401)
||+||||||||||+||++|+++ .+.|++||+|||+||.|++|+++++++.+|++++||+||+|++++
T Consensus 137 ~~~VAaASIlAKv~Rd~~m~~l------~~~~~~~g~Gy~sd~~t~~~l~~~~~~~g~~~~~~R~sf~~~~~~ 203 (204)
T cd07180 137 YPVVSAASIIAKVERDREIEEL------KEEYGDFGSGYPSDPRTIKFLRNYYREHGELPPIVRKSWKTVKRL 203 (204)
T ss_pred CchhhHHHHHHHHHHHHHHHHH------HHhcccCCCcCCCCHHHHHHHHHHHHhhCCCChhheecccchhhc
Confidence 9999999999999999999985 577899999999999999999988877677999999999999864
No 4
>PRK14551 rnhB ribonuclease HII; Provisional
Probab=100.00 E-value=1.4e-55 Score=415.30 Aligned_cols=201 Identities=29% Similarity=0.447 Sum_probs=172.9
Q ss_pred cEeeeccCCCCCCccceeEEEEEeeCCCChhHhhhcCCCCCCcCCHHHHHHHHHHHhhccceeeEEEEEEChHhHHHHhH
Q psy12553 41 CVLGIDEAGRGPVLGPMVYGTAYCPKDNNEELLKNLGCADSKALTEKKRDDILDSICKENAWLGWMVEIISPNVICNSML 120 (401)
Q Consensus 41 ~viGIDEAGRGpv~GPmVvaav~~p~~~~~~~L~~lGv~DSKkLSe~kRe~L~~~I~~~~~~v~~aV~visp~eId~~ml 120 (401)
.++|||||||||||||||||||+++.+.. ..||+|||+||+++|++|+++|++. ..+.|++.+++|++||+.
T Consensus 1 ~~iGiDEaGRG~v~GPlVvaav~~~~~~~-----~~gv~DSK~Ls~~~R~~l~~~I~~~-~~~~~~i~~isp~~Id~~-- 72 (212)
T PRK14551 1 MRFGVDEAGKGPVLGSMFAAAVRADPAAL-----PDGIDDSKRLSPERREELAAELRED-DAIAVGVAEIPPARIDDP-- 72 (212)
T ss_pred CeeCccCCCCCCccccceEEEEEECcccC-----cCCCcCcccCCHHHHHHHHHHHHhc-cCceEEEEEeCHHHHCcc--
Confidence 37999999999999999999999997644 3599999999999999999999952 137899999999999963
Q ss_pred hHhHhhHHHHHHHHHHHHHHHHHHcCCCccEEEEcCCC-Cccchhhhhhhcc-CcceEEEeecCCCCCccccccccccCC
Q psy12553 121 RRQKYSLNEVSHDAAIGLIRKVIAAGVNVREVYVDTVG-PPESYKKKLSEIF-PELIITVASKADSTYPVVGAAIASKAD 198 (401)
Q Consensus 121 ~~~~~NLN~l~~~aai~lI~~~l~~gv~~~~V~VD~~g-~p~~Y~~~L~~~f-p~i~i~v~~KADs~y~v~~~~~~~kgD 198 (401)
.+|||.+.+.++.++|.+++ ..+..|+||+++ ++.+|+.+|++.+ +++++++++|||++
T Consensus 73 ---~~nln~~~~~a~~~ai~~l~---~~~~~v~iD~~~~~~~~~~~~l~~~~~~~~~~~~~~KaD~~------------- 133 (212)
T PRK14551 73 ---ETDMNTLTVAAHAEALSGVA---TDGITGLCDAGDVDAGRFARRVADRVALDVSVSAEHGADEE------------- 133 (212)
T ss_pred ---ccCHHHHHHHHHHHHHHhhc---cCCCEEEECCCCCchHHHHHhhhhccCCCCceEEEecccch-------------
Confidence 36999999988888887653 356789999985 5667888887765 34677888999999
Q ss_pred CccchhhhhhHHHHHHHHHHHhhhhhhhhhhhhcCCCCCCCCCCHHHHHHHHhcCCCCcccccccccCchhHHHHhhc
Q psy12553 199 STYPVVGAASICAKVSRDSALKSWTFQEGIQIENNAWGSGYPGDPVTKKFLSENIDPVFGFPQLVRFSWSTASKILKE 276 (401)
Q Consensus 199 ~~yp~VAAASIvAKVtRD~~m~~~~~~e~l~~~~~~yGsGYPSDp~Tk~~L~~~i~~~fG~p~~hR~SW~tvk~il~~ 276 (401)
||+||||||||||+||+.|+++ ...||+|||||||||.|++||++++++.+++|++||+||+|+++++++
T Consensus 134 --~~~VAAASIlAKv~RD~~m~~l------~~~y~~~GsGYpsd~~t~~~l~~~~~~~g~~p~~~R~Sw~~~~~~~~~ 203 (212)
T PRK14551 134 --DPLVGAASIVAKVARDAHVAAL------AAEYGDVGSGYPSDPTTREFLREYVREHGELPACARRSWSTCDDVLAA 203 (212)
T ss_pred --hHHHHHHHHHHHHHHHHHHHHH------HHHCCCCCCcCCCcHHHHHHHHHHHHHhCCCchhhccCcHHHHHHHHH
Confidence 9999999999999999999985 578899999999999999999887765444566999999999999976
No 5
>TIGR00729 ribonuclease H, mammalian HI/archaeal HII subfamily. Archaeal members of this subfamily of RNase H are designated RNase HII and one has been shown to be active as a monomer. A member from Homo sapiens was characterized as RNase HI, large subunit.
Probab=100.00 E-value=2.3e-55 Score=411.22 Aligned_cols=202 Identities=38% Similarity=0.563 Sum_probs=171.4
Q ss_pred EeeeccCCCCCCccceeEEEEEeeCCCChhHhhhcCCCCCCcCCHHHHHHHHHHHhhccceeeEEEEEEChHhHHHHhHh
Q psy12553 42 VLGIDEAGRGPVLGPMVYGTAYCPKDNNEELLKNLGCADSKALTEKKRDDILDSICKENAWLGWMVEIISPNVICNSMLR 121 (401)
Q Consensus 42 viGIDEAGRGpv~GPmVvaav~~p~~~~~~~L~~lGv~DSKkLSe~kRe~L~~~I~~~~~~v~~aV~visp~eId~~ml~ 121 (401)
++|||||||||+|||||||||+++.+.. ..|..+||+|||+||+++|++|++.|++ ..+.|++.+++|++||+.+
T Consensus 1 iiGiDEaGrG~~~GPlvva~v~~~~~~~-~~l~~~gv~DSK~Ls~~~r~~l~~~I~~--~~~~~~i~~i~p~~id~~~-- 75 (206)
T TIGR00729 1 VAGIDEAGRGPVIGPLVVGVFAIEEKRE-EELRKLGVKDSKKLTPGRREELFSKIRN--KLGRYEVLKITPEEIDRER-- 75 (206)
T ss_pred CcCccCCCCCCccCceEEEEEEechhhh-hhHhhcCCccCCcCCHHHHHHHHHHHHh--hcCcEEEEEEcHHHHChHH--
Confidence 5899999999999999997777776544 5678899999999999999999999984 4678999999999999864
Q ss_pred HhHhhHHHHHHHHHHHHHHHHHHcCCCccEEEEcCCCCccchhh---hhhhccCcceEEEeecCCCCCccccccccccCC
Q psy12553 122 RQKYSLNEVSHDAAIGLIRKVIAAGVNVREVYVDTVGPPESYKK---KLSEIFPELIITVASKADSTYPVVGAAIASKAD 198 (401)
Q Consensus 122 ~~~~NLN~l~~~aai~lI~~~l~~gv~~~~V~VD~~g~p~~Y~~---~L~~~fp~i~i~v~~KADs~y~v~~~~~~~kgD 198 (401)
..|||.+++.++.++|+++. ..+..||||+++.++.|.. .+...+|+.++++++|||++
T Consensus 76 --~~nln~~~~~a~~~~i~~l~---~~~~~v~iD~~~~~~~~~~~~~~~~~~~~~~~~~~~~KaD~~------------- 137 (206)
T TIGR00729 76 --NINLNENEIEKFSKAAIILI---EKPSEVYVDSVDVNPKRFKREIKIKERIEGIKVIAEHKADAK------------- 137 (206)
T ss_pred --HhhHHHHHHHHHHHHHHHHh---cCCcEEEEcCCCCcHHHHHHHHHHhccCCCCcEEEEeccccc-------------
Confidence 37999999999888887653 3467899999997765322 22234777788889999999
Q ss_pred CccchhhhhhHHHHHHHHHHHhhhhhhhhhhhhcCCCCCCCCCCHHHHHHHHhcCCCCcccccccccCchhHHHHh
Q psy12553 199 STYPVVGAASICAKVSRDSALKSWTFQEGIQIENNAWGSGYPGDPVTKKFLSENIDPVFGFPQLVRFSWSTASKIL 274 (401)
Q Consensus 199 ~~yp~VAAASIvAKVtRD~~m~~~~~~e~l~~~~~~yGsGYPSDp~Tk~~L~~~i~~~fG~p~~hR~SW~tvk~il 274 (401)
||+||||||||||+||++|+.+ .+.++.|||||||||+|++||++++++.+++|++||+||+|+++++
T Consensus 138 --~~~VAAASIlAKv~RD~~m~~l------~~~~~~~GsGY~sd~~t~~~l~~~~~~~g~~~~~~R~sf~~~~~~~ 205 (206)
T TIGR00729 138 --YPVVSAASIIAKVERDREIESL------KRKYGDFGSGYPSDPRTREWLEEYFKSHGELPDIVRRTWKTVRKLL 205 (206)
T ss_pred --cchhhHHHHHHHHHHHHHHHHH------HHhcCCCCCcCCCCHHHHHHHHHHHHhhCCCCcccccCcHHHHHhh
Confidence 9999999999999999999986 5778999999999999999999877544335679999999999876
No 6
>COG0164 RnhB Ribonuclease HII [DNA replication, recombination, and repair]
Probab=100.00 E-value=1.9e-51 Score=383.01 Aligned_cols=186 Identities=35% Similarity=0.511 Sum_probs=154.2
Q ss_pred cEeeeccCCCCCCccceeEEEEEeeCCCChhHhhhcCCCCCCcCCHHHHHHHHHHHhhccceeeEEEEEEChHhHHHHhH
Q psy12553 41 CVLGIDEAGRGPVLGPMVYGTAYCPKDNNEELLKNLGCADSKALTEKKRDDILDSICKENAWLGWMVEIISPNVICNSML 120 (401)
Q Consensus 41 ~viGIDEAGRGpv~GPmVvaav~~p~~~~~~~L~~lGv~DSKkLSe~kRe~L~~~I~~~~~~v~~aV~visp~eId~~ml 120 (401)
.++||||||||||+||||+|||++|.+.. . +.+|++|||+||+++|++||++|+. .++.|.|.++++++||+
T Consensus 1 ~vaGIDEAGRGpl~GPvV~Aavil~~~~~-~--~~~Gl~DSKkLs~~kRe~L~~~I~~--~a~~~~v~~~~~~~Id~--- 72 (199)
T COG0164 1 LVAGVDEAGRGPLAGPVVAAAVILPPDRL-P--KKLGLKDSKKLSPKKREELFEEIKE--KALAWGVGIIPAEEIDE--- 72 (199)
T ss_pred CcCcccCCCcCCcccceeEEEEEECcccc-c--cccCccccccCCHHHHHHHHHHHHh--hccEEEEEEcCHHHHhh---
Confidence 47899999999999999999999998875 2 5699999999999999999999993 67899999999999997
Q ss_pred hHhHhhHHHHHHHHHHHHHHHHHHcCCCccEEEEcCCCCccchhhhhhhccCcceEEEeecCCCCCccccccccccCCCc
Q psy12553 121 RRQKYSLNEVSHDAAIGLIRKVIAAGVNVREVYVDTVGPPESYKKKLSEIFPELIITVASKADSTYPVVGAAIASKADST 200 (401)
Q Consensus 121 ~~~~~NLN~l~~~aai~lI~~~l~~gv~~~~V~VD~~g~p~~Y~~~L~~~fp~i~i~v~~KADs~y~v~~~~~~~kgD~~ 200 (401)
.|+|..++.++...+.. +..++..||||+++.+.. ++.. .++++|||++
T Consensus 73 ----~ni~~a~~~am~~av~~---l~~~~~~vlvD~~~~~~~--------l~~~-~~a~~KgDa~--------------- 121 (199)
T COG0164 73 ----LNILEATKLAMRRAVAG---LSSQPDLVLVDGNDLPLG--------LPQP-AVAIIKGDAK--------------- 121 (199)
T ss_pred ----hhHHHHHHHHHHHHHHh---ccccCCEEEEeCCCcccc--------CCCC-cceeeccchh---------------
Confidence 57776666655555543 245568999999984422 1211 2667899999
Q ss_pred cchhhhhhHHHHHHHHHHHhhhhhhhhhhhhcCCCC----CCCCCCHHHHHHHHhcCCCCcccccccccCchhHHHHhhc
Q psy12553 201 YPVVGAASICAKVSRDSALKSWTFQEGIQIENNAWG----SGYPGDPVTKKFLSENIDPVFGFPQLVRFSWSTASKILKE 276 (401)
Q Consensus 201 yp~VAAASIvAKVtRD~~m~~~~~~e~l~~~~~~yG----sGYPSDp~Tk~~L~~~i~~~fG~p~~hR~SW~tvk~il~~ 276 (401)
|++||||||||||+||++|+.+ ++.||+|| |||||||.|.+|++. ++.+++||+||+|++++++.
T Consensus 122 ~~~IaAASIvAKV~RDr~m~~l------~~~yp~Y~~~~~~GY~T~~h~~a~~~~-----~~~~~~hR~Sf~~vk~~~~~ 190 (199)
T COG0164 122 SPSIAAASILAKVTRDRLMEEL------AKEYPEYGFDKGSGYPTDPHTEALLKK-----GGTPGIHRRSFAPVRRLLGL 190 (199)
T ss_pred hHHHHHHHHHHHHHHHHHHHHH------HhhCcCcCcccCCCCCChHHHHHHHHh-----CCCCceeecccHHHHHhhhh
Confidence 9999999999999999999985 67887774 999999999999975 34445999999999999965
No 7
>PRK00015 rnhB ribonuclease HII; Validated
Probab=100.00 E-value=4.5e-51 Score=380.91 Aligned_cols=178 Identities=30% Similarity=0.419 Sum_probs=153.8
Q ss_pred CCCcEeeeccCCCCCCccceeEEEEEeeCCCChhHhhhcCCCCCCcCCHHHHHHHHHHHhhccceeeEEEEEEChHhHHH
Q psy12553 38 SQPCVLGIDEAGRGPVLGPMVYGTAYCPKDNNEELLKNLGCADSKALTEKKRDDILDSICKENAWLGWMVEIISPNVICN 117 (401)
Q Consensus 38 ~~~~viGIDEAGRGpv~GPmVvaav~~p~~~~~~~L~~lGv~DSKkLSe~kRe~L~~~I~~~~~~v~~aV~visp~eId~ 117 (401)
+..+++|||||||||++||||||||+++.+.. + +||+|||+||+++|++|++.|++ .++.|++.+++|++||+
T Consensus 16 ~~~~viGiDEaGrG~v~GPlvvaav~~~~~~~---l--~gv~DSK~Ls~~~R~~l~~~I~~--~~~~~~i~~isp~~id~ 88 (197)
T PRK00015 16 GLGLIAGVDEAGRGPLAGPVVAAAVILDPDRP---I--EGLNDSKKLSEKKREELYEEIKE--KALAYSVGIASPEEIDE 88 (197)
T ss_pred CCcEEEeecCcCCCCcccceeEEEEEECcccc---c--CCCCCcccCCHHHHHHHHHHHHH--hCceEEEEEcCHHHHHH
Confidence 45689999999999999999999999986532 2 79999999999999999999995 46789999999999997
Q ss_pred HhHhHhHhhHHHHHHHHHHHHHHHHHHcCCCccEEEEcCCCCccchhhhhhhccCcceEEEeecCCCCCccccccccccC
Q psy12553 118 SMLRRQKYSLNEVSHDAAIGLIRKVIAAGVNVREVYVDTVGPPESYKKKLSEIFPELIITVASKADSTYPVVGAAIASKA 197 (401)
Q Consensus 118 ~ml~~~~~NLN~l~~~aai~lI~~~l~~gv~~~~V~VD~~g~p~~Y~~~L~~~fp~i~i~v~~KADs~y~v~~~~~~~kg 197 (401)
+|+|.+++.++.++|+++ .++..|+||+++.|..+ + ++++++|||++
T Consensus 89 -------~nln~~~~~a~~~~i~~l----~~~~~i~vD~~~~~~~~-------~---~~~~~~kaD~~------------ 135 (197)
T PRK00015 89 -------LNILEATLLAMRRAVEGL----VKPDYVLVDGNRVPKLP-------I---PQEAIVKGDAK------------ 135 (197)
T ss_pred -------hhHHHHHHHHHHHHHHhc----CCCCEEEECCCCCCCCC-------C---CeEEEEcCCcc------------
Confidence 589998888877777653 46788999999876421 2 34566799999
Q ss_pred CCccchhhhhhHHHHHHHHHHHhhhhhhhhhhhhcCCCC----CCCCCCHHHHHHHHhcCCCCcccccccccCchhH
Q psy12553 198 DSTYPVVGAASICAKVSRDSALKSWTFQEGIQIENNAWG----SGYPGDPVTKKFLSENIDPVFGFPQLVRFSWSTA 270 (401)
Q Consensus 198 D~~yp~VAAASIvAKVtRD~~m~~~~~~e~l~~~~~~yG----sGYPSDp~Tk~~L~~~i~~~fG~p~~hR~SW~tv 270 (401)
||+||||||||||+||++|+.| ++.+++|| |||||||.|++|++ +|++++||+||+|+
T Consensus 136 ---~~~VaAASIvAKv~RD~~m~~l------~~~~~~yg~~~~sGY~s~~~~~a~~~------~G~~~~~R~Sw~~~ 197 (197)
T PRK00015 136 ---SPSIAAASILAKVTRDRLMEEL------DKEYPGYGFAKHKGYGTKEHLEALAK------YGPTPIHRRSFAPV 197 (197)
T ss_pred ---cHHHHHHHHHHHHHHHHHHHHH------HHhCcCCCCcCCCcCCCHHHHHHHHH------cCCChhhcCcCcCC
Confidence 9999999999999999999986 57789999 99999999999775 59999999999985
No 8
>cd06266 RNaseH_typeII Ribonuclease H type II. Ribonuclease H (RNase H) is classified into two families, type I (prokaryotic RNase HI, eukaryotic RNase H1 and viral RNase H) and type II (prokaryotic RNase HII and HIII, and eukaryotic RNase H2/HII). RNase H endonucleolytically hydrolyzes an RNA strand when it is annealed to a complementary DNA strand in the presence of divalent cations, in DNA replication and repair. The enzyme can be found in bacteria, archaea, and eukaryotes. Most prokaryotic and eukaryotic genomes contain multiple RNase H genes, however, no prokaryotic genome contained the combination of only RNase HI and HIII. Despite a lack of evidence for homology from sequence comparisons, type I and type II RNase H share a common fold and similar steric configurations of the four acidic active-site residues, suggesting identical or very similar catalytic mechanisms. It appears that type I and type II RNases H also have overlapping functions in cells, as over-expression of Escheri
Probab=100.00 E-value=2.4e-51 Score=379.35 Aligned_cols=189 Identities=41% Similarity=0.571 Sum_probs=164.9
Q ss_pred eeeccCCCCCCccceeEEEEEeeCCCChhHhhhcCCCCCCcCCHHHHHHHHHHHhhccceeeEEEEEEChHhHHHHhHhH
Q psy12553 43 LGIDEAGRGPVLGPMVYGTAYCPKDNNEELLKNLGCADSKALTEKKRDDILDSICKENAWLGWMVEIISPNVICNSMLRR 122 (401)
Q Consensus 43 iGIDEAGRGpv~GPmVvaav~~p~~~~~~~L~~lGv~DSKkLSe~kRe~L~~~I~~~~~~v~~aV~visp~eId~~ml~~ 122 (401)
+|||||||||||||||||||+++.+.. ..|..+||+|||+||+++|++|++.|++ ..++|.+.+++|++||+
T Consensus 1 iGiDEaGrG~~~GPlvva~v~~~~~~~-~~l~~~gv~DSK~Lt~~~r~~l~~~I~~--~~~~~~v~~~~p~~id~----- 72 (193)
T cd06266 1 AGIDEAGRGPLAGPVVAAAVILPKENI-EILKILGVKDSKKLSEKKREELFEEIKE--EALAYAIGIISPEEIDE----- 72 (193)
T ss_pred CCCcccCcCCcchheEEEEEEEchhhc-ccccccCCCCcccCCHHHHHHHHHHHHh--hCCeEEEEEECHHHHCH-----
Confidence 699999999999999999999999877 7788999999999999999999999995 57899999999999997
Q ss_pred hHhhHHHHHHHHHHHHHHHHHHcCCCccEEEEcCCCCccchhhhhhhccCcceEEEeecCCCCCccccccccccCCCccc
Q psy12553 123 QKYSLNEVSHDAAIGLIRKVIAAGVNVREVYVDTVGPPESYKKKLSEIFPELIITVASKADSTYPVVGAAIASKADSTYP 202 (401)
Q Consensus 123 ~~~NLN~l~~~aai~lI~~~l~~gv~~~~V~VD~~g~p~~Y~~~L~~~fp~i~i~v~~KADs~y~v~~~~~~~kgD~~yp 202 (401)
.|+|.+....+.++|..+ ..++..|+||+++.++.|+. +...++..++++++|||++ ||
T Consensus 73 --~nl~~~~~~~~~~~i~~l---~~~~~~i~iD~~~~~~~~~~-~~~~~~~~~~~~~~kaD~~---------------~~ 131 (193)
T cd06266 73 --LNILQATALAMARAILNL---GVKPDEVLVDGNGVPEKYFA-LEKKFLPIPVTAIVKGDSK---------------SP 131 (193)
T ss_pred --HHHHHHHHHHHHHHHHhc---CCCCCEEEECCCCChhhhhh-hcccCCCCCeEEEeccccc---------------cH
Confidence 388887777766666543 35788999999999999987 5555677888899999999 99
Q ss_pred hhhhhhHHHHHHHHHHHhhhhhhhhhhhhcC----CCCCCCCCCHHHHHHHHhcCCCCcccccccccCchhHH
Q psy12553 203 VVGAASICAKVSRDSALKSWTFQEGIQIENN----AWGSGYPGDPVTKKFLSENIDPVFGFPQLVRFSWSTAS 271 (401)
Q Consensus 203 ~VAAASIvAKVtRD~~m~~~~~~e~l~~~~~----~yGsGYPSDp~Tk~~L~~~i~~~fG~p~~hR~SW~tvk 271 (401)
+||||||||||+||+.|+.+ +..++ ..|+|||+||.|++|++.+.. +++||+||+|++
T Consensus 132 ~VaAASIiAKv~rd~~m~~l------~~~~~~~~~~~gsGy~s~~~~~~~~~~~~~-----~~~~R~sf~~~~ 193 (193)
T cd06266 132 SVAAASILAKVTRDRLMEEL------DEEYPGYGFAKGKGYPTDPHTEAILKYGPT-----EPIHRRSFKTVK 193 (193)
T ss_pred hHHHHHHHHHHHHHHHHHHH------HHHCCCCCCcCCcCcCcHHHHHHHHHhCcC-----CCeeeCCCCCCC
Confidence 99999999999999999986 45555 667999999999999987432 299999999863
No 9
>PRK14550 rnhB ribonuclease HII; Provisional
Probab=100.00 E-value=1.9e-50 Score=378.66 Aligned_cols=193 Identities=27% Similarity=0.334 Sum_probs=152.2
Q ss_pred cEeeeccCCCCCCccceeEEEEEeeCCCChhHhhhcCCCCCCcCCHHHHHHHHHHHhhccceeeEEEEEEChHhHHHHhH
Q psy12553 41 CVLGIDEAGRGPVLGPMVYGTAYCPKDNNEELLKNLGCADSKALTEKKRDDILDSICKENAWLGWMVEIISPNVICNSML 120 (401)
Q Consensus 41 ~viGIDEAGRGpv~GPmVvaav~~p~~~~~~~L~~lGv~DSKkLSe~kRe~L~~~I~~~~~~v~~aV~visp~eId~~ml 120 (401)
.++|||||||||++||||||||++|.+.. ..+..+||+|||+||+++|++|++.|++. ..+.|.+.+++|++||+
T Consensus 1 ~~~GiDEAGRGpl~GPvVvaav~~~~~~~-~~l~~~gv~DSKkLs~~~Re~L~~~I~~~-~~~~~~i~~~~~~eID~--- 75 (204)
T PRK14550 1 MTLGIDEAGRGCLAGSLFVAGVACNEKTA-LEFLKMGLKDSKKLSPKKRFFLEDKIKTH-GEVGFFVVKKSANEIDS--- 75 (204)
T ss_pred CeeCccCcCCCCccchheEEEEEEChhhc-cchhhcCccChhhCCHHHHHHHHHHHHhc-cCcEEEEEEECHHHHHH---
Confidence 47999999999999999999999998765 55668899999999999999999999852 23789999999999997
Q ss_pred hHhHhhHHHHHHHHHHHHHHHHHHcCCCccEEEEcCCCCccchhhhhhhccCcceEEEeecCCCCCccccccccccCCCc
Q psy12553 121 RRQKYSLNEVSHDAAIGLIRKVIAAGVNVREVYVDTVGPPESYKKKLSEIFPELIITVASKADSTYPVVGAAIASKADST 200 (401)
Q Consensus 121 ~~~~~NLN~l~~~aai~lI~~~l~~gv~~~~V~VD~~g~p~~Y~~~L~~~fp~i~i~v~~KADs~y~v~~~~~~~kgD~~ 200 (401)
.|+|..+..++.+++.. ....++.|+||++..+..+. .+| .+..++|||++
T Consensus 76 ----~ni~~a~~~am~~al~~---l~~~~~~vliDg~~~~~~~~-----~~~--~~~~~~KgD~~--------------- 126 (204)
T PRK14550 76 ----LGLGACLKLAIQEILEN---GCSLANEIKIDGNTAFGLNK-----RYP--NIQTIIKGDET--------------- 126 (204)
T ss_pred ----HHHHHHHHHHHHHHHHh---CCCCCCEEEECCccCccccc-----cCc--ceeEEEccccc---------------
Confidence 46775543333333322 23456789999885443221 122 23455788888
Q ss_pred cchhhhhhHHHHHHHHHHHhhhhhhhhhhhhcCCCC----CCCCCCHHHHHHHHhcCCCCcccccccccCchhHHHHhhc
Q psy12553 201 YPVVGAASICAKVSRDSALKSWTFQEGIQIENNAWG----SGYPGDPVTKKFLSENIDPVFGFPQLVRFSWSTASKILKE 276 (401)
Q Consensus 201 yp~VAAASIvAKVtRD~~m~~~~~~e~l~~~~~~yG----sGYPSDp~Tk~~L~~~i~~~fG~p~~hR~SW~tvk~il~~ 276 (401)
||+||||||||||+||++|.++ ++.||+|| |||| |++|++++ ..+|++++||+||+|++++|..
T Consensus 127 ~~~VAAASIiAKV~RD~~M~~l------~~~~p~Ygf~~~kGY~----T~~h~~ai--~~~G~~p~hR~Sf~t~~~~~~~ 194 (204)
T PRK14550 127 IAQIAMASVLAKAFKDREMLEL------HALFKEYGWDKNCGYG----TKQHIEAI--IKLGATPFHRHSFTLKNRILNP 194 (204)
T ss_pred chhHHHHHHHHHHHHHHHHHHH------HHhCCCCCCcCCCCCC----CHHHHHHH--HHhCcCHHHcCCcCCCCcccCh
Confidence 9999999999999999999985 56778777 9999 57788774 4589999999999999998876
Q ss_pred cCc
Q psy12553 277 KAV 279 (401)
Q Consensus 277 ~~~ 279 (401)
+-.
T Consensus 195 ~~~ 197 (204)
T PRK14550 195 KLL 197 (204)
T ss_pred HHH
Confidence 543
No 10
>cd07182 RNaseH_typeII_bacteria_HII_like bacterial Ribonuclease HII-like. Bacterial ribonuclease (RNase) HII has a role in primer removal based on its involvement in ribonucleotide-specific catalytic activity in the presence of RNA/DNA hybrid substrates. RNase H is classified into two families, type I (prokaryotic RNase HI, eukaryotic RNase H1 and viral RNase H) and type II (prokaryotic RNase HII and HIII, and eukaryotic RNase H2). RNase H endonucleolytically hydrolyzes an RNA strand when it is annealed to a complementary DNA strand in the presence of divalent cations, in DNA replication and repair. Several bacteria, such as Bacillus subtilis, have two different type II RNases H, RNases HII and HIII- double deletion of these leads to cellular lethality. It appears that type I and type II RNases H also have overlapping functions in cells, as over-expression of Escherichia coli RNase HII can complement an RNase HI deletion phenotype in E. coli.
Probab=100.00 E-value=6.1e-50 Score=368.06 Aligned_cols=174 Identities=30% Similarity=0.424 Sum_probs=147.9
Q ss_pred eeeccCCCCCCccceeEEEEEeeCCCChhHhhhcCCCCCCcCCHHHHHHHHHHHhhccceeeEEEEEEChHhHHHHhHhH
Q psy12553 43 LGIDEAGRGPVLGPMVYGTAYCPKDNNEELLKNLGCADSKALTEKKRDDILDSICKENAWLGWMVEIISPNVICNSMLRR 122 (401)
Q Consensus 43 iGIDEAGRGpv~GPmVvaav~~p~~~~~~~L~~lGv~DSKkLSe~kRe~L~~~I~~~~~~v~~aV~visp~eId~~ml~~ 122 (401)
+|||||||||++||||||||+++.+.. .+||+|||+||+++|++|++.|++ ..+.|++.+++|++||+
T Consensus 1 ~GiDEaGRG~~~GPlvvaav~~~~~~~-----~~gv~DSK~Ls~~~R~~l~~~I~~--~~~~~~v~~~~~~~Id~----- 68 (179)
T cd07182 1 AGVDEAGRGPLAGPVVAAAVILPPDFE-----IEGLNDSKKLSEKKREELYEEIKE--KALAWGIGIASPEEIDR----- 68 (179)
T ss_pred CCCcCccCCCcccceEEEEEEECcccC-----cCCCCCcccCCHHHHHHHHHHHHH--hcccEEEEEECHHHHCH-----
Confidence 699999999999999999999987754 389999999999999999999995 56889999999999996
Q ss_pred hHhhHHHHHHHHHHHHHHHHHHcCCCccEEEEcCCCCccchhhhhhhccCcceEEEeecCCCCCccccccccccCCCccc
Q psy12553 123 QKYSLNEVSHDAAIGLIRKVIAAGVNVREVYVDTVGPPESYKKKLSEIFPELIITVASKADSTYPVVGAAIASKADSTYP 202 (401)
Q Consensus 123 ~~~NLN~l~~~aai~lI~~~l~~gv~~~~V~VD~~g~p~~Y~~~L~~~fp~i~i~v~~KADs~y~v~~~~~~~kgD~~yp 202 (401)
.|+|.+.+.++.++|.++ ...+..|+||+++.+.. ..++++++|||++ ||
T Consensus 69 --~nl~~~~~~a~~~ai~~l---~~~~~~v~iD~~~~~~~----------~~~~~~~~KaD~~---------------~~ 118 (179)
T cd07182 69 --INILQATLLAMRRAVEGL---PVKPDYVLVDGNRLPPL----------PIPQEAIVKGDAK---------------SA 118 (179)
T ss_pred --hhHHHHHHHHHHHHHHhC---CCCCCEEEECCcCCCCC----------CCCeEEEeccccc---------------cH
Confidence 588888887777766543 44678899999986542 2345677899999 99
Q ss_pred hhhhhhHHHHHHHHHHHhhhhhhhhhhhhcCCCC----CCCCCCHHHHHHHHhcCCCCcccccccccCchhH
Q psy12553 203 VVGAASICAKVSRDSALKSWTFQEGIQIENNAWG----SGYPGDPVTKKFLSENIDPVFGFPQLVRFSWSTA 270 (401)
Q Consensus 203 ~VAAASIvAKVtRD~~m~~~~~~e~l~~~~~~yG----sGYPSDp~Tk~~L~~~i~~~fG~p~~hR~SW~tv 270 (401)
+||||||||||+||++|+.| ++.+|+|| |||||++ +++++++ ||++++||+||+|+
T Consensus 119 ~VaAASIvAKv~RD~~m~~l------~~~~~~yg~~~~~GY~s~~-h~~~i~~-----~G~~~~hR~s~~~~ 178 (179)
T cd07182 119 SIAAASILAKVTRDRLMIEL------DKKYPGYGFAKHKGYGTKE-HLEALKK-----YGPTPIHRRSFAPV 178 (179)
T ss_pred HHHHHHHHHHHHHHHHHHHH------HHHCcCCCCcCCCCCCcHH-HHHHHHH-----hCcCHhhcCCCCCC
Confidence 99999999999999999986 57888887 9999866 4444443 79999999999986
No 11
>cd06590 RNaseH_typeII_bacteria_HIII_like bacterial Ribonuclease HIII-like. Ribonuclease H (RNase H) is classified into two families, type I (prokaryotic RNase HI, eukaryotic RNase H1 and viral RNase H) and type II (prokaryotic RNase HII and HIII, and eukaryotic RNase H2). RNase H endonucleolytically hydrolyzes an RNA strand when it is annealed to a complementary DNA strand in the presence of divalent cations, in DNA replication and repair. Several bacteria, such as Bacillus subtilis, have two different type II RNases H, RNases HII and HIII. RNases HIII are distinguished by having a large (70-90 residues) N-terminal extension of unknown function. In addition, the active site of RNase HIII differs from that of other RNases H; replacing the fourth residue (aspartate) of the acidic "DEDD" motif with a glutamate. Most prokaryotic and eukaryotic genomes contain multiple RNase H genes, however, no prokaryotic genomes contain the combination of both RNase HI and HIII. This mutual exclusive gen
Probab=100.00 E-value=4.6e-50 Score=375.55 Aligned_cols=202 Identities=22% Similarity=0.275 Sum_probs=174.4
Q ss_pred eeeccCCCCCCccceeEEEEEeeCCCChhHhhhcCCCCCCcCCHHHHHHHHHHHhhccceeeEEEEEEChHhHHHHhHhH
Q psy12553 43 LGIDEAGRGPVLGPMVYGTAYCPKDNNEELLKNLGCADSKALTEKKRDDILDSICKENAWLGWMVEIISPNVICNSMLRR 122 (401)
Q Consensus 43 iGIDEAGRGpv~GPmVvaav~~p~~~~~~~L~~lGv~DSKkLSe~kRe~L~~~I~~~~~~v~~aV~visp~eId~~ml~~ 122 (401)
+|||||||||++||||+|||+++.+.. ..|..+|++|||+||+++|++|++.|++ .+.|++.+++|++||..+ .
T Consensus 1 iGiDEaGRG~~~GPlVvaav~~~~~~~-~~l~~~gv~DSK~Ls~~~r~~l~~~I~~---~~~~~v~~i~~~~in~~~--~ 74 (208)
T cd06590 1 IGSDEVGKGDYFGPLVVAAVYVDKENI-SKLKKLGVKDSKKLTDKKIIRLAPKIKK---KIPYSVLSLGPEKYNELY--K 74 (208)
T ss_pred CCCCCCCCCCCcCccEEEEEEEcHHHH-HHHHHCCCCcCCcCCHHHHHHHHHHHHh---cCCEEEEecCHHHHHHHH--H
Confidence 699999999999999999999998765 6678899999999999999999999985 478999999999999753 2
Q ss_pred hHhhHHHHHHHHHHHHHHHHHHcCCCccEEEEcCCCCccchhhhhhhcc--CcceEEEeecCCCCCccccccccccCCCc
Q psy12553 123 QKYSLNEVSHDAAIGLIRKVIAAGVNVREVYVDTVGPPESYKKKLSEIF--PELIITVASKADSTYPVVGAAIASKADST 200 (401)
Q Consensus 123 ~~~NLN~l~~~aai~lI~~~l~~gv~~~~V~VD~~g~p~~Y~~~L~~~f--p~i~i~v~~KADs~y~v~~~~~~~kgD~~ 200 (401)
...|||.+...++.++|++++..+..+..|+||+++.+++|+.+|++.+ +++++++++|||++
T Consensus 75 ~~~nln~l~~~~~~~ai~~l~~~~~~~~~v~vD~~~~~~~~~~~l~~~~~~~~~~~~~~~kaD~~--------------- 139 (208)
T cd06590 75 KGKNLNKLKALLHNKAINNLLEKPKKPVAILIDQFASEKVYKRYLKKEKKIVKEPLIFRTKAESK--------------- 139 (208)
T ss_pred ccCCHHHHHHHHHHHHHHHHHHhcCCCCEEEecCCCCHHHHHHHHHhhccCCCCceEEEecCccc---------------
Confidence 2579999988888888888765456788999999999999999998887 56788889999999
Q ss_pred cchhhhhhHHHHHHHHHHHhhhhhhhhhhhhcC---CCCCCCCCCHHHHHHHHhcCCCCcccccccccCchhHHHH
Q psy12553 201 YPVVGAASICAKVSRDSALKSWTFQEGIQIENN---AWGSGYPGDPVTKKFLSENIDPVFGFPQLVRFSWSTASKI 273 (401)
Q Consensus 201 yp~VAAASIvAKVtRD~~m~~~~~~e~l~~~~~---~yGsGYPSDp~Tk~~L~~~i~~~fG~p~~hR~SW~tvk~i 273 (401)
||+||||||||||+||+.|+.+ ++.|+ +.|+|||+|+.|++|++.+.. -.+|+++|+||+|++++
T Consensus 140 ~~~VaAASIlAKv~Rd~~m~~l------~~~yg~~~~~G~g~~~~~~~~~~l~~~g~--~~l~~~~k~~~~t~~~~ 207 (208)
T cd06590 140 HLAVAAASILARYAFLEKMEKL------SKQYGMKLPKGASSKVDEQAAEIIKKYGL--EELKKVAKLHFKNTKKA 207 (208)
T ss_pred chHHHHHHHHHHHHHHHHHHHH------HHHhCCCCCCCCCcHHHHHHHHHHHHhhH--hHHHHHHHHhchhhHhh
Confidence 9999999999999999999986 34443 578999999999999998421 11567999999999876
No 12
>PRK13926 ribonuclease HII; Provisional
Probab=100.00 E-value=2.1e-49 Score=372.32 Aligned_cols=182 Identities=27% Similarity=0.425 Sum_probs=156.3
Q ss_pred CCCCcEeeeccCCCCCCccceeEEEEEeeCCCChhHhhhcCCCCCCcCCHHHHHHHHHHHhhccceeeEEEEEEChHhHH
Q psy12553 37 KSQPCVLGIDEAGRGPVLGPMVYGTAYCPKDNNEELLKNLGCADSKALTEKKRDDILDSICKENAWLGWMVEIISPNVIC 116 (401)
Q Consensus 37 ~~~~~viGIDEAGRGpv~GPmVvaav~~p~~~~~~~L~~lGv~DSKkLSe~kRe~L~~~I~~~~~~v~~aV~visp~eId 116 (401)
.+..+++|||||||||++||||||||+++.+. +|++|||+||+++|++|++.|++ .++.|.+.+++|++||
T Consensus 19 ~~~~~i~GiDEAGRG~~~GPlVvaav~~~~~~-------~~~~DSK~Ls~~~R~~L~~~I~~--~~~~~~i~~isp~~Id 89 (207)
T PRK13926 19 RGYLRVAGVDEAGRGAWAGPVVVAAVILPPGE-------YPFRDSKTLSPAAREALAEEVRR--VALAWAVGHAEAAEID 89 (207)
T ss_pred CCCcEEEeecCcCCCCccccceEEEEEECccC-------CCccccccCCHHHHHHHHHHHHH--hCceEEEEEeCHHHHh
Confidence 34568999999999999999999999998753 57999999999999999999985 4678999999999999
Q ss_pred HHhHhHhHhhHHHHHHHHHHHHHHHHHHcCCCccEEEEcCCCCccchhhhhhhccCcceEEEeecCCCCCcccccccccc
Q psy12553 117 NSMLRRQKYSLNEVSHDAAIGLIRKVIAAGVNVREVYVDTVGPPESYKKKLSEIFPELIITVASKADSTYPVVGAAIASK 196 (401)
Q Consensus 117 ~~ml~~~~~NLN~l~~~aai~lI~~~l~~gv~~~~V~VD~~g~p~~Y~~~L~~~fp~i~i~v~~KADs~y~v~~~~~~~k 196 (401)
+ .|+|.++|+++.++++++ .++++.+++|....+ + .+++++++|||++
T Consensus 90 ~-------~ni~~a~~~a~~~~l~~l---~~~~~~v~~D~~~~~----------~-~~~~~~~~KgD~~----------- 137 (207)
T PRK13926 90 R-------LNVLKATHLAAARALARL---AVAPEALVTDYLRLP----------T-PLPLLAPPKADAL----------- 137 (207)
T ss_pred H-------HHHHHHHHHHHHHHHHhc---CCCCCEEEECcccCC----------C-CCCeEEEecCccc-----------
Confidence 6 489999999888877542 456788999964211 1 2356778899999
Q ss_pred CCCccchhhhhhHHHHHHHHHHHhhhhhhhhhhhhcCCCC----CCCCCCHHHHHHHHhcCCCCcccccccccCchhHHH
Q psy12553 197 ADSTYPVVGAASICAKVSRDSALKSWTFQEGIQIENNAWG----SGYPGDPVTKKFLSENIDPVFGFPQLVRFSWSTASK 272 (401)
Q Consensus 197 gD~~yp~VAAASIvAKVtRD~~m~~~~~~e~l~~~~~~yG----sGYPSDp~Tk~~L~~~i~~~fG~p~~hR~SW~tvk~ 272 (401)
||+||||||||||+||++|++| ++.+++|| |||| ++.|++||+. ||++++||+||+|+++
T Consensus 138 ----~~~VaAASIvAKv~RD~~m~~l------~~~~~~yg~~~~kGY~-t~~h~~~l~~-----~G~~~~hR~s~~~~~~ 201 (207)
T PRK13926 138 ----SPTVAAASLLAKTERDRLMREL------DARYPGYGFARHKGYG-TPAHREALAA-----LGPSPVHRRSFAPVRR 201 (207)
T ss_pred ----cHHHHHHHHHHHHHHHHHHHHH------HHhCccCCCcCCCCCC-CHHHHHHHHH-----hCcCHHHcCCcHHHHH
Confidence 9999999999999999999986 67889988 9999 7999999986 7999999999999998
Q ss_pred Hhh
Q psy12553 273 ILK 275 (401)
Q Consensus 273 il~ 275 (401)
++.
T Consensus 202 ~~~ 204 (207)
T PRK13926 202 LLT 204 (207)
T ss_pred hhh
Confidence 763
No 13
>PRK13925 rnhB ribonuclease HII; Provisional
Probab=100.00 E-value=1.1e-49 Score=372.07 Aligned_cols=186 Identities=26% Similarity=0.338 Sum_probs=151.1
Q ss_pred CCcEeeeccCCCCCCccceeEEEEEeeCCCChhHhhhcCCCCCCcCCHHHHHHHHHHHhhccceeeEEEEEEChHhHHHH
Q psy12553 39 QPCVLGIDEAGRGPVLGPMVYGTAYCPKDNNEELLKNLGCADSKALTEKKRDDILDSICKENAWLGWMVEIISPNVICNS 118 (401)
Q Consensus 39 ~~~viGIDEAGRGpv~GPmVvaav~~p~~~~~~~L~~lGv~DSKkLSe~kRe~L~~~I~~~~~~v~~aV~visp~eId~~ 118 (401)
.++++||||||||||+||||||||++|.+.. ..|+.+||+|||+||+++|++||+.|++ .+..|++.+++|++||+
T Consensus 7 ~~~iiGiDEAGRGpv~GPmVvaav~~~~~~~-~~L~~~gv~DSK~Ls~~~Re~l~~~I~~--~~~~~~i~~i~~~eId~- 82 (198)
T PRK13925 7 SELIAGVDEVGRGALFGPVFAAAVILSEKAE-PQLLQAGLTDSKKLSPKRRAQLVPLILT--LASDWGIGQASAREIDR- 82 (198)
T ss_pred CCeEEeecCCCCCCChHHhEEEEEEEchHhh-hhhhhcCCCCcccCCHHHHHHHHHHHHh--hCCcEEEEEECHHHhCH-
Confidence 4689999999999999999999999998876 7788999999999999999999999985 45679999999999997
Q ss_pred hHhHhHhhHHHHHHHHHHHHHHHHHHcCCCccEEEEcCCCCccchhhhhhhccCcceEEEeecCCCCCccccccccccCC
Q psy12553 119 MLRRQKYSLNEVSHDAAIGLIRKVIAAGVNVREVYVDTVGPPESYKKKLSEIFPELIITVASKADSTYPVVGAAIASKAD 198 (401)
Q Consensus 119 ml~~~~~NLN~l~~~aai~lI~~~l~~gv~~~~V~VD~~g~p~~Y~~~L~~~fp~i~i~v~~KADs~y~v~~~~~~~kgD 198 (401)
.|+|.+...++.+++.+ ...++..|+||+++... .++....+ .+|||++
T Consensus 83 ------~ni~~~~~~a~~~~i~~---l~~~~~~v~iD~~~~~~--------~~~~~~~~-v~kaD~~------------- 131 (198)
T PRK13925 83 ------LGIRQATELAMLRALKK---LKSPPSLCLVDGNLPLR--------LWPGPQRT-IVKGDSK------------- 131 (198)
T ss_pred ------hhHHHHHHHHHHHHHHh---cCCCCCEEEECCccccC--------cCCCCcee-ecccccc-------------
Confidence 47777766665555543 24567889999987421 12322222 3588888
Q ss_pred CccchhhhhhHHHHHHHHHHHhhhhhhhhhhhhcCCCC----CCCCCCHHHHHHHHhcCCCCcccccccccCchhHHHH
Q psy12553 199 STYPVVGAASICAKVSRDSALKSWTFQEGIQIENNAWG----SGYPGDPVTKKFLSENIDPVFGFPQLVRFSWSTASKI 273 (401)
Q Consensus 199 ~~yp~VAAASIvAKVtRD~~m~~~~~~e~l~~~~~~yG----sGYPSDp~Tk~~L~~~i~~~fG~p~~hR~SW~tvk~i 273 (401)
||+||||||||||+||++|+.| ++.||+|| +|||+++ |++++. .||++++||+||+|.-.+
T Consensus 132 --~~~VaAASIiAKV~RD~~m~~l------~~~yp~y~f~~~kGY~t~~-h~~~i~-----~~G~~p~hR~sf~~~~~~ 196 (198)
T PRK13925 132 --SAAIAAASILAKVWRDDLIKRL------AKKYPGYGLEKNKGYGTAQ-HRQALL-----KLGPTPLHRKSFLPKLIL 196 (198)
T ss_pred --cHHHHHHHHHHHHHHHHHHHHH------HHHCCCCCcccCCCCCcHH-HHHHHH-----HhCcCHHHcCCCcchhhc
Confidence 9999999999999999999986 67899998 9999633 444444 489999999999987554
No 14
>PF01351 RNase_HII: Ribonuclease HII; InterPro: IPR024567 Ribonuclease HII and HIII are endonucleases that specifically degrade the RNA of RNA-DNA hybrids. Proteins which belong to this family have been found in bacteria, archaea, and eukaryota. The domain represented by this entry is found in ribonucleases HII aand HIII.; PDB: 2ETJ_A 3O3H_A 3O3G_A 3O3F_A 3KIO_A 3P5J_A 1UAX_B 2DFF_A 1IO2_A 2DFH_A ....
Probab=100.00 E-value=4e-48 Score=358.88 Aligned_cols=195 Identities=40% Similarity=0.662 Sum_probs=161.9
Q ss_pred eeeccCCCCCCccceeEEEEEeeCCCChhHhhhcCCCCCCcCCHHHHHHHHHHHhhccceeeEEEEEEChHhHHHHhHhH
Q psy12553 43 LGIDEAGRGPVLGPMVYGTAYCPKDNNEELLKNLGCADSKALTEKKRDDILDSICKENAWLGWMVEIISPNVICNSMLRR 122 (401)
Q Consensus 43 iGIDEAGRGpv~GPmVvaav~~p~~~~~~~L~~lGv~DSKkLSe~kRe~L~~~I~~~~~~v~~aV~visp~eId~~ml~~ 122 (401)
+|||||||||+|||||||||+++.+.. ..|+.+||+|||+||+++|++|++.|+ .+.+. .+.+..+.. ...
T Consensus 1 iG~DEaGrG~~~GPlvvaav~~~~~~~-~~l~~~gv~DSK~Ls~~~r~~l~~~I~----~i~~~--~~~~~~~~~--~~~ 71 (198)
T PF01351_consen 1 IGIDEAGRGDVFGPLVVAAVYLPEEDI-EKLKELGVKDSKKLSDKKREELAEKIK----KISYS--EVSPYPIGY--ISP 71 (198)
T ss_dssp EEEEEESSS-SBS-EEEEEEEEEGGGH-HHHHHTTGCCGTTS-HHHHHHHHHHHH----EEEEE--EEECHHHHH--HHT
T ss_pred CCCCCCCCCCcccchheEEEEeccccH-HHHHhhccCccccCCHHHHHHHHHHHH----hhchh--hhhhccccc--cch
Confidence 799999999999999999999999988 788999999999999999999999999 23333 344444432 122
Q ss_pred hHhhHHHHHHHHHHHHHHHHHHcCCCccEEEEcCCCCccchhhhhhhccCcceEEEeecCCCCCccccccccccCCCccc
Q psy12553 123 QKYSLNEVSHDAAIGLIRKVIAAGVNVREVYVDTVGPPESYKKKLSEIFPELIITVASKADSTYPVVGAAIASKADSTYP 202 (401)
Q Consensus 123 ~~~NLN~l~~~aai~lI~~~l~~gv~~~~V~VD~~g~p~~Y~~~L~~~fp~i~i~v~~KADs~y~v~~~~~~~kgD~~yp 202 (401)
...|+|.+.+....++++.+.+.+..++.|+||+++.+..|..++++.++ .++++++|||++ ||
T Consensus 72 ~~in~n~i~~~~~~~~~~~l~~~~~~~~~v~iD~~~~~~~~~~~~~~~~~-~~~~~~~Kad~~---------------~~ 135 (198)
T PF01351_consen 72 KEINLNNILAALHNAMIRALLKLGVQPDEVLIDQFGSPEKYYNKLEKIFK-IKVVFEPKADSK---------------YP 135 (198)
T ss_dssp TTSCHHHHHHHHHHHHHHHHHHTTSEESEEEEEESSSHHHHHHHHHHHST-SEEEEETTHHHC---------------SH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhccCCceeecchhhcchhcccchheecC-cceeeecccchh---------------hH
Confidence 45799999888888888887777788899999999999989999998888 788999999999 99
Q ss_pred hhhhhhHHHHHHHHHHHhhhhhhhhhhhhcC---CCCCCCCCCHHHHHHHHhcCCCCcccccccccCchhH
Q psy12553 203 VVGAASICAKVSRDSALKSWTFQEGIQIENN---AWGSGYPGDPVTKKFLSENIDPVFGFPQLVRFSWSTA 270 (401)
Q Consensus 203 ~VAAASIvAKVtRD~~m~~~~~~e~l~~~~~---~yGsGYPSDp~Tk~~L~~~i~~~fG~p~~hR~SW~tv 270 (401)
+||||||||||+||..|+.+ .+.++ ..|||||+||.|++|++....+ +++++||+||+|+
T Consensus 136 ~VAAASIvAK~~rd~~~~~~------~~~~~~~~~~gsGy~s~~~~~~~~~~~~~~--~l~~~~R~sf~tv 198 (198)
T PF01351_consen 136 SVAAASIVAKVTRDEMIELL------SKYPGYGFPKGSGYPSDPHTRAILKKGGSP--ELPQIHRLSFKTV 198 (198)
T ss_dssp HHHHHHHHHHHHHHHHHHHH------HHHHTS-HCCTSSSTTSHHHHHHHHHHHHH--SSHTTB-TTSHHH
T ss_pred HHHHHHHHHHHHHHHHHHHH------HhCcCCCCccCCCCChHHHHHHHHHhCCCC--CCCccccCCCcCC
Confidence 99999999999999877764 22222 6789999999999999987654 7888999999996
No 15
>PRK00996 ribonuclease HIII; Provisional
Probab=100.00 E-value=9.3e-44 Score=350.84 Aligned_cols=205 Identities=25% Similarity=0.350 Sum_probs=165.3
Q ss_pred CCcEeeeccCCCCCCccceeEEEEEeeCCCChhHhhhcCCCCCCcCCHHHHHHHHHHHhhccceeeEEEEEEChHhHHHH
Q psy12553 39 QPCVLGIDEAGRGPVLGPMVYGTAYCPKDNNEELLKNLGCADSKALTEKKRDDILDSICKENAWLGWMVEIISPNVICNS 118 (401)
Q Consensus 39 ~~~viGIDEAGRGpv~GPmVvaav~~p~~~~~~~L~~lGv~DSKkLSe~kRe~L~~~I~~~~~~v~~aV~visp~eId~~ 118 (401)
...++|||||||||+|||||||||+++.+.. ..|+.+||+|||+||+++|++|++.|++ . +.|.+.+++|++||..
T Consensus 86 ~~~viGiDEaGrG~~fGPlvvaav~v~~~~~-~~l~~lgv~DSK~Ls~~kr~~La~~I~~--~-~~~~v~~~~p~~~n~l 161 (304)
T PRK00996 86 NLSLIGSDEVGKGDYFGPLTVAAVYVDKEQI-PFLKKLGVKDSKKLTDTKIRQIAPQLRE--K-IPHSVLLLSPEKYNEL 161 (304)
T ss_pred CceEEeecCCCCCCcccceEEEEEEEchhhc-chhhhcCCCccccCCHHHHHHHHHHHHH--h-cCEEEEEeCHHHhhhH
Confidence 3568999999999999999999999998877 7888999999999999999999999995 2 6899999999999975
Q ss_pred hHhHhHhhHHHHHHHHHHHHHHHHHHc--CCCccEEEEcCCCCccchhhhhhhc--cCcceEEEeecCCCCCcccccccc
Q psy12553 119 MLRRQKYSLNEVSHDAAIGLIRKVIAA--GVNVREVYVDTVGPPESYKKKLSEI--FPELIITVASKADSTYPVVGAAIA 194 (401)
Q Consensus 119 ml~~~~~NLN~l~~~aai~lI~~~l~~--gv~~~~V~VD~~g~p~~Y~~~L~~~--fp~i~i~v~~KADs~y~v~~~~~~ 194 (401)
+ ...+|+|.+....+.++|..+++. +..++.|+||+++.|+.|+.+|... .+..++++++|||++
T Consensus 162 ~--~~~~nln~l~a~~h~~ai~~l~~k~~~~~p~~iliD~f~~~~~y~~~l~~e~~~~~~~~~~~~KaD~~--------- 230 (304)
T PRK00996 162 Q--AKGYNQNKLKAWLHNQAIDNLLQKIAGIQPEKIVIDQFASPEVYQKYLKKEKNKFRDNVTFETKAESK--------- 230 (304)
T ss_pred H--HhhhhHHHHHHHHHHHHHHHHHhhccCCCCCEEEECCCCCchHHHHHhhhhccCCCCceEEEeccchh---------
Confidence 3 245799987544444455554432 5678899999999999999999763 234567788999999
Q ss_pred ccCCCccchhhhhhHHHHHHHHHHHhhhhhhhhhhhhcCCC------CCCCCCCHHHHHHHHhcCCCCcccccccccCch
Q psy12553 195 SKADSTYPVVGAASICAKVSRDSALKSWTFQEGIQIENNAW------GSGYPGDPVTKKFLSENIDPVFGFPQLVRFSWS 268 (401)
Q Consensus 195 ~kgD~~yp~VAAASIvAKVtRD~~m~~~~~~e~l~~~~~~y------GsGYPSDp~Tk~~L~~~i~~~fG~p~~hR~SW~ 268 (401)
|++|||||||| ||++|+.+ ++++++| |+|||+|+.+++||+++- .-.++.++|++|+
T Consensus 231 ------~~~VAAASIiA---R~~~l~~~------~~l~~~yg~~~~kGag~~~d~~a~~~i~~~G--~~~L~~~aK~hfk 293 (304)
T PRK00996 231 ------HLAVAAASIIA---RYAFLENM------DKLSKEAGMTLPKGAGAKVDKVAAQILKKYG--KEALEKFAKLHFK 293 (304)
T ss_pred ------hHHHHHHHHHH---HHHHHHHH------HHhCcCCCCCCCCCCCCHHHHHHHHHHHHhC--cchhHHHHHHhch
Confidence 99999999999 77777664 2334444 688888999999998741 1225789999999
Q ss_pred hHHHHhh
Q psy12553 269 TASKILK 275 (401)
Q Consensus 269 tvk~il~ 275 (401)
|+++++.
T Consensus 294 ~~~k~~~ 300 (304)
T PRK00996 294 NTEKAQK 300 (304)
T ss_pred hHHHHHH
Confidence 9998875
No 16
>TIGR00716 rnhC ribonuclease HIII. Two types of ribonuclease H in Bacillus subtilis, RNase HII (rnhB) and RNase HIII (rnhC), are both known experimentally and are quite similar to each other. The only RNase H homolog in the Mycoplasmas resembles rnhC. Archaeal forms resemble HII more closely than HIII. This model describes bacterial RNase III.
Probab=100.00 E-value=7.2e-39 Score=313.59 Aligned_cols=192 Identities=25% Similarity=0.314 Sum_probs=148.9
Q ss_pred CCcEeeeccCCCCCCccceeEEEEEeeCCCChhHhhhcCCCCCCcCCHHHHHHHHHHHhhccceeeEEEEEEChHhHHHH
Q psy12553 39 QPCVLGIDEAGRGPVLGPMVYGTAYCPKDNNEELLKNLGCADSKALTEKKRDDILDSICKENAWLGWMVEIISPNVICNS 118 (401)
Q Consensus 39 ~~~viGIDEAGRGpv~GPmVvaav~~p~~~~~~~L~~lGv~DSKkLSe~kRe~L~~~I~~~~~~v~~aV~visp~eId~~ 118 (401)
..+++|||||||||+|||||||||+++.+.. ..|+.+||+|||+||+++|++|++.|++ .+.|.+.+++|++||..
T Consensus 80 ~~~viGiDEaGrG~~fGPlvvaav~v~~~~~-~~L~~lGv~DSK~Ls~~kr~~la~~I~~---~~~~~i~~l~p~~~n~~ 155 (284)
T TIGR00716 80 PRSVIGCDESGKGDIFGPLVLCCVYIPEENY-LKVSSLNPRDSKRLSDKRIERLALNLKP---LVKAYCYELKPEKYNKL 155 (284)
T ss_pred CceEEeecCCCCCCcccceEEEEEEEChhhh-hhhhhcCCCCcccCCHHHHHHHHHHHHH---hCCEEEEEeCHHHhcHH
Confidence 3679999999999999999999999998876 7889999999999999999999999995 35799999999999964
Q ss_pred hHhHhHhhHHHHHHHHHHHHHHHHHHcCCCccEEEEcCCCCccchhhhhhhc-cCcceEEEeecCCCCCccccccccccC
Q psy12553 119 MLRRQKYSLNEVSHDAAIGLIRKVIAAGVNVREVYVDTVGPPESYKKKLSEI-FPELIITVASKADSTYPVVGAAIASKA 197 (401)
Q Consensus 119 ml~~~~~NLN~l~~~aai~lI~~~l~~gv~~~~V~VD~~g~p~~Y~~~L~~~-fp~i~i~v~~KADs~y~v~~~~~~~kg 197 (401)
+ ...+|+|.+....+.++|.+++.....+..|+||+++.++.|+.++... ++..++++++|||+
T Consensus 156 ~--~~~~nln~l~a~~h~~aI~~l~~~~~~~~~i~ID~f~~~~~y~~~l~~~~~~~~~~~~~~KaE~------------- 220 (284)
T TIGR00716 156 Y--RKFRNLNKMMAHFHKLLIERLLKEECGVSEVVVDQFAPSNPFFNHLKGRDIVGEDVIFETEAER------------- 220 (284)
T ss_pred H--HHHHHHHHHHHHHHHHHHHHHhhCcCCCcEEEECCCCCchHhhhhcccccccCCceeeeccccc-------------
Confidence 2 3458999998888888888776433334579999999888887776542 33445666667664
Q ss_pred CCccchhhhhhHHHHHHHHHHHhhhhhhhhhhhhcCCCC----CCCCCCHHHHHHHHhcCCCCcccccccc
Q psy12553 198 DSTYPVVGAASICAKVSRDSALKSWTFQEGIQIENNAWG----SGYPGDPVTKKFLSENIDPVFGFPQLVR 264 (401)
Q Consensus 198 D~~yp~VAAASIvAKVtRD~~m~~~~~~e~l~~~~~~yG----sGYPSDp~Tk~~L~~~i~~~fG~p~~hR 264 (401)
||+|||||||| ||++|+.+ ++.+++|| +||++ . +.+.-++.+ +.||++.++.
T Consensus 221 ---~~aVAAASIiA---R~~~l~~l------~~l~~~yg~~~pkGa~~-~-v~~~a~~~i-~~~G~~~L~~ 276 (284)
T TIGR00716 221 ---NLAVAAASIFA---RYKFLQSL------KELERELGIKLPKGASK-E-VKELAKSLI-LKKGPSALER 276 (284)
T ss_pred ---chhhhHHHHHH---HHHHHHHH------HHhCcccCCcCCCCCCh-H-HHHHHHHHH-HHhCccHHHH
Confidence 79999999999 77777764 45677777 99995 2 222111222 3579886544
No 17
>COG1039 RnhC Ribonuclease HIII [DNA replication, recombination, and repair]
Probab=99.97 E-value=1.5e-31 Score=259.84 Aligned_cols=204 Identities=26% Similarity=0.346 Sum_probs=165.3
Q ss_pred CCcEeeeccCCCCCCccceeEEEEEeeCCCChhHhhhcCCCCCCcCCHHHHHHHHHHHhhccceeeEEEEEEChHhHHHH
Q psy12553 39 QPCVLGIDEAGRGPVLGPMVYGTAYCPKDNNEELLKNLGCADSKALTEKKRDDILDSICKENAWLGWMVEIISPNVICNS 118 (401)
Q Consensus 39 ~~~viGIDEAGRGpv~GPmVvaav~~p~~~~~~~L~~lGv~DSKkLSe~kRe~L~~~I~~~~~~v~~aV~visp~eId~~ 118 (401)
...++|+||+|.|++|||+|||||+++++.. ..|+.+||+|||+||+.++.+|++.|+. .+.+.+..++|++|++.
T Consensus 82 ~~~~IGsDEvG~GDyFGpl~v~av~v~~e~~-~~L~~lgV~DSKkL~D~kI~~la~~ik~---~i~~~~l~l~p~kYNel 157 (297)
T COG1039 82 AKNLIGSDEVGKGDYFGPLVVCAVYVSKENL-PKLKELGVKDSKKLSDKKIQQLAPIIKP---LIPHSVLTLDPKKYNEL 157 (297)
T ss_pred cccccCCCCCCCCCccCCceEEEEEcCHHHH-HHHHhcCCcccccCCHHHHHHHHHHHHH---hcCceEEEEChHHHHHH
Confidence 4689999999999999999999999999888 8999999999999999999999999994 67899999999999873
Q ss_pred hHhHhHhhHHHHHHHHHHHHHHHHHH-cCCCccEEEEcCCCCccchhhhhhhcc--CcceEEEeecCCCCCccccccccc
Q psy12553 119 MLRRQKYSLNEVSHDAAIGLIRKVIA-AGVNVREVYVDTVGPPESYKKKLSEIF--PELIITVASKADSTYPVVGAAIAS 195 (401)
Q Consensus 119 ml~~~~~NLN~l~~~aai~lI~~~l~-~gv~~~~V~VD~~g~p~~Y~~~L~~~f--p~i~i~v~~KADs~y~v~~~~~~~ 195 (401)
.+..+|+|.+....+..+|..++. .+..++.|+||++...+.|..+|.+.. +..++.+..||++.
T Consensus 158 --~~k~~N~n~mkt~lH~~ai~~ll~~~~~~~~~ivIDqFa~~~~~~~yl~k~~~~~~~p~~f~~kaEs~---------- 225 (297)
T COG1039 158 --YKKFNNANSMKTFLHNQAIQNLLPQKGAQPEFIVIDQFASSENYKNYLQKETNKFSEPVLFLTKAESK---------- 225 (297)
T ss_pred --HHhhhhHHHHHHHHHHHHHHHHHHhccCCCeEEEeccccchhHHHHHHHhhccCCCCceeeeeccccc----------
Confidence 346789998866666677777764 688999999999999999999998763 23356677888888
Q ss_pred cCCCccchhhhhhHHHHHHHHHHHhhhhhhhhhhhhcCCCC----CCCCCCHHHHHHHHhcCCCCcccc---cccccCch
Q psy12553 196 KADSTYPVVGAASICAKVSRDSALKSWTFQEGIQIENNAWG----SGYPGDPVTKKFLSENIDPVFGFP---QLVRFSWS 268 (401)
Q Consensus 196 kgD~~yp~VAAASIvAKVtRD~~m~~~~~~e~l~~~~~~yG----sGYPSDp~Tk~~L~~~i~~~fG~p---~~hR~SW~ 268 (401)
+.+||||||+| ||.++..++ ....+|| +|-+ |..++..++++ ..+|+. .+...+|+
T Consensus 226 -----~laVAvASIiA---R~~Fl~~~~------~l~~~~gv~LPkGAg--~~V~~~a~~i~-~k~g~~~L~~~~k~hf~ 288 (297)
T COG1039 226 -----SLAVAVASIIA---RYAFLQSLK------QLSRQYGVQLPKGAG--PAVDQAAAEII-QKRGFSKLEQVAKLHFK 288 (297)
T ss_pred -----chhHHHHHHHH---HHHHHHHHH------HHHHHhCCcCCCCCc--hhHHHHHHHHH-HHhhHHHHHHHHHHHHH
Confidence 99999999999 999999873 3333344 5555 45555555544 457875 46777777
Q ss_pred hHHHHhh
Q psy12553 269 TASKILK 275 (401)
Q Consensus 269 tvk~il~ 275 (401)
+.++.+.
T Consensus 289 n~~k~~k 295 (297)
T COG1039 289 NFQKALK 295 (297)
T ss_pred HHHHHHh
Confidence 7776653
No 18
>PRK04342 DNA topoisomerase VI subunit A; Provisional
Probab=29.67 E-value=27 Score=36.29 Aligned_cols=17 Identities=24% Similarity=0.423 Sum_probs=15.0
Q ss_pred CCCCCCCCHHHHHHHHhc
Q psy12553 235 WGSGYPGDPVTKKFLSEN 252 (401)
Q Consensus 235 yGsGYPSDp~Tk~~L~~~ 252 (401)
+|+||| |..|+++|+..
T Consensus 220 tgkG~P-d~~TR~fl~~L 236 (367)
T PRK04342 220 HLKGQP-ARATRRFIKRL 236 (367)
T ss_pred ECCCCC-CHHHHHHHHHH
Confidence 589999 79999999874
No 19
>PRK12362 germination protease; Provisional
Probab=25.70 E-value=47 Score=34.13 Aligned_cols=34 Identities=18% Similarity=0.487 Sum_probs=26.1
Q ss_pred CcCCHHHHHHHHHHHhhccceeeEEEEEEChHhHHHHh
Q psy12553 82 KALTEKKRDDILDSICKENAWLGWMVEIISPNVICNSM 119 (401)
Q Consensus 82 KkLSe~kRe~L~~~I~~~~~~v~~aV~visp~eId~~m 119 (401)
|.|+++++.+|+.++.+. ..+ -.+++|++||..+
T Consensus 264 ~~~~~~ek~~li~evl~p--~~~--~l~VTPKeID~~i 297 (318)
T PRK12362 264 KSLNQEEKQQLIKEVLSP--YVG--NLIVTPKEIDELI 297 (318)
T ss_pred hccCHHHHHHHHHHHhCc--cCC--cceECcHhHHHHH
Confidence 578999999999888852 222 2689999999864
No 20
>cd00223 TOPRIM_TopoIIB_SPO TOPRIM_TopoIIB_SPO: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in the type IIB family of DNA topoisomerases and Spo11. This subgroup contains proteins similar to Sulfolobus shibatae topoisomerase VI (TopoVI) and Saccharomyces cerevisiae meiotic recombination factor: Spo11. Type II DNA topoisomerases catalyze the ATP-dependent transport of one DNA duplex through another, in the process generating transient double strand breaks via covalent attachments to both DNA strands at the 5' positions. TopoVI enzymes are heterotetramers found in archaea and plants. Spo11 plays a role in generating the double strand breaks that initiate homologous recombination during meiosis. S. shibatae TopoVI relaxes both positive and negative supercoils, and in addition has a strong decatenase activity. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspart
Probab=24.35 E-value=48 Score=29.86 Aligned_cols=16 Identities=50% Similarity=1.003 Sum_probs=14.1
Q ss_pred CCCCCCCCHHHHHHHHh
Q psy12553 235 WGSGYPGDPVTKKFLSE 251 (401)
Q Consensus 235 yGsGYPSDp~Tk~~L~~ 251 (401)
+|+||| |..|+.+|+.
T Consensus 30 t~kG~P-~~~tr~~l~~ 45 (160)
T cd00223 30 TGKGYP-DRATRRFLRR 45 (160)
T ss_pred EcCCcC-CHHHHHHHHH
Confidence 589999 6889999987
No 21
>KOG3495|consensus
Probab=24.35 E-value=69 Score=24.50 Aligned_cols=19 Identities=21% Similarity=0.265 Sum_probs=16.9
Q ss_pred hhhhhHHHHHHHHHHHhhh
Q psy12553 204 VGAASICAKVSRDSALKSW 222 (401)
Q Consensus 204 VAAASIvAKVtRD~~m~~~ 222 (401)
|.=++|+|++.|+.++.++
T Consensus 12 i~Ys~I~A~vvR~~LK~e~ 30 (50)
T KOG3495|consen 12 IRYSQIAAQVVRQALKTEL 30 (50)
T ss_pred HHHHHHHHHHHHHHHhHHH
Confidence 6778999999999999875
No 22
>PF09010 AsiA: Anti-Sigma Factor A; InterPro: IPR015100 Anti-sigma factor A is a transcriptional inhibitor that inhibits sigma 70-directed transcription by weakening its interaction with the core of the host's RNA polymerase. It is an all-helical protein, composed of six helical segments and intervening loops and turns, as well as a helix-turn-helix DNA binding motif, although neither free anti-sigma factor nor anti-sigma factor bound to sigma-70 has been shown to interact directly with DNA. In solution, the protein forms a symmetric dimer of small (10.59 kDa) protomers, which are composed of helix and coil regions and are devoid of beta-strand/sheet secondary structural elements []. ; PDB: 1TKV_A 1JR5_B 1TLH_A 1TL6_A.
Probab=22.86 E-value=40 Score=28.70 Aligned_cols=20 Identities=35% Similarity=0.526 Sum_probs=18.3
Q ss_pred chhhhhhHHHHHHHHHHHhh
Q psy12553 202 PVVGAASICAKVSRDSALKS 221 (401)
Q Consensus 202 p~VAAASIvAKVtRD~~m~~ 221 (401)
-+||.|||+-|.-||.+++.
T Consensus 10 eIia~aSiLIKfg~ddIl~~ 29 (91)
T PF09010_consen 10 EIIAVASILIKFGRDDILEN 29 (91)
T ss_dssp HHHHHHHHHHHTTTHHHHTS
T ss_pred HHHHHHHHHHHcChHHHHHh
Confidence 47999999999999999986
No 23
>TIGR01441 GPR GPR endopeptidase. This model describes a tetrameric protease that makes the rate-limiting first cut in the small, acid-soluble spore proteins (SASP) of Bacillus subtilis and related species. The enzyme lacks clear homology to other known proteases. It processes its own amino end before becoming active to cleave SASPs.
Probab=20.52 E-value=1.5e+02 Score=31.10 Aligned_cols=34 Identities=9% Similarity=0.178 Sum_probs=21.7
Q ss_pred CcCCHHHHHHHHHHHhhccceeeEEEEEEChHhHHHHh
Q psy12553 82 KALTEKKRDDILDSICKENAWLGWMVEIISPNVICNSM 119 (401)
Q Consensus 82 KkLSe~kRe~L~~~I~~~~~~v~~aV~visp~eId~~m 119 (401)
|.|+++++.+|+.++.+ ...+ . .+++|++||..+
T Consensus 296 ~~~~~~Ek~~li~EvL~--P~~~-~-L~VTPKeID~~i 329 (358)
T TIGR01441 296 GTLDEEEKRQLIYEVLN--PLGH-N-LMVTPKEVDMFI 329 (358)
T ss_pred ccCCHHHHHHHHHHHhC--cccC-c-ceECcHhHHHHH
Confidence 34566666666666663 2222 2 689999999864
Done!