Query 027718
Match_columns 219
No_of_seqs 114 out of 1077
Neff 6.6
Searched_HMMs 46136
Date Fri Mar 29 14:07:56 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/027718.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/027718hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 cd07181 RNaseH_typeII_eukaryot 100.0 4.7E-60 1E-64 403.5 18.7 191 17-207 1-192 (216)
2 KOG2299 Ribonuclease HI [Repli 100.0 1.1E-55 2.4E-60 376.8 15.3 203 9-211 23-229 (301)
3 cd07180 RNaseH_typeII_Archaea_ 100.0 6.1E-54 1.3E-58 363.0 18.6 186 17-217 1-188 (204)
4 cd06266 RNaseH_typeII Ribonucl 100.0 2.4E-53 5.3E-58 356.2 17.3 178 17-208 1-178 (193)
5 PRK14551 rnhB ribonuclease HII 100.0 2E-52 4.4E-57 355.5 18.9 174 16-207 2-177 (212)
6 TIGR00729 ribonuclease H, mamm 100.0 2.8E-52 6.1E-57 353.3 18.8 179 16-208 1-182 (206)
7 COG0164 RnhB Ribonuclease HII 100.0 1.5E-52 3.3E-57 350.4 16.0 177 15-215 1-181 (199)
8 cd06590 RNaseH_typeII_bacteria 100.0 7.1E-52 1.5E-56 351.2 18.3 184 17-207 1-186 (208)
9 PRK13925 rnhB ribonuclease HII 100.0 1.2E-51 2.7E-56 347.2 17.0 181 13-215 7-190 (198)
10 PRK00015 rnhB ribonuclease HII 100.0 4.8E-51 1E-55 343.5 17.6 166 14-207 18-183 (197)
11 cd07182 RNaseH_typeII_bacteria 100.0 2E-50 4.3E-55 335.4 16.9 162 17-205 1-162 (179)
12 PRK14550 rnhB ribonuclease HII 100.0 3.3E-50 7.3E-55 339.7 16.1 182 15-215 1-185 (204)
13 PRK00996 ribonuclease HIII; Pr 100.0 3.7E-49 8.1E-54 351.4 19.7 187 14-207 87-277 (304)
14 PF01351 RNase_HII: Ribonuclea 100.0 3.8E-49 8.3E-54 331.8 15.9 181 17-208 1-181 (198)
15 PRK13926 ribonuclease HII; Pro 100.0 1.8E-47 3.9E-52 323.7 19.0 163 14-207 22-184 (207)
16 TIGR00716 rnhC ribonuclease HI 100.0 1.4E-45 3E-50 325.7 17.8 179 14-202 81-260 (284)
17 COG1039 RnhC Ribonuclease HIII 100.0 8.7E-42 1.9E-46 296.9 16.7 185 14-205 83-270 (297)
18 TIGR01441 GPR GPR endopeptidas 48.1 25 0.00055 32.5 4.0 34 55-91 296-329 (358)
19 PRK05473 hypothetical protein; 45.6 22 0.00048 26.2 2.6 22 163-184 60-81 (86)
20 PRK12362 germination protease; 43.9 34 0.00073 31.2 4.1 34 55-91 264-297 (318)
21 PHA03297 envelope glycoprotein 38.3 15 0.00032 30.1 0.8 10 24-33 148-157 (185)
22 PF06135 DUF965: Bacterial pro 34.8 41 0.0009 24.4 2.6 21 163-183 57-77 (79)
23 PF09010 AsiA: Anti-Sigma Fact 29.1 25 0.00053 26.2 0.7 20 159-178 10-29 (91)
24 PF12686 DUF3800: Protein of u 27.7 3.2E+02 0.0069 21.9 14.3 162 16-177 1-213 (235)
25 KOG0179 20S proteasome, regula 25.2 30 0.00065 29.8 0.6 16 14-29 128-143 (235)
26 PRK02858 germination protease; 25.0 81 0.0018 29.3 3.4 34 55-91 307-340 (369)
27 KOG3495 Mitochondrial F1F0-ATP 23.5 1E+02 0.0022 20.4 2.7 20 161-180 12-31 (50)
No 1
>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=4.7e-60 Score=403.49 Aligned_cols=191 Identities=63% Similarity=1.014 Sum_probs=173.7
Q ss_pred eeeecCCcCCcccceeeEEEEcccccchhhhccCcCCCCCCCHHHHHHHHHHhhhcC-cccEEEEEEChhhHhHHhhhhh
Q 027718 17 MGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLKVND-SVGWAVDIIDPRELSAKMLNKN 95 (219)
Q Consensus 17 iGiDEaGrG~~~GPlvvaav~~~~~~~~~l~~~gv~DSK~Ls~~~r~~l~~~I~~~~-~~~~~v~~i~p~~id~~~~~~~ 95 (219)
+|||||||||+|||||||||+++.+..+.|..+||+|||+||+++|++|+++|++.. ++.|.+.+++|++||+.|...+
T Consensus 1 iGiDEaGRG~~~GPlvvaav~~~~~~~~~l~~~gv~DSK~Ls~~~r~~L~~~I~~~~~~~~~~i~~i~~~~id~~~~~~~ 80 (216)
T cd07181 1 LGIDEAGRGPVLGPMVYGIAYCPISYEEDLKKLGFADSKTLTEEKREELFKKIKEKSEALGWATRILSPQYISAKMLART 80 (216)
T ss_pred CCCcCCCCCCChhhhEEEEEEEchHhhhhhhhcCCCcCCcCCHHHHHHHHHHHHhccccceEEEEEECHHHHCHHhhhcc
Confidence 699999999999999999999998876778778999999999999999999999742 5789999999999998765434
Q ss_pred hchHHHHHHHHHHHHHHHHHhcCCCCCEEEECCCCChHHHHHHhhccCCCcceEEeecCccchhhHHHHhHHhHHHHHHH
Q 027718 96 KINLNEISHDSAIGLITRVLNIGILLTEVYLDTVGDAEKYQAKLSQRFPSIKFVVSKKADSLYPVVSGASIVAKVTRDRT 175 (219)
Q Consensus 96 ~~Nin~~~~~~~~~li~~~l~~~~~~~~i~iD~~~~~~~~~~~L~~~~~~~~~~~~~KaD~~~~sVAAASIlAKv~RD~~ 175 (219)
..|||+++++++.+++++++..+..++.++||+++++++|.++|+..+|+.++++++|||++|++||||||||||+||++
T Consensus 81 ~~nln~~~~~~~~~~i~~~~~~~~~~~~vliD~~~~~~~~~~~L~~~~~~~~~~~~~kaD~~~~~VAAASIvAKV~RD~~ 160 (216)
T cd07181 81 KYNLNEISHDAAIGLIKSVLDKGVNVTEVYVDTVGPPEKYQAKLKKLFPGIKFTVEKKADSLYPIVSAASIVAKVTRDRA 160 (216)
T ss_pred cccHHHHHHHHHHHHHHHHHcCCCCCCEEEECCCCChhHHHHhhhhcCCCCceEEeeCcccccHHHHHHHHHHHHHHHHH
Confidence 57999999999999998877655567899999999888999999876677778889999999999999999999999999
Q ss_pred HHHhhHhcccccccCCCccccCCchhhhhhhh
Q 027718 176 LRGWIFEETAENMHRNFGSGYPGGARCLKLSI 207 (219)
Q Consensus 176 m~~l~~~~p~y~~~~~~GsGYpsd~~t~~~~~ 207 (219)
|++|++.||.|+|.+++|||||||+||++|..
T Consensus 161 m~~l~~~~~~~~~~~~~gsGYpsd~~t~~~l~ 192 (216)
T cd07181 161 LKNWQFDEYLIDPDGDFGSGYPSDPKTKKWLK 192 (216)
T ss_pred HHHHHhhCccccccCCCceECCCHHHHHHHHH
Confidence 99999999999999999999999999999994
No 2
>KOG2299 consensus Ribonuclease HI [Replication, recombination and repair]
Probab=100.00 E-value=1.1e-55 Score=376.77 Aligned_cols=203 Identities=59% Similarity=0.978 Sum_probs=190.1
Q ss_pred CCCCCCcEeeeecCCcCCcccceeeEEEEcccccchhhhccCcCCCCCCCHHHHHHHHHHhhhc----CcccEEEEEECh
Q 027718 9 KWASNPCIMGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLKVN----DSVGWAVDIIDP 84 (219)
Q Consensus 9 ~~~~~~~~iGiDEaGrG~~~GPlvvaav~~~~~~~~~l~~~gv~DSK~Ls~~~r~~l~~~I~~~----~~~~~~v~~i~p 84 (219)
+|++.++++|||||||||++||||+|+++||.+....|..+|+.|||+|++.+|++|+++|+++ ..++|++.+++|
T Consensus 23 ~~~~~PcvlGIDEAGRGPVLGPMVYa~~ycP~~~~~~l~~lgfaDSK~L~e~kRe~lf~~i~~d~~~~~~vgwA~~~isP 102 (301)
T KOG2299|consen 23 EQKSEPCVLGIDEAGRGPVLGPMVYAAAYCPLDYLEDLENLGFADSKTLTEAKREELFNKIKEDEELTSNVGWATDCISP 102 (301)
T ss_pred cccCCceEeeccccCCCCcccceeeEEEeccchhhhhhhhcCccchhhccHHHHHHHHHHHhhhhhhhhceeeEeeecCH
Confidence 5666799999999999999999999999999998888999999999999999999999999763 237899999999
Q ss_pred hhHhHHhhhhhhchHHHHHHHHHHHHHHHHHhcCCCCCEEEECCCCChHHHHHHhhccCCCcceEEeecCccchhhHHHH
Q 027718 85 RELSAKMLNKNKINLNEISHDSAIGLITRVLNIGILLTEVYLDTVGDAEKYQAKLSQRFPSIKFVVSKKADSLYPVVSGA 164 (219)
Q Consensus 85 ~~id~~~~~~~~~Nin~~~~~~~~~li~~~l~~~~~~~~i~iD~~~~~~~~~~~L~~~~~~~~~~~~~KaD~~~~sVAAA 164 (219)
.+|...|++++.+|||..+|++++.+|+.+++.++....|++|+.|+|.+|...|++.||++++++..|||+.|+.||||
T Consensus 103 ~~IS~~Ml~r~kynLNevshdsam~LI~~v~~~gvnvteiyVDTVGpp~~Yq~kLek~FP~~k~tV~kKADSlfpiVS~A 182 (301)
T KOG2299|consen 103 REISASMLRRNKYNLNEVSHDSAMGLIDEVLDQGVNVTEIYVDTVGPPAKYQEKLEKRFPGIKFTVTKKADSLFPIVSAA 182 (301)
T ss_pred HHHHHHHHHHhcCCchhhhhHHHHHHHHHHHHhCCceEEEEEecCCChHHHHHHHHhhCCCeEEEEeecccccccchhhh
Confidence 99999999888999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hHHhHHHHHHHHHHhhHhcccccccCCCccccCCchhhhhhhhhhhh
Q 027718 165 SIVAKVTRDRTLRGWIFEETAENMHRNFGSGYPGGARCLKLSIVCNN 211 (219)
Q Consensus 165 SIlAKv~RD~~m~~l~~~~p~y~~~~~~GsGYpsd~~t~~~~~~~~~ 211 (219)
||+|||+||+.+++|+..+.....+.++|||||+||.|++|++.+.+
T Consensus 183 SI~AKVtRD~alk~w~~~E~~~~~d~~~GSGYP~DP~T~~wLk~~v~ 229 (301)
T KOG2299|consen 183 SIVAKVTRDRALKEWQFEEKLSDPDEDLGSGYPSDPETKAWLKENVD 229 (301)
T ss_pred hhhhhhhhccccceeeeeeecccCCccccCCCCCChhHHHHHHhccc
Confidence 99999999999999987777777788999999999999999986543
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=6.1e-54 Score=362.97 Aligned_cols=186 Identities=37% Similarity=0.590 Sum_probs=162.9
Q ss_pred eeeecCCcCCcccceeeEEEEcccccchhhhccCcCCCCCCCHHHHHHHHHHhhhcCcccEEEEEEChhhHhHHhhhhhh
Q 027718 17 MGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLKVNDSVGWAVDIIDPRELSAKMLNKNK 96 (219)
Q Consensus 17 iGiDEaGrG~~~GPlvvaav~~~~~~~~~l~~~gv~DSK~Ls~~~r~~l~~~I~~~~~~~~~v~~i~p~~id~~~~~~~~ 96 (219)
||||||||||+|||||||||+++.+....|..+||+|||+||+++|++|+++|++. .+.|++.+++|++||+++ ..
T Consensus 1 iGiDEaGrG~~~GPlvvaav~~~~~~~~~l~~~gv~DSK~Ls~~~r~~l~~~I~~~-~~~~~i~~i~~~~id~~~---~~ 76 (204)
T cd07180 1 CGIDEAGRGPVIGPMVVAGVAIDEESLKKLKSLGVKDSKKLTPKKREELYNEILKV-ADDVVIVIVSPEEIDERR---EA 76 (204)
T ss_pred CCCCCCCCCCcccceEEEEEEECHHHhhhHhhcCCCcCCCCCHHHHHHHHHHHHhc-CCeEEEEEECHHHhChhh---hh
Confidence 69999999999999999999999987778888999999999999999999999984 678999999999999876 36
Q ss_pred chHHHHHHHHHHHHHHHHHhcCCCCCEEEECCC-CChHHHHHHhhccC-CCcceEEeecCccchhhHHHHhHHhHHHHHH
Q 027718 97 INLNEISHDSAIGLITRVLNIGILLTEVYLDTV-GDAEKYQAKLSQRF-PSIKFVVSKKADSLYPVVSGASIVAKVTRDR 174 (219)
Q Consensus 97 ~Nin~~~~~~~~~li~~~l~~~~~~~~i~iD~~-~~~~~~~~~L~~~~-~~~~~~~~~KaD~~~~sVAAASIlAKv~RD~ 174 (219)
.|||.++.++|.++++++. .++..++||++ +++++|.++|++.+ ++.++++++|||+++++||||||||||+||+
T Consensus 77 ~nln~~~~~~~~~~i~~l~---~~~~~iliD~~~~~~~~~~~~l~~~~~~~~~~~~~~KgD~~~~~VAaASIlAKv~Rd~ 153 (204)
T cd07180 77 HNLNELEAEAFAELINRLS---DKPDIVYVDACDVNEERFAEELRERLNSGVEVIAEHKADAKYPVVSAASIIAKVERDR 153 (204)
T ss_pred cCHHHHHHHHHHHHHHHhh---cCCCEEEEeCCCCCHHHHHHHHHHhcCCCCcEEEEeCCcccCchhhHHHHHHHHHHHH
Confidence 7999999999999998875 24678999999 46778888887654 3567788999999999999999999999999
Q ss_pred HHHHhhHhcccccccCCCccccCCchhhhhhhhhhhhhccccC
Q 027718 175 TLRGWIFEETAENMHRNFGSGYPGGARCLKLSIVCNNFQSFGG 217 (219)
Q Consensus 175 ~m~~l~~~~p~y~~~~~~GsGYpsd~~t~~~~~~~~~~~~~~~ 217 (219)
+|++|++.|| ++|+|||+|+.|++|.+ +++..|||
T Consensus 154 ~m~~l~~~~~------~~g~Gy~sd~~t~~~l~--~~~~~~g~ 188 (204)
T cd07180 154 EIEELKEEYG------DFGSGYPSDPRTIKFLR--NYYREHGE 188 (204)
T ss_pred HHHHHHHhcc------cCCCcCCCCHHHHHHHH--HHHHhhCC
Confidence 9999998885 56799999999999985 33444444
No 4
>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-53 Score=356.16 Aligned_cols=178 Identities=37% Similarity=0.522 Sum_probs=161.2
Q ss_pred eeeecCCcCCcccceeeEEEEcccccchhhhccCcCCCCCCCHHHHHHHHHHhhhcCcccEEEEEEChhhHhHHhhhhhh
Q 027718 17 MGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLKVNDSVGWAVDIIDPRELSAKMLNKNK 96 (219)
Q Consensus 17 iGiDEaGrG~~~GPlvvaav~~~~~~~~~l~~~gv~DSK~Ls~~~r~~l~~~I~~~~~~~~~v~~i~p~~id~~~~~~~~ 96 (219)
+|||||||||+|||||||||+++.+..+.|..+||+|||+||+++|++|+++|++ ..+.|.+.+++|++||+
T Consensus 1 iGiDEaGrG~~~GPlvva~v~~~~~~~~~l~~~gv~DSK~Lt~~~r~~l~~~I~~-~~~~~~v~~~~p~~id~------- 72 (193)
T cd06266 1 AGIDEAGRGPLAGPVVAAAVILPKENIEILKILGVKDSKKLSEKKREELFEEIKE-EALAYAIGIISPEEIDE------- 72 (193)
T ss_pred CCCcccCcCCcchheEEEEEEEchhhcccccccCCCCcccCCHHHHHHHHHHHHh-hCCeEEEEEECHHHHCH-------
Confidence 6999999999999999999999999888888999999999999999999999998 36899999999999974
Q ss_pred chHHHHHHHHHHHHHHHHHhcCCCCCEEEECCCCChHHHHHHhhccCCCcceEEeecCccchhhHHHHhHHhHHHHHHHH
Q 027718 97 INLNEISHDSAIGLITRVLNIGILLTEVYLDTVGDAEKYQAKLSQRFPSIKFVVSKKADSLYPVVSGASIVAKVTRDRTL 176 (219)
Q Consensus 97 ~Nin~~~~~~~~~li~~~l~~~~~~~~i~iD~~~~~~~~~~~L~~~~~~~~~~~~~KaD~~~~sVAAASIlAKv~RD~~m 176 (219)
.|||.++..+|.+++.++. .++..++||++++++.|.. +....++.++++++|||++|++||||||||||+||+.|
T Consensus 73 ~nl~~~~~~~~~~~i~~l~---~~~~~i~iD~~~~~~~~~~-~~~~~~~~~~~~~~kaD~~~~~VaAASIiAKv~rd~~m 148 (193)
T cd06266 73 LNILQATALAMARAILNLG---VKPDEVLVDGNGVPEKYFA-LEKKFLPIPVTAIVKGDSKSPSVAAASILAKVTRDRLM 148 (193)
T ss_pred HHHHHHHHHHHHHHHHhcC---CCCCEEEECCCCChhhhhh-hcccCCCCCeEEEeccccccHhHHHHHHHHHHHHHHHH
Confidence 5999999999998888764 3568999999999988876 44445678889999999999999999999999999999
Q ss_pred HHhhHhcccccccCCCccccCCchhhhhhhhh
Q 027718 177 RGWIFEETAENMHRNFGSGYPGGARCLKLSIV 208 (219)
Q Consensus 177 ~~l~~~~p~y~~~~~~GsGYpsd~~t~~~~~~ 208 (219)
+.|+..||.|+| ++|+|||+|+||++|.+-
T Consensus 149 ~~l~~~~~~~~~--~~gsGy~s~~~~~~~~~~ 178 (193)
T cd06266 149 EELDEEYPGYGF--AKGKGYPTDPHTEAILKY 178 (193)
T ss_pred HHHHHHCCCCCC--cCCcCcCcHHHHHHHHHh
Confidence 999999999887 577999999999999764
No 5
>PRK14551 rnhB ribonuclease HII; Provisional
Probab=100.00 E-value=2e-52 Score=355.54 Aligned_cols=174 Identities=29% Similarity=0.426 Sum_probs=151.6
Q ss_pred EeeeecCCcCCcccceeeEEEEcccccchhhhccCcCCCCCCCHHHHHHHHHHhhhcCcccEEEEEEChhhHhHHhhhhh
Q 027718 16 IMGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLKVNDSVGWAVDIIDPRELSAKMLNKN 95 (219)
Q Consensus 16 ~iGiDEaGrG~~~GPlvvaav~~~~~~~~~l~~~gv~DSK~Ls~~~r~~l~~~I~~~~~~~~~v~~i~p~~id~~~~~~~ 95 (219)
++|||||||||+|||||||||+++.+. + ..||+|||+||+++|++|+++|++...+.|++.+++|++||+ .
T Consensus 2 ~iGiDEaGRG~v~GPlVvaav~~~~~~---~-~~gv~DSK~Ls~~~R~~l~~~I~~~~~~~~~i~~isp~~Id~-----~ 72 (212)
T PRK14551 2 RFGVDEAGKGPVLGSMFAAAVRADPAA---L-PDGIDDSKRLSPERREELAAELREDDAIAVGVAEIPPARIDD-----P 72 (212)
T ss_pred eeCccCCCCCCccccceEEEEEECccc---C-cCCCcCcccCCHHHHHHHHHHHHhccCceEEEEEeCHHHHCc-----c
Confidence 799999999999999999999999763 2 359999999999999999999997423689999999999985 2
Q ss_pred hchHHHHHHHHHHHHHHHHHhcCCCCCEEEECCCC-ChHHHHHHhhccC-CCcceEEeecCccchhhHHHHhHHhHHHHH
Q 027718 96 KINLNEISHDSAIGLITRVLNIGILLTEVYLDTVG-DAEKYQAKLSQRF-PSIKFVVSKKADSLYPVVSGASIVAKVTRD 173 (219)
Q Consensus 96 ~~Nin~~~~~~~~~li~~~l~~~~~~~~i~iD~~~-~~~~~~~~L~~~~-~~~~~~~~~KaD~~~~sVAAASIlAKv~RD 173 (219)
..|||.++..+|.+++++++. ++..++||++. ++++|..++++.+ ++.++++++|||++|++||||||||||+||
T Consensus 73 ~~nln~~~~~a~~~ai~~l~~---~~~~v~iD~~~~~~~~~~~~l~~~~~~~~~~~~~~KaD~~~~~VAAASIlAKv~RD 149 (212)
T PRK14551 73 ETDMNTLTVAAHAEALSGVAT---DGITGLCDAGDVDAGRFARRVADRVALDVSVSAEHGADEEDPLVGAASIVAKVARD 149 (212)
T ss_pred ccCHHHHHHHHHHHHHHhhcc---CCCEEEECCCCCchHHHHHhhhhccCCCCceEEEecccchhHHHHHHHHHHHHHHH
Confidence 479999999999999987642 35789999984 6677887887664 356778899999999999999999999999
Q ss_pred HHHHHhhHhcccccccCCCccccCCchhhhhhhh
Q 027718 174 RTLRGWIFEETAENMHRNFGSGYPGGARCLKLSI 207 (219)
Q Consensus 174 ~~m~~l~~~~p~y~~~~~~GsGYpsd~~t~~~~~ 207 (219)
+.|++|++.|| ++|||||||++|++|.+
T Consensus 150 ~~m~~l~~~y~------~~GsGYpsd~~t~~~l~ 177 (212)
T PRK14551 150 AHVAALAAEYG------DVGSGYPSDPTTREFLR 177 (212)
T ss_pred HHHHHHHHHCC------CCCCcCCCcHHHHHHHH
Confidence 99999998886 56799999999999964
No 6
>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=2.8e-52 Score=353.32 Aligned_cols=179 Identities=37% Similarity=0.568 Sum_probs=153.3
Q ss_pred EeeeecCCcCCcccceeeEEEEcccccchhhhccCcCCCCCCCHHHHHHHHHHhhhcCcccEEEEEEChhhHhHHhhhhh
Q 027718 16 IMGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLKVNDSVGWAVDIIDPRELSAKMLNKN 95 (219)
Q Consensus 16 ~iGiDEaGrG~~~GPlvvaav~~~~~~~~~l~~~gv~DSK~Ls~~~r~~l~~~I~~~~~~~~~v~~i~p~~id~~~~~~~ 95 (219)
++|||||||||+|||||||||+++.+....|..+||+|||+||+++|++|+++|++. .+.|++..++|++||+.+
T Consensus 1 iiGiDEaGrG~~~GPlvva~v~~~~~~~~~l~~~gv~DSK~Ls~~~r~~l~~~I~~~-~~~~~i~~i~p~~id~~~---- 75 (206)
T TIGR00729 1 VAGIDEAGRGPVIGPLVVGVFAIEEKREEELRKLGVKDSKKLTPGRREELFSKIRNK-LGRYEVLKITPEEIDRER---- 75 (206)
T ss_pred CcCccCCCCCCccCceEEEEEEechhhhhhHhhcCCccCCcCCHHHHHHHHHHHHhh-cCcEEEEEEcHHHHChHH----
Confidence 589999999999999999888877765667778899999999999999999999974 578999999999999754
Q ss_pred hchHHHHHHHHHHHHHHHHHhcCCCCCEEEECCCCChHH-HHHHhh--ccCCCcceEEeecCccchhhHHHHhHHhHHHH
Q 027718 96 KINLNEISHDSAIGLITRVLNIGILLTEVYLDTVGDAEK-YQAKLS--QRFPSIKFVVSKKADSLYPVVSGASIVAKVTR 172 (219)
Q Consensus 96 ~~Nin~~~~~~~~~li~~~l~~~~~~~~i~iD~~~~~~~-~~~~L~--~~~~~~~~~~~~KaD~~~~sVAAASIlAKv~R 172 (219)
..|||.++..++.++++++.. ++..++||+++.++. |...+. ..+|+.++++++|||+++++||||||||||+|
T Consensus 76 ~~nln~~~~~a~~~~i~~l~~---~~~~v~iD~~~~~~~~~~~~~~~~~~~~~~~~~~~~KaD~~~~~VAAASIlAKv~R 152 (206)
T TIGR00729 76 NINLNENEIEKFSKAAIILIE---KPSEVYVDSVDVNPKRFKREIKIKERIEGIKVIAEHKADAKYPVVSAASIIAKVER 152 (206)
T ss_pred HhhHHHHHHHHHHHHHHHHhc---CCcEEEEcCCCCcHHHHHHHHHHhccCCCCcEEEEeccccccchhhHHHHHHHHHH
Confidence 479999999999999887642 357899999986654 332222 23566788899999999999999999999999
Q ss_pred HHHHHHhhHhcccccccCCCccccCCchhhhhhhhh
Q 027718 173 DRTLRGWIFEETAENMHRNFGSGYPGGARCLKLSIV 208 (219)
Q Consensus 173 D~~m~~l~~~~p~y~~~~~~GsGYpsd~~t~~~~~~ 208 (219)
|++|++|++.||. +|+|||||++|++|.+.
T Consensus 153 D~~m~~l~~~~~~------~GsGY~sd~~t~~~l~~ 182 (206)
T TIGR00729 153 DREIESLKRKYGD------FGSGYPSDPRTREWLEE 182 (206)
T ss_pred HHHHHHHHHhcCC------CCCcCCCCHHHHHHHHH
Confidence 9999999988865 57999999999999864
No 7
>COG0164 RnhB Ribonuclease HII [DNA replication, recombination, and repair]
Probab=100.00 E-value=1.5e-52 Score=350.41 Aligned_cols=177 Identities=32% Similarity=0.450 Sum_probs=149.3
Q ss_pred cEeeeecCCcCCcccceeeEEEEcccccchhhhccCcCCCCCCCHHHHHHHHHHhhhcCcccEEEEEEChhhHhHHhhhh
Q 027718 15 CIMGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLKVNDSVGWAVDIIDPRELSAKMLNK 94 (219)
Q Consensus 15 ~~iGiDEaGrG~~~GPlvvaav~~~~~~~~~l~~~gv~DSK~Ls~~~r~~l~~~I~~~~~~~~~v~~i~p~~id~~~~~~ 94 (219)
.++|||||||||++||||+|||++|.+... ..+|++|||+||+++|++|+++|++ .++.|.+.++++++||
T Consensus 1 ~vaGIDEAGRGpl~GPvV~Aavil~~~~~~--~~~Gl~DSKkLs~~kRe~L~~~I~~-~a~~~~v~~~~~~~Id------ 71 (199)
T COG0164 1 LVAGVDEAGRGPLAGPVVAAAVILPPDRLP--KKLGLKDSKKLSPKKREELFEEIKE-KALAWGVGIIPAEEID------ 71 (199)
T ss_pred CcCcccCCCcCCcccceeEEEEEECccccc--cccCccccccCCHHHHHHHHHHHHh-hccEEEEEEcCHHHHh------
Confidence 378999999999999999999999997543 5589999999999999999999995 4789999999999995
Q ss_pred hhchHHHHHHHHHHHHHHHHHhcCCCCCEEEECCCCChHHHHHHhhccCCCcceEEeecCccchhhHHHHhHHhHHHHHH
Q 027718 95 NKINLNEISHDSAIGLITRVLNIGILLTEVYLDTVGDAEKYQAKLSQRFPSIKFVVSKKADSLYPVVSGASIVAKVTRDR 174 (219)
Q Consensus 95 ~~~Nin~~~~~~~~~li~~~l~~~~~~~~i~iD~~~~~~~~~~~L~~~~~~~~~~~~~KaD~~~~sVAAASIlAKv~RD~ 174 (219)
+.||+++++.++.+++..+. .+++.++||+++.+. .++.. .++++|||+++++||||||||||+||+
T Consensus 72 -~~ni~~a~~~am~~av~~l~---~~~~~vlvD~~~~~~--------~l~~~-~~a~~KgDa~~~~IaAASIvAKV~RDr 138 (199)
T COG0164 72 -ELNILEATKLAMRRAVAGLS---SQPDLVLVDGNDLPL--------GLPQP-AVAIIKGDAKSPSIAAASILAKVTRDR 138 (199)
T ss_pred -hhhHHHHHHHHHHHHHHhcc---ccCCEEEEeCCCccc--------cCCCC-cceeeccchhhHHHHHHHHHHHHHHHH
Confidence 58999999988887777653 234889999886221 11111 277899999999999999999999999
Q ss_pred HHHHhhHhcccccccCCCccccCCchhhhhhhh---hh-hhhccc
Q 027718 175 TLRGWIFEETAENMHRNFGSGYPGGARCLKLSI---VC-NNFQSF 215 (219)
Q Consensus 175 ~m~~l~~~~p~y~~~~~~GsGYpsd~~t~~~~~---~~-~~~~~~ 215 (219)
+|++|++.||+|+|+.| ||||||+||.+|.+ +. .|+++|
T Consensus 139 ~m~~l~~~yp~Y~~~~~--~GY~T~~h~~a~~~~~~~~~~hR~Sf 181 (199)
T COG0164 139 LMEELAKEYPEYGFDKG--SGYPTDPHTEALLKKGGTPGIHRRSF 181 (199)
T ss_pred HHHHHHhhCcCcCcccC--CCCCChHHHHHHHHhCCCCceeeccc
Confidence 99999999999999655 99999999999983 22 455555
No 8
>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=7.1e-52 Score=351.23 Aligned_cols=184 Identities=21% Similarity=0.248 Sum_probs=165.7
Q ss_pred eeeecCCcCCcccceeeEEEEcccccchhhhccCcCCCCCCCHHHHHHHHHHhhhcCcccEEEEEEChhhHhHHhhhhhh
Q 027718 17 MGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLKVNDSVGWAVDIIDPRELSAKMLNKNK 96 (219)
Q Consensus 17 iGiDEaGrG~~~GPlvvaav~~~~~~~~~l~~~gv~DSK~Ls~~~r~~l~~~I~~~~~~~~~v~~i~p~~id~~~~~~~~ 96 (219)
+|||||||||+|||||||||+++.+....|..+||+|||+||+++|++|++.|++ .+.|++..++|++||.++. +.
T Consensus 1 iGiDEaGRG~~~GPlVvaav~~~~~~~~~l~~~gv~DSK~Ls~~~r~~l~~~I~~--~~~~~v~~i~~~~in~~~~--~~ 76 (208)
T cd06590 1 IGSDEVGKGDYFGPLVVAAVYVDKENISKLKKLGVKDSKKLTDKKIIRLAPKIKK--KIPYSVLSLGPEKYNELYK--KG 76 (208)
T ss_pred CCCCCCCCCCCcCccEEEEEEEcHHHHHHHHHCCCCcCCcCCHHHHHHHHHHHHh--cCCEEEEecCHHHHHHHHH--cc
Confidence 6999999999999999999999987777788899999999999999999999998 3789999999999998752 36
Q ss_pred chHHHHHHHHHHHHHHHHHhcCCCCCEEEECCCCChHHHHHHhhccC--CCcceEEeecCccchhhHHHHhHHhHHHHHH
Q 027718 97 INLNEISHDSAIGLITRVLNIGILLTEVYLDTVGDAEKYQAKLSQRF--PSIKFVVSKKADSLYPVVSGASIVAKVTRDR 174 (219)
Q Consensus 97 ~Nin~~~~~~~~~li~~~l~~~~~~~~i~iD~~~~~~~~~~~L~~~~--~~~~~~~~~KaD~~~~sVAAASIlAKv~RD~ 174 (219)
.|+|.++.++|.+++++++..+..++.+++|+++.+++|..+|++.+ +++++++++|||++|++||||||||||+||+
T Consensus 77 ~nln~l~~~~~~~ai~~l~~~~~~~~~v~vD~~~~~~~~~~~l~~~~~~~~~~~~~~~kaD~~~~~VaAASIlAKv~Rd~ 156 (208)
T cd06590 77 KNLNKLKALLHNKAINNLLEKPKKPVAILIDQFASEKVYKRYLKKEKKIVKEPLIFRTKAESKHLAVAAASILARYAFLE 156 (208)
T ss_pred CCHHHHHHHHHHHHHHHHHHhcCCCCEEEecCCCCHHHHHHHHHhhccCCCCceEEEecCcccchHHHHHHHHHHHHHHH
Confidence 79999999999999998875445678899999999889988888765 5678889999999999999999999999999
Q ss_pred HHHHhhHhcccccccCCCccccCCchhhhhhhh
Q 027718 175 TLRGWIFEETAENMHRNFGSGYPGGARCLKLSI 207 (219)
Q Consensus 175 ~m~~l~~~~p~y~~~~~~GsGYpsd~~t~~~~~ 207 (219)
.|++|++. |+|..++|+|||+|+.|++|.+
T Consensus 157 ~m~~l~~~---yg~~~~~G~g~~~~~~~~~~l~ 186 (208)
T cd06590 157 KMEKLSKQ---YGMKLPKGASSKVDEQAAEIIK 186 (208)
T ss_pred HHHHHHHH---hCCCCCCCCCcHHHHHHHHHHH
Confidence 99998655 6899999999999999999876
No 9
>PRK13925 rnhB ribonuclease HII; Provisional
Probab=100.00 E-value=1.2e-51 Score=347.21 Aligned_cols=181 Identities=21% Similarity=0.313 Sum_probs=153.4
Q ss_pred CCcEeeeecCCcCCcccceeeEEEEcccccchhhhccCcCCCCCCCHHHHHHHHHHhhhcCcccEEEEEEChhhHhHHhh
Q 027718 13 NPCIMGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLKVNDSVGWAVDIIDPRELSAKML 92 (219)
Q Consensus 13 ~~~~iGiDEaGrG~~~GPlvvaav~~~~~~~~~l~~~gv~DSK~Ls~~~r~~l~~~I~~~~~~~~~v~~i~p~~id~~~~ 92 (219)
.+.++|||||||||+|||||||||+++.+....|..+||+|||+||+++|++|+++|++. ...|++.+++|++||
T Consensus 7 ~~~iiGiDEAGRGpv~GPmVvaav~~~~~~~~~L~~~gv~DSK~Ls~~~Re~l~~~I~~~-~~~~~i~~i~~~eId---- 81 (198)
T PRK13925 7 SELIAGVDEVGRGALFGPVFAAAVILSEKAEPQLLQAGLTDSKKLSPKRRAQLVPLILTL-ASDWGIGQASAREID---- 81 (198)
T ss_pred CCeEEeecCCCCCCChHHhEEEEEEEchHhhhhhhhcCCCCcccCCHHHHHHHHHHHHhh-CCcEEEEEECHHHhC----
Confidence 468999999999999999999999999887777888999999999999999999999874 567999999999996
Q ss_pred hhhhchHHHHHHHHHHHHHHHHHhcCCCCCEEEECCCCChHHHHHHhhccCCCcceEEeecCccchhhHHHHhHHhHHHH
Q 027718 93 NKNKINLNEISHDSAIGLITRVLNIGILLTEVYLDTVGDAEKYQAKLSQRFPSIKFVVSKKADSLYPVVSGASIVAKVTR 172 (219)
Q Consensus 93 ~~~~~Nin~~~~~~~~~li~~~l~~~~~~~~i~iD~~~~~~~~~~~L~~~~~~~~~~~~~KaD~~~~sVAAASIlAKv~R 172 (219)
..|||.++..++.++++++ ..+++.|++|+++... .+++.. ..++|||++|++||||||||||+|
T Consensus 82 ---~~ni~~~~~~a~~~~i~~l---~~~~~~v~iD~~~~~~--------~~~~~~-~~v~kaD~~~~~VaAASIiAKV~R 146 (198)
T PRK13925 82 ---RLGIRQATELAMLRALKKL---KSPPSLCLVDGNLPLR--------LWPGPQ-RTIVKGDSKSAAIAAASILAKVWR 146 (198)
T ss_pred ---HhhHHHHHHHHHHHHHHhc---CCCCCEEEECCccccC--------cCCCCc-eeecccccccHHHHHHHHHHHHHH
Confidence 4689999988888777654 2346789999986321 122222 345799999999999999999999
Q ss_pred HHHHHHhhHhcccccccCCCccccCCchhhhh---hhhhhhhhccc
Q 027718 173 DRTLRGWIFEETAENMHRNFGSGYPGGARCLK---LSIVCNNFQSF 215 (219)
Q Consensus 173 D~~m~~l~~~~p~y~~~~~~GsGYpsd~~t~~---~~~~~~~~~~~ 215 (219)
|++|+.|++.||+|+|+.| +||||++|+.. +.....|+++|
T Consensus 147 D~~m~~l~~~yp~y~f~~~--kGY~t~~h~~~i~~~G~~p~hR~sf 190 (198)
T PRK13925 147 DDLIKRLAKKYPGYGLEKN--KGYGTAQHRQALLKLGPTPLHRKSF 190 (198)
T ss_pred HHHHHHHHHHCCCCCcccC--CCCCcHHHHHHHHHhCcCHHHcCCC
Confidence 9999999999999999877 89999999865 45566777766
No 10
>PRK00015 rnhB ribonuclease HII; Validated
Probab=100.00 E-value=4.8e-51 Score=343.55 Aligned_cols=166 Identities=30% Similarity=0.411 Sum_probs=145.6
Q ss_pred CcEeeeecCCcCCcccceeeEEEEcccccchhhhccCcCCCCCCCHHHHHHHHHHhhhcCcccEEEEEEChhhHhHHhhh
Q 027718 14 PCIMGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLKVNDSVGWAVDIIDPRELSAKMLN 93 (219)
Q Consensus 14 ~~~iGiDEaGrG~~~GPlvvaav~~~~~~~~~l~~~gv~DSK~Ls~~~r~~l~~~I~~~~~~~~~v~~i~p~~id~~~~~ 93 (219)
..++|||||||||+|||||||||+++.+.. + +||+|||+||+++|++|+++|++. .+.|++.+++|++||+
T Consensus 18 ~~viGiDEaGrG~v~GPlvvaav~~~~~~~--l--~gv~DSK~Ls~~~R~~l~~~I~~~-~~~~~i~~isp~~id~---- 88 (197)
T PRK00015 18 GLIAGVDEAGRGPLAGPVVAAAVILDPDRP--I--EGLNDSKKLSEKKREELYEEIKEK-ALAYSVGIASPEEIDE---- 88 (197)
T ss_pred cEEEeecCcCCCCcccceeEEEEEECcccc--c--CCCCCcccCCHHHHHHHHHHHHHh-CceEEEEEcCHHHHHH----
Confidence 579999999999999999999999987632 2 699999999999999999999984 5789999999999974
Q ss_pred hhhchHHHHHHHHHHHHHHHHHhcCCCCCEEEECCCCChHHHHHHhhccCCCcceEEeecCccchhhHHHHhHHhHHHHH
Q 027718 94 KNKINLNEISHDSAIGLITRVLNIGILLTEVYLDTVGDAEKYQAKLSQRFPSIKFVVSKKADSLYPVVSGASIVAKVTRD 173 (219)
Q Consensus 94 ~~~~Nin~~~~~~~~~li~~~l~~~~~~~~i~iD~~~~~~~~~~~L~~~~~~~~~~~~~KaD~~~~sVAAASIlAKv~RD 173 (219)
.|+|+++..++.++++++ ..+..++||+++.++. ..++++++|||++|++||||||||||+||
T Consensus 89 ---~nln~~~~~a~~~~i~~l----~~~~~i~vD~~~~~~~----------~~~~~~~~kaD~~~~~VaAASIvAKv~RD 151 (197)
T PRK00015 89 ---LNILEATLLAMRRAVEGL----VKPDYVLVDGNRVPKL----------PIPQEAIVKGDAKSPSIAAASILAKVTRD 151 (197)
T ss_pred ---hhHHHHHHHHHHHHHHhc----CCCCEEEECCCCCCCC----------CCCeEEEEcCCcccHHHHHHHHHHHHHHH
Confidence 699999999988888765 2457899999986521 12356678999999999999999999999
Q ss_pred HHHHHhhHhcccccccCCCccccCCchhhhhhhh
Q 027718 174 RTLRGWIFEETAENMHRNFGSGYPGGARCLKLSI 207 (219)
Q Consensus 174 ~~m~~l~~~~p~y~~~~~~GsGYpsd~~t~~~~~ 207 (219)
++|+.|+++||.|+|..+ ||||||+||++|.+
T Consensus 152 ~~m~~l~~~~~~yg~~~~--sGY~s~~~~~a~~~ 183 (197)
T PRK00015 152 RLMEELDKEYPGYGFAKH--KGYGTKEHLEALAK 183 (197)
T ss_pred HHHHHHHHhCcCCCCcCC--CcCCCHHHHHHHHH
Confidence 999999999999998766 89999999999875
No 11
>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=2e-50 Score=335.36 Aligned_cols=162 Identities=30% Similarity=0.429 Sum_probs=141.5
Q ss_pred eeeecCCcCCcccceeeEEEEcccccchhhhccCcCCCCCCCHHHHHHHHHHhhhcCcccEEEEEEChhhHhHHhhhhhh
Q 027718 17 MGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLKVNDSVGWAVDIIDPRELSAKMLNKNK 96 (219)
Q Consensus 17 iGiDEaGrG~~~GPlvvaav~~~~~~~~~l~~~gv~DSK~Ls~~~r~~l~~~I~~~~~~~~~v~~i~p~~id~~~~~~~~ 96 (219)
+|||||||||+|||||||||+++.+... +||+|||+||+++|++|+++|++. .+.|++.+++|++||+
T Consensus 1 ~GiDEaGRG~~~GPlvvaav~~~~~~~~----~gv~DSK~Ls~~~R~~l~~~I~~~-~~~~~v~~~~~~~Id~------- 68 (179)
T cd07182 1 AGVDEAGRGPLAGPVVAAAVILPPDFEI----EGLNDSKKLSEKKREELYEEIKEK-ALAWGIGIASPEEIDR------- 68 (179)
T ss_pred CCCcCccCCCcccceEEEEEEECcccCc----CCCCCcccCCHHHHHHHHHHHHHh-cccEEEEEECHHHHCH-------
Confidence 6999999999999999999999886422 799999999999999999999984 6789999999999964
Q ss_pred chHHHHHHHHHHHHHHHHHhcCCCCCEEEECCCCChHHHHHHhhccCCCcceEEeecCccchhhHHHHhHHhHHHHHHHH
Q 027718 97 INLNEISHDSAIGLITRVLNIGILLTEVYLDTVGDAEKYQAKLSQRFPSIKFVVSKKADSLYPVVSGASIVAKVTRDRTL 176 (219)
Q Consensus 97 ~Nin~~~~~~~~~li~~~l~~~~~~~~i~iD~~~~~~~~~~~L~~~~~~~~~~~~~KaD~~~~sVAAASIlAKv~RD~~m 176 (219)
.|||+++..++.++++++ ...++.+++|++..++. ..++++++|||+++++||||||||||+||++|
T Consensus 69 ~nl~~~~~~a~~~ai~~l---~~~~~~v~iD~~~~~~~----------~~~~~~~~KaD~~~~~VaAASIvAKv~RD~~m 135 (179)
T cd07182 69 INILQATLLAMRRAVEGL---PVKPDYVLVDGNRLPPL----------PIPQEAIVKGDAKSASIAAASILAKVTRDRLM 135 (179)
T ss_pred hhHHHHHHHHHHHHHHhC---CCCCCEEEECCcCCCCC----------CCCeEEEeccccccHHHHHHHHHHHHHHHHHH
Confidence 699999999988888765 23567899999875432 23567789999999999999999999999999
Q ss_pred HHhhHhcccccccCCCccccCCchhhhhh
Q 027718 177 RGWIFEETAENMHRNFGSGYPGGARCLKL 205 (219)
Q Consensus 177 ~~l~~~~p~y~~~~~~GsGYpsd~~t~~~ 205 (219)
++|+++||+|+|+.| +||||++|+..+
T Consensus 136 ~~l~~~~~~yg~~~~--~GY~s~~h~~~i 162 (179)
T cd07182 136 IELDKKYPGYGFAKH--KGYGTKEHLEAL 162 (179)
T ss_pred HHHHHHCcCCCCcCC--CCCCcHHHHHHH
Confidence 999999999999666 899999998653
No 12
>PRK14550 rnhB ribonuclease HII; Provisional
Probab=100.00 E-value=3.3e-50 Score=339.68 Aligned_cols=182 Identities=23% Similarity=0.271 Sum_probs=148.0
Q ss_pred cEeeeecCCcCCcccceeeEEEEcccccchhhhccCcCCCCCCCHHHHHHHHHHhhhcCcccEEEEEEChhhHhHHhhhh
Q 027718 15 CIMGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLKVNDSVGWAVDIIDPRELSAKMLNK 94 (219)
Q Consensus 15 ~~iGiDEaGrG~~~GPlvvaav~~~~~~~~~l~~~gv~DSK~Ls~~~r~~l~~~I~~~~~~~~~v~~i~p~~id~~~~~~ 94 (219)
.++|||||||||+|||||||||+++.+....+..+||+|||+||+++|++|+++|++...+.|.+..++|++||
T Consensus 1 ~~~GiDEAGRGpl~GPvVvaav~~~~~~~~~l~~~gv~DSKkLs~~~Re~L~~~I~~~~~~~~~i~~~~~~eID------ 74 (204)
T PRK14550 1 MTLGIDEAGRGCLAGSLFVAGVACNEKTALEFLKMGLKDSKKLSPKKRFFLEDKIKTHGEVGFFVVKKSANEID------ 74 (204)
T ss_pred CeeCccCcCCCCccchheEEEEEEChhhccchhhcCccChhhCCHHHHHHHHHHHHhccCcEEEEEEECHHHHH------
Confidence 37999999999999999999999998765566678999999999999999999999753368999999999996
Q ss_pred hhchHHHHHHHHHHHHHHHHHhcCCCCCEEEECCCCChHHHHHHhhccCCCcceEEeecCccchhhHHHHhHHhHHHHHH
Q 027718 95 NKINLNEISHDSAIGLITRVLNIGILLTEVYLDTVGDAEKYQAKLSQRFPSIKFVVSKKADSLYPVVSGASIVAKVTRDR 174 (219)
Q Consensus 95 ~~~Nin~~~~~~~~~li~~~l~~~~~~~~i~iD~~~~~~~~~~~L~~~~~~~~~~~~~KaD~~~~sVAAASIlAKv~RD~ 174 (219)
..|||.++..++.++++++ ...++.+++|++..+..+ ..++ ++.+++|||++|++||||||||||+||+
T Consensus 75 -~~ni~~a~~~am~~al~~l---~~~~~~vliDg~~~~~~~-----~~~~--~~~~~~KgD~~~~~VAAASIiAKV~RD~ 143 (204)
T PRK14550 75 -SLGLGACLKLAIQEILENG---CSLANEIKIDGNTAFGLN-----KRYP--NIQTIIKGDETIAQIAMASVLAKAFKDR 143 (204)
T ss_pred -HHHHHHHHHHHHHHHHHhC---CCCCCEEEECCccCcccc-----ccCc--ceeEEEcccccchhHHHHHHHHHHHHHH
Confidence 4689988876666666543 234578999987533211 1112 3457799999999999999999999999
Q ss_pred HHHHhhHhcccccccCCCccccCCchhhhhh---hhhhhhhccc
Q 027718 175 TLRGWIFEETAENMHRNFGSGYPGGARCLKL---SIVCNNFQSF 215 (219)
Q Consensus 175 ~m~~l~~~~p~y~~~~~~GsGYpsd~~t~~~---~~~~~~~~~~ 215 (219)
+|++|+++||+|+|+.| |||||.+|..++ ...-.|+++|
T Consensus 144 ~M~~l~~~~p~Ygf~~~--kGY~T~~h~~ai~~~G~~p~hR~Sf 185 (204)
T PRK14550 144 EMLELHALFKEYGWDKN--CGYGTKQHIEAIIKLGATPFHRHSF 185 (204)
T ss_pred HHHHHHHhCCCCCCcCC--CCCCCHHHHHHHHHhCcCHHHcCCc
Confidence 99999999999999755 899999998654 3445566666
No 13
>PRK00996 ribonuclease HIII; Provisional
Probab=100.00 E-value=3.7e-49 Score=351.39 Aligned_cols=187 Identities=22% Similarity=0.260 Sum_probs=166.0
Q ss_pred CcEeeeecCCcCCcccceeeEEEEcccccchhhhccCcCCCCCCCHHHHHHHHHHhhhcCcccEEEEEEChhhHhHHhhh
Q 027718 14 PCIMGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLKVNDSVGWAVDIIDPRELSAKMLN 93 (219)
Q Consensus 14 ~~~iGiDEaGrG~~~GPlvvaav~~~~~~~~~l~~~gv~DSK~Ls~~~r~~l~~~I~~~~~~~~~v~~i~p~~id~~~~~ 93 (219)
..+||||||||||+|||||||||+++.+....|..+||+|||+||+++|++|+++|++. +.|++.+++|++||+++.
T Consensus 87 ~~viGiDEaGrG~~fGPlvvaav~v~~~~~~~l~~lgv~DSK~Ls~~kr~~La~~I~~~--~~~~v~~~~p~~~n~l~~- 163 (304)
T PRK00996 87 LSLIGSDEVGKGDYFGPLTVAAVYVDKEQIPFLKKLGVKDSKKLTDTKIRQIAPQLREK--IPHSVLLLSPEKYNELQA- 163 (304)
T ss_pred ceEEeecCCCCCCcccceEEEEEEEchhhcchhhhcCCCccccCCHHHHHHHHHHHHHh--cCEEEEEeCHHHhhhHHH-
Confidence 45899999999999999999999999888888889999999999999999999999984 689999999999998763
Q ss_pred hhhchHHHHHHHHHHHHHHHHHhc--CCCCCEEEECCCCChHHHHHHhhcc--CCCcceEEeecCccchhhHHHHhHHhH
Q 027718 94 KNKINLNEISHDSAIGLITRVLNI--GILLTEVYLDTVGDAEKYQAKLSQR--FPSIKFVVSKKADSLYPVVSGASIVAK 169 (219)
Q Consensus 94 ~~~~Nin~~~~~~~~~li~~~l~~--~~~~~~i~iD~~~~~~~~~~~L~~~--~~~~~~~~~~KaD~~~~sVAAASIlAK 169 (219)
...|+|.++.+.|.+++.++++. +..++.|+||+|+.+++|.++|... .+..++++++|||++|++||||||||
T Consensus 164 -~~~nln~l~a~~h~~ai~~l~~k~~~~~p~~iliD~f~~~~~y~~~l~~e~~~~~~~~~~~~KaD~~~~~VAAASIiA- 241 (304)
T PRK00996 164 -KGYNQNKLKAWLHNQAIDNLLQKIAGIQPEKIVIDQFASPEVYQKYLKKEKNKFRDNVTFETKAESKHLAVAAASIIA- 241 (304)
T ss_pred -hhhhHHHHHHHHHHHHHHHHHhhccCCCCCEEEECCCCCchHHHHHhhhhccCCCCceEEEeccchhhHHHHHHHHHH-
Confidence 35799999888888888887653 4456799999999999999999753 23456788999999999999999999
Q ss_pred HHHHHHHHHhhHhcccccccCCCccccCCchhhhhhhh
Q 027718 170 VTRDRTLRGWIFEETAENMHRNFGSGYPGGARCLKLSI 207 (219)
Q Consensus 170 v~RD~~m~~l~~~~p~y~~~~~~GsGYpsd~~t~~~~~ 207 (219)
||++|++|++++|+|+|..++|+|||+|+.+++|.+
T Consensus 242 --R~~~l~~~~~l~~~yg~~~~kGag~~~d~~a~~~i~ 277 (304)
T PRK00996 242 --RYAFLENMDKLSKEAGMTLPKGAGAKVDKVAAQILK 277 (304)
T ss_pred --HHHHHHHHHHhCcCCCCCCCCCCCCHHHHHHHHHHH
Confidence 999999999999999999999999999999877654
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=3.8e-49 Score=331.83 Aligned_cols=181 Identities=39% Similarity=0.585 Sum_probs=148.6
Q ss_pred eeeecCCcCCcccceeeEEEEcccccchhhhccCcCCCCCCCHHHHHHHHHHhhhcCcccEEEEEEChhhHhHHhhhhhh
Q 027718 17 MGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLKVNDSVGWAVDIIDPRELSAKMLNKNK 96 (219)
Q Consensus 17 iGiDEaGrG~~~GPlvvaav~~~~~~~~~l~~~gv~DSK~Ls~~~r~~l~~~I~~~~~~~~~v~~i~p~~id~~~~~~~~ 96 (219)
+|||||||||+|||||||||+++.+..+.|..+||+|||+||+++|++|+++|+. +.+.. +.+..++.. ..+.
T Consensus 1 iG~DEaGrG~~~GPlvvaav~~~~~~~~~l~~~gv~DSK~Ls~~~r~~l~~~I~~---i~~~~--~~~~~~~~~--~~~~ 73 (198)
T PF01351_consen 1 IGIDEAGRGDVFGPLVVAAVYLPEEDIEKLKELGVKDSKKLSDKKREELAEKIKK---ISYSE--VSPYPIGYI--SPKE 73 (198)
T ss_dssp EEEEEESSS-SBS-EEEEEEEEEGGGHHHHHHTTGCCGTTS-HHHHHHHHHHHHE---EEEEE--EECHHHHHH--HTTT
T ss_pred CCCCCCCCCCcccchheEEEEeccccHHHHHhhccCccccCCHHHHHHHHHHHHh---hchhh--hhhcccccc--chHH
Confidence 7999999999999999999999999999999999999999999999999999992 33443 344444321 1256
Q ss_pred chHHHHHHHHHHHHHHHHHhcCCCCCEEEECCCCChHHHHHHhhccCCCcceEEeecCccchhhHHHHhHHhHHHHHHHH
Q 027718 97 INLNEISHDSAIGLITRVLNIGILLTEVYLDTVGDAEKYQAKLSQRFPSIKFVVSKKADSLYPVVSGASIVAKVTRDRTL 176 (219)
Q Consensus 97 ~Nin~~~~~~~~~li~~~l~~~~~~~~i~iD~~~~~~~~~~~L~~~~~~~~~~~~~KaD~~~~sVAAASIlAKv~RD~~m 176 (219)
+|+|.+++..+..+++.+.+.+..++.++||+|+.++++...+++.++ .++++++|||++|++|||||||||++||+.|
T Consensus 74 in~n~i~~~~~~~~~~~l~~~~~~~~~v~iD~~~~~~~~~~~~~~~~~-~~~~~~~Kad~~~~~VAAASIvAK~~rd~~~ 152 (198)
T PF01351_consen 74 INLNNILAALHNAMIRALLKLGVQPDEVLIDQFGSPEKYYNKLEKIFK-IKVVFEPKADSKYPSVAAASIVAKVTRDEMI 152 (198)
T ss_dssp SCHHHHHHHHHHHHHHHHHHTTSEESEEEEEESSSHHHHHHHHHHHST-SEEEEETTHHHCSHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHhccCCceeecchhhcchhcccchheecC-cceeeecccchhhHHHHHHHHHHHHHHHHHH
Confidence 888888888888888887776667789999999999888888888777 7889999999999999999999999999555
Q ss_pred HHhhHhcccccccCCCccccCCchhhhhhhhh
Q 027718 177 RGWIFEETAENMHRNFGSGYPGGARCLKLSIV 208 (219)
Q Consensus 177 ~~l~~~~p~y~~~~~~GsGYpsd~~t~~~~~~ 208 (219)
+. .+.+|.|+| ++|+|||+|+||++|.+.
T Consensus 153 ~~-~~~~~~~~~--~~gsGy~s~~~~~~~~~~ 181 (198)
T PF01351_consen 153 EL-LSKYPGYGF--PKGSGYPSDPHTRAILKK 181 (198)
T ss_dssp HH-HHHHHTS-H--CCTSSSTTSHHHHHHHHH
T ss_pred HH-HHhCcCCCC--ccCCCCChHHHHHHHHHh
Confidence 55 445666665 678999999999999764
No 15
>PRK13926 ribonuclease HII; Provisional
Probab=100.00 E-value=1.8e-47 Score=323.71 Aligned_cols=163 Identities=30% Similarity=0.448 Sum_probs=138.2
Q ss_pred CcEeeeecCCcCCcccceeeEEEEcccccchhhhccCcCCCCCCCHHHHHHHHHHhhhcCcccEEEEEEChhhHhHHhhh
Q 027718 14 PCIMGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLKVNDSVGWAVDIIDPRELSAKMLN 93 (219)
Q Consensus 14 ~~~iGiDEaGrG~~~GPlvvaav~~~~~~~~~l~~~gv~DSK~Ls~~~r~~l~~~I~~~~~~~~~v~~i~p~~id~~~~~ 93 (219)
..++|||||||||+|||||||||+++... ++++|||+||+++|++|+++|++. ...|++.+++|++||+
T Consensus 22 ~~i~GiDEAGRG~~~GPlVvaav~~~~~~------~~~~DSK~Ls~~~R~~L~~~I~~~-~~~~~i~~isp~~Id~---- 90 (207)
T PRK13926 22 LRVAGVDEAGRGAWAGPVVVAAVILPPGE------YPFRDSKTLSPAAREALAEEVRRV-ALAWAVGHAEAAEIDR---- 90 (207)
T ss_pred cEEEeecCcCCCCccccceEEEEEECccC------CCccccccCCHHHHHHHHHHHHHh-CceEEEEEeCHHHHhH----
Confidence 57999999999999999999999998753 479999999999999999999975 5689999999999964
Q ss_pred hhhchHHHHHHHHHHHHHHHHHhcCCCCCEEEECCCCChHHHHHHhhccCCCcceEEeecCccchhhHHHHhHHhHHHHH
Q 027718 94 KNKINLNEISHDSAIGLITRVLNIGILLTEVYLDTVGDAEKYQAKLSQRFPSIKFVVSKKADSLYPVVSGASIVAKVTRD 173 (219)
Q Consensus 94 ~~~~Nin~~~~~~~~~li~~~l~~~~~~~~i~iD~~~~~~~~~~~L~~~~~~~~~~~~~KaD~~~~sVAAASIlAKv~RD 173 (219)
.|||.++++++.++++++ ...++.+++|... +. ...++++++|||++|++||||||||||+||
T Consensus 91 ---~ni~~a~~~a~~~~l~~l---~~~~~~v~~D~~~--------~~---~~~~~~~~~KgD~~~~~VaAASIvAKv~RD 153 (207)
T PRK13926 91 ---LNVLKATHLAAARALARL---AVAPEALVTDYLR--------LP---TPLPLLAPPKADALSPTVAAASLLAKTERD 153 (207)
T ss_pred ---HHHHHHHHHHHHHHHHhc---CCCCCEEEECccc--------CC---CCCCeEEEecCccccHHHHHHHHHHHHHHH
Confidence 689999999988888654 2346789999531 11 124577889999999999999999999999
Q ss_pred HHHHHhhHhcccccccCCCccccCCchhhhhhhh
Q 027718 174 RTLRGWIFEETAENMHRNFGSGYPGGARCLKLSI 207 (219)
Q Consensus 174 ~~m~~l~~~~p~y~~~~~~GsGYpsd~~t~~~~~ 207 (219)
++|++|+++||+|+|..| +|||+..| ++|.+
T Consensus 154 ~~m~~l~~~~~~yg~~~~--kGY~t~~h-~~~l~ 184 (207)
T PRK13926 154 RLMRELDARYPGYGFARH--KGYGTPAH-REALA 184 (207)
T ss_pred HHHHHHHHhCccCCCcCC--CCCCCHHH-HHHHH
Confidence 999999999999999777 89995554 55543
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=1.4e-45 Score=325.66 Aligned_cols=179 Identities=25% Similarity=0.312 Sum_probs=152.7
Q ss_pred CcEeeeecCCcCCcccceeeEEEEcccccchhhhccCcCCCCCCCHHHHHHHHHHhhhcCcccEEEEEEChhhHhHHhhh
Q 027718 14 PCIMGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLKVNDSVGWAVDIIDPRELSAKMLN 93 (219)
Q Consensus 14 ~~~iGiDEaGrG~~~GPlvvaav~~~~~~~~~l~~~gv~DSK~Ls~~~r~~l~~~I~~~~~~~~~v~~i~p~~id~~~~~ 93 (219)
..+||||||||||+|||||||||+++.+....|+.+||+|||+||+++|++|+++|++. +.|++.+++|++||.++.
T Consensus 81 ~~viGiDEaGrG~~fGPlvvaav~v~~~~~~~L~~lGv~DSK~Ls~~kr~~la~~I~~~--~~~~i~~l~p~~~n~~~~- 157 (284)
T TIGR00716 81 RSVIGCDESGKGDIFGPLVLCCVYIPEENYLKVSSLNPRDSKRLSDKRIERLALNLKPL--VKAYCYELKPEKYNKLYR- 157 (284)
T ss_pred ceEEeecCCCCCCcccceEEEEEEEChhhhhhhhhcCCCCcccCCHHHHHHHHHHHHHh--CCEEEEEeCHHHhcHHHH-
Confidence 34999999999999999999999999887788889999999999999999999999984 579999999999997653
Q ss_pred hhhchHHHHHHHHHHHHHHHHHhcCCCCCEEEECCCCChHHHHHHhhcc-CCCcceEEeecCccchhhHHHHhHHhHHHH
Q 027718 94 KNKINLNEISHDSAIGLITRVLNIGILLTEVYLDTVGDAEKYQAKLSQR-FPSIKFVVSKKADSLYPVVSGASIVAKVTR 172 (219)
Q Consensus 94 ~~~~Nin~~~~~~~~~li~~~l~~~~~~~~i~iD~~~~~~~~~~~L~~~-~~~~~~~~~~KaD~~~~sVAAASIlAKv~R 172 (219)
...|+|.++.+.|.++|.+++......+.|+||+|+.++.|.+++... ++..++++++|||+ |++|||||||| |
T Consensus 158 -~~~nln~l~a~~h~~aI~~l~~~~~~~~~i~ID~f~~~~~y~~~l~~~~~~~~~~~~~~KaE~-~~aVAAASIiA---R 232 (284)
T TIGR00716 158 -KFRNLNKMMAHFHKLLIERLLKEECGVSEVVVDQFAPSNPFFNHLKGRDIVGEDVIFETEAER-NLAVAAASIFA---R 232 (284)
T ss_pred -HHHHHHHHHHHHHHHHHHHHhhCcCCCcEEEECCCCCchHhhhhcccccccCCceeeeccccc-chhhhHHHHHH---H
Confidence 357999999999999998886533233579999999888777666542 34567888999998 99999999999 9
Q ss_pred HHHHHHhhHhcccccccCCCccccCCchhh
Q 027718 173 DRTLRGWIFEETAENMHRNFGSGYPGGARC 202 (219)
Q Consensus 173 D~~m~~l~~~~p~y~~~~~~GsGYpsd~~t 202 (219)
|++|++|++++|+|+|..++ ||++..+.
T Consensus 233 ~~~l~~l~~l~~~yg~~~pk--Ga~~~v~~ 260 (284)
T TIGR00716 233 YKFLQSLKELERELGIKLPK--GASKEVKE 260 (284)
T ss_pred HHHHHHHHHhCcccCCcCCC--CCChHHHH
Confidence 99999999999999999885 55544433
No 17
>COG1039 RnhC Ribonuclease HIII [DNA replication, recombination, and repair]
Probab=100.00 E-value=8.7e-42 Score=296.92 Aligned_cols=185 Identities=23% Similarity=0.251 Sum_probs=169.1
Q ss_pred CcEeeeecCCcCCcccceeeEEEEcccccchhhhccCcCCCCCCCHHHHHHHHHHhhhcCcccEEEEEEChhhHhHHhhh
Q 027718 14 PCIMGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLKVNDSVGWAVDIIDPRELSAKMLN 93 (219)
Q Consensus 14 ~~~iGiDEaGrG~~~GPlvvaav~~~~~~~~~l~~~gv~DSK~Ls~~~r~~l~~~I~~~~~~~~~v~~i~p~~id~~~~~ 93 (219)
..+||+||+|+||+||||+||||++++++++.|.++||+|||+|||.++.+|++.|++ .+.+.+..++|++||+++.
T Consensus 83 ~~~IGsDEvG~GDyFGpl~v~av~v~~e~~~~L~~lgV~DSKkL~D~kI~~la~~ik~--~i~~~~l~l~p~kYNel~~- 159 (297)
T COG1039 83 KNLIGSDEVGKGDYFGPLVVCAVYVSKENLPKLKELGVKDSKKLSDKKIQQLAPIIKP--LIPHSVLTLDPKKYNELYK- 159 (297)
T ss_pred ccccCCCCCCCCCccCCceEEEEEcCHHHHHHHHhcCCcccccCCHHHHHHHHHHHHH--hcCceEEEEChHHHHHHHH-
Confidence 5799999999999999999999999999999999999999999999999999999998 4899999999999999885
Q ss_pred hhhchHHHHHHHHHHHHHHHHHh-cCCCCCEEEECCCCChHHHHHHhhcc--CCCcceEEeecCccchhhHHHHhHHhHH
Q 027718 94 KNKINLNEISHDSAIGLITRVLN-IGILLTEVYLDTVGDAEKYQAKLSQR--FPSIKFVVSKKADSLYPVVSGASIVAKV 170 (219)
Q Consensus 94 ~~~~Nin~~~~~~~~~li~~~l~-~~~~~~~i~iD~~~~~~~~~~~L~~~--~~~~~~~~~~KaD~~~~sVAAASIlAKv 170 (219)
+..|.|.+..+.|.++|++++. .+.+++.|+||+|.+.+.|.+||++. .+..++.+.+|||++|++||||||+|
T Consensus 160 -k~~N~n~mkt~lH~~ai~~ll~~~~~~~~~ivIDqFa~~~~~~~yl~k~~~~~~~p~~f~~kaEs~~laVAvASIiA-- 236 (297)
T COG1039 160 -KFNNANSMKTFLHNQAIQNLLPQKGAQPEFIVIDQFASSENYKNYLQKETNKFSEPVLFLTKAESKSLAVAVASIIA-- 236 (297)
T ss_pred -hhhhHHHHHHHHHHHHHHHHHHhccCCCeEEEeccccchhHHHHHHHhhccCCCCceeeeecccccchhHHHHHHHH--
Confidence 5689999988889999999885 66778999999999999999999876 23556778999999999999999999
Q ss_pred HHHHHHHHhhHhcccccccCCCccccCCchhhhhh
Q 027718 171 TRDRTLRGWIFEETAENMHRNFGSGYPGGARCLKL 205 (219)
Q Consensus 171 ~RD~~m~~l~~~~p~y~~~~~~GsGYpsd~~t~~~ 205 (219)
||.|+..|+++..+|++..++|+|-.+|.-.+++
T Consensus 237 -R~~Fl~~~~~l~~~~gv~LPkGAg~~V~~~a~~i 270 (297)
T COG1039 237 -RYAFLQSLKQLSRQYGVQLPKGAGPAVDQAAAEI 270 (297)
T ss_pred -HHHHHHHHHHHHHHhCCcCCCCCchhHHHHHHHH
Confidence 9999999999999999999999997777766554
No 18
>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=48.08 E-value=25 Score=32.46 Aligned_cols=34 Identities=21% Similarity=0.297 Sum_probs=22.4
Q ss_pred CCCCHHHHHHHHHHhhhcCcccEEEEEEChhhHhHHh
Q 027718 55 KTLKEEKREELFEDLKVNDSVGWAVDIIDPRELSAKM 91 (219)
Q Consensus 55 K~Ls~~~r~~l~~~I~~~~~~~~~v~~i~p~~id~~~ 91 (219)
|.|+++++.+|..++.+ +... . ..++|++||+.+
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 34556666666666665 2222 2 789999999876
No 19
>PRK05473 hypothetical protein; Provisional
Probab=45.64 E-value=22 Score=26.23 Aligned_cols=22 Identities=18% Similarity=0.291 Sum_probs=18.7
Q ss_pred HHhHHhHHHHHHHHHHhhHhcc
Q 027718 163 GASIVAKVTRDRTLRGWIFEET 184 (219)
Q Consensus 163 AASIlAKv~RD~~m~~l~~~~p 184 (219)
|=|+|-|+.||++++++-+.|-
T Consensus 60 AR~lIrkiERDEilEeLv~~Yl 81 (86)
T PRK05473 60 ARNLIRKLERDEILEELVKSYL 81 (86)
T ss_pred HHHHHHHHhHHHHHHHHHHHHH
Confidence 4588999999999999877664
No 20
>PRK12362 germination protease; Provisional
Probab=43.86 E-value=34 Score=31.19 Aligned_cols=34 Identities=26% Similarity=0.546 Sum_probs=26.5
Q ss_pred CCCCHHHHHHHHHHhhhcCcccEEEEEEChhhHhHHh
Q 027718 55 KTLKEEKREELFEDLKVNDSVGWAVDIIDPRELSAKM 91 (219)
Q Consensus 55 K~Ls~~~r~~l~~~I~~~~~~~~~v~~i~p~~id~~~ 91 (219)
|.|+++.+.+|.+++.+ +... -..++|++||+.+
T Consensus 264 ~~~~~~ek~~li~evl~-p~~~--~l~VTPKeID~~i 297 (318)
T PRK12362 264 KSLNQEEKQQLIKEVLS-PYVG--NLIVTPKEIDELI 297 (318)
T ss_pred hccCHHHHHHHHHHHhC-ccCC--cceECcHhHHHHH
Confidence 56889999999888887 2222 2789999999876
No 21
>PHA03297 envelope glycoprotein L; Provisional
Probab=38.27 E-value=15 Score=30.06 Aligned_cols=10 Identities=30% Similarity=0.534 Sum_probs=8.5
Q ss_pred cCCcccceee
Q 027718 24 RGPVLGPMVY 33 (219)
Q Consensus 24 rG~~~GPlvv 33 (219)
-||++||.+.
T Consensus 148 lGCv~Gpffl 157 (185)
T PHA03297 148 LGCFTGPFFL 157 (185)
T ss_pred CCceecceec
Confidence 5999999885
No 22
>PF06135 DUF965: Bacterial protein of unknown function (DUF965); InterPro: IPR009309 This family consists of several hypothetical bacterial proteins. The function of the family is unknown.
Probab=34.79 E-value=41 Score=24.41 Aligned_cols=21 Identities=19% Similarity=0.271 Sum_probs=17.9
Q ss_pred HHhHHhHHHHHHHHHHhhHhc
Q 027718 163 GASIVAKVTRDRTLRGWIFEE 183 (219)
Q Consensus 163 AASIlAKv~RD~~m~~l~~~~ 183 (219)
|=|+|-|+.||.+++++-+.|
T Consensus 57 AR~lIr~~eRDellEeLv~~Y 77 (79)
T PF06135_consen 57 ARNLIRKIERDELLEELVRFY 77 (79)
T ss_pred HHHHHHHHhHHHHHHHHHHHH
Confidence 568899999999999986655
No 23
>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=29.14 E-value=25 Score=26.21 Aligned_cols=20 Identities=35% Similarity=0.478 Sum_probs=17.1
Q ss_pred hhHHHHhHHhHHHHHHHHHH
Q 027718 159 PVVSGASIVAKVTRDRTLRG 178 (219)
Q Consensus 159 ~sVAAASIlAKv~RD~~m~~ 178 (219)
-.||-||||=|.-||.+++.
T Consensus 10 eIia~aSiLIKfg~ddIl~~ 29 (91)
T PF09010_consen 10 EIIAVASILIKFGRDDILEN 29 (91)
T ss_dssp HHHHHHHHHHHTTTHHHHTS
T ss_pred HHHHHHHHHHHcChHHHHHh
Confidence 46899999999999988765
No 24
>PF12686 DUF3800: Protein of unknown function (DUF3800); InterPro: IPR024524 This family of proteins is functionally uncharacterised. Some family members possess a DE motif at their N terminus and a QXXD motif at their C terminus that may be functionally important.
Probab=27.70 E-value=3.2e+02 Score=21.86 Aligned_cols=162 Identities=18% Similarity=0.128 Sum_probs=76.2
Q ss_pred EeeeecCCcCCc-----ccce-eeEEEEcccccchhh----h----ccCc------------------CCCCCCCHHHH-
Q 027718 16 IMGIDEAGRGPV-----LGPM-VYGCLYCPCSYQQTL----A----TLNF------------------ADSKTLKEEKR- 62 (219)
Q Consensus 16 ~iGiDEaGrG~~-----~GPl-vvaav~~~~~~~~~l----~----~~gv------------------~DSK~Ls~~~r- 62 (219)
++.+||+|.-.. -.|. |+|+++++.+....+ . ..+. .+-..++..+|
T Consensus 1 ~iyiDESG~~~~~~~~~~~~~fvl~gv~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lh~~~i~~~~~~~~~~~~~~~~ 80 (235)
T PF12686_consen 1 IIYIDESGNTGPNYSDKNSPYFVLGGVIIEDEDWKKIINEIRSLKKKYGFKEEVEKSELHASDISNGKKDFSKLSKDERQ 80 (235)
T ss_pred CEEEeCCCCCCCCcCCCCCCEEEEEEEEEcHHHHHHHHHHHHHHHHHhCccccchhhhhhHHHhhhcccccccCCHHHHH
Confidence 478999996544 3454 567788876543111 1 1111 12223444455
Q ss_pred ---HHHHHHhhhcCcccEEEEEEChhhHhHHhhhh-hhchHHHHHHHHHHHHHHHHHh---cCCCCCEEEECCCCCh--H
Q 027718 63 ---EELFEDLKVNDSVGWAVDIIDPRELSAKMLNK-NKINLNEISHDSAIGLITRVLN---IGILLTEVYLDTVGDA--E 133 (219)
Q Consensus 63 ---~~l~~~I~~~~~~~~~v~~i~p~~id~~~~~~-~~~Nin~~~~~~~~~li~~~l~---~~~~~~~i~iD~~~~~--~ 133 (219)
..++..|.+.....+.+.++....++...... .....+.........+++++.. .....-.|++|..... .
T Consensus 81 ~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~y~~~~~~ll~~~~~~~~~~~~~~~iv~D~~~~~~~~ 160 (235)
T PF12686_consen 81 EFFKDLFDIISELKFIIFIAVIDDKKLYNRSSLDNNKPRDPNKFYNLALRFLLERINMYLQRPNENIIIVIDNGDRKKDN 160 (235)
T ss_pred HHHHHHHHHHHhCCCceEEEEEEeccccchhhhcccccchhHHHHHHHHHHHHHHHHHhhcCCCceEEEEEeCCCchHHH
Confidence 67777777643244566666666665432211 1112222233333444555441 1223357889932221 2
Q ss_pred HHHHHhhc----cCC----CcceEEeecCccch-hhHHHHhHHhHHHHHHHHH
Q 027718 134 KYQAKLSQ----RFP----SIKFVVSKKADSLY-PVVSGASIVAKVTRDRTLR 177 (219)
Q Consensus 134 ~~~~~L~~----~~~----~~~~~~~~KaD~~~-~sVAAASIlAKv~RD~~m~ 177 (219)
.+..++.. ... ...+....-.|++. +.+=+|=++|=..|-.+..
T Consensus 161 ~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~S~~s~~lQiAD~ia~~i~r~~~~ 213 (235)
T PF12686_consen 161 KLKEYLRKQYSKGSKRDKLKNIIEEIFFVDSKDSPGLQIADLIAGAIRRYLEK 213 (235)
T ss_pred HHHHHHHHhcccccccccccccccceeecCCCCCHhHHHHHHHHHHHHHHHHh
Confidence 23333311 000 00111122333333 7788888888666655543
No 25
>KOG0179 consensus 20S proteasome, regulatory subunit beta type PSMB1/PRE7 [Posttranslational modification, protein turnover, chaperones]
Probab=25.20 E-value=30 Score=29.81 Aligned_cols=16 Identities=44% Similarity=0.812 Sum_probs=13.3
Q ss_pred CcEeeeecCCcCCccc
Q 027718 14 PCIMGIDEAGRGPVLG 29 (219)
Q Consensus 14 ~~~iGiDEaGrG~~~G 29 (219)
..+.|+||=|||+++-
T Consensus 128 ~ilaGiDeeGKG~VyS 143 (235)
T KOG0179|consen 128 NILAGIDEEGKGAVYS 143 (235)
T ss_pred eeeecccccCceeEEe
Confidence 4578999999999863
No 26
>PRK02858 germination protease; Provisional
Probab=24.99 E-value=81 Score=29.31 Aligned_cols=34 Identities=26% Similarity=0.478 Sum_probs=22.2
Q ss_pred CCCCHHHHHHHHHHhhhcCcccEEEEEEChhhHhHHh
Q 027718 55 KTLKEEKREELFEDLKVNDSVGWAVDIIDPRELSAKM 91 (219)
Q Consensus 55 K~Ls~~~r~~l~~~I~~~~~~~~~v~~i~p~~id~~~ 91 (219)
+.|+++.+.+|..++.+ + .+ .=..++|++||+.+
T Consensus 307 ~~~~~~Ek~~li~Evl~-P-~g-~~L~VTPKeID~~I 340 (369)
T PRK02858 307 GTLEEEEKRQLIYEVLA-P-LG-HNLMVTPKEVDAFI 340 (369)
T ss_pred ccCCHHHHHHHHHHHhc-c-cC-CceeECcHhHHHHH
Confidence 34556666676666665 2 22 11579999999876
No 27
>KOG3495 consensus Mitochondrial F1F0-ATP synthase, subunit epsilon/ATP15 [Energy production and conversion]
Probab=23.55 E-value=1e+02 Score=20.44 Aligned_cols=20 Identities=20% Similarity=0.159 Sum_probs=16.5
Q ss_pred HHHHhHHhHHHHHHHHHHhh
Q 027718 161 VSGASIVAKVTRDRTLRGWI 180 (219)
Q Consensus 161 VAAASIlAKv~RD~~m~~l~ 180 (219)
|.=++|-|++.|+.++.++-
T Consensus 12 i~Ys~I~A~vvR~~LK~e~k 31 (50)
T KOG3495|consen 12 IRYSQIAAQVVRQALKTELK 31 (50)
T ss_pred HHHHHHHHHHHHHHHhHHHH
Confidence 45578999999999998863
Done!