Query 023038
Match_columns 288
No_of_seqs 256 out of 1499
Neff 5.9
Searched_HMMs 46136
Date Fri Mar 29 08:00:20 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/023038.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/023038hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2299 Ribonuclease HI [Repli 100.0 1.3E-80 2.9E-85 559.5 16.0 268 5-286 18-300 (301)
2 cd07181 RNaseH_typeII_eukaryot 100.0 7.5E-63 1.6E-67 443.7 19.0 206 17-222 1-216 (216)
3 cd07180 RNaseH_typeII_Archaea_ 100.0 1.8E-55 3.9E-60 392.5 18.0 192 17-221 1-203 (204)
4 COG0164 RnhB Ribonuclease HII 100.0 2.6E-55 5.6E-60 387.8 16.1 185 15-223 1-189 (199)
5 PRK14551 rnhB ribonuclease HII 100.0 7.8E-55 1.7E-59 390.7 18.6 192 15-224 1-203 (212)
6 PRK14550 rnhB ribonuclease HII 100.0 3.1E-55 6.8E-60 390.9 13.4 190 15-223 1-193 (204)
7 TIGR00729 ribonuclease H, mamm 100.0 2.7E-54 5.8E-59 385.6 19.2 193 16-222 1-205 (206)
8 cd06266 RNaseH_typeII Ribonucl 100.0 1.5E-54 3.2E-59 383.0 15.3 188 17-218 1-192 (193)
9 cd07182 RNaseH_typeII_bacteria 100.0 1.8E-54 3.9E-59 379.3 15.2 175 17-218 1-178 (179)
10 PRK13925 rnhB ribonuclease HII 100.0 2.4E-54 5.2E-59 383.8 16.0 186 14-221 8-196 (198)
11 PRK00015 rnhB ribonuclease HII 100.0 3.7E-54 8.1E-59 382.4 15.2 177 14-218 18-197 (197)
12 PRK13926 ribonuclease HII; Pro 100.0 5.2E-53 1.1E-57 377.4 17.8 180 14-223 22-204 (207)
13 cd06590 RNaseH_typeII_bacteria 100.0 3.6E-53 7.7E-58 378.6 16.0 198 17-222 1-208 (208)
14 PF01351 RNase_HII: Ribonuclea 100.0 5.7E-50 1.2E-54 354.9 14.0 191 17-218 1-198 (198)
15 PRK00996 ribonuclease HIII; Pr 100.0 3.1E-48 6.8E-53 364.6 18.5 204 13-223 86-300 (304)
16 TIGR00716 rnhC ribonuclease HI 100.0 5.5E-43 1.2E-47 326.3 15.6 190 14-212 81-276 (284)
17 COG1039 RnhC Ribonuclease HIII 100.0 1.6E-35 3.4E-40 272.5 13.6 179 14-199 83-264 (297)
18 PF12686 DUF3800: Protein of u 71.6 64 0.0014 27.6 11.3 161 16-177 1-213 (235)
19 TIGR01441 GPR GPR endopeptidas 37.8 34 0.00075 33.5 3.4 33 56-91 297-329 (358)
20 KOG3495 Mitochondrial F1F0-ATP 37.7 34 0.00074 24.2 2.5 20 161-180 12-31 (50)
21 PRK12362 germination protease; 34.1 45 0.00098 32.2 3.5 34 55-91 264-297 (318)
22 PF09010 AsiA: Anti-Sigma Fact 32.9 18 0.00039 28.7 0.5 20 159-178 10-29 (91)
23 PRK05473 hypothetical protein; 31.7 48 0.001 26.0 2.7 22 163-184 60-81 (86)
24 KOG0189 Phosphoadenosine phosp 29.5 3.3E+02 0.0072 25.2 8.0 82 58-150 18-104 (261)
25 KOG3840 Uncharaterized conserv 26.5 33 0.00071 33.3 1.2 23 194-217 299-334 (438)
26 PF06135 DUF965: Bacterial pro 21.7 94 0.002 24.1 2.7 21 163-183 57-77 (79)
27 COG3817 Predicted membrane pro 20.7 26 0.00056 33.1 -0.7 48 25-72 49-96 (313)
No 1
>KOG2299 consensus Ribonuclease HI [Replication, recombination and repair]
Probab=100.00 E-value=1.3e-80 Score=559.50 Aligned_cols=268 Identities=53% Similarity=0.900 Sum_probs=239.2
Q ss_pred CCcCCcCCC-CceecccccCcCCcccceeeEEEEecccccccccccCcCCCCCCCHHHHHHHHHHhhhc----CcccEEE
Q 023038 5 AALPKWASN-PCIMGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLKVN----DSVGWAV 79 (288)
Q Consensus 5 ~~~p~~~~~-~~viGiDEAGRGpv~GPmVvaav~~~~~~~~~L~~~gv~DSK~Ls~~kRe~L~~~I~~~----~~~~~~v 79 (288)
|++|+.|.+ ||++||||||||||+||||||++|||.+....|..+|++|||+|++.+|++||++|++. ..++|++
T Consensus 18 s~vp~~~~~~PcvlGIDEAGRGPVLGPMVYa~~ycP~~~~~~l~~lgfaDSK~L~e~kRe~lf~~i~~d~~~~~~vgwA~ 97 (301)
T KOG2299|consen 18 SPVPDEQKSEPCVLGIDEAGRGPVLGPMVYAAAYCPLDYLEDLENLGFADSKTLTEAKREELFNKIKEDEELTSNVGWAT 97 (301)
T ss_pred cCCcccccCCceEeeccccCCCCcccceeeEEEeccchhhhhhhhcCccchhhccHHHHHHHHHHHhhhhhhhhceeeEe
Confidence 688999987 99999999999999999999999999999889999999999999999999999999753 3589999
Q ss_pred EEECHhhHhHHhhccccchHHHHHHHHHHHHHHHHHccCCCcceEEECCCCChHHHHHHhhccCCCcceEEeecCCccCc
Q 023038 80 DIIDPRELSAKMLNKNKINLNEISHDSAIGLITRVLNIGILLTEVYLDTVGDAEKYQAKLSQRFPSIKFVVSKKADSLYP 159 (288)
Q Consensus 80 ~~isp~eId~~~~~~~~~NlN~l~~~~~~~li~~~l~~~~~~~~v~VD~~g~~~~y~~~L~~~~p~i~v~~~~KADs~~~ 159 (288)
.+|+|++|++.|++++++|||+++|++++.||+.+++.|+++.+|||||+|+|.+||.+|++.||+++++|.+|||++||
T Consensus 98 ~~isP~~IS~~Ml~r~kynLNevshdsam~LI~~v~~~gvnvteiyVDTVGpp~~Yq~kLek~FP~~k~tV~kKADSlfp 177 (301)
T KOG2299|consen 98 DCISPREISASMLRRNKYNLNEVSHDSAMGLIDEVLDQGVNVTEIYVDTVGPPAKYQEKLEKRFPGIKFTVTKKADSLFP 177 (301)
T ss_pred eecCHHHHHHHHHHHhcCCchhhhhHHHHHHHHHHHHhCCceEEEEEecCCChHHHHHHHHhhCCCeEEEEeeccccccc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred chhhhhHHHHHHHHHHHHhhhhhhcccccCCCCcccCccc---------ccccccCCCcccccccHhHHHhh-hccceeE
Q 023038 160 VVSGASIVAKVTRDRTLRGWIFEETAENMHRNFGSGYPGD---------HKHIIFGFPSLVRFSWGTCTSHF-KDIVEVL 229 (288)
Q Consensus 160 ~VAAASIiAKV~RD~~m~~~~~~~~~~~~~~~~GsGYPsd---------h~~~~~G~p~~~R~Sw~t~~~~l-~~~~~~~ 229 (288)
+||||||||||+||+.+++|++.+.....+.++|||||+| |++.+||||++|||||+|++++| +.+.++.
T Consensus 178 iVS~ASI~AKVtRD~alk~w~~~E~~~~~d~~~GSGYP~DP~T~~wLk~~v~~VFGfp~lVRfSW~Ta~t~L~~~~~~~~ 257 (301)
T KOG2299|consen 178 IVSAASIVAKVTRDRALKEWQFEEKLSDPDEDLGSGYPSDPETKAWLKENVDSVFGFPSLVRFSWKTAKTLLEDRSEPLK 257 (301)
T ss_pred chhhhhhhhhhhhccccceeeeeeecccCCccccCCCCCChhHHHHHHhcccccccCccceeeeHHHHHHHHhcccccce
Confidence 9999999999999999999999999888899999999999 88899999999999999999999 5799999
Q ss_pred eecCcccccccccccccccceecccccCcccCcchhhhccCccccchhhhccccccc
Q 023038 230 WESDEMDEDVSSRRSGKRQLKLSDIGFSSSKRRSEEIESSGKGRCKFLEARKLEQLT 286 (288)
Q Consensus 230 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~~r~l~~~~ 286 (288)
|+++..+.+... . .++++|..+... +.. ..|..+| +|+|+++.
T Consensus 258 ~e~~~~e~~~~~--~----~~~T~~~~~~~~--s~~-----~~r~~~~-~r~l~~~~ 300 (301)
T KOG2299|consen 258 WEESGFELDKTP--L----LKFTKKFKPNPA--SRS-----VPRSERF-ERHLENWY 300 (301)
T ss_pred eecccccccchH--H----HHHHHHhcCCCc--ccc-----cchhHHH-HHhhhhhc
Confidence 999876532211 1 367775222211 111 2344466 99999875
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=7.5e-63 Score=443.67 Aligned_cols=206 Identities=64% Similarity=1.063 Sum_probs=187.5
Q ss_pred ecccccCcCCcccceeeEEEEecccccccccccCcCCCCCCCHHHHHHHHHHhhhcC-cccEEEEEECHhhHhHHhhccc
Q 023038 17 MGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLKVND-SVGWAVDIIDPRELSAKMLNKN 95 (288)
Q Consensus 17 iGiDEAGRGpv~GPmVvaav~~~~~~~~~L~~~gv~DSK~Ls~~kRe~L~~~I~~~~-~~~~~v~~isp~eId~~~~~~~ 95 (288)
+|||||||||+|||||||||+++.+....|..+||+|||+||+++|++|++.|++.. ++.|.+.+++|++||+.|++..
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 699999999999999999999998766677778999999999999999999998742 5789999999999999876555
Q ss_pred cchHHHHHHHHHHHHHHHHHccCCCcceEEECCCCChHHHHHHhhccCCCcceEEeecCCccCcchhhhhHHHHHHHHHH
Q 023038 96 KINLNEISHDSAIGLITRVLNIGILLTEVYLDTVGDAEKYQAKLSQRFPSIKFVVSKKADSLYPVVSGASIVAKVTRDRT 175 (288)
Q Consensus 96 ~~NlN~l~~~~~~~li~~~l~~~~~~~~v~VD~~g~~~~y~~~L~~~~p~i~v~~~~KADs~~~~VAAASIiAKV~RD~~ 175 (288)
.+|||+++|+++..++++++..+..+..||||+++++++|..+|+..+|++++++++|||++|++||||||||||+||++
T Consensus 81 ~~nln~~~~~~~~~~i~~~~~~~~~~~~vliD~~~~~~~~~~~L~~~~~~~~~~~~~kaD~~~~~VAAASIvAKV~RD~~ 160 (216)
T cd07181 81 KYNLNEISHDAAIGLIKSVLDKGVNVTEVYVDTVGPPEKYQAKLKKLFPGIKFTVEKKADSLYPIVSAASIVAKVTRDRA 160 (216)
T ss_pred cccHHHHHHHHHHHHHHHHHcCCCCCCEEEECCCCChhHHHHhhhhcCCCCceEEeeCcccccHHHHHHHHHHHHHHHHH
Confidence 68999999999999998887777778899999999999999999877777788899999999999999999999999999
Q ss_pred HHhhhhhhcccccCCCCcccCccc---------ccccccCCCcccccccHhHHHhh
Q 023038 176 LRGWIFEETAENMHRNFGSGYPGD---------HKHIIFGFPSLVRFSWGTCTSHF 222 (288)
Q Consensus 176 m~~~~~~~~~~~~~~~~GsGYPsd---------h~~~~~G~p~~~R~Sw~t~~~~l 222 (288)
|++|+..+|.|++.+++||||||| ++...+|+|++||+||+|++++|
T Consensus 161 m~~l~~~~~~~~~~~~~gsGYpsd~~t~~~l~~~~~~~~~~~~~~R~sw~t~~~~l 216 (216)
T cd07181 161 LKNWQFDEYLIDPDGDFGSGYPSDPKTKKWLKKNVDPVFGFPSLVRFSWSTAKKLL 216 (216)
T ss_pred HHHHHhhCccccccCCCceECCCHHHHHHHHHhcCCCcCCCCCceEccccchHhcC
Confidence 999999999999999999999999 34446899999999999999875
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=1.8e-55 Score=392.48 Aligned_cols=192 Identities=38% Similarity=0.576 Sum_probs=168.3
Q ss_pred ecccccCcCCcccceeeEEEEecccccccccccCcCCCCCCCHHHHHHHHHHhhhcCcccEEEEEECHhhHhHHhhcccc
Q 023038 17 MGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLKVNDSVGWAVDIIDPRELSAKMLNKNK 96 (288)
Q Consensus 17 iGiDEAGRGpv~GPmVvaav~~~~~~~~~L~~~gv~DSK~Ls~~kRe~L~~~I~~~~~~~~~v~~isp~eId~~~~~~~~ 96 (288)
+|||||||||+|||||||||++|.+....|..+||+|||+||+++|++|+++|++. ++.|.+.+++|++||++| ..
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 69999999999999999999999887777888999999999999999999999974 578999999999999887 35
Q ss_pred chHHHHHHHHHHHHHHHHHccCCCcceEEECCC-CChHHHHHHhhccC-CCcceEEeecCCccCcchhhhhHHHHHHHHH
Q 023038 97 INLNEISHDSAIGLITRVLNIGILLTEVYLDTV-GDAEKYQAKLSQRF-PSIKFVVSKKADSLYPVVSGASIVAKVTRDR 174 (288)
Q Consensus 97 ~NlN~l~~~~~~~li~~~l~~~~~~~~v~VD~~-g~~~~y~~~L~~~~-p~i~v~~~~KADs~~~~VAAASIiAKV~RD~ 174 (288)
.|||++++.++.++|+.+. ..+..|+||++ +++++|.++|++.+ +++++++++|||++|++||||||||||+||+
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 7999999999999998765 34678999999 57788998887765 3567888999999999999999999999999
Q ss_pred HHHhhhhhhcccccCCCCcccCccc-----cccc----ccCCCcccccccHhHHHh
Q 023038 175 TLRGWIFEETAENMHRNFGSGYPGD-----HKHI----IFGFPSLVRFSWGTCTSH 221 (288)
Q Consensus 175 ~m~~~~~~~~~~~~~~~~GsGYPsd-----h~~~----~~G~p~~~R~Sw~t~~~~ 221 (288)
+|++|+..|+ +||+|||+| |+.. .+|+|++||+||+|++++
T Consensus 154 ~m~~l~~~~~------~~g~Gy~sd~~t~~~l~~~~~~~g~~~~~~R~sf~~~~~~ 203 (204)
T cd07180 154 EIEELKEEYG------DFGSGYPSDPRTIKFLRNYYREHGELPPIVRKSWKTVKRL 203 (204)
T ss_pred HHHHHHHhcc------cCCCcCCCCHHHHHHHHHHHHhhCCCChhheecccchhhc
Confidence 9999987764 678999998 3332 246899999999999864
No 4
>COG0164 RnhB Ribonuclease HII [DNA replication, recombination, and repair]
Probab=100.00 E-value=2.6e-55 Score=387.79 Aligned_cols=185 Identities=33% Similarity=0.465 Sum_probs=157.8
Q ss_pred ceecccccCcCCcccceeeEEEEecccccccccccCcCCCCCCCHHHHHHHHHHhhhcCcccEEEEEECHhhHhHHhhcc
Q 023038 15 CIMGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLKVNDSVGWAVDIIDPRELSAKMLNK 94 (288)
Q Consensus 15 ~viGiDEAGRGpv~GPmVvaav~~~~~~~~~L~~~gv~DSK~Ls~~kRe~L~~~I~~~~~~~~~v~~isp~eId~~~~~~ 94 (288)
.++||||||||||+||||+|||++|+.... ..+|++|||+||+++||+||++|+. .++.|.|.++++++||
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 478999999999999999999999987533 5689999999999999999999994 4789999999999995
Q ss_pred ccchHHHHHHHHHHHHHHHHHccCCCcceEEECCCCChHHHHHHhhccCCCcceEEeecCCccCcchhhhhHHHHHHHHH
Q 023038 95 NKINLNEISHDSAIGLITRVLNIGILLTEVYLDTVGDAEKYQAKLSQRFPSIKFVVSKKADSLYPVVSGASIVAKVTRDR 174 (288)
Q Consensus 95 ~~~NlN~l~~~~~~~li~~~l~~~~~~~~v~VD~~g~~~~y~~~L~~~~p~i~v~~~~KADs~~~~VAAASIiAKV~RD~ 174 (288)
++|||+++++++..++..+ ...+..||||+++-+. .|. .| .++++|||++|++||||||||||+||+
T Consensus 72 -~~ni~~a~~~am~~av~~l---~~~~~~vlvD~~~~~~----~l~--~~---~~a~~KgDa~~~~IaAASIvAKV~RDr 138 (199)
T COG0164 72 -ELNILEATKLAMRRAVAGL---SSQPDLVLVDGNDLPL----GLP--QP---AVAIIKGDAKSPSIAAASILAKVTRDR 138 (199)
T ss_pred -hhhHHHHHHHHHHHHHHhc---cccCCEEEEeCCCccc----cCC--CC---cceeeccchhhHHHHHHHHHHHHHHHH
Confidence 6899999998887666553 4455889999997321 121 12 277899999999999999999999999
Q ss_pred HHHhhhhhhcccccCCCCcccCccc-cccc--ccCCCc-ccccccHhHHHhhh
Q 023038 175 TLRGWIFEETAENMHRNFGSGYPGD-HKHI--IFGFPS-LVRFSWGTCTSHFK 223 (288)
Q Consensus 175 ~m~~~~~~~~~~~~~~~~GsGYPsd-h~~~--~~G~p~-~~R~Sw~t~~~~l~ 223 (288)
+|++++..||.|+|+ +||||||| |..+ .+|.++ +||+||+|+++++.
T Consensus 139 ~m~~l~~~yp~Y~~~--~~~GY~T~~h~~a~~~~~~~~~~hR~Sf~~vk~~~~ 189 (199)
T COG0164 139 LMEELAKEYPEYGFD--KGSGYPTDPHTEALLKKGGTPGIHRRSFAPVRRLLG 189 (199)
T ss_pred HHHHHHhhCcCcCcc--cCCCCCChHHHHHHHHhCCCCceeecccHHHHHhhh
Confidence 999999999999986 55999999 8777 366655 99999999999984
No 5
>PRK14551 rnhB ribonuclease HII; Provisional
Probab=100.00 E-value=7.8e-55 Score=390.73 Aligned_cols=192 Identities=31% Similarity=0.472 Sum_probs=163.1
Q ss_pred ceecccccCcCCcccceeeEEEEecccccccccccCcCCCCCCCHHHHHHHHHHhhhcCcccEEEEEECHhhHhHHhhcc
Q 023038 15 CIMGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLKVNDSVGWAVDIIDPRELSAKMLNK 94 (288)
Q Consensus 15 ~viGiDEAGRGpv~GPmVvaav~~~~~~~~~L~~~gv~DSK~Ls~~kRe~L~~~I~~~~~~~~~v~~isp~eId~~~~~~ 94 (288)
.++|||||||||||||||||||+++.+. + ..||+|||+||+++|++||++|++...+.|++.+++|++||+
T Consensus 1 ~~iGiDEaGRG~v~GPlVvaav~~~~~~---~-~~gv~DSK~Ls~~~R~~l~~~I~~~~~~~~~i~~isp~~Id~----- 71 (212)
T PRK14551 1 MRFGVDEAGKGPVLGSMFAAAVRADPAA---L-PDGIDDSKRLSPERREELAAELREDDAIAVGVAEIPPARIDD----- 71 (212)
T ss_pred CeeCccCCCCCCccccceEEEEEECccc---C-cCCCcCcccCCHHHHHHHHHHHHhccCceEEEEEeCHHHHCc-----
Confidence 3799999999999999999999999753 2 359999999999999999999987433689999999999985
Q ss_pred ccchHHHHHHHHHHHHHHHHHccCCCcceEEECCCC-ChHHHHHHhhccC-CCcceEEeecCCccCcchhhhhHHHHHHH
Q 023038 95 NKINLNEISHDSAIGLITRVLNIGILLTEVYLDTVG-DAEKYQAKLSQRF-PSIKFVVSKKADSLYPVVSGASIVAKVTR 172 (288)
Q Consensus 95 ~~~NlN~l~~~~~~~li~~~l~~~~~~~~v~VD~~g-~~~~y~~~L~~~~-p~i~v~~~~KADs~~~~VAAASIiAKV~R 172 (288)
..+|||.+++.+|.++|++++ ..+..||||++. ++++|+.+|.+.+ +++++++++|||++|++||||||||||+|
T Consensus 72 ~~~nln~~~~~a~~~ai~~l~---~~~~~v~iD~~~~~~~~~~~~l~~~~~~~~~~~~~~KaD~~~~~VAAASIlAKv~R 148 (212)
T PRK14551 72 PETDMNTLTVAAHAEALSGVA---TDGITGLCDAGDVDAGRFARRVADRVALDVSVSAEHGADEEDPLVGAASIVAKVAR 148 (212)
T ss_pred cccCHHHHHHHHHHHHHHhhc---cCCCEEEECCCCCchHHHHHhhhhccCCCCceEEEecccchhHHHHHHHHHHHHHH
Confidence 247999999999998888764 245789999985 6778888887765 35678889999999999999999999999
Q ss_pred HHHHHhhhhhhcccccCCCCcccCccc-----ccc-c--ccC-CCcccccccHhHHHhhhc
Q 023038 173 DRTLRGWIFEETAENMHRNFGSGYPGD-----HKH-I--IFG-FPSLVRFSWGTCTSHFKD 224 (288)
Q Consensus 173 D~~m~~~~~~~~~~~~~~~~GsGYPsd-----h~~-~--~~G-~p~~~R~Sw~t~~~~l~~ 224 (288)
|+.|++|+..|+ ++|+|||+| |+. . .|| +|++||+||+|+++++++
T Consensus 149 D~~m~~l~~~y~------~~GsGYpsd~~t~~~l~~~~~~~g~~p~~~R~Sw~~~~~~~~~ 203 (212)
T PRK14551 149 DAHVAALAAEYG------DVGSGYPSDPTTREFLREYVREHGELPACARRSWSTCDDVLAA 203 (212)
T ss_pred HHHHHHHHHHCC------CCCCcCCCcHHHHHHHHHHHHHhCCCchhhccCcHHHHHHHHH
Confidence 999999988775 678999998 532 2 356 555999999999999853
No 6
>PRK14550 rnhB ribonuclease HII; Provisional
Probab=100.00 E-value=3.1e-55 Score=390.88 Aligned_cols=190 Identities=22% Similarity=0.267 Sum_probs=159.9
Q ss_pred ceecccccCcCCcccceeeEEEEecccccccccccCcCCCCCCCHHHHHHHHHHhhhcCcccEEEEEECHhhHhHHhhcc
Q 023038 15 CIMGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLKVNDSVGWAVDIIDPRELSAKMLNK 94 (288)
Q Consensus 15 ~viGiDEAGRGpv~GPmVvaav~~~~~~~~~L~~~gv~DSK~Ls~~kRe~L~~~I~~~~~~~~~v~~isp~eId~~~~~~ 94 (288)
.++||||||||||+||||||||+++.+....+..+||+|||+||+++|++||++|++...+.|.+.+++|++||
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 47999999999999999999999998765566778999999999999999999998753478999999999996
Q ss_pred ccchHHHHHHHHHHHHHHHHHccCCCcceEEECCCCChHHHHHHhhccCCCcceEEeecCCccCcchhhhhHHHHHHHHH
Q 023038 95 NKINLNEISHDSAIGLITRVLNIGILLTEVYLDTVGDAEKYQAKLSQRFPSIKFVVSKKADSLYPVVSGASIVAKVTRDR 174 (288)
Q Consensus 95 ~~~NlN~l~~~~~~~li~~~l~~~~~~~~v~VD~~g~~~~y~~~L~~~~p~i~v~~~~KADs~~~~VAAASIiAKV~RD~ 174 (288)
++|||.++..++.+++.. +...++.++||++..+..+ ..+| .+.+++|||++|++||||||||||+||+
T Consensus 75 -~~ni~~a~~~am~~al~~---l~~~~~~vliDg~~~~~~~-----~~~~--~~~~~~KgD~~~~~VAAASIiAKV~RD~ 143 (204)
T PRK14550 75 -SLGLGACLKLAIQEILEN---GCSLANEIKIDGNTAFGLN-----KRYP--NIQTIIKGDETIAQIAMASVLAKAFKDR 143 (204)
T ss_pred -HHHHHHHHHHHHHHHHHh---CCCCCCEEEECCccCcccc-----ccCc--ceeEEEcccccchhHHHHHHHHHHHHHH
Confidence 469999887766655554 2345678999988543211 1123 3456789999999999999999999999
Q ss_pred HHHhhhhhhcccccCCCCcccCccc-cccc--ccCCCcccccccHhHHHhhh
Q 023038 175 TLRGWIFEETAENMHRNFGSGYPGD-HKHI--IFGFPSLVRFSWGTCTSHFK 223 (288)
Q Consensus 175 ~m~~~~~~~~~~~~~~~~GsGYPsd-h~~~--~~G~p~~~R~Sw~t~~~~l~ 223 (288)
+|++|+..||.|+|. +|+||||+ |+.+ .+|++|+||+||+|.+++|.
T Consensus 144 ~M~~l~~~~p~Ygf~--~~kGY~T~~h~~ai~~~G~~p~hR~Sf~t~~~~~~ 193 (204)
T PRK14550 144 EMLELHALFKEYGWD--KNCGYGTKQHIEAIIKLGATPFHRHSFTLKNRILN 193 (204)
T ss_pred HHHHHHHhCCCCCCc--CCCCCCCHHHHHHHHHhCcCHHHcCCcCCCCcccC
Confidence 999999999999987 45999998 8877 59999999999999998883
No 7
>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=2.7e-54 Score=385.56 Aligned_cols=193 Identities=38% Similarity=0.580 Sum_probs=161.9
Q ss_pred eecccccCcCCcccceeeEEEEecccccccccccCcCCCCCCCHHHHHHHHHHhhhcCcccEEEEEECHhhHhHHhhccc
Q 023038 16 IMGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLKVNDSVGWAVDIIDPRELSAKMLNKN 95 (288)
Q Consensus 16 viGiDEAGRGpv~GPmVvaav~~~~~~~~~L~~~gv~DSK~Ls~~kRe~L~~~I~~~~~~~~~v~~isp~eId~~~~~~~ 95 (288)
++|||||||||||||||||||+++......|..+||+|||+||+++|++|+++|++. .+.|.+.+++|++||+.+
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 589999999999999999877777665566778999999999999999999999874 578999999999999865
Q ss_pred cchHHHHHHHHHHHHHHHHHccCCCcceEEECCCCChHHHHH---HhhccCCCcceEEeecCCccCcchhhhhHHHHHHH
Q 023038 96 KINLNEISHDSAIGLITRVLNIGILLTEVYLDTVGDAEKYQA---KLSQRFPSIKFVVSKKADSLYPVVSGASIVAKVTR 172 (288)
Q Consensus 96 ~~NlN~l~~~~~~~li~~~l~~~~~~~~v~VD~~g~~~~y~~---~L~~~~p~i~v~~~~KADs~~~~VAAASIiAKV~R 172 (288)
..|||.++++++.++|+.+. ..+..||||+++.++.|.. .+...+|+.++++++|||++|++||||||||||+|
T Consensus 76 ~~nln~~~~~a~~~~i~~l~---~~~~~v~iD~~~~~~~~~~~~~~~~~~~~~~~~~~~~KaD~~~~~VAAASIlAKv~R 152 (206)
T TIGR00729 76 NINLNENEIEKFSKAAIILI---EKPSEVYVDSVDVNPKRFKREIKIKERIEGIKVIAEHKADAKYPVVSAASIIAKVER 152 (206)
T ss_pred HhhHHHHHHHHHHHHHHHHh---cCCcEEEEcCCCCcHHHHHHHHHHhccCCCCcEEEEeccccccchhhHHHHHHHHHH
Confidence 47999999999998887753 2457899999987655322 22235777888999999999999999999999999
Q ss_pred HHHHHhhhhhhcccccCCCCcccCccc-----cccc---ccC-CCcccccccHhHHHhh
Q 023038 173 DRTLRGWIFEETAENMHRNFGSGYPGD-----HKHI---IFG-FPSLVRFSWGTCTSHF 222 (288)
Q Consensus 173 D~~m~~~~~~~~~~~~~~~~GsGYPsd-----h~~~---~~G-~p~~~R~Sw~t~~~~l 222 (288)
|++|+.|+..|+. ||+|||+| |+.. .+| +|++||+||+|+++++
T Consensus 153 D~~m~~l~~~~~~------~GsGY~sd~~t~~~l~~~~~~~g~~~~~~R~sf~~~~~~~ 205 (206)
T TIGR00729 153 DREIESLKRKYGD------FGSGYPSDPRTREWLEEYFKSHGELPDIVRRTWKTVRKLL 205 (206)
T ss_pred HHHHHHHHHhcCC------CCCcCCCCHHHHHHHHHHHHhhCCCCcccccCcHHHHHhh
Confidence 9999999887653 68999998 4432 356 5679999999999875
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=1.5e-54 Score=383.03 Aligned_cols=188 Identities=38% Similarity=0.550 Sum_probs=167.5
Q ss_pred ecccccCcCCcccceeeEEEEecccccccccccCcCCCCCCCHHHHHHHHHHhhhcCcccEEEEEECHhhHhHHhhcccc
Q 023038 17 MGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLKVNDSVGWAVDIIDPRELSAKMLNKNK 96 (288)
Q Consensus 17 iGiDEAGRGpv~GPmVvaav~~~~~~~~~L~~~gv~DSK~Ls~~kRe~L~~~I~~~~~~~~~v~~isp~eId~~~~~~~~ 96 (288)
+|||||||||||||||||||+++.+..+.|..+||+|||+||+++|++|++.|++ ..+.|.+.+++|++||+
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 6999999999999999999999998888889999999999999999999999997 35889999999999975
Q ss_pred chHHHHHHHHHHHHHHHHHccCCCcceEEECCCCChHHHHHHhhccCCCcceEEeecCCccCcchhhhhHHHHHHHHHHH
Q 023038 97 INLNEISHDSAIGLITRVLNIGILLTEVYLDTVGDAEKYQAKLSQRFPSIKFVVSKKADSLYPVVSGASIVAKVTRDRTL 176 (288)
Q Consensus 97 ~NlN~l~~~~~~~li~~~l~~~~~~~~v~VD~~g~~~~y~~~L~~~~p~i~v~~~~KADs~~~~VAAASIiAKV~RD~~m 176 (288)
.|||.++..++.+++..+. ..+..||||++++++.|+. +...++++++++++|||++|++||||||||||+||+.|
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 4999999888877776643 5678999999999999987 55556788899999999999999999999999999999
Q ss_pred HhhhhhhcccccCCCCcccCccc-cccc--ccCCC-cccccccHhH
Q 023038 177 RGWIFEETAENMHRNFGSGYPGD-HKHI--IFGFP-SLVRFSWGTC 218 (288)
Q Consensus 177 ~~~~~~~~~~~~~~~~GsGYPsd-h~~~--~~G~p-~~~R~Sw~t~ 218 (288)
+.|+..|+.|++ ++|+|||+| |... .+|+. ++||+||+|+
T Consensus 149 ~~l~~~~~~~~~--~~gsGy~s~~~~~~~~~~~~~~~~~R~sf~~~ 192 (193)
T cd06266 149 EELDEEYPGYGF--AKGKGYPTDPHTEAILKYGPTEPIHRRSFKTV 192 (193)
T ss_pred HHHHHHCCCCCC--cCCcCcCcHHHHHHHHHhCcCCCeeeCCCCCC
Confidence 999999988776 478999999 5554 35666 9999999986
No 9
>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=1.8e-54 Score=379.28 Aligned_cols=175 Identities=29% Similarity=0.439 Sum_probs=153.1
Q ss_pred ecccccCcCCcccceeeEEEEecccccccccccCcCCCCCCCHHHHHHHHHHhhhcCcccEEEEEECHhhHhHHhhcccc
Q 023038 17 MGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLKVNDSVGWAVDIIDPRELSAKMLNKNK 96 (288)
Q Consensus 17 iGiDEAGRGpv~GPmVvaav~~~~~~~~~L~~~gv~DSK~Ls~~kRe~L~~~I~~~~~~~~~v~~isp~eId~~~~~~~~ 96 (288)
+|||||||||||||||||||+++.+.. .+||+|||+||+++|++|++.|++. .+.|++.+++|++|| +
T Consensus 1 ~GiDEaGRG~~~GPlvvaav~~~~~~~----~~gv~DSK~Ls~~~R~~l~~~I~~~-~~~~~v~~~~~~~Id-------~ 68 (179)
T cd07182 1 AGVDEAGRGPLAGPVVAAAVILPPDFE----IEGLNDSKKLSEKKREELYEEIKEK-ALAWGIGIASPEEID-------R 68 (179)
T ss_pred CCCcCccCCCcccceEEEEEEECcccC----cCCCCCcccCCHHHHHHHHHHHHHh-cccEEEEEECHHHHC-------H
Confidence 699999999999999999999987632 2899999999999999999999874 578999999999996 4
Q ss_pred chHHHHHHHHHHHHHHHHHccCCCcceEEECCCCChHHHHHHhhccCCCcceEEeecCCccCcchhhhhHHHHHHHHHHH
Q 023038 97 INLNEISHDSAIGLITRVLNIGILLTEVYLDTVGDAEKYQAKLSQRFPSIKFVVSKKADSLYPVVSGASIVAKVTRDRTL 176 (288)
Q Consensus 97 ~NlN~l~~~~~~~li~~~l~~~~~~~~v~VD~~g~~~~y~~~L~~~~p~i~v~~~~KADs~~~~VAAASIiAKV~RD~~m 176 (288)
+|||++++.++.++|.++ ...+..|+||+++.+.. ..++++++|||++|++||||||||||+||++|
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 699999999888777653 34678899999976532 24567889999999999999999999999999
Q ss_pred HhhhhhhcccccCCCCcccCccc-cccc--ccCCCcccccccHhH
Q 023038 177 RGWIFEETAENMHRNFGSGYPGD-HKHI--IFGFPSLVRFSWGTC 218 (288)
Q Consensus 177 ~~~~~~~~~~~~~~~~GsGYPsd-h~~~--~~G~p~~~R~Sw~t~ 218 (288)
++|+..+|.|+|.. |+||||+ |... .||++++||+||+|+
T Consensus 136 ~~l~~~~~~yg~~~--~~GY~s~~h~~~i~~~G~~~~hR~s~~~~ 178 (179)
T cd07182 136 IELDKKYPGYGFAK--HKGYGTKEHLEALKKYGPTPIHRRSFAPV 178 (179)
T ss_pred HHHHHHCcCCCCcC--CCCCCcHHHHHHHHHhCcCHhhcCCCCCC
Confidence 99999999999864 5999999 7666 599999999999986
No 10
>PRK13925 rnhB ribonuclease HII; Provisional
Probab=100.00 E-value=2.4e-54 Score=383.78 Aligned_cols=186 Identities=22% Similarity=0.317 Sum_probs=159.5
Q ss_pred CceecccccCcCCcccceeeEEEEecccccccccccCcCCCCCCCHHHHHHHHHHhhhcCcccEEEEEECHhhHhHHhhc
Q 023038 14 PCIMGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLKVNDSVGWAVDIIDPRELSAKMLN 93 (288)
Q Consensus 14 ~~viGiDEAGRGpv~GPmVvaav~~~~~~~~~L~~~gv~DSK~Ls~~kRe~L~~~I~~~~~~~~~v~~isp~eId~~~~~ 93 (288)
.+++|||||||||||||||||||++|.+....|..+||+|||+||+++|++||++|++. +..|++.+++|++||
T Consensus 8 ~~iiGiDEAGRGpv~GPmVvaav~~~~~~~~~L~~~gv~DSK~Ls~~~Re~l~~~I~~~-~~~~~i~~i~~~eId----- 81 (198)
T PRK13925 8 ELIAGVDEVGRGALFGPVFAAAVILSEKAEPQLLQAGLTDSKKLSPKRRAQLVPLILTL-ASDWGIGQASAREID----- 81 (198)
T ss_pred CeEEeecCCCCCCChHHhEEEEEEEchHhhhhhhhcCCCCcccCCHHHHHHHHHHHHhh-CCcEEEEEECHHHhC-----
Confidence 78999999999999999999999999887677888999999999999999999999874 567999999999996
Q ss_pred cccchHHHHHHHHHHHHHHHHHccCCCcceEEECCCCChHHHHHHhhccCCCcceEEeecCCccCcchhhhhHHHHHHHH
Q 023038 94 KNKINLNEISHDSAIGLITRVLNIGILLTEVYLDTVGDAEKYQAKLSQRFPSIKFVVSKKADSLYPVVSGASIVAKVTRD 173 (288)
Q Consensus 94 ~~~~NlN~l~~~~~~~li~~~l~~~~~~~~v~VD~~g~~~~y~~~L~~~~p~i~v~~~~KADs~~~~VAAASIiAKV~RD 173 (288)
..|||.++..++.+++..+ ..++..|+||+++... .+++.. ...+|||++|++||||||||||+||
T Consensus 82 --~~ni~~~~~~a~~~~i~~l---~~~~~~v~iD~~~~~~--------~~~~~~-~~v~kaD~~~~~VaAASIiAKV~RD 147 (198)
T PRK13925 82 --RLGIRQATELAMLRALKKL---KSPPSLCLVDGNLPLR--------LWPGPQ-RTIVKGDSKSAAIAAASILAKVWRD 147 (198)
T ss_pred --HhhHHHHHHHHHHHHHHhc---CCCCCEEEECCccccC--------cCCCCc-eeecccccccHHHHHHHHHHHHHHH
Confidence 4699999988877666553 3456789999986421 133322 2346999999999999999999999
Q ss_pred HHHHhhhhhhcccccCCCCcccCccc-cccc--ccCCCcccccccHhHHHh
Q 023038 174 RTLRGWIFEETAENMHRNFGSGYPGD-HKHI--IFGFPSLVRFSWGTCTSH 221 (288)
Q Consensus 174 ~~m~~~~~~~~~~~~~~~~GsGYPsd-h~~~--~~G~p~~~R~Sw~t~~~~ 221 (288)
++|+.|+..||.|+|..| +||||+ |..+ .||++|+||+||+|.-.+
T Consensus 148 ~~m~~l~~~yp~y~f~~~--kGY~t~~h~~~i~~~G~~p~hR~sf~~~~~~ 196 (198)
T PRK13925 148 DLIKRLAKKYPGYGLEKN--KGYGTAQHRQALLKLGPTPLHRKSFLPKLIL 196 (198)
T ss_pred HHHHHHHHHCCCCCcccC--CCCCcHHHHHHHHHhCcCHHHcCCCcchhhc
Confidence 999999999999999866 899999 8887 599999999999986543
No 11
>PRK00015 rnhB ribonuclease HII; Validated
Probab=100.00 E-value=3.7e-54 Score=382.40 Aligned_cols=177 Identities=30% Similarity=0.418 Sum_probs=154.2
Q ss_pred CceecccccCcCCcccceeeEEEEecccccccccccCcCCCCCCCHHHHHHHHHHhhhcCcccEEEEEECHhhHhHHhhc
Q 023038 14 PCIMGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLKVNDSVGWAVDIIDPRELSAKMLN 93 (288)
Q Consensus 14 ~~viGiDEAGRGpv~GPmVvaav~~~~~~~~~L~~~gv~DSK~Ls~~kRe~L~~~I~~~~~~~~~v~~isp~eId~~~~~ 93 (288)
..++|||||||||+|||||||||+++.+.. + +||+|||+||+++|++|+++|++. ++.|++.+++|++||+
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 579999999999999999999999987532 3 799999999999999999999974 5789999999999974
Q ss_pred cccchHHHHHHHHHHHHHHHHHccCCCcceEEECCCCChHHHHHHhhccCCCcceEEeecCCccCcchhhhhHHHHHHHH
Q 023038 94 KNKINLNEISHDSAIGLITRVLNIGILLTEVYLDTVGDAEKYQAKLSQRFPSIKFVVSKKADSLYPVVSGASIVAKVTRD 173 (288)
Q Consensus 94 ~~~~NlN~l~~~~~~~li~~~l~~~~~~~~v~VD~~g~~~~y~~~L~~~~p~i~v~~~~KADs~~~~VAAASIiAKV~RD 173 (288)
+|||++++.++.++|+++ ..+..||||+++.++. . +++++++|||++|++||||||||||+||
T Consensus 89 ---~nln~~~~~a~~~~i~~l----~~~~~i~vD~~~~~~~-------~---~~~~~~~kaD~~~~~VaAASIvAKv~RD 151 (197)
T PRK00015 89 ---LNILEATLLAMRRAVEGL----VKPDYVLVDGNRVPKL-------P---IPQEAIVKGDAKSPSIAAASILAKVTRD 151 (197)
T ss_pred ---hhHHHHHHHHHHHHHHhc----CCCCEEEECCCCCCCC-------C---CCeEEEEcCCcccHHHHHHHHHHHHHHH
Confidence 699999999888777764 4567899999986631 1 2356678999999999999999999999
Q ss_pred HHHHhhhhhhcccccCCCCcccCccc-cccc--ccCCCcccccccHhH
Q 023038 174 RTLRGWIFEETAENMHRNFGSGYPGD-HKHI--IFGFPSLVRFSWGTC 218 (288)
Q Consensus 174 ~~m~~~~~~~~~~~~~~~~GsGYPsd-h~~~--~~G~p~~~R~Sw~t~ 218 (288)
++|+.|+..++.|+|.. |||||+| |..+ .+|++++||+||+|+
T Consensus 152 ~~m~~l~~~~~~yg~~~--~sGY~s~~~~~a~~~~G~~~~~R~Sw~~~ 197 (197)
T PRK00015 152 RLMEELDKEYPGYGFAK--HKGYGTKEHLEALAKYGPTPIHRRSFAPV 197 (197)
T ss_pred HHHHHHHHhCcCCCCcC--CCcCCCHHHHHHHHHcCCChhhcCcCcCC
Confidence 99999999999998865 4999999 6665 589999999999984
No 12
>PRK13926 ribonuclease HII; Provisional
Probab=100.00 E-value=5.2e-53 Score=377.39 Aligned_cols=180 Identities=29% Similarity=0.445 Sum_probs=155.2
Q ss_pred CceecccccCcCCcccceeeEEEEecccccccccccCcCCCCCCCHHHHHHHHHHhhhcCcccEEEEEECHhhHhHHhhc
Q 023038 14 PCIMGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLKVNDSVGWAVDIIDPRELSAKMLN 93 (288)
Q Consensus 14 ~~viGiDEAGRGpv~GPmVvaav~~~~~~~~~L~~~gv~DSK~Ls~~kRe~L~~~I~~~~~~~~~v~~isp~eId~~~~~ 93 (288)
.+++|||||||||+|||||||||+++... ++++|||+||+++|++|+++|++. ...|.+.+++|++||+
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 67999999999999999999999998753 579999999999999999999874 4679999999999964
Q ss_pred cccchHHHHHHHHHHHHHHHHHccCCCcceEEECCCCChHHHHHHhhccCCCcceEEeecCCccCcchhhhhHHHHHHHH
Q 023038 94 KNKINLNEISHDSAIGLITRVLNIGILLTEVYLDTVGDAEKYQAKLSQRFPSIKFVVSKKADSLYPVVSGASIVAKVTRD 173 (288)
Q Consensus 94 ~~~~NlN~l~~~~~~~li~~~l~~~~~~~~v~VD~~g~~~~y~~~L~~~~p~i~v~~~~KADs~~~~VAAASIiAKV~RD 173 (288)
+|||+++|+++.++++++ .+.+..+++|... +. + .+++++++|||++|++||||||||||+||
T Consensus 91 ---~ni~~a~~~a~~~~l~~l---~~~~~~v~~D~~~--------~~--~-~~~~~~~~KgD~~~~~VaAASIvAKv~RD 153 (207)
T PRK13926 91 ---LNVLKATHLAAARALARL---AVAPEALVTDYLR--------LP--T-PLPLLAPPKADALSPTVAAASLLAKTERD 153 (207)
T ss_pred ---HHHHHHHHHHHHHHHHhc---CCCCCEEEECccc--------CC--C-CCCeEEEecCccccHHHHHHHHHHHHHHH
Confidence 699999999888777553 3557789999531 11 1 24678899999999999999999999999
Q ss_pred HHHHhhhhhhcccccCCCCcccCccc-cccc--ccCCCcccccccHhHHHhhh
Q 023038 174 RTLRGWIFEETAENMHRNFGSGYPGD-HKHI--IFGFPSLVRFSWGTCTSHFK 223 (288)
Q Consensus 174 ~~m~~~~~~~~~~~~~~~~GsGYPsd-h~~~--~~G~p~~~R~Sw~t~~~~l~ 223 (288)
++|++|+..|+.|+|..| +|||++ |+.. .||+||+||+||+|++++++
T Consensus 154 ~~m~~l~~~~~~yg~~~~--kGY~t~~h~~~l~~~G~~~~hR~s~~~~~~~~~ 204 (207)
T PRK13926 154 RLMRELDARYPGYGFARH--KGYGTPAHREALAALGPSPVHRRSFAPVRRLLT 204 (207)
T ss_pred HHHHHHHHhCccCCCcCC--CCCCCHHHHHHHHHhCcCHHHcCCcHHHHHhhh
Confidence 999999999999998765 888876 7666 59999999999999998763
No 13
>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=3.6e-53 Score=378.62 Aligned_cols=198 Identities=21% Similarity=0.282 Sum_probs=174.7
Q ss_pred ecccccCcCCcccceeeEEEEecccccccccccCcCCCCCCCHHHHHHHHHHhhhcCcccEEEEEECHhhHhHHhhcccc
Q 023038 17 MGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLKVNDSVGWAVDIIDPRELSAKMLNKNK 96 (288)
Q Consensus 17 iGiDEAGRGpv~GPmVvaav~~~~~~~~~L~~~gv~DSK~Ls~~kRe~L~~~I~~~~~~~~~v~~isp~eId~~~~~~~~ 96 (288)
+|||||||||+|||||+|||+++.+....|..+||+|||+||+++|++|++.|++ .+.|.+.+++|++||.++. ..
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 6999999999999999999999987666778899999999999999999999987 3789999999999998763 36
Q ss_pred chHHHHHHHHHHHHHHHHHccCCCcceEEECCCCChHHHHHHhhccC--CCcceEEeecCCccCcchhhhhHHHHHHHHH
Q 023038 97 INLNEISHDSAIGLITRVLNIGILLTEVYLDTVGDAEKYQAKLSQRF--PSIKFVVSKKADSLYPVVSGASIVAKVTRDR 174 (288)
Q Consensus 97 ~NlN~l~~~~~~~li~~~l~~~~~~~~v~VD~~g~~~~y~~~L~~~~--p~i~v~~~~KADs~~~~VAAASIiAKV~RD~ 174 (288)
.|||.++..++.++++.++..+..+..|+||+++.+++|+.+|.+.+ +++++++++|||++|++||||||||||+||+
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 79999999999999998865455678899999999999999998876 6678899999999999999999999999999
Q ss_pred HHHhhhhhhcccccCCCCcccCccccc---cc--ccC---CCcccccccHhHHHhh
Q 023038 175 TLRGWIFEETAENMHRNFGSGYPGDHK---HI--IFG---FPSLVRFSWGTCTSHF 222 (288)
Q Consensus 175 ~m~~~~~~~~~~~~~~~~GsGYPsdh~---~~--~~G---~p~~~R~Sw~t~~~~l 222 (288)
.|++++.. |+|..++|||||++ . .. .+| +|+++|+||+|+++++
T Consensus 157 ~m~~l~~~---yg~~~~~G~g~~~~-~~~~~~l~~~g~~~l~~~~k~~~~t~~~~~ 208 (208)
T cd06590 157 KMEKLSKQ---YGMKLPKGASSKVD-EQAAEIIKKYGLEELKKVAKLHFKNTKKAL 208 (208)
T ss_pred HHHHHHHH---hCCCCCCCCCcHHH-HHHHHHHHHhhHhHHHHHHHHhchhhHhhC
Confidence 99998655 57888999999995 3 21 367 6789999999998763
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=5.7e-50 Score=354.89 Aligned_cols=191 Identities=40% Similarity=0.606 Sum_probs=155.4
Q ss_pred ecccccCcCCcccceeeEEEEecccccccccccCcCCCCCCCHHHHHHHHHHhhhcCcccEEEEEECHhhHhHHhhcccc
Q 023038 17 MGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLKVNDSVGWAVDIIDPRELSAKMLNKNK 96 (288)
Q Consensus 17 iGiDEAGRGpv~GPmVvaav~~~~~~~~~L~~~gv~DSK~Ls~~kRe~L~~~I~~~~~~~~~v~~isp~eId~~~~~~~~ 96 (288)
+|||||||||+|||||||||+++.+....|..+||+|||+||+++|++|+++|+. +.+. .+.+..|... ....
T Consensus 1 iG~DEaGrG~~~GPlvvaav~~~~~~~~~l~~~gv~DSK~Ls~~~r~~l~~~I~~---i~~~--~~~~~~~~~~--~~~~ 73 (198)
T PF01351_consen 1 IGIDEAGRGDVFGPLVVAAVYLPEEDIEKLKELGVKDSKKLSDKKREELAEKIKK---ISYS--EVSPYPIGYI--SPKE 73 (198)
T ss_dssp EEEEEESSS-SBS-EEEEEEEEEGGGHHHHHHTTGCCGTTS-HHHHHHHHHHHHE---EEEE--EEECHHHHHH--HTTT
T ss_pred CCCCCCCCCCcccchheEEEEeccccHHHHHhhccCccccCCHHHHHHHHHHHHh---hchh--hhhhcccccc--chHH
Confidence 7999999999999999999999999888899999999999999999999999991 3333 3444444321 1256
Q ss_pred chHHHHHHHHHHHHHHHHHccCCCcceEEECCCCChHHHHHHhhccCCCcceEEeecCCccCcchhhhhHHHHHHHHHHH
Q 023038 97 INLNEISHDSAIGLITRVLNIGILLTEVYLDTVGDAEKYQAKLSQRFPSIKFVVSKKADSLYPVVSGASIVAKVTRDRTL 176 (288)
Q Consensus 97 ~NlN~l~~~~~~~li~~~l~~~~~~~~v~VD~~g~~~~y~~~L~~~~p~i~v~~~~KADs~~~~VAAASIiAKV~RD~~m 176 (288)
+|+|.+++..+.++++.+.+.+..+..|+||+++.+++|...+.+.++ .++++++|||++|++||||||||||+||+.|
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 899999999999999988888788899999999999999999988888 8899999999999999999999999999666
Q ss_pred HhhhhhhcccccCCCCcccCccc-cccc------ccCCCcccccccHhH
Q 023038 177 RGWIFEETAENMHRNFGSGYPGD-HKHI------IFGFPSLVRFSWGTC 218 (288)
Q Consensus 177 ~~~~~~~~~~~~~~~~GsGYPsd-h~~~------~~G~p~~~R~Sw~t~ 218 (288)
+.+ ..+++|++ ++|+|||+| |... .-++|++||+||+|+
T Consensus 153 ~~~-~~~~~~~~--~~gsGy~s~~~~~~~~~~~~~~~l~~~~R~sf~tv 198 (198)
T PF01351_consen 153 ELL-SKYPGYGF--PKGSGYPSDPHTRAILKKGGSPELPQIHRLSFKTV 198 (198)
T ss_dssp HHH-HHHHTS-H--CCTSSSTTSHHHHHHHHHHHHHSSHTTB-TTSHHH
T ss_pred HHH-HhCcCCCC--ccCCCCChHHHHHHHHHhCCCCCCCccccCCCcCC
Confidence 654 44555655 688999999 3332 116788999999996
No 15
>PRK00996 ribonuclease HIII; Provisional
Probab=100.00 E-value=3.1e-48 Score=364.58 Aligned_cols=204 Identities=23% Similarity=0.284 Sum_probs=177.1
Q ss_pred CCceecccccCcCCcccceeeEEEEecccccccccccCcCCCCCCCHHHHHHHHHHhhhcCcccEEEEEECHhhHhHHhh
Q 023038 13 NPCIMGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLKVNDSVGWAVDIIDPRELSAKML 92 (288)
Q Consensus 13 ~~~viGiDEAGRGpv~GPmVvaav~~~~~~~~~L~~~gv~DSK~Ls~~kRe~L~~~I~~~~~~~~~v~~isp~eId~~~~ 92 (288)
...+||||||||||+|||||||||+++.+....|..+||+|||+||+++|++|++.|++. +.|.+.+++|++||+++.
T Consensus 86 ~~~viGiDEaGrG~~fGPlvvaav~v~~~~~~~l~~lgv~DSK~Ls~~kr~~La~~I~~~--~~~~v~~~~p~~~n~l~~ 163 (304)
T PRK00996 86 NLSLIGSDEVGKGDYFGPLTVAAVYVDKEQIPFLKKLGVKDSKKLTDTKIRQIAPQLREK--IPHSVLLLSPEKYNELQA 163 (304)
T ss_pred CceEEeecCCCCCCcccceEEEEEEEchhhcchhhhcCCCccccCCHHHHHHHHHHHHHh--cCEEEEEeCHHHhhhHHH
Confidence 356899999999999999999999999887788889999999999999999999999974 689999999999998753
Q ss_pred ccccchHHHHHHHHHHHHHHHHHcc--CCCcceEEECCCCChHHHHHHhhcc--CCCcceEEeecCCccCcchhhhhHHH
Q 023038 93 NKNKINLNEISHDSAIGLITRVLNI--GILLTEVYLDTVGDAEKYQAKLSQR--FPSIKFVVSKKADSLYPVVSGASIVA 168 (288)
Q Consensus 93 ~~~~~NlN~l~~~~~~~li~~~l~~--~~~~~~v~VD~~g~~~~y~~~L~~~--~p~i~v~~~~KADs~~~~VAAASIiA 168 (288)
..+|+|.+....|.++|..+++. +..+..|+||+++.+++|+.+|... .+..++++++|||++|++||||||||
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 35799998877777777777653 5667899999999999999999752 23457888999999999999999999
Q ss_pred HHHHHHHHHhhhhhhcccccCCCCcccCcccccc----cccC---CCcccccccHhHHHhhh
Q 023038 169 KVTRDRTLRGWIFEETAENMHRNFGSGYPGDHKH----IIFG---FPSLVRFSWGTCTSHFK 223 (288)
Q Consensus 169 KV~RD~~m~~~~~~~~~~~~~~~~GsGYPsdh~~----~~~G---~p~~~R~Sw~t~~~~l~ 223 (288)
||++|+.|+.+++.|++..++|+|||+|... ..|| ++.++|.+|+|.+++++
T Consensus 242 ---R~~~l~~~~~l~~~yg~~~~kGag~~~d~~a~~~i~~~G~~~L~~~aK~hfk~~~k~~~ 300 (304)
T PRK00996 242 ---RYAFLENMDKLSKEAGMTLPKGAGAKVDKVAAQILKKYGKEALEKFAKLHFKNTEKAQK 300 (304)
T ss_pred ---HHHHHHHHHHhCcCCCCCCCCCCCCHHHHHHHHHHHHhCcchhHHHHHHhchhHHHHHH
Confidence 9999999999999999999999999996221 1467 78899999999988764
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=5.5e-43 Score=326.27 Aligned_cols=190 Identities=25% Similarity=0.293 Sum_probs=159.1
Q ss_pred CceecccccCcCCcccceeeEEEEecccccccccccCcCCCCCCCHHHHHHHHHHhhhcCcccEEEEEECHhhHhHHhhc
Q 023038 14 PCIMGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLKVNDSVGWAVDIIDPRELSAKMLN 93 (288)
Q Consensus 14 ~~viGiDEAGRGpv~GPmVvaav~~~~~~~~~L~~~gv~DSK~Ls~~kRe~L~~~I~~~~~~~~~v~~isp~eId~~~~~ 93 (288)
.++||||||||||+|||||||||+++.+....|+.+||+|||+||+++|++|+++|++. +.|.+.+++|++||.++.
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 56999999999999999999999999887778889999999999999999999999874 579999999999997643
Q ss_pred cccchHHHHHHHHHHHHHHHHHccCCCcceEEECCCCChHHHHHHhhc-cCCCcceEEeecCCccCcchhhhhHHHHHHH
Q 023038 94 KNKINLNEISHDSAIGLITRVLNIGILLTEVYLDTVGDAEKYQAKLSQ-RFPSIKFVVSKKADSLYPVVSGASIVAKVTR 172 (288)
Q Consensus 94 ~~~~NlN~l~~~~~~~li~~~l~~~~~~~~v~VD~~g~~~~y~~~L~~-~~p~i~v~~~~KADs~~~~VAAASIiAKV~R 172 (288)
...|+|.+....|.++|..++........|+||+++.++.|+.++.. .++..++++++|||+ |++|||||||| |
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 35799999999999999887643333347999999988888877754 245667889999998 99999999999 9
Q ss_pred HHHHHhhhhhhcccccCCCCcccCccccccc-----ccCCCcccc
Q 023038 173 DRTLRGWIFEETAENMHRNFGSGYPGDHKHI-----IFGFPSLVR 212 (288)
Q Consensus 173 D~~m~~~~~~~~~~~~~~~~GsGYPsdh~~~-----~~G~p~~~R 212 (288)
|++|+.|+.+++.|++..+.|+|-.. |..+ .||+..++.
T Consensus 233 ~~~l~~l~~l~~~yg~~~pkGa~~~v-~~~a~~~i~~~G~~~L~~ 276 (284)
T TIGR00716 233 YKFLQSLKELERELGIKLPKGASKEV-KELAKSLILKKGPSALER 276 (284)
T ss_pred HHHHHHHHHhCcccCCcCCCCCChHH-HHHHHHHHHHhCccHHHH
Confidence 99999999999999998885555444 4332 478875443
No 17
>COG1039 RnhC Ribonuclease HIII [DNA replication, recombination, and repair]
Probab=100.00 E-value=1.6e-35 Score=272.45 Aligned_cols=179 Identities=25% Similarity=0.265 Sum_probs=162.2
Q ss_pred CceecccccCcCCcccceeeEEEEecccccccccccCcCCCCCCCHHHHHHHHHHhhhcCcccEEEEEECHhhHhHHhhc
Q 023038 14 PCIMGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLKVNDSVGWAVDIIDPRELSAKMLN 93 (288)
Q Consensus 14 ~~viGiDEAGRGpv~GPmVvaav~~~~~~~~~L~~~gv~DSK~Ls~~kRe~L~~~I~~~~~~~~~v~~isp~eId~~~~~ 93 (288)
..+||+||+|.|++|||||||||+++++....|.++||+|||+|+|.++.+|++.|++ .+.+.+..+.|++||+++.
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 5789999999999999999999999999999999999999999999999999999998 4789999999999999874
Q ss_pred cccchHHHHHHHHHHHHHHHHHc-cCCCcceEEECCCCChHHHHHHhhccC--CCcceEEeecCCccCcchhhhhHHHHH
Q 023038 94 KNKINLNEISHDSAIGLITRVLN-IGILLTEVYLDTVGDAEKYQAKLSQRF--PSIKFVVSKKADSLYPVVSGASIVAKV 170 (288)
Q Consensus 94 ~~~~NlN~l~~~~~~~li~~~l~-~~~~~~~v~VD~~g~~~~y~~~L~~~~--p~i~v~~~~KADs~~~~VAAASIiAKV 170 (288)
...|.|.+....|..+|..++. .+..++.|+||+|.+.+.|..+|.+.. +..++.+.+||++++.+||||||+|
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 4589998877777788888884 688899999999999999999998762 3446778999999999999999999
Q ss_pred HHHHHHHhhhhhhcccccCCCCcccCccc
Q 023038 171 TRDRTLRGWIFEETAENMHRNFGSGYPGD 199 (288)
Q Consensus 171 ~RD~~m~~~~~~~~~~~~~~~~GsGYPsd 199 (288)
||.++..|+..+..|++..+.|+|--.|
T Consensus 237 -R~~Fl~~~~~l~~~~gv~LPkGAg~~V~ 264 (297)
T COG1039 237 -RYAFLQSLKQLSRQYGVQLPKGAGPAVD 264 (297)
T ss_pred -HHHHHHHHHHHHHHhCCcCCCCCchhHH
Confidence 9999999999999999999999996665
No 18
>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=71.61 E-value=64 Score=27.58 Aligned_cols=161 Identities=19% Similarity=0.183 Sum_probs=76.4
Q ss_pred eecccccCcCCc-----ccc-eeeEEEEecccccccc--------cccCcC------------------CCCCCCHHHH-
Q 023038 16 IMGIDEAGRGPV-----LGP-MVYGCLYCPCSYQQTL--------ATLNFA------------------DSKTLKEEKR- 62 (288)
Q Consensus 16 viGiDEAGRGpv-----~GP-mVvaav~~~~~~~~~L--------~~~gv~------------------DSK~Ls~~kR- 62 (288)
++.|||+|.-.. -.| .|+|+++++.+....+ ..++.. +=..++..+|
T Consensus 1 ~iyiDESG~~~~~~~~~~~~~fvl~gv~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lh~~~i~~~~~~~~~~~~~~~~ 80 (235)
T PF12686_consen 1 IIYIDESGNTGPNYSDKNSPYFVLGGVIIEDEDWKKIINEIRSLKKKYGFKEEVEKSELHASDISNGKKDFSKLSKDERQ 80 (235)
T ss_pred CEEEeCCCCCCCCcCCCCCCEEEEEEEEEcHHHHHHHHHHHHHHHHHhCccccchhhhhhHHHhhhcccccccCCHHHHH
Confidence 368999995433 344 5688888887543211 112211 1123444444
Q ss_pred ---HHHHHHhhhcCcccEEEEEECHhhHhHHhhccc-cchHHHHHHHHHHHHHHHHH---ccCCCcceEEECCCCC--hH
Q 023038 63 ---EELFEDLKVNDSVGWAVDIIDPRELSAKMLNKN-KINLNEISHDSAIGLITRVL---NIGILLTEVYLDTVGD--AE 133 (288)
Q Consensus 63 ---e~L~~~I~~~~~~~~~v~~isp~eId~~~~~~~-~~NlN~l~~~~~~~li~~~l---~~~~~~~~v~VD~~g~--~~ 133 (288)
+.++..|.+.....+.+.++....++....... ....+..-..+...+++++. ........|++|.... ..
T Consensus 81 ~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~y~~~~~~ll~~~~~~~~~~~~~~~iv~D~~~~~~~~ 160 (235)
T PF12686_consen 81 EFFKDLFDIISELKFIIFIAVIDDKKLYNRSSLDNNKPRDPNKFYNLALRFLLERINMYLQRPNENIIIVIDNGDRKKDN 160 (235)
T ss_pred HHHHHHHHHHHhCCCceEEEEEEeccccchhhhcccccchhHHHHHHHHHHHHHHHHHhhcCCCceEEEEEeCCCchHHH
Confidence 667777776432445556666666654432111 11222233333444555544 1222335688893222 12
Q ss_pred HHHHHhhc---------cCCCcceEEeecCCccC-cchhhhhHHHHHHHHHHHH
Q 023038 134 KYQAKLSQ---------RFPSIKFVVSKKADSLY-PVVSGASIVAKVTRDRTLR 177 (288)
Q Consensus 134 ~y~~~L~~---------~~p~i~v~~~~KADs~~-~~VAAASIiAKV~RD~~m~ 177 (288)
....++.. ....+ +....-.||+. +-|=+|=+||=..|-.+..
T Consensus 161 ~l~~~~~~~~~~~~~~~~~~~~-~~~~~~~~S~~s~~lQiAD~ia~~i~r~~~~ 213 (235)
T PF12686_consen 161 KLKEYLRKQYSKGSKRDKLKNI-IEEIFFVDSKDSPGLQIADLIAGAIRRYLEK 213 (235)
T ss_pred HHHHHHHHhccccccccccccc-ccceeecCCCCCHhHHHHHHHHHHHHHHHHh
Confidence 22222210 00111 11222334444 7888888888655555443
No 19
>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=37.84 E-value=34 Score=33.48 Aligned_cols=33 Identities=21% Similarity=0.317 Sum_probs=19.6
Q ss_pred CCCHHHHHHHHHHhhhcCcccEEEEEECHhhHhHHh
Q 023038 56 TLKEEKREELFEDLKVNDSVGWAVDIIDPRELSAKM 91 (288)
Q Consensus 56 ~Ls~~kRe~L~~~I~~~~~~~~~v~~isp~eId~~~ 91 (288)
.|+++++.+|+.++.+ ...+ . ..++|.|||+.+
T Consensus 297 ~~~~~Ek~~li~EvL~-P~~~-~-L~VTPKeID~~i 329 (358)
T TIGR01441 297 TLDEEEKRQLIYEVLN-PLGH-N-LMVTPKEVDMFI 329 (358)
T ss_pred cCCHHHHHHHHHHHhC-cccC-c-ceECcHhHHHHH
Confidence 3445555555554443 1122 2 789999999876
No 20
>KOG3495 consensus Mitochondrial F1F0-ATP synthase, subunit epsilon/ATP15 [Energy production and conversion]
Probab=37.74 E-value=34 Score=24.21 Aligned_cols=20 Identities=20% Similarity=0.159 Sum_probs=16.8
Q ss_pred hhhhhHHHHHHHHHHHHhhh
Q 023038 161 VSGASIVAKVTRDRTLRGWI 180 (288)
Q Consensus 161 VAAASIiAKV~RD~~m~~~~ 180 (288)
|.=++|+|++.|+.++.++.
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 45579999999999998863
No 21
>PRK12362 germination protease; Provisional
Probab=34.05 E-value=45 Score=32.21 Aligned_cols=34 Identities=26% Similarity=0.544 Sum_probs=26.0
Q ss_pred CCCCHHHHHHHHHHhhhcCcccEEEEEECHhhHhHHh
Q 023038 55 KTLKEEKREELFEDLKVNDSVGWAVDIIDPRELSAKM 91 (288)
Q Consensus 55 K~Ls~~kRe~L~~~I~~~~~~~~~v~~isp~eId~~~ 91 (288)
|.|+++++.+|+.++.+- ..+ -..++|.+||+.+
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 578999999998887752 222 2689999999876
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=32.89 E-value=18 Score=28.66 Aligned_cols=20 Identities=35% Similarity=0.478 Sum_probs=17.9
Q ss_pred cchhhhhHHHHHHHHHHHHh
Q 023038 159 PVVSGASIVAKVTRDRTLRG 178 (288)
Q Consensus 159 ~~VAAASIiAKV~RD~~m~~ 178 (288)
-+||-|||+-|.-||.+++.
T Consensus 10 eIia~aSiLIKfg~ddIl~~ 29 (91)
T PF09010_consen 10 EIIAVASILIKFGRDDILEN 29 (91)
T ss_dssp HHHHHHHHHHHTTTHHHHTS
T ss_pred HHHHHHHHHHHcChHHHHHh
Confidence 47899999999999998876
No 23
>PRK05473 hypothetical protein; Provisional
Probab=31.68 E-value=48 Score=26.04 Aligned_cols=22 Identities=18% Similarity=0.291 Sum_probs=19.0
Q ss_pred hhhHHHHHHHHHHHHhhhhhhc
Q 023038 163 GASIVAKVTRDRTLRGWIFEET 184 (288)
Q Consensus 163 AASIiAKV~RD~~m~~~~~~~~ 184 (288)
|=|+|-|+.||.+|+++-..|.
T Consensus 60 AR~lIrkiERDEilEeLv~~Yl 81 (86)
T PRK05473 60 ARNLIRKLERDEILEELVKSYL 81 (86)
T ss_pred HHHHHHHHhHHHHHHHHHHHHH
Confidence 6699999999999999877664
No 24
>KOG0189 consensus Phosphoadenosine phosphosulfate reductase [Amino acid transport and metabolism]
Probab=29.48 E-value=3.3e+02 Score=25.16 Aligned_cols=82 Identities=22% Similarity=0.306 Sum_probs=46.9
Q ss_pred CHHHHHHHHHHhhhcCcccEEEEEECHhhHhHHhhccccchHHHHHHHHH--HHHHHHHHccCCCcceEEECCCC-ChHH
Q 023038 58 KEEKREELFEDLKVNDSVGWAVDIIDPRELSAKMLNKNKINLNEISHDSA--IGLITRVLNIGILLTEVYLDTVG-DAEK 134 (288)
Q Consensus 58 s~~kRe~L~~~I~~~~~~~~~v~~isp~eId~~~~~~~~~NlN~l~~~~~--~~li~~~l~~~~~~~~v~VD~~g-~~~~ 134 (288)
..+.-|+|..+|.+ +||.||-.+-+- .--|+-+++...+ ..+|.-+-..+.++.-++|||-. +|++
T Consensus 18 ~~E~~e~l~kqL~~----------~sP~eIm~~al~-tf~~~~q~a~~G~~~lvlid~~~~~~~~~~l~~idT~~~~PeT 86 (261)
T KOG0189|consen 18 EVEDLEELNKQLEN----------LSPQEIMDWALE-TFPNLFQTAASGLEGLVLIDMLSKTGRPFRLFFIDTLHHFPET 86 (261)
T ss_pred cHHHHHHHHHHHhh----------CCHHHHHHHHHH-HhhhHHHHHhccccchHHHHHHHHcCCCceeEEeeccccChHH
Confidence 44556666666653 579998554331 1224433332111 22344444456677788999986 8988
Q ss_pred HH--HHhhccCCCcceEE
Q 023038 135 YQ--AKLSQRFPSIKFVV 150 (288)
Q Consensus 135 y~--~~L~~~~p~i~v~~ 150 (288)
|. +..++.++++++.+
T Consensus 87 ~~l~d~VekkY~~i~I~~ 104 (261)
T KOG0189|consen 87 LRLFDAVEKKYGNIRIHV 104 (261)
T ss_pred HHHHHHHHHhcCceEEEE
Confidence 74 44566677766554
No 25
>KOG3840 consensus Uncharaterized conserved protein, contains BTB/POZ domain [General function prediction only]
Probab=26.47 E-value=33 Score=33.29 Aligned_cols=23 Identities=35% Similarity=0.787 Sum_probs=15.3
Q ss_pred ccCccccccc-----------c--cCCCcccccccHh
Q 023038 194 SGYPGDHKHI-----------I--FGFPSLVRFSWGT 217 (288)
Q Consensus 194 sGYPsdh~~~-----------~--~G~p~~~R~Sw~t 217 (288)
-|||+ |.+. + |--.|++|.||..
T Consensus 299 EGYPT-hKEKikkRPGGRaEVIYnYVQRPFIhMSWEK 334 (438)
T KOG3840|consen 299 EGYPT-HKEKIKKRPGGRAEVIYNYVQRPFIHMSWEK 334 (438)
T ss_pred ccCcc-hHHHhhcCCCCCchhhHhhhcCcceeechhh
Confidence 39999 5443 1 2245799999963
No 26
>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=21.67 E-value=94 Score=24.05 Aligned_cols=21 Identities=19% Similarity=0.271 Sum_probs=18.0
Q ss_pred hhhHHHHHHHHHHHHhhhhhh
Q 023038 163 GASIVAKVTRDRTLRGWIFEE 183 (288)
Q Consensus 163 AASIiAKV~RD~~m~~~~~~~ 183 (288)
|=|+|-|+.||.+++++-..|
T Consensus 57 AR~lIr~~eRDellEeLv~~Y 77 (79)
T PF06135_consen 57 ARNLIRKIERDELLEELVRFY 77 (79)
T ss_pred HHHHHHHHhHHHHHHHHHHHH
Confidence 679999999999999986554
No 27
>COG3817 Predicted membrane protein [Function unknown]
Probab=20.73 E-value=26 Score=33.09 Aligned_cols=48 Identities=19% Similarity=0.203 Sum_probs=37.1
Q ss_pred CCcccceeeEEEEecccccccccccCcCCCCCCCHHHHHHHHHHhhhc
Q 023038 25 GPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLKVN 72 (288)
Q Consensus 25 Gpv~GPmVvaav~~~~~~~~~L~~~gv~DSK~Ls~~kRe~L~~~I~~~ 72 (288)
|+.++++|+++.++-.....-+...++.-=+.+|+++||+.++.+..+
T Consensus 49 g~~lp~~viG~ivillAliagf~~v~~G~~~~~~~e~re~~A~rlgnr 96 (313)
T COG3817 49 GDRLPNIVIGLIVILLALIAGFGQVKIGALPELSPEEREKSANRLGNR 96 (313)
T ss_pred cccccchhHhHHHHHHHHHHhcCCcccCCCCCCCHHHHHHHHHHhcCE
Confidence 368999999987665554444566778888999999999999888753
Done!