Query 022427
Match_columns 297
No_of_seqs 261 out of 1474
Neff 5.8
Searched_HMMs 46136
Date Fri Mar 29 03:27:58 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/022427.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/022427hhsearch_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 2.8E-85 6E-90 593.1 17.3 277 5-295 18-300 (301)
2 cd07181 RNaseH_typeII_eukaryot 100.0 4E-66 8.7E-71 467.3 20.7 215 17-231 1-216 (216)
3 cd07180 RNaseH_typeII_Archaea_ 100.0 8.9E-59 1.9E-63 415.9 19.9 201 17-230 1-203 (204)
4 PRK14551 rnhB ribonuclease HII 100.0 2.5E-58 5.3E-63 415.6 20.1 201 15-233 1-203 (212)
5 TIGR00729 ribonuclease H, mamm 100.0 7.7E-58 1.7E-62 410.5 21.2 202 16-231 1-205 (206)
6 COG0164 RnhB Ribonuclease HII 100.0 8.6E-56 1.9E-60 393.1 18.2 189 15-232 1-189 (199)
7 cd06266 RNaseH_typeII Ribonucl 100.0 1.3E-55 2.8E-60 391.8 17.8 193 17-228 1-193 (193)
8 cd06590 RNaseH_typeII_bacteria 100.0 3.3E-55 7.2E-60 393.8 18.2 206 17-231 1-208 (208)
9 PRK00015 rnhB ribonuclease HII 100.0 9.7E-55 2.1E-59 388.2 18.0 180 14-227 18-197 (197)
10 PRK13926 ribonuclease HII; Pro 100.0 6.9E-54 1.5E-58 385.1 21.2 185 12-232 19-204 (207)
11 PRK14550 rnhB ribonuclease HII 100.0 1.5E-54 3.2E-59 388.6 15.4 193 15-232 1-193 (204)
12 PRK13925 rnhB ribonuclease HII 100.0 7.4E-54 1.6E-58 382.7 18.7 194 9-230 2-196 (198)
13 cd07182 RNaseH_typeII_bacteria 100.0 5.8E-54 1.3E-58 378.1 17.7 178 17-227 1-178 (179)
14 PF01351 RNase_HII: Ribonuclea 100.0 9.2E-53 2E-57 374.7 15.8 198 17-227 1-198 (198)
15 PRK00996 ribonuclease HIII; Pr 100.0 4.4E-50 9.6E-55 379.1 20.8 211 13-232 86-300 (304)
16 TIGR00716 rnhC ribonuclease HI 100.0 1.6E-43 3.4E-48 331.7 18.2 194 14-220 81-275 (284)
17 COG1039 RnhC Ribonuclease HIII 100.0 1.8E-36 4E-41 280.2 15.7 206 14-231 83-294 (297)
18 PF12686 DUF3800: Protein of u 74.0 57 0.0012 28.1 11.6 160 16-176 1-212 (235)
19 cd00223 TOPRIM_TopoIIB_SPO TOP 41.5 17 0.00038 31.1 1.9 18 192-210 30-47 (160)
20 TIGR01441 GPR GPR endopeptidas 41.1 37 0.00079 33.5 4.2 34 56-92 297-330 (358)
21 PRK12362 germination protease; 36.3 51 0.0011 32.1 4.3 35 55-92 264-298 (318)
22 KOG3495 Mitochondrial F1F0-ATP 34.2 44 0.00096 23.8 2.6 20 161-180 12-31 (50)
23 PRK04342 DNA topoisomerase VI 33.7 27 0.00058 34.5 2.0 19 192-211 220-238 (367)
24 PLN00060 meiotic recombination 33.2 28 0.00061 34.7 2.0 17 193-210 242-258 (384)
25 PF09345 DUF1987: Domain of un 28.1 84 0.0018 25.3 3.7 54 193-246 16-90 (99)
26 KOG2795 Catalytic subunit of t 27.5 34 0.00074 33.9 1.5 20 192-212 224-243 (372)
27 PRK05473 hypothetical protein; 26.2 71 0.0015 25.3 2.8 22 163-184 60-81 (86)
28 KOG0189 Phosphoadenosine phosp 25.7 4.5E+02 0.0098 24.5 8.3 82 58-150 18-104 (261)
29 PF09010 AsiA: Anti-Sigma Fact 25.5 28 0.00062 27.7 0.5 20 159-178 10-29 (91)
No 1
>KOG2299 consensus Ribonuclease HI [Replication, recombination and repair]
Probab=100.00 E-value=2.8e-85 Score=593.15 Aligned_cols=277 Identities=54% Similarity=0.919 Sum_probs=248.5
Q ss_pred CCCCCcCCC-CceeeecccCCCCcccceeEEEEEecccccchhcccCCCCCCCCCHHHHHHHHHHhhhc----CcccEEE
Q 022427 5 AALPKWASN-PCIMGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLKVN----DSVGWAV 79 (297)
Q Consensus 5 ~~~~~~~~~-~~viGiDEAGRGpv~GPmVvaav~~~~~~~~~L~~lgv~DSK~Ls~~kRe~L~~~I~~~----~~~~~~v 79 (297)
|++|+.|.+ ||++||||||||||+||||||++|||.+....|..+|++|||+|++.+|++||+.|++. ..++|++
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 688999988 99999999999999999999999999999999999999999999999999999999753 2489999
Q ss_pred EEEChhhHhHHhhhhhhhhHHHHHHHHHHHHHHHHHccCCCcceEEECCCCChHHHHHHhhccCCCcceEEeecCccccc
Q 022427 80 DIIDPRELSAKMLNKNKINLNEISHDSAIGLITRVLNIGILLTEVYLDTVGDAEKYQAKLSQRFPSIKFVVSKKADSLYP 159 (297)
Q Consensus 80 ~~isp~eId~~m~~~~~~NLN~l~~~~~~~li~~~l~~~~~~~~v~VD~~g~~~~y~~~L~~~~p~~~~~~~~KaDs~~~ 159 (297)
.+|+|++|++.|++++++|||+++|++++.||+.+++.|+++.+|||||+|+|++||.+|+++||+++++|..|||++||
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 hhhhhHHHHHHHHHHHHHHhhHhhcccccCCCCCccCCCCHHHHHHHHhcccccCCCCccccccchhHHHhh-cccceEE
Q 022427 160 VVSGASIVAKVTRDRTLRGWIFEETAENMHRNFGSGYPGDPETKAWLTDHKHIIFGFPSLVRFSWGTCTSHF-KDIVEVL 238 (297)
Q Consensus 160 ~VAAASIiAKV~RD~~m~~~~~~~~~~~~~~~~GsGYpsDp~T~~~L~~~~~~~~G~~~~~R~Sw~t~~~~l-~~~~~~~ 238 (297)
+||||||||||+||+.+++|.+.+.....+.+||||||+||+|++||++|++.+||||++|||||+|++.+| ..+.++.
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 999999999999999999999999988889999999999999999999999999999999999999999999 5899999
Q ss_pred eccCcccccccccccccccceecccccCcccCcchhhhccCccccchhhhccccccc
Q 022427 239 WESDEMDEDVSSRRSGKRQLKLSDIGFSSSKRRSEEIESSGKGRCKFLEARKLEQLT 295 (297)
Q Consensus 239 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~~r~l~~~~ 295 (297)
|+++..+.+... . .++++|..+... +.. ..|..+| +|+|+++.
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 998875532211 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=4e-66 Score=467.34 Aligned_cols=215 Identities=64% Similarity=1.069 Sum_probs=199.0
Q ss_pred eeecccCCCCcccceeEEEEEecccccchhcccCCCCCCCCCHHHHHHHHHHhhhcC-cccEEEEEEChhhHhHHhhhhh
Q 022427 17 MGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLKVND-SVGWAVDIIDPRELSAKMLNKN 95 (297)
Q Consensus 17 iGiDEAGRGpv~GPmVvaav~~~~~~~~~L~~lgv~DSK~Ls~~kRe~L~~~I~~~~-~~~~~v~~isp~eId~~m~~~~ 95 (297)
+|||||||||+|||||||||+++.+..+.|..+||+|||+||+++|++|++.|++.. .+.|.+.+++|++||+.|....
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 699999999999999999999998766678789999999999999999999998742 4789999999999999876545
Q ss_pred hhhHHHHHHHHHHHHHHHHHccCCCcceEEECCCCChHHHHHHhhccCCCcceEEeecCccccchhhhhHHHHHHHHHHH
Q 022427 96 KINLNEISHDSAIGLITRVLNIGILLTEVYLDTVGDAEKYQAKLSQRFPSIKFVVSKKADSLYPVVSGASIVAKVTRDRT 175 (297)
Q Consensus 96 ~~NLN~l~~~~~~~li~~~l~~~~~~~~v~VD~~g~~~~y~~~L~~~~p~~~~~~~~KaDs~~~~VAAASIiAKV~RD~~ 175 (297)
..|||+++|+++..++++++..+..+..|+||+++++++|.++|+..+|++++++++|||++|++||||||||||+||++
T Consensus 81 ~~nln~~~~~~~~~~i~~~~~~~~~~~~vliD~~~~~~~~~~~L~~~~~~~~~~~~~kaD~~~~~VAAASIvAKV~RD~~ 160 (216)
T cd07181 81 KYNLNEISHDAAIGLIKSVLDKGVNVTEVYVDTVGPPEKYQAKLKKLFPGIKFTVEKKADSLYPIVSAASIVAKVTRDRA 160 (216)
T ss_pred cccHHHHHHHHHHHHHHHHHcCCCCCCEEEECCCCChhHHHHhhhhcCCCCceEEeeCcccccHHHHHHHHHHHHHHHHH
Confidence 67999999999999998887767778899999999999999999877777888899999999999999999999999999
Q ss_pred HHHhhHhhcccccCCCCCccCCCCHHHHHHHHhcccccCCCCccccccchhHHHhh
Q 022427 176 LRGWIFEETAENMHRNFGSGYPGDPETKAWLTDHKHIIFGFPSLVRFSWGTCTSHF 231 (297)
Q Consensus 176 m~~~~~~~~~~~~~~~~GsGYpsDp~T~~~L~~~~~~~~G~~~~~R~Sw~t~~~~l 231 (297)
|++|+..+|.|++.+++||||||||.|++||++++++.+|+|++||+||+|++++|
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 99999999999999999999999999999999999999999999999999999875
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=8.9e-59 Score=415.91 Aligned_cols=201 Identities=37% Similarity=0.576 Sum_probs=180.8
Q ss_pred eeecccCCCCcccceeEEEEEecccccchhcccCCCCCCCCCHHHHHHHHHHhhhcCcccEEEEEEChhhHhHHhhhhhh
Q 022427 17 MGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLKVNDSVGWAVDIIDPRELSAKMLNKNK 96 (297)
Q Consensus 17 iGiDEAGRGpv~GPmVvaav~~~~~~~~~L~~lgv~DSK~Ls~~kRe~L~~~I~~~~~~~~~v~~isp~eId~~m~~~~~ 96 (297)
+|||||||||+|||||||||++|.+....|..+||+|||+||+++|++|+++|++. .+.|.+.+++|++||++| ..
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 69999999999999999999999887777888999999999999999999999975 578999999999999876 35
Q ss_pred hhHHHHHHHHHHHHHHHHHccCCCcceEEECCC-CChHHHHHHhhccC-CCcceEEeecCccccchhhhhHHHHHHHHHH
Q 022427 97 INLNEISHDSAIGLITRVLNIGILLTEVYLDTV-GDAEKYQAKLSQRF-PSIKFVVSKKADSLYPVVSGASIVAKVTRDR 174 (297)
Q Consensus 97 ~NLN~l~~~~~~~li~~~l~~~~~~~~v~VD~~-g~~~~y~~~L~~~~-p~~~~~~~~KaDs~~~~VAAASIiAKV~RD~ 174 (297)
.|||.+++.++.++|+.+. ..+..|+||++ +++++|.++|++.+ +++++++++|||++|++||||||||||+||+
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 7999999999999988765 34678999999 57788998887765 3567888999999999999999999999999
Q ss_pred HHHHhhHhhcccccCCCCCccCCCCHHHHHHHHhcccccCCCCccccccchhHHHh
Q 022427 175 TLRGWIFEETAENMHRNFGSGYPGDPETKAWLTDHKHIIFGFPSLVRFSWGTCTSH 230 (297)
Q Consensus 175 ~m~~~~~~~~~~~~~~~~GsGYpsDp~T~~~L~~~~~~~~G~~~~~R~Sw~t~~~~ 230 (297)
+|++|+..++ +||+|||+||.|++||++++++.+|+|++||+||+|++++
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 9999877663 6789999999999999999988888999999999999865
No 4
>PRK14551 rnhB ribonuclease HII; Provisional
Probab=100.00 E-value=2.5e-58 Score=415.58 Aligned_cols=201 Identities=30% Similarity=0.463 Sum_probs=174.8
Q ss_pred ceeeecccCCCCcccceeEEEEEecccccchhcccCCCCCCCCCHHHHHHHHHHhhhcCcccEEEEEEChhhHhHHhhhh
Q 022427 15 CIMGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLKVNDSVGWAVDIIDPRELSAKMLNK 94 (297)
Q Consensus 15 ~viGiDEAGRGpv~GPmVvaav~~~~~~~~~L~~lgv~DSK~Ls~~kRe~L~~~I~~~~~~~~~v~~isp~eId~~m~~~ 94 (297)
.++|||||||||||||||||||+++.+. + ..||+|||+||+++|++||++|++...+.|.+.+++|++||+.
T Consensus 1 ~~iGiDEaGRG~v~GPlVvaav~~~~~~---~-~~gv~DSK~Ls~~~R~~l~~~I~~~~~~~~~i~~isp~~Id~~---- 72 (212)
T PRK14551 1 MRFGVDEAGKGPVLGSMFAAAVRADPAA---L-PDGIDDSKRLSPERREELAAELREDDAIAVGVAEIPPARIDDP---- 72 (212)
T ss_pred CeeCccCCCCCCccccceEEEEEECccc---C-cCCCcCcccCCHHHHHHHHHHHHhccCceEEEEEeCHHHHCcc----
Confidence 3799999999999999999999999753 2 3599999999999999999999975336899999999999852
Q ss_pred hhhhHHHHHHHHHHHHHHHHHccCCCcceEEECCCC-ChHHHHHHhhccC-CCcceEEeecCccccchhhhhHHHHHHHH
Q 022427 95 NKINLNEISHDSAIGLITRVLNIGILLTEVYLDTVG-DAEKYQAKLSQRF-PSIKFVVSKKADSLYPVVSGASIVAKVTR 172 (297)
Q Consensus 95 ~~~NLN~l~~~~~~~li~~~l~~~~~~~~v~VD~~g-~~~~y~~~L~~~~-p~~~~~~~~KaDs~~~~VAAASIiAKV~R 172 (297)
.+|||.+++.+|.++|.+++ ..++.||||++. ++++|..+|.+.+ +++++++++|||++|++||||||||||+|
T Consensus 73 -~~nln~~~~~a~~~ai~~l~---~~~~~v~iD~~~~~~~~~~~~l~~~~~~~~~~~~~~KaD~~~~~VAAASIlAKv~R 148 (212)
T PRK14551 73 -ETDMNTLTVAAHAEALSGVA---TDGITGLCDAGDVDAGRFARRVADRVALDVSVSAEHGADEEDPLVGAASIVAKVAR 148 (212)
T ss_pred -ccCHHHHHHHHHHHHHHhhc---cCCCEEEECCCCCchHHHHHhhhhccCCCCceEEEecccchhHHHHHHHHHHHHHH
Confidence 47999999999998887754 245789999984 6778888887765 35778889999999999999999999999
Q ss_pred HHHHHHhhHhhcccccCCCCCccCCCCHHHHHHHHhcccccCCCCccccccchhHHHhhcc
Q 022427 173 DRTLRGWIFEETAENMHRNFGSGYPGDPETKAWLTDHKHIIFGFPSLVRFSWGTCTSHFKD 233 (297)
Q Consensus 173 D~~m~~~~~~~~~~~~~~~~GsGYpsDp~T~~~L~~~~~~~~G~~~~~R~Sw~t~~~~l~~ 233 (297)
|+.|++|+..++ ++|||||+||.|++||++++++.+++|++||+||+|+++++++
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 999999987764 6789999999999999998877666777999999999998853
No 5
>TIGR00729 ribonuclease H, mammalian HI/archaeal HII subfamily. Archaeal members of this subfamily of RNase H are designated RNase HII and one has been shown to be active as a monomer. A member from Homo sapiens was characterized as RNase HI, large subunit.
Probab=100.00 E-value=7.7e-58 Score=410.52 Aligned_cols=202 Identities=38% Similarity=0.585 Sum_probs=173.2
Q ss_pred eeeecccCCCCcccceeEEEEEecccccchhcccCCCCCCCCCHHHHHHHHHHhhhcCcccEEEEEEChhhHhHHhhhhh
Q 022427 16 IMGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLKVNDSVGWAVDIIDPRELSAKMLNKN 95 (297)
Q Consensus 16 viGiDEAGRGpv~GPmVvaav~~~~~~~~~L~~lgv~DSK~Ls~~kRe~L~~~I~~~~~~~~~v~~isp~eId~~m~~~~ 95 (297)
++|||||||||+|||||||||+++.+....|..+||+|||+||+++|++|+++|++. .+.|.+.+++|++||+.+
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 589999999999999999888777665566788999999999999999999999874 478999999999999865
Q ss_pred hhhHHHHHHHHHHHHHHHHHccCCCcceEEECCCCChHHHHHH-h--hccCCCcceEEeecCccccchhhhhHHHHHHHH
Q 022427 96 KINLNEISHDSAIGLITRVLNIGILLTEVYLDTVGDAEKYQAK-L--SQRFPSIKFVVSKKADSLYPVVSGASIVAKVTR 172 (297)
Q Consensus 96 ~~NLN~l~~~~~~~li~~~l~~~~~~~~v~VD~~g~~~~y~~~-L--~~~~p~~~~~~~~KaDs~~~~VAAASIiAKV~R 172 (297)
..|||.++++++.++|+.+. ..+..||||+++.++.|..+ + ...+|+.++++++|||++|++||||||||||+|
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 24578999999876653322 2 235777888899999999999999999999999
Q ss_pred HHHHHHhhHhhcccccCCCCCccCCCCHHHHHHHHhcccccCCCCccccccchhHHHhh
Q 022427 173 DRTLRGWIFEETAENMHRNFGSGYPGDPETKAWLTDHKHIIFGFPSLVRFSWGTCTSHF 231 (297)
Q Consensus 173 D~~m~~~~~~~~~~~~~~~~GsGYpsDp~T~~~L~~~~~~~~G~~~~~R~Sw~t~~~~l 231 (297)
|++|+.|+..++. +|||||+||.|++||++++++.+++|++||+||+|+++++
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 9999999877653 6899999999999999988776557789999999999875
No 6
>COG0164 RnhB Ribonuclease HII [DNA replication, recombination, and repair]
Probab=100.00 E-value=8.6e-56 Score=393.06 Aligned_cols=189 Identities=34% Similarity=0.500 Sum_probs=161.6
Q ss_pred ceeeecccCCCCcccceeEEEEEecccccchhcccCCCCCCCCCHHHHHHHHHHhhhcCcccEEEEEEChhhHhHHhhhh
Q 022427 15 CIMGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLKVNDSVGWAVDIIDPRELSAKMLNK 94 (297)
Q Consensus 15 ~viGiDEAGRGpv~GPmVvaav~~~~~~~~~L~~lgv~DSK~Ls~~kRe~L~~~I~~~~~~~~~v~~isp~eId~~m~~~ 94 (297)
.++||||||||||+||||+|||++|++... ..+|++|||+||+++|++||++|+. .++.|.+.++++++||
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 379999999999999999999999987543 5689999999999999999999994 4689999999999995
Q ss_pred hhhhHHHHHHHHHHHHHHHHHccCCCcceEEECCCCChHHHHHHhhccCCCcceEEeecCccccchhhhhHHHHHHHHHH
Q 022427 95 NKINLNEISHDSAIGLITRVLNIGILLTEVYLDTVGDAEKYQAKLSQRFPSIKFVVSKKADSLYPVVSGASIVAKVTRDR 174 (297)
Q Consensus 95 ~~~NLN~l~~~~~~~li~~~l~~~~~~~~v~VD~~g~~~~y~~~L~~~~p~~~~~~~~KaDs~~~~VAAASIiAKV~RD~ 174 (297)
++|||++++.+|..++..+ ...++.||||+++-+.. | ..| .++++|||++|++||||||||||+||+
T Consensus 72 -~~ni~~a~~~am~~av~~l---~~~~~~vlvD~~~~~~~----l--~~~---~~a~~KgDa~~~~IaAASIvAKV~RDr 138 (199)
T COG0164 72 -ELNILEATKLAMRRAVAGL---SSQPDLVLVDGNDLPLG----L--PQP---AVAIIKGDAKSPSIAAASILAKVTRDR 138 (199)
T ss_pred -hhhHHHHHHHHHHHHHHhc---cccCCEEEEeCCCcccc----C--CCC---cceeeccchhhHHHHHHHHHHHHHHHH
Confidence 5899999999887666553 34458999999863311 1 112 267899999999999999999999999
Q ss_pred HHHHhhHhhcccccCCCCCccCCCCHHHHHHHHhcccccCCCCccccccchhHHHhhc
Q 022427 175 TLRGWIFEETAENMHRNFGSGYPGDPETKAWLTDHKHIIFGFPSLVRFSWGTCTSHFK 232 (297)
Q Consensus 175 ~m~~~~~~~~~~~~~~~~GsGYpsDp~T~~~L~~~~~~~~G~~~~~R~Sw~t~~~~l~ 232 (297)
+|++++..||.|+|+ +|||||+||.|.+|++.+ +.+++||+||+|+++++.
T Consensus 139 ~m~~l~~~yp~Y~~~--~~~GY~T~~h~~a~~~~~-----~~~~~hR~Sf~~vk~~~~ 189 (199)
T COG0164 139 LMEELAKEYPEYGFD--KGSGYPTDPHTEALLKKG-----GTPGIHRRSFAPVRRLLG 189 (199)
T ss_pred HHHHHHhhCcCcCcc--cCCCCCChHHHHHHHHhC-----CCCceeecccHHHHHhhh
Confidence 999999999999876 569999999999999854 445599999999999984
No 7
>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=1.3e-55 Score=391.79 Aligned_cols=193 Identities=38% Similarity=0.530 Sum_probs=172.6
Q ss_pred eeecccCCCCcccceeEEEEEecccccchhcccCCCCCCCCCHHHHHHHHHHhhhcCcccEEEEEEChhhHhHHhhhhhh
Q 022427 17 MGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLKVNDSVGWAVDIIDPRELSAKMLNKNK 96 (297)
Q Consensus 17 iGiDEAGRGpv~GPmVvaav~~~~~~~~~L~~lgv~DSK~Ls~~kRe~L~~~I~~~~~~~~~v~~isp~eId~~m~~~~~ 96 (297)
+|||||||||||||||||||+++.+..+.|..+||+|||+||+++|++|+++|++ ..+.|.+.+++|++||+
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 35899999999999974
Q ss_pred hhHHHHHHHHHHHHHHHHHccCCCcceEEECCCCChHHHHHHhhccCCCcceEEeecCccccchhhhhHHHHHHHHHHHH
Q 022427 97 INLNEISHDSAIGLITRVLNIGILLTEVYLDTVGDAEKYQAKLSQRFPSIKFVVSKKADSLYPVVSGASIVAKVTRDRTL 176 (297)
Q Consensus 97 ~NLN~l~~~~~~~li~~~l~~~~~~~~v~VD~~g~~~~y~~~L~~~~p~~~~~~~~KaDs~~~~VAAASIiAKV~RD~~m 176 (297)
.|||.++..++.+++..+. ..+..||||++++++.|+. +...+++.++++++|||++|++||||||||||+||+.|
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 5999999888877776643 5678999999999999987 55556778899999999999999999999999999999
Q ss_pred HHhhHhhcccccCCCCCccCCCCHHHHHHHHhcccccCCCCccccccchhHH
Q 022427 177 RGWIFEETAENMHRNFGSGYPGDPETKAWLTDHKHIIFGFPSLVRFSWGTCT 228 (297)
Q Consensus 177 ~~~~~~~~~~~~~~~~GsGYpsDp~T~~~L~~~~~~~~G~~~~~R~Sw~t~~ 228 (297)
+.|+..++.|++ ++|||||+|+.|++|++.+..+ ++||+||+|++
T Consensus 149 ~~l~~~~~~~~~--~~gsGy~s~~~~~~~~~~~~~~-----~~~R~sf~~~~ 193 (193)
T cd06266 149 EELDEEYPGYGF--AKGKGYPTDPHTEAILKYGPTE-----PIHRRSFKTVK 193 (193)
T ss_pred HHHHHHCCCCCC--cCCcCcCcHHHHHHHHHhCcCC-----CeeeCCCCCCC
Confidence 999998887665 5789999999999999976332 89999999863
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=3.3e-55 Score=393.76 Aligned_cols=206 Identities=19% Similarity=0.235 Sum_probs=183.6
Q ss_pred eeecccCCCCcccceeEEEEEecccccchhcccCCCCCCCCCHHHHHHHHHHhhhcCcccEEEEEEChhhHhHHhhhhhh
Q 022427 17 MGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLKVNDSVGWAVDIIDPRELSAKMLNKNK 96 (297)
Q Consensus 17 iGiDEAGRGpv~GPmVvaav~~~~~~~~~L~~lgv~DSK~Ls~~kRe~L~~~I~~~~~~~~~v~~isp~eId~~m~~~~~ 96 (297)
+|||||||||++||||+|||+++.+....|..+||+|||+||+++|++||+.|++ .+.|.+.+++|++||.++. ..
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 6999999999999999999999987667788899999999999999999999987 3789999999999998763 25
Q ss_pred hhHHHHHHHHHHHHHHHHHccCCCcceEEECCCCChHHHHHHhhccC--CCcceEEeecCccccchhhhhHHHHHHHHHH
Q 022427 97 INLNEISHDSAIGLITRVLNIGILLTEVYLDTVGDAEKYQAKLSQRF--PSIKFVVSKKADSLYPVVSGASIVAKVTRDR 174 (297)
Q Consensus 97 ~NLN~l~~~~~~~li~~~l~~~~~~~~v~VD~~g~~~~y~~~L~~~~--p~~~~~~~~KaDs~~~~VAAASIiAKV~RD~ 174 (297)
.|||.++..++.++++.++..+..+..|+||+++.+++|+.+|.+.+ +++++++++|||++|++||||||||||+||+
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 79999999999999988765455678899999999999999998876 5678899999999999999999999999999
Q ss_pred HHHHhhHhhcccccCCCCCccCCCCHHHHHHHHhcccccCCCCccccccchhHHHhh
Q 022427 175 TLRGWIFEETAENMHRNFGSGYPGDPETKAWLTDHKHIIFGFPSLVRFSWGTCTSHF 231 (297)
Q Consensus 175 ~m~~~~~~~~~~~~~~~~GsGYpsDp~T~~~L~~~~~~~~G~~~~~R~Sw~t~~~~l 231 (297)
.|+.++.. |++..++|+|||+|+.|++||+++.... +|+++|+||+|++++.
T Consensus 157 ~m~~l~~~---yg~~~~~G~g~~~~~~~~~~l~~~g~~~--l~~~~k~~~~t~~~~~ 208 (208)
T cd06590 157 KMEKLSKQ---YGMKLPKGASSKVDEQAAEIIKKYGLEE--LKKVAKLHFKNTKKAL 208 (208)
T ss_pred HHHHHHHH---hCCCCCCCCCcHHHHHHHHHHHHhhHhH--HHHHHHHhchhhHhhC
Confidence 99998654 6788999999999999999999884322 7789999999998863
No 9
>PRK00015 rnhB ribonuclease HII; Validated
Probab=100.00 E-value=9.7e-55 Score=388.23 Aligned_cols=180 Identities=29% Similarity=0.410 Sum_probs=157.6
Q ss_pred CceeeecccCCCCcccceeEEEEEecccccchhcccCCCCCCCCCHHHHHHHHHHhhhcCcccEEEEEEChhhHhHHhhh
Q 022427 14 PCIMGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLKVNDSVGWAVDIIDPRELSAKMLN 93 (297)
Q Consensus 14 ~~viGiDEAGRGpv~GPmVvaav~~~~~~~~~L~~lgv~DSK~Ls~~kRe~L~~~I~~~~~~~~~v~~isp~eId~~m~~ 93 (297)
..++|||||||||+|||||||||+++.+.. + +||+|||+||+++|++||+.|++. .+.|.+.+++|++||+
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 579999999999999999999999986532 3 799999999999999999999975 5789999999999974
Q ss_pred hhhhhHHHHHHHHHHHHHHHHHccCCCcceEEECCCCChHHHHHHhhccCCCcceEEeecCccccchhhhhHHHHHHHHH
Q 022427 94 KNKINLNEISHDSAIGLITRVLNIGILLTEVYLDTVGDAEKYQAKLSQRFPSIKFVVSKKADSLYPVVSGASIVAKVTRD 173 (297)
Q Consensus 94 ~~~~NLN~l~~~~~~~li~~~l~~~~~~~~v~VD~~g~~~~y~~~L~~~~p~~~~~~~~KaDs~~~~VAAASIiAKV~RD 173 (297)
+|||++++.++.++|+++ ..++.+|||+++.++. . .++++++|||++|++||||||||||+||
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 699999999988777764 3567899999987632 1 2356678999999999999999999999
Q ss_pred HHHHHhhHhhcccccCCCCCccCCCCHHHHHHHHhcccccCCCCccccccchhH
Q 022427 174 RTLRGWIFEETAENMHRNFGSGYPGDPETKAWLTDHKHIIFGFPSLVRFSWGTC 227 (297)
Q Consensus 174 ~~m~~~~~~~~~~~~~~~~GsGYpsDp~T~~~L~~~~~~~~G~~~~~R~Sw~t~ 227 (297)
++|+.|+..++.|+|.. |||||+||.|++|++ +|++++||+||+|+
T Consensus 152 ~~m~~l~~~~~~yg~~~--~sGY~s~~~~~a~~~------~G~~~~~R~Sw~~~ 197 (197)
T PRK00015 152 RLMEELDKEYPGYGFAK--HKGYGTKEHLEALAK------YGPTPIHRRSFAPV 197 (197)
T ss_pred HHHHHHHHhCcCCCCcC--CCcCCCHHHHHHHHH------cCCChhhcCcCcCC
Confidence 99999999999888765 599999999999776 49999999999984
No 10
>PRK13926 ribonuclease HII; Provisional
Probab=100.00 E-value=6.9e-54 Score=385.12 Aligned_cols=185 Identities=29% Similarity=0.433 Sum_probs=160.6
Q ss_pred CC-CceeeecccCCCCcccceeEEEEEecccccchhcccCCCCCCCCCHHHHHHHHHHhhhcCcccEEEEEEChhhHhHH
Q 022427 12 SN-PCIMGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLKVNDSVGWAVDIIDPRELSAK 90 (297)
Q Consensus 12 ~~-~~viGiDEAGRGpv~GPmVvaav~~~~~~~~~L~~lgv~DSK~Ls~~kRe~L~~~I~~~~~~~~~v~~isp~eId~~ 90 (297)
.+ .+++|||||||||++||||||||+++... ++++|||+||+++|++||++|++. ...|.+.+++|++||+
T Consensus 19 ~~~~~i~GiDEAGRG~~~GPlVvaav~~~~~~------~~~~DSK~Ls~~~R~~L~~~I~~~-~~~~~i~~isp~~Id~- 90 (207)
T PRK13926 19 RGYLRVAGVDEAGRGAWAGPVVVAAVILPPGE------YPFRDSKTLSPAAREALAEEVRRV-ALAWAVGHAEAAEIDR- 90 (207)
T ss_pred CCCcEEEeecCcCCCCccccceEEEEEECccC------CCccccccCCHHHHHHHHHHHHHh-CceEEEEEeCHHHHhH-
Confidence 45 67999999999999999999999998752 579999999999999999999875 4679999999999964
Q ss_pred hhhhhhhhHHHHHHHHHHHHHHHHHccCCCcceEEECCCCChHHHHHHhhccCCCcceEEeecCccccchhhhhHHHHHH
Q 022427 91 MLNKNKINLNEISHDSAIGLITRVLNIGILLTEVYLDTVGDAEKYQAKLSQRFPSIKFVVSKKADSLYPVVSGASIVAKV 170 (297)
Q Consensus 91 m~~~~~~NLN~l~~~~~~~li~~~l~~~~~~~~v~VD~~g~~~~y~~~L~~~~p~~~~~~~~KaDs~~~~VAAASIiAKV 170 (297)
.|||.++|+++.++++++ .+.++.+++|... + .+ .+++++++|||++|++||||||||||
T Consensus 91 ------~ni~~a~~~a~~~~l~~l---~~~~~~v~~D~~~--------~--~~-~~~~~~~~KgD~~~~~VaAASIvAKv 150 (207)
T PRK13926 91 ------LNVLKATHLAAARALARL---AVAPEALVTDYLR--------L--PT-PLPLLAPPKADALSPTVAAASLLAKT 150 (207)
T ss_pred ------HHHHHHHHHHHHHHHHhc---CCCCCEEEECccc--------C--CC-CCCeEEEecCccccHHHHHHHHHHHH
Confidence 699999999988777553 3556789999531 1 11 24677889999999999999999999
Q ss_pred HHHHHHHHhhHhhcccccCCCCCccCCCCHHHHHHHHhcccccCCCCccccccchhHHHhhc
Q 022427 171 TRDRTLRGWIFEETAENMHRNFGSGYPGDPETKAWLTDHKHIIFGFPSLVRFSWGTCTSHFK 232 (297)
Q Consensus 171 ~RD~~m~~~~~~~~~~~~~~~~GsGYpsDp~T~~~L~~~~~~~~G~~~~~R~Sw~t~~~~l~ 232 (297)
+||++|++|+..++.|+|..| |||| ++.|++||++| |+|++||+||+|++++++
T Consensus 151 ~RD~~m~~l~~~~~~yg~~~~--kGY~-t~~h~~~l~~~-----G~~~~hR~s~~~~~~~~~ 204 (207)
T PRK13926 151 ERDRLMRELDARYPGYGFARH--KGYG-TPAHREALAAL-----GPSPVHRRSFAPVRRLLT 204 (207)
T ss_pred HHHHHHHHHHHhCccCCCcCC--CCCC-CHHHHHHHHHh-----CcCHHHcCCcHHHHHhhh
Confidence 999999999999999988755 9999 89999999864 999999999999998763
No 11
>PRK14550 rnhB ribonuclease HII; Provisional
Probab=100.00 E-value=1.5e-54 Score=388.64 Aligned_cols=193 Identities=23% Similarity=0.276 Sum_probs=160.1
Q ss_pred ceeeecccCCCCcccceeEEEEEecccccchhcccCCCCCCCCCHHHHHHHHHHhhhcCcccEEEEEEChhhHhHHhhhh
Q 022427 15 CIMGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLKVNDSVGWAVDIIDPRELSAKMLNK 94 (297)
Q Consensus 15 ~viGiDEAGRGpv~GPmVvaav~~~~~~~~~L~~lgv~DSK~Ls~~kRe~L~~~I~~~~~~~~~v~~isp~eId~~m~~~ 94 (297)
.++|||||||||++||||||||+++.+....+..+||+|||+||+++|++||++|++...+.|.+.+++|++||
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 37999999999999999999999998766667778999999999999999999998753478999999999996
Q ss_pred hhhhHHHHHHHHHHHHHHHHHccCCCcceEEECCCCChHHHHHHhhccCCCcceEEeecCccccchhhhhHHHHHHHHHH
Q 022427 95 NKINLNEISHDSAIGLITRVLNIGILLTEVYLDTVGDAEKYQAKLSQRFPSIKFVVSKKADSLYPVVSGASIVAKVTRDR 174 (297)
Q Consensus 95 ~~~NLN~l~~~~~~~li~~~l~~~~~~~~v~VD~~g~~~~y~~~L~~~~p~~~~~~~~KaDs~~~~VAAASIiAKV~RD~ 174 (297)
++|||.++..++.+++.++ ...++.++||++..+..+ ..+| .+.+++|||++|++||||||||||+||+
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 4799998877766565542 345678999987543211 1122 3456789999999999999999999999
Q ss_pred HHHHhhHhhcccccCCCCCccCCCCHHHHHHHHhcccccCCCCccccccchhHHHhhc
Q 022427 175 TLRGWIFEETAENMHRNFGSGYPGDPETKAWLTDHKHIIFGFPSLVRFSWGTCTSHFK 232 (297)
Q Consensus 175 ~m~~~~~~~~~~~~~~~~GsGYpsDp~T~~~L~~~~~~~~G~~~~~R~Sw~t~~~~l~ 232 (297)
+|++++..+|.|+|. +||||| |++|++.. ..+|++|+||+||+|++++|.
T Consensus 144 ~M~~l~~~~p~Ygf~--~~kGY~----T~~h~~ai--~~~G~~p~hR~Sf~t~~~~~~ 193 (204)
T PRK14550 144 EMLELHALFKEYGWD--KNCGYG----TKQHIEAI--IKLGATPFHRHSFTLKNRILN 193 (204)
T ss_pred HHHHHHHhCCCCCCc--CCCCCC----CHHHHHHH--HHhCcCHHHcCCcCCCCcccC
Confidence 999999999999986 459999 67777663 346999999999999999883
No 12
>PRK13925 rnhB ribonuclease HII; Provisional
Probab=100.00 E-value=7.4e-54 Score=382.72 Aligned_cols=194 Identities=21% Similarity=0.286 Sum_probs=161.4
Q ss_pred CcCCC-CceeeecccCCCCcccceeEEEEEecccccchhcccCCCCCCCCCHHHHHHHHHHhhhcCcccEEEEEEChhhH
Q 022427 9 KWASN-PCIMGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLKVNDSVGWAVDIIDPREL 87 (297)
Q Consensus 9 ~~~~~-~~viGiDEAGRGpv~GPmVvaav~~~~~~~~~L~~lgv~DSK~Ls~~kRe~L~~~I~~~~~~~~~v~~isp~eI 87 (297)
...+. .+++||||||||||+||||||||++|.+....|..+||+|||+||+++|++||++|++. ...|.+.+++|++|
T Consensus 2 ~~~~~~~~iiGiDEAGRGpv~GPmVvaav~~~~~~~~~L~~~gv~DSK~Ls~~~Re~l~~~I~~~-~~~~~i~~i~~~eI 80 (198)
T PRK13925 2 MMENISELIAGVDEVGRGALFGPVFAAAVILSEKAEPQLLQAGLTDSKKLSPKRRAQLVPLILTL-ASDWGIGQASAREI 80 (198)
T ss_pred cccCCCCeEEeecCCCCCCChHHhEEEEEEEchHhhhhhhhcCCCCcccCCHHHHHHHHHHHHhh-CCcEEEEEECHHHh
Confidence 33443 78999999999999999999999999887777888999999999999999999999875 46799999999999
Q ss_pred hHHhhhhhhhhHHHHHHHHHHHHHHHHHccCCCcceEEECCCCChHHHHHHhhccCCCcceEEeecCccccchhhhhHHH
Q 022427 88 SAKMLNKNKINLNEISHDSAIGLITRVLNIGILLTEVYLDTVGDAEKYQAKLSQRFPSIKFVVSKKADSLYPVVSGASIV 167 (297)
Q Consensus 88 d~~m~~~~~~NLN~l~~~~~~~li~~~l~~~~~~~~v~VD~~g~~~~y~~~L~~~~p~~~~~~~~KaDs~~~~VAAASIi 167 (297)
| +.|||.++..++.+++..+ ...++.|+||++++.. .+++... ..+|||++|++|||||||
T Consensus 81 d-------~~ni~~~~~~a~~~~i~~l---~~~~~~v~iD~~~~~~--------~~~~~~~-~v~kaD~~~~~VaAASIi 141 (198)
T PRK13925 81 D-------RLGIRQATELAMLRALKKL---KSPPSLCLVDGNLPLR--------LWPGPQR-TIVKGDSKSAAIAAASIL 141 (198)
T ss_pred C-------HhhHHHHHHHHHHHHHHhc---CCCCCEEEECCccccC--------cCCCCce-eecccccccHHHHHHHHH
Confidence 6 4699999988887766553 3456789999986421 2333222 346999999999999999
Q ss_pred HHHHHHHHHHHhhHhhcccccCCCCCccCCCCHHHHHHHHhcccccCCCCccccccchhHHHh
Q 022427 168 AKVTRDRTLRGWIFEETAENMHRNFGSGYPGDPETKAWLTDHKHIIFGFPSLVRFSWGTCTSH 230 (297)
Q Consensus 168 AKV~RD~~m~~~~~~~~~~~~~~~~GsGYpsDp~T~~~L~~~~~~~~G~~~~~R~Sw~t~~~~ 230 (297)
|||+||++|+.|+..+|.|+|..| +|||+++ |++++++ ||++|+||+||.|+-.+
T Consensus 142 AKV~RD~~m~~l~~~yp~y~f~~~--kGY~t~~-h~~~i~~-----~G~~p~hR~sf~~~~~~ 196 (198)
T PRK13925 142 AKVWRDDLIKRLAKKYPGYGLEKN--KGYGTAQ-HRQALLK-----LGPTPLHRKSFLPKLIL 196 (198)
T ss_pred HHHHHHHHHHHHHHHCCCCCcccC--CCCCcHH-HHHHHHH-----hCcCHHHcCCCcchhhc
Confidence 999999999999999999998766 9999533 5666665 49999999999986544
No 13
>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=5.8e-54 Score=378.08 Aligned_cols=178 Identities=29% Similarity=0.419 Sum_probs=153.5
Q ss_pred eeecccCCCCcccceeEEEEEecccccchhcccCCCCCCCCCHHHHHHHHHHhhhcCcccEEEEEEChhhHhHHhhhhhh
Q 022427 17 MGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLKVNDSVGWAVDIIDPRELSAKMLNKNK 96 (297)
Q Consensus 17 iGiDEAGRGpv~GPmVvaav~~~~~~~~~L~~lgv~DSK~Ls~~kRe~L~~~I~~~~~~~~~v~~isp~eId~~m~~~~~ 96 (297)
+|||||||||+|||||||||+++.+.. .+||+|||+||+++|++||+.|++. .+.|++.+++|++||+
T Consensus 1 ~GiDEaGRG~~~GPlvvaav~~~~~~~----~~gv~DSK~Ls~~~R~~l~~~I~~~-~~~~~v~~~~~~~Id~------- 68 (179)
T cd07182 1 AGVDEAGRGPLAGPVVAAAVILPPDFE----IEGLNDSKKLSEKKREELYEEIKEK-ALAWGIGIASPEEIDR------- 68 (179)
T ss_pred CCCcCccCCCcccceEEEEEEECcccC----cCCCCCcccCCHHHHHHHHHHHHHh-cccEEEEEECHHHHCH-------
Confidence 699999999999999999999987632 2899999999999999999999974 5789999999999963
Q ss_pred hhHHHHHHHHHHHHHHHHHccCCCcceEEECCCCChHHHHHHhhccCCCcceEEeecCccccchhhhhHHHHHHHHHHHH
Q 022427 97 INLNEISHDSAIGLITRVLNIGILLTEVYLDTVGDAEKYQAKLSQRFPSIKFVVSKKADSLYPVVSGASIVAKVTRDRTL 176 (297)
Q Consensus 97 ~NLN~l~~~~~~~li~~~l~~~~~~~~v~VD~~g~~~~y~~~L~~~~p~~~~~~~~KaDs~~~~VAAASIiAKV~RD~~m 176 (297)
+|||++++.++.++|.++ ...++.|+||+++.+.. ..++++++|||++|++||||||||||+||++|
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 699999999988777653 34678899999976532 24567889999999999999999999999999
Q ss_pred HHhhHhhcccccCCCCCccCCCCHHHHHHHHhcccccCCCCccccccchhH
Q 022427 177 RGWIFEETAENMHRNFGSGYPGDPETKAWLTDHKHIIFGFPSLVRFSWGTC 227 (297)
Q Consensus 177 ~~~~~~~~~~~~~~~~GsGYpsDp~T~~~L~~~~~~~~G~~~~~R~Sw~t~ 227 (297)
+.|+..++.|+|.. |||||+++ +++++++ +|++++||+||+|+
T Consensus 136 ~~l~~~~~~yg~~~--~~GY~s~~-h~~~i~~-----~G~~~~hR~s~~~~ 178 (179)
T cd07182 136 IELDKKYPGYGFAK--HKGYGTKE-HLEALKK-----YGPTPIHRRSFAPV 178 (179)
T ss_pred HHHHHHCcCCCCcC--CCCCCcHH-HHHHHHH-----hCcCHhhcCCCCCC
Confidence 99999999998865 59999866 5556655 59999999999986
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=9.2e-53 Score=374.65 Aligned_cols=198 Identities=40% Similarity=0.601 Sum_probs=166.0
Q ss_pred eeecccCCCCcccceeEEEEEecccccchhcccCCCCCCCCCHHHHHHHHHHhhhcCcccEEEEEEChhhHhHHhhhhhh
Q 022427 17 MGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLKVNDSVGWAVDIIDPRELSAKMLNKNK 96 (297)
Q Consensus 17 iGiDEAGRGpv~GPmVvaav~~~~~~~~~L~~lgv~DSK~Ls~~kRe~L~~~I~~~~~~~~~v~~isp~eId~~m~~~~~ 96 (297)
+|||||||||+|||||||||+++.+....|..+||+|||+||+++|++|+++|+. +.+. .+.+..|... ..+.
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 7999999999999999999999999888999999999999999999999999991 3333 3444444321 1256
Q ss_pred hhHHHHHHHHHHHHHHHHHccCCCcceEEECCCCChHHHHHHhhccCCCcceEEeecCccccchhhhhHHHHHHHHHHHH
Q 022427 97 INLNEISHDSAIGLITRVLNIGILLTEVYLDTVGDAEKYQAKLSQRFPSIKFVVSKKADSLYPVVSGASIVAKVTRDRTL 176 (297)
Q Consensus 97 ~NLN~l~~~~~~~li~~~l~~~~~~~~v~VD~~g~~~~y~~~L~~~~p~~~~~~~~KaDs~~~~VAAASIiAKV~RD~~m 176 (297)
+|+|.+++..+.++++.+.+.+..++.|+||+++.+++|..++.+.++ .++++++|||++|++||||||||||+||..|
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 899999999998899988887778889999999999999999988888 8899999999999999999999999999666
Q ss_pred HHhhHhhcccccCCCCCccCCCCHHHHHHHHhcccccCCCCccccccchhH
Q 022427 177 RGWIFEETAENMHRNFGSGYPGDPETKAWLTDHKHIIFGFPSLVRFSWGTC 227 (297)
Q Consensus 177 ~~~~~~~~~~~~~~~~GsGYpsDp~T~~~L~~~~~~~~G~~~~~R~Sw~t~ 227 (297)
+.+. .+++ +..++|||||+||.|++|++.+..+ ++|++||+||+|+
T Consensus 153 ~~~~-~~~~--~~~~~gsGy~s~~~~~~~~~~~~~~--~l~~~~R~sf~tv 198 (198)
T PF01351_consen 153 ELLS-KYPG--YGFPKGSGYPSDPHTRAILKKGGSP--ELPQIHRLSFKTV 198 (198)
T ss_dssp HHHH-HHHT--S-HCCTSSSTTSHHHHHHHHHHHHH--SSHTTB-TTSHHH
T ss_pred HHHH-hCcC--CCCccCCCCChHHHHHHHHHhCCCC--CCCccccCCCcCC
Confidence 6543 3444 4457899999999999999999877 8999999999996
No 15
>PRK00996 ribonuclease HIII; Provisional
Probab=100.00 E-value=4.4e-50 Score=379.13 Aligned_cols=211 Identities=22% Similarity=0.257 Sum_probs=185.1
Q ss_pred CCceeeecccCCCCcccceeEEEEEecccccchhcccCCCCCCCCCHHHHHHHHHHhhhcCcccEEEEEEChhhHhHHhh
Q 022427 13 NPCIMGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLKVNDSVGWAVDIIDPRELSAKML 92 (297)
Q Consensus 13 ~~~viGiDEAGRGpv~GPmVvaav~~~~~~~~~L~~lgv~DSK~Ls~~kRe~L~~~I~~~~~~~~~v~~isp~eId~~m~ 92 (297)
...+||||||||||+|||||||||+++.+....|..+||+|||+||+++|++|++.|++. +.|.+.+++|++||+++.
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 356899999999999999999999999888888899999999999999999999999974 689999999999998753
Q ss_pred hhhhhhHHHHHHHHHHHHHHHHHcc--CCCcceEEECCCCChHHHHHHhhcc--CCCcceEEeecCccccchhhhhHHHH
Q 022427 93 NKNKINLNEISHDSAIGLITRVLNI--GILLTEVYLDTVGDAEKYQAKLSQR--FPSIKFVVSKKADSLYPVVSGASIVA 168 (297)
Q Consensus 93 ~~~~~NLN~l~~~~~~~li~~~l~~--~~~~~~v~VD~~g~~~~y~~~L~~~--~p~~~~~~~~KaDs~~~~VAAASIiA 168 (297)
...|+|.+....+.++|..+++. +..++.|+||+|+.++.|+++|... .+..++++++|||++|++||||||||
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 34799998776666667776543 5667899999999999999999752 23467888999999999999999999
Q ss_pred HHHHHHHHHHhhHhhcccccCCCCCccCCCCHHHHHHHHhcccccCCCCccccccchhHHHhhc
Q 022427 169 KVTRDRTLRGWIFEETAENMHRNFGSGYPGDPETKAWLTDHKHIIFGFPSLVRFSWGTCTSHFK 232 (297)
Q Consensus 169 KV~RD~~m~~~~~~~~~~~~~~~~GsGYpsDp~T~~~L~~~~~~~~G~~~~~R~Sw~t~~~~l~ 232 (297)
||++|+.|+.+++.|++..++|+|||+|+.+++||+++.. -.++.++|.+|+|++++++
T Consensus 242 ---R~~~l~~~~~l~~~yg~~~~kGag~~~d~~a~~~i~~~G~--~~L~~~aK~hfk~~~k~~~ 300 (304)
T PRK00996 242 ---RYAFLENMDKLSKEAGMTLPKGAGAKVDKVAAQILKKYGK--EALEKFAKLHFKNTEKAQK 300 (304)
T ss_pred ---HHHHHHHHHHhCcCCCCCCCCCCCCHHHHHHHHHHHHhCc--chhHHHHHHhchhHHHHHH
Confidence 9999999999999999999999999999999999998742 2378899999999988764
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=1.6e-43 Score=331.71 Aligned_cols=194 Identities=24% Similarity=0.296 Sum_probs=160.9
Q ss_pred CceeeecccCCCCcccceeEEEEEecccccchhcccCCCCCCCCCHHHHHHHHHHhhhcCcccEEEEEEChhhHhHHhhh
Q 022427 14 PCIMGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLKVNDSVGWAVDIIDPRELSAKMLN 93 (297)
Q Consensus 14 ~~viGiDEAGRGpv~GPmVvaav~~~~~~~~~L~~lgv~DSK~Ls~~kRe~L~~~I~~~~~~~~~v~~isp~eId~~m~~ 93 (297)
.++||||||||||+|||||||||+++.+....|+.+||+|||+||+++|++|+++|++. +.|.+.+++|++||.++.
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 56999999999999999999999999887778899999999999999999999999974 579999999999997642
Q ss_pred hhhhhHHHHHHHHHHHHHHHHHccCCCcceEEECCCCChHHHHHHhhc-cCCCcceEEeecCccccchhhhhHHHHHHHH
Q 022427 94 KNKINLNEISHDSAIGLITRVLNIGILLTEVYLDTVGDAEKYQAKLSQ-RFPSIKFVVSKKADSLYPVVSGASIVAKVTR 172 (297)
Q Consensus 94 ~~~~NLN~l~~~~~~~li~~~l~~~~~~~~v~VD~~g~~~~y~~~L~~-~~p~~~~~~~~KaDs~~~~VAAASIiAKV~R 172 (297)
...|+|.+....+.++|..++........|+||+++.++.|+.+|.. .++..++++++|||+ |++|||||||| |
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 35799999999998888887643323347999999988888877754 345678889999998 99999999999 9
Q ss_pred HHHHHHhhHhhcccccCCCCCccCCCCHHHHHHHHhcccccCCCCccc
Q 022427 173 DRTLRGWIFEETAENMHRNFGSGYPGDPETKAWLTDHKHIIFGFPSLV 220 (297)
Q Consensus 173 D~~m~~~~~~~~~~~~~~~~GsGYpsDp~T~~~L~~~~~~~~G~~~~~ 220 (297)
|++|+.|+.+++.|++..+.|+|-..|....+++++| |+..++
T Consensus 233 ~~~l~~l~~l~~~yg~~~pkGa~~~v~~~a~~~i~~~-----G~~~L~ 275 (284)
T TIGR00716 233 YKFLQSLKELERELGIKLPKGASKEVKELAKSLILKK-----GPSALE 275 (284)
T ss_pred HHHHHHHHHhCcccCCcCCCCCChHHHHHHHHHHHHh-----CccHHH
Confidence 9999999999999999887444433344444566654 777544
No 17
>COG1039 RnhC Ribonuclease HIII [DNA replication, recombination, and repair]
Probab=100.00 E-value=1.8e-36 Score=280.20 Aligned_cols=206 Identities=22% Similarity=0.273 Sum_probs=178.1
Q ss_pred CceeeecccCCCCcccceeEEEEEecccccchhcccCCCCCCCCCHHHHHHHHHHhhhcCcccEEEEEEChhhHhHHhhh
Q 022427 14 PCIMGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLKVNDSVGWAVDIIDPRELSAKMLN 93 (297)
Q Consensus 14 ~~viGiDEAGRGpv~GPmVvaav~~~~~~~~~L~~lgv~DSK~Ls~~kRe~L~~~I~~~~~~~~~v~~isp~eId~~m~~ 93 (297)
..+||+||+|.|++|||||||||+++++....|..+||+|||+|++.++.+|++.|++ .+.+.+..++|++||++..
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 6789999999999999999999999999999999999999999999999999999998 4788999999999999874
Q ss_pred hhhhhHHHHHHHHHHHHHHHHHc-cCCCcceEEECCCCChHHHHHHhhccC--CCcceEEeecCccccchhhhhHHHHHH
Q 022427 94 KNKINLNEISHDSAIGLITRVLN-IGILLTEVYLDTVGDAEKYQAKLSQRF--PSIKFVVSKKADSLYPVVSGASIVAKV 170 (297)
Q Consensus 94 ~~~~NLN~l~~~~~~~li~~~l~-~~~~~~~v~VD~~g~~~~y~~~L~~~~--p~~~~~~~~KaDs~~~~VAAASIiAKV 170 (297)
...|.|.+....+..+|+.++. .+..++.|+||+|.+.+.|..+|.+.. +..++.+.+||++++.+||||||+|
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 4578888877777777888874 678899999999999999999998762 3456778999999999999999999
Q ss_pred HHHHHHHHhhHhhcccccCCCCCccCCCCHHHHHHHHhcccccCCCC---ccccccchhHHHhh
Q 022427 171 TRDRTLRGWIFEETAENMHRNFGSGYPGDPETKAWLTDHKHIIFGFP---SLVRFSWGTCTSHF 231 (297)
Q Consensus 171 ~RD~~m~~~~~~~~~~~~~~~~GsGYpsDp~T~~~L~~~~~~~~G~~---~~~R~Sw~t~~~~l 231 (297)
||.|+..|+.++.+|++..+.|+|-.+|....+.+++. |+. .+....|++.++.+
T Consensus 237 -R~~Fl~~~~~l~~~~gv~LPkGAg~~V~~~a~~i~~k~-----g~~~L~~~~k~hf~n~~k~~ 294 (297)
T COG1039 237 -RYAFLQSLKQLSRQYGVQLPKGAGPAVDQAAAEIIQKR-----GFSKLEQVAKLHFKNFQKAL 294 (297)
T ss_pred -HHHHHHHHHHHHHHhCCcCCCCCchhHHHHHHHHHHHh-----hHHHHHHHHHHHHHHHHHHH
Confidence 99999999999999999999999977777776666654 543 35556666665554
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=74.03 E-value=57 Score=28.06 Aligned_cols=160 Identities=19% Similarity=0.175 Sum_probs=76.5
Q ss_pred eeeecccCCCCc-----ccce-eEEEEEecccccchh--------cccCCC------------------CCCCCCHHHH-
Q 022427 16 IMGIDEAGRGPV-----LGPM-VYGCLYCPCSYQQTL--------ATLNFA------------------DSKTLKEEKR- 62 (297)
Q Consensus 16 viGiDEAGRGpv-----~GPm-Vvaav~~~~~~~~~L--------~~lgv~------------------DSK~Ls~~kR- 62 (297)
++.|||+|.-.. -.|. |+|+++++.+....+ ..++.. +-..++..+|
T Consensus 1 ~iyiDESG~~~~~~~~~~~~~fvl~gv~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lh~~~i~~~~~~~~~~~~~~~~ 80 (235)
T PF12686_consen 1 IIYIDESGNTGPNYSDKNSPYFVLGGVIIEDEDWKKIINEIRSLKKKYGFKEEVEKSELHASDISNGKKDFSKLSKDERQ 80 (235)
T ss_pred CEEEeCCCCCCCCcCCCCCCEEEEEEEEEcHHHHHHHHHHHHHHHHHhCccccchhhhhhHHHhhhcccccccCCHHHHH
Confidence 478999995433 3443 578888877543211 112221 1123444444
Q ss_pred ---HHHHHHhhhcCcccEEEEEEChhhHhHHhhhhh-hhhHHHHHHHHHHHHHHHHH---ccCCCcceEEECCCCC--hH
Q 022427 63 ---EELFEDLKVNDSVGWAVDIIDPRELSAKMLNKN-KINLNEISHDSAIGLITRVL---NIGILLTEVYLDTVGD--AE 133 (297)
Q Consensus 63 ---e~L~~~I~~~~~~~~~v~~isp~eId~~m~~~~-~~NLN~l~~~~~~~li~~~l---~~~~~~~~v~VD~~g~--~~ 133 (297)
+.++..|.+.....+.+.++....++....... ....+..-..+...+++++. ...-....|++|.... ..
T Consensus 81 ~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~y~~~~~~ll~~~~~~~~~~~~~~~iv~D~~~~~~~~ 160 (235)
T PF12686_consen 81 EFFKDLFDIISELKFIIFIAVIDDKKLYNRSSLDNNKPRDPNKFYNLALRFLLERINMYLQRPNENIIIVIDNGDRKKDN 160 (235)
T ss_pred HHHHHHHHHHHhCCCceEEEEEEeccccchhhhcccccchhHHHHHHHHHHHHHHHHHhhcCCCceEEEEEeCCCchHHH
Confidence 667777776432445566666666654432111 11222333334444555544 1122334688893221 22
Q ss_pred HHHHHhhc---------cCCCcceEEeecCcccc-chhhhhHHHHHHHHHHHH
Q 022427 134 KYQAKLSQ---------RFPSIKFVVSKKADSLY-PVVSGASIVAKVTRDRTL 176 (297)
Q Consensus 134 ~y~~~L~~---------~~p~~~~~~~~KaDs~~-~~VAAASIiAKV~RD~~m 176 (297)
....++.. ....+ +....-.||+. +-|=+|=+||=..|-.+.
T Consensus 161 ~l~~~~~~~~~~~~~~~~~~~~-~~~~~~~~S~~s~~lQiAD~ia~~i~r~~~ 212 (235)
T PF12686_consen 161 KLKEYLRKQYSKGSKRDKLKNI-IEEIFFVDSKDSPGLQIADLIAGAIRRYLE 212 (235)
T ss_pred HHHHHHHHhccccccccccccc-ccceeecCCCCCHhHHHHHHHHHHHHHHHH
Confidence 22233210 01111 11123344443 888899999965555443
No 19
>cd00223 TOPRIM_TopoIIB_SPO TOPRIM_TopoIIB_SPO: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in the type IIB family of DNA topoisomerases and Spo11. This subgroup contains proteins similar to Sulfolobus shibatae topoisomerase VI (TopoVI) and Saccharomyces cerevisiae meiotic recombination factor: Spo11. Type II DNA topoisomerases catalyze the ATP-dependent transport of one DNA duplex through another, in the process generating transient double strand breaks via covalent attachments to both DNA strands at the 5' positions. TopoVI enzymes are heterotetramers found in archaea and plants. Spo11 plays a role in generating the double strand breaks that initiate homologous recombination during meiosis. S. shibatae TopoVI relaxes both positive and negative supercoils, and in addition has a strong decatenase activity. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspart
Probab=41.54 E-value=17 Score=31.05 Aligned_cols=18 Identities=39% Similarity=0.754 Sum_probs=15.0
Q ss_pred CCccCCCCHHHHHHHHhcc
Q 022427 192 FGSGYPGDPETKAWLTDHK 210 (297)
Q Consensus 192 ~GsGYpsDp~T~~~L~~~~ 210 (297)
.|+||| |..|+.||+...
T Consensus 30 t~kG~P-~~~tr~~l~~L~ 47 (160)
T cd00223 30 TGKGYP-DRATRRFLRRLH 47 (160)
T ss_pred EcCCcC-CHHHHHHHHHHH
Confidence 479999 799999999753
No 20
>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=41.07 E-value=37 Score=33.51 Aligned_cols=34 Identities=21% Similarity=0.280 Sum_probs=20.6
Q ss_pred CCCHHHHHHHHHHhhhcCcccEEEEEEChhhHhHHhh
Q 022427 56 TLKEEKREELFEDLKVNDSVGWAVDIIDPRELSAKML 92 (297)
Q Consensus 56 ~Ls~~kRe~L~~~I~~~~~~~~~v~~isp~eId~~m~ 92 (297)
.|+++.+.+|+.++.+ +..+ . .+++|++||+.+.
T Consensus 297 ~~~~~Ek~~li~EvL~-P~~~-~-L~VTPKeID~~i~ 330 (358)
T TIGR01441 297 TLDEEEKRQLIYEVLN-PLGH-N-LMVTPKEVDMFIE 330 (358)
T ss_pred cCCHHHHHHHHHHHhC-cccC-c-ceECcHhHHHHHH
Confidence 4455555555555543 2122 2 7899999998763
No 21
>PRK12362 germination protease; Provisional
Probab=36.32 E-value=51 Score=32.08 Aligned_cols=35 Identities=26% Similarity=0.520 Sum_probs=26.5
Q ss_pred CCCCHHHHHHHHHHhhhcCcccEEEEEEChhhHhHHhh
Q 022427 55 KTLKEEKREELFEDLKVNDSVGWAVDIIDPRELSAKML 92 (297)
Q Consensus 55 K~Ls~~kRe~L~~~I~~~~~~~~~v~~isp~eId~~m~ 92 (297)
|.|+++.+.+|+.++.+- ..+ . .+++|++||+.+.
T Consensus 264 ~~~~~~ek~~li~evl~p-~~~-~-l~VTPKeID~~i~ 298 (318)
T PRK12362 264 KSLNQEEKQQLIKEVLSP-YVG-N-LIVTPKEIDELIE 298 (318)
T ss_pred hccCHHHHHHHHHHHhCc-cCC-c-ceECcHhHHHHHH
Confidence 578999999998887752 222 2 6899999998763
No 22
>KOG3495 consensus Mitochondrial F1F0-ATP synthase, subunit epsilon/ATP15 [Energy production and conversion]
Probab=34.22 E-value=44 Score=23.81 Aligned_cols=20 Identities=20% Similarity=0.159 Sum_probs=16.8
Q ss_pred hhhhHHHHHHHHHHHHHHhh
Q 022427 161 VSGASIVAKVTRDRTLRGWI 180 (297)
Q Consensus 161 VAAASIiAKV~RD~~m~~~~ 180 (297)
|.=++|+|++.|+.++.++.
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 45679999999999998863
No 23
>PRK04342 DNA topoisomerase VI subunit A; Provisional
Probab=33.71 E-value=27 Score=34.46 Aligned_cols=19 Identities=16% Similarity=0.300 Sum_probs=16.0
Q ss_pred CCccCCCCHHHHHHHHhccc
Q 022427 192 FGSGYPGDPETKAWLTDHKH 211 (297)
Q Consensus 192 ~GsGYpsDp~T~~~L~~~~~ 211 (297)
.|+||| |..|+.||+...+
T Consensus 220 tgkG~P-d~~TR~fl~~L~~ 238 (367)
T PRK04342 220 HLKGQP-ARATRRFIKRLNE 238 (367)
T ss_pred ECCCCC-CHHHHHHHHHHHH
Confidence 489999 7999999997654
No 24
>PLN00060 meiotic recombination protein SPO11-2; Provisional
Probab=33.21 E-value=28 Score=34.67 Aligned_cols=17 Identities=35% Similarity=0.544 Sum_probs=14.9
Q ss_pred CccCCCCHHHHHHHHhcc
Q 022427 193 GSGYPGDPETKAWLTDHK 210 (297)
Q Consensus 193 GsGYpsDp~T~~~L~~~~ 210 (297)
|+||| |-.|+.||+...
T Consensus 242 gKGyP-D~aTR~fL~~L~ 258 (384)
T PLN00060 242 AKGYP-DLATRFILHRLS 258 (384)
T ss_pred cCCCC-CHHHHHHHHHHH
Confidence 79999 899999999753
No 25
>PF09345 DUF1987: Domain of unknown function (DUF1987); InterPro: IPR018530 This family of proteins are functionally uncharacterised.
Probab=28.09 E-value=84 Score=25.25 Aligned_cols=54 Identities=24% Similarity=0.330 Sum_probs=29.5
Q ss_pred CccCCCCHH-----HHHHHHhcccccCCCCc-cccccc---hhHHHh------hc------ccceEEeccCcccc
Q 022427 193 GSGYPGDPE-----TKAWLTDHKHIIFGFPS-LVRFSW---GTCTSH------FK------DIVEVLWESDEMDE 246 (297)
Q Consensus 193 GsGYpsDp~-----T~~~L~~~~~~~~G~~~-~~R~Sw---~t~~~~------l~------~~~~~~~~~~~~~~ 246 (297)
|..||-|+. ..+||++++....+... -+++++ ++.+.+ |+ ..|.|.|--|++|+
T Consensus 16 GeSypEn~~~Fy~Pi~~wl~~Yl~~~~~~i~~~~~L~YfNTSSsk~l~~i~~~Le~~~~~g~~V~v~Wyyd~dD~ 90 (99)
T PF09345_consen 16 GESYPENAFAFYQPILDWLEAYLAEPNKPITFNFKLSYFNTSSSKALMDIFDLLEDAAQKGGKVTVNWYYDEDDE 90 (99)
T ss_pred cccCccCHHHHHHHHHHHHHHHHhCCCCcEEEEEEEEEEecHhHHHHHHHHHHHHHHHhcCCcEEEEEEECCCCc
Confidence 566776664 46888888766322222 244444 333332 11 45889996665443
No 26
>KOG2795 consensus Catalytic subunit of the meiotic double strand break transesterase [Replication, recombination and repair]
Probab=27.48 E-value=34 Score=33.87 Aligned_cols=20 Identities=35% Similarity=0.640 Sum_probs=16.5
Q ss_pred CCccCCCCHHHHHHHHhcccc
Q 022427 192 FGSGYPGDPETKAWLTDHKHI 212 (297)
Q Consensus 192 ~GsGYpsDp~T~~~L~~~~~~ 212 (297)
-|+||| |-.|+.||+...+.
T Consensus 224 TgKGyP-D~~TR~fLkkL~~~ 243 (372)
T KOG2795|consen 224 TGKGYP-DIATRLFLKKLEEK 243 (372)
T ss_pred ecCCCC-cHHHHHHHHHHHHH
Confidence 489999 99999999976543
No 27
>PRK05473 hypothetical protein; Provisional
Probab=26.20 E-value=71 Score=25.27 Aligned_cols=22 Identities=18% Similarity=0.291 Sum_probs=18.3
Q ss_pred hhHHHHHHHHHHHHHHhhHhhc
Q 022427 163 GASIVAKVTRDRTLRGWIFEET 184 (297)
Q Consensus 163 AASIiAKV~RD~~m~~~~~~~~ 184 (297)
|=|+|-|+.||.+|+++-..|.
T Consensus 60 AR~lIrkiERDEilEeLv~~Yl 81 (86)
T PRK05473 60 ARNLIRKLERDEILEELVKSYL 81 (86)
T ss_pred HHHHHHHHhHHHHHHHHHHHHH
Confidence 6699999999999999765543
No 28
>KOG0189 consensus Phosphoadenosine phosphosulfate reductase [Amino acid transport and metabolism]
Probab=25.72 E-value=4.5e+02 Score=24.46 Aligned_cols=82 Identities=22% Similarity=0.306 Sum_probs=46.9
Q ss_pred CHHHHHHHHHHhhhcCcccEEEEEEChhhHhHHhhhhhhhhHHHHHHHHH--HHHHHHHHccCCCcceEEECCCC-ChHH
Q 022427 58 KEEKREELFEDLKVNDSVGWAVDIIDPRELSAKMLNKNKINLNEISHDSA--IGLITRVLNIGILLTEVYLDTVG-DAEK 134 (297)
Q Consensus 58 s~~kRe~L~~~I~~~~~~~~~v~~isp~eId~~m~~~~~~NLN~l~~~~~--~~li~~~l~~~~~~~~v~VD~~g-~~~~ 134 (297)
..+.-|+|.++|.+ +||.+|=.+-+. ..-|+-+++...+ ..+|.-+-..+.++..++|||-. +|++
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 45556666666553 578888544321 1224433332221 22344444456677889999975 8998
Q ss_pred HH--HHhhccCCCcceEE
Q 022427 135 YQ--AKLSQRFPSIKFVV 150 (297)
Q Consensus 135 y~--~~L~~~~p~~~~~~ 150 (297)
|. +...+.++++.+.+
T Consensus 87 ~~l~d~VekkY~~i~I~~ 104 (261)
T KOG0189|consen 87 LRLFDAVEKKYGNIRIHV 104 (261)
T ss_pred HHHHHHHHHhcCceEEEE
Confidence 74 44566677766543
No 29
>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=25.51 E-value=28 Score=27.73 Aligned_cols=20 Identities=35% Similarity=0.478 Sum_probs=17.9
Q ss_pred chhhhhHHHHHHHHHHHHHH
Q 022427 159 PVVSGASIVAKVTRDRTLRG 178 (297)
Q Consensus 159 ~~VAAASIiAKV~RD~~m~~ 178 (297)
-+||-|||+-|.-||.+++.
T Consensus 10 eIia~aSiLIKfg~ddIl~~ 29 (91)
T PF09010_consen 10 EIIAVASILIKFGRDDILEN 29 (91)
T ss_dssp HHHHHHHHHHHTTTHHHHTS
T ss_pred HHHHHHHHHHHcChHHHHHh
Confidence 47999999999999988876
Done!