Query 026552
Match_columns 237
No_of_seqs 248 out of 1283
Neff 5.7
Searched_HMMs 46136
Date Fri Mar 29 09:29:56 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/026552.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/026552hhsearch_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 4.4E-62 9.6E-67 430.0 11.9 218 4-235 77-300 (301)
2 cd07181 RNaseH_typeII_eukaryot 100.0 1.6E-43 3.5E-48 309.1 16.4 162 4-171 47-216 (216)
3 PRK14551 rnhB ribonuclease HII 100.0 5E-40 1.1E-44 286.7 15.2 155 4-172 45-202 (212)
4 cd07180 RNaseH_typeII_Archaea_ 100.0 2.2E-39 4.7E-44 280.6 15.6 155 4-170 47-203 (204)
5 TIGR00729 ribonuclease H, mamm 100.0 4.6E-39 1E-43 279.1 16.1 155 4-171 48-205 (206)
6 COG0164 RnhB Ribonuclease HII 100.0 3.8E-35 8.3E-40 253.0 14.0 140 3-172 46-189 (199)
7 PRK00015 rnhB ribonuclease HII 100.0 1.3E-34 2.7E-39 250.3 13.1 131 4-167 63-197 (197)
8 cd06266 RNaseH_typeII Ribonucl 100.0 9.3E-34 2E-38 243.0 14.1 143 4-168 47-193 (193)
9 cd07182 RNaseH_typeII_bacteria 100.0 8.3E-34 1.8E-38 241.8 13.1 132 4-167 43-178 (179)
10 PRK13926 ribonuclease HII; Pro 100.0 5E-33 1.1E-37 242.0 14.8 135 4-171 65-203 (207)
11 cd06590 RNaseH_typeII_bacteria 100.0 3.5E-33 7.7E-38 242.3 12.9 157 4-171 47-208 (208)
12 PRK14550 rnhB ribonuclease HII 100.0 9.6E-33 2.1E-37 239.7 10.5 140 4-172 49-193 (204)
13 PRK13925 rnhB ribonuclease HII 100.0 4.4E-31 9.5E-36 228.4 13.2 136 4-170 57-196 (198)
14 PF01351 RNase_HII: Ribonuclea 100.0 5E-30 1.1E-34 220.5 12.6 149 4-167 47-198 (198)
15 PRK00996 ribonuclease HIII; Pr 99.9 1.8E-26 4E-31 211.0 13.1 158 4-172 136-300 (304)
16 TIGR00716 rnhC ribonuclease HI 99.8 6.7E-20 1.5E-24 166.5 11.9 121 4-137 130-255 (284)
17 COG1039 RnhC Ribonuclease HIII 99.6 1.4E-14 3.1E-19 130.9 11.0 154 4-170 132-293 (297)
18 PRK04342 DNA topoisomerase VI 49.3 10 0.00022 36.0 1.8 19 132-151 220-238 (367)
19 cd00223 TOPRIM_TopoIIB_SPO TOP 46.6 13 0.00027 30.8 1.7 18 132-150 30-47 (160)
20 KOG3495 Mitochondrial F1F0-ATP 43.9 25 0.00054 24.3 2.5 19 101-119 12-30 (50)
21 PF09010 AsiA: Anti-Sigma Fact 41.4 15 0.00032 28.4 1.2 20 99-118 10-29 (91)
22 KOG1532 GTPase XAB1, interacts 40.0 1.4E+02 0.0031 28.2 7.6 70 38-110 96-180 (366)
23 PLN00060 meiotic recombination 38.1 21 0.00045 34.3 2.0 16 133-149 242-257 (384)
24 KOG2795 Catalytic subunit of t 27.9 35 0.00076 32.7 1.6 19 132-151 224-242 (372)
25 cd07015 Clp_protease_NfeD Nodu 25.3 2.5E+02 0.0053 23.8 6.2 73 39-116 10-88 (172)
26 PRK05473 hypothetical protein; 25.0 61 0.0013 24.9 2.2 17 103-119 60-76 (86)
27 PRK04860 hypothetical protein; 21.0 95 0.0021 26.2 2.8 30 131-164 79-108 (160)
28 PF09345 DUF1987: Domain of un 20.1 1.4E+02 0.0029 23.3 3.3 54 133-186 16-90 (99)
No 1
>KOG2299 consensus Ribonuclease HI [Replication, recombination and repair]
Probab=100.00 E-value=4.4e-62 Score=429.95 Aligned_cols=218 Identities=50% Similarity=0.826 Sum_probs=189.7
Q ss_pred cchhHHHhcC-----CceEEEEEEChhhHhhhcccCChhhHHHHHHHHHHHHHHHHHhcCCCccEEEEcCCCChhHHHHH
Q 026552 4 EAALPKWASN-----PFGWAVDIIDPRELSAKMLNKNKINLNEISHDSAIGLITRVLNIGILLTEVYLDTVGDAEKYQAK 78 (237)
Q Consensus 4 ~~~~~~i~~~-----a~~~~v~~isp~eId~~ml~~~~~nLN~ls~~a~~~~I~~ll~~~~~~~~V~VD~~g~~~~y~~~ 78 (237)
|.|+..|.++ .+||++.+|||++|++.||+++++|||+++|++++.||+.++++|+++++|||||+|+|++||++
T Consensus 77 e~lf~~i~~d~~~~~~vgwA~~~isP~~IS~~Ml~r~kynLNevshdsam~LI~~v~~~gvnvteiyVDTVGpp~~Yq~k 156 (301)
T KOG2299|consen 77 EELFNKIKEDEELTSNVGWATDCISPREISASMLRRNKYNLNEVSHDSAMGLIDEVLDQGVNVTEIYVDTVGPPAKYQEK 156 (301)
T ss_pred HHHHHHHhhhhhhhhceeeEeeecCHHHHHHHHHHHhcCCchhhhhHHHHHHHHHHHHhCCceEEEEEecCCChHHHHHH
Confidence 5577777655 39999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhccCCCceeEEEecCCccchhHHHHHHHHHHHHHHHHhhhchhhHHhhhcCCCCccCCCCHHHHHHHHhccccccCCCc
Q 026552 79 LSQRFPSIKFVVSKKADSLYPVVSGASIVAKVTRDRTLRGWIFEETAENMHRNFGSGYPGDPETKAWLTDHKHIIFGFPS 158 (237)
Q Consensus 79 L~~~~p~i~v~v~~KADs~~p~VsAASIvAKV~RD~~m~~~~~~e~~~~~~~~yGsGYPsDp~Tk~~L~~~~~~~fG~p~ 158 (237)
|+++||+++++|.+||||+||+||||||||||+||+.+++|+|.|.+.....+|||||||||+|++||+.|++++||||+
T Consensus 157 Lek~FP~~k~tV~kKADSlfpiVS~ASI~AKVtRD~alk~w~~~E~~~~~d~~~GSGYP~DP~T~~wLk~~v~~VFGfp~ 236 (301)
T KOG2299|consen 157 LEKRFPGIKFTVTKKADSLFPIVSAASIVAKVTRDRALKEWQFEEKLSDPDEDLGSGYPSDPETKAWLKENVDSVFGFPS 236 (301)
T ss_pred HHhhCCCeEEEEeecccccccchhhhhhhhhhhhccccceeeeeeecccCCccccCCCCCChhHHHHHHhcccccccCcc
Confidence 99999999999999999999999999999999999999999999988888889999999999999999999999999999
Q ss_pred cccccchhhHhhc-cccceeeeccCcccccccccccccccccccccccCcccCchhhhhccCccccchhhhccccccc
Q 026552 159 LVRFSWGTCTSHF-KDIVEVLWESDEMDEDVSSRRSGKRQLKLSDIGFSSSKRRSEEIESSGKGRCKFLEARKLEQLT 235 (237)
Q Consensus 159 ~~R~Sw~t~~~~l-~~~~~v~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~~r~l~~~~ 235 (237)
+|||||+|++.+| +++.++.|+++..+.+.. .. .++++|..+.. .+.. ..|..+| +|+|+++.
T Consensus 237 lVRfSW~Ta~t~L~~~~~~~~~e~~~~e~~~~---~~---~~~T~~~~~~~--~s~~-----~~r~~~~-~r~l~~~~ 300 (301)
T KOG2299|consen 237 LVRFSWKTAKTLLEDRSEPLKWEESGFELDKT---PL---LKFTKKFKPNP--ASRS-----VPRSERF-ERHLENWY 300 (301)
T ss_pred ceeeeHHHHHHHHhcccccceeecccccccch---HH---HHHHHHhcCCC--cccc-----cchhHHH-HHhhhhhc
Confidence 9999999999999 589999999886543211 11 26777522221 1111 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=1.6e-43 Score=309.14 Aligned_cols=162 Identities=60% Similarity=0.989 Sum_probs=145.8
Q ss_pred cchhHHHhcC--CceEEEEEEChhhHhhhcccCChhhHHHHHHHHHHHHHHHHHhcCCCccEEEEcCCCChhHHHHHhhc
Q 026552 4 EAALPKWASN--PFGWAVDIIDPRELSAKMLNKNKINLNEISHDSAIGLITRVLNIGILLTEVYLDTVGDAEKYQAKLSQ 81 (237)
Q Consensus 4 ~~~~~~i~~~--a~~~~v~~isp~eId~~ml~~~~~nLN~ls~~a~~~~I~~ll~~~~~~~~V~VD~~g~~~~y~~~L~~ 81 (237)
|.|++.|.+. ++.|.+.+++|++||+.|++...+|||+++++++.+++..++..+.+++.||||+++++++|.++|+.
T Consensus 47 ~~L~~~I~~~~~~~~~~i~~i~~~~id~~~~~~~~~nln~~~~~~~~~~i~~~~~~~~~~~~vliD~~~~~~~~~~~L~~ 126 (216)
T cd07181 47 EELFKKIKEKSEALGWATRILSPQYISAKMLARTKYNLNEISHDAAIGLIKSVLDKGVNVTEVYVDTVGPPEKYQAKLKK 126 (216)
T ss_pred HHHHHHHHhccccceEEEEEECHHHHCHHhhhcccccHHHHHHHHHHHHHHHHHcCCCCCCEEEECCCCChhHHHHhhhh
Confidence 5688999887 88999999999999998766567899999999999999887766677899999999988999999987
Q ss_pred cCCCceeEEEecCCccchhHHHHHHHHHHHHHHHHhhhchhhHHhhhc------CCCCccCCCCHHHHHHHHhccccccC
Q 026552 82 RFPSIKFVVSKKADSLYPVVSGASIVAKVTRDRTLRGWIFEETAENMH------RNFGSGYPGDPETKAWLTDHKHIIFG 155 (237)
Q Consensus 82 ~~p~i~v~v~~KADs~~p~VsAASIvAKV~RD~~m~~~~~~e~~~~~~------~~yGsGYPsDp~Tk~~L~~~~~~~fG 155 (237)
.+|++++++++|||++||+||||||||||+||++|+.+ ++.+ +++||||||||+|++||++++++.+|
T Consensus 127 ~~~~~~~~~~~kaD~~~~~VAAASIvAKV~RD~~m~~l------~~~~~~~~~~~~~gsGYpsd~~t~~~l~~~~~~~~~ 200 (216)
T cd07181 127 LFPGIKFTVEKKADSLYPIVSAASIVAKVTRDRALKNW------QFDEYLIDPDGDFGSGYPSDPKTKKWLKKNVDPVFG 200 (216)
T ss_pred cCCCCceEEeeCcccccHHHHHHHHHHHHHHHHHHHHH------HhhCccccccCCCceECCCHHHHHHHHHhcCCCcCC
Confidence 67777888999999999999999999999999999995 4444 46799999999999999999999999
Q ss_pred CCccccccchhhHhhc
Q 026552 156 FPSLVRFSWGTCTSHF 171 (237)
Q Consensus 156 ~p~~~R~Sw~t~~~~l 171 (237)
+|++||+||+|++++|
T Consensus 201 ~~~~~R~sw~t~~~~l 216 (216)
T cd07181 201 FPSLVRFSWSTAKKLL 216 (216)
T ss_pred CCCceEccccchHhcC
Confidence 9999999999999875
No 3
>PRK14551 rnhB ribonuclease HII; Provisional
Probab=100.00 E-value=5e-40 Score=286.70 Aligned_cols=155 Identities=25% Similarity=0.373 Sum_probs=136.1
Q ss_pred cchhHHHhcCC-ceEEEEEEChhhHhhhcccCChhhHHHHHHHHHHHHHHHHHhcCCCccEEEEcCCC-ChhHHHHHhhc
Q 026552 4 EAALPKWASNP-FGWAVDIIDPRELSAKMLNKNKINLNEISHDSAIGLITRVLNIGILLTEVYLDTVG-DAEKYQAKLSQ 81 (237)
Q Consensus 4 ~~~~~~i~~~a-~~~~v~~isp~eId~~ml~~~~~nLN~ls~~a~~~~I~~ll~~~~~~~~V~VD~~g-~~~~y~~~L~~ 81 (237)
|.|++.|.+.+ ++|++.+++|++||+. .+|||.++..+|.++|.+++. .++.||||+++ ++++|+.+|.+
T Consensus 45 ~~l~~~I~~~~~~~~~i~~isp~~Id~~-----~~nln~~~~~a~~~ai~~l~~---~~~~v~iD~~~~~~~~~~~~l~~ 116 (212)
T PRK14551 45 EELAAELREDDAIAVGVAEIPPARIDDP-----ETDMNTLTVAAHAEALSGVAT---DGITGLCDAGDVDAGRFARRVAD 116 (212)
T ss_pred HHHHHHHHhccCceEEEEEeCHHHHCcc-----ccCHHHHHHHHHHHHHHhhcc---CCCEEEECCCCCchHHHHHhhhh
Confidence 57889998875 8899999999999983 359999999999999998742 46789999985 67889988876
Q ss_pred cC-CCceeEEEecCCccchhHHHHHHHHHHHHHHHHhhhchhhHHhhhcCCCCccCCCCHHHHHHHHhccccccCCCccc
Q 026552 82 RF-PSIKFVVSKKADSLYPVVSGASIVAKVTRDRTLRGWIFEETAENMHRNFGSGYPGDPETKAWLTDHKHIIFGFPSLV 160 (237)
Q Consensus 82 ~~-p~i~v~v~~KADs~~p~VsAASIvAKV~RD~~m~~~~~~e~~~~~~~~yGsGYPsDp~Tk~~L~~~~~~~fG~p~~~ 160 (237)
.+ +++++++++|||++||+||||||||||+||+.|+. +.+.||+|||||||||.|++||++++++.+++|++|
T Consensus 117 ~~~~~~~~~~~~KaD~~~~~VAAASIlAKv~RD~~m~~------l~~~y~~~GsGYpsd~~t~~~l~~~~~~~g~~p~~~ 190 (212)
T PRK14551 117 RVALDVSVSAEHGADEEDPLVGAASIVAKVARDAHVAA------LAAEYGDVGSGYPSDPTTREFLREYVREHGELPACA 190 (212)
T ss_pred ccCCCCceEEEecccchhHHHHHHHHHHHHHHHHHHHH------HHHHCCCCCCcCCCcHHHHHHHHHHHHHhCCCchhh
Confidence 65 35778899999999999999999999999999999 567789999999999999999999888765577799
Q ss_pred cccchhhHhhcc
Q 026552 161 RFSWGTCTSHFK 172 (237)
Q Consensus 161 R~Sw~t~~~~l~ 172 (237)
|+||+|++++++
T Consensus 191 R~Sw~~~~~~~~ 202 (212)
T PRK14551 191 RRSWSTCDDVLA 202 (212)
T ss_pred ccCcHHHHHHHH
Confidence 999999999884
No 4
>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=2.2e-39 Score=280.63 Aligned_cols=155 Identities=32% Similarity=0.499 Sum_probs=138.5
Q ss_pred cchhHHHhcCCceEEEEEEChhhHhhhcccCChhhHHHHHHHHHHHHHHHHHhcCCCccEEEEcCC-CChhHHHHHhhcc
Q 026552 4 EAALPKWASNPFGWAVDIIDPRELSAKMLNKNKINLNEISHDSAIGLITRVLNIGILLTEVYLDTV-GDAEKYQAKLSQR 82 (237)
Q Consensus 4 ~~~~~~i~~~a~~~~v~~isp~eId~~ml~~~~~nLN~ls~~a~~~~I~~ll~~~~~~~~V~VD~~-g~~~~y~~~L~~~ 82 (237)
+.|++.|.+.++.|++.+++|++||++| ...|||++++.+|.++|++|. ..++.|+||++ +++++|.+.|+..
T Consensus 47 ~~l~~~I~~~~~~~~i~~i~~~~id~~~---~~~nln~~~~~~~~~~i~~l~---~~~~~iliD~~~~~~~~~~~~l~~~ 120 (204)
T cd07180 47 EELYNEILKVADDVVIVIVSPEEIDERR---EAHNLNELEAEAFAELINRLS---DKPDIVYVDACDVNEERFAEELRER 120 (204)
T ss_pred HHHHHHHHhcCCeEEEEEECHHHhChhh---hhcCHHHHHHHHHHHHHHHhh---cCCCEEEEeCCCCCHHHHHHHHHHh
Confidence 5788999988899999999999999986 367999999999999999874 34688999999 4778999888765
Q ss_pred C-CCceeEEEecCCccchhHHHHHHHHHHHHHHHHhhhchhhHHhhhcCCCCccCCCCHHHHHHHHhccccccCCCcccc
Q 026552 83 F-PSIKFVVSKKADSLYPVVSGASIVAKVTRDRTLRGWIFEETAENMHRNFGSGYPGDPETKAWLTDHKHIIFGFPSLVR 161 (237)
Q Consensus 83 ~-p~i~v~v~~KADs~~p~VsAASIvAKV~RD~~m~~~~~~e~~~~~~~~yGsGYPsDp~Tk~~L~~~~~~~fG~p~~~R 161 (237)
+ +++++++++|||++||+||||||||||+||++|+. +...|++||+|||+||.|++||++++++.+|+|++||
T Consensus 121 ~~~~~~~~~~~KgD~~~~~VAaASIlAKv~Rd~~m~~------l~~~~~~~g~Gy~sd~~t~~~l~~~~~~~g~~~~~~R 194 (204)
T cd07180 121 LNSGVEVIAEHKADAKYPVVSAASIIAKVERDREIEE------LKEEYGDFGSGYPSDPRTIKFLRNYYREHGELPPIVR 194 (204)
T ss_pred cCCCCcEEEEeCCcccCchhhHHHHHHHHHHHHHHHH------HHHhcccCCCcCCCCHHHHHHHHHHHHhhCCCChhhe
Confidence 5 35678889999999999999999999999999999 4667799999999999999999998888777999999
Q ss_pred ccchhhHhh
Q 026552 162 FSWGTCTSH 170 (237)
Q Consensus 162 ~Sw~t~~~~ 170 (237)
+||+|++++
T Consensus 195 ~sf~~~~~~ 203 (204)
T cd07180 195 KSWKTVKRL 203 (204)
T ss_pred ecccchhhc
Confidence 999999864
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=4.6e-39 Score=279.07 Aligned_cols=155 Identities=34% Similarity=0.531 Sum_probs=132.6
Q ss_pred cchhHHHhcCCceEEEEEEChhhHhhhcccCChhhHHHHHHHHHHHHHHHHHhcCCCccEEEEcCCCChhH-HHHHh--h
Q 026552 4 EAALPKWASNPFGWAVDIIDPRELSAKMLNKNKINLNEISHDSAIGLITRVLNIGILLTEVYLDTVGDAEK-YQAKL--S 80 (237)
Q Consensus 4 ~~~~~~i~~~a~~~~v~~isp~eId~~ml~~~~~nLN~ls~~a~~~~I~~ll~~~~~~~~V~VD~~g~~~~-y~~~L--~ 80 (237)
|.|++.|.+.++.|++.+++|++||+.+ .+|||.+++++|.++|++|. ..++.||||+++.++. |...+ .
T Consensus 48 ~~l~~~I~~~~~~~~i~~i~p~~id~~~----~~nln~~~~~a~~~~i~~l~---~~~~~v~iD~~~~~~~~~~~~~~~~ 120 (206)
T TIGR00729 48 EELFSKIRNKLGRYEVLKITPEEIDRER----NINLNENEIEKFSKAAIILI---EKPSEVYVDSVDVNPKRFKREIKIK 120 (206)
T ss_pred HHHHHHHHhhcCcEEEEEEcHHHHChHH----HhhHHHHHHHHHHHHHHHHh---cCCcEEEEcCCCCcHHHHHHHHHHh
Confidence 5788999887889999999999999964 46999999999999999873 2457899999985544 33323 2
Q ss_pred ccCCCceeEEEecCCccchhHHHHHHHHHHHHHHHHhhhchhhHHhhhcCCCCccCCCCHHHHHHHHhccccccCCCccc
Q 026552 81 QRFPSIKFVVSKKADSLYPVVSGASIVAKVTRDRTLRGWIFEETAENMHRNFGSGYPGDPETKAWLTDHKHIIFGFPSLV 160 (237)
Q Consensus 81 ~~~p~i~v~v~~KADs~~p~VsAASIvAKV~RD~~m~~~~~~e~~~~~~~~yGsGYPsDp~Tk~~L~~~~~~~fG~p~~~ 160 (237)
..+|++++++++|||++||+||||||||||+||++|+. +.+.|+.|||||||||+|++||++++++.+++|++|
T Consensus 121 ~~~~~~~~~~~~KaD~~~~~VAAASIlAKv~RD~~m~~------l~~~~~~~GsGY~sd~~t~~~l~~~~~~~g~~~~~~ 194 (206)
T TIGR00729 121 ERIEGIKVIAEHKADAKYPVVSAASIIAKVERDREIES------LKRKYGDFGSGYPSDPRTREWLEEYFKSHGELPDIV 194 (206)
T ss_pred ccCCCCcEEEEeccccccchhhHHHHHHHHHHHHHHHH------HHHhcCCCCCcCCCCHHHHHHHHHHHHhhCCCCccc
Confidence 34677888999999999999999999999999999999 466789999999999999999999887764467799
Q ss_pred cccchhhHhhc
Q 026552 161 RFSWGTCTSHF 171 (237)
Q Consensus 161 R~Sw~t~~~~l 171 (237)
|+||+|+++++
T Consensus 195 R~sf~~~~~~~ 205 (206)
T TIGR00729 195 RRTWKTVRKLL 205 (206)
T ss_pred ccCcHHHHHhh
Confidence 99999998875
No 6
>COG0164 RnhB Ribonuclease HII [DNA replication, recombination, and repair]
Probab=100.00 E-value=3.8e-35 Score=253.03 Aligned_cols=140 Identities=29% Similarity=0.389 Sum_probs=118.6
Q ss_pred ccchhHHHhcCCceEEEEEEChhhHhhhcccCChhhHHHHHHHHHHHHHHHHHhcCCCccEEEEcCCCChhHHHHHhhcc
Q 026552 3 SEAALPKWASNPFGWAVDIIDPRELSAKMLNKNKINLNEISHDSAIGLITRVLNIGILLTEVYLDTVGDAEKYQAKLSQR 82 (237)
Q Consensus 3 ~~~~~~~i~~~a~~~~v~~isp~eId~~ml~~~~~nLN~ls~~a~~~~I~~ll~~~~~~~~V~VD~~g~~~~y~~~L~~~ 82 (237)
-|.|+++|.+.++.|.|.++++++||+. |||++++++|.++|.+|. ..++.||||+++-+ ..| .
T Consensus 46 Re~L~~~I~~~a~~~~v~~~~~~~Id~~-------ni~~a~~~am~~av~~l~---~~~~~vlvD~~~~~----~~l--~ 109 (199)
T COG0164 46 REELFEEIKEKALAWGVGIIPAEEIDEL-------NILEATKLAMRRAVAGLS---SQPDLVLVDGNDLP----LGL--P 109 (199)
T ss_pred HHHHHHHHHhhccEEEEEEcCHHHHhhh-------hHHHHHHHHHHHHHHhcc---ccCCEEEEeCCCcc----ccC--C
Confidence 3789999998889999999999999995 999999999999999983 34589999998721 112 1
Q ss_pred CCCceeEEEecCCccchhHHHHHHHHHHHHHHHHhhhchhhHHhhhcCCC----CccCCCCHHHHHHHHhccccccCCCc
Q 026552 83 FPSIKFVVSKKADSLYPVVSGASIVAKVTRDRTLRGWIFEETAENMHRNF----GSGYPGDPETKAWLTDHKHIIFGFPS 158 (237)
Q Consensus 83 ~p~i~v~v~~KADs~~p~VsAASIvAKV~RD~~m~~~~~~e~~~~~~~~y----GsGYPsDp~Tk~~L~~~~~~~fG~p~ 158 (237)
.| .++++|||++|++||||||||||+||++|++ +++.||+| ||||||||.|.+|++.+ +.|+
T Consensus 110 ~~---~~a~~KgDa~~~~IaAASIvAKV~RDr~m~~------l~~~yp~Y~~~~~~GY~T~~h~~a~~~~~-----~~~~ 175 (199)
T COG0164 110 QP---AVAIIKGDAKSPSIAAASILAKVTRDRLMEE------LAKEYPEYGFDKGSGYPTDPHTEALLKKG-----GTPG 175 (199)
T ss_pred CC---cceeeccchhhHHHHHHHHHHHHHHHHHHHH------HHhhCcCcCcccCCCCCChHHHHHHHHhC-----CCCc
Confidence 22 2788999999999999999999999999999 56677665 59999999999999863 4555
Q ss_pred cccccchhhHhhcc
Q 026552 159 LVRFSWGTCTSHFK 172 (237)
Q Consensus 159 ~~R~Sw~t~~~~l~ 172 (237)
+||+||+|+++++.
T Consensus 176 ~hR~Sf~~vk~~~~ 189 (199)
T COG0164 176 IHRRSFAPVRRLLG 189 (199)
T ss_pred eeecccHHHHHhhh
Confidence 99999999999884
No 7
>PRK00015 rnhB ribonuclease HII; Validated
Probab=100.00 E-value=1.3e-34 Score=250.29 Aligned_cols=131 Identities=24% Similarity=0.328 Sum_probs=114.4
Q ss_pred cchhHHHhcCCceEEEEEEChhhHhhhcccCChhhHHHHHHHHHHHHHHHHHhcCCCccEEEEcCCCChhHHHHHhhccC
Q 026552 4 EAALPKWASNPFGWAVDIIDPRELSAKMLNKNKINLNEISHDSAIGLITRVLNIGILLTEVYLDTVGDAEKYQAKLSQRF 83 (237)
Q Consensus 4 ~~~~~~i~~~a~~~~v~~isp~eId~~ml~~~~~nLN~ls~~a~~~~I~~ll~~~~~~~~V~VD~~g~~~~y~~~L~~~~ 83 (237)
+.|++.|.+.+++|++.+++|++||+. |||++++++|.++|++| ..++.||||+++.+. + .+
T Consensus 63 ~~l~~~I~~~~~~~~i~~isp~~id~~-------nln~~~~~a~~~~i~~l----~~~~~i~vD~~~~~~-----~--~~ 124 (197)
T PRK00015 63 EELYEEIKEKALAYSVGIASPEEIDEL-------NILEATLLAMRRAVEGL----VKPDYVLVDGNRVPK-----L--PI 124 (197)
T ss_pred HHHHHHHHHhCceEEEEEcCHHHHHHh-------hHHHHHHHHHHHHHHhc----CCCCEEEECCCCCCC-----C--CC
Confidence 578899998889999999999999994 99999999999999986 356899999998552 1 12
Q ss_pred CCceeEEEecCCccchhHHHHHHHHHHHHHHHHhhhchhhHHhhhcCCCC----ccCCCCHHHHHHHHhccccccCCCcc
Q 026552 84 PSIKFVVSKKADSLYPVVSGASIVAKVTRDRTLRGWIFEETAENMHRNFG----SGYPGDPETKAWLTDHKHIIFGFPSL 159 (237)
Q Consensus 84 p~i~v~v~~KADs~~p~VsAASIvAKV~RD~~m~~~~~~e~~~~~~~~yG----sGYPsDp~Tk~~L~~~~~~~fG~p~~ 159 (237)
| +++++|||++||+||||||||||+||++|+. +++.+++|| |||||||+|++|++ +|++++
T Consensus 125 ~---~~~~~kaD~~~~~VaAASIvAKv~RD~~m~~------l~~~~~~yg~~~~sGY~s~~~~~a~~~------~G~~~~ 189 (197)
T PRK00015 125 P---QEAIVKGDAKSPSIAAASILAKVTRDRLMEE------LDKEYPGYGFAKHKGYGTKEHLEALAK------YGPTPI 189 (197)
T ss_pred C---eEEEEcCCcccHHHHHHHHHHHHHHHHHHHH------HHHhCcCCCCcCCCcCCCHHHHHHHHH------cCCChh
Confidence 3 5667899999999999999999999999999 467788888 99999999999766 389999
Q ss_pred ccccchhh
Q 026552 160 VRFSWGTC 167 (237)
Q Consensus 160 ~R~Sw~t~ 167 (237)
||+||+|+
T Consensus 190 ~R~Sw~~~ 197 (197)
T PRK00015 190 HRRSFAPV 197 (197)
T ss_pred hcCcCcCC
Confidence 99999985
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=9.3e-34 Score=242.98 Aligned_cols=143 Identities=32% Similarity=0.421 Sum_probs=125.6
Q ss_pred cchhHHHhcCCceEEEEEEChhhHhhhcccCChhhHHHHHHHHHHHHHHHHHhcCCCccEEEEcCCCChhHHHHHhhccC
Q 026552 4 EAALPKWASNPFGWAVDIIDPRELSAKMLNKNKINLNEISHDSAIGLITRVLNIGILLTEVYLDTVGDAEKYQAKLSQRF 83 (237)
Q Consensus 4 ~~~~~~i~~~a~~~~v~~isp~eId~~ml~~~~~nLN~ls~~a~~~~I~~ll~~~~~~~~V~VD~~g~~~~y~~~L~~~~ 83 (237)
+.|++.|.+..++|.+.+++|++||+. |||.++..+|.++|..+. ..++.||||++++++.|+. +...+
T Consensus 47 ~~l~~~I~~~~~~~~v~~~~p~~id~~-------nl~~~~~~~~~~~i~~l~---~~~~~i~iD~~~~~~~~~~-~~~~~ 115 (193)
T cd06266 47 EELFEEIKEEALAYAIGIISPEEIDEL-------NILQATALAMARAILNLG---VKPDEVLVDGNGVPEKYFA-LEKKF 115 (193)
T ss_pred HHHHHHHHhhCCeEEEEEECHHHHCHH-------HHHHHHHHHHHHHHHhcC---CCCCEEEECCCCChhhhhh-hcccC
Confidence 578899998889999999999999995 999999999999999873 4678999999999998887 54556
Q ss_pred CCceeEEEecCCccchhHHHHHHHHHHHHHHHHhhhchhhHHhhhcC----CCCccCCCCHHHHHHHHhccccccCCCcc
Q 026552 84 PSIKFVVSKKADSLYPVVSGASIVAKVTRDRTLRGWIFEETAENMHR----NFGSGYPGDPETKAWLTDHKHIIFGFPSL 159 (237)
Q Consensus 84 p~i~v~v~~KADs~~p~VsAASIvAKV~RD~~m~~~~~~e~~~~~~~----~yGsGYPsDp~Tk~~L~~~~~~~fG~p~~ 159 (237)
+++++++++|||++||+||||||||||+||+.|+.+ +..|+ +.|||||+||.|++|++.+.. +++
T Consensus 116 ~~~~~~~~~kaD~~~~~VaAASIiAKv~rd~~m~~l------~~~~~~~~~~~gsGy~s~~~~~~~~~~~~~-----~~~ 184 (193)
T cd06266 116 LPIPVTAIVKGDSKSPSVAAASILAKVTRDRLMEEL------DEEYPGYGFAKGKGYPTDPHTEAILKYGPT-----EPI 184 (193)
T ss_pred CCCCeEEEeccccccHhHHHHHHHHHHHHHHHHHHH------HHHCCCCCCcCCcCcCcHHHHHHHHHhCcC-----CCe
Confidence 778899999999999999999999999999999994 44454 778999999999999997532 299
Q ss_pred ccccchhhH
Q 026552 160 VRFSWGTCT 168 (237)
Q Consensus 160 ~R~Sw~t~~ 168 (237)
||+||+|++
T Consensus 185 ~R~sf~~~~ 193 (193)
T cd06266 185 HRRSFKTVK 193 (193)
T ss_pred eeCCCCCCC
Confidence 999999863
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=8.3e-34 Score=241.76 Aligned_cols=132 Identities=21% Similarity=0.278 Sum_probs=112.1
Q ss_pred cchhHHHhcCCceEEEEEEChhhHhhhcccCChhhHHHHHHHHHHHHHHHHHhcCCCccEEEEcCCCChhHHHHHhhccC
Q 026552 4 EAALPKWASNPFGWAVDIIDPRELSAKMLNKNKINLNEISHDSAIGLITRVLNIGILLTEVYLDTVGDAEKYQAKLSQRF 83 (237)
Q Consensus 4 ~~~~~~i~~~a~~~~v~~isp~eId~~ml~~~~~nLN~ls~~a~~~~I~~ll~~~~~~~~V~VD~~g~~~~y~~~L~~~~ 83 (237)
|.|++.|.++++.|++.+++|++||+. |||+++..+|.++|.+| ...++.|+||+++.+..
T Consensus 43 ~~l~~~I~~~~~~~~v~~~~~~~Id~~-------nl~~~~~~a~~~ai~~l---~~~~~~v~iD~~~~~~~--------- 103 (179)
T cd07182 43 EELYEEIKEKALAWGIGIASPEEIDRI-------NILQATLLAMRRAVEGL---PVKPDYVLVDGNRLPPL--------- 103 (179)
T ss_pred HHHHHHHHHhcccEEEEEECHHHHCHh-------hHHHHHHHHHHHHHHhC---CCCCCEEEECCcCCCCC---------
Confidence 678999998889999999999999984 99999999999999886 24578999999874321
Q ss_pred CCceeEEEecCCccchhHHHHHHHHHHHHHHHHhhhchhhHHhhhcCCCC----ccCCCCHHHHHHHHhccccccCCCcc
Q 026552 84 PSIKFVVSKKADSLYPVVSGASIVAKVTRDRTLRGWIFEETAENMHRNFG----SGYPGDPETKAWLTDHKHIIFGFPSL 159 (237)
Q Consensus 84 p~i~v~v~~KADs~~p~VsAASIvAKV~RD~~m~~~~~~e~~~~~~~~yG----sGYPsDp~Tk~~L~~~~~~~fG~p~~ 159 (237)
...+++++|||++||+||||||||||+||++|+.| ++.+|+|| |||||++ +++++++ +|+|++
T Consensus 104 -~~~~~~~~KaD~~~~~VaAASIvAKv~RD~~m~~l------~~~~~~yg~~~~~GY~s~~-h~~~i~~-----~G~~~~ 170 (179)
T cd07182 104 -PIPQEAIVKGDAKSASIAAASILAKVTRDRLMIEL------DKKYPGYGFAKHKGYGTKE-HLEALKK-----YGPTPI 170 (179)
T ss_pred -CCCeEEEeccccccHHHHHHHHHHHHHHHHHHHHH------HHHCcCCCCcCCCCCCcHH-HHHHHHH-----hCcCHh
Confidence 24467889999999999999999999999999994 56778876 9999877 4445554 599999
Q ss_pred ccccchhh
Q 026552 160 VRFSWGTC 167 (237)
Q Consensus 160 ~R~Sw~t~ 167 (237)
||+||+|+
T Consensus 171 hR~s~~~~ 178 (179)
T cd07182 171 HRRSFAPV 178 (179)
T ss_pred hcCCCCCC
Confidence 99999986
No 10
>PRK13926 ribonuclease HII; Provisional
Probab=100.00 E-value=5e-33 Score=241.96 Aligned_cols=135 Identities=25% Similarity=0.401 Sum_probs=116.9
Q ss_pred cchhHHHhcCCceEEEEEEChhhHhhhcccCChhhHHHHHHHHHHHHHHHHHhcCCCccEEEEcCCCChhHHHHHhhccC
Q 026552 4 EAALPKWASNPFGWAVDIIDPRELSAKMLNKNKINLNEISHDSAIGLITRVLNIGILLTEVYLDTVGDAEKYQAKLSQRF 83 (237)
Q Consensus 4 ~~~~~~i~~~a~~~~v~~isp~eId~~ml~~~~~nLN~ls~~a~~~~I~~ll~~~~~~~~V~VD~~g~~~~y~~~L~~~~ 83 (237)
|.|++.|.+.++.|.+.+++|++||+. |||++++++|.++|+++ .++++.|++|... +.
T Consensus 65 ~~L~~~I~~~~~~~~i~~isp~~Id~~-------ni~~a~~~a~~~~l~~l---~~~~~~v~~D~~~--------~~--- 123 (207)
T PRK13926 65 EALAEEVRRVALAWAVGHAEAAEIDRL-------NVLKATHLAAARALARL---AVAPEALVTDYLR--------LP--- 123 (207)
T ss_pred HHHHHHHHHhCceEEEEEeCHHHHhHH-------HHHHHHHHHHHHHHHhc---CCCCCEEEECccc--------CC---
Confidence 678899998888999999999999985 99999999999999875 2567889999531 11
Q ss_pred CCceeEEEecCCccchhHHHHHHHHHHHHHHHHhhhchhhHHhhhcCCCC----ccCCCCHHHHHHHHhccccccCCCcc
Q 026552 84 PSIKFVVSKKADSLYPVVSGASIVAKVTRDRTLRGWIFEETAENMHRNFG----SGYPGDPETKAWLTDHKHIIFGFPSL 159 (237)
Q Consensus 84 p~i~v~v~~KADs~~p~VsAASIvAKV~RD~~m~~~~~~e~~~~~~~~yG----sGYPsDp~Tk~~L~~~~~~~fG~p~~ 159 (237)
..+++++++|||++||+||||||||||+||++|+.| ++.|++|| |||| ++.|++||++ +|+||+
T Consensus 124 ~~~~~~~~~KgD~~~~~VaAASIvAKv~RD~~m~~l------~~~~~~yg~~~~kGY~-t~~h~~~l~~-----~G~~~~ 191 (207)
T PRK13926 124 TPLPLLAPPKADALSPTVAAASLLAKTERDRLMREL------DARYPGYGFARHKGYG-TPAHREALAA-----LGPSPV 191 (207)
T ss_pred CCCCeEEEecCccccHHHHHHHHHHHHHHHHHHHHH------HHhCccCCCcCCCCCC-CHHHHHHHHH-----hCcCHH
Confidence 134678889999999999999999999999999994 67788877 9999 8889999986 489999
Q ss_pred ccccchhhHhhc
Q 026552 160 VRFSWGTCTSHF 171 (237)
Q Consensus 160 ~R~Sw~t~~~~l 171 (237)
||+||+|+++++
T Consensus 192 hR~s~~~~~~~~ 203 (207)
T PRK13926 192 HRRSFAPVRRLL 203 (207)
T ss_pred HcCCcHHHHHhh
Confidence 999999999876
No 11
>cd06590 RNaseH_typeII_bacteria_HIII_like bacterial Ribonuclease HIII-like. Ribonuclease H (RNase H) is classified into two families, type I (prokaryotic RNase HI, eukaryotic RNase H1 and viral RNase H) and type II (prokaryotic RNase HII and HIII, and eukaryotic RNase H2). RNase H endonucleolytically hydrolyzes an RNA strand when it is annealed to a complementary DNA strand in the presence of divalent cations, in DNA replication and repair. Several bacteria, such as Bacillus subtilis, have two different type II RNases H, RNases HII and HIII. RNases HIII are distinguished by having a large (70-90 residues) N-terminal extension of unknown function. In addition, the active site of RNase HIII differs from that of other RNases H; replacing the fourth residue (aspartate) of the acidic "DEDD" motif with a glutamate. Most prokaryotic and eukaryotic genomes contain multiple RNase H genes, however, no prokaryotic genomes contain the combination of both RNase HI and HIII. This mutual exclusive gen
Probab=100.00 E-value=3.5e-33 Score=242.34 Aligned_cols=157 Identities=15% Similarity=0.141 Sum_probs=135.9
Q ss_pred cchhHHHhcCCceEEEEEEChhhHhhhcccCChhhHHHHHHHHHHHHHHHHHhcCCCccEEEEcCCCChhHHHHHhhccC
Q 026552 4 EAALPKWASNPFGWAVDIIDPRELSAKMLNKNKINLNEISHDSAIGLITRVLNIGILLTEVYLDTVGDAEKYQAKLSQRF 83 (237)
Q Consensus 4 ~~~~~~i~~~a~~~~v~~isp~eId~~ml~~~~~nLN~ls~~a~~~~I~~ll~~~~~~~~V~VD~~g~~~~y~~~L~~~~ 83 (237)
|.|++.|.+ .+.|++.+++|++||.++ ....|||.++.++|.++|..|+..++.++.|+||+++.+++|+..|.+.+
T Consensus 47 ~~l~~~I~~-~~~~~v~~i~~~~in~~~--~~~~nln~l~~~~~~~ai~~l~~~~~~~~~v~vD~~~~~~~~~~~l~~~~ 123 (208)
T cd06590 47 IRLAPKIKK-KIPYSVLSLGPEKYNELY--KKGKNLNKLKALLHNKAINNLLEKPKKPVAILIDQFASEKVYKRYLKKEK 123 (208)
T ss_pred HHHHHHHHh-cCCEEEEecCHHHHHHHH--HccCCHHHHHHHHHHHHHHHHHHhcCCCCEEEecCCCCHHHHHHHHHhhc
Confidence 568888887 578999999999999875 22579999999999999999875556678999999998899999998776
Q ss_pred --CCceeEEEecCCccchhHHHHHHHHHHHHHHHHhhhchhhHHhhhcC---CCCccCCCCHHHHHHHHhccccccCCCc
Q 026552 84 --PSIKFVVSKKADSLYPVVSGASIVAKVTRDRTLRGWIFEETAENMHR---NFGSGYPGDPETKAWLTDHKHIIFGFPS 158 (237)
Q Consensus 84 --p~i~v~v~~KADs~~p~VsAASIvAKV~RD~~m~~~~~~e~~~~~~~---~yGsGYPsDp~Tk~~L~~~~~~~fG~p~ 158 (237)
+++++++++|||++||+||||||||||+||+.|+.+ .+.|+ +.|+|||+|+.|++||+++... .+|+
T Consensus 124 ~~~~~~~~~~~kaD~~~~~VaAASIlAKv~Rd~~m~~l------~~~yg~~~~~G~g~~~~~~~~~~l~~~g~~--~l~~ 195 (208)
T cd06590 124 KIVKEPLIFRTKAESKHLAVAAASILARYAFLEKMEKL------SKQYGMKLPKGASSKVDEQAAEIIKKYGLE--ELKK 195 (208)
T ss_pred cCCCCceEEEecCcccchHHHHHHHHHHHHHHHHHHHH------HHHhCCCCCCCCCcHHHHHHHHHHHHhhHh--HHHH
Confidence 567889999999999999999999999999999994 44444 6799999999999999997543 2788
Q ss_pred cccccchhhHhhc
Q 026552 159 LVRFSWGTCTSHF 171 (237)
Q Consensus 159 ~~R~Sw~t~~~~l 171 (237)
++|+||+|+++++
T Consensus 196 ~~k~~~~t~~~~~ 208 (208)
T cd06590 196 VAKLHFKNTKKAL 208 (208)
T ss_pred HHHHhchhhHhhC
Confidence 9999999998763
No 12
>PRK14550 rnhB ribonuclease HII; Provisional
Probab=99.98 E-value=9.6e-33 Score=239.74 Aligned_cols=140 Identities=19% Similarity=0.238 Sum_probs=115.2
Q ss_pred cchhHHHhcCC-ceEEEEEEChhhHhhhcccCChhhHHHHHHHHHHHHHHHHHhcCCCccEEEEcCCCChhHHHHHhhcc
Q 026552 4 EAALPKWASNP-FGWAVDIIDPRELSAKMLNKNKINLNEISHDSAIGLITRVLNIGILLTEVYLDTVGDAEKYQAKLSQR 82 (237)
Q Consensus 4 ~~~~~~i~~~a-~~~~v~~isp~eId~~ml~~~~~nLN~ls~~a~~~~I~~ll~~~~~~~~V~VD~~g~~~~y~~~L~~~ 82 (237)
|.|+++|.+.+ +.|.+.+++|++||+. |||.++..+|.++|.++ ...++.|+||++..+. +...
T Consensus 49 e~L~~~I~~~~~~~~~i~~~~~~eID~~-------ni~~a~~~am~~al~~l---~~~~~~vliDg~~~~~-----~~~~ 113 (204)
T PRK14550 49 FFLEDKIKTHGEVGFFVVKKSANEIDSL-------GLGACLKLAIQEILENG---CSLANEIKIDGNTAFG-----LNKR 113 (204)
T ss_pred HHHHHHHHhccCcEEEEEEECHHHHHHH-------HHHHHHHHHHHHHHHhC---CCCCCEEEECCccCcc-----cccc
Confidence 67899998775 8999999999999985 99999999999999886 2457889999875322 1111
Q ss_pred CCCceeEEEecCCccchhHHHHHHHHHHHHHHHHhhhchhhHHhhhcCCCC----ccCCCCHHHHHHHHhccccccCCCc
Q 026552 83 FPSIKFVVSKKADSLYPVVSGASIVAKVTRDRTLRGWIFEETAENMHRNFG----SGYPGDPETKAWLTDHKHIIFGFPS 158 (237)
Q Consensus 83 ~p~i~v~v~~KADs~~p~VsAASIvAKV~RD~~m~~~~~~e~~~~~~~~yG----sGYPsDp~Tk~~L~~~~~~~fG~p~ 158 (237)
+|+ +.+++|||++||+||||||||||+||++|++ +++.||+|| |||| |++|++. +++ +|++|
T Consensus 114 ~~~--~~~~~KgD~~~~~VAAASIiAKV~RD~~M~~------l~~~~p~Ygf~~~kGY~----T~~h~~a-i~~-~G~~p 179 (204)
T PRK14550 114 YPN--IQTIIKGDETIAQIAMASVLAKAFKDREMLE------LHALFKEYGWDKNCGYG----TKQHIEA-IIK-LGATP 179 (204)
T ss_pred Ccc--eeEEEcccccchhHHHHHHHHHHHHHHHHHH------HHHhCCCCCCcCCCCCC----CHHHHHH-HHH-hCcCH
Confidence 232 4566899999999999999999999999999 456677765 9999 8888887 443 69999
Q ss_pred cccccchhhHhhcc
Q 026552 159 LVRFSWGTCTSHFK 172 (237)
Q Consensus 159 ~~R~Sw~t~~~~l~ 172 (237)
+||+||+|+.++|.
T Consensus 180 ~hR~Sf~t~~~~~~ 193 (204)
T PRK14550 180 FHRHSFTLKNRILN 193 (204)
T ss_pred HHcCCcCCCCcccC
Confidence 99999999999884
No 13
>PRK13925 rnhB ribonuclease HII; Provisional
Probab=99.97 E-value=4.4e-31 Score=228.41 Aligned_cols=136 Identities=18% Similarity=0.216 Sum_probs=110.1
Q ss_pred cchhHHHhcCCceEEEEEEChhhHhhhcccCChhhHHHHHHHHHHHHHHHHHhcCCCccEEEEcCCCChhHHHHHhhccC
Q 026552 4 EAALPKWASNPFGWAVDIIDPRELSAKMLNKNKINLNEISHDSAIGLITRVLNIGILLTEVYLDTVGDAEKYQAKLSQRF 83 (237)
Q Consensus 4 ~~~~~~i~~~a~~~~v~~isp~eId~~ml~~~~~nLN~ls~~a~~~~I~~ll~~~~~~~~V~VD~~g~~~~y~~~L~~~~ 83 (237)
|.|++.|.+.+..|++.+++|++||+. |||.++..+|.++|..+ ...++.|+||+++... .+
T Consensus 57 e~l~~~I~~~~~~~~i~~i~~~eId~~-------ni~~~~~~a~~~~i~~l---~~~~~~v~iD~~~~~~--------~~ 118 (198)
T PRK13925 57 AQLVPLILTLASDWGIGQASAREIDRL-------GIRQATELAMLRALKKL---KSPPSLCLVDGNLPLR--------LW 118 (198)
T ss_pred HHHHHHHHhhCCcEEEEEECHHHhCHh-------hHHHHHHHHHHHHHHhc---CCCCCEEEECCccccC--------cC
Confidence 678899998888999999999999985 89999999999999886 2456889999986311 13
Q ss_pred CCceeEEEecCCccchhHHHHHHHHHHHHHHHHhhhchhhHHhhhcCCCC----ccCCCCHHHHHHHHhccccccCCCcc
Q 026552 84 PSIKFVVSKKADSLYPVVSGASIVAKVTRDRTLRGWIFEETAENMHRNFG----SGYPGDPETKAWLTDHKHIIFGFPSL 159 (237)
Q Consensus 84 p~i~v~v~~KADs~~p~VsAASIvAKV~RD~~m~~~~~~e~~~~~~~~yG----sGYPsDp~Tk~~L~~~~~~~fG~p~~ 159 (237)
+.... ..+|||++||+||||||||||+||++|+. +++.||+|| +|||+++ ++++++. +|++|+
T Consensus 119 ~~~~~-~v~kaD~~~~~VaAASIiAKV~RD~~m~~------l~~~yp~y~f~~~kGY~t~~-h~~~i~~-----~G~~p~ 185 (198)
T PRK13925 119 PGPQR-TIVKGDSKSAAIAAASILAKVWRDDLIKR------LAKKYPGYGLEKNKGYGTAQ-HRQALLK-----LGPTPL 185 (198)
T ss_pred CCCce-eecccccccHHHHHHHHHHHHHHHHHHHH------HHHHCCCCCcccCCCCCcHH-HHHHHHH-----hCcCHH
Confidence 33222 33699999999999999999999999999 467888888 9999555 4444444 599999
Q ss_pred ccccchhhHhh
Q 026552 160 VRFSWGTCTSH 170 (237)
Q Consensus 160 ~R~Sw~t~~~~ 170 (237)
||+||.|.-.+
T Consensus 186 hR~sf~~~~~~ 196 (198)
T PRK13925 186 HRKSFLPKLIL 196 (198)
T ss_pred HcCCCcchhhc
Confidence 99999886543
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=99.97 E-value=5e-30 Score=220.51 Aligned_cols=149 Identities=37% Similarity=0.522 Sum_probs=121.6
Q ss_pred cchhHHHhcCCceEEEEEEChhhHhhhcccCChhhHHHHHHHHHHHHHHHHHhcCCCccEEEEcCCCChhHHHHHhhccC
Q 026552 4 EAALPKWASNPFGWAVDIIDPRELSAKMLNKNKINLNEISHDSAIGLITRVLNIGILLTEVYLDTVGDAEKYQAKLSQRF 83 (237)
Q Consensus 4 ~~~~~~i~~~a~~~~v~~isp~eId~~ml~~~~~nLN~ls~~a~~~~I~~ll~~~~~~~~V~VD~~g~~~~y~~~L~~~~ 83 (237)
|.|++.|. .+.+ ..+.+..|... ....+|+|.+++.++.++++.+.+.+..++.|+||+++.+++|...+...+
T Consensus 47 ~~l~~~I~--~i~~--~~~~~~~~~~~--~~~~in~n~i~~~~~~~~~~~l~~~~~~~~~v~iD~~~~~~~~~~~~~~~~ 120 (198)
T PF01351_consen 47 EELAEKIK--KISY--SEVSPYPIGYI--SPKEINLNNILAALHNAMIRALLKLGVQPDEVLIDQFGSPEKYYNKLEKIF 120 (198)
T ss_dssp HHHHHHHH--EEEE--EEEECHHHHHH--HTTTSCHHHHHHHHHHHHHHHHHHTTSEESEEEEEESSSHHHHHHHHHHHS
T ss_pred HHHHHHHH--hhch--hhhhhcccccc--chHHHHHHHHHHHHHHHHHHHHHHhccCCceeecchhhcchhcccchheec
Confidence 56788888 2333 34444444432 125579999999999999998877777889999999999998999998878
Q ss_pred CCceeEEEecCCccchhHHHHHHHHHHHHHHHHhhhchhhHHhhhcC---CCCccCCCCHHHHHHHHhccccccCCCccc
Q 026552 84 PSIKFVVSKKADSLYPVVSGASIVAKVTRDRTLRGWIFEETAENMHR---NFGSGYPGDPETKAWLTDHKHIIFGFPSLV 160 (237)
Q Consensus 84 p~i~v~v~~KADs~~p~VsAASIvAKV~RD~~m~~~~~~e~~~~~~~---~yGsGYPsDp~Tk~~L~~~~~~~fG~p~~~ 160 (237)
+ .++++++|||++||+||||||||||+||..|+. +.+.++ +.|||||+||.|++|++.+..+ ++|++|
T Consensus 121 ~-~~~~~~~Kad~~~~~VAAASIvAK~~rd~~~~~------~~~~~~~~~~~gsGy~s~~~~~~~~~~~~~~--~l~~~~ 191 (198)
T PF01351_consen 121 K-IKVVFEPKADSKYPSVAAASIVAKVTRDEMIEL------LSKYPGYGFPKGSGYPSDPHTRAILKKGGSP--ELPQIH 191 (198)
T ss_dssp T-SEEEEETTHHHCSHHHHHHHHHHHHHHHHHHHH------HHHHHTS-HCCTSSSTTSHHHHHHHHHHHHH--SSHTTB
T ss_pred C-cceeeecccchhhHHHHHHHHHHHHHHHHHHHH------HHhCcCCCCccCCCCChHHHHHHHHHhCCCC--CCCccc
Confidence 8 889999999999999999999999999987776 333333 7899999999999999998877 899999
Q ss_pred cccchhh
Q 026552 161 RFSWGTC 167 (237)
Q Consensus 161 R~Sw~t~ 167 (237)
|+||+|+
T Consensus 192 R~sf~tv 198 (198)
T PF01351_consen 192 RLSFKTV 198 (198)
T ss_dssp -TTSHHH
T ss_pred cCCCcCC
Confidence 9999986
No 15
>PRK00996 ribonuclease HIII; Provisional
Probab=99.94 E-value=1.8e-26 Score=211.01 Aligned_cols=158 Identities=18% Similarity=0.174 Sum_probs=128.0
Q ss_pred cchhHHHhcCCceEEEEEEChhhHhhhcccCChhhHHHHHHHHHHHHHHHHHhc--CCCccEEEEcCCCChhHHHHHhhc
Q 026552 4 EAALPKWASNPFGWAVDIIDPRELSAKMLNKNKINLNEISHDSAIGLITRVLNI--GILLTEVYLDTVGDAEKYQAKLSQ 81 (237)
Q Consensus 4 ~~~~~~i~~~a~~~~v~~isp~eId~~ml~~~~~nLN~ls~~a~~~~I~~ll~~--~~~~~~V~VD~~g~~~~y~~~L~~ 81 (237)
+.|++.|.+. +.|.+.+++|++||+++ ...+|+|.+...+|.++|.+|++. +..|+.|+||+++.+++|+++|..
T Consensus 136 ~~La~~I~~~-~~~~v~~~~p~~~n~l~--~~~~nln~l~a~~h~~ai~~l~~k~~~~~p~~iliD~f~~~~~y~~~l~~ 212 (304)
T PRK00996 136 RQIAPQLREK-IPHSVLLLSPEKYNELQ--AKGYNQNKLKAWLHNQAIDNLLQKIAGIQPEKIVIDQFASPEVYQKYLKK 212 (304)
T ss_pred HHHHHHHHHh-cCEEEEEeCHHHhhhHH--HhhhhHHHHHHHHHHHHHHHHHhhccCCCCCEEEECCCCCchHHHHHhhh
Confidence 5788999877 68999999999999874 245799999999999999998764 567889999999989999999975
Q ss_pred c--CCCceeEEEecCCccchhHHHHHHHHHHHHHHHHhhhchhhHHhhhcC---CCCccCCCCHHHHHHHHhccccccCC
Q 026552 82 R--FPSIKFVVSKKADSLYPVVSGASIVAKVTRDRTLRGWIFEETAENMHR---NFGSGYPGDPETKAWLTDHKHIIFGF 156 (237)
Q Consensus 82 ~--~p~i~v~v~~KADs~~p~VsAASIvAKV~RD~~m~~~~~~e~~~~~~~---~yGsGYPsDp~Tk~~L~~~~~~~fG~ 156 (237)
. .+..++++++|||++||+|||||||| ||++|+.++ + +...|+ +.|+|||+|+.+++||++++.. .+
T Consensus 213 e~~~~~~~~~~~~KaD~~~~~VAAASIiA---R~~~l~~~~--~-l~~~yg~~~~kGag~~~d~~a~~~i~~~G~~--~L 284 (304)
T PRK00996 213 EKNKFRDNVTFETKAESKHLAVAAASIIA---RYAFLENMD--K-LSKEAGMTLPKGAGAKVDKVAAQILKKYGKE--AL 284 (304)
T ss_pred hccCCCCceEEEeccchhhHHHHHHHHHH---HHHHHHHHH--H-hCcCCCCCCCCCCCCHHHHHHHHHHHHhCcc--hh
Confidence 2 23457889999999999999999999 666666631 1 122222 3478999999999999997542 48
Q ss_pred CccccccchhhHhhcc
Q 026552 157 PSLVRFSWGTCTSHFK 172 (237)
Q Consensus 157 p~~~R~Sw~t~~~~l~ 172 (237)
+.++|.+|+|.+++++
T Consensus 285 ~~~aK~hfk~~~k~~~ 300 (304)
T PRK00996 285 EKFAKLHFKNTEKAQK 300 (304)
T ss_pred HHHHHHhchhHHHHHH
Confidence 8999999999988764
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=99.82 E-value=6.7e-20 Score=166.46 Aligned_cols=121 Identities=20% Similarity=0.219 Sum_probs=96.2
Q ss_pred cchhHHHhcCCceEEEEEEChhhHhhhcccCChhhHHHHHHHHHHHHHHHHHhcCCCccEEEEcCCCChhHHHHHhhc-c
Q 026552 4 EAALPKWASNPFGWAVDIIDPRELSAKMLNKNKINLNEISHDSAIGLITRVLNIGILLTEVYLDTVGDAEKYQAKLSQ-R 82 (237)
Q Consensus 4 ~~~~~~i~~~a~~~~v~~isp~eId~~ml~~~~~nLN~ls~~a~~~~I~~ll~~~~~~~~V~VD~~g~~~~y~~~L~~-~ 82 (237)
+.|++.|.+. +.|.+.+++|++||.++ ...+|+|.+..++|.++|.+|+.....++.|+||+++.++.|.+.+.. .
T Consensus 130 ~~la~~I~~~-~~~~i~~l~p~~~n~~~--~~~~nln~l~a~~h~~aI~~l~~~~~~~~~i~ID~f~~~~~y~~~l~~~~ 206 (284)
T TIGR00716 130 ERLALNLKPL-VKAYCYELKPEKYNKLY--RKFRNLNKMMAHFHKLLIERLLKEECGVSEVVVDQFAPSNPFFNHLKGRD 206 (284)
T ss_pred HHHHHHHHHh-CCEEEEEeCHHHhcHHH--HHHHHHHHHHHHHHHHHHHHHhhCcCCCcEEEECCCCCchHhhhhccccc
Confidence 5678888876 47999999999999763 245799999999999999998654333357999999988888777643 2
Q ss_pred CCCceeEEEecCCccchhHHHHHHHHHHHHHHHHhhhchhhHHhhhcCCCC----ccCC
Q 026552 83 FPSIKFVVSKKADSLYPVVSGASIVAKVTRDRTLRGWIFEETAENMHRNFG----SGYP 137 (237)
Q Consensus 83 ~p~i~v~v~~KADs~~p~VsAASIvAKV~RD~~m~~~~~~e~~~~~~~~yG----sGYP 137 (237)
++...+++++|||+ ||+|||||||| ||++|+. +++++++|| +||+
T Consensus 207 ~~~~~~~~~~KaE~-~~aVAAASIiA---R~~~l~~------l~~l~~~yg~~~pkGa~ 255 (284)
T TIGR00716 207 IVGEDVIFETEAER-NLAVAAASIFA---RYKFLQS------LKELERELGIKLPKGAS 255 (284)
T ss_pred ccCCceeeeccccc-chhhhHHHHHH---HHHHHHH------HHHhCcccCCcCCCCCC
Confidence 44567889999998 99999999999 7777776 344556665 8999
No 17
>COG1039 RnhC Ribonuclease HIII [DNA replication, recombination, and repair]
Probab=99.57 E-value=1.4e-14 Score=130.92 Aligned_cols=154 Identities=19% Similarity=0.192 Sum_probs=116.4
Q ss_pred cchhHHHhcCCceEEEEEEChhhHhhhcccCChhhHHHHHHHHHHHHHHHHHh-cCCCccEEEEcCCCChhHHHHHhhcc
Q 026552 4 EAALPKWASNPFGWAVDIIDPRELSAKMLNKNKINLNEISHDSAIGLITRVLN-IGILLTEVYLDTVGDAEKYQAKLSQR 82 (237)
Q Consensus 4 ~~~~~~i~~~a~~~~v~~isp~eId~~ml~~~~~nLN~ls~~a~~~~I~~ll~-~~~~~~~V~VD~~g~~~~y~~~L~~~ 82 (237)
.++++.|+. .+.+.+..+.|++++++. ...+|+|.+....|.++|++|+. .+..++.|+||.+...++|..+|.+.
T Consensus 132 ~~la~~ik~-~i~~~~l~l~p~kYNel~--~k~~N~n~mkt~lH~~ai~~ll~~~~~~~~~ivIDqFa~~~~~~~yl~k~ 208 (297)
T COG1039 132 QQLAPIIKP-LIPHSVLTLDPKKYNELY--KKFNNANSMKTFLHNQAIQNLLPQKGAQPEFIVIDQFASSENYKNYLQKE 208 (297)
T ss_pred HHHHHHHHH-hcCceEEEEChHHHHHHH--HhhhhHHHHHHHHHHHHHHHHHHhccCCCeEEEeccccchhHHHHHHHhh
Confidence 357788887 678999999999999985 45689999999999999999984 67889999999999999999998765
Q ss_pred C--CCceeEEEecCCccchhHHHHHHHHHHHHHHHHhhhchhhHHhhhcC--CCCccCCCCHHHHHHHHhccccccCCC-
Q 026552 83 F--PSIKFVVSKKADSLYPVVSGASIVAKVTRDRTLRGWIFEETAENMHR--NFGSGYPGDPETKAWLTDHKHIIFGFP- 157 (237)
Q Consensus 83 ~--p~i~v~v~~KADs~~p~VsAASIvAKV~RD~~m~~~~~~e~~~~~~~--~yGsGYPsDp~Tk~~L~~~~~~~fG~p- 157 (237)
. +...+....||++.|.+||||||+| ||.++..++ ++.++++- +-|+|-.+|...++.+++ +|+.
T Consensus 209 ~~~~~~p~~f~~kaEs~~laVAvASIiA---R~~Fl~~~~--~l~~~~gv~LPkGAg~~V~~~a~~i~~k-----~g~~~ 278 (297)
T COG1039 209 TNKFSEPVLFLTKAESKSLAVAVASIIA---RYAFLQSLK--QLSRQYGVQLPKGAGPAVDQAAAEIIQK-----RGFSK 278 (297)
T ss_pred ccCCCCceeeeecccccchhHHHHHHHH---HHHHHHHHH--HHHHHhCCcCCCCCchhHHHHHHHHHHH-----hhHHH
Confidence 2 3345678899999999999999999 999999953 22233222 345665566655555554 4543
Q ss_pred --ccccccchhhHhh
Q 026552 158 --SLVRFSWGTCTSH 170 (237)
Q Consensus 158 --~~~R~Sw~t~~~~ 170 (237)
.+....|++.++.
T Consensus 279 L~~~~k~hf~n~~k~ 293 (297)
T COG1039 279 LEQVAKLHFKNFQKA 293 (297)
T ss_pred HHHHHHHHHHHHHHH
Confidence 3444444444433
No 18
>PRK04342 DNA topoisomerase VI subunit A; Provisional
Probab=49.28 E-value=10 Score=36.04 Aligned_cols=19 Identities=16% Similarity=0.300 Sum_probs=15.8
Q ss_pred CCccCCCCHHHHHHHHhccc
Q 026552 132 FGSGYPGDPETKAWLTDHKH 151 (237)
Q Consensus 132 yGsGYPsDp~Tk~~L~~~~~ 151 (237)
+|+||| |..|+.||+...+
T Consensus 220 tgkG~P-d~~TR~fl~~L~~ 238 (367)
T PRK04342 220 HLKGQP-ARATRRFIKRLNE 238 (367)
T ss_pred ECCCCC-CHHHHHHHHHHHH
Confidence 589999 7789999998543
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=46.63 E-value=13 Score=30.77 Aligned_cols=18 Identities=39% Similarity=0.754 Sum_probs=14.8
Q ss_pred CCccCCCCHHHHHHHHhcc
Q 026552 132 FGSGYPGDPETKAWLTDHK 150 (237)
Q Consensus 132 yGsGYPsDp~Tk~~L~~~~ 150 (237)
+|+||| |..|+.+|+...
T Consensus 30 t~kG~P-~~~tr~~l~~L~ 47 (160)
T cd00223 30 TGKGYP-DRATRRFLRRLH 47 (160)
T ss_pred EcCCcC-CHHHHHHHHHHH
Confidence 589999 677999999753
No 20
>KOG3495 consensus Mitochondrial F1F0-ATP synthase, subunit epsilon/ATP15 [Energy production and conversion]
Probab=43.86 E-value=25 Score=24.33 Aligned_cols=19 Identities=21% Similarity=0.204 Sum_probs=16.1
Q ss_pred HHHHHHHHHHHHHHHHhhh
Q 026552 101 VSGASIVAKVTRDRTLRGW 119 (237)
Q Consensus 101 VsAASIvAKV~RD~~m~~~ 119 (237)
|.=++|||+|+|+.++.+.
T Consensus 12 i~Ys~I~A~vvR~~LK~e~ 30 (50)
T KOG3495|consen 12 IRYSQIAAQVVRQALKTEL 30 (50)
T ss_pred HHHHHHHHHHHHHHHhHHH
Confidence 4557999999999999874
No 21
>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=41.38 E-value=15 Score=28.44 Aligned_cols=20 Identities=35% Similarity=0.478 Sum_probs=18.5
Q ss_pred hhHHHHHHHHHHHHHHHHhh
Q 026552 99 PVVSGASIVAKVTRDRTLRG 118 (237)
Q Consensus 99 p~VsAASIvAKV~RD~~m~~ 118 (237)
-+||-|||+-|.-||.+++.
T Consensus 10 eIia~aSiLIKfg~ddIl~~ 29 (91)
T PF09010_consen 10 EIIAVASILIKFGRDDILEN 29 (91)
T ss_dssp HHHHHHHHHHHTTTHHHHTS
T ss_pred HHHHHHHHHHHcChHHHHHh
Confidence 57999999999999999987
No 22
>KOG1532 consensus GTPase XAB1, interacts with DNA repair protein XPA [Replication, recombination and repair]
Probab=40.04 E-value=1.4e+02 Score=28.19 Aligned_cols=70 Identities=29% Similarity=0.360 Sum_probs=43.7
Q ss_pred hHHHHHHHHHHHHHHHHHhcCCCccEEEEcCCCChhH---------HHHHhhccCCCceeEEEecCCccchhH------H
Q 026552 38 NLNEISHDSAIGLITRVLNIGILLTEVYLDTVGDAEK---------YQAKLSQRFPSIKFVVSKKADSLYPVV------S 102 (237)
Q Consensus 38 nLN~ls~~a~~~~I~~ll~~~~~~~~V~VD~~g~~~~---------y~~~L~~~~p~i~v~v~~KADs~~p~V------s 102 (237)
||-....+-.+++|++. .-..+.|+|||.|.-+. .-+-|...||.+-+.+.--.-+..|++ =
T Consensus 96 NLF~tk~dqv~~~iek~---~~~~~~~liDTPGQIE~FtWSAsGsIIte~lass~ptvv~YvvDt~rs~~p~tFMSNMlY 172 (366)
T KOG1532|consen 96 NLFATKFDQVIELIEKR---AEEFDYVLIDTPGQIEAFTWSASGSIITETLASSFPTVVVYVVDTPRSTSPTTFMSNMLY 172 (366)
T ss_pred HHHHHHHHHHHHHHHHh---hcccCEEEEcCCCceEEEEecCCccchHhhHhhcCCeEEEEEecCCcCCCchhHHHHHHH
Confidence 44444555555666664 23467999999984332 234455667876555555556666765 4
Q ss_pred HHHHHHHH
Q 026552 103 GASIVAKV 110 (237)
Q Consensus 103 AASIvAKV 110 (237)
|+||+-|.
T Consensus 173 AcSilykt 180 (366)
T KOG1532|consen 173 ACSILYKT 180 (366)
T ss_pred HHHHHHhc
Confidence 89999864
No 23
>PLN00060 meiotic recombination protein SPO11-2; Provisional
Probab=38.09 E-value=21 Score=34.35 Aligned_cols=16 Identities=38% Similarity=0.576 Sum_probs=14.3
Q ss_pred CccCCCCHHHHHHHHhc
Q 026552 133 GSGYPGDPETKAWLTDH 149 (237)
Q Consensus 133 GsGYPsDp~Tk~~L~~~ 149 (237)
|+||| |-.|+.+|+..
T Consensus 242 gKGyP-D~aTR~fL~~L 257 (384)
T PLN00060 242 AKGYP-DLATRFILHRL 257 (384)
T ss_pred cCCCC-CHHHHHHHHHH
Confidence 89999 77799999985
No 24
>KOG2795 consensus Catalytic subunit of the meiotic double strand break transesterase [Replication, recombination and repair]
Probab=27.87 E-value=35 Score=32.73 Aligned_cols=19 Identities=37% Similarity=0.711 Sum_probs=15.9
Q ss_pred CCccCCCCHHHHHHHHhccc
Q 026552 132 FGSGYPGDPETKAWLTDHKH 151 (237)
Q Consensus 132 yGsGYPsDp~Tk~~L~~~~~ 151 (237)
-|+||| |-.|+.+|+..-+
T Consensus 224 TgKGyP-D~~TR~fLkkL~~ 242 (372)
T KOG2795|consen 224 TGKGYP-DIATRLFLKKLEE 242 (372)
T ss_pred ecCCCC-cHHHHHHHHHHHH
Confidence 389999 9999999988543
No 25
>cd07015 Clp_protease_NfeD Nodulation formation efficiency D (NfeD) is a membrane-bound ClpP-class protease. Nodulation formation efficiency D (NfeD; stomatin operon partner protein, STOPP; DUF107) is a member of membrane-anchored ClpP-class proteases. Currently, more than 300 NfeD homologs have been identified - all of which are bacterial or archaeal in origin. Majority of these genomes have been shown to possess operons containing a homologous NfeD/stomatin gene pair, causing NfeD to be previously named STOPP (stomatin operon partner protein). NfeD homologs can be divided into two groups: long and short forms. Long-form homologs have a putative ClpP-class serine protease domain while the short form homologs do not. Downstream from the ClpP-class domain is the so-called NfeD or DUF107 domain. N-terminal region of the NfeD homolog PH1510 (1510-N or PH1510-N) from Pyrococcus horikoshii has been shown to possess serine protease activity and has a Ser-Lys catalytic dyad, preferentially cle
Probab=25.27 E-value=2.5e+02 Score=23.84 Aligned_cols=73 Identities=16% Similarity=0.129 Sum_probs=38.0
Q ss_pred HHHHHHHHHHHHHHHHHhcCCCccEEEEcCCC-Chh---HHHHHhhccCCCceeEEEe--cCCccchhHHHHHHHHHHHH
Q 026552 39 LNEISHDSAIGLITRVLNIGILLTEVYLDTVG-DAE---KYQAKLSQRFPSIKFVVSK--KADSLYPVVSGASIVAKVTR 112 (237)
Q Consensus 39 LN~ls~~a~~~~I~~ll~~~~~~~~V~VD~~g-~~~---~y~~~L~~~~p~i~v~v~~--KADs~~p~VsAASIvAKV~R 112 (237)
|+..+.+...++++...+.+...-.++||+.| ... ...+.+... ...+++.. .|+ .+.||+++|+=-..
T Consensus 10 I~~~~~~~l~~~l~~A~~~~~~~i~l~inSPGG~v~~~~~I~~~i~~~--~~pvv~~v~p~g~---~AaSag~~I~~a~~ 84 (172)
T cd07015 10 ITSYTYDQFDRYITIAEQDNAEAIIIELDTPGGRADAAGNIVQRIQQS--KIPVIIYVYPPGA---SAASAGTYIALGSH 84 (172)
T ss_pred ECHhHHHHHHHHHHHHhcCCCCeEEEEEECCCCCHHHHHHHHHHHHhc--CcCEEEEEecCCC---eehhHHHHHHHhcC
Confidence 44444555566666654445666678999997 221 222223221 12233322 222 34799999985444
Q ss_pred HHHH
Q 026552 113 DRTL 116 (237)
Q Consensus 113 D~~m 116 (237)
-++|
T Consensus 85 ~i~m 88 (172)
T cd07015 85 LIAM 88 (172)
T ss_pred ceEE
Confidence 4444
No 26
>PRK05473 hypothetical protein; Provisional
Probab=25.05 E-value=61 Score=24.88 Aligned_cols=17 Identities=24% Similarity=0.454 Sum_probs=15.2
Q ss_pred HHHHHHHHHHHHHHhhh
Q 026552 103 GASIVAKVTRDRTLRGW 119 (237)
Q Consensus 103 AASIvAKV~RD~~m~~~ 119 (237)
|=|+|-|+.||.+|+++
T Consensus 60 AR~lIrkiERDEilEeL 76 (86)
T PRK05473 60 ARNLIRKLERDEILEEL 76 (86)
T ss_pred HHHHHHHHhHHHHHHHH
Confidence 66899999999999984
No 27
>PRK04860 hypothetical protein; Provisional
Probab=20.99 E-value=95 Score=26.18 Aligned_cols=30 Identities=20% Similarity=0.341 Sum_probs=22.7
Q ss_pred CCCccCCCCHHHHHHHHhccccccCCCccccccc
Q 026552 131 NFGSGYPGDPETKAWLTDHKHIIFGFPSLVRFSW 164 (237)
Q Consensus 131 ~yGsGYPsDp~Tk~~L~~~~~~~fG~p~~~R~Sw 164 (237)
.||.|||-|+.=+.++++ +||++|=.-.|+
T Consensus 79 ~~g~~~~Hg~ewk~lm~~----v~g~~~r~~h~~ 108 (160)
T PRK04860 79 LFGRVAPHGKEWQWMMES----VLGVPARRTHQF 108 (160)
T ss_pred HcCCCCCCCHHHHHHHHH----hcCCCCcccCCC
Confidence 578999999999998887 478765444444
No 28
>PF09345 DUF1987: Domain of unknown function (DUF1987); InterPro: IPR018530 This family of proteins are functionally uncharacterised.
Probab=20.07 E-value=1.4e+02 Score=23.25 Aligned_cols=54 Identities=24% Similarity=0.263 Sum_probs=29.6
Q ss_pred CccCCCCHH-----HHHHHHhccccccCCC-ccccccc---hhhHhh----------c--cccceeeeccCcccc
Q 026552 133 GSGYPGDPE-----TKAWLTDHKHIIFGFP-SLVRFSW---GTCTSH----------F--KDIVEVLWESDEMDE 186 (237)
Q Consensus 133 GsGYPsDp~-----Tk~~L~~~~~~~fG~p-~~~R~Sw---~t~~~~----------l--~~~~~v~w~~~~~~~ 186 (237)
|.-||-|+. ..+||++++....+.. =.+++++ ++.+.+ . +..|.|.|.-|++|+
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 556886663 4589999886522211 1334444 222221 1 256789997765443
Done!