Query gi|254781076|ref|YP_003065489.1| ribonuclease HII [Candidatus Liberibacter asiaticus str. psy62] Match_columns 209 No_of_seqs 132 out of 2742 Neff 6.2 Searched_HMMs 39220 Date Mon May 30 04:13:51 2011 Command /home/congqian_1/programs/hhpred/hhsearch -i 254781076.hhm -d /home/congqian_1/database/cdd/Cdd.hhm No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 PRK13926 junction RNase; Provi 100.0 0 0 493.0 17.8 200 7-208 5-205 (212) 2 PRK00015 rnhB ribonuclease HII 100.0 0 0 468.1 16.1 195 8-204 2-197 (197) 3 PRK13925 rnhB ribonuclease HII 100.0 0 0 460.0 15.5 184 23-206 7-195 (200) 4 cd07182 RNaseH_typeII_bacteria 100.0 0 0 445.8 12.9 178 27-205 1-179 (179) 5 COG0164 RnhB Ribonuclease HII 100.0 0 0 430.8 14.8 184 25-208 1-188 (199) 6 cd06266 RNaseH_typeII Ribonucl 100.0 0 0 389.5 13.1 179 27-205 1-193 (193) 7 pfam01351 RNase_HII Ribonuclea 100.0 0 0 385.6 11.0 177 27-204 1-197 (197) 8 cd07180 RNaseH_typeII_Archaea_ 100.0 0 0 376.7 14.1 177 27-207 1-203 (204) 9 cd07181 RNaseH_typeII_eukaryot 100.0 0 0 362.6 12.8 181 27-207 1-215 (216) 10 cd06590 RNaseH_typeII_bacteria 100.0 0 0 338.8 11.5 178 27-207 1-207 (208) 11 TIGR00729 TIGR00729 ribonuclea 100.0 0 0 329.2 10.4 179 26-208 1-234 (235) 12 KOG2299 consensus 100.0 2.2E-36 5.7E-41 247.8 9.8 182 21-207 25-248 (301) 13 PRK00996 ribonuclease HIII; Pr 100.0 3.2E-35 8.1E-40 240.6 12.1 182 22-206 86-299 (303) 14 COG1039 RnhC Ribonuclease HIII 100.0 1.3E-29 3.2E-34 205.7 9.7 180 23-205 82-294 (297) 15 TIGR00716 rnhC ribonuclease HI 99.9 5.7E-26 1.5E-30 182.9 9.5 170 25-197 92-289 (298) 16 cd06559 Endonuclease_V Endonuc 64.9 3 7.6E-05 22.4 1.1 26 102-127 81-106 (208) 17 pfam04493 Endonuclease_5 Endon 62.8 3.5 8.9E-05 22.0 1.1 80 23-127 21-101 (205) 18 PRK11617 endonuclease V; Provi 62.5 3.3 8.3E-05 22.2 1.0 25 103-127 85-109 (223) 19 TIGR00538 hemN oxygen-independ 55.2 15 0.00038 18.1 3.3 31 63-93 118-154 (462) 20 cd01674 Homoaconitase_Swivel H 52.2 15 0.00039 18.0 3.0 30 175-204 53-84 (129) 21 pfam06135 DUF965 Bacterial pro 48.7 16 0.0004 17.9 2.6 32 137-168 44-77 (79) 22 PRK05473 hypothetical protein; 46.4 17 0.00043 17.7 2.5 31 138-168 48-80 (86) 23 COG1515 Nfi Deoxyinosine 3'end 42.2 11 0.00027 19.0 0.9 26 101-126 82-107 (212) 24 pfam01314 AFOR_C Aldehyde ferr 40.9 20 0.00052 17.3 2.2 32 155-187 348-379 (382) 25 pfam08893 DUF1839 Domain of un 40.1 20 0.00051 17.3 2.0 27 182-208 219-245 (320) 26 PRK01641 leuD isopropylmalate 39.2 32 0.00082 16.0 3.0 12 155-166 164-175 (201) 27 KOG3407 consensus 38.1 16 0.00042 17.8 1.3 17 114-130 53-69 (151) 28 PRK09849 putative oxidoreducta 37.3 24 0.00062 16.8 2.1 32 154-185 651-682 (702) 29 cd01218 PH_phafin2 Phafin2 Pl 34.9 28 0.0007 16.4 2.1 31 134-167 67-97 (104) 30 COG0066 LeuD 3-isopropylmalate 34.4 39 0.00099 15.5 2.8 11 68-78 78-88 (191) 31 pfam07286 DUF1445 Protein of u 34.1 28 0.00073 16.3 2.0 44 11-54 8-63 (143) 32 pfam04084 ORC2 Origin recognit 34.0 20 0.00052 17.3 1.3 13 66-78 118-130 (316) 33 cd01577 IPMI_Swivel Aconatase- 31.2 44 0.0011 15.2 2.8 30 175-204 25-56 (91) 34 TIGR01070 mutS1 DNA mismatch r 30.5 15 0.00037 18.1 0.1 15 116-130 410-424 (863) 35 KOG2745 consensus 29.4 47 0.0012 15.0 2.6 27 146-172 93-119 (321) 36 pfam11641 Antigen_Bd37 Glycosy 29.4 47 0.0012 15.0 2.9 34 154-187 138-179 (224) 37 cd01220 PH_CDEP Chondrocyte-de 29.1 39 0.001 15.5 2.1 34 131-167 63-96 (99) 38 KOG3495 consensus 28.7 48 0.0012 14.9 2.7 21 146-166 12-32 (50) 39 pfam04870 DUF644 Protein of un 27.4 51 0.0013 14.8 2.7 31 178-208 286-316 (323) 40 COG2238 RPS19A Ribosomal prote 26.1 54 0.0014 14.6 2.6 55 140-194 47-111 (147) 41 PRK00439 leuD 3-isopropylmalat 24.7 57 0.0015 14.5 2.9 12 68-79 64-75 (163) 42 cd01219 PH_FGD FGD (faciogenit 23.3 59 0.0015 14.4 2.1 36 129-167 63-98 (101) 43 TIGR02177 PorB_KorB 2-oxoacid: 23.3 61 0.0015 14.3 3.0 39 137-175 77-115 (302) 44 pfam08589 DUF1770 Fungal prote 23.2 50 0.0013 14.8 1.7 15 6-20 67-81 (96) 45 COG2247 LytB Putative cell wal 22.9 62 0.0016 14.2 3.0 13 183-196 146-158 (337) 46 pfam12149 HSV_VP16_C Herpes si 22.8 38 0.00096 15.6 1.0 21 8-33 9-29 (30) 47 pfam09974 DUF2209 Uncharacteri 22.8 62 0.0016 14.2 5.6 116 27-166 1-127 (128) 48 PRK11181 23S rRNA (guanosine-2 22.4 63 0.0016 14.2 3.4 15 115-129 95-109 (244) 49 pfam08459 UvrC_HhH_N UvrC Heli 22.1 64 0.0016 14.1 2.9 37 106-142 70-116 (154) 50 KOG3668 consensus 21.4 55 0.0014 14.5 1.6 15 152-167 212-226 (269) 51 COG3081 Nucleoid-associated pr 21.4 66 0.0017 14.1 3.4 22 161-182 242-269 (335) 52 pfam09288 UBA_3 Fungal ubiquit 21.0 68 0.0017 14.0 2.5 25 177-206 19-43 (55) 53 pfam09010 AsiA Anti-Sigma Fact 20.7 68 0.0017 14.0 2.2 23 144-166 10-32 (91) 54 pfam08714 Fae Formaldehyde-act 20.6 62 0.0016 14.2 1.7 34 80-114 106-144 (160) 55 KOG3062 consensus 20.6 69 0.0018 13.9 2.6 34 113-146 72-105 (281) 56 pfam02334 RTP Replication term 20.3 51 0.0013 14.8 1.3 13 154-166 104-116 (122) 57 COG3596 Predicted GTPase [Gene 20.2 59 0.0015 14.4 1.6 23 144-166 221-243 (296) No 1 >PRK13926 junction RNase; Provisional Probab=100.00 E-value=0 Score=492.97 Aligned_cols=200 Identities=36% Similarity=0.527 Sum_probs=190.7 Q ss_pred CCCCCHHHHHHHHHCCCCEEEEEECCCCCCCCCCEEEEEEEECCCCCCCCCCCCCCCCHHHHHHHHHHHCCCC-EEEEEC Q ss_conf 7886888999999779948999842787775222559999987010823311520289999987552110123-078851 Q gi|254781076|r 7 PERPHFELEAMVREKNMWPVAGIDEVGRGALAGPVVVAAIILDPNNIPFGINDSKKISHKKREELYEKITSSA-IISISS 85 (209) Q Consensus 7 ~~~p~~~~E~~l~~~~~~~IiGvDEaGRG~~~GPlvvaav~~~~~~~~~~i~DSK~Ls~~~R~~l~~~i~~~~-~~~i~~ 85 (209) +..|||++|++|++.|+.+|||||||||||||||||+|||+++......+++|||+||+++|++||+.|++++ .|++++ T Consensus 5 ~~~p~~~~E~~l~~~G~~~I~GVDEaGRG~laGPvvvaaVil~~~~~~~~~~DSKkLs~kkRe~l~~~I~~~~~~~~i~~ 84 (212) T PRK13926 5 STMPDWALEREHWRRGLFRVAGVDEAGRGAWAGPITVAAVILPGTPGEYPFRDSKQLSPAARERLAAKVREVAVAWAVEH 84 (212) T ss_pred CCCCCHHHHHHHHHCCCCEEEEECCCCCCCCHHHHEEEEEEECCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHEEEE T ss_conf 89969799999998799719866576866553433479999788666357870353999999999999986412331366 Q ss_pred CCHHHHHHHCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 56799852047999886543210025753211012653224662122687114786520023666654775899999998 Q gi|254781076|r 86 ASHQYIDKHNIHKATLDAIYHAVENLQVIPRSALIDGRSIPEDLPCQAFAVIKGDSISLSIAAASIIAKVTRDRLMRIAH 165 (209) Q Consensus 86 ~~~~eID~~ni~~A~~~a~~~ai~~l~~~~~~ilIDg~~~~~~~~~~~~~i~KgD~~~~~VaaASIiAKv~RD~~m~~l~ 165 (209) ++++|||++||++||.+||++|+.+|...++.+++|+...+. +.++.+++|||+++++||||||||||+||++|.+|+ T Consensus 85 ~s~~eID~~nI~~At~~am~rai~~l~~~~~~v~~D~~~~~~--~~~~~~~~KGD~~~~~IAAASIiAKV~RD~~M~~l~ 162 (212) T PRK13926 85 AWPEEIDRLNVLGATHAAAERALARLPPPPQALVTDYLRLRT--PLPLLAPPKADALSYSVAAASLLAKTERDRLMAELD 162 (212) T ss_pred ECHHHHHHHCHHHHHHHHHHHHHHHCCCCCCEEEECCCCCCC--CCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHH T ss_conf 589998750709999999999998658887679856874799--988050278634433127889999999899999999 Q ss_pred HHCCCCCCCCCCCCCCHHHHHHHHHCCCCCCCCCCHHHHHHHC Q ss_conf 8777988102899999899999998285830107848886403 Q gi|254781076|r 166 KKYPDYGFDSHVGYPTAKHQQVIKEKGPSCIHRLTFRPLRNLS 208 (209) Q Consensus 166 ~~~p~Ygf~~nkGYgT~~H~~ai~~~G~~~~HR~Sf~~vk~l~ 208 (209) ++||+|||++||||||++|+++|++||+|++||+||+||+++- T Consensus 163 ~~yP~Ygf~~nkGYgTk~H~~ai~~~G~~~~HR~Sf~Pi~~~~ 205 (212) T PRK13926 163 ALYPGYGFAAHKGYGAPAHRAALLALGVSEVHRRRYAPIAQLL 205 (212) T ss_pred HHCCCCCCCCCCCCCCHHHHHHHHHHCCCHHHCCCCHHHHHHH T ss_conf 8787998200579782999999998495976768868799999 No 2 >PRK00015 rnhB ribonuclease HII; Validated Probab=100.00 E-value=0 Score=468.07 Aligned_cols=195 Identities=51% Similarity=0.766 Sum_probs=187.3 Q ss_pred CCCCHHHHHHHHHCCCCEEEEEECCCCCCCCCCEEEEEEEECCCCCCCCCCCCCCCCHHHHHHHHHHHCCCC-EEEEECC Q ss_conf 886888999999779948999842787775222559999987010823311520289999987552110123-0788515 Q gi|254781076|r 8 ERPHFELEAMVREKNMWPVAGIDEVGRGALAGPVVVAAIILDPNNIPFGINDSKKISHKKREELYEKITSSA-IISISSA 86 (209) Q Consensus 8 ~~p~~~~E~~l~~~~~~~IiGvDEaGRG~~~GPlvvaav~~~~~~~~~~i~DSK~Ls~~~R~~l~~~i~~~~-~~~i~~~ 86 (209) .+|++++|+.|+..|+.+|+|||||||||++||||+|||+++++..+.||+|||+||+++|++||+.|++++ .|+++++ T Consensus 2 ~~p~~~~e~~l~~~g~~~ViGiDEaGRG~~~GP~vvaav~~~~~~~~~gv~DSK~Ls~~kR~~l~~~I~~~~~~~~i~~~ 81 (197) T PRK00015 2 LVPMLSFEKALLKQGLGLIAGVDEAGRGPLAGPVVAAAVILDPNRIILGLNDSKKLSEKKREALYEEIKEKALAWSVGIA 81 (197) T ss_pred CCCCHHHHHHHHHCCCCEEEEECCCCCCCCCCCEEEEEEEECCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHEEEC T ss_conf 98727999999987990799863688787600016899998875676777310109999999999999998877631315 Q ss_pred CHHHHHHHCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 67998520479998865432100257532110126532246621226871147865200236666547758999999988 Q gi|254781076|r 87 SHQYIDKHNIHKATLDAIYHAVENLQVIPRSALIDGRSIPEDLPCQAFAVIKGDSISLSIAAASIIAKVTRDRLMRIAHK 166 (209) Q Consensus 87 ~~~eID~~ni~~A~~~a~~~ai~~l~~~~~~ilIDg~~~~~~~~~~~~~i~KgD~~~~~VaaASIiAKv~RD~~m~~l~~ 166 (209) +|+|||++||++|+.++|++++.+|..+|+.++|||+..+. +.++.+++|||++|++||||||||||+||++|.+|++ T Consensus 82 ~~~eID~~ni~~a~~~a~~~al~~l~~~~~~i~vDg~~~~~--~~~~~~~~KaD~~~~~VaAASIvAKv~RD~~m~~l~~ 159 (197) T PRK00015 82 SPEEIDELNILEATMLAMRRAVAGLSVKPDYVLIDGNPVPV--PIPQEAIVKGDAKSPSIAAASILAKVTRDRLMEELDK 159 (197) T ss_pred CHHHHHHHCCHHHHHHHHHHHHHHCCCCCCEEEECCCCCCC--CCCEEEEECCCCCCHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 79997400709999999999999649999999985999999--9974888525210035778899999899999999998 Q ss_pred HCCCCCCCCCCCCCCHHHHHHHHHCCCCCCCCCCHHHH Q ss_conf 77798810289999989999999828583010784888 Q gi|254781076|r 167 KYPDYGFDSHVGYPTAKHQQVIKEKGPSCIHRLTFRPL 204 (209) Q Consensus 167 ~~p~Ygf~~nkGYgT~~H~~ai~~~G~~~~HR~Sf~~v 204 (209) +||+|||++||||||++|+++|+++|+|++||+||+|| T Consensus 160 ~yp~Yg~~~nkGY~T~~H~~ai~~~G~~~~HR~S~~pi 197 (197) T PRK00015 160 EYPGYGFAKHKGYGTKAHLEALKKHGPTPIHRRSFAPV 197 (197) T ss_pred HCCCCCCCCCCCCCCHHHHHHHHHHCCCHHHCCCCCCC T ss_conf 78898986587869799999999849698873998899 No 3 >PRK13925 rnhB ribonuclease HII; Provisional Probab=100.00 E-value=0 Score=459.96 Aligned_cols=184 Identities=43% Similarity=0.618 Sum_probs=174.7 Q ss_pred CCEEEEEECCCCCCCCCCEEEEEEEECCCCC----CCCCCCCCCCCHHHHHHHHHHHCCCC-EEEEECCCHHHHHHHCHH Q ss_conf 9489998427877752225599999870108----23311520289999987552110123-078851567998520479 Q gi|254781076|r 23 MWPVAGIDEVGRGALAGPVVVAAIILDPNNI----PFGINDSKKISHKKREELYEKITSSA-IISISSASHQYIDKHNIH 97 (209) Q Consensus 23 ~~~IiGvDEaGRG~~~GPlvvaav~~~~~~~----~~~i~DSK~Ls~~~R~~l~~~i~~~~-~~~i~~~~~~eID~~ni~ 97 (209) -.+|||||||||||||||||+|||+++++.. ..||+|||+||+++|++||+.|++++ .|+++.++++|||++||+ T Consensus 7 ~g~IiGvDEaGRG~laGPvvvaav~~~~~~~~~l~~~gv~DSKkLs~kkR~~l~~~I~~~~~~~~i~~~s~~eID~~nI~ 86 (200) T PRK13925 7 SGLIAGVDEVGRGCLFGPVVAAAVILPESAAEELLAAGLTDSKKLSQRRRAQLVPLIETVAIAWGIGQASAREIDRLNIL 86 (200) T ss_pred CCCEEEECCCCCCCCHHCEEEEEEEEECCCCHHHHHCCCHHHHHCCHHHHHHHHHHHHHHHHEEEEEEECHHHHHHHCHH T ss_conf 99899872888666410017999998065542230123404551578889999887875211028999089999875849 Q ss_pred HHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCC Q ss_conf 99886543210025753211012653224662122687114786520023666654775899999998877798810289 Q gi|254781076|r 98 KATLDAIYHAVENLQVIPRSALIDGRSIPEDLPCQAFAVIKGDSISLSIAAASIIAKVTRDRLMRIAHKKYPDYGFDSHV 177 (209) Q Consensus 98 ~A~~~a~~~ai~~l~~~~~~ilIDg~~~~~~~~~~~~~i~KgD~~~~~VaaASIiAKv~RD~~m~~l~~~~p~Ygf~~nk 177 (209) +||.+||++|+.+|..+|+.++|||+...+.++.++.+++|||+++++||||||||||+||++|.+|+++||+|||++|| T Consensus 87 ~At~~am~~ai~~l~~~~~~vlvDG~~~~~~~~~~~~~ivKgD~~~~~IaAASIIAKV~RD~~M~~l~~~yP~Y~f~~nk 166 (200) T PRK13925 87 QATELAMLRALQKLPSPPDLCLVDGNQPIRLLPGPQRTVVKGDSRSAAIAAASILAKVWRDALIKRLARRYPGYGLERNK 166 (200) T ss_pred HHHHHHHHHHHHHCCCCCCEEEEECCCCCCCCCCCEEEECCCCCEEEEEHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCC T ss_conf 99999999999863899778997368556778867477528971111005888999999999999999878699841265 Q ss_pred CCCCHHHHHHHHHCCCCCCCCCCHHHHHH Q ss_conf 99998999999982858301078488864 Q gi|254781076|r 178 GYPTAKHQQVIKEKGPSCIHRLTFRPLRN 206 (209) Q Consensus 178 GYgT~~H~~ai~~~G~~~~HR~Sf~~vk~ 206 (209) ||||++|+++|++||+|++||+||+||.. T Consensus 167 GYgTk~H~~ai~~~G~s~~HRkSf~P~~~ 195 (200) T PRK13925 167 GYGTAKHRQALLQLGPTPLHRQSFLPCLI 195 (200) T ss_pred CCCCHHHHHHHHHHCCCHHHCCCCHHHHH T ss_conf 87819999999983949778698687999 No 4 >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=0 Score=445.76 Aligned_cols=178 Identities=56% Similarity=0.803 Sum_probs=171.6 Q ss_pred EEEECCCCCCCCCCEEEEEEEECCCCCCCCCCCCCCCCHHHHHHHHHHHCCCC-EEEEECCCHHHHHHHCHHHHHHHHHH Q ss_conf 99842787775222559999987010823311520289999987552110123-07885156799852047999886543 Q gi|254781076|r 27 AGIDEVGRGALAGPVVVAAIILDPNNIPFGINDSKKISHKKREELYEKITSSA-IISISSASHQYIDKHNIHKATLDAIY 105 (209) Q Consensus 27 iGvDEaGRG~~~GPlvvaav~~~~~~~~~~i~DSK~Ls~~~R~~l~~~i~~~~-~~~i~~~~~~eID~~ni~~A~~~a~~ 105 (209) +|||||||||++||||+|+|+++.+..+.||+|||+||+++|++||+.|++++ .|++++++|+|||++||++|+.+||+ T Consensus 1 aGiDEaGRG~~~GP~vvaav~~~~~~~~~gv~DSK~Lt~k~R~~l~~~I~~~~~~~~v~~~s~~eID~~ni~~A~~~a~~ 80 (179) T cd07182 1 AGVDEAGRGPLAGPVVAAAVILPPDFEIEGLNDSKKLSEKKREELYEEIKEKALAWGIGIASPEEIDRINILQATLLAMR 80 (179) T ss_pred CCCCCCCCCCCCCCEEEEEEEECCCCCCCCCCHHHHCCHHHHHHHHHHHHHCCCEEEEEECCHHHHHHCCHHHHHHHHHH T ss_conf 99876686662100158999988867866542665389999999999986211306778669999986399999999999 Q ss_pred HHCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCHHHH Q ss_conf 21002575321101265322466212268711478652002366665477589999999887779881028999998999 Q gi|254781076|r 106 HAVENLQVIPRSALIDGRSIPEDLPCQAFAVIKGDSISLSIAAASIIAKVTRDRLMRIAHKKYPDYGFDSHVGYPTAKHQ 185 (209) Q Consensus 106 ~ai~~l~~~~~~ilIDg~~~~~~~~~~~~~i~KgD~~~~~VaaASIiAKv~RD~~m~~l~~~~p~Ygf~~nkGYgT~~H~ 185 (209) +++++|...++.++|||+.++ .+++++.+++|||++|++||||||||||+||++|.+|+++||+|||++||||||++|+ T Consensus 81 ~ai~~l~~~~~~i~vDg~~~~-~~~~~~~~i~kaD~~~~~VaaASIiAKv~RD~~m~~l~~~yP~Yg~~~nkGYgT~~H~ 159 (179) T cd07182 81 RAVEGLPVKPDYVLVDGNRLP-PLPIPQEAIVKGDAKSASIAAASILAKVTRDRLMIELDKKYPGYGFAKHKGYGTKEHL 159 (179) T ss_pred HHHHHCCCCCCEEEEECCCCC-CCCCCEEEEECCCCEEEEEEHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHH T ss_conf 999866899868997466388-9998869995487356565277889898899999999987879884127688809999 Q ss_pred HHHHHCCCCCCCCCCHHHHH Q ss_conf 99998285830107848886 Q gi|254781076|r 186 QVIKEKGPSCIHRLTFRPLR 205 (209) Q Consensus 186 ~ai~~~G~~~~HR~Sf~~vk 205 (209) ++|++||+|++||+||+|++ T Consensus 160 ~aI~~~G~~~~HR~Sf~~~~ 179 (179) T cd07182 160 EALKKYGPTPIHRRSFAPVK 179 (179) T ss_pred HHHHHHCCCHHHCCCCCCCC T ss_conf 99998494977757986869 No 5 >COG0164 RnhB Ribonuclease HII [DNA replication, recombination, and repair] Probab=100.00 E-value=0 Score=430.82 Aligned_cols=184 Identities=52% Similarity=0.788 Sum_probs=174.6 Q ss_pred EEEEEECCCCCCCCCCEEEEEEEECCCCCC--CCCCCCCCCCHHHHHHHHHHHCCCC-EEEEECCCHHHHHHHCHHHHHH Q ss_conf 899984278777522255999998701082--3311520289999987552110123-0788515679985204799988 Q gi|254781076|r 25 PVAGIDEVGRGALAGPVVVAAIILDPNNIP--FGINDSKKISHKKREELYEKITSSA-IISISSASHQYIDKHNIHKATL 101 (209) Q Consensus 25 ~IiGvDEaGRG~~~GPlvvaav~~~~~~~~--~~i~DSK~Ls~~~R~~l~~~i~~~~-~~~i~~~~~~eID~~ni~~A~~ 101 (209) +|+|||||||||++||||+|||+++++..+ .|++||||||+++|++||+.|++.+ .|+++++++++||++||++|++ T Consensus 1 ~vaGIDEAGRGpl~GPvV~Aavil~~~~~~~~~Gl~DSKkLs~~kRe~L~~~I~~~a~~~~v~~~~~~~Id~~ni~~a~~ 80 (199) T COG0164 1 LVAGVDEAGRGPLAGPVVAAAVILPPDRLPKKLGLKDSKKLSPKKREELFEEIKEKALAWGVGIIPAEEIDELNILEATK 80 (199) T ss_pred CCCCCCCCCCCCCCCCEEEEEEEECCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCEEEEEECCHHHHHHHHHHHHHH T ss_conf 92760577867752622589999773223334586652307999999999999865227999972789886742999999 Q ss_pred HHHHHHCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCC Q ss_conf 65432100257532110126532246621226871147865200236666547758999999988777988102899999 Q gi|254781076|r 102 DAIYHAVENLQVIPRSALIDGRSIPEDLPCQAFAVIKGDSISLSIAAASIIAKVTRDRLMRIAHKKYPDYGFDSHVGYPT 181 (209) Q Consensus 102 ~a~~~ai~~l~~~~~~ilIDg~~~~~~~~~~~~~i~KgD~~~~~VaaASIiAKv~RD~~m~~l~~~~p~Ygf~~nkGYgT 181 (209) +||++|+.+|..+++.++|||+.++..++.+..+++|||++|++||||||||||+||++|.+|++.||+|||+.|||||| T Consensus 81 ~am~~av~~l~~~~~~vlvD~~~~~~~l~~~~~a~~KgDa~~~~IaAASIvAKV~RDr~m~~l~~~yp~Y~~~~~~GY~T 160 (199) T COG0164 81 LAMRRAVAGLSSQPDLVLVDGNDLPLGLPQPAVAIIKGDAKSPSIAAASILAKVTRDRLMEELAKEYPEYGFDKGSGYPT 160 (199) T ss_pred HHHHHHHHHCCCCCCEEEEECCCCCCCCCCCCCEEECCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCC T ss_conf 99999998266668889981788642378776034535311378999999999999999999986586767625787798 Q ss_pred HHHHHHHHHCCCCC-CCCCCHHHHHHHC Q ss_conf 89999999828583-0107848886403 Q gi|254781076|r 182 AKHQQVIKEKGPSC-IHRLTFRPLRNLS 208 (209) Q Consensus 182 ~~H~~ai~~~G~~~-~HR~Sf~~vk~l~ 208 (209) +.|.+++.++|+++ +||+||+|++++. T Consensus 161 ~~h~~a~~~~~~~~~~hR~Sf~~vk~~~ 188 (199) T COG0164 161 DPHTEALLKKGGTPGIHRRSFAPVRRLL 188 (199) T ss_pred HHHHHHHHHHCCCCCEEECCCHHHHHHH T ss_conf 3999999985699862222428899874 No 6 >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=0 Score=389.53 Aligned_cols=179 Identities=53% Similarity=0.779 Sum_probs=167.3 Q ss_pred EEEECCCCCCCCCCEEEEEEEECCCCC----CCCCCCCCCCCHHHHHHHHHHHCCCC-EEEEECCCHHHHHHHCHHHHHH Q ss_conf 998427877752225599999870108----23311520289999987552110123-0788515679985204799988 Q gi|254781076|r 27 AGIDEVGRGALAGPVVVAAIILDPNNI----PFGINDSKKISHKKREELYEKITSSA-IISISSASHQYIDKHNIHKATL 101 (209) Q Consensus 27 iGvDEaGRG~~~GPlvvaav~~~~~~~----~~~i~DSK~Ls~~~R~~l~~~i~~~~-~~~i~~~~~~eID~~ni~~A~~ 101 (209) +|||||||||+|||||+|||+++.+.. ..||+|||+||+++|++||+.|++.+ .|++++++|+|||++||++++. T Consensus 1 ~GiDEaGRG~~~GP~vvaav~~~~~~~~~l~~~gv~DSK~Ls~~kR~~l~~~I~~~~~~~~v~~~s~~~Id~~ni~~~~~ 80 (193) T cd06266 1 AGIDEAGRGPLAGPVVAAAVILPKENIEILKILGVKDSKKLSEKKREELFEEIKEEALAYAIGIISPEEIDELNILQATA 80 (193) T ss_pred CCCCCCCCCCCCCCEEEEEEEECHHHHHHHHHCCCCCHHHCCHHHHHHHHHHHCCCCEEEEEEECCHHHHHHCCHHHHHH T ss_conf 99857786772044068999981354003432577511018999999998752356448999967899997557899999 Q ss_pred HHHHHHCCCCCCCCCCCCCCCCCCCC--------CCCEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCC Q ss_conf 65432100257532110126532246--------6212268711478652002366665477589999999887779881 Q gi|254781076|r 102 DAIYHAVENLQVIPRSALIDGRSIPE--------DLPCQAFAVIKGDSISLSIAAASIIAKVTRDRLMRIAHKKYPDYGF 173 (209) Q Consensus 102 ~a~~~ai~~l~~~~~~ilIDg~~~~~--------~~~~~~~~i~KgD~~~~~VaaASIiAKv~RD~~m~~l~~~~p~Ygf 173 (209) ++|.+++.++..+++.++|||+..++ ..+.++.+++|||++|++||||||+|||+||++|.+|+++||+|+| T Consensus 81 ~~~~~ai~~l~~~~~~v~vD~~~~~~~~~~~~~~~~~~~~~~~~kaD~~~~~VaAASIiAKv~RD~~m~~l~~~~p~y~~ 160 (193) T cd06266 81 LAMARAILNLGVKPDEVLVDGNGVPEKYFALEKKFLPIPVTAIVKGDSKSPSVAAASILAKVTRDRLMEELDEEYPGYGF 160 (193) T ss_pred HHHHHHHHHCCCCCCEEEECCCCCHHHHHHHHCCCCCCCEEEEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCC T ss_conf 99999999648999999989999827776542026898717886155421788899999999999999999987879998 Q ss_pred CCCCCCCCHHHHHHHHHCCCC-CCCCCCHHHHH Q ss_conf 028999998999999982858-30107848886 Q gi|254781076|r 174 DSHVGYPTAKHQQVIKEKGPS-CIHRLTFRPLR 205 (209) Q Consensus 174 ~~nkGYgT~~H~~ai~~~G~~-~~HR~Sf~~vk 205 (209) +.|+||||+.|.+++.++|++ ++||+||+|++ T Consensus 161 ~~g~GY~t~~h~~~~~~~g~~~~~hR~sf~~~~ 193 (193) T cd06266 161 AKGKGYPTDPHTEAILKYGPTEPIHRRSFKTVK 193 (193) T ss_pred CCCCCCCCHHHHHHHHHHCCCCHHHCCCCCCCC T ss_conf 577583999999999986859566566876869 No 7 >pfam01351 RNase_HII Ribonuclease HII. Probab=100.00 E-value=0 Score=385.57 Aligned_cols=177 Identities=46% Similarity=0.674 Sum_probs=159.5 Q ss_pred EEEECCCCCCCCCCEEEEEEEECCCCCC----CCCCCCCCCCHHHHHHHHHHHCCCC------EEEEECCCHHHHHHHCH Q ss_conf 9984278777522255999998701082----3311520289999987552110123------07885156799852047 Q gi|254781076|r 27 AGIDEVGRGALAGPVVVAAIILDPNNIP----FGINDSKKISHKKREELYEKITSSA------IISISSASHQYIDKHNI 96 (209) Q Consensus 27 iGvDEaGRG~~~GPlvvaav~~~~~~~~----~~i~DSK~Ls~~~R~~l~~~i~~~~------~~~i~~~~~~eID~~ni 96 (209) +|||||||||+|||||+|||+++++... .||+|||+||+++|+++++.|++.+ .|.+...++++||+.|| T Consensus 1 aGiDEaGRG~~~GPlvvaav~l~~~~~~~l~~~gv~DSK~Ls~kkR~~l~~~I~~~~~~~~~~~~~i~~~~~~~id~~~i 80 (197) T pfam01351 1 AGIDEVGRGPLAGPLVVAAVYLPPERLIELRKLGVKDSKKLSDKKREELAELIKKRIETRKLVAGNIKYAEANEINLNNI 80 (197) T ss_pred CCCCCCCCCCCCCCEEEEEEEEECCCCHHHHHCCCHHHHHCCHHHHHHHHHHHHHHHHHHHCEEEEEEEECHHHHCHHHH T ss_conf 99877587676022068999980221556664332022017999999999999974101110244556603756269999 Q ss_pred HHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCC------EEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCC Q ss_conf 9998865432100257532110126532246621------2268711478652002366665477589999999887779 Q gi|254781076|r 97 HKATLDAIYHAVENLQVIPRSALIDGRSIPEDLP------CQAFAVIKGDSISLSIAAASIIAKVTRDRLMRIAHKKYPD 170 (209) Q Consensus 97 ~~A~~~a~~~ai~~l~~~~~~ilIDg~~~~~~~~------~~~~~i~KgD~~~~~VaaASIiAKv~RD~~m~~l~~~~p~ 170 (209) .+++..+|.+++..+...++.++|||+..+..+. .++.+++|||++|++||||||||||+||+.|+ +..+||+ T Consensus 81 ~~a~~~~~~~~l~~~~~~~~~i~vD~~~~~~~~~~~~~~~~~~~~~~KaD~~~~~VAAASIlAKv~RD~~i~-~~~~~p~ 159 (197) T pfam01351 81 LHALHLAMIRAVQKLGVKPDEILVDGFTPPKSLPMKQEAIFKVTAEHKADSKYLSVAAASIIAKVTRDEMLE-LLKRFPG 159 (197) T ss_pred HHHHHHHHHHHHHHCCCCCCEEEECCCCCCCCCCHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHH-HHHHCCC T ss_conf 999999999999845999998998898894201222430257623232012203431437899999999999-9866879 Q ss_pred CCCCCCCCCCCHHHHHHHHHCCCCC----CCCCCHHHH Q ss_conf 8810289999989999999828583----010784888 Q gi|254781076|r 171 YGFDSHVGYPTAKHQQVIKEKGPSC----IHRLTFRPL 204 (209) Q Consensus 171 Ygf~~nkGYgT~~H~~ai~~~G~~~----~HR~Sf~~v 204 (209) |+|++||||||++|+++|.++|++| +||+||+|| T Consensus 160 y~f~~~~GY~t~~h~~~i~~~g~~~~~~~~hR~Sf~~v 197 (197) T pfam01351 160 YGLDKGSGYPSDPHTEALLKLGATPWLPDFHRRSFATV 197 (197) T ss_pred CCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCCCCCCCC T ss_conf 99624868498999999999682999884126888897 No 8 >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=0 Score=376.72 Aligned_cols=177 Identities=36% Similarity=0.585 Sum_probs=154.4 Q ss_pred EEEECCCCCCCCCCEEEEEEEECCCCC----CCCCCCCCCCCHHHHHHHHHHHCCCC-EEEEECCCHHHHHH----HCHH Q ss_conf 998427877752225599999870108----23311520289999987552110123-07885156799852----0479 Q gi|254781076|r 27 AGIDEVGRGALAGPVVVAAIILDPNNI----PFGINDSKKISHKKREELYEKITSSA-IISISSASHQYIDK----HNIH 97 (209) Q Consensus 27 iGvDEaGRG~~~GPlvvaav~~~~~~~----~~~i~DSK~Ls~~~R~~l~~~i~~~~-~~~i~~~~~~eID~----~ni~ 97 (209) ||||||||||||||||+|||+++++.. ..||+|||+||+++|++|++.|++++ .|++++++++|||+ .||+ T Consensus 1 ~GvDEaGRG~laGPvvvaav~~~~~~~~~l~~~gv~DSKkLs~kkR~~l~~~I~~~~~~~~i~~~s~~eID~~~~~~nln 80 (204) T cd07180 1 CGIDEAGRGPVIGPMVVAGVAIDEESLKKLKSLGVKDSKKLTPKKREELYNEILKVADDVVIVIVSPEEIDERREAHNLN 80 (204) T ss_pred CCCCCCCCCCCCCCCEEEEEEECHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHCCEEEEEEECHHHHHHHHHHHHHH T ss_conf 99987787662101168999984553335553677535008899999999999973537899997799997885899999 Q ss_pred HHHHHHHHHHCCCCCCCCCCCCCCCCCCC---------C--CCCEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 99886543210025753211012653224---------6--621226871147865200236666547758999999988 Q gi|254781076|r 98 KATLDAIYHAVENLQVIPRSALIDGRSIP---------E--DLPCQAFAVIKGDSISLSIAAASIIAKVTRDRLMRIAHK 166 (209) Q Consensus 98 ~A~~~a~~~ai~~l~~~~~~ilIDg~~~~---------~--~~~~~~~~i~KgD~~~~~VaaASIiAKv~RD~~m~~l~~ 166 (209) .++..+|.++++++..+++.+++|+.... . ..+..+.+++|||+++++||||||||||+||++|.+|++ T Consensus 81 ~~~~~a~~~~i~~l~~~~~~i~iD~~~~~~~~~~~~~~~~~~~~~~v~~~~KgD~k~~~IAAASIiAKv~RD~~M~~l~~ 160 (204) T cd07180 81 ELEAEAFAELINRLSDKPDIVYVDACDVNEERFAEELRERLNSGVEVIAEHKADAKYPVVSAASIIAKVERDREIEELKE 160 (204) T ss_pred HHHHHHHHHHHHHCCCCCCEEEEECCCCCCHHHHHHCCCCCCCCCCEEEECCCCHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 99999999999955778999998167876134433033235888726873375222177899999999999999999998 Q ss_pred HCCCCCCCCCCCCCC-HHHHHH----HHHCC-CCCCCCCCHHHHHHH Q ss_conf 777988102899999-899999----99828-583010784888640 Q gi|254781076|r 167 KYPDYGFDSHVGYPT-AKHQQV----IKEKG-PSCIHRLTFRPLRNL 207 (209) Q Consensus 167 ~~p~Ygf~~nkGYgT-~~H~~a----i~~~G-~~~~HR~Sf~~vk~l 207 (209) +||+|| +|||| |.|+++ |+++| ++++||+||+|||+| T Consensus 161 ~yp~yG----~GYpsd~~t~~~l~~~i~~~g~~~~~hR~S~~~vk~~ 203 (204) T cd07180 161 EYGDFG----SGYPSDPRTIKFLRNYYREHGELPPIVRKSWKTVKRL 203 (204) T ss_pred HCCCCC----CCCCCCHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHH T ss_conf 769989----8799977899999999873289996631881758975 No 9 >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=0 Score=362.64 Aligned_cols=181 Identities=31% Similarity=0.390 Sum_probs=146.0 Q ss_pred EEEECCCCCCCCCCEEEEEEEECCCCC----CCCCCCCCCCCHHHHHHHHHHHCCCC---EEEEECCCHHHHHHH----- Q ss_conf 998427877752225599999870108----23311520289999987552110123---078851567998520----- Q gi|254781076|r 27 AGIDEVGRGALAGPVVVAAIILDPNNI----PFGINDSKKISHKKREELYEKITSSA---IISISSASHQYIDKH----- 94 (209) Q Consensus 27 iGvDEaGRG~~~GPlvvaav~~~~~~~----~~~i~DSK~Ls~~~R~~l~~~i~~~~---~~~i~~~~~~eID~~----- 94 (209) ||||||||||||||||+|||+++.+.. ..||+|||+||+++|++||+.|++.+ .|+++.++++|||+. T Consensus 1 IGvDEaGRGplaGPvV~aav~~~~~~~~~l~~~gv~DSKkLs~kkRe~l~~~I~~~~~~~~~~i~~~~~~eId~~~l~~~ 80 (216) T cd07181 1 LGIDEAGRGPVLGPMVYGIAYCPISYEEDLKKLGFADSKTLTEEKREELFKKIKEKSEALGWATRILSPQYISAKMLART 80 (216) T ss_pred CCCCCCCCCCCCCCCEEEEEEEECCCCCHHHHCCCCHHCCCCHHHHHHHHHHHHHHCCCEEEEEEEECHHHHHHHHHHHH T ss_conf 99778786662164057999970222303431487120119999999999999852735078999946999889898864 Q ss_pred --CHHHHHHHHHHH---HCCCCCCCCCCCCCCCCCCCC---------CCCEEEEEECCCCCCCHHHHHHHHHHHHHHHHH Q ss_conf --479998865432---100257532110126532246---------621226871147865200236666547758999 Q gi|254781076|r 95 --NIHKATLDAIYH---AVENLQVIPRSALIDGRSIPE---------DLPCQAFAVIKGDSISLSIAAASIIAKVTRDRL 160 (209) Q Consensus 95 --ni~~A~~~a~~~---ai~~l~~~~~~ilIDg~~~~~---------~~~~~~~~i~KgD~~~~~VaaASIiAKv~RD~~ 160 (209) |++.....++.+ .+.....+++.++||+...+. ..+.+..+++|||++|++||||||||||+||++ T Consensus 81 ~~~ln~l~~~~~~~~i~~~~~~~~~~~~i~iD~~g~~~~~~~~l~~~~~~~~~~~~~KgD~~~~~IaAASIlAKV~RD~~ 160 (216) T cd07181 81 KYNLNEISHDAAIGLIKSVLDKGVNVTEVYVDTVGPPEKYQAKLKKLFPGIKFTVEKKADSLYPIVSAASIVAKVTRDRA 160 (216) T ss_pred HHHHHHHHHHHHHHHHHHHHHCCCCCCEEEEECCCCHHHHHHHHHCCCCCCCEEEEECCCCCCCCHHHHHHHHHHHCCHH T ss_conf 75599999999999999999659998779981899867887653103899654772126545520237888999974599 Q ss_pred HHHHHHHCCCCCCCCC--CCCCC-HHHHHHHHH-----CCCCCCCCCCHHHHHHH Q ss_conf 9999887779881028--99999-899999998-----28583010784888640 Q gi|254781076|r 161 MRIAHKKYPDYGFDSH--VGYPT-AKHQQVIKE-----KGPSCIHRLTFRPLRNL 207 (209) Q Consensus 161 m~~l~~~~p~Ygf~~n--kGYgT-~~H~~ai~~-----~G~~~~HR~Sf~~vk~l 207 (209) |.+|+..||.|+|..| +|||| +.|+++|++ +|+|++||+||+||++| T Consensus 161 m~~l~~~~~~~~~~~~~GsGYPsdp~t~~~L~~~~~~~~g~~~~hR~Sw~~v~~l 215 (216) T cd07181 161 LKNWQFDEYLIDPDGDFGSGYPSDPKTKKWLKKNVDPVFGFPSLVRFSWSTAKKL 215 (216) T ss_pred HHHHHHHCCCCCCCCCCCEECCCCHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHH T ss_conf 9987645645544688785789838899999955556689996640782999985 No 10 >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=0 Score=338.80 Aligned_cols=178 Identities=30% Similarity=0.358 Sum_probs=147.5 Q ss_pred EEEECCCCCCCCCCEEEEEEEECCCCC----CCCCCCCCCCCHHHHHHHHHHHCCCCEEEEECCCHHHHHHHCHHHH--- Q ss_conf 998427877752225599999870108----2331152028999998755211012307885156799852047999--- Q gi|254781076|r 27 AGIDEVGRGALAGPVVVAAIILDPNNI----PFGINDSKKISHKKREELYEKITSSAIISISSASHQYIDKHNIHKA--- 99 (209) Q Consensus 27 iGvDEaGRG~~~GPlvvaav~~~~~~~----~~~i~DSK~Ls~~~R~~l~~~i~~~~~~~i~~~~~~eID~~ni~~A--- 99 (209) ||+|||||||||||||+|||+++++.. ..||+|||+||+++|++||+.|++.+.|++..+++++||.+..... T Consensus 1 IGiDEaGRG~l~GPvv~aav~~~~~~~~~l~~lgv~DSKkLs~kkR~~l~~~I~~~~~~~~~~~~~~~~n~~~~~~~n~n 80 (208) T cd06590 1 IGSDEVGKGDYFGPLVVAAVYVDKENISKLKKLGVKDSKKLTDKKIIRLAPKIKKKIPYSVLSLGPEKYNELYKKGKNLN 80 (208) T ss_pred CCCCCCCCCCCHHCCEEEEEEECHHHHHHHHHCCCCCHHHCCHHHHHHHHHHHHHHCCEEEEEECHHHHHHHHHHHHHHH T ss_conf 98767787765102078999986575477876598532125899999999999984866899987899999998798899 Q ss_pred --HHHHHHHHCCCCC---CCCCCCCCCCCCCC-----------CCCCEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHH Q ss_conf --8865432100257---53211012653224-----------6621226871147865200236666547758999999 Q gi|254781076|r 100 --TLDAIYHAVENLQ---VIPRSALIDGRSIP-----------EDLPCQAFAVIKGDSISLSIAAASIIAKVTRDRLMRI 163 (209) Q Consensus 100 --~~~a~~~ai~~l~---~~~~~ilIDg~~~~-----------~~~~~~~~~i~KgD~~~~~VaaASIiAKv~RD~~m~~ 163 (209) ...++.++++++. ..++.++||++..+ ...+.++.+++|||++|++||||||||||+||+.|.+ T Consensus 81 ~~~~~~~~~ai~~~~~~~~~~~~v~iD~~~~~~~~~~~l~~~~~~~~~~~~~~~KgD~k~~~VaAASIiAKv~rd~~m~~ 160 (208) T cd06590 81 KLKALLHNKAINNLLEKPKKPVAILIDQFASEKVYKRYLKKEKKIVKEPLIFRTKAESKHLAVAAASILARYAFLEKMEK 160 (208) T ss_pred HHHHHHHHHHHHHHHHCCCCCCEEEECCCCCCHHHHHHHHCCCCCCCCCEEEEECHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 99999999999999836899998998898870478898731367889876998223332278899999999999999999 Q ss_pred HHHHCCCCCCCCCCCCCCHHHHHH---HHHCCCCCCCCC---CHHHHHHH Q ss_conf 988777988102899999899999---998285830107---84888640 Q gi|254781076|r 164 AHKKYPDYGFDSHVGYPTAKHQQV---IKEKGPSCIHRL---TFRPLRNL 207 (209) Q Consensus 164 l~~~~p~Ygf~~nkGYgT~~H~~a---i~~~G~~~~HR~---Sf~~vk~l 207 (209) |+++ |||..||||||+.|+++ |++||++++||. +|+|+++. T Consensus 161 l~~~---Yg~~~~kGyGt~~~~~a~~~i~~yG~~~lhr~~k~~f~~~k~~ 207 (208) T cd06590 161 LSKQ---YGMKLPKGASSKVDEQAAEIIKKYGLEELKKVAKLHFKNTKKA 207 (208) T ss_pred HHHH---CCCCCCCCCCCHHHHHHHHHHHHHCCHHHHHHHHHHCHHHHHH T ss_conf 8786---4987688998288999999999849618788998702158750 No 11 >TIGR00729 TIGR00729 ribonuclease HII; InterPro: IPR004649 Ribonuclease HII 3.1.26.4 from EC cleaves RNA from DNA-RNA hybrids. 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 characterised as RNase HI, large subunit.; GO: 0004523 ribonuclease H activity, 0016070 RNA metabolic process. Probab=100.00 E-value=0 Score=329.17 Aligned_cols=179 Identities=34% Similarity=0.521 Sum_probs=149.6 Q ss_pred EEEEECCCCCCCCCCEEEE-EEEECCCCC----CCCCCCCCCCCHHHHHHHHHHHCC------CCEEEEECCCHHHHHH- Q ss_conf 9998427877752225599-999870108----233115202899999875521101------2307885156799852- Q gi|254781076|r 26 VAGIDEVGRGALAGPVVVA-AIILDPNNI----PFGINDSKKISHKKREELYEKITS------SAIISISSASHQYIDK- 93 (209) Q Consensus 26 IiGvDEaGRG~~~GPlvva-av~~~~~~~----~~~i~DSK~Ls~~~R~~l~~~i~~------~~~~~i~~~~~~eID~- 93 (209) |+|||||||||+.|||||| +.+.++..+ ..||+|||+||+.+|+.||..|.+ .+.|.+..++|+|||+ T Consensus 1 v~GiDEAGRGpV~GPlVvag~~~~e~~~~~~L~~lGVkDSK~Lt~~~R~~L~~~i~~DneeL~~~~~~~~~i~p~eId~G 80 (235) T TIGR00729 1 VAGIDEAGRGPVIGPLVVAGVFAIEEKREEELRKLGVKDSKKLTPGRRRELFRKIRQDNEELKLGRVEVLKITPEEIDRG 80 (235) T ss_pred CCEEECCCCCCCCCCCEEEEEEEECHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHCCCCCEEEEEEEEEEEEECCCCCCC T ss_conf 91110058887206523687765313566454406844630169668999999860886527886689998630014662 Q ss_pred ----HC-HH----HHHHHHHHHHCCCCCCCC------CCCCCCCCCCCC------------------CCCEEEEEECCCC Q ss_conf ----04-79----998865432100257532------110126532246------------------6212268711478 Q gi|254781076|r 94 ----HN-IH----KATLDAIYHAVENLQVIP------RSALIDGRSIPE------------------DLPCQAFAVIKGD 140 (209) Q Consensus 94 ----~n-i~----~A~~~a~~~ai~~l~~~~------~~ilIDg~~~~~------------------~~~~~~~~i~KgD 140 (209) .+ ++ .+..+....++..|..+| +.++||.....+ ..+.++...|||| T Consensus 81 mskf~~~~~~~~n~~e~~~~~~~~~~l~~kpnir~~~~~vyvD~~~~~~~rfedsfk~~~~~~~~~~~~~~~v~aEhKAD 160 (235) T TIGR00729 81 MSKFERTRNINLNENEIEKFSAAVIILIVKPNIRVKLSEVYVDSVDVKPKRFEDSFKLKREIKLKERGEEIKVIAEHKAD 160 (235) T ss_pred HHHHHHHHHHHCCHHHHHHHHHHHHHHHHCCCCCCCCCEEEEECCCCCCCHHHHHHHHHHHHHHHHCCCCCEEEEECCCC T ss_conf 12014227662058899999999864420466321412788833888840112457679999987517981899974778 Q ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHH---CCCCCCCCCCCCCC-HHHHHHHHH----C-C-CCCCCCCCHHHHHHHC Q ss_conf 652002366665477589999999887---77988102899999-899999998----2-8-5830107848886403 Q gi|254781076|r 141 SISLSIAAASIIAKVTRDRLMRIAHKK---YPDYGFDSHVGYPT-AKHQQVIKE----K-G-PSCIHRLTFRPLRNLS 208 (209) Q Consensus 141 ~~~~~VaaASIiAKv~RD~~m~~l~~~---~p~Ygf~~nkGYgT-~~H~~ai~~----~-G-~~~~HR~Sf~~vk~l~ 208 (209) ++|+.||||||||||+||+.++.|.++ |+..| +|||| |.|++||++ | | ++++.|.||+||++|. T Consensus 161 ~kY~~VSAASIiAKV~RD~~ie~lk~~~rkyG~~G----SGYPSDP~T~ewL~~~~~~~mG~~P~~vR~~W~Tv~~l~ 234 (235) T TIGR00729 161 SKYPVVSAASIIAKVERDREIESLKRKPRKYGDIG----SGYPSDPRTREWLEEYFKSLMGELPDIVRRSWKTVRKLL 234 (235) T ss_pred CCCCCEEEEEEEEHHHHHHHHHHHHHCCCCCCCCC----CCCCCCHHHHHHHHHHHHHHCCCCCCCEECCCHHHHHCC T ss_conf 88862232334202245688998720232146557----878976356899999999862765300006506755115 No 12 >KOG2299 consensus Probab=100.00 E-value=2.2e-36 Score=247.81 Aligned_cols=182 Identities=32% Similarity=0.448 Sum_probs=140.1 Q ss_pred CCCCEEEEEECCCCCCCCCCEEEEEEEECCCCC----CCCCCCCCCCCHHHHHHHHHHHCCC------CEEEEECCCHHH Q ss_conf 799489998427877752225599999870108----2331152028999998755211012------307885156799 Q gi|254781076|r 21 KNMWPVAGIDEVGRGALAGPVVVAAIILDPNNI----PFGINDSKKISHKKREELYEKITSS------AIISISSASHQY 90 (209) Q Consensus 21 ~~~~~IiGvDEaGRG~~~GPlvvaav~~~~~~~----~~~i~DSK~Ls~~~R~~l~~~i~~~------~~~~i~~~~~~e 90 (209) +....+.|||||||||+.||||.|+++.|.+.. ..|+.|||+|++.+|++||+.|++. .-|++..++|.+ T Consensus 25 ~~~PcvlGIDEAGRGPVLGPMVYa~~ycP~~~~~~l~~lgfaDSK~L~e~kRe~lf~~i~~d~~~~~~vgwA~~~isP~~ 104 (301) T KOG2299 25 KSEPCVLGIDEAGRGPVLGPMVYAAAYCPLDYLEDLENLGFADSKTLTEAKREELFNKIKEDEELTSNVGWATDCISPRE 104 (301) T ss_pred CCCCEEEECCCCCCCCCCCCEEEEEEECCCHHHHHHHHCCCCCHHHCCHHHHHHHHHHHHHHHHHHHCEEEEEEECCHHH T ss_conf 48864864343577875442045788435045435654586631110678999999998630133210035765268899 Q ss_pred HH-------HHCHHHHHHHHH----HHHCCCCCCCCCCCCCCCCCCCC--------CCC-EEEEEECCCCCCCHHHHHHH Q ss_conf 85-------204799988654----32100257532110126532246--------621-22687114786520023666 Q gi|254781076|r 91 ID-------KHNIHKATLDAI----YHAVENLQVIPRSALIDGRSIPE--------DLP-CQAFAVIKGDSISLSIAAAS 150 (209) Q Consensus 91 ID-------~~ni~~A~~~a~----~~ai~~l~~~~~~ilIDg~~~~~--------~~~-~~~~~i~KgD~~~~~VaaAS 150 (209) |- ++|+++....+. +++++. ......++||....+. .+| +++..-.|||+.|+.|+||| T Consensus 105 IS~~Ml~r~kynLNevshdsam~LI~~v~~~-gvnvteiyVDTVGpp~~Yq~kLek~FP~~k~tV~kKADSlfpiVS~AS 183 (301) T KOG2299 105 ISASMLRRNKYNLNEVSHDSAMGLIDEVLDQ-GVNVTEIYVDTVGPPAKYQEKLEKRFPGIKFTVTKKADSLFPIVSAAS 183 (301) T ss_pred HHHHHHHHHCCCCHHHHHHHHHHHHHHHHHH-CCCEEEEEEECCCCHHHHHHHHHHHCCCEEEEEEECCCCCCCCHHHHH T ss_conf 8899888714780134358899999999984-875279997057985999999996589708998503665243201545 Q ss_pred HHHHHHHHHHHHHHHH------HCCCCCCCCCCCCCC-HHHHHHHHH-----CCCCCCCCCCHHHHHHH Q ss_conf 6547758999999988------777988102899999-899999998-----28583010784888640 Q gi|254781076|r 151 IIAKVTRDRLMRIAHK------KYPDYGFDSHVGYPT-AKHQQVIKE-----KGPSCIHRLTFRPLRNL 207 (209) Q Consensus 151 IiAKv~RD~~m~~l~~------~~p~Ygf~~nkGYgT-~~H~~ai~~-----~G~~~~HR~Sf~~vk~l 207 (209) |+|||+||+.+++..- .-..|| +|||+ |++++||++ ||.+.+.|.||+|+++| T Consensus 184 I~AKVtRD~alk~w~~~E~~~~~d~~~G----SGYP~DP~T~~wLk~~v~~VFGfp~lVRfSW~Ta~t~ 248 (301) T KOG2299 184 IVAKVTRDRALKEWQFEEKLSDPDEDLG----SGYPSDPETKAWLKENVDSVFGFPSLVRFSWKTAKTL 248 (301) T ss_pred HHHHHHHCCCCCEEEEEEECCCCCCCCC----CCCCCCHHHHHHHHHCCCCCCCCCCCEEEEHHHHHHH T ss_conf 6665530110100454440346775556----8899980678999964640026850206438889998 No 13 >PRK00996 ribonuclease HIII; Provisional Probab=100.00 E-value=3.2e-35 Score=240.62 Aligned_cols=182 Identities=28% Similarity=0.382 Sum_probs=142.0 Q ss_pred CCCEEEEEECCCCCCCCCCEEEEEEEECCCCC----CCCCCCCCCCCHHHHHHHHHHHCCCCEEEEECCCHHHHHHH--- Q ss_conf 99489998427877752225599999870108----23311520289999987552110123078851567998520--- Q gi|254781076|r 22 NMWPVAGIDEVGRGALAGPVVVAAIILDPNNI----PFGINDSKKISHKKREELYEKITSSAIISISSASHQYIDKH--- 94 (209) Q Consensus 22 ~~~~IiGvDEaGRG~~~GPlvvaav~~~~~~~----~~~i~DSK~Ls~~~R~~l~~~i~~~~~~~i~~~~~~eID~~--- 94 (209) ..+++||+||||+||+|||||||||+++++.+ ..||+|||+||+++|.+|++.|++.+.|++..++|+++|++ T Consensus 86 ~~~~~iGsDE~G~Gd~FGPlvVaav~v~~~~~~~L~~lGVkDSK~Lsd~kI~~la~~I~~~~~~~~~~l~p~kYNel~~k 165 (303) T PRK00996 86 DLRPHIGSDEVGKGDYFGPLTVAAVYVDKEQIPFLKKLGVDDSKKLTDTKIRQIAPQLREKIPHSVLLLSPEKYNELQAK 165 (303) T ss_pred CCCCCEEECCCCCCCCCCCCEEEEEEECHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHCCEEEEEECHHHHHHHHHH T ss_conf 56762003587788876771899999779999999975996601189999999999999748779999886878999984 Q ss_pred CHHHHHHHHHH--HHCCCC---CCCCCCCCCCCCCCCC-----------CCCEEEEEECCCCCCCHHHHHHHHHHHHHHH Q ss_conf 47999886543--210025---7532110126532246-----------6212268711478652002366665477589 Q gi|254781076|r 95 NIHKATLDAIY--HAVENL---QVIPRSALIDGRSIPE-----------DLPCQAFAVIKGDSISLSIAAASIIAKVTRD 158 (209) Q Consensus 95 ni~~A~~~a~~--~ai~~l---~~~~~~ilIDg~~~~~-----------~~~~~~~~i~KgD~~~~~VaaASIiAKv~RD 158 (209) +++...++||. +||.+| ...|+.++||++..+. ....+....+|||+++++|||||||| |+ T Consensus 166 ~~Nln~ika~lH~~aI~~ll~k~~~~~~ilIDqF~~~~~~~~yl~~~~~~~~~~i~~~~Kae~~~~aVAAASIiA---R~ 242 (303) T PRK00996 166 GYNQNKLKAWLHNQAIDNLLQKPSQPEAIVIDQFASPEVYLKYLAKEKNKFRDPVTFETKAESKHLAVAAASIIA---RY 242 (303) T ss_pred HCCHHHHHHHHHHHHHHHHHHCCCCCCEEEECCCCCHHHHHHHHHHHCCCCCCCEEEEECCCCCCHHHHHHHHHH---HH T ss_conf 348999999999999999983578998799716888078999987540478764488731554007899999999---99 Q ss_pred HHHHHHHHHCCCCCCCCCCCCCCHHH---HHHHHHCC------CCCCCCCCHHHHHH Q ss_conf 99999988777988102899999899---99999828------58301078488864 Q gi|254781076|r 159 RLMRIAHKKYPDYGFDSHVGYPTAKH---QQVIKEKG------PSCIHRLTFRPLRN 206 (209) Q Consensus 159 ~~m~~l~~~~p~Ygf~~nkGYgT~~H---~~ai~~~G------~~~~HR~Sf~~vk~ 206 (209) .++..++++-.+||+.--+|-|++.- .+.++++| ++..|=++.+-++. T Consensus 243 ~Fl~~m~~ls~~~g~~lPkGAg~~v~~~a~~i~~~~G~~~L~~~aKlHFknt~ka~~ 299 (303) T PRK00996 243 AFLENMDKLSKEAGMTLPKGAGAKVDKVAAQIIKKYGKEALEKIAKLHFANTEKAQK 299 (303) T ss_pred HHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHH T ss_conf 999999999998199787888788999999999985999999999886113999999 No 14 >COG1039 RnhC Ribonuclease HIII [DNA replication, recombination, and repair] Probab=99.96 E-value=1.3e-29 Score=205.70 Aligned_cols=180 Identities=27% Similarity=0.382 Sum_probs=138.7 Q ss_pred CCEEEEEECCCCCCCCCCEEEEEEEECCCCCC----CCCCCCCCCCHHHHHHHHHHHCCCCEEEEECCCHHHHHHH---C Q ss_conf 94899984278777522255999998701082----3311520289999987552110123078851567998520---4 Q gi|254781076|r 23 MWPVAGIDEVGRGALAGPVVVAAIILDPNNIP----FGINDSKKISHKKREELYEKITSSAIISISSASHQYIDKH---N 95 (209) Q Consensus 23 ~~~IiGvDEaGRG~~~GPlvvaav~~~~~~~~----~~i~DSK~Ls~~~R~~l~~~i~~~~~~~i~~~~~~eID~~---n 95 (209) ..+++|+||+|.|++||||+||||+++++.++ .||+|||+|++.++.+|++.|++.+.+.+..++|++.+++ + T Consensus 82 ~~~~IGsDEvG~GDyFGpl~v~av~v~~e~~~~L~~lgV~DSKkL~D~kI~~la~~ik~~i~~~~l~l~p~kYNel~~k~ 161 (297) T COG1039 82 AKNLIGSDEVGKGDYFGPLVVCAVYVSKENLPKLKELGVKDSKKLSDKKIQQLAPIIKPLIPHSVLTLDPKKYNELYKKF 161 (297) T ss_pred CCCCCCCCCCCCCCCCCCCEEEEEECCHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHCCCEEEEECHHHHHHHHHHH T ss_conf 46314777878887557716899973899979998639853032887889999999997568249997868889999854 Q ss_pred HHHHHHHHHH--HHCC----CCCCCCCCCCCCCCCCCC-----------CCCEEEEEECCCCCCCHHHHHHHHHHHHHHH Q ss_conf 7999886543--2100----257532110126532246-----------6212268711478652002366665477589 Q gi|254781076|r 96 IHKATLDAIY--HAVE----NLQVIPRSALIDGRSIPE-----------DLPCQAFAVIKGDSISLSIAAASIIAKVTRD 158 (209) Q Consensus 96 i~~A~~~a~~--~ai~----~l~~~~~~ilIDg~~~~~-----------~~~~~~~~i~KgD~~~~~VaaASIiAKv~RD 158 (209) .+...++++. +|+. .....++.++||.+...+ ...-+.....||++++.+||+|||+| || T Consensus 162 ~N~n~mkt~lH~~ai~~ll~~~~~~~~~ivIDqFa~~~~~~~yl~k~~~~~~~p~~f~~kaEs~~laVAvASIiA---R~ 238 (297) T COG1039 162 NNANSMKTFLHNQAIQNLLPQKGAQPEFIVIDQFASSENYKNYLQKETNKFSEPVLFLTKAESKSLAVAVASIIA---RY 238 (297) T ss_pred HHHHHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCCHHHHHHHHHHHCCCCCCCEEEEECCCCCCHHHHHHHHHH---HH T ss_conf 239999999999999999875368973887320136568999988602578996024423354102688899999---99 Q ss_pred HHHHHHHHHCCCCCCCCCCCCCCH---HHHHHHHHCC------CCCCCCCCHHHHH Q ss_conf 999999887779881028999998---9999999828------5830107848886 Q gi|254781076|r 159 RLMRIAHKKYPDYGFDSHVGYPTA---KHQQVIKEKG------PSCIHRLTFRPLR 205 (209) Q Consensus 159 ~~m~~l~~~~p~Ygf~~nkGYgT~---~H~~ai~~~G------~~~~HR~Sf~~vk 205 (209) .++..+++...+||..--||-|.. .-.+-++++| .+..|-++|.-+. T Consensus 239 ~Fl~~~~~l~~~~gv~LPkGAg~~V~~~a~~i~~k~g~~~L~~~~k~hf~n~~k~~ 294 (297) T COG1039 239 AFLQSLKQLSRQYGVQLPKGAGPAVDQAAAEIIQKRGFSKLEQVAKLHFKNFQKAL 294 (297) T ss_pred HHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 99999999999959737788746489999999987427999999999998799887 No 15 >TIGR00716 rnhC ribonuclease HIII; InterPro: IPR004641 Ribonuclease HIII 3.1.26 from EC cleaves RNA from DNA-RNA hybrids. It catalyses endonucleolytic cleavage to 5'-phospho-monoesters. 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 homologue in the Mycoplasmas resembles rnhC. Archaeal forms resemble HII more closely than HIII. This family describes bacterial RNase HIII .; GO: 0004523 ribonuclease H activity, 0016070 RNA metabolic process, 0005737 cytoplasm. Probab=99.93 E-value=5.7e-26 Score=182.89 Aligned_cols=170 Identities=24% Similarity=0.352 Sum_probs=133.2 Q ss_pred EEEEEECCCCCCCCCCEEEEEEEECC-CCCC----CCCCCCCCCCHHHHHHHHHHHCCCCEEEEECCCHHHHHHH---CH Q ss_conf 89998427877752225599999870-1082----3311520289999987552110123078851567998520---47 Q gi|254781076|r 25 PVAGIDEVGRGALAGPVVVAAIILDP-NNIP----FGINDSKKISHKKREELYEKITSSAIISISSASHQYIDKH---NI 96 (209) Q Consensus 25 ~IiGvDEaGRG~~~GPlvvaav~~~~-~~~~----~~i~DSK~Ls~~~R~~l~~~i~~~~~~~i~~~~~~eID~~---ni 96 (209) .+||+||+|+|++||||++|||+++. ..++ .+++|||.|+++|+++|+..|+..+.+.+..+-||+.+.+ +. T Consensus 92 S~IG~DEsGkGD~FGpl~~~cvy~~~P~~~~~~~~l~~~DsK~l~D~~i~~la~nl~~l~~~~~~~lkpEkYN~ly~kf~ 171 (298) T TIGR00716 92 SVIGVDESGKGDYFGPLVVVCVYVDEPEALEKLKELSVKDSKRLKDKKILELARNLKKLVKAKVLVLKPEKYNKLYEKFR 171 (298) T ss_pred CEEECCCCCCCCCCCCEEEEEEECCCHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHCEEEEEECCCCHHHHHHHCC T ss_conf 23302456887634141688775187568899884688655558867899999987764122455753740378886002 Q ss_pred HHHHHHHHH--HHCCCC-----CCCCCCCCCCCCCCCCCC----------CEEEEEECCCCCCCHHHHHHHHHHHHHHHH Q ss_conf 999886543--210025-----753211012653224662----------122687114786520023666654775899 Q gi|254781076|r 97 HKATLDAIY--HAVENL-----QVIPRSALIDGRSIPEDL----------PCQAFAVIKGDSISLSIAAASIIAKVTRDR 159 (209) Q Consensus 97 ~~A~~~a~~--~ai~~l-----~~~~~~ilIDg~~~~~~~----------~~~~~~i~KgD~~~~~VaaASIiAKv~RD~ 159 (209) +...++|+. .+|++| +..|+.+++|.+..+..+ +......++|+...++||||||+| |.. T Consensus 172 nlnkm~a~~h~~~I~~l~~~~~Gv~Pe~~~~Dqfa~s~~~l~~~~~~~~~~~~~if~t~AE~i~laVAaASI~A---Ry~ 248 (298) T TIGR00716 172 NLNKMLALLHKLLIERLLKKEAGVKPEAVVVDQFAESERYLLQLKRKDIVDEEVIFETKAERIDLAVAAASILA---RYK 248 (298) T ss_pred CHHHHHHHHHHHHHHHHHHHCCCCCCCEEEEEEECCCHHHHHHHHCCCCCCEEEEEECCCCCCCHHHHHHHHHH---HHH T ss_conf 65579999999999975111048985547872004733788864214200000022101253305777888999---999 Q ss_pred HHHHHHHHCCCCCCCCCCCCCCHHHHHH---HHHCCCCCCC Q ss_conf 9999988777988102899999899999---9982858301 Q gi|254781076|r 160 LMRIAHKKYPDYGFDSHVGYPTAKHQQV---IKEKGPSCIH 197 (209) Q Consensus 160 ~m~~l~~~~p~Ygf~~nkGYgT~~H~~a---i~~~G~~~~H 197 (209) |+..+++..-+||..--||-+.+.-..| |.+-|.+.+- T Consensus 249 FL~s~~~ler~~gi~lpKGas~~Vke~Ak~l~~~Kg~~~Le 289 (298) T TIGR00716 249 FLSSLKKLERELGIKLPKGASKKVKELAKELLLKKGAVVLE 289 (298) T ss_pred HHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHCCHHHHH T ss_conf 99899998898486714899854899999997605844545 No 16 >cd06559 Endonuclease_V Endonuclease_V, a DNA repair enzyme that initiates repair of nitrosative deaminated purine bases. Endonuclease_V (EndoV) is an enzyme that can initiate repair of all possible deaminated DNA bases. EndoV cleaves the DNA strand containing lesions at the second phosphodiester bond 3' to the lesion using Mg2+ as a cofactor. EndoV homologs are conserved throughout all domains of life from bacteria to humans. EndoV is encoded by the nfi gene and nfi null mutant mice have a phenotype prone to cancer. The ability of endonuclease V to recognize mismatches and abnormal replicative DNA structures suggests that the enzyme plays an important role in DNA metabolism. The details of downstream processing for the EndoV pathway remain unknown. Probab=64.94 E-value=3 Score=22.44 Aligned_cols=26 Identities=31% Similarity=0.551 Sum_probs=20.1 Q ss_pred HHHHHHCCCCCCCCCCCCCCCCCCCC Q ss_conf 65432100257532110126532246 Q gi|254781076|r 102 DAIYHAVENLQVIPRSALIDGRSIPE 127 (209) Q Consensus 102 ~a~~~ai~~l~~~~~~ilIDg~~~~~ 127 (209) -.|..|+++|...||.++|||+.... T Consensus 81 p~~l~a~~~l~~~PdlllvDG~Gi~H 106 (208) T cd06559 81 PPLLEALEKLKTKPDLLLVDGHGIAH 106 (208) T ss_pred HHHHHHHHHCCCCCCEEEECCCCCCC T ss_conf 89999998557799999986887526 No 17 >pfam04493 Endonuclease_5 Endonuclease V. Endonuclease V is specific for single-stranded DNA or for duplex DNA that contains uracil or that is damaged by a variety of agents. Probab=62.77 E-value=3.5 Score=22.04 Aligned_cols=80 Identities=21% Similarity=0.194 Sum_probs=41.2 Q ss_pred CCEEEEEECCC-CCCCCCCEEEEEEEECCCCCCCCCCCCCCCCHHHHHHHHHHHCCCCEEEEECCCHHHHHHHCHHHHHH Q ss_conf 94899984278-77752225599999870108233115202899999875521101230788515679985204799988 Q gi|254781076|r 23 MWPVAGIDEVG-RGALAGPVVVAAIILDPNNIPFGINDSKKISHKKREELYEKITSSAIISISSASHQYIDKHNIHKATL 101 (209) Q Consensus 23 ~~~IiGvDEaG-RG~~~GPlvvaav~~~~~~~~~~i~DSK~Ls~~~R~~l~~~i~~~~~~~i~~~~~~eID~~ni~~A~~ 101 (209) .+.|+|+|=+= +|.. .++|+|+++..++.. -+. .+....-...|-=|..+=.| . T Consensus 21 l~~VaGvDvSf~~~~~---~~aa~Vvl~~p~l~~--v~~----------~~~~~~~~fPYIPG~LaFRE----------~ 75 (205) T pfam04493 21 LRYVAGVDVSYDKETR---AVAALVVLDFPSLEV--IEK----------KVIRGEISFPYIPGFLAFRE----------L 75 (205) T ss_pred EEEEEEEEEEEECCCE---EEEEEEEEECCCCCE--EEE----------EEEEEEECCCCCCCHHHHHH----------H T ss_conf 5699999973757984---999999998899839--999----------99997623665540343310----------1 Q ss_pred HHHHHHCCCCCCCCCCCCCCCCCCCC Q ss_conf 65432100257532110126532246 Q gi|254781076|r 102 DAIYHAVENLQVIPRSALIDGRSIPE 127 (209) Q Consensus 102 ~a~~~ai~~l~~~~~~ilIDg~~~~~ 127 (209) -+|.+++++|...||.++|||+.+.. T Consensus 76 p~~l~a~~~L~~~PDvllvDG~Gi~H 101 (205) T pfam04493 76 PLLLKALKKLYDEPDVLLVDGNGIAH 101 (205) T ss_pred HHHHHHHHHCCCCCCEEEECCCCCCC T ss_conf 89999999657799999987876437 No 18 >PRK11617 endonuclease V; Provisional Probab=62.49 E-value=3.3 Score=22.20 Aligned_cols=25 Identities=32% Similarity=0.489 Sum_probs=19.6 Q ss_pred HHHHHCCCCCCCCCCCCCCCCCCCC Q ss_conf 5432100257532110126532246 Q gi|254781076|r 103 AIYHAVENLQVIPRSALIDGRSIPE 127 (209) Q Consensus 103 a~~~ai~~l~~~~~~ilIDg~~~~~ 127 (209) ++..++++|+..||.++|||+.+.. T Consensus 85 ~ll~a~~~L~~~PDvllvDG~Gi~H 109 (223) T PRK11617 85 ALLAAWEQLSQKPDLVFVDGHGISH 109 (223) T ss_pred HHHHHHHHCCCCCCEEEECCCCCCC T ss_conf 9999999627799999987975437 No 19 >TIGR00538 hemN oxygen-independent coproporphyrinogen III oxidase; InterPro: IPR004558 This family represents HemN, the oxygen-independent coproporphyrinogen III oxidase that replaces HemF function under anaerobic conditions. HemN catalyses the anaerobic transformation of coproporhyrinogen-III into protoporphyrinogen-IX during porphyrin biosynthesis. Several species, including Escherichia coli, Helicobacter pylori, and Aquifex aeolicus, have both a member of this family and a member of another, closely related family for which there is no evidence of coproporphyrinogen III oxidase activity, IPR004559 from INTERPRO. Members of this family have a perfectly conserved motif PYRT[SC]YP in a region N-terminal to the region of homology with the related uncharacterised protein.; GO: 0004109 coproporphyrinogen oxidase activity, 0006779 porphyrin biosynthetic process, 0005737 cytoplasm. Probab=55.23 E-value=15 Score=18.12 Aligned_cols=31 Identities=26% Similarity=0.340 Sum_probs=21.6 Q ss_pred CCHHHHHHHHHHHCCCCE-EE-----EECCCHHHHHH Q ss_conf 899999875521101230-78-----85156799852 Q gi|254781076|r 63 ISHKKREELYEKITSSAI-IS-----ISSASHQYIDK 93 (209) Q Consensus 63 Ls~~~R~~l~~~i~~~~~-~~-----i~~~~~~eID~ 93 (209) ||+.|.+.|.+.|++... ++ -..++|.++|+ T Consensus 118 L~~~Q~~~l~~~i~~~F~nf~~daEiSiEidPR~~~~ 154 (462) T TIGR00538 118 LSPEQIEELMKEIREAFPNFSEDAEISIEIDPRYLTK 154 (462) T ss_pred CCHHHHHHHHHHHHHHHHHHCCCCEEEEEECCCCCCH T ss_conf 7889999999999987320115844776523741378 No 20 >cd01674 Homoaconitase_Swivel Homoaconitase swivel domain. This family includes homoaconitase and other uncharacterized proteins of the Aconitase family. Homoaconitase is part of an unusual lysine biosynthesis pathway found only in filamentous fungi, in which lysine is synthesized via the alpha-aminoadipate pathway. In this pathway, homoaconitase catalyzes the conversion of cis-homoaconitic acid into homoisocitric acid. The reaction mechanism is believed to be similar to that of other aconitases. This is the swivel domain, which is believed to undergo swivelling conformational change in the enzyme mechanism. Probab=52.21 E-value=15 Score=18.01 Aligned_cols=30 Identities=13% Similarity=0.196 Sum_probs=23.2 Q ss_pred CCCCCCC-HHH-HHHHHHCCCCCCCCCCHHHH Q ss_conf 2899999-899-99999828583010784888 Q gi|254781076|r 175 SHVGYPT-AKH-QQVIKEKGPSCIHRLTFRPL 204 (209) Q Consensus 175 ~nkGYgT-~~H-~~ai~~~G~~~~HR~Sf~~v 204 (209) .|.|-|| .+| ..+|+.+|+..+.-+||.-| T Consensus 53 ~NFGcGSSREhA~~aL~~~Gi~aVIA~SFa~I 84 (129) T cd01674 53 FNFGTGSSREQAATALLAKGIPLVVSGSFGNI 84 (129) T ss_pred CCCCCCCCHHHHHHHHHHCCCCEEEECHHHHH T ss_conf 86576734889999999849979998529999 No 21 >pfam06135 DUF965 Bacterial protein of unknown function (DUF965). This family consists of several hypothetical bacterial proteins. The function of the family is unknown. Probab=48.74 E-value=16 Score=17.93 Aligned_cols=32 Identities=28% Similarity=0.513 Sum_probs=22.7 Q ss_pred CCCCCCCHH--HHHHHHHHHHHHHHHHHHHHHHC Q ss_conf 147865200--23666654775899999998877 Q gi|254781076|r 137 IKGDSISLS--IAAASIIAKVTRDRLMRIAHKKY 168 (209) Q Consensus 137 ~KgD~~~~~--VaaASIiAKv~RD~~m~~l~~~~ 168 (209) .-||-.|.+ --|-|++-|+.||.++++|=+.| T Consensus 44 lSgDPtYItsh~nAR~lIrkiERDEilEelv~~Y 77 (79) T pfam06135 44 LSGDPAYITRHNDARNLIRKIERDEILEELVKSY 77 (79) T ss_pred CCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHH T ss_conf 2489775277525999999985889999999997 No 22 >PRK05473 hypothetical protein; Provisional Probab=46.42 E-value=17 Score=17.75 Aligned_cols=31 Identities=29% Similarity=0.474 Sum_probs=22.4 Q ss_pred CCCCCCHH--HHHHHHHHHHHHHHHHHHHHHHC Q ss_conf 47865200--23666654775899999998877 Q gi|254781076|r 138 KGDSISLS--IAAASIIAKVTRDRLMRIAHKKY 168 (209) Q Consensus 138 KgD~~~~~--VaaASIiAKv~RD~~m~~l~~~~ 168 (209) -||-.|.+ --|-|++-|+.||.++++|=+.| T Consensus 48 SGDPaYItsh~~AR~lIrk~eRDEilEELv~~Y 80 (86) T PRK05473 48 SGDPAYIPRHNDARNLIRKLERDEILEELVKSY 80 (86) T ss_pred CCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHH T ss_conf 489763167402999999986889999999999 No 23 >COG1515 Nfi Deoxyinosine 3'endonuclease (endonuclease V) [DNA replication, recombination, and repair] Probab=42.16 E-value=11 Score=19.02 Aligned_cols=26 Identities=38% Similarity=0.607 Sum_probs=21.2 Q ss_pred HHHHHHHCCCCCCCCCCCCCCCCCCC Q ss_conf 86543210025753211012653224 Q gi|254781076|r 101 LDAIYHAVENLQVIPRSALIDGRSIP 126 (209) Q Consensus 101 ~~a~~~ai~~l~~~~~~ilIDg~~~~ 126 (209) .-+|.++++.|..+++.++|||+.+. T Consensus 82 ~p~~l~a~~~l~~~~d~ilVDG~Gia 107 (212) T COG1515 82 LPLLLKALEKLSVKPDLLLVDGHGIA 107 (212) T ss_pred HHHHHHHHHHCCCCCCEEEECCCCEE T ss_conf 28899999864888889998686514 No 24 >pfam01314 AFOR_C Aldehyde ferredoxin oxidoreductase, domains 2 & 3. Aldehyde ferredoxin oxidoreductase (AOR) catalyses the reversible oxidation of aldehydes to their corresponding carboxylic acids with their accompanying reduction of the redox protein ferredoxin. This family is composed of two structural domains that bind the tungsten cofactor via DXXGL(C/D) motifs. In addition to maintaining specific binding interactions with the cofactor, another role for domains 2 and 3 may be to regulate substrate access to AOR. Probab=40.91 E-value=20 Score=17.25 Aligned_cols=32 Identities=25% Similarity=0.430 Sum_probs=25.7 Q ss_pred HHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHH Q ss_conf 758999999988777988102899999899999 Q gi|254781076|r 155 VTRDRLMRIAHKKYPDYGFDSHVGYPTAKHQQV 187 (209) Q Consensus 155 v~RD~~m~~l~~~~p~Ygf~~nkGYgT~~H~~a 187 (209) +.|+.+-+.+...|...||+. .|-||+++.+- T Consensus 348 ~~~e~~~~~l~~YY~~rGWd~-~G~Pt~e~L~~ 379 (382) T pfam01314 348 LDREDLEEMLDEYYRLRGWDE-EGVPTPETLKE 379 (382) T ss_pred CCHHHHHHHHHHHHHHCCCCC-CCCCCHHHHHH T ss_conf 699999999999999829898-99889899987 No 25 >pfam08893 DUF1839 Domain of unknown function (DUF1839). This family of proteins are functionally uncharacterized. Probab=40.05 E-value=20 Score=17.28 Aligned_cols=27 Identities=26% Similarity=0.492 Sum_probs=24.4 Q ss_pred HHHHHHHHHCCCCCCCCCCHHHHHHHC Q ss_conf 899999998285830107848886403 Q gi|254781076|r 182 AKHQQVIKEKGPSCIHRLTFRPLRNLS 208 (209) Q Consensus 182 ~~H~~ai~~~G~~~~HR~Sf~~vk~l~ 208 (209) +.|.++|...|..-+|-+||.+.++|+ T Consensus 219 ~~~l~~l~~r~~~~FH~YsFn~lRQlG 245 (320) T pfam08893 219 PAHLETLLARGEPFFHLYAFNVLRQLG 245 (320) T ss_pred HHHHHHHHHCCCCCCHHHHHHHHHHCC T ss_conf 999999985895400076540387633 No 26 >PRK01641 leuD isopropylmalate isomerase small subunit; Provisional Probab=39.21 E-value=32 Score=16.02 Aligned_cols=12 Identities=17% Similarity=0.144 Sum_probs=5.8 Q ss_pred HHHHHHHHHHHH Q ss_conf 758999999988 Q gi|254781076|r 155 VTRDRLMRIAHK 166 (209) Q Consensus 155 v~RD~~m~~l~~ 166 (209) ..|.++|.-++. T Consensus 164 ~~k~~LL~GlD~ 175 (201) T PRK01641 164 FRRHCLLNGLDD 175 (201) T ss_pred HHHHHHHHCCCH T ss_conf 999999919688 No 27 >KOG3407 consensus Probab=38.10 E-value=16 Score=17.82 Aligned_cols=17 Identities=35% Similarity=0.630 Sum_probs=6.7 Q ss_pred CCCCCCCCCCCCCCCCC Q ss_conf 32110126532246621 Q gi|254781076|r 114 IPRSALIDGRSIPEDLP 130 (209) Q Consensus 114 ~~~~ilIDg~~~~~~~~ 130 (209) .|+.-..||+..++.++ T Consensus 53 ~Pe~e~~~g~~~p~~~~ 69 (151) T KOG3407 53 KPEVEPKDGFVVPPELP 69 (151) T ss_pred CCCCCCCCCCCCCCCCC T ss_conf 97533334734797643 No 28 >PRK09849 putative oxidoreductase; Provisional Probab=37.35 E-value=24 Score=16.78 Aligned_cols=32 Identities=28% Similarity=0.486 Sum_probs=19.9 Q ss_pred HHHHHHHHHHHHHHCCCCCCCCCCCCCCHHHH Q ss_conf 77589999999887779881028999998999 Q gi|254781076|r 154 KVTRDRLMRIAHKKYPDYGFDSHVGYPTAKHQ 185 (209) Q Consensus 154 Kv~RD~~m~~l~~~~p~Ygf~~nkGYgT~~H~ 185 (209) |..|+.+-+.|.+.|..-||+...|-||+++. T Consensus 651 ~~d~e~~e~ml~~YY~~rGWD~e~G~Pt~etL 682 (702) T PRK09849 651 KMDRDDMQASLTMFYKEMGWDPQTGCPTRATL 682 (702) T ss_pred CCCHHHHHHHHHHHHHHHCCCCCCCCCCHHHH T ss_conf 68999999999999997099855884289999 No 29 >cd01218 PH_phafin2 Phafin2 Pleckstrin Homology (PH) domain. Phafin contains a PH domain and a FYVE domain. PH domains share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains also have diverse functions. They are often involved in targeting proteins to the plasma membrane, but few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinsases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. Probab=34.94 E-value=28 Score=16.43 Aligned_cols=31 Identities=23% Similarity=0.121 Sum_probs=24.7 Q ss_pred EEECCCCCCCHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 8711478652002366665477589999999887 Q gi|254781076|r 134 FAVIKGDSISLSIAAASIIAKVTRDRLMRIAHKK 167 (209) Q Consensus 134 ~~i~KgD~~~~~VaaASIiAKv~RD~~m~~l~~~ 167 (209) ...+.+-.++.+|+|+|--. ++.||..|.+- T Consensus 67 ~f~I~s~~KSF~v~A~s~~E---k~~Wm~~i~~a 97 (104) T cd01218 67 GWIIKTPTKSFAVYAATETE---KREWMLHINKC 97 (104) T ss_pred EEEEECCCCEEEEEECCHHH---HHHHHHHHHHH T ss_conf 69997388189999699999---99999999999 No 30 >COG0066 LeuD 3-isopropylmalate dehydratase small subunit [Amino acid transport and metabolism] Probab=34.42 E-value=39 Score=15.51 Aligned_cols=11 Identities=18% Similarity=0.039 Sum_probs=3.6 Q ss_pred HHHHHHHHCCC Q ss_conf 98755211012 Q gi|254781076|r 68 REELYEKITSS 78 (209) Q Consensus 68 R~~l~~~i~~~ 78 (209) ||...-.|+.. T Consensus 78 REHApwALk~~ 88 (191) T COG0066 78 REHAPWALKDY 88 (191) T ss_pred HHHHHHHHHHC T ss_conf 77899999975 No 31 >pfam07286 DUF1445 Protein of unknown function (DUF1445). This family represents a conserved region approximately 150 residues long within a number of hypothetical bacterial and eukaryotic proteins of unknown function. Probab=34.13 E-value=28 Score=16.34 Aligned_cols=44 Identities=18% Similarity=0.286 Sum_probs=30.9 Q ss_pred CHHHHHHHHHCCCCE------------EEEEECCCCCCCCCCEEEEEEEECCCCCC Q ss_conf 888999999779948------------99984278777522255999998701082 Q gi|254781076|r 11 HFELEAMVREKNMWP------------VAGIDEVGRGALAGPVVVAAIILDPNNIP 54 (209) Q Consensus 11 ~~~~E~~l~~~~~~~------------IiGvDEaGRG~~~GPlvvaav~~~~~~~~ 54 (209) +|++|..|.+.|..+ .--++=.--|++.|||||.---++++.+. T Consensus 8 SFSFE~aL~~aGip~rhi~~~~nV~MY~Tni~~~~aG~F~g~mVVSMRp~~~~~~~ 63 (143) T pfam07286 8 SFSFEEALLAAGIPVRHIEEGRNVPMYRTNIPCRPAGPFSGPMVVSMRPIPADDVI 63 (143) T ss_pred CCCHHHHHHHCCCCCCCCCCCCCCCEEECCCCCCCCCCCCCCEEEEEECCCHHHHH T ss_conf 30589999987998533235866683865865535677567547874038989988 No 32 >pfam04084 ORC2 Origin recognition complex subunit 2. All DNA replication initiation is driven by a single conserved eukaryotic initiator complex termed he origin recognition complex (ORC). The ORC is a six protein complex. The function of ORC is reviewed in. Probab=33.98 E-value=20 Score=17.25 Aligned_cols=13 Identities=8% Similarity=0.115 Sum_probs=6.4 Q ss_pred HHHHHHHHHHCCC Q ss_conf 9998755211012 Q gi|254781076|r 66 KKREELYEKITSS 78 (209) Q Consensus 66 ~~R~~l~~~i~~~ 78 (209) .+-..+.+.+.+. T Consensus 118 ~~~~~i~~~~~~~ 130 (316) T pfam04084 118 EQLDFIVSYLNSR 130 (316) T ss_pred HHHHHHHHHHHCC T ss_conf 9999999998368 No 33 >cd01577 IPMI_Swivel Aconatase-like swivel domain of 3-isopropylmalate dehydratase and related uncharacterized proteins. 3-isopropylmalate dehydratase catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate, via the formation of 2-isopropylmaleate 3-isopropylmalate. IPMI is involved in fungal and bacterial leucine biosynthesis and is also found in eukaryotes. This is the aconitase-like swivel domain, which is believed to undergo swivelling conformational change in the enzyme mechanism. Probab=31.19 E-value=44 Score=15.18 Aligned_cols=30 Identities=17% Similarity=0.347 Sum_probs=19.6 Q ss_pred CCCCCCC-HHHH-HHHHHCCCCCCCCCCHHHH Q ss_conf 2899999-8999-9999828583010784888 Q gi|254781076|r 175 SHVGYPT-AKHQ-QVIKEKGPSCIHRLTFRPL 204 (209) Q Consensus 175 ~nkGYgT-~~H~-~ai~~~G~~~~HR~Sf~~v 204 (209) .|.|-|| .+|- .+++.+|+..+.-+||.-+ T Consensus 25 ~NFG~GSSREhA~~al~~~Gi~~VIa~SFa~I 56 (91) T cd01577 25 KNFGCGSSREHAPWALKDAGIRAVIAESFARI 56 (91) T ss_pred CCCCCCCCHHHHHHHHHHCCCEEEEEHHHHHH T ss_conf 86577852899999999849549997239999 No 34 >TIGR01070 mutS1 DNA mismatch repair protein MutS; InterPro: IPR005748 Mismatch repair contributes to the overall fidelity of DNA replication and is essential for combating the adverse effects of damage to the genome. It involves the correction of mismatched base pairs that have been missed by the proofreading element of the DNA polymerase complex. The post-replicative Mismatch Repair System (MMRS) of Escherichia coli involves MutS (Mutator S), MutL and MutH proteins, and acts to correct point mutations or small insertion/deletion loops produced during DNA replication . MutS and MutL are involved in preventing recombination between partially homologous DNA sequences. The assembly of MMRS is initiated by MutS, which recognises and binds to mispaired nucleotides and allows further action of MutL and MutH to eliminate a portion of newly synthesized DNA strand containing the mispaired base . MutS can also collaborate with methyltransferases in the repair of O(6)-methylguanine damage, which would otherwise pair with thymine during replication to create an O(6)mG:T mismatch . MutS exists as a dimer, where the two monomers have different conformations and form a heterodimer at the structural level . Only one monomer recognises the mismatch specifically and has ADP bound. Non-specific major groove DNA-binding domains from both monomers embrace the DNA in a clamp-like structure. Mismatch binding induces ATP uptake and a conformational change in the MutS protein, resulting in a clamp that translocates on DNA. MutS is a modular protein with a complex structure , and is composed of: N-terminal mismatch-recognition domain, which is similar in structure to tRNA endonuclease. Connector domain, which is similar in structure to Holliday junction resolvase ruvC. Core domain, which is composed of two separate subdomains that join together to form a helical bundle; from within the core domain, two helices act as levers that extend towards (but do not touch) the DNA. Clamp domain, which is inserted between the two subdomains of the core domain at the top of the lever helices; the clamp domain has a beta-sheet structure. ATPase domain (connected to the core domain), which has a classical Walker A motif. HTH (helix-turn-helix) domain, which is involved in dimer contacts. Homologues of MutS have been found in many species including eukaryotes (MSH 1, 2, 3, 4, 5, and 6 proteins), archaea and bacteria, and together these proteins have been grouped into the MutS family. Although many of these proteins have similar activities to the E. coli MutS, there is significant diversity of function among the MutS family members. This diversity is even seen within species, where many species encode multiple MutS homologues with distinct functions . Inter-species homologues may have arisen through frequent ancient horizontal gene transfer of MutS (and MutL) from bacteria to archaea and eukaryotes via endosymbiotic ancestors of mitochondria and chloroplasts . This entry represents a family of MutS proteins.; GO: 0005524 ATP binding, 0030983 mismatched DNA binding, 0006298 mismatch repair. Probab=30.54 E-value=15 Score=18.14 Aligned_cols=15 Identities=27% Similarity=0.266 Sum_probs=6.3 Q ss_pred CCCCCCCCCCCCCCC Q ss_conf 110126532246621 Q gi|254781076|r 116 RSALIDGRSIPEDLP 130 (209) Q Consensus 116 ~~ilIDg~~~~~~~~ 130 (209) ..++=||.-+..+++ T Consensus 410 P~~v~dGG~I~~GYd 424 (863) T TIGR01070 410 PLVVRDGGVIREGYD 424 (863) T ss_pred CCEEECCCEECCCCC T ss_conf 926504861235788 No 35 >KOG2745 consensus Probab=29.38 E-value=47 Score=14.99 Aligned_cols=27 Identities=33% Similarity=0.536 Sum_probs=17.7 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHCCCCC Q ss_conf 236666547758999999988777988 Q gi|254781076|r 146 IAAASIIAKVTRDRLMRIAHKKYPDYG 172 (209) Q Consensus 146 VaaASIiAKv~RD~~m~~l~~~~p~Yg 172 (209) -=|||+++-|.+|+..+.+++.||+-| T Consensus 93 rL~a~~v~~v~~~rv~q~l~~~~p~~~ 119 (321) T KOG2745 93 RLAASAVQTVVSDRVLQYLDEYYPNEG 119 (321) T ss_pred HHHHHHHHHHHHHHHHHHHHHHCCCCC T ss_conf 999999999971179987521086768 No 36 >pfam11641 Antigen_Bd37 Glycosylphosphatidylinositol-anchored merozoite surface protein. This family of proteins represents the core region of Bd37, a surface antigen of B.divergens which is GPI-anchored at the surface of the merozoite. The structure of the protein consists of mainly alpha folds and has three sub domains. Probab=29.36 E-value=47 Score=14.98 Aligned_cols=34 Identities=24% Similarity=0.369 Sum_probs=24.8 Q ss_pred HHHHHHHHHHHHHHCCC-------CCCCCCCCCCCH-HHHHH Q ss_conf 77589999999887779-------881028999998-99999 Q gi|254781076|r 154 KVTRDRLMRIAHKKYPD-------YGFDSHVGYPTA-KHQQV 187 (209) Q Consensus 154 Kv~RD~~m~~l~~~~p~-------Ygf~~nkGYgT~-~H~~a 187 (209) ++.||.+|+++....|. |||-.---||.| .|-.| T Consensus 138 ~~~~del~kKf~a~~psflt~eDIs~fLTVPeYG~p~na~kw 179 (224) T pfam11641 138 RVQRDELVKKFTARAPSFLTSEDISGFLTVPEYGVPMNAAKW 179 (224) T ss_pred HHHHHHHHHHHHHCCCCCCCHHHHHHHEECCCCCCCCCHHHH T ss_conf 553999999888508976648766222106656897638899 No 37 >cd01220 PH_CDEP Chondrocyte-derived ezrin-like domain containing protein (CDEP) Pleckstrin homology (PH) domain. CDEP consists of a Ferm domain, a rhoGEF (DH) domain followed by two PH domains. PH domains share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains also have diverse functions. They are often involved in targeting proteins to the plasma membrane, but few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. Probab=29.14 E-value=39 Score=15.45 Aligned_cols=34 Identities=15% Similarity=0.220 Sum_probs=26.0 Q ss_pred EEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 2268711478652002366665477589999999887 Q gi|254781076|r 131 CQAFAVIKGDSISLSIAAASIIAKVTRDRLMRIAHKK 167 (209) Q Consensus 131 ~~~~~i~KgD~~~~~VaaASIiAKv~RD~~m~~l~~~ 167 (209) .+....+.+-+++..|+|+|--- ||.||..+.+. T Consensus 63 ~~n~f~I~~~~ks~~v~A~s~~E---k~~W~~~i~~a 96 (99) T cd01220 63 VPHCFTIFGGQCAITVAASTRAE---KEKWLADLSKA 96 (99) T ss_pred CCCEEEEECCCEEEEEEECCHHH---HHHHHHHHHHH T ss_conf 87379996588799999599999---99999999998 No 38 >KOG3495 consensus Probab=28.69 E-value=48 Score=14.91 Aligned_cols=21 Identities=29% Similarity=0.267 Sum_probs=17.5 Q ss_pred HHHHHHHHHHHHHHHHHHHHH Q ss_conf 236666547758999999988 Q gi|254781076|r 146 IAAASIIAKVTRDRLMRIAHK 166 (209) Q Consensus 146 VaaASIiAKv~RD~~m~~l~~ 166 (209) |.=++|.|++.|+.++.++.. T Consensus 12 i~Ys~I~A~vvR~~LK~e~ka 32 (50) T KOG3495 12 IRYSQIAAQVVRQALKTELKA 32 (50) T ss_pred HHHHHHHHHHHHHHHHHHHHH T ss_conf 999999999999998577777 No 39 >pfam04870 DUF644 Protein of unknown function (DUF644). This family of proteins with unknown function are from C.elegans. The GO annotation for this protein indicates that this protein is involved in nematode larval development and is a positive regulator of growth rate. This protein is possibly an integral membrane protein. Probab=27.37 E-value=51 Score=14.76 Aligned_cols=31 Identities=13% Similarity=0.215 Sum_probs=20.5 Q ss_pred CCCCHHHHHHHHHCCCCCCCCCCHHHHHHHC Q ss_conf 9999899999998285830107848886403 Q gi|254781076|r 178 GYPTAKHQQVIKEKGPSCIHRLTFRPLRNLS 208 (209) Q Consensus 178 GYgT~~H~~ai~~~G~~~~HR~Sf~~vk~l~ 208 (209) -|.+++-.+..+.+-...+||.=|++|+.|+ T Consensus 286 p~~ns~~L~~~k~lt~~~~~~sI~~tIr~lA 316 (323) T pfam04870 286 PFNNSKALKEYRNLTRAEIPRSIHSTIRDIA 316 (323) T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH T ss_conf 8888899999874587679999999999999 No 40 >COG2238 RPS19A Ribosomal protein S19E (S16A) [Translation, ribosomal structure and biogenesis] Probab=26.11 E-value=54 Score=14.62 Aligned_cols=55 Identities=20% Similarity=0.115 Sum_probs=37.8 Q ss_pred CCCCHHHHHHHHHHHHHHHHH--HHHHHHHCCCC------CCCCCCCCCC--HHHHHHHHHCCCC Q ss_conf 865200236666547758999--99998877798------8102899999--8999999982858 Q gi|254781076|r 140 DSISLSIAAASIIAKVTRDRL--MRIAHKKYPDY------GFDSHVGYPT--AKHQQVIKEKGPS 194 (209) Q Consensus 140 D~~~~~VaaASIiAKv~RD~~--m~~l~~~~p~Y------gf~~nkGYgT--~~H~~ai~~~G~~ 194 (209) +....-+-||||+-|+.=|-. +..|...|++- -...-+|+|+ ..-.+.|++.|.- T Consensus 47 ~~DWwY~RaASilRkiyi~gpvGi~rL~t~YGg~k~rG~rP~~~~~gsgsI~RkilqqLE~~G~V 111 (147) T COG2238 47 QEDWWYVRAASILRKIYIDGPVGIERLRTAYGGRKNRGSRPEKFRKGSGSIIRKVLQQLEKAGLV 111 (147) T ss_pred CCCHHHHHHHHHHHHHHHCCCHHHHHHHHHHCCCCCCCCCCHHHHCCCCHHHHHHHHHHHHCCCE T ss_conf 87549999999999998537601999999878666688894344237736999999999977856 No 41 >PRK00439 leuD 3-isopropylmalate dehydratase small subunit; Reviewed Probab=24.73 E-value=57 Score=14.46 Aligned_cols=12 Identities=17% Similarity=0.191 Sum_probs=4.8 Q ss_pred HHHHHHHHCCCC Q ss_conf 987552110123 Q gi|254781076|r 68 REELYEKITSSA 79 (209) Q Consensus 68 R~~l~~~i~~~~ 79 (209) ||.....++... T Consensus 64 RE~A~~al~~~G 75 (163) T PRK00439 64 REHAPLALKAAG 75 (163) T ss_pred HHHHHHHHHHCC T ss_conf 799999999859 No 42 >cd01219 PH_FGD FGD (faciogenital dysplasia protein) pleckstrin homology (PH) domain. FGD has a RhoGEF (DH) domain, followed by a PH domain, a FYVE domain and a C-terminal PH domain. FGD is a guanine nucleotide exchange factor that activates the Rho GTPase Cdc42. PH domains share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains also have diverse functions. They are often involved in targeting proteins to the plasma membrane, but few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. Probab=23.33 E-value=59 Score=14.35 Aligned_cols=36 Identities=11% Similarity=0.137 Sum_probs=28.3 Q ss_pred CCEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 212268711478652002366665477589999999887 Q gi|254781076|r 129 LPCQAFAVIKGDSISLSIAAASIIAKVTRDRLMRIAHKK 167 (209) Q Consensus 129 ~~~~~~~i~KgD~~~~~VaaASIiAKv~RD~~m~~l~~~ 167 (209) ...++...+.|.+++..++|.|--- ||.||+.+... T Consensus 63 ~~~~~~F~I~~~~rsl~l~A~s~eE---k~~W~~~i~~a 98 (101) T cd01219 63 LERPHSFLVSGKQRCLELQARTQKE---KNDWVQAIFSI 98 (101) T ss_pred CCCCEEEEEEECCEEEEEECCCHHH---HHHHHHHHHHH T ss_conf 7877079998465699998799899---99999999987 No 43 >TIGR02177 PorB_KorB 2-oxoacid:acceptor oxidoreductase, beta subunit, pyruvate/2-ketoisovalerate family; InterPro: IPR011896 A number of anaerobic and microaerophilic species lack pyruvate dehydrogenase and have instead a four subunit, oxygen-sensitive pyruvate oxidoreductase, with either ferredoxins or flavodoxins used as the acceptor. Several related four-subunit enzymes may exist in the same species. This entry describes the beta subunits, representing mostly pyruvate and 2-ketoisovalerate specific enzymes.. Probab=23.25 E-value=61 Score=14.29 Aligned_cols=39 Identities=18% Similarity=0.271 Sum_probs=22.9 Q ss_pred CCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCC Q ss_conf 147865200236666547758999999988777988102 Q gi|254781076|r 137 IKGDSISLSIAAASIIAKVTRDRLMRIAHKKYPDYGFDS 175 (209) Q Consensus 137 ~KgD~~~~~VaaASIiAKv~RD~~m~~l~~~~p~Ygf~~ 175 (209) ..||-.-..++++=.||---|--=|..|=-...-||.-+ T Consensus 77 ~GGDGD~~GIG~~Hfva~gRRN~dIt~l~~DN~VYGLTK 115 (302) T TIGR02177 77 VGGDGDLYGIGGNHFVAAGRRNVDITVLVHDNQVYGLTK 115 (302) T ss_pred EECCCCCHHHHHHHHHHHHCCCCCCEEEEECCEECCCCC T ss_conf 606864101105778754114788248842470546665 No 44 >pfam08589 DUF1770 Fungal protein of unknown function (DUF1770). The function of this family is unknown. These proteins are rather dissimilar except for a single strongly conserved motif (PDLRFEQ). Probab=23.24 E-value=50 Score=14.82 Aligned_cols=15 Identities=20% Similarity=0.419 Sum_probs=5.8 Q ss_pred CCCCCCHHHHHHHHH Q ss_conf 878868889999997 Q gi|254781076|r 6 IPERPHFELEAMVRE 20 (209) Q Consensus 6 ~~~~p~~~~E~~l~~ 20 (209) +|-.|||++|+.+++ T Consensus 67 lPPlPDLRFEQSYL~ 81 (96) T pfam08589 67 LPPLPDLRFEQSYLA 81 (96) T ss_pred CCCCCCHHHHHHHHH T ss_conf 988965137899999 No 45 >COG2247 LytB Putative cell wall-binding domain [Cell envelope biogenesis, outer membrane] Probab=22.86 E-value=62 Score=14.24 Aligned_cols=13 Identities=23% Similarity=0.322 Sum_probs=8.2 Q ss_pred HHHHHHHHCCCCCC Q ss_conf 99999998285830 Q gi|254781076|r 183 KHQQVIKEKGPSCI 196 (209) Q Consensus 183 ~H~~ai~~~G~~~~ 196 (209) +.++++++ |++|. T Consensus 146 ~~~e~~k~-~~~p~ 158 (337) T COG2247 146 ALMELMKE-GIVPV 158 (337) T ss_pred HHHHHHHC-CCCEE T ss_conf 78888753-75326 No 46 >pfam12149 HSV_VP16_C Herpes simplex virus virion protein 16 C terminal. This domain is found in viruses, and is about 30 amino acids in length. It is found in association with pfam02232. This domain is the C terminal of the HSV virion protein 16. This protein is a transcription promoter. The C terminal domain is the carboxyl subdomain of the acidic transcriptional activation domain. The protein binds to DNA binding proteins to carry out its function. Such proteins include TATA binding protein, CBP, TBP-binding protein, etc. Probab=22.85 E-value=38 Score=15.58 Aligned_cols=21 Identities=38% Similarity=0.757 Sum_probs=15.5 Q ss_pred CCCCHHHHHHHHHCCCCEEEEEECCC Q ss_conf 88688899999977994899984278 Q gi|254781076|r 8 ERPHFELEAMVREKNMWPVAGIDEVG 33 (209) Q Consensus 8 ~~p~~~~E~~l~~~~~~~IiGvDEaG 33 (209) +..+|++|+++-.. .|+||-| T Consensus 9 dmadfefeqmftda-----lgidd~g 29 (30) T pfam12149 9 DMADFEFEQMFTDA-----LGIDDFG 29 (30) T ss_pred HHHHHHHHHHHHHH-----HCCCCCC T ss_conf 05567899998664-----0764558 No 47 >pfam09974 DUF2209 Uncharacterized protein conserved in archaea (DUF2209). This domain, found in various hypothetical archaeal proteins, has no known function. Probab=22.82 E-value=62 Score=14.23 Aligned_cols=116 Identities=15% Similarity=0.182 Sum_probs=60.2 Q ss_pred EEEECCCCCCCCCC--EEEEEEEECCCCCCCCCCCCCCCCHHHHHHHHHHHCCCCEEEEECCCHHHHHHHCHHHHHHHHH Q ss_conf 99842787775222--5599999870108233115202899999875521101230788515679985204799988654 Q gi|254781076|r 27 AGIDEVGRGALAGP--VVVAAIILDPNNIPFGINDSKKISHKKREELYEKITSSAIISISSASHQYIDKHNIHKATLDAI 104 (209) Q Consensus 27 iGvDEaGRG~~~GP--lvvaav~~~~~~~~~~i~DSK~Ls~~~R~~l~~~i~~~~~~~i~~~~~~eID~~ni~~A~~~a~ 104 (209) +|||=.||--..|- +|.|||.+.-+.... + .+.+...+.+-.-.+ -|+ .....-. T Consensus 1 vaVDISGRH~e~dgy~~V~AaV~~ev~a~~I-------------~----~Ve~v~v~~v~~~~~-----~~L-~diV~~v 57 (128) T pfam09974 1 IAVDISGRHAEKDGYYRVCAAVALEVSADHI-------------E----TVRQVNVFPVCTREP-----PNL-RDIVEEV 57 (128) T ss_pred CEEECCCCCCCCCCEEEEEEEEEEEECHHHE-------------E----EEECCEEEEEECCCC-----CCH-HHHHHHH T ss_conf 9140456431168479999889899724465-------------7----653132799864788-----518-9999999 Q ss_pred HHHCCCCCCCCCC-CCCC-CCCCCCCCCEEEEEECCCCCCCH-------HHHHHHHHHHHHHHHHHHHHHH Q ss_conf 3210025753211-0126-53224662122687114786520-------0236666547758999999988 Q gi|254781076|r 105 YHAVENLQVIPRS-ALID-GRSIPEDLPCQAFAVIKGDSISL-------SIAAASIIAKVTRDRLMRIAHK 166 (209) Q Consensus 105 ~~ai~~l~~~~~~-ilID-g~~~~~~~~~~~~~i~KgD~~~~-------~VaaASIiAKv~RD~~m~~l~~ 166 (209) .++++++...++. ++.. |.++ ....+.+.++-+++=+|+ +|-.|-=++-..|+-+|.+|.. T Consensus 58 ~~~v~~l~~~f~g~Iv~E~Gefy-n~P~w~v~a~l~~~fky~es~gEreaIe~AHhvSysvrklL~~el~i 127 (128) T pfam09974 58 ERTLDGLDKDFEYTIVAEKGEFF-NQPEWRVSAMLSAPFKYQETVAEREAIEMAHHVSYSVRKLLIKELKI 127 (128) T ss_pred HHHHHHCCCCCCCCEEECCCCCC-CCCHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCC T ss_conf 99997267688852895173201-48166888772566204154888999999999999999999886057 No 48 >PRK11181 23S rRNA (guanosine-2'-O-)-methyltransferase; Provisional Probab=22.43 E-value=63 Score=14.19 Aligned_cols=15 Identities=33% Similarity=0.620 Sum_probs=8.1 Q ss_pred CCCCCCCCCCCCCCC Q ss_conf 211012653224662 Q gi|254781076|r 115 PRSALIDGRSIPEDL 129 (209) Q Consensus 115 ~~~ilIDg~~~~~~~ 129 (209) |-.+++|+-.-|.++ T Consensus 95 ~lil~LD~I~DP~Nl 109 (244) T PRK11181 95 PFLLILDGVTDPHNL 109 (244) T ss_pred CEEEEECCCCCCCHH T ss_conf 879998188787389 No 49 >pfam08459 UvrC_HhH_N UvrC Helix-hairpin-helix N-terminal. This domain is found in the C subunits of the bacterial and archaeal UvrABC system which catalyses nucleotide excision repair in a multi-step process. UvrC catalyses the first incision on the fourth or fifth phosphodiester bond 3' and on the eighth phosphodiester bond 5' from the damage that is to be excised. The domain described here is found to the N-terminus of a helix hairpin helix (pfam00633) motif and also co-occurs with the pfam01541 catalytic domain which is found at the N-terminus of the same proteins. Probab=22.07 E-value=64 Score=14.14 Aligned_cols=37 Identities=22% Similarity=0.345 Sum_probs=23.2 Q ss_pred HHCCCCCCCCCCCCCCCCC---------C-CCCCCEEEEEECCCCCC Q ss_conf 2100257532110126532---------2-46621226871147865 Q gi|254781076|r 106 HAVENLQVIPRSALIDGRS---------I-PEDLPCQAFAVIKGDSI 142 (209) Q Consensus 106 ~ai~~l~~~~~~ilIDg~~---------~-~~~~~~~~~~i~KgD~~ 142 (209) +..+.-..-|+.++|||-. + ..+++.++.++.|++.. T Consensus 70 ~~~~~~~~~PDLilIDGGkgQl~~a~~~l~~~~~~i~vi~iaK~~~~ 116 (154) T pfam08459 70 RLLKEKLPLPDLILIDGGKGQLNAAKEVLEELGLDIPVIGLAKGEEH 116 (154) T ss_pred HHHHCCCCCCCEEEECCCHHHHHHHHHHHHHCCCCCEEEEEEECCCC T ss_conf 65411689998899759989999999999985999529999735655 No 50 >KOG3668 consensus Probab=21.44 E-value=55 Score=14.55 Aligned_cols=15 Identities=47% Similarity=0.722 Sum_probs=7.7 Q ss_pred HHHHHHHHHHHHHHHH Q ss_conf 5477589999999887 Q gi|254781076|r 152 IAKVTRDRLMRIAHKK 167 (209) Q Consensus 152 iAKv~RD~~m~~l~~~ 167 (209) +-||.| ++|...+.+ T Consensus 212 Ihk~~~-rv~~~~HRq 226 (269) T KOG3668 212 IHKVER-RVFTRAHRQ 226 (269) T ss_pred HHHHHH-HHHHHHHHH T ss_conf 999999-999998878 No 51 >COG3081 Nucleoid-associated protein [General function prediction only] Probab=21.36 E-value=66 Score=14.05 Aligned_cols=22 Identities=27% Similarity=0.584 Sum_probs=16.1 Q ss_pred HHHHHHHCCC------CCCCCCCCCCCH Q ss_conf 9999887779------881028999998 Q gi|254781076|r 161 MRIAHKKYPD------YGFDSHVGYPTA 182 (209) Q Consensus 161 m~~l~~~~p~------Ygf~~nkGYgT~ 182 (209) +.+|++.-|. |.|..++|||-. T Consensus 242 l~~LS~~lp~~~e~~F~~f~~eq~YgLe 269 (335) T COG3081 242 LQELSKELPGLNEVAFYDFTAEKGYGLE 269 (335) T ss_pred HHHHHHHCCCCCCCHHHHHHHHCCCCCC T ss_conf 9998734788674129998886056777 No 52 >pfam09288 UBA_3 Fungal ubiquitin-associated domain. Members of this family of ubiquitin binding domains adopt a structure consisting of a three alpha-helix bundle. They are predominantly found in fungal ubiquitin-protein ligases. Probab=20.96 E-value=68 Score=14.00 Aligned_cols=25 Identities=28% Similarity=0.444 Sum_probs=17.4 Q ss_pred CCCCCHHHHHHHHHCCCCCCCCCCHHHHHH Q ss_conf 999998999999982858301078488864 Q gi|254781076|r 177 VGYPTAKHQQVIKEKGPSCIHRLTFRPLRN 206 (209) Q Consensus 177 kGYgT~~H~~ai~~~G~~~~HR~Sf~~vk~ 206 (209) -|++..+.++.+|+.|+- |+.|+.| T Consensus 19 ~GF~r~KvIevLrRlgiK-----s~~~~~n 43 (55) T pfam09288 19 QGFEKDKVIEVLKRLGIK-----SMDPNDN 43 (55) T ss_pred CCCCHHHHHHHHHHHCCC-----CCCCCCH T ss_conf 488623399999995856-----5797552 No 53 >pfam09010 AsiA Anti-Sigma Factor A. 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. Probab=20.73 E-value=68 Score=13.97 Aligned_cols=23 Identities=26% Similarity=0.316 Sum_probs=17.7 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 00236666547758999999988 Q gi|254781076|r 144 LSIAAASIIAKVTRDRLMRIAHK 166 (209) Q Consensus 144 ~~VaaASIiAKv~RD~~m~~l~~ 166 (209) -.||-|||+-|..||.++..-+. T Consensus 10 eIia~aSlLIK~~~edI~~~q~~ 32 (91) T pfam09010 10 DIIATASLLIKFGREDIVENQAN 32 (91) T ss_pred HHHHHHHHHHHCCHHHHHHHHHH T ss_conf 99999999998269999871999 No 54 >pfam08714 Fae Formaldehyde-activating enzyme (Fae). Formaldehyde-activating enzyme is an enzyme required for energy metabolism and formaldehyde detoxification. It catalyses the condensation of formaldehyde and tetrahydromethanopterin to methylene tetrahydromethanopterin. Probab=20.58 E-value=62 Score=14.24 Aligned_cols=34 Identities=29% Similarity=0.187 Sum_probs=20.3 Q ss_pred EEEEECCCHHHHH-----HHCHHHHHHHHHHHHCCCCCCC Q ss_conf 0788515679985-----2047999886543210025753 Q gi|254781076|r 80 IISISSASHQYID-----KHNIHKATLDAIYHAVENLQVI 114 (209) Q Consensus 80 ~~~i~~~~~~eID-----~~ni~~A~~~a~~~ai~~l~~~ 114 (209) +..-.+++|+-.| ++| .+||.+|++||++..+.. T Consensus 106 iiv~V~i~p~a~D~~kiy~~N-y~ATk~AI~rAm~~~Ps~ 144 (160) T pfam08714 106 IIVSVFIHPEALDDKKIYRYN-YEATKLAIKRAMKGEPSI 144 (160) T ss_pred EEEEEECCCCCCCHHHHHHHH-HHHHHHHHHHHHCCCCCH T ss_conf 999997183303689999999-999999999998089998 No 55 >KOG3062 consensus Probab=20.56 E-value=69 Score=13.95 Aligned_cols=34 Identities=6% Similarity=0.123 Sum_probs=24.2 Q ss_pred CCCCCCCCCCCCCCCCCCEEEEEECCCCCCCHHH Q ss_conf 5321101265322466212268711478652002 Q gi|254781076|r 113 VIPRSALIDGRSIPEDLPCQAFAVIKGDSISLSI 146 (209) Q Consensus 113 ~~~~~ilIDg~~~~~~~~~~~~~i~KgD~~~~~V 146 (209) .+.+.|++|.-...+++.+...|+.|+-..-.+| T Consensus 72 sk~~iVI~DslNyIKGfRYeLyC~ak~~~tt~Cv 105 (281) T KOG3062 72 SKGDIVIVDSLNYIKGFRYELYCEAKAARTTYCV 105 (281) T ss_pred CCCCEEEEECCCCCCCCEEEEEEEHHCCCEEEEE T ss_conf 5686899814441122020365510105446899 No 56 >pfam02334 RTP Replication terminator protein. The bacterial replication terminator protein (RTP) plays a role in the termination of DNA replication by impeding replication fork movement. Two RTP dimers bind to the two inverted repeat regions at the termination site. Probab=20.29 E-value=51 Score=14.75 Aligned_cols=13 Identities=38% Similarity=0.491 Sum_probs=6.5 Q ss_pred HHHHHHHHHHHHH Q ss_conf 7758999999988 Q gi|254781076|r 154 KVTRDRLMRIAHK 166 (209) Q Consensus 154 Kv~RD~~m~~l~~ 166 (209) |+.=||....+++ T Consensus 104 K~eLdRc~~ll~K 116 (122) T pfam02334 104 KVELDRCKKLIEK 116 (122) T ss_pred HHHHHHHHHHHHH T ss_conf 9889999999999 No 57 >COG3596 Predicted GTPase [General function prediction only] Probab=20.16 E-value=59 Score=14.36 Aligned_cols=23 Identities=26% Similarity=0.294 Sum_probs=13.3 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 00236666547758999999988 Q gi|254781076|r 144 LSIAAASIIAKVTRDRLMRIAHK 166 (209) Q Consensus 144 ~~VaaASIiAKv~RD~~m~~l~~ 166 (209) .++.++|++|+..-|.+=..... T Consensus 221 lp~e~rs~~a~~~~d~~~~~~~~ 243 (296) T COG3596 221 LPVEARSPLAARLQDELRTQSAR 243 (296) T ss_pred CCCCCCCHHHHHHHHHHHHHHHH T ss_conf 73100240243301687777788 Done!