Query gi|254780940|ref|YP_003065353.1| ribonuclease III [Candidatus Liberibacter asiaticus str. psy62] Match_columns 227 No_of_seqs 139 out of 3294 Neff 7.6 Searched_HMMs 39220 Date Mon May 30 02:29:16 2011 Command /home/congqian_1/programs/hhpred/hhsearch -i 254780940.hhm -d /home/congqian_1/database/cdd/Cdd.hhm No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 TIGR02191 RNaseIII ribonucleas 100.0 0 0 487.5 15.7 215 9-223 1-228 (228) 2 PRK12371 ribonuclease III; Rev 100.0 0 0 479.5 18.1 227 1-227 7-233 (235) 3 PRK00102 rnc ribonuclease III; 100.0 0 0 443.7 17.1 221 4-224 2-226 (228) 4 COG0571 Rnc dsRNA-specific rib 100.0 0 0 434.0 17.8 226 2-227 4-233 (235) 5 PRK12372 ribonuclease III; Rev 100.0 0 0 431.1 16.1 216 4-222 1-219 (425) 6 KOG1817 consensus 100.0 0 0 325.1 12.3 219 5-224 274-502 (533) 7 smart00535 RIBOc Ribonuclease 100.0 2.5E-36 6.3E-41 243.5 6.6 127 21-148 1-127 (129) 8 cd00593 RIBOc RIBOc. Ribonucle 100.0 6.8E-35 1.7E-39 234.7 5.3 129 21-149 1-130 (133) 9 KOG3769 consensus 99.9 1.1E-23 2.9E-28 165.7 11.6 217 6-225 65-303 (333) 10 pfam00636 Ribonuclease_3 RNase 99.9 1.1E-23 2.7E-28 165.8 6.8 91 41-131 1-96 (96) 11 KOG0701 consensus 99.8 1.4E-21 3.7E-26 152.7 4.6 133 4-138 979-1174(1606) 12 KOG0701 consensus 99.8 5.7E-20 1.4E-24 142.9 7.4 203 5-223 1370-1596(1606) 13 KOG1817 consensus 99.8 2.8E-20 7.2E-25 144.7 4.8 135 6-140 43-232 (533) 14 cd00048 DSRM Double-stranded R 99.6 5.2E-16 1.3E-20 118.5 7.2 68 156-223 1-68 (68) 15 smart00358 DSRM Double-strande 99.6 2E-15 5.1E-20 114.9 7.3 67 157-224 1-67 (67) 16 KOG3732 consensus 99.3 4E-12 1E-16 94.6 7.5 73 151-224 138-210 (339) 17 pfam00035 dsrm Double-stranded 99.3 4.9E-12 1.3E-16 94.0 7.5 66 157-223 1-66 (66) 18 KOG3732 consensus 99.0 5.6E-10 1.4E-14 81.4 7.0 70 155-226 38-107 (339) 19 KOG2777 consensus 98.3 1.8E-06 4.5E-11 59.8 6.3 65 154-224 89-153 (542) 20 KOG4334 consensus 98.1 1.3E-06 3.2E-11 60.7 2.8 63 159-223 379-441 (650) 21 COG1939 Ribonuclease III famil 97.8 4.8E-05 1.2E-09 51.0 5.3 98 40-143 15-127 (132) 22 KOG2334 consensus 95.2 0.0064 1.6E-07 37.9 0.8 138 75-227 299-444 (477) 23 KOG3792 consensus 92.3 0.058 1.5E-06 32.0 1.2 48 177-225 396-443 (816) 24 KOG3792 consensus 91.5 0.22 5.5E-06 28.5 3.4 49 174-223 520-569 (816) 25 pfam03368 dsRNA_bind Double st 87.2 2.1 5.2E-05 22.5 5.8 63 158-226 2-77 (91) 26 pfam11469 DUF3204 Protein of u 79.1 4.8 0.00012 20.2 4.9 84 43-145 3-90 (120) 27 PRK07009 consensus 58.3 8.2 0.00021 18.8 2.4 82 40-126 75-172 (241) 28 PRK06859 consensus 53.7 8.4 0.00021 18.8 1.8 82 40-126 83-180 (253) 29 KOG2783 consensus 51.9 4.5 0.00012 20.4 0.2 42 158-199 231-272 (436) 30 TIGR01854 lipid_A_lpxH UDP-2,3 48.8 3.3 8.4E-05 21.3 -0.9 52 58-140 8-59 (241) 31 PRK13184 pknD serine/threonine 47.0 21 0.00055 16.2 3.1 38 41-80 551-597 (933) 32 PRK06022 consensus 39.0 24 0.00062 15.9 2.3 80 41-125 76-169 (234) 33 pfam04034 DUF367 Domain of unk 37.4 19 0.00048 16.6 1.5 40 109-149 61-101 (128) 34 pfam06754 PhnG Phosphonate met 36.5 32 0.00081 15.2 4.6 36 188-223 65-102 (147) 35 PRK06631 consensus 36.5 14 0.00035 17.4 0.7 40 81-125 136-175 (229) 36 PRK00394 transcription factor; 34.8 34 0.00087 15.0 5.8 27 186-213 139-165 (178) 37 TIGR02195 heptsyl_trn_II lipop 34.4 26 0.00065 15.8 1.8 24 44-67 8-31 (361) 38 PRK08816 consensus 32.8 13 0.00034 17.5 0.2 82 40-126 75-173 (244) 39 COG2042 Uncharacterized conser 32.0 25 0.00064 15.8 1.5 39 110-149 110-149 (179) 40 PRK08858 consensus 31.8 22 0.00057 16.1 1.2 40 81-125 147-186 (246) 41 PRK02287 hypothetical protein; 31.6 27 0.00068 15.7 1.5 41 108-149 99-140 (169) 42 KOG2146 consensus 31.6 38 0.00098 14.7 3.1 73 1-81 22-110 (354) 43 pfam11324 DUF3126 Protein of u 30.8 40 0.001 14.6 4.5 40 159-203 3-42 (63) 44 COG4148 ModC ABC-type molybdat 30.7 19 0.00048 16.6 0.6 60 3-70 68-133 (352) 45 cd00652 TBP_TLF TATA box bindi 30.1 41 0.001 14.5 5.5 26 187-213 138-163 (174) 46 cd04518 TBP_archaea archaeal T 29.3 42 0.0011 14.5 5.5 27 186-213 136-162 (174) 47 LOAD_cdc45 consensus 28.7 43 0.0011 14.4 5.5 73 61-144 338-411 (578) 48 pfam00333 Ribosomal_S5 Ribosom 28.6 43 0.0011 14.4 6.2 39 185-223 20-62 (67) 49 TIGR02706 P_butyryltrans phosp 28.2 44 0.0011 14.3 3.0 51 38-105 127-179 (295) 50 pfam07125 DUF1378 Protein of u 28.0 21 0.00054 16.3 0.5 30 118-147 10-40 (59) 51 KOG3302 consensus 27.6 45 0.0011 14.3 5.2 17 187-203 158-174 (200) 52 TIGR02587 TIGR02587 putative i 27.5 45 0.0012 14.3 2.3 28 112-139 154-181 (284) 53 TIGR01088 aroQ 3-dehydroquinat 26.4 18 0.00047 16.6 -0.0 18 98-116 5-22 (144) 54 PRK05711 DNA polymerase III su 26.2 36 0.00091 14.9 1.4 40 81-125 136-175 (240) 55 PRK10916 ADP-heptose:LPS hepto 26.2 36 0.00091 14.9 1.4 24 44-67 9-32 (348) 56 TIGR01256 modA molybdate ABC t 25.8 42 0.0011 14.5 1.7 13 214-226 120-132 (225) 57 PRK10422 lipopolysaccharide co 25.3 37 0.00095 14.8 1.4 10 95-104 184-193 (352) 58 COG1737 RpiR Transcriptional r 25.2 40 0.001 14.6 1.5 44 54-97 22-66 (281) 59 cd04516 TBP_eukaryotes eukaryo 24.8 50 0.0013 14.0 5.5 26 187-213 137-162 (174) 60 cd01831 Endoglucanase_E_like E 24.5 9.7 0.00025 18.4 -1.7 20 199-218 145-164 (169) 61 cd04517 TLF TBP-like factors ( 24.3 52 0.0013 13.9 5.6 27 186-213 137-163 (174) 62 pfam11940 DUF3458 Domain of un 23.5 54 0.0014 13.8 4.7 26 7-32 134-159 (408) 63 PRK07982 consensus 22.7 29 0.00075 15.4 0.4 81 40-125 84-181 (243) 64 pfam01418 HTH_6 Helix-turn-hel 21.8 41 0.001 14.5 1.0 41 55-97 21-64 (106) 65 TIGR02087 LEUD_arch 3-isopropy 21.6 50 0.0013 14.0 1.4 49 161-225 27-76 (159) 66 TIGR00677 fadh2_euk methylenet 20.7 61 0.0016 13.5 2.0 18 210-227 293-310 (312) 67 COG0859 RfaF ADP-heptose:LPS h 20.5 49 0.0012 14.0 1.2 24 43-66 9-32 (334) 68 pfam00352 TBP Transcription fa 20.2 62 0.0016 13.4 5.7 39 185-224 46-86 (86) 69 PRK11557 putative DNA-binding 20.1 45 0.0011 14.3 0.9 40 55-96 21-63 (282) No 1 >TIGR02191 RNaseIII ribonuclease III; InterPro: IPR011907 This family consists almost exclusively of bacterial examples of ribonuclease III (RNase III). This ubiquitous enzyme specifically cleaves double-stranded rRNA and is found in all bacteria and eukaryotes . In bacteria its main role is the processing of pre-rRNAs, where the large precursor ribosomal RNA molecules are at cleaved at specific sites to produce the immediate precursors of the functional molecules. RNase III also functions in the maturation and degradation of mRNAs, and the maturaton of tRNAs. In some organisms (eg. E. coli) cells are viable without this enzyme, though they are impeded in growth, but in others (eg. B. subtilis and M. genitalium) this enzyme is essential. The bacterial RNase III enzymes so far characterised are homodimers with a molecular mass of ~50 kDa , . The endonuclease domain is located within the N-terminal two-thirds of the protein, containing several alpha helices, but no beta strands. The double-stranded RNA binding domain is found at the C-terminal third of the protein, forming the alpha-beta(3)-alpha fold common to dsRNA-binding proteins. A signature box of 11 conserved amino acids found in the N-terminal region of RNase III may contain the active site, though this has not been proven.; GO: 0003723 RNA binding, 0004525 ribonuclease III activity, 0016075 rRNA catabolic process. Probab=100.00 E-value=0 Score=487.46 Aligned_cols=215 Identities=45% Similarity=0.634 Sum_probs=205.7 Q ss_pred HHHHHCCCCCCHHHHHHHCCCHHHCCCCC-----CCHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHH Q ss_conf 99983696589899998424612126676-----6547788745868864547877641046887899888888874433 Q gi|254780940|r 9 LEKRIGYAFANRSLLEKALTHSSISHSYQ-----ESYERLEFLGDRILGLLISTLLFNHFDSAKEGELSVRFNSLVSAET 83 (227) Q Consensus 9 l~~~lgy~f~~~~ll~~A~th~S~~~~~~-----~~~erLEflGDavL~~~v~~~l~~~~p~~~eG~lt~lr~~lV~n~~ 83 (227) |+++|||+|+|+.||.+||||+||.+++. +|||||||||||||+++||+|||++||+.+||+||++|+.|||.++ T Consensus 1 l~~~lg~~f~~~~lL~~ALTH~S~~ne~~~~~~~~~nERLEFLGDaVL~l~~~~~Lf~~~P~~~EG~Ls~~Ra~lV~~~~ 80 (228) T TIGR02191 1 LEKRLGYKFKNPELLEQALTHSSYANEHNESKKAKHNERLEFLGDAVLGLVVAEYLFKNFPDASEGELSKLRAALVSEES 80 (228) T ss_pred CHHHCCCCCCCHHHHHHHCCCCCHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHCHHH T ss_conf 90123888888899986201543233221146888511456788999999999999974789880258999998617488 Q ss_pred HHHHHH-HCCCCCEEEECCCCCCCCCCCCCCCCHHHHHHHHHHHHHCCC--CCCCHHHHHCCCCCCCCC--CCC-CCCCH Q ss_conf 454543-138772001036631237531333332669999999964155--422001221025643111--000-13452 Q gi|254780940|r 84 CSQVAR-ELDLASFIRVSSDLRKDVCSFMTSIQADVVESLIAALYLDGG--IEVAGTFVDKYWKQRALK--SGK-FRRDA 157 (227) Q Consensus 84 La~~a~-~lgl~~~l~~~~~~~~~~~~~~~~ilad~fEA~iGAiy~d~G--~~~~~~~i~~~~~~~~~~--~~~-~~~dp 157 (227) |+.+|+ .+||++||++|++++.++++.+++||||+|||+|||||+|+| ++.|+.||.++|.+.+.. ... ..+|| T Consensus 81 La~~A~~~~~L~~~l~LG~GE~~~gGr~r~siLaDa~EAliGAiYLD~G~e~~~a~~f~~~~~~~~~~~~~~~~~~~~D~ 160 (228) T TIGR02191 81 LAKVARKELGLGEYLLLGKGEEKSGGRRRDSILADAFEALIGAIYLDSGLELEAARKFILKLLIPRIDAIEKEEIAIKDY 160 (228) T ss_pred HHHHHHHHHCCCCEEEECHHHHHCCCCCCHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCC T ss_conf 99999997188651542502543265442468999999999999841796689999999998999986655312456886 Q ss_pred HHHHHHHHHCCCCC-CCCCCEECCCCCCCCCEEEEEEEEC-CEEEEEEEECCHHHHHHHHHHHHHHHC Q ss_conf 58898753202233-3343101020778884599999999-989999996898999999999999974 Q gi|254780940|r 158 KTELQEWAHAKFGV-TPEYKVTFRSGPDHDPRFTVVVEIS-GLAPAQGMDCSKRAAEQVAAAEVLKRE 223 (227) Q Consensus 158 K~~Lqe~~q~~~~~-~P~Y~~~~~~g~~~~~~f~v~v~v~-g~~~g~g~g~SkK~Ae~~AA~~AL~kl 223 (227) ||+||||.|+++.. +|+|+++.++||+|++.|+|.|+|+ +..+|+|+|+|||+|||.||+.||++| T Consensus 161 Kt~LQE~~Q~~~~~~~P~Y~l~~~~Gp~H~~~F~v~V~~~~~~~~g~G~G~SKKeAEQ~AA~~al~~l 228 (228) T TIGR02191 161 KTALQEWAQARGKPELPEYRLIKEEGPDHDKEFTVEVSVNGGEPLGEGKGKSKKEAEQAAAKAALEKL 228 (228) T ss_pred CHHHHHHHHHCCCCCCCEEEEEECCCCCCCCEEEEEEEECCCEEEEEEEECCHHHHHHHHHHHHHHHC T ss_conf 31789999854887672488874147889965899999738757888751776899999999999829 No 2 >PRK12371 ribonuclease III; Reviewed Probab=100.00 E-value=0 Score=479.54 Aligned_cols=227 Identities=55% Similarity=0.897 Sum_probs=218.4 Q ss_pred CCCCCHHHHHHHHCCCCCCHHHHHHHCCCHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHH Q ss_conf 97358899999836965898999984246121266766547788745868864547877641046887899888888874 Q gi|254780940|r 1 MSALRYSTLEKRIGYAFANRSLLEKALTHSSISHSYQESYERLEFLGDRILGLLISTLLFNHFDSAKEGELSVRFNSLVS 80 (227) Q Consensus 1 m~~~~~~~l~~~lgy~f~~~~ll~~A~th~S~~~~~~~~~erLEflGDavL~~~v~~~l~~~~p~~~eG~lt~lr~~lV~ 80 (227) |++.+++.||++|||+|+|++||.+||||+|+......|||||||||||||+++||+|||.+||+.+||+||++|+.+|| T Consensus 7 ~~~~~~~~le~~igy~F~d~~Ll~~AlTH~S~~~~~~~nyERLEFLGDaVL~lvvs~~Ly~~fP~~~EG~LT~~Rs~lV~ 86 (235) T PRK12371 7 LANKTASILEERTGHRFANKERLDRALTHSSVQAPAGGNYERLEFLGDRVLGLCVAEMLFEAFPDASEGELSVRLNALVN 86 (235) T ss_pred HCCCCHHHHHHHHCCCCCCHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHH T ss_conf 25252999999979800888999987178686667767615553023999999999999986898883257999999971 Q ss_pred HHHHHHHHHHCCCCCEEEECCCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCHHHHHCCCCCCCCCCCCCCCCHHHH Q ss_conf 43345454313877200103663123753133333266999999996415542200122102564311100013452588 Q gi|254780940|r 81 AETCSQVARELDLASFIRVSSDLRKDVCSFMTSIQADVVESLIAALYLDGGIEVAGTFVDKYWKQRALKSGKFRRDAKTE 160 (227) Q Consensus 81 n~~La~~a~~lgl~~~l~~~~~~~~~~~~~~~~ilad~fEA~iGAiy~d~G~~~~~~~i~~~~~~~~~~~~~~~~dpK~~ 160 (227) +++|+.+|.++||+++++++.++....++.+++++||+|||+|||||+|+|++.|+.||.++|.+.....+....|||+. T Consensus 87 ~~~La~iA~~lgL~~~i~~g~~~~~~~~~~~~silaD~~EAliGAiyLD~G~~~a~~fv~~~~~~~~~~~~~~~~d~Ks~ 166 (235) T PRK12371 87 AETCAAIADEIGLHDLIRTGSDVKKLTGKRLLNVRADVVEALIAVIYLDGGLEAARPFIQRYWQKRALETDAARRDAKTE 166 (235) T ss_pred HHHHHHHHHHCCHHHHHHHCCCHHHCCCCCCCHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHCCCCCCCHHHH T ss_conf 99999999875737765224462212885421088899999999999865799999999999888865214443577999 Q ss_pred HHHHHHCCCCCCCCCCEECCCCCCCCCEEEEEEEECCEEEEEEEECCHHHHHHHHHHHHHHHCCCCC Q ss_conf 9875320223333431010207788845999999999899999968989999999999999748899 Q gi|254780940|r 161 LQEWAHAKFGVTPEYKVTFRSGPDHDPRFTVVVEISGLAPAQGMDCSKRAAEQVAAAEVLKREGIWT 227 (227) Q Consensus 161 Lqe~~q~~~~~~P~Y~~~~~~g~~~~~~f~v~v~v~g~~~g~g~g~SkK~Ae~~AA~~AL~klgi~t 227 (227) ||||||+++...|.|+++.++||+|+|+|+|.|+++|..+|+|.|+|||+||+.||++||+|+|||- T Consensus 167 LqE~~q~~~~~~P~Y~~~~~~G~~h~~~F~v~v~i~~~~~~~G~G~SKK~AEq~AA~~aL~k~g~~k 233 (235) T PRK12371 167 LQEWAHQQGGVTPVYRIDSRSGPDHDPLFTVEVEVKGFAPETGEGRSKRIAEQVAAEKMLEREGVWK 233 (235) T ss_pred HHHHHHHHCCCCCEEEEEECCCCCCCCEEEEEEEECCEEEEEEEECCHHHHHHHHHHHHHHHHCCCC T ss_conf 9999997089997489830427898980899999999688998708999999999999999858866 No 3 >PRK00102 rnc ribonuclease III; Reviewed Probab=100.00 E-value=0 Score=443.68 Aligned_cols=221 Identities=39% Similarity=0.561 Sum_probs=208.0 Q ss_pred CCHHHHHHHHCCCCCCHHHHHHHCCCHHHCCC--CCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHH Q ss_conf 58899999836965898999984246121266--7665477887458688645478776410468878998888888744 Q gi|254780940|r 4 LRYSTLEKRIGYAFANRSLLEKALTHSSISHS--YQESYERLEFLGDRILGLLISTLLFNHFDSAKEGELSVRFNSLVSA 81 (227) Q Consensus 4 ~~~~~l~~~lgy~f~~~~ll~~A~th~S~~~~--~~~~~erLEflGDavL~~~v~~~l~~~~p~~~eG~lt~lr~~lV~n 81 (227) -++++||++|||+|+|++||.+||||+||.+. ...|||||||||||||+++||+|||.+||+.+||+||++|+++||+ T Consensus 2 ~~~~~le~~lg~~f~~~~ll~~AlTH~S~~~~~~~~~~~erLEfLGDavL~~~vs~~L~~~~p~~~eG~LT~~R~~lV~~ 81 (228) T PRK00102 2 KDLEELQKKLGYTFKDPELLIQALTHRSYANENKGLKHNERLEFLGDAVLNLVISEYLFHRFPDLDEGDLSKLRAALVRE 81 (228) T ss_pred CCHHHHHHHHCCCCCCHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHH T ss_conf 57999999959862888999998568172244778763489998659999999999999878899844899999998628 Q ss_pred HHHHHHHHHCCCCCEEEECCCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCHHHHHCCCCCCCCCC--CCCCCCHHH Q ss_conf 334545431387720010366312375313333326699999999641554220012210256431110--001345258 Q gi|254780940|r 82 ETCSQVARELDLASFIRVSSDLRKDVCSFMTSIQADVVESLIAALYLDGGIEVAGTFVDKYWKQRALKS--GKFRRDAKT 159 (227) Q Consensus 82 ~~La~~a~~lgl~~~l~~~~~~~~~~~~~~~~ilad~fEA~iGAiy~d~G~~~~~~~i~~~~~~~~~~~--~~~~~dpK~ 159 (227) ++|+.+|.++||++++++++++..+.++.+++++||+|||+|||||+|+|++.|+.||.++|.+..... .....|||+ T Consensus 82 ~~La~ia~~lgL~~~i~~s~~e~~~~~~~~~~ilaD~fEA~iGAiylD~G~~~~~~fv~~~~~~~l~~~~~~~~~~d~Ks 161 (228) T PRK00102 82 ESLAEIARELGLGEYLLLGKGEEKSGGRRRPSILADAFEALIGAIYLDSGLETARKFILKLFEPRIDEIDLGDLVKDYKT 161 (228) T ss_pred HHHHHHHHHCCHHHHHHHCCHHHHCCCCCCHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCHHH T ss_conf 89999999659899998633687739966500888999999989996267999999999999999863110444368799 Q ss_pred HHHHHHHCCCCCCCCCCEECCCCCCCCCEEEEEEEECCEEEEEEEECCHHHHHHHHHHHHHHHCC Q ss_conf 89875320223333431010207788845999999999899999968989999999999999748 Q gi|254780940|r 160 ELQEWAHAKFGVTPEYKVTFRSGPDHDPRFTVVVEISGLAPAQGMDCSKRAAEQVAAAEVLKREG 224 (227) Q Consensus 160 ~Lqe~~q~~~~~~P~Y~~~~~~g~~~~~~f~v~v~v~g~~~g~g~g~SkK~Ae~~AA~~AL~klg 224 (227) .||||||+.+...|+|+++.++||+|++.|+|+|+++|..+|+|+|+|||+||+.||++||++|. T Consensus 162 ~Lqe~~q~~~~~~p~Y~~~~~~g~~~~~~f~v~v~i~~~~~g~G~G~SkK~Ae~~AA~~AL~~Lk 226 (228) T PRK00102 162 RLQELLQGRGLPLPEYELVKEEGPAHDKEFTVEVIVNGKELGEGTGSSKKEAEQAAAKQALKKLK 226 (228) T ss_pred HHHHHHHHHCCCCCEEEEEEEECCCCCCCEEEEEEECCEEEEEEEECCHHHHHHHHHHHHHHHHH T ss_conf 99999998289998468863157999961899999999899998858999999999999999985 No 4 >COG0571 Rnc dsRNA-specific ribonuclease [Transcription] Probab=100.00 E-value=0 Score=434.00 Aligned_cols=226 Identities=41% Similarity=0.592 Sum_probs=215.2 Q ss_pred CCCCHHHHHHHHCCCCCCHHHHHHHCCCHHHCCCC--CCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHH Q ss_conf 73588999998369658989999842461212667--6654778874586886454787764104688789988888887 Q gi|254780940|r 2 SALRYSTLEKRIGYAFANRSLLEKALTHSSISHSY--QESYERLEFLGDRILGLLISTLLFNHFDSAKEGELSVRFNSLV 79 (227) Q Consensus 2 ~~~~~~~l~~~lgy~f~~~~ll~~A~th~S~~~~~--~~~~erLEflGDavL~~~v~~~l~~~~p~~~eG~lt~lr~~lV 79 (227) ....+..|++.+||+|+|++||.+||||+||.+++ ..|||||||||||||+++|+++||++||+.+||+||++|+.+| T Consensus 4 ~~~~~~~l~~~lg~~f~~~~lL~~AltH~S~~~e~~~~~~nERLEFLGDavL~l~vae~Lf~~yP~~~EG~Ls~~ra~lV 83 (235) T COG0571 4 MIKKLEALEKKLGYTFKDKELLEQALTHRSYANEHKAVENNERLEFLGDAVLGLVVAEYLFKKYPNLPEGELSKLRAALV 83 (235) T ss_pred CHHHHHHHHHHHCCCCCCHHHHHHHHCCCCHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHH T ss_conf 16899999998298978989999986474122346677523888751899999999999999789998778999999997 Q ss_pred HHHHHHHHHHHCCCCCEEEECCCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCHHHHHCCCCCCCCCCCCCC--CCH Q ss_conf 443345454313877200103663123753133333266999999996415542200122102564311100013--452 Q gi|254780940|r 80 SAETCSQVARELDLASFIRVSSDLRKDVCSFMTSIQADVVESLIAALYLDGGIEVAGTFVDKYWKQRALKSGKFR--RDA 157 (227) Q Consensus 80 ~n~~La~~a~~lgl~~~l~~~~~~~~~~~~~~~~ilad~fEA~iGAiy~d~G~~~~~~~i~~~~~~~~~~~~~~~--~dp 157 (227) |+++|+.+|+.+||++|+++++++..++++.+++++||+|||+|||||+|+|++.++.|+.++|.+.+....... +|| T Consensus 84 ~~~~La~ia~~l~l~~~l~lg~ge~~~gg~~~~silaD~~EAligAiylD~g~~~~~~~i~~l~~~~~~~~~~~~~~~D~ 163 (235) T COG0571 84 SEESLAEIARELGLGDYLRLGKGEEKSGGRRRESILADAFEALIGAIYLDSGLEAARKFILKLFLPRLEEIDAGDQFKDP 163 (235) T ss_pred HHHHHHHHHHHHCCCCHHHCCCCHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHCCCCCCCCCH T ss_conf 78999999998097423230577655289886239999999999999981780999999999999998631434312584 Q ss_pred HHHHHHHHHCCCCCCCCCCEECCCCCCCCCEEEEEEEECCEEEEEEEECCHHHHHHHHHHHHHHHCCCCC Q ss_conf 5889875320223333431010207788845999999999899999968989999999999999748899 Q gi|254780940|r 158 KTELQEWAHAKFGVTPEYKVTFRSGPDHDPRFTVVVEISGLAPAQGMDCSKRAAEQVAAAEVLKREGIWT 227 (227) Q Consensus 158 K~~Lqe~~q~~~~~~P~Y~~~~~~g~~~~~~f~v~v~v~g~~~g~g~g~SkK~Ae~~AA~~AL~klgi~t 227 (227) |++||||+|+++...|+|+++..+||+|++.|+|.|.+++..+|+|.|+|||+|||.||+.||+++++|. T Consensus 164 Kt~LQe~~q~~~~~~p~Y~~v~~~g~~h~~~F~v~v~v~~~~~g~G~G~skk~AEq~AA~~al~~l~~~~ 233 (235) T COG0571 164 KTRLQELLQAQGLVLPEYRLVKEEGPAHDKEFTVEVAVGGKELGTGKGRSKKEAEQAAAEQALKKLGVKE 233 (235) T ss_pred HHHHHHHHHHCCCCCCEEEEECCCCCCCCCEEEEEEEECCEEEEEECCCCHHHHHHHHHHHHHHHHCCCC T ss_conf 4899999996489997479840568877866899999899457773466889999999999999860304 No 5 >PRK12372 ribonuclease III; Reviewed Probab=100.00 E-value=0 Score=431.10 Aligned_cols=216 Identities=35% Similarity=0.496 Sum_probs=204.5 Q ss_pred CCHHHHHHHHCCCCCCHHHHHHHCCCHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHH Q ss_conf 58899999836965898999984246121266766547788745868864547877641046887899888888874433 Q gi|254780940|r 4 LRYSTLEKRIGYAFANRSLLEKALTHSSISHSYQESYERLEFLGDRILGLLISTLLFNHFDSAKEGELSVRFNSLVSAET 83 (227) Q Consensus 4 ~~~~~l~~~lgy~f~~~~ll~~A~th~S~~~~~~~~~erLEflGDavL~~~v~~~l~~~~p~~~eG~lt~lr~~lV~n~~ 83 (227) |.++.||++|||+|+|++||.+||||+||.. .||||||||||+||+++|+++||.+||+.+||.||++|+.||+.++ T Consensus 1 MpLs~LE~rLGY~Fkd~~LL~~ALTHRS~~~---~~NERLEFLGDAVLglvIae~Ly~~fP~~~EG~LSrlRA~LV~~~t 77 (425) T PRK12372 1 MPLSQLESRLRYEFRNAELLRQALTHRSHSA---THNERLEFLGDSVLNCAVAALLFQRFGKLDEGDLSRVRANLVKQQS 77 (425) T ss_pred CCHHHHHHHHCCEECCHHHHHHHHCCCCCCC---CCCCHHHCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHCHHH T ss_conf 9868999983977688899999851657888---8871022205999999999999987889885478999999969799 Q ss_pred HHHHHHHCCCCCEEEECCCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCHHHHHCCCCCCCCCC--CCCCCCHHHHH Q ss_conf 4545431387720010366312375313333326699999999641554220012210256431110--00134525889 Q gi|254780940|r 84 CSQVARELDLASFIRVSSDLRKDVCSFMTSIQADVVESLIAALYLDGGIEVAGTFVDKYWKQRALKS--GKFRRDAKTEL 161 (227) Q Consensus 84 La~~a~~lgl~~~l~~~~~~~~~~~~~~~~ilad~fEA~iGAiy~d~G~~~~~~~i~~~~~~~~~~~--~~~~~dpK~~L 161 (227) |+.+|++++|.+||++|+++..++++.+++||+|+|||+|||||+|+||+.++.||.++|.+.+..+ ....+||||+| T Consensus 78 LAeiAr~l~Lg~~L~LG~GE~kSGGr~R~SILADA~EAlIGAIYLD~G~eaA~~~I~rlf~~~L~~i~~~~~~KD~KT~L 157 (425) T PRK12372 78 LYEIAQALNISDGLRLGEGELRSGGFRRPSILADAFEAIIGAVFLDGGFEAAQGVIKRLYVPILDHIDPRTLGKDAKTLL 157 (425) T ss_pred HHHHHHHCCCCHHEEECCCHHHCCCCCCCHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCHHH T ss_conf 99999976962014236740104897760089999999887963135589999999999999986089552367800899 Q ss_pred HHHHHCCCCCCCCCCEECCCCCCCCCEEEEEEEECCEEE-EEEEECCHHHHHHHHHHHHHHH Q ss_conf 875320223333431010207788845999999999899-9999689899999999999997 Q gi|254780940|r 162 QEWAHAKFGVTPEYKVTFRSGPDHDPRFTVVVEISGLAP-AQGMDCSKRAAEQVAAAEVLKR 222 (227) Q Consensus 162 qe~~q~~~~~~P~Y~~~~~~g~~~~~~f~v~v~v~g~~~-g~g~g~SkK~Ae~~AA~~AL~k 222 (227) |||+|.++..+|+|.++..+|++|++.|+|.|.|.+..+ ..|.|.|+|.|||.||++||+. T Consensus 158 QE~LQ~rk~~LP~Y~Vv~~~G~aH~Q~F~V~C~V~~l~~~~~G~G~SRR~AEQ~AAk~ALee 219 (425) T PRK12372 158 QEYLQGHKIALPTYTVVATHGAAHNQQFEVECTVPKLDVKVSGSGASRRAAEQAAAKKALDE 219 (425) T ss_pred HHHHHHCCCCCCCEEEEEEECCCCCCEEEEEEEECCCCCEEEEEECCCHHHHHHHHHHHHHH T ss_conf 99985179999961786315477577079998854887314742377169999999999999 No 6 >KOG1817 consensus Probab=100.00 E-value=0 Score=325.14 Aligned_cols=219 Identities=32% Similarity=0.441 Sum_probs=196.6 Q ss_pred CHHHHHHHHCCCCCCHHHHHHHCCCHHHCCC--CCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHH Q ss_conf 8899999836965898999984246121266--76654778874586886454787764104688789988888887443 Q gi|254780940|r 5 RYSTLEKRIGYAFANRSLLEKALTHSSISHS--YQESYERLEFLGDRILGLLISTLLFNHFDSAKEGELSVRFNSLVSAE 82 (227) Q Consensus 5 ~~~~l~~~lgy~f~~~~ll~~A~th~S~~~~--~~~~~erLEflGDavL~~~v~~~l~~~~p~~~eG~lt~lr~~lV~n~ 82 (227) .+-++|+++|..|.+.+++.+|||-+|.... ...+|||||||||+||++++|++||.+||+.+||.||.+|+.+|||+ T Consensus 274 p~~~~e~~~g~vF~Hirlla~aft~rs~~~n~Lt~gHNqRLEFLGDSilqlv~T~ily~kFPdhhEGhLSlLRssLVsNe 353 (533) T KOG1817 274 PLTQFEEIIGIVFIHIRLLARAFTLRSIPFNHLTLGHNQRLEFLGDSILQLVMTEILYRKFPDHHEGHLSLLRSSLVSNE 353 (533) T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHCCH T ss_conf 50357998778999999999986315797125565256788886788999999999997587546436999999873627 Q ss_pred HHHHHHHHCCCCCEEEECCCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCHHHHHCCCCCCCCCC--CCCCCCHHHH Q ss_conf 34545431387720010366312375313333326699999999641554220012210256431110--0013452588 Q gi|254780940|r 83 TCSQVARELDLASFIRVSSDLRKDVCSFMTSIQADVVESLIAALYLDGGIEVAGTFVDKYWKQRALKS--GKFRRDAKTE 160 (227) Q Consensus 83 ~La~~a~~lgl~~~l~~~~~~~~~~~~~~~~ilad~fEA~iGAiy~d~G~~~~~~~i~~~~~~~~~~~--~~~~~dpK~~ 160 (227) +.+.+|..+|+++++........ ..+.+.|.+||+|||||||+|+|.|.+.|+.|+..++.|++... .....|||+. T Consensus 354 tqakva~~lgf~e~li~n~~~k~-~~~lk~K~~ADlfEAfiGaLyvD~~le~~~qf~~~l~~Prl~~fi~nq~wndpksk 432 (533) T KOG1817 354 TQAKVADDLGFHEYLITNFDLKD-FQNLKLKDYADLFEAFIGALYVDKGLEYCRQFLRVLFFPRLKEFIRNQDWNDPKSK 432 (533) T ss_pred HHHHHHHHHCCCHHHHHCCCHHH-HHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCHHH T ss_conf 89999998097353440766233-33124778999999998788526880899999999831789999874011582779 Q ss_pred HHHHHHCC------CCCCCCCCEECCCCCCCCCEEEEEEEECCEEEEEEEECCHHHHHHHHHHHHHHHCC Q ss_conf 98753202------23333431010207788845999999999899999968989999999999999748 Q gi|254780940|r 161 LQEWAHAK------FGVTPEYKVTFRSGPDHDPRFTVVVEISGLAPAQGMDCSKRAAEQVAAAEVLKREG 224 (227) Q Consensus 161 Lqe~~q~~------~~~~P~Y~~~~~~g~~~~~~f~v~v~v~g~~~g~g~g~SkK~Ae~~AA~~AL~klg 224 (227) ||++|... ....|.|++....||.+++.|+|.||++|+.+|+|+|+|.|.|+.+||.+||+++. T Consensus 433 Lqq~cl~~rys~~~epdip~y~V~~~~gpa~~r~y~Vavyf~gkrlat~~G~nik~Ae~rAA~~ALe~~~ 502 (533) T KOG1817 433 LQQCCLTLRYSLGGEPDIPLYKVLGAKGPANDRNYKVAVYFKGKRLATGVGSNIKQAEMRAAMQALENLK 502 (533) T ss_pred HHHHHHHHHCCCCCCCCCCEEEEECCCCCCCCCCEEEEEEECCEEEEECCCCHHHHHHHHHHHHHHHHHH T ss_conf 9999888741568888872378723468877873589999888788624674076887789999999987 No 7 >smart00535 RIBOc Ribonuclease III family. Probab=100.00 E-value=2.5e-36 Score=243.54 Aligned_cols=127 Identities=42% Similarity=0.583 Sum_probs=118.2 Q ss_pred HHHHHHCCCHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEC Q ss_conf 99998424612126676654778874586886454787764104688789988888887443345454313877200103 Q gi|254780940|r 21 SLLEKALTHSSISHSYQESYERLEFLGDRILGLLISTLLFNHFDSAKEGELSVRFNSLVSAETCSQVARELDLASFIRVS 100 (227) Q Consensus 21 ~ll~~A~th~S~~~~~~~~~erLEflGDavL~~~v~~~l~~~~p~~~eG~lt~lr~~lV~n~~La~~a~~lgl~~~l~~~ 100 (227) ++|.+||||+|+.... +||||||||||+||+++|++|||.+||+.+||.||.+|+.+|||++|+++|.++||+++++++ T Consensus 1 ~ll~~Alth~S~~~~~-~~yerLEfLGDavL~~~v~~~l~~~~p~~~eg~lt~~r~~lvsn~~La~ia~~lgL~~~i~~~ 79 (129) T smart00535 1 SLLLRALTHASYSNEH-EHNERLEFLGDAVLELVVTEYLYKKYPDLSEGDLSRLRSALVSNETLARLAKKLGLGEFIRLG 79 (129) T ss_pred CHHHHHHCCCCCCCCC-CCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHC T ss_conf 9788976461646788-755999998999999999999998588888017999999998588999999986909997626 Q ss_pred CCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCHHHHHCCCCCCCC Q ss_conf 663123753133333266999999996415542200122102564311 Q gi|254780940|r 101 SDLRKDVCSFMTSIQADVVESLIAALYLDGGIEVAGTFVDKYWKQRAL 148 (227) Q Consensus 101 ~~~~~~~~~~~~~ilad~fEA~iGAiy~d~G~~~~~~~i~~~~~~~~~ 148 (227) ++...+..+..++++||+|||+|||||+|+|++.|+.|+.++|.+.+. T Consensus 80 ~~~~~~~~~~~~ki~ad~~EAliGAiyld~G~~~~~~~l~~~~~~~l~ 127 (129) T smart00535 80 RGEAISGGRDKPSILADVFEALIGAIYLDSGLEAAREFIRDLLGPRLE 127 (129) T ss_pred CCHHHCCCCCCCCCHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHH T ss_conf 613213664466621069999999999976799999999999999986 No 8 >cd00593 RIBOc RIBOc. Ribonuclease III C terminal domain. This group consists of eukaryotic, bacterial and archeal ribonuclease III (RNAse III) proteins. RNAse III is a double stranded RNA-specific endonuclease. Prokaryotic RNAse III is important in post-transcriptional control of mRNA stability and translational efficiency. It is involved in the processing of ribosomal RNA precursors. Prokaryotic RNAse III also plays a role in the maturation of tRNA precursors and in the processing of phage and plasmid transcripts. Eukaryotic RNase III's participate (through direct cleavage) in rRNA processing, in processing of small nucleolar RNAs (snoRNAs) and snRNA's (components of the spliceosome). In eukaryotes RNase III or RNaseIII like enzymes such as Dicer are involved in RNAi (RNA interference) and miRNA (micro-RNA) gene silencing. Probab=100.00 E-value=6.8e-35 Score=234.69 Aligned_cols=129 Identities=40% Similarity=0.583 Sum_probs=118.4 Q ss_pred HHHHHHCCCHHHCCCC-CCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEE Q ss_conf 9999842461212667-665477887458688645478776410468878998888888744334545431387720010 Q gi|254780940|r 21 SLLEKALTHSSISHSY-QESYERLEFLGDRILGLLISTLLFNHFDSAKEGELSVRFNSLVSAETCSQVARELDLASFIRV 99 (227) Q Consensus 21 ~ll~~A~th~S~~~~~-~~~~erLEflGDavL~~~v~~~l~~~~p~~~eG~lt~lr~~lV~n~~La~~a~~lgl~~~l~~ 99 (227) .++.+||||+|+.... ..|||||||||||||+++|+.++|.+||+.+||.||++|+.+|||++|+++|.++||+++++. T Consensus 1 ~ll~~Alth~S~~~~~~~~~~erLEflGDavL~~~v~~~l~~~~p~~~~g~lt~~r~~lV~n~~L~~~a~~~gl~~~i~~ 80 (133) T cd00593 1 SLLLEALTHPSYANEHGRFNNERLEFLGDAVLELVVTEYLFKKFPDLSEGDLTRLRSALVSNETLARLARELGLGKYLRL 80 (133) T ss_pred CHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCHHHHHHH T ss_conf 97889764616012688743499999889999999999999858578876208999999739999999998871999860 Q ss_pred CCCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCHHHHHCCCCCCCCC Q ss_conf 36631237531333332669999999964155422001221025643111 Q gi|254780940|r 100 SSDLRKDVCSFMTSIQADVVESLIAALYLDGGIEVAGTFVDKYWKQRALK 149 (227) Q Consensus 100 ~~~~~~~~~~~~~~ilad~fEA~iGAiy~d~G~~~~~~~i~~~~~~~~~~ 149 (227) ++.........+++++||+|||+|||||+|+|++.++.|+..+|.+.... T Consensus 81 ~~~~~~~~~~~~~k~~aD~~EAliGAiyld~g~~~~~~~i~~l~~~~~~~ 130 (133) T cd00593 81 GKGEEKSGGRLRPKILADVFEALIGAIYLDGGFEAARKFLLRLLGPLIEE 130 (133) T ss_pred CCHHHHCCCCHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHH T ss_conf 87576548730256898999999999999647999999999999999976 No 9 >KOG3769 consensus Probab=99.91 E-value=1.1e-23 Score=165.67 Aligned_cols=217 Identities=21% Similarity=0.210 Sum_probs=183.4 Q ss_pred HHHHHHHHC-CCCCCHHHHHHHCCCHHHCCC-----------------CCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCC Q ss_conf 899999836-965898999984246121266-----------------76654778874586886454787764104688 Q gi|254780940|r 6 YSTLEKRIG-YAFANRSLLEKALTHSSISHS-----------------YQESYERLEFLGDRILGLLISTLLFNHFDSAK 67 (227) Q Consensus 6 ~~~l~~~lg-y~f~~~~ll~~A~th~S~~~~-----------------~~~~~erLEflGDavL~~~v~~~l~~~~p~~~ 67 (227) +.+|.++|| -.|. .+.+.+|||.+|+... ...+|+.|--.|...+++.|++||-.+||.++ T Consensus 65 l~afg~RL~~~~is-~~~l~ka~t~~s~~~~~kv~~~~lg~~~~~~~~~~~~N~~L~~~Gk~~~~~~v~~~l~~kyPrlP 143 (333) T KOG3769 65 LSAFGKRLQSEEIS-LSYLLKALTNLSFSYPEKVLRQQLGAETVAQVNPQYSNEELVEIGKQFLSFYVTEYLKCKYPRLP 143 (333) T ss_pred HHHHHHHHCCCCCC-HHHHHHHHHCCCCCCHHHHHHHHHCCHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCC T ss_conf 99988774442104-99999997173200648776665321046552577550889998899999999999997556885 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEECCCCCCCCCCC-CCCCCHHHHHHHHHHHHHCCCCCCCHHHHHCCCCCC Q ss_conf 7899888888874433454543138772001036631237531-333332669999999964155422001221025643 Q gi|254780940|r 68 EGELSVRFNSLVSAETCSQVARELDLASFIRVSSDLRKDVCSF-MTSIQADVVESLIAALYLDGGIEVAGTFVDKYWKQR 146 (227) Q Consensus 68 eG~lt~lr~~lV~n~~La~~a~~lgl~~~l~~~~~~~~~~~~~-~~~ilad~fEA~iGAiy~d~G~~~~~~~i~~~~~~~ 146 (227) +--+--+-+.+.+.++||++|..+|+.++++.-.-... ... .+....+++-|++|+++.+.|++.+++||...+... T Consensus 144 ~E~l~ai~n~ll~ee~LahiAt~lGie~l~~seeFp~~--~eisq~ess~~aI~Al~~~~~~ek~~~~v~dFI~~qi~~k 221 (333) T KOG3769 144 EEGLHAIVNGLLGEEVLAHIATHLGIEELGLSEEFPKV--GEISQDESSRRAIGALLGSVGLEKGFNFVRDFINDQILSK 221 (333) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCC--HHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH T ss_conf 89999999875218999999987538988622668994--3666788899999999832117777899999998775311 Q ss_pred CCCCCC--CCCCHHHHHHHHHHCCCCCCCCCCEECCCCCC-CCCEEEEEEEECCEEEEEEEECCHHHHHHHHHHHHHHHC Q ss_conf 111000--13452588987532022333343101020778-884599999999989999996898999999999999974 Q gi|254780940|r 147 ALKSGK--FRRDAKTELQEWAHAKFGVTPEYKVTFRSGPD-HDPRFTVVVEISGLAPAQGMDCSKRAAEQVAAAEVLKRE 223 (227) Q Consensus 147 ~~~~~~--~~~dpK~~Lqe~~q~~~~~~P~Y~~~~~~g~~-~~~~f~v~v~v~g~~~g~g~g~SkK~Ae~~AA~~AL~kl 223 (227) ...... ...+|...|.+.|+..+...|+++++.++|.. -.|.|.|++|.|.+.+|+|.|+|-+.|++.||++||.++ T Consensus 222 ~L~~~~m~ql~~P~~~L~~lckr~~l~epe~Rll~esGr~S~~PvyvVgiYs~kkllGqG~Gesl~~A~e~AA~dAL~k~ 301 (333) T KOG3769 222 DLDPREMWQLQWPRRLLSRLCKRRGLKEPESRLLAESGRNSAEPVYVVGIYSGKKLLGQGQGESLKLAEEQAARDALIKL 301 (333) T ss_pred CCCHHHHCCCCCHHHHHHHHHHHCCCCCCHHHHHHHHCCCCCCCEEEEEEECCCHHHCCCCCHHHHHHHHHHHHHHHHHH T ss_conf 02667641523669999999987487884068998716676675278886317412135852078999999999999999 Q ss_pred CC Q ss_conf 88 Q gi|254780940|r 224 GI 225 (227) Q Consensus 224 gi 225 (227) =. T Consensus 302 y~ 303 (333) T KOG3769 302 YD 303 (333) T ss_pred HC T ss_conf 72 No 10 >pfam00636 Ribonuclease_3 RNase3 domain. Probab=99.89 E-value=1.1e-23 Score=165.78 Aligned_cols=91 Identities=44% Similarity=0.705 Sum_probs=81.2 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEECCCCC-----CCCCCCCCCCC Q ss_conf 7788745868864547877641046887899888888874433454543138772001036631-----23753133333 Q gi|254780940|r 41 ERLEFLGDRILGLLISTLLFNHFDSAKEGELSVRFNSLVSAETCSQVARELDLASFIRVSSDLR-----KDVCSFMTSIQ 115 (227) Q Consensus 41 erLEflGDavL~~~v~~~l~~~~p~~~eG~lt~lr~~lV~n~~La~~a~~lgl~~~l~~~~~~~-----~~~~~~~~~il 115 (227) ||||||||+||++++++|+|.+||+.+||.||.+|+.+|||++|+.+|.++||++|++.++... .......++++ T Consensus 1 erLefLGD~vL~~~~~~~l~~~~p~~~eg~l~~~~~~lv~~~~L~~~a~~~gl~~~i~~~~~~~~~~~~~~~~~~~~k~~ 80 (96) T pfam00636 1 ERLEFLGDAVLELIVSEYLYEKYPDLSEGELTRLRSALVSNETLAKLARKLGLDKYIRRGRNALSKGEKAKSASLSPKVL 80 (96) T ss_pred CCHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHCCCCCCCCHHHCCCCCCCHHH T ss_conf 90998799999999999999878998766899999999748999999999797899860862101321221466540388 Q ss_pred HHHHHHHHHHHHHCCC Q ss_conf 2669999999964155 Q gi|254780940|r 116 ADVVESLIAALYLDGG 131 (227) Q Consensus 116 ad~fEA~iGAiy~d~G 131 (227) ||+|||+|||||+|+| T Consensus 81 ad~~EAliGAiyld~g 96 (96) T pfam00636 81 ADVFEALIGAIYLDGG 96 (96) T ss_pred HHHHHHHHHHHHHCCC T ss_conf 7899999999997679 No 11 >KOG0701 consensus Probab=99.84 E-value=1.4e-21 Score=152.71 Aligned_cols=133 Identities=33% Similarity=0.426 Sum_probs=109.2 Q ss_pred CCHHHHHHHHC--CCCCCH--------HHHHHHCCCHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHH Q ss_conf 58899999836--965898--------99998424612126676654778874586886454787764104688789988 Q gi|254780940|r 4 LRYSTLEKRIG--YAFANR--------SLLEKALTHSSISHSYQESYERLEFLGDRILGLLISTLLFNHFDSAKEGELSV 73 (227) Q Consensus 4 ~~~~~l~~~lg--y~f~~~--------~ll~~A~th~S~~~~~~~~~erLEflGDavL~~~v~~~l~~~~p~~~eG~lt~ 73 (227) ++.+.+++++. |.|.+. .++.+|||+.|+.. ..++||||+|||++|++.++.++|.+||+.+||.+|. T Consensus 979 ~~~E~~e~i~n~~~~Fs~~~~~i~~~~s~LLEAlT~~~~~~--s~s~Erle~Lgds~Lk~avsr~l~L~ypd~~Egqls~ 1056 (1606) T KOG0701 979 SDWEAVEKILNFRYVFSISLASIALSTSLLLEALTTSSCQD--SFSLERLELLGDSLLKLAVSRHLFLTYPDLDEGQLSR 1056 (1606) T ss_pred CCCCCCCCCCCCCEECCCCCCCCCCCHHHHHHHHHCCCCCC--CHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHH T ss_conf 44222102344000014122311255268999860576544--2007888766778887789999997287324106899 Q ss_pred HHHHHHHHHHHHHHHHHCCCCCEEEEC--CCC-----------------------------CC----------------C Q ss_conf 888887443345454313877200103--663-----------------------------12----------------3 Q gi|254780940|r 74 RFNSLVSAETCSQVARELDLASFIRVS--SDL-----------------------------RK----------------D 106 (227) Q Consensus 74 lr~~lV~n~~La~~a~~lgl~~~l~~~--~~~-----------------------------~~----------------~ 106 (227) +|+.+|++++++.+|...|+..+++.+ ... .. . T Consensus 1057 lr~~~~~~~nl~~la~~~gl~~~~~~~~fep~~~~~p~~~~~~~~~~k~~~~~~~~~~~~e~~e~~~df~e~~~~~~~~~ 1136 (1606) T KOG0701 1057 LRDVNVSNDNLARLAVKKGLYSYLRHEGFEPSRWWVPGQLDVNNVDCKDLSGDQNYILYKELDEKIKDFQEAMEKEDGDS 1136 (1606) T ss_pred HHHHCCCCCCHHHHHHCCCCHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCC T ss_conf 98724663102233220253544014442445111555666552001245443320012132233167887643037765 Q ss_pred ------CCCCCCCCCHHHHHHHHHHHHHCCCCCCCHHH Q ss_conf ------75313333326699999999641554220012 Q gi|254780940|r 107 ------VCSFMTSIQADVVESLIAALYLDGGIEVAGTF 138 (227) Q Consensus 107 ------~~~~~~~ilad~fEA~iGAiy~d~G~~~~~~~ 138 (227) .....++.++|++||++||+|+|+|+.....+ T Consensus 1137 ~~~~~~~~~~~~ks~adl~eaLlga~~vD~~~~~~~~~ 1174 (1606) T KOG0701 1137 RSKGGDHDWLAPKSPADLLEALLGAIYVDGGLLETFET 1174 (1606) T ss_pred CCCCCCCCEECCCCHHHHHHHHHHHHHHHCCCHHHHHH T ss_conf 23332120015887899999987764322220234457 No 12 >KOG0701 consensus Probab=99.81 E-value=5.7e-20 Score=142.88 Aligned_cols=203 Identities=24% Similarity=0.328 Sum_probs=138.2 Q ss_pred CHHHHHHHHCCCCCCHHHHHHHCCCHHHCCCC-CCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHH Q ss_conf 88999998369658989999842461212667-66547788745868864547877641046887899888888874433 Q gi|254780940|r 5 RYSTLEKRIGYAFANRSLLEKALTHSSISHSY-QESYERLEFLGDRILGLLISTLLFNHFDSAKEGELSVRFNSLVSAET 83 (227) Q Consensus 5 ~~~~l~~~lgy~f~~~~ll~~A~th~S~~~~~-~~~~erLEflGDavL~~~v~~~l~~~~p~~~eG~lt~lr~~lV~n~~ 83 (227) .+..+++.++|.|.+..++.+|+||-||..+. ..+||||||+||+|++..|++++|...|..++|.+|.+|+++|+|+- T Consensus 1370 ~~~~~e~~l~y~f~~~~~l~~a~th~s~~~~~~~~C~qrleflgd~vld~~it~hl~~~~~~~sp~~~td~rsa~vnn~~ 1449 (1606) T KOG0701 1370 SFGKFEEKLNYRFKLKPYLTQATTHASYIYNRITDCYQRLEFLGDAVLDYLITKHLYEDPRQHSPGVLTDLRSALVNNTI 1449 (1606) T ss_pred HHHHHHCCCCHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHCCCC T ss_conf 78765401106665410342001466312576630455677767765236665325445333472033322667641553 Q ss_pred HHHHHHHCCCCCEEEECCCCC------------C---------CCCCCCCCCCHHHHHHHHHHHHHCCCCCCCHHHHHCC Q ss_conf 454543138772001036631------------2---------3753133333266999999996415542200122102 Q gi|254780940|r 84 CSQVARELDLASFIRVSSDLR------------K---------DVCSFMTSIQADVVESLIAALYLDGGIEVAGTFVDKY 142 (227) Q Consensus 84 La~~a~~lgl~~~l~~~~~~~------------~---------~~~~~~~~ilad~fEA~iGAiy~d~G~~~~~~~i~~~ 142 (227) .+.+|.+.++++++..-.... . ...-.-+|.++|+||++.||||+|+|. --+-.+..+ T Consensus 1450 ~a~~av~~~~~K~~~~~~~~l~~~I~~~v~~~~q~~~~~~~~~~edievpKa~gdi~esiagai~~dsg~-~~~~~~~~~ 1528 (1606) T KOG0701 1450 FASLAVKADLHKFIIAASPGLIHNIDRFVSFQLQSNLDSLFGWEEDIEVPKALGDIFESIAGAIKLDSGN-MMEPCIEKF 1528 (1606) T ss_pred CHHHHHHHCCHHHHHHHCCCCCCCHHHHHHHHHHHCCCCCCCCHHHCCCCHHHHHHHHCCCCEEECCCCC-CCCHHHHCC T ss_conf 1256776212567776233126516778888876122457786121024044433321034400147665-410576507 Q ss_pred CCCCCCC--CCCCCCCHHHHHHHHHHCCCCCCCCCCEECCCCCCCCCEEEEEEEECCEEEEEEEECCHHHHHHHHHHHHH Q ss_conf 5643111--00013452588987532022333343101020778884599999999989999996898999999999999 Q gi|254780940|r 143 WKQRALK--SGKFRRDAKTELQEWAHAKFGVTPEYKVTFRSGPDHDPRFTVVVEISGLAPAQGMDCSKRAAEQVAAAEVL 220 (227) Q Consensus 143 ~~~~~~~--~~~~~~dpK~~Lqe~~q~~~~~~P~Y~~~~~~g~~~~~~f~v~v~v~g~~~g~g~g~SkK~Ae~~AA~~AL 220 (227) |..+-.. ......+|++.+-.-+++ +.. .+.-.+.|.+.+.....|.|...+.|+..|++.|+ T Consensus 1529 ~a~p~~s~~~E~~~~h~~~~~~~~~~k----------~~d-----~~~~~~tv~~~~~~~~~~~g~~~~~aK~s~~k~A~ 1593 (1606) T KOG0701 1529 WALPPRSPIRELLELHPERALFGKCEK----------VAD-----AGKVRVTVDVFNKEVFAGEGRNYRIAKASAAKAAL 1593 (1606) T ss_pred CCCCCCCCHHHHCCCCCEEECCCHHHH----------HHH-----CCCEEEEEEECCCCHHHHCCHHHHHHHHHHHHHHH T ss_conf 689985520000345540000230120----------011-----55157999841420022213123445666777999 Q ss_pred HHC Q ss_conf 974 Q gi|254780940|r 221 KRE 223 (227) Q Consensus 221 ~kl 223 (227) +.+ T Consensus 1594 ~ll 1596 (1606) T KOG0701 1594 KLL 1596 (1606) T ss_pred HHH T ss_conf 999 No 13 >KOG1817 consensus Probab=99.80 E-value=2.8e-20 Score=144.74 Aligned_cols=135 Identities=33% Similarity=0.488 Sum_probs=111.0 Q ss_pred HHHHHHHHCCCCCCHHHHHHHCCCHHHCCC-------------------------------------------------- Q ss_conf 899999836965898999984246121266-------------------------------------------------- Q gi|254780940|r 6 YSTLEKRIGYAFANRSLLEKALTHSSISHS-------------------------------------------------- 35 (227) Q Consensus 6 ~~~l~~~lgy~f~~~~ll~~A~th~S~~~~-------------------------------------------------- 35 (227) +.-||+.|||+|+|..|++.|+||||+... T Consensus 43 l~~~e~~i~y~f~~r~~~~lal~h~s~~~~~Gt~~dh~kns~tncg~r~~~yg~~~~~~~~kr~~gin~li~imk~l~~~ 122 (533) T KOG1817 43 LDHLEELIGYTFQDRCLLQLALTHPSHKLNYGTNPDHAKNSLTNCGIRQPKYGDRKEHIMTKRKLGINTLINIMKRLGVI 122 (533) T ss_pred HHHHHHHHCEEECCHHHHHHHHCCCHHHHHCCCCCHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCC T ss_conf 99999984713121678999851842776079991565403432475775532267777777775034777887650678 Q ss_pred -----CCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEECCCCCCCCCCC Q ss_conf -----766547788745868864547877641046887899888888874433454543138772001036631237531 Q gi|254780940|r 36 -----YQESYERLEFLGDRILGLLISTLLFNHFDSAKEGELSVRFNSLVSAETCSQVARELDLASFIRVSSDLRKDVCSF 110 (227) Q Consensus 36 -----~~~~~erLEflGDavL~~~v~~~l~~~~p~~~eG~lt~lr~~lV~n~~La~~a~~lgl~~~l~~~~~~~~~~~~~ 110 (227) ....||||||+||+|.+++++.++|..+|...+|.|...|+++|.|..++.+++++.++.|+...-+....-... T Consensus 123 ~~~~s~i~hnErle~lgdavve~~ss~hl~~~~~r~~eggLatyrta~vqnr~la~lakklrkd~fl~yahg~dl~~~~E 202 (533) T KOG1817 123 QPTHSVIKHNERLEFLGDAVVELLSSNHLYFMFPRLEEGGLATYRTAIVQNRHLAKLAKKLRKDEFLLYAHGYDLCFETE 202 (533) T ss_pred CCCHHHHHHHHHHHHHHHCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHH T ss_conf 87325767888999875210777777888873663002540578899997689999998877999999850732122788 Q ss_pred CCCCCHHHHHHHHHHHHHCCCCCCCHHHHH Q ss_conf 333332669999999964155422001221 Q gi|254780940|r 111 MTSIQADVVESLIAALYLDGGIEVAGTFVD 140 (227) Q Consensus 111 ~~~ilad~fEA~iGAiy~d~G~~~~~~~i~ 140 (227) -....+++|||++||+|+|+|...+..... T Consensus 203 ~Kha~an~feavi~a~~l~g~~~~~e~lfs 232 (533) T KOG1817 203 LKHAMANCFEAVIGAKYLDGGLVVAEKLFS 232 (533) T ss_pred HHHHHHHHHHHHHHHHHHHCCHHHHHHHHH T ss_conf 777799999998588887243278999987 No 14 >cd00048 DSRM Double-stranded RNA binding motif. Binding is not sequence specific but is highly specific for double stranded RNA. Found in a variety of proteins including dsRNA dependent protein kinase PKR, RNA helicases, Drosophila staufen protein, E. coli RNase III, RNases H1, and dsRNA dependent adenosine deaminases. Probab=99.64 E-value=5.2e-16 Score=118.51 Aligned_cols=68 Identities=40% Similarity=0.581 Sum_probs=65.7 Q ss_pred CHHHHHHHHHHCCCCCCCCCCEECCCCCCCCCEEEEEEEECCEEEEEEEECCHHHHHHHHHHHHHHHC Q ss_conf 52588987532022333343101020778884599999999989999996898999999999999974 Q gi|254780940|r 156 DAKTELQEWAHAKFGVTPEYKVTFRSGPDHDPRFTVVVEISGLAPAQGMDCSKRAAEQVAAAEVLKRE 223 (227) Q Consensus 156 dpK~~Lqe~~q~~~~~~P~Y~~~~~~g~~~~~~f~v~v~v~g~~~g~g~g~SkK~Ae~~AA~~AL~kl 223 (227) |||+.||||||+.+...|.|.++.++||+|+++|+|.|.++|..+++|.|+|||+||+.||+.||+.| T Consensus 1 ~pks~LqE~~q~~~~~~p~Y~~~~~~g~~h~~~F~~~v~i~~~~~~~g~g~sKK~Aeq~AA~~aL~~L 68 (68) T cd00048 1 NPKSLLQELAQKRGKPLPEYELVEEEGPDHAPRFTVEVTVGGKITGEGEGSSKKEAKQNAAEAALRKL 68 (68) T ss_pred CCHHHHHHHHHHCCCCCCEEEECCCCCCCCCCEEEEEEEECCEEEECCCCCCHHHHHHHHHHHHHHHC T ss_conf 95789999999749999979616540898773499999999988615777769999999999999849 No 15 >smart00358 DSRM Double-stranded RNA binding motif. Probab=99.60 E-value=2e-15 Score=114.90 Aligned_cols=67 Identities=40% Similarity=0.568 Sum_probs=63.6 Q ss_pred HHHHHHHHHHCCCCCCCCCCEECCCCCCCCCEEEEEEEECCEEEEEEEECCHHHHHHHHHHHHHHHCC Q ss_conf 25889875320223333431010207788845999999999899999968989999999999999748 Q gi|254780940|r 157 AKTELQEWAHAKFGVTPEYKVTFRSGPDHDPRFTVVVEISGLAPAQGMDCSKRAAEQVAAAEVLKREG 224 (227) Q Consensus 157 pK~~Lqe~~q~~~~~~P~Y~~~~~~g~~~~~~f~v~v~v~g~~~g~g~g~SkK~Ae~~AA~~AL~klg 224 (227) ||+.||||||+.+. .|.|.++.++||+|+++|+|.|.++|..++.|.|+|||.||+.||+.||++|. T Consensus 1 pks~L~E~~qk~~~-~~~y~~~~~~g~~h~~~F~~~v~i~g~~~~~g~g~sKK~Ae~~AA~~al~~L~ 67 (67) T smart00358 1 PKSLLQELAQKRGL-PPEYELVKEEGPDHAPRFTVTVKVGGEYTGEGEGSSKKEAKQRAAEAALRSLK 67 (67) T ss_pred CCHHHHHHHHHCCC-CCEEEEEEEECCCCCCEEEEEEEECCEEEECCCCCCHHHHHHHHHHHHHHHHC T ss_conf 94099999987798-98799997158997847999999999998435789999999999999999739 No 16 >KOG3732 consensus Probab=99.33 E-value=4e-12 Score=94.57 Aligned_cols=73 Identities=29% Similarity=0.330 Sum_probs=68.1 Q ss_pred CCCCCCHHHHHHHHHHCCCCCCCCCCEECCCCCCCCCEEEEEEEECCEEEEEEEECCHHHHHHHHHHHHHHHCC Q ss_conf 00134525889875320223333431010207788845999999999899999968989999999999999748 Q gi|254780940|r 151 GKFRRDAKTELQEWAHAKFGVTPEYKVTFRSGPDHDPRFTVVVEISGLAPAQGMDCSKRAAEQVAAAEVLKREG 224 (227) Q Consensus 151 ~~~~~dpK~~Lqe~~q~~~~~~P~Y~~~~~~g~~~~~~f~v~v~v~g~~~g~g~g~SkK~Ae~~AA~~AL~klg 224 (227) .....||.++|||+||++++..|+|.++.+.|++|.+.|++.|.+.+.. .+|+|.|||.|+++||+..|..+| T Consensus 138 ~~~~~NPI~~L~e~~q~k~~k~P~yelv~E~G~~~~rEFv~q~sv~~~~-~~GkG~sKKiAKRnAAeamLe~l~ 210 (339) T KOG3732 138 YGQVLNPIGRLQELAQAKKWKLPEYELVQESGVPHRREFVIQCSVENFT-EEGKGPSKKIAKRNAAEAMLESLG 210 (339) T ss_pred CCCCCCHHHHHHHHHHHHCCCCCCEEEEECCCCCCCCEEEEEEEECCEE-EECCCCHHHHHHHHHHHHHHHHHC T ss_conf 0125586999999999837899955887325777664489998750302-246785088999999999999836 No 17 >pfam00035 dsrm Double-stranded RNA binding motif. Putative motif shared by proteins that bind to dsRNA. At least some DSRM proteins seem to bind to specific RNA targets. Exemplified by Staufen, which is involved in localization of at least five different mRNAs in the early Drosophila embryo. Also by interferon-induced protein kinase in humans, which is part of the cellular response to dsRNA. Probab=99.33 E-value=4.9e-12 Score=94.03 Aligned_cols=66 Identities=36% Similarity=0.534 Sum_probs=60.6 Q ss_pred HHHHHHHHHHCCCCCCCCCCEECCCCCCCCCEEEEEEEECCEEEEEEEECCHHHHHHHHHHHHHHHC Q ss_conf 2588987532022333343101020778884599999999989999996898999999999999974 Q gi|254780940|r 157 AKTELQEWAHAKFGVTPEYKVTFRSGPDHDPRFTVVVEISGLAPAQGMDCSKRAAEQVAAAEVLKRE 223 (227) Q Consensus 157 pK~~Lqe~~q~~~~~~P~Y~~~~~~g~~~~~~f~v~v~v~g~~~g~g~g~SkK~Ae~~AA~~AL~kl 223 (227) ||+.||||||..+. .|.|..+...|++|++.|.|.|.++|..++.|.|+|||+||+.||..||+.| T Consensus 1 ~ks~L~e~~~~~~~-~~~~~~~~~~~~~~~~~F~~~v~v~~~~~~~g~g~sKK~A~~~AA~~aL~~L 66 (66) T pfam00035 1 PKSLLQELCQKKGK-KPPYEYVEEEGPSHSPTFTVTVTVGGKKYGTGTGSSKKEAKQLAAEKALQKL 66 (66) T ss_pred CCHHHHHHHHHCCC-CCCEEEEEEECCCCCCEEEEEEEECCEEEEECCCCCHHHHHHHHHHHHHHHC T ss_conf 94499999996295-9899999848899886599999979989874388889999999999999849 No 18 >KOG3732 consensus Probab=99.05 E-value=5.6e-10 Score=81.37 Aligned_cols=70 Identities=31% Similarity=0.366 Sum_probs=63.2 Q ss_pred CCHHHHHHHHHHCCCCCCCCCCEECCCCCCCCCEEEEEEEECCEEEEEEEECCHHHHHHHHHHHHHHHCCCC Q ss_conf 452588987532022333343101020778884599999999989999996898999999999999974889 Q gi|254780940|r 155 RDAKTELQEWAHAKFGVTPEYKVTFRSGPDHDPRFTVVVEISGLAPAQGMDCSKRAAEQVAAAEVLKREGIW 226 (227) Q Consensus 155 ~dpK~~Lqe~~q~~~~~~P~Y~~~~~~g~~~~~~f~v~v~v~g~~~g~g~g~SkK~Ae~~AA~~AL~klgi~ 226 (227) +-|.+.|||++.+.+. .|.|.+..++||.|++.|++.|.|. ...++|.|+|||.|+++||..+|..|.-+ T Consensus 38 KS~IS~l~E~~~r~~~-~v~fevl~eeGp~H~~~fv~rvtvg-~~~a~GeG~sKK~AKh~AA~~~L~~lk~l 107 (339) T KOG3732 38 KSPISLLQEYGLRRGL-TPVYEVLREEGPPHMPNFVFRVTVG-EITATGEGKSKKLAKHRAAEALLKELKKL 107 (339) T ss_pred CCHHHHHHHHHHHHCC-CCCEEEEECCCCCCCCCEEEEEEEE-EEEEECCCCCHHHHHHHHHHHHHHHHHHC T ss_conf 7708999999997089-7550542134886578768999986-46886378742688999999999998507 No 19 >KOG2777 consensus Probab=98.30 E-value=1.8e-06 Score=59.82 Aligned_cols=65 Identities=29% Similarity=0.347 Sum_probs=58.6 Q ss_pred CCCHHHHHHHHHHCCCCCCCCCCEECCCCCCCCCEEEEEEEECCEEEEEEEECCHHHHHHHHHHHHHHHCC Q ss_conf 34525889875320223333431010207788845999999999899999968989999999999999748 Q gi|254780940|r 154 RRDAKTELQEWAHAKFGVTPEYKVTFRSGPDHDPRFTVVVEISGLAPAQGMDCSKRAAEQVAAAEVLKREG 224 (227) Q Consensus 154 ~~dpK~~Lqe~~q~~~~~~P~Y~~~~~~g~~~~~~f~v~v~v~g~~~g~g~g~SkK~Ae~~AA~~AL~klg 224 (227) .++|.+.|.|+.+ .|.|......||.|.+.|.|.|.+||...-.| |.|||+|++.||..||+.+. T Consensus 89 ~~npv~ll~e~~~-----~~~~~~~~~~~~~~~~~F~~~~~vdg~~~~~~-~~sKk~ak~~aa~~al~~l~ 153 (542) T KOG2777 89 GKNPVSLLHELAN-----GLFFDFVNESGPQHAPKFVMSVVVDGRWFEGG-GRSKKEAKQEAAMAALQVLF 153 (542) T ss_pred CCCCHHHHHHHHC-----CCCEEEECCCCCCCCCEEEEEEEECCEECCCC-CCCHHHHHHHHHHHHHHHHH T ss_conf 6780587997750-----62434200578888860799999899873587-86237899999999999997 No 20 >KOG4334 consensus Probab=98.15 E-value=1.3e-06 Score=60.73 Aligned_cols=63 Identities=22% Similarity=0.254 Sum_probs=55.5 Q ss_pred HHHHHHHHCCCCCCCCCCEECCCCCCCCCEEEEEEEECCEEEEEEEECCHHHHHHHHHHHHHHHC Q ss_conf 88987532022333343101020778884599999999989999996898999999999999974 Q gi|254780940|r 159 TELQEWAHAKFGVTPEYKVTFRSGPDHDPRFTVVVEISGLAPAQGMDCSKRAAEQVAAAEVLKRE 223 (227) Q Consensus 159 ~~Lqe~~q~~~~~~P~Y~~~~~~g~~~~~~f~v~v~v~g~~~g~g~g~SkK~Ae~~AA~~AL~kl 223 (227) -.|.||.|.-....|+|..-+.+.+ ...|..+|.+|+..+|+|+|.|||.|+..||+.+|+.| T Consensus 379 CiLhEy~q~~lk~~pvyef~e~~n~--stpysa~v~~d~~~yGsG~g~sKK~Ak~~AAR~tLeiL 441 (650) T KOG4334 379 CILHEYAQQCLKSLPVYEFAENDNN--STPYSAGVLPDLFPYGSGVGASKKTAKLVAARDTLEIL 441 (650) T ss_pred EHHHHHHHHHHHHCCEEEHHHCCCC--CCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHH T ss_conf 3299999988642220003321588--98655411136500256645206777778899999975 No 21 >COG1939 Ribonuclease III family protein [Replication, recombination, and repair] Probab=97.77 E-value=4.8e-05 Score=51.01 Aligned_cols=98 Identities=22% Similarity=0.294 Sum_probs=65.2 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCEE--------EECCCCCCCCCCCC Q ss_conf 4778874586886454787764104688789988888887443345454313877200--------10366312375313 Q gi|254780940|r 40 YERLEFLGDRILGLLISTLLFNHFDSAKEGELSVRFNSLVSAETCSQVARELDLASFI--------RVSSDLRKDVCSFM 111 (227) Q Consensus 40 ~erLEflGDavL~~~v~~~l~~~~p~~~eG~lt~lr~~lV~n~~La~~a~~lgl~~~l--------~~~~~~~~~~~~~~ 111 (227) ==-|.|+||||+++.|-.|+...+.. .++.|.+.-.+.||.+..|.+-..+ .+++ +-|.+.. .... T Consensus 15 ~laLAy~GDAV~e~yVR~~~l~~g~~-k~~~lH~~a~~~VsAk~QA~il~~~--~~~Lte~E~~I~KRgRNak---s~T~ 88 (132) T COG1939 15 GLALAYLGDAVYELYVREYLLLKGKT-KPNDLHKRATAYVSAKAQALILKAL--LEFLTEEEEEIVKRGRNAK---SGTK 88 (132) T ss_pred HHHHHHHHHHHHHHHHHHHHHHCCCC-CHHHHHHHHHHHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHCCCC---CCCC T ss_conf 89999953599999999999722457-8689999999994588899999999--9986189999999701543---6789 Q ss_pred CC-------CCHHHHHHHHHHHHHCCCCCCCHHHHHCCC Q ss_conf 33-------332669999999964155422001221025 Q gi|254780940|r 112 TS-------IQADVVESLIAALYLDGGIEVAGTFVDKYW 143 (227) Q Consensus 112 ~~-------ilad~fEA~iGAiy~d~G~~~~~~~i~~~~ 143 (227) ++ -.+.-|||++|.+|+..-.+....++...+ T Consensus 89 ~kn~dv~tYr~sTgfEAliGyLyL~~~~eRL~ell~~~i 127 (132) T COG1939 89 PKNTDVETYRMSTGFEALIGYLYLTKQEERLEELLNKVI 127 (132) T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHH T ss_conf 887976788885019999999998455999999999998 No 22 >KOG2334 consensus Probab=95.20 E-value=0.0064 Score=37.94 Aligned_cols=138 Identities=20% Similarity=0.232 Sum_probs=85.0 Q ss_pred HHHHHHHHHHHHHHHHCCCCCEEEECCCCCCCCCCCCCCCC---HHHH---HHHHHHHHHCCCCCCCHHHH-HCCCCCCC Q ss_conf 88887443345454313877200103663123753133333---2669---99999996415542200122-10256431 Q gi|254780940|r 75 FNSLVSAETCSQVARELDLASFIRVSSDLRKDVCSFMTSIQ---ADVV---ESLIAALYLDGGIEVAGTFV-DKYWKQRA 147 (227) Q Consensus 75 r~~lV~n~~La~~a~~lgl~~~l~~~~~~~~~~~~~~~~il---ad~f---EA~iGAiy~d~G~~~~~~~i-~~~~~~~~ 147 (227) ...+....+.+.+++-.+++++....+.+...... +.+.+ +|+. |.+. |.| +-.+- ...|..+. T Consensus 299 ~~~~~~~~~~~~i~k~~~i~d~~~~~~~el~~~~~-k~Rl~~~~~d~~~~~~~le-----~~~---~l~i~~r~~f~r~~ 369 (477) T KOG2334 299 GKRIQAAQTVAQICKAFEIEDIYATLKRELDTPVC-KKRLLVSPADTVNLAERLE-----DLS---ALAIHGRKIFDRPT 369 (477) T ss_pred HHHHHCCHHHHHHHHHHCCHHHHHHHHHHHCCCCC-CCEEEECCCHHHHHHHHHH-----HCC---CHHHHHCCCCCCCC T ss_conf 66765305599998886014587764775156110-0024407300055766677-----501---02342011125667 Q ss_pred CCCCCCCCCHHHHHHHHHHCCCCCCCCCCEECCCCCCCCCEEEEEEEECCEEEEEE-EECCHHHHHHHHHHHHHHHCCCC Q ss_conf 11000134525889875320223333431010207788845999999999899999-96898999999999999974889 Q gi|254780940|r 148 LKSGKFRRDAKTELQEWAHAKFGVTPEYKVTFRSGPDHDPRFTVVVEISGLAPAQG-MDCSKRAAEQVAAAEVLKREGIW 226 (227) Q Consensus 148 ~~~~~~~~dpK~~Lqe~~q~~~~~~P~Y~~~~~~g~~~~~~f~v~v~v~g~~~g~g-~g~SkK~Ae~~AA~~AL~klgi~ 226 (227) ... -+..||..|..||-......|.|.++... +..|...+..+|..+-.+ +.+++|.|+|.||..+|.++|+| T Consensus 370 ~pa--~~~~~k~~l~~~~~~~~~~~~~ye~~~~~----d~lf~si~~~~~~~~~ssi~~~n~k~aeq~aa~~~l~~s~l~ 443 (477) T KOG2334 370 DPA--KWDTPKMVLADLCVKTKANGPVYETVQRT----DKLFSSIATARGQKYNSSIWSPNKKSAEQDAAIVALRKSNLW 443 (477) T ss_pred CCC--CCCCHHHHHHHHHHHHCCCCCCHHHHHHH----HHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHCCCC T ss_conf 876--78878789887435312787601355666----666677732521322123468433367888899998754762 Q ss_pred C Q ss_conf 9 Q gi|254780940|r 227 T 227 (227) Q Consensus 227 t 227 (227) - T Consensus 444 e 444 (477) T KOG2334 444 E 444 (477) T ss_pred H T ss_conf 1 No 23 >KOG3792 consensus Probab=92.30 E-value=0.058 Score=32.04 Aligned_cols=48 Identities=35% Similarity=0.487 Sum_probs=37.3 Q ss_pred EECCCCCCCCCEEEEEEEECCEEEEEEEECCHHHHHHHHHHHHHHHCCC Q ss_conf 0102077888459999999998999999689899999999999997488 Q gi|254780940|r 177 VTFRSGPDHDPRFTVVVEISGLAPAQGMDCSKRAAEQVAAAEVLKREGI 225 (227) Q Consensus 177 ~~~~~g~~~~~~f~v~v~v~g~~~g~g~g~SkK~Ae~~AA~~AL~klgi 225 (227) ++...+|.|.++|+.++.+|+.. .++.|.|++.|+.-||++.|+.+|. T Consensus 396 Lvv~t~Ps~~~~~t~e~r~~~~~-~~a~gps~~~~~wh~~~k~lq~~~~ 443 (816) T KOG3792 396 LVVDTKPSHRPRRTMEVRVNGLP-AEAEGPSKKTAKWHAARKRLQNEGR 443 (816) T ss_pred CEECCCCCCCCHHHHHHHHCCCC-CCCCCCCCCCCHHHHHHHHHHCCCC T ss_conf 42126876620243566632774-1147862123038888877632589 No 24 >KOG3792 consensus Probab=91.45 E-value=0.22 Score=28.54 Aligned_cols=49 Identities=27% Similarity=0.321 Sum_probs=43.1 Q ss_pred CCCEECCCC-CCCCCEEEEEEEECCEEEEEEEECCHHHHHHHHHHHHHHHC Q ss_conf 431010207-78884599999999989999996898999999999999974 Q gi|254780940|r 174 EYKVTFRSG-PDHDPRFTVVVEISGLAPAQGMDCSKRAAEQVAAAEVLKRE 223 (227) Q Consensus 174 ~Y~~~~~~g-~~~~~~f~v~v~v~g~~~g~g~g~SkK~Ae~~AA~~AL~kl 223 (227) .|+++.+.| -.|+++|..+|.++|++ +.|.+.+++.|...|+-.|++++ T Consensus 520 k~El~set~~gs~~~R~v~gV~rvG~~-akG~~~~gd~a~~~a~Lca~~pt 569 (816) T KOG3792 520 KYELPSETGTGSHDKRFVKGVMRVGIL-AKGLLLNGDRAVELALLCAEKPT 569 (816) T ss_pred CEECCCCCCCCCCCCCEEEEEEEEEHH-HCCCCCCCHHHHHHHHHHCCCCC T ss_conf 210454467888886035543430010-00444464178889887515766 No 25 >pfam03368 dsRNA_bind Double stranded RNA binding domain. This domain is a divergent double stranded RNA-binding domain. It is found in members of the Dicer protein family which function in RNA interference, an evolutionarily conserved mechanism for gene silencing using double-stranded RNA (dsRNA) molecules. Probab=87.23 E-value=2.1 Score=22.51 Aligned_cols=63 Identities=24% Similarity=0.164 Sum_probs=40.6 Q ss_pred HHHHHHHHHC-----CCCCCCCCCEECCCCCCCCCEEEEEEEECC-----EEEEEEEECCHHHHHHHHHHHHHHH---CC Q ss_conf 5889875320-----223333431010207788845999999999-----8999999689899999999999997---48 Q gi|254780940|r 158 KTELQEWAHA-----KFGVTPEYKVTFRSGPDHDPRFTVVVEISG-----LAPAQGMDCSKRAAEQVAAAEVLKR---EG 224 (227) Q Consensus 158 K~~Lqe~~q~-----~~~~~P~Y~~~~~~g~~~~~~f~v~v~v~g-----~~~g~g~g~SkK~Ae~~AA~~AL~k---lg 224 (227) .+.|..||.+ -....|+|.+...+ +.|.|+|.+-- ...|. .-.|++.|++.||-+|.++ +| T Consensus 2 i~lL~~yCa~LP~d~f~~~~P~~~~~~~~-----~~~~~~v~LP~~splr~i~g~-~~~~~~~Ak~~aAf~ac~~L~~~G 75 (91) T pfam03368 2 ISLLHRYCAKLPSDPFTKLKPEFSVEPDE-----GGYVCTVILPLNSPVREIVGP-PMKSKRLAKQSAAFEACKKLHELG 75 (91) T ss_pred HHHHHHHHHCCCCCCCCCCCEEEEEEECC-----CCEEEEEECCCCCCCCEEECC-CCCCHHHHHHHHHHHHHHHHHHCC T ss_conf 78999998218998655774169999659-----917999987899985735877-331189999999999999999868 Q ss_pred CC Q ss_conf 89 Q gi|254780940|r 225 IW 226 (227) Q Consensus 225 i~ 226 (227) .+ T Consensus 76 ~L 77 (91) T pfam03368 76 EL 77 (91) T ss_pred CC T ss_conf 76 No 26 >pfam11469 DUF3204 Protein of unknown function (DUF3204). This archaeal family of proteins has no known function. Probab=79.07 E-value=4.8 Score=20.23 Aligned_cols=84 Identities=20% Similarity=0.218 Sum_probs=49.5 Q ss_pred HHHHHHHHHHHHHHHHHH--HHCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEECCCCCCCCCCCCCCCCHHHHH Q ss_conf 887458688645478776--410468878998888888744334545431387720010366312375313333326699 Q gi|254780940|r 43 LEFLGDRILGLLISTLLF--NHFDSAKEGELSVRFNSLVSAETCSQVARELDLASFIRVSSDLRKDVCSFMTSIQADVVE 120 (227) Q Consensus 43 LEflGDavL~~~v~~~l~--~~~p~~~eG~lt~lr~~lV~n~~La~~a~~lgl~~~l~~~~~~~~~~~~~~~~ilad~fE 120 (227) |.-+||+.++|++|--|- .-+|... -|-|.+|+---..-||...+. + +....-.+|.-| T Consensus 3 Lak~GDSLiNfl~SlALse~lG~Ptg~----------rVPnasLaiale~agL~~~~~---P------Rtdkh~kGd~aE 63 (120) T pfam11469 3 LAKLGDSLINFLVSLALTELLGKPTGV----------RVPNASLAIALESSGLSKLGK---P------RTDKHAKGDAAE 63 (120) T ss_pred HHHHHHHHHHHHHHHHHHHHHCCCCCC----------CCCCHHHHHHHHHHHHHHCCC---C------CCCCCCCCHHHH T ss_conf 777738999999999999993898878----------788739999999870651389---7------657677518999 Q ss_pred HHHHHHHHCCCCC--CCHHHHHCCCCC Q ss_conf 9999996415542--200122102564 Q gi|254780940|r 121 SLIAALYLDGGIE--VAGTFVDKYWKQ 145 (227) Q Consensus 121 A~iGAiy~d~G~~--~~~~~i~~~~~~ 145 (227) |+++--|+.+-+. .+-.++..-+.+ T Consensus 64 A~iAyAWleg~is~eEavEil~~nl~~ 90 (120) T pfam11469 64 ALLAYAWLKGSISCEEAVEILYTNLDD 90 (120) T ss_pred HHHHHHHHHCCCCHHHHHHHHHHCCCH T ss_conf 999999980535199999999964745 No 27 >PRK07009 consensus Probab=58.29 E-value=8.2 Score=18.84 Aligned_cols=82 Identities=12% Similarity=0.113 Sum_probs=44.1 Q ss_pred HHHHHHHHHHHH---------HHHHHHHHHHHCCCCCH------HHHHHHHHHHH-HHHHHHHHHHHCCCCCEEEECCCC Q ss_conf 477887458688---------64547877641046887------89988888887-443345454313877200103663 Q gi|254780940|r 40 YERLEFLGDRIL---------GLLISTLLFNHFDSAKE------GELSVRFNSLV-SAETCSQVARELDLASFIRVSSDL 103 (227) Q Consensus 40 ~erLEflGDavL---------~~~v~~~l~~~~p~~~e------G~lt~lr~~lV-~n~~La~~a~~lgl~~~l~~~~~~ 103 (227) -|-+||+||++| +|+-.++--..+|.+.+ ..|..-|...- ...+|-.+|+.++++..=+.--++ T Consensus 75 ~efl~Fi~~a~LVaHNA~FD~~FLn~EL~r~G~~~~~~~~~~viDTL~lAR~~~Pg~~~sLdaLc~R~~I~~~~r~~HgA 154 (241) T PRK07009 75 DQIRDFVQDAELIIHNAPFDLGFLDAEFALLGLPPFTEHCAGVIDTLVQAKQMFPGKRNSLDALCDRFGISNAHRTLHGA 154 (241) T ss_pred HHHHHHHCCCEEEEECHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHCCCCCCCCCCCCC T ss_conf 99999966992788676999999999999839973102444476799999997899987889999982869887330242 Q ss_pred CCCCCCCCCCCCHHHHHHHHHHH Q ss_conf 12375313333326699999999 Q gi|254780940|r 104 RKDVCSFMTSIQADVVESLIAAL 126 (227) Q Consensus 104 ~~~~~~~~~~ilad~fEA~iGAi 126 (227) .. ...+||+++=++.|+- T Consensus 155 L~-----Da~lLa~vyl~mtgGq 172 (241) T PRK07009 155 LL-----DSELLAEVYLAMTRGQ 172 (241) T ss_pred HH-----HHHHHHHHHHHHHCCC T ss_conf 87-----7999999999983897 No 28 >PRK06859 consensus Probab=53.69 E-value=8.4 Score=18.76 Aligned_cols=82 Identities=12% Similarity=0.107 Sum_probs=43.9 Q ss_pred HHHHHHHHHHHH---------HHHHHHHHHHHCCCCCH------HHHHHHHHHHH-HHHHHHHHHHHCCCCCEEEECCCC Q ss_conf 477887458688---------64547877641046887------89988888887-443345454313877200103663 Q gi|254780940|r 40 YERLEFLGDRIL---------GLLISTLLFNHFDSAKE------GELSVRFNSLV-SAETCSQVARELDLASFIRVSSDL 103 (227) Q Consensus 40 ~erLEflGDavL---------~~~v~~~l~~~~p~~~e------G~lt~lr~~lV-~n~~La~~a~~lgl~~~l~~~~~~ 103 (227) .|-++|+||++| +|+=.++--...|...+ ..|..-|...- ...+|-.+|+.++++..-|.--++ T Consensus 83 ~efl~Fi~~a~LVaHNa~FD~~FLn~El~r~g~~~~~~~~~~viDTL~lAR~~~Pg~~~sLdaLc~r~~id~~~R~~HgA 162 (253) T PRK06859 83 QEFIDYIKGAELLIHNAPFDVGFMDYEFRKLNLNVKTDDICLVTDTLQMARQMYPGKRNNLDALCDRLGIDNSKRTLHGA 162 (253) T ss_pred HHHHHHHCCCEEEEECHHHHHHHHHHHHHHCCCCCCCCCCCCEEEHHHHHHHHCCCCCCCHHHHHHHCCCCCCCCCCCCH T ss_conf 99999967997999571888999999999749996532200113399999987879977999999973998766330132 Q ss_pred CCCCCCCCCCCCHHHHHHHHHHH Q ss_conf 12375313333326699999999 Q gi|254780940|r 104 RKDVCSFMTSIQADVVESLIAAL 126 (227) Q Consensus 104 ~~~~~~~~~~ilad~fEA~iGAi 126 (227) .. ...+|||++=++.|+- T Consensus 163 ll-----Da~lLa~VYl~mtGGQ 180 (253) T PRK06859 163 LL-----DAEILADVYLMMTGGQ 180 (253) T ss_pred HH-----HHHHHHHHHHHHCCCC T ss_conf 88-----8999999999872675 No 29 >KOG2783 consensus Probab=51.95 E-value=4.5 Score=20.41 Aligned_cols=42 Identities=21% Similarity=0.248 Sum_probs=24.1 Q ss_pred HHHHHHHHHCCCCCCCCCCEECCCCCCCCCEEEEEEEECCEE Q ss_conf 588987532022333343101020778884599999999989 Q gi|254780940|r 158 KTELQEWAHAKFGVTPEYKVTFRSGPDHDPRFTVVVEISGLA 199 (227) Q Consensus 158 K~~Lqe~~q~~~~~~P~Y~~~~~~g~~~~~~f~v~v~v~g~~ 199 (227) |..|--++.--++...+|+-+...-|-..|.|..+|+..|.. T Consensus 231 k~~l~~L~~~Lf~~~~~~rwV~~yfpft~ps~eleI~~~~~w 272 (436) T KOG2783 231 KQTLEGLCDELFGKEVEYRWVDAYFPFTHPSWELEIYFKGEW 272 (436) T ss_pred HHHHHHHHHHHCCCHHHEEHEEEECCCCCCCEEEEEEECCCC T ss_conf 999988999862604411011057666898758999965876 No 30 >TIGR01854 lipid_A_lpxH UDP-2,3-diacylglucosamine hydrolase; InterPro: IPR010138 This entry represents LpxH, or UDP-2,3-diacylglucosamine hydrolase (or pyrophosphatase), which is an essential enzyme in Escherichia coli that catalyses the fourth step in lipid A biosynthesis. This reaction involves pyrophosphate bond hydrolysis of the precursor UDP-2,3-diacylglucosamine to yield 2,3-diacylglucosamine 1-phosphate and UMP . Several Gram-negative bacteria have homologues of LpxH and/or LpxH2, while others have only distant orthologues of LpxH or LpxH2, or lack these enzymes altogether .; GO: 0016462 pyrophosphatase activity, 0009245 lipid A biosynthetic process, 0005737 cytoplasm. Probab=48.81 E-value=3.3 Score=21.27 Aligned_cols=52 Identities=15% Similarity=-0.049 Sum_probs=29.8 Q ss_pred HHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEECCCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCHH Q ss_conf 77641046887899888888874433454543138772001036631237531333332669999999964155422001 Q gi|254780940|r 58 LLFNHFDSAKEGELSVRFNSLVSAETCSQVARELDLASFIRVSSDLRKDVCSFMTSIQADVVESLIAALYLDGGIEVAGT 137 (227) Q Consensus 58 ~l~~~~p~~~eG~lt~lr~~lV~n~~La~~a~~lgl~~~l~~~~~~~~~~~~~~~~ilad~fEA~iGAiy~d~G~~~~~~ 137 (227) ||-..-|+.++++|.=|++... +.+..-=||+|+|||.|| |-+.+.... T Consensus 8 HL~~~~P~iTa~Fl~FL~~~A~---------------------------G~AdALYILGDLFeaWIG----DD~~~~l~~ 56 (241) T TIGR01854 8 HLSEERPDITALFLDFLREEAR---------------------------GKADALYILGDLFEAWIG----DDDPSALAR 56 (241) T ss_pred CCCCCCCHHHHHHHHHHHHHCC---------------------------CCCHHHHHHCCHHHCEEC----CCCCCHHHH T ss_conf 5882460789999999875233---------------------------400002210120001146----897217999 Q ss_pred HHH Q ss_conf 221 Q gi|254780940|r 138 FVD 140 (227) Q Consensus 138 ~i~ 140 (227) =|. T Consensus 57 ~va 59 (241) T TIGR01854 57 SVA 59 (241) T ss_pred HHH T ss_conf 999 No 31 >PRK13184 pknD serine/threonine-protein kinase; Reviewed Probab=47.05 E-value=21 Score=16.25 Aligned_cols=38 Identities=16% Similarity=0.294 Sum_probs=23.1 Q ss_pred HHHHHHHHHHHHHHHHHH---------HHHHCCCCCHHHHHHHHHHHHH Q ss_conf 778874586886454787---------7641046887899888888874 Q gi|254780940|r 41 ERLEFLGDRILGLLISTL---------LFNHFDSAKEGELSVRFNSLVS 80 (227) Q Consensus 41 erLEflGDavL~~~v~~~---------l~~~~p~~~eG~lt~lr~~lV~ 80 (227) --||+||.|..---..+| -+++||+.+| +.+++..+|. T Consensus 551 apleylgkalvyq~~~~~~eeik~~~la~kry~~hp~--i~~l~~h~~~ 597 (933) T PRK13184 551 APLEYLGKALVYQRLGEYNEEIKSLLLALKRYSQHPE--IPRLKDHVVY 597 (933) T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCC--CHHHHHHHHH T ss_conf 7578888899998730078999999999975679987--3678989999 No 32 >PRK06022 consensus Probab=39.03 E-value=24 Score=15.93 Aligned_cols=80 Identities=15% Similarity=0.151 Sum_probs=38.3 Q ss_pred HHHHHHHHHHH---------HHHHHHHHHHHCCCCCHHH-H-H--HHHHHHH-HHHHHHHHHHHCCCCCEEEECCCCCCC Q ss_conf 77887458688---------6454787764104688789-9-8--8888887-443345454313877200103663123 Q gi|254780940|r 41 ERLEFLGDRIL---------GLLISTLLFNHFDSAKEGE-L-S--VRFNSLV-SAETCSQVARELDLASFIRVSSDLRKD 106 (227) Q Consensus 41 erLEflGDavL---------~~~v~~~l~~~~p~~~eG~-l-t--~lr~~lV-~n~~La~~a~~lgl~~~l~~~~~~~~~ 106 (227) +-++|+||++| +|+-.++--...|...... + | .-|...- ...+|-.+|+.++++.--|.--++.. T Consensus 76 ~fl~Fi~~a~LVaHNA~FD~gFLn~El~r~G~~~~~~~~viDTL~LAR~~~Pg~~~sLdaLc~r~~Id~~~R~~HgAL~- 154 (234) T PRK06022 76 EFLEFFDGARLVAHNATFDLGFINAEFARLGQPEITSERVVDTLALARRKHPMGPNSLDALCRRYGIDNSHRTKHGALL- 154 (234) T ss_pred HHHHHHCCCEEEEECHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHCCCCCCCHHHHHHHCCCCCCCCCCCCCHH- T ss_conf 9999818985999557872999999999859987778887469999998688998898999998399977735376288- Q ss_pred CCCCCCCCCHHHHHHHHHH Q ss_conf 7531333332669999999 Q gi|254780940|r 107 VCSFMTSIQADVVESLIAA 125 (227) Q Consensus 107 ~~~~~~~ilad~fEA~iGA 125 (227) -..+||+++=.+.|+ T Consensus 155 ----Da~lLa~VyleL~GG 169 (234) T PRK06022 155 ----DSELLAEVYIELIGG 169 (234) T ss_pred ----HHHHHHHHHHHHCCC T ss_conf ----899999999997288 No 33 >pfam04034 DUF367 Domain of unknown function (DUF367). Probab=37.36 E-value=19 Score=16.59 Aligned_cols=40 Identities=30% Similarity=0.412 Sum_probs=27.9 Q ss_pred CCCCCCCHHHHHHHHHHHHHCCCCCCCHHHHHCC-CCCCCCC Q ss_conf 3133333266999999996415542200122102-5643111 Q gi|254780940|r 109 SFMTSIQADVVESLIAALYLDGGIEVAGTFVDKY-WKQRALK 149 (227) Q Consensus 109 ~~~~~ilad~fEA~iGAiy~d~G~~~~~~~i~~~-~~~~~~~ 149 (227) -+++-.|+ +.||+.+|+|+-+-.+.++.++..| |.+.... T Consensus 61 YGKP~kLs-~vEAlAAaLyI~G~~~~A~~lL~~FkWG~~Fl~ 101 (128) T pfam04034 61 YGKPCKLS-CVEALAAALYIVGFKDEASELLSKFKWGHTFLE 101 (128) T ss_pred CCCCCCCC-HHHHHHHHHHHCCCHHHHHHHHHCCCCCHHHHH T ss_conf 68876212-799999999994999999999850897178999 No 34 >pfam06754 PhnG Phosphonate metabolism protein PhnG. This family consists of several bacterial phosphonate metabolism protein PhnG sequences. In Escherichia coli, the phn operon encodes proteins responsible for the uptake and breakdown of phosphonates. The exact function of PhnG is unknown, however it is thought likely that along with six other proteins PhnG makes up the the C-P (carbon-phosphorus) lyase. Probab=36.49 E-value=32 Score=15.19 Aligned_cols=36 Identities=19% Similarity=0.183 Sum_probs=27.5 Q ss_pred EEEEEEEECCEEEEEEE--ECCHHHHHHHHHHHHHHHC Q ss_conf 59999999998999999--6898999999999999974 Q gi|254780940|r 188 RFTVVVEISGLAPAQGM--DCSKRAAEQVAAAEVLKRE 223 (227) Q Consensus 188 ~f~v~v~v~g~~~g~g~--g~SkK~Ae~~AA~~AL~kl 223 (227) +-.|.|.+++-.+|-|. |.+|+.||.-|--+||-|- T Consensus 65 VTRc~VrL~~G~~G~~yv~GRdk~~AelaA~~DALlQ~ 102 (147) T pfam06754 65 VTRAAVRLASGTVGHSYVLGRDKRHAELAALIDALLQD 102 (147) T ss_pred EEEEEEEECCCCEEEEEEECCCHHHHHHHHHHHHHHCC T ss_conf 88899994899756887635899999999999998479 No 35 >PRK06631 consensus Probab=36.46 E-value=14 Score=17.43 Aligned_cols=40 Identities=13% Similarity=0.086 Sum_probs=23.9 Q ss_pred HHHHHHHHHHCCCCCEEEECCCCCCCCCCCCCCCCHHHHHHHHHH Q ss_conf 433454543138772001036631237531333332669999999 Q gi|254780940|r 81 AETCSQVARELDLASFIRVSSDLRKDVCSFMTSIQADVVESLIAA 125 (227) Q Consensus 81 n~~La~~a~~lgl~~~l~~~~~~~~~~~~~~~~ilad~fEA~iGA 125 (227) ..+|..+|+.++++.--+..-++.. -..++|++|=++.|+ T Consensus 136 ~~sLdaLc~r~~I~~s~r~~H~AL~-----DA~llA~Vyl~l~gG 175 (229) T PRK06631 136 KYNLDALCKRFKVDNSGRQLHGALK-----DAALLAEVYVELTGG 175 (229) T ss_pred CCCHHHHHHHCCCCCCCCCCCCCHH-----HHHHHHHHHHHHHCC T ss_conf 8899999998499999855568689-----999999999997178 No 36 >PRK00394 transcription factor; Reviewed Probab=34.80 E-value=34 Score=15.02 Aligned_cols=27 Identities=33% Similarity=0.380 Sum_probs=18.1 Q ss_pred CCEEEEEEEECCEEEEEEEECCHHHHHH Q ss_conf 8459999999998999999689899999 Q gi|254780940|r 186 DPRFTVVVEISGLAPAQGMDCSKRAAEQ 213 (227) Q Consensus 186 ~~~f~v~v~v~g~~~g~g~g~SkK~Ae~ 213 (227) +|.-++-++..|+.+-+|. +|..++++ T Consensus 139 ~pk~~~liF~sGkivitGa-ks~~~~~~ 165 (178) T PRK00394 139 DPKVVVLLFGSGKLVITGA-KSEEDAEK 165 (178) T ss_pred CCCEEEEEECCCEEEEECC-CCHHHHHH T ss_conf 9978999977984999866-99999999 No 37 >TIGR02195 heptsyl_trn_II lipopolysaccharide heptosyltransferase II; InterPro: IPR011910 This family consists of examples of ADP-heptose:LPS heptosyltransferase II, an enzyme of LPS inner core region biosynthesis. LPS, composed of lipid A, a core region, and O antigen, is found in the outer membrane of Gram-negative bacteria.; GO: 0016757 transferase activity transferring glycosyl groups, 0009103 lipopolysaccharide biosynthetic process. Probab=34.44 E-value=26 Score=15.79 Aligned_cols=24 Identities=21% Similarity=0.409 Sum_probs=18.6 Q ss_pred HHHHHHHHHHHHHHHHHHHCCCCC Q ss_conf 874586886454787764104688 Q gi|254780940|r 44 EFLGDRILGLLISTLLFNHFDSAK 67 (227) Q Consensus 44 EflGDavL~~~v~~~l~~~~p~~~ 67 (227) .|+||+|+.-..=.-|.++||+.. T Consensus 8 sWVGDmvMaQ~Lf~~Lk~~yP~~~ 31 (361) T TIGR02195 8 SWVGDMVMAQSLFRLLKKRYPDAV 31 (361) T ss_pred CCHHHHHHHHHHHHHHHHHCCCCE T ss_conf 736555676899999998589838 No 38 >PRK08816 consensus Probab=32.78 E-value=13 Score=17.52 Aligned_cols=82 Identities=17% Similarity=0.151 Sum_probs=41.6 Q ss_pred HHHHHHHHHHHH---------HHHHHHHHHH--HCCCCC-----HHHHHHHHHHHH-HHHHHHHHHHHCCCCCEEEECCC Q ss_conf 477887458688---------6454787764--104688-----789988888887-44334545431387720010366 Q gi|254780940|r 40 YERLEFLGDRIL---------GLLISTLLFN--HFDSAK-----EGELSVRFNSLV-SAETCSQVARELDLASFIRVSSD 102 (227) Q Consensus 40 ~erLEflGDavL---------~~~v~~~l~~--~~p~~~-----eG~lt~lr~~lV-~n~~La~~a~~lgl~~~l~~~~~ 102 (227) -|-++|+||++| +|+=.++-.. .+|... ...|..-|...= ...+|-.+|+.++++..=|.--+ T Consensus 75 ~efl~Fi~ds~LVaHNa~FDi~FLn~El~r~g~~~~~~~~~~~v~DTl~lAr~~~Pg~~nsLDaLc~r~~id~~~R~~Hg 154 (244) T PRK08816 75 DEFLAYIDGAELIIHNAAFDLGFLDNELSLLGDQYGRIVDRATVVDTLMMARERYPGQRNSLDALCKRLGVDNSHRQLHG 154 (244) T ss_pred HHHHHHHCCCEEEEECCHHHHHHHHHHHHHHCCCCCCCCCCCCEEEHHHHHHHHCCCCCCCHHHHHHHCCCCCCCCCCCC T ss_conf 99999828998999663652989999999848875676431010438999998787997789999997497887735014 Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHH Q ss_conf 312375313333326699999999 Q gi|254780940|r 103 LRKDVCSFMTSIQADVVESLIAAL 126 (227) Q Consensus 103 ~~~~~~~~~~~ilad~fEA~iGAi 126 (227) +.. ...+|||++=++.|+- T Consensus 155 ALl-----Da~lLa~VYl~mtgGq 173 (244) T PRK08816 155 ALL-----DAQILADVYIALTSGQ 173 (244) T ss_pred HHH-----HHHHHHHHHHHHCCCC T ss_conf 888-----7999999999974786 No 39 >COG2042 Uncharacterized conserved protein [Function unknown] Probab=32.00 E-value=25 Score=15.82 Aligned_cols=39 Identities=28% Similarity=0.372 Sum_probs=27.2 Q ss_pred CCCCCCHHHHHHHHHHHHHCCCCCCCHHHHHCC-CCCCCCC Q ss_conf 133333266999999996415542200122102-5643111 Q gi|254780940|r 110 FMTSIQADVVESLIAALYLDGGIEVAGTFVDKY-WKQRALK 149 (227) Q Consensus 110 ~~~~ilad~fEA~iGAiy~d~G~~~~~~~i~~~-~~~~~~~ 149 (227) +++=.| .+.||+++|+|+-+-.+.+..++..| |.+..+. T Consensus 110 Gkp~kL-ss~EAlaAaLYI~G~~deA~~lls~F~WG~~Fle 149 (179) T COG2042 110 GKPFKL-SSAEALAAALYIVGFKDEASELLSKFKWGHTFLE 149 (179) T ss_pred CCCCHH-CHHHHHHHHHHHHCCHHHHHHHHHHCCCCHHHHH T ss_conf 875010-4499999999982769799999842760188999 No 40 >PRK08858 consensus Probab=31.80 E-value=22 Score=16.14 Aligned_cols=40 Identities=13% Similarity=0.042 Sum_probs=22.6 Q ss_pred HHHHHHHHHHCCCCCEEEECCCCCCCCCCCCCCCCHHHHHHHHHH Q ss_conf 433454543138772001036631237531333332669999999 Q gi|254780940|r 81 AETCSQVARELDLASFIRVSSDLRKDVCSFMTSIQADVVESLIAA 125 (227) Q Consensus 81 n~~La~~a~~lgl~~~l~~~~~~~~~~~~~~~~ilad~fEA~iGA 125 (227) ..+|-.+|+.++++.-=|.--++.. -..+||+++=++.|+ T Consensus 147 ~~sLdaLc~r~~Id~s~R~~HgALl-----Da~lLa~Vyl~mtgG 186 (246) T PRK08858 147 RNNLDVLCERYGIDNSHRTLHGALL-----DAEILADVYLLMTGG 186 (246) T ss_pred CCCHHHHHHHCCCCCCCCCCCCHHH-----HHHHHHHHHHHHCCC T ss_conf 8888999998198988834023088-----899999999997289 No 41 >PRK02287 hypothetical protein; Provisional Probab=31.59 E-value=27 Score=15.67 Aligned_cols=41 Identities=29% Similarity=0.355 Sum_probs=27.7 Q ss_pred CCCCCCCCHHHHHHHHHHHHHCCCCCCCHHHHHCC-CCCCCCC Q ss_conf 53133333266999999996415542200122102-5643111 Q gi|254780940|r 108 CSFMTSIQADVVESLIAALYLDGGIEVAGTFVDKY-WKQRALK 149 (227) Q Consensus 108 ~~~~~~ilad~fEA~iGAiy~d~G~~~~~~~i~~~-~~~~~~~ 149 (227) +-+++-.|+ +.||+.+|+|+-+-.+.+..++..| |.+.... T Consensus 99 NYGkP~kLs-~vEAlAAaLyI~G~~~~A~~lL~~FkWG~~Fl~ 140 (169) T PRK02287 99 NYGKPCKLS-SVEAFAAALYILGYKEEAEKILSKFKWGHTFLE 140 (169) T ss_pred CCCCCCCCC-HHHHHHHHHHHCCCHHHHHHHHHCCCCCHHHHH T ss_conf 668876212-799999999994999999999850897278999 No 42 >KOG2146 consensus Probab=31.56 E-value=38 Score=14.70 Aligned_cols=73 Identities=21% Similarity=0.276 Sum_probs=39.0 Q ss_pred CCCCCHHH-HHHHHCCCCCCHHHHHHHCCCHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCC------------ Q ss_conf 97358899-99983696589899998424612126676654778874586886454787764104688------------ Q gi|254780940|r 1 MSALRYST-LEKRIGYAFANRSLLEKALTHSSISHSYQESYERLEFLGDRILGLLISTLLFNHFDSAK------------ 67 (227) Q Consensus 1 m~~~~~~~-l~~~lgy~f~~~~ll~~A~th~S~~~~~~~~~erLEflGDavL~~~v~~~l~~~~p~~~------------ 67 (227) |+.++|.+ |++++...=-|.++|.-=+|- .-||-|-|--|-|++||....=-..+|+-. T Consensus 22 mkqmKF~~~lekkVDmsKvnleVlkPWItk--------rvneilgfEDdVViefvynqLee~k~ldpkkmQiNlTGFLng 93 (354) T KOG2146 22 MKQMKFPACLEKKVDMSKVNLEVLKPWITK--------RVNEILGFEDDVVIEFVYNQLEEAKNLDPKKMQINLTGFLNG 93 (354) T ss_pred HHHCCCHHHHHHHCCHHHCCHHHHHHHHHH--------HHHHHHCCCCCHHHHHHHHHHHHHCCCCCHHEEEEEEHHCCC T ss_conf 986353777765312433034453389988--------788763664203599988777651278813146521000254 Q ss_pred ---HHHHHHHHHHHHHH Q ss_conf ---78998888888744 Q gi|254780940|r 68 ---EGELSVRFNSLVSA 81 (227) Q Consensus 68 ---eG~lt~lr~~lV~n 81 (227) -.+|-+|.+.|+++ T Consensus 94 rnAreFmgeLW~LliS~ 110 (354) T KOG2146 94 RNAREFMGELWSLLISE 110 (354) T ss_pred CCHHHHHHHHHHHHHHH T ss_conf 20899999999998720 No 43 >pfam11324 DUF3126 Protein of unknown function (DUF3126). This family of proteins with unknown function appear to be restricted to Alphaproteobacteria. Probab=30.77 E-value=40 Score=14.61 Aligned_cols=40 Identities=25% Similarity=0.233 Sum_probs=25.8 Q ss_pred HHHHHHHHCCCCCCCCCCEECCCCCCCCCEEEEEEEECCEEEEEE Q ss_conf 889875320223333431010207788845999999999899999 Q gi|254780940|r 159 TELQEWAHAKFGVTPEYKVTFRSGPDHDPRFTVVVEISGLAPAQG 203 (227) Q Consensus 159 ~~Lqe~~q~~~~~~P~Y~~~~~~g~~~~~~f~v~v~v~g~~~g~g 203 (227) .+||.|+++.++. |...+.....++ =.|+|+++++.+|.- T Consensus 3 ~klq~yLr~~F~n-~~i~v~~r~k~~----DSaEV~~~~EFiGvi 42 (63) T pfam11324 3 KKLQAYLKRKFGN-PTLRVKARPKKG----DSAEVYIGDEFIGVL 42 (63) T ss_pred HHHHHHHHHHHCC-CCEEEECCCCCC----CCEEEEECCEEEEEE T ss_conf 8999999997199-965997679999----876998589899999 No 44 >COG4148 ModC ABC-type molybdate transport system, ATPase component [Inorganic ion transport and metabolism] Probab=30.66 E-value=19 Score=16.59 Aligned_cols=60 Identities=25% Similarity=0.510 Sum_probs=36.2 Q ss_pred CCCHHHHHHHHCCCCCCHHHHHHHCCCHHHCCCCCCCHH----HH-HHHHHHHHHHHHHHHHHHHCCC-CCHHH Q ss_conf 358899999836965898999984246121266766547----78-8745868864547877641046-88789 Q gi|254780940|r 3 ALRYSTLEKRIGYAFANRSLLEKALTHSSISHSYQESYE----RL-EFLGDRILGLLISTLLFNHFDS-AKEGE 70 (227) Q Consensus 3 ~~~~~~l~~~lgy~f~~~~ll~~A~th~S~~~~~~~~~e----rL-EflGDavL~~~v~~~l~~~~p~-~~eG~ 70 (227) ++.+..=+.++||-|+|-+| |-|=|...+. .|- +. +| |.+.++.-..+|..+||. ++-|+ T Consensus 68 ~i~lp~~~RriGYVFQDARL----FpH~tVrgNL--~YG~~~~~~~~f--d~iv~lLGI~hLL~R~P~~LSGGE 133 (352) T COG4148 68 GIFLPPEKRRIGYVFQDARL----FPHYTVRGNL--RYGMWKSMRAQF--DQLVALLGIEHLLDRYPGTLSGGE 133 (352) T ss_pred CCCCCHHHHEEEEEEECCCC----CCCEEEECCH--HHHCCCCCHHHH--HHHHHHHCCHHHHHCCCCCCCCCH T ss_conf 74467546113567400201----6651773220--010143536779--999998484867850877567615 No 45 >cd00652 TBP_TLF TATA box binding protein (TBP): Present in archaea and eukaryotes, TBPs are transcription factors that recognize promoters and initiate transcription. TBP has been shown to be an essential component of three different transcription initiation complexes: SL1, TFIID and TFIIIB, directing transcription by RNA polymerases I, II and III, respectively. TBP binds directly to the TATA box promoter element, where it nucleates polymerase assembly, thus defining the transcription start site. TBP's binding in the minor groove induces a dramatic DNA bending while its own structure barely changes. The conserved core domain of TBP, which binds to the TATA box, has a bipartite structure, with intramolecular symmetry generating a saddle-shaped structure that sits astride the DNA. New members of the TBP family, called TBP-like proteins (TBLP, TLF, TLP) or TBP-related factors (TRF1, TRF2,TRP), are similar to the core domain of TBPs, with identical or chemically similar amino acids at many Probab=30.12 E-value=41 Score=14.55 Aligned_cols=26 Identities=19% Similarity=0.333 Sum_probs=16.3 Q ss_pred CEEEEEEEECCEEEEEEEECCHHHHHH Q ss_conf 459999999998999999689899999 Q gi|254780940|r 187 PRFTVVVEISGLAPAQGMDCSKRAAEQ 213 (227) Q Consensus 187 ~~f~v~v~v~g~~~g~g~g~SkK~Ae~ 213 (227) +.-++-++..|+.+-+|. +|..++++ T Consensus 138 pk~~~liF~sGkvvitGa-ks~~~~~~ 163 (174) T cd00652 138 PKVVLLIFVSGKIVITGA-KSREDIYE 163 (174) T ss_pred CCEEEEEECCCEEEEECC-CCHHHHHH T ss_conf 978999977987999747-99999999 No 46 >cd04518 TBP_archaea archaeal TATA box binding protein (TBP): TBPs are transcription factors present in archaea and eukaryotes, that recognize promoters and initiate transcription. TBP has been shown to be an essential component of three different transcription initiation complexes: SL1, TFIID and TFIIIB, directing transcription by RNA polymerases I, II and III, respectively. TBP binds directly to the TATA box promoter element, where it nucleates polymerase assembly, thus defining the transcription start site. TBP's binding in the minor groove induces a dramatic DNA bending while its own structure barely changes. The conserved core domain of TBP, which binds to the TATA box, has a bipartite structure, with intramolecular symmetry generating a saddle-shaped structure that sits astride the DNA. Probab=29.31 E-value=42 Score=14.46 Aligned_cols=27 Identities=22% Similarity=0.346 Sum_probs=17.9 Q ss_pred CCEEEEEEEECCEEEEEEEECCHHHHHH Q ss_conf 8459999999998999999689899999 Q gi|254780940|r 186 DPRFTVVVEISGLAPAQGMDCSKRAAEQ 213 (227) Q Consensus 186 ~~~f~v~v~v~g~~~g~g~g~SkK~Ae~ 213 (227) +|.-++-++..|+.+-+|. +|..+++. T Consensus 136 ~pk~~~liF~SGKivitGa-ks~~~~~~ 162 (174) T cd04518 136 EPKVVLLLFSSGKMVITGA-KSEEDAKR 162 (174) T ss_pred CCCEEEEEECCCEEEEECC-CCHHHHHH T ss_conf 9978999987984999867-99999999 No 47 >LOAD_cdc45 consensus Probab=28.74 E-value=43 Score=14.40 Aligned_cols=73 Identities=18% Similarity=0.191 Sum_probs=33.7 Q ss_pred HHCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEECCCCCCCCCCCCCCCC-HHHHHHHHHHHHHCCCCCCCHHHH Q ss_conf 4104688789988888887443345454313877200103663123753133333-266999999996415542200122 Q gi|254780940|r 61 NHFDSAKEGELSVRFNSLVSAETCSQVARELDLASFIRVSSDLRKDVCSFMTSIQ-ADVVESLIAALYLDGGIEVAGTFV 139 (227) Q Consensus 61 ~~~p~~~eG~lt~lr~~lV~n~~La~~a~~lgl~~~l~~~~~~~~~~~~~~~~il-ad~fEA~iGAiy~d~G~~~~~~~i 139 (227) ++|..++.. +|..+ .+.|.+.|.++||.++...+-. ..-+.+. ++- +|+++|+.+-+ ++|-+.-+.|. T Consensus 338 Q~y~~Md~~----lK~~L--~~~l~k~a~~ygL~~l~~~sF~-r~~Gyk~--~lsAsD~v~a~~AlL--E~~~~~~~~~~ 406 (578) T LOAD_cdc45 338 QTYEAMDLS----LKREL--VSMLEKSADKYGLTDIIYQGFT-RTLGFRD--KLAASDVVEALSALL--EMGTARRRSGT 406 (578) T ss_pred HHHHHCCHH----HHHHH--HHHHHHHHHHCCCCCEEECCEE-EEECCCC--CEEHHHHHHHHHHHH--HCCCCCCCCHH T ss_conf 455427999----99999--9999998876699752526456-7852665--202899999989998--33854456588 Q ss_pred HCCCC Q ss_conf 10256 Q gi|254780940|r 140 DKYWK 144 (227) Q Consensus 140 ~~~~~ 144 (227) .+||. T Consensus 407 ~nFw~ 411 (578) T LOAD_cdc45 407 SNFYE 411 (578) T ss_pred HHHHH T ss_conf 89999 No 48 >pfam00333 Ribosomal_S5 Ribosomal protein S5, N-terminal domain. Probab=28.55 E-value=43 Score=14.38 Aligned_cols=39 Identities=13% Similarity=0.041 Sum_probs=27.0 Q ss_pred CCCEEEEEEEECCE--E--EEEEEECCHHHHHHHHHHHHHHHC Q ss_conf 88459999999998--9--999996898999999999999974 Q gi|254780940|r 185 HDPRFTVVVEISGL--A--PAQGMDCSKRAAEQVAAAEVLKRE 223 (227) Q Consensus 185 ~~~~f~v~v~v~g~--~--~g~g~g~SkK~Ae~~AA~~AL~kl 223 (227) ....|.+-|.+++. . +|.|.+..-..|-++|-..|-++| T Consensus 20 r~~~f~alvvVGn~~G~vG~G~gKa~ev~~Ai~KA~~~Ak~nm 62 (67) T pfam00333 20 RRFSFRALVVVGDKNGHVGLGEGKAKEVPGAIRKAIEDAKLNL 62 (67) T ss_pred CCEEEEEEEEEECCCCCEEEEEEECCCHHHHHHHHHHHHHHCC T ss_conf 6115899999977998397746643618999999999998676 No 49 >TIGR02706 P_butyryltrans phosphate butyryltransferase; InterPro: IPR014079 Members of this family are phosphate butyryltransferase enzymes, also called phosphotransbutyrylase. In general, this enzyme is found in butyrate-producing anaerobic bacteria, encoded next to the gene for butyrate kinase. Together, these two enzymes represent what may be the less common of two pathways for butyrate production from butyryl-CoA. The alternative is transfer of the CoA group to acetate by butyryl-CoA:acetate CoA transferase. This entry does not include the homologue from Thermotoga maritima, whose activity on butyryl-CoA is only 30 0f its activity with acetyl-CoA.. Probab=28.21 E-value=44 Score=14.34 Aligned_cols=51 Identities=18% Similarity=0.275 Sum_probs=34.8 Q ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCC--CCEEEECCCCCC Q ss_conf 65477887458688645478776410468878998888888744334545431387--720010366312 Q gi|254780940|r 38 ESYERLEFLGDRILGLLISTLLFNHFDSAKEGELSVRFNSLVSAETCSQVARELDL--ASFIRVSSDLRK 105 (227) Q Consensus 38 ~~~erLEflGDavL~~~v~~~l~~~~p~~~eG~lt~lr~~lV~n~~La~~a~~lgl--~~~l~~~~~~~~ 105 (227) +.|+||=||- +-=|..||++.+ +..+|+|..= +|+..|+ ++--.++.-|-- T Consensus 127 P~~dRLl~lT---------DaAfN~yP~Lk~------K~~ii~NaV~--VAha~Gi~~PkVA~l~AVEvV 179 (295) T TIGR02706 127 PGFDRLLFLT---------DAAFNIYPELKD------KVQIINNAVK--VAHAIGIEVPKVAVLAAVEVV 179 (295) T ss_pred CCCCHHHHHH---------HHHHCCCCCHHH------HHHHHHHHHH--HHHCCCCCCCCEEEECCEEEE T ss_conf 9855143231---------266502878789------9999764755--023217886861153026356 No 50 >pfam07125 DUF1378 Protein of unknown function (DUF1378). This family consists of hypothetical bacterial and phage proteins of around 59 residues in length. Bacterial members of this family seem to be specific to Enterobacteria. The function of this family is unknown. Probab=27.96 E-value=21 Score=16.26 Aligned_cols=30 Identities=27% Similarity=0.526 Sum_probs=23.2 Q ss_pred HHHHHHHHHHH-CCCCCCCHHHHHCCCCCCC Q ss_conf 69999999964-1554220012210256431 Q gi|254780940|r 118 VVESLIAALYL-DGGIEVAGTFVDKYWKQRA 147 (227) Q Consensus 118 ~fEA~iGAiy~-d~G~~~~~~~i~~~~~~~~ 147 (227) -|...|.++|+ .+|+.+++.++.+-+.... T Consensus 10 YFCtvVc~lYL~sGGYk~iR~~~rrkID~~A 40 (59) T pfam07125 10 YFCTVVCALYLVSGGYKVIRNYIRRKIDDAA 40 (59) T ss_pred HHHHHHHHHHHHHCCHHHHHHHHHHHHHHHH T ss_conf 9999999999983439999999999875999 No 51 >KOG3302 consensus Probab=27.64 E-value=45 Score=14.28 Aligned_cols=17 Identities=18% Similarity=0.536 Sum_probs=10.5 Q ss_pred CEEEEEEEECCEEEEEE Q ss_conf 45999999999899999 Q gi|254780940|r 187 PRFTVVVEISGLAPAQG 203 (227) Q Consensus 187 ~~f~v~v~v~g~~~g~g 203 (227) +.-+..+++.|.++-+| T Consensus 158 pkv~l~IF~tG~Vvvtg 174 (200) T KOG3302 158 PKVVLLIFVTGKVVVTG 174 (200) T ss_pred CCEEEEEECCCEEEEEE T ss_conf 86899992377799970 No 52 >TIGR02587 TIGR02587 putative integral membrane protein TIGR02587; InterPro: IPR013416 This entry is found in Nostoc sp. PCC 7120, Agrobacterium tumefaciens, Rhizobium meliloti, and Gloeobacter violaceus in a conserved two-gene neighbourhood. Proteins containing this entry appear to span the membrane seven times.. Probab=27.45 E-value=45 Score=14.26 Aligned_cols=28 Identities=25% Similarity=0.287 Sum_probs=23.1 Q ss_pred CCCCHHHHHHHHHHHHHCCCCCCCHHHH Q ss_conf 3333266999999996415542200122 Q gi|254780940|r 112 TSIQADVVESLIAALYLDGGIEVAGTFV 139 (227) Q Consensus 112 ~~ilad~fEA~iGAiy~d~G~~~~~~~i 139 (227) +--++|+|--+|||+++.-+...+++.+ T Consensus 154 ~gyl~eLf~~~vGAl~ls~NiAPTeEv~ 181 (284) T TIGR02587 154 YGYLAELFLMLVGALFLSLNIAPTEEVV 181 (284) T ss_pred CHHHHHHHHHHHHHHHHHHCCCCCHHHH T ss_conf 0359999999999999984279831189 No 53 >TIGR01088 aroQ 3-dehydroquinate dehydratase, type II; InterPro: IPR001874 3-dehydroquinate dehydratase (4.2.1.10 from EC), or dehydroquinase, catalyzes the conversion of 3-dehydroquinate into 3-dehydroshikimate. It is the third step in the shikimate pathway for the biosynthesis of aromatic amino acids from chorismate. Two classes of dehydroquinases exist, known as types I and II. Class-II enzymes are homododecameric enzymes of about 17 kDa. They are found in some bacteria such as actinomycetales , and some fungi where they act in a catabolic pathway that allows the use of quinic acid as a carbon source.; GO: 0003855 3-dehydroquinate dehydratase activity, 0009073 aromatic amino acid family biosynthetic process. Probab=26.41 E-value=18 Score=16.65 Aligned_cols=18 Identities=6% Similarity=-0.164 Sum_probs=6.9 Q ss_pred EECCCCCCCCCCCCCCCCH Q ss_conf 1036631237531333332 Q gi|254780940|r 98 RVSSDLRKDVCSFMTSIQA 116 (227) Q Consensus 98 ~~~~~~~~~~~~~~~~ila 116 (227) +-||+..+-+.|+ |.+++ T Consensus 5 lnGPNLN~LG~RE-P~~YG 22 (144) T TIGR01088 5 LNGPNLNMLGLRE-PGVYG 22 (144) T ss_pred ECCCCCCCCCCCC-CCCCC T ss_conf 2088747578746-53247 No 54 >PRK05711 DNA polymerase III subunit epsilon; Provisional Probab=26.18 E-value=36 Score=14.89 Aligned_cols=40 Identities=10% Similarity=0.091 Sum_probs=23.6 Q ss_pred HHHHHHHHHHCCCCCEEEECCCCCCCCCCCCCCCCHHHHHHHHHH Q ss_conf 433454543138772001036631237531333332669999999 Q gi|254780940|r 81 AETCSQVARELDLASFIRVSSDLRKDVCSFMTSIQADVVESLIAA 125 (227) Q Consensus 81 n~~La~~a~~lgl~~~l~~~~~~~~~~~~~~~~ilad~fEA~iGA 125 (227) ..+|-.+|+.++++.--|.--++.. -..++|++|=++.|+ T Consensus 136 ~~sLdaLc~r~~I~~s~R~~HgAL~-----Da~llA~Vyl~l~gG 175 (240) T PRK05711 136 RNSLDALCKRYGIDNSHRTLHGALL-----DAEILAEVYLAMTGG 175 (240) T ss_pred CCCHHHHHHHCCCCCCCCCCCCHHH-----HHHHHHHHHHHHCCC T ss_conf 8899999998098988756576488-----899999999997178 No 55 >PRK10916 ADP-heptose:LPS heptosyltransferase II; Provisional Probab=26.16 E-value=36 Score=14.90 Aligned_cols=24 Identities=17% Similarity=0.314 Sum_probs=12.6 Q ss_pred HHHHHHHHHHHHHHHHHHHCCCCC Q ss_conf 874586886454787764104688 Q gi|254780940|r 44 EFLGDRILGLLISTLLFNHFDSAK 67 (227) Q Consensus 44 EflGDavL~~~v~~~l~~~~p~~~ 67 (227) -++||.|+..-+...|-++||+.. T Consensus 9 ~~iGDvvlttP~l~aLr~~~P~a~ 32 (348) T PRK10916 9 SWVGDMMMSQSLYRTLKARYPQAI 32 (348) T ss_pred CCHHHHHHHHHHHHHHHHHCCCCE T ss_conf 764699999999999998789988 No 56 >TIGR01256 modA molybdate ABC transporter, periplasmic molybdate-binding protein; InterPro: IPR005950 ABC transporters belong to the ATP-Binding Cassette (ABC) superfamily, which uses the hydrolysis of ATP to energize diverse biological systems. ABC transporters are minimally constituted of two conserved regions: a highly conserved ATP binding cassette (ABC) and a less conserved transmembrane domain (TMD). These regions can be found on the same protein or on two different ones. Most ABC transporters function as a dimer and therefore are constituted of four domains, two ABC modules and two TMDs. ABC transporters are involved in the export or import of a wide variety of substrates ranging from small ions to macromolecules. The major function of ABC import systems is to provide essential nutrients to bacteria. They are found only in prokaryotes and their four constitutive domains are usually encoded by independent polypeptides (two ABC proteins and two TMD proteins). Prokaryotic importers require additional extracytoplasmic binding proteins (one or more per systems) for function. In contrast, export systems are involved in the extrusion of noxious substances, the export of extracellular toxins and the targeting of membrane components. They are found in all living organisms and in general the TMD is fused to the ABC module in a variety of combinations. Some eukaryotic exporters encode the four domains on the same polypeptide chain . The ABC module (approximately two hundred amino acid residues) is known to bind and hydrolyze ATP, thereby coupling transport to ATP hydrolysis in a large number of biological processes. The cassette is duplicated in several subfamilies. Its primary sequence is highly conserved, displaying a typical phosphate-binding loop: Walker A, and a magnesium binding site: Walker B. Besides these two regions, three other conserved motifs are present in the ABC cassette: the switch region which contains a histidine loop, postulated to polarize the attaching water molecule for hydrolysis, the signature conserved motif (LSGGQ) specific to the ABC transporter, and the Q-motif (between Walker A and the signature), which interacts with the gamma phosphate through a water bond. The Walker A, Walker B, Q-loop and switch region form the nucleotide binding site , , . The 3D structure of a monomeric ABC module adopts a stubby L-shape with two distinct arms. ArmI (mainly beta-strand) contains Walker A and Walker B. The important residues for ATP hydrolysis and/or binding are located in the P-loop. The ATP-binding pocket is located at the extremity of armI. The perpendicular armII contains mostly the alpha helical subdomain with the signature motif. It only seems to be required for structural integrity of the ABC module. ArmII is in direct contact with the TMD. The hinge between armI and armII contains both the histidine loop and the Q-loop, making contact with the gamma phosphate of the ATP molecule. ATP hydrolysis leads to a conformational change that could facilitate ADP release. In the dimer the two ABC cassettes contact each other through hydrophobic interactions at the antiparallel beta-sheet of armI by a two-fold axis , , , , , . Proteins known to belong to this family are classified in several functional subfamilies depending on the substrate used (for further information see http://www.tcdb.org/tcdb/index.php?tc=3.A.1). This entry describes the molybdate ABC transporter periplasmic binding protein in bacteria and archae. Several of the periplasmic receptors constitute a diverse class of binding proteins that differ widely in size, sequence and ligand specificity. It has been shown experimentally by radioactive labeling that ModA represents a hydrophylioc periplasmic-binding protein in Gram-negative organisms and its counterpart in Gram-positive organisms is a lipoprotein. The other components of the system include ModB, an integral membrane protein and ModC, the ATP-binding subunit. Almost all of them display a common beta/alpha folding motif and have similar tertiary structures consisting of two globular domains.; GO: 0015412 molybdate transmembrane-transporting ATPase activity, 0015689 molybdate ion transport, 0030288 outer membrane-bounded periplasmic space. Probab=25.84 E-value=42 Score=14.47 Aligned_cols=13 Identities=54% Similarity=1.038 Sum_probs=8.2 Q ss_pred HHHHHHHHHCCCC Q ss_conf 9999999974889 Q gi|254780940|r 214 VAAAEVLKREGIW 226 (227) Q Consensus 214 ~AA~~AL~klgi~ 226 (227) .||.++|+++|+| T Consensus 120 ~~A~E~L~~lgl~ 132 (225) T TIGR01256 120 AAAKEVLQKLGLW 132 (225) T ss_pred HHHHHHHHHCCCC T ss_conf 9999999707976 No 57 >PRK10422 lipopolysaccharide core biosynthesis protein; Provisional Probab=25.25 E-value=37 Score=14.76 Aligned_cols=10 Identities=10% Similarity=0.478 Sum_probs=4.2 Q ss_pred CEEEECCCCC Q ss_conf 2001036631 Q gi|254780940|r 95 SFIRVSSDLR 104 (227) Q Consensus 95 ~~l~~~~~~~ 104 (227) +|+.++++.. T Consensus 184 ~~ivi~pga~ 193 (352) T PRK10422 184 NYVVIQPTAR 193 (352) T ss_pred CEEEEECCCC T ss_conf 8799967899 No 58 >COG1737 RpiR Transcriptional regulators [Transcription] Probab=25.25 E-value=40 Score=14.57 Aligned_cols=44 Identities=20% Similarity=0.187 Sum_probs=31.5 Q ss_pred HHHHHHHHHCCCCCHHHHHHH-HHHHHHHHHHHHHHHHCCCCCEE Q ss_conf 547877641046887899888-88887443345454313877200 Q gi|254780940|r 54 LISTLLFNHFDSAKEGELSVR-FNSLVSAETCSQVARELDLASFI 97 (227) Q Consensus 54 ~v~~~l~~~~p~~~eG~lt~l-r~~lV~n~~La~~a~~lgl~~~l 97 (227) -|.+|+..+.+....+....+ ...=||..++.+.|+++|+..|= T Consensus 22 ~iA~yil~~~~~~~~~si~elA~~a~VS~aTv~Rf~~kLGf~Gf~ 66 (281) T COG1737 22 KIADYILANPDEVALLSIAELAERAGVSPATVVRFARKLGFEGFS 66 (281) T ss_pred HHHHHHHHCHHHHHHCCHHHHHHHHCCCHHHHHHHHHHCCCCCHH T ss_conf 999999939678856149999988199888999999985999889 No 59 >cd04516 TBP_eukaryotes eukaryotic TATA box binding protein (TBP): Present in archaea and eukaryotes, TBPs are transcription factors that recognize promoters and initiate transcription. TBP has been shown to be an essential component of three different transcription initiation complexes: SL1, TFIID and TFIIIB, directing transcription by RNA polymerases I, II and III, respectively. TBP binds directly to the TATA box promoter element, where it nucleates polymerase assembly, thus defining the transcription start site. TBP's binding in the minor groove induces a dramatic DNA bending while its own structure barely changes. The conserved core domain of TBP, which binds to the TATA box, has a bipartite structure, with intramolecular symmetry generating a saddle-shaped structure that sits astride the DNA. Probab=24.85 E-value=50 Score=13.97 Aligned_cols=26 Identities=23% Similarity=0.356 Sum_probs=16.6 Q ss_pred CEEEEEEEECCEEEEEEEECCHHHHHH Q ss_conf 459999999998999999689899999 Q gi|254780940|r 187 PRFTVVVEISGLAPAQGMDCSKRAAEQ 213 (227) Q Consensus 187 ~~f~v~v~v~g~~~g~g~g~SkK~Ae~ 213 (227) +.-++-++..|+.+-+|. +|..+++. T Consensus 137 ~~~~~liF~sGkvvitGa-ks~~~~~~ 162 (174) T cd04516 137 PKIVLLIFVSGKIVLTGA-KSREEIYQ 162 (174) T ss_pred CCEEEEEECCCEEEEECC-CCHHHHHH T ss_conf 988999967987999767-99999999 No 60 >cd01831 Endoglucanase_E_like Endoglucanase E-like members of the SGNH hydrolase family; Endoglucanase E catalyzes the endohydrolysis of 1,4-beta-glucosidic linkages in cellulose, lichenin and cereal beta-D-glucans. Probab=24.49 E-value=9.7 Score=18.37 Aligned_cols=20 Identities=5% Similarity=-0.077 Sum_probs=13.8 Q ss_pred EEEEEEECCHHHHHHHHHHH Q ss_conf 99999968989999999999 Q gi|254780940|r 199 APAQGMDCSKRAAEQVAAAE 218 (227) Q Consensus 199 ~~g~g~g~SkK~Ae~~AA~~ 218 (227) .+|.+.++|...-++.|.+- T Consensus 145 ~~g~~~HPs~~gh~kmA~~L 164 (169) T cd01831 145 DIGCDWHPTVAGHQKIAKHL 164 (169) T ss_pred CCCCCCCCCHHHHHHHHHHH T ss_conf 76898894999999999999 No 61 >cd04517 TLF TBP-like factors (TLF; also called TLP, TRF, TRP), which are found in most metazoans. TLFs and TBPs have well-conserved core domains; however, they only share about 60% similarity. TLFs, like TBPs, interact with TFIIA and TFIIB, which are part of the basal transcription machinery. Yet, in contrast to TBPs, TLFs seem not to interact with the TATA-box and even have a negative effect on the transcription of TATA-containing promoters. Recent results indicate that TLFs are involved in the transcription via TATA-less promoters. Probab=24.29 E-value=52 Score=13.90 Aligned_cols=27 Identities=22% Similarity=0.297 Sum_probs=16.6 Q ss_pred CCEEEEEEEECCEEEEEEEECCHHHHHH Q ss_conf 8459999999998999999689899999 Q gi|254780940|r 186 DPRFTVVVEISGLAPAQGMDCSKRAAEQ 213 (227) Q Consensus 186 ~~~f~v~v~v~g~~~g~g~g~SkK~Ae~ 213 (227) ++.-++-++..|+.+-+|. +|..+++. T Consensus 137 ~pk~~~lIF~sGkvvitGa-ks~~e~~~ 163 (174) T cd04517 137 GPRATLSIFSTGSVTVTGA-RSMEDVRE 163 (174) T ss_pred CCCEEEEEECCCEEEEECC-CCHHHHHH T ss_conf 9968999967977999806-99899999 No 62 >pfam11940 DUF3458 Domain of unknown function (DUF3458). This presumed domain is functionally uncharacterized. This domain is found in bacteria, archaea and eukaryotes. This domain is typically between 402 to 419 amino acids in length. This domain is found associated with pfam01433. This domain has a conserved FSAPV sequence motif. Probab=23.47 E-value=54 Score=13.80 Aligned_cols=26 Identities=12% Similarity=0.013 Sum_probs=13.5 Q ss_pred HHHHHHHCCCCCCHHHHHHHCCCHHH Q ss_conf 99999836965898999984246121 Q gi|254780940|r 7 STLEKRIGYAFANRSLLEKALTHSSI 32 (227) Q Consensus 7 ~~l~~~lgy~f~~~~ll~~A~th~S~ 32 (227) .++...|.=.--|+.+..++||=||. T Consensus 134 ~a~~~~L~d~~lD~a~~A~~L~LPse 159 (408) T pfam11940 134 DAFRALLADESLDPAFRALLLTLPSE 159 (408) T ss_pred HHHHHHHCCCCCCHHHHHHHHCCCCH T ss_conf 99999975987799999998639997 No 63 >PRK07982 consensus Probab=22.69 E-value=29 Score=15.42 Aligned_cols=81 Identities=11% Similarity=0.119 Sum_probs=40.0 Q ss_pred HHHHHHHHHHHH-------HHHHHHHHHHH----CCCCCH-----HHHHHHHHHHH-HHHHHHHHHHHCCCCCEEEECCC Q ss_conf 477887458688-------64547877641----046887-----89988888887-44334545431387720010366 Q gi|254780940|r 40 YERLEFLGDRIL-------GLLISTLLFNH----FDSAKE-----GELSVRFNSLV-SAETCSQVARELDLASFIRVSSD 102 (227) Q Consensus 40 ~erLEflGDavL-------~~~v~~~l~~~----~p~~~e-----G~lt~lr~~lV-~n~~La~~a~~lgl~~~l~~~~~ 102 (227) .|-++|+||++| ++-.-++=+.+ .|.... ..|..-|...- ...+|-.+|+.++++..-|.--+ T Consensus 84 ~efl~Fi~~a~LVaHNA~FD~~FLn~El~r~g~~~~~~~~~~~v~DTL~lAR~~~Pg~~~sLDaLc~R~~Id~s~R~~Hg 163 (243) T PRK07982 84 DEFLDYIRGAELVIHNAAFDIGFMDYEFSLLKRDIPKTNTFCKVTDSLALARKMFPGKRNSLDALCDRYEIDNSKRTLHG 163 (243) T ss_pred HHHHHHHCCCEEEEECCHHHHHHHHHHHHHCCCCCCCCCCCCCEEEHHHHHHHHCCCCCCCHHHHHHHCCCCCCCCCCCC T ss_conf 99999967998999733888999999999708898861012431349999888788986899999875487765655233 Q ss_pred CCCCCCCCCCCCCHHHHHHHHHH Q ss_conf 31237531333332669999999 Q gi|254780940|r 103 LRKDVCSFMTSIQADVVESLIAA 125 (227) Q Consensus 103 ~~~~~~~~~~~ilad~fEA~iGA 125 (227) +.. ...+||+++=++.|+ T Consensus 164 ALl-----Da~lLAeVYl~ltgG 181 (243) T PRK07982 164 ALL-----DAQILAEVYLAMTGG 181 (243) T ss_pred HHH-----HHHHHHHHHHHHCCC T ss_conf 377-----488999999997289 No 64 >pfam01418 HTH_6 Helix-turn-helix domain, rpiR family. This domain contains a helix-turn-helix motif. The best characterized member of this family is RpiR, a regulator of the expression of rpiB gene. Probab=21.78 E-value=41 Score=14.51 Aligned_cols=41 Identities=22% Similarity=0.299 Sum_probs=26.6 Q ss_pred HHHHHHHHCCC---CCHHHHHHHHHHHHHHHHHHHHHHHCCCCCEE Q ss_conf 47877641046---88789988888887443345454313877200 Q gi|254780940|r 55 ISTLLFNHFDS---AKEGELSVRFNSLVSAETCSQVARELDLASFI 97 (227) Q Consensus 55 v~~~l~~~~p~---~~eG~lt~lr~~lV~n~~La~~a~~lgl~~~l 97 (227) |++|+..+... ++-.++. ...-||..+..+.|+++|+..|- T Consensus 21 ia~yil~~~~~~~~~si~~lA--~~~~vS~atv~Rf~kklG~~Gf~ 64 (106) T pfam01418 21 IADYILASPDNAIHLSIAELA--KAAGVSEASVVRFCRKLGFSGFS 64 (106) T ss_pred HHHHHHHCHHHHHHCCHHHHH--HHHCCCHHHHHHHHHHHCCCCHH T ss_conf 999999299999883399999--89699899999999995899899 No 65 >TIGR02087 LEUD_arch 3-isopropylmalate dehydratase, small subunit; InterPro: IPR011827 3-isopropylmalate dehydratase (or isopropylmalate isomerase; 4.2.1.33 from EC) catalyses the stereo-specific isomerisation of 2-isopropylmalate and 3-isopropylmalate, via the formation of 2-isopropylmaleate. This enzyme performs the second step in the biosynthesis of leucine, and is present in most prokaryotes and many fungal species. The prokaryotic enzyme is a heterodimer composed of a large (LeuC) and small (LeuD) subunit, while the fungal form is a monomeric enzyme. Both forms of isopropylmalate are related and are part of the larger aconitase family . Aconitases are mostly monomeric proteins which share four domains in common and contain a single, labile [4Fe-4S] cluster. Three structural domains (1, 2 and 3) are tightly packed around the iron-sulphur cluster, while a fourth domain (4) forms a deep active-site cleft. The prokaryotic enzyme is encoded by two adjacent genes, leuC and leuD, corresponding to aconitase domains 1-3 and 4 respectively , . LeuC does not bind an iron-sulphur cluster. It is thought that some prokaryotic isopropylamalate dehydrogenases can also function as homoaconitase 4.2.1.36 from EC, converting cis-homoaconitate to homoisocitric acid in lysine biosynthesis . Homoaconitase has been identified in higher fungi (mitochondria) and several archaea and one thermophilic species of bacteria, Thermus thermophilus . This entry is most closely related to the 3-isopropylmalate dehydratase IPR004431 from INTERPRO. It also includes members, which cluster with other genes of leucine biosynthesis. The structure of the Pyrococcus horikoshii small subunit (O59393 from SWISSPROT) has recently been determined . As expected the structure of this polypeptide is similar to that of aconitase domain 4, though one alpha helix is replaced by a short loop with relatively high temperature factor values. This loop region is thought to be important for substrate recognition. Unlike other aconitase family proteins, this subunit formed a tetramer through disulphide linkages, though it is not expected to interfere with its interaction with the large subunit. These disulphide linkages would be expected to confer thermostability on the enzyme, reflecting the thermophilic lifestyle of the organism.; GO: 0003861 3-isopropylmalate dehydratase activity, 0009098 leucine biosynthetic process, 0009316 3-isopropylmalate dehydratase complex. Probab=21.64 E-value=50 Score=13.99 Aligned_cols=49 Identities=35% Similarity=0.473 Sum_probs=25.3 Q ss_pred HHHHHH-CCCCCCCCCCEECCCCCCCCCEEEEEEEECCEEEEEEEECCHHHHHHHHHHHHHHHCCC Q ss_conf 987532-02233334310102077888459999999998999999689899999999999997488 Q gi|254780940|r 161 LQEWAH-AKFGVTPEYKVTFRSGPDHDPRFTVVVEISGLAPAQGMDCSKRAAEQVAAAEVLKREGI 225 (227) Q Consensus 161 Lqe~~q-~~~~~~P~Y~~~~~~g~~~~~~f~v~v~v~g~~~g~g~g~SkK~Ae~~AA~~AL~klgi 225 (227) +||+.+ +.-+..|+|--.-..| .|.|=|+- -|+|+|.-+ |-.|||+.|| T Consensus 27 ~~eLA~haM~g~~PeF~~kvr~G---------DviVAGkN--FGcGSSREQ-----A~~ALK~aGv 76 (159) T TIGR02087 27 PDELASHAMEGIDPEFAKKVREG---------DVIVAGKN--FGCGSSREQ-----AALALKAAGV 76 (159) T ss_pred HHHHHHHCCCCCCCCHHHHCCCC---------CEEEECCC--CCCCCCHHH-----HHHHHHHCCE T ss_conf 78899870558996313407899---------78871416--477887788-----9999974790 No 66 >TIGR00677 fadh2_euk methylenetetrahydrofolate reductase; InterPro: IPR004621 The enzyme activities methylenetetrahydrofolate reductase (1.5.1.20 from EC) and 5,10-methylenetetrahydrofolate reductase (FADH) (1.7.99.5 from EC) differ in that the former (assigned in many eukaryotes) is defined to use NADP+ as an acceptor, while the latter (assigned in many bacteria) is flexible with respect to the acceptor. Both convert 5-methyltetrahydrofolate to 5,10-methylenetetrahydrofolate. From a larger set of proteins assigned as one or the other, this family describes the subset of proteins found in eukaryotes, and currently designated methylenetetrahydrofolate reductase (1.5.1.20 from EC). This protein is an FAD-containing flavoprotein.; GO: 0004489 methylenetetrahydrofolate reductase (NADPH) activity, 0006555 methionine metabolic process. Probab=20.72 E-value=61 Score=13.46 Aligned_cols=18 Identities=28% Similarity=0.302 Sum_probs=14.6 Q ss_pred HHHHHHHHHHHHHCCCCC Q ss_conf 999999999999748899 Q gi|254780940|r 210 AAEQVAAAEVLKREGIWT 227 (227) Q Consensus 210 ~Ae~~AA~~AL~klgi~t 227 (227) .=-++|+.+.|++||+|+ T Consensus 293 lNlEKA~~~Il~rLg~l~ 310 (312) T TIGR00677 293 LNLEKAALMILERLGLLD 310 (312) T ss_pred CCHHHHHHHHHHHCCCCC T ss_conf 017789999998478877 No 67 >COG0859 RfaF ADP-heptose:LPS heptosyltransferase [Cell envelope biogenesis, outer membrane] Probab=20.47 E-value=49 Score=14.05 Aligned_cols=24 Identities=33% Similarity=0.411 Sum_probs=11.9 Q ss_pred HHHHHHHHHHHHHHHHHHHHCCCC Q ss_conf 887458688645478776410468 Q gi|254780940|r 43 LEFLGDRILGLLISTLLFNHFDSA 66 (227) Q Consensus 43 LEflGDavL~~~v~~~l~~~~p~~ 66 (227) +.++||.|+...+-..|-+.||+. T Consensus 9 ~~~iGD~vlt~p~~~~lk~~~P~a 32 (334) T COG0859 9 LSKLGDVVLTLPLLRTLKKAYPNA 32 (334) T ss_pred CCCHHHHHHHHHHHHHHHHHCCCC T ss_conf 574013776999999999878997 No 68 >pfam00352 TBP Transcription factor TFIID (or TATA-binding protein, TBP). Probab=20.23 E-value=62 Score=13.39 Aligned_cols=39 Identities=26% Similarity=0.337 Sum_probs=25.7 Q ss_pred CCCEEEEEEEECCEEEEEEEECCHHHHHHHHHHHH--HHHCC Q ss_conf 88459999999998999999689899999999999--99748 Q gi|254780940|r 185 HDPRFTVVVEISGLAPAQGMDCSKRAAEQVAAAEV--LKREG 224 (227) Q Consensus 185 ~~~~f~v~v~v~g~~~g~g~g~SkK~Ae~~AA~~A--L~klg 224 (227) ++|.-++-++..|+.+.+|. +|..++++.+.+-+ |+++| T Consensus 46 ~~pk~t~liF~SGkivitGa-ks~~~~~~a~~~i~~~L~~~g 86 (86) T pfam00352 46 REPKATALIFSSGKVVITGA-KSEEDAKKAVRKIAPILKKLG 86 (86) T ss_pred CCCCEEEEEECCCEEEEECC-CCHHHHHHHHHHHHHHHHHCC T ss_conf 78854999983885999842-999999999999999999758 No 69 >PRK11557 putative DNA-binding transcriptional regulator; Provisional Probab=20.07 E-value=45 Score=14.29 Aligned_cols=40 Identities=20% Similarity=0.269 Sum_probs=24.1 Q ss_pred HHHHHHHHCC---CCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCE Q ss_conf 4787764104---68878998888888744334545431387720 Q gi|254780940|r 55 ISTLLFNHFD---SAKEGELSVRFNSLVSAETCSQVARELDLASF 96 (227) Q Consensus 55 v~~~l~~~~p---~~~eG~lt~lr~~lV~n~~La~~a~~lgl~~~ 96 (227) |++|+..+.. .++-.+|. ...-||..+..+.|+++|+..| T Consensus 21 IA~yIl~n~~~v~~~si~eLA--~~~~vS~aTVvRf~kkLGf~Gf 63 (282) T PRK11557 21 LADYLLLQPDTARHLSSQQLA--NEAGVSQSSVVKFAQKLGYKGF 63 (282) T ss_pred HHHHHHCCHHHHHHCCHHHHH--HHHCCCHHHHHHHHHHHCCCCH T ss_conf 999998098999765699999--8969998899999999389989 Done!