Query gi|254780720|ref|YP_003065133.1| Ferroxidase [Candidatus Liberibacter asiaticus str. psy62] Match_columns 164 No_of_seqs 118 out of 1088 Neff 7.7 Searched_HMMs 39220 Date Sun May 29 20:28:23 2011 Command /home/congqian_1/programs/hhpred/hhsearch -i 254780720.hhm -d /home/congqian_1/database/cdd/Cdd.hhm No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 PRK10304 ferritin; Provisional 100.0 0 0 336.2 22.5 164 1-164 2-165 (165) 2 cd01055 Nonheme_Ferritin nonhe 100.0 0 0 317.6 19.1 156 2-157 1-156 (156) 3 COG1528 Ftn Ferritin-like prot 100.0 0 0 313.6 21.7 163 1-163 2-164 (167) 4 cd00904 Ferritin Ferritin iron 100.0 0 0 303.2 18.3 154 2-155 1-160 (160) 5 cd01056 Euk_Ferritin eukaryoti 100.0 5.2E-44 0 287.2 19.5 155 2-156 1-161 (161) 6 cd00907 Bacterioferritin Bacte 100.0 5.7E-31 1.5E-35 207.9 20.0 143 2-145 3-145 (153) 7 KOG2332 consensus 100.0 9.3E-32 2.4E-36 212.7 13.0 158 2-159 14-177 (178) 8 PRK10635 bacterioferritin, iro 100.0 9.4E-28 2.4E-32 188.4 19.3 147 2-152 4-150 (158) 9 pfam00210 Ferritin Ferritin-li 100.0 3.1E-26 7.8E-31 179.2 19.3 138 6-143 1-142 (142) 10 COG2193 Bfr Bacterioferritin ( 99.9 5.2E-24 1.3E-28 165.6 17.5 147 2-152 4-150 (157) 11 cd01052 DPSL DPS-like protein, 99.9 4.9E-23 1.3E-27 159.7 18.6 134 3-137 5-148 (148) 12 PRK13456 DNA protection protei 99.8 2.9E-18 7.3E-23 130.7 17.6 135 3-138 17-161 (184) 13 TIGR00754 bfr bacterioferritin 99.6 5.9E-14 1.5E-18 104.5 13.8 147 2-152 4-150 (157) 14 cd00657 Ferritin_like Ferritin 99.5 4.8E-12 1.2E-16 92.9 15.6 124 7-136 1-129 (130) 15 cd07908 Mn_catalase_like Manga 99.4 6E-11 1.5E-15 86.3 16.4 131 2-136 11-153 (154) 16 COG2406 Protein distantly rela 99.3 1E-09 2.6E-14 78.8 16.8 135 3-138 16-160 (172) 17 cd01041 Rubrerythrin Rubreryth 99.2 3.9E-09 9.9E-14 75.2 16.8 129 7-140 4-133 (134) 18 PRK09448 DNA starvation/statio 98.9 2.5E-07 6.5E-12 64.2 16.5 122 3-125 20-150 (164) 19 cd01046 Rubrerythrin_like rubr 98.9 4.6E-07 1.2E-11 62.6 16.9 122 4-140 1-122 (123) 20 pfam02915 Rubrerythrin Rubrery 98.9 4.8E-07 1.2E-11 62.5 16.3 126 8-137 2-137 (137) 21 cd01043 DPS DPS protein, ferri 98.8 7.2E-07 1.8E-11 61.5 16.3 118 8-125 2-127 (139) 22 COG0783 Dps DNA-binding ferrit 98.8 1.8E-06 4.7E-11 59.0 16.9 123 3-126 14-144 (156) 23 COG1633 Uncharacterized conser 98.7 4.1E-06 1E-10 56.9 17.6 133 3-141 23-170 (176) 24 cd01045 Ferritin_like_AB Uncha 98.6 4.8E-06 1.2E-10 56.4 15.7 124 7-136 1-138 (139) 25 cd01051 Mn_catalase Manganese 98.6 7.9E-06 2E-10 55.1 16.0 134 2-140 18-155 (156) 26 COG1592 Rubrerythrin [Energy p 98.4 4.2E-05 1.1E-09 50.7 15.4 127 3-141 3-130 (166) 27 pfam05067 Mn_catalase Manganes 97.7 0.0036 9.3E-08 38.9 14.6 134 2-141 18-190 (272) 28 cd01042 DMQH Demethoxyubiquino 97.4 0.0097 2.5E-07 36.4 12.6 117 14-136 10-137 (165) 29 COG3546 Mn-containing catalase 97.3 0.0076 1.9E-07 37.0 11.1 138 2-145 18-194 (277) 30 pfam09537 DUF2383 Domain of un 97.1 0.019 4.9E-07 34.5 11.7 98 5-105 2-110 (111) 31 cd01044 Ferritin_CCC1_N Ferrit 96.6 0.056 1.4E-06 31.7 13.3 115 9-138 3-124 (125) 32 pfam03232 COQ7 Ubiquinone bios 96.2 0.094 2.4E-06 30.4 13.5 117 14-135 12-141 (171) 33 COG1633 Uncharacterized conser 95.6 0.12 3.1E-06 29.7 8.4 66 76-144 19-84 (176) 34 cd07910 MiaE MiaE tRNA-modifyi 95.3 0.23 5.7E-06 28.1 18.3 134 3-146 17-161 (180) 35 pfam04305 DUF455 Protein of un 95.3 0.23 5.8E-06 28.0 14.0 131 5-138 65-207 (250) 36 pfam05974 DUF892 Domain of unk 94.7 0.33 8.5E-06 27.0 17.0 132 4-138 5-151 (159) 37 cd01050 Acyl_ACP_Desat Acyl AC 93.7 0.54 1.4E-05 25.7 8.2 108 34-144 91-209 (297) 38 PRK13654 magnesium-protoporphy 92.3 0.88 2.3E-05 24.5 9.6 121 4-125 81-202 (351) 39 pfam03405 FA_desaturase_2 Fatt 91.4 1.1 2.8E-05 23.9 8.4 105 36-141 98-212 (330) 40 cd07909 YciF YciF bacterial st 91.3 1.1 2.8E-05 23.8 16.9 120 6-128 5-138 (147) 41 cd01047 ACSF Aerobic Cyclase S 90.9 1.2 3.1E-05 23.6 9.1 121 4-125 63-184 (323) 42 CHL00185 ycf59 magnesium-proto 90.5 1.3 3.4E-05 23.3 10.3 120 5-125 78-198 (349) 43 pfam06175 MiaE tRNA-(MS[2]IO[6 90.4 1.4 3.5E-05 23.3 17.8 133 4-146 27-170 (199) 44 PRK09101 nrdB ribonucleotide-d 80.6 4.4 0.00011 20.2 6.9 81 18-100 205-291 (376) 45 COG2833 Uncharacterized protei 80.1 4.5 0.00012 20.1 10.7 121 5-131 76-207 (268) 46 COG3685 Uncharacterized protei 79.1 4.9 0.00013 19.9 15.7 129 5-136 10-152 (167) 47 PRK13965 ribonucleotide-diphos 78.3 5.2 0.00013 19.8 5.2 82 17-103 175-261 (337) 48 TIGR02284 TIGR02284 conserved 77.9 5.3 0.00014 19.7 8.5 129 6-140 2-141 (142) 49 COG2941 CAT5 Ubiquinone biosyn 76.4 5.9 0.00015 19.5 12.6 113 14-133 51-174 (204) 50 pfam08066 PMC2NT PMC2NT (NUC01 74.9 4.6 0.00012 20.1 3.9 58 34-91 21-79 (91) 51 PRK09614 nrdF ribonucleotide-d 74.0 6.8 0.00017 19.1 7.8 79 20-102 168-250 (325) 52 PRK13966 nrdF2 ribonucleotide- 67.5 9.5 0.00024 18.2 5.6 83 19-104 164-249 (324) 53 TIGR02630 xylose_isom_A xylose 60.1 9.9 0.00025 18.1 3.1 42 34-75 188-233 (437) 54 COG2996 Predicted RNA-bindinin 54.0 14 0.00037 17.1 3.1 50 43-92 216-269 (287) 55 PRK07209 ribonucleotide-diphos 53.0 17 0.00044 16.6 6.6 41 100-140 244-284 (391) 56 pfam10152 DUF2360 Predicted co 39.4 28 0.00071 15.3 4.1 43 114-162 7-49 (147) 57 cd07911 RNRR2_Rv0233_like Ribo 38.4 29 0.00074 15.2 7.8 38 31-68 73-110 (280) 58 pfam04518 DUF582 Protein of un 36.7 31 0.00078 15.1 4.0 56 5-60 158-220 (380) 59 pfam10666 Phage_Gp14 Phage pro 34.5 33 0.00085 14.9 2.6 92 10-107 4-99 (140) 60 cd01058 AAMH_B Aromatic and Al 33.8 34 0.00088 14.8 16.3 108 35-145 128-256 (304) 61 pfam04332 DUF475 Protein of un 33.0 35 0.0009 14.7 3.4 65 79-145 48-113 (294) 62 pfam03202 Lipoprotein_10 Putat 32.8 13 0.00034 17.3 0.2 17 110-126 16-32 (134) 63 TIGR02858 spore_III_AA stage I 29.0 34 0.00088 14.8 1.7 47 35-81 91-137 (282) 64 cd01048 Ferritin_like_AB2 Unch 28.6 42 0.0011 14.3 14.9 96 6-108 2-109 (135) 65 TIGR02146 LysS_fung_arch homoc 28.2 43 0.0011 14.2 2.7 80 13-92 68-157 (355) 66 pfam02332 Phenol_Hydrox Methan 26.8 45 0.0012 14.1 14.6 105 35-143 102-227 (233) 67 TIGR02110 PQQ_syn_pqqF coenzym 26.7 36 0.00092 14.7 1.5 54 33-86 43-100 (737) 68 PTZ00211 ribonucleotide reduct 25.9 47 0.0012 14.0 7.6 60 29-98 186-246 (330) 69 TIGR01582 FDH-beta formate deh 25.9 47 0.0012 14.0 2.3 21 46-66 191-212 (293) 70 cd01049 RNRR2 Ribonucleotide R 25.8 47 0.0012 14.0 9.9 63 35-101 176-239 (288) 71 pfam00268 Ribonuc_red_sm Ribon 23.3 53 0.0013 13.7 10.7 20 35-54 180-199 (281) 72 COG4445 MiaE Hydroxylase for s 23.3 53 0.0013 13.7 13.7 126 8-144 32-168 (203) 73 TIGR02024 FtcD glutamate formi 22.2 55 0.0014 13.5 3.3 59 40-98 56-117 (331) 74 TIGR01924 rsbW_low_gc anti-sig 21.7 35 0.0009 14.7 0.7 17 139-155 108-124 (161) 75 cd07648 F-BAR_FCHO The F-BAR ( 21.7 57 0.0014 13.5 10.3 35 35-69 21-55 (261) 76 cd00886 MogA_MoaB MogA_MoaB fa 20.6 25 0.00063 15.7 -0.3 39 32-70 88-126 (152) 77 cd07647 F-BAR_PSTPIP The F-BAR 20.2 61 0.0016 13.3 10.4 91 35-140 21-111 (239) No 1 >PRK10304 ferritin; Provisional Probab=100.00 E-value=0 Score=336.18 Aligned_cols=164 Identities=34% Similarity=0.628 Sum_probs=161.9 Q ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEECCCCCCCCCCC Q ss_conf 99899999999999999999999999999815994789999999999999999999999995399714378225720488 Q gi|254780720|r 1 MTNTRDRVLNELMNMEYVAQYHYMQAAAWAASHNLDGCCNFLLKHAMEEHSHVIRIFKHLTDLGVEAKFSSIEAPVISAN 80 (164) Q Consensus 1 ~s~~~~~~Ln~qi~~El~as~~Yl~~a~~~~~~~~~g~a~~f~~~a~EE~~HA~~l~~yi~~rgg~~~~~~i~~p~~~~~ 80 (164) ||++|.++||+|||.|+.||++|++||+||+..|+||||+||+.+|.||++||++|++||++|||.|.+++|++|+.+|. T Consensus 2 l~~~l~~~LN~Qin~E~~as~~Ylama~w~~~~~l~G~a~~f~~qa~EE~~Ha~k~~~yl~~rg~~v~l~~I~~P~~~~~ 81 (165) T PRK10304 2 LKPEMIEKLNEQMNLELYSSLLYQQMSAWCSYHTFEGAAAFLRRHAQEEMTHMQRLFDYLTDTGNLPRINTVESPFAEYS 81 (165) T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCEEECCCCCCCCCCC T ss_conf 88899999999999999999999999999877799249999999999999999999999996799844499899733407 Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHH Q ss_conf 98999999999999999999999999997099889999999999999999999999999995288751699999999965 Q gi|254780720|r 81 DVEGLFSLMYEHENKVTIAYDDAIETILAEKDHQTFQFLQWFVKEQHEEMALFRRILDKIRLIGSGPHSRYMFDLEIEKI 160 (164) Q Consensus 81 ~~~e~~~~al~~E~~vt~~~~~l~~~A~~~~D~~t~~fl~~fl~EQ~eee~~~~~ll~~l~~~g~~~~glyl~D~~l~~~ 160 (164) ++.++|+.+|+||+.||.+|++|+++|.+++|++|.+||+|||+||++||+.+++++++++++|++|.|+|++|++|+++ T Consensus 82 s~~~vf~~al~hE~~VT~~I~~L~~~A~~~~D~~t~~FL~wFv~EQvEEE~~~~~il~~l~~~g~~~~~l~~lD~eL~~~ 161 (165) T PRK10304 82 SLDELFQETYKHEQLITQKINELAHAAMTNQDYPTFNFLQWYVSEQHEEEKLFKSIIDKLSLAGKSGEGLYFIDKELSTL 161 (165) T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHH T ss_conf 89999999999999999999999999988488838999999999999999999999999998179974596896888640 Q ss_pred HCCC Q ss_conf 3189 Q gi|254780720|r 161 ANKS 164 (164) Q Consensus 161 ~~~~ 164 (164) ..++ T Consensus 162 ~~q~ 165 (165) T PRK10304 162 DTQN 165 (165) T ss_pred CCCC T ss_conf 0479 No 2 >cd01055 Nonheme_Ferritin nonheme-containing ferritins. Nonheme Ferritin domain, found in archaea and bacteria, is a member of a broad superfamily of ferritin-like diiron-carboxylate proteins. The ferritin protein shell is composed of 24 protein subunits arranged in 432 symmetry. Each protein subunit, a four-helix bundle with a fifth short terminal helix, contains a dinuclear ferroxidase center (H type). Unique to this group of proteins is a third metal site in the ferroxidase center. Iron storage involves the uptake of iron (II) at the protein shell, its oxidation by molecular oxygen at the ferroxidase centers, and the movement of iron (III) into the cavity for deposition as ferrihydrite. Probab=100.00 E-value=0 Score=317.57 Aligned_cols=156 Identities=42% Similarity=0.664 Sum_probs=154.0 Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEECCCCCCCCCCCC Q ss_conf 98999999999999999999999999998159947899999999999999999999999953997143782257204889 Q gi|254780720|r 2 TNTRDRVLNELMNMEYVAQYHYMQAAAWAASHNLDGCCNFLLKHAMEEHSHVIRIFKHLTDLGVEAKFSSIEAPVISAND 81 (164) Q Consensus 2 s~~~~~~Ln~qi~~El~as~~Yl~~a~~~~~~~~~g~a~~f~~~a~EE~~HA~~l~~yi~~rgg~~~~~~i~~p~~~~~~ 81 (164) |++|+++||+|||.|++||++|++||+||++.|+||||+||+.+|.|||+||++|++|+++|||+|.+++|++|+.+|.+ T Consensus 1 s~~~~~~LN~qin~El~as~~Yl~ma~~~~~~~l~g~a~ff~~~a~EEr~HA~kl~~yl~~rgg~~~l~~I~~p~~~~~~ 80 (156) T cd01055 1 SEKLEKALNEQINLELYSSYLYLAMAAWFDSKGLDGFANFFRVQAQEEREHAMKFFDYLNDRGGRVELPAIEAPPSEFES 80 (156) T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCEECCCCCCCCCCCCC T ss_conf 97999999999999999999999999997266876899999999999999999999999976997230896898767599 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHH Q ss_conf 8999999999999999999999999997099889999999999999999999999999995288751699999999 Q gi|254780720|r 82 VEGLFSLMYEHENKVTIAYDDAIETILAEKDHQTFQFLQWFVKEQHEEMALFRRILDKIRLIGSGPHSRYMFDLEI 157 (164) Q Consensus 82 ~~e~~~~al~~E~~vt~~~~~l~~~A~~~~D~~t~~fl~~fl~EQ~eee~~~~~ll~~l~~~g~~~~glyl~D~~l 157 (164) +.++|+.+|++|+.||+++++++++|++++|++|.+||+|||+||+++++++++++++++++|++|.|+|+||++| T Consensus 81 ~~~~~~~al~~E~~vt~~i~~l~~~A~~~~D~~t~~FL~~fl~EQveee~~~~~~l~~l~~~g~~~~gl~~~D~~l 156 (156) T cd01055 81 LLEVFEAALEHEQKVTESINNLVDLALEEKDYATFNFLQWFVKEQVEEEALARDILDKLKLAGDDGGGLYMLDKEL 156 (156) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEHHCCCC T ss_conf 9999999999999999999999999988588718999999999999999999999999997179977100106759 No 3 >COG1528 Ftn Ferritin-like protein [Inorganic ion transport and metabolism] Probab=100.00 E-value=0 Score=313.58 Aligned_cols=163 Identities=39% Similarity=0.633 Sum_probs=159.9 Q ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEECCCCCCCCCCC Q ss_conf 99899999999999999999999999999815994789999999999999999999999995399714378225720488 Q gi|254780720|r 1 MTNTRDRVLNELMNMEYVAQYHYMQAAAWAASHNLDGCCNFLLKHAMEEHSHVIRIFKHLTDLGVEAKFSSIEAPVISAN 80 (164) Q Consensus 1 ~s~~~~~~Ln~qi~~El~as~~Yl~~a~~~~~~~~~g~a~~f~~~a~EE~~HA~~l~~yi~~rgg~~~~~~i~~p~~~~~ 80 (164) +|.+|.++||+|||.||.||++|++||+||+..|+||+|+||+.||+||+.||++|++|++.||++|.++.|.+|+.+|. T Consensus 2 ls~~~~~~LN~Q~N~E~yas~lYl~maa~~~~~~l~G~A~f~~~qa~EE~~H~~k~~~yl~~~g~~~~l~~I~~P~~~~~ 81 (167) T COG1528 2 LSEKMIELLNEQMNLEFYASNLYLQMAAWCSSESLPGFAKFLRAQAQEELTHAMKLFNYLNERGARPELKAIEAPPNKFS 81 (167) T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEECCCCCCCCCCC T ss_conf 21899999999999999999999999999866499049999999978999999999999985699862167679866647 Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHH Q ss_conf 98999999999999999999999999997099889999999999999999999999999995288751699999999965 Q gi|254780720|r 81 DVEGLFSLMYEHENKVTIAYDDAIETILAEKDHQTFQFLQWFVKEQHEEMALFRRILDKIRLIGSGPHSRYMFDLEIEKI 160 (164) Q Consensus 81 ~~~e~~~~al~~E~~vt~~~~~l~~~A~~~~D~~t~~fl~~fl~EQ~eee~~~~~ll~~l~~~g~~~~glyl~D~~l~~~ 160 (164) ++.++|+.+|+||+.||++|++|+++|.+++|+.|.+||+|||+||++|++.+++|+++++++|++|.|+|++|++|+++ T Consensus 82 s~~e~f~~tlehEq~vt~~I~~L~~~a~~~kD~~T~nFLqWfv~EQ~eEe~~~~~I~d~~~~ag~~~~~l~~~D~~L~~~ 161 (167) T COG1528 82 SLKELFEKTLEHEQKVTSSINELAEVAREEKDYATFNFLQWFVAEQVEEEKLFKTILDKLELAGNDGEGLYLIDKELKNR 161 (167) T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHH T ss_conf 89999999999999999999999999988164779999999999888899889999999998277755202467889864 Q ss_pred HCC Q ss_conf 318 Q gi|254780720|r 161 ANK 163 (164) Q Consensus 161 ~~~ 163 (164) +.. T Consensus 162 ~~~ 164 (167) T COG1528 162 ASS 164 (167) T ss_pred CCC T ss_conf 036 No 4 >cd00904 Ferritin Ferritin iron storage proteins. Ferritins are the primary iron storage proteins of most living organisms and members of a broad superfamily of ferritin-like diiron-carboxylate proteins. The iron-free (apoferritin) ferritin molecule is a protein shell composed of 24 protein chains arranged in 432 symmetry. Iron storage involves the uptake of iron (II) at the protein shell, its oxidation by molecular oxygen at the dinuclear ferroxidase centers, and the movement of iron (III) into the cavity for deposition as ferrihydrite; the protein shell can hold up to 4500 iron atoms. In vertebrates, two types of chains (subunits) have been characterized, H or M (fast) and L (slow), which differ in rates of iron uptake and mineralization. Bacterial non-heme ferritins are composed only of H chains. Fe(II) oxidation in the H/M subunits take place initially at the ferroxidase center, a carboxylate-bridged diiron center, located within the subunit four-helix bundle. In a complementary rol Probab=100.00 E-value=0 Score=303.24 Aligned_cols=154 Identities=25% Similarity=0.369 Sum_probs=148.6 Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEECCCCCCCC-C Q ss_conf 989999999999999999999999999981--5994789999999999999999999999995399714378225720-4 Q gi|254780720|r 2 TNTRDRVLNELMNMEYVAQYHYMQAAAWAA--SHNLDGCCNFLLKHAMEEHSHVIRIFKHLTDLGVEAKFSSIEAPVI-S 78 (164) Q Consensus 2 s~~~~~~Ln~qi~~El~as~~Yl~~a~~~~--~~~~~g~a~~f~~~a~EE~~HA~~l~~yi~~rgg~~~~~~i~~p~~-~ 78 (164) |++|+++||+|||.|+.|||+|++||+||+ +.++|||++||+.+|.|||+||++|++|+++|||+|++++|++|+. . T Consensus 1 S~~~~~alN~qIn~El~as~~Yl~ma~~f~~~~~~l~Gfa~ff~~~a~EE~~Ha~~l~~Yl~~RGg~v~~~~i~~p~~~~ 80 (160) T cd00904 1 SEKVEAAVNRQLNLELYASYTYLSMATYFDRDDVALKGVAHFFKEQAQEEREHAEKFYKYQNERGGRVELQDIEKPPSDE 80 (160) T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCEEECCCCCCCCCCC T ss_conf 97999999999999999999999999996514567476999999999999999999999999779923348867888877 Q ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHCC--CCCHHHHHHHH Q ss_conf 8898999999999999999999999999997099889999999-99999999999999999999528--87516999999 Q gi|254780720|r 79 ANDVEGLFSLMYEHENKVTIAYDDAIETILAEKDHQTFQFLQW-FVKEQHEEMALFRRILDKIRLIG--SGPHSRYMFDL 155 (164) Q Consensus 79 ~~~~~e~~~~al~~E~~vt~~~~~l~~~A~~~~D~~t~~fl~~-fl~EQ~eee~~~~~ll~~l~~~g--~~~~glyl~D~ 155 (164) |.++.++|+.+|++|+.||+++++|+++|.+++|+.|.+||+| ||+||+++++++++++++++++| +.|+|+|+||| T Consensus 81 ~~s~~~~~~~al~~Ek~vt~~i~~L~~~A~~~~D~~~~~fLe~~Fv~eQ~ee~~~~~~~l~~l~~~g~~~~glg~ylfDk 160 (160) T cd00904 81 WGGTLDAMEAALKLEKFVNQALLDLHELASEEKDPHLCDFLESHFLDEQVKEIKQVGDILTNLERLNGQQAGSGEYLFDR 160 (160) T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHCCCCCCCEEEEEECC T ss_conf 79889999999999999999999999999886997599887165379999999999999999998089998703410086 No 5 >cd01056 Euk_Ferritin eukaryotic ferritins. Eukaryotic Ferritin (Euk_Ferritin) domain. Ferritins are the primary iron storage proteins of most living organisms and members of a broad superfamily of ferritin-like diiron-carboxylate proteins. The iron-free (apoferritin) ferritin molecule is a protein shell composed of 24 protein chains arranged in 432 symmetry. Iron storage involves the uptake of iron (II) at the protein shell, its oxidation by molecular oxygen at the dinuclear ferroxidase centers, and the movement of iron (III) into the cavity for deposition as ferrihydrite; the protein shell can hold up to 4500 iron atoms. In vertebrates, two types of chains (subunits) have been characterized, H or M (fast) and L (slow), which differ in rates of iron uptake and mineralization. Fe(II) oxidation in the H/M subunits take place initially at the ferroxidase center, a carboxylate-bridged diiron center, located within the subunit four-helix bundle. In a complementary role, negatively charged r Probab=100.00 E-value=5.2e-44 Score=287.18 Aligned_cols=155 Identities=23% Similarity=0.306 Sum_probs=148.5 Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEECCCCCCC-CC Q ss_conf 989999999999999999999999999981--599478999999999999999999999999539971437822572-04 Q gi|254780720|r 2 TNTRDRVLNELMNMEYVAQYHYMQAAAWAA--SHNLDGCCNFLLKHAMEEHSHVIRIFKHLTDLGVEAKFSSIEAPV-IS 78 (164) Q Consensus 2 s~~~~~~Ln~qi~~El~as~~Yl~~a~~~~--~~~~~g~a~~f~~~a~EE~~HA~~l~~yi~~rgg~~~~~~i~~p~-~~ 78 (164) +++|+++||+||+.|+.|||.|++||+||+ ++++|||++||+.+|+|||+||.+|++|+++|||+|.+++|++|+ .. T Consensus 1 ~~~~e~aln~qi~~El~asy~Yl~ma~~f~~~~~~l~Gfa~~f~~~s~Ee~~ha~kl~~Yl~~RG~~v~~~~i~~p~~~~ 80 (161) T cd01056 1 HEECEAALNKQINLELNASYVYLSMAAYFDRDDVALPGFAKFFRKLSDEEREHAEKLIKYQNKRGGRVVLQDIKKPEKDE 80 (161) T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCEEECCCCCCCCCCC T ss_conf 96899999999999999999999999986713578576999999999999999999999999869920258868887777 Q ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHCCCC--CHHHHHHHH Q ss_conf 8898999999999999999999999999997099889999999-9999999999999999999952887--516999999 Q gi|254780720|r 79 ANDVEGLFSLMYEHENKVTIAYDDAIETILAEKDHQTFQFLQW-FVKEQHEEMALFRRILDKIRLIGSG--PHSRYMFDL 155 (164) Q Consensus 79 ~~~~~e~~~~al~~E~~vt~~~~~l~~~A~~~~D~~t~~fl~~-fl~EQ~eee~~~~~ll~~l~~~g~~--~~glyl~D~ 155 (164) |.++.++|+.||++|+.||+++++|+++|.+++|++|.+||+| ||.||+++++++++++++++++|++ |+|+|+||+ T Consensus 81 ~~s~l~~~~~al~~Ek~vt~~i~~L~~~A~~~~D~~~~~fLe~~fi~eQ~e~~~~~~~~l~~l~~~~~~~~glg~ylfDk 160 (161) T cd01056 81 WGSGLEALELALDLEKLVNQSLLDLHKLASEHNDPHLADFLESEFLEEQVESIKKLAGYITNLKRVGKPQSGLGEYLFDK 160 (161) T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCC T ss_conf 79999999999999999999999999999876996699999888789999999999999999998479986500003488 Q ss_pred H Q ss_conf 9 Q gi|254780720|r 156 E 156 (164) Q Consensus 156 ~ 156 (164) . T Consensus 161 ~ 161 (161) T cd01056 161 Y 161 (161) T ss_pred C T ss_conf 9 No 6 >cd00907 Bacterioferritin Bacterioferritin, ferritin-like diiron-binding domain. Bacterioferritins, also known as cytochrome b1, are members of a broad superfamily of ferritin-like diiron-carboxylate proteins. Similar to ferritin in architecture, Bfr forms an oligomer of 24 subunits that assembles to form a hollow sphere with 432 symmetry. Up to 12 heme cofactor groups (iron protoporphyrin IX or coproporphyrin III) are bound between dimer pairs. The role of the heme is unknown, although it may be involved in mediating iron-core reduction and iron release. Each subunit is composed of a four-helix bundle which carries a diiron ferroxidase center; it is here that initial oxidation of ferrous iron by molecular oxygen occurs, facilitating the detoxification of iron, protection against dioxygen and radical products, and storage of ferric-hydroxyphosphate at the core. Some bacterioferritins are composed of two subunit types, one conferring heme-binding ability (alpha) and the other (beta) best Probab=100.00 E-value=5.7e-31 Score=207.91 Aligned_cols=143 Identities=17% Similarity=0.181 Sum_probs=135.2 Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEECCCCCCCCCCCC Q ss_conf 98999999999999999999999999998159947899999999999999999999999953997143782257204889 Q gi|254780720|r 2 TNTRDRVLNELMNMEYVAQYHYMQAAAWAASHNLDGCCNFLLKHAMEEHSHVIRIFKHLTDLGVEAKFSSIEAPVISAND 81 (164) Q Consensus 2 s~~~~~~Ln~qi~~El~as~~Yl~~a~~~~~~~~~g~a~~f~~~a~EE~~HA~~l~~yi~~rgg~~~~~~i~~p~~~~~~ 81 (164) +++|.++||++++.|++|+++|+.+|.+|+++|++++|++|+.+|.|||+||.++++||+++||.|++++.+.|. .++| T Consensus 3 ~~kvi~~LN~~L~~El~A~~qY~~~a~~~~~~g~~~la~~~~~~a~eE~~HA~~l~~rIl~LgG~P~~~~~~~~~-~~~~ 81 (153) T cd00907 3 DPKVIEALNKALTGELTAINQYFLHARMLEDWGLEKLAERFRKESIEEMKHADKLIERILFLEGLPNLQRLGKLR-IGED 81 (153) T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCC-CCCC T ss_conf 689999999999999999999999999998849798999999998999999999999999839998766667785-7877 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC Q ss_conf 8999999999999999999999999997099889999999999999999999999999995288 Q gi|254780720|r 82 VEGLFSLMYEHENKVTIAYDDAIETILAEKDHQTFQFLQWFVKEQHEEMALFRRILDKIRLIGS 145 (164) Q Consensus 82 ~~e~~~~al~~E~~vt~~~~~l~~~A~~~~D~~t~~fl~~fl~EQ~eee~~~~~ll~~l~~~g~ 145 (164) +.++|+.+++.|..++..|++++..|.+.+|++|+.+++||+.++.++..++.+.++.++++|. T Consensus 82 v~e~L~~dl~~E~~ai~~y~e~i~~a~~~~D~~t~~ll~~il~dEeeH~~~le~~L~li~~~G~ 145 (153) T cd00907 82 VPEMLENDLALEYEAIAALNEAIALCEEVGDYVSRDLLEEILEDEEEHIDWLETQLDLIDKMGL 145 (153) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 9999999999999999999999999877898989999999999999999999999999999778 No 7 >KOG2332 consensus Probab=99.98 E-value=9.3e-32 Score=212.70 Aligned_cols=158 Identities=22% Similarity=0.335 Sum_probs=149.8 Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEECCCCCCC-CC Q ss_conf 989999999999999999999999999981--599478999999999999999999999999539971437822572-04 Q gi|254780720|r 2 TNTRDRVLNELMNMEYVAQYHYMQAAAWAA--SHNLDGCCNFLLKHAMEEHSHVIRIFKHLTDLGVEAKFSSIEAPV-IS 78 (164) Q Consensus 2 s~~~~~~Ln~qi~~El~as~~Yl~~a~~~~--~~~~~g~a~~f~~~a~EE~~HA~~l~~yi~~rgg~~~~~~i~~p~-~~ 78 (164) ++..+.++|.|||.|+++||.|++||+||+ ++.++||++||..+|.|||+||.+++.|+++|||.+++++|.+|. .+ T Consensus 14 ~~~~~~~in~~in~el~~sy~Ylsma~yf~rd~v~l~g~~~ff~~~s~eereha~klm~~~n~rgg~i~l~~i~~P~~~e 93 (178) T KOG2332 14 HDEAEAAINSQINLELNASYVYLSMAAYFDRDDVALKGFAKFFLKQSQEEREHAEKLMKTQNMRGGRIELQDIKKPELDE 93 (178) T ss_pred HHHCCCHHHHHCCCHHCCCHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCHH T ss_conf 00020012011040220014554135326811023020666624430202225999999998717853135444554203 Q ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHCCC--CCHHHHHHHH Q ss_conf 8898999999999999999999999999997099889999999-999999999999999999995288--7516999999 Q gi|254780720|r 79 ANDVEGLFSLMYEHENKVTIAYDDAIETILAEKDHQTFQFLQW-FVKEQHEEMALFRRILDKIRLIGS--GPHSRYMFDL 155 (164) Q Consensus 79 ~~~~~e~~~~al~~E~~vt~~~~~l~~~A~~~~D~~t~~fl~~-fl~EQ~eee~~~~~ll~~l~~~g~--~~~glyl~D~ 155 (164) |.+-..+++.|+.+|+.|+.++.+|+.+|.+.+|++..+|++. |+.||++..+++++.+++++++|. .|+|.|+||+ T Consensus 94 w~~~l~ale~al~LEk~vn~sLl~Lh~lA~~knD~hL~dflE~~fL~eQVksIkeL~~~~~~l~k~~~~~~g~~~~lfd~ 173 (178) T KOG2332 94 WGKGLEALEAALHLEKNVNQSLLELHSLATKKNDPHLCDFLESHFLNEQVKSIKELSDYLANLKKMGAPDGGLGEYLFDK 173 (178) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHH T ss_conf 77689998889999999879999999999864980788999984009999999999998876675057888702431466 Q ss_pred HHHH Q ss_conf 9996 Q gi|254780720|r 156 EIEK 159 (164) Q Consensus 156 ~l~~ 159 (164) .+.. T Consensus 174 ~~~~ 177 (178) T KOG2332 174 YLLS 177 (178) T ss_pred HHHC T ss_conf 5405 No 8 >PRK10635 bacterioferritin, iron storage and detoxification protein; Provisional Probab=99.96 E-value=9.4e-28 Score=188.36 Aligned_cols=147 Identities=16% Similarity=0.130 Sum_probs=132.9 Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEECCCCCCCCCCCC Q ss_conf 98999999999999999999999999998159947899999999999999999999999953997143782257204889 Q gi|254780720|r 2 TNTRDRVLNELMNMEYVAQYHYMQAAAWAASHNLDGCCNFLLKHAMEEHSHVIRIFKHLTDLGVEAKFSSIEAPVISAND 81 (164) Q Consensus 2 s~~~~~~Ln~qi~~El~as~~Yl~~a~~~~~~~~~g~a~~f~~~a~EE~~HA~~l~~yi~~rgg~~~~~~i~~p~~~~~~ 81 (164) +++|...||+.+..|++|++||+.+|..|++||++.+++.|+++|.|||.||.++++||+++||.|++++.+++. ...+ T Consensus 4 ~~~vi~~LN~~L~~ELtAinQYf~harm~~~wG~~~La~~~~~esieEm~HAd~LieRILfLeG~Pn~~~l~~~~-ig~~ 82 (158) T PRK10635 4 DVKIINYLNKLLGNELVAINQYFLHARMFKNWGLMRLNDVEYHESIDEMKHADKYIERILFLEGIPNLQDLGKLG-IGED 82 (158) T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCC-CCCC T ss_conf 789999999999999999999999999987389499999999998999999999999999828996601077677-6868 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHH Q ss_conf 89999999999999999999999999970998899999999999999999999999999952887516999 Q gi|254780720|r 82 VEGLFSLMYEHENKVTIAYDDAIETILAEKDHQTFQFLQWFVKEQHEEMALFRRILDKIRLIGSGPHSRYM 152 (164) Q Consensus 82 ~~e~~~~al~~E~~vt~~~~~l~~~A~~~~D~~t~~fl~~fl~EQ~eee~~~~~ll~~l~~~g~~~~glyl 152 (164) +.++|+.+++.|..++..|++.+..|++.+|++|++++..++.+ |+.++.|+-+++.+++.-|...|+ T Consensus 83 v~Eml~~Dl~~E~~ai~~y~~ai~~ce~~~D~~sr~ll~~iL~d---EEeH~dwlEtQl~lI~~~G~~nYl 150 (158) T PRK10635 83 VEEMLRSDLRLELEGAKDLREAIAYADSVHDYVSRDMMIEILAD---EEGHIDWLETELDLIGKLGLQNYL 150 (158) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 89999978999999999999999999885889789999999997---888999999999999997689999 No 9 >pfam00210 Ferritin Ferritin-like domain. This family contains ferritins and other ferritin-like proteins such as members of the DPS family and bacterioferritins. Probab=99.95 E-value=3.1e-26 Score=179.17 Aligned_cols=138 Identities=30% Similarity=0.436 Sum_probs=129.4 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEECCCCC----CCCCCCC Q ss_conf 999999999999999999999999815994789999999999999999999999995399714378225----7204889 Q gi|254780720|r 6 DRVLNELMNMEYVAQYHYMQAAAWAASHNLDGCCNFLLKHAMEEHSHVIRIFKHLTDLGVEAKFSSIEA----PVISAND 81 (164) Q Consensus 6 ~~~Ln~qi~~El~as~~Yl~~a~~~~~~~~~g~a~~f~~~a~EE~~HA~~l~~yi~~rgg~~~~~~i~~----p~~~~~~ 81 (164) .++||++|+.|+.++++|++++.+|.+.+++|++++|+.++.++++||+++++||+.|||.|..+.++. |+..+.+ T Consensus 1 ~~~Ln~~l~~e~~a~~~y~~~~~~~~g~~f~~l~~~f~~~~~ee~~had~laeri~~lgg~p~~~~~~~~~~~~~~~~~~ 80 (142) T pfam00210 1 IEALNEQLADELTASYQYLQMAWYFDGPGLPGLAEFFDEQAEEEREHADKLAERILALGGKPVLTPVELLKIEPPDEFGS 80 (142) T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHCCCCCCCCCCC T ss_conf 96989999999999999999999874998189999899999999999999999999859988876112223678777899 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC Q ss_conf 89999999999999999999999999970998899999999999999999999999999952 Q gi|254780720|r 82 VEGLFSLMYEHENKVTIAYDDAIETILAEKDHQTFQFLQWFVKEQHEEMALFRRILDKIRLI 143 (164) Q Consensus 82 ~~e~~~~al~~E~~vt~~~~~l~~~A~~~~D~~t~~fl~~fl~EQ~eee~~~~~ll~~l~~~ 143 (164) +.++++.+++.|+.++..|+++++.|.+.+|+.|.+|++||+.+|.+++..++.++++++++ T Consensus 81 ~~~~l~~~l~~e~~~~~~~~~~~~~a~~~~D~~t~~ll~~~l~e~~~~~~~l~~~L~~~~~~ 142 (142) T pfam00210 81 VLEALEAALEHEKEVTESLRELIELAEEEGDYATADFLEWFLEEQEEHEWMLEALLEKLKRI 142 (142) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC T ss_conf 99999999999999999999999999823758899999999999999999999999986639 No 10 >COG2193 Bfr Bacterioferritin (cytochrome b1) [Inorganic ion transport and metabolism] Probab=99.93 E-value=5.2e-24 Score=165.60 Aligned_cols=147 Identities=16% Similarity=0.198 Sum_probs=129.4 Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEECCCCCCCCCCCC Q ss_conf 98999999999999999999999999998159947899999999999999999999999953997143782257204889 Q gi|254780720|r 2 TNTRDRVLNELMNMEYVAQYHYMQAAAWAASHNLDGCCNFLLKHAMEEHSHVIRIFKHLTDLGVEAKFSSIEAPVISAND 81 (164) Q Consensus 2 s~~~~~~Ln~qi~~El~as~~Yl~~a~~~~~~~~~g~a~~f~~~a~EE~~HA~~l~~yi~~rgg~~~~~~i~~p~~~~~~ 81 (164) .++|...||+++..|+.|.++|+.+|.++.+||+..++++++++|.+||.||++++++|++++|.|++++.++ -....+ T Consensus 4 ~~~Vi~~LN~~L~~EL~ainQYflHsrM~~~WG~~~L~~~~~~esi~Em~HAd~lieRIlfLeG~Pnlq~~~~-l~iG~t 82 (157) T COG2193 4 DPKVIRLLNEALGLELAAINQYFLHSRMYKNWGLTKLAAHEYHESIEEMKHADQLIERILFLEGLPNLQDLGK-LRIGET 82 (157) T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCC-CCCCCC T ss_conf 1899999999999899999999999999816474789999999879999989999999994168987230333-225887 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHH Q ss_conf 89999999999999999999999999970998899999999999999999999999999952887516999 Q gi|254780720|r 82 VEGLFSLMYEHENKVTIAYDDAIETILAEKDHQTFQFLQWFVKEQHEEMALFRRILDKIRLIGSGPHSRYM 152 (164) Q Consensus 82 ~~e~~~~al~~E~~vt~~~~~l~~~A~~~~D~~t~~fl~~fl~EQ~eee~~~~~ll~~l~~~g~~~~glyl 152 (164) +.++++.+|.+|..+...+.+.+..|.+.+||+|++.+..++..+-++.+++. +++.+++.-|...|+ T Consensus 83 v~E~L~~DL~~E~~a~~~lk~~i~~~e~~~Dyvsrdl~~~iL~deEEHid~Le---tqL~li~~~G~~nY~ 150 (157) T COG2193 83 VKEMLEADLALEYEARDALKEAIAYCEEVQDYVSRDLLEEILADEEEHIDWLE---TQLDLIAKIGEENYL 150 (157) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHCCHHHHHHHHH---HHHHHHHHHHHHHHH T ss_conf 79999978898899999999999999860563389999999816077799999---999999997677799 No 11 >cd01052 DPSL DPS-like protein, ferritin-like diiron-binding domain. DPSL (DPS-like). DPSL is a phylogenetically distinct class within the ferritin-like superfamily, and similar in many ways to the DPS (DNA Protecting protein under Starved conditions) proteins. Like DPS, these proteins are expressed in response to oxidative stress, form dodecameric cage-like particles, preferentially utilize hydrogen peroxide in the controlled oxidation of iron, and possess a short N-terminal extension implicated in stabilizing cellular DNA. This domain is a member of a broad superfamily of ferritin-like diiron-carboxylate proteins. These proteins are distantly related to bacterial ferritins which assemble 24 monomers, each of which have a four-helix bundle with a fifth shorter helix at the C terminus and a diiron (ferroxidase) center. Ferritins contain a center where oxidation of ferrous iron by molecular oxygen occurs, facilitating the detoxification of iron, protection against dioxygen and radical Probab=99.92 E-value=4.9e-23 Score=159.70 Aligned_cols=134 Identities=19% Similarity=0.218 Sum_probs=120.5 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEECCCC--------- Q ss_conf 89999999999999999999999999981599478999999999999999999999999539971437822--------- Q gi|254780720|r 3 NTRDRVLNELMNMEYVAQYHYMQAAAWAASHNLDGCCNFLLKHAMEEHSHVIRIFKHLTDLGVEAKFSSIE--------- 73 (164) Q Consensus 3 ~~~~~~Ln~qi~~El~as~~Yl~~a~~~~~~~~~g~a~~f~~~a~EE~~HA~~l~~yi~~rgg~~~~~~i~--------- 73 (164) +++.+.||+.+..|++|+++|+.+|.+|.++++++++++|+.+|.|||.||.+++++|+++||.|.+++-. T Consensus 5 ~~vIe~LN~aL~~El~ai~qY~~~a~~~~g~~~~~l~~~~~e~a~eE~~HA~~laeRI~~LgG~P~~~~~~~~~~~~~~~ 84 (148) T cd01052 5 DELIELLNKAFADEWLAYYYYTILAKHVKGPEGEGIKEELEEAAEEELNHAELLAERIYELGGTPPRDPKDWYEISGCKC 84 (148) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHCCCC T ss_conf 99999999999999999999999999982888068999999998999999999999999859958988889999803656 Q ss_pred -CCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf -5720488989999999999999999999999999970998899999999999999999999999 Q gi|254780720|r 74 -APVISANDVEGLFSLMYEHENKVTIAYDDAIETILAEKDHQTFQFLQWFVKEQHEEMALFRRIL 137 (164) Q Consensus 74 -~p~~~~~~~~e~~~~al~~E~~vt~~~~~l~~~A~~~~D~~t~~fl~~fl~EQ~eee~~~~~ll 137 (164) .++.+..++.++++.+++.|+.++..|+++++.|.. +|++|++++..++.+..++..++.+++ T Consensus 85 ~~~~~~~~dv~emL~~~l~~E~~AI~~Y~e~i~~~~~-~D~~t~~l~~~IL~dEeeH~~~le~lL 148 (148) T cd01052 85 GYLPPDPPDVKGILKVNLKAERCAIKVYKELCDMTHG-KDPVTYDLALAILNEEIEHEEDLEELL 148 (148) T ss_pred CCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHC-CCHHHHHHHHHHHHHHHHHHHHHHHHC T ss_conf 6788887779999999999999999999999999878-998999999999999998999999769 No 12 >PRK13456 DNA protection protein DPS; Provisional Probab=99.82 E-value=2.9e-18 Score=130.74 Aligned_cols=135 Identities=17% Similarity=0.239 Sum_probs=123.0 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEECCCC-------C- Q ss_conf 89999999999999999999999999981599478999999999999999999999999539971437822-------5- Q gi|254780720|r 3 NTRDRVLNELMNMEYVAQYHYMQAAAWAASHNLDGCCNFLLKHAMEEHSHVIRIFKHLTDLGVEAKFSSIE-------A- 74 (164) Q Consensus 3 ~~~~~~Ln~qi~~El~as~~Yl~~a~~~~~~~~~g~a~~f~~~a~EE~~HA~~l~~yi~~rgg~~~~~~i~-------~- 74 (164) +++.++||+.+..|+.|.|+|..++..+.+..-++++..|...+.||+.||+++.++|.++||.|...+-. . T Consensus 17 d~lI~lLn~A~A~E~~ayy~Y~~~~~~~~G~~~e~iae~~e~aa~Ee~~HAd~la~RI~QLGG~pp~dp~~~~~~s~c~~ 96 (184) T PRK13456 17 DKLVELLVKNAAAEFTTYYYYTILRAHLIGLEGEGLKEIAEDARLEDRNHFEALVPRIYELGGSLPRDMKEFHDISACPP 96 (184) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHCCCCC T ss_conf 99999999999999999999999999973635088999999999999999999999999809989999799998826985 Q ss_pred --CCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf --7204889899999999999999999999999999709988999999999999999999999999 Q gi|254780720|r 75 --PVISANDVEGLFSLMYEHENKVTIAYDDAIETILAEKDHQTFQFLQWFVKEQHEEMALFRRILD 138 (164) Q Consensus 75 --p~~~~~~~~e~~~~al~~E~~vt~~~~~l~~~A~~~~D~~t~~fl~~fl~EQ~eee~~~~~ll~ 138 (164) .+.+++++.++++.++..|+.++..|+++++... .+|++|++++..+|.+.++++++|.+++. T Consensus 97 ~y~P~~~tDl~~ml~~nl~AErcAI~~Y~eii~~t~-gKDP~T~~la~~IL~dE~EHe~~f~ell~ 161 (184) T PRK13456 97 AYLPENPTDIKEILKVLLEAEQCAVRQYTEICNMTA-GKDHRTYDLALAILNEEIEHESWFSEFLG 161 (184) T ss_pred CCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHC-CCCCCHHHHHHHHHHHHHHHHHHHHHHHC T ss_conf 468999632999999999999999999999999975-89941999999999999998999999975 No 13 >TIGR00754 bfr bacterioferritin; InterPro: IPR002024 Bacterioferritin (BFR; also known as cytochrome b1 or cytochrome b557) , of Escherichia coli is an iron-storage protein consisting of 24 identical subunits that pack together to form a highly symmetrical, nearly spherical shell surrounding a central cavity of about 8 nm diameter , . X-ray crystallographic studies have revealed a close structural similarity between BFR and the ferritins, a family of iron-storage proteins found in both eukaryotes and bacteria . Common to both ferritins and BFRs is a capacity to store large quantities of iron within their hollow interior, in the form of a hydrated ferric oxide mineral containing variable amounts of phosphate anion. However, a major difference between them is that BFR contains up 12 b-type haem groups, while ferritins, as isolated, do not contain haem. The building block for the BFR shell is a protein dimer (subunits A and B) binding the single haem group. Each subunit consists of four nearly parallel alpha-helices. The haem is bound symmetrically to subunits A and B by Met(A)-52 and Met(B)-52 residues . Each subunit includes a binuclear metal-binding site linking together the four major helices of the subunit, which has been identified as the ferroxidase centre of BFR . BFR mutants with Met-52 replaced are haem-free, but appear to be correctly assembled and are capable of accumulating iron .; GO: 0008199 ferric iron binding, 0006826 iron ion transport, 0006879 cellular iron ion homeostasis. Probab=99.59 E-value=5.9e-14 Score=104.53 Aligned_cols=147 Identities=16% Similarity=0.164 Sum_probs=131.7 Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEECCCCCCCCCCCC Q ss_conf 98999999999999999999999999998159947899999999999999999999999953997143782257204889 Q gi|254780720|r 2 TNTRDRVLNELMNMEYVAQYHYMQAAAWAASHNLDGCCNFLLKHAMEEHSHVIRIFKHLTDLGVEAKFSSIEAPVISAND 81 (164) Q Consensus 2 s~~~~~~Ln~qi~~El~as~~Yl~~a~~~~~~~~~g~a~~f~~~a~EE~~HA~~l~~yi~~rgg~~~~~~i~~p~~~~~~ 81 (164) +..+...||+++..|+.|.++|+.++..|++||+..++.+-++.+.+++.||..++++++.+.|.|.++.+.+... ..+ T Consensus 4 ~~~~~~~ln~~l~~~l~~~n~yflh~~~~~~Wg~~~l~~~~~~~~~~~~~~~~~~~~~~l~l~g~pn~~~~g~l~~-g~~ 82 (157) T TIGR00754 4 DPDVLQHLNKLLGNELTAINQYFLHARMCKNWGLKELADHEYHESIDEMKHADELIERILFLEGLPNLQDLGKLLI-GET 82 (157) T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHC-CCH T ss_conf 3789999999887677788788887665410251456666777668887667889988987615754344545430-311 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHH Q ss_conf 89999999999999999999999999970998899999999999999999999999999952887516999 Q gi|254780720|r 82 VEGLFSLMYEHENKVTIAYDDAIETILAEKDHQTFQFLQWFVKEQHEEMALFRRILDKIRLIGSGPHSRYM 152 (164) Q Consensus 82 ~~e~~~~al~~E~~vt~~~~~l~~~A~~~~D~~t~~fl~~fl~EQ~eee~~~~~ll~~l~~~g~~~~glyl 152 (164) +.+++...+..+..+...+...+..|++..|+.+++.+..++.+ ++.+++++-+++.++...|...|+ T Consensus 83 ~~e~~~~dl~~~~~~~~~l~~~~~~~~~~~d~~~~~~~~~~~~~---~e~~~dwle~~~~l~~~~g~~~y~ 150 (157) T TIGR00754 83 VPELLEADLALELDVLDGLKEGIAYAEEVRDYVSRDLLEEILED---EEEHIDWLETQLWLIDKLGLENYL 150 (157) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 58875212344343210245667765444456779999999732---223456778889998752167788 No 14 >cd00657 Ferritin_like Ferritin-like superfamily of diiron-containing four-helix-bundle proteins. Ferritin-like, diiron-carboxylate proteins participate in a range of functions including iron regulation, mono-oxygenation, and reactive radical production. These proteins are characterized by the fact that they catalyze dioxygen-dependent oxidation-hydroxylation reactions within diiron centers; one exception is manganese catalase, which catalyzes peroxide-dependent oxidation-reduction within a dimanganese center. Diiron-carboxylate proteins are further characterized by the presence of duplicate metal ligands, glutamates and histidines (ExxH) and two additional glutamates within a four-helix bundle. Outside of these conserved residues there is little obvious homology. Members include bacterioferritin, ferritin, rubrerythrin, aromatic and alkene monooxygenase hydroxylases (AAMH), ribonucleotide reductase R2 (RNRR2), acyl-ACP-desaturases (Acyl_ACP_Desat), manganese (Mn) catalases, demethoxyub Probab=99.48 E-value=4.8e-12 Score=92.92 Aligned_cols=124 Identities=27% Similarity=0.322 Sum_probs=108.4 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEECC-----CCCCCCCCCC Q ss_conf 99999999999999999999999815994789999999999999999999999995399714378-----2257204889 Q gi|254780720|r 7 RVLNELMNMEYVAQYHYMQAAAWAASHNLDGCCNFLLKHAMEEHSHVIRIFKHLTDLGVEAKFSS-----IEAPVISAND 81 (164) Q Consensus 7 ~~Ln~qi~~El~as~~Yl~~a~~~~~~~~~g~a~~f~~~a~EE~~HA~~l~~yi~~rgg~~~~~~-----i~~p~~~~~~ 81 (164) +.||..++.|+.|+..|..++..+. .|.+.+.|+..+.+|+.|+..+.+++..+||.|..+. ...+.....+ T Consensus 1 ~~L~~~l~~E~~a~~~Y~~~a~~~~---~~~~~~~~~~~a~eE~~H~~~l~~~~~~l~~~p~~~~~~~~~~~~~~~~~~~ 77 (130) T cd00657 1 RLLNDALAGEYAAIIAYGQLAARAP---DPDLKDELLEIADEERRHADALAERLRELGGTPPLPPAHLLAAYALPKTSDD 77 (130) T ss_pred CHHHHHHHHHHHHHHHHHHHHHHCC---CHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHCCCCCCCCC T ss_conf 9888999999999999999998889---9779999999999999999999999998089888875033330001458999 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 8999999999999999999999999997099889999999999999999999999 Q gi|254780720|r 82 VEGLFSLMYEHENKVTIAYDDAIETILAEKDHQTFQFLQWFVKEQHEEMALFRRI 136 (164) Q Consensus 82 ~~e~~~~al~~E~~vt~~~~~l~~~A~~~~D~~t~~fl~~fl~EQ~eee~~~~~l 136 (164) +.+++..++..|..+...|.+++..+ .|+.+..++..++.+...+...+..+ T Consensus 78 ~~~~l~~~~~~E~~a~~~y~~~~~~~---~d~~~~~~~~~i~~dE~~H~~~~~~~ 129 (130) T cd00657 78 PAEALRAALEVEARAIAAYRELIEQA---DDPELRRLLERILADEQRHAAWFRKL 129 (130) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHC---CCHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 99999999999999999999999872---88999999999999999999999966 No 15 >cd07908 Mn_catalase_like Manganese catalase-like protein, ferritin-like diiron-binding domain. This uncharacterized bacterial protein family has a ferritin-like domain similar to that of the manganese catalase protein of Lactobacillus plantarum and the bll3758 protein of Bradyrhizobium japonicum. Ferritin-like, diiron-carboxylate proteins participate in a range of functions including iron regulation, mono-oxygenation, and reactive radical production. These proteins are characterized by the fact that they catalyze dioxygen-dependent oxidation-hydroxylation reactions within diiron centers; one exception is manganese catalase, which catalyzes peroxide-dependent oxidation-reduction within a dimanganese center. Diiron-carboxylate proteins are further characterized by the presence of duplicate metal ligands, glutamates and histidines (ExxH) and two additional glutamates within a four-helix bundle. Outside of these conserved residues there is little obvious homology. Members include bacterio Probab=99.39 E-value=6e-11 Score=86.26 Aligned_cols=131 Identities=16% Similarity=0.203 Sum_probs=110.7 Q ss_pred CHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEECCCCCC--- Q ss_conf 9899999999999---9999999999999998159947899999999999999999999999953997143782257--- Q gi|254780720|r 2 TNTRDRVLNELMN---MEYVAQYHYMQAAAWAASHNLDGCCNFLLKHAMEEHSHVIRIFKHLTDLGVEAKFSSIEAP--- 75 (164) Q Consensus 2 s~~~~~~Ln~qi~---~El~as~~Yl~~a~~~~~~~~~g~a~~f~~~a~EE~~HA~~l~~yi~~rgg~~~~~~i~~p--- 75 (164) +..+.+.|-+|+. .|++|+.+|+..+..+++ +++.+++.|.+-|.|||.|.+.+...|..+||.|........ T Consensus 11 np~~A~~l~~~~gG~~gElsA~~qYl~q~~~~~~-~~~~i~~ll~dIa~eEm~HlE~i~~~I~~Lgg~p~~~~~~~~~~~ 89 (154) T cd07908 11 NPRYAELLLDDYAGTNSELTAISQYIYQHLISEE-KYPEIAETFLGIAIVEMHHLEILGQLIVLLGGDPRYRSSSSDKFT 89 (154) T ss_pred CHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHCCC-CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEECCCCCC T ss_conf 9899999999848961689999999998970789-847999999999999999999999999991899841303688777 Q ss_pred ------CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf ------2048898999999999999999999999999997099889999999999999999999999 Q gi|254780720|r 76 ------VISANDVEGLFSLMYEHENKVTIAYDDAIETILAEKDHQTFQFLQWFVKEQHEEMALFRRI 136 (164) Q Consensus 76 ------~~~~~~~~e~~~~al~~E~~vt~~~~~l~~~A~~~~D~~t~~fl~~fl~EQ~eee~~~~~l 136 (164) .....++.+.+..+++.|+.....|.+++..+ +|+.+.+.|+.++.....|...|+.. T Consensus 90 ~wt~~yv~~~~~~~~~L~~diaaE~~A~~~Y~~~~~~i---~D~~vk~~L~~ii~dE~~H~~~F~e~ 153 (154) T cd07908 90 YWTGKYVNYGESIKEMLKLDIASEKAAIAKYKRQAETI---KDPYIRALLNRIILDEKLHIKILEEL 153 (154) T ss_pred CCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHC---CCHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 48875558899999999999999999999999999976---88879999999999999999999975 No 16 >COG2406 Protein distantly related to bacterial ferritins [General function prediction only] Probab=99.27 E-value=1e-09 Score=78.80 Aligned_cols=135 Identities=16% Similarity=0.218 Sum_probs=115.0 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCE--------ECCCCC Q ss_conf 899999999999999999999999999815994789999999999999999999999995399714--------378225 Q gi|254780720|r 3 NTRDRVLNELMNMEYVAQYHYMQAAAWAASHNLDGCCNFLLKHAMEEHSHVIRIFKHLTDLGVEAK--------FSSIEA 74 (164) Q Consensus 3 ~~~~~~Ln~qi~~El~as~~Yl~~a~~~~~~~~~g~a~~f~~~a~EE~~HA~~l~~yi~~rgg~~~--------~~~i~~ 74 (164) +++.++|-..-..|+++.|.|+..+....+..-.|...+...--.|-+.|+..+..+|.+.||.|. ++.-+. T Consensus 16 ~kli~~Llka~AaE~tt~YYYtilr~~l~Gle~e~~keiae~Ar~E~r~H~e~i~~Ri~elg~~~Prd~~~l~dISgC~~ 95 (172) T COG2406 16 DKLIELLLKAAAAEWTTYYYYTILRYALKGLEGEGIKEIAEEAREEDRKHFELIAPRIYELGGDLPRDMKKLHDISGCKP 95 (172) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHCCCCC T ss_conf 99999999999999999999999999980321578999999999999989999999999828998266999876417998 Q ss_pred --CCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf --7204889899999999999999999999999999709988999999999999999999999999 Q gi|254780720|r 75 --PVISANDVEGLFSLMYEHENKVTIAYDDAIETILAEKDHQTFQFLQWFVKEQHEEMALFRRILD 138 (164) Q Consensus 75 --p~~~~~~~~e~~~~al~~E~~vt~~~~~l~~~A~~~~D~~t~~fl~~fl~EQ~eee~~~~~ll~ 138 (164) .|.++.++.+++..+++.|+.+++.|.++++.... +|+.|.++-+.+++|.++++.++..++. T Consensus 96 a~LPedp~D~~~~l~vlv~AE~CAir~ykeic~~T~G-kDprTyeLa~~IL~eEi~hr~~~~~ll~ 160 (172) T COG2406 96 AYLPEDPYDIDEILAVLVKAERCAIRAYKEICNLTAG-KDPRTYELAEAILREEIEHRTWFLELLG 160 (172) T ss_pred CCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCC-CCCCHHHHHHHHHHHHHHHHHHHHHHHC T ss_conf 8999996578999999999999999999999731048-9943599999999999999999999813 No 17 >cd01041 Rubrerythrin Rubrerythrin, ferritin-like diiron-binding domain. Rubrerythrin domain is a nonheme iron binding domain found in many air-sensitive bacteria and archaea and member of a broad superfamily of ferritin-like diiron-carboxylate proteins. The homodimeric rubrerythrin protein contains a binuclear metal center located within a four helix bundle. Many, but not all, rubrerythrin proteins have a second domain with a rubredoxin-like hexacoordinated iron center. Rubrerythrin is thought to reduce hydrogen peroxide as part of an oxidative stress protection system but its function is still poorly understood. Probab=99.20 E-value=3.9e-09 Score=75.24 Aligned_cols=129 Identities=18% Similarity=0.178 Sum_probs=116.2 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEECCCCCCCCCCCCHHHHH Q ss_conf 99999999999999999999999815994789999999999999999999999995399714378225720488989999 Q gi|254780720|r 7 RVLNELMNMEYVAQYHYMQAAAWAASHNLDGCCNFLLKHAMEEHSHVIRIFKHLTDLGVEAKFSSIEAPVISANDVEGLF 86 (164) Q Consensus 7 ~~Ln~qi~~El~as~~Yl~~a~~~~~~~~~g~a~~f~~~a~EE~~HA~~l~~yi~~rgg~~~~~~i~~p~~~~~~~~e~~ 86 (164) +-|-.....|-.|...|+.+|..++..|++.++..|+.-|..|..||..+++.+...++.+. .|+....+..+.| T Consensus 4 ~NL~~AfaGEs~A~~rY~~fA~~A~~eG~~~iA~lF~~tA~~E~~HA~~~~~~l~~~~~~~~-----~~~~~~~~t~~NL 78 (134) T cd01041 4 KNLLAAFAGESQARNRYTYFAEKARKEGYEQIARLFRATAENEKEHAKGHFKLLKGLGGGDT-----GPPIGIGDTLENL 78 (134) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCC-----CCCCCCCCHHHHH T ss_conf 89999984789999999999999988677999999999999999999999999734576655-----5555646599999 Q ss_pred HHHHHHHH-HHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 99999999-9999999999999970998899999999999999999999999999 Q gi|254780720|r 87 SLMYEHEN-KVTIAYDDAIETILAEKDHQTFQFLQWFVKEQHEEMALFRRILDKI 140 (164) Q Consensus 87 ~~al~~E~-~vt~~~~~l~~~A~~~~D~~t~~fl~~fl~EQ~eee~~~~~ll~~l 140 (164) +.+.+.|. +.+..|-...+.|+++++......+.+..+-...+.+.+..+++.+ T Consensus 79 ~~Ai~GE~~E~~~mYP~fa~~A~~EG~~~aA~~F~~i~~~E~~H~~~y~~~l~~l 133 (134) T cd01041 79 KAAIAGETYEYTEMYPEFAEVAEEEGFKEAARSFEAIAEAEKVHAERYKKALENL 133 (134) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHC T ss_conf 9998513778999719999999886749999999999999999999999998745 No 18 >PRK09448 DNA starvation/stationary phase protection protein Dps; Provisional Probab=98.92 E-value=2.5e-07 Score=64.21 Aligned_cols=122 Identities=13% Similarity=0.115 Sum_probs=97.2 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH-HHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEE--------CCCC Q ss_conf 899999999999999999999999999-8159947899999999999999999999999953997143--------7822 Q gi|254780720|r 3 NTRDRVLNELMNMEYVAQYHYMQAAAW-AASHNLDGCCNFLLKHAMEEHSHVIRIFKHLTDLGVEAKF--------SSIE 73 (164) Q Consensus 3 ~~~~~~Ln~qi~~El~as~~Yl~~a~~-~~~~~~~g~a~~f~~~a~EE~~HA~~l~~yi~~rgg~~~~--------~~i~ 73 (164) +++.+.||..+..-..-...+ ..+.| ..+.+|-.+-.+|..+..+=.++++.+.+||..+||.|.- +.++ T Consensus 20 ~~~v~~Ln~~LAd~~~L~~k~-~~~HWnV~G~~F~~lH~~fee~y~e~~~~iD~iAERi~~LG~~p~~s~~~~~~~s~i~ 98 (164) T PRK09448 20 KATIELLNQQLAQFIDLSLIT-KQAHWNMKGANFIAVHEMLDGFRTALEDHLDTVAERAVQLGGTALGTTQVVASKTPLK 98 (164) T ss_pred HHHHHHHHHHHHHHHHHHHHH-HCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHCCCC T ss_conf 999999999999999999998-6377162484699999979999999999889999999986999998999999778798 Q ss_pred CCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHH Q ss_conf 5720488989999999999999999999999999970998899999999999 Q gi|254780720|r 74 APVISANDVEGLFSLMYEHENKVTIAYDDAIETILAEKDHQTFQFLQWFVKE 125 (164) Q Consensus 74 ~p~~~~~~~~e~~~~al~~E~~vt~~~~~l~~~A~~~~D~~t~~fl~~fl~E 125 (164) ..+....+..++++..++.-..+...+++.++.|.+.+|++|.+++..++.. T Consensus 99 e~~~~~~~~~~~l~~l~~~~~~~~~~~r~~i~~a~e~~D~~T~dll~~~~~~ 150 (164) T PRK09448 99 SYPLDIHNVQDHLKALADRYAIVANDVRKAIDEADEAGDADTADIFTAASRD 150 (164) T ss_pred CCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHH T ss_conf 7789999999999999999999999999999998877898899999999999 No 19 >cd01046 Rubrerythrin_like rubrerythrin-like, diiron-binding domain. Rubrerythrin-like domain, similar to rubrerythrin, a nonheme iron binding domain found in many air-sensitive bacteria and archaea, and member of a broad superfamily of ferritin-like diiron-carboxylate proteins. Rubrerythrin is thought to reduce hydrogen peroxide as part of an oxidative stress protection system. The rubrerythrin protein has two domains, a binuclear metal center located within a four-helix bundle of the rubrerythrin domain, and a rubredoxin domain. The Rubrerythrin-like domains in this CD are singular domains (no C-terminus rubredoxin domain) and are phylogenetically distinct from rubrerythrin domains of rubrerythrin-rubredoxin proteins. Probab=98.89 E-value=4.6e-07 Score=62.63 Aligned_cols=122 Identities=20% Similarity=0.220 Sum_probs=106.1 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEECCCCCCCCCCCCHH Q ss_conf 99999999999999999999999999815994789999999999999999999999995399714378225720488989 Q gi|254780720|r 4 TRDRVLNELMNMEYVAQYHYMQAAAWAASHNLDGCCNFLLKHAMEEHSHVIRIFKHLTDLGVEAKFSSIEAPVISANDVE 83 (164) Q Consensus 4 ~~~~~Ln~qi~~El~as~~Yl~~a~~~~~~~~~g~a~~f~~~a~EE~~HA~~l~~yi~~rgg~~~~~~i~~p~~~~~~~~ 83 (164) ++++-|.....-|-++...|+.+|...+..|||.+|..|+.-|..|..||..+.+. .|+.+ .|.. T Consensus 1 ~~E~nL~~aFaGESqA~~kY~~~A~~A~keGy~~IA~~F~~tA~~E~~HA~~~~~~---~g~~~------------~~t~ 65 (123) T cd01046 1 DLEEDLEANFKGETTEVGMYLAMARVAQREGYPEVAEELKRIAMEEAEHAARFAEL---LGKVS------------EDTK 65 (123) T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHH---CCCCC------------CCHH T ss_conf 98879999983679999999999999988584999999999999899999999987---39998------------6699 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 999999999999999999999999970998899999999999999999999999999 Q gi|254780720|r 84 GLFSLMYEHENKVTIAYDDAIETILAEKDHQTFQFLQWFVKEQHEEMALFRRILDKI 140 (164) Q Consensus 84 e~~~~al~~E~~vt~~~~~l~~~A~~~~D~~t~~fl~~fl~EQ~eee~~~~~ll~~l 140 (164) +-++.+.+-|...+..+....+.|++++.....+++....+-.-.+.+.+..+|++. T Consensus 66 eNL~~a~~GE~~e~~~~~~~a~~A~eEGf~eia~~f~~~a~~E~~H~~r~~~lLery 122 (123) T cd01046 66 ENLEMMLEGEAGANEGKKDAATEAKAEGLDEAHDFFHEAAKDEARHGKMLKGLLERY 122 (123) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 999999975167886059999999887879999999999999999999999998764 No 20 >pfam02915 Rubrerythrin Rubrerythrin. This domain has a ferritin-like fold. Probab=98.87 E-value=4.8e-07 Score=62.52 Aligned_cols=126 Identities=18% Similarity=0.175 Sum_probs=101.0 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEECCCCC-------CCC--- Q ss_conf 9999999999999999999999815994789999999999999999999999995399714378225-------720--- Q gi|254780720|r 8 VLNELMNMEYVAQYHYMQAAAWAASHNLDGCCNFLLKHAMEEHSHVIRIFKHLTDLGVEAKFSSIEA-------PVI--- 77 (164) Q Consensus 8 ~Ln~qi~~El~as~~Yl~~a~~~~~~~~~g~a~~f~~~a~EE~~HA~~l~~yi~~rgg~~~~~~i~~-------p~~--- 77 (164) .|...|..|..|...|..+|....+.| |.+++.|+.-|.+|..|+..+.+.+..+++....+.... |.. T Consensus 2 ~L~~Ai~~E~~a~~~Y~~~A~~a~~~g-~~i~~~F~~lA~~E~~Ha~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 80 (137) T pfam02915 2 ILEYAIAGESSARRRYKELAEKAKGEG-PQIAELFEEMAEEERRHAGFLNKLLKDLFPGLEPVILKEHVEYTFFPVADEL 80 (137) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHC-HHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHCCCCCCCCCCC T ss_conf 699999709999999999999997848-8999999999999999999999998763466563022443111113556363 Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 488989999999999999999999999999970998899999999999999999999999 Q gi|254780720|r 78 SANDVEGLFSLMYEHENKVTIAYDDAIETILAEKDHQTFQFLQWFVKEQHEEMALFRRIL 137 (164) Q Consensus 78 ~~~~~~e~~~~al~~E~~vt~~~~~l~~~A~~~~D~~t~~fl~~fl~EQ~eee~~~~~ll 137 (164) .-.++.++++.++..|+.....|. .+|...+|..+..++.++......|.+.+..++ T Consensus 81 ~~~nl~~a~~~a~~~e~~~y~~y~---~~A~~~~~~~~~~~f~~la~~E~~H~~~f~~ll 137 (137) T pfam02915 81 TRENLKEAIEGAMLEEKEAYPFYI---EIAEKEGEEEARRLFEDLAEAEKRHEERFRKLL 137 (137) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHH---HHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHC T ss_conf 663399999999999999999999---999887788999999999999999999999769 No 21 >cd01043 DPS DPS protein, ferritin-like diiron-binding domain. DPS (DNA Protecting protein under Starved conditions) domain is a member of a broad superfamily of ferritin-like diiron-carboxylate proteins. Some DPS proteins nonspecifically bind DNA, protecting it from cleavage caused by reactive oxygen species such as the hydroxyl radicals produced during oxidation of Fe(II) by hydrogen peroxide. These proteins assemble into dodecameric structures, some form DPS-DNA co-crystalline complexes, and possess iron and H2O2 detoxification capabilities. Expression of DPS is induced by oxidative or nutritional stress, including metal ion starvation. Members of the DPS family are homopolymers formed by 12 four-helix bundle subunits that assemble with 23 symmetry into a hollow shell. The DPS ferroxidase site is unusual in that it is not located in a four-helix bundle as in ferritin, but is shared by 2-fold symmetry-related subunits providing the iron ligands. Many DPS sequences (e.g., E. coli) disp Probab=98.83 E-value=7.2e-07 Score=61.47 Aligned_cols=118 Identities=17% Similarity=0.139 Sum_probs=96.2 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCE--------ECCCCCCCCCC Q ss_conf 9999999999999999999999815994789999999999999999999999995399714--------37822572048 Q gi|254780720|r 8 VLNELMNMEYVAQYHYMQAAAWAASHNLDGCCNFLLKHAMEEHSHVIRIFKHLTDLGVEAK--------FSSIEAPVISA 79 (164) Q Consensus 8 ~Ln~qi~~El~as~~Yl~~a~~~~~~~~~g~a~~f~~~a~EE~~HA~~l~~yi~~rgg~~~--------~~~i~~p~~~~ 79 (164) .||..+..-+.-...+-.+.=...+.++..+-.+|..+..+-.++.+.+.++|..+||.|. .+.++.++... T Consensus 2 ~Ln~~lA~~~~l~~k~~~~HWnv~G~~F~~lH~~~ee~y~~~~~~~D~iAERi~~lG~~p~~~~~~~~~~s~i~e~~~~~ 81 (139) T cd01043 2 ALNQLLADLYVLYLKLKNYHWNVKGPNFFALHELFEELYDELREAIDEIAERIRALGGKPLGTLKEYAELSTIKEEPAGV 81 (139) T ss_pred HHHHHHHHHHHHHHHHHHCCHHEECCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHCCCCCCCCCC T ss_conf 58899988999999984010001787789999999999999999999999999986999997799999768898778999 Q ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHH Q ss_conf 8989999999999999999999999999970998899999999999 Q gi|254780720|r 80 NDVEGLFSLMYEHENKVTIAYDDAIETILAEKDHQTFQFLQWFVKE 125 (164) Q Consensus 80 ~~~~e~~~~al~~E~~vt~~~~~l~~~A~~~~D~~t~~fl~~fl~E 125 (164) .+..++++..++.-..+...++++++.|.+.+|++|.+++..++.+ T Consensus 82 ~~~~~m~~~l~~~~~~~~~~~r~~~~~a~~~~D~~t~dll~~~~~~ 127 (139) T cd01043 82 LSAKEMVAELLEDYETLIEELREAIELADEAGDPATADLLTEIIRE 127 (139) T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHH T ss_conf 9999999999999999999999999998777889899999999999 No 22 >COG0783 Dps DNA-binding ferritin-like protein (oxidative damage protectant) [Inorganic ion transport and metabolism] Probab=98.78 E-value=1.8e-06 Score=58.97 Aligned_cols=123 Identities=19% Similarity=0.096 Sum_probs=98.3 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCE--------ECCCCC Q ss_conf 899999999999999999999999999815994789999999999999999999999995399714--------378225 Q gi|254780720|r 3 NTRDRVLNELMNMEYVAQYHYMQAAAWAASHNLDGCCNFLLKHAMEEHSHVIRIFKHLTDLGVEAK--------FSSIEA 74 (164) Q Consensus 3 ~~~~~~Ln~qi~~El~as~~Yl~~a~~~~~~~~~g~a~~f~~~a~EE~~HA~~l~~yi~~rgg~~~--------~~~i~~ 74 (164) .++.+.||.++..=.......-.+.=...+-++--+-.+|..+..+-..|.+.+.+|+..+||.|. .+.++. T Consensus 14 ~~~~~~Ln~~lAd~~~Ly~k~~~~HWnV~G~~F~~lHe~~ee~y~~l~~~~DeiAERi~~LGg~p~~t~~~~~~~s~ike 93 (156) T COG0783 14 KKIAEALNQLLADLYVLYLKTHNYHWNVKGPNFFALHEKLEELYEELAEHVDEIAERIRALGGVPLGTLSEYLKLSSIKE 93 (156) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHCCCCEECCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHCCCCC T ss_conf 99999999999999999999752341301865999999999999999999899999999859999523999998687754 Q ss_pred CCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHH Q ss_conf 7204889899999999999999999999999999709988999999999999 Q gi|254780720|r 75 PVISANDVEGLFSLMYEHENKVTIAYDDAIETILAEKDHQTFQFLQWFVKEQ 126 (164) Q Consensus 75 p~~~~~~~~e~~~~al~~E~~vt~~~~~l~~~A~~~~D~~t~~fl~~fl~EQ 126 (164) .+.+ .++.++++...+--..+++.+++.+++|.+.+|..|.+++..++.+. T Consensus 94 ~~~~-~~~~~~l~~l~~~~~~l~~~~r~~~~~a~e~gD~~Tadl~~~~~~~~ 144 (156) T COG0783 94 EPGD-YTAREMLKELVEDYEYLIKELRKGIELADEAGDEVTADLLTDIIREL 144 (156) T ss_pred CCCC-CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHH T ss_conf 6899-99999999999999999999999987630048863799999999999 No 23 >COG1633 Uncharacterized conserved protein [Function unknown] Probab=98.74 E-value=4.1e-06 Score=56.87 Aligned_cols=133 Identities=11% Similarity=0.138 Sum_probs=105.5 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCE-------------E Q ss_conf 899999999999999999999999999815994789999999999999999999999995399714-------------3 Q gi|254780720|r 3 NTRDRVLNELMNMEYVAQYHYMQAAAWAASHNLDGCCNFLLKHAMEEHSHVIRIFKHLTDLGVEAK-------------F 69 (164) Q Consensus 3 ~~~~~~Ln~qi~~El~as~~Yl~~a~~~~~~~~~g~a~~f~~~a~EE~~HA~~l~~yi~~rgg~~~-------------~ 69 (164) ..+.++|+..|..|..|..+|..+|....+- -+.+.|..-|.+|++|...|-+.+..+++.+. + T Consensus 23 ~~~~e~L~~Ai~~E~eA~~fY~~lae~~~~~---~~rk~~~~la~eE~~H~~~f~~l~~~~~~~~~~~~~~~~~~~~~~~ 99 (176) T COG1633 23 LSIEELLAIAIRGELEAIKFYEELAERIEDE---EIRKLFEDLADEEMRHLRKFEKLLEKLTPKEVSSEEEEGEIESEIL 99 (176) T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHHCCCH---HHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHCCHHHHHC T ss_conf 1199999999997999999999999765877---6999999999999999999999999866775430221010122322 Q ss_pred CCCCC--CCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 78225--7204889899999999999999999999999999709988999999999999999999999999999 Q gi|254780720|r 70 SSIEA--PVISANDVEGLFSLMYEHENKVTIAYDDAIETILAEKDHQTFQFLQWFVKEQHEEMALFRRILDKIR 141 (164) Q Consensus 70 ~~i~~--p~~~~~~~~e~~~~al~~E~~vt~~~~~l~~~A~~~~D~~t~~fl~~fl~EQ~eee~~~~~ll~~l~ 141 (164) +.... +.....++.+.+..+...|+.....|..+.... .|.....++.++++..-.+...+...++.+- T Consensus 100 ~~~~~~~~~~~~~~~~~~I~~a~~~E~~t~~~Y~~~~~~~---~~~~~~~~~~~~a~~E~~H~~~l~~~~~~~~ 170 (176) T COG1633 100 EYLQPGKEMEKSVSYLEAIEAAMEAEKDTIEFYEELLDEL---VNEEAKKLFKTIADDEKGHASGLLSLYNRLT 170 (176) T ss_pred CCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHC---CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 4467662134642288999999999998999999999973---6788999999999999889999999999774 No 24 >cd01045 Ferritin_like_AB Uncharacterized family of ferritin-like proteins found in archaea and bacteria. Ferritin-like domain found in archaea and bacteria (Ferritin_like_AB). This uncharacterized domain is a member of a broad superfamily of ferritin-like diiron-carboxylate proteins whose function is unknown. This family includes unknown or hypothetical proteins which were sequenced from mostly anaerobic or microaerophilic metal-metabolizing and/or nitrogen-fixing microbes. The family includes sequences from ferric-, sulfate-, and arsenic-reducing bacteria, Geobacter, Magnetospirillum, Desulfovibrio, and Desulfitobacterium. Also included are several nitrogen-fixing endosymbiotic bacteria, Rhizobium, Mesorhizobium, and Bradyrhizobium; also phototrophic purple nonsulfur bacteria, Rhodobacter and Rhodopseudomonas, as well as, obligate thermophiles, Thermotoga, Thermoanaerobacter, and Pyrococcus. The conserved residues of a diiron center are present in this uncharacterized domain. Probab=98.64 E-value=4.8e-06 Score=56.44 Aligned_cols=124 Identities=20% Similarity=0.221 Sum_probs=99.0 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCE--ECCCC-------CC-- Q ss_conf 99999999999999999999999815994789999999999999999999999995399714--37822-------57-- Q gi|254780720|r 7 RVLNELMNMEYVAQYHYMQAAAWAASHNLDGCCNFLLKHAMEEHSHVIRIFKHLTDLGVEAK--FSSIE-------AP-- 75 (164) Q Consensus 7 ~~Ln~qi~~El~as~~Yl~~a~~~~~~~~~g~a~~f~~~a~EE~~HA~~l~~yi~~rgg~~~--~~~i~-------~p-- 75 (164) ++|.-.|..|-.+.-+|..+|..+.+ |+..+.|..-|.+|..|...|.+......+.+. .+... .| T Consensus 1 eil~~Ai~~E~~~~~fY~~~a~~~~~---~~~k~~f~~LA~eE~~H~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~ 77 (139) T cd01045 1 EILALAIKMEEEAAEFYLELAEKAKD---PELKKLFEELAEEEKEHAERLEELYEKLFGEELPELEPEDYKEEVEEEPEF 77 (139) T ss_pred CHHHHHHHHHHHHHHHHHHHHHHCCC---HHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHCCCHHHH T ss_conf 99999999899999999999987798---899999999999999999999999865137777731034431000000668 Q ss_pred ---CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf ---2048898999999999999999999999999997099889999999999999999999999 Q gi|254780720|r 76 ---VISANDVEGLFSLMYEHENKVTIAYDDAIETILAEKDHQTFQFLQWFVKEQHEEMALFRRI 136 (164) Q Consensus 76 ---~~~~~~~~e~~~~al~~E~~vt~~~~~l~~~A~~~~D~~t~~fl~~fl~EQ~eee~~~~~l 136 (164) .....++.++++.|+..|+.....|..+...+ .|..+..++.++..+...|...+..+ T Consensus 78 ~~~~~~~~~~~~~l~~Ai~~E~~a~~fY~~la~~~---~d~~~r~l~~~La~eE~~H~~~L~~~ 138 (139) T cd01045 78 KKALESLMDPLEALRLAIEIEKDAIEFYEELAEKA---EDPEVKKLFEELAEEERGHLRLLEEL 138 (139) T ss_pred HHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHC---CCHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 88630359999999999999999999999998768---99999999999999999999999976 No 25 >cd01051 Mn_catalase Manganese catalase, ferritin-like diiron-binding domain. Manganese (Mn) catalase is a member of a broad superfamily of ferritin-like diiron enzymes. While many diiron enzymes catalyze dioxygen-dependent reactions, manganese catalase performs peroxide-dependent oxidation-reduction. Catalases are important antioxidant metalloenzymes that catalyze disproportionation of hydrogen peroxide, forming dioxygen and water. Manganese catalase, a nonheme type II catalase, contains a binuclear manganese cluster that catalyzes the redox dismutation of hydrogen peroxide, interconverting between dimanganese(II) [(2,2)] and dimanganese(III) [(3,3)] oxidation states during turnover. Mn catalases are found in a broad range of microorganisms in microaerophilic environments, including the mesophilic lactic acid bacteria (e.g., Lactobacillus plantarum) and bacterial and archaeal thermophiles (e.g., Thermus thermophilus and Pyrobaculum caldifontis). L. plantarum and T. thermophilus holoenz Probab=98.61 E-value=7.9e-06 Score=55.13 Aligned_cols=134 Identities=16% Similarity=0.158 Sum_probs=104.8 Q ss_pred CHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEECCCC-CCCC Q ss_conf 9899999999999---99999999999999981599478999999999999999999999999539971437822-5720 Q gi|254780720|r 2 TNTRDRVLNELMN---MEYVAQYHYMQAAAWAASHNLDGCCNFLLKHAMEEHSHVIRIFKHLTDLGVEAKFSSIE-APVI 77 (164) Q Consensus 2 s~~~~~~Ln~qi~---~El~as~~Yl~~a~~~~~~~~~g~a~~f~~~a~EE~~HA~~l~~yi~~rgg~~~~~~i~-~p~~ 77 (164) +....++|.+|+. .|++|+.+|+..+.-+. ..+.+...+.+-+.||+.|.+.+..-|..++..+.-.+=. .-.. T Consensus 18 np~~A~~l~e~~GG~~GElsa~~qYl~Q~~~~~--~~~~~~dll~dI~teEl~HlEml~t~I~~L~~ds~G~pWt~~yv~ 95 (156) T cd01051 18 DPRFAKLLQEQLGGAFGELSAAMQYLFQSFNFR--EDPKYRDLLLDIGTEELSHLEMVATLIAMLLKDSQGVPWTAAYIQ 95 (156) T ss_pred CHHHHHHHHHHHCCCCHHHHHHHHHHHHHHCCC--CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHH T ss_conf 989999999986897248999999999886046--777799999999999999999999999997168899989736870 Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 488989999999999999999999999999970998899999999999999999999999999 Q gi|254780720|r 78 SANDVEGLFSLMYEHENKVTIAYDDAIETILAEKDHQTFQFLQWFVKEQHEEMALFRRILDKI 140 (164) Q Consensus 78 ~~~~~~e~~~~al~~E~~vt~~~~~l~~~A~~~~D~~t~~fl~~fl~EQ~eee~~~~~ll~~l 140 (164) ...++...+...++.|......|.+++... +|+...+.|...+...+-+..-+...+..+ T Consensus 96 ~~gdl~~dL~~niaaE~~Ar~~y~rl~~~~---dDp~v~~~L~fL~~rE~~H~~~f~~ale~l 155 (156) T cd01051 96 SSGNLVADLRSNIAAESRARLTYERLYEMT---DDPGVKDTLSFLLVREIVHQNAFGKALESL 155 (156) T ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHHHHC---CCCCHHHHHHHHHHHHHHHHHHHHHHHHHC T ss_conf 689799999989999999999999999854---981099999999998899999999999972 No 26 >COG1592 Rubrerythrin [Energy production and conversion] Probab=98.41 E-value=4.2e-05 Score=50.71 Aligned_cols=127 Identities=18% Similarity=0.145 Sum_probs=106.2 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEECCCCCCCCCCCCH Q ss_conf 89999999999999999999999999981599478999999999999999999999999539971437822572048898 Q gi|254780720|r 3 NTRDRVLNELMNMEYVAQYHYMQAAAWAASHNLDGCCNFLLKHAMEEHSHVIRIFKHLTDLGVEAKFSSIEAPVISANDV 82 (164) Q Consensus 3 ~~~~~~Ln~qi~~El~as~~Yl~~a~~~~~~~~~g~a~~f~~~a~EE~~HA~~l~~yi~~rgg~~~~~~i~~p~~~~~~~ 82 (164) ...++-|-+...-|-.|...|+.||...+..|+|.+|+.|+..|.+|..||..+.+-+...+ ....+. T Consensus 3 ~~t~~~L~~aF~GEs~a~~rY~~~A~~A~~eG~~~va~lfr~iA~~E~~HA~~~~~~l~~~~------------~~~~~~ 70 (166) T COG1592 3 METEENLRKAFAGESMAVMRYLIFAKVAEEEGYPEIARLFRAIAEAEAVHAKNHLKLLGKLL------------LVLGDT 70 (166) T ss_pred CHHHHHHHHHHCCHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCC------------CCCCCH T ss_conf 13899999996310999999999999999877889999999999999999999999963000------------122638 Q ss_pred HHHHHHHHHHHHHH-HHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 99999999999999-999999999999709988999999999999999999999999999 Q gi|254780720|r 83 EGLFSLMYEHENKV-TIAYDDAIETILAEKDHQTFQFLQWFVKEQHEEMALFRRILDKIR 141 (164) Q Consensus 83 ~e~~~~al~~E~~v-t~~~~~l~~~A~~~~D~~t~~fl~~fl~EQ~eee~~~~~ll~~l~ 141 (164) .+-++.+.+-|..- +..+......|...++-.....+.+...-.-.+...+..+++.++ T Consensus 71 ~eNl~~aieGE~~e~~emyp~~ae~A~~~g~~~~a~~f~~~~~~Ek~H~~~~~~~Le~~~ 130 (166) T COG1592 71 RENLEEAIEGETYEITEMYPVFAEVAEEEGFKEAARSFRAAAKAEKRHAEMFRGLLERLE 130 (166) T ss_pred HHHHHHHHCCCHHHHHHHCHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 999999986610778886768999999858089999999999899998999999998660 No 27 >pfam05067 Mn_catalase Manganese containing catalase. Catalases are important antioxidant metalloenzymes that catalyse disproportionation of hydrogen peroxide, forming dioxygen and water. Two families of catalases are known, one having a heme cofactor, and this family that is a structurally distinct family containing non-heme manganese. Probab=97.74 E-value=0.0036 Score=38.94 Aligned_cols=134 Identities=16% Similarity=0.206 Sum_probs=98.5 Q ss_pred CHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEC-------- Q ss_conf 98999999999999---9999999999999981599478999999999999999999999999539971437-------- Q gi|254780720|r 2 TNTRDRVLNELMNM---EYVAQYHYMQAAAWAASHNLDGCCNFLLKHAMEEHSHVIRIFKHLTDLGVEAKFS-------- 70 (164) Q Consensus 2 s~~~~~~Ln~qi~~---El~as~~Yl~~a~~~~~~~~~g~a~~f~~~a~EE~~HA~~l~~yi~~rgg~~~~~-------- 70 (164) +....++|.+|+.- |+.++.+|+..+.-|.+.+. ...+...+.||+.|.+.+..-|..+-...... T Consensus 18 DP~~A~~lqeq~GG~~GElsaamqYl~Q~~~~r~~~~---kdLL~dI~tEEl~HvEmvat~I~~Ll~ga~~~~~~~a~~~ 94 (272) T pfam05067 18 DPVLAKKLQEQLGGQFGELSAAMRYLFQGFNTRDKGK---KDLLMDIGTEELGHVEMIATMIARLLKGATPDQQEDAAEI 94 (272) T ss_pred CHHHHHHHHHHHCCCCHHHHHHHHHHHHHHCCCCHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHH T ss_conf 9899999999957972499999999998727898058---7899887789988999999999998169983101455566 Q ss_pred ---------------C--------CCCC-----CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHH Q ss_conf ---------------8--------2257-----20488989999999999999999999999999970998899999999 Q gi|254780720|r 71 ---------------S--------IEAP-----VISANDVEGLFSLMYEHENKVTIAYDDAIETILAEKDHQTFQFLQWF 122 (164) Q Consensus 71 ---------------~--------i~~p-----~~~~~~~~e~~~~al~~E~~vt~~~~~l~~~A~~~~D~~t~~fl~~f 122 (164) . ...| .....++..=|...+..|......+.+|++.+ .|+...+.|... T Consensus 95 ~~~~~~~n~~h~i~~g~g~~p~ds~G~PWt~~Yi~~sGnl~aDL~~N~aaE~~aR~~y~rL~~mT---dDp~vkd~L~FL 171 (272) T pfam05067 95 GSVLGGMNPQHAIVSGLGAMPHDSAGVPWTADYIVASGNLIADLRANLAAESQARLQYTRLYEMT---DDPGVRDMLSFL 171 (272) T ss_pred HHHHCCCCCCEEEECCCCCCCCCCCCCCCCCCEEEECCCHHHHHHHHHHHHHHHHHHHHHHHHHC---CCCCHHHHHHHH T ss_conf 76543788400230388777467899956600023148778889998999975499999999810---882399999999 Q ss_pred HHHHHHHHHHHHHHHHHHH Q ss_conf 9999999999999999999 Q gi|254780720|r 123 VKEQHEEMALFRRILDKIR 141 (164) Q Consensus 123 l~EQ~eee~~~~~ll~~l~ 141 (164) +.-.+-+..-+...|..|. T Consensus 172 ~~Re~~Hq~~f~~ALe~l~ 190 (272) T pfam05067 172 IVRDTVHQNAFAKALEILE 190 (272) T ss_pred HHHHHHHHHHHHHHHHHHC T ss_conf 9998999999999999830 No 28 >cd01042 DMQH Demethoxyubiquinone hydroxylase, ferritin-like diiron-binding domain. Demethoxyubiquinone hydroxylases (DMQH) are members of the ferritin-like, diiron-carboxylate family which are present in eukaryotes (the CLK-1/CAT5 family) and prokaryotes (the Coq7 family). DMQH participates in one of the last steps of ubiquinone biosysnthesis and is responsible for DMQ hydroxylation, resulting in the formation of hydroxyubiquinone, a precursor of ubiquinone. CLK-1 is a mitochondrial inner membrane protein and Coq7 is a proposed interfacial integral membrane protein. Mutations in the Caenorhabditis elegans gene clk-1 affect biological timing and extend longevity. The conserved residues of a diiron center are present in this domain. Probab=97.38 E-value=0.0097 Score=36.36 Aligned_cols=117 Identities=18% Similarity=0.189 Sum_probs=89.6 Q ss_pred HHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEECCCCCCCCCC-----------CCH Q ss_conf 999999999999999981599478999999999999999999999999539971437822572048-----------898 Q gi|254780720|r 14 NMEYVAQYHYMQAAAWAASHNLDGCCNFLLKHAMEEHSHVIRIFKHLTDLGVEAKFSSIEAPVISA-----------NDV 82 (164) Q Consensus 14 ~~El~as~~Yl~~a~~~~~~~~~g~a~~f~~~a~EE~~HA~~l~~yi~~rgg~~~~~~i~~p~~~~-----------~~~ 82 (164) .-|..|...|.....++.+ |.+..++.....+|..|-..|-+.|..++++|..- .|.... -.. T Consensus 10 AGE~gAv~IY~Gql~~~~~---~~~~~~~~~~~~~E~~HL~~f~~~l~~~~~r~s~l---~PlW~~~gf~lG~~~al~G~ 83 (165) T cd01042 10 AGEVGAVRIYRGQLAVARD---PAVRPLIKEMLDEEKDHLAWFEELLPELGVRPSLL---LPLWYVAGFALGALTALLGK 83 (165) T ss_pred CHHHHHHHHHHHHHHHCCC---HHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHH---HHHHHHHHHHHHHHHHHHCC T ss_conf 4189999999999988499---88999999999999999999999888659998607---88899968899999998276 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 999999999999999999999999997099889999999999999999999999 Q gi|254780720|r 83 EGLFSLMYEHENKVTIAYDDAIETILAEKDHQTFQFLQWFVKEQHEEMALFRRI 136 (164) Q Consensus 83 ~e~~~~al~~E~~vt~~~~~l~~~A~~~~D~~t~~fl~~fl~EQ~eee~~~~~l 136 (164) .-++-..-+.|..|-..|.+-++.-...+|..+...++.|-.|.+++.+.+... T Consensus 84 ~~~~~~~~aVE~~V~~Hy~~Qi~~L~~~~d~~l~~~l~~~r~DE~eH~~~A~~~ 137 (165) T cd01042 84 KAAMACTAAVETVVEEHYNDQLRELPAQPDKELRAIIEQFRDDELEHADIAEEL 137 (165) T ss_pred CEEEEHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHC T ss_conf 600200799999999999999998650778889999999997599999999887 No 29 >COG3546 Mn-containing catalase [Inorganic ion transport and metabolism] Probab=97.28 E-value=0.0076 Score=37.02 Aligned_cols=138 Identities=15% Similarity=0.148 Sum_probs=104.2 Q ss_pred CHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEC-------- Q ss_conf 9899999999999---99999999999999981599478999999999999999999999999539971437-------- Q gi|254780720|r 2 TNTRDRVLNELMN---MEYVAQYHYMQAAAWAASHNLDGCCNFLLKHAMEEHSHVIRIFKHLTDLGVEAKFS-------- 70 (164) Q Consensus 2 s~~~~~~Ln~qi~---~El~as~~Yl~~a~~~~~~~~~g~a~~f~~~a~EE~~HA~~l~~yi~~rgg~~~~~-------- 70 (164) +....++|.+|+. -|+.++.+|+..+.-|.+ +++-..+.+.+.||+.|.+.+..-|..+-.....+ T Consensus 18 dp~~A~~lqEqlGG~~GElsaamqYl~Q~fn~r~---~~~~dll~DI~TEEl~HlEmvat~I~~L~~ga~~e~~~~~~l~ 94 (277) T COG3546 18 NPQLAKLLQEQLGGAFGELSAAMQYLFQGFNVRD---AKYKDLLMDIGTEELSHLEMVATMINLLNKGATGEGAEEAELY 94 (277) T ss_pred CHHHHHHHHHHHCCCCHHHHHHHHHHHHHCCCCC---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHH T ss_conf 9699999999967962479999999875346675---3799999986478888999999999999569998887402557 Q ss_pred ---------------CCCCCCCC-----C--------CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHH Q ss_conf ---------------82257204-----8--------8989999999999999999999999999970998899999999 Q gi|254780720|r 71 ---------------SIEAPVIS-----A--------NDVEGLFSLMYEHENKVTIAYDDAIETILAEKDHQTFQFLQWF 122 (164) Q Consensus 71 ---------------~i~~p~~~-----~--------~~~~e~~~~al~~E~~vt~~~~~l~~~A~~~~D~~t~~fl~~f 122 (164) -...++.+ | .++..=|...+..|......+..+++++ .|+...+.|... T Consensus 95 ~s~~~~~n~~h~~~~~~g~~p~dS~G~pWta~YI~~sGnliaDlr~NiaaE~~aR~~y~rLy~mt---dDpgvrd~L~fL 171 (277) T COG3546 95 GSGLGGMNPHHISVLLYGAGPADSAGVPWTAAYIVASGNLIADLRSNIAAEARARLQYERLYEMT---DDPGVRDTLSFL 171 (277) T ss_pred HHHCCCCCCHHHHHHCCCCCCCCCCCCCCCHHHHHCCCCCHHHHHHHHHHHHCCCEEEEEEEECC---CCCCHHHHHHHH T ss_conf 75325787202665304778765689965023443368508999998888741500000201047---880289999999 Q ss_pred HHHHHHHHHHHHHHHHHHHHCCC Q ss_conf 99999999999999999995288 Q gi|254780720|r 123 VKEQHEEMALFRRILDKIRLIGS 145 (164) Q Consensus 123 l~EQ~eee~~~~~ll~~l~~~g~ 145 (164) +.-.+-+...+...|..++-.+. T Consensus 172 l~Re~~H~~~f~kAL~~l~~~~~ 194 (277) T COG3546 172 LTREIAHQNAFRKALESLENEED 194 (277) T ss_pred HHHHHHHHHHHHHHHHHHHHCCC T ss_conf 99878999999999999872256 No 30 >pfam09537 DUF2383 Domain of unknown function (DUF2383). Members of this protein family are found mostly in the Proteobacteria, although one member is found in the the marine planctomycete Pirellula sp. strain 1. The function is unknown. Probab=97.10 E-value=0.019 Score=34.53 Aligned_cols=98 Identities=20% Similarity=0.194 Sum_probs=74.4 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEECCCCC--CCCCC--- Q ss_conf 9999999999999999999999999815994789999999999999999999999995399714378225--72048--- Q gi|254780720|r 5 RDRVLNELMNMEYVAQYHYMQAAAWAASHNLDGCCNFLLKHAMEEHSHVIRIFKHLTDLGVEAKFSSIEA--PVISA--- 79 (164) Q Consensus 5 ~~~~Ln~qi~~El~as~~Yl~~a~~~~~~~~~g~a~~f~~~a~EE~~HA~~l~~yi~~rgg~~~~~~i~~--p~~~~--- 79 (164) +.+.||+.|..-..+..-|..++.-+++ |.+..+|...+.+...|+..|-.+|...||.|.....-. .-.-| T Consensus 2 ~i~~Ln~Li~~~~D~~~gy~~aae~~~~---~~lk~~f~~~~~~r~~~~~eL~~~i~~~Gg~p~~~gs~~g~lhr~w~~l 78 (111) T pfam09537 2 TINALNDLIETLYDGEEGYEKAAEKVKD---PQLKALFQRRAAERRQAAAELQAEIRALGGEPEDGGSFAGTLHRAWMDL 78 (111) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHCCC---HHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHH T ss_conf 7889999999937799999999987678---7899999999999999999999999996899888985677999999999 Q ss_pred ------CCHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf ------89899999999999999999999999 Q gi|254780720|r 80 ------NDVEGLFSLMYEHENKVTIAYDDAIE 105 (164) Q Consensus 80 ------~~~~e~~~~al~~E~~vt~~~~~l~~ 105 (164) .+-..+++.+..-|..+...|.+..+ T Consensus 79 ks~~~~~d~~~il~~~e~gE~~~~~~y~~aL~ 110 (111) T pfam09537 79 KSALTGDDDEAVLEECERGEDAALEEYDEALE 110 (111) T ss_pred HHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 99982897899999999889999999999971 No 31 >cd01044 Ferritin_CCC1_N Ferritin-CCC1, N-terminal ferritin-like diiron-binding domain. Ferritin-like N-terminal domain present in an uncharacterized family of proteins found in bacteria and archaea. These proteins also have a C-terminal CCC1-like transmembrane domain and are thought to be involved in iron and/or manganese transport. This domain has the conserved residues of a diiron center found in other ferritin-like proteins. Probab=96.62 E-value=0.056 Score=31.74 Aligned_cols=115 Identities=21% Similarity=0.158 Sum_probs=79.7 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEECCCCCCCCCC-------CC Q ss_conf 99999999999999999999981599478999999999999999999999999539971437822572048-------89 Q gi|254780720|r 9 LNELMNMEYVAQYHYMQAAAWAASHNLDGCCNFLLKHAMEEHSHVIRIFKHLTDLGVEAKFSSIEAPVISA-------ND 81 (164) Q Consensus 9 Ln~qi~~El~as~~Yl~~a~~~~~~~~~g~a~~f~~~a~EE~~HA~~l~~yi~~rgg~~~~~~i~~p~~~~-------~~ 81 (164) +.+....|++.+.+|..+|..-.+ |...+-|..-|..|..||..+-+++..+|..|.. +..+.-+ -. T Consensus 3 ~~~~~~~E~~~~~~Y~~LA~~ekd---~~~reil~~lA~~E~~Ha~~W~~~l~~~~~~~~~---~~~k~~~~~~L~r~fG 76 (125) T cd01044 3 LRKFQKDEITEAAIYRKLAKREKD---PENREILLKLAEDERRHAEFWKKFLGKRGVPPPR---PKLKIFFYKLLARIFG 76 (125) T ss_pred HHHHHHHHHHHHHHHHHHHHHCCC---HHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCC---CHHHHHHHHHHHHHHH T ss_conf 889999899899999999976479---8999999999999999999999998865788888---6399999999999967 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 899999999999999999999999999709988999999999999999999999999 Q gi|254780720|r 82 VEGLFSLMYEHENKVTIAYDDAIETILAEKDHQTFQFLQWFVKEQHEEMALFRRILD 138 (164) Q Consensus 82 ~~e~~~~al~~E~~vt~~~~~l~~~A~~~~D~~t~~fl~~fl~EQ~eee~~~~~ll~ 138 (164) +.=+++..-..|......|....+. ..-+..++.+..+++..+..+++ T Consensus 77 ~~fvl~llE~~E~~a~~~Y~~~~~~---------~~~~~~I~~DE~~HE~~l~~l~~ 124 (125) T cd01044 77 PTFVLKLLERGEERAIEKYDRLLEE---------RPELKEIIADELEHEEVLIALLD 124 (125) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH---------HHHHHHHHHHHHHHHHHHHHHHC T ss_conf 9999999998876148889866876---------78899999999999999997745 No 32 >pfam03232 COQ7 Ubiquinone biosynthesis protein COQ7. Members of this family contain two repeats of about 90 amino acids, that contains two conserved motifs. One of these DXEXXH may be part of an enzyme active site. Probab=96.24 E-value=0.094 Score=30.36 Aligned_cols=117 Identities=14% Similarity=0.088 Sum_probs=84.2 Q ss_pred HHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEECCCCCCCCCC-----------CCH Q ss_conf 999999999999999981599478999999999999999999999999539971437822572048-----------898 Q gi|254780720|r 14 NMEYVAQYHYMQAAAWAASHNLDGCCNFLLKHAMEEHSHVIRIFKHLTDLGVEAKFSSIEAPVISA-----------NDV 82 (164) Q Consensus 14 ~~El~as~~Yl~~a~~~~~~~~~g~a~~f~~~a~EE~~HA~~l~~yi~~rgg~~~~~~i~~p~~~~-----------~~~ 82 (164) .-|+.|...|.....++.+ -|....+++....+|..|-..|-+.+..++++|.+- .|-... -.. T Consensus 12 AGE~gAv~IY~GQ~a~~~~--~~~~~~~~~~~~~~E~~HL~~f~~~l~e~~~Rps~l---~PlW~~~gf~lG~~~al~G~ 86 (171) T pfam03232 12 AGELGAVRIYAGQLAVLGP--RPSLGPLIKEMWDQEKVHLATFNELIAERRVRPTLL---LPLWHVAGFALGAGTALLGK 86 (171) T ss_pred CHHHHHHHHHHHHHHHHCC--CHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCH---HHHHHHHHHHHHHHHHHCCC T ss_conf 3389999999999999789--978999999999999999999998889829998406---77799989999999873377 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH--HHCCHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 99999999999999999999999999--709988999999999999999999999 Q gi|254780720|r 83 EGLFSLMYEHENKVTIAYDDAIETIL--AEKDHQTFQFLQWFVKEQHEEMALFRR 135 (164) Q Consensus 83 ~e~~~~al~~E~~vt~~~~~l~~~A~--~~~D~~t~~fl~~fl~EQ~eee~~~~~ 135 (164) ..++...-+.|..|-+.|.+-++.-. ...|..+...+..|-.|.+++-+.+.+ T Consensus 87 ~~~~a~t~aVE~~V~~Hy~~Qi~~L~~~~~~d~~l~~~l~~~~~dE~~H~~~A~~ 141 (171) T pfam03232 87 KAAMACTAAVETVIGEHYNDQLRELEELEEDDKELKETIAKFRDEELEHRDTAIE 141 (171) T ss_pred CEEEEEHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 6124005999999999999999998617833299999999999889999999998 No 33 >COG1633 Uncharacterized conserved protein [Function unknown] Probab=95.60 E-value=0.12 Score=29.70 Aligned_cols=66 Identities=17% Similarity=0.331 Sum_probs=56.2 Q ss_pred CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC Q ss_conf 204889899999999999999999999999999709988999999999999999999999999999528 Q gi|254780720|r 76 VISANDVEGLFSLMYEHENKVTIAYDDAIETILAEKDHQTFQFLQWFVKEQHEEMALFRRILDKIRLIG 144 (164) Q Consensus 76 ~~~~~~~~e~~~~al~~E~~vt~~~~~l~~~A~~~~D~~t~~fl~~fl~EQ~eee~~~~~ll~~l~~~g 144 (164) +....++.+++..|...|...++-|..+++.+ .|..+..++.++..+...|.+.|..++.++..-+ T Consensus 19 ~~~~~~~~e~L~~Ai~~E~eA~~fY~~lae~~---~~~~~rk~~~~la~eE~~H~~~f~~l~~~~~~~~ 84 (176) T COG1633 19 LVKELSIEELLAIAIRGELEAIKFYEELAERI---EDEEIRKLFEDLADEEMRHLRKFEKLLEKLTPKE 84 (176) T ss_pred HHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHC---CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCC T ss_conf 75031199999999997999999999999765---8776999999999999999999999999866775 No 34 >cd07910 MiaE MiaE tRNA-modifying nonheme diiron monooxygenase, ferritin-like diiron-binding domain. MiaE is a nonheme diiron monooxygenase that catalyzes the posttranscriptional allylic hydroxylation of a modified nucleoside in tRNA called 2-methylthio-N-6-isopentenyl adenosine (ms2i6A). ms2i6A is found at position 37, next to the anticodon at the 3' position in almost all eukaryotic and bacterial tRNA's that read codons beginning with uridine. The miaE gene is absent in Escherichia coli, a finding consistent with the absence of the hydroxylated derivative of ms2i6A in this species. Probab=95.32 E-value=0.23 Score=28.07 Aligned_cols=134 Identities=14% Similarity=0.049 Sum_probs=92.1 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEECCCCCCCCC---- Q ss_conf 8999999999999999999999999998159947899999999999999999999999953997143782257204---- Q gi|254780720|r 3 NTRDRVLNELMNMEYVAQYHYMQAAAWAASHNLDGCCNFLLKHAMEEHSHVIRIFKHLTDLGVEAKFSSIEAPVIS---- 78 (164) Q Consensus 3 ~~~~~~Ln~qi~~El~as~~Yl~~a~~~~~~~~~g~a~~f~~~a~EE~~HA~~l~~yi~~rgg~~~~~~i~~p~~~---- 78 (164) .++...|.+|-+-|-.|+..=+++-..+ -+.+.+..-+-.-|.||+.|..++.+-|..||.... ++.+.+.- T Consensus 17 ~~~~~~L~DHA~cEkKAAs~Amsli~ry--p~~~~Lv~~m~~lA~EEL~HF~qV~~lm~~Rgi~l~--~~~~~~Y~~~L~ 92 (180) T cd07910 17 ANLDEILIDHAHCEKKAASSAMSLIFRY--PEKPELVEAMSDLAREELQHFEQVLKIMKKRGIPLG--PDSKDPYASGLR 92 (180) T ss_pred HCHHHHHHHHHHHHHHHHHHHHHHHHHC--CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCC--CCCCCHHHHHHH T ss_conf 8889999999999999999999999988--993899999999999999999999999998499789--999788999999 Q ss_pred ----CCC---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCC Q ss_conf ----889---89999999999999999999999999970998899999999999999999999999999952887 Q gi|254780720|r 79 ----AND---VEGLFSLMYEHENKVTIAYDDAIETILAEKDHQTFQFLQWFVKEQHEEMALFRRILDKIRLIGSG 146 (164) Q Consensus 79 ----~~~---~~e~~~~al~~E~~vt~~~~~l~~~A~~~~D~~t~~fl~~fl~EQ~eee~~~~~ll~~l~~~g~~ 146 (164) ... ..+.+-.+-=.|- ++-.+..-+|....|.....|-..++. .|.+++.+-++..+.+++. T Consensus 93 ~~~r~~~~~~llD~Llv~a~IEA---RscERF~lLa~~l~D~eL~~FY~~L~~---SEarH~~~yl~LA~~~~~~ 161 (180) T cd07910 93 KLVRKGEPERLLDRLLVAALIEA---RSCERFALLAPALPDPELKKFYRGLLE---SEARHYELFLDLARKYFDE 161 (180) T ss_pred HHCCCCCHHHHHHHHHHHHHHHH---HHHHHHHHHHHHCCCHHHHHHHHHHHH---HHHHHHHHHHHHHHHHCCH T ss_conf 87357971889999999999985---567689999855886899999999999---9988999999999988786 No 35 >pfam04305 DUF455 Protein of unknown function (DUF455). Probab=95.30 E-value=0.23 Score=28.02 Aligned_cols=131 Identities=19% Similarity=0.177 Sum_probs=86.9 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEECCCCCCCCCCC---- Q ss_conf 9999999999999999999999999815994789999999999999999999999995399714378225720488---- Q gi|254780720|r 5 RDRVLNELMNMEYVAQYHYMQAAAWAASHNLDGCCNFLLKHAMEEHSHVIRIFKHLTDLGVEAKFSSIEAPVISAN---- 80 (164) Q Consensus 5 ~~~~Ln~qi~~El~as~~Yl~~a~~~~~~~~~g~a~~f~~~a~EE~~HA~~l~~yi~~rgg~~~~~~i~~p~~~~~---- 80 (164) -..+|-..-+.||.|+.+.+-+..-|.+.-..-+..| -.-|.||-.|...+.+++..+|.. .++.++=..-|. T Consensus 65 r~~llHa~AHIE~nAIdLa~Da~~RF~~lP~~Fy~Dw-~~VA~dEa~Hf~ll~~rL~~lG~~--YGd~PaH~gLW~~a~~ 141 (250) T pfam04305 65 RAALLHALAHIELNAIDLALDAVARFRGLPREFYDDW-LKVADDEAKHFRLLRERLEELGSE--YGDLPAHDGLWEAAEK 141 (250) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHH-HHHHHHHHHHHHHHHHHHHHHCCC--CCCCCCCHHHHHHHHH T ss_conf 9999999999999999999999987236778999999-999999999999999999982987--5797100499999998 Q ss_pred ---CHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHH----HHHHHHHH Q ss_conf ---989999-99999999999999999999997099889999999999999999----99999999 Q gi|254780720|r 81 ---DVEGLF-SLMYEHENKVTIAYDDAIETILAEKDHQTFQFLQWFVKEQHEEM----ALFRRILD 138 (164) Q Consensus 81 ---~~~e~~-~~al~~E~~vt~~~~~l~~~A~~~~D~~t~~fl~~fl~EQ~eee----~~~~~ll~ 138 (164) |+..=+ -.-+-+|..-.+.--.+++.-...+|..+...|+-++.|++.++ +++..+.. T Consensus 142 T~~dllaRmAivp~vlEArGLD~tp~~~~kl~~~gD~~sa~iL~~I~~dEI~HVa~G~rWF~~~c~ 207 (250) T pfam04305 142 TADDLLARLALVPRVLEARGLDATPGIIAKLEGAGDNESAAILEVILRDEIGHVAIGNRWFRFLCE 207 (250) T ss_pred HHCCHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 533899999886888886067667899999997798678999999999988899987999999998 No 36 >pfam05974 DUF892 Domain of unknown function (DUF892). This family consists of several hypothetical bacterial proteins of unknown function. Probab=94.72 E-value=0.33 Score=27.04 Aligned_cols=132 Identities=14% Similarity=0.047 Sum_probs=96.0 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEECCCC---------- Q ss_conf 9999999999999999999999999981599478999999999999999999999999539971437822---------- Q gi|254780720|r 4 TRDRVLNELMNMEYVAQYHYMQAAAWAASHNLDGCCNFLLKHAMEEHSHVIRIFKHLTDLGVEAKFSSIE---------- 73 (164) Q Consensus 4 ~~~~~Ln~qi~~El~as~~Yl~~a~~~~~~~~~g~a~~f~~~a~EE~~HA~~l~~yi~~rgg~~~~~~i~---------- 73 (164) -....|.+....|-++.-.--.|+.-+.+ |.+..-|..+..|-++|..++-+-+..+|..|.-..-+ T Consensus 5 lf~~~L~d~y~aE~q~~~al~~~~~~a~~---peLk~~l~~H~~eT~~qi~rLe~i~~~lg~~~~~~~c~~m~gli~e~~ 81 (159) T pfam05974 5 LFIDELRDIYAAEKQALKALPKMAKAAED---PELKAALEQHLEETEGQIERLEQIFERLGESPSGKKCDAMEGLVAEGQ 81 (159) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHCC---HHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHH T ss_conf 99999999999999999999999988589---999999999999999999999999998299955573489999999999 Q ss_pred CC-CCCC--CCHHHH--HHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 57-2048--898999--99999999999999999999999709988999999999999999999999999 Q gi|254780720|r 74 AP-VISA--NDVEGL--FSLMYEHENKVTIAYDDAIETILAEKDHQTFQFLQWFVKEQHEEMALFRRILD 138 (164) Q Consensus 74 ~p-~~~~--~~~~e~--~~~al~~E~~vt~~~~~l~~~A~~~~D~~t~~fl~~fl~EQ~eee~~~~~ll~ 138 (164) .. .... ..++++ +-.+...|.+-+.+|..++..|..-++......|+..+.|...--+++..+.. T Consensus 82 ~~~~~~~~d~~vkda~li~aaq~~EhyEIA~YgtL~~~A~~lG~~~~a~lL~~~L~EE~~~d~~L~~~a~ 151 (159) T pfam05974 82 ELLEEDAGDEVVKDAALIAAAQAVEHYEIAAYGTLIAAAEQLGLKDAAALLEQTLDEEKATDEKLTQLAE 151 (159) T ss_pred HHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 9871456736887389999999999999999999999998869888999999999999999999999999 No 37 >cd01050 Acyl_ACP_Desat Acyl ACP desaturase, ferritin-like diiron-binding domain. Acyl-Acyl Carrier Protein Desaturase (Acyl_ACP_Desat) is a mu-oxo-bridged diiron-carboxylate enzyme, which belongs to a broad superfamily of ferritin-like proteins and catalyzes the NADPH and O2-dependent formation of a cis-double bond in acyl-ACPs. Acyl-ACP desaturases are found in higher plants and a few bacterial species (Mycobacterium tuberculosis, M. leprae, M. avium and Streptomyces avermitilis, S. coelicolor). In plants, Acyl-ACP desaturase is a plastid-localized, covalently ACP linked, soluble desaturase that introduces the first double bound into saturated fatty acids, resulting in the corresponding monounsaturated fatty acid. Members of this class of soluble desaturases are specific for a particular substrate chain length and introduce the double bond between specific carbon atoms. For example, delta 9 stearoyl-ACP is specific for stearic acid and introduces a double bond between carbon 9 and 1 Probab=93.70 E-value=0.54 Score=25.74 Aligned_cols=108 Identities=16% Similarity=0.116 Sum_probs=85.5 Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEECCCC-----------CCCCCCCCHHHHHHHHHHHHHHHHHHHHH Q ss_conf 9478999999999999999999999999539971437822-----------57204889899999999999999999999 Q gi|254780720|r 34 NLDGCCNFLLKHAMEEHSHVIRIFKHLTDLGVEAKFSSIE-----------APVISANDVEGLFSLMYEHENKVTIAYDD 102 (164) Q Consensus 34 ~~~g~a~~f~~~a~EE~~HA~~l~~yi~~rgg~~~~~~i~-----------~p~~~~~~~~e~~~~al~~E~~vt~~~~~ 102 (164) +-.+-+.|.+....||-.|+.-+-+|+.-.|.. ....++ .|+. ..++...|-..-=+|+....+..+ T Consensus 91 ~~~~W~~Wv~~WTAEEnRHg~~Lr~YL~~tr~V-Dp~~lE~~r~~~i~~G~~~~~-~~~p~~~~~YtsfQElAT~IsH~N 168 (297) T cd01050 91 SPTAWARWVRRWTAEENRHGDLLNKYLYLTGRV-DPRALERTRQYLIGSGFDPGT-DNSPYRGFVYTSFQELATRISHRN 168 (297) T ss_pred CCCCHHHHCCCCCCCCCHHHHHHHHHEEECCCC-CHHHHHHHHHHHHHCCCCCCC-CCCHHHHHHHHHHHHHCCHHHHHH T ss_conf 898256520652644240378886310005677-829999999999837889999-877899999999987501333623 Q ss_pred HHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC Q ss_conf 999999709988999999999999999999999999999528 Q gi|254780720|r 103 AIETILAEKDHQTFQFLQWFVKEQHEEMALFRRILDKIRLIG 144 (164) Q Consensus 103 l~~~A~~~~D~~t~~fl~~fl~EQ~eee~~~~~ll~~l~~~g 144 (164) ..++|. .+|+....++..+-.+.--++.-.+++++.+=-+. T Consensus 169 t~rla~-~gDp~l~~i~~rIA~DE~rH~~fYr~iv~~~le~d 209 (297) T cd01050 169 TARLAG-AGDPVLAKLLGRIAADEARHEAFYRDIVEALFELD 209 (297) T ss_pred HHHHHH-CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC T ss_conf 888750-59979999998875168899999999999998339 No 38 >PRK13654 magnesium-protoporphyrin IX monomethyl ester cyclase; Provisional Probab=92.26 E-value=0.88 Score=24.46 Aligned_cols=121 Identities=12% Similarity=0.094 Sum_probs=100.2 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEECCCCCCC-CCCCCH Q ss_conf 9999999999999999999999999981599478999999999999999999999999539971437822572-048898 Q gi|254780720|r 4 TRDRVLNELMNMEYVAQYHYMQAAAWAASHNLDGCCNFLLKHAMEEHSHVIRIFKHLTDLGVEAKFSSIEAPV-ISANDV 82 (164) Q Consensus 4 ~~~~~Ln~qi~~El~as~~Yl~~a~~~~~~~~~g~a~~f~~~a~EE~~HA~~l~~yi~~rgg~~~~~~i~~p~-~~~~~~ 82 (164) ...+-|..-+..||....+|--++.-..+ .-|-+++.|.-.|.+|-.||--+-+-+.+-|..++++-..+.+ ..+--| T Consensus 81 ~f~dfL~~SctsEFSG~lLykEl~rr~k~-~np~l~e~F~~MaRDEaRHAGFlN~am~df~i~lDLgfLtk~k~YTfF~P 159 (351) T PRK13654 81 EFIDFLERSCTAEFSGFLLYKELSRRLKD-RNPLLAELFQLMARDEARHAGFLNKAMKDFGLSLDLGFLTKKKKYTFFPP 159 (351) T ss_pred HHHHHHHHHHHHHHCHHHHHHHHHHHCCC-CCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHCCCCEEEECC T ss_conf 99999998767660123699999987033-78189999999864377777789999998195302576635662266466 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHH Q ss_conf 9999999999999999999999999970998899999999999 Q gi|254780720|r 83 EGLFSLMYEHENKVTIAYDDAIETILAEKDHQTFQFLQWFVKE 125 (164) Q Consensus 83 ~e~~~~al~~E~~vt~~~~~l~~~A~~~~D~~t~~fl~~fl~E 125 (164) +=+|=..+=-||-=.-.|-.++..-+++-+..-...++||=.= T Consensus 160 kfI~YatYLSEKIGY~RYItIyRHLe~hPe~r~~PiF~~Fe~W 202 (351) T PRK13654 160 KFIFYATYLSEKIGYWRYITIYRHLEKHPEHRIHPIFKFFENW 202 (351) T ss_pred CEEEHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHH T ss_conf 4243144877654067877999998869210335389999998 No 39 >pfam03405 FA_desaturase_2 Fatty acid desaturase. Probab=91.43 E-value=1.1 Score=23.90 Aligned_cols=105 Identities=15% Similarity=0.049 Sum_probs=80.1 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCE----------ECCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 789999999999999999999999995399714----------3782257204889899999999999999999999999 Q gi|254780720|r 36 DGCCNFLLKHAMEEHSHVIRIFKHLTDLGVEAK----------FSSIEAPVISANDVEGLFSLMYEHENKVTIAYDDAIE 105 (164) Q Consensus 36 ~g~a~~f~~~a~EE~~HA~~l~~yi~~rgg~~~----------~~~i~~p~~~~~~~~e~~~~al~~E~~vt~~~~~l~~ 105 (164) .+-+.|.+....||-.|..-+-+|+.-.|..=. ++..-.|.. ..++...|-..-=+|.....+-.+..+ T Consensus 98 ~~W~~Wv~~WTAEEnRHg~~Lr~YL~ltr~VD~~~lE~~~~~~i~~G~~p~~-~~~py~~~vYtSFQElAT~ISH~NTgr 176 (330) T pfam03405 98 TPWAIWTRAWTAEENRHGDLLNKYLYLSGRVDMRQIEKTIQYLIGSGMDPGT-ENNPYLGFIYTSFQERATFISHGNTAR 176 (330) T ss_pred CCHHHHCCCCCCCCCHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHCCCCCCC-CCCCHHHHHHHHHHHHHHHCCHHHHHH T ss_conf 5065321752644341478997655522467859999999999827889987-668104330455788876511411999 Q ss_pred HHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 999709988999999999999999999999999999 Q gi|254780720|r 106 TILAEKDHQTFQFLQWFVKEQHEEMALFRRILDKIR 141 (164) Q Consensus 106 ~A~~~~D~~t~~fl~~fl~EQ~eee~~~~~ll~~l~ 141 (164) +|.+.+|+....++..+-.+.--++.--+++++.+= T Consensus 177 la~~~GDp~la~i~~rIAaDE~rH~~fYr~iv~~~~ 212 (330) T pfam03405 177 LAKEHGDTKLAQICGTIASDEKRHETAYTKIVEKLF 212 (330) T ss_pred HHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 988729989999998874337789999999999998 No 40 >cd07909 YciF YciF bacterial stress response protein, ferritin-like iron-binding domain. YciF is a bacterial protein of unknown function that is up-regulated when bacteria experience stress conditions, and is highly conserved in a broad range of bacterial species. YciF has a ferritin-like domain. Ferritin-like, diiron-carboxylate proteins participate in a range of functions including iron regulation, mono-oxygenation, and reactive radical production. These proteins are characterized by the fact that they catalyze dioxygen-dependent oxidation-hydroxylation reactions within diiron centers; one exception is manganese catalase, which catalyzes peroxide-dependent oxidation-reduction within a dimanganese center. Diiron-carboxylate proteins are further characterized by the presence of duplicate metal ligands, glutamates and histidines (ExxH) and two additional glutamates within a four-helix bundle. Outside of these conserved residues there is little obvious homology. Members include bacterio Probab=91.34 E-value=1.1 Score=23.84 Aligned_cols=120 Identities=16% Similarity=0.061 Sum_probs=88.1 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEECCCCC----------C Q ss_conf 999999999999999999999999815994789999999999999999999999995399714378225----------7 Q gi|254780720|r 6 DRVLNELMNMEYVAQYHYMQAAAWAASHNLDGCCNFLLKHAMEEHSHVIRIFKHLTDLGVEAKFSSIEA----------P 75 (164) Q Consensus 6 ~~~Ln~qi~~El~as~~Yl~~a~~~~~~~~~g~a~~f~~~a~EE~~HA~~l~~yi~~rgg~~~~~~i~~----------p 75 (164) ...|.+....|-++.-.--.|+.-. .-|-+..-|..+..|-.+|..++-+=+..+|+.|.-..-+. . T Consensus 5 ~~~L~d~y~aE~Q~~~~l~~m~~~a---~~peLk~~l~~H~~eT~~qi~rLe~i~~~lg~~~~~~~c~am~gli~e~~~~ 81 (147) T cd07909 5 VHELRDLYSAEKQLVKALPKMAKAA---TSEELKEAFESHLEETEGQVERLEQIFESLGEKPEGKKCKAMEGLIKEAEEL 81 (147) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH---CCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHH T ss_conf 9999999999999999999999883---8999999999999999999999999999819996667408999999999999 Q ss_pred CCCC--CCHHH--HHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHH Q ss_conf 2048--89899--99999999999999999999999970998899999999999999 Q gi|254780720|r 76 VISA--NDVEG--LFSLMYEHENKVTIAYDDAIETILAEKDHQTFQFLQWFVKEQHE 128 (164) Q Consensus 76 ~~~~--~~~~e--~~~~al~~E~~vt~~~~~l~~~A~~~~D~~t~~fl~~fl~EQ~e 128 (164) -..+ ..+.+ ++-.+...|.+-+.+|..++..|...++......|+..+.|..+ T Consensus 82 ~~~~~~~~v~Da~li~aaq~~EHyEIA~YgtL~~~A~~lG~~e~a~lL~~~L~EE~~ 138 (147) T cd07909 82 IEETGDSAVLDAALIAAAQKVEHYEIAGYGTLRALAKLLGLDDAADLLQETLDEEKA 138 (147) T ss_pred HHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHH T ss_conf 864488889999999999999999999999999999885987899999999999999 No 41 >cd01047 ACSF Aerobic Cyclase System Fe-containing subunit (ACSF), ferritin-like diiron-binding domain. Aerobic Cyclase System, Fe-containing subunit (ACSF) is a member of a broad superfamily of ferritin-like diiron-carboxylate proteins. Rubrivivax gelatinosus acsF codes for a conserved, putative binuclear iron-cluster-containing protein involved in aerobic oxidative cyclization of Mg-protoporphyrin IX monomethyl ester. AcsF and homologs have a leucine zipper and two copies of the conserved glutamate and histidine residues predicted to act as ligands for iron in the Ex(29-35)DExRH motifs. Several homologs of AcsF are found in a wide range of photosynthetic organisms, including Chlamydomonas reinhardtii Crd1 and Pharbitis nil PNZIP, suggesting that this aerobic oxidative cyclization mechanism is conserved from bacteria to plants. Probab=90.90 E-value=1.2 Score=23.58 Aligned_cols=121 Identities=12% Similarity=0.077 Sum_probs=98.5 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEECCCCCCC-CCCCCH Q ss_conf 9999999999999999999999999981599478999999999999999999999999539971437822572-048898 Q gi|254780720|r 4 TRDRVLNELMNMEYVAQYHYMQAAAWAASHNLDGCCNFLLKHAMEEHSHVIRIFKHLTDLGVEAKFSSIEAPV-ISANDV 82 (164) Q Consensus 4 ~~~~~Ln~qi~~El~as~~Yl~~a~~~~~~~~~g~a~~f~~~a~EE~~HA~~l~~yi~~rgg~~~~~~i~~p~-~~~~~~ 82 (164) ...+-|..-+..||..-.+|--++.-..+. -|-+++.|.-.|.+|-.||--+=+-+.+-|..++++-..+.+ ..+-.| T Consensus 63 ~f~dfL~~SctsEFSG~lLykEl~rr~k~~-nP~l~e~f~~MaRDEaRHAGFlN~al~d~~~~lDLgfLtk~k~YT~F~p 141 (323) T cd01047 63 IFLEFLERSCTSEFSGFLLYKELGRRLKNT-NPVVAELFRLMARDEARHAGFLNKALSDFNLALDLGFLTKTRKYTFFKP 141 (323) T ss_pred HHHHHHHHHHHHHHCHHHHHHHHHHHHCCC-CCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHCCCCCEEEECC T ss_conf 999999987677601236899999874237-9079999999865477777678899998495202476516673266576 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHH Q ss_conf 9999999999999999999999999970998899999999999 Q gi|254780720|r 83 EGLFSLMYEHENKVTIAYDDAIETILAEKDHQTFQFLQWFVKE 125 (164) Q Consensus 83 ~e~~~~al~~E~~vt~~~~~l~~~A~~~~D~~t~~fl~~fl~E 125 (164) +=+|=..+=-||-=.-.|-.++..-+++-+..-...+.||=.= T Consensus 142 kfI~YatYLSEKIGY~RYItIyRhLe~~Pe~rf~PiF~~Fe~W 184 (323) T cd01047 142 KFIFYATYLSEKIGYWRYITIYRHLERNPENQFHPIFKYFENW 184 (323) T ss_pred CEEEEHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHH T ss_conf 0454034666543167887999999869110236079989988 No 42 >CHL00185 ycf59 magnesium-protoporphyrin IX monomethyl ester cyclase; Provisional Probab=90.48 E-value=1.3 Score=23.35 Aligned_cols=120 Identities=12% Similarity=0.099 Sum_probs=100.2 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEECCCCCCC-CCCCCHH Q ss_conf 999999999999999999999999981599478999999999999999999999999539971437822572-0488989 Q gi|254780720|r 5 RDRVLNELMNMEYVAQYHYMQAAAWAASHNLDGCCNFLLKHAMEEHSHVIRIFKHLTDLGVEAKFSSIEAPV-ISANDVE 83 (164) Q Consensus 5 ~~~~Ln~qi~~El~as~~Yl~~a~~~~~~~~~g~a~~f~~~a~EE~~HA~~l~~yi~~rgg~~~~~~i~~p~-~~~~~~~ 83 (164) ..+-|..-+..||..-.+|--++.-..+. -|-+++.|.-.|.+|-.||-.+-+-+.+-|..++++-..+.+ ..+-.|+ T Consensus 78 FidfL~~SctsEFSG~lLykEl~rr~k~~-nP~l~e~f~~MaRDEaRHAGFlNkam~df~~~lDLgfLtk~k~YTfF~Pk 156 (349) T CHL00185 78 FIEFLERSCTAEFSGFLLYKELSRKLKDR-NPLLAECFLLMSRDEARHAGFLNKAMADFNLSLDLGFLTKSRKYTFFAPK 156 (349) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHCCC-CCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHCCCCCEEEECCC T ss_conf 99999987677601236999999871337-90799999998765777878899999984952024765056612654644 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHH Q ss_conf 999999999999999999999999970998899999999999 Q gi|254780720|r 84 GLFSLMYEHENKVTIAYDDAIETILAEKDHQTFQFLQWFVKE 125 (164) Q Consensus 84 e~~~~al~~E~~vt~~~~~l~~~A~~~~D~~t~~fl~~fl~E 125 (164) =+|=..+=-||--.-.|-.++..-+++-+..-...+.||-.= T Consensus 157 fI~YatYLSEKIGY~RYItIyRhLe~~Pe~r~~PiF~~Fe~W 198 (349) T CHL00185 157 FIFYATYLSEKIGYWRYITIYRHLEKHPEHRIYPIFKFFENW 198 (349) T ss_pred EEEHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHH T ss_conf 011355877654267887999998869100226389999998 No 43 >pfam06175 MiaE tRNA-(MS[2]IO[6]A)-hydroxylase (MiaE). This family consists of several bacterial tRNA-(MS[2]IO[6]A)-hydroxylase (MiaE) proteins. The modified nucleoside 2-methylthio-N-6-isopentenyl adenosine (ms2i6A) is present at position 37 (3' of the anticodon) of tRNAs that read codons beginning with U except tRNA(I,V Ser) in Escherichia coli. Salmonella typhimurium 2-methylthio-cis-ribozeatin (ms2io6A) is found in tRNA, probably in the corresponding species that have ms2i6A in E. coli. The miaE gene is absent in E. coli, a finding consistent with the absence of the hydroxylated derivative of ms2i6A in this species. Probab=90.37 E-value=1.4 Score=23.29 Aligned_cols=133 Identities=16% Similarity=0.059 Sum_probs=88.5 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEECCCCCCCC------ Q ss_conf 99999999999999999999999999815994789999999999999999999999995399714378225720------ Q gi|254780720|r 4 TRDRVLNELMNMEYVAQYHYMQAAAWAASHNLDGCCNFLLKHAMEEHSHVIRIFKHLTDLGVEAKFSSIEAPVI------ 77 (164) Q Consensus 4 ~~~~~Ln~qi~~El~as~~Yl~~a~~~~~~~~~g~a~~f~~~a~EE~~HA~~l~~yi~~rgg~~~~~~i~~p~~------ 77 (164) ++...|.+|-+-|-.|+..-+++-..+. -..+.+..-+-.-|.||+.|..++.+-|..||.... .+.+.+. T Consensus 27 ~~~~lL~DHA~CEkKAAstAmsli~rY~-p~~~~Lv~~ms~LArEEL~HF~qV~~im~~Rgi~l~--~~~~~~Ya~~L~~ 103 (199) T pfam06175 27 NLDVLLLDHSHCELKAAQTAMNLMRRYA-PSNQDLVNKLTRLAKEELHHFEQVLEILEARNIPYA--PISASRYAKGLLA 103 (199) T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHCC-CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCC--CCCCCHHHHHHHH T ss_conf 7889999989899999999999999839-982789999999999999999999999998599688--9997889999998 Q ss_pred -----CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCC Q ss_conf -----488989999999999999999999999999970998899999999999999999999999999952887 Q gi|254780720|r 78 -----SANDVEGLFSLMYEHENKVTIAYDDAIETILAEKDHQTFQFLQWFVKEQHEEMALFRRILDKIRLIGSG 146 (164) Q Consensus 78 -----~~~~~~e~~~~al~~E~~vt~~~~~l~~~A~~~~D~~t~~fl~~fl~EQ~eee~~~~~ll~~l~~~g~~ 146 (164) ...-+.+.+-.+-=.|-.--..+ .-+|... |.....|-..+++ .|.+++.+-++..+.+++. T Consensus 104 ~vr~~~~~rllD~Llv~AlIEARScERF---~lLa~~l-d~eL~~FY~~L~~---SEarH~~~yl~LA~~~~~~ 170 (199) T pfam06175 104 AVRTHEPQRLLDKLIVGAYIEARSCERF---ALLAPHL-DAELAKFYVSLLR---SEARHFQDYLKLAYQYFDE 170 (199) T ss_pred HCCCCCHHHHHHHHHHHHHHHHHHHHHH---HHHHHHC-CHHHHHHHHHHHH---HHHHHHHHHHHHHHHHCCH T ss_conf 7447874889999999999976567799---9999866-6999999999999---9988999999999988687 No 44 >PRK09101 nrdB ribonucleotide-diphosphate reductase subunit beta; Reviewed Probab=80.60 E-value=4.4 Score=20.23 Aligned_cols=81 Identities=16% Similarity=0.157 Sum_probs=41.1 Q ss_pred HHHHHHHHHHHHH--HCCC-HHHHHHHHHHHHHHHHHHHHH---HHHHHHHCCCCCEECCCCCCCCCCCCHHHHHHHHHH Q ss_conf 9999999999998--1599-478999999999999999999---999999539971437822572048898999999999 Q gi|254780720|r 18 VAQYHYMQAAAWA--ASHN-LDGCCNFLLKHAMEEHSHVIR---IFKHLTDLGVEAKFSSIEAPVISANDVEGLFSLMYE 91 (164) Q Consensus 18 ~as~~Yl~~a~~~--~~~~-~~g~a~~f~~~a~EE~~HA~~---l~~yi~~rgg~~~~~~i~~p~~~~~~~~e~~~~al~ 91 (164) ...++|-+.+..+ .+.| ++|.+.-.+--+.+|.-|... +++.+..-.-.|.+..+. +..-..+.++|..|.+ T Consensus 205 Egi~F~~~F~~~~~~~~~~~m~g~~~~~~~i~rDE~~Hl~~~~~ii~~l~~~~e~pe~~~~~--~e~~~~v~~m~~~ave 282 (376) T PRK09101 205 EAIRFYVSFACSFAFAERELMEGNAKIIRLIARDEALHLTGTQHMLNLMRSGKDDPEMAEIA--EECKQECYDLFVQAAE 282 (376) T ss_pred HHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHH--HHHHHHHHHHHHHHHH T ss_conf 68998999999999986488845799999999719989999999999998538982788999--9999999999999999 Q ss_pred HHHHHHHHH Q ss_conf 999999999 Q gi|254780720|r 92 HENKVTIAY 100 (164) Q Consensus 92 ~E~~vt~~~ 100 (164) +|++-...+ T Consensus 283 ~E~~wa~yl 291 (376) T PRK09101 283 QEKEWADYL 291 (376) T ss_pred HHHHHHHHH T ss_conf 999999996 No 45 >COG2833 Uncharacterized protein conserved in bacteria [Function unknown] Probab=80.13 E-value=4.5 Score=20.13 Aligned_cols=121 Identities=18% Similarity=0.155 Sum_probs=79.5 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEECCCCCCCCCC----- Q ss_conf 999999999999999999999999981599478999999999999999999999999539971437822572048----- Q gi|254780720|r 5 RDRVLNELMNMEYVAQYHYMQAAAWAASHNLDGCCNFLLKHAMEEHSHVIRIFKHLTDLGVEAKFSSIEAPVISA----- 79 (164) Q Consensus 5 ~~~~Ln~qi~~El~as~~Yl~~a~~~~~~~~~g~a~~f~~~a~EE~~HA~~l~~yi~~rgg~~~~~~i~~p~~~~----- 79 (164) ...+|...-..||.|+++-+--+.-|....+.-+-.|++ -|.||-.|...+-+++..+|...- ..++-..-| T Consensus 76 ~aallHAiAHIEfNAInLaLDa~~RF~~~p~~F~~dWm~-VA~EE~~HF~Ll~~~L~~LG~~YG--DfpaHdgLw~~a~~ 152 (268) T COG2833 76 RAALLHAIAHIEFNAINLALDAVYRFAPLPLQFYDDWMR-VADEEAKHFRLLRERLKSLGYDYG--DFPAHDGLWQMAEA 152 (268) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHH-HHHHHHHHHHHHHHHHHHHCCCCC--CCCCCCCHHHHHHH T ss_conf 999999998976425778889999846886789999999-999998999999999998188757--88130518999987 Q ss_pred --CCHHHHHH-HHHHHHHH---HHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHH Q ss_conf --89899999-99999999---999999999999970998899999999999999999 Q gi|254780720|r 80 --NDVEGLFS-LMYEHENK---VTIAYDDAIETILAEKDHQTFQFLQWFVKEQHEEMA 131 (164) Q Consensus 80 --~~~~e~~~-~al~~E~~---vt~~~~~l~~~A~~~~D~~t~~fl~~fl~EQ~eee~ 131 (164) .++..-+. .-+-.|.. +|-.+. .++ .+.+|..+...|+=++++.+.++. T Consensus 153 T~~dl~~RmalVprvLEARGLDatP~l~--aK~-~~~gD~~~~~iLdIIlrDEigHVa 207 (268) T COG2833 153 TANDLLARMALVPRVLEARGLDATPSLR--AKL-AETGDSEAAAILDIILRDEIGHVA 207 (268) T ss_pred HHCCHHHHHHHHHHHHHHCCCCCCHHHH--HHH-HHCCCHHHHHHHHHHHHCCCCCEE T ss_conf 6408898865446677642677887899--999-873864888899999731234222 No 46 >COG3685 Uncharacterized protein conserved in bacteria [Function unknown] Probab=79.06 E-value=4.9 Score=19.92 Aligned_cols=129 Identities=16% Similarity=0.174 Sum_probs=82.8 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEC---CCCCCCCCCC- Q ss_conf 999999999999999999999999981599478999999999999999999999999539971437---8225720488- Q gi|254780720|r 5 RDRVLNELMNMEYVAQYHYMQAAAWAASHNLDGCCNFLLKHAMEEHSHVIRIFKHLTDLGVEAKFS---SIEAPVISAN- 80 (164) Q Consensus 5 ~~~~Ln~qi~~El~as~~Yl~~a~~~~~~~~~g~a~~f~~~a~EE~~HA~~l~~yi~~rgg~~~~~---~i~~p~~~~~- 80 (164) ....|.+....|-+..-.--.||.-+. +|-+..-|..+-.|.-.|..++-+-....|..+.-. .+........ T Consensus 10 f~~~LrD~y~aEkq~~kaL~kma~~~~---~~~Lka~~E~Hl~ET~~qi~rLe~Vfe~~g~~~~~~~cda~~giiaegq~ 86 (167) T COG3685 10 FIDTLRDIYAAEKQILKALPKMARRAQ---YPELKAAIEKHLEETKGQIERLEQVFERLGKKARRVTCDAMEGLIAEGQE 86 (167) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHC---CHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHH T ss_conf 999999999999999999899998714---79999999999998888999999999984865322328889979998899 Q ss_pred --------CH--HHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf --------98--999999999999999999999999997099889999999999999999999999 Q gi|254780720|r 81 --------DV--EGLFSLMYEHENKVTIAYDDAIETILAEKDHQTFQFLQWFVKEQHEEMALFRRI 136 (164) Q Consensus 81 --------~~--~e~~~~al~~E~~vt~~~~~l~~~A~~~~D~~t~~fl~~fl~EQ~eee~~~~~l 136 (164) .+ ..+.-.+...|..-+.+|.-|+..|.+.+|-.+...|...|+|...--.++.++ T Consensus 87 i~~~~~~~evlda~L~~aaq~vEhyEIA~YgtL~a~A~qlG~~~a~~ll~~~L~eEkatd~~Lt~~ 152 (167) T COG3685 87 IMEEFKSNEVLDAGLIGAAQKVEHYEIACYGTLIAAAEQLGDDEAVKLLEAILEEEKATDEKLTQL 152 (167) T ss_pred HHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 987656408888998999999999999999999999998283889999999988899899999997 No 47 >PRK13965 ribonucleotide-diphosphate reductase subunit beta; Provisional Probab=78.26 E-value=5.2 Score=19.78 Aligned_cols=82 Identities=9% Similarity=-0.038 Sum_probs=48.7 Q ss_pred HHHHHHHHHHHH--HHHCCC-HHHHHHHHHHHHHHHHHHHHHHH-HHHHHCC-CCCEECCCCCCCCCCCCHHHHHHHHHH Q ss_conf 999999999999--981599-47899999999999999999999-9999539-971437822572048898999999999 Q gi|254780720|r 17 YVAQYHYMQAAA--WAASHN-LDGCCNFLLKHAMEEHSHVIRIF-KHLTDLG-VEAKFSSIEAPVISANDVEGLFSLMYE 91 (164) Q Consensus 17 l~as~~Yl~~a~--~~~~~~-~~g~a~~f~~~a~EE~~HA~~l~-~yi~~rg-g~~~~~~i~~p~~~~~~~~e~~~~al~ 91 (164) +.+.++|-..+. ++.+.| ++|.+.-++-.+.+|--|..... .+..... -.|. ..+ ..-..+.++++.+++ T Consensus 175 lEGi~FysgFa~~l~l~~~gkM~g~~~ii~~I~RDEslH~~~~~~~~~~~~~~~~~e----~~~-e~~~~v~~~~~~aVe 249 (337) T PRK13965 175 MPGFLLYGGFYLPFYLSARGKLPNTSDIIRLILRDKVIHNYYSGYKYQQKVARLSPE----KQA-EMKAFVFDLLYELID 249 (337) T ss_pred HHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHH----HHH-HHHHHHHHHHHHHHH T ss_conf 999999999999999886698723798878998704888889999999998742987----789-999999999999999 Q ss_pred HHHHHHHHHHHH Q ss_conf 999999999999 Q gi|254780720|r 92 HENKVTIAYDDA 103 (164) Q Consensus 92 ~E~~vt~~~~~l 103 (164) +|+.-+..+-.. T Consensus 250 lE~~~~~~~~~~ 261 (337) T PRK13965 250 LEKAYLRELYAG 261 (337) T ss_pred HHHHHHHHHHHC T ss_conf 999999999836 No 48 >TIGR02284 TIGR02284 conserved hypothetical protein; InterPro: IPR011971 Members of this protein family are found mostly in the Proteobacteria, although one member is found in the the marine planctomycete Pirellula sp. strain 1. The function is unknown.. Probab=77.93 E-value=5.3 Score=19.72 Aligned_cols=129 Identities=16% Similarity=0.085 Sum_probs=85.0 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEECCCCC---------C- Q ss_conf 999999999999999999999999815994789999999999999999999999995399714378225---------7- Q gi|254780720|r 6 DRVLNELMNMEYVAQYHYMQAAAWAASHNLDGCCNFLLKHAMEEHSHVIRIFKHLTDLGVEAKFSSIEA---------P- 75 (164) Q Consensus 6 ~~~Ln~qi~~El~as~~Yl~~a~~~~~~~~~g~a~~f~~~a~EE~~HA~~l~~yi~~rgg~~~~~~i~~---------p- 75 (164) ...||+.|..-...-. .+..-....+=|.++.+|+..|.+...-+.-|-+|+..+||.|....--. . T Consensus 2 ~~~Ln~LI~~~~d~~~---~f~~sA~~~~d~~l~tlf~~~a~~~~a~v~eLqq~V~~~Gg~ped~Gs~~g~lh~~w~~ir 78 (142) T TIGR02284 2 IESLNDLIEVSIDGKD---GFEESAEEVKDPELATLFRRIADEKSAIVSELQQLVESLGGKPEDSGSVAGKLHRIWVKIR 78 (142) T ss_pred HHHHHHHHHHCCCCCH---HHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHH T ss_conf 1556778860799702---4788786328767999998742455689998899999717954656510155657655552 Q ss_pred -CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf -20488989999999999999999999999999970998899999999999999999999999999 Q gi|254780720|r 76 -VISANDVEGLFSLMYEHENKVTIAYDDAIETILAEKDHQTFQFLQWFVKEQHEEMALFRRILDKI 140 (164) Q Consensus 76 -~~~~~~~~e~~~~al~~E~~vt~~~~~l~~~A~~~~D~~t~~fl~~fl~EQ~eee~~~~~ll~~l 140 (164) ....++-..++..+=.-|-.+...|.+..+...+. .+..-+..-+.-|.++++.-.+-+..+ T Consensus 79 ~~l~~~d~~~~l~e~Er~ED~~~~aY~~~L~~~~ek---G~~aa~~~v~~~qy~~v~~~hd~~~~~ 141 (142) T TIGR02284 79 AKLTSNDDLVVLEEAERGEDVAKKAYDETLKDQDEK---GVPAAVRDVVERQYEGVKANHDKIRAL 141 (142) T ss_pred HHCCCCCHHHHHHHHCCHHHHHHHHHHHHHHHHCCC---CCCHHHHHHHHHHHHHHHHHHHHHHCC T ss_conf 102898403467543000018889999998630146---988889999999889888524765306 No 49 >COG2941 CAT5 Ubiquinone biosynthesis protein COQ7 [Coenzyme metabolism] Probab=76.39 E-value=5.9 Score=19.45 Aligned_cols=113 Identities=23% Similarity=0.192 Sum_probs=80.2 Q ss_pred HHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEECCCCCCCCCC-----------CCH Q ss_conf 999999999999999981599478999999999999999999999999539971437822572048-----------898 Q gi|254780720|r 14 NMEYVAQYHYMQAAAWAASHNLDGCCNFLLKHAMEEHSHVIRIFKHLTDLGVEAKFSSIEAPVISA-----------NDV 82 (164) Q Consensus 14 ~~El~as~~Yl~~a~~~~~~~~~g~a~~f~~~a~EE~~HA~~l~~yi~~rgg~~~~~~i~~p~~~~-----------~~~ 82 (164) .-|+.|-..|.-.+.+.... .+.. -++..+++|..|--.+-++++++|..|.+- .|-... -.. T Consensus 51 aGE~~A~~iY~GQ~~~~r~~-~~R~--~l~em~d~E~~HL~~f~~~l~e~~vRPsll---~P~W~~~~FalGA~a~Llgd 124 (204) T COG2941 51 AGELGAQAIYQGQAAVARSP-EPRI--QLKEMADEEIDHLAWFEQRLLELGVRPSLL---NPLWYAAAFALGAGAGLLGD 124 (204) T ss_pred HHHHHHHHHHHHHHHHHCCC-CHHH--HHHHHHHHHHHHHHHHHHHHHHCCCCCCHH---HHHHHHHHHHHHHHHHHCCC T ss_conf 24788999984279998182-3689--999999878899999999999815782078---79999888998777763053 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHH Q ss_conf 999999999999999999999999997099889999999999999999999 Q gi|254780720|r 83 EGLFSLMYEHENKVTIAYDDAIETILAEKDHQTFQFLQWFVKEQHEEMALF 133 (164) Q Consensus 83 ~e~~~~al~~E~~vt~~~~~l~~~A~~~~D~~t~~fl~~fl~EQ~eee~~~ 133 (164) +..+-..-+.|..+-+.|..-...- .+.|..+...+..|=.+.+++-+.+ T Consensus 125 k~am~~teavE~vIe~Hy~~ql~~L-~~~d~~lr~~l~qfR~DE~eH~d~A 174 (204) T COG2941 125 KAAMGFTEAVETVIEKHYDGQLREL-PNLDAELRAILAQFRDDELEHLDNA 174 (204) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH-HHCCHHHHHHHHHHHHHHHHHHHHH T ss_conf 8888878999999999999999987-4116999999999866999877789 No 50 >pfam08066 PMC2NT PMC2NT (NUC016) domain. This domain is found at the N-terminus of 3'-5' exonucleases with HRDC domains, and also in putative exosome components. Probab=74.91 E-value=4.6 Score=20.09 Aligned_cols=58 Identities=9% Similarity=-0.059 Sum_probs=41.3 Q ss_pred CH-HHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEECCCCCCCCCCCCHHHHHHHHHH Q ss_conf 94-78999999999999999999999999539971437822572048898999999999 Q gi|254780720|r 34 NL-DGCCNFLLKHAMEEHSHVIRIFKHLTDLGVEAKFSSIEAPVISANDVEGLFSLMYE 91 (164) Q Consensus 34 ~~-~g~a~~f~~~a~EE~~HA~~l~~yi~~rgg~~~~~~i~~p~~~~~~~~e~~~~al~ 91 (164) .+ |+|++++..++..=+.-+..+++.+..++..+..+....+...|..+.++....++ T Consensus 21 S~dp~~~~~ld~~s~rLl~l~n~ll~~~~~~~~~~~~~~~~~~e~~w~~vvdv~D~llE 79 (91) T pfam08066 21 SFDPEFSQSLDEQSQRLLSLINDLLQSAGSKSDIPDRSDEDDVEDQWEGVVDVNDSLLE 79 (91) T ss_pred HCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHH T ss_conf 50888999999999999999999998447667887875423188999999999999999 No 51 >PRK09614 nrdF ribonucleotide-diphosphate reductase subunit beta; Reviewed Probab=74.01 E-value=6.8 Score=19.08 Aligned_cols=79 Identities=16% Similarity=0.110 Sum_probs=50.2 Q ss_pred HHHHHHHHH--HHHCCC-HHHHHHHHHHHHHHHHHHHHHHHHHHHHCC-CCCEECCCCCCCCCCCCHHHHHHHHHHHHHH Q ss_conf 999999999--981599-478999999999999999999999999539-9714378225720488989999999999999 Q gi|254780720|r 20 QYHYMQAAA--WAASHN-LDGCCNFLLKHAMEEHSHVIRIFKHLTDLG-VEAKFSSIEAPVISANDVEGLFSLMYEHENK 95 (164) Q Consensus 20 s~~Yl~~a~--~~~~~~-~~g~a~~f~~~a~EE~~HA~~l~~yi~~rg-g~~~~~~i~~p~~~~~~~~e~~~~al~~E~~ 95 (164) .++|-+.+. |+.+.| ++|++.-.+--+.+|--|..-...-++..- ..|. ...+.. ...+.++++.+.++|+. T Consensus 168 i~FyssFa~~~~f~~~g~m~G~~~~i~~I~RDE~lH~~~~~~l~~~l~~e~p~---~~~~~~-~~~i~~~~~eave~E~~ 243 (325) T PRK09614 168 FLFYSGFYYPLYLARQGKMTGTGQIIRLIIRDESLHGYYIGYLFQAGLEELPE---LEQEEL-KDEIYDLLYELYENEEA 243 (325) T ss_pred HHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCH---HHHHHH-HHHHHHHHHHHHHHHHH T ss_conf 99998899999999859662589999999987888899999999999863988---557999-99999999999999999 Q ss_pred HHHHHHH Q ss_conf 9999999 Q gi|254780720|r 96 VTIAYDD 102 (164) Q Consensus 96 vt~~~~~ 102 (164) -+..+-. T Consensus 244 ~~~~~~~ 250 (325) T PRK09614 244 YTELLYD 250 (325) T ss_pred HHHHHHC T ss_conf 9999855 No 52 >PRK13966 nrdF2 ribonucleotide-diphosphate reductase subunit beta; Provisional Probab=67.49 E-value=9.5 Score=18.20 Aligned_cols=83 Identities=16% Similarity=0.111 Sum_probs=43.6 Q ss_pred HHHHHHHHHH--HHHCC-CHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEECCCCCCCCCCCCHHHHHHHHHHHHHH Q ss_conf 9999999999--98159-94789999999999999999999999995399714378225720488989999999999999 Q gi|254780720|r 19 AQYHYMQAAA--WAASH-NLDGCCNFLLKHAMEEHSHVIRIFKHLTDLGVEAKFSSIEAPVISANDVEGLFSLMYEHENK 95 (164) Q Consensus 19 as~~Yl~~a~--~~~~~-~~~g~a~~f~~~a~EE~~HA~~l~~yi~~rgg~~~~~~i~~p~~~~~~~~e~~~~al~~E~~ 95 (164) +.++|-..+. ++.+. -++|.+.-++-.+.+|.-|...+.. +..++ ....+.+..+.. -..+.+++..+.+.|+. T Consensus 164 g~~FysgFa~~l~l~~~~kM~G~~~ii~~I~RDEs~H~~~~~~-l~~~~-~~~~~~~~~~e~-~~~i~~~~~~~v~~E~~ 240 (324) T PRK13966 164 SFLFYSGFYLPMYWSSRAKLTNTADMIRLIIRDEAVHGYYIGY-KFQRG-LALVDDVTRAEL-KDYTYELLFELYDNEVE 240 (324) T ss_pred HHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHH-HHHHH-HHHCCHHHHHHH-HHHHHHHHHHHHHHHHH T ss_conf 9999999999999985699867899999999837888879999-99998-885487768999-99999999999999999 Q ss_pred HHHHHHHHH Q ss_conf 999999999 Q gi|254780720|r 96 VTIAYDDAI 104 (164) Q Consensus 96 vt~~~~~l~ 104 (164) -+..+-... T Consensus 241 ~~~~l~~~~ 249 (324) T PRK13966 241 YTQDLYDEV 249 (324) T ss_pred HHHHHHCCC T ss_conf 999875237 No 53 >TIGR02630 xylose_isom_A xylose isomerase; InterPro: IPR013452 Xylose isomerase (5.3.1.5 from EC) is an enzyme which interconverts D-xylose and D-xylulose.; GO: 0009045 xylose isomerase activity. Probab=60.14 E-value=9.9 Score=18.09 Aligned_cols=42 Identities=19% Similarity=0.299 Sum_probs=31.0 Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHH----HHHHHCCCCCEECCCCCC Q ss_conf 947899999999999999999999----999953997143782257 Q gi|254780720|r 34 NLDGCCNFLLKHAMEEHSHVIRIF----KHLTDLGVEAKFSSIEAP 75 (164) Q Consensus 34 ~~~g~a~~f~~~a~EE~~HA~~l~----~yi~~rgg~~~~~~i~~p 75 (164) |+.|-...+.....-|++|.-+|+ +|-...|-.+.+=--|+| T Consensus 188 GREGYetLLNTD~~~Eld~lArF~~mAvdYa~~IGF~G~fLIEPKP 233 (437) T TIGR02630 188 GREGYETLLNTDMKLELDHLARFLQMAVDYAKKIGFKGQFLIEPKP 233 (437) T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCC T ss_conf 5303321445217789999988999999998846899844116763 No 54 >COG2996 Predicted RNA-bindining protein (contains S1 and HTH domains) [General function prediction only] Probab=54.00 E-value=14 Score=17.08 Aligned_cols=50 Identities=18% Similarity=0.097 Sum_probs=33.3 Q ss_pred HHHHHHHHH-HHHHHHHHHHHCCCCCEECCCCCCC---CCCCCHHHHHHHHHHH Q ss_conf 999999999-9999999999539971437822572---0488989999999999 Q gi|254780720|r 43 LKHAMEEHS-HVIRIFKHLTDLGVEAKFSSIEAPV---ISANDVEGLFSLMYEH 92 (164) Q Consensus 43 ~~~a~EE~~-HA~~l~~yi~~rgg~~~~~~i~~p~---~~~~~~~e~~~~al~~ 92 (164) +..+.|.+. .|+++..|+..+||...++.-..|. ..|.--+..|+.|+.+ T Consensus 216 ~p~~~E~l~~daq~Il~yL~~~gG~mpf~DKSsPEdIk~~FgiSKg~FKrAiGg 269 (287) T COG2996 216 RPRAHEMLDEDAQMILTYLESNGGFMPFNDKSSPEDIKATFGISKGQFKRAIGG 269 (287) T ss_pred CCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHH T ss_conf 563177654148999999997499244678999899998868178899998888 No 55 >PRK07209 ribonucleotide-diphosphate reductase subunit beta; Validated Probab=52.96 E-value=17 Score=16.64 Aligned_cols=41 Identities=7% Similarity=0.181 Sum_probs=17.0 Q ss_pred HHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 99999999970998899999999999999999999999999 Q gi|254780720|r 100 YDDAIETILAEKDHQTFQFLQWFVKEQHEEMALFRRILDKI 140 (164) Q Consensus 100 ~~~l~~~A~~~~D~~t~~fl~~fl~EQ~eee~~~~~ll~~l 140 (164) .--+..+.+..+=..+...++|++++..-|..-..+++..+ T Consensus 244 Fa~il~l~RrgkM~G~~~~~~~i~RDEslH~~f~~~li~~i 284 (391) T PRK07209 244 FTQILSLGRQNKMTGAAEQYQYILRDESMHLNFGIDLINQI 284 (391) T ss_pred HHHHHHHHHHCCCCCHHHHHHHHHCCHHHHHHHHHHHHHHH T ss_conf 99999987514575758776463202788999999999998 No 56 >pfam10152 DUF2360 Predicted coiled-coil domain-containing protein (DUF2360). This is the conserved 140 amino acid region of a family of proteins conserved from nematodes to humans. One C. elegans member is annotated as a Daf-16-dependent longevity protein 1 but this could not be confirmed. The function is unknown. Probab=39.39 E-value=28 Score=15.34 Aligned_cols=43 Identities=14% Similarity=0.224 Sum_probs=21.1 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHC Q ss_conf 8999999999999999999999999999528875169999999996531 Q gi|254780720|r 114 QTFQFLQWFVKEQHEEMALFRRILDKIRLIGSGPHSRYMFDLEIEKIAN 162 (164) Q Consensus 114 ~t~~fl~~fl~EQ~eee~~~~~ll~~l~~~g~~~~glyl~D~~l~~~~~ 162 (164) .|.+||+.|-.. =|.++.++-.+|.++.- .+-+++.+|+.|++ T Consensus 7 ~Tv~FLNrFs~~---CE~KL~~~e~~LQ~lE~---~l~ILEaKL~SIpg 49 (147) T pfam10152 7 STVQFLNRFSAV---CESKLVEAERSLQQLET---TLSLLEAKLASIPG 49 (147) T ss_pred HHHHHHHHHHHH---HHHHHHHHHHHHHHHHH---HHHHHHHHHCCCCC T ss_conf 999999999999---99999999999999999---99999999746975 No 57 >cd07911 RNRR2_Rv0233_like Ribonucleotide Reductase R2-like protein, ferritin-like diiron-binding domain. Rv0233 is a Mycobacterium tuberculosis ribonucleotide reductase R2 protein with a heterodinuclear manganese/iron-carboxylate cofactor located in its metal center. The Rv0233-like family may represent a structural/functional counterpart of the evolutionary ancestor of the RNRR2's (Ribonucleotide Reductase, R2/beta subunit) and the bacterial multicomponent monooxygenases. RNRR2s belong to a broad superfamily of ferritin-like diiron-carboxylate proteins. The RNR protein catalyzes the conversion of ribonucleotides to deoxyribonucleotides and is found in prokaryotes and archaea. The catalytically active form of RNR is a proposed alpha2-beta2 tetramer. The homodimeric alpha subunit (R1) contains the active site and redox active cysteines as well as the allosteric binding sites. Probab=38.37 E-value=29 Score=15.25 Aligned_cols=38 Identities=21% Similarity=0.176 Sum_probs=26.5 Q ss_pred HCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCE Q ss_conf 15994789999999999999999999999995399714 Q gi|254780720|r 31 ASHNLDGCCNFLLKHAMEEHSHVIRIFKHLTDLGVEAK 68 (164) Q Consensus 31 ~~~~~~g~a~~f~~~a~EE~~HA~~l~~yi~~rgg~~~ 68 (164) ...+.+....|+-.++-+|--|++.+.-.+-..|.... T Consensus 73 ~~~~~~e~~~~l~~q~~eEaiH~~sYs~~~~tl~~~~~ 110 (280) T cd07911 73 AAEGRLEEEMYLTQFLFEEAKHTDFFRRWLDAVGVSDD 110 (280) T ss_pred HCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHH T ss_conf 20375899999999999999999999999998467565 No 58 >pfam04518 DUF582 Protein of unknown function, DUF582. This family contains several uncharacterized chlamydial proteins. Probab=36.74 E-value=31 Score=15.09 Aligned_cols=56 Identities=16% Similarity=0.256 Sum_probs=27.1 Q ss_pred HHHHHHHHHHH--HHHHHHHHHHHHHHHHC--CC---HHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 99999999999--99999999999999815--99---47899999999999999999999999 Q gi|254780720|r 5 RDRVLNELMNM--EYVAQYHYMQAAAWAAS--HN---LDGCCNFLLKHAMEEHSHVIRIFKHL 60 (164) Q Consensus 5 ~~~~Ln~qi~~--El~as~~Yl~~a~~~~~--~~---~~g~a~~f~~~a~EE~~HA~~l~~yi 60 (164) -.+++|..|.. +|..+-.|..+|+|... .| +||-..-....-.+|+.++.+-+++- T Consensus 158 aa~~~N~ll~~i~~F~ta~vYynl~sYl~Q~~~g~~~F~g~~~~a~~~l~~Ek~~~~~di~~~ 220 (380) T pfam04518 158 AANYGNDLLDIISSFQTASVYYNLASYLGQGKMGTNAFPGSYDEALAKLEKEKEQIRRDIKRC 220 (380) T ss_pred HHHHHHHHHHHHHHCCCCCEEEEHHHHHCCCCCCHHHCCCHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 788767999999855475224537888535302321156629999999999999999999999 No 59 >pfam10666 Phage_Gp14 Phage protein Gp14. This phage protein family is of unknown function but is expressed from within a cluster of tail- and base plate-producing genes. Probab=34.47 E-value=33 Score=14.87 Aligned_cols=92 Identities=15% Similarity=0.115 Sum_probs=43.9 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHH---HHHH-HHHHHHHHHHHCCCCCEECCCCCCCCCCCCHHHH Q ss_conf 99999999999999999999815994789999999999---9999-9999999999539971437822572048898999 Q gi|254780720|r 10 NELMNMEYVAQYHYMQAAAWAASHNLDGCCNFLLKHAM---EEHS-HVIRIFKHLTDLGVEAKFSSIEAPVISANDVEGL 85 (164) Q Consensus 10 n~qi~~El~as~~Yl~~a~~~~~~~~~g~a~~f~~~a~---EE~~-HA~~l~~yi~~rgg~~~~~~i~~p~~~~~~~~e~ 85 (164) |..||..+.-||+=+.++.-.-++|+. .-+|..-. |... .-.++-+|-.+.-|...+..... --.++.++ T Consensus 4 nnviniqleesyqef~lgtelfrv~l~---d~mrr~wieadekyk~kl~kl~kyn~d~~~ems~~~y~~---l~~~v~ea 77 (140) T pfam10666 4 NNVINIQLEESYQEFQLGTELFRVGLG---DKMRRKWIEADEKYKKKLEKLNKYNIDNTDEMSSEEYFT---LEEDVKEA 77 (140) T ss_pred CCEEEEEHHHHHHHHHHHHHHHHHCCC---HHHHHHHHHCCHHHHHHHHHHHHCCCCCCCCCHHHHHHH---HHHHHHHH T ss_conf 653655338888998520678541024---899999997009999999886204865434230888999---99999999 Q ss_pred HHHHHHHHHHHHHHHHHHHHHH Q ss_conf 9999999999999999999999 Q gi|254780720|r 86 FSLMYEHENKVTIAYDDAIETI 107 (164) Q Consensus 86 ~~~al~~E~~vt~~~~~l~~~A 107 (164) +..|++.=..--..+...+..| T Consensus 78 l~~a~~ill~d~~afdkcya~c 99 (140) T pfam10666 78 LTEAYAILLDDEKAFDKCYAQC 99 (140) T ss_pred HHHHHHHHHCCCHHHHHHHHHH T ss_conf 9998898826513488999999 No 60 >cd01058 AAMH_B Aromatic and Alkene Monooxygenase Hydroxylase, subunit B, ferritin-like diiron-binding domain. Aromatic and Alkene Monooxygenase Hydroxylases, subunit B (AAMH_B). Subunit B (beta) of the soluble hydroxylase of multicomponent, aromatic and alkene monooxygenases are members of a superfamily of ferritin-like iron-storage proteins. AAMH exists as a hexamer (an alpha2-beta2-gamma2 homodimer) with each alpha-subunit housing one nonheme diiron center embedded in a four-helix bundle. The N-terminal domain of the alpha- and noncatalytic beta-subunits possess nearly identical folds; the beta-subunit lacks the C-terminal domain found in the alpha-subunit. Methane monooxygenase is a multicomponent enzyme found in methanotrophic bacteria that catalyzes the hydroxylation of methane and higher alkenes (as large as octane). Phenol monooxygenase, found in a diverse group of bacteria, catalyses the hydroxylation of phenol, chloro- and methyl-phenol and naphthol. Both enzyme systems consis Probab=33.76 E-value=34 Score=14.80 Aligned_cols=108 Identities=10% Similarity=-0.044 Sum_probs=68.8 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEECCCCCCCC------CCCCHHHHHHHHH--------------HHHH Q ss_conf 4789999999999999999999999995399714378225720------4889899999999--------------9999 Q gi|254780720|r 35 LDGCCNFLLKHAMEEHSHVIRIFKHLTDLGVEAKFSSIEAPVI------SANDVEGLFSLMY--------------EHEN 94 (164) Q Consensus 35 ~~g~a~~f~~~a~EE~~HA~~l~~yi~~rgg~~~~~~i~~p~~------~~~~~~e~~~~al--------------~~E~ 94 (164) =..+..-+.-+|.+++.||+.+.-|.+.+++...-......+. .|..+.+.++..+ -.|- T Consensus 128 ~~~i~~a~~f~a~D~Lr~aQ~i~~~~~~L~~~~~~~~~~~~k~~W~~dp~WQ~~R~~vE~~l~~~Dw~E~~vA~nlv~d~ 207 (304) T cd01058 128 STTITNAAAFQAMDKLRIAQDIAYRGLELDGNTPGFDGDAAKEAWEEDPAWQGLRELVEKLLVTYDWGEAFVAQNLVFDP 207 (304) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCCHHHHHHHHHHHHHHCCHHHHHHHHHHHHHH T ss_conf 09999999999888867999999999984656898772689998830840131899999998613559999999887998 Q ss_pred HHHHH-HHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC Q ss_conf 99999-9999999997099889999999999999999999999999995288 Q gi|254780720|r 95 KVTIA-YDDAIETILAEKDHQTFQFLQWFVKEQHEEMALFRRILDKIRLIGS 145 (164) Q Consensus 95 ~vt~~-~~~l~~~A~~~~D~~t~~fl~~fl~EQ~eee~~~~~ll~~l~~~g~ 145 (164) -+... +..+...|...+|..|..+...... ...++.++....+|.+-. T Consensus 208 ll~~L~~~~f~~~a~~~Gd~~t~~l~~~~~~---d~~r~~~w~~alvk~~~~ 256 (304) T cd01058 208 LVGELVRRELDRLAASNGDTLTPLLTEFMLD---DAQRHRRWTDALVKTAAE 256 (304) T ss_pred HHHHHHHHHHHHHHHHCCCCCHHHHHHHHHH---HHHHHHHHHHHHHHHHHH T ss_conf 8799999999999998699513999999999---999999999999999981 No 61 >pfam04332 DUF475 Protein of unknown function (DUF475). Predicted to be an integral membrane protein with multiple membrane spans. Probab=32.97 E-value=35 Score=14.72 Aligned_cols=65 Identities=17% Similarity=0.221 Sum_probs=43.6 Q ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC Q ss_conf 88989999999999999999999999999-97099889999999999999999999999999995288 Q gi|254780720|r 79 ANDVEGLFSLMYEHENKVTIAYDDAIETI-LAEKDHQTFQFLQWFVKEQHEEMALFRRILDKIRLIGS 145 (164) Q Consensus 79 ~~~~~e~~~~al~~E~~vt~~~~~l~~~A-~~~~D~~t~~fl~~fl~EQ~eee~~~~~ll~~l~~~g~ 145 (164) .-+|.++++.|+..-....+.+.+.+..- .=-+=+-..-||+||++| ++++++.++...+.+.|. T Consensus 48 ~lgp~ea~~lAl~~p~~Y~~~l~~ahp~IaaFGG~FLlmvfL~fffde--k~~~Wl~~iE~~l~k~g~ 113 (294) T pfam04332 48 GLDPIEAMKLALENPDRYEELLTAAHPSIAAFGGMFLLMVFLDFFFDD--RDIKWLKWIERPLARIGK 113 (294) T ss_pred CCCHHHHHHHHHCCHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHCCC--CCCCEEHHHHHHHHHCCC T ss_conf 889899999983697889999984368899885999999999870206--636543698799987277 No 62 >pfam03202 Lipoprotein_10 Putative mycoplasma lipoprotein, C-terminal region. Probab=32.85 E-value=13 Score=17.28 Aligned_cols=17 Identities=24% Similarity=0.819 Sum_probs=8.4 Q ss_pred HCCHHHHHHHHHHHHHH Q ss_conf 09988999999999999 Q gi|254780720|r 110 EKDHQTFQFLQWFVKEQ 126 (164) Q Consensus 110 ~~D~~t~~fl~~fl~EQ 126 (164) ..|-+|..|++|||..+ T Consensus 16 ked~aTk~FV~W~l~~~ 32 (134) T pfam03202 16 KENAETQKFVNWFLNTE 32 (134) T ss_pred CCCHHHHHHHHHHHCCC T ss_conf 55689999999996374 No 63 >TIGR02858 spore_III_AA stage III sporulation protein AA; InterPro: IPR014217 Proteins in this entry include the stage III sporulation protein AA that is encoded by one of several genes in the spoIIIA locus. This protein is only found in species that are capable of endospore formation.. Probab=28.97 E-value=34 Score=14.79 Aligned_cols=47 Identities=15% Similarity=0.114 Sum_probs=36.8 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEECCCCCCCCCCCC Q ss_conf 47899999999999999999999999953997143782257204889 Q gi|254780720|r 35 LDGCCNFLLKHAMEEHSHVIRIFKHLTDLGVEAKFSSIEAPVISAND 81 (164) Q Consensus 35 ~~g~a~~f~~~a~EE~~HA~~l~~yi~~rgg~~~~~~i~~p~~~~~~ 81 (164) +...|.|=-.-|.|-.+=|++++.||.+++|.+...=|=.||...++ T Consensus 91 ik~v~S~NiRIaRE~~G~A~~~~~yL~d~~~~~~NTLiIsPPq~GKT 137 (282) T TIGR02858 91 IKNVASLNIRIAREVLGAADKILPYLVDRNGRVLNTLIISPPQCGKT 137 (282) T ss_pred EECCCCCCEEEEEECCCCCHHHHHHHHCCCCCEEEEEEECCCCCCCC T ss_conf 10546421330200057756668877305894467888868898851 No 64 >cd01048 Ferritin_like_AB2 Uncharacterized family of ferritin-like proteins found in archaea and bacteria. Ferritin-like domain found in archaea and bacteria, subgroup 2 (Ferritin_like_AB2). This uncharacterized domain is a member of a broad superfamily of ferritin-like diiron-carboxylate proteins whose function is unknown. The conserved residues of a diiron center are present within the putative active site. Probab=28.61 E-value=42 Score=14.27 Aligned_cols=96 Identities=15% Similarity=0.100 Sum_probs=68.1 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHCCC-HHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEECCCCC-C-------- Q ss_conf 99999999999999999999999981599-4789999999999999999999999995399714378225-7-------- Q gi|254780720|r 6 DRVLNELMNMEYVAQYHYMQAAAWAASHN-LDGCCNFLLKHAMEEHSHVIRIFKHLTDLGVEAKFSSIEA-P-------- 75 (164) Q Consensus 6 ~~~Ln~qi~~El~as~~Yl~~a~~~~~~~-~~g~a~~f~~~a~EE~~HA~~l~~yi~~rgg~~~~~~i~~-p-------- 75 (164) .+.|...+..|.-|--+|+... +.+| .+ -|...+.-|..|+..+..-+...|-.....+-+. . T Consensus 2 ~~~L~~~~eeEklArdvY~~l~---~~~G~~~----~F~nI~~SE~~H~~al~~Ll~~y~l~~P~~~~~~~~f~~~~y~~ 74 (135) T cd01048 2 IAALLYALEEEKLARDVYLALY---EKFGGLR----PFSNIAESEQRHMDALKTLLERYGLPDPVDPFSGGVFTNPQYNQ 74 (135) T ss_pred HHHHHHHHHHHHHHHHHHHHHH---HHHCCCC----HHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHH T ss_conf 5789999999999999999999---9878863----28999999999999999999985999999877667567611789 Q ss_pred --CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf --204889899999999999999999999999999 Q gi|254780720|r 76 --VISANDVEGLFSLMYEHENKVTIAYDDAIETIL 108 (164) Q Consensus 76 --~~~~~~~~e~~~~al~~E~~vt~~~~~l~~~A~ 108 (164) .....|..++++.....|..-+..|.++...+. T Consensus 75 l~~~g~~Sl~~Al~vGv~iE~~dI~dl~~~l~~t~ 109 (135) T cd01048 75 LVEQGPKSLQDALEVGVLIEELDIADYDRLLERTQ 109 (135) T ss_pred HHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCC T ss_conf 99875323999999999999962999999987658 No 65 >TIGR02146 LysS_fung_arch homocitrate synthase; InterPro: IPR011872 This entry includes the yeast LYS21 gene which carries out the first step of the alpha-aminoadipate (AAA) lysine biosynthesis pathway. A related pathway is found in Thermus thermophilus . This enzyme is closely related to 2-isopropylmalate synthase (LeuA) and citramalate synthase (CimA), both of which are present in the euryarchaeota. Some archaea have a separate homocitrate synthase (AksA) which also synthesizes longer homocitrate analogs .; GO: 0046912 transferase activity transferring acyl groups acyl groups converted into alkyl on transfer, 0019752 carboxylic acid metabolic process. Probab=28.15 E-value=43 Score=14.22 Aligned_cols=80 Identities=15% Similarity=0.168 Sum_probs=54.1 Q ss_pred HHHHHHHHHHHHHHHHHHH--CCC-HHHHHHHHHHH-----HHHHHHHHHHHHHHHHHCC--CCCEECCCCCCCCCCCCH Q ss_conf 9999999999999999981--599-47899999999-----9999999999999999539--971437822572048898 Q gi|254780720|r 13 MNMEYVAQYHYMQAAAWAA--SHN-LDGCCNFLLKH-----AMEEHSHVIRIFKHLTDLG--VEAKFSSIEAPVISANDV 82 (164) Q Consensus 13 i~~El~as~~Yl~~a~~~~--~~~-~~g~a~~f~~~-----a~EE~~HA~~l~~yi~~rg--g~~~~~~i~~p~~~~~~~ 82 (164) |-.+..|...=.-.|.-.+ +++ +=|.|+++++. -.+=++-+...|.|+..-| -.+.+++-..-.++|.++ T Consensus 68 iv~Hsra~~~D~~~a~~~~Vd~i~~~~G~S~~~l~~~h~~~~~~al~~i~e~I~y~K~~Gphv~VRFtaED~~R~d~~~L 147 (355) T TIGR02146 68 IVTHSRAVLDDIEVAVETEVDRIDVFFGVSKLLLKYKHRKDLEEALEIIAEVIEYAKSHGPHVKVRFTAEDTFRSDLDDL 147 (355) T ss_pred HHHHHHHHHHHHHHHHHCCCCEEEEEEECHHHHHCCCCCCCHHHHHHHHHHHHHHHHHCCCEEEEEECCCCCCHHHHHHH T ss_conf 56778999999877642278657874300588851025778899999999999999724882478864788851218999 Q ss_pred HHHHHHHHHH Q ss_conf 9999999999 Q gi|254780720|r 83 EGLFSLMYEH 92 (164) Q Consensus 83 ~e~~~~al~~ 92 (164) ..+.+.+.+. T Consensus 148 ~~v~k~a~~~ 157 (355) T TIGR02146 148 LKVYKTAKEA 157 (355) T ss_pred HHHHHHHHHC T ss_conf 9999999761 No 66 >pfam02332 Phenol_Hydrox Methane/Phenol/Toluene Hydroxylase. Bacterial phenol hydroxylase is a multicomponent enzyme that catabolizes phenol and some of its methylated derivatives. This Pfam family contains both the P1 and P3 polypeptides of phenol hydroxylase and the alpha and beta chain of methane hydroxylase protein A. Probab=26.83 E-value=45 Score=14.07 Aligned_cols=105 Identities=16% Similarity=0.015 Sum_probs=66.4 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEECCCCCCCCCC-------------------CCH-HHHHHHHHHHHH Q ss_conf 478999999999999999999999999539971437822572048-------------------898-999999999999 Q gi|254780720|r 35 LDGCCNFLLKHAMEEHSHVIRIFKHLTDLGVEAKFSSIEAPVISA-------------------NDV-EGLFSLMYEHEN 94 (164) Q Consensus 35 ~~g~a~~f~~~a~EE~~HA~~l~~yi~~rgg~~~~~~i~~p~~~~-------------------~~~-~e~~~~al~~E~ 94 (164) =+++..-+--++.+|+.|++.++-++..+.+...-..- ..+..| .+. .-.+...+..|- T Consensus 102 ~~~~~n~~~~~a~DelR~~Q~~~~~~~~l~~~~~~~~~-~~k~~w~~dp~wq~~R~~~E~~~~~~Dw~E~~va~nlv~e~ 180 (233) T pfam02332 102 APTIRNCATFQALDELRHLQRQAYFLHELAKADPDFDW-GQRAYWTNDPAWQGLRRLFEDILVTQDWVEAFIALNLVFEP 180 (233) T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCH-HHHHHHHHCCHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHH T ss_conf 89999999998879999999999999877522888684-89998861833789999999888607899999999888997 Q ss_pred HHHHH-HHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC Q ss_conf 99999-99999999970998899999999999999999999999999952 Q gi|254780720|r 95 KVTIA-YDDAIETILAEKDHQTFQFLQWFVKEQHEEMALFRRILDKIRLI 143 (164) Q Consensus 95 ~vt~~-~~~l~~~A~~~~D~~t~~fl~~fl~EQ~eee~~~~~ll~~l~~~ 143 (164) -++.. +..+...|...+|..|..++..... ++.++.++....+|.+ T Consensus 181 ~~~~l~~~~~~~~A~~~GD~~~~~l~~s~q~---D~~Rh~~~~~alvk~~ 227 (233) T pfam02332 181 LFTNLVFVALAEDAAENGDTLTALLTSSIQT---DEARHARWGDALVKTA 227 (233) T ss_pred HHHHHHHHHHHHHHHHCCCHHHHHHHHHHHH---HHHHHHHHHHHHHHHH T ss_conf 5368999999999998699037999999998---9999999999999999 No 67 >TIGR02110 PQQ_syn_pqqF coenzyme PQQ biosynthesis protein PqqF; InterPro: IPR011844 Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site . The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases . Peptidases are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry. Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. This family of metallopeptidases belong to MEROPS peptidase family M16, subfamily M16A (clan ME). In the subset of species that make coenzyme PQQ (pyrrolo-quinoline-quinone), this peptidase is found in the PQQ biosynthesis region and is thought to act as a protease on PqqA (IPR011725 from INTERPRO), a probable peptide precursor of the coenzyme. PQQ is required for some glucose dehydrogenases and alcohol dehydrogenases .; GO: 0008234 cysteine-type peptidase activity, 0008270 zinc ion binding, 0018189 pyrroloquinoline quinone biosynthetic process. Probab=26.67 E-value=36 Score=14.67 Aligned_cols=54 Identities=15% Similarity=0.094 Sum_probs=37.1 Q ss_pred CCHHHHHHHHHHHH---HHHHHHHHHHHHHHHHCCCCCEECCCCCCC-CCCCCHHHHH Q ss_conf 99478999999999---999999999999999539971437822572-0488989999 Q gi|254780720|r 33 HNLDGCCNFLLKHA---MEEHSHVIRIFKHLTDLGVEAKFSSIEAPV-ISANDVEGLF 86 (164) Q Consensus 33 ~~~~g~a~~f~~~a---~EE~~HA~~l~~yi~~rgg~~~~~~i~~p~-~~~~~~~e~~ 86 (164) ..+||+|+|+.+-. -|-..--+++|-|+..+||.|+=++..+-. .-|+=+-+.| T Consensus 43 ~awPGLAHfLEHLlFlG~ErF~~d~rLM~wvQ~qGGQVNA~T~~r~t~fFFElpA~Al 100 (737) T TIGR02110 43 SAWPGLAHFLEHLLFLGGERFQGDDRLMPWVQRQGGQVNASTLERTTDFFFELPAEAL 100 (737) T ss_pred CCCCCHHHHHHHHHHCCCCCCCCCCCCCHHHHHCCCCCCCCHHCCCCHHHHHHHHHHH T ss_conf 1466548899999730311145766620898623885100020134203455799999 No 68 >PTZ00211 ribonucleotide reductase small subunit; Provisional Probab=25.92 E-value=47 Score=13.97 Aligned_cols=60 Identities=15% Similarity=0.092 Sum_probs=30.3 Q ss_pred HHHCCC-HHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEECCCCCCCCCCCCHHHHHHHHHHHHHHHHH Q ss_conf 981599-4789999999999999999999999995399714378225720488989999999999999999 Q gi|254780720|r 29 WAASHN-LDGCCNFLLKHAMEEHSHVIRIFKHLTDLGVEAKFSSIEAPVISANDVEGLFSLMYEHENKVTI 98 (164) Q Consensus 29 ~~~~~~-~~g~a~~f~~~a~EE~~HA~~l~~yi~~rgg~~~~~~i~~p~~~~~~~~e~~~~al~~E~~vt~ 98 (164) |+.+.| ++|++.-..--+.+|--|..-...-+...-.. .|+ ..+.++++.|.+.|+..+. T Consensus 186 ~l~~~g~m~g~~~~i~~I~RDE~~H~~f~~~l~~~l~~e-------~~~---e~v~~~~~eAvelE~~f~~ 246 (330) T PTZ00211 186 WLKKRGLMPGLTFSNELISRDEGLHTDFACLLYSHLKNK-------LPR---ERVQEIIKDAVEIEREFIC 246 (330) T ss_pred HHHHCCCCCCHHHHHHHHHCCHHHHHHHHHHHHHHHHHC-------CCH---HHHHHHHHHHHHHHHHHHH T ss_conf 999749741179988899820999999999999997562-------999---9999999999999999999 No 69 >TIGR01582 FDH-beta formate dehydrogenase, beta subunit; InterPro: IPR006470 The sequences in this group represent the beta subunit of the gamma-proteobacterial formate dehydrogenase. This subunit contains four 4Fe-4S clusters and is involved in transmitting electrons from the alpha subunit (IPR006443 from INTERPRO) at the periplasmic space to the gamma subunit which spans the cytoplasmic membrane . In addition to the gamma proteobacteria, a sequence from Aquifex aolicus falls within this group. This appears to be the case for the alpha, gamma and epsilon (accessory protein IPR006452 from INTERPRO) chains as well. ; GO: 0008863 formate dehydrogenase activity, 0045333 cellular respiration, 0016021 integral to membrane. Probab=25.89 E-value=47 Score=13.97 Aligned_cols=21 Identities=19% Similarity=0.181 Sum_probs=17.4 Q ss_pred HHHHHH-HHHHHHHHHHHCCCC Q ss_conf 999999-999999999953997 Q gi|254780720|r 46 AMEEHS-HVIRIFKHLTDLGVE 66 (164) Q Consensus 46 a~EE~~-HA~~l~~yi~~rgg~ 66 (164) +.|+|. ||++.++.|..||.. T Consensus 191 ~KEdM~~~a~~~vadLK~RGY~ 212 (293) T TIGR01582 191 FKEDMKERAEKRVADLKSRGYE 212 (293) T ss_pred CHHHHHHHHHHHHHHHHHCCCC T ss_conf 7578999987888887634888 No 70 >cd01049 RNRR2 Ribonucleotide Reductase, R2/beta subunit, ferritin-like diiron-binding domain. Ribonucleotide Reductase, R2/beta subunit (RNRR2) is a member of a broad superfamily of ferritin-like diiron-carboxylate proteins. The RNR protein catalyzes the conversion of ribonucleotides to deoxyribonucleotides and is found in all eukaryotes, many prokaryotes, several viruses, and few archaea. The catalytically active form of RNR is a proposed alpha2-beta2 tetramer. The homodimeric alpha subunit (R1) contains the active site and redox active cysteines as well as the allosteric binding sites. The beta subunit (R2) contains a diiron cluster that, in its reduced state, reacts with dioxygen to form a stable tyrosyl radical and a diiron(III) cluster. This essential tyrosyl radical is proposed to generate a thiyl radical, located on a cysteine residue in the R1 active site that initiates ribonucleotide reduction. The beta subunit is composed of 10-13 helices, the 8 longest helices form an alpha- Probab=25.76 E-value=47 Score=13.95 Aligned_cols=63 Identities=14% Similarity=0.029 Sum_probs=28.5 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCC-CEECCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHH Q ss_conf 47899999999999999999999999953997-14378225720488989999999999999999999 Q gi|254780720|r 35 LDGCCNFLLKHAMEEHSHVIRIFKHLTDLGVE-AKFSSIEAPVISANDVEGLFSLMYEHENKVTIAYD 101 (164) Q Consensus 35 ~~g~a~~f~~~a~EE~~HA~~l~~yi~~rgg~-~~~~~i~~p~~~~~~~~e~~~~al~~E~~vt~~~~ 101 (164) ++|++.-.+--+.+|.-|..-...-+..+-.. |. +... .....+.++++.+.+.|+.-+..+. T Consensus 176 m~g~~~~i~~I~rDE~lH~~f~~~l~~~l~~e~~~---~~~~-~~~~~i~~~~~eav~~E~~~~~~~~ 239 (288) T cd01049 176 MPGLAEIIELISRDESLHGDFACLLIRELLNENPE---LFTE-EFKEEVYELIKEAVELEKEFARDLL 239 (288) T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCH---HHHH-HHHHHHHHHHHHHHHHHHHHHHHHC T ss_conf 60099999999998999999999999998862988---5656-6799999999999999999999980 No 71 >pfam00268 Ribonuc_red_sm Ribonucleotide reductase, small chain. Probab=23.31 E-value=53 Score=13.67 Aligned_cols=20 Identities=20% Similarity=0.210 Sum_probs=9.1 Q ss_pred HHHHHHHHHHHHHHHHHHHH Q ss_conf 47899999999999999999 Q gi|254780720|r 35 LDGCCNFLLKHAMEEHSHVI 54 (164) Q Consensus 35 ~~g~a~~f~~~a~EE~~HA~ 54 (164) ++|++.-.+--+.+|--|.. T Consensus 180 m~g~~~~i~~I~RDE~lH~~ 199 (281) T pfam00268 180 MPGTCQSNELISRDEALHTD 199 (281) T ss_pred HHHHHHHHHHHHHHHHHHHH T ss_conf 34499999999998999999 No 72 >COG4445 MiaE Hydroxylase for synthesis of 2-methylthio-cis-ribozeatin in tRNA [Nucleotide transport and metabolism / Translation, ribosomal structure and biogenesis] Probab=23.31 E-value=53 Score=13.67 Aligned_cols=126 Identities=16% Similarity=0.114 Sum_probs=70.3 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEECCCCCCCCCCCCHHHHHH Q ss_conf 99999999999999999999998159947899999999999999999999999953997143782257204889899999 Q gi|254780720|r 8 VLNELMNMEYVAQYHYMQAAAWAASHNLDGCCNFLLKHAMEEHSHVIRIFKHLTDLGVEAKFSSIEAPVISANDVEGLFS 87 (164) Q Consensus 8 ~Ln~qi~~El~as~~Yl~~a~~~~~~~~~g~a~~f~~~a~EE~~HA~~l~~yi~~rgg~~~~~~i~~p~~~~~~~~e~~~ 87 (164) +|-++..-|+.|+..-+.+-.-+ .+-..+-..+-.-+.||+.|.....+.+..||.... ++++++. ...+.. T Consensus 32 lLlDH~~CE~KAa~tAl~li~kY--~~~~~lv~km~~larEEL~HFeqV~eilq~RnI~~~--~i~asrY----a~~l~~ 103 (203) T COG4445 32 LLLDHLHCELKAAQTALNLIRKY--PSNTDLVDKMVLLAREELHHFEQVLEILQARNIPYV--PIPASRY----AKGLLA 103 (203) T ss_pred EHHHHHHHHHHHHHHHHHHHHHC--CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCC--CCCCCHH----HHHHHH T ss_conf 20356888888789999999983--426789999999999999999999999998399512--1795577----899999 Q ss_pred HHHHHHHH--HHHHHHHHHHHHHHH---------CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC Q ss_conf 99999999--999999999999970---------9988999999999999999999999999999528 Q gi|254780720|r 88 LMYEHENK--VTIAYDDAIETILAE---------KDHQTFQFLQWFVKEQHEEMALFRRILDKIRLIG 144 (164) Q Consensus 88 ~al~~E~~--vt~~~~~l~~~A~~~---------~D~~t~~fl~~fl~EQ~eee~~~~~ll~~l~~~g 144 (164) .+..+|-. .-+.+-..+-.|++. -|-....|....++ .|-+++++-+....-++ T Consensus 104 ~~rt~EPqrliD~Livga~IEARScERfa~LaphldeelakFY~gLl~---SEaRHfqdYl~LA~qy~ 168 (203) T COG4445 104 AVRTHEPQRLIDKLIVGAYIEARSCERFAALAPHLDEELAKFYKGLLR---SEARHFQDYLVLADQYF 168 (203) T ss_pred HHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHH T ss_conf 987248199999999988876644888986423564999999999999---88899888999999980 No 73 >TIGR02024 FtcD glutamate formiminotransferase; InterPro: IPR004227 This entry represents the formiminotransferase (FT) domain of formiminotransferase-cyclodeaminase (FTCD), which forms a homodimer, with each protomer being comprised of two subdomains. Tetrahydrofolate (THF)-dependent glutamate formiminotransferase is involved in the histidine utilization pathway. This enzyme interconverts L-glutamate and N-formimino-L-glutamate. The enzyme is bifunctional as it also catalyzes the cyclodeaminase reaction on N-formimino-THF, converting it to 5,10-methenyl-THF and releasing ammonia; part of the process of regenerating THF. This model covers enzymes from metazoa as well as Gram-positive bacteria and archaea. In humans, deficiency of this enzyme results in a disease phenotype . The crystal structure of the enzyme has been studied in the context of the catalytic mechanism . ; GO: 0005542 folic acid binding, 0016740 transferase activity, 0008152 metabolic process. Probab=22.24 E-value=55 Score=13.54 Aligned_cols=59 Identities=8% Similarity=0.139 Sum_probs=43.2 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHCCCCCEECCCCCCC---CCCCCHHHHHHHHHHHHHHHHH Q ss_conf 9999999999999999999999539971437822572---0488989999999999999999 Q gi|254780720|r 40 NFLLKHAMEEHSHVIRIFKHLTDLGVEAKFSSIEAPV---ISANDVEGLFSLMYEHENKVTI 98 (164) Q Consensus 40 ~~f~~~a~EE~~HA~~l~~yi~~rgg~~~~~~i~~p~---~~~~~~~e~~~~al~~E~~vt~ 98 (164) +-.-+-+-.--.-|..|||--+.+|+||.+++..-.| ..-.+..+|.+.|-+.=|.+-. T Consensus 56 e~v~~A~~~~aK~A~eLIDm~~H~G~HPRMGA~DViPF~Pv~~~~~EECV~~A~~~Gkr~GE 117 (331) T TIGR02024 56 EKVVNAALKLAKKAAELIDMRNHKGEHPRMGAVDVIPFIPVKDVTMEECVELAKELGKRLGE 117 (331) T ss_pred HHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCEEECCCCCCCCCCHHHHHHHHHHHHHHHHH T ss_conf 89999999988786765300147877795244100053137898489999999986158566 No 74 >TIGR01924 rsbW_low_gc anti-sigma B factor; InterPro: IPR010193 This entry describes the anti-sigma B factor also known as serine-protein kinase RsbW. Sigma B controls the general stress regulon in B subtilis and is activated by cell stresses such as stationary phase and heat shock. RsbW binds to sigma B and prevents formation of the transcription complex at the promoter . RsbV (anti-anti-sigma factor) binds to RsbW to inhibit association with sigma B, however RsbW can phosphorylate RsbV, causing disassociation of the RsbV/RsbW complex . Low ATP level or environmental stress causes the dephosphorylation of RsbV .; GO: 0004674 protein serine/threonine kinase activity, 0005524 ATP binding, 0016989 sigma factor antagonist activity, 0006468 protein amino acid phosphorylation, 0045892 negative regulation of transcription DNA-dependent. Probab=21.67 E-value=35 Score=14.72 Aligned_cols=17 Identities=12% Similarity=0.319 Sum_probs=11.3 Q ss_pred HHHHCCCCCHHHHHHHH Q ss_conf 99952887516999999 Q gi|254780720|r 139 KIRLIGSGPHSRYMFDL 155 (164) Q Consensus 139 ~l~~~g~~~~glyl~D~ 155 (164) .++.+...||||||+.- T Consensus 108 ~i~~L~eGGLGLFLiet 124 (161) T TIGR01924 108 DIDQLREGGLGLFLIET 124 (161) T ss_pred CHHHHHCCCCHHHHHHC T ss_conf 75432017713664510 No 75 >cd07648 F-BAR_FCHO The F-BAR (FES-CIP4 Homology and Bin/Amphiphysin/Rvs) domain of FCH domain Only proteins. F-BAR domains are dimerization modules that bind and bend membranes and are found in proteins involved in membrane dynamics and actin reorganization. Proteins in this group have been named FCH domain Only (FCHO) proteins. Vertebrates have two members, FCHO1 and FCHO2. These proteins contain an F-BAR domain and a C-terminal domain of unknown function named SAFF which is also present in endophilin interacting protein 1. F-BAR domains form banana-shaped dimers with a positively-charged concave surface that binds to negatively-charged lipid membranes. They can induce membrane deformation in the form of long tubules. Probab=21.67 E-value=57 Score=13.47 Aligned_cols=35 Identities=14% Similarity=0.141 Sum_probs=27.6 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEE Q ss_conf 47899999999999999999999999953997143 Q gi|254780720|r 35 LDGCCNFLLKHAMEEHSHVIRIFKHLTDLGVEAKF 69 (164) Q Consensus 35 ~~g~a~~f~~~a~EE~~HA~~l~~yi~~rgg~~~~ 69 (164) ..-++.||+..|.=|-..|..|.+.....++.... T Consensus 21 ~~el~~f~kERa~IEe~YAK~L~kLakk~~~~~e~ 55 (261) T cd07648 21 VKELADFLRERATIEETYSKALNKLAKQASNSSQL 55 (261) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCC T ss_conf 99999999999999999999999998410467775 No 76 >cd00886 MogA_MoaB MogA_MoaB family. Members of this family are involved in biosynthesis of the molybdenum cofactor (MoCF) an essential cofactor of a diverse group of redox enzymes. MoCF biosynthesis is an evolutionarily conserved pathway present in eubacteria, archaea, and eukaryotes. MoCF contains a tricyclic pyranopterin, termed molybdopterin (MPT). MogA, together with MoeA, is responsible for the metal incorporation into MPT, the third step in MoCF biosynthesis. The plant homolog Cnx1 is a MoeA-MogA fusion protein. The mammalian homolog gephyrin is a MogA-MoeA fusion protein, that plays a critical role in postsynaptic anchoring of inhibitory glycine receptors and major GABAa receptor subtypes. In contrast, MoaB shows high similarity to MogA, but little is known about its physiological role. All well studied members of this family form highly stable trimers. Probab=20.59 E-value=25 Score=15.68 Aligned_cols=39 Identities=15% Similarity=0.076 Sum_probs=25.0 Q ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEC Q ss_conf 599478999999999999999999999999539971437 Q gi|254780720|r 32 SHNLDGCCNFLLKHAMEEHSHVIRIFKHLTDLGVEAKFS 70 (164) Q Consensus 32 ~~~~~g~a~~f~~~a~EE~~HA~~l~~yi~~rgg~~~~~ 70 (164) +..+|||+..|+..+.++-.+|..=..-.--+|+.+.++ T Consensus 88 ~k~~pG~~e~~r~~s~~~~~~a~lSR~~aGi~~~tlI~~ 126 (152) T cd00886 88 DKELPGFGEAFRALSLEETGTAMLSRAVAGIRGGTLIFN 126 (152) T ss_pred HHCCCCHHHHHHHHHHCCCCHHHEEHHHEEEECCEEEEE T ss_conf 516965999999987553866312203138989999998 No 77 >cd07647 F-BAR_PSTPIP The F-BAR (FES-CIP4 Homology and Bin/Amphiphysin/Rvs) domain of Proline-Serine-Threonine Phosphatase-Interacting Proteins. F-BAR domains are dimerization modules that bind and bend membranes and are found in proteins involved in membrane dynamics and actin reorganization. Vetebrates contain two Proline-Serine-Threonine Phosphatase-Interacting Proteins (PSTPIPs), PSTPIP1 and PSTPIP2. PSTPIPs are mainly expressed in hematopoietic cells and are involved in the regulation of cell adhesion and motility. Mutations in PSTPIPs have been shown to cause autoinflammatory disorders. PSTPIP1 contains an N-terminal F-BAR domain, PEST motifs, and a C-terminal SH3 domain, while PSTPIP2 contains only the N-terminal F-BAR domain. F-BAR domains form banana-shaped dimers with a positively-charged concave surface that binds to negatively-charged lipid membranes. They can induce membrane deformation in the form of long tubules. Probab=20.20 E-value=61 Score=13.28 Aligned_cols=91 Identities=16% Similarity=0.146 Sum_probs=47.0 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEECCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHH Q ss_conf 47899999999999999999999999953997143782257204889899999999999999999999999999709988 Q gi|254780720|r 35 LDGCCNFLLKHAMEEHSHVIRIFKHLTDLGVEAKFSSIEAPVISANDVEGLFSLMYEHENKVTIAYDDAIETILAEKDHQ 114 (164) Q Consensus 35 ~~g~a~~f~~~a~EE~~HA~~l~~yi~~rgg~~~~~~i~~p~~~~~~~~e~~~~al~~E~~vt~~~~~l~~~A~~~~D~~ 114 (164) ..-++.||+..|.=|...|..|.+.-...++. ....++..++..... |.+....++.-....... + T Consensus 21 ckel~~f~kERa~IEe~YaK~L~kLsk~~~~~----------~e~Gtl~~sw~~~~~-e~e~~a~~H~~l~~~L~~-~-- 86 (239) T cd07647 21 CKELEDFLKQRAKAEEDYGKALLKLSKSAGPG----------DEIGTLKSSWDSLRK-ETENVANAHIQLAQSLRE-E-- 86 (239) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCC----------CCCCCHHHHHHHHHH-HHHHHHHHHHHHHHHHHH-H-- T ss_conf 99999999998899999989999997144688----------888929999999999-999999999999999998-8-- Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 99999999999999999999999999 Q gi|254780720|r 115 TFQFLQWFVKEQHEEMALFRRILDKI 140 (164) Q Consensus 115 t~~fl~~fl~EQ~eee~~~~~ll~~l 140 (164) ... +..|..+|.++-+.+.+...++ T Consensus 87 ~~~-~~~~~~~q~k~rK~~e~~~~K~ 111 (239) T cd07647 87 AEK-LEEFREKQKEERKKTEDIMKRS 111 (239) T ss_pred HHH-HHHHHHHHHHHHHHHHHHHHHH T ss_conf 899-9999999999999999899999 Done!