Query 025459
Match_columns 252
No_of_seqs 136 out of 362
Neff 4.5
Searched_HMMs 46136
Date Fri Mar 29 06:03:17 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/025459.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/025459hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN02478 alternative oxidase 100.0 6E-116 1E-120 803.9 20.9 252 1-252 77-328 (328)
2 PF01786 AOX: Alternative oxid 100.0 5.2E-89 1.1E-93 601.4 20.6 203 32-234 3-207 (207)
3 cd01053 AOX Alternative oxidas 100.0 2.6E-82 5.7E-87 542.8 17.9 167 69-235 1-167 (168)
4 cd01042 DMQH Demethoxyubiquino 97.9 0.00021 4.5E-09 61.9 11.2 102 108-231 29-136 (165)
5 PF03232 COQ7: Ubiquinone bios 97.8 0.00036 7.7E-09 60.8 11.4 102 110-230 34-141 (172)
6 COG2941 CAT5 Ubiquinone biosyn 97.0 0.0092 2E-07 53.3 10.5 97 112-231 75-176 (204)
7 cd07908 Mn_catalase_like Manga 96.7 0.0045 9.7E-08 51.3 6.4 126 79-228 18-149 (154)
8 cd01045 Ferritin_like_AB Uncha 95.9 0.33 7.2E-06 37.6 12.4 99 109-228 28-134 (139)
9 cd01051 Mn_catalase Manganese 94.4 0.12 2.7E-06 44.1 6.3 120 79-228 25-147 (156)
10 cd01044 Ferritin_CCC1_N Ferrit 93.7 1.1 2.3E-05 36.2 10.3 93 100-228 20-118 (125)
11 cd00657 Ferritin_like Ferritin 93.6 0.94 2E-05 33.2 9.1 96 106-229 26-126 (130)
12 KOG4061 DMQ mono-oxygenase/Ubi 86.4 2.8 6.1E-05 37.7 7.0 92 119-229 89-185 (217)
13 PRK13456 DNA protection protei 83.4 3 6.5E-05 37.2 5.8 117 96-240 42-169 (186)
14 COG1633 Uncharacterized conser 65.4 15 0.00033 32.0 5.4 55 155-230 20-74 (176)
15 cd01045 Ferritin_like_AB Uncha 64.3 12 0.00026 28.8 4.1 46 169-235 8-53 (139)
16 PF02915 Rubrerythrin: Rubrery 62.1 13 0.00028 28.7 4.0 99 109-228 30-132 (137)
17 cd01041 Rubrerythrin Rubreryth 50.9 1.3E+02 0.0028 24.2 8.2 86 108-228 34-125 (134)
18 PF02915 Rubrerythrin: Rubrery 48.1 38 0.00082 26.0 4.6 47 170-236 9-56 (137)
19 PRK12775 putative trifunctiona 47.5 42 0.00092 36.6 6.2 108 110-240 891-1002(1006)
20 cd00657 Ferritin_like Ferritin 41.8 44 0.00095 24.1 3.8 45 170-235 9-53 (130)
21 PF13413 HTH_25: Helix-turn-he 41.5 23 0.00049 25.7 2.2 25 179-203 24-48 (62)
22 PF13668 Ferritin_2: Ferritin- 39.3 40 0.00086 27.1 3.5 54 166-232 8-61 (137)
23 PRK10635 bacterioferritin; Pro 39.3 64 0.0014 27.5 4.9 87 111-228 42-133 (158)
24 cd01044 Ferritin_CCC1_N Ferrit 29.4 91 0.002 24.9 4.1 40 170-230 9-48 (125)
25 cd01048 Ferritin_like_AB2 Unch 29.3 2.4E+02 0.0052 23.1 6.7 51 155-226 78-128 (135)
26 PF10785 NADH-u_ox-rdase: NADH 25.3 1.4E+02 0.003 23.2 4.3 30 139-171 57-86 (86)
27 PF05669 Med31: SOH1; InterPr 24.3 69 0.0015 26.1 2.5 15 168-182 28-42 (101)
28 COG1633 Uncharacterized conser 22.9 3.4E+02 0.0073 23.7 6.7 100 109-229 54-162 (176)
29 PF06480 FtsH_ext: FtsH Extrac 22.0 27 0.00058 25.9 -0.2 21 172-192 26-46 (110)
30 COG1614 CdhC CO dehydrogenase/ 21.9 13 0.00029 36.5 -2.4 26 86-111 325-350 (470)
31 PRK00046 murB UDP-N-acetylenol 20.3 46 0.00099 32.0 0.9 17 79-95 108-124 (334)
No 1
>PLN02478 alternative oxidase
Probab=100.00 E-value=5.8e-116 Score=803.92 Aligned_cols=252 Identities=86% Similarity=1.459 Sum_probs=250.4
Q ss_pred CCcceeeecCCCCCCCCCCccccccccccccccchhhhccccCCCCCccchHHHHHHHHHhhhcccccccccccceeeee
Q 025459 1 MIVSYWGVEAPKVNKDDGSEWKWNCFRPWEAYEADLSIDLKKHHAPTTFSDKMALWTVKSLRWPTDLFFQRRYGCRAMML 80 (252)
Q Consensus 1 ~~~~ywg~~~~k~~~~DGt~w~W~~f~p~~tY~~~~~~~~~~h~~P~~~~D~~A~~~vk~lr~~~D~~~~~r~~~R~~~L 80 (252)
+++|||||.|+|+++||||+|+|+||+||++|+++..+++.+|++|++++||+|+++||+||+++|+||++||++|++||
T Consensus 77 ~~~~ywg~~~~~~~~~dg~~~~w~~~~p~~~y~~~~~~~~~~H~~P~~~~Dk~A~~~Vk~lR~~~D~~f~~R~~~R~ifL 156 (328)
T PLN02478 77 AIVSYWGIEPAKITKEDGTEWKWNCFRPWETYKADLSIDLKKHHVPKTLLDKIAYWTVKSLRVPTDLFFQRRYGCRAMML 156 (328)
T ss_pred eeeeecccCCcccccCCCCCCCccCcCCCccccHhhhchhhcCCCCCchHHHHHHHHHHHHHHHHHHHhhcchhhHHHHH
Confidence 47999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ehhccCChhHHHHHHHhhhhhccccCcchHHHHHHHHHhHHHHHHHHHHHhCCchHHHHHHHHHHHHHHHHHHHHHHhCh
Q 025459 81 ETVAAVPGMVGGMLLHCKSLRRFEHSGGWIKALLEEAENERMHLMTFMEVAKPKWYERALVFAVQGVFFNAYFLGYLISP 160 (252)
Q Consensus 81 ETVA~VPgmv~~~~~Hl~sLr~~~rd~gwI~~lleEaeNErmHLl~~~el~~p~~~~R~lv~~~Q~vf~~~~~~~YlvsP 160 (252)
||||||||||+||++||+|||+|+||+|||++||||||||||||||||++++|+|++|++++++|++|||+||++||+||
T Consensus 157 ETVA~VPGmV~gmlrHL~SLRr~krd~gWIrtLLeEAeNERMHLLtf~~l~~p~w~eR~lv~~aQgvf~~~ff~~YLiSP 236 (328)
T PLN02478 157 ETVAAVPGMVGGMLLHLKSLRRFEHSGGWIKALLEEAENERMHLMTFMEVAKPKWYERALVIAVQGVFFNAYFLGYLISP 236 (328)
T ss_pred HHHhcCchHHHHHHHHHHHHhhhhccCchHHHHHHHHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHHHHHHHHHhH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhHhhhhhhhhhhHHHHHHHHHHHhcCCCCCCCCCCHHHHHhhCCCCCCCHHHHHHHHHhhhhHhHhhhhhccccccccc
Q 025459 161 KFAHRMVGYLEEEAIHSYTEFLKELDKGNIENVPAPAIATDYWRLPPNSTLKDVVLVVRADEAHHRDVNHYASDIHYQGR 240 (252)
Q Consensus 161 r~ahrfvgylEEeAv~tYt~~l~~id~g~l~~~paP~iA~~Yw~Lp~~atlrDvi~~IRaDEa~Hr~vNH~~ad~~~~~~ 240 (252)
|+|||||||||||||+|||+||++||+|+|+|+|||+||++||+||+++||||||++||+||++||+|||++||++.||+
T Consensus 237 r~aHRfvGYLEEEAV~TYT~~L~eid~G~l~n~pAP~IAi~YW~LP~~atLrDVi~~IRaDEa~HRdVNH~~sd~~~~~~ 316 (328)
T PLN02478 237 KFAHRIVGYLEEEAIHSYTEFLKDLDAGKIENVPAPAIAIDYWRLPADATLRDVVTVVRADEAHHRDVNHFASDIHYQGK 316 (328)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhhcCcccCCCCChHHHHHhCCCCCCcHHHHHHHHHhhhhhhhccCcchhhhhhccc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cccCCCCCCCCC
Q 025459 241 QLRESPAPLGYH 252 (252)
Q Consensus 241 ~~~~~~~~~~~~ 252 (252)
+++++|+|+|||
T Consensus 317 ~~~~~~~~~~~~ 328 (328)
T PLN02478 317 ELKEAPAPIGYH 328 (328)
T ss_pred ccCCCCCCCCCC
Confidence 999999999999
No 2
>PF01786 AOX: Alternative oxidase; InterPro: IPR002680 The alternative oxidase is used as a second terminal oxidase in the mitochondria, electrons are transferred directly from reduced ubiquinol to oxygen forming water []. This is not coupled to ATP synthesis and is not inhibited by cyanide, this pathway is a single step process []. In Oryza sativa (Rice) the transcript levels of the alternative oxidase are increased by low temperature []. It has been predicted to contain a coupled diiron centre on the basis of a conserved sequence motif consisting of the proposed iron ligands, four Glu and two His residues []. The EPR study of Arabidopsis thaliana (Mouse-ear cress) alternative oxidase AOX1a shows that the enzyme contains a hydroxo-bridged mixed-valent Fe(II)/Fe(III) binuclear iron centre []. A catalytic cycle has been proposed that involves diiron centre and at least one transient protein-derived radical, most probably an invariant Tyr residue [].; GO: 0007585 respiratory gaseous exchange, 0055114 oxidation-reduction process, 0005740 mitochondrial envelope
Probab=100.00 E-value=5.2e-89 Score=601.38 Aligned_cols=203 Identities=59% Similarity=1.037 Sum_probs=197.9
Q ss_pred ccchhhhcc-ccCCCCCccchHHHHHHHHHhhhcccccccccccceeeeeehhccCChhHHHHHHHhhhhhccccCcchH
Q 025459 32 YEADLSIDL-KKHHAPTTFSDKMALWTVKSLRWPTDLFFQRRYGCRAMMLETVAAVPGMVGGMLLHCKSLRRFEHSGGWI 110 (252)
Q Consensus 32 Y~~~~~~~~-~~h~~P~~~~D~~A~~~vk~lr~~~D~~~~~r~~~R~~~LETVA~VPgmv~~~~~Hl~sLr~~~rd~gwI 110 (252)
|+.+...++ .+|++|++++|++|+++||+||+++|++|++||++|++||||||||||||++|++||+|||+|+||+|||
T Consensus 3 ~~~~~~~~v~~~h~~p~~~~d~~A~~~v~~lr~~~D~~~~~r~~~R~~~LEtVA~VPg~v~~~~~Hl~slr~~~rd~g~I 82 (207)
T PF01786_consen 3 YTEEELESVQVTHREPKTFSDRVAYGIVKFLRWFFDLLFEKRWLHRFIFLETVAGVPGMVGGMVRHLRSLRRMKRDGGWI 82 (207)
T ss_pred CCHHHHhhcccccCCCCcHHHHHHHHHHHHHHHHHHHhccccchhheeeeeecccCChHHHHHHHHHHHHhCCCCCCcHH
Confidence 556555555 5999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHhHHHHHHHHHHHhCCchHHHHHHHHHHHHHHHHHHHHHHhChhhHhhhhhhhhhhHHHHHHHHHHHhcCCCC
Q 025459 111 KALLEEAENERMHLMTFMEVAKPKWYERALVFAVQGVFFNAYFLGYLISPKFAHRMVGYLEEEAIHSYTEFLKELDKGNI 190 (252)
Q Consensus 111 ~~lleEaeNErmHLl~~~el~~p~~~~R~lv~~~Q~vf~~~~~~~YlvsPr~ahrfvgylEEeAv~tYt~~l~~id~g~l 190 (252)
++|+|||||||||||||+++++|+|++|++++++|++|||+|+++|++|||+|||||||||||||+|||+||+|||+|+|
T Consensus 83 ~~lleEaeNErmHLli~~~l~~p~~~~R~lv~~~q~vf~~~~~~~Yl~sPr~ahrfvgylEeeAv~tYt~~l~di~~g~l 162 (207)
T PF01786_consen 83 KTLLEEAENERMHLLIFEELGKPSWFDRFLVLHAQGVFYNIFFLLYLVSPRTAHRFVGYLEEEAVHTYTEFLEDIDEGKL 162 (207)
T ss_pred HHHHHHHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHHHHHHHHcCHHHHHHHHHHHHHHHHHHHHHHHHHcccCCC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCCCHHHHHhhCCCC-CCCHHHHHHHHHhhhhHhHhhhhhccc
Q 025459 191 ENVPAPAIATDYWRLPP-NSTLKDVVLVVRADEAHHRDVNHYASD 234 (252)
Q Consensus 191 ~~~paP~iA~~Yw~Lp~-~atlrDvi~~IRaDEa~Hr~vNH~~ad 234 (252)
+|+|||+||++||+||+ ++||||||++||+||++||++||++||
T Consensus 163 ~~~paP~iAi~Yw~l~~~~atlrDvi~~IRaDEa~Hr~vNH~~a~ 207 (207)
T PF01786_consen 163 PNMPAPEIAIDYWGLPELDATLRDVILAIRADEAEHRDVNHTLAD 207 (207)
T ss_pred CCCCCCHHHHHHhCCCccCchHHHHHHHHHhhHHHHHHhhhhhcC
Confidence 99999999999999999 999999999999999999999999997
No 3
>cd01053 AOX Alternative oxidase, ferritin-like diiron-binding domain. Alternative oxidase (AOX) is a mitochondrial ubiquinol oxidase found in plants and some fungi and protists. AOX is a member of the ferritin-like diiron-carboxylate superfamily. The plant mitochondrial protein alternative oxidase catalyses dioxygen dependent ubiquinol oxidation to yield ubiquinone and water. AOX is a cyanide-resistant, salicylhydroxamic acid-sensitive oxidase that transfers electrons from ubiquinol to oxygen, bypassing the cytochrome chain. AOX has been proposed to contain a hydroxo-bridged diiron center within a four-helix bundle and a proximal redox-active tyrosine residue. AOX is proposed to be peripherally associated with the matrix side of the inner mitochondrial membrane. Fungal and protozoan AOXs generally exist as monomers. In plants, AOX is dimeric. Pyruvate is an allosteric activator of plant AOX involved in the reversible inactivation of the enzyme though the formation of an intermolecular
Probab=100.00 E-value=2.6e-82 Score=542.77 Aligned_cols=167 Identities=58% Similarity=0.979 Sum_probs=165.3
Q ss_pred ccccccceeeeeehhccCChhHHHHHHHhhhhhccccCcchHHHHHHHHHhHHHHHHHHHHHhCCchHHHHHHHHHHHHH
Q 025459 69 FQRRYGCRAMMLETVAAVPGMVGGMLLHCKSLRRFEHSGGWIKALLEEAENERMHLMTFMEVAKPKWYERALVFAVQGVF 148 (252)
Q Consensus 69 ~~~r~~~R~~~LETVA~VPgmv~~~~~Hl~sLr~~~rd~gwI~~lleEaeNErmHLl~~~el~~p~~~~R~lv~~~Q~vf 148 (252)
|++||++||+||||||||||||++|++||+|||+|+||+||||+|||||||||||||||+++++|++++|.++..+|++|
T Consensus 1 ~~~r~~~R~~~LEtVA~vPgmv~~~~~HL~slr~~~rd~~wi~~lleEaeNErmHLltf~~l~~p~~~~r~~v~~~q~vf 80 (168)
T cd01053 1 YEDRWLARFIFLETVARVPGMVAGMLLHLYSLRGMWRDGGWIKTLLEEAENERMHLLIFEELGGPGWWFRRFVAQHQAVF 80 (168)
T ss_pred CCCcceehhhhhhHhccCcHHHHHHHHHHHHHhCCcccCCHHHHHHHHHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHH
Confidence 57899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHhChhhHhhhhhhhhhhHHHHHHHHHHHhcCCCCCCCCCCHHHHHhhCCCCCCCHHHHHHHHHhhhhHhHhh
Q 025459 149 FNAYFLGYLISPKFAHRMVGYLEEEAIHSYTEFLKELDKGNIENVPAPAIATDYWRLPPNSTLKDVVLVVRADEAHHRDV 228 (252)
Q Consensus 149 ~~~~~~~YlvsPr~ahrfvgylEEeAv~tYt~~l~~id~g~l~~~paP~iA~~Yw~Lp~~atlrDvi~~IRaDEa~Hr~v 228 (252)
||+|+++|++|||+|||||||||||||+|||+||++||+|+++|+|||+||++||+||+++||||||++||+||++||+|
T Consensus 81 y~~~~~~YlisPr~ahrfvgylEEeAV~TYt~~L~~id~g~~~~~paP~iAi~Yw~l~~~atl~Dvi~~IR~DEa~Hr~v 160 (168)
T cd01053 81 YNAYFLLYLISPRLAHRFVGYLEEEAVDTYTEFLKDIEEGLKPDLPAPEIAIEYYRLGEDATLYDVFVAIRADEAEHRKV 160 (168)
T ss_pred HHHHHHHHHhhHHHHHHHHHhhhHHHHHHHHHHHHHhhccccCCCCCCHHHHHHhCCCCCCcHHHHHHHHHhhHHhHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhhcccc
Q 025459 229 NHYASDI 235 (252)
Q Consensus 229 NH~~ad~ 235 (252)
||++||+
T Consensus 161 nh~~~~~ 167 (168)
T cd01053 161 NHACADL 167 (168)
T ss_pred HHHhhcC
Confidence 9999986
No 4
>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=97.86 E-value=0.00021 Score=61.89 Aligned_cols=102 Identities=25% Similarity=0.324 Sum_probs=79.4
Q ss_pred chHHHHHHH-HHhHHHHHHHHHHHh-----CCchHHHHHHHHHHHHHHHHHHHHHHhChhhHhhhhhhhhhhHHHHHHHH
Q 025459 108 GWIKALLEE-AENERMHLMTFMEVA-----KPKWYERALVFAVQGVFFNAYFLGYLISPKFAHRMVGYLEEEAIHSYTEF 181 (252)
Q Consensus 108 gwI~~lleE-aeNErmHLl~~~el~-----~p~~~~R~lv~~~Q~vf~~~~~~~YlvsPr~ahrfvgylEEeAv~tYt~~ 181 (252)
.-++..++| ++.|.-||..|.+.. +|+++--+.-. .=|.+-++.=++.++.++-|+.-+|+....-|.+-
T Consensus 29 ~~~~~~l~~~~~~E~~Hl~~f~~~i~~~~~rps~l~PlW~~----~gf~lG~~tal~G~~~a~~~~~avE~~V~~Hy~~q 104 (165)
T cd01042 29 PAVRPLIKEMLDEEKDHLAWFEELLPELGVRPSLLLPLWYV----AGFALGALTALLGKKAAMACTAAVETVVEEHYNDQ 104 (165)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCchHHHHHHH----HHHHHHHHHHhhChHHHHHHHHHHHHHHHHHHHHH
Confidence 345555555 788999999998885 57766554422 22445666778899999999999999999999999
Q ss_pred HHHhcCCCCCCCCCCHHHHHhhCCCCCCCHHHHHHHHHhhhhHhHhhhhh
Q 025459 182 LKELDKGNIENVPAPAIATDYWRLPPNSTLKDVVLVVRADEAHHRDVNHY 231 (252)
Q Consensus 182 l~~id~g~l~~~paP~iA~~Yw~Lp~~atlrDvi~~IRaDEa~Hr~vNH~ 231 (252)
|+++..- .|..+++.|..+|+||.+|++.--.
T Consensus 105 l~~L~~~------------------~d~~l~~~l~~~r~DE~~H~d~A~~ 136 (165)
T cd01042 105 LRELPAQ------------------PDKELRAIIEQFRDDELEHADIAEE 136 (165)
T ss_pred HHHhhcc------------------CCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 9998321 2688999999999999999987543
No 5
>PF03232 COQ7: Ubiquinone biosynthesis protein COQ7; InterPro: IPR011566 Coq7 (also known as Clk-1) is a di-iron carboxylate protein occuring in both prokaryotes and eukaryotes that is essential for ubiquinone biosynthesis [, ]. It has been implicated in the aging process as mutations in the Caenorhabditis elegans gene lead to increased lifespan []. Coq7 is a membrane-bound protein that functions as a monooxygenase to hydroxylate demethoxyubiquinone (2-methoxy-5-methyl-6-polyprenyl-1,4-benzoquinone) in the penultimate step of ubiquinone biosynthesis []. Biochemical studies indicate that NADH can serve directly as a reductant for catalytic activation of dioxygen and substrate oxidation by the enzyme, with no requirement for an additional reductase protein component []. This direct reaction with NADH is so far unique amongst members of the di-iron carboxylate protein family. This entry is specific for the bacterial Coq7 proteins.; GO: 0006744 ubiquinone biosynthetic process, 0055114 oxidation-reduction process
Probab=97.78 E-value=0.00036 Score=60.77 Aligned_cols=102 Identities=25% Similarity=0.311 Sum_probs=79.0
Q ss_pred HHHHHHH-HHhHHHHHHHHHHHh-----CCchHHHHHHHHHHHHHHHHHHHHHHhChhhHhhhhhhhhhhHHHHHHHHHH
Q 025459 110 IKALLEE-AENERMHLMTFMEVA-----KPKWYERALVFAVQGVFFNAYFLGYLISPKFAHRMVGYLEEEAIHSYTEFLK 183 (252)
Q Consensus 110 I~~lleE-aeNErmHLl~~~el~-----~p~~~~R~lv~~~Q~vf~~~~~~~YlvsPr~ahrfvgylEEeAv~tYt~~l~ 183 (252)
++..+.| ++.|.-||..|.++. .|+++.-+.- +.-|.+-++.=++.++.+.-++.-+|+....-|.+-|+
T Consensus 34 ~~~~l~~~~~~E~~Hl~~f~~~l~~~~~RpS~l~Plw~----~~g~~LG~~tal~G~~~~~a~t~avE~~V~~Hy~~Ql~ 109 (172)
T PF03232_consen 34 LRPFLKEMAEEEKDHLAWFEQLLPELRVRPSLLNPLWY----VAGFALGALTALLGDKAAMACTAAVETVVEEHYNDQLR 109 (172)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhHHcCCCCcHHHHHHH----HHHHHHHHHHHhhchHHHHHHHHHHHHHHHHHHHHHHH
Confidence 5554444 668999999999886 4777655543 22245566678999999999999999999999999999
Q ss_pred HhcCCCCCCCCCCHHHHHhhCCCCCCCHHHHHHHHHhhhhHhHhhhh
Q 025459 184 ELDKGNIENVPAPAIATDYWRLPPNSTLKDVVLVVRADEAHHRDVNH 230 (252)
Q Consensus 184 ~id~g~l~~~paP~iA~~Yw~Lp~~atlrDvi~~IRaDEa~Hr~vNH 230 (252)
++.... .++|..++++|..+|+||.+|++.--
T Consensus 110 ~L~~~~---------------~~~d~~l~~~i~~~r~DE~~H~d~A~ 141 (172)
T PF03232_consen 110 ELPAMG---------------EEEDPELRAIIEQFRDDELEHRDTAI 141 (172)
T ss_pred HHHhcc---------------ccchHHHHHHHHHHHHHHHHHHHHHH
Confidence 983211 13456799999999999999998653
No 6
>COG2941 CAT5 Ubiquinone biosynthesis protein COQ7 [Coenzyme metabolism]
Probab=96.96 E-value=0.0092 Score=53.30 Aligned_cols=97 Identities=24% Similarity=0.197 Sum_probs=74.1
Q ss_pred HHHHHHHhHHHHHHHHHHHh-----CCchHHHHHHHHHHHHHHHHHHHHHHhChhhHhhhhhhhhhhHHHHHHHHHHHhc
Q 025459 112 ALLEEAENERMHLMTFMEVA-----KPKWYERALVFAVQGVFFNAYFLGYLISPKFAHRMVGYLEEEAIHSYTEFLKELD 186 (252)
Q Consensus 112 ~lleEaeNErmHLl~~~el~-----~p~~~~R~lv~~~Q~vf~~~~~~~YlvsPr~ahrfvgylEEeAv~tYt~~l~~id 186 (252)
.+.|-++.|-.||-+|.+.. .|+++--+--- .=|.+-.+.=|+++++|.-|++-.|+.-..-|.+-|+.+.
T Consensus 75 ~l~em~d~E~~HL~~f~~~l~e~~vRPsll~P~W~~----~~FalGA~a~Llgdk~am~~teavE~vIe~Hy~~ql~~L~ 150 (204)
T COG2941 75 QLKEMADEEIDHLAWFEQRLLELGVRPSLLNPLWYA----AAFALGAGAGLLGDKAAMGFTEAVETVIEKHYDGQLRELP 150 (204)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHccCCccHHHHHHHH----HHHHHHHHHhhcccHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 34445677889999988774 58765543321 1134455688999999999999999999999999998872
Q ss_pred CCCCCCCCCCHHHHHhhCCCCCCCHHHHHHHHHhhhhHhHhhhhh
Q 025459 187 KGNIENVPAPAIATDYWRLPPNSTLKDVVLVVRADEAHHRDVNHY 231 (252)
Q Consensus 187 ~g~l~~~paP~iA~~Yw~Lp~~atlrDvi~~IRaDEa~Hr~vNH~ 231 (252)
..|+.++--+...|.||..|.+.--.
T Consensus 151 -------------------~~d~~lr~~l~qfR~DE~eH~d~Ai~ 176 (204)
T COG2941 151 -------------------NLDAELRAILAQFRDDELEHLDNAIA 176 (204)
T ss_pred -------------------hccHHHHHHHHHHhhHHHHHHHHHHH
Confidence 13568999999999999999886443
No 7
>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=96.72 E-value=0.0045 Score=51.33 Aligned_cols=126 Identities=16% Similarity=0.135 Sum_probs=89.1
Q ss_pred eeehhccCChhHHHHHHHhhhhhccccCcchH-HHHHHHHHhHHHHHHHHHHHh-----CCchHHHHHHHHHHHHHHHHH
Q 025459 79 MLETVAAVPGMVGGMLLHCKSLRRFEHSGGWI-KALLEEAENERMHLMTFMEVA-----KPKWYERALVFAVQGVFFNAY 152 (252)
Q Consensus 79 ~LETVA~VPgmv~~~~~Hl~sLr~~~rd~gwI-~~lleEaeNErmHLl~~~el~-----~p~~~~R~lv~~~Q~vf~~~~ 152 (252)
++|-++|.-|=-.++.+.++.....+....-+ +.+...|.-|.-|..++.++. +|.+...+.. .+.++..-
T Consensus 18 ~~~~~~g~~~E~~ai~~Y~y~~~~~~~~~~~~k~~f~~lA~eE~~H~~~l~~~i~~lgg~p~~~~~~~~---~~~~~~~~ 94 (154)
T cd07908 18 LLDDYAGTNSELTAISQYIYQHLISEEKYPEIAETFLGIAIVEMHHLEILGQLIVLLGGDPRYRSSSSD---KFTYWTGK 94 (154)
T ss_pred HHHHhCCcchHHHHHHHHHHHHHHccCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCcchhhccc---cCCcCCcc
Confidence 56677777777788888888877666533334 456677999999999998883 4654332111 11111111
Q ss_pred HHHHHhChhhHhhhhhhhhhhHHHHHHHHHHHhcCCCCCCCCCCHHHHHhhCCCCCCCHHHHHHHHHhhhhHhHhh
Q 025459 153 FLGYLISPKFAHRMVGYLEEEAIHSYTEFLKELDKGNIENVPAPAIATDYWRLPPNSTLKDVVLVVRADEAHHRDV 228 (252)
Q Consensus 153 ~~~YlvsPr~ahrfvgylEEeAv~tYt~~l~~id~g~l~~~paP~iA~~Yw~Lp~~atlrDvi~~IRaDEa~Hr~v 228 (252)
.+...-++..+.++.--+|+.|+..|.+.++.+ +|...++++..|.+||..|.+.
T Consensus 95 ~~~~~~~~~~~L~~~~~~E~~ai~~Y~~~~~~~---------------------~d~~~r~ll~~I~~eE~~H~~~ 149 (154)
T cd07908 95 YVNYGESIKEMLKLDIASEKAAIAKYKRQAETI---------------------KDPYIRALLNRIILDEKLHIKI 149 (154)
T ss_pred ccCCccCHHHHHHHHHHHHHHHHHHHHHHHHHc---------------------CCHHHHHHHHHHHHHHHHHHHH
Confidence 112334667799999999999999999999864 3578999999999999999764
No 8
>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=95.87 E-value=0.33 Score=37.58 Aligned_cols=99 Identities=22% Similarity=0.203 Sum_probs=67.0
Q ss_pred hHHH-HHHHHHhHHHHHHHHHHHhC-------CchHHHHHHHHHHHHHHHHHHHHHHhChhhHhhhhhhhhhhHHHHHHH
Q 025459 109 WIKA-LLEEAENERMHLMTFMEVAK-------PKWYERALVFAVQGVFFNAYFLGYLISPKFAHRMVGYLEEEAIHSYTE 180 (252)
Q Consensus 109 wI~~-lleEaeNErmHLl~~~el~~-------p~~~~R~lv~~~Q~vf~~~~~~~YlvsPr~ahrfvgylEEeAv~tYt~ 180 (252)
-++. +..-|..|+.|..++.++.. |..-............+..-......+++.+-+..--+|..|+..|.+
T Consensus 28 ~~~~~~~~la~eE~~H~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~E~~~~~~Y~~ 107 (139)
T cd01045 28 ELKKLFEELAEEEKEHAERLEELYEKLFGEELPELEPEDYKEEVEEEPEFKKALESLMDPLEALRLAIEIEKDAIEFYEE 107 (139)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhccccCCcccHHHHHHHHhhhhhHHHHHHhccCHHHHHHHHHHHHHHHHHHHHH
Confidence 3554 45569999999999988841 222111111011111111123455667788999999999999999999
Q ss_pred HHHHhcCCCCCCCCCCHHHHHhhCCCCCCCHHHHHHHHHhhhhHhHhh
Q 025459 181 FLKELDKGNIENVPAPAIATDYWRLPPNSTLKDVVLVVRADEAHHRDV 228 (252)
Q Consensus 181 ~l~~id~g~l~~~paP~iA~~Yw~Lp~~atlrDvi~~IRaDEa~Hr~v 228 (252)
+++.+ .|...++++..|..||..|...
T Consensus 108 ~~~~~---------------------~d~~~~~~~~~l~~~E~~H~~~ 134 (139)
T cd01045 108 LAEKA---------------------EDPEVKKLFEELAEEERGHLRL 134 (139)
T ss_pred HHHHc---------------------CCHHHHHHHHHHHHHHHHHHHH
Confidence 99876 2357899999999999999754
No 9
>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=94.39 E-value=0.12 Score=44.06 Aligned_cols=120 Identities=18% Similarity=0.159 Sum_probs=79.2
Q ss_pred eeehhccCChhHHHHHHHhhhhhccccCcchHHHHHHHHHhHHHHHHHHHHHhCCchHHHHHHHHHHHHHHHHHHHHHHh
Q 025459 79 MLETVAAVPGMVGGMLLHCKSLRRFEHSGGWIKALLEEAENERMHLMTFMEVAKPKWYERALVFAVQGVFFNAYFLGYLI 158 (252)
Q Consensus 79 ~LETVA~VPgmv~~~~~Hl~sLr~~~rd~gwI~~lleEaeNErmHLl~~~el~~p~~~~R~lv~~~Q~vf~~~~~~~Ylv 158 (252)
++|-++|.-|=..++++-++.-..++.+...-..+++.|-.|..|+.++.++-.- +.. -..+..| ...|+.
T Consensus 25 l~~~~gG~~gEl~ai~qYl~q~~~~~~~~~~~d~l~~ia~eEm~H~e~la~~I~~-----Lg~-~~~g~pw---~~~yv~ 95 (156)
T cd01051 25 LQEQLGGAFGELSAAMQYLFQSFNFREDPKYRDLLLDIGTEELSHLEMVATLIAM-----LLK-DSQGVPW---TAAYIQ 95 (156)
T ss_pred HHHHhCCccHHHHHHHHHHHHHhhcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH-----HcC-CCCCCcC---CCcccC
Confidence 6677777777777777777776666433344456778899999999987776210 000 0011111 223322
Q ss_pred ---ChhhHhhhhhhhhhhHHHHHHHHHHHhcCCCCCCCCCCHHHHHhhCCCCCCCHHHHHHHHHhhhhHhHhh
Q 025459 159 ---SPKFAHRMVGYLEEEAIHSYTEFLKELDKGNIENVPAPAIATDYWRLPPNSTLKDVVLVVRADEAHHRDV 228 (252)
Q Consensus 159 ---sPr~ahrfvgylEEeAv~tYt~~l~~id~g~l~~~paP~iA~~Yw~Lp~~atlrDvi~~IRaDEa~Hr~v 228 (252)
.+...-+-+=-.|+.|..+|.+.++.+ +|.+.+|++..|++||..|.+.
T Consensus 96 ~~~d~~~~L~~ni~aE~~Ai~~Y~~l~~~~---------------------~Dp~v~~~l~~I~~rE~~H~~~ 147 (156)
T cd01051 96 SSGNLVADLRSNIAAESRARLTYERLYEMT---------------------DDPGVKDTLSFLLVREIVHQNA 147 (156)
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHHHHc---------------------CCHHHHHHHHHHHHHHHHHHHH
Confidence 223333333445999999999999987 3688999999999999999763
No 10
>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=93.74 E-value=1.1 Score=36.16 Aligned_cols=93 Identities=28% Similarity=0.435 Sum_probs=63.8
Q ss_pred hhccccCcchHHH-HHHHHHhHHHHHHHHHHHhC-----CchHHHHHHHHHHHHHHHHHHHHHHhChhhHhhhhhhhhhh
Q 025459 100 LRRFEHSGGWIKA-LLEEAENERMHLMTFMEVAK-----PKWYERALVFAVQGVFFNAYFLGYLISPKFAHRMVGYLEEE 173 (252)
Q Consensus 100 Lr~~~rd~gwI~~-lleEaeNErmHLl~~~el~~-----p~~~~R~lv~~~Q~vf~~~~~~~YlvsPr~ahrfvgylEEe 173 (252)
|-....|.. ++. +..-|+.|+.|..+|.++.+ |. ... ....++ .++.=+++|..+.++..-.|+.
T Consensus 20 la~~~~~~~-~k~~f~~lA~~E~~H~~~~~~~~~~~~~~~~-~~~-----~~~~~~--~~l~~~~g~~~~l~~~~~~E~~ 90 (125)
T cd01044 20 LAKREKDPE-NREILLKLAEDERRHAEFWKKFLGKRGVPPP-RPK-----LKIFFY--KLLARIFGPTFVLKLLERGEER 90 (125)
T ss_pred HHHHcCCHH-HHHHHHHHHHHHHHHHHHHHHHHhhccCCCC-Ccc-----HHHHHH--HHHHHHHhHHHHHHHHHHhHHh
Confidence 333343433 554 55569999999999999862 22 111 111111 1233456888899999999999
Q ss_pred HHHHHHHHHHHhcCCCCCCCCCCHHHHHhhCCCCCCCHHHHHHHHHhhhhHhHhh
Q 025459 174 AIHSYTEFLKELDKGNIENVPAPAIATDYWRLPPNSTLKDVVLVVRADEAHHRDV 228 (252)
Q Consensus 174 Av~tYt~~l~~id~g~l~~~paP~iA~~Yw~Lp~~atlrDvi~~IRaDEa~Hr~v 228 (252)
|+..|++..+. +..+..|-.||..|...
T Consensus 91 ai~~Y~~~~~~---------------------------~~~~~~Ii~dE~~H~~~ 118 (125)
T cd01044 91 AIEKYDRLLEE---------------------------RPELKEIIADELEHEEV 118 (125)
T ss_pred hHhhHHhhhhh---------------------------hHHHHHHHHHHHHHHHH
Confidence 99999998776 35778999999999765
No 11
>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=93.60 E-value=0.94 Score=33.19 Aligned_cols=96 Identities=24% Similarity=0.222 Sum_probs=65.5
Q ss_pred CcchHHHHHHHHHhHHHHHHHHHHHh-----CCchHHHHHHHHHHHHHHHHHHHHHHhChhhHhhhhhhhhhhHHHHHHH
Q 025459 106 SGGWIKALLEEAENERMHLMTFMEVA-----KPKWYERALVFAVQGVFFNAYFLGYLISPKFAHRMVGYLEEEAIHSYTE 180 (252)
Q Consensus 106 d~gwI~~lleEaeNErmHLl~~~el~-----~p~~~~R~lv~~~Q~vf~~~~~~~YlvsPr~ahrfvgylEEeAv~tYt~ 180 (252)
+.+..+.+...+..|+.|...+.++. +|....... ....-......+|..+-...--.|..+...|..
T Consensus 26 ~~~~~~~~~~~a~~E~~H~~~l~~~~~~~g~~~~~~~~~~-------~~~~~~~~~~~~~~~~l~~~~~~E~~~~~~y~~ 98 (130)
T cd00657 26 DPDLKDELLEIADEERRHADALAERLRELGGTPPLPPAHL-------LAAYALPKTSDDPAEALRAALEVEARAIAAYRE 98 (130)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCCHHHH-------HHhcccCCCccCHHHHHHHHHHHHHHHHHHHHH
Confidence 44556667777999999999999884 343322210 001111123345666666667778889998988
Q ss_pred HHHHhcCCCCCCCCCCHHHHHhhCCCCCCCHHHHHHHHHhhhhHhHhhh
Q 025459 181 FLKELDKGNIENVPAPAIATDYWRLPPNSTLKDVVLVVRADEAHHRDVN 229 (252)
Q Consensus 181 ~l~~id~g~l~~~paP~iA~~Yw~Lp~~atlrDvi~~IRaDEa~Hr~vN 229 (252)
+++.. + |..+++++..+..||..|...-
T Consensus 99 ~~~~~--------------------~-d~~~~~~~~~~~~~E~~H~~~~ 126 (130)
T cd00657 99 LIEQA--------------------D-DPELRRLLERILADEQRHAAWF 126 (130)
T ss_pred HHHhc--------------------C-ChHHHHHHHHHHHHHHHHHHHH
Confidence 88765 1 6778999999999999998753
No 12
>KOG4061 consensus DMQ mono-oxygenase/Ubiquinone biosynthesis protein COQ7/CLK-1/CAT5 [General function prediction only]
Probab=86.41 E-value=2.8 Score=37.70 Aligned_cols=92 Identities=23% Similarity=0.242 Sum_probs=66.2
Q ss_pred hHHHHHHHHHHHh-----CCchHHHHHHHHHHHHHHHHHHHHHHhChhhHhhhhhhhhhhHHHHHHHHHHHhcCCCCCCC
Q 025459 119 NERMHLMTFMEVA-----KPKWYERALVFAVQGVFFNAYFLGYLISPKFAHRMVGYLEEEAIHSYTEFLKELDKGNIENV 193 (252)
Q Consensus 119 NErmHLl~~~el~-----~p~~~~R~lv~~~Q~vf~~~~~~~YlvsPr~ahrfvgylEEeAv~tYt~~l~~id~g~l~~~ 193 (252)
.|-.||.+|.++. .|+.+.-+--+.+ |-+-...-|++|+.|-.-..-+|+--..-|-.-|+++-+..
T Consensus 89 qEk~Hl~tf~~l~~k~rVrpT~l~P~w~vag----falGaGTALlg~eaAMACT~AVEtvIg~HYNdQlr~l~~~~---- 160 (217)
T KOG4061|consen 89 QEKEHLKTFENLALKHRVRPTVLTPLWNVAG----FALGAGTALLGKEAAMACTEAVETVIGGHYNDQLRELAEDD---- 160 (217)
T ss_pred HHHHHHHHHHHHHHHccCCchhhhhHHHHHH----HHhccchhhhChHHHHHHHHHHHHHHHHhhhHHHHHHHHhC----
Confidence 4678999999986 4776655443222 23444578999999988888888888888887777762211
Q ss_pred CCCHHHHHhhCCCCCCCHHHHHHHHHhhhhHhHhhh
Q 025459 194 PAPAIATDYWRLPPNSTLKDVVLVVRADEAHHRDVN 229 (252)
Q Consensus 194 paP~iA~~Yw~Lp~~atlrDvi~~IRaDEa~Hr~vN 229 (252)
-+++-.|+-.|...|+||.+|.|+-
T Consensus 161 -----------pe~~kell~~i~~fRDeEleHhdtg 185 (217)
T KOG4061|consen 161 -----------PEEHKELLSTITKFRDEELEHHDTG 185 (217)
T ss_pred -----------cHhHHHHHHHHHHHhHHHHHhhccc
Confidence 1344678899999999999998764
No 13
>PRK13456 DNA protection protein DPS; Provisional
Probab=83.39 E-value=3 Score=37.17 Aligned_cols=117 Identities=21% Similarity=0.215 Sum_probs=69.7
Q ss_pred HhhhhhccccCcchHHHHHHHHH-hHHHHHHHHHH----Hh-CCch-HHHHHHHHHHHHHHHHHHHHHHhC-hhhHhhhh
Q 025459 96 HCKSLRRFEHSGGWIKALLEEAE-NERMHLMTFME----VA-KPKW-YERALVFAVQGVFFNAYFLGYLIS-PKFAHRMV 167 (252)
Q Consensus 96 Hl~sLr~~~rd~gwI~~lleEae-NErmHLl~~~e----l~-~p~~-~~R~lv~~~Q~vf~~~~~~~Ylvs-Pr~ahrfv 167 (252)
|-..+.|+.++. |+..|+++- -|+-|-..+.+ |+ .|.. ...|.-+..+. .+++-. |...-.++
T Consensus 42 ~a~~~~G~~~e~--V~e~le~a~~EEl~HA~~lAeRI~qLGG~P~~~p~~~~~ls~~~-------~~~~p~d~tdv~~mL 112 (186)
T PRK13456 42 LRAHLIGLEGEG--LKEIAEDARLEDRNHFEALVPRIYELGGKLPRDIREFHDISACP-------DAYLPENPTDPKEIL 112 (186)
T ss_pred HHHHHhCcCcHH--HHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCChHHHhhhhcCc-------cccCCCCcchHHHHH
Confidence 444456666543 666666655 88889876542 33 3432 22222222221 011211 22233333
Q ss_pred hhh---hhhHHHHHHHHHHHhcCCCCCCCCCCHHHHHhhCCCCCCCHHHHHHHHHhhhhHhHhhhhhccccccccc
Q 025459 168 GYL---EEEAIHSYTEFLKELDKGNIENVPAPAIATDYWRLPPNSTLKDVVLVVRADEAHHRDVNHYASDIHYQGR 240 (252)
Q Consensus 168 gyl---EEeAv~tYt~~l~~id~g~l~~~paP~iA~~Yw~Lp~~atlrDvi~~IRaDEa~Hr~vNH~~ad~~~~~~ 240 (252)
... |..|+.+|++.++... ..|-+=+|+++.|-+||.+|.+--..+=...+.|.
T Consensus 113 ~~~L~AEr~AI~~Y~eii~~~~-------------------~kDp~T~~l~~~IL~dE~eH~~dl~~lL~~~~~~~ 169 (186)
T PRK13456 113 KVLLEAERCAIRTYTEICDMTA-------------------GKDPRTYDLALAILQEEIEHEAWFSELLGGGPSGH 169 (186)
T ss_pred HHHHHHHHHHHHHHHHHHHHHh-------------------cCCccHHHHHHHHHHHHHHHHHHHHHHHhcCCCcc
Confidence 322 7899999999999983 34677889999999999999987766655444443
No 14
>COG1633 Uncharacterized conserved protein [Function unknown]
Probab=65.40 E-value=15 Score=32.03 Aligned_cols=55 Identities=16% Similarity=0.093 Sum_probs=44.0
Q ss_pred HHHhChhhHhhhhhhhhhhHHHHHHHHHHHhcCCCCCCCCCCHHHHHhhCCCCCCCHHHHHHHHHhhhhHhHhhhh
Q 025459 155 GYLISPKFAHRMVGYLEEEAIHSYTEFLKELDKGNIENVPAPAIATDYWRLPPNSTLKDVVLVVRADEAHHRDVNH 230 (252)
Q Consensus 155 ~YlvsPr~ahrfvgylEEeAv~tYt~~l~~id~g~l~~~paP~iA~~Yw~Lp~~atlrDvi~~IRaDEa~Hr~vNH 230 (252)
....++.=+-+...-.|.+|+.-|.+..+-+ +|..+|.+|..|.+||..|...=-
T Consensus 20 ~~~~~~~e~L~~Ai~~E~eA~~fY~~lae~~---------------------~~~~~rk~~~~la~eE~~H~~~f~ 74 (176)
T COG1633 20 VKELSIEELLAIAIRGELEAIKFYEELAERI---------------------EDEEIRKLFEDLADEEMRHLRKFE 74 (176)
T ss_pred hhhccHHHHHHHHHHHHHHHHHHHHHHHHhc---------------------CCHhHHHHHHHHHHHHHHHHHHHH
Confidence 4455666666777778999999999988876 356899999999999999976533
No 15
>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=64.26 E-value=12 Score=28.77 Aligned_cols=46 Identities=22% Similarity=0.258 Sum_probs=36.6
Q ss_pred hhhhhHHHHHHHHHHHhcCCCCCCCCCCHHHHHhhCCCCCCCHHHHHHHHHhhhhHhHhhhhhcccc
Q 025459 169 YLEEEAIHSYTEFLKELDKGNIENVPAPAIATDYWRLPPNSTLKDVVLVVRADEAHHRDVNHYASDI 235 (252)
Q Consensus 169 ylEEeAv~tYt~~l~~id~g~l~~~paP~iA~~Yw~Lp~~atlrDvi~~IRaDEa~Hr~vNH~~ad~ 235 (252)
-+|..++..|..+.+.. ++..+++++..+..||..|.+.=..+...
T Consensus 8 ~~E~~~~~~Y~~~a~~~---------------------~~~~~~~~~~~la~eE~~H~~~l~~~~~~ 53 (139)
T cd01045 8 KMEEEAAEFYLELAEKA---------------------KDPELKKLFEELAEEEKEHAERLEELYEK 53 (139)
T ss_pred HHHHHHHHHHHHHHhHC---------------------CCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 46889999999998875 22368999999999999999876655444
No 16
>PF02915 Rubrerythrin: Rubrerythrin; InterPro: IPR003251 Rubrerythrin (Rr), found in anaerobic sulphate-reducing bacteria [], is a fusion protein containing an N-terminal diiron-binding domain and a C-terminal domain homologous to rubredoxin []. The physiological role of Rr has not been identified. The 3-D structure of Desulphovibrio vulgaris rubrerythrin has been solved []. The structure reveals a tetramer of two-domain subunits. In each monomer, the N-terminal 146 residues form a four-alpha-helix bundle containing the diiron-oxo site (centre I), and the C-terminal 45 residues form a rubredoxin-like FeS4 domain.; GO: 0016491 oxidoreductase activity, 0046872 metal ion binding, 0055114 oxidation-reduction process; PDB: 1VJX_A 2FZF_A 3SID_B 3QHC_B 3QHB_B 4DI0_A 1J30_B 1YV1_A 1YUZ_B 1YUX_B ....
Probab=62.15 E-value=13 Score=28.66 Aligned_cols=99 Identities=20% Similarity=0.182 Sum_probs=61.6
Q ss_pred hHHHHHHH-HHhHHHHHHHHHHHhCCch-HHHHH--HHHHHHHHHHHHHHHHHhChhhHhhhhhhhhhhHHHHHHHHHHH
Q 025459 109 WIKALLEE-AENERMHLMTFMEVAKPKW-YERAL--VFAVQGVFFNAYFLGYLISPKFAHRMVGYLEEEAIHSYTEFLKE 184 (252)
Q Consensus 109 wI~~lleE-aeNErmHLl~~~el~~p~~-~~R~l--v~~~Q~vf~~~~~~~YlvsPr~ahrfvgylEEeAv~tYt~~l~~ 184 (252)
.++.+|.+ |+-|+.|...|.++.+..- -.+-. ..-....++......-.-++..+.+..-..|..++..|.+..+.
T Consensus 30 ~~~~~f~~lA~~E~~H~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~E~~~~~~Y~~~a~~ 109 (137)
T PF02915_consen 30 ELKELFRRLAEEEQEHAKFLEKLLRKLGPGEEPPFLEEKVEYSFFPKLEEETDENLEEALEMAIKEEKDAYEFYAELARK 109 (137)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHCHCSTTHHTHCHCCCCCHCCCCTCCSSHHHHHHHHHHHHHHHHHTHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhhccccCcchhhhhhhhhhcchhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 46655544 9999999999998863210 00000 00000000000000000067788888888899999999999998
Q ss_pred hcCCCCCCCCCCHHHHHhhCCCCCCCHHHHHHHHHhhhhHhHhh
Q 025459 185 LDKGNIENVPAPAIATDYWRLPPNSTLKDVVLVVRADEAHHRDV 228 (252)
Q Consensus 185 id~g~l~~~paP~iA~~Yw~Lp~~atlrDvi~~IRaDEa~Hr~v 228 (252)
. .+.-.+++|..|..||..|.+.
T Consensus 110 ~---------------------~~~~~~~~~~~l~~~E~~H~~~ 132 (137)
T PF02915_consen 110 A---------------------PDPEIRKLFEELAKEEKEHEDL 132 (137)
T ss_dssp T---------------------TSHHHHHHHHHHHHHHHHHHHH
T ss_pred C---------------------CCHHHHHHHHHHHHHHHHHHHH
Confidence 6 2345678899999999999764
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=50.89 E-value=1.3e+02 Score=24.22 Aligned_cols=86 Identities=14% Similarity=0.041 Sum_probs=53.4
Q ss_pred chHHHHHHHHHhHHHHHHHHHHHh-----CCchHHHHHHHHHHHHHHHHHHHHHHhChhhHhhhhhhhhh-hHHHHHHHH
Q 025459 108 GWIKALLEEAENERMHLMTFMEVA-----KPKWYERALVFAVQGVFFNAYFLGYLISPKFAHRMVGYLEE-EAIHSYTEF 181 (252)
Q Consensus 108 gwI~~lleEaeNErmHLl~~~el~-----~p~~~~R~lv~~~Q~vf~~~~~~~YlvsPr~ahrfvgylEE-eAv~tYt~~ 181 (252)
|.-+.+..+|..|+.|-.-|.+.. .|. .+ .. -.=+.+....-.--.|. ++...|-++
T Consensus 34 ~~a~~f~~~a~eE~~HA~~~~~~l~~l~g~~~-----~~----~~--------~~~~~~~~l~~~~~~E~~e~~~~y~~~ 96 (134)
T cd01041 34 QIARLFRATAENEKEHAKGHFKLLKGLGGGDT-----GP----PI--------GIGDTLENLKAAIAGETYEYTEMYPEF 96 (134)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCc-----CC----CC--------CcchHHHHHHHHHHhhHHHHHHHHHHH
Confidence 667778889999999998877764 232 00 00 00011111111222344 355777777
Q ss_pred HHHhcCCCCCCCCCCHHHHHhhCCCCCCCHHHHHHHHHhhhhHhHhh
Q 025459 182 LKELDKGNIENVPAPAIATDYWRLPPNSTLKDVVLVVRADEAHHRDV 228 (252)
Q Consensus 182 l~~id~g~l~~~paP~iA~~Yw~Lp~~atlrDvi~~IRaDEa~Hr~v 228 (252)
++.-.. -.|.+.+|.|..|.+||..|.+.
T Consensus 97 ~~~A~~------------------e~d~~~~~~f~~i~~~E~~H~~~ 125 (134)
T cd01041 97 AEVAEE------------------EGFKEAARSFEAIAEAEKVHAER 125 (134)
T ss_pred HHHHHH------------------cCCHHHHHHHHHHHHHHHHHHHH
Confidence 766532 56788999999999999999864
No 18
>PF02915 Rubrerythrin: Rubrerythrin; InterPro: IPR003251 Rubrerythrin (Rr), found in anaerobic sulphate-reducing bacteria [], is a fusion protein containing an N-terminal diiron-binding domain and a C-terminal domain homologous to rubredoxin []. The physiological role of Rr has not been identified. The 3-D structure of Desulphovibrio vulgaris rubrerythrin has been solved []. The structure reveals a tetramer of two-domain subunits. In each monomer, the N-terminal 146 residues form a four-alpha-helix bundle containing the diiron-oxo site (centre I), and the C-terminal 45 residues form a rubredoxin-like FeS4 domain.; GO: 0016491 oxidoreductase activity, 0046872 metal ion binding, 0055114 oxidation-reduction process; PDB: 1VJX_A 2FZF_A 3SID_B 3QHC_B 3QHB_B 4DI0_A 1J30_B 1YV1_A 1YUZ_B 1YUX_B ....
Probab=48.11 E-value=38 Score=26.01 Aligned_cols=47 Identities=19% Similarity=0.222 Sum_probs=37.3
Q ss_pred hhhhHHHHHHHHHHHhcCCCCCCCCCCHHHHHhhCCCCC-CCHHHHHHHHHhhhhHhHhhhhhccccc
Q 025459 170 LEEEAIHSYTEFLKELDKGNIENVPAPAIATDYWRLPPN-STLKDVVLVVRADEAHHRDVNHYASDIH 236 (252)
Q Consensus 170 lEEeAv~tYt~~l~~id~g~l~~~paP~iA~~Yw~Lp~~-atlrDvi~~IRaDEa~Hr~vNH~~ad~~ 236 (252)
.|.+++..|..+.+.... + .-++++|..+..||..|.+.-..+....
T Consensus 9 ~E~~~~~~Y~~~a~~~~~--------------------~~p~~~~~f~~lA~~E~~H~~~~~~l~~~~ 56 (137)
T PF02915_consen 9 MELEAAKFYRELAEKAKD--------------------EGPELKELFRRLAEEEQEHAKFLEKLLRKL 56 (137)
T ss_dssp HHHHHHHHHHHHHHHHHH--------------------TTHHHHHHHHHHHHHHHHHHHHHHHHHCHC
T ss_pred HHHHHHHHHHHHHHHhhh--------------------cccHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 588899999999888621 1 2388999999999999998887776554
No 19
>PRK12775 putative trifunctional 2-polyprenylphenol hydroxylase/glutamate synthase subunit beta/ferritin domain-containing protein; Provisional
Probab=47.48 E-value=42 Score=36.56 Aligned_cols=108 Identities=20% Similarity=0.214 Sum_probs=70.8
Q ss_pred HHHHHHH-HHhHHHHHHHHHHHhC---CchHHHHHHHHHHHHHHHHHHHHHHhChhhHhhhhhhhhhhHHHHHHHHHHHh
Q 025459 110 IKALLEE-AENERMHLMTFMEVAK---PKWYERALVFAVQGVFFNAYFLGYLISPKFAHRMVGYLEEEAIHSYTEFLKEL 185 (252)
Q Consensus 110 I~~lleE-aeNErmHLl~~~el~~---p~~~~R~lv~~~Q~vf~~~~~~~YlvsPr~ahrfvgylEEeAv~tYt~~l~~i 185 (252)
++.+|.+ |+-|+.|..+|.++.+ |..-+-+.. ....++-- +..+.-+|..++++---+|+.|+.-|.++.+..
T Consensus 891 ~K~lF~~LA~eE~~H~~~l~~~~~~~~~~~~~~~~~--~~~~~~~~-~~~~~~~~~~al~lAm~~Ekdai~fY~~la~~~ 967 (1006)
T PRK12775 891 LKELFLKFAGMEQEHMATLARRYHAAAPSPTEGFKI--ERAAIMAG-VKGRPDDPGNLFRIAIEFERRAVKFFKERVAET 967 (1006)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhccCCccccccc--chhhhhhh-hccccCCHHHHHHHHHHHHHHHHHHHHHHHhhC
Confidence 6666655 8889999999988853 111111100 00111111 112345688899999999999999999999886
Q ss_pred cCCCCCCCCCCHHHHHhhCCCCCCCHHHHHHHHHhhhhHhHhhhhhccccccccc
Q 025459 186 DKGNIENVPAPAIATDYWRLPPNSTLKDVVLVVRADEAHHRDVNHYASDIHYQGR 240 (252)
Q Consensus 186 d~g~l~~~paP~iA~~Yw~Lp~~atlrDvi~~IRaDEa~Hr~vNH~~ad~~~~~~ 240 (252)
++....+.++..+-+-|..|...=-..=|...||+
T Consensus 968 --------------------~d~e~~k~l~~~LA~EEk~Hl~~L~~~~d~~~~~~ 1002 (1006)
T PRK12775 968 --------------------PDGSVERQLYKELAAEEREHVALLTTEFERWKQGK 1002 (1006)
T ss_pred --------------------CChHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccC
Confidence 22234789999999999999876554444444553
No 20
>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=41.83 E-value=44 Score=24.13 Aligned_cols=45 Identities=27% Similarity=0.301 Sum_probs=36.7
Q ss_pred hhhhHHHHHHHHHHHhcCCCCCCCCCCHHHHHhhCCCCCCCHHHHHHHHHhhhhHhHhhhhhcccc
Q 025459 170 LEEEAIHSYTEFLKELDKGNIENVPAPAIATDYWRLPPNSTLKDVVLVVRADEAHHRDVNHYASDI 235 (252)
Q Consensus 170 lEEeAv~tYt~~l~~id~g~l~~~paP~iA~~Yw~Lp~~atlrDvi~~IRaDEa~Hr~vNH~~ad~ 235 (252)
.|..|+..|..+...+ + +..++.++..+-.||..|.+.-..+...
T Consensus 9 ~E~~a~~~y~~~~~~~--------------------~-~~~~~~~~~~~a~~E~~H~~~l~~~~~~ 53 (130)
T cd00657 9 GEYAAIIAYGQLAARA--------------------P-DPDLKDELLEIADEERRHADALAERLRE 53 (130)
T ss_pred HHHHHHHHHHHHHHHc--------------------C-CHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 5778899999888876 2 4568899999999999999988776544
No 21
>PF13413 HTH_25: Helix-turn-helix domain; PDB: 2WUS_R 3FYM_A.
Probab=41.54 E-value=23 Score=25.74 Aligned_cols=25 Identities=24% Similarity=0.761 Sum_probs=21.3
Q ss_pred HHHHHHhcCCCCCCCCCCHHHHHhh
Q 025459 179 TEFLKELDKGNIENVPAPAIATDYW 203 (252)
Q Consensus 179 t~~l~~id~g~l~~~paP~iA~~Yw 203 (252)
..+|+.|++|.+..+|.|..+++|=
T Consensus 24 ~~~l~aiE~~~~~~lp~~~y~rg~l 48 (62)
T PF13413_consen 24 VSYLEAIENGDFDSLPSPVYARGYL 48 (62)
T ss_dssp HHHHHHHHCT-GCCSSSHHHHHHHH
T ss_pred HHHHHHHHCcChhhCCcHHHHHHHH
Confidence 4689999999999999999898885
No 22
>PF13668 Ferritin_2: Ferritin-like domain
Probab=39.32 E-value=40 Score=27.05 Aligned_cols=54 Identities=15% Similarity=0.157 Sum_probs=37.9
Q ss_pred hhhhhhhhHHHHHHHHHHHhcCCCCCCCCCCHHHHHhhCCCCCCCHHHHHHHHHhhhhHhHhhhhhc
Q 025459 166 MVGYLEEEAIHSYTEFLKELDKGNIENVPAPAIATDYWRLPPNSTLKDVVLVVRADEAHHRDVNHYA 232 (252)
Q Consensus 166 fvgylEEeAv~tYt~~l~~id~g~l~~~paP~iA~~Yw~Lp~~atlrDvi~~IRaDEa~Hr~vNH~~ 232 (252)
|.--+|..++.-|++.++....+. . ....+...++++..|+++|..|.+.=...
T Consensus 8 ~Al~lE~l~~~fY~~~~~~~~~~~-~------------~~~~~~~~~~~~~~i~~~E~~H~~~l~~~ 61 (137)
T PF13668_consen 8 FALNLEYLEADFYQQAAEGFTLQD-N------------KAALDPEVRDLFQEIADQEQGHVDFLQAA 61 (137)
T ss_pred HHHHHHHHHHHHHHHHHhcCChhh-h------------hccCCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 334567888888888887542211 0 23556788999999999999998864443
No 23
>PRK10635 bacterioferritin; Provisional
Probab=39.31 E-value=64 Score=27.50 Aligned_cols=87 Identities=21% Similarity=0.179 Sum_probs=58.6
Q ss_pred HHHHHHHHhHHHHHHHHHHH----h-CCchHHHHHHHHHHHHHHHHHHHHHHhChhhHhhhhhhhhhhHHHHHHHHHHHh
Q 025459 111 KALLEEAENERMHLMTFMEV----A-KPKWYERALVFAVQGVFFNAYFLGYLISPKFAHRMVGYLEEEAIHSYTEFLKEL 185 (252)
Q Consensus 111 ~~lleEaeNErmHLl~~~el----~-~p~~~~R~lv~~~Q~vf~~~~~~~YlvsPr~ahrfvgylEEeAv~tYt~~l~~i 185 (252)
+....||..|+-|..-+.+- + .|+.-..--+ -.. -+++-.....=-.|.+|+..|.+.++.-
T Consensus 42 ~~~~~ea~eEm~HA~~l~eRIl~LgG~P~~~~~~~~-----------~~g--~~v~eml~~dl~~E~~ai~~y~e~i~~a 108 (158)
T PRK10635 42 DVEYHESIDEMKHADKYIERILFLEGIPNLQDLGKL-----------NIG--EDVEEMLRSDLRLELEGAKDLREAIAYA 108 (158)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHcCCCCCCCCCCCC-----------CCC--CCHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34566788999998876643 1 3543211000 000 2555556666667999999999999865
Q ss_pred cCCCCCCCCCCHHHHHhhCCCCCCCHHHHHHHHHhhhhHhHhh
Q 025459 186 DKGNIENVPAPAIATDYWRLPPNSTLKDVVLVVRADEAHHRDV 228 (252)
Q Consensus 186 d~g~l~~~paP~iA~~Yw~Lp~~atlrDvi~~IRaDEa~Hr~v 228 (252)
++ ..|.+-++++..|-+||-+|.+-
T Consensus 109 ~~------------------~~D~~s~~ll~~iL~dEe~H~~~ 133 (158)
T PRK10635 109 DS------------------VHDYVSRDMMIEILADEEGHIDW 133 (158)
T ss_pred HH------------------cCCHHHHHHHHHHHHHHHHHHHH
Confidence 32 35678899999999999999764
No 24
>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=29.43 E-value=91 Score=24.87 Aligned_cols=40 Identities=18% Similarity=0.252 Sum_probs=31.6
Q ss_pred hhhhHHHHHHHHHHHhcCCCCCCCCCCHHHHHhhCCCCCCCHHHHHHHHHhhhhHhHhhhh
Q 025459 170 LEEEAIHSYTEFLKELDKGNIENVPAPAIATDYWRLPPNSTLKDVVLVVRADEAHHRDVNH 230 (252)
Q Consensus 170 lEEeAv~tYt~~l~~id~g~l~~~paP~iA~~Yw~Lp~~atlrDvi~~IRaDEa~Hr~vNH 230 (252)
.|.++...|....+.. +|..++++|..+..+|..|.+.=.
T Consensus 9 ~E~~~~~~Y~~la~~~---------------------~~~~~k~~f~~lA~~E~~H~~~~~ 48 (125)
T cd01044 9 DEITEAAIYRKLAKRE---------------------KDPENREILLKLAEDERRHAEFWK 48 (125)
T ss_pred HHHHHHHHHHHHHHHc---------------------CCHHHHHHHHHHHHHHHHHHHHHH
Confidence 4677788888777664 345699999999999999998633
No 25
>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=29.34 E-value=2.4e+02 Score=23.07 Aligned_cols=51 Identities=24% Similarity=0.224 Sum_probs=43.7
Q ss_pred HHHhChhhHhhhhhhhhhhHHHHHHHHHHHhcCCCCCCCCCCHHHHHhhCCCCCCCHHHHHHHHHhhhhHhH
Q 025459 155 GYLISPKFAHRMVGYLEEEAIHSYTEFLKELDKGNIENVPAPAIATDYWRLPPNSTLKDVVLVVRADEAHHR 226 (252)
Q Consensus 155 ~YlvsPr~ahrfvgylEEeAv~tYt~~l~~id~g~l~~~paP~iA~~Yw~Lp~~atlrDvi~~IRaDEa~Hr 226 (252)
.=..|..-|+++.-.+|+..+.-|.++++.. +|..+++|+..+++-|..|-
T Consensus 78 ~~~~s~~~al~~g~~~E~~~i~~ye~~~~~~---------------------~d~d~k~v~~~L~~~e~~H~ 128 (135)
T cd01048 78 QGPKSLQDALEVGVLIEELDIADYDRLLERT---------------------QNPDIRDVFENLQAASRNHH 128 (135)
T ss_pred hccccHHHHHHHHHHHHHHHHHHHHHHHHhc---------------------ccHHHHHHHHHHHHHHHHHH
Confidence 3355788999999999999999999999986 34668999999999999884
No 26
>PF10785 NADH-u_ox-rdase: NADH-ubiquinone oxidoreductase complex I, 21 kDa subunit; InterPro: IPR019721 This domain is found in the N-terminal region of NADH-ubiquinone oxidoreductase 21kDa subunits from plants and fungi [].
Probab=25.31 E-value=1.4e+02 Score=23.22 Aligned_cols=30 Identities=27% Similarity=0.464 Sum_probs=17.6
Q ss_pred HHHHHHHHHHHHHHHHHHHhChhhHhhhhhhhh
Q 025459 139 ALVFAVQGVFFNAYFLGYLISPKFAHRMVGYLE 171 (252)
Q Consensus 139 ~lv~~~Q~vf~~~~~~~YlvsPr~ahrfvgylE 171 (252)
.+.+..-+.|.-.|++. .-|.|.||.|+.|
T Consensus 57 ~~~~a~~ig~~gGfl~a---yqrS~~Rf~G~~e 86 (86)
T PF10785_consen 57 AMRLAGAIGFFGGFLLA---YQRSSLRFMGFTE 86 (86)
T ss_pred HHHHHHHHHHHHHHHHH---HHHhhhhhcCCCC
Confidence 33333333433344333 4588999999987
No 27
>PF05669 Med31: SOH1; InterPro: IPR008831 The Mediator complex is a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. The Mediator complex, having a compact conformation in its free form, is recruited to promoters by direct interactions with regulatory proteins and serves for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. On recruitment the Mediator complex unfolds to an extended conformation and partially surrounds RNA polymerase II, specifically interacting with the unphosphorylated form of the C-terminal domain (CTD) of RNA polymerase II. The Mediator complex dissociates from the RNA polymerase II holoenzyme and stays at the promoter when transcriptional elongation begins. The Mediator complex is composed of at least 31 subunits: MED1, MED4, MED6, MED7, MED8, MED9, MED10, MED11, MED12, MED13, MED13L, MED14, MED15, MED16, MED17, MED18, MED19, MED20, MED21, MED22, MED23, MED24, MED25, MED26, MED27, MED29, MED30, MED31, CCNC, CDK8 and CDC2L6/CDK11. The subunits form at least three structurally distinct submodules. The head and the middle modules interact directly with RNA polymerase II, whereas the elongated tail module interacts with gene-specific regulatory proteins. Mediator containing the CDK8 module is less active than Mediator lacking this module in supporting transcriptional activation. The head module contains: MED6, MED8, MED11, SRB4/MED17, SRB5/MED18, ROX3/MED19, SRB2/MED20 and SRB6/MED22. The middle module contains: MED1, MED4, NUT1/MED5, MED7, CSE2/MED9, NUT2/MED10, SRB7/MED21 and SOH1/MED31. CSE2/MED9 interacts directly with MED4. The tail module contains: MED2, PGD1/MED3, RGR1/MED14, GAL11/MED15 and SIN4/MED16. The CDK8 module contains: MED12, MED13, CCNC and CDK8. Individual preparations of the Mediator complex lacking one or more distinct subunits have been variously termed ARC, CRSP, DRIP, PC2, SMCC and TRAP. This entry represents subunit Med31 of the Mediator complex. It contains the Saccharomyces cerevisiae SOH1 homologues. SOH1 is responsible for the repression of temperature sensitive growth of the HPR1 mutant [] and has been found to be a component of the RNA polymerase II transcription complex. SOH1 not only interacts with factors involved in DNA repair, but transcription as well. Thus, the SOH1 protein may serve to couple these two processes [].; GO: 0001104 RNA polymerase II transcription cofactor activity, 0006355 regulation of transcription, DNA-dependent, 0016592 mediator complex; PDB: 3FBI_D 3FBN_D.
Probab=24.34 E-value=69 Score=26.11 Aligned_cols=15 Identities=40% Similarity=0.913 Sum_probs=13.8
Q ss_pred hhhhhhHHHHHHHHH
Q 025459 168 GYLEEEAIHSYTEFL 182 (252)
Q Consensus 168 gylEEeAv~tYt~~l 182 (252)
||++++|...|-++|
T Consensus 28 ~y~~d~~F~nYLkYL 42 (101)
T PF05669_consen 28 GYFEDPAFINYLKYL 42 (101)
T ss_dssp GGGTSTHHHHHHHHG
T ss_pred CccCCHHHHHHHHHH
Confidence 999999999888887
No 28
>COG1633 Uncharacterized conserved protein [Function unknown]
Probab=22.86 E-value=3.4e+02 Score=23.67 Aligned_cols=100 Identities=24% Similarity=0.168 Sum_probs=56.5
Q ss_pred hHHHHHHH-HHhHHHHHHHHHHHh-----CCchHHHHHHHHHHHHHHHHHH---HHHHhChhhHhhhhhhhhhhHHHHHH
Q 025459 109 WIKALLEE-AENERMHLMTFMEVA-----KPKWYERALVFAVQGVFFNAYF---LGYLISPKFAHRMVGYLEEEAIHSYT 179 (252)
Q Consensus 109 wI~~lleE-aeNErmHLl~~~el~-----~p~~~~R~lv~~~Q~vf~~~~~---~~YlvsPr~ahrfvgylEEeAv~tYt 179 (252)
-++.++++ |.-|+-|+-.|.++. ++-..+--.....+.++--..- .-=-.|..-+=+..-..|..++.+|.
T Consensus 54 ~~rk~~~~la~eE~~H~~~f~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~I~~a~~~E~~t~~~Y~ 133 (176)
T COG1633 54 EIRKLFEDLADEEMRHLRKFEKLLEKLTPKEVSSEEEEGEIESEILEYLQPGKEMEKSVSYLEAIEAAMEAEKDTIEFYE 133 (176)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHhcCCccchhhhhcchhhhhccccCcccccccchhHHHHHHHHHHHHHHHHHHHH
Confidence 46655554 999999999999775 1211111111111111110000 00011222333333444999999999
Q ss_pred HHHHHhcCCCCCCCCCCHHHHHhhCCCCCCCHHHHHHHHHhhhhHhHhhh
Q 025459 180 EFLKELDKGNIENVPAPAIATDYWRLPPNSTLKDVVLVVRADEAHHRDVN 229 (252)
Q Consensus 180 ~~l~~id~g~l~~~paP~iA~~Yw~Lp~~atlrDvi~~IRaDEa~Hr~vN 229 (252)
..++.+ .+...+-++..+=.||-.|...=
T Consensus 134 ~~~~~~---------------------~~~~~~~~~~~~a~~E~~H~~~l 162 (176)
T COG1633 134 ELLDEL---------------------VNEEAKKLFKTIADDEKGHASGL 162 (176)
T ss_pred HHHHHc---------------------cCHHHHHHHHHHHHHHHHHHHHH
Confidence 999987 34666778888888998886543
No 29
>PF06480 FtsH_ext: FtsH Extracellular; InterPro: IPR011546 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: 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-, N-, 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. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; 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. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. 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 []. This domain is found in the FtsH family of proteins that include FtsH a membrane-bound ATP-dependent protease universally conserved in prokaryotes []. The FtsH peptidases, which belong to MEROPS peptidase family M41 (clan MA(E)), efficiently degrade proteins that have a low thermodynamic stability - e.g. they lack robust unfoldase activity. This feature may be key and implies that this could be a criterion for degrading a protein. In Oenococcus oeni (Leuconostoc oenos) FtsH is involved in protection against environmental stress [], and shows increased expression under heat or osmotic stress. These two lines of evidence suggest that it is a fundamental prokaryotic self-protection mechanism that checks if proteins are correctly folded. The precise function of this N-terminal region is unclear. ; GO: 0004222 metalloendopeptidase activity, 0005524 ATP binding, 0008270 zinc ion binding, 0016021 integral to membrane; PDB: 2LNA_A.
Probab=22.03 E-value=27 Score=25.92 Aligned_cols=21 Identities=43% Similarity=0.751 Sum_probs=14.6
Q ss_pred hhHHHHHHHHHHHhcCCCCCC
Q 025459 172 EEAIHSYTEFLKELDKGNIEN 192 (252)
Q Consensus 172 EeAv~tYt~~l~~id~g~l~~ 192 (252)
.--..+|++|++++++|++++
T Consensus 26 ~~~~i~YS~F~~~l~~g~V~~ 46 (110)
T PF06480_consen 26 QTKEISYSEFLQMLEKGNVKK 46 (110)
T ss_dssp SSEE--HHHHHHTGGGT-EEE
T ss_pred CCcEECHHHHHHHHHcCCEEE
Confidence 334578999999999999863
No 30
>COG1614 CdhC CO dehydrogenase/acetyl-CoA synthase beta subunit [Energy production and conversion]
Probab=21.94 E-value=13 Score=36.55 Aligned_cols=26 Identities=35% Similarity=0.690 Sum_probs=24.0
Q ss_pred CChhHHHHHHHhhhhhccccCcchHH
Q 025459 86 VPGMVGGMLLHCKSLRRFEHSGGWIK 111 (252)
Q Consensus 86 VPgmv~~~~~Hl~sLr~~~rd~gwI~ 111 (252)
||||++.++.-++|-.-++-||||=+
T Consensus 325 v~GF~Gisi~Ym~SpKFlQ~DGGw~R 350 (470)
T COG1614 325 VPGFVGISISYMRSPKFLQADGGWER 350 (470)
T ss_pred ccceeeeeeeeecCccceecCCCeeE
Confidence 89999999999999999999999933
No 31
>PRK00046 murB UDP-N-acetylenolpyruvoylglucosamine reductase; Provisional
Probab=20.34 E-value=46 Score=31.99 Aligned_cols=17 Identities=41% Similarity=0.679 Sum_probs=15.2
Q ss_pred eeehhccCChhHHHHHH
Q 025459 79 MLETVAAVPGMVGGMLL 95 (252)
Q Consensus 79 ~LETVA~VPgmv~~~~~ 95 (252)
=||..+++||.|||.+.
T Consensus 108 GlE~l~gIPGTVGGAv~ 124 (334)
T PRK00046 108 GLENLALIPGTVGAAPI 124 (334)
T ss_pred hhHHhcCCCcchhHHHH
Confidence 48999999999998876
Done!