Query 030082
Match_columns 183
No_of_seqs 208 out of 762
Neff 4.4
Searched_HMMs 46136
Date Fri Mar 29 08:14:23 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/030082.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/030082hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PTZ00173 60S ribosomal protein 100.0 1.8E-78 4E-83 511.4 18.8 174 1-174 38-211 (213)
2 KOG0857 60s ribosomal protein 100.0 1.4E-61 3E-66 407.0 7.0 173 1-173 38-211 (212)
3 TIGR00279 L10e ribosomal prote 100.0 1.2E-55 2.6E-60 363.2 15.0 131 6-136 40-170 (172)
4 PRK04199 rpl10e 50S ribosomal 100.0 1.2E-53 2.6E-58 351.5 14.4 129 7-135 41-169 (172)
5 COG0197 RplP Ribosomal protein 100.0 9.4E-43 2E-47 280.5 12.9 113 8-137 30-144 (146)
6 cd01433 Ribosomal_L16_L10e Rib 100.0 1.1E-37 2.4E-42 238.7 12.5 111 5-129 2-112 (112)
7 PRK09203 rplP 50S ribosomal pr 100.0 6.6E-36 1.4E-40 238.1 12.7 104 12-131 31-134 (138)
8 CHL00044 rpl16 ribosomal prote 100.0 3.4E-35 7.3E-40 233.6 12.4 104 12-131 31-134 (135)
9 TIGR01164 rplP_bact ribosomal 100.0 7.6E-35 1.6E-39 229.0 11.5 97 12-124 30-126 (126)
10 PF00252 Ribosomal_L16: Riboso 100.0 1.5E-33 3.3E-38 222.3 9.8 104 12-130 30-133 (133)
11 KOG3422 Mitochondrial ribosoma 99.9 1.4E-22 3E-27 171.9 9.9 107 13-132 71-177 (221)
12 PF07831 PYNP_C: Pyrimidine nu 69.2 11 0.00023 27.2 4.4 28 91-118 43-71 (75)
13 PF13533 Biotin_lipoyl_2: Biot 57.0 12 0.00027 24.5 2.6 14 91-104 23-36 (50)
14 cd00992 PDZ_signaling PDZ doma 46.4 35 0.00076 22.9 3.6 34 83-117 36-72 (82)
15 smart00380 AP2 DNA-binding dom 40.7 26 0.00056 23.9 2.3 50 87-145 12-63 (64)
16 COG0504 PyrG CTP synthase (UTP 36.4 40 0.00086 33.0 3.5 52 109-161 305-356 (533)
17 PRK06770 hypothetical protein; 36.4 30 0.00066 29.4 2.5 39 107-150 68-106 (180)
18 COG1242 Predicted Fe-S oxidore 26.8 75 0.0016 29.2 3.5 49 7-65 180-228 (312)
19 PF02391 MoaE: MoaE protein; 26.6 1.8E+02 0.004 22.2 5.2 31 88-118 79-109 (117)
20 cd03777 MATH_TRAF3 Tumor Necro 26.0 2.1E+02 0.0044 23.9 5.7 108 43-163 70-182 (186)
21 PF13872 AAA_34: P-loop contai 25.9 57 0.0012 29.7 2.5 27 14-40 27-55 (303)
22 PRK15052 D-tagatose-1,6-bispho 25.9 1.6E+02 0.0034 28.2 5.5 49 97-150 15-70 (421)
23 PF06572 DUF1131: Protein of u 23.5 60 0.0013 27.4 2.1 32 73-104 48-79 (171)
24 PF02749 QRPTase_N: Quinolinat 23.0 83 0.0018 22.7 2.5 56 8-105 15-70 (88)
25 PRK15458 tagatose 6-phosphate 22.4 2.1E+02 0.0045 27.5 5.6 49 97-150 18-73 (426)
26 TIGR02810 agaZ_gatZ D-tagatose 22.3 2.1E+02 0.0046 27.4 5.6 49 97-150 14-69 (420)
27 PF13580 SIS_2: SIS domain; PD 22.3 83 0.0018 24.2 2.6 39 82-121 91-129 (138)
28 PRK10718 RpoE-regulated lipopr 22.0 96 0.0021 26.7 3.0 32 73-104 69-100 (191)
29 COG0279 GmhA Phosphoheptose is 21.8 93 0.002 26.5 2.9 28 93-121 108-135 (176)
30 PF04320 DUF469: Protein with 21.0 71 0.0015 24.7 1.9 40 1-40 4-44 (101)
31 cd04275 ZnMc_pappalysin_like Z 20.5 2.3E+02 0.0051 24.3 5.1 35 8-42 3-41 (225)
32 cd00136 PDZ PDZ domain, also c 20.3 1.2E+02 0.0026 19.7 2.7 28 90-117 29-59 (70)
No 1
>PTZ00173 60S ribosomal protein L10; Provisional
Probab=100.00 E-value=1.8e-78 Score=511.42 Aligned_cols=174 Identities=68% Similarity=1.125 Sum_probs=170.9
Q ss_pred CCcCCCCCCceeeEEeeccccccChHHHHHHHHHHHhhhhhhhCCcceeEEEEecCCceeeeccccccccchhhhccccC
Q 030082 1 MKKKGVDEFPFCVHLVSWEKENVSSEALEAARIACNKYMAKFAGKDAFHLRVRVHPFHVLRINKMLSCAGADRLQTGMRG 80 (183)
Q Consensus 1 ~kka~v~~fp~~~~Lvs~E~~qiss~aLEAARi~~nkyl~k~~Gk~~f~l~IRv~P~~vir~nkmls~agAdRlq~GMr~ 80 (183)
+++|+|||||+|+||+|+|++||||+||||||+|+||||.|++|+|+||||||+|||||||||||||||||||||+|||+
T Consensus 38 ~~~a~~~~fp~~v~Lvs~E~~qIss~aLEAaRia~nr~l~K~~Gk~~fhl~IRv~P~hvlR~nKm~T~AgAdrlq~gMr~ 117 (213)
T PTZ00173 38 RKKATVDEFPVCVHIVSDEYEQISSEALEAARISANKYMVKRAGKDGFHLRIRVHPFHVLRINKMLSCAGADRLQTGMRG 117 (213)
T ss_pred CCcCCcccCCeEEEEEEcccccccHHHHHHHHHHHHHhhhhhcCCccceEEEEEcCCcccccccccccccCchhhhhccc
Confidence 57899999999999999999999999999999999999988899999999999999999999999999999999999999
Q ss_pred CCCCcceEEEEeeCCCEEEEEEeeCCCHHHHHHHHHHccccCCCceEEEEecCCcccccChHHHHHhhhcCeEeeccceE
Q 030082 81 AFGKPQGTCARVAIGQVLLSVRCKDSNSLHAQEALRRAKFKFPGRQKIIVSRKWGFTKFSRSDYLRFKSENRIVPDGVNA 160 (183)
Q Consensus 81 akGkp~g~vArV~~Gqiifei~~~~~~~~~a~eALrrA~~KlP~~~kIv~~~~~gft~~~~~e~~~~~~~~~l~~dG~~v 160 (183)
|||+|+||||||++|||||||++++++.++|+|||++|++|||++|+|+++++||||+|++|||++|+++|+|++|||+|
T Consensus 118 gfGkp~g~vArVk~Gqiifei~~~~~~~~~AkeALrrA~~KlP~~~kIv~~~~wgft~~~~~~~~~~~~~~~~~~~g~~~ 197 (213)
T PTZ00173 118 AFGKPNGTCARVRIGQILLSIRTKEAYVPQAIEALRRAKYKFPGRQKIVVSNKWGFTNYTREEYQKLRAEGKLIQDGVHV 197 (213)
T ss_pred CCCCccEEEEEECcCCEEEEEecccCCHHHHHHHHHHhcccCCCeEEEEEecccCccccCHHHHHHHHHCCeEecCCceE
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEeCCCCCCCCCCC
Q 030082 161 KLLGCHGPLASRQP 174 (183)
Q Consensus 161 k~~~~~gpl~~~~~ 174 (183)
|++++||||++|..
T Consensus 198 ~~~~~~g~l~~~~~ 211 (213)
T PTZ00173 198 KLISPKGPLTKVNP 211 (213)
T ss_pred EEeCCCCChhhhhc
Confidence 99999999999854
No 2
>KOG0857 consensus 60s ribosomal protein L10 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.4e-61 Score=407.00 Aligned_cols=173 Identities=71% Similarity=1.082 Sum_probs=170.7
Q ss_pred CCcCCCCCCceeeEEeeccccccChHHHHHHHHHHHhhhhhhhCCcceeEEEEecC-Cceeeeccccccccchhhhcccc
Q 030082 1 MKKKGVDEFPFCVHLVSWEKENVSSEALEAARIACNKYMAKFAGKDAFHLRVRVHP-FHVLRINKMLSCAGADRLQTGMR 79 (183)
Q Consensus 1 ~kka~v~~fp~~~~Lvs~E~~qiss~aLEAARi~~nkyl~k~~Gk~~f~l~IRv~P-~~vir~nkmls~agAdRlq~GMr 79 (183)
+||+.|++||+|+|+++.|.++|+++|+||+|+|+|+|+.+.+|+|+||+++|+|| +||+++|+||||||||||||||+
T Consensus 38 ~~k~~~~e~~l~v~~~~~~~~~l~~~~~eA~ri~~~~~~~~~~~~d~~~~r~~~~~~fhv~~i~k~ls~~~~~RLQtgmr 117 (212)
T KOG0857|consen 38 RKKAGVDEFPLCVHLVSNEIEQLSSEALEAARICANKPMVKSKGKDAFHLRVRVHPNFHVLRINKMLSCAGADRLQTGMR 117 (212)
T ss_pred CcCCCCcccchhhhhhhHHHHhHHHHHHHHhhhcccCcccccccccchhhhhhcccchhHHHHhhhhcccchhhhhhccc
Confidence 47999999999999999999999999999999999999999999999999999999 99999999999999999999999
Q ss_pred CCCCCcceEEEEeeCCCEEEEEEeeCCCHHHHHHHHHHccccCCCceEEEEecCCcccccChHHHHHhhhcCeEeeccce
Q 030082 80 GAFGKPQGTCARVAIGQVLLSVRCKDSNSLHAQEALRRAKFKFPGRQKIIVSRKWGFTKFSRSDYLRFKSENRIVPDGVN 159 (183)
Q Consensus 80 ~akGkp~g~vArV~~Gqiifei~~~~~~~~~a~eALrrA~~KlP~~~kIv~~~~~gft~~~~~e~~~~~~~~~l~~dG~~ 159 (183)
++||+|+|+||||.+|||||||+++++|.++++|||++|++|||+.++|+++++||||+|++|||++|++++++++|||+
T Consensus 118 ga~gkp~G~varV~iGqvi~Svrtk~~nkeh~ieal~rak~kfpG~qki~vs~kwgftk~~~def~~~~~~~~~~~~g~~ 197 (212)
T KOG0857|consen 118 GAFGKPQGTVARVHIGQVIMSVRTKLQNKEHVIEALRRAKFKFPGRQKIVVSKKWGFTKFDRDEFEDLRARKRLEPDGCG 197 (212)
T ss_pred ccccCccceEEEEEcCceEEEeecCcccHHHHHHHHHhccccCCCceeEEeeeecCccccchhHHHHHHhhcceeccCCc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEEeCCCCCCCCCC
Q 030082 160 AKLLGCHGPLASRQ 173 (183)
Q Consensus 160 vk~~~~~gpl~~~~ 173 (183)
|+|++.+|||+++.
T Consensus 198 vk~~~~~gp~~~~~ 211 (212)
T KOG0857|consen 198 VKFIPVCGPLQAII 211 (212)
T ss_pred eeeecccCchhhcc
Confidence 99999999999874
No 3
>TIGR00279 L10e ribosomal protein L10.e. L10.e is distantly related to eubacterial ribosomal protein L16.
Probab=100.00 E-value=1.2e-55 Score=363.23 Aligned_cols=131 Identities=58% Similarity=0.889 Sum_probs=128.6
Q ss_pred CCCCceeeEEeeccccccChHHHHHHHHHHHhhhhhhhCCcceeEEEEecCCceeeeccccccccchhhhccccCCCCCc
Q 030082 6 VDEFPFCVHLVSWEKENVSSEALEAARIACNKYMAKFAGKDAFHLRVRVHPFHVLRINKMLSCAGADRLQTGMRGAFGKP 85 (183)
Q Consensus 6 v~~fp~~~~Lvs~E~~qiss~aLEAARi~~nkyl~k~~Gk~~f~l~IRv~P~~vir~nkmls~agAdRlq~GMr~akGkp 85 (183)
.+|||+|++|+++|++||||+||||||+++||||++..|+++||+|||+|||||||+|||++++||||||+|||+|||+|
T Consensus 40 ~~~fp~~~~L~a~E~~~I~~~qiEAaR~a~~r~lkk~~g~~~~k~wIRvfP~~~lt~kp~~trmGaDRlq~GMr~gkG~p 119 (172)
T TIGR00279 40 SAEFPVCVHLVAKEPEQIRHNALEAARIAANKYMTRRAGRMGYHLKIRVYPHHILRENKMATGAGADRIQQGMRGAFGKP 119 (172)
T ss_pred cCCCCEEEEEEECccceecHHHHHHHHHHHHHHHHhhcCccceEEEEEECCCCceecCchhhhcCchhhhcccccCCCCc
Confidence 57899999999999999999999999999999999989999999999999999999999999999999999999999999
Q ss_pred ceEEEEeeCCCEEEEEEeeCCCHHHHHHHHHHccccCCCceEEEEecCCcc
Q 030082 86 QGTCARVAIGQVLLSVRCKDSNSLHAQEALRRAKFKFPGRQKIIVSRKWGF 136 (183)
Q Consensus 86 ~g~vArV~~Gqiifei~~~~~~~~~a~eALrrA~~KlP~~~kIv~~~~~gf 136 (183)
++|||+|++|||||||+++++++++|+|||++|++|||++|+|+++++|+.
T Consensus 120 ~~wvArVk~Gqiifei~~~~~~~~~AkeAlr~A~~KLP~~~kiv~~~~~~~ 170 (172)
T TIGR00279 120 VGTAARVKIGQKIFSVWTKPSNFDVAKEALRRAAMKFPVPCKIVIEKGWEL 170 (172)
T ss_pred cEEEEEECcCCEEEEEEeecCCHHHHHHHHHHHhccCCCcEEEEEecCccc
Confidence 999999999999999999999999999999999999999999999999985
No 4
>PRK04199 rpl10e 50S ribosomal protein L10e; Reviewed
Probab=100.00 E-value=1.2e-53 Score=351.47 Aligned_cols=129 Identities=50% Similarity=0.723 Sum_probs=125.5
Q ss_pred CCCceeeEEeeccccccChHHHHHHHHHHHhhhhhhhCCcceeEEEEecCCceeeeccccccccchhhhccccCCCCCcc
Q 030082 7 DEFPFCVHLVSWEKENVSSEALEAARIACNKYMAKFAGKDAFHLRVRVHPFHVLRINKMLSCAGADRLQTGMRGAFGKPQ 86 (183)
Q Consensus 7 ~~fp~~~~Lvs~E~~qiss~aLEAARi~~nkyl~k~~Gk~~f~l~IRv~P~~vir~nkmls~agAdRlq~GMr~akGkp~ 86 (183)
+|||+|++|+|+|++||||+||||||+++||||++.+|+++||+|||+|||||||+|||.+++||||||+|||+|||+|+
T Consensus 41 ~~~~~~~~L~a~E~~~I~~~qiEAaR~ai~r~lkk~~G~~~~k~wIrvfP~~~lt~kp~~~rmGAdRmg~GMr~akG~p~ 120 (172)
T PRK04199 41 GDFPVEVSLVVEEPCQIRHNALEAARIAANKYLTKTVGRSNYHLKIRVYPHHVLRENKMATGAGADRVSDGMRLAFGKPV 120 (172)
T ss_pred CCCCEEEEEEEcccccccHHHHHHHHHHHHHHHHhccCCcccEEEEEeCCCcceecChhHhhcchhhhccCcccCCCCcc
Confidence 89999999999999999999999999999999998779999999999999999999999999999999999999999999
Q ss_pred eEEEEeeCCCEEEEEEeeCCCHHHHHHHHHHccccCCCceEEEEecCCc
Q 030082 87 GTCARVAIGQVLLSVRCKDSNSLHAQEALRRAKFKFPGRQKIIVSRKWG 135 (183)
Q Consensus 87 g~vArV~~Gqiifei~~~~~~~~~a~eALrrA~~KlP~~~kIv~~~~~g 135 (183)
+|||+|++|||||||+++.+++++|+|||++|++|||++|+|+++++-+
T Consensus 121 ~wva~Vk~G~ilfei~~~~~~~~~akeAlr~a~~KLP~k~kiv~~~~~~ 169 (172)
T PRK04199 121 GTAARVEKGQKIFTVRVNPEHLEAAKEALRRAAMKLPTPCRIVVEKGKE 169 (172)
T ss_pred EEEEEECcCCEEEEEEecCCCHHHHHHHHHHhhccCCCcEEEEEecccc
Confidence 9999999999999999999999999999999999999999999887643
No 5
>COG0197 RplP Ribosomal protein L16/L10E [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=9.4e-43 Score=280.48 Aligned_cols=113 Identities=38% Similarity=0.531 Sum_probs=102.3
Q ss_pred CCceeeEEeeccccccChHHHHHHHHHHHhhhhhhhCCcceeEEEEecCCceeeeccccccccchhhhccccCCCCCcce
Q 030082 8 EFPFCVHLVSWEKENVSSEALEAARIACNKYMAKFAGKDAFHLRVRVHPFHVLRINKMLSCAGADRLQTGMRGAFGKPQG 87 (183)
Q Consensus 8 ~fp~~~~Lvs~E~~qiss~aLEAARi~~nkyl~k~~Gk~~f~l~IRv~P~~vir~nkmls~agAdRlq~GMr~akGkp~g 87 (183)
+||.+++|++.|.+|||++||||||+|+||||++ .|+ +|||+|||||||+|| ||||||+|| |+|+|
T Consensus 30 ~~fg~~gL~a~e~~~It~~qiEAARia~~R~lkr-~g~----~wIRvfP~~~~~~kp-----~e~Rmg~Gk----G~peg 95 (146)
T COG0197 30 VFFGEYGLVALEPGQITARQIEAARIAANRYLKR-GGG----LWIRVFPDKPLTEKP-----GEDRMGKGK----GKPEG 95 (146)
T ss_pred ccceEEEEEEcccceecHHHHHHHHHHHHHHhhh-cCC----EEEEEcCCceeeeCC-----CcccccCCC----CCccE
Confidence 8999999999999999999999999999999987 553 999999999999999 888888886 99999
Q ss_pred EEEEeeCCCEEEEEEeeCCCHHHHHHHHHHccccCCCceEEEEe--cCCccc
Q 030082 88 TCARVAIGQVLLSVRCKDSNSLHAQEALRRAKFKFPGRQKIIVS--RKWGFT 137 (183)
Q Consensus 88 ~vArV~~Gqiifei~~~~~~~~~a~eALrrA~~KlP~~~kIv~~--~~~gft 137 (183)
|||||+||||||||+++++ +.|+|||++|++|||++|++++. + +.++
T Consensus 96 waArVkpG~vlfei~g~~e--~~A~EAlr~Aa~KLP~~~~~v~~~~~-~~~~ 144 (146)
T COG0197 96 WAARVKPGRVLFEIAGVPE--ELAREALRRAAAKLPVKTKFVIRIEK-REGT 144 (146)
T ss_pred EEEEecCCcEEEEEecCcH--HHHHHHHHHHhhcCCCceEEEEEEec-chhc
Confidence 9999999999999999955 66999999999999999666544 4 5544
No 6
>cd01433 Ribosomal_L16_L10e Ribosomal_L16_L10e: L16 is an essential protein in the large ribosomal subunit of bacteria, mitochondria, and chloroplasts. Large subunits that lack L16 are defective in peptidyl transferase activity, peptidyl-tRNA hydrolysis activity, association with the 30S subunit, binding of aminoacyl-tRNA and interaction with antibiotics. L16 is required for the function of elongation factor P (EF-P), a protein involved in peptide bond synthesis through the stimulation of peptidyl transferase activity by the ribosome. Mutations in L16 and the adjoining bases of 23S rRNA confer antibiotic resistance in bacteria, suggesting a role for L16 in the formation of the antibiotic binding site. The GTPase RbgA (YlqF) is essential for the assembly of the large subunit, and it is believed to regulate the incorporation of L16. L10e is the archaeal and eukaryotic cytosolic homolog of bacterial L16. L16 and L10e exhibit structural differences at the N-terminus.
Probab=100.00 E-value=1.1e-37 Score=238.67 Aligned_cols=111 Identities=42% Similarity=0.502 Sum_probs=104.4
Q ss_pred CCCCCceeeEEeeccccccChHHHHHHHHHHHhhhhhhhCCcceeEEEEecCCceeeeccccccccchhhhccccCCCCC
Q 030082 5 GVDEFPFCVHLVSWEKENVSSEALEAARIACNKYMAKFAGKDAFHLRVRVHPFHVLRINKMLSCAGADRLQTGMRGAFGK 84 (183)
Q Consensus 5 ~v~~fp~~~~Lvs~E~~qiss~aLEAARi~~nkyl~k~~Gk~~f~l~IRv~P~~vir~nkmls~agAdRlq~GMr~akGk 84 (183)
..+.++.+++|+++|++|||++||||||+++||||.+. +|++|||+|||+|+|+|| +++|||+|||+
T Consensus 2 ~~~~~~g~~gL~a~e~~~i~~~~lEa~R~~i~r~l~k~----~~~~~ir~~p~~~vt~k~---------~~~rMGkGKG~ 68 (112)
T cd01433 2 GNKLFFGEYGLVALEPGRITAEQLEAARIAINRYLKKK----GGKLWIRVFPDHPVTKKP---------LETRMGKGKGK 68 (112)
T ss_pred CceeccceEEEEECcCCeECHHHHHHHHHHHHHHhhhc----CceEEEEecCCccEEECc---------cccccCCCCCC
Confidence 35678999999999999999999999999999999874 469999999999999999 89999999999
Q ss_pred cceEEEEeeCCCEEEEEEeeCCCHHHHHHHHHHccccCCCceEEE
Q 030082 85 PQGTCARVAIGQVLLSVRCKDSNSLHAQEALRRAKFKFPGRQKII 129 (183)
Q Consensus 85 p~g~vArV~~Gqiifei~~~~~~~~~a~eALrrA~~KlP~~~kIv 129 (183)
|++|||+|++||+|||+.+++. .+.|++||++|++|||++|+|+
T Consensus 69 ~~~~~a~v~~G~iifEi~~~~~-~~~~~~alk~a~~Klp~~~k~i 112 (112)
T cd01433 69 PEGWVARVKPGQILFEVRGVPE-EEVAKEALRRAAKKLPIKTKIV 112 (112)
T ss_pred ccEEEEEECCCCEEEEEeCcCc-HHHHHHHHHHhhccCCCcEEEC
Confidence 9999999999999999999854 8999999999999999999985
No 7
>PRK09203 rplP 50S ribosomal protein L16; Reviewed
Probab=100.00 E-value=6.6e-36 Score=238.12 Aligned_cols=104 Identities=26% Similarity=0.336 Sum_probs=98.5
Q ss_pred eeEEeeccccccChHHHHHHHHHHHhhhhhhhCCcceeEEEEecCCceeeeccccccccchhhhccccCCCCCcceEEEE
Q 030082 12 CVHLVSWEKENVSSEALEAARIACNKYMAKFAGKDAFHLRVRVHPFHVLRINKMLSCAGADRLQTGMRGAFGKPQGTCAR 91 (183)
Q Consensus 12 ~~~Lvs~E~~qiss~aLEAARi~~nkyl~k~~Gk~~f~l~IRv~P~~vir~nkmls~agAdRlq~GMr~akGkp~g~vAr 91 (183)
...|+++|++|||++||||||+++||||++ .| ++|||+|||+|||++| +++|||+|||+|++|||+
T Consensus 31 ~~gL~a~e~g~i~~~qlEaaR~~i~r~Lkk-~g----~~~irv~P~~~vt~k~---------~~~RMGkGKG~~~~~var 96 (138)
T PRK09203 31 EFGLKALEPGWITARQIEAARIAMTRHIKR-GG----KVWIRIFPDKPVTKKP---------AEVRMGKGKGSPEYWVAV 96 (138)
T ss_pred cEEEEECcCCeEcHHHHHHHHHHHHHHhhc-Cc----eEEEEeCCCccEEcCh---------hhccccCCCCCCcEEEEE
Confidence 568999999999999999999999999965 67 7999999999999999 789999999999999999
Q ss_pred eeCCCEEEEEEeeCCCHHHHHHHHHHccccCCCceEEEEe
Q 030082 92 VAIGQVLLSVRCKDSNSLHAQEALRRAKFKFPGRQKIIVS 131 (183)
Q Consensus 92 V~~Gqiifei~~~~~~~~~a~eALrrA~~KlP~~~kIv~~ 131 (183)
|++|||||||++ .+.++|++||++|++|||++|+|+..
T Consensus 97 Vk~G~iifEi~~--~~~~~a~~al~~a~~KLP~~~kii~~ 134 (138)
T PRK09203 97 VKPGRILFEIAG--VSEELAREALRLAAAKLPIKTKFVKR 134 (138)
T ss_pred ECCCCEEEEEeC--CCHHHHHHHHHHHhccCCCcEEEEEe
Confidence 999999999999 48899999999999999999999975
No 8
>CHL00044 rpl16 ribosomal protein L16
Probab=100.00 E-value=3.4e-35 Score=233.55 Aligned_cols=104 Identities=24% Similarity=0.338 Sum_probs=96.5
Q ss_pred eeEEeeccccccChHHHHHHHHHHHhhhhhhhCCcceeEEEEecCCceeeeccccccccchhhhccccCCCCCcceEEEE
Q 030082 12 CVHLVSWEKENVSSEALEAARIACNKYMAKFAGKDAFHLRVRVHPFHVLRINKMLSCAGADRLQTGMRGAFGKPQGTCAR 91 (183)
Q Consensus 12 ~~~Lvs~E~~qiss~aLEAARi~~nkyl~k~~Gk~~f~l~IRv~P~~vir~nkmls~agAdRlq~GMr~akGkp~g~vAr 91 (183)
..+|+++|.+|||++||||||+++||+|++ +|++|||+|||+|||+|| .+++||+|||+|++|||+
T Consensus 31 ~~GL~a~e~~~i~~~qiEaaR~~i~r~lkk-----~~~i~irv~P~~pvtkkp---------~e~RMGkGKG~~~~~va~ 96 (135)
T CHL00044 31 RYALQALEPAWITSRQIEAGRRAITRYARR-----GGKIWIRIFPDKPVTMRP---------AETRMGSGKGSPEYWVAV 96 (135)
T ss_pred cEEEEEccCcEECHHHHHHHHHHHHHhhhc-----CcEEEEEECCCcceEeCc---------ccccccCCCCCccEEEEE
Confidence 468999999999999999999999999965 458999999999999999 667788889999999999
Q ss_pred eeCCCEEEEEEeeCCCHHHHHHHHHHccccCCCceEEEEe
Q 030082 92 VAIGQVLLSVRCKDSNSLHAQEALRRAKFKFPGRQKIIVS 131 (183)
Q Consensus 92 V~~Gqiifei~~~~~~~~~a~eALrrA~~KlP~~~kIv~~ 131 (183)
|++|||||||.++ ++++|++||++|++|||++|+|+..
T Consensus 97 V~~G~ilfEi~g~--~~~~ak~al~~a~~KLP~k~~~v~~ 134 (135)
T CHL00044 97 VKPGRILYEMGGV--SETIARAAIKIAAYKMPIKTQFIIS 134 (135)
T ss_pred ECCCcEEEEEeCC--CHHHHHHHHHHHhhcCCCcEEEEec
Confidence 9999999999997 5589999999999999999999864
No 9
>TIGR01164 rplP_bact ribosomal protein L16, bacterial/organelle. This model describes bacterial and organellar ribosomal protein L16. The homologous protein of the eukaryotic cytosol is designated L10
Probab=100.00 E-value=7.6e-35 Score=228.97 Aligned_cols=97 Identities=28% Similarity=0.332 Sum_probs=91.9
Q ss_pred eeEEeeccccccChHHHHHHHHHHHhhhhhhhCCcceeEEEEecCCceeeeccccccccchhhhccccCCCCCcceEEEE
Q 030082 12 CVHLVSWEKENVSSEALEAARIACNKYMAKFAGKDAFHLRVRVHPFHVLRINKMLSCAGADRLQTGMRGAFGKPQGTCAR 91 (183)
Q Consensus 12 ~~~Lvs~E~~qiss~aLEAARi~~nkyl~k~~Gk~~f~l~IRv~P~~vir~nkmls~agAdRlq~GMr~akGkp~g~vAr 91 (183)
+..|+++|.+|||++||||||+++||||.+ +|++|||+|||+|||++| +++|||+|||+|++|||+
T Consensus 30 ~~gL~a~e~~~i~~~qlEaaR~~i~r~l~~-----~~~~~irv~P~~~vt~k~---------~~~RMGkGKG~~~~~var 95 (126)
T TIGR01164 30 EYGLQALEPGWITARQIEAARVAMTRYVKR-----GGKLWIRIFPDKPYTKKP---------LETRMGKGKGNPEYWVAV 95 (126)
T ss_pred cEeeEECcCCeEcHHHHHHHHHHHHHHHhh-----CceEEEEECCCcCEEeCc---------hhccccCCCCCCCEEEEE
Confidence 568999999999999999999999999974 569999999999999999 778999999999999999
Q ss_pred eeCCCEEEEEEeeCCCHHHHHHHHHHccccCCC
Q 030082 92 VAIGQVLLSVRCKDSNSLHAQEALRRAKFKFPG 124 (183)
Q Consensus 92 V~~Gqiifei~~~~~~~~~a~eALrrA~~KlP~ 124 (183)
|++|||||||++ .++++|++||++|++|||+
T Consensus 96 V~~G~ilfEi~~--~~~~~a~~al~~a~~KLP~ 126 (126)
T TIGR01164 96 VKPGKILFEIAG--VPEEVAREAFRLAASKLPI 126 (126)
T ss_pred ECCCCEEEEEeC--CCHHHHHHHHHHHHhcCCC
Confidence 999999999999 4889999999999999995
No 10
>PF00252 Ribosomal_L16: Ribosomal protein L16p/L10e; InterPro: IPR016180 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This entry represents a structural domain with an alpha/beta-hammerhead fold, where the beta-hammerhead motif is similar to that in barrel-sandwich hybrids. Domains of this structure can be found in ribosomal proteins L10e and L16. ; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005840 ribosome; PDB: 2ZJR_J 1Y69_K 3DLL_J 2ZJQ_J 2ZJP_J 3PIO_J 3CF5_J 3PIP_J 2ZKR_h 3J11_O ....
Probab=100.00 E-value=1.5e-33 Score=222.34 Aligned_cols=104 Identities=38% Similarity=0.500 Sum_probs=95.3
Q ss_pred eeEEeeccccccChHHHHHHHHHHHhhhhhhhCCcceeEEEEecCCceeeeccccccccchhhhccccCCCCCcceEEEE
Q 030082 12 CVHLVSWEKENVSSEALEAARIACNKYMAKFAGKDAFHLRVRVHPFHVLRINKMLSCAGADRLQTGMRGAFGKPQGTCAR 91 (183)
Q Consensus 12 ~~~Lvs~E~~qiss~aLEAARi~~nkyl~k~~Gk~~f~l~IRv~P~~vir~nkmls~agAdRlq~GMr~akGkp~g~vAr 91 (183)
.++|+++|.++||++||||||+++||+|++ .| ++|||+|||+|+|++| ++++||+|+|+|++|||+
T Consensus 30 ~~gl~a~~~g~l~~~qlEa~R~~i~r~lkk-~~----~~~i~v~p~~~vTkk~---------~~~RMG~GKG~~~~~~a~ 95 (133)
T PF00252_consen 30 DYGLKALEPGRLTSNQLEAARIAINRYLKK-NG----KLWIRVFPHHPVTKKP---------LETRMGKGKGKIDHWVAR 95 (133)
T ss_dssp SEEEEESS-EEEEHHHHHHHHHHHHHHHHH-TS----TEEESSSCEEEEEE-S---------SSSSSSSSSCEEEEEEEE
T ss_pred eeeEEEeeeeeechhhhHHHHHHHHHHhhh-he----eEEEEeeeeeeeeeeh---------hhhhhccCCCCccEEEEE
Confidence 489999999999999999999999999987 55 5999999999999999 789999999999999999
Q ss_pred eeCCCEEEEEEeeCCCHHHHHHHHHHccccCCCceEEEE
Q 030082 92 VAIGQVLLSVRCKDSNSLHAQEALRRAKFKFPGRQKIIV 130 (183)
Q Consensus 92 V~~Gqiifei~~~~~~~~~a~eALrrA~~KlP~~~kIv~ 130 (183)
|++||||||+.+. .+.+.|++||++|++|||++++||.
T Consensus 96 V~~G~iifEi~~~-v~~~~a~~alk~a~~KLP~~~~~v~ 133 (133)
T PF00252_consen 96 VKPGQIIFEIGGK-VNEEEAKEALKRAAKKLPIKTKFVS 133 (133)
T ss_dssp ESTTEEEEEEESG-SCHHHHHHHHHHHHHTSSSCEEEE-
T ss_pred ECCCcEEEEECCc-CCHHHHHHHHHHHHhhCCCCEEEeC
Confidence 9999999999872 3889999999999999999999984
No 11
>KOG3422 consensus Mitochondrial ribosomal protein L16 [Translation, ribosomal structure and biogenesis]
Probab=99.88 E-value=1.4e-22 Score=171.85 Aligned_cols=107 Identities=21% Similarity=0.243 Sum_probs=97.2
Q ss_pred eEEeeccccccChHHHHHHHHHHHhhhhhhhCCcceeEEEEecCCceeeeccccccccchhhhccccCCCCCcceEEEEe
Q 030082 13 VHLVSWEKENVSSEALEAARIACNKYMAKFAGKDAFHLRVRVHPFHVLRINKMLSCAGADRLQTGMRGAFGKPQGTCARV 92 (183)
Q Consensus 13 ~~Lvs~E~~qiss~aLEAARi~~nkyl~k~~Gk~~f~l~IRv~P~~vir~nkmls~agAdRlq~GMr~akGkp~g~vArV 92 (183)
..|++++.++|+|.|+|++|..+++++.= ..+|+||.|++|+.|+|.++ -+++||+|||+|++||++|
T Consensus 71 Ygl~a~~~g~l~~~~~e~~r~~~~r~~~~---~~~~~iWrr~~p~~Pvt~K~---------~etRMG~GKGa~d~wva~V 138 (221)
T KOG3422|consen 71 YGLRAKSGGILDSAQFEAMRLTRARKMNP---RNNGKIWRRPAPNLPVTVKG---------NETRMGGGKGAIDHWVARV 138 (221)
T ss_pred hhheeccCceeeHHHHHHHHHHHHHhcCc---ccCccEEEEecCCCceeecC---------cceeccCCCCCcceeEEEe
Confidence 46899999999999999999777777742 23679999999999999888 7899999999999999999
Q ss_pred eCCCEEEEEEeeCCCHHHHHHHHHHccccCCCceEEEEec
Q 030082 93 AIGQVLLSVRCKDSNSLHAQEALRRAKFKFPGRQKIIVSR 132 (183)
Q Consensus 93 ~~Gqiifei~~~~~~~~~a~eALrrA~~KlP~~~kIv~~~ 132 (183)
++|+|||||.|. ..++.|++||..|++|||++++||++.
T Consensus 139 ~~GrIl~EmgG~-~~~~~Ar~al~~aa~klp~~~efVs~~ 177 (221)
T KOG3422|consen 139 KAGRILFEMGGD-VEEEEARQALLQAAHKLPFKYEFVSEE 177 (221)
T ss_pred cCCcEEEEeCCc-ccHHHHHHHHHHHHhcCCccEEEeeHh
Confidence 999999999995 688999999999999999999999874
No 12
>PF07831 PYNP_C: Pyrimidine nucleoside phosphorylase C-terminal domain; InterPro: IPR013102 This domain is found at the C-terminal end of the large alpha/beta domain making up various pyrimidine nucleoside phosphorylases [, ]. It has slightly different conformations in different members of this family. For example, in pyrimidine nucleoside phosphorylase (PYNP, P77826 from SWISSPROT) there is an added three-stranded anti-parallel beta sheet as compared to other members of the family, such as Escherichia coli thymidine phosphorylase (TP, P07650 from SWISSPROT) []. The domain contains an alpha/ beta hammerhead fold and residues in this domain seem to be important in formation of the homodimer []. ; GO: 0016763 transferase activity, transferring pentosyl groups, 0006213 pyrimidine nucleoside metabolic process; PDB: 1AZY_A 1OTP_A 2TPT_A 3H5Q_A 1BRW_A 2WK5_C 2J0F_C 2WK6_B 1UOU_A 2DSJ_B ....
Probab=69.24 E-value=11 Score=27.18 Aligned_cols=28 Identities=36% Similarity=0.395 Sum_probs=20.8
Q ss_pred EeeCCCEEEEEEeeCCC-HHHHHHHHHHc
Q 030082 91 RVAIGQVLLSVRCKDSN-SLHAQEALRRA 118 (183)
Q Consensus 91 rV~~Gqiifei~~~~~~-~~~a~eALrrA 118 (183)
+|+.||+|++|...++. .+.|.+.|+.|
T Consensus 43 ~V~~Gd~l~~i~~~~~~~~~~a~~~~~~a 71 (75)
T PF07831_consen 43 RVEKGDPLATIYANDEARLEEAVERLRAA 71 (75)
T ss_dssp EEBTTSEEEEEEESSSSHHHHHHHHHHHH
T ss_pred EECCCCeEEEEEcCChHHHHHHHHHHHhC
Confidence 68999999999998665 55555555443
No 13
>PF13533 Biotin_lipoyl_2: Biotin-lipoyl like
Probab=56.99 E-value=12 Score=24.45 Aligned_cols=14 Identities=36% Similarity=0.508 Sum_probs=12.5
Q ss_pred EeeCCCEEEEEEee
Q 030082 91 RVAIGQVLLSVRCK 104 (183)
Q Consensus 91 rV~~Gqiifei~~~ 104 (183)
.|+.||+||+++..
T Consensus 23 ~VkkGd~L~~ld~~ 36 (50)
T PF13533_consen 23 QVKKGDVLLVLDSP 36 (50)
T ss_pred EEcCCCEEEEECcH
Confidence 79999999999864
No 14
>cd00992 PDZ_signaling PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. In this subfamily of PDZ domains an N-terminal beta-strand forms the peptide-binding groove base, a circular permutation with respect to PDZ domains found in proteases.
Probab=46.36 E-value=35 Score=22.87 Aligned_cols=34 Identities=24% Similarity=0.353 Sum_probs=23.3
Q ss_pred CCcceEEEEeeCCCEEEEEEeeCC---CHHHHHHHHHH
Q 030082 83 GKPQGTCARVAIGQVLLSVRCKDS---NSLHAQEALRR 117 (183)
Q Consensus 83 Gkp~g~vArV~~Gqiifei~~~~~---~~~~a~eALrr 117 (183)
|+|..- +.+++|++|.+|.+.+. +.+.+.++|+.
T Consensus 36 ~s~a~~-~gl~~GD~I~~ing~~i~~~~~~~~~~~l~~ 72 (82)
T cd00992 36 GGPAER-GGLRVGDRILEVNGVSVEGLTHEEAVELLKN 72 (82)
T ss_pred CChHHh-CCCCCCCEEEEECCEEcCccCHHHHHHHHHh
Confidence 344333 57899999999998754 45566666654
No 15
>smart00380 AP2 DNA-binding domain in plant proteins such as APETALA2 and EREBPs.
Probab=40.66 E-value=26 Score=23.86 Aligned_cols=50 Identities=24% Similarity=0.169 Sum_probs=35.4
Q ss_pred eEEEEeeC--CCEEEEEEeeCCCHHHHHHHHHHccccCCCceEEEEecCCcccccChHHHH
Q 030082 87 GTCARVAI--GQVLLSVRCKDSNSLHAQEALRRAKFKFPGRQKIIVSRKWGFTKFSRSDYL 145 (183)
Q Consensus 87 g~vArV~~--Gqiifei~~~~~~~~~a~eALrrA~~KlP~~~kIv~~~~~gft~~~~~e~~ 145 (183)
-|.|+|.. +..-..+.. -.+.+.|..|..+|..++=+ ....+||+.++|+
T Consensus 12 kw~A~I~~~~~~k~~~lG~-f~t~eeAa~Ayd~a~~~~~g--------~~a~~Nf~~~~y~ 63 (64)
T smart00380 12 KWVAEIRDPSKGKRVWLGT-FDTAEEAARAYDRAAFKFRG--------RSARLNFPNSLYD 63 (64)
T ss_pred eEEEEEEecCCCcEEecCC-CCCHHHHHHHHHHHHHHhcC--------CccccCCCCccCC
Confidence 49999987 655555544 34678899999999888744 3346678777764
No 16
>COG0504 PyrG CTP synthase (UTP-ammonia lyase) [Nucleotide transport and metabolism]
Probab=36.44 E-value=40 Score=33.02 Aligned_cols=52 Identities=15% Similarity=0.192 Sum_probs=44.4
Q ss_pred HHHHHHHHHccccCCCceEEEEecCCcccccChHHHHHhhhcCeEeeccceEE
Q 030082 109 LHAQEALRRAKFKFPGRQKIIVSRKWGFTKFSRSDYLRFKSENRIVPDGVNAK 161 (183)
Q Consensus 109 ~~a~eALrrA~~KlP~~~kIv~~~~~gft~~~~~e~~~~~~~~~l~~dG~~vk 161 (183)
.-+.|||+-|...+..+..|.--..-.++.-+.++++++ ..|-|+|-|-|.+
T Consensus 305 ~Sv~EAL~hag~~~~~~v~i~wIdse~le~~~~~~~~~~-~dgIlVPGGFG~R 356 (533)
T COG0504 305 KSVIEALKHAGIALGVKVNIKWIDSEDLEEENAAELEKL-VDGILVPGGFGYR 356 (533)
T ss_pred HHHHHHHHhhhhhcCCceeeEEEccccccccchhhhhhc-CCEEEeCCCCCcC
Confidence 457899999999999999998888888888887788776 8999999998754
No 17
>PRK06770 hypothetical protein; Provisional
Probab=36.39 E-value=30 Score=29.41 Aligned_cols=39 Identities=21% Similarity=0.445 Sum_probs=32.4
Q ss_pred CHHHHHHHHHHccccCCCceEEEEecCCcccccChHHHHHhhhc
Q 030082 107 NSLHAQEALRRAKFKFPGRQKIIVSRKWGFTKFSRSDYLRFKSE 150 (183)
Q Consensus 107 ~~~~a~eALrrA~~KlP~~~kIv~~~~~gft~~~~~e~~~~~~~ 150 (183)
+++....|++.-.+ ||+.-.++|||+..+.+.-+.++.-
T Consensus 68 tE~~ii~~MH~MtH-----QKV~A~~KwG~~~mT~enI~~l~~~ 106 (180)
T PRK06770 68 TEEEIITAMHKMTH-----QKVKADEKWGFIEMTQENIEKLKDI 106 (180)
T ss_pred CHHHHHHHHHHHHh-----hhhhhhcccceEecCHHHHHHHHHH
Confidence 56778888877665 8889999999999999999888643
No 18
>COG1242 Predicted Fe-S oxidoreductase [General function prediction only]
Probab=26.83 E-value=75 Score=29.20 Aligned_cols=49 Identities=29% Similarity=0.533 Sum_probs=39.0
Q ss_pred CCCceeeEEeeccccccChHHHHHHHHHHHhhhhhhhCCcceeEEEEecCCceeeeccc
Q 030082 7 DEFPFCVHLVSWEKENVSSEALEAARIACNKYMAKFAGKDAFHLRVRVHPFHVLRINKM 65 (183)
Q Consensus 7 ~~fp~~~~Lvs~E~~qiss~aLEAARi~~nkyl~k~~Gk~~f~l~IRv~P~~vir~nkm 65 (183)
..--+|.||+--=++-=..+-||+|++.+.-=+ -| |.+||-|++.-.||
T Consensus 180 rgIkvc~HiI~GLPgE~~~~mleTak~v~~~~v---~G-------IKlH~LhvvkgT~m 228 (312)
T COG1242 180 RGIKVCTHLINGLPGETRDEMLETAKIVAELGV---DG-------IKLHPLHVVKGTPM 228 (312)
T ss_pred cCCeEEEEEeeCCCCCCHHHHHHHHHHHHhcCC---ce-------EEEEEEEEecCChH
Confidence 345689999999888889999999997665322 34 88999999987775
No 19
>PF02391 MoaE: MoaE protein; InterPro: IPR003448 This family contains the MoaE protein that is involved in biosynthesis of molybdopterin []. Molybdopterin, the universal component of the pterin molybdenum cofactors, contains a dithiolene group serving to bind Mo. Addition of the dithiolene sulphurs to a molybdopterin precursor requires the activity of the converting factor. Converting factor contains the MoaE and MoaD proteins.; GO: 0006777 Mo-molybdopterin cofactor biosynthetic process; PDB: 2WP4_B 2OMD_B 1NVJ_E 1FM0_E 3BII_E 1NVI_E 1FMA_E 2QIE_K 2Q5W_E 3RPF_A ....
Probab=26.58 E-value=1.8e+02 Score=22.24 Aligned_cols=31 Identities=19% Similarity=0.248 Sum_probs=26.2
Q ss_pred EEEEeeCCCEEEEEEeeCCCHHHHHHHHHHc
Q 030082 88 TCARVAIGQVLLSVRCKDSNSLHAQEALRRA 118 (183)
Q Consensus 88 ~vArV~~Gqiifei~~~~~~~~~a~eALrrA 118 (183)
.+-++++|+.++-|-.-..|...|.+|++.+
T Consensus 79 R~G~l~vGe~~v~V~vsa~hR~eaf~A~~~~ 109 (117)
T PF02391_consen 79 RVGRLKVGEPIVLVAVSAPHRKEAFEACEYI 109 (117)
T ss_dssp EEEEEETTSEEEEEEEEESSHHHHHHHHHHH
T ss_pred eeCCCCCCCeEEEEEEecCCHHHHHHHHHHH
Confidence 3448999999999999888999999998754
No 20
>cd03777 MATH_TRAF3 Tumor Necrosis Factor Receptor (TNFR)-Associated Factor (TRAF) family, TRAF3 subfamily, TRAF domain; TRAF molecules serve as adapter proteins that link TNFRs and downstream kinase cascades resulting in the activation of transcription factors and the regulation of cell survival, proliferation and stress responses. TRAF3 was first described as a molecule that binds the cytoplasmic tail of CD40. However, it is not required for CD40 signaling. More recently, TRAF3 has been identified as a key regulator of type I interferon (IFN) production and the mammalian innate antiviral immunity. It mediates IFN responses in Toll-like receptor (TLR)-dependent as well as TLR-independent viral recognition pathways. It is also a key element in immunological homeostasis through its regulation of the anti-inflammatory cytokine interleukin-10. TRAF3 contains a RING finger domain, five zinc finger domains, and a TRAF domain. The TRAF domain can be divided into a more divergent N-terminal al
Probab=25.99 E-value=2.1e+02 Score=23.88 Aligned_cols=108 Identities=18% Similarity=0.137 Sum_probs=53.4
Q ss_pred hCCcceeEEEEecCCceeeeccccccccch-hhhccccCCCCCcceEEEEeeCCCEEEEEEeeCCCHHHHHHHHHHc---
Q 030082 43 AGKDAFHLRVRVHPFHVLRINKMLSCAGAD-RLQTGMRGAFGKPQGTCARVAIGQVLLSVRCKDSNSLHAQEALRRA--- 118 (183)
Q Consensus 43 ~Gk~~f~l~IRv~P~~vir~nkmls~agAd-Rlq~GMr~akGkp~g~vArV~~Gqiifei~~~~~~~~~a~eALrrA--- 118 (183)
.|.-+|++.||+||+=.-..+. +..+.= .| |.+.+...-.| .|+ .++-|++-....+..++.+.++-.
T Consensus 70 vg~~GY~w~i~~ypnG~g~~~~--~~iSvyl~L---~~ge~D~~L~W--P~~-~~~tfsLlDQ~~~~~~~~~~~~p~p~~ 141 (186)
T cd03777 70 TGYFGYKMCARVYLNGDGMGKG--THLSLFFVI---MRGEYDALLPW--PFK-QKVTLMLMDQGSSRRHLGDAFKPDPNS 141 (186)
T ss_pred eCCCCeeEEEEEEcCCCCCCCC--CEEEEEEEE---ecCCcccccCC--cee-EEEEEEEEcCCCccccccceeccCCcc
Confidence 3555899999999984221100 000000 12 33344444455 333 777777764322333344433311
Q ss_pred -cccCCCceEEEEecCCcccccChHHHHHhhhcCeEeeccceEEEe
Q 030082 119 -KFKFPGRQKIIVSRKWGFTKFSRSDYLRFKSENRIVPDGVNAKLL 163 (183)
Q Consensus 119 -~~KlP~~~kIv~~~~~gft~~~~~e~~~~~~~~~l~~dG~~vk~~ 163 (183)
.|.-|..- ....|||.+|-. .++|...+.|..|--.+++.
T Consensus 142 ~~F~rp~~~---~n~~~G~~~Fi~--~~~Le~~~ylkdD~l~Irv~ 182 (186)
T cd03777 142 SSFKKPTGE---MNIASGCPVFVA--QTVLENGTYIKDDTIFIKVI 182 (186)
T ss_pred ccccCCccC---CCCCCCchheeE--HHHhccCCcEeCCEEEEEEE
Confidence 11113211 134799988842 23455677887776666553
No 21
>PF13872 AAA_34: P-loop containing NTP hydrolase pore-1
Probab=25.93 E-value=57 Score=29.73 Aligned_cols=27 Identities=30% Similarity=0.342 Sum_probs=22.4
Q ss_pred EEee--ccccccChHHHHHHHHHHHhhhh
Q 030082 14 HLVS--WEKENVSSEALEAARIACNKYMA 40 (183)
Q Consensus 14 ~Lvs--~E~~qiss~aLEAARi~~nkyl~ 40 (183)
+|-. .+.+.||+.||||.--|+.+.-.
T Consensus 27 ~lp~~~~~~g~LS~~QLEaV~yA~q~h~~ 55 (303)
T PF13872_consen 27 HLPEEVIDSGLLSALQLEAVIYACQRHEQ 55 (303)
T ss_pred CCCHHHHhcccccHHHHHHHHHHHHHHHh
Confidence 4444 68899999999999999988764
No 22
>PRK15052 D-tagatose-1,6-bisphosphate aldolase subunit GatZ; Provisional
Probab=25.91 E-value=1.6e+02 Score=28.23 Aligned_cols=49 Identities=22% Similarity=0.120 Sum_probs=33.9
Q ss_pred EEEEEEeeCCCHHHHHHH-HHHccc-cCCCceEEE-----EecCCcccccChHHHHHhhhc
Q 030082 97 VLLSVRCKDSNSLHAQEA-LRRAKF-KFPGRQKII-----VSRKWGFTKFSRSDYLRFKSE 150 (183)
Q Consensus 97 iifei~~~~~~~~~a~eA-LrrA~~-KlP~~~kIv-----~~~~~gft~~~~~e~~~~~~~ 150 (183)
=|+||+.- |. .++|| |++|+- ..|. -|. +...-|||.++..+|.+.+.+
T Consensus 15 Gi~SVCsa--hp-~VieAAl~~a~~~~~pv--LiEAT~NQVdq~GGYTGmtP~dF~~~V~~ 70 (421)
T PRK15052 15 GICSVCSA--HP-LVIEAALAFDLNSTRKV--LIEATSNQVNQFGGYTGMTPADFREFVYG 70 (421)
T ss_pred ceeeECCC--CH-HHHHHHHHHHhhcCCcE--EEEeccccccccCCcCCCCHHHHHHHHHH
Confidence 37888854 54 55555 988876 3333 333 224469999999999999877
No 23
>PF06572 DUF1131: Protein of unknown function (DUF1131); InterPro: IPR010938 This entry consists of several hypothetical bacterial proteins of unknown function.; PDB: 2QZB_B.
Probab=23.46 E-value=60 Score=27.39 Aligned_cols=32 Identities=28% Similarity=0.294 Sum_probs=29.2
Q ss_pred hhhccccCCCCCcceEEEEeeCCCEEEEEEee
Q 030082 73 RLQTGMRGAFGKPQGTCARVAIGQVLLSVRCK 104 (183)
Q Consensus 73 Rlq~GMr~akGkp~g~vArV~~Gqiifei~~~ 104 (183)
||..||..+-|++..+..-.+-+|+.++|.+.
T Consensus 48 ~lrsGm~t~nG~~v~~~qA~~~d~v~lvI~G~ 79 (171)
T PF06572_consen 48 RLRSGMQTANGNIVSFFQAMKDDQVKLVISGD 79 (171)
T ss_dssp EEEEEEEEETTEEEEEEEEEETTEEEEEEEE-
T ss_pred EEecceecCCCCeEEeeeeecCCeEEEEEecC
Confidence 77899999999999999999999999999986
No 24
>PF02749 QRPTase_N: Quinolinate phosphoribosyl transferase, N-terminal domain; InterPro: IPR022412 Quinolinate phosphoribosyl transferase (QPRTase) or nicotinate-nucleotide pyrophosphorylase 2.4.2.19 from EC is involved in the de novo synthesis of NAD in both prokaryotes and eukaryotes. It catalyses the reaction of quinolinic acid with 5-phosphoribosyl-1-pyrophosphate (PRPP) in the presence of Mg2+ to give rise to nicotinic acid mononucleotide (NaMN), pyrophosphate and carbon dioxide [, ]. Unlike IPR004393 from INTERPRO, this domain also includes the molybdenum transport system protein ModD.; GO: 0016763 transferase activity, transferring pentosyl groups; PDB: 3L0G_B 1QAP_A 3C2O_A 3C2F_A 3C2E_A 3C2R_A 3C2V_A 2I14_C 1X1O_B 2B7Q_B ....
Probab=23.00 E-value=83 Score=22.69 Aligned_cols=56 Identities=25% Similarity=0.328 Sum_probs=35.0
Q ss_pred CCceeeEEeeccccccChHHHHHHHHHHHhhhhhhhCCcceeEEEEecCCceeeeccccccccchhhhccccCCCCCcce
Q 030082 8 EFPFCVHLVSWEKENVSSEALEAARIACNKYMAKFAGKDAFHLRVRVHPFHVLRINKMLSCAGADRLQTGMRGAFGKPQG 87 (183)
Q Consensus 8 ~fp~~~~Lvs~E~~qiss~aLEAARi~~nkyl~k~~Gk~~f~l~IRv~P~~vir~nkmls~agAdRlq~GMr~akGkp~g 87 (183)
+-+....+++-|.+-++- +|-+...+... | +.+..+ ...|.
T Consensus 15 ~~~~~a~i~are~gV~aG--~~~~~~i~~~l-----~-----~~v~~~------------------~~dG~--------- 55 (88)
T PF02749_consen 15 DKTGTATIIAREDGVLAG--LEEAEEIFEKL-----G-----LEVEWL------------------VKDGD--------- 55 (88)
T ss_dssp TSEEEEEEEESSSEEE-S--HHHHHHHHHHC-----T-----EEEEES------------------S-TT----------
T ss_pred CCEEEEEEEeCCCEEEEC--HHHHHHHHhhc-----c-----EEEEEE------------------eCCCC---------
Confidence 345667788888877753 55555544433 3 444433 34563
Q ss_pred EEEEeeCCCEEEEEEeeC
Q 030082 88 TCARVAIGQVLLSVRCKD 105 (183)
Q Consensus 88 ~vArV~~Gqiifei~~~~ 105 (183)
+|.+|++|+++.|..
T Consensus 56 ---~v~~g~~i~~i~G~a 70 (88)
T PF02749_consen 56 ---RVEPGDVILEIEGPA 70 (88)
T ss_dssp ---EEETTCEEEEEEEEH
T ss_pred ---CccCCcEEEEEEeCH
Confidence 899999999999963
No 25
>PRK15458 tagatose 6-phosphate aldolase subunit KbaZ; Provisional
Probab=22.40 E-value=2.1e+02 Score=27.48 Aligned_cols=49 Identities=24% Similarity=0.260 Sum_probs=33.6
Q ss_pred EEEEEEeeCCCHHHHHHH-HHHcccc-CCCceEEE-----EecCCcccccChHHHHHhhhc
Q 030082 97 VLLSVRCKDSNSLHAQEA-LRRAKFK-FPGRQKII-----VSRKWGFTKFSRSDYLRFKSE 150 (183)
Q Consensus 97 iifei~~~~~~~~~a~eA-LrrA~~K-lP~~~kIv-----~~~~~gft~~~~~e~~~~~~~ 150 (183)
-|+||+.- |. .++|| |++|+-+ .|. -|. +...-|||.++..+|.+.+.+
T Consensus 18 gI~sVCsa--hp-~VieAAl~~a~~~~~pv--LiEAT~NQVnq~GGYTGmtP~dF~~~V~~ 73 (426)
T PRK15458 18 GIYAVCSA--HP-LVLEAAIRYALANDSPL--LIEATSNQVDQFGGYTGMTPADFRGFVCQ 73 (426)
T ss_pred eEEEecCC--CH-HHHHHHHHHHhhcCCcE--EEEeccccccccCCcCCCCHHHHHHHHHH
Confidence 47888853 54 55555 9888763 332 333 224469999999999999877
No 26
>TIGR02810 agaZ_gatZ D-tagatose-bisphosphate aldolase, class II, non-catalytic subunit. Aldolases specific for D-tagatose-bisphosphate occur in distinct pathways in Escherichia coli and other bacteria, one for the degradation of galactitol (formerly dulcitol) and one for degradation of N-acetyl-galactosamine and D-galactosamine. This family represents a protein of both systems that behaves as a non-catalytic subunit of D-tagatose-bisphosphate aldolase, required both for full activity and for good stability of the aldolase. Note that members of this protein family appear in public databases annotated as putative tagatose 6-phosphate kinases, possibly in error.
Probab=22.32 E-value=2.1e+02 Score=27.40 Aligned_cols=49 Identities=29% Similarity=0.347 Sum_probs=33.6
Q ss_pred EEEEEEeeCCCHHHHHHH-HHHcccc-CCCceEEE-----EecCCcccccChHHHHHhhhc
Q 030082 97 VLLSVRCKDSNSLHAQEA-LRRAKFK-FPGRQKII-----VSRKWGFTKFSRSDYLRFKSE 150 (183)
Q Consensus 97 iifei~~~~~~~~~a~eA-LrrA~~K-lP~~~kIv-----~~~~~gft~~~~~e~~~~~~~ 150 (183)
-|+||+.- |. .++|| |++|+-+ .|. -|. +...-|||.++..+|.+.+.+
T Consensus 14 gI~sVCsa--hp-~VieAAl~~a~~~~~pv--LiEAT~NQVnq~GGYTGmtP~dF~~~V~~ 69 (420)
T TIGR02810 14 GIYSVCSA--HP-LVLEAAIRRARASGTPV--LIEATSNQVNQFGGYTGMTPADFRDFVET 69 (420)
T ss_pred eEEEECCC--CH-HHHHHHHHHHhhcCCcE--EEEeccccccccCCcCCCCHHHHHHHHHH
Confidence 47888753 54 55555 9888763 333 333 224469999999999999877
No 27
>PF13580 SIS_2: SIS domain; PDB: 1TK9_C 2I22_B 2I2W_A 1X92_A 3BJZ_D 2XBL_B 2X3Y_F 2YVA_B 3CVJ_D 3TRJ_D ....
Probab=22.32 E-value=83 Score=24.22 Aligned_cols=39 Identities=21% Similarity=0.236 Sum_probs=24.3
Q ss_pred CCCcceEEEEeeCCCEEEEEEeeCCCHHHHHHHHHHcccc
Q 030082 82 FGKPQGTCARVAIGQVLLSVRCKDSNSLHAQEALRRAKFK 121 (183)
Q Consensus 82 kGkp~g~vArV~~Gqiifei~~~~~~~~~a~eALrrA~~K 121 (183)
|+.+.--...+++|++|+-|++...+ ...++|++.|+.+
T Consensus 91 ~~~~~~~~~~~~~gDvli~iS~SG~s-~~vi~a~~~Ak~~ 129 (138)
T PF13580_consen 91 FARQLLALYDIRPGDVLIVISNSGNS-PNVIEAAEEAKER 129 (138)
T ss_dssp HHHHHHHHTT--TT-EEEEEESSS-S-HHHHHHHHHHHHT
T ss_pred HHHHHHHHcCCCCCCEEEEECCCCCC-HHHHHHHHHHHHC
Confidence 44433223348999999999986544 7888999988654
No 28
>PRK10718 RpoE-regulated lipoprotein; Provisional
Probab=22.04 E-value=96 Score=26.68 Aligned_cols=32 Identities=25% Similarity=0.306 Sum_probs=30.0
Q ss_pred hhhccccCCCCCcceEEEEeeCCCEEEEEEee
Q 030082 73 RLQTGMRGAFGKPQGTCARVAIGQVLLSVRCK 104 (183)
Q Consensus 73 Rlq~GMr~akGkp~g~vArV~~Gqiifei~~~ 104 (183)
||.+||+-.-|....+..-++-+||.++|.+.
T Consensus 69 ~lrsGm~t~~G~iv~~~qa~~~d~v~lvi~G~ 100 (191)
T PRK10718 69 RLRSGMKTANGNVVRFFQAMKGDQVAMVINGQ 100 (191)
T ss_pred eEeccccCCCCCEEEeeeeecCCceEEEEECC
Confidence 78899999999999999999999999999985
No 29
>COG0279 GmhA Phosphoheptose isomerase [Carbohydrate transport and metabolism]
Probab=21.78 E-value=93 Score=26.45 Aligned_cols=28 Identities=32% Similarity=0.389 Sum_probs=23.9
Q ss_pred eCCCEEEEEEeeCCCHHHHHHHHHHcccc
Q 030082 93 AIGQVLLSVRCKDSNSLHAQEALRRAKFK 121 (183)
Q Consensus 93 ~~Gqiifei~~~~~~~~~a~eALrrA~~K 121 (183)
++|+||+=|++-. |...+.+|++.|+.|
T Consensus 108 ~~GDvLigISTSG-NS~nVl~Ai~~Ak~~ 135 (176)
T COG0279 108 QPGDVLIGISTSG-NSKNVLKAIEAAKEK 135 (176)
T ss_pred CCCCEEEEEeCCC-CCHHHHHHHHHHHHc
Confidence 5699999999965 778999999999875
No 30
>PF04320 DUF469: Protein with unknown function (DUF469); InterPro: IPR007416 This entry represents a family of uncharacterised proteins which are predicted to function as phosphotransferases.
Probab=21.01 E-value=71 Score=24.72 Aligned_cols=40 Identities=28% Similarity=0.130 Sum_probs=33.8
Q ss_pred CCcCCCCCCceeeEEeeccccc-cChHHHHHHHHHHHhhhh
Q 030082 1 MKKKGVDEFPFCVHLVSWEKEN-VSSEALEAARIACNKYMA 40 (183)
Q Consensus 1 ~kka~v~~fp~~~~Lvs~E~~q-iss~aLEAARi~~nkyl~ 40 (183)
|||-.++||.-.+..++..... ++.+++++.=-+.--++.
T Consensus 4 RKKL~l~EFqelGF~v~~~~~~~~~~e~~D~~~D~fId~Ie 44 (101)
T PF04320_consen 4 RKKLHLDEFQELGFEVSCRFAEGTSEEQIDAFVDAFIDVIE 44 (101)
T ss_pred hhhhhhhhhheeEEEEEEEECCCCCHHHHHHHHHHHHHHHH
Confidence 6999999999999999999988 999999987665555553
No 31
>cd04275 ZnMc_pappalysin_like Zinc-dependent metalloprotease, pappalysin_like subfamily. The pregnancy-associated plasma protein A (PAPP-A or pappalysin-1) cleaves insulin-like growth factor-binding proteins 4 and 5, thereby promoting cell growth by releasing bound growth factor. This model includes pappalysins and related metalloprotease domains from all three kingdoms of life. The three-dimensional structure of an archaeal representative, ulilysin, has been solved.
Probab=20.46 E-value=2.3e+02 Score=24.27 Aligned_cols=35 Identities=14% Similarity=0.174 Sum_probs=30.2
Q ss_pred CCceeeEEeecc----ccccChHHHHHHHHHHHhhhhhh
Q 030082 8 EFPFCVHLVSWE----KENVSSEALEAARIACNKYMAKF 42 (183)
Q Consensus 8 ~fp~~~~Lvs~E----~~qiss~aLEAARi~~nkyl~k~ 42 (183)
..|+.+|++... .+.|+..+|++.=..+|+.....
T Consensus 3 ~ipVvfHVi~~~~~~~~~~i~d~~i~~qi~vlN~~y~~~ 41 (225)
T cd04275 3 VIPVYFHVIYNNSAVSGGNISDAQITDQIDVLNDDYSGL 41 (225)
T ss_pred EeCeEEEEEeCCCCccCCccCHHHHHHHHHHHHHHhhcc
Confidence 469999999766 59999999999999999998653
No 32
>cd00136 PDZ PDZ domain, also called DHR (Dlg homologous region) or GLGF (after a conserved sequence motif). Many PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. Heterodimerization through PDZ-PDZ domain interactions adds to the domain's versatility, and PDZ domain-mediated interactions may be modulated dynamically through target phosphorylation. Some PDZ domains play a role in scaffolding supramolecular complexes. PDZ domains are found in diverse signaling proteins in bacteria, archebacteria, and eurkayotes. This CD contains two distinct structural subgroups with either a N- or C-terminal beta-strand forming the peptide-binding groove base. The circular permutation placing the strand on the N-terminus appears to be found in Eumetazoa only, while the C-terminal variant is found in all three kingdoms of life, and seems to co-occur with protease domains. PDZ domains have been named after PSD95(pos
Probab=20.33 E-value=1.2e+02 Score=19.69 Aligned_cols=28 Identities=29% Similarity=0.448 Sum_probs=18.4
Q ss_pred EEeeCCCEEEEEEeeCCCH---HHHHHHHHH
Q 030082 90 ARVAIGQVLLSVRCKDSNS---LHAQEALRR 117 (183)
Q Consensus 90 ArV~~Gqiifei~~~~~~~---~~a~eALrr 117 (183)
+.+++|++|.+|.+.+... +.+.+.|+.
T Consensus 29 ~gl~~GD~I~~Ing~~v~~~~~~~~~~~l~~ 59 (70)
T cd00136 29 AGLQAGDVILAVNGTDVKNLTLEDVAELLKK 59 (70)
T ss_pred cCCCCCCEEEEECCEECCCCCHHHHHHHHhh
Confidence 4688999999998875322 344444443
Done!