Query 029194
Match_columns 197
No_of_seqs 175 out of 295
Neff 3.9
Searched_HMMs 46136
Date Fri Mar 29 09:00:24 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/029194.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/029194hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1696 60s ribosomal protein 100.0 1.5E-86 3.3E-91 554.1 16.9 187 1-187 1-187 (193)
2 PTZ00097 60S ribosomal protein 100.0 1.9E-80 4E-85 516.9 19.3 174 3-176 1-174 (175)
3 cd01417 Ribosomal_L19e_E Ribos 100.0 4.6E-79 1E-83 504.4 17.5 164 4-167 1-164 (164)
4 PTZ00436 60S ribosomal protein 100.0 2.6E-77 5.7E-82 533.2 20.1 170 1-170 1-170 (357)
5 PF01280 Ribosomal_L19e: Ribos 100.0 1E-74 2.2E-79 472.4 14.1 148 2-149 1-148 (148)
6 cd00481 Ribosomal_L19e Ribosom 100.0 2.9E-73 6.3E-78 462.4 15.0 145 4-148 1-145 (145)
7 PRK08570 rpl19e 50S ribosomal 100.0 4E-73 8.6E-78 463.7 15.7 147 1-147 1-147 (150)
8 cd01418 Ribosomal_L19e_A Ribos 100.0 2.4E-71 5.1E-76 451.1 15.5 142 4-145 1-142 (145)
9 COG2147 RPL19A Ribosomal prote 100.0 9.6E-68 2.1E-72 430.7 14.9 149 1-149 1-149 (150)
10 TIGR01764 excise DNA binding d 69.2 3.1 6.7E-05 25.8 1.4 29 23-52 1-29 (49)
11 PF12728 HTH_17: Helix-turn-he 68.8 3.3 7.1E-05 27.0 1.5 29 23-52 1-29 (51)
12 PRK00247 putative inner membra 58.6 84 0.0018 30.4 9.4 69 92-167 291-363 (429)
13 PF13453 zf-TFIIB: Transcripti 55.2 5.3 0.00012 25.7 0.6 15 20-34 26-40 (41)
14 PF13880 Acetyltransf_13: ESCO 49.3 5.4 0.00012 29.4 -0.1 14 16-29 5-18 (70)
15 TIGR02075 pyrH_bact uridylate 43.3 26 0.00056 29.9 3.2 48 5-52 77-125 (233)
16 PRK05920 aromatic acid decarbo 41.0 32 0.00069 29.7 3.3 47 9-58 121-167 (204)
17 PF01479 S4: S4 domain; Inter 38.9 23 0.00049 22.7 1.7 27 30-56 8-34 (48)
18 TIGR01610 phage_O_Nterm phage 33.8 49 0.0011 24.6 3.0 38 16-54 40-81 (95)
19 PRK06029 3-octaprenyl-4-hydrox 33.4 53 0.0011 27.8 3.5 46 9-57 106-151 (185)
20 PF12802 MarR_2: MarR family; 33.2 38 0.00083 22.2 2.1 52 7-60 7-61 (62)
21 PHA00616 hypothetical protein 31.9 27 0.00058 23.8 1.2 17 129-145 8-24 (44)
22 smart00345 HTH_GNTR helix_turn 31.5 38 0.00081 21.5 1.8 25 32-56 32-56 (60)
23 cd04254 AAK_UMPK-PyrH-Ec UMP k 28.8 56 0.0012 27.7 2.9 44 9-52 81-124 (231)
24 PF09851 SHOCT: Short C-termin 28.4 70 0.0015 19.6 2.6 20 104-123 6-25 (31)
25 COG3592 Uncharacterized conser 28.3 28 0.00061 26.2 0.9 19 11-30 35-53 (74)
26 PRK11548 outer membrane biogen 27.0 44 0.00096 25.8 1.8 26 22-47 36-61 (113)
27 TIGR02988 YaaA_near_RecF S4 do 25.3 52 0.0011 22.2 1.7 21 35-55 21-41 (59)
28 PF08535 KorB: KorB domain; I 25.2 62 0.0013 23.8 2.2 39 6-51 5-43 (93)
29 PRK00083 frr ribosome recyclin 24.4 3.9E+02 0.0085 22.6 7.2 84 22-125 69-158 (185)
30 TIGR00421 ubiX_pad polyprenyl 24.2 95 0.0021 26.0 3.4 47 9-58 103-149 (181)
31 PF15319 RHINO: RAD9, RAD1, HU 24.2 27 0.00059 31.4 0.2 34 83-120 201-234 (236)
32 PF00096 zf-C2H2: Zinc finger, 23.9 60 0.0013 17.5 1.5 16 129-144 7-22 (23)
33 PF14468 DUF4427: Protein of u 23.9 55 0.0012 27.1 1.9 33 12-53 30-62 (132)
34 PF06353 DUF1062: Protein of u 23.7 59 0.0013 26.8 2.0 23 34-56 113-135 (142)
35 smart00420 HTH_DEOR helix_turn 21.7 78 0.0017 19.5 1.9 25 32-56 26-50 (53)
36 PF01047 MarR: MarR family; I 21.5 61 0.0013 21.2 1.4 26 34-59 31-56 (59)
37 PF13412 HTH_24: Winged helix- 21.2 68 0.0015 20.4 1.6 20 32-51 29-48 (48)
38 PF10625 UspB: Universal stres 20.9 1.4E+02 0.0031 24.0 3.5 32 95-133 19-50 (107)
39 smart00099 btg1 tob/btg1 famil 20.7 36 0.00079 27.0 0.2 10 21-30 93-102 (108)
40 KOG1596 Fibrillarin and relate 20.4 64 0.0014 30.0 1.7 22 6-28 137-158 (317)
41 PRK13982 bifunctional SbtC-lik 20.3 1.4E+02 0.0031 29.0 4.2 49 10-59 172-221 (475)
42 PF00392 GntR: Bacterial regul 20.1 84 0.0018 21.3 1.9 27 31-57 35-61 (64)
43 cd04762 HTH_MerR-trunc Helix-T 20.0 87 0.0019 18.8 1.8 17 36-52 12-28 (49)
No 1
>KOG1696 consensus 60s ribosomal protein L19 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.5e-86 Score=554.13 Aligned_cols=187 Identities=73% Similarity=1.102 Sum_probs=185.2
Q ss_pred CCcchhhHHHHHHHhccCCCceecCccchhHHHhhhhhHHHHhhhhcCceeecCCCCCChhHHHHHHHHHhcCcCCCcCC
Q 029194 1 MVSLKLQKRLSASVLKCGRGKVWLDPNEVNEISMANSRQNIRKLVKDGFIIRKPTKIHSRSRARRMKEAKRKGRHSGYGK 80 (197)
Q Consensus 1 M~~l~~QKRLAA~VL~cGk~rVWlDPne~~eIa~A~sR~~IRkLIkdG~Ii~kp~~~~SR~R~r~~~~ak~kGRh~G~Gk 80 (197)
|++|++|||||||||+||+.+|||||||++||++|||||+|++||+||+||.+|+++|||+||+++.+++++|||+|+|+
T Consensus 1 Ms~lrlqKRLAssVl~cGKkKvWlDpNE~~eI~~ansRq~irkLikdg~iI~Kp~~vhsr~r~rk~~~akrkgrH~G~GK 80 (193)
T KOG1696|consen 1 MSNLRLQKRLAASVLKCGKKKVWLDPNEISEISGANSRQNIRKLIKDGLIIRKPVTVHSRSRCRKRLEAKRKGRHMGYGK 80 (193)
T ss_pred CchHHHHHHHHHHHHHhcccceeeCccHHHHhcccchHHHHHHHHhCCeEeecchhhhHHHHHHHHHHHHHhccccCccc
Confidence 89999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cccccccCCcchHHHHHHHHHHHHHHHHHHhcCCCChHhhHHHHhhhcCCccccHHHHHHHHHHHhhHHHHhhhhhHHHH
Q 029194 81 RKGTREARLPTKILWMRRMRVLRRLLRKYRESKKIDKHMYHDMYMKVKGNVFKNKRVLMESIHKSKAEKAREKTLSDQFE 160 (197)
Q Consensus 81 RKGt~~AR~p~K~~Wm~RiR~lRrlLr~~Re~~kID~~~Yr~LY~kaKGn~Fknk~~L~e~I~k~kae~~r~k~l~dQae 160 (197)
|+||+|||||+|++||+|||+||++|++|||+|+||+|+||+||+++|||+|+|+.+||||||+.|||++++|+|+||||
T Consensus 81 RkGTanArmP~k~~Wmrr~RvlRrlL~kyR~skKIdkh~YH~lY~k~KGnvFKnK~~LmE~I~K~KAe~~r~K~LadQae 160 (193)
T KOG1696|consen 81 RKGTANARMPSKVLWMRRMRVLRRLLKKYRDSKKIDKHMYHDLYLKVKGNVFKNKRVLMEHIHKSKAEKAREKLLADQAE 160 (193)
T ss_pred ccccccccCchhHHHHHHHHHHHHHHHHhhhcccchHHHHHHHHHHHhcchhhhHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHhhhHHHHHHHHHHHHHHHhcCCCC
Q 029194 161 AKRAKNKASRERKLARREERLAQGPGE 187 (197)
Q Consensus 161 A~r~k~k~~r~rr~~r~~~k~~~~~~~ 187 (197)
|+|.++++++++++|++++++++++..
T Consensus 161 Arr~k~k~ar~rreer~~~k~~~~~~~ 187 (193)
T KOG1696|consen 161 ARRLKNKAARKRREERLAAKPQELIKT 187 (193)
T ss_pred HHHhhhHHHhhhHHHHHhhchhhhhcc
Confidence 999999999999999999999998863
No 2
>PTZ00097 60S ribosomal protein L19; Provisional
Probab=100.00 E-value=1.9e-80 Score=516.89 Aligned_cols=174 Identities=71% Similarity=1.152 Sum_probs=171.3
Q ss_pred cchhhHHHHHHHhccCCCceecCccchhHHHhhhhhHHHHhhhhcCceeecCCCCCChhHHHHHHHHHhcCcCCCcCCcc
Q 029194 3 SLKLQKRLSASVLKCGRGKVWLDPNEVNEISMANSRQNIRKLVKDGFIIRKPTKIHSRSRARRMKEAKRKGRHSGYGKRK 82 (197)
Q Consensus 3 ~l~~QKRLAA~VL~cGk~rVWlDPne~~eIa~A~sR~~IRkLIkdG~Ii~kp~~~~SR~R~r~~~~ak~kGRh~G~GkRK 82 (197)
+|++||||||+||+||+++||||||+++||++||||+|||+||+||+|+++|++||||+|++++++++++|||+|+|||+
T Consensus 1 ~l~~QKRLAA~vL~cG~~rVWiDP~~~~eI~~A~tR~dIR~LIkdG~I~~kp~kg~SR~R~r~~~~~k~kGR~~G~G~RK 80 (175)
T PTZ00097 1 NLRLQKRLAASVLKCGKNRVWLDPNEASEISLANSRFSIRKLIKDGLIIRKPVAVHSRARARRFHEAKRKGRHTGIGKRR 80 (175)
T ss_pred CchHHHHHHHHHHCCCCCceeeCHHHHHHHHHhhhHHHHHHHHHCCCeeecCCCCCChHHHHHHHHHHHhCCCCCCCCCc
Confidence 58999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cccccCCcchHHHHHHHHHHHHHHHHHHhcCCCChHhhHHHHhhhcCCccccHHHHHHHHHHHhhHHHHhhhhhHHHHHH
Q 029194 83 GTREARLPTKILWMRRMRVLRRLLRKYRESKKIDKHMYHDMYMKVKGNVFKNKRVLMESIHKSKAEKAREKTLSDQFEAK 162 (197)
Q Consensus 83 Gt~~AR~p~K~~Wm~RiR~lRrlLr~~Re~~kID~~~Yr~LY~kaKGn~Fknk~~L~e~I~k~kae~~r~k~l~dQaeA~ 162 (197)
||+|||||+|+.||++||+||++|++|||+|+||+|+||.||++||||+|+|++||++|||+.|||+++++.|+||+||+
T Consensus 81 Gtk~AR~p~K~~W~~riR~lRr~Lk~~R~~~kIdk~~Yr~lY~kaKGn~Fknk~~L~~~I~~~kae~~r~k~l~~q~~a~ 160 (175)
T PTZ00097 81 GTREARMPTKVLWMRRQRVLRRLLRKYRAAKKIDRHMYHEFYLKSKGNQFKNKRVLIEAIHKTKNEKVKEKKIQDQLEAR 160 (175)
T ss_pred CcccccCcHHHHHHHHHHHHHHHHHHHHHcCCCCHHHHHHHHHHhcCCCcCcHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HhhhHHHHHHHHHH
Q 029194 163 RAKNKASRERKLAR 176 (197)
Q Consensus 163 r~k~k~~r~rr~~r 176 (197)
+.++++++++++++
T Consensus 161 r~k~~~~~~~r~~~ 174 (175)
T PTZ00097 161 RAKAKALRNKRKAK 174 (175)
T ss_pred HHHHHHHHHHHhhc
Confidence 99999999987653
No 3
>cd01417 Ribosomal_L19e_E Ribosomal protein L19e, eukaryotic. L19e is found in the large ribosomal subunit of eukaryotes and archaea. L19e is distinct from the ribosomal subunit L19, which is found in prokaryotes. It consists of two small globular domains connected by an extended segment. It is located toward the surface of the large subunit, with one exposed end involved in forming the intersubunit bridge with the small subunit. The other exposed end is involved in forming the translocon binding site, along with L22, L23, L24, L29, and L31e subunits.
Probab=100.00 E-value=4.6e-79 Score=504.43 Aligned_cols=164 Identities=79% Similarity=1.221 Sum_probs=162.0
Q ss_pred chhhHHHHHHHhccCCCceecCccchhHHHhhhhhHHHHhhhhcCceeecCCCCCChhHHHHHHHHHhcCcCCCcCCccc
Q 029194 4 LKLQKRLSASVLKCGRGKVWLDPNEVNEISMANSRQNIRKLVKDGFIIRKPTKIHSRSRARRMKEAKRKGRHSGYGKRKG 83 (197)
Q Consensus 4 l~~QKRLAA~VL~cGk~rVWlDPne~~eIa~A~sR~~IRkLIkdG~Ii~kp~~~~SR~R~r~~~~ak~kGRh~G~GkRKG 83 (197)
|++||||||+||+||+++||||||+++||++||||+|||+||+||+|+++|++||||+|++++++++++|||+|+|||+|
T Consensus 1 l~~QKRLAA~vL~cG~~rVW~DP~~~~eI~~A~tR~dIR~LIkdG~I~~kp~kg~SR~R~r~~~~~k~kGR~~G~G~RkG 80 (164)
T cd01417 1 LRLQKRLAASVLKCGKRKVWLDPNEISEISNANSRQSIRKLIKDGLIIKKPVKVHSRSRARKRHEAKRKGRHMGYGKRKG 80 (164)
T ss_pred CcHHHHHHHHHHCCCCCceeeCHHHHHHHHHhhhHHHHHHHHHCCCeeecCCCcCCHHHHHHHHHHHHhCCCCCCCCCcC
Confidence 68999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccccCCcchHHHHHHHHHHHHHHHHHHhcCCCChHhhHHHHhhhcCCccccHHHHHHHHHHHhhHHHHhhhhhHHHHHHH
Q 029194 84 TREARLPTKILWMRRMRVLRRLLRKYRESKKIDKHMYHDMYMKVKGNVFKNKRVLMESIHKSKAEKAREKTLSDQFEAKR 163 (197)
Q Consensus 84 t~~AR~p~K~~Wm~RiR~lRrlLr~~Re~~kID~~~Yr~LY~kaKGn~Fknk~~L~e~I~k~kae~~r~k~l~dQaeA~r 163 (197)
|+|||||+|+.||++||+||++|++|||+|+||+|+||.||++||||+|+|+++|++|||+.|||+++++.|+||+||++
T Consensus 81 t~~AR~p~K~~W~~riR~lRr~Lk~~R~~~kIdk~~Yr~lY~kaKGn~Fknk~~L~~~I~~~kae~~r~k~l~~q~~a~r 160 (164)
T cd01417 81 TANARMPSKVLWMRRQRVLRRLLKKYRESKKIDKHLYHELYLKAKGNVFKNKRVLMEHIHKAKAEKAREKELADQAEARR 160 (164)
T ss_pred cccccCcHHHHHHHHHHHHHHHHHHHHHcCCCCHHHHHHHHHHhcCCCcCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhhH
Q 029194 164 AKNK 167 (197)
Q Consensus 164 ~k~k 167 (197)
++++
T Consensus 161 ~~~~ 164 (164)
T cd01417 161 AKNK 164 (164)
T ss_pred hccC
Confidence 8863
No 4
>PTZ00436 60S ribosomal protein L19-like protein; Provisional
Probab=100.00 E-value=2.6e-77 Score=533.24 Aligned_cols=170 Identities=67% Similarity=1.101 Sum_probs=167.6
Q ss_pred CCcchhhHHHHHHHhccCCCceecCccchhHHHhhhhhHHHHhhhhcCceeecCCCCCChhHHHHHHHHHhcCcCCCcCC
Q 029194 1 MVSLKLQKRLSASVLKCGRGKVWLDPNEVNEISMANSRQNIRKLVKDGFIIRKPTKIHSRSRARRMKEAKRKGRHSGYGK 80 (197)
Q Consensus 1 M~~l~~QKRLAA~VL~cGk~rVWlDPne~~eIa~A~sR~~IRkLIkdG~Ii~kp~~~~SR~R~r~~~~ak~kGRh~G~Gk 80 (197)
|++|++||||||+||+||++|||||||+++||++||||+|||+||+||+|+++|++||||+|+|++++++++|||+|+||
T Consensus 1 M~dLklQKRLAAsVL~cGk~RVWiDPnel~eIa~AiTReDIRkLIkdGlIikKp~KGhSRgRaRkr~eaKrKGRhrG~Gs 80 (357)
T PTZ00436 1 MVSLKLQARLAADILRCGRHRVWLDPNEASEISNANSRKSVRKLIKDGLIIRKPVKVHSRSRWRHMKEAKSMGRHEGAGR 80 (357)
T ss_pred CcchHHHHHHHHHHhCCCCCceeeCHHHHHHHHHhhhHHHHHHHHHCCCeeecCcccCChHHHHHHHHHHHhCcCCCCCC
Confidence 89999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cccccccCCcchHHHHHHHHHHHHHHHHHHhcCCCChHhhHHHHhhhcCCccccHHHHHHHHHHHhhHHHHhhhhhHHHH
Q 029194 81 RKGTREARLPTKILWMRRMRVLRRLLRKYRESKKIDKHMYHDMYMKVKGNVFKNKRVLMESIHKSKAEKAREKTLSDQFE 160 (197)
Q Consensus 81 RKGt~~AR~p~K~~Wm~RiR~lRrlLr~~Re~~kID~~~Yr~LY~kaKGn~Fknk~~L~e~I~k~kae~~r~k~l~dQae 160 (197)
|+||+|||||+|++||+|||+||++|++|||+|+||+|+||+||+++|||+|+|++||++|||+.|+|+.+++.|+||+|
T Consensus 81 RKGTk~AR~P~K~~WIrRIRaLRRlLKklRd~gKIDkh~YR~LYrKAKGn~FKNK~~L~e~I~k~KaE~~R~K~L~dQ~e 160 (357)
T PTZ00436 81 REGTREARMPSKELWMRRLRILRRLLRKYREEKKIDRHIYRELYVKAKGNVFRNKRNLMEHIHKVKNEKKKERQLAEQLA 160 (357)
T ss_pred CcCcccccCcHHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHhcCCccCcHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHhhhHHHH
Q 029194 161 AKRAKNKASR 170 (197)
Q Consensus 161 A~r~k~k~~r 170 (197)
|+|.++++.|
T Consensus 161 ArR~k~~~~r 170 (357)
T PTZ00436 161 AKRLKDEQHR 170 (357)
T ss_pred HHHHHhhhhh
Confidence 9999987543
No 5
>PF01280 Ribosomal_L19e: Ribosomal protein L19e; InterPro: IPR000196 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 structural domain of the ribosomal protein L19 from eukaryotes, as well as L19e from archaea []. L19/L19e is absent in bacteria. L19/L19e is part of the large ribosomal subunit, whose structure has been determined in a number of eukaryotic and archaeal species []. L19/L19e is a multi-helical protein consisting of two different 3-helical domains connected by a long, partly helical linker.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3IZR_T 3O58_S 3O5H_S 3IZS_T 2WWA_J 1S1I_P 2WW9_J 2ZKR_7 4A1A_O 4A1C_O ....
Probab=100.00 E-value=1e-74 Score=472.37 Aligned_cols=148 Identities=68% Similarity=1.093 Sum_probs=131.0
Q ss_pred CcchhhHHHHHHHhccCCCceecCccchhHHHhhhhhHHHHhhhhcCceeecCCCCCChhHHHHHHHHHhcCcCCCcCCc
Q 029194 2 VSLKLQKRLSASVLKCGRGKVWLDPNEVNEISMANSRQNIRKLVKDGFIIRKPTKIHSRSRARRMKEAKRKGRHSGYGKR 81 (197)
Q Consensus 2 ~~l~~QKRLAA~VL~cGk~rVWlDPne~~eIa~A~sR~~IRkLIkdG~Ii~kp~~~~SR~R~r~~~~ak~kGRh~G~GkR 81 (197)
|+|++||||||+||+||++||||||||++||++||||+|||+||+||+|+++|++|||||||+++++++++|||+|+|+|
T Consensus 1 m~l~~QKRLAa~vL~~G~~rVw~DP~~~~eI~~A~tR~~IR~LIk~G~I~~k~~k~~Sr~R~r~~~~~r~kGr~~G~G~R 80 (148)
T PF01280_consen 1 MDLKLQKRLAASVLGCGKNRVWIDPNELEEIANAITREDIRKLIKDGLIIKKPVKGHSRGRARKRKEARRKGRHRGPGKR 80 (148)
T ss_dssp -STHHHHHHHHHHHTS-GGGEEE-STTHHHHHH--SHHHHHHHHHTTSEEE---S--STHHHHHHHHHHHCTTS-SSTTS
T ss_pred CccHHHHHHHHHHHCCCCCcEEeCHHHHHHHHhhhhHHHHHHHHHCCCeEeCCCCCCchHHHHHHHHHHhhccccccccc
Confidence 59999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccccccCCcchHHHHHHHHHHHHHHHHHHhcCCCChHhhHHHHhhhcCCccccHHHHHHHHHHHhhHH
Q 029194 82 KGTREARLPTKILWMRRMRVLRRLLRKYRESKKIDKHMYHDMYMKVKGNVFKNKRVLMESIHKSKAEK 149 (197)
Q Consensus 82 KGt~~AR~p~K~~Wm~RiR~lRrlLr~~Re~~kID~~~Yr~LY~kaKGn~Fknk~~L~e~I~k~kae~ 149 (197)
+||+|||+|+|+.||++||+||++|++|||+|+||+|+||+||++||||+|+|+++|++|||++++|+
T Consensus 81 kGt~~AR~~~K~~W~~riR~lRr~Lk~~r~~~kID~~~Yr~lY~kaKGn~Fkn~~~L~~~i~~~k~e~ 148 (148)
T PF01280_consen 81 KGTKNARMPEKELWMRRIRALRRLLKRLRDSGKIDRHMYRSLYRKAKGNVFKNKRHLMEHIHKLKAEK 148 (148)
T ss_dssp -S-HHHHS-HHHHHHHHHHHHHHHHHHHHHTTSS-HHHHHHHHHHHHTTS-SSHHHHHHHHHHHHHCH
T ss_pred cccccccccHHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHhcCCcccCHHHHHHHHHHhccCC
Confidence 99999999999999999999999999999999999999999999999999999999999999999985
No 6
>cd00481 Ribosomal_L19e Ribosomal protein L19e. L19e is found in the large ribosomal subunit of eukaryotes and archaea. L19e is distinct from the ribosomal subunit L19, which is found in prokaryotes. It consists of two small globular domains connected by an extended segment. It is located toward the surface of the large subunit, with one exposed end involved in forming the intersubunit bridge with the small subunit. The other exposed end is involved in forming the translocon binding site, along with L22, L23, L24, L29, and L31e subunits.
Probab=100.00 E-value=2.9e-73 Score=462.38 Aligned_cols=145 Identities=66% Similarity=1.102 Sum_probs=143.1
Q ss_pred chhhHHHHHHHhccCCCceecCccchhHHHhhhhhHHHHhhhhcCceeecCCCCCChhHHHHHHHHHhcCcCCCcCCccc
Q 029194 4 LKLQKRLSASVLKCGRGKVWLDPNEVNEISMANSRQNIRKLVKDGFIIRKPTKIHSRSRARRMKEAKRKGRHSGYGKRKG 83 (197)
Q Consensus 4 l~~QKRLAA~VL~cGk~rVWlDPne~~eIa~A~sR~~IRkLIkdG~Ii~kp~~~~SR~R~r~~~~ak~kGRh~G~GkRKG 83 (197)
|++||||||+||+||+++||||||+++||++||||+|||+||+||+|+++|++||||+|++++++++++|||+|+|||+|
T Consensus 1 l~~QkRLAA~vL~~G~~rVW~DP~~~~eI~~A~tR~dIR~LIkdG~I~~kp~kg~Sr~R~r~~~~~r~kGr~~G~G~RkG 80 (145)
T cd00481 1 LRLQKRLAADILKCGKNRVWIDPNELEEIANANTREDIRKLIKDGLIIKKPKKGHSRGRARKRHEARRKGRHRGPGSRKG 80 (145)
T ss_pred CcHHHHHHHHHHCCCCCceeeCHHHHHHHHHhhhHHHHHHHHHCCCeeecCCCCCChHHHHHHHHHHHhCcCCCCCCccC
Confidence 68999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccccCCcchHHHHHHHHHHHHHHHHHHhcCCCChHhhHHHHhhhcCCccccHHHHHHHHHHHhhH
Q 029194 84 TREARLPTKILWMRRMRVLRRLLRKYRESKKIDKHMYHDMYMKVKGNVFKNKRVLMESIHKSKAE 148 (197)
Q Consensus 84 t~~AR~p~K~~Wm~RiR~lRrlLr~~Re~~kID~~~Yr~LY~kaKGn~Fknk~~L~e~I~k~kae 148 (197)
|++||||+|+.||++||+||++|++|||+|+||+|+||.||++||||+|+|+++|++|||+.++|
T Consensus 81 t~~AR~p~K~~W~~riR~lRr~Lk~~R~~~kIdk~~Yr~lY~kaKG~~Fknk~~L~~~i~~~~~~ 145 (145)
T cd00481 81 TKGARMPSKELWIRRIRALRRLLKKLRDSGKIDKHTYRELYLKAKGNVFKNKRHLKEYIHKAKAE 145 (145)
T ss_pred ccccCCcHHHHHHHHHHHHHHHHHHHHHcCCCCHHHHHHHHHHhcCCCcCCHHHHHHHHHHhccC
Confidence 99999999999999999999999999999999999999999999999999999999999998764
No 7
>PRK08570 rpl19e 50S ribosomal protein L19e; Reviewed
Probab=100.00 E-value=4e-73 Score=463.71 Aligned_cols=147 Identities=42% Similarity=0.736 Sum_probs=145.2
Q ss_pred CCcchhhHHHHHHHhccCCCceecCccchhHHHhhhhhHHHHhhhhcCceeecCCCCCChhHHHHHHHHHhcCcCCCcCC
Q 029194 1 MVSLKLQKRLSASVLKCGRGKVWLDPNEVNEISMANSRQNIRKLVKDGFIIRKPTKIHSRSRARRMKEAKRKGRHSGYGK 80 (197)
Q Consensus 1 M~~l~~QKRLAA~VL~cGk~rVWlDPne~~eIa~A~sR~~IRkLIkdG~Ii~kp~~~~SR~R~r~~~~ak~kGRh~G~Gk 80 (197)
|++|++||||||+||+||+++||||||+++||++||||+|||+||+||+|+++|++||||+|++++++++++|||+|+||
T Consensus 1 M~~l~~qkRLAA~iL~~G~~rVw~DP~~~~eI~~A~tR~dIR~LI~~G~I~~kp~kg~Sr~R~r~~~~~r~kGr~~G~G~ 80 (150)
T PRK08570 1 MMDLSAQKRLAADILGVGVSRVWIDPEALEDVAEAITREDIRELIKEGVIKAKPKKGISRGRARERHEKRKKGRRRGPGS 80 (150)
T ss_pred CcchHHHHHHHHHHHCCCccceeeCHHHHHHHHHHhhHHHHHHHHHCCCeeecCccCCChHHHHHHHHHHHhCCCCCCCC
Confidence 89999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cccccccCCcchHHHHHHHHHHHHHHHHHHhcCCCChHhhHHHHhhhcCCccccHHHHHHHHHHHhh
Q 029194 81 RKGTREARLPTKILWMRRMRVLRRLLRKYRESKKIDKHMYHDMYMKVKGNVFKNKRVLMESIHKSKA 147 (197)
Q Consensus 81 RKGt~~AR~p~K~~Wm~RiR~lRrlLr~~Re~~kID~~~Yr~LY~kaKGn~Fknk~~L~e~I~k~ka 147 (197)
|+||+|||+|+|+.||++||+||++|++|||+|+||+|+||.||++||||+|+|+++|++||+....
T Consensus 81 RkGt~~AR~p~K~~W~~riR~lRr~Lk~lR~~~kId~~~Yr~lY~kaKGn~Fkn~~~L~~~i~~~~~ 147 (150)
T PRK08570 81 RKGKKGARTPKKERWINRIRALRRYLRELRDEGKIDRKTYRKLYRKAKGGEFRSVSHLKTYIEEHGL 147 (150)
T ss_pred CCCcccCCCCHHHHHHHHHHHHHHHHHHHHHcCCCCHHHHHHHHHHhcCCccCCHHHHHHHHHHhcc
Confidence 9999999999999999999999999999999999999999999999999999999999999998753
No 8
>cd01418 Ribosomal_L19e_A Ribosomal protein L19e, archaeal. L19e is found in the large ribosomal subunit of eukaryotes and archaea. L19e is distinct from the ribosomal subunit L19, which is found in prokaryotes. It consists of two small globular domains connected by an extended segment. It is located toward the surface of the large subunit, with one exposed end involved in forming the intersubunit bridge with the small subunit. The other exposed end is involved in forming the translocon binding site, along with L22, L23, L24, L29, and L31e subunits.
Probab=100.00 E-value=2.4e-71 Score=451.11 Aligned_cols=142 Identities=40% Similarity=0.723 Sum_probs=140.4
Q ss_pred chhhHHHHHHHhccCCCceecCccchhHHHhhhhhHHHHhhhhcCceeecCCCCCChhHHHHHHHHHhcCcCCCcCCccc
Q 029194 4 LKLQKRLSASVLKCGRGKVWLDPNEVNEISMANSRQNIRKLVKDGFIIRKPTKIHSRSRARRMKEAKRKGRHSGYGKRKG 83 (197)
Q Consensus 4 l~~QKRLAA~VL~cGk~rVWlDPne~~eIa~A~sR~~IRkLIkdG~Ii~kp~~~~SR~R~r~~~~ak~kGRh~G~GkRKG 83 (197)
|++||||||+||+||+++||||||+++||++||||+|||+||+||+|+++|++||||+|++++++++++|||+|+|||+|
T Consensus 1 l~~QkRLAA~iL~~G~~rVw~DP~~~~eI~~A~tR~dIR~LI~~G~I~~kp~kg~Sr~R~r~~~~~r~kGr~~G~G~RkG 80 (145)
T cd01418 1 LSSQRRLAADILGVGINRVWIDPERLEEVAEAITRDDIRALIKEGVIKAKPKKGISRGRLKERHEKRKKGRRRGPGSRKG 80 (145)
T ss_pred CcHHHHHHHHHHCCCCCeeeeChHHHHHHHHhhhHHHHHHHHHCCCeeecCCCCCCHHHHHHHHHHHHhCcCCCCCCCCC
Confidence 67999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccccCCcchHHHHHHHHHHHHHHHHHHhcCCCChHhhHHHHhhhcCCccccHHHHHHHHHHH
Q 029194 84 TREARLPTKILWMRRMRVLRRLLRKYRESKKIDKHMYHDMYMKVKGNVFKNKRVLMESIHKS 145 (197)
Q Consensus 84 t~~AR~p~K~~Wm~RiR~lRrlLr~~Re~~kID~~~Yr~LY~kaKGn~Fknk~~L~e~I~k~ 145 (197)
|+|||||+|+.||++||+||++|++|||+|+||+|+||.||++||||+|+|+++|++||...
T Consensus 81 t~~AR~p~K~~W~~riR~lRr~Lk~~R~~~kId~~~Yr~lY~kaKGn~Fkn~~~L~~~I~~~ 142 (145)
T cd01418 81 KKGARTPKKERWIKTIRALRRYLKELRDKGKIDKKTYRKLYRKAKGGSFRSLSHLKSYLKQH 142 (145)
T ss_pred ccccCCCHHHHHHHHHHHHHHHHHHHHHcCCCCHHHHHHHHHHhcCCCcCCHHHHHHHHHHh
Confidence 99999999999999999999999999999999999999999999999999999999999875
No 9
>COG2147 RPL19A Ribosomal protein L19E [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=9.6e-68 Score=430.72 Aligned_cols=149 Identities=50% Similarity=0.809 Sum_probs=146.6
Q ss_pred CCcchhhHHHHHHHhccCCCceecCccchhHHHhhhhhHHHHhhhhcCceeecCCCCCChhHHHHHHHHHhcCcCCCcCC
Q 029194 1 MVSLKLQKRLSASVLKCGRGKVWLDPNEVNEISMANSRQNIRKLVKDGFIIRKPTKIHSRSRARRMKEAKRKGRHSGYGK 80 (197)
Q Consensus 1 M~~l~~QKRLAA~VL~cGk~rVWlDPne~~eIa~A~sR~~IRkLIkdG~Ii~kp~~~~SR~R~r~~~~ak~kGRh~G~Gk 80 (197)
|+||++|+||||+|||||++|||||||+++||++|+||+|||.||+||+|+.+|++|+|++|+++++++++||||+||||
T Consensus 1 M~nl~~qkRLAA~il~vG~~Rvwidp~~~eei~~A~TR~dIr~LIk~g~I~~k~~kg~SrgR~rkr~~qkkkgr~rG~Gs 80 (150)
T COG2147 1 MSNLRTQKRLAADILGVGENRVWIDPNEIEEIASAITREDIRALIKDGVIKAKPKKGISRGRARKRHAQKKKGRRRGPGS 80 (150)
T ss_pred CchHHHHHHHHHHHHccCcceeeeChHHHHHHHHhhhHHHHHHHHHCCCeeeccccccchHHHHHHHHHHhcccCCCCCc
Confidence 88999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cccccccCCcchHHHHHHHHHHHHHHHHHHhcCCCChHhhHHHHhhhcCCccccHHHHHHHHHHHhhHH
Q 029194 81 RKGTREARLPTKILWMRRMRVLRRLLRKYRESKKIDKHMYHDMYMKVKGNVFKNKRVLMESIHKSKAEK 149 (197)
Q Consensus 81 RKGt~~AR~p~K~~Wm~RiR~lRrlLr~~Re~~kID~~~Yr~LY~kaKGn~Fknk~~L~e~I~k~kae~ 149 (197)
|+||++||||+|+.||.+||+||++|++|||+|+||+|+||.||+++|||.|+++++|.+||.+++.++
T Consensus 81 RKG~k~AR~p~K~~Wi~~IRalR~~Lr~lrd~gkIdk~~YR~lY~~aKGg~fk~~~~L~~~i~~~~~~k 149 (150)
T COG2147 81 RKGTKGARMPSKERWIKRIRALRRELRKLRDDGKIDKHTYRKLYRMAKGGAFKSKSHLKSYIEEAKLLK 149 (150)
T ss_pred cccccccCCCHHHHHHHHHHHHHHHHHHHHHcCCcCHHHHHHHHHHHcCCccccHHHHHHHHHHhcccc
Confidence 999999999999999999999999999999999999999999999999999999999999999987653
No 10
>TIGR01764 excise DNA binding domain, excisionase family. An excisionase, or Xis protein, is a small protein that binds and promotes excisive recombination; it is not enzymatically active. This model represents a number of putative excisionases and related proteins from temperate phage, plasmids, and transposons, as well as DNA binding domains of other proteins, such as a DNA modification methylase. This model identifies mostly small proteins and N-terminal regions of large proteins, but some proteins appear to have two copies. This domain appears similar, in both sequence and predicted secondary structure (PSIPRED) to the MerR family of transcriptional regulators (pfam00376).
Probab=69.22 E-value=3.1 Score=25.82 Aligned_cols=29 Identities=21% Similarity=0.331 Sum_probs=24.3
Q ss_pred ecCccchhHHHhhhhhHHHHhhhhcCceee
Q 029194 23 WLDPNEVNEISMANSRQNIRKLVKDGFIIR 52 (197)
Q Consensus 23 WlDPne~~eIa~A~sR~~IRkLIkdG~Ii~ 52 (197)
||++.|+.++-. +|+..|+.|+++|.|-.
T Consensus 1 ~lt~~e~a~~lg-is~~ti~~~~~~g~i~~ 29 (49)
T TIGR01764 1 YLTVEEAAEYLG-VSKDTVYRLIHEGELPA 29 (49)
T ss_pred CCCHHHHHHHHC-CCHHHHHHHHHcCCCCe
Confidence 677888888876 78999999999998765
No 11
>PF12728 HTH_17: Helix-turn-helix domain
Probab=68.79 E-value=3.3 Score=26.97 Aligned_cols=29 Identities=24% Similarity=0.345 Sum_probs=24.8
Q ss_pred ecCccchhHHHhhhhhHHHHhhhhcCceee
Q 029194 23 WLDPNEVNEISMANSRQNIRKLVKDGFIIR 52 (197)
Q Consensus 23 WlDPne~~eIa~A~sR~~IRkLIkdG~Ii~ 52 (197)
||++.|+-++-. +|+..|+++++.|.|..
T Consensus 1 ~lt~~e~a~~l~-is~~tv~~~~~~g~i~~ 29 (51)
T PF12728_consen 1 YLTVKEAAELLG-ISRSTVYRWIRQGKIPP 29 (51)
T ss_pred CCCHHHHHHHHC-cCHHHHHHHHHcCCCCe
Confidence 688899999888 79999999999997643
No 12
>PRK00247 putative inner membrane protein translocase component YidC; Validated
Probab=58.56 E-value=84 Score=30.36 Aligned_cols=69 Identities=16% Similarity=0.254 Sum_probs=37.8
Q ss_pred hHHHHHHHHHHHHHHHHHHhcC---CCChHhhHHHHhhhcCCccccHHHHHHHHHHHhhHHHHhhhhhHH-HHHHHhhhH
Q 029194 92 KILWMRRMRVLRRLLRKYRESK---KIDKHMYHDMYMKVKGNVFKNKRVLMESIHKSKAEKAREKTLSDQ-FEAKRAKNK 167 (197)
Q Consensus 92 K~~Wm~RiR~lRrlLr~~Re~~---kID~~~Yr~LY~kaKGn~Fknk~~L~e~I~k~kae~~r~k~l~dQ-aeA~r~k~k 167 (197)
+..|..+.+..+..++..|... .|.+..+..|..- |...=.+.=...+++|+++|.++.+ -||.|.-++
T Consensus 291 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~-------~~~~~~~~~~~~~~~k~~~k~~~~~~~~~~~~~~~ 363 (429)
T PRK00247 291 RAQYREKQKEKKAFLWTLRRNRLRMIITPWRAPELHAE-------NAEIKKTRTAEKNEAKARKKEIAQKRRAAEREINR 363 (429)
T ss_pred HHHHHHHHHHHHHHHHHHHhccccccCCcccHHHHHHH-------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4456666666655555555544 7888877777432 2222233334446667777766543 344444444
No 13
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=55.18 E-value=5.3 Score=25.69 Aligned_cols=15 Identities=27% Similarity=0.809 Sum_probs=12.4
Q ss_pred CceecCccchhHHHh
Q 029194 20 GKVWLDPNEVNEISM 34 (197)
Q Consensus 20 ~rVWlDPne~~eIa~ 34 (197)
.-||||++|++.|.+
T Consensus 26 ~G~W~d~~el~~~~e 40 (41)
T PF13453_consen 26 GGIWFDAGELEKLLE 40 (41)
T ss_pred CeEEccHHHHHHHHh
Confidence 569999999988753
No 14
>PF13880 Acetyltransf_13: ESCO1/2 acetyl-transferase
Probab=49.28 E-value=5.4 Score=29.39 Aligned_cols=14 Identities=29% Similarity=1.037 Sum_probs=12.0
Q ss_pred ccCCCceecCccch
Q 029194 16 KCGRGKVWLDPNEV 29 (197)
Q Consensus 16 ~cGk~rVWlDPne~ 29 (197)
-||.++||..|..-
T Consensus 5 ~~GI~RIWV~~~~R 18 (70)
T PF13880_consen 5 VCGISRIWVSPSHR 18 (70)
T ss_pred EEEeEEEEeChhhh
Confidence 59999999999763
No 15
>TIGR02075 pyrH_bact uridylate kinase. This protein, also called UMP kinase, converts UMP to UDP by adding a phosphate from ATP. It is the first step in pyrimidine biosynthesis. GTP is an allosteric activator. In a large fraction of all bacterial genomes, the gene tends to be located immediately downstream of elongation factor Ts and upstream of ribosome recycling factor. A related protein family, believed to be equivalent in function and found in the archaea and in spirochetes, is described by a separate model, TIGR02076.
Probab=43.32 E-value=26 Score=29.86 Aligned_cols=48 Identities=15% Similarity=0.126 Sum_probs=38.1
Q ss_pred hhhHHH-HHHHhccCCCceecCccchhHHHhhhhhHHHHhhhhcCceee
Q 029194 5 KLQKRL-SASVLKCGRGKVWLDPNEVNEISMANSRQNIRKLVKDGFIIR 52 (197)
Q Consensus 5 ~~QKRL-AA~VL~cGk~rVWlDPne~~eIa~A~sR~~IRkLIkdG~Ii~ 52 (197)
+++-+| +..+...|.+-++|+|.....+..-.+.+.+..|++.|.|..
T Consensus 77 ~l~~~l~~~~L~~~Gi~a~~l~~~~~~~~~~~~~~~~i~~ll~~g~VpV 125 (233)
T TIGR02075 77 VINGLALRDALEKLGVKTRVLSAISMPQICESYIRRKAIKHLEKGKVVI 125 (233)
T ss_pred HHHHHHHHHHHHhCCCCcEEeccccCCCCccccCHHHHHHHHHCCCEEE
Confidence 456665 677778999999999998765555567899999999999843
No 16
>PRK05920 aromatic acid decarboxylase; Validated
Probab=41.03 E-value=32 Score=29.71 Aligned_cols=47 Identities=32% Similarity=0.289 Sum_probs=36.6
Q ss_pred HHHHHHhccCCCceecCccchhHHHhhhhhHHHHhhhhcCceeecCCCCC
Q 029194 9 RLSASVLKCGRGKVWLDPNEVNEISMANSRQNIRKLVKDGFIIRKPTKIH 58 (197)
Q Consensus 9 RLAA~VL~cGk~rVWlDPne~~eIa~A~sR~~IRkLIkdG~Ii~kp~~~~ 58 (197)
+.|...|+.+. .|.|=|.+... ++.+++++..|-..|.++.-|+.+.
T Consensus 121 ~~a~~~L~~~~-pvvi~P~~m~~--~~~~~~nl~~L~~~G~~ii~P~~g~ 167 (204)
T PRK05920 121 RAADVVLKERR-KLILVPRETPL--SLIHLENMLKLAEAGAIILPAIPAF 167 (204)
T ss_pred HHHHHHHhcCC-CEEEEeCCCCC--CHHHHHHHHHHHHCCCEEeCCcccc
Confidence 55556788777 55555765444 7889999999999999999999874
No 17
>PF01479 S4: S4 domain; InterPro: IPR002942 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 [, ]. The S4 domain is a small domain consisting of 60-65 amino acid residues that was detected in the bacterial ribosomal protein S4, eukaryotic ribosomal S9, two families of pseudouridine synthases, a novel family of predicted RNA methylases, a yeast protein containing a pseudouridine synthetase and a deaminase domain, bacterial tyrosyl-tRNA synthetases, and a number of uncharacterised, small proteins that may be involved in translation regulation []. The S4 domain probably mediates binding to RNA.; GO: 0003723 RNA binding; PDB: 3BBU_A 1DM9_B 2K6P_A 3U5G_E 3U5C_E 3IZB_D 2XZM_D 2XZN_D 3O30_E 3O2Z_E ....
Probab=38.92 E-value=23 Score=22.67 Aligned_cols=27 Identities=26% Similarity=0.450 Sum_probs=20.6
Q ss_pred hHHHhhhhhHHHHhhhhcCceeecCCC
Q 029194 30 NEISMANSRQNIRKLVKDGFIIRKPTK 56 (197)
Q Consensus 30 ~eIa~A~sR~~IRkLIkdG~Ii~kp~~ 56 (197)
.+...+.||.++++||+.|.|..--..
T Consensus 8 ~~~~~~~sr~~a~~~I~~g~V~VNg~~ 34 (48)
T PF01479_consen 8 SRLGLASSRSEARRLIKQGRVKVNGKV 34 (48)
T ss_dssp HHTTSSSSHHHHHHHHHTTTEEETTEE
T ss_pred HHcCCcCCHHHHHHhcCCCEEEECCEE
Confidence 344557799999999999998765443
No 18
>TIGR01610 phage_O_Nterm phage replication protein O, N-terminal domain. This model represents the N-terminal region of the phage lambda replication protein O and homologous regions of other phage proteins.
Probab=33.81 E-value=49 Score=24.65 Aligned_cols=38 Identities=18% Similarity=0.305 Sum_probs=26.2
Q ss_pred ccCCCceecCccchhHHHhhhhhHH----HHhhhhcCceeecC
Q 029194 16 KCGRGKVWLDPNEVNEISMANSRQN----IRKLVKDGFIIRKP 54 (197)
Q Consensus 16 ~cGk~rVWlDPne~~eIa~A~sR~~----IRkLIkdG~Ii~kp 54 (197)
|.++..+++.+.|+.++... ||+. |..|.++|+|....
T Consensus 40 G~~~~~~~is~~eLa~~~g~-sr~tVsr~L~~Le~~GlI~r~~ 81 (95)
T TIGR01610 40 GWNKKQDRVTATVIAELTGL-SRTHVSDAIKSLARRRIIFRQG 81 (95)
T ss_pred CccccCCccCHHHHHHHHCc-CHHHHHHHHHHHHHCCCeeeec
Confidence 44556777777777766554 4544 55799999998654
No 19
>PRK06029 3-octaprenyl-4-hydroxybenzoate carboxy-lyase; Provisional
Probab=33.37 E-value=53 Score=27.85 Aligned_cols=46 Identities=26% Similarity=0.255 Sum_probs=35.7
Q ss_pred HHHHHHhccCCCceecCccchhHHHhhhhhHHHHhhhhcCceeecCCCC
Q 029194 9 RLSASVLKCGRGKVWLDPNEVNEISMANSRQNIRKLVKDGFIIRKPTKI 57 (197)
Q Consensus 9 RLAA~VL~cGk~rVWlDPne~~eIa~A~sR~~IRkLIkdG~Ii~kp~~~ 57 (197)
+.|...|.+++ .|.|=|. +--.+..+.+++.+|-+.|.++..|..|
T Consensus 106 ~~a~~~L~~~~-pvii~P~--~M~~~p~~~~Nl~~L~~~G~~vi~P~~g 151 (185)
T PRK06029 106 RAADVMLKERR-RLVLCVR--ETPLHLGHLRNMTKLAEMGAIIMPPVPA 151 (185)
T ss_pred HHHHHHHhcCC-CEEEEec--cccCCHHHHHHHHHHHHCcCEEECCCcc
Confidence 44556777765 5555574 4566889999999999999999999876
No 20
>PF12802 MarR_2: MarR family; PDB: 3ECO_B 2QWW_B 3KP6_B 3KP4_B 3KP2_A 3KP5_A 3KP3_B 3KP7_A 3NQO_B 3K0L_B ....
Probab=33.25 E-value=38 Score=22.17 Aligned_cols=52 Identities=23% Similarity=0.283 Sum_probs=31.0
Q ss_pred hHHHHHHHhccCCCceecCccchhH---HHhhhhhHHHHhhhhcCceeecCCCCCCh
Q 029194 7 QKRLSASVLKCGRGKVWLDPNEVNE---ISMANSRQNIRKLVKDGFIIRKPTKIHSR 60 (197)
Q Consensus 7 QKRLAA~VL~cGk~rVWlDPne~~e---Ia~A~sR~~IRkLIkdG~Ii~kp~~~~SR 60 (197)
|-++-..|..+|.. ++-+.++.+ ++-...-.-|.+|++.|+|.+.+.....|
T Consensus 7 q~~vL~~l~~~~~~--~~t~~~la~~l~~~~~~vs~~v~~L~~~Glv~r~~~~~D~R 61 (62)
T PF12802_consen 7 QFRVLMALARHPGE--ELTQSELAERLGISKSTVSRIVKRLEKKGLVERERDPGDRR 61 (62)
T ss_dssp HHHHHHHHHHSTTS--GEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEE-SSSTT
T ss_pred HHHHHHHHHHCCCC--CcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEeCCCCCCC
Confidence 44445555555554 333444333 22334446788999999999998877665
No 21
>PHA00616 hypothetical protein
Probab=31.89 E-value=27 Score=23.76 Aligned_cols=17 Identities=24% Similarity=0.634 Sum_probs=15.1
Q ss_pred CCccccHHHHHHHHHHH
Q 029194 129 GNVFKNKRVLMESIHKS 145 (197)
Q Consensus 129 Gn~Fknk~~L~e~I~k~ 145 (197)
|..|.+++.|..|+.+.
T Consensus 8 G~~F~~~s~l~~H~r~~ 24 (44)
T PHA00616 8 GGIFRKKKEVIEHLLSV 24 (44)
T ss_pred hHHHhhHHHHHHHHHHh
Confidence 78999999999999664
No 22
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=31.49 E-value=38 Score=21.53 Aligned_cols=25 Identities=24% Similarity=0.578 Sum_probs=18.1
Q ss_pred HHhhhhhHHHHhhhhcCceeecCCC
Q 029194 32 ISMANSRQNIRKLVKDGFIIRKPTK 56 (197)
Q Consensus 32 Ia~A~sR~~IRkLIkdG~Ii~kp~~ 56 (197)
|+.+.-+..+..|.++|+|...|-.
T Consensus 32 vs~~tv~~~l~~L~~~g~i~~~~~~ 56 (60)
T smart00345 32 VSRTTVREALSRLEAEGLVQRRPGS 56 (60)
T ss_pred CCHHHHHHHHHHHHHCCCEEEecCC
Confidence 3445567778889999999876643
No 23
>cd04254 AAK_UMPK-PyrH-Ec UMP kinase (UMPK)-Ec, the microbial/chloroplast uridine monophosphate kinase (uridylate kinase) enzyme that catalyzes UMP phosphorylation and plays a key role in pyrimidine nucleotide biosynthesis; regulation of this process is via feed-back control and via gene repression of carbamoyl phosphate synthetase (the first enzyme of the pyrimidine biosynthesis pathway). The UMP kinase of E. coli (Ec) is known to function as a homohexamer, with GTP and UTP being allosteric effectors. Like other related enzymes (carbamate kinase, aspartokinase, and N-acetylglutamate kinase) the E. coli and most bacterial and chloroplast UMPKs (this CD) have a conserved, N-terminal, lysine residue proposed to function in the catalysis of the phosphoryl group transfer, whereas most archaeal UMPKs appear to lack this residue and the Pyrococcus furiosus structure has an additional Mg ion bound to the ATP molecule which is proposed to function as the catalysis instead. Members of this CD be
Probab=28.80 E-value=56 Score=27.72 Aligned_cols=44 Identities=9% Similarity=0.130 Sum_probs=35.6
Q ss_pred HHHHHHhccCCCceecCccchhHHHhhhhhHHHHhhhhcCceee
Q 029194 9 RLSASVLKCGRGKVWLDPNEVNEISMANSRQNIRKLVKDGFIIR 52 (197)
Q Consensus 9 RLAA~VL~cGk~rVWlDPne~~eIa~A~sR~~IRkLIkdG~Ii~ 52 (197)
-|++.+...|.+-+||+|-+++.+.....-+.+..+++.|.|..
T Consensus 81 ll~~~L~~~Gv~a~~l~~~~~~~~~~~~~~~~l~~~l~~g~ipV 124 (231)
T cd04254 81 ALQDALESLGVKTRVMSAIPMQGVAEPYIRRRAIRHLEKGRVVI 124 (231)
T ss_pred HHHHHHHHcCCCeEEEcHHHhhhhhcccCHHHHHHHHHCCCEEE
Confidence 35667778999999999999876655566789999999998743
No 24
>PF09851 SHOCT: Short C-terminal domain; InterPro: IPR018649 This family of hypothetical prokaryotic proteins has no known function.
Probab=28.44 E-value=70 Score=19.60 Aligned_cols=20 Identities=15% Similarity=0.320 Sum_probs=16.9
Q ss_pred HHHHHHHhcCCCChHhhHHH
Q 029194 104 RLLRKYRESKKIDKHMYHDM 123 (197)
Q Consensus 104 rlLr~~Re~~kID~~~Yr~L 123 (197)
..|+.+.+.|.|+...|...
T Consensus 6 ~~L~~l~~~G~IseeEy~~~ 25 (31)
T PF09851_consen 6 EKLKELYDKGEISEEEYEQK 25 (31)
T ss_pred HHHHHHHHcCCCCHHHHHHH
Confidence 45788999999999999764
No 25
>COG3592 Uncharacterized conserved protein [Function unknown]
Probab=28.30 E-value=28 Score=26.18 Aligned_cols=19 Identities=32% Similarity=0.789 Sum_probs=14.7
Q ss_pred HHHHhccCCCceecCccchh
Q 029194 11 SASVLKCGRGKVWLDPNEVN 30 (197)
Q Consensus 11 AA~VL~cGk~rVWlDPne~~ 30 (197)
+++|+++|..= ||+|+..+
T Consensus 35 n~~vF~~~rkP-WI~Pd~~~ 53 (74)
T COG3592 35 NPKVFNLGRKP-WIMPDAVD 53 (74)
T ss_pred CHhhcccCCCC-ccCCCCCC
Confidence 56788888765 99998754
No 26
>PRK11548 outer membrane biogenesis protein BamE; Provisional
Probab=26.97 E-value=44 Score=25.83 Aligned_cols=26 Identities=23% Similarity=0.440 Sum_probs=23.0
Q ss_pred eecCccchhHHHhhhhhHHHHhhhhc
Q 029194 22 VWLDPNEVNEISMANSRQNIRKLVKD 47 (197)
Q Consensus 22 VWlDPne~~eIa~A~sR~~IRkLIkd 47 (197)
-++||+.+++|.--.|+++|+.|+-.
T Consensus 36 ~~~~~~~l~~l~~GmTk~qV~~lLGt 61 (113)
T PRK11548 36 NYLTPNDVAKIHVGMTQQQVAYTLGT 61 (113)
T ss_pred ccCCHHHHHHhcCCCCHHHHHHHcCC
Confidence 37899999999999999999999843
No 27
>TIGR02988 YaaA_near_RecF S4 domain protein YaaA. This small protein has a single S4 domain (pfam01479), as do bacterial ribosomal protein S4, some pseudouridine synthases, tyrosyl-tRNA synthetases. The S4 domain may bind RNA. Members of this protein family are found almost exclusively in the Firmicutes, and almost invariably just a few nucleotides upstream of the gene for the DNA replication and repair protein RecF. The few members of this family that are not near recF are found instead near dnaA and/or dnaN, the usual neighbors of recF, near the origin of replication. The conserved location suggests a possible role in replication in the Firmicutes lineage.
Probab=25.31 E-value=52 Score=22.18 Aligned_cols=21 Identities=5% Similarity=0.132 Sum_probs=17.5
Q ss_pred hhhhHHHHhhhhcCceeecCC
Q 029194 35 ANSRQNIRKLVKDGFIIRKPT 55 (197)
Q Consensus 35 A~sR~~IRkLIkdG~Ii~kp~ 55 (197)
+.||..+++||++|.|..--.
T Consensus 21 ~~SR~~~k~li~~G~V~VNg~ 41 (59)
T TIGR02988 21 IDSGGQAKWFLQENEVLVNGE 41 (59)
T ss_pred ccCHHHHHHHHHcCCEEECCE
Confidence 349999999999999988443
No 28
>PF08535 KorB: KorB domain; InterPro: IPR013741 This entry contains several KorB transcriptional repressor proteins. The korB gene is a major regulatory element in the replication and maintenance of broad host-range plasmid RK2. It negatively controls the replication gene trfA, the host-lethal determinants kilA and kilB, and the korA-korB operon []. This domain includes the DNA-binding HTH motif []. ; PDB: 1R71_C.
Probab=25.24 E-value=62 Score=23.78 Aligned_cols=39 Identities=23% Similarity=0.600 Sum_probs=24.1
Q ss_pred hhHHHHHHHhccCCCceecCccchhHHHhhhhhHHHHhhhhcCcee
Q 029194 6 LQKRLSASVLKCGRGKVWLDPNEVNEISMANSRQNIRKLVKDGFII 51 (197)
Q Consensus 6 ~QKRLAA~VL~cGk~rVWlDPne~~eIa~A~sR~~IRkLIkdG~Ii 51 (197)
.|.-+|..| |+++-|+ .+-++-+.-=++|+.|+.+|.|.
T Consensus 5 tq~eIA~~l---Gks~s~V----s~~l~Ll~lP~~i~~~v~~g~~~ 43 (93)
T PF08535_consen 5 TQEEIAKRL---GKSRSWV----SNHLALLDLPEEIKELVRSGRIS 43 (93)
T ss_dssp -HHHHHHHT---T--HHHH----HHHHGGGS--HHHHHHHHTTS--
T ss_pred CHHHHHHHH---CCCHHHH----HHHHHHHcCCHHHHHHHHcCCCc
Confidence 466777765 9999887 34455556667899999999764
No 29
>PRK00083 frr ribosome recycling factor; Reviewed
Probab=24.42 E-value=3.9e+02 Score=22.63 Aligned_cols=84 Identities=23% Similarity=0.312 Sum_probs=55.6
Q ss_pred eecCccchhHHHhhhhhHHHH-hhhhcCceeecCCCCCChhHHH-HHHHHHhcCcCCCcCCcccccccCCcchHHHHHHH
Q 029194 22 VWLDPNEVNEISMANSRQNIR-KLVKDGFIIRKPTKIHSRSRAR-RMKEAKRKGRHSGYGKRKGTREARLPTKILWMRRM 99 (197)
Q Consensus 22 VWlDPne~~eIa~A~sR~~IR-kLIkdG~Ii~kp~~~~SR~R~r-~~~~ak~kGRh~G~GkRKGt~~AR~p~K~~Wm~Ri 99 (197)
+| ||+-+..|..|+.-.++- .-+.||-.++-|+.--+.-|-. --+.++..+ +.+-..|
T Consensus 69 p~-D~~~i~~I~kAI~~s~lgl~P~~dg~~Iri~iP~lT~E~R~elvK~~k~~~-------------------E~aKv~i 128 (185)
T PRK00083 69 PW-DKSMLKAIEKAIRASDLGLNPSNDGTVIRLPIPPLTEERRKELVKQVKKEA-------------------EEAKVAI 128 (185)
T ss_pred eC-CHhHHHHHHHHHHHCCCCCCcccCCCEEEecCCCCCHHHHHHHHHHHHHHH-------------------HHHHHHH
Confidence 45 999999999999876653 3345888888887666654433 223333322 2344578
Q ss_pred HHHHHH----HHHHHhcCCCChHhhHHHHh
Q 029194 100 RVLRRL----LRKYRESKKIDKHMYHDMYM 125 (197)
Q Consensus 100 R~lRrl----Lr~~Re~~kID~~~Yr~LY~ 125 (197)
|-+|+- |+++...|.|....++.+..
T Consensus 129 RniRr~~~~~iKk~~k~~~iseD~~k~~e~ 158 (185)
T PRK00083 129 RNIRRDANDKLKKLEKDKEISEDELKRAED 158 (185)
T ss_pred HHHHHHHHHHHHHHhhcCCCChHHHHHHHH
Confidence 888876 66666677888888777655
No 30
>TIGR00421 ubiX_pad polyprenyl P-hydroxybenzoate and phenylacrylic acid decarboxylases. In E.coli, the protein UbiX (3-octaprenyl-4-hydroxybenzoate carboxy-lyase) has been shown to be involved in the third step of ubiquinone biosynthesis. It catalyzes the reaction [3-octaprenyl-4-hydroxybenzoate = 2-octaprenylphenol + CO2]. The knockout of the homologous protein in yeast confers sensitivity to phenylacrylic acid. Members are not restricted to ubiquinone-synthesizing species. This family represents a distinct clade within the flavoprotein family of Pfam model pfam02441.
Probab=24.22 E-value=95 Score=25.98 Aligned_cols=47 Identities=30% Similarity=0.295 Sum_probs=35.4
Q ss_pred HHHHHHhccCCCceecCccchhHHHhhhhhHHHHhhhhcCceeecCCCCC
Q 029194 9 RLSASVLKCGRGKVWLDPNEVNEISMANSRQNIRKLVKDGFIIRKPTKIH 58 (197)
Q Consensus 9 RLAA~VL~cGk~rVWlDPne~~eIa~A~sR~~IRkLIkdG~Ii~kp~~~~ 58 (197)
+.|...|++++ .|.|=|.+. -.++.+.+++..|-+.|.++.-|..+.
T Consensus 103 ~~a~~~L~~~~-pv~i~P~~m--~~~~~~~~Nl~~L~~~G~~ii~P~~g~ 149 (181)
T TIGR00421 103 RAADVCLKERR-KLVLVPRET--PLNSIHLENMLRLSRMGAIILPPMPAF 149 (181)
T ss_pred HHHHHHHhcCC-CEEEEeCCC--cCCHHHHHHHHHHHHCCCEEECCCCcc
Confidence 44555778775 555557544 458888999999999999999998763
No 31
>PF15319 RHINO: RAD9, RAD1, HUS1-interacting nuclear orphan protein
Probab=24.17 E-value=27 Score=31.35 Aligned_cols=34 Identities=35% Similarity=0.622 Sum_probs=25.9
Q ss_pred cccccCCcchHHHHHHHHHHHHHHHHHHhcCCCChHhh
Q 029194 83 GTREARLPTKILWMRRMRVLRRLLRKYRESKKIDKHMY 120 (197)
Q Consensus 83 Gt~~AR~p~K~~Wm~RiR~lRrlLr~~Re~~kID~~~Y 120 (197)
-|-.--..-|++|-+| +-||..|||.|++++..|
T Consensus 201 DTPE~~YGiKvTWRRR----~hL~~yLrerGkL~~sq~ 234 (236)
T PF15319_consen 201 DTPEEKYGIKVTWRRR----RHLLAYLRERGKLSRSQF 234 (236)
T ss_pred cCCcccccceeeeecc----HHHHHHHHHhCccchhhc
Confidence 3444455669999776 478999999999998764
No 32
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=23.94 E-value=60 Score=17.55 Aligned_cols=16 Identities=25% Similarity=0.497 Sum_probs=13.2
Q ss_pred CCccccHHHHHHHHHH
Q 029194 129 GNVFKNKRVLMESIHK 144 (197)
Q Consensus 129 Gn~Fknk~~L~e~I~k 144 (197)
|-+|.+...|..||..
T Consensus 7 ~~~f~~~~~l~~H~~~ 22 (23)
T PF00096_consen 7 GKSFSSKSNLKRHMRR 22 (23)
T ss_dssp TEEESSHHHHHHHHHH
T ss_pred CCccCCHHHHHHHHhH
Confidence 5679999999999853
No 33
>PF14468 DUF4427: Protein of unknown function (DUF4427)
Probab=23.91 E-value=55 Score=27.07 Aligned_cols=33 Identities=21% Similarity=0.399 Sum_probs=25.4
Q ss_pred HHHhccCCCceecCccchhHHHhhhhhHHHHhhhhcCceeec
Q 029194 12 ASVLKCGRGKVWLDPNEVNEISMANSRQNIRKLVKDGFIIRK 53 (197)
Q Consensus 12 A~VL~cGk~rVWlDPne~~eIa~A~sR~~IRkLIkdG~Ii~k 53 (197)
.-++.-|.-.||| |+ |+.+=+|.||++|.|+.-
T Consensus 30 ~~~~e~G~~wvWi-~D--------N~~~~vRALl~~grV~v~ 62 (132)
T PF14468_consen 30 DYDREFGNAWVWI-HD--------NQSEVVRALLQAGRVKVN 62 (132)
T ss_pred cchhhcCceEEEE-ec--------CcCHHHHHHHHcCceeec
Confidence 3456789999999 33 456678999999998754
No 34
>PF06353 DUF1062: Protein of unknown function (DUF1062); InterPro: IPR009412 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=23.68 E-value=59 Score=26.81 Aligned_cols=23 Identities=30% Similarity=0.673 Sum_probs=20.5
Q ss_pred hhhhhHHHHhhhhcCceeecCCC
Q 029194 34 MANSRQNIRKLVKDGFIIRKPTK 56 (197)
Q Consensus 34 ~A~sR~~IRkLIkdG~Ii~kp~~ 56 (197)
.-+||.+|..|+++|.|...|.+
T Consensus 113 L~lSrs~l~~l~~~G~I~~~~~~ 135 (142)
T PF06353_consen 113 LGLSRSRLKRLIEQGLIRSDPDK 135 (142)
T ss_pred hCcCHHHHHHHHHCCCEEecCcc
Confidence 35799999999999999998876
No 35
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=21.73 E-value=78 Score=19.46 Aligned_cols=25 Identities=24% Similarity=0.411 Sum_probs=18.1
Q ss_pred HHhhhhhHHHHhhhhcCceeecCCC
Q 029194 32 ISMANSRQNIRKLVKDGFIIRKPTK 56 (197)
Q Consensus 32 Ia~A~sR~~IRkLIkdG~Ii~kp~~ 56 (197)
++.+.-+..|..|.+.|+|...+.-
T Consensus 26 ~s~~tv~~~l~~L~~~g~i~~~~~~ 50 (53)
T smart00420 26 VSEMTIRRDLNKLEEQGLLTRVHGG 50 (53)
T ss_pred CCHHHHHHHHHHHHHCCCEEEeecC
Confidence 3445567788899999999876543
No 36
>PF01047 MarR: MarR family; InterPro: IPR000835 The MarR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 135 amino acids present in transcription regulators of the MarR/SlyA family, involved in the development of antibiotic resistance. This family of transcription regulators is named after Escherichia coli MarR, a repressor of genes which activate the multiple antibiotic resistance and oxidative stress regulons, and after slyA from Salmonella typhimurium and E. coli, a transcription regulator that is required for virulence and survival in the macrophage environment. Regulators with the MarR-type HTH domain are present in bacteria and archaea and control a variety of biological functions, including resistance to multiple antibiotics, household disinfectants, organic solvents, oxidative stress agents and regulation of the virulence factor synthesis in pathogens of humans and plants. Many of the MarR-like regulators respond to aromatic compounds [, , ]. The crystal structures of MarR, MexR and SlyA have been determined and show a winged HTH DNA-binding core flanked by helices involved in dimerisation. The DNA-binding domains are ascribed to the superfamily of winged helix proteins, containing a three (four)-helix (H) bundle and a three-stranded antiparallel beta-sheet (B) in the topology: H1-(H1')-H2-B1-H3-H4-B2-B3-H5-H6. Helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing. Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. The helices 1, 5 and 6 are involved in dimerisation, as most MarR-like transcription regulators form dimers [, ]. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1JGS_A 2NYX_D 2PEX_B 2PFB_A 3BPX_A 3BPV_A 2BV6_A 3BJA_A 3E6M_B 2ETH_A ....
Probab=21.48 E-value=61 Score=21.16 Aligned_cols=26 Identities=23% Similarity=0.300 Sum_probs=19.2
Q ss_pred hhhhhHHHHhhhhcCceeecCCCCCC
Q 029194 34 MANSRQNIRKLVKDGFIIRKPTKIHS 59 (197)
Q Consensus 34 ~A~sR~~IRkLIkdG~Ii~kp~~~~S 59 (197)
.++.-.-|.+|++.|+|.+.+....-
T Consensus 31 ~~~~t~~i~~L~~~g~I~r~~~~~D~ 56 (59)
T PF01047_consen 31 RSTVTRIIKRLEKKGLIERERDPDDR 56 (59)
T ss_dssp HHHHHHHHHHHHHTTSEEEEEETTET
T ss_pred hhHHHHHHHHHHHCCCEEeccCCCCC
Confidence 34445678999999999988765443
No 37
>PF13412 HTH_24: Winged helix-turn-helix DNA-binding; PDB: 1I1G_B 2IA0_B 3I4P_A 2GQQ_A 2L4A_A 2CFX_B 2DBB_B 2EFO_A 2EFQ_A 2PN6_A ....
Probab=21.22 E-value=68 Score=20.39 Aligned_cols=20 Identities=30% Similarity=0.466 Sum_probs=15.4
Q ss_pred HHhhhhhHHHHhhhhcCcee
Q 029194 32 ISMANSRQNIRKLVKDGFII 51 (197)
Q Consensus 32 Ia~A~sR~~IRkLIkdG~Ii 51 (197)
|+.+.....+++|+++|+|.
T Consensus 29 is~~tv~~~l~~L~~~g~I~ 48 (48)
T PF13412_consen 29 ISRSTVNRYLKKLEEKGLIE 48 (48)
T ss_dssp S-HHHHHHHHHHHHHTTSEE
T ss_pred CCHHHHHHHHHHHHHCcCcC
Confidence 45566778899999999984
No 38
>PF10625 UspB: Universal stress protein B (UspB); InterPro: IPR019598 Universal stress protein B (UspB) in Escherichia coli is a 14kDa protein which is predicted to be an integral membrane protein. Over expression of UspB results in cell death in stationary phase, and mutants of UspB are sensitive to ethanol exposure during stationary phase [].
Probab=20.86 E-value=1.4e+02 Score=23.95 Aligned_cols=32 Identities=38% Similarity=0.537 Sum_probs=24.6
Q ss_pred HHHHHHHHHHHHHHHHhcCCCChHhhHHHHhhhcCCccc
Q 029194 95 WMRRMRVLRRLLRKYRESKKIDKHMYHDMYMKVKGNVFK 133 (197)
Q Consensus 95 Wm~RiR~lRrlLr~~Re~~kID~~~Yr~LY~kaKGn~Fk 133 (197)
+++=.=.||-+|--|||...+ ||..+.||-|=
T Consensus 19 m~RY~SsLR~LL~imR~~dPL-------LYQ~VDG~GFF 50 (107)
T PF10625_consen 19 MARYFSSLRALLYIMREADPL-------LYQQVDGNGFF 50 (107)
T ss_pred HHHHHHHHHHHHHHHhcCCcH-------HHHhccCCCce
Confidence 556667899999999995443 77788888773
No 39
>smart00099 btg1 tob/btg1 family. The tob/btg1 is a family of proteins that inhibit cell proliferation.
Probab=20.67 E-value=36 Score=27.04 Aligned_cols=10 Identities=50% Similarity=1.165 Sum_probs=8.2
Q ss_pred ceecCccchh
Q 029194 21 KVWLDPNEVN 30 (197)
Q Consensus 21 rVWlDPne~~ 30 (197)
.||+||.|+.
T Consensus 93 tiwvDP~eVs 102 (108)
T smart00099 93 TLWVDPFEVS 102 (108)
T ss_pred EEEECCCEEE
Confidence 5899999863
No 40
>KOG1596 consensus Fibrillarin and related nucleolar RNA-binding proteins [RNA processing and modification]
Probab=20.38 E-value=64 Score=29.96 Aligned_cols=22 Identities=23% Similarity=0.599 Sum_probs=18.8
Q ss_pred hhHHHHHHHhccCCCceecCccc
Q 029194 6 LQKRLSASVLKCGRGKVWLDPNE 28 (197)
Q Consensus 6 ~QKRLAA~VL~cGk~rVWlDPne 28 (197)
.|-.|||.||+ |..-+||.|-.
T Consensus 137 frSKLAA~I~g-GvdnihikpGs 158 (317)
T KOG1596|consen 137 FRSKLAAGILG-GVDNIHIKPGS 158 (317)
T ss_pred HHHHHHHHhhc-CccceeecCCc
Confidence 46789999986 99999999953
No 41
>PRK13982 bifunctional SbtC-like/phosphopantothenoylcysteine decarboxylase/phosphopantothenate synthase; Provisional
Probab=20.33 E-value=1.4e+02 Score=29.02 Aligned_cols=49 Identities=24% Similarity=0.310 Sum_probs=36.5
Q ss_pred HHHHHhccCCCceecCccchhH-HHhhhhhHHHHhhhhcCceeecCCCCCC
Q 029194 10 LSASVLKCGRGKVWLDPNEVNE-ISMANSRQNIRKLVKDGFIIRKPTKIHS 59 (197)
Q Consensus 10 LAA~VL~cGk~rVWlDPne~~e-Ia~A~sR~~IRkLIkdG~Ii~kp~~~~S 59 (197)
|++-+|.++. .|-|=|.+... ..+..+++++..|-.+|.++..|..|.-
T Consensus 172 lt~v~La~~~-PvliaPaMN~~M~~npat~~Nl~~L~~~G~~vi~P~~g~l 221 (475)
T PRK13982 172 ASAILLAANR-PILLAPAMNPLMWNNPATRRNVAQLKRDGVHMIGPNAGEM 221 (475)
T ss_pred HHHHHHhcCC-CEEEEEcCCHHHhcCHHHHHHHHHHHHCCCEEECCCCCcc
Confidence 3455566654 55555766655 4589999999999999999999998743
No 42
>PF00392 GntR: Bacterial regulatory proteins, gntR family; InterPro: IPR000524 Many bacterial transcription regulation proteins bind DNA through a helix-turn-helix (HTH) motif, which can be classified into subfamilies on the basis of sequence similarities. The HTH GntR family has many members distributed among diverse bacterial groups that regulate various biological processes. It was named GntR after the Bacillus subtilis repressor of the gluconate operon []. Family members include GntR, HutC, KorA, NtaR, FadR, ExuR, FarR, DgoR and PhnF. The crystal structure of the FadR protein has been determined []. In general, these proteins contain a DNA-binding HTH domain at the N terminus, and an effector-binding or oligomerisation domain at the C terminus (IPR011711 from INTERPRO). The DNA-binding domain is well conserved in structure for the whole of the GntR family, consisting of a 3-helical bundle core with a small beta-sheet (wing); the GntR winged helix structure is similar to that found in several other transcriptional regulator families. The regions outside the DNA-binding domain are more variable and are consequently used to define GntR subfamilies []. This entry represents the N-terminal DNA-binding domain of the GntR family.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1HW1_B 1H9T_A 1HW2_A 1H9G_A 1E2X_A 3IHU_A 3C7J_A 2RA5_A 3BY6_C 3IC7_A ....
Probab=20.09 E-value=84 Score=21.27 Aligned_cols=27 Identities=30% Similarity=0.564 Sum_probs=21.1
Q ss_pred HHHhhhhhHHHHhhhhcCceeecCCCC
Q 029194 31 EISMANSRQNIRKLVKDGFIIRKPTKI 57 (197)
Q Consensus 31 eIa~A~sR~~IRkLIkdG~Ii~kp~~~ 57 (197)
.++-..-|+-+..|..+|+|...|-.|
T Consensus 35 ~vsr~tvr~al~~L~~~g~i~~~~~~G 61 (64)
T PF00392_consen 35 GVSRTTVREALRRLEAEGLIERRPGRG 61 (64)
T ss_dssp TS-HHHHHHHHHHHHHTTSEEEETTTE
T ss_pred ccCCcHHHHHHHHHHHCCcEEEECCce
Confidence 345566778888999999999998766
No 43
>cd04762 HTH_MerR-trunc Helix-Turn-Helix DNA binding domain of truncated MerR-like proteins. Proteins in this family mostly have a truncated helix-turn-helix (HTH) MerR-like domain. They lack a portion of the C-terminal region, called Wing 2 and the long dimerization helix that is typically present in MerR-like proteins. These truncated domains are found in response regulator receiver (REC) domain proteins (i.e., CheY), cytosine-C5 specific DNA methylases, IS607 transposase-like proteins, and RacA, a bacterial protein that anchors chromosomes to cell poles.
Probab=20.05 E-value=87 Score=18.82 Aligned_cols=17 Identities=29% Similarity=0.432 Sum_probs=14.4
Q ss_pred hhhHHHHhhhhcCceee
Q 029194 36 NSRQNIRKLVKDGFIIR 52 (197)
Q Consensus 36 ~sR~~IRkLIkdG~Ii~ 52 (197)
+|+..|+.++++|.|..
T Consensus 12 vs~~tl~~~~~~g~~~~ 28 (49)
T cd04762 12 VSPSTLRRWVKEGKLKA 28 (49)
T ss_pred cCHHHHHHHHHcCCCCc
Confidence 68899999999998743
Done!