Query 028729
Match_columns 204
No_of_seqs 176 out of 296
Neff 3.8
Searched_HMMs 46136
Date Fri Mar 29 16:05:48 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/028729.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/028729hhsearch_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 1.6E-86 3.4E-91 557.0 17.1 186 1-186 1-186 (193)
2 PTZ00097 60S ribosomal protein 100.0 3.5E-80 7.7E-85 517.8 19.2 174 3-176 1-174 (175)
3 cd01417 Ribosomal_L19e_E Ribos 100.0 7.5E-79 1.6E-83 505.7 17.4 164 4-167 1-164 (164)
4 PTZ00436 60S ribosomal protein 100.0 2.9E-77 6.4E-82 535.6 20.0 170 1-170 1-170 (357)
5 PF01280 Ribosomal_L19e: Ribos 100.0 1.1E-74 2.3E-79 474.6 14.1 148 2-149 1-148 (148)
6 cd00481 Ribosomal_L19e Ribosom 100.0 3.9E-73 8.4E-78 464.0 14.9 145 4-148 1-145 (145)
7 PRK08570 rpl19e 50S ribosomal 100.0 5.9E-73 1.3E-77 465.0 15.6 147 1-147 1-147 (150)
8 cd01418 Ribosomal_L19e_A Ribos 100.0 3.3E-71 7.2E-76 452.5 15.5 142 4-145 1-142 (145)
9 COG2147 RPL19A Ribosomal prote 100.0 1.8E-67 3.8E-72 431.4 14.8 149 1-149 1-149 (150)
10 TIGR01764 excise DNA binding d 70.2 2.8 6E-05 26.1 1.4 30 23-53 1-30 (49)
11 PF12728 HTH_17: Helix-turn-he 69.6 3 6.5E-05 27.3 1.5 29 23-52 1-29 (51)
12 PF13453 zf-TFIIB: Transcripti 53.8 5.8 0.00013 25.7 0.6 15 20-34 26-40 (41)
13 PF13880 Acetyltransf_13: ESCO 46.3 6.4 0.00014 29.2 -0.1 14 16-29 5-18 (70)
14 TIGR02075 pyrH_bact uridylate 44.7 24 0.00051 30.3 3.1 48 5-52 77-125 (233)
15 PRK05920 aromatic acid decarbo 39.9 33 0.00071 29.8 3.3 47 9-58 121-167 (204)
16 PRK00247 putative inner membra 36.3 4.2E+02 0.0091 25.9 10.7 69 92-167 291-363 (429)
17 PF01479 S4: S4 domain; Inter 35.7 27 0.00058 22.5 1.6 27 31-57 9-35 (48)
18 TIGR01610 phage_O_Nterm phage 34.6 45 0.00098 25.0 2.9 38 16-54 40-81 (95)
19 PF12802 MarR_2: MarR family; 31.6 41 0.00089 22.1 2.1 52 7-60 7-61 (62)
20 smart00345 HTH_GNTR helix_turn 31.6 40 0.00086 21.5 1.9 25 32-56 32-56 (60)
21 PRK06029 3-octaprenyl-4-hydrox 31.3 58 0.0013 27.8 3.4 46 9-57 106-151 (185)
22 PHA00616 hypothetical protein 30.4 29 0.00063 23.7 1.2 17 129-145 8-24 (44)
23 cd04254 AAK_UMPK-PyrH-Ec UMP k 29.2 54 0.0012 28.0 2.9 42 10-51 82-123 (231)
24 PF08535 KorB: KorB domain; I 28.6 48 0.001 24.5 2.2 39 6-51 5-43 (93)
25 PRK11548 outer membrane biogen 27.5 43 0.00092 26.1 1.8 26 22-47 36-61 (113)
26 PF09851 SHOCT: Short C-termin 26.4 80 0.0017 19.5 2.6 20 104-123 6-25 (31)
27 COG3592 Uncharacterized conser 25.3 34 0.00074 25.9 0.9 19 11-30 35-53 (74)
28 PF10625 UspB: Universal stres 24.5 1.1E+02 0.0023 24.8 3.6 33 94-133 18-50 (107)
29 PF01047 MarR: MarR family; I 22.9 60 0.0013 21.3 1.6 25 35-59 32-56 (59)
30 TIGR02988 YaaA_near_RecF S4 do 22.9 61 0.0013 22.0 1.7 21 36-56 22-42 (59)
31 PRK04960 universal stress prot 22.8 1E+02 0.0022 25.0 3.2 33 94-133 18-50 (111)
32 PF14468 DUF4427: Protein of u 22.7 59 0.0013 27.1 1.9 33 12-53 30-62 (132)
33 TIGR00421 ubiX_pad polyprenyl 22.4 1.1E+02 0.0023 25.9 3.4 47 9-58 103-149 (181)
34 PF00096 zf-C2H2: Zinc finger, 22.3 67 0.0014 17.5 1.5 16 129-144 7-22 (23)
35 PF13412 HTH_24: Winged helix- 21.7 65 0.0014 20.6 1.6 20 32-51 29-48 (48)
36 smart00420 HTH_DEOR helix_turn 21.5 77 0.0017 19.6 1.9 24 32-55 26-49 (53)
37 PF06353 DUF1062: Protein of u 20.8 71 0.0015 26.5 2.0 23 34-56 113-135 (142)
38 cd04762 HTH_MerR-trunc Helix-T 20.4 81 0.0017 19.1 1.8 17 36-52 12-28 (49)
39 smart00099 btg1 tob/btg1 famil 20.2 38 0.00082 27.1 0.2 10 21-30 93-102 (108)
No 1
>KOG1696 consensus 60s ribosomal protein L19 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.6e-86 Score=556.96 Aligned_cols=186 Identities=74% Similarity=1.108 Sum_probs=184.9
Q ss_pred CCcchhhHHHHHHHhccCCCceecCccchhHHHhhhhhHHHHhhhhcCceeeccCCccChhHHHHHHHHHhcCcCCCCCC
Q 028729 1 MVSLKLQKRLSASVLKCGRGKVWLDPNEVNEISMANSRQNIRKLVKDGFIIRKPTKIHSRSRARRMKEAKRKGRHSGYGK 80 (204)
Q Consensus 1 M~~l~~QKRLAA~VL~cGk~rVWlDPne~~eIa~A~sR~~IRkLIkdG~Ii~Kp~~~~SR~R~r~~~~ak~kGRh~G~Gk 80 (204)
|++|++|||||||||+||+.+|||||||++||++|||||+|++||+||+||.+|+++|||+||+++.+++++|||+|+|+
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 028729 81 RKGTREARLPTKILWMRRMRVLRRLLRKYRESKKIDKHMYHDMYMKVKGNVFKNKRVLMESIHKSKAEKAREKTLSDQFE 160 (204)
Q Consensus 81 RKGt~~AR~p~K~~WmrRiR~lRrlLr~~Re~~kID~~~Y~~LY~kaKGn~Fknk~~L~e~I~k~kae~~r~k~l~dQae 160 (204)
|+||+|||||+|++||+|||+||++|++|||+|+||+|+||+||+++|||+|+|+++||||||+.+||++++|+|+||||
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 HHHhhhHHHHHHHHHHHHHHHhcCCC
Q 028729 161 AKRAKNKASRERKLARREERLAQGPG 186 (204)
Q Consensus 161 A~r~k~k~~r~rr~~r~~~k~~~~~~ 186 (204)
|+|.++++++++++|++++++++++.
T Consensus 161 Arr~k~k~ar~rreer~~~k~~~~~~ 186 (193)
T KOG1696|consen 161 ARRLKNKAARKRREERLAAKPQELIK 186 (193)
T ss_pred HHHhhhHHHhhhHHHHHhhchhhhhc
Confidence 99999999999999999999999886
No 2
>PTZ00097 60S ribosomal protein L19; Provisional
Probab=100.00 E-value=3.5e-80 Score=517.77 Aligned_cols=174 Identities=71% Similarity=1.152 Sum_probs=171.3
Q ss_pred cchhhHHHHHHHhccCCCceecCccchhHHHhhhhhHHHHhhhhcCceeeccCCccChhHHHHHHHHHhcCcCCCCCCcc
Q 028729 3 SLKLQKRLSASVLKCGRGKVWLDPNEVNEISMANSRQNIRKLVKDGFIIRKPTKIHSRSRARRMKEAKRKGRHSGYGKRK 82 (204)
Q Consensus 3 ~l~~QKRLAA~VL~cGk~rVWlDPne~~eIa~A~sR~~IRkLIkdG~Ii~Kp~~~~SR~R~r~~~~ak~kGRh~G~GkRK 82 (204)
+|++||||||+||+||+++||||||+++||++||||+|||+||+||+|+++|++||||+|++++++++++|||+|||||+
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 028729 83 GTREARLPTKILWMRRMRVLRRLLRKYRESKKIDKHMYHDMYMKVKGNVFKNKRVLMESIHKSKAEKAREKTLSDQFEAK 162 (204)
Q Consensus 83 Gt~~AR~p~K~~WmrRiR~lRrlLr~~Re~~kID~~~Y~~LY~kaKGn~Fknk~~L~e~I~k~kae~~r~k~l~dQaeA~ 162 (204)
||+|||||+|+.||++||+||++|++|||+|+||+|+||.||++||||+|+|++||++|||+.++|+++++.|+||+||+
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 028729 163 RAKNKASRERKLAR 176 (204)
Q Consensus 163 r~k~k~~r~rr~~r 176 (204)
+.++++++++++++
T Consensus 161 r~k~~~~~~~r~~~ 174 (175)
T PTZ00097 161 RAKAKALRNKRKAK 174 (175)
T ss_pred HHHHHHHHHHHhhc
Confidence 99999999987753
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=7.5e-79 Score=505.66 Aligned_cols=164 Identities=79% Similarity=1.221 Sum_probs=162.0
Q ss_pred chhhHHHHHHHhccCCCceecCccchhHHHhhhhhHHHHhhhhcCceeeccCCccChhHHHHHHHHHhcCcCCCCCCccc
Q 028729 4 LKLQKRLSASVLKCGRGKVWLDPNEVNEISMANSRQNIRKLVKDGFIIRKPTKIHSRSRARRMKEAKRKGRHSGYGKRKG 83 (204)
Q Consensus 4 l~~QKRLAA~VL~cGk~rVWlDPne~~eIa~A~sR~~IRkLIkdG~Ii~Kp~~~~SR~R~r~~~~ak~kGRh~G~GkRKG 83 (204)
|++|+||||+||+||+++||||||+++||++||||+|||+||+||+|+++|++||||+|++++++++++|||+|+|||+|
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 028729 84 TREARLPTKILWMRRMRVLRRLLRKYRESKKIDKHMYHDMYMKVKGNVFKNKRVLMESIHKSKAEKAREKTLSDQFEAKR 163 (204)
Q Consensus 84 t~~AR~p~K~~WmrRiR~lRrlLr~~Re~~kID~~~Y~~LY~kaKGn~Fknk~~L~e~I~k~kae~~r~k~l~dQaeA~r 163 (204)
|+|||||+|+.||++||+||++|++|||+|+||+|+||.||++||||+|+|+++|++|||+.++|+++++.|+||+||++
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 028729 164 AKNK 167 (204)
Q Consensus 164 ~k~k 167 (204)
++++
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=2.9e-77 Score=535.61 Aligned_cols=170 Identities=67% Similarity=1.101 Sum_probs=167.5
Q ss_pred CCcchhhHHHHHHHhccCCCceecCccchhHHHhhhhhHHHHhhhhcCceeeccCCccChhHHHHHHHHHhcCcCCCCCC
Q 028729 1 MVSLKLQKRLSASVLKCGRGKVWLDPNEVNEISMANSRQNIRKLVKDGFIIRKPTKIHSRSRARRMKEAKRKGRHSGYGK 80 (204)
Q Consensus 1 M~~l~~QKRLAA~VL~cGk~rVWlDPne~~eIa~A~sR~~IRkLIkdG~Ii~Kp~~~~SR~R~r~~~~ak~kGRh~G~Gk 80 (204)
|++|++||||||+||+||++|||||||+++||++||||+|||+||+||+|+++|++||||+|+|++++++++|||+|+||
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 028729 81 RKGTREARLPTKILWMRRMRVLRRLLRKYRESKKIDKHMYHDMYMKVKGNVFKNKRVLMESIHKSKAEKAREKTLSDQFE 160 (204)
Q Consensus 81 RKGt~~AR~p~K~~WmrRiR~lRrlLr~~Re~~kID~~~Y~~LY~kaKGn~Fknk~~L~e~I~k~kae~~r~k~l~dQae 160 (204)
|+||+|||||+|++||+|||+||++|++|||+|+||+|+||+||+++|||+|+|++||++|||+.++|+.+++.|.||+|
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 028729 161 AKRAKNKASR 170 (204)
Q Consensus 161 A~r~k~k~~r 170 (204)
|+|.++++.|
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=1.1e-74 Score=474.58 Aligned_cols=148 Identities=68% Similarity=1.093 Sum_probs=131.0
Q ss_pred CcchhhHHHHHHHhccCCCceecCccchhHHHhhhhhHHHHhhhhcCceeeccCCccChhHHHHHHHHHhcCcCCCCCCc
Q 028729 2 VSLKLQKRLSASVLKCGRGKVWLDPNEVNEISMANSRQNIRKLVKDGFIIRKPTKIHSRSRARRMKEAKRKGRHSGYGKR 81 (204)
Q Consensus 2 ~~l~~QKRLAA~VL~cGk~rVWlDPne~~eIa~A~sR~~IRkLIkdG~Ii~Kp~~~~SR~R~r~~~~ak~kGRh~G~GkR 81 (204)
|+|++||||||+||+||+++|||||||++||++||||+|||+||+||+|+++|++|||||||+++++++++|||+|+|+|
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 028729 82 KGTREARLPTKILWMRRMRVLRRLLRKYRESKKIDKHMYHDMYMKVKGNVFKNKRVLMESIHKSKAEK 149 (204)
Q Consensus 82 KGt~~AR~p~K~~WmrRiR~lRrlLr~~Re~~kID~~~Y~~LY~kaKGn~Fknk~~L~e~I~k~kae~ 149 (204)
+||+|||||+|++||++||+||++|++|||+|+||+|+||+||++||||+|+|+++|++|||++++|+
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=3.9e-73 Score=463.96 Aligned_cols=145 Identities=66% Similarity=1.102 Sum_probs=143.0
Q ss_pred chhhHHHHHHHhccCCCceecCccchhHHHhhhhhHHHHhhhhcCceeeccCCccChhHHHHHHHHHhcCcCCCCCCccc
Q 028729 4 LKLQKRLSASVLKCGRGKVWLDPNEVNEISMANSRQNIRKLVKDGFIIRKPTKIHSRSRARRMKEAKRKGRHSGYGKRKG 83 (204)
Q Consensus 4 l~~QKRLAA~VL~cGk~rVWlDPne~~eIa~A~sR~~IRkLIkdG~Ii~Kp~~~~SR~R~r~~~~ak~kGRh~G~GkRKG 83 (204)
|++||||||+||+||+++||||||+++||++||||+|||+||+||+|+++|++||||+|++++++++++|||+|+|||+|
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 028729 84 TREARLPTKILWMRRMRVLRRLLRKYRESKKIDKHMYHDMYMKVKGNVFKNKRVLMESIHKSKAE 148 (204)
Q Consensus 84 t~~AR~p~K~~WmrRiR~lRrlLr~~Re~~kID~~~Y~~LY~kaKGn~Fknk~~L~e~I~k~kae 148 (204)
|+|||||+|+.||++||+||++|++|||+|+||+|+||.||++||||+|+|+++|++|||+.++|
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=5.9e-73 Score=464.98 Aligned_cols=147 Identities=42% Similarity=0.736 Sum_probs=145.2
Q ss_pred CCcchhhHHHHHHHhccCCCceecCccchhHHHhhhhhHHHHhhhhcCceeeccCCccChhHHHHHHHHHhcCcCCCCCC
Q 028729 1 MVSLKLQKRLSASVLKCGRGKVWLDPNEVNEISMANSRQNIRKLVKDGFIIRKPTKIHSRSRARRMKEAKRKGRHSGYGK 80 (204)
Q Consensus 1 M~~l~~QKRLAA~VL~cGk~rVWlDPne~~eIa~A~sR~~IRkLIkdG~Ii~Kp~~~~SR~R~r~~~~ak~kGRh~G~Gk 80 (204)
|++|++|+||||+||+||+++||||||+++||++||||+|||+||+||+|+++|++||||+|++++++++++|||+|+||
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 028729 81 RKGTREARLPTKILWMRRMRVLRRLLRKYRESKKIDKHMYHDMYMKVKGNVFKNKRVLMESIHKSKA 147 (204)
Q Consensus 81 RKGt~~AR~p~K~~WmrRiR~lRrlLr~~Re~~kID~~~Y~~LY~kaKGn~Fknk~~L~e~I~k~ka 147 (204)
|+||+|||+|+|+.||++||+||++|++|||+|+||+|+||.||++||||+|+|+++|++||+....
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=3.3e-71 Score=452.49 Aligned_cols=142 Identities=40% Similarity=0.723 Sum_probs=140.4
Q ss_pred chhhHHHHHHHhccCCCceecCccchhHHHhhhhhHHHHhhhhcCceeeccCCccChhHHHHHHHHHhcCcCCCCCCccc
Q 028729 4 LKLQKRLSASVLKCGRGKVWLDPNEVNEISMANSRQNIRKLVKDGFIIRKPTKIHSRSRARRMKEAKRKGRHSGYGKRKG 83 (204)
Q Consensus 4 l~~QKRLAA~VL~cGk~rVWlDPne~~eIa~A~sR~~IRkLIkdG~Ii~Kp~~~~SR~R~r~~~~ak~kGRh~G~GkRKG 83 (204)
|++||||||+||+||+++||||||+++||++||||+|||+||+||+|+++|++||||+|++++++++++|||+|+|||+|
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 68999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccccCCcchHHHHHHHHHHHHHHHHHHhcCCCChHhhHHHHhhhcCCccccHHHHHHHHHHH
Q 028729 84 TREARLPTKILWMRRMRVLRRLLRKYRESKKIDKHMYHDMYMKVKGNVFKNKRVLMESIHKS 145 (204)
Q Consensus 84 t~~AR~p~K~~WmrRiR~lRrlLr~~Re~~kID~~~Y~~LY~kaKGn~Fknk~~L~e~I~k~ 145 (204)
|+|||||+|+.||++||+||++|++|||+|+||+|+||.||++||||+|+|+++|++||...
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=1.8e-67 Score=431.39 Aligned_cols=149 Identities=50% Similarity=0.809 Sum_probs=146.7
Q ss_pred CCcchhhHHHHHHHhccCCCceecCccchhHHHhhhhhHHHHhhhhcCceeeccCCccChhHHHHHHHHHhcCcCCCCCC
Q 028729 1 MVSLKLQKRLSASVLKCGRGKVWLDPNEVNEISMANSRQNIRKLVKDGFIIRKPTKIHSRSRARRMKEAKRKGRHSGYGK 80 (204)
Q Consensus 1 M~~l~~QKRLAA~VL~cGk~rVWlDPne~~eIa~A~sR~~IRkLIkdG~Ii~Kp~~~~SR~R~r~~~~ak~kGRh~G~Gk 80 (204)
|+||++|+||||+||+||+++||||||+++||++|+||+|||.||+||+|+.+|++|+|++|+++++++++||||+||||
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 028729 81 RKGTREARLPTKILWMRRMRVLRRLLRKYRESKKIDKHMYHDMYMKVKGNVFKNKRVLMESIHKSKAEK 149 (204)
Q Consensus 81 RKGt~~AR~p~K~~WmrRiR~lRrlLr~~Re~~kID~~~Y~~LY~kaKGn~Fknk~~L~e~I~k~kae~ 149 (204)
|+||++||||+|+.||.+||+||++|++||++|+||+|+||.||+++|||.|+++++|.+||.+.+.++
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=70.23 E-value=2.8 Score=26.15 Aligned_cols=30 Identities=20% Similarity=0.297 Sum_probs=24.8
Q ss_pred ecCccchhHHHhhhhhHHHHhhhhcCceeec
Q 028729 23 WLDPNEVNEISMANSRQNIRKLVKDGFIIRK 53 (204)
Q Consensus 23 WlDPne~~eIa~A~sR~~IRkLIkdG~Ii~K 53 (204)
||++.|+.++-. +|+..|+.|+++|.|-.-
T Consensus 1 ~lt~~e~a~~lg-is~~ti~~~~~~g~i~~~ 30 (49)
T TIGR01764 1 YLTVEEAAEYLG-VSKDTVYRLIHEGELPAY 30 (49)
T ss_pred CCCHHHHHHHHC-CCHHHHHHHHHcCCCCeE
Confidence 677888888876 789999999999987653
No 11
>PF12728 HTH_17: Helix-turn-helix domain
Probab=69.58 E-value=3 Score=27.29 Aligned_cols=29 Identities=24% Similarity=0.345 Sum_probs=24.9
Q ss_pred ecCccchhHHHhhhhhHHHHhhhhcCceee
Q 028729 23 WLDPNEVNEISMANSRQNIRKLVKDGFIIR 52 (204)
Q Consensus 23 WlDPne~~eIa~A~sR~~IRkLIkdG~Ii~ 52 (204)
||++.|+-++-. +|+..|+.+++.|.|..
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
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=53.77 E-value=5.8 Score=25.67 Aligned_cols=15 Identities=27% Similarity=0.809 Sum_probs=12.3
Q ss_pred CceecCccchhHHHh
Q 028729 20 GKVWLDPNEVNEISM 34 (204)
Q Consensus 20 ~rVWlDPne~~eIa~ 34 (204)
.-||||++|++.|.+
T Consensus 26 ~G~W~d~~el~~~~e 40 (41)
T PF13453_consen 26 GGIWFDAGELEKLLE 40 (41)
T ss_pred CeEEccHHHHHHHHh
Confidence 469999999988753
No 13
>PF13880 Acetyltransf_13: ESCO1/2 acetyl-transferase
Probab=46.30 E-value=6.4 Score=29.18 Aligned_cols=14 Identities=29% Similarity=1.037 Sum_probs=11.9
Q ss_pred ccCCCceecCccch
Q 028729 16 KCGRGKVWLDPNEV 29 (204)
Q Consensus 16 ~cGk~rVWlDPne~ 29 (204)
-||.++||..|..-
T Consensus 5 ~~GI~RIWV~~~~R 18 (70)
T PF13880_consen 5 VCGISRIWVSPSHR 18 (70)
T ss_pred EEEeEEEEeChhhh
Confidence 49999999999753
No 14
>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=44.67 E-value=24 Score=30.26 Aligned_cols=48 Identities=15% Similarity=0.126 Sum_probs=38.2
Q ss_pred hhhHHH-HHHHhccCCCceecCccchhHHHhhhhhHHHHhhhhcCceee
Q 028729 5 KLQKRL-SASVLKCGRGKVWLDPNEVNEISMANSRQNIRKLVKDGFIIR 52 (204)
Q Consensus 5 ~~QKRL-AA~VL~cGk~rVWlDPne~~eIa~A~sR~~IRkLIkdG~Ii~ 52 (204)
+++-+| +..+...|.+-++|+|.....+..-++.+.+..|++.|.|..
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 777778999999999998765555567899999999999843
No 15
>PRK05920 aromatic acid decarboxylase; Validated
Probab=39.88 E-value=33 Score=29.77 Aligned_cols=47 Identities=32% Similarity=0.289 Sum_probs=36.4
Q ss_pred HHHHHHhccCCCceecCccchhHHHhhhhhHHHHhhhhcCceeeccCCcc
Q 028729 9 RLSASVLKCGRGKVWLDPNEVNEISMANSRQNIRKLVKDGFIIRKPTKIH 58 (204)
Q Consensus 9 RLAA~VL~cGk~rVWlDPne~~eIa~A~sR~~IRkLIkdG~Ii~Kp~~~~ 58 (204)
+.|...|+.|. .|.|=|.+... ++.++++|..|-..|.++.-|..+.
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 45556788776 55555765444 7889999999999999999999874
No 16
>PRK00247 putative inner membrane protein translocase component YidC; Validated
Probab=36.29 E-value=4.2e+02 Score=25.86 Aligned_cols=69 Identities=16% Similarity=0.254 Sum_probs=37.3
Q ss_pred hHHHHHHHHHHHHHHHHHHhcC---CCChHhhHHHHhhhcCCccccHHHHHHHHHHHhhHHHHhhhhhHH-HHHHHhhhH
Q 028729 92 KILWMRRMRVLRRLLRKYRESK---KIDKHMYHDMYMKVKGNVFKNKRVLMESIHKSKAEKAREKTLSDQ-FEAKRAKNK 167 (204)
Q Consensus 92 K~~WmrRiR~lRrlLr~~Re~~---kID~~~Y~~LY~kaKGn~Fknk~~L~e~I~k~kae~~r~k~l~dQ-aeA~r~k~k 167 (204)
+..|..+.+..+..++..|... .|.+..+..|..- |...=.+.=...+++|+++|.++.+ -||.|.-++
T Consensus 291 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~-------~~~~~~~~~~~~~~~k~~~k~~~~~~~~~~~~~~~ 363 (429)
T PRK00247 291 RAQYREKQKEKKAFLWTLRRNRLRMIITPWRAPELHAE-------NAEIKKTRTAEKNEAKARKKEIAQKRRAAEREINR 363 (429)
T ss_pred HHHHHHHHHHHHHHHHHHHhccccccCCcccHHHHHHH-------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4456666666555555555544 7888877777432 2222233334446666766666543 344444444
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=35.67 E-value=27 Score=22.46 Aligned_cols=27 Identities=26% Similarity=0.477 Sum_probs=20.8
Q ss_pred HHHhhhhhHHHHhhhhcCceeeccCCc
Q 028729 31 EISMANSRQNIRKLVKDGFIIRKPTKI 57 (204)
Q Consensus 31 eIa~A~sR~~IRkLIkdG~Ii~Kp~~~ 57 (204)
+...+.||.++++||+.|.|...-..+
T Consensus 9 ~~~~~~sr~~a~~~I~~g~V~VNg~~v 35 (48)
T PF01479_consen 9 RLGLASSRSEARRLIKQGRVKVNGKVV 35 (48)
T ss_dssp HTTSSSSHHHHHHHHHTTTEEETTEEE
T ss_pred HcCCcCCHHHHHHhcCCCEEEECCEEE
Confidence 344567999999999999987655443
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=34.60 E-value=45 Score=24.99 Aligned_cols=38 Identities=18% Similarity=0.305 Sum_probs=26.1
Q ss_pred ccCCCceecCccchhHHHhhhhhHH----HHhhhhcCceeecc
Q 028729 16 KCGRGKVWLDPNEVNEISMANSRQN----IRKLVKDGFIIRKP 54 (204)
Q Consensus 16 ~cGk~rVWlDPne~~eIa~A~sR~~----IRkLIkdG~Ii~Kp 54 (204)
|.++..++|.+.|+.++... ||+. |..|.++|+|....
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 34456777777777766554 4444 56799999998654
No 19
>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=31.59 E-value=41 Score=22.14 Aligned_cols=52 Identities=21% Similarity=0.242 Sum_probs=31.4
Q ss_pred hHHHHHHHhccCCCceecCccchhHH---HhhhhhHHHHhhhhcCceeeccCCccCh
Q 028729 7 QKRLSASVLKCGRGKVWLDPNEVNEI---SMANSRQNIRKLVKDGFIIRKPTKIHSR 60 (204)
Q Consensus 7 QKRLAA~VL~cGk~rVWlDPne~~eI---a~A~sR~~IRkLIkdG~Ii~Kp~~~~SR 60 (204)
|-++-..|..+|.. ++-+.++.+. +-...-.-|..|++.|+|.+.+.....|
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 44555556566655 3334444332 2334456788999999999998877655
No 20
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=31.58 E-value=40 Score=21.53 Aligned_cols=25 Identities=24% Similarity=0.578 Sum_probs=18.0
Q ss_pred HHhhhhhHHHHhhhhcCceeeccCC
Q 028729 32 ISMANSRQNIRKLVKDGFIIRKPTK 56 (204)
Q Consensus 32 Ia~A~sR~~IRkLIkdG~Ii~Kp~~ 56 (204)
|+.+.-+..+..|.++|+|...|-.
T Consensus 32 vs~~tv~~~l~~L~~~g~i~~~~~~ 56 (60)
T smart00345 32 VSRTTVREALSRLEAEGLVQRRPGS 56 (60)
T ss_pred CCHHHHHHHHHHHHHCCCEEEecCC
Confidence 3344557778899999999876643
No 21
>PRK06029 3-octaprenyl-4-hydroxybenzoate carboxy-lyase; Provisional
Probab=31.34 E-value=58 Score=27.76 Aligned_cols=46 Identities=26% Similarity=0.255 Sum_probs=35.5
Q ss_pred HHHHHHhccCCCceecCccchhHHHhhhhhHHHHhhhhcCceeeccCCc
Q 028729 9 RLSASVLKCGRGKVWLDPNEVNEISMANSRQNIRKLVKDGFIIRKPTKI 57 (204)
Q Consensus 9 RLAA~VL~cGk~rVWlDPne~~eIa~A~sR~~IRkLIkdG~Ii~Kp~~~ 57 (204)
+.|...|.+++ .|.|=|. +--.+..+.+++.+|-+.|.++..|..|
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 44556677765 5555575 4556889999999999999999999876
No 22
>PHA00616 hypothetical protein
Probab=30.42 E-value=29 Score=23.73 Aligned_cols=17 Identities=24% Similarity=0.634 Sum_probs=15.1
Q ss_pred CCccccHHHHHHHHHHH
Q 028729 129 GNVFKNKRVLMESIHKS 145 (204)
Q Consensus 129 Gn~Fknk~~L~e~I~k~ 145 (204)
|..|.++++|..|+.+.
T Consensus 8 G~~F~~~s~l~~H~r~~ 24 (44)
T PHA00616 8 GGIFRKKKEVIEHLLSV 24 (44)
T ss_pred hHHHhhHHHHHHHHHHh
Confidence 78999999999999664
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=29.19 E-value=54 Score=27.98 Aligned_cols=42 Identities=10% Similarity=0.160 Sum_probs=35.0
Q ss_pred HHHHHhccCCCceecCccchhHHHhhhhhHHHHhhhhcCcee
Q 028729 10 LSASVLKCGRGKVWLDPNEVNEISMANSRQNIRKLVKDGFII 51 (204)
Q Consensus 10 LAA~VL~cGk~rVWlDPne~~eIa~A~sR~~IRkLIkdG~Ii 51 (204)
|++.+...|.+-+||+|-+++.+.....-+.+..+++.|.|.
T Consensus 82 l~~~L~~~Gv~a~~l~~~~~~~~~~~~~~~~l~~~l~~g~ip 123 (231)
T cd04254 82 LQDALESLGVKTRVMSAIPMQGVAEPYIRRRAIRHLEKGRVV 123 (231)
T ss_pred HHHHHHHcCCCeEEEcHHHhhhhhcccCHHHHHHHHHCCCEE
Confidence 566777899999999999987665556679999999999873
No 24
>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=28.60 E-value=48 Score=24.49 Aligned_cols=39 Identities=23% Similarity=0.600 Sum_probs=24.5
Q ss_pred hhHHHHHHHhccCCCceecCccchhHHHhhhhhHHHHhhhhcCcee
Q 028729 6 LQKRLSASVLKCGRGKVWLDPNEVNEISMANSRQNIRKLVKDGFII 51 (204)
Q Consensus 6 ~QKRLAA~VL~cGk~rVWlDPne~~eIa~A~sR~~IRkLIkdG~Ii 51 (204)
+|.-+|..| |+++-|+ .+-++-+.--++|+.|+.+|.|.
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 466677754 8998887 45566667778999999999774
No 25
>PRK11548 outer membrane biogenesis protein BamE; Provisional
Probab=27.45 E-value=43 Score=26.07 Aligned_cols=26 Identities=23% Similarity=0.440 Sum_probs=23.1
Q ss_pred eecCccchhHHHhhhhhHHHHhhhhc
Q 028729 22 VWLDPNEVNEISMANSRQNIRKLVKD 47 (204)
Q Consensus 22 VWlDPne~~eIa~A~sR~~IRkLIkd 47 (204)
-++||+.+++|.--.|+++|+.|+-.
T Consensus 36 ~~~~~~~l~~l~~GmTk~qV~~lLGt 61 (113)
T PRK11548 36 NYLTPNDVAKIHVGMTQQQVAYTLGT 61 (113)
T ss_pred ccCCHHHHHHhcCCCCHHHHHHHcCC
Confidence 38899999999999999999999844
No 26
>PF09851 SHOCT: Short C-terminal domain; InterPro: IPR018649 This family of hypothetical prokaryotic proteins has no known function.
Probab=26.36 E-value=80 Score=19.48 Aligned_cols=20 Identities=15% Similarity=0.320 Sum_probs=17.0
Q ss_pred HHHHHHHhcCCCChHhhHHH
Q 028729 104 RLLRKYRESKKIDKHMYHDM 123 (204)
Q Consensus 104 rlLr~~Re~~kID~~~Y~~L 123 (204)
..|+.+.+.|.|+...|...
T Consensus 6 ~~L~~l~~~G~IseeEy~~~ 25 (31)
T PF09851_consen 6 EKLKELYDKGEISEEEYEQK 25 (31)
T ss_pred HHHHHHHHcCCCCHHHHHHH
Confidence 45788999999999999764
No 27
>COG3592 Uncharacterized conserved protein [Function unknown]
Probab=25.27 E-value=34 Score=25.90 Aligned_cols=19 Identities=32% Similarity=0.789 Sum_probs=14.6
Q ss_pred HHHHhccCCCceecCccchh
Q 028729 11 SASVLKCGRGKVWLDPNEVN 30 (204)
Q Consensus 11 AA~VL~cGk~rVWlDPne~~ 30 (204)
+++|+++|..= ||+|+..+
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 28
>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=24.51 E-value=1.1e+02 Score=24.77 Aligned_cols=33 Identities=36% Similarity=0.491 Sum_probs=25.3
Q ss_pred HHHHHHHHHHHHHHHHHhcCCCChHhhHHHHhhhcCCccc
Q 028729 94 LWMRRMRVLRRLLRKYRESKKIDKHMYHDMYMKVKGNVFK 133 (204)
Q Consensus 94 ~WmrRiR~lRrlLr~~Re~~kID~~~Y~~LY~kaKGn~Fk 133 (204)
-++|=.=.||-+|--|||...+ ||..+.||-|=
T Consensus 18 Nm~RY~SsLR~LL~imR~~dPL-------LYQ~VDG~GFF 50 (107)
T PF10625_consen 18 NMARYFSSLRALLYIMREADPL-------LYQQVDGNGFF 50 (107)
T ss_pred HHHHHHHHHHHHHHHHhcCCcH-------HHHhccCCCce
Confidence 3566667899999999996543 78888888774
No 29
>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=22.87 E-value=60 Score=21.31 Aligned_cols=25 Identities=24% Similarity=0.335 Sum_probs=19.0
Q ss_pred hhhhHHHHhhhhcCceeeccCCccC
Q 028729 35 ANSRQNIRKLVKDGFIIRKPTKIHS 59 (204)
Q Consensus 35 A~sR~~IRkLIkdG~Ii~Kp~~~~S 59 (204)
++.-.-|.+|++.|+|.+.+....-
T Consensus 32 ~~~t~~i~~L~~~g~I~r~~~~~D~ 56 (59)
T PF01047_consen 32 STVTRIIKRLEKKGLIERERDPDDR 56 (59)
T ss_dssp HHHHHHHHHHHHTTSEEEEEETTET
T ss_pred hHHHHHHHHHHHCCCEEeccCCCCC
Confidence 4445678999999999998765543
No 30
>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=22.86 E-value=61 Score=21.98 Aligned_cols=21 Identities=5% Similarity=0.112 Sum_probs=17.6
Q ss_pred hhhHHHHhhhhcCceeeccCC
Q 028729 36 NSRQNIRKLVKDGFIIRKPTK 56 (204)
Q Consensus 36 ~sR~~IRkLIkdG~Ii~Kp~~ 56 (204)
.||..+++||++|.|...-..
T Consensus 22 ~SR~~~k~li~~G~V~VNg~~ 42 (59)
T TIGR02988 22 DSGGQAKWFLQENEVLVNGEL 42 (59)
T ss_pred cCHHHHHHHHHcCCEEECCEE
Confidence 499999999999999885443
No 31
>PRK04960 universal stress protein UspB; Provisional
Probab=22.84 E-value=1e+02 Score=25.03 Aligned_cols=33 Identities=30% Similarity=0.370 Sum_probs=26.4
Q ss_pred HHHHHHHHHHHHHHHHHhcCCCChHhhHHHHhhhcCCccc
Q 028729 94 LWMRRMRVLRRLLRKYRESKKIDKHMYHDMYMKVKGNVFK 133 (204)
Q Consensus 94 ~WmrRiR~lRrlLr~~Re~~kID~~~Y~~LY~kaKGn~Fk 133 (204)
-++|=.=.||-+|--|||...+ ||..+.||-|=
T Consensus 18 Nm~RY~SsLR~LL~imRe~dPL-------LYQ~VDG~GFF 50 (111)
T PRK04960 18 NMARYFSSLRALLVVLRGCDPL-------LYQYVDGGGFF 50 (111)
T ss_pred HHHHHHHHHHHHHHHHHccCch-------hheeecCCcee
Confidence 4666777899999999996554 88889998774
No 32
>PF14468 DUF4427: Protein of unknown function (DUF4427)
Probab=22.71 E-value=59 Score=27.08 Aligned_cols=33 Identities=21% Similarity=0.399 Sum_probs=25.3
Q ss_pred HHHhccCCCceecCccchhHHHhhhhhHHHHhhhhcCceeec
Q 028729 12 ASVLKCGRGKVWLDPNEVNEISMANSRQNIRKLVKDGFIIRK 53 (204)
Q Consensus 12 A~VL~cGk~rVWlDPne~~eIa~A~sR~~IRkLIkdG~Ii~K 53 (204)
.-++.-|...||| |+ |+.+=+|.||++|.|+.-
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 33
>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=22.37 E-value=1.1e+02 Score=25.87 Aligned_cols=47 Identities=30% Similarity=0.295 Sum_probs=35.1
Q ss_pred HHHHHHhccCCCceecCccchhHHHhhhhhHHHHhhhhcCceeeccCCcc
Q 028729 9 RLSASVLKCGRGKVWLDPNEVNEISMANSRQNIRKLVKDGFIIRKPTKIH 58 (204)
Q Consensus 9 RLAA~VL~cGk~rVWlDPne~~eIa~A~sR~~IRkLIkdG~Ii~Kp~~~~ 58 (204)
+.|...|+++. .|.|=|.+. -.++.+.+++..|-+.|.++.-|..+.
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 44445777765 555557544 457888999999999999999998763
No 34
>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=22.31 E-value=67 Score=17.46 Aligned_cols=16 Identities=25% Similarity=0.497 Sum_probs=13.2
Q ss_pred CCccccHHHHHHHHHH
Q 028729 129 GNVFKNKRVLMESIHK 144 (204)
Q Consensus 129 Gn~Fknk~~L~e~I~k 144 (204)
|-+|.+...|..||..
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 35
>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=21.67 E-value=65 Score=20.63 Aligned_cols=20 Identities=30% Similarity=0.466 Sum_probs=15.4
Q ss_pred HHhhhhhHHHHhhhhcCcee
Q 028729 32 ISMANSRQNIRKLVKDGFII 51 (204)
Q Consensus 32 Ia~A~sR~~IRkLIkdG~Ii 51 (204)
|+.+.....|++|+++|+|.
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 36
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=21.49 E-value=77 Score=19.60 Aligned_cols=24 Identities=25% Similarity=0.443 Sum_probs=17.7
Q ss_pred HHhhhhhHHHHhhhhcCceeeccC
Q 028729 32 ISMANSRQNIRKLVKDGFIIRKPT 55 (204)
Q Consensus 32 Ia~A~sR~~IRkLIkdG~Ii~Kp~ 55 (204)
++.+.-+..|..|.+.|+|...+.
T Consensus 26 ~s~~tv~~~l~~L~~~g~i~~~~~ 49 (53)
T smart00420 26 VSEMTIRRDLNKLEEQGLLTRVHG 49 (53)
T ss_pred CCHHHHHHHHHHHHHCCCEEEeec
Confidence 344555778889999999987654
No 37
>PF06353 DUF1062: Protein of unknown function (DUF1062); InterPro: IPR009412 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=20.79 E-value=71 Score=26.49 Aligned_cols=23 Identities=30% Similarity=0.673 Sum_probs=20.5
Q ss_pred hhhhhHHHHhhhhcCceeeccCC
Q 028729 34 MANSRQNIRKLVKDGFIIRKPTK 56 (204)
Q Consensus 34 ~A~sR~~IRkLIkdG~Ii~Kp~~ 56 (204)
--+||.+|..|+++|.|...|.+
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 38
>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=20.42 E-value=81 Score=19.08 Aligned_cols=17 Identities=29% Similarity=0.432 Sum_probs=14.4
Q ss_pred hhhHHHHhhhhcCceee
Q 028729 36 NSRQNIRKLVKDGFIIR 52 (204)
Q Consensus 36 ~sR~~IRkLIkdG~Ii~ 52 (204)
+|+..|+.++++|.|..
T Consensus 12 vs~~tl~~~~~~g~~~~ 28 (49)
T cd04762 12 VSPSTLRRWVKEGKLKA 28 (49)
T ss_pred cCHHHHHHHHHcCCCCc
Confidence 68899999999998743
No 39
>smart00099 btg1 tob/btg1 family. The tob/btg1 is a family of proteins that inhibit cell proliferation.
Probab=20.20 E-value=38 Score=27.12 Aligned_cols=10 Identities=50% Similarity=1.165 Sum_probs=8.3
Q ss_pred ceecCccchh
Q 028729 21 KVWLDPNEVN 30 (204)
Q Consensus 21 rVWlDPne~~ 30 (204)
.||+||.|+.
T Consensus 93 tiwvDP~eVs 102 (108)
T smart00099 93 TLWVDPFEVS 102 (108)
T ss_pred EEEECCCEEE
Confidence 5999999863
Done!