Query 028425
Match_columns 209
No_of_seqs 161 out of 300
Neff 3.7
Searched_HMMs 46136
Date Fri Mar 29 11:20:00 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/028425.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/028425hhsearch_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 1.3E-87 2.9E-92 565.5 16.5 186 1-186 1-186 (193)
2 PTZ00097 60S ribosomal protein 100.0 4.5E-80 9.6E-85 518.9 19.3 174 3-176 1-174 (175)
3 cd01417 Ribosomal_L19e_E Ribos 100.0 9.8E-79 2.1E-83 506.6 17.5 164 4-167 1-164 (164)
4 PTZ00436 60S ribosomal protein 100.0 5.3E-78 1.2E-82 542.2 17.9 170 1-170 1-170 (357)
5 PF01280 Ribosomal_L19e: Ribos 100.0 1.4E-74 3E-79 475.4 14.0 148 2-149 1-148 (148)
6 cd00481 Ribosomal_L19e Ribosom 100.0 5.6E-73 1.2E-77 464.5 14.9 145 4-148 1-145 (145)
7 PRK08570 rpl19e 50S ribosomal 100.0 1.2E-72 2.6E-77 464.7 15.7 147 1-147 1-147 (150)
8 cd01418 Ribosomal_L19e_A Ribos 100.0 5.7E-71 1.2E-75 452.6 15.6 142 4-145 1-142 (145)
9 COG2147 RPL19A Ribosomal prote 100.0 6.2E-67 1.3E-71 429.7 14.9 149 1-149 1-149 (150)
10 PRK00247 putative inner membra 80.6 31 0.00067 33.6 11.9 69 92-167 291-363 (429)
11 TIGR01764 excise DNA binding d 70.4 2.7 5.9E-05 26.3 1.3 29 23-52 1-29 (49)
12 PF12728 HTH_17: Helix-turn-he 69.5 3 6.5E-05 27.4 1.4 28 23-51 1-28 (51)
13 PF13453 zf-TFIIB: Transcripti 51.8 6.4 0.00014 25.6 0.6 15 20-34 26-40 (41)
14 PF12802 MarR_2: MarR family; 47.1 28 0.00061 23.0 3.2 53 6-60 6-61 (62)
15 PF13880 Acetyltransf_13: ESCO 46.0 6.5 0.00014 29.3 -0.1 14 16-29 5-18 (70)
16 TIGR02075 pyrH_bact uridylate 44.0 25 0.00053 30.3 3.1 48 5-52 77-125 (233)
17 PRK05920 aromatic acid decarbo 38.4 36 0.00079 29.6 3.3 47 9-58 121-167 (204)
18 PF01479 S4: S4 domain; Inter 37.1 25 0.00054 22.7 1.7 27 30-56 8-34 (48)
19 TIGR01610 phage_O_Nterm phage 35.6 43 0.00093 25.2 3.0 38 16-54 40-81 (95)
20 PHA00616 hypothetical protein 32.7 25 0.00055 24.2 1.2 17 129-145 8-24 (44)
21 PRK06029 3-octaprenyl-4-hydrox 32.5 56 0.0012 28.0 3.5 46 9-57 106-151 (185)
22 smart00345 HTH_GNTR helix_turn 32.2 39 0.00085 21.6 2.0 25 32-56 32-56 (60)
23 PF08535 KorB: KorB domain; I 28.3 50 0.0011 24.5 2.2 39 6-51 5-43 (93)
24 PRK11548 outer membrane biogen 28.1 40 0.00088 26.3 1.8 26 22-47 36-61 (113)
25 cd04254 AAK_UMPK-PyrH-Ec UMP k 26.6 63 0.0014 27.6 2.9 43 10-52 82-124 (231)
26 TIGR02988 YaaA_near_RecF S4 do 23.8 50 0.0011 22.5 1.4 21 35-55 21-41 (59)
27 PF14468 DUF4427: Protein of u 23.6 56 0.0012 27.4 1.9 32 13-53 31-62 (132)
28 PF01047 MarR: MarR family; I 23.3 52 0.0011 21.7 1.4 25 34-58 31-55 (59)
29 COG3592 Uncharacterized conser 23.0 40 0.00088 25.7 0.9 19 11-30 35-53 (74)
30 TIGR00421 ubiX_pad polyprenyl 22.6 1.1E+02 0.0023 25.9 3.4 47 9-58 103-149 (181)
31 smart00420 HTH_DEOR helix_turn 22.5 73 0.0016 19.8 1.9 25 32-56 26-50 (53)
32 PF13412 HTH_24: Winged helix- 22.5 62 0.0013 20.8 1.6 20 32-51 29-48 (48)
33 COG5104 PRP40 Splicing factor 21.9 3.2E+02 0.0068 27.7 6.9 50 5-55 425-487 (590)
34 PF09851 SHOCT: Short C-termin 21.7 1.1E+02 0.0024 18.9 2.6 20 104-123 6-25 (31)
35 PF00096 zf-C2H2: Zinc finger, 21.7 70 0.0015 17.5 1.5 16 129-144 7-22 (23)
36 smart00099 btg1 tob/btg1 famil 21.2 35 0.00076 27.4 0.2 10 21-30 93-102 (108)
37 PF15319 RHINO: RAD9, RAD1, HU 20.9 40 0.00086 30.6 0.6 35 82-120 200-234 (236)
38 TIGR02337 HpaR homoprotocatech 20.6 92 0.002 23.5 2.4 36 25-60 44-82 (118)
39 PF06353 DUF1062: Protein of u 20.3 75 0.0016 26.5 2.0 23 34-56 113-135 (142)
No 1
>KOG1696 consensus 60s ribosomal protein L19 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.3e-87 Score=565.47 Aligned_cols=186 Identities=73% Similarity=1.106 Sum_probs=184.7
Q ss_pred CCcchhhHHHHHHHhccCCCceecCccchhHHHhhhhhHHHHhhhhcCceeecCCCCCChhHHHHHHHHHhcCcCCCCCC
Q 028425 1 MVSLKLQKRLSASVLKCGRGKVWLDPNEVNEISMANSRQNIRKLVKDGFIIRKPTKIHSRSRARRMKEAKRKGRHSGYGK 80 (209)
Q Consensus 1 M~~l~~QKRLAAsVL~cGk~kVWlDPne~~eIa~AnsR~~IRkLIKdGlIi~Kp~~~hSR~R~r~~~~ak~kGRh~G~Gk 80 (209)
|++|++|||||||||+||+.+|||||||++||++|||||+|++||+||+||.+|+++|||+||+++.+++++|||+|+|+
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 cccccccCCchhHHHHHHHHHHHHHHHHHHhcCCCChhhhHHHHhhhcCCccccHHHHHHHHHHHhhHHHHhhhhhHHHH
Q 028425 81 RKGTREARLPTKVLWMRRMRVLRRLLRKYREAKKIDRHMYHDMYMKVKGNVFKNKRVLMESIHKSKAEKAREKTLSDQFE 160 (209)
Q Consensus 81 RKGt~~AR~p~K~~WmrRiR~lRrlLr~~Re~~kID~h~Yr~LY~kaKGn~Fknk~~L~e~I~k~Kaek~r~k~l~dQae 160 (209)
|+||+|||||+|++||+||||||+||++|||+|+||+||||+||+++|||+|||+++||||||+.|||++++|+|+||||
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 028425 161 AKRAKNKASRERKIARREERLAQGPG 186 (209)
Q Consensus 161 A~r~k~k~~r~rr~~r~~~kk~~~~~ 186 (209)
|+|.++++++++++|++++++++++.
T Consensus 161 Arr~k~k~ar~rreer~~~k~~~~~~ 186 (193)
T KOG1696|consen 161 ARRLKNKAARKRREERLAAKPQELIK 186 (193)
T ss_pred HHHhhhHHHhhhHHHHHhhchhhhhc
Confidence 99999999999999999999998875
No 2
>PTZ00097 60S ribosomal protein L19; Provisional
Probab=100.00 E-value=4.5e-80 Score=518.88 Aligned_cols=174 Identities=72% Similarity=1.159 Sum_probs=171.3
Q ss_pred cchhhHHHHHHHhccCCCceecCccchhHHHhhhhhHHHHhhhhcCceeecCCCCCChhHHHHHHHHHhcCcCCCCCCcc
Q 028425 3 SLKLQKRLSASVLKCGRGKVWLDPNEVNEISMANSRQNIRKLVKDGFIIRKPTKIHSRSRARRMKEAKRKGRHSGYGKRK 82 (209)
Q Consensus 3 ~l~~QKRLAAsVL~cGk~kVWlDPne~~eIa~AnsR~~IRkLIKdGlIi~Kp~~~hSR~R~r~~~~ak~kGRh~G~GkRK 82 (209)
+|++||||||+||+||+++||||||+++||++||||+|||+||+||+|+.+|++||||+|++++++++++|||+|+|+|+
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 cccccCCchhHHHHHHHHHHHHHHHHHHhcCCCChhhhHHHHhhhcCCccccHHHHHHHHHHHhhHHHHhhhhhHHHHHH
Q 028425 83 GTREARLPTKVLWMRRMRVLRRLLRKYREAKKIDRHMYHDMYMKVKGNVFKNKRVLMESIHKSKAEKAREKTLSDQFEAK 162 (209)
Q Consensus 83 Gt~~AR~p~K~~WmrRiR~lRrlLr~~Re~~kID~h~Yr~LY~kaKGn~Fknk~~L~e~I~k~Kaek~r~k~l~dQaeA~ 162 (209)
||+|||||+|+.||++||+||++|++|||+|+||+|+||.||++||||+|+|+++|++|||+.|+|+++++.|+||+||+
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 028425 163 RAKNKASRERKIAR 176 (209)
Q Consensus 163 r~k~k~~r~rr~~r 176 (209)
+.++++++++++++
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=9.8e-79 Score=506.64 Aligned_cols=164 Identities=78% Similarity=1.218 Sum_probs=162.0
Q ss_pred chhhHHHHHHHhccCCCceecCccchhHHHhhhhhHHHHhhhhcCceeecCCCCCChhHHHHHHHHHhcCcCCCCCCccc
Q 028425 4 LKLQKRLSASVLKCGRGKVWLDPNEVNEISMANSRQNIRKLVKDGFIIRKPTKIHSRSRARRMKEAKRKGRHSGYGKRKG 83 (209)
Q Consensus 4 l~~QKRLAAsVL~cGk~kVWlDPne~~eIa~AnsR~~IRkLIKdGlIi~Kp~~~hSR~R~r~~~~ak~kGRh~G~GkRKG 83 (209)
|++|+||||+||+||+++||||||+++||++||||+|||+||+||+|+++|++||||+|++++++++++|||+|+|+|+|
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 ccccCCchhHHHHHHHHHHHHHHHHHHhcCCCChhhhHHHHhhhcCCccccHHHHHHHHHHHhhHHHHhhhhhHHHHHHH
Q 028425 84 TREARLPTKVLWMRRMRVLRRLLRKYREAKKIDRHMYHDMYMKVKGNVFKNKRVLMESIHKSKAEKAREKTLSDQFEAKR 163 (209)
Q Consensus 84 t~~AR~p~K~~WmrRiR~lRrlLr~~Re~~kID~h~Yr~LY~kaKGn~Fknk~~L~e~I~k~Kaek~r~k~l~dQaeA~r 163 (209)
|+|||||+|+.||++||+||++|++|||+|+||+|+||.||++||||+|+|+++|++|||+.|+|+++++.|+||+||++
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 028425 164 AKNK 167 (209)
Q Consensus 164 ~k~k 167 (209)
++++
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=5.3e-78 Score=542.25 Aligned_cols=170 Identities=68% Similarity=1.106 Sum_probs=167.5
Q ss_pred CCcchhhHHHHHHHhccCCCceecCccchhHHHhhhhhHHHHhhhhcCceeecCCCCCChhHHHHHHHHHhcCcCCCCCC
Q 028425 1 MVSLKLQKRLSASVLKCGRGKVWLDPNEVNEISMANSRQNIRKLVKDGFIIRKPTKIHSRSRARRMKEAKRKGRHSGYGK 80 (209)
Q Consensus 1 M~~l~~QKRLAAsVL~cGk~kVWlDPne~~eIa~AnsR~~IRkLIKdGlIi~Kp~~~hSR~R~r~~~~ak~kGRh~G~Gk 80 (209)
|++|++||||||+||+||++||||||||++||++||||+|||+||+||+|+++|++||||+|+|++++++++|||+|+||
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 cccccccCCchhHHHHHHHHHHHHHHHHHHhcCCCChhhhHHHHhhhcCCccccHHHHHHHHHHHhhHHHHhhhhhHHHH
Q 028425 81 RKGTREARLPTKVLWMRRMRVLRRLLRKYREAKKIDRHMYHDMYMKVKGNVFKNKRVLMESIHKSKAEKAREKTLSDQFE 160 (209)
Q Consensus 81 RKGt~~AR~p~K~~WmrRiR~lRrlLr~~Re~~kID~h~Yr~LY~kaKGn~Fknk~~L~e~I~k~Kaek~r~k~l~dQae 160 (209)
|+||+|||||+|++||+|||+||++|++|||+|+||+|+||.||+++|||+|+|++||++|||+.|+|+.|++.|.||+|
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 028425 161 AKRAKNKASR 170 (209)
Q Consensus 161 A~r~k~k~~r 170 (209)
|+|.++++.|
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=1.4e-74 Score=475.41 Aligned_cols=148 Identities=68% Similarity=1.097 Sum_probs=130.9
Q ss_pred CcchhhHHHHHHHhccCCCceecCccchhHHHhhhhhHHHHhhhhcCceeecCCCCCChhHHHHHHHHHhcCcCCCCCCc
Q 028425 2 VSLKLQKRLSASVLKCGRGKVWLDPNEVNEISMANSRQNIRKLVKDGFIIRKPTKIHSRSRARRMKEAKRKGRHSGYGKR 81 (209)
Q Consensus 2 ~~l~~QKRLAAsVL~cGk~kVWlDPne~~eIa~AnsR~~IRkLIKdGlIi~Kp~~~hSR~R~r~~~~ak~kGRh~G~GkR 81 (209)
|+|++||||||+||+||+++|||||||++||++||||+|||+||+||+|+++|++|||||||+++++++++|||+|+|+|
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 58999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccccccCCchhHHHHHHHHHHHHHHHHHHhcCCCChhhhHHHHhhhcCCccccHHHHHHHHHHHhhHH
Q 028425 82 KGTREARLPTKVLWMRRMRVLRRLLRKYREAKKIDRHMYHDMYMKVKGNVFKNKRVLMESIHKSKAEK 149 (209)
Q Consensus 82 KGt~~AR~p~K~~WmrRiR~lRrlLr~~Re~~kID~h~Yr~LY~kaKGn~Fknk~~L~e~I~k~Kaek 149 (209)
+||+|||||+|+.||++||+||++|++|||+|+||+|+||+||++||||+|+|+++|+||||++++|+
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 99999999999999999999999999999999999999999999999999999999999999999875
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=5.6e-73 Score=464.52 Aligned_cols=145 Identities=64% Similarity=1.101 Sum_probs=143.0
Q ss_pred chhhHHHHHHHhccCCCceecCccchhHHHhhhhhHHHHhhhhcCceeecCCCCCChhHHHHHHHHHhcCcCCCCCCccc
Q 028425 4 LKLQKRLSASVLKCGRGKVWLDPNEVNEISMANSRQNIRKLVKDGFIIRKPTKIHSRSRARRMKEAKRKGRHSGYGKRKG 83 (209)
Q Consensus 4 l~~QKRLAAsVL~cGk~kVWlDPne~~eIa~AnsR~~IRkLIKdGlIi~Kp~~~hSR~R~r~~~~ak~kGRh~G~GkRKG 83 (209)
|++|+||||+||+||+++||||||+++||++||||+|||+||+||+|+++|++||||+|++++++++++|||+|+|||+|
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 ccccCCchhHHHHHHHHHHHHHHHHHHhcCCCChhhhHHHHhhhcCCccccHHHHHHHHHHHhhH
Q 028425 84 TREARLPTKVLWMRRMRVLRRLLRKYREAKKIDRHMYHDMYMKVKGNVFKNKRVLMESIHKSKAE 148 (209)
Q Consensus 84 t~~AR~p~K~~WmrRiR~lRrlLr~~Re~~kID~h~Yr~LY~kaKGn~Fknk~~L~e~I~k~Kae 148 (209)
|+|||||+|+.||++||+||++|++|||+|+||+|+||.||++||||+|+|+++|++|||+.++|
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=1.2e-72 Score=464.70 Aligned_cols=147 Identities=43% Similarity=0.742 Sum_probs=145.2
Q ss_pred CCcchhhHHHHHHHhccCCCceecCccchhHHHhhhhhHHHHhhhhcCceeecCCCCCChhHHHHHHHHHhcCcCCCCCC
Q 028425 1 MVSLKLQKRLSASVLKCGRGKVWLDPNEVNEISMANSRQNIRKLVKDGFIIRKPTKIHSRSRARRMKEAKRKGRHSGYGK 80 (209)
Q Consensus 1 M~~l~~QKRLAAsVL~cGk~kVWlDPne~~eIa~AnsR~~IRkLIKdGlIi~Kp~~~hSR~R~r~~~~ak~kGRh~G~Gk 80 (209)
|++|++|+||||+||+||+++||||||+++||++||||+|||+||+||+|+++|++||||+|++++++++++|||+|+||
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 cccccccCCchhHHHHHHHHHHHHHHHHHHhcCCCChhhhHHHHhhhcCCccccHHHHHHHHHHHhh
Q 028425 81 RKGTREARLPTKVLWMRRMRVLRRLLRKYREAKKIDRHMYHDMYMKVKGNVFKNKRVLMESIHKSKA 147 (209)
Q Consensus 81 RKGt~~AR~p~K~~WmrRiR~lRrlLr~~Re~~kID~h~Yr~LY~kaKGn~Fknk~~L~e~I~k~Ka 147 (209)
|+||+|||||+|+.||++||+||++|++|||+|+||+|+||.||++||||+|+|+++|++||+....
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=5.7e-71 Score=452.63 Aligned_cols=142 Identities=39% Similarity=0.722 Sum_probs=140.4
Q ss_pred chhhHHHHHHHhccCCCceecCccchhHHHhhhhhHHHHhhhhcCceeecCCCCCChhHHHHHHHHHhcCcCCCCCCccc
Q 028425 4 LKLQKRLSASVLKCGRGKVWLDPNEVNEISMANSRQNIRKLVKDGFIIRKPTKIHSRSRARRMKEAKRKGRHSGYGKRKG 83 (209)
Q Consensus 4 l~~QKRLAAsVL~cGk~kVWlDPne~~eIa~AnsR~~IRkLIKdGlIi~Kp~~~hSR~R~r~~~~ak~kGRh~G~GkRKG 83 (209)
|++||||||+||+||+++||||||+++||++||||+|||+||+||+|+++|++||||+|++++++++++|||+|+|||+|
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 ccccCCchhHHHHHHHHHHHHHHHHHHhcCCCChhhhHHHHhhhcCCccccHHHHHHHHHHH
Q 028425 84 TREARLPTKVLWMRRMRVLRRLLRKYREAKKIDRHMYHDMYMKVKGNVFKNKRVLMESIHKS 145 (209)
Q Consensus 84 t~~AR~p~K~~WmrRiR~lRrlLr~~Re~~kID~h~Yr~LY~kaKGn~Fknk~~L~e~I~k~ 145 (209)
|+|||||+|+.||++||+||++|++|||+|+||+|+||.||++||||+|+|+++|++||...
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=6.2e-67 Score=429.68 Aligned_cols=149 Identities=49% Similarity=0.808 Sum_probs=146.6
Q ss_pred CCcchhhHHHHHHHhccCCCceecCccchhHHHhhhhhHHHHhhhhcCceeecCCCCCChhHHHHHHHHHhcCcCCCCCC
Q 028425 1 MVSLKLQKRLSASVLKCGRGKVWLDPNEVNEISMANSRQNIRKLVKDGFIIRKPTKIHSRSRARRMKEAKRKGRHSGYGK 80 (209)
Q Consensus 1 M~~l~~QKRLAAsVL~cGk~kVWlDPne~~eIa~AnsR~~IRkLIKdGlIi~Kp~~~hSR~R~r~~~~ak~kGRh~G~Gk 80 (209)
|+||+.|+||||+||+||+++||||||+++||++|+||+|||.||+||+|+.+|++|+|++|++++++++++|||+||||
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 cccccccCCchhHHHHHHHHHHHHHHHHHHhcCCCChhhhHHHHhhhcCCccccHHHHHHHHHHHhhHH
Q 028425 81 RKGTREARLPTKVLWMRRMRVLRRLLRKYREAKKIDRHMYHDMYMKVKGNVFKNKRVLMESIHKSKAEK 149 (209)
Q Consensus 81 RKGt~~AR~p~K~~WmrRiR~lRrlLr~~Re~~kID~h~Yr~LY~kaKGn~Fknk~~L~e~I~k~Kaek 149 (209)
|+||++||||+|+.||.+||+||++|++||++|+||+|+||.||+++|||.|+++++|.+||.+++.++
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
>PRK00247 putative inner membrane protein translocase component YidC; Validated
Probab=80.65 E-value=31 Score=33.57 Aligned_cols=69 Identities=16% Similarity=0.252 Sum_probs=36.4
Q ss_pred hHHHHHHHHHHHHHHHHHHhcC---CCChhhhHHHHhhhcCCccccHHHHHHHHHHHhhHHHHhhhhhHH-HHHHHhhhH
Q 028425 92 KVLWMRRMRVLRRLLRKYREAK---KIDRHMYHDMYMKVKGNVFKNKRVLMESIHKSKAEKAREKTLSDQ-FEAKRAKNK 167 (209)
Q Consensus 92 K~~WmrRiR~lRrlLr~~Re~~---kID~h~Yr~LY~kaKGn~Fknk~~L~e~I~k~Kaek~r~k~l~dQ-aeA~r~k~k 167 (209)
+..|..+.+..+..++..|... .|..+.+..|..- |...=.+.=...+++|+++|.++.+ -||.|.-++
T Consensus 291 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~-------~~~~~~~~~~~~~~~k~~~k~~~~~~~~~~~~~~~ 363 (429)
T PRK00247 291 RAQYREKQKEKKAFLWTLRRNRLRMIITPWRAPELHAE-------NAEIKKTRTAEKNEAKARKKEIAQKRRAAEREINR 363 (429)
T ss_pred HHHHHHHHHHHHHHHHHHHhccccccCCcccHHHHHHH-------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4456666655555555555444 7777777766432 2222233334446667776666543 344444444
No 11
>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=70.39 E-value=2.7 Score=26.29 Aligned_cols=29 Identities=21% Similarity=0.331 Sum_probs=24.3
Q ss_pred ecCccchhHHHhhhhhHHHHhhhhcCceee
Q 028425 23 WLDPNEVNEISMANSRQNIRKLVKDGFIIR 52 (209)
Q Consensus 23 WlDPne~~eIa~AnsR~~IRkLIKdGlIi~ 52 (209)
||++.|+.++-. .|+..|+.|+++|.|-.
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 78999999999998764
No 12
>PF12728 HTH_17: Helix-turn-helix domain
Probab=69.53 E-value=3 Score=27.40 Aligned_cols=28 Identities=25% Similarity=0.368 Sum_probs=24.4
Q ss_pred ecCccchhHHHhhhhhHHHHhhhhcCcee
Q 028425 23 WLDPNEVNEISMANSRQNIRKLVKDGFII 51 (209)
Q Consensus 23 WlDPne~~eIa~AnsR~~IRkLIKdGlIi 51 (209)
||++.|+.++-. +|+..|+++++.|.|.
T Consensus 1 ~lt~~e~a~~l~-is~~tv~~~~~~g~i~ 28 (51)
T PF12728_consen 1 YLTVKEAAELLG-ISRSTVYRWIRQGKIP 28 (51)
T ss_pred CCCHHHHHHHHC-cCHHHHHHHHHcCCCC
Confidence 688899999888 6999999999999663
No 13
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=51.84 E-value=6.4 Score=25.58 Aligned_cols=15 Identities=27% Similarity=0.809 Sum_probs=12.3
Q ss_pred CceecCccchhHHHh
Q 028425 20 GKVWLDPNEVNEISM 34 (209)
Q Consensus 20 ~kVWlDPne~~eIa~ 34 (209)
.-||||++|++.|.+
T Consensus 26 ~G~W~d~~el~~~~e 40 (41)
T PF13453_consen 26 GGIWFDAGELEKLLE 40 (41)
T ss_pred CeEEccHHHHHHHHh
Confidence 469999999988753
No 14
>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=47.10 E-value=28 Score=23.03 Aligned_cols=53 Identities=21% Similarity=0.224 Sum_probs=32.6
Q ss_pred hhHHHHHHHhccCCCceecCccchhHH---HhhhhhHHHHhhhhcCceeecCCCCCCh
Q 028425 6 LQKRLSASVLKCGRGKVWLDPNEVNEI---SMANSRQNIRKLVKDGFIIRKPTKIHSR 60 (209)
Q Consensus 6 ~QKRLAAsVL~cGk~kVWlDPne~~eI---a~AnsR~~IRkLIKdGlIi~Kp~~~hSR 60 (209)
.|-++-..|..+|.. ++-++++.+. +-..--..|.+|++.|+|.+.+.....|
T Consensus 6 ~q~~vL~~l~~~~~~--~~t~~~la~~l~~~~~~vs~~v~~L~~~Glv~r~~~~~D~R 61 (62)
T PF12802_consen 6 SQFRVLMALARHPGE--ELTQSELAERLGISKSTVSRIVKRLEKKGLVERERDPGDRR 61 (62)
T ss_dssp HHHHHHHHHHHSTTS--GEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEE-SSSTT
T ss_pred HHHHHHHHHHHCCCC--CcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEeCCCCCCC
Confidence 344555556666655 3334444432 3344456789999999999998877655
No 15
>PF13880 Acetyltransf_13: ESCO1/2 acetyl-transferase
Probab=46.01 E-value=6.5 Score=29.27 Aligned_cols=14 Identities=29% Similarity=1.037 Sum_probs=11.9
Q ss_pred ccCCCceecCccch
Q 028425 16 KCGRGKVWLDPNEV 29 (209)
Q Consensus 16 ~cGk~kVWlDPne~ 29 (209)
-||.++||..|..-
T Consensus 5 ~~GI~RIWV~~~~R 18 (70)
T PF13880_consen 5 VCGISRIWVSPSHR 18 (70)
T ss_pred EEEeEEEEeChhhh
Confidence 49999999999753
No 16
>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=44.05 E-value=25 Score=30.26 Aligned_cols=48 Identities=15% Similarity=0.126 Sum_probs=38.1
Q ss_pred hhhHHH-HHHHhccCCCceecCccchhHHHhhhhhHHHHhhhhcCceee
Q 028425 5 KLQKRL-SASVLKCGRGKVWLDPNEVNEISMANSRQNIRKLVKDGFIIR 52 (209)
Q Consensus 5 ~~QKRL-AAsVL~cGk~kVWlDPne~~eIa~AnsR~~IRkLIKdGlIi~ 52 (209)
+++-+| +..+...|.+-++|+|.....+..-++.+.+..|++.|.|..
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 777778999999999998765555567899999999999743
No 17
>PRK05920 aromatic acid decarboxylase; Validated
Probab=38.43 E-value=36 Score=29.62 Aligned_cols=47 Identities=32% Similarity=0.289 Sum_probs=36.5
Q ss_pred HHHHHHhccCCCceecCccchhHHHhhhhhHHHHhhhhcCceeecCCCCC
Q 028425 9 RLSASVLKCGRGKVWLDPNEVNEISMANSRQNIRKLVKDGFIIRKPTKIH 58 (209)
Q Consensus 9 RLAAsVL~cGk~kVWlDPne~~eIa~AnsR~~IRkLIKdGlIi~Kp~~~h 58 (209)
+.|...|++|. .|.|=|.+... ++.++++|..|-..|.++.-|+.+.
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 55556788776 55556865444 7888999999999999999999874
No 18
>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=37.10 E-value=25 Score=22.71 Aligned_cols=27 Identities=26% Similarity=0.450 Sum_probs=20.6
Q ss_pred hHHHhhhhhHHHHhhhhcCceeecCCC
Q 028425 30 NEISMANSRQNIRKLVKDGFIIRKPTK 56 (209)
Q Consensus 30 ~eIa~AnsR~~IRkLIKdGlIi~Kp~~ 56 (209)
.+...+.||.++++||+.|.|...-..
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 19
>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=35.56 E-value=43 Score=25.21 Aligned_cols=38 Identities=18% Similarity=0.305 Sum_probs=26.4
Q ss_pred ccCCCceecCccchhHHHhhhhhHH----HHhhhhcCceeecC
Q 028425 16 KCGRGKVWLDPNEVNEISMANSRQN----IRKLVKDGFIIRKP 54 (209)
Q Consensus 16 ~cGk~kVWlDPne~~eIa~AnsR~~----IRkLIKdGlIi~Kp 54 (209)
|+++..++|.+.|+.++... ||+. |..|.++|+|.+..
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 44556777777777776654 4444 56799999998654
No 20
>PHA00616 hypothetical protein
Probab=32.69 E-value=25 Score=24.15 Aligned_cols=17 Identities=24% Similarity=0.634 Sum_probs=15.1
Q ss_pred CCccccHHHHHHHHHHH
Q 028425 129 GNVFKNKRVLMESIHKS 145 (209)
Q Consensus 129 Gn~Fknk~~L~e~I~k~ 145 (209)
|..|.++++|..|+.+.
T Consensus 8 G~~F~~~s~l~~H~r~~ 24 (44)
T PHA00616 8 GGIFRKKKEVIEHLLSV 24 (44)
T ss_pred hHHHhhHHHHHHHHHHh
Confidence 78999999999999664
No 21
>PRK06029 3-octaprenyl-4-hydroxybenzoate carboxy-lyase; Provisional
Probab=32.52 E-value=56 Score=27.97 Aligned_cols=46 Identities=26% Similarity=0.255 Sum_probs=35.8
Q ss_pred HHHHHHhccCCCceecCccchhHHHhhhhhHHHHhhhhcCceeecCCCC
Q 028425 9 RLSASVLKCGRGKVWLDPNEVNEISMANSRQNIRKLVKDGFIIRKPTKI 57 (209)
Q Consensus 9 RLAAsVL~cGk~kVWlDPne~~eIa~AnsR~~IRkLIKdGlIi~Kp~~~ 57 (209)
+.|...|.+++ .|.|=|. +--.+..+++++.+|-+.|.++.-|..|
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 44556677665 5555675 4566889999999999999999999876
No 22
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=32.19 E-value=39 Score=21.64 Aligned_cols=25 Identities=24% Similarity=0.578 Sum_probs=18.2
Q ss_pred HHhhhhhHHHHhhhhcCceeecCCC
Q 028425 32 ISMANSRQNIRKLVKDGFIIRKPTK 56 (209)
Q Consensus 32 Ia~AnsR~~IRkLIKdGlIi~Kp~~ 56 (209)
|+.+.-++.+..|.++|+|...|-.
T Consensus 32 vs~~tv~~~l~~L~~~g~i~~~~~~ 56 (60)
T smart00345 32 VSRTTVREALSRLEAEGLVQRRPGS 56 (60)
T ss_pred CCHHHHHHHHHHHHHCCCEEEecCC
Confidence 3345557778899999999876643
No 23
>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=28.32 E-value=50 Score=24.52 Aligned_cols=39 Identities=23% Similarity=0.600 Sum_probs=24.6
Q ss_pred hhHHHHHHHhccCCCceecCccchhHHHhhhhhHHHHhhhhcCcee
Q 028425 6 LQKRLSASVLKCGRGKVWLDPNEVNEISMANSRQNIRKLVKDGFII 51 (209)
Q Consensus 6 ~QKRLAAsVL~cGk~kVWlDPne~~eIa~AnsR~~IRkLIKdGlIi 51 (209)
+|.-||..| |+++-|+ .+-++-++--++|+.|+.+|.|.
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 466777754 8999887 45566667778999999999764
No 24
>PRK11548 outer membrane biogenesis protein BamE; Provisional
Probab=28.11 E-value=40 Score=26.30 Aligned_cols=26 Identities=23% Similarity=0.440 Sum_probs=23.0
Q ss_pred eecCccchhHHHhhhhhHHHHhhhhc
Q 028425 22 VWLDPNEVNEISMANSRQNIRKLVKD 47 (209)
Q Consensus 22 VWlDPne~~eIa~AnsR~~IRkLIKd 47 (209)
-++||+.+++|.--.|+++|+.|+-.
T Consensus 36 ~~~~~~~l~~l~~GmTk~qV~~lLGt 61 (113)
T PRK11548 36 NYLTPNDVAKIHVGMTQQQVAYTLGT 61 (113)
T ss_pred ccCCHHHHHHhcCCCCHHHHHHHcCC
Confidence 38899999999999999999998843
No 25
>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=26.62 E-value=63 Score=27.65 Aligned_cols=43 Identities=9% Similarity=0.138 Sum_probs=35.1
Q ss_pred HHHHHhccCCCceecCccchhHHHhhhhhHHHHhhhhcCceee
Q 028425 10 LSASVLKCGRGKVWLDPNEVNEISMANSRQNIRKLVKDGFIIR 52 (209)
Q Consensus 10 LAAsVL~cGk~kVWlDPne~~eIa~AnsR~~IRkLIKdGlIi~ 52 (209)
|++.+...|.+-+||+|-+++.+.....-+.+..++..|.|..
T Consensus 82 l~~~L~~~Gv~a~~l~~~~~~~~~~~~~~~~l~~~l~~g~ipV 124 (231)
T cd04254 82 LQDALESLGVKTRVMSAIPMQGVAEPYIRRRAIRHLEKGRVVI 124 (231)
T ss_pred HHHHHHHcCCCeEEEcHHHhhhhhcccCHHHHHHHHHCCCEEE
Confidence 5667778999999999999876655556789999999998743
No 26
>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=23.79 E-value=50 Score=22.51 Aligned_cols=21 Identities=5% Similarity=0.132 Sum_probs=17.4
Q ss_pred hhhhHHHHhhhhcCceeecCC
Q 028425 35 ANSRQNIRKLVKDGFIIRKPT 55 (209)
Q Consensus 35 AnsR~~IRkLIKdGlIi~Kp~ 55 (209)
+.||..+++||++|.|...-.
T Consensus 21 ~~SR~~~k~li~~G~V~VNg~ 41 (59)
T TIGR02988 21 IDSGGQAKWFLQENEVLVNGE 41 (59)
T ss_pred ccCHHHHHHHHHcCCEEECCE
Confidence 349999999999999987443
No 27
>PF14468 DUF4427: Protein of unknown function (DUF4427)
Probab=23.62 E-value=56 Score=27.36 Aligned_cols=32 Identities=22% Similarity=0.430 Sum_probs=25.0
Q ss_pred HHhccCCCceecCccchhHHHhhhhhHHHHhhhhcCceeec
Q 028425 13 SVLKCGRGKVWLDPNEVNEISMANSRQNIRKLVKDGFIIRK 53 (209)
Q Consensus 13 sVL~cGk~kVWlDPne~~eIa~AnsR~~IRkLIKdGlIi~K 53 (209)
-++.-|...|||- + |+.+=+|.||++|.|+.-
T Consensus 31 ~~~e~G~~wvWi~-D--------N~~~~vRALl~~grV~v~ 62 (132)
T PF14468_consen 31 YDREFGNAWVWIH-D--------NQSEVVRALLQAGRVKVN 62 (132)
T ss_pred chhhcCceEEEEe-c--------CcCHHHHHHHHcCceeec
Confidence 4567899999993 3 456778999999998754
No 28
>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=23.33 E-value=52 Score=21.68 Aligned_cols=25 Identities=24% Similarity=0.315 Sum_probs=19.0
Q ss_pred hhhhhHHHHhhhhcCceeecCCCCC
Q 028425 34 MANSRQNIRKLVKDGFIIRKPTKIH 58 (209)
Q Consensus 34 ~AnsR~~IRkLIKdGlIi~Kp~~~h 58 (209)
.++.-.-|.+|++.|+|.+.+....
T Consensus 31 ~~~~t~~i~~L~~~g~I~r~~~~~D 55 (59)
T PF01047_consen 31 RSTVTRIIKRLEKKGLIERERDPDD 55 (59)
T ss_dssp HHHHHHHHHHHHHTTSEEEEEETTE
T ss_pred hhHHHHHHHHHHHCCCEEeccCCCC
Confidence 3445567899999999998876543
No 29
>COG3592 Uncharacterized conserved protein [Function unknown]
Probab=22.96 E-value=40 Score=25.65 Aligned_cols=19 Identities=32% Similarity=0.789 Sum_probs=14.5
Q ss_pred HHHHhccCCCceecCccchh
Q 028425 11 SASVLKCGRGKVWLDPNEVN 30 (209)
Q Consensus 11 AAsVL~cGk~kVWlDPne~~ 30 (209)
+++|+++|..= ||+|+..+
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 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=22.57 E-value=1.1e+02 Score=25.94 Aligned_cols=47 Identities=30% Similarity=0.295 Sum_probs=35.3
Q ss_pred HHHHHHhccCCCceecCccchhHHHhhhhhHHHHhhhhcCceeecCCCCC
Q 028425 9 RLSASVLKCGRGKVWLDPNEVNEISMANSRQNIRKLVKDGFIIRKPTKIH 58 (209)
Q Consensus 9 RLAAsVL~cGk~kVWlDPne~~eIa~AnsR~~IRkLIKdGlIi~Kp~~~h 58 (209)
+.|...|+++. .|.|=|.+. -.++.+.+++.+|-..|.++.-|..+.
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 44455777765 555567544 457888999999999999999998763
No 31
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=22.51 E-value=73 Score=19.77 Aligned_cols=25 Identities=24% Similarity=0.411 Sum_probs=18.2
Q ss_pred HHhhhhhHHHHhhhhcCceeecCCC
Q 028425 32 ISMANSRQNIRKLVKDGFIIRKPTK 56 (209)
Q Consensus 32 Ia~AnsR~~IRkLIKdGlIi~Kp~~ 56 (209)
++.+.-+..|..|.+.|+|...+.-
T Consensus 26 ~s~~tv~~~l~~L~~~g~i~~~~~~ 50 (53)
T smart00420 26 VSEMTIRRDLNKLEEQGLLTRVHGG 50 (53)
T ss_pred CCHHHHHHHHHHHHHCCCEEEeecC
Confidence 3445557788899999999876543
No 32
>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=22.45 E-value=62 Score=20.80 Aligned_cols=20 Identities=30% Similarity=0.466 Sum_probs=15.4
Q ss_pred HHhhhhhHHHHhhhhcCcee
Q 028425 32 ISMANSRQNIRKLVKDGFII 51 (209)
Q Consensus 32 Ia~AnsR~~IRkLIKdGlIi 51 (209)
|+.+.....|++|+++|+|.
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 45566788899999999983
No 33
>COG5104 PRP40 Splicing factor [RNA processing and modification]
Probab=21.94 E-value=3.2e+02 Score=27.71 Aligned_cols=50 Identities=22% Similarity=0.235 Sum_probs=37.6
Q ss_pred hhhHHHHHHHhccCCCceecCccchhHHHhhhhh-------------HHHHhhhhcCceeecCC
Q 028425 5 KLQKRLSASVLKCGRGKVWLDPNEVNEISMANSR-------------QNIRKLVKDGFIIRKPT 55 (209)
Q Consensus 5 ~~QKRLAAsVL~cGk~kVWlDPne~~eIa~AnsR-------------~~IRkLIKdGlIi~Kp~ 55 (209)
..-+|+.+..+-+|..-+| |-..++||-.+++- ..+-.||-||+|..+..
T Consensus 425 ~~~r~~~~~~~~~~qis~~-d~~~vdei~~~~~Ek~eE~e~~~d~v~kE~is~i~D~~I~qr~E 487 (590)
T COG5104 425 GFARRSYERETRTGQISPT-DRRAVDEIFEAIAEKKEEGEIKFDKVDKEDISLIVDGLIKQRNE 487 (590)
T ss_pred HHHHHHHHHHHHhccCCCc-cccchHHHHHHHHHHHhhcchhhhhhhHHHHHHHHHHHHHHhHH
Confidence 3446778888888999999 88899999888873 23346788888865443
No 34
>PF09851 SHOCT: Short C-terminal domain; InterPro: IPR018649 This family of hypothetical prokaryotic proteins has no known function.
Probab=21.74 E-value=1.1e+02 Score=18.94 Aligned_cols=20 Identities=15% Similarity=0.298 Sum_probs=16.7
Q ss_pred HHHHHHHhcCCCChhhhHHH
Q 028425 104 RLLRKYREAKKIDRHMYHDM 123 (209)
Q Consensus 104 rlLr~~Re~~kID~h~Yr~L 123 (209)
.-|+.+.+.|.|+-..|...
T Consensus 6 ~~L~~l~~~G~IseeEy~~~ 25 (31)
T PF09851_consen 6 EKLKELYDKGEISEEEYEQK 25 (31)
T ss_pred HHHHHHHHcCCCCHHHHHHH
Confidence 45788899999999999764
No 35
>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=21.71 E-value=70 Score=17.47 Aligned_cols=16 Identities=25% Similarity=0.497 Sum_probs=13.3
Q ss_pred CCccccHHHHHHHHHH
Q 028425 129 GNVFKNKRVLMESIHK 144 (209)
Q Consensus 129 Gn~Fknk~~L~e~I~k 144 (209)
|-+|.+...|..||..
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 36
>smart00099 btg1 tob/btg1 family. The tob/btg1 is a family of proteins that inhibit cell proliferation.
Probab=21.19 E-value=35 Score=27.42 Aligned_cols=10 Identities=50% Similarity=1.165 Sum_probs=8.3
Q ss_pred ceecCccchh
Q 028425 21 KVWLDPNEVN 30 (209)
Q Consensus 21 kVWlDPne~~ 30 (209)
.||+||.|+.
T Consensus 93 tiwvDP~eVs 102 (108)
T smart00099 93 TLWVDPFEVS 102 (108)
T ss_pred EEEECCCEEE
Confidence 5899999864
No 37
>PF15319 RHINO: RAD9, RAD1, HUS1-interacting nuclear orphan protein
Probab=20.88 E-value=40 Score=30.62 Aligned_cols=35 Identities=40% Similarity=0.634 Sum_probs=26.9
Q ss_pred ccccccCCchhHHHHHHHHHHHHHHHHHHhcCCCChhhh
Q 028425 82 KGTREARLPTKVLWMRRMRVLRRLLRKYREAKKIDRHMY 120 (209)
Q Consensus 82 KGt~~AR~p~K~~WmrRiR~lRrlLr~~Re~~kID~h~Y 120 (209)
+-|-.--+.-|++|-+| +-||..|||.|++++..|
T Consensus 200 ~DTPE~~YGiKvTWRRR----~hL~~yLrerGkL~~sq~ 234 (236)
T PF15319_consen 200 EDTPEEKYGIKVTWRRR----RHLLAYLRERGKLSRSQF 234 (236)
T ss_pred ccCCcccccceeeeecc----HHHHHHHHHhCccchhhc
Confidence 34545566779999776 478899999999998764
No 38
>TIGR02337 HpaR homoprotocatechuate degradation operon regulator, HpaR. This Helix-Turn-Helix transcriptional regulator is a member of the MarR family (pfam01047) and is found in association with operons for the degradation of 4-hydroxyphenylacetic acid via homoprotocatechuate.
Probab=20.60 E-value=92 Score=23.51 Aligned_cols=36 Identities=14% Similarity=0.220 Sum_probs=24.0
Q ss_pred CccchhHH---HhhhhhHHHHhhhhcCceeecCCCCCCh
Q 028425 25 DPNEVNEI---SMANSRQNIRKLVKDGFIIRKPTKIHSR 60 (209)
Q Consensus 25 DPne~~eI---a~AnsR~~IRkLIKdGlIi~Kp~~~hSR 60 (209)
.+.++.+. +.++--..|.+|.++|+|.+.+.....|
T Consensus 44 t~~ela~~~~~~~~tvs~~l~~Le~~GlI~r~~~~~D~R 82 (118)
T TIGR02337 44 EFTQLANQACILRPSLTGILARLERDGLVTRLKASNDQR 82 (118)
T ss_pred CHHHHHHHhCCCchhHHHHHHHHHHCCCEEeccCCCCCC
Confidence 44444444 2334456788999999999988766544
No 39
>PF06353 DUF1062: Protein of unknown function (DUF1062); InterPro: IPR009412 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=20.28 E-value=75 Score=26.46 Aligned_cols=23 Identities=30% Similarity=0.673 Sum_probs=20.5
Q ss_pred hhhhhHHHHhhhhcCceeecCCC
Q 028425 34 MANSRQNIRKLVKDGFIIRKPTK 56 (209)
Q Consensus 34 ~AnsR~~IRkLIKdGlIi~Kp~~ 56 (209)
.-.||.+|..|+++|.|...|.+
T Consensus 113 L~lSrs~l~~l~~~G~I~~~~~~ 135 (142)
T PF06353_consen 113 LGLSRSRLKRLIEQGLIRSDPDK 135 (142)
T ss_pred hCcCHHHHHHHHHCCCEEecCcc
Confidence 35799999999999999998876
Done!