Query 046974
Match_columns 212
No_of_seqs 175 out of 290
Neff 3.6
Searched_HMMs 46136
Date Fri Mar 29 06:24:20 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/046974.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/046974hhsearch_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 5.7E-87 1.2E-91 562.9 16.7 185 1-185 1-187 (193)
2 PTZ00097 60S ribosomal protein 100.0 2.7E-79 5.8E-84 515.1 18.7 169 3-171 1-169 (175)
3 cd01417 Ribosomal_L19e_E Ribos 100.0 7.4E-79 1.6E-83 508.3 17.8 164 4-167 1-164 (164)
4 PTZ00436 60S ribosomal protein 100.0 1.4E-77 3.1E-82 540.5 18.9 171 1-171 1-171 (357)
5 PF01280 Ribosomal_L19e: Ribos 100.0 1E-74 2.3E-79 477.0 13.5 148 2-149 1-148 (148)
6 cd00481 Ribosomal_L19e Ribosom 100.0 4.5E-73 9.8E-78 466.0 14.5 145 4-148 1-145 (145)
7 PRK08570 rpl19e 50S ribosomal 100.0 7.9E-73 1.7E-77 466.7 15.5 147 1-147 1-147 (150)
8 cd01418 Ribosomal_L19e_A Ribos 100.0 4.3E-71 9.3E-76 454.2 15.3 142 4-145 1-142 (145)
9 COG2147 RPL19A Ribosomal prote 100.0 4.9E-67 1.1E-71 431.2 14.7 149 1-149 1-149 (150)
10 TIGR01764 excise DNA binding d 68.6 3 6.6E-05 26.1 1.3 29 23-52 1-29 (49)
11 PF12728 HTH_17: Helix-turn-he 68.0 3.3 7.1E-05 27.3 1.4 28 23-51 1-28 (51)
12 PF13453 zf-TFIIB: Transcripti 53.3 6 0.00013 25.8 0.6 15 20-34 26-40 (41)
13 PF13880 Acetyltransf_13: ESCO 48.1 5.8 0.00013 29.6 -0.1 14 16-29 5-18 (70)
14 TIGR02075 pyrH_bact uridylate 48.0 20 0.00043 30.9 3.2 48 5-52 77-125 (233)
15 PRK05920 aromatic acid decarbo 41.6 31 0.00067 30.1 3.4 47 9-58 121-167 (204)
16 PRK00247 putative inner membra 35.8 4.3E+02 0.0094 25.9 11.2 59 93-158 292-353 (429)
17 PRK06029 3-octaprenyl-4-hydrox 34.7 49 0.0011 28.3 3.5 46 9-57 106-151 (185)
18 TIGR01610 phage_O_Nterm phage 34.0 48 0.001 25.0 3.0 38 16-54 40-81 (95)
19 PF01479 S4: S4 domain; Inter 33.4 30 0.00065 22.4 1.6 25 31-55 9-33 (48)
20 PF12802 MarR_2: MarR family; 32.9 36 0.00077 22.6 1.9 52 7-60 7-61 (62)
21 smart00345 HTH_GNTR helix_turn 31.6 39 0.00084 21.7 1.9 23 34-56 34-56 (60)
22 cd04254 AAK_UMPK-PyrH-Ec UMP k 31.2 49 0.0011 28.4 2.9 44 9-52 81-124 (231)
23 PHA00616 hypothetical protein 30.7 27 0.00059 24.1 1.1 17 129-145 8-24 (44)
24 PF15319 RHINO: RAD9, RAD1, HU 29.5 24 0.00052 32.1 0.8 33 84-120 202-234 (236)
25 PF10625 UspB: Universal stres 28.0 79 0.0017 25.7 3.4 33 94-133 18-50 (107)
26 PRK04960 universal stress prot 26.3 76 0.0016 26.0 3.0 33 94-133 18-50 (111)
27 PF08535 KorB: KorB domain; I 25.8 57 0.0012 24.2 2.2 39 6-51 5-43 (93)
28 TIGR00421 ubiX_pad polyprenyl 25.0 90 0.002 26.4 3.5 47 9-58 103-149 (181)
29 PF09851 SHOCT: Short C-termin 24.9 88 0.0019 19.5 2.6 20 104-123 6-25 (31)
30 PRK11548 outer membrane biogen 23.7 54 0.0012 25.6 1.8 26 22-47 36-61 (113)
31 COG3592 Uncharacterized conser 22.4 41 0.00088 25.7 0.8 19 11-30 35-53 (74)
32 PF01047 MarR: MarR family; I 21.8 53 0.0011 21.7 1.2 25 35-59 32-56 (59)
33 TIGR02988 YaaA_near_RecF S4 do 21.7 57 0.0012 22.3 1.4 20 36-55 22-41 (59)
34 COG5104 PRP40 Splicing factor 21.7 3.2E+02 0.007 27.7 6.9 50 4-54 424-486 (590)
35 PRK13982 bifunctional SbtC-lik 21.6 1.4E+02 0.003 29.5 4.4 49 10-59 172-221 (475)
36 PF00096 zf-C2H2: Zinc finger, 21.4 70 0.0015 17.5 1.5 16 129-144 7-22 (23)
37 KOG1596 Fibrillarin and relate 21.3 62 0.0013 30.4 1.9 72 6-93 137-220 (317)
38 PF13412 HTH_24: Winged helix- 20.9 66 0.0014 20.7 1.5 20 32-51 29-48 (48)
39 smart00420 HTH_DEOR helix_turn 20.5 77 0.0017 19.7 1.7 23 33-55 27-49 (53)
40 PF03428 RP-C: Replication pro 20.2 4E+02 0.0086 22.9 6.4 57 90-146 71-140 (177)
41 smart00099 btg1 tob/btg1 famil 20.1 39 0.00085 27.2 0.3 10 21-30 93-102 (108)
No 1
>KOG1696 consensus 60s ribosomal protein L19 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=5.7e-87 Score=562.93 Aligned_cols=185 Identities=72% Similarity=1.112 Sum_probs=183.7
Q ss_pred CCchhhhHHHHHHHhccCCCceecCccchhHHHhhhhhHHHHhhhhcCceeecCCCCCChhHHHHHHHHHhcCCCCCCCC
Q 046974 1 MVSLKLQKRLAASMLKCGRGMVWLDPNEVNEISMANSRQNIRKLVKGGFIIRKPTKIHSRSRALRMKEAKRKGRHSGYGK 80 (212)
Q Consensus 1 M~~L~lQKRLAA~VL~cGk~kVWlDPne~~eIa~A~SRq~IRkLIkdGlIi~Kpv~~hSR~R~R~~~~ar~kGRh~G~Gk 80 (212)
|++|++|||||||||+||+.+|||||||++||++|||||+||+||+||+||.+|+++|||+|||++.+++++|||+|+|+
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 CccccccCCCCchHHHHHHHHHHHHHHHHHhcCCCChhhhHHHHhhhcCCccccHHHHHHHHHHHHHHHHHHHhhHHHHH
Q 046974 81 RRGTREARLPTKIPWMRRMRVLRRLLRRYREAKKIDRHMYHDMYMKVKGNVFKNKRVLMESIHKSRAEKAREKILSDQLE 160 (212)
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 (212)
|+||+|||||+|++||+|||+||++|++|||+|+||+|+||+||+++|||+|+|+++||||||+.|||++|+|+|+||||
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 HHHhhhhhhhH--HHHhccCCCCCCCC
Q 046974 161 AKRAKNKASRS--EERLAKGPGGAPTT 185 (212)
Q Consensus 161 Arr~k~k~~r~--eerl~~k~~e~~~~ 185 (212)
|+|.+++++++ ||++|++++|++.+
T Consensus 161 Arr~k~k~ar~rreer~~~k~~~~~~~ 187 (193)
T KOG1696|consen 161 ARRLKNKAARKRREERLAAKPQELIKT 187 (193)
T ss_pred HHHhhhHHHhhhHHHHHhhchhhhhcc
Confidence 99999999999 99999999999983
No 2
>PTZ00097 60S ribosomal protein L19; Provisional
Probab=100.00 E-value=2.7e-79 Score=515.12 Aligned_cols=169 Identities=72% Similarity=1.133 Sum_probs=167.6
Q ss_pred chhhhHHHHHHHhccCCCceecCccchhHHHhhhhhHHHHhhhhcCceeecCCCCCChhHHHHHHHHHhcCCCCCCCCCc
Q 046974 3 SLKLQKRLAASMLKCGRGMVWLDPNEVNEISMANSRQNIRKLVKGGFIIRKPTKIHSRSRALRMKEAKRKGRHSGYGKRR 82 (212)
Q Consensus 3 ~L~lQKRLAA~VL~cGk~kVWlDPne~~eIa~A~SRq~IRkLIkdGlIi~Kpv~~hSR~R~R~~~~ar~kGRh~G~GkRK 82 (212)
+|++||||||+||+||+++||||||+++||++||||+|||+||+||+|+++|++||||+|++++++++++|||+|+|||+
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 cccccCCCCchHHHHHHHHHHHHHHHHHhcCCCChhhhHHHHhhhcCCccccHHHHHHHHHHHHHHHHHHHhhHHHHHHH
Q 046974 83 GTREARLPTKIPWMRRMRVLRRLLRRYREAKKIDRHMYHDMYMKVKGNVFKNKRVLMESIHKSRAEKAREKILSDQLEAK 162 (212)
Q Consensus 83 Gt~~AR~p~K~~WmrRiR~lRrlLr~~Re~~kID~h~Yr~LY~kaKGn~Fknk~~L~e~I~k~kaek~r~k~L~dQaeAr 162 (212)
||+|||||+|+.||++||+||++|++|||+|+||+|+||.||++||||+|+|++||++|||+.++|++++++|+||+||+
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 HhhhhhhhH
Q 046974 163 RAKNKASRS 171 (212)
Q Consensus 163 r~k~k~~r~ 171 (212)
+.+++++++
T Consensus 161 r~k~~~~~~ 169 (175)
T PTZ00097 161 RAKAKALRN 169 (175)
T ss_pred HHHHHHHHH
Confidence 999999987
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=7.4e-79 Score=508.31 Aligned_cols=164 Identities=73% Similarity=1.165 Sum_probs=162.1
Q ss_pred hhhhHHHHHHHhccCCCceecCccchhHHHhhhhhHHHHhhhhcCceeecCCCCCChhHHHHHHHHHhcCCCCCCCCCcc
Q 046974 4 LKLQKRLAASMLKCGRGMVWLDPNEVNEISMANSRQNIRKLVKGGFIIRKPTKIHSRSRALRMKEAKRKGRHSGYGKRRG 83 (212)
Q Consensus 4 L~lQKRLAA~VL~cGk~kVWlDPne~~eIa~A~SRq~IRkLIkdGlIi~Kpv~~hSR~R~R~~~~ar~kGRh~G~GkRKG 83 (212)
|++|+||||+||+||+++||||||+++||++||||+|||+||+||+|+++|++||||+|++++++++++|||+|+|||+|
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 ccccCCCCchHHHHHHHHHHHHHHHHHhcCCCChhhhHHHHhhhcCCccccHHHHHHHHHHHHHHHHHHHhhHHHHHHHH
Q 046974 84 TREARLPTKIPWMRRMRVLRRLLRRYREAKKIDRHMYHDMYMKVKGNVFKNKRVLMESIHKSRAEKAREKILSDQLEAKR 163 (212)
Q Consensus 84 t~~AR~p~K~~WmrRiR~lRrlLr~~Re~~kID~h~Yr~LY~kaKGn~Fknk~~L~e~I~k~kaek~r~k~L~dQaeArr 163 (212)
|+|||||+|+.||++||+||++|++|||+|+||+|+||.||++||||+|+|+++|++|||+.++|++|++.|+||+||++
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 046974 164 AKNK 167 (212)
Q Consensus 164 ~k~k 167 (212)
++++
T Consensus 161 ~~~~ 164 (164)
T cd01417 161 AKNK 164 (164)
T ss_pred hccC
Confidence 9874
No 4
>PTZ00436 60S ribosomal protein L19-like protein; Provisional
Probab=100.00 E-value=1.4e-77 Score=540.55 Aligned_cols=171 Identities=65% Similarity=1.053 Sum_probs=168.7
Q ss_pred CCchhhhHHHHHHHhccCCCceecCccchhHHHhhhhhHHHHhhhhcCceeecCCCCCChhHHHHHHHHHhcCCCCCCCC
Q 046974 1 MVSLKLQKRLAASMLKCGRGMVWLDPNEVNEISMANSRQNIRKLVKGGFIIRKPTKIHSRSRALRMKEAKRKGRHSGYGK 80 (212)
Q Consensus 1 M~~L~lQKRLAA~VL~cGk~kVWlDPne~~eIa~A~SRq~IRkLIkdGlIi~Kpv~~hSR~R~R~~~~ar~kGRh~G~Gk 80 (212)
|++|++||||||+||+||++|||||||+++||++||||+|||+||+||+|+++|++||||+|+|++++++++|||+|+||
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 CccccccCCCCchHHHHHHHHHHHHHHHHHhcCCCChhhhHHHHhhhcCCccccHHHHHHHHHHHHHHHHHHHhhHHHHH
Q 046974 81 RRGTREARLPTKIPWMRRMRVLRRLLRRYREAKKIDRHMYHDMYMKVKGNVFKNKRVLMESIHKSRAEKAREKILSDQLE 160 (212)
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 (212)
|+||+|||||+|++||+|||+||++|++|||+|+||+|+||+||+++|||+|+|++||++|||+.|+|+.|+++|.||+|
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 HHHhhhhhhhH
Q 046974 161 AKRAKNKASRS 171 (212)
Q Consensus 161 Arr~k~k~~r~ 171 (212)
|+|.|+++.|-
T Consensus 161 ArR~k~~~~r~ 171 (357)
T PTZ00436 161 AKRLKDEQHRH 171 (357)
T ss_pred HHHHHhhhhhh
Confidence 99999987654
No 5
>PF01280 Ribosomal_L19e: Ribosomal protein L19e; InterPro: IPR000196 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This entry represents structural domain of the ribosomal protein L19 from eukaryotes, as well as L19e from archaea []. L19/L19e is absent in bacteria. L19/L19e is part of the large ribosomal subunit, whose structure has been determined in a number of eukaryotic and archaeal species []. L19/L19e is a multi-helical protein consisting of two different 3-helical domains connected by a long, partly helical linker.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3IZR_T 3O58_S 3O5H_S 3IZS_T 2WWA_J 1S1I_P 2WW9_J 2ZKR_7 4A1A_O 4A1C_O ....
Probab=100.00 E-value=1e-74 Score=476.99 Aligned_cols=148 Identities=65% Similarity=1.047 Sum_probs=130.9
Q ss_pred CchhhhHHHHHHHhccCCCceecCccchhHHHhhhhhHHHHhhhhcCceeecCCCCCChhHHHHHHHHHhcCCCCCCCCC
Q 046974 2 VSLKLQKRLAASMLKCGRGMVWLDPNEVNEISMANSRQNIRKLVKGGFIIRKPTKIHSRSRALRMKEAKRKGRHSGYGKR 81 (212)
Q Consensus 2 ~~L~lQKRLAA~VL~cGk~kVWlDPne~~eIa~A~SRq~IRkLIkdGlIi~Kpv~~hSR~R~R~~~~ar~kGRh~G~GkR 81 (212)
|+|++||||||+||+||+++|||||||++||++||||||||+||+||+|+++|++|||||||+++++++++|||+|+|+|
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 ccccccCCCCchHHHHHHHHHHHHHHHHHhcCCCChhhhHHHHhhhcCCccccHHHHHHHHHHHHHHH
Q 046974 82 RGTREARLPTKIPWMRRMRVLRRLLRRYREAKKIDRHMYHDMYMKVKGNVFKNKRVLMESIHKSRAEK 149 (212)
Q Consensus 82 KGt~~AR~p~K~~WmrRiR~lRrlLr~~Re~~kID~h~Yr~LY~kaKGn~Fknk~~L~e~I~k~kaek 149 (212)
+||+|||||+|+.||++||+||++|++|||+|+||+|+||+||++||||+|+|++||+||||++++|+
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=4.5e-73 Score=465.98 Aligned_cols=145 Identities=61% Similarity=1.046 Sum_probs=142.9
Q ss_pred hhhhHHHHHHHhccCCCceecCccchhHHHhhhhhHHHHhhhhcCceeecCCCCCChhHHHHHHHHHhcCCCCCCCCCcc
Q 046974 4 LKLQKRLAASMLKCGRGMVWLDPNEVNEISMANSRQNIRKLVKGGFIIRKPTKIHSRSRALRMKEAKRKGRHSGYGKRRG 83 (212)
Q Consensus 4 L~lQKRLAA~VL~cGk~kVWlDPne~~eIa~A~SRq~IRkLIkdGlIi~Kpv~~hSR~R~R~~~~ar~kGRh~G~GkRKG 83 (212)
|++||||||+||+||+++||||||+++||++||||+|||+||+||+|+++|++||||+|++++++++++|||+|+|||+|
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 ccccCCCCchHHHHHHHHHHHHHHHHHhcCCCChhhhHHHHhhhcCCccccHHHHHHHHHHHHHH
Q 046974 84 TREARLPTKIPWMRRMRVLRRLLRRYREAKKIDRHMYHDMYMKVKGNVFKNKRVLMESIHKSRAE 148 (212)
Q Consensus 84 t~~AR~p~K~~WmrRiR~lRrlLr~~Re~~kID~h~Yr~LY~kaKGn~Fknk~~L~e~I~k~kae 148 (212)
|+|||||+|+.||++||+||++|++|||+|+||+|+||.||++||||+|+|+++|++|||+.++|
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=7.9e-73 Score=466.67 Aligned_cols=147 Identities=42% Similarity=0.708 Sum_probs=145.1
Q ss_pred CCchhhhHHHHHHHhccCCCceecCccchhHHHhhhhhHHHHhhhhcCceeecCCCCCChhHHHHHHHHHhcCCCCCCCC
Q 046974 1 MVSLKLQKRLAASMLKCGRGMVWLDPNEVNEISMANSRQNIRKLVKGGFIIRKPTKIHSRSRALRMKEAKRKGRHSGYGK 80 (212)
Q Consensus 1 M~~L~lQKRLAA~VL~cGk~kVWlDPne~~eIa~A~SRq~IRkLIkdGlIi~Kpv~~hSR~R~R~~~~ar~kGRh~G~Gk 80 (212)
|++|++||||||+||+||+++||||||+++||++||||+|||+||+||+|+++|++||||+|++++++++++|||+|+||
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 CccccccCCCCchHHHHHHHHHHHHHHHHHhcCCCChhhhHHHHhhhcCCccccHHHHHHHHHHHHH
Q 046974 81 RRGTREARLPTKIPWMRRMRVLRRLLRRYREAKKIDRHMYHDMYMKVKGNVFKNKRVLMESIHKSRA 147 (212)
Q Consensus 81 RKGt~~AR~p~K~~WmrRiR~lRrlLr~~Re~~kID~h~Yr~LY~kaKGn~Fknk~~L~e~I~k~ka 147 (212)
|+||+|||||+|+.||++||+||++|++|||+|+||+|+||.||++||||+|+|+++|++||+....
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 9999999999999999999999999999999999999999999999999999999999999998653
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=4.3e-71 Score=454.22 Aligned_cols=142 Identities=39% Similarity=0.692 Sum_probs=140.3
Q ss_pred hhhhHHHHHHHhccCCCceecCccchhHHHhhhhhHHHHhhhhcCceeecCCCCCChhHHHHHHHHHhcCCCCCCCCCcc
Q 046974 4 LKLQKRLAASMLKCGRGMVWLDPNEVNEISMANSRQNIRKLVKGGFIIRKPTKIHSRSRALRMKEAKRKGRHSGYGKRRG 83 (212)
Q Consensus 4 L~lQKRLAA~VL~cGk~kVWlDPne~~eIa~A~SRq~IRkLIkdGlIi~Kpv~~hSR~R~R~~~~ar~kGRh~G~GkRKG 83 (212)
|++||||||+||+||+++||||||+++||++||||+|||+||+||+|+++|++||||+|++++++++++|||+|+|||+|
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 ccccCCCCchHHHHHHHHHHHHHHHHHhcCCCChhhhHHHHhhhcCCccccHHHHHHHHHHH
Q 046974 84 TREARLPTKIPWMRRMRVLRRLLRRYREAKKIDRHMYHDMYMKVKGNVFKNKRVLMESIHKS 145 (212)
Q Consensus 84 t~~AR~p~K~~WmrRiR~lRrlLr~~Re~~kID~h~Yr~LY~kaKGn~Fknk~~L~e~I~k~ 145 (212)
|+|||||+|+.||++||+||++|++|||+|+||+|+||.||++||||+|+|+++|++||...
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=4.9e-67 Score=431.18 Aligned_cols=149 Identities=46% Similarity=0.772 Sum_probs=146.5
Q ss_pred CCchhhhHHHHHHHhccCCCceecCccchhHHHhhhhhHHHHhhhhcCceeecCCCCCChhHHHHHHHHHhcCCCCCCCC
Q 046974 1 MVSLKLQKRLAASMLKCGRGMVWLDPNEVNEISMANSRQNIRKLVKGGFIIRKPTKIHSRSRALRMKEAKRKGRHSGYGK 80 (212)
Q Consensus 1 M~~L~lQKRLAA~VL~cGk~kVWlDPne~~eIa~A~SRq~IRkLIkdGlIi~Kpv~~hSR~R~R~~~~ar~kGRh~G~Gk 80 (212)
|+||+.|+||||+||+||+++||||||+++||++|+||+|||.||+||+|+.+|++|+|++|+++++++++||||+||||
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 CccccccCCCCchHHHHHHHHHHHHHHHHHhcCCCChhhhHHHHhhhcCCccccHHHHHHHHHHHHHHH
Q 046974 81 RRGTREARLPTKIPWMRRMRVLRRLLRRYREAKKIDRHMYHDMYMKVKGNVFKNKRVLMESIHKSRAEK 149 (212)
Q Consensus 81 RKGt~~AR~p~K~~WmrRiR~lRrlLr~~Re~~kID~h~Yr~LY~kaKGn~Fknk~~L~e~I~k~kaek 149 (212)
|+||++||||+|+.||.+||+||++|++||++|+||+|+||.||+++|||.|+++++|.+||.+.+.++
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=68.60 E-value=3 Score=26.11 Aligned_cols=29 Identities=21% Similarity=0.291 Sum_probs=24.2
Q ss_pred ecCccchhHHHhhhhhHHHHhhhhcCceee
Q 046974 23 WLDPNEVNEISMANSRQNIRKLVKGGFIIR 52 (212)
Q Consensus 23 WlDPne~~eIa~A~SRq~IRkLIkdGlIi~ 52 (212)
||++.|+.++-. +|+..|+.|+++|.|-.
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 677788888776 78999999999998765
No 11
>PF12728 HTH_17: Helix-turn-helix domain
Probab=68.02 E-value=3.3 Score=27.26 Aligned_cols=28 Identities=25% Similarity=0.345 Sum_probs=24.4
Q ss_pred ecCccchhHHHhhhhhHHHHhhhhcCcee
Q 046974 23 WLDPNEVNEISMANSRQNIRKLVKGGFII 51 (212)
Q Consensus 23 WlDPne~~eIa~A~SRq~IRkLIkdGlIi 51 (212)
||++.|+-++-. +|+..|+++++.|.|.
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 688889999888 7999999999999763
No 12
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=53.31 E-value=6 Score=25.79 Aligned_cols=15 Identities=27% Similarity=0.756 Sum_probs=12.4
Q ss_pred CceecCccchhHHHh
Q 046974 20 GMVWLDPNEVNEISM 34 (212)
Q Consensus 20 ~kVWlDPne~~eIa~ 34 (212)
.-||||++|++.|.+
T Consensus 26 ~G~W~d~~el~~~~e 40 (41)
T PF13453_consen 26 GGIWFDAGELEKLLE 40 (41)
T ss_pred CeEEccHHHHHHHHh
Confidence 469999999998753
No 13
>PF13880 Acetyltransf_13: ESCO1/2 acetyl-transferase
Probab=48.14 E-value=5.8 Score=29.60 Aligned_cols=14 Identities=29% Similarity=0.933 Sum_probs=12.0
Q ss_pred ccCCCceecCccch
Q 046974 16 KCGRGMVWLDPNEV 29 (212)
Q Consensus 16 ~cGk~kVWlDPne~ 29 (212)
-||+++||..|..-
T Consensus 5 ~~GI~RIWV~~~~R 18 (70)
T PF13880_consen 5 VCGISRIWVSPSHR 18 (70)
T ss_pred EEEeEEEEeChhhh
Confidence 49999999999863
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=47.96 E-value=20 Score=30.89 Aligned_cols=48 Identities=15% Similarity=0.115 Sum_probs=38.3
Q ss_pred hhhHHH-HHHHhccCCCceecCccchhHHHhhhhhHHHHhhhhcCceee
Q 046974 5 KLQKRL-AASMLKCGRGMVWLDPNEVNEISMANSRQNIRKLVKGGFIIR 52 (212)
Q Consensus 5 ~lQKRL-AA~VL~cGk~kVWlDPne~~eIa~A~SRq~IRkLIkdGlIi~ 52 (212)
+++-+| +..+...|.+-++|+|.....+..-++.+.+..|++.|.|..
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 15
>PRK05920 aromatic acid decarboxylase; Validated
Probab=41.57 E-value=31 Score=30.10 Aligned_cols=47 Identities=30% Similarity=0.259 Sum_probs=36.5
Q ss_pred HHHHHHhccCCCceecCccchhHHHhhhhhHHHHhhhhcCceeecCCCCC
Q 046974 9 RLAASMLKCGRGMVWLDPNEVNEISMANSRQNIRKLVKGGFIIRKPTKIH 58 (212)
Q Consensus 9 RLAA~VL~cGk~kVWlDPne~~eIa~A~SRq~IRkLIkdGlIi~Kpv~~h 58 (212)
+.|...|++|. .|.|=|.+... ++.++++|..|-..|.++.-|+.+.
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 55555765444 7889999999999999999999874
No 16
>PRK00247 putative inner membrane protein translocase component YidC; Validated
Probab=35.83 E-value=4.3e+02 Score=25.91 Aligned_cols=59 Identities=14% Similarity=0.186 Sum_probs=30.9
Q ss_pred hHHHHHHHHHHHHHHHHHhc---CCCChhhhHHHHhhhcCCccccHHHHHHHHHHHHHHHHHHHhhHHH
Q 046974 93 IPWMRRMRVLRRLLRRYREA---KKIDRHMYHDMYMKVKGNVFKNKRVLMESIHKSRAEKAREKILSDQ 158 (212)
Q Consensus 93 ~~WmrRiR~lRrlLr~~Re~---~kID~h~Yr~LY~kaKGn~Fknk~~L~e~I~k~kaek~r~k~L~dQ 158 (212)
..|..+.+..+..++..|.. ..|..+.+..|..- |...=.+.=...+++|+++|.++.+
T Consensus 292 ~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~-------~~~~~~~~~~~~~~~k~~~k~~~~~ 353 (429)
T PRK00247 292 AQYREKQKEKKAFLWTLRRNRLRMIITPWRAPELHAE-------NAEIKKTRTAEKNEAKARKKEIAQK 353 (429)
T ss_pred HHHHHHHHHHHHHHHHHHhccccccCCcccHHHHHHH-------HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34555555555555544444 37777777766432 2222233334446666666666543
No 17
>PRK06029 3-octaprenyl-4-hydroxybenzoate carboxy-lyase; Provisional
Probab=34.72 E-value=49 Score=28.34 Aligned_cols=46 Identities=30% Similarity=0.248 Sum_probs=35.8
Q ss_pred HHHHHHhccCCCceecCccchhHHHhhhhhHHHHhhhhcCceeecCCCC
Q 046974 9 RLAASMLKCGRGMVWLDPNEVNEISMANSRQNIRKLVKGGFIIRKPTKI 57 (212)
Q Consensus 9 RLAA~VL~cGk~kVWlDPne~~eIa~A~SRq~IRkLIkdGlIi~Kpv~~ 57 (212)
+.|.-.|.+++ .|.|=|. +--.+..+++++.+|-+.|.++..|..|
T Consensus 106 ~~a~~~L~~~~-pvii~P~--~M~~~p~~~~Nl~~L~~~G~~vi~P~~g 151 (185)
T PRK06029 106 RAADVMLKERR-RLVLCVR--ETPLHLGHLRNMTKLAEMGAIIMPPVPA 151 (185)
T ss_pred HHHHHHHhcCC-CEEEEec--cccCCHHHHHHHHHHHHCcCEEECCCcc
Confidence 44556777765 5555574 4566889999999999999999999976
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=34.00 E-value=48 Score=25.01 Aligned_cols=38 Identities=18% Similarity=0.277 Sum_probs=25.9
Q ss_pred ccCCCceecCccchhHHHhhhhhHH----HHhhhhcCceeecC
Q 046974 16 KCGRGMVWLDPNEVNEISMANSRQN----IRKLVKGGFIIRKP 54 (212)
Q Consensus 16 ~cGk~kVWlDPne~~eIa~A~SRq~----IRkLIkdGlIi~Kp 54 (212)
|+++..++|.+.|+.++... ||+. |..|.++|+|.+..
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
>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=33.40 E-value=30 Score=22.38 Aligned_cols=25 Identities=28% Similarity=0.472 Sum_probs=19.6
Q ss_pred HHHhhhhhHHHHhhhhcCceeecCC
Q 046974 31 EISMANSRQNIRKLVKGGFIIRKPT 55 (212)
Q Consensus 31 eIa~A~SRq~IRkLIkdGlIi~Kpv 55 (212)
+...+.||.++++||+.|.|...-.
T Consensus 9 ~~~~~~sr~~a~~~I~~g~V~VNg~ 33 (48)
T PF01479_consen 9 RLGLASSRSEARRLIKQGRVKVNGK 33 (48)
T ss_dssp HTTSSSSHHHHHHHHHTTTEEETTE
T ss_pred HcCCcCCHHHHHHhcCCCEEEECCE
Confidence 3445679999999999999876543
No 20
>PF12802 MarR_2: MarR family; PDB: 3ECO_B 2QWW_B 3KP6_B 3KP4_B 3KP2_A 3KP5_A 3KP3_B 3KP7_A 3NQO_B 3K0L_B ....
Probab=32.86 E-value=36 Score=22.56 Aligned_cols=52 Identities=21% Similarity=0.244 Sum_probs=31.3
Q ss_pred hHHHHHHHhccCCCceecCccchhHH---HhhhhhHHHHhhhhcCceeecCCCCCCh
Q 046974 7 QKRLAASMLKCGRGMVWLDPNEVNEI---SMANSRQNIRKLVKGGFIIRKPTKIHSR 60 (212)
Q Consensus 7 QKRLAA~VL~cGk~kVWlDPne~~eI---a~A~SRq~IRkLIkdGlIi~Kpv~~hSR 60 (212)
|-++=..|..+|.. ++-++++.+. +-..--.-|..|++.|+|.+.+.....|
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 44555556566554 3334444332 2233456789999999999998877655
No 21
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=31.65 E-value=39 Score=21.69 Aligned_cols=23 Identities=22% Similarity=0.501 Sum_probs=17.3
Q ss_pred hhhhhHHHHhhhhcCceeecCCC
Q 046974 34 MANSRQNIRKLVKGGFIIRKPTK 56 (212)
Q Consensus 34 ~A~SRq~IRkLIkdGlIi~Kpv~ 56 (212)
.+.-++.+..|.++|+|...|-.
T Consensus 34 ~~tv~~~l~~L~~~g~i~~~~~~ 56 (60)
T smart00345 34 RTTVREALSRLEAEGLVQRRPGS 56 (60)
T ss_pred HHHHHHHHHHHHHCCCEEEecCC
Confidence 34557778899999999876643
No 22
>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=31.18 E-value=49 Score=28.39 Aligned_cols=44 Identities=9% Similarity=0.117 Sum_probs=35.8
Q ss_pred HHHHHHhccCCCceecCccchhHHHhhhhhHHHHhhhhcCceee
Q 046974 9 RLAASMLKCGRGMVWLDPNEVNEISMANSRQNIRKLVKGGFIIR 52 (212)
Q Consensus 9 RLAA~VL~cGk~kVWlDPne~~eIa~A~SRq~IRkLIkdGlIi~ 52 (212)
-|++.+...|.+-+||+|-+++.+.....-+.+..+++.|.|..
T Consensus 81 ll~~~L~~~Gv~a~~l~~~~~~~~~~~~~~~~l~~~l~~g~ipV 124 (231)
T cd04254 81 ALQDALESLGVKTRVMSAIPMQGVAEPYIRRRAIRHLEKGRVVI 124 (231)
T ss_pred HHHHHHHHcCCCeEEEcHHHhhhhhcccCHHHHHHHHHCCCEEE
Confidence 35667778999999999999877655566799999999998733
No 23
>PHA00616 hypothetical protein
Probab=30.70 E-value=27 Score=24.07 Aligned_cols=17 Identities=24% Similarity=0.634 Sum_probs=15.0
Q ss_pred CCccccHHHHHHHHHHH
Q 046974 129 GNVFKNKRVLMESIHKS 145 (212)
Q Consensus 129 Gn~Fknk~~L~e~I~k~ 145 (212)
|..|.++++|..|+.+.
T Consensus 8 G~~F~~~s~l~~H~r~~ 24 (44)
T PHA00616 8 GGIFRKKKEVIEHLLSV 24 (44)
T ss_pred hHHHhhHHHHHHHHHHh
Confidence 78999999999999654
No 24
>PF15319 RHINO: RAD9, RAD1, HUS1-interacting nuclear orphan protein
Probab=29.47 E-value=24 Score=32.11 Aligned_cols=33 Identities=39% Similarity=0.673 Sum_probs=25.4
Q ss_pred ccccCCCCchHHHHHHHHHHHHHHHHHhcCCCChhhh
Q 046974 84 TREARLPTKIPWMRRMRVLRRLLRRYREAKKIDRHMY 120 (212)
Q Consensus 84 t~~AR~p~K~~WmrRiR~lRrlLr~~Re~~kID~h~Y 120 (212)
|-.--..-|++|-+| +-||..|||.|++++..|
T Consensus 202 TPE~~YGiKvTWRRR----~hL~~yLrerGkL~~sq~ 234 (236)
T PF15319_consen 202 TPEEKYGIKVTWRRR----RHLLAYLRERGKLSRSQF 234 (236)
T ss_pred CCcccccceeeeecc----HHHHHHHHHhCccchhhc
Confidence 444455669999766 578999999999998764
No 25
>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=27.99 E-value=79 Score=25.72 Aligned_cols=33 Identities=39% Similarity=0.522 Sum_probs=25.8
Q ss_pred HHHHHHHHHHHHHHHHHhcCCCChhhhHHHHhhhcCCccc
Q 046974 94 PWMRRMRVLRRLLRRYREAKKIDRHMYHDMYMKVKGNVFK 133 (212)
Q Consensus 94 ~WmrRiR~lRrlLr~~Re~~kID~h~Yr~LY~kaKGn~Fk 133 (212)
-++|=.=.||-||--|||...+ ||..|.||-|=
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 3566667899999999996554 88889998774
No 26
>PRK04960 universal stress protein UspB; Provisional
Probab=26.27 E-value=76 Score=25.99 Aligned_cols=33 Identities=30% Similarity=0.392 Sum_probs=26.8
Q ss_pred HHHHHHHHHHHHHHHHHhcCCCChhhhHHHHhhhcCCccc
Q 046974 94 PWMRRMRVLRRLLRRYREAKKIDRHMYHDMYMKVKGNVFK 133 (212)
Q Consensus 94 ~WmrRiR~lRrlLr~~Re~~kID~h~Yr~LY~kaKGn~Fk 133 (212)
-++|=.=.||-||--|||...+ ||..|.||-|=
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 3566677899999999997665 88899998874
No 27
>PF08535 KorB: KorB domain; InterPro: IPR013741 This entry contains several KorB transcriptional repressor proteins. The korB gene is a major regulatory element in the replication and maintenance of broad host-range plasmid RK2. It negatively controls the replication gene trfA, the host-lethal determinants kilA and kilB, and the korA-korB operon []. This domain includes the DNA-binding HTH motif []. ; PDB: 1R71_C.
Probab=25.76 E-value=57 Score=24.22 Aligned_cols=39 Identities=26% Similarity=0.581 Sum_probs=24.5
Q ss_pred hhHHHHHHHhccCCCceecCccchhHHHhhhhhHHHHhhhhcCcee
Q 046974 6 LQKRLAASMLKCGRGMVWLDPNEVNEISMANSRQNIRKLVKGGFII 51 (212)
Q Consensus 6 lQKRLAA~VL~cGk~kVWlDPne~~eIa~A~SRq~IRkLIkdGlIi 51 (212)
.|.-+|..| |+++-|+ .+-++-+.-=++|+.|+.+|.|.
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 466677654 8998887 45566667778999999999764
No 28
>TIGR00421 ubiX_pad polyprenyl P-hydroxybenzoate and phenylacrylic acid decarboxylases. In E.coli, the protein UbiX (3-octaprenyl-4-hydroxybenzoate carboxy-lyase) has been shown to be involved in the third step of ubiquinone biosynthesis. It catalyzes the reaction [3-octaprenyl-4-hydroxybenzoate = 2-octaprenylphenol + CO2]. The knockout of the homologous protein in yeast confers sensitivity to phenylacrylic acid. Members are not restricted to ubiquinone-synthesizing species. This family represents a distinct clade within the flavoprotein family of Pfam model pfam02441.
Probab=24.96 E-value=90 Score=26.42 Aligned_cols=47 Identities=30% Similarity=0.262 Sum_probs=35.3
Q ss_pred HHHHHHhccCCCceecCccchhHHHhhhhhHHHHhhhhcCceeecCCCCC
Q 046974 9 RLAASMLKCGRGMVWLDPNEVNEISMANSRQNIRKLVKGGFIIRKPTKIH 58 (212)
Q Consensus 9 RLAA~VL~cGk~kVWlDPne~~eIa~A~SRq~IRkLIkdGlIi~Kpv~~h 58 (212)
+.|...|+++. .|.|=|.+. -.++.+.+++..|-+.|.++.-|..|.
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 44555778765 555557544 458888999999999999999998763
No 29
>PF09851 SHOCT: Short C-terminal domain; InterPro: IPR018649 This family of hypothetical prokaryotic proteins has no known function.
Probab=24.93 E-value=88 Score=19.46 Aligned_cols=20 Identities=15% Similarity=0.285 Sum_probs=16.9
Q ss_pred HHHHHHHhcCCCChhhhHHH
Q 046974 104 RLLRRYREAKKIDRHMYHDM 123 (212)
Q Consensus 104 rlLr~~Re~~kID~h~Yr~L 123 (212)
..|+.+.+.|.|+-..|...
T Consensus 6 ~~L~~l~~~G~IseeEy~~~ 25 (31)
T PF09851_consen 6 EKLKELYDKGEISEEEYEQK 25 (31)
T ss_pred HHHHHHHHcCCCCHHHHHHH
Confidence 45788999999999999764
No 30
>PRK11548 outer membrane biogenesis protein BamE; Provisional
Probab=23.73 E-value=54 Score=25.64 Aligned_cols=26 Identities=23% Similarity=0.426 Sum_probs=22.9
Q ss_pred eecCccchhHHHhhhhhHHHHhhhhc
Q 046974 22 VWLDPNEVNEISMANSRQNIRKLVKG 47 (212)
Q Consensus 22 VWlDPne~~eIa~A~SRq~IRkLIkd 47 (212)
-++||+.+++|.--.|++||+.|+=.
T Consensus 36 ~~~~~~~l~~l~~GmTk~qV~~lLGt 61 (113)
T PRK11548 36 NYLTPNDVAKIHVGMTQQQVAYTLGT 61 (113)
T ss_pred ccCCHHHHHHhcCCCCHHHHHHHcCC
Confidence 38899999999999999999998843
No 31
>COG3592 Uncharacterized conserved protein [Function unknown]
Probab=22.45 E-value=41 Score=25.73 Aligned_cols=19 Identities=26% Similarity=0.705 Sum_probs=14.6
Q ss_pred HHHHhccCCCceecCccchh
Q 046974 11 AASMLKCGRGMVWLDPNEVN 30 (212)
Q Consensus 11 AA~VL~cGk~kVWlDPne~~ 30 (212)
+++|+++|.+= ||+|+..+
T Consensus 35 n~~vF~~~rkP-WI~Pd~~~ 53 (74)
T COG3592 35 NPKVFNLGRKP-WIMPDAVD 53 (74)
T ss_pred CHhhcccCCCC-ccCCCCCC
Confidence 46788888765 99998754
No 32
>PF01047 MarR: MarR family; InterPro: IPR000835 The MarR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 135 amino acids present in transcription regulators of the MarR/SlyA family, involved in the development of antibiotic resistance. This family of transcription regulators is named after Escherichia coli MarR, a repressor of genes which activate the multiple antibiotic resistance and oxidative stress regulons, and after slyA from Salmonella typhimurium and E. coli, a transcription regulator that is required for virulence and survival in the macrophage environment. Regulators with the MarR-type HTH domain are present in bacteria and archaea and control a variety of biological functions, including resistance to multiple antibiotics, household disinfectants, organic solvents, oxidative stress agents and regulation of the virulence factor synthesis in pathogens of humans and plants. Many of the MarR-like regulators respond to aromatic compounds [, , ]. The crystal structures of MarR, MexR and SlyA have been determined and show a winged HTH DNA-binding core flanked by helices involved in dimerisation. The DNA-binding domains are ascribed to the superfamily of winged helix proteins, containing a three (four)-helix (H) bundle and a three-stranded antiparallel beta-sheet (B) in the topology: H1-(H1')-H2-B1-H3-H4-B2-B3-H5-H6. Helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing. Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. The helices 1, 5 and 6 are involved in dimerisation, as most MarR-like transcription regulators form dimers [, ]. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1JGS_A 2NYX_D 2PEX_B 2PFB_A 3BPX_A 3BPV_A 2BV6_A 3BJA_A 3E6M_B 2ETH_A ....
Probab=21.83 E-value=53 Score=21.71 Aligned_cols=25 Identities=24% Similarity=0.314 Sum_probs=18.8
Q ss_pred hhhhHHHHhhhhcCceeecCCCCCC
Q 046974 35 ANSRQNIRKLVKGGFIIRKPTKIHS 59 (212)
Q Consensus 35 A~SRq~IRkLIkdGlIi~Kpv~~hS 59 (212)
++.-.-|.+|++.|+|.+.+....-
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 3445678999999999988765443
No 33
>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=21.74 E-value=57 Score=22.27 Aligned_cols=20 Identities=5% Similarity=0.094 Sum_probs=17.0
Q ss_pred hhhHHHHhhhhcCceeecCC
Q 046974 36 NSRQNIRKLVKGGFIIRKPT 55 (212)
Q Consensus 36 ~SRq~IRkLIkdGlIi~Kpv 55 (212)
.||..+++||++|.|...-.
T Consensus 22 ~SR~~~k~li~~G~V~VNg~ 41 (59)
T TIGR02988 22 DSGGQAKWFLQENEVLVNGE 41 (59)
T ss_pred cCHHHHHHHHHcCCEEECCE
Confidence 49999999999999987443
No 34
>COG5104 PRP40 Splicing factor [RNA processing and modification]
Probab=21.70 E-value=3.2e+02 Score=27.72 Aligned_cols=50 Identities=20% Similarity=0.193 Sum_probs=37.3
Q ss_pred hhhhHHHHHHHhccCCCceecCccchhHHHhhhhh-------------HHHHhhhhcCceeecC
Q 046974 4 LKLQKRLAASMLKCGRGMVWLDPNEVNEISMANSR-------------QNIRKLVKGGFIIRKP 54 (212)
Q Consensus 4 L~lQKRLAA~VL~cGk~kVWlDPne~~eIa~A~SR-------------q~IRkLIkdGlIi~Kp 54 (212)
+..-+|+.+..+-+|..-+| |-..++||-.+++- ..+-.||-||+|..+.
T Consensus 424 y~~~r~~~~~~~~~~qis~~-d~~~vdei~~~~~Ek~eE~e~~~d~v~kE~is~i~D~~I~qr~ 486 (590)
T COG5104 424 YGFARRSYERETRTGQISPT-DRRAVDEIFEAIAEKKEEGEIKFDKVDKEDISLIVDGLIKQRN 486 (590)
T ss_pred HHHHHHHHHHHHHhccCCCc-cccchHHHHHHHHHHHhhcchhhhhhhHHHHHHHHHHHHHHhH
Confidence 34446778888888999999 88889999888873 2334678888886543
No 35
>PRK13982 bifunctional SbtC-like/phosphopantothenoylcysteine decarboxylase/phosphopantothenate synthase; Provisional
Probab=21.58 E-value=1.4e+02 Score=29.51 Aligned_cols=49 Identities=20% Similarity=0.266 Sum_probs=36.4
Q ss_pred HHHHHhccCCCceecCccchhH-HHhhhhhHHHHhhhhcCceeecCCCCCC
Q 046974 10 LAASMLKCGRGMVWLDPNEVNE-ISMANSRQNIRKLVKGGFIIRKPTKIHS 59 (212)
Q Consensus 10 LAA~VL~cGk~kVWlDPne~~e-Ia~A~SRq~IRkLIkdGlIi~Kpv~~hS 59 (212)
|++-+|.++. .|-|=|.+... ..+..+++++..|-.+|.++..|..|.-
T Consensus 172 lt~v~La~~~-PvliaPaMN~~M~~npat~~Nl~~L~~~G~~vi~P~~g~l 221 (475)
T PRK13982 172 ASAILLAANR-PILLAPAMNPLMWNNPATRRNVAQLKRDGVHMIGPNAGEM 221 (475)
T ss_pred HHHHHHhcCC-CEEEEEcCCHHHhcCHHHHHHHHHHHHCCCEEECCCCCcc
Confidence 3455566554 55555666555 4589999999999999999999998743
No 36
>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=21.39 E-value=70 Score=17.52 Aligned_cols=16 Identities=25% Similarity=0.497 Sum_probs=13.2
Q ss_pred CCccccHHHHHHHHHH
Q 046974 129 GNVFKNKRVLMESIHK 144 (212)
Q Consensus 129 Gn~Fknk~~L~e~I~k 144 (212)
|-.|.+...|..||..
T Consensus 7 ~~~f~~~~~l~~H~~~ 22 (23)
T PF00096_consen 7 GKSFSSKSNLKRHMRR 22 (23)
T ss_dssp TEEESSHHHHHHHHHH
T ss_pred CCccCCHHHHHHHHhH
Confidence 5579999999999853
No 37
>KOG1596 consensus Fibrillarin and related nucleolar RNA-binding proteins [RNA processing and modification]
Probab=21.26 E-value=62 Score=30.44 Aligned_cols=72 Identities=25% Similarity=0.305 Sum_probs=40.9
Q ss_pred hhHHHHHHHhccCCCceecCccc------------hhHHHhhhhhHHHHhhhhcCceeecCCCCCChhHHHHHHHHHhcC
Q 046974 6 LQKRLAASMLKCGRGMVWLDPNE------------VNEISMANSRQNIRKLVKGGFIIRKPTKIHSRSRALRMKEAKRKG 73 (212)
Q Consensus 6 lQKRLAA~VL~cGk~kVWlDPne------------~~eIa~A~SRq~IRkLIkdGlIi~Kpv~~hSR~R~R~~~~ar~kG 73 (212)
.|-.|||.|| ||...+||.|-. ++.|++-.- .+|++..-.. .|-.+|---+..+|+--
T Consensus 137 frSKLAA~I~-gGvdnihikpGsKVLYLGAasGttVSHvSDiVG--------peG~VYAVEf-s~rsGRdL~nmAkkRtN 206 (317)
T KOG1596|consen 137 FRSKLAAGIL-GGVDNIHIKPGSKVLYLGAASGTTVSHVSDIVG--------PEGCVYAVEF-SHRSGRDLINMAKKRTN 206 (317)
T ss_pred HHHHHHHHhh-cCccceeecCCceEEEeeccCCceeehhhcccC--------CCceEEEEEe-cccchHHHHHHhhccCC
Confidence 4668999999 699999999953 233333222 4566665443 34445655555544310
Q ss_pred CCCCCCCCccccccCCCCch
Q 046974 74 RHSGYGKRRGTREARLPTKI 93 (212)
Q Consensus 74 Rh~G~GkRKGt~~AR~p~K~ 93 (212)
== -=--.||+|.|-
T Consensus 207 ii------PIiEDArhP~KY 220 (317)
T KOG1596|consen 207 II------PIIEDARHPAKY 220 (317)
T ss_pred ce------eeeccCCCchhe
Confidence 00 012357888763
No 38
>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=20.91 E-value=66 Score=20.70 Aligned_cols=20 Identities=30% Similarity=0.439 Sum_probs=15.2
Q ss_pred HHhhhhhHHHHhhhhcCcee
Q 046974 32 ISMANSRQNIRKLVKGGFII 51 (212)
Q Consensus 32 Ia~A~SRq~IRkLIkdGlIi 51 (212)
|+.+.....|++|+++|+|.
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 44556678899999999984
No 39
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=20.49 E-value=77 Score=19.69 Aligned_cols=23 Identities=26% Similarity=0.390 Sum_probs=17.2
Q ss_pred HhhhhhHHHHhhhhcCceeecCC
Q 046974 33 SMANSRQNIRKLVKGGFIIRKPT 55 (212)
Q Consensus 33 a~A~SRq~IRkLIkdGlIi~Kpv 55 (212)
+.+.-+..|..|.+.|+|...+.
T Consensus 27 s~~tv~~~l~~L~~~g~i~~~~~ 49 (53)
T smart00420 27 SEMTIRRDLNKLEEQGLLTRVHG 49 (53)
T ss_pred CHHHHHHHHHHHHHCCCEEEeec
Confidence 44455778889999999987654
No 40
>PF03428 RP-C: Replication protein C N-terminal domain; InterPro: IPR005090 Proteins in this group have homology with the RepC protein of Agrobacterium Ri and Ti plasmids []. They may be involved in plasmid replication and stabilisation functions.
Probab=20.16 E-value=4e+02 Score=22.89 Aligned_cols=57 Identities=26% Similarity=0.300 Sum_probs=39.1
Q ss_pred CCchHHHHHH-----HHHHHHHHHHHhcCCCCh---hhhHHHHhhhcCCc----cc-cHHHHHHHHHHHH
Q 046974 90 PTKIPWMRRM-----RVLRRLLRRYREAKKIDR---HMYHDMYMKVKGNV----FK-NKRVLMESIHKSR 146 (212)
Q Consensus 90 p~K~~WmrRi-----R~lRrlLr~~Re~~kID~---h~Yr~LY~kaKGn~----Fk-nk~~L~e~I~k~k 146 (212)
|+...-..++ +-|||.|+.|-|.|.|-+ ..++.+..+-.+|. |= |.+-|..-..+..
T Consensus 71 pSN~~La~r~~G~s~~tlrR~l~~LveaGLI~rrDS~NgkRy~~R~~~G~I~~A~GfdLsPL~~R~~El~ 140 (177)
T PF03428_consen 71 PSNAQLAERLNGMSERTLRRHLARLVEAGLIVRRDSPNGKRYARRDRGGRIVEAFGFDLSPLIARAEELA 140 (177)
T ss_pred cCHHHHHHHHcCCCHHHHHHHHHHHHHCCCeeeccCCCCCccCccCCCCCEEeEeCcCHHHHHHHHHHHH
Confidence 3334444555 889999999999999954 56887777766554 33 6677766655543
No 41
>smart00099 btg1 tob/btg1 family. The tob/btg1 is a family of proteins that inhibit cell proliferation.
Probab=20.05 E-value=39 Score=27.23 Aligned_cols=10 Identities=50% Similarity=1.142 Sum_probs=8.3
Q ss_pred ceecCccchh
Q 046974 21 MVWLDPNEVN 30 (212)
Q Consensus 21 kVWlDPne~~ 30 (212)
.||+||.|+.
T Consensus 93 tiwvDP~eVs 102 (108)
T smart00099 93 TLWVDPFEVS 102 (108)
T ss_pred EEEECCCEEE
Confidence 5899999864
Done!