Query psy17505
Match_columns 199
No_of_seqs 156 out of 295
Neff 3.9
Searched_HMMs 46136
Date Sat Aug 17 00:16:47 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy17505.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/17505hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1696|consensus 100.0 5.5E-90 1.2E-94 575.5 16.9 193 1-193 1-193 (193)
2 PTZ00097 60S ribosomal protein 100.0 3.1E-80 6.8E-85 516.2 19.3 174 3-176 1-174 (175)
3 cd01417 Ribosomal_L19e_E Ribos 100.0 5.4E-79 1.2E-83 504.7 17.5 164 4-167 1-164 (164)
4 PTZ00436 60S ribosomal protein 100.0 5.1E-77 1.1E-81 532.1 21.7 170 1-170 1-170 (357)
5 PF01280 Ribosomal_L19e: Ribos 100.0 1.1E-74 2.4E-79 472.8 14.7 148 2-149 1-148 (148)
6 cd00481 Ribosomal_L19e Ribosom 100.0 3.7E-73 8.1E-78 462.4 15.0 145 4-148 1-145 (145)
7 PRK08570 rpl19e 50S ribosomal 100.0 1.3E-72 2.8E-77 461.3 15.6 146 1-146 1-146 (150)
8 cd01418 Ribosomal_L19e_A Ribos 100.0 4.6E-71 9.9E-76 450.0 15.4 142 4-145 1-142 (145)
9 COG2147 RPL19A Ribosomal prote 100.0 3.6E-67 7.8E-72 427.9 15.0 149 1-149 1-149 (150)
10 PF07946 DUF1682: Protein of u 74.3 9.8 0.00021 34.5 6.3 52 144-195 257-309 (321)
11 TIGR01764 excise DNA binding d 69.5 3.3 7.1E-05 25.7 1.6 29 23-52 1-29 (49)
12 PF12728 HTH_17: Helix-turn-he 68.9 3.5 7.5E-05 26.9 1.7 28 23-51 1-28 (51)
13 PF13453 zf-TFIIB: Transcripti 55.3 5.1 0.00011 25.8 0.5 15 20-34 26-40 (41)
14 PF14468 DUF4427: Protein of u 54.2 11 0.00024 31.1 2.4 33 12-53 30-62 (132)
15 PF12802 MarR_2: MarR family; 48.1 29 0.00062 22.8 3.3 53 6-60 6-61 (62)
16 PRK00247 putative inner membra 47.9 2.7E+02 0.0059 27.0 11.4 77 92-175 291-371 (429)
17 PF13880 Acetyltransf_13: ESCO 47.1 6.2 0.00013 29.1 -0.1 14 16-29 5-18 (70)
18 TIGR02075 pyrH_bact uridylate 44.0 30 0.00064 29.6 3.6 48 5-52 77-125 (233)
19 PRK05920 aromatic acid decarbo 41.6 35 0.00076 29.5 3.7 47 9-58 121-167 (204)
20 PF01479 S4: S4 domain; Inter 38.5 27 0.00059 22.3 2.0 29 30-58 8-36 (48)
21 PRK06029 3-octaprenyl-4-hydrox 35.7 53 0.0011 27.9 3.8 47 9-58 106-152 (185)
22 smart00345 HTH_GNTR helix_turn 33.7 37 0.0008 21.6 2.1 25 32-56 32-56 (60)
23 TIGR01610 phage_O_Nterm phage 33.3 31 0.00068 25.7 1.9 38 16-54 40-81 (95)
24 PF08535 KorB: KorB domain; I 31.5 45 0.00098 24.6 2.5 39 6-51 5-43 (93)
25 PRK11548 outer membrane biogen 30.5 38 0.00083 26.2 2.0 26 22-47 36-61 (113)
26 PHA00616 hypothetical protein 29.5 28 0.00062 23.7 1.0 17 129-145 8-24 (44)
27 cd04254 AAK_UMPK-PyrH-Ec UMP k 27.4 69 0.0015 27.2 3.2 43 10-52 82-124 (231)
28 TIGR00421 ubiX_pad polyprenyl 25.9 98 0.0021 25.9 3.8 47 9-58 103-149 (181)
29 COG3592 Uncharacterized conser 25.2 35 0.00075 25.7 0.9 19 11-30 35-53 (74)
30 TIGR02988 YaaA_near_RecF S4 do 24.6 62 0.0013 21.8 2.0 22 35-56 21-42 (59)
31 COG5104 PRP40 Splicing factor 24.2 3.2E+02 0.007 27.4 7.3 51 4-55 424-487 (590)
32 PF01047 MarR: MarR family; I 24.0 54 0.0012 21.4 1.6 26 34-59 31-56 (59)
33 PF04703 FaeA: FaeA-like prote 24.0 76 0.0016 22.7 2.4 33 25-57 14-52 (62)
34 smart00099 btg1 tob/btg1 famil 23.5 30 0.00065 27.6 0.3 10 21-30 93-102 (108)
35 PF15319 RHINO: RAD9, RAD1, HU 23.1 33 0.00072 30.8 0.5 35 82-120 200-234 (236)
36 smart00420 HTH_DEOR helix_turn 22.9 77 0.0017 19.5 2.1 25 32-56 26-50 (53)
37 KOG1596|consensus 22.5 55 0.0012 30.4 1.8 22 6-28 137-158 (317)
38 PF09851 SHOCT: Short C-termin 22.2 1.1E+02 0.0023 18.8 2.5 20 104-123 6-25 (31)
39 PF00096 zf-C2H2: Zinc finger, 22.1 62 0.0014 17.5 1.3 15 129-143 7-21 (23)
40 TIGR02337 HpaR homoprotocatech 21.8 91 0.002 23.4 2.6 36 25-60 44-82 (118)
41 PF13412 HTH_24: Winged helix- 21.3 72 0.0016 20.3 1.7 20 32-51 29-48 (48)
42 PF07742 BTG: BTG family; Int 20.3 31 0.00067 27.5 -0.2 10 21-30 95-104 (118)
43 PF00392 GntR: Bacterial regul 20.0 93 0.002 21.1 2.2 27 31-57 35-61 (64)
No 1
>KOG1696|consensus
Probab=100.00 E-value=5.5e-90 Score=575.52 Aligned_cols=193 Identities=76% Similarity=1.149 Sum_probs=191.9
Q ss_pred CCchhhHHHHHHHHhhcCCCceecCccchhhHhhhhhhHHHHHHhhcCceeecCCCccchhhhHHhHHHHhcCcCCCCCC
Q psy17505 1 MSSLKLQKRLAASVMRCGKKKVWLDPNEINEIAITNSRQNIRKLIKDGLIIKKPVAVHSRARTRKNKEARRKGRHCGFGK 80 (199)
Q Consensus 1 m~~l~~QKRLAA~vL~cGk~kVWlDPne~~eI~~A~sR~~IRkLIkdG~Ii~kp~~~~Sr~R~r~~~~ak~kGRh~G~Gk 80 (199)
|++|++|+|||||||+||+.+|||||||+++|++|||||+|++||+||+||.+|+++|||+||+++.+++++|||+|+|+
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 cccccccCCchhHHHHHHHHHHHHHHHHHHhcCCCChHhhHHHHHhhhCCCcccHHHHHHHHHHHhhHHHHhhhhHHHHH
Q psy17505 81 RKGTANARMPQKILWVNRMRVLRRLLKKYRQAKKIDKHLYHQLYMKAKGNVFKNKRVLMEFIHKKKAEKSRAKLLSDQAE 160 (199)
Q Consensus 81 RkGt~~AR~p~K~~Wm~riR~lRrlLr~~re~~kID~~~Y~~lY~kaKGn~Fknk~~L~e~I~k~Kae~~r~k~l~dQae 160 (199)
|+||+|||||+|++||+||||||++|++|||+|+||+|+||+||++||||+|+|+++||||||++|||++++|+|+||||
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 HHHHhhHHHHHHHHHHHHHHHHHHHhhhhhHhh
Q psy17505 161 ARRQKVKEAKKRREERIQMKRQELLASYAREDE 193 (199)
Q Consensus 161 Arr~k~k~~r~rr~~r~~~kk~~~~~~~~~~~e 193 (199)
|+|.++++++++++|++++++++++.+++++||
T Consensus 161 Arr~k~k~ar~rreer~~~k~~~~~~~~~k~ee 193 (193)
T KOG1696|consen 161 ARRLKNKAARKRREERLAAKPQELIKTLSKEEE 193 (193)
T ss_pred HHHhhhHHHhhhHHHHHhhchhhhhcccccccC
Confidence 999999999999999999999999999999986
No 2
>PTZ00097 60S ribosomal protein L19; Provisional
Probab=100.00 E-value=3.1e-80 Score=516.23 Aligned_cols=174 Identities=66% Similarity=1.082 Sum_probs=171.2
Q ss_pred chhhHHHHHHHHhhcCCCceecCccchhhHhhhhhhHHHHHHhhcCceeecCCCccchhhhHHhHHHHhcCcCCCCCCcc
Q psy17505 3 SLKLQKRLAASVMRCGKKKVWLDPNEINEIAITNSRQNIRKLIKDGLIIKKPVAVHSRARTRKNKEARRKGRHCGFGKRK 82 (199)
Q Consensus 3 ~l~~QKRLAA~vL~cGk~kVWlDPne~~eI~~A~sR~~IRkLIkdG~Ii~kp~~~~Sr~R~r~~~~ak~kGRh~G~GkRk 82 (199)
+|++|+||||+||+||+++||||||+++||++||||+|||+||+||+|+++|++||||||++++++++++|||+|||+|+
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 cccccCCchhHHHHHHHHHHHHHHHHHHhcCCCChHhhHHHHHhhhCCCcccHHHHHHHHHHHhhHHHHhhhhHHHHHHH
Q psy17505 83 GTANARMPQKILWVNRMRVLRRLLKKYRQAKKIDKHLYHQLYMKAKGNVFKNKRVLMEFIHKKKAEKSRAKLLSDQAEAR 162 (199)
Q Consensus 83 Gt~~AR~p~K~~Wm~riR~lRrlLr~~re~~kID~~~Y~~lY~kaKGn~Fknk~~L~e~I~k~Kae~~r~k~l~dQaeAr 162 (199)
||+|||||+|+.||++||+||++|++|||+|+||+|+||.||++||||+|+|+++|++|||+.|+|+++++.|+||+||+
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 psy17505 163 RQKVKEAKKRREER 176 (199)
Q Consensus 163 r~k~k~~r~rr~~r 176 (199)
+.++++++++++++
T Consensus 161 r~k~~~~~~~r~~~ 174 (175)
T PTZ00097 161 RAKAKALRNKRKAK 174 (175)
T ss_pred HHHHHHHHHHHhhc
Confidence 99999999987653
No 3
>cd01417 Ribosomal_L19e_E Ribosomal protein L19e, eukaryotic. L19e is found in the large ribosomal subunit of eukaryotes and archaea. L19e is distinct from the ribosomal subunit L19, which is found in prokaryotes. It consists of two small globular domains connected by an extended segment. It is located toward the surface of the large subunit, with one exposed end involved in forming the intersubunit bridge with the small subunit. The other exposed end is involved in forming the translocon binding site, along with L22, L23, L24, L29, and L31e subunits.
Probab=100.00 E-value=5.4e-79 Score=504.72 Aligned_cols=164 Identities=79% Similarity=1.202 Sum_probs=161.9
Q ss_pred hhhHHHHHHHHhhcCCCceecCccchhhHhhhhhhHHHHHHhhcCceeecCCCccchhhhHHhHHHHhcCcCCCCCCccc
Q psy17505 4 LKLQKRLAASVMRCGKKKVWLDPNEINEIAITNSRQNIRKLIKDGLIIKKPVAVHSRARTRKNKEARRKGRHCGFGKRKG 83 (199)
Q Consensus 4 l~~QKRLAA~vL~cGk~kVWlDPne~~eI~~A~sR~~IRkLIkdG~Ii~kp~~~~Sr~R~r~~~~ak~kGRh~G~GkRkG 83 (199)
|++|+||||+||+||+++||||||+++||++||||+|||+||+||+|+++|++||||||++++++++++|||+|+|+|+|
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 67999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccccCCchhHHHHHHHHHHHHHHHHHHhcCCCChHhhHHHHHhhhCCCcccHHHHHHHHHHHhhHHHHhhhhHHHHHHHH
Q psy17505 84 TANARMPQKILWVNRMRVLRRLLKKYRQAKKIDKHLYHQLYMKAKGNVFKNKRVLMEFIHKKKAEKSRAKLLSDQAEARR 163 (199)
Q Consensus 84 t~~AR~p~K~~Wm~riR~lRrlLr~~re~~kID~~~Y~~lY~kaKGn~Fknk~~L~e~I~k~Kae~~r~k~l~dQaeArr 163 (199)
|+|||||+|+.||++||+||++|++|||+|+||+|+||.||++||||+|+|+++|++|||+.|+|+++++.|+||+||++
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 psy17505 164 QKVK 167 (199)
Q Consensus 164 ~k~k 167 (199)
++++
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=5.1e-77 Score=532.08 Aligned_cols=170 Identities=61% Similarity=1.007 Sum_probs=168.0
Q ss_pred CCchhhHHHHHHHHhhcCCCceecCccchhhHhhhhhhHHHHHHhhcCceeecCCCccchhhhHHhHHHHhcCcCCCCCC
Q psy17505 1 MSSLKLQKRLAASVMRCGKKKVWLDPNEINEIAITNSRQNIRKLIKDGLIIKKPVAVHSRARTRKNKEARRKGRHCGFGK 80 (199)
Q Consensus 1 m~~l~~QKRLAA~vL~cGk~kVWlDPne~~eI~~A~sR~~IRkLIkdG~Ii~kp~~~~Sr~R~r~~~~ak~kGRh~G~Gk 80 (199)
|++|++|+||||+||+||++|||||||+++||++||||+|||+||+||+|+++|++||||+|+|++++++++|||+|+||
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 cccccccCCchhHHHHHHHHHHHHHHHHHHhcCCCChHhhHHHHHhhhCCCcccHHHHHHHHHHHhhHHHHhhhhHHHHH
Q psy17505 81 RKGTANARMPQKILWVNRMRVLRRLLKKYRQAKKIDKHLYHQLYMKAKGNVFKNKRVLMEFIHKKKAEKSRAKLLSDQAE 160 (199)
Q Consensus 81 RkGt~~AR~p~K~~Wm~riR~lRrlLr~~re~~kID~~~Y~~lY~kaKGn~Fknk~~L~e~I~k~Kae~~r~k~l~dQae 160 (199)
|+||+|||||+|++||+|||+||++|++|||+|+||+|+||.||+++|||+|+|++||++|||+.|+|+.+++.|.||+|
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 psy17505 161 ARRQKVKEAK 170 (199)
Q Consensus 161 Arr~k~k~~r 170 (199)
|+|.++++.|
T Consensus 161 ArR~k~~~~r 170 (357)
T PTZ00436 161 AKRLKDEQHR 170 (357)
T ss_pred HHHHHhhhhh
Confidence 9999988654
No 5
>PF01280 Ribosomal_L19e: Ribosomal protein L19e; InterPro: IPR000196 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This entry represents structural domain of the ribosomal protein L19 from eukaryotes, as well as L19e from archaea []. L19/L19e is absent in bacteria. L19/L19e is part of the large ribosomal subunit, whose structure has been determined in a number of eukaryotic and archaeal species []. L19/L19e is a multi-helical protein consisting of two different 3-helical domains connected by a long, partly helical linker.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3IZR_T 3O58_S 3O5H_S 3IZS_T 2WWA_J 1S1I_P 2WW9_J 2ZKR_7 4A1A_O 4A1C_O ....
Probab=100.00 E-value=1.1e-74 Score=472.82 Aligned_cols=148 Identities=72% Similarity=1.088 Sum_probs=131.0
Q ss_pred CchhhHHHHHHHHhhcCCCceecCccchhhHhhhhhhHHHHHHhhcCceeecCCCccchhhhHHhHHHHhcCcCCCCCCc
Q psy17505 2 SSLKLQKRLAASVMRCGKKKVWLDPNEINEIAITNSRQNIRKLIKDGLIIKKPVAVHSRARTRKNKEARRKGRHCGFGKR 81 (199)
Q Consensus 2 ~~l~~QKRLAA~vL~cGk~kVWlDPne~~eI~~A~sR~~IRkLIkdG~Ii~kp~~~~Sr~R~r~~~~ak~kGRh~G~GkR 81 (199)
|+|++|+||||+||+||+++|||||||++||++||||+|||+||+||+|+++|++|||||||+++++++++|||+|||+|
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 ccccccCCchhHHHHHHHHHHHHHHHHHHhcCCCChHhhHHHHHhhhCCCcccHHHHHHHHHHHhhHH
Q psy17505 82 KGTANARMPQKILWVNRMRVLRRLLKKYRQAKKIDKHLYHQLYMKAKGNVFKNKRVLMEFIHKKKAEK 149 (199)
Q Consensus 82 kGt~~AR~p~K~~Wm~riR~lRrlLr~~re~~kID~~~Y~~lY~kaKGn~Fknk~~L~e~I~k~Kae~ 149 (199)
+||+|||||+|++||++||+||++|++|||+|+||+|+||+||++||||+|+|+++|+||||+.++|+
T Consensus 81 kGt~~AR~~~K~~W~~riR~lRr~Lk~~r~~~kID~~~Yr~lY~kaKGn~Fkn~~~L~~~i~~~k~e~ 148 (148)
T PF01280_consen 81 KGTKNARMPEKELWMRRIRALRRLLKRLRDSGKIDRHMYRSLYRKAKGNVFKNKRHLMEHIHKLKAEK 148 (148)
T ss_dssp -S-HHHHS-HHHHHHHHHHHHHHHHHHHHHTTSS-HHHHHHHHHHHHTTS-SSHHHHHHHHHHHHHCH
T ss_pred cccccccccHHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHhcCCcccCHHHHHHHHHHhccCC
Confidence 99999999999999999999999999999999999999999999999999999999999999999985
No 6
>cd00481 Ribosomal_L19e Ribosomal protein L19e. L19e is found in the large ribosomal subunit of eukaryotes and archaea. L19e is distinct from the ribosomal subunit L19, which is found in prokaryotes. It consists of two small globular domains connected by an extended segment. It is located toward the surface of the large subunit, with one exposed end involved in forming the intersubunit bridge with the small subunit. The other exposed end is involved in forming the translocon binding site, along with L22, L23, L24, L29, and L31e subunits.
Probab=100.00 E-value=3.7e-73 Score=462.38 Aligned_cols=145 Identities=69% Similarity=1.100 Sum_probs=143.0
Q ss_pred hhhHHHHHHHHhhcCCCceecCccchhhHhhhhhhHHHHHHhhcCceeecCCCccchhhhHHhHHHHhcCcCCCCCCccc
Q psy17505 4 LKLQKRLAASVMRCGKKKVWLDPNEINEIAITNSRQNIRKLIKDGLIIKKPVAVHSRARTRKNKEARRKGRHCGFGKRKG 83 (199)
Q Consensus 4 l~~QKRLAA~vL~cGk~kVWlDPne~~eI~~A~sR~~IRkLIkdG~Ii~kp~~~~Sr~R~r~~~~ak~kGRh~G~GkRkG 83 (199)
|++|+||||+||+||+++||||||+++||++||||+|||+||+||+|+++|++||||+|++++++++++|||+|||+|+|
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 ccccCCchhHHHHHHHHHHHHHHHHHHhcCCCChHhhHHHHHhhhCCCcccHHHHHHHHHHHhhH
Q psy17505 84 TANARMPQKILWVNRMRVLRRLLKKYRQAKKIDKHLYHQLYMKAKGNVFKNKRVLMEFIHKKKAE 148 (199)
Q Consensus 84 t~~AR~p~K~~Wm~riR~lRrlLr~~re~~kID~~~Y~~lY~kaKGn~Fknk~~L~e~I~k~Kae 148 (199)
|++||||+|+.||++||+||++|++|||+|+||+|+||.||++||||+|+|+++|++|||+.++|
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=1.3e-72 Score=461.31 Aligned_cols=146 Identities=44% Similarity=0.761 Sum_probs=144.3
Q ss_pred CCchhhHHHHHHHHhhcCCCceecCccchhhHhhhhhhHHHHHHhhcCceeecCCCccchhhhHHhHHHHhcCcCCCCCC
Q psy17505 1 MSSLKLQKRLAASVMRCGKKKVWLDPNEINEIAITNSRQNIRKLIKDGLIIKKPVAVHSRARTRKNKEARRKGRHCGFGK 80 (199)
Q Consensus 1 m~~l~~QKRLAA~vL~cGk~kVWlDPne~~eI~~A~sR~~IRkLIkdG~Ii~kp~~~~Sr~R~r~~~~ak~kGRh~G~Gk 80 (199)
|++|++|+||||+||+||+++||||||+++||++||||+|||+||+||+|+++|++||||||++++++++++|||+|+||
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 cccccccCCchhHHHHHHHHHHHHHHHHHHhcCCCChHhhHHHHHhhhCCCcccHHHHHHHHHHHh
Q psy17505 81 RKGTANARMPQKILWVNRMRVLRRLLKKYRQAKKIDKHLYHQLYMKAKGNVFKNKRVLMEFIHKKK 146 (199)
Q Consensus 81 RkGt~~AR~p~K~~Wm~riR~lRrlLr~~re~~kID~~~Y~~lY~kaKGn~Fknk~~L~e~I~k~K 146 (199)
|+||+|||+|+|+.||++||+||++|++|||+|+||+|+||.||++||||+|+|+++|++||+...
T Consensus 81 RkGt~~AR~p~K~~W~~riR~lRr~Lk~lR~~~kId~~~Yr~lY~kaKGn~Fkn~~~L~~~i~~~~ 146 (150)
T PRK08570 81 RKGKKGARTPKKERWINRIRALRRYLRELRDEGKIDRKTYRKLYRKAKGGEFRSVSHLKTYIEEHG 146 (150)
T ss_pred CCCcccCCCCHHHHHHHHHHHHHHHHHHHHHcCCCCHHHHHHHHHHhcCCccCCHHHHHHHHHHhc
Confidence 999999999999999999999999999999999999999999999999999999999999999754
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=4.6e-71 Score=450.04 Aligned_cols=142 Identities=43% Similarity=0.746 Sum_probs=140.0
Q ss_pred hhhHHHHHHHHhhcCCCceecCccchhhHhhhhhhHHHHHHhhcCceeecCCCccchhhhHHhHHHHhcCcCCCCCCccc
Q psy17505 4 LKLQKRLAASVMRCGKKKVWLDPNEINEIAITNSRQNIRKLIKDGLIIKKPVAVHSRARTRKNKEARRKGRHCGFGKRKG 83 (199)
Q Consensus 4 l~~QKRLAA~vL~cGk~kVWlDPne~~eI~~A~sR~~IRkLIkdG~Ii~kp~~~~Sr~R~r~~~~ak~kGRh~G~GkRkG 83 (199)
|++|+||||+||+||+++||||||+++||++||||+|||+||+||+|+++|++||||+|++++++++++|||+|+|||+|
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 ccccCCchhHHHHHHHHHHHHHHHHHHhcCCCChHhhHHHHHhhhCCCcccHHHHHHHHHHH
Q psy17505 84 TANARMPQKILWVNRMRVLRRLLKKYRQAKKIDKHLYHQLYMKAKGNVFKNKRVLMEFIHKK 145 (199)
Q Consensus 84 t~~AR~p~K~~Wm~riR~lRrlLr~~re~~kID~~~Y~~lY~kaKGn~Fknk~~L~e~I~k~ 145 (199)
|+|||||+|+.||++||+||++|++|||+|+||+|+||.||++||||+|+|+++|++||...
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 99999999999999999999999999999999999999999999999999999999999754
No 9
>COG2147 RPL19A Ribosomal protein L19E [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=3.6e-67 Score=427.94 Aligned_cols=149 Identities=52% Similarity=0.815 Sum_probs=146.3
Q ss_pred CCchhhHHHHHHHHhhcCCCceecCccchhhHhhhhhhHHHHHHhhcCceeecCCCccchhhhHHhHHHHhcCcCCCCCC
Q psy17505 1 MSSLKLQKRLAASVMRCGKKKVWLDPNEINEIAITNSRQNIRKLIKDGLIIKKPVAVHSRARTRKNKEARRKGRHCGFGK 80 (199)
Q Consensus 1 m~~l~~QKRLAA~vL~cGk~kVWlDPne~~eI~~A~sR~~IRkLIkdG~Ii~kp~~~~Sr~R~r~~~~ak~kGRh~G~Gk 80 (199)
|+||+.|+||||+|||||+++||||||+++||++|+||+|||.||+||+|+.+|++|+|++|++++++++++|||+||||
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 cccccccCCchhHHHHHHHHHHHHHHHHHHhcCCCChHhhHHHHHhhhCCCcccHHHHHHHHHHHhhHH
Q psy17505 81 RKGTANARMPQKILWVNRMRVLRRLLKKYRQAKKIDKHLYHQLYMKAKGNVFKNKRVLMEFIHKKKAEK 149 (199)
Q Consensus 81 RkGt~~AR~p~K~~Wm~riR~lRrlLr~~re~~kID~~~Y~~lY~kaKGn~Fknk~~L~e~I~k~Kae~ 149 (199)
|+||++||||+|+.||.+||+||++|++|+++|+||+|+||.||+++|||.|+++++|.+||.+.+.++
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 999999999999999999999999999999999999999999999999999999999999999887653
No 10
>PF07946 DUF1682: Protein of unknown function (DUF1682); InterPro: IPR012879 The members of this family are all hypothetical eukaryotic proteins of unknown function. One member (Q920S6 from SWISSPROT) is described as being an adipocyte-specific protein, but no evidence of this was found.
Probab=74.34 E-value=9.8 Score=34.48 Aligned_cols=52 Identities=27% Similarity=0.404 Sum_probs=33.7
Q ss_pred HHhhHHHHhhhhHHHHHHHHHhhHH-HHHHHHHHHHHHHHHHHhhhhhHhhHh
Q psy17505 144 KKKAEKSRAKLLSDQAEARRQKVKE-AKKRREERIQMKRQELLASYAREDEKA 195 (199)
Q Consensus 144 k~Kae~~r~k~l~dQaeArr~k~k~-~r~rr~~r~~~kk~~~~~~~~~~~e~~ 195 (199)
..|+++.|++.+++-..+......+ +.+++++...+++++.++.++.||..+
T Consensus 257 ~~K~~k~R~~~~~~~~K~~~~~r~E~~~~~k~e~kr~e~~~~~~~lspeeQrK 309 (321)
T PF07946_consen 257 KKKAKKNREEEEEKILKEAHQERQEEAQEKKEEKKREERERKLSKLSPEEQRK 309 (321)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCHHHHHH
Confidence 3466777777766654444444333 445666666677788899999888744
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=69.54 E-value=3.3 Score=25.75 Aligned_cols=29 Identities=24% Similarity=0.345 Sum_probs=24.3
Q ss_pred ecCccchhhHhhhhhhHHHHHHhhcCceee
Q psy17505 23 WLDPNEINEIAITNSRQNIRKLIKDGLIIK 52 (199)
Q Consensus 23 WlDPne~~eI~~A~sR~~IRkLIkdG~Ii~ 52 (199)
||++.|+.++-. .|+..|+.|+++|.|-.
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 677888888776 78999999999998765
No 12
>PF12728 HTH_17: Helix-turn-helix domain
Probab=68.87 E-value=3.5 Score=26.88 Aligned_cols=28 Identities=29% Similarity=0.381 Sum_probs=24.4
Q ss_pred ecCccchhhHhhhhhhHHHHHHhhcCcee
Q psy17505 23 WLDPNEINEIAITNSRQNIRKLIKDGLII 51 (199)
Q Consensus 23 WlDPne~~eI~~A~sR~~IRkLIkdG~Ii 51 (199)
||++.|+-++-. +|+..|+.+++.|.|.
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 6999999999999763
No 13
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=55.27 E-value=5.1 Score=25.82 Aligned_cols=15 Identities=20% Similarity=0.665 Sum_probs=12.3
Q ss_pred CceecCccchhhHhh
Q psy17505 20 KKVWLDPNEINEIAI 34 (199)
Q Consensus 20 ~kVWlDPne~~eI~~ 34 (199)
.-||||++|++.|.+
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
>PF14468 DUF4427: Protein of unknown function (DUF4427)
Probab=54.17 E-value=11 Score=31.14 Aligned_cols=33 Identities=21% Similarity=0.415 Sum_probs=26.0
Q ss_pred HHHhhcCCCceecCccchhhHhhhhhhHHHHHHhhcCceeec
Q psy17505 12 ASVMRCGKKKVWLDPNEINEIAITNSRQNIRKLIKDGLIIKK 53 (199)
Q Consensus 12 A~vL~cGk~kVWlDPne~~eI~~A~sR~~IRkLIkdG~Ii~k 53 (199)
.-++.-|...||| |+ |+.+=+|.||++|.|+.-
T Consensus 30 ~~~~e~G~~wvWi-~D--------N~~~~vRALl~~grV~v~ 62 (132)
T PF14468_consen 30 DYDREFGNAWVWI-HD--------NQSEVVRALLQAGRVKVN 62 (132)
T ss_pred cchhhcCceEEEE-ec--------CcCHHHHHHHHcCceeec
Confidence 3456789999999 33 667789999999998764
No 15
>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=48.08 E-value=29 Score=22.82 Aligned_cols=53 Identities=21% Similarity=0.245 Sum_probs=32.6
Q ss_pred hHHHHHHHHhhcCCCceecCccchhhH---hhhhhhHHHHHHhhcCceeecCCCccch
Q psy17505 6 LQKRLAASVMRCGKKKVWLDPNEINEI---AITNSRQNIRKLIKDGLIIKKPVAVHSR 60 (199)
Q Consensus 6 ~QKRLAA~vL~cGk~kVWlDPne~~eI---~~A~sR~~IRkLIkdG~Ii~kp~~~~Sr 60 (199)
.|-++-..|..+|.. ++-++++.+. +-+.--..|..|++.|+|.+.+.....|
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 344555566666655 3344444432 3344456788999999999998877655
No 16
>PRK00247 putative inner membrane protein translocase component YidC; Validated
Probab=47.94 E-value=2.7e+02 Score=27.02 Aligned_cols=77 Identities=18% Similarity=0.251 Sum_probs=40.3
Q ss_pred hHHHHHHHHHHHHHHHHHHhcC---CCChHhhHHHHHhhhCCCcccHHHHHHHHHHHhhHHHHhhhhHHH-HHHHHHhhH
Q psy17505 92 KILWVNRMRVLRRLLKKYRQAK---KIDKHLYHQLYMKAKGNVFKNKRVLMEFIHKKKAEKSRAKLLSDQ-AEARRQKVK 167 (199)
Q Consensus 92 K~~Wm~riR~lRrlLr~~re~~---kID~~~Y~~lY~kaKGn~Fknk~~L~e~I~k~Kae~~r~k~l~dQ-aeArr~k~k 167 (199)
+..|..+.+..+..++..|... .|....+..|..- |...=.+.=...+++++++|.++.+ -||.|.-++
T Consensus 291 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~-------~~~~~~~~~~~~~~~k~~~k~~~~~~~~~~~~~~~ 363 (429)
T PRK00247 291 RAQYREKQKEKKAFLWTLRRNRLRMIITPWRAPELHAE-------NAEIKKTRTAEKNEAKARKKEIAQKRRAAEREINR 363 (429)
T ss_pred HHHHHHHHHHHHHHHHHHHhccccccCCcccHHHHHHH-------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4456666666555555555544 7777777666432 2222223333446666777766554 344444455
Q ss_pred HHHHHHHH
Q psy17505 168 EAKKRREE 175 (199)
Q Consensus 168 ~~r~rr~~ 175 (199)
++++.+.+
T Consensus 364 ~~~~~~~~ 371 (429)
T PRK00247 364 EARQERAA 371 (429)
T ss_pred HhhhhHHH
Confidence 44444333
No 17
>PF13880 Acetyltransf_13: ESCO1/2 acetyl-transferase
Probab=47.10 E-value=6.2 Score=29.11 Aligned_cols=14 Identities=29% Similarity=1.020 Sum_probs=11.9
Q ss_pred hcCCCceecCccch
Q psy17505 16 RCGKKKVWLDPNEI 29 (199)
Q Consensus 16 ~cGk~kVWlDPne~ 29 (199)
-||.++||..|..-
T Consensus 5 ~~GI~RIWV~~~~R 18 (70)
T PF13880_consen 5 VCGISRIWVSPSHR 18 (70)
T ss_pred EEEeEEEEeChhhh
Confidence 49999999999753
No 18
>TIGR02075 pyrH_bact uridylate kinase. This protein, also called UMP kinase, converts UMP to UDP by adding a phosphate from ATP. It is the first step in pyrimidine biosynthesis. GTP is an allosteric activator. In a large fraction of all bacterial genomes, the gene tends to be located immediately downstream of elongation factor Ts and upstream of ribosome recycling factor. A related protein family, believed to be equivalent in function and found in the archaea and in spirochetes, is described by a separate model, TIGR02076.
Probab=43.99 E-value=30 Score=29.56 Aligned_cols=48 Identities=15% Similarity=0.182 Sum_probs=38.2
Q ss_pred hhHHHH-HHHHhhcCCCceecCccchhhHhhhhhhHHHHHHhhcCceee
Q psy17505 5 KLQKRL-AASVMRCGKKKVWLDPNEINEIAITNSRQNIRKLIKDGLIIK 52 (199)
Q Consensus 5 ~~QKRL-AA~vL~cGk~kVWlDPne~~eI~~A~sR~~IRkLIkdG~Ii~ 52 (199)
.++-+| +..+...|.+-++++|.....+..-++.+.+..|++.|.|..
T Consensus 77 ~l~~~l~~~~L~~~Gi~a~~l~~~~~~~~~~~~~~~~i~~ll~~g~VpV 125 (233)
T TIGR02075 77 VINGLALRDALEKLGVKTRVLSAISMPQICESYIRRKAIKHLEKGKVVI 125 (233)
T ss_pred HHHHHHHHHHHHhCCCCcEEeccccCCCCccccCHHHHHHHHHCCCEEE
Confidence 456665 777778999999999998765555567899999999999843
No 19
>PRK05920 aromatic acid decarboxylase; Validated
Probab=41.64 E-value=35 Score=29.50 Aligned_cols=47 Identities=28% Similarity=0.306 Sum_probs=36.6
Q ss_pred HHHHHHhhcCCCceecCccchhhHhhhhhhHHHHHHhhcCceeecCCCcc
Q psy17505 9 RLAASVMRCGKKKVWLDPNEINEIAITNSRQNIRKLIKDGLIIKKPVAVH 58 (199)
Q Consensus 9 RLAA~vL~cGk~kVWlDPne~~eI~~A~sR~~IRkLIkdG~Ii~kp~~~~ 58 (199)
+.|...|+.|. .|.|=|.+... ++.+++++..|-..|.++.-|..+.
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 7788999999999999999999875
No 20
>PF01479 S4: S4 domain; InterPro: IPR002942 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. The S4 domain is a small domain consisting of 60-65 amino acid residues that was detected in the bacterial ribosomal protein S4, eukaryotic ribosomal S9, two families of pseudouridine synthases, a novel family of predicted RNA methylases, a yeast protein containing a pseudouridine synthetase and a deaminase domain, bacterial tyrosyl-tRNA synthetases, and a number of uncharacterised, small proteins that may be involved in translation regulation []. The S4 domain probably mediates binding to RNA.; GO: 0003723 RNA binding; PDB: 3BBU_A 1DM9_B 2K6P_A 3U5G_E 3U5C_E 3IZB_D 2XZM_D 2XZN_D 3O30_E 3O2Z_E ....
Probab=38.52 E-value=27 Score=22.33 Aligned_cols=29 Identities=28% Similarity=0.471 Sum_probs=21.9
Q ss_pred hhHhhhhhhHHHHHHhhcCceeecCCCcc
Q psy17505 30 NEIAITNSRQNIRKLIKDGLIIKKPVAVH 58 (199)
Q Consensus 30 ~eI~~A~sR~~IRkLIkdG~Ii~kp~~~~ 58 (199)
.+...+.||.++++||+.|.|..--..+.
T Consensus 8 ~~~~~~~sr~~a~~~I~~g~V~VNg~~v~ 36 (48)
T PF01479_consen 8 SRLGLASSRSEARRLIKQGRVKVNGKVVK 36 (48)
T ss_dssp HHTTSSSSHHHHHHHHHTTTEEETTEEES
T ss_pred HHcCCcCCHHHHHHhcCCCEEEECCEEEc
Confidence 34455789999999999999877554443
No 21
>PRK06029 3-octaprenyl-4-hydroxybenzoate carboxy-lyase; Provisional
Probab=35.68 E-value=53 Score=27.89 Aligned_cols=47 Identities=23% Similarity=0.271 Sum_probs=36.3
Q ss_pred HHHHHHhhcCCCceecCccchhhHhhhhhhHHHHHHhhcCceeecCCCcc
Q psy17505 9 RLAASVMRCGKKKVWLDPNEINEIAITNSRQNIRKLIKDGLIIKKPVAVH 58 (199)
Q Consensus 9 RLAA~vL~cGk~kVWlDPne~~eI~~A~sR~~IRkLIkdG~Ii~kp~~~~ 58 (199)
+.|.-.|.+++ .|.|=|. +--.+..+.+++.+|-+.|.++..|..|.
T Consensus 106 ~~a~~~L~~~~-pvii~P~--~M~~~p~~~~Nl~~L~~~G~~vi~P~~g~ 152 (185)
T PRK06029 106 RAADVMLKERR-RLVLCVR--ETPLHLGHLRNMTKLAEMGAIIMPPVPAF 152 (185)
T ss_pred HHHHHHHhcCC-CEEEEec--cccCCHHHHHHHHHHHHCcCEEECCCccc
Confidence 44556677665 5555685 45668899999999999999999999763
No 22
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=33.75 E-value=37 Score=21.61 Aligned_cols=25 Identities=24% Similarity=0.553 Sum_probs=18.2
Q ss_pred HhhhhhhHHHHHHhhcCceeecCCC
Q psy17505 32 IAITNSRQNIRKLIKDGLIIKKPVA 56 (199)
Q Consensus 32 I~~A~sR~~IRkLIkdG~Ii~kp~~ 56 (199)
|+.+.-+..+..|.++|+|...|-.
T Consensus 32 vs~~tv~~~l~~L~~~g~i~~~~~~ 56 (60)
T smart00345 32 VSRTTVREALSRLEAEGLVQRRPGS 56 (60)
T ss_pred CCHHHHHHHHHHHHHCCCEEEecCC
Confidence 3445567777889999999876643
No 23
>TIGR01610 phage_O_Nterm phage replication protein O, N-terminal domain. This model represents the N-terminal region of the phage lambda replication protein O and homologous regions of other phage proteins.
Probab=33.34 E-value=31 Score=25.74 Aligned_cols=38 Identities=24% Similarity=0.329 Sum_probs=26.5
Q ss_pred hcCCCceecCccchhhHhhhhhhHH----HHHHhhcCceeecC
Q psy17505 16 RCGKKKVWLDPNEINEIAITNSRQN----IRKLIKDGLIIKKP 54 (199)
Q Consensus 16 ~cGk~kVWlDPne~~eI~~A~sR~~----IRkLIkdG~Ii~kp 54 (199)
|.++..+++.+.|+.++... ||+. |..|.++|+|....
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 4544 55799999998654
No 24
>PF08535 KorB: KorB domain; InterPro: IPR013741 This entry contains several KorB transcriptional repressor proteins. The korB gene is a major regulatory element in the replication and maintenance of broad host-range plasmid RK2. It negatively controls the replication gene trfA, the host-lethal determinants kilA and kilB, and the korA-korB operon []. This domain includes the DNA-binding HTH motif []. ; PDB: 1R71_C.
Probab=31.45 E-value=45 Score=24.55 Aligned_cols=39 Identities=28% Similarity=0.622 Sum_probs=24.9
Q ss_pred hHHHHHHHHhhcCCCceecCccchhhHhhhhhhHHHHHHhhcCcee
Q psy17505 6 LQKRLAASVMRCGKKKVWLDPNEINEIAITNSRQNIRKLIKDGLII 51 (199)
Q Consensus 6 ~QKRLAA~vL~cGk~kVWlDPne~~eI~~A~sR~~IRkLIkdG~Ii 51 (199)
+|.-+|..| |+++-|+ .+-++-++--++|+.|+.+|.|.
T Consensus 5 tq~eIA~~l---Gks~s~V----s~~l~Ll~lP~~i~~~v~~g~~~ 43 (93)
T PF08535_consen 5 TQEEIAKRL---GKSRSWV----SNHLALLDLPEEIKELVRSGRIS 43 (93)
T ss_dssp -HHHHHHHT---T--HHHH----HHHHGGGS--HHHHHHHHTTS--
T ss_pred CHHHHHHHH---CCCHHHH----HHHHHHHcCCHHHHHHHHcCCCc
Confidence 466677754 8999887 45666677788999999999774
No 25
>PRK11548 outer membrane biogenesis protein BamE; Provisional
Probab=30.49 E-value=38 Score=26.24 Aligned_cols=26 Identities=19% Similarity=0.440 Sum_probs=23.3
Q ss_pred eecCccchhhHhhhhhhHHHHHHhhc
Q psy17505 22 VWLDPNEINEIAITNSRQNIRKLIKD 47 (199)
Q Consensus 22 VWlDPne~~eI~~A~sR~~IRkLIkd 47 (199)
-++||+.+++|.--.|+++|+.|+-.
T Consensus 36 ~~~~~~~l~~l~~GmTk~qV~~lLGt 61 (113)
T PRK11548 36 NYLTPNDVAKIHVGMTQQQVAYTLGT 61 (113)
T ss_pred ccCCHHHHHHhcCCCCHHHHHHHcCC
Confidence 37899999999999999999999854
No 26
>PHA00616 hypothetical protein
Probab=29.49 E-value=28 Score=23.65 Aligned_cols=17 Identities=24% Similarity=0.622 Sum_probs=14.9
Q ss_pred CCCcccHHHHHHHHHHH
Q psy17505 129 GNVFKNKRVLMEFIHKK 145 (199)
Q Consensus 129 Gn~Fknk~~L~e~I~k~ 145 (199)
|..|.+++.|..|+.+.
T Consensus 8 G~~F~~~s~l~~H~r~~ 24 (44)
T PHA00616 8 GGIFRKKKEVIEHLLSV 24 (44)
T ss_pred hHHHhhHHHHHHHHHHh
Confidence 78999999999999654
No 27
>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=27.45 E-value=69 Score=27.23 Aligned_cols=43 Identities=14% Similarity=0.202 Sum_probs=35.2
Q ss_pred HHHHHhhcCCCceecCccchhhHhhhhhhHHHHHHhhcCceee
Q psy17505 10 LAASVMRCGKKKVWLDPNEINEIAITNSRQNIRKLIKDGLIIK 52 (199)
Q Consensus 10 LAA~vL~cGk~kVWlDPne~~eI~~A~sR~~IRkLIkdG~Ii~ 52 (199)
|++.+...|.+-+||+|-+++.+.....-+.+..++..|.|..
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 5667778999999999999876655566789999999998743
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=25.92 E-value=98 Score=25.94 Aligned_cols=47 Identities=26% Similarity=0.310 Sum_probs=35.4
Q ss_pred HHHHHHhhcCCCceecCccchhhHhhhhhhHHHHHHhhcCceeecCCCcc
Q psy17505 9 RLAASVMRCGKKKVWLDPNEINEIAITNSRQNIRKLIKDGLIIKKPVAVH 58 (199)
Q Consensus 9 RLAA~vL~cGk~kVWlDPne~~eI~~A~sR~~IRkLIkdG~Ii~kp~~~~ 58 (199)
+.|...|+++. .|.|=|.+. -.++.+.+++..|-..|.++.-|..+.
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 555568544 457888999999999999999998763
No 29
>COG3592 Uncharacterized conserved protein [Function unknown]
Probab=25.19 E-value=35 Score=25.74 Aligned_cols=19 Identities=26% Similarity=0.788 Sum_probs=14.6
Q ss_pred HHHHhhcCCCceecCccchh
Q psy17505 11 AASVMRCGKKKVWLDPNEIN 30 (199)
Q Consensus 11 AA~vL~cGk~kVWlDPne~~ 30 (199)
+++|+++|..= ||+|+..+
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
>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=24.59 E-value=62 Score=21.85 Aligned_cols=22 Identities=5% Similarity=0.120 Sum_probs=18.1
Q ss_pred hhhhHHHHHHhhcCceeecCCC
Q psy17505 35 TNSRQNIRKLIKDGLIIKKPVA 56 (199)
Q Consensus 35 A~sR~~IRkLIkdG~Ii~kp~~ 56 (199)
+.||..+++||++|.|...-..
T Consensus 21 ~~SR~~~k~li~~G~V~VNg~~ 42 (59)
T TIGR02988 21 IDSGGQAKWFLQENEVLVNGEL 42 (59)
T ss_pred ccCHHHHHHHHHcCCEEECCEE
Confidence 3499999999999999885443
No 31
>COG5104 PRP40 Splicing factor [RNA processing and modification]
Probab=24.20 E-value=3.2e+02 Score=27.41 Aligned_cols=51 Identities=24% Similarity=0.254 Sum_probs=38.6
Q ss_pred hhhHHHHHHHHhhcCCCceecCccchhhHhhhhhhH-------------HHHHHhhcCceeecCC
Q psy17505 4 LKLQKRLAASVMRCGKKKVWLDPNEINEIAITNSRQ-------------NIRKLIKDGLIIKKPV 55 (199)
Q Consensus 4 l~~QKRLAA~vL~cGk~kVWlDPne~~eI~~A~sR~-------------~IRkLIkdG~Ii~kp~ 55 (199)
+..-+|+.+..+-+|..-+| |...++||-.+++=. .+-.||-||+|..+..
T Consensus 424 y~~~r~~~~~~~~~~qis~~-d~~~vdei~~~~~Ek~eE~e~~~d~v~kE~is~i~D~~I~qr~E 487 (590)
T COG5104 424 YGFARRSYERETRTGQISPT-DRRAVDEIFEAIAEKKEEGEIKFDKVDKEDISLIVDGLIKQRNE 487 (590)
T ss_pred HHHHHHHHHHHHHhccCCCc-cccchHHHHHHHHHHHhhcchhhhhhhHHHHHHHHHHHHHHhHH
Confidence 34446788888889999999 888999998888742 3447888888866543
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=24.01 E-value=54 Score=21.44 Aligned_cols=26 Identities=23% Similarity=0.272 Sum_probs=19.4
Q ss_pred hhhhhHHHHHHhhcCceeecCCCccc
Q psy17505 34 ITNSRQNIRKLIKDGLIIKKPVAVHS 59 (199)
Q Consensus 34 ~A~sR~~IRkLIkdG~Ii~kp~~~~S 59 (199)
.++.-.-|.+|++.|+|.+.+....-
T Consensus 31 ~~~~t~~i~~L~~~g~I~r~~~~~D~ 56 (59)
T PF01047_consen 31 RSTVTRIIKRLEKKGLIERERDPDDR 56 (59)
T ss_dssp HHHHHHHHHHHHHTTSEEEEEETTET
T ss_pred hhHHHHHHHHHHHCCCEEeccCCCCC
Confidence 34455678999999999998765543
No 33
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=23.99 E-value=76 Score=22.67 Aligned_cols=33 Identities=36% Similarity=0.391 Sum_probs=22.1
Q ss_pred CccchhhHhhh--hhhHHHH----HHhhcCceeecCCCc
Q psy17505 25 DPNEINEIAIT--NSRQNIR----KLIKDGLIIKKPVAV 57 (199)
Q Consensus 25 DPne~~eI~~A--~sR~~IR----kLIkdG~Ii~kp~~~ 57 (199)
.|=-+.|||+| .|+.++| .|.++|.|..-|+.-
T Consensus 14 ~p~~T~eiA~~~gls~~~aR~yL~~Le~eG~V~~~~~~r 52 (62)
T PF04703_consen 14 GPLKTREIADALGLSIYQARYYLEKLEKEGKVERSPVRR 52 (62)
T ss_dssp S-EEHHHHHHHHTS-HHHHHHHHHHHHHCTSEEEES-SS
T ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEecCCC
Confidence 35667788776 4555655 799999999888643
No 34
>smart00099 btg1 tob/btg1 family. The tob/btg1 is a family of proteins that inhibit cell proliferation.
Probab=23.51 E-value=30 Score=27.58 Aligned_cols=10 Identities=40% Similarity=1.155 Sum_probs=8.3
Q ss_pred ceecCccchh
Q psy17505 21 KVWLDPNEIN 30 (199)
Q Consensus 21 kVWlDPne~~ 30 (199)
.||+||.|+.
T Consensus 93 tiwvDP~eVs 102 (108)
T smart00099 93 TLWVDPFEVS 102 (108)
T ss_pred EEEECCCEEE
Confidence 5899999864
No 35
>PF15319 RHINO: RAD9, RAD1, HUS1-interacting nuclear orphan protein
Probab=23.15 E-value=33 Score=30.84 Aligned_cols=35 Identities=26% Similarity=0.517 Sum_probs=26.5
Q ss_pred ccccccCCchhHHHHHHHHHHHHHHHHHHhcCCCChHhh
Q psy17505 82 KGTANARMPQKILWVNRMRVLRRLLKKYRQAKKIDKHLY 120 (199)
Q Consensus 82 kGt~~AR~p~K~~Wm~riR~lRrlLr~~re~~kID~~~Y 120 (199)
+.|-.--+.-|++|-+| +.||..|||.|++++..|
T Consensus 200 ~DTPE~~YGiKvTWRRR----~hL~~yLrerGkL~~sq~ 234 (236)
T PF15319_consen 200 EDTPEEKYGIKVTWRRR----RHLLAYLRERGKLSRSQF 234 (236)
T ss_pred ccCCcccccceeeeecc----HHHHHHHHHhCccchhhc
Confidence 34545556679999666 578899999999998754
No 36
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=22.87 E-value=77 Score=19.51 Aligned_cols=25 Identities=20% Similarity=0.369 Sum_probs=18.2
Q ss_pred HhhhhhhHHHHHHhhcCceeecCCC
Q psy17505 32 IAITNSRQNIRKLIKDGLIIKKPVA 56 (199)
Q Consensus 32 I~~A~sR~~IRkLIkdG~Ii~kp~~ 56 (199)
++.+.-+..|..|.+.|+|...+.-
T Consensus 26 ~s~~tv~~~l~~L~~~g~i~~~~~~ 50 (53)
T smart00420 26 VSEMTIRRDLNKLEEQGLLTRVHGG 50 (53)
T ss_pred CCHHHHHHHHHHHHHCCCEEEeecC
Confidence 4445567788899999999876543
No 37
>KOG1596|consensus
Probab=22.53 E-value=55 Score=30.38 Aligned_cols=22 Identities=23% Similarity=0.598 Sum_probs=18.7
Q ss_pred hHHHHHHHHhhcCCCceecCccc
Q psy17505 6 LQKRLAASVMRCGKKKVWLDPNE 28 (199)
Q Consensus 6 ~QKRLAA~vL~cGk~kVWlDPne 28 (199)
.|-.|||.|| ||...|||.|-.
T Consensus 137 frSKLAA~I~-gGvdnihikpGs 158 (317)
T KOG1596|consen 137 FRSKLAAGIL-GGVDNIHIKPGS 158 (317)
T ss_pred HHHHHHHHhh-cCccceeecCCc
Confidence 4668999999 599999999953
No 38
>PF09851 SHOCT: Short C-terminal domain; InterPro: IPR018649 This family of hypothetical prokaryotic proteins has no known function.
Probab=22.20 E-value=1.1e+02 Score=18.80 Aligned_cols=20 Identities=25% Similarity=0.295 Sum_probs=16.7
Q ss_pred HHHHHHHhcCCCChHhhHHH
Q psy17505 104 RLLKKYRQAKKIDKHLYHQL 123 (199)
Q Consensus 104 rlLr~~re~~kID~~~Y~~l 123 (199)
..|+.+.+.|.|+-..|...
T Consensus 6 ~~L~~l~~~G~IseeEy~~~ 25 (31)
T PF09851_consen 6 EKLKELYDKGEISEEEYEQK 25 (31)
T ss_pred HHHHHHHHcCCCCHHHHHHH
Confidence 35788899999999999764
No 39
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=22.07 E-value=62 Score=17.50 Aligned_cols=15 Identities=27% Similarity=0.472 Sum_probs=12.8
Q ss_pred CCCcccHHHHHHHHH
Q psy17505 129 GNVFKNKRVLMEFIH 143 (199)
Q Consensus 129 Gn~Fknk~~L~e~I~ 143 (199)
|-.|.+...|..||.
T Consensus 7 ~~~f~~~~~l~~H~~ 21 (23)
T PF00096_consen 7 GKSFSSKSNLKRHMR 21 (23)
T ss_dssp TEEESSHHHHHHHHH
T ss_pred CCccCCHHHHHHHHh
Confidence 557999999999985
No 40
>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=21.81 E-value=91 Score=23.36 Aligned_cols=36 Identities=14% Similarity=0.232 Sum_probs=24.2
Q ss_pred CccchhhH---hhhhhhHHHHHHhhcCceeecCCCccch
Q psy17505 25 DPNEINEI---AITNSRQNIRKLIKDGLIIKKPVAVHSR 60 (199)
Q Consensus 25 DPne~~eI---~~A~sR~~IRkLIkdG~Ii~kp~~~~Sr 60 (199)
.+.++.+. +.++--..|.+|.++|+|.+.|.....|
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 44454444 2334446788999999999988766544
No 41
>PF13412 HTH_24: Winged helix-turn-helix DNA-binding; PDB: 1I1G_B 2IA0_B 3I4P_A 2GQQ_A 2L4A_A 2CFX_B 2DBB_B 2EFO_A 2EFQ_A 2PN6_A ....
Probab=21.35 E-value=72 Score=20.32 Aligned_cols=20 Identities=30% Similarity=0.463 Sum_probs=15.4
Q ss_pred HhhhhhhHHHHHHhhcCcee
Q psy17505 32 IAITNSRQNIRKLIKDGLII 51 (199)
Q Consensus 32 I~~A~sR~~IRkLIkdG~Ii 51 (199)
|+.+.....|++|+++|+|.
T Consensus 29 is~~tv~~~l~~L~~~g~I~ 48 (48)
T PF13412_consen 29 ISRSTVNRYLKKLEEKGLIE 48 (48)
T ss_dssp S-HHHHHHHHHHHHHTTSEE
T ss_pred CCHHHHHHHHHHHHHCcCcC
Confidence 45566778899999999984
No 42
>PF07742 BTG: BTG family; InterPro: IPR002087 Anti-proliferative proteins have been shown to include mammalian and avian protein BTG1 (which appears to be involved in negative regulation of cell proliferation) and rat/mouse NGF-inducible protein PC3/TIS21 (BTG2) [, , ]. These proteins have from 158 to 363 amino acid residues, that are highly similar and include 3 conserved cysteine residues. BTG2 seems to have a signal sequence; while the other proteins may lack such a domain. The sequence of the N-terminal half of these proteins is well conserved.; PDB: 3DJU_B 3E9V_A 2Z15_D 2D5R_B 3DJN_B.
Probab=20.31 E-value=31 Score=27.48 Aligned_cols=10 Identities=40% Similarity=1.272 Sum_probs=8.3
Q ss_pred ceecCccchh
Q psy17505 21 KVWLDPNEIN 30 (199)
Q Consensus 21 kVWlDPne~~ 30 (199)
-||+||.|+.
T Consensus 95 tlWvDPgeVs 104 (118)
T PF07742_consen 95 TLWVDPGEVS 104 (118)
T ss_dssp EEEEETTEEE
T ss_pred EEEECCCEEE
Confidence 6899999864
No 43
>PF00392 GntR: Bacterial regulatory proteins, gntR family; InterPro: IPR000524 Many bacterial transcription regulation proteins bind DNA through a helix-turn-helix (HTH) motif, which can be classified into subfamilies on the basis of sequence similarities. The HTH GntR family has many members distributed among diverse bacterial groups that regulate various biological processes. It was named GntR after the Bacillus subtilis repressor of the gluconate operon []. Family members include GntR, HutC, KorA, NtaR, FadR, ExuR, FarR, DgoR and PhnF. The crystal structure of the FadR protein has been determined []. In general, these proteins contain a DNA-binding HTH domain at the N terminus, and an effector-binding or oligomerisation domain at the C terminus (IPR011711 from INTERPRO). The DNA-binding domain is well conserved in structure for the whole of the GntR family, consisting of a 3-helical bundle core with a small beta-sheet (wing); the GntR winged helix structure is similar to that found in several other transcriptional regulator families. The regions outside the DNA-binding domain are more variable and are consequently used to define GntR subfamilies []. This entry represents the N-terminal DNA-binding domain of the GntR family.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1HW1_B 1H9T_A 1HW2_A 1H9G_A 1E2X_A 3IHU_A 3C7J_A 2RA5_A 3BY6_C 3IC7_A ....
Probab=20.04 E-value=93 Score=21.08 Aligned_cols=27 Identities=30% Similarity=0.502 Sum_probs=21.1
Q ss_pred hHhhhhhhHHHHHHhhcCceeecCCCc
Q psy17505 31 EIAITNSRQNIRKLIKDGLIIKKPVAV 57 (199)
Q Consensus 31 eI~~A~sR~~IRkLIkdG~Ii~kp~~~ 57 (199)
.++-..-|+-+..|..+|+|...|-.|
T Consensus 35 ~vsr~tvr~al~~L~~~g~i~~~~~~G 61 (64)
T PF00392_consen 35 GVSRTTVREALRRLEAEGLIERRPGRG 61 (64)
T ss_dssp TS-HHHHHHHHHHHHHTTSEEEETTTE
T ss_pred ccCCcHHHHHHHHHHHCCcEEEECCce
Confidence 345566678888999999999998766
Done!