Query 028783
Match_columns 204
No_of_seqs 167 out of 287
Neff 3.6
Searched_HMMs 46136
Date Fri Mar 29 02:28:07 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/028783.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/028783hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1696 60s ribosomal protein 100.0 1.6E-79 3.5E-84 515.1 12.7 179 6-184 2-184 (193)
2 PTZ00097 60S ribosomal protein 100.0 5.4E-74 1.2E-78 480.6 14.2 168 8-175 2-173 (175)
3 cd01417 Ribosomal_L19e_E Ribos 100.0 5E-73 1.1E-77 470.9 13.0 159 9-167 2-164 (164)
4 PTZ00436 60S ribosomal protein 100.0 6.1E-70 1.3E-74 488.7 15.0 164 7-170 3-170 (357)
5 PF01280 Ribosomal_L19e: Ribos 100.0 9.7E-68 2.1E-72 433.5 9.7 141 9-149 4-148 (148)
6 cd00481 Ribosomal_L19e Ribosom 100.0 5E-67 1.1E-71 428.0 10.5 140 9-148 2-145 (145)
7 cd01418 Ribosomal_L19e_A Ribos 100.0 1.1E-64 2.4E-69 414.2 11.0 136 9-144 2-141 (145)
8 PRK08570 rpl19e 50S ribosomal 100.0 1.2E-64 2.7E-69 415.9 10.3 140 7-146 3-146 (150)
9 COG2147 RPL19A Ribosomal prote 100.0 5.5E-59 1.2E-63 381.6 10.0 141 8-148 4-148 (150)
10 PRK00247 putative inner membra 65.1 87 0.0019 30.4 10.8 69 92-167 291-363 (429)
11 TIGR01764 excise DNA binding d 59.9 2.9 6.2E-05 26.1 -0.1 29 23-52 1-29 (49)
12 PF12728 HTH_17: Helix-turn-he 59.1 3.3 7.1E-05 27.1 0.1 28 23-51 1-28 (51)
13 PF13453 zf-TFIIB: Transcripti 55.9 2.3 4.9E-05 27.6 -1.0 15 19-33 25-39 (41)
14 PF01479 S4: S4 domain; Inter 38.7 25 0.00054 22.6 1.9 25 31-55 9-33 (48)
15 PF12802 MarR_2: MarR family; 37.1 25 0.00054 23.2 1.7 26 35-60 36-61 (62)
16 smart00345 HTH_GNTR helix_turn 35.4 25 0.00055 22.4 1.5 25 32-56 32-56 (60)
17 PF11823 DUF3343: Protein of u 33.2 10 0.00022 27.0 -0.7 31 9-39 32-62 (73)
18 PHA00616 hypothetical protein 29.2 30 0.00064 23.7 1.0 17 129-145 8-24 (44)
19 PF11868 DUF3388: Protein of u 28.8 24 0.00051 31.0 0.6 29 14-48 72-102 (192)
20 PF09851 SHOCT: Short C-termin 26.7 79 0.0017 19.5 2.6 20 104-123 6-25 (31)
21 TIGR02988 YaaA_near_RecF S4 do 25.4 49 0.0011 22.5 1.6 21 35-55 21-41 (59)
22 smart00420 HTH_DEOR helix_turn 25.4 54 0.0012 20.3 1.7 26 31-56 25-50 (53)
23 PF03428 RP-C: Replication pro 24.6 2.6E+02 0.0056 23.9 6.1 57 89-145 70-139 (177)
24 PF00096 zf-C2H2: Zinc finger, 21.9 57 0.0012 17.8 1.1 15 129-143 7-21 (23)
25 PF13412 HTH_24: Winged helix- 21.8 47 0.001 21.3 0.9 20 32-51 29-48 (48)
26 PF06353 DUF1062: Protein of u 21.1 74 0.0016 26.4 2.1 23 34-56 113-135 (142)
27 PF01047 MarR: MarR family; I 20.7 48 0.001 21.8 0.8 26 33-58 30-55 (59)
No 1
>KOG1696 consensus 60s ribosomal protein L19 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.6e-79 Score=515.13 Aligned_cols=179 Identities=64% Similarity=0.954 Sum_probs=172.0
Q ss_pred CCCCCCccccccc--ccc--eeccCCCcccccCcchhHHHHHhhhcCceeecCCCCCChhHHHHHHHHHhcCCCCCCCCc
Q 028783 6 SPWPTPHRIFSSV--CES--HITSKSEIPSLLLPSAGQNIRKLVKDGFIIRKPTKIHSRSRARRMKEAKRKGRHSGYGKR 81 (204)
Q Consensus 6 ~~~~~q~rla~~V--~gk--vWlDPne~~eIa~AnSR~~IRkLIKdGlIi~Kp~~~hSR~R~R~~~~ak~KGRh~G~GkR 81 (204)
|--++|+|||||| ||+ |||||||++||++|||||+|++||+||+||.+|+++|||+||+++.+++++|||+|||+|
T Consensus 2 s~lrlqKRLAssVl~cGKkKvWlDpNE~~eI~~ansRq~irkLikdg~iI~Kp~~vhsr~r~rk~~~akrkgrH~G~GKR 81 (193)
T KOG1696|consen 2 SNLRLQKRLAASVLKCGKKKVWLDPNEISEISGANSRQNIRKLIKDGLIIRKPVTVHSRSRCRKRLEAKRKGRHMGYGKR 81 (193)
T ss_pred chHHHHHHHHHHHHHhcccceeeCccHHHHhcccchHHHHHHHHhCCeEeecchhhhHHHHHHHHHHHHHhccccCcccc
Confidence 3457899999999 994 999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccccccCCchhHHHHHHHHHHHHHHHHHHhcCCCChHhhHHHHHhhcCCccccHHHHHHHHHHhhhHHHHhhhhhHHHHH
Q 028783 82 KGTREARLPTKILWMRRMRVLRRLLRKYRESKKIDKHMYHDMYMKVKGNVFKNKRVLMESIHKSKAEKAREKTLSDQFEA 161 (204)
Q Consensus 82 KGtk~AR~p~K~~WmrRiR~lRRlLr~yRe~kkID~h~Yr~LY~kaKGn~FKnk~~L~e~Ihk~Kaek~r~k~l~dQaeA 161 (204)
+||+|||||+|++||+||||||++|++|||+|+||+||||+||+++|||+|||+++|||||||+|||++++|+|+|||||
T Consensus 82 kGTanArmP~k~~Wmrr~RvlRrlL~kyR~skKIdkh~YH~lY~k~KGnvFKnK~~LmE~I~K~KAe~~r~K~LadQaeA 161 (193)
T KOG1696|consen 82 KGTANARMPSKVLWMRRMRVLRRLLKKYRDSKKIDKHMYHDLYLKVKGNVFKNKRVLMEHIHKSKAEKAREKLLADQAEA 161 (193)
T ss_pred cccccccCchhHHHHHHHHHHHHHHHHhhhcccchHHHHHHHHHHHhcchhhhHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHhhhHHHHHHHHHHHHHHHhcC
Q 028783 162 KRAKNKASRERKLARREERLAQG 184 (204)
Q Consensus 162 rr~k~k~~r~r~~~r~~~~~~~~ 184 (204)
+|.++++++++++++.+++.+..
T Consensus 162 rr~k~k~ar~rreer~~~k~~~~ 184 (193)
T KOG1696|consen 162 RRLKNKAARKRREERLAAKPQEL 184 (193)
T ss_pred HHhhhHHHhhhHHHHHhhchhhh
Confidence 99999999999888777665443
No 2
>PTZ00097 60S ribosomal protein L19; Provisional
Probab=100.00 E-value=5.4e-74 Score=480.58 Aligned_cols=168 Identities=61% Similarity=0.971 Sum_probs=164.3
Q ss_pred CCCCccccccc--cc--ceeccCCCcccccCcchhHHHHHhhhcCceeecCCCCCChhHHHHHHHHHhcCCCCCCCCccc
Q 028783 8 WPTPHRIFSSV--CE--SHITSKSEIPSLLLPSAGQNIRKLVKDGFIIRKPTKIHSRSRARRMKEAKRKGRHSGYGKRKG 83 (204)
Q Consensus 8 ~~~q~rla~~V--~g--kvWlDPne~~eIa~AnSR~~IRkLIKdGlIi~Kp~~~hSR~R~R~~~~ak~KGRh~G~GkRKG 83 (204)
..+|+||||+| || +||||||+++||++||||+|||+||+||+|+++|++||||+|++++++++++|||+|||+|+|
T Consensus 2 l~~QKRLAA~vL~cG~~rVWiDP~~~~eI~~A~tR~dIR~LIkdG~I~~kp~kg~SR~R~r~~~~~k~kGR~~G~G~RKG 81 (175)
T PTZ00097 2 LRLQKRLAASVLKCGKNRVWLDPNEASEISLANSRFSIRKLIKDGLIIRKPVAVHSRARARRFHEAKRKGRHTGIGKRRG 81 (175)
T ss_pred chHHHHHHHHHHCCCCCceeeCHHHHHHHHHhhhHHHHHHHHHCCCeeecCCCCCChHHHHHHHHHHHhCCCCCCCCCcC
Confidence 35899999999 88 499999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccccCCchhHHHHHHHHHHHHHHHHHHhcCCCChHhhHHHHHhhcCCccccHHHHHHHHHHhhhHHHHhhhhhHHHHHHH
Q 028783 84 TREARLPTKILWMRRMRVLRRLLRKYRESKKIDKHMYHDMYMKVKGNVFKNKRVLMESIHKSKAEKAREKTLSDQFEAKR 163 (204)
Q Consensus 84 tk~AR~p~K~~WmrRiR~lRRlLr~yRe~kkID~h~Yr~LY~kaKGn~FKnk~~L~e~Ihk~Kaek~r~k~l~dQaeArr 163 (204)
|+|||||+|+.||++||+||++|++|||+|+||+|+||.||++||||+|+|+++|++|||+.|+|++++++|+||+||++
T Consensus 82 tk~AR~p~K~~W~~riR~lRr~Lk~~R~~~kIdk~~Yr~lY~kaKGn~Fknk~~L~~~I~~~kae~~r~k~l~~q~~a~r 161 (175)
T PTZ00097 82 TREARMPTKVLWMRRQRVLRRLLRKYRAAKKIDRHMYHEFYLKSKGNQFKNKRVLIEAIHKTKNEKVKEKKIQDQLEARR 161 (175)
T ss_pred cccccCcHHHHHHHHHHHHHHHHHHHHHcCCCCHHHHHHHHHHhcCCCcCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhhHHHHHHHHH
Q 028783 164 AKNKASRERKLA 175 (204)
Q Consensus 164 ~k~k~~r~r~~~ 175 (204)
.+++++++++.+
T Consensus 162 ~k~~~~~~~r~~ 173 (175)
T PTZ00097 162 AKAKALRNKRKA 173 (175)
T ss_pred HHHHHHHHHHhh
Confidence 999999998664
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=5e-73 Score=470.91 Aligned_cols=159 Identities=67% Similarity=1.036 Sum_probs=156.1
Q ss_pred CCCccccccc--cc--ceeccCCCcccccCcchhHHHHHhhhcCceeecCCCCCChhHHHHHHHHHhcCCCCCCCCcccc
Q 028783 9 PTPHRIFSSV--CE--SHITSKSEIPSLLLPSAGQNIRKLVKDGFIIRKPTKIHSRSRARRMKEAKRKGRHSGYGKRKGT 84 (204)
Q Consensus 9 ~~q~rla~~V--~g--kvWlDPne~~eIa~AnSR~~IRkLIKdGlIi~Kp~~~hSR~R~R~~~~ak~KGRh~G~GkRKGt 84 (204)
.+|+||||+| || +||||||+++||++||||+|||+||+||+|+++|++||||+|++++++++++|||+|+|+|+||
T Consensus 2 ~~QKRLAA~vL~cG~~rVW~DP~~~~eI~~A~tR~dIR~LIkdG~I~~kp~kg~SR~R~r~~~~~k~kGR~~G~G~RkGt 81 (164)
T cd01417 2 RLQKRLAASVLKCGKRKVWLDPNEISEISNANSRQSIRKLIKDGLIIKKPVKVHSRSRARKRHEAKRKGRHMGYGKRKGT 81 (164)
T ss_pred cHHHHHHHHHHCCCCCceeeCHHHHHHHHHhhhHHHHHHHHHCCCeeecCCCcCCHHHHHHHHHHHHhCCCCCCCCCcCc
Confidence 5799999999 88 4999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cccCCchhHHHHHHHHHHHHHHHHHHhcCCCChHhhHHHHHhhcCCccccHHHHHHHHHHhhhHHHHhhhhhHHHHHHHh
Q 028783 85 REARLPTKILWMRRMRVLRRLLRKYRESKKIDKHMYHDMYMKVKGNVFKNKRVLMESIHKSKAEKAREKTLSDQFEAKRA 164 (204)
Q Consensus 85 k~AR~p~K~~WmrRiR~lRRlLr~yRe~kkID~h~Yr~LY~kaKGn~FKnk~~L~e~Ihk~Kaek~r~k~l~dQaeArr~ 164 (204)
+|||||+|+.||++||+||++|++|||+|+||+|+||.||++||||+|+|+++|++|||+.|+|+++++.|+||+||+++
T Consensus 82 ~~AR~p~K~~W~~riR~lRr~Lk~~R~~~kIdk~~Yr~lY~kaKGn~Fknk~~L~~~I~~~kae~~r~k~l~~q~~a~r~ 161 (164)
T cd01417 82 ANARMPSKVLWMRRQRVLRRLLKKYRESKKIDKHLYHELYLKAKGNVFKNKRVLMEHIHKAKAEKAREKELADQAEARRA 161 (164)
T ss_pred ccccCcHHHHHHHHHHHHHHHHHHHHHcCCCCHHHHHHHHHHhcCCCcCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999998
Q ss_pred hhH
Q 028783 165 KNK 167 (204)
Q Consensus 165 k~k 167 (204)
+++
T Consensus 162 ~~~ 164 (164)
T cd01417 162 KNK 164 (164)
T ss_pred ccC
Confidence 864
No 4
>PTZ00436 60S ribosomal protein L19-like protein; Provisional
Probab=100.00 E-value=6.1e-70 Score=488.71 Aligned_cols=164 Identities=54% Similarity=0.903 Sum_probs=159.7
Q ss_pred CCCCCccccccc--cc--ceeccCCCcccccCcchhHHHHHhhhcCceeecCCCCCChhHHHHHHHHHhcCCCCCCCCcc
Q 028783 7 PWPTPHRIFSSV--CE--SHITSKSEIPSLLLPSAGQNIRKLVKDGFIIRKPTKIHSRSRARRMKEAKRKGRHSGYGKRK 82 (204)
Q Consensus 7 ~~~~q~rla~~V--~g--kvWlDPne~~eIa~AnSR~~IRkLIKdGlIi~Kp~~~hSR~R~R~~~~ak~KGRh~G~GkRK 82 (204)
-..+|+|||++| || +|||||||++||++||||+|||+||+||+|+++|++||||+|+|++++++++|||+|+|||+
T Consensus 3 dLklQKRLAAsVL~cGk~RVWiDPnel~eIa~AiTReDIRkLIkdGlIikKp~KGhSRgRaRkr~eaKrKGRhrG~GsRK 82 (357)
T PTZ00436 3 SLKLQARLAADILRCGRHRVWLDPNEASEISNANSRKSVRKLIKDGLIIRKPVKVHSRSRWRHMKEAKSMGRHEGAGRRE 82 (357)
T ss_pred chHHHHHHHHHHhCCCCCceeeCHHHHHHHHHhhhHHHHHHHHHCCCeeecCcccCChHHHHHHHHHHHhCcCCCCCCCc
Confidence 457899999999 88 49999999999999999999999999999999999999999999999999999999999999
Q ss_pred cccccCCchhHHHHHHHHHHHHHHHHHHhcCCCChHhhHHHHHhhcCCccccHHHHHHHHHHhhhHHHHhhhhhHHHHHH
Q 028783 83 GTREARLPTKILWMRRMRVLRRLLRKYRESKKIDKHMYHDMYMKVKGNVFKNKRVLMESIHKSKAEKAREKTLSDQFEAK 162 (204)
Q Consensus 83 Gtk~AR~p~K~~WmrRiR~lRRlLr~yRe~kkID~h~Yr~LY~kaKGn~FKnk~~L~e~Ihk~Kaek~r~k~l~dQaeAr 162 (204)
||+|||||+|++||+|||+|||+|++|||+|+||+|+||+||+++|||+|+|++||++|||+.|+|+.++++|.||+||+
T Consensus 83 GTk~AR~P~K~~WIrRIRaLRRlLKklRd~gKIDkh~YR~LYrKAKGn~FKNK~~L~e~I~k~KaE~~R~K~L~dQ~eAr 162 (357)
T PTZ00436 83 GTREARMPSKELWMRRLRILRRLLRKYREEKKIDRHIYRELYVKAKGNVFRNKRNLMEHIHKVKNEKKKERQLAEQLAAK 162 (357)
T ss_pred CcccccCcHHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHhcCCccCcHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HhhhHHHH
Q 028783 163 RAKNKASR 170 (204)
Q Consensus 163 r~k~k~~r 170 (204)
|.++++.|
T Consensus 163 R~k~~~~r 170 (357)
T PTZ00436 163 RLKDEQHR 170 (357)
T ss_pred HHHhhhhh
Confidence 99987654
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=9.7e-68 Score=433.46 Aligned_cols=141 Identities=58% Similarity=0.915 Sum_probs=123.6
Q ss_pred CCCccccccc--cc--ceeccCCCcccccCcchhHHHHHhhhcCceeecCCCCCChhHHHHHHHHHhcCCCCCCCCcccc
Q 028783 9 PTPHRIFSSV--CE--SHITSKSEIPSLLLPSAGQNIRKLVKDGFIIRKPTKIHSRSRARRMKEAKRKGRHSGYGKRKGT 84 (204)
Q Consensus 9 ~~q~rla~~V--~g--kvWlDPne~~eIa~AnSR~~IRkLIKdGlIi~Kp~~~hSR~R~R~~~~ak~KGRh~G~GkRKGt 84 (204)
.+|+||||+| || +|||||||++||++||||+|||+||+||+|+++|++|||||||+++++++++|||+|+|+|+||
T Consensus 4 ~~QKRLAa~vL~~G~~rVw~DP~~~~eI~~A~tR~~IR~LIk~G~I~~k~~k~~Sr~R~r~~~~~r~kGr~~G~G~RkGt 83 (148)
T PF01280_consen 4 KLQKRLAASVLGCGKNRVWIDPNELEEIANAITREDIRKLIKDGLIIKKPVKGHSRGRARKRKEARRKGRHRGPGKRKGT 83 (148)
T ss_dssp HHHHHHHHHHHTS-GGGEEE-STTHHHHHH--SHHHHHHHHHTTSEEE---S--STHHHHHHHHHHHCTTS-SSTTS-S-
T ss_pred HHHHHHHHHHHCCCCCcEEeCHHHHHHHHhhhhHHHHHHHHHCCCeEeCCCCCCchHHHHHHHHHHhhcccccccccccc
Confidence 5799999999 88 4999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cccCCchhHHHHHHHHHHHHHHHHHHhcCCCChHhhHHHHHhhcCCccccHHHHHHHHHHhhhHH
Q 028783 85 REARLPTKILWMRRMRVLRRLLRKYRESKKIDKHMYHDMYMKVKGNVFKNKRVLMESIHKSKAEK 149 (204)
Q Consensus 85 k~AR~p~K~~WmrRiR~lRRlLr~yRe~kkID~h~Yr~LY~kaKGn~FKnk~~L~e~Ihk~Kaek 149 (204)
+|||+|+|+.||++||+||++|++|||+|+||+|+||+||++||||+|+|+++|+||||+.|+|+
T Consensus 84 ~~AR~~~K~~W~~riR~lRr~Lk~~r~~~kID~~~Yr~lY~kaKGn~Fkn~~~L~~~i~~~k~e~ 148 (148)
T PF01280_consen 84 KNARMPEKELWMRRIRALRRLLKRLRDSGKIDRHMYRSLYRKAKGNVFKNKRHLMEHIHKLKAEK 148 (148)
T ss_dssp HHHHS-HHHHHHHHHHHHHHHHHHHHHTTSS-HHHHHHHHHHHHTTS-SSHHHHHHHHHHHHHCH
T ss_pred ccccccHHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHhcCCcccCHHHHHHHHHHhccCC
Confidence 99999999999999999999999999999999999999999999999999999999999999985
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=5e-67 Score=428.04 Aligned_cols=140 Identities=54% Similarity=0.893 Sum_probs=137.0
Q ss_pred CCCccccccc--cc--ceeccCCCcccccCcchhHHHHHhhhcCceeecCCCCCChhHHHHHHHHHhcCCCCCCCCcccc
Q 028783 9 PTPHRIFSSV--CE--SHITSKSEIPSLLLPSAGQNIRKLVKDGFIIRKPTKIHSRSRARRMKEAKRKGRHSGYGKRKGT 84 (204)
Q Consensus 9 ~~q~rla~~V--~g--kvWlDPne~~eIa~AnSR~~IRkLIKdGlIi~Kp~~~hSR~R~R~~~~ak~KGRh~G~GkRKGt 84 (204)
.+|+||||+| || .||||||+++||++||||+|||+||+||+|+++|++||||+|++++++++++|||+|+|+|+||
T Consensus 2 ~~QkRLAA~vL~~G~~rVW~DP~~~~eI~~A~tR~dIR~LIkdG~I~~kp~kg~Sr~R~r~~~~~r~kGr~~G~G~RkGt 81 (145)
T cd00481 2 RLQKRLAADILKCGKNRVWIDPNELEEIANANTREDIRKLIKDGLIIKKPKKGHSRGRARKRHEARRKGRHRGPGSRKGT 81 (145)
T ss_pred cHHHHHHHHHHCCCCCceeeCHHHHHHHHHhhhHHHHHHHHHCCCeeecCCCCCChHHHHHHHHHHHhCcCCCCCCccCc
Confidence 5799999999 88 4999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cccCCchhHHHHHHHHHHHHHHHHHHhcCCCChHhhHHHHHhhcCCccccHHHHHHHHHHhhhH
Q 028783 85 REARLPTKILWMRRMRVLRRLLRKYRESKKIDKHMYHDMYMKVKGNVFKNKRVLMESIHKSKAE 148 (204)
Q Consensus 85 k~AR~p~K~~WmrRiR~lRRlLr~yRe~kkID~h~Yr~LY~kaKGn~FKnk~~L~e~Ihk~Kae 148 (204)
++||||+|+.||++||+||++|++|||+|+||+|+||.||++||||+|+|+++|++|||+.++|
T Consensus 82 ~~AR~p~K~~W~~riR~lRr~Lk~~R~~~kIdk~~Yr~lY~kaKG~~Fknk~~L~~~i~~~~~~ 145 (145)
T cd00481 82 KGARMPSKELWIRRIRALRRLLKKLRDSGKIDKHTYRELYLKAKGNVFKNKRHLKEYIHKAKAE 145 (145)
T ss_pred cccCCcHHHHHHHHHHHHHHHHHHHHHcCCCCHHHHHHHHHHhcCCCcCCHHHHHHHHHHhccC
Confidence 9999999999999999999999999999999999999999999999999999999999998764
No 7
>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=1.1e-64 Score=414.22 Aligned_cols=136 Identities=32% Similarity=0.569 Sum_probs=133.4
Q ss_pred CCCccccccc--cc--ceeccCCCcccccCcchhHHHHHhhhcCceeecCCCCCChhHHHHHHHHHhcCCCCCCCCcccc
Q 028783 9 PTPHRIFSSV--CE--SHITSKSEIPSLLLPSAGQNIRKLVKDGFIIRKPTKIHSRSRARRMKEAKRKGRHSGYGKRKGT 84 (204)
Q Consensus 9 ~~q~rla~~V--~g--kvWlDPne~~eIa~AnSR~~IRkLIKdGlIi~Kp~~~hSR~R~R~~~~ak~KGRh~G~GkRKGt 84 (204)
.+|+||||+| || .||||||+++||++||||+|||+||+||+|+++|++||||+|++++++++++|||+|+|+|+||
T Consensus 2 ~~QkRLAA~iL~~G~~rVw~DP~~~~eI~~A~tR~dIR~LI~~G~I~~kp~kg~Sr~R~r~~~~~r~kGr~~G~G~RkGt 81 (145)
T cd01418 2 SSQRRLAADILGVGINRVWIDPERLEEVAEAITRDDIRALIKEGVIKAKPKKGISRGRLKERHEKRKKGRRRGPGSRKGK 81 (145)
T ss_pred cHHHHHHHHHHCCCCCeeeeChHHHHHHHHhhhHHHHHHHHHCCCeeecCCCCCCHHHHHHHHHHHHhCcCCCCCCCCCc
Confidence 5799999999 88 4999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cccCCchhHHHHHHHHHHHHHHHHHHhcCCCChHhhHHHHHhhcCCccccHHHHHHHHHH
Q 028783 85 REARLPTKILWMRRMRVLRRLLRKYRESKKIDKHMYHDMYMKVKGNVFKNKRVLMESIHK 144 (204)
Q Consensus 85 k~AR~p~K~~WmrRiR~lRRlLr~yRe~kkID~h~Yr~LY~kaKGn~FKnk~~L~e~Ihk 144 (204)
+|||||+|+.||++||+||++|++|||+|+||+|+||.||++||||+|+|+++|++||..
T Consensus 82 ~~AR~p~K~~W~~riR~lRr~Lk~~R~~~kId~~~Yr~lY~kaKGn~Fkn~~~L~~~I~~ 141 (145)
T cd01418 82 KGARTPKKERWIKTIRALRRYLKELRDKGKIDKKTYRKLYRKAKGGSFRSLSHLKSYLKQ 141 (145)
T ss_pred cccCCCHHHHHHHHHHHHHHHHHHHHHcCCCCHHHHHHHHHHhcCCCcCCHHHHHHHHHH
Confidence 999999999999999999999999999999999999999999999999999999999975
No 8
>PRK08570 rpl19e 50S ribosomal protein L19e; Reviewed
Probab=100.00 E-value=1.2e-64 Score=415.85 Aligned_cols=140 Identities=34% Similarity=0.573 Sum_probs=135.9
Q ss_pred CCCCCccccccc--cc--ceeccCCCcccccCcchhHHHHHhhhcCceeecCCCCCChhHHHHHHHHHhcCCCCCCCCcc
Q 028783 7 PWPTPHRIFSSV--CE--SHITSKSEIPSLLLPSAGQNIRKLVKDGFIIRKPTKIHSRSRARRMKEAKRKGRHSGYGKRK 82 (204)
Q Consensus 7 ~~~~q~rla~~V--~g--kvWlDPne~~eIa~AnSR~~IRkLIKdGlIi~Kp~~~hSR~R~R~~~~ak~KGRh~G~GkRK 82 (204)
...+|+||||+| || .||||||+++||++||||+|||+||+||+|+++|++||||+|++++++++++|||+|+|+|+
T Consensus 3 ~l~~qkRLAA~iL~~G~~rVw~DP~~~~eI~~A~tR~dIR~LI~~G~I~~kp~kg~Sr~R~r~~~~~r~kGr~~G~G~Rk 82 (150)
T PRK08570 3 DLSAQKRLAADILGVGVSRVWIDPEALEDVAEAITREDIRELIKEGVIKAKPKKGISRGRARERHEKRKKGRRRGPGSRK 82 (150)
T ss_pred chHHHHHHHHHHHCCCccceeeCHHHHHHHHHHhhHHHHHHHHHCCCeeecCccCCChHHHHHHHHHHHhCCCCCCCCCC
Confidence 346899999999 88 49999999999999999999999999999999999999999999999999999999999999
Q ss_pred cccccCCchhHHHHHHHHHHHHHHHHHHhcCCCChHhhHHHHHhhcCCccccHHHHHHHHHHhh
Q 028783 83 GTREARLPTKILWMRRMRVLRRLLRKYRESKKIDKHMYHDMYMKVKGNVFKNKRVLMESIHKSK 146 (204)
Q Consensus 83 Gtk~AR~p~K~~WmrRiR~lRRlLr~yRe~kkID~h~Yr~LY~kaKGn~FKnk~~L~e~Ihk~K 146 (204)
||+|||+|+|+.||++||+||++|++|||+|+||+|+||.||++||||+|+|+++|++||+...
T Consensus 83 Gt~~AR~p~K~~W~~riR~lRr~Lk~lR~~~kId~~~Yr~lY~kaKGn~Fkn~~~L~~~i~~~~ 146 (150)
T PRK08570 83 GKKGARTPKKERWINRIRALRRYLRELRDEGKIDRKTYRKLYRKAKGGEFRSVSHLKTYIEEHG 146 (150)
T ss_pred CcccCCCCHHHHHHHHHHHHHHHHHHHHHcCCCCHHHHHHHHHHhcCCccCCHHHHHHHHHHhc
Confidence 9999999999999999999999999999999999999999999999999999999999999753
No 9
>COG2147 RPL19A Ribosomal protein L19E [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=5.5e-59 Score=381.57 Aligned_cols=141 Identities=41% Similarity=0.636 Sum_probs=136.9
Q ss_pred CCCCccccccc--cc--ceeccCCCcccccCcchhHHHHHhhhcCceeecCCCCCChhHHHHHHHHHhcCCCCCCCCccc
Q 028783 8 WPTPHRIFSSV--CE--SHITSKSEIPSLLLPSAGQNIRKLVKDGFIIRKPTKIHSRSRARRMKEAKRKGRHSGYGKRKG 83 (204)
Q Consensus 8 ~~~q~rla~~V--~g--kvWlDPne~~eIa~AnSR~~IRkLIKdGlIi~Kp~~~hSR~R~R~~~~ak~KGRh~G~GkRKG 83 (204)
..+|+||||+| || .||||||+++||++|+||+|||.||+||+|+.+|++|+|++|+++++++++||||+|||||+|
T Consensus 4 l~~qkRLAA~il~vG~~Rvwidp~~~eei~~A~TR~dIr~LIk~g~I~~k~~kg~SrgR~rkr~~qkkkgr~rG~GsRKG 83 (150)
T COG2147 4 LRTQKRLAADILGVGENRVWIDPNEIEEIASAITREDIRALIKDGVIKAKPKKGISRGRARKRHAQKKKGRRRGPGSRKG 83 (150)
T ss_pred HHHHHHHHHHHHccCcceeeeChHHHHHHHHhhhHHHHHHHHHCCCeeeccccccchHHHHHHHHHHhcccCCCCCcccc
Confidence 35899999999 88 399999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccccCCchhHHHHHHHHHHHHHHHHHHhcCCCChHhhHHHHHhhcCCccccHHHHHHHHHHhhhH
Q 028783 84 TREARLPTKILWMRRMRVLRRLLRKYRESKKIDKHMYHDMYMKVKGNVFKNKRVLMESIHKSKAE 148 (204)
Q Consensus 84 tk~AR~p~K~~WmrRiR~lRRlLr~yRe~kkID~h~Yr~LY~kaKGn~FKnk~~L~e~Ihk~Kae 148 (204)
|++||||+|+.||.+||+||++|++||++|+||+|+||.||+++|||.|+++++|.+||...+.+
T Consensus 84 ~k~AR~p~K~~Wi~~IRalR~~Lr~lrd~gkIdk~~YR~lY~~aKGg~fk~~~~L~~~i~~~~~~ 148 (150)
T COG2147 84 TKGARMPSKERWIKRIRALRRELRKLRDDGKIDKHTYRKLYRMAKGGAFKSKSHLKSYIEEAKLL 148 (150)
T ss_pred ccccCCCHHHHHHHHHHHHHHHHHHHHHcCCcCHHHHHHHHHHHcCCccccHHHHHHHHHHhccc
Confidence 99999999999999999999999999999999999999999999999999999999999987654
No 10
>PRK00247 putative inner membrane protein translocase component YidC; Validated
Probab=65.06 E-value=87 Score=30.43 Aligned_cols=69 Identities=16% Similarity=0.254 Sum_probs=36.9
Q ss_pred hHHHHHHHHHHHHHHHHHHhcC---CCChHhhHHHHHhhcCCccccHHHHHHHHHHhhhHHHHhhhhhHH-HHHHHhhhH
Q 028783 92 KILWMRRMRVLRRLLRKYRESK---KIDKHMYHDMYMKVKGNVFKNKRVLMESIHKSKAEKAREKTLSDQ-FEAKRAKNK 167 (204)
Q Consensus 92 K~~WmrRiR~lRRlLr~yRe~k---kID~h~Yr~LY~kaKGn~FKnk~~L~e~Ihk~Kaek~r~k~l~dQ-aeArr~k~k 167 (204)
+..|..+.+..+..++..|... .|....+..|..- |...=.+.=...+++|+++|.++.+ -||.|.-++
T Consensus 291 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~-------~~~~~~~~~~~~~~~k~~~k~~~~~~~~~~~~~~~ 363 (429)
T PRK00247 291 RAQYREKQKEKKAFLWTLRRNRLRMIITPWRAPELHAE-------NAEIKKTRTAEKNEAKARKKEIAQKRRAAEREINR 363 (429)
T ss_pred HHHHHHHHHHHHHHHHHHHhccccccCCcccHHHHHHH-------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4456666666555555555544 7888877777432 1222222333346667777766544 344444444
No 11
>TIGR01764 excise DNA binding domain, excisionase family. An excisionase, or Xis protein, is a small protein that binds and promotes excisive recombination; it is not enzymatically active. This model represents a number of putative excisionases and related proteins from temperate phage, plasmids, and transposons, as well as DNA binding domains of other proteins, such as a DNA modification methylase. This model identifies mostly small proteins and N-terminal regions of large proteins, but some proteins appear to have two copies. This domain appears similar, in both sequence and predicted secondary structure (PSIPRED) to the MerR family of transcriptional regulators (pfam00376).
Probab=59.91 E-value=2.9 Score=26.06 Aligned_cols=29 Identities=14% Similarity=0.209 Sum_probs=23.2
Q ss_pred eccCCCcccccCcchhHHHHHhhhcCceee
Q 028783 23 ITSKSEIPSLLLPSAGQNIRKLVKDGFIIR 52 (204)
Q Consensus 23 WlDPne~~eIa~AnSR~~IRkLIKdGlIi~ 52 (204)
||++.|+.++-. +|+..|+.||++|.|-.
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 566677777765 79999999999998764
No 12
>PF12728 HTH_17: Helix-turn-helix domain
Probab=59.11 E-value=3.3 Score=27.10 Aligned_cols=28 Identities=18% Similarity=0.222 Sum_probs=23.8
Q ss_pred eccCCCcccccCcchhHHHHHhhhcCcee
Q 028783 23 ITSKSEIPSLLLPSAGQNIRKLVKDGFII 51 (204)
Q Consensus 23 WlDPne~~eIa~AnSR~~IRkLIKdGlIi 51 (204)
||++.|+-++-. +|+..|++|++.|.|.
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 678888888888 6999999999999663
No 13
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=55.91 E-value=2.3 Score=27.61 Aligned_cols=15 Identities=27% Similarity=0.432 Sum_probs=12.3
Q ss_pred ccceeccCCCccccc
Q 028783 19 CESHITSKSEIPSLL 33 (204)
Q Consensus 19 ~gkvWlDPne~~eIa 33 (204)
|+-+|||++|++.|.
T Consensus 25 C~G~W~d~~el~~~~ 39 (41)
T PF13453_consen 25 CGGIWFDAGELEKLL 39 (41)
T ss_pred CCeEEccHHHHHHHH
Confidence 556999999988764
No 14
>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=38.66 E-value=25 Score=22.60 Aligned_cols=25 Identities=28% Similarity=0.356 Sum_probs=20.1
Q ss_pred cccCcchhHHHHHhhhcCceeecCC
Q 028783 31 SLLLPSAGQNIRKLVKDGFIIRKPT 55 (204)
Q Consensus 31 eIa~AnSR~~IRkLIKdGlIi~Kp~ 55 (204)
+...+.||.++++||+.|.|...-.
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 4556789999999999999876543
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=37.10 E-value=25 Score=23.18 Aligned_cols=26 Identities=19% Similarity=0.376 Sum_probs=19.5
Q ss_pred cchhHHHHHhhhcCceeecCCCCCCh
Q 028783 35 PSAGQNIRKLVKDGFIIRKPTKIHSR 60 (204)
Q Consensus 35 AnSR~~IRkLIKdGlIi~Kp~~~hSR 60 (204)
...-..|.+|++.|+|.+.+.....|
T Consensus 36 ~~vs~~v~~L~~~Glv~r~~~~~D~R 61 (62)
T PF12802_consen 36 STVSRIVKRLEKKGLVERERDPGDRR 61 (62)
T ss_dssp HHHHHHHHHHHHTTSEEEEE-SSSTT
T ss_pred HHHHHHHHHHHHCCCEEEeCCCCCCC
Confidence 33446788999999999998877655
No 16
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=35.39 E-value=25 Score=22.43 Aligned_cols=25 Identities=16% Similarity=0.442 Sum_probs=18.5
Q ss_pred ccCcchhHHHHHhhhcCceeecCCC
Q 028783 32 LLLPSAGQNIRKLVKDGFIIRKPTK 56 (204)
Q Consensus 32 Ia~AnSR~~IRkLIKdGlIi~Kp~~ 56 (204)
|+.+.-++.+..|.++|+|...|-.
T Consensus 32 vs~~tv~~~l~~L~~~g~i~~~~~~ 56 (60)
T smart00345 32 VSRTTVREALSRLEAEGLVQRRPGS 56 (60)
T ss_pred CCHHHHHHHHHHHHHCCCEEEecCC
Confidence 4455667778889999999876643
No 17
>PF11823 DUF3343: Protein of unknown function (DUF3343); InterPro: IPR021778 This family of proteins are functionally uncharacterised. This protein is found in bacteria and archaea. Proteins in this family are typically between 78 to 102 amino acids in length.
Probab=33.21 E-value=10 Score=27.00 Aligned_cols=31 Identities=13% Similarity=0.101 Sum_probs=21.5
Q ss_pred CCCcccccccccceeccCCCcccccCcchhH
Q 028783 9 PTPHRIFSSVCESHITSKSEIPSLLLPSAGQ 39 (204)
Q Consensus 9 ~~q~rla~~V~gkvWlDPne~~eIa~AnSR~ 39 (204)
|++.-+.+|||-.+++++++.+.|.+.....
T Consensus 32 P~P~~i~~~CG~al~~~~~d~~~i~~~l~~~ 62 (73)
T PF11823_consen 32 PTPREISAGCGLALRFEPEDLEKIKEILEEN 62 (73)
T ss_pred CCChhccCCCCEEEEEChhhHHHHHHHHHHC
Confidence 6777776666558999998877766554433
No 18
>PHA00616 hypothetical protein
Probab=29.18 E-value=30 Score=23.74 Aligned_cols=17 Identities=24% Similarity=0.634 Sum_probs=14.8
Q ss_pred CCccccHHHHHHHHHHh
Q 028783 129 GNVFKNKRVLMESIHKS 145 (204)
Q Consensus 129 Gn~FKnk~~L~e~Ihk~ 145 (204)
|..|.+++.|..|+-+.
T Consensus 8 G~~F~~~s~l~~H~r~~ 24 (44)
T PHA00616 8 GGIFRKKKEVIEHLLSV 24 (44)
T ss_pred hHHHhhHHHHHHHHHHh
Confidence 78999999999999653
No 19
>PF11868 DUF3388: Protein of unknown function (DUF3388); InterPro: IPR024514 This domain is found in a family of bacterial proteins that are functionally uncharacterised. Proteins in this family are typically between 261 to 275 amino acids in length and have a N-terminal ACT domain.
Probab=28.84 E-value=24 Score=30.98 Aligned_cols=29 Identities=28% Similarity=0.381 Sum_probs=23.5
Q ss_pred ccccccc-ceeccCCCcccccCcchhHHHHH-hhhcC
Q 028783 14 IFSSVCE-SHITSKSEIPSLLLPSAGQNIRK-LVKDG 48 (204)
Q Consensus 14 la~~V~g-kvWlDPne~~eIa~AnSR~~IRk-LIKdG 48 (204)
+|+|||. |.|+ -|++..-||.||. |++|-
T Consensus 72 vAasVcAnKrW~------f~SSTlikQTvRs~L~~dE 102 (192)
T PF11868_consen 72 VAASVCANKRWL------FLSSTLIKQTVRSQLIEDE 102 (192)
T ss_pred HHHhhhcCceEE------EeeHHHHHHHHHHHhhhcc
Confidence 6899988 6998 6788888999997 66653
No 20
>PF09851 SHOCT: Short C-terminal domain; InterPro: IPR018649 This family of hypothetical prokaryotic proteins has no known function.
Probab=26.72 E-value=79 Score=19.54 Aligned_cols=20 Identities=15% Similarity=0.320 Sum_probs=16.9
Q ss_pred HHHHHHHhcCCCChHhhHHH
Q 028783 104 RLLRKYRESKKIDKHMYHDM 123 (204)
Q Consensus 104 RlLr~yRe~kkID~h~Yr~L 123 (204)
..|+.+.+.|.|+-..|...
T Consensus 6 ~~L~~l~~~G~IseeEy~~~ 25 (31)
T PF09851_consen 6 EKLKELYDKGEISEEEYEQK 25 (31)
T ss_pred HHHHHHHHcCCCCHHHHHHH
Confidence 45788899999999999764
No 21
>TIGR02988 YaaA_near_RecF S4 domain protein YaaA. This small protein has a single S4 domain (pfam01479), as do bacterial ribosomal protein S4, some pseudouridine synthases, tyrosyl-tRNA synthetases. The S4 domain may bind RNA. Members of this protein family are found almost exclusively in the Firmicutes, and almost invariably just a few nucleotides upstream of the gene for the DNA replication and repair protein RecF. The few members of this family that are not near recF are found instead near dnaA and/or dnaN, the usual neighbors of recF, near the origin of replication. The conserved location suggests a possible role in replication in the Firmicutes lineage.
Probab=25.39 E-value=49 Score=22.48 Aligned_cols=21 Identities=5% Similarity=0.180 Sum_probs=17.6
Q ss_pred cchhHHHHHhhhcCceeecCC
Q 028783 35 PSAGQNIRKLVKDGFIIRKPT 55 (204)
Q Consensus 35 AnSR~~IRkLIKdGlIi~Kp~ 55 (204)
+.||..|++||++|.|...-.
T Consensus 21 ~~SR~~~k~li~~G~V~VNg~ 41 (59)
T TIGR02988 21 IDSGGQAKWFLQENEVLVNGE 41 (59)
T ss_pred ccCHHHHHHHHHcCCEEECCE
Confidence 359999999999999987443
No 22
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=25.37 E-value=54 Score=20.29 Aligned_cols=26 Identities=15% Similarity=0.249 Sum_probs=19.8
Q ss_pred cccCcchhHHHHHhhhcCceeecCCC
Q 028783 31 SLLLPSAGQNIRKLVKDGFIIRKPTK 56 (204)
Q Consensus 31 eIa~AnSR~~IRkLIKdGlIi~Kp~~ 56 (204)
+++.+.-+..|..|.++|+|...+.-
T Consensus 25 ~~s~~tv~~~l~~L~~~g~i~~~~~~ 50 (53)
T smart00420 25 GVSEMTIRRDLNKLEEQGLLTRVHGG 50 (53)
T ss_pred CCCHHHHHHHHHHHHHCCCEEEeecC
Confidence 45666678888999999999876543
No 23
>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=24.62 E-value=2.6e+02 Score=23.88 Aligned_cols=57 Identities=21% Similarity=0.276 Sum_probs=40.7
Q ss_pred CchhHHHHHHH-----HHHHHHHHHHHhcCCCCh---HhhHHHHHhhcCCc----cc-cHHHHHHHHHHh
Q 028783 89 LPTKILWMRRM-----RVLRRLLRKYRESKKIDK---HMYHDMYMKVKGNV----FK-NKRVLMESIHKS 145 (204)
Q Consensus 89 ~p~K~~WmrRi-----R~lRRlLr~yRe~kkID~---h~Yr~LY~kaKGn~----FK-nk~~L~e~Ihk~ 145 (204)
.|+...-..++ +-|||.|..|-|.|.|-+ ..++.+..+-.+|. |= |.+-|..-....
T Consensus 70 fpSN~~La~r~~G~s~~tlrR~l~~LveaGLI~rrDS~NgkRy~~R~~~G~I~~A~GfdLsPL~~R~~El 139 (177)
T PF03428_consen 70 FPSNAQLAERLNGMSERTLRRHLARLVEAGLIVRRDSPNGKRYARRDRGGRIVEAFGFDLSPLIARAEEL 139 (177)
T ss_pred ecCHHHHHHHHcCCCHHHHHHHHHHHHHCCCeeeccCCCCCccCccCCCCCEEeEeCcCHHHHHHHHHHH
Confidence 34455555666 889999999999999954 56887777766554 33 677777766655
No 24
>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=21.87 E-value=57 Score=17.79 Aligned_cols=15 Identities=27% Similarity=0.470 Sum_probs=12.7
Q ss_pred CCccccHHHHHHHHH
Q 028783 129 GNVFKNKRVLMESIH 143 (204)
Q Consensus 129 Gn~FKnk~~L~e~Ih 143 (204)
|-.|.+...|..||.
T Consensus 7 ~~~f~~~~~l~~H~~ 21 (23)
T PF00096_consen 7 GKSFSSKSNLKRHMR 21 (23)
T ss_dssp TEEESSHHHHHHHHH
T ss_pred CCccCCHHHHHHHHh
Confidence 557999999999975
No 25
>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=21.81 E-value=47 Score=21.31 Aligned_cols=20 Identities=20% Similarity=0.391 Sum_probs=15.5
Q ss_pred ccCcchhHHHHHhhhcCcee
Q 028783 32 LLLPSAGQNIRKLVKDGFII 51 (204)
Q Consensus 32 Ia~AnSR~~IRkLIKdGlIi 51 (204)
|+.+.....|++|+++|+|.
T Consensus 29 is~~tv~~~l~~L~~~g~I~ 48 (48)
T PF13412_consen 29 ISRSTVNRYLKKLEEKGLIE 48 (48)
T ss_dssp S-HHHHHHHHHHHHHTTSEE
T ss_pred CCHHHHHHHHHHHHHCcCcC
Confidence 55566778899999999983
No 26
>PF06353 DUF1062: Protein of unknown function (DUF1062); InterPro: IPR009412 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=21.06 E-value=74 Score=26.41 Aligned_cols=23 Identities=26% Similarity=0.574 Sum_probs=20.6
Q ss_pred CcchhHHHHHhhhcCceeecCCC
Q 028783 34 LPSAGQNIRKLVKDGFIIRKPTK 56 (204)
Q Consensus 34 ~AnSR~~IRkLIKdGlIi~Kp~~ 56 (204)
.-.||.+|..|+++|.|...|.+
T Consensus 113 L~lSrs~l~~l~~~G~I~~~~~~ 135 (142)
T PF06353_consen 113 LGLSRSRLKRLIEQGLIRSDPDK 135 (142)
T ss_pred hCcCHHHHHHHHHCCCEEecCcc
Confidence 45799999999999999988876
No 27
>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=20.73 E-value=48 Score=21.77 Aligned_cols=26 Identities=23% Similarity=0.276 Sum_probs=19.1
Q ss_pred cCcchhHHHHHhhhcCceeecCCCCC
Q 028783 33 LLPSAGQNIRKLVKDGFIIRKPTKIH 58 (204)
Q Consensus 33 a~AnSR~~IRkLIKdGlIi~Kp~~~h 58 (204)
+.++.=.-|.+|++.|+|.+.+....
T Consensus 30 ~~~~~t~~i~~L~~~g~I~r~~~~~D 55 (59)
T PF01047_consen 30 SRSTVTRIIKRLEKKGLIERERDPDD 55 (59)
T ss_dssp -HHHHHHHHHHHHHTTSEEEEEETTE
T ss_pred ChhHHHHHHHHHHHCCCEEeccCCCC
Confidence 34455567899999999998876544
Done!