Query psy3939
Match_columns 123
No_of_seqs 161 out of 404
Neff 4.9
Searched_HMMs 46136
Date Fri Aug 16 21:12:10 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy3939.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/3939hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PTZ00074 60S ribosomal protein 100.0 2.7E-45 5.9E-50 272.8 6.5 98 4-101 19-116 (135)
2 KOG1790|consensus 100.0 5.8E-40 1.3E-44 239.3 2.7 91 5-95 20-110 (121)
3 COG2174 RPL34A Ribosomal prote 100.0 6.2E-39 1.3E-43 224.8 7.5 82 4-85 12-93 (93)
4 PLN03166 60S ribosomal protein 100.0 4.4E-38 9.6E-43 222.8 7.3 76 4-79 19-96 (96)
5 PF01199 Ribosomal_L34e: Ribos 100.0 4.6E-38 1E-42 221.9 4.9 75 5-79 20-94 (94)
6 PRK04059 rpl34e 50S ribosomal 100.0 5.6E-35 1.2E-39 204.2 7.3 74 4-77 12-85 (88)
7 PRK04059 rpl34e 50S ribosomal 99.5 2.3E-15 5E-20 105.4 0.6 49 61-123 32-80 (88)
8 PLN03166 60S ribosomal protein 99.4 1.4E-14 3E-19 102.9 0.4 48 62-123 40-89 (96)
9 PTZ00074 60S ribosomal protein 99.4 3.4E-14 7.3E-19 106.2 0.5 48 62-123 40-87 (135)
10 PF01199 Ribosomal_L34e: Ribos 99.4 1.2E-14 2.6E-19 102.8 -2.6 47 63-123 41-87 (94)
11 KOG1790|consensus 99.3 2.5E-13 5.4E-18 99.6 -0.2 46 64-123 42-87 (121)
12 COG2174 RPL34A Ribosomal prote 99.2 2.4E-12 5.2E-17 90.7 0.3 49 61-123 32-80 (93)
13 COG1571 Predicted DNA-binding 63.0 3.8 8.3E-05 36.1 1.2 60 24-105 348-407 (421)
14 PRK00415 rps27e 30S ribosomal 50.8 23 0.00049 23.2 3.1 33 3-36 7-40 (59)
15 COG1381 RecO Recombinational D 47.1 9.3 0.0002 30.6 0.9 30 25-70 153-182 (251)
16 PRK00085 recO DNA repair prote 46.8 9.2 0.0002 29.7 0.9 30 25-70 148-177 (247)
17 COG3813 Uncharacterized protei 41.7 18 0.00039 25.1 1.6 34 28-62 43-77 (84)
18 PRK00420 hypothetical protein; 39.4 16 0.00034 26.7 1.1 30 27-76 24-53 (112)
19 PRK00398 rpoP DNA-directed RNA 36.3 9.9 0.00021 22.7 -0.3 9 28-36 5-13 (46)
20 PLN00209 ribosomal protein S27 35.6 40 0.00086 23.7 2.6 32 4-36 33-65 (86)
21 PF14471 DUF4428: Domain of un 35.3 32 0.00069 21.5 1.9 29 28-72 1-29 (51)
22 PTZ00083 40S ribosomal protein 35.1 40 0.00087 23.6 2.5 32 4-36 32-64 (85)
23 PRK12495 hypothetical protein; 31.6 22 0.00049 29.0 0.9 14 24-37 40-53 (226)
24 PF06689 zf-C4_ClpX: ClpX C4-t 30.9 54 0.0012 19.4 2.3 31 27-71 2-32 (41)
25 PTZ00218 40S ribosomal protein 28.0 48 0.001 21.4 1.8 38 17-73 6-44 (54)
26 PF13248 zf-ribbon_3: zinc-rib 28.0 29 0.00062 18.5 0.7 11 26-36 16-26 (26)
27 KOG1842|consensus 27.5 20 0.00044 32.2 -0.0 36 23-71 177-212 (505)
28 COG1996 RPC10 DNA-directed RNA 26.5 22 0.00048 22.4 0.1 25 28-71 8-32 (49)
29 cd00065 FYVE FYVE domain; Zinc 26.3 39 0.00085 20.3 1.2 38 27-77 3-40 (57)
30 PF01667 Ribosomal_S27e: Ribos 26.2 51 0.0011 21.2 1.7 32 4-36 4-36 (55)
31 COG2906 Bfd Bacterioferritin-a 26.0 44 0.00095 22.2 1.4 19 63-83 35-53 (63)
32 PF01412 ArfGap: Putative GTPa 26.0 45 0.00098 23.5 1.6 39 22-79 9-47 (116)
33 COG5347 GTPase-activating prot 25.6 11 0.00023 32.0 -2.0 38 17-71 11-48 (319)
34 PF09237 GAGA: GAGA factor; I 24.9 14 0.00031 23.9 -1.0 34 5-38 3-36 (54)
35 smart00064 FYVE Protein presen 23.8 49 0.0011 20.7 1.3 39 26-77 10-48 (68)
36 PF10764 Gin: Inhibitor of sig 23.8 43 0.00092 20.6 1.0 27 28-73 1-28 (46)
37 PF13408 Zn_ribbon_recom: Reco 23.7 29 0.00064 20.7 0.2 13 26-38 5-17 (58)
38 KOG1819|consensus 23.6 19 0.00042 33.3 -0.9 35 24-71 899-933 (990)
39 PF13240 zinc_ribbon_2: zinc-r 20.5 59 0.0013 17.1 1.0 10 28-37 1-10 (23)
No 1
>PTZ00074 60S ribosomal protein L34; Provisional
Probab=100.00 E-value=2.7e-45 Score=272.77 Aligned_cols=98 Identities=39% Similarity=0.716 Sum_probs=93.3
Q ss_pred eeeeeeCCCCceEEEEeeeCCCCCCcCCCCCCCCCccccchhhHhhcccCccccccccCCccchhhHhhHHHHhhhhhcc
Q psy3939 4 YLPSVKTPGGRLVYHYLKKAGKVPRCGHCKIKLPGIEKARSIERSRMSRRRKMVKRSYGGVLCHKCVKEKFIYCFFYSHC 83 (123)
Q Consensus 4 ~~~~vkTPGgrlv~~y~kK~~~~pkC~~c~~~L~Gi~~~rp~~~~~l~k~~k~v~R~YGG~lC~~cvr~rI~raFL~ee~ 83 (123)
.++++|||||+|||||.+|+++.|+|||||.+|+||+++||.++++|++++|||||||||++||+||+|||++|||||||
T Consensus 19 k~r~vrTPGGrlV~~y~KK~~~~pkC~~cg~~L~GI~~~Rp~e~~rlsK~~KtvsRaYGG~lC~~CVr~rIirAFLiEEq 98 (135)
T PTZ00074 19 KVRLVKTPGGRLVVQKRKKKSSGPKCGDCGKVLAGIKALRPTEYKQLSRRERTVSRAYGGVLCHKCVRDRIVRAFLVEEQ 98 (135)
T ss_pred eeEEEECCCCceEEEEeccCCCCCCCCCCCCccCCccCCchHHHHHccccCCCccCCCccchhHHHHHHHHHHHHHHHHH
Confidence 36899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccccccchhhhhHHHHhc
Q psy3939 84 KIKLPGIEKARSIERSRM 101 (123)
Q Consensus 84 KivkkgVKakrp~ekkrl 101 (123)
|||+++++++...+++..
T Consensus 99 Kivkkv~k~~~~~~k~~~ 116 (135)
T PTZ00074 99 KIVKQVLKEKAKQKKQKK 116 (135)
T ss_pred HHHHHHHHHHHHHHHhhh
Confidence 999999999887666543
No 2
>KOG1790|consensus
Probab=100.00 E-value=5.8e-40 Score=239.28 Aligned_cols=91 Identities=45% Similarity=0.851 Sum_probs=87.8
Q ss_pred eeeeeCCCCceEEEEeeeCCCCCCcCCCCCCCCCccccchhhHhhcccCccccccccCCccchhhHhhHHHHhhhhhccc
Q psy3939 5 LPSVKTPGGRLVYHYLKKAGKVPRCGHCKIKLPGIEKARSIERSRMSRRRKMVKRSYGGVLCHKCVKEKFIYCFFYSHCK 84 (123)
Q Consensus 5 ~~~vkTPGgrlv~~y~kK~~~~pkC~~c~~~L~Gi~~~rp~~~~~l~k~~k~v~R~YGG~lC~~cvr~rI~raFL~ee~K 84 (123)
++++|||||+||++|.||.++.|+|+||+..|+||+++||.++.+||++.|+|||+|||++|++||+|||++||||||||
T Consensus 20 ~r~vrTPg~~lv~q~~kK~~~~pkc~~c~~~l~Gi~~~RPk~~~rlsk~~KtVsRayGG~~ca~~vrerI~rAFLi~EQk 99 (121)
T KOG1790|consen 20 TRLVRTPGGRLVYQYVKKKAKLPKCGDCGMRLQGIPALRPKELMRLSKSHKTVSRAYGGVLCAKCVRERIIRAFLIEEQK 99 (121)
T ss_pred cccccCCCceehhHhhHhhccCCCCCcCCcccCCCCCcCHHHHHHHhhhHHHhhhhccccchHHHHHHHHHHHHHhhHHH
Confidence 47899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cccccchhhhh
Q psy3939 85 IKLPGIEKARS 95 (123)
Q Consensus 85 ivkkgVKakrp 95 (123)
||.+.++++..
T Consensus 100 IV~k~~~~~~~ 110 (121)
T KOG1790|consen 100 IVKKVLKAQEA 110 (121)
T ss_pred HHHHHHHHHHH
Confidence 99998887644
No 3
>COG2174 RPL34A Ribosomal protein L34E [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=6.2e-39 Score=224.79 Aligned_cols=82 Identities=43% Similarity=0.732 Sum_probs=80.4
Q ss_pred eeeeeeCCCCceEEEEeeeCCCCCCcCCCCCCCCCccccchhhHhhcccCccccccccCCccchhhHhhHHHHhhhhhcc
Q psy3939 4 YLPSVKTPGGRLVYHYLKKAGKVPRCGHCKIKLPGIEKARSIERSRMSRRRKMVKRSYGGVLCHKCVKEKFIYCFFYSHC 83 (123)
Q Consensus 4 ~~~~vkTPGgrlv~~y~kK~~~~pkC~~c~~~L~Gi~~~rp~~~~~l~k~~k~v~R~YGG~lC~~cvr~rI~raFL~ee~ 83 (123)
.+++||||||++|+||+||+++.|+|++||.+|+||+++||.|+++||+++|+|+|||||++|++|++++|++|||+|||
T Consensus 12 rr~~vkTPgGr~v~h~~kK~~~~p~C~~cg~pL~Gi~r~RP~e~~r~skt~krp~RpYGG~lc~~c~~~~i~~a~r~~~~ 91 (93)
T COG2174 12 RRRYVKTPGGRTVIHYEKKKPTIPKCAICGRPLGGIPRGRPREFRRLSKTKKRPERPYGGYLCANCVRERIKRAFRIEEQ 91 (93)
T ss_pred eeEEEECCCCcEEEeeeeccCCCCcccccCCccCCccCCCcHHHHhccccccCcCCCcCceecHHHHHHHHHHHHHHHHh
Confidence 46899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cc
Q psy3939 84 KI 85 (123)
Q Consensus 84 Ki 85 (123)
+|
T Consensus 92 ki 93 (93)
T COG2174 92 KI 93 (93)
T ss_pred cC
Confidence 86
No 4
>PLN03166 60S ribosomal protein L34; Provisional
Probab=100.00 E-value=4.4e-38 Score=222.78 Aligned_cols=76 Identities=42% Similarity=0.716 Sum_probs=74.1
Q ss_pred eeeeeeCCCCceEEEEeeeCCCCCCcCCCCCCCCCccccchhhHh--hcccCccccccccCCccchhhHhhHHHHhhh
Q psy3939 4 YLPSVKTPGGRLVYHYLKKAGKVPRCGHCKIKLPGIEKARSIERS--RMSRRRKMVKRSYGGVLCHKCVKEKFIYCFF 79 (123)
Q Consensus 4 ~~~~vkTPGgrlv~~y~kK~~~~pkC~~c~~~L~Gi~~~rp~~~~--~l~k~~k~v~R~YGG~lC~~cvr~rI~raFL 79 (123)
.++++|||||+||+||+||+++.|+|||||.+|+||+++||.|++ +|+|++|+|||||||++||+||+|+|++|||
T Consensus 19 k~r~vkTPGGrlv~~y~kK~~~~pkC~~cg~~L~Gi~~~Rp~~~~~~~lsK~~K~vsRaYGG~lc~~cvr~rIvrAFL 96 (96)
T PLN03166 19 QHRVVKTPGGKLVYQTTKKRASGPKCPVTGKRIQGIPHLRPAEYKRSRLSRNRRTVNRAYGGVLSGSAVRERIIRAFL 96 (96)
T ss_pred eeEEEECCCCcEEEEEeccCCCCCcCCCCCCccCCccCCChhhhhhhhcccCcCccccCcCCcccHHHHHHHHHHHhC
Confidence 368999999999999999999999999999999999999999997 8999999999999999999999999999998
No 5
>PF01199 Ribosomal_L34e: Ribosomal protein L34e; InterPro: IPR008195 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 [, ]. A number of eukaryotic and archaebacterial ribosomal proteins belong to the L34e family. These include, vertebrate L34, mosquito L31 [], plant L34 [], yeast putative ribosomal protein YIL052c and archaebacterial L34e.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3IZR_i 3IZS_i 4A19_L 4A1D_L 4A18_L 4A1B_L.
Probab=100.00 E-value=4.6e-38 Score=221.94 Aligned_cols=75 Identities=53% Similarity=1.021 Sum_probs=61.1
Q ss_pred eeeeeCCCCceEEEEeeeCCCCCCcCCCCCCCCCccccchhhHhhcccCccccccccCCccchhhHhhHHHHhhh
Q psy3939 5 LPSVKTPGGRLVYHYLKKAGKVPRCGHCKIKLPGIEKARSIERSRMSRRRKMVKRSYGGVLCHKCVKEKFIYCFF 79 (123)
Q Consensus 5 ~~~vkTPGgrlv~~y~kK~~~~pkC~~c~~~L~Gi~~~rp~~~~~l~k~~k~v~R~YGG~lC~~cvr~rI~raFL 79 (123)
++++|||||+|||||++|+++.|+|||||.+|+||+++||.|+++|+|++|||||||||++||+||+|+|++|||
T Consensus 20 ~~~vrTPGGrlv~~y~kK~~~~pkC~~cg~~L~Gi~~~rp~~~~rl~k~~k~vsRaYGG~lc~~cvr~rI~rAFL 94 (94)
T PF01199_consen 20 RRYVRTPGGRLVYHYIKKKPKKPKCGDCGKPLNGIPALRPVELRRLSKRQKTVSRAYGGSLCHKCVRERIKRAFL 94 (94)
T ss_dssp SEEEE-SSSEEEEEE-S--TT--BSTSSS-BSSSS-SS-SSTTGTS-CHCH--CCTSSSS-HHHHHHHHHHHHHH
T ss_pred EEEeEcCCCcEEEEeccccCCCCCcCccCCcccccccccHHHHhhcccCCCCCCCCCCccchHHHHHHHHHHHhC
Confidence 679999999999999999999999999999999999999999999999999999999999999999999999998
No 6
>PRK04059 rpl34e 50S ribosomal protein L34e; Validated
Probab=100.00 E-value=5.6e-35 Score=204.16 Aligned_cols=74 Identities=35% Similarity=0.664 Sum_probs=72.0
Q ss_pred eeeeeeCCCCceEEEEeeeCCCCCCcCCCCCCCCCccccchhhHhhcccCccccccccCCccchhhHhhHHHHh
Q psy3939 4 YLPSVKTPGGRLVYHYLKKAGKVPRCGHCKIKLPGIEKARSIERSRMSRRRKMVKRSYGGVLCHKCVKEKFIYC 77 (123)
Q Consensus 4 ~~~~vkTPGgrlv~~y~kK~~~~pkC~~c~~~L~Gi~~~rp~~~~~l~k~~k~v~R~YGG~lC~~cvr~rI~ra 77 (123)
.+++||||||+|||||.+|+++.|+|||||.+|+||+++||.|+++|+|++|+|||||||++||+||+|+|+.+
T Consensus 12 k~r~vrTPGGrlv~~y~kK~~~~pkC~~c~~~L~Gi~~~Rp~~~~rlsK~~K~vsRaYGG~lc~~cvr~rI~~~ 85 (88)
T PRK04059 12 RRVYVRTPGGRTVIHYERKKPSKAKCAICGKPLNGVPRGRPVEIRKLGKTEKRPERPYGGYLCPKCLKRLIKAK 85 (88)
T ss_pred ceEEEECCCCCEEEEEeccCCCCCcCCCCCCccCCccCcchHHHHhcccccCCcccCcCceecHHHHHHHHHHH
Confidence 46899999999999999999999999999999999999999999999999999999999999999999999876
No 7
>PRK04059 rpl34e 50S ribosomal protein L34e; Validated
Probab=99.51 E-value=2.3e-15 Score=105.39 Aligned_cols=49 Identities=35% Similarity=0.731 Sum_probs=45.7
Q ss_pred cCCccchhhHhhHHHHhhhhhccccccccchhhhhHHHHhcccCCCccccccCCccccccccC
Q psy3939 61 YGGVLCHKCVKEKFIYCFFYSHCKIKLPGIEKARSIERSRMSRRRKMVKRSYGGVLCHKCVKE 123 (123)
Q Consensus 61 YGG~lC~~cvr~rI~raFL~ee~KivkkgVKakrp~ekkrl~k~~ktV~RayGG~lc~~cvr~ 123 (123)
-.++.|+.|-. .|+||++.+|.++++|||++|||||||||++||+||+|
T Consensus 32 ~~~pkC~~c~~--------------~L~Gi~~~Rp~~~~rlsK~~K~vsRaYGG~lc~~cvr~ 80 (88)
T PRK04059 32 PSKAKCAICGK--------------PLNGVPRGRPVEIRKLGKTEKRPERPYGGYLCPKCLKR 80 (88)
T ss_pred CCCCcCCCCCC--------------ccCCccCcchHHHHhcccccCCcccCcCceecHHHHHH
Confidence 34667999998 99999999999999999999999999999999999986
No 8
>PLN03166 60S ribosomal protein L34; Provisional
Probab=99.45 E-value=1.4e-14 Score=102.87 Aligned_cols=48 Identities=42% Similarity=0.702 Sum_probs=44.8
Q ss_pred CCccchhhHhhHHHHhhhhhccccccccchhhhhHHHH--hcccCCCccccccCCccccccccC
Q psy3939 62 GGVLCHKCVKEKFIYCFFYSHCKIKLPGIEKARSIERS--RMSRRRKMVKRSYGGVLCHKCVKE 123 (123)
Q Consensus 62 GG~lC~~cvr~rI~raFL~ee~KivkkgVKakrp~ekk--rl~k~~ktV~RayGG~lc~~cvr~ 123 (123)
.++.|+.|-. .|+||++.+|.+++ +|||++|+|||||||++||+||+|
T Consensus 40 ~~pkC~~cg~--------------~L~Gi~~~Rp~~~~~~~lsK~~K~vsRaYGG~lc~~cvr~ 89 (96)
T PLN03166 40 SGPKCPVTGK--------------RIQGIPHLRPAEYKRSRLSRNRRTVNRAYGGVLSGSAVRE 89 (96)
T ss_pred CCCcCCCCCC--------------ccCCccCCChhhhhhhhcccCcCccccCcCCcccHHHHHH
Confidence 4567999999 99999999999997 899999999999999999999986
No 9
>PTZ00074 60S ribosomal protein L34; Provisional
Probab=99.41 E-value=3.4e-14 Score=106.20 Aligned_cols=48 Identities=50% Similarity=0.981 Sum_probs=45.5
Q ss_pred CCccchhhHhhHHHHhhhhhccccccccchhhhhHHHHhcccCCCccccccCCccccccccC
Q psy3939 62 GGVLCHKCVKEKFIYCFFYSHCKIKLPGIEKARSIERSRMSRRRKMVKRSYGGVLCHKCVKE 123 (123)
Q Consensus 62 GG~lC~~cvr~rI~raFL~ee~KivkkgVKakrp~ekkrl~k~~ktV~RayGG~lc~~cvr~ 123 (123)
.++.|+.|-. .|+||++.+|.++++|++++|||||||||++||.||+|
T Consensus 40 ~~pkC~~cg~--------------~L~GI~~~Rp~e~~rlsK~~KtvsRaYGG~lC~~CVr~ 87 (135)
T PTZ00074 40 SGPKCGDCGK--------------VLAGIKALRPTEYKQLSRRERTVSRAYGGVLCHKCVRD 87 (135)
T ss_pred CCCCCCCCCC--------------ccCCccCCchHHHHHccccCCCccCCCccchhHHHHHH
Confidence 4677999999 99999999999999999999999999999999999985
No 10
>PF01199 Ribosomal_L34e: Ribosomal protein L34e; InterPro: IPR008195 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 [, ]. A number of eukaryotic and archaebacterial ribosomal proteins belong to the L34e family. These include, vertebrate L34, mosquito L31 [], plant L34 [], yeast putative ribosomal protein YIL052c and archaebacterial L34e.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3IZR_i 3IZS_i 4A19_L 4A1D_L 4A18_L 4A1B_L.
Probab=99.40 E-value=1.2e-14 Score=102.84 Aligned_cols=47 Identities=51% Similarity=0.948 Sum_probs=36.7
Q ss_pred CccchhhHhhHHHHhhhhhccccccccchhhhhHHHHhcccCCCccccccCCccccccccC
Q psy3939 63 GVLCHKCVKEKFIYCFFYSHCKIKLPGIEKARSIERSRMSRRRKMVKRSYGGVLCHKCVKE 123 (123)
Q Consensus 63 G~lC~~cvr~rI~raFL~ee~KivkkgVKakrp~ekkrl~k~~ktV~RayGG~lc~~cvr~ 123 (123)
++.|+.|-+ .|+||++.+|.+.++|+|++|||||||||++||+||+|
T Consensus 41 ~pkC~~cg~--------------~L~Gi~~~rp~~~~rl~k~~k~vsRaYGG~lc~~cvr~ 87 (94)
T PF01199_consen 41 KPKCGDCGK--------------PLNGIPALRPVELRRLSKRQKTVSRAYGGSLCHKCVRE 87 (94)
T ss_dssp --BSTSSS---------------BSSSS-SS-SSTTGTS-CHCH--CCTSSSS-HHHHHHH
T ss_pred CCCcCccCC--------------cccccccccHHHHhhcccCCCCCCCCCCccchHHHHHH
Confidence 467999999 99999999999999999999999999999999999985
No 11
>KOG1790|consensus
Probab=99.31 E-value=2.5e-13 Score=99.59 Aligned_cols=46 Identities=48% Similarity=0.867 Sum_probs=42.6
Q ss_pred ccchhhHhhHHHHhhhhhccccccccchhhhhHHHHhcccCCCccccccCCccccccccC
Q psy3939 64 VLCHKCVKEKFIYCFFYSHCKIKLPGIEKARSIERSRMSRRRKMVKRSYGGVLCHKCVKE 123 (123)
Q Consensus 64 ~lC~~cvr~rI~raFL~ee~KivkkgVKakrp~ekkrl~k~~ktV~RayGG~lc~~cvr~ 123 (123)
+.|++|.. .++||.+.+|.+++++|+++|||||+|||++|++||+|
T Consensus 42 pkc~~c~~--------------~l~Gi~~~RPk~~~rlsk~~KtVsRayGG~~ca~~vre 87 (121)
T KOG1790|consen 42 PKCGDCGM--------------RLQGIPALRPKELMRLSKSHKTVSRAYGGVLCAKCVRE 87 (121)
T ss_pred CCCCcCCc--------------ccCCCCCcCHHHHHHHhhhHHHhhhhccccchHHHHHH
Confidence 34777777 99999999999999999999999999999999999986
No 12
>COG2174 RPL34A Ribosomal protein L34E [Translation, ribosomal structure and biogenesis]
Probab=99.21 E-value=2.4e-12 Score=90.71 Aligned_cols=49 Identities=39% Similarity=0.697 Sum_probs=45.9
Q ss_pred cCCccchhhHhhHHHHhhhhhccccccccchhhhhHHHHhcccCCCccccccCCccccccccC
Q psy3939 61 YGGVLCHKCVKEKFIYCFFYSHCKIKLPGIEKARSIERSRMSRRRKMVKRSYGGVLCHKCVKE 123 (123)
Q Consensus 61 YGG~lC~~cvr~rI~raFL~ee~KivkkgVKakrp~ekkrl~k~~ktV~RayGG~lc~~cvr~ 123 (123)
=+=+.|+.|.+ .|+||+..+|.+..++|+++|+|+|+|||++|+.||+|
T Consensus 32 ~~~p~C~~cg~--------------pL~Gi~r~RP~e~~r~skt~krp~RpYGG~lc~~c~~~ 80 (93)
T COG2174 32 PTIPKCAICGR--------------PLGGIPRGRPREFRRLSKTKKRPERPYGGYLCANCVRE 80 (93)
T ss_pred CCCCcccccCC--------------ccCCccCCCcHHHHhccccccCcCCCcCceecHHHHHH
Confidence 34578999999 99999999999999999999999999999999999975
No 13
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=63.02 E-value=3.8 Score=36.06 Aligned_cols=60 Identities=20% Similarity=0.346 Sum_probs=37.5
Q ss_pred CCCCCcCCCCCCCCCccccchhhHhhcccCccccccccCCccchhhHhhHHHHhhhhhccccccccchhhhhHHHHhccc
Q psy3939 24 GKVPRCGHCKIKLPGIEKARSIERSRMSRRRKMVKRSYGGVLCHKCVKEKFIYCFFYSHCKIKLPGIEKARSIERSRMSR 103 (123)
Q Consensus 24 ~~~pkC~~c~~~L~Gi~~~rp~~~~~l~k~~k~v~R~YGG~lC~~cvr~rI~raFL~ee~KivkkgVKakrp~ekkrl~k 103 (123)
...|+|+.||..+..- -| ||..|.+|-..-=-..+. |-..-+-.|+ +..+....+|||
T Consensus 348 ~~~p~Cp~Cg~~m~S~------------------G~--~g~rC~kCg~~~~~~~~~-~v~r~l~~g~-evp~~arRHLsk 405 (421)
T COG1571 348 RVNPVCPRCGGRMKSA------------------GR--NGFRCKKCGTRARETLIK-EVPRDLEPGV-EVPPVARRHLSK 405 (421)
T ss_pred EcCCCCCccCCchhhc------------------CC--CCcccccccccCCccccc-ccccccCCCC-cCCchhhhhccC
Confidence 3568999999865332 22 399999998522112222 4455566777 777777777776
Q ss_pred CC
Q psy3939 104 RR 105 (123)
Q Consensus 104 ~~ 105 (123)
-.
T Consensus 406 P~ 407 (421)
T COG1571 406 PL 407 (421)
T ss_pred Cc
Confidence 43
No 14
>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed
Probab=50.84 E-value=23 Score=23.23 Aligned_cols=33 Identities=30% Similarity=0.436 Sum_probs=26.5
Q ss_pred eeeeeeeCCC-CceEEEEeeeCCCCCCcCCCCCCC
Q psy3939 3 TYLPSVKTPG-GRLVYHYLKKAGKVPRCGHCKIKL 36 (123)
Q Consensus 3 ~~~~~vkTPG-grlv~~y~kK~~~~pkC~~c~~~L 36 (123)
.|...|+=|+ +...+.|- ...+.-.|..||..|
T Consensus 7 S~F~~VkCp~C~n~q~vFs-ha~t~V~C~~Cg~~L 40 (59)
T PRK00415 7 SRFLKVKCPDCGNEQVVFS-HASTVVRCLVCGKTL 40 (59)
T ss_pred CeEEEEECCCCCCeEEEEe-cCCcEEECcccCCCc
Confidence 3667788898 78888777 677788899999877
No 15
>COG1381 RecO Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]
Probab=47.06 E-value=9.3 Score=30.65 Aligned_cols=30 Identities=27% Similarity=0.698 Sum_probs=24.1
Q ss_pred CCCCcCCCCCCCCCccccchhhHhhcccCccccccccCCccchhhH
Q psy3939 25 KVPRCGHCKIKLPGIEKARSIERSRMSRRRKMVKRSYGGVLCHKCV 70 (123)
Q Consensus 25 ~~pkC~~c~~~L~Gi~~~rp~~~~~l~k~~k~v~R~YGG~lC~~cv 70 (123)
+-..|+.||.+.+= -.++..+||.+|+.|.
T Consensus 153 ~l~~Ca~cg~~~~~----------------~~~s~~~~~~~C~~~~ 182 (251)
T COG1381 153 NLTSCARCGTPVDP----------------VYFSPKSGGFLCSKCA 182 (251)
T ss_pred chHHHhCcCCcCCC----------------cceeeccCcccchhcc
Confidence 34579999988653 3788999999999986
No 16
>PRK00085 recO DNA repair protein RecO; Reviewed
Probab=46.79 E-value=9.2 Score=29.68 Aligned_cols=30 Identities=20% Similarity=0.553 Sum_probs=23.1
Q ss_pred CCCCcCCCCCCCCCccccchhhHhhcccCccccccccCCccchhhH
Q psy3939 25 KVPRCGHCKIKLPGIEKARSIERSRMSRRRKMVKRSYGGVLCHKCV 70 (123)
Q Consensus 25 ~~pkC~~c~~~L~Gi~~~rp~~~~~l~k~~k~v~R~YGG~lC~~cv 70 (123)
....|+.||.++.. -..+-..||.+|..|.
T Consensus 148 ~l~~C~~Cg~~~~~----------------~~f~~~~gg~~c~~c~ 177 (247)
T PRK00085 148 DLDHCAVCGAPGDH----------------RYFSPKEGGAVCSECG 177 (247)
T ss_pred chhhHhcCCCCCCc----------------eEEecccCCccccccc
Confidence 34569999998761 2467789999999995
No 17
>COG3813 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=41.74 E-value=18 Score=25.07 Aligned_cols=34 Identities=24% Similarity=0.341 Sum_probs=25.3
Q ss_pred CcCCCCCCCCCccccchh-hHhhcccCccccccccC
Q psy3939 28 RCGHCKIKLPGIEKARSI-ERSRMSRRRKMVKRSYG 62 (123)
Q Consensus 28 kC~~c~~~L~Gi~~~rp~-~~~~l~k~~k~v~R~YG 62 (123)
.|++||..|---| .||. .+.+-+-+.++|-|+-|
T Consensus 43 ~CPnCGGelv~RP-~RPaa~L~r~PASt~Rv~r~~G 77 (84)
T COG3813 43 LCPNCGGELVARP-IRPAAKLARYPASTRRVLRPEG 77 (84)
T ss_pred cCCCCCchhhcCc-CChHHHHhhCchhhhheecccC
Confidence 4888887776544 4554 47888888999999876
No 18
>PRK00420 hypothetical protein; Validated
Probab=39.38 E-value=16 Score=26.67 Aligned_cols=30 Identities=23% Similarity=0.453 Sum_probs=22.6
Q ss_pred CCcCCCCCCCCCccccchhhHhhcccCccccccccCCccchhhHhhHHHH
Q psy3939 27 PRCGHCKIKLPGIEKARSIERSRMSRRRKMVKRSYGGVLCHKCVKEKFIY 76 (123)
Q Consensus 27 pkC~~c~~~L~Gi~~~rp~~~~~l~k~~k~v~R~YGG~lC~~cvr~rI~r 76 (123)
..|+.||.+|-+... |-..|+.|-..-++.
T Consensus 24 ~~CP~Cg~pLf~lk~--------------------g~~~Cp~Cg~~~~v~ 53 (112)
T PRK00420 24 KHCPVCGLPLFELKD--------------------GEVVCPVHGKVYIVK 53 (112)
T ss_pred CCCCCCCCcceecCC--------------------CceECCCCCCeeeec
Confidence 579999999877654 567899998755543
No 19
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=36.27 E-value=9.9 Score=22.71 Aligned_cols=9 Identities=22% Similarity=0.973 Sum_probs=5.4
Q ss_pred CcCCCCCCC
Q psy3939 28 RCGHCKIKL 36 (123)
Q Consensus 28 kC~~c~~~L 36 (123)
+|++||..+
T Consensus 5 ~C~~CG~~~ 13 (46)
T PRK00398 5 KCARCGREV 13 (46)
T ss_pred ECCCCCCEE
Confidence 466666654
No 20
>PLN00209 ribosomal protein S27; Provisional
Probab=35.60 E-value=40 Score=23.71 Aligned_cols=32 Identities=25% Similarity=0.498 Sum_probs=25.3
Q ss_pred eeeeeeCCC-CceEEEEeeeCCCCCCcCCCCCCC
Q psy3939 4 YLPSVKTPG-GRLVYHYLKKAGKVPRCGHCKIKL 36 (123)
Q Consensus 4 ~~~~vkTPG-grlv~~y~kK~~~~pkC~~c~~~L 36 (123)
|...|+=|| +.+.+.|- ...+...|..||..|
T Consensus 33 ~Fm~VkCp~C~n~q~VFS-hA~t~V~C~~Cg~~L 65 (86)
T PLN00209 33 FFMDVKCQGCFNITTVFS-HSQTVVVCGSCQTVL 65 (86)
T ss_pred EEEEEECCCCCCeeEEEe-cCceEEEccccCCEe
Confidence 667788888 77777777 566777799999876
No 21
>PF14471 DUF4428: Domain of unknown function (DUF4428)
Probab=35.31 E-value=32 Score=21.46 Aligned_cols=29 Identities=24% Similarity=0.689 Sum_probs=19.0
Q ss_pred CcCCCCCCCCCccccchhhHhhcccCccccccccCCccchhhHhh
Q psy3939 28 RCGHCKIKLPGIEKARSIERSRMSRRRKMVKRSYGGVLCHKCVKE 72 (123)
Q Consensus 28 kC~~c~~~L~Gi~~~rp~~~~~l~k~~k~v~R~YGG~lC~~cvr~ 72 (123)
+|+.||..+.=+.. ..-=.|++|.+|...
T Consensus 1 ~C~iCg~kigl~~~----------------~k~~DG~iC~~C~~K 29 (51)
T PF14471_consen 1 KCAICGKKIGLFKR----------------FKIKDGYICKDCLKK 29 (51)
T ss_pred CCCccccccccccc----------------eeccCccchHHHHHH
Confidence 58999987643322 112246899999974
No 22
>PTZ00083 40S ribosomal protein S27; Provisional
Probab=35.14 E-value=40 Score=23.64 Aligned_cols=32 Identities=34% Similarity=0.682 Sum_probs=25.3
Q ss_pred eeeeeeCCC-CceEEEEeeeCCCCCCcCCCCCCC
Q psy3939 4 YLPSVKTPG-GRLVYHYLKKAGKVPRCGHCKIKL 36 (123)
Q Consensus 4 ~~~~vkTPG-grlv~~y~kK~~~~pkC~~c~~~L 36 (123)
|...|+-|| +.+.+.|- ...+...|..||..|
T Consensus 32 ~Fm~VkCp~C~n~q~VFS-hA~t~V~C~~Cg~~L 64 (85)
T PTZ00083 32 YFMDVKCPGCSQITTVFS-HAQTVVLCGGCSSQL 64 (85)
T ss_pred eEEEEECCCCCCeeEEEe-cCceEEEccccCCEe
Confidence 667788888 77777777 567777799999876
No 23
>PRK12495 hypothetical protein; Provisional
Probab=31.60 E-value=22 Score=28.97 Aligned_cols=14 Identities=14% Similarity=0.294 Sum_probs=11.2
Q ss_pred CCCCCcCCCCCCCC
Q psy3939 24 GKVPRCGHCKIKLP 37 (123)
Q Consensus 24 ~~~pkC~~c~~~L~ 37 (123)
.+.-.|.+||.+|.
T Consensus 40 msa~hC~~CG~PIp 53 (226)
T PRK12495 40 MTNAHCDECGDPIF 53 (226)
T ss_pred cchhhcccccCccc
Confidence 34567999999987
No 24
>PF06689 zf-C4_ClpX: ClpX C4-type zinc finger; InterPro: IPR010603 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 ClpX heat shock protein of Escherichia coli is a member of the universally conserved Hsp100 family of proteins, and possesses a putative zinc finger motif of the C4 type []. This presumed zinc binding domain (ZBD) is found at the N terminus of the ClpX protein. ClpX is an ATPase which functions both as a substrate specificity component of the ClpXP protease and as a molecular chaperone. ZBD is a member of the treble clef zinc finger family, a motif known to facilitate protein-ligand, protein-DNA, and protein-protein interactions and forms a constitutive dimer that is essential for the degradation of some, but not all, ClpX substrates []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0016887 ATPase activity, 0046983 protein dimerization activity, 0006200 ATP catabolic process, 0019538 protein metabolic process; PDB: 2DS8_B 2DS6_B 2DS5_A 1OVX_A 2DS7_A.
Probab=30.89 E-value=54 Score=19.39 Aligned_cols=31 Identities=23% Similarity=0.722 Sum_probs=19.3
Q ss_pred CCcCCCCCCCCCccccchhhHhhcccCccccccccCCccchhhHh
Q psy3939 27 PRCGHCKIKLPGIEKARSIERSRMSRRRKMVKRSYGGVLCHKCVK 71 (123)
Q Consensus 27 pkC~~c~~~L~Gi~~~rp~~~~~l~k~~k~v~R~YGG~lC~~cvr 71 (123)
..|.=||++-.-+.. -++-+-|+++|..|+.
T Consensus 2 ~~CSFCgr~~~~v~~--------------li~g~~~~~IC~~Cv~ 32 (41)
T PF06689_consen 2 KRCSFCGRPESEVGR--------------LISGPNGAYICDECVE 32 (41)
T ss_dssp -B-TTT--BTTTSSS--------------EEEES-SEEEEHHHHH
T ss_pred CCccCCCCCHHHHhc--------------eecCCCCcEECHHHHH
Confidence 357778877665544 4667778999999996
No 25
>PTZ00218 40S ribosomal protein S29; Provisional
Probab=27.97 E-value=48 Score=21.35 Aligned_cols=38 Identities=29% Similarity=0.610 Sum_probs=27.1
Q ss_pred EEEeeeCCCCCC-cCCCCCCCCCccccchhhHhhcccCccccccccCCccchhhHhhH
Q psy3939 17 YHYLKKAGKVPR-CGHCKIKLPGIEKARSIERSRMSRRRKMVKRSYGGVLCHKCVKEK 73 (123)
Q Consensus 17 ~~y~kK~~~~pk-C~~c~~~L~Gi~~~rp~~~~~l~k~~k~v~R~YGG~lC~~cvr~r 73 (123)
.-+.++-++..+ |..||.+ .-+-|.||=.+|-.|.+|.
T Consensus 6 ~shpr~yGkGsr~C~vCg~~-------------------~gliRkygL~~CRqCFRe~ 44 (54)
T PTZ00218 6 NTHPRTYGKGSRQCRVCSNR-------------------HGLIRKYGLNVCRQCFREN 44 (54)
T ss_pred cCCCCcCCCCCCeeecCCCc-------------------chhhhhcCcchhhHHHHHh
Confidence 334555666554 9999874 2456789999999999863
No 26
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=27.96 E-value=29 Score=18.51 Aligned_cols=11 Identities=36% Similarity=0.733 Sum_probs=7.0
Q ss_pred CCCcCCCCCCC
Q psy3939 26 VPRCGHCKIKL 36 (123)
Q Consensus 26 ~pkC~~c~~~L 36 (123)
..-|+.||.+|
T Consensus 16 ~~fC~~CG~~L 26 (26)
T PF13248_consen 16 AKFCPNCGAKL 26 (26)
T ss_pred cccChhhCCCC
Confidence 34477777765
No 27
>KOG1842|consensus
Probab=27.49 E-value=20 Score=32.20 Aligned_cols=36 Identities=31% Similarity=0.689 Sum_probs=28.0
Q ss_pred CCCCCCcCCCCCCCCCccccchhhHhhcccCccccccccCCccchhhHh
Q psy3939 23 AGKVPRCGHCKIKLPGIEKARSIERSRMSRRRKMVKRSYGGVLCHKCVK 71 (123)
Q Consensus 23 ~~~~pkC~~c~~~L~Gi~~~rp~~~~~l~k~~k~v~R~YGG~lC~~cvr 71 (123)
=.+++-|++|+.+. ||.. .++-.|--|+++|++|.+
T Consensus 177 Ds~V~~CP~Ca~~F-~l~r------------RrHHCRLCG~VmC~~C~k 212 (505)
T KOG1842|consen 177 DSSVQFCPECANSF-GLTR------------RRHHCRLCGRVMCRDCSK 212 (505)
T ss_pred CCcccccccccchh-hhHH------------HhhhhhhcchHHHHHHHH
Confidence 35778899998774 3332 357789999999999998
No 28
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=26.46 E-value=22 Score=22.42 Aligned_cols=25 Identities=20% Similarity=0.541 Sum_probs=17.0
Q ss_pred CcCCCCCCCCCccccchhhHhhcccCccccccccCCccchhhHh
Q psy3939 28 RCGHCKIKLPGIEKARSIERSRMSRRRKMVKRSYGGVLCHKCVK 71 (123)
Q Consensus 28 kC~~c~~~L~Gi~~~rp~~~~~l~k~~k~v~R~YGG~lC~~cvr 71 (123)
+|+.||+.+.=+ -.+.|..|+.|--
T Consensus 8 ~C~~Cg~~~~~~-------------------~~~~~irCp~Cg~ 32 (49)
T COG1996 8 KCARCGREVELD-------------------QETRGIRCPYCGS 32 (49)
T ss_pred EhhhcCCeeehh-------------------hccCceeCCCCCc
Confidence 488898876211 1366888888875
No 29
>cd00065 FYVE FYVE domain; Zinc-binding domain; targets proteins to membrane lipids via interaction with phosphatidylinositol-3-phosphate, PI3P; present in Fab1, YOTB, Vac1, and EEA1;
Probab=26.26 E-value=39 Score=20.27 Aligned_cols=38 Identities=21% Similarity=0.467 Sum_probs=27.7
Q ss_pred CCcCCCCCCCCCccccchhhHhhcccCccccccccCCccchhhHhhHHHHh
Q psy3939 27 PRCGHCKIKLPGIEKARSIERSRMSRRRKMVKRSYGGVLCHKCVKEKFIYC 77 (123)
Q Consensus 27 pkC~~c~~~L~Gi~~~rp~~~~~l~k~~k~v~R~YGG~lC~~cvr~rI~ra 77 (123)
..|..|++.+.-.. .+.--|.=|...|.+|...+....
T Consensus 3 ~~C~~C~~~F~~~~-------------rk~~Cr~Cg~~~C~~C~~~~~~~~ 40 (57)
T cd00065 3 SSCMGCGKPFTLTR-------------RRHHCRNCGRIFCSKCSSNRIPLP 40 (57)
T ss_pred CcCcccCccccCCc-------------cccccCcCcCCcChHHcCCeeecC
Confidence 45888888877543 256778889999999998654443
No 30
>PF01667 Ribosomal_S27e: Ribosomal protein S27; InterPro: IPR000592 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 [, ]. A number of eukaryotic and archaeal ribosomal proteins can be grouped on the basis of sequence similarities. One of these families include mammalian, yeast, Chlamydomonas reinhardtii and Entamoeba histolytica S27, and Methanocaldococcus jannaschii (Methanococcus jannaschii) MJ0250 []. These proteins have from 62 to 87 amino acids. They contain, in their central section, a putative zinc-finger region of the type C-x(2)-C-x(14)-C-x(2)-C.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 1QXF_A 3IZ6_X 2XZN_6 2XZM_6 3U5G_b 3IZB_X 3U5C_b.
Probab=26.19 E-value=51 Score=21.20 Aligned_cols=32 Identities=31% Similarity=0.517 Sum_probs=20.2
Q ss_pred eeeeeeCCC-CceEEEEeeeCCCCCCcCCCCCCC
Q psy3939 4 YLPSVKTPG-GRLVYHYLKKAGKVPRCGHCKIKL 36 (123)
Q Consensus 4 ~~~~vkTPG-grlv~~y~kK~~~~pkC~~c~~~L 36 (123)
|...|+=|| +.+.+.|- .....-.|..||..|
T Consensus 4 ~Fm~VkCp~C~~~q~vFS-ha~t~V~C~~Cg~~L 36 (55)
T PF01667_consen 4 YFMDVKCPGCYNIQTVFS-HAQTVVKCVVCGTVL 36 (55)
T ss_dssp -EEEEE-TTT-SEEEEET-T-SS-EE-SSSTSEE
T ss_pred cEEEEECCCCCCeeEEEe-cCCeEEEcccCCCEe
Confidence 667788888 77777776 566677799999866
No 31
>COG2906 Bfd Bacterioferritin-associated ferredoxin [Inorganic ion transport and metabolism]
Probab=25.97 E-value=44 Score=22.20 Aligned_cols=19 Identities=26% Similarity=0.427 Sum_probs=14.5
Q ss_pred CccchhhHhhHHHHhhhhhcc
Q psy3939 63 GVLCHKCVKEKFIYCFFYSHC 83 (123)
Q Consensus 63 G~lC~~cvr~rI~raFL~ee~ 83 (123)
|+-|++|++ --++||.|+.
T Consensus 35 Gs~CGkC~~--~Arevl~e~~ 53 (63)
T COG2906 35 GSQCGKCVR--AAREVLEEAL 53 (63)
T ss_pred ccchHHHHH--HHHHHHHHHH
Confidence 899999997 4567776653
No 32
>PF01412 ArfGap: Putative GTPase activating protein for Arf; InterPro: IPR001164 This entry describes a family of small GTPase activating proteins, for example ARF1-directed GTPase-activating protein, the cycle control GTPase activating protein (GAP) GCS1 which is important for the regulation of the ADP ribosylation factor ARF, a member of the Ras superfamily of GTP-binding proteins []. The GTP-bound form of ARF is essential for the maintenance of normal Golgi morphology, it participates in recruitment of coat proteins which are required for budding and fission of membranes. Before the fusion with an acceptor compartment the membrane must be uncoated. This step required the hydrolysis of GTP associated to ARF. These proteins contain a characteristic zinc finger motif (Cys-x2-Cys-x(16,17)-x2-Cys) which displays some similarity to the C4-type GATA zinc finger. The ARFGAP domain display no obvious similarity to other GAP proteins. The 3D structure of the ARFGAP domain of the PYK2-associated protein beta has been solved []. It consists of a three-stranded beta-sheet surrounded by 5 alpha helices. The domain is organised around a central zinc atom which is coordinated by 4 cysteines. The ARFGAP domain is clearly unrelated to the other GAP proteins structures which are exclusively helical. Classical GAP proteins accelerate GTPase activity by supplying an arginine finger to the active site. The crystal structure of ARFGAP bound to ARF revealed that the ARFGAP domain does not supply an arginine to the active site which suggests a more indirect role of the ARFGAP domain in the GTPase hydrolysis []. The Rev protein of human immunodeficiency virus type 1 (HIV-1) facilitates nuclear export of unspliced and partly-spliced viral RNAs []. Rev contains an RNA-binding domain and an effector domain; the latter is believed to interact with a cellular cofactor required for the Rev response and hence HIV-1 replication. Human Rev interacting protein (hRIP) specifically interacts with the Rev effector. The amino acid sequence of hRIP is characterised by an N-terminal, C-4 class zinc finger motif.; GO: 0008060 ARF GTPase activator activity, 0008270 zinc ion binding, 0032312 regulation of ARF GTPase activity; PDB: 2P57_A 2CRR_A 2OWA_B 3O47_B 3DWD_A 1DCQ_A 2CRW_A 3MDB_D 3FEH_A 3LJU_X ....
Probab=25.96 E-value=45 Score=23.53 Aligned_cols=39 Identities=23% Similarity=0.416 Sum_probs=23.4
Q ss_pred eCCCCCCcCCCCCCCCCccccchhhHhhcccCccccccccCCccchhhHhhHHHHhhh
Q psy3939 22 KAGKVPRCGHCKIKLPGIEKARSIERSRMSRRRKMVKRSYGGVLCHKCVKEKFIYCFF 79 (123)
Q Consensus 22 K~~~~pkC~~c~~~L~Gi~~~rp~~~~~l~k~~k~v~R~YGG~lC~~cvr~rI~raFL 79 (123)
+.+..-.|+|||.+=+ .=++=.||=.+|..|-. |-|.|-
T Consensus 9 ~~~~N~~CaDCg~~~p-----------------~w~s~~~GiflC~~Cag--~HR~lg 47 (116)
T PF01412_consen 9 KKPGNKVCADCGAPNP-----------------TWASLNYGIFLCLECAG--IHRSLG 47 (116)
T ss_dssp CSTTCTB-TTT-SBS-------------------EEETTTTEEE-HHHHH--HHHHHT
T ss_pred cCcCcCcCCCCCCCCC-----------------CEEEeecChhhhHHHHH--HHHHhc
Confidence 3456678999984421 24555699999999985 555554
No 33
>COG5347 GTPase-activating protein that regulates ARFs (ADP-ribosylation factors), involved in ARF-mediated vesicular transport [Intracellular trafficking and secretion]
Probab=25.61 E-value=11 Score=31.99 Aligned_cols=38 Identities=21% Similarity=0.455 Sum_probs=28.0
Q ss_pred EEEeeeCCCCCCcCCCCCCCCCccccchhhHhhcccCccccccccCCccchhhHh
Q psy3939 17 YHYLKKAGKVPRCGHCKIKLPGIEKARSIERSRMSRRRKMVKRSYGGVLCHKCVK 71 (123)
Q Consensus 17 ~~y~kK~~~~pkC~~c~~~L~Gi~~~rp~~~~~l~k~~k~v~R~YGG~lC~~cvr 71 (123)
..++++....-+|+|||.+- |. =+|=.||=.+|-+|-.
T Consensus 11 l~~l~~~~~Nk~CaDCga~~---P~--------------W~S~nlGvfiCi~Cag 48 (319)
T COG5347 11 LKLLKSDSSNKKCADCGAPN---PT--------------WASVNLGVFLCIDCAG 48 (319)
T ss_pred HHHHhhccccCccccCCCCC---Cc--------------eEecccCeEEEeecch
Confidence 34456677778899999885 22 3455799999999964
No 34
>PF09237 GAGA: GAGA factor; InterPro: IPR015318 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. Members of this entry bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognises the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognises the A in the fourth position of the consensus sequence []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1YUI_A 1YUJ_A.
Probab=24.94 E-value=14 Score=23.85 Aligned_cols=34 Identities=9% Similarity=0.101 Sum_probs=10.4
Q ss_pred eeeeeCCCCceEEEEeeeCCCCCCcCCCCCCCCC
Q psy3939 5 LPSVKTPGGRLVYHYLKKAGKVPRCGHCKIKLPG 38 (123)
Q Consensus 5 ~~~vkTPGgrlv~~y~kK~~~~pkC~~c~~~L~G 38 (123)
+.+.+++-+..-..-.......+.|++|+..+.-
T Consensus 3 ~~~~~~~~~~~~~k~~~~S~~PatCP~C~a~~~~ 36 (54)
T PF09237_consen 3 AAVIKRKPSTKKPKSKSQSEQPATCPICGAVIRQ 36 (54)
T ss_dssp ----S-SS-----CCCCTTS--EE-TTT--EESS
T ss_pred ccccccchhhhHHHHhhccCCCCCCCcchhhccc
Confidence 3344444442222223344456779999887554
No 35
>smart00064 FYVE Protein present in Fab1, YOTB, Vac1, and EEA1. The FYVE zinc finger is named after four proteins where it was first found: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two Zn2+ ions. The FYVE finger has eight potential zinc coordinating cysteine positions. The FYVE finger is structurally related to the PF10764 Gin: Inhibitor of sigma-G Gin; InterPro: IPR019700 Gin allows sigma-F to delay late forespore transcription by preventing sigma-G to take over before the cell has reached a critical stage of development. Gin is also known as CsfB [].
Probab=23.79 E-value=43 Score=20.61 Aligned_cols=27 Identities=37% Similarity=0.813 Sum_probs=19.6
Q ss_pred CcCCCCCCCC-CccccchhhHhhcccCccccccccCCccchhhHhhH
Q psy3939 28 RCGHCKIKLP-GIEKARSIERSRMSRRRKMVKRSYGGVLCHKCVKEK 73 (123)
Q Consensus 28 kC~~c~~~L~-Gi~~~rp~~~~~l~k~~k~v~R~YGG~lC~~cvr~r 73 (123)
+|-.|+++.+ ||- .||-.+|.+|-++.
T Consensus 1 ~CiiC~~~~~~GI~-------------------I~~~fIC~~CE~~i 28 (46)
T PF10764_consen 1 KCIICGKEKEEGIH-------------------IYGKFICSDCEKEI 28 (46)
T ss_pred CeEeCCCcCCCCEE-------------------EECeEehHHHHHHh
Confidence 3667777655 654 58899999998754
No 37
>PF13408 Zn_ribbon_recom: Recombinase zinc beta ribbon domain
Probab=23.74 E-value=29 Score=20.69 Aligned_cols=13 Identities=46% Similarity=1.076 Sum_probs=10.8
Q ss_pred CCCcCCCCCCCCC
Q psy3939 26 VPRCGHCKIKLPG 38 (123)
Q Consensus 26 ~pkC~~c~~~L~G 38 (123)
...|++||.+|..
T Consensus 5 ~l~C~~CG~~m~~ 17 (58)
T PF13408_consen 5 LLRCGHCGSKMTR 17 (58)
T ss_pred cEEcccCCcEeEE
Confidence 4569999999877
No 38
>KOG1819|consensus
Probab=23.60 E-value=19 Score=33.32 Aligned_cols=35 Identities=23% Similarity=0.663 Sum_probs=27.4
Q ss_pred CCCCCcCCCCCCCCCccccchhhHhhcccCccccccccCCccchhhHh
Q psy3939 24 GKVPRCGHCKIKLPGIEKARSIERSRMSRRRKMVKRSYGGVLCHKCVK 71 (123)
Q Consensus 24 ~~~pkC~~c~~~L~Gi~~~rp~~~~~l~k~~k~v~R~YGG~lC~~cvr 71 (123)
...+.|-.|-.|.+.+++ ++-.|--||.+|+.|--
T Consensus 899 ~~a~~cmacq~pf~afrr-------------rhhcrncggifcg~cs~ 933 (990)
T KOG1819|consen 899 EDAEQCMACQMPFNAFRR-------------RHHCRNCGGIFCGKCSC 933 (990)
T ss_pred CcchhhhhccCcHHHHHH-------------hhhhcccCceeeccccc
Confidence 356778888887766553 57789999999999985
No 39
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=20.51 E-value=59 Score=17.05 Aligned_cols=10 Identities=20% Similarity=0.747 Sum_probs=6.8
Q ss_pred CcCCCCCCCC
Q psy3939 28 RCGHCKIKLP 37 (123)
Q Consensus 28 kC~~c~~~L~ 37 (123)
.|+.||..|.
T Consensus 1 ~Cp~CG~~~~ 10 (23)
T PF13240_consen 1 YCPNCGAEIE 10 (23)
T ss_pred CCcccCCCCC
Confidence 3777877764
Done!