Query gi|254780266|ref|YP_003064679.1| 30S ribosomal protein S12 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 124
No_of_seqs 127 out of 756
Neff 3.8
Searched_HMMs 39220
Date Tue May 24 09:29:54 2011
Command /home/congqian_1/programs/hhpred/hhsearch -i 254780266.hhm -d /home/congqian_1/database/cdd/Cdd.hhm
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 CHL00051 rps12 ribosomal prote 100.0 0 0 414.3 12.2 123 1-124 1-123 (123)
2 PRK05163 rpsL 30S ribosomal pr 100.0 0 0 413.6 12.1 123 1-124 1-123 (124)
3 TIGR00981 rpsL_bact ribosomal 100.0 0 0 401.2 9.5 123 1-124 1-123 (124)
4 COG0048 RpsL Ribosomal protein 100.0 0 0 371.8 10.6 123 1-124 7-129 (129)
5 PTZ00115 40S ribosomal protein 100.0 0 0 364.7 9.5 105 19-123 113-217 (288)
6 pfam00164 Ribosomal_S12 Riboso 100.0 0 0 361.5 11.3 109 16-124 4-112 (112)
7 cd03368 Ribosomal_S12 S12-like 100.0 0 0 347.1 11.3 108 3-111 1-108 (108)
8 cd00319 Ribosomal_S12_like Rib 100.0 0 0 319.7 10.5 94 18-111 2-95 (95)
9 KOG1750 consensus 100.0 0 0 305.8 8.5 112 1-112 28-139 (139)
10 cd03367 Ribosomal_S23 S12-like 100.0 5.4E-43 0 272.7 10.0 102 12-113 3-114 (115)
11 PTZ00067 40S ribosomal S23; Pr 100.0 9.7E-38 2.5E-42 241.9 8.5 101 13-113 29-139 (143)
12 PRK04211 rps12P 30S ribosomal 100.0 5.6E-34 1.4E-38 219.9 7.5 102 13-114 31-143 (146)
13 TIGR00982 S23_S12_E_A ribosoma 99.9 7.8E-25 2E-29 166.4 6.8 102 14-115 25-137 (139)
14 KOG1749 consensus 99.9 1.5E-24 3.8E-29 164.8 7.0 98 15-112 31-138 (143)
15 COG0361 InfA Translation initi 88.3 0.83 2.1E-05 25.9 4.3 32 53-84 21-56 (75)
16 PRK00276 infA translation init 87.1 1.2 3.1E-05 24.9 4.5 64 30-116 8-71 (72)
17 PRK12442 translation initiatio 84.9 2 5.1E-05 23.6 4.7 65 30-117 8-72 (87)
18 CHL00010 infA translation init 83.4 2.2 5.5E-05 23.4 4.4 63 31-116 9-71 (78)
19 TIGR00008 infA translation ini 78.4 4.4 0.00011 21.6 4.6 43 53-106 19-61 (69)
20 cd04451 S1_IF1 S1_IF1: Transla 77.0 4.8 0.00012 21.4 4.4 54 32-106 4-57 (64)
21 PRK00347 sugar fermentation st 71.9 9.4 0.00024 19.7 5.2 35 50-84 17-54 (234)
22 pfam01176 eIF-1a Translation i 68.0 8.8 0.00023 19.9 4.0 32 53-84 17-51 (65)
23 TIGR02062 RNase_B exoribonucle 61.5 5.9 0.00015 20.9 2.1 48 51-100 595-654 (664)
24 pfam06246 Isy1 Isy1-like splic 60.0 2.2 5.5E-05 23.4 -0.3 11 86-96 128-138 (253)
25 pfam03749 SfsA Sugar fermentat 59.5 17 0.00042 18.3 5.0 35 50-85 5-42 (215)
26 KOG3068 consensus 58.5 2.5 6.5E-05 23.0 -0.2 14 83-96 118-135 (268)
27 COG1489 SfsA DNA-binding prote 50.9 23 0.00059 17.4 4.9 34 50-84 17-53 (235)
28 cd01726 LSm6 The eukaryotic Sm 39.9 34 0.00088 16.4 4.0 24 47-70 6-29 (67)
29 TIGR01810 betA choline dehydro 36.2 11 0.00029 19.2 0.2 24 61-84 282-305 (540)
30 PRK00737 small nuclear ribonuc 34.3 42 0.0011 15.9 3.7 26 47-72 10-35 (72)
31 COG1768 Predicted phosphohydro 32.0 42 0.0011 15.9 2.6 30 75-105 41-85 (230)
32 COG3970 Fumarylacetoacetate (F 31.3 36 0.00092 16.3 2.2 12 80-91 29-40 (379)
33 cd01722 Sm_F The eukaryotic Sm 28.3 54 0.0014 15.3 4.4 22 47-68 7-28 (68)
34 cd05793 S1_IF1A S1_IF1A: Trans 26.7 57 0.0015 15.1 4.1 31 54-84 15-48 (77)
35 PRK08393 N-ethylammeline chlor 26.0 58 0.0015 15.1 2.5 26 58-88 3-28 (419)
36 TIGR00758 UDG_fam4 uracil-DNA 24.7 39 0.00098 16.1 1.4 31 63-96 9-42 (185)
37 TIGR00337 PyrG CTP synthase; I 24.4 44 0.0011 15.8 1.6 19 76-94 141-160 (571)
38 KOG1646 consensus 23.5 56 0.0014 15.2 2.0 33 62-97 95-127 (237)
39 KOG0784 consensus 23.3 24 0.0006 17.4 0.0 85 28-114 96-186 (375)
40 PRK02106 choline dehydrogenase 23.3 47 0.0012 15.6 1.6 23 62-84 279-301 (555)
No 1
>CHL00051 rps12 ribosomal protein S12
Probab=100.00 E-value=0 Score=414.25 Aligned_cols=123 Identities=66% Similarity=1.092 Sum_probs=119.5
Q ss_pred CCCCHHHHHCCCCCCCCCCCCCCCCCCCCCCCEEEEEEEECCCCCCCCCCCEEEEEEECCCCEEEEEECCCCCCCCCCCE
Q ss_conf 95502354268737864666677000686212478756751845674424328899966996999980788875464678
Q gi|254780266|r 1 MPTVNQLIRKPRKGSFRACAKVTALRGNPQKRGVCLRVYTVTPKKPNSALRKVIKARLTSGVEVIAYVPGEGHNLQEHSV 80 (124)
Q Consensus 1 MpTinQlir~~Rkk~~~~~~K~~~L~~~PqkkGVclkv~~~~PKKPNSA~RKvarV~Lsng~~v~ayIPGeGhnlqehs~ 80 (124)
|||||||++++|+++. .+.+++||++|||++|||+++++++|||||||+||||+|+||||++|+||||||||||||||+
T Consensus 1 M~TinQl~r~~r~~~~-~k~k~~aL~~~Pq~kGvclkv~~~tPKKPNSA~RKvakVrLsng~~v~ayIPGeghnlqehs~ 79 (123)
T CHL00051 1 MPTIKQLIRNTRQPIR-NKTKSPALRGCPQRRGTCTRVYTITPKKPNSALRKVARVRLTSGFEITAYIPGIGHNLQEHSV 79 (123)
T ss_pred CCCHHHHHHCCCCCCC-CCCCCCCCCCCCCCCEEEEEEEEECCCCCCCCCCEEEEEEECCCCEEEEECCCCCCCCCCCCE
T ss_conf 9657787633776665-557685224796525588998750678998310217999953898999981798768531578
Q ss_pred EEEECCCCCCCCCCEEEEEECCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf 99953783888875478980400144334200121125610789
Q gi|254780266|r 81 VMLCGGRVKDLPGVKYRVIRGVLDAQGVKNRKQARSRYGAERPK 124 (124)
Q Consensus 81 VLvrGGrv~DlPGVry~ivRG~~D~~gv~~Rk~~RSkYG~kkpk 124 (124)
|||||||++|||||+||+|||+|||+||.+|+++|||||+|+||
T Consensus 80 VLvrGGrv~DLPGVky~ivRG~~D~~gv~~R~~~RSkYG~KkpK 123 (123)
T CHL00051 80 VLVRGGRVKDLPGVRYHIVRGTLDAVGVKDRQQGRSKYGVKKPK 123 (123)
T ss_pred EEEECCCCCCCCCCEEEEEEEEECCCCCCCCCCCCCCCCCCCCC
T ss_conf 99938876879983279960420255446552134315667899
No 2
>PRK05163 rpsL 30S ribosomal protein S12; Validated
Probab=100.00 E-value=0 Score=413.60 Aligned_cols=123 Identities=70% Similarity=1.131 Sum_probs=119.6
Q ss_pred CCCCHHHHHCCCCCCCCCCCCCCCCCCCCCCCEEEEEEEECCCCCCCCCCCEEEEEEECCCCEEEEEECCCCCCCCCCCE
Q ss_conf 95502354268737864666677000686212478756751845674424328899966996999980788875464678
Q gi|254780266|r 1 MPTVNQLIRKPRKGSFRACAKVTALRGNPQKRGVCLRVYTVTPKKPNSALRKVIKARLTSGVEVIAYVPGEGHNLQEHSV 80 (124)
Q Consensus 1 MpTinQlir~~Rkk~~~~~~K~~~L~~~PqkkGVclkv~~~~PKKPNSA~RKvarV~Lsng~~v~ayIPGeGhnlqehs~ 80 (124)
|||||||++++|+++. ++.++++|++|||++|||++|++++|||||||+||||+|+||||++|+||||||||||||||+
T Consensus 1 M~T~nQl~r~~r~kk~-~k~k~paL~~~Pq~kGvc~kv~~~~PKKPNSA~RKvakVrLsng~~v~ayIPGeGHnlqeHs~ 79 (124)
T PRK05163 1 MPTINQLVRKGRKSKV-KKSKSPALEACPQKRGVCTRVYTTTPKKPNSALRKVARVRLTNGFEVTAYIPGEGHNLQEHSV 79 (124)
T ss_pred CCCHHHHHHCCCCCCC-CCCCCCCCCCCCCCCEEEEEEEEECCCCCCCCCCEEEEEEECCCCEEEEECCCCCCCCCCCCE
T ss_conf 9657787634787766-556680002796525488997750568998521207999952898999980899877631578
Q ss_pred EEEECCCCCCCCCCEEEEEECCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf 99953783888875478980400144334200121125610789
Q gi|254780266|r 81 VMLCGGRVKDLPGVKYRVIRGVLDAQGVKNRKQARSRYGAERPK 124 (124)
Q Consensus 81 VLvrGGrv~DlPGVry~ivRG~~D~~gv~~Rk~~RSkYG~kkpk 124 (124)
|||||||++|||||+||+|||+|||+||.+|+++|||||+|+||
T Consensus 80 VLvrGGrvkDLPGVky~iVRG~~D~~gv~~R~~~RSkYG~KkpK 123 (124)
T PRK05163 80 VLIRGGRVKDLPGVRYHIVRGALDTAGVKDRKQGRSKYGAKRPK 123 (124)
T ss_pred EEEECCCCCCCCCCEEEEEEEECCCCCCCCCCCCCCCCCCCCCC
T ss_conf 99948876879983289960520254446552134315657889
No 3
>TIGR00981 rpsL_bact ribosomal protein S12; InterPro: IPR005679 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 of 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 , . Ribosomal protein S12 is one of the proteins from the small ribosomal subunit. In Escherichia coli, S12 is known to be involved in the translation initiation step. It is a very basic protein of 120 to 150 amino-acid residues. S12 belongs to a family of ribosomal proteins which are grouped on the basis of sequence similarities. This family consists of ribosomal protein S12 from bacteria, mitochondria, and chloroplasts.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0015935 small ribosomal subunit.
Probab=100.00 E-value=0 Score=401.23 Aligned_cols=123 Identities=72% Similarity=1.132 Sum_probs=119.7
Q ss_pred CCCCHHHHHCCCCCCCCCCCCCCCCCCCCCCCEEEEEEEECCCCCCCCCCCEEEEEEECCCCEEEEEECCCCCCCCCCCE
Q ss_conf 95502354268737864666677000686212478756751845674424328899966996999980788875464678
Q gi|254780266|r 1 MPTVNQLIRKPRKGSFRACAKVTALRGNPQKRGVCLRVYTVTPKKPNSALRKVIKARLTSGVEVIAYVPGEGHNLQEHSV 80 (124)
Q Consensus 1 MpTinQlir~~Rkk~~~~~~K~~~L~~~PqkkGVclkv~~~~PKKPNSA~RKvarV~Lsng~~v~ayIPGeGhnlqehs~ 80 (124)
|||||||+|..|.... .+.++|+|+.|||++|||++|+|++|||||||+||+|+|+|||+.+|+||||||||||||||+
T Consensus 1 mpT~~Ql~r~~r~~~~-~~~~~paL~~~P~krGvc~~V~t~tPkKPNSAlRK~a~vrL~~~~~V~aYIpG~gH~lqEHs~ 79 (124)
T TIGR00981 1 MPTINQLIRKGRKKKV-KKSKSPALEKCPQKRGVCTRVYTVTPKKPNSALRKVARVRLTNGFEVTAYIPGEGHNLQEHSV 79 (124)
T ss_pred CCCHHHHHCCCCHHHH-HHHCCCHHHHCCCCCCEEEEEEEECCCCCCHHHCCEEEEEECCCCEEEEEECCCCCCCCCCCE
T ss_conf 9303645505530222-310240456088767737887753599986201314678724884898851887766443327
Q ss_pred EEEECCCCCCCCCCEEEEEECCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf 99953783888875478980400144334200121125610789
Q gi|254780266|r 81 VMLCGGRVKDLPGVKYRVIRGVLDAQGVKNRKQARSRYGAERPK 124 (124)
Q Consensus 81 VLvrGGrv~DlPGVry~ivRG~~D~~gv~~Rk~~RSkYG~kkpk 124 (124)
||||||||+|||||+||||||.+|+.||.+|+++||+||+|+|+
T Consensus 80 vl~rGGrv~dLPGVrYhivrGa~D~~GV~~R~~~Rs~YG~k~~~ 123 (124)
T TIGR00981 80 VLVRGGRVKDLPGVRYHIVRGALDTAGVKNRKQSRSKYGAKKPK 123 (124)
T ss_pred EEECCCEECCCCCCEEEEEECCCCHHHHHHHHHCCCCCCCCCCC
T ss_conf 88507844278983279984551013465432011104744788
No 4
>COG0048 RpsL Ribosomal protein S12 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=0 Score=371.81 Aligned_cols=123 Identities=67% Similarity=1.089 Sum_probs=119.1
Q ss_pred CCCCHHHHHCCCCCCCCCCCCCCCCCCCCCCCEEEEEEEECCCCCCCCCCCEEEEEEECCCCEEEEEECCCCCCCCCCCE
Q ss_conf 95502354268737864666677000686212478756751845674424328899966996999980788875464678
Q gi|254780266|r 1 MPTVNQLIRKPRKGSFRACAKVTALRGNPQKRGVCLRVYTVTPKKPNSALRKVIKARLTSGVEVIAYVPGEGHNLQEHSV 80 (124)
Q Consensus 1 MpTinQlir~~Rkk~~~~~~K~~~L~~~PqkkGVclkv~~~~PKKPNSA~RKvarV~Lsng~~v~ayIPGeGhnlqehs~ 80 (124)
|+|+||++|..|+.. ..+.|+|||++|||++|||++++++||||||||+||||||||+||++||||||||||||||||+
T Consensus 7 m~t~~q~~R~~rr~~-~~k~Ks~~L~g~Pq~RGV~~~v~~~~pKkPNSAlRK~~RVrL~NG~~VtAyiPg~Gh~lqEH~~ 85 (129)
T COG0048 7 MPTINQLVRKKRRSL-GLKSKSPALEGAPQARGVCTRVYTVTPKKPNSALRKVARVRLINGKEVTAYIPGEGHNLQEHSE 85 (129)
T ss_pred HHHHHHHHHCCCCCC-CCCCCCCCCCCCCCCCEEEEEEEECCCCCCCHHHHEEEEEEEECCCEEEEECCCCCCCCCCCCE
T ss_conf 257777764144312-4224477334797405578998752548977655206899952696999975789854353578
Q ss_pred EEEECCCCCCCCCCEEEEEECCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf 99953783888875478980400144334200121125610789
Q gi|254780266|r 81 VMLCGGRVKDLPGVKYRVIRGVLDAQGVKNRKQARSRYGAERPK 124 (124)
Q Consensus 81 VLvrGGrv~DlPGVry~ivRG~~D~~gv~~Rk~~RSkYG~kkpk 124 (124)
|||||||++||||||||||||.+|.++|..|.++||+||+|+||
T Consensus 86 Vli~G~~v~DlPGVRy~vvrg~~ds~gv~~r~~~rs~yg~k~~k 129 (129)
T COG0048 86 VLIRGGRVKDLPGVRYKVVRGALDSLGVLDRGQKRSKYGAKRPK 129 (129)
T ss_pred EEEECCCCCCCCCCEEEEEEECCHHHHHHHHCCCCCCCCCCCCC
T ss_conf 99966765888971589998723012323313233645566899
No 5
>PTZ00115 40S ribosomal protein S12; Provisional
Probab=100.00 E-value=0 Score=364.73 Aligned_cols=105 Identities=49% Similarity=0.850 Sum_probs=101.6
Q ss_pred CCCCCCCCCCCCCCEEEEEEEECCCCCCCCCCCEEEEEEECCCCEEEEEECCCCCCCCCCCEEEEECCCCCCCCCCEEEE
Q ss_conf 66677000686212478756751845674424328899966996999980788875464678999537838888754789
Q gi|254780266|r 19 CAKVTALRGNPQKRGVCLRVYTVTPKKPNSALRKVIKARLTSGVEVIAYVPGEGHNLQEHSVVMLCGGRVKDLPGVKYRV 98 (124)
Q Consensus 19 ~~K~~~L~~~PqkkGVclkv~~~~PKKPNSA~RKvarV~Lsng~~v~ayIPGeGhnlqehs~VLvrGGrv~DlPGVry~i 98 (124)
+.++.+|+||||++|||++|+|++|||||||+||||+|+||||++|+||||||||||||||+||||||||+|||||+||+
T Consensus 113 ~~rs~~LegcPQKkGVC~kV~t~tPKKPNSAlRKvAkVrLsng~~v~aYIPGeGHnLQEHsvVLVRGGRvkDLPGVkY~i 192 (288)
T PTZ00115 113 NRRSCWLEGAPQKKGICVTVRVVTPRKPNSGLRKVARVRLSTGRTVTCHIPGIGHNLHTHSVVLVRGGRCQDVSGCHYKV 192 (288)
T ss_pred HHHHHHHHCCCCCCEEEEEEEECCCCCCCCHHCCEEEEECCCCCEEEEECCCCCCCCCCCCEEEEECCCCCCCCCCEEEE
T ss_conf 04556652598316488996766999987211016999956998899972688757520327999588767799851799
Q ss_pred EECCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf 8040014433420012112561078
Q gi|254780266|r 99 IRGVLDAQGVKNRKQARSRYGAERP 123 (124)
Q Consensus 99 vRG~~D~~gv~~Rk~~RSkYG~kkp 123 (124)
|||+||++||.+|+++|||||+|-+
T Consensus 193 VRG~~D~~gV~~Rk~sRSKYG~Kl~ 217 (288)
T PTZ00115 193 VRGKYDLLPVKNRASSRSKYGVKLS 217 (288)
T ss_pred EEECCCCCCCCCCCCCCCCCCCCCC
T ss_conf 6030234344655333322451674
No 6
>pfam00164 Ribosomal_S12 Ribosomal protein S12.
Probab=100.00 E-value=0 Score=361.49 Aligned_cols=109 Identities=68% Similarity=1.127 Sum_probs=106.1
Q ss_pred CCCCCCCCCCCCCCCCCEEEEEEEECCCCCCCCCCCEEEEEEECCCCEEEEEECCCCCCCCCCCEEEEECCCCCCCCCCE
Q ss_conf 64666677000686212478756751845674424328899966996999980788875464678999537838888754
Q gi|254780266|r 16 FRACAKVTALRGNPQKRGVCLRVYTVTPKKPNSALRKVIKARLTSGVEVIAYVPGEGHNLQEHSVVMLCGGRVKDLPGVK 95 (124)
Q Consensus 16 ~~~~~K~~~L~~~PqkkGVclkv~~~~PKKPNSA~RKvarV~Lsng~~v~ayIPGeGhnlqehs~VLvrGGrv~DlPGVr 95 (124)
+..+.|++||++|||++|||+++++++|||||||+||||+|+|+||++||||||||||||||||+|||||||++|||||+
T Consensus 4 ~~~k~k~~~L~g~Pq~kGi~l~v~~~~pKKPNSA~RKvarV~L~ng~~vtayIPG~Gh~lqehs~VLVrGgrv~DlPGVr 83 (112)
T pfam00164 4 LGLKTKSPALEGCPQKRGVCLEVYTITPKKPNSALRKVARVRLINGKEVTAYIPGDGHNLQEHSEVLIRGGRVKDLPGVR 83 (112)
T ss_pred CCCCCCCCCCCCCCCCCEEEEEEEECCCCCCCHHHEEEEEEEECCCCEEEEEECCCCCCCCCCCEEEEECCCCCCCCCCE
T ss_conf 34334588546897516588886640679998003018999904998999982899778543788999488768899740
Q ss_pred EEEEECCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf 78980400144334200121125610789
Q gi|254780266|r 96 YRVIRGVLDAQGVKNRKQARSRYGAERPK 124 (124)
Q Consensus 96 y~ivRG~~D~~gv~~Rk~~RSkYG~kkpk 124 (124)
||+|||+|||+||.+|+++|||||+|+||
T Consensus 84 ykivrG~~D~~gv~~r~~~RSkyG~kkpk 112 (112)
T pfam00164 84 YKVVRGALDVAGVSDRKQARSKYGKEKPK 112 (112)
T ss_pred EEEEEEECCCCCCCCCCCCCCCCCCCCCC
T ss_conf 89972300263446320023114666899
No 7
>cd03368 Ribosomal_S12 S12-like family, 30S ribosomal protein S12 subfamily; S12 is located at the interface of the large and small ribosomal subunits of prokaryotes, chloroplasts and mitochondria, where it plays an important role in both tRNA and ribosomal subunit interactions. S12 is essential for maintenance of a pretranslocation state and, together with S13, functions as a control element for the rRNA- and tRNA-driven movements of translocation. Antibiotics such as streptomycin bind S12 and cause the ribosome to misread the genetic code.
Probab=100.00 E-value=0 Score=347.11 Aligned_cols=108 Identities=70% Similarity=1.107 Sum_probs=103.9
Q ss_pred CCHHHHHCCCCCCCCCCCCCCCCCCCCCCCEEEEEEEECCCCCCCCCCCEEEEEEECCCCEEEEEECCCCCCCCCCCEEE
Q ss_conf 50235426873786466667700068621247875675184567442432889996699699998078887546467899
Q gi|254780266|r 3 TVNQLIRKPRKGSFRACAKVTALRGNPQKRGVCLRVYTVTPKKPNSALRKVIKARLTSGVEVIAYVPGEGHNLQEHSVVM 82 (124)
Q Consensus 3 TinQlir~~Rkk~~~~~~K~~~L~~~PqkkGVclkv~~~~PKKPNSA~RKvarV~Lsng~~v~ayIPGeGhnlqehs~VL 82 (124)
|+|||++++|+++. .+.++++|++|||++|||+++++++|||||||+||||+|+||||++||||||||||||||||+||
T Consensus 1 T~nQl~~~~r~~~~-~k~k~~aL~g~Pq~kGi~l~v~~~~pKKPNSA~RKvarV~Lsng~~vtAyIPG~ghnlqehs~VL 79 (108)
T cd03368 1 TINQLIRKGRKKKK-KKSKSPALEGCPQKKGVCLKVYTTTPKKPNSALRKVARVRLSNGKEVTAYIPGEGHNLQEHSVVL 79 (108)
T ss_pred CCHHHHCCCCCCCC-CCCCCCCCCCCCCCCEEEEEEEECCCCCCCCCCCEEEEEEECCCCEEEEEECCCCCCCCCCCEEE
T ss_conf 91154134887766-55778322379762569988765166899841001799992389899998068877755478899
Q ss_pred EECCCCCCCCCCEEEEEECCCCCCCCCCC
Q ss_conf 95378388887547898040014433420
Q gi|254780266|r 83 LCGGRVKDLPGVKYRVIRGVLDAQGVKNR 111 (124)
Q Consensus 83 vrGGrv~DlPGVry~ivRG~~D~~gv~~R 111 (124)
|||||++|||||+||+|||+|||+||.+|
T Consensus 80 vrGGrv~DlPGVry~vvrG~~D~~gv~~R 108 (108)
T cd03368 80 VRGGRVKDLPGVRYHIVRGVLDLAGVKNR 108 (108)
T ss_pred EECCCCCCCCCCEEEEEEEEECCCCCCCC
T ss_conf 95877788998348996063115565689
No 8
>cd00319 Ribosomal_S12_like Ribosomal protein S12-like family; composed of prokaryotic 30S ribosomal protein S12, eukaryotic 40S ribosomal protein S23 and similar proteins. S12 and S23 are located at the interface of the large and small ribosomal subunits, adjacent to the decoding center. They play an important role in translocation during the peptide elongation step of protein synthesis. They are also involved in important RNA and protein interactions. Ribosomal protein S12 is essential for maintenance of a pretranslocation state and, together with S13, functions as a control element for the rRNA- and tRNA-driven movements of translocation. S23 interacts with domain III of the eukaryotic elongation factor 2 (eEF2), which catalyzes translocation. Mutations in S12 and S23 have been found to affect translational accuracy. Antibiotics such as streptomycin may also bind S12/S23 and cause the ribosome to misread the genetic code.
Probab=100.00 E-value=0 Score=319.72 Aligned_cols=94 Identities=72% Similarity=1.132 Sum_probs=91.5
Q ss_pred CCCCCCCCCCCCCCCEEEEEEEECCCCCCCCCCCEEEEEEECCCCEEEEEECCCCCCCCCCCEEEEECCCCCCCCCCEEE
Q ss_conf 66667700068621247875675184567442432889996699699998078887546467899953783888875478
Q gi|254780266|r 18 ACAKVTALRGNPQKRGVCLRVYTVTPKKPNSALRKVIKARLTSGVEVIAYVPGEGHNLQEHSVVMLCGGRVKDLPGVKYR 97 (124)
Q Consensus 18 ~~~K~~~L~~~PqkkGVclkv~~~~PKKPNSA~RKvarV~Lsng~~v~ayIPGeGhnlqehs~VLvrGGrv~DlPGVry~ 97 (124)
++.++++|++|||++|||+++++++|||||||+||||+|+|+||++||||||||||||||||+|||||||++|||||+||
T Consensus 2 ~k~k~~~L~g~Pq~kGi~l~v~~~~pKKPNSA~RKvarV~L~ng~~vtayIPG~gh~lqeh~~VLvrGGr~~DlPGVry~ 81 (95)
T cd00319 2 KKSKVPALKGAPFRRGVCTVVRTVTPKKPNSALRKVAKVRLTSGYEVTAYIPGEGHNLQEHSVVLIRGGRVKDLPGVRYH 81 (95)
T ss_pred CCCCCCCCCCCCCCCEEEEEEEEECCCCCCCCCCCEEEEEECCCCEEEEECCCCCCCCCCCCEEEEECCCCCCCCCCEEE
T ss_conf 75448854589761668899876568998830020899996089899998288987754378899948876889983189
Q ss_pred EEECCCCCCCCCCC
Q ss_conf 98040014433420
Q gi|254780266|r 98 VIRGVLDAQGVKNR 111 (124)
Q Consensus 98 ivRG~~D~~gv~~R 111 (124)
+|||+|||+||.+|
T Consensus 82 virG~~D~~gv~~r 95 (95)
T cd00319 82 IVRGVYDAAGVKDR 95 (95)
T ss_pred EEEEEECCCCCCCC
T ss_conf 97260025565689
No 9
>KOG1750 consensus
Probab=100.00 E-value=0 Score=305.80 Aligned_cols=112 Identities=59% Similarity=0.911 Sum_probs=105.0
Q ss_pred CCCCHHHHHCCCCCCCCCCCCCCCCCCCCCCCEEEEEEEECCCCCCCCCCCEEEEEEECCCCEEEEEECCCCCCCCCCCE
Q ss_conf 95502354268737864666677000686212478756751845674424328899966996999980788875464678
Q gi|254780266|r 1 MPTVNQLIRKPRKGSFRACAKVTALRGNPQKRGVCLRVYTVTPKKPNSALRKVIKARLTSGVEVIAYVPGEGHNLQEHSV 80 (124)
Q Consensus 1 MpTinQlir~~Rkk~~~~~~K~~~L~~~PqkkGVclkv~~~~PKKPNSA~RKvarV~Lsng~~v~ayIPGeGhnlqehs~ 80 (124)
|||+|||||++-...++...++++|++|||.+|||++|++++|||||||.||||+|+||||.+|+|||||||||+|||+.
T Consensus 28 m~T~nQliR~~~r~~kRr~~~~~~L~g~p~~kgvv~~v~t~~pkkPnsa~rK~~~vrlstg~~i~ayipg~ghn~qehs~ 107 (139)
T KOG1750 28 MATLNQLIRNGGRPPKRRPRKSPALDGCPQRKGVVLRVFTRKPKKPNSANRKCARVRLSTGREVTAYIPGIGHNLQEHSI 107 (139)
T ss_pred HHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCEEEEEEEEECCCCCCHHHEEEEEEEECCCHHEEEECCCCCCCCEEEEE
T ss_conf 37699998548998766776441224776323189999973489997310015678733760001237775623167789
Q ss_pred EEEECCCCCCCCCCEEEEEECCCCCCCCCCCC
Q ss_conf 99953783888875478980400144334200
Q gi|254780266|r 81 VMLCGGRVKDLPGVKYRVIRGVLDAQGVKNRK 112 (124)
Q Consensus 81 VLvrGGrv~DlPGVry~ivRG~~D~~gv~~Rk 112 (124)
||+||||++|+|||+||+|||+|||.||.+|.
T Consensus 108 Vlvrggr~qd~pgvk~~~vRg~~d~~~V~~r~ 139 (139)
T KOG1750 108 VLVRGGRVQDLPGVKYHVVRGVYDLAGVVGRI 139 (139)
T ss_pred EEEECCCCCCCCCEEEEEEEEHHHHCCCCCCC
T ss_conf 99946400116420011200012202456689
No 10
>cd03367 Ribosomal_S23 S12-like family, 40S ribosomal protein S23 subfamily; S23 is located at the interface of the large and small ribosomal subunits of eukaryotes, adjacent to the decoding center. It interacts with domain III of the eukaryotic elongation factor 2 (eEF2), which catalyzes the translocation of the growing peptidyl-tRNA to the P site to make room for the next aminoacyl-tRNA at the A (acceptor) site. Through its interaction with eEF2, S23 may play an important role in translocation. Also members of this subfamily are the archaeal 30S ribosomal S12 proteins. Prokaryotic S12 is essential for maintenance of a pretranslocation state and, together with S13, functions as control element for the rRNA- and tRNA-driven movements of translocation. S12 and S23 are also implicated in translation accuracy. Antibiotics such as streptomycin bind S12/S23 and cause the ribosome to misread the genetic code.
Probab=100.00 E-value=5.4e-43 Score=272.68 Aligned_cols=102 Identities=34% Similarity=0.647 Sum_probs=94.6
Q ss_pred CCCCCCCCCCCCCCCCCCCCCEEEEEEEECCCCCCCCCCCEEEEEEE-CCCCEEEEEECCCC--CCCCCCCEEEE-----
Q ss_conf 73786466667700068621247875675184567442432889996-69969999807888--75464678999-----
Q gi|254780266|r 12 RKGSFRACAKVTALRGNPQKRGVCLRVYTVTPKKPNSALRKVIKARL-TSGVEVIAYVPGEG--HNLQEHSVVML----- 83 (124)
Q Consensus 12 Rkk~~~~~~K~~~L~~~PqkkGVclkv~~~~PKKPNSA~RKvarV~L-sng~~v~ayIPGeG--hnlqehs~VLv----- 83 (124)
+++.+..+.|+++|++|||++|||+++++++|||||||+|||||||| +||++||||||||| |||||||+|||
T Consensus 3 ~r~~~~~~~K~~pl~g~pq~kGIvl~~~~~~pKkPNSA~RK~~rVqL~kngk~vtAyiPg~G~~h~lqEh~~Vlv~g~g~ 82 (115)
T cd03367 3 KKRHLGTKYKADPLGGAPHAKGIVLEKVGVEAKQPNSAIRKCVRVQLIKNGKKITAFVPGDGCLNFIDENDEVLVAGFGR 82 (115)
T ss_pred CCCCCCCCCCCCCCCCCCCCCEEEEEEEEECCCCCCCCEEEEEEEEECCCCEEEEEEECCCCCCCCCCCCCEEEEEECCC
T ss_conf 31201741257855689651668999988534899741017999999149919999917998424356488999972277
Q ss_pred ECCCCCCCCCCEEEEEE--CCCCCCCCCCCCC
Q ss_conf 53783888875478980--4001443342001
Q gi|254780266|r 84 CGGRVKDLPGVKYRVIR--GVLDAQGVKNRKQ 113 (124)
Q Consensus 84 rGGrv~DlPGVry~ivR--G~~D~~gv~~Rk~ 113 (124)
+|++++|||||+||+|| |+.+.+.+.+++.
T Consensus 83 ~G~~v~DlPGVrykvvrV~~vsl~~l~~gkke 114 (115)
T cd03367 83 KGRAVGDIPGVRFKVVKVNGVSLLALFKGKKE 114 (115)
T ss_pred CCCCCCCCCCEEEEEEEECCEEHHHHHCCCCC
T ss_conf 88725879970689999988668997513035
No 11
>PTZ00067 40S ribosomal S23; Provisional
Probab=100.00 E-value=9.7e-38 Score=241.92 Aligned_cols=101 Identities=31% Similarity=0.633 Sum_probs=92.0
Q ss_pred CCCCCCCCCCCCCCCCCCCCEEEEEEEECCCCCCCCCCCEEEEEEE-CCCCEEEEEECCCC--CCCCCCCEEEEEC-CC-
Q ss_conf 3786466667700068621247875675184567442432889996-69969999807888--7546467899953-78-
Q gi|254780266|r 13 KGSFRACAKVTALRGNPQKRGVCLRVYTVTPKKPNSALRKVIKARL-TSGVEVIAYVPGEG--HNLQEHSVVMLCG-GR- 87 (124)
Q Consensus 13 kk~~~~~~K~~~L~~~PqkkGVclkv~~~~PKKPNSA~RKvarV~L-sng~~v~ayIPGeG--hnlqehs~VLvrG-Gr- 87 (124)
+..+....|+++|+|+||++||||++++++|||||||+|||+|||| +||++||||||||| |||||||+|||+| ||
T Consensus 29 k~~lg~~~K~~Pl~Gap~akGIvlekv~veaKqPNSAiRKcvrVqLikNgk~vtAfvPgdG~l~~i~EhdeVlv~g~Gr~ 108 (143)
T PTZ00067 29 KAHTGTRYKANPFGGSSHAKGIVVEKIGVEAKQPNSAVRKCVRVQLIKNGKKITAFVPNDGCLNFIEENDEVLVAGFGRS 108 (143)
T ss_pred HHHHCCCCCCCCCCCCCCCCEEEEEEEEEECCCCCHHHHEEEEEEEECCCCEEEEEECCCCCCCCCCCCCEEEEEECCCC
T ss_conf 87616520038768985405278999885025886012158999991499199999169963112566888999833757
Q ss_pred ---CCCCCCCEEEEEE--CCCCCCCCCCCCC
Q ss_conf ---3888875478980--4001443342001
Q gi|254780266|r 88 ---VKDLPGVKYRVIR--GVLDAQGVKNRKQ 113 (124)
Q Consensus 88 ---v~DlPGVry~ivR--G~~D~~gv~~Rk~ 113 (124)
++|||||+|++|. |+.-.+.+.+++.
T Consensus 109 G~s~gDiPGVr~kvvkV~~vSL~aL~kgkkE 139 (143)
T PTZ00067 109 GHAVGDIPGVRFKIVKVSGVSLLALYRQKKE 139 (143)
T ss_pred CCCCCCCCCEEEEEEEECCEEHHHHHHCCCC
T ss_conf 7756889960799999998879999704132
No 12
>PRK04211 rps12P 30S ribosomal protein S12P; Reviewed
Probab=100.00 E-value=5.6e-34 Score=219.91 Aligned_cols=102 Identities=37% Similarity=0.682 Sum_probs=91.2
Q ss_pred CCCCCCCCCCCCCCCCCCCCEEEEEEEECCCCCCCCCCCEEEEEEE-CCCCEEEEEECCCC--CCCCCCCEEEEEC----
Q ss_conf 3786466667700068621247875675184567442432889996-69969999807888--7546467899953----
Q gi|254780266|r 13 KGSFRACAKVTALRGNPQKRGVCLRVYTVTPKKPNSALRKVIKARL-TSGVEVIAYVPGEG--HNLQEHSVVMLCG---- 85 (124)
Q Consensus 13 kk~~~~~~K~~~L~~~PqkkGVclkv~~~~PKKPNSA~RKvarV~L-sng~~v~ayIPGeG--hnlqehs~VLvrG---- 85 (124)
++.+....|+++|+|+||++||||+++.+++||||||+|||+|||| +||++||||+||+| |+|||||+|||.|
T Consensus 31 kr~lg~~~K~dPl~GapqAkGIVlEKvgvEakqPnSa~RKcvrVqLikNgk~vtAfvPgdgal~~i~ehdeV~v~g~gGr 110 (146)
T PRK04211 31 RRMLGLKEKADPLEGAPQARGIVLEKVGVEAKQPNSAIRKCVRVQLIKNGRQVTAFAPGDGAINFIDEHDEVVIEGIGGP 110 (146)
T ss_pred HHHHCCCCCCCCCCCCCCCCEEEEEEEEEECCCCCHHHHHEEEEEEECCCCEEEEEECCCCCCCCCCCCCEEEEEECCCC
T ss_conf 98857520138667875425269999986125987654116799994389599999358853112556888999743655
Q ss_pred --CCCCCCCCCEEEEEE--CCCCCCCCCCCCCC
Q ss_conf --783888875478980--40014433420012
Q gi|254780266|r 86 --GRVKDLPGVKYRVIR--GVLDAQGVKNRKQA 114 (124)
Q Consensus 86 --Grv~DlPGVry~ivR--G~~D~~gv~~Rk~~ 114 (124)
+.++|||||+|+||. |+.-.+.+.+++..
T Consensus 111 ~g~s~gDiPGVr~kVvkVngvsL~al~kgkkEK 143 (146)
T PRK04211 111 MGRSMGDIPGVRYKVVKVNGVSLRELVRGRKEK 143 (146)
T ss_pred CCCCCCCCCCEEEEEEEECCEEHHHHHCCCCCC
T ss_conf 677657788706899999786799997052224
No 13
>TIGR00982 S23_S12_E_A ribosomal protein S23 (S12); InterPro: IPR005680 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 of 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 , . Ribosomal protein S12 is one of the proteins from the small ribosomal subunit. In Escherichia coli, S12 is known to be involved in the translation initiation step. It is a very basic protein of 120 to 150 amino-acid residues. S12 belongs to a family of ribosomal proteins which are grouped on the basis of sequence similarities. This family represents the eukaryotic and archaeal homologs of bacterial ribosomal protein S12. This protein is known typically as S23 in eukaryotes and as either S12 or S23 in the Archaea.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0015935 small ribosomal subunit.
Probab=99.91 E-value=7.8e-25 Score=166.44 Aligned_cols=102 Identities=40% Similarity=0.692 Sum_probs=86.5
Q ss_pred CCCCCCCCCCCCCCCCCCCEEEEEEEECCCCCCCCCCCEEEEEEE-CCCCEEEEEECCCC--CCCCCCCEEEEEC--CC-
Q ss_conf 786466667700068621247875675184567442432889996-69969999807888--7546467899953--78-
Q gi|254780266|r 14 GSFRACAKVTALRGNPQKRGVCLRVYTVTPKKPNSALRKVIKARL-TSGVEVIAYVPGEG--HNLQEHSVVMLCG--GR- 87 (124)
Q Consensus 14 k~~~~~~K~~~L~~~PqkkGVclkv~~~~PKKPNSA~RKvarV~L-sng~~v~ayIPGeG--hnlqehs~VLvrG--Gr- 87 (124)
+.+....|.++|+|+|+++||+++.+.++.++||||+|||+||+| .|++.||||+|++| .+++||++|+|++ |.
T Consensus 25 r~l~l~~k~dPleGaP~arGivlek~~~ea~qPns~~rk~vrvql~kn~~~~taf~P~dG~i~f~dehdev~~e~iGG~~ 104 (139)
T TIGR00982 25 RVLRLKEKADPLEGAPQARGIVLEKVGVEAKQPNSALRKAVRVQLIKNGKVVTAFVPGDGAINFIDEHDEVIVEGIGGPK 104 (139)
T ss_pred HHHHHHHCCCCCCCCCCCCCEEEEEEEEECCCCCHHHHHEEEEEEEECCCEEEEEECCCCCEEEEECCCEEEEECCCCCC
T ss_conf 43222110576467855352576532210128602331112245652573688870689834454246607884357888
Q ss_pred ---CCCCCCCEEEEEE--CCCCCCCCCCCCCCC
Q ss_conf ---3888875478980--400144334200121
Q gi|254780266|r 88 ---VKDLPGVKYRVIR--GVLDAQGVKNRKQAR 115 (124)
Q Consensus 88 ---v~DlPGVry~ivR--G~~D~~gv~~Rk~~R 115 (124)
+.|+|||+|+++. .+.--.-+.+++..+
T Consensus 105 G~smGdiPGvry~v~~vn~~sl~~l~~G~~~k~ 137 (139)
T TIGR00982 105 GRSMGDIPGVRYKVVKVNNVSLKELVKGKKEKP 137 (139)
T ss_pred CCCCCCCCCCEEEEEEECHHHHHHHHHHHHHCC
T ss_conf 873346786037988751036888862232125
No 14
>KOG1749 consensus
Probab=99.91 E-value=1.5e-24 Score=164.78 Aligned_cols=98 Identities=33% Similarity=0.647 Sum_probs=83.7
Q ss_pred CCCCCCCCCCCCCCCCCCEEEEEEEECCCCCCCCCCCEEEEEEE-CCCCEEEEEECCCC--CCCCCCCEEEEEC-C----
Q ss_conf 86466667700068621247875675184567442432889996-69969999807888--7546467899953-7----
Q gi|254780266|r 15 SFRACAKVTALRGNPQKRGVCLRVYTVTPKKPNSALRKVIKARL-TSGVEVIAYVPGEG--HNLQEHSVVMLCG-G---- 86 (124)
Q Consensus 15 ~~~~~~K~~~L~~~PqkkGVclkv~~~~PKKPNSA~RKvarV~L-sng~~v~ayIPGeG--hnlqehs~VLvrG-G---- 86 (124)
......|+.++.++++++||+|+.+.+++||||||+|||+|||| .||++||||+|-+| .+++|+++|||.| |
T Consensus 31 ~lGta~K~~pfggashAKgIvLEKigVEAKQPNSAiRKcvRvQLIkngKKITafVp~dgcln~ieendevlv~gfgrkg~ 110 (143)
T KOG1749 31 LLGTAYKSSPFGGASHAKGIVLEKIGVEAKQPNSAIRKCVRVQLIKNGKKITAFVPNDGCLNFIEENDEVLVAGFGRKGH 110 (143)
T ss_pred HHCCHHHCCCCCCCCCCCEEEEEEEEEECCCCCHHHHHHEEEEEEECCCEEEEEECCCCCEEEECCCCEEEEECCCCCCC
T ss_conf 64513322877886556446888610311497378765316645307846789826887152112587566440475675
Q ss_pred CCCCCCCCEEEEEE--CCCCCCCCCCCC
Q ss_conf 83888875478980--400144334200
Q gi|254780266|r 87 RVKDLPGVKYRVIR--GVLDAQGVKNRK 112 (124)
Q Consensus 87 rv~DlPGVry~ivR--G~~D~~gv~~Rk 112 (124)
.+.|+|||||++|. |+..++--.+.+
T Consensus 111 avgdipgvrfkvvkv~~vsl~alf~~kk 138 (143)
T KOG1749 111 AVGDIPGVRFKVVKVSGVSLLALFKEKK 138 (143)
T ss_pred CCCCCCCEEEEEEEECCCCHHHHHHCCC
T ss_conf 0367786378999970737456553444
No 15
>COG0361 InfA Translation initiation factor 1 (IF-1) [Translation, ribosomal structure and biogenesis]
Probab=88.26 E-value=0.83 Score=25.87 Aligned_cols=32 Identities=22% Similarity=0.352 Sum_probs=26.3
Q ss_pred EEEEEECCCCEEEEEECCCC--CC--CCCCCEEEEE
Q ss_conf 88999669969999807888--75--4646789995
Q gi|254780266|r 53 VIKARLTSGVEVIAYVPGEG--HN--LQEHSVVMLC 84 (124)
Q Consensus 53 varV~Lsng~~v~ayIPGeG--hn--lqehs~VLvr 84 (124)
-.+|+|.||.+++|+|||-. |+ +-+-++|+|+
T Consensus 21 ~f~v~~eng~~~~ahI~GKmr~~~i~I~~GD~V~Ve 56 (75)
T COG0361 21 RFRVELENGHERLAHISGKMRKNRIRILPGDVVLVE 56 (75)
T ss_pred EEEEEECCCCEEEEECCCCCCEEEEEECCCCEEEEE
T ss_conf 899994699699988258744004885799999997
No 16
>PRK00276 infA translation initiation factor IF-1; Validated
Probab=87.13 E-value=1.2 Score=24.92 Aligned_cols=64 Identities=30% Similarity=0.434 Sum_probs=42.1
Q ss_pred CCCEEEEEEEECCCCCCCCCCCEEEEEEECCCCEEEEEECCCCCCCCCCCEEEEECCCCCCCCCCEEEEEECCCCCCCCC
Q ss_conf 21247875675184567442432889996699699998078887546467899953783888875478980400144334
Q gi|254780266|r 30 QKRGVCLRVYTVTPKKPNSALRKVIKARLTSGVEVIAYVPGEGHNLQEHSVVMLCGGRVKDLPGVKYRVIRGVLDAQGVK 109 (124)
Q Consensus 30 qkkGVclkv~~~~PKKPNSA~RKvarV~Lsng~~v~ayIPGeGhnlqehs~VLvrGGrv~DlPGVry~ivRG~~D~~gv~ 109 (124)
+..|++++++ ||.- -+|+|.||.+|+||+.|- +|-.+.+=|||=+-++----||+. +
T Consensus 8 ~~~G~V~e~l------pn~~----F~V~Leng~~v~a~~sGK-----------mR~~~Iril~GD~V~vE~spYDlt--k 64 (72)
T PRK00276 8 EMEGTVLETL------PNAM----FRVELENGHEVLAHISGK-----------MRKNYIRILPGDKVTVELSPYDLT--K 64 (72)
T ss_pred EEEEEEEEEC------CCCE----EEEEECCCCEEEEEECHH-----------EEEEEEEECCCCEEEEEECCCCCC--C
T ss_conf 9999999985------9988----999978999999997413-----------110169975899899998866799--5
Q ss_pred CCCCCCC
Q ss_conf 2001211
Q gi|254780266|r 110 NRKQARS 116 (124)
Q Consensus 110 ~Rk~~RS 116 (124)
||..-|-
T Consensus 65 GRIv~R~ 71 (72)
T PRK00276 65 GRITYRY 71 (72)
T ss_pred EEEEEEC
T ss_conf 7899974
No 17
>PRK12442 translation initiation factor IF-1; Reviewed
Probab=84.95 E-value=2 Score=23.64 Aligned_cols=65 Identities=29% Similarity=0.415 Sum_probs=44.5
Q ss_pred CCCEEEEEEEECCCCCCCCCCCEEEEEEECCCCEEEEEECCCCCCCCCCCEEEEECCCCCCCCCCEEEEEECCCCCCCCC
Q ss_conf 21247875675184567442432889996699699998078887546467899953783888875478980400144334
Q gi|254780266|r 30 QKRGVCLRVYTVTPKKPNSALRKVIKARLTSGVEVIAYVPGEGHNLQEHSVVMLCGGRVKDLPGVKYRVIRGVLDAQGVK 109 (124)
Q Consensus 30 qkkGVclkv~~~~PKKPNSA~RKvarV~Lsng~~v~ayIPGeGhnlqehs~VLvrGGrv~DlPGVry~ivRG~~D~~gv~ 109 (124)
+..|++++++ ||. .-+|+|.||.+|+|||-|- +|--+.+=|||=+-++----||+. .
T Consensus 8 e~eG~V~e~l------pn~----~FrV~LeNg~~Vla~~sGK-----------mR~~~IrIl~GD~V~VElSpYDlt--k 64 (87)
T PRK12442 8 ELDGIVDEVL------PDS----RYRVTLENGVEVGAYASGR-----------MRKHRIRILAGDRVTLELSPYDLT--K 64 (87)
T ss_pred EEEEEEEEEC------CCC----EEEEEECCCCEEEEEEECC-----------EEEEEEEECCCCEEEEEECCCCCC--C
T ss_conf 9878999987------998----7999977998999998550-----------133027776899899998877788--7
Q ss_pred CCCCCCCC
Q ss_conf 20012112
Q gi|254780266|r 110 NRKQARSR 117 (124)
Q Consensus 110 ~Rk~~RSk 117 (124)
+|.+-|-|
T Consensus 65 GRIvyR~k 72 (87)
T PRK12442 65 GRINFRHK 72 (87)
T ss_pred EEEEEEEC
T ss_conf 48998847
No 18
>CHL00010 infA translation initiation factor 1
Probab=83.36 E-value=2.2 Score=23.43 Aligned_cols=63 Identities=27% Similarity=0.454 Sum_probs=41.6
Q ss_pred CCEEEEEEEECCCCCCCCCCCEEEEEEECCCCEEEEEECCCCCCCCCCCEEEEECCCCCCCCCCEEEEEECCCCCCCCCC
Q ss_conf 12478756751845674424328899966996999980788875464678999537838888754789804001443342
Q gi|254780266|r 31 KRGVCLRVYTVTPKKPNSALRKVIKARLTSGVEVIAYVPGEGHNLQEHSVVMLCGGRVKDLPGVKYRVIRGVLDAQGVKN 110 (124)
Q Consensus 31 kkGVclkv~~~~PKKPNSA~RKvarV~Lsng~~v~ayIPGeGhnlqehs~VLvrGGrv~DlPGVry~ivRG~~D~~gv~~ 110 (124)
..|++.++. ||. .-+|+|.||.+|+|||-|- +|--+.+=|||=+-++----||+. ++
T Consensus 9 ~eG~V~e~L------pn~----~F~V~Leng~~Vla~~sGK-----------mR~~~Iril~GD~V~VE~SpYDlt--kG 65 (78)
T CHL00010 9 MEGLVTESL------PNG----MFRVRLDNGDLVLGYISGK-----------IRRNSIRILPGDRVKVELSPYDLT--KG 65 (78)
T ss_pred EEEEEEEEC------CCC----EEEEEECCCCEEEEEECCH-----------HEECEEEECCCCEEEEEECCCCCC--CE
T ss_conf 989999986------998----8999978999999999805-----------200318974899899998756788--57
Q ss_pred CCCCCC
Q ss_conf 001211
Q gi|254780266|r 111 RKQARS 116 (124)
Q Consensus 111 Rk~~RS 116 (124)
|..-|-
T Consensus 66 RI~~R~ 71 (78)
T CHL00010 66 RIIYRL 71 (78)
T ss_pred EEEEEE
T ss_conf 899990
No 19
>TIGR00008 infA translation initiation factor IF-1; InterPro: IPR004368 This family consists of translation initiation factor IF-1 as found in bacteria and chloroplasts. This protein, about 70 residues in length, consists largely of an S1 RNA binding domain (IPR003029 from INTERPRO).; GO: 0003743 translation initiation factor activity, 0006413 translational initiation.
Probab=78.42 E-value=4.4 Score=21.61 Aligned_cols=43 Identities=28% Similarity=0.494 Sum_probs=33.0
Q ss_pred EEEEEECCCCEEEEEECCCCCCCCCCCEEEEECCCCCCCCCCEEEEEECCCCCC
Q ss_conf 889996699699998078887546467899953783888875478980400144
Q gi|254780266|r 53 VIKARLTSGVEVIAYVPGEGHNLQEHSVVMLCGGRVKDLPGVKYRVIRGVLDAQ 106 (124)
Q Consensus 53 varV~Lsng~~v~ayIPGeGhnlqehs~VLvrGGrv~DlPGVry~ivRG~~D~~ 106 (124)
-=+|.|-|+..|.|||-| .+..|+ .+=|||=+-+|----||+.
T Consensus 19 ~f~V~LeN~~~v~a~iSG---k~r~~~--------iriLpGD~V~ve~SpYdl~ 61 (69)
T TIGR00008 19 MFRVELENGHEVLAHISG---KIRKNY--------IRILPGDKVKVELSPYDLT 61 (69)
T ss_pred EEEEEECCCCEEEEEECC---EEECCE--------EEECCCCEEEEEECCCCCC
T ss_conf 269994799789899710---341351--------7554798789987136487
No 20
>cd04451 S1_IF1 S1_IF1: Translation Initiation Factor IF1, S1-like RNA-binding domain. IF1 contains an S1-like RNA-binding domain, which is found in a wide variety of RNA-associated proteins. Translation initiation includes a number of interrelated steps preceding the formation of the first peptide bond. In Escherichia coli, the initiation mechanism requires, in addition to mRNA, fMet-tRNA, and ribosomal subunits, the presence of three additional proteins (initiation factors IF1, IF2, and IF3) and at least one GTP molecule. The three initiation factors influence both the kinetics and the stability of ternary complex formation. IF1 is the smallest of the three factors. IF1 enhances the rate of 70S ribosome subunit association and dissociation and the interaction of 30S ribosomal subunit with IF2 and IF3. It stimulates 30S complex formation. In addition, by binding to the A-site of the 30S ribosomal subunit, IF1 may contribute to the fidelity of the selection of the initiation site of th
Probab=77.01 E-value=4.8 Score=21.43 Aligned_cols=54 Identities=28% Similarity=0.473 Sum_probs=34.1
Q ss_pred CEEEEEEEECCCCCCCCCCCEEEEEEECCCCEEEEEECCCCCCCCCCCEEEEECCCCCCCCCCEEEEEECCCCCC
Q ss_conf 247875675184567442432889996699699998078887546467899953783888875478980400144
Q gi|254780266|r 32 RGVCLRVYTVTPKKPNSALRKVIKARLTSGVEVIAYVPGEGHNLQEHSVVMLCGGRVKDLPGVKYRVIRGVLDAQ 106 (124)
Q Consensus 32 kGVclkv~~~~PKKPNSA~RKvarV~Lsng~~v~ayIPGeGhnlqehs~VLvrGGrv~DlPGVry~ivRG~~D~~ 106 (124)
.|++++++ ||. .-+|+|.||.+|.||+.|- + |--+.+=|||=+-++----||+.
T Consensus 4 ~G~V~e~l------pn~----~F~V~Leng~~v~a~~sGK---m--------r~~~Iril~GD~V~VE~SpYDlt 57 (64)
T cd04451 4 EGVVTEAL------PNA----MFRVELENGHEVLAHISGK---M--------RMNYIRILPGDRVKVELSPYDLT 57 (64)
T ss_pred EEEEEEEC------CCC----EEEEEECCCCEEEEEECCH---H--------EEEEEEECCCCEEEEEECCCCCC
T ss_conf 89999987------998----8999978998999997233---0--------41269845899899998866788
No 21
>PRK00347 sugar fermentation stimulation protein A; Reviewed
Probab=71.92 E-value=9.4 Score=19.71 Aligned_cols=35 Identities=29% Similarity=0.359 Sum_probs=30.2
Q ss_pred CCEEEEEEECCCCEEEEEECCCC---CCCCCCCEEEEE
Q ss_conf 43288999669969999807888---754646789995
Q gi|254780266|r 50 LRKVIKARLTSGVEVIAYVPGEG---HNLQEHSVVMLC 84 (124)
Q Consensus 50 ~RKvarV~Lsng~~v~ayIPGeG---hnlqehs~VLvr 84 (124)
.|=+|.|.|.+|.+++||+|--| .-|.+-+.||++
T Consensus 17 nRF~a~v~l~~G~~~~aH~pntGrl~~ll~pG~~v~l~ 54 (234)
T PRK00347 17 KRFLADVELDDGEEITAHCPNTGRMTGCLTPGNTVWLS 54 (234)
T ss_pred CCEEEEEEECCCCEEEEECCCCCCCCCCCCCCCEEEEE
T ss_conf 74799999899989999878987661115689899999
No 22
>pfam01176 eIF-1a Translation initiation factor 1A / IF-1. This family includes both the eukaryotic translation factor eIF-1A and the bacterial translation initiation factor IF-1.
Probab=68.04 E-value=8.8 Score=19.86 Aligned_cols=32 Identities=22% Similarity=0.362 Sum_probs=23.3
Q ss_pred EEEEEECCCCEEEEEECCCCC---CCCCCCEEEEE
Q ss_conf 889996699699998078887---54646789995
Q gi|254780266|r 53 VIKARLTSGVEVIAYVPGEGH---NLQEHSVVMLC 84 (124)
Q Consensus 53 varV~Lsng~~v~ayIPGeGh---nlqehs~VLvr 84 (124)
-.+|.+.||.+++|+|||-=- -+.+.+.|||.
T Consensus 17 ~~~V~~~dg~~~l~~i~GK~rkriwi~~GD~VlV~ 51 (65)
T pfam01176 17 RFEVELEDGHERLAHIPGKRRKRIWILRGDFVLVE 51 (65)
T ss_pred EEEEEECCCCEEEEEECCCEEEEEEECCCCEEEEE
T ss_conf 89999799999999982205457997499999999
No 23
>TIGR02062 RNase_B exoribonuclease II; InterPro: IPR011804 This family consists of exoribonuclease II (RNase II), the product of the rnb gene, as found in a number of gamma proteobacteria. In Escherichia coli, it is one of eight different exoribonucleases. It is involved in mRNA degradation and tRNA precursor end processing.; GO: 0003723 RNA binding, 0008859 exoribonuclease II activity, 0006401 RNA catabolic process.
Probab=61.45 E-value=5.9 Score=20.87 Aligned_cols=48 Identities=29% Similarity=0.459 Sum_probs=36.2
Q ss_pred CEEEEEEE-CCCCEEEEEECCCC-CCC-------CCCCEEEEECCC---CCCCCCCEEEEEE
Q ss_conf 32889996-69969999807888-754-------646789995378---3888875478980
Q gi|254780266|r 51 RKVIKARL-TSGVEVIAYVPGEG-HNL-------QEHSVVMLCGGR---VKDLPGVKYRVIR 100 (124)
Q Consensus 51 RKvarV~L-sng~~v~ayIPGeG-hnl-------qehs~VLvrGGr---v~DlPGVry~ivR 100 (124)
|-=-|||| -|| ..+|||+-= |+. ||...|+|.|-. +.|+--|...=||
T Consensus 595 R~G~Rv~LleNG--A~~FIPA~~Lh~~keel~~n~e~G~v~Ikge~~YKi~D~~~v~LtEv~ 654 (664)
T TIGR02062 595 RAGMRVRLLENG--ASAFIPAAFLHDNKEELVCNQEEGTVYIKGEVVYKIGDVIEVVLTEVR 654 (664)
T ss_pred CCCCEEEEECCC--CCHHCCHHHHCCCCCEEEEECCCCEEEEEEEEEEEEEEEEEEEEEEEE
T ss_conf 787434312056--311114344303321366506876388710789866106999984540
No 24
>pfam06246 Isy1 Isy1-like splicing family. Isy1 protein is important in the optimisation of splicing.
Probab=60.04 E-value=2.2 Score=23.43 Aligned_cols=11 Identities=73% Similarity=1.192 Sum_probs=9.9
Q ss_pred CCCCCCCCCEE
Q ss_conf 78388887547
Q gi|254780266|r 86 GRVKDLPGVKY 96 (124)
Q Consensus 86 Grv~DlPGVry 96 (124)
||++|||||+=
T Consensus 128 GrAkeLPgVkE 138 (253)
T pfam06246 128 GRAKELPGVKE 138 (253)
T ss_pred CHHHCCCCHHH
T ss_conf 05421721799
No 25
>pfam03749 SfsA Sugar fermentation stimulation protein. This family contains Sugar fermentation stimulation proteins. Which is probably a regulatory factor involved in maltose metabolism. SfsA has been shown to bind DNA and it contains a helix-turn-helix motif that probably binds DNA at its C-terminus.
Probab=59.47 E-value=17 Score=18.26 Aligned_cols=35 Identities=29% Similarity=0.332 Sum_probs=29.0
Q ss_pred CCEEEEEEECCCCEEEEEECCCC---CCCCCCCEEEEEC
Q ss_conf 43288999669969999807888---7546467899953
Q gi|254780266|r 50 LRKVIKARLTSGVEVIAYVPGEG---HNLQEHSVVMLCG 85 (124)
Q Consensus 50 ~RKvarV~Lsng~~v~ayIPGeG---hnlqehs~VLvrG 85 (124)
.|=+|.|.| +|.+++||+|.-| .-|.+-+.|+++-
T Consensus 5 nRF~a~v~~-~g~~~~aH~pntGrm~~ll~pG~~v~l~~ 42 (215)
T pfam03749 5 NRFLVDVEL-DGEVVTAHCPNTGRLTELLEPGNRVWLSR 42 (215)
T ss_pred CCEEEEEEE-CCEEEEEECCCCCCCCCCCCCCCEEEEEE
T ss_conf 757999999-99899998589767702146998999998
No 26
>KOG3068 consensus
Probab=58.51 E-value=2.5 Score=23.03 Aligned_cols=14 Identities=57% Similarity=1.018 Sum_probs=11.2
Q ss_pred EEC----CCCCCCCCCEE
Q ss_conf 953----78388887547
Q gi|254780266|r 83 LCG----GRVKDLPGVKY 96 (124)
Q Consensus 83 vrG----Grv~DlPGVry 96 (124)
+|| |+++||||||-
T Consensus 118 ~rGyrYFGaAkdLPgVrE 135 (268)
T KOG3068 118 IRGYRYFGAAKDLPGVRE 135 (268)
T ss_pred CCCCHHHHHHCCCCCHHH
T ss_conf 775022213203831799
No 27
>COG1489 SfsA DNA-binding protein, stimulates sugar fermentation [General function prediction only]
Probab=50.88 E-value=23 Score=17.43 Aligned_cols=34 Identities=32% Similarity=0.365 Sum_probs=29.2
Q ss_pred CCEEEEEEECCCCEEEEEECCCC---CCCCCCCEEEEE
Q ss_conf 43288999669969999807888---754646789995
Q gi|254780266|r 50 LRKVIKARLTSGVEVIAYVPGEG---HNLQEHSVVMLC 84 (124)
Q Consensus 50 ~RKvarV~Lsng~~v~ayIPGeG---hnlqehs~VLvr 84 (124)
.|=.|-|.|. |.+++|++|.-| +-+..-+.|+++
T Consensus 17 nRFl~dv~l~-G~~~~~H~~ntGrm~~l~~pG~~v~l~ 53 (235)
T COG1489 17 NRFLADVELD-GEEVTAHCPNTGRMTELLTPGNTVWLS 53 (235)
T ss_pred CCEEEEEEEC-CEEEEEECCCCCCCCCCCCCCCEEEEE
T ss_conf 0169999978-959999838987652136799779999
No 28
>cd01726 LSm6 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm6 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=39.89 E-value=34 Score=16.41 Aligned_cols=24 Identities=17% Similarity=0.332 Sum_probs=18.2
Q ss_pred CCCCCEEEEEEECCCCEEEEEECC
Q ss_conf 442432889996699699998078
Q gi|254780266|r 47 NSALRKVIKARLTSGVEVIAYVPG 70 (124)
Q Consensus 47 NSA~RKvarV~Lsng~~v~ayIPG 70 (124)
++++-|.+.|+|++|.+.....-.
T Consensus 6 ~~~~gk~V~VkLk~G~ey~G~L~s 29 (67)
T cd01726 6 KAIIGRPVVVKLNSGVDYRGILAC 29 (67)
T ss_pred HHCCCCEEEEEECCCCEEEEEEEE
T ss_conf 660599099998899898999998
No 29
>TIGR01810 betA choline dehydrogenase; InterPro: IPR011533 Choline dehydrogenase catalyzes the conversion of exogenously supplied choline into the intermediate glycine betaine aldehyde, as part of a two-step oxidative reaction leading to the formation of osmoprotectant betaine. This enzymatic system can be found in both Gram-positive and Gram-negative bacteria. As in Escherichia coli , Staphylococcus xylosus , and Sinorhizobium meliloti , this enzyme is found associated in a transcriptionally co-induced gene cluster with betaine aldehyde dehydrogenase, the second catalytic enzyme in this reaction. Other Gram-positive organisms have been shown to employ a different enzymatic system, utilising a soluble choline oxidase or type III alcohol dehydrogenase instead of choline dehydrogenase . This enzyme is a member of the GMC oxidoreductase family, sharing a common evolutionary origin and enzymatic reaction with alcohol dehydrogenase . Out grouping from this model, Caulobacter crescentus shares sequence homology with choline dehydrogenase, yet other genes participating in this enzymatic reaction have not currently been identified. ; GO: 0008812 choline dehydrogenase activity, 0019285 glycine betaine biosynthetic process from choline.
Probab=36.18 E-value=11 Score=19.24 Aligned_cols=24 Identities=46% Similarity=0.715 Sum_probs=19.4
Q ss_pred CCEEEEEECCCCCCCCCCCEEEEE
Q ss_conf 969999807888754646789995
Q gi|254780266|r 61 GVEVIAYVPGEGHNLQEHSVVMLC 84 (124)
Q Consensus 61 g~~v~ayIPGeGhnlqehs~VLvr 84 (124)
+-++-...||.|-|||+|=++.+.
T Consensus 282 gI~~~~~lPGVGeNl~DHlE~Y~Q 305 (540)
T TIGR01810 282 GIELKVELPGVGENLQDHLEVYLQ 305 (540)
T ss_pred CCCEEECCCCCCCCHHHHHHHHHH
T ss_conf 896065278787633435642322
No 30
>PRK00737 small nuclear ribonucleoprotein; Provisional
Probab=34.32 E-value=42 Score=15.88 Aligned_cols=26 Identities=27% Similarity=0.360 Sum_probs=19.9
Q ss_pred CCCCCEEEEEEECCCCEEEEEECCCC
Q ss_conf 44243288999669969999807888
Q gi|254780266|r 47 NSALRKVIKARLTSGVEVIAYVPGEG 72 (124)
Q Consensus 47 NSA~RKvarV~Lsng~~v~ayIPGeG 72 (124)
++++-|-+.|+|++|+++....-|.-
T Consensus 10 ~~~~~k~V~V~Lk~gr~~~G~L~~~D 35 (72)
T PRK00737 10 NNSLNSPVLVRLKGGREFRGELQGYD 35 (72)
T ss_pred HHHCCCEEEEEECCCCEEEEEEEEEC
T ss_conf 98749849999989989999999985
No 31
>COG1768 Predicted phosphohydrolase [General function prediction only]
Probab=32.03 E-value=42 Score=15.91 Aligned_cols=30 Identities=43% Similarity=0.757 Sum_probs=18.4
Q ss_pred CCCCCEEEEECCC---------------CCCCCCCEEEEEECCCCC
Q ss_conf 4646789995378---------------388887547898040014
Q gi|254780266|r 75 LQEHSVVMLCGGR---------------VKDLPGVKYRVIRGVLDA 105 (124)
Q Consensus 75 lqehs~VLvrGGr---------------v~DlPGVry~ivRG~~D~ 105 (124)
+.+-++||+-|-- ..||||.+| ++||--|.
T Consensus 41 v~~eDiVllpGDiSWaM~l~ea~~Dl~~i~~LPG~K~-m~rGNHDY 85 (230)
T COG1768 41 VSPEDIVLLPGDISWAMRLEEAEEDLRFIGDLPGTKY-MIRGNHDY 85 (230)
T ss_pred CCHHHEEEECCCCHHHEECHHHHHHHHHHHCCCCCEE-EEECCCCC
T ss_conf 7841278843652454105344431456504899679-87267763
No 32
>COG3970 Fumarylacetoacetate (FAA) hydrolase family protein [General function prediction only]
Probab=31.35 E-value=36 Score=16.29 Aligned_cols=12 Identities=50% Similarity=0.819 Sum_probs=4.4
Q ss_pred EEEEECCCCCCC
Q ss_conf 899953783888
Q gi|254780266|r 80 VVMLCGGRVKDL 91 (124)
Q Consensus 80 ~VLvrGGrv~Dl 91 (124)
.||||||++-|+
T Consensus 29 ~vlvr~g~v~di 40 (379)
T COG3970 29 PVLVRGGRVFDI 40 (379)
T ss_pred EEEEECCEEEEE
T ss_conf 489748779872
No 33
>cd01722 Sm_F The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit F is capable of forming both homo- and hetero-heptamer ring structures. To form the hetero-heptamer, Sm subunit F initially binds subunits E and G to form a trimer which then assembles onto snRNA along with the D3/B and D1/D2 heterodimers.
Probab=28.31 E-value=54 Score=15.28 Aligned_cols=22 Identities=23% Similarity=0.241 Sum_probs=16.0
Q ss_pred CCCCCEEEEEEECCCCEEEEEE
Q ss_conf 4424328899966996999980
Q gi|254780266|r 47 NSALRKVIKARLTSGVEVIAYV 68 (124)
Q Consensus 47 NSA~RKvarV~Lsng~~v~ayI 68 (124)
|++.-|-+.|+|++|.+.....
T Consensus 7 ~~~~gk~V~V~LK~G~~y~G~L 28 (68)
T cd01722 7 NDLTGKPVIVKLKWGMEYKGTL 28 (68)
T ss_pred HHCCCCEEEEEECCCCEEEEEE
T ss_conf 7607982999988998999999
No 34
>cd05793 S1_IF1A S1_IF1A: Translation initiation factor IF1A, also referred to as eIF1A in eukaryotes and aIF1A in archaea, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. IF1A is essential for translation initiation. eIF1A acts synergistically with eIF1 to mediate assembly of ribosomal initiation complexes at the initiation codon and maintain the accuracy of this process by recognizing and destabilizing aberrant preinitiation complexes from the mRNA. Without eIF1A and eIF1, 43S ribosomal preinitiation complexes can bind to the cap-proximal region, but are unable to reach the initiation codon. eIF1a also enhances the formation of 5'-terminal complexes in the presence of other translation initiation factors. This protein family is only found in eukaryotes and archaea.
Probab=26.69 E-value=57 Score=15.10 Aligned_cols=31 Identities=16% Similarity=0.323 Sum_probs=25.5
Q ss_pred EEEEECCCCEEEEEECCCC---CCCCCCCEEEEE
Q ss_conf 8999669969999807888---754646789995
Q gi|254780266|r 54 IKARLTSGVEVIAYVPGEG---HNLQEHSVVMLC 84 (124)
Q Consensus 54 arV~Lsng~~v~ayIPGeG---hnlqehs~VLvr 84 (124)
+.|..++|.+..|.|||-= ..+++-+.|||.
T Consensus 15 ~~v~c~Dg~~ri~~IrGk~rkR~wi~~gdiVLV~ 48 (77)
T cd05793 15 LEVRCFDGKKRLCRIRGKMRKRVWINEGDIVLVA 48 (77)
T ss_pred EEEEECCCCEEEEEECCCEEEEEEECCCCEEEEE
T ss_conf 9999689999999984620203696489999997
No 35
>PRK08393 N-ethylammeline chlorohydrolase; Provisional
Probab=26.05 E-value=58 Score=15.10 Aligned_cols=26 Identities=15% Similarity=0.402 Sum_probs=17.2
Q ss_pred ECCCCEEEEEECCCCCCCCCCCEEEEECCCC
Q ss_conf 6699699998078887546467899953783
Q gi|254780266|r 58 LTSGVEVIAYVPGEGHNLQEHSVVMLCGGRV 88 (124)
Q Consensus 58 Lsng~~v~ayIPGeGhnlqehs~VLvrGGrv 88 (124)
+.||..|+ |+...+-+. .|||+|||.
T Consensus 3 ikng~Vv~----~d~~~~~~~-dVlIe~g~I 28 (419)
T PRK08393 3 IKNGMVIY----GENLTVVRA-DVLIESNKI 28 (419)
T ss_pred EECCEEEE----CCCCCEECC-CEEEECCEE
T ss_conf 96869998----899855014-399999999
No 36
>TIGR00758 UDG_fam4 uracil-DNA glycosylase, family 4; InterPro: IPR005273 This well-conserved family of proteins is about 200 residues in length and homologous to the N-terminus of the DNA polymerase of phage SPO1 of Bacillus subtilis. The function of these proteins is unknown. .
Probab=24.70 E-value=39 Score=16.11 Aligned_cols=31 Identities=32% Similarity=0.641 Sum_probs=20.3
Q ss_pred EEEEEECCCCCCCCCCCEEEEEC---CCCCCCCCCEE
Q ss_conf 99998078887546467899953---78388887547
Q gi|254780266|r 63 EVIAYVPGEGHNLQEHSVVMLCG---GRVKDLPGVKY 96 (124)
Q Consensus 63 ~v~ayIPGeGhnlqehs~VLvrG---Grv~DlPGVry 96 (124)
.=|-++||||. +.+.||+=| |+.-|+-|-=|
T Consensus 9 ~rT~~VpGdG~---~~a~i~~VGEAPG~~EDr~G~PF 42 (185)
T TIGR00758 9 TRTNAVPGDGN---PDAEIMFVGEAPGREEDRKGRPF 42 (185)
T ss_pred CCCCCCCCCCC---CCCCEEEEEECCCHHHHHCCCCC
T ss_conf 37764107775---64547898547882242078983
No 37
>TIGR00337 PyrG CTP synthase; InterPro: IPR004468 CTP synthase is involved in pyrimidine ribonucleotide/ribonucleoside metabolism. The enzyme catalyzes the reaction L-glutamine + H2O + UTP + ATP = CTP + phosphate + ADP + L-glutamate. The enzyme exists as a dimer of identical chains that aggregates as a tetramer. This gene has been found circa 500 bp 5 upstream of enolase in both beta (Nitrosomonas europaea) and gamma (Escherichia coli) subdivisions of Proteobacterium .; GO: 0003883 CTP synthase activity, 0006221 pyrimidine nucleotide biosynthetic process.
Probab=24.36 E-value=44 Score=15.79 Aligned_cols=19 Identities=32% Similarity=0.557 Sum_probs=13.9
Q ss_pred CCCCEEEEE-CCCCCCCCCC
Q ss_conf 646789995-3783888875
Q gi|254780266|r 76 QEHSVVMLC-GGRVKDLPGV 94 (124)
Q Consensus 76 qehs~VLvr-GGrv~DlPGV 94 (124)
.++++|+|+ ||-|+|+=|.
T Consensus 141 ~~~Dv~IvEiGGTVGDIEs~ 160 (571)
T TIGR00337 141 SGADVVIVEIGGTVGDIESL 160 (571)
T ss_pred CCCCEEEEEECCCCCCCCCH
T ss_conf 99747999837700000362
No 38
>KOG1646 consensus
Probab=23.45 E-value=56 Score=15.17 Aligned_cols=33 Identities=27% Similarity=0.424 Sum_probs=22.2
Q ss_pred CEEEEEECCCCCCCCCCCEEEEECCCCCCCCCCEEE
Q ss_conf 699998078887546467899953783888875478
Q gi|254780266|r 62 VEVIAYVPGEGHNLQEHSVVMLCGGRVKDLPGVKYR 97 (124)
Q Consensus 62 ~~v~ayIPGeGhnlqehs~VLvrGGrv~DlPGVry~ 97 (124)
+.|-.+|-+ -||.--+.|.|+-|- +||||.--.
T Consensus 95 KSVRGcIV~--anlsvLnLvIvKkGe-kdipGLTdt 127 (237)
T KOG1646 95 KSVRGCIVS--ANLSVLNLVIVKKGE-KDIPGLTDT 127 (237)
T ss_pred CCCCCEEEC--CCCEEEEEEEECCCC-CCCCCCCCC
T ss_conf 221224532--541002456751476-557775455
No 39
>KOG0784 consensus
Probab=23.33 E-value=24 Score=17.38 Aligned_cols=85 Identities=22% Similarity=0.323 Sum_probs=58.2
Q ss_pred CCCCCEEEEEEEECCCCCCCCC------CCEEEEEEECCCCEEEEEECCCCCCCCCCCEEEEECCCCCCCCCCEEEEEEC
Q ss_conf 8621247875675184567442------4328899966996999980788875464678999537838888754789804
Q gi|254780266|r 28 NPQKRGVCLRVYTVTPKKPNSA------LRKVIKARLTSGVEVIAYVPGEGHNLQEHSVVMLCGGRVKDLPGVKYRVIRG 101 (124)
Q Consensus 28 ~PqkkGVclkv~~~~PKKPNSA------~RKvarV~Lsng~~v~ayIPGeGhnlqehs~VLvrGGrv~DlPGVry~ivRG 101 (124)
+-.+.+||++.-+-||--|-++ +|+- .-|--...-+--+||.-.--..-+.|+||----+.--|.-|-.|.|
T Consensus 96 Si~rNkValkG~i~t~~~~g~~~s~n~~LR~~--LDLyanvv~~~slpG~~tRh~~vDiviIRENTEGEYs~LEHE~VpG 173 (375)
T KOG0784 96 SIKRNKVALKGNIETPDLPGGAKSLNVKLRKE--LDLYANVVHCKSLPGVKTRHENVDIVIIRENTEGEYSGLEHESVPG 173 (375)
T ss_pred HHHHCCEEEEECCCCCCCCCCHHHHHHHHHHH--HHHHHHEEEEECCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCC
T ss_conf 98735536850225888764234667888876--5355420133026885445689548998137754324445666746
Q ss_pred CCCCCCCCCCCCC
Q ss_conf 0014433420012
Q gi|254780266|r 102 VLDAQGVKNRKQA 114 (124)
Q Consensus 102 ~~D~~gv~~Rk~~ 114 (124)
+-.+.-|..|..+
T Consensus 174 VVEsLKVvT~~ks 186 (375)
T KOG0784 174 VVESLKVVTRFKS 186 (375)
T ss_pred HHHEEEEEHHHHH
T ss_conf 3211343026406
No 40
>PRK02106 choline dehydrogenase; Validated
Probab=23.29 E-value=47 Score=15.62 Aligned_cols=23 Identities=43% Similarity=0.718 Sum_probs=16.5
Q ss_pred CEEEEEECCCCCCCCCCCEEEEE
Q ss_conf 69999807888754646789995
Q gi|254780266|r 62 VEVIAYVPGEGHNLQEHSVVMLC 84 (124)
Q Consensus 62 ~~v~ayIPGeGhnlqehs~VLvr 84 (124)
..+.+-.||.|.|||+|-.+.+.
T Consensus 279 I~~v~dlPgVG~NLqDH~~~~~~ 301 (555)
T PRK02106 279 IEVVHDLPGVGENLQDHLEVYIQ 301 (555)
T ss_pred CCEECCCCCCCHHHHCCCCEEEE
T ss_conf 95562184424113227334799
Done!