254780266

 Score =  215 bits (548), Expect = 1e-54,   Method: Compositional matrix adjust.
 Identities = 105/124 (84%), Positives = 112/124 (90%)

Query: 1   MPTVNQLIRKPRKGSFRACAKVTALRGNPQKRGVCLRVYTVTPKKPNSALRKVIKARLTS 60
           MPTVNQLIRKPRK + R CAKVTALRG+PQKRGVCLRVYT TPKKPNSALRKV K RLT+
Sbjct: 1   MPTVNQLIRKPRKSAIRTCAKVTALRGSPQKRGVCLRVYTSTPKKPNSALRKVTKVRLTN 60

Query: 61  GVEVIAYVPGEGHNLQEHSVVMLCGGRVKDLPGVKYRVIRGVLDAQGVKNRKQARSRYGA 120
           G EVI Y+PG GHNLQEHSVVMLCGGRVKDLPGVKYRV+RGVLD  GVK+RKQ+RSRYGA
Sbjct: 61  GAEVIGYIPGVGHNLQEHSVVMLCGGRVKDLPGVKYRVVRGVLDTAGVKDRKQSRSRYGA 120

Query: 121 ERPK 124
            RPK
Sbjct: 121 GRPK 124

Species: Candidatus Liberibacter solanacearum
Genus: Candidatus Liberibacter
Family: Rhizobiaceae
Order: Rhizobiales
Class: Alphaproteobacteria
Phylum: Proteobacteria
Superkingdom: Bacteria

 Score =  193 bits (490), Expect = 8e-48,   Method: Compositional matrix adjust.
 Identities = 96/124 (77%), Positives = 105/124 (84%), Gaps = 1/124 (0%)

Query: 1   MPTVNQLIRKPRKGSFRACAKVTALRGNPQKRGVCLRVYTVTPKKPNSALRKVIKARLTS 60
           MPTVNQLIRKPR    +   KV AL+ NPQKRGVC RVYT TPKKPNSALRKV K RLT+
Sbjct: 32  MPTVNQLIRKPRTAPVKRN-KVPALQANPQKRGVCTRVYTTTPKKPNSALRKVAKVRLTN 90

Query: 61  GVEVIAYVPGEGHNLQEHSVVMLCGGRVKDLPGVKYRVIRGVLDAQGVKNRKQARSRYGA 120
           G EVI Y+PGEGHNLQEHSVVM+ GGRVKDLPGV+Y +IRGVLD QGVKNRKQ RS+YGA
Sbjct: 91  GFEVIGYIPGEGHNLQEHSVVMIRGGRVKDLPGVRYHIIRGVLDTQGVKNRKQRRSKYGA 150

Query: 121 ERPK 124
           +RPK
Sbjct: 151 KRPK 154

Species: Brucella ceti
Genus: Brucella
Family: Brucellaceae
Order: Rhizobiales
Class: Alphaproteobacteria
Phylum: Proteobacteria
Superkingdom: Bacteria

 Score =  192 bits (488), Expect = 1e-47,   Method: Compositional matrix adjust.
 Identities = 96/124 (77%), Positives = 107/124 (86%), Gaps = 1/124 (0%)

Query: 1   MPTVNQLIRKPRKGSFRACAKVTALRGNPQKRGVCLRVYTVTPKKPNSALRKVIKARLTS 60
           MPTVNQLIRKPR+ + +   KV AL+ NPQKRGVC RVYT TPKKPNSALRKV K RLT+
Sbjct: 1   MPTVNQLIRKPRQANVKR-NKVPALQENPQKRGVCTRVYTTTPKKPNSALRKVAKIRLTN 59

Query: 61  GVEVIAYVPGEGHNLQEHSVVMLCGGRVKDLPGVKYRVIRGVLDAQGVKNRKQARSRYGA 120
           G EVI Y+PGEGHNLQEHSVVM+ GGRVKDLPGV+Y +IRGVLD QGVKNRKQ RS+YGA
Sbjct: 60  GFEVIGYIPGEGHNLQEHSVVMIRGGRVKDLPGVRYHIIRGVLDTQGVKNRKQRRSKYGA 119

Query: 121 ERPK 124
           +RPK
Sbjct: 120 KRPK 123

Species: Rhizobium etli
Genus: Rhizobium
Family: Rhizobiaceae
Order: Rhizobiales
Class: Alphaproteobacteria
Phylum: Proteobacteria
Superkingdom: Bacteria

 Score =  192 bits (487), Expect = 2e-47,   Method: Compositional matrix adjust.
 Identities = 96/124 (77%), Positives = 105/124 (84%), Gaps = 1/124 (0%)

Query: 1   MPTVNQLIRKPRKGSFRACAKVTALRGNPQKRGVCLRVYTVTPKKPNSALRKVIKARLTS 60
           MPTVNQLIRKPR    +   KV AL+ NPQKRGVC RVYT TPKKPNSALRKV K RLT+
Sbjct: 12  MPTVNQLIRKPRTAPVKR-NKVPALQANPQKRGVCTRVYTTTPKKPNSALRKVAKVRLTN 70

Query: 61  GVEVIAYVPGEGHNLQEHSVVMLCGGRVKDLPGVKYRVIRGVLDAQGVKNRKQARSRYGA 120
           G EVI Y+PGEGHNLQEHSVVM+ GGRVKDLPGV+Y +IRGVLD QGVKNRKQ RS+YGA
Sbjct: 71  GFEVIGYIPGEGHNLQEHSVVMIRGGRVKDLPGVRYHIIRGVLDTQGVKNRKQRRSKYGA 130

Query: 121 ERPK 124
           +RPK
Sbjct: 131 KRPK 134

Species: Brucella melitensis
Genus: Brucella
Family: Brucellaceae
Order: Rhizobiales
Class: Alphaproteobacteria
Phylum: Proteobacteria
Superkingdom: Bacteria

 Score =  192 bits (487), Expect = 2e-47,   Method: Compositional matrix adjust.
 Identities = 96/124 (77%), Positives = 106/124 (85%), Gaps = 1/124 (0%)

Query: 1   MPTVNQLIRKPRKGSFRACAKVTALRGNPQKRGVCLRVYTVTPKKPNSALRKVIKARLTS 60
           MPTVNQLIRKPR+   +   KV AL+ NPQKRGVC RVYT TPKKPNSALRKV K RLT+
Sbjct: 80  MPTVNQLIRKPRQAQVKR-NKVPALQENPQKRGVCTRVYTTTPKKPNSALRKVAKIRLTN 138

Query: 61  GVEVIAYVPGEGHNLQEHSVVMLCGGRVKDLPGVKYRVIRGVLDAQGVKNRKQARSRYGA 120
           G EVI Y+PGEGHNLQEHSVVM+ GGRVKDLPGV+Y +IRGVLD QGVKNRKQ RS+YGA
Sbjct: 139 GFEVIGYIPGEGHNLQEHSVVMIRGGRVKDLPGVRYHIIRGVLDTQGVKNRKQRRSKYGA 198

Query: 121 ERPK 124
           +RPK
Sbjct: 199 KRPK 202

Species: Agrobacterium vitis
Genus: Agrobacterium
Family: Rhizobiaceae
Order: Rhizobiales
Class: Alphaproteobacteria
Phylum: Proteobacteria
Superkingdom: Bacteria

 Score =  192 bits (487), Expect = 2e-47,   Method: Compositional matrix adjust.
 Identities = 96/124 (77%), Positives = 106/124 (85%), Gaps = 1/124 (0%)

Query: 1   MPTVNQLIRKPRKGSFRACAKVTALRGNPQKRGVCLRVYTVTPKKPNSALRKVIKARLTS 60
           MPTVNQLIRKPR+   +   KV AL+ NPQKRGVC RVYT TPKKPNSALRKV K RLT+
Sbjct: 1   MPTVNQLIRKPRQAQVKR-NKVPALQENPQKRGVCTRVYTTTPKKPNSALRKVAKIRLTN 59

Query: 61  GVEVIAYVPGEGHNLQEHSVVMLCGGRVKDLPGVKYRVIRGVLDAQGVKNRKQARSRYGA 120
           G EVI Y+PGEGHNLQEHSVVM+ GGRVKDLPGV+Y +IRGVLD QGVKNRKQ RS+YGA
Sbjct: 60  GFEVIGYIPGEGHNLQEHSVVMIRGGRVKDLPGVRYHIIRGVLDTQGVKNRKQRRSKYGA 119

Query: 121 ERPK 124
           +RPK
Sbjct: 120 KRPK 123

Species: Sinorhizobium medicae
Genus: Sinorhizobium
Family: Rhizobiaceae
Order: Rhizobiales
Class: Alphaproteobacteria
Phylum: Proteobacteria
Superkingdom: Bacteria

 Score =  192 bits (487), Expect = 2e-47,   Method: Compositional matrix adjust.
 Identities = 96/124 (77%), Positives = 105/124 (84%), Gaps = 1/124 (0%)

Query: 1   MPTVNQLIRKPRKGSFRACAKVTALRGNPQKRGVCLRVYTVTPKKPNSALRKVIKARLTS 60
           MPTVNQLIRKPR    +   KV AL+ NPQKRGVC RVYT TPKKPNSALRKV K RLT+
Sbjct: 1   MPTVNQLIRKPRTAPVKR-NKVPALQANPQKRGVCTRVYTTTPKKPNSALRKVAKVRLTN 59

Query: 61  GVEVIAYVPGEGHNLQEHSVVMLCGGRVKDLPGVKYRVIRGVLDAQGVKNRKQARSRYGA 120
           G EVI Y+PGEGHNLQEHSVVM+ GGRVKDLPGV+Y +IRGVLD QGVKNRKQ RS+YGA
Sbjct: 60  GFEVIGYIPGEGHNLQEHSVVMIRGGRVKDLPGVRYHIIRGVLDTQGVKNRKQRRSKYGA 119

Query: 121 ERPK 124
           +RPK
Sbjct: 120 KRPK 123

Species: Brucella suis
Genus: Brucella
Family: Brucellaceae
Order: Rhizobiales
Class: Alphaproteobacteria
Phylum: Proteobacteria
Superkingdom: Bacteria

 Score =  191 bits (486), Expect = 2e-47,   Method: Compositional matrix adjust.
 Identities = 95/124 (76%), Positives = 107/124 (86%), Gaps = 1/124 (0%)

Query: 1   MPTVNQLIRKPRKGSFRACAKVTALRGNPQKRGVCLRVYTVTPKKPNSALRKVIKARLTS 60
           MPT+NQLIRKPR+   RA  KV AL+ +PQKRGVC RVYT TPKKPNSALRKV K RLT+
Sbjct: 1   MPTINQLIRKPREAQ-RARNKVPALQASPQKRGVCTRVYTTTPKKPNSALRKVAKVRLTN 59

Query: 61  GVEVIAYVPGEGHNLQEHSVVMLCGGRVKDLPGVKYRVIRGVLDAQGVKNRKQARSRYGA 120
           G EVI Y+PGEGHNLQEHSVVM+ GGRVKDLPGV+Y ++RGVLD QGVKNRKQ RS+YGA
Sbjct: 60  GYEVIGYIPGEGHNLQEHSVVMIRGGRVKDLPGVRYHILRGVLDTQGVKNRKQRRSKYGA 119

Query: 121 ERPK 124
           +RPK
Sbjct: 120 KRPK 123

Species: Starkeya novella
Genus: Starkeya
Family: Xanthobacteraceae
Order: Rhizobiales
Class: Alphaproteobacteria
Phylum: Proteobacteria
Superkingdom: Bacteria

 Score =  191 bits (485), Expect = 3e-47,   Method: Compositional matrix adjust.
 Identities = 96/124 (77%), Positives = 105/124 (84%), Gaps = 1/124 (0%)

Query: 1   MPTVNQLIRKPRKGSFRACAKVTALRGNPQKRGVCLRVYTVTPKKPNSALRKVIKARLTS 60
           MPTVNQLIRKPR    +   KV AL+ NPQKRGVC RVYT TPKKPNSALRKV K RLT+
Sbjct: 1   MPTVNQLIRKPRTAPVKR-NKVPALQANPQKRGVCTRVYTTTPKKPNSALRKVAKIRLTN 59

Query: 61  GVEVIAYVPGEGHNLQEHSVVMLCGGRVKDLPGVKYRVIRGVLDAQGVKNRKQARSRYGA 120
           G EVI Y+PGEGHNLQEHSVVM+ GGRVKDLPGV+Y +IRGVLD QGVKNRKQ RS+YGA
Sbjct: 60  GFEVIGYIPGEGHNLQEHSVVMIRGGRVKDLPGVRYHIIRGVLDTQGVKNRKQRRSKYGA 119

Query: 121 ERPK 124
           +RPK
Sbjct: 120 KRPK 123

Species: Brucella ceti
Genus: Brucella
Family: Brucellaceae
Order: Rhizobiales
Class: Alphaproteobacteria
Phylum: Proteobacteria
Superkingdom: Bacteria

 Score =  191 bits (485), Expect = 3e-47,   Method: Compositional matrix adjust.
 Identities = 95/124 (76%), Positives = 107/124 (86%), Gaps = 1/124 (0%)

Query: 1   MPTVNQLIRKPRKGSFRACAKVTALRGNPQKRGVCLRVYTVTPKKPNSALRKVIKARLTS 60
           MPTVNQLIRKPR+ + +   KV AL+ NPQKRGVC RVYT TP+KPNSALRKV K RLT+
Sbjct: 1   MPTVNQLIRKPRQANVKR-NKVPALQENPQKRGVCTRVYTTTPRKPNSALRKVAKIRLTN 59

Query: 61  GVEVIAYVPGEGHNLQEHSVVMLCGGRVKDLPGVKYRVIRGVLDAQGVKNRKQARSRYGA 120
           G EVI Y+PGEGHNLQEHSVVM+ GGRVKDLPGV+Y +IRGVLD QGVKNRKQ RS+YGA
Sbjct: 60  GFEVIGYIPGEGHNLQEHSVVMIRGGRVKDLPGVRYHIIRGVLDTQGVKNRKQRRSKYGA 119

Query: 121 ERPK 124
           +RPK
Sbjct: 120 KRPK 123

Species: Rhizobium etli
Genus: Rhizobium
Family: Rhizobiaceae
Order: Rhizobiales
Class: Alphaproteobacteria
Phylum: Proteobacteria
Superkingdom: Bacteria

 Score =  210 bits (536), Expect = 9e-56
 Identities = 87/124 (70%), Positives = 101/124 (81%), Gaps = 1/124 (0%)

Query: 1   MPTVNQLIRKPRKGSFRACAKVTALRGNPQKRGVCLRVYTVTPKKPNSALRKVIKARLTS 60
           MPT+NQL+RK RK S    +K  AL   PQKRGVC RVYT TPKKPNSALRKV + RLT+
Sbjct: 1   MPTINQLVRKGRK-SKVKKSKSPALNACPQKRGVCTRVYTTTPKKPNSALRKVARVRLTN 59

Query: 61  GVEVIAYVPGEGHNLQEHSVVMLCGGRVKDLPGVKYRVIRGVLDAQGVKNRKQARSRYGA 120
           G EV AY+PGEGHNLQEHSVV++ GGRVKDLPGV+Y ++RG LD  GVK+RKQ RS+YGA
Sbjct: 60  GFEVTAYIPGEGHNLQEHSVVLIRGGRVKDLPGVRYHIVRGALDTAGVKDRKQGRSKYGA 119

Query: 121 ERPK 124
           +RPK
Sbjct: 120 KRPK 123

Length = 124

 Score =  182 bits (464), Expect = 2e-47
 Identities = 88/124 (70%), Positives = 101/124 (81%), Gaps = 1/124 (0%)

Query: 1   MPTVNQLIRKPRKGSFRACAKVTALRGNPQKRGVCLRVYTVTPKKPNSALRKVIKARLTS 60
           MPT+NQLIRK RK   +  +K  AL   PQKRGVC RVYT TPKKPNSALRKV + RLT+
Sbjct: 1   MPTINQLIRKGRKKKKKK-SKSPALEACPQKRGVCTRVYTTTPKKPNSALRKVARVRLTN 59

Query: 61  GVEVIAYVPGEGHNLQEHSVVMLCGGRVKDLPGVKYRVIRGVLDAQGVKNRKQARSRYGA 120
           G EV AY+PGEGHNLQEHSVV++ GGRVKDLPGV+Y ++RG LD  GVKNRKQ RS+YGA
Sbjct: 60  GFEVTAYIPGEGHNLQEHSVVLIRGGRVKDLPGVRYHIVRGALDTAGVKNRKQGRSKYGA 119

Query: 121 ERPK 124
           +RPK
Sbjct: 120 KRPK 123

This model recognizes ribosomal protein S12 of Bacteria, mitochondria, and chloroplasts. The homologous ribosomal proteins of Archaea and Eukarya, termed S23 in Eukarya and S12 or S23 in Archaea, score below the trusted cutoff. Length = 124

 Score =  159 bits (404), Expect = 2e-40
 Identities = 84/124 (67%), Positives = 100/124 (80%), Gaps = 1/124 (0%)

Query: 1   MPTVNQLIRKPRKGSFRACAKVTALRGNPQKRGVCLRVYTVTPKKPNSALRKVIKARLTS 60
           MPT+NQL+RK R+ S    +K  AL G PQ RGVC RVYTVTPKKPNSALRKV + RL +
Sbjct: 7   MPTINQLVRKKRR-SLGLKSKSPALEGAPQARGVCTRVYTVTPKKPNSALRKVARVRLIN 65

Query: 61  GVEVIAYVPGEGHNLQEHSVVMLCGGRVKDLPGVKYRVIRGVLDAQGVKNRKQARSRYGA 120
           G EV AY+PGEGHNLQEHS V++ GGRVKDLPGV+Y+V+RG LD+ GV +R Q RS+YGA
Sbjct: 66  GKEVTAYIPGEGHNLQEHSEVLIRGGRVKDLPGVRYKVVRGALDSLGVLDRGQKRSKYGA 125

Query: 121 ERPK 124
           +RPK
Sbjct: 126 KRPK 129

Length = 129

 Score =  159 bits (403), Expect = 3e-40
 Identities = 74/104 (71%), Positives = 87/104 (83%)

Query: 21  KVTALRGNPQKRGVCLRVYTVTPKKPNSALRKVIKARLTSGVEVIAYVPGEGHNLQEHSV 80
           K  AL G PQKRGVCL VYT+TPKKPNSALRKV + RL +G EV AY+PG+GHNLQEHS 
Sbjct: 9   KSPALEGCPQKRGVCLEVYTITPKKPNSALRKVARVRLINGKEVTAYIPGDGHNLQEHSE 68

Query: 81  VMLCGGRVKDLPGVKYRVIRGVLDAQGVKNRKQARSRYGAERPK 124
           V++ GGRVKDLPGV+Y+V+RG LD  GV +RKQARS+YG E+PK
Sbjct: 69  VLIRGGRVKDLPGVRYKVVRGALDVAGVSDRKQARSKYGKEKPK 112

Length = 112

 Score =  155 bits (393), Expect = 3e-39
 Identities = 76/109 (69%), Positives = 90/109 (82%), Gaps = 1/109 (0%)

Query: 3   TVNQLIRKPRKGSFRACAKVTALRGNPQKRGVCLRVYTVTPKKPNSALRKVIKARLTSGV 62
           T+NQLIRK RK   +  +K  AL G PQK+GVCL+VYT TPKKPNSALRKV + RL++G 
Sbjct: 1   TINQLIRKGRK-KKKKKSKSPALEGCPQKKGVCLKVYTTTPKKPNSALRKVARVRLSNGK 59

Query: 63  EVIAYVPGEGHNLQEHSVVMLCGGRVKDLPGVKYRVIRGVLDAQGVKNR 111
           EV AY+PGEGHNLQEHSVV++ GGRVKDLPGV+Y ++RGVLD  GVKNR
Sbjct: 60  EVTAYIPGEGHNLQEHSVVLVRGGRVKDLPGVRYHIVRGVLDLAGVKNR 108

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.. Length = 108

 Score =  135 bits (341), Expect = 3e-33
 Identities = 66/112 (58%), Positives = 80/112 (71%)

Query: 1   MPTVNQLIRKPRKGSFRACAKVTALRGNPQKRGVCLRVYTVTPKKPNSALRKVIKARLTS 60
           M T+NQLIR   +   R   K  AL G PQ++GV LRV+T  PKKPNSA RK  + RL++
Sbjct: 28  MATLNQLIRNGGRPPKRRPRKSPALDGCPQRKGVVLRVFTRKPKKPNSANRKCARVRLST 87

Query: 61  GVEVIAYVPGEGHNLQEHSVVMLCGGRVKDLPGVKYRVIRGVLDAQGVKNRK 112
           G EV AY+PG GHNLQEHS+V++ GGRV+DLPGVKY V+RGV D  GV  R 
Sbjct: 88  GREVTAYIPGIGHNLQEHSIVLVRGGRVQDLPGVKYHVVRGVYDLAGVVGRI 139

Length = 139

 Score =  124 bits (313), Expect = 6e-30
 Identities = 53/95 (55%), Positives = 70/95 (73%)

Query: 25  LRGNPQKRGVCLRVYTVTPKKPNSALRKVIKARLTSGVEVIAYVPGEGHNLQEHSVVMLC 84
           L G PQK+G+C++V   TP+KPNS LRKV + RL++G  V  Y+PG GHNL  HSVV++ 
Sbjct: 120 LEGAPQKKGICVKVRVQTPRKPNSGLRKVARVRLSTGRTVTVYIPGIGHNLNTHSVVLVR 179

Query: 85  GGRVKDLPGVKYRVIRGVLDAQGVKNRKQARSRYG 119
           GGR KD+PG  Y+ +RGV D   VKNR ++RS+YG
Sbjct: 180 GGRCKDVPGCNYKAVRGVYDLLPVKNRARSRSKYG 214

Length = 290

 Score = 70.5 bits (172), Expect = 1e-13
 Identities = 62/82 (75%), Positives = 70/82 (85%)

Query: 21  KVTALRGNPQKRGVCLRVYTVTPKKPNSALRKVIKARLTSGVEVIAYVPGEGHNLQEHSV 80
           KV AL+G P +RGVC  V TVTPKKPNSALRKV K RLTSG EV AY+PGEGHNLQEHSV
Sbjct: 5   KVPALKGAPFRRGVCTVVRTVTPKKPNSALRKVAKVRLTSGYEVTAYIPGEGHNLQEHSV 64

Query: 81  VMLCGGRVKDLPGVKYRVIRGV 102
           V++ GGRVKDLPGV+Y ++RGV
Sbjct: 65  VLIRGGRVKDLPGVRYHIVRGV 86

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.. Length = 95

 Score = 54.8 bits (132), Expect = 6e-09
 Identities = 33/97 (34%), Positives = 57/97 (58%), Gaps = 8/97 (8%)

Query: 12  RKGSFRACAKVTALRGNPQKRGVCLRVYTVTPKKPNSALRKVIKARLT-SGVEVIAYVPG 70
           +K       K   L G P  +G+ L    V  K+PNSA+RK ++ +L  +G ++ A+VPG
Sbjct: 3   KKRHLGTKYKADPLGGAPHAKGIVLEKVGVEAKQPNSAIRKCVRVQLIKNGKKITAFVPG 62

Query: 71  EG--HNLQEHSVVMLCG----GR-VKDLPGVKYRVIR 100
           +G  + + E+  V++ G    GR V D+PGV+++V++
Sbjct: 63  DGCLNFIDENDEVLVAGFGRKGRAVGDIPGVRFKVVK 99

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.. Length = 115

 Score = 54.6 bits (132), Expect = 7e-09
 Identities = 41/108 (37%), Positives = 62/108 (57%), Gaps = 11/108 (10%)

Query: 21  KVTALRGNPQKRGVCLRVYTVTPKKPNSALRKVIKARLT-SGVEVIAYVPGEG--HNLQE 77
           K   L G P  RG+ L    V  K+PNSA+RK ++ +L  +G +V A+ PG+G  + + E
Sbjct: 38  KADPLEGAPMARGIVLEKVGVEAKQPNSAIRKCVRVQLIKNGKQVTAFCPGDGAINFIDE 97

Query: 78  HSVVMLCG-----GRVK-DLPGVKYRVIR--GVLDAQGVKNRKQARSR 117
           H  V++ G     GR   D+PGV+Y+VI+  GV   + VK +K+   R
Sbjct: 98  HDEVVIEGIGGPKGRSMGDIPGVRYKVIKVNGVSLKELVKGKKEKPVR 145

Length = 145

 Score = 54.1 bits (130), Expect = 1e-08
 Identities = 38/120 (31%), Positives = 64/120 (53%), Gaps = 11/120 (9%)

Query: 9   RKPRKGSFRACAKVTALRGNPQKRGVCLRVYTVTPKKPNSALRKVIKARLT-SGVEVIAY 67
           R+ ++   R   K   L G P  RG+ L    V  ++PNSA+RK ++ +L  +G  V A+
Sbjct: 20  RRFKRRMLRLKRKADPLEGAPMARGIVLEKVGVEARQPNSAIRKCVRVQLIKNGKVVTAF 79

Query: 68  VPGEG--HNLQEHSVVML------CGGRVKDLPGVKYRVIR--GVLDAQGVKNRKQARSR 117
            PG+G  + + EH  V++       G  + D+PGV+Y+V++   V   + VK +K+   R
Sbjct: 80  CPGDGAINFIDEHDEVIIEGIGGPRGRSMGDIPGVRYKVVKVNNVSLKELVKGKKEKPRR 139

This model 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. Length = 139

 Score = 43.6 bits (103), Expect = 2e-05
 Identities = 28/97 (28%), Positives = 54/97 (55%), Gaps = 8/97 (8%)

Query: 12  RKGSFRACAKVTALRGNPQKRGVCLRVYTVTPKKPNSALRKVIKARLT-SGVEVIAYVPG 70
           +K       K     G    +G+ +    +  K+PNSA+RK ++ +L  +G ++ A+VP 
Sbjct: 28  KKAHLGTRYKANPFGGASHAKGIVVEKIGIEAKQPNSAIRKCVRVQLIKNGKKITAFVPN 87

Query: 71  EG--HNLQEHSVVMLCG-GR----VKDLPGVKYRVIR 100
           +G  + + E+  V++ G GR    V D+PGV+++V++
Sbjct: 88  DGCLNFINENDEVLVSGFGRSGHAVGDIPGVRFKVVK 124

Length = 143

 Score = 42.6 bits (100), Expect = 3e-05
 Identities = 29/88 (32%), Positives = 54/88 (61%), Gaps = 8/88 (9%)

Query: 21  KVTALRGNPQKRGVCLRVYTVTPKKPNSALRKVIKARL-TSGVEVIAYVPGEG--HNLQE 77
           K +   G    +G+ L    V  K+PNSA+RK ++ +L  +G ++ A+VP +G  + ++E
Sbjct: 37  KSSPFGGASHAKGIVLEKIGVEAKQPNSAIRKCVRVQLIKNGKKITAFVPNDGCLNFIEE 96

Query: 78  HSVVMLCG-GR----VKDLPGVKYRVIR 100
           +  V++ G GR    V D+PGV+++V++
Sbjct: 97  NDEVLVAGFGRKGHAVGDIPGVRFKVVK 124

Length = 143

 Score =  186 bits (475), Expect = 1e-48
 Identities = 82/124 (66%), Positives = 99/124 (79%), Gaps = 1/124 (0%)

Query: 1   MPTVNQLIRKPRKGSFRACAKVTALRGNPQKRGVCLRVYTVTPKKPNSALRKVIKARLTS 60
           MPT+ QLIR  R+   R   K  ALRG PQ+RG C RVYT+TPKKPNSALRKV + RLTS
Sbjct: 1   MPTIKQLIRNTRQ-PIRNKTKSPALRGCPQRRGTCTRVYTITPKKPNSALRKVARVRLTS 59

Query: 61  GVEVIAYVPGEGHNLQEHSVVMLCGGRVKDLPGVKYRVIRGVLDAQGVKNRKQARSRYGA 120
           G E+ AY+PG GHNLQEHSVV++ GGRVKDLPGV+Y ++RG LDA GVK+R+Q RS+YG 
Sbjct: 60  GFEITAYIPGIGHNLQEHSVVLVRGGRVKDLPGVRYHIVRGTLDAVGVKDRQQGRSKYGV 119

Query: 121 ERPK 124
           ++PK
Sbjct: 120 KKPK 123

Length = 123

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

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

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

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=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

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

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

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

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=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

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=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

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

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=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

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

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

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=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

 Score =  166 bits (421), Expect = 1e-42
 Identities = 84/124 (67%), Positives = 103/124 (83%), Gaps = 1/124 (0%)

Query: 1   MPTVNQLIRKPRKGSFRACAKVTALRGNPQKRGVCLRVYTVTPKKPNSALRKVIKARLTS 60
           +PT+NQL+RK R+   R  +KV AL+G P +RGVC  V TVTPKKPNSALRKV K RLTS
Sbjct: 4   LPTINQLVRKGRE-KVRKKSKVPALKGAPFRRGVCTVVRTVTPKKPNSALRKVAKVRLTS 62

Query: 61  GVEVIAYVPGEGHNLQEHSVVMLCGGRVKDLPGVKYRVIRGVLDAQGVKNRKQARSRYGA 120
           G EV AY+PGEGHNLQEHSVV++ GGRVKDLPGV+Y ++RGV DA GVK+RK++RS+YG 
Sbjct: 63  GYEVTAYIPGEGHNLQEHSVVLIRGGRVKDLPGVRYHIVRGVYDAAGVKDRKKSRSKYGT 122

Query: 121 ERPK 124
           ++PK
Sbjct: 123 KKPK 126

 Score = 95.7 bits (238), Expect = 2e-21
 Identities = 32/119 (26%), Positives = 61/119 (51%), Gaps = 11/119 (9%)

Query: 9   RKPRKGSFRACAKVTALRGNPQKRGVCLRVYTVTPKKPNSALRKVIKARLTS-GVEVIAY 67
           ++ +K       K     G    +G+ L    V  K+PNSA+RK ++ +L   G ++ A+
Sbjct: 25  KQYKKAHLGTALKANPFGGASHAKGIVLEKVGVEAKQPNSAIRKCVRVQLIKNGKKITAF 84

Query: 68  VPGEG--HNLQEHSVVMLC-----GGRVKDLPGVKYRVIRGV---LDAQGVKNRKQARS 116
           VP +G  + ++E+  V++      G  V D+PGV+++V++     L A     +++ RS
Sbjct: 85  VPNDGCLNFIEENDEVLVAGFGRKGHAVGDIPGVRFKVVKVANVSLLALYKGKKERPRS 143

Probab=100.00  E-value=0  Score=414.85  Aligned_cols=123  Identities=67%  Similarity=1.086  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         4 M~T~nQl~r~~R~~~~-~k~k~~aL~~~PqkkGvc~kv~~~tPKKPNSA~RKvarVrLsng~~vtayIPGeGhnlqEHs~   82 (135)
T 2vqe_L            4 LPTINQLVRKGREKVR-KKSKVPALKGAPFRRGVCTVVRTVTPKKPNSALRKVAKVRLTSGYEVTAYIPGEGHNLQEHSV   82 (135)
T ss_dssp             -CCHHHHHHTCCCCCC-CCCSCCCSSSCSEEEEEESCCCEECCCTTCCCCEECCEEEETTSCEEEEECCSSCCCCCTTCE
T ss_pred             CCCHHHHHCCCCCCCC-CCCCCCCCCCCCCCCEEEEEEEEECCCCCCCCEEEEEEEEECCCCEEEEECCCCCCCCCCCCE
T ss_conf             4768897514888776-567785023797415588997774689965300137899936997999981899867554788


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        83 VLvrGGrv~DLPGVry~vvRG~~D~~gV~~Rk~~RSkYG~Kkpk  126 (135)
T 2vqe_L           83 VLIRGGRVKDLPGVRYHIVRGVYDAAGVKDRKKSRSKYGTKKPK  126 (135)
T ss_dssp             EEEEECCCTTSTTCCEEECTTSTTSCCCTTCCSSGGGGTCCCCC
T ss_pred             EEEECCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCCCCCCCCC
T ss_conf             99928877889984079964112243346642145546646852

Probab=100.00  E-value=4.1e-44  Score=278.00  Aligned_cols=104  Identities=29%  Similarity=0.592  Sum_probs=93.4

Q ss_pred             CCCCCCCCCCCCCCCCCCCEEEEEEEECCCCCCCCCCCEEEEEEE-CCCCEEEEEECCCC--CCCCCCCEEEE-----EC
Q ss_conf             786466667700068621247875675184567442432889996-69969999807888--75464678999-----53
Q gi|254780266|r   14 GSFRACAKVTALRGNPQKRGVCLRVYTVTPKKPNSALRKVIKARL-TSGVEVIAYVPGEG--HNLQEHSVVML-----CG   85 (124)
Q Consensus        14 k~~~~~~K~~~L~~~PqkkGVclkv~~~~PKKPNSA~RKvarV~L-sng~~v~ayIPGeG--hnlqehs~VLv-----rG   85 (124)
                      +......|+++|++|||++|||+++++++|||||||+||||+|+| +||++|||||||||  |||||||+|||     +|
T Consensus        30 ~~~~~~~K~~pl~g~Pq~kGivl~~~~~~pKkPNSA~RK~~rV~L~~ngk~vtA~iPG~G~~h~l~eh~~Vlv~g~G~rG  109 (143)
T 2zkq_l           30 AHLGTALKANPFGGASHAKGIVLEKVGVEAKQPNSAIRKCVRVQLIKNGKKITAFVPNDGCLNFIEENDEVLVAGFGRKG  109 (143)
T ss_dssp             CCCCCCCCCCCSTTCSCEEEEEEEEEEEECCTTCCCEEEEEEEEESGGGCEEEEECCSSCSSCCCCTTCCEEECSSSSSS
T ss_pred             HHHCCCCCCCCCCCCCCCCEEEEEEEEECCCCCCCCCEEEEEEEEECCCEEEEEEECCCCCCCCCCCCCEEEEEECCCCC
T ss_conf             43033313583458975256899976733579875201699999905990999992798650556648899997357578


Q ss_pred             CCCCCCCCCEEEEEECC-CCCCCCCCCCCCCCC
Q ss_conf             78388887547898040-014433420012112
Q gi|254780266|r   86 GRVKDLPGVKYRVIRGV-LDAQGVKNRKQARSR  117 (124)
Q Consensus        86 Grv~DlPGVry~ivRG~-~D~~gv~~Rk~~RSk  117 (124)
                      |+++|||||+|++|||. +++..+..++..+|+
T Consensus       110 g~~~DlPGVrykvvr~~~~~l~~l~~gkkekpr  142 (143)
T 2zkq_l          110 HAVGDIPGVRFKVVKVANVSLLALYKGKKERPR  142 (143)
T ss_dssp             CCBTTBTTCCEECCTTSTTSCSTTTTCCCCC--
T ss_pred             CCCCCCCCEEEEEEEECCCCHHHHHCCCCCCCC
T ss_conf             867889971389999648318988636343789

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: Ribosomal protein S12
species: Thermus thermophilus [TaxId: 274]

 Score =  164 bits (417), Expect = 2e-42
 Identities = 82/118 (69%), Positives = 98/118 (83%), Gaps = 1/118 (0%)

Query: 2   PTVNQLIRKPRKGSFRACAKVTALRGNPQKRGVCLRVYTVTPKKPNSALRKVIKARLTSG 61
           PT+NQL+RK R+   R  +KV AL+G P +RGVC  V TVTPKKPNSALRKV K RLTSG
Sbjct: 1   PTINQLVRKGRE-KVRKKSKVPALKGAPFRRGVCTVVRTVTPKKPNSALRKVAKVRLTSG 59

Query: 62  VEVIAYVPGEGHNLQEHSVVMLCGGRVKDLPGVKYRVIRGVLDAQGVKNRKQARSRYG 119
            EV AY+PGEGHNLQEHSVV++ GGRVKDLPGV+Y ++RGV DA GVK+RK++RS+YG
Sbjct: 60  YEVTAYIPGEGHNLQEHSVVLIRGGRVKDLPGVRYHIVRGVYDAAGVKDRKKSRSKYG 117

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: Ribosomal protein S12
species: Thermus thermophilus [TaxId: 274]

Probab=100.00  E-value=0  Score=395.87  Aligned_cols=118  Identities=69%  Similarity=1.083  Sum_probs=114.6

Q ss_pred             CCCHHHHHCCCCCCCCCCCCCCCCCCCCCCCEEEEEEEECCCCCCCCCCCEEEEEEECCCCEEEEEECCCCCCCCCCCEE
Q ss_conf             55023542687378646666770006862124787567518456744243288999669969999807888754646789
Q gi|254780266|r    2 PTVNQLIRKPRKGSFRACAKVTALRGNPQKRGVCLRVYTVTPKKPNSALRKVIKARLTSGVEVIAYVPGEGHNLQEHSVV   81 (124)
Q Consensus         2 pTinQlir~~Rkk~~~~~~K~~~L~~~PqkkGVclkv~~~~PKKPNSA~RKvarV~Lsng~~v~ayIPGeGhnlqehs~V   81 (124)
                      ||||||+|++|+++. .+.++++|++|||++|||++++|++|||||||+||||+|+||||++||||||||||||||||+|
T Consensus         1 PTinQL~rk~R~kk~-~k~k~~aL~~~PqkkGvc~kv~~~~PKKPNSA~RKvarVrLsng~~v~AyIPG~GhnlqEHs~V   79 (118)
T d2uubl1           1 PTINQLVRKGREKVR-KKSKVPALKGAPFRRGVCTVVRTVTPKKPNSALRKVAKVRLTSGYEVTAYIPGEGHNLQEHSVV   79 (118)
T ss_dssp             CCHHHHHHHCCCCCC-CCCSCCCTTTCSCEEEEEEEEEEECCCTTCCSCEEEEEEEETTSCEEEEECCSSCCCCCTTCEE
T ss_pred             CCHHHHCCCCCCCCC-CCCCCCCCCCCCCCCEEEEEEEEECCCCCCCEEEEEEEEEECCCEEEEEECCCCCCCCCCCCEE
T ss_conf             987671036888776-6788852236976043888988822688861021389999629909999818997674557889


Q ss_pred             EEECCCCCCCCCCEEEEEECCCCCCCCCCCCCCCCCCCC
Q ss_conf             995378388887547898040014433420012112561
Q gi|254780266|r   82 MLCGGRVKDLPGVKYRVIRGVLDAQGVKNRKQARSRYGA  120 (124)
Q Consensus        82 LvrGGrv~DlPGVry~ivRG~~D~~gv~~Rk~~RSkYG~  120 (124)
                      ||||||++|||||+||+|||+|||++|.+|+++||||||
T Consensus        80 LvrGGrv~DlPGVry~vvrG~~D~~~v~~Rk~~RSkYGt  118 (118)
T d2uubl1          80 LIRGGRVKDLPGVRYHIVRGVYDAAGVKDRKKSRSKYGT  118 (118)
T ss_dssp             EECCCCCTTSTTCCEEBCTTSTTCCCCTTCCSSTTTTTC
T ss_pred             EEECCCCCCCCCCEEEEEEEEECCCCCCCCCCCCCCCCC
T ss_conf             994886666777478997231014333665326676789

 Score =  141 bits (358), Expect = 2e-35
 Identities = 75/104 (72%), Positives = 89/104 (85%)

Query: 21  KVTALRGNPQKRGVCLRVYTVTPKKPNSALRKVIKARLTSGVEVIAYVPGEGHNLQEHSV 80
           KV AL+G P +RGVC  V TVTPKKPNSALRKV K RLTSG EV AY+PGEGHNLQEHSV
Sbjct: 1   KVPALKGAPFRRGVCTVVRTVTPKKPNSALRKVAKVRLTSGYEVTAYIPGEGHNLQEHSV 60

Query: 81  VMLCGGRVKDLPGVKYRVIRGVLDAQGVKNRKQARSRYGAERPK 124
           V++ GGRVKDLPGV+Y ++RGV DA GVK+RK++RS+YG ++PK
Sbjct: 61  VLIRGGRVKDLPGVRYHIVRGVYDAAGVKDRKKSRSKYGTKKPK 104

 Score =  106 bits (266), Expect = 1e-24
 Identities = 32/132 (24%), Positives = 60/132 (45%), Gaps = 20/132 (15%)

Query: 6   QLIRKPRK-----------GSFRACAKVTALRGNPQKRGVCLRVYTVTPKKPNSALRKVI 54
           + +R  R+                  K     G    +G+ L    V  K+PNSA+RK +
Sbjct: 11  RKLRSHRRDQKWHDKQYKKAHLGTALKANPFGGASHAKGIVLEKVGVEAKQPNSAIRKCV 70

Query: 55  KARLTS-GVEVIAYVPGEG--HNLQEHSVVMLCG-----GRVKDLPGVKYRVIRGVLD-A 105
           + +L   G ++ A+VP +G  + ++E+  V++ G       V D+PGV+++V++      
Sbjct: 71  RVQLIKNGKKITAFVPNDGCLNFIEENDEVLVAGFGRKGHAVGDIPGVRFKVVKVANVSL 130

Query: 106 QGVKNRKQARSR 117
             +   K+ R R
Sbjct: 131 LALYKGKKERPR 142

Probab=100.00  E-value=0  Score=356.93  Aligned_cols=104  Identities=72%  Similarity=1.174  Sum_probs=102.6

Q ss_pred             CCCCCCCCCCCCEEEEEEEECCCCCCCCCCCEEEEEEECCCCEEEEEECCCCCCCCCCCEEEEECCCCCCCCCCEEEEEE
Q ss_conf             67700068621247875675184567442432889996699699998078887546467899953783888875478980
Q gi|254780266|r   21 KVTALRGNPQKRGVCLRVYTVTPKKPNSALRKVIKARLTSGVEVIAYVPGEGHNLQEHSVVMLCGGRVKDLPGVKYRVIR  100 (124)
Q Consensus        21 K~~~L~~~PqkkGVclkv~~~~PKKPNSA~RKvarV~Lsng~~v~ayIPGeGhnlqehs~VLvrGGrv~DlPGVry~ivR  100 (124)
                      |+++|++|||++|||+++++++|||||||+||||+|+|+||++||||||||||||||||+|||||||++|||||+||+||
T Consensus         1 K~~~L~g~Pq~kGi~l~v~~~~pKKPNSA~RKvarVrL~ngk~v~AyIPG~ghnlqehs~VLVrGgrv~DlPGVrykiVr   80 (113)
T 2vqe_L            1 KVPALKGAPFRRGVCTVVRTVTPKKPNSALRKVAKVRLTSGYEVTAYIPGEGHNLQEHSVVLIRGGRVKDLPGVRYHIVR   80 (113)
T ss_dssp             SCCCSSSCSEEEEEESCCCEECCCTTCCCCEECCEEEETTSCEEEEECCSSCCCCCTTCEEEEEECCCTTSTTCCEEECT
T ss_pred             CCCCCCCCCCCCEEEEEEEEECCCCCCCEEEEEEEEEECCCCEEEEEECCCCCCCCCCCEEEEECCCCCCCCCCEEEEEE
T ss_conf             88534799751079988878336776501312789996699599999578886555378899958756778875789984


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             400144334200121125610789
Q gi|254780266|r  101 GVLDAQGVKNRKQARSRYGAERPK  124 (124)
Q Consensus       101 G~~D~~gv~~Rk~~RSkYG~kkpk  124 (124)
                      |+|||++|.+|+++||+||+|+||
T Consensus        81 G~~d~~~v~~Rk~~rSkyG~k~~k  104 (113)
T 2vqe_L           81 GVYDAAGVKDRKKSRSKYGTKKPK  104 (113)
T ss_dssp             TSTTSCCCTTCCSSGGGGTCCCCC
T ss_pred             EECCCCCCCCCCCCCCCCCCCCCH
T ss_conf             501364446653245546645730

Probab=100.00  E-value=0  Score=321.39  Aligned_cols=115  Identities=27%  Similarity=0.503  Sum_probs=103.2

Q ss_pred             CCCCHHHHHCCCCCCCCCCCCCCCCCCCCCCCEEEEEEEECCCCCCCCCCCEEEEEEEC-CCCEEEEEECCCC--CCCCC
Q ss_conf             95502354268737864666677000686212478756751845674424328899966-9969999807888--75464
Q gi|254780266|r    1 MPTVNQLIRKPRKGSFRACAKVTALRGNPQKRGVCLRVYTVTPKKPNSALRKVIKARLT-SGVEVIAYVPGEG--HNLQE   77 (124)
Q Consensus         1 MpTinQlir~~Rkk~~~~~~K~~~L~~~PqkkGVclkv~~~~PKKPNSA~RKvarV~Ls-ng~~v~ayIPGeG--hnlqe   77 (124)
                      |.|++|.....+  ....+.++++|++|||++|||++++++||||||||+||||+|+|+ ||++|||||||||  |||||
T Consensus        19 ~~~~~~~~~~r~--~~~~k~k~~~l~g~Pq~kGivl~~~~~~pKKPNSA~RK~arV~L~~Ngk~vtAyIPGeG~~hnlqE   96 (143)
T 2zkq_l           19 DQKWHDKQYKKA--HLGTALKANPFGGASHAKGIVLEKVGVEAKQPNSAIRKCVRVQLIKNGKKITAFVPNDGCLNFIEE   96 (143)
T ss_dssp             -------CCCSC--CCCCCCCCCCSTTCSCEEEEEEEEEEEECCTTCCCEEEEEEEEESGGGCEEEEECCSSCSSCCCCT
T ss_pred             HHCCCCCHHHHH--HCCCCCCCCCCCCCCCCCEEEEEEEEECCCCCCCHHHEEEEEEEECCCEEEEEECCCCCCCCCCCC
T ss_conf             630012046665--404430258344894042478999984257887002226899990599799999179853033453


Q ss_pred             CCEEEEEC-----CCCCCCCCCEEEEEECCCCC-CCCCCCCCCCCC
Q ss_conf             67899953-----78388887547898040014-433420012112
Q gi|254780266|r   78 HSVVMLCG-----GRVKDLPGVKYRVIRGVLDA-QGVKNRKQARSR  117 (124)
Q Consensus        78 hs~VLvrG-----Grv~DlPGVry~ivRG~~D~-~gv~~Rk~~RSk  117 (124)
                      ||+|||||     ||++|||||+||||||+||+ .++.+|+++|||
T Consensus        97 hs~VlVrG~G~~gGrv~DLPGVrykvIrg~~d~l~~v~~rk~~rsk  142 (143)
T 2zkq_l           97 NDEVLVAGFGRKGHAVGDIPGVRFKVVKVANVSLLALYKGKKERPR  142 (143)
T ss_dssp             TCCEEECSSSSSSCCBTTBTTCCEECCTTSTTSCSTTTTCCCCC--
T ss_pred             CCEEEEEECCCCCCCCCCCCCEEEEEEEECCCCHHHHHCCCCCCCC
T ss_conf             6489998467467766889972799999758119998603130589