Query psy7476
Match_columns 143
No_of_seqs 121 out of 359
Neff 3.6
Searched_HMMs 46136
Date Fri Aug 16 19:17:37 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy7476.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/7476hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PTZ00067 40S ribosomal S23; Pr 100.0 5.3E-74 1.1E-78 445.6 14.1 143 1-143 1-143 (143)
2 PRK04211 rps12P 30S ribosomal 100.0 1.1E-71 2.3E-76 433.5 13.6 141 3-143 4-145 (145)
3 TIGR00982 S23_S12_E_A ribosoma 100.0 9.1E-71 2E-75 425.9 13.4 138 6-143 1-139 (139)
4 KOG1749|consensus 100.0 3.8E-69 8.3E-74 414.6 11.6 143 1-143 1-143 (143)
5 cd03367 Ribosomal_S23 S12-like 100.0 2.6E-61 5.5E-66 363.8 12.3 115 26-140 1-115 (115)
6 COG0048 RpsL Ribosomal protein 100.0 4.9E-55 1.1E-59 334.5 10.6 123 7-142 1-123 (129)
7 cd00319 Ribosomal_S12_like Rib 100.0 6.4E-48 1.4E-52 283.1 9.4 94 34-137 2-95 (95)
8 PF00164 Ribosom_S12_S23: Ribo 100.0 2.5E-48 5.5E-53 295.6 6.8 106 29-142 11-122 (122)
9 cd03368 Ribosomal_S12 S12-like 100.0 1.2E-44 2.6E-49 270.9 9.7 84 35-126 16-99 (108)
10 PRK05163 rpsL 30S ribosomal pr 100.0 6.4E-44 1.4E-48 272.2 9.9 88 36-132 19-106 (124)
11 CHL00051 rps12 ribosomal prote 100.0 5.8E-44 1.3E-48 272.2 9.5 90 35-133 18-107 (123)
12 TIGR00981 rpsL_bact ribosomal 100.0 8.9E-44 1.9E-48 271.4 9.9 88 36-132 19-106 (124)
13 PTZ00115 40S ribosomal protein 100.0 2.6E-39 5.7E-44 272.3 9.8 93 36-138 115-207 (290)
14 KOG1750|consensus 100.0 1E-32 2.2E-37 213.5 5.8 83 36-126 47-129 (139)
15 TIGR00008 infA translation ini 94.0 0.1 2.2E-06 36.6 4.1 46 47-103 7-54 (68)
16 COG0361 InfA Translation initi 92.4 0.25 5.4E-06 35.4 4.1 47 46-103 8-56 (75)
17 PRK12442 translation initiatio 85.4 1.4 3.1E-05 32.4 3.9 46 47-103 9-56 (87)
18 smart00652 eIF1a eukaryotic tr 83.2 2.2 4.8E-05 30.4 4.0 35 69-104 19-54 (83)
19 cd04456 S1_IF1A_like S1_IF1A_l 80.3 3.4 7.3E-05 29.2 4.1 34 69-103 14-48 (78)
20 TIGR00523 eIF-1A eukaryotic/ar 72.6 6.1 0.00013 29.2 3.8 53 40-103 14-67 (99)
21 PLN00208 translation initiatio 68.1 7.8 0.00017 30.8 3.7 53 40-103 27-80 (145)
22 PTZ00329 eukaryotic translatio 66.4 9.3 0.0002 30.7 3.9 54 40-104 27-81 (155)
23 TIGR00230 sfsA sugar fermentat 62.0 39 0.00084 28.4 6.9 35 67-103 20-55 (232)
24 cd05793 S1_IF1A S1_IF1A: Trans 56.7 12 0.00026 26.3 2.7 35 69-104 14-49 (77)
25 PRK00347 putative DNA-binding 55.7 46 0.001 27.8 6.4 36 67-103 18-54 (234)
26 PF01176 eIF-1a: Translation i 53.2 12 0.00027 25.0 2.2 32 70-103 18-51 (65)
27 PF03749 SfsA: Sugar fermentat 52.3 68 0.0015 26.5 6.8 38 66-104 5-43 (215)
28 PRK04012 translation initiatio 48.7 19 0.0004 26.7 2.7 53 40-103 16-69 (100)
29 cd01726 LSm6 The eukaryotic Sm 48.0 31 0.00067 23.0 3.5 58 63-129 6-64 (67)
30 COG1489 SfsA DNA-binding prote 45.9 48 0.001 28.3 5.0 36 66-103 17-53 (235)
31 cd01724 Sm_D1 The eukaryotic S 39.6 43 0.00093 24.0 3.3 29 63-92 7-36 (90)
32 PRK00284 pqqA coenzyme PQQ syn 32.6 59 0.0013 19.2 2.6 13 77-89 12-24 (26)
33 PLN02856 fumarylacetoacetase 30.2 91 0.002 28.6 4.6 34 71-105 369-402 (424)
34 cd01731 archaeal_Sm1 The archa 29.6 1.1E+02 0.0024 20.3 3.9 28 64-92 7-35 (68)
35 TIGR01266 fum_ac_acetase fumar 28.8 1.1E+02 0.0024 28.0 4.9 34 71-105 361-394 (415)
36 PF00386 C1q: C1q domain; Int 28.4 1.6E+02 0.0034 21.0 4.8 41 64-104 55-105 (127)
37 COG4776 Rnb Exoribonuclease II 28.1 62 0.0014 31.1 3.2 37 66-104 573-615 (645)
38 cd05792 S1_eIF1AD_like S1_eIF1 26.4 1.1E+02 0.0024 21.8 3.6 34 70-104 15-49 (78)
39 COG2302 Uncharacterized conser 25.7 67 0.0015 27.9 2.8 16 92-107 219-234 (257)
40 cd01733 LSm10 The eukaryotic S 25.6 1.4E+02 0.0031 20.7 4.0 38 63-102 15-53 (78)
41 PRK00737 small nuclear ribonuc 24.8 1.3E+02 0.0027 20.4 3.6 24 63-87 10-33 (72)
42 PRK00276 infA translation init 23.1 2.3E+02 0.0049 19.2 4.5 33 70-103 22-56 (72)
43 PLN00051 RNA-binding S4 domain 23.0 51 0.0011 28.1 1.6 15 93-107 231-245 (267)
44 TIGR02107 PQQ_syn_pqqA coenzym 21.3 1.3E+02 0.0027 17.8 2.5 13 77-89 11-23 (26)
45 PF11975 Glyco_hydro_4C: Famil 21.2 1.3E+02 0.0028 24.1 3.5 29 76-104 148-177 (232)
46 cd03109 DTBS Dethiobiotin synt 21.0 1.2E+02 0.0025 22.3 3.0 24 76-106 25-48 (134)
47 cd01722 Sm_F The eukaryotic Sm 20.9 2.6E+02 0.0057 18.6 4.5 32 63-95 7-39 (68)
48 PF02080 TrkA_C: TrkA-C domain 20.6 93 0.002 19.6 2.1 21 82-104 38-58 (71)
49 TIGR03069 PS_II_S4 photosystem 20.6 1.1E+02 0.0024 25.7 3.1 15 93-107 223-237 (257)
No 1
>PTZ00067 40S ribosomal S23; Provisional
Probab=100.00 E-value=5.3e-74 Score=445.62 Aligned_cols=143 Identities=85% Similarity=1.350 Sum_probs=141.5
Q ss_pred CCCCcchhhhHhhhhhhccccccchhhhhhcccccccCCCCCCCCccceeEEeeeeccccCCCcccccEEEEEEeecCeE
Q psy7476 1 MGKPRGIRTARKHVNNRRVQRWADKDYKKAHLGTRWKANPFGGASHAKGIVLEKVGVEAKQPNSAIRKCVRVQLIKNGKK 80 (143)
Q Consensus 1 ~~k~~Gl~~arkl~~~r~~~r~~dk~ykk~~lg~~~k~~~l~g~Pq~kGivl~~~~~~pKkPNSA~RK~~rV~L~kngk~ 80 (143)
|++++||||||+|+++|+++||+|++|++++|++.+|.+||+++||++|||++++++||||||||+||||+|||++||++
T Consensus 1 m~~~~Gl~aarkl~~~r~~~rw~d~~y~k~~lg~~~k~~pl~g~pq~kGivl~~~~~~pKkPNSA~RK~~rV~L~kngk~ 80 (143)
T PTZ00067 1 MGKPRGLRAARKLRRHRRVNRWADKEYKKAHLGTRYKANPFGGASHAKGIVVEKIGIEAKQPNSAIRKCVRVQLIKNGKK 80 (143)
T ss_pred CCCcchhHHHHHHHHHHHHhhhhhHHHHHHhcCCccccCcccCCCccceEEEEEEeecCCCCChhhceEEEEEEccCCcE
Confidence 88999999999999999999999999999999999999999999999999999999999999999999999999889999
Q ss_pred EEEeecCCCccCCcccccEEEEeeecCCCCcCCCCCCceEEEEEeccccHHHHHhhhccCCCC
Q psy7476 81 ITAFVPRDGCLNYIEENDEVLVAGFGRKGHAVGDIPGVRFKVVKVANVSLLALYKEKKERPRS 143 (143)
Q Consensus 81 v~A~IPg~G~l~~lqeh~~VLV~G~G~~Gg~v~DlPGVrykvvrv~~vsl~~l~~gkkekp~r 143 (143)
|||||||||+||||||||+|||+|||++||+++|||||+|+||+|+||||+|||+||||||+|
T Consensus 81 vtAyiPg~G~lh~lqEh~~VLV~G~Gr~g~~v~DlPGVrykvVrV~~vsL~~l~kgkkekp~r 143 (143)
T PTZ00067 81 ITAFVPNDGCLNFINENDEVLVSGFGRSGHAVGDIPGVRFKVVKVAGVSLLALYKGKKEKPRN 143 (143)
T ss_pred EEEEeCCCCcccccccCCEEEEEecCcCCCccCCCCceEEEEEEECCEeHHHHHhcccccCCC
Confidence 999999999999999999999999999999999999999999999999999999999999986
No 2
>PRK04211 rps12P 30S ribosomal protein S12P; Reviewed
Probab=100.00 E-value=1.1e-71 Score=433.50 Aligned_cols=141 Identities=61% Similarity=0.988 Sum_probs=139.1
Q ss_pred CCcchhhhHhhhhhhccccccchhhhhhcccccccCCCCCCCCccceeEEeeeeccccCCCcccccEEEEEEeecCeEEE
Q psy7476 3 KPRGIRTARKHVNNRRVQRWADKDYKKAHLGTRWKANPFGGASHAKGIVLEKVGVEAKQPNSAIRKCVRVQLIKNGKKIT 82 (143)
Q Consensus 3 k~~Gl~~arkl~~~r~~~r~~dk~ykk~~lg~~~k~~~l~g~Pq~kGivl~~~~~~pKkPNSA~RK~~rV~L~kngk~v~ 82 (143)
+|+||||||+|+++|++|||+|++|++++|++++|++||+|+||++|||++++++||||||||+||||+|||++||++||
T Consensus 4 ~~~Gl~aarkl~~~r~~~rw~d~~y~k~~lg~~~K~~~l~g~Pq~kGivl~~~~v~pKKPNSA~RK~arV~L~~Ngk~vt 83 (145)
T PRK04211 4 SPNGLFAARKLKLKRKKFRWSDRRYKRRMLGLKEKADPLEGAPMARGIVLEKVGVEAKQPNSAIRKCVRVQLIKNGKQVT 83 (145)
T ss_pred CcchhhHHHHHHHHHHHhhhhhHHHHHHHhCcccccCcccCCCccCeEEEEEeeecCCCCchhhceeEEEEEccCCeEEE
Confidence 49999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EeecCCCccCCcccccEEEEeeec-CCCCcCCCCCCceEEEEEeccccHHHHHhhhccCCCC
Q psy7476 83 AFVPRDGCLNYIEENDEVLVAGFG-RKGHAVGDIPGVRFKVVKVANVSLLALYKEKKERPRS 143 (143)
Q Consensus 83 A~IPg~G~l~~lqeh~~VLV~G~G-~~Gg~v~DlPGVrykvvrv~~vsl~~l~~gkkekp~r 143 (143)
||||||||+|||||||+|||+||| ++||+++|||||+|+||+|+||||+|||+||||||+|
T Consensus 84 AyIPg~G~~~~lqEh~~VLV~G~gg~~gg~v~DlPGVrykvVkV~~vsL~~l~~gkkekp~r 145 (145)
T PRK04211 84 AFCPGDGAINFIDEHDEVVIEGIGGPKGRSMGDIPGVRYKVIKVNGVSLKELVKGKKEKPVR 145 (145)
T ss_pred EEeCCCccccccccCCEEEEeecCccCCCCcCCCCceEEEEEEECCEeHHHHHhcccccCCC
Confidence 999999999999999999999998 9999999999999999999999999999999999986
No 3
>TIGR00982 S23_S12_E_A ribosomal protein S23 (S12). 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.
Probab=100.00 E-value=9.1e-71 Score=425.93 Aligned_cols=138 Identities=61% Similarity=0.997 Sum_probs=136.6
Q ss_pred chhhhHhhhhhhccccccchhhhhhcccccccCCCCCCCCccceeEEeeeeccccCCCcccccEEEEEEeecCeEEEEee
Q psy7476 6 GIRTARKHVNNRRVQRWADKDYKKAHLGTRWKANPFGGASHAKGIVLEKVGVEAKQPNSAIRKCVRVQLIKNGKKITAFV 85 (143)
Q Consensus 6 Gl~~arkl~~~r~~~r~~dk~ykk~~lg~~~k~~~l~g~Pq~kGivl~~~~~~pKkPNSA~RK~~rV~L~kngk~v~A~I 85 (143)
|||||++|+++|++|||+|++|+++++++..|++||+|+||++|||++++++||||||||+||||+|||++||++|||||
T Consensus 1 Gl~aarkl~~~r~~~rw~d~~y~k~~~~~~~K~~~l~g~Pq~kGivl~~~~~~pKkPNSA~RK~~rV~L~~ngk~vtAyi 80 (139)
T TIGR00982 1 GLFAARKLKRKRKKFRWSDRRFKRRMLRLKRKADPLEGAPMARGIVLEKVGVEARQPNSAIRKCVRVQLIKNGKVVTAFC 80 (139)
T ss_pred CchhHHHHHHHHHHhhhhhHHHHHHhhccccccCcccCCCccCeEEEEEEeecCCCCCcccceEEEEEEccCCeEEEEEe
Confidence 89999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cCCCccCCcccccEEEEeeec-CCCCcCCCCCCceEEEEEeccccHHHHHhhhccCCCC
Q psy7476 86 PRDGCLNYIEENDEVLVAGFG-RKGHAVGDIPGVRFKVVKVANVSLLALYKEKKERPRS 143 (143)
Q Consensus 86 Pg~G~l~~lqeh~~VLV~G~G-~~Gg~v~DlPGVrykvvrv~~vsl~~l~~gkkekp~r 143 (143)
|||||+|||||||+|||+||| ++||+++|||||+|+||+|+||||+|||+||||||+|
T Consensus 81 Pg~G~~~~lqeh~~VLV~G~gg~~gg~v~DlPGVrykvVkV~~vsL~~l~~gkkekp~r 139 (139)
T TIGR00982 81 PGDGAINFIDEHDEVIIEGIGGPRGRSMGDIPGVRYKVVKVNNVSLKELVKGKKEKPRR 139 (139)
T ss_pred CCCccccccccCCEEEEEecCccCCCCcCCCCceEEEEEEECCEeHHHHHhcccccCCC
Confidence 999999999999999999999 9999999999999999999999999999999999986
No 4
>KOG1749|consensus
Probab=100.00 E-value=3.8e-69 Score=414.60 Aligned_cols=143 Identities=85% Similarity=1.297 Sum_probs=142.0
Q ss_pred CCCCcchhhhHhhhhhhccccccchhhhhhcccccccCCCCCCCCccceeEEeeeeccccCCCcccccEEEEEEeecCeE
Q psy7476 1 MGKPRGIRTARKHVNNRRVQRWADKDYKKAHLGTRWKANPFGGASHAKGIVLEKVGVEAKQPNSAIRKCVRVQLIKNGKK 80 (143)
Q Consensus 1 ~~k~~Gl~~arkl~~~r~~~r~~dk~ykk~~lg~~~k~~~l~g~Pq~kGivl~~~~~~pKkPNSA~RK~~rV~L~kngk~ 80 (143)
||++.||||||+|+.+|+.|||+|++|+++++|+++|++||+|+||+||||||++++|+||||||+|||+|||||+||++
T Consensus 1 mgk~~Gl~aarklr~~r~~~rwad~~ykk~~lGta~K~~pfggashAKgIvLEKigVEAKQPNSAiRKcvRvQLIkngKK 80 (143)
T KOG1749|consen 1 MGKPRGLFAARKLRTHRRNQRWADKHYKKRLLGTAYKSSPFGGASHAKGIVLEKIGVEAKQPNSAIRKCVRVQLIKNGKK 80 (143)
T ss_pred CCCcccchhHHHHHhhhhhhccchhhhhhhhhcchhhcCCCCCccccceeEEEeeeeeccCCcHHHhhheeeeeeeCCce
Confidence 89999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEEeecCCCccCCcccccEEEEeeecCCCCcCCCCCCceEEEEEeccccHHHHHhhhccCCCC
Q psy7476 81 ITAFVPRDGCLNYIEENDEVLVAGFGRKGHAVGDIPGVRFKVVKVANVSLLALYKEKKERPRS 143 (143)
Q Consensus 81 v~A~IPg~G~l~~lqeh~~VLV~G~G~~Gg~v~DlPGVrykvvrv~~vsl~~l~~gkkekp~r 143 (143)
||||+|.||||||++|||||||.|||++|++++|||||||+|++|+||||+|||+||||||++
T Consensus 81 ITafVp~dgcln~ieendevlv~gfgrkg~avgdipgvrfkvvkv~~vsl~alf~~kkekpr~ 143 (143)
T KOG1749|consen 81 ITAFVPNDGCLNFIEENDEVLVAGFGRKGHAVGDIPGVRFKVVKVSGVSLLALFKEKKEKPRS 143 (143)
T ss_pred EEEEecCCCceeeeccCCeeeeeccCccCccccCCCceEEEEEEEcCcChhhhhhccccCCCC
Confidence 999999999999999999999999999999999999999999999999999999999999985
No 5
>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=2.6e-61 Score=363.83 Aligned_cols=115 Identities=86% Similarity=1.319 Sum_probs=113.3
Q ss_pred hhhhhcccccccCCCCCCCCccceeEEeeeeccccCCCcccccEEEEEEeecCeEEEEeecCCCccCCcccccEEEEeee
Q psy7476 26 DYKKAHLGTRWKANPFGGASHAKGIVLEKVGVEAKQPNSAIRKCVRVQLIKNGKKITAFVPRDGCLNYIEENDEVLVAGF 105 (143)
Q Consensus 26 ~ykk~~lg~~~k~~~l~g~Pq~kGivl~~~~~~pKkPNSA~RK~~rV~L~kngk~v~A~IPg~G~l~~lqeh~~VLV~G~ 105 (143)
.|++++++++.|++||+|+||++|||++++++||||||||+||||||||++||++||||||||||||||||||+|||+||
T Consensus 1 ~~~~~~~~~~~k~~~l~g~Pq~kGivl~~~~~~pKkPNSA~RK~~rV~L~~ngk~itAyIPG~G~~~~lqeh~~VLV~G~ 80 (115)
T cd03367 1 RYKKRHLGTKYKADPLGGAPHAKGIVLEKVGVEAKQPNSAIRKCVRVQLIKNGKKITAFVPGDGCLNFIDENDEVLVAGF 80 (115)
T ss_pred ChhhhhccccccCCcccCCCccCeEEEEEeecCCCCCChhhceEEEEEEccCCeEEEEEeCCCCcccccccCCEEEEEec
Confidence 48999999999999999999999999999999999999999999999998899999999999999999999999999999
Q ss_pred cCCCCcCCCCCCceEEEEEeccccHHHHHhhhccC
Q psy7476 106 GRKGHAVGDIPGVRFKVVKVANVSLLALYKEKKER 140 (143)
Q Consensus 106 G~~Gg~v~DlPGVrykvvrv~~vsl~~l~~gkkek 140 (143)
|++||+++|||||+|+||+|+||||+|||+|||||
T Consensus 81 G~~Gg~v~DlPGVrykvVkV~~vsl~~l~~gkkek 115 (115)
T cd03367 81 GRKGRAVGDIPGVRFKVVKVNGVSLLALFKGKKEK 115 (115)
T ss_pred ccCCCccCCCCceEEEEEEECCEEHHHHhhhhccC
Confidence 99999999999999999999999999999999997
No 6
>COG0048 RpsL Ribosomal protein S12 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=4.9e-55 Score=334.51 Aligned_cols=123 Identities=41% Similarity=0.609 Sum_probs=118.5
Q ss_pred hhhhHhhhhhhccccccchhhhhhcccccccCCCCCCCCccceeEEeeeeccccCCCcccccEEEEEEeecCeEEEEeec
Q psy7476 7 IRTARKHVNNRRVQRWADKDYKKAHLGTRWKANPFGGASHAKGIVLEKVGVEAKQPNSAIRKCVRVQLIKNGKKITAFVP 86 (143)
Q Consensus 7 l~~arkl~~~r~~~r~~dk~ykk~~lg~~~k~~~l~g~Pq~kGivl~~~~~~pKkPNSA~RK~~rV~L~kngk~v~A~IP 86 (143)
+|||++|...++..| |.++.++++.|++||+||||++|||++++++||||||||+||||||||+ ||++||||||
T Consensus 1 ~~a~~km~t~~q~~R-----~~rr~~~~k~Ks~~L~g~Pq~RGv~~~v~~~~pKkPNSAlRK~~RVrL~-NG~~VtAyiP 74 (129)
T COG0048 1 LFAARKMPTINQLVR-----KKRRSLGLKSKSPALEGAPQARGVCTRVYTVTPKKPNSALRKVARVRLI-NGKEVTAYIP 74 (129)
T ss_pred CcccchhhhHHHHhh-----cccccccccccCCcccCCCccceEEEEEEecccCCCChhhheeEEEEee-CCcEEEEEcC
Confidence 589999999999777 9999999999999999999999999999999999999999999999995 9999999999
Q ss_pred CCCccCCcccccEEEEeeecCCCCcCCCCCCceEEEEEeccccHHHHHhhhccCCC
Q psy7476 87 RDGCLNYIEENDEVLVAGFGRKGHAVGDIPGVRFKVVKVANVSLLALYKEKKERPR 142 (143)
Q Consensus 87 g~G~l~~lqeh~~VLV~G~G~~Gg~v~DlPGVrykvvrv~~vsl~~l~~gkkekp~ 142 (143)
|||| +|||||+||||| ++++|||||+||||||+++||.+++++++|+|.
T Consensus 75 g~Gh--~lqEH~~Vli~G-----~~v~DlPGVRy~vvrg~~ds~~v~~r~~~rs~y 123 (129)
T COG0048 75 GEGH--NLQEHSEVLIRG-----GRVKDLPGVRYKVVRGALDSLGVLDRGQKRSKY 123 (129)
T ss_pred CCCc--cccccCEEEEec-----CccCCCCCceEEEEEEcchhhhhhhhccccccc
Confidence 9999 799999999998 679999999999999999999999999999875
No 7
>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=6.4e-48 Score=283.14 Aligned_cols=94 Identities=35% Similarity=0.605 Sum_probs=89.7
Q ss_pred ccccCCCCCCCCccceeEEeeeeccccCCCcccccEEEEEEeecCeEEEEeecCCCccCCcccccEEEEeeecCCCCcCC
Q psy7476 34 TRWKANPFGGASHAKGIVLEKVGVEAKQPNSAIRKCVRVQLIKNGKKITAFVPRDGCLNYIEENDEVLVAGFGRKGHAVG 113 (143)
Q Consensus 34 ~~~k~~~l~g~Pq~kGivl~~~~~~pKkPNSA~RK~~rV~L~kngk~v~A~IPg~G~l~~lqeh~~VLV~G~G~~Gg~v~ 113 (143)
++.|++||+++||++|||+++++++|||||||+|||||||| +||++|||||||||| ||||||+|||+| |++.
T Consensus 2 ~~~k~~~l~~~Pq~kGi~l~~~~~~pKkPNSA~RK~arV~L-~ngk~v~ayIPg~Gh--~lqeh~~VLvrG-----Gr~~ 73 (95)
T cd00319 2 KKSKVPALKGAPFRRGVCTVVRTVTPKKPNSALRKVAKVRL-TSGYEVTAYIPGEGH--NLQEHSVVLIRG-----GRVK 73 (95)
T ss_pred CccccCcccCCcccCeEEEEEEeccccCCChhhceEEEEEc-cCCCEEEEECCCCCc--ccccccEEEEeC-----CCcC
Confidence 55788999999999999999999999999999999999999 699999999999996 999999999998 8899
Q ss_pred CCCCceEEEEEeccccHHHHHhhh
Q psy7476 114 DIPGVRFKVVKVANVSLLALYKEK 137 (143)
Q Consensus 114 DlPGVrykvvrv~~vsl~~l~~gk 137 (143)
|||||+|+||| |+++.++++|+
T Consensus 74 DlPGVrykvVr--G~~d~~~v~~R 95 (95)
T cd00319 74 DLPGVRYHIVR--GVYDAAGVKDR 95 (95)
T ss_pred CCCCcEEEEEc--ccchhhhccCC
Confidence 99999999999 89999999875
No 8
>PF00164 Ribosom_S12_S23: Ribosomal protein S12/S23; InterPro: IPR006032 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. 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 protein is known typically as S12 in bacteria, S23 in eukaryotes and as either S12 or S23 in the Archaea []. Bacterial S12 molecules contain a conserved aspartic acid residue which undergoes a novel post-translational modification, beta-methylthiolation, to form the corresponding 3-methylthioaspartic acid.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 2ZKQ_l 3BBN_L 3PYU_L 3D5A_L 3MS0_L 3MR8_L 3F1G_L 2OW8_m 3PYS_L 2QNH_m ....
Probab=100.00 E-value=2.5e-48 Score=295.56 Aligned_cols=106 Identities=47% Similarity=0.747 Sum_probs=100.5
Q ss_pred hhcccccccCCCCCCCCccceeEEeeeeccccCCCcccccEEEEEEeecCeEEEEeecCCCccCCcccccEEEEeeecCC
Q psy7476 29 KAHLGTRWKANPFGGASHAKGIVLEKVGVEAKQPNSAIRKCVRVQLIKNGKKITAFVPRDGCLNYIEENDEVLVAGFGRK 108 (143)
Q Consensus 29 k~~lg~~~k~~~l~g~Pq~kGivl~~~~~~pKkPNSA~RK~~rV~L~kngk~v~A~IPg~G~l~~lqeh~~VLV~G~G~~ 108 (143)
+.+++++.|+++|+++||++|||+++++++|||||||+||||+||| +||++|+|||||||| ||||||+|||+|
T Consensus 11 r~~~~~~~k~~~l~~~Pq~kGi~l~~~~~~pKKPNSA~RK~arVrL-~n~k~v~AyIPg~Gh--nlqehs~VLVrG---- 83 (122)
T PF00164_consen 11 RKKKKRKSKSPALGGCPQKKGICLKVVTVKPKKPNSAIRKVARVRL-SNGKKVTAYIPGEGH--NLQEHSVVLVRG---- 83 (122)
T ss_dssp CHSSTCSHSSSSSTTSSEEEEEEEEEEEEEESTTTCSEEEEEEEEE-TTSEEEEEEC-SSSC--CSTTTSEEEEEE----
T ss_pred CCCCCccccCCccCCCCccCcEEeecccccccCccchhhhcceeee-ccCceEEEEecCCcc--cccccceEEEec----
Confidence 5777888999999999999999999999999999999999999999 699999999999996 999999999998
Q ss_pred CCcCCCCCCceEEEEE----ecccc--HHHHHhhhccCCC
Q psy7476 109 GHAVGDIPGVRFKVVK----VANVS--LLALYKEKKERPR 142 (143)
Q Consensus 109 Gg~v~DlPGVrykvvr----v~~vs--l~~l~~gkkekp~ 142 (143)
|+++|||||+|+||| +++|+ +.+++++.++||+
T Consensus 84 -grv~DlPGVkykvVRG~~D~~gV~~r~~~rskyg~kkPk 122 (122)
T PF00164_consen 84 -GRVGDLPGVKYKVVRGVYDVAGVSNRKKARSKYGKKKPK 122 (122)
T ss_dssp -ESBTTSTTECEEBETTSTTCSSSTT-SSSCTTTTCCCCH
T ss_pred -cccCCCCceEEEEEeeccccccccHHHHhhhhcCCcCCC
Confidence 779999999999999 88999 9999999999984
No 9
>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=1.2e-44 Score=270.93 Aligned_cols=84 Identities=40% Similarity=0.726 Sum_probs=81.1
Q ss_pred cccCCCCCCCCccceeEEeeeeccccCCCcccccEEEEEEeecCeEEEEeecCCCccCCcccccEEEEeeecCCCCcCCC
Q psy7476 35 RWKANPFGGASHAKGIVLEKVGVEAKQPNSAIRKCVRVQLIKNGKKITAFVPRDGCLNYIEENDEVLVAGFGRKGHAVGD 114 (143)
Q Consensus 35 ~~k~~~l~g~Pq~kGivl~~~~~~pKkPNSA~RK~~rV~L~kngk~v~A~IPg~G~l~~lqeh~~VLV~G~G~~Gg~v~D 114 (143)
..|++||+++||++|||+++++++|||||||+||||+||| +||++|+|||||||| ||||||+|||+| |+++|
T Consensus 16 ~~k~~~l~g~Pq~kGi~l~v~~~~pKKPNSA~RKvarV~L-~ngk~v~AyIPG~Gh--nlqehs~VLvrG-----Grv~D 87 (108)
T cd03368 16 KSKSPALEGCPQKKGVCLKVYTTTPKKPNSALRKVARVRL-SNGKEVTAYIPGEGH--NLQEHSVVLVRG-----GRVKD 87 (108)
T ss_pred cccCCcccCCcccCcEEEEEEeccccCCChhheeeEEEEe-cCCCEEEEEcCCCCC--CccccCEEEEeC-----CccCC
Confidence 4578999999999999999999999999999999999999 699999999999996 999999999998 99999
Q ss_pred CCCceEEEEEec
Q psy7476 115 IPGVRFKVVKVA 126 (143)
Q Consensus 115 lPGVrykvvrv~ 126 (143)
||||+|++||+.
T Consensus 88 lPGVkykvvRG~ 99 (108)
T cd03368 88 LPGVRYHIVRGV 99 (108)
T ss_pred CCCeEEEEEeee
Confidence 999999999997
No 10
>PRK05163 rpsL 30S ribosomal protein S12; Validated
Probab=100.00 E-value=6.4e-44 Score=272.22 Aligned_cols=88 Identities=34% Similarity=0.624 Sum_probs=83.8
Q ss_pred ccCCCCCCCCccceeEEeeeeccccCCCcccccEEEEEEeecCeEEEEeecCCCccCCcccccEEEEeeecCCCCcCCCC
Q psy7476 36 WKANPFGGASHAKGIVLEKVGVEAKQPNSAIRKCVRVQLIKNGKKITAFVPRDGCLNYIEENDEVLVAGFGRKGHAVGDI 115 (143)
Q Consensus 36 ~k~~~l~g~Pq~kGivl~~~~~~pKkPNSA~RK~~rV~L~kngk~v~A~IPg~G~l~~lqeh~~VLV~G~G~~Gg~v~Dl 115 (143)
.|++||+++||++|||+++++++|||||||+||||+||| +||++|||||||||| ||||||+|||+| |+++||
T Consensus 19 ~k~~~l~~~Pq~kGv~l~v~~~~pKKPNSA~RKvarVrL-~ngk~v~AyIPGeGh--nlqehs~VLvrG-----Grv~Dl 90 (124)
T PRK05163 19 SKSPALNACPQKRGVCTRVYTTTPKKPNSALRKVARVRL-TNGFEVTAYIPGEGH--NLQEHSVVLIRG-----GRVKDL 90 (124)
T ss_pred ccCcccccCcccCcEEEEEEecCccCCCchhheEEEEEe-CCCCEEEEEcCCCCC--CccccCEEEEeC-----CccCCC
Confidence 478999999999999999999999999999999999999 999999999999996 999999999997 999999
Q ss_pred CCceEEEEEeccccHHH
Q psy7476 116 PGVRFKVVKVANVSLLA 132 (143)
Q Consensus 116 PGVrykvvrv~~vsl~~ 132 (143)
|||+|+|||+. .++..
T Consensus 91 PGVrykvVrG~-~D~~g 106 (124)
T PRK05163 91 PGVRYHIVRGA-LDTAG 106 (124)
T ss_pred CCcEEEEeeee-ecccc
Confidence 99999999998 66655
No 11
>CHL00051 rps12 ribosomal protein S12
Probab=100.00 E-value=5.8e-44 Score=272.16 Aligned_cols=90 Identities=34% Similarity=0.615 Sum_probs=85.1
Q ss_pred cccCCCCCCCCccceeEEeeeeccccCCCcccccEEEEEEeecCeEEEEeecCCCccCCcccccEEEEeeecCCCCcCCC
Q psy7476 35 RWKANPFGGASHAKGIVLEKVGVEAKQPNSAIRKCVRVQLIKNGKKITAFVPRDGCLNYIEENDEVLVAGFGRKGHAVGD 114 (143)
Q Consensus 35 ~~k~~~l~g~Pq~kGivl~~~~~~pKkPNSA~RK~~rV~L~kngk~v~A~IPg~G~l~~lqeh~~VLV~G~G~~Gg~v~D 114 (143)
..|++||+++||++|||+++++++|||||||+||||+||| +||++|+|||||||| ||||||+|||+| |+++|
T Consensus 18 ~~k~~~L~g~Pq~kGv~lkv~~~~pKKPNSA~RKvarVrL-sngk~v~AyIPGeGh--nlqehs~VLvrG-----Grv~D 89 (123)
T CHL00051 18 KTKSPALRGCPQRRGTCTRVYTITPKKPNSALRKVARVRL-TSGFEITAYIPGIGH--NLQEHSVVLVRG-----GRVKD 89 (123)
T ss_pred cccCcccccCcccCeEEEEEEeccccCCChhheeEEEEEc-cCCCEEEEEcCCCCc--cccccCEEEEeC-----CccCC
Confidence 3578999999999999999999999999999999999999 999999999999998 999999999997 99999
Q ss_pred CCCceEEEEEeccccHHHH
Q psy7476 115 IPGVRFKVVKVANVSLLAL 133 (143)
Q Consensus 115 lPGVrykvvrv~~vsl~~l 133 (143)
||||+|+|||+. .++..+
T Consensus 90 lPGVrykvVRG~-~D~~gv 107 (123)
T CHL00051 90 LPGVRYHIVRGT-LDAVGV 107 (123)
T ss_pred CCCeeEEEEeee-eccccc
Confidence 999999999998 666653
No 12
>TIGR00981 rpsL_bact ribosomal protein S12, bacterial/organelle. 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.
Probab=100.00 E-value=8.9e-44 Score=271.44 Aligned_cols=88 Identities=34% Similarity=0.619 Sum_probs=83.9
Q ss_pred ccCCCCCCCCccceeEEeeeeccccCCCcccccEEEEEEeecCeEEEEeecCCCccCCcccccEEEEeeecCCCCcCCCC
Q psy7476 36 WKANPFGGASHAKGIVLEKVGVEAKQPNSAIRKCVRVQLIKNGKKITAFVPRDGCLNYIEENDEVLVAGFGRKGHAVGDI 115 (143)
Q Consensus 36 ~k~~~l~g~Pq~kGivl~~~~~~pKkPNSA~RK~~rV~L~kngk~v~A~IPg~G~l~~lqeh~~VLV~G~G~~Gg~v~Dl 115 (143)
.|++||+|+||++||||++++++|||||||+||||+||| +||++|||||||||| ||||||+|||+| |+++||
T Consensus 19 ~k~~~l~g~Pq~kGi~l~~~~~~pKKPNSA~RKvarVrL-~ngk~v~AyIPG~Gh--nlqehs~VLvrG-----Grv~Dl 90 (124)
T TIGR00981 19 SKSPALEACPQKRGVCTRVYTTTPKKPNSALRKVARVRL-TNGFEVTAYIPGEGH--NLQEHSVVLIRG-----GRVKDL 90 (124)
T ss_pred ccCcccccCCccCcEEEEEEeccccCCCchhheeEEEEe-CCCCEEEEEcCCCCC--CccccCEEEEeC-----CccCCC
Confidence 478999999999999999999999999999999999999 999999999999996 999999999997 999999
Q ss_pred CCceEEEEEeccccHHH
Q psy7476 116 PGVRFKVVKVANVSLLA 132 (143)
Q Consensus 116 PGVrykvvrv~~vsl~~ 132 (143)
|||+|+|||+. .+|..
T Consensus 91 PGVkykvVrG~-~D~~g 106 (124)
T TIGR00981 91 PGVRYHIVRGA-LDTAG 106 (124)
T ss_pred CCeEEEEEeEe-ecccc
Confidence 99999999998 66665
No 13
>PTZ00115 40S ribosomal protein S12; Provisional
Probab=100.00 E-value=2.6e-39 Score=272.30 Aligned_cols=93 Identities=31% Similarity=0.556 Sum_probs=85.6
Q ss_pred ccCCCCCCCCccceeEEeeeeccccCCCcccccEEEEEEeecCeEEEEeecCCCccCCcccccEEEEeeecCCCCcCCCC
Q psy7476 36 WKANPFGGASHAKGIVLEKVGVEAKQPNSAIRKCVRVQLIKNGKKITAFVPRDGCLNYIEENDEVLVAGFGRKGHAVGDI 115 (143)
Q Consensus 36 ~k~~~l~g~Pq~kGivl~~~~~~pKkPNSA~RK~~rV~L~kngk~v~A~IPg~G~l~~lqeh~~VLV~G~G~~Gg~v~Dl 115 (143)
.++.+|+|+||++|||+++++++|||||||+||||+||| +||++|+|||||||| ||||||+|||+| |+++||
T Consensus 115 ~k~paL~g~PQkKGIclkv~~~tPKKPNSA~RKvarVrL-sNGk~VtAyIPGeGH--nLQEHs~VLVRG-----GrvkDL 186 (290)
T PTZ00115 115 RRSKWLEGAPQKKGICVKVRVQTPRKPNSGLRKVARVRL-STGRTVTVYIPGIGH--NLNTHSVVLVRG-----GRCKDV 186 (290)
T ss_pred CcCccccCCcccCeEEEEeeecCCCCCCccccceEEEEe-cCCCEEEEEcCCCCc--ccccCCEEEEeC-----CCcCCC
Confidence 467899999999999999999999999999999999999 799999999999998 999999999997 999999
Q ss_pred CCceEEEEEeccccHHHHHhhhc
Q psy7476 116 PGVRFKVVKVANVSLLALYKEKK 138 (143)
Q Consensus 116 PGVrykvvrv~~vsl~~l~~gkk 138 (143)
|||+|+|||+. .++.. +.+++
T Consensus 187 PGVrYkvVRG~-~D~~g-V~~Rk 207 (290)
T PTZ00115 187 PGCNYKAVRGV-YDLLP-VKNRA 207 (290)
T ss_pred CCceEEEeeee-ccccc-ccccc
Confidence 99999999998 55555 44443
No 14
>KOG1750|consensus
Probab=99.97 E-value=1e-32 Score=213.53 Aligned_cols=83 Identities=41% Similarity=0.719 Sum_probs=80.3
Q ss_pred ccCCCCCCCCccceeEEeeeeccccCCCcccccEEEEEEeecCeEEEEeecCCCccCCcccccEEEEeeecCCCCcCCCC
Q psy7476 36 WKANPFGGASHAKGIVLEKVGVEAKQPNSAIRKCVRVQLIKNGKKITAFVPRDGCLNYIEENDEVLVAGFGRKGHAVGDI 115 (143)
Q Consensus 36 ~k~~~l~g~Pq~kGivl~~~~~~pKkPNSA~RK~~rV~L~kngk~v~A~IPg~G~l~~lqeh~~VLV~G~G~~Gg~v~Dl 115 (143)
.++.+|+|+||.+|||+.+++++|||||||+|||++|+| +||.+|+|||||+|| |+|||+.|||+| |+++|+
T Consensus 47 ~~~~~L~g~p~~kgvvl~v~t~~pkkPnsa~rK~~~vrl-stg~~i~ayipg~gh--nlqehs~Vlvrg-----gr~qdl 118 (139)
T KOG1750|consen 47 RKSPALDGCPQRKGVVLRVFTRKPKKPNSANRKCARVRL-STGREVTAYIPGIGH--NLQEHSIVLVRG-----GRVQDL 118 (139)
T ss_pred cccccccCCcccccEEEEEEEecCCCCCccceeeEEEEe-cCchheeeeCCCccc--cceeEEEEEEec-----ceeccC
Confidence 456899999999999999999999999999999999999 999999999999998 999999999998 999999
Q ss_pred CCceEEEEEec
Q psy7476 116 PGVRFKVVKVA 126 (143)
Q Consensus 116 PGVrykvvrv~ 126 (143)
|||+|++||+.
T Consensus 119 pgvk~~~vRg~ 129 (139)
T KOG1750|consen 119 PGVKYHVVRGV 129 (139)
T ss_pred cchhhhhhhhh
Confidence 99999999986
No 15
>TIGR00008 infA translation initiation factor IF-1. 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 (pfam00575).
Probab=93.99 E-value=0.1 Score=36.57 Aligned_cols=46 Identities=33% Similarity=0.478 Sum_probs=34.0
Q ss_pred cceeEEeeeeccccCCCcccccEEEEEEeecCeEEEEeecCCCccC--CcccccEEEEe
Q psy7476 47 AKGIVLEKVGVEAKQPNSAIRKCVRVQLIKNGKKITAFVPRDGCLN--YIEENDEVLVA 103 (143)
Q Consensus 47 ~kGivl~~~~~~pKkPNSA~RK~~rV~L~kngk~v~A~IPg~G~l~--~lqeh~~VLV~ 103 (143)
..|+|++.+ ||. -.+|+| -||.++.|||||-=-.| -|.+.|.|+|+
T Consensus 7 ~~G~V~e~L------~~~----~f~V~l-~ng~~vla~i~GKmr~~rI~I~~GD~V~Ve 54 (68)
T TIGR00008 7 MEGKVTESL------PNA----MFRVEL-ENGHEVLAHISGKIRMHYIRILPGDKVKVE 54 (68)
T ss_pred EEEEEEEEC------CCC----EEEEEE-CCCCEEEEEecCcchhccEEECCCCEEEEE
Confidence 346666654 454 467899 79999999999954322 27899999998
No 16
>COG0361 InfA Translation initiation factor 1 (IF-1) [Translation, ribosomal structure and biogenesis]
Probab=92.36 E-value=0.25 Score=35.37 Aligned_cols=47 Identities=34% Similarity=0.393 Sum_probs=36.7
Q ss_pred ccceeEEeeeeccccCCCcccccEEEEEEeecCeEEEEeecCCCccCC--cccccEEEEe
Q psy7476 46 HAKGIVLEKVGVEAKQPNSAIRKCVRVQLIKNGKKITAFVPRDGCLNY--IEENDEVLVA 103 (143)
Q Consensus 46 q~kGivl~~~~~~pKkPNSA~RK~~rV~L~kngk~v~A~IPg~G~l~~--lqeh~~VLV~ 103 (143)
+.-|+|++.++ |. =++|+| -||.+++|+|||-.-.|+ |-+-|.|+|+
T Consensus 8 e~~g~V~e~L~------~~----~f~v~~-edg~~~~ahI~GKmr~~~i~I~~GD~V~Ve 56 (75)
T COG0361 8 EMEGTVIEMLP------NG----RFRVEL-ENGHERLAHISGKMRKNRIRILPGDVVLVE 56 (75)
T ss_pred EEEEEEEEecC------CC----EEEEEe-cCCcEEEEEccCcchheeEEeCCCCEEEEE
Confidence 45566666653 33 367999 899999999999998655 5799999998
No 17
>PRK12442 translation initiation factor IF-1; Reviewed
Probab=85.40 E-value=1.4 Score=32.40 Aligned_cols=46 Identities=33% Similarity=0.414 Sum_probs=34.9
Q ss_pred cceeEEeeeeccccCCCcccccEEEEEEeecCeEEEEeecCCCccCC--cccccEEEEe
Q psy7476 47 AKGIVLEKVGVEAKQPNSAIRKCVRVQLIKNGKKITAFVPRDGCLNY--IEENDEVLVA 103 (143)
Q Consensus 47 ~kGivl~~~~~~pKkPNSA~RK~~rV~L~kngk~v~A~IPg~G~l~~--lqeh~~VLV~ 103 (143)
..|+|++.+ ||. -.+|+| -||.+|+|||+|-=-.|+ |.+.|.|+|+
T Consensus 9 ~~G~V~e~L------p~~----~frV~L-enG~~vla~isGKmR~~rIrIl~GD~V~VE 56 (87)
T PRK12442 9 LDGIVDEVL------PDS----RFRVTL-ENGVEVGAYASGRMRKHRIRILAGDRVTLE 56 (87)
T ss_pred EEEEEEEEC------CCC----EEEEEe-CCCCEEEEEeccceeeeeEEecCCCEEEEE
Confidence 456666654 454 467999 799999999999765444 5689999998
No 18
>smart00652 eIF1a eukaryotic translation initiation factor 1A.
Probab=83.20 E-value=2.2 Score=30.39 Aligned_cols=35 Identities=29% Similarity=0.283 Sum_probs=27.1
Q ss_pred EEEEEEeecCeEEEEeecCCCc-cCCcccccEEEEee
Q psy7476 69 CVRVQLIKNGKKITAFVPRDGC-LNYIEENDEVLVAG 104 (143)
Q Consensus 69 ~~rV~L~kngk~v~A~IPg~G~-l~~lqeh~~VLV~G 104 (143)
-.+|+| .||.++.|+|||-=. ---|.+.|.|+|+=
T Consensus 19 ~~~V~~-~dG~~~la~ipgK~Rk~iwI~~GD~VlVe~ 54 (83)
T smart00652 19 RLEVMC-ADGKERLARIPGKMRKKVWIRRGDIVLVDP 54 (83)
T ss_pred EEEEEE-CCCCEEEEEEchhhcccEEEcCCCEEEEEe
Confidence 367888 899999999999321 02488999999983
No 19
>cd04456 S1_IF1A_like S1_IF1A_like: Translation initiation factor IF1A-like, S1-like RNA-binding domain. IF1A is also referred to as eIF1A in eukaryotes and aIF1A in archaea. 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=80.27 E-value=3.4 Score=29.19 Aligned_cols=34 Identities=18% Similarity=0.230 Sum_probs=26.9
Q ss_pred EEEEEEeecCeEEEEeecCCCcc-CCcccccEEEEe
Q psy7476 69 CVRVQLIKNGKKITAFVPRDGCL-NYIEENDEVLVA 103 (143)
Q Consensus 69 ~~rV~L~kngk~v~A~IPg~G~l-~~lqeh~~VLV~ 103 (143)
-.+|++ .||.++.|.|||-=.= --+.+.|.|+|+
T Consensus 14 ~~~V~~-~dg~~~l~~i~gK~Rk~iwI~~GD~VlV~ 48 (78)
T cd04456 14 RHEVEC-ADGQRRLVSIPGKLRKNIWIKRGDFLIVD 48 (78)
T ss_pred EEEEEE-CCCCEEEEEEchhhccCEEEcCCCEEEEE
Confidence 467888 7999999999993210 258899999997
No 20
>TIGR00523 eIF-1A eukaryotic/archaeal initiation factor 1A. Recommended nomenclature: eIF-1A for eukaryotes, aIF-1A for Archaea. Also called eIF-4C
Probab=72.59 E-value=6.1 Score=29.20 Aligned_cols=53 Identities=25% Similarity=0.323 Sum_probs=38.0
Q ss_pred CCCCCCccceeEEeeeeccccCCCcccccEEEEEEeecCeEEEEeecCCCc-cCCcccccEEEEe
Q psy7476 40 PFGGASHAKGIVLEKVGVEAKQPNSAIRKCVRVQLIKNGKKITAFVPRDGC-LNYIEENDEVLVA 103 (143)
Q Consensus 40 ~l~g~Pq~kGivl~~~~~~pKkPNSA~RK~~rV~L~kngk~v~A~IPg~G~-l~~lqeh~~VLV~ 103 (143)
|+...-|.-|.|++..+ | --.+|+| .||.++.|+|||-=. --.|.+.|.|+|.
T Consensus 14 p~~~e~e~~g~V~~~lG------~----~~~~V~~-~dG~~~la~i~GK~Rk~iwI~~GD~VlVs 67 (99)
T TIGR00523 14 PRKEEGEILGVIEQMLG------A----GRVKVRC-LDGKTRLGRIPGKLKKRIWIREGDVVIVK 67 (99)
T ss_pred CCCCCCEEEEEEEEEcC------C----CEEEEEe-CCCCEEEEEEchhhcccEEecCCCEEEEE
Confidence 44344577788877765 2 1577888 799999999999321 1248899999994
No 21
>PLN00208 translation initiation factor (eIF); Provisional
Probab=68.09 E-value=7.8 Score=30.84 Aligned_cols=53 Identities=19% Similarity=0.181 Sum_probs=38.3
Q ss_pred CCCCCCccceeEEeeeeccccCCCcccccEEEEEEeecCeEEEEeecCCCc-cCCcccccEEEEe
Q psy7476 40 PFGGASHAKGIVLEKVGVEAKQPNSAIRKCVRVQLIKNGKKITAFVPRDGC-LNYIEENDEVLVA 103 (143)
Q Consensus 40 ~l~g~Pq~kGivl~~~~~~pKkPNSA~RK~~rV~L~kngk~v~A~IPg~G~-l~~lqeh~~VLV~ 103 (143)
+|-.--|.-|+|++.++- . -++|++ .||.+++|+|||-=. ---|.+.|.|||+
T Consensus 27 ~~p~egq~~g~V~~~lGn------~----~~~V~c-~dG~~rLa~IpGKmRKrIWI~~GD~VlVe 80 (145)
T PLN00208 27 IFKEDGQEYAQVLRMLGN------G----RCEALC-IDGTKRLCHIRGKMRKKVWIAAGDIILVG 80 (145)
T ss_pred ccCCCCcEEEEEEEEcCC------C----EEEEEE-CCCCEEEEEEeccceeeEEecCCCEEEEE
Confidence 333445777888877642 2 477888 799999999999321 0258899999998
No 22
>PTZ00329 eukaryotic translation initiation factor 1A; Provisional
Probab=66.35 E-value=9.3 Score=30.74 Aligned_cols=54 Identities=20% Similarity=0.178 Sum_probs=38.4
Q ss_pred CCCCCCccceeEEeeeeccccCCCcccccEEEEEEeecCeEEEEeecCCCcc-CCcccccEEEEee
Q psy7476 40 PFGGASHAKGIVLEKVGVEAKQPNSAIRKCVRVQLIKNGKKITAFVPRDGCL-NYIEENDEVLVAG 104 (143)
Q Consensus 40 ~l~g~Pq~kGivl~~~~~~pKkPNSA~RK~~rV~L~kngk~v~A~IPg~G~l-~~lqeh~~VLV~G 104 (143)
++..--|.-|.|++.++ |. -++|+| -||.+++|+|||-=.- --|.+.|.|||+-
T Consensus 27 ~~~eegq~~g~V~~~LG------n~----~f~V~c-~dG~~rLa~I~GKmRK~IWI~~GD~VlVel 81 (155)
T PTZ00329 27 VFKEEGQEYAQVLRMLG------NG----RLEAYC-FDGVKRLCHIRGKMRKRVWINIGDIILVSL 81 (155)
T ss_pred ccCCCCcEEEEEEEEcC------CC----EEEEEE-CCCCEEEEEeeccceeeEEecCCCEEEEec
Confidence 33345577788877764 32 467888 7999999999994210 2488999999973
No 23
>TIGR00230 sfsA sugar fermentation stimulation protein. probable regulatory factor involved in maltose metabolism contains a putative DNA binding domain. Isolated as a gene which enabled E.coli strain MK2001 to use maltose.
Probab=62.02 E-value=39 Score=28.38 Aligned_cols=35 Identities=31% Similarity=0.479 Sum_probs=30.6
Q ss_pred ccEEEEEEeecCeEEEEeecCCCcc-CCcccccEEEEe
Q psy7476 67 RKCVRVQLIKNGKKITAFVPRDGCL-NYIEENDEVLVA 103 (143)
Q Consensus 67 RK~~rV~L~kngk~v~A~IPg~G~l-~~lqeh~~VLV~ 103 (143)
|=.|.|.+ +|.+++|++|+-|.| .-+.+...|+++
T Consensus 20 RF~~~V~~--~G~~~~aH~pNtGrl~ell~pG~~vll~ 55 (232)
T TIGR00230 20 RFLVDVEV--DGRRETAHCPNTGRLTELIFPGNDVGLS 55 (232)
T ss_pred CEEEEEEE--CCeEEEEEcCCCCCChhhcCCCCEEEEE
Confidence 88899988 899999999999976 447788999997
No 24
>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=56.74 E-value=12 Score=26.26 Aligned_cols=35 Identities=31% Similarity=0.260 Sum_probs=27.0
Q ss_pred EEEEEEeecCeEEEEeecCCCc-cCCcccccEEEEee
Q psy7476 69 CVRVQLIKNGKKITAFVPRDGC-LNYIEENDEVLVAG 104 (143)
Q Consensus 69 ~~rV~L~kngk~v~A~IPg~G~-l~~lqeh~~VLV~G 104 (143)
-.+|+| -||.++.|+|||-=. --.+.+.|.|+|+=
T Consensus 14 ~~~V~~-~~g~~~la~i~gK~rk~iwI~~GD~V~Ve~ 49 (77)
T cd05793 14 RLEVRC-FDGKKRLCRIRGKMRKRVWINEGDIVLVAP 49 (77)
T ss_pred EEEEEE-CCCCEEEEEEchhhcccEEEcCCCEEEEEe
Confidence 367888 799999999998522 02478899999983
No 25
>PRK00347 putative DNA-binding transcriptional regulator; Reviewed
Probab=55.71 E-value=46 Score=27.77 Aligned_cols=36 Identities=25% Similarity=0.500 Sum_probs=30.6
Q ss_pred ccEEEEEEeecCeEEEEeecCCCcc-CCcccccEEEEe
Q psy7476 67 RKCVRVQLIKNGKKITAFVPRDGCL-NYIEENDEVLVA 103 (143)
Q Consensus 67 RK~~rV~L~kngk~v~A~IPg~G~l-~~lqeh~~VLV~ 103 (143)
|=.|.|++ -+|..++||+|+-|.| ..+.+...|+++
T Consensus 18 RF~~~V~~-~~g~~~~aH~pntGRl~ell~pG~~v~l~ 54 (234)
T PRK00347 18 RFLADVEL-DDGEELTAHCPNTGRMTGLLTPGNTVWLS 54 (234)
T ss_pred CEEEEEEE-CCCCEEEEEcCCCCCChhhccCCCEEEEE
Confidence 88899998 4699999999999976 447788889987
No 26
>PF01176 eIF-1a: Translation initiation factor 1A / IF-1; InterPro: IPR006196 The S1 domain of around 70 amino acids, originally identified in ribosomal protein S1, is found in a large number of RNA-associated proteins. It has been shown that S1 proteins bind RNA through their S1 domains with some degree of sequence specificity. This type of S1 domain is found in translation initiation factor 1. The solution structure of one S1 RNA-binding domain from Escherichia coli polynucleotide phosphorylase has been determined []. It displays some similarity with the cold shock domain (CSD) (IPR002059 from INTERPRO). Both the S1 and the CSD domain consist of an antiparallel beta barrel of the same topology with 5 beta strands. This fold is also shared by many other proteins of unrelated function and is known as the OB fold. However, the S1 and CSD fold can be distinguished from the other OB folds by the presence of a short 3(10) helix at the end of strand 3. This unique feature is likely to form a part of the DNA/RNA-binding site. This entry is specific for bacterial, chloroplastic and eukaryotic IF-1 type S1 domains.; GO: 0003723 RNA binding, 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 1JT8_A 3I4O_A 1AH9_A 1ZO1_W 1D7Q_A 2OQK_A 2DGY_A 1HR0_W.
Probab=53.19 E-value=12 Score=24.96 Aligned_cols=32 Identities=28% Similarity=0.435 Sum_probs=23.9
Q ss_pred EEEEEeecCeEEEEeecCCCccC--CcccccEEEEe
Q psy7476 70 VRVQLIKNGKKITAFVPRDGCLN--YIEENDEVLVA 103 (143)
Q Consensus 70 ~rV~L~kngk~v~A~IPg~G~l~--~lqeh~~VLV~ 103 (143)
.+|+| .||.+++|+|||- --+ .|.+.|.|+|+
T Consensus 18 ~~V~~-~dg~~~l~~i~gK-~r~~iwI~~GD~V~V~ 51 (65)
T PF01176_consen 18 FEVEC-EDGEERLARIPGK-FRKRIWIKRGDFVLVE 51 (65)
T ss_dssp EEEEE-TTSEEEEEEE-HH-HHTCC---TTEEEEEE
T ss_pred EEEEe-CCCCEEEEEeccc-eeeeEecCCCCEEEEE
Confidence 67898 8999999999996 323 47899999997
No 27
>PF03749 SfsA: Sugar fermentation stimulation protein; InterPro: IPR005224 The sugar fermentation stimulation protein is a probable regulatory factor involved in maltose metabolism. It contains a putative DNA-binding domain, and was isolated as a gene which enabled Escherichia coli W3110 (strain MK2001) to use maltose [].
Probab=52.30 E-value=68 Score=26.50 Aligned_cols=38 Identities=29% Similarity=0.464 Sum_probs=30.8
Q ss_pred cccEEEEEEeecCeEEEEeecCCCccC-CcccccEEEEee
Q psy7476 66 IRKCVRVQLIKNGKKITAFVPRDGCLN-YIEENDEVLVAG 104 (143)
Q Consensus 66 ~RK~~rV~L~kngk~v~A~IPg~G~l~-~lqeh~~VLV~G 104 (143)
+|=.|.|.| .+|..++||+|+-|.|. .|.+...|+++=
T Consensus 5 nRF~~~v~l-~~g~~~~~H~pntGRl~ell~pG~~v~l~~ 43 (215)
T PF03749_consen 5 NRFLADVEL-DDGEEVTAHCPNTGRLKELLVPGARVLLSK 43 (215)
T ss_pred CcEEEEEEE-CCCCEEEEEcCCCCcchhhccCCCEEEEEE
Confidence 355788888 45999999999999887 456888999973
No 28
>PRK04012 translation initiation factor IF-1A; Provisional
Probab=48.66 E-value=19 Score=26.74 Aligned_cols=53 Identities=28% Similarity=0.389 Sum_probs=37.7
Q ss_pred CCCCCCccceeEEeeeeccccCCCcccccEEEEEEeecCeEEEEeecCCCc-cCCcccccEEEEe
Q psy7476 40 PFGGASHAKGIVLEKVGVEAKQPNSAIRKCVRVQLIKNGKKITAFVPRDGC-LNYIEENDEVLVA 103 (143)
Q Consensus 40 ~l~g~Pq~kGivl~~~~~~pKkPNSA~RK~~rV~L~kngk~v~A~IPg~G~-l~~lqeh~~VLV~ 103 (143)
|+-..-|.-|+|++..+- . -.+|+| .||..+.|+|||-=. --.|.+.|.|+|+
T Consensus 16 ~~p~e~e~~g~V~~~lG~------~----~~~V~~-~dG~~~la~i~GK~Rk~IwI~~GD~VlVe 69 (100)
T PRK04012 16 PMPEEGEVFGVVEQMLGA------N----RVRVRC-MDGVERMGRIPGKMKKRMWIREGDVVIVA 69 (100)
T ss_pred cCCCCCEEEEEEEEEcCC------C----EEEEEe-CCCCEEEEEEchhhcccEEecCCCEEEEE
Confidence 444445777777776542 2 577888 799999999997421 1247889999997
No 29
>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=47.99 E-value=31 Score=22.99 Aligned_cols=58 Identities=24% Similarity=0.317 Sum_probs=32.1
Q ss_pred CcccccEEEEEEeecCeEEEEeecC-CCccCCcccccEEEEeeecCCCCcCCCCCCceEEEEEecccc
Q psy7476 63 NSAIRKCVRVQLIKNGKKITAFVPR-DGCLNYIEENDEVLVAGFGRKGHAVGDIPGVRFKVVKVANVS 129 (143)
Q Consensus 63 NSA~RK~~rV~L~kngk~v~A~IPg-~G~l~~lqeh~~VLV~G~G~~Gg~v~DlPGVrykvvrv~~vs 129 (143)
++++-+-+.|+| +||.++...+=+ |.++|-.=++-+....| +....++=| +||+++|-
T Consensus 6 ~~~~~~~V~V~L-k~g~~~~G~L~~~D~~mNlvL~~~~~~~~~-----~~~~~~~~v---~IRG~~I~ 64 (67)
T cd01726 6 KAIIGRPVVVKL-NSGVDYRGILACLDGYMNIALEQTEEYVNG-----QLKNKYGDA---FIRGNNVL 64 (67)
T ss_pred HhhCCCeEEEEE-CCCCEEEEEEEEEccceeeEEeeEEEEeCC-----ceeeEeCCE---EEECCEEE
Confidence 356778899999 899987765443 44444333333332221 223333332 67777653
No 30
>COG1489 SfsA DNA-binding protein, stimulates sugar fermentation [General function prediction only]
Probab=45.91 E-value=48 Score=28.34 Aligned_cols=36 Identities=25% Similarity=0.473 Sum_probs=30.4
Q ss_pred cccEEEEEEeecCeEEEEeecCCCccC-CcccccEEEEe
Q psy7476 66 IRKCVRVQLIKNGKKITAFVPRDGCLN-YIEENDEVLVA 103 (143)
Q Consensus 66 ~RK~~rV~L~kngk~v~A~IPg~G~l~-~lqeh~~VLV~ 103 (143)
+|=.+.|.| +|.+++|++|+-|.+. -+.+.+.|.++
T Consensus 17 nRFl~dv~l--~G~~~~~H~~ntGrm~~l~~pG~~v~l~ 53 (235)
T COG1489 17 NRFLADVEL--DGEEVTAHCPNTGRMTELLTPGNTVWLS 53 (235)
T ss_pred cceEEEEEE--CCeEEEEEcCCCCccccccCCCCEEEEE
Confidence 366788888 5999999999999876 56788999987
No 31
>cd01724 Sm_D1 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 D1 heterodimerizes with subunit D2 and three such heterodimers form a hexameric ring structure with alternating D1 and D2 subunits. The D1 - D2 heterodimer also assembles into a heptameric ring containing DB, D3, E, F, and G subunits. Sm-like proteins exist in archaea as well as prokaryotes which form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=39.63 E-value=43 Score=24.04 Aligned_cols=29 Identities=24% Similarity=0.378 Sum_probs=19.3
Q ss_pred CcccccEEEEEEeecCeEEEEeec-CCCccC
Q psy7476 63 NSAIRKCVRVQLIKNGKKITAFVP-RDGCLN 92 (143)
Q Consensus 63 NSA~RK~~rV~L~kngk~v~A~IP-g~G~l~ 92 (143)
++..-+-+.|.| +||..+...+= =|+++|
T Consensus 7 ~~l~g~~V~VeL-Kng~~~~G~L~~vD~~MN 36 (90)
T cd01724 7 MKLTNETVTIEL-KNGTIVHGTITGVDPSMN 36 (90)
T ss_pred HhCCCCEEEEEE-CCCCEEEEEEEEEcCcee
Confidence 355678899999 89987765432 244444
No 32
>PRK00284 pqqA coenzyme PQQ synthesis protein PqqA; Provisional
Probab=32.60 E-value=59 Score=19.15 Aligned_cols=13 Identities=15% Similarity=0.335 Sum_probs=10.8
Q ss_pred cCeEEEEeecCCC
Q psy7476 77 NGKKITAFVPRDG 89 (143)
Q Consensus 77 ngk~v~A~IPg~G 89 (143)
-|.+|+.|+|...
T Consensus 12 ~G~EItmY~~~r~ 24 (26)
T PRK00284 12 VGMEVTMYFSARX 24 (26)
T ss_pred cceEEEEEEeccc
Confidence 4999999999754
No 33
>PLN02856 fumarylacetoacetase
Probab=30.18 E-value=91 Score=28.60 Aligned_cols=34 Identities=21% Similarity=0.431 Sum_probs=23.8
Q ss_pred EEEEeecCeEEEEeecCCCccCCcccccEEEEeee
Q psy7476 71 RVQLIKNGKKITAFVPRDGCLNYIEENDEVLVAGF 105 (143)
Q Consensus 71 rV~L~kngk~v~A~IPg~G~l~~lqeh~~VLV~G~ 105 (143)
-+.|.-+|++.++.-.|+ .-.||+..|+|.++|+
T Consensus 369 llElt~~G~~p~~l~~g~-~r~fL~dGD~V~l~g~ 402 (424)
T PLN02856 369 LLELTWAGSREVSLEGGT-RRKFLEDGDEVVLSGW 402 (424)
T ss_pred EEEEEeCCccceEeccCC-ccccCCCCCEEEEEEE
Confidence 344444677766654454 2359999999999997
No 34
>cd01731 archaeal_Sm1 The archaeal sm1 proteins: The Sm proteins are conserved in all three domains of life and are always associated with U-rich RNA sequences. They function to mediate RNA-RNA interactions and RNA biogenesis. All Sm proteins contain a common sequence motif in two segments, Sm1 and Sm2, separated by a short variable linker. Eukaryotic Sm proteins form part of specific small nuclear ribonucleoproteins (snRNPs) that are involved in the processing of pre-mRNAs to mature mRNAs, and are a major component of the eukaryotic spliceosome. Most snRNPs consist of seven Sm proteins (B/B', D1, D2, D3, E, F and G) arranged in a ring on a uridine-rich sequence (Sm site), plus a small nuclear RNA (snRNA) (either U1, U2, U5 or U4/6). Since archaebacteria do not have any splicing apparatus, Sm proteins of archaebacteria may play a more general role. Archaeal Lsm proteins are likely to represent the ancestral Sm domain.
Probab=29.62 E-value=1.1e+02 Score=20.27 Aligned_cols=28 Identities=32% Similarity=0.473 Sum_probs=20.0
Q ss_pred cccccEEEEEEeecCeEEEEeecC-CCccC
Q psy7476 64 SAIRKCVRVQLIKNGKKITAFVPR-DGCLN 92 (143)
Q Consensus 64 SA~RK~~rV~L~kngk~v~A~IPg-~G~l~ 92 (143)
+++-|-+.|.| +||+.+....=+ |.++|
T Consensus 7 ~~~~~~V~V~l-~~g~~~~G~L~~~D~~mN 35 (68)
T cd01731 7 DSLNKPVLVKL-KGGKEVRGRLKSYDQHMN 35 (68)
T ss_pred HhcCCEEEEEE-CCCCEEEEEEEEECCcce
Confidence 45677899999 899998876544 34444
No 35
>TIGR01266 fum_ac_acetase fumarylacetoacetase. This enzyme catalyzes the final step in the breakdown of tyrosine or phenylalanine to fumarate and acetoacetate.
Probab=28.79 E-value=1.1e+02 Score=27.97 Aligned_cols=34 Identities=26% Similarity=0.424 Sum_probs=26.3
Q ss_pred EEEEeecCeEEEEeecCCCccCCcccccEEEEeee
Q psy7476 71 RVQLIKNGKKITAFVPRDGCLNYIEENDEVLVAGF 105 (143)
Q Consensus 71 rV~L~kngk~v~A~IPg~G~l~~lqeh~~VLV~G~ 105 (143)
-+.+.-+|++.++.-.|+-. .||+..|+|.++|+
T Consensus 361 ~lE~t~~g~~~v~l~~g~~r-~fL~dGD~V~~~~~ 394 (415)
T TIGR01266 361 MLELSWKGKKPIDVGQGETR-TFLEDGDEVILRGH 394 (415)
T ss_pred EEEEEeCCeeeeecCCCCCC-CCCCCCCEEEEEEE
Confidence 34554578777777667665 89999999999997
No 36
>PF00386 C1q: C1q domain; InterPro: IPR001073 This entry represents the C-terminal domain of C1q. C1q is a subunit of the C1 enzyme complex that activates the serum complement system. C1q comprises 6 A, 6 B and 6 C chains. These share the same topology, each possessing a small, globular N-terminal domain, a collagen-like Gly/Pro-rich central region, and a conserved C-terminal region, the C1q domain []. The C1q protein is produced in collagen-producing cells and shows sequence and structural similarity to collagens VIII and X [, ]. This domain is also found in multimerin and EMILIN proteins.; PDB: 1O91_C 2JG8_D 2JG9_A 2WNV_A 2WNU_A 1PK6_A 4DOU_A 1C3H_C 1C28_C 2OII_A ....
Probab=28.41 E-value=1.6e+02 Score=21.04 Aligned_cols=41 Identities=22% Similarity=0.323 Sum_probs=25.8
Q ss_pred cccccEEEEEEeecCeEEEEeecCCCc----------cCCcccccEEEEee
Q psy7476 64 SAIRKCVRVQLIKNGKKITAFVPRDGC----------LNYIEENDEVLVAG 104 (143)
Q Consensus 64 SA~RK~~rV~L~kngk~v~A~IPg~G~----------l~~lqeh~~VLV~G 104 (143)
+.....+.++|.+|+..+....-.... +-.|++.|+|-|+=
T Consensus 55 ~~~~~~~~~~L~~N~~~~~~~~~~~~~~~~~~~s~s~vl~L~~GD~V~v~~ 105 (127)
T PF00386_consen 55 TSSGSSVWVELMKNGNPVASTYASNSSGNYDSASNSAVLQLNKGDTVWVRL 105 (127)
T ss_dssp SEEEEEEEEEEEETTEEEEEEEECSBTTBEEEEEEEEEEEE-TT-EEEEEE
T ss_pred ccCCchhHHhhhhhccceeeEeecCCCCccceEEEEEEEEeCCCCEEEEEE
Confidence 556677888899999987665422222 11378888888874
No 37
>COG4776 Rnb Exoribonuclease II [Transcription]
Probab=28.14 E-value=62 Score=31.06 Aligned_cols=37 Identities=38% Similarity=0.528 Sum_probs=27.6
Q ss_pred cccEEEEEEeecCeEEEEeecCCC------ccCCcccccEEEEee
Q psy7476 66 IRKCVRVQLIKNGKKITAFVPRDG------CLNYIEENDEVLVAG 104 (143)
Q Consensus 66 ~RK~~rV~L~kngk~v~A~IPg~G------~l~~lqeh~~VLV~G 104 (143)
.|--.||||+-||- .||||+-= .|+.-||.-.|.|.|
T Consensus 573 ~R~G~RvrLleNGA--~~FIPa~lih~~reei~~n~e~gtv~I~g 615 (645)
T COG4776 573 SRGGMRVRLLENGA--IAFIPAPLIHANREELVCNQENGTVQIKG 615 (645)
T ss_pred ccCceEEEeccCCc--ceecchhhhccchhheEecCCCceEEEcc
Confidence 36678999999997 48999852 233446788888886
No 38
>cd05792 S1_eIF1AD_like S1_eIF1AD_like: eukaryotic translation initiation factor 1A domain containing protein (eIF1AD)-like, S1-like RNA-binding domain. eIF1AD is also known as MGC11102 protein. Little is known about the function of eIF1AD. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins, including translation initiation factor IF1A (also referred to as eIF1A in eukaryotes). eIF1A 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.
Probab=26.38 E-value=1.1e+02 Score=21.80 Aligned_cols=34 Identities=26% Similarity=0.261 Sum_probs=25.6
Q ss_pred EEEEEeecCeEEEEeecCCCc-cCCcccccEEEEee
Q psy7476 70 VRVQLIKNGKKITAFVPRDGC-LNYIEENDEVLVAG 104 (143)
Q Consensus 70 ~rV~L~kngk~v~A~IPg~G~-l~~lqeh~~VLV~G 104 (143)
..|++ -+|.+..|-||+-=. ---+.+.|.|||.=
T Consensus 15 ~~V~~-~dG~~~l~~iP~KfRk~iWIkrGd~VlV~p 49 (78)
T cd05792 15 HEVET-PNGSRYLVSMPTKFRKNIWIKRGDFVLVEP 49 (78)
T ss_pred EEEEc-CCCCEEEEEechhhcccEEEEeCCEEEEEe
Confidence 56677 699999999999311 02589999999973
No 39
>COG2302 Uncharacterized conserved protein, contains S4-like domain [Function unknown]
Probab=25.75 E-value=67 Score=27.91 Aligned_cols=16 Identities=38% Similarity=0.729 Sum_probs=14.3
Q ss_pred CCcccccEEEEeeecC
Q psy7476 92 NYIEENDEVLVAGFGR 107 (143)
Q Consensus 92 ~~lqeh~~VLV~G~G~ 107 (143)
-.+++.|.+.||||||
T Consensus 219 ~~v~~GDliSirG~GR 234 (257)
T COG2302 219 YEVQEGDLISIRGFGR 234 (257)
T ss_pred ceeccCCEEEEecccc
Confidence 3699999999999996
No 40
>cd01733 LSm10 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. LSm10 is an SmD1-like protein which is thought to bind U7 snRNA along with LSm11 and five other Sm subunits to form a 7-member ring structure. LSm10 and the U7 snRNP of which it is a part are thought to play an important role in histone mRNA 3' processing.
Probab=25.58 E-value=1.4e+02 Score=20.75 Aligned_cols=38 Identities=24% Similarity=0.364 Sum_probs=24.0
Q ss_pred CcccccEEEEEEeecCeEEEEeecC-CCccCCcccccEEEE
Q psy7476 63 NSAIRKCVRVQLIKNGKKITAFVPR-DGCLNYIEENDEVLV 102 (143)
Q Consensus 63 NSA~RK~~rV~L~kngk~v~A~IPg-~G~l~~lqeh~~VLV 102 (143)
+++.-+-+.|.| +||..+...+-+ |+++| ++=-|...+
T Consensus 15 ~~l~g~~V~VeL-Kng~~~~G~L~~vD~~MN-l~L~~~~~~ 53 (78)
T cd01733 15 QGLQGKVVTVEL-RNETTVTGRIASVDAFMN-IRLAKVTII 53 (78)
T ss_pred HHCCCCEEEEEE-CCCCEEEEEEEEEcCCce-eEEEEEEEE
Confidence 345667799999 999988876554 44443 444444444
No 41
>PRK00737 small nuclear ribonucleoprotein; Provisional
Probab=24.79 E-value=1.3e+02 Score=20.38 Aligned_cols=24 Identities=29% Similarity=0.409 Sum_probs=18.2
Q ss_pred CcccccEEEEEEeecCeEEEEeecC
Q psy7476 63 NSAIRKCVRVQLIKNGKKITAFVPR 87 (143)
Q Consensus 63 NSA~RK~~rV~L~kngk~v~A~IPg 87 (143)
++++-|-+.|.| +||+.+...+=|
T Consensus 10 ~~~~~k~V~V~l-k~g~~~~G~L~~ 33 (72)
T PRK00737 10 NNALNSPVLVRL-KGGREFRGELQG 33 (72)
T ss_pred HHhCCCEEEEEE-CCCCEEEEEEEE
Confidence 456778899999 899998765444
No 42
>PRK00276 infA translation initiation factor IF-1; Validated
Probab=23.10 E-value=2.3e+02 Score=19.19 Aligned_cols=33 Identities=30% Similarity=0.350 Sum_probs=24.1
Q ss_pred EEEEEeecCeEEEEeecCCCcc--CCcccccEEEEe
Q psy7476 70 VRVQLIKNGKKITAFVPRDGCL--NYIEENDEVLVA 103 (143)
Q Consensus 70 ~rV~L~kngk~v~A~IPg~G~l--~~lqeh~~VLV~ 103 (143)
..|++ .||..+.|+++|-=-. ..+-..|.|+|+
T Consensus 22 y~V~~-~~g~~~~c~~~Gklr~~~i~i~vGD~V~ve 56 (72)
T PRK00276 22 FRVEL-ENGHEVLAHISGKMRKNYIRILPGDKVTVE 56 (72)
T ss_pred EEEEe-CCCCEEEEEEccceeeCCcccCCCCEEEEE
Confidence 45666 6899999999984221 136789999998
No 43
>PLN00051 RNA-binding S4 domain-containing protein; Provisional
Probab=23.00 E-value=51 Score=28.11 Aligned_cols=15 Identities=40% Similarity=0.570 Sum_probs=13.4
Q ss_pred CcccccEEEEeeecC
Q psy7476 93 YIEENDEVLVAGFGR 107 (143)
Q Consensus 93 ~lqeh~~VLV~G~G~ 107 (143)
.+.+.|+|.|||+|+
T Consensus 231 ~v~~gD~isiRG~GR 245 (267)
T PLN00051 231 TLKTGDVVSVSGKGR 245 (267)
T ss_pred CCCCCCEEEEeeCCE
Confidence 789999999999884
No 44
>TIGR02107 PQQ_syn_pqqA coenzyme PQQ biosynthesis protein A. This model describes a very small protein, coenzyme PQQ biosynthesis protein A, which is smaller than 25 amino acids in many species. It is proposed to serve as a peptide precursor of coenzyme pyrrolo-quinoline-quinone (PQQ), with Glu and Tyr of a conserved motif Glu-Xxx-Xxx-Xxx-Tyr becoming part of the product.
Probab=21.28 E-value=1.3e+02 Score=17.80 Aligned_cols=13 Identities=23% Similarity=0.419 Sum_probs=10.6
Q ss_pred cCeEEEEeecCCC
Q psy7476 77 NGKKITAFVPRDG 89 (143)
Q Consensus 77 ngk~v~A~IPg~G 89 (143)
-|.+||+|++...
T Consensus 11 ~G~EVTmY~~~~~ 23 (26)
T TIGR02107 11 LGMEVTMYVSAXX 23 (26)
T ss_pred ccEEEEEEeeccc
Confidence 4899999998654
No 45
>PF11975 Glyco_hydro_4C: Family 4 glycosyl hydrolase C-terminal domain; InterPro: IPR022616 This domain is found primarily in bacterial family 4 glycosyl hydrolases. It is found in the C terminus. ; GO: 0004553 hydrolase activity, hydrolyzing O-glycosyl compounds; PDB: 1UP4_A 1UP6_C 1UP7_E 1VJT_A 1U8X_X 1S6Y_A 3FEF_D 1OBB_A.
Probab=21.16 E-value=1.3e+02 Score=24.09 Aligned_cols=29 Identities=21% Similarity=0.329 Sum_probs=21.0
Q ss_pred ecCeEEEEe-ecCCCccCCcccccEEEEee
Q psy7476 76 KNGKKITAF-VPRDGCLNYIEENDEVLVAG 104 (143)
Q Consensus 76 kngk~v~A~-IPg~G~l~~lqeh~~VLV~G 104 (143)
.|...++.. +|++|+|.||...++|-|-.
T Consensus 148 ~~~~~~~~vNv~N~G~I~nLp~davVEvp~ 177 (232)
T PF11975_consen 148 NDKPKRFVVNVPNNGAIPNLPDDAVVEVPC 177 (232)
T ss_dssp HSSEEEEEEEEE-TTSSTTS-TTSEEEEEE
T ss_pred cCCCeEEEEECCCCCccCCCCCCcEEEEEE
Confidence 344444555 99999999999999998875
No 46
>cd03109 DTBS Dethiobiotin synthetase (DTBS) is the penultimate enzyme in the biotin biosynthesis pathway in Escherichia coli and other microorganisms. The enzyme catalyzes formation of the ureido ring of dethiobiotin from (7R,8S)-7,8-diaminononanoic acid (DAPA) and carbon dioxide. The enzyme utilizes carbon dioxide instead of hydrogen carbonate as substrate and is dependent on ATP and divalent metal ions as cofactors.
Probab=20.97 E-value=1.2e+02 Score=22.33 Aligned_cols=24 Identities=33% Similarity=0.556 Sum_probs=19.0
Q ss_pred ecCeEEEEeecCCCccCCcccccEEEEeeec
Q psy7476 76 KNGKKITAFVPRDGCLNYIEENDEVLVAGFG 106 (143)
Q Consensus 76 kngk~v~A~IPg~G~l~~lqeh~~VLV~G~G 106 (143)
..|..|-+|=|... +|.|+|||-|
T Consensus 25 ~~~~~v~~~kp~~~-------~d~vliEGaG 48 (134)
T cd03109 25 EKGYRVAPLKPVQT-------YDFVLVEGAG 48 (134)
T ss_pred HCCCeEEEEecCCC-------CCEEEEECCC
Confidence 35778888877765 7999999976
No 47
>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=20.91 E-value=2.6e+02 Score=18.56 Aligned_cols=32 Identities=28% Similarity=0.226 Sum_probs=21.1
Q ss_pred CcccccEEEEEEeecCeEEEEeecC-CCccCCcc
Q psy7476 63 NSAIRKCVRVQLIKNGKKITAFVPR-DGCLNYIE 95 (143)
Q Consensus 63 NSA~RK~~rV~L~kngk~v~A~IPg-~G~l~~lq 95 (143)
++++-+-+.|.| +||..+...+=+ |.++|-+=
T Consensus 7 ~~~~g~~V~V~L-k~g~~~~G~L~~~D~~mNi~L 39 (68)
T cd01722 7 NDLTGKPVIVKL-KWGMEYKGTLVSVDSYMNLQL 39 (68)
T ss_pred HHcCCCEEEEEE-CCCcEEEEEEEEECCCEEEEE
Confidence 355667899999 899987765333 45544433
No 48
>PF02080 TrkA_C: TrkA-C domain; InterPro: IPR006037 The regulator of K+ conductance (RCK) domain is found in many ligand-gated K+ channels, most often attached to the intracellular carboxy terminus. The domain is prevalent among prokaryotic K+ channels, and also found in eukaryotic, high-conductance Ca2+-activated K+ channels (BK channels) [, , ]. Largely involved in redox-linked regulation of potassium channels, the N-terminal part of the RCK domain is predicted to be an active dehydrogenase at least in some cases []. Some have a conserved sequence motif (G-x-G-x-x-G-x(n)-[DE]) for NAD+ binding [], but others do not, reflecting the diversity of ligands for RCK domains. The C-terminal part is less conserved, being absent in some channels, such as the kefC antiporter from Escherichia coli. It is predicted to bind unidentified ligands and to regulate sulphate, sodium and other transporters. The X-ray structure of several RCK domains has been solved [, , ]. It reveals an alpha-beta fold similar to dehydrogenase enzymes. The domain forms a homodimer, producing a cleft between two lobes. It has a composite structure, with an N-terminal (RCK-N), and a C-terminal (RCK-C) subdomain. The RCK-N subdomain forms a Rossmann fold with two alpha helices on one side of a six stranded parallel beta sheet and three alpha helices on the other side. The RCK-C subdomain is an all-beta-strand fold. It forms an extention of the dimer interface and further stabilises the RCK homodimer [, , ]. Ca2+ is a ligand that opens the channel in a concentration-dependent manner. Two Ca2+ ions are located at the base of a cleft between two RCK domains, coordinated by the carboxylate groups of two glutamate residues, and by an aspartate residue [, , ]. RCK domains occur in at least five different contexts: As a single domain on the C terminus of some K+ channels (for example, many prokaryotic K+ channels). As two tandem RCK domains on the C terminus of some transporters that form gating rings (for example, eukaryotic BK channels). The gating ring has an arrangement of eight identical RCK domains, one from each of the four pore-forming subunits and four from the intracellular solution. As two domains, one at the N terminus and another at the C terminus of transporter (for example, the prokaryotic trk system potassium uptake protein A). As a soluble protein (not part of a K+ channel) consisting of two tandem RCK domains. As a soluble protein consisting of a single RCK domain. This entry represents the C-terminal subdomain of RCK.; GO: 0008324 cation transmembrane transporter activity, 0006813 potassium ion transport; PDB: 2BKP_A 1VCT_A 2BKO_A 2BKN_A 3L4B_C 2FY8_D 2AEF_A 1LNQ_E 3RBX_C 3KXD_A ....
Probab=20.65 E-value=93 Score=19.63 Aligned_cols=21 Identities=19% Similarity=0.488 Sum_probs=13.8
Q ss_pred EEeecCCCccCCcccccEEEEee
Q psy7476 82 TAFVPRDGCLNYIEENDEVLVAG 104 (143)
Q Consensus 82 ~A~IPg~G~l~~lqeh~~VLV~G 104 (143)
..++|.... .|+++|.++|.|
T Consensus 38 ~~~~p~~~~--~l~~gD~l~v~g 58 (71)
T PF02080_consen 38 EIIIPDGDT--VLQAGDILIVVG 58 (71)
T ss_dssp EEES--TT---BE-TTEEEEEEE
T ss_pred EEECCCCCC--EECCCCEEEEEE
Confidence 356777765 899999999986
No 49
>TIGR03069 PS_II_S4 photosystem II S4 domain protein. Members of this protein family are about 265 residues long and each contains an S4 RNA-binding domain of about 48 residues. The member from the Cyanobacterium, Synechocystis sp. PCC 6803, was detected as a novel polypeptide in a highly purified preparation of active photosystem II (Kashino, et al., 2002). The phylogenetic distribution, including Cyanobacteria and Arabidopsis, supports a role in photosystem II, although the high bit score cutoffs for this model reflect similar sequences in non-photosynthetic organisms such as Carboxydothermus hydrogenoformans, a Gram-positive bacterium.
Probab=20.61 E-value=1.1e+02 Score=25.74 Aligned_cols=15 Identities=27% Similarity=0.465 Sum_probs=13.0
Q ss_pred CcccccEEEEeeecC
Q psy7476 93 YIEENDEVLVAGFGR 107 (143)
Q Consensus 93 ~lqeh~~VLV~G~G~ 107 (143)
.+.+.|+|.|+|+|+
T Consensus 223 ~v~~gD~IsvrG~Gr 237 (257)
T TIGR03069 223 ELKVGDRLQLRGKGR 237 (257)
T ss_pred cCCCCCEEEEcCCce
Confidence 678899999999874
Done!