Query 032641
Match_columns 136
No_of_seqs 118 out of 360
Neff 3.5
Searched_HMMs 46136
Date Fri Mar 29 04:03:54 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/032641.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/032641hhsearch_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 3E-72 6.5E-77 432.8 13.6 136 1-136 7-143 (143)
2 TIGR00982 S23_S12_E_A ribosoma 100.0 8.5E-71 1.8E-75 423.1 13.5 136 1-136 2-139 (139)
3 PRK04211 rps12P 30S ribosomal 100.0 8.1E-71 1.7E-75 425.6 13.2 136 1-136 8-145 (145)
4 KOG1749 40S ribosomal protein 100.0 6.2E-69 1.3E-73 410.8 11.1 136 1-136 7-143 (143)
5 cd03367 Ribosomal_S23 S12-like 100.0 4.8E-62 1E-66 365.2 12.1 114 20-133 1-115 (115)
6 COG0048 RpsL Ribosomal protein 100.0 1.6E-55 3.5E-60 334.9 11.3 122 1-135 1-123 (129)
7 PF00164 Ribosom_S12_S23: Ribo 100.0 1.6E-48 3.4E-53 294.5 8.1 105 23-135 11-122 (122)
8 cd00319 Ribosomal_S12_like Rib 100.0 6.8E-48 1.5E-52 281.0 9.6 94 27-130 1-95 (95)
9 cd03368 Ribosomal_S12 S12-like 100.0 8.6E-44 1.9E-48 264.4 9.9 80 32-119 20-99 (108)
10 PRK05163 rpsL 30S ribosomal pr 100.0 3E-43 6.5E-48 266.7 9.8 80 32-119 22-101 (124)
11 CHL00051 rps12 ribosomal prote 100.0 2.8E-43 6.1E-48 266.5 9.5 80 32-119 22-101 (123)
12 TIGR00981 rpsL_bact ribosomal 100.0 3.4E-43 7.4E-48 266.4 9.7 80 32-119 22-101 (124)
13 PTZ00115 40S ribosomal protein 100.0 3E-38 6.5E-43 264.1 9.9 79 33-119 119-197 (290)
14 KOG1750 Mitochondrial/chloropl 100.0 2E-31 4.2E-36 205.0 5.8 80 32-119 50-129 (139)
15 TIGR00008 infA translation ini 94.3 0.09 1.9E-06 36.6 4.4 34 62-96 19-54 (68)
16 COG0361 InfA Translation initi 92.7 0.23 4.9E-06 35.3 4.3 34 63-97 22-57 (75)
17 PRK12442 translation initiatio 86.2 1.3 2.8E-05 32.4 4.0 39 54-97 17-57 (87)
18 smart00652 eIF1a eukaryotic tr 84.2 2.1 4.6E-05 30.3 4.2 34 63-97 20-54 (83)
19 cd04456 S1_IF1A_like S1_IF1A_l 81.9 3.1 6.6E-05 29.2 4.3 35 62-97 14-49 (78)
20 TIGR00523 eIF-1A eukaryotic/ar 74.6 5.7 0.00012 29.1 4.0 54 32-96 13-67 (99)
21 PLN00208 translation initiatio 69.9 7.3 0.00016 30.7 3.9 53 33-97 27-81 (145)
22 PTZ00329 eukaryotic translatio 68.3 8.7 0.00019 30.7 4.0 53 33-97 27-81 (155)
23 TIGR00230 sfsA sugar fermentat 65.3 16 0.00034 30.4 5.2 36 60-97 20-56 (232)
24 PF03749 SfsA: Sugar fermentat 61.8 20 0.00044 29.3 5.2 37 60-97 6-43 (215)
25 cd05793 S1_IF1A S1_IF1A: Trans 56.3 13 0.00029 25.8 2.8 34 63-97 15-49 (77)
26 PRK00347 putative DNA-binding 54.9 32 0.00069 28.5 5.3 37 60-97 18-55 (234)
27 PF01176 eIF-1a: Translation i 51.7 14 0.0003 24.6 2.2 33 63-97 18-52 (65)
28 COG1489 SfsA DNA-binding prote 50.1 39 0.00085 28.6 5.1 37 59-97 17-54 (235)
29 PRK04012 translation initiatio 47.6 21 0.00046 26.2 2.8 53 33-96 16-69 (100)
30 PRK00284 pqqA coenzyme PQQ syn 36.3 50 0.0011 19.3 2.6 12 71-82 13-24 (26)
31 PLN02856 fumarylacetoacetase 35.0 66 0.0014 29.2 4.5 33 66-99 371-403 (424)
32 COG2302 Uncharacterized conser 32.8 43 0.00094 28.8 2.8 26 85-122 219-244 (257)
33 cd01726 LSm6 The eukaryotic Sm 32.7 68 0.0015 21.1 3.2 29 56-85 6-35 (67)
34 PF00386 C1q: C1q domain; Int 32.3 1.2E+02 0.0025 21.5 4.6 41 57-97 55-105 (127)
35 TIGR01266 fum_ac_acetase fumar 32.1 86 0.0019 28.4 4.7 33 65-98 362-394 (415)
36 cd05792 S1_eIF1AD_like S1_eIF1 29.6 97 0.0021 21.9 3.7 34 63-97 15-49 (78)
37 COG4776 Rnb Exoribonuclease II 29.1 51 0.0011 31.4 2.9 37 59-97 573-615 (645)
38 cd01724 Sm_D1 The eukaryotic S 27.6 1.4E+02 0.003 21.3 4.3 21 56-77 7-27 (90)
39 PF02080 TrkA_C: TrkA-C domain 25.8 66 0.0014 20.2 2.2 21 75-97 38-58 (71)
40 PLN00051 RNA-binding S4 domain 25.1 44 0.00095 28.2 1.6 15 86-100 231-245 (267)
41 TIGR02107 PQQ_syn_pqqA coenzym 24.4 97 0.0021 18.1 2.5 13 70-82 11-23 (26)
42 PRK00276 infA translation init 24.1 2.3E+02 0.005 19.0 4.7 33 63-96 22-56 (72)
43 KOG4716 Thioredoxin reductase 23.8 1.5E+02 0.0032 27.7 4.7 46 62-114 123-185 (503)
44 cd01732 LSm5 The eukaryotic Sm 22.8 1.5E+02 0.0032 20.4 3.6 30 56-86 9-39 (76)
45 TIGR03069 PS_II_S4 photosystem 22.4 93 0.002 25.9 3.0 15 86-100 223-237 (257)
46 PF11975 Glyco_hydro_4C: Famil 22.1 1.1E+02 0.0025 24.2 3.3 30 69-98 148-178 (232)
47 cd04497 hPOT1_OB1_like hPOT1_O 20.9 2.1E+02 0.0045 21.2 4.3 65 61-131 37-107 (138)
48 cd03109 DTBS Dethiobiotin synt 20.4 1.3E+02 0.0028 21.8 3.1 24 69-99 25-48 (134)
49 PF06565 DUF1126: Repeat of un 20.3 40 0.00086 20.2 0.3 12 48-59 12-23 (33)
No 1
>PTZ00067 40S ribosomal S23; Provisional
Probab=100.00 E-value=3e-72 Score=432.80 Aligned_cols=136 Identities=80% Similarity=1.298 Sum_probs=134.3
Q ss_pred CchhhhhHhhhhhccccchhhhhhccCCccc-CCCCCCCCccceEEeeeeecccCCCcccceEEEEEEecCCcEEEEEeC
Q 032641 1 MGAGRKLKSHRRRQRWADKSYKKSHLGNEWK-KPFAGSSHAKGIVLEKIGIEAKQPNSAIRKCARVQLIKNGKKIAAFVP 79 (136)
Q Consensus 1 l~~arkl~~~r~~~rw~d~~ykk~~lg~~~k-~pl~g~pq~kGivl~~~~~~pKkPNSA~RK~~rVqLikngk~v~A~IP 79 (136)
|||||||+++|+.+||+|++|+++|||+.+| |||+++||++|||++++++||||||||+||||+|||++||++||||||
T Consensus 7 l~aarkl~~~r~~~rw~d~~y~k~~lg~~~k~~pl~g~pq~kGivl~~~~~~pKkPNSA~RK~~rV~L~kngk~vtAyiP 86 (143)
T PTZ00067 7 LRAARKLRRHRRVNRWADKEYKKAHLGTRYKANPFGGASHAKGIVVEKIGIEAKQPNSAIRKCVRVQLIKNGKKITAFVP 86 (143)
T ss_pred hHHHHHHHHHHHHhhhhhHHHHHHhcCCccccCcccCCCccceEEEEEEeecCCCCChhhceEEEEEEccCCcEEEEEeC
Confidence 6999999999999999999999999999999 999999999999999999999999999999999999889999999999
Q ss_pred CCCccCcccccCeEEEeeecCCCCcCCCCCCceEEEEEecChhHHHHhhhhccCCCC
Q 032641 80 NDGCLNYIEENDEVLIAGFGRKGHAVGDIPGVRFKVVKVSGVSLLALFKEKKEKPRS 136 (136)
Q Consensus 80 g~G~l~~lqeh~~VLV~G~G~~gg~v~DlPGVrykvvrv~~vsl~al~~gkkekp~~ 136 (136)
||||||||||||+|||+|||++||+++|||||+|+||+||||||+|||+||||||++
T Consensus 87 g~G~lh~lqEh~~VLV~G~Gr~g~~v~DlPGVrykvVrV~~vsL~~l~kgkkekp~r 143 (143)
T PTZ00067 87 NDGCLNFINENDEVLVSGFGRSGHAVGDIPGVRFKVVKVAGVSLLALYKGKKEKPRN 143 (143)
T ss_pred CCCcccccccCCEEEEEecCcCCCccCCCCceEEEEEEECCEeHHHHHhcccccCCC
Confidence 999999999999999999999999999999999999999999999999999999985
No 2
>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=8.5e-71 Score=423.14 Aligned_cols=136 Identities=59% Similarity=0.999 Sum_probs=134.1
Q ss_pred CchhhhhHhhhhhccccchhhhhhccCCccc-CCCCCCCCccceEEeeeeecccCCCcccceEEEEEEecCCcEEEEEeC
Q 032641 1 MGAGRKLKSHRRRQRWADKSYKKSHLGNEWK-KPFAGSSHAKGIVLEKIGIEAKQPNSAIRKCARVQLIKNGKKIAAFVP 79 (136)
Q Consensus 1 l~~arkl~~~r~~~rw~d~~ykk~~lg~~~k-~pl~g~pq~kGivl~~~~~~pKkPNSA~RK~~rVqLikngk~v~A~IP 79 (136)
|||||||+++|++|||+|++|+++++|+..| +||+|+||++|||++++++||||||||+||||||||++||++||||||
T Consensus 2 l~aarkl~~~r~~~rw~d~~y~k~~~~~~~K~~~l~g~Pq~kGivl~~~~~~pKkPNSA~RK~~rV~L~~ngk~vtAyiP 81 (139)
T TIGR00982 2 LFAARKLKRKRKKFRWSDRRFKRRMLRLKRKADPLEGAPMARGIVLEKVGVEARQPNSAIRKCVRVQLIKNGKVVTAFCP 81 (139)
T ss_pred chhHHHHHHHHHHhhhhhHHHHHHhhccccccCcccCCCccCeEEEEEEeecCCCCCcccceEEEEEEccCCeEEEEEeC
Confidence 7999999999999999999999999999999 999999999999999999999999999999999999999999999999
Q ss_pred CCCccCcccccCeEEEeeec-CCCCcCCCCCCceEEEEEecChhHHHHhhhhccCCCC
Q 032641 80 NDGCLNYIEENDEVLIAGFG-RKGHAVGDIPGVRFKVVKVSGVSLLALFKEKKEKPRS 136 (136)
Q Consensus 80 g~G~l~~lqeh~~VLV~G~G-~~gg~v~DlPGVrykvvrv~~vsl~al~~gkkekp~~ 136 (136)
||||+|||||||+|||+||| ++||+++|||||+|+||+|+||||+|||+||||||++
T Consensus 82 g~G~~~~lqeh~~VLV~G~gg~~gg~v~DlPGVrykvVkV~~vsL~~l~~gkkekp~r 139 (139)
T TIGR00982 82 GDGAINFIDEHDEVIIEGIGGPRGRSMGDIPGVRYKVVKVNNVSLKELVKGKKEKPRR 139 (139)
T ss_pred CCccccccccCCEEEEEecCccCCCCcCCCCceEEEEEEECCEeHHHHHhcccccCCC
Confidence 99999999999999999998 9999999999999999999999999999999999985
No 3
>PRK04211 rps12P 30S ribosomal protein S12P; Reviewed
Probab=100.00 E-value=8.1e-71 Score=425.64 Aligned_cols=136 Identities=61% Similarity=1.018 Sum_probs=134.0
Q ss_pred CchhhhhHhhhhhccccchhhhhhccCCccc-CCCCCCCCccceEEeeeeecccCCCcccceEEEEEEecCCcEEEEEeC
Q 032641 1 MGAGRKLKSHRRRQRWADKSYKKSHLGNEWK-KPFAGSSHAKGIVLEKIGIEAKQPNSAIRKCARVQLIKNGKKIAAFVP 79 (136)
Q Consensus 1 l~~arkl~~~r~~~rw~d~~ykk~~lg~~~k-~pl~g~pq~kGivl~~~~~~pKkPNSA~RK~~rVqLikngk~v~A~IP 79 (136)
|||||||+++|++|||+|++|++++||+.+| +||+|+||++|||++++++||||||||+||||+|||++||++||||||
T Consensus 8 l~aarkl~~~r~~~rw~d~~y~k~~lg~~~K~~~l~g~Pq~kGivl~~~~v~pKKPNSA~RK~arV~L~~Ngk~vtAyIP 87 (145)
T PRK04211 8 LFAARKLKLKRKKFRWSDRRYKRRMLGLKEKADPLEGAPMARGIVLEKVGVEAKQPNSAIRKCVRVQLIKNGKQVTAFCP 87 (145)
T ss_pred hhHHHHHHHHHHHhhhhhHHHHHHHhCcccccCcccCCCccCeEEEEEeeecCCCCchhhceeEEEEEccCCeEEEEEeC
Confidence 6899999999999999999999999999999 999999999999999999999999999999999999999999999999
Q ss_pred CCCccCcccccCeEEEeeec-CCCCcCCCCCCceEEEEEecChhHHHHhhhhccCCCC
Q 032641 80 NDGCLNYIEENDEVLIAGFG-RKGHAVGDIPGVRFKVVKVSGVSLLALFKEKKEKPRS 136 (136)
Q Consensus 80 g~G~l~~lqeh~~VLV~G~G-~~gg~v~DlPGVrykvvrv~~vsl~al~~gkkekp~~ 136 (136)
||||+|||||||+|||+||| ++||+++|||||+|+||+|+||||+|||+||||||++
T Consensus 88 g~G~~~~lqEh~~VLV~G~gg~~gg~v~DlPGVrykvVkV~~vsL~~l~~gkkekp~r 145 (145)
T PRK04211 88 GDGAINFIDEHDEVVIEGIGGPKGRSMGDIPGVRYKVIKVNGVSLKELVKGKKEKPVR 145 (145)
T ss_pred CCccccccccCCEEEEeecCccCCCCcCCCCceEEEEEEECCEeHHHHHhcccccCCC
Confidence 99999999999999999988 9999999999999999999999999999999999985
No 4
>KOG1749 consensus 40S ribosomal protein S23 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=6.2e-69 Score=410.80 Aligned_cols=136 Identities=85% Similarity=1.318 Sum_probs=134.8
Q ss_pred CchhhhhHhhhhhccccchhhhhhccCCccc-CCCCCCCCccceEEeeeeecccCCCcccceEEEEEEecCCcEEEEEeC
Q 032641 1 MGAGRKLKSHRRRQRWADKSYKKSHLGNEWK-KPFAGSSHAKGIVLEKIGIEAKQPNSAIRKCARVQLIKNGKKIAAFVP 79 (136)
Q Consensus 1 l~~arkl~~~r~~~rw~d~~ykk~~lg~~~k-~pl~g~pq~kGivl~~~~~~pKkPNSA~RK~~rVqLikngk~v~A~IP 79 (136)
|+|||+|+.+|+.+||+|.+|++++|||++| |||+|+||+||||||++++|+||||||||||+|||||+||++||||+|
T Consensus 7 l~aarklr~~r~~~rwad~~ykk~~lGta~K~~pfggashAKgIvLEKigVEAKQPNSAiRKcvRvQLIkngKKITafVp 86 (143)
T KOG1749|consen 7 LFAARKLRTHRRNQRWADKHYKKRLLGTAYKSSPFGGASHAKGIVLEKIGVEAKQPNSAIRKCVRVQLIKNGKKITAFVP 86 (143)
T ss_pred chhHHHHHhhhhhhccchhhhhhhhhcchhhcCCCCCccccceeEEEeeeeeccCCcHHHhhheeeeeeeCCceEEEEec
Confidence 6899999999999999999999999999999 999999999999999999999999999999999999999999999999
Q ss_pred CCCccCcccccCeEEEeeecCCCCcCCCCCCceEEEEEecChhHHHHhhhhccCCCC
Q 032641 80 NDGCLNYIEENDEVLIAGFGRKGHAVGDIPGVRFKVVKVSGVSLLALFKEKKEKPRS 136 (136)
Q Consensus 80 g~G~l~~lqeh~~VLV~G~G~~gg~v~DlPGVrykvvrv~~vsl~al~~gkkekp~~ 136 (136)
.||||||++|||||||.|||++|++++|||||||+||+|+||||+|||+||||||++
T Consensus 87 ~dgcln~ieendevlv~gfgrkg~avgdipgvrfkvvkv~~vsl~alf~~kkekpr~ 143 (143)
T KOG1749|consen 87 NDGCLNFIEENDEVLVAGFGRKGHAVGDIPGVRFKVVKVSGVSLLALFKEKKEKPRS 143 (143)
T ss_pred CCCceeeeccCCeeeeeccCccCccccCCCceEEEEEEEcCcChhhhhhccccCCCC
Confidence 999999999999999999999999999999999999999999999999999999986
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=4.8e-62 Score=365.23 Aligned_cols=114 Identities=82% Similarity=1.303 Sum_probs=112.3
Q ss_pred hhhhhccCCccc-CCCCCCCCccceEEeeeeecccCCCcccceEEEEEEecCCcEEEEEeCCCCccCcccccCeEEEeee
Q 032641 20 SYKKSHLGNEWK-KPFAGSSHAKGIVLEKIGIEAKQPNSAIRKCARVQLIKNGKKIAAFVPNDGCLNYIEENDEVLIAGF 98 (136)
Q Consensus 20 ~ykk~~lg~~~k-~pl~g~pq~kGivl~~~~~~pKkPNSA~RK~~rVqLikngk~v~A~IPg~G~l~~lqeh~~VLV~G~ 98 (136)
.|+++++|+..| +||+|+||++|||++++++||||||||+||||||||++||++||||||||||||||||||+|||+||
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 499999999999 9999999999999999999999999999999999998899999999999999999999999999999
Q ss_pred cCCCCcCCCCCCceEEEEEecChhHHHHhhhhccC
Q 032641 99 GRKGHAVGDIPGVRFKVVKVSGVSLLALFKEKKEK 133 (136)
Q Consensus 99 G~~gg~v~DlPGVrykvvrv~~vsl~al~~gkkek 133 (136)
|++||+++|||||+|+||+||||||+|||+|||||
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=1.6e-55 Score=334.94 Aligned_cols=122 Identities=39% Similarity=0.601 Sum_probs=117.6
Q ss_pred CchhhhhHhhhhhccccchhhhhhccCCccc-CCCCCCCCccceEEeeeeecccCCCcccceEEEEEEecCCcEEEEEeC
Q 032641 1 MGAGRKLKSHRRRQRWADKSYKKSHLGNEWK-KPFAGSSHAKGIVLEKIGIEAKQPNSAIRKCARVQLIKNGKKIAAFVP 79 (136)
Q Consensus 1 l~~arkl~~~r~~~rw~d~~ykk~~lg~~~k-~pl~g~pq~kGivl~~~~~~pKkPNSA~RK~~rVqLikngk~v~A~IP 79 (136)
+|||++|...++..| |.++.++++.| +||+|+||++|||++++++||||||||+||||||||+ ||++||||||
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 689999999999888 99999999999 8899999999999999999999999999999999996 9999999999
Q ss_pred CCCccCcccccCeEEEeeecCCCCcCCCCCCceEEEEEecChhHHHHhhhhccCCC
Q 032641 80 NDGCLNYIEENDEVLIAGFGRKGHAVGDIPGVRFKVVKVSGVSLLALFKEKKEKPR 135 (136)
Q Consensus 80 g~G~l~~lqeh~~VLV~G~G~~gg~v~DlPGVrykvvrv~~vsl~al~~gkkekp~ 135 (136)
|||| +|||||+||||| ++++||||||||||||+++||.++++|++|+|.
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 799999999999 469999999999999999999999999999985
No 7
>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=1.6e-48 Score=294.54 Aligned_cols=105 Identities=45% Similarity=0.747 Sum_probs=99.2
Q ss_pred hhccCCccc-CCCCCCCCccceEEeeeeecccCCCcccceEEEEEEecCCcEEEEEeCCCCccCcccccCeEEEeeecCC
Q 032641 23 KSHLGNEWK-KPFAGSSHAKGIVLEKIGIEAKQPNSAIRKCARVQLIKNGKKIAAFVPNDGCLNYIEENDEVLIAGFGRK 101 (136)
Q Consensus 23 k~~lg~~~k-~pl~g~pq~kGivl~~~~~~pKkPNSA~RK~~rVqLikngk~v~A~IPg~G~l~~lqeh~~VLV~G~G~~ 101 (136)
+.+++++.+ +||+++||++|||+++++++|||||||+||||+||| +||++|+|||||||| ||||||+|||+|
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 677888888 899999999999999999999999999999999999 699999999999996 999999999999
Q ss_pred CCcCCCCCCceEEEEE----ecChh--HHHHhhhhccCCC
Q 032641 102 GHAVGDIPGVRFKVVK----VSGVS--LLALFKEKKEKPR 135 (136)
Q Consensus 102 gg~v~DlPGVrykvvr----v~~vs--l~al~~gkkekp~ 135 (136)
|+++|||||+|+||| +++|+ +.+++++.++||+
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 569999999999999 99999 9999999999984
No 8
>cd00319 Ribosomal_S12_like Ribosomal protein S12-like family; composed of prokaryotic 30S ribosomal protein S12, eukaryotic 40S ribosomal protein S23 and similar proteins. S12 and S23 are located at the interface of the large and small ribosomal subunits, adjacent to the decoding center. They play an important role in translocation during the peptide elongation step of protein synthesis. They are also involved in important RNA and protein interactions. Ribosomal protein S12 is essential for maintenance of a pretranslocation state and, together with S13, functions as a control element for the rRNA- and tRNA-driven movements of translocation. S23 interacts with domain III of the eukaryotic elongation factor 2 (eEF2), which catalyzes translocation. Mutations in S12 and S23 have been found to affect translational accuracy. Antibiotics such as streptomycin may also bind S12/S23 and cause the ribosome to misread the genetic code.
Probab=100.00 E-value=6.8e-48 Score=281.02 Aligned_cols=94 Identities=35% Similarity=0.631 Sum_probs=88.9
Q ss_pred CCccc-CCCCCCCCccceEEeeeeecccCCCcccceEEEEEEecCCcEEEEEeCCCCccCcccccCeEEEeeecCCCCcC
Q 032641 27 GNEWK-KPFAGSSHAKGIVLEKIGIEAKQPNSAIRKCARVQLIKNGKKIAAFVPNDGCLNYIEENDEVLIAGFGRKGHAV 105 (136)
Q Consensus 27 g~~~k-~pl~g~pq~kGivl~~~~~~pKkPNSA~RK~~rVqLikngk~v~A~IPg~G~l~~lqeh~~VLV~G~G~~gg~v 105 (136)
+++.| +||+++||++|||+++++++|||||||+|||||||| +||++|||||||||| ||||||+|||+| |++
T Consensus 1 ~~~~k~~~l~~~Pq~kGi~l~~~~~~pKkPNSA~RK~arV~L-~ngk~v~ayIPg~Gh--~lqeh~~VLvrG-----Gr~ 72 (95)
T cd00319 1 RKKSKVPALKGAPFRRGVCTVVRTVTPKKPNSALRKVAKVRL-TSGYEVTAYIPGEGH--NLQEHSVVLIRG-----GRV 72 (95)
T ss_pred CCccccCcccCCcccCeEEEEEEeccccCCChhhceEEEEEc-cCCCEEEEECCCCCc--ccccccEEEEeC-----CCc
Confidence 35567 899999999999999999999999999999999999 699999999999996 999999999999 778
Q ss_pred CCCCCceEEEEEecChhHHHHhhhh
Q 032641 106 GDIPGVRFKVVKVSGVSLLALFKEK 130 (136)
Q Consensus 106 ~DlPGVrykvvrv~~vsl~al~~gk 130 (136)
.|||||+|+||| |+++.++++|+
T Consensus 73 ~DlPGVrykvVr--G~~d~~~v~~R 95 (95)
T cd00319 73 KDLPGVRYHIVR--GVYDAAGVKDR 95 (95)
T ss_pred CCCCCcEEEEEc--ccchhhhccCC
Confidence 899999999999 99999999885
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=8.6e-44 Score=264.44 Aligned_cols=80 Identities=40% Similarity=0.750 Sum_probs=77.6
Q ss_pred CCCCCCCCccceEEeeeeecccCCCcccceEEEEEEecCCcEEEEEeCCCCccCcccccCeEEEeeecCCCCcCCCCCCc
Q 032641 32 KPFAGSSHAKGIVLEKIGIEAKQPNSAIRKCARVQLIKNGKKIAAFVPNDGCLNYIEENDEVLIAGFGRKGHAVGDIPGV 111 (136)
Q Consensus 32 ~pl~g~pq~kGivl~~~~~~pKkPNSA~RK~~rVqLikngk~v~A~IPg~G~l~~lqeh~~VLV~G~G~~gg~v~DlPGV 111 (136)
+||+|+||++|||+++++++|||||||+||||+||| +||++|+|||||||| ||||||+|||+| |+++|||||
T Consensus 20 ~~l~g~Pq~kGi~l~v~~~~pKKPNSA~RKvarV~L-~ngk~v~AyIPG~Gh--nlqehs~VLvrG-----Grv~DlPGV 91 (108)
T cd03368 20 PALEGCPQKKGVCLKVYTTTPKKPNSALRKVARVRL-SNGKEVTAYIPGEGH--NLQEHSVVLVRG-----GRVKDLPGV 91 (108)
T ss_pred CcccCCcccCcEEEEEEeccccCCChhheeeEEEEe-cCCCEEEEEcCCCCC--CccccCEEEEeC-----CccCCCCCe
Confidence 789999999999999999999999999999999999 699999999999996 999999999999 899999999
Q ss_pred eEEEEEec
Q 032641 112 RFKVVKVS 119 (136)
Q Consensus 112 rykvvrv~ 119 (136)
+|+|||+.
T Consensus 92 kykvvRG~ 99 (108)
T cd03368 92 RYHIVRGV 99 (108)
T ss_pred EEEEEeee
Confidence 99999964
No 10
>PRK05163 rpsL 30S ribosomal protein S12; Validated
Probab=100.00 E-value=3e-43 Score=266.66 Aligned_cols=80 Identities=36% Similarity=0.682 Sum_probs=77.8
Q ss_pred CCCCCCCCccceEEeeeeecccCCCcccceEEEEEEecCCcEEEEEeCCCCccCcccccCeEEEeeecCCCCcCCCCCCc
Q 032641 32 KPFAGSSHAKGIVLEKIGIEAKQPNSAIRKCARVQLIKNGKKIAAFVPNDGCLNYIEENDEVLIAGFGRKGHAVGDIPGV 111 (136)
Q Consensus 32 ~pl~g~pq~kGivl~~~~~~pKkPNSA~RK~~rVqLikngk~v~A~IPg~G~l~~lqeh~~VLV~G~G~~gg~v~DlPGV 111 (136)
+||+++||++|||+++++++|||||||+||||+||| +||++|||||||||| ||||||+|||+| |+++|||||
T Consensus 22 ~~l~~~Pq~kGv~l~v~~~~pKKPNSA~RKvarVrL-~ngk~v~AyIPGeGh--nlqehs~VLvrG-----Grv~DlPGV 93 (124)
T PRK05163 22 PALNACPQKRGVCTRVYTTTPKKPNSALRKVARVRL-TNGFEVTAYIPGEGH--NLQEHSVVLIRG-----GRVKDLPGV 93 (124)
T ss_pred cccccCcccCcEEEEEEecCccCCCchhheEEEEEe-CCCCEEEEEcCCCCC--CccccCEEEEeC-----CccCCCCCc
Confidence 789999999999999999999999999999999999 999999999999996 999999999998 899999999
Q ss_pred eEEEEEec
Q 032641 112 RFKVVKVS 119 (136)
Q Consensus 112 rykvvrv~ 119 (136)
+|+|||+.
T Consensus 94 rykvVrG~ 101 (124)
T PRK05163 94 RYHIVRGA 101 (124)
T ss_pred EEEEeeee
Confidence 99999964
No 11
>CHL00051 rps12 ribosomal protein S12
Probab=100.00 E-value=2.8e-43 Score=266.51 Aligned_cols=80 Identities=38% Similarity=0.671 Sum_probs=78.0
Q ss_pred CCCCCCCCccceEEeeeeecccCCCcccceEEEEEEecCCcEEEEEeCCCCccCcccccCeEEEeeecCCCCcCCCCCCc
Q 032641 32 KPFAGSSHAKGIVLEKIGIEAKQPNSAIRKCARVQLIKNGKKIAAFVPNDGCLNYIEENDEVLIAGFGRKGHAVGDIPGV 111 (136)
Q Consensus 32 ~pl~g~pq~kGivl~~~~~~pKkPNSA~RK~~rVqLikngk~v~A~IPg~G~l~~lqeh~~VLV~G~G~~gg~v~DlPGV 111 (136)
+||+|+||++|||+++++++|||||||+|||||||| +||++|||||||||| ||||||+|||+| |+++|||||
T Consensus 22 ~~L~g~Pq~kGv~lkv~~~~pKKPNSA~RKvarVrL-sngk~v~AyIPGeGh--nlqehs~VLvrG-----Grv~DlPGV 93 (123)
T CHL00051 22 PALRGCPQRRGTCTRVYTITPKKPNSALRKVARVRL-TSGFEITAYIPGIGH--NLQEHSVVLVRG-----GRVKDLPGV 93 (123)
T ss_pred cccccCcccCeEEEEEEeccccCCChhheeEEEEEc-cCCCEEEEEcCCCCc--cccccCEEEEeC-----CccCCCCCe
Confidence 789999999999999999999999999999999999 999999999999998 999999999998 899999999
Q ss_pred eEEEEEec
Q 032641 112 RFKVVKVS 119 (136)
Q Consensus 112 rykvvrv~ 119 (136)
+|+|||+.
T Consensus 94 rykvVRG~ 101 (123)
T CHL00051 94 RYHIVRGT 101 (123)
T ss_pred eEEEEeee
Confidence 99999965
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=3.4e-43 Score=266.38 Aligned_cols=80 Identities=36% Similarity=0.683 Sum_probs=77.8
Q ss_pred CCCCCCCCccceEEeeeeecccCCCcccceEEEEEEecCCcEEEEEeCCCCccCcccccCeEEEeeecCCCCcCCCCCCc
Q 032641 32 KPFAGSSHAKGIVLEKIGIEAKQPNSAIRKCARVQLIKNGKKIAAFVPNDGCLNYIEENDEVLIAGFGRKGHAVGDIPGV 111 (136)
Q Consensus 32 ~pl~g~pq~kGivl~~~~~~pKkPNSA~RK~~rVqLikngk~v~A~IPg~G~l~~lqeh~~VLV~G~G~~gg~v~DlPGV 111 (136)
+||+|+||++||||++++++|||||||+||||+||| +||++|||||||||| ||||||+|||+| |+++|||||
T Consensus 22 ~~l~g~Pq~kGi~l~~~~~~pKKPNSA~RKvarVrL-~ngk~v~AyIPG~Gh--nlqehs~VLvrG-----Grv~DlPGV 93 (124)
T TIGR00981 22 PALEACPQKRGVCTRVYTTTPKKPNSALRKVARVRL-TNGFEVTAYIPGEGH--NLQEHSVVLIRG-----GRVKDLPGV 93 (124)
T ss_pred cccccCCccCcEEEEEEeccccCCCchhheeEEEEe-CCCCEEEEEcCCCCC--CccccCEEEEeC-----CccCCCCCe
Confidence 789999999999999999999999999999999999 999999999999996 999999999998 899999999
Q ss_pred eEEEEEec
Q 032641 112 RFKVVKVS 119 (136)
Q Consensus 112 rykvvrv~ 119 (136)
+|+|||+.
T Consensus 94 kykvVrG~ 101 (124)
T TIGR00981 94 RYHIVRGA 101 (124)
T ss_pred EEEEEeEe
Confidence 99999964
No 13
>PTZ00115 40S ribosomal protein S12; Provisional
Probab=100.00 E-value=3e-38 Score=264.11 Aligned_cols=79 Identities=30% Similarity=0.583 Sum_probs=76.6
Q ss_pred CCCCCCCccceEEeeeeecccCCCcccceEEEEEEecCCcEEEEEeCCCCccCcccccCeEEEeeecCCCCcCCCCCCce
Q 032641 33 PFAGSSHAKGIVLEKIGIEAKQPNSAIRKCARVQLIKNGKKIAAFVPNDGCLNYIEENDEVLIAGFGRKGHAVGDIPGVR 112 (136)
Q Consensus 33 pl~g~pq~kGivl~~~~~~pKkPNSA~RK~~rVqLikngk~v~A~IPg~G~l~~lqeh~~VLV~G~G~~gg~v~DlPGVr 112 (136)
.|+|+||++|||+++++++|||||||+||||+||| +||++|||||||||| ||||||+|||+| |+++|||||+
T Consensus 119 aL~g~PQkKGIclkv~~~tPKKPNSA~RKvarVrL-sNGk~VtAyIPGeGH--nLQEHs~VLVRG-----GrvkDLPGVr 190 (290)
T PTZ00115 119 WLEGAPQKKGICVKVRVQTPRKPNSGLRKVARVRL-STGRTVTVYIPGIGH--NLNTHSVVLVRG-----GRCKDVPGCN 190 (290)
T ss_pred cccCCcccCeEEEEeeecCCCCCCccccceEEEEe-cCCCEEEEEcCCCCc--ccccCCEEEEeC-----CCcCCCCCce
Confidence 49999999999999999999999999999999999 799999999999998 999999999999 8899999999
Q ss_pred EEEEEec
Q 032641 113 FKVVKVS 119 (136)
Q Consensus 113 ykvvrv~ 119 (136)
|+|||+.
T Consensus 191 YkvVRG~ 197 (290)
T PTZ00115 191 YKAVRGV 197 (290)
T ss_pred EEEeeee
Confidence 9999965
No 14
>KOG1750 consensus Mitochondrial/chloroplast ribosomal protein S12 [Translation, ribosomal structure and biogenesis]
Probab=99.97 E-value=2e-31 Score=205.04 Aligned_cols=80 Identities=40% Similarity=0.736 Sum_probs=77.7
Q ss_pred CCCCCCCCccceEEeeeeecccCCCcccceEEEEEEecCCcEEEEEeCCCCccCcccccCeEEEeeecCCCCcCCCCCCc
Q 032641 32 KPFAGSSHAKGIVLEKIGIEAKQPNSAIRKCARVQLIKNGKKIAAFVPNDGCLNYIEENDEVLIAGFGRKGHAVGDIPGV 111 (136)
Q Consensus 32 ~pl~g~pq~kGivl~~~~~~pKkPNSA~RK~~rVqLikngk~v~A~IPg~G~l~~lqeh~~VLV~G~G~~gg~v~DlPGV 111 (136)
.+|.|+||.+|||+.+++++|||||||.|||++|+| +||.+|+|||||+|| |+|||+.|||+| |++.|+|||
T Consensus 50 ~~L~g~p~~kgvvl~v~t~~pkkPnsa~rK~~~vrl-stg~~i~ayipg~gh--nlqehs~Vlvrg-----gr~qdlpgv 121 (139)
T KOG1750|consen 50 PALDGCPQRKGVVLRVFTRKPKKPNSANRKCARVRL-STGREVTAYIPGIGH--NLQEHSIVLVRG-----GRVQDLPGV 121 (139)
T ss_pred ccccCCcccccEEEEEEEecCCCCCccceeeEEEEe-cCchheeeeCCCccc--cceeEEEEEEec-----ceeccCcch
Confidence 679999999999999999999999999999999999 999999999999998 999999999999 899999999
Q ss_pred eEEEEEec
Q 032641 112 RFKVVKVS 119 (136)
Q Consensus 112 rykvvrv~ 119 (136)
+|++||+.
T Consensus 122 k~~~vRg~ 129 (139)
T KOG1750|consen 122 KYHVVRGV 129 (139)
T ss_pred hhhhhhhh
Confidence 99999964
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=94.32 E-value=0.09 Score=36.58 Aligned_cols=34 Identities=26% Similarity=0.388 Sum_probs=27.3
Q ss_pred EEEEEEecCCcEEEEEeCCCCccC--cccccCeEEEe
Q 032641 62 CARVQLIKNGKKIAAFVPNDGCLN--YIEENDEVLIA 96 (136)
Q Consensus 62 ~~rVqLikngk~v~A~IPg~G~l~--~lqeh~~VLV~ 96 (136)
-.+|+| -||.++.|||||-=-.| -|.+.|.|+|+
T Consensus 19 ~f~V~l-~ng~~vla~i~GKmr~~rI~I~~GD~V~Ve 54 (68)
T TIGR00008 19 MFRVEL-ENGHEVLAHISGKIRMHYIRILPGDKVKVE 54 (68)
T ss_pred EEEEEE-CCCCEEEEEecCcchhccEEECCCCEEEEE
Confidence 356898 89999999999954322 37899999998
No 16
>COG0361 InfA Translation initiation factor 1 (IF-1) [Translation, ribosomal structure and biogenesis]
Probab=92.73 E-value=0.23 Score=35.31 Aligned_cols=34 Identities=32% Similarity=0.317 Sum_probs=29.5
Q ss_pred EEEEEecCCcEEEEEeCCCCccCc--ccccCeEEEee
Q 032641 63 ARVQLIKNGKKIAAFVPNDGCLNY--IEENDEVLIAG 97 (136)
Q Consensus 63 ~rVqLikngk~v~A~IPg~G~l~~--lqeh~~VLV~G 97 (136)
++|+| -||.+++|+|||-.-.|+ |-+.|.|+|+=
T Consensus 22 f~v~~-edg~~~~ahI~GKmr~~~i~I~~GD~V~Ve~ 57 (75)
T COG0361 22 FRVEL-ENGHERLAHISGKMRKNRIRILPGDVVLVEL 57 (75)
T ss_pred EEEEe-cCCcEEEEEccCcchheeEEeCCCCEEEEEe
Confidence 67898 899999999999998654 57999999984
No 17
>PRK12442 translation initiation factor IF-1; Reviewed
Probab=86.24 E-value=1.3 Score=32.36 Aligned_cols=39 Identities=28% Similarity=0.340 Sum_probs=30.7
Q ss_pred CCCcccceEEEEEEecCCcEEEEEeCCCCccCc--ccccCeEEEee
Q 032641 54 QPNSAIRKCARVQLIKNGKKIAAFVPNDGCLNY--IEENDEVLIAG 97 (136)
Q Consensus 54 kPNSA~RK~~rVqLikngk~v~A~IPg~G~l~~--lqeh~~VLV~G 97 (136)
-||. -.+|+| -||.+|.|||+|-=-.|+ |.+.|.|+|+=
T Consensus 17 Lp~~----~frV~L-enG~~vla~isGKmR~~rIrIl~GD~V~VE~ 57 (87)
T PRK12442 17 LPDS----RFRVTL-ENGVEVGAYASGRMRKHRIRILAGDRVTLEL 57 (87)
T ss_pred CCCC----EEEEEe-CCCCEEEEEeccceeeeeEEecCCCEEEEEE
Confidence 4565 467899 899999999999765443 57899999983
No 18
>smart00652 eIF1a eukaryotic translation initiation factor 1A.
Probab=84.21 E-value=2.1 Score=30.25 Aligned_cols=34 Identities=26% Similarity=0.296 Sum_probs=26.8
Q ss_pred EEEEEecCCcEEEEEeCCCCc-cCcccccCeEEEee
Q 032641 63 ARVQLIKNGKKIAAFVPNDGC-LNYIEENDEVLIAG 97 (136)
Q Consensus 63 ~rVqLikngk~v~A~IPg~G~-l~~lqeh~~VLV~G 97 (136)
.+|+| .||.++.|+|||-=. --.|.+.|.|+|+=
T Consensus 20 ~~V~~-~dG~~~la~ipgK~Rk~iwI~~GD~VlVe~ 54 (83)
T smart00652 20 LEVMC-ADGKERLARIPGKMRKKVWIRRGDIVLVDP 54 (83)
T ss_pred EEEEE-CCCCEEEEEEchhhcccEEEcCCCEEEEEe
Confidence 56888 899999999999321 12588999999984
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=81.93 E-value=3.1 Score=29.19 Aligned_cols=35 Identities=14% Similarity=0.231 Sum_probs=27.3
Q ss_pred EEEEEEecCCcEEEEEeCCCCcc-CcccccCeEEEee
Q 032641 62 CARVQLIKNGKKIAAFVPNDGCL-NYIEENDEVLIAG 97 (136)
Q Consensus 62 ~~rVqLikngk~v~A~IPg~G~l-~~lqeh~~VLV~G 97 (136)
-.+|++ .||.++.|.|||-=.= --+.+.|.|+|+=
T Consensus 14 ~~~V~~-~dg~~~l~~i~gK~Rk~iwI~~GD~VlV~~ 49 (78)
T cd04456 14 RHEVEC-ADGQRRLVSIPGKLRKNIWIKRGDFLIVDP 49 (78)
T ss_pred EEEEEE-CCCCEEEEEEchhhccCEEEcCCCEEEEEe
Confidence 467888 8999999999993210 2589999999974
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=74.60 E-value=5.7 Score=29.15 Aligned_cols=54 Identities=20% Similarity=0.312 Sum_probs=38.6
Q ss_pred CCCCCCCCccceEEeeeeecccCCCcccceEEEEEEecCCcEEEEEeCCCCc-cCcccccCeEEEe
Q 032641 32 KPFAGSSHAKGIVLEKIGIEAKQPNSAIRKCARVQLIKNGKKIAAFVPNDGC-LNYIEENDEVLIA 96 (136)
Q Consensus 32 ~pl~g~pq~kGivl~~~~~~pKkPNSA~RK~~rVqLikngk~v~A~IPg~G~-l~~lqeh~~VLV~ 96 (136)
-|+...-|.-|.|++..+ |. -.+|+| -||.++.|+|||-=. --.|.+.|.|+|.
T Consensus 13 ~p~~~e~e~~g~V~~~lG------~~----~~~V~~-~dG~~~la~i~GK~Rk~iwI~~GD~VlVs 67 (99)
T TIGR00523 13 LPRKEEGEILGVIEQMLG------AG----RVKVRC-LDGKTRLGRIPGKLKKRIWIREGDVVIVK 67 (99)
T ss_pred CCCCCCCEEEEEEEEEcC------CC----EEEEEe-CCCCEEEEEEchhhcccEEecCCCEEEEE
Confidence 355555677777777665 22 467888 799999999999311 1248899999994
No 21
>PLN00208 translation initiation factor (eIF); Provisional
Probab=69.95 E-value=7.3 Score=30.75 Aligned_cols=53 Identities=19% Similarity=0.226 Sum_probs=38.2
Q ss_pred CCCCCCCccceEEeeeeecccCCCcccceEEEEEEecCCcEEEEEeCCCC--ccCcccccCeEEEee
Q 032641 33 PFAGSSHAKGIVLEKIGIEAKQPNSAIRKCARVQLIKNGKKIAAFVPNDG--CLNYIEENDEVLIAG 97 (136)
Q Consensus 33 pl~g~pq~kGivl~~~~~~pKkPNSA~RK~~rVqLikngk~v~A~IPg~G--~l~~lqeh~~VLV~G 97 (136)
||-.--|.=|.|++.++ |. -++|++ -||.+++|+|||-= . --|.+.|.|||+-
T Consensus 27 ~~p~egq~~g~V~~~lG------n~----~~~V~c-~dG~~rLa~IpGKmRKr-IWI~~GD~VlVel 81 (145)
T PLN00208 27 IFKEDGQEYAQVLRMLG------NG----RCEALC-IDGTKRLCHIRGKMRKK-VWIAAGDIILVGL 81 (145)
T ss_pred ccCCCCcEEEEEEEEcC------CC----EEEEEE-CCCCEEEEEEeccceee-EEecCCCEEEEEc
Confidence 44445566677776654 32 467888 79999999999931 2 2589999999984
No 22
>PTZ00329 eukaryotic translation initiation factor 1A; Provisional
Probab=68.31 E-value=8.7 Score=30.66 Aligned_cols=53 Identities=19% Similarity=0.196 Sum_probs=37.9
Q ss_pred CCCCCCCccceEEeeeeecccCCCcccceEEEEEEecCCcEEEEEeCCCC--ccCcccccCeEEEee
Q 032641 33 PFAGSSHAKGIVLEKIGIEAKQPNSAIRKCARVQLIKNGKKIAAFVPNDG--CLNYIEENDEVLIAG 97 (136)
Q Consensus 33 pl~g~pq~kGivl~~~~~~pKkPNSA~RK~~rVqLikngk~v~A~IPg~G--~l~~lqeh~~VLV~G 97 (136)
||-.--|.=|.|++.++ |. -.+|+| -||.+++|+|||-= . --|.+.|.|||+-
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-FDGVKRLCHIRGKMRKR-VWINIGDIILVSL 81 (155)
T ss_pred ccCCCCcEEEEEEEEcC------CC----EEEEEE-CCCCEEEEEeeccceee-EEecCCCEEEEec
Confidence 44455666677766654 33 467888 79999999999932 2 2488999999974
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=65.25 E-value=16 Score=30.44 Aligned_cols=36 Identities=28% Similarity=0.449 Sum_probs=31.0
Q ss_pred ceEEEEEEecCCcEEEEEeCCCCcc-CcccccCeEEEee
Q 032641 60 RKCARVQLIKNGKKIAAFVPNDGCL-NYIEENDEVLIAG 97 (136)
Q Consensus 60 RK~~rVqLikngk~v~A~IPg~G~l-~~lqeh~~VLV~G 97 (136)
|=.|.|.+ +|.+++|++|+-|.| .-+.+...|+++=
T Consensus 20 RF~~~V~~--~G~~~~aH~pNtGrl~ell~pG~~vll~~ 56 (232)
T TIGR00230 20 RFLVDVEV--DGRRETAHCPNTGRLTELIFPGNDVGLSK 56 (232)
T ss_pred CEEEEEEE--CCeEEEEEcCCCCCChhhcCCCCEEEEEE
Confidence 88899998 899999999999976 4478899999973
No 24
>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=61.83 E-value=20 Score=29.30 Aligned_cols=37 Identities=32% Similarity=0.546 Sum_probs=30.7
Q ss_pred ceEEEEEEecCCcEEEEEeCCCCccC-cccccCeEEEee
Q 032641 60 RKCARVQLIKNGKKIAAFVPNDGCLN-YIEENDEVLIAG 97 (136)
Q Consensus 60 RK~~rVqLikngk~v~A~IPg~G~l~-~lqeh~~VLV~G 97 (136)
|=.|.|+| .+|..++||+|+-|.|. .+.+...|+++=
T Consensus 6 RF~~~v~l-~~g~~~~~H~pntGRl~ell~pG~~v~l~~ 43 (215)
T PF03749_consen 6 RFLADVEL-DDGEEVTAHCPNTGRLKELLVPGARVLLSK 43 (215)
T ss_pred cEEEEEEE-CCCCEEEEEcCCCCcchhhccCCCEEEEEE
Confidence 55788888 45999999999999987 456889999874
No 25
>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=56.29 E-value=13 Score=25.83 Aligned_cols=34 Identities=29% Similarity=0.271 Sum_probs=26.9
Q ss_pred EEEEEecCCcEEEEEeCCCCc-cCcccccCeEEEee
Q 032641 63 ARVQLIKNGKKIAAFVPNDGC-LNYIEENDEVLIAG 97 (136)
Q Consensus 63 ~rVqLikngk~v~A~IPg~G~-l~~lqeh~~VLV~G 97 (136)
.+|+| -||.++.|+|||-=. --.+.+.|.|+|+=
T Consensus 15 ~~V~~-~~g~~~la~i~gK~rk~iwI~~GD~V~Ve~ 49 (77)
T cd05793 15 LEVRC-FDGKKRLCRIRGKMRKRVWINEGDIVLVAP 49 (77)
T ss_pred EEEEE-CCCCEEEEEEchhhcccEEEcCCCEEEEEe
Confidence 67888 799999999998522 12478999999984
No 26
>PRK00347 putative DNA-binding transcriptional regulator; Reviewed
Probab=54.91 E-value=32 Score=28.47 Aligned_cols=37 Identities=27% Similarity=0.521 Sum_probs=31.1
Q ss_pred ceEEEEEEecCCcEEEEEeCCCCcc-CcccccCeEEEee
Q 032641 60 RKCARVQLIKNGKKIAAFVPNDGCL-NYIEENDEVLIAG 97 (136)
Q Consensus 60 RK~~rVqLikngk~v~A~IPg~G~l-~~lqeh~~VLV~G 97 (136)
|=.|.|++ -+|..++|++|+-|.| ..+.+...|+++=
T Consensus 18 RF~~~V~~-~~g~~~~aH~pntGRl~ell~pG~~v~l~~ 55 (234)
T PRK00347 18 RFLADVEL-DDGEELTAHCPNTGRMTGLLTPGNTVWLST 55 (234)
T ss_pred CEEEEEEE-CCCCEEEEEcCCCCCChhhccCCCEEEEEE
Confidence 88899998 4699999999999976 4477888999873
No 27
>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=51.74 E-value=14 Score=24.56 Aligned_cols=33 Identities=24% Similarity=0.394 Sum_probs=24.1
Q ss_pred EEEEEecCCcEEEEEeCCCCccC--cccccCeEEEee
Q 032641 63 ARVQLIKNGKKIAAFVPNDGCLN--YIEENDEVLIAG 97 (136)
Q Consensus 63 ~rVqLikngk~v~A~IPg~G~l~--~lqeh~~VLV~G 97 (136)
.+|+| .||.++.|+|||- --+ .+.+.|.|+|+=
T Consensus 18 ~~V~~-~dg~~~l~~i~gK-~r~~iwI~~GD~V~V~~ 52 (65)
T PF01176_consen 18 FEVEC-EDGEERLARIPGK-FRKRIWIKRGDFVLVEP 52 (65)
T ss_dssp EEEEE-TTSEEEEEEE-HH-HHTCC---TTEEEEEEE
T ss_pred EEEEe-CCCCEEEEEeccc-eeeeEecCCCCEEEEEe
Confidence 67888 8999999999986 322 478999999973
No 28
>COG1489 SfsA DNA-binding protein, stimulates sugar fermentation [General function prediction only]
Probab=50.10 E-value=39 Score=28.62 Aligned_cols=37 Identities=27% Similarity=0.495 Sum_probs=30.8
Q ss_pred cceEEEEEEecCCcEEEEEeCCCCccC-cccccCeEEEee
Q 032641 59 IRKCARVQLIKNGKKIAAFVPNDGCLN-YIEENDEVLIAG 97 (136)
Q Consensus 59 ~RK~~rVqLikngk~v~A~IPg~G~l~-~lqeh~~VLV~G 97 (136)
.|=.|.|.| +|..++|++|+-|.+. -+.+.+.|.++-
T Consensus 17 nRFl~dv~l--~G~~~~~H~~ntGrm~~l~~pG~~v~l~~ 54 (235)
T COG1489 17 NRFLADVEL--DGEEVTAHCPNTGRMTELLTPGNTVWLSR 54 (235)
T ss_pred cceEEEEEE--CCeEEEEEcCCCCccccccCCCCEEEEEE
Confidence 356788888 4999999999999877 567899998874
No 29
>PRK04012 translation initiation factor IF-1A; Provisional
Probab=47.55 E-value=21 Score=26.23 Aligned_cols=53 Identities=25% Similarity=0.392 Sum_probs=37.7
Q ss_pred CCCCCCCccceEEeeeeecccCCCcccceEEEEEEecCCcEEEEEeCCCCc-cCcccccCeEEEe
Q 032641 33 PFAGSSHAKGIVLEKIGIEAKQPNSAIRKCARVQLIKNGKKIAAFVPNDGC-LNYIEENDEVLIA 96 (136)
Q Consensus 33 pl~g~pq~kGivl~~~~~~pKkPNSA~RK~~rVqLikngk~v~A~IPg~G~-l~~lqeh~~VLV~ 96 (136)
|+-..-|.-|.|++..+ |. -.+|+| .||..+.|+|||-=. --.|.+.|.|+|+
T Consensus 16 ~~p~e~e~~g~V~~~lG------~~----~~~V~~-~dG~~~la~i~GK~Rk~IwI~~GD~VlVe 69 (100)
T PRK04012 16 PMPEEGEVFGVVEQMLG------AN----RVRVRC-MDGVERMGRIPGKMKKRMWIREGDVVIVA 69 (100)
T ss_pred cCCCCCEEEEEEEEEcC------CC----EEEEEe-CCCCEEEEEEchhhcccEEecCCCEEEEE
Confidence 44455666777776654 22 467888 899999999997421 1257899999997
No 30
>PRK00284 pqqA coenzyme PQQ synthesis protein PqqA; Provisional
Probab=36.26 E-value=50 Score=19.34 Aligned_cols=12 Identities=8% Similarity=0.379 Sum_probs=10.4
Q ss_pred CcEEEEEeCCCC
Q 032641 71 GKKIAAFVPNDG 82 (136)
Q Consensus 71 gk~v~A~IPg~G 82 (136)
|.+||.|+|+..
T Consensus 13 G~EItmY~~~r~ 24 (26)
T PRK00284 13 GMEVTMYFSARX 24 (26)
T ss_pred ceEEEEEEeccc
Confidence 899999999754
No 31
>PLN02856 fumarylacetoacetase
Probab=34.99 E-value=66 Score=29.25 Aligned_cols=33 Identities=21% Similarity=0.453 Sum_probs=22.1
Q ss_pred EEecCCcEEEEEeCCCCccCcccccCeEEEeeec
Q 032641 66 QLIKNGKKIAAFVPNDGCLNYIEENDEVLIAGFG 99 (136)
Q Consensus 66 qLikngk~v~A~IPg~G~l~~lqeh~~VLV~G~G 99 (136)
.|.-+|++.++.-.|+ .-.||+..|+|.++|+.
T Consensus 371 Elt~~G~~p~~l~~g~-~r~fL~dGD~V~l~g~~ 403 (424)
T PLN02856 371 ELTWAGSREVSLEGGT-RRKFLEDGDEVVLSGWC 403 (424)
T ss_pred EEEeCCccceEeccCC-ccccCCCCCEEEEEEEE
Confidence 3333566655544444 23599999999999973
No 32
>COG2302 Uncharacterized conserved protein, contains S4-like domain [Function unknown]
Probab=32.84 E-value=43 Score=28.84 Aligned_cols=26 Identities=38% Similarity=0.804 Sum_probs=19.9
Q ss_pred CcccccCeEEEeeecCCCCcCCCCCCceEEEEEecChh
Q 032641 85 NYIEENDEVLIAGFGRKGHAVGDIPGVRFKVVKVSGVS 122 (136)
Q Consensus 85 ~~lqeh~~VLV~G~G~~gg~v~DlPGVrykvvrv~~vs 122 (136)
-.+++.|.+-|||||| +++-+++|+.
T Consensus 219 ~~v~~GDliSirG~GR------------~~i~~i~g~T 244 (257)
T COG2302 219 YEVQEGDLISIRGFGR------------LKILEINGVT 244 (257)
T ss_pred ceeccCCEEEEecccc------------EEEEeecCcc
Confidence 3699999999999985 5666666553
No 33
>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=32.69 E-value=68 Score=21.13 Aligned_cols=29 Identities=24% Similarity=0.411 Sum_probs=19.8
Q ss_pred CcccceEEEEEEecCCcEEEEEeCC-CCccC
Q 032641 56 NSAIRKCARVQLIKNGKKIAAFVPN-DGCLN 85 (136)
Q Consensus 56 NSA~RK~~rVqLikngk~v~A~IPg-~G~l~ 85 (136)
++++-+-+.|+| +||..+...+=+ |.++|
T Consensus 6 ~~~~~~~V~V~L-k~g~~~~G~L~~~D~~mN 35 (67)
T cd01726 6 KAIIGRPVVVKL-NSGVDYRGILACLDGYMN 35 (67)
T ss_pred HhhCCCeEEEEE-CCCCEEEEEEEEEcccee
Confidence 356778899999 899987755333 44444
No 34
>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=32.33 E-value=1.2e+02 Score=21.51 Aligned_cols=41 Identities=22% Similarity=0.311 Sum_probs=26.3
Q ss_pred cccceEEEEEEecCCcEEEEEe-CCCCc---------cCcccccCeEEEee
Q 032641 57 SAIRKCARVQLIKNGKKIAAFV-PNDGC---------LNYIEENDEVLIAG 97 (136)
Q Consensus 57 SA~RK~~rVqLikngk~v~A~I-Pg~G~---------l~~lqeh~~VLV~G 97 (136)
+...+.+.++|.+|+..+.... ...+. +-.|++.|+|-|+=
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 5666778889999998876654 22222 22388889988875
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=32.07 E-value=86 Score=28.41 Aligned_cols=33 Identities=27% Similarity=0.476 Sum_probs=24.8
Q ss_pred EEEecCCcEEEEEeCCCCccCcccccCeEEEeee
Q 032641 65 VQLIKNGKKIAAFVPNDGCLNYIEENDEVLIAGF 98 (136)
Q Consensus 65 VqLikngk~v~A~IPg~G~l~~lqeh~~VLV~G~ 98 (136)
+.+.-+|++..+.-.|+-. .||+..|+|.++|+
T Consensus 362 lE~t~~g~~~v~l~~g~~r-~fL~dGD~V~~~~~ 394 (415)
T TIGR01266 362 LELSWKGKKPIDVGQGETR-TFLEDGDEVILRGH 394 (415)
T ss_pred EEEEeCCeeeeecCCCCCC-CCCCCCCEEEEEEE
Confidence 3444467776666666655 89999999999997
No 36
>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=29.56 E-value=97 Score=21.91 Aligned_cols=34 Identities=24% Similarity=0.278 Sum_probs=25.8
Q ss_pred EEEEEecCCcEEEEEeCCCCc-cCcccccCeEEEee
Q 032641 63 ARVQLIKNGKKIAAFVPNDGC-LNYIEENDEVLIAG 97 (136)
Q Consensus 63 ~rVqLikngk~v~A~IPg~G~-l~~lqeh~~VLV~G 97 (136)
..|++ -+|.+..|-||+-=. ---+.+.|.|||.=
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 45676 689999999998311 12589999999975
No 37
>COG4776 Rnb Exoribonuclease II [Transcription]
Probab=29.06 E-value=51 Score=31.37 Aligned_cols=37 Identities=41% Similarity=0.516 Sum_probs=28.2
Q ss_pred cceEEEEEEecCCcEEEEEeCCCC------ccCcccccCeEEEee
Q 032641 59 IRKCARVQLIKNGKKIAAFVPNDG------CLNYIEENDEVLIAG 97 (136)
Q Consensus 59 ~RK~~rVqLikngk~v~A~IPg~G------~l~~lqeh~~VLV~G 97 (136)
.|--.||||+-||- .||||+-= .|..-||+-.|.|.|
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 36678899999997 48999852 233457888999988
No 38
>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=27.56 E-value=1.4e+02 Score=21.26 Aligned_cols=21 Identities=19% Similarity=0.287 Sum_probs=15.6
Q ss_pred CcccceEEEEEEecCCcEEEEE
Q 032641 56 NSAIRKCARVQLIKNGKKIAAF 77 (136)
Q Consensus 56 NSA~RK~~rVqLikngk~v~A~ 77 (136)
++..-+-+.|.| +||..+...
T Consensus 7 ~~l~g~~V~VeL-Kng~~~~G~ 27 (90)
T cd01724 7 MKLTNETVTIEL-KNGTIVHGT 27 (90)
T ss_pred HhCCCCEEEEEE-CCCCEEEEE
Confidence 355678899999 899776644
No 39
>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=25.78 E-value=66 Score=20.15 Aligned_cols=21 Identities=14% Similarity=0.525 Sum_probs=14.2
Q ss_pred EEEeCCCCccCcccccCeEEEee
Q 032641 75 AAFVPNDGCLNYIEENDEVLIAG 97 (136)
Q Consensus 75 ~A~IPg~G~l~~lqeh~~VLV~G 97 (136)
..++|.... .|+++|.++|.|
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 456777765 899999999987
No 40
>PLN00051 RNA-binding S4 domain-containing protein; Provisional
Probab=25.10 E-value=44 Score=28.25 Aligned_cols=15 Identities=33% Similarity=0.563 Sum_probs=13.4
Q ss_pred cccccCeEEEeeecC
Q 032641 86 YIEENDEVLIAGFGR 100 (136)
Q Consensus 86 ~lqeh~~VLV~G~G~ 100 (136)
.+.+.|.|.|||+|+
T Consensus 231 ~v~~gD~isiRG~GR 245 (267)
T PLN00051 231 TLKTGDVVSVSGKGR 245 (267)
T ss_pred CCCCCCEEEEeeCCE
Confidence 789999999999874
No 41
>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=24.41 E-value=97 Score=18.13 Aligned_cols=13 Identities=15% Similarity=0.378 Sum_probs=10.5
Q ss_pred CCcEEEEEeCCCC
Q 032641 70 NGKKIAAFVPNDG 82 (136)
Q Consensus 70 ngk~v~A~IPg~G 82 (136)
=|.+||+|++...
T Consensus 11 ~G~EVTmY~~~~~ 23 (26)
T TIGR02107 11 LGMEVTMYVSAXX 23 (26)
T ss_pred ccEEEEEEeeccc
Confidence 3899999998654
No 42
>PRK00276 infA translation initiation factor IF-1; Validated
Probab=24.07 E-value=2.3e+02 Score=19.00 Aligned_cols=33 Identities=27% Similarity=0.338 Sum_probs=24.1
Q ss_pred EEEEEecCCcEEEEEeCCCCcc--CcccccCeEEEe
Q 032641 63 ARVQLIKNGKKIAAFVPNDGCL--NYIEENDEVLIA 96 (136)
Q Consensus 63 ~rVqLikngk~v~A~IPg~G~l--~~lqeh~~VLV~ 96 (136)
..|++ .||..+.|.++|-=-. ..+-..|.|+|+
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 44566 6899999999984221 136789999998
No 43
>KOG4716 consensus Thioredoxin reductase [Posttranslational modification, protein turnover, chaperones]
Probab=23.78 E-value=1.5e+02 Score=27.66 Aligned_cols=46 Identities=30% Similarity=0.473 Sum_probs=29.3
Q ss_pred EEEEEEecCCcEEEEEeCCCCccCcccccC----------------eEEEeeecCCCCcCCCCCC-ceEE
Q 032641 62 CARVQLIKNGKKIAAFVPNDGCLNYIEEND----------------EVLIAGFGRKGHAVGDIPG-VRFK 114 (136)
Q Consensus 62 ~~rVqLikngk~v~A~IPg~G~l~~lqeh~----------------~VLV~G~G~~gg~v~DlPG-Vryk 114 (136)
.-|||| +-|+| .||-.-|. |++.|- .++|.-++| -+..|||| +.|-
T Consensus 123 ~yRv~L--reKkV-~Y~Nsyge--Fv~~h~I~at~~~gk~~~~ta~~fvIatG~R--PrYp~IpG~~Ey~ 185 (503)
T KOG4716|consen 123 GYRVQL--REKKV-EYINSYGE--FVDPHKIKATNKKGKERFLTAENFVIATGLR--PRYPDIPGAKEYG 185 (503)
T ss_pred eEEEEe--cccee-eeeeccee--ecccceEEEecCCCceEEeecceEEEEecCC--CCCCCCCCceeee
Confidence 468998 44443 67777776 666553 345554444 57889999 4453
No 44
>cd01732 LSm5 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. LSm4 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=22.82 E-value=1.5e+02 Score=20.42 Aligned_cols=30 Identities=17% Similarity=0.261 Sum_probs=20.7
Q ss_pred CcccceEEEEEEecCCcEEEEEeCC-CCccCc
Q 032641 56 NSAIRKCARVQLIKNGKKIAAFVPN-DGCLNY 86 (136)
Q Consensus 56 NSA~RK~~rVqLikngk~v~A~IPg-~G~l~~ 86 (136)
+.++.|=+.|.| ++|.++...+=| |.|+|-
T Consensus 9 ~~~~~~~V~V~l-~~gr~~~G~L~g~D~~mNl 39 (76)
T cd01732 9 DKCIGSRIWIVM-KSDKEFVGTLLGFDDYVNM 39 (76)
T ss_pred HHhCCCEEEEEE-CCCeEEEEEEEEeccceEE
Confidence 455677789999 899888766433 555543
No 45
>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=22.39 E-value=93 Score=25.92 Aligned_cols=15 Identities=27% Similarity=0.488 Sum_probs=13.0
Q ss_pred cccccCeEEEeeecC
Q 032641 86 YIEENDEVLIAGFGR 100 (136)
Q Consensus 86 ~lqeh~~VLV~G~G~ 100 (136)
.+.+.|.|.|+|+|+
T Consensus 223 ~v~~gD~IsvrG~Gr 237 (257)
T TIGR03069 223 ELKVGDRLQLRGKGR 237 (257)
T ss_pred cCCCCCEEEEcCCce
Confidence 688999999999874
No 46
>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=22.09 E-value=1.1e+02 Score=24.19 Aligned_cols=30 Identities=20% Similarity=0.409 Sum_probs=21.2
Q ss_pred cCCcEEEEE-eCCCCccCcccccCeEEEeee
Q 032641 69 KNGKKIAAF-VPNDGCLNYIEENDEVLIAGF 98 (136)
Q Consensus 69 kngk~v~A~-IPg~G~l~~lqeh~~VLV~G~ 98 (136)
.|...+... +|++|+|.||...+.|-|-..
T Consensus 148 ~~~~~~~~vNv~N~G~I~nLp~davVEvp~~ 178 (232)
T PF11975_consen 148 NDKPKRFVVNVPNNGAIPNLPDDAVVEVPCY 178 (232)
T ss_dssp HSSEEEEEEEEE-TTSSTTS-TTSEEEEEEE
T ss_pred cCCCeEEEEECCCCCccCCCCCCcEEEEEEE
Confidence 344444555 999999999999999987653
No 47
>cd04497 hPOT1_OB1_like hPOT1_OB1_like: A subfamily of OB folds similar to the first OB fold (OB1) of human protection of telomeres 1 protein (hPOT1), the single OB fold of the N-terminal domain of Schizosaccharomyces pombe POT1 (SpPOT1), and the first OB fold of the N-terminal domain of the alpha subunit (OB1Nalpha) of Oxytricha nova telomere end binding protein (OnTEBP). POT1 proteins recognize single-stranded (ss) 3-prime ends of the telomere. A 3-prime ss overhang is conserved in ciliated protozoa, yeast, and mammals. SpPOT1 is essential for telomere maintenance. It binds specifically to the ss G-rich telomeric sequence (GGTTAC) of S. pombe. hPOT1 binds specifically to ss telomeric DNA repeats ending with the sequence GGTTAG. Deletion of the S. pombe pot1+ gene results in a rapid loss of telomere sequences, chromosome mis-segregation and chromosome circularization. hPOT1 is implicated in telomere length regulation. The hPOT1 monomer consists of two closely connected OB folds (OB1-OB
Probab=20.93 E-value=2.1e+02 Score=21.22 Aligned_cols=65 Identities=18% Similarity=0.343 Sum_probs=42.3
Q ss_pred eEEEEEEec------CCcEEEEEeCCCCccCcccccCeEEEeeecCCCCcCCCCCCceEEEEEecChhHHHHhhhhc
Q 032641 61 KCARVQLIK------NGKKIAAFVPNDGCLNYIEENDEVLIAGFGRKGHAVGDIPGVRFKVVKVSGVSLLALFKEKK 131 (136)
Q Consensus 61 K~~rVqLik------ngk~v~A~IPg~G~l~~lqeh~~VLV~G~G~~gg~v~DlPGVrykvvrv~~vsl~al~~gkk 131 (136)
-|+.+.|+= .+-+|+-|-|-.-+|-.+++.|+|+++++ .+++.-|--+=+..- ..|-.|+|.|..
T Consensus 37 ~~~tl~i~D~S~~~~~~l~v~~F~~~~~~LP~v~~GDVIll~~~-----kv~~~~g~~~~~~~~-~~ss~avf~~~~ 107 (138)
T cd04497 37 YCCTLTITDPSLANSDGLTVKLFRPNEESLPIVKVGDIILLRRV-----KIQSYNGKPQGISND-RGSSWAVFRGDD 107 (138)
T ss_pred EEEEEEEECCCCCCCCcEEEEEECCChhhCCCCCCCCEEEEEEE-----EEEEECCceEEEECC-CceeEEEEcCCC
Confidence 455555532 34678888888888887899999999995 566665553333222 255566666653
No 48
>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=20.40 E-value=1.3e+02 Score=21.85 Aligned_cols=24 Identities=33% Similarity=0.574 Sum_probs=19.0
Q ss_pred cCCcEEEEEeCCCCccCcccccCeEEEeeec
Q 032641 69 KNGKKIAAFVPNDGCLNYIEENDEVLIAGFG 99 (136)
Q Consensus 69 kngk~v~A~IPg~G~l~~lqeh~~VLV~G~G 99 (136)
..|.+|-+|=|... +|.|+|||-|
T Consensus 25 ~~~~~v~~~kp~~~-------~d~vliEGaG 48 (134)
T cd03109 25 EKGYRVAPLKPVQT-------YDFVLVEGAG 48 (134)
T ss_pred HCCCeEEEEecCCC-------CCEEEEECCC
Confidence 35778888877765 7999999964
No 49
>PF06565 DUF1126: Repeat of unknown function (DUF1126); InterPro: IPR010554 This group contains several eukaryote specific repeats of around 35 residues in length. The function of this family is unknown.; PDB: 2Z14_A 2Z13_A.
Probab=20.29 E-value=40 Score=20.20 Aligned_cols=12 Identities=25% Similarity=-0.006 Sum_probs=1.6
Q ss_pred eeecccCCCccc
Q 032641 48 IGIEAKQPNSAI 59 (136)
Q Consensus 48 ~~~~pKkPNSA~ 59 (136)
-..||.++||++
T Consensus 12 ~I~E~~~~NSG~ 23 (33)
T PF06565_consen 12 SIFEPPVRNSGR 23 (33)
T ss_dssp EEE---------
T ss_pred EEEEeccCCCCC
Confidence 356899999987
Done!