Query 031206
Match_columns 164
No_of_seqs 145 out of 1185
Neff 3.3
Searched_HMMs 46136
Date Fri Mar 29 10:46:37 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/031206.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/031206hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3419 Mitochondrial/chloropl 100.0 4E-35 8.6E-40 224.8 8.1 93 1-93 1-108 (112)
2 PRK14525 rpsP 30S ribosomal pr 100.0 4.7E-33 1E-37 205.7 9.4 74 1-74 1-85 (88)
3 PRK14521 rpsP 30S ribosomal pr 100.0 2.7E-32 5.9E-37 224.2 8.7 84 1-84 1-95 (186)
4 CHL00005 rps16 ribosomal prote 100.0 5.2E-32 1.1E-36 197.9 8.3 71 2-72 1-80 (82)
5 PRK14524 rpsP 30S ribosomal pr 100.0 1E-31 2.2E-36 200.6 7.3 76 2-77 1-87 (94)
6 PRK14522 rpsP 30S ribosomal pr 100.0 9.1E-32 2E-36 207.7 6.4 80 1-80 1-92 (116)
7 TIGR00002 S16 ribosomal protei 100.0 5.7E-31 1.2E-35 190.5 8.7 67 3-69 1-78 (78)
8 PRK14520 rpsP 30S ribosomal pr 100.0 6.1E-31 1.3E-35 211.2 8.1 71 1-71 1-82 (155)
9 PRK14523 rpsP 30S ribosomal pr 100.0 2.3E-30 4.9E-35 204.6 7.8 83 2-84 1-96 (137)
10 COG0228 RpsP Ribosomal protein 100.0 3.5E-30 7.5E-35 190.8 7.9 66 2-67 1-78 (87)
11 PRK00040 rpsP 30S ribosomal pr 100.0 9.4E-30 2E-34 183.0 6.9 62 2-63 1-75 (75)
12 PF00886 Ribosomal_S16: Riboso 99.8 1.1E-21 2.4E-26 136.1 3.4 48 9-56 1-62 (62)
13 TIGR02097 yccV hemimethylated 57.6 8 0.00017 29.5 2.0 14 13-26 46-59 (101)
14 PRK14129 heat shock protein Hs 48.1 14 0.0003 28.9 2.0 14 13-26 47-60 (105)
15 PF03484 B5: tRNA synthetase B 44.6 33 0.00071 23.5 3.3 33 36-69 2-34 (70)
16 PF08755 YccV-like: Hemimethyl 39.7 19 0.00042 26.5 1.6 15 13-27 46-60 (100)
17 PF03649 UPF0014: Uncharacteri 33.5 36 0.00077 29.3 2.5 31 36-66 150-180 (250)
18 TIGR00245 conserved hypothetic 30.5 43 0.00092 28.9 2.4 36 36-71 144-182 (248)
19 smart00874 B5 tRNA synthetase 30.4 93 0.002 20.6 3.6 32 36-68 2-33 (71)
20 COG3323 Uncharacterized protei 28.2 26 0.00057 27.5 0.7 23 123-145 34-56 (109)
21 PF13592 HTH_33: Winged helix- 21.8 1.7E+02 0.0037 19.3 3.7 37 39-75 4-43 (60)
22 cd07762 CYTH-like_Pase_1 Uncha 20.5 2.8E+02 0.0062 22.1 5.3 35 36-70 72-106 (180)
No 1
>KOG3419 consensus Mitochondrial/chloroplast ribosomal protein S16 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=4e-35 Score=224.79 Aligned_cols=93 Identities=59% Similarity=0.989 Sum_probs=86.1
Q ss_pred CceEEeeccCCCCCCCeeEEEEeecCCCCCCCC--------------CCccEEEehHHHHHHHHCCCccCHHHHHHHHHc
Q 031206 1 MVVRIRLARFGCKNKPFYRVMAADSRSPRDGQD--------------SGKRMGLNFDRVKYWLSVGAQPSDPVQRILFRA 66 (164)
Q Consensus 1 MaVKIRLaR~G~KnrPFYRIVVaDsRspRDGk~--------------~~k~I~Ln~eRIkyWL~~GAQPTdtV~~LLkka 66 (164)
|+|+|||+|+||||||||||||+|+|++|||++ +++.+.||+|||+|||++|||||+||.+||+++
T Consensus 1 ~~vkIRLar~GcknRPfY~Ivva~~r~~rdgk~iE~lG~ydPlp~~~~~~~v~Ln~dRikyWl~~GAqpS~tv~~Ll~~a 80 (112)
T KOG3419|consen 1 MVVKIRLARFGCKNRPFYRIVVADSRKRRDGKPIEQLGTYDPLPNQDNEKLVALNFDRIKYWLGVGAQPSDTVEELLGKA 80 (112)
T ss_pred CeEEEeehhcCccCCCeeEEEEeeccccccCCchhheecccCCCCCCCCcceeecHHHHHHHHhcCCccChHHHHHHHhc
Confidence 789999999999999999999999999999953 357899999999999999999999999999999
Q ss_pred CCCCCCCcccccccCCCCCC-CCCCCCC
Q 031206 67 GLLPPPPMVAMGRKGGPRDT-RPVDPMT 93 (164)
Q Consensus 67 Gil~~~p~~~~~~kg~~~~~-~p~~~~~ 93 (164)
|++|.+|+..++.|.+.+.. ++++|++
T Consensus 81 Gl~p~~p~~~~~a~~~rr~~a~~~~~~~ 108 (112)
T KOG3419|consen 81 GLFPIHPMTFMNAKRNRRLTAEQVLPVE 108 (112)
T ss_pred CCCCCchhhhhccccchhhhhhhccchh
Confidence 99999999999999999776 6666654
No 2
>PRK14525 rpsP 30S ribosomal protein S16; Provisional
Probab=100.00 E-value=4.7e-33 Score=205.72 Aligned_cols=74 Identities=43% Similarity=0.733 Sum_probs=67.8
Q ss_pred CceEEeeccCCCCCCCeeEEEEeecCCCCCCCCC-----------CccEEEehHHHHHHHHCCCccCHHHHHHHHHcCCC
Q 031206 1 MVVRIRLARFGCKNKPFYRVMAADSRSPRDGQDS-----------GKRMGLNFDRVKYWLSVGAQPSDPVQRILFRAGLL 69 (164)
Q Consensus 1 MaVKIRLaR~G~KnrPFYRIVVaDsRspRDGk~~-----------~k~I~Ln~eRIkyWL~~GAQPTdtV~~LLkkaGil 69 (164)
|+|+|||+|+|+||+|||||||+|+|++|||+.+ ++.+.||+||++|||++|||||+||.+||+++|+.
T Consensus 1 M~VkIRL~R~G~k~~P~YrIVv~dsr~~RdGk~IE~lG~YnP~~~~~~i~ln~eri~~WL~~GAqpT~tV~~Ll~~~g~~ 80 (88)
T PRK14525 1 MAVVLRLSRAGTHKAPFYHVVATDSRNARDGKYLEDVGIYDPTKRPERIELKVERIEHWLKAGAKPSQTVAMILKRAAKA 80 (88)
T ss_pred CcEEEehhhCCCCCCCeEEEEEeecCCCCCCCceeEEecccCCCCCceEEEcHHHHHHHHHCCCccCHHHHHHHHHcCcc
Confidence 8999999999999999999999999999999532 35799999999999999999999999999999998
Q ss_pred CCCCc
Q 031206 70 PPPPM 74 (164)
Q Consensus 70 ~~~p~ 74 (164)
..+|.
T Consensus 81 ~~~~~ 85 (88)
T PRK14525 81 AAPAA 85 (88)
T ss_pred CCCCC
Confidence 65443
No 3
>PRK14521 rpsP 30S ribosomal protein S16; Provisional
Probab=99.97 E-value=2.7e-32 Score=224.18 Aligned_cols=84 Identities=46% Similarity=0.716 Sum_probs=77.2
Q ss_pred CceEEeeccCCCCCCCeeEEEEeecCCCCCCCCC-----------CccEEEehHHHHHHHHCCCccCHHHHHHHHHcCCC
Q 031206 1 MVVRIRLARFGCKNKPFYRVMAADSRSPRDGQDS-----------GKRMGLNFDRVKYWLSVGAQPSDPVQRILFRAGLL 69 (164)
Q Consensus 1 MaVKIRLaR~G~KnrPFYRIVVaDsRspRDGk~~-----------~k~I~Ln~eRIkyWL~~GAQPTdtV~~LLkkaGil 69 (164)
|+|||||+|+|+|++|||||||+|+|++|||+++ +..|.||+|||+|||++|||||+||.+||+++|++
T Consensus 1 M~VkIRL~R~G~KkrPfYrIVVaDsR~~RDGk~IE~lG~YnP~~~~~~i~Ln~eRi~~WL~~GAqPTdtV~~lL~~~g~~ 80 (186)
T PRK14521 1 MAVKIRLQRHGRKGKAFYWIVAADSRAPRDGKFIEKIGTYNPNTNPATVDLNFDRAVYWLMNGAQPTDTARNILSYEGVL 80 (186)
T ss_pred CcEeehhhhCCCCCCCeEEEEEEeCCCCCCCCceeeeeecCCCCCCceEEEcHHHHHHHHHCCCcCCHHHHHHHHHcccc
Confidence 9999999999999999999999999999999532 35899999999999999999999999999999999
Q ss_pred CCCCcccccccCCCC
Q 031206 70 PPPPMVAMGRKGGPR 84 (164)
Q Consensus 70 ~~~p~~~~~~kg~~~ 84 (164)
++++...+.+||...
T Consensus 81 ~k~~~~~~~~kg~~~ 95 (186)
T PRK14521 81 LKKHLLGGVAKGAFT 95 (186)
T ss_pred hhhhhhcccCCCccc
Confidence 988888788787654
No 4
>CHL00005 rps16 ribosomal protein S16
Probab=99.97 E-value=5.2e-32 Score=197.89 Aligned_cols=71 Identities=37% Similarity=0.596 Sum_probs=65.6
Q ss_pred ceEEeeccCCCCCCCeeEEEEeecCCCCCCC---------CCCccEEEehHHHHHHHHCCCccCHHHHHHHHHcCCCCCC
Q 031206 2 VVRIRLARFGCKNKPFYRVMAADSRSPRDGQ---------DSGKRMGLNFDRVKYWLSVGAQPSDPVQRILFRAGLLPPP 72 (164)
Q Consensus 2 aVKIRLaR~G~KnrPFYRIVVaDsRspRDGk---------~~~k~I~Ln~eRIkyWL~~GAQPTdtV~~LLkkaGil~~~ 72 (164)
||+|||+|+|+||+|||||||+|+|++|||+ |..+.+.||+||++|||++|||||+||.+||+++|++++.
T Consensus 1 ~vkIRL~R~G~kk~P~YrIVvadsr~~RdGk~iE~lG~YnP~~~~~~ln~eri~~Wl~~GAqpt~tV~~Ll~~~g~~~~~ 80 (82)
T CHL00005 1 MVKLRLKRCGRKQQAVYRIVAIDVRSRREGRDLEKVGFYDPIKNQTYLNVPAILYFLEKGAQPTETVYDILKKAEVFKEL 80 (82)
T ss_pred CeEEecccCCCCCCCeEEEEEEeCCCCCCCcceeEeeeccCCCcccEEeHHHHHHHHHCcCccCHHHHHHHHHcCchhhh
Confidence 5899999999999999999999999999995 3456799999999999999999999999999999987643
No 5
>PRK14524 rpsP 30S ribosomal protein S16; Provisional
Probab=99.97 E-value=1e-31 Score=200.55 Aligned_cols=76 Identities=38% Similarity=0.677 Sum_probs=68.1
Q ss_pred ceEEeeccCCCCCCCeeEEEEeecCCCCCCCCC-----------CccEEEehHHHHHHHHCCCccCHHHHHHHHHcCCCC
Q 031206 2 VVRIRLARFGCKNKPFYRVMAADSRSPRDGQDS-----------GKRMGLNFDRVKYWLSVGAQPSDPVQRILFRAGLLP 70 (164)
Q Consensus 2 aVKIRLaR~G~KnrPFYRIVVaDsRspRDGk~~-----------~k~I~Ln~eRIkyWL~~GAQPTdtV~~LLkkaGil~ 70 (164)
||+|||+|+|+||+|||||||+|+|++|||+++ +..+.||+||++|||++|||||+||.+||+++|+++
T Consensus 1 mVkIRL~R~G~KkrPfYrIVvadsr~~RdGk~iE~lG~YnP~~~~~~i~l~~eri~~Wl~~GAqpT~tV~~Llkk~g~~~ 80 (94)
T PRK14524 1 MVRIRLTRMGKRKQPFYRIVVVDSRKRRDGAYIESLGYYNPLKEPYEIKVDVERAVEWILKGAQPSDTVRDILRKFGVMK 80 (94)
T ss_pred CcEEhhccCCCCCCCeEEEEEEecCCCCCCCceeEeeecCCCCCCceEEEcHHHHHHHHHcCCccCHHHHHHHHHccchh
Confidence 489999999999999999999999999999532 357899999999999999999999999999999987
Q ss_pred CCCcccc
Q 031206 71 PPPMVAM 77 (164)
Q Consensus 71 ~~p~~~~ 77 (164)
+....+.
T Consensus 81 ~~~~~~~ 87 (94)
T PRK14524 81 KVHEIKY 87 (94)
T ss_pred hhHHhhh
Confidence 6654443
No 6
>PRK14522 rpsP 30S ribosomal protein S16; Provisional
Probab=99.97 E-value=9.1e-32 Score=207.75 Aligned_cols=80 Identities=31% Similarity=0.552 Sum_probs=72.0
Q ss_pred CceEEeeccCCCCCCCeeEEEEeecCCCCCCCCC----------CccEEEehHHHHHHHHCCCccCHHHHHHHHH--cCC
Q 031206 1 MVVRIRLARFGCKNKPFYRVMAADSRSPRDGQDS----------GKRMGLNFDRVKYWLSVGAQPSDPVQRILFR--AGL 68 (164)
Q Consensus 1 MaVKIRLaR~G~KnrPFYRIVVaDsRspRDGk~~----------~k~I~Ln~eRIkyWL~~GAQPTdtV~~LLkk--aGi 68 (164)
|+|+|||+|+|+||+|||||||+|+|++|||+++ .+.+.||+|||+|||++|||||+||.+||++ +|+
T Consensus 1 MmVkIRLaR~G~KkrPfYrIVVaDsR~~RDGk~IE~lG~YdP~~~~~v~Ln~eRi~yWL~~GAqPS~tV~~LLkk~~~Gi 80 (116)
T PRK14522 1 MALKIRLRQQGRRNHVVYRLVLADVESPRDGKYIELLGWYDPHSEQNYQLKSERIFYWLNQGAELTEKAGALVKQGAPGV 80 (116)
T ss_pred CcEEEecccCCCCCCCeEEEEEeecCCCCCCCcceeeeccCCCCCCceEECHHHHHHHHHCCCccCHHHHHHHHhhhccc
Confidence 9999999999999999999999999999999542 2579999999999999999999999999999 699
Q ss_pred CCCCCccccccc
Q 031206 69 LPPPPMVAMGRK 80 (164)
Q Consensus 69 l~~~p~~~~~~k 80 (164)
+++....+-.+|
T Consensus 81 ~~~~~~~k~~~~ 92 (116)
T PRK14522 81 YSELMAKKVARK 92 (116)
T ss_pred chhHHHHHHHHH
Confidence 998876654433
No 7
>TIGR00002 S16 ribosomal protein S16. This model describes ribosomal S16 of bacteria and organelles.
Probab=99.97 E-value=5.7e-31 Score=190.50 Aligned_cols=67 Identities=55% Similarity=0.952 Sum_probs=62.6
Q ss_pred eEEeeccCCCCCCCeeEEEEeecCCCCCCCCC-----------CccEEEehHHHHHHHHCCCccCHHHHHHHHHcCCC
Q 031206 3 VRIRLARFGCKNKPFYRVMAADSRSPRDGQDS-----------GKRMGLNFDRVKYWLSVGAQPSDPVQRILFRAGLL 69 (164)
Q Consensus 3 VKIRLaR~G~KnrPFYRIVVaDsRspRDGk~~-----------~k~I~Ln~eRIkyWL~~GAQPTdtV~~LLkkaGil 69 (164)
|+|||+|+|+||+|||||||+|+|++|||+++ ++.+.||+||++|||++|||||+||++||+++|++
T Consensus 1 vkIRL~R~G~k~~PfYrIVv~d~r~~RdGk~iE~lG~YnP~~~~~~i~l~~~ri~~Wl~~GAqps~tV~~Ll~~~g~~ 78 (78)
T TIGR00002 1 VKIRLKRGGRKKRPFYRIVVADSRSRRDGRYIEELGFYNPLTKESRVKLNVERIKYWLSKGAQPTDTVRNLLKKAGVF 78 (78)
T ss_pred CEEecccCCCCCCCeEEEEEEecCCCCCCCceeEeeeccCCCCCcEEEEcHHHHHHHHHCCCccCHHHHHHHHHccCC
Confidence 79999999999999999999999999999532 36799999999999999999999999999999974
No 8
>PRK14520 rpsP 30S ribosomal protein S16; Provisional
Probab=99.97 E-value=6.1e-31 Score=211.21 Aligned_cols=71 Identities=42% Similarity=0.755 Sum_probs=66.0
Q ss_pred CceEEeeccCCCCCCCeeEEEEeecCCCCCCCC-----------CCccEEEehHHHHHHHHCCCccCHHHHHHHHHcCCC
Q 031206 1 MVVRIRLARFGCKNKPFYRVMAADSRSPRDGQD-----------SGKRMGLNFDRVKYWLSVGAQPSDPVQRILFRAGLL 69 (164)
Q Consensus 1 MaVKIRLaR~G~KnrPFYRIVVaDsRspRDGk~-----------~~k~I~Ln~eRIkyWL~~GAQPTdtV~~LLkkaGil 69 (164)
|+|||||+|+|+||+|||||||+|+|++|||+. .+..|.||+||++|||++|||||++|.+||+++|++
T Consensus 1 MaVkIRL~R~G~kk~PfYrIVVaDsR~~RDGk~IE~lG~YnP~~~~~~i~ln~eRi~yWL~~GAQPT~~V~~LLk~~g~~ 80 (155)
T PRK14520 1 MAVKIKLKRLGKIRNPQYRIVVADSRTKRDGRAIEEIGRYHPKEEPSLIEIDSERAQYWLSVGAQPTEPVLALLKITGDW 80 (155)
T ss_pred CcEEehhhhCCCCCCCeEEEEEeecCCCCCCCceeeeeccCCCCCCceEEEcHHHHHHHHHCCCccCHHHHHHHHHcchh
Confidence 999999999999999999999999999999953 235789999999999999999999999999999987
Q ss_pred CC
Q 031206 70 PP 71 (164)
Q Consensus 70 ~~ 71 (164)
.+
T Consensus 81 ~~ 82 (155)
T PRK14520 81 QK 82 (155)
T ss_pred hh
Confidence 54
No 9
>PRK14523 rpsP 30S ribosomal protein S16; Provisional
Probab=99.96 E-value=2.3e-30 Score=204.64 Aligned_cols=83 Identities=39% Similarity=0.576 Sum_probs=72.7
Q ss_pred ceEEeeccCCCCCCCeeEEEEeecCCCCCCCCC-------------CccEEEehHHHHHHHHCCCccCHHHHHHHHHcCC
Q 031206 2 VVRIRLARFGCKNKPFYRVMAADSRSPRDGQDS-------------GKRMGLNFDRVKYWLSVGAQPSDPVQRILFRAGL 68 (164)
Q Consensus 2 aVKIRLaR~G~KnrPFYRIVVaDsRspRDGk~~-------------~k~I~Ln~eRIkyWL~~GAQPTdtV~~LLkkaGi 68 (164)
||+|||+|+|+||+|||||||+|+|++|||+++ .+.+.||+|||+|||++|||||+||.+||+++|+
T Consensus 1 mVkIRL~R~GrKkrPfYRIVVaDsRs~RDGK~IE~LG~YdP~~~~~~~~i~Ln~eRi~yWL~~GAQPS~tV~~LLkkag~ 80 (137)
T PRK14523 1 MVVIRLARGGSKKNPFYHIVVADRRKPRDGRFIERVGYYNPMARGQDIRLQLEKERISHWLNQGAQTSLRVKHLIKKLEK 80 (137)
T ss_pred CcEehhhcCCCCCCCeEEEEEEecCCCCCCCceeeeeecCCCCCCCCceEEECHHHHHHHHHCCCccCHHHHHHHHHccc
Confidence 489999999999999999999999999999532 2479999999999999999999999999999999
Q ss_pred CCCCCcccccccCCCC
Q 031206 69 LPPPPMVAMGRKGGPR 84 (164)
Q Consensus 69 l~~~p~~~~~~kg~~~ 84 (164)
++......+.++|.+.
T Consensus 81 ~~~~~~~~g~~~~~~~ 96 (137)
T PRK14523 81 SPEEAQKGGMRKGEFK 96 (137)
T ss_pred chHHHHhcccccCCcc
Confidence 8887766555555443
No 10
>COG0228 RpsP Ribosomal protein S16 [Translation, ribosomal structure and biogenesis]
Probab=99.96 E-value=3.5e-30 Score=190.75 Aligned_cols=66 Identities=59% Similarity=0.993 Sum_probs=61.8
Q ss_pred ceEEeeccCCCCCCCeeEEEEeecCCCCCCCCC------------CccEEEehHHHHHHHHCCCccCHHHHHHHHHcC
Q 031206 2 VVRIRLARFGCKNKPFYRVMAADSRSPRDGQDS------------GKRMGLNFDRVKYWLSVGAQPSDPVQRILFRAG 67 (164)
Q Consensus 2 aVKIRLaR~G~KnrPFYRIVVaDsRspRDGk~~------------~k~I~Ln~eRIkyWL~~GAQPTdtV~~LLkkaG 67 (164)
+|||||+|+|+||+|||||||||||+||||+.+ ++.++||.||+.|||++||||||||++||+++|
T Consensus 1 ~vkIRL~R~G~kk~P~YrIVVaDsrs~RDGr~IE~lG~ynP~~~~~~~v~l~~eri~~Wl~~GAqpSdtV~~ll~~~g 78 (87)
T COG0228 1 MVKIRLARGGSKKRPFYRIVVADSRSPRDGRFIERLGTYNPLLGKEERVKLDEERILYWLSQGAQPSDTVRRLLKKAG 78 (87)
T ss_pred CeEEehhhCCCccCCeEEEEEeccCCCCCCcchhhhcccCCCCCccceEEEcHHHHHHHHHcCCcccHHHHHHHHHhh
Confidence 589999999999999999999999999999532 258999999999999999999999999999998
No 11
>PRK00040 rpsP 30S ribosomal protein S16; Reviewed
Probab=99.96 E-value=9.4e-30 Score=183.04 Aligned_cols=62 Identities=56% Similarity=0.979 Sum_probs=57.3
Q ss_pred ceEEeeccCCCCCCCeeEEEEeecCCCCCCCCC-------------CccEEEehHHHHHHHHCCCccCHHHHHHH
Q 031206 2 VVRIRLARFGCKNKPFYRVMAADSRSPRDGQDS-------------GKRMGLNFDRVKYWLSVGAQPSDPVQRIL 63 (164)
Q Consensus 2 aVKIRLaR~G~KnrPFYRIVVaDsRspRDGk~~-------------~k~I~Ln~eRIkyWL~~GAQPTdtV~~LL 63 (164)
||+|||+|+|+||+|||||||+|+|++|||+++ ++.+.||+||++|||++|||||++|++||
T Consensus 1 ~vkIRL~R~G~k~~P~YrIVv~d~r~~RdGk~iE~lG~ydP~~~~~~~~i~ln~eri~~Wl~~GAqpt~~V~~Ll 75 (75)
T PRK00040 1 MVKIRLARGGAKKRPFYRIVVADSRSPRDGRFIERVGFYNPLAKPAEEEVKLDEERVLYWLGQGAQPTDTVRRLL 75 (75)
T ss_pred CeEEhhhhCCCCCCCeEEEEEEecCCCCCCCceeEEeecCCCCCCCcceEEEcHHHHHHHHHCCCccCHHHHHhC
Confidence 589999999999999999999999999999532 24899999999999999999999999986
No 12
>PF00886 Ribosomal_S16: Ribosomal protein S16; InterPro: IPR000307 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 S16 is one of the proteins from the small ribosomal subunit. It belongs to a family of ribosomal proteins which, on the basis of sequence similarities [], groups: Eubacterial S16. Algal and plant chloroplast S16. Cyanelle S16. Neurospora crassa mitochondrial S24 (cyt-21). S16 proteins have about 100 amino-acid residues.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 2Y14_P 3UZ6_S 2J02_P 1HNZ_P 3V26_P 3KNL_P 1N34_P 2J00_P 1HNW_P 3OHC_P ....
Probab=99.84 E-value=1.1e-21 Score=136.07 Aligned_cols=48 Identities=63% Similarity=1.147 Sum_probs=44.0
Q ss_pred cCCCCCCCeeEEEEeecCCCCCCCC---------C-----CccEEEehHHHHHHHHCCCccC
Q 031206 9 RFGCKNKPFYRVMAADSRSPRDGQD---------S-----GKRMGLNFDRVKYWLSVGAQPS 56 (164)
Q Consensus 9 R~G~KnrPFYRIVVaDsRspRDGk~---------~-----~k~I~Ln~eRIkyWL~~GAQPT 56 (164)
|+|||++|||||||+|+|++|||+. . ++.+.||+|||+|||++|||||
T Consensus 1 R~G~k~~P~YrIVv~d~r~~RdGk~iE~lG~YdP~~~~~~~~~~~l~~eri~~Wl~~GAqpT 62 (62)
T PF00886_consen 1 RMGRKKRPFYRIVVADSRSPRDGKFIEELGFYDPIPNPDEEKQIKLNFERIKYWLSKGAQPT 62 (62)
T ss_dssp EESSTTEEEEEEEEEETTSSTTSSESEEEEEEETTSSSSSSTSEEETHHHHHHHHHTTEEEE
T ss_pred CCCCCCCCeEEEEEEeCCcccccchhhccceEcCCCCCCCceeEEeCHHHHHHHHHcCcCCC
Confidence 7899999999999999999999942 2 3589999999999999999998
No 13
>TIGR02097 yccV hemimethylated DNA binding domain. This model describes the small protein from E. coli YccV and its homologs in other Proteobacteria. YccV is now described as a hemimethylated DNA binding protein. The model also describes a domain in longer eukaryotic proteins.
Probab=57.57 E-value=8 Score=29.46 Aligned_cols=14 Identities=43% Similarity=1.037 Sum_probs=12.1
Q ss_pred CCCCeeEEEEeecC
Q 031206 13 KNKPFYRVMAADSR 26 (164)
Q Consensus 13 KnrPFYRIVVaDsR 26 (164)
|++|||+++|-|..
T Consensus 46 ~~qPfYhvLv~~~~ 59 (101)
T TIGR02097 46 RDQPFYHVLAEDDE 59 (101)
T ss_pred cCCCceEEEEeCCC
Confidence 89999999988754
No 14
>PRK14129 heat shock protein HspQ; Provisional
Probab=48.13 E-value=14 Score=28.91 Aligned_cols=14 Identities=29% Similarity=0.733 Sum_probs=11.7
Q ss_pred CCCCeeEEEEeecC
Q 031206 13 KNKPFYRVMAADSR 26 (164)
Q Consensus 13 KnrPFYRIVVaDsR 26 (164)
|.+|||+++|-|.-
T Consensus 47 kdqPwYHvl~en~~ 60 (105)
T PRK14129 47 RAAPWYHVVMEDDD 60 (105)
T ss_pred cCCCceEEEEEcCC
Confidence 79999999996644
No 15
>PF03484 B5: tRNA synthetase B5 domain; InterPro: IPR005147 Domain B5 is found in phenylalanine-tRNA synthetase beta subunits. This domain has been shown to bind DNA through a winged helix-turn-helix motif []. Phenylalanine-tRNA synthetase may influence common cellular processes via DNA binding, in addition to its aminoacylation function.; GO: 0000287 magnesium ion binding, 0003723 RNA binding, 0005524 ATP binding, 0006432 phenylalanyl-tRNA aminoacylation; PDB: 2AKW_B 1B70_B 1B7Y_B 2ALY_B 2IY5_B 2AMC_B 3PCO_D 2CXI_C 1JJC_B 1EIY_B ....
Probab=44.63 E-value=33 Score=23.46 Aligned_cols=33 Identities=24% Similarity=0.502 Sum_probs=25.8
Q ss_pred ccEEEehHHHHHHHHCCCccCHHHHHHHHHcCCC
Q 031206 36 KRMGLNFDRVKYWLSVGAQPSDPVQRILFRAGLL 69 (164)
Q Consensus 36 k~I~Ln~eRIkyWL~~GAQPTdtV~~LLkkaGil 69 (164)
+.+.++.+++...|+. .-..+.+.++|++.|+-
T Consensus 2 ~~i~~~~~~i~~~lG~-~i~~~~i~~~L~~lg~~ 34 (70)
T PF03484_consen 2 KKITLSLDKINKLLGI-DISPEEIIKILKRLGFK 34 (70)
T ss_dssp EEEEEEHHHHHHHHTS----HHHHHHHHHHTT-E
T ss_pred eEEEecHHHHHHHhCC-CCCHHHHHHHHHHCCCE
Confidence 5789999999999997 55568899999998863
No 16
>PF08755 YccV-like: Hemimethylated DNA-binding protein YccV like; InterPro: IPR011722 This entry describes the small protein from Escherichia coli YccV and its homologs in other Proteobacteria. YccV is now described as a hemimethylated DNA binding protein []. The model entry describes a domain in longer eukaryotic proteins.; PDB: 1VBV_A.
Probab=39.71 E-value=19 Score=26.55 Aligned_cols=15 Identities=47% Similarity=0.964 Sum_probs=7.5
Q ss_pred CCCCeeEEEEeecCC
Q 031206 13 KNKPFYRVMAADSRS 27 (164)
Q Consensus 13 KnrPFYRIVVaDsRs 27 (164)
+++|||+|.|-+...
T Consensus 46 ~~qPfY~vLv~~~~~ 60 (100)
T PF08755_consen 46 RNQPFYHVLVDDRDS 60 (100)
T ss_dssp ----EEEEEEE-SS-
T ss_pred CCCCcEEEEEecCCc
Confidence 899999998877643
No 17
>PF03649 UPF0014: Uncharacterised protein family (UPF0014); InterPro: IPR005226 This family has no known function. It includes potential membrane proteins.
Probab=33.49 E-value=36 Score=29.34 Aligned_cols=31 Identities=26% Similarity=0.443 Sum_probs=27.0
Q ss_pred ccEEEehHHHHHHHHCCCccCHHHHHHHHHc
Q 031206 36 KRMGLNFDRVKYWLSVGAQPSDPVQRILFRA 66 (164)
Q Consensus 36 k~I~Ln~eRIkyWL~~GAQPTdtV~~LLkka 66 (164)
.+++-+.+++.+||+.||.|.+.++.+++++
T Consensus 150 ~~l~~~~~~ie~~LalGat~~eA~~~~~r~a 180 (250)
T PF03649_consen 150 SELRERRDEIEALLALGATPREAVRPFIRRA 180 (250)
T ss_pred HHHHHhHHHHHHHHHCCCCHHHHHHHHHHHH
Confidence 4566688999999999999999999988874
No 18
>TIGR00245 conserved hypothetical protein TIGR00245.
Probab=30.48 E-value=43 Score=28.89 Aligned_cols=36 Identities=25% Similarity=0.468 Sum_probs=30.5
Q ss_pred ccEEEehHHHHHHHHCCCccCHHHHHHHHHc---CCCCC
Q 031206 36 KRMGLNFDRVKYWLSVGAQPSDPVQRILFRA---GLLPP 71 (164)
Q Consensus 36 k~I~Ln~eRIkyWL~~GAQPTdtV~~LLkka---Gil~~ 71 (164)
++++-+.+++.+||+.||.|.+.++.+++++ +++|.
T Consensus 144 ~~l~~~~~~ie~~LaLGat~~~A~~~~~r~Ai~aaliP~ 182 (248)
T TIGR00245 144 SMVKSERDEIQGYLSLGATPKQAIAPFIRNAIKASLIPT 182 (248)
T ss_pred HHHHHhhHHHHHHHHCCCCHHHHHHHHHHHHHHHHhhch
Confidence 4577788999999999999999999999874 55554
No 19
>smart00874 B5 tRNA synthetase B5 domain. This domain is found in phenylalanine-tRNA synthetase beta subunits.
Probab=30.38 E-value=93 Score=20.63 Aligned_cols=32 Identities=22% Similarity=0.466 Sum_probs=26.5
Q ss_pred ccEEEehHHHHHHHHCCCccCHHHHHHHHHcCC
Q 031206 36 KRMGLNFDRVKYWLSVGAQPSDPVQRILFRAGL 68 (164)
Q Consensus 36 k~I~Ln~eRIkyWL~~GAQPTdtV~~LLkkaGi 68 (164)
..+.++.+++...|+.-- ..+.+.++|++.|+
T Consensus 2 ~~i~~~~~~i~~llG~~i-~~~ei~~~L~~lg~ 33 (71)
T smart00874 2 RTITLRRERINRLLGLDL-SAEEIEEILKRLGF 33 (71)
T ss_pred cEEEecHHHHHHHHCCCC-CHHHHHHHHHHCCC
Confidence 468999999999999743 34679999999986
No 20
>COG3323 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=28.23 E-value=26 Score=27.47 Aligned_cols=23 Identities=39% Similarity=0.481 Sum_probs=20.7
Q ss_pred eeeccccccceeeccccccCCCe
Q 031206 123 VFMHCTSSSILKLQHMPVQGSNE 145 (164)
Q Consensus 123 ~~~~~~~~~~~~~~~~~~~~~~~ 145 (164)
-+-||+.++.-.=|-.|++|+|-
T Consensus 34 ~Y~~C~~~~~g~G~frP~egAnP 56 (109)
T COG3323 34 NYDHCTFSSEGTGQFRPLEGANP 56 (109)
T ss_pred ccceEEEEeeeeEEEeecCCCCC
Confidence 46799999999999999999984
No 21
>PF13592 HTH_33: Winged helix-turn helix
Probab=21.77 E-value=1.7e+02 Score=19.35 Aligned_cols=37 Identities=22% Similarity=0.294 Sum_probs=29.1
Q ss_pred EEehHHHHHHHHC--CCccCH-HHHHHHHHcCCCCCCCcc
Q 031206 39 GLNFDRVKYWLSV--GAQPSD-PVQRILFRAGLLPPPPMV 75 (164)
Q Consensus 39 ~Ln~eRIkyWL~~--GAQPTd-tV~~LLkkaGil~~~p~~ 75 (164)
.+....|..||.. |..-|. +|.+||++.|+-.+.|..
T Consensus 4 ~wt~~~i~~~I~~~fgv~ys~~~v~~lL~r~G~s~~kp~~ 43 (60)
T PF13592_consen 4 RWTLKEIAAYIEEEFGVKYSPSGVYRLLKRLGFSYQKPRP 43 (60)
T ss_pred cccHHHHHHHHHHHHCCEEcHHHHHHHHHHcCCccccCCC
Confidence 4567788888877 887774 689999999998777654
No 22
>cd07762 CYTH-like_Pase_1 Uncharacterized subgroup 1 of the CYTH-like superfamily. Enzymes belonging to the CYTH-like (also known as triphosphate tunnel metalloenzyme (TTM)-like) superfamily hydrolyze triphosphate-containing substrates, require metal cations as cofactors, and have a unique active site located at the center of an eight-stranded antiparallel beta barrel tunnel (the triphosphate tunnel). The name CYTH originated from the gene designation for bacterial class IV adenylyl cyclases (CyaB) and from thiamine triphosphatase. Class IV adenylate cyclases catalyze the conversion of ATP to 3',5'-cyclic AMP (cAMP) and PPi. Thiamine triphosphatase is a soluble cytosolic enzyme which converts thiamine triphosphate to thiamine diphosphate. This domain superfamily also contains RNA triphosphatases, membrane-associated polyphosphate polymerases, tripolyphosphatases, nucleoside triphosphatases, nucleoside tetraphosphatases and other proteins with unknown functions. Proteins of this subgroup
Probab=20.49 E-value=2.8e+02 Score=22.15 Aligned_cols=35 Identities=17% Similarity=0.292 Sum_probs=29.0
Q ss_pred ccEEEehHHHHHHHHCCCccCHHHHHHHHHcCCCC
Q 031206 36 KRMGLNFDRVKYWLSVGAQPSDPVQRILFRAGLLP 70 (164)
Q Consensus 36 k~I~Ln~eRIkyWL~~GAQPTdtV~~LLkkaGil~ 70 (164)
-++.|+.+...-++..|.-|.+.+..+|...|+-+
T Consensus 72 ~e~~l~~~~~~~~~~~~~~~~~~~~~~L~~lg~~~ 106 (180)
T cd07762 72 TNQPLTLEEAEKLIKGGTLPEGEILDKLKELGIDP 106 (180)
T ss_pred EeecCCHHHHHHHhccccCCchHHHHHHHHhCCCc
Confidence 34556666888899999999999999999999753
Done!