Query 033524
Match_columns 117
No_of_seqs 123 out of 1197
Neff 4.1
Searched_HMMs 46136
Date Fri Mar 29 03:17:25 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/033524.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/033524hhsearch_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 6.5E-36 1.4E-40 216.6 8.0 93 1-93 1-108 (112)
2 PRK14525 rpsP 30S ribosomal pr 100.0 6.7E-35 1.4E-39 204.4 8.8 72 1-72 1-83 (88)
3 PRK14521 rpsP 30S ribosomal pr 100.0 3.2E-34 7E-39 223.2 8.7 89 1-89 1-100 (186)
4 CHL00005 rps16 ribosomal prote 100.0 1.4E-33 3.1E-38 195.4 8.2 71 2-72 1-80 (82)
5 PRK14524 rpsP 30S ribosomal pr 100.0 8.9E-34 1.9E-38 200.6 7.1 76 2-77 1-87 (94)
6 PRK14522 rpsP 30S ribosomal pr 100.0 1.8E-33 3.8E-38 205.7 6.3 77 1-77 1-89 (116)
7 TIGR00002 S16 ribosomal protei 100.0 6.3E-33 1.4E-37 190.4 8.2 67 3-69 1-78 (78)
8 PRK14520 rpsP 30S ribosomal pr 100.0 8.5E-33 1.8E-37 210.3 7.9 71 1-71 1-82 (155)
9 COG0228 RpsP Ribosomal protein 100.0 2.5E-32 5.4E-37 191.3 7.5 66 2-67 1-78 (87)
10 PRK14523 rpsP 30S ribosomal pr 100.0 2.3E-32 5E-37 204.5 7.8 86 2-87 1-99 (137)
11 PRK00040 rpsP 30S ribosomal pr 100.0 3.3E-31 7.1E-36 180.8 6.8 62 2-63 1-75 (75)
12 PF00886 Ribosomal_S16: Riboso 99.9 8.6E-23 1.9E-27 134.4 3.3 48 9-56 1-62 (62)
13 TIGR02097 yccV hemimethylated 69.9 3.7 8.1E-05 29.4 2.1 14 13-26 46-59 (101)
14 PRK14129 heat shock protein Hs 65.5 5.1 0.00011 29.4 2.0 14 13-26 47-60 (105)
15 PF08755 YccV-like: Hemimethyl 54.5 8.7 0.00019 26.8 1.6 15 13-27 46-60 (100)
16 PF03484 B5: tRNA synthetase B 49.2 26 0.00057 22.6 3.2 33 36-69 2-34 (70)
17 PF03649 UPF0014: Uncharacteri 33.6 37 0.00081 27.5 2.5 31 36-66 150-180 (250)
18 smart00874 B5 tRNA synthetase 32.8 85 0.0018 19.6 3.6 33 36-69 2-34 (71)
19 TIGR01071 rplO_bact ribosomal 30.9 1E+02 0.0022 22.8 4.3 33 36-71 73-105 (145)
20 PF13592 HTH_33: Winged helix- 30.5 1E+02 0.0022 19.2 3.6 36 39-74 4-42 (60)
21 TIGR00245 conserved hypothetic 29.5 48 0.001 26.9 2.5 31 36-66 144-174 (248)
22 KOG3471 RNA polymerase II tran 26.7 57 0.0012 29.4 2.6 62 11-72 121-185 (465)
23 PF03540 TFIID_30kDa: Transcri 26.7 71 0.0015 20.5 2.4 24 43-66 6-31 (51)
24 PF07022 Phage_CI_repr: Bacter 26.0 63 0.0014 20.5 2.1 32 37-68 21-53 (66)
25 COG3785 Uncharacterized conser 24.7 52 0.0011 24.5 1.7 17 12-28 56-72 (116)
26 cd07762 CYTH-like_Pase_1 Uncha 22.9 2.4E+02 0.0051 21.3 5.1 34 37-70 73-106 (180)
No 1
>KOG3419 consensus Mitochondrial/chloroplast ribosomal protein S16 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=6.5e-36 Score=216.62 Aligned_cols=93 Identities=59% Similarity=0.989 Sum_probs=85.8
Q ss_pred CccEEeeccCCCCCCCeeEEEEeccCCCCCCCC--------------CCcceEEehHHHHHHHHCCCccCHHHHHHHHHc
Q 033524 1 MVVRIRLARFGCKNKPFYRVMAADSRSPRDGQD--------------SGKRMGLNFDRVKYWLSVGAQPSDPVQRILFRA 66 (117)
Q Consensus 1 MaVkIRLaR~G~KkrPfYrIVVadsR~~RDGk~--------------~~k~i~Ln~eRi~yWL~~GAqPT~tV~~LLk~a 66 (117)
|+|+|||+|+||||||||||||+|+|++|||++ +++.+.||+|||+|||++|||||++|.+||+++
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 346799999999999999999999999999999
Q ss_pred CCCCCCCcccccccCCCCCC-CCCCCCC
Q 033524 67 GLLPPPPMVAMGRKGGPRDT-RPVDPMT 93 (117)
Q Consensus 67 Gil~~~p~~~~~~~g~~~~~-~~~~~~~ 93 (117)
|+++.||++.+..+.+.+.+ +.++|.+
T Consensus 81 Gl~p~~p~~~~~a~~~rr~~a~~~~~~~ 108 (112)
T KOG3419|consen 81 GLFPIHPMTFMNAKRNRRLTAEQVLPVE 108 (112)
T ss_pred CCCCCchhhhhccccchhhhhhhccchh
Confidence 99999999999999888877 6776665
No 2
>PRK14525 rpsP 30S ribosomal protein S16; Provisional
Probab=100.00 E-value=6.7e-35 Score=204.38 Aligned_cols=72 Identities=44% Similarity=0.755 Sum_probs=66.7
Q ss_pred CccEEeeccCCCCCCCeeEEEEeccCCCCCCCCC-----------CcceEEehHHHHHHHHCCCccCHHHHHHHHHcCCC
Q 033524 1 MVVRIRLARFGCKNKPFYRVMAADSRSPRDGQDS-----------GKRMGLNFDRVKYWLSVGAQPSDPVQRILFRAGLL 69 (117)
Q Consensus 1 MaVkIRLaR~G~KkrPfYrIVVadsR~~RDGk~~-----------~k~i~Ln~eRi~yWL~~GAqPT~tV~~LLk~aGil 69 (117)
|||+|||+|+||||+|||||||+|+|++|||+++ +..+.||+|||+|||++|||||+||.+||+++|+.
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 9999999999999999999999999999999542 35799999999999999999999999999999998
Q ss_pred CCC
Q 033524 70 PPP 72 (117)
Q Consensus 70 ~~~ 72 (117)
...
T Consensus 81 ~~~ 83 (88)
T PRK14525 81 AAP 83 (88)
T ss_pred CCC
Confidence 543
No 3
>PRK14521 rpsP 30S ribosomal protein S16; Provisional
Probab=100.00 E-value=3.2e-34 Score=223.24 Aligned_cols=89 Identities=44% Similarity=0.688 Sum_probs=80.7
Q ss_pred CccEEeeccCCCCCCCeeEEEEeccCCCCCCCCC-----------CcceEEehHHHHHHHHCCCccCHHHHHHHHHcCCC
Q 033524 1 MVVRIRLARFGCKNKPFYRVMAADSRSPRDGQDS-----------GKRMGLNFDRVKYWLSVGAQPSDPVQRILFRAGLL 69 (117)
Q Consensus 1 MaVkIRLaR~G~KkrPfYrIVVadsR~~RDGk~~-----------~k~i~Ln~eRi~yWL~~GAqPT~tV~~LLk~aGil 69 (117)
|+|+|||+|+||||+|||||||+|+|++|||+++ +..|.||++||+|||++|||||+||.+||+++|++
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 9999999999999999999999999999999542 35799999999999999999999999999999999
Q ss_pred CCCCcccccccCCCCCCCCC
Q 033524 70 PPPPMVAMGRKGGPRDTRPV 89 (117)
Q Consensus 70 ~~~p~~~~~~~g~~~~~~~~ 89 (117)
.++++..+.++|.+......
T Consensus 81 ~k~~~~~~~~kg~~~~~~~~ 100 (186)
T PRK14521 81 LKKHLLGGVAKGAFTEAQAE 100 (186)
T ss_pred hhhhhhcccCCCcccccchh
Confidence 99888888888877655443
No 4
>CHL00005 rps16 ribosomal protein S16
Probab=100.00 E-value=1.4e-33 Score=195.43 Aligned_cols=71 Identities=38% Similarity=0.622 Sum_probs=65.7
Q ss_pred ccEEeeccCCCCCCCeeEEEEeccCCCCCCCC---------CCcceEEehHHHHHHHHCCCccCHHHHHHHHHcCCCCCC
Q 033524 2 VVRIRLARFGCKNKPFYRVMAADSRSPRDGQD---------SGKRMGLNFDRVKYWLSVGAQPSDPVQRILFRAGLLPPP 72 (117)
Q Consensus 2 aVkIRLaR~G~KkrPfYrIVVadsR~~RDGk~---------~~k~i~Ln~eRi~yWL~~GAqPT~tV~~LLk~aGil~~~ 72 (117)
||+|||+|+||||+|||||||+|+|++|||++ ..+.+.||+||++|||++|||||+||.+||+++|+++++
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 59999999999999999999999999999954 346789999999999999999999999999999987654
No 5
>PRK14524 rpsP 30S ribosomal protein S16; Provisional
Probab=100.00 E-value=8.9e-34 Score=200.65 Aligned_cols=76 Identities=38% Similarity=0.677 Sum_probs=68.2
Q ss_pred ccEEeeccCCCCCCCeeEEEEeccCCCCCCCCC-----------CcceEEehHHHHHHHHCCCccCHHHHHHHHHcCCCC
Q 033524 2 VVRIRLARFGCKNKPFYRVMAADSRSPRDGQDS-----------GKRMGLNFDRVKYWLSVGAQPSDPVQRILFRAGLLP 70 (117)
Q Consensus 2 aVkIRLaR~G~KkrPfYrIVVadsR~~RDGk~~-----------~k~i~Ln~eRi~yWL~~GAqPT~tV~~LLk~aGil~ 70 (117)
||+|||+|+||||+|||||||+|+|++|||+++ +..+.||+||++|||++|||||+||.+||+++|+++
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 599999999999999999999999999999543 257899999999999999999999999999999987
Q ss_pred CCCcccc
Q 033524 71 PPPMVAM 77 (117)
Q Consensus 71 ~~p~~~~ 77 (117)
+....+.
T Consensus 81 ~~~~~~~ 87 (94)
T PRK14524 81 KVHEIKY 87 (94)
T ss_pred hhHHhhh
Confidence 6654433
No 6
>PRK14522 rpsP 30S ribosomal protein S16; Provisional
Probab=100.00 E-value=1.8e-33 Score=205.70 Aligned_cols=77 Identities=30% Similarity=0.537 Sum_probs=70.7
Q ss_pred CccEEeeccCCCCCCCeeEEEEeccCCCCCCCCC----------CcceEEehHHHHHHHHCCCccCHHHHHHHHH--cCC
Q 033524 1 MVVRIRLARFGCKNKPFYRVMAADSRSPRDGQDS----------GKRMGLNFDRVKYWLSVGAQPSDPVQRILFR--AGL 68 (117)
Q Consensus 1 MaVkIRLaR~G~KkrPfYrIVVadsR~~RDGk~~----------~k~i~Ln~eRi~yWL~~GAqPT~tV~~LLk~--aGi 68 (117)
|||+|||+|+||||+|||||||+|+|++|||+++ .+.+.||+|||.|||++|||||++|.+||++ .|+
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 9999999999999999999999999999999643 2579999999999999999999999999999 699
Q ss_pred CCCCCcccc
Q 033524 69 LPPPPMVAM 77 (117)
Q Consensus 69 l~~~p~~~~ 77 (117)
++++...+-
T Consensus 81 ~~~~~~~k~ 89 (116)
T PRK14522 81 YSELMAKKV 89 (116)
T ss_pred chhHHHHHH
Confidence 998876553
No 7
>TIGR00002 S16 ribosomal protein S16. This model describes ribosomal S16 of bacteria and organelles.
Probab=100.00 E-value=6.3e-33 Score=190.40 Aligned_cols=67 Identities=55% Similarity=0.952 Sum_probs=62.6
Q ss_pred cEEeeccCCCCCCCeeEEEEeccCCCCCCCCC-----------CcceEEehHHHHHHHHCCCccCHHHHHHHHHcCCC
Q 033524 3 VRIRLARFGCKNKPFYRVMAADSRSPRDGQDS-----------GKRMGLNFDRVKYWLSVGAQPSDPVQRILFRAGLL 69 (117)
Q Consensus 3 VkIRLaR~G~KkrPfYrIVVadsR~~RDGk~~-----------~k~i~Ln~eRi~yWL~~GAqPT~tV~~LLk~aGil 69 (117)
|+|||+|+||||+|||||||+|+|++|||+++ ++.+.||+||++|||++|||||++|.+||+++|++
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 79999999999999999999999999999643 35799999999999999999999999999999975
No 8
>PRK14520 rpsP 30S ribosomal protein S16; Provisional
Probab=99.98 E-value=8.5e-33 Score=210.31 Aligned_cols=71 Identities=42% Similarity=0.746 Sum_probs=66.0
Q ss_pred CccEEeeccCCCCCCCeeEEEEeccCCCCCCCCC-----------CcceEEehHHHHHHHHCCCccCHHHHHHHHHcCCC
Q 033524 1 MVVRIRLARFGCKNKPFYRVMAADSRSPRDGQDS-----------GKRMGLNFDRVKYWLSVGAQPSDPVQRILFRAGLL 69 (117)
Q Consensus 1 MaVkIRLaR~G~KkrPfYrIVVadsR~~RDGk~~-----------~k~i~Ln~eRi~yWL~~GAqPT~tV~~LLk~aGil 69 (117)
|||+|||+|+||||+|||||||+|+|++|||+++ +..|.||++|++|||++|||||++|.+||++.|++
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 9999999999999999999999999999999542 35789999999999999999999999999999987
Q ss_pred CC
Q 033524 70 PP 71 (117)
Q Consensus 70 ~~ 71 (117)
..
T Consensus 81 ~~ 82 (155)
T PRK14520 81 QK 82 (155)
T ss_pred hh
Confidence 54
No 9
>COG0228 RpsP Ribosomal protein S16 [Translation, ribosomal structure and biogenesis]
Probab=99.97 E-value=2.5e-32 Score=191.31 Aligned_cols=66 Identities=59% Similarity=0.993 Sum_probs=61.8
Q ss_pred ccEEeeccCCCCCCCeeEEEEeccCCCCCCCCC------------CcceEEehHHHHHHHHCCCccCHHHHHHHHHcC
Q 033524 2 VVRIRLARFGCKNKPFYRVMAADSRSPRDGQDS------------GKRMGLNFDRVKYWLSVGAQPSDPVQRILFRAG 67 (117)
Q Consensus 2 aVkIRLaR~G~KkrPfYrIVVadsR~~RDGk~~------------~k~i~Ln~eRi~yWL~~GAqPT~tV~~LLk~aG 67 (117)
||+|||+|+|+||+|||||||+|||++|||+++ +..++||.||+.|||++||||||||++||+++|
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 599999999999999999999999999999532 258999999999999999999999999999998
No 10
>PRK14523 rpsP 30S ribosomal protein S16; Provisional
Probab=99.97 E-value=2.3e-32 Score=204.46 Aligned_cols=86 Identities=37% Similarity=0.555 Sum_probs=76.6
Q ss_pred ccEEeeccCCCCCCCeeEEEEeccCCCCCCCCC-------------CcceEEehHHHHHHHHCCCccCHHHHHHHHHcCC
Q 033524 2 VVRIRLARFGCKNKPFYRVMAADSRSPRDGQDS-------------GKRMGLNFDRVKYWLSVGAQPSDPVQRILFRAGL 68 (117)
Q Consensus 2 aVkIRLaR~G~KkrPfYrIVVadsR~~RDGk~~-------------~k~i~Ln~eRi~yWL~~GAqPT~tV~~LLk~aGi 68 (117)
||+|||+|+||||+|||||||+|+|++|||+++ .+.|.||++||+|||++|||||++|.+||+++|+
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 599999999999999999999999999999532 2478999999999999999999999999999999
Q ss_pred CCCCCcccccccCCCCCCC
Q 033524 69 LPPPPMVAMGRKGGPRDTR 87 (117)
Q Consensus 69 l~~~p~~~~~~~g~~~~~~ 87 (117)
++.+.+..+.++|.+..-.
T Consensus 81 ~~~~~~~~g~~~~~~~~~~ 99 (137)
T PRK14523 81 SPEEAQKGGMRKGEFKRLQ 99 (137)
T ss_pred chHHHHhcccccCCcchhh
Confidence 9988887777777765433
No 11
>PRK00040 rpsP 30S ribosomal protein S16; Reviewed
Probab=99.97 E-value=3.3e-31 Score=180.77 Aligned_cols=62 Identities=56% Similarity=0.979 Sum_probs=57.3
Q ss_pred ccEEeeccCCCCCCCeeEEEEeccCCCCCCCCC-------------CcceEEehHHHHHHHHCCCccCHHHHHHH
Q 033524 2 VVRIRLARFGCKNKPFYRVMAADSRSPRDGQDS-------------GKRMGLNFDRVKYWLSVGAQPSDPVQRIL 63 (117)
Q Consensus 2 aVkIRLaR~G~KkrPfYrIVVadsR~~RDGk~~-------------~k~i~Ln~eRi~yWL~~GAqPT~tV~~LL 63 (117)
||+|||+|+||||+|||||||+|+|++|||+++ ++.+.||+||++|||++|||||++|++||
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 599999999999999999999999999999532 24789999999999999999999999986
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=99.86 E-value=8.6e-23 Score=134.41 Aligned_cols=48 Identities=63% Similarity=1.147 Sum_probs=44.0
Q ss_pred cCCCCCCCeeEEEEeccCCCCCCCC---------C-----CcceEEehHHHHHHHHCCCccC
Q 033524 9 RFGCKNKPFYRVMAADSRSPRDGQD---------S-----GKRMGLNFDRVKYWLSVGAQPS 56 (117)
Q Consensus 9 R~G~KkrPfYrIVVadsR~~RDGk~---------~-----~k~i~Ln~eRi~yWL~~GAqPT 56 (117)
|+||||+|||||||+|+|++|||++ . ++.+.||+|||+|||++|||||
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 7999999999999999999999953 2 2589999999999999999998
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=69.91 E-value=3.7 Score=29.44 Aligned_cols=14 Identities=43% Similarity=1.037 Sum_probs=12.2
Q ss_pred CCCCeeEEEEeccC
Q 033524 13 KNKPFYRVMAADSR 26 (117)
Q Consensus 13 KkrPfYrIVVadsR 26 (117)
+++|||+++|-|..
T Consensus 46 ~~qPfYhvLv~~~~ 59 (101)
T TIGR02097 46 RDQPFYHVLAEDDE 59 (101)
T ss_pred cCCCceEEEEeCCC
Confidence 89999999988854
No 14
>PRK14129 heat shock protein HspQ; Provisional
Probab=65.45 E-value=5.1 Score=29.38 Aligned_cols=14 Identities=29% Similarity=0.733 Sum_probs=12.0
Q ss_pred CCCCeeEEEEeccC
Q 033524 13 KNKPFYRVMAADSR 26 (117)
Q Consensus 13 KkrPfYrIVVadsR 26 (117)
|.+||||++|-|.-
T Consensus 47 kdqPwYHvl~en~~ 60 (105)
T PRK14129 47 RAAPWYHVVMEDDD 60 (105)
T ss_pred cCCCceEEEEEcCC
Confidence 79999999997654
No 15
>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=54.52 E-value=8.7 Score=26.80 Aligned_cols=15 Identities=47% Similarity=0.964 Sum_probs=7.6
Q ss_pred CCCCeeEEEEeccCC
Q 033524 13 KNKPFYRVMAADSRS 27 (117)
Q Consensus 13 KkrPfYrIVVadsR~ 27 (117)
+++|||+|.|-+..+
T Consensus 46 ~~qPfY~vLv~~~~~ 60 (100)
T PF08755_consen 46 RNQPFYHVLVDDRDS 60 (100)
T ss_dssp ----EEEEEEE-SS-
T ss_pred CCCCcEEEEEecCCc
Confidence 899999998887654
No 16
>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=49.20 E-value=26 Score=22.56 Aligned_cols=33 Identities=24% Similarity=0.502 Sum_probs=25.5
Q ss_pred cceEEehHHHHHHHHCCCccCHHHHHHHHHcCCC
Q 033524 36 KRMGLNFDRVKYWLSVGAQPSDPVQRILFRAGLL 69 (117)
Q Consensus 36 k~i~Ln~eRi~yWL~~GAqPT~tV~~LLk~aGil 69 (117)
+.+.++.+++...|+. --..+.+.++|++.|+-
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 5689999999999997 45558899999998864
No 17
>PF03649 UPF0014: Uncharacterised protein family (UPF0014); InterPro: IPR005226 This family has no known function. It includes potential membrane proteins.
Probab=33.60 E-value=37 Score=27.55 Aligned_cols=31 Identities=26% Similarity=0.443 Sum_probs=26.8
Q ss_pred cceEEehHHHHHHHHCCCccCHHHHHHHHHc
Q 033524 36 KRMGLNFDRVKYWLSVGAQPSDPVQRILFRA 66 (117)
Q Consensus 36 k~i~Ln~eRi~yWL~~GAqPT~tV~~LLk~a 66 (117)
.+++-+.+++.+||+.||.|.+.++.+++++
T Consensus 150 ~~l~~~~~~ie~~LalGat~~eA~~~~~r~a 180 (250)
T PF03649_consen 150 SELRERRDEIEALLALGATPREAVRPFIRRA 180 (250)
T ss_pred HHHHHhHHHHHHHHHCCCCHHHHHHHHHHHH
Confidence 3566688999999999999999999998874
No 18
>smart00874 B5 tRNA synthetase B5 domain. This domain is found in phenylalanine-tRNA synthetase beta subunits.
Probab=32.77 E-value=85 Score=19.61 Aligned_cols=33 Identities=21% Similarity=0.423 Sum_probs=26.6
Q ss_pred cceEEehHHHHHHHHCCCccCHHHHHHHHHcCCC
Q 033524 36 KRMGLNFDRVKYWLSVGAQPSDPVQRILFRAGLL 69 (117)
Q Consensus 36 k~i~Ln~eRi~yWL~~GAqPT~tV~~LLk~aGil 69 (117)
..+.++.+++...|+.-- ..+.+.++|++.|+-
T Consensus 2 ~~i~~~~~~i~~llG~~i-~~~ei~~~L~~lg~~ 34 (71)
T smart00874 2 RTITLRRERINRLLGLDL-SAEEIEEILKRLGFE 34 (71)
T ss_pred cEEEecHHHHHHHHCCCC-CHHHHHHHHHHCCCe
Confidence 458999999999998743 346789999999863
No 19
>TIGR01071 rplO_bact ribosomal protein L15, bacterial/organelle.
Probab=30.90 E-value=1e+02 Score=22.81 Aligned_cols=33 Identities=12% Similarity=0.224 Sum_probs=23.7
Q ss_pred cceEEehHHHHHHHHCCCccCHHHHHHHHHcCCCCC
Q 033524 36 KRMGLNFDRVKYWLSVGAQPSDPVQRILFRAGLLPP 71 (117)
Q Consensus 36 k~i~Ln~eRi~yWL~~GAqPT~tV~~LLk~aGil~~ 71 (117)
....||+.+|++|+..|.. .+...|.. ++++..
T Consensus 73 ~~~~VNL~~L~~~~~~g~~--i~~~~L~~-~gli~~ 105 (145)
T TIGR01071 73 EYAEVNLGKLAKLFPNGEV--VTLETLKE-KGLITK 105 (145)
T ss_pred ceeEEEHHHHhhhhhcCCE--ecHHHHhh-CccCcC
Confidence 3468999999999988854 34445554 888864
No 20
>PF13592 HTH_33: Winged helix-turn helix
Probab=30.48 E-value=1e+02 Score=19.23 Aligned_cols=36 Identities=22% Similarity=0.319 Sum_probs=28.6
Q ss_pred EEehHHHHHHHHC--CCccCH-HHHHHHHHcCCCCCCCc
Q 033524 39 GLNFDRVKYWLSV--GAQPSD-PVQRILFRAGLLPPPPM 74 (117)
Q Consensus 39 ~Ln~eRi~yWL~~--GAqPT~-tV~~LLk~aGil~~~p~ 74 (117)
.++...|..||.. |..-|. +|.+||++.|+-...|.
T Consensus 4 ~wt~~~i~~~I~~~fgv~ys~~~v~~lL~r~G~s~~kp~ 42 (60)
T PF13592_consen 4 RWTLKEIAAYIEEEFGVKYSPSGVYRLLKRLGFSYQKPR 42 (60)
T ss_pred cccHHHHHHHHHHHHCCEEcHHHHHHHHHHcCCccccCC
Confidence 4567788889887 887775 68999999998776664
No 21
>TIGR00245 conserved hypothetical protein TIGR00245.
Probab=29.51 E-value=48 Score=26.94 Aligned_cols=31 Identities=23% Similarity=0.383 Sum_probs=27.6
Q ss_pred cceEEehHHHHHHHHCCCccCHHHHHHHHHc
Q 033524 36 KRMGLNFDRVKYWLSVGAQPSDPVQRILFRA 66 (117)
Q Consensus 36 k~i~Ln~eRi~yWL~~GAqPT~tV~~LLk~a 66 (117)
++++-+.+.+.+||+.||.|.+.++.+++++
T Consensus 144 ~~l~~~~~~ie~~LaLGat~~~A~~~~~r~A 174 (248)
T TIGR00245 144 SMVKSERDEIQGYLSLGATPKQAIAPFIRNA 174 (248)
T ss_pred HHHHHhhHHHHHHHHCCCCHHHHHHHHHHHH
Confidence 4577788999999999999999999999884
No 22
>KOG3471 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit TFB2 [Transcription; Replication, recombination and repair]
Probab=26.74 E-value=57 Score=29.36 Aligned_cols=62 Identities=19% Similarity=0.251 Sum_probs=36.9
Q ss_pred CCCCCCeeEEEEeccCCCCCCCCCCcceEEehHHHHHHHHC---CCccCHHHHHHHHHcCCCCCC
Q 033524 11 GCKNKPFYRVMAADSRSPRDGQDSGKRMGLNFDRVKYWLSV---GAQPSDPVQRILFRAGLLPPP 72 (117)
Q Consensus 11 G~KkrPfYrIVVadsR~~RDGk~~~k~i~Ln~eRi~yWL~~---GAqPT~tV~~LLk~aGil~~~ 72 (117)
|.+.++|=..|+=+....||++...+.-.=..|-|.+.+-- -.-||+.|.+||+.+|++...
T Consensus 121 g~~~~s~~s~~l~~~~~~r~v~~ld~ya~~rwe~ILh~mvgt~~a~~~se~v~~ll~~a~lm~~~ 185 (465)
T KOG3471|consen 121 GGKQNSFGSLVLGEDKHNRDVDFLDKYASERWECILHFMVGTPEAKAVSEGVLNLLKHAGLMSRD 185 (465)
T ss_pred CCCcccCCCcccCCCcCcccchhhHHHHHHHHHHHHHHHhCCccccccChhHHHHHHhcCccCCC
Confidence 44444443445555566777764433333334445444432 246899999999999997543
No 23
>PF03540 TFIID_30kDa: Transcription initiation factor TFIID 23-30kDa subunit; InterPro: IPR003923 Transcription initiation factor TFIID is a multimeric protein complex that plays a central role in mediating promoter responses to various activators and repressors. The complex includes TATA binding protein (TBP) and various TBP-associated factors (TAFS). TFIID a bona fide RNA polymerase II-specific TATA-binding protein-associated factor (TAF) and is essential for viability []. TFIID acts to nucleate the transcription complex, recruiting the rest of the factors through a direct interaction with TFIIB. The TBP subunit of TFIID is sufficient for TATA-element binding and TFIIB interaction, and can support basal transcription. The protein belongs to the TAF2H family.; GO: 0006352 transcription initiation, DNA-dependent, 0005634 nucleus
Probab=26.72 E-value=71 Score=20.46 Aligned_cols=24 Identities=38% Similarity=0.556 Sum_probs=17.8
Q ss_pred HHHHHHHHC-CCccCH-HHHHHHHHc
Q 033524 43 DRVKYWLSV-GAQPSD-PVQRILFRA 66 (117)
Q Consensus 43 eRi~yWL~~-GAqPT~-tV~~LLk~a 66 (117)
+-+.|||.. |.+.+| +|.+|++.+
T Consensus 6 ~v~~~yL~~~G~~~~D~rv~RLvSLa 31 (51)
T PF03540_consen 6 EVTDYYLERSGFQTSDPRVKRLVSLA 31 (51)
T ss_pred HHHHHHHHHCCCCCCCHhHHHHHHHH
Confidence 457888887 888876 577777765
No 24
>PF07022 Phage_CI_repr: Bacteriophage CI repressor helix-turn-helix domain; InterPro: IPR010744 This family consists of several phage CI repressor proteins and related bacterial sequences. The CI repressor is known to function as a transcriptional switch, determining whether transcription is lytic or lysogenic [].; GO: 0003677 DNA binding, 0045892 negative regulation of transcription, DNA-dependent; PDB: 2FJR_B.
Probab=25.97 E-value=63 Score=20.50 Aligned_cols=32 Identities=22% Similarity=0.568 Sum_probs=22.7
Q ss_pred ceEEehHHHH-HHHHCCCccCHHHHHHHHHcCC
Q 033524 37 RMGLNFDRVK-YWLSVGAQPSDPVQRILFRAGL 68 (117)
Q Consensus 37 ~i~Ln~eRi~-yWL~~GAqPT~tV~~LLk~aGi 68 (117)
.+.+...-+. .|..+|.-|.+-+..|-...|+
T Consensus 21 ~lgis~st~s~~~~~r~~~P~~~l~~ia~~~gv 53 (66)
T PF07022_consen 21 RLGISKSTLSNNWKKRGSIPAEWLIKIALETGV 53 (66)
T ss_dssp CTT--HHHHH-HHHHSSS--HHHHHHHHHHH--
T ss_pred HhCcCHHHhhHHHHhCCCCCHHHHHHHHHHHCc
Confidence 4667788899 9999999999999998888775
No 25
>COG3785 Uncharacterized conserved protein [Function unknown]
Probab=24.71 E-value=52 Score=24.50 Aligned_cols=17 Identities=24% Similarity=0.765 Sum_probs=13.1
Q ss_pred CCCCCeeEEEEeccCCC
Q 033524 12 CKNKPFYRVMAADSRSP 28 (117)
Q Consensus 12 ~KkrPfYrIVVadsR~~ 28 (117)
.|-.||||+++=|.-.+
T Consensus 56 ~rdqPfYHllaEnde~~ 72 (116)
T COG3785 56 LRDQPFYHLLAENDETE 72 (116)
T ss_pred cccCCceeeeeecCCcc
Confidence 36789999999887643
No 26
>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=22.88 E-value=2.4e+02 Score=21.31 Aligned_cols=34 Identities=18% Similarity=0.300 Sum_probs=28.7
Q ss_pred ceEEehHHHHHHHHCCCccCHHHHHHHHHcCCCC
Q 033524 37 RMGLNFDRVKYWLSVGAQPSDPVQRILFRAGLLP 70 (117)
Q Consensus 37 ~i~Ln~eRi~yWL~~GAqPT~tV~~LLk~aGil~ 70 (117)
++.|+.+...-++..|.-|.+.+..+|...|+-+
T Consensus 73 e~~l~~~~~~~~~~~~~~~~~~~~~~L~~lg~~~ 106 (180)
T cd07762 73 NQPLTLEEAEKLIKGGTLPEGEILDKLKELGIDP 106 (180)
T ss_pred eecCCHHHHHHHhccccCCchHHHHHHHHhCCCc
Confidence 4556666888999999999999999999999853
Done!