Query 032887
Match_columns 131
No_of_seqs 118 out of 1137
Neff 4.3
Searched_HMMs 46136
Date Fri Mar 29 07:10:16 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/032887.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/032887hhsearch_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 1.2E-45 2.6E-50 271.1 8.7 100 1-100 1-100 (112)
2 PRK14525 rpsP 30S ribosomal pr 100.0 6.4E-44 1.4E-48 253.8 10.3 83 1-86 1-83 (88)
3 PRK14521 rpsP 30S ribosomal pr 100.0 4.1E-43 8.9E-48 277.5 9.6 94 1-97 1-94 (186)
4 PRK14524 rpsP 30S ribosomal pr 100.0 9.3E-43 2E-47 250.4 8.5 86 2-90 1-86 (94)
5 TIGR00002 S16 ribosomal protei 100.0 3.2E-42 6.9E-47 240.2 9.6 78 3-83 1-78 (78)
6 CHL00005 rps16 ribosomal prote 100.0 2.8E-42 6.2E-47 242.6 9.1 80 2-86 1-80 (82)
7 PRK14522 rpsP 30S ribosomal pr 100.0 1.2E-41 2.5E-46 252.5 8.1 86 1-90 1-88 (116)
8 PRK14520 rpsP 30S ribosomal pr 100.0 1.5E-41 3.2E-46 262.4 8.9 82 1-85 1-82 (155)
9 COG0228 RpsP Ribosomal protein 100.0 2.9E-41 6.4E-46 239.8 8.0 78 2-81 1-78 (87)
10 PRK14523 rpsP 30S ribosomal pr 100.0 2.7E-41 5.8E-46 256.4 8.0 93 2-95 1-93 (137)
11 PRK00040 rpsP 30S ribosomal pr 100.0 4.5E-41 9.8E-46 232.9 8.1 75 2-77 1-75 (75)
12 PF00886 Ribosomal_S16: Riboso 100.0 1.4E-33 3.1E-38 188.7 5.0 62 9-70 1-62 (62)
13 TIGR02097 yccV hemimethylated 57.3 8.6 0.00019 28.1 2.0 14 13-26 46-59 (101)
14 PRK14129 heat shock protein Hs 52.4 11 0.00024 28.0 2.0 14 13-26 47-60 (105)
15 PF03484 B5: tRNA synthetase B 51.1 23 0.00049 23.3 3.2 33 50-83 2-34 (70)
16 PF08755 YccV-like: Hemimethyl 48.5 14 0.00031 26.2 2.0 23 13-43 46-68 (100)
17 smart00874 B5 tRNA synthetase 33.3 80 0.0017 20.1 3.6 32 50-82 2-33 (71)
18 PF03649 UPF0014: Uncharacteri 30.3 44 0.00096 27.6 2.5 30 51-80 151-180 (250)
19 KOG0135 Pristanoyl-CoA/acyl-Co 30.2 58 0.0013 30.9 3.4 80 30-123 170-254 (661)
20 KOG2618 Uncharacterized conser 28.5 92 0.002 27.6 4.1 35 8-49 134-168 (366)
21 PF11875 DUF3395: Domain of un 27.8 36 0.00077 26.0 1.4 12 33-44 108-119 (151)
22 PRK13149 H/ACA RNA-protein com 26.8 46 0.00099 22.5 1.6 27 13-39 21-47 (73)
23 TIGR00245 conserved hypothetic 25.9 59 0.0013 26.9 2.4 30 51-80 145-174 (248)
24 PF07022 Phage_CI_repr: Bacter 22.8 72 0.0016 20.6 2.0 32 51-82 21-53 (66)
25 cd06392 PBP1_iGluR_delta_1 N-t 22.8 1.2E+02 0.0027 26.3 4.0 40 4-44 357-396 (400)
No 1
>KOG3419 consensus Mitochondrial/chloroplast ribosomal protein S16 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.2e-45 Score=271.06 Aligned_cols=100 Identities=63% Similarity=1.063 Sum_probs=96.8
Q ss_pred CceEEeeccCCCCCCCeeEEEEeccCCCCCCcceeeeeeecCCCCCCCCcceEEeHHHHHHHHHCCCccCHHHHHHHHHc
Q 032887 1 MVVRIRLARFGCKNKPFYRVMAADSRSPRDGKHLEVLGYYNPLPGQDSGKRMGLNFDRVKYWLSVGAQPSDPVQRILFRA 80 (131)
Q Consensus 1 M~VkIRL~R~G~K~rPfYrIVv~dsr~~RdGk~IE~LG~YdP~~~~~~~k~i~Ln~eRi~yWL~~GAqpT~tV~~LL~~~ 80 (131)
|+|+|||+|+||||||||||||+|+|++|||++||+||||||+++.++++.+.||+|||+|||++|||||+||.+||+++
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 89999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCCCCccccccCCCCCCC
Q 032887 81 GLLPPPPMVAMGRKGGPRDT 100 (131)
Q Consensus 81 g~l~~~p~~~~~~kg~~~~~ 100 (131)
|++|.+|+..+.++.+.+..
T Consensus 81 Gl~p~~p~~~~~a~~~rr~~ 100 (112)
T KOG3419|consen 81 GLFPIHPMTFMNAKRNRRLT 100 (112)
T ss_pred CCCCCchhhhhccccchhhh
Confidence 99999999999998877655
No 2
>PRK14525 rpsP 30S ribosomal protein S16; Provisional
Probab=100.00 E-value=6.4e-44 Score=253.84 Aligned_cols=83 Identities=46% Similarity=0.787 Sum_probs=78.9
Q ss_pred CceEEeeccCCCCCCCeeEEEEeccCCCCCCcceeeeeeecCCCCCCCCcceEEeHHHHHHHHHCCCccCHHHHHHHHHc
Q 032887 1 MVVRIRLARFGCKNKPFYRVMAADSRSPRDGKHLEVLGYYNPLPGQDSGKRMGLNFDRVKYWLSVGAQPSDPVQRILFRA 80 (131)
Q Consensus 1 M~VkIRL~R~G~K~rPfYrIVv~dsr~~RdGk~IE~LG~YdP~~~~~~~k~i~Ln~eRi~yWL~~GAqpT~tV~~LL~~~ 80 (131)
|||+|||+|+||||+|||||||+|+|++|||+|||+||||||+.++ +.+.||+|||+|||++|||||+||.+||+++
T Consensus 1 M~VkIRL~R~G~k~~P~YrIVv~dsr~~RdGk~IE~lG~YnP~~~~---~~i~ln~eri~~WL~~GAqpT~tV~~Ll~~~ 77 (88)
T PRK14525 1 MAVVLRLSRAGTHKAPFYHVVATDSRNARDGKYLEDVGIYDPTKRP---ERIELKVERIEHWLKAGAKPSQTVAMILKRA 77 (88)
T ss_pred CcEEEehhhCCCCCCCeEEEEEeecCCCCCCCceeEEecccCCCCC---ceEEEcHHHHHHHHHCCCccCHHHHHHHHHc
Confidence 9999999999999999999999999999999999999999999653 5899999999999999999999999999999
Q ss_pred CCCCCC
Q 032887 81 GLLPPP 86 (131)
Q Consensus 81 g~l~~~ 86 (131)
|+...+
T Consensus 78 g~~~~~ 83 (88)
T PRK14525 78 AKAAAP 83 (88)
T ss_pred CccCCC
Confidence 998553
No 3
>PRK14521 rpsP 30S ribosomal protein S16; Provisional
Probab=100.00 E-value=4.1e-43 Score=277.48 Aligned_cols=94 Identities=48% Similarity=0.776 Sum_probs=88.4
Q ss_pred CceEEeeccCCCCCCCeeEEEEeccCCCCCCcceeeeeeecCCCCCCCCcceEEeHHHHHHHHHCCCccCHHHHHHHHHc
Q 032887 1 MVVRIRLARFGCKNKPFYRVMAADSRSPRDGKHLEVLGYYNPLPGQDSGKRMGLNFDRVKYWLSVGAQPSDPVQRILFRA 80 (131)
Q Consensus 1 M~VkIRL~R~G~K~rPfYrIVv~dsr~~RdGk~IE~LG~YdP~~~~~~~k~i~Ln~eRi~yWL~~GAqpT~tV~~LL~~~ 80 (131)
|+|+|||+|+|||++|||||||+|+|++|||+|||+||||||+.++ ..|.||++||+|||++|||||+||.+||+++
T Consensus 1 M~VkIRL~R~G~KkrPfYrIVVaDsR~~RDGk~IE~lG~YnP~~~~---~~i~Ln~eRi~~WL~~GAqPTdtV~~lL~~~ 77 (186)
T PRK14521 1 MAVKIRLQRHGRKGKAFYWIVAADSRAPRDGKFIEKIGTYNPNTNP---ATVDLNFDRAVYWLMNGAQPTDTARNILSYE 77 (186)
T ss_pred CcEeehhhhCCCCCCCeEEEEEEeCCCCCCCCceeeeeecCCCCCC---ceEEEcHHHHHHHHHCCCcCCHHHHHHHHHc
Confidence 9999999999999999999999999999999999999999999764 5899999999999999999999999999999
Q ss_pred CCCCCCCccccccCCCC
Q 032887 81 GLLPPPPMVAMGRKGGP 97 (131)
Q Consensus 81 g~l~~~p~~~~~~kg~~ 97 (131)
|+|.+++...+.+||..
T Consensus 78 g~~~k~~~~~~~~kg~~ 94 (186)
T PRK14521 78 GVLLKKHLLGGVAKGAF 94 (186)
T ss_pred ccchhhhhhcccCCCcc
Confidence 99998887777777643
No 4
>PRK14524 rpsP 30S ribosomal protein S16; Provisional
Probab=100.00 E-value=9.3e-43 Score=250.37 Aligned_cols=86 Identities=43% Similarity=0.789 Sum_probs=80.1
Q ss_pred ceEEeeccCCCCCCCeeEEEEeccCCCCCCcceeeeeeecCCCCCCCCcceEEeHHHHHHHHHCCCccCHHHHHHHHHcC
Q 032887 2 VVRIRLARFGCKNKPFYRVMAADSRSPRDGKHLEVLGYYNPLPGQDSGKRMGLNFDRVKYWLSVGAQPSDPVQRILFRAG 81 (131)
Q Consensus 2 ~VkIRL~R~G~K~rPfYrIVv~dsr~~RdGk~IE~LG~YdP~~~~~~~k~i~Ln~eRi~yWL~~GAqpT~tV~~LL~~~g 81 (131)
||+|||+|+||||+|||||||+|+|++|||+|||+||||||+.++ ..+.||++|++|||++|||||+||.+||+++|
T Consensus 1 mVkIRL~R~G~KkrPfYrIVvadsr~~RdGk~iE~lG~YnP~~~~---~~i~l~~eri~~Wl~~GAqpT~tV~~Llkk~g 77 (94)
T PRK14524 1 MVRIRLTRMGKRKQPFYRIVVVDSRKRRDGAYIESLGYYNPLKEP---YEIKVDVERAVEWILKGAQPSDTVRDILRKFG 77 (94)
T ss_pred CcEEhhccCCCCCCCeEEEEEEecCCCCCCCceeEeeecCCCCCC---ceEEEcHHHHHHHHHcCCccCHHHHHHHHHcc
Confidence 589999999999999999999999999999999999999999764 58999999999999999999999999999999
Q ss_pred CCCCCCccc
Q 032887 82 LLPPPPMVA 90 (131)
Q Consensus 82 ~l~~~p~~~ 90 (131)
++++....+
T Consensus 78 ~~~~~~~~~ 86 (94)
T PRK14524 78 VMKKVHEIK 86 (94)
T ss_pred chhhhHHhh
Confidence 987765443
No 5
>TIGR00002 S16 ribosomal protein S16. This model describes ribosomal S16 of bacteria and organelles.
Probab=100.00 E-value=3.2e-42 Score=240.21 Aligned_cols=78 Identities=56% Similarity=1.025 Sum_probs=75.0
Q ss_pred eEEeeccCCCCCCCeeEEEEeccCCCCCCcceeeeeeecCCCCCCCCcceEEeHHHHHHHHHCCCccCHHHHHHHHHcCC
Q 032887 3 VRIRLARFGCKNKPFYRVMAADSRSPRDGKHLEVLGYYNPLPGQDSGKRMGLNFDRVKYWLSVGAQPSDPVQRILFRAGL 82 (131)
Q Consensus 3 VkIRL~R~G~K~rPfYrIVv~dsr~~RdGk~IE~LG~YdP~~~~~~~k~i~Ln~eRi~yWL~~GAqpT~tV~~LL~~~g~ 82 (131)
|+|||+|+||||+|||||||+|+|++|||+|||+||||||+.++ +.+.||+||++|||++|||||++|++||+++|+
T Consensus 1 vkIRL~R~G~k~~PfYrIVv~d~r~~RdGk~iE~lG~YnP~~~~---~~i~l~~~ri~~Wl~~GAqps~tV~~Ll~~~g~ 77 (78)
T TIGR00002 1 VKIRLKRGGRKKRPFYRIVVADSRSRRDGRYIEELGFYNPLTKE---SRVKLNVERIKYWLSKGAQPTDTVRNLLKKAGV 77 (78)
T ss_pred CEEecccCCCCCCCeEEEEEEecCCCCCCCceeEeeeccCCCCC---cEEEEcHHHHHHHHHCCCccCHHHHHHHHHccC
Confidence 79999999999999999999999999999999999999999764 689999999999999999999999999999997
Q ss_pred C
Q 032887 83 L 83 (131)
Q Consensus 83 l 83 (131)
+
T Consensus 78 ~ 78 (78)
T TIGR00002 78 F 78 (78)
T ss_pred C
Confidence 5
No 6
>CHL00005 rps16 ribosomal protein S16
Probab=100.00 E-value=2.8e-42 Score=242.63 Aligned_cols=80 Identities=39% Similarity=0.712 Sum_probs=75.7
Q ss_pred ceEEeeccCCCCCCCeeEEEEeccCCCCCCcceeeeeeecCCCCCCCCcceEEeHHHHHHHHHCCCccCHHHHHHHHHcC
Q 032887 2 VVRIRLARFGCKNKPFYRVMAADSRSPRDGKHLEVLGYYNPLPGQDSGKRMGLNFDRVKYWLSVGAQPSDPVQRILFRAG 81 (131)
Q Consensus 2 ~VkIRL~R~G~K~rPfYrIVv~dsr~~RdGk~IE~LG~YdP~~~~~~~k~i~Ln~eRi~yWL~~GAqpT~tV~~LL~~~g 81 (131)
||+|||+|+|+||+|||||||+|+|++|||+|||+||||||+.+ .+.||+||++|||++|||||+||.+||+++|
T Consensus 1 ~vkIRL~R~G~kk~P~YrIVvadsr~~RdGk~iE~lG~YnP~~~-----~~~ln~eri~~Wl~~GAqpt~tV~~Ll~~~g 75 (82)
T CHL00005 1 MVKLRLKRCGRKQQAVYRIVAIDVRSRREGRDLEKVGFYDPIKN-----QTYLNVPAILYFLEKGAQPTETVYDILKKAE 75 (82)
T ss_pred CeEEecccCCCCCCCeEEEEEEeCCCCCCCcceeEeeeccCCCc-----ccEEeHHHHHHHHHCcCccCHHHHHHHHHcC
Confidence 58999999999999999999999999999999999999999863 5799999999999999999999999999999
Q ss_pred CCCCC
Q 032887 82 LLPPP 86 (131)
Q Consensus 82 ~l~~~ 86 (131)
+++++
T Consensus 76 ~~~~~ 80 (82)
T CHL00005 76 VFKEL 80 (82)
T ss_pred chhhh
Confidence 87653
No 7
>PRK14522 rpsP 30S ribosomal protein S16; Provisional
Probab=100.00 E-value=1.2e-41 Score=252.49 Aligned_cols=86 Identities=34% Similarity=0.642 Sum_probs=81.5
Q ss_pred CceEEeeccCCCCCCCeeEEEEeccCCCCCCcceeeeeeecCCCCCCCCcceEEeHHHHHHHHHCCCccCHHHHHHHHH-
Q 032887 1 MVVRIRLARFGCKNKPFYRVMAADSRSPRDGKHLEVLGYYNPLPGQDSGKRMGLNFDRVKYWLSVGAQPSDPVQRILFR- 79 (131)
Q Consensus 1 M~VkIRL~R~G~K~rPfYrIVv~dsr~~RdGk~IE~LG~YdP~~~~~~~k~i~Ln~eRi~yWL~~GAqpT~tV~~LL~~- 79 (131)
|||+|||+|+||||+|||||||+|+|++|||+|||+||||||+.+ +.+.||+|||.|||++|||||+||.+||++
T Consensus 1 MmVkIRLaR~G~KkrPfYrIVVaDsR~~RDGk~IE~lG~YdP~~~----~~v~Ln~eRi~yWL~~GAqPS~tV~~LLkk~ 76 (116)
T PRK14522 1 MALKIRLRQQGRRNHVVYRLVLADVESPRDGKYIELLGWYDPHSE----QNYQLKSERIFYWLNQGAELTEKAGALVKQG 76 (116)
T ss_pred CcEEEecccCCCCCCCeEEEEEeecCCCCCCCcceeeeccCCCCC----CceEECHHHHHHHHHCCCccCHHHHHHHHhh
Confidence 999999999999999999999999999999999999999999865 379999999999999999999999999999
Q ss_pred -cCCCCCCCccc
Q 032887 80 -AGLLPPPPMVA 90 (131)
Q Consensus 80 -~g~l~~~p~~~ 90 (131)
+|+++++...+
T Consensus 77 ~~Gi~~~~~~~k 88 (116)
T PRK14522 77 APGVYSELMAKK 88 (116)
T ss_pred hcccchhHHHHH
Confidence 69999877654
No 8
>PRK14520 rpsP 30S ribosomal protein S16; Provisional
Probab=100.00 E-value=1.5e-41 Score=262.42 Aligned_cols=82 Identities=41% Similarity=0.764 Sum_probs=78.6
Q ss_pred CceEEeeccCCCCCCCeeEEEEeccCCCCCCcceeeeeeecCCCCCCCCcceEEeHHHHHHHHHCCCccCHHHHHHHHHc
Q 032887 1 MVVRIRLARFGCKNKPFYRVMAADSRSPRDGKHLEVLGYYNPLPGQDSGKRMGLNFDRVKYWLSVGAQPSDPVQRILFRA 80 (131)
Q Consensus 1 M~VkIRL~R~G~K~rPfYrIVv~dsr~~RdGk~IE~LG~YdP~~~~~~~k~i~Ln~eRi~yWL~~GAqpT~tV~~LL~~~ 80 (131)
|+|+|||+|+||||+|||||||+|+|++|||+|||+||||||+.++ ..|.||++|++|||++|||||++|.+||++.
T Consensus 1 MaVkIRL~R~G~kk~PfYrIVVaDsR~~RDGk~IE~lG~YnP~~~~---~~i~ln~eRi~yWL~~GAQPT~~V~~LLk~~ 77 (155)
T PRK14520 1 MAVKIKLKRLGKIRNPQYRIVVADSRTKRDGRAIEEIGRYHPKEEP---SLIEIDSERAQYWLSVGAQPTEPVLALLKIT 77 (155)
T ss_pred CcEEehhhhCCCCCCCeEEEEEeecCCCCCCCceeeeeccCCCCCC---ceEEEcHHHHHHHHHCCCccCHHHHHHHHHc
Confidence 9999999999999999999999999999999999999999998764 5899999999999999999999999999999
Q ss_pred CCCCC
Q 032887 81 GLLPP 85 (131)
Q Consensus 81 g~l~~ 85 (131)
|++.+
T Consensus 78 g~~~~ 82 (155)
T PRK14520 78 GDWQK 82 (155)
T ss_pred chhhh
Confidence 98764
No 9
>COG0228 RpsP Ribosomal protein S16 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=2.9e-41 Score=239.80 Aligned_cols=78 Identities=59% Similarity=1.017 Sum_probs=74.1
Q ss_pred ceEEeeccCCCCCCCeeEEEEeccCCCCCCcceeeeeeecCCCCCCCCcceEEeHHHHHHHHHCCCccCHHHHHHHHHcC
Q 032887 2 VVRIRLARFGCKNKPFYRVMAADSRSPRDGKHLEVLGYYNPLPGQDSGKRMGLNFDRVKYWLSVGAQPSDPVQRILFRAG 81 (131)
Q Consensus 2 ~VkIRL~R~G~K~rPfYrIVv~dsr~~RdGk~IE~LG~YdP~~~~~~~k~i~Ln~eRi~yWL~~GAqpT~tV~~LL~~~g 81 (131)
||+|||+|+|+||+|||||||+|||++|||+|||.||||||+. ..+..+.||.||+.|||++||||||||++||+++|
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 MVKIRLARGGSKKRPFYRIVVADSRSPRDGRFIERLGTYNPLL--GKEERVKLDEERILYWLSQGAQPSDTVRRLLKKAG 78 (87)
T ss_pred CeEEehhhCCCccCCeEEEEEeccCCCCCCcchhhhcccCCCC--CccceEEEcHHHHHHHHHcCCcccHHHHHHHHHhh
Confidence 5899999999999999999999999999999999999999977 23468999999999999999999999999999998
No 10
>PRK14523 rpsP 30S ribosomal protein S16; Provisional
Probab=100.00 E-value=2.7e-41 Score=256.35 Aligned_cols=93 Identities=41% Similarity=0.697 Sum_probs=84.1
Q ss_pred ceEEeeccCCCCCCCeeEEEEeccCCCCCCcceeeeeeecCCCCCCCCcceEEeHHHHHHHHHCCCccCHHHHHHHHHcC
Q 032887 2 VVRIRLARFGCKNKPFYRVMAADSRSPRDGKHLEVLGYYNPLPGQDSGKRMGLNFDRVKYWLSVGAQPSDPVQRILFRAG 81 (131)
Q Consensus 2 ~VkIRL~R~G~K~rPfYrIVv~dsr~~RdGk~IE~LG~YdP~~~~~~~k~i~Ln~eRi~yWL~~GAqpT~tV~~LL~~~g 81 (131)
||+|||+|+||||+|||||||+|+|++|||+|||+||||||+.+.. .+.|.||++||+|||++|||||+||.+||+++|
T Consensus 1 mVkIRL~R~GrKkrPfYRIVVaDsRs~RDGK~IE~LG~YdP~~~~~-~~~i~Ln~eRi~yWL~~GAQPS~tV~~LLkkag 79 (137)
T PRK14523 1 MVVIRLARGGSKKNPFYHIVVADRRKPRDGRFIERVGYYNPMARGQ-DIRLQLEKERISHWLNQGAQTSLRVKHLIKKLE 79 (137)
T ss_pred CcEehhhcCCCCCCCeEEEEEEecCCCCCCCceeeeeecCCCCCCC-CceEEECHHHHHHHHHCCCccCHHHHHHHHHcc
Confidence 5899999999999999999999999999999999999999997653 358999999999999999999999999999999
Q ss_pred CCCCCCccccccCC
Q 032887 82 LLPPPPMVAMGRKG 95 (131)
Q Consensus 82 ~l~~~p~~~~~~kg 95 (131)
+++.+....+.++|
T Consensus 80 ~~~~~~~~~g~~~~ 93 (137)
T PRK14523 80 KSPEEAQKGGMRKG 93 (137)
T ss_pred cchHHHHhcccccC
Confidence 98887665544444
No 11
>PRK00040 rpsP 30S ribosomal protein S16; Reviewed
Probab=100.00 E-value=4.5e-41 Score=232.92 Aligned_cols=75 Identities=55% Similarity=1.025 Sum_probs=71.0
Q ss_pred ceEEeeccCCCCCCCeeEEEEeccCCCCCCcceeeeeeecCCCCCCCCcceEEeHHHHHHHHHCCCccCHHHHHHH
Q 032887 2 VVRIRLARFGCKNKPFYRVMAADSRSPRDGKHLEVLGYYNPLPGQDSGKRMGLNFDRVKYWLSVGAQPSDPVQRIL 77 (131)
Q Consensus 2 ~VkIRL~R~G~K~rPfYrIVv~dsr~~RdGk~IE~LG~YdP~~~~~~~k~i~Ln~eRi~yWL~~GAqpT~tV~~LL 77 (131)
||+|||+|+||||+|||||||+|+|++|||+|||+||||||+.+. +++.+.||+|||+|||++|||||++|++||
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 MVKIRLARGGAKKRPFYRIVVADSRSPRDGRFIERVGFYNPLAKP-AEEEVKLDEERVLYWLGQGAQPTDTVRRLL 75 (75)
T ss_pred CeEEhhhhCCCCCCCeEEEEEEecCCCCCCCceeEEeecCCCCCC-CcceEEEcHHHHHHHHHCCCccCHHHHHhC
Confidence 589999999999999999999999999999999999999999864 346899999999999999999999999986
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=100.00 E-value=1.4e-33 Score=188.67 Aligned_cols=62 Identities=61% Similarity=1.217 Sum_probs=59.6
Q ss_pred cCCCCCCCeeEEEEeccCCCCCCcceeeeeeecCCCCCCCCcceEEeHHHHHHHHHCCCccC
Q 032887 9 RFGCKNKPFYRVMAADSRSPRDGKHLEVLGYYNPLPGQDSGKRMGLNFDRVKYWLSVGAQPS 70 (131)
Q Consensus 9 R~G~K~rPfYrIVv~dsr~~RdGk~IE~LG~YdP~~~~~~~k~i~Ln~eRi~yWL~~GAqpT 70 (131)
|+||||+|||||||+|+|++|||++||+||+|||+++..+++.+.||+|||+|||++|||||
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 78999999999999999999999999999999999987666899999999999999999997
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=57.27 E-value=8.6 Score=28.05 Aligned_cols=14 Identities=43% Similarity=1.037 Sum_probs=12.2
Q ss_pred CCCCeeEEEEeccC
Q 032887 13 KNKPFYRVMAADSR 26 (131)
Q Consensus 13 K~rPfYrIVv~dsr 26 (131)
|++|||+++|-|..
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=52.43 E-value=11 Score=28.02 Aligned_cols=14 Identities=29% Similarity=0.733 Sum_probs=11.9
Q ss_pred CCCCeeEEEEeccC
Q 032887 13 KNKPFYRVMAADSR 26 (131)
Q Consensus 13 K~rPfYrIVv~dsr 26 (131)
|.+||||++|-|.-
T Consensus 47 kdqPwYHvl~en~~ 60 (105)
T PRK14129 47 RAAPWYHVVMEDDD 60 (105)
T ss_pred cCCCceEEEEEcCC
Confidence 79999999996654
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=51.11 E-value=23 Score=23.30 Aligned_cols=33 Identities=24% Similarity=0.502 Sum_probs=25.8
Q ss_pred cceEEeHHHHHHHHHCCCccCHHHHHHHHHcCCC
Q 032887 50 KRMGLNFDRVKYWLSVGAQPSDPVQRILFRAGLL 83 (131)
Q Consensus 50 k~i~Ln~eRi~yWL~~GAqpT~tV~~LL~~~g~l 83 (131)
+.+.++.+++...|+. .-..+.+.++|++.|+-
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 5799999999999987 45558899999999863
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=48.45 E-value=14 Score=26.20 Aligned_cols=23 Identities=35% Similarity=0.641 Sum_probs=12.0
Q ss_pred CCCCeeEEEEeccCCCCCCcceeeeeeecCC
Q 032887 13 KNKPFYRVMAADSRSPRDGKHLEVLGYYNPL 43 (131)
Q Consensus 13 K~rPfYrIVv~dsr~~RdGk~IE~LG~YdP~ 43 (131)
+++|||+|.|-+..+ +.+ +|-|-
T Consensus 46 ~~qPfY~vLv~~~~~-------~~~-~YVaE 68 (100)
T PF08755_consen 46 RNQPFYHVLVDDRDS-------PPV-RYVAE 68 (100)
T ss_dssp ----EEEEEEE-SS---------EE-EEEEG
T ss_pred CCCCcEEEEEecCCc-------cce-EEecc
Confidence 899999998877654 344 88774
No 17
>smart00874 B5 tRNA synthetase B5 domain. This domain is found in phenylalanine-tRNA synthetase beta subunits.
Probab=33.34 E-value=80 Score=20.12 Aligned_cols=32 Identities=22% Similarity=0.466 Sum_probs=26.3
Q ss_pred cceEEeHHHHHHHHHCCCccCHHHHHHHHHcCC
Q 032887 50 KRMGLNFDRVKYWLSVGAQPSDPVQRILFRAGL 82 (131)
Q Consensus 50 k~i~Ln~eRi~yWL~~GAqpT~tV~~LL~~~g~ 82 (131)
..+.++.+++...|+.-- ..+.+.++|.+.|+
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 368999999999998743 34679999999996
No 18
>PF03649 UPF0014: Uncharacterised protein family (UPF0014); InterPro: IPR005226 This family has no known function. It includes potential membrane proteins.
Probab=30.34 E-value=44 Score=27.63 Aligned_cols=30 Identities=27% Similarity=0.457 Sum_probs=25.9
Q ss_pred ceEEeHHHHHHHHHCCCccCHHHHHHHHHc
Q 032887 51 RMGLNFDRVKYWLSVGAQPSDPVQRILFRA 80 (131)
Q Consensus 51 ~i~Ln~eRi~yWL~~GAqpT~tV~~LL~~~ 80 (131)
+++-+.+++.+||+.||-+.+.++.+++++
T Consensus 151 ~l~~~~~~ie~~LalGat~~eA~~~~~r~a 180 (250)
T PF03649_consen 151 ELRERRDEIEALLALGATPREAVRPFIRRA 180 (250)
T ss_pred HHHHhHHHHHHHHHCCCCHHHHHHHHHHHH
Confidence 456678899999999999999999888764
No 19
>KOG0135 consensus Pristanoyl-CoA/acyl-CoA oxidase [Lipid transport and metabolism; Secondary metabolites biosynthesis, transport and catabolism]
Probab=30.24 E-value=58 Score=30.93 Aligned_cols=80 Identities=18% Similarity=0.262 Sum_probs=45.2
Q ss_pred CCcceeeeeeecCCCCCCCCcceEE---eHHHHHHHHHCCCccCHHHHHHHHHcCCCCCCCccccccCCCC-CCCCC-CC
Q 032887 30 DGKHLEVLGYYNPLPGQDSGKRMGL---NFDRVKYWLSVGAQPSDPVQRILFRAGLLPPPPMVAMGRKGGP-RDTRP-VD 104 (131)
Q Consensus 30 dGk~IE~LG~YdP~~~~~~~k~i~L---n~eRi~yWL~~GAqpT~tV~~LL~~~g~l~~~p~~~~~~kg~~-~~~~~-~~ 104 (131)
+-+-|+..-+|||... ++.| |++.++||+++=|. +.|..-.+.+--+ + ++..|. .=..| -+
T Consensus 170 Nt~~I~TtatyDP~t~-----EfVinTP~~~A~K~WiGn~a~-~athavvfa~L~~-~-------g~n~G~H~FiiqIRd 235 (661)
T KOG0135|consen 170 NTKGIQTTATYDPTTE-----EFVINTPDFSAIKCWIGNAAK-HATHAVVFAQLHV-P-------GQNHGLHGFIIQIRD 235 (661)
T ss_pred cccceeeeeeecCCCC-----eeEecCCcHHHHHHHhccccc-cceEEEEEEEeee-c-------CccCceeeEEEEeec
Confidence 4578999999999864 4666 57999999998664 2232222221110 0 011111 00111 35
Q ss_pred CCCCccCCCCcccCCCCCC
Q 032887 105 PMTGRVLEKPTNAKQIKAD 123 (131)
Q Consensus 105 ~~~~~~~~~~~~~~~~~~~ 123 (131)
|-+...++|+.|.|--.-.
T Consensus 236 pkT~~t~PgV~igD~G~K~ 254 (661)
T KOG0135|consen 236 PKTLQTLPGVRIGDCGHKI 254 (661)
T ss_pred ccccCCCCCceeccccccc
Confidence 6667777888887754443
No 20
>KOG2618 consensus Uncharacterized conserved protein [Function unknown]
Probab=28.53 E-value=92 Score=27.64 Aligned_cols=35 Identities=23% Similarity=0.532 Sum_probs=27.9
Q ss_pred ccCCCCCCCeeEEEEeccCCCCCCcceeeeeeecCCCCCCCC
Q 032887 8 ARFGCKNKPFYRVMAADSRSPRDGKHLEVLGYYNPLPGQDSG 49 (131)
Q Consensus 8 ~R~G~K~rPfYrIVv~dsr~~RdGk~IE~LG~YdP~~~~~~~ 49 (131)
++.|.+++|+|--+ |||+.+=.-|.||=..+..|.
T Consensus 134 kt~gskkqpYfI~f-------~dgRlL~mAglfD~wE~egGD 168 (366)
T KOG2618|consen 134 KTVGSKKQPYFISF-------RDGRLLFMAGLFDYWEKEGGD 168 (366)
T ss_pred eeccccCCceEEEE-------ecCceeEeeeehheecccCCc
Confidence 56799999987555 999999999999987664333
No 21
>PF11875 DUF3395: Domain of unknown function (DUF3395); InterPro: IPR024586 Chaperone DnaJ was originally characterised from Escherichia coli as a 41 kDa heat shock protein. DnaJ has a modular structure consisting of a J-domain, a proximal G/F-domain, and a distal zinc finger domain, followed by less conserved C-terminal sequences. Since then, a large number of DnaJ-related proteins containing a J-domain have been characterised from a variety of different organisms. In the genome of Arabidopsis thaliana a total of 89 J-domain proteins have been identified []. This entry represents a C-terminal domain found in some eukaryotic DnaJ-like proteins, including member 11 from the subfamily C1 and protein DnaJ 13 from Arabidopsis. This domain is typically between 147 to 176 amino acids in length.
Probab=27.82 E-value=36 Score=26.02 Aligned_cols=12 Identities=33% Similarity=0.905 Sum_probs=9.4
Q ss_pred ceeeeeeecCCC
Q 032887 33 HLEVLGYYNPLP 44 (131)
Q Consensus 33 ~IE~LG~YdP~~ 44 (131)
.=..+|||||-+
T Consensus 108 Ks~L~GF~DP~p 119 (151)
T PF11875_consen 108 KSGLPGFYDPCP 119 (151)
T ss_pred hhhCCCCCCCcc
Confidence 334789999987
No 22
>PRK13149 H/ACA RNA-protein complex component Gar1; Reviewed
Probab=26.81 E-value=46 Score=22.52 Aligned_cols=27 Identities=22% Similarity=0.351 Sum_probs=23.3
Q ss_pred CCCCeeEEEEeccCCCCCCcceeeeee
Q 032887 13 KNKPFYRVMAADSRSPRDGKHLEVLGY 39 (131)
Q Consensus 13 K~rPfYrIVv~dsr~~RdGk~IE~LG~ 39 (131)
.+.|.+.-+|.+....+=|+..|.+|-
T Consensus 21 ~~~P~~n~~V~~~~~~~IGkV~dIfGP 47 (73)
T PRK13149 21 DKQPPIGSVVYDKKLKKIGKVVDVFGP 47 (73)
T ss_pred CCCCCCCCEeECCCCCEeEEEEEEECC
Confidence 567877888889888999999999994
No 23
>TIGR00245 conserved hypothetical protein TIGR00245.
Probab=25.93 E-value=59 Score=26.93 Aligned_cols=30 Identities=23% Similarity=0.395 Sum_probs=26.5
Q ss_pred ceEEeHHHHHHHHHCCCccCHHHHHHHHHc
Q 032887 51 RMGLNFDRVKYWLSVGAQPSDPVQRILFRA 80 (131)
Q Consensus 51 ~i~Ln~eRi~yWL~~GAqpT~tV~~LL~~~ 80 (131)
+++-+.+++.+||..||-|-+.++.+++++
T Consensus 145 ~l~~~~~~ie~~LaLGat~~~A~~~~~r~A 174 (248)
T TIGR00245 145 MVKSERDEIQGYLSLGATPKQAIAPFIRNA 174 (248)
T ss_pred HHHHhhHHHHHHHHCCCCHHHHHHHHHHHH
Confidence 466788999999999999999999999874
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=22.80 E-value=72 Score=20.60 Aligned_cols=32 Identities=22% Similarity=0.568 Sum_probs=22.9
Q ss_pred ceEEeHHHHH-HHHHCCCccCHHHHHHHHHcCC
Q 032887 51 RMGLNFDRVK-YWLSVGAQPSDPVQRILFRAGL 82 (131)
Q Consensus 51 ~i~Ln~eRi~-yWL~~GAqpT~tV~~LL~~~g~ 82 (131)
.+.+...-+. .|..+|.-|.+-+..|-...|+
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 4678888999 9999999999999998888775
No 25
>cd06392 PBP1_iGluR_delta_1 N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the delta1 receptor of an orphan glutamate receptor family. N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the delta1 receptor of an orphan glutamate receptor family. While this N-terminal domain belongs to the periplasmic-binding fold type I superfamily, the glutamate-binding domain of the iGluR is structurally homologous to the periplasmic-binding fold type II. The LIVBP-like domain of iGluRs is thought to play a role in the initial assembly of iGluR subunits, but it is not well understood how this domain is arranged and functions in intact iGluR. Although the delta receptors are a member of the ionotropic glutamate receptor family, they cannot be activated by AMPA, kainate, NMDA, glutamate, or any other ligands. Phylogenetic analysis shows that both GluRdelta1 and GluRalpha2 may be closer related to non-NMDA receptors. In contrast to GluRdelta2, GluRdel
Probab=22.80 E-value=1.2e+02 Score=26.34 Aligned_cols=40 Identities=10% Similarity=0.198 Sum_probs=28.4
Q ss_pred EEeeccCCCCCCCeeEEEEeccCCCCCCcceeeeeeecCCC
Q 032887 4 RIRLARFGCKNKPFYRVMAADSRSPRDGKHLEVLGYYNPLP 44 (131)
Q Consensus 4 kIRL~R~G~K~rPfYrIVv~dsr~~RdGk~IE~LG~YdP~~ 44 (131)
.|++--.|.+..+.|.|+=.... ---|+-+.+||||+|..
T Consensus 357 ~I~F~~~G~r~~~~ldIi~l~~~-~~~g~g~~~iG~W~~~~ 396 (400)
T cd06392 357 VMEFKEDGANPHVQFEILGTSYS-ETFGKDVRRLATWDSEK 396 (400)
T ss_pred ceeECCCCCCcCCceEEEecccc-ccCCCCceEeEEecCCC
Confidence 46777778778888888765511 13377789999999953
Done!