Query 030410
Match_columns 178
No_of_seqs 125 out of 1143
Neff 3.4
Searched_HMMs 46136
Date Fri Mar 29 13:18:50 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/030410.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/030410hhsearch_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 1.5E-44 3.2E-49 279.5 8.8 107 1-107 1-108 (112)
2 PRK14525 rpsP 30S ribosomal pr 100.0 2.5E-42 5.4E-47 258.0 10.6 84 1-87 1-84 (88)
3 PRK14521 rpsP 30S ribosomal pr 100.0 4E-41 8.8E-46 279.4 10.1 94 1-97 1-94 (186)
4 PRK14524 rpsP 30S ribosomal pr 100.0 4.9E-41 1.1E-45 253.4 8.8 86 2-90 1-86 (94)
5 TIGR00002 S16 ribosomal protei 100.0 1.2E-40 2.6E-45 243.7 9.9 78 3-83 1-78 (78)
6 CHL00005 rps16 ribosomal prote 100.0 1.1E-40 2.3E-45 246.3 9.2 79 2-85 1-79 (82)
7 PRK14522 rpsP 30S ribosomal pr 100.0 4.3E-40 9.3E-45 256.7 7.3 87 1-91 1-89 (116)
8 COG0228 RpsP Ribosomal protein 100.0 8.9E-40 1.9E-44 244.3 8.1 78 2-81 1-78 (87)
9 PRK14520 rpsP 30S ribosomal pr 100.0 1E-39 2.2E-44 264.8 9.2 82 1-85 1-82 (155)
10 PRK00040 rpsP 30S ribosomal pr 100.0 1.3E-39 2.9E-44 236.7 8.4 75 2-77 1-75 (75)
11 PRK14523 rpsP 30S ribosomal pr 100.0 4.6E-39 1E-43 256.7 9.2 93 2-95 1-93 (137)
12 PF00886 Ribosomal_S16: Riboso 100.0 2.5E-32 5.5E-37 191.5 5.2 62 9-70 1-62 (62)
13 TIGR02097 yccV hemimethylated 50.5 12 0.00027 28.8 2.1 14 13-26 46-59 (101)
14 PF03484 B5: tRNA synthetase B 47.6 30 0.00065 24.0 3.5 34 50-84 2-35 (70)
15 PRK14129 heat shock protein Hs 42.0 20 0.00043 28.4 2.0 14 13-26 47-60 (105)
16 PF08755 YccV-like: Hemimethyl 39.8 22 0.00049 26.6 2.0 23 13-43 46-68 (100)
17 smart00874 B5 tRNA synthetase 31.4 92 0.002 21.0 3.8 33 50-83 2-34 (71)
18 COG3323 Uncharacterized protei 28.9 26 0.00057 27.8 0.8 22 138-159 35-56 (109)
19 PF03649 UPF0014: Uncharacteri 27.0 54 0.0012 28.6 2.5 35 51-85 151-188 (250)
20 KOG0135 Pristanoyl-CoA/acyl-Co 26.9 70 0.0015 32.1 3.5 93 30-140 170-267 (661)
21 TIGR00245 conserved hypothetic 23.8 66 0.0014 28.1 2.5 36 50-85 144-182 (248)
22 PF11875 DUF3395: Domain of un 20.5 63 0.0014 26.1 1.6 13 32-44 107-119 (151)
23 KOG2618 Uncharacterized conser 20.0 1.6E+02 0.0035 27.7 4.2 35 8-49 134-168 (366)
No 1
>KOG3419 consensus Mitochondrial/chloroplast ribosomal protein S16 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.5e-44 Score=279.49 Aligned_cols=107 Identities=61% Similarity=1.021 Sum_probs=101.3
Q ss_pred CceEEeeccCCCCCCCeeEEEEeecCCCCCCcceeeeeeecCCCCCCCCceEEEeHHHHHHHHHCCCccCHHHHHHHHHc
Q 030410 1 MVVRIRLARFGCKNKPFYRVMAADSRSPRDGKHLEVLGYYNPLPGQDSGKRMGLNFDRVKYWLSVGAQPSDPVQRILFRA 80 (178)
Q Consensus 1 M~VkIRLaR~G~KkrPfYRIVVaDsRspRDGK~IE~LG~YdPl~~~~~~K~i~Ln~eRIkyWL~~GAQPTdtV~~LL~ka 80 (178)
|+|+|||+|+||||||||||||+|+|++||||+||+||+|||+++.++++.+.||+|||+|||++|||||+||.+||+++
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 88999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCCCCccccccCCCCCCC-CCCCCCC
Q 030410 81 GLLPPPPMVAMGRKGGPRDT-RPVDPMT 107 (178)
Q Consensus 81 Gllp~~p~~~~~~kg~~~~~-~p~~~~~ 107 (178)
|++|.+|+..+.++.+.+.. ++++|.+
T Consensus 81 Gl~p~~p~~~~~a~~~rr~~a~~~~~~~ 108 (112)
T KOG3419|consen 81 GLFPIHPMTFMNAKRNRRLTAEQVLPVE 108 (112)
T ss_pred CCCCCchhhhhccccchhhhhhhccchh
Confidence 99999999999999988776 4455544
No 2
>PRK14525 rpsP 30S ribosomal protein S16; Provisional
Probab=100.00 E-value=2.5e-42 Score=257.96 Aligned_cols=84 Identities=45% Similarity=0.779 Sum_probs=79.6
Q ss_pred CceEEeeccCCCCCCCeeEEEEeecCCCCCCcceeeeeeecCCCCCCCCceEEEeHHHHHHHHHCCCccCHHHHHHHHHc
Q 030410 1 MVVRIRLARFGCKNKPFYRVMAADSRSPRDGKHLEVLGYYNPLPGQDSGKRMGLNFDRVKYWLSVGAQPSDPVQRILFRA 80 (178)
Q Consensus 1 M~VkIRLaR~G~KkrPfYRIVVaDsRspRDGK~IE~LG~YdPl~~~~~~K~i~Ln~eRIkyWL~~GAQPTdtV~~LL~ka 80 (178)
|+|+|||+|+|+||+|||||||+|+|++|||+|||+||+|||+.++ +.+.||+|||+|||++|||||+||++||+++
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 9999999999999999999999999999999999999999999753 5899999999999999999999999999999
Q ss_pred CCCCCCC
Q 030410 81 GLLPPPP 87 (178)
Q Consensus 81 Gllp~~p 87 (178)
|+.+++|
T Consensus 78 g~~~~~~ 84 (88)
T PRK14525 78 AKAAAPA 84 (88)
T ss_pred CccCCCC
Confidence 9986543
No 3
>PRK14521 rpsP 30S ribosomal protein S16; Provisional
Probab=100.00 E-value=4e-41 Score=279.41 Aligned_cols=94 Identities=48% Similarity=0.776 Sum_probs=87.9
Q ss_pred CceEEeeccCCCCCCCeeEEEEeecCCCCCCcceeeeeeecCCCCCCCCceEEEeHHHHHHHHHCCCccCHHHHHHHHHc
Q 030410 1 MVVRIRLARFGCKNKPFYRVMAADSRSPRDGKHLEVLGYYNPLPGQDSGKRMGLNFDRVKYWLSVGAQPSDPVQRILFRA 80 (178)
Q Consensus 1 M~VkIRLaR~G~KkrPfYRIVVaDsRspRDGK~IE~LG~YdPl~~~~~~K~i~Ln~eRIkyWL~~GAQPTdtV~~LL~ka 80 (178)
|+|||||+|+|+|++|||||||+|+|++|||||||+||||||+.++ ..|.||+|||+|||++|||||+||++||+++
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 030410 81 GLLPPPPMVAMGRKGGP 97 (178)
Q Consensus 81 Gllp~~p~~~~~~kg~~ 97 (178)
|+|++++...+.+||..
T Consensus 78 g~~~k~~~~~~~~kg~~ 94 (186)
T PRK14521 78 GVLLKKHLLGGVAKGAF 94 (186)
T ss_pred ccchhhhhhcccCCCcc
Confidence 99998887776666644
No 4
>PRK14524 rpsP 30S ribosomal protein S16; Provisional
Probab=100.00 E-value=4.9e-41 Score=253.43 Aligned_cols=86 Identities=43% Similarity=0.789 Sum_probs=80.0
Q ss_pred ceEEeeccCCCCCCCeeEEEEeecCCCCCCcceeeeeeecCCCCCCCCceEEEeHHHHHHHHHCCCccCHHHHHHHHHcC
Q 030410 2 VVRIRLARFGCKNKPFYRVMAADSRSPRDGKHLEVLGYYNPLPGQDSGKRMGLNFDRVKYWLSVGAQPSDPVQRILFRAG 81 (178)
Q Consensus 2 ~VkIRLaR~G~KkrPfYRIVVaDsRspRDGK~IE~LG~YdPl~~~~~~K~i~Ln~eRIkyWL~~GAQPTdtV~~LL~kaG 81 (178)
||+|||+|+|+|++|||||||+|+|++|||+|||+||+|||+.++ ..+.||+||++|||++|||||+||.+||+++|
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 030410 82 LLPPPPMVA 90 (178)
Q Consensus 82 llp~~p~~~ 90 (178)
++++....+
T Consensus 78 ~~~~~~~~~ 86 (94)
T PRK14524 78 VMKKVHEIK 86 (94)
T ss_pred chhhhHHhh
Confidence 987655443
No 5
>TIGR00002 S16 ribosomal protein S16. This model describes ribosomal S16 of bacteria and organelles.
Probab=100.00 E-value=1.2e-40 Score=243.69 Aligned_cols=78 Identities=56% Similarity=1.025 Sum_probs=75.1
Q ss_pred eEEeeccCCCCCCCeeEEEEeecCCCCCCcceeeeeeecCCCCCCCCceEEEeHHHHHHHHHCCCccCHHHHHHHHHcCC
Q 030410 3 VRIRLARFGCKNKPFYRVMAADSRSPRDGKHLEVLGYYNPLPGQDSGKRMGLNFDRVKYWLSVGAQPSDPVQRILFRAGL 82 (178)
Q Consensus 3 VkIRLaR~G~KkrPfYRIVVaDsRspRDGK~IE~LG~YdPl~~~~~~K~i~Ln~eRIkyWL~~GAQPTdtV~~LL~kaGl 82 (178)
|+|||+|+|+||+|||||||+|+|++|||||||+||+|||++++ +.+.||+||++|||++|||||+||++||+++|+
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 79999999999999999999999999999999999999999864 689999999999999999999999999999997
Q ss_pred C
Q 030410 83 L 83 (178)
Q Consensus 83 l 83 (178)
+
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=1.1e-40 Score=246.34 Aligned_cols=79 Identities=39% Similarity=0.731 Sum_probs=75.3
Q ss_pred ceEEeeccCCCCCCCeeEEEEeecCCCCCCcceeeeeeecCCCCCCCCceEEEeHHHHHHHHHCCCccCHHHHHHHHHcC
Q 030410 2 VVRIRLARFGCKNKPFYRVMAADSRSPRDGKHLEVLGYYNPLPGQDSGKRMGLNFDRVKYWLSVGAQPSDPVQRILFRAG 81 (178)
Q Consensus 2 ~VkIRLaR~G~KkrPfYRIVVaDsRspRDGK~IE~LG~YdPl~~~~~~K~i~Ln~eRIkyWL~~GAQPTdtV~~LL~kaG 81 (178)
||+|||+|+|+|++|||||||+|+|++|||+|||+||+|||+.+ .+.||+||++|||++|||||+||++||+++|
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 58999999999999999999999999999999999999999864 5799999999999999999999999999999
Q ss_pred CCCC
Q 030410 82 LLPP 85 (178)
Q Consensus 82 llp~ 85 (178)
++++
T Consensus 76 ~~~~ 79 (82)
T CHL00005 76 VFKE 79 (82)
T ss_pred chhh
Confidence 8765
No 7
>PRK14522 rpsP 30S ribosomal protein S16; Provisional
Probab=100.00 E-value=4.3e-40 Score=256.69 Aligned_cols=87 Identities=33% Similarity=0.641 Sum_probs=82.0
Q ss_pred CceEEeeccCCCCCCCeeEEEEeecCCCCCCcceeeeeeecCCCCCCCCceEEEeHHHHHHHHHCCCccCHHHHHHHHH-
Q 030410 1 MVVRIRLARFGCKNKPFYRVMAADSRSPRDGKHLEVLGYYNPLPGQDSGKRMGLNFDRVKYWLSVGAQPSDPVQRILFR- 79 (178)
Q Consensus 1 M~VkIRLaR~G~KkrPfYRIVVaDsRspRDGK~IE~LG~YdPl~~~~~~K~i~Ln~eRIkyWL~~GAQPTdtV~~LL~k- 79 (178)
|+|+|||+|+|+||+|||||||+|+|++|||+|||+||||||+.+ +.+.||+|||+|||++|||||+||.+||++
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 999999999999999999999999999999999999999999875 379999999999999999999999999999
Q ss_pred -cCCCCCCCcccc
Q 030410 80 -AGLLPPPPMVAM 91 (178)
Q Consensus 80 -aGllp~~p~~~~ 91 (178)
+|++++....+-
T Consensus 77 ~~Gi~~~~~~~k~ 89 (116)
T PRK14522 77 APGVYSELMAKKV 89 (116)
T ss_pred hcccchhHHHHHH
Confidence 699998776553
No 8
>COG0228 RpsP Ribosomal protein S16 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=8.9e-40 Score=244.33 Aligned_cols=78 Identities=59% Similarity=1.017 Sum_probs=74.4
Q ss_pred ceEEeeccCCCCCCCeeEEEEeecCCCCCCcceeeeeeecCCCCCCCCceEEEeHHHHHHHHHCCCccCHHHHHHHHHcC
Q 030410 2 VVRIRLARFGCKNKPFYRVMAADSRSPRDGKHLEVLGYYNPLPGQDSGKRMGLNFDRVKYWLSVGAQPSDPVQRILFRAG 81 (178)
Q Consensus 2 ~VkIRLaR~G~KkrPfYRIVVaDsRspRDGK~IE~LG~YdPl~~~~~~K~i~Ln~eRIkyWL~~GAQPTdtV~~LL~kaG 81 (178)
||||||+|+|+|++|||||||+|||+||||+|||.||+|||+. +.+..+.||.||+.|||++||||||||++||+++|
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 33468999999999999999999999999999998
No 9
>PRK14520 rpsP 30S ribosomal protein S16; Provisional
Probab=100.00 E-value=1e-39 Score=264.78 Aligned_cols=82 Identities=41% Similarity=0.764 Sum_probs=78.5
Q ss_pred CceEEeeccCCCCCCCeeEEEEeecCCCCCCcceeeeeeecCCCCCCCCceEEEeHHHHHHHHHCCCccCHHHHHHHHHc
Q 030410 1 MVVRIRLARFGCKNKPFYRVMAADSRSPRDGKHLEVLGYYNPLPGQDSGKRMGLNFDRVKYWLSVGAQPSDPVQRILFRA 80 (178)
Q Consensus 1 M~VkIRLaR~G~KkrPfYRIVVaDsRspRDGK~IE~LG~YdPl~~~~~~K~i~Ln~eRIkyWL~~GAQPTdtV~~LL~ka 80 (178)
|+|||||+|+|+|++|||||||+|+|++|||+|||+||+|||+.++ ..|.||++|++|||++|||||+||.+||+++
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 030410 81 GLLPP 85 (178)
Q Consensus 81 Gllp~ 85 (178)
|++.+
T Consensus 78 g~~~~ 82 (155)
T PRK14520 78 GDWQK 82 (155)
T ss_pred chhhh
Confidence 98754
No 10
>PRK00040 rpsP 30S ribosomal protein S16; Reviewed
Probab=100.00 E-value=1.3e-39 Score=236.71 Aligned_cols=75 Identities=55% Similarity=1.025 Sum_probs=71.1
Q ss_pred ceEEeeccCCCCCCCeeEEEEeecCCCCCCcceeeeeeecCCCCCCCCceEEEeHHHHHHHHHCCCccCHHHHHHH
Q 030410 2 VVRIRLARFGCKNKPFYRVMAADSRSPRDGKHLEVLGYYNPLPGQDSGKRMGLNFDRVKYWLSVGAQPSDPVQRIL 77 (178)
Q Consensus 2 ~VkIRLaR~G~KkrPfYRIVVaDsRspRDGK~IE~LG~YdPl~~~~~~K~i~Ln~eRIkyWL~~GAQPTdtV~~LL 77 (178)
||+|||+|+|+||+|||||||+|+|++|||||||+||+|||++++ +++.+.||+|||+|||++|||||+||++||
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 347999999999999999999999999986
No 11
>PRK14523 rpsP 30S ribosomal protein S16; Provisional
Probab=100.00 E-value=4.6e-39 Score=256.69 Aligned_cols=93 Identities=41% Similarity=0.697 Sum_probs=83.4
Q ss_pred ceEEeeccCCCCCCCeeEEEEeecCCCCCCcceeeeeeecCCCCCCCCceEEEeHHHHHHHHHCCCccCHHHHHHHHHcC
Q 030410 2 VVRIRLARFGCKNKPFYRVMAADSRSPRDGKHLEVLGYYNPLPGQDSGKRMGLNFDRVKYWLSVGAQPSDPVQRILFRAG 81 (178)
Q Consensus 2 ~VkIRLaR~G~KkrPfYRIVVaDsRspRDGK~IE~LG~YdPl~~~~~~K~i~Ln~eRIkyWL~~GAQPTdtV~~LL~kaG 81 (178)
||+|||+|+|+||+|||||||+|+|++|||+|||+||||||+.++. ++.|.||++||+|||++|||||+||.+||+++|
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 5899999999999999999999999999999999999999998653 358999999999999999999999999999999
Q ss_pred CCCCCCccccccCC
Q 030410 82 LLPPPPMVAMGRKG 95 (178)
Q Consensus 82 llp~~p~~~~~~kg 95 (178)
+++......+.++|
T Consensus 80 ~~~~~~~~~g~~~~ 93 (137)
T PRK14523 80 KSPEEAQKGGMRKG 93 (137)
T ss_pred cchHHHHhcccccC
Confidence 88876654433443
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=99.97 E-value=2.5e-32 Score=191.45 Aligned_cols=62 Identities=61% Similarity=1.217 Sum_probs=59.8
Q ss_pred cCCCCCCCeeEEEEeecCCCCCCcceeeeeeecCCCCCCCCceEEEeHHHHHHHHHCCCccC
Q 030410 9 RFGCKNKPFYRVMAADSRSPRDGKHLEVLGYYNPLPGQDSGKRMGLNFDRVKYWLSVGAQPS 70 (178)
Q Consensus 9 R~G~KkrPfYRIVVaDsRspRDGK~IE~LG~YdPl~~~~~~K~i~Ln~eRIkyWL~~GAQPT 70 (178)
|+|+|++|||||||+|+|++|||++||+||+|||++++.+++.+.||+|||+|||++|||||
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 78999999999999999999999999999999999987667899999999999999999998
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=50.48 E-value=12 Score=28.79 Aligned_cols=14 Identities=43% Similarity=1.037 Sum_probs=12.2
Q ss_pred CCCCeeEEEEeecC
Q 030410 13 KNKPFYRVMAADSR 26 (178)
Q Consensus 13 KkrPfYRIVVaDsR 26 (178)
|++|||+++|-|..
T Consensus 46 ~~qPfYhvLv~~~~ 59 (101)
T TIGR02097 46 RDQPFYHVLAEDDE 59 (101)
T ss_pred cCCCceEEEEeCCC
Confidence 89999999988854
No 14
>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=47.59 E-value=30 Score=23.99 Aligned_cols=34 Identities=24% Similarity=0.470 Sum_probs=26.6
Q ss_pred ceEEEeHHHHHHHHHCCCccCHHHHHHHHHcCCCC
Q 030410 50 KRMGLNFDRVKYWLSVGAQPSDPVQRILFRAGLLP 84 (178)
Q Consensus 50 K~i~Ln~eRIkyWL~~GAQPTdtV~~LL~kaGllp 84 (178)
+.+.++.+++...|+. .-..+.+.++|++.|+--
T Consensus 2 ~~i~~~~~~i~~~lG~-~i~~~~i~~~L~~lg~~~ 35 (70)
T PF03484_consen 2 KKITLSLDKINKLLGI-DISPEEIIKILKRLGFKV 35 (70)
T ss_dssp EEEEEEHHHHHHHHTS----HHHHHHHHHHTT-EE
T ss_pred eEEEecHHHHHHHhCC-CCCHHHHHHHHHHCCCEE
Confidence 5799999999999997 556688999999998643
No 15
>PRK14129 heat shock protein HspQ; Provisional
Probab=41.99 E-value=20 Score=28.37 Aligned_cols=14 Identities=29% Similarity=0.733 Sum_probs=11.9
Q ss_pred CCCCeeEEEEeecC
Q 030410 13 KNKPFYRVMAADSR 26 (178)
Q Consensus 13 KkrPfYRIVVaDsR 26 (178)
|.+|||+++|-|..
T Consensus 47 kdqPwYHvl~en~~ 60 (105)
T PRK14129 47 RAAPWYHVVMEDDD 60 (105)
T ss_pred cCCCceEEEEEcCC
Confidence 79999999996654
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=39.75 E-value=22 Score=26.57 Aligned_cols=23 Identities=35% Similarity=0.641 Sum_probs=11.7
Q ss_pred CCCCeeEEEEeecCCCCCCcceeeeeeecCC
Q 030410 13 KNKPFYRVMAADSRSPRDGKHLEVLGYYNPL 43 (178)
Q Consensus 13 KkrPfYRIVVaDsRspRDGK~IE~LG~YdPl 43 (178)
+++|||+|.|-+..+ +.+ +|-|-
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 333 77763
No 17
>smart00874 B5 tRNA synthetase B5 domain. This domain is found in phenylalanine-tRNA synthetase beta subunits.
Probab=31.40 E-value=92 Score=20.95 Aligned_cols=33 Identities=21% Similarity=0.419 Sum_probs=27.1
Q ss_pred ceEEEeHHHHHHHHHCCCccCHHHHHHHHHcCCC
Q 030410 50 KRMGLNFDRVKYWLSVGAQPSDPVQRILFRAGLL 83 (178)
Q Consensus 50 K~i~Ln~eRIkyWL~~GAQPTdtV~~LL~kaGll 83 (178)
+.+.++.+++...|+.- -..+.+.++|.+.|+-
T Consensus 2 ~~i~~~~~~i~~llG~~-i~~~ei~~~L~~lg~~ 34 (71)
T smart00874 2 RTITLRRERINRLLGLD-LSAEEIEEILKRLGFE 34 (71)
T ss_pred cEEEecHHHHHHHHCCC-CCHHHHHHHHHHCCCe
Confidence 36899999999999873 3456799999999963
No 18
>COG3323 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=28.89 E-value=26 Score=27.81 Aligned_cols=22 Identities=41% Similarity=0.535 Sum_probs=20.2
Q ss_pred eeecccccceeeccccccCCCe
Q 030410 138 FMHCTSSSILKLQHMPVQGSNE 159 (178)
Q Consensus 138 ~~~~~~~~~~~~~~~~~~~~~~ 159 (178)
+-||+.++.-.=|-.|++|+|-
T Consensus 35 Y~~C~~~~~g~G~frP~egAnP 56 (109)
T COG3323 35 YDHCTFSSEGTGQFRPLEGANP 56 (109)
T ss_pred cceEEEEeeeeEEEeecCCCCC
Confidence 5699999999999999999984
No 19
>PF03649 UPF0014: Uncharacterised protein family (UPF0014); InterPro: IPR005226 This family has no known function. It includes potential membrane proteins.
Probab=26.99 E-value=54 Score=28.64 Aligned_cols=35 Identities=29% Similarity=0.534 Sum_probs=28.3
Q ss_pred eEEEeHHHHHHHHHCCCccCHHHHHHHHHc---CCCCC
Q 030410 51 RMGLNFDRVKYWLSVGAQPSDPVQRILFRA---GLLPP 85 (178)
Q Consensus 51 ~i~Ln~eRIkyWL~~GAQPTdtV~~LL~ka---Gllp~ 85 (178)
+++-+.+++.+||+.||.|.+.++.+++++ +++|.
T Consensus 151 ~l~~~~~~ie~~LalGat~~eA~~~~~r~ai~~al~P~ 188 (250)
T PF03649_consen 151 ELRERRDEIEALLALGATPREAVRPFIRRAIRAALIPT 188 (250)
T ss_pred HHHHhHHHHHHHHHCCCCHHHHHHHHHHHHHHHHhHhH
Confidence 455678899999999999999999888875 44443
No 20
>KOG0135 consensus Pristanoyl-CoA/acyl-CoA oxidase [Lipid transport and metabolism; Secondary metabolites biosynthesis, transport and catabolism]
Probab=26.90 E-value=70 Score=32.13 Aligned_cols=93 Identities=19% Similarity=0.340 Sum_probs=56.2
Q ss_pred CCcceeeeeeecCCCCCCCCceEEE---eHHHHHHHHHCCCccCHHHHHHHHHcCCCCCCCccccccCCCC-CCCCC-CC
Q 030410 30 DGKHLEVLGYYNPLPGQDSGKRMGL---NFDRVKYWLSVGAQPSDPVQRILFRAGLLPPPPMVAMGRKGGP-RDTRP-VD 104 (178)
Q Consensus 30 DGK~IE~LG~YdPl~~~~~~K~i~L---n~eRIkyWL~~GAQPTdtV~~LL~kaGllp~~p~~~~~~kg~~-~~~~p-~~ 104 (178)
+-+-||..-+|||... ++.| |++.+|||++.=|.- .|.+-.+.+-- +| +...|. .=..| -|
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-----EFVINTPDFSAIKCWIGNAAKH-ATHAVVFAQLH-VP-------GQNHGLHGFIIQIRD 235 (661)
T ss_pred cccceeeeeeecCCCC-----eeEecCCcHHHHHHHhcccccc-ceEEEEEEEee-ec-------CccCceeeEEEEeec
Confidence 4578999999999874 4555 579999999976642 22221111110 01 111111 11112 57
Q ss_pred CCCCcccCCCcccCCCCCcccccccCCcceeeeeee
Q 030410 105 PMTGRVLEKPTNAKQIKADDICSHMNGLDLAFVFMH 140 (178)
Q Consensus 105 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 140 (178)
|.+.+.++++.+.|-- +-|+ .||+|=.|+..+
T Consensus 236 pkT~~t~PgV~igD~G---~K~G-lnGVDNG~l~F~ 267 (661)
T KOG0135|consen 236 PKTLQTLPGVRIGDCG---HKIG-LNGVDNGFLWFD 267 (661)
T ss_pred ccccCCCCCceecccc---cccc-cccccCceEEEe
Confidence 8888888998887532 2344 799998887765
No 21
>TIGR00245 conserved hypothetical protein TIGR00245.
Probab=23.82 E-value=66 Score=28.10 Aligned_cols=36 Identities=25% Similarity=0.468 Sum_probs=29.8
Q ss_pred ceEEEeHHHHHHHHHCCCccCHHHHHHHHHc---CCCCC
Q 030410 50 KRMGLNFDRVKYWLSVGAQPSDPVQRILFRA---GLLPP 85 (178)
Q Consensus 50 K~i~Ln~eRIkyWL~~GAQPTdtV~~LL~ka---Gllp~ 85 (178)
++++-+.+++.+||+.||.|-+.++.+++++ +++|.
T Consensus 144 ~~l~~~~~~ie~~LaLGat~~~A~~~~~r~Ai~aaliP~ 182 (248)
T TIGR00245 144 SMVKSERDEIQGYLSLGATPKQAIAPFIRNAIKASLIPT 182 (248)
T ss_pred HHHHHhhHHHHHHHHCCCCHHHHHHHHHHHHHHHHhhch
Confidence 3466678999999999999999999999874 66654
No 22
>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=20.50 E-value=63 Score=26.05 Aligned_cols=13 Identities=31% Similarity=0.838 Sum_probs=10.0
Q ss_pred cceeeeeeecCCC
Q 030410 32 KHLEVLGYYNPLP 44 (178)
Q Consensus 32 K~IE~LG~YdPl~ 44 (178)
..=..+|||||-+
T Consensus 107 sKs~L~GF~DP~p 119 (151)
T PF11875_consen 107 SKSGLPGFYDPCP 119 (151)
T ss_pred chhhCCCCCCCcc
Confidence 3445789999987
No 23
>KOG2618 consensus Uncharacterized conserved protein [Function unknown]
Probab=20.04 E-value=1.6e+02 Score=27.73 Aligned_cols=35 Identities=23% Similarity=0.532 Sum_probs=28.0
Q ss_pred ccCCCCCCCeeEEEEeecCCCCCCcceeeeeeecCCCCCCCC
Q 030410 8 ARFGCKNKPFYRVMAADSRSPRDGKHLEVLGYYNPLPGQDSG 49 (178)
Q Consensus 8 aR~G~KkrPfYRIVVaDsRspRDGK~IE~LG~YdPl~~~~~~ 49 (178)
++.|.+++|+|--+ ||||.+=.-|.||=-.+..|+
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 56799999987554 999999999999987764443
Done!