Query 032855
Match_columns 132
No_of_seqs 120 out of 1079
Neff 4.5
Searched_HMMs 46136
Date Fri Mar 29 06:45:54 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/032855.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/032855hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PTZ00241 40S ribosomal protein 100.0 8.6E-50 1.9E-54 308.2 13.7 115 18-132 44-158 (158)
2 PRK08572 rps17p 30S ribosomal 100.0 3.4E-46 7.4E-51 273.4 13.7 105 16-120 3-107 (108)
3 TIGR03630 arch_S17P archaeal r 100.0 4.1E-46 8.8E-51 270.7 13.1 101 17-117 2-102 (102)
4 KOG1728 40S ribosomal protein 100.0 2.5E-42 5.3E-47 263.3 5.2 111 19-132 45-156 (156)
5 COG0186 RpsQ Ribosomal protein 100.0 2.1E-38 4.4E-43 224.7 11.5 86 35-121 1-86 (87)
6 CHL00142 rps17 ribosomal prote 100.0 4.2E-35 9.2E-40 206.5 11.9 79 42-121 3-81 (84)
7 PRK05610 rpsQ 30S ribosomal pr 100.0 7.6E-35 1.6E-39 204.9 11.7 79 41-120 5-83 (84)
8 TIGR03635 S17_bact 30S ribosom 100.0 1.7E-33 3.6E-38 192.7 10.0 71 42-113 1-71 (71)
9 PF00366 Ribosomal_S17: Riboso 100.0 6.6E-32 1.4E-36 183.5 9.5 69 47-116 1-69 (69)
10 KOG1740 Predicted mitochondria 100.0 7.5E-30 1.6E-34 185.5 -0.3 78 42-120 2-79 (107)
11 KOG3447 Mitochondrial/chloropl 99.4 6.6E-14 1.4E-18 106.9 0.8 81 38-119 6-87 (150)
12 KOG3416 Predicted nucleic acid 65.7 27 0.00059 26.9 6.1 60 33-101 12-72 (134)
13 PF10844 DUF2577: Protein of u 63.0 51 0.0011 23.3 7.2 23 90-115 76-98 (100)
14 PF10650 zf-C3H1: Putative zin 56.9 5.5 0.00012 22.0 0.8 14 21-34 6-19 (23)
15 cd03695 CysN_NodQ_II CysN_NodQ 50.6 59 0.0013 21.7 5.3 26 75-100 41-66 (81)
16 cd03698 eRF3_II_like eRF3_II_l 47.2 63 0.0014 21.4 4.9 25 76-100 42-66 (83)
17 cd03693 EF1_alpha_II EF1_alpha 42.4 76 0.0016 21.5 4.9 26 75-100 45-70 (91)
18 PF13550 Phage-tail_3: Putativ 39.7 80 0.0017 22.6 4.9 38 76-117 126-163 (164)
19 cd03697 EFTU_II EFTU_II: Elong 38.6 1E+02 0.0022 20.7 5.0 52 42-100 15-68 (87)
20 PRK00276 infA translation init 36.8 1.3E+02 0.0027 20.0 8.1 59 43-110 7-65 (72)
21 cd03696 selB_II selB_II: this 35.5 1.3E+02 0.0028 19.8 5.5 26 75-100 41-66 (83)
22 PF09740 DUF2043: Uncharacteri 34.3 17 0.00038 27.0 0.6 10 28-37 86-95 (110)
23 TIGR00008 infA translation ini 32.8 1.6E+02 0.0035 20.0 5.5 53 43-109 5-62 (68)
24 cd03694 GTPBP_II Domain II of 31.7 94 0.002 20.9 3.9 26 75-100 45-70 (87)
25 PF04246 RseC_MucC: Positive r 31.4 56 0.0012 23.8 2.9 21 79-101 42-62 (135)
26 PF06107 DUF951: Bacterial pro 31.3 75 0.0016 21.1 3.2 25 91-116 2-26 (57)
27 PRK10413 hydrogenase 2 accesso 30.0 1.9E+02 0.0042 20.1 6.0 19 89-107 41-59 (82)
28 KOG1698 Mitochondrial/chloropl 29.9 98 0.0021 25.4 4.3 30 90-119 96-125 (201)
29 COG0361 InfA Translation initi 29.5 2E+02 0.0043 20.0 5.6 51 43-108 7-63 (75)
30 TIGR03595 Obg_CgtA_exten Obg f 29.4 37 0.00081 22.6 1.6 12 90-101 53-64 (69)
31 KOG1730 Thioredoxin-like prote 28.4 41 0.00089 27.5 1.9 39 9-48 50-91 (206)
32 cd04466 S1_YloQ_GTPase S1_YloQ 27.9 95 0.0021 19.3 3.2 28 89-120 36-63 (68)
33 CHL00010 infA translation init 26.6 2.1E+02 0.0045 19.4 8.4 62 45-115 9-70 (78)
34 cd04456 S1_IF1A_like S1_IF1A_l 26.5 2.2E+02 0.0047 19.5 5.5 52 45-110 2-58 (78)
35 cd00174 SH3 Src homology 3 dom 25.1 1E+02 0.0022 17.3 2.8 22 81-102 8-29 (54)
36 PF09269 DUF1967: Domain of un 24.6 37 0.00079 22.6 0.8 12 90-101 53-64 (69)
37 smart00652 eIF1a eukaryotic tr 24.5 2.4E+02 0.0053 19.4 5.9 55 43-111 5-63 (83)
38 PF07653 SH3_2: Variant SH3 do 24.2 47 0.001 20.3 1.2 24 77-100 4-27 (55)
39 PF11347 DUF3148: Protein of u 23.8 59 0.0013 22.1 1.7 17 92-108 1-17 (63)
40 PRK05338 rplS 50S ribosomal pr 23.7 1.6E+02 0.0034 22.0 4.1 20 42-61 39-61 (116)
41 COG0227 RpmB Ribosomal protein 23.6 74 0.0016 22.2 2.2 50 30-84 3-52 (77)
42 smart00326 SH3 Src homology 3 23.6 1.4E+02 0.003 16.9 3.2 17 87-103 17-33 (58)
43 PRK05753 nucleoside diphosphat 23.5 2.1E+02 0.0046 21.3 4.9 30 90-121 101-130 (137)
44 cd04451 S1_IF1 S1_IF1: Transla 23.5 2E+02 0.0044 18.2 6.5 48 45-100 3-50 (64)
45 cd04089 eRF3_II eRF3_II: domai 23.4 2.3E+02 0.0049 18.7 5.2 25 76-100 41-65 (82)
46 cd05793 S1_IF1A S1_IF1A: Trans 22.7 2.6E+02 0.0056 19.0 5.4 53 45-111 2-58 (77)
47 cd04460 S1_RpoE S1_RpoE: RpoE, 22.4 2.6E+02 0.0056 19.0 5.0 13 88-100 51-63 (99)
48 smart00357 CSP Cold shock prot 21.3 1.7E+02 0.0037 17.3 3.4 26 79-104 21-50 (64)
49 PF02887 PK_C: Pyruvate kinase 20.9 1.6E+02 0.0034 20.7 3.6 29 89-117 88-116 (117)
50 cd05698 S1_Rrp5_repeat_hs6_sc5 20.8 89 0.0019 19.5 2.1 58 42-107 1-63 (70)
51 PF09926 DUF2158: Uncharacteri 20.6 71 0.0015 20.6 1.5 13 92-104 2-14 (53)
52 PF08980 DUF1883: Domain of un 20.5 38 0.00081 24.5 0.3 19 80-100 2-20 (94)
53 COG0853 PanD Aspartate 1-decar 20.3 85 0.0018 24.0 2.1 17 90-106 77-93 (126)
54 PRK10862 SoxR reducing system 20.2 1.2E+02 0.0025 23.2 2.9 52 46-100 5-68 (154)
No 1
>PTZ00241 40S ribosomal protein S11; Provisional
Probab=100.00 E-value=8.6e-50 Score=308.24 Aligned_cols=115 Identities=66% Similarity=1.094 Sum_probs=109.9
Q ss_pred chhhhcccccccCCCCCcceeeeecEEEEEEEEecCCCCeEEEEEeEEEeeeeeeeEEeeeeeEEEEcCCCCCCCCCCEE
Q 032855 18 LMSLCFSGTYIDKKCPFTGTVSIRGRILAGTCHSAKMNRTIIVRRNYLHFVKKYQRYEKRHSNIPAHISPCFRVKEGDHV 97 (132)
Q Consensus 18 ~~~~~~~~~~~d~~cp~~g~~~vr~k~l~G~VVS~Km~KTivV~v~~~~~hpkY~K~ikr~kky~vHD~e~n~~kvGD~V 97 (132)
.|.+|++|+|+|++||||||++|||++|+|+|+|+||+|||+|+++++++||+|+|+++++++|+|||||||+|++||+|
T Consensus 44 ~P~~~~~~~yiD~kCPf~G~~~iRgril~G~VvS~KM~KTIVV~ve~~~~h~kY~K~~kr~kk~~aHd~~~~~~kvGD~V 123 (158)
T PTZ00241 44 TPKEAIEGKYIDKKCPFTGNVSIRGRILRGVVISTKMKRTIIIRRDYLHYVKKYNRYEKRHKNIPVHCSPCFDVKEGDIV 123 (158)
T ss_pred CChhhhcccccCCCCCccceeeEcceEEEEEEEEccCCccEEEEEEEEEecCccceEEEeeecEEEeCCccCCCCCCCEE
Confidence 47899999999999999999999999999999999999999999999999999999999999999999889999999999
Q ss_pred EEeecccCCCeeeEEEEEeeecCCCCCcccccccC
Q 032855 98 IIGQCRPLSKTVRFNVLKVIPAGSSGGAKKAFTAM 132 (132)
Q Consensus 98 ~I~ecRPiSKtK~~~V~~Ii~k~~~~~~~~~f~~~ 132 (132)
+|+|||||||+|+|+|++|++++.+++.++||++|
T Consensus 124 ~I~EcRPLSKTKrf~Vv~V~~~~~~~~~~k~f~~f 158 (158)
T PTZ00241 124 VVGQCRPLSKTVRFNVLKVEKNEIIGNVRKQFVLF 158 (158)
T ss_pred EEEEcCCCCCceeEEEEEEEecccccccccccccC
Confidence 99999999999999999999987544459999987
No 2
>PRK08572 rps17p 30S ribosomal protein S17P; Reviewed
Probab=100.00 E-value=3.4e-46 Score=273.37 Aligned_cols=105 Identities=47% Similarity=0.760 Sum_probs=99.4
Q ss_pred ccchhhhcccccccCCCCCcceeeeecEEEEEEEEecCCCCeEEEEEeEEEeeeeeeeEEeeeeeEEEEcCCCCCCCCCC
Q 032855 16 RVLMSLCFSGTYIDKKCPFTGTVSIRGRILAGTCHSAKMNRTIIVRRNYLHFVKKYQRYEKRHSNIPAHISPCFRVKEGD 95 (132)
Q Consensus 16 ~~~~~~~~~~~~~d~~cp~~g~~~vr~k~l~G~VVS~Km~KTivV~v~~~~~hpkY~K~ikr~kky~vHD~e~n~~kvGD 95 (132)
.||.-++-++.|+|++|||||+|+|||+.|+|+|+|++|+|||+|+++++++||+|+|+++++++|+||||+||+|++||
T Consensus 3 ig~~~~~p~~~~~d~~cP~~g~l~irgk~l~G~VvS~Km~KTvvV~v~r~~~hpkY~K~i~r~kky~aHDe~cn~~kvGD 82 (108)
T PRK08572 3 IGLDVKPPEEECDDPNCPFHGTLPVRGQVLEGTVVSDKMHKTVVVEREYLHYVPKYERYEKRRSRIHAHNPPCIDAKVGD 82 (108)
T ss_pred cccCCCCCcccccCCCCCCcceeeeeeEEEEEEEEecCCCceEEEEEEEEEecCCccEEEEEeeeEEEECCCCCCCCCCC
Confidence 46666677788999999999999999999999999999999999999999999999999999999999996569999999
Q ss_pred EEEEeecccCCCeeeEEEEEeeecC
Q 032855 96 HVIIGQCRPLSKTVRFNVLKVIPAG 120 (132)
Q Consensus 96 ~V~I~ecRPiSKtK~~~V~~Ii~k~ 120 (132)
.|+|+|||||||+|+|.|.+|++++
T Consensus 83 ~V~I~E~RPiSKtK~w~v~~i~~~~ 107 (108)
T PRK08572 83 KVKIAECRPLSKTKSFVVVEKKERA 107 (108)
T ss_pred EEEEEEcCCCCCceEEEEEEEEEcC
Confidence 9999999999999999999999875
No 3
>TIGR03630 arch_S17P archaeal ribosomal protein S17P. This model describes exclusively the archaeal ribosomal protein S17P. It excludes homologous ribosomal proteins S11 from eukaryotes and S17 from bacteria.
Probab=100.00 E-value=4.1e-46 Score=270.65 Aligned_cols=101 Identities=50% Similarity=0.802 Sum_probs=96.0
Q ss_pred cchhhhcccccccCCCCCcceeeeecEEEEEEEEecCCCCeEEEEEeEEEeeeeeeeEEeeeeeEEEEcCCCCCCCCCCE
Q 032855 17 VLMSLCFSGTYIDKKCPFTGTVSIRGRILAGTCHSAKMNRTIIVRRNYLHFVKKYQRYEKRHSNIPAHISPCFRVKEGDH 96 (132)
Q Consensus 17 ~~~~~~~~~~~~d~~cp~~g~~~vr~k~l~G~VVS~Km~KTivV~v~~~~~hpkY~K~ikr~kky~vHD~e~n~~kvGD~ 96 (132)
||+-.+=+++|+|++|||||+|+|||++|+|+|+|+||+|||+|+|+++++||+|+|+++++++|+||||+||+|++||+
T Consensus 2 g~~~~~p~~~~~d~~cpf~g~l~irgk~l~G~VvS~Km~KTivV~V~r~~~hpkY~K~i~r~kky~aHDe~cn~~kvGD~ 81 (102)
T TIGR03630 2 GIPVKPPERECNDPKCPFHGHLKVRGQILEGVVVSDKMNKTVVVEREYLYYDRKYERYERRRSKIHAHNPPCIDVKEGDI 81 (102)
T ss_pred CcccCCCCccccCCCCCccceeeeeeEEEEEEEEecCCCceEEEEEEEEEecCCccEEEEEeeeEEEECCCCCCCCCCCE
Confidence 66666678899999999999999999999999999999999999999999999999999999999999966699999999
Q ss_pred EEEeecccCCCeeeEEEEEee
Q 032855 97 VIIGQCRPLSKTVRFNVLKVI 117 (132)
Q Consensus 97 V~I~ecRPiSKtK~~~V~~Ii 117 (132)
|+|+|||||||+|+|+|.+|+
T Consensus 82 V~I~E~RPlSKtK~w~vv~i~ 102 (102)
T TIGR03630 82 VIIGETRPLSKTKSFVVLGKV 102 (102)
T ss_pred EEEEEcCCCCCceEEEEEEeC
Confidence 999999999999999999874
No 4
>KOG1728 consensus 40S ribosomal protein S11 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=2.5e-42 Score=263.32 Aligned_cols=111 Identities=68% Similarity=1.172 Sum_probs=108.5
Q ss_pred hhhhcccccccCCCCCcceeeeecEEEEEEEEecCCCCeEEEEEeEEEeeeeeeeEEeeeeeEEEEcCCCCC-CCCCCEE
Q 032855 19 MSLCFSGTYIDKKCPFTGTVSIRGRILAGTCHSAKMNRTIIVRRNYLHFVKKYQRYEKRHSNIPAHISPCFR-VKEGDHV 97 (132)
Q Consensus 19 ~~~~~~~~~~d~~cp~~g~~~vr~k~l~G~VVS~Km~KTivV~v~~~~~hpkY~K~ikr~kky~vHD~e~n~-~kvGD~V 97 (132)
|.|||+|+|+|++|||+||++|||++|.|+|+++||++||+|+.+|+|+.+||++|.+||+++.||.+||+. .++||+|
T Consensus 45 P~eAiegtYIDKKCPftG~vsIRGril~G~V~k~Km~rTIvvrrdYlHy~~KY~ryekrHkN~svh~SPcFrdi~~gDiV 124 (156)
T KOG1728|consen 45 PREAIEGTYIDKKCPFTGNVSIRGRILTGTVVKMKMQRTIVVRRDYLHYIKKYNRYEKRHKNMSVHVSPCFRDIQEGDIV 124 (156)
T ss_pred hHHhhcceeecccCCcccceeEeeEEEeeEEeeeceeEEEEEEhhhhhHhHHhhHHHHhccCCccccchhhhccccCCEE
Confidence 899999999999999999999999999999999999999999999999999999999999999999999997 9999999
Q ss_pred EEeecccCCCeeeEEEEEeeecCCCCCcccccccC
Q 032855 98 IIGQCRPLSKTVRFNVLKVIPAGSSGGAKKAFTAM 132 (132)
Q Consensus 98 ~I~ecRPiSKtK~~~V~~Ii~k~~~~~~~~~f~~~ 132 (132)
+|+|||||||+++|.|++++++ ||.++||++|
T Consensus 125 tvGecrPLSKtvrfnVLkv~k~---~g~~k~~~k~ 156 (156)
T KOG1728|consen 125 TVGECRPLSKTVRFNVLKVIKA---AGSKKQFKKF 156 (156)
T ss_pred EEeecccccceEEEEEEEEeec---CCCccccccC
Confidence 9999999999999999999999 4689999987
No 5
>COG0186 RpsQ Ribosomal protein S17 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=2.1e-38 Score=224.73 Aligned_cols=86 Identities=37% Similarity=0.618 Sum_probs=83.8
Q ss_pred cceeeeecEEEEEEEEecCCCCeEEEEEeEEEeeeeeeeEEeeeeeEEEEcCCCCCCCCCCEEEEeecccCCCeeeEEEE
Q 032855 35 TGTVSIRGRILAGTCHSAKMNRTIIVRRNYLHFVKKYQRYEKRHSNIPAHISPCFRVKEGDHVIIGQCRPLSKTVRFNVL 114 (132)
Q Consensus 35 ~g~~~vr~k~l~G~VVS~Km~KTivV~v~~~~~hpkY~K~ikr~kky~vHD~e~n~~kvGD~V~I~ecRPiSKtK~~~V~ 114 (132)
||++++++++|+|+|+|+||+|||+|++++.++||+|+|+++++++|+||| |||+|++||+|+|+|||||||||+|+|+
T Consensus 1 ~~~~~~~~k~l~G~VvS~Km~KTvvV~ve~~~~hp~Y~K~v~r~kK~~aHd-e~~~~k~GD~V~I~EtRPLSKtK~~~vv 79 (87)
T COG0186 1 HGKLRVRGRVLEGVVVSDKMDKTVVVEVERKVYHPKYGKYVRRSKKYHAHD-ECNEAKVGDIVRIAETRPLSKTKRFVVV 79 (87)
T ss_pred CCccccCceEEEEEEEEccCceeEEEEEEEEEecccceEEEEEEeeeEeec-ccccCCCCCEEEEEEccccCCcceEEEE
Confidence 689999999999999999999999999999999999999999999999999 9999999999999999999999999999
Q ss_pred EeeecCC
Q 032855 115 KVIPAGS 121 (132)
Q Consensus 115 ~Ii~k~~ 121 (132)
+|++++.
T Consensus 80 ~i~~~a~ 86 (87)
T COG0186 80 EIVEKAV 86 (87)
T ss_pred EEeeecc
Confidence 9999864
No 6
>CHL00142 rps17 ribosomal protein S17; Validated
Probab=100.00 E-value=4.2e-35 Score=206.45 Aligned_cols=79 Identities=28% Similarity=0.307 Sum_probs=76.8
Q ss_pred cEEEEEEEEecCCCCeEEEEEeEEEeeeeeeeEEeeeeeEEEEcCCCCCCCCCCEEEEeecccCCCeeeEEEEEeeecCC
Q 032855 42 GRILAGTCHSAKMNRTIIVRRNYLHFVKKYQRYEKRHSNIPAHISPCFRVKEGDHVIIGQCRPLSKTVRFNVLKVIPAGS 121 (132)
Q Consensus 42 ~k~l~G~VVS~Km~KTivV~v~~~~~hpkY~K~ikr~kky~vHD~e~n~~kvGD~V~I~ecRPiSKtK~~~V~~Ii~k~~ 121 (132)
.+.++|+|+|++|+|||+|+++++++||+|+|+++++++|+||| |+|+|++||+|+|+|||||||+|+|+|.+|++++.
T Consensus 3 ~~~~~G~Vvs~km~KTivV~v~r~~~h~kY~K~~~r~kk~~aHD-e~n~~~~GD~V~I~e~RPlSKtK~~~v~~i~~~~~ 81 (84)
T CHL00142 3 VKEKIGIVVSNKMNKTIVVAVENRYKHPIYGKIITKTKKYLVHD-EENECNIGDQVLIEETRPLSKTKRWILKEILSKSS 81 (84)
T ss_pred ceEEEEEEEeCCCCceEEEEEEEEEEcCcccEEEEeeEEEEEeC-CCCCCCCCCEEEEEEcCCCCCcEEEEEEEEEEeee
Confidence 57899999999999999999999999999999999999999999 89999999999999999999999999999999875
No 7
>PRK05610 rpsQ 30S ribosomal protein S17; Reviewed
Probab=100.00 E-value=7.6e-35 Score=204.94 Aligned_cols=79 Identities=32% Similarity=0.364 Sum_probs=76.4
Q ss_pred ecEEEEEEEEecCCCCeEEEEEeEEEeeeeeeeEEeeeeeEEEEcCCCCCCCCCCEEEEeecccCCCeeeEEEEEeeecC
Q 032855 41 RGRILAGTCHSAKMNRTIIVRRNYLHFVKKYQRYEKRHSNIPAHISPCFRVKEGDHVIIGQCRPLSKTVRFNVLKVIPAG 120 (132)
Q Consensus 41 r~k~l~G~VVS~Km~KTivV~v~~~~~hpkY~K~ikr~kky~vHD~e~n~~kvGD~V~I~ecRPiSKtK~~~V~~Ii~k~ 120 (132)
.++.|.|+|+|++|+||++|+++++++||+|+|+++++++|+||| |+|+|++||+|+|+|||||||+|+|+|.+|++++
T Consensus 5 ~~~~l~G~Vvs~km~KTvvV~v~r~~~h~kY~K~~~r~kk~~aHD-~~n~~k~GD~V~I~e~rPlSK~K~~~v~~i~~~~ 83 (84)
T PRK05610 5 PRKTLQGRVVSDKMDKTIVVLVERRVKHPLYGKIVKRSKKYHAHD-ENNEAKIGDVVRIMETRPLSKTKRWRLVEIVEKA 83 (84)
T ss_pred CCCEEEEEEEcccCCceEEEEEEEEEEeccccEEEEcceEEEEEC-CCCCCCCCCEEEEEEcccCCCCEEEEEEEEEecc
Confidence 368999999999999999999999999999999999999999999 7899999999999999999999999999999875
No 8
>TIGR03635 S17_bact 30S ribosomal protein S17. This model describes the bacterial ribosomal small subunit protein S17, while excluding cytosolic eukaryotic homologs and archaeal homologs. The model finds many, but not, chloroplast and mitochondrial counterparts to bacterial S17.
Probab=100.00 E-value=1.7e-33 Score=192.66 Aligned_cols=71 Identities=35% Similarity=0.367 Sum_probs=68.6
Q ss_pred cEEEEEEEEecCCCCeEEEEEeEEEeeeeeeeEEeeeeeEEEEcCCCCCCCCCCEEEEeecccCCCeeeEEE
Q 032855 42 GRILAGTCHSAKMNRTIIVRRNYLHFVKKYQRYEKRHSNIPAHISPCFRVKEGDHVIIGQCRPLSKTVRFNV 113 (132)
Q Consensus 42 ~k~l~G~VVS~Km~KTivV~v~~~~~hpkY~K~ikr~kky~vHD~e~n~~kvGD~V~I~ecRPiSKtK~~~V 113 (132)
.++|.|+|+|++|+||++|+++++++||+|+|+++++++|+||| |+|+|++||+|.|+|||||||+|+|.|
T Consensus 1 ~~~l~G~Vvs~km~KTvvV~v~~~~~h~ky~k~~~r~kk~~aHD-~~~~~k~GD~V~I~ecrPlSK~K~~~~ 71 (71)
T TIGR03635 1 RKTLQGVVVSDKMDKTIVVLVERRVKHPLYGKIVKRTKKYHAHD-ENNECKVGDVVRIIETRPLSKTKRWRL 71 (71)
T ss_pred CeEEEEEEEcccCCceEEEEEEEEEEeccccEEEEccEEEEEEC-CCCCCCCCCEEEEEEcCCcCCceEeEC
Confidence 37899999999999999999999999999999999999999999 789999999999999999999999985
No 9
>PF00366 Ribosomal_S17: Ribosomal protein S17; InterPro: IPR000266 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 [, ]. The ribosomal proteins catalyse ribosome assembly and stabilise the rRNA, tuning the structure of the ribosome for optimal function. Evidence suggests that, in prokaryotes, the peptidyl transferase reaction is performed by the large subunit 23S rRNA, whereas proteins probably have a greater role in eukaryotic ribosomes. Most of the proteins lie close to, or on the surface of, the 30S subunit, arranged peripherally around the rRNA []. The small subunit ribosomal proteins can be categorised as primary binding proteins, which bind directly and independently to 16S rRNA; secondary binding proteins, which display no specific affinity for 16S rRNA, but its assembly is contingent upon the presence of one or more primary binding proteins; and tertiary binding proteins, which require the presence of one or more secondary binding proteins and sometimes other tertiary binding proteins. The small ribosomal subunit protein S17 is known to bind specifically to the 5' end of 16S ribosomal RNA in Escherichia coli (primary rRNA binding protein), and is thought to be involved in the recognition of termination codons. Experimental evidence [] has revealed that S17 has virtually no groups exposed on the ribosomal surface.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 2YKR_Q 2VHP_Q 3BBN_Q 2QAL_Q 3OAR_Q 1VS5_Q 3KC4_Q 2AW7_Q 3E1C_J 2AVY_Q ....
Probab=99.97 E-value=6.6e-32 Score=183.45 Aligned_cols=69 Identities=43% Similarity=0.632 Sum_probs=66.6
Q ss_pred EEEEecCCCCeEEEEEeEEEeeeeeeeEEeeeeeEEEEcCCCCCCCCCCEEEEeecccCCCeeeEEEEEe
Q 032855 47 GTCHSAKMNRTIIVRRNYLHFVKKYQRYEKRHSNIPAHISPCFRVKEGDHVIIGQCRPLSKTVRFNVLKV 116 (132)
Q Consensus 47 G~VVS~Km~KTivV~v~~~~~hpkY~K~ikr~kky~vHD~e~n~~kvGD~V~I~ecRPiSKtK~~~V~~I 116 (132)
|+|+|++|+||++|+++++++||+|+|+++++++|+||| |.|+|++||+|+|.|||||||+|+|.|.++
T Consensus 1 G~Vvs~km~KTv~V~v~~~~~~~ky~K~~~~~kk~~aHD-~~~~~~vGD~V~I~e~rPiSk~K~~~v~~v 69 (69)
T PF00366_consen 1 GVVVSDKMDKTVVVRVERLVYHPKYKKYIKRTKKYMAHD-ENNICKVGDKVRIRECRPISKTKRFVVVEV 69 (69)
T ss_dssp EEEEEEESTTEEEEEEEEEEEETTTEEEEEEEEEEEEE--TTSSSTTTSEEEEEEEEEEETTEEEEEEEE
T ss_pred CEEEEcCCCCeEEEEEEEEEEcceEeeccCccccEEEeC-CccCCCCCCEEEEEeeeccCCcEeEEEEEC
Confidence 899999999999999999999999999999999999999 899999999999999999999999999986
No 10
>KOG1740 consensus Predicted mitochondrial/chloroplast ribosomal protein S17 [Translation, ribosomal structure and biogenesis]
Probab=99.95 E-value=7.5e-30 Score=185.54 Aligned_cols=78 Identities=38% Similarity=0.498 Sum_probs=75.0
Q ss_pred cEEEEEEEEecCCCCeEEEEEeEEEeeeeeeeEEeeeeeEEEEcCCCCCCCCCCEEEEeecccCCCeeeEEEEEeeecC
Q 032855 42 GRILAGTCHSAKMNRTIIVRRNYLHFVKKYQRYEKRHSNIPAHISPCFRVKEGDHVIIGQCRPLSKTVRFNVLKVIPAG 120 (132)
Q Consensus 42 ~k~l~G~VVS~Km~KTivV~v~~~~~hpkY~K~ikr~kky~vHD~e~n~~kvGD~V~I~ecRPiSKtK~~~V~~Ii~k~ 120 (132)
.+.+.|+|+|.+|+||++|+|+++..||+|+|+++++++|+||| |.|.|++||.|+|.+||||||+|+|.+.+||.++
T Consensus 2 m~~~vg~VvS~kmqKTv~V~V~rl~~n~~ynryv~~~~kymahD-~~n~cnvGD~VrlepsRPlSk~K~f~i~eII~~a 79 (107)
T KOG1740|consen 2 MKNVVGTVVSNKMQKTVKVRVDRLFFNPKYNRYVKRTSKYMAHD-DKNQCNVGDRVRLEPSRPLSKTKHFIIAEIIKKA 79 (107)
T ss_pred CccceeeeeecccCceeEEEeeeccccHHHHHHHHHhhheeecC-ccccccccceEEeccCCcccccceeehHHHHHHH
Confidence 35689999999999999999999999999999999999999999 8999999999999999999999999999999874
No 11
>KOG3447 consensus Mitochondrial/chloroplast ribosomal S17-like protein [Translation, ribosomal structure and biogenesis]
Probab=99.39 E-value=6.6e-14 Score=106.92 Aligned_cols=81 Identities=25% Similarity=0.274 Sum_probs=74.5
Q ss_pred eeeecEEEEEEEEecCCCCeEEEEEeEEEeeeeeeeEEeeeeeEEEEcCCCCCCCCCCEEEEeec-ccCCCeeeEEEEEe
Q 032855 38 VSIRGRILAGTCHSAKMNRTIIVRRNYLHFVKKYQRYEKRHSNIPAHISPCFRVKEGDHVIIGQC-RPLSKTVRFNVLKV 116 (132)
Q Consensus 38 ~~vr~k~l~G~VVS~Km~KTivV~v~~~~~hpkY~K~ikr~kky~vHD~e~n~~kvGD~V~I~ec-RPiSKtK~~~V~~I 116 (132)
.+++++.|.|.|+..+|++|+.|++.++..+|..+||+++.+.|+||| +...|++||+|.|++. -|..+..+|.|.+|
T Consensus 6 ~s~~~~~lmGk~ig~~~q~~akVR~~r~eld~yL~kYf~k~~~yfAhD-~~~~c~vGDtVLir~lp~r~t~~V~H~v~~V 84 (150)
T KOG3447|consen 6 SSVHAQWLMGKVIGTKMQKTAKVRVTRLELDPYLLKYFNKRKTYFAHD-ALQQCTVGDTVLIRALPVRRTKHVKHEVAEV 84 (150)
T ss_pred eecccEEEEeeeeeccccccceeeeehhhcCHHHHHHhccccceeecc-hhhccccCCEEEEecCCcchhhhhhhhhHhh
Confidence 467899999999999999999999999999999999999999999999 8999999999999996 56677788888888
Q ss_pred eec
Q 032855 117 IPA 119 (132)
Q Consensus 117 i~k 119 (132)
+.+
T Consensus 85 Vfk 87 (150)
T KOG3447|consen 85 VFK 87 (150)
T ss_pred eee
Confidence 765
No 12
>KOG3416 consensus Predicted nucleic acid binding protein [General function prediction only]
Probab=65.70 E-value=27 Score=26.88 Aligned_cols=60 Identities=13% Similarity=0.056 Sum_probs=39.2
Q ss_pred CCcceeee-ecEEEEEEEEecCCCCeEEEEEeEEEeeeeeeeEEeeeeeEEEEcCCCCCCCCCCEEEEee
Q 032855 33 PFTGTVSI-RGRILAGTCHSAKMNRTIIVRRNYLHFVKKYQRYEKRHSNIPAHISPCFRVKEGDHVIIGQ 101 (132)
Q Consensus 33 p~~g~~~v-r~k~l~G~VVS~Km~KTivV~v~~~~~hpkY~K~ikr~kky~vHD~e~n~~kvGD~V~I~e 101 (132)
|.--|..+ .--...|.+.++|.++++.+..--- ..-+=++.+-|++++..++||+|++..
T Consensus 12 P~~kN~~v~fIvl~~g~~tkTkdg~~v~~~kVaD---------~TgsI~isvW~e~~~~~~PGDIirLt~ 72 (134)
T KOG3416|consen 12 PGLKNINVTFIVLEYGRATKTKDGHEVRSCKVAD---------ETGSINISVWDEEGCLIQPGDIIRLTG 72 (134)
T ss_pred hhhhcceEEEEEEeeceeeeccCCCEEEEEEEec---------ccceEEEEEecCcCcccCCccEEEecc
Confidence 44344443 3345678888899888887652111 123445667787888999999999764
No 13
>PF10844 DUF2577: Protein of unknown function (DUF2577); InterPro: IPR022555 This family of proteins has no known function
Probab=63.04 E-value=51 Score=23.28 Aligned_cols=23 Identities=26% Similarity=0.420 Sum_probs=16.1
Q ss_pred CCCCCCEEEEeecccCCCeeeEEEEE
Q 032855 90 RVKEGDHVIIGQCRPLSKTVRFNVLK 115 (132)
Q Consensus 90 ~~kvGD~V~I~ecRPiSKtK~~~V~~ 115 (132)
.+++||.|.+. |.-.-.+|.|+.
T Consensus 76 ~Lk~GD~V~ll---~~~~gQ~yiVlD 98 (100)
T PF10844_consen 76 GLKVGDKVLLL---RVQGGQKYIVLD 98 (100)
T ss_pred CCcCCCEEEEE---EecCCCEEEEEE
Confidence 78999999988 444445555543
No 14
>PF10650 zf-C3H1: Putative zinc-finger domain; InterPro: IPR019607 This domain is conserved in fungi and might be a zinc-finger domain as it contains three conserved Cs and an H in the C-x8-C-x5-C-x3-H conformation typical of a zinc-finger.
Probab=56.93 E-value=5.5 Score=22.02 Aligned_cols=14 Identities=29% Similarity=0.472 Sum_probs=11.2
Q ss_pred hhcccccccCCCCC
Q 032855 21 LCFSGTYIDKKCPF 34 (132)
Q Consensus 21 ~~~~~~~~d~~cp~ 34 (132)
|+.-|.|+|..|+|
T Consensus 6 El~Gg~Cnd~~C~~ 19 (23)
T PF10650_consen 6 ELTGGVCNDPDCEF 19 (23)
T ss_pred ccCCCeeCCCCCCc
Confidence 44456999999998
No 15
>cd03695 CysN_NodQ_II CysN_NodQ_II: This subfamily represents the domain II of the large subunit of ATP sulfurylase (ATPS): CysN or the N-terminal portion of NodQ, found mainly in proteobacteria and homologous to the domain II of EF-Tu. Escherichia coli ATPS consists of CysN and a smaller subunit CysD and CysN. ATPS produces adenosine-5'-phosphosulfate (APS) from ATP and sulfate, coupled with GTP hydrolysis. In the subsequent reaction APS is phosphorylated by an APS kinase (CysC), to produce 3'-phosphoadenosine-5'-phosphosulfate (PAPS) for use in amino acid (aa) biosynthesis. The Rhizobiaceae group (alpha-proteobacteria) appears to carry out the same chemistry for the sufation of a nodulation factor. In Rhizobium meliloti, a the hererodimeric complex comprised of NodP and NodQ appears to possess both ATPS and APS kinase activities. The N and C termini of NodQ correspond to CysN and CysC, respectively. Other eubacteria, Archaea, and eukaryotes use a different ATP sulfurylase, which sho
Probab=50.64 E-value=59 Score=21.73 Aligned_cols=26 Identities=15% Similarity=0.141 Sum_probs=21.0
Q ss_pred EeeeeeEEEEcCCCCCCCCCCEEEEe
Q 032855 75 EKRHSNIPAHISPCFRVKEGDHVIIG 100 (132)
Q Consensus 75 ikr~kky~vHD~e~n~~kvGD~V~I~ 100 (132)
.-.-+.+.+|+.+.+.+..||.|.|.
T Consensus 41 ~~~V~si~~~~~~~~~a~aGd~v~l~ 66 (81)
T cd03695 41 TSRVKSIETFDGELDEAGAGESVTLT 66 (81)
T ss_pred eEEEEEEEECCcEeCEEcCCCEEEEE
Confidence 45667778888778889999999885
No 16
>cd03698 eRF3_II_like eRF3_II_like: domain similar to domain II of the eukaryotic class II release factor (eRF3). In eukaryotes, translation termination is mediated by two interacting release factors, eRF1 and eRF3, which act as class I and II factors, respectively. eRF1 functions as an omnipotent release factor, decoding all three stop codons and triggering the release of the nascent peptide catalyzed by the ribsome. eRF3 is a GTPase, which enhances the termination efficiency by stimulating the eRF1 activity in a GTP-dependent manner. Sequence comparison of class II release factors with elongation factors shows that eRF3 is more similar to eEF1alpha whereas prokaryote RF3 is more similar to EF-G, implying that their precise function may differ. Only eukaryote RF3s are found in this group. Saccharomyces cerevisiae eRF3 (Sup35p) is a translation termination factor which is divided into three regions N, M and a C-terminal eEF1a-like region essential for translation termination. Sup35NM
Probab=47.18 E-value=63 Score=21.43 Aligned_cols=25 Identities=12% Similarity=0.006 Sum_probs=19.6
Q ss_pred eeeeeEEEEcCCCCCCCCCCEEEEe
Q 032855 76 KRHSNIPAHISPCFRVKEGDHVIIG 100 (132)
Q Consensus 76 kr~kky~vHD~e~n~~kvGD~V~I~ 100 (132)
-.-+.+..|+.+.+++..||.|.|.
T Consensus 42 ~~V~si~~~~~~~~~a~aGd~v~~~ 66 (83)
T cd03698 42 VEVKSIYVDDEEVDYAVAGENVRLK 66 (83)
T ss_pred EEEEEEEECCeECCEECCCCEEEEE
Confidence 4556677788778889999999864
No 17
>cd03693 EF1_alpha_II EF1_alpha_II: this family represents the domain II of elongation factor 1-alpha (EF-1a) that is found in archaea and all eukaryotic lineages. EF-1A is very abundant in the cytosol, where it is involved in the GTP-dependent binding of aminoacyl-tRNAs to the A site of the ribosomes in the second step of translation from mRNAs to proteins. Both domain II of EF1A and domain IV of IF2/eIF5B have been implicated in recognition of the 3'-ends of tRNA. More than 61% of eukaryotic elongation factor 1A (eEF-1A) in cells is estimated to be associated with actin cytoskeleton. The binding of eEF1A to actin is a noncanonical function that may link two distinct cellular processes, cytoskeleton organization and gene expression.
Probab=42.41 E-value=76 Score=21.50 Aligned_cols=26 Identities=19% Similarity=0.220 Sum_probs=20.4
Q ss_pred EeeeeeEEEEcCCCCCCCCCCEEEEe
Q 032855 75 EKRHSNIPAHISPCFRVKEGDHVIIG 100 (132)
Q Consensus 75 ikr~kky~vHD~e~n~~kvGD~V~I~ 100 (132)
...-+.+..|+.+...+..||.|.|.
T Consensus 45 ~~~V~sI~~~~~~~~~a~aG~~v~i~ 70 (91)
T cd03693 45 TGEVKSVEMHHEPLEEALPGDNVGFN 70 (91)
T ss_pred EEEEEEEEECCcCcCEECCCCEEEEE
Confidence 45566677888777889999999874
No 18
>PF13550 Phage-tail_3: Putative phage tail protein
Probab=39.75 E-value=80 Score=22.62 Aligned_cols=38 Identities=13% Similarity=0.326 Sum_probs=27.1
Q ss_pred eeeeeEEEEcCCCCCCCCCCEEEEeecccCCCeeeEEEEEee
Q 032855 76 KRHSNIPAHISPCFRVKEGDHVIIGQCRPLSKTVRFNVLKVI 117 (132)
Q Consensus 76 kr~kky~vHD~e~n~~kvGD~V~I~ecRPiSKtK~~~V~~Ii 117 (132)
+++=.|.+-- +...+.+||+|.|..- .+...|+|.+|-
T Consensus 126 r~t~~f~~~~-~~~~l~pGDvi~l~~~---~~~~~~RI~~i~ 163 (164)
T PF13550_consen 126 RRTVSFTLPP-DGLALEPGDVIALSDD---GRDMRFRITEIE 163 (164)
T ss_pred ceEEEEEECh-hhccCCCCCEEEEEeC---CCceEEEEEEEe
Confidence 3344555553 5668999999999866 557888888774
No 19
>cd03697 EFTU_II EFTU_II: Elongation factor Tu domain II. Elongation factors Tu (EF-Tu) are three-domain GTPases with an essential function in the elongation phase of mRNA translation. The GTPase center of EF-Tu is in the N-terminal domain (domain I), also known as the catalytic or G-domain. The G-domain is composed of about 200 amino acid residues, arranged into a predominantly parallel six-stranded beta-sheet core surrounded by seven a-helices. Non-catalytic domains II and III are beta-barrels of seven and six, respectively, antiparallel beta-strands that share an extended interface. Either non-catalytic domain is composed of about 100 amino acid residues. EF-Tu proteins exist in two principal conformations: in a compact one, EF-Tu*GTP, with tight interfaces between all three domains and a high affinity for aminoacyl-tRNA, and in an open one, EF-Tu*GDP, with essentially no G-domain-domain II interactions and a low affinity for aminoacyl-tRNA. EF-Tu has approximately a 100-fold higher
Probab=38.63 E-value=1e+02 Score=20.66 Aligned_cols=52 Identities=12% Similarity=0.183 Sum_probs=31.2
Q ss_pred cEEEEEEEEecCC--CCeEEEEEeEEEeeeeeeeEEeeeeeEEEEcCCCCCCCCCCEEEEe
Q 032855 42 GRILAGTCHSAKM--NRTIIVRRNYLHFVKKYQRYEKRHSNIPAHISPCFRVKEGDHVIIG 100 (132)
Q Consensus 42 ~k~l~G~VVS~Km--~KTivV~v~~~~~hpkY~K~ikr~kky~vHD~e~n~~kvGD~V~I~ 100 (132)
|.++.|+|.+-.+ .-.+.+.- .+. .....-+.+.+|+.+..++..||.|.|.
T Consensus 15 G~vv~G~v~~G~v~~gd~v~~~p-----~~~--~~~~~V~si~~~~~~~~~a~~G~~v~l~ 68 (87)
T cd03697 15 GTVVTGRIERGTIKVGDEVEIVG-----FGE--TLKTTVTGIEMFRKTLDEAEAGDNVGVL 68 (87)
T ss_pred EEEEEEEECCCCCccCCEEEEeC-----CCC--CceEEEEEEEECCcCCCEECCCCEEEEE
Confidence 5567888776532 33333221 011 1223455577888777889999999875
No 20
>PRK00276 infA translation initiation factor IF-1; Validated
Probab=36.84 E-value=1.3e+02 Score=19.98 Aligned_cols=59 Identities=19% Similarity=0.098 Sum_probs=33.1
Q ss_pred EEEEEEEEecCCCCeEEEEEeEEEeeeeeeeEEeeeeeEEEEcCCCCCCCCCCEEEEeecccCCCeee
Q 032855 43 RILAGTCHSAKMNRTIIVRRNYLHFVKKYQRYEKRHSNIPAHISPCFRVKEGDHVIIGQCRPLSKTVR 110 (132)
Q Consensus 43 k~l~G~VVS~Km~KTivV~v~~~~~hpkY~K~ikr~kky~vHD~e~n~~kvGD~V~I~ecRPiSKtK~ 110 (132)
-.+.|+|++.-.+..-.|..+ -...|...++..-+ +. .....+||.|.+.. +|...++-
T Consensus 7 ~~~~G~Vi~~~~~~~y~V~~~---~g~~~~c~~~Gklr---~~--~i~i~vGD~V~ve~-~~~~~~~g 65 (72)
T PRK00276 7 IEMEGTVVEALPNAMFRVELE---NGHEVLAHISGKMR---KN--YIRILPGDKVTVEL-SPYDLTKG 65 (72)
T ss_pred EEEEEEEEEEcCCCEEEEEeC---CCCEEEEEEcccee---eC--CcccCCCCEEEEEE-cccCCCeE
Confidence 456788888654544444321 11244455444433 22 24588999999875 45555554
No 21
>cd03696 selB_II selB_II: this subfamily represents the domain of elongation factor SelB, homologous to domain II of EF-Tu. SelB may function by replacing EF-Tu. In prokaryotes, the incorporation of selenocysteine as the 21st amino acid, encoded by TGA, requires several elements: SelC is the tRNA itself, SelD acts as a donor of reduced selenium, SelA modifies a serine residue on SelC into selenocysteine, and SelB is a selenocysteine-specific translation elongation factor. 3' or 5' non-coding elements of mRNA have been found as probable structures for directing selenocysteine incorporation.
Probab=35.49 E-value=1.3e+02 Score=19.76 Aligned_cols=26 Identities=31% Similarity=0.378 Sum_probs=19.7
Q ss_pred EeeeeeEEEEcCCCCCCCCCCEEEEe
Q 032855 75 EKRHSNIPAHISPCFRVKEGDHVIIG 100 (132)
Q Consensus 75 ikr~kky~vHD~e~n~~kvGD~V~I~ 100 (132)
.-.-+.+..|+.+..++..||.|.|.
T Consensus 41 ~~~V~sI~~~~~~~~~a~aGd~v~i~ 66 (83)
T cd03696 41 ETRVRSIQVHGKDVEEAKAGDRVALN 66 (83)
T ss_pred eEEEEEEEECCcCcCEEcCCCEEEEE
Confidence 45556677777666789999999874
No 22
>PF09740 DUF2043: Uncharacterized conserved protein (DUF2043); InterPro: IPR018610 This entry consists of uncharacterised proteins of unknown function. They contain three conserved cysteines and a {CP}{y/l}{HG} motif.
Probab=34.32 E-value=17 Score=27.00 Aligned_cols=10 Identities=60% Similarity=1.159 Sum_probs=7.9
Q ss_pred ccCCCCCcce
Q 032855 28 IDKKCPFTGT 37 (132)
Q Consensus 28 ~d~~cp~~g~ 37 (132)
+-.+|||||-
T Consensus 86 D~~kCPfHG~ 95 (110)
T PF09740_consen 86 DRKKCPFHGK 95 (110)
T ss_pred CcccCCCCCc
Confidence 4468999996
No 23
>TIGR00008 infA translation initiation factor IF-1. This family consists of translation initiation factor IF-1 as found in bacteria and chloroplasts. This protein, about 70 residues in length, consists largely of an S1 RNA binding domain (pfam00575).
Probab=32.82 E-value=1.6e+02 Score=19.98 Aligned_cols=53 Identities=25% Similarity=0.253 Sum_probs=32.7
Q ss_pred EEEEEEEEecCCCCeEEEEEeEEEeeeeeeeEEeeeeeEEEEcCCCC-----CCCCCCEEEEeecccCCCee
Q 032855 43 RILAGTCHSAKMNRTIIVRRNYLHFVKKYQRYEKRHSNIPAHISPCF-----RVKEGDHVIIGQCRPLSKTV 109 (132)
Q Consensus 43 k~l~G~VVS~Km~KTivV~v~~~~~hpkY~K~ikr~kky~vHD~e~n-----~~kvGD~V~I~ecRPiSKtK 109 (132)
-.+.|+|+..-.+-...|..+- -...++|-+-.. -..+||.|.+. -+|...+|
T Consensus 5 ie~~G~V~e~L~~~~f~V~l~n-------------g~~vla~i~GKmr~~rI~I~~GD~V~Ve-~spyd~tk 62 (68)
T TIGR00008 5 IEMEGKVTESLPNAMFRVELEN-------------GHEVLAHISGKIRMHYIRILPGDKVKVE-LSPYDLTR 62 (68)
T ss_pred EEEEEEEEEECCCCEEEEEECC-------------CCEEEEEecCcchhccEEECCCCEEEEE-ECcccCCc
Confidence 4678999988777777776542 123344442111 25679999965 56666555
No 24
>cd03694 GTPBP_II Domain II of the GP-1 family of GTPase. This group includes proteins similar to GTPBP1 and GTPBP2. GTPB1 is structurally, related to elongation factor 1 alpha, a key component of protein biosynthesis machinery. Immunohistochemical analyses on mouse tissues revealed that GTPBP1 is expressed in some neurons and smooth muscle cells of various organs as well as macrophages. Immunofluorescence analyses revealed that GTPBP1 is localized exclusively in cytoplasm and shows a diffuse granular network forming a gradient from the nucleus to the periphery of the cells in smooth muscle cell lines and macrophages. No significant difference was observed in the immune response to protein antigen between mutant mice and wild-type mice, suggesting normal function of antigen-presenting cells of the mutant mice. The absence of an eminent phenotype in GTPBP1-deficient mice may be due to functional compensation by GTPBP2, which is similar to GTPBP1 in structure and tissue distribution.
Probab=31.71 E-value=94 Score=20.91 Aligned_cols=26 Identities=19% Similarity=0.224 Sum_probs=20.3
Q ss_pred EeeeeeEEEEcCCCCCCCCCCEEEEe
Q 032855 75 EKRHSNIPAHISPCFRVKEGDHVIIG 100 (132)
Q Consensus 75 ikr~kky~vHD~e~n~~kvGD~V~I~ 100 (132)
.-.-+.+..|+.+.+++..||.|.|.
T Consensus 45 ~~~V~sI~~~~~~~~~a~aGd~v~l~ 70 (87)
T cd03694 45 PVTVKSIHRNRSPVRVVRAGQSASLA 70 (87)
T ss_pred EEEEEEEEECCeECCEECCCCEEEEE
Confidence 35556677888777789999999874
No 25
>PF04246 RseC_MucC: Positive regulator of sigma(E), RseC/MucC; InterPro: IPR007359 This bacterial family of integral membrane proteins represents a positive regulator of the sigma(E) transcription factor, namely RseC/MucC. The sigma(E) transcription factor is up-regulated by cell envelope protein misfolding, and regulates the expression of genes that are collectively termed ECF (devoted to Extra-Cellular Functions) []. In Pseudomonas aeruginosa, derepression of sigma(E) is associated with the alginate-overproducing phenotype characteristic of chronic respiratory tract colonization in cystic fibrosis patients. The mechanism by which RseC/MucC positively regulates the sigma(E) transcription factor is unknown. RseC is also thought to have a role in thiamine biosynthesis in Salmonella typhimurium []. In addition, this family also includes an N-terminal part of RnfF, a Rhodobacter capsulatus protein, of unknown function, that is essential for nitrogen fixation. This protein also contains a domain found in ApbE protein IPR003374 from INTERPRO, which is itself involved in thiamine biosynthesis.
Probab=31.37 E-value=56 Score=23.77 Aligned_cols=21 Identities=24% Similarity=0.139 Sum_probs=15.0
Q ss_pred eeEEEEcCCCCCCCCCCEEEEee
Q 032855 79 SNIPAHISPCFRVKEGDHVIIGQ 101 (132)
Q Consensus 79 kky~vHD~e~n~~kvGD~V~I~e 101 (132)
..+.+++ ...+++||.|+|.-
T Consensus 42 ~~~~~~~--~~~~~~GD~V~v~i 62 (135)
T PF04246_consen 42 ITFRAPN--PIGAKVGDRVEVEI 62 (135)
T ss_pred EEEEecC--CCCCCCCCEEEEEe
Confidence 3444555 36899999999864
No 26
>PF06107 DUF951: Bacterial protein of unknown function (DUF951); InterPro: IPR009296 This family consists of several short hypothetical bacterial proteins of unknown function.
Probab=31.30 E-value=75 Score=21.11 Aligned_cols=25 Identities=16% Similarity=0.393 Sum_probs=20.6
Q ss_pred CCCCCEEEEeecccCCCeeeEEEEEe
Q 032855 91 VKEGDHVIIGQCRPLSKTVRFNVLKV 116 (132)
Q Consensus 91 ~kvGD~V~I~ecRPiSKtK~~~V~~I 116 (132)
..+||+|....-.|=-. ..|.|..+
T Consensus 2 ~~vgDiV~mKK~HPCG~-~~Wei~R~ 26 (57)
T PF06107_consen 2 YEVGDIVEMKKPHPCGS-NEWEIIRI 26 (57)
T ss_pred ccCCCEEEEcCCCCCCC-CEEEEEEc
Confidence 57899999999988655 67988775
No 27
>PRK10413 hydrogenase 2 accessory protein HypG; Provisional
Probab=29.98 E-value=1.9e+02 Score=20.11 Aligned_cols=19 Identities=16% Similarity=-0.017 Sum_probs=14.4
Q ss_pred CCCCCCCEEEEeecccCCC
Q 032855 89 FRVKEGDHVIIGQCRPLSK 107 (132)
Q Consensus 89 n~~kvGD~V~I~ecRPiSK 107 (132)
.+.++||.|.+...--+|+
T Consensus 41 ~~~~vGDyVLVHaGfAi~~ 59 (82)
T PRK10413 41 PADLLGQWVLVHVGFAMSI 59 (82)
T ss_pred cccccCCEEEEecchhhhh
Confidence 4789999999987655543
No 28
>KOG1698 consensus Mitochondrial/chloroplast ribosomal protein L19 [Translation, ribosomal structure and biogenesis]
Probab=29.89 E-value=98 Score=25.37 Aligned_cols=30 Identities=17% Similarity=0.056 Sum_probs=27.1
Q ss_pred CCCCCCEEEEeecccCCCeeeEEEEEeeec
Q 032855 90 RVKEGDHVIIGQCRPLSKTVRFNVLKVIPA 119 (132)
Q Consensus 90 ~~kvGD~V~I~ecRPiSKtK~~~V~~Ii~k 119 (132)
+.++||+|.|..--|-++.|.++...|.-.
T Consensus 96 e~~~G~Iv~V~s~~p~~k~k~s~f~Gi~I~ 125 (201)
T KOG1698|consen 96 EFKVGSIVRVTSEDPENKRKVSRFKGICIR 125 (201)
T ss_pred ccccccEEEEEecCCccCCceeEEEEEEEE
Confidence 899999999999999999999999887544
No 29
>COG0361 InfA Translation initiation factor 1 (IF-1) [Translation, ribosomal structure and biogenesis]
Probab=29.47 E-value=2e+02 Score=20.00 Aligned_cols=51 Identities=29% Similarity=0.255 Sum_probs=33.5
Q ss_pred EEEEEEEEecCCCCeEEEEEeEEEeeeeeeeEEeeeeeEEEEcCCCC------CCCCCCEEEEeecccCCCe
Q 032855 43 RILAGTCHSAKMNRTIIVRRNYLHFVKKYQRYEKRHSNIPAHISPCF------RVKEGDHVIIGQCRPLSKT 108 (132)
Q Consensus 43 k~l~G~VVS~Km~KTivV~v~~~~~hpkY~K~ikr~kky~vHD~e~n------~~kvGD~V~I~ecRPiSKt 108 (132)
-.+.|+|+..-.+....|..+--+ ..+||-+ .. -..+||+|.+. .+|..-+
T Consensus 7 ~e~~g~V~e~L~~~~f~v~~edg~-------------~~~ahI~-GKmr~~~i~I~~GD~V~Ve-~~~~d~~ 63 (75)
T COG0361 7 IEMEGTVIEMLPNGRFRVELENGH-------------ERLAHIS-GKMRKNRIRILPGDVVLVE-LSPYDLT 63 (75)
T ss_pred cEEEEEEEEecCCCEEEEEecCCc-------------EEEEEcc-CcchheeEEeCCCCEEEEE-ecccccc
Confidence 467899999988888888765444 2345552 21 25679999864 5565533
No 30
>TIGR03595 Obg_CgtA_exten Obg family GTPase CgtA, C-terminal extension. CgtA (see model TIGR02729) is a broadly conserved member of the obg family of GTPases associated with ribosome maturation. This model represents a unique C-terminal domain found in some but not all sequences of CgtA. This region is preceded, and may be followed, by a region of low-complexity sequence.
Probab=29.41 E-value=37 Score=22.62 Aligned_cols=12 Identities=50% Similarity=0.792 Sum_probs=10.3
Q ss_pred CCCCCCEEEEee
Q 032855 90 RVKEGDHVIIGQ 101 (132)
Q Consensus 90 ~~kvGD~V~I~e 101 (132)
-++.||+|.|..
T Consensus 53 G~~~GD~V~Ig~ 64 (69)
T TIGR03595 53 GAKDGDTVRIGD 64 (69)
T ss_pred CCCCCCEEEEcc
Confidence 589999999975
No 31
>KOG1730 consensus Thioredoxin-like protein [Posttranslational modification, protein turnover, chaperones]
Probab=28.44 E-value=41 Score=27.52 Aligned_cols=39 Identities=23% Similarity=0.469 Sum_probs=25.3
Q ss_pred EEEEeeeccchhhhcccccccC---CCCCcceeeeecEEEEEE
Q 032855 9 IRVWERTRVLMSLCFSGTYIDK---KCPFTGTVSIRGRILAGT 48 (132)
Q Consensus 9 ~~~~~~~~~~~~~~~~~~~~d~---~cp~~g~~~vr~k~l~G~ 48 (132)
...||.-.-.- +-+|..+++. .-|||||+++.+-.+.|-
T Consensus 50 FKpwe~R~d~s-e~vESDaD~eLLfniPFtg~vkLkgI~I~g~ 91 (206)
T KOG1730|consen 50 FKPWEKRTDRS-EYVESDADEELLFNIPFTGNVKLKGISIMGE 91 (206)
T ss_pred cchhhhhcchh-hhhhccCCceeEEeccccCceeEEEEEEEeC
Confidence 35677544444 5566666554 469999988887666663
No 32
>cd04466 S1_YloQ_GTPase S1_YloQ_GTPase: YloQ GTase family (also known as YjeQ and CpgA), S1-like RNA-binding domain. Proteins in the YloQ GTase family bind the ribosome and have GTPase activity. The precise role of this family is unknown. The protein structure is composed of three domains: an N-terminal S1 domain, a central GTPase domain, and a C-terminal zinc finger domain. This N-terminal S1 domain binds ssRNA. The central GTPase domain contains nucleotide-binding signature motifs: G1 (walker A), G3 (walker B) and G4 motifs. Experiments show that the bacterial YloQ and YjeQ proteins have low intrinsic GTPase activity. The C-terminal zinc-finger domain has structural similarity to a portion of the DNA-repair protein Rad51. This suggests a possible role for this GTPase as a regulator of translation, perhaps as a translation initiation factor. This family is classified based on the N-terminal S1 domain.
Probab=27.91 E-value=95 Score=19.32 Aligned_cols=28 Identities=14% Similarity=0.064 Sum_probs=18.6
Q ss_pred CCCCCCCEEEEeecccCCCeeeEEEEEeeecC
Q 032855 89 FRVKEGDHVIIGQCRPLSKTVRFNVLKVIPAG 120 (132)
Q Consensus 89 n~~kvGD~V~I~ecRPiSKtK~~~V~~Ii~k~ 120 (132)
...-+||+|.+.. .. .-.+.+.+++++.
T Consensus 36 ~~~~VGD~V~~~~---~~-~~~~~I~~vl~R~ 63 (68)
T cd04466 36 NPPAVGDRVEFEP---ED-DGEGVIEEILPRK 63 (68)
T ss_pred CCCCCCcEEEEEE---CC-CCcEEEEEEeccc
Confidence 4568999999853 11 1246777888763
No 33
>CHL00010 infA translation initiation factor 1
Probab=26.58 E-value=2.1e+02 Score=19.36 Aligned_cols=62 Identities=18% Similarity=0.157 Sum_probs=34.0
Q ss_pred EEEEEEecCCCCeEEEEEeEEEeeeeeeeEEeeeeeEEEEcCCCCCCCCCCEEEEeecccCCCeeeEEEEE
Q 032855 45 LAGTCHSAKMNRTIIVRRNYLHFVKKYQRYEKRHSNIPAHISPCFRVKEGDHVIIGQCRPLSKTVRFNVLK 115 (132)
Q Consensus 45 l~G~VVS~Km~KTivV~v~~~~~hpkY~K~ikr~kky~vHD~e~n~~kvGD~V~I~ecRPiSKtK~~~V~~ 115 (132)
+.|+|++.-....-.|..+ -...|...++..-+ +. .....+||.|.+.. +|...++--++.+
T Consensus 9 ~~G~Vik~lg~~~y~V~~~---~g~~~~c~~rGklr---~~--~i~~~vGD~V~ve~-~~~~~~~g~Ii~r 70 (78)
T CHL00010 9 MEGLVTESLPNGMFRVRLD---NGCQVLGYISGKIR---RN--SIRILPGDRVKVEL-SPYDLTKGRIIYR 70 (78)
T ss_pred EEEEEEEEcCCCEEEEEeC---CCCEEEEEecccee---cC--CcccCCCCEEEEEE-cccCCCeEEEEEE
Confidence 6788887654444444321 11244444444433 21 34578999999875 5666666544433
No 34
>cd04456 S1_IF1A_like S1_IF1A_like: Translation initiation factor IF1A-like, S1-like RNA-binding domain. IF1A is also referred to as eIF1A in eukaryotes and aIF1A in archaea. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. IF1A is essential for translation initiation. eIF1A acts synergistically with eIF1 to mediate assembly of ribosomal initiation complexes at the initiation codon and maintain the accuracy of this process by recognizing and destabilizing aberrant preinitiation complexes from the mRNA. Without eIF1A and eIF1, 43S ribosomal preinitiation complexes can bind to the cap-proximal region, but are unable to reach the initiation codon. eIF1a also enhances the formation of 5'-terminal complexes in the presence of other translation initiation factors. This protein family is only found in eukaryotes and archaea.
Probab=26.50 E-value=2.2e+02 Score=19.49 Aligned_cols=52 Identities=13% Similarity=-0.033 Sum_probs=30.7
Q ss_pred EEEEEEecCCCCeEEEEEeEEEeeeeeeeEEeeeeeEEEEcCCCC----CCCCCCEEEEeecccC-CCeee
Q 032855 45 LAGTCHSAKMNRTIIVRRNYLHFVKKYQRYEKRHSNIPAHISPCF----RVKEGDHVIIGQCRPL-SKTVR 110 (132)
Q Consensus 45 l~G~VVS~Km~KTivV~v~~~~~hpkY~K~ikr~kky~vHD~e~n----~~kvGD~V~I~ecRPi-SKtK~ 110 (132)
..|+|+....+....|..+- -+.++||-|... -.+.||.|.+. .+|. .+.|.
T Consensus 2 ~i~~V~~~lG~~~~~V~~~d-------------g~~~l~~i~gK~Rk~iwI~~GD~VlV~-~~~~~~~~kg 58 (78)
T cd04456 2 QIVRVLRMLGNNRHEVECAD-------------GQRRLVSIPGKLRKNIWIKRGDFLIVD-PIEEGEDVKA 58 (78)
T ss_pred eEEEEEEECCCCEEEEEECC-------------CCEEEEEEchhhccCEEEcCCCEEEEE-ecccCCCceE
Confidence 46778877777777666431 133444542211 25669999984 6777 45554
No 35
>cd00174 SH3 Src homology 3 domains; SH3 domains bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs; they play a role in the regulation of enzymes by intramolecular interactions, changing the subcellular localization of signal pathway components and mediate multiprotein complex assemblies.
Probab=25.07 E-value=1e+02 Score=17.33 Aligned_cols=22 Identities=18% Similarity=0.122 Sum_probs=15.3
Q ss_pred EEEEcCCCCCCCCCCEEEEeec
Q 032855 81 IPAHISPCFRVKEGDHVIIGQC 102 (132)
Q Consensus 81 y~vHD~e~n~~kvGD~V~I~ec 102 (132)
|.++++....+..||.|.+.+.
T Consensus 8 ~~~~~~~~l~~~~Gd~v~v~~~ 29 (54)
T cd00174 8 YDARDPDELSFKKGDIIEVLEK 29 (54)
T ss_pred eCCCCCCCCCCCCCCEEEEEEc
Confidence 4444433446899999999876
No 36
>PF09269 DUF1967: Domain of unknown function (DUF1967); InterPro: IPR015349 The Obg family comprises a group of ancient P-loop small G proteins (GTPases) belonging to the TRAFAC (for translation factors) class and can be subdivided into several distinct protein subfamilies []. OBG GTPases have been found in both prokaryotes and eukaryotes []. The structure of the OBG GTPase from Thermus thermophilus has been determined []. This entry represents a C-terminal domain found in certain OBG GTPases. This domain contains a four-stranded beta sheet and three alpha helices flanked by an additional beta strand. It is predominantly found in the bacterial GTP-binding protein Obg, and is functionally uncharacterised. ; GO: 0000166 nucleotide binding; PDB: 1UDX_A.
Probab=24.60 E-value=37 Score=22.62 Aligned_cols=12 Identities=58% Similarity=0.817 Sum_probs=7.3
Q ss_pred CCCCCCEEEEee
Q 032855 90 RVKEGDHVIIGQ 101 (132)
Q Consensus 90 ~~kvGD~V~I~e 101 (132)
-++.||+|.|..
T Consensus 53 G~~~GD~V~Ig~ 64 (69)
T PF09269_consen 53 GAKEGDTVRIGD 64 (69)
T ss_dssp T--TT-EEEETT
T ss_pred CCCCCCEEEEcC
Confidence 588999999974
No 37
>smart00652 eIF1a eukaryotic translation initiation factor 1A.
Probab=24.48 E-value=2.4e+02 Score=19.41 Aligned_cols=55 Identities=13% Similarity=-0.009 Sum_probs=32.2
Q ss_pred EEEEEEEEecCCCCeEEEEEeEEEeeeeeeeEEeeeeeEEEEcCCCC----CCCCCCEEEEeecccCCCeeeE
Q 032855 43 RILAGTCHSAKMNRTIIVRRNYLHFVKKYQRYEKRHSNIPAHISPCF----RVKEGDHVIIGQCRPLSKTVRF 111 (132)
Q Consensus 43 k~l~G~VVS~Km~KTivV~v~~~~~hpkY~K~ikr~kky~vHD~e~n----~~kvGD~V~I~ecRPiSKtK~~ 111 (132)
....|+|+....+.-..|..+- -..++||-|... -.+.||.|.+. -+|..+.|-=
T Consensus 5 ~q~~g~V~~~lG~~~~~V~~~d-------------G~~~la~ipgK~Rk~iwI~~GD~VlVe-~~~~~~~kg~ 63 (83)
T smart00652 5 GQEIAQVVKMLGNGRLEVMCAD-------------GKERLARIPGKMRKKVWIRRGDIVLVD-PWDFQDVKAD 63 (83)
T ss_pred CcEEEEEEEEcCCCEEEEEECC-------------CCEEEEEEchhhcccEEEcCCCEEEEE-ecCCCCCEEE
Confidence 3467888888777777776331 122233332111 24569999985 5677765543
No 38
>PF07653 SH3_2: Variant SH3 domain; InterPro: IPR011511 SH3 (src Homology-3) domains are small protein modules containing approximately 50 amino acid residues [, ]. They are found in a great variety of intracellular or membrane-associated proteins [, , ] for example, in a variety of proteins with enzymatic activity, in adaptor proteins that lack catalytic sequences and in cytoskeletal proteins, such as fodrin and yeast actin binding protein ABP-1. The SH3 domain has a characteristic fold which consists of five or six beta-strands arranged as two tightly packed anti-parallel beta sheets. The linker regions may contain short helices []. The surface of the SH3-domain bears a flat, hydrophobic ligand-binding pocket which consists of three shallow grooves defined by conservative aromatic residues in which the ligand adopts an extended left-handed helical arrangement. The ligand binds with low affinity but this may be enhanced by multiple interactions. The region bound by the SH3 domain is in all cases proline-rich and contains PXXP as a core-conserved binding motif. The function of the SH3 domain is not well understood but they may mediate many diverse processes such as increasing local concentration of proteins, altering their subcellular location and mediating the assembly of large multiprotein complexes []. This entry represents a variant of the SH3 domain.; PDB: 1I1J_B 1K0X_A 1HJD_A 2KEA_A 1KJW_A 1JXM_A 1JXO_B 2EBP_A 2DL3_A 2EYX_A ....
Probab=24.15 E-value=47 Score=20.33 Aligned_cols=24 Identities=17% Similarity=0.065 Sum_probs=15.3
Q ss_pred eeeeEEEEcCCCCCCCCCCEEEEe
Q 032855 77 RHSNIPAHISPCFRVKEGDHVIIG 100 (132)
Q Consensus 77 r~kky~vHD~e~n~~kvGD~V~I~ 100 (132)
-...|.+-++....++.||+|.|.
T Consensus 4 a~~d~~~~~~~~Ls~~~Gd~i~v~ 27 (55)
T PF07653_consen 4 AIFDYVAEDPDELSFKKGDVIEVL 27 (55)
T ss_dssp ESSSBESSSTTB-EB-TTEEEEEE
T ss_pred EeEEECCCCCCceEEecCCEEEEE
Confidence 344555555445579999999998
No 39
>PF11347 DUF3148: Protein of unknown function (DUF3148); InterPro: IPR021495 This family of proteins has no known function.
Probab=23.83 E-value=59 Score=22.09 Aligned_cols=17 Identities=35% Similarity=0.415 Sum_probs=13.5
Q ss_pred CCCCEEEEeecccCCCe
Q 032855 92 KEGDHVIIGQCRPLSKT 108 (132)
Q Consensus 92 kvGD~V~I~ecRPiSKt 108 (132)
++||.|.+.+-.|.=||
T Consensus 1 ~iG~~V~l~~~ppylKT 17 (63)
T PF11347_consen 1 SIGDKVRLIEAPPYLKT 17 (63)
T ss_pred CCCCeEEEeecCCceec
Confidence 47999999988887665
No 40
>PRK05338 rplS 50S ribosomal protein L19; Provisional
Probab=23.72 E-value=1.6e+02 Score=22.01 Aligned_cols=20 Identities=25% Similarity=0.335 Sum_probs=16.1
Q ss_pred cEEEEEEEEec---CCCCeEEEE
Q 032855 42 GRILAGTCHSA---KMNRTIIVR 61 (132)
Q Consensus 42 ~k~l~G~VVS~---Km~KTivV~ 61 (132)
-+.++|+|++. .++.|++|+
T Consensus 39 ~q~f~GvvI~~~~~G~~~tftvR 61 (116)
T PRK05338 39 IQAFEGVVIARRGRGLNETFTVR 61 (116)
T ss_pred eccEEEEEEEEeCCCCCceEEEE
Confidence 45799999985 478888886
No 41
>COG0227 RpmB Ribosomal protein L28 [Translation, ribosomal structure and biogenesis]
Probab=23.59 E-value=74 Score=22.24 Aligned_cols=50 Identities=20% Similarity=0.267 Sum_probs=33.0
Q ss_pred CCCCCcceeeeecEEEEEEEEecCCCCeEEEEEeEEEeeeeeeeEEeeeeeEEEE
Q 032855 30 KKCPFTGTVSIRGRILAGTCHSAKMNRTIIVRRNYLHFVKKYQRYEKRHSNIPAH 84 (132)
Q Consensus 30 ~~cp~~g~~~vr~k~l~G~VVS~Km~KTivV~v~~~~~hpkY~K~ikr~kky~vH 84 (132)
..|..||. ....|-=+|.+|++|=.+-.+.+..+..|--...+..++.|-
T Consensus 3 r~C~lTGk-----~~~~GnnvShs~~kTkRr~~pNlq~~~~~~~~~g~~~~l~Vs 52 (77)
T COG0227 3 RRCQLTGK-----GPMSGNNVSHSHNKTKRRFLPNLQKVRFWSLSDGRFKRLRVS 52 (77)
T ss_pred ceeeeccc-----cccccccccccccccceeecCccEEEEEEEccCCcEEEEEEE
Confidence 45888887 344455589999998877666666555555555555555554
No 42
>smart00326 SH3 Src homology 3 domains. Src homology 3 (SH3) domains bind to target proteins through sequences containing proline and hydrophobic amino acids. Pro-containing polypeptides may bind to SH3 domains in 2 different binding orientations.
Probab=23.56 E-value=1.4e+02 Score=16.89 Aligned_cols=17 Identities=18% Similarity=0.229 Sum_probs=13.4
Q ss_pred CCCCCCCCCEEEEeecc
Q 032855 87 PCFRVKEGDHVIIGQCR 103 (132)
Q Consensus 87 e~n~~kvGD~V~I~ecR 103 (132)
....++.||.|.+.+..
T Consensus 17 ~~l~~~~Gd~v~v~~~~ 33 (58)
T smart00326 17 DELSFKKGDIITVLEKS 33 (58)
T ss_pred CCCCCCCCCEEEEEEcC
Confidence 34578999999988764
No 43
>PRK05753 nucleoside diphosphate kinase regulator; Provisional
Probab=23.53 E-value=2.1e+02 Score=21.25 Aligned_cols=30 Identities=20% Similarity=0.166 Sum_probs=23.6
Q ss_pred CCCCCCEEEEeecccCCCeeeEEEEEeeecCC
Q 032855 90 RVKEGDHVIIGQCRPLSKTVRFNVLKVIPAGS 121 (132)
Q Consensus 90 ~~kvGD~V~I~ecRPiSKtK~~~V~~Ii~k~~ 121 (132)
-.++||.|.+. .|-.....+.|.+|.....
T Consensus 101 G~~~Gd~v~v~--~p~G~~~~~~I~~I~y~p~ 130 (137)
T PRK05753 101 GLSVGQSIDWP--LPGGKETHLEVLEVEYQPE 130 (137)
T ss_pred CCCCCCEEEEE--CCCCCEEEEEEEEEEeCCc
Confidence 57899999987 5655567899999986654
No 44
>cd04451 S1_IF1 S1_IF1: Translation Initiation Factor IF1, S1-like RNA-binding domain. IF1 contains an S1-like RNA-binding domain, which is found in a wide variety of RNA-associated proteins. Translation initiation includes a number of interrelated steps preceding the formation of the first peptide bond. In Escherichia coli, the initiation mechanism requires, in addition to mRNA, fMet-tRNA, and ribosomal subunits, the presence of three additional proteins (initiation factors IF1, IF2, and IF3) and at least one GTP molecule. The three initiation factors influence both the kinetics and the stability of ternary complex formation. IF1 is the smallest of the three factors. IF1 enhances the rate of 70S ribosome subunit association and dissociation and the interaction of 30S ribosomal subunit with IF2 and IF3. It stimulates 30S complex formation. In addition, by binding to the A-site of the 30S ribosomal subunit, IF1 may contribute to the fidelity of the selection of the initiation site of th
Probab=23.49 E-value=2e+02 Score=18.17 Aligned_cols=48 Identities=17% Similarity=0.111 Sum_probs=26.8
Q ss_pred EEEEEEecCCCCeEEEEEeEEEeeeeeeeEEeeeeeEEEEcCCCCCCCCCCEEEEe
Q 032855 45 LAGTCHSAKMNRTIIVRRNYLHFVKKYQRYEKRHSNIPAHISPCFRVKEGDHVIIG 100 (132)
Q Consensus 45 l~G~VVS~Km~KTivV~v~~~~~hpkY~K~ikr~kky~vHD~e~n~~kvGD~V~I~ 100 (132)
..|+|++.-...-..|..+ -...|....+..-+ + ..+.+.+||.|.+.
T Consensus 3 ~~G~Vi~~~~g~~~~V~~~---~g~~~~c~~rGklr---~--~~~~~~vGD~V~~~ 50 (64)
T cd04451 3 MEGVVTEALPNAMFRVELE---NGHEVLAHISGKMR---M--NYIRILPGDRVKVE 50 (64)
T ss_pred EEEEEEEEeCCCEEEEEeC---CCCEEEEEECceee---c--CCcccCCCCEEEEE
Confidence 5677776553334444321 12355555555433 2 23458999999877
No 45
>cd04089 eRF3_II eRF3_II: domain II of the eukaryotic class II release factor (eRF3). In eukaryotes, translation termination is mediated by two interacting release factors, eRF1 and eRF3, which act as class I and II factors, respectively. eRF1 functions as an omnipotent release factor, decoding all three stop codons and triggering the release of the nascent peptide catalyzed by the ribsome. eRF3 is a GTPase, which enhances the termination efficiency by stimulating the eRF1 activity in a GTP-dependent manner. Sequence comparison of class II release factors with elongation factors shows that eRF3 is more similar to eEF1alpha whereas prokaryote RF3 is more similar to EF-G, implying that their precise function may differ. Only eukaryote RF3s are found in this group. Saccharomyces cerevisiae eRF3 (Sup35p) is a translation termination factor which is divided into three regions N, M and a C-terminal eEF1a-like region essential for translation termination. Sup35NM is a non-pathogenic prion-li
Probab=23.42 E-value=2.3e+02 Score=18.67 Aligned_cols=25 Identities=12% Similarity=0.026 Sum_probs=18.6
Q ss_pred eeeeeEEEEcCCCCCCCCCCEEEEe
Q 032855 76 KRHSNIPAHISPCFRVKEGDHVIIG 100 (132)
Q Consensus 76 kr~kky~vHD~e~n~~kvGD~V~I~ 100 (132)
-.-+.+..|+.+.+++..||.|.|.
T Consensus 41 ~~V~si~~~~~~~~~a~aGd~v~l~ 65 (82)
T cd04089 41 VEVLSIYNEDVEVRYARPGENVRLR 65 (82)
T ss_pred EEEEEEEECCEECCEECCCCEEEEE
Confidence 3445566777677789999999874
No 46
>cd05793 S1_IF1A S1_IF1A: Translation initiation factor IF1A, also referred to as eIF1A in eukaryotes and aIF1A in archaea, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. IF1A is essential for translation initiation. eIF1A acts synergistically with eIF1 to mediate assembly of ribosomal initiation complexes at the initiation codon and maintain the accuracy of this process by recognizing and destabilizing aberrant preinitiation complexes from the mRNA. Without eIF1A and eIF1, 43S ribosomal preinitiation complexes can bind to the cap-proximal region, but are unable to reach the initiation codon. eIF1a also enhances the formation of 5'-terminal complexes in the presence of other translation initiation factors. This protein family is only found in eukaryotes and archaea.
Probab=22.73 E-value=2.6e+02 Score=19.03 Aligned_cols=53 Identities=17% Similarity=0.051 Sum_probs=31.9
Q ss_pred EEEEEEecCCCCeEEEEEeEEEeeeeeeeEEeeeeeEEEEcCCCC----CCCCCCEEEEeecccCCCeeeE
Q 032855 45 LAGTCHSAKMNRTIIVRRNYLHFVKKYQRYEKRHSNIPAHISPCF----RVKEGDHVIIGQCRPLSKTVRF 111 (132)
Q Consensus 45 l~G~VVS~Km~KTivV~v~~~~~hpkY~K~ikr~kky~vHD~e~n----~~kvGD~V~I~ecRPiSKtK~~ 111 (132)
..|+|+....+....|..+-- ..++||-|... -.+.||.|.+. -+|..++|-=
T Consensus 2 ~~g~V~~~~g~~~~~V~~~~g-------------~~~la~i~gK~rk~iwI~~GD~V~Ve-~~~~d~~kg~ 58 (77)
T cd05793 2 EYGQVEKMLGNGRLEVRCFDG-------------KKRLCRIRGKMRKRVWINEGDIVLVA-PWDFQDDKAD 58 (77)
T ss_pred EEEEEEEEcCCCEEEEEECCC-------------CEEEEEEchhhcccEEEcCCCEEEEE-eccccCCEEE
Confidence 468888887777777764321 12334432111 24569999976 5677776643
No 47
>cd04460 S1_RpoE S1_RpoE: RpoE, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. RpoE is subunit E of archaeal RNA polymerase. Archaeal cells contain a single RNA polymerase made up of 12 subunits, which are homologous to the 12 subunits (RPB1-12) of eukaryotic RNA polymerase II. RpoE is homologous to Rpa43 of eukaryotic RNA polymerase I, RPB7 of eukaryotic RNA polymerase II, and Rpc25 of eukaryotic RNA polymerase III. RpoE is composed of two domains, the N-terminal RNP (ribonucleoprotein) domain and the C-terminal S1 domain. This S1 domain binds ssRNA and ssDNA. This family is classified based on the C-terminal S1 domain. The function of RpoE is not fully understood. In eukaryotes, RPB7 and RPB4 form a heterodimer that reversibly associates with the RNA polymerase II core.
Probab=22.39 E-value=2.6e+02 Score=18.97 Aligned_cols=13 Identities=31% Similarity=0.095 Sum_probs=10.0
Q ss_pred CCCCCCCCEEEEe
Q 032855 88 CFRVKEGDHVIIG 100 (132)
Q Consensus 88 ~n~~kvGD~V~I~ 100 (132)
....++||.|.+.
T Consensus 51 ~~~~~~Gd~v~vk 63 (99)
T cd04460 51 KRVLKVGDVVRAR 63 (99)
T ss_pred CCEECCCCEEEEE
Confidence 4568999998764
No 48
>smart00357 CSP Cold shock protein domain. RNA-binding domain that functions as a RNA-chaperone in bacteria and is involved in regulating translation in eukaryotes. Contains sub-family of RNA-binding domains in the Rho transcription termination factor.
Probab=21.30 E-value=1.7e+02 Score=17.35 Aligned_cols=26 Identities=27% Similarity=0.365 Sum_probs=17.8
Q ss_pred eeEEEEcCC----CCCCCCCCEEEEeeccc
Q 032855 79 SNIPAHISP----CFRVKEGDHVIIGQCRP 104 (132)
Q Consensus 79 kky~vHD~e----~n~~kvGD~V~I~ecRP 104 (132)
..+++|.+. .+.+..||.|.+.-..|
T Consensus 21 ~~i~v~~~~~~~~~~~~~~Gd~V~~~i~~~ 50 (64)
T smart00357 21 KDVFVHPSQIQGGLKSLREGDEVEFKVVSP 50 (64)
T ss_pred ccEEEEhHHhhcCCCcCCCCCEEEEEEEEc
Confidence 366677522 35688899999886554
No 49
>PF02887 PK_C: Pyruvate kinase, alpha/beta domain; InterPro: IPR015795 Pyruvate kinase (2.7.1.40 from EC) (PK) catalyses the final step in glycolysis [], the conversion of phosphoenolpyruvate to pyruvate with concomitant phosphorylation of ADP to ATP: ADP + phosphoenolpyruvate = ATP + pyruvate The enzyme, which is found in all living organisms, requires both magnesium and potassium ions for its activity. In vertebrates, there are four tissue-specific isozymes: L (liver), R (red cells), M1 (muscle, heart and brain), and M2 (early foetal tissue). In plants, PK exists as cytoplasmic and plastid isozymes, while most bacteria and lower eukaryotes have one form, except in certain bacteria, such as Escherichia coli, that have two isozymes. All isozymes appear to be tetramers of identical subunits of ~500 residues. PK helps control the rate of glycolysis, along with phosphofructokinase (IPR000023 from INTERPRO) and hexokinase (IPR001312 from INTERPRO). PK possesses allosteric sites for numerous effectors, yet the isozymes respond differently, in keeping with their different tissue distributions []. The activity of L-type (liver) PK is increased by fructose-1,6-bisphosphate (F1,6BP) and lowered by ATP and alanine (gluconeogenic precursor), therefore when glucose levels are high, glycolysis is promoted, and when levels are low, gluconeogenesis is promoted. L-type PK is also hormonally regulated, being activated by insulin and inhibited by glucagon, which covalently modifies the PK enzyme. M1-type (muscle, brain) PK is inhibited by ATP, but F1,6BP and alanine have no effect, which correlates with the function of muscle and brain, as opposed to the liver. The structure of several pyruvate kinases from various organisms have been determined [, ]. The protein comprises three-four domains: a small N-terminal helical domain (absent in bacterial PK), a beta/alpha-barrel domain, a beta-barrel domain (inserted within the beta/alpha-barrel domain), and a 3-layer alpha/beta/alpha sandwich domain. This entry represents the 3-layer alpha/beta/alpha sandwich domain. This domain has a similar topology to the archaeal hypothetical protein, MTH1675 from Methanobacterium thermoautotrophicum.; PDB: 3QTG_B 1VP8_A 1T57_C 3N25_A 1AQF_C 2G50_B 1F3X_G 1A5U_F 1A49_E 1F3W_C ....
Probab=20.92 E-value=1.6e+02 Score=20.68 Aligned_cols=29 Identities=24% Similarity=0.357 Sum_probs=22.0
Q ss_pred CCCCCCCEEEEeecccCCCeeeEEEEEee
Q 032855 89 FRVKEGDHVIIGQCRPLSKTVRFNVLKVI 117 (132)
Q Consensus 89 n~~kvGD~V~I~ecRPiSKtK~~~V~~Ii 117 (132)
.-++.||.|.+....|......-...+|+
T Consensus 88 g~~~~gd~vVv~~g~~~~~~g~tn~~~v~ 116 (117)
T PF02887_consen 88 GLLKPGDKVVVVAGMPFGTPGGTNTIRVV 116 (117)
T ss_dssp TSS-TTSEEEEEEESSTTTTSSEEEEEEE
T ss_pred CCCCCCCEEEEEeCCCCCCCCCCEEEEEE
Confidence 45899999999999888776666666654
No 50
>cd05698 S1_Rrp5_repeat_hs6_sc5 S1_Rrp5_repeat_hs6_sc5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 6 (hs6) and S. cerevisiae S1 repeat 5 (sc5). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=20.78 E-value=89 Score=19.46 Aligned_cols=58 Identities=19% Similarity=0.200 Sum_probs=31.7
Q ss_pred cEEEEEEEEecCCCCeEEEEEeEEEeeeeeeeEEeee---eeEEEEcCCCCCCCCCCEEEEe--ecccCCC
Q 032855 42 GRILAGTCHSAKMNRTIIVRRNYLHFVKKYQRYEKRH---SNIPAHISPCFRVKEGDHVIIG--QCRPLSK 107 (132)
Q Consensus 42 ~k~l~G~VVS~Km~KTivV~v~~~~~hpkY~K~ikr~---kky~vHD~e~n~~kvGD~V~I~--ecRPiSK 107 (132)
|.++.|+|++.. +.-+.|..... ..-++..+ ..+ ++| +....++||.|.+. +.-|-++
T Consensus 1 g~~~~g~V~~v~-~~G~~V~l~~~-----~~gli~~s~l~~~~-~~~-~~~~~~~G~~i~v~v~~~d~~~~ 63 (70)
T cd05698 1 GLKTHGTIVKVK-PNGCIVSFYNN-----VKGFLPKSELSEAF-IKD-PEEHFRVGQVVKVKVLSCDPEQQ 63 (70)
T ss_pred CCEEEEEEEEEe-cCcEEEEECCC-----CEEEEEHHHcChhh-cCC-HHHcccCCCEEEEEEEEEcCCCC
Confidence 456788888775 66777775321 11121111 111 445 45679999998764 4444433
No 51
>PF09926 DUF2158: Uncharacterized small protein (DUF2158); InterPro: IPR019226 This entry represents a family of predominantly prokaryotic proteins with no known function.
Probab=20.57 E-value=71 Score=20.59 Aligned_cols=13 Identities=38% Similarity=0.457 Sum_probs=11.1
Q ss_pred CCCCEEEEeeccc
Q 032855 92 KEGDHVIIGQCRP 104 (132)
Q Consensus 92 kvGD~V~I~ecRP 104 (132)
++||+|.+.+.=|
T Consensus 2 ~~GDvV~LKSGGp 14 (53)
T PF09926_consen 2 KIGDVVQLKSGGP 14 (53)
T ss_pred CCCCEEEEccCCC
Confidence 6899999998766
No 52
>PF08980 DUF1883: Domain of unknown function (DUF1883); InterPro: IPR015073 This family consist of hypothetical bacterial proteins. ; PDB: 2B1Y_A.
Probab=20.46 E-value=38 Score=24.54 Aligned_cols=19 Identities=21% Similarity=0.200 Sum_probs=1.9
Q ss_pred eEEEEcCCCCCCCCCCEEEEe
Q 032855 80 NIPAHISPCFRVKEGDHVIIG 100 (132)
Q Consensus 80 ky~vHD~e~n~~kvGD~V~I~ 100 (132)
+|..|| ...++.||+|.|.
T Consensus 2 ~~~~~~--~~~~~~Gd~V~V~ 20 (94)
T PF08980_consen 2 KFIHYD--LGHLKRGDTVVVR 20 (94)
T ss_dssp -------------TT------
T ss_pred ceeeec--hhccCCCCEEEEE
Confidence 355676 5689999999986
No 53
>COG0853 PanD Aspartate 1-decarboxylase [Coenzyme metabolism]
Probab=20.29 E-value=85 Score=23.99 Aligned_cols=17 Identities=41% Similarity=0.432 Sum_probs=14.5
Q ss_pred CCCCCCEEEEeecccCC
Q 032855 90 RVKEGDHVIIGQCRPLS 106 (132)
Q Consensus 90 ~~kvGD~V~I~ecRPiS 106 (132)
-+++||.|+|...-.+|
T Consensus 77 l~~~GD~VII~sy~~~~ 93 (126)
T COG0853 77 LVQVGDLVIIMSYAQMS 93 (126)
T ss_pred hCCCCCEEEEEEcccCC
Confidence 48999999999877775
No 54
>PRK10862 SoxR reducing system protein RseC; Provisional
Probab=20.15 E-value=1.2e+02 Score=23.17 Aligned_cols=52 Identities=13% Similarity=0.092 Sum_probs=28.1
Q ss_pred EEEEEecCCCCeEEEEEeEEEe-----------eeeeeeEE-eeeeeEEEEcCCCCCCCCCCEEEEe
Q 032855 46 AGTCHSAKMNRTIIVRRNYLHF-----------VKKYQRYE-KRHSNIPAHISPCFRVKEGDHVIIG 100 (132)
Q Consensus 46 ~G~VVS~Km~KTivV~v~~~~~-----------hpkY~K~i-kr~kky~vHD~e~n~~kvGD~V~I~ 100 (132)
.|+|++.. +..+.|+..+.-- +....|.. .++..+.+.. ...+++||.|.|.
T Consensus 5 ~~~Vv~v~-~~~a~Ve~~r~saCg~C~a~~gCG~~~l~~~~~~~~~~~~v~~--~~~~~vGD~V~v~ 68 (154)
T PRK10862 5 WATVVSWQ-NGIALLRCEVKAGCSSCASRAGCGSRLLNKLGPQTTHQLVVPS--SQPLVPGQKVELG 68 (154)
T ss_pred EEEEEEEE-CCEEEEEEecCCCCcCcCCCCCchhhHHHHhcCCCceEEEecC--CCCCCCCCEEEEe
Confidence 57777764 3456666554320 00111111 1234455665 3568999999985
Done!