Query 041511
Match_columns 147
No_of_seqs 109 out of 1038
Neff 4.3
Searched_HMMs 46136
Date Fri Mar 29 07:56:03 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/041511.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/041511hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG0186 RpsQ Ribosomal protein 100.0 5.4E-35 1.2E-39 211.3 11.4 82 39-120 5-86 (87)
2 CHL00142 rps17 ribosomal prote 100.0 1.7E-34 3.7E-39 207.3 11.8 80 42-121 3-82 (84)
3 PRK05610 rpsQ 30S ribosomal pr 100.0 3.4E-34 7.4E-39 205.4 12.0 78 42-119 6-83 (84)
4 PRK08572 rps17p 30S ribosomal 100.0 1.6E-33 3.6E-38 210.4 11.6 81 39-119 26-107 (108)
5 TIGR03630 arch_S17P archaeal r 100.0 3.9E-33 8.5E-38 206.6 10.9 78 39-116 24-102 (102)
6 TIGR03635 S17_bact 30S ribosom 100.0 1.2E-32 2.6E-37 192.0 9.8 70 43-112 2-71 (71)
7 PF00366 Ribosomal_S17: Riboso 100.0 9.2E-32 2E-36 186.2 9.0 69 47-115 1-69 (69)
8 PTZ00241 40S ribosomal protein 100.0 1.2E-30 2.6E-35 205.8 11.1 82 38-119 64-146 (158)
9 KOG1740 Predicted mitochondria 100.0 9.8E-32 2.1E-36 199.3 1.3 95 42-136 2-96 (107)
10 KOG1728 40S ribosomal protein 99.8 2.9E-22 6.4E-27 156.3 3.4 84 38-121 64-149 (156)
11 KOG3447 Mitochondrial/chloropl 99.7 1.4E-18 3E-23 135.1 2.5 98 33-130 1-99 (150)
12 PF10844 DUF2577: Protein of u 71.2 36 0.00078 24.6 8.1 63 43-114 18-98 (100)
13 TIGR00523 eIF-1A eukaryotic/ar 69.2 31 0.00068 25.4 6.9 49 43-105 19-72 (99)
14 cd05793 S1_IF1A S1_IF1A: Trans 68.3 24 0.00052 24.7 5.9 51 45-109 2-57 (77)
15 smart00652 eIF1a eukaryotic tr 67.9 27 0.00057 24.8 6.1 52 44-109 6-62 (83)
16 PTZ00329 eukaryotic translatio 64.8 53 0.0012 26.3 7.9 57 44-114 33-94 (155)
17 PLN00208 translation initiatio 63.7 63 0.0014 25.6 8.0 57 44-114 33-94 (145)
18 cd04451 S1_IF1 S1_IF1: Transla 58.1 49 0.0011 21.6 5.7 50 44-100 2-51 (64)
19 cd04456 S1_IF1A_like S1_IF1A_l 57.7 47 0.001 23.3 5.8 51 45-109 2-58 (78)
20 cd01854 YjeQ_engC YjeQ/EngC. 55.5 44 0.00096 28.0 6.3 38 87-128 32-69 (287)
21 PRK04012 translation initiatio 54.0 52 0.0011 24.3 5.8 52 43-108 21-77 (100)
22 cd05791 S1_CSL4 S1_CSL4: CSL4, 47.8 34 0.00074 24.2 3.9 60 39-99 4-70 (92)
23 cd01342 Translation_Factor_II_ 45.3 70 0.0015 19.5 4.9 57 39-100 12-69 (83)
24 PF13550 Phage-tail_3: Putativ 45.0 48 0.001 24.3 4.5 36 78-116 128-163 (164)
25 PF11302 DUF3104: Protein of u 43.7 50 0.0011 23.6 4.1 37 89-125 5-43 (75)
26 cd03693 EF1_alpha_II EF1_alpha 43.6 64 0.0014 22.3 4.7 53 40-99 17-70 (91)
27 cd03695 CysN_NodQ_II CysN_NodQ 40.7 49 0.0011 22.6 3.7 49 44-99 17-66 (81)
28 PRK10413 hydrogenase 2 accesso 39.5 1.2E+02 0.0027 21.6 5.7 51 46-105 6-58 (82)
29 cd04092 mtEFG2_II_like mtEFG2_ 37.8 83 0.0018 21.1 4.4 56 39-100 12-71 (83)
30 cd03690 Tet_II Tet_II: This su 37.4 1E+02 0.0022 21.1 4.9 57 38-101 14-74 (85)
31 cd03698 eRF3_II_like eRF3_II_l 37.2 57 0.0012 22.1 3.6 52 41-99 14-66 (83)
32 PRK12442 translation initiatio 36.8 1.7E+02 0.0036 21.4 6.5 53 43-108 7-64 (87)
33 PRK10862 SoxR reducing system 35.6 73 0.0016 24.8 4.4 53 45-99 4-68 (154)
34 cd03696 selB_II selB_II: this 35.1 1.1E+02 0.0023 20.6 4.7 52 41-99 14-66 (83)
35 PF06107 DUF951: Bacterial pro 34.6 65 0.0014 21.9 3.4 25 90-115 2-26 (57)
36 cd03697 EFTU_II EFTU_II: Elong 34.4 1.3E+02 0.0028 20.5 5.1 54 41-99 14-68 (87)
37 PRK00276 infA translation init 33.9 1.5E+02 0.0033 20.0 7.8 59 43-109 7-65 (72)
38 cd04466 S1_YloQ_GTPase S1_YloQ 33.9 67 0.0015 20.5 3.3 29 88-120 36-64 (68)
39 PRK11637 AmiB activator; Provi 33.7 91 0.002 27.6 5.1 80 45-125 329-422 (428)
40 TIGR03595 Obg_CgtA_exten Obg f 33.0 29 0.00063 23.6 1.5 13 89-101 53-65 (69)
41 cd03694 GTPBP_II Domain II of 31.8 70 0.0015 22.0 3.3 55 40-99 13-70 (87)
42 KOG1698 Mitochondrial/chloropl 31.6 59 0.0013 27.2 3.4 35 80-116 89-123 (201)
43 PRK01889 GTPase RsgA; Reviewed 31.3 1.7E+02 0.0036 25.5 6.3 73 45-128 29-101 (356)
44 COG0361 InfA Translation initi 30.2 2E+02 0.0044 20.4 5.6 46 43-101 7-58 (75)
45 cd04088 EFG_mtEFG_II EFG_mtEFG 29.6 1.5E+02 0.0032 19.6 4.6 58 39-100 12-71 (83)
46 TIGR00008 infA translation ini 28.9 2E+02 0.0044 19.9 6.3 51 44-108 6-62 (68)
47 cd03699 lepA_II lepA_II: This 28.8 1.5E+02 0.0034 20.0 4.7 54 39-99 12-69 (86)
48 PF04246 RseC_MucC: Positive r 28.5 63 0.0014 24.0 2.8 21 79-100 42-62 (135)
49 PRK05753 nucleoside diphosphat 27.9 1.4E+02 0.0031 22.7 4.7 27 89-117 101-127 (137)
50 PF13567 DUF4131: Domain of un 27.2 2.3E+02 0.0049 20.0 7.1 62 43-107 78-147 (176)
51 TIGR00157 ribosome small subun 27.0 83 0.0018 25.8 3.5 38 91-132 2-39 (245)
52 PF09926 DUF2158: Uncharacteri 26.8 48 0.001 21.9 1.7 13 91-103 2-14 (53)
53 PF09269 DUF1967: Domain of un 26.7 33 0.00072 23.3 0.9 12 89-100 53-64 (69)
54 cd03689 RF3_II RF3_II: this su 25.5 2.2E+02 0.0049 19.5 5.0 14 88-101 60-73 (85)
55 cd04454 S1_Rrp4_like S1_Rrp4_l 25.5 2.1E+02 0.0045 19.0 5.0 58 39-102 4-63 (82)
56 PF07347 CI-B14_5a: NADH:ubiqu 25.2 50 0.0011 24.6 1.7 29 2-30 26-63 (97)
57 cd05789 S1_Rrp4 S1_Rrp4: Rrp4 25.2 1.5E+02 0.0032 19.8 4.0 57 39-101 4-66 (86)
58 COG2012 RPB5 DNA-directed RNA 25.2 42 0.00091 24.3 1.3 21 80-100 42-65 (80)
59 cd05698 S1_Rrp5_repeat_hs6_sc5 23.7 84 0.0018 20.0 2.4 51 43-99 2-54 (70)
60 PRK10409 hydrogenase assembly 23.0 58 0.0013 23.8 1.7 18 88-105 40-57 (90)
61 PF01938 TRAM: TRAM domain; I 23.0 2.1E+02 0.0045 18.1 4.8 42 55-99 5-47 (61)
62 PF10377 ATG11: Autophagy-rela 22.9 1.1E+02 0.0023 23.3 3.2 15 89-103 42-56 (129)
63 cd04089 eRF3_II eRF3_II: domai 22.3 1.4E+02 0.0031 20.1 3.5 50 42-98 14-64 (82)
64 KOG3507 DNA-directed RNA polym 22.0 45 0.00098 23.1 0.9 15 87-101 29-43 (62)
65 smart00357 CSP Cold shock prot 21.2 1.8E+02 0.004 17.6 3.6 25 79-103 21-50 (64)
66 cd05692 S1_RPS1_repeat_hs4 S1_ 21.1 1.5E+02 0.0033 18.0 3.2 51 43-99 2-54 (69)
67 PF08605 Rad9_Rad53_bind: Fung 20.7 1.1E+02 0.0024 23.6 2.9 61 41-118 21-83 (131)
68 COG3655 Predicted transcriptio 20.1 56 0.0012 23.2 1.1 12 89-100 56-67 (73)
No 1
>COG0186 RpsQ Ribosomal protein S17 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=5.4e-35 Score=211.31 Aligned_cols=82 Identities=48% Similarity=0.750 Sum_probs=79.0
Q ss_pred cCccceEEEEEEeCCCCceEEEEEeeEEeecceeeEEeeeceEEEECCCCCCCCCCEEEEeecCcCCcceeEEEEEEEec
Q 041511 39 PSQMKSVVGLVVSNKMQKSVVVAVDRLFHHKVYNRYVKRTSKFMAHDENNECNIGDRVRLDPSRPLSKHKHWLVAEILKK 118 (147)
Q Consensus 39 ~~~~k~l~G~VVS~km~KTvvV~V~r~~~hpkY~K~i~r~kK~~vHDp~n~~kvGDiV~I~ecRPiSK~K~f~V~eIi~k 118 (147)
+.+++.|+|+|+|++|+|||+|.+++.++||+|+||+++++||+||||+++|++||+|+|+|||||||+|+|+|++|+++
T Consensus 5 ~~~~k~l~G~VvS~Km~KTvvV~ve~~~~hp~Y~K~v~r~kK~~aHde~~~~k~GD~V~I~EtRPLSKtK~~~vv~i~~~ 84 (87)
T COG0186 5 RVRGRVLEGVVVSDKMDKTVVVEVERKVYHPKYGKYVRRSKKYHAHDECNEAKVGDIVRIAETRPLSKTKRFVVVEIVEK 84 (87)
T ss_pred ccCceEEEEEEEEccCceeEEEEEEEEEecccceEEEEEEeeeEeecccccCCCCCEEEEEEccccCCcceEEEEEEeee
Confidence 56788999999999999999999999999999999999999999999999999999999999999999999999999987
Q ss_pred cc
Q 041511 119 AR 120 (147)
Q Consensus 119 ~~ 120 (147)
+.
T Consensus 85 a~ 86 (87)
T COG0186 85 AV 86 (87)
T ss_pred cc
Confidence 64
No 2
>CHL00142 rps17 ribosomal protein S17; Validated
Probab=100.00 E-value=1.7e-34 Score=207.27 Aligned_cols=80 Identities=49% Similarity=0.944 Sum_probs=77.3
Q ss_pred cceEEEEEEeCCCCceEEEEEeeEEeecceeeEEeeeceEEEECCCCCCCCCCEEEEeecCcCCcceeEEEEEEEecccc
Q 041511 42 MKSVVGLVVSNKMQKSVVVAVDRLFHHKVYNRYVKRTSKFMAHDENNECNIGDRVRLDPSRPLSKHKHWLVAEILKKARI 121 (147)
Q Consensus 42 ~k~l~G~VVS~km~KTvvV~V~r~~~hpkY~K~i~r~kK~~vHDp~n~~kvGDiV~I~ecRPiSK~K~f~V~eIi~k~~~ 121 (147)
.+.|+|+|+|++|+|||+|+|++++|||+|+|+++++++|+||||+|+|++||+|+|+|||||||+|+|.|.+|+++++.
T Consensus 3 ~~~~~G~Vvs~km~KTivV~v~r~~~h~kY~K~~~r~kk~~aHDe~n~~~~GD~V~I~e~RPlSKtK~~~v~~i~~~~~~ 82 (84)
T CHL00142 3 VKEKIGIVVSNKMNKTIVVAVENRYKHPIYGKIITKTKKYLVHDEENECNIGDQVLIEETRPLSKTKRWILKEILSKSSL 82 (84)
T ss_pred ceEEEEEEEeCCCCceEEEEEEEEEEcCcccEEEEeeEEEEEeCCCCCCCCCCEEEEEEcCCCCCcEEEEEEEEEEeeec
Confidence 46799999999999999999999999999999999999999999999999999999999999999999999999998764
No 3
>PRK05610 rpsQ 30S ribosomal protein S17; Reviewed
Probab=100.00 E-value=3.4e-34 Score=205.44 Aligned_cols=78 Identities=53% Similarity=0.829 Sum_probs=76.2
Q ss_pred cceEEEEEEeCCCCceEEEEEeeEEeecceeeEEeeeceEEEECCCCCCCCCCEEEEeecCcCCcceeEEEEEEEecc
Q 041511 42 MKSVVGLVVSNKMQKSVVVAVDRLFHHKVYNRYVKRTSKFMAHDENNECNIGDRVRLDPSRPLSKHKHWLVAEILKKA 119 (147)
Q Consensus 42 ~k~l~G~VVS~km~KTvvV~V~r~~~hpkY~K~i~r~kK~~vHDp~n~~kvGDiV~I~ecRPiSK~K~f~V~eIi~k~ 119 (147)
++.|+|+|+|++|+||++|+|++++|||+|+||++++++|+||||+|+|++||+|+|+|||||||+|+|+|.+|++++
T Consensus 6 ~~~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 6 RKTLQGRVVSDKMDKTIVVLVERRVKHPLYGKIVKRSKKYHAHDENNEAKIGDVVRIMETRPLSKTKRWRLVEIVEKA 83 (84)
T ss_pred CCEEEEEEEcccCCceEEEEEEEEEEeccccEEEEcceEEEEECCCCCCCCCCEEEEEEcccCCCCEEEEEEEEEecc
Confidence 578999999999999999999999999999999999999999999999999999999999999999999999999875
No 4
>PRK08572 rps17p 30S ribosomal protein S17P; Reviewed
Probab=100.00 E-value=1.6e-33 Score=210.43 Aligned_cols=81 Identities=40% Similarity=0.608 Sum_probs=78.0
Q ss_pred cCccceEEEEEEeCCCCceEEEEEeeEEeecceeeEEeeeceEEEECCC-CCCCCCCEEEEeecCcCCcceeEEEEEEEe
Q 041511 39 PSQMKSVVGLVVSNKMQKSVVVAVDRLFHHKVYNRYVKRTSKFMAHDEN-NECNIGDRVRLDPSRPLSKHKHWLVAEILK 117 (147)
Q Consensus 39 ~~~~k~l~G~VVS~km~KTvvV~V~r~~~hpkY~K~i~r~kK~~vHDp~-n~~kvGDiV~I~ecRPiSK~K~f~V~eIi~ 117 (147)
+.+++.|+|+|+|++|+|||+|+|+++++||+|+|+++++++|+||||+ |+|++||+|+|+|||||||+|+|.|.+|++
T Consensus 26 ~irgk~l~G~VvS~Km~KTvvV~v~r~~~hpkY~K~i~r~kky~aHDe~cn~~kvGD~V~I~E~RPiSKtK~w~v~~i~~ 105 (108)
T PRK08572 26 PVRGQVLEGTVVSDKMHKTVVVEREYLHYVPKYERYEKRRSRIHAHNPPCIDAKVGDKVKIAECRPLSKTKSFVVVEKKE 105 (108)
T ss_pred eeeeEEEEEEEEecCCCceEEEEEEEEEecCCccEEEEEeeeEEEECCCCCCCCCCCEEEEEEcCCCCCceEEEEEEEEE
Confidence 4567899999999999999999999999999999999999999999999 799999999999999999999999999998
Q ss_pred cc
Q 041511 118 KA 119 (147)
Q Consensus 118 k~ 119 (147)
++
T Consensus 106 ~~ 107 (108)
T PRK08572 106 RA 107 (108)
T ss_pred cC
Confidence 75
No 5
>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=3.9e-33 Score=206.63 Aligned_cols=78 Identities=37% Similarity=0.554 Sum_probs=75.3
Q ss_pred cCccceEEEEEEeCCCCceEEEEEeeEEeecceeeEEeeeceEEEECCC-CCCCCCCEEEEeecCcCCcceeEEEEEEE
Q 041511 39 PSQMKSVVGLVVSNKMQKSVVVAVDRLFHHKVYNRYVKRTSKFMAHDEN-NECNIGDRVRLDPSRPLSKHKHWLVAEIL 116 (147)
Q Consensus 39 ~~~~k~l~G~VVS~km~KTvvV~V~r~~~hpkY~K~i~r~kK~~vHDp~-n~~kvGDiV~I~ecRPiSK~K~f~V~eIi 116 (147)
+.+++.|+|+|+|++|+|||+|+|+|+++||+|+|+++++++|+||||+ |+|++||+|+|+|||||||+|+|.|.+|+
T Consensus 24 ~irgk~l~G~VvS~Km~KTivV~V~r~~~hpkY~K~i~r~kky~aHDe~cn~~kvGD~V~I~E~RPlSKtK~w~vv~i~ 102 (102)
T TIGR03630 24 KVRGQILEGVVVSDKMNKTVVVEREYLYYDRKYERYERRRSKIHAHNPPCIDVKEGDIVIIGETRPLSKTKSFVVLGKV 102 (102)
T ss_pred eeeeEEEEEEEEecCCCceEEEEEEEEEecCCccEEEEEeeeEEEECCCCCCCCCCCEEEEEEcCCCCCceEEEEEEeC
Confidence 5578899999999999999999999999999999999999999999999 79999999999999999999999999985
No 6
>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=1.2e-32 Score=192.00 Aligned_cols=70 Identities=54% Similarity=0.922 Sum_probs=68.6
Q ss_pred ceEEEEEEeCCCCceEEEEEeeEEeecceeeEEeeeceEEEECCCCCCCCCCEEEEeecCcCCcceeEEE
Q 041511 43 KSVVGLVVSNKMQKSVVVAVDRLFHHKVYNRYVKRTSKFMAHDENNECNIGDRVRLDPSRPLSKHKHWLV 112 (147)
Q Consensus 43 k~l~G~VVS~km~KTvvV~V~r~~~hpkY~K~i~r~kK~~vHDp~n~~kvGDiV~I~ecRPiSK~K~f~V 112 (147)
+.|+|+|+|++|+||++|+|++++|||+|+|+++++++|+||||+|+|++||+|+|+|||||||+|+|.|
T Consensus 2 ~~l~G~Vvs~km~KTvvV~v~~~~~h~ky~k~~~r~kk~~aHD~~~~~k~GD~V~I~ecrPlSK~K~~~~ 71 (71)
T TIGR03635 2 KTLQGVVVSDKMDKTIVVLVERRVKHPLYGKIVKRTKKYHAHDENNECKVGDVVRIIETRPLSKTKRWRL 71 (71)
T ss_pred eEEEEEEEcccCCceEEEEEEEEEEeccccEEEEccEEEEEECCCCCCCCCCEEEEEEcCCcCCceEeEC
Confidence 5799999999999999999999999999999999999999999999999999999999999999999985
No 7
>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=9.2e-32 Score=186.16 Aligned_cols=69 Identities=57% Similarity=0.989 Sum_probs=67.1
Q ss_pred EEEEeCCCCceEEEEEeeEEeecceeeEEeeeceEEEECCCCCCCCCCEEEEeecCcCCcceeEEEEEE
Q 041511 47 GLVVSNKMQKSVVVAVDRLFHHKVYNRYVKRTSKFMAHDENNECNIGDRVRLDPSRPLSKHKHWLVAEI 115 (147)
Q Consensus 47 G~VVS~km~KTvvV~V~r~~~hpkY~K~i~r~kK~~vHDp~n~~kvGDiV~I~ecRPiSK~K~f~V~eI 115 (147)
|+|+|++|+||++|+|++++|||+|+|+++++++|+||||+|+|++||+|+|+|||||||+|+|.|.++
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 GVVVSDKMDKTVVVRVERLVYHPKYKKYIKRTKKYMAHDENNICKVGDKVRIRECRPISKTKRFVVVEV 69 (69)
T ss_dssp EEEEEEESTTEEEEEEEEEEEETTTEEEEEEEEEEEEE-TTSSSTTTSEEEEEEEEEEETTEEEEEEEE
T ss_pred CEEEEcCCCCeEEEEEEEEEEcceEeeccCccccEEEeCCccCCCCCCEEEEEeeeccCCcEeEEEEEC
Confidence 999999999999999999999999999999999999999999999999999999999999999999986
No 8
>PTZ00241 40S ribosomal protein S11; Provisional
Probab=99.97 E-value=1.2e-30 Score=205.79 Aligned_cols=82 Identities=30% Similarity=0.426 Sum_probs=78.3
Q ss_pred ccCccceEEEEEEeCCCCceEEEEEeeEEeecceeeEEeeeceEEEECC-CCCCCCCCEEEEeecCcCCcceeEEEEEEE
Q 041511 38 GPSQMKSVVGLVVSNKMQKSVVVAVDRLFHHKVYNRYVKRTSKFMAHDE-NNECNIGDRVRLDPSRPLSKHKHWLVAEIL 116 (147)
Q Consensus 38 ~~~~~k~l~G~VVS~km~KTvvV~V~r~~~hpkY~K~i~r~kK~~vHDp-~n~~kvGDiV~I~ecRPiSK~K~f~V~eIi 116 (147)
.+.++++|+|+|+|++|+|||+|++++++|||+|+||++++++|+|||+ .++|++||+|+|+|||||||+|+|+|++|+
T Consensus 64 ~~iRgril~G~VvS~KM~KTIVV~ve~~~~h~kY~K~~kr~kk~~aHd~~~~~~kvGD~V~I~EcRPLSKTKrf~Vv~V~ 143 (158)
T PTZ00241 64 VSIRGRILRGVVISTKMKRTIIIRRDYLHYVKKYNRYEKRHKNIPVHCSPCFDVKEGDIVVVGQCRPLSKTVRFNVLKVE 143 (158)
T ss_pred eeEcceEEEEEEEEccCCccEEEEEEEEEecCccceEEEeeecEEEeCCccCCCCCCCEEEEEEcCCCCCceeEEEEEEE
Confidence 4778999999999999999999999999999999999999999999996 579999999999999999999999999999
Q ss_pred ecc
Q 041511 117 KKA 119 (147)
Q Consensus 117 ~k~ 119 (147)
+++
T Consensus 144 ~~~ 146 (158)
T PTZ00241 144 KNE 146 (158)
T ss_pred ecc
Confidence 865
No 9
>KOG1740 consensus Predicted mitochondrial/chloroplast ribosomal protein S17 [Translation, ribosomal structure and biogenesis]
Probab=99.97 E-value=9.8e-32 Score=199.26 Aligned_cols=95 Identities=66% Similarity=1.037 Sum_probs=86.6
Q ss_pred cceEEEEEEeCCCCceEEEEEeeEEeecceeeEEeeeceEEEECCCCCCCCCCEEEEeecCcCCcceeEEEEEEEecccc
Q 041511 42 MKSVVGLVVSNKMQKSVVVAVDRLFHHKVYNRYVKRTSKFMAHDENNECNIGDRVRLDPSRPLSKHKHWLVAEILKKARI 121 (147)
Q Consensus 42 ~k~l~G~VVS~km~KTvvV~V~r~~~hpkY~K~i~r~kK~~vHDp~n~~kvGDiV~I~ecRPiSK~K~f~V~eIi~k~~~ 121 (147)
++.++|+|+|.+|+||++|+|+++.+||+|+||++++++|+|||+.|.|++||.|+|.+||||||+|+|++.+||+++++
T Consensus 2 m~~~vg~VvS~kmqKTv~V~V~rl~~n~~ynryv~~~~kymahD~~n~cnvGD~VrlepsRPlSk~K~f~i~eII~~a~r 81 (107)
T KOG1740|consen 2 MKNVVGTVVSNKMQKTVKVRVDRLFFNPKYNRYVKRTSKYMAHDDKNQCNVGDRVRLEPSRPLSKTKHFIIAEIIKKARR 81 (107)
T ss_pred CccceeeeeecccCceeEEEeeeccccHHHHHHHHHhhheeecCccccccccceEEeccCCcccccceeehHHHHHHHhh
Confidence 45689999999999999999999999999999999999999999999999999999999999999999999999999998
Q ss_pred cCCCCccchhccccc
Q 041511 122 YVPPSADNAAAAAVS 136 (147)
Q Consensus 122 ~~~p~~~~~~~~~~~ 136 (147)
..+.....+..+..+
T Consensus 82 ~spa~~~ea~~s~~~ 96 (107)
T KOG1740|consen 82 YSPAAEAEALGSSAS 96 (107)
T ss_pred hCcchhhhhhcCchh
Confidence 877666555444333
No 10
>KOG1728 consensus 40S ribosomal protein S11 [Translation, ribosomal structure and biogenesis]
Probab=99.85 E-value=2.9e-22 Score=156.32 Aligned_cols=84 Identities=35% Similarity=0.434 Sum_probs=80.1
Q ss_pred ccCccceEEEEEEeCCCCceEEEEEeeEEeecceeeEEeeeceEEEECCCC--CCCCCCEEEEeecCcCCcceeEEEEEE
Q 041511 38 GPSQMKSVVGLVVSNKMQKSVVVAVDRLFHHKVYNRYVKRTSKFMAHDENN--ECNIGDRVRLDPSRPLSKHKHWLVAEI 115 (147)
Q Consensus 38 ~~~~~k~l~G~VVS~km~KTvvV~V~r~~~hpkY~K~i~r~kK~~vHDp~n--~~kvGDiV~I~ecRPiSK~K~f~V~eI 115 (147)
.+.++++|.|+|++.||++||+|+.++++|.+||++|.+|++++.||...+ ++++||+|+|+|||||||+++|.|+++
T Consensus 64 vsIRGril~G~V~k~Km~rTIvvrrdYlHy~~KY~ryekrHkN~svh~SPcFrdi~~gDiVtvGecrPLSKtvrfnVLkv 143 (156)
T KOG1728|consen 64 VSIRGRILTGTVVKMKMQRTIVVRRDYLHYIKKYNRYEKRHKNMSVHVSPCFRDIQEGDIVTVGECRPLSKTVRFNVLKV 143 (156)
T ss_pred eeEeeEEEeeEEeeeceeEEEEEEhhhhhHhHHhhHHHHhccCCccccchhhhccccCCEEEEeecccccceEEEEEEEE
Confidence 477899999999999999999999999999999999999999999999997 799999999999999999999999999
Q ss_pred Eecccc
Q 041511 116 LKKARI 121 (147)
Q Consensus 116 i~k~~~ 121 (147)
++.++.
T Consensus 144 ~k~~g~ 149 (156)
T KOG1728|consen 144 IKAAGS 149 (156)
T ss_pred eecCCC
Confidence 988753
No 11
>KOG3447 consensus Mitochondrial/chloroplast ribosomal S17-like protein [Translation, ribosomal structure and biogenesis]
Probab=99.72 E-value=1.4e-18 Score=135.08 Aligned_cols=98 Identities=27% Similarity=0.407 Sum_probs=92.8
Q ss_pred cceeeccCccceEEEEEEeCCCCceEEEEEeeEEeecceeeEEeeeceEEEECCCCCCCCCCEEEEeec-CcCCcceeEE
Q 041511 33 LSIQIGPSQMKSVVGLVVSNKMQKSVVVAVDRLFHHKVYNRYVKRTSKFMAHDENNECNIGDRVRLDPS-RPLSKHKHWL 111 (147)
Q Consensus 33 ~~~~~~~~~~k~l~G~VVS~km~KTvvV~V~r~~~hpkY~K~i~r~kK~~vHDp~n~~kvGDiV~I~ec-RPiSK~K~f~ 111 (147)
||+.-.+..++.|.|.|+..+|+|+++|++.++.++|..+||+.+++.|+|||+...|++||+|+|++. -+..+..+|.
T Consensus 1 ~sv~~~s~~~~~lmGk~ig~~~q~~akVR~~r~eld~yL~kYf~k~~~yfAhD~~~~c~vGDtVLir~lp~r~t~~V~H~ 80 (150)
T KOG3447|consen 1 MSVVKSSVHAQWLMGKVIGTKMQKTAKVRVTRLELDPYLLKYFNKRKTYFAHDALQQCTVGDTVLIRALPVRRTKHVKHE 80 (150)
T ss_pred CceEEeecccEEEEeeeeeccccccceeeeehhhcCHHHHHHhccccceeecchhhccccCCEEEEecCCcchhhhhhhh
Confidence 456667888999999999999999999999999999999999999999999999999999999999999 6889999999
Q ss_pred EEEEEecccccCCCCccch
Q 041511 112 VAEILKKARIYVPPSADNA 130 (147)
Q Consensus 112 V~eIi~k~~~~~~p~~~~~ 130 (147)
|.+|+.+-|.+.||.||.-
T Consensus 81 v~~VVfk~G~IidPvTGkk 99 (150)
T KOG3447|consen 81 VAEVVFKVGKIIDPVTGKK 99 (150)
T ss_pred hHhheeecccccCCCcCcc
Confidence 9999999999999999974
No 12
>PF10844 DUF2577: Protein of unknown function (DUF2577); InterPro: IPR022555 This family of proteins has no known function
Probab=71.24 E-value=36 Score=24.58 Aligned_cols=63 Identities=24% Similarity=0.360 Sum_probs=34.0
Q ss_pred ceEEEEEEeCCCCceEEEEEee-EEeecc---eeeEEeeece--------------EEEECCCCCCCCCCEEEEeecCcC
Q 041511 43 KSVVGLVVSNKMQKSVVVAVDR-LFHHKV---YNRYVKRTSK--------------FMAHDENNECNIGDRVRLDPSRPL 104 (147)
Q Consensus 43 k~l~G~VVS~km~KTvvV~V~r-~~~hpk---Y~K~i~r~kK--------------~~vHDp~n~~kvGDiV~I~ecRPi 104 (147)
....|+|+|..- .+|.++- +..... .-..+++++. +..+| .++.||.|.+.. .
T Consensus 18 ~i~~G~V~s~~P---L~I~i~~~liL~~~~L~i~~~l~~~~~~~~~~~~~~~~~~~i~~~~---~Lk~GD~V~ll~---~ 88 (100)
T PF10844_consen 18 DIVIGTVVSVPP---LKIKIDQKLILDKDFLIIPELLKDYTRDITIEHNSETDNITITFTD---GLKVGDKVLLLR---V 88 (100)
T ss_pred eeEEEEEEeccc---EEEEECCeEEEchHHEEeehhccceEEEEEEeccccccceeEEEec---CCcCCCEEEEEE---e
Confidence 357999998764 6666666 222210 1112222222 33333 589999999876 3
Q ss_pred CcceeEEEEE
Q 041511 105 SKHKHWLVAE 114 (147)
Q Consensus 105 SK~K~f~V~e 114 (147)
-.-.+|.|+.
T Consensus 89 ~~gQ~yiVlD 98 (100)
T PF10844_consen 89 QGGQKYIVLD 98 (100)
T ss_pred cCCCEEEEEE
Confidence 3344555543
No 13
>TIGR00523 eIF-1A eukaryotic/archaeal initiation factor 1A. Recommended nomenclature: eIF-1A for eukaryotes, aIF-1A for Archaea. Also called eIF-4C
Probab=69.18 E-value=31 Score=25.37 Aligned_cols=49 Identities=16% Similarity=0.133 Sum_probs=31.9
Q ss_pred ceEEEEEEeCCCCceEEEEEe----eEEeec-ceeeEEeeeceEEEECCCCCCCCCCEEEEeecCcCC
Q 041511 43 KSVVGLVVSNKMQKSVVVAVD----RLFHHK-VYNRYVKRTSKFMAHDENNECNIGDRVRLDPSRPLS 105 (147)
Q Consensus 43 k~l~G~VVS~km~KTvvV~V~----r~~~hp-kY~K~i~r~kK~~vHDp~n~~kvGDiV~I~ecRPiS 105 (147)
.+..|+|+....+....|..+ ++...| |++| ++| .+.||.|++ +.+.++
T Consensus 19 ~e~~g~V~~~lG~~~~~V~~~dG~~~la~i~GK~Rk------~iw-------I~~GD~VlV-sp~d~~ 72 (99)
T TIGR00523 19 GEILGVIEQMLGAGRVKVRCLDGKTRLGRIPGKLKK------RIW-------IREGDVVIV-KPWEFQ 72 (99)
T ss_pred CEEEEEEEEEcCCCEEEEEeCCCCEEEEEEchhhcc------cEE-------ecCCCEEEE-EEccCC
Confidence 457999998877777777744 333333 2222 333 578999999 567777
No 14
>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=68.27 E-value=24 Score=24.68 Aligned_cols=51 Identities=20% Similarity=0.136 Sum_probs=31.1
Q ss_pred EEEEEEeCCCCceEEEEEe----eEEeec-ceeeEEeeeceEEEECCCCCCCCCCEEEEeecCcCCccee
Q 041511 45 VVGLVVSNKMQKSVVVAVD----RLFHHK-VYNRYVKRTSKFMAHDENNECNIGDRVRLDPSRPLSKHKH 109 (147)
Q Consensus 45 l~G~VVS~km~KTvvV~V~----r~~~hp-kY~K~i~r~kK~~vHDp~n~~kvGDiV~I~ecRPiSK~K~ 109 (147)
..|+|+....++...|..+ ++...| |++| +++ .+.||.|++. ..|..+.|.
T Consensus 2 ~~g~V~~~~g~~~~~V~~~~g~~~la~i~gK~rk------~iw-------I~~GD~V~Ve-~~~~d~~kg 57 (77)
T cd05793 2 EYGQVEKMLGNGRLEVRCFDGKKRLCRIRGKMRK------RVW-------INEGDIVLVA-PWDFQDDKA 57 (77)
T ss_pred EEEEEEEEcCCCEEEEEECCCCEEEEEEchhhcc------cEE-------EcCCCEEEEE-eccccCCEE
Confidence 4788888777777777644 222222 2221 233 5789999987 556676654
No 15
>smart00652 eIF1a eukaryotic translation initiation factor 1A.
Probab=67.86 E-value=27 Score=24.82 Aligned_cols=52 Identities=21% Similarity=0.151 Sum_probs=32.6
Q ss_pred eEEEEEEeCCCCceEEEEEe----eEEeec-ceeeEEeeeceEEEECCCCCCCCCCEEEEeecCcCCccee
Q 041511 44 SVVGLVVSNKMQKSVVVAVD----RLFHHK-VYNRYVKRTSKFMAHDENNECNIGDRVRLDPSRPLSKHKH 109 (147)
Q Consensus 44 ~l~G~VVS~km~KTvvV~V~----r~~~hp-kY~K~i~r~kK~~vHDp~n~~kvGDiV~I~ecRPiSK~K~ 109 (147)
+..|+|+....++-..|..+ ++...| |++| +++ .+.||.|++. ..|..+.|-
T Consensus 6 q~~g~V~~~lG~~~~~V~~~dG~~~la~ipgK~Rk------~iw-------I~~GD~VlVe-~~~~~~~kg 62 (83)
T smart00652 6 QEIAQVVKMLGNGRLEVMCADGKERLARIPGKMRK------KVW-------IRRGDIVLVD-PWDFQDVKA 62 (83)
T ss_pred cEEEEEEEEcCCCEEEEEECCCCEEEEEEchhhcc------cEE-------EcCCCEEEEE-ecCCCCCEE
Confidence 46899998777777777743 333333 3322 233 5789999995 556665543
No 16
>PTZ00329 eukaryotic translation initiation factor 1A; Provisional
Probab=64.80 E-value=53 Score=26.35 Aligned_cols=57 Identities=18% Similarity=0.169 Sum_probs=38.7
Q ss_pred eEEEEEEeCCCCceEEEEEe----eEEeec-ceeeEEeeeceEEEECCCCCCCCCCEEEEeecCcCCcceeEEEEE
Q 041511 44 SVVGLVVSNKMQKSVVVAVD----RLFHHK-VYNRYVKRTSKFMAHDENNECNIGDRVRLDPSRPLSKHKHWLVAE 114 (147)
Q Consensus 44 ~l~G~VVS~km~KTvvV~V~----r~~~hp-kY~K~i~r~kK~~vHDp~n~~kvGDiV~I~ecRPiSK~K~f~V~e 114 (147)
...|+|+....+..+.|... ++...| |++| ++| ++.||+|++. .+|..+.|.=++..
T Consensus 33 q~~g~V~~~LGn~~f~V~c~dG~~rLa~I~GKmRK------~IW-------I~~GD~VlVe-l~~yd~~KgdIi~R 94 (155)
T PTZ00329 33 QEYAQVLRMLGNGRLEAYCFDGVKRLCHIRGKMRK------RVW-------INIGDIILVS-LRDFQDSKADVILK 94 (155)
T ss_pred cEEEEEEEEcCCCEEEEEECCCCEEEEEeecccee------eEE-------ecCCCEEEEe-ccCCCCCEEEEEEE
Confidence 35899998888888888743 444444 3333 244 5789999995 49988887654443
No 17
>PLN00208 translation initiation factor (eIF); Provisional
Probab=63.66 E-value=63 Score=25.64 Aligned_cols=57 Identities=16% Similarity=0.134 Sum_probs=38.7
Q ss_pred eEEEEEEeCCCCceEEEEE----eeEEeec-ceeeEEeeeceEEEECCCCCCCCCCEEEEeecCcCCcceeEEEEE
Q 041511 44 SVVGLVVSNKMQKSVVVAV----DRLFHHK-VYNRYVKRTSKFMAHDENNECNIGDRVRLDPSRPLSKHKHWLVAE 114 (147)
Q Consensus 44 ~l~G~VVS~km~KTvvV~V----~r~~~hp-kY~K~i~r~kK~~vHDp~n~~kvGDiV~I~ecRPiSK~K~f~V~e 114 (147)
...|+|+....+..+.|.. .++...| |++| ++| .+.||+|++. .++..+.|.=++..
T Consensus 33 q~~g~V~~~lGn~~~~V~c~dG~~rLa~IpGKmRK------rIW-------I~~GD~VlVe-l~~~d~~KgdIv~r 94 (145)
T PLN00208 33 QEYAQVLRMLGNGRCEALCIDGTKRLCHIRGKMRK------KVW-------IAAGDIILVG-LRDYQDDKADVILK 94 (145)
T ss_pred cEEEEEEEEcCCCEEEEEECCCCEEEEEEecccee------eEE-------ecCCCEEEEE-ccCCCCCEEEEEEE
Confidence 4689999887778788773 4555555 4443 244 5689999987 77887776654443
No 18
>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=58.07 E-value=49 Score=21.61 Aligned_cols=50 Identities=14% Similarity=0.139 Sum_probs=27.5
Q ss_pred eEEEEEEeCCCCceEEEEEeeEEeecceeeEEeeeceEEEECCCCCCCCCCEEEEee
Q 041511 44 SVVGLVVSNKMQKSVVVAVDRLFHHKVYNRYVKRTSKFMAHDENNECNIGDRVRLDP 100 (147)
Q Consensus 44 ~l~G~VVS~km~KTvvV~V~r~~~hpkY~K~i~r~kK~~vHDp~n~~kvGDiV~I~e 100 (147)
++.|+|++.....-..|..+ --..|....+..-+ + ....+.+||.|.+.-
T Consensus 2 ~~~G~Vi~~~~g~~~~V~~~---~g~~~~c~~rGklr---~-~~~~~~vGD~V~~~~ 51 (64)
T cd04451 2 EMEGVVTEALPNAMFRVELE---NGHEVLAHISGKMR---M-NYIRILPGDRVKVEL 51 (64)
T ss_pred eEEEEEEEEeCCCEEEEEeC---CCCEEEEEECceee---c-CCcccCCCCEEEEEE
Confidence 35788886553333444321 11355555554333 1 334589999998873
No 19
>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=57.68 E-value=47 Score=23.29 Aligned_cols=51 Identities=12% Similarity=-0.033 Sum_probs=30.1
Q ss_pred EEEEEEeCCCCceEEEEEeeEEeecceeeEEeeeceEEEECCCC-----CCCCCCEEEEeecCcC-Cccee
Q 041511 45 VVGLVVSNKMQKSVVVAVDRLFHHKVYNRYVKRTSKFMAHDENN-----ECNIGDRVRLDPSRPL-SKHKH 109 (147)
Q Consensus 45 l~G~VVS~km~KTvvV~V~r~~~hpkY~K~i~r~kK~~vHDp~n-----~~kvGDiV~I~ecRPi-SK~K~ 109 (147)
..|+|+....++-..|..+- -+.+++|-|.. =.+.||.|++. .+|. .+.|.
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 46888877777777776441 12223333321 26789999995 5666 35443
No 20
>cd01854 YjeQ_engC YjeQ/EngC. YjeQ (YloQ in Bacillus subtilis) represents a protein family whose members are broadly conserved in bacteria and have been shown to be essential to the growth of E. coli and B. subtilis. Proteins of the YjeQ family contain all sequence motifs typical of the vast class of P-loop-containing GTPases, but show a circular permutation, with a G4-G1-G3 pattern of motifs as opposed to the regular G1-G3-G4 pattern seen in most GTPases. All YjeQ family proteins display a unique domain architecture, which includes an N-terminal OB-fold RNA-binding domain, the central permuted GTPase domain, and a zinc knuckle-like C-terminal cysteine domain. This domain architecture suggests a role for YjeQ as a regulator of translation.
Probab=55.49 E-value=44 Score=27.99 Aligned_cols=38 Identities=18% Similarity=0.393 Sum_probs=27.4
Q ss_pred CCCCCCCCEEEEeecCcCCcceeEEEEEEEecccccCCCCcc
Q 041511 87 NNECNIGDRVRLDPSRPLSKHKHWLVAEILKKARIYVPPSAD 128 (147)
Q Consensus 87 ~n~~kvGDiV~I~ecRPiSK~K~f~V~eIi~k~~~~~~p~~~ 128 (147)
.....+||.|.+...- ...+.|.+|+.+...+.-|..+
T Consensus 32 ~~~~~vGD~V~~~~~~----~~~~~i~~i~~R~~~l~R~~~~ 69 (287)
T cd01854 32 GIKPVVGDWVEVEPDD----DGEGVIVRVLPRKNLLSRPAAG 69 (287)
T ss_pred CCCccCCCEEEEEecC----CCcEEEEEEECCCceEEccCCC
Confidence 4458999999997432 3468899999887766666643
No 21
>PRK04012 translation initiation factor IF-1A; Provisional
Probab=54.02 E-value=52 Score=24.29 Aligned_cols=52 Identities=21% Similarity=0.203 Sum_probs=33.0
Q ss_pred ceEEEEEEeCCCCceEEEEEe----eEEeec-ceeeEEeeeceEEEECCCCCCCCCCEEEEeecCcCCcce
Q 041511 43 KSVVGLVVSNKMQKSVVVAVD----RLFHHK-VYNRYVKRTSKFMAHDENNECNIGDRVRLDPSRPLSKHK 108 (147)
Q Consensus 43 k~l~G~VVS~km~KTvvV~V~----r~~~hp-kY~K~i~r~kK~~vHDp~n~~kvGDiV~I~ecRPiSK~K 108 (147)
.+..|+|+....+.-..|..+ ++...| |++| ++| .+.||.|++.. +|....|
T Consensus 21 ~e~~g~V~~~lG~~~~~V~~~dG~~~la~i~GK~Rk------~Iw-------I~~GD~VlVe~-~~~~~~k 77 (100)
T PRK04012 21 GEVFGVVEQMLGANRVRVRCMDGVERMGRIPGKMKK------RMW-------IREGDVVIVAP-WDFQDEK 77 (100)
T ss_pred CEEEEEEEEEcCCCEEEEEeCCCCEEEEEEchhhcc------cEE-------ecCCCEEEEEe-cccCCCE
Confidence 457899998777777777744 333333 3332 233 45899999874 5556554
No 22
>cd05791 S1_CSL4 S1_CSL4: CSL4, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. ScCSL4 protein is a subunit of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In S. cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".
Probab=47.79 E-value=34 Score=24.25 Aligned_cols=60 Identities=13% Similarity=0.080 Sum_probs=33.0
Q ss_pred cCccceEEEEEEeCCCCceEEEEEee---EEeecceeeEEeee----ceEEEECCCCCCCCCCEEEEe
Q 041511 39 PSQMKSVVGLVVSNKMQKSVVVAVDR---LFHHKVYNRYVKRT----SKFMAHDENNECNIGDRVRLD 99 (147)
Q Consensus 39 ~~~~k~l~G~VVS~km~KTvvV~V~r---~~~hpkY~K~i~r~----kK~~vHDp~n~~kvGDiV~I~ 99 (147)
|+.+-...|+|++-. .+-+.|.+.. .....-|.-+++.. ...--.+..+..++||+|+.+
T Consensus 4 P~~GDiVig~V~~v~-~~~~~v~I~~v~~~~l~~~~~g~l~~~dv~~~~~d~~~~~~~f~~GDiV~Ak 70 (92)
T cd05791 4 PKVGSIVIARVTRIN-PRFAKVDILCVGGRPLKESFRGVIRKEDIRATEKDKVEMYKCFRPGDIVRAK 70 (92)
T ss_pred CCCCCEEEEEEEEEc-CCEEEEEEEEecCeecCCCcccEEEHHHccccccchHHHHhhcCCCCEEEEE
Confidence 567778899999754 4556666532 22233344444422 111111223567999999753
No 23
>cd01342 Translation_Factor_II_like Translation_Factor_II_like: Elongation factor Tu (EF-Tu) domain II-like proteins. Elongation factor Tu consists of three structural domains, this family represents the second domain. Domain II adopts a beta barrel structure and is involved in binding to charged tRNA. Domain II is found in other proteins such as elongation factor G and translation initiation factor IF-2. This group also includes the C2 subdomain of domain IV of IF-2 that has the same fold as domain II of (EF-Tu). Like IF-2 from certain prokaryotes such as Thermus thermophilus, mitochondrial IF-2 lacks domain II, which is thought to be involved in binding of E.coli IF-2 to 30S subunits.
Probab=45.29 E-value=70 Score=19.52 Aligned_cols=57 Identities=21% Similarity=0.101 Sum_probs=31.6
Q ss_pred cCccceEEEEEEeCCCCceEEEEEeeEEeecceeeEEeeeceEE-EECCCCCCCCCCEEEEee
Q 041511 39 PSQMKSVVGLVVSNKMQKSVVVAVDRLFHHKVYNRYVKRTSKFM-AHDENNECNIGDRVRLDP 100 (147)
Q Consensus 39 ~~~~k~l~G~VVS~km~KTvvV~V~r~~~hpkY~K~i~r~kK~~-vHDp~n~~kvGDiV~I~e 100 (147)
+..++...|+|.++...+--.+.+... ...+...+ +.+. .+.+.+++..||.+.+.-
T Consensus 12 ~~~g~v~~~rv~~G~l~~g~~v~~~~~--~~~~~~~i---~~i~~~~~~~~~~~aG~~~~~~~ 69 (83)
T cd01342 12 KGRGTVATGRVESGTLKKGDKVRVGPG--GGGVKGKV---KSLKRFKGEVDEAVAGDIVGIVL 69 (83)
T ss_pred CCceEEEEEEEeeCEEecCCEEEEecC--CceeEEEE---eEeEecCceeceecCCCEEEEEE
Confidence 345667788888876554444444332 11111111 1233 234456899999998865
No 24
>PF13550 Phage-tail_3: Putative phage tail protein
Probab=44.95 E-value=48 Score=24.28 Aligned_cols=36 Identities=19% Similarity=0.285 Sum_probs=25.7
Q ss_pred eceEEEECCCCCCCCCCEEEEeecCcCCcceeEEEEEEE
Q 041511 78 TSKFMAHDENNECNIGDRVRLDPSRPLSKHKHWLVAEIL 116 (147)
Q Consensus 78 ~kK~~vHDp~n~~kvGDiV~I~ecRPiSK~K~f~V~eIi 116 (147)
+=.|.+--..-.+.+||+|.|..- .+...|+|.+|-
T Consensus 128 t~~f~~~~~~~~l~pGDvi~l~~~---~~~~~~RI~~i~ 163 (164)
T PF13550_consen 128 TVSFTLPPDGLALEPGDVIALSDD---GRDMRFRITEIE 163 (164)
T ss_pred EEEEEEChhhccCCCCCEEEEEeC---CCceEEEEEEEe
Confidence 334444444458999999999876 557788888774
No 25
>PF11302 DUF3104: Protein of unknown function (DUF3104); InterPro: IPR021453 This family of proteins with unknown function appears to be restricted to Cyanobacteria.
Probab=43.67 E-value=50 Score=23.59 Aligned_cols=37 Identities=16% Similarity=0.315 Sum_probs=28.6
Q ss_pred CCCCCCEEEEeecC--cCCcceeEEEEEEEecccccCCC
Q 041511 89 ECNIGDRVRLDPSR--PLSKHKHWLVAEILKKARIYVPP 125 (147)
Q Consensus 89 ~~kvGDiV~I~ecR--PiSK~K~f~V~eIi~k~~~~~~p 125 (147)
.+|.||.|++.... -..+.+.|-+-+||...+-.-+|
T Consensus 5 ~Vk~Gd~ViV~~~~~~~~~~~~dWWmg~Vi~~~ggaR~P 43 (75)
T PF11302_consen 5 SVKPGDTVIVQDEQEVGQKQDKDWWMGQVIHCEGGARDP 43 (75)
T ss_pred ccCCCCEEEEecCccccccCCCCcEEEEEEEEeccccCC
Confidence 57899999999985 45677899999999876543333
No 26
>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=43.60 E-value=64 Score=22.35 Aligned_cols=53 Identities=21% Similarity=0.226 Sum_probs=33.9
Q ss_pred CccceEEEEEEeCCCCceEEEEEeeEEeecceeeEEeeeceEEEECCC-CCCCCCCEEEEe
Q 041511 40 SQMKSVVGLVVSNKMQKSVVVAVDRLFHHKVYNRYVKRTSKFMAHDEN-NECNIGDRVRLD 99 (147)
Q Consensus 40 ~~~k~l~G~VVS~km~KTvvV~V~r~~~hpkY~K~i~r~kK~~vHDp~-n~~kvGDiV~I~ 99 (147)
..+..+.|+|.++...+--+|.+- |- +....-+.+..|+.. ..+..||.|.|.
T Consensus 17 g~g~vv~G~v~~G~i~~gd~v~i~-----P~--~~~~~V~sI~~~~~~~~~a~aG~~v~i~ 70 (91)
T cd03693 17 GIGTVPVGRVETGVLKPGMVVTFA-----PA--GVTGEVKSVEMHHEPLEEALPGDNVGFN 70 (91)
T ss_pred CceEEEEEEEecceeecCCEEEEC-----CC--CcEEEEEEEEECCcCcCEECCCCEEEEE
Confidence 345678899998765543333322 21 134556667777777 589999999874
No 27
>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=40.68 E-value=49 Score=22.59 Aligned_cols=49 Identities=20% Similarity=0.262 Sum_probs=31.1
Q ss_pred eEEEEEEeCCCCceEEEEEeeEEeecceeeEEeeeceEEEECCC-CCCCCCCEEEEe
Q 041511 44 SVVGLVVSNKMQKSVVVAVDRLFHHKVYNRYVKRTSKFMAHDEN-NECNIGDRVRLD 99 (147)
Q Consensus 44 ~l~G~VVS~km~KTvvV~V~r~~~hpkY~K~i~r~kK~~vHDp~-n~~kvGDiV~I~ 99 (147)
...|+|.++...+--+|.+- |- .....-+.+.+|+.. +.|..||.|.|.
T Consensus 17 ~v~Gkv~~G~v~~Gd~v~~~-----P~--~~~~~V~si~~~~~~~~~a~aGd~v~l~ 66 (81)
T cd03695 17 GYAGTIASGSIRVGDEVVVL-----PS--GKTSRVKSIETFDGELDEAGAGESVTLT 66 (81)
T ss_pred EEEEEEccceEECCCEEEEc-----CC--CCeEEEEEEEECCcEeCEEcCCCEEEEE
Confidence 57888887654333223221 21 234566677777777 589999999874
No 28
>PRK10413 hydrogenase 2 accessory protein HypG; Provisional
Probab=39.47 E-value=1.2e+02 Score=21.58 Aligned_cols=51 Identities=16% Similarity=0.096 Sum_probs=27.5
Q ss_pred EEEEEeCCCC--ceEEEEEeeEEeecceeeEEeeeceEEEECCCCCCCCCCEEEEeecCcCC
Q 041511 46 VGLVVSNKMQ--KSVVVAVDRLFHHKVYNRYVKRTSKFMAHDENNECNIGDRVRLDPSRPLS 105 (147)
Q Consensus 46 ~G~VVS~km~--KTvvV~V~r~~~hpkY~K~i~r~kK~~vHDp~n~~kvGDiV~I~ecRPiS 105 (147)
=|+|++-..+ ++++|...- ..+.-.-.++-+++.++++||+|++.-.--|+
T Consensus 6 P~kVi~i~~~~~~~A~vd~~G---------v~r~V~l~Lv~~~~~~~~vGDyVLVHaGfAi~ 58 (82)
T PRK10413 6 PGQVLAVGEDIHQLAQVEVCG---------IKRDVNIALICEGNPADLLGQWVLVHVGFAMS 58 (82)
T ss_pred ceEEEEECCCCCcEEEEEcCC---------eEEEEEeeeeccCCcccccCCEEEEecchhhh
Confidence 3667663332 566665322 22222223444443478999999997654333
No 29
>cd04092 mtEFG2_II_like mtEFG2_C: C-terminus of mitochondrial Elongation factor G2 (mtEFG2)-like proteins found in eukaryotes. Eukaryotic cells harbor 2 protein synthesis systems: one localized in the cytoplasm, the other in the mitochondria. Most factors regulating mitochondrial protein synthesis are encoded by nuclear genes, translated in the cytoplasm, and then transported to the mitochondria. The eukaryotic system of elongation factor (EF) components is more complex than that in prokaryotes, with both cytoplasmic and mitochondrial elongation factors and multiple isoforms being expressed in certain species. Eukaryotic EF-2 operates in the cytosolic protein synthesis machinery of eukaryotes, EF-Gs in protein synthesis in bacteria. Eukaryotic mtEFG1 proteins show significant homology to bacterial EF-Gs. No clear phenotype has been found for mutants in the yeast homologue of mtEFG2, MEF2. There are two forms of mtEFG present in mammals (designated mtEFG1s and mtEFG2s) mtEFG1s are n
Probab=37.77 E-value=83 Score=21.11 Aligned_cols=56 Identities=9% Similarity=0.039 Sum_probs=28.9
Q ss_pred cCccceEEEEEEeCCCCceEEEEEeeEEeecceeeEEeeeceEEEEC----CCCCCCCCCEEEEee
Q 041511 39 PSQMKSVVGLVVSNKMQKSVVVAVDRLFHHKVYNRYVKRTSKFMAHD----ENNECNIGDRVRLDP 100 (147)
Q Consensus 39 ~~~~k~l~G~VVS~km~KTvvV~V~r~~~hpkY~K~i~r~kK~~vHD----p~n~~kvGDiV~I~e 100 (147)
+..++.-.++|.++...+--.|.+... ++..+-.+=+..|- +-+++..||+|.|..
T Consensus 12 ~~~g~i~~~Ri~sGtl~~g~~v~~~~~------~~~~~v~~l~~~~g~~~~~v~~~~aGdI~~i~g 71 (83)
T cd04092 12 PQRGPLTFVRVYSGTLKRGSALYNTNT------GKKERISRLLQPFADQYQEIPSLSAGNIGVITG 71 (83)
T ss_pred CCCCeEEEEEEecCEECCCCEEEECCC------CCEEEeeEEEEEECCCceECCeeCCCCEEEEEC
Confidence 445666777777766554433432221 11122122222222 125899999999865
No 30
>cd03690 Tet_II Tet_II: This subfamily represents domain II of ribosomal protection proteins Tet(M) and Tet(O). This domain has homology to domain II of the elongation factors EF-G and EF-2. Tet(M) and Tet(O) catalyze the release of tetracycline (Tc) from the ribosome in a GTP-dependent manner thereby mediating Tc resistance. Tcs are broad-spectrum antibiotics. Typical Tcs bind to the ribosome and inhibit the elongation phase of protein synthesis, by inhibiting the occupation of site A by aminoacyl-tRNA.
Probab=37.40 E-value=1e+02 Score=21.09 Aligned_cols=57 Identities=16% Similarity=0.089 Sum_probs=30.8
Q ss_pred ccCccceEEEEEEeCCCCceEEEEEeeEEeecceeeEEeeeceEEEECC----CCCCCCCCEEEEeec
Q 041511 38 GPSQMKSVVGLVVSNKMQKSVVVAVDRLFHHKVYNRYVKRTSKFMAHDE----NNECNIGDRVRLDPS 101 (147)
Q Consensus 38 ~~~~~k~l~G~VVS~km~KTvvV~V~r~~~hpkY~K~i~r~kK~~vHDp----~n~~kvGDiV~I~ec 101 (147)
.+..++.-.|+|.|+...+--.|.+.. .+..+-.+=|..+-. -+++..||++-|...
T Consensus 14 d~~~G~la~~RV~sG~l~~g~~v~~~~-------~~~~~v~~l~~~~g~~~~~v~~~~aGdI~ai~gl 74 (85)
T cd03690 14 DDKGERLAYLRLYSGTLRLRDSVRVNR-------EEKIKITELRVFNNGEVVTADTVTAGDIAILTGL 74 (85)
T ss_pred CCCCCeEEEEEEccCEEcCCCEEEeCC-------CcEEEeceeEEEeCCCeEECcEECCCCEEEEECC
Confidence 356677778888886654444443322 111111122222221 158999999988764
No 31
>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=37.18 E-value=57 Score=22.08 Aligned_cols=52 Identities=25% Similarity=0.219 Sum_probs=30.5
Q ss_pred ccceEEEEEEeCCCCceEEEEEeeEEeecceeeEEeeeceEEEECCC-CCCCCCCEEEEe
Q 041511 41 QMKSVVGLVVSNKMQKSVVVAVDRLFHHKVYNRYVKRTSKFMAHDEN-NECNIGDRVRLD 99 (147)
Q Consensus 41 ~~k~l~G~VVS~km~KTvvV~V~r~~~hpkY~K~i~r~kK~~vHDp~-n~~kvGDiV~I~ 99 (147)
.+..+.|+|.++...+--.|.+- |-- ...+-+.+..|+.. ++|..||.|.|.
T Consensus 14 ~g~vv~G~v~~G~i~~Gd~v~i~-----P~~--~~~~V~si~~~~~~~~~a~aGd~v~~~ 66 (83)
T cd03698 14 GGTVVSGKVESGSIQKGDTLLVM-----PSK--ESVEVKSIYVDDEEVDYAVAGENVRLK 66 (83)
T ss_pred CCcEEEEEEeeeEEeCCCEEEEe-----CCC--cEEEEEEEEECCeECCEECCCCEEEEE
Confidence 45567888887554333222221 211 22455567777766 589999999863
No 32
>PRK12442 translation initiation factor IF-1; Reviewed
Probab=36.83 E-value=1.7e+02 Score=21.45 Aligned_cols=53 Identities=21% Similarity=0.133 Sum_probs=31.7
Q ss_pred ceEEEEEEeCCCCceEEEEEe----eEEeec-ceeeEEeeeceEEEECCCCCCCCCCEEEEeecCcCCcce
Q 041511 43 KSVVGLVVSNKMQKSVVVAVD----RLFHHK-VYNRYVKRTSKFMAHDENNECNIGDRVRLDPSRPLSKHK 108 (147)
Q Consensus 43 k~l~G~VVS~km~KTvvV~V~----r~~~hp-kY~K~i~r~kK~~vHDp~n~~kvGDiV~I~ecRPiSK~K 108 (147)
-++.|+|+...-+-...|..+ .+.+.+ |+++... -..+||.|.++-+ |..-+|
T Consensus 7 ie~~G~V~e~Lp~~~frV~LenG~~vla~isGKmR~~rI------------rIl~GD~V~VE~s-pYDltk 64 (87)
T PRK12442 7 IELDGIVDEVLPDSRFRVTLENGVEVGAYASGRMRKHRI------------RILAGDRVTLELS-PYDLTK 64 (87)
T ss_pred EEEEEEEEEECCCCEEEEEeCCCCEEEEEeccceeeeeE------------EecCCCEEEEEEC-cccCCc
Confidence 368999998777777777765 222222 2222111 2568999998765 555444
No 33
>PRK10862 SoxR reducing system protein RseC; Provisional
Probab=35.57 E-value=73 Score=24.81 Aligned_cols=53 Identities=15% Similarity=0.130 Sum_probs=29.7
Q ss_pred EEEEEEeCCCCceEEEEEeeEEe-----------ecceeeEEe-eeceEEEECCCCCCCCCCEEEEe
Q 041511 45 VVGLVVSNKMQKSVVVAVDRLFH-----------HKVYNRYVK-RTSKFMAHDENNECNIGDRVRLD 99 (147)
Q Consensus 45 l~G~VVS~km~KTvvV~V~r~~~-----------hpkY~K~i~-r~kK~~vHDp~n~~kvGDiV~I~ 99 (147)
-.|+|++... ..+.|+.++.-- +-...|..- ++..+.+.++ ..+++||.|.|.
T Consensus 4 e~~~Vv~v~~-~~a~Ve~~r~saCg~C~a~~gCG~~~l~~~~~~~~~~~~v~~~-~~~~vGD~V~v~ 68 (154)
T PRK10862 4 EWATVVSWQN-GIALLRCEVKAGCSSCASRAGCGSRLLNKLGPQTTHQLVVPSS-QPLVPGQKVELG 68 (154)
T ss_pred eEEEEEEEEC-CEEEEEEecCCCCcCcCCCCCchhhHHHHhcCCCceEEEecCC-CCCCCCCEEEEe
Confidence 3688887643 457777665431 111122222 2334555554 468999999875
No 34
>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=35.13 E-value=1.1e+02 Score=20.59 Aligned_cols=52 Identities=27% Similarity=0.320 Sum_probs=31.7
Q ss_pred ccceEEEEEEeCCCCceEEEEEeeEEeecceeeEEeeeceEEEECCC-CCCCCCCEEEEe
Q 041511 41 QMKSVVGLVVSNKMQKSVVVAVDRLFHHKVYNRYVKRTSKFMAHDEN-NECNIGDRVRLD 99 (147)
Q Consensus 41 ~~k~l~G~VVS~km~KTvvV~V~r~~~hpkY~K~i~r~kK~~vHDp~-n~~kvGDiV~I~ 99 (147)
.+..+.|+|.++....--.|.+- | .+....-+.+..|+.. ..+..||.|.|.
T Consensus 14 ~g~vv~G~v~sG~i~~g~~v~~~-----p--~~~~~~V~sI~~~~~~~~~a~aGd~v~i~ 66 (83)
T cd03696 14 QGTVVTGTVLSGSVKVGDKVEIL-----P--LGEETRVRSIQVHGKDVEEAKAGDRVALN 66 (83)
T ss_pred cEEEEEEEEeecEEeCCCEEEEC-----C--CCceEEEEEEEECCcCcCEEcCCCEEEEE
Confidence 34467888887654333333321 2 1234556667777776 689999999874
No 35
>PF06107 DUF951: Bacterial protein of unknown function (DUF951); InterPro: IPR009296 This family consists of several short hypothetical bacterial proteins of unknown function.
Probab=34.61 E-value=65 Score=21.91 Aligned_cols=25 Identities=24% Similarity=0.611 Sum_probs=20.3
Q ss_pred CCCCCEEEEeecCcCCcceeEEEEEE
Q 041511 90 CNIGDRVRLDPSRPLSKHKHWLVAEI 115 (147)
Q Consensus 90 ~kvGDiV~I~ecRPiSK~K~f~V~eI 115 (147)
..+||+|....-.|=.- ..|.|+.+
T Consensus 2 ~~vgDiV~mKK~HPCG~-~~Wei~R~ 26 (57)
T PF06107_consen 2 YEVGDIVEMKKPHPCGS-NEWEIIRI 26 (57)
T ss_pred ccCCCEEEEcCCCCCCC-CEEEEEEc
Confidence 57899999999888665 58988765
No 36
>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=34.39 E-value=1.3e+02 Score=20.52 Aligned_cols=54 Identities=13% Similarity=0.139 Sum_probs=32.3
Q ss_pred ccceEEEEEEeCCCCceEEEEEeeEEeecceeeEEeeeceEEEECCC-CCCCCCCEEEEe
Q 041511 41 QMKSVVGLVVSNKMQKSVVVAVDRLFHHKVYNRYVKRTSKFMAHDEN-NECNIGDRVRLD 99 (147)
Q Consensus 41 ~~k~l~G~VVS~km~KTvvV~V~r~~~hpkY~K~i~r~kK~~vHDp~-n~~kvGDiV~I~ 99 (147)
.+..+.|+|.++.+..--.|.+--. +. .....-+.+.+|+.. +++..||.|.|.
T Consensus 14 ~G~vv~G~v~~G~v~~gd~v~~~p~---~~--~~~~~V~si~~~~~~~~~a~~G~~v~l~ 68 (87)
T cd03697 14 RGTVVTGRIERGTIKVGDEVEIVGF---GE--TLKTTVTGIEMFRKTLDEAEAGDNVGVL 68 (87)
T ss_pred cEEEEEEEECCCCCccCCEEEEeCC---CC--CceEEEEEEEECCcCCCEECCCCEEEEE
Confidence 4456899999877654433432110 11 122344457777777 588899999874
No 37
>PRK00276 infA translation initiation factor IF-1; Validated
Probab=33.88 E-value=1.5e+02 Score=20.03 Aligned_cols=59 Identities=15% Similarity=0.140 Sum_probs=31.6
Q ss_pred ceEEEEEEeCCCCceEEEEEeeEEeecceeeEEeeeceEEEECCCCCCCCCCEEEEeecCcCCccee
Q 041511 43 KSVVGLVVSNKMQKSVVVAVDRLFHHKVYNRYVKRTSKFMAHDENNECNIGDRVRLDPSRPLSKHKH 109 (147)
Q Consensus 43 k~l~G~VVS~km~KTvvV~V~r~~~hpkY~K~i~r~kK~~vHDp~n~~kvGDiV~I~ecRPiSK~K~ 109 (147)
-++.|+|++........|..+ -...|....+..-+ +. ...+.+||.|.+.- .+...++-
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 467899997665444444321 11244444443322 11 23478999999985 33444443
No 38
>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=33.88 E-value=67 Score=20.48 Aligned_cols=29 Identities=31% Similarity=0.566 Sum_probs=19.2
Q ss_pred CCCCCCCEEEEeecCcCCcceeEEEEEEEeccc
Q 041511 88 NECNIGDRVRLDPSRPLSKHKHWLVAEILKKAR 120 (147)
Q Consensus 88 n~~kvGDiV~I~ecRPiSK~K~f~V~eIi~k~~ 120 (147)
....+||+|.+.... .-.+.+.+|+.+..
T Consensus 36 ~~~~VGD~V~~~~~~----~~~~~I~~vl~R~s 64 (68)
T cd04466 36 NPPAVGDRVEFEPED----DGEGVIEEILPRKN 64 (68)
T ss_pred CCCCCCcEEEEEECC----CCcEEEEEEeccce
Confidence 456899999986321 12467778887654
No 39
>PRK11637 AmiB activator; Provisional
Probab=33.72 E-value=91 Score=27.56 Aligned_cols=80 Identities=18% Similarity=0.168 Sum_probs=40.5
Q ss_pred EEEEEEeCCCCceEEEE----EeeEEeecceeeEEe-e----eceEEEECCCCCCCCCCEEEEeec----CcC-CcceeE
Q 041511 45 VVGLVVSNKMQKSVVVA----VDRLFHHKVYNRYVK-R----TSKFMAHDENNECNIGDRVRLDPS----RPL-SKHKHW 110 (147)
Q Consensus 45 l~G~VVS~km~KTvvV~----V~r~~~hpkY~K~i~-r----~kK~~vHDp~n~~kvGDiV~I~ec----RPi-SK~K~f 110 (147)
-.|+.+...-.-.|+-. |.+.-|.+-|+.++. . +..++.|...-.++.||.|.-++. .-- ..+-.+
T Consensus 329 ~~Gi~i~~~~g~~v~A~~~G~V~~~~~~~~~G~~vii~hg~g~~t~Y~~~~~~~v~~G~~V~~G~~ig~~g~~g~~~~~~ 408 (428)
T PRK11637 329 WKGMVIGASEGTEVKAIADGRVLLADWLQGYGLVVVVEHGKGDMSLYGYNQSALVSVGAQVRAGQPIALVGSSGGQGRPS 408 (428)
T ss_pred CCCEEeecCCCCeEEecCCeEEEEeeccCCcccEEEEEeCCCcEEEccCCCcCCCCCcCEECCCCeEEeecCCCCCCCCe
Confidence 45777754433333221 122245566665432 2 344567877778889998854442 110 123345
Q ss_pred EEEEEEecccccCCC
Q 041511 111 LVAEILKKARIYVPP 125 (147)
Q Consensus 111 ~V~eIi~k~~~~~~p 125 (147)
.-++|-..+. ..||
T Consensus 409 l~fei~~~~~-~vnP 422 (428)
T PRK11637 409 LYFEIRRQGQ-AVNP 422 (428)
T ss_pred EEEEEEECCE-EeCh
Confidence 5556665443 3444
No 40
>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=33.03 E-value=29 Score=23.64 Aligned_cols=13 Identities=31% Similarity=0.394 Sum_probs=11.0
Q ss_pred CCCCCCEEEEeec
Q 041511 89 ECNIGDRVRLDPS 101 (147)
Q Consensus 89 ~~kvGDiV~I~ec 101 (147)
-|+.||+|.|...
T Consensus 53 G~~~GD~V~Ig~~ 65 (69)
T TIGR03595 53 GAKDGDTVRIGDF 65 (69)
T ss_pred CCCCCCEEEEccE
Confidence 6899999999853
No 41
>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=31.80 E-value=70 Score=22.03 Aligned_cols=55 Identities=9% Similarity=-0.024 Sum_probs=31.9
Q ss_pred CccceEEEEEEeCCCCceEEEEEeeEEeecce-ee-EEeeeceEEEECCC-CCCCCCCEEEEe
Q 041511 40 SQMKSVVGLVVSNKMQKSVVVAVDRLFHHKVY-NR-YVKRTSKFMAHDEN-NECNIGDRVRLD 99 (147)
Q Consensus 40 ~~~k~l~G~VVS~km~KTvvV~V~r~~~hpkY-~K-~i~r~kK~~vHDp~-n~~kvGDiV~I~ 99 (147)
..+-.+.|+|.++...+--.+. .-|-. ++ +..+-+.+..|+.. +++..||.|.|.
T Consensus 13 g~GtVv~G~v~~G~v~~g~~v~-----~~P~~~g~~~~~~V~sI~~~~~~~~~a~aGd~v~l~ 70 (87)
T cd03694 13 GVGTVVGGTVSKGVIRLGDTLL-----LGPDQDGSFRPVTVKSIHRNRSPVRVVRAGQSASLA 70 (87)
T ss_pred CcceEEEEEEecCEEeCCCEEE-----ECCCCCCCEeEEEEEEEEECCeECCEECCCCEEEEE
Confidence 3444677777765543322222 22321 11 34555667777777 589999999874
No 42
>KOG1698 consensus Mitochondrial/chloroplast ribosomal protein L19 [Translation, ribosomal structure and biogenesis]
Probab=31.65 E-value=59 Score=27.22 Aligned_cols=35 Identities=23% Similarity=0.237 Sum_probs=29.3
Q ss_pred eEEEECCCCCCCCCCEEEEeecCcCCcceeEEEEEEE
Q 041511 80 KFMAHDENNECNIGDRVRLDPSRPLSKHKHWLVAEIL 116 (147)
Q Consensus 80 K~~vHDp~n~~kvGDiV~I~ecRPiSK~K~f~V~eIi 116 (147)
.+.-+-| +.++||+|.|..--|-+|.|.++...|+
T Consensus 89 r~~r~iP--e~~~G~Iv~V~s~~p~~k~k~s~f~Gi~ 123 (201)
T KOG1698|consen 89 RKVRDIP--EFKVGSIVRVTSEDPENKRKVSRFKGIC 123 (201)
T ss_pred HhcccCC--ccccccEEEEEecCCccCCceeEEEEEE
Confidence 3444455 8999999999999999999999988886
No 43
>PRK01889 GTPase RsgA; Reviewed
Probab=31.30 E-value=1.7e+02 Score=25.55 Aligned_cols=73 Identities=22% Similarity=0.247 Sum_probs=42.0
Q ss_pred EEEEEEeCCCCceEEEEEeeEEeecceeeEEeeeceEEEECCCCCCCCCCEEEEeecCcCCcceeEEEEEEEecccccCC
Q 041511 45 VVGLVVSNKMQKSVVVAVDRLFHHKVYNRYVKRTSKFMAHDENNECNIGDRVRLDPSRPLSKHKHWLVAEILKKARIYVP 124 (147)
Q Consensus 45 l~G~VVS~km~KTvvV~V~r~~~hpkY~K~i~r~kK~~vHDp~n~~kvGDiV~I~ecRPiSK~K~f~V~eIi~k~~~~~~ 124 (147)
..|+|++.... -..|..+. -.|....+..-+...+......-+||+|.+.. .-..++.+|+.+...+.-
T Consensus 29 ~~g~v~~~~~~-~~~v~~~~----~~~~~~~~gk~~~~~~~~~~~~~vGD~V~~~~------~~~g~I~~i~pR~~~L~R 97 (356)
T PRK01889 29 EPGRVVEEHRS-GYVVATEE----GEVRAEVSGKWRHEAFPPGDRPAVGDWVLLDN------EKKARIVRLLPRRSLFSR 97 (356)
T ss_pred ccEEEEEEECC-EEEEEECC----cEEEEEecchhhccccccCCCCccCcEEEEec------CCceEEEEEECCCceEEc
Confidence 47999874432 23343322 23333333332333344445689999999963 134778899988766666
Q ss_pred CCcc
Q 041511 125 PSAD 128 (147)
Q Consensus 125 p~~~ 128 (147)
|..+
T Consensus 98 ~~~~ 101 (356)
T PRK01889 98 KAAG 101 (356)
T ss_pred CCCC
Confidence 6554
No 44
>COG0361 InfA Translation initiation factor 1 (IF-1) [Translation, ribosomal structure and biogenesis]
Probab=30.18 E-value=2e+02 Score=20.38 Aligned_cols=46 Identities=20% Similarity=0.145 Sum_probs=31.4
Q ss_pred ceEEEEEEeCCCCceEEEEEeeEEeecceeeEEeeeceEEEECCCC------CCCCCCEEEEeec
Q 041511 43 KSVVGLVVSNKMQKSVVVAVDRLFHHKVYNRYVKRTSKFMAHDENN------ECNIGDRVRLDPS 101 (147)
Q Consensus 43 k~l~G~VVS~km~KTvvV~V~r~~~hpkY~K~i~r~kK~~vHDp~n------~~kvGDiV~I~ec 101 (147)
-++.|+|+....+..+.|..+--+ ..++|-+.. -..+||+|++...
T Consensus 7 ~e~~g~V~e~L~~~~f~v~~edg~-------------~~~ahI~GKmr~~~i~I~~GD~V~Ve~~ 58 (75)
T COG0361 7 IEMEGTVIEMLPNGRFRVELENGH-------------ERLAHISGKMRKNRIRILPGDVVLVELS 58 (75)
T ss_pred cEEEEEEEEecCCCEEEEEecCCc-------------EEEEEccCcchheeEEeCCCCEEEEEec
Confidence 368999999888888888765432 344555542 3568999987643
No 45
>cd04088 EFG_mtEFG_II EFG_mtEFG_II: this subfamily represents the domain II of elongation factor G (EF-G) in bacteria and, the C-terminus of mitochondrial Elongation factor G1 (mtEFG1) and G2 (mtEFG2)_like proteins found in eukaryotes. During the process of peptide synthesis and tRNA site changes, the ribosome is moved along the mRNA a distance equal to one codon with the addition of each amino acid. In bacteria this translocation step is catalyzed by EF-G_GTP, which is hydrolyzed to provide the required energy. Thus, this action releases the uncharged tRNA from the P site and transfers the newly formed peptidyl-tRNA from the A site to the P site. Eukaryotic cells harbor 2 protein synthesis systems: one localized in the cytoplasm, the other in the mitochondria. Most factors regulating mitochondrial protein synthesis are encoded by nuclear genes, translated in the cytoplasm, and then transported to the mitochondria. The eukaryotic system of elongation factor (EF) components is more compl
Probab=29.61 E-value=1.5e+02 Score=19.65 Aligned_cols=58 Identities=16% Similarity=0.078 Sum_probs=29.0
Q ss_pred cCccceEEEEEEeCCCCceEEEEEeeEEeecceeeEEeeeceEEEE--CCCCCCCCCCEEEEee
Q 041511 39 PSQMKSVVGLVVSNKMQKSVVVAVDRLFHHKVYNRYVKRTSKFMAH--DENNECNIGDRVRLDP 100 (147)
Q Consensus 39 ~~~~k~l~G~VVS~km~KTvvV~V~r~~~hpkY~K~i~r~kK~~vH--Dp~n~~kvGDiV~I~e 100 (147)
+..++...++|.++...+--.|.+.....-.+..+. -.++.. -+-+++..||++.|..
T Consensus 12 ~~~G~~~~~Rv~sG~l~~g~~v~~~~~~~~~~v~~l----~~~~g~~~~~v~~~~aGdI~~i~g 71 (83)
T cd04088 12 PFVGKLSFVRVYSGTLKAGSTLYNSTKGKKERVGRL----LRMHGKKQEEVEEAGAGDIGAVAG 71 (83)
T ss_pred CCCceEEEEEEecCEEcCCCEEEECCCCcEEEeeEE----EEEcCCCceECCEeCCCCEEEEEC
Confidence 556677788888766655444433221000011111 111111 1115899999999954
No 46
>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=28.89 E-value=2e+02 Score=19.92 Aligned_cols=51 Identities=18% Similarity=0.281 Sum_probs=32.3
Q ss_pred eEEEEEEeCCCCceEEEEEeeEEeecceeeEEeeeceEEEECCCC------CCCCCCEEEEeecCcCCcce
Q 041511 44 SVVGLVVSNKMQKSVVVAVDRLFHHKVYNRYVKRTSKFMAHDENN------ECNIGDRVRLDPSRPLSKHK 108 (147)
Q Consensus 44 ~l~G~VVS~km~KTvvV~V~r~~~hpkY~K~i~r~kK~~vHDp~n------~~kvGDiV~I~ecRPiSK~K 108 (147)
++.|+|+....+-...|..+- -..+++|-+.. -...||.|.+. ..|...+|
T Consensus 6 e~~G~V~e~L~~~~f~V~l~n-------------g~~vla~i~GKmr~~rI~I~~GD~V~Ve-~spyd~tk 62 (68)
T TIGR00008 6 EMEGKVTESLPNAMFRVELEN-------------GHEVLAHISGKIRMHYIRILPGDKVKVE-LSPYDLTR 62 (68)
T ss_pred EEEEEEEEECCCCEEEEEECC-------------CCEEEEEecCcchhccEEECCCCEEEEE-ECcccCCc
Confidence 678999987777777777552 23334444431 25689999887 44555444
No 47
>cd03699 lepA_II lepA_II: This subfamily represents the domain II of LepA, a GTP-binding protein localized in the cytoplasmic membrane. The N-terminal domain of LepA shares regions of homology to translation factors. In terms of interaction with the ribosome, EF-G, EF-Tu and IF2 have all been demonstrated to interact at overlapping sites on the ribosome. Chemical protection studies demonstrate that they all include the universally conserved alpha-sarcin loop as part of their binding site. These data indicate that LepA may bind to this location on the ribosome as well. LepA has never been observed in archaea, and eukaryl LepA is organellar. LepA is therefore a true bacterial GTPase, found only in the bacterial lineage.
Probab=28.84 E-value=1.5e+02 Score=20.05 Aligned_cols=54 Identities=11% Similarity=0.023 Sum_probs=28.8
Q ss_pred cCccceEEEEEEeCCCCceEEEEEeeEEeecceeeEEeeeceEEE-EC---CCCCCCCCCEEEEe
Q 041511 39 PSQMKSVVGLVVSNKMQKSVVVAVDRLFHHKVYNRYVKRTSKFMA-HD---ENNECNIGDRVRLD 99 (147)
Q Consensus 39 ~~~~k~l~G~VVS~km~KTvvV~V~r~~~hpkY~K~i~r~kK~~v-HD---p~n~~kvGDiV~I~ 99 (147)
+..++...|+|.++...+--.|..... +.+ .+ -.+++. +. +-.++..||++.|.
T Consensus 12 ~~~G~i~~~Rv~sG~l~~~~~v~~~~~--~~~----~~-i~~l~~~~~~~~~~~~~~aGdI~~v~ 69 (86)
T cd03699 12 PYRGVIALVRVFDGTLKKGDKIRFMST--GKE----YE-VEEVGIFRPEMTPTDELSAGQVGYII 69 (86)
T ss_pred CCCCEEEEEEEEcCEEcCCCEEEEecC--CCe----EE-EEEEEEECCCccCCceECCCCEEEEE
Confidence 556778888898877654333322211 111 11 111222 22 22588999999885
No 48
>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=28.50 E-value=63 Score=23.99 Aligned_cols=21 Identities=29% Similarity=0.463 Sum_probs=14.4
Q ss_pred ceEEEECCCCCCCCCCEEEEee
Q 041511 79 SKFMAHDENNECNIGDRVRLDP 100 (147)
Q Consensus 79 kK~~vHDp~n~~kvGDiV~I~e 100 (147)
..+.++++. .+++||.|.|.-
T Consensus 42 ~~~~~~~~~-~~~~GD~V~v~i 62 (135)
T PF04246_consen 42 ITFRAPNPI-GAKVGDRVEVEI 62 (135)
T ss_pred EEEEecCCC-CCCCCCEEEEEe
Confidence 344454443 799999999864
No 49
>PRK05753 nucleoside diphosphate kinase regulator; Provisional
Probab=27.94 E-value=1.4e+02 Score=22.71 Aligned_cols=27 Identities=22% Similarity=0.273 Sum_probs=21.8
Q ss_pred CCCCCCEEEEeecCcCCcceeEEEEEEEe
Q 041511 89 ECNIGDRVRLDPSRPLSKHKHWLVAEILK 117 (147)
Q Consensus 89 ~~kvGDiV~I~ecRPiSK~K~f~V~eIi~ 117 (147)
-.++||.|.+. .|-...+.+.|.+|.+
T Consensus 101 G~~~Gd~v~v~--~p~G~~~~~~I~~I~y 127 (137)
T PRK05753 101 GLSVGQSIDWP--LPGGKETHLEVLEVEY 127 (137)
T ss_pred CCCCCCEEEEE--CCCCCEEEEEEEEEEe
Confidence 57899999987 5666667899999974
No 50
>PF13567 DUF4131: Domain of unknown function (DUF4131)
Probab=27.20 E-value=2.3e+02 Score=19.97 Aligned_cols=62 Identities=21% Similarity=0.282 Sum_probs=34.7
Q ss_pred ceEEEEEEeCC--CCce--EEEEEeeEEeecceeeEEeeeceEEEECCCC--C-CCCCCEEEEeec-CcCCcc
Q 041511 43 KSVVGLVVSNK--MQKS--VVVAVDRLFHHKVYNRYVKRTSKFMAHDENN--E-CNIGDRVRLDPS-RPLSKH 107 (147)
Q Consensus 43 k~l~G~VVS~k--m~KT--vvV~V~r~~~hpkY~K~i~r~kK~~vHDp~n--~-~kvGDiV~I~ec-RPiSK~ 107 (147)
..++|+|.+.. ..++ ..+.+++. ..-.......-++.+..+.+ . ...||.+++... +|++..
T Consensus 78 ~~v~g~V~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~i~~~~~~~~~~~l~~Gd~i~~~g~l~~~~~~ 147 (176)
T PF13567_consen 78 VTVQGTVESVPQIDGRGQRFTLRVERV---LAGGNWIPVSGKILLYLPKDSQPRLQPGDRIRVRGKLKPPSGP 147 (176)
T ss_pred EEEEEEEcccccccCceEEEEEEEEEe---eccccccccceeeEEEeccccccccCCCCEEEEEEEEecCCCC
Confidence 35899998632 2223 34444444 33333444444555555554 3 679999999774 665543
No 51
>TIGR00157 ribosome small subunit-dependent GTPase A. The Aquifex aeolicus ortholog is split into consecutive open reading frames. Consequently, this model was build in fragment mode (-f option).
Probab=27.02 E-value=83 Score=25.77 Aligned_cols=38 Identities=21% Similarity=0.280 Sum_probs=26.2
Q ss_pred CCCCEEEEeecCcCCcceeEEEEEEEecccccCCCCccchhc
Q 041511 91 NIGDRVRLDPSRPLSKHKHWLVAEILKKARIYVPPSADNAAA 132 (147)
Q Consensus 91 kvGDiV~I~ecRPiSK~K~f~V~eIi~k~~~~~~p~~~~~~~ 132 (147)
.+||+|.+... ......+.+|+++-..+.++...++..
T Consensus 2 ~vGD~V~~~~~----~~~~~~i~~i~eR~~~L~r~~~~n~D~ 39 (245)
T TIGR00157 2 VVGDRVVWEPG----NVVKVYGGAIAERKNELTRPIVANIDQ 39 (245)
T ss_pred CCCcEEEEEec----CCCceEEEEEecccceEECcccccCCE
Confidence 58999999742 124578999998877777665444433
No 52
>PF09926 DUF2158: Uncharacterized small protein (DUF2158); InterPro: IPR019226 This entry represents a family of predominantly prokaryotic proteins with no known function.
Probab=26.83 E-value=48 Score=21.87 Aligned_cols=13 Identities=46% Similarity=0.792 Sum_probs=11.4
Q ss_pred CCCCEEEEeecCc
Q 041511 91 NIGDRVRLDPSRP 103 (147)
Q Consensus 91 kvGDiV~I~ecRP 103 (147)
++||+|++...-|
T Consensus 2 ~~GDvV~LKSGGp 14 (53)
T PF09926_consen 2 KIGDVVQLKSGGP 14 (53)
T ss_pred CCCCEEEEccCCC
Confidence 6899999998876
No 53
>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=26.69 E-value=33 Score=23.32 Aligned_cols=12 Identities=33% Similarity=0.534 Sum_probs=7.6
Q ss_pred CCCCCCEEEEee
Q 041511 89 ECNIGDRVRLDP 100 (147)
Q Consensus 89 ~~kvGDiV~I~e 100 (147)
-|+.||+|.|..
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 588999999975
No 54
>cd03689 RF3_II RF3_II: this subfamily represents the domain II of bacterial Release Factor 3 (RF3). Termination of protein synthesis by the ribosome requires two release factor (RF) classes. The class II RF3 is a GTPase that removes class I RFs (RF1 or RF2) from the ribosome after release of the nascent polypeptide. RF3 in the GDP state binds to the ribosomal class I RF complex, followed by an exchange of GDP for GTP and release of the class I RF. Sequence comparison of class II release factors with elongation factors shows that prokaryotic RF3 is more similar to EF-G whereas eukaryotic eRF3 is more similar to eEF1A, implying that their precise function may differ.
Probab=25.54 E-value=2.2e+02 Score=19.50 Aligned_cols=14 Identities=29% Similarity=0.332 Sum_probs=11.6
Q ss_pred CCCCCCCEEEEeec
Q 041511 88 NECNIGDRVRLDPS 101 (147)
Q Consensus 88 n~~kvGDiV~I~ec 101 (147)
+++..||+|.+...
T Consensus 60 ~~a~aGdIv~v~gl 73 (85)
T cd03689 60 DEAYPGDIIGLVNP 73 (85)
T ss_pred CEECCCCEEEEECC
Confidence 57899999998764
No 55
>cd04454 S1_Rrp4_like S1_Rrp4_like: Rrp4-like, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Rrp4 protein, and Rrp40 and Csl4 proteins, also represented in this group, are subunits of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In Saccharomyces cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".
Probab=25.46 E-value=2.1e+02 Score=18.98 Aligned_cols=58 Identities=14% Similarity=0.088 Sum_probs=32.7
Q ss_pred cCccceEEEEEEeCCCCceEEEEEeeEEeecceeeEEeeeceEE--EECCCCCCCCCCEEEEeecC
Q 041511 39 PSQMKSVVGLVVSNKMQKSVVVAVDRLFHHKVYNRYVKRTSKFM--AHDENNECNIGDRVRLDPSR 102 (147)
Q Consensus 39 ~~~~k~l~G~VVS~km~KTvvV~V~r~~~hpkY~K~i~r~kK~~--vHDp~n~~kvGDiV~I~ecR 102 (147)
|..+....|+|++-. ++-+.|.+... +.-++....--. .-+.....++||.+...=++
T Consensus 4 p~~GdiV~G~V~~v~-~~~~~V~i~~~-----~~g~l~~~~~~~~~~~~~~~~~~~GD~i~~~V~~ 63 (82)
T cd04454 4 PDVGDIVIGIVTEVN-SRFWKVDILSR-----GTARLEDSSATEKDKKEIRKSLQPGDLILAKVIS 63 (82)
T ss_pred CCCCCEEEEEEEEEc-CCEEEEEeCCC-----ceEEeechhccCcchHHHHhcCCCCCEEEEEEEE
Confidence 567778899999764 56677766431 222222221110 11112358999999776553
No 56
>PF07347 CI-B14_5a: NADH:ubiquinone oxidoreductase subunit B14.5a (Complex I-B14.5a); InterPro: IPR009947 NADH:ubiquinone oxidoreductase (complex I) (1.6.5.3 from EC) is a respiratory-chain enzyme that catalyses the transfer of two electrons from NADH to ubiquinone in a reaction that is associated with proton translocation across the membrane (NADH + ubiquinone = NAD+ + ubiquinol) []. Complex I is a major source of reactive oxygen species (ROS) that are predominantly formed by electron transfer from FMNH(2). Complex I is found in bacteria, cyanobacteria (as a NADH-plastoquinone oxidoreductase), archaea [], mitochondira, and in the hydrogenosome, a mitochondria-derived organelle. In general, the bacterial complex consists of 14 different subunits, while the mitochondrial complex contains homologues to these subunits in addition to approximately 31 additional proteins []. Mitochondrial complex I, which is located in the inner mitochondrial membrane, is the largest multimeric respiratory enzyme in the mitochondria, consisting of more than 40 subunits, one FMN co-factor and eight FeS clusters []. The assembly of mitochondrial complex I is an intricate process that requires the cooperation of the nuclear and mitochondrial genomes [, ]. Mitochondrial complex I can cycle between active and deactive forms that can be distinguished by the reactivity towards divalent cations and thiol-reactive agents. All redox prosthetic groups reside in the peripheral arm of the L-shaped structure. The NADH oxidation domain harbouring the FMN cofactor is connected via a chain of iron-sulphur clusters to the ubiquinone reduction site that is located in a large pocket formed by the PSST and 49kDa subunits of complex I []. This family contains the eukaryotic NADH:ubiquinone oxidoreductase subunit B14.5a (Complex I-B14.5a). This is approximately 100 residues long, and forms part of a multiprotein complex that resides on the inner mitochondrial membrane [].; GO: 0008137 NADH dehydrogenase (ubiquinone) activity, 0042773 ATP synthesis coupled electron transport, 0005743 mitochondrial inner membrane
Probab=25.22 E-value=50 Score=24.57 Aligned_cols=29 Identities=41% Similarity=0.638 Sum_probs=21.1
Q ss_pred CCCCCCCCC------ceeeeecc---ccceecccCCCC
Q 041511 2 NSPRTVPPP------HHRFLSCA---VDLRQLLWPPSV 30 (147)
Q Consensus 2 ~~~~~~~~~------h~~~~~~~---~~~~~~~~~~~~ 30 (147)
-|+|||||| ||..-.+- -|-|+-.=||-+
T Consensus 26 ~s~RTqPpP~lP~Gp~hkls~NyYy~RD~RRev~PP~~ 63 (97)
T PF07347_consen 26 ISPRTQPPPNLPGGPSHKLSANYYYTRDARREVQPPID 63 (97)
T ss_pred cccCCCCCCCCCCCCccccccccccccccccccCCCeE
Confidence 489999998 77665553 378888777644
No 57
>cd05789 S1_Rrp4 S1_Rrp4: Rrp4 S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Rrp4 protein is a subunit of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In Saccharomyces cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".
Probab=25.21 E-value=1.5e+02 Score=19.83 Aligned_cols=57 Identities=16% Similarity=0.117 Sum_probs=32.2
Q ss_pred cCccceEEEEEEeCCCCceEEEEEeeEEeecceeeEEeeeceE------EEECCCCCCCCCCEEEEeec
Q 041511 39 PSQMKSVVGLVVSNKMQKSVVVAVDRLFHHKVYNRYVKRTSKF------MAHDENNECNIGDRVRLDPS 101 (147)
Q Consensus 39 ~~~~k~l~G~VVS~km~KTvvV~V~r~~~hpkY~K~i~r~kK~------~vHDp~n~~kvGDiV~I~ec 101 (147)
++.+....|+|++. .++-+.|.+.. .+.-++....-. ..-+.....++||.|.+.=.
T Consensus 4 p~~GdiV~g~V~~i-~~~g~~v~i~~-----~~~G~l~~se~~~~~~~~~~~~~~~~l~vGd~i~~~V~ 66 (86)
T cd05789 4 PEVGDVVIGRVTEV-GFKRWKVDINS-----PYDAVLPLSEVNLPRTDEDELNMRSYLDEGDLIVAEVQ 66 (86)
T ss_pred CCCCCEEEEEEEEE-CCCEEEEECCC-----CeEEEEEHHHccCCCCccchHHHHhhCCCCCEEEEEEE
Confidence 45677889999984 45667776642 233333322111 01122235899999976544
No 58
>COG2012 RPB5 DNA-directed RNA polymerase, subunit H, RpoH/RPB5 [Transcription]
Probab=25.17 E-value=42 Score=24.32 Aligned_cols=21 Identities=29% Similarity=0.260 Sum_probs=15.7
Q ss_pred eEEEECCC---CCCCCCCEEEEee
Q 041511 80 KFMAHDEN---NECNIGDRVRLDP 100 (147)
Q Consensus 80 K~~vHDp~---n~~kvGDiV~I~e 100 (147)
++.+-||- -.++.||+|.|.-
T Consensus 42 kI~~~DPva~~lgak~GdvVkIvR 65 (80)
T COG2012 42 KIKASDPVAKALGAKPGDVVKIVR 65 (80)
T ss_pred cccccChhHHHccCCCCcEEEEEe
Confidence 56677884 4899999887754
No 59
>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=23.72 E-value=84 Score=20.00 Aligned_cols=51 Identities=14% Similarity=0.294 Sum_probs=29.1
Q ss_pred ceEEEEEEeCCCCceEEEEEeeEEeecceeeEEeeec--eEEEECCCCCCCCCCEEEEe
Q 041511 43 KSVVGLVVSNKMQKSVVVAVDRLFHHKVYNRYVKRTS--KFMAHDENNECNIGDRVRLD 99 (147)
Q Consensus 43 k~l~G~VVS~km~KTvvV~V~r~~~hpkY~K~i~r~k--K~~vHDp~n~~kvGDiV~I~ 99 (147)
..+.|+|++-. ++-+.|.+... ..-++.... .-.+.|+....++||.|.+.
T Consensus 2 ~~~~g~V~~v~-~~G~~V~l~~~-----~~gli~~s~l~~~~~~~~~~~~~~G~~i~v~ 54 (70)
T cd05698 2 LKTHGTIVKVK-PNGCIVSFYNN-----VKGFLPKSELSEAFIKDPEEHFRVGQVVKVK 54 (70)
T ss_pred CEEEEEEEEEe-cCcEEEEECCC-----CEEEEEHHHcChhhcCCHHHcccCCCEEEEE
Confidence 45788888654 46677776421 111111110 01255666789999998765
No 60
>PRK10409 hydrogenase assembly chaperone; Provisional
Probab=23.01 E-value=58 Score=23.79 Aligned_cols=18 Identities=17% Similarity=0.231 Sum_probs=13.6
Q ss_pred CCCCCCCEEEEeecCcCC
Q 041511 88 NECNIGDRVRLDPSRPLS 105 (147)
Q Consensus 88 n~~kvGDiV~I~ecRPiS 105 (147)
.++++||+|++.-.--||
T Consensus 40 ~~~~vGDyVLVHaGfAi~ 57 (90)
T PRK10409 40 GQPRVGQWVLVHVGFAMS 57 (90)
T ss_pred CccCCCCEEEEecChHHh
Confidence 379999999998754443
No 61
>PF01938 TRAM: TRAM domain; InterPro: IPR002792 The TRAM (after TRM2 and miaB) domain is a 60-70-residue-long module that is found in: Two distinct classes of tRNA-modifying enzymes, namely uridine methylases of the TRM2 family and enzymes of the miaB family that are involved in 2- methylthioadenine formation In several other proteins associated with the translation machinery In a family of small uncharacterised archaeal proteins that are predicted to have a role in the regulation of tRNA modification and/or translation The TRAM domain can be found alone or in association with other domains, such as the catalytic biotin/lipoate synthetase-like domain, the RNA methylase domain, the ribosomal S2 domain and the eIF2-beta domain. The TRAM domain is predicted to bind tRNA and deliver the RNA-modifying enzymatic domain to their targets []. Secondary structure prediction indicates that the TRAM domain adopts a simple beta-barrel fold. The conservation pattern of the TRAM domain consists primarily of small and hydrophobic residues that correspond to five beta-strands in the predicted secondary structure [].; PDB: 1YEZ_A 2BH2_A 1UWV_A 1YVC_A.
Probab=23.00 E-value=2.1e+02 Score=18.12 Aligned_cols=42 Identities=21% Similarity=0.190 Sum_probs=23.6
Q ss_pred CceEEEEEeeEEeecceeeEEeeec-eEEEECCCCCCCCCCEEEEe
Q 041511 55 QKSVVVAVDRLFHHKVYNRYVKRTS-KFMAHDENNECNIGDRVRLD 99 (147)
Q Consensus 55 ~KTvvV~V~r~~~hpkY~K~i~r~k-K~~vHDp~n~~kvGDiV~I~ 99 (147)
.+++.|.|+... ++ +..+=|+. ...++-+.....+||.|.++
T Consensus 5 G~~~~VlVe~~~-~~--g~~~gr~~~~~~V~v~~~~~~iG~~v~v~ 47 (61)
T PF01938_consen 5 GKTLEVLVEELG-DE--GQGIGRTDNGKVVFVPGGLPLIGEFVKVR 47 (61)
T ss_dssp TEEEEEEEEEE--TT--SEEEEEET-TEEEEETT--T--TEEEEEE
T ss_pred CcEEEEEEEEec-CC--CEEEEEeCCCeEEEECCCCCCCCCEEEEE
Confidence 467888888887 22 22344444 56666666544489998665
No 62
>PF10377 ATG11: Autophagy-related protein 11; InterPro: IPR019460 This family consists of proteins involved in telomere maintenance. In Schizosaccharomyces pombe (fission yeast) this protein is called Taf1 (taz1 interacting factor) and is part of the telomere cap complex. In Saccharomyces cerevisiae (baker's yeast) this protein is called ATG11 and is known to be involved in vacuolar targeting and peroxisome degradation [, ].
Probab=22.88 E-value=1.1e+02 Score=23.34 Aligned_cols=15 Identities=33% Similarity=0.558 Sum_probs=13.0
Q ss_pred CCCCCCEEEEeecCc
Q 041511 89 ECNIGDRVRLDPSRP 103 (147)
Q Consensus 89 ~~kvGDiV~I~ecRP 103 (147)
.|++||.|++..++.
T Consensus 42 ~f~~GDlvLflpt~~ 56 (129)
T PF10377_consen 42 NFQVGDLVLFLPTRN 56 (129)
T ss_pred cCCCCCEEEEEecCC
Confidence 689999999998854
No 63
>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=22.26 E-value=1.4e+02 Score=20.10 Aligned_cols=50 Identities=22% Similarity=0.173 Sum_probs=27.1
Q ss_pred cceEEEEEEeCCCCceEEEEEeeEEeecceeeEEeeeceEEEECCC-CCCCCCCEEEE
Q 041511 42 MKSVVGLVVSNKMQKSVVVAVDRLFHHKVYNRYVKRTSKFMAHDEN-NECNIGDRVRL 98 (147)
Q Consensus 42 ~k~l~G~VVS~km~KTvvV~V~r~~~hpkY~K~i~r~kK~~vHDp~-n~~kvGDiV~I 98 (147)
+....|+|.++....--+|.+ -|-- ....-+.+..|+.. +++..||.|.|
T Consensus 14 g~vv~G~v~~G~i~~G~~v~i-----~P~~--~~~~V~si~~~~~~~~~a~aGd~v~l 64 (82)
T cd04089 14 GTVVLGKVESGTIKKGDKLLV-----MPNK--TQVEVLSIYNEDVEVRYARPGENVRL 64 (82)
T ss_pred CEEEEEEEeeeEEecCCEEEE-----eCCC--cEEEEEEEEECCEECCEECCCCEEEE
Confidence 446777777655433222221 1221 23445556666655 47888888876
No 64
>KOG3507 consensus DNA-directed RNA polymerase, subunit RPB7.0 [Transcription]
Probab=21.95 E-value=45 Score=23.08 Aligned_cols=15 Identities=27% Similarity=0.366 Sum_probs=13.9
Q ss_pred CCCCCCCCEEEEeec
Q 041511 87 NNECNIGDRVRLDPS 101 (147)
Q Consensus 87 ~n~~kvGDiV~I~ec 101 (147)
+|+++-||.|+.+||
T Consensus 29 en~lk~~D~irCReC 43 (62)
T KOG3507|consen 29 ENTLKRGDVIRCREC 43 (62)
T ss_pred cccccCCCcEehhhc
Confidence 479999999999999
No 65
>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=21.24 E-value=1.8e+02 Score=17.57 Aligned_cols=25 Identities=20% Similarity=0.379 Sum_probs=17.1
Q ss_pred ceEEEECCC-----CCCCCCCEEEEeecCc
Q 041511 79 SKFMAHDEN-----NECNIGDRVRLDPSRP 103 (147)
Q Consensus 79 kK~~vHDp~-----n~~kvGDiV~I~ecRP 103 (147)
..+++|... ..+..||.|.+.-..+
T Consensus 21 ~~i~v~~~~~~~~~~~~~~Gd~V~~~i~~~ 50 (64)
T smart00357 21 KDVFVHPSQIQGGLKSLREGDEVEFKVVSP 50 (64)
T ss_pred ccEEEEhHHhhcCCCcCCCCCEEEEEEEEc
Confidence 356666444 4678899999986543
No 66
>cd05692 S1_RPS1_repeat_hs4 S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 4 (hs4) of the H. sapiens RPS1 homolog. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=21.07 E-value=1.5e+02 Score=18.03 Aligned_cols=51 Identities=20% Similarity=0.192 Sum_probs=26.5
Q ss_pred ceEEEEEEeCCCCceEEEEEeeEEeecceeeEEeeec--eEEEECCCCCCCCCCEEEEe
Q 041511 43 KSVVGLVVSNKMQKSVVVAVDRLFHHKVYNRYVKRTS--KFMAHDENNECNIGDRVRLD 99 (147)
Q Consensus 43 k~l~G~VVS~km~KTvvV~V~r~~~hpkY~K~i~r~k--K~~vHDp~n~~kvGDiV~I~ 99 (147)
..+.|+|+.-. +.-+.|.+.. .+.-++.... .-...++....++||.|.+.
T Consensus 2 ~~~~g~V~~i~-~~g~~v~i~~-----~~~g~l~~~~l~~~~~~~~~~~~~~Gd~v~v~ 54 (69)
T cd05692 2 SVVEGTVTRLK-PFGAFVELGG-----GISGLVHISQIAHKRVKDVKDVLKEGDKVKVK 54 (69)
T ss_pred CEEEEEEEEEE-eeeEEEEECC-----CCEEEEEhHHcCCcccCCHHHccCCCCEEEEE
Confidence 46788887633 3556665541 1222222211 00123444568999999765
No 67
>PF08605 Rad9_Rad53_bind: Fungal Rad9-like Rad53-binding; InterPro: IPR013914 In Saccharomyces cerevisiae (Baker s yeast), the Rad9 is a key adaptor protein in DNA damage checkpoint pathways. DNA damage induces Rad9 phosphorylation, and Rad53 specifically associates with this region of Rad9, when phosphorylated, via the Rad53 IPR000253 from INTERPRO domain []. There is no clear higher eukaryotic ortholog to Rad9.
Probab=20.74 E-value=1.1e+02 Score=23.60 Aligned_cols=61 Identities=18% Similarity=0.236 Sum_probs=36.6
Q ss_pred ccceEEEEEEeCCC-CceEEEEEeeEEeecceeeEEeeeceEEEECCC-CCCCCCCEEEEeecCcCCcceeEEEEEEEec
Q 041511 41 QMKSVVGLVVSNKM-QKSVVVAVDRLFHHKVYNRYVKRTSKFMAHDEN-NECNIGDRVRLDPSRPLSKHKHWLVAEILKK 118 (147)
Q Consensus 41 ~~k~l~G~VVS~km-~KTvvV~V~r~~~hpkY~K~i~r~kK~~vHDp~-n~~kvGDiV~I~ecRPiSK~K~f~V~eIi~k 118 (147)
..+..-|++++... .....|..+--. ..+-..|=. -++++||.|.+.. ++-.|+|...-.+
T Consensus 21 ~~~yYPa~~~~~~~~~~~~~V~Fedg~------------~~i~~~dv~~LDlRIGD~Vkv~~-----~k~~yiV~Gl~~~ 83 (131)
T PF08605_consen 21 NLKYYPATCVGSGVDRDRSLVRFEDGT------------YEIKNEDVKYLDLRIGDTVKVDG-----PKVTYIVVGLECK 83 (131)
T ss_pred CCeEeeEEEEeecCCCCeEEEEEecCc------------eEeCcccEeeeeeecCCEEEECC-----CCccEEEEEeeec
Confidence 45667888887433 324555543322 112222222 3899999999998 3346888887766
No 68
>COG3655 Predicted transcriptional regulator [Transcription]
Probab=20.10 E-value=56 Score=23.15 Aligned_cols=12 Identities=42% Similarity=0.805 Sum_probs=10.0
Q ss_pred CCCCCCEEEEee
Q 041511 89 ECNIGDRVRLDP 100 (147)
Q Consensus 89 ~~kvGDiV~I~e 100 (147)
+|++||++.+..
T Consensus 56 eCqpgDiley~~ 67 (73)
T COG3655 56 ECQPGDILEYVP 67 (73)
T ss_pred CCChhheeEEec
Confidence 799999998753
Done!