Query 033970
Match_columns 107
No_of_seqs 113 out of 1009
Neff 5.0
Searched_HMMs 46136
Date Fri Mar 29 08:19:39 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/033970.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/033970hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 CHL00142 rps17 ribosomal prote 100.0 9.2E-37 2E-41 206.2 11.9 80 1-80 3-82 (84)
2 PRK05610 rpsQ 30S ribosomal pr 100.0 3E-36 6.6E-41 203.5 11.8 77 2-78 7-83 (84)
3 COG0186 RpsQ Ribosomal protein 100.0 3E-36 6.5E-41 205.0 11.1 78 2-79 9-86 (87)
4 PRK08572 rps17p 30S ribosomal 100.0 8.1E-35 1.7E-39 204.6 11.7 77 2-78 30-107 (108)
5 TIGR03635 S17_bact 30S ribosom 100.0 7.7E-35 1.7E-39 191.3 10.0 70 2-71 2-71 (71)
6 TIGR03630 arch_S17P archaeal r 100.0 1.7E-34 3.6E-39 201.3 11.4 74 2-75 28-102 (102)
7 KOG1740 Predicted mitochondria 100.0 1.1E-35 2.3E-40 207.1 0.8 99 1-104 2-100 (107)
8 PF00366 Ribosomal_S17: Riboso 100.0 6.7E-34 1.5E-38 185.6 9.2 69 6-74 1-69 (69)
9 PTZ00241 40S ribosomal protein 100.0 6.7E-32 1.4E-36 200.2 11.6 77 2-78 69-146 (158)
10 KOG1728 40S ribosomal protein 99.8 5E-22 1.1E-26 145.7 3.5 81 2-82 69-151 (156)
11 KOG3447 Mitochondrial/chloropl 99.8 6.3E-21 1.4E-25 139.1 1.9 105 2-106 11-117 (150)
12 cd05793 S1_IF1A S1_IF1A: Trans 63.9 26 0.00056 22.9 5.1 52 4-69 2-58 (77)
13 cd04451 S1_IF1 S1_IF1: Transla 59.4 39 0.00083 20.7 5.5 51 3-60 2-52 (64)
14 PF10844 DUF2577: Protein of u 55.1 63 0.0014 21.8 8.2 61 3-72 19-97 (100)
15 PF13550 Phage-tail_3: Putativ 53.6 37 0.0008 23.4 4.8 36 37-75 128-163 (164)
16 cd04466 S1_YloQ_GTPase S1_YloQ 52.3 26 0.00055 21.1 3.4 29 47-79 36-64 (68)
17 cd01854 YjeQ_engC YjeQ/EngC. 49.7 54 0.0012 25.8 5.6 32 46-81 32-63 (287)
18 TIGR00008 infA translation ini 48.6 73 0.0016 20.7 6.0 51 3-67 6-62 (68)
19 PTZ00329 eukaryotic translatio 46.9 1.2E+02 0.0026 22.7 7.2 60 4-73 34-94 (155)
20 TIGR00523 eIF-1A eukaryotic/ar 46.8 94 0.002 21.4 5.9 48 3-64 20-72 (99)
21 smart00652 eIF1a eukaryotic tr 44.3 83 0.0018 20.8 5.1 52 3-68 6-62 (83)
22 cd04486 YhcR_OBF_like YhcR_OBF 42.9 36 0.00078 22.0 3.1 19 40-58 35-54 (78)
23 COG0361 InfA Translation initi 41.5 1E+02 0.0023 20.4 5.7 45 3-60 8-58 (75)
24 PRK10413 hydrogenase 2 accesso 40.1 1.1E+02 0.0024 20.4 6.0 51 6-65 7-59 (82)
25 cd04456 S1_IF1A_like S1_IF1A_l 38.8 97 0.0021 20.3 4.7 51 4-68 2-58 (78)
26 PF04246 RseC_MucC: Positive r 38.2 41 0.00089 23.4 3.0 22 37-59 41-62 (135)
27 PF01176 eIF-1a: Translation i 37.6 77 0.0017 19.7 4.0 52 3-68 4-60 (65)
28 cd04089 eRF3_II eRF3_II: domai 36.1 45 0.00098 21.2 2.8 42 44-90 21-62 (82)
29 PRK00276 infA translation init 35.9 1.1E+02 0.0025 19.3 7.8 58 3-68 8-65 (72)
30 PF11302 DUF3104: Protein of u 35.1 57 0.0012 21.7 3.1 33 48-80 5-39 (75)
31 PRK12442 translation initiatio 35.0 1.5E+02 0.0032 20.3 5.8 51 3-67 8-64 (87)
32 PLN00208 translation initiatio 34.9 1.9E+02 0.0041 21.5 7.4 58 3-73 33-94 (145)
33 PF09926 DUF2158: Uncharacteri 34.3 31 0.00067 21.3 1.6 13 50-62 2-14 (53)
34 cd03698 eRF3_II_like eRF3_II_l 34.0 44 0.00095 21.2 2.4 40 45-89 23-62 (83)
35 PF10377 ATG11: Autophagy-rela 32.9 64 0.0014 23.0 3.4 27 48-74 42-69 (129)
36 PRK05753 nucleoside diphosphat 32.6 1E+02 0.0023 21.9 4.4 29 48-78 101-129 (137)
37 KOG1698 Mitochondrial/chloropl 31.8 75 0.0016 24.9 3.8 33 41-75 91-123 (201)
38 PRK10409 hydrogenase assembly 31.3 35 0.00076 23.3 1.7 50 6-65 7-58 (90)
39 cd03697 EFTU_II EFTU_II: Elong 30.7 1.1E+02 0.0025 19.5 4.0 15 45-59 23-37 (87)
40 cd04460 S1_RpoE S1_RpoE: RpoE, 30.7 1.6E+02 0.0034 19.2 5.1 14 46-59 51-64 (99)
41 TIGR03595 Obg_CgtA_exten Obg f 30.5 36 0.00078 21.7 1.6 12 48-59 53-64 (69)
42 PRK10862 SoxR reducing system 30.5 1.4E+02 0.003 21.8 4.8 56 1-58 1-68 (154)
43 PRK01889 GTPase RsgA; Reviewed 28.2 1.9E+02 0.0041 23.6 5.7 66 5-81 30-95 (356)
44 smart00357 CSP Cold shock prot 27.5 1.1E+02 0.0024 17.4 3.3 25 38-62 21-50 (64)
45 PF15057 DUF4537: Domain of un 27.0 1.7E+02 0.0037 20.5 4.7 49 4-58 15-65 (124)
46 PF09269 DUF1967: Domain of un 26.1 40 0.00088 21.4 1.2 12 48-59 53-64 (69)
47 cd00174 SH3 Src homology 3 dom 26.0 75 0.0016 17.2 2.2 13 48-60 17-29 (54)
48 PF02887 PK_C: Pyruvate kinase 25.9 1.2E+02 0.0025 20.4 3.6 30 46-75 87-116 (117)
49 TIGR00157 ribosome small subun 25.2 94 0.002 23.9 3.3 28 50-81 2-29 (245)
50 PF06107 DUF951: Bacterial pro 25.1 1.3E+02 0.0027 19.1 3.3 25 49-74 2-26 (57)
51 PF01938 TRAM: TRAM domain; I 24.5 1.6E+02 0.0035 17.4 4.6 42 14-58 5-47 (61)
52 cd05791 S1_CSL4 S1_CSL4: CSL4, 24.2 1.2E+02 0.0025 20.1 3.3 55 3-58 9-70 (92)
53 PRK10371 DNA-binding transcrip 22.9 83 0.0018 24.7 2.7 42 23-64 40-83 (302)
54 PF08980 DUF1883: Domain of un 22.7 32 0.00069 23.8 0.3 20 39-59 2-21 (94)
55 COG0853 PanD Aspartate 1-decar 22.6 78 0.0017 23.1 2.2 18 48-65 77-94 (126)
56 PRK04012 translation initiatio 22.4 2.3E+02 0.005 19.5 4.5 51 3-67 22-77 (100)
57 PRK00098 GTPase RsgA; Reviewed 22.4 2.8E+02 0.0062 21.8 5.6 65 5-81 2-66 (298)
58 COG3655 Predicted transcriptio 22.3 49 0.0011 21.9 1.1 12 48-59 56-67 (73)
59 PRK09570 rpoH DNA-directed RNA 22.3 69 0.0015 21.4 1.8 33 39-71 39-75 (79)
60 CHL00010 infA translation init 22.3 2.3E+02 0.0049 18.3 8.4 58 3-68 8-65 (78)
61 cd03693 EF1_alpha_II EF1_alpha 22.2 1.2E+02 0.0027 19.5 3.0 36 44-84 26-61 (91)
62 cd04498 hPOT1_OB2 hPOT1_OB2: A 21.7 1.2E+02 0.0027 21.6 3.2 24 37-60 61-88 (123)
63 PRK13168 rumA 23S rRNA m(5)U19 21.5 1.8E+02 0.0039 24.2 4.5 51 49-99 43-96 (443)
64 PRK10807 paraquat-inducible pr 21.1 1.8E+02 0.0038 25.5 4.5 70 3-75 68-149 (547)
65 KOG3507 DNA-directed RNA polym 20.9 48 0.001 21.4 0.8 16 45-60 28-43 (62)
66 COG1326 Uncharacterized archae 20.3 4.3E+02 0.0093 20.7 6.0 69 5-87 36-107 (201)
67 PRK12288 GTPase RsgA; Reviewed 20.0 3.3E+02 0.0071 22.3 5.7 33 48-81 72-105 (347)
No 1
>CHL00142 rps17 ribosomal protein S17; Validated
Probab=100.00 E-value=9.2e-37 Score=206.24 Aligned_cols=80 Identities=39% Similarity=0.576 Sum_probs=77.0
Q ss_pred CceEEEEEEeCCCCCeEEEEEeEEEeccccceEEEeeeeEEEECCCCCCCCCCEEEEeecccCCCceeEEEEEeecCCcc
Q 033970 1 MKKMQGRVVCASSDKTVAVEVVRLDPHPKYKRRIRKKKKYQAHDPENQFQVGDLVQLEKSRPISKTKSFIAVAMPPRNAS 80 (107)
Q Consensus 1 ~k~l~G~VVs~km~KTvvV~V~r~~~hpky~K~~~r~kk~~vHDe~~~~~vGD~V~I~e~RPiSK~K~~~V~~Iv~~~~~ 80 (107)
++.|.|+|+|++|+|||+|+|+|+++||+|+|+++++++|+||||.|+|++||+|+|.|||||||+|+|.|.+|++++..
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 47899999999999999999999999999999999999999999999999999999999999999999999999987753
No 2
>PRK05610 rpsQ 30S ribosomal protein S17; Reviewed
Probab=100.00 E-value=3e-36 Score=203.53 Aligned_cols=77 Identities=42% Similarity=0.682 Sum_probs=75.2
Q ss_pred ceEEEEEEeCCCCCeEEEEEeEEEeccccceEEEeeeeEEEECCCCCCCCCCEEEEeecccCCCceeEEEEEeecCC
Q 033970 2 KKMQGRVVCASSDKTVAVEVVRLDPHPKYKRRIRKKKKYQAHDPENQFQVGDLVQLEKSRPISKTKSFIAVAMPPRN 78 (107)
Q Consensus 2 k~l~G~VVs~km~KTvvV~V~r~~~hpky~K~~~r~kk~~vHDe~~~~~vGD~V~I~e~RPiSK~K~~~V~~Iv~~~ 78 (107)
+.|.|+|+|++|+|||+|+|+++++||+|+|+++++++|+||||.|.|++||+|+|.|||||||+|+|.|.+|++++
T Consensus 7 ~~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 7 KTLQGRVVSDKMDKTIVVLVERRVKHPLYGKIVKRSKKYHAHDENNEAKIGDVVRIMETRPLSKTKRWRLVEIVEKA 83 (84)
T ss_pred CEEEEEEEcccCCceEEEEEEEEEEeccccEEEEcceEEEEECCCCCCCCCCEEEEEEcccCCCCEEEEEEEEEecc
Confidence 57999999999999999999999999999999999999999999999999999999999999999999999999875
No 3
>COG0186 RpsQ Ribosomal protein S17 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=3e-36 Score=204.96 Aligned_cols=78 Identities=45% Similarity=0.724 Sum_probs=75.8
Q ss_pred ceEEEEEEeCCCCCeEEEEEeEEEeccccceEEEeeeeEEEECCCCCCCCCCEEEEeecccCCCceeEEEEEeecCCc
Q 033970 2 KKMQGRVVCASSDKTVAVEVVRLDPHPKYKRRIRKKKKYQAHDPENQFQVGDLVQLEKSRPISKTKSFIAVAMPPRNA 79 (107)
Q Consensus 2 k~l~G~VVs~km~KTvvV~V~r~~~hpky~K~~~r~kk~~vHDe~~~~~vGD~V~I~e~RPiSK~K~~~V~~Iv~~~~ 79 (107)
+.|+|+|+|++|+|||+|++++.++||+|+|+++++++|+||||.|+|++||+|+|.|||||||+|+|.|++|++++.
T Consensus 9 k~l~G~VvS~Km~KTvvV~ve~~~~hp~Y~K~v~r~kK~~aHde~~~~k~GD~V~I~EtRPLSKtK~~~vv~i~~~a~ 86 (87)
T COG0186 9 RVLEGVVVSDKMDKTVVVEVERKVYHPKYGKYVRRSKKYHAHDECNEAKVGDIVRIAETRPLSKTKRFVVVEIVEKAV 86 (87)
T ss_pred eEEEEEEEEccCceeEEEEEEEEEecccceEEEEEEeeeEeecccccCCCCCEEEEEEccccCCcceEEEEEEeeecc
Confidence 589999999999999999999999999999999999999999999999999999999999999999999999998864
No 4
>PRK08572 rps17p 30S ribosomal protein S17P; Reviewed
Probab=100.00 E-value=8.1e-35 Score=204.64 Aligned_cols=77 Identities=39% Similarity=0.598 Sum_probs=74.9
Q ss_pred ceEEEEEEeCCCCCeEEEEEeEEEeccccceEEEeeeeEEEECCC-CCCCCCCEEEEeecccCCCceeEEEEEeecCC
Q 033970 2 KKMQGRVVCASSDKTVAVEVVRLDPHPKYKRRIRKKKKYQAHDPE-NQFQVGDLVQLEKSRPISKTKSFIAVAMPPRN 78 (107)
Q Consensus 2 k~l~G~VVs~km~KTvvV~V~r~~~hpky~K~~~r~kk~~vHDe~-~~~~vGD~V~I~e~RPiSK~K~~~V~~Iv~~~ 78 (107)
+.|.|+|+|++|+|||+|+|+++++||+|+|+++++++|+||||+ |+|++||.|+|+|||||||+|+|.|.+|++++
T Consensus 30 k~l~G~VvS~Km~KTvvV~v~r~~~hpkY~K~i~r~kky~aHDe~cn~~kvGD~V~I~E~RPiSKtK~w~v~~i~~~~ 107 (108)
T PRK08572 30 QVLEGTVVSDKMHKTVVVEREYLHYVPKYERYEKRRSRIHAHNPPCIDAKVGDKVKIAECRPLSKTKSFVVVEKKERA 107 (108)
T ss_pred EEEEEEEEecCCCceEEEEEEEEEecCCccEEEEEeeeEEEECCCCCCCCCCCEEEEEEcCCCCCceEEEEEEEEEcC
Confidence 579999999999999999999999999999999999999999999 79999999999999999999999999999876
No 5
>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=7.7e-35 Score=191.30 Aligned_cols=70 Identities=44% Similarity=0.694 Sum_probs=68.6
Q ss_pred ceEEEEEEeCCCCCeEEEEEeEEEeccccceEEEeeeeEEEECCCCCCCCCCEEEEeecccCCCceeEEE
Q 033970 2 KKMQGRVVCASSDKTVAVEVVRLDPHPKYKRRIRKKKKYQAHDPENQFQVGDLVQLEKSRPISKTKSFIA 71 (107)
Q Consensus 2 k~l~G~VVs~km~KTvvV~V~r~~~hpky~K~~~r~kk~~vHDe~~~~~vGD~V~I~e~RPiSK~K~~~V 71 (107)
++|.|+|+|++|+||++|+|+++++||+|+|+++++++|+||||.|+|++||+|.|.|||||||+|+|.|
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 5799999999999999999999999999999999999999999999999999999999999999999975
No 6
>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=1.7e-34 Score=201.30 Aligned_cols=74 Identities=38% Similarity=0.559 Sum_probs=72.1
Q ss_pred ceEEEEEEeCCCCCeEEEEEeEEEeccccceEEEeeeeEEEECCC-CCCCCCCEEEEeecccCCCceeEEEEEee
Q 033970 2 KKMQGRVVCASSDKTVAVEVVRLDPHPKYKRRIRKKKKYQAHDPE-NQFQVGDLVQLEKSRPISKTKSFIAVAMP 75 (107)
Q Consensus 2 k~l~G~VVs~km~KTvvV~V~r~~~hpky~K~~~r~kk~~vHDe~-~~~~vGD~V~I~e~RPiSK~K~~~V~~Iv 75 (107)
+.|+|+|+|++|+|||+|+|+|+++||+|+|+++++++|+||||+ |+|++||.|+|+|||||||+|+|.|.+|+
T Consensus 28 k~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 28 QILEGVVVSDKMNKTVVVEREYLYYDRKYERYERRRSKIHAHNPPCIDVKEGDIVIIGETRPLSKTKSFVVLGKV 102 (102)
T ss_pred EEEEEEEEecCCCceEEEEEEEEEecCCccEEEEEeeeEEEECCCCCCCCCCCEEEEEEcCCCCCceEEEEEEeC
Confidence 689999999999999999999999999999999999999999999 79999999999999999999999999985
No 7
>KOG1740 consensus Predicted mitochondrial/chloroplast ribosomal protein S17 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.1e-35 Score=207.14 Aligned_cols=99 Identities=45% Similarity=0.619 Sum_probs=92.7
Q ss_pred CceEEEEEEeCCCCCeEEEEEeEEEeccccceEEEeeeeEEEECCCCCCCCCCEEEEeecccCCCceeEEEEEeecCCcc
Q 033970 1 MKKMQGRVVCASSDKTVAVEVVRLDPHPKYKRRIRKKKKYQAHDPENQFQVGDLVQLEKSRPISKTKSFIAVAMPPRNAS 80 (107)
Q Consensus 1 ~k~l~G~VVs~km~KTvvV~V~r~~~hpky~K~~~r~kk~~vHDe~~~~~vGD~V~I~e~RPiSK~K~~~V~~Iv~~~~~ 80 (107)
|+-++|+|+|.+|+||++|+|+++.+||+|+||++++++|+|||+.|.|++||.|+|++||||||+|+|++.+||.++.+
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 67899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccccccCCCCCCccccccccchhh
Q 033970 81 KKAAGESSNAGNNELGIPLESEQQ 104 (107)
Q Consensus 81 ~~~a~~~~~~~~~~~~~~~~~~~~ 104 (107)
..+|.|.+. ||+|..+|||
T Consensus 82 ~spa~~~ea-----~~s~~~~~~~ 100 (107)
T KOG1740|consen 82 YSPAAEAEA-----LGSSASSQQQ 100 (107)
T ss_pred hCcchhhhh-----hcCchhhhcc
Confidence 877766654 6778888887
No 8
>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=100.00 E-value=6.7e-34 Score=185.57 Aligned_cols=69 Identities=54% Similarity=0.791 Sum_probs=67.0
Q ss_pred EEEEeCCCCCeEEEEEeEEEeccccceEEEeeeeEEEECCCCCCCCCCEEEEeecccCCCceeEEEEEe
Q 033970 6 GRVVCASSDKTVAVEVVRLDPHPKYKRRIRKKKKYQAHDPENQFQVGDLVQLEKSRPISKTKSFIAVAM 74 (107)
Q Consensus 6 G~VVs~km~KTvvV~V~r~~~hpky~K~~~r~kk~~vHDe~~~~~vGD~V~I~e~RPiSK~K~~~V~~I 74 (107)
|+|+|++|+||++|+|+++++||+|+|+++++++|+||||+|.|++||+|+|+|||||||+|+|.|.+|
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 9
>PTZ00241 40S ribosomal protein S11; Provisional
Probab=99.98 E-value=6.7e-32 Score=200.16 Aligned_cols=77 Identities=23% Similarity=0.369 Sum_probs=74.1
Q ss_pred ceEEEEEEeCCCCCeEEEEEeEEEeccccceEEEeeeeEEEECC-CCCCCCCCEEEEeecccCCCceeEEEEEeecCC
Q 033970 2 KKMQGRVVCASSDKTVAVEVVRLDPHPKYKRRIRKKKKYQAHDP-ENQFQVGDLVQLEKSRPISKTKSFIAVAMPPRN 78 (107)
Q Consensus 2 k~l~G~VVs~km~KTvvV~V~r~~~hpky~K~~~r~kk~~vHDe-~~~~~vGD~V~I~e~RPiSK~K~~~V~~Iv~~~ 78 (107)
++|.|+|+|++|+|||+|+++++++||+|+||++++++|+|||| .+.|++||+|+|.|||||||+|+|+|++|+.++
T Consensus 69 ril~G~VvS~KM~KTIVV~ve~~~~h~kY~K~~kr~kk~~aHd~~~~~~kvGD~V~I~EcRPLSKTKrf~Vv~V~~~~ 146 (158)
T PTZ00241 69 RILRGVVISTKMKRTIIIRRDYLHYVKKYNRYEKRHKNIPVHCSPCFDVKEGDIVVVGQCRPLSKTVRFNVLKVEKNE 146 (158)
T ss_pred eEEEEEEEEccCCccEEEEEEEEEecCccceEEEeeecEEEeCCccCCCCCCCEEEEEEcCCCCCceeEEEEEEEecc
Confidence 68999999999999999999999999999999999999999995 669999999999999999999999999999865
No 10
>KOG1728 consensus 40S ribosomal protein S11 [Translation, ribosomal structure and biogenesis]
Probab=99.85 E-value=5e-22 Score=145.68 Aligned_cols=81 Identities=30% Similarity=0.396 Sum_probs=76.3
Q ss_pred ceEEEEEEeCCCCCeEEEEEeEEEeccccceEEEeeeeEEEECCCC--CCCCCCEEEEeecccCCCceeEEEEEeecCCc
Q 033970 2 KKMQGRVVCASSDKTVAVEVVRLDPHPKYKRRIRKKKKYQAHDPEN--QFQVGDLVQLEKSRPISKTKSFIAVAMPPRNA 79 (107)
Q Consensus 2 k~l~G~VVs~km~KTvvV~V~r~~~hpky~K~~~r~kk~~vHDe~~--~~~vGD~V~I~e~RPiSK~K~~~V~~Iv~~~~ 79 (107)
++|.|+|++.+|++||+|+.+|++|.++|++|.+|++++-||-..+ ..++||+|.|.|||||||+++|.|++++..++
T Consensus 69 ril~G~V~k~Km~rTIvvrrdYlHy~~KY~ryekrHkN~svh~SPcFrdi~~gDiVtvGecrPLSKtvrfnVLkv~k~~g 148 (156)
T KOG1728|consen 69 RILTGTVVKMKMQRTIVVRRDYLHYIKKYNRYEKRHKNMSVHVSPCFRDIQEGDIVTVGECRPLSKTVRFNVLKVIKAAG 148 (156)
T ss_pred EEEeeEEeeeceeEEEEEEhhhhhHhHHhhHHHHhccCCccccchhhhccccCCEEEEeecccccceEEEEEEEEeecCC
Confidence 5899999999999999999999999999999999999999999887 69999999999999999999999999998875
Q ss_pred ccc
Q 033970 80 SKK 82 (107)
Q Consensus 80 ~~~ 82 (107)
..+
T Consensus 149 ~~k 151 (156)
T KOG1728|consen 149 SKK 151 (156)
T ss_pred Ccc
Confidence 443
No 11
>KOG3447 consensus Mitochondrial/chloroplast ribosomal S17-like protein [Translation, ribosomal structure and biogenesis]
Probab=99.81 E-value=6.3e-21 Score=139.15 Aligned_cols=105 Identities=26% Similarity=0.299 Sum_probs=99.3
Q ss_pred ceEEEEEEeCCCCCeEEEEEeEEEeccccceEEEeeeeEEEECCCCCCCCCCEEEEeec-ccCCCceeEEEEEeecCCcc
Q 033970 2 KKMQGRVVCASSDKTVAVEVVRLDPHPKYKRRIRKKKKYQAHDPENQFQVGDLVQLEKS-RPISKTKSFIAVAMPPRNAS 80 (107)
Q Consensus 2 k~l~G~VVs~km~KTvvV~V~r~~~hpky~K~~~r~kk~~vHDe~~~~~vGD~V~I~e~-RPiSK~K~~~V~~Iv~~~~~ 80 (107)
..|.|.|+..+|++|++|++.++.++|+..|||.|++.|||||+-..|++||+|+|++. -|..+..+|.|.+|+++-+-
T Consensus 11 ~~lmGk~ig~~~q~~akVR~~r~eld~yL~kYf~k~~~yfAhD~~~~c~vGDtVLir~lp~r~t~~V~H~v~~VVfk~G~ 90 (150)
T KOG3447|consen 11 QWLMGKVIGTKMQKTAKVRVTRLELDPYLLKYFNKRKTYFAHDALQQCTVGDTVLIRALPVRRTKHVKHEVAEVVFKVGK 90 (150)
T ss_pred EEEEeeeeeccccccceeeeehhhcCHHHHHHhccccceeecchhhccccCCEEEEecCCcchhhhhhhhhHhheeeccc
Confidence 47899999999999999999999999999999999999999999999999999999998 78889999999999999888
Q ss_pred c-cccccCCCCCCccccccccchhhhc
Q 033970 81 K-KAAGESSNAGNNELGIPLESEQQLE 106 (107)
Q Consensus 81 ~-~~a~~~~~~~~~~~~~~~~~~~~~~ 106 (107)
- ++.|+.+|++-||+++|..-+-|++
T Consensus 91 IidPvTGkk~~~~ty~e~~~~~~~~~~ 117 (150)
T KOG3447|consen 91 IIDPVTGKKCAGDTYLESPLSKETTQL 117 (150)
T ss_pred ccCCCcCccccCcchhcchHHHHHHHh
Confidence 7 9999999999999999988776653
No 12
>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=63.87 E-value=26 Score=22.95 Aligned_cols=52 Identities=17% Similarity=0.107 Sum_probs=33.6
Q ss_pred EEEEEEeCCCCCeEEEEEeEEEeccccceEEEeeeeEEEECCCC-----CCCCCCEEEEeecccCCCceeE
Q 033970 4 MQGRVVCASSDKTVAVEVVRLDPHPKYKRRIRKKKKYQAHDPEN-----QFQVGDLVQLEKSRPISKTKSF 69 (107)
Q Consensus 4 l~G~VVs~km~KTvvV~V~r~~~hpky~K~~~r~kk~~vHDe~~-----~~~vGD~V~I~e~RPiSK~K~~ 69 (107)
..|+|+....++...|..+-- ..+++|-|.. -.+.||.|++. ..|..+.|-=
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 578899888888777775521 2333333322 26889999988 4566766543
No 13
>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=59.38 E-value=39 Score=20.67 Aligned_cols=51 Identities=25% Similarity=0.219 Sum_probs=28.7
Q ss_pred eEEEEEEeCCCCCeEEEEEeEEEeccccceEEEeeeeEEEECCCCCCCCCCEEEEeec
Q 033970 3 KMQGRVVCASSDKTVAVEVVRLDPHPKYKRRIRKKKKYQAHDPENQFQVGDLVQLEKS 60 (107)
Q Consensus 3 ~l~G~VVs~km~KTvvV~V~r~~~hpky~K~~~r~kk~~vHDe~~~~~vGD~V~I~e~ 60 (107)
++.|+|++.....-..|..+ -...|....+..-+ + ....+.+||.|.+..+
T Consensus 2 ~~~G~Vi~~~~g~~~~V~~~---~g~~~~c~~rGklr---~-~~~~~~vGD~V~~~~~ 52 (64)
T cd04451 2 EMEGVVTEALPNAMFRVELE---NGHEVLAHISGKMR---M-NYIRILPGDRVKVELS 52 (64)
T ss_pred eEEEEEEEEeCCCEEEEEeC---CCCEEEEEECceee---c-CCcccCCCCEEEEEEe
Confidence 46788887654344444321 12345555444322 1 3345899999988743
No 14
>PF10844 DUF2577: Protein of unknown function (DUF2577); InterPro: IPR022555 This family of proteins has no known function
Probab=55.14 E-value=63 Score=21.81 Aligned_cols=61 Identities=18% Similarity=0.278 Sum_probs=33.2
Q ss_pred eEEEEEEeCCCCCeEEEEEeEEEeccc----cceEEEeeee--------------EEEECCCCCCCCCCEEEEeecccCC
Q 033970 3 KMQGRVVCASSDKTVAVEVVRLDPHPK----YKRRIRKKKK--------------YQAHDPENQFQVGDLVQLEKSRPIS 64 (107)
Q Consensus 3 ~l~G~VVs~km~KTvvV~V~r~~~hpk----y~K~~~r~kk--------------~~vHDe~~~~~vGD~V~I~e~RPiS 64 (107)
...|+|+|... .+|.++....-+. .-..+.+++. +..|| .+++||.|.+.. .-
T Consensus 19 i~~G~V~s~~P---L~I~i~~~liL~~~~L~i~~~l~~~~~~~~~~~~~~~~~~~i~~~~---~Lk~GD~V~ll~---~~ 89 (100)
T PF10844_consen 19 IVIGTVVSVPP---LKIKIDQKLILDKDFLIIPELLKDYTRDITIEHNSETDNITITFTD---GLKVGDKVLLLR---VQ 89 (100)
T ss_pred eEEEEEEeccc---EEEEECCeEEEchHHEEeehhccceEEEEEEeccccccceeEEEec---CCcCCCEEEEEE---ec
Confidence 56899998764 7777776211111 0111222222 23333 589999998876 33
Q ss_pred CceeEEEE
Q 033970 65 KTKSFIAV 72 (107)
Q Consensus 65 K~K~~~V~ 72 (107)
.--+|.|.
T Consensus 90 ~gQ~yiVl 97 (100)
T PF10844_consen 90 GGQKYIVL 97 (100)
T ss_pred CCCEEEEE
Confidence 34455544
No 15
>PF13550 Phage-tail_3: Putative phage tail protein
Probab=53.63 E-value=37 Score=23.38 Aligned_cols=36 Identities=11% Similarity=0.245 Sum_probs=25.9
Q ss_pred eeeEEEECCCCCCCCCCEEEEeecccCCCceeEEEEEee
Q 033970 37 KKKYQAHDPENQFQVGDLVQLEKSRPISKTKSFIAVAMP 75 (107)
Q Consensus 37 ~kk~~vHDe~~~~~vGD~V~I~e~RPiSK~K~~~V~~Iv 75 (107)
+-.|.+--..-.+.+||+|.|..- .+...|.|.+|-
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 444444444558999999999876 557888888773
No 16
>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=52.35 E-value=26 Score=21.09 Aligned_cols=29 Identities=28% Similarity=0.339 Sum_probs=19.5
Q ss_pred CCCCCCCEEEEeecccCCCceeEEEEEeecCCc
Q 033970 47 NQFQVGDLVQLEKSRPISKTKSFIAVAMPPRNA 79 (107)
Q Consensus 47 ~~~~vGD~V~I~e~RPiSK~K~~~V~~Iv~~~~ 79 (107)
...-+||+|.+...- .-.+.+.+|+++..
T Consensus 36 ~~~~VGD~V~~~~~~----~~~~~I~~vl~R~s 64 (68)
T cd04466 36 NPPAVGDRVEFEPED----DGEGVIEEILPRKN 64 (68)
T ss_pred CCCCCCcEEEEEECC----CCcEEEEEEeccce
Confidence 457899999986421 12467788887654
No 17
>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=49.75 E-value=54 Score=25.75 Aligned_cols=32 Identities=25% Similarity=0.248 Sum_probs=23.2
Q ss_pred CCCCCCCCEEEEeecccCCCceeEEEEEeecCCccc
Q 033970 46 ENQFQVGDLVQLEKSRPISKTKSFIAVAMPPRNASK 81 (107)
Q Consensus 46 ~~~~~vGD~V~I~e~RPiSK~K~~~V~~Iv~~~~~~ 81 (107)
...+-+||+|.+...- ...+.+.+|++|....
T Consensus 32 ~~~~~vGD~V~~~~~~----~~~~~i~~i~~R~~~l 63 (287)
T cd01854 32 GIKPVVGDWVEVEPDD----DGEGVIVRVLPRKNLL 63 (287)
T ss_pred CCCccCCCEEEEEecC----CCcEEEEEEECCCceE
Confidence 4458999999997432 3467888998876654
No 18
>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=48.61 E-value=73 Score=20.65 Aligned_cols=51 Identities=25% Similarity=0.354 Sum_probs=33.9
Q ss_pred eEEEEEEeCCCCCeEEEEEeEEEeccccceEEEeeeeEEEECCCC------CCCCCCEEEEeecccCCCce
Q 033970 3 KMQGRVVCASSDKTVAVEVVRLDPHPKYKRRIRKKKKYQAHDPEN------QFQVGDLVQLEKSRPISKTK 67 (107)
Q Consensus 3 ~l~G~VVs~km~KTvvV~V~r~~~hpky~K~~~r~kk~~vHDe~~------~~~vGD~V~I~e~RPiSK~K 67 (107)
++.|+|+....+-...|..+- -...++|-+.. -..+||.|.+.- .|...+|
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-------------GHEVLAHISGKIRMHYIRILPGDKVKVEL-SPYDLTR 62 (68)
T ss_pred EEEEEEEEECCCCEEEEEECC-------------CCEEEEEecCcchhccEEECCCCEEEEEE-CcccCCc
Confidence 578999988777777777653 34455555542 267899998874 4544444
No 19
>PTZ00329 eukaryotic translation initiation factor 1A; Provisional
Probab=46.90 E-value=1.2e+02 Score=22.72 Aligned_cols=60 Identities=12% Similarity=0.223 Sum_probs=35.5
Q ss_pred EEEEEEeCCCCCeEEEEEeE-EEeccccceEEEeeeeEEEECCCCCCCCCCEEEEeecccCCCceeEEEEE
Q 033970 4 MQGRVVCASSDKTVAVEVVR-LDPHPKYKRRIRKKKKYQAHDPENQFQVGDLVQLEKSRPISKTKSFIAVA 73 (107)
Q Consensus 4 l~G~VVs~km~KTvvV~V~r-~~~hpky~K~~~r~kk~~vHDe~~~~~vGD~V~I~e~RPiSK~K~~~V~~ 73 (107)
..|+|+....+..+.|...- ....-++.--|++ ++| .+.||+|++.. +|..+.|.=++..
T Consensus 34 ~~g~V~~~LGn~~f~V~c~dG~~rLa~I~GKmRK--~IW-------I~~GD~VlVel-~~yd~~KgdIi~R 94 (155)
T PTZ00329 34 EYAQVLRMLGNGRLEAYCFDGVKRLCHIRGKMRK--RVW-------INIGDIILVSL-RDFQDSKADVILK 94 (155)
T ss_pred EEEEEEEEcCCCEEEEEECCCCEEEEEeecccee--eEE-------ecCCCEEEEec-cCCCCCEEEEEEE
Confidence 56788887777777777441 0011111111222 344 67899999965 9998887655443
No 20
>TIGR00523 eIF-1A eukaryotic/archaeal initiation factor 1A. Recommended nomenclature: eIF-1A for eukaryotes, aIF-1A for Archaea. Also called eIF-4C
Probab=46.76 E-value=94 Score=21.36 Aligned_cols=48 Identities=19% Similarity=0.219 Sum_probs=30.4
Q ss_pred eEEEEEEeCCCCCeEEEEEeEEEeccccceEEEeeeeEEEECCCC-----CCCCCCEEEEeecccCC
Q 033970 3 KMQGRVVCASSDKTVAVEVVRLDPHPKYKRRIRKKKKYQAHDPEN-----QFQVGDLVQLEKSRPIS 64 (107)
Q Consensus 3 ~l~G~VVs~km~KTvvV~V~r~~~hpky~K~~~r~kk~~vHDe~~-----~~~vGD~V~I~e~RPiS 64 (107)
...|+|+....+....|..+ --..+++|-|.. -.+.||.|++ +.+.++
T Consensus 20 e~~g~V~~~lG~~~~~V~~~-------------dG~~~la~i~GK~Rk~iwI~~GD~VlV-sp~d~~ 72 (99)
T TIGR00523 20 EILGVIEQMLGAGRVKVRCL-------------DGKTRLGRIPGKLKKRIWIREGDVVIV-KPWEFQ 72 (99)
T ss_pred EEEEEEEEEcCCCEEEEEeC-------------CCCEEEEEEchhhcccEEecCCCEEEE-EEccCC
Confidence 45677777766666666644 123444444432 2688999999 557777
No 21
>smart00652 eIF1a eukaryotic translation initiation factor 1A.
Probab=44.27 E-value=83 Score=20.81 Aligned_cols=52 Identities=19% Similarity=0.221 Sum_probs=32.2
Q ss_pred eEEEEEEeCCCCCeEEEEEeEEEeccccceEEEeeeeEEEECCCC-----CCCCCCEEEEeecccCCCcee
Q 033970 3 KMQGRVVCASSDKTVAVEVVRLDPHPKYKRRIRKKKKYQAHDPEN-----QFQVGDLVQLEKSRPISKTKS 68 (107)
Q Consensus 3 ~l~G~VVs~km~KTvvV~V~r~~~hpky~K~~~r~kk~~vHDe~~-----~~~vGD~V~I~e~RPiSK~K~ 68 (107)
...|+|+....+.-..|..+- -..++||-|.. -.+.||.|++. ..|..+.|-
T Consensus 6 q~~g~V~~~lG~~~~~V~~~d-------------G~~~la~ipgK~Rk~iwI~~GD~VlVe-~~~~~~~kg 62 (83)
T smart00652 6 QEIAQVVKMLGNGRLEVMCAD-------------GKERLARIPGKMRKKVWIRRGDIVLVD-PWDFQDVKA 62 (83)
T ss_pred cEEEEEEEEcCCCEEEEEECC-------------CCEEEEEEchhhcccEEEcCCCEEEEE-ecCCCCCEE
Confidence 467888877777777776542 23334444422 26889999995 456666544
No 22
>cd04486 YhcR_OBF_like YhcR_OBF_like: A subfamily of OB-fold domains similar to the OB folds of Bacillus subtilis YhcR. YhcR is a sugar-nonspecific nuclease, which is active in the presence of Ca2+ and Mn2+. It cleaves RNA endonucleolytically, producing 3'-monophosphate nucleosides. YhcR appears to be the major Ca2+ activated nuclease of B. subtilis. YhcR may be localized in the cell wall.
Probab=42.88 E-value=36 Score=22.01 Aligned_cols=19 Identities=26% Similarity=0.317 Sum_probs=13.4
Q ss_pred EEEECC-CCCCCCCCEEEEe
Q 033970 40 YQAHDP-ENQFQVGDLVQLE 58 (107)
Q Consensus 40 ~~vHDe-~~~~~vGD~V~I~ 58 (107)
+++..+ .....+||+|+|.
T Consensus 35 ifV~~~~~~~~~~Gd~V~vt 54 (78)
T cd04486 35 IFVYTGSGADVAVGDLVRVT 54 (78)
T ss_pred EEEecCCCCCCCCCCEEEEE
Confidence 444444 5578999999885
No 23
>COG0361 InfA Translation initiation factor 1 (IF-1) [Translation, ribosomal structure and biogenesis]
Probab=41.50 E-value=1e+02 Score=20.40 Aligned_cols=45 Identities=27% Similarity=0.304 Sum_probs=32.0
Q ss_pred eEEEEEEeCCCCCeEEEEEeEEEeccccceEEEeeeeEEEECCCC------CCCCCCEEEEeec
Q 033970 3 KMQGRVVCASSDKTVAVEVVRLDPHPKYKRRIRKKKKYQAHDPEN------QFQVGDLVQLEKS 60 (107)
Q Consensus 3 ~l~G~VVs~km~KTvvV~V~r~~~hpky~K~~~r~kk~~vHDe~~------~~~vGD~V~I~e~ 60 (107)
.+.|+|+..-.+..+.|..+-- ...++|-+.. -..+||+|.++..
T Consensus 8 e~~g~V~e~L~~~~f~v~~edg-------------~~~~ahI~GKmr~~~i~I~~GD~V~Ve~~ 58 (75)
T COG0361 8 EMEGTVIEMLPNGRFRVELENG-------------HERLAHISGKMRKNRIRILPGDVVLVELS 58 (75)
T ss_pred EEEEEEEEecCCCEEEEEecCC-------------cEEEEEccCcchheeEEeCCCCEEEEEec
Confidence 5789999888888888876643 2455666643 3678999988654
No 24
>PRK10413 hydrogenase 2 accessory protein HypG; Provisional
Probab=40.06 E-value=1.1e+02 Score=20.36 Aligned_cols=51 Identities=20% Similarity=0.174 Sum_probs=28.6
Q ss_pred EEEEeCCCC--CeEEEEEeEEEeccccceEEEeeeeEEEECCCCCCCCCCEEEEeecccCCC
Q 033970 6 GRVVCASSD--KTVAVEVVRLDPHPKYKRRIRKKKKYQAHDPENQFQVGDLVQLEKSRPISK 65 (107)
Q Consensus 6 G~VVs~km~--KTvvV~V~r~~~hpky~K~~~r~kk~~vHDe~~~~~vGD~V~I~e~RPiSK 65 (107)
|+|++-.-+ ++++|.... ..+.-.-.++-++.....+||+|++.-.--|++
T Consensus 7 ~kVi~i~~~~~~~A~vd~~G---------v~r~V~l~Lv~~~~~~~~vGDyVLVHaGfAi~~ 59 (82)
T PRK10413 7 GQVLAVGEDIHQLAQVEVCG---------IKRDVNIALICEGNPADLLGQWVLVHVGFAMSI 59 (82)
T ss_pred eEEEEECCCCCcEEEEEcCC---------eEEEEEeeeeccCCcccccCCEEEEecchhhhh
Confidence 667765332 456665432 222323334444434689999999987644443
No 25
>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=38.77 E-value=97 Score=20.27 Aligned_cols=51 Identities=16% Similarity=0.168 Sum_probs=32.2
Q ss_pred EEEEEEeCCCCCeEEEEEeEEEeccccceEEEeeeeEEEECCCC-----CCCCCCEEEEeecccC-CCcee
Q 033970 4 MQGRVVCASSDKTVAVEVVRLDPHPKYKRRIRKKKKYQAHDPEN-----QFQVGDLVQLEKSRPI-SKTKS 68 (107)
Q Consensus 4 l~G~VVs~km~KTvvV~V~r~~~hpky~K~~~r~kk~~vHDe~~-----~~~vGD~V~I~e~RPi-SK~K~ 68 (107)
..|+|+....++-..|..+- -..+++|-|.. =.+.||.|++. ..|. .+.|-
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 46888887777777776542 23344444432 27889999995 5666 35443
No 26
>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=38.23 E-value=41 Score=23.41 Aligned_cols=22 Identities=32% Similarity=0.478 Sum_probs=15.8
Q ss_pred eeeEEEECCCCCCCCCCEEEEee
Q 033970 37 KKKYQAHDPENQFQVGDLVQLEK 59 (107)
Q Consensus 37 ~kk~~vHDe~~~~~vGD~V~I~e 59 (107)
...+.++++. .+++||.|.|.-
T Consensus 41 ~~~~~~~~~~-~~~~GD~V~v~i 62 (135)
T PF04246_consen 41 PITFRAPNPI-GAKVGDRVEVEI 62 (135)
T ss_pred cEEEEecCCC-CCCCCCEEEEEe
Confidence 4556665555 699999998864
No 27
>PF01176 eIF-1a: Translation initiation factor 1A / IF-1; InterPro: IPR006196 The S1 domain of around 70 amino acids, originally identified in ribosomal protein S1, is found in a large number of RNA-associated proteins. It has been shown that S1 proteins bind RNA through their S1 domains with some degree of sequence specificity. This type of S1 domain is found in translation initiation factor 1. The solution structure of one S1 RNA-binding domain from Escherichia coli polynucleotide phosphorylase has been determined []. It displays some similarity with the cold shock domain (CSD) (IPR002059 from INTERPRO). Both the S1 and the CSD domain consist of an antiparallel beta barrel of the same topology with 5 beta strands. This fold is also shared by many other proteins of unrelated function and is known as the OB fold. However, the S1 and CSD fold can be distinguished from the other OB folds by the presence of a short 3(10) helix at the end of strand 3. This unique feature is likely to form a part of the DNA/RNA-binding site. This entry is specific for bacterial, chloroplastic and eukaryotic IF-1 type S1 domains.; GO: 0003723 RNA binding, 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 1JT8_A 3I4O_A 1AH9_A 1ZO1_W 1D7Q_A 2OQK_A 2DGY_A 1HR0_W.
Probab=37.61 E-value=77 Score=19.66 Aligned_cols=52 Identities=27% Similarity=0.342 Sum_probs=28.5
Q ss_pred eEEEEEEeCCCCCeEEEEEeEEEeccccceEEEeeeeEEEECCCC-----CCCCCCEEEEeecccCCCcee
Q 033970 3 KMQGRVVCASSDKTVAVEVVRLDPHPKYKRRIRKKKKYQAHDPEN-----QFQVGDLVQLEKSRPISKTKS 68 (107)
Q Consensus 3 ~l~G~VVs~km~KTvvV~V~r~~~hpky~K~~~r~kk~~vHDe~~-----~~~vGD~V~I~e~RPiSK~K~ 68 (107)
...|+|+....+....|..+- -..+++|-|.. -.+.||.|++.. .|..++|-
T Consensus 4 e~~~~V~~~lG~~~~~V~~~d-------------g~~~l~~i~gK~r~~iwI~~GD~V~V~~-~~~d~~kG 60 (65)
T PF01176_consen 4 EVIGRVTEMLGNNLFEVECED-------------GEERLARIPGKFRKRIWIKRGDFVLVEP-SPYDKVKG 60 (65)
T ss_dssp EEEEEEEEEESSSEEEEEETT-------------SEEEEEEE-HHHHTCC---TTEEEEEEE-STTCTTEE
T ss_pred EEEEEEEEECCCCEEEEEeCC-------------CCEEEEEeccceeeeEecCCCCEEEEEe-cccCCCeE
Confidence 456777776666666665432 22333443311 378999997776 66666654
No 28
>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=36.06 E-value=45 Score=21.17 Aligned_cols=42 Identities=10% Similarity=0.133 Sum_probs=24.7
Q ss_pred CCCCCCCCCCEEEEeecccCCCceeEEEEEeecCCccccccccCCCC
Q 033970 44 DPENQFQVGDLVQLEKSRPISKTKSFIAVAMPPRNASKKAAGESSNA 90 (107)
Q Consensus 44 De~~~~~vGD~V~I~e~RPiSK~K~~~V~~Iv~~~~~~~~a~~~~~~ 90 (107)
-+...+++||.|.|.+.. +...|.+|-......+.|.-+++.
T Consensus 21 v~~G~i~~G~~v~i~P~~-----~~~~V~si~~~~~~~~~a~aGd~v 62 (82)
T cd04089 21 VESGTIKKGDKLLVMPNK-----TQVEVLSIYNEDVEVRYARPGENV 62 (82)
T ss_pred EeeeEEecCCEEEEeCCC-----cEEEEEEEEECCEECCEECCCCEE
Confidence 345567888888887653 356677775444444544444443
No 29
>PRK00276 infA translation initiation factor IF-1; Validated
Probab=35.86 E-value=1.1e+02 Score=19.26 Aligned_cols=58 Identities=29% Similarity=0.308 Sum_probs=31.1
Q ss_pred eEEEEEEeCCCCCeEEEEEeEEEeccccceEEEeeeeEEEECCCCCCCCCCEEEEeecccCCCcee
Q 033970 3 KMQGRVVCASSDKTVAVEVVRLDPHPKYKRRIRKKKKYQAHDPENQFQVGDLVQLEKSRPISKTKS 68 (107)
Q Consensus 3 ~l~G~VVs~km~KTvvV~V~r~~~hpky~K~~~r~kk~~vHDe~~~~~vGD~V~I~e~RPiSK~K~ 68 (107)
++.|+|++........|..+ -...|...++..-+ +. ...+.+||.|.+..+ |.+.++-
T Consensus 8 ~~~G~Vi~~~~~~~y~V~~~---~g~~~~c~~~Gklr---~~-~i~i~vGD~V~ve~~-~~~~~~g 65 (72)
T PRK00276 8 EMEGTVVEALPNAMFRVELE---NGHEVLAHISGKMR---KN-YIRILPGDKVTVELS-PYDLTKG 65 (72)
T ss_pred EEEEEEEEEcCCCEEEEEeC---CCCEEEEEEcccee---eC-CcccCCCCEEEEEEc-ccCCCeE
Confidence 56788887665544555321 12234444433222 11 234899999999863 3444443
No 30
>PF11302 DUF3104: Protein of unknown function (DUF3104); InterPro: IPR021453 This family of proteins with unknown function appears to be restricted to Cyanobacteria.
Probab=35.15 E-value=57 Score=21.74 Aligned_cols=33 Identities=12% Similarity=0.145 Sum_probs=26.8
Q ss_pred CCCCCCEEEEeecc--cCCCceeEEEEEeecCCcc
Q 033970 48 QFQVGDLVQLEKSR--PISKTKSFIAVAMPPRNAS 80 (107)
Q Consensus 48 ~~~vGD~V~I~e~R--PiSK~K~~~V~~Iv~~~~~ 80 (107)
.++.||.|+++... -.++.+.|-+-.||...+.
T Consensus 5 ~Vk~Gd~ViV~~~~~~~~~~~~dWWmg~Vi~~~gg 39 (75)
T PF11302_consen 5 SVKPGDTVIVQDEQEVGQKQDKDWWMGQVIHCEGG 39 (75)
T ss_pred ccCCCCEEEEecCccccccCCCCcEEEEEEEEecc
Confidence 57899999999975 3466779999999987664
No 31
>PRK12442 translation initiation factor IF-1; Reviewed
Probab=34.96 E-value=1.5e+02 Score=20.27 Aligned_cols=51 Identities=27% Similarity=0.247 Sum_probs=32.1
Q ss_pred eEEEEEEeCCCCCeEEEEEeEEEeccccceEEEeeeeEEEECCCC------CCCCCCEEEEeecccCCCce
Q 033970 3 KMQGRVVCASSDKTVAVEVVRLDPHPKYKRRIRKKKKYQAHDPEN------QFQVGDLVQLEKSRPISKTK 67 (107)
Q Consensus 3 ~l~G~VVs~km~KTvvV~V~r~~~hpky~K~~~r~kk~~vHDe~~------~~~vGD~V~I~e~RPiSK~K 67 (107)
++.|+|+....+-...|..+-- ..+++|-+.. -..+||.|.++-+ |..-+|
T Consensus 8 e~~G~V~e~Lp~~~frV~LenG-------------~~vla~isGKmR~~rIrIl~GD~V~VE~s-pYDltk 64 (87)
T PRK12442 8 ELDGIVDEVLPDSRFRVTLENG-------------VEVGAYASGRMRKHRIRILAGDRVTLELS-PYDLTK 64 (87)
T ss_pred EEEEEEEEECCCCEEEEEeCCC-------------CEEEEEeccceeeeeEEecCCCEEEEEEC-cccCCc
Confidence 5788888877777777776621 2233333322 2568999998876 444444
No 32
>PLN00208 translation initiation factor (eIF); Provisional
Probab=34.93 E-value=1.9e+02 Score=21.45 Aligned_cols=58 Identities=17% Similarity=0.217 Sum_probs=35.7
Q ss_pred eEEEEEEeCCCCCeEEEEEe----EEEeccccceEEEeeeeEEEECCCCCCCCCCEEEEeecccCCCceeEEEEE
Q 033970 3 KMQGRVVCASSDKTVAVEVV----RLDPHPKYKRRIRKKKKYQAHDPENQFQVGDLVQLEKSRPISKTKSFIAVA 73 (107)
Q Consensus 3 ~l~G~VVs~km~KTvvV~V~----r~~~hpky~K~~~r~kk~~vHDe~~~~~vGD~V~I~e~RPiSK~K~~~V~~ 73 (107)
...|+|+....+..+.|... ++...| --+++ ++| .+.||+|++. .+|..+.|-=++..
T Consensus 33 q~~g~V~~~lGn~~~~V~c~dG~~rLa~Ip---GKmRK--rIW-------I~~GD~VlVe-l~~~d~~KgdIv~r 94 (145)
T PLN00208 33 QEYAQVLRMLGNGRCEALCIDGTKRLCHIR---GKMRK--KVW-------IAAGDIILVG-LRDYQDDKADVILK 94 (145)
T ss_pred cEEEEEEEEcCCCEEEEEECCCCEEEEEEe---cccee--eEE-------ecCCCEEEEE-ccCCCCCEEEEEEE
Confidence 35688888777777777744 222211 11222 355 6789999887 77887777654433
No 33
>PF09926 DUF2158: Uncharacterized small protein (DUF2158); InterPro: IPR019226 This entry represents a family of predominantly prokaryotic proteins with no known function.
Probab=34.27 E-value=31 Score=21.28 Aligned_cols=13 Identities=46% Similarity=0.925 Sum_probs=11.1
Q ss_pred CCCCEEEEeeccc
Q 033970 50 QVGDLVQLEKSRP 62 (107)
Q Consensus 50 ~vGD~V~I~e~RP 62 (107)
++||+|.+.+.-|
T Consensus 2 ~~GDvV~LKSGGp 14 (53)
T PF09926_consen 2 KIGDVVQLKSGGP 14 (53)
T ss_pred CCCCEEEEccCCC
Confidence 6899999998855
No 34
>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=33.97 E-value=44 Score=21.23 Aligned_cols=40 Identities=18% Similarity=0.141 Sum_probs=20.3
Q ss_pred CCCCCCCCCEEEEeecccCCCceeEEEEEeecCCccccccccCCC
Q 033970 45 PENQFQVGDLVQLEKSRPISKTKSFIAVAMPPRNASKKAAGESSN 89 (107)
Q Consensus 45 e~~~~~vGD~V~I~e~RPiSK~K~~~V~~Iv~~~~~~~~a~~~~~ 89 (107)
+...+++||.|.|.+.. ....|.+|-......+.|.-+++
T Consensus 23 ~~G~i~~Gd~v~i~P~~-----~~~~V~si~~~~~~~~~a~aGd~ 62 (83)
T cd03698 23 ESGSIQKGDTLLVMPSK-----ESVEVKSIYVDDEEVDYAVAGEN 62 (83)
T ss_pred eeeEEeCCCEEEEeCCC-----cEEEEEEEEECCeECCEECCCCE
Confidence 44456677777776543 23455555443333344443333
No 35
>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=32.88 E-value=64 Score=22.95 Aligned_cols=27 Identities=37% Similarity=0.560 Sum_probs=18.0
Q ss_pred CCCCCCEEEEeecccCC-CceeEEEEEe
Q 033970 48 QFQVGDLVQLEKSRPIS-KTKSFIAVAM 74 (107)
Q Consensus 48 ~~~vGD~V~I~e~RPiS-K~K~~~V~~I 74 (107)
.|.+||.|++-.++.-. +..-|.+..+
T Consensus 42 ~f~~GDlvLflpt~~~~~~~~~~~af~~ 69 (129)
T PF10377_consen 42 NFQVGDLVLFLPTRNHNNKKQPWAAFNV 69 (129)
T ss_pred cCCCCCEEEEEecCCCCccccceEEeeC
Confidence 69999999999985533 3333444443
No 36
>PRK05753 nucleoside diphosphate kinase regulator; Provisional
Probab=32.62 E-value=1e+02 Score=21.93 Aligned_cols=29 Identities=14% Similarity=0.196 Sum_probs=22.4
Q ss_pred CCCCCCEEEEeecccCCCceeEEEEEeecCC
Q 033970 48 QFQVGDLVQLEKSRPISKTKSFIAVAMPPRN 78 (107)
Q Consensus 48 ~~~vGD~V~I~e~RPiSK~K~~~V~~Iv~~~ 78 (107)
-.++||.|.+. .|-...++|.|.+|.+.+
T Consensus 101 G~~~Gd~v~v~--~p~G~~~~~~I~~I~y~p 129 (137)
T PRK05753 101 GLSVGQSIDWP--LPGGKETHLEVLEVEYQP 129 (137)
T ss_pred CCCCCCEEEEE--CCCCCEEEEEEEEEEeCC
Confidence 46899999987 565556789999997543
No 37
>KOG1698 consensus Mitochondrial/chloroplast ribosomal protein L19 [Translation, ribosomal structure and biogenesis]
Probab=31.81 E-value=75 Score=24.87 Aligned_cols=33 Identities=24% Similarity=0.344 Sum_probs=27.2
Q ss_pred EEECCCCCCCCCCEEEEeecccCCCceeEEEEEee
Q 033970 41 QAHDPENQFQVGDLVQLEKSRPISKTKSFIAVAMP 75 (107)
Q Consensus 41 ~vHDe~~~~~vGD~V~I~e~RPiSK~K~~~V~~Iv 75 (107)
.-|-| +.++||+|+|..--|-++.+.+...-|.
T Consensus 91 ~r~iP--e~~~G~Iv~V~s~~p~~k~k~s~f~Gi~ 123 (201)
T KOG1698|consen 91 VRDIP--EFKVGSIVRVTSEDPENKRKVSRFKGIC 123 (201)
T ss_pred cccCC--ccccccEEEEEecCCccCCceeEEEEEE
Confidence 33445 7999999999999999999988887773
No 38
>PRK10409 hydrogenase assembly chaperone; Provisional
Probab=31.28 E-value=35 Score=23.27 Aligned_cols=50 Identities=20% Similarity=0.199 Sum_probs=27.7
Q ss_pred EEEEeCCCCCeEEEEEeEEEeccccceEEEeeeeEEEE--CCCCCCCCCCEEEEeecccCCC
Q 033970 6 GRVVCASSDKTVAVEVVRLDPHPKYKRRIRKKKKYQAH--DPENQFQVGDLVQLEKSRPISK 65 (107)
Q Consensus 6 G~VVs~km~KTvvV~V~r~~~hpky~K~~~r~kk~~vH--De~~~~~vGD~V~I~e~RPiSK 65 (107)
|+|++..- .+++|.+.- ..+.-.-.++- |+...+++||+|++.-.--|||
T Consensus 7 ~kVv~i~~-~~A~vd~~G---------v~reV~l~Lv~~~~~~~~~~vGDyVLVHaGfAi~~ 58 (90)
T PRK10409 7 GQIRTIDG-NQAKVDVCG---------IQRDVDLTLVGSCDENGQPRVGQWVLVHVGFAMSV 58 (90)
T ss_pred eEEEEEcC-CeEEEEcCC---------eEEEEEEeeecccCCCCccCCCCEEEEecChHHhh
Confidence 67776542 356665432 22222233332 2233799999999987644444
No 39
>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=30.72 E-value=1.1e+02 Score=19.49 Aligned_cols=15 Identities=27% Similarity=0.437 Sum_probs=8.3
Q ss_pred CCCCCCCCCEEEEee
Q 033970 45 PENQFQVGDLVQLEK 59 (107)
Q Consensus 45 e~~~~~vGD~V~I~e 59 (107)
+.-.+++||.|.+.+
T Consensus 23 ~~G~v~~gd~v~~~p 37 (87)
T cd03697 23 ERGTIKVGDEVEIVG 37 (87)
T ss_pred CCCCCccCCEEEEeC
Confidence 444556666665544
No 40
>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=30.70 E-value=1.6e+02 Score=19.21 Aligned_cols=14 Identities=29% Similarity=0.525 Sum_probs=10.5
Q ss_pred CCCCCCCCEEEEee
Q 033970 46 ENQFQVGDLVQLEK 59 (107)
Q Consensus 46 ~~~~~vGD~V~I~e 59 (107)
....++||.|.+.-
T Consensus 51 ~~~~~~Gd~v~vkI 64 (99)
T cd04460 51 KRVLKVGDVVRARI 64 (99)
T ss_pred CCEECCCCEEEEEE
Confidence 46779999987653
No 41
>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=30.49 E-value=36 Score=21.67 Aligned_cols=12 Identities=25% Similarity=0.354 Sum_probs=10.3
Q ss_pred CCCCCCEEEEee
Q 033970 48 QFQVGDLVQLEK 59 (107)
Q Consensus 48 ~~~vGD~V~I~e 59 (107)
-|+.||+|.|..
T Consensus 53 G~~~GD~V~Ig~ 64 (69)
T TIGR03595 53 GAKDGDTVRIGD 64 (69)
T ss_pred CCCCCCEEEEcc
Confidence 589999999975
No 42
>PRK10862 SoxR reducing system protein RseC; Provisional
Probab=30.47 E-value=1.4e+02 Score=21.77 Aligned_cols=56 Identities=13% Similarity=0.044 Sum_probs=33.2
Q ss_pred CceEEEEEEeCCCCCeEEEEEeEEE-----------eccccceEEEe-eeeEEEECCCCCCCCCCEEEEe
Q 033970 1 MKKMQGRVVCASSDKTVAVEVVRLD-----------PHPKYKRRIRK-KKKYQAHDPENQFQVGDLVQLE 58 (107)
Q Consensus 1 ~k~l~G~VVs~km~KTvvV~V~r~~-----------~hpky~K~~~r-~kk~~vHDe~~~~~vGD~V~I~ 58 (107)
|=+=.|+|++.. +..+.|+..|.- -+-...|.+.. ...+.+..+. .+++||.|.|.
T Consensus 1 Mmee~~~Vv~v~-~~~a~Ve~~r~saCg~C~a~~gCG~~~l~~~~~~~~~~~~v~~~~-~~~vGD~V~v~ 68 (154)
T PRK10862 1 MIKEWATVVSWQ-NGIALLRCEVKAGCSSCASRAGCGSRLLNKLGPQTTHQLVVPSSQ-PLVPGQKVELG 68 (154)
T ss_pred CcceEEEEEEEE-CCEEEEEEecCCCCcCcCCCCCchhhHHHHhcCCCceEEEecCCC-CCCCCCEEEEe
Confidence 334579999874 356888887752 11122222222 3445555543 58999999875
No 43
>PRK01889 GTPase RsgA; Reviewed
Probab=28.16 E-value=1.9e+02 Score=23.61 Aligned_cols=66 Identities=26% Similarity=0.306 Sum_probs=35.7
Q ss_pred EEEEEeCCCCCeEEEEEeEEEeccccceEEEeeeeEEEECCCCCCCCCCEEEEeecccCCCceeEEEEEeecCCccc
Q 033970 5 QGRVVCASSDKTVAVEVVRLDPHPKYKRRIRKKKKYQAHDPENQFQVGDLVQLEKSRPISKTKSFIAVAMPPRNASK 81 (107)
Q Consensus 5 ~G~VVs~km~KTvvV~V~r~~~hpky~K~~~r~kk~~vHDe~~~~~vGD~V~I~e~RPiSK~K~~~V~~Iv~~~~~~ 81 (107)
.|+|++.... -..|..+ +-.|....+..-+...|.....+-+||+|.+.. .-.+.+.+|+++....
T Consensus 30 ~g~v~~~~~~-~~~v~~~----~~~~~~~~~gk~~~~~~~~~~~~~vGD~V~~~~------~~~g~I~~i~pR~~~L 95 (356)
T PRK01889 30 PGRVVEEHRS-GYVVATE----EGEVRAEVSGKWRHEAFPPGDRPAVGDWVLLDN------EKKARIVRLLPRRSLF 95 (356)
T ss_pred cEEEEEEECC-EEEEEEC----CcEEEEEecchhhccccccCCCCccCcEEEEec------CCceEEEEEECCCceE
Confidence 5777765432 2333322 122323333322222334445689999999973 1347788888877654
No 44
>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=27.51 E-value=1.1e+02 Score=17.41 Aligned_cols=25 Identities=24% Similarity=0.423 Sum_probs=17.5
Q ss_pred eeEEEECCC-----CCCCCCCEEEEeeccc
Q 033970 38 KKYQAHDPE-----NQFQVGDLVQLEKSRP 62 (107)
Q Consensus 38 kk~~vHDe~-----~~~~vGD~V~I~e~RP 62 (107)
..+++|... +.+..||.|...-..+
T Consensus 21 ~~i~v~~~~~~~~~~~~~~Gd~V~~~i~~~ 50 (64)
T smart00357 21 KDVFVHPSQIQGGLKSLREGDEVEFKVVSP 50 (64)
T ss_pred ccEEEEhHHhhcCCCcCCCCCEEEEEEEEc
Confidence 356666544 4578899999886654
No 45
>PF15057 DUF4537: Domain of unknown function (DUF4537)
Probab=26.98 E-value=1.7e+02 Score=20.47 Aligned_cols=49 Identities=24% Similarity=0.171 Sum_probs=27.1
Q ss_pred EEEEEEeCCCCCeEEEEEeEEEeccccceEEEeeeeEEEE-CC-CCCCCCCCEEEEe
Q 033970 4 MQGRVVCASSDKTVAVEVVRLDPHPKYKRRIRKKKKYQAH-DP-ENQFQVGDLVQLE 58 (107)
Q Consensus 4 l~G~VVs~km~KTvvV~V~r~~~hpky~K~~~r~kk~~vH-De-~~~~~vGD~V~I~ 58 (107)
..|+|.+.-......|+- +.-.....-...+... |. ...+++||.|+-.
T Consensus 15 Y~GtV~~~~~~~~~lV~f------~~~~~~~v~~~~iI~~~~~~~~~L~~GD~VLA~ 65 (124)
T PF15057_consen 15 YPGTVKKCVSSGQFLVEF------DDGDTQEVPISDIIALSDAMRHSLQVGDKVLAP 65 (124)
T ss_pred EeEEEEEccCCCEEEEEE------CCCCEEEeChHHeEEccCcccCcCCCCCEEEEe
Confidence 568888876566666665 1111111112222222 22 3489999999877
No 46
>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=26.09 E-value=40 Score=21.40 Aligned_cols=12 Identities=25% Similarity=0.382 Sum_probs=7.3
Q ss_pred CCCCCCEEEEee
Q 033970 48 QFQVGDLVQLEK 59 (107)
Q Consensus 48 ~~~vGD~V~I~e 59 (107)
-++.||+|.|..
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 578999999864
No 47
>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=25.96 E-value=75 Score=17.16 Aligned_cols=13 Identities=23% Similarity=0.672 Sum_probs=11.4
Q ss_pred CCCCCCEEEEeec
Q 033970 48 QFQVGDLVQLEKS 60 (107)
Q Consensus 48 ~~~vGD~V~I~e~ 60 (107)
.+..||.|.+.+.
T Consensus 17 ~~~~Gd~v~v~~~ 29 (54)
T cd00174 17 SFKKGDIIEVLEK 29 (54)
T ss_pred CCCCCCEEEEEEc
Confidence 6899999998877
No 48
>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=25.91 E-value=1.2e+02 Score=20.39 Aligned_cols=30 Identities=13% Similarity=0.186 Sum_probs=22.9
Q ss_pred CCCCCCCCEEEEeecccCCCceeEEEEEee
Q 033970 46 ENQFQVGDLVQLEKSRPISKTKSFIAVAMP 75 (107)
Q Consensus 46 ~~~~~vGD~V~I~e~RPiSK~K~~~V~~Iv 75 (107)
.+.++.||.|.+-...|......-...+|+
T Consensus 87 ~g~~~~gd~vVv~~g~~~~~~g~tn~~~v~ 116 (117)
T PF02887_consen 87 RGLLKPGDKVVVVAGMPFGTPGGTNTIRVV 116 (117)
T ss_dssp TTSS-TTSEEEEEEESSTTTTSSEEEEEEE
T ss_pred cCCCCCCCEEEEEeCCCCCCCCCCEEEEEE
Confidence 346899999999999888877777666665
No 49
>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=25.18 E-value=94 Score=23.86 Aligned_cols=28 Identities=25% Similarity=0.233 Sum_probs=19.2
Q ss_pred CCCCEEEEeecccCCCceeEEEEEeecCCccc
Q 033970 50 QVGDLVQLEKSRPISKTKSFIAVAMPPRNASK 81 (107)
Q Consensus 50 ~vGD~V~I~e~RPiSK~K~~~V~~Iv~~~~~~ 81 (107)
-+||+|.+... -.....+.+|+++-..-
T Consensus 2 ~vGD~V~~~~~----~~~~~~i~~i~eR~~~L 29 (245)
T TIGR00157 2 VVGDRVVWEPG----NVVKVYGGAIAERKNEL 29 (245)
T ss_pred CCCcEEEEEec----CCCceEEEEEecccceE
Confidence 58999999732 12447788888875544
No 50
>PF06107 DUF951: Bacterial protein of unknown function (DUF951); InterPro: IPR009296 This family consists of several short hypothetical bacterial proteins of unknown function.
Probab=25.13 E-value=1.3e+02 Score=19.10 Aligned_cols=25 Identities=24% Similarity=0.695 Sum_probs=19.8
Q ss_pred CCCCCEEEEeecccCCCceeEEEEEe
Q 033970 49 FQVGDLVQLEKSRPISKTKSFIAVAM 74 (107)
Q Consensus 49 ~~vGD~V~I~e~RPiSK~K~~~V~~I 74 (107)
..+||+|....--|=. ...|.|..+
T Consensus 2 ~~vgDiV~mKK~HPCG-~~~Wei~R~ 26 (57)
T PF06107_consen 2 YEVGDIVEMKKPHPCG-SNEWEIIRI 26 (57)
T ss_pred ccCCCEEEEcCCCCCC-CCEEEEEEc
Confidence 4689999999887754 478988765
No 51
>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=24.53 E-value=1.6e+02 Score=17.41 Aligned_cols=42 Identities=21% Similarity=0.271 Sum_probs=23.7
Q ss_pred CCeEEEEEeEEEeccccceEEEeee-eEEEECCCCCCCCCCEEEEe
Q 033970 14 DKTVAVEVVRLDPHPKYKRRIRKKK-KYQAHDPENQFQVGDLVQLE 58 (107)
Q Consensus 14 ~KTvvV~V~r~~~hpky~K~~~r~k-k~~vHDe~~~~~vGD~V~I~ 58 (107)
-+++.|.|+..- ++ +..+-|+. ...++-+.....+||.|.++
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 23344444 56666666544479998664
No 52
>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=24.19 E-value=1.2e+02 Score=20.05 Aligned_cols=55 Identities=18% Similarity=0.299 Sum_probs=29.4
Q ss_pred eEEEEEEeCCCCCeEEEEEeEE---EeccccceEEEeee----eEEEECCCCCCCCCCEEEEe
Q 033970 3 KMQGRVVCASSDKTVAVEVVRL---DPHPKYKRRIRKKK----KYQAHDPENQFQVGDLVQLE 58 (107)
Q Consensus 3 ~l~G~VVs~km~KTvvV~V~r~---~~hpky~K~~~r~k----k~~vHDe~~~~~vGD~V~I~ 58 (107)
+..|+|++.. .+.+.|.+-.. ....-|.-.++... ..--.+.....++||+|+-+
T Consensus 9 iVig~V~~v~-~~~~~v~I~~v~~~~l~~~~~g~l~~~dv~~~~~d~~~~~~~f~~GDiV~Ak 70 (92)
T cd05791 9 IVIARVTRIN-PRFAKVDILCVGGRPLKESFRGVIRKEDIRATEKDKVEMYKCFRPGDIVRAK 70 (92)
T ss_pred EEEEEEEEEc-CCEEEEEEEEecCeecCCCcccEEEHHHccccccchHHHHhhcCCCCEEEEE
Confidence 5689998764 55577766332 22333444444211 11111234568999999643
No 53
>PRK10371 DNA-binding transcriptional regulator MelR; Provisional
Probab=22.87 E-value=83 Score=24.69 Aligned_cols=42 Identities=12% Similarity=0.141 Sum_probs=32.3
Q ss_pred EEEeccccceEEEe--eeeEEEECCCCCCCCCCEEEEeecccCC
Q 033970 23 RLDPHPKYKRRIRK--KKKYQAHDPENQFQVGDLVQLEKSRPIS 64 (107)
Q Consensus 23 r~~~hpky~K~~~r--~kk~~vHDe~~~~~vGD~V~I~e~RPiS 64 (107)
..+||..|.=.+.. .-.|.+.+....+..||.+.|..+.|-+
T Consensus 40 ~~HwH~e~Ei~yv~~G~~~~~i~g~~~~l~~Gd~ili~s~~~H~ 83 (302)
T PRK10371 40 TSHWHGQVEVNVPFDGDVEYLINNEKVQINQGHITLFWACTPHQ 83 (302)
T ss_pred CCCccccEEEEEecCCcEEEEECCEEEEEcCCcEEEEecCCccc
Confidence 56899999886654 4455555556689999999999998865
No 54
>PF08980 DUF1883: Domain of unknown function (DUF1883); InterPro: IPR015073 This family consist of hypothetical bacterial proteins. ; PDB: 2B1Y_A.
Probab=22.73 E-value=32 Score=23.80 Aligned_cols=20 Identities=25% Similarity=0.330 Sum_probs=1.9
Q ss_pred eEEEECCCCCCCCCCEEEEee
Q 033970 39 KYQAHDPENQFQVGDLVQLEK 59 (107)
Q Consensus 39 k~~vHDe~~~~~vGD~V~I~e 59 (107)
+|..||-. .++.||+|.|.=
T Consensus 2 ~~~~~~~~-~~~~Gd~V~V~l 21 (94)
T PF08980_consen 2 KFIHYDLG-HLKRGDTVVVRL 21 (94)
T ss_dssp ------------TT-------
T ss_pred ceeeechh-ccCCCCEEEEEe
Confidence 34557765 588999998863
No 55
>COG0853 PanD Aspartate 1-decarboxylase [Coenzyme metabolism]
Probab=22.63 E-value=78 Score=23.10 Aligned_cols=18 Identities=39% Similarity=0.473 Sum_probs=14.9
Q ss_pred CCCCCCEEEEeecccCCC
Q 033970 48 QFQVGDLVQLEKSRPISK 65 (107)
Q Consensus 48 ~~~vGD~V~I~e~RPiSK 65 (107)
.|.+||.|.|...-.++-
T Consensus 77 l~~~GD~VII~sy~~~~e 94 (126)
T COG0853 77 LVQVGDLVIIMSYAQMSE 94 (126)
T ss_pred hCCCCCEEEEEEcccCCH
Confidence 689999999998766653
No 56
>PRK04012 translation initiation factor IF-1A; Provisional
Probab=22.41 E-value=2.3e+02 Score=19.45 Aligned_cols=51 Identities=18% Similarity=0.175 Sum_probs=29.8
Q ss_pred eEEEEEEeCCCCCeEEEEEeEEEeccccceEEEeeeeEEEECCCC-----CCCCCCEEEEeecccCCCce
Q 033970 3 KMQGRVVCASSDKTVAVEVVRLDPHPKYKRRIRKKKKYQAHDPEN-----QFQVGDLVQLEKSRPISKTK 67 (107)
Q Consensus 3 ~l~G~VVs~km~KTvvV~V~r~~~hpky~K~~~r~kk~~vHDe~~-----~~~vGD~V~I~e~RPiSK~K 67 (107)
...|+|+....+.-..|..+- -..++||-|.. -.+.||.|++.. .|....|
T Consensus 22 e~~g~V~~~lG~~~~~V~~~d-------------G~~~la~i~GK~Rk~IwI~~GD~VlVe~-~~~~~~k 77 (100)
T PRK04012 22 EVFGVVEQMLGANRVRVRCMD-------------GVERMGRIPGKMKKRMWIREGDVVIVAP-WDFQDEK 77 (100)
T ss_pred EEEEEEEEEcCCCEEEEEeCC-------------CCEEEEEEchhhcccEEecCCCEEEEEe-cccCCCE
Confidence 467777777767766666441 12233333311 256899998874 5555554
No 57
>PRK00098 GTPase RsgA; Reviewed
Probab=22.40 E-value=2.8e+02 Score=21.79 Aligned_cols=65 Identities=22% Similarity=0.221 Sum_probs=33.9
Q ss_pred EEEEEeCCCCCeEEEEEeEEEeccccceEEEeeeeEEEECCCCCCCCCCEEEEeecccCCCceeEEEEEeecCCccc
Q 033970 5 QGRVVCASSDKTVAVEVVRLDPHPKYKRRIRKKKKYQAHDPENQFQVGDLVQLEKSRPISKTKSFIAVAMPPRNASK 81 (107)
Q Consensus 5 ~G~VVs~km~KTvvV~V~r~~~hpky~K~~~r~kk~~vHDe~~~~~vGD~V~I~e~RPiSK~K~~~V~~Iv~~~~~~ 81 (107)
.|+|++.... -..|..+. .-.|....+..-+ + ....+-+||+|.+....| ....+.+|..+....
T Consensus 2 ~g~v~~~~~~-~~~v~~~~---~~~~~~~~~g~~~---~-~~~~~~vGD~V~~~~~~~----~~g~i~~i~~R~~~l 66 (298)
T PRK00098 2 EGLIIKALGG-FYYVESED---GQVYQCRARGKFR---K-KTNTPAVGDRVEFSAENN----DEGVILEIHERKNLL 66 (298)
T ss_pred eEEEEEEECC-EEEEEECC---CCEEEEEeccccc---c-CCCCcCCCCEEEEEECCC----CcEEEEEEeCCCceE
Confidence 5888865432 33443321 1123333333222 2 234578999999974322 345667777766554
No 58
>COG3655 Predicted transcriptional regulator [Transcription]
Probab=22.33 E-value=49 Score=21.89 Aligned_cols=12 Identities=25% Similarity=0.470 Sum_probs=10.0
Q ss_pred CCCCCCEEEEee
Q 033970 48 QFQVGDLVQLEK 59 (107)
Q Consensus 48 ~~~vGD~V~I~e 59 (107)
+|.+||++.+..
T Consensus 56 eCqpgDiley~~ 67 (73)
T COG3655 56 ECQPGDILEYVP 67 (73)
T ss_pred CCChhheeEEec
Confidence 799999998753
No 59
>PRK09570 rpoH DNA-directed RNA polymerase subunit H; Reviewed
Probab=22.30 E-value=69 Score=21.40 Aligned_cols=33 Identities=18% Similarity=0.312 Sum_probs=21.0
Q ss_pred eEEEECCCC---CCCCCCEEEEeec-ccCCCceeEEE
Q 033970 39 KYQAHDPEN---QFQVGDLVQLEKS-RPISKTKSFIA 71 (107)
Q Consensus 39 k~~vHDe~~---~~~vGD~V~I~e~-RPiSK~K~~~V 71 (107)
++...||-. .++.||+|.|.-- .--.....|++
T Consensus 39 ~I~~~DPv~r~~g~k~GdVvkI~R~S~taG~~v~YR~ 75 (79)
T PRK09570 39 KIKASDPVVKAIGAKPGDVIKIVRKSPTAGEAVYYRL 75 (79)
T ss_pred ceeccChhhhhcCCCCCCEEEEEECCCCCCccEEEEE
Confidence 566778743 7899999988543 33344445544
No 60
>CHL00010 infA translation initiation factor 1
Probab=22.30 E-value=2.3e+02 Score=18.29 Aligned_cols=58 Identities=22% Similarity=0.223 Sum_probs=31.1
Q ss_pred eEEEEEEeCCCCCeEEEEEeEEEeccccceEEEeeeeEEEECCCCCCCCCCEEEEeecccCCCcee
Q 033970 3 KMQGRVVCASSDKTVAVEVVRLDPHPKYKRRIRKKKKYQAHDPENQFQVGDLVQLEKSRPISKTKS 68 (107)
Q Consensus 3 ~l~G~VVs~km~KTvvV~V~r~~~hpky~K~~~r~kk~~vHDe~~~~~vGD~V~I~e~RPiSK~K~ 68 (107)
.+.|+|++........|..+ -...|...++..-+ +. .....+||.|.+.. .|...++-
T Consensus 8 ~~~G~Vik~lg~~~y~V~~~---~g~~~~c~~rGklr---~~-~i~~~vGD~V~ve~-~~~~~~~g 65 (78)
T CHL00010 8 EMEGLVTESLPNGMFRVRLD---NGCQVLGYISGKIR---RN-SIRILPGDRVKVEL-SPYDLTKG 65 (78)
T ss_pred EEEEEEEEEcCCCEEEEEeC---CCCEEEEEecccee---cC-CcccCCCCEEEEEE-cccCCCeE
Confidence 46788887654444555321 11234444443333 22 34578999999986 34455443
No 61
>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=22.23 E-value=1.2e+02 Score=19.54 Aligned_cols=36 Identities=8% Similarity=0.014 Sum_probs=17.9
Q ss_pred CCCCCCCCCCEEEEeecccCCCceeEEEEEeecCCcccccc
Q 033970 44 DPENQFQVGDLVQLEKSRPISKTKSFIAVAMPPRNASKKAA 84 (107)
Q Consensus 44 De~~~~~vGD~V~I~e~RPiSK~K~~~V~~Iv~~~~~~~~a 84 (107)
-+...++.||.|.|.+.. ....|.+|-......+.|
T Consensus 26 v~~G~i~~gd~v~i~P~~-----~~~~V~sI~~~~~~~~~a 61 (91)
T cd03693 26 VETGVLKPGMVVTFAPAG-----VTGEVKSVEMHHEPLEEA 61 (91)
T ss_pred EecceeecCCEEEECCCC-----cEEEEEEEEECCcCcCEE
Confidence 344556666666666542 334555554333333333
No 62
>cd04498 hPOT1_OB2 hPOT1_OB2: A subfamily of OB folds similar to the second OB fold (OB2) of human protection of telomeres 1 protein (hPOT1). POT1 proteins bind to the single-stranded (ss) 3-prime ends of the telomere. hPOT1 binds specifically to ss telomeric DNA repeats ending with the sequence GGTTAG. The hPOT1 monomer consists of two closely connected OB folds (OB1-OB2) which cooperate to bind telomeric ssDNA. OB1 makes more extensive contact with the ssDNA than OB2. OB2 protects the 3' end of the ssDNA. hPOT1 is implicated in telomere length regulation.
Probab=21.74 E-value=1.2e+02 Score=21.64 Aligned_cols=24 Identities=17% Similarity=0.225 Sum_probs=17.7
Q ss_pred eeeEEEECCCC----CCCCCCEEEEeec
Q 033970 37 KKKYQAHDPEN----QFQVGDLVQLEKS 60 (107)
Q Consensus 37 ~kk~~vHDe~~----~~~vGD~V~I~e~ 60 (107)
+-.+.+-||.. +++.||.|+|.-.
T Consensus 61 ti~It~yD~H~~~ar~lK~GdfV~L~NV 88 (123)
T cd04498 61 TIDILVYDNHVELAKSLKPGDFVRIYNV 88 (123)
T ss_pred EEEEEEEcchHHHHhhCCCCCEEEEEEE
Confidence 34556667743 6999999999876
No 63
>PRK13168 rumA 23S rRNA m(5)U1939 methyltransferase; Reviewed
Probab=21.52 E-value=1.8e+02 Score=24.19 Aligned_cols=51 Identities=8% Similarity=0.041 Sum_probs=34.3
Q ss_pred CCCCCEEEEeecccCCCceeEEEEEeecCCccccccc---cCCCCCCccccccc
Q 033970 49 FQVGDLVQLEKSRPISKTKSFIAVAMPPRNASKKAAG---ESSNAGNNELGIPL 99 (107)
Q Consensus 49 ~~vGD~V~I~e~RPiSK~K~~~V~~Iv~~~~~~~~a~---~~~~~~~~~~~~~~ 99 (107)
+-+||.|++.=++.-.+.-.-.+.+|++.+..+-.+. -..|-|-+....+-
T Consensus 43 ~lPGe~v~v~i~~~~~~~~~~~~~~vl~~sp~Rv~p~C~~~~~CGGC~~qh~~y 96 (443)
T PRK13168 43 ALPGERVEVQVTEDKKQYARAKVVRILKPSPERVTPRCPHFGVCGGCQLQHLSI 96 (443)
T ss_pred CCCCCEEEEEEEEecCcEEEEEEEEEecCCcccCCCCCCcCCcCcCchhcCCCH
Confidence 5589999998876544444667999999988884321 12466666655553
No 64
>PRK10807 paraquat-inducible protein B; Provisional
Probab=21.08 E-value=1.8e+02 Score=25.52 Aligned_cols=70 Identities=14% Similarity=0.209 Sum_probs=48.0
Q ss_pred eEEEEEEeCCCC---CeEEEEEeEEEeccccceEEEeeeeEEEECCCCC---------CCCCCEEEEeecccCCCceeEE
Q 033970 3 KMQGRVVCASSD---KTVAVEVVRLDPHPKYKRRIRKKKKYQAHDPENQ---------FQVGDLVQLEKSRPISKTKSFI 70 (107)
Q Consensus 3 ~l~G~VVs~km~---KTvvV~V~r~~~hpky~K~~~r~kk~~vHDe~~~---------~~vGD~V~I~e~RPiSK~K~~~ 70 (107)
.-+|.|.+...+ +.|.|.+ ..++.|..+++..++||+-+|.-. +--|..+.+.+..+-....+|.
T Consensus 68 v~VG~V~~v~l~~d~~~V~~~~---~i~~~~~~ll~~~trFWvv~p~is~~GvsgL~tLlsG~yi~~~pG~~~~~~~~F~ 144 (547)
T PRK10807 68 VDVGVVESVTLSDDLTHVEIKA---RLNSGMEKLLHKDSVFWVVKPQIGREGISGLGTLLSGAYIELQPGSKGSKPDKYD 144 (547)
T ss_pred ceEEEEEEEEECCCCCeEEEEE---EECccHHHhhcCCCEEEEeeeeEcCCCCcChHHhhccceEEecCCCCCCcCceeE
Confidence 347888875443 3343333 345779999999999999998532 3447887776665666678888
Q ss_pred EEEee
Q 033970 71 AVAMP 75 (107)
Q Consensus 71 V~~Iv 75 (107)
+.+--
T Consensus 145 ~~~~~ 149 (547)
T PRK10807 145 LLDSP 149 (547)
T ss_pred eccCC
Confidence 76543
No 65
>KOG3507 consensus DNA-directed RNA polymerase, subunit RPB7.0 [Transcription]
Probab=20.94 E-value=48 Score=21.41 Aligned_cols=16 Identities=25% Similarity=0.555 Sum_probs=14.4
Q ss_pred CCCCCCCCCEEEEeec
Q 033970 45 PENQFQVGDLVQLEKS 60 (107)
Q Consensus 45 e~~~~~vGD~V~I~e~ 60 (107)
.+|+.+.||.++.+||
T Consensus 28 ~en~lk~~D~irCReC 43 (62)
T KOG3507|consen 28 QENTLKRGDVIRCREC 43 (62)
T ss_pred ccccccCCCcEehhhc
Confidence 3679999999999999
No 66
>COG1326 Uncharacterized archaeal Zn-finger protein [General function prediction only]
Probab=20.33 E-value=4.3e+02 Score=20.74 Aligned_cols=69 Identities=22% Similarity=0.292 Sum_probs=40.6
Q ss_pred EEEEEeC--CCCCeEEEEEeEEEeccccceEEEeeeeEEEECCCCCCCCCCEEEEeecccCCCceeEEEEEeecC-Cccc
Q 033970 5 QGRVVCA--SSDKTVAVEVVRLDPHPKYKRRIRKKKKYQAHDPENQFQVGDLVQLEKSRPISKTKSFIAVAMPPR-NASK 81 (107)
Q Consensus 5 ~G~VVs~--km~KTvvV~V~r~~~hpky~K~~~r~kk~~vHDe~~~~~vGD~V~I~e~RPiSK~K~~~V~~Iv~~-~~~~ 81 (107)
.|.|-.+ +..|.+.|.+-- .+|..-+++..+ -||...+++||.+.+..-+ ..+.+|--. ..+.
T Consensus 36 CG~V~~~~i~~~k~~~v~viV----S~~~~S~~~~ve---l~~gE~l~vGDei~vd~e~-------veITSIE~~~gkRV 101 (201)
T COG1326 36 CGTVHPAIIKTPKPVRVRVIV----SRHEESFTKEVE---LDPGETLKVGDEIEVDGEE-------VEITSIELGGGKRV 101 (201)
T ss_pred CCcEeeceeeccccceEEEEE----ecCCcccceeEe---cCCCCeEecCCEEEEcCCE-------EEEEEEeeCCCccc
Confidence 3666633 445555554432 334444433333 4788899999999887655 666676555 3444
Q ss_pred cccccC
Q 033970 82 KAAGES 87 (107)
Q Consensus 82 ~~a~~~ 87 (107)
++|.+.
T Consensus 102 ~~A~ve 107 (201)
T COG1326 102 KSAKVE 107 (201)
T ss_pred cccccc
Confidence 666543
No 67
>PRK12288 GTPase RsgA; Reviewed
Probab=20.04 E-value=3.3e+02 Score=22.31 Aligned_cols=33 Identities=21% Similarity=0.255 Sum_probs=21.8
Q ss_pred CCCCCCEEEEeec-ccCCCceeEEEEEeecCCccc
Q 033970 48 QFQVGDLVQLEKS-RPISKTKSFIAVAMPPRNASK 81 (107)
Q Consensus 48 ~~~vGD~V~I~e~-RPiSK~K~~~V~~Iv~~~~~~ 81 (107)
.+-+||+|.+... -.. ....+.+.+|+++-...
T Consensus 72 ~~~vGD~V~~~~~~~~~-~~~~~~I~~il~R~n~L 105 (347)
T PRK12288 72 SLVTGDRVVWRPGKEAL-EGVSGVVEAVHPRTSVL 105 (347)
T ss_pred CCCCCcEEEEEeCCCcc-cccceEEEEEecccceE
Confidence 3789999999732 111 11347888998877665
Done!