Query 034020
Match_columns 106
No_of_seqs 131 out of 1020
Neff 4.9
Searched_HMMs 46136
Date Fri Mar 29 08:53:38 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/034020.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/034020hhsearch_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 1.7E-37 3.8E-42 209.8 12.1 80 1-80 3-82 (84)
2 COG0186 RpsQ Ribosomal protein 100.0 2.5E-37 5.5E-42 210.3 11.3 78 2-79 9-86 (87)
3 PRK05610 rpsQ 30S ribosomal pr 100.0 7.4E-37 1.6E-41 206.5 11.9 77 2-78 7-83 (84)
4 PRK08572 rps17p 30S ribosomal 100.0 2.1E-35 4.4E-40 207.7 11.8 77 2-78 30-107 (108)
5 TIGR03635 S17_bact 30S ribosom 100.0 1.8E-35 3.9E-40 194.3 9.9 70 2-71 2-71 (71)
6 TIGR03630 arch_S17P archaeal r 100.0 4.2E-35 9E-40 204.4 11.1 74 2-75 28-102 (102)
7 PF00366 Ribosomal_S17: Riboso 100.0 2.3E-34 5.1E-39 187.7 9.3 69 6-74 1-69 (69)
8 PTZ00241 40S ribosomal protein 100.0 9.7E-33 2.1E-37 204.7 11.3 77 2-78 69-146 (158)
9 KOG1740 Predicted mitochondria 100.0 2.4E-33 5.1E-38 195.5 0.4 86 1-86 2-87 (107)
10 KOG1728 40S ribosomal protein 99.9 9.4E-24 2E-28 154.8 3.1 79 2-80 69-149 (156)
11 KOG3447 Mitochondrial/chloropl 99.7 1.9E-18 4.2E-23 126.2 1.4 90 2-91 11-101 (150)
12 PTZ00329 eukaryotic translatio 67.5 50 0.0011 24.8 8.0 57 3-73 33-94 (155)
13 PF11302 DUF3104: Protein of u 64.7 16 0.00035 24.4 4.2 38 48-85 5-44 (75)
14 smart00652 eIF1a eukaryotic tr 64.4 39 0.00085 22.4 6.1 52 3-68 6-62 (83)
15 PF10844 DUF2577: Protein of u 63.0 44 0.00096 22.6 8.9 62 3-73 19-98 (100)
16 TIGR00523 eIF-1A eukaryotic/ar 61.8 50 0.0011 22.7 6.8 48 3-64 20-72 (99)
17 PF13550 Phage-tail_3: Putativ 57.6 28 0.0006 24.0 4.7 35 37-74 128-162 (164)
18 cd04456 S1_IF1A_like S1_IF1A_l 56.6 54 0.0012 21.5 5.9 50 4-67 2-57 (78)
19 PLN00208 translation initiatio 56.0 82 0.0018 23.4 8.2 57 3-73 33-94 (145)
20 cd01854 YjeQ_engC YjeQ/EngC. 55.8 45 0.00098 26.2 6.1 37 46-86 32-68 (287)
21 cd05793 S1_IF1A S1_IF1A: Trans 52.1 53 0.0012 21.4 5.0 52 3-68 1-57 (77)
22 PRK00276 infA translation init 51.5 61 0.0013 20.6 7.1 57 3-67 8-64 (72)
23 COG0361 InfA Translation initi 50.5 60 0.0013 21.6 5.1 45 3-60 8-58 (75)
24 cd04466 S1_YloQ_GTPase S1_YloQ 48.1 32 0.00069 20.6 3.3 30 47-80 36-65 (68)
25 cd04451 S1_IF1 S1_IF1: Transla 46.5 66 0.0014 19.6 5.9 51 3-60 2-52 (64)
26 COG1489 SfsA DNA-binding prote 43.3 1.5E+02 0.0032 23.7 7.1 63 38-101 28-98 (235)
27 TIGR00157 ribosome small subun 43.0 32 0.0007 26.4 3.4 36 50-89 2-37 (245)
28 PRK10862 SoxR reducing system 42.6 61 0.0013 23.7 4.6 56 1-58 1-68 (154)
29 KOG1698 Mitochondrial/chloropl 41.7 33 0.00072 26.8 3.2 33 41-75 91-123 (201)
30 PF06107 DUF951: Bacterial pro 41.3 49 0.0011 21.0 3.4 25 49-74 2-26 (57)
31 PF04246 RseC_MucC: Positive r 40.1 35 0.00077 23.7 2.9 21 38-59 42-62 (135)
32 cd04089 eRF3_II eRF3_II: domai 39.8 32 0.00069 21.9 2.5 49 43-96 20-68 (82)
33 cd03698 eRF3_II_like eRF3_II_l 37.1 28 0.0006 22.2 1.9 46 44-94 22-67 (83)
34 TIGR03595 Obg_CgtA_exten Obg f 36.7 24 0.00053 22.5 1.5 13 48-60 53-65 (69)
35 cd03693 EF1_alpha_II EF1_alpha 36.2 1E+02 0.0022 20.0 4.5 23 35-57 46-69 (91)
36 COG1162 Predicted GTPases [Gen 36.2 1.8E+02 0.0038 24.0 6.7 73 4-86 5-77 (301)
37 TIGR00008 infA translation ini 34.0 1.3E+02 0.0029 19.4 5.8 51 3-67 6-62 (68)
38 PRK10413 hydrogenase 2 accesso 33.6 1.5E+02 0.0032 19.8 5.9 51 6-65 7-59 (82)
39 PRK00098 GTPase RsgA; Reviewed 33.5 1.7E+02 0.0037 23.0 6.2 35 47-85 36-70 (298)
40 PRK12288 GTPase RsgA; Reviewed 33.1 1.1E+02 0.0024 25.1 5.2 34 48-82 72-106 (347)
41 PRK10409 hydrogenase assembly 33.1 32 0.0007 23.5 1.7 19 47-65 40-58 (90)
42 PRK09570 rpoH DNA-directed RNA 33.0 83 0.0018 21.0 3.7 33 39-71 39-75 (79)
43 PRK04012 translation initiatio 32.6 1.7E+02 0.0036 20.2 6.2 51 3-67 22-77 (100)
44 cd03695 CysN_NodQ_II CysN_NodQ 32.2 85 0.0018 20.0 3.6 24 35-58 42-66 (81)
45 PRK01889 GTPase RsgA; Reviewed 32.0 1.9E+02 0.004 23.6 6.3 38 43-86 63-100 (356)
46 cd00174 SH3 Src homology 3 dom 32.0 46 0.001 18.1 2.1 13 48-60 17-29 (54)
47 PF02887 PK_C: Pyruvate kinase 31.9 83 0.0018 21.1 3.7 30 47-76 88-117 (117)
48 PF13567 DUF4131: Domain of un 31.6 1.6E+02 0.0034 19.5 6.6 60 3-65 79-146 (176)
49 PF09269 DUF1967: Domain of un 31.4 25 0.00055 22.4 1.0 12 48-59 53-64 (69)
50 PRK10371 DNA-binding transcrip 31.3 53 0.0011 25.8 2.9 43 22-64 39-83 (302)
51 cd03694 GTPBP_II Domain II of 31.1 85 0.0018 20.2 3.5 24 35-58 46-70 (87)
52 PF09926 DUF2158: Uncharacteri 31.1 38 0.00083 20.9 1.7 13 50-62 2-14 (53)
53 COG1499 NMD3 NMD protein affec 29.6 1.1E+02 0.0023 25.7 4.6 42 40-90 240-281 (355)
54 cd03696 selB_II selB_II: this 29.4 1.5E+02 0.0032 18.6 4.5 23 35-57 42-65 (83)
55 PRK05753 nucleoside diphosphat 29.4 1.4E+02 0.0031 21.2 4.7 27 48-76 101-127 (137)
56 cd03697 EFTU_II EFTU_II: Elong 28.1 1E+02 0.0022 19.7 3.4 14 46-59 24-37 (87)
57 COG3655 Predicted transcriptio 27.5 34 0.00074 22.6 1.1 12 48-59 56-67 (73)
58 PRK14120 gpmA phosphoglyceromu 27.3 18 0.0004 28.1 -0.3 23 75-97 224-246 (249)
59 COG2012 RPB5 DNA-directed RNA 27.1 84 0.0018 21.3 2.9 33 39-71 42-78 (80)
60 cd04486 YhcR_OBF_like YhcR_OBF 26.8 93 0.002 20.0 3.1 20 39-58 34-54 (78)
61 PRK12442 translation initiatio 26.3 2.2E+02 0.0047 19.5 5.9 51 3-67 8-64 (87)
62 PF10377 ATG11: Autophagy-rela 26.1 93 0.002 22.1 3.2 28 47-74 41-69 (129)
63 PF01200 Ribosomal_S28e: Ribos 25.8 68 0.0015 21.1 2.2 18 44-61 45-62 (69)
64 smart00357 CSP Cold shock prot 25.7 1.2E+02 0.0025 17.3 3.1 25 38-62 21-50 (64)
65 PF01938 TRAM: TRAM domain; I 25.6 1.5E+02 0.0033 17.5 4.6 42 14-58 5-47 (61)
66 PF11347 DUF3148: Protein of u 24.8 59 0.0013 21.1 1.8 17 50-66 1-17 (63)
67 smart00326 SH3 Src homology 3 24.6 1.3E+02 0.0028 16.3 3.2 23 48-74 20-42 (58)
68 cd04460 S1_RpoE S1_RpoE: RpoE, 24.6 2.1E+02 0.0045 18.6 4.9 13 46-58 51-63 (99)
69 PF07653 SH3_2: Variant SH3 do 24.6 44 0.00096 19.5 1.1 22 37-58 5-27 (55)
70 cd05791 S1_CSL4 S1_CSL4: CSL4, 24.3 1.3E+02 0.0028 19.8 3.5 54 3-57 9-69 (92)
71 COG4591 LolE ABC-type transpor 24.3 1.4E+02 0.0029 25.3 4.3 32 48-79 157-194 (408)
72 PF02359 CDC48_N: Cell divisio 24.2 56 0.0012 21.1 1.7 15 48-62 72-86 (87)
73 COG0853 PanD Aspartate 1-decar 23.8 70 0.0015 23.4 2.2 18 48-65 77-94 (126)
74 PF02311 AraC_binding: AraC-li 23.0 99 0.0022 19.6 2.7 41 23-63 17-59 (136)
75 TIGR02657 amicyanin amicyanin. 23.0 1.1E+02 0.0024 19.4 2.9 28 41-68 6-34 (83)
76 cd04457 S1_S28E S1_S28E: S28E, 22.9 1.1E+02 0.0024 19.6 2.8 15 46-60 38-52 (60)
77 PF08605 Rad9_Rad53_bind: Fung 22.9 1.2E+02 0.0026 21.9 3.3 25 48-77 59-83 (131)
78 COG2053 RPS28A Ribosomal prote 22.7 72 0.0016 21.0 1.9 20 41-60 40-59 (69)
79 smart00739 KOW KOW (Kyprides, 22.2 88 0.0019 15.4 1.9 12 49-60 2-13 (28)
80 PF08980 DUF1883: Domain of un 21.3 35 0.00077 23.6 0.3 20 39-59 2-21 (94)
81 cd04498 hPOT1_OB2 hPOT1_OB2: A 21.2 90 0.002 22.4 2.3 23 39-61 63-89 (123)
82 PRK12289 GTPase RsgA; Reviewed 21.1 1.1E+02 0.0025 25.1 3.2 36 48-85 51-86 (352)
83 PRK10807 paraquat-inducible pr 20.8 1.6E+02 0.0034 25.8 4.2 68 3-73 68-147 (547)
No 1
>CHL00142 rps17 ribosomal protein S17; Validated
Probab=100.00 E-value=1.7e-37 Score=209.77 Aligned_cols=80 Identities=48% Similarity=0.921 Sum_probs=77.5
Q ss_pred CceEEEEEEeCCCCCeEEEEEeeEEeecceeeEEEeeeeEEEECCCCCCCCCCEEEEeecccCCcceeEEEEEEEeeccc
Q 034020 1 MKSVVGLVVSNKMQKSVVVAVDRLFHHKVYNRYVKRTSKFMAHDENNQCNIGDRVRLDPSRPLSKHKHWAVAEILKKARI 80 (106)
Q Consensus 1 ~k~l~G~VvS~km~KTvvV~V~r~~~hpkY~K~~~r~kk~~vHDe~~~~k~GD~V~I~e~RPiSK~K~f~V~~Ii~k~~~ 80 (106)
++.++|+|+|++|+|||+|+|+|+++||+|+|+++++++|+||||+|+|++||+|+|+|||||||+|+|+|.+|++++..
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 47899999999999999999999999999999999999999999999999999999999999999999999999998764
No 2
>COG0186 RpsQ Ribosomal protein S17 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=2.5e-37 Score=210.28 Aligned_cols=78 Identities=49% Similarity=0.790 Sum_probs=75.8
Q ss_pred ceEEEEEEeCCCCCeEEEEEeeEEeecceeeEEEeeeeEEEECCCCCCCCCCEEEEeecccCCcceeEEEEEEEeecc
Q 034020 2 KSVVGLVVSNKMQKSVVVAVDRLFHHKVYNRYVKRTSKFMAHDENNQCNIGDRVRLDPSRPLSKHKHWAVAEILKKAR 79 (106)
Q Consensus 2 k~l~G~VvS~km~KTvvV~V~r~~~hpkY~K~~~r~kk~~vHDe~~~~k~GD~V~I~e~RPiSK~K~f~V~~Ii~k~~ 79 (106)
+.|+|+|+|++|+||++|.+++.++||+|+||+++++||+||||+|+|++||.|+|+|||||||+|+|+|++|++++.
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 3
>PRK05610 rpsQ 30S ribosomal protein S17; Reviewed
Probab=100.00 E-value=7.4e-37 Score=206.51 Aligned_cols=77 Identities=52% Similarity=0.846 Sum_probs=75.3
Q ss_pred ceEEEEEEeCCCCCeEEEEEeeEEeecceeeEEEeeeeEEEECCCCCCCCCCEEEEeecccCCcceeEEEEEEEeec
Q 034020 2 KSVVGLVVSNKMQKSVVVAVDRLFHHKVYNRYVKRTSKFMAHDENNQCNIGDRVRLDPSRPLSKHKHWAVAEILKKA 78 (106)
Q Consensus 2 k~l~G~VvS~km~KTvvV~V~r~~~hpkY~K~~~r~kk~~vHDe~~~~k~GD~V~I~e~RPiSK~K~f~V~~Ii~k~ 78 (106)
+.|.|+|+|++|+||++|+++|++|||+|+||++++++|+||||+|+|++||+|+|+|||||||+|+|+|.+|++++
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 4
>PRK08572 rps17p 30S ribosomal protein S17P; Reviewed
Probab=100.00 E-value=2.1e-35 Score=207.68 Aligned_cols=77 Identities=40% Similarity=0.605 Sum_probs=74.8
Q ss_pred ceEEEEEEeCCCCCeEEEEEeeEEeecceeeEEEeeeeEEEECCC-CCCCCCCEEEEeecccCCcceeEEEEEEEeec
Q 034020 2 KSVVGLVVSNKMQKSVVVAVDRLFHHKVYNRYVKRTSKFMAHDEN-NQCNIGDRVRLDPSRPLSKHKHWAVAEILKKA 78 (106)
Q Consensus 2 k~l~G~VvS~km~KTvvV~V~r~~~hpkY~K~~~r~kk~~vHDe~-~~~k~GD~V~I~e~RPiSK~K~f~V~~Ii~k~ 78 (106)
+.|+|+|+|++|+|||+|+|+|+++||+|+|+++++++|+||||+ |+|++||.|+|+|||||||+|+|.|.+|++++
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 79999999999999999999999999999875
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=1.8e-35 Score=194.27 Aligned_cols=70 Identities=53% Similarity=0.920 Sum_probs=68.7
Q ss_pred ceEEEEEEeCCCCCeEEEEEeeEEeecceeeEEEeeeeEEEECCCCCCCCCCEEEEeecccCCcceeEEE
Q 034020 2 KSVVGLVVSNKMQKSVVVAVDRLFHHKVYNRYVKRTSKFMAHDENNQCNIGDRVRLDPSRPLSKHKHWAV 71 (106)
Q Consensus 2 k~l~G~VvS~km~KTvvV~V~r~~~hpkY~K~~~r~kk~~vHDe~~~~k~GD~V~I~e~RPiSK~K~f~V 71 (106)
++|.|+|+|++|+||++|++++++|||+|+|+++++++|+||||+|+|++||+|+|+|||||||+|+|+|
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 6899999999999999999999999999999999999999999999999999999999999999999985
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=4.2e-35 Score=204.38 Aligned_cols=74 Identities=39% Similarity=0.584 Sum_probs=72.0
Q ss_pred ceEEEEEEeCCCCCeEEEEEeeEEeecceeeEEEeeeeEEEECCC-CCCCCCCEEEEeecccCCcceeEEEEEEE
Q 034020 2 KSVVGLVVSNKMQKSVVVAVDRLFHHKVYNRYVKRTSKFMAHDEN-NQCNIGDRVRLDPSRPLSKHKHWAVAEIL 75 (106)
Q Consensus 2 k~l~G~VvS~km~KTvvV~V~r~~~hpkY~K~~~r~kk~~vHDe~-~~~k~GD~V~I~e~RPiSK~K~f~V~~Ii 75 (106)
+.|+|+|+|++|+|||+|+|+|+++||+|+|+++++++|+||||+ |+|++||.|+|+|||||||+|+|+|++|+
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 79999999999999999999999999874
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=100.00 E-value=2.3e-34 Score=187.71 Aligned_cols=69 Identities=57% Similarity=0.984 Sum_probs=67.0
Q ss_pred EEEEeCCCCCeEEEEEeeEEeecceeeEEEeeeeEEEECCCCCCCCCCEEEEeecccCCcceeEEEEEE
Q 034020 6 GLVVSNKMQKSVVVAVDRLFHHKVYNRYVKRTSKFMAHDENNQCNIGDRVRLDPSRPLSKHKHWAVAEI 74 (106)
Q Consensus 6 G~VvS~km~KTvvV~V~r~~~hpkY~K~~~r~kk~~vHDe~~~~k~GD~V~I~e~RPiSK~K~f~V~~I 74 (106)
|+|+|++|+||++|++++++|||+|+|+++++++|+||||+|+|++||+|+|+|||||||+|+|.|.++
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=100.00 E-value=9.7e-33 Score=204.68 Aligned_cols=77 Identities=32% Similarity=0.487 Sum_probs=73.9
Q ss_pred ceEEEEEEeCCCCCeEEEEEeeEEeecceeeEEEeeeeEEEECC-CCCCCCCCEEEEeecccCCcceeEEEEEEEeec
Q 034020 2 KSVVGLVVSNKMQKSVVVAVDRLFHHKVYNRYVKRTSKFMAHDE-NNQCNIGDRVRLDPSRPLSKHKHWAVAEILKKA 78 (106)
Q Consensus 2 k~l~G~VvS~km~KTvvV~V~r~~~hpkY~K~~~r~kk~~vHDe-~~~~k~GD~V~I~e~RPiSK~K~f~V~~Ii~k~ 78 (106)
++|+|+|+|++|+|||+|+++|+++||+|+||++++++|+|||| .++|++||+|+|+|||||||+|+|+|++|++++
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 68999999999999999999999999999999999999999996 459999999999999999999999999999864
No 9
>KOG1740 consensus Predicted mitochondrial/chloroplast ribosomal protein S17 [Translation, ribosomal structure and biogenesis]
Probab=99.97 E-value=2.4e-33 Score=195.52 Aligned_cols=86 Identities=72% Similarity=1.108 Sum_probs=81.9
Q ss_pred CceEEEEEEeCCCCCeEEEEEeeEEeecceeeEEEeeeeEEEECCCCCCCCCCEEEEeecccCCcceeEEEEEEEeeccc
Q 034020 1 MKSVVGLVVSNKMQKSVVVAVDRLFHHKVYNRYVKRTSKFMAHDENNQCNIGDRVRLDPSRPLSKHKHWAVAEILKKARI 80 (106)
Q Consensus 1 ~k~l~G~VvS~km~KTvvV~V~r~~~hpkY~K~~~r~kk~~vHDe~~~~k~GD~V~I~e~RPiSK~K~f~V~~Ii~k~~~ 80 (106)
|+.++|+|+|.+|+||++|+|+++.+||+|+||++++++|+||||.|+|++||.|+|.+||||||+|+|.+.+||.++..
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 67899999999999999999999999999999999999999999999999999999999999999999999999999998
Q ss_pred cCCCCc
Q 034020 81 YVPPSA 86 (106)
Q Consensus 81 ~~~p~t 86 (106)
..|...
T Consensus 82 ~spa~~ 87 (107)
T KOG1740|consen 82 YSPAAE 87 (107)
T ss_pred hCcchh
Confidence 766433
No 10
>KOG1728 consensus 40S ribosomal protein S11 [Translation, ribosomal structure and biogenesis]
Probab=99.88 E-value=9.4e-24 Score=154.84 Aligned_cols=79 Identities=37% Similarity=0.493 Sum_probs=75.8
Q ss_pred ceEEEEEEeCCCCCeEEEEEeeEEeecceeeEEEeeeeEEEECCCC--CCCCCCEEEEeecccCCcceeEEEEEEEeecc
Q 034020 2 KSVVGLVVSNKMQKSVVVAVDRLFHHKVYNRYVKRTSKFMAHDENN--QCNIGDRVRLDPSRPLSKHKHWAVAEILKKAR 79 (106)
Q Consensus 2 k~l~G~VvS~km~KTvvV~V~r~~~hpkY~K~~~r~kk~~vHDe~~--~~k~GD~V~I~e~RPiSK~K~f~V~~Ii~k~~ 79 (106)
++|.|+|.+.||++||+|+.+|++|.++|++|.+|++++.||..+| ++++||+|+|.|||||||+++|+|+++++.++
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 5899999999999999999999999999999999999999999998 69999999999999999999999999998875
Q ss_pred c
Q 034020 80 I 80 (106)
Q Consensus 80 ~ 80 (106)
.
T Consensus 149 ~ 149 (156)
T KOG1728|consen 149 S 149 (156)
T ss_pred C
Confidence 3
No 11
>KOG3447 consensus Mitochondrial/chloroplast ribosomal S17-like protein [Translation, ribosomal structure and biogenesis]
Probab=99.71 E-value=1.9e-18 Score=126.24 Aligned_cols=90 Identities=30% Similarity=0.450 Sum_probs=86.1
Q ss_pred ceEEEEEEeCCCCCeEEEEEeeEEeecceeeEEEeeeeEEEECCCCCCCCCCEEEEeec-ccCCcceeEEEEEEEeeccc
Q 034020 2 KSVVGLVVSNKMQKSVVVAVDRLFHHKVYNRYVKRTSKFMAHDENNQCNIGDRVRLDPS-RPLSKHKHWAVAEILKKARI 80 (106)
Q Consensus 2 k~l~G~VvS~km~KTvvV~V~r~~~hpkY~K~~~r~kk~~vHDe~~~~k~GD~V~I~e~-RPiSK~K~f~V~~Ii~k~~~ 80 (106)
+.|.|.|+..+|+++.+|++.|+.++|..+||+.+++.|||||+...|++||.|+|++. -|.-+..+|.|.+|+.+-+.
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 58888999999999999999
Q ss_pred cCCCCcchhhh
Q 034020 81 YVPPSADNAAA 91 (106)
Q Consensus 81 ~~~p~t~~~~~ 91 (106)
++||.||...+
T Consensus 91 IidPvTGkk~~ 101 (150)
T KOG3447|consen 91 IIDPVTGKKCA 101 (150)
T ss_pred ccCCCcCcccc
Confidence 99999998765
No 12
>PTZ00329 eukaryotic translation initiation factor 1A; Provisional
Probab=67.54 E-value=50 Score=24.78 Aligned_cols=57 Identities=18% Similarity=0.158 Sum_probs=37.5
Q ss_pred eEEEEEEeCCCCCeEEEEEe----eEEeec-ceeeEEEeeeeEEEECCCCCCCCCCEEEEeecccCCcceeEEEEE
Q 034020 3 SVVGLVVSNKMQKSVVVAVD----RLFHHK-VYNRYVKRTSKFMAHDENNQCNIGDRVRLDPSRPLSKHKHWAVAE 73 (106)
Q Consensus 3 ~l~G~VvS~km~KTvvV~V~----r~~~hp-kY~K~~~r~kk~~vHDe~~~~k~GD~V~I~e~RPiSK~K~f~V~~ 73 (106)
+..|+|+...-+....|... ++...| +++| ++| .+.||+|++.. +|..+.|.=++..
T Consensus 33 q~~g~V~~~LGn~~f~V~c~dG~~rLa~I~GKmRK------~IW-------I~~GD~VlVel-~~yd~~KgdIi~R 94 (155)
T PTZ00329 33 QEYAQVLRMLGNGRLEAYCFDGVKRLCHIRGKMRK------RVW-------INIGDIILVSL-RDFQDSKADVILK 94 (155)
T ss_pred cEEEEEEEEcCCCEEEEEECCCCEEEEEeecccee------eEE-------ecCCCEEEEec-cCCCCCEEEEEEE
Confidence 45788888777777777743 343333 2222 244 67899999965 9998887655544
No 13
>PF11302 DUF3104: Protein of unknown function (DUF3104); InterPro: IPR021453 This family of proteins with unknown function appears to be restricted to Cyanobacteria.
Probab=64.71 E-value=16 Score=24.40 Aligned_cols=38 Identities=16% Similarity=0.282 Sum_probs=31.2
Q ss_pred CCCCCCEEEEeecc--cCCcceeEEEEEEEeeccccCCCC
Q 034020 48 QCNIGDRVRLDPSR--PLSKHKHWAVAEILKKARIYVPPS 85 (106)
Q Consensus 48 ~~k~GD~V~I~e~R--PiSK~K~f~V~~Ii~k~~~~~~p~ 85 (106)
.++.||.|+++... -..+.+.|-+-+||...+.--||.
T Consensus 5 ~Vk~Gd~ViV~~~~~~~~~~~~dWWmg~Vi~~~ggaR~P~ 44 (75)
T PF11302_consen 5 SVKPGDTVIVQDEQEVGQKQDKDWWMGQVIHCEGGARDPK 44 (75)
T ss_pred ccCCCCEEEEecCccccccCCCCcEEEEEEEEeccccCCC
Confidence 68999999999985 346677999999999888666665
No 14
>smart00652 eIF1a eukaryotic translation initiation factor 1A.
Probab=64.38 E-value=39 Score=22.40 Aligned_cols=52 Identities=17% Similarity=0.082 Sum_probs=31.9
Q ss_pred eEEEEEEeCCCCCeEEEEEeeEEeecceeeEEEeeeeEEEECCCC-----CCCCCCEEEEeecccCCccee
Q 034020 3 SVVGLVVSNKMQKSVVVAVDRLFHHKVYNRYVKRTSKFMAHDENN-----QCNIGDRVRLDPSRPLSKHKH 68 (106)
Q Consensus 3 ~l~G~VvS~km~KTvvV~V~r~~~hpkY~K~~~r~kk~~vHDe~~-----~~k~GD~V~I~e~RPiSK~K~ 68 (106)
+..|+|+....+.-..|..+- -..+++|-|.. =.+.||.|.+. ..|..+.|-
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 567888887777777777442 12233333321 26789999995 457665543
No 15
>PF10844 DUF2577: Protein of unknown function (DUF2577); InterPro: IPR022555 This family of proteins has no known function
Probab=63.02 E-value=44 Score=22.56 Aligned_cols=62 Identities=23% Similarity=0.367 Sum_probs=34.7
Q ss_pred eEEEEEEeCCCCCeEEEEEee--------EEeecceeeEEEeeee----------EEEECCCCCCCCCCEEEEeecccCC
Q 034020 3 SVVGLVVSNKMQKSVVVAVDR--------LFHHKVYNRYVKRTSK----------FMAHDENNQCNIGDRVRLDPSRPLS 64 (106)
Q Consensus 3 ~l~G~VvS~km~KTvvV~V~r--------~~~hpkY~K~~~r~kk----------~~vHDe~~~~k~GD~V~I~e~RPiS 64 (106)
...|+|+|... .+|.++- ++.-....+|.+.-+- +..|| ..+.||.|.+.+ .-
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 46899999774 6666665 2222222222222110 33333 589999998876 44
Q ss_pred cceeEEEEE
Q 034020 65 KHKHWAVAE 73 (106)
Q Consensus 65 K~K~f~V~~ 73 (106)
.-.+|.|+.
T Consensus 90 ~gQ~yiVlD 98 (100)
T PF10844_consen 90 GGQKYIVLD 98 (100)
T ss_pred CCCEEEEEE
Confidence 445666654
No 16
>TIGR00523 eIF-1A eukaryotic/archaeal initiation factor 1A. Recommended nomenclature: eIF-1A for eukaryotes, aIF-1A for Archaea. Also called eIF-4C
Probab=61.76 E-value=50 Score=22.73 Aligned_cols=48 Identities=13% Similarity=0.060 Sum_probs=30.2
Q ss_pred eEEEEEEeCCCCCeEEEEEeeEEeecceeeEEEeeeeEEEECCCC-----CCCCCCEEEEeecccCC
Q 034020 3 SVVGLVVSNKMQKSVVVAVDRLFHHKVYNRYVKRTSKFMAHDENN-----QCNIGDRVRLDPSRPLS 64 (106)
Q Consensus 3 ~l~G~VvS~km~KTvvV~V~r~~~hpkY~K~~~r~kk~~vHDe~~-----~~k~GD~V~I~e~RPiS 64 (106)
+..|+|+....+....|..+- -..+++|-|.- =.+.||.|++ +.+.++
T Consensus 20 e~~g~V~~~lG~~~~~V~~~d-------------G~~~la~i~GK~Rk~iwI~~GD~VlV-sp~d~~ 72 (99)
T TIGR00523 20 EILGVIEQMLGAGRVKVRCLD-------------GKTRLGRIPGKLKKRIWIREGDVVIV-KPWEFQ 72 (99)
T ss_pred EEEEEEEEEcCCCEEEEEeCC-------------CCEEEEEEchhhcccEEecCCCEEEE-EEccCC
Confidence 467788877767777766431 22334444321 2678999999 556777
No 17
>PF13550 Phage-tail_3: Putative phage tail protein
Probab=57.63 E-value=28 Score=23.98 Aligned_cols=35 Identities=20% Similarity=0.333 Sum_probs=24.6
Q ss_pred eeeEEEECCCCCCCCCCEEEEeecccCCcceeEEEEEE
Q 034020 37 TSKFMAHDENNQCNIGDRVRLDPSRPLSKHKHWAVAEI 74 (106)
Q Consensus 37 ~kk~~vHDe~~~~k~GD~V~I~e~RPiSK~K~f~V~~I 74 (106)
+=.|.+--+...+.+||+|.|..- .+...|+|.+|
T Consensus 128 t~~f~~~~~~~~l~pGDvi~l~~~---~~~~~~RI~~i 162 (164)
T PF13550_consen 128 TVSFTLPPDGLALEPGDVIALSDD---GRDMRFRITEI 162 (164)
T ss_pred EEEEEEChhhccCCCCCEEEEEeC---CCceEEEEEEE
Confidence 333443334458999999999876 55778888776
No 18
>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=56.63 E-value=54 Score=21.50 Aligned_cols=50 Identities=12% Similarity=-0.018 Sum_probs=31.3
Q ss_pred EEEEEEeCCCCCeEEEEEeeEEeecceeeEEEeeeeEEEECCCC-----CCCCCCEEEEeecccC-Ccce
Q 034020 4 VVGLVVSNKMQKSVVVAVDRLFHHKVYNRYVKRTSKFMAHDENN-----QCNIGDRVRLDPSRPL-SKHK 67 (106)
Q Consensus 4 l~G~VvS~km~KTvvV~V~r~~~hpkY~K~~~r~kk~~vHDe~~-----~~k~GD~V~I~e~RPi-SK~K 67 (106)
..|+|+....++...|..+- -..+++|-|.. =.+.||.|.+. ..|. .+.|
T Consensus 2 ~i~~V~~~lG~~~~~V~~~d-------------g~~~l~~i~gK~Rk~iwI~~GD~VlV~-~~~~~~~~k 57 (78)
T cd04456 2 QIVRVLRMLGNNRHEVECAD-------------GQRRLVSIPGKLRKNIWIKRGDFLIVD-PIEEGEDVK 57 (78)
T ss_pred eEEEEEEECCCCEEEEEECC-------------CCEEEEEEchhhccCEEEcCCCEEEEE-ecccCCCce
Confidence 46888887777777777442 23344444431 36889999995 5667 3544
No 19
>PLN00208 translation initiation factor (eIF); Provisional
Probab=56.01 E-value=82 Score=23.38 Aligned_cols=57 Identities=16% Similarity=0.124 Sum_probs=37.5
Q ss_pred eEEEEEEeCCCCCeEEEEE----eeEEeec-ceeeEEEeeeeEEEECCCCCCCCCCEEEEeecccCCcceeEEEEE
Q 034020 3 SVVGLVVSNKMQKSVVVAV----DRLFHHK-VYNRYVKRTSKFMAHDENNQCNIGDRVRLDPSRPLSKHKHWAVAE 73 (106)
Q Consensus 3 ~l~G~VvS~km~KTvvV~V----~r~~~hp-kY~K~~~r~kk~~vHDe~~~~k~GD~V~I~e~RPiSK~K~f~V~~ 73 (106)
+..|+|+...-+....|.. .++...| +++| ++| .+.||.|++. .+|..+.|.=++..
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 4578888877777777773 3444444 2222 355 5789999887 77888776655544
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=55.83 E-value=45 Score=26.18 Aligned_cols=37 Identities=19% Similarity=0.390 Sum_probs=26.7
Q ss_pred CCCCCCCCEEEEeecccCCcceeEEEEEEEeeccccCCCCc
Q 034020 46 NNQCNIGDRVRLDPSRPLSKHKHWAVAEILKKARIYVPPSA 86 (106)
Q Consensus 46 ~~~~k~GD~V~I~e~RPiSK~K~f~V~~Ii~k~~~~~~p~t 86 (106)
....-+||+|.+.... ...+.+.+|+.+...+.=|..
T Consensus 32 ~~~~~vGD~V~~~~~~----~~~~~i~~i~~R~~~l~R~~~ 68 (287)
T cd01854 32 GIKPVVGDWVEVEPDD----DGEGVIVRVLPRKNLLSRPAA 68 (287)
T ss_pred CCCccCCCEEEEEecC----CCcEEEEEEECCCceEEccCC
Confidence 3458999999996432 346889999988876655553
No 21
>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=52.14 E-value=53 Score=21.45 Aligned_cols=52 Identities=17% Similarity=0.023 Sum_probs=33.0
Q ss_pred eEEEEEEeCCCCCeEEEEEeeEEeecceeeEEEeeeeEEEECCCC-----CCCCCCEEEEeecccCCccee
Q 034020 3 SVVGLVVSNKMQKSVVVAVDRLFHHKVYNRYVKRTSKFMAHDENN-----QCNIGDRVRLDPSRPLSKHKH 68 (106)
Q Consensus 3 ~l~G~VvS~km~KTvvV~V~r~~~hpkY~K~~~r~kk~~vHDe~~-----~~k~GD~V~I~e~RPiSK~K~ 68 (106)
+..|+|+....+....|..+-- ..+++|-|.. -.+.||.|.+. ..|..+.|.
T Consensus 1 e~~g~V~~~~g~~~~~V~~~~g-------------~~~la~i~gK~rk~iwI~~GD~V~Ve-~~~~d~~kg 57 (77)
T cd05793 1 EEYGQVEKMLGNGRLEVRCFDG-------------KKRLCRIRGKMRKRVWINEGDIVLVA-PWDFQDDKA 57 (77)
T ss_pred CEEEEEEEEcCCCEEEEEECCC-------------CEEEEEEchhhcccEEEcCCCEEEEE-eccccCCEE
Confidence 3578888887788777775421 2333333321 36789999988 446676654
No 22
>PRK00276 infA translation initiation factor IF-1; Validated
Probab=51.53 E-value=61 Score=20.57 Aligned_cols=57 Identities=18% Similarity=0.186 Sum_probs=29.6
Q ss_pred eEEEEEEeCCCCCeEEEEEeeEEeecceeeEEEeeeeEEEECCCCCCCCCCEEEEeecccCCcce
Q 034020 3 SVVGLVVSNKMQKSVVVAVDRLFHHKVYNRYVKRTSKFMAHDENNQCNIGDRVRLDPSRPLSKHK 67 (106)
Q Consensus 3 ~l~G~VvS~km~KTvvV~V~r~~~hpkY~K~~~r~kk~~vHDe~~~~k~GD~V~I~e~RPiSK~K 67 (106)
++.|+|++......-.|..+ -...|....+-.-+ +. .....+||.|.+..+ |...++
T Consensus 8 ~~~G~Vi~~~~~~~y~V~~~---~g~~~~c~~~Gklr---~~-~i~i~vGD~V~ve~~-~~~~~~ 64 (72)
T PRK00276 8 EMEGTVVEALPNAMFRVELE---NGHEVLAHISGKMR---KN-YIRILPGDKVTVELS-PYDLTK 64 (72)
T ss_pred EEEEEEEEEcCCCEEEEEeC---CCCEEEEEEcccee---eC-CcccCCCCEEEEEEc-ccCCCe
Confidence 56788887664444444321 11233333332222 11 234789999999863 344444
No 23
>COG0361 InfA Translation initiation factor 1 (IF-1) [Translation, ribosomal structure and biogenesis]
Probab=50.53 E-value=60 Score=21.57 Aligned_cols=45 Identities=20% Similarity=0.171 Sum_probs=31.4
Q ss_pred eEEEEEEeCCCCCeEEEEEeeEEeecceeeEEEeeeeEEEECCCC------CCCCCCEEEEeec
Q 034020 3 SVVGLVVSNKMQKSVVVAVDRLFHHKVYNRYVKRTSKFMAHDENN------QCNIGDRVRLDPS 60 (106)
Q Consensus 3 ~l~G~VvS~km~KTvvV~V~r~~~hpkY~K~~~r~kk~~vHDe~~------~~k~GD~V~I~e~ 60 (106)
++.|+|+..-.+....|..+-- ...++|-+.- -..+||+|.+...
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 5788998888888888876543 2345666542 3678999987654
No 24
>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=48.10 E-value=32 Score=20.64 Aligned_cols=30 Identities=30% Similarity=0.563 Sum_probs=20.0
Q ss_pred CCCCCCCEEEEeecccCCcceeEEEEEEEeeccc
Q 034020 47 NQCNIGDRVRLDPSRPLSKHKHWAVAEILKKARI 80 (106)
Q Consensus 47 ~~~k~GD~V~I~e~RPiSK~K~f~V~~Ii~k~~~ 80 (106)
...-+||+|.+.... .-.+.+.+++.+.+.
T Consensus 36 ~~~~VGD~V~~~~~~----~~~~~I~~vl~R~s~ 65 (68)
T cd04466 36 NPPAVGDRVEFEPED----DGEGVIEEILPRKNL 65 (68)
T ss_pred CCCCCCcEEEEEECC----CCcEEEEEEeccceE
Confidence 456899999986321 124677788877653
No 25
>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=46.51 E-value=66 Score=19.58 Aligned_cols=51 Identities=16% Similarity=0.158 Sum_probs=27.5
Q ss_pred eEEEEEEeCCCCCeEEEEEeeEEeecceeeEEEeeeeEEEECCCCCCCCCCEEEEeec
Q 034020 3 SVVGLVVSNKMQKSVVVAVDRLFHHKVYNRYVKRTSKFMAHDENNQCNIGDRVRLDPS 60 (106)
Q Consensus 3 ~l~G~VvS~km~KTvvV~V~r~~~hpkY~K~~~r~kk~~vHDe~~~~k~GD~V~I~e~ 60 (106)
+..|+|++.....-..|..+ -...|....+-.-+ + ....+.+||.|.+..+
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 45788887554344444321 11344444443322 1 3345899999988743
No 26
>COG1489 SfsA DNA-binding protein, stimulates sugar fermentation [General function prediction only]
Probab=43.31 E-value=1.5e+02 Score=23.74 Aligned_cols=63 Identities=21% Similarity=0.205 Sum_probs=38.6
Q ss_pred eeEEEECCC-----CCCCCCCEEEEeec-ccCCcceeEEEEEEEeecc--ccCCCCcchhhhhhcccccccc
Q 034020 38 SKFMAHDEN-----NQCNIGDRVRLDPS-RPLSKHKHWAVAEILKKAR--IYVPPSADNAAAAAVSNTQTEA 101 (106)
Q Consensus 38 kk~~vHDe~-----~~~k~GD~V~I~e~-RPiSK~K~f~V~~Ii~k~~--~~~~p~t~~~~~~~~~~~~~~~ 101 (106)
+...+|.++ .-+.+|+.|.+.+. .|.-|+ .|.+.-+-.... .+.--+.++.++-|+.|.|...
T Consensus 28 ~~~~~H~~ntGrm~~l~~pG~~v~l~~sd~~~rK~-~~~~~~~~~~~~~v~VnT~l~N~l~~eai~~~~~~~ 98 (235)
T COG1489 28 EEVTAHCPNTGRMTELLTPGNTVWLSRSDNPKRKY-RYTLELVEADNTLVCVNTGLPNRLAEEAIPNGQIPE 98 (235)
T ss_pred eEEEEEcCCCCccccccCCCCEEEEEEecCCCccc-eEEEEEEEcCCeEEEEeCCccHHHHHHHHhhCcccc
Confidence 344556554 36889999999998 576664 555544433331 2344455666777777765433
No 27
>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=42.96 E-value=32 Score=26.41 Aligned_cols=36 Identities=22% Similarity=0.279 Sum_probs=26.3
Q ss_pred CCCCEEEEeecccCCcceeEEEEEEEeeccccCCCCcchh
Q 034020 50 NIGDRVRLDPSRPLSKHKHWAVAEILKKARIYVPPSADNA 89 (106)
Q Consensus 50 k~GD~V~I~e~RPiSK~K~f~V~~Ii~k~~~~~~p~t~~~ 89 (106)
-+||+|.+... ......+.+|+++-..+.+|...++
T Consensus 2 ~vGD~V~~~~~----~~~~~~i~~i~eR~~~L~r~~~~n~ 37 (245)
T TIGR00157 2 VVGDRVVWEPG----NVVKVYGGAIAERKNELTRPIVANI 37 (245)
T ss_pred CCCcEEEEEec----CCCceEEEEEecccceEECcccccC
Confidence 58999999743 1245789999999888787765443
No 28
>PRK10862 SoxR reducing system protein RseC; Provisional
Probab=42.55 E-value=61 Score=23.65 Aligned_cols=56 Identities=16% Similarity=0.156 Sum_probs=32.4
Q ss_pred CceEEEEEEeCCCCCeEEEEEeeEE-----------eecceeeEEE-eeeeEEEECCCCCCCCCCEEEEe
Q 034020 1 MKSVVGLVVSNKMQKSVVVAVDRLF-----------HHKVYNRYVK-RTSKFMAHDENNQCNIGDRVRLD 58 (106)
Q Consensus 1 ~k~l~G~VvS~km~KTvvV~V~r~~-----------~hpkY~K~~~-r~kk~~vHDe~~~~k~GD~V~I~ 58 (106)
|=+-+|+|++.. +..+.|+.+|.- -+....|... ++..+-+..+ ..+++||.|.|.
T Consensus 1 Mmee~~~Vv~v~-~~~a~Ve~~r~saCg~C~a~~gCG~~~l~~~~~~~~~~~~v~~~-~~~~vGD~V~v~ 68 (154)
T PRK10862 1 MIKEWATVVSWQ-NGIALLRCEVKAGCSSCASRAGCGSRLLNKLGPQTTHQLVVPSS-QPLVPGQKVELG 68 (154)
T ss_pred CcceEEEEEEEE-CCEEEEEEecCCCCcCcCCCCCchhhHHHHhcCCCceEEEecCC-CCCCCCCEEEEe
Confidence 335579999875 356888876632 1112222222 2334555444 468999999875
No 29
>KOG1698 consensus Mitochondrial/chloroplast ribosomal protein L19 [Translation, ribosomal structure and biogenesis]
Probab=41.73 E-value=33 Score=26.84 Aligned_cols=33 Identities=21% Similarity=0.254 Sum_probs=28.0
Q ss_pred EEECCCCCCCCCCEEEEeecccCCcceeEEEEEEE
Q 034020 41 MAHDENNQCNIGDRVRLDPSRPLSKHKHWAVAEIL 75 (106)
Q Consensus 41 ~vHDe~~~~k~GD~V~I~e~RPiSK~K~f~V~~Ii 75 (106)
.-|-| +.++||+|.|...-|-++.+.++...|+
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 33444 8999999999999999999999988874
No 30
>PF06107 DUF951: Bacterial protein of unknown function (DUF951); InterPro: IPR009296 This family consists of several short hypothetical bacterial proteins of unknown function.
Probab=41.27 E-value=49 Score=20.99 Aligned_cols=25 Identities=24% Similarity=0.648 Sum_probs=21.0
Q ss_pred CCCCCEEEEeecccCCcceeEEEEEE
Q 034020 49 CNIGDRVRLDPSRPLSKHKHWAVAEI 74 (106)
Q Consensus 49 ~k~GD~V~I~e~RPiSK~K~f~V~~I 74 (106)
..+||+|+...-.|=.- ..|.|+++
T Consensus 2 ~~vgDiV~mKK~HPCG~-~~Wei~R~ 26 (57)
T PF06107_consen 2 YEVGDIVEMKKPHPCGS-NEWEIIRI 26 (57)
T ss_pred ccCCCEEEEcCCCCCCC-CEEEEEEc
Confidence 57899999999888765 69999875
No 31
>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=40.15 E-value=35 Score=23.73 Aligned_cols=21 Identities=29% Similarity=0.460 Sum_probs=14.6
Q ss_pred eeEEEECCCCCCCCCCEEEEee
Q 034020 38 SKFMAHDENNQCNIGDRVRLDP 59 (106)
Q Consensus 38 kk~~vHDe~~~~k~GD~V~I~e 59 (106)
..+.++++. .+++||.|++.-
T Consensus 42 ~~~~~~~~~-~~~~GD~V~v~i 62 (135)
T PF04246_consen 42 ITFRAPNPI-GAKVGDRVEVEI 62 (135)
T ss_pred EEEEecCCC-CCCCCCEEEEEe
Confidence 445554443 799999998864
No 32
>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=39.76 E-value=32 Score=21.90 Aligned_cols=49 Identities=12% Similarity=0.144 Sum_probs=29.7
Q ss_pred ECCCCCCCCCCEEEEeecccCCcceeEEEEEEEeeccccCCCCcchhhhhhccc
Q 034020 43 HDENNQCNIGDRVRLDPSRPLSKHKHWAVAEILKKARIYVPPSADNAAAAAVSN 96 (106)
Q Consensus 43 HDe~~~~k~GD~V~I~e~RPiSK~K~f~V~~Ii~k~~~~~~p~t~~~~~~~~~~ 96 (106)
.-+...+++||.|.|.+.. +...|..|-...........|+.++-++.+
T Consensus 20 ~v~~G~i~~G~~v~i~P~~-----~~~~V~si~~~~~~~~~a~aGd~v~l~l~~ 68 (82)
T cd04089 20 KVESGTIKKGDKLLVMPNK-----TQVEVLSIYNEDVEVRYARPGENVRLRLKG 68 (82)
T ss_pred EEeeeEEecCCEEEEeCCC-----cEEEEEEEEECCEECCEECCCCEEEEEecC
Confidence 3445567888888887653 346666665444444555566666555543
No 33
>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=37.09 E-value=28 Score=22.18 Aligned_cols=46 Identities=17% Similarity=0.136 Sum_probs=22.1
Q ss_pred CCCCCCCCCCEEEEeecccCCcceeEEEEEEEeeccccCCCCcchhhhhhc
Q 034020 44 DENNQCNIGDRVRLDPSRPLSKHKHWAVAEILKKARIYVPPSADNAAAAAV 94 (106)
Q Consensus 44 De~~~~k~GD~V~I~e~RPiSK~K~f~V~~Ii~k~~~~~~p~t~~~~~~~~ 94 (106)
-+...+++||.|.|.+.. ....|.+|-...........|+.++-++
T Consensus 22 v~~G~i~~Gd~v~i~P~~-----~~~~V~si~~~~~~~~~a~aGd~v~~~l 67 (83)
T cd03698 22 VESGSIQKGDTLLVMPSK-----ESVEVKSIYVDDEEVDYAVAGENVRLKL 67 (83)
T ss_pred EeeeEEeCCCEEEEeCCC-----cEEEEEEEEECCeECCEECCCCEEEEEE
Confidence 344456667777666543 2345555543333333344444444333
No 34
>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=36.75 E-value=24 Score=22.48 Aligned_cols=13 Identities=31% Similarity=0.389 Sum_probs=10.9
Q ss_pred CCCCCCEEEEeec
Q 034020 48 QCNIGDRVRLDPS 60 (106)
Q Consensus 48 ~~k~GD~V~I~e~ 60 (106)
-++.||.|.|...
T Consensus 53 G~~~GD~V~Ig~~ 65 (69)
T TIGR03595 53 GAKDGDTVRIGDF 65 (69)
T ss_pred CCCCCCEEEEccE
Confidence 5899999999753
No 35
>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=36.23 E-value=1e+02 Score=19.95 Aligned_cols=23 Identities=22% Similarity=0.228 Sum_probs=11.7
Q ss_pred EeeeeEEEECCCC-CCCCCCEEEE
Q 034020 35 KRTSKFMAHDENN-QCNIGDRVRL 57 (106)
Q Consensus 35 ~r~kk~~vHDe~~-~~k~GD~V~I 57 (106)
..-+.++.|+.+. .+..||.|.|
T Consensus 46 ~~V~sI~~~~~~~~~a~aG~~v~i 69 (91)
T cd03693 46 GEVKSVEMHHEPLEEALPGDNVGF 69 (91)
T ss_pred EEEEEEEECCcCcCEECCCCEEEE
Confidence 3334444554443 5666666654
No 36
>COG1162 Predicted GTPases [General function prediction only]
Probab=36.18 E-value=1.8e+02 Score=23.98 Aligned_cols=73 Identities=18% Similarity=0.252 Sum_probs=40.6
Q ss_pred EEEEEEeCCCCCeEEEEEeeEEeecceeeEEEeeeeEEEECCCCCCCCCCEEEEeecccCCcceeEEEEEEEeeccccCC
Q 034020 4 VVGLVVSNKMQKSVVVAVDRLFHHKVYNRYVKRTSKFMAHDENNQCNIGDRVRLDPSRPLSKHKHWAVAEILKKARIYVP 83 (106)
Q Consensus 4 l~G~VvS~km~KTvvV~V~r~~~hpkY~K~~~r~kk~~vHDe~~~~k~GD~V~I~e~RPiSK~K~f~V~~Ii~k~~~~~~ 83 (106)
..|.|++.- ..-..|..+...-...|.-..+ .++--. ...+-+||.|.+.....- .++.+|..+...+.=
T Consensus 5 ~~g~v~~~~-~g~y~v~~~~~~~~~~~~~~~r--~~lr~~--~~~~vVGD~V~~~~~~~~-----g~I~~i~~Rkn~L~R 74 (301)
T COG1162 5 KRGRVVKVD-AGFYGVRLEEEVDGEVYRCRAR--GNLRKK--DLKPVVGDRVVFEDENNN-----GVIEKILPRKNVLIR 74 (301)
T ss_pred cCcEEEEee-CCEEEEEEccccccceeeeeee--cceecc--CccccccCeEEEecCCCc-----ceEEEEecccCceeC
Confidence 456666544 3445555553322223332222 222222 447899999999877433 778888887765444
Q ss_pred CCc
Q 034020 84 PSA 86 (106)
Q Consensus 84 p~t 86 (106)
|--
T Consensus 75 p~v 77 (301)
T COG1162 75 PPV 77 (301)
T ss_pred Ccc
Confidence 433
No 37
>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=34.01 E-value=1.3e+02 Score=19.43 Aligned_cols=51 Identities=18% Similarity=0.287 Sum_probs=32.8
Q ss_pred eEEEEEEeCCCCCeEEEEEeeEEeecceeeEEEeeeeEEEECCCC------CCCCCCEEEEeecccCCcce
Q 034020 3 SVVGLVVSNKMQKSVVVAVDRLFHHKVYNRYVKRTSKFMAHDENN------QCNIGDRVRLDPSRPLSKHK 67 (106)
Q Consensus 3 ~l~G~VvS~km~KTvvV~V~r~~~hpkY~K~~~r~kk~~vHDe~~------~~k~GD~V~I~e~RPiSK~K 67 (106)
++.|+|+..-.+-...|..+- -...++|-+.- -..+||.|.+.. .|...+|
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 578888887777777777553 23444555431 367899998874 4555444
No 38
>PRK10413 hydrogenase 2 accessory protein HypG; Provisional
Probab=33.61 E-value=1.5e+02 Score=19.80 Aligned_cols=51 Identities=16% Similarity=0.092 Sum_probs=28.1
Q ss_pred EEEEeCCCC--CeEEEEEeeEEeecceeeEEEeeeeEEEECCCCCCCCCCEEEEeecccCCc
Q 034020 6 GLVVSNKMQ--KSVVVAVDRLFHHKVYNRYVKRTSKFMAHDENNQCNIGDRVRLDPSRPLSK 65 (106)
Q Consensus 6 G~VvS~km~--KTvvV~V~r~~~hpkY~K~~~r~kk~~vHDe~~~~k~GD~V~I~e~RPiSK 65 (106)
|+|++-.-+ ++++|...- ..+.-.-.++-+++.+..+||+|++.-.--|++
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 667763322 456665322 222222234444334789999999987655444
No 39
>PRK00098 GTPase RsgA; Reviewed
Probab=33.52 E-value=1.7e+02 Score=23.03 Aligned_cols=35 Identities=26% Similarity=0.452 Sum_probs=23.4
Q ss_pred CCCCCCCEEEEeecccCCcceeEEEEEEEeeccccCCCC
Q 034020 47 NQCNIGDRVRLDPSRPLSKHKHWAVAEILKKARIYVPPS 85 (106)
Q Consensus 47 ~~~k~GD~V~I~e~RPiSK~K~f~V~~Ii~k~~~~~~p~ 85 (106)
...-+||+|.+....| ....+.+|..+...+.-|.
T Consensus 36 ~~~~vGD~V~~~~~~~----~~g~i~~i~~R~~~l~R~~ 70 (298)
T PRK00098 36 NTPAVGDRVEFSAENN----DEGVILEIHERKNLLVRPP 70 (298)
T ss_pred CCcCCCCEEEEEECCC----CcEEEEEEeCCCceEECCC
Confidence 4578999999964322 3466777888777554444
No 40
>PRK12288 GTPase RsgA; Reviewed
Probab=33.09 E-value=1.1e+02 Score=25.05 Aligned_cols=34 Identities=21% Similarity=0.310 Sum_probs=23.6
Q ss_pred CCCCCCEEEEeecc-cCCcceeEEEEEEEeeccccC
Q 034020 48 QCNIGDRVRLDPSR-PLSKHKHWAVAEILKKARIYV 82 (106)
Q Consensus 48 ~~k~GD~V~I~e~R-PiSK~K~f~V~~Ii~k~~~~~ 82 (106)
..-+||+|.+...- .. ....+++.+|+.+...+.
T Consensus 72 ~~~vGD~V~~~~~~~~~-~~~~~~I~~il~R~n~L~ 106 (347)
T PRK12288 72 SLVTGDRVVWRPGKEAL-EGVSGVVEAVHPRTSVLT 106 (347)
T ss_pred CCCCCcEEEEEeCCCcc-cccceEEEEEecccceEE
Confidence 37889999996321 11 113488899999988777
No 41
>PRK10409 hydrogenase assembly chaperone; Provisional
Probab=33.08 E-value=32 Score=23.48 Aligned_cols=19 Identities=21% Similarity=0.207 Sum_probs=14.8
Q ss_pred CCCCCCCEEEEeecccCCc
Q 034020 47 NQCNIGDRVRLDPSRPLSK 65 (106)
Q Consensus 47 ~~~k~GD~V~I~e~RPiSK 65 (106)
.++++||+|++.-.--|||
T Consensus 40 ~~~~vGDyVLVHaGfAi~~ 58 (90)
T PRK10409 40 GQPRVGQWVLVHVGFAMSV 58 (90)
T ss_pred CccCCCCEEEEecChHHhh
Confidence 3799999999987655554
No 42
>PRK09570 rpoH DNA-directed RNA polymerase subunit H; Reviewed
Probab=32.96 E-value=83 Score=21.03 Aligned_cols=33 Identities=15% Similarity=0.173 Sum_probs=21.6
Q ss_pred eEEEECCCC---CCCCCCEEEEeec-ccCCcceeEEE
Q 034020 39 KFMAHDENN---QCNIGDRVRLDPS-RPLSKHKHWAV 71 (106)
Q Consensus 39 k~~vHDe~~---~~k~GD~V~I~e~-RPiSK~K~f~V 71 (106)
++..-||-. .++.||+|.|.-- .--.....|++
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 566778753 8999999988543 44444455554
No 43
>PRK04012 translation initiation factor IF-1A; Provisional
Probab=32.64 E-value=1.7e+02 Score=20.17 Aligned_cols=51 Identities=22% Similarity=0.214 Sum_probs=30.4
Q ss_pred eEEEEEEeCCCCCeEEEEEe----eEEeec-ceeeEEEeeeeEEEECCCCCCCCCCEEEEeecccCCcce
Q 034020 3 SVVGLVVSNKMQKSVVVAVD----RLFHHK-VYNRYVKRTSKFMAHDENNQCNIGDRVRLDPSRPLSKHK 67 (106)
Q Consensus 3 ~l~G~VvS~km~KTvvV~V~----r~~~hp-kY~K~~~r~kk~~vHDe~~~~k~GD~V~I~e~RPiSK~K 67 (106)
+..|+|+....+....|..+ ++...| ++.| ++| .+.||.|++.. +|....|
T Consensus 22 e~~g~V~~~lG~~~~~V~~~dG~~~la~i~GK~Rk------~Iw-------I~~GD~VlVe~-~~~~~~k 77 (100)
T PRK04012 22 EVFGVVEQMLGANRVRVRCMDGVERMGRIPGKMKK------RMW-------IREGDVVIVAP-WDFQDEK 77 (100)
T ss_pred EEEEEEEEEcCCCEEEEEeCCCCEEEEEEchhhcc------cEE-------ecCCCEEEEEe-cccCCCE
Confidence 56788887777777777644 222222 1111 344 56899998874 5666554
No 44
>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=32.25 E-value=85 Score=20.01 Aligned_cols=24 Identities=21% Similarity=0.412 Sum_probs=14.7
Q ss_pred EeeeeEEEECCC-CCCCCCCEEEEe
Q 034020 35 KRTSKFMAHDEN-NQCNIGDRVRLD 58 (106)
Q Consensus 35 ~r~kk~~vHDe~-~~~k~GD~V~I~ 58 (106)
..-+.+..|+.+ +.+..||.|.|.
T Consensus 42 ~~V~si~~~~~~~~~a~aGd~v~l~ 66 (81)
T cd03695 42 SRVKSIETFDGELDEAGAGESVTLT 66 (81)
T ss_pred EEEEEEEECCcEeCEEcCCCEEEEE
Confidence 444555556554 367778887663
No 45
>PRK01889 GTPase RsgA; Reviewed
Probab=32.05 E-value=1.9e+02 Score=23.62 Aligned_cols=38 Identities=21% Similarity=0.368 Sum_probs=26.4
Q ss_pred ECCCCCCCCCCEEEEeecccCCcceeEEEEEEEeeccccCCCCc
Q 034020 43 HDENNQCNIGDRVRLDPSRPLSKHKHWAVAEILKKARIYVPPSA 86 (106)
Q Consensus 43 HDe~~~~k~GD~V~I~e~RPiSK~K~f~V~~Ii~k~~~~~~p~t 86 (106)
|......-+||+|.+.. .-.+++.+|+.+...+.=|..
T Consensus 63 ~~~~~~~~vGD~V~~~~------~~~g~I~~i~pR~~~L~R~~~ 100 (356)
T PRK01889 63 FPPGDRPAVGDWVLLDN------EKKARIVRLLPRRSLFSRKAA 100 (356)
T ss_pred cccCCCCccCcEEEEec------CCceEEEEEECCCceEEcCCC
Confidence 33445688999999963 134788888888776655554
No 46
>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=31.99 E-value=46 Score=18.06 Aligned_cols=13 Identities=15% Similarity=0.204 Sum_probs=11.7
Q ss_pred CCCCCCEEEEeec
Q 034020 48 QCNIGDRVRLDPS 60 (106)
Q Consensus 48 ~~k~GD~V~I~e~ 60 (106)
.+..||.|.+.+.
T Consensus 17 ~~~~Gd~v~v~~~ 29 (54)
T cd00174 17 SFKKGDIIEVLEK 29 (54)
T ss_pred CCCCCCEEEEEEc
Confidence 7899999999887
No 47
>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=31.89 E-value=83 Score=21.12 Aligned_cols=30 Identities=13% Similarity=0.210 Sum_probs=23.7
Q ss_pred CCCCCCCEEEEeecccCCcceeEEEEEEEe
Q 034020 47 NQCNIGDRVRLDPSRPLSKHKHWAVAEILK 76 (106)
Q Consensus 47 ~~~k~GD~V~I~e~RPiSK~K~f~V~~Ii~ 76 (106)
+.++.||.|.+....|......-...+|++
T Consensus 88 g~~~~gd~vVv~~g~~~~~~g~tn~~~v~~ 117 (117)
T PF02887_consen 88 GLLKPGDKVVVVAGMPFGTPGGTNTIRVVR 117 (117)
T ss_dssp TSS-TTSEEEEEEESSTTTTSSEEEEEEEE
T ss_pred CCCCCCCEEEEEeCCCCCCCCCCEEEEEEC
Confidence 468999999999999988877777777753
No 48
>PF13567 DUF4131: Domain of unknown function (DUF4131)
Probab=31.58 E-value=1.6e+02 Score=19.51 Aligned_cols=60 Identities=22% Similarity=0.308 Sum_probs=31.7
Q ss_pred eEEEEEEeCC--CCCe--EEEEEeeEEeecceeeEEEeeeeEEEECCCC--C-CCCCCEEEEeec-ccCCc
Q 034020 3 SVVGLVVSNK--MQKS--VVVAVDRLFHHKVYNRYVKRTSKFMAHDENN--Q-CNIGDRVRLDPS-RPLSK 65 (106)
Q Consensus 3 ~l~G~VvS~k--m~KT--vvV~V~r~~~hpkY~K~~~r~kk~~vHDe~~--~-~k~GD~V~I~e~-RPiSK 65 (106)
.++|+|.+.. ..++ ..+.+++. ..-.......-++.+..+.. . ...||.+++.-. +|++.
T Consensus 79 ~v~g~V~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~i~~~~~~~~~~~l~~Gd~i~~~g~l~~~~~ 146 (176)
T PF13567_consen 79 TVQGTVESVPQIDGRGQRFTLRVERV---LAGGNWIPVSGKILLYLPKDSQPRLQPGDRIRVRGKLKPPSG 146 (176)
T ss_pred EEEEEEcccccccCceEEEEEEEEEe---eccccccccceeeEEEeccccccccCCCCEEEEEEEEecCCC
Confidence 3678887622 2222 34444443 22233333444455555444 3 679999988764 55554
No 49
>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=31.42 E-value=25 Score=22.35 Aligned_cols=12 Identities=33% Similarity=0.529 Sum_probs=7.5
Q ss_pred CCCCCCEEEEee
Q 034020 48 QCNIGDRVRLDP 59 (106)
Q Consensus 48 ~~k~GD~V~I~e 59 (106)
.++.||+|.|..
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 589999999975
No 50
>PRK10371 DNA-binding transcriptional regulator MelR; Provisional
Probab=31.29 E-value=53 Score=25.79 Aligned_cols=43 Identities=16% Similarity=0.102 Sum_probs=31.3
Q ss_pred eeEEeecceeeEEEeeeeE--EEECCCCCCCCCCEEEEeecccCC
Q 034020 22 DRLFHHKVYNRYVKRTSKF--MAHDENNQCNIGDRVRLDPSRPLS 64 (106)
Q Consensus 22 ~r~~~hpkY~K~~~r~kk~--~vHDe~~~~k~GD~V~I~e~RPiS 64 (106)
...+||..|.=.+-..-.. .+.+....+..||.+.|-.++|-+
T Consensus 39 ~~~HwH~e~Ei~yv~~G~~~~~i~g~~~~l~~Gd~ili~s~~~H~ 83 (302)
T PRK10371 39 PTSHWHGQVEVNVPFDGDVEYLINNEKVQINQGHITLFWACTPHQ 83 (302)
T ss_pred CCCCccccEEEEEecCCcEEEEECCEEEEEcCCcEEEEecCCccc
Confidence 3679999998766554443 333344499999999999998865
No 51
>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=31.13 E-value=85 Score=20.20 Aligned_cols=24 Identities=8% Similarity=0.097 Sum_probs=14.4
Q ss_pred EeeeeEEEECCC-CCCCCCCEEEEe
Q 034020 35 KRTSKFMAHDEN-NQCNIGDRVRLD 58 (106)
Q Consensus 35 ~r~kk~~vHDe~-~~~k~GD~V~I~ 58 (106)
.+-+.+..|+.. +++..||.|.|.
T Consensus 46 ~~V~sI~~~~~~~~~a~aGd~v~l~ 70 (87)
T cd03694 46 VTVKSIHRNRSPVRVVRAGQSASLA 70 (87)
T ss_pred EEEEEEEECCeECCEECCCCEEEEE
Confidence 444455566554 367778877663
No 52
>PF09926 DUF2158: Uncharacterized small protein (DUF2158); InterPro: IPR019226 This entry represents a family of predominantly prokaryotic proteins with no known function.
Probab=31.09 E-value=38 Score=20.86 Aligned_cols=13 Identities=46% Similarity=0.792 Sum_probs=11.2
Q ss_pred CCCCEEEEeeccc
Q 034020 50 NIGDRVRLDPSRP 62 (106)
Q Consensus 50 k~GD~V~I~e~RP 62 (106)
++||+|.+.+.-|
T Consensus 2 ~~GDvV~LKSGGp 14 (53)
T PF09926_consen 2 KIGDVVQLKSGGP 14 (53)
T ss_pred CCCCEEEEccCCC
Confidence 6899999988866
No 53
>COG1499 NMD3 NMD protein affecting ribosome stability and mRNA decay [Translation, ribosomal structure and biogenesis]
Probab=29.59 E-value=1.1e+02 Score=25.70 Aligned_cols=42 Identities=10% Similarity=0.165 Sum_probs=32.7
Q ss_pred EEEECCCCCCCCCCEEEEeecccCCcceeEEEEEEEeeccccCCCCcchhh
Q 034020 40 FMAHDENNQCNIGDRVRLDPSRPLSKHKHWAVAEILKKARIYVPPSADNAA 90 (106)
Q Consensus 40 ~~vHDe~~~~k~GD~V~I~e~RPiSK~K~f~V~~Ii~k~~~~~~p~t~~~~ 90 (106)
|.+--| +.++||+|.+.- +.+.+..+..+.-.+.|+.|++..
T Consensus 240 ~Svrip--~~~~gDiV~~~~-------~~~~~v~~~~~~~~~~dl~t~e~~ 281 (355)
T COG1499 240 YSVRIP--EFRPGDIVSVRG-------RQLVLVRSIGKGIVVLDLETGEPV 281 (355)
T ss_pred EEEECC--CCCCCCEEEECC-------CeEEEEEEecCceEEEecccCCcc
Confidence 444444 689999997765 688899999988888999888543
No 54
>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=29.42 E-value=1.5e+02 Score=18.59 Aligned_cols=23 Identities=30% Similarity=0.583 Sum_probs=12.9
Q ss_pred EeeeeEEEECCC-CCCCCCCEEEE
Q 034020 35 KRTSKFMAHDEN-NQCNIGDRVRL 57 (106)
Q Consensus 35 ~r~kk~~vHDe~-~~~k~GD~V~I 57 (106)
..-+.+..|+++ .++..||.|.|
T Consensus 42 ~~V~sI~~~~~~~~~a~aGd~v~i 65 (83)
T cd03696 42 TRVRSIQVHGKDVEEAKAGDRVAL 65 (83)
T ss_pred EEEEEEEECCcCcCEEcCCCEEEE
Confidence 444445555544 36667777765
No 55
>PRK05753 nucleoside diphosphate kinase regulator; Provisional
Probab=29.36 E-value=1.4e+02 Score=21.21 Aligned_cols=27 Identities=22% Similarity=0.305 Sum_probs=21.5
Q ss_pred CCCCCCEEEEeecccCCcceeEEEEEEEe
Q 034020 48 QCNIGDRVRLDPSRPLSKHKHWAVAEILK 76 (106)
Q Consensus 48 ~~k~GD~V~I~e~RPiSK~K~f~V~~Ii~ 76 (106)
..++||.|.+. -|-...+++.+.+|..
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 48999999987 5656567899999974
No 56
>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=28.09 E-value=1e+02 Score=19.74 Aligned_cols=14 Identities=21% Similarity=0.413 Sum_probs=6.6
Q ss_pred CCCCCCCCEEEEee
Q 034020 46 NNQCNIGDRVRLDP 59 (106)
Q Consensus 46 ~~~~k~GD~V~I~e 59 (106)
...+++||.|.+.+
T Consensus 24 ~G~v~~gd~v~~~p 37 (87)
T cd03697 24 RGTIKVGDEVEIVG 37 (87)
T ss_pred CCCCccCCEEEEeC
Confidence 33445555554443
No 57
>COG3655 Predicted transcriptional regulator [Transcription]
Probab=27.46 E-value=34 Score=22.64 Aligned_cols=12 Identities=33% Similarity=0.753 Sum_probs=10.1
Q ss_pred CCCCCCEEEEee
Q 034020 48 QCNIGDRVRLDP 59 (106)
Q Consensus 48 ~~k~GD~V~I~e 59 (106)
+|.+||++.+..
T Consensus 56 eCqpgDiley~~ 67 (73)
T COG3655 56 ECQPGDILEYVP 67 (73)
T ss_pred CCChhheeEEec
Confidence 799999998753
No 58
>PRK14120 gpmA phosphoglyceromutase; Provisional
Probab=27.29 E-value=18 Score=28.06 Aligned_cols=23 Identities=43% Similarity=0.580 Sum_probs=20.0
Q ss_pred EeeccccCCCCcchhhhhhcccc
Q 034020 75 LKKARIYVPPSADNAAAAAVSNT 97 (106)
Q Consensus 75 i~k~~~~~~p~t~~~~~~~~~~~ 97 (106)
+.-++...||.++.|.||||.|.
T Consensus 224 ~~~~~~~~~~~~~~~~~~~~~~~ 246 (249)
T PRK14120 224 LNPGGTYLDPEAAAAGAAAVANQ 246 (249)
T ss_pred ecccceecCHHHHHHHHHHHHhc
Confidence 66677899999999999999885
No 59
>COG2012 RPB5 DNA-directed RNA polymerase, subunit H, RpoH/RPB5 [Transcription]
Probab=27.06 E-value=84 Score=21.27 Aligned_cols=33 Identities=18% Similarity=0.174 Sum_probs=19.6
Q ss_pred eEEEECCC---CCCCCCCEEEEeec-ccCCcceeEEE
Q 034020 39 KFMAHDEN---NQCNIGDRVRLDPS-RPLSKHKHWAV 71 (106)
Q Consensus 39 k~~vHDe~---~~~k~GD~V~I~e~-RPiSK~K~f~V 71 (106)
++.+-||- -.++.||+|.|.-- .--.....|++
T Consensus 42 kI~~~DPva~~lgak~GdvVkIvRkS~TaGe~v~YR~ 78 (80)
T COG2012 42 KIKASDPVAKALGAKPGDVVKIVRKSPTAGESVYYRL 78 (80)
T ss_pred cccccChhHHHccCCCCcEEEEEecCCCCCceEEEEE
Confidence 45666773 37999999977543 33333344433
No 60
>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=26.80 E-value=93 Score=20.05 Aligned_cols=20 Identities=20% Similarity=0.358 Sum_probs=14.3
Q ss_pred eEEEECC-CCCCCCCCEEEEe
Q 034020 39 KFMAHDE-NNQCNIGDRVRLD 58 (106)
Q Consensus 39 k~~vHDe-~~~~k~GD~V~I~ 58 (106)
-+++..+ ....++||+|++.
T Consensus 34 gifV~~~~~~~~~~Gd~V~vt 54 (78)
T cd04486 34 GIFVYTGSGADVAVGDLVRVT 54 (78)
T ss_pred eEEEecCCCCCCCCCCEEEEE
Confidence 3555555 5578999999885
No 61
>PRK12442 translation initiation factor IF-1; Reviewed
Probab=26.32 E-value=2.2e+02 Score=19.47 Aligned_cols=51 Identities=24% Similarity=0.229 Sum_probs=31.4
Q ss_pred eEEEEEEeCCCCCeEEEEEeeEEeecceeeEEEeeeeEEEECCCC------CCCCCCEEEEeecccCCcce
Q 034020 3 SVVGLVVSNKMQKSVVVAVDRLFHHKVYNRYVKRTSKFMAHDENN------QCNIGDRVRLDPSRPLSKHK 67 (106)
Q Consensus 3 ~l~G~VvS~km~KTvvV~V~r~~~hpkY~K~~~r~kk~~vHDe~~------~~k~GD~V~I~e~RPiSK~K 67 (106)
++.|+|+....+-...|..+-- ..+++|-+.- -..+||.|.+.-+ |..-+|
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 5788888877777777776521 2223333321 2568999988776 555444
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=26.11 E-value=93 Score=22.13 Aligned_cols=28 Identities=29% Similarity=0.558 Sum_probs=19.0
Q ss_pred CCCCCCCEEEEeecccCC-cceeEEEEEE
Q 034020 47 NQCNIGDRVRLDPSRPLS-KHKHWAVAEI 74 (106)
Q Consensus 47 ~~~k~GD~V~I~e~RPiS-K~K~f~V~~I 74 (106)
..|++||.|++.+++.-. +..-|.+...
T Consensus 41 ~~f~~GDlvLflpt~~~~~~~~~~~af~~ 69 (129)
T PF10377_consen 41 RNFQVGDLVLFLPTRNHNNKKQPWAAFNV 69 (129)
T ss_pred ecCCCCCEEEEEecCCCCccccceEEeeC
Confidence 369999999999996533 3444555443
No 63
>PF01200 Ribosomal_S28e: Ribosomal protein S28e; InterPro: IPR000289 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 [, ]. A number of eukaryotic and archaebacterial ribosomal proteins can be grouped on the basis of sequence similarities. Examples are: Mammalian S28 [] Plant S28 [] Fungi S33 [] Archaebacterial S28e. These proteins have from 64 to 78 amino acids and a highly conserved C-terminal region.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3IZ6_Y 2XZN_1 2XZM_1 1NY4_A 1NE3_A 3U5C_c 3U5G_c 3O30_R 3O2Z_R 3IZB_Y.
Probab=25.80 E-value=68 Score=21.09 Aligned_cols=18 Identities=17% Similarity=0.202 Sum_probs=13.6
Q ss_pred CCCCCCCCCCEEEEeecc
Q 034020 44 DENNQCNIGDRVRLDPSR 61 (106)
Q Consensus 44 De~~~~k~GD~V~I~e~R 61 (106)
.-...+++||++.+.||.
T Consensus 45 NVkGPVr~GDil~LlEtE 62 (69)
T PF01200_consen 45 NVKGPVREGDILTLLETE 62 (69)
T ss_dssp EECSTTSTT-EEEESSSS
T ss_pred cccCCcccCcEEEEeehh
Confidence 334579999999999994
No 64
>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=25.74 E-value=1.2e+02 Score=17.31 Aligned_cols=25 Identities=20% Similarity=0.379 Sum_probs=17.7
Q ss_pred eeEEEECCC-----CCCCCCCEEEEeeccc
Q 034020 38 SKFMAHDEN-----NQCNIGDRVRLDPSRP 62 (106)
Q Consensus 38 kk~~vHDe~-----~~~k~GD~V~I~e~RP 62 (106)
..+++|... +.+..||.|.+.-..+
T Consensus 21 ~~i~v~~~~~~~~~~~~~~Gd~V~~~i~~~ 50 (64)
T smart00357 21 KDVFVHPSQIQGGLKSLREGDEVEFKVVSP 50 (64)
T ss_pred ccEEEEhHHhhcCCCcCCCCCEEEEEEEEc
Confidence 366676554 4688899999886554
No 65
>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=25.64 E-value=1.5e+02 Score=17.52 Aligned_cols=42 Identities=21% Similarity=0.199 Sum_probs=24.0
Q ss_pred CCeEEEEEeeEEeecceeeEEEeee-eEEEECCCCCCCCCCEEEEe
Q 034020 14 QKSVVVAVDRLFHHKVYNRYVKRTS-KFMAHDENNQCNIGDRVRLD 58 (106)
Q Consensus 14 ~KTvvV~V~r~~~hpkY~K~~~r~k-k~~vHDe~~~~k~GD~V~I~ 58 (106)
-+++.|.|+... ++ +..+-|+. ...++-+.....+||.|.++
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 467888888888 22 22344444 66777776644479998654
No 66
>PF11347 DUF3148: Protein of unknown function (DUF3148); InterPro: IPR021495 This family of proteins has no known function.
Probab=24.77 E-value=59 Score=21.06 Aligned_cols=17 Identities=47% Similarity=0.692 Sum_probs=13.7
Q ss_pred CCCCEEEEeecccCCcc
Q 034020 50 NIGDRVRLDPSRPLSKH 66 (106)
Q Consensus 50 k~GD~V~I~e~RPiSK~ 66 (106)
++||.|++.+..|.=||
T Consensus 1 ~iG~~V~l~~~ppylKT 17 (63)
T PF11347_consen 1 SIGDKVRLIEAPPYLKT 17 (63)
T ss_pred CCCCeEEEeecCCceec
Confidence 47999999988887665
No 67
>smart00326 SH3 Src homology 3 domains. Src homology 3 (SH3) domains bind to target proteins through sequences containing proline and hydrophobic amino acids. Pro-containing polypeptides may bind to SH3 domains in 2 different binding orientations.
Probab=24.61 E-value=1.3e+02 Score=16.28 Aligned_cols=23 Identities=13% Similarity=0.280 Sum_probs=16.1
Q ss_pred CCCCCCEEEEeecccCCcceeEEEEEE
Q 034020 48 QCNIGDRVRLDPSRPLSKHKHWAVAEI 74 (106)
Q Consensus 48 ~~k~GD~V~I~e~RPiSK~K~f~V~~I 74 (106)
.++.||.|.+.+.. .--|...+.
T Consensus 20 ~~~~Gd~v~v~~~~----~~~w~~~~~ 42 (58)
T smart00326 20 SFKKGDIITVLEKS----DDGWWKGRL 42 (58)
T ss_pred CCCCCCEEEEEEcC----CCCeEEEEe
Confidence 78999999998775 234554443
No 68
>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=24.59 E-value=2.1e+02 Score=18.60 Aligned_cols=13 Identities=31% Similarity=0.460 Sum_probs=9.9
Q ss_pred CCCCCCCCEEEEe
Q 034020 46 NNQCNIGDRVRLD 58 (106)
Q Consensus 46 ~~~~k~GD~V~I~ 58 (106)
....++||.|.+.
T Consensus 51 ~~~~~~Gd~v~vk 63 (99)
T cd04460 51 KRVLKVGDVVRAR 63 (99)
T ss_pred CCEECCCCEEEEE
Confidence 4567999998764
No 69
>PF07653 SH3_2: Variant SH3 domain; InterPro: IPR011511 SH3 (src Homology-3) domains are small protein modules containing approximately 50 amino acid residues [, ]. They are found in a great variety of intracellular or membrane-associated proteins [, , ] for example, in a variety of proteins with enzymatic activity, in adaptor proteins that lack catalytic sequences and in cytoskeletal proteins, such as fodrin and yeast actin binding protein ABP-1. The SH3 domain has a characteristic fold which consists of five or six beta-strands arranged as two tightly packed anti-parallel beta sheets. The linker regions may contain short helices []. The surface of the SH3-domain bears a flat, hydrophobic ligand-binding pocket which consists of three shallow grooves defined by conservative aromatic residues in which the ligand adopts an extended left-handed helical arrangement. The ligand binds with low affinity but this may be enhanced by multiple interactions. The region bound by the SH3 domain is in all cases proline-rich and contains PXXP as a core-conserved binding motif. The function of the SH3 domain is not well understood but they may mediate many diverse processes such as increasing local concentration of proteins, altering their subcellular location and mediating the assembly of large multiprotein complexes []. This entry represents a variant of the SH3 domain.; PDB: 1I1J_B 1K0X_A 1HJD_A 2KEA_A 1KJW_A 1JXM_A 1JXO_B 2EBP_A 2DL3_A 2EYX_A ....
Probab=24.56 E-value=44 Score=19.55 Aligned_cols=22 Identities=18% Similarity=0.344 Sum_probs=14.9
Q ss_pred eeeEEEECCCC-CCCCCCEEEEe
Q 034020 37 TSKFMAHDENN-QCNIGDRVRLD 58 (106)
Q Consensus 37 ~kk~~vHDe~~-~~k~GD~V~I~ 58 (106)
...|..-+++. .++.||+|.|.
T Consensus 5 ~~d~~~~~~~~Ls~~~Gd~i~v~ 27 (55)
T PF07653_consen 5 IFDYVAEDPDELSFKKGDVIEVL 27 (55)
T ss_dssp SSSBESSSTTB-EB-TTEEEEEE
T ss_pred eEEECCCCCCceEEecCCEEEEE
Confidence 34455555555 89999999998
No 70
>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=24.32 E-value=1.3e+02 Score=19.85 Aligned_cols=54 Identities=13% Similarity=0.066 Sum_probs=27.3
Q ss_pred eEEEEEEeCCCCCeEEEEEee---EEeecceeeEEEeee----eEEEECCCCCCCCCCEEEE
Q 034020 3 SVVGLVVSNKMQKSVVVAVDR---LFHHKVYNRYVKRTS----KFMAHDENNQCNIGDRVRL 57 (106)
Q Consensus 3 ~l~G~VvS~km~KTvvV~V~r---~~~hpkY~K~~~r~k----k~~vHDe~~~~k~GD~V~I 57 (106)
...|+|++.. .+.+.|.+.. .....-|.-+++... ..--.+.....++||+|+-
T Consensus 9 iVig~V~~v~-~~~~~v~I~~v~~~~l~~~~~g~l~~~dv~~~~~d~~~~~~~f~~GDiV~A 69 (92)
T cd05791 9 IVIARVTRIN-PRFAKVDILCVGGRPLKESFRGVIRKEDIRATEKDKVEMYKCFRPGDIVRA 69 (92)
T ss_pred EEEEEEEEEc-CCEEEEEEEEecCeecCCCcccEEEHHHccccccchHHHHhhcCCCCEEEE
Confidence 4678988754 4556666532 222333444443111 1100122346799999954
No 71
>COG4591 LolE ABC-type transport system, involved in lipoprotein release, permease component [Cell envelope biogenesis, outer membrane]
Probab=24.28 E-value=1.4e+02 Score=25.32 Aligned_cols=32 Identities=25% Similarity=0.520 Sum_probs=26.0
Q ss_pred CCCCCCEEEEeecc---cC---CcceeEEEEEEEeecc
Q 034020 48 QCNIGDRVRLDPSR---PL---SKHKHWAVAEILKKAR 79 (106)
Q Consensus 48 ~~k~GD~V~I~e~R---Pi---SK~K~f~V~~Ii~k~~ 79 (106)
.+++||+|.+.-.. |. -+.|+|.|..|.+.+.
T Consensus 157 gv~~GD~v~li~p~~~~~~g~~p~~~~f~V~Gif~tG~ 194 (408)
T COG4591 157 GVRVGDKVTLITPESNTPFGRGPRQKRFTVVGIFSTGL 194 (408)
T ss_pred CCCCCCEEEEEeecCCcccccCcceEEEEEEEEEecCc
Confidence 68999999888776 42 3679999999988775
No 72
>PF02359 CDC48_N: Cell division protein 48 (CDC48), N-terminal domain; InterPro: IPR003338 AAA ATPases (ATPases Associated with diverse cellular Activities) form a large protein family and play a number of roles in the cell including cell-cycle regulation, protein proteolysis and disaggregation, organelle biogenesis and intracellular transport. Some of them function as molecular chaperones, subunits of proteolytic complexes or independent proteases (FtsH, Lon). They also act as DNA helicases and transcription factors []. AAA ATPases belong to the AAA+ superfamily of ringshaped P-loop NTPases, which act via the energy-dependent unfolding of macromolecules [, ]. There are six major clades of AAA domains (proteasome subunits, metalloproteases, domains D1 and D2 of ATPases with two AAA domains, the MSP1/katanin/spastin group and BCS1 and it homologues), as well as a number of deeply branching minor clades []. They assemble into oligomeric assemblies (often hexamers) that form a ring-shaped structure with a central pore. These proteins produce a molecular motor that couples ATP binding and hydrolysis to changes in conformational states that act upon a target substrate, either translocating or remodelling it []. They are found in all living organisms and share the common feature of the presence of a highly conserved AAA domain called the AAA module. This domain is responsible for ATP binding and hydrolysis. It contains 200-250 residues, among them there are two classical motifs, Walker A (GX4GKT) and Walker B (HyDE) []. The VAT protein of the archaebacterium Thermoplasma acidophilum, like all other members of the Cdc48/p97 family of AAA ATPases, has two ATPase domains and a 185-residue amino-terminal substrate-recognition domain, VAT-N. VAT shows activity in protein folding and unfolding and thus shares the common function of these ATPases in disassembly and/or degradation of protein complexes. VAT-N is composed of two equally sized subdomains. The amino-terminal subdomain VAT-Nn forms a double-psi beta-barrel whose pseudo-twofold symmetry is mirrored by an internal sequence repeat of 42 residues. The carboxy-terminal subdomain VAT-Nc forms a novel six-stranded beta-clam fold []. Together, VAT-Nn and VAT-Nc form a kidney-shaped structure, in close agreement with results from electron microscopy. VAT-Nn is related to numerous proteins including prokaryotic transcription factors, metabolic enzymes, the protease cofactors UFD1 and PrlF, and aspartic proteinases. ; GO: 0005524 ATP binding; PDB: 1CZ4_A 1CZ5_A 3CF3_C 3CF1_A 3CF2_A 1S3S_D 1E32_A 1R7R_A 2PJH_B 1CR5_B ....
Probab=24.20 E-value=56 Score=21.11 Aligned_cols=15 Identities=47% Similarity=0.835 Sum_probs=11.7
Q ss_pred CCCCCCEEEEeeccc
Q 034020 48 QCNIGDRVRLDPSRP 62 (106)
Q Consensus 48 ~~k~GD~V~I~e~RP 62 (106)
.+..||.|.|.++.|
T Consensus 72 ~v~igd~V~V~~~~~ 86 (87)
T PF02359_consen 72 GVSIGDRVTVRPYDP 86 (87)
T ss_dssp T--TTSEEEEEEETT
T ss_pred CcCCCCEEEEEECCC
Confidence 688999999999877
No 73
>COG0853 PanD Aspartate 1-decarboxylase [Coenzyme metabolism]
Probab=23.78 E-value=70 Score=23.36 Aligned_cols=18 Identities=22% Similarity=0.298 Sum_probs=15.0
Q ss_pred CCCCCCEEEEeecccCCc
Q 034020 48 QCNIGDRVRLDPSRPLSK 65 (106)
Q Consensus 48 ~~k~GD~V~I~e~RPiSK 65 (106)
-|.+||.|+|...-.++-
T Consensus 77 l~~~GD~VII~sy~~~~e 94 (126)
T COG0853 77 LVQVGDLVIIMSYAQMSE 94 (126)
T ss_pred hCCCCCEEEEEEcccCCH
Confidence 589999999998877654
No 74
>PF02311 AraC_binding: AraC-like ligand binding domain; InterPro: IPR003313 This entry defines the arabinose-binding and dimerisation domain of the bacterial gene regulatory protein AraC. The crystal structure of the arabinose-binding and dimerization domain of the Escherichia coli gene regulatory protein AraC was determined in the presence and absence of L-arabinose. The arabinose-bound molecule shows that the protein adopts an unusual fold, binding sugar within a beta barrel and completely burying the arabinose with the amino-terminal arm of the protein. Dimer contacts in the presence of arabinose are mediated by an antiparallel coiled-coil. In the uncomplexed protein, the amino-terminal arm is disordered, uncovering the sugar-binding pocket and allowing it to serve as an oligomerization interface [].; GO: 0006355 regulation of transcription, DNA-dependent; PDB: 1XJA_B 2ARA_A 2AAC_B 2ARC_A.
Probab=22.99 E-value=99 Score=19.59 Aligned_cols=41 Identities=17% Similarity=0.196 Sum_probs=23.1
Q ss_pred eEEeecceeeEEEeeeeEEEECCC--CCCCCCCEEEEeecccC
Q 034020 23 RLFHHKVYNRYVKRTSKFMAHDEN--NQCNIGDRVRLDPSRPL 63 (106)
Q Consensus 23 r~~~hpkY~K~~~r~kk~~vHDe~--~~~k~GD~V~I~e~RPi 63 (106)
..++|+.|.=.+.-.=....+... -.++.||.+.|.+..+-
T Consensus 17 ~~h~h~~~~i~~v~~G~~~~~~~~~~~~l~~g~~~li~p~~~H 59 (136)
T PF02311_consen 17 PPHWHDFYEIIYVLSGEGTLHIDGQEYPLKPGDLFLIPPGQPH 59 (136)
T ss_dssp EEETT-SEEEEEEEEE-EEEEETTEEEEE-TT-EEEE-TTS-E
T ss_pred CCEECCCEEEEEEeCCEEEEEECCEEEEEECCEEEEecCCccE
Confidence 347788777655554444444443 48999999999887543
No 75
>TIGR02657 amicyanin amicyanin. Members of this family are amicyanin, a type I blue copper protein that accepts electrons from the tryptophan tryptophylquinone (TTQ) cofactor of the methylamine dehydrogenase light chain and then transfers them to the heme group of cytochrome c-551i. Amicyanin, methylamine dehydrogenase, and cytochrome c-551i are periplasmic and form a complex. This system has been studied primarily in Paracoccus denitrificans and Methylobacterium extorquens. Related type I blue copper proteins include plastocyanin, pseudoazurin, halocyanin, etc.
Probab=22.98 E-value=1.1e+02 Score=19.39 Aligned_cols=28 Identities=18% Similarity=0.336 Sum_probs=19.7
Q ss_pred EEECCCC-CCCCCCEEEEeecccCCccee
Q 034020 41 MAHDENN-QCNIGDRVRLDPSRPLSKHKH 68 (106)
Q Consensus 41 ~vHDe~~-~~k~GD~V~I~e~RPiSK~K~ 68 (106)
++.+|.. .++.||.|.+...-+...+..
T Consensus 6 ~~F~P~~i~v~~GdtVt~~N~d~~~Hnv~ 34 (83)
T TIGR02657 6 MKYETPELHVKVGDTVTWINREAMPHNVH 34 (83)
T ss_pred eEEcCCEEEECCCCEEEEEECCCCCccEE
Confidence 3456665 799999999987666554443
No 76
>cd04457 S1_S28E S1_S28E: S28E, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. S28E protein is a component of the 30S ribosomal subunit. S28E is highly conserved among archaea and eukaryotes. S28E may control precursor RNA splicing and turnover in mRNA maturation process but its function in the ribosome is largely unknown. The structure contains an OB-fold found in many oligosaccharide and nucleic acid binding proteins. This implies that S28E might be involved in protein synthesis.
Probab=22.93 E-value=1.1e+02 Score=19.60 Aligned_cols=15 Identities=20% Similarity=0.193 Sum_probs=13.1
Q ss_pred CCCCCCCCEEEEeec
Q 034020 46 NNQCNIGDRVRLDPS 60 (106)
Q Consensus 46 ~~~~k~GD~V~I~e~ 60 (106)
...+++||++.+.|+
T Consensus 38 KGPVr~GDIl~L~Et 52 (60)
T cd04457 38 KGPVREGDILMLLET 52 (60)
T ss_pred cCCcccCcEEeehhh
Confidence 457999999999998
No 77
>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=22.89 E-value=1.2e+02 Score=21.88 Aligned_cols=25 Identities=28% Similarity=0.404 Sum_probs=19.9
Q ss_pred CCCCCCEEEEeecccCCcceeEEEEEEEee
Q 034020 48 QCNIGDRVRLDPSRPLSKHKHWAVAEILKK 77 (106)
Q Consensus 48 ~~k~GD~V~I~e~RPiSK~K~f~V~~Ii~k 77 (106)
+.++||.|.+.. ++-.|+|...-.+
T Consensus 59 DlRIGD~Vkv~~-----~k~~yiV~Gl~~~ 83 (131)
T PF08605_consen 59 DLRIGDTVKVDG-----PKVTYIVVGLECK 83 (131)
T ss_pred eeecCCEEEECC-----CCccEEEEEeeec
Confidence 799999999988 3345888887666
No 78
>COG2053 RPS28A Ribosomal protein S28E/S33 [Translation, ribosomal structure and biogenesis]
Probab=22.72 E-value=72 Score=20.99 Aligned_cols=20 Identities=15% Similarity=0.308 Sum_probs=15.0
Q ss_pred EEECCCCCCCCCCEEEEeec
Q 034020 41 MAHDENNQCNIGDRVRLDPS 60 (106)
Q Consensus 41 ~vHDe~~~~k~GD~V~I~e~ 60 (106)
....-...+++||++.+.||
T Consensus 40 itRNV~GPVrvgDIl~L~Et 59 (69)
T COG2053 40 ITRNVKGPVRVGDILMLLET 59 (69)
T ss_pred EeeeccCCcccccEEeehhh
Confidence 33333457999999999998
No 79
>smart00739 KOW KOW (Kyprides, Ouzounis, Woese) motif. Motif in ribosomal proteins, NusG, Spt5p, KIN17 and T54.
Probab=22.17 E-value=88 Score=15.39 Aligned_cols=12 Identities=33% Similarity=0.587 Sum_probs=9.7
Q ss_pred CCCCCEEEEeec
Q 034020 49 CNIGDRVRLDPS 60 (106)
Q Consensus 49 ~k~GD~V~I~e~ 60 (106)
..+||.|.|..-
T Consensus 2 ~~~G~~V~I~~G 13 (28)
T smart00739 2 FEVGDTVRVIAG 13 (28)
T ss_pred CCCCCEEEEeEC
Confidence 468999999884
No 80
>PF08980 DUF1883: Domain of unknown function (DUF1883); InterPro: IPR015073 This family consist of hypothetical bacterial proteins. ; PDB: 2B1Y_A.
Probab=21.28 E-value=35 Score=23.58 Aligned_cols=20 Identities=30% Similarity=0.365 Sum_probs=1.9
Q ss_pred eEEEECCCCCCCCCCEEEEee
Q 034020 39 KFMAHDENNQCNIGDRVRLDP 59 (106)
Q Consensus 39 k~~vHDe~~~~k~GD~V~I~e 59 (106)
+|..||-. .++.||+|.|.=
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 34556654 689999998863
No 81
>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=21.24 E-value=90 Score=22.36 Aligned_cols=23 Identities=22% Similarity=0.271 Sum_probs=17.3
Q ss_pred eEEEECCCC----CCCCCCEEEEeecc
Q 034020 39 KFMAHDENN----QCNIGDRVRLDPSR 61 (106)
Q Consensus 39 k~~vHDe~~----~~k~GD~V~I~e~R 61 (106)
-+.+.||.. ++++||.|+|..-+
T Consensus 63 ~It~yD~H~~~ar~lK~GdfV~L~NVh 89 (123)
T cd04498 63 DILVYDNHVELAKSLKPGDFVRIYNVH 89 (123)
T ss_pred EEEEEcchHHHHhhCCCCCEEEEEEEE
Confidence 455667753 69999999998765
No 82
>PRK12289 GTPase RsgA; Reviewed
Probab=21.15 E-value=1.1e+02 Score=25.11 Aligned_cols=36 Identities=28% Similarity=0.403 Sum_probs=25.9
Q ss_pred CCCCCCEEEEeecccCCcceeEEEEEEEeeccccCCCC
Q 034020 48 QCNIGDRVRLDPSRPLSKHKHWAVAEILKKARIYVPPS 85 (106)
Q Consensus 48 ~~k~GD~V~I~e~RPiSK~K~f~V~~Ii~k~~~~~~p~ 85 (106)
..-+||+|.+.+- +. ......+.+|+.+...+.-|.
T Consensus 51 ~~~vGD~V~~~~~-~~-~~~~~~I~~vlpR~~~L~R~~ 86 (352)
T PRK12289 51 QVMVGDRVIVEEP-DW-QGQRGAIAEVLPRKTELDRPP 86 (352)
T ss_pred CcccCCEEEEeec-CC-CCCceEEEEEeccccceechh
Confidence 4889999999752 11 114578899999888766664
No 83
>PRK10807 paraquat-inducible protein B; Provisional
Probab=20.78 E-value=1.6e+02 Score=25.83 Aligned_cols=68 Identities=18% Similarity=0.190 Sum_probs=45.6
Q ss_pred eEEEEEEeCCC---CCeEEEEEeeEEeecceeeEEEeeeeEEEECCCCC---------CCCCCEEEEeecccCCcceeEE
Q 034020 3 SVVGLVVSNKM---QKSVVVAVDRLFHHKVYNRYVKRTSKFMAHDENNQ---------CNIGDRVRLDPSRPLSKHKHWA 70 (106)
Q Consensus 3 ~l~G~VvS~km---~KTvvV~V~r~~~hpkY~K~~~r~kk~~vHDe~~~---------~k~GD~V~I~e~RPiSK~K~f~ 70 (106)
.-+|.|.+... .+.|.+. ...++.|..+++..++||+-+|.-. +--|..+.+.+..+-....+|.
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 VDVGVVESVTLSDDLTHVEIK---ARLNSGMEKLLHKDSVFWVVKPQIGREGISGLGTLLSGAYIELQPGSKGSKPDKYD 144 (547)
T ss_pred ceEEEEEEEEECCCCCeEEEE---EEECccHHHhhcCCCEEEEeeeeEcCCCCcChHHhhccceEEecCCCCCCcCceeE
Confidence 34788887433 3344444 3456789999999999999988532 3347777776655555566776
Q ss_pred EEE
Q 034020 71 VAE 73 (106)
Q Consensus 71 V~~ 73 (106)
+.+
T Consensus 145 ~~~ 147 (547)
T PRK10807 145 LLD 147 (547)
T ss_pred ecc
Confidence 654
Done!