Query 031480
Match_columns 159
No_of_seqs 209 out of 1232
Neff 4.5
Searched_HMMs 46136
Date Fri Mar 29 14:42:52 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/031480.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/031480hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PTZ00241 40S ribosomal protein 100.0 1.8E-73 4E-78 453.1 15.4 157 1-159 2-158 (158)
2 KOG1728 40S ribosomal protein 100.0 2.3E-70 5E-75 429.1 6.8 154 1-159 2-156 (156)
3 PRK08572 rps17p 30S ribosomal 100.0 2E-51 4.3E-56 310.1 13.5 107 37-147 1-107 (108)
4 TIGR03630 arch_S17P archaeal r 100.0 8.4E-49 1.8E-53 293.2 13.0 102 39-144 1-102 (102)
5 COG0186 RpsQ Ribosomal protein 100.0 1.1E-38 2.4E-43 232.8 11.1 85 62-147 1-85 (87)
6 CHL00142 rps17 ribosomal prote 100.0 4.4E-34 9.6E-39 207.3 11.6 79 69-148 3-81 (84)
7 PRK05610 rpsQ 30S ribosomal pr 100.0 4.9E-34 1.1E-38 206.9 11.5 78 69-147 6-83 (84)
8 TIGR03635 S17_bact 30S ribosom 100.0 6E-33 1.3E-37 195.6 9.8 70 70-140 2-71 (71)
9 PF00366 Ribosomal_S17: Riboso 100.0 6.1E-31 1.3E-35 184.1 9.9 69 74-143 1-69 (69)
10 KOG1740 Predicted mitochondria 99.9 2.9E-28 6.3E-33 182.4 -0.5 78 69-147 2-79 (107)
11 KOG3447 Mitochondrial/chloropl 99.2 3.6E-12 7.8E-17 100.4 0.5 82 64-146 5-87 (150)
12 PF10915 DUF2709: Protein of u 81.2 0.77 1.7E-05 39.0 1.2 58 5-66 31-97 (238)
13 TIGR00008 infA translation ini 69.3 27 0.00058 24.6 6.3 52 71-136 6-62 (68)
14 COG0361 InfA Translation initi 66.2 34 0.00073 24.6 6.4 52 71-136 8-64 (75)
15 cd03698 eRF3_II_like eRF3_II_l 65.3 22 0.00048 24.5 5.3 25 103-127 42-66 (83)
16 TIGR00523 eIF-1A eukaryotic/ar 60.9 37 0.0008 25.3 6.0 49 71-133 20-72 (99)
17 cd05793 S1_IF1A S1_IF1A: Trans 60.7 37 0.0008 24.0 5.7 55 72-140 2-60 (77)
18 KOG3416 Predicted nucleic acid 57.6 39 0.00085 26.9 5.9 50 69-127 22-71 (134)
19 PF10844 DUF2577: Protein of u 57.4 73 0.0016 23.3 7.5 23 117-142 76-98 (100)
20 cd04456 S1_IF1A_like S1_IF1A_l 56.7 50 0.0011 23.5 5.9 55 72-140 2-61 (78)
21 cd03693 EF1_alpha_II EF1_alpha 53.7 38 0.00082 23.8 4.9 26 102-127 45-70 (91)
22 cd03697 EFTU_II EFTU_II: Elong 49.5 48 0.001 23.0 4.9 53 68-127 14-68 (87)
23 cd03696 selB_II selB_II: this 49.0 78 0.0017 21.6 5.8 26 102-127 41-66 (83)
24 PF09740 DUF2043: Uncharacteri 48.6 6.1 0.00013 30.4 0.1 13 56-68 87-99 (110)
25 cd03694 GTPBP_II Domain II of 48.1 35 0.00077 23.8 4.0 26 102-127 45-70 (87)
26 PRK12442 translation initiatio 47.9 85 0.0018 23.2 6.0 62 70-145 7-73 (87)
27 cd03695 CysN_NodQ_II CysN_NodQ 47.8 40 0.00086 23.4 4.2 49 67-127 18-66 (81)
28 smart00652 eIF1a eukaryotic tr 44.2 1.1E+02 0.0023 21.9 6.0 56 71-140 6-65 (83)
29 PRK04012 translation initiatio 42.5 1.4E+02 0.0031 22.2 7.5 56 71-140 22-81 (100)
30 PTZ00329 eukaryotic translatio 41.2 1.9E+02 0.0041 23.5 7.6 58 72-143 34-95 (155)
31 PF13550 Phage-tail_3: Putativ 41.1 60 0.0013 24.1 4.5 39 102-144 125-163 (164)
32 COG1786 Swiveling domain assoc 41.0 17 0.00038 28.8 1.6 24 46-73 32-55 (131)
33 cd04089 eRF3_II eRF3_II: domai 39.4 1.2E+02 0.0027 20.7 5.9 25 103-127 41-65 (82)
34 TIGR03595 Obg_CgtA_exten Obg f 37.5 24 0.00051 24.4 1.7 13 117-129 53-65 (69)
35 cd01342 Translation_Factor_II_ 37.3 1E+02 0.0022 19.1 5.3 22 107-128 48-69 (83)
36 CHL00071 tufA elongation facto 36.7 1.3E+02 0.0028 26.9 6.6 25 103-127 264-288 (409)
37 KOG1730 Thioredoxin-like prote 31.9 30 0.00066 29.2 1.7 18 58-75 74-91 (206)
38 PF09269 DUF1967: Domain of un 31.5 23 0.0005 24.4 0.8 12 117-128 53-64 (69)
39 PRK12736 elongation factor Tu; 31.5 1.3E+02 0.0029 26.6 5.9 23 104-126 255-277 (394)
40 PF04246 RseC_MucC: Positive r 28.4 65 0.0014 24.2 2.9 13 115-127 49-61 (135)
41 cd04092 mtEFG2_II_like mtEFG2_ 28.3 1.9E+02 0.0042 19.5 5.3 15 114-128 57-71 (83)
42 cd03689 RF3_II RF3_II: this su 28.2 1.8E+02 0.0039 20.2 5.0 14 115-128 59-72 (85)
43 cd04466 S1_YloQ_GTPase S1_YloQ 27.9 81 0.0018 20.4 3.0 28 116-147 36-63 (68)
44 PF01176 eIF-1a: Translation i 27.6 1.2E+02 0.0027 20.3 3.9 52 72-137 5-60 (65)
45 PF06107 DUF951: Bacterial pro 27.4 84 0.0018 21.6 3.0 25 118-143 2-26 (57)
46 TIGR02657 amicyanin amicyanin. 27.3 70 0.0015 22.1 2.7 29 110-138 7-35 (83)
47 PF07653 SH3_2: Variant SH3 do 27.1 41 0.00089 21.3 1.4 23 105-127 5-27 (55)
48 cd00174 SH3 Src homology 3 dom 25.6 68 0.0015 18.8 2.1 21 109-129 9-29 (54)
49 PLN00208 translation initiatio 25.0 3.6E+02 0.0079 21.6 7.3 58 72-143 34-95 (145)
50 cd05789 S1_Rrp4 S1_Rrp4: Rrp4 24.9 2.2E+02 0.0049 19.2 5.2 22 68-90 6-27 (86)
51 PRK01777 hypothetical protein; 24.2 80 0.0017 23.2 2.7 18 114-133 61-78 (95)
52 cd05698 S1_Rrp5_repeat_hs6_sc5 23.7 1.9E+02 0.0042 18.5 4.3 58 69-134 1-63 (70)
53 PF11302 DUF3104: Protein of u 23.3 1.5E+02 0.0033 21.3 3.9 31 117-147 5-37 (75)
54 cd05752 Ig1_FcgammaR_like Frst 22.6 1E+02 0.0022 21.0 2.8 27 113-140 7-37 (78)
55 TIGR00483 EF-1_alpha translati 22.2 2E+02 0.0043 25.6 5.2 49 69-126 242-292 (426)
56 smart00326 SH3 Src homology 3 22.0 1.4E+02 0.0031 17.5 3.1 19 112-130 15-33 (58)
57 PF03658 Ub-RnfH: RnfH family 21.8 63 0.0014 23.6 1.7 18 114-133 58-75 (84)
58 KOG1698 Mitochondrial/chloropl 21.7 1.6E+02 0.0034 25.0 4.2 46 108-156 90-135 (201)
59 PF01200 Ribosomal_S28e: Ribos 20.1 63 0.0014 23.0 1.3 14 117-130 49-62 (69)
60 PRK05807 hypothetical protein; 20.0 3.6E+02 0.0078 20.7 5.7 60 69-144 6-76 (136)
61 cd05687 S1_RPS1_repeat_ec1_hs1 20.0 2.4E+02 0.0052 18.1 4.1 53 69-127 1-54 (70)
No 1
>PTZ00241 40S ribosomal protein S11; Provisional
Probab=100.00 E-value=1.8e-73 Score=453.06 Aligned_cols=157 Identities=66% Similarity=1.076 Sum_probs=144.9
Q ss_pred CchhhHHhhccCcceeecccccCCCCCCCCCCceeeeeecccccCChhhhcccccCCCCCceeeeeeeceEEEEEEEecC
Q 031480 1 MAEQTEKAFLKQPKVFLSSKKAGKGKRPGKGGNRFWKSIGLGFKTPREAIEGTYIDKKCPFTGTVSIRGRILAGTCHSAK 80 (159)
Q Consensus 1 m~~q~~~a~qkq~~i~~~~~~~~~~~~~~~~~~r~~~~igl~~~~P~~~~~~~yiD~kcPf~g~~sirg~il~G~VvS~K 80 (159)
|++|+|||||||++||+|+++.+.++ ..+.+||++||||||++|++||||+|||++|||||||||||++|+|+|+|+|
T Consensus 2 ~~~q~e~a~qkq~~i~~~~~~~~~~~--~~~~~r~~k~iGl~~~~P~~~~~~~yiD~kCPf~G~~~iRgril~G~VvS~K 79 (158)
T PTZ00241 2 ADVQTERAFQKQEGVFQNSKRLLKKK--TSKGVRYWKKVGLGFKTPKEAIEGKYIDKKCPFTGNVSIRGRILRGVVISTK 79 (158)
T ss_pred ccccchhhhccCCceeeccccccccc--cccccchhhhcCCCCcCChhhhcccccCCCCCccceeeEcceEEEEEEEEcc
Confidence 35599999999999999999965332 2237899999999999999999999999999999999999999999999999
Q ss_pred CCCeEEEEEeEEEeeeeeeeEEeeeeeEEEEcCCCCCCCCCCEEEEeeeecCCCeeeEEEEEEeecCCCCCcccccccC
Q 031480 81 MNRTIIVRRNYLHFVKKYQRYEKRHSNIPAHISPCFRVKEGDHVIIGQCRPLSKTVRFNVLKVIPAGSSGGAKKAFTAM 159 (159)
Q Consensus 81 M~KTvvV~v~~~~~~pKY~K~~kr~kk~~vHd~p~~~~kvGD~V~I~ecRPLSKtK~f~V~~Ii~~~~~~~~~k~f~~f 159 (159)
|+|||+|+++|++|||+|+||++|+++|+|||||||+|++||+|+|+|||||||||+|+|++|++++..++.+|||++|
T Consensus 80 M~KTIVV~ve~~~~h~kY~K~~kr~kk~~aHd~~~~~~kvGD~V~I~EcRPLSKTKrf~Vv~V~~~~~~~~~~k~f~~f 158 (158)
T PTZ00241 80 MKRTIIIRRDYLHYVKKYNRYEKRHKNIPVHCSPCFDVKEGDIVVVGQCRPLSKTVRFNVLKVEKNEIIGNVRKQFVLF 158 (158)
T ss_pred CCccEEEEEEEEEecCccceEEEeeecEEEeCCccCCCCCCCEEEEEEcCCCCCceeEEEEEEEecccccccccccccC
Confidence 9999999999999999999999999999999989999999999999999999999999999999975322259999987
No 2
>KOG1728 consensus 40S ribosomal protein S11 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=2.3e-70 Score=429.11 Aligned_cols=154 Identities=71% Similarity=1.179 Sum_probs=147.9
Q ss_pred CchhhHHhhccCcceeecccccCCCCCCCCCCceeeeeecccccCChhhhcccccCCCCCceeeeeeeceEEEEEEEecC
Q 031480 1 MAEQTEKAFLKQPKVFLSSKKAGKGKRPGKGGNRFWKSIGLGFKTPREAIEGTYIDKKCPFTGTVSIRGRILAGTCHSAK 80 (159)
Q Consensus 1 m~~q~~~a~qkq~~i~~~~~~~~~~~~~~~~~~r~~~~igl~~~~P~~~~~~~yiD~kcPf~g~~sirg~il~G~VvS~K 80 (159)
|++|+|+|||+|++||+|.|.. +...+++.+||++|||||||+|+||++|+|||+||||||+|||||+||+|+|+++|
T Consensus 2 ~~vq~eraF~kq~~v~~~~k~~--~~~~~k~~~r~~~~iglGFKtP~eAiegtYIDKKCPftG~vsIRGril~G~V~k~K 79 (156)
T KOG1728|consen 2 MAVQTERAFQKQPGVFLNAKAS--GKRTSKKGKRRYKNIGLGFKTPREAIEGTYIDKKCPFTGNVSIRGRILTGTVVKMK 79 (156)
T ss_pred cchhhhHHhhhCccccccCccc--ccccccccchhhhhcCcccCChHHhhcceeecccCCcccceeEeeEEEeeEEeeec
Confidence 6789999999999999999987 35578899999999999999999999999999999999999999999999999999
Q ss_pred CCCeEEEEEeEEEeeeeeeeEEeeeeeEEEEcCCCCC-CCCCCEEEEeeeecCCCeeeEEEEEEeecCCCCCcccccccC
Q 031480 81 MNRTIIVRRNYLHFVKKYQRYEKRHSNIPAHISPCFR-VKEGDHVIIGQCRPLSKTVRFNVLKVIPAGSSGGAKKAFTAM 159 (159)
Q Consensus 81 M~KTvvV~v~~~~~~pKY~K~~kr~kk~~vHd~p~~~-~kvGD~V~I~ecRPLSKtK~f~V~~Ii~~~~~~~~~k~f~~f 159 (159)
|++||||++|||||.+||++|++||+|++||.|||++ +++||+|+|+||||||||+||+|+++++. ++.+|+|.+|
T Consensus 80 m~rTIvvrrdYlHy~~KY~ryekrHkN~svh~SPcFrdi~~gDiVtvGecrPLSKtvrfnVLkv~k~---~g~~k~~~k~ 156 (156)
T KOG1728|consen 80 MQRTIVVRRDYLHYIKKYNRYEKRHKNMSVHVSPCFRDIQEGDIVTVGECRPLSKTVRFNVLKVIKA---AGSKKQFKKF 156 (156)
T ss_pred eeEEEEEEhhhhhHhHHhhHHHHhccCCccccchhhhccccCCEEEEeecccccceEEEEEEEEeec---CCCccccccC
Confidence 9999999999999999999999999999999999997 99999999999999999999999999999 4579999987
No 3
>PRK08572 rps17p 30S ribosomal protein S17P; Reviewed
Probab=100.00 E-value=2e-51 Score=310.06 Aligned_cols=107 Identities=50% Similarity=0.915 Sum_probs=104.2
Q ss_pred eeecccccCChhhhcccccCCCCCceeeeeeeceEEEEEEEecCCCCeEEEEEeEEEeeeeeeeEEeeeeeEEEEcCCCC
Q 031480 37 KSIGLGFKTPREAIEGTYIDKKCPFTGTVSIRGRILAGTCHSAKMNRTIIVRRNYLHFVKKYQRYEKRHSNIPAHISPCF 116 (159)
Q Consensus 37 ~~igl~~~~P~~~~~~~yiD~kcPf~g~~sirg~il~G~VvS~KM~KTvvV~v~~~~~~pKY~K~~kr~kk~~vHd~p~~ 116 (159)
+||||||++|+++|| |++|||||+|+|||++|+|+|+|++|+|||+|++++++|||+|+|+++++++|+|||++||
T Consensus 1 ~~ig~~~~~p~~~~~----d~~cP~~g~l~irgk~l~G~VvS~Km~KTvvV~v~r~~~hpkY~K~i~r~kky~aHDe~cn 76 (108)
T PRK08572 1 RNIGLDVKPPEEECD----DPNCPFHGTLPVRGQVLEGTVVSDKMHKTVVVEREYLHYVPKYERYEKRRSRIHAHNPPCI 76 (108)
T ss_pred CccccCCCCCccccc----CCCCCCcceeeeeeEEEEEEEEecCCCceEEEEEEEEEecCCccEEEEEeeeEEEECCCCC
Confidence 589999999999999 9999999999999999999999999999999999999999999999999999999997789
Q ss_pred CCCCCCEEEEeeeecCCCeeeEEEEEEeecC
Q 031480 117 RVKEGDHVIIGQCRPLSKTVRFNVLKVIPAG 147 (159)
Q Consensus 117 ~~kvGD~V~I~ecRPLSKtK~f~V~~Ii~~~ 147 (159)
+|++||+|+|+|||||||+|+|+|++|++++
T Consensus 77 ~~kvGD~V~I~E~RPiSKtK~w~v~~i~~~~ 107 (108)
T PRK08572 77 DAKVGDKVKIAECRPLSKTKSFVVVEKKERA 107 (108)
T ss_pred CCCCCCEEEEEEcCCCCCceEEEEEEEEEcC
Confidence 9999999999999999999999999999874
No 4
>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=8.4e-49 Score=293.24 Aligned_cols=102 Identities=53% Similarity=0.926 Sum_probs=98.3
Q ss_pred ecccccCChhhhcccccCCCCCceeeeeeeceEEEEEEEecCCCCeEEEEEeEEEeeeeeeeEEeeeeeEEEEcCCCCCC
Q 031480 39 IGLGFKTPREAIEGTYIDKKCPFTGTVSIRGRILAGTCHSAKMNRTIIVRRNYLHFVKKYQRYEKRHSNIPAHISPCFRV 118 (159)
Q Consensus 39 igl~~~~P~~~~~~~yiD~kcPf~g~~sirg~il~G~VvS~KM~KTvvV~v~~~~~~pKY~K~~kr~kk~~vHd~p~~~~ 118 (159)
|||++++|+++|+ |++|||||+|+|||++|+|+|+|+||+|||+|+++++++||+|+|+++++++|+|||++||+|
T Consensus 1 ig~~~~~p~~~~~----d~~cpf~g~l~irgk~l~G~VvS~Km~KTivV~V~r~~~hpkY~K~i~r~kky~aHDe~cn~~ 76 (102)
T TIGR03630 1 IGIPVKPPERECN----DPKCPFHGHLKVRGQILEGVVVSDKMNKTVVVEREYLYYDRKYERYERRRSKIHAHNPPCIDV 76 (102)
T ss_pred CCcccCCCCcccc----CCCCCccceeeeeeEEEEEEEEecCCCceEEEEEEEEEecCCccEEEEEeeeEEEECCCCCCC
Confidence 7999999997666 999999999999999999999999999999999999999999999999999999999777999
Q ss_pred CCCCEEEEeeeecCCCeeeEEEEEEe
Q 031480 119 KEGDHVIIGQCRPLSKTVRFNVLKVI 144 (159)
Q Consensus 119 kvGD~V~I~ecRPLSKtK~f~V~~Ii 144 (159)
++||+|+|+|||||||+|+|+|++|+
T Consensus 77 kvGD~V~I~E~RPlSKtK~w~vv~i~ 102 (102)
T TIGR03630 77 KEGDIVIIGETRPLSKTKSFVVLGKV 102 (102)
T ss_pred CCCCEEEEEEcCCCCCceEEEEEEeC
Confidence 99999999999999999999999974
No 5
>COG0186 RpsQ Ribosomal protein S17 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.1e-38 Score=232.79 Aligned_cols=85 Identities=38% Similarity=0.629 Sum_probs=83.2
Q ss_pred eeeeeeeceEEEEEEEecCCCCeEEEEEeEEEeeeeeeeEEeeeeeEEEEcCCCCCCCCCCEEEEeeeecCCCeeeEEEE
Q 031480 62 TGTVSIRGRILAGTCHSAKMNRTIIVRRNYLHFVKKYQRYEKRHSNIPAHISPCFRVKEGDHVIIGQCRPLSKTVRFNVL 141 (159)
Q Consensus 62 ~g~~sirg~il~G~VvS~KM~KTvvV~v~~~~~~pKY~K~~kr~kk~~vHd~p~~~~kvGD~V~I~ecRPLSKtK~f~V~ 141 (159)
||+++++|++|+|+|+|+||+|||+|++++.+|||+|+||++++++|+||| |||+|++||+|+|+|||||||||+|+|+
T Consensus 1 ~~~~~~~~k~l~G~VvS~Km~KTvvV~ve~~~~hp~Y~K~v~r~kK~~aHd-e~~~~k~GD~V~I~EtRPLSKtK~~~vv 79 (87)
T COG0186 1 HGKLRVRGRVLEGVVVSDKMDKTVVVEVERKVYHPKYGKYVRRSKKYHAHD-ECNEAKVGDIVRIAETRPLSKTKRFVVV 79 (87)
T ss_pred CCccccCceEEEEEEEEccCceeEEEEEEEEEecccceEEEEEEeeeEeec-ccccCCCCCEEEEEEccccCCcceEEEE
Confidence 689999999999999999999999999999999999999999999999999 9999999999999999999999999999
Q ss_pred EEeecC
Q 031480 142 KVIPAG 147 (159)
Q Consensus 142 ~Ii~~~ 147 (159)
+|++++
T Consensus 80 ~i~~~a 85 (87)
T COG0186 80 EIVEKA 85 (87)
T ss_pred EEeeec
Confidence 999874
No 6
>CHL00142 rps17 ribosomal protein S17; Validated
Probab=100.00 E-value=4.4e-34 Score=207.34 Aligned_cols=79 Identities=28% Similarity=0.307 Sum_probs=76.1
Q ss_pred ceEEEEEEEecCCCCeEEEEEeEEEeeeeeeeEEeeeeeEEEEcCCCCCCCCCCEEEEeeeecCCCeeeEEEEEEeecCC
Q 031480 69 GRILAGTCHSAKMNRTIIVRRNYLHFVKKYQRYEKRHSNIPAHISPCFRVKEGDHVIIGQCRPLSKTVRFNVLKVIPAGS 148 (159)
Q Consensus 69 g~il~G~VvS~KM~KTvvV~v~~~~~~pKY~K~~kr~kk~~vHd~p~~~~kvGD~V~I~ecRPLSKtK~f~V~~Ii~~~~ 148 (159)
.+.|.|+|+|++|+|||+|++++++|||+|+|+++++++|+||| |+|+|++||+|+|+|||||||||+|+|++|++++.
T Consensus 3 ~~~~~G~Vvs~km~KTivV~v~r~~~h~kY~K~~~r~kk~~aHD-e~n~~~~GD~V~I~e~RPlSKtK~~~v~~i~~~~~ 81 (84)
T CHL00142 3 VKEKIGIVVSNKMNKTIVVAVENRYKHPIYGKIITKTKKYLVHD-EENECNIGDQVLIEETRPLSKTKRWILKEILSKSS 81 (84)
T ss_pred ceEEEEEEEeCCCCceEEEEEEEEEEcCcccEEEEeeEEEEEeC-CCCCCCCCCEEEEEEcCCCCCcEEEEEEEEEEeee
Confidence 47899999999999999999999999999999999999999999 89999999999999999999999999999998854
No 7
>PRK05610 rpsQ 30S ribosomal protein S17; Reviewed
Probab=100.00 E-value=4.9e-34 Score=206.89 Aligned_cols=78 Identities=32% Similarity=0.373 Sum_probs=75.6
Q ss_pred ceEEEEEEEecCCCCeEEEEEeEEEeeeeeeeEEeeeeeEEEEcCCCCCCCCCCEEEEeeeecCCCeeeEEEEEEeecC
Q 031480 69 GRILAGTCHSAKMNRTIIVRRNYLHFVKKYQRYEKRHSNIPAHISPCFRVKEGDHVIIGQCRPLSKTVRFNVLKVIPAG 147 (159)
Q Consensus 69 g~il~G~VvS~KM~KTvvV~v~~~~~~pKY~K~~kr~kk~~vHd~p~~~~kvGD~V~I~ecRPLSKtK~f~V~~Ii~~~ 147 (159)
+++|.|+|+|++|+|||+|++++++|||+|+||++++++|+||| |+|+|++||+|+|+|||||||+|+|+|++|++++
T Consensus 6 ~~~l~G~Vvs~km~KTvvV~v~r~~~h~kY~K~~~r~kk~~aHD-~~n~~k~GD~V~I~e~rPlSK~K~~~v~~i~~~~ 83 (84)
T PRK05610 6 RKTLQGRVVSDKMDKTIVVLVERRVKHPLYGKIVKRSKKYHAHD-ENNEAKIGDVVRIMETRPLSKTKRWRLVEIVEKA 83 (84)
T ss_pred CCEEEEEEEcccCCceEEEEEEEEEEeccccEEEEcceEEEEEC-CCCCCCCCCEEEEEEcccCCCCEEEEEEEEEecc
Confidence 78999999999999999999999999999999999999999999 7889999999999999999999999999999864
No 8
>TIGR03635 S17_bact 30S ribosomal protein S17. This model describes the bacterial ribosomal small subunit protein S17, while excluding cytosolic eukaryotic homologs and archaeal homologs. The model finds many, but not, chloroplast and mitochondrial counterparts to bacterial S17.
Probab=100.00 E-value=6e-33 Score=195.61 Aligned_cols=70 Identities=36% Similarity=0.377 Sum_probs=68.1
Q ss_pred eEEEEEEEecCCCCeEEEEEeEEEeeeeeeeEEeeeeeEEEEcCCCCCCCCCCEEEEeeeecCCCeeeEEE
Q 031480 70 RILAGTCHSAKMNRTIIVRRNYLHFVKKYQRYEKRHSNIPAHISPCFRVKEGDHVIIGQCRPLSKTVRFNV 140 (159)
Q Consensus 70 ~il~G~VvS~KM~KTvvV~v~~~~~~pKY~K~~kr~kk~~vHd~p~~~~kvGD~V~I~ecRPLSKtK~f~V 140 (159)
++|.|+|+|++|+|||+|++++++|||+|+|+++++++|+||| |+|+|++||+|+|+|||||||+|+|+|
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 KTLQGVVVSDKMDKTIVVLVERRVKHPLYGKIVKRTKKYHAHD-ENNECKVGDVVRIIETRPLSKTKRWRL 71 (71)
T ss_pred eEEEEEEEcccCCceEEEEEEEEEEeccccEEEEccEEEEEEC-CCCCCCCCCEEEEEEcCCcCCceEeEC
Confidence 6899999999999999999999999999999999999999999 788999999999999999999999985
No 9
>PF00366 Ribosomal_S17: Ribosomal protein S17; InterPro: IPR000266 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. The ribosomal proteins catalyse ribosome assembly and stabilise the rRNA, tuning the structure of the ribosome for optimal function. Evidence suggests that, in prokaryotes, the peptidyl transferase reaction is performed by the large subunit 23S rRNA, whereas proteins probably have a greater role in eukaryotic ribosomes. Most of the proteins lie close to, or on the surface of, the 30S subunit, arranged peripherally around the rRNA []. The small subunit ribosomal proteins can be categorised as primary binding proteins, which bind directly and independently to 16S rRNA; secondary binding proteins, which display no specific affinity for 16S rRNA, but its assembly is contingent upon the presence of one or more primary binding proteins; and tertiary binding proteins, which require the presence of one or more secondary binding proteins and sometimes other tertiary binding proteins. The small ribosomal subunit protein S17 is known to bind specifically to the 5' end of 16S ribosomal RNA in Escherichia coli (primary rRNA binding protein), and is thought to be involved in the recognition of termination codons. Experimental evidence [] has revealed that S17 has virtually no groups exposed on the ribosomal surface.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 2YKR_Q 2VHP_Q 3BBN_Q 2QAL_Q 3OAR_Q 1VS5_Q 3KC4_Q 2AW7_Q 3E1C_J 2AVY_Q ....
Probab=99.97 E-value=6.1e-31 Score=184.08 Aligned_cols=69 Identities=43% Similarity=0.632 Sum_probs=66.4
Q ss_pred EEEEecCCCCeEEEEEeEEEeeeeeeeEEeeeeeEEEEcCCCCCCCCCCEEEEeeeecCCCeeeEEEEEE
Q 031480 74 GTCHSAKMNRTIIVRRNYLHFVKKYQRYEKRHSNIPAHISPCFRVKEGDHVIIGQCRPLSKTVRFNVLKV 143 (159)
Q Consensus 74 G~VvS~KM~KTvvV~v~~~~~~pKY~K~~kr~kk~~vHd~p~~~~kvGD~V~I~ecRPLSKtK~f~V~~I 143 (159)
|+|+|++|+|||+|++++++|||+|+|+++++++|+||| |.+.|++||+|+|.|||||||+|+|+|++|
T Consensus 1 G~Vvs~km~KTv~V~v~~~~~~~ky~K~~~~~kk~~aHD-~~~~~~vGD~V~I~e~rPiSk~K~~~v~~v 69 (69)
T PF00366_consen 1 GVVVSDKMDKTVVVRVERLVYHPKYKKYIKRTKKYMAHD-ENNICKVGDKVRIRECRPISKTKRFVVVEV 69 (69)
T ss_dssp EEEEEEESTTEEEEEEEEEEEETTTEEEEEEEEEEEEE--TTSSSTTTSEEEEEEEEEEETTEEEEEEEE
T ss_pred CEEEEcCCCCeEEEEEEEEEEcceEeeccCccccEEEeC-CccCCCCCCEEEEEeeeccCCcEeEEEEEC
Confidence 899999999999999999999999999999999999999 788899999999999999999999999986
No 10
>KOG1740 consensus Predicted mitochondrial/chloroplast ribosomal protein S17 [Translation, ribosomal structure and biogenesis]
Probab=99.94 E-value=2.9e-28 Score=182.44 Aligned_cols=78 Identities=38% Similarity=0.498 Sum_probs=74.5
Q ss_pred ceEEEEEEEecCCCCeEEEEEeEEEeeeeeeeEEeeeeeEEEEcCCCCCCCCCCEEEEeeeecCCCeeeEEEEEEeecC
Q 031480 69 GRILAGTCHSAKMNRTIIVRRNYLHFVKKYQRYEKRHSNIPAHISPCFRVKEGDHVIIGQCRPLSKTVRFNVLKVIPAG 147 (159)
Q Consensus 69 g~il~G~VvS~KM~KTvvV~v~~~~~~pKY~K~~kr~kk~~vHd~p~~~~kvGD~V~I~ecRPLSKtK~f~V~~Ii~~~ 147 (159)
.+-+.|+|+|.+|+||++|+|+++.+||+|+||++++++|+||| |.+.|++||.|+|..||||||||+|.+.+|++++
T Consensus 2 m~~~vg~VvS~kmqKTv~V~V~rl~~n~~ynryv~~~~kymahD-~~n~cnvGD~VrlepsRPlSk~K~f~i~eII~~a 79 (107)
T KOG1740|consen 2 MKNVVGTVVSNKMQKTVKVRVDRLFFNPKYNRYVKRTSKYMAHD-DKNQCNVGDRVRLEPSRPLSKTKHFIIAEIIKKA 79 (107)
T ss_pred CccceeeeeecccCceeEEEeeeccccHHHHHHHHHhhheeecC-ccccccccceEEeccCCcccccceeehHHHHHHH
Confidence 34688999999999999999999999999999999999999999 8999999999999999999999999999999874
No 11
>KOG3447 consensus Mitochondrial/chloroplast ribosomal S17-like protein [Translation, ribosomal structure and biogenesis]
Probab=99.19 E-value=3.6e-12 Score=100.38 Aligned_cols=82 Identities=24% Similarity=0.271 Sum_probs=76.0
Q ss_pred eeeeeceEEEEEEEecCCCCeEEEEEeEEEeeeeeeeEEeeeeeEEEEcCCCCCCCCCCEEEEeee-ecCCCeeeEEEEE
Q 031480 64 TVSIRGRILAGTCHSAKMNRTIIVRRNYLHFVKKYQRYEKRHSNIPAHISPCFRVKEGDHVIIGQC-RPLSKTVRFNVLK 142 (159)
Q Consensus 64 ~~sirg~il~G~VvS~KM~KTvvV~v~~~~~~pKY~K~~kr~kk~~vHd~p~~~~kvGD~V~I~ec-RPLSKtK~f~V~~ 142 (159)
.-|+++++|.|.|+-.+|++|+.|++.++.++|..++|+.+++.|.||| +...|++||+|.|.+- -|+.+.+++.|.+
T Consensus 5 ~~s~~~~~lmGk~ig~~~q~~akVR~~r~eld~yL~kYf~k~~~yfAhD-~~~~c~vGDtVLir~lp~r~t~~V~H~v~~ 83 (150)
T KOG3447|consen 5 KSSVHAQWLMGKVIGTKMQKTAKVRVTRLELDPYLLKYFNKRKTYFAHD-ALQQCTVGDTVLIRALPVRRTKHVKHEVAE 83 (150)
T ss_pred EeecccEEEEeeeeeccccccceeeeehhhcCHHHHHHhccccceeecc-hhhccccCCEEEEecCCcchhhhhhhhhHh
Confidence 3589999999999999999999999999999999999999999999999 8999999999999995 6778888999988
Q ss_pred Eeec
Q 031480 143 VIPA 146 (159)
Q Consensus 143 Ii~~ 146 (159)
|+-+
T Consensus 84 VVfk 87 (150)
T KOG3447|consen 84 VVFK 87 (150)
T ss_pred heee
Confidence 8765
No 12
>PF10915 DUF2709: Protein of unknown function (DUF2709); InterPro: IPR024484 Members of this family appear restricted to Chlamydiales. Their function is unknown.
Probab=81.24 E-value=0.77 Score=39.02 Aligned_cols=58 Identities=29% Similarity=0.337 Sum_probs=35.0
Q ss_pred hHHhhccCcceeecccccCCCC-------CCCCCCceeeeeecccccCChhhh--cccccCCCCCceeeee
Q 031480 5 TEKAFLKQPKVFLSSKKAGKGK-------RPGKGGNRFWKSIGLGFKTPREAI--EGTYIDKKCPFTGTVS 66 (159)
Q Consensus 5 ~~~a~qkq~~i~~~~~~~~~~~-------~~~~~~~r~~~~igl~~~~P~~~~--~~~yiD~kcPf~g~~s 66 (159)
-|.+|+-||.+|...|-.-+.. ...+|.+|=. .|-+++-.|+--. .--|| |||||.|.
T Consensus 31 lE~k~~l~PVlF~rdK~I~qs~e~ai~~lE~e~KlWret-eI~I~~g~p~VNE~TkkIYI---CPFTGKVF 97 (238)
T PF10915_consen 31 LEQKFNLQPVLFVRDKIIFQSAEDAIRILEEEGKLWRET-EIKIQSGKPSVNEQTKKIYI---CPFTGKVF 97 (238)
T ss_pred HHHhcCCCceeeecchhhccCHHHHHHHHHHhcchheee-eEEEecCCcccccccceEEE---cCCcCccc
Confidence 5889999998888776332110 0123433332 5777777775322 22377 99999774
No 13
>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=69.35 E-value=27 Score=24.56 Aligned_cols=52 Identities=25% Similarity=0.273 Sum_probs=34.5
Q ss_pred EEEEEEEecCCCCeEEEEEeEEEeeeeeeeEEeeeeeEEEEcCCCC-----CCCCCCEEEEeeeecCCCee
Q 031480 71 ILAGTCHSAKMNRTIIVRRNYLHFVKKYQRYEKRHSNIPAHISPCF-----RVKEGDHVIIGQCRPLSKTV 136 (159)
Q Consensus 71 il~G~VvS~KM~KTvvV~v~~~~~~pKY~K~~kr~kk~~vHd~p~~-----~~kvGD~V~I~ecRPLSKtK 136 (159)
.+.|+|+..-.+-...|..+- -..+.||.|-.. .+.+||.|.+. -+|...++
T Consensus 6 e~~G~V~e~L~~~~f~V~l~n-------------g~~vla~i~GKmr~~rI~I~~GD~V~Ve-~spyd~tk 62 (68)
T TIGR00008 6 EMEGKVTESLPNAMFRVELEN-------------GHEVLAHISGKIRMHYIRILPGDKVKVE-LSPYDLTR 62 (68)
T ss_pred EEEEEEEEECCCCEEEEEECC-------------CCEEEEEecCcchhccEEECCCCEEEEE-ECcccCCc
Confidence 578999988766666666442 234556664322 37899999994 66766555
No 14
>COG0361 InfA Translation initiation factor 1 (IF-1) [Translation, ribosomal structure and biogenesis]
Probab=66.22 E-value=34 Score=24.63 Aligned_cols=52 Identities=29% Similarity=0.287 Sum_probs=36.4
Q ss_pred EEEEEEEecCCCCeEEEEEeEEEeeeeeeeEEeeeeeEEEEcCCCC-----CCCCCCEEEEeeeecCCCee
Q 031480 71 ILAGTCHSAKMNRTIIVRRNYLHFVKKYQRYEKRHSNIPAHISPCF-----RVKEGDHVIIGQCRPLSKTV 136 (159)
Q Consensus 71 il~G~VvS~KM~KTvvV~v~~~~~~pKY~K~~kr~kk~~vHd~p~~-----~~kvGD~V~I~ecRPLSKtK 136 (159)
.+.|+|+..-.+....|..+--+ ..+||.|-.. ...+||+|++ |.+|..-++
T Consensus 8 e~~g~V~e~L~~~~f~v~~edg~-------------~~~ahI~GKmr~~~i~I~~GD~V~V-e~~~~d~~k 64 (75)
T COG0361 8 EMEGTVIEMLPNGRFRVELENGH-------------ERLAHISGKMRKNRIRILPGDVVLV-ELSPYDLTK 64 (75)
T ss_pred EEEEEEEEecCCCEEEEEecCCc-------------EEEEEccCcchheeEEeCCCCEEEE-Eeccccccc
Confidence 57899999888888888755444 4567774322 3689999998 566665443
No 15
>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=65.33 E-value=22 Score=24.51 Aligned_cols=25 Identities=12% Similarity=0.006 Sum_probs=20.1
Q ss_pred eeeeeEEEEcCCCCCCCCCCEEEEe
Q 031480 103 KRHSNIPAHISPCFRVKEGDHVIIG 127 (159)
Q Consensus 103 kr~kk~~vHd~p~~~~kvGD~V~I~ 127 (159)
-.-+.+..|+.+...+..||.|.|.
T Consensus 42 ~~V~si~~~~~~~~~a~aGd~v~~~ 66 (83)
T cd03698 42 VEVKSIYVDDEEVDYAVAGENVRLK 66 (83)
T ss_pred EEEEEEEECCeECCEECCCCEEEEE
Confidence 4556677888788889999999874
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=60.88 E-value=37 Score=25.29 Aligned_cols=49 Identities=18% Similarity=0.152 Sum_probs=33.6
Q ss_pred EEEEEEEecCCCCeEEEEEeEEEeeeeeeeEEeeeeeEEEEcCCCC----CCCCCCEEEEeeeecCC
Q 031480 71 ILAGTCHSAKMNRTIIVRRNYLHFVKKYQRYEKRHSNIPAHISPCF----RVKEGDHVIIGQCRPLS 133 (159)
Q Consensus 71 il~G~VvS~KM~KTvvV~v~~~~~~pKY~K~~kr~kk~~vHd~p~~----~~kvGD~V~I~ecRPLS 133 (159)
...|+|+....+....|..+- -..++||.|..+ -++.||.|.| +.+.++
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 467888888777766665331 235566664433 2889999999 677888
No 17
>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=60.68 E-value=37 Score=24.04 Aligned_cols=55 Identities=16% Similarity=0.069 Sum_probs=35.9
Q ss_pred EEEEEEecCCCCeEEEEEeEEEeeeeeeeEEeeeeeEEEEcCCCC----CCCCCCEEEEeeeecCCCeeeEEE
Q 031480 72 LAGTCHSAKMNRTIIVRRNYLHFVKKYQRYEKRHSNIPAHISPCF----RVKEGDHVIIGQCRPLSKTVRFNV 140 (159)
Q Consensus 72 l~G~VvS~KM~KTvvV~v~~~~~~pKY~K~~kr~kk~~vHd~p~~----~~kvGD~V~I~ecRPLSKtK~f~V 140 (159)
..|+|+....+....|..+- -..++||.|..+ -++.||.|.+. -+|..+++-=.+
T Consensus 2 ~~g~V~~~~g~~~~~V~~~~-------------g~~~la~i~gK~rk~iwI~~GD~V~Ve-~~~~d~~kg~Iv 60 (77)
T cd05793 2 EYGQVEKMLGNGRLEVRCFD-------------GKKRLCRIRGKMRKRVWINEGDIVLVA-PWDFQDDKADII 60 (77)
T ss_pred EEEEEEEEcCCCEEEEEECC-------------CCEEEEEEchhhcccEEEcCCCEEEEE-eccccCCEEEEE
Confidence 46788887777766665331 234566764444 38899999996 667777665443
No 18
>KOG3416 consensus Predicted nucleic acid binding protein [General function prediction only]
Probab=57.57 E-value=39 Score=26.87 Aligned_cols=50 Identities=14% Similarity=0.052 Sum_probs=36.0
Q ss_pred ceEEEEEEEecCCCCeEEEEEeEEEeeeeeeeEEeeeeeEEEEcCCCCCCCCCCEEEEe
Q 031480 69 GRILAGTCHSAKMNRTIIVRRNYLHFVKKYQRYEKRHSNIPAHISPCFRVKEGDHVIIG 127 (159)
Q Consensus 69 g~il~G~VvS~KM~KTvvV~v~~~~~~pKY~K~~kr~kk~~vHd~p~~~~kvGD~V~I~ 127 (159)
=-+..|.+.++|..++|.+.. .- =+.-.=++.+-|++|...++||+|.+.
T Consensus 22 Ivl~~g~~tkTkdg~~v~~~k---Va------D~TgsI~isvW~e~~~~~~PGDIirLt 71 (134)
T KOG3416|consen 22 IVLEYGRATKTKDGHEVRSCK---VA------DETGSINISVWDEEGCLIQPGDIIRLT 71 (134)
T ss_pred EEEeeceeeeccCCCEEEEEE---Ee------cccceEEEEEecCcCcccCCccEEEec
Confidence 346778999999888887651 10 012345677888888999999999874
No 19
>PF10844 DUF2577: Protein of unknown function (DUF2577); InterPro: IPR022555 This family of proteins has no known function
Probab=57.45 E-value=73 Score=23.26 Aligned_cols=23 Identities=26% Similarity=0.420 Sum_probs=16.8
Q ss_pred CCCCCCEEEEeeeecCCCeeeEEEEE
Q 031480 117 RVKEGDHVIIGQCRPLSKTVRFNVLK 142 (159)
Q Consensus 117 ~~kvGD~V~I~ecRPLSKtK~f~V~~ 142 (159)
.+++||.|.+- |...--+|.|+.
T Consensus 76 ~Lk~GD~V~ll---~~~~gQ~yiVlD 98 (100)
T PF10844_consen 76 GLKVGDKVLLL---RVQGGQKYIVLD 98 (100)
T ss_pred CCcCCCEEEEE---EecCCCEEEEEE
Confidence 59999999986 355566666654
No 20
>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=56.75 E-value=50 Score=23.45 Aligned_cols=55 Identities=13% Similarity=-0.037 Sum_probs=34.7
Q ss_pred EEEEEEecCCCCeEEEEEeEEEeeeeeeeEEeeeeeEEEEcCCCC----CCCCCCEEEEeeeecC-CCeeeEEE
Q 031480 72 LAGTCHSAKMNRTIIVRRNYLHFVKKYQRYEKRHSNIPAHISPCF----RVKEGDHVIIGQCRPL-SKTVRFNV 140 (159)
Q Consensus 72 l~G~VvS~KM~KTvvV~v~~~~~~pKY~K~~kr~kk~~vHd~p~~----~~kvGD~V~I~ecRPL-SKtK~f~V 140 (159)
..|+|+....+....|..+ --..++||.|..+ -++.||.|.+ +-+|. .+++-=.+
T Consensus 2 ~i~~V~~~lG~~~~~V~~~-------------dg~~~l~~i~gK~Rk~iwI~~GD~VlV-~~~~~~~~~kg~Iv 61 (78)
T cd04456 2 QIVRVLRMLGNNRHEVECA-------------DGQRRLVSIPGKLRKNIWIKRGDFLIV-DPIEEGEDVKADII 61 (78)
T ss_pred eEEEEEEECCCCEEEEEEC-------------CCCEEEEEEchhhccCEEEcCCCEEEE-EecccCCCceEEEE
Confidence 3577777766666655533 1245667775544 2899999999 56777 46554333
No 21
>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=53.73 E-value=38 Score=23.82 Aligned_cols=26 Identities=19% Similarity=0.220 Sum_probs=20.7
Q ss_pred EeeeeeEEEEcCCCCCCCCCCEEEEe
Q 031480 102 EKRHSNIPAHISPCFRVKEGDHVIIG 127 (159)
Q Consensus 102 ~kr~kk~~vHd~p~~~~kvGD~V~I~ 127 (159)
.-.-+.+..|+.+...+..||.|.|.
T Consensus 45 ~~~V~sI~~~~~~~~~a~aG~~v~i~ 70 (91)
T cd03693 45 TGEVKSVEMHHEPLEEALPGDNVGFN 70 (91)
T ss_pred EEEEEEEEECCcCcCEECCCCEEEEE
Confidence 45566777888777889999999985
No 22
>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=49.49 E-value=48 Score=23.02 Aligned_cols=53 Identities=13% Similarity=0.201 Sum_probs=31.3
Q ss_pred eceEEEEEEEecCCCC--eEEEEEeEEEeeeeeeeEEeeeeeEEEEcCCCCCCCCCCEEEEe
Q 031480 68 RGRILAGTCHSAKMNR--TIIVRRNYLHFVKKYQRYEKRHSNIPAHISPCFRVKEGDHVIIG 127 (159)
Q Consensus 68 rg~il~G~VvS~KM~K--TvvV~v~~~~~~pKY~K~~kr~kk~~vHd~p~~~~kvGD~V~I~ 127 (159)
+|.++.|+|.+-.+.. .+.+.- .+. ...-.-+.+.+|+.+...+..||.|.|.
T Consensus 14 ~G~vv~G~v~~G~v~~gd~v~~~p-----~~~--~~~~~V~si~~~~~~~~~a~~G~~v~l~ 68 (87)
T cd03697 14 RGTVVTGRIERGTIKVGDEVEIVG-----FGE--TLKTTVTGIEMFRKTLDEAEAGDNVGVL 68 (87)
T ss_pred cEEEEEEEECCCCCccCCEEEEeC-----CCC--CceEEEEEEEECCcCCCEECCCCEEEEE
Confidence 3556777777654332 333221 000 1123445577888777889999999985
No 23
>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=48.99 E-value=78 Score=21.57 Aligned_cols=26 Identities=31% Similarity=0.378 Sum_probs=19.7
Q ss_pred EeeeeeEEEEcCCCCCCCCCCEEEEe
Q 031480 102 EKRHSNIPAHISPCFRVKEGDHVIIG 127 (159)
Q Consensus 102 ~kr~kk~~vHd~p~~~~kvGD~V~I~ 127 (159)
.-.-+.+..|+.+...+..||.|.|.
T Consensus 41 ~~~V~sI~~~~~~~~~a~aGd~v~i~ 66 (83)
T cd03696 41 ETRVRSIQVHGKDVEEAKAGDRVALN 66 (83)
T ss_pred eEEEEEEEECCcCcCEEcCCCEEEEE
Confidence 45556667777677789999999984
No 24
>PF09740 DUF2043: Uncharacterized conserved protein (DUF2043); InterPro: IPR018610 This entry consists of uncharacterised proteins of unknown function. They contain three conserved cysteines and a {CP}{y/l}{HG} motif.
Probab=48.57 E-value=6.1 Score=30.36 Aligned_cols=13 Identities=54% Similarity=1.076 Sum_probs=9.7
Q ss_pred CCCCCceeeeeee
Q 031480 56 DKKCPFTGTVSIR 68 (159)
Q Consensus 56 D~kcPf~g~~sir 68 (159)
-.+|||||-+--|
T Consensus 87 ~~kCPfHG~IIpR 99 (110)
T PF09740_consen 87 RKKCPFHGKIIPR 99 (110)
T ss_pred cccCCCCCcccCC
Confidence 4589999977544
No 25
>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=48.08 E-value=35 Score=23.83 Aligned_cols=26 Identities=19% Similarity=0.224 Sum_probs=20.9
Q ss_pred EeeeeeEEEEcCCCCCCCCCCEEEEe
Q 031480 102 EKRHSNIPAHISPCFRVKEGDHVIIG 127 (159)
Q Consensus 102 ~kr~kk~~vHd~p~~~~kvGD~V~I~ 127 (159)
.-.-+.+..|+.+...+..||.|.|.
T Consensus 45 ~~~V~sI~~~~~~~~~a~aGd~v~l~ 70 (87)
T cd03694 45 PVTVKSIHRNRSPVRVVRAGQSASLA 70 (87)
T ss_pred EEEEEEEEECCeECCEECCCCEEEEE
Confidence 45566788888777889999999985
No 26
>PRK12442 translation initiation factor IF-1; Reviewed
Probab=47.89 E-value=85 Score=23.24 Aligned_cols=62 Identities=18% Similarity=0.081 Sum_probs=38.2
Q ss_pred eEEEEEEEecCCCCeEEEEEeEEEeeeeeeeEEeeeeeEEEEcCCC-----CCCCCCCEEEEeeeecCCCeeeEEEEEEe
Q 031480 70 RILAGTCHSAKMNRTIIVRRNYLHFVKKYQRYEKRHSNIPAHISPC-----FRVKEGDHVIIGQCRPLSKTVRFNVLKVI 144 (159)
Q Consensus 70 ~il~G~VvS~KM~KTvvV~v~~~~~~pKY~K~~kr~kk~~vHd~p~-----~~~kvGD~V~I~ecRPLSKtK~f~V~~Ii 144 (159)
-.++|+|+..--+-...|+.+-=+ .++||.|-. ..+.+||.|++. -.|..-++-=.+.+-.
T Consensus 7 ie~~G~V~e~Lp~~~frV~LenG~-------------~vla~isGKmR~~rIrIl~GD~V~VE-~spYDltkGRIiyR~~ 72 (87)
T PRK12442 7 IELDGIVDEVLPDSRFRVTLENGV-------------EVGAYASGRMRKHRIRILAGDRVTLE-LSPYDLTKGRINFRHK 72 (87)
T ss_pred EEEEEEEEEECCCCEEEEEeCCCC-------------EEEEEeccceeeeeEEecCCCEEEEE-ECcccCCceeEEEEec
Confidence 357888888766667777644222 334554322 247899999994 4577666655555444
Q ss_pred e
Q 031480 145 P 145 (159)
Q Consensus 145 ~ 145 (159)
.
T Consensus 73 ~ 73 (87)
T PRK12442 73 D 73 (87)
T ss_pred C
Confidence 3
No 27
>cd03695 CysN_NodQ_II CysN_NodQ_II: This subfamily represents the domain II of the large subunit of ATP sulfurylase (ATPS): CysN or the N-terminal portion of NodQ, found mainly in proteobacteria and homologous to the domain II of EF-Tu. Escherichia coli ATPS consists of CysN and a smaller subunit CysD and CysN. ATPS produces adenosine-5'-phosphosulfate (APS) from ATP and sulfate, coupled with GTP hydrolysis. In the subsequent reaction APS is phosphorylated by an APS kinase (CysC), to produce 3'-phosphoadenosine-5'-phosphosulfate (PAPS) for use in amino acid (aa) biosynthesis. The Rhizobiaceae group (alpha-proteobacteria) appears to carry out the same chemistry for the sufation of a nodulation factor. In Rhizobium meliloti, a the hererodimeric complex comprised of NodP and NodQ appears to possess both ATPS and APS kinase activities. The N and C termini of NodQ correspond to CysN and CysC, respectively. Other eubacteria, Archaea, and eukaryotes use a different ATP sulfurylase, which sho
Probab=47.83 E-value=40 Score=23.37 Aligned_cols=49 Identities=16% Similarity=0.207 Sum_probs=31.5
Q ss_pred eeceEEEEEEEecCCCCeEEEEEeEEEeeeeeeeEEeeeeeEEEEcCCCCCCCCCCEEEEe
Q 031480 67 IRGRILAGTCHSAKMNRTIIVRRNYLHFVKKYQRYEKRHSNIPAHISPCFRVKEGDHVIIG 127 (159)
Q Consensus 67 irg~il~G~VvS~KM~KTvvV~v~~~~~~pKY~K~~kr~kk~~vHd~p~~~~kvGD~V~I~ 127 (159)
+-|++..|.|-. .-++.+. |- ...-.-+.+.+|+.+...+..||.|.|.
T Consensus 18 v~Gkv~~G~v~~---Gd~v~~~-------P~--~~~~~V~si~~~~~~~~~a~aGd~v~l~ 66 (81)
T cd03695 18 YAGTIASGSIRV---GDEVVVL-------PS--GKTSRVKSIETFDGELDEAGAGESVTLT 66 (81)
T ss_pred EEEEEccceEEC---CCEEEEc-------CC--CCeEEEEEEEECCcEeCEEcCCCEEEEE
Confidence 556666665442 2344333 21 2345667788888778889999999985
No 28
>smart00652 eIF1a eukaryotic translation initiation factor 1A.
Probab=44.20 E-value=1.1e+02 Score=21.93 Aligned_cols=56 Identities=13% Similarity=0.003 Sum_probs=34.9
Q ss_pred EEEEEEEecCCCCeEEEEEeEEEeeeeeeeEEeeeeeEEEEcCCCC----CCCCCCEEEEeeeecCCCeeeEEE
Q 031480 71 ILAGTCHSAKMNRTIIVRRNYLHFVKKYQRYEKRHSNIPAHISPCF----RVKEGDHVIIGQCRPLSKTVRFNV 140 (159)
Q Consensus 71 il~G~VvS~KM~KTvvV~v~~~~~~pKY~K~~kr~kk~~vHd~p~~----~~kvGD~V~I~ecRPLSKtK~f~V 140 (159)
...|+|+....+.-..|.-+- -..++||.|..+ -++.||.|.| +-+|-.+.+-=++
T Consensus 6 q~~g~V~~~lG~~~~~V~~~d-------------G~~~la~ipgK~Rk~iwI~~GD~VlV-e~~~~~~~kg~Iv 65 (83)
T smart00652 6 QEIAQVVKMLGNGRLEVMCAD-------------GKERLARIPGKMRKKVWIRRGDIVLV-DPWDFQDVKADII 65 (83)
T ss_pred cEEEEEEEEcCCCEEEEEECC-------------CCEEEEEEchhhcccEEEcCCCEEEE-EecCCCCCEEEEE
Confidence 356788877666666665321 234566664443 2889999999 4567766554433
No 29
>PRK04012 translation initiation factor IF-1A; Provisional
Probab=42.54 E-value=1.4e+02 Score=22.24 Aligned_cols=56 Identities=16% Similarity=0.087 Sum_probs=34.8
Q ss_pred EEEEEEEecCCCCeEEEEEeEEEeeeeeeeEEeeeeeEEEEcCCCC----CCCCCCEEEEeeeecCCCeeeEEE
Q 031480 71 ILAGTCHSAKMNRTIIVRRNYLHFVKKYQRYEKRHSNIPAHISPCF----RVKEGDHVIIGQCRPLSKTVRFNV 140 (159)
Q Consensus 71 il~G~VvS~KM~KTvvV~v~~~~~~pKY~K~~kr~kk~~vHd~p~~----~~kvGD~V~I~ecRPLSKtK~f~V 140 (159)
...|+|+....+....|..+- -..++||.|..+ -++.||.|.|. -+|...++.=++
T Consensus 22 e~~g~V~~~lG~~~~~V~~~d-------------G~~~la~i~GK~Rk~IwI~~GD~VlVe-~~~~~~~kg~Iv 81 (100)
T PRK04012 22 EVFGVVEQMLGANRVRVRCMD-------------GVERMGRIPGKMKKRMWIREGDVVIVA-PWDFQDEKADII 81 (100)
T ss_pred EEEEEEEEEcCCCEEEEEeCC-------------CCEEEEEEchhhcccEEecCCCEEEEE-ecccCCCEEEEE
Confidence 467888887777766665331 123455553333 27899999995 577776654333
No 30
>PTZ00329 eukaryotic translation initiation factor 1A; Provisional
Probab=41.21 E-value=1.9e+02 Score=23.49 Aligned_cols=58 Identities=14% Similarity=0.038 Sum_probs=37.3
Q ss_pred EEEEEEecCCCCeEEEEEeEEEeeeeeeeEEeeeeeEEEEcCCCC----CCCCCCEEEEeeeecCCCeeeEEEEEE
Q 031480 72 LAGTCHSAKMNRTIIVRRNYLHFVKKYQRYEKRHSNIPAHISPCF----RVKEGDHVIIGQCRPLSKTVRFNVLKV 143 (159)
Q Consensus 72 l~G~VvS~KM~KTvvV~v~~~~~~pKY~K~~kr~kk~~vHd~p~~----~~kvGD~V~I~ecRPLSKtK~f~V~~I 143 (159)
..|+|++...+....|...- -...+||.|-.+ -+.+||+|+|. -+|-..+|.=++...
T Consensus 34 ~~g~V~~~LGn~~f~V~c~d-------------G~~rLa~I~GKmRK~IWI~~GD~VlVe-l~~yd~~KgdIi~Ry 95 (155)
T PTZ00329 34 EYAQVLRMLGNGRLEAYCFD-------------GVKRLCHIRGKMRKRVWINIGDIILVS-LRDFQDSKADVILKY 95 (155)
T ss_pred EEEEEEEEcCCCEEEEEECC-------------CCEEEEEeeccceeeEEecCCCEEEEe-ccCCCCCEEEEEEEc
Confidence 47888888777777776321 112233432211 27889999995 599988887665554
No 31
>PF13550 Phage-tail_3: Putative phage tail protein
Probab=41.08 E-value=60 Score=24.11 Aligned_cols=39 Identities=15% Similarity=0.348 Sum_probs=26.8
Q ss_pred EeeeeeEEEEcCCCCCCCCCCEEEEeeeecCCCeeeEEEEEEe
Q 031480 102 EKRHSNIPAHISPCFRVKEGDHVIIGQCRPLSKTVRFNVLKVI 144 (159)
Q Consensus 102 ~kr~kk~~vHd~p~~~~kvGD~V~I~ecRPLSKtK~f~V~~Ii 144 (159)
.+++=.+.+-. ....+.+||+|.|..- .+...|.|.+|.
T Consensus 125 ~r~t~~f~~~~-~~~~l~pGDvi~l~~~---~~~~~~RI~~i~ 163 (164)
T PF13550_consen 125 ERRTVSFTLPP-DGLALEPGDVIALSDD---GRDMRFRITEIE 163 (164)
T ss_pred cceEEEEEECh-hhccCCCCCEEEEEeC---CCceEEEEEEEe
Confidence 33344444443 4567999999999755 557888888764
No 32
>COG1786 Swiveling domain associated with predicted aconitase [Energy production and conversion]
Probab=41.04 E-value=17 Score=28.77 Aligned_cols=24 Identities=42% Similarity=0.793 Sum_probs=19.2
Q ss_pred ChhhhcccccCCCCCceeeeeeeceEEE
Q 031480 46 PREAIEGTYIDKKCPFTGTVSIRGRILA 73 (159)
Q Consensus 46 P~~~~~~~yiD~kcPf~g~~sirg~il~ 73 (159)
|++ |.-||++||-+| -++.|++|.
T Consensus 32 PeT---G~vid~~h~l~G-~~l~Gkilv 55 (131)
T COG1786 32 PET---GKVIDPHHPLHG-ESLTGKILV 55 (131)
T ss_pred ccc---ccCcCCCCCccc-ccccceEEE
Confidence 555 666999999999 688888874
No 33
>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=39.35 E-value=1.2e+02 Score=20.67 Aligned_cols=25 Identities=12% Similarity=0.026 Sum_probs=19.1
Q ss_pred eeeeeEEEEcCCCCCCCCCCEEEEe
Q 031480 103 KRHSNIPAHISPCFRVKEGDHVIIG 127 (159)
Q Consensus 103 kr~kk~~vHd~p~~~~kvGD~V~I~ 127 (159)
-.-+.+..|+.+..++..||.|.|.
T Consensus 41 ~~V~si~~~~~~~~~a~aGd~v~l~ 65 (82)
T cd04089 41 VEVLSIYNEDVEVRYARPGENVRLR 65 (82)
T ss_pred EEEEEEEECCEECCEECCCCEEEEE
Confidence 3455567777677889999999984
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=37.49 E-value=24 Score=24.40 Aligned_cols=13 Identities=46% Similarity=0.710 Sum_probs=10.9
Q ss_pred CCCCCCEEEEeee
Q 031480 117 RVKEGDHVIIGQC 129 (159)
Q Consensus 117 ~~kvGD~V~I~ec 129 (159)
-|+.||+|.|+..
T Consensus 53 G~~~GD~V~Ig~~ 65 (69)
T TIGR03595 53 GAKDGDTVRIGDF 65 (69)
T ss_pred CCCCCCEEEEccE
Confidence 4899999999853
No 35
>cd01342 Translation_Factor_II_like Translation_Factor_II_like: Elongation factor Tu (EF-Tu) domain II-like proteins. Elongation factor Tu consists of three structural domains, this family represents the second domain. Domain II adopts a beta barrel structure and is involved in binding to charged tRNA. Domain II is found in other proteins such as elongation factor G and translation initiation factor IF-2. This group also includes the C2 subdomain of domain IV of IF-2 that has the same fold as domain II of (EF-Tu). Like IF-2 from certain prokaryotes such as Thermus thermophilus, mitochondrial IF-2 lacks domain II, which is thought to be involved in binding of E.coli IF-2 to 30S subunits.
Probab=37.27 E-value=1e+02 Score=19.05 Aligned_cols=22 Identities=18% Similarity=0.027 Sum_probs=15.5
Q ss_pred eEEEEcCCCCCCCCCCEEEEee
Q 031480 107 NIPAHISPCFRVKEGDHVIIGQ 128 (159)
Q Consensus 107 k~~vHd~p~~~~kvGD~V~I~e 128 (159)
.+..+..+...+..||.+.+.-
T Consensus 48 ~i~~~~~~~~~~~aG~~~~~~~ 69 (83)
T cd01342 48 SLKRFKGEVDEAVAGDIVGIVL 69 (83)
T ss_pred EeEecCceeceecCCCEEEEEE
Confidence 4444445777899999998853
No 36
>CHL00071 tufA elongation factor Tu
Probab=36.73 E-value=1.3e+02 Score=26.85 Aligned_cols=25 Identities=16% Similarity=-0.003 Sum_probs=19.0
Q ss_pred eeeeeEEEEcCCCCCCCCCCEEEEe
Q 031480 103 KRHSNIPAHISPCFRVKEGDHVIIG 127 (159)
Q Consensus 103 kr~kk~~vHd~p~~~~kvGD~V~I~ 127 (159)
-+-+.+..|+.+...+..||.|.|.
T Consensus 264 ~~VksI~~~~~~v~~a~aGd~v~i~ 288 (409)
T CHL00071 264 TTVTGLEMFQKTLDEGLAGDNVGIL 288 (409)
T ss_pred EEEEEEEEcCcCCCEECCCceeEEE
Confidence 4667778888677779999998654
No 37
>KOG1730 consensus Thioredoxin-like protein [Posttranslational modification, protein turnover, chaperones]
Probab=31.87 E-value=30 Score=29.16 Aligned_cols=18 Identities=39% Similarity=0.813 Sum_probs=15.1
Q ss_pred CCCceeeeeeeceEEEEE
Q 031480 58 KCPFTGTVSIRGRILAGT 75 (159)
Q Consensus 58 kcPf~g~~sirg~il~G~ 75 (159)
+-||||++.+.|-++.|-
T Consensus 74 niPFtg~vkLkgI~I~g~ 91 (206)
T KOG1730|consen 74 NIPFTGNVKLKGISIMGE 91 (206)
T ss_pred eccccCceeEEEEEEEeC
Confidence 469999999988888774
No 38
>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=31.53 E-value=23 Score=24.41 Aligned_cols=12 Identities=58% Similarity=0.817 Sum_probs=7.5
Q ss_pred CCCCCCEEEEee
Q 031480 117 RVKEGDHVIIGQ 128 (159)
Q Consensus 117 ~~kvGD~V~I~e 128 (159)
-++.||+|.|+.
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 489999999975
No 39
>PRK12736 elongation factor Tu; Reviewed
Probab=31.52 E-value=1.3e+02 Score=26.60 Aligned_cols=23 Identities=13% Similarity=0.034 Sum_probs=15.4
Q ss_pred eeeeEEEEcCCCCCCCCCCEEEE
Q 031480 104 RHSNIPAHISPCFRVKEGDHVII 126 (159)
Q Consensus 104 r~kk~~vHd~p~~~~kvGD~V~I 126 (159)
+-+.+.+|..+...+..||.|.|
T Consensus 255 ~V~sI~~~~~~~~~a~aGd~v~l 277 (394)
T PRK12736 255 VVTGVEMFRKLLDEGQAGDNVGV 277 (394)
T ss_pred EEEEEEECCEEccEECCCCEEEE
Confidence 45556666656667788887755
No 40
>PF04246 RseC_MucC: Positive regulator of sigma(E), RseC/MucC; InterPro: IPR007359 This bacterial family of integral membrane proteins represents a positive regulator of the sigma(E) transcription factor, namely RseC/MucC. The sigma(E) transcription factor is up-regulated by cell envelope protein misfolding, and regulates the expression of genes that are collectively termed ECF (devoted to Extra-Cellular Functions) []. In Pseudomonas aeruginosa, derepression of sigma(E) is associated with the alginate-overproducing phenotype characteristic of chronic respiratory tract colonization in cystic fibrosis patients. The mechanism by which RseC/MucC positively regulates the sigma(E) transcription factor is unknown. RseC is also thought to have a role in thiamine biosynthesis in Salmonella typhimurium []. In addition, this family also includes an N-terminal part of RnfF, a Rhodobacter capsulatus protein, of unknown function, that is essential for nitrogen fixation. This protein also contains a domain found in ApbE protein IPR003374 from INTERPRO, which is itself involved in thiamine biosynthesis.
Probab=28.44 E-value=65 Score=24.23 Aligned_cols=13 Identities=31% Similarity=0.340 Sum_probs=11.1
Q ss_pred CCCCCCCCEEEEe
Q 031480 115 CFRVKEGDHVIIG 127 (159)
Q Consensus 115 ~~~~kvGD~V~I~ 127 (159)
...+++||.|+|+
T Consensus 49 ~~~~~~GD~V~v~ 61 (135)
T PF04246_consen 49 PIGAKVGDRVEVE 61 (135)
T ss_pred CCCCCCCCEEEEE
Confidence 4579999999986
No 41
>cd04092 mtEFG2_II_like mtEFG2_C: C-terminus of mitochondrial Elongation factor G2 (mtEFG2)-like proteins found in eukaryotes. Eukaryotic cells harbor 2 protein synthesis systems: one localized in the cytoplasm, the other in the mitochondria. Most factors regulating mitochondrial protein synthesis are encoded by nuclear genes, translated in the cytoplasm, and then transported to the mitochondria. The eukaryotic system of elongation factor (EF) components is more complex than that in prokaryotes, with both cytoplasmic and mitochondrial elongation factors and multiple isoforms being expressed in certain species. Eukaryotic EF-2 operates in the cytosolic protein synthesis machinery of eukaryotes, EF-Gs in protein synthesis in bacteria. Eukaryotic mtEFG1 proteins show significant homology to bacterial EF-Gs. No clear phenotype has been found for mutants in the yeast homologue of mtEFG2, MEF2. There are two forms of mtEFG present in mammals (designated mtEFG1s and mtEFG2s) mtEFG1s are n
Probab=28.34 E-value=1.9e+02 Score=19.52 Aligned_cols=15 Identities=13% Similarity=0.105 Sum_probs=11.6
Q ss_pred CCCCCCCCCEEEEee
Q 031480 114 PCFRVKEGDHVIIGQ 128 (159)
Q Consensus 114 p~~~~kvGD~V~I~e 128 (159)
|..++..||+|.|.-
T Consensus 57 ~v~~~~aGdI~~i~g 71 (83)
T cd04092 57 EIPSLSAGNIGVITG 71 (83)
T ss_pred ECCeeCCCCEEEEEC
Confidence 445799999998853
No 42
>cd03689 RF3_II RF3_II: this subfamily represents the domain II of bacterial Release Factor 3 (RF3). Termination of protein synthesis by the ribosome requires two release factor (RF) classes. The class II RF3 is a GTPase that removes class I RFs (RF1 or RF2) from the ribosome after release of the nascent polypeptide. RF3 in the GDP state binds to the ribosomal class I RF complex, followed by an exchange of GDP for GTP and release of the class I RF. Sequence comparison of class II release factors with elongation factors shows that prokaryotic RF3 is more similar to EF-G whereas eukaryotic eRF3 is more similar to eEF1A, implying that their precise function may differ.
Probab=28.24 E-value=1.8e+02 Score=20.25 Aligned_cols=14 Identities=14% Similarity=0.033 Sum_probs=11.3
Q ss_pred CCCCCCCCEEEEee
Q 031480 115 CFRVKEGDHVIIGQ 128 (159)
Q Consensus 115 ~~~~kvGD~V~I~e 128 (159)
..++..||+|.+.-
T Consensus 59 v~~a~aGdIv~v~g 72 (85)
T cd03689 59 VDEAYPGDIIGLVN 72 (85)
T ss_pred cCEECCCCEEEEEC
Confidence 45689999999865
No 43
>cd04466 S1_YloQ_GTPase S1_YloQ_GTPase: YloQ GTase family (also known as YjeQ and CpgA), S1-like RNA-binding domain. Proteins in the YloQ GTase family bind the ribosome and have GTPase activity. The precise role of this family is unknown. The protein structure is composed of three domains: an N-terminal S1 domain, a central GTPase domain, and a C-terminal zinc finger domain. This N-terminal S1 domain binds ssRNA. The central GTPase domain contains nucleotide-binding signature motifs: G1 (walker A), G3 (walker B) and G4 motifs. Experiments show that the bacterial YloQ and YjeQ proteins have low intrinsic GTPase activity. The C-terminal zinc-finger domain has structural similarity to a portion of the DNA-repair protein Rad51. This suggests a possible role for this GTPase as a regulator of translation, perhaps as a translation initiation factor. This family is classified based on the N-terminal S1 domain.
Probab=27.91 E-value=81 Score=20.36 Aligned_cols=28 Identities=14% Similarity=0.064 Sum_probs=18.5
Q ss_pred CCCCCCCEEEEeeeecCCCeeeEEEEEEeecC
Q 031480 116 FRVKEGDHVIIGQCRPLSKTVRFNVLKVIPAG 147 (159)
Q Consensus 116 ~~~kvGD~V~I~ecRPLSKtK~f~V~~Ii~~~ 147 (159)
...-+||+|.+.. .. .-.+.+.+++++.
T Consensus 36 ~~~~VGD~V~~~~---~~-~~~~~I~~vl~R~ 63 (68)
T cd04466 36 NPPAVGDRVEFEP---ED-DGEGVIEEILPRK 63 (68)
T ss_pred CCCCCCcEEEEEE---CC-CCcEEEEEEeccc
Confidence 3478999999852 11 2346777888763
No 44
>PF01176 eIF-1a: Translation initiation factor 1A / IF-1; InterPro: IPR006196 The S1 domain of around 70 amino acids, originally identified in ribosomal protein S1, is found in a large number of RNA-associated proteins. It has been shown that S1 proteins bind RNA through their S1 domains with some degree of sequence specificity. This type of S1 domain is found in translation initiation factor 1. The solution structure of one S1 RNA-binding domain from Escherichia coli polynucleotide phosphorylase has been determined []. It displays some similarity with the cold shock domain (CSD) (IPR002059 from INTERPRO). Both the S1 and the CSD domain consist of an antiparallel beta barrel of the same topology with 5 beta strands. This fold is also shared by many other proteins of unrelated function and is known as the OB fold. However, the S1 and CSD fold can be distinguished from the other OB folds by the presence of a short 3(10) helix at the end of strand 3. This unique feature is likely to form a part of the DNA/RNA-binding site. This entry is specific for bacterial, chloroplastic and eukaryotic IF-1 type S1 domains.; GO: 0003723 RNA binding, 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 1JT8_A 3I4O_A 1AH9_A 1ZO1_W 1D7Q_A 2OQK_A 2DGY_A 1HR0_W.
Probab=27.63 E-value=1.2e+02 Score=20.29 Aligned_cols=52 Identities=21% Similarity=0.238 Sum_probs=28.2
Q ss_pred EEEEEEecCCCCeEEEEEeEEEeeeeeeeEEeeeeeEEEEcCC----CCCCCCCCEEEEeeeecCCCeee
Q 031480 72 LAGTCHSAKMNRTIIVRRNYLHFVKKYQRYEKRHSNIPAHISP----CFRVKEGDHVIIGQCRPLSKTVR 137 (159)
Q Consensus 72 l~G~VvS~KM~KTvvV~v~~~~~~pKY~K~~kr~kk~~vHd~p----~~~~kvGD~V~I~ecRPLSKtK~ 137 (159)
..|+|+..-.+....|..+ --..+.||.|. ..-++.||.|.+.. +|..+++-
T Consensus 5 ~~~~V~~~lG~~~~~V~~~-------------dg~~~l~~i~gK~r~~iwI~~GD~V~V~~-~~~d~~kG 60 (65)
T PF01176_consen 5 VIGRVTEMLGNNLFEVECE-------------DGEERLARIPGKFRKRIWIKRGDFVLVEP-SPYDKVKG 60 (65)
T ss_dssp EEEEEEEEESSSEEEEEET-------------TSEEEEEEE-HHHHTCC---TTEEEEEEE-STTCTTEE
T ss_pred EEEEEEEECCCCEEEEEeC-------------CCCEEEEEeccceeeeEecCCCCEEEEEe-cccCCCeE
Confidence 4677777766666666521 12233344421 12488999998854 77776654
No 45
>PF06107 DUF951: Bacterial protein of unknown function (DUF951); InterPro: IPR009296 This family consists of several short hypothetical bacterial proteins of unknown function.
Probab=27.41 E-value=84 Score=21.59 Aligned_cols=25 Identities=16% Similarity=0.392 Sum_probs=20.7
Q ss_pred CCCCCEEEEeeeecCCCeeeEEEEEE
Q 031480 118 VKEGDHVIIGQCRPLSKTVRFNVLKV 143 (159)
Q Consensus 118 ~kvGD~V~I~ecRPLSKtK~f~V~~I 143 (159)
..+||+|....-.|= -+..|.|+++
T Consensus 2 ~~vgDiV~mKK~HPC-G~~~Wei~R~ 26 (57)
T PF06107_consen 2 YEVGDIVEMKKPHPC-GSNEWEIIRI 26 (57)
T ss_pred ccCCCEEEEcCCCCC-CCCEEEEEEc
Confidence 578999999988884 4588998876
No 46
>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=27.28 E-value=70 Score=22.06 Aligned_cols=29 Identities=28% Similarity=0.347 Sum_probs=20.3
Q ss_pred EEcCCCCCCCCCCEEEEeeeecCCCeeeE
Q 031480 110 AHISPCFRVKEGDHVIIGQCRPLSKTVRF 138 (159)
Q Consensus 110 vHd~p~~~~kvGD~V~I~ecRPLSKtK~f 138 (159)
+.+|+...+.+||.|++.-.-+.+.+..+
T Consensus 7 ~F~P~~i~v~~GdtVt~~N~d~~~Hnv~~ 35 (83)
T TIGR02657 7 KYETPELHVKVGDTVTWINREAMPHNVHF 35 (83)
T ss_pred EEcCCEEEECCCCEEEEEECCCCCccEEe
Confidence 45556667999999999766555555543
No 47
>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=27.11 E-value=41 Score=21.34 Aligned_cols=23 Identities=17% Similarity=0.076 Sum_probs=14.8
Q ss_pred eeeEEEEcCCCCCCCCCCEEEEe
Q 031480 105 HSNIPAHISPCFRVKEGDHVIIG 127 (159)
Q Consensus 105 ~kk~~vHd~p~~~~kvGD~V~I~ 127 (159)
...|.+-++....++.||+|.|.
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 34455555555679999999997
No 48
>cd00174 SH3 Src homology 3 domains; SH3 domains bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs; they play a role in the regulation of enzymes by intramolecular interactions, changing the subcellular localization of signal pathway components and mediate multiprotein complex assemblies.
Probab=25.61 E-value=68 Score=18.79 Aligned_cols=21 Identities=19% Similarity=0.139 Sum_probs=14.7
Q ss_pred EEEcCCCCCCCCCCEEEEeee
Q 031480 109 PAHISPCFRVKEGDHVIIGQC 129 (159)
Q Consensus 109 ~vHd~p~~~~kvGD~V~I~ec 129 (159)
.++++....+..||.|.+.+.
T Consensus 9 ~~~~~~~l~~~~Gd~v~v~~~ 29 (54)
T cd00174 9 DARDPDELSFKKGDIIEVLEK 29 (54)
T ss_pred CCCCCCCCCCCCCCEEEEEEc
Confidence 334433456899999999876
No 49
>PLN00208 translation initiation factor (eIF); Provisional
Probab=25.00 E-value=3.6e+02 Score=21.60 Aligned_cols=58 Identities=16% Similarity=0.054 Sum_probs=35.6
Q ss_pred EEEEEEecCCCCeEEEEEeEEEeeeeeeeEEeeeeeEEEEcCCCC----CCCCCCEEEEeeeecCCCeeeEEEEEE
Q 031480 72 LAGTCHSAKMNRTIIVRRNYLHFVKKYQRYEKRHSNIPAHISPCF----RVKEGDHVIIGQCRPLSKTVRFNVLKV 143 (159)
Q Consensus 72 l~G~VvS~KM~KTvvV~v~~~~~~pKY~K~~kr~kk~~vHd~p~~----~~kvGD~V~I~ecRPLSKtK~f~V~~I 143 (159)
..|+|++...+..+.|...- -...+||.|-.+ -+++||+|+|. -+|-.++|.=++...
T Consensus 34 ~~g~V~~~lGn~~~~V~c~d-------------G~~rLa~IpGKmRKrIWI~~GD~VlVe-l~~~d~~KgdIv~ry 95 (145)
T PLN00208 34 EYAQVLRMLGNGRCEALCID-------------GTKRLCHIRGKMRKKVWIAAGDIILVG-LRDYQDDKADVILKY 95 (145)
T ss_pred EEEEEEEEcCCCEEEEEECC-------------CCEEEEEEeccceeeEEecCCCEEEEE-ccCCCCCEEEEEEEc
Confidence 56888888777777766221 122233332111 27889999996 788887776555544
No 50
>cd05789 S1_Rrp4 S1_Rrp4: Rrp4 S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Rrp4 protein is a subunit of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In Saccharomyces cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".
Probab=24.94 E-value=2.2e+02 Score=19.15 Aligned_cols=22 Identities=18% Similarity=0.173 Sum_probs=16.5
Q ss_pred eceEEEEEEEecCCCCeEEEEEe
Q 031480 68 RGRILAGTCHSAKMNRTIIVRRN 90 (159)
Q Consensus 68 rg~il~G~VvS~KM~KTvvV~v~ 90 (159)
.|.+..|.|++. ++..+.|...
T Consensus 6 ~GdiV~g~V~~i-~~~g~~v~i~ 27 (86)
T cd05789 6 VGDVVIGRVTEV-GFKRWKVDIN 27 (86)
T ss_pred CCCEEEEEEEEE-CCCEEEEECC
Confidence 588999999985 4566777654
No 51
>PRK01777 hypothetical protein; Validated
Probab=24.22 E-value=80 Score=23.21 Aligned_cols=18 Identities=39% Similarity=0.523 Sum_probs=14.3
Q ss_pred CCCCCCCCCEEEEeeeecCC
Q 031480 114 PCFRVKEGDHVIIGQCRPLS 133 (159)
Q Consensus 114 p~~~~kvGD~V~I~ecRPLS 133 (159)
....++.||.|.| .|||.
T Consensus 61 ~d~~L~dGDRVeI--yrPL~ 78 (95)
T PRK01777 61 LTDVLRDGDRVEI--YRPLL 78 (95)
T ss_pred CCCcCCCCCEEEE--ecCCC
Confidence 4457999999998 57775
No 52
>cd05698 S1_Rrp5_repeat_hs6_sc5 S1_Rrp5_repeat_hs6_sc5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 6 (hs6) and S. cerevisiae S1 repeat 5 (sc5). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=23.74 E-value=1.9e+02 Score=18.48 Aligned_cols=58 Identities=21% Similarity=0.208 Sum_probs=31.2
Q ss_pred ceEEEEEEEecCCCCeEEEEEeEEEeeeeeeeEEeeeeeE---EEEcCCCCCCCCCCEEEEe--eeecCCC
Q 031480 69 GRILAGTCHSAKMNRTIIVRRNYLHFVKKYQRYEKRHSNI---PAHISPCFRVKEGDHVIIG--QCRPLSK 134 (159)
Q Consensus 69 g~il~G~VvS~KM~KTvvV~v~~~~~~pKY~K~~kr~kk~---~vHd~p~~~~kvGD~V~I~--ecRPLSK 134 (159)
|.++.|.|++.. +..+.|....- -.-++.. +.+ .+++ |....++||.|.+. +.-|-++
T Consensus 1 g~~~~g~V~~v~-~~G~~V~l~~~-----~~gli~~-s~l~~~~~~~-~~~~~~~G~~i~v~v~~~d~~~~ 63 (70)
T cd05698 1 GLKTHGTIVKVK-PNGCIVSFYNN-----VKGFLPK-SELSEAFIKD-PEEHFRVGQVVKVKVLSCDPEQQ 63 (70)
T ss_pred CCEEEEEEEEEe-cCcEEEEECCC-----CEEEEEH-HHcChhhcCC-HHHcccCCCEEEEEEEEEcCCCC
Confidence 567889988764 56777775321 1111111 111 1333 44568999988764 3444433
No 53
>PF11302 DUF3104: Protein of unknown function (DUF3104); InterPro: IPR021453 This family of proteins with unknown function appears to be restricted to Cyanobacteria.
Probab=23.35 E-value=1.5e+02 Score=21.35 Aligned_cols=31 Identities=26% Similarity=0.303 Sum_probs=24.1
Q ss_pred CCCCCCEEEEeeeec--CCCeeeEEEEEEeecC
Q 031480 117 RVKEGDHVIIGQCRP--LSKTVRFNVLKVIPAG 147 (159)
Q Consensus 117 ~~kvGD~V~I~ecRP--LSKtK~f~V~~Ii~~~ 147 (159)
.++.||.|.+....- .+..+.|-+-.|+...
T Consensus 5 ~Vk~Gd~ViV~~~~~~~~~~~~dWWmg~Vi~~~ 37 (75)
T PF11302_consen 5 SVKPGDTVIVQDEQEVGQKQDKDWWMGQVIHCE 37 (75)
T ss_pred ccCCCCEEEEecCccccccCCCCcEEEEEEEEe
Confidence 589999999988752 3456789888888764
No 54
>cd05752 Ig1_FcgammaR_like Frst immunoglobulin (Ig)-like domain of Fcgamma-receptors (FcgammaRs) and similar proteins. Ig1_FcgammaR_like: domain similar to the first immunoglobulin (Ig)-like domain of Fcgamma-receptors (FcgammaRs). Interactions between IgG and FcgammaR are important to the initiation of cellular and humoral response. IgG binding to FcgammaR leads to a cascade of signals and ultimately to functions such as antibody-dependent-cellular-cytotoxicity (ADCC), endocytosis, phagocytosis, release of inflammatory mediators, etc. FcgammaR has two Ig-like domains. This group also contains FcepsilonRI, which binds IgE with high affinity.
Probab=22.56 E-value=1e+02 Score=20.98 Aligned_cols=27 Identities=19% Similarity=0.524 Sum_probs=19.0
Q ss_pred CCCCCCCCCCEEEEeeee----cCCCeeeEEE
Q 031480 113 SPCFRVKEGDHVIIGQCR----PLSKTVRFNV 140 (159)
Q Consensus 113 ~p~~~~kvGD~V~I~ecR----PLSKtK~f~V 140 (159)
|+...+.+||.|++ .|. |......|.-
T Consensus 7 P~~~~v~~G~~V~L-~C~~~~~p~~~~~~W~k 37 (78)
T cd05752 7 PPWTTIFQGEKVTL-TCNGFNSPEQNSTQWYH 37 (78)
T ss_pred CCCeEeeCCCCEEE-EEeCCCCCCCccEEEEE
Confidence 34457999999999 686 5545567744
No 55
>TIGR00483 EF-1_alpha translation elongation factor EF-1 alpha. This model represents the counterpart of bacterial EF-Tu for the Archaea (aEF-1 alpha) and Eukaryotes (eEF-1 alpha). The trusted cutoff is set fairly high so that incomplete sequences will score between suggested and trusted cutoff levels.
Probab=22.15 E-value=2e+02 Score=25.63 Aligned_cols=49 Identities=14% Similarity=0.241 Sum_probs=31.2
Q ss_pred ceEEEEEEEec--CCCCeEEEEEeEEEeeeeeeeEEeeeeeEEEEcCCCCCCCCCCEEEE
Q 031480 69 GRILAGTCHSA--KMNRTIIVRRNYLHFVKKYQRYEKRHSNIPAHISPCFRVKEGDHVII 126 (159)
Q Consensus 69 g~il~G~VvS~--KM~KTvvV~v~~~~~~pKY~K~~kr~kk~~vHd~p~~~~kvGD~V~I 126 (159)
|.+..|+|.+- +..-++.+. |- .....-+.+.+|+.+...+..||.|.|
T Consensus 242 G~vv~G~v~~G~i~~gd~v~i~-------P~--~~~~~VksI~~~~~~~~~a~aG~~v~i 292 (426)
T TIGR00483 242 GTVPVGRVETGVLKPGDKVVFE-------PA--GVSGEVKSIEMHHEQIEQAEPGDNIGF 292 (426)
T ss_pred eEEEEEEEccceeecCCEEEEC-------CC--CcEEEEEEEEECCcccCEEcCCCEEEE
Confidence 55677777764 333444443 21 123456777888877778999999877
No 56
>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=21.95 E-value=1.4e+02 Score=17.47 Aligned_cols=19 Identities=16% Similarity=0.146 Sum_probs=14.1
Q ss_pred cCCCCCCCCCCEEEEeeee
Q 031480 112 ISPCFRVKEGDHVIIGQCR 130 (159)
Q Consensus 112 d~p~~~~kvGD~V~I~ecR 130 (159)
.+....++.||.|.+.+..
T Consensus 15 ~~~~l~~~~Gd~v~v~~~~ 33 (58)
T smart00326 15 DPDELSFKKGDIITVLEKS 33 (58)
T ss_pred CCCCCCCCCCCEEEEEEcC
Confidence 3345579999999998664
No 57
>PF03658 Ub-RnfH: RnfH family Ubiquitin; InterPro: IPR005346 This is a small family of proteins of unknown function.; PDB: 2HJ1_B.
Probab=21.84 E-value=63 Score=23.56 Aligned_cols=18 Identities=39% Similarity=0.582 Sum_probs=8.7
Q ss_pred CCCCCCCCCEEEEeeeecCC
Q 031480 114 PCFRVKEGDHVIIGQCRPLS 133 (159)
Q Consensus 114 p~~~~kvGD~V~I~ecRPLS 133 (159)
+...++.||.|.| .|||.
T Consensus 58 ~d~~L~~GDRVEI--YRPL~ 75 (84)
T PF03658_consen 58 LDTVLRDGDRVEI--YRPLT 75 (84)
T ss_dssp TT-B--TT-EEEE--E-S--
T ss_pred CCCcCCCCCEEEE--eccCc
Confidence 3456999999998 68885
No 58
>KOG1698 consensus Mitochondrial/chloroplast ribosomal protein L19 [Translation, ribosomal structure and biogenesis]
Probab=21.68 E-value=1.6e+02 Score=24.97 Aligned_cols=46 Identities=20% Similarity=0.190 Sum_probs=33.1
Q ss_pred EEEEcCCCCCCCCCCEEEEeeeecCCCeeeEEEEEEeecCCCCCccccc
Q 031480 108 IPAHISPCFRVKEGDHVIIGQCRPLSKTVRFNVLKVIPAGSSGGAKKAF 156 (159)
Q Consensus 108 ~~vHd~p~~~~kvGD~V~I~ecRPLSKtK~f~V~~Ii~~~~~~~~~k~f 156 (159)
++-|. | +.++||+|.|..--|-++.+-++...|.=+-..+|-.-+|
T Consensus 90 ~~r~i-P--e~~~G~Iv~V~s~~p~~k~k~s~f~Gi~I~R~~~Gl~atf 135 (201)
T KOG1698|consen 90 KVRDI-P--EFKVGSIVRVTSEDPENKRKVSRFKGICIRRRNAGLNATF 135 (201)
T ss_pred hcccC-C--ccccccEEEEEecCCccCCceeEEEEEEEEecccCCcceE
Confidence 34454 4 8999999999999999999999988885443333333333
No 59
>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=20.06 E-value=63 Score=23.01 Aligned_cols=14 Identities=29% Similarity=0.456 Sum_probs=11.4
Q ss_pred CCCCCCEEEEeeee
Q 031480 117 RVKEGDHVIIGQCR 130 (159)
Q Consensus 117 ~~kvGD~V~I~ecR 130 (159)
.+++||++.+.||-
T Consensus 49 PVr~GDil~LlEtE 62 (69)
T PF01200_consen 49 PVREGDILTLLETE 62 (69)
T ss_dssp TTSTT-EEEESSSS
T ss_pred CcccCcEEEEeehh
Confidence 49999999999983
No 60
>PRK05807 hypothetical protein; Provisional
Probab=20.04 E-value=3.6e+02 Score=20.66 Aligned_cols=60 Identities=22% Similarity=0.208 Sum_probs=35.7
Q ss_pred ceEEEEEEEecCCCCeEEEEEeEEEeeeeeeeEEeeeeeEEEEcCC---------CCCCCCCCEEEEe--eeecCCCeee
Q 031480 69 GRILAGTCHSAKMNRTIIVRRNYLHFVKKYQRYEKRHSNIPAHISP---------CFRVKEGDHVIIG--QCRPLSKTVR 137 (159)
Q Consensus 69 g~il~G~VvS~KM~KTvvV~v~~~~~~pKY~K~~kr~kk~~vHd~p---------~~~~kvGD~V~I~--ecRPLSKtK~ 137 (159)
|.++.|+|+.... --+-|..+.. .-++|.++ ....++||.|.+. +..+ .....
T Consensus 6 G~vv~G~Vt~i~~-~GafV~L~~~--------------~Glvhiseis~~~v~~~~~~~kvGd~V~VkV~~id~-~gkI~ 69 (136)
T PRK05807 6 GSILEGTVVNITN-FGAFVEVEGK--------------TGLVHISEVADTYVKDIREHLKEQDKVKVKVISIDD-NGKIS 69 (136)
T ss_pred CCEEEEEEEEEEC-CeEEEEECCE--------------EEEEEhhhcccccccCccccCCCCCEEEEEEEEECC-CCcEE
Confidence 7899999988653 4455554311 23333322 3457999998754 3445 45666
Q ss_pred EEEEEEe
Q 031480 138 FNVLKVI 144 (159)
Q Consensus 138 f~V~~Ii 144 (159)
+.+..+.
T Consensus 70 LSlk~~~ 76 (136)
T PRK05807 70 LSIKQAM 76 (136)
T ss_pred EEEEecc
Confidence 6666654
No 61
>cd05687 S1_RPS1_repeat_ec1_hs1 S1_RPS1_repeat_ec1_hs1: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 1 of the Escherichia coli and Homo sapiens RPS1 (ec1 and hs1, respectively). Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=20.03 E-value=2.4e+02 Score=18.09 Aligned_cols=53 Identities=26% Similarity=0.248 Sum_probs=27.3
Q ss_pred ceEEEEEEEecCCCCeEEEEEeEEEeeeeeeeEEeeeeeEEEEc-CCCCCCCCCCEEEEe
Q 031480 69 GRILAGTCHSAKMNRTIIVRRNYLHFVKKYQRYEKRHSNIPAHI-SPCFRVKEGDHVIIG 127 (159)
Q Consensus 69 g~il~G~VvS~KM~KTvvV~v~~~~~~pKY~K~~kr~kk~~vHd-~p~~~~kvGD~V~I~ 127 (159)
|.+..|.|++.. +.-+.|.... .+.-++....--.-.. .+....++||+|.+.
T Consensus 1 G~iv~g~V~~i~-~~~~~v~l~~-----~~~g~l~~~e~~~~~~~~~~~~~~~Gd~i~~~ 54 (70)
T cd05687 1 GDIVKGTVVSVD-DDEVLVDIGY-----KSEGIIPISEFSDDPIENGEDEVKVGDEVEVY 54 (70)
T ss_pred CCEEEEEEEEEe-CCEEEEEeCC-----CceEEEEHHHhCccccCCHhHcCCCCCEEEEE
Confidence 567899998875 4567776532 1111221110000000 023348999998764
Done!