Query 032281
Match_columns 144
No_of_seqs 219 out of 1230
Neff 4.6
Searched_HMMs 46136
Date Fri Mar 29 12:01:25 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/032281.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/032281hhsearch_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 6.6E-70 1.4E-74 425.4 14.6 144 1-144 2-158 (158)
2 KOG1728 40S ribosomal protein 100.0 1E-66 2.2E-71 401.6 6.1 141 1-144 2-156 (156)
3 PRK08572 rps17p 30S ribosomal 100.0 1.4E-52 3E-57 311.1 13.7 107 22-132 1-107 (108)
4 TIGR03630 arch_S17P archaeal r 100.0 8E-50 1.7E-54 293.7 13.3 102 24-129 1-102 (102)
5 COG0186 RpsQ Ribosomal protein 100.0 1.5E-39 3.2E-44 233.4 11.0 85 47-132 1-85 (87)
6 CHL00142 rps17 ribosomal prote 100.0 1E-34 2.2E-39 207.1 11.9 79 54-133 3-81 (84)
7 PRK05610 rpsQ 30S ribosomal pr 100.0 1E-34 2.3E-39 206.9 11.5 78 54-132 6-83 (84)
8 TIGR03635 S17_bact 30S ribosom 100.0 1.2E-33 2.7E-38 195.8 9.9 70 55-125 2-71 (71)
9 PF00366 Ribosomal_S17: Riboso 100.0 1.6E-31 3.5E-36 183.9 10.3 69 59-128 1-69 (69)
10 KOG1740 Predicted mitochondria 99.9 1E-28 2.2E-33 181.7 -0.3 77 55-132 3-79 (107)
11 KOG3447 Mitochondrial/chloropl 99.2 1.3E-12 2.9E-17 101.0 0.9 81 50-131 6-87 (150)
12 cd03698 eRF3_II_like eRF3_II_l 68.3 19 0.00041 24.4 5.3 25 88-112 42-66 (83)
13 KOG3416 Predicted nucleic acid 64.2 29 0.00063 27.1 6.1 49 55-112 23-71 (134)
14 PF10844 DUF2577: Protein of u 61.9 56 0.0012 23.4 7.6 23 102-127 76-98 (100)
15 cd05793 S1_IF1A S1_IF1A: Trans 61.5 35 0.00077 23.7 5.7 53 57-123 2-58 (77)
16 cd04456 S1_IF1A_like S1_IF1A_l 58.0 47 0.001 23.1 5.8 53 57-123 2-59 (78)
17 cd03695 CysN_NodQ_II CysN_NodQ 57.1 40 0.00086 22.9 5.3 26 87-112 41-66 (81)
18 cd03693 EF1_alpha_II EF1_alpha 56.3 34 0.00073 23.6 4.9 26 87-112 45-70 (91)
19 COG0361 InfA Translation initi 56.3 54 0.0012 23.1 5.9 49 56-118 8-61 (75)
20 TIGR00523 eIF-1A eukaryotic/ar 55.0 81 0.0017 23.0 7.1 49 56-118 20-72 (99)
21 smart00652 eIF1a eukaryotic tr 54.9 56 0.0012 23.0 5.9 53 57-123 7-63 (83)
22 PF09740 DUF2043: Uncharacteri 54.7 4.4 9.5E-05 30.6 0.2 13 41-53 87-99 (110)
23 TIGR00008 infA translation ini 53.9 70 0.0015 22.0 6.2 52 56-121 6-62 (68)
24 cd03697 EFTU_II EFTU_II: Elong 52.1 45 0.00098 22.7 5.0 53 53-112 14-68 (87)
25 cd03696 selB_II selB_II: this 48.0 81 0.0018 21.1 5.7 26 87-112 41-66 (83)
26 cd03694 GTPBP_II Domain II of 46.0 48 0.001 22.7 4.3 26 87-112 45-70 (87)
27 cd04089 eRF3_II eRF3_II: domai 41.4 1.1E+02 0.0023 20.6 6.0 25 88-112 41-65 (82)
28 CHL00071 tufA elongation facto 41.2 1.1E+02 0.0025 26.7 6.9 25 88-112 264-288 (409)
29 TIGR03595 Obg_CgtA_exten Obg f 40.9 19 0.00042 24.3 1.7 13 102-114 53-65 (69)
30 PF13550 Phage-tail_3: Putativ 40.7 66 0.0014 23.5 4.6 40 86-129 124-163 (164)
31 PRK04012 translation initiatio 40.4 1.3E+02 0.0029 22.0 6.1 53 56-122 22-78 (100)
32 cd03689 RF3_II RF3_II: this su 40.1 1E+02 0.0022 21.1 5.3 14 100-113 59-72 (85)
33 COG1786 Swiveling domain assoc 39.4 20 0.00043 27.9 1.7 21 37-58 35-55 (131)
34 cd01342 Translation_Factor_II_ 35.9 1E+02 0.0022 18.7 5.5 22 92-113 48-69 (83)
35 PTZ00329 eukaryotic translatio 35.9 2.2E+02 0.0049 22.6 7.2 58 57-128 34-95 (155)
36 PRK12442 translation initiatio 35.3 1.5E+02 0.0032 21.5 5.5 61 56-130 8-73 (87)
37 KOG1730 Thioredoxin-like prote 34.7 26 0.00057 29.0 1.8 18 43-60 74-91 (206)
38 PF09269 DUF1967: Domain of un 34.6 19 0.0004 24.4 0.8 12 102-113 53-64 (69)
39 PF10915 DUF2709: Protein of u 33.9 19 0.00042 30.1 0.9 25 23-50 70-96 (238)
40 PRK12736 elongation factor Tu; 30.6 1.8E+02 0.0039 25.3 6.4 23 89-111 255-277 (394)
41 PF07653 SH3_2: Variant SH3 do 30.1 34 0.00074 21.3 1.4 23 90-112 5-27 (55)
42 PF04246 RseC_MucC: Positive r 30.1 59 0.0013 24.0 2.9 19 93-113 44-62 (135)
43 PF06107 DUF951: Bacterial pro 30.0 72 0.0016 21.5 3.0 25 103-128 2-26 (57)
44 cd04092 mtEFG2_II_like mtEFG2_ 30.0 1.7E+02 0.0037 19.4 5.5 15 99-113 57-71 (83)
45 PF11302 DUF3104: Protein of u 29.1 1.1E+02 0.0024 21.7 3.9 32 101-132 4-37 (75)
46 cd00174 SH3 Src homology 3 dom 28.6 56 0.0012 18.8 2.1 21 94-114 9-29 (54)
47 cd04466 S1_YloQ_GTPase S1_YloQ 27.1 87 0.0019 19.8 3.0 28 101-132 36-63 (68)
48 cd05789 S1_Rrp4 S1_Rrp4: Rrp4 27.0 1.9E+02 0.0042 19.1 5.2 22 53-75 6-27 (86)
49 PRK06763 F0F1 ATP synthase sub 25.9 1.7E+02 0.0036 24.6 5.1 45 55-112 40-84 (213)
50 TIGR02657 amicyanin amicyanin. 25.7 81 0.0018 21.3 2.8 29 95-123 7-35 (83)
51 PRK05807 hypothetical protein; 24.9 2.7E+02 0.0058 21.0 5.7 60 54-129 6-76 (136)
52 TIGR00483 EF-1_alpha translati 24.4 1.7E+02 0.0038 25.5 5.2 49 54-111 242-292 (426)
53 smart00326 SH3 Src homology 3 24.3 1.3E+02 0.0027 17.4 3.2 19 97-115 15-33 (58)
54 PF01176 eIF-1a: Translation i 23.9 2E+02 0.0042 18.9 4.3 52 57-122 5-60 (65)
55 cd06827 PLPDE_III_AR_proteobac 23.7 2.1E+02 0.0046 24.6 5.6 12 101-112 310-321 (354)
56 cd04451 S1_IF1 S1_IF1: Transla 23.3 2.1E+02 0.0046 18.3 6.3 49 56-112 2-50 (64)
57 PRK09521 exosome complex RNA-b 23.0 1.2E+02 0.0027 23.7 3.7 66 45-112 54-128 (189)
58 COG2012 RPB5 DNA-directed RNA 22.9 1.1E+02 0.0025 21.9 3.1 22 92-114 42-66 (80)
59 cd05698 S1_Rrp5_repeat_hs6_sc5 22.8 1.8E+02 0.0039 18.3 3.9 58 54-119 1-63 (70)
60 PF02887 PK_C: Pyruvate kinase 22.4 1.5E+02 0.0032 21.1 3.7 30 101-130 88-117 (117)
61 PLN00043 elongation factor 1-a 22.3 1.5E+02 0.0032 26.6 4.5 50 54-112 248-299 (447)
62 PF01200 Ribosomal_S28e: Ribos 22.0 53 0.0012 22.9 1.2 14 102-115 49-62 (69)
63 KOG1698 Mitochondrial/chloropl 21.3 1.7E+02 0.0037 24.3 4.2 36 93-131 90-125 (201)
64 PRK01678 rpmE2 50S ribosomal p 20.5 2.8E+02 0.006 20.0 4.8 33 80-124 6-38 (87)
No 1
>PTZ00241 40S ribosomal protein S11; Provisional
Probab=100.00 E-value=6.6e-70 Score=425.44 Aligned_cols=144 Identities=69% Similarity=1.142 Sum_probs=134.0
Q ss_pred CchhhhHhhccCC----------CCC---CCeeeeeecccccCCcccccccccCcCCCceeeeeEeceEEEEEEEecCCC
Q 032281 1 MAEQTEKAFLKQP----------GKG---GNRFWKSIGLGFKTPREAIEGTYIDKKCPFTGTVSIRGRILAGTCHSAKMN 67 (144)
Q Consensus 1 m~~~~~~a~~kq~----------~~~---~~r~~~~igl~~k~P~~~~~~~y~D~kcPf~g~~sirg~il~G~VvS~KM~ 67 (144)
|++|+|||||||+ +++ .+||++||||||++|++||||+|||++|||||||||||++|+|+|+|+||+
T Consensus 2 ~~~q~e~a~qkq~~i~~~~~~~~~~~~~~~~r~~k~iGl~~~~P~~~~~~~yiD~kCPf~G~~~iRgril~G~VvS~KM~ 81 (158)
T PTZ00241 2 ADVQTERAFQKQEGVFQNSKRLLKKKTSKGVRYWKKVGLGFKTPKEAIEGKYIDKKCPFTGNVSIRGRILRGVVISTKMK 81 (158)
T ss_pred ccccchhhhccCCceeeccccccccccccccchhhhcCCCCcCChhhhcccccCCCCCccceeeEcceEEEEEEEEccCC
Confidence 3459999999994 222 379999999999999999999999999999999999999999999999999
Q ss_pred CeEEEEEeEEEeeceeeeEEeeeeeEEEEcCCCCCCCCCCEEEEeeeecCCCeeeEEEEEeeecCCCCCcccccccC
Q 032281 68 RTIIVRRNYLHFVKKYQRYEKRHSNIPAHISPCFRVKEGDHVIIGQCRPLSKTVRFNVLKVIPAGSSGGAKKAFTAM 144 (144)
Q Consensus 68 KTvvV~v~~~~~~pkY~K~~kr~kk~~vHd~p~~~~kvGD~V~I~ecRPlSKtK~f~V~~ii~~~~~~~~~k~f~~f 144 (144)
|||+|+++|++|||+|+||++|+++|+|||||||+|++||+|+|+|||||||||+|+|++|++++..++.+|||++|
T Consensus 82 KTIVV~ve~~~~h~kY~K~~kr~kk~~aHd~~~~~~kvGD~V~I~EcRPLSKTKrf~Vv~V~~~~~~~~~~k~f~~f 158 (158)
T PTZ00241 82 RTIIIRRDYLHYVKKYNRYEKRHKNIPVHCSPCFDVKEGDIVVVGQCRPLSKTVRFNVLKVEKNEIIGNVRKQFVLF 158 (158)
T ss_pred ccEEEEEEEEEecCccceEEEeeecEEEeCCccCCCCCCCEEEEEEcCCCCCceeEEEEEEEecccccccccccccC
Confidence 99999999999999999999999999999989999999999999999999999999999999976333359999988
No 2
>KOG1728 consensus 40S ribosomal protein S11 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1e-66 Score=401.62 Aligned_cols=141 Identities=72% Similarity=1.207 Sum_probs=135.5
Q ss_pred CchhhhHhhccCC-------------CCCCCeeeeeecccccCCcccccccccCcCCCceeeeeEeceEEEEEEEecCCC
Q 032281 1 MAEQTEKAFLKQP-------------GKGGNRFWKSIGLGFKTPREAIEGTYIDKKCPFTGTVSIRGRILAGTCHSAKMN 67 (144)
Q Consensus 1 m~~~~~~a~~kq~-------------~~~~~r~~~~igl~~k~P~~~~~~~y~D~kcPf~g~~sirg~il~G~VvS~KM~ 67 (144)
|++|+|+|||+|+ +++.+||++|||||||||+||++|+|||+||||+|+|||||++|+|+|+++||+
T Consensus 2 ~~vq~eraF~kq~~v~~~~k~~~~~~~k~~~r~~~~iglGFKtP~eAiegtYIDKKCPftG~vsIRGril~G~V~k~Km~ 81 (156)
T KOG1728|consen 2 MAVQTERAFQKQPGVFLNAKASGKRTSKKGKRRYKNIGLGFKTPREAIEGTYIDKKCPFTGNVSIRGRILTGTVVKMKMQ 81 (156)
T ss_pred cchhhhHHhhhCccccccCcccccccccccchhhhhcCcccCChHHhhcceeecccCCcccceeEeeEEEeeEEeeecee
Confidence 6789999999994 357899999999999999999999999999999999999999999999999999
Q ss_pred CeEEEEEeEEEeeceeeeEEeeeeeEEEEcCCCCC-CCCCCEEEEeeeecCCCeeeEEEEEeeecCCCCCcccccccC
Q 032281 68 RTIIVRRNYLHFVKKYQRYEKRHSNIPAHISPCFR-VKEGDHVIIGQCRPLSKTVRFNVLKVIPAGSSGGAKKAFTAM 144 (144)
Q Consensus 68 KTvvV~v~~~~~~pkY~K~~kr~kk~~vHd~p~~~-~kvGD~V~I~ecRPlSKtK~f~V~~ii~~~~~~~~~k~f~~f 144 (144)
+||+|++|||||.+||++|++||+|++||.|||+. +++||+|+|+||||||||+||+|+++++.+ +..|||.+|
T Consensus 82 rTIvvrrdYlHy~~KY~ryekrHkN~svh~SPcFrdi~~gDiVtvGecrPLSKtvrfnVLkv~k~~---g~~k~~~k~ 156 (156)
T KOG1728|consen 82 RTIVVRRDYLHYIKKYNRYEKRHKNMSVHVSPCFRDIQEGDIVTVGECRPLSKTVRFNVLKVIKAA---GSKKQFKKF 156 (156)
T ss_pred EEEEEEhhhhhHhHHhhHHHHhccCCccccchhhhccccCCEEEEeecccccceEEEEEEEEeecC---CCccccccC
Confidence 99999999999999999999999999999999997 999999999999999999999999999986 568999987
No 3
>PRK08572 rps17p 30S ribosomal protein S17P; Reviewed
Probab=100.00 E-value=1.4e-52 Score=311.08 Aligned_cols=107 Identities=50% Similarity=0.915 Sum_probs=104.3
Q ss_pred eeecccccCCcccccccccCcCCCceeeeeEeceEEEEEEEecCCCCeEEEEEeEEEeeceeeeEEeeeeeEEEEcCCCC
Q 032281 22 KSIGLGFKTPREAIEGTYIDKKCPFTGTVSIRGRILAGTCHSAKMNRTIIVRRNYLHFVKKYQRYEKRHSNIPAHISPCF 101 (144)
Q Consensus 22 ~~igl~~k~P~~~~~~~y~D~kcPf~g~~sirg~il~G~VvS~KM~KTvvV~v~~~~~~pkY~K~~kr~kk~~vHd~p~~ 101 (144)
+||||||++|+++|| |++|||||+|+|||++|+|+|+|++|+|||+|++++++|||+|+|+++++++|+|||++||
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 9999999999999999999999999999999999999999999999999999999997779
Q ss_pred CCCCCCEEEEeeeecCCCeeeEEEEEeeecC
Q 032281 102 RVKEGDHVIIGQCRPLSKTVRFNVLKVIPAG 132 (144)
Q Consensus 102 ~~kvGD~V~I~ecRPlSKtK~f~V~~ii~~~ 132 (144)
+|++||+|+|+|||||||+|+|+|++|++++
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=8e-50 Score=293.72 Aligned_cols=102 Identities=53% Similarity=0.926 Sum_probs=98.7
Q ss_pred ecccccCCcccccccccCcCCCceeeeeEeceEEEEEEEecCCCCeEEEEEeEEEeeceeeeEEeeeeeEEEEcCCCCCC
Q 032281 24 IGLGFKTPREAIEGTYIDKKCPFTGTVSIRGRILAGTCHSAKMNRTIIVRRNYLHFVKKYQRYEKRHSNIPAHISPCFRV 103 (144)
Q Consensus 24 igl~~k~P~~~~~~~y~D~kcPf~g~~sirg~il~G~VvS~KM~KTvvV~v~~~~~~pkY~K~~kr~kk~~vHd~p~~~~ 103 (144)
|||++++|+++|+ |++|||||+|+|||++|+|+|+|+||+|||+|+++++++||+|+|+++++++|+|||++||+|
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 7999999998777 999999999999999999999999999999999999999999999999999999999777999
Q ss_pred CCCCEEEEeeeecCCCeeeEEEEEee
Q 032281 104 KEGDHVIIGQCRPLSKTVRFNVLKVI 129 (144)
Q Consensus 104 kvGD~V~I~ecRPlSKtK~f~V~~ii 129 (144)
++||+|+|+|||||||||+|+|++|+
T Consensus 77 kvGD~V~I~E~RPlSKtK~w~vv~i~ 102 (102)
T TIGR03630 77 KEGDIVIIGETRPLSKTKSFVVLGKV 102 (102)
T ss_pred CCCCEEEEEEcCCCCCceEEEEEEeC
Confidence 99999999999999999999999874
No 5
>COG0186 RpsQ Ribosomal protein S17 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.5e-39 Score=233.39 Aligned_cols=85 Identities=38% Similarity=0.629 Sum_probs=83.4
Q ss_pred eeeeeEeceEEEEEEEecCCCCeEEEEEeEEEeeceeeeEEeeeeeEEEEcCCCCCCCCCCEEEEeeeecCCCeeeEEEE
Q 032281 47 TGTVSIRGRILAGTCHSAKMNRTIIVRRNYLHFVKKYQRYEKRHSNIPAHISPCFRVKEGDHVIIGQCRPLSKTVRFNVL 126 (144)
Q Consensus 47 ~g~~sirg~il~G~VvS~KM~KTvvV~v~~~~~~pkY~K~~kr~kk~~vHd~p~~~~kvGD~V~I~ecRPlSKtK~f~V~ 126 (144)
||+++++|++|+|+|+|+||+|||+|++++.+|||+|+||++++++|+||| |||+|++||+|+|+|||||||||+|+|+
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 032281 127 KVIPAG 132 (144)
Q Consensus 127 ~ii~~~ 132 (144)
++++++
T Consensus 80 ~i~~~a 85 (87)
T COG0186 80 EIVEKA 85 (87)
T ss_pred EEeeec
Confidence 999875
No 6
>CHL00142 rps17 ribosomal protein S17; Validated
Probab=100.00 E-value=1e-34 Score=207.15 Aligned_cols=79 Identities=28% Similarity=0.307 Sum_probs=76.2
Q ss_pred ceEEEEEEEecCCCCeEEEEEeEEEeeceeeeEEeeeeeEEEEcCCCCCCCCCCEEEEeeeecCCCeeeEEEEEeeecCC
Q 032281 54 GRILAGTCHSAKMNRTIIVRRNYLHFVKKYQRYEKRHSNIPAHISPCFRVKEGDHVIIGQCRPLSKTVRFNVLKVIPAGS 133 (144)
Q Consensus 54 g~il~G~VvS~KM~KTvvV~v~~~~~~pkY~K~~kr~kk~~vHd~p~~~~kvGD~V~I~ecRPlSKtK~f~V~~ii~~~~ 133 (144)
.+.|.|+|+|++|+|||+|++++++|||+|+|+++++++|+||| |+|+|++||+|+|+|||||||||+|+|++|++++.
T Consensus 3 ~~~~~G~Vvs~km~KTivV~v~r~~~h~kY~K~~~r~kk~~aHD-e~n~~~~GD~V~I~e~RPlSKtK~~~v~~i~~~~~ 81 (84)
T CHL00142 3 VKEKIGIVVSNKMNKTIVVAVENRYKHPIYGKIITKTKKYLVHD-EENECNIGDQVLIEETRPLSKTKRWILKEILSKSS 81 (84)
T ss_pred ceEEEEEEEeCCCCceEEEEEEEEEEcCcccEEEEeeEEEEEeC-CCCCCCCCCEEEEEEcCCCCCcEEEEEEEEEEeee
Confidence 57899999999999999999999999999999999999999999 89999999999999999999999999999998864
No 7
>PRK05610 rpsQ 30S ribosomal protein S17; Reviewed
Probab=100.00 E-value=1e-34 Score=206.90 Aligned_cols=78 Identities=32% Similarity=0.373 Sum_probs=75.7
Q ss_pred ceEEEEEEEecCCCCeEEEEEeEEEeeceeeeEEeeeeeEEEEcCCCCCCCCCCEEEEeeeecCCCeeeEEEEEeeecC
Q 032281 54 GRILAGTCHSAKMNRTIIVRRNYLHFVKKYQRYEKRHSNIPAHISPCFRVKEGDHVIIGQCRPLSKTVRFNVLKVIPAG 132 (144)
Q Consensus 54 g~il~G~VvS~KM~KTvvV~v~~~~~~pkY~K~~kr~kk~~vHd~p~~~~kvGD~V~I~ecRPlSKtK~f~V~~ii~~~ 132 (144)
+++|.|+|+|++|+|||+|++++++|||+|+||++++++|+||| |+|+|++||+|+|+|||||||+|+|+|++|++++
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=1.2e-33 Score=195.81 Aligned_cols=70 Identities=36% Similarity=0.377 Sum_probs=68.2
Q ss_pred eEEEEEEEecCCCCeEEEEEeEEEeeceeeeEEeeeeeEEEEcCCCCCCCCCCEEEEeeeecCCCeeeEEE
Q 032281 55 RILAGTCHSAKMNRTIIVRRNYLHFVKKYQRYEKRHSNIPAHISPCFRVKEGDHVIIGQCRPLSKTVRFNV 125 (144)
Q Consensus 55 ~il~G~VvS~KM~KTvvV~v~~~~~~pkY~K~~kr~kk~~vHd~p~~~~kvGD~V~I~ecRPlSKtK~f~V 125 (144)
++|.|+|+|++|+|||+|++++++|||+|+|+++++++|+||| |+|+|++||+|+|+|||||||+|+|+|
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 7899999999999999999999999999999999999999999 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=1.6e-31 Score=183.91 Aligned_cols=69 Identities=43% Similarity=0.632 Sum_probs=66.4
Q ss_pred EEEEecCCCCeEEEEEeEEEeeceeeeEEeeeeeEEEEcCCCCCCCCCCEEEEeeeecCCCeeeEEEEEe
Q 032281 59 GTCHSAKMNRTIIVRRNYLHFVKKYQRYEKRHSNIPAHISPCFRVKEGDHVIIGQCRPLSKTVRFNVLKV 128 (144)
Q Consensus 59 G~VvS~KM~KTvvV~v~~~~~~pkY~K~~kr~kk~~vHd~p~~~~kvGD~V~I~ecRPlSKtK~f~V~~i 128 (144)
|+|+|++|+|||+|++++++|||+|+|+++++++|+||| |.+.|++||+|+|.|||||||+|+|+|++|
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=1e-28 Score=181.68 Aligned_cols=77 Identities=39% Similarity=0.519 Sum_probs=74.2
Q ss_pred eEEEEEEEecCCCCeEEEEEeEEEeeceeeeEEeeeeeEEEEcCCCCCCCCCCEEEEeeeecCCCeeeEEEEEeeecC
Q 032281 55 RILAGTCHSAKMNRTIIVRRNYLHFVKKYQRYEKRHSNIPAHISPCFRVKEGDHVIIGQCRPLSKTVRFNVLKVIPAG 132 (144)
Q Consensus 55 ~il~G~VvS~KM~KTvvV~v~~~~~~pkY~K~~kr~kk~~vHd~p~~~~kvGD~V~I~ecRPlSKtK~f~V~~ii~~~ 132 (144)
+-+.|+|+|.+|+||++|+|+++.+||+|+||++++++|+||| |.+.|++||.|+|..||||||||+|.+.+|++++
T Consensus 3 ~~~vg~VvS~kmqKTv~V~V~rl~~n~~ynryv~~~~kymahD-~~n~cnvGD~VrlepsRPlSk~K~f~i~eII~~a 79 (107)
T KOG1740|consen 3 KNVVGTVVSNKMQKTVKVRVDRLFFNPKYNRYVKRTSKYMAHD-DKNQCNVGDRVRLEPSRPLSKTKHFIIAEIIKKA 79 (107)
T ss_pred ccceeeeeecccCceeEEEeeeccccHHHHHHHHHhhheeecC-ccccccccceEEeccCCcccccceeehHHHHHHH
Confidence 4678999999999999999999999999999999999999999 8999999999999999999999999999999875
No 11
>KOG3447 consensus Mitochondrial/chloroplast ribosomal S17-like protein [Translation, ribosomal structure and biogenesis]
Probab=99.25 E-value=1.3e-12 Score=100.99 Aligned_cols=81 Identities=25% Similarity=0.274 Sum_probs=75.8
Q ss_pred eeEeceEEEEEEEecCCCCeEEEEEeEEEeeceeeeEEeeeeeEEEEcCCCCCCCCCCEEEEeee-ecCCCeeeEEEEEe
Q 032281 50 VSIRGRILAGTCHSAKMNRTIIVRRNYLHFVKKYQRYEKRHSNIPAHISPCFRVKEGDHVIIGQC-RPLSKTVRFNVLKV 128 (144)
Q Consensus 50 ~sirg~il~G~VvS~KM~KTvvV~v~~~~~~pkY~K~~kr~kk~~vHd~p~~~~kvGD~V~I~ec-RPlSKtK~f~V~~i 128 (144)
-|+++++|.|.|+..+|++|..|++.++.++|..++|+++++.|.||| +...|++||+|.|.+. -|+.+.+++.|.+|
T Consensus 6 ~s~~~~~lmGk~ig~~~q~~akVR~~r~eld~yL~kYf~k~~~yfAhD-~~~~c~vGDtVLir~lp~r~t~~V~H~v~~V 84 (150)
T KOG3447|consen 6 SSVHAQWLMGKVIGTKMQKTAKVRVTRLELDPYLLKYFNKRKTYFAHD-ALQQCTVGDTVLIRALPVRRTKHVKHEVAEV 84 (150)
T ss_pred eecccEEEEeeeeeccccccceeeeehhhcCHHHHHHhccccceeecc-hhhccccCCEEEEecCCcchhhhhhhhhHhh
Confidence 589999999999999999999999999999999999999999999999 8999999999999996 67778888988888
Q ss_pred eec
Q 032281 129 IPA 131 (144)
Q Consensus 129 i~~ 131 (144)
+-+
T Consensus 85 Vfk 87 (150)
T KOG3447|consen 85 VFK 87 (150)
T ss_pred eee
Confidence 765
No 12
>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=68.28 E-value=19 Score=24.40 Aligned_cols=25 Identities=12% Similarity=0.006 Sum_probs=20.0
Q ss_pred eeeeeEEEEcCCCCCCCCCCEEEEe
Q 032281 88 KRHSNIPAHISPCFRVKEGDHVIIG 112 (144)
Q Consensus 88 kr~kk~~vHd~p~~~~kvGD~V~I~ 112 (144)
-.-+.+..|+.+...+..||.|.|.
T Consensus 42 ~~V~si~~~~~~~~~a~aGd~v~~~ 66 (83)
T cd03698 42 VEVKSIYVDDEEVDYAVAGENVRLK 66 (83)
T ss_pred EEEEEEEECCeECCEECCCCEEEEE
Confidence 4556677888788889999999874
No 13
>KOG3416 consensus Predicted nucleic acid binding protein [General function prediction only]
Probab=64.23 E-value=29 Score=27.06 Aligned_cols=49 Identities=14% Similarity=0.083 Sum_probs=35.2
Q ss_pred eEEEEEEEecCCCCeEEEEEeEEEeeceeeeEEeeeeeEEEEcCCCCCCCCCCEEEEe
Q 032281 55 RILAGTCHSAKMNRTIIVRRNYLHFVKKYQRYEKRHSNIPAHISPCFRVKEGDHVIIG 112 (144)
Q Consensus 55 ~il~G~VvS~KM~KTvvV~v~~~~~~pkY~K~~kr~kk~~vHd~p~~~~kvGD~V~I~ 112 (144)
-+..|.+.++|..++|.+..-- =+.-.=++.+-|++|...++||+|.+.
T Consensus 23 vl~~g~~tkTkdg~~v~~~kVa---------D~TgsI~isvW~e~~~~~~PGDIirLt 71 (134)
T KOG3416|consen 23 VLEYGRATKTKDGHEVRSCKVA---------DETGSINISVWDEEGCLIQPGDIIRLT 71 (134)
T ss_pred EEeeceeeeccCCCEEEEEEEe---------cccceEEEEEecCcCcccCCccEEEec
Confidence 4667888899988887664110 012345677888888899999999874
No 14
>PF10844 DUF2577: Protein of unknown function (DUF2577); InterPro: IPR022555 This family of proteins has no known function
Probab=61.92 E-value=56 Score=23.40 Aligned_cols=23 Identities=26% Similarity=0.455 Sum_probs=16.8
Q ss_pred CCCCCCEEEEeeeecCCCeeeEEEEE
Q 032281 102 RVKEGDHVIIGQCRPLSKTVRFNVLK 127 (144)
Q Consensus 102 ~~kvGD~V~I~ecRPlSKtK~f~V~~ 127 (144)
.+++||.|.+.. ...--+|.|+.
T Consensus 76 ~Lk~GD~V~ll~---~~~gQ~yiVlD 98 (100)
T PF10844_consen 76 GLKVGDKVLLLR---VQGGQKYIVLD 98 (100)
T ss_pred CCcCCCEEEEEE---ecCCCEEEEEE
Confidence 599999999873 55556666654
No 15
>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=61.53 E-value=35 Score=23.67 Aligned_cols=53 Identities=17% Similarity=0.070 Sum_probs=34.3
Q ss_pred EEEEEEecCCCCeEEEEEeEEEeeceeeeEEeeeeeEEEEcCCCC----CCCCCCEEEEeeeecCCCeeeE
Q 032281 57 LAGTCHSAKMNRTIIVRRNYLHFVKKYQRYEKRHSNIPAHISPCF----RVKEGDHVIIGQCRPLSKTVRF 123 (144)
Q Consensus 57 l~G~VvS~KM~KTvvV~v~~~~~~pkY~K~~kr~kk~~vHd~p~~----~~kvGD~V~I~ecRPlSKtK~f 123 (144)
..|+|+....+....|..+- -..++||.|..+ -++.||.|.+. -+|..+++-=
T Consensus 2 ~~g~V~~~~g~~~~~V~~~~-------------g~~~la~i~gK~rk~iwI~~GD~V~Ve-~~~~d~~kg~ 58 (77)
T cd05793 2 EYGQVEKMLGNGRLEVRCFD-------------GKKRLCRIRGKMRKRVWINEGDIVLVA-PWDFQDDKAD 58 (77)
T ss_pred EEEEEEEEcCCCEEEEEECC-------------CCEEEEEEchhhcccEEEcCCCEEEEE-eccccCCEEE
Confidence 46788887777766666332 124456664433 37899999987 5577766543
No 16
>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=58.02 E-value=47 Score=23.13 Aligned_cols=53 Identities=13% Similarity=-0.061 Sum_probs=33.4
Q ss_pred EEEEEEecCCCCeEEEEEeEEEeeceeeeEEeeeeeEEEEcCCCC----CCCCCCEEEEeeeecC-CCeeeE
Q 032281 57 LAGTCHSAKMNRTIIVRRNYLHFVKKYQRYEKRHSNIPAHISPCF----RVKEGDHVIIGQCRPL-SKTVRF 123 (144)
Q Consensus 57 l~G~VvS~KM~KTvvV~v~~~~~~pkY~K~~kr~kk~~vHd~p~~----~~kvGD~V~I~ecRPl-SKtK~f 123 (144)
..|+|+....+....|+.+- -..++||.|..+ -++.||.|.+. -+|. .++|-=
T Consensus 2 ~i~~V~~~lG~~~~~V~~~d-------------g~~~l~~i~gK~Rk~iwI~~GD~VlV~-~~~~~~~~kg~ 59 (78)
T cd04456 2 QIVRVLRMLGNNRHEVECAD-------------GQRRLVSIPGKLRKNIWIKRGDFLIVD-PIEEGEDVKAD 59 (78)
T ss_pred eEEEEEEECCCCEEEEEECC-------------CCEEEEEEchhhccCEEEcCCCEEEEE-ecccCCCceEE
Confidence 35777777666666665331 234567775444 28899999984 6777 455543
No 17
>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=57.05 E-value=40 Score=22.93 Aligned_cols=26 Identities=15% Similarity=0.141 Sum_probs=21.2
Q ss_pred EeeeeeEEEEcCCCCCCCCCCEEEEe
Q 032281 87 EKRHSNIPAHISPCFRVKEGDHVIIG 112 (144)
Q Consensus 87 ~kr~kk~~vHd~p~~~~kvGD~V~I~ 112 (144)
.-.-+.+.+|+.+...+..||.|.|.
T Consensus 41 ~~~V~si~~~~~~~~~a~aGd~v~l~ 66 (81)
T cd03695 41 TSRVKSIETFDGELDEAGAGESVTLT 66 (81)
T ss_pred eEEEEEEEECCcEeCEEcCCCEEEEE
Confidence 45667778888778889999999985
No 18
>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=56.31 E-value=34 Score=23.64 Aligned_cols=26 Identities=19% Similarity=0.220 Sum_probs=20.6
Q ss_pred EeeeeeEEEEcCCCCCCCCCCEEEEe
Q 032281 87 EKRHSNIPAHISPCFRVKEGDHVIIG 112 (144)
Q Consensus 87 ~kr~kk~~vHd~p~~~~kvGD~V~I~ 112 (144)
.-.-+.+..|+.+...+..||.|.|.
T Consensus 45 ~~~V~sI~~~~~~~~~a~aG~~v~i~ 70 (91)
T cd03693 45 TGEVKSVEMHHEPLEEALPGDNVGFN 70 (91)
T ss_pred EEEEEEEEECCcCcCEECCCCEEEEE
Confidence 45566777888777789999999975
No 19
>COG0361 InfA Translation initiation factor 1 (IF-1) [Translation, ribosomal structure and biogenesis]
Probab=56.31 E-value=54 Score=23.11 Aligned_cols=49 Identities=29% Similarity=0.296 Sum_probs=33.8
Q ss_pred EEEEEEEecCCCCeEEEEEeEEEeeceeeeEEeeeeeEEEEcCCCC-----CCCCCCEEEEeeeecCC
Q 032281 56 ILAGTCHSAKMNRTIIVRRNYLHFVKKYQRYEKRHSNIPAHISPCF-----RVKEGDHVIIGQCRPLS 118 (144)
Q Consensus 56 il~G~VvS~KM~KTvvV~v~~~~~~pkY~K~~kr~kk~~vHd~p~~-----~~kvGD~V~I~ecRPlS 118 (144)
.+.|+|+..-.+....|.-+--+ ...||.|-.. ...+||+|++. .+|..
T Consensus 8 e~~g~V~e~L~~~~f~v~~edg~-------------~~~ahI~GKmr~~~i~I~~GD~V~Ve-~~~~d 61 (75)
T COG0361 8 EMEGTVIEMLPNGRFRVELENGH-------------ERLAHISGKMRKNRIRILPGDVVLVE-LSPYD 61 (75)
T ss_pred EEEEEEEEecCCCEEEEEecCCc-------------EEEEEccCcchheeEEeCCCCEEEEE-ecccc
Confidence 57899999988888888755444 3467773222 36789999865 44544
No 20
>TIGR00523 eIF-1A eukaryotic/archaeal initiation factor 1A. Recommended nomenclature: eIF-1A for eukaryotes, aIF-1A for Archaea. Also called eIF-4C
Probab=55.03 E-value=81 Score=23.03 Aligned_cols=49 Identities=18% Similarity=0.152 Sum_probs=33.1
Q ss_pred EEEEEEEecCCCCeEEEEEeEEEeeceeeeEEeeeeeEEEEcCCCC----CCCCCCEEEEeeeecCC
Q 032281 56 ILAGTCHSAKMNRTIIVRRNYLHFVKKYQRYEKRHSNIPAHISPCF----RVKEGDHVIIGQCRPLS 118 (144)
Q Consensus 56 il~G~VvS~KM~KTvvV~v~~~~~~pkY~K~~kr~kk~~vHd~p~~----~~kvGD~V~I~ecRPlS 118 (144)
...|+|++...+....|.-+- -..++||.|..+ -++.||.|.| +.+.++
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 467888888777777666331 124456664333 2889999999 667788
No 21
>smart00652 eIF1a eukaryotic translation initiation factor 1A.
Probab=54.94 E-value=56 Score=22.96 Aligned_cols=53 Identities=13% Similarity=0.008 Sum_probs=33.3
Q ss_pred EEEEEEecCCCCeEEEEEeEEEeeceeeeEEeeeeeEEEEcCCCC----CCCCCCEEEEeeeecCCCeeeE
Q 032281 57 LAGTCHSAKMNRTIIVRRNYLHFVKKYQRYEKRHSNIPAHISPCF----RVKEGDHVIIGQCRPLSKTVRF 123 (144)
Q Consensus 57 l~G~VvS~KM~KTvvV~v~~~~~~pkY~K~~kr~kk~~vHd~p~~----~~kvGD~V~I~ecRPlSKtK~f 123 (144)
..|+|+....+.-..|.-+- -..+.||.|..+ -++.||.|.|. -+|-.+.+-=
T Consensus 7 ~~g~V~~~lG~~~~~V~~~d-------------G~~~la~ipgK~Rk~iwI~~GD~VlVe-~~~~~~~kg~ 63 (83)
T smart00652 7 EIAQVVKMLGNGRLEVMCAD-------------GKERLARIPGKMRKKVWIRRGDIVLVD-PWDFQDVKAD 63 (83)
T ss_pred EEEEEEEEcCCCEEEEEECC-------------CCEEEEEEchhhcccEEEcCCCEEEEE-ecCCCCCEEE
Confidence 56788877766666665321 133456664433 28899999995 5676665543
No 22
>PF09740 DUF2043: Uncharacterized conserved protein (DUF2043); InterPro: IPR018610 This entry consists of uncharacterised proteins of unknown function. They contain three conserved cysteines and a {CP}{y/l}{HG} motif.
Probab=54.66 E-value=4.4 Score=30.58 Aligned_cols=13 Identities=54% Similarity=1.076 Sum_probs=9.6
Q ss_pred CcCCCceeeeeEe
Q 032281 41 DKKCPFTGTVSIR 53 (144)
Q Consensus 41 D~kcPf~g~~sir 53 (144)
-.+|||||-+--|
T Consensus 87 ~~kCPfHG~IIpR 99 (110)
T PF09740_consen 87 RKKCPFHGKIIPR 99 (110)
T ss_pred cccCCCCCcccCC
Confidence 4589999976544
No 23
>TIGR00008 infA translation initiation factor IF-1. This family consists of translation initiation factor IF-1 as found in bacteria and chloroplasts. This protein, about 70 residues in length, consists largely of an S1 RNA binding domain (pfam00575).
Probab=53.95 E-value=70 Score=22.02 Aligned_cols=52 Identities=25% Similarity=0.273 Sum_probs=33.5
Q ss_pred EEEEEEEecCCCCeEEEEEeEEEeeceeeeEEeeeeeEEEEcCCCC-----CCCCCCEEEEeeeecCCCee
Q 032281 56 ILAGTCHSAKMNRTIIVRRNYLHFVKKYQRYEKRHSNIPAHISPCF-----RVKEGDHVIIGQCRPLSKTV 121 (144)
Q Consensus 56 il~G~VvS~KM~KTvvV~v~~~~~~pkY~K~~kr~kk~~vHd~p~~-----~~kvGD~V~I~ecRPlSKtK 121 (144)
.+.|+|+..-.+-...|..+- -....||.+-.. ...+||.|.+. -+|...++
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 578999988777777776442 123456664322 37899999976 55655554
No 24
>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=52.07 E-value=45 Score=22.74 Aligned_cols=53 Identities=13% Similarity=0.192 Sum_probs=31.3
Q ss_pred eceEEEEEEEecCCC--CeEEEEEeEEEeeceeeeEEeeeeeEEEEcCCCCCCCCCCEEEEe
Q 032281 53 RGRILAGTCHSAKMN--RTIIVRRNYLHFVKKYQRYEKRHSNIPAHISPCFRVKEGDHVIIG 112 (144)
Q Consensus 53 rg~il~G~VvS~KM~--KTvvV~v~~~~~~pkY~K~~kr~kk~~vHd~p~~~~kvGD~V~I~ 112 (144)
+|.++.|+|.+-.+. -.+.+.-. +. ...-.-+.+.+|+.+...+..||.|.|.
T Consensus 14 ~G~vv~G~v~~G~v~~gd~v~~~p~-----~~--~~~~~V~si~~~~~~~~~a~~G~~v~l~ 68 (87)
T cd03697 14 RGTVVTGRIERGTIKVGDEVEIVGF-----GE--TLKTTVTGIEMFRKTLDEAEAGDNVGVL 68 (87)
T ss_pred cEEEEEEEECCCCCccCCEEEEeCC-----CC--CceEEEEEEEECCcCCCEECCCCEEEEE
Confidence 355677777765332 23332210 00 1123445577888777889999999875
No 25
>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=48.04 E-value=81 Score=21.09 Aligned_cols=26 Identities=31% Similarity=0.378 Sum_probs=19.6
Q ss_pred EeeeeeEEEEcCCCCCCCCCCEEEEe
Q 032281 87 EKRHSNIPAHISPCFRVKEGDHVIIG 112 (144)
Q Consensus 87 ~kr~kk~~vHd~p~~~~kvGD~V~I~ 112 (144)
.-.-+.+..|+.+...+..||.|.|.
T Consensus 41 ~~~V~sI~~~~~~~~~a~aGd~v~i~ 66 (83)
T cd03696 41 ETRVRSIQVHGKDVEEAKAGDRVALN 66 (83)
T ss_pred eEEEEEEEECCcCcCEEcCCCEEEEE
Confidence 44556667777677789999999985
No 26
>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=45.97 E-value=48 Score=22.72 Aligned_cols=26 Identities=19% Similarity=0.224 Sum_probs=20.7
Q ss_pred EeeeeeEEEEcCCCCCCCCCCEEEEe
Q 032281 87 EKRHSNIPAHISPCFRVKEGDHVIIG 112 (144)
Q Consensus 87 ~kr~kk~~vHd~p~~~~kvGD~V~I~ 112 (144)
.-.-+.+..|+.+...+..||.|.|.
T Consensus 45 ~~~V~sI~~~~~~~~~a~aGd~v~l~ 70 (87)
T cd03694 45 PVTVKSIHRNRSPVRVVRAGQSASLA 70 (87)
T ss_pred EEEEEEEEECCeECCEECCCCEEEEE
Confidence 45566678888777789999999985
No 27
>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=41.41 E-value=1.1e+02 Score=20.57 Aligned_cols=25 Identities=12% Similarity=0.026 Sum_probs=19.0
Q ss_pred eeeeeEEEEcCCCCCCCCCCEEEEe
Q 032281 88 KRHSNIPAHISPCFRVKEGDHVIIG 112 (144)
Q Consensus 88 kr~kk~~vHd~p~~~~kvGD~V~I~ 112 (144)
-.-+.+..|+.+...+..||.|.|.
T Consensus 41 ~~V~si~~~~~~~~~a~aGd~v~l~ 65 (82)
T cd04089 41 VEVLSIYNEDVEVRYARPGENVRLR 65 (82)
T ss_pred EEEEEEEECCEECCEECCCCEEEEE
Confidence 3445567777677789999999975
No 28
>CHL00071 tufA elongation factor Tu
Probab=41.20 E-value=1.1e+02 Score=26.71 Aligned_cols=25 Identities=16% Similarity=-0.003 Sum_probs=18.7
Q ss_pred eeeeeEEEEcCCCCCCCCCCEEEEe
Q 032281 88 KRHSNIPAHISPCFRVKEGDHVIIG 112 (144)
Q Consensus 88 kr~kk~~vHd~p~~~~kvGD~V~I~ 112 (144)
-+-+.+..|+.+...+..||.|.|.
T Consensus 264 ~~VksI~~~~~~v~~a~aGd~v~i~ 288 (409)
T CHL00071 264 TTVTGLEMFQKTLDEGLAGDNVGIL 288 (409)
T ss_pred EEEEEEEEcCcCCCEECCCceeEEE
Confidence 4666777887667779999988654
No 29
>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=40.92 E-value=19 Score=24.34 Aligned_cols=13 Identities=46% Similarity=0.710 Sum_probs=11.0
Q ss_pred CCCCCCEEEEeee
Q 032281 102 RVKEGDHVIIGQC 114 (144)
Q Consensus 102 ~~kvGD~V~I~ec 114 (144)
-++.||+|.|+..
T Consensus 53 G~~~GD~V~Ig~~ 65 (69)
T TIGR03595 53 GAKDGDTVRIGDF 65 (69)
T ss_pred CCCCCCEEEEccE
Confidence 5899999999854
No 30
>PF13550 Phage-tail_3: Putative phage tail protein
Probab=40.68 E-value=66 Score=23.45 Aligned_cols=40 Identities=18% Similarity=0.404 Sum_probs=27.6
Q ss_pred EEeeeeeEEEEcCCCCCCCCCCEEEEeeeecCCCeeeEEEEEee
Q 032281 86 YEKRHSNIPAHISPCFRVKEGDHVIIGQCRPLSKTVRFNVLKVI 129 (144)
Q Consensus 86 ~~kr~kk~~vHd~p~~~~kvGD~V~I~ecRPlSKtK~f~V~~ii 129 (144)
+.+++=.+.+-. ....+.+||+|.|..- .+...|+|.+|.
T Consensus 124 ~~r~t~~f~~~~-~~~~l~pGDvi~l~~~---~~~~~~RI~~i~ 163 (164)
T PF13550_consen 124 YERRTVSFTLPP-DGLALEPGDVIALSDD---GRDMRFRITEIE 163 (164)
T ss_pred ccceEEEEEECh-hhccCCCCCEEEEEeC---CCceEEEEEEEe
Confidence 334444455543 4567999999998865 567888887764
No 31
>PRK04012 translation initiation factor IF-1A; Provisional
Probab=40.39 E-value=1.3e+02 Score=21.96 Aligned_cols=53 Identities=17% Similarity=0.119 Sum_probs=32.9
Q ss_pred EEEEEEEecCCCCeEEEEEeEEEeeceeeeEEeeeeeEEEEcCCCC----CCCCCCEEEEeeeecCCCeee
Q 032281 56 ILAGTCHSAKMNRTIIVRRNYLHFVKKYQRYEKRHSNIPAHISPCF----RVKEGDHVIIGQCRPLSKTVR 122 (144)
Q Consensus 56 il~G~VvS~KM~KTvvV~v~~~~~~pkY~K~~kr~kk~~vHd~p~~----~~kvGD~V~I~ecRPlSKtK~ 122 (144)
...|+|+....+....|..+- -..++||.|..+ -++.||.|.|. -+|...+|-
T Consensus 22 e~~g~V~~~lG~~~~~V~~~d-------------G~~~la~i~GK~Rk~IwI~~GD~VlVe-~~~~~~~kg 78 (100)
T PRK04012 22 EVFGVVEQMLGANRVRVRCMD-------------GVERMGRIPGKMKKRMWIREGDVVIVA-PWDFQDEKA 78 (100)
T ss_pred EEEEEEEEEcCCCEEEEEeCC-------------CCEEEEEEchhhcccEEecCCCEEEEE-ecccCCCEE
Confidence 467888888777766666331 122345553333 27789999987 466666653
No 32
>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=40.11 E-value=1e+02 Score=21.10 Aligned_cols=14 Identities=14% Similarity=0.033 Sum_probs=11.2
Q ss_pred CCCCCCCCEEEEee
Q 032281 100 CFRVKEGDHVIIGQ 113 (144)
Q Consensus 100 ~~~~kvGD~V~I~e 113 (144)
..++..||+|.+.-
T Consensus 59 v~~a~aGdIv~v~g 72 (85)
T cd03689 59 VDEAYPGDIIGLVN 72 (85)
T ss_pred cCEECCCCEEEEEC
Confidence 34689999999875
No 33
>COG1786 Swiveling domain associated with predicted aconitase [Energy production and conversion]
Probab=39.43 E-value=20 Score=27.91 Aligned_cols=21 Identities=43% Similarity=0.781 Sum_probs=16.9
Q ss_pred ccccCcCCCceeeeeEeceEEE
Q 032281 37 GTYIDKKCPFTGTVSIRGRILA 58 (144)
Q Consensus 37 ~~y~D~kcPf~g~~sirg~il~ 58 (144)
|.-||++||-+| -++.|++|.
T Consensus 35 G~vid~~h~l~G-~~l~Gkilv 55 (131)
T COG1786 35 GKVIDPHHPLHG-ESLTGKILV 55 (131)
T ss_pred ccCcCCCCCccc-ccccceEEE
Confidence 566899999998 677777774
No 34
>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=35.90 E-value=1e+02 Score=18.68 Aligned_cols=22 Identities=18% Similarity=0.027 Sum_probs=15.4
Q ss_pred eEEEEcCCCCCCCCCCEEEEee
Q 032281 92 NIPAHISPCFRVKEGDHVIIGQ 113 (144)
Q Consensus 92 k~~vHd~p~~~~kvGD~V~I~e 113 (144)
.+..+..+...+..||.+.+.-
T Consensus 48 ~i~~~~~~~~~~~aG~~~~~~~ 69 (83)
T cd01342 48 SLKRFKGEVDEAVAGDIVGIVL 69 (83)
T ss_pred EeEecCceeceecCCCEEEEEE
Confidence 3444445777899999998763
No 35
>PTZ00329 eukaryotic translation initiation factor 1A; Provisional
Probab=35.88 E-value=2.2e+02 Score=22.62 Aligned_cols=58 Identities=14% Similarity=0.037 Sum_probs=36.8
Q ss_pred EEEEEEecCCCCeEEEEEeEEEeeceeeeEEeeeeeEEEEcCCCC----CCCCCCEEEEeeeecCCCeeeEEEEEe
Q 032281 57 LAGTCHSAKMNRTIIVRRNYLHFVKKYQRYEKRHSNIPAHISPCF----RVKEGDHVIIGQCRPLSKTVRFNVLKV 128 (144)
Q Consensus 57 l~G~VvS~KM~KTvvV~v~~~~~~pkY~K~~kr~kk~~vHd~p~~----~~kvGD~V~I~ecRPlSKtK~f~V~~i 128 (144)
..|+|++...+....|...- -...+||.|-.+ -+.+||+|+|.. +|-.++|-=++...
T Consensus 34 ~~g~V~~~LGn~~f~V~c~d-------------G~~rLa~I~GKmRK~IWI~~GD~VlVel-~~yd~~KgdIi~Ry 95 (155)
T PTZ00329 34 EYAQVLRMLGNGRLEAYCFD-------------GVKRLCHIRGKMRKRVWINIGDIILVSL-RDFQDSKADVILKY 95 (155)
T ss_pred EEEEEEEEcCCCEEEEEECC-------------CCEEEEEeeccceeeEEecCCCEEEEec-cCCCCCEEEEEEEc
Confidence 57888888878777776321 112233332211 277899999964 99988886655544
No 36
>PRK12442 translation initiation factor IF-1; Reviewed
Probab=35.29 E-value=1.5e+02 Score=21.54 Aligned_cols=61 Identities=18% Similarity=0.097 Sum_probs=36.5
Q ss_pred EEEEEEEecCCCCeEEEEEeEEEeeceeeeEEeeeeeEEEEcCCC-----CCCCCCCEEEEeeeecCCCeeeEEEEEeee
Q 032281 56 ILAGTCHSAKMNRTIIVRRNYLHFVKKYQRYEKRHSNIPAHISPC-----FRVKEGDHVIIGQCRPLSKTVRFNVLKVIP 130 (144)
Q Consensus 56 il~G~VvS~KM~KTvvV~v~~~~~~pkY~K~~kr~kk~~vHd~p~-----~~~kvGD~V~I~ecRPlSKtK~f~V~~ii~ 130 (144)
.++|+|+..-.+-...|+.+-=+ .+.||.|-- ..+.+||.|.+.-+ |..-++-=.+..-..
T Consensus 8 e~~G~V~e~Lp~~~frV~LenG~-------------~vla~isGKmR~~rIrIl~GD~V~VE~s-pYDltkGRIiyR~~~ 73 (87)
T PRK12442 8 ELDGIVDEVLPDSRFRVTLENGV-------------EVGAYASGRMRKHRIRILAGDRVTLELS-PYDLTKGRINFRHKD 73 (87)
T ss_pred EEEEEEEEECCCCEEEEEeCCCC-------------EEEEEeccceeeeeEEecCCCEEEEEEC-cccCCceeEEEEecC
Confidence 57889988877777777744221 233444222 24778999997654 666565444444433
No 37
>KOG1730 consensus Thioredoxin-like protein [Posttranslational modification, protein turnover, chaperones]
Probab=34.75 E-value=26 Score=28.98 Aligned_cols=18 Identities=39% Similarity=0.813 Sum_probs=15.2
Q ss_pred CCCceeeeeEeceEEEEE
Q 032281 43 KCPFTGTVSIRGRILAGT 60 (144)
Q Consensus 43 kcPf~g~~sirg~il~G~ 60 (144)
+-|||||+.+.|-++.|-
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=34.64 E-value=19 Score=24.39 Aligned_cols=12 Identities=58% Similarity=0.817 Sum_probs=7.6
Q ss_pred CCCCCCEEEEee
Q 032281 102 RVKEGDHVIIGQ 113 (144)
Q Consensus 102 ~~kvGD~V~I~e 113 (144)
.++.||+|.|+.
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 39
>PF10915 DUF2709: Protein of unknown function (DUF2709); InterPro: IPR024484 Members of this family appear restricted to Chlamydiales. Their function is unknown.
Probab=33.85 E-value=19 Score=30.14 Aligned_cols=25 Identities=40% Similarity=0.743 Sum_probs=15.8
Q ss_pred eecccccCCccc--ccccccCcCCCceeee
Q 032281 23 SIGLGFKTPREA--IEGTYIDKKCPFTGTV 50 (144)
Q Consensus 23 ~igl~~k~P~~~--~~~~y~D~kcPf~g~~ 50 (144)
.|-+++-.|.-- -.--|| |||||.|
T Consensus 70 eI~I~~g~p~VNE~TkkIYI---CPFTGKV 96 (238)
T PF10915_consen 70 EIKIQSGKPSVNEQTKKIYI---CPFTGKV 96 (238)
T ss_pred eEEEecCCcccccccceEEE---cCCcCcc
Confidence 566677777532 222366 9999965
No 40
>PRK12736 elongation factor Tu; Reviewed
Probab=30.58 E-value=1.8e+02 Score=25.29 Aligned_cols=23 Identities=13% Similarity=0.034 Sum_probs=15.2
Q ss_pred eeeeEEEEcCCCCCCCCCCEEEE
Q 032281 89 RHSNIPAHISPCFRVKEGDHVII 111 (144)
Q Consensus 89 r~kk~~vHd~p~~~~kvGD~V~I 111 (144)
+-+.+.+|..+...+..||.|.|
T Consensus 255 ~V~sI~~~~~~~~~a~aGd~v~l 277 (394)
T PRK12736 255 VVTGVEMFRKLLDEGQAGDNVGV 277 (394)
T ss_pred EEEEEEECCEEccEECCCCEEEE
Confidence 45556666656667778887755
No 41
>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=30.14 E-value=34 Score=21.32 Aligned_cols=23 Identities=17% Similarity=0.076 Sum_probs=14.9
Q ss_pred eeeEEEEcCCCCCCCCCCEEEEe
Q 032281 90 HSNIPAHISPCFRVKEGDHVIIG 112 (144)
Q Consensus 90 ~kk~~vHd~p~~~~kvGD~V~I~ 112 (144)
...|.+-++....++.||+|.|.
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 42
>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=30.09 E-value=59 Score=24.02 Aligned_cols=19 Identities=26% Similarity=0.176 Sum_probs=13.7
Q ss_pred EEEEcCCCCCCCCCCEEEEee
Q 032281 93 IPAHISPCFRVKEGDHVIIGQ 113 (144)
Q Consensus 93 ~~vHd~p~~~~kvGD~V~I~e 113 (144)
+.+++ ...+++||.|+|+-
T Consensus 44 ~~~~~--~~~~~~GD~V~v~i 62 (135)
T PF04246_consen 44 FRAPN--PIGAKVGDRVEVEI 62 (135)
T ss_pred EEecC--CCCCCCCCEEEEEe
Confidence 34444 45799999999873
No 43
>PF06107 DUF951: Bacterial protein of unknown function (DUF951); InterPro: IPR009296 This family consists of several short hypothetical bacterial proteins of unknown function.
Probab=30.05 E-value=72 Score=21.49 Aligned_cols=25 Identities=16% Similarity=0.392 Sum_probs=20.7
Q ss_pred CCCCCEEEEeeeecCCCeeeEEEEEe
Q 032281 103 VKEGDHVIIGQCRPLSKTVRFNVLKV 128 (144)
Q Consensus 103 ~kvGD~V~I~ecRPlSKtK~f~V~~i 128 (144)
..+||+|....-.|= -+..|.|+.+
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 4588988876
No 44
>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=29.99 E-value=1.7e+02 Score=19.42 Aligned_cols=15 Identities=13% Similarity=0.105 Sum_probs=11.5
Q ss_pred CCCCCCCCCEEEEee
Q 032281 99 PCFRVKEGDHVIIGQ 113 (144)
Q Consensus 99 p~~~~kvGD~V~I~e 113 (144)
|..++..||+|.|.-
T Consensus 57 ~v~~~~aGdI~~i~g 71 (83)
T cd04092 57 EIPSLSAGNIGVITG 71 (83)
T ss_pred ECCeeCCCCEEEEEC
Confidence 345799999998753
No 45
>PF11302 DUF3104: Protein of unknown function (DUF3104); InterPro: IPR021453 This family of proteins with unknown function appears to be restricted to Cyanobacteria.
Probab=29.06 E-value=1.1e+02 Score=21.68 Aligned_cols=32 Identities=25% Similarity=0.314 Sum_probs=24.8
Q ss_pred CCCCCCCEEEEeeeec--CCCeeeEEEEEeeecC
Q 032281 101 FRVKEGDHVIIGQCRP--LSKTVRFNVLKVIPAG 132 (144)
Q Consensus 101 ~~~kvGD~V~I~ecRP--lSKtK~f~V~~ii~~~ 132 (144)
..++.||.|.+....- .++.+.|-+-.|+...
T Consensus 4 L~Vk~Gd~ViV~~~~~~~~~~~~dWWmg~Vi~~~ 37 (75)
T PF11302_consen 4 LSVKPGDTVIVQDEQEVGQKQDKDWWMGQVIHCE 37 (75)
T ss_pred cccCCCCEEEEecCccccccCCCCcEEEEEEEEe
Confidence 3699999999998752 3456789898888764
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=28.58 E-value=56 Score=18.81 Aligned_cols=21 Identities=19% Similarity=0.139 Sum_probs=15.0
Q ss_pred EEEcCCCCCCCCCCEEEEeee
Q 032281 94 PAHISPCFRVKEGDHVIIGQC 114 (144)
Q Consensus 94 ~vHd~p~~~~kvGD~V~I~ec 114 (144)
.++++....+..||.|.+.+.
T Consensus 9 ~~~~~~~l~~~~Gd~v~v~~~ 29 (54)
T cd00174 9 DARDPDELSFKKGDIIEVLEK 29 (54)
T ss_pred CCCCCCCCCCCCCCEEEEEEc
Confidence 344433456899999999877
No 47
>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=27.11 E-value=87 Score=19.81 Aligned_cols=28 Identities=14% Similarity=0.064 Sum_probs=18.6
Q ss_pred CCCCCCCEEEEeeeecCCCeeeEEEEEeeecC
Q 032281 101 FRVKEGDHVIIGQCRPLSKTVRFNVLKVIPAG 132 (144)
Q Consensus 101 ~~~kvGD~V~I~ecRPlSKtK~f~V~~ii~~~ 132 (144)
...-+||+|.+.. .. .-.+.+.+++++.
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 3478999998852 11 2346777888764
No 48
>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=26.98 E-value=1.9e+02 Score=19.11 Aligned_cols=22 Identities=18% Similarity=0.173 Sum_probs=16.4
Q ss_pred eceEEEEEEEecCCCCeEEEEEe
Q 032281 53 RGRILAGTCHSAKMNRTIIVRRN 75 (144)
Q Consensus 53 rg~il~G~VvS~KM~KTvvV~v~ 75 (144)
.|.+..|.|++. ++..+.|...
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 588999999995 4566777653
No 49
>PRK06763 F0F1 ATP synthase subunit alpha; Validated
Probab=25.92 E-value=1.7e+02 Score=24.56 Aligned_cols=45 Identities=22% Similarity=0.371 Sum_probs=26.8
Q ss_pred eEEEEEEEecCCCCeEEEEEeEEEeeceeeeEEeeeeeEEEEcCCCCCCCCCCEEEEe
Q 032281 55 RILAGTCHSAKMNRTIIVRRNYLHFVKKYQRYEKRHSNIPAHISPCFRVKEGDHVIIG 112 (144)
Q Consensus 55 ~il~G~VvS~KM~KTvvV~v~~~~~~pkY~K~~kr~kk~~vHd~p~~~~kvGD~V~I~ 112 (144)
..++|+|+-.. +.++.|+.. -|+.- +.+|.+-.-.+++||.|...
T Consensus 40 ~tiEGrVvEV~-~~~i~iesk------~yn~~------v~i~~d~~~nvKVGD~VKaT 84 (213)
T PRK06763 40 STIEGRVVEVD-NGVIVIKSK------QYEEP------VSVYIDSLSNVKVGDEVKAT 84 (213)
T ss_pred ceeeeEEEEEe-CCEEEEEec------cCCCc------eEEEecCCCCcccCcEEEEc
Confidence 35677777554 566666643 22221 45554333357999999987
No 50
>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=25.69 E-value=81 Score=21.30 Aligned_cols=29 Identities=28% Similarity=0.347 Sum_probs=20.4
Q ss_pred EEcCCCCCCCCCCEEEEeeeecCCCeeeE
Q 032281 95 AHISPCFRVKEGDHVIIGQCRPLSKTVRF 123 (144)
Q Consensus 95 vHd~p~~~~kvGD~V~I~ecRPlSKtK~f 123 (144)
+-+|+...+.+||.|++.-.-+.+.+..+
T Consensus 7 ~F~P~~i~v~~GdtVt~~N~d~~~Hnv~~ 35 (83)
T TIGR02657 7 KYETPELHVKVGDTVTWINREAMPHNVHF 35 (83)
T ss_pred EEcCCEEEECCCCEEEEEECCCCCccEEe
Confidence 45556668999999999766565555543
No 51
>PRK05807 hypothetical protein; Provisional
Probab=24.89 E-value=2.7e+02 Score=20.97 Aligned_cols=60 Identities=22% Similarity=0.208 Sum_probs=34.9
Q ss_pred ceEEEEEEEecCCCCeEEEEEeEEEeeceeeeEEeeeeeEEEEcCC---------CCCCCCCCEEEEe--eeecCCCeee
Q 032281 54 GRILAGTCHSAKMNRTIIVRRNYLHFVKKYQRYEKRHSNIPAHISP---------CFRVKEGDHVIIG--QCRPLSKTVR 122 (144)
Q Consensus 54 g~il~G~VvS~KM~KTvvV~v~~~~~~pkY~K~~kr~kk~~vHd~p---------~~~~kvGD~V~I~--ecRPlSKtK~ 122 (144)
|.++.|+|+.... --+-|..+-. .-++|.++ ....++||.|.+. +..+ .....
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 7889999998653 3444544311 22333322 3458999998754 3444 45566
Q ss_pred EEEEEee
Q 032281 123 FNVLKVI 129 (144)
Q Consensus 123 f~V~~ii 129 (144)
+.+..+.
T Consensus 70 LSlk~~~ 76 (136)
T PRK05807 70 LSIKQAM 76 (136)
T ss_pred EEEEecc
Confidence 6665554
No 52
>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=24.43 E-value=1.7e+02 Score=25.52 Aligned_cols=49 Identities=14% Similarity=0.241 Sum_probs=30.9
Q ss_pred ceEEEEEEEec--CCCCeEEEEEeEEEeeceeeeEEeeeeeEEEEcCCCCCCCCCCEEEE
Q 032281 54 GRILAGTCHSA--KMNRTIIVRRNYLHFVKKYQRYEKRHSNIPAHISPCFRVKEGDHVII 111 (144)
Q Consensus 54 g~il~G~VvS~--KM~KTvvV~v~~~~~~pkY~K~~kr~kk~~vHd~p~~~~kvGD~V~I 111 (144)
|.+..|+|.+- +..-++.+. |- ...-.-+.+.+|+.+...+..||.|.|
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 55677777754 333444443 21 123456777888877778999999877
No 53
>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=24.33 E-value=1.3e+02 Score=17.37 Aligned_cols=19 Identities=16% Similarity=0.146 Sum_probs=14.4
Q ss_pred cCCCCCCCCCCEEEEeeee
Q 032281 97 ISPCFRVKEGDHVIIGQCR 115 (144)
Q Consensus 97 d~p~~~~kvGD~V~I~ecR 115 (144)
.+....++.||.|.+.+..
T Consensus 15 ~~~~l~~~~Gd~v~v~~~~ 33 (58)
T smart00326 15 DPDELSFKKGDIITVLEKS 33 (58)
T ss_pred CCCCCCCCCCCEEEEEEcC
Confidence 3345579999999988764
No 54
>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=23.89 E-value=2e+02 Score=18.92 Aligned_cols=52 Identities=21% Similarity=0.238 Sum_probs=28.0
Q ss_pred EEEEEEecCCCCeEEEEEeEEEeeceeeeEEeeeeeEEEEcCC----CCCCCCCCEEEEeeeecCCCeee
Q 032281 57 LAGTCHSAKMNRTIIVRRNYLHFVKKYQRYEKRHSNIPAHISP----CFRVKEGDHVIIGQCRPLSKTVR 122 (144)
Q Consensus 57 l~G~VvS~KM~KTvvV~v~~~~~~pkY~K~~kr~kk~~vHd~p----~~~~kvGD~V~I~ecRPlSKtK~ 122 (144)
..|+|+..-.+....|..+ --..+.||.|. ..-++.||.|.+.. +|..+++-
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 5677777776666666521 11122334321 12478899997765 77776653
No 55
>cd06827 PLPDE_III_AR_proteobact Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes, Proteobacterial Alanine Racemases. This subfamily is composed mainly of proteobacterial alanine racemases (EC 5.1.1.1), fold type III PLP-dependent enzymes that catalyze the interconversion between L- and D-alanine, which is an essential component of the peptidoglycan layer of bacterial cell walls. hese proteins are similar to other bacterial ARs and are fold type III PLP-dependent enzymes containing contains an N-terminal PLP-binding TIM-barrel domain and a C-terminal beta-sandwich domain. They exist as homodimers with active sites that lie at the interface between the TIM barrel domain of one subunit and the beta-sandwich domain of the other subunit. Homodimer formation and the presence of the PLP cofactor are required for catalytic activity.
Probab=23.68 E-value=2.1e+02 Score=24.61 Aligned_cols=12 Identities=33% Similarity=0.216 Sum_probs=9.3
Q ss_pred CCCCCCCEEEEe
Q 032281 101 FRVKEGDHVIIG 112 (144)
Q Consensus 101 ~~~kvGD~V~I~ 112 (144)
.++++||.|++-
T Consensus 310 ~~~~~Gd~v~l~ 321 (354)
T cd06827 310 PEAKVGDPVELW 321 (354)
T ss_pred CCCCCCCEEEEE
Confidence 368899999664
No 56
>cd04451 S1_IF1 S1_IF1: Translation Initiation Factor IF1, S1-like RNA-binding domain. IF1 contains an S1-like RNA-binding domain, which is found in a wide variety of RNA-associated proteins. Translation initiation includes a number of interrelated steps preceding the formation of the first peptide bond. In Escherichia coli, the initiation mechanism requires, in addition to mRNA, fMet-tRNA, and ribosomal subunits, the presence of three additional proteins (initiation factors IF1, IF2, and IF3) and at least one GTP molecule. The three initiation factors influence both the kinetics and the stability of ternary complex formation. IF1 is the smallest of the three factors. IF1 enhances the rate of 70S ribosome subunit association and dissociation and the interaction of 30S ribosomal subunit with IF2 and IF3. It stimulates 30S complex formation. In addition, by binding to the A-site of the 30S ribosomal subunit, IF1 may contribute to the fidelity of the selection of the initiation site of th
Probab=23.27 E-value=2.1e+02 Score=18.33 Aligned_cols=49 Identities=16% Similarity=0.091 Sum_probs=25.4
Q ss_pred EEEEEEEecCCCCeEEEEEeEEEeeceeeeEEeeeeeEEEEcCCCCCCCCCCEEEEe
Q 032281 56 ILAGTCHSAKMNRTIIVRRNYLHFVKKYQRYEKRHSNIPAHISPCFRVKEGDHVIIG 112 (144)
Q Consensus 56 il~G~VvS~KM~KTvvV~v~~~~~~pkY~K~~kr~kk~~vHd~p~~~~kvGD~V~I~ 112 (144)
++.|+|++.-...-..|..+ -...|....+.+-+ + ..+.+.+||.|.+.
T Consensus 2 ~~~G~Vi~~~~g~~~~V~~~---~g~~~~c~~rGklr---~--~~~~~~vGD~V~~~ 50 (64)
T cd04451 2 EMEGVVTEALPNAMFRVELE---NGHEVLAHISGKMR---M--NYIRILPGDRVKVE 50 (64)
T ss_pred eEEEEEEEEeCCCEEEEEeC---CCCEEEEEECceee---c--CCcccCCCCEEEEE
Confidence 35677776553333334321 01344444444322 1 23458999999876
No 57
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=23.04 E-value=1.2e+02 Score=23.70 Aligned_cols=66 Identities=23% Similarity=0.221 Sum_probs=35.0
Q ss_pred Cceeee--eEeceEEEEEEEecCCCCeEEEEEeEE-----EeeceeeeEEeeeeeEEEE--cCCCCCCCCCCEEEEe
Q 032281 45 PFTGTV--SIRGRILAGTCHSAKMNRTIIVRRNYL-----HFVKKYQRYEKRHSNIPAH--ISPCFRVKEGDHVIIG 112 (144)
Q Consensus 45 Pf~g~~--sirg~il~G~VvS~KM~KTvvV~v~~~-----~~~pkY~K~~kr~kk~~vH--d~p~~~~kvGD~V~I~ 112 (144)
||.+.. .-.|.+..|+|++.. ++-+.|..... ...+-+.-++.... +.-. ++....+++||+|...
T Consensus 54 P~~~~~~~~~~GdiV~GkV~~i~-~~g~~V~I~~~~~~~~~l~~~~~G~l~~s~-i~~~~~~~~~~~~~~GD~V~ak 128 (189)
T PRK09521 54 PFKKTPPLLKKGDIVYGRVVDVK-EQRALVRIVSIEGSERELATSKLAYIHISQ-VSDGYVESLTDAFKIGDIVRAK 128 (189)
T ss_pred cCcCCCCCCCCCCEEEEEEEEEc-CCeEEEEEEEecccccccCCCceeeEEhhH-cChhhhhhHHhccCCCCEEEEE
Confidence 777633 236999999999884 46666665321 01122333332221 1100 0112348999999765
No 58
>COG2012 RPB5 DNA-directed RNA polymerase, subunit H, RpoH/RPB5 [Transcription]
Probab=22.94 E-value=1.1e+02 Score=21.88 Aligned_cols=22 Identities=36% Similarity=0.365 Sum_probs=14.5
Q ss_pred eEEEEcCCC---CCCCCCCEEEEeee
Q 032281 92 NIPAHISPC---FRVKEGDHVIIGQC 114 (144)
Q Consensus 92 k~~vHd~p~---~~~kvGD~V~I~ec 114 (144)
++.+-| |- ..++.||+|.|.--
T Consensus 42 kI~~~D-Pva~~lgak~GdvVkIvRk 66 (80)
T COG2012 42 KIKASD-PVAKALGAKPGDVVKIVRK 66 (80)
T ss_pred cccccC-hhHHHccCCCCcEEEEEec
Confidence 345666 52 36999998877643
No 59
>cd05698 S1_Rrp5_repeat_hs6_sc5 S1_Rrp5_repeat_hs6_sc5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 6 (hs6) and S. cerevisiae S1 repeat 5 (sc5). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=22.83 E-value=1.8e+02 Score=18.27 Aligned_cols=58 Identities=21% Similarity=0.208 Sum_probs=31.0
Q ss_pred ceEEEEEEEecCCCCeEEEEEeEEEeeceeeeEEeeeeeE---EEEcCCCCCCCCCCEEEEe--eeecCCC
Q 032281 54 GRILAGTCHSAKMNRTIIVRRNYLHFVKKYQRYEKRHSNI---PAHISPCFRVKEGDHVIIG--QCRPLSK 119 (144)
Q Consensus 54 g~il~G~VvS~KM~KTvvV~v~~~~~~pkY~K~~kr~kk~---~vHd~p~~~~kvGD~V~I~--ecRPlSK 119 (144)
|.++.|.|++.. +.-+.|....- -.-++.. +.+ .+++ +....++||.|.+. +.-|-++
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 567889988875 56677765320 1111111 111 1333 44568999988764 3444433
No 60
>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=22.43 E-value=1.5e+02 Score=21.15 Aligned_cols=30 Identities=23% Similarity=0.335 Sum_probs=23.8
Q ss_pred CCCCCCCEEEEeeeecCCCeeeEEEEEeee
Q 032281 101 FRVKEGDHVIIGQCRPLSKTVRFNVLKVIP 130 (144)
Q Consensus 101 ~~~kvGD~V~I~ecRPlSKtK~f~V~~ii~ 130 (144)
.-++.||.|.+....|....-.-+.++|++
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 458999999999999988877877777763
No 61
>PLN00043 elongation factor 1-alpha; Provisional
Probab=22.29 E-value=1.5e+02 Score=26.61 Aligned_cols=50 Identities=14% Similarity=0.169 Sum_probs=26.8
Q ss_pred ceEEEEEEEec--CCCCeEEEEEeEEEeeceeeeEEeeeeeEEEEcCCCCCCCCCCEEEEe
Q 032281 54 GRILAGTCHSA--KMNRTIIVRRNYLHFVKKYQRYEKRHSNIPAHISPCFRVKEGDHVIIG 112 (144)
Q Consensus 54 g~il~G~VvS~--KM~KTvvV~v~~~~~~pkY~K~~kr~kk~~vHd~p~~~~kvGD~V~I~ 112 (144)
|.+..|+|.+- +..-.+.+. |-- ..-+-+.+..|+.+...+..||.|.|.
T Consensus 248 G~vv~G~V~~G~l~~Gd~v~~~-------P~~--~~~~VksI~~~~~~v~~a~aGd~v~i~ 299 (447)
T PLN00043 248 GTVPVGRVETGVIKPGMVVTFG-------PTG--LTTEVKSVEMHHESLQEALPGDNVGFN 299 (447)
T ss_pred EEEEEEEEECCEEeeCCEEEEc-------CCC--CEEEEEEEEECCeEeCEecCCCeEEEE
Confidence 55677777764 223333332 211 123445556666566677777777664
No 62
>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=21.97 E-value=53 Score=22.91 Aligned_cols=14 Identities=29% Similarity=0.456 Sum_probs=11.3
Q ss_pred CCCCCCEEEEeeee
Q 032281 102 RVKEGDHVIIGQCR 115 (144)
Q Consensus 102 ~~kvGD~V~I~ecR 115 (144)
.+++||++.+.||-
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 63
>KOG1698 consensus Mitochondrial/chloroplast ribosomal protein L19 [Translation, ribosomal structure and biogenesis]
Probab=21.32 E-value=1.7e+02 Score=24.33 Aligned_cols=36 Identities=19% Similarity=0.116 Sum_probs=29.3
Q ss_pred EEEEcCCCCCCCCCCEEEEeeeecCCCeeeEEEEEeeec
Q 032281 93 IPAHISPCFRVKEGDHVIIGQCRPLSKTVRFNVLKVIPA 131 (144)
Q Consensus 93 ~~vHd~p~~~~kvGD~V~I~ecRPlSKtK~f~V~~ii~~ 131 (144)
++-|. | +.++||+|.|..--|-++.+-++...|.=.
T Consensus 90 ~~r~i-P--e~~~G~Iv~V~s~~p~~k~k~s~f~Gi~I~ 125 (201)
T KOG1698|consen 90 KVRDI-P--EFKVGSIVRVTSEDPENKRKVSRFKGICIR 125 (201)
T ss_pred hcccC-C--ccccccEEEEEecCCccCCceeEEEEEEEE
Confidence 34454 4 899999999999999999999988888543
No 64
>PRK01678 rpmE2 50S ribosomal protein L31 type B; Reviewed
Probab=20.47 E-value=2.8e+02 Score=19.96 Aligned_cols=33 Identities=15% Similarity=0.243 Sum_probs=26.1
Q ss_pred eceeeeEEeeeeeEEEEcCCCCCCCCCCEEEEeeeecCCCeeeEE
Q 032281 80 VKKYQRYEKRHSNIPAHISPCFRVKEGDHVIIGQCRPLSKTVRFN 124 (144)
Q Consensus 80 ~pkY~K~~kr~kk~~vHd~p~~~~kvGD~V~I~ecRPlSKtK~f~ 124 (144)
||.|... .++| +.-|....++.+.+-..|..|.
T Consensus 6 HP~y~~v-------~~~~-----~t~g~~f~~~ST~~~~~t~~~~ 38 (87)
T PRK01678 6 HPEYRPV-------VFHD-----TSTGFKFLTGSTITTDETIEWE 38 (87)
T ss_pred CCCCEEE-------EEEE-----CCCCCEEEEeeeccccceeeec
Confidence 7888765 4776 5668899999999988888884
Done!