Query psy10000
Match_columns 193
No_of_seqs 292 out of 1370
Neff 4.7
Searched_HMMs 46136
Date Fri Aug 16 15:20:15 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy10000.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/10000hhsearch_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 4.4E-67 9.6E-72 427.3 14.8 149 44-193 4-158 (158)
2 KOG1728|consensus 100.0 1.6E-66 3.4E-71 416.6 6.4 150 44-193 4-156 (156)
3 PRK08572 rps17p 30S ribosomal 100.0 3.7E-50 8.1E-55 310.9 13.7 107 73-184 1-107 (108)
4 TIGR03630 arch_S17P archaeal r 100.0 1.5E-47 3.2E-52 293.8 13.3 102 75-181 1-102 (102)
5 COG0186 RpsQ Ribosomal protein 100.0 2.3E-37 5E-42 231.4 11.3 86 98-185 1-86 (87)
6 CHL00142 rps17 ribosomal prote 100.0 4.3E-33 9.4E-38 207.4 11.8 79 105-185 3-81 (84)
7 PRK05610 rpsQ 30S ribosomal pr 100.0 4.3E-33 9.3E-38 207.3 11.5 78 105-184 6-83 (84)
8 TIGR03635 S17_bact 30S ribosom 100.0 5E-32 1.1E-36 195.9 9.8 70 106-177 2-71 (71)
9 PF00366 Ribosomal_S17: Riboso 100.0 2.3E-30 5.1E-35 186.0 10.5 69 110-180 1-69 (69)
10 KOG1740|consensus 99.9 1.1E-27 2.5E-32 183.2 -0.1 78 106-185 3-80 (107)
11 KOG1728|consensus 99.8 7.8E-20 1.7E-24 147.4 1.3 62 1-62 2-65 (156)
12 PTZ00241 40S ribosomal protein 99.7 9.2E-18 2E-22 137.7 2.1 63 1-63 2-66 (158)
13 KOG3447|consensus 98.9 2.8E-10 6.1E-15 91.8 1.4 83 100-184 5-88 (150)
14 PRK08572 rps17p 30S ribosomal 93.5 0.027 5.8E-07 44.2 0.6 27 34-63 1-27 (108)
15 PF10915 DUF2709: Protein of u 91.4 0.13 2.9E-06 44.6 2.2 64 5-101 31-96 (238)
16 COG0361 InfA Translation initi 64.2 30 0.00065 25.5 6.0 52 106-171 7-62 (75)
17 TIGR00008 infA translation ini 61.7 42 0.0009 24.2 6.2 54 106-173 5-62 (68)
18 PF10844 DUF2577: Protein of u 61.0 68 0.0015 24.1 7.7 23 154-179 76-98 (100)
19 TIGR00523 eIF-1A eukaryotic/ar 55.3 49 0.0011 25.3 6.0 50 107-170 20-72 (99)
20 cd05793 S1_IF1A S1_IF1A: Trans 53.3 48 0.001 24.1 5.5 56 108-177 2-60 (77)
21 PTZ00329 eukaryotic translatio 51.2 1.2E+02 0.0026 25.3 8.1 59 108-180 34-95 (155)
22 cd04456 S1_IF1A_like S1_IF1A_l 50.4 67 0.0015 23.5 5.9 56 108-177 2-61 (78)
23 PF09740 DUF2043: Uncharacteri 47.9 6.9 0.00015 30.9 0.3 13 92-104 87-99 (110)
24 smart00652 eIF1a eukaryotic tr 47.1 81 0.0018 23.2 5.9 57 107-177 6-65 (83)
25 cd03698 eRF3_II_like eRF3_II_l 45.0 68 0.0015 22.7 5.1 24 140-164 43-66 (83)
26 PLN00208 translation initiatio 42.5 1.9E+02 0.0042 23.8 8.2 59 108-180 34-95 (145)
27 COG2053 RPS28A Ribosomal prote 40.1 39 0.00085 24.6 3.1 13 154-166 47-59 (69)
28 PRK12442 translation initiatio 39.9 1E+02 0.0022 23.5 5.5 62 106-181 7-72 (87)
29 cd03693 EF1_alpha_II EF1_alpha 36.5 1.1E+02 0.0023 22.2 5.2 25 139-164 46-70 (91)
30 TIGR03595 Obg_CgtA_exten Obg f 34.3 28 0.00061 24.7 1.7 13 154-166 53-65 (69)
31 PF11604 CusF_Ec: Copper bindi 33.5 1.7E+02 0.0037 20.5 7.1 66 110-181 1-67 (70)
32 PF04246 RseC_MucC: Positive r 33.2 47 0.001 25.8 3.0 19 144-165 44-62 (135)
33 PF13550 Phage-tail_3: Putativ 31.1 1.1E+02 0.0025 23.4 4.8 40 137-181 124-163 (164)
34 KOG3416|consensus 30.8 2E+02 0.0044 23.5 6.2 50 105-164 22-71 (134)
35 cd03695 CysN_NodQ_II CysN_NodQ 29.8 1.6E+02 0.0035 20.9 5.1 26 139-165 42-67 (81)
36 PF09269 DUF1967: Domain of un 28.7 27 0.00058 24.8 0.8 12 154-165 53-64 (69)
37 PF06107 DUF951: Bacterial pro 28.7 81 0.0017 22.2 3.2 25 155-180 2-26 (57)
38 cd03696 selB_II selB_II: this 25.8 2.4E+02 0.0051 19.7 5.4 25 139-164 42-66 (83)
39 cd03694 GTPBP_II Domain II of 25.6 1.4E+02 0.003 21.4 4.1 25 139-164 46-70 (87)
40 PRK01678 rpmE2 50S ribosomal p 25.6 2E+02 0.0042 21.8 5.0 34 130-176 5-38 (87)
41 KOG1730|consensus 24.9 47 0.001 28.8 1.7 18 94-111 74-91 (206)
42 PRK04012 translation initiatio 24.6 3.2E+02 0.007 20.9 7.5 57 107-177 22-81 (100)
43 PF11302 DUF3104: Protein of u 24.1 1.3E+02 0.0028 22.3 3.7 34 152-185 3-38 (75)
44 cd03697 EFTU_II EFTU_II: Elong 23.9 2.1E+02 0.0045 20.4 4.8 53 104-164 14-68 (87)
45 cd05789 S1_Rrp4 S1_Rrp4: Rrp4 23.4 2.4E+02 0.0052 19.6 5.0 21 104-125 6-26 (86)
46 cd03689 RF3_II RF3_II: this su 21.8 2.6E+02 0.0056 20.0 5.0 12 154-165 61-72 (85)
47 smart00380 AP2 DNA-binding dom 21.5 43 0.00092 22.9 0.7 19 35-53 25-44 (64)
48 PF08605 Rad9_Rad53_bind: Fung 21.4 1.1E+02 0.0024 24.6 3.2 25 154-183 59-83 (131)
49 cd00018 AP2 DNA-binding domain 21.0 45 0.00098 22.4 0.7 19 34-52 25-44 (61)
50 PF13567 DUF4131: Domain of un 20.7 3.6E+02 0.0077 19.9 7.2 62 107-171 79-146 (176)
51 PF07653 SH3_2: Variant SH3 do 20.7 54 0.0012 21.4 1.1 23 141-164 5-27 (55)
52 cd04089 eRF3_II eRF3_II: domai 20.5 3.1E+02 0.0068 19.2 5.6 23 141-164 43-65 (82)
53 cd00174 SH3 Src homology 3 dom 20.2 98 0.0021 18.7 2.2 13 154-166 17-29 (54)
54 PRK10862 SoxR reducing system 20.0 1.1E+02 0.0025 24.8 3.0 19 143-164 50-68 (154)
No 1
>PTZ00241 40S ribosomal protein S11; Provisional
Probab=100.00 E-value=4.4e-67 Score=427.27 Aligned_cols=149 Identities=70% Similarity=1.141 Sum_probs=141.0
Q ss_pred hhhhhhhccCcceeeecccccccc---cceeeeeecccccCCcccccccccCcCCCceeeeeeeceEEEEEEEeccCCce
Q psy10000 44 RETERAFQKQPTIFLARKPTYKKK---SLRYHKTVGLGFKTPREAIDGTYIDKKCPFTGNVSIRGRILIGIVRKMKMQRT 120 (193)
Q Consensus 44 ~eAe~ayqKQ~~if~~~~~~~~~~---~~r~~~~igl~~~~P~~~~~~~y~d~~cPf~g~~~irg~~l~G~Vvs~Km~KT 120 (193)
.|+|+|||+|++||+|+++..+++ .+||++||||||++|++||||+|||++|||||||||||++|+|+|+|++|+||
T Consensus 4 ~q~e~a~qkq~~i~~~~~~~~~~~~~~~~r~~k~iGl~~~~P~~~~~~~yiD~kCPf~G~~~iRgril~G~VvS~KM~KT 83 (158)
T PTZ00241 4 VQTERAFQKQEGVFQNSKRLLKKKTSKGVRYWKKVGLGFKTPKEAIEGKYIDKKCPFTGNVSIRGRILRGVVISTKMKRT 83 (158)
T ss_pred ccchhhhccCCceeeccccccccccccccchhhhcCCCCcCChhhhcccccCCCCCccceeeEcceEEEEEEEEccCCcc
Confidence 578999999999999999853333 48999999999999999999999999999999999999999999999999999
Q ss_pred EEEEEeEEeeecceeeEEeeeeeEEEEcCCCCCCCCCCCEEEEeeeecCCCceeEEEEEEEecC--cc-ccccccC
Q psy10000 121 IVIRRDYLHYIKKYNRFEKRHRNMSVHLSPAFRDVEIGDVVTVGECRPLSKTVRFNVLKVTKGT--GS-KKAFKKF 193 (193)
Q Consensus 121 vvV~~~~~~~~~KYkk~~kr~kk~~vHd~~~~~~~kvGD~V~I~ecRPlSKtK~f~V~~v~~~~--~~-~k~f~~~ 193 (193)
|||+++|++|||+|+||++|+++|+||||+|+ +|++||+|+|+|||||||||+|+|++|++++ ++ +|||++|
T Consensus 84 IVV~ve~~~~h~kY~K~~kr~kk~~aHd~~~~-~~kvGD~V~I~EcRPLSKTKrf~Vv~V~~~~~~~~~~k~f~~f 158 (158)
T PTZ00241 84 IIIRRDYLHYVKKYNRYEKRHKNIPVHCSPCF-DVKEGDIVVVGQCRPLSKTVRFNVLKVEKNEIIGNVRKQFVLF 158 (158)
T ss_pred EEEEEEEEEecCccceEEEeeecEEEeCCccC-CCCCCCEEEEEEcCCCCCceeEEEEEEEecccccccccccccC
Confidence 99999999999999999999999999999996 7999999999999999999999999999987 44 9999987
No 2
>KOG1728|consensus
Probab=100.00 E-value=1.6e-66 Score=416.62 Aligned_cols=150 Identities=78% Similarity=1.218 Sum_probs=145.6
Q ss_pred hhhhhhhccCcceeeecccc---cccccceeeeeecccccCCcccccccccCcCCCceeeeeeeceEEEEEEEeccCCce
Q psy10000 44 RETERAFQKQPTIFLARKPT---YKKKSLRYHKTVGLGFKTPREAIDGTYIDKKCPFTGNVSIRGRILIGIVRKMKMQRT 120 (193)
Q Consensus 44 ~eAe~ayqKQ~~if~~~~~~---~~~~~~r~~~~igl~~~~P~~~~~~~y~d~~cPf~g~~~irg~~l~G~Vvs~Km~KT 120 (193)
.+.|+|||+|+++|+|.|+. .+++.+|+++||||||+||+||++|+|||+||||||+|||||++|+|+|+++||++|
T Consensus 4 vq~eraF~kq~~v~~~~k~~~~~~~k~~~r~~~~iglGFKtP~eAiegtYIDKKCPftG~vsIRGril~G~V~k~Km~rT 83 (156)
T KOG1728|consen 4 VQTERAFQKQPGVFLNAKASGKRTSKKGKRRYKNIGLGFKTPREAIEGTYIDKKCPFTGNVSIRGRILTGTVVKMKMQRT 83 (156)
T ss_pred hhhhHHhhhCccccccCcccccccccccchhhhhcCcccCChHHhhcceeecccCCcccceeEeeEEEeeEEeeeceeEE
Confidence 46799999999999999964 568999999999999999999999999999999999999999999999999999999
Q ss_pred EEEEEeEEeeecceeeEEeeeeeEEEEcCCCCCCCCCCCEEEEeeeecCCCceeEEEEEEEecCccccccccC
Q psy10000 121 IVIRRDYLHYIKKYNRFEKRHRNMSVHLSPAFRDVEIGDVVTVGECRPLSKTVRFNVLKVTKGTGSKKAFKKF 193 (193)
Q Consensus 121 vvV~~~~~~~~~KYkk~~kr~kk~~vHd~~~~~~~kvGD~V~I~ecRPlSKtK~f~V~~v~~~~~~~k~f~~~ 193 (193)
|||++|||||++||+||++||+|++||.+|||+++++||+|+|+||||||||+||+|++|+++++..++|.+|
T Consensus 84 IvvrrdYlHy~~KY~ryekrHkN~svh~SPcFrdi~~gDiVtvGecrPLSKtvrfnVLkv~k~~g~~k~~~k~ 156 (156)
T KOG1728|consen 84 IVVRRDYLHYIKKYNRYEKRHKNMSVHVSPCFRDIQEGDIVTVGECRPLSKTVRFNVLKVIKAAGSKKQFKKF 156 (156)
T ss_pred EEEEhhhhhHhHHhhHHHHhccCCccccchhhhccccCCEEEEeecccccceEEEEEEEEeecCCCccccccC
Confidence 9999999999999999999999999999999999999999999999999999999999999999999999987
No 3
>PRK08572 rps17p 30S ribosomal protein S17P; Reviewed
Probab=100.00 E-value=3.7e-50 Score=310.94 Aligned_cols=107 Identities=44% Similarity=0.879 Sum_probs=104.2
Q ss_pred eeecccccCCcccccccccCcCCCceeeeeeeceEEEEEEEeccCCceEEEEEeEEeeecceeeEEeeeeeEEEEcCCCC
Q psy10000 73 KTVGLGFKTPREAIDGTYIDKKCPFTGNVSIRGRILIGIVRKMKMQRTIVIRRDYLHYIKKYNRFEKRHRNMSVHLSPAF 152 (193)
Q Consensus 73 ~~igl~~~~P~~~~~~~y~d~~cPf~g~~~irg~~l~G~Vvs~Km~KTvvV~~~~~~~~~KYkk~~kr~kk~~vHd~~~~ 152 (193)
+||||||++|+++|+ |++|||||+|+|||++|+|+|+|++|+|||+|++++++|||+|+||++++++|+||||+|+
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 9999999999999999999999999999999999999999999999999999999999984
Q ss_pred CCCCCCCEEEEeeeecCCCceeEEEEEEEecC
Q psy10000 153 RDVEIGDVVTVGECRPLSKTVRFNVLKVTKGT 184 (193)
Q Consensus 153 ~~~kvGD~V~I~ecRPlSKtK~f~V~~v~~~~ 184 (193)
+|++||+|+|+|||||||+|+|+|++|++++
T Consensus 77 -~~kvGD~V~I~E~RPiSKtK~w~v~~i~~~~ 107 (108)
T PRK08572 77 -DAKVGDKVKIAECRPLSKTKSFVVVEKKERA 107 (108)
T ss_pred -CCCCCCEEEEEEcCCCCCceEEEEEEEEEcC
Confidence 8999999999999999999999999999865
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=1.5e-47 Score=293.80 Aligned_cols=102 Identities=45% Similarity=0.839 Sum_probs=98.2
Q ss_pred ecccccCCcccccccccCcCCCceeeeeeeceEEEEEEEeccCCceEEEEEeEEeeecceeeEEeeeeeEEEEcCCCCCC
Q psy10000 75 VGLGFKTPREAIDGTYIDKKCPFTGNVSIRGRILIGIVRKMKMQRTIVIRRDYLHYIKKYNRFEKRHRNMSVHLSPAFRD 154 (193)
Q Consensus 75 igl~~~~P~~~~~~~y~d~~cPf~g~~~irg~~l~G~Vvs~Km~KTvvV~~~~~~~~~KYkk~~kr~kk~~vHd~~~~~~ 154 (193)
|||++++|+++|+ |++|||||+|+|||++|+|+|+|++|+|||+|+++++++||+|+|+++++++|+||||+| |+
T Consensus 1 ig~~~~~p~~~~~----d~~cpf~g~l~irgk~l~G~VvS~Km~KTivV~V~r~~~hpkY~K~i~r~kky~aHDe~c-n~ 75 (102)
T TIGR03630 1 IGIPVKPPERECN----DPKCPFHGHLKVRGQILEGVVVSDKMNKTVVVEREYLYYDRKYERYERRRSKIHAHNPPC-ID 75 (102)
T ss_pred CCcccCCCCcccc----CCCCCccceeeeeeEEEEEEEEecCCCceEEEEEEEEEecCCccEEEEEeeeEEEECCCC-CC
Confidence 7999999997766 999999999999999999999999999999999999999999999999999999999997 48
Q ss_pred CCCCCEEEEeeeecCCCceeEEEEEEE
Q psy10000 155 VEIGDVVTVGECRPLSKTVRFNVLKVT 181 (193)
Q Consensus 155 ~kvGD~V~I~ecRPlSKtK~f~V~~v~ 181 (193)
|++||+|+|+|||||||||+|+|++|+
T Consensus 76 ~kvGD~V~I~E~RPlSKtK~w~vv~i~ 102 (102)
T TIGR03630 76 VKEGDIVIIGETRPLSKTKSFVVLGKV 102 (102)
T ss_pred CCCCCEEEEEEcCCCCCceEEEEEEeC
Confidence 999999999999999999999999984
No 5
>COG0186 RpsQ Ribosomal protein S17 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=2.3e-37 Score=231.42 Aligned_cols=86 Identities=34% Similarity=0.623 Sum_probs=82.7
Q ss_pred eeeeeeeceEEEEEEEeccCCceEEEEEeEEeeecceeeEEeeeeeEEEEcCCCCCCCCCCCEEEEeeeecCCCceeEEE
Q psy10000 98 TGNVSIRGRILIGIVRKMKMQRTIVIRRDYLHYIKKYNRFEKRHRNMSVHLSPAFRDVEIGDVVTVGECRPLSKTVRFNV 177 (193)
Q Consensus 98 ~g~~~irg~~l~G~Vvs~Km~KTvvV~~~~~~~~~KYkk~~kr~kk~~vHd~~~~~~~kvGD~V~I~ecRPlSKtK~f~V 177 (193)
||+++++|++|+|+|+|++|+|||+|++++.++||+|+||++++++|+||| +|+ +|++||+|+|+|||||||||+|+|
T Consensus 1 ~~~~~~~~k~l~G~VvS~Km~KTvvV~ve~~~~hp~Y~K~v~r~kK~~aHd-e~~-~~k~GD~V~I~EtRPLSKtK~~~v 78 (87)
T COG0186 1 HGKLRVRGRVLEGVVVSDKMDKTVVVEVERKVYHPKYGKYVRRSKKYHAHD-ECN-EAKVGDIVRIAETRPLSKTKRFVV 78 (87)
T ss_pred CCccccCceEEEEEEEEccCceeEEEEEEEEEecccceEEEEEEeeeEeec-ccc-cCCCCCEEEEEEccccCCcceEEE
Confidence 689999999999999999999999999999999999999999999999999 664 899999999999999999999999
Q ss_pred EEEEecCc
Q psy10000 178 LKVTKGTG 185 (193)
Q Consensus 178 ~~v~~~~~ 185 (193)
+++++++.
T Consensus 79 v~i~~~a~ 86 (87)
T COG0186 79 VEIVEKAV 86 (87)
T ss_pred EEEeeecc
Confidence 99998864
No 6
>CHL00142 rps17 ribosomal protein S17; Validated
Probab=100.00 E-value=4.3e-33 Score=207.42 Aligned_cols=79 Identities=30% Similarity=0.397 Sum_probs=76.0
Q ss_pred ceEEEEEEEeccCCceEEEEEeEEeeecceeeEEeeeeeEEEEcCCCCCCCCCCCEEEEeeeecCCCceeEEEEEEEecC
Q psy10000 105 GRILIGIVRKMKMQRTIVIRRDYLHYIKKYNRFEKRHRNMSVHLSPAFRDVEIGDVVTVGECRPLSKTVRFNVLKVTKGT 184 (193)
Q Consensus 105 g~~l~G~Vvs~Km~KTvvV~~~~~~~~~KYkk~~kr~kk~~vHd~~~~~~~kvGD~V~I~ecRPlSKtK~f~V~~v~~~~ 184 (193)
.+.|.|+|+|++|+|||+|++++++|||+|+|+++++++|+||||.| +|++||+|+|+|||||||||+|+|++|++++
T Consensus 3 ~~~~~G~Vvs~km~KTivV~v~r~~~h~kY~K~~~r~kk~~aHDe~n--~~~~GD~V~I~e~RPlSKtK~~~v~~i~~~~ 80 (84)
T CHL00142 3 VKEKIGIVVSNKMNKTIVVAVENRYKHPIYGKIITKTKKYLVHDEEN--ECNIGDQVLIEETRPLSKTKRWILKEILSKS 80 (84)
T ss_pred ceEEEEEEEeCCCCceEEEEEEEEEEcCcccEEEEeeEEEEEeCCCC--CCCCCCEEEEEEcCCCCCcEEEEEEEEEEee
Confidence 47899999999999999999999999999999999999999999987 8999999999999999999999999999877
Q ss_pred c
Q psy10000 185 G 185 (193)
Q Consensus 185 ~ 185 (193)
.
T Consensus 81 ~ 81 (84)
T CHL00142 81 S 81 (84)
T ss_pred e
Confidence 4
No 7
>PRK05610 rpsQ 30S ribosomal protein S17; Reviewed
Probab=100.00 E-value=4.3e-33 Score=207.33 Aligned_cols=78 Identities=32% Similarity=0.453 Sum_probs=75.7
Q ss_pred ceEEEEEEEeccCCceEEEEEeEEeeecceeeEEeeeeeEEEEcCCCCCCCCCCCEEEEeeeecCCCceeEEEEEEEecC
Q psy10000 105 GRILIGIVRKMKMQRTIVIRRDYLHYIKKYNRFEKRHRNMSVHLSPAFRDVEIGDVVTVGECRPLSKTVRFNVLKVTKGT 184 (193)
Q Consensus 105 g~~l~G~Vvs~Km~KTvvV~~~~~~~~~KYkk~~kr~kk~~vHd~~~~~~~kvGD~V~I~ecRPlSKtK~f~V~~v~~~~ 184 (193)
+++|.|+|+|++|+|||+|++++++|||+|+||++++++|+||||+| +|++||+|+|+|||||||+|+|+|++|++++
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 RKTLQGRVVSDKMDKTIVVLVERRVKHPLYGKIVKRSKKYHAHDENN--EAKIGDVVRIMETRPLSKTKRWRLVEIVEKA 83 (84)
T ss_pred CCEEEEEEEcccCCceEEEEEEEEEEeccccEEEEcceEEEEECCCC--CCCCCCEEEEEEcccCCCCEEEEEEEEEecc
Confidence 68999999999999999999999999999999999999999999987 8999999999999999999999999999865
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=99.97 E-value=5e-32 Score=195.95 Aligned_cols=70 Identities=34% Similarity=0.493 Sum_probs=68.2
Q ss_pred eEEEEEEEeccCCceEEEEEeEEeeecceeeEEeeeeeEEEEcCCCCCCCCCCCEEEEeeeecCCCceeEEE
Q psy10000 106 RILIGIVRKMKMQRTIVIRRDYLHYIKKYNRFEKRHRNMSVHLSPAFRDVEIGDVVTVGECRPLSKTVRFNV 177 (193)
Q Consensus 106 ~~l~G~Vvs~Km~KTvvV~~~~~~~~~KYkk~~kr~kk~~vHd~~~~~~~kvGD~V~I~ecRPlSKtK~f~V 177 (193)
++|.|+|+|++|+|||+|++++++|||+|+|+++++++|+||||+| +|++||+|+|+|||||||+|+|+|
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 KTLQGVVVSDKMDKTIVVLVERRVKHPLYGKIVKRTKKYHAHDENN--ECKVGDVVRIIETRPLSKTKRWRL 71 (71)
T ss_pred eEEEEEEEcccCCceEEEEEEEEEEeccccEEEEccEEEEEECCCC--CCCCCCEEEEEEcCCcCCceEeEC
Confidence 6899999999999999999999999999999999999999999987 899999999999999999999985
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=2.3e-30 Score=186.03 Aligned_cols=69 Identities=41% Similarity=0.679 Sum_probs=66.6
Q ss_pred EEEEeccCCceEEEEEeEEeeecceeeEEeeeeeEEEEcCCCCCCCCCCCEEEEeeeecCCCceeEEEEEE
Q psy10000 110 GIVRKMKMQRTIVIRRDYLHYIKKYNRFEKRHRNMSVHLSPAFRDVEIGDVVTVGECRPLSKTVRFNVLKV 180 (193)
Q Consensus 110 G~Vvs~Km~KTvvV~~~~~~~~~KYkk~~kr~kk~~vHd~~~~~~~kvGD~V~I~ecRPlSKtK~f~V~~v 180 (193)
|+|+|++|+|||+|++++++|||+|+|+++++++|+||||+| .|++||+|+|.|||||||+|+|+|++|
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 GVVVSDKMDKTVVVRVERLVYHPKYKKYIKRTKKYMAHDENN--ICKVGDKVRIRECRPISKTKRFVVVEV 69 (69)
T ss_dssp EEEEEEESTTEEEEEEEEEEEETTTEEEEEEEEEEEEE-TTS--SSTTTSEEEEEEEEEEETTEEEEEEEE
T ss_pred CEEEEcCCCCeEEEEEEEEEEcceEeeccCccccEEEeCCcc--CCCCCCEEEEEeeeccCCcEeEEEEEC
Confidence 899999999999999999999999999999999999999998 699999999999999999999999986
No 10
>KOG1740|consensus
Probab=99.93 E-value=1.1e-27 Score=183.22 Aligned_cols=78 Identities=35% Similarity=0.534 Sum_probs=74.7
Q ss_pred eEEEEEEEeccCCceEEEEEeEEeeecceeeEEeeeeeEEEEcCCCCCCCCCCCEEEEeeeecCCCceeEEEEEEEecCc
Q psy10000 106 RILIGIVRKMKMQRTIVIRRDYLHYIKKYNRFEKRHRNMSVHLSPAFRDVEIGDVVTVGECRPLSKTVRFNVLKVTKGTG 185 (193)
Q Consensus 106 ~~l~G~Vvs~Km~KTvvV~~~~~~~~~KYkk~~kr~kk~~vHd~~~~~~~kvGD~V~I~ecRPlSKtK~f~V~~v~~~~~ 185 (193)
..+.|+|+|++|+|||+|+++++.+||+|+||++++++|+|||+.+ .|++||.|+|..||||||||+|.+.+|+++++
T Consensus 3 ~~~vg~VvS~kmqKTv~V~V~rl~~n~~ynryv~~~~kymahD~~n--~cnvGD~VrlepsRPlSk~K~f~i~eII~~a~ 80 (107)
T KOG1740|consen 3 KNVVGTVVSNKMQKTVKVRVDRLFFNPKYNRYVKRTSKYMAHDDKN--QCNVGDRVRLEPSRPLSKTKHFIIAEIIKKAR 80 (107)
T ss_pred ccceeeeeecccCceeEEEeeeccccHHHHHHHHHhhheeecCccc--cccccceEEeccCCcccccceeehHHHHHHHh
Confidence 4688999999999999999999999999999999999999999986 79999999999999999999999999998764
No 11
>KOG1728|consensus
Probab=99.77 E-value=7.8e-20 Score=147.40 Aligned_cols=62 Identities=44% Similarity=0.702 Sum_probs=56.3
Q ss_pred CccchhhhhccCcceeeceecccc-cCCCccceeeccCcccccchhh-hhhhccCcceeeeccc
Q psy10000 1 MAEQNERSFQKQPTVFLNRKKGLS-KKRKELRYFRDVGLGFKSPRET-ERAFQKQPTIFLARKP 62 (193)
Q Consensus 1 m~~q~e~afqKQ~~if~~~k~~~~-~~~k~~R~~K~IGLGfKtP~eA-e~ayqKQ~~if~~~~~ 62 (193)
|++|+|+|||+|++||+|.+.... .+++.+|||+|||||||||+|| |+.|+|++|+|++.-.
T Consensus 2 ~~vq~eraF~kq~~v~~~~k~~~~~~~k~~~r~~~~iglGFKtP~eAiegtYIDKKCPftG~vs 65 (156)
T KOG1728|consen 2 MAVQTERAFQKQPGVFLNAKASGKRTSKKGKRRYKNIGLGFKTPREAIEGTYIDKKCPFTGNVS 65 (156)
T ss_pred cchhhhHHhhhCccccccCcccccccccccchhhhhcCcccCChHHhhcceeecccCCccccee
Confidence 678999999999999999997733 3577899999999999999999 9999999999999774
No 12
>PTZ00241 40S ribosomal protein S11; Provisional
Probab=99.68 E-value=9.2e-18 Score=137.67 Aligned_cols=63 Identities=43% Similarity=0.670 Sum_probs=54.4
Q ss_pred CccchhhhhccCcceeeceecccccC-CCccceeeccCcccccchhh-hhhhccCcceeeecccc
Q psy10000 1 MAEQNERSFQKQPTVFLNRKKGLSKK-RKELRYFRDVGLGFKSPRET-ERAFQKQPTIFLARKPT 63 (193)
Q Consensus 1 m~~q~e~afqKQ~~if~~~k~~~~~~-~k~~R~~K~IGLGfKtP~eA-e~ayqKQ~~if~~~~~~ 63 (193)
|++|+|+|||||++||+|++..++++ .+..||+|||||||++|++| ++.|+|.+|||++.-..
T Consensus 2 ~~~q~e~a~qkq~~i~~~~~~~~~~~~~~~~r~~k~iGl~~~~P~~~~~~~yiD~kCPf~G~~~i 66 (158)
T PTZ00241 2 ADVQTERAFQKQEGVFQNSKRLLKKKTSKGVRYWKKVGLGFKTPKEAIEGKYIDKKCPFTGNVSI 66 (158)
T ss_pred ccccchhhhccCCceeeccccccccccccccchhhhcCCCCcCChhhhcccccCCCCCccceeeE
Confidence 45599999999999999999865432 23589999999999999999 99999999999998753
No 13
>KOG3447|consensus
Probab=98.93 E-value=2.8e-10 Score=91.77 Aligned_cols=83 Identities=22% Similarity=0.256 Sum_probs=75.3
Q ss_pred eeeeeceEEEEEEEeccCCceEEEEEeEEeeecceeeEEeeeeeEEEEcCCCCCCCCCCCEEEEeee-ecCCCceeEEEE
Q psy10000 100 NVSIRGRILIGIVRKMKMQRTIVIRRDYLHYIKKYNRFEKRHRNMSVHLSPAFRDVEIGDVVTVGEC-RPLSKTVRFNVL 178 (193)
Q Consensus 100 ~~~irg~~l~G~Vvs~Km~KTvvV~~~~~~~~~KYkk~~kr~kk~~vHd~~~~~~~kvGD~V~I~ec-RPlSKtK~f~V~ 178 (193)
.-|+++++|-|.|+..+|++|..|++.++..++-.++|..++..|.|||+-. .|++||+|.|.+- -|+.+.+++.|.
T Consensus 5 ~~s~~~~~lmGk~ig~~~q~~akVR~~r~eld~yL~kYf~k~~~yfAhD~~~--~c~vGDtVLir~lp~r~t~~V~H~v~ 82 (150)
T KOG3447|consen 5 KSSVHAQWLMGKVIGTKMQKTAKVRVTRLELDPYLLKYFNKRKTYFAHDALQ--QCTVGDTVLIRALPVRRTKHVKHEVA 82 (150)
T ss_pred EeecccEEEEeeeeeccccccceeeeehhhcCHHHHHHhccccceeecchhh--ccccCCEEEEecCCcchhhhhhhhhH
Confidence 3589999999999999999999999999999999999999999999999986 7999999999995 567788888888
Q ss_pred EEEecC
Q psy10000 179 KVTKGT 184 (193)
Q Consensus 179 ~v~~~~ 184 (193)
+|+-+-
T Consensus 83 ~VVfk~ 88 (150)
T KOG3447|consen 83 EVVFKV 88 (150)
T ss_pred hheeec
Confidence 886553
No 14
>PRK08572 rps17p 30S ribosomal protein S17P; Reviewed
Probab=93.54 E-value=0.027 Score=44.18 Aligned_cols=27 Identities=30% Similarity=0.492 Sum_probs=22.3
Q ss_pred eccCcccccchhhhhhhccCcceeeecccc
Q psy10000 34 RDVGLGFKSPRETERAFQKQPTIFLARKPT 63 (193)
Q Consensus 34 K~IGLGfKtP~eAe~ayqKQ~~if~~~~~~ 63 (193)
+||||||++|++|-. |..|||.+.-+.
T Consensus 1 ~~ig~~~~~p~~~~~---d~~cP~~g~l~i 27 (108)
T PRK08572 1 RNIGLDVKPPEEECD---DPNCPFHGTLPV 27 (108)
T ss_pred CccccCCCCCccccc---CCCCCCcceeee
Confidence 589999999988722 788999998764
No 15
>PF10915 DUF2709: Protein of unknown function (DUF2709); InterPro: IPR024484 Members of this family appear restricted to Chlamydiales. Their function is unknown.
Probab=91.41 E-value=0.13 Score=44.57 Aligned_cols=64 Identities=33% Similarity=0.568 Sum_probs=35.4
Q ss_pred hhhhhccCcceeeceecccccCCCccceeeccCcccccchhhhhhhccCcceeeecccccccccceeeeeecccccCCc-
Q psy10000 5 NERSFQKQPTVFLNRKKGLSKKRKELRYFRDVGLGFKSPRETERAFQKQPTIFLARKPTYKKKSLRYHKTVGLGFKTPR- 83 (193)
Q Consensus 5 ~e~afqKQ~~if~~~k~~~~~~~k~~R~~K~IGLGfKtP~eAe~ayqKQ~~if~~~~~~~~~~~~r~~~~igl~~~~P~- 83 (193)
.|.+|+=||.+|...|- =|+++++|.+..-.- +|..|-. .|-+++-.|.
T Consensus 31 lE~k~~l~PVlF~rdK~-----------------I~qs~e~ai~~lE~e------------~KlWret-eI~I~~g~p~V 80 (238)
T PF10915_consen 31 LEQKFNLQPVLFVRDKI-----------------IFQSAEDAIRILEEE------------GKLWRET-EIKIQSGKPSV 80 (238)
T ss_pred HHHhcCCCceeeecchh-----------------hccCHHHHHHHHHHh------------cchheee-eEEEecCCccc
Confidence 36677777777765442 166666664433221 2333322 4666666664
Q ss_pred -ccccccccCcCCCceeee
Q psy10000 84 -EAIDGTYIDKKCPFTGNV 101 (193)
Q Consensus 84 -~~~~~~y~d~~cPf~g~~ 101 (193)
|...--|| |||||.|
T Consensus 81 NE~TkkIYI---CPFTGKV 96 (238)
T PF10915_consen 81 NEQTKKIYI---CPFTGKV 96 (238)
T ss_pred ccccceEEE---cCCcCcc
Confidence 22223388 9999876
No 16
>COG0361 InfA Translation initiation factor 1 (IF-1) [Translation, ribosomal structure and biogenesis]
Probab=64.18 E-value=30 Score=25.52 Aligned_cols=52 Identities=25% Similarity=0.231 Sum_probs=36.0
Q ss_pred eEEEEEEEeccCCceEEEEEeEEeeecceeeEEeeeeeEEEEcCCCCC----CCCCCCEEEEeeeecCCC
Q psy10000 106 RILIGIVRKMKMQRTIVIRRDYLHYIKKYNRFEKRHRNMSVHLSPAFR----DVEIGDVVTVGECRPLSK 171 (193)
Q Consensus 106 ~~l~G~Vvs~Km~KTvvV~~~~~~~~~KYkk~~kr~kk~~vHd~~~~~----~~kvGD~V~I~ecRPlSK 171 (193)
-.+.|+|+..-.+....|.-+--|. ..||.|.-.+ -+.+||+|++. .+|..-
T Consensus 7 ~e~~g~V~e~L~~~~f~v~~edg~~-------------~~ahI~GKmr~~~i~I~~GD~V~Ve-~~~~d~ 62 (75)
T COG0361 7 IEMEGTVIEMLPNGRFRVELENGHE-------------RLAHISGKMRKNRIRILPGDVVLVE-LSPYDL 62 (75)
T ss_pred cEEEEEEEEecCCCEEEEEecCCcE-------------EEEEccCcchheeEEeCCCCEEEEE-eccccc
Confidence 3578999999888888887655443 3688876432 26789999874 455543
No 17
>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=61.68 E-value=42 Score=24.24 Aligned_cols=54 Identities=20% Similarity=0.177 Sum_probs=35.0
Q ss_pred eEEEEEEEeccCCceEEEEEeEEeeecceeeEEeeeeeEEEEcCCCCC----CCCCCCEEEEeeeecCCCce
Q psy10000 106 RILIGIVRKMKMQRTIVIRRDYLHYIKKYNRFEKRHRNMSVHLSPAFR----DVEIGDVVTVGECRPLSKTV 173 (193)
Q Consensus 106 ~~l~G~Vvs~Km~KTvvV~~~~~~~~~KYkk~~kr~kk~~vHd~~~~~----~~kvGD~V~I~ecRPlSKtK 173 (193)
-.+.|+|+..-.+-...|.-+-- ..+.||.+--++ -+.+||.|.++ -+|..-++
T Consensus 5 ie~~G~V~e~L~~~~f~V~l~ng-------------~~vla~i~GKmr~~rI~I~~GD~V~Ve-~spyd~tk 62 (68)
T TIGR00008 5 IEMEGKVTESLPNAMFRVELENG-------------HEVLAHISGKIRMHYIRILPGDKVKVE-LSPYDLTR 62 (68)
T ss_pred EEEEEEEEEECCCCEEEEEECCC-------------CEEEEEecCcchhccEEECCCCEEEEE-ECcccCCc
Confidence 36789999886666666664321 234677766432 27899999986 55655554
No 18
>PF10844 DUF2577: Protein of unknown function (DUF2577); InterPro: IPR022555 This family of proteins has no known function
Probab=60.97 E-value=68 Score=24.12 Aligned_cols=23 Identities=22% Similarity=0.391 Sum_probs=16.1
Q ss_pred CCCCCCEEEEeeeecCCCceeEEEEE
Q psy10000 154 DVEIGDVVTVGECRPLSKTVRFNVLK 179 (193)
Q Consensus 154 ~~kvGD~V~I~ecRPlSKtK~f~V~~ 179 (193)
.+++||.|.+-. ...--+|.|+.
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 589999999765 44555666554
No 19
>TIGR00523 eIF-1A eukaryotic/archaeal initiation factor 1A. Recommended nomenclature: eIF-1A for eukaryotes, aIF-1A for Archaea. Also called eIF-4C
Probab=55.27 E-value=49 Score=25.35 Aligned_cols=50 Identities=16% Similarity=0.209 Sum_probs=33.9
Q ss_pred EEEEEEEeccCCceEEEEEeEEeeecceeeEEeeeeeEEEEcCCCCC---CCCCCCEEEEeeeecCC
Q psy10000 107 ILIGIVRKMKMQRTIVIRRDYLHYIKKYNRFEKRHRNMSVHLSPAFR---DVEIGDVVTVGECRPLS 170 (193)
Q Consensus 107 ~l~G~Vvs~Km~KTvvV~~~~~~~~~KYkk~~kr~kk~~vHd~~~~~---~~kvGD~V~I~ecRPlS 170 (193)
...|+|+....+....|.-+- -..++||.|.-|+ -++.||.|.| +.+.++
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 477888888777766665331 1234566665543 2889999999 678888
No 20
>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=53.30 E-value=48 Score=24.14 Aligned_cols=56 Identities=18% Similarity=0.113 Sum_probs=35.7
Q ss_pred EEEEEEeccCCceEEEEEeEEeeecceeeEEeeeeeEEEEcCCCCC---CCCCCCEEEEeeeecCCCceeEEE
Q psy10000 108 LIGIVRKMKMQRTIVIRRDYLHYIKKYNRFEKRHRNMSVHLSPAFR---DVEIGDVVTVGECRPLSKTVRFNV 177 (193)
Q Consensus 108 l~G~Vvs~Km~KTvvV~~~~~~~~~KYkk~~kr~kk~~vHd~~~~~---~~kvGD~V~I~ecRPlSKtK~f~V 177 (193)
..|+|+....+....|.-+- -..++||.|.-|+ -++.||.|.+. -+|.++++-=++
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 46788887766666665331 1234566665543 27899999997 567777665433
No 21
>PTZ00329 eukaryotic translation initiation factor 1A; Provisional
Probab=51.21 E-value=1.2e+02 Score=25.33 Aligned_cols=59 Identities=19% Similarity=0.103 Sum_probs=37.5
Q ss_pred EEEEEEeccCCceEEEEEeEEeeecceeeEEeeeeeEEEEcCCCCC---CCCCCCEEEEeeeecCCCceeEEEEEE
Q psy10000 108 LIGIVRKMKMQRTIVIRRDYLHYIKKYNRFEKRHRNMSVHLSPAFR---DVEIGDVVTVGECRPLSKTVRFNVLKV 180 (193)
Q Consensus 108 l~G~Vvs~Km~KTvvV~~~~~~~~~KYkk~~kr~kk~~vHd~~~~~---~~kvGD~V~I~ecRPlSKtK~f~V~~v 180 (193)
..|+|++...+....|...-- ..++||.|.-++ -+..||+|+|.. ||-..+|-=++...
T Consensus 34 ~~g~V~~~LGn~~f~V~c~dG-------------~~rLa~I~GKmRK~IWI~~GD~VlVel-~~yd~~KgdIi~Ry 95 (155)
T PTZ00329 34 EYAQVLRMLGNGRLEAYCFDG-------------VKRLCHIRGKMRKRVWINIGDIILVSL-RDFQDSKADVILKY 95 (155)
T ss_pred EEEEEEEEcCCCEEEEEECCC-------------CEEEEEeeccceeeEEecCCCEEEEec-cCCCCCEEEEEEEc
Confidence 478888887777777763211 112333333221 288999999965 99998886655554
No 22
>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=50.40 E-value=67 Score=23.45 Aligned_cols=56 Identities=14% Similarity=0.037 Sum_probs=34.9
Q ss_pred EEEEEEeccCCceEEEEEeEEeeecceeeEEeeeeeEEEEcCCCCCC---CCCCCEEEEeeeecC-CCceeEEE
Q psy10000 108 LIGIVRKMKMQRTIVIRRDYLHYIKKYNRFEKRHRNMSVHLSPAFRD---VEIGDVVTVGECRPL-SKTVRFNV 177 (193)
Q Consensus 108 l~G~Vvs~Km~KTvvV~~~~~~~~~KYkk~~kr~kk~~vHd~~~~~~---~kvGD~V~I~ecRPl-SKtK~f~V 177 (193)
..|+|+....+....|+.+- -..++||.|.-|+. ++.||.|.|. -+|. ++++-=++
T Consensus 2 ~i~~V~~~lG~~~~~V~~~d-------------g~~~l~~i~gK~Rk~iwI~~GD~VlV~-~~~~~~~~kg~Iv 61 (78)
T cd04456 2 QIVRVLRMLGNNRHEVECAD-------------GQRRLVSIPGKLRKNIWIKRGDFLIVD-PIEEGEDVKADII 61 (78)
T ss_pred eEEEEEEECCCCEEEEEECC-------------CCEEEEEEchhhccCEEEcCCCEEEEE-ecccCCCceEEEE
Confidence 35777777666655555321 23446777765532 8899999994 6777 46554333
No 23
>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=47.92 E-value=6.9 Score=30.88 Aligned_cols=13 Identities=54% Similarity=1.094 Sum_probs=10.0
Q ss_pred CcCCCceeeeeee
Q psy10000 92 DKKCPFTGNVSIR 104 (193)
Q Consensus 92 d~~cPf~g~~~ir 104 (193)
-.+|||||.+--|
T Consensus 87 ~~kCPfHG~IIpR 99 (110)
T PF09740_consen 87 RKKCPFHGKIIPR 99 (110)
T ss_pred cccCCCCCcccCC
Confidence 3579999987655
No 24
>smart00652 eIF1a eukaryotic translation initiation factor 1A.
Probab=47.13 E-value=81 Score=23.24 Aligned_cols=57 Identities=16% Similarity=0.067 Sum_probs=35.4
Q ss_pred EEEEEEEeccCCceEEEEEeEEeeecceeeEEeeeeeEEEEcCCCCC---CCCCCCEEEEeeeecCCCceeEEE
Q psy10000 107 ILIGIVRKMKMQRTIVIRRDYLHYIKKYNRFEKRHRNMSVHLSPAFR---DVEIGDVVTVGECRPLSKTVRFNV 177 (193)
Q Consensus 107 ~l~G~Vvs~Km~KTvvV~~~~~~~~~KYkk~~kr~kk~~vHd~~~~~---~~kvGD~V~I~ecRPlSKtK~f~V 177 (193)
...|+|+....+.-..|.-+- -..+.||.|.-|+ -++.||.|.|. -+|-.+.+-=++
T Consensus 6 q~~g~V~~~lG~~~~~V~~~d-------------G~~~la~ipgK~Rk~iwI~~GD~VlVe-~~~~~~~kg~Iv 65 (83)
T smart00652 6 QEIAQVVKMLGNGRLEVMCAD-------------GKERLARIPGKMRKKVWIRRGDIVLVD-PWDFQDVKADII 65 (83)
T ss_pred cEEEEEEEEcCCCEEEEEECC-------------CCEEEEEEchhhcccEEEcCCCEEEEE-ecCCCCCEEEEE
Confidence 357888887666666655321 1233566666553 28899999995 567776554433
No 25
>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=44.95 E-value=68 Score=22.72 Aligned_cols=24 Identities=13% Similarity=0.106 Sum_probs=18.2
Q ss_pred eeeeEEEEcCCCCCCCCCCCEEEEe
Q psy10000 140 RHRNMSVHLSPAFRDVEIGDVVTVG 164 (193)
Q Consensus 140 r~kk~~vHd~~~~~~~kvGD~V~I~ 164 (193)
.=+.+..|+.+. ..+..||.|.|.
T Consensus 43 ~V~si~~~~~~~-~~a~aGd~v~~~ 66 (83)
T cd03698 43 EVKSIYVDDEEV-DYAVAGENVRLK 66 (83)
T ss_pred EEEEEEECCeEC-CEECCCCEEEEE
Confidence 445677888876 479999999864
No 26
>PLN00208 translation initiation factor (eIF); Provisional
Probab=42.53 E-value=1.9e+02 Score=23.80 Aligned_cols=59 Identities=19% Similarity=0.084 Sum_probs=35.8
Q ss_pred EEEEEEeccCCceEEEEEeEEeeecceeeEEeeeeeEEEEcCCCCC---CCCCCCEEEEeeeecCCCceeEEEEEE
Q psy10000 108 LIGIVRKMKMQRTIVIRRDYLHYIKKYNRFEKRHRNMSVHLSPAFR---DVEIGDVVTVGECRPLSKTVRFNVLKV 180 (193)
Q Consensus 108 l~G~Vvs~Km~KTvvV~~~~~~~~~KYkk~~kr~kk~~vHd~~~~~---~~kvGD~V~I~ecRPlSKtK~f~V~~v 180 (193)
..|+|++...+..+.|...-- ...+||.|.-++ -+++||+|+|. -||-.++|-=++...
T Consensus 34 ~~g~V~~~lGn~~~~V~c~dG-------------~~rLa~IpGKmRKrIWI~~GD~VlVe-l~~~d~~KgdIv~ry 95 (145)
T PLN00208 34 EYAQVLRMLGNGRCEALCIDG-------------TKRLCHIRGKMRKKVWIAAGDIILVG-LRDYQDDKADVILKY 95 (145)
T ss_pred EEEEEEEEcCCCEEEEEECCC-------------CEEEEEEeccceeeEEecCCCEEEEE-ccCCCCCEEEEEEEc
Confidence 568888887777676663210 112333333221 28899999987 788887776555443
No 27
>COG2053 RPS28A Ribosomal protein S28E/S33 [Translation, ribosomal structure and biogenesis]
Probab=40.07 E-value=39 Score=24.59 Aligned_cols=13 Identities=31% Similarity=0.572 Sum_probs=11.8
Q ss_pred CCCCCCEEEEeee
Q psy10000 154 DVEIGDVVTVGEC 166 (193)
Q Consensus 154 ~~kvGD~V~I~ec 166 (193)
.+++||++.+.||
T Consensus 47 PVrvgDIl~L~Et 59 (69)
T COG2053 47 PVRVGDILMLLET 59 (69)
T ss_pred CcccccEEeehhh
Confidence 5999999999987
No 28
>PRK12442 translation initiation factor IF-1; Reviewed
Probab=39.87 E-value=1e+02 Score=23.47 Aligned_cols=62 Identities=19% Similarity=0.116 Sum_probs=37.3
Q ss_pred eEEEEEEEeccCCceEEEEEeEEeeecceeeEEeeeeeEEEEcCCCCC----CCCCCCEEEEeeeecCCCceeEEEEEEE
Q psy10000 106 RILIGIVRKMKMQRTIVIRRDYLHYIKKYNRFEKRHRNMSVHLSPAFR----DVEIGDVVTVGECRPLSKTVRFNVLKVT 181 (193)
Q Consensus 106 ~~l~G~Vvs~Km~KTvvV~~~~~~~~~KYkk~~kr~kk~~vHd~~~~~----~~kvGD~V~I~ecRPlSKtK~f~V~~v~ 181 (193)
-.++|+|+..--+-...|+-+--+ .+.||.+--++ -+.+||.|.|+-+ |..-++-=++-+-.
T Consensus 7 ie~~G~V~e~Lp~~~frV~LenG~-------------~vla~isGKmR~~rIrIl~GD~V~VE~s-pYDltkGRIiyR~~ 72 (87)
T PRK12442 7 IELDGIVDEVLPDSRFRVTLENGV-------------EVGAYASGRMRKHRIRILAGDRVTLELS-PYDLTKGRINFRHK 72 (87)
T ss_pred EEEEEEEEEECCCCEEEEEeCCCC-------------EEEEEeccceeeeeEEecCCCEEEEEEC-cccCCceeEEEEec
Confidence 367899998866666777644222 12455544321 3678999998654 66656544444443
No 29
>cd03693 EF1_alpha_II EF1_alpha_II: this family represents the domain II of elongation factor 1-alpha (EF-1a) that is found in archaea and all eukaryotic lineages. EF-1A is very abundant in the cytosol, where it is involved in the GTP-dependent binding of aminoacyl-tRNAs to the A site of the ribosomes in the second step of translation from mRNAs to proteins. Both domain II of EF1A and domain IV of IF2/eIF5B have been implicated in recognition of the 3'-ends of tRNA. More than 61% of eukaryotic elongation factor 1A (eEF-1A) in cells is estimated to be associated with actin cytoskeleton. The binding of eEF1A to actin is a noncanonical function that may link two distinct cellular processes, cytoskeleton organization and gene expression.
Probab=36.54 E-value=1.1e+02 Score=22.17 Aligned_cols=25 Identities=20% Similarity=0.331 Sum_probs=18.9
Q ss_pred eeeeeEEEEcCCCCCCCCCCCEEEEe
Q psy10000 139 KRHRNMSVHLSPAFRDVEIGDVVTVG 164 (193)
Q Consensus 139 kr~kk~~vHd~~~~~~~kvGD~V~I~ 164 (193)
-.-+.+..|+.+. ..+..||.|.|.
T Consensus 46 ~~V~sI~~~~~~~-~~a~aG~~v~i~ 70 (91)
T cd03693 46 GEVKSVEMHHEPL-EEALPGDNVGFN 70 (91)
T ss_pred EEEEEEEECCcCc-CEECCCCEEEEE
Confidence 4456667888876 479999999874
No 30
>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=34.28 E-value=28 Score=24.70 Aligned_cols=13 Identities=31% Similarity=0.608 Sum_probs=11.1
Q ss_pred CCCCCCEEEEeee
Q psy10000 154 DVEIGDVVTVGEC 166 (193)
Q Consensus 154 ~~kvGD~V~I~ec 166 (193)
.++.||+|.|+..
T Consensus 53 G~~~GD~V~Ig~~ 65 (69)
T TIGR03595 53 GAKDGDTVRIGDF 65 (69)
T ss_pred CCCCCCEEEEccE
Confidence 5899999999863
No 31
>PF11604 CusF_Ec: Copper binding periplasmic protein CusF; InterPro: IPR021647 CusF is a periplasmic protein involved in copper and silver resistance in Escherichia coil. CusF forms a five-stranded beta-barrel OB fold. Cu(I) binds to H36, M47 and M49 which are conserved residues in the protein []. ; PDB: 2L55_A 2VB3_X 1ZEQ_X 2QCP_X 3E6Z_X 2VB2_X.
Probab=33.48 E-value=1.7e+02 Score=20.53 Aligned_cols=66 Identities=15% Similarity=0.187 Sum_probs=37.3
Q ss_pred EEEEec-cCCceEEEEEeEEeeecceeeEEeeeeeEEEEcCCCCCCCCCCCEEEEeeeecCCCceeEEEEEEE
Q psy10000 110 GIVRKM-KMQRTIVIRRDYLHYIKKYNRFEKRHRNMSVHLSPAFRDVEIGDVVTVGECRPLSKTVRFNVLKVT 181 (193)
Q Consensus 110 G~Vvs~-Km~KTvvV~~~~~~~~~KYkk~~kr~kk~~vHd~~~~~~~kvGD~V~I~ecRPlSKtK~f~V~~v~ 181 (193)
|+|.+. ...++|+|.++-.-- -..---+-.|.+-++..+..+++||.|.+.=.+ .....|+|.+|-
T Consensus 1 G~V~~vd~~~~~iti~H~pIp~----l~wpaMTM~F~v~~~~~l~~l~~Gd~V~F~~~~--~~~~~~~I~~i~ 67 (70)
T PF11604_consen 1 GVVKSVDPEAGTITISHEPIPE----LGWPAMTMDFPVADPVDLAGLKPGDKVRFTFER--TDDGSYVITAIE 67 (70)
T ss_dssp EEEEEEETTTTEEEEEE--BCC----CTB-SEEEEEE--TTSEESS-STT-EEEEEEEE--ETTCEEEEEEEE
T ss_pred CEEEEEecCCCEEEEecCcccc----CCCCCeEEEEEcCChhhhhcCCCCCEEEEEEEE--CCCCcEEEEEEE
Confidence 778874 678999998653321 012234455566666656689999999987655 223346666654
No 32
>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=33.17 E-value=47 Score=25.81 Aligned_cols=19 Identities=21% Similarity=0.216 Sum_probs=14.1
Q ss_pred EEEEcCCCCCCCCCCCEEEEee
Q psy10000 144 MSVHLSPAFRDVEIGDVVTVGE 165 (193)
Q Consensus 144 ~~vHd~~~~~~~kvGD~V~I~e 165 (193)
+.++++. .+++||.|+|+-
T Consensus 44 ~~~~~~~---~~~~GD~V~v~i 62 (135)
T PF04246_consen 44 FRAPNPI---GAKVGDRVEVEI 62 (135)
T ss_pred EEecCCC---CCCCCCEEEEEe
Confidence 3455654 699999999864
No 33
>PF13550 Phage-tail_3: Putative phage tail protein
Probab=31.08 E-value=1.1e+02 Score=23.41 Aligned_cols=40 Identities=20% Similarity=0.486 Sum_probs=26.7
Q ss_pred EEeeeeeEEEEcCCCCCCCCCCCEEEEeeeecCCCceeEEEEEEE
Q psy10000 137 FEKRHRNMSVHLSPAFRDVEIGDVVTVGECRPLSKTVRFNVLKVT 181 (193)
Q Consensus 137 ~~kr~kk~~vHd~~~~~~~kvGD~V~I~ecRPlSKtK~f~V~~v~ 181 (193)
+.+++=.+.+-.+. -.+.+||+|.|..- .....|.|.+|.
T Consensus 124 ~~r~t~~f~~~~~~--~~l~pGDvi~l~~~---~~~~~~RI~~i~ 163 (164)
T PF13550_consen 124 YERRTVSFTLPPDG--LALEPGDVIALSDD---GRDMRFRITEIE 163 (164)
T ss_pred ccceEEEEEEChhh--ccCCCCCEEEEEeC---CCceEEEEEEEe
Confidence 33444444444443 27999999999876 557888888764
No 34
>KOG3416|consensus
Probab=30.75 E-value=2e+02 Score=23.50 Aligned_cols=50 Identities=18% Similarity=0.087 Sum_probs=33.6
Q ss_pred ceEEEEEEEeccCCceEEEEEeEEeeecceeeEEeeeeeEEEEcCCCCCCCCCCCEEEEe
Q psy10000 105 GRILIGIVRKMKMQRTIVIRRDYLHYIKKYNRFEKRHRNMSVHLSPAFRDVEIGDVVTVG 164 (193)
Q Consensus 105 g~~l~G~Vvs~Km~KTvvV~~~~~~~~~KYkk~~kr~kk~~vHd~~~~~~~kvGD~V~I~ 164 (193)
=-+..|.+.+++..++|.+..--- +.-.=++.+-|++|- ..+.||+|.+.
T Consensus 22 Ivl~~g~~tkTkdg~~v~~~kVaD---------~TgsI~isvW~e~~~-~~~PGDIirLt 71 (134)
T KOG3416|consen 22 IVLEYGRATKTKDGHEVRSCKVAD---------ETGSINISVWDEEGC-LIQPGDIIRLT 71 (134)
T ss_pred EEEeeceeeeccCCCEEEEEEEec---------ccceEEEEEecCcCc-ccCCccEEEec
Confidence 356778999999888876642100 122335677788773 79999999863
No 35
>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=29.80 E-value=1.6e+02 Score=20.90 Aligned_cols=26 Identities=15% Similarity=0.216 Sum_probs=19.6
Q ss_pred eeeeeEEEEcCCCCCCCCCCCEEEEee
Q psy10000 139 KRHRNMSVHLSPAFRDVEIGDVVTVGE 165 (193)
Q Consensus 139 kr~kk~~vHd~~~~~~~kvGD~V~I~e 165 (193)
-.-+.+.+|+.+. +.+..||.|.|.=
T Consensus 42 ~~V~si~~~~~~~-~~a~aGd~v~l~l 67 (81)
T cd03695 42 SRVKSIETFDGEL-DEAGAGESVTLTL 67 (81)
T ss_pred EEEEEEEECCcEe-CEEcCCCEEEEEE
Confidence 4556677888875 4799999998853
No 36
>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=28.71 E-value=27 Score=24.78 Aligned_cols=12 Identities=33% Similarity=0.711 Sum_probs=7.6
Q ss_pred CCCCCCEEEEee
Q psy10000 154 DVEIGDVVTVGE 165 (193)
Q Consensus 154 ~~kvGD~V~I~e 165 (193)
.++.||+|.|+.
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 37
>PF06107 DUF951: Bacterial protein of unknown function (DUF951); InterPro: IPR009296 This family consists of several short hypothetical bacterial proteins of unknown function.
Probab=28.69 E-value=81 Score=22.21 Aligned_cols=25 Identities=20% Similarity=0.581 Sum_probs=21.4
Q ss_pred CCCCCEEEEeeeecCCCceeEEEEEE
Q psy10000 155 VEIGDVVTVGECRPLSKTVRFNVLKV 180 (193)
Q Consensus 155 ~kvGD~V~I~ecRPlSKtK~f~V~~v 180 (193)
..+||+|....-.|--. ..|.|+++
T Consensus 2 ~~vgDiV~mKK~HPCG~-~~Wei~R~ 26 (57)
T PF06107_consen 2 YEVGDIVEMKKPHPCGS-NEWEIIRI 26 (57)
T ss_pred ccCCCEEEEcCCCCCCC-CEEEEEEc
Confidence 57999999999999754 88999876
No 38
>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=25.82 E-value=2.4e+02 Score=19.74 Aligned_cols=25 Identities=28% Similarity=0.464 Sum_probs=18.1
Q ss_pred eeeeeEEEEcCCCCCCCCCCCEEEEe
Q psy10000 139 KRHRNMSVHLSPAFRDVEIGDVVTVG 164 (193)
Q Consensus 139 kr~kk~~vHd~~~~~~~kvGD~V~I~ 164 (193)
-.-+.+..|+++. ..+..||.|.|.
T Consensus 42 ~~V~sI~~~~~~~-~~a~aGd~v~i~ 66 (83)
T cd03696 42 TRVRSIQVHGKDV-EEAKAGDRVALN 66 (83)
T ss_pred EEEEEEEECCcCc-CEEcCCCEEEEE
Confidence 4445666777775 479999999884
No 39
>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=25.60 E-value=1.4e+02 Score=21.44 Aligned_cols=25 Identities=20% Similarity=0.323 Sum_probs=19.0
Q ss_pred eeeeeEEEEcCCCCCCCCCCCEEEEe
Q psy10000 139 KRHRNMSVHLSPAFRDVEIGDVVTVG 164 (193)
Q Consensus 139 kr~kk~~vHd~~~~~~~kvGD~V~I~ 164 (193)
-.-+.+..|+.+. +.+..||.|.|.
T Consensus 46 ~~V~sI~~~~~~~-~~a~aGd~v~l~ 70 (87)
T cd03694 46 VTVKSIHRNRSPV-RVVRAGQSASLA 70 (87)
T ss_pred EEEEEEEECCeEC-CEECCCCEEEEE
Confidence 4455677888875 479999999885
No 40
>PRK01678 rpmE2 50S ribosomal protein L31 type B; Reviewed
Probab=25.60 E-value=2e+02 Score=21.77 Aligned_cols=34 Identities=15% Similarity=0.224 Sum_probs=26.1
Q ss_pred eecceeeEEeeeeeEEEEcCCCCCCCCCCCEEEEeeeecCCCceeEE
Q psy10000 130 YIKKYNRFEKRHRNMSVHLSPAFRDVEIGDVVTVGECRPLSKTVRFN 176 (193)
Q Consensus 130 ~~~KYkk~~kr~kk~~vHd~~~~~~~kvGD~V~I~ecRPlSKtK~f~ 176 (193)
.||.|... .+||..| |....+.++.+-..|..|.
T Consensus 5 IHP~y~~v-------~~~~~t~------g~~f~~~ST~~~~~t~~~~ 38 (87)
T PRK01678 5 IHPEYRPV-------VFHDTST------GFKFLTGSTITTDETIEWE 38 (87)
T ss_pred CCCCCEEE-------EEEECCC------CCEEEEeeeccccceeeec
Confidence 36888766 6777555 8889999999988888883
No 41
>KOG1730|consensus
Probab=24.93 E-value=47 Score=28.78 Aligned_cols=18 Identities=44% Similarity=0.885 Sum_probs=15.2
Q ss_pred CCCceeeeeeeceEEEEE
Q psy10000 94 KCPFTGNVSIRGRILIGI 111 (193)
Q Consensus 94 ~cPf~g~~~irg~~l~G~ 111 (193)
.-||||+|.+.|-++.|-
T Consensus 74 niPFtg~vkLkgI~I~g~ 91 (206)
T KOG1730|consen 74 NIPFTGNVKLKGISIMGE 91 (206)
T ss_pred eccccCceeEEEEEEEeC
Confidence 469999999998888774
No 42
>PRK04012 translation initiation factor IF-1A; Provisional
Probab=24.60 E-value=3.2e+02 Score=20.89 Aligned_cols=57 Identities=16% Similarity=0.099 Sum_probs=35.2
Q ss_pred EEEEEEEeccCCceEEEEEeEEeeecceeeEEeeeeeEEEEcCCCCC---CCCCCCEEEEeeeecCCCceeEEE
Q psy10000 107 ILIGIVRKMKMQRTIVIRRDYLHYIKKYNRFEKRHRNMSVHLSPAFR---DVEIGDVVTVGECRPLSKTVRFNV 177 (193)
Q Consensus 107 ~l~G~Vvs~Km~KTvvV~~~~~~~~~KYkk~~kr~kk~~vHd~~~~~---~~kvGD~V~I~ecRPlSKtK~f~V 177 (193)
...|+|+....+....|..+-- ..++||.|.-|+ -+..||.|.|. -+|...++-=++
T Consensus 22 e~~g~V~~~lG~~~~~V~~~dG-------------~~~la~i~GK~Rk~IwI~~GD~VlVe-~~~~~~~kg~Iv 81 (100)
T PRK04012 22 EVFGVVEQMLGANRVRVRCMDG-------------VERMGRIPGKMKKRMWIREGDVVIVA-PWDFQDEKADII 81 (100)
T ss_pred EEEEEEEEEcCCCEEEEEeCCC-------------CEEEEEEchhhcccEEecCCCEEEEE-ecccCCCEEEEE
Confidence 4678888887666666653311 123555555443 27899999987 467776654333
No 43
>PF11302 DUF3104: Protein of unknown function (DUF3104); InterPro: IPR021453 This family of proteins with unknown function appears to be restricted to Cyanobacteria.
Probab=24.10 E-value=1.3e+02 Score=22.28 Aligned_cols=34 Identities=24% Similarity=0.287 Sum_probs=25.4
Q ss_pred CCCCCCCCEEEEeeeec--CCCceeEEEEEEEecCc
Q psy10000 152 FRDVEIGDVVTVGECRP--LSKTVRFNVLKVTKGTG 185 (193)
Q Consensus 152 ~~~~kvGD~V~I~ecRP--lSKtK~f~V~~v~~~~~ 185 (193)
|-.++.||.|.|....- .+..+.|-+-.|+.-.+
T Consensus 3 FL~Vk~Gd~ViV~~~~~~~~~~~~dWWmg~Vi~~~g 38 (75)
T PF11302_consen 3 FLSVKPGDTVIVQDEQEVGQKQDKDWWMGQVIHCEG 38 (75)
T ss_pred ccccCCCCEEEEecCccccccCCCCcEEEEEEEEec
Confidence 33699999999998762 34556888888876554
No 44
>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=23.86 E-value=2.1e+02 Score=20.40 Aligned_cols=53 Identities=17% Similarity=0.276 Sum_probs=29.9
Q ss_pred eceEEEEEEEecc--CCceEEEEEeEEeeecceeeEEeeeeeEEEEcCCCCCCCCCCCEEEEe
Q psy10000 104 RGRILIGIVRKMK--MQRTIVIRRDYLHYIKKYNRFEKRHRNMSVHLSPAFRDVEIGDVVTVG 164 (193)
Q Consensus 104 rg~~l~G~Vvs~K--m~KTvvV~~~~~~~~~KYkk~~kr~kk~~vHd~~~~~~~kvGD~V~I~ 164 (193)
+|.++.|+|.+-. ..-.+.+.- .+. .....-+.+.+|+.+. ..+..||.|.|.
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--TLKTTVTGIEMFRKTL-DEAEAGDNVGVL 68 (87)
T ss_pred cEEEEEEEECCCCCccCCEEEEeC-----CCC--CceEEEEEEEECCcCC-CEECCCCEEEEE
Confidence 3556777777643 223333321 000 1122334577888876 479999999875
No 45
>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=23.44 E-value=2.4e+02 Score=19.62 Aligned_cols=21 Identities=19% Similarity=0.305 Sum_probs=15.8
Q ss_pred eceEEEEEEEeccCCceEEEEE
Q psy10000 104 RGRILIGIVRKMKMQRTIVIRR 125 (193)
Q Consensus 104 rg~~l~G~Vvs~Km~KTvvV~~ 125 (193)
.|.+..|.|++.. +..+.|..
T Consensus 6 ~GdiV~g~V~~i~-~~g~~v~i 26 (86)
T cd05789 6 VGDVVIGRVTEVG-FKRWKVDI 26 (86)
T ss_pred CCCEEEEEEEEEC-CCEEEEEC
Confidence 5888999999954 56677754
No 46
>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=21.76 E-value=2.6e+02 Score=20.04 Aligned_cols=12 Identities=17% Similarity=0.371 Sum_probs=10.2
Q ss_pred CCCCCCEEEEee
Q psy10000 154 DVEIGDVVTVGE 165 (193)
Q Consensus 154 ~~kvGD~V~I~e 165 (193)
++..||+|.+.-
T Consensus 61 ~a~aGdIv~v~g 72 (85)
T cd03689 61 EAYPGDIIGLVN 72 (85)
T ss_pred EECCCCEEEEEC
Confidence 688999999865
No 47
>smart00380 AP2 DNA-binding domain in plant proteins such as APETALA2 and EREBPs.
Probab=21.50 E-value=43 Score=22.90 Aligned_cols=19 Identities=37% Similarity=0.688 Sum_probs=14.3
Q ss_pred ccCcc-cccchhhhhhhccC
Q psy10000 35 DVGLG-FKSPRETERAFQKQ 53 (193)
Q Consensus 35 ~IGLG-fKtP~eAe~ayqKQ 53 (193)
.+-|| |.||+||..||-..
T Consensus 25 ~~~lG~f~t~eeAa~Ayd~a 44 (64)
T smart00380 25 RVWLGTFDTAEEAARAYDRA 44 (64)
T ss_pred EEecCCCCCHHHHHHHHHHH
Confidence 45555 88999999998554
No 48
>PF08605 Rad9_Rad53_bind: Fungal Rad9-like Rad53-binding; InterPro: IPR013914 In Saccharomyces cerevisiae (Baker s yeast), the Rad9 is a key adaptor protein in DNA damage checkpoint pathways. DNA damage induces Rad9 phosphorylation, and Rad53 specifically associates with this region of Rad9, when phosphorylated, via the Rad53 IPR000253 from INTERPRO domain []. There is no clear higher eukaryotic ortholog to Rad9.
Probab=21.43 E-value=1.1e+02 Score=24.57 Aligned_cols=25 Identities=32% Similarity=0.472 Sum_probs=20.0
Q ss_pred CCCCCCEEEEeeeecCCCceeEEEEEEEec
Q psy10000 154 DVEIGDVVTVGECRPLSKTVRFNVLKVTKG 183 (193)
Q Consensus 154 ~~kvGD~V~I~ecRPlSKtK~f~V~~v~~~ 183 (193)
++++||.|.+.. +...|+|.....+
T Consensus 59 DlRIGD~Vkv~~-----~k~~yiV~Gl~~~ 83 (131)
T PF08605_consen 59 DLRIGDTVKVDG-----PKVTYIVVGLECK 83 (131)
T ss_pred eeecCCEEEECC-----CCccEEEEEeeec
Confidence 899999999998 3345888887655
No 49
>cd00018 AP2 DNA-binding domain found in transcription regulators in plants such as APETALA2 and EREBP (ethylene responsive element binding protein). In EREBPs the domain specifically binds to the 11bp GCC box of the ethylene response element (ERE), a promotor element essential for ethylene responsiveness. EREBPs and the C-repeat binding factor CBF1, which is involved in stress response, contain a single copy of the AP2 domain. APETALA2-like proteins, which play a role in plant development contain two copies.
Probab=20.97 E-value=45 Score=22.39 Aligned_cols=19 Identities=37% Similarity=0.768 Sum_probs=14.4
Q ss_pred eccCcc-cccchhhhhhhcc
Q psy10000 34 RDVGLG-FKSPRETERAFQK 52 (193)
Q Consensus 34 K~IGLG-fKtP~eAe~ayqK 52 (193)
+.+-|| |.||+||..||..
T Consensus 25 k~~~lG~f~t~eeAa~Ayd~ 44 (61)
T cd00018 25 RRIWLGTFDTAEEAARAYDR 44 (61)
T ss_pred ceEccCCCCCHHHHHHHHHH
Confidence 355566 8899999999854
No 50
>PF13567 DUF4131: Domain of unknown function (DUF4131)
Probab=20.74 E-value=3.6e+02 Score=19.94 Aligned_cols=62 Identities=16% Similarity=0.190 Sum_probs=32.5
Q ss_pred EEEEEEEecc--CCce--EEEEEeEEeeecceeeEEeeeeeEEEEcCCCCCC-CCCCCEEEEee-eecCCC
Q psy10000 107 ILIGIVRKMK--MQRT--IVIRRDYLHYIKKYNRFEKRHRNMSVHLSPAFRD-VEIGDVVTVGE-CRPLSK 171 (193)
Q Consensus 107 ~l~G~Vvs~K--m~KT--vvV~~~~~~~~~KYkk~~kr~kk~~vHd~~~~~~-~kvGD~V~I~e-cRPlSK 171 (193)
.++|+|.+.. ...+ .+++++++ ..-......+-++.+..+..-.. ...||.+++.. .+|++.
T Consensus 79 ~v~g~V~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~i~~~~~~~~~~~l~~Gd~i~~~g~l~~~~~ 146 (176)
T PF13567_consen 79 TVQGTVESVPQIDGRGQRFTLRVERV---LAGGNWIPVSGKILLYLPKDSQPRLQPGDRIRVRGKLKPPSG 146 (176)
T ss_pred EEEEEEcccccccCceEEEEEEEEEe---eccccccccceeeEEEeccccccccCCCCEEEEEEEEecCCC
Confidence 3677776641 2222 34444443 22233334444555555443213 68999999866 466654
No 51
>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=20.65 E-value=54 Score=21.40 Aligned_cols=23 Identities=17% Similarity=0.150 Sum_probs=15.0
Q ss_pred eeeEEEEcCCCCCCCCCCCEEEEe
Q psy10000 141 HRNMSVHLSPAFRDVEIGDVVTVG 164 (193)
Q Consensus 141 ~kk~~vHd~~~~~~~kvGD~V~I~ 164 (193)
...|.+-++..+ .++.||+|.|.
T Consensus 5 ~~d~~~~~~~~L-s~~~Gd~i~v~ 27 (55)
T PF07653_consen 5 IFDYVAEDPDEL-SFKKGDVIEVL 27 (55)
T ss_dssp SSSBESSSTTB--EB-TTEEEEEE
T ss_pred eEEECCCCCCce-EEecCCEEEEE
Confidence 344455566655 79999999997
No 52
>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=20.47 E-value=3.1e+02 Score=19.20 Aligned_cols=23 Identities=13% Similarity=0.017 Sum_probs=16.5
Q ss_pred eeeEEEEcCCCCCCCCCCCEEEEe
Q psy10000 141 HRNMSVHLSPAFRDVEIGDVVTVG 164 (193)
Q Consensus 141 ~kk~~vHd~~~~~~~kvGD~V~I~ 164 (193)
-+.+..|+.+. ..+..||.|.|.
T Consensus 43 V~si~~~~~~~-~~a~aGd~v~l~ 65 (82)
T cd04089 43 VLSIYNEDVEV-RYARPGENVRLR 65 (82)
T ss_pred EEEEEECCEEC-CEECCCCEEEEE
Confidence 34566777665 479999999874
No 53
>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=20.20 E-value=98 Score=18.68 Aligned_cols=13 Identities=31% Similarity=0.434 Sum_probs=11.6
Q ss_pred CCCCCCEEEEeee
Q psy10000 154 DVEIGDVVTVGEC 166 (193)
Q Consensus 154 ~~kvGD~V~I~ec 166 (193)
.+..||.|.+.+.
T Consensus 17 ~~~~Gd~v~v~~~ 29 (54)
T cd00174 17 SFKKGDIIEVLEK 29 (54)
T ss_pred CCCCCCEEEEEEc
Confidence 6899999999887
No 54
>PRK10862 SoxR reducing system protein RseC; Provisional
Probab=20.03 E-value=1.1e+02 Score=24.76 Aligned_cols=19 Identities=26% Similarity=0.331 Sum_probs=13.7
Q ss_pred eEEEEcCCCCCCCCCCCEEEEe
Q psy10000 143 NMSVHLSPAFRDVEIGDVVTVG 164 (193)
Q Consensus 143 k~~vHd~~~~~~~kvGD~V~I~ 164 (193)
.+.+.++. ++++||.|.|+
T Consensus 50 ~~~v~~~~---~~~vGD~V~v~ 68 (154)
T PRK10862 50 QLVVPSSQ---PLVPGQKVELG 68 (154)
T ss_pred EEEecCCC---CCCCCCEEEEe
Confidence 34555553 69999999986
Done!