Query 042342
Match_columns 87
No_of_seqs 109 out of 300
Neff 3.5
Searched_HMMs 46136
Date Fri Mar 29 05:20:11 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/042342.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/042342hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 cd03367 Ribosomal_S23 S12-like 100.0 5.3E-49 1.1E-53 275.7 9.3 81 1-81 15-95 (115)
2 PTZ00067 40S ribosomal S23; Pr 100.0 1E-47 2.2E-52 277.2 9.5 81 1-81 40-120 (143)
3 TIGR00982 S23_S12_E_A ribosoma 100.0 2.1E-47 4.6E-52 274.5 9.5 81 1-81 35-116 (139)
4 PRK04211 rps12P 30S ribosomal 100.0 2E-47 4.4E-52 276.1 9.3 81 1-81 41-122 (145)
5 KOG1749 40S ribosomal protein 100.0 3.5E-46 7.6E-51 267.8 7.6 81 1-81 40-120 (143)
6 cd00319 Ribosomal_S12_like Rib 100.0 1.1E-44 2.5E-49 246.9 8.2 73 1-81 8-80 (95)
7 COG0048 RpsL Ribosomal protein 100.0 1.9E-44 4.2E-49 256.6 8.2 73 1-81 29-101 (129)
8 cd03368 Ribosomal_S12 S12-like 100.0 7.5E-44 1.6E-48 247.5 8.2 73 1-81 21-93 (108)
9 PRK05163 rpsL 30S ribosomal pr 100.0 2.6E-43 5.7E-48 249.5 8.4 73 1-81 23-95 (124)
10 CHL00051 rps12 ribosomal prote 100.0 2.6E-43 5.7E-48 249.2 8.1 73 1-81 23-95 (123)
11 TIGR00981 rpsL_bact ribosomal 100.0 3.2E-43 6.9E-48 249.0 8.3 73 1-81 23-95 (124)
12 PF00164 Ribosom_S12_S23: Ribo 100.0 8.6E-43 1.9E-47 245.7 8.8 73 1-81 22-94 (122)
13 PTZ00115 40S ribosomal protein 100.0 1.2E-38 2.5E-43 249.0 8.5 73 1-81 119-191 (290)
14 KOG1750 Mitochondrial/chloropl 100.0 1.6E-32 3.6E-37 197.4 6.0 73 1-81 51-123 (139)
15 TIGR00008 infA translation ini 95.2 0.045 9.7E-07 35.4 4.4 34 30-64 19-54 (68)
16 COG0361 InfA Translation initi 93.6 0.16 3.5E-06 33.6 4.3 34 31-65 22-57 (75)
17 PRK12442 translation initiatio 90.2 0.64 1.4E-05 31.6 4.3 35 30-65 21-57 (87)
18 smart00652 eIF1a eukaryotic tr 88.3 1.1 2.4E-05 29.4 4.2 34 31-65 20-54 (83)
19 cd04456 S1_IF1A_like S1_IF1A_l 86.6 1.7 3.6E-05 28.3 4.3 35 30-65 14-49 (78)
20 TIGR00523 eIF-1A eukaryotic/ar 81.5 3.1 6.6E-05 28.3 4.0 34 30-64 33-67 (99)
21 PF01176 eIF-1a: Translation i 79.6 1.9 4.1E-05 26.6 2.3 33 31-65 18-52 (65)
22 cd05793 S1_IF1A S1_IF1A: Trans 79.3 4 8.7E-05 26.4 3.9 35 30-65 14-49 (77)
23 PLN00208 translation initiatio 77.1 4.3 9.3E-05 29.7 3.9 35 30-65 46-81 (145)
24 PTZ00329 eukaryotic translatio 75.8 5.2 0.00011 29.6 4.0 35 30-65 46-81 (155)
25 TIGR00230 sfsA sugar fermentat 72.1 9.9 0.00021 29.3 4.9 35 28-64 20-55 (232)
26 PF03749 SfsA: Sugar fermentat 70.0 12 0.00027 28.3 5.0 38 27-65 5-43 (215)
27 PRK00347 putative DNA-binding 64.6 19 0.00041 27.6 5.1 36 28-64 18-54 (234)
28 PF06246 Isy1: Isy1-like splic 64.0 2.2 4.9E-05 33.3 0.0 16 64-83 124-139 (255)
29 PRK04012 translation initiatio 58.5 12 0.00026 25.5 2.8 34 30-64 35-69 (100)
30 KOG3068 mRNA splicing factor [ 52.5 3.7 8E-05 32.9 -0.5 15 64-82 122-136 (268)
31 PLN00051 RNA-binding S4 domain 51.3 9.7 0.00021 29.7 1.6 15 54-68 231-245 (267)
32 PF14890 Intein_splicing: Inte 51.1 35 0.00076 26.0 4.6 39 25-64 47-92 (323)
33 COG1489 SfsA DNA-binding prote 49.7 42 0.0009 26.4 4.9 37 27-65 17-54 (235)
34 PF02210 Laminin_G_2: Laminin 48.9 52 0.0011 20.2 4.4 9 79-87 113-121 (128)
35 cd01732 LSm5 The eukaryotic Sm 45.4 43 0.00092 21.4 3.7 31 24-55 9-40 (76)
36 TIGR03069 PS_II_S4 photosystem 45.3 25 0.00054 27.1 3.0 15 54-68 223-237 (257)
37 COG2302 Uncharacterized conser 45.1 13 0.00028 29.7 1.5 15 54-68 220-234 (257)
38 PRK00284 pqqA coenzyme PQQ syn 44.6 32 0.0007 18.7 2.6 17 31-50 8-24 (26)
39 cd01724 Sm_D1 The eukaryotic S 44.1 60 0.0013 21.4 4.3 21 24-45 7-27 (90)
40 PF00386 C1q: C1q domain; Int 43.7 50 0.0011 21.6 3.9 41 25-65 55-105 (127)
41 cd05792 S1_eIF1AD_like S1_eIF1 40.4 59 0.0013 21.3 3.8 32 31-65 15-49 (78)
42 PLN02856 fumarylacetoacetase 39.8 52 0.0011 27.7 4.2 34 32-66 369-402 (424)
43 KOG2820 FAD-dependent oxidored 39.6 12 0.00026 31.6 0.5 37 40-86 338-375 (399)
44 TIGR01266 fum_ac_acetase fumar 38.8 61 0.0013 27.2 4.5 34 32-66 361-394 (415)
45 PF02080 TrkA_C: TrkA-C domain 38.4 31 0.00068 20.0 2.1 21 43-65 38-58 (71)
46 COG1768 Predicted phosphohydro 36.9 22 0.00049 28.0 1.6 10 73-82 69-78 (230)
47 PF07593 UnbV_ASPIC: ASPIC and 34.4 96 0.0021 19.0 3.9 36 31-68 5-40 (71)
48 PF04435 SPK: Domain of unknow 29.9 43 0.00092 21.4 1.8 26 26-52 82-107 (109)
49 TIGR02107 PQQ_syn_pqqA coenzym 28.5 72 0.0016 17.4 2.3 12 39-50 12-23 (26)
50 PF12869 tRNA_anti-like: tRNA_ 28.1 25 0.00053 23.4 0.5 41 41-85 99-143 (144)
51 PRK00276 infA translation init 27.8 1.6E+02 0.0034 18.3 4.6 33 31-64 22-56 (72)
52 COG4776 Rnb Exoribonuclease II 27.2 58 0.0013 28.9 2.7 50 27-80 573-628 (645)
53 TIGR00176 mobB molybdopterin-g 26.9 38 0.00082 23.7 1.3 16 53-68 85-100 (155)
54 cd03116 MobB Molybdenum is an 26.3 49 0.0011 23.4 1.8 16 53-68 88-103 (159)
55 PF14020 DUF4236: Protein of u 26.2 76 0.0017 19.6 2.4 25 26-50 26-50 (55)
56 PF11975 Glyco_hydro_4C: Famil 25.6 91 0.002 22.8 3.1 29 37-65 148-177 (232)
57 PRK10664 transcriptional regul 25.4 33 0.00071 22.3 0.7 15 54-68 35-49 (90)
58 smart00110 C1Q Complement comp 24.9 1.9E+02 0.0041 20.0 4.5 36 30-65 65-110 (135)
59 PF06565 DUF1126: Repeat of un 24.9 37 0.0008 18.9 0.7 12 16-27 12-23 (33)
60 cd03109 DTBS Dethiobiotin synt 23.9 1.2E+02 0.0026 20.3 3.3 25 37-68 25-49 (134)
61 cd01731 archaeal_Sm1 The archa 23.7 1.1E+02 0.0025 18.5 2.9 29 25-54 7-36 (68)
62 CHL00010 infA translation init 22.2 2.2E+02 0.0048 18.1 4.4 34 30-64 21-56 (78)
63 smart00651 Sm snRNP Sm protein 22.1 1.2E+02 0.0026 17.7 2.7 28 25-53 5-33 (67)
64 cd01726 LSm6 The eukaryotic Sm 21.3 1.4E+02 0.003 18.1 2.9 31 24-55 6-37 (67)
65 PRK06151 N-ethylammeline chlor 21.1 96 0.0021 25.2 2.7 29 35-68 4-32 (488)
66 PF00054 Laminin_G_1: Laminin 20.8 2.6E+02 0.0056 18.4 5.4 49 38-87 72-121 (131)
67 PF12663 DUF3788: Protein of u 20.8 1.7E+02 0.0038 20.3 3.6 30 31-68 50-79 (133)
68 PRK14494 putative molybdopteri 20.6 80 0.0017 24.1 2.0 12 57-68 85-96 (229)
69 cd01730 LSm3 The eukaryotic Sm 20.4 1.7E+02 0.0036 18.6 3.2 29 26-55 9-38 (82)
70 cd04497 hPOT1_OB1_like hPOT1_O 20.3 1.5E+02 0.0032 20.3 3.2 28 39-66 53-80 (138)
No 1
>cd03367 Ribosomal_S23 S12-like family, 40S ribosomal protein S23 subfamily; S23 is located at the interface of the large and small ribosomal subunits of eukaryotes, adjacent to the decoding center. It interacts with domain III of the eukaryotic elongation factor 2 (eEF2), which catalyzes the translocation of the growing peptidyl-tRNA to the P site to make room for the next aminoacyl-tRNA at the A (acceptor) site. Through its interaction with eEF2, S23 may play an important role in translocation. Also members of this subfamily are the archaeal 30S ribosomal S12 proteins. Prokaryotic S12 is essential for maintenance of a pretranslocation state and, together with S13, functions as control element for the rRNA- and tRNA-driven movements of translocation. S12 and S23 are also implicated in translation accuracy. Antibiotics such as streptomycin bind S12/S23 and cause the ribosome to misread the genetic code.
Probab=100.00 E-value=5.3e-49 Score=275.72 Aligned_cols=81 Identities=72% Similarity=1.175 Sum_probs=80.0
Q ss_pred CCCCCCccceeEEeeeeeeecCCCcccccEEEEEEecCCcEEEEEeCCCCcccccccCCeEEEeecCCCCCCCCCCCCce
Q 042342 1 PFAGPSHAKGIVLEKIGIEAKQPNFAIRKCSRVQLIKNGKKIVTFVPSDGCLNYIEENDKVLIAGFGRKGHAVATSPPII 80 (87)
Q Consensus 1 pl~~~pq~kGivl~~~~~~pKkPNSA~RK~~rV~Likngk~v~A~IPg~G~ln~lqeh~~VLV~GfGr~g~~v~DlPGV~ 80 (87)
||+++||+||||++++++||||||||+||||||||++||++|||||||||||+||||||+|||+|||++|++++|||||+
T Consensus 15 ~l~g~Pq~kGivl~~~~~~pKkPNSA~RK~~rV~L~~ngk~itAyIPG~G~~~~lqeh~~VLV~G~G~~Gg~v~DlPGVr 94 (115)
T cd03367 15 PLGGAPHAKGIVLEKVGVEAKQPNSAIRKCVRVQLIKNGKKITAFVPGDGCLNFIDENDEVLVAGFGRKGRAVGDIPGVR 94 (115)
T ss_pred cccCCCccCeEEEEEeecCCCCCChhhceEEEEEEccCCeEEEEEeCCCCcccccccCCEEEEEecccCCCccCCCCceE
Confidence 79999999999999999999999999999999999899999999999999999999999999999999999999999999
Q ss_pred e
Q 042342 81 S 81 (87)
Q Consensus 81 y 81 (87)
|
T Consensus 95 y 95 (115)
T cd03367 95 F 95 (115)
T ss_pred E
Confidence 8
No 2
>PTZ00067 40S ribosomal S23; Provisional
Probab=100.00 E-value=1e-47 Score=277.17 Aligned_cols=81 Identities=74% Similarity=1.200 Sum_probs=79.9
Q ss_pred CCCCCCccceeEEeeeeeeecCCCcccccEEEEEEecCCcEEEEEeCCCCcccccccCCeEEEeecCCCCCCCCCCCCce
Q 042342 1 PFAGPSHAKGIVLEKIGIEAKQPNFAIRKCSRVQLIKNGKKIVTFVPSDGCLNYIEENDKVLIAGFGRKGHAVATSPPII 80 (87)
Q Consensus 1 pl~~~pq~kGivl~~~~~~pKkPNSA~RK~~rV~Likngk~v~A~IPg~G~ln~lqeh~~VLV~GfGr~g~~v~DlPGV~ 80 (87)
||+++||++|||++++++||||||||+||||||||++||++|||||||||+|+||||||+|||+||||+|++++|||||+
T Consensus 40 pl~g~pq~kGivl~~~~~~pKkPNSA~RK~~rV~L~kngk~vtAyiPg~G~lh~lqEh~~VLV~G~Gr~g~~v~DlPGVr 119 (143)
T PTZ00067 40 PFGGASHAKGIVVEKIGIEAKQPNSAIRKCVRVQLIKNGKKITAFVPNDGCLNFINENDEVLVSGFGRSGHAVGDIPGVR 119 (143)
T ss_pred cccCCCccceEEEEEEeecCCCCChhhceEEEEEEccCCcEEEEEeCCCCcccccccCCEEEEEecCcCCCccCCCCceE
Confidence 89999999999999999999999999999999999889999999999999888999999999999999999999999999
Q ss_pred e
Q 042342 81 S 81 (87)
Q Consensus 81 y 81 (87)
|
T Consensus 120 y 120 (143)
T PTZ00067 120 F 120 (143)
T ss_pred E
Confidence 8
No 3
>TIGR00982 S23_S12_E_A ribosomal protein S23 (S12). This model represents the eukaryotic and archaeal homologs of bacterial ribosomal protein S12. This protein is known typically as S23 in eukaryotes and as either S12 or S23 in the Archaea.
Probab=100.00 E-value=2.1e-47 Score=274.50 Aligned_cols=81 Identities=53% Similarity=0.971 Sum_probs=79.9
Q ss_pred CCCCCCccceeEEeeeeeeecCCCcccccEEEEEEecCCcEEEEEeCCCCcccccccCCeEEEeecC-CCCCCCCCCCCc
Q 042342 1 PFAGPSHAKGIVLEKIGIEAKQPNFAIRKCSRVQLIKNGKKIVTFVPSDGCLNYIEENDKVLIAGFG-RKGHAVATSPPI 79 (87)
Q Consensus 1 pl~~~pq~kGivl~~~~~~pKkPNSA~RK~~rV~Likngk~v~A~IPg~G~ln~lqeh~~VLV~GfG-r~g~~v~DlPGV 79 (87)
||+++||+||||++++++||||||||+||||||||++||++||||||||||+|||||||+|||+||| ++|++++|||||
T Consensus 35 ~l~g~Pq~kGivl~~~~~~pKkPNSA~RK~~rV~L~~ngk~vtAyiPg~G~~~~lqeh~~VLV~G~gg~~gg~v~DlPGV 114 (139)
T TIGR00982 35 PLEGAPMARGIVLEKVGVEARQPNSAIRKCVRVQLIKNGKVVTAFCPGDGAINFIDEHDEVIIEGIGGPRGRSMGDIPGV 114 (139)
T ss_pred cccCCCccCeEEEEEEeecCCCCCcccceEEEEEEccCCeEEEEEeCCCccccccccCCEEEEEecCccCCCCcCCCCce
Confidence 7999999999999999999999999999999999999999999999999999999999999999998 999999999999
Q ss_pred ee
Q 042342 80 IS 81 (87)
Q Consensus 80 ~y 81 (87)
+|
T Consensus 115 ry 116 (139)
T TIGR00982 115 RY 116 (139)
T ss_pred EE
Confidence 99
No 4
>PRK04211 rps12P 30S ribosomal protein S12P; Reviewed
Probab=100.00 E-value=2e-47 Score=276.07 Aligned_cols=81 Identities=56% Similarity=0.984 Sum_probs=79.9
Q ss_pred CCCCCCccceeEEeeeeeeecCCCcccccEEEEEEecCCcEEEEEeCCCCcccccccCCeEEEeecC-CCCCCCCCCCCc
Q 042342 1 PFAGPSHAKGIVLEKIGIEAKQPNFAIRKCSRVQLIKNGKKIVTFVPSDGCLNYIEENDKVLIAGFG-RKGHAVATSPPI 79 (87)
Q Consensus 1 pl~~~pq~kGivl~~~~~~pKkPNSA~RK~~rV~Likngk~v~A~IPg~G~ln~lqeh~~VLV~GfG-r~g~~v~DlPGV 79 (87)
||+++||++|||++++++||||||||+||||||||++||++||||||||||+|||||||+|||+||| ++|++++|||||
T Consensus 41 ~l~g~Pq~kGivl~~~~v~pKKPNSA~RK~arV~L~~Ngk~vtAyIPg~G~~~~lqEh~~VLV~G~gg~~gg~v~DlPGV 120 (145)
T PRK04211 41 PLEGAPMARGIVLEKVGVEAKQPNSAIRKCVRVQLIKNGKQVTAFCPGDGAINFIDEHDEVVIEGIGGPKGRSMGDIPGV 120 (145)
T ss_pred cccCCCccCeEEEEEeeecCCCCchhhceeEEEEEccCCeEEEEEeCCCccccccccCCEEEEeecCccCCCCcCCCCce
Confidence 7999999999999999999999999999999999999999999999999999999999999999998 999999999999
Q ss_pred ee
Q 042342 80 IS 81 (87)
Q Consensus 80 ~y 81 (87)
+|
T Consensus 121 ry 122 (145)
T PRK04211 121 RY 122 (145)
T ss_pred EE
Confidence 98
No 5
>KOG1749 consensus 40S ribosomal protein S23 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=3.5e-46 Score=267.79 Aligned_cols=81 Identities=78% Similarity=1.235 Sum_probs=80.3
Q ss_pred CCCCCCccceeEEeeeeeeecCCCcccccEEEEEEecCCcEEEEEeCCCCcccccccCCeEEEeecCCCCCCCCCCCCce
Q 042342 1 PFAGPSHAKGIVLEKIGIEAKQPNFAIRKCSRVQLIKNGKKIVTFVPSDGCLNYIEENDKVLIAGFGRKGHAVATSPPII 80 (87)
Q Consensus 1 pl~~~pq~kGivl~~~~~~pKkPNSA~RK~~rV~Likngk~v~A~IPg~G~ln~lqeh~~VLV~GfGr~g~~v~DlPGV~ 80 (87)
||+|+||+||||||++++|+||||||+|||+|||||+|||+||||+|.||||||++|||+|||.||||+||+++||||||
T Consensus 40 pfggashAKgIvLEKigVEAKQPNSAiRKcvRvQLIkngKKITafVp~dgcln~ieendevlv~gfgrkg~avgdipgvr 119 (143)
T KOG1749|consen 40 PFGGASHAKGIVLEKIGVEAKQPNSAIRKCVRVQLIKNGKKITAFVPNDGCLNFIEENDEVLVAGFGRKGHAVGDIPGVR 119 (143)
T ss_pred CCCCccccceeEEEeeeeeccCCcHHHhhheeeeeeeCCceEEEEecCCCceeeeccCCeeeeeccCccCccccCCCceE
Confidence 89999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred e
Q 042342 81 S 81 (87)
Q Consensus 81 y 81 (87)
+
T Consensus 120 f 120 (143)
T KOG1749|consen 120 F 120 (143)
T ss_pred E
Confidence 7
No 6
>cd00319 Ribosomal_S12_like Ribosomal protein S12-like family; composed of prokaryotic 30S ribosomal protein S12, eukaryotic 40S ribosomal protein S23 and similar proteins. S12 and S23 are located at the interface of the large and small ribosomal subunits, adjacent to the decoding center. They play an important role in translocation during the peptide elongation step of protein synthesis. They are also involved in important RNA and protein interactions. Ribosomal protein S12 is essential for maintenance of a pretranslocation state and, together with S13, functions as a control element for the rRNA- and tRNA-driven movements of translocation. S23 interacts with domain III of the eukaryotic elongation factor 2 (eEF2), which catalyzes translocation. Mutations in S12 and S23 have been found to affect translational accuracy. Antibiotics such as streptomycin may also bind S12/S23 and cause the ribosome to misread the genetic code.
Probab=100.00 E-value=1.1e-44 Score=246.87 Aligned_cols=73 Identities=30% Similarity=0.597 Sum_probs=71.5
Q ss_pred CCCCCCccceeEEeeeeeeecCCCcccccEEEEEEecCCcEEEEEeCCCCcccccccCCeEEEeecCCCCCCCCCCCCce
Q 042342 1 PFAGPSHAKGIVLEKIGIEAKQPNFAIRKCSRVQLIKNGKKIVTFVPSDGCLNYIEENDKVLIAGFGRKGHAVATSPPII 80 (87)
Q Consensus 1 pl~~~pq~kGivl~~~~~~pKkPNSA~RK~~rV~Likngk~v~A~IPg~G~ln~lqeh~~VLV~GfGr~g~~v~DlPGV~ 80 (87)
||+++||+||||+++++++|||||||+|||||||| +||++|+|||||||| ||||||+|||+| || ++|||||+
T Consensus 8 ~l~~~Pq~kGi~l~~~~~~pKkPNSA~RK~arV~L-~ngk~v~ayIPg~Gh--~lqeh~~VLvrG-Gr----~~DlPGVr 79 (95)
T cd00319 8 ALKGAPFRRGVCTVVRTVTPKKPNSALRKVAKVRL-TSGYEVTAYIPGEGH--NLQEHSVVLIRG-GR----VKDLPGVR 79 (95)
T ss_pred cccCCcccCeEEEEEEeccccCCChhhceEEEEEc-cCCCEEEEECCCCCc--ccccccEEEEeC-CC----cCCCCCcE
Confidence 79999999999999999999999999999999999 699999999999999 999999999999 99 99999999
Q ss_pred e
Q 042342 81 S 81 (87)
Q Consensus 81 y 81 (87)
|
T Consensus 80 y 80 (95)
T cd00319 80 Y 80 (95)
T ss_pred E
Confidence 9
No 7
>COG0048 RpsL Ribosomal protein S12 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.9e-44 Score=256.64 Aligned_cols=73 Identities=37% Similarity=0.714 Sum_probs=71.4
Q ss_pred CCCCCCccceeEEeeeeeeecCCCcccccEEEEEEecCCcEEEEEeCCCCcccccccCCeEEEeecCCCCCCCCCCCCce
Q 042342 1 PFAGPSHAKGIVLEKIGIEAKQPNFAIRKCSRVQLIKNGKKIVTFVPSDGCLNYIEENDKVLIAGFGRKGHAVATSPPII 80 (87)
Q Consensus 1 pl~~~pq~kGivl~~~~~~pKkPNSA~RK~~rV~Likngk~v~A~IPg~G~ln~lqeh~~VLV~GfGr~g~~v~DlPGV~ 80 (87)
||+++||++|||+|++++||||||||+||||||||+ ||++|||||||||| +|||||+||||| |+ ++||||||
T Consensus 29 ~L~g~Pq~RGv~~~v~~~~pKkPNSAlRK~~RVrL~-NG~~VtAyiPg~Gh--~lqEH~~Vli~G-~~----v~DlPGVR 100 (129)
T COG0048 29 ALEGAPQARGVCTRVYTVTPKKPNSALRKVARVRLI-NGKEVTAYIPGEGH--NLQEHSEVLIRG-GR----VKDLPGVR 100 (129)
T ss_pred cccCCCccceEEEEEEecccCCCChhhheeEEEEee-CCcEEEEEcCCCCc--cccccCEEEEec-Cc----cCCCCCce
Confidence 799999999999999999999999999999999995 99999999999999 899999999999 78 99999999
Q ss_pred e
Q 042342 81 S 81 (87)
Q Consensus 81 y 81 (87)
|
T Consensus 101 y 101 (129)
T COG0048 101 Y 101 (129)
T ss_pred E
Confidence 9
No 8
>cd03368 Ribosomal_S12 S12-like family, 30S ribosomal protein S12 subfamily; S12 is located at the interface of the large and small ribosomal subunits of prokaryotes, chloroplasts and mitochondria, where it plays an important role in both tRNA and ribosomal subunit interactions. S12 is essential for maintenance of a pretranslocation state and, together with S13, functions as a control element for the rRNA- and tRNA-driven movements of translocation. Antibiotics such as streptomycin bind S12 and cause the ribosome to misread the genetic code.
Probab=100.00 E-value=7.5e-44 Score=247.46 Aligned_cols=73 Identities=36% Similarity=0.664 Sum_probs=71.7
Q ss_pred CCCCCCccceeEEeeeeeeecCCCcccccEEEEEEecCCcEEEEEeCCCCcccccccCCeEEEeecCCCCCCCCCCCCce
Q 042342 1 PFAGPSHAKGIVLEKIGIEAKQPNFAIRKCSRVQLIKNGKKIVTFVPSDGCLNYIEENDKVLIAGFGRKGHAVATSPPII 80 (87)
Q Consensus 1 pl~~~pq~kGivl~~~~~~pKkPNSA~RK~~rV~Likngk~v~A~IPg~G~ln~lqeh~~VLV~GfGr~g~~v~DlPGV~ 80 (87)
||+++||+||||+++++++|||||||+|||||||| +||++|+|||||||| ||||||+|||+| || ++|||||+
T Consensus 21 ~l~g~Pq~kGi~l~v~~~~pKKPNSA~RKvarV~L-~ngk~v~AyIPG~Gh--nlqehs~VLvrG-Gr----v~DlPGVk 92 (108)
T cd03368 21 ALEGCPQKKGVCLKVYTTTPKKPNSALRKVARVRL-SNGKEVTAYIPGEGH--NLQEHSVVLVRG-GR----VKDLPGVR 92 (108)
T ss_pred cccCCcccCcEEEEEEeccccCCChhheeeEEEEe-cCCCEEEEEcCCCCC--CccccCEEEEeC-Cc----cCCCCCeE
Confidence 68999999999999999999999999999999999 699999999999999 999999999999 99 99999999
Q ss_pred e
Q 042342 81 S 81 (87)
Q Consensus 81 y 81 (87)
|
T Consensus 93 y 93 (108)
T cd03368 93 Y 93 (108)
T ss_pred E
Confidence 9
No 9
>PRK05163 rpsL 30S ribosomal protein S12; Validated
Probab=100.00 E-value=2.6e-43 Score=249.46 Aligned_cols=73 Identities=32% Similarity=0.579 Sum_probs=71.9
Q ss_pred CCCCCCccceeEEeeeeeeecCCCcccccEEEEEEecCCcEEEEEeCCCCcccccccCCeEEEeecCCCCCCCCCCCCce
Q 042342 1 PFAGPSHAKGIVLEKIGIEAKQPNFAIRKCSRVQLIKNGKKIVTFVPSDGCLNYIEENDKVLIAGFGRKGHAVATSPPII 80 (87)
Q Consensus 1 pl~~~pq~kGivl~~~~~~pKkPNSA~RK~~rV~Likngk~v~A~IPg~G~ln~lqeh~~VLV~GfGr~g~~v~DlPGV~ 80 (87)
||+++||++|||+++++++|||||||+|||||||| +||++|+|||||||| ||||||+|||+| |+ ++|||||+
T Consensus 23 ~l~~~Pq~kGv~l~v~~~~pKKPNSA~RKvarVrL-~ngk~v~AyIPGeGh--nlqehs~VLvrG-Gr----v~DlPGVr 94 (124)
T PRK05163 23 ALNACPQKRGVCTRVYTTTPKKPNSALRKVARVRL-TNGFEVTAYIPGEGH--NLQEHSVVLIRG-GR----VKDLPGVR 94 (124)
T ss_pred ccccCcccCcEEEEEEecCccCCCchhheEEEEEe-CCCCEEEEEcCCCCC--CccccCEEEEeC-Cc----cCCCCCcE
Confidence 68999999999999999999999999999999999 999999999999999 999999999999 99 99999999
Q ss_pred e
Q 042342 81 S 81 (87)
Q Consensus 81 y 81 (87)
|
T Consensus 95 y 95 (124)
T PRK05163 95 Y 95 (124)
T ss_pred E
Confidence 9
No 10
>CHL00051 rps12 ribosomal protein S12
Probab=100.00 E-value=2.6e-43 Score=249.19 Aligned_cols=73 Identities=33% Similarity=0.566 Sum_probs=72.0
Q ss_pred CCCCCCccceeEEeeeeeeecCCCcccccEEEEEEecCCcEEEEEeCCCCcccccccCCeEEEeecCCCCCCCCCCCCce
Q 042342 1 PFAGPSHAKGIVLEKIGIEAKQPNFAIRKCSRVQLIKNGKKIVTFVPSDGCLNYIEENDKVLIAGFGRKGHAVATSPPII 80 (87)
Q Consensus 1 pl~~~pq~kGivl~~~~~~pKkPNSA~RK~~rV~Likngk~v~A~IPg~G~ln~lqeh~~VLV~GfGr~g~~v~DlPGV~ 80 (87)
||+++||++|||+++++++|||||||+|||||||| +||++|+|||||||| ||||||+||||| || ++|||||+
T Consensus 23 ~L~g~Pq~kGv~lkv~~~~pKKPNSA~RKvarVrL-sngk~v~AyIPGeGh--nlqehs~VLvrG-Gr----v~DlPGVr 94 (123)
T CHL00051 23 ALRGCPQRRGTCTRVYTITPKKPNSALRKVARVRL-TSGFEITAYIPGIGH--NLQEHSVVLVRG-GR----VKDLPGVR 94 (123)
T ss_pred ccccCcccCeEEEEEEeccccCCChhheeEEEEEc-cCCCEEEEEcCCCCc--cccccCEEEEeC-Cc----cCCCCCee
Confidence 68999999999999999999999999999999999 999999999999999 999999999999 99 99999999
Q ss_pred e
Q 042342 81 S 81 (87)
Q Consensus 81 y 81 (87)
|
T Consensus 95 y 95 (123)
T CHL00051 95 Y 95 (123)
T ss_pred E
Confidence 9
No 11
>TIGR00981 rpsL_bact ribosomal protein S12, bacterial/organelle. This model recognizes ribosomal protein S12 of Bacteria, mitochondria, and chloroplasts. The homologous ribosomal proteins of Archaea and Eukarya, termed S23 in Eukarya and S12 or S23 in Archaea, score below the trusted cutoff.
Probab=100.00 E-value=3.2e-43 Score=249.05 Aligned_cols=73 Identities=32% Similarity=0.580 Sum_probs=71.9
Q ss_pred CCCCCCccceeEEeeeeeeecCCCcccccEEEEEEecCCcEEEEEeCCCCcccccccCCeEEEeecCCCCCCCCCCCCce
Q 042342 1 PFAGPSHAKGIVLEKIGIEAKQPNFAIRKCSRVQLIKNGKKIVTFVPSDGCLNYIEENDKVLIAGFGRKGHAVATSPPII 80 (87)
Q Consensus 1 pl~~~pq~kGivl~~~~~~pKkPNSA~RK~~rV~Likngk~v~A~IPg~G~ln~lqeh~~VLV~GfGr~g~~v~DlPGV~ 80 (87)
||+++||++|||+++++++|||||||+|||||||| +||++|+|||||||| ||||||+||||| || ++|||||+
T Consensus 23 ~l~g~Pq~kGi~l~~~~~~pKKPNSA~RKvarVrL-~ngk~v~AyIPG~Gh--nlqehs~VLvrG-Gr----v~DlPGVk 94 (124)
T TIGR00981 23 ALEACPQKRGVCTRVYTTTPKKPNSALRKVARVRL-TNGFEVTAYIPGEGH--NLQEHSVVLIRG-GR----VKDLPGVR 94 (124)
T ss_pred ccccCCccCcEEEEEEeccccCCCchhheeEEEEe-CCCCEEEEEcCCCCC--CccccCEEEEeC-Cc----cCCCCCeE
Confidence 68999999999999999999999999999999999 999999999999999 999999999999 99 99999999
Q ss_pred e
Q 042342 81 S 81 (87)
Q Consensus 81 y 81 (87)
|
T Consensus 95 y 95 (124)
T TIGR00981 95 Y 95 (124)
T ss_pred E
Confidence 9
No 12
>PF00164 Ribosom_S12_S23: Ribosomal protein S12/S23; InterPro: IPR006032 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 [, ]. Ribosomal protein S12 is one of the proteins from the small ribosomal subunit. In Escherichia coli, S12 is known to be involved in the translation initiation step. It is a very basic protein of 120 to 150 amino-acid residues. S12 belongs to a family of ribosomal proteins which are grouped on the basis of sequence similarities. This protein is known typically as S12 in bacteria, S23 in eukaryotes and as either S12 or S23 in the Archaea []. Bacterial S12 molecules contain a conserved aspartic acid residue which undergoes a novel post-translational modification, beta-methylthiolation, to form the corresponding 3-methylthioaspartic acid.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 2ZKQ_l 3BBN_L 3PYU_L 3D5A_L 3MS0_L 3MR8_L 3F1G_L 2OW8_m 3PYS_L 2QNH_m ....
Probab=100.00 E-value=8.6e-43 Score=245.73 Aligned_cols=73 Identities=40% Similarity=0.730 Sum_probs=70.5
Q ss_pred CCCCCCccceeEEeeeeeeecCCCcccccEEEEEEecCCcEEEEEeCCCCcccccccCCeEEEeecCCCCCCCCCCCCce
Q 042342 1 PFAGPSHAKGIVLEKIGIEAKQPNFAIRKCSRVQLIKNGKKIVTFVPSDGCLNYIEENDKVLIAGFGRKGHAVATSPPII 80 (87)
Q Consensus 1 pl~~~pq~kGivl~~~~~~pKkPNSA~RK~~rV~Likngk~v~A~IPg~G~ln~lqeh~~VLV~GfGr~g~~v~DlPGV~ 80 (87)
||+++||+||||+++++++|||||||+|||||||| +|+++|+|||||||| ||||||+|||+| |+ ++|||||+
T Consensus 22 ~l~~~Pq~kGi~l~~~~~~pKKPNSA~RK~arVrL-~n~k~v~AyIPg~Gh--nlqehs~VLVrG-gr----v~DlPGVk 93 (122)
T PF00164_consen 22 ALGGCPQKKGICLKVVTVKPKKPNSAIRKVARVRL-SNGKKVTAYIPGEGH--NLQEHSVVLVRG-GR----VGDLPGVK 93 (122)
T ss_dssp SSTTSSEEEEEEEEEEEEEESTTTCSEEEEEEEEE-TTSEEEEEEC-SSSC--CSTTTSEEEEEE-ES----BTTSTTEC
T ss_pred ccCCCCccCcEEeecccccccCccchhhhcceeee-ccCceEEEEecCCcc--cccccceEEEec-cc----cCCCCceE
Confidence 68999999999999999999999999999999999 699999999999999 999999999999 88 99999999
Q ss_pred e
Q 042342 81 S 81 (87)
Q Consensus 81 y 81 (87)
|
T Consensus 94 y 94 (122)
T PF00164_consen 94 Y 94 (122)
T ss_dssp E
T ss_pred E
Confidence 8
No 13
>PTZ00115 40S ribosomal protein S12; Provisional
Probab=100.00 E-value=1.2e-38 Score=249.04 Aligned_cols=73 Identities=27% Similarity=0.508 Sum_probs=71.4
Q ss_pred CCCCCCccceeEEeeeeeeecCCCcccccEEEEEEecCCcEEEEEeCCCCcccccccCCeEEEeecCCCCCCCCCCCCce
Q 042342 1 PFAGPSHAKGIVLEKIGIEAKQPNFAIRKCSRVQLIKNGKKIVTFVPSDGCLNYIEENDKVLIAGFGRKGHAVATSPPII 80 (87)
Q Consensus 1 pl~~~pq~kGivl~~~~~~pKkPNSA~RK~~rV~Likngk~v~A~IPg~G~ln~lqeh~~VLV~GfGr~g~~v~DlPGV~ 80 (87)
.|+++||+||||+++++++|||||||+|||||||| +||++|+|||||||| ||||||+|||+| |+ ++|||||+
T Consensus 119 aL~g~PQkKGIclkv~~~tPKKPNSA~RKvarVrL-sNGk~VtAyIPGeGH--nLQEHs~VLVRG-Gr----vkDLPGVr 190 (290)
T PTZ00115 119 WLEGAPQKKGICVKVRVQTPRKPNSGLRKVARVRL-STGRTVTVYIPGIGH--NLNTHSVVLVRG-GR----CKDVPGCN 190 (290)
T ss_pred cccCCcccCeEEEEeeecCCCCCCccccceEEEEe-cCCCEEEEEcCCCCc--ccccCCEEEEeC-CC----cCCCCCce
Confidence 37899999999999999999999999999999999 899999999999999 999999999999 99 99999999
Q ss_pred e
Q 042342 81 S 81 (87)
Q Consensus 81 y 81 (87)
|
T Consensus 191 Y 191 (290)
T PTZ00115 191 Y 191 (290)
T ss_pred E
Confidence 9
No 14
>KOG1750 consensus Mitochondrial/chloroplast ribosomal protein S12 [Translation, ribosomal structure and biogenesis]
Probab=99.97 E-value=1.6e-32 Score=197.38 Aligned_cols=73 Identities=36% Similarity=0.659 Sum_probs=71.7
Q ss_pred CCCCCCccceeEEeeeeeeecCCCcccccEEEEEEecCCcEEEEEeCCCCcccccccCCeEEEeecCCCCCCCCCCCCce
Q 042342 1 PFAGPSHAKGIVLEKIGIEAKQPNFAIRKCSRVQLIKNGKKIVTFVPSDGCLNYIEENDKVLIAGFGRKGHAVATSPPII 80 (87)
Q Consensus 1 pl~~~pq~kGivl~~~~~~pKkPNSA~RK~~rV~Likngk~v~A~IPg~G~ln~lqeh~~VLV~GfGr~g~~v~DlPGV~ 80 (87)
+|+++||.+|||+++++++|||||||.|||++|+| +||.+|+|||||+|| |+|||+.||++| || ++|+|||+
T Consensus 51 ~L~g~p~~kgvvl~v~t~~pkkPnsa~rK~~~vrl-stg~~i~ayipg~gh--nlqehs~Vlvrg-gr----~qdlpgvk 122 (139)
T KOG1750|consen 51 ALDGCPQRKGVVLRVFTRKPKKPNSANRKCARVRL-STGREVTAYIPGIGH--NLQEHSIVLVRG-GR----VQDLPGVK 122 (139)
T ss_pred cccCCcccccEEEEEEEecCCCCCccceeeEEEEe-cCchheeeeCCCccc--cceeEEEEEEec-ce----eccCcchh
Confidence 58899999999999999999999999999999999 999999999999999 999999999999 99 99999999
Q ss_pred e
Q 042342 81 S 81 (87)
Q Consensus 81 y 81 (87)
|
T Consensus 123 ~ 123 (139)
T KOG1750|consen 123 Y 123 (139)
T ss_pred h
Confidence 7
No 15
>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=95.21 E-value=0.045 Score=35.43 Aligned_cols=34 Identities=26% Similarity=0.415 Sum_probs=27.7
Q ss_pred EEEEEEecCCcEEEEEeCCCCccc--ccccCCeEEEe
Q 042342 30 CSRVQLIKNGKKIVTFVPSDGCLN--YIEENDKVLIA 64 (87)
Q Consensus 30 ~~rV~Likngk~v~A~IPg~G~ln--~lqeh~~VLV~ 64 (87)
-.+|+| -||+++.|||||-=-.| -+.+.|.|+|+
T Consensus 19 ~f~V~l-~ng~~vla~i~GKmr~~rI~I~~GD~V~Ve 54 (68)
T TIGR00008 19 MFRVEL-ENGHEVLAHISGKIRMHYIRILPGDKVKVE 54 (68)
T ss_pred EEEEEE-CCCCEEEEEecCcchhccEEECCCCEEEEE
Confidence 467899 89999999999954422 37899999998
No 16
>COG0361 InfA Translation initiation factor 1 (IF-1) [Translation, ribosomal structure and biogenesis]
Probab=93.57 E-value=0.16 Score=33.56 Aligned_cols=34 Identities=29% Similarity=0.326 Sum_probs=29.4
Q ss_pred EEEEEecCCcEEEEEeCCCCcccc--cccCCeEEEee
Q 042342 31 SRVQLIKNGKKIVTFVPSDGCLNY--IEENDKVLIAG 65 (87)
Q Consensus 31 ~rV~Likngk~v~A~IPg~G~ln~--lqeh~~VLV~G 65 (87)
.+|+| -||+++.|+|||-.-.|+ |-+-|.|+|+=
T Consensus 22 f~v~~-edg~~~~ahI~GKmr~~~i~I~~GD~V~Ve~ 57 (75)
T COG0361 22 FRVEL-ENGHERLAHISGKMRKNRIRILPGDVVLVEL 57 (75)
T ss_pred EEEEe-cCCcEEEEEccCcchheeEEeCCCCEEEEEe
Confidence 67999 999999999999997544 67999999984
No 17
>PRK12442 translation initiation factor IF-1; Reviewed
Probab=90.25 E-value=0.64 Score=31.64 Aligned_cols=35 Identities=23% Similarity=0.244 Sum_probs=28.6
Q ss_pred EEEEEEecCCcEEEEEeCCCCcccc--cccCCeEEEee
Q 042342 30 CSRVQLIKNGKKIVTFVPSDGCLNY--IEENDKVLIAG 65 (87)
Q Consensus 30 ~~rV~Likngk~v~A~IPg~G~ln~--lqeh~~VLV~G 65 (87)
-.+|+| -||..|.|||+|-=-.|+ |.+.|.|+|+=
T Consensus 21 ~frV~L-enG~~vla~isGKmR~~rIrIl~GD~V~VE~ 57 (87)
T PRK12442 21 RFRVTL-ENGVEVGAYASGRMRKHRIRILAGDRVTLEL 57 (87)
T ss_pred EEEEEe-CCCCEEEEEeccceeeeeEEecCCCEEEEEE
Confidence 467999 899999999999765443 57889999983
No 18
>smart00652 eIF1a eukaryotic translation initiation factor 1A.
Probab=88.34 E-value=1.1 Score=29.40 Aligned_cols=34 Identities=24% Similarity=0.304 Sum_probs=27.0
Q ss_pred EEEEEecCCcEEEEEeCCCCc-ccccccCCeEEEee
Q 042342 31 SRVQLIKNGKKIVTFVPSDGC-LNYIEENDKVLIAG 65 (87)
Q Consensus 31 ~rV~Likngk~v~A~IPg~G~-ln~lqeh~~VLV~G 65 (87)
.+|++ .||+++.|+|||-=. --.+.+.|.|+|+=
T Consensus 20 ~~V~~-~dG~~~la~ipgK~Rk~iwI~~GD~VlVe~ 54 (83)
T smart00652 20 LEVMC-ADGKERLARIPGKMRKKVWIRRGDIVLVDP 54 (83)
T ss_pred EEEEE-CCCCEEEEEEchhhcccEEEcCCCEEEEEe
Confidence 57888 899999999999421 12588999999984
No 19
>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=86.57 E-value=1.7 Score=28.30 Aligned_cols=35 Identities=14% Similarity=0.262 Sum_probs=27.4
Q ss_pred EEEEEEecCCcEEEEEeCCCCc-ccccccCCeEEEee
Q 042342 30 CSRVQLIKNGKKIVTFVPSDGC-LNYIEENDKVLIAG 65 (87)
Q Consensus 30 ~~rV~Likngk~v~A~IPg~G~-ln~lqeh~~VLV~G 65 (87)
-.+|++ .||+++.|.|||-=. ---+.+.|.|+|+=
T Consensus 14 ~~~V~~-~dg~~~l~~i~gK~Rk~iwI~~GD~VlV~~ 49 (78)
T cd04456 14 RHEVEC-ADGQRRLVSIPGKLRKNIWIKRGDFLIVDP 49 (78)
T ss_pred EEEEEE-CCCCEEEEEEchhhccCEEEcCCCEEEEEe
Confidence 467888 899999999999421 02688999999973
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=81.48 E-value=3.1 Score=28.33 Aligned_cols=34 Identities=24% Similarity=0.313 Sum_probs=26.8
Q ss_pred EEEEEEecCCcEEEEEeCCCC-cccccccCCeEEEe
Q 042342 30 CSRVQLIKNGKKIVTFVPSDG-CLNYIEENDKVLIA 64 (87)
Q Consensus 30 ~~rV~Likngk~v~A~IPg~G-~ln~lqeh~~VLV~ 64 (87)
-.+|++ -||+++.|+|||-= .--.+.+.|.|+|.
T Consensus 33 ~~~V~~-~dG~~~la~i~GK~Rk~iwI~~GD~VlVs 67 (99)
T TIGR00523 33 RVKVRC-LDGKTRLGRIPGKLKKRIWIREGDVVIVK 67 (99)
T ss_pred EEEEEe-CCCCEEEEEEchhhcccEEecCCCEEEEE
Confidence 467888 89999999999942 12258899999994
No 21
>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=79.57 E-value=1.9 Score=26.62 Aligned_cols=33 Identities=21% Similarity=0.407 Sum_probs=24.2
Q ss_pred EEEEEecCCcEEEEEeCCCCccc--ccccCCeEEEee
Q 042342 31 SRVQLIKNGKKIVTFVPSDGCLN--YIEENDKVLIAG 65 (87)
Q Consensus 31 ~rV~Likngk~v~A~IPg~G~ln--~lqeh~~VLV~G 65 (87)
.+|+| .||.++.|+|||- --+ .+.+.|.|+|.=
T Consensus 18 ~~V~~-~dg~~~l~~i~gK-~r~~iwI~~GD~V~V~~ 52 (65)
T PF01176_consen 18 FEVEC-EDGEERLARIPGK-FRKRIWIKRGDFVLVEP 52 (65)
T ss_dssp EEEEE-TTSEEEEEEE-HH-HHTCC---TTEEEEEEE
T ss_pred EEEEe-CCCCEEEEEeccc-eeeeEecCCCCEEEEEe
Confidence 67898 8999999999997 322 478999999973
No 22
>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=79.28 E-value=4 Score=26.39 Aligned_cols=35 Identities=29% Similarity=0.259 Sum_probs=27.5
Q ss_pred EEEEEEecCCcEEEEEeCCCCc-ccccccCCeEEEee
Q 042342 30 CSRVQLIKNGKKIVTFVPSDGC-LNYIEENDKVLIAG 65 (87)
Q Consensus 30 ~~rV~Likngk~v~A~IPg~G~-ln~lqeh~~VLV~G 65 (87)
-.+|++ -||+++.|+|||-=. --.+.+.|.|+|+=
T Consensus 14 ~~~V~~-~~g~~~la~i~gK~rk~iwI~~GD~V~Ve~ 49 (77)
T cd05793 14 RLEVRC-FDGKKRLCRIRGKMRKRVWINEGDIVLVAP 49 (77)
T ss_pred EEEEEE-CCCCEEEEEEchhhcccEEEcCCCEEEEEe
Confidence 367888 899999999998532 12578899999974
No 23
>PLN00208 translation initiation factor (eIF); Provisional
Probab=77.14 E-value=4.3 Score=29.74 Aligned_cols=35 Identities=14% Similarity=0.141 Sum_probs=27.4
Q ss_pred EEEEEEecCCcEEEEEeCCCCc-ccccccCCeEEEee
Q 042342 30 CSRVQLIKNGKKIVTFVPSDGC-LNYIEENDKVLIAG 65 (87)
Q Consensus 30 ~~rV~Likngk~v~A~IPg~G~-ln~lqeh~~VLV~G 65 (87)
-.+|++ -||.+++|+|||-=. ---+.+.|.|||+-
T Consensus 46 ~~~V~c-~dG~~rLa~IpGKmRKrIWI~~GD~VlVel 81 (145)
T PLN00208 46 RCEALC-IDGTKRLCHIRGKMRKKVWIAAGDIILVGL 81 (145)
T ss_pred EEEEEE-CCCCEEEEEEeccceeeEEecCCCEEEEEc
Confidence 367888 799999999999421 12688999999984
No 24
>PTZ00329 eukaryotic translation initiation factor 1A; Provisional
Probab=75.77 E-value=5.2 Score=29.64 Aligned_cols=35 Identities=14% Similarity=0.078 Sum_probs=27.1
Q ss_pred EEEEEEecCCcEEEEEeCCCCc-ccccccCCeEEEee
Q 042342 30 CSRVQLIKNGKKIVTFVPSDGC-LNYIEENDKVLIAG 65 (87)
Q Consensus 30 ~~rV~Likngk~v~A~IPg~G~-ln~lqeh~~VLV~G 65 (87)
-.+|++ -||.+++|+|||-=. ---|.+.|.|||+-
T Consensus 46 ~f~V~c-~dG~~rLa~I~GKmRK~IWI~~GD~VlVel 81 (155)
T PTZ00329 46 RLEAYC-FDGVKRLCHIRGKMRKRVWINIGDIILVSL 81 (155)
T ss_pred EEEEEE-CCCCEEEEEeeccceeeEEecCCCEEEEec
Confidence 367788 799999999999421 12588999999974
No 25
>TIGR00230 sfsA sugar fermentation stimulation protein. probable regulatory factor involved in maltose metabolism contains a putative DNA binding domain. Isolated as a gene which enabled E.coli strain MK2001 to use maltose.
Probab=72.07 E-value=9.9 Score=29.27 Aligned_cols=35 Identities=23% Similarity=0.391 Sum_probs=30.6
Q ss_pred ccEEEEEEecCCcEEEEEeCCCCcc-cccccCCeEEEe
Q 042342 28 RKCSRVQLIKNGKKIVTFVPSDGCL-NYIEENDKVLIA 64 (87)
Q Consensus 28 RK~~rV~Likngk~v~A~IPg~G~l-n~lqeh~~VLV~ 64 (87)
|=.+.|++ +|.+++|++|+-|.+ .-+.+...|+++
T Consensus 20 RF~~~V~~--~G~~~~aH~pNtGrl~ell~pG~~vll~ 55 (232)
T TIGR00230 20 RFLVDVEV--DGRRETAHCPNTGRLTELIFPGNDVGLS 55 (232)
T ss_pred CEEEEEEE--CCeEEEEEcCCCCCChhhcCCCCEEEEE
Confidence 78899998 899999999999976 457888999987
No 26
>PF03749 SfsA: Sugar fermentation stimulation protein; InterPro: IPR005224 The sugar fermentation stimulation protein is a probable regulatory factor involved in maltose metabolism. It contains a putative DNA-binding domain, and was isolated as a gene which enabled Escherichia coli W3110 (strain MK2001) to use maltose [].
Probab=69.98 E-value=12 Score=28.28 Aligned_cols=38 Identities=24% Similarity=0.469 Sum_probs=30.9
Q ss_pred cccEEEEEEecCCcEEEEEeCCCCccc-ccccCCeEEEee
Q 042342 27 IRKCSRVQLIKNGKKIVTFVPSDGCLN-YIEENDKVLIAG 65 (87)
Q Consensus 27 ~RK~~rV~Likngk~v~A~IPg~G~ln-~lqeh~~VLV~G 65 (87)
+|=.|.|+| .+|..++||+|+-|.|. .+.+...|+++=
T Consensus 5 nRF~~~v~l-~~g~~~~~H~pntGRl~ell~pG~~v~l~~ 43 (215)
T PF03749_consen 5 NRFLADVEL-DDGEEVTAHCPNTGRLKELLVPGARVLLSK 43 (215)
T ss_pred CcEEEEEEE-CCCCEEEEEcCCCCcchhhccCCCEEEEEE
Confidence 355788998 55999999999999876 556888888874
No 27
>PRK00347 putative DNA-binding transcriptional regulator; Reviewed
Probab=64.56 E-value=19 Score=27.59 Aligned_cols=36 Identities=19% Similarity=0.487 Sum_probs=30.9
Q ss_pred ccEEEEEEecCCcEEEEEeCCCCccc-ccccCCeEEEe
Q 042342 28 RKCSRVQLIKNGKKIVTFVPSDGCLN-YIEENDKVLIA 64 (87)
Q Consensus 28 RK~~rV~Likngk~v~A~IPg~G~ln-~lqeh~~VLV~ 64 (87)
|=.|.|++ -+|..++|++|+-|.+. .+.+...|+++
T Consensus 18 RF~~~V~~-~~g~~~~aH~pntGRl~ell~pG~~v~l~ 54 (234)
T PRK00347 18 RFLADVEL-DDGEELTAHCPNTGRMTGLLTPGNTVWLS 54 (234)
T ss_pred CEEEEEEE-CCCCEEEEEcCCCCCChhhccCCCEEEEE
Confidence 88899998 56999999999999764 57788889987
No 28
>PF06246 Isy1: Isy1-like splicing family; InterPro: IPR009360 Isy1 protein is important in the optimisation of splicing [].; PDB: 1X4T_A.
Probab=64.04 E-value=2.2 Score=33.34 Aligned_cols=16 Identities=31% Similarity=0.399 Sum_probs=0.0
Q ss_pred eecCCCCCCCCCCCCceecc
Q 042342 64 AGFGRKGHAVATSPPIISLK 83 (87)
Q Consensus 64 ~GfGr~g~~v~DlPGV~y~~ 83 (87)
+=||| .+|||||+-|-
T Consensus 124 rYFGr----AkeLPgVkeL~ 139 (255)
T PF06246_consen 124 RYFGR----AKELPGVKELF 139 (255)
T ss_dssp --------------------
T ss_pred eEeeh----hccCccHHHHH
Confidence 66999 99999999773
No 29
>PRK04012 translation initiation factor IF-1A; Provisional
Probab=58.52 E-value=12 Score=25.52 Aligned_cols=34 Identities=26% Similarity=0.343 Sum_probs=26.7
Q ss_pred EEEEEEecCCcEEEEEeCCCCc-ccccccCCeEEEe
Q 042342 30 CSRVQLIKNGKKIVTFVPSDGC-LNYIEENDKVLIA 64 (87)
Q Consensus 30 ~~rV~Likngk~v~A~IPg~G~-ln~lqeh~~VLV~ 64 (87)
-.+|+| .||+.+.|+|||-=. --.+.+.|.|+|+
T Consensus 35 ~~~V~~-~dG~~~la~i~GK~Rk~IwI~~GD~VlVe 69 (100)
T PRK04012 35 RVRVRC-MDGVERMGRIPGKMKKRMWIREGDVVIVA 69 (100)
T ss_pred EEEEEe-CCCCEEEEEEchhhcccEEecCCCEEEEE
Confidence 467888 899999999997431 1257889999996
No 30
>KOG3068 consensus mRNA splicing factor [RNA processing and modification]
Probab=52.49 E-value=3.7 Score=32.92 Aligned_cols=15 Identities=27% Similarity=0.377 Sum_probs=12.8
Q ss_pred eecCCCCCCCCCCCCceec
Q 042342 64 AGFGRKGHAVATSPPIISL 82 (87)
Q Consensus 64 ~GfGr~g~~v~DlPGV~y~ 82 (87)
+-||+ .+||||||-|
T Consensus 122 rYFGa----AkdLPgVrEl 136 (268)
T KOG3068|consen 122 RYFGA----AKDLPGVREL 136 (268)
T ss_pred hhhhh----hccCccHHHH
Confidence 55888 9999999976
No 31
>PLN00051 RNA-binding S4 domain-containing protein; Provisional
Probab=51.25 E-value=9.7 Score=29.73 Aligned_cols=15 Identities=33% Similarity=0.567 Sum_probs=14.1
Q ss_pred ccccCCeEEEeecCC
Q 042342 54 YIEENDKVLIAGFGR 68 (87)
Q Consensus 54 ~lqeh~~VLV~GfGr 68 (87)
.+.+.|.+.|||+||
T Consensus 231 ~v~~gD~isiRG~GR 245 (267)
T PLN00051 231 TLKTGDVVSVSGKGR 245 (267)
T ss_pred CCCCCCEEEEeeCCE
Confidence 789999999999997
No 32
>PF14890 Intein_splicing: Intein splicing domain; PDB: 1MI8_A 2CW7_A 2CW8_A.
Probab=51.14 E-value=35 Score=25.97 Aligned_cols=39 Identities=15% Similarity=0.366 Sum_probs=27.5
Q ss_pred cccccEEEEEEecCCcEEEE------EeCCCC-cccccccCCeEEEe
Q 042342 25 FAIRKCSRVQLIKNGKKIVT------FVPSDG-CLNYIEENDKVLIA 64 (87)
Q Consensus 25 SA~RK~~rV~Likngk~v~A------~IPg~G-~ln~lqeh~~VLV~ 64 (87)
++..++.||++ ++|++|+| |++.++ -+..|++.|.|.+.
T Consensus 47 ~g~k~v~ri~t-~~GreI~~T~~H~~lt~~~wk~~~~Lk~GD~I~v~ 92 (323)
T PF14890_consen 47 NGEKPVYRIRT-RSGREIKATPDHPFLTPDGWKRLEELKPGDRIAVP 92 (323)
T ss_dssp EEEEEEEEEEE-TTS-EEEEETT-EEEECCCCCECCC--TT-EEEEE
T ss_pred cCCceEEEEEe-CCCCEEEEcCCCcEEEccCCEEhHHhhcccccccc
Confidence 56778999999 99999985 577766 45568888998876
No 33
>COG1489 SfsA DNA-binding protein, stimulates sugar fermentation [General function prediction only]
Probab=49.74 E-value=42 Score=26.40 Aligned_cols=37 Identities=19% Similarity=0.438 Sum_probs=30.3
Q ss_pred cccEEEEEEecCCcEEEEEeCCCCccc-ccccCCeEEEee
Q 042342 27 IRKCSRVQLIKNGKKIVTFVPSDGCLN-YIEENDKVLIAG 65 (87)
Q Consensus 27 ~RK~~rV~Likngk~v~A~IPg~G~ln-~lqeh~~VLV~G 65 (87)
+|=.+.|.| +|.+++|++|+-|.+. -+.+.+.|.++-
T Consensus 17 nRFl~dv~l--~G~~~~~H~~ntGrm~~l~~pG~~v~l~~ 54 (235)
T COG1489 17 NRFLADVEL--DGEEVTAHCPNTGRMTELLTPGNTVWLSR 54 (235)
T ss_pred cceEEEEEE--CCeEEEEEcCCCCccccccCCCCEEEEEE
Confidence 356788887 4999999999999877 667888888874
No 34
>PF02210 Laminin_G_2: Laminin G domain; InterPro: IPR012680 Laminins are large heterotrimeric glycoproteins involved in basement membrane function []. The laminin globular (G) domain can be found in one to several copies in various laminin family members, including a large number of extracellular proteins. The C terminus of the laminin alpha chain contains a tandem repeat of five laminin G domains, which are critical for heparin-binding and cell attachment activity []. Laminin alpha4 is distributed in a variety of tissues including peripheral nerves, dorsal root ganglion, skeletal muscle and capillaries; in the neuromuscular junction, it is required for synaptic specialisation []. The structure of the laminin-G domain has been predicted to resemble that of pentraxin []. Laminin G domains can vary in their function, and a variety of binding functions have been ascribed to different LamG modules. For example, the laminin alpha1 and alpha2 chains each have five C-teminal laminin G domains, where only domains LG4 and LG5 contain binding sites for heparin, sulphatides and the cell surface receptor dystroglycan []. Laminin G-containing proteins appear to have a wide variety of roles in cell adhesion, signalling, migration, assembly and differentiation. This entry represents one subtype of laminin G domains, which is sometimes found in association with thrombospondin-type laminin G domains (IPR012679 from INTERPRO).; PDB: 3POY_A 3QCW_B 3R05_B 3ASI_A 3MW4_B 3MW3_A 1QU0_D 1DYK_A 1OKQ_A 3SH4_A ....
Probab=48.85 E-value=52 Score=20.18 Aligned_cols=9 Identities=33% Similarity=0.844 Sum_probs=6.5
Q ss_pred ceecccccC
Q 042342 79 IISLKGCMR 87 (87)
Q Consensus 79 V~y~~~~~~ 87 (87)
.....|||+
T Consensus 113 ~~~f~Gci~ 121 (128)
T PF02210_consen 113 TPGFVGCIR 121 (128)
T ss_dssp TSB-EEEEE
T ss_pred CCCcEEEcC
Confidence 678899985
No 35
>cd01732 LSm5 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm4 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=45.43 E-value=43 Score=21.43 Aligned_cols=31 Identities=19% Similarity=0.257 Sum_probs=21.2
Q ss_pred CcccccEEEEEEecCCcEEEEEeCC-CCccccc
Q 042342 24 NFAIRKCSRVQLIKNGKKIVTFVPS-DGCLNYI 55 (87)
Q Consensus 24 NSA~RK~~rV~Likngk~v~A~IPg-~G~ln~l 55 (87)
+.++.|-+.|.| ++|+++...+=| |.|.|-+
T Consensus 9 ~~~~~~~V~V~l-~~gr~~~G~L~g~D~~mNlv 40 (76)
T cd01732 9 DKCIGSRIWIVM-KSDKEFVGTLLGFDDYVNMV 40 (76)
T ss_pred HHhCCCEEEEEE-CCCeEEEEEEEEeccceEEE
Confidence 456678889999 899888766433 4455543
No 36
>TIGR03069 PS_II_S4 photosystem II S4 domain protein. Members of this protein family are about 265 residues long and each contains an S4 RNA-binding domain of about 48 residues. The member from the Cyanobacterium, Synechocystis sp. PCC 6803, was detected as a novel polypeptide in a highly purified preparation of active photosystem II (Kashino, et al., 2002). The phylogenetic distribution, including Cyanobacteria and Arabidopsis, supports a role in photosystem II, although the high bit score cutoffs for this model reflect similar sequences in non-photosynthetic organisms such as Carboxydothermus hydrogenoformans, a Gram-positive bacterium.
Probab=45.31 E-value=25 Score=27.08 Aligned_cols=15 Identities=27% Similarity=0.539 Sum_probs=13.7
Q ss_pred ccccCCeEEEeecCC
Q 042342 54 YIEENDKVLIAGFGR 68 (87)
Q Consensus 54 ~lqeh~~VLV~GfGr 68 (87)
.+++.|.|.|+|+||
T Consensus 223 ~v~~gD~IsvrG~Gr 237 (257)
T TIGR03069 223 ELKVGDRLQLRGKGR 237 (257)
T ss_pred cCCCCCEEEEcCCce
Confidence 678899999999997
No 37
>COG2302 Uncharacterized conserved protein, contains S4-like domain [Function unknown]
Probab=45.11 E-value=13 Score=29.69 Aligned_cols=15 Identities=47% Similarity=0.844 Sum_probs=14.3
Q ss_pred ccccCCeEEEeecCC
Q 042342 54 YIEENDKVLIAGFGR 68 (87)
Q Consensus 54 ~lqeh~~VLV~GfGr 68 (87)
.+++.|.+.||||||
T Consensus 220 ~v~~GDliSirG~GR 234 (257)
T COG2302 220 EVQEGDLISIRGFGR 234 (257)
T ss_pred eeccCCEEEEecccc
Confidence 789999999999998
No 38
>PRK00284 pqqA coenzyme PQQ synthesis protein PqqA; Provisional
Probab=44.63 E-value=32 Score=18.73 Aligned_cols=17 Identities=6% Similarity=0.423 Sum_probs=12.6
Q ss_pred EEEEEecCCcEEEEEeCCCC
Q 042342 31 SRVQLIKNGKKIVTFVPSDG 50 (87)
Q Consensus 31 ~rV~Likngk~v~A~IPg~G 50 (87)
.-+++ |.+|+.|+|.+.
T Consensus 8 ~e~~~---G~EItmY~~~r~ 24 (26)
T PRK00284 8 TELRV---GMEVTMYFSARX 24 (26)
T ss_pred EEeec---ceEEEEEEeccc
Confidence 34454 999999999753
No 39
>cd01724 Sm_D1 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit D1 heterodimerizes with subunit D2 and three such heterodimers form a hexameric ring structure with alternating D1 and D2 subunits. The D1 - D2 heterodimer also assembles into a heptameric ring containing DB, D3, E, F, and G subunits. Sm-like proteins exist in archaea as well as prokaryotes which form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=44.09 E-value=60 Score=21.37 Aligned_cols=21 Identities=19% Similarity=0.172 Sum_probs=15.8
Q ss_pred CcccccEEEEEEecCCcEEEEE
Q 042342 24 NFAIRKCSRVQLIKNGKKIVTF 45 (87)
Q Consensus 24 NSA~RK~~rV~Likngk~v~A~ 45 (87)
++..-+-+.|.| |||..+...
T Consensus 7 ~~l~g~~V~VeL-Kng~~~~G~ 27 (90)
T cd01724 7 MKLTNETVTIEL-KNGTIVHGT 27 (90)
T ss_pred HhCCCCEEEEEE-CCCCEEEEE
Confidence 356778899999 999776643
No 40
>PF00386 C1q: C1q domain; InterPro: IPR001073 This entry represents the C-terminal domain of C1q. C1q is a subunit of the C1 enzyme complex that activates the serum complement system. C1q comprises 6 A, 6 B and 6 C chains. These share the same topology, each possessing a small, globular N-terminal domain, a collagen-like Gly/Pro-rich central region, and a conserved C-terminal region, the C1q domain []. The C1q protein is produced in collagen-producing cells and shows sequence and structural similarity to collagens VIII and X [, ]. This domain is also found in multimerin and EMILIN proteins.; PDB: 1O91_C 2JG8_D 2JG9_A 2WNV_A 2WNU_A 1PK6_A 4DOU_A 1C3H_C 1C28_C 2OII_A ....
Probab=43.66 E-value=50 Score=21.57 Aligned_cols=41 Identities=17% Similarity=0.235 Sum_probs=26.4
Q ss_pred cccccEEEEEEecCCcEEEEEe-CCCCc---------ccccccCCeEEEee
Q 042342 25 FAIRKCSRVQLIKNGKKIVTFV-PSDGC---------LNYIEENDKVLIAG 65 (87)
Q Consensus 25 SA~RK~~rV~Likngk~v~A~I-Pg~G~---------ln~lqeh~~VLV~G 65 (87)
+...+-+.++|.+|+..+.... ...+. +-.|++.|+|-|+=
T Consensus 55 ~~~~~~~~~~L~~N~~~~~~~~~~~~~~~~~~~s~s~vl~L~~GD~V~v~~ 105 (127)
T PF00386_consen 55 TSSGSSVWVELMKNGNPVASTYASNSSGNYDSASNSAVLQLNKGDTVWVRL 105 (127)
T ss_dssp SEEEEEEEEEEEETTEEEEEEEECSBTTBEEEEEEEEEEEE-TT-EEEEEE
T ss_pred ccCCchhHHhhhhhccceeeEeecCCCCccceEEEEEEEEeCCCCEEEEEE
Confidence 5566778889999998876653 22222 22488999998875
No 41
>cd05792 S1_eIF1AD_like S1_eIF1AD_like: eukaryotic translation initiation factor 1A domain containing protein (eIF1AD)-like, S1-like RNA-binding domain. eIF1AD is also known as MGC11102 protein. Little is known about the function of eIF1AD. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins, including translation initiation factor IF1A (also referred to as eIF1A in eukaryotes). eIF1A 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.
Probab=40.40 E-value=59 Score=21.32 Aligned_cols=32 Identities=25% Similarity=0.478 Sum_probs=25.9
Q ss_pred EEEEEecCCcEEEEEeCCC---CcccccccCCeEEEee
Q 042342 31 SRVQLIKNGKKIVTFVPSD---GCLNYIEENDKVLIAG 65 (87)
Q Consensus 31 ~rV~Likngk~v~A~IPg~---G~ln~lqeh~~VLV~G 65 (87)
..|++ -+|.+..|.||+- -- -+.+.|.|||.=
T Consensus 15 ~~V~~-~dG~~~l~~iP~KfRk~i--WIkrGd~VlV~p 49 (78)
T cd05792 15 HEVET-PNGSRYLVSMPTKFRKNI--WIKRGDFVLVEP 49 (78)
T ss_pred EEEEc-CCCCEEEEEechhhcccE--EEEeCCEEEEEe
Confidence 45676 6899999999993 33 689999999975
No 42
>PLN02856 fumarylacetoacetase
Probab=39.82 E-value=52 Score=27.71 Aligned_cols=34 Identities=21% Similarity=0.468 Sum_probs=24.5
Q ss_pred EEEEecCCcEEEEEeCCCCcccccccCCeEEEeec
Q 042342 32 RVQLIKNGKKIVTFVPSDGCLNYIEENDKVLIAGF 66 (87)
Q Consensus 32 rV~Likngk~v~A~IPg~G~ln~lqeh~~VLV~Gf 66 (87)
-+.|.-+|++-++.-.|+ .-.||+..|+|.++|+
T Consensus 369 llElt~~G~~p~~l~~g~-~r~fL~dGD~V~l~g~ 402 (424)
T PLN02856 369 LLELTWAGSREVSLEGGT-RRKFLEDGDEVVLSGW 402 (424)
T ss_pred EEEEEeCCccceEeccCC-ccccCCCCCEEEEEEE
Confidence 344545777777754444 3459999999999997
No 43
>KOG2820 consensus FAD-dependent oxidoreductase [General function prediction only]
Probab=39.62 E-value=12 Score=31.62 Aligned_cols=37 Identities=24% Similarity=0.408 Sum_probs=28.4
Q ss_pred cEEEEEeCCCCcccccccCCeEEEeecCCCCCCCCCCCCc-eeccccc
Q 042342 40 KKIVTFVPSDGCLNYIEENDKVLIAGFGRKGHAVATSPPI-ISLKGCM 86 (87)
Q Consensus 40 k~v~A~IPg~G~ln~lqeh~~VLV~GfGr~g~~v~DlPGV-~y~~~~~ 86 (87)
.-|+-|+|..- -|+|-| |-+||..+=.|+| |||-+||
T Consensus 338 ~FviD~~P~~~---------Nv~Vg~-G~SGHGFK~aP~iGk~lae~~ 375 (399)
T KOG2820|consen 338 NFVIDKHPQYD---------NVFVGG-GGSGHGFKFAPNIGKYLAEMA 375 (399)
T ss_pred CeeeecCCCcc---------cEEEec-CCCCcceeecchHHHHHHHHh
Confidence 44566666543 488888 9999999999998 6777775
No 44
>TIGR01266 fum_ac_acetase fumarylacetoacetase. This enzyme catalyzes the final step in the breakdown of tyrosine or phenylalanine to fumarate and acetoacetate.
Probab=38.84 E-value=61 Score=27.19 Aligned_cols=34 Identities=24% Similarity=0.463 Sum_probs=25.6
Q ss_pred EEEEecCCcEEEEEeCCCCcccccccCCeEEEeec
Q 042342 32 RVQLIKNGKKIVTFVPSDGCLNYIEENDKVLIAGF 66 (87)
Q Consensus 32 rV~Likngk~v~A~IPg~G~ln~lqeh~~VLV~Gf 66 (87)
-+.+..+|++.++.--|+-. .||+..|+|.++|+
T Consensus 361 ~lE~t~~g~~~v~l~~g~~r-~fL~dGD~V~~~~~ 394 (415)
T TIGR01266 361 MLELSWKGKKPIDVGQGETR-TFLEDGDEVILRGH 394 (415)
T ss_pred EEEEEeCCeeeeecCCCCCC-CCCCCCCEEEEEEE
Confidence 34454577777776666654 79999999999997
No 45
>PF02080 TrkA_C: TrkA-C domain; InterPro: IPR006037 The regulator of K+ conductance (RCK) domain is found in many ligand-gated K+ channels, most often attached to the intracellular carboxy terminus. The domain is prevalent among prokaryotic K+ channels, and also found in eukaryotic, high-conductance Ca2+-activated K+ channels (BK channels) [, , ]. Largely involved in redox-linked regulation of potassium channels, the N-terminal part of the RCK domain is predicted to be an active dehydrogenase at least in some cases []. Some have a conserved sequence motif (G-x-G-x-x-G-x(n)-[DE]) for NAD+ binding [], but others do not, reflecting the diversity of ligands for RCK domains. The C-terminal part is less conserved, being absent in some channels, such as the kefC antiporter from Escherichia coli. It is predicted to bind unidentified ligands and to regulate sulphate, sodium and other transporters. The X-ray structure of several RCK domains has been solved [, , ]. It reveals an alpha-beta fold similar to dehydrogenase enzymes. The domain forms a homodimer, producing a cleft between two lobes. It has a composite structure, with an N-terminal (RCK-N), and a C-terminal (RCK-C) subdomain. The RCK-N subdomain forms a Rossmann fold with two alpha helices on one side of a six stranded parallel beta sheet and three alpha helices on the other side. The RCK-C subdomain is an all-beta-strand fold. It forms an extention of the dimer interface and further stabilises the RCK homodimer [, , ]. Ca2+ is a ligand that opens the channel in a concentration-dependent manner. Two Ca2+ ions are located at the base of a cleft between two RCK domains, coordinated by the carboxylate groups of two glutamate residues, and by an aspartate residue [, , ]. RCK domains occur in at least five different contexts: As a single domain on the C terminus of some K+ channels (for example, many prokaryotic K+ channels). As two tandem RCK domains on the C terminus of some transporters that form gating rings (for example, eukaryotic BK channels). The gating ring has an arrangement of eight identical RCK domains, one from each of the four pore-forming subunits and four from the intracellular solution. As two domains, one at the N terminus and another at the C terminus of transporter (for example, the prokaryotic trk system potassium uptake protein A). As a soluble protein (not part of a K+ channel) consisting of two tandem RCK domains. As a soluble protein consisting of a single RCK domain. This entry represents the C-terminal subdomain of RCK.; GO: 0008324 cation transmembrane transporter activity, 0006813 potassium ion transport; PDB: 2BKP_A 1VCT_A 2BKO_A 2BKN_A 3L4B_C 2FY8_D 2AEF_A 1LNQ_E 3RBX_C 3KXD_A ....
Probab=38.35 E-value=31 Score=19.99 Aligned_cols=21 Identities=14% Similarity=0.480 Sum_probs=14.5
Q ss_pred EEEeCCCCcccccccCCeEEEee
Q 042342 43 VTFVPSDGCLNYIEENDKVLIAG 65 (87)
Q Consensus 43 ~A~IPg~G~ln~lqeh~~VLV~G 65 (87)
..++|.... .|+++|.++|.|
T Consensus 38 ~~~~p~~~~--~l~~gD~l~v~g 58 (71)
T PF02080_consen 38 EIIIPDGDT--VLQAGDILIVVG 58 (71)
T ss_dssp EEES--TT---BE-TTEEEEEEE
T ss_pred EEECCCCCC--EECCCCEEEEEE
Confidence 457788878 999999999987
No 46
>COG1768 Predicted phosphohydrolase [General function prediction only]
Probab=36.89 E-value=22 Score=27.95 Aligned_cols=10 Identities=10% Similarity=0.192 Sum_probs=9.1
Q ss_pred CCCCCCceec
Q 042342 73 VATSPPIISL 82 (87)
Q Consensus 73 v~DlPGV~y~ 82 (87)
.+||||.+|+
T Consensus 69 i~~LPG~K~m 78 (230)
T COG1768 69 IGDLPGTKYM 78 (230)
T ss_pred hhcCCCcEEE
Confidence 6899999997
No 47
>PF07593 UnbV_ASPIC: ASPIC and UnbV; InterPro: IPR011519 This conserved sequence is found associated with IPR001440 from INTERPRO in several paralogous proteins in Rhodopirellula baltica. It is also found associated with IPR000413 from INTERPRO in several eukaryotic integrin-like proteins (e.g. human ASPIC Q9NQ78 from SWISSPROT) and in several other bacterial proteins (e.g. Q84HN1 from SWISSPROT) [].
Probab=34.42 E-value=96 Score=18.96 Aligned_cols=36 Identities=28% Similarity=0.500 Sum_probs=23.2
Q ss_pred EEEEEecCCcEEEEEeCCCCcccccccCCeEEEeecCC
Q 042342 31 SRVQLIKNGKKIVTFVPSDGCLNYIEENDKVLIAGFGR 68 (87)
Q Consensus 31 ~rV~Likngk~v~A~IPg~G~ln~lqeh~~VLV~GfGr 68 (87)
|+|++..++...+..+-+.+. ++..++-.+-=|+|.
T Consensus 5 A~V~v~~~~~~q~~~v~~g~g--y~s~~~~~lhFGLG~ 40 (71)
T PF07593_consen 5 ARVTVTADGRTQTREVTSGGG--YLSQSEPRLHFGLGD 40 (71)
T ss_pred eEEEEEECCeEEEEEEeCCCC--EeecCCCCEEEECCC
Confidence 688887787776766554444 455556666657664
No 48
>PF04435 SPK: Domain of unknown function (DUF545) ; InterPro: IPR006570 SPK is a domain of unknown function found in SET and PHD domain containing proteins and protein kinases.
Probab=29.90 E-value=43 Score=21.41 Aligned_cols=26 Identities=31% Similarity=0.612 Sum_probs=21.6
Q ss_pred ccccEEEEEEecCCcEEEEEeCCCCcc
Q 042342 26 AIRKCSRVQLIKNGKKIVTFVPSDGCL 52 (87)
Q Consensus 26 A~RK~~rV~Likngk~v~A~IPg~G~l 52 (87)
.+|+.+.|+| -....|+.|...||.+
T Consensus 82 ~L~~~a~v~l-D~~~rI~~Y~s~dg~l 107 (109)
T PF04435_consen 82 ELRKHADVEL-DEKGRIIKYKSKDGSL 107 (109)
T ss_pred HHHhCcEEEE-cCCCCEEEEEeCCCEE
Confidence 3678899999 6667899999999974
No 49
>TIGR02107 PQQ_syn_pqqA coenzyme PQQ biosynthesis protein A. This model describes a very small protein, coenzyme PQQ biosynthesis protein A, which is smaller than 25 amino acids in many species. It is proposed to serve as a peptide precursor of coenzyme pyrrolo-quinoline-quinone (PQQ), with Glu and Tyr of a conserved motif Glu-Xxx-Xxx-Xxx-Tyr becoming part of the product.
Probab=28.50 E-value=72 Score=17.39 Aligned_cols=12 Identities=17% Similarity=0.517 Sum_probs=10.0
Q ss_pred CcEEEEEeCCCC
Q 042342 39 GKKIVTFVPSDG 50 (87)
Q Consensus 39 gk~v~A~IPg~G 50 (87)
|.+|++|++...
T Consensus 12 G~EVTmY~~~~~ 23 (26)
T TIGR02107 12 GMEVTMYVSAXX 23 (26)
T ss_pred cEEEEEEeeccc
Confidence 999999998543
No 50
>PF12869 tRNA_anti-like: tRNA_anti-like; InterPro: IPR024422 The function of the proteins in this entry is not known, but they contain a novel variant of the nucleic acid-binding OB fold [].; PDB: 3F1Z_I.
Probab=28.14 E-value=25 Score=23.43 Aligned_cols=41 Identities=17% Similarity=0.374 Sum_probs=22.0
Q ss_pred EEEEEeCCCC----cccccccCCeEEEeecCCCCCCCCCCCCceecccc
Q 042342 41 KIVTFVPSDG----CLNYIEENDKVLIAGFGRKGHAVATSPPIISLKGC 85 (87)
Q Consensus 41 ~v~A~IPg~G----~ln~lqeh~~VLV~GfGr~g~~v~DlPGV~y~~~~ 85 (87)
.|.+++..+- ..+.|++.|.|.|.|-.. .+. +-|+-.|+.|
T Consensus 99 ~v~~~~~~~~~~~~~~~~l~~G~~Vti~G~~~---g~~-~~~~v~l~~c 143 (144)
T PF12869_consen 99 GVQCYFSNDQEKRASVAKLKKGQKVTIKGICT---GYS-LMGVVMLDDC 143 (144)
T ss_dssp S--EEEEEEGGGHHHHHH--TTSEEEEEEE---------SSS-EEEE--
T ss_pred eEEEEEccchhhhhhHhcCCCCCEEEEEEEEE---eee-cCCcEEeecc
Confidence 3677877666 344599999999999532 133 5688888877
No 51
>PRK00276 infA translation initiation factor IF-1; Validated
Probab=27.76 E-value=1.6e+02 Score=18.30 Aligned_cols=33 Identities=30% Similarity=0.431 Sum_probs=24.4
Q ss_pred EEEEEecCCcEEEEEeCCCCccc--ccccCCeEEEe
Q 042342 31 SRVQLIKNGKKIVTFVPSDGCLN--YIEENDKVLIA 64 (87)
Q Consensus 31 ~rV~Likngk~v~A~IPg~G~ln--~lqeh~~VLV~ 64 (87)
..|++ .||..+.|+++|-=-.+ .+-..|.|+++
T Consensus 22 y~V~~-~~g~~~~c~~~Gklr~~~i~i~vGD~V~ve 56 (72)
T PRK00276 22 FRVEL-ENGHEVLAHISGKMRKNYIRILPGDKVTVE 56 (72)
T ss_pred EEEEe-CCCCEEEEEEccceeeCCcccCCCCEEEEE
Confidence 45666 68899999999853321 36789999998
No 52
>COG4776 Rnb Exoribonuclease II [Transcription]
Probab=27.17 E-value=58 Score=28.95 Aligned_cols=50 Identities=30% Similarity=0.344 Sum_probs=34.3
Q ss_pred cccEEEEEEecCCcEEEEEeCCCC------cccccccCCeEEEeecCCCCCCCCCCCCce
Q 042342 27 IRKCSRVQLIKNGKKIVTFVPSDG------CLNYIEENDKVLIAGFGRKGHAVATSPPII 80 (87)
Q Consensus 27 ~RK~~rV~Likngk~v~A~IPg~G------~ln~lqeh~~VLV~GfGr~g~~v~DlPGV~ 80 (87)
.|--.||||+-||- .||||+-= .|+.-||+-.|.|.|-= --.++|+--|.
T Consensus 573 ~R~G~RvrLleNGA--~~FIPa~lih~~reei~~n~e~gtv~I~ge~--~Yk~~D~i~V~ 628 (645)
T COG4776 573 SRGGMRVRLLENGA--IAFIPAPLIHANREELVCNQENGTVQIKGET--VYKVGDVIDVT 628 (645)
T ss_pred ccCceEEEeccCCc--ceecchhhhccchhheEecCCCceEEEccEE--EEeeccEEEEE
Confidence 36668999999997 48999842 35566889999998721 11255655444
No 53
>TIGR00176 mobB molybdopterin-guanine dinucleotide biosynthesis protein MobB. This molybdenum cofactor biosynthesis enzyme is similar to the urease accessory protein UreG and to the hydrogenase accessory protein HypB, both GTP hydrolases involved in loading nickel into the metallocenters of their respective target enzymes.
Probab=26.92 E-value=38 Score=23.66 Aligned_cols=16 Identities=25% Similarity=0.571 Sum_probs=12.3
Q ss_pred cccccCCeEEEeecCC
Q 042342 53 NYIEENDKVLIAGFGR 68 (87)
Q Consensus 53 n~lqeh~~VLV~GfGr 68 (87)
+.+...|.|||+||+.
T Consensus 85 ~~~~~~D~vlVEG~k~ 100 (155)
T TIGR00176 85 DRLPDLDIILVEGFKD 100 (155)
T ss_pred hhCCCCCEEEECCCCC
Confidence 3445689999999765
No 54
>cd03116 MobB Molybdenum is an essential trace element in the form of molybdenum cofactor (Moco) which is associated with the metabolism of nitrogen, carbon and sulfur by redox active enzymes. In E. coli, the synthesis of Moco involves genes from several loci: moa, mob, mod, moe and mog. The mob locus contains mobA and mobB genes. MobB catalyzes the attachment of the guanine dinucleotide to molybdopterin.
Probab=26.33 E-value=49 Score=23.40 Aligned_cols=16 Identities=31% Similarity=0.453 Sum_probs=12.6
Q ss_pred cccccCCeEEEeecCC
Q 042342 53 NYIEENDKVLIAGFGR 68 (87)
Q Consensus 53 n~lqeh~~VLV~GfGr 68 (87)
..+.+.|.|||+||..
T Consensus 88 ~~~~~~D~vlvEG~k~ 103 (159)
T cd03116 88 LRLLDVDLVLVEGFKE 103 (159)
T ss_pred hhCCCCCEEEEccCCC
Confidence 3556789999999765
No 55
>PF14020 DUF4236: Protein of unknown function (DUF4236)
Probab=26.17 E-value=76 Score=19.61 Aligned_cols=25 Identities=24% Similarity=0.395 Sum_probs=18.4
Q ss_pred ccccEEEEEEecCCcEEEEEeCCCC
Q 042342 26 AIRKCSRVQLIKNGKKIVTFVPSDG 50 (87)
Q Consensus 26 A~RK~~rV~Likngk~v~A~IPg~G 50 (87)
.=.+.+++..-++|..+++.|||-|
T Consensus 26 ~G~~g~~~t~~~~G~~~t~~iPGtG 50 (55)
T PF14020_consen 26 VGPKGARITVGKRGRRTTVGIPGTG 50 (55)
T ss_pred eCCCCcceEeCCCCcEEEEEcCCCc
Confidence 3445667776677888888999887
No 56
>PF11975 Glyco_hydro_4C: Family 4 glycosyl hydrolase C-terminal domain; InterPro: IPR022616 This domain is found primarily in bacterial family 4 glycosyl hydrolases. It is found in the C terminus. ; GO: 0004553 hydrolase activity, hydrolyzing O-glycosyl compounds; PDB: 1UP4_A 1UP6_C 1UP7_E 1VJT_A 1U8X_X 1S6Y_A 3FEF_D 1OBB_A.
Probab=25.60 E-value=91 Score=22.80 Aligned_cols=29 Identities=17% Similarity=0.360 Sum_probs=20.2
Q ss_pred cCCcEEEEE-eCCCCcccccccCCeEEEee
Q 042342 37 KNGKKIVTF-VPSDGCLNYIEENDKVLIAG 65 (87)
Q Consensus 37 kngk~v~A~-IPg~G~ln~lqeh~~VLV~G 65 (87)
.|...+... +|++|+|.+|...+.|-|-.
T Consensus 148 ~~~~~~~~vNv~N~G~I~nLp~davVEvp~ 177 (232)
T PF11975_consen 148 NDKPKRFVVNVPNNGAIPNLPDDAVVEVPC 177 (232)
T ss_dssp HSSEEEEEEEEE-TTSSTTS-TTSEEEEEE
T ss_pred cCCCeEEEEECCCCCccCCCCCCcEEEEEE
Confidence 344444555 99999999999999997654
No 57
>PRK10664 transcriptional regulator HU subunit beta; Provisional
Probab=25.38 E-value=33 Score=22.31 Aligned_cols=15 Identities=40% Similarity=0.809 Sum_probs=12.8
Q ss_pred ccccCCeEEEeecCC
Q 042342 54 YIEENDKVLIAGFGR 68 (87)
Q Consensus 54 ~lqeh~~VLV~GfGr 68 (87)
.|.+++.|.++|||.
T Consensus 35 ~L~~~~~v~l~gfG~ 49 (90)
T PRK10664 35 SLKEGDDVALVGFGT 49 (90)
T ss_pred HHhCCCEEEECCcEE
Confidence 578899999999993
No 58
>smart00110 C1Q Complement component C1q domain. Globular domain found in many collagens and eponymously in complement C1q. When part of full length proteins these domains form a 'bouquet' due to the multimerization of heterotrimers. The C1q fold is similar to that of tumour necrosis factor.
Probab=24.89 E-value=1.9e+02 Score=19.97 Aligned_cols=36 Identities=25% Similarity=0.386 Sum_probs=24.0
Q ss_pred EEEEEEecCCcEEEEE-eCCC---------CcccccccCCeEEEee
Q 042342 30 CSRVQLIKNGKKIVTF-VPSD---------GCLNYIEENDKVLIAG 65 (87)
Q Consensus 30 ~~rV~Likngk~v~A~-IPg~---------G~ln~lqeh~~VLV~G 65 (87)
-+.|.|.+|++.+..+ -... +-+-.|++.|+|-|+=
T Consensus 65 ~~~v~L~~N~~~~~~~~~~~~~~~~~~~S~s~vL~L~~GD~Vwl~l 110 (135)
T smart00110 65 NVKVSLMKNGIQVMSTYDEYQKGLYDVASGGALLQLRQGDQVWLEL 110 (135)
T ss_pred EEEEEEEECCceeEEEEhhcCCCCceeecCcEEEEECCCCEEEEEE
Confidence 4678999999887643 2111 2233578999999884
No 59
>PF06565 DUF1126: Repeat of unknown function (DUF1126); InterPro: IPR010554 This group contains several eukaryote specific repeats of around 35 residues in length. The function of this family is unknown.; PDB: 2Z14_A 2Z13_A.
Probab=24.86 E-value=37 Score=18.88 Aligned_cols=12 Identities=17% Similarity=-0.144 Sum_probs=1.7
Q ss_pred eeeeecCCCccc
Q 042342 16 IGIEAKQPNFAI 27 (87)
Q Consensus 16 ~~~~pKkPNSA~ 27 (87)
-..||.++||++
T Consensus 12 ~I~E~~~~NSG~ 23 (33)
T PF06565_consen 12 SIFEPPVRNSGR 23 (33)
T ss_dssp EEE---------
T ss_pred EEEEeccCCCCC
Confidence 457899999987
No 60
>cd03109 DTBS Dethiobiotin synthetase (DTBS) is the penultimate enzyme in the biotin biosynthesis pathway in Escherichia coli and other microorganisms. The enzyme catalyzes formation of the ureido ring of dethiobiotin from (7R,8S)-7,8-diaminononanoic acid (DAPA) and carbon dioxide. The enzyme utilizes carbon dioxide instead of hydrogen carbonate as substrate and is dependent on ATP and divalent metal ions as cofactors.
Probab=23.85 E-value=1.2e+02 Score=20.29 Aligned_cols=25 Identities=28% Similarity=0.529 Sum_probs=19.0
Q ss_pred cCCcEEEEEeCCCCcccccccCCeEEEeecCC
Q 042342 37 KNGKKIVTFVPSDGCLNYIEENDKVLIAGFGR 68 (87)
Q Consensus 37 kngk~v~A~IPg~G~ln~lqeh~~VLV~GfGr 68 (87)
+.|.+|-.|=|... +|.|+|+|-|.
T Consensus 25 ~~~~~v~~~kp~~~-------~d~vliEGaGg 49 (134)
T cd03109 25 EKGYRVAPLKPVQT-------YDFVLVEGAGG 49 (134)
T ss_pred HCCCeEEEEecCCC-------CCEEEEECCCc
Confidence 35777878877665 79999999654
No 61
>cd01731 archaeal_Sm1 The archaeal sm1 proteins: The Sm proteins are conserved in all three domains of life and are always associated with U-rich RNA sequences. They function to mediate RNA-RNA interactions and RNA biogenesis. All Sm proteins contain a common sequence motif in two segments, Sm1 and Sm2, separated by a short variable linker. Eukaryotic Sm proteins form part of specific small nuclear ribonucleoproteins (snRNPs) that are involved in the processing of pre-mRNAs to mature mRNAs, and are a major component of the eukaryotic spliceosome. Most snRNPs consist of seven Sm proteins (B/B', D1, D2, D3, E, F and G) arranged in a ring on a uridine-rich sequence (Sm site), plus a small nuclear RNA (snRNA) (either U1, U2, U5 or U4/6). Since archaebacteria do not have any splicing apparatus, Sm proteins of archaebacteria may play a more general role. Archaeal Lsm proteins are likely to represent the ancestral Sm domain.
Probab=23.73 E-value=1.1e+02 Score=18.48 Aligned_cols=29 Identities=31% Similarity=0.338 Sum_probs=20.3
Q ss_pred cccccEEEEEEecCCcEEEEEeCC-CCcccc
Q 042342 25 FAIRKCSRVQLIKNGKKIVTFVPS-DGCLNY 54 (87)
Q Consensus 25 SA~RK~~rV~Likngk~v~A~IPg-~G~ln~ 54 (87)
+++-|-+.|+| +||+.+....=+ |.|+|-
T Consensus 7 ~~~~~~V~V~l-~~g~~~~G~L~~~D~~mNl 36 (68)
T cd01731 7 DSLNKPVLVKL-KGGKEVRGRLKSYDQHMNL 36 (68)
T ss_pred HhcCCEEEEEE-CCCCEEEEEEEEECCcceE
Confidence 45678899999 999998866444 334443
No 62
>CHL00010 infA translation initiation factor 1
Probab=22.19 E-value=2.2e+02 Score=18.08 Aligned_cols=34 Identities=24% Similarity=0.317 Sum_probs=24.9
Q ss_pred EEEEEEecCCcEEEEEeCCCCcc--cccccCCeEEEe
Q 042342 30 CSRVQLIKNGKKIVTFVPSDGCL--NYIEENDKVLIA 64 (87)
Q Consensus 30 ~~rV~Likngk~v~A~IPg~G~l--n~lqeh~~VLV~ 64 (87)
...|++ .||..+.|+++|-=-. ..+-..|.|+++
T Consensus 21 ~y~V~~-~~g~~~~c~~rGklr~~~i~~~vGD~V~ve 56 (78)
T CHL00010 21 MFRVRL-DNGCQVLGYISGKIRRNSIRILPGDRVKVE 56 (78)
T ss_pred EEEEEe-CCCCEEEEEeccceecCCcccCCCCEEEEE
Confidence 345677 7899999999985331 125779999998
No 63
>smart00651 Sm snRNP Sm proteins. small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA splicing
Probab=22.13 E-value=1.2e+02 Score=17.70 Aligned_cols=28 Identities=32% Similarity=0.335 Sum_probs=19.3
Q ss_pred cccccEEEEEEecCCcEEEEEeCC-CCccc
Q 042342 25 FAIRKCSRVQLIKNGKKIVTFVPS-DGCLN 53 (87)
Q Consensus 25 SA~RK~~rV~Likngk~v~A~IPg-~G~ln 53 (87)
+.+.+.++|.| +||..+...+=+ |.+.|
T Consensus 5 ~~~~~~V~V~l-~~g~~~~G~L~~~D~~~N 33 (67)
T smart00651 5 KLIGKRVLVEL-KNGREYRGTLKGFDQFMN 33 (67)
T ss_pred HhCCcEEEEEE-CCCcEEEEEEEEECcccc
Confidence 56778899999 899887755333 33443
No 64
>cd01726 LSm6 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm6 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=21.34 E-value=1.4e+02 Score=18.13 Aligned_cols=31 Identities=23% Similarity=0.309 Sum_probs=20.9
Q ss_pred CcccccEEEEEEecCCcEEEEEeCC-CCccccc
Q 042342 24 NFAIRKCSRVQLIKNGKKIVTFVPS-DGCLNYI 55 (87)
Q Consensus 24 NSA~RK~~rV~Likngk~v~A~IPg-~G~ln~l 55 (87)
++++-|-+.|+| +||.++...+=+ |.++|-.
T Consensus 6 ~~~~~~~V~V~L-k~g~~~~G~L~~~D~~mNlv 37 (67)
T cd01726 6 KAIIGRPVVVKL-NSGVDYRGILACLDGYMNIA 37 (67)
T ss_pred HhhCCCeEEEEE-CCCCEEEEEEEEEccceeeE
Confidence 356778899999 999987755433 3454443
No 65
>PRK06151 N-ethylammeline chlorohydrolase; Provisional
Probab=21.11 E-value=96 Score=25.17 Aligned_cols=29 Identities=21% Similarity=0.263 Sum_probs=18.7
Q ss_pred EecCCcEEEEEeCCCCcccccccCCeEEEeecCC
Q 042342 35 LIKNGKKIVTFVPSDGCLNYIEENDKVLIAGFGR 68 (87)
Q Consensus 35 Likngk~v~A~IPg~G~ln~lqeh~~VLV~GfGr 68 (87)
||+|+..++ +.+++. .+.++..|+|+| |+
T Consensus 4 li~~~~v~~--~d~~~~--~~~~~~~VlVe~-g~ 32 (488)
T PRK06151 4 LIKARWVLG--FDDGDH--RLLRDGEVVFEG-DR 32 (488)
T ss_pred EEEccEEEE--EcCCCC--eEEeCcEEEEEC-CE
Confidence 567775544 345555 566778888888 74
No 66
>PF00054 Laminin_G_1: Laminin G domain; InterPro: IPR012679 Laminins are large heterotrimeric glycoproteins involved in basement membrane function []. The laminin globular (G) domain can be found in one to several copies in various laminin family members, which includes a large number of extracellular proteins. The C terminus of laminin alpha chain contains a tandem repeat of five laminin G domains, which are critical for heparin-binding and cell attachment activity []. Laminin alpha4 is distributed in a variety of tissues including peripheral nerves, dorsal root ganglion, skeletal muscle and capillaries; in the neuromuscular junction, it is required for synaptic specialisation []. The structure of the laminin-G domain has been predicted to resemble that of pentraxin []. Laminin G domains can vary in their function, and a variety of binding functions has been ascribed to different LamG modules. For example, the laminin alpha1 and alpha2 chains each has five C-teminal laminin G domains, where only domains LG4 and LG5 contain binding sites for heparin, sulphatides and the cell surface receptor dystroglycan []. Laminin G-containing proteins appear to have a wide variety of roles in cell adhesion, signalling, migration, assembly and differentiation. This entry represents one subtype of laminin G domains, which is sometimes found in association with thrombospondin-type laminin G domains (IPR012680 from INTERPRO).; PDB: 1OKQ_A 1DYK_A 2C5D_A 1H30_A 1LHW_A 1KDK_A 1LHU_A 1KDM_A 1LHO_A 1D2S_A ....
Probab=20.83 E-value=2.6e+02 Score=18.36 Aligned_cols=49 Identities=18% Similarity=0.403 Sum_probs=25.9
Q ss_pred CCcEE-EEEeCCCCcccccccCCeEEEeecCCCCCCCCCCCCceecccccC
Q 042342 38 NGKKI-VTFVPSDGCLNYIEENDKVLIAGFGRKGHAVATSPPIISLKGCMR 87 (87)
Q Consensus 38 ngk~v-~A~IPg~G~ln~lqeh~~VLV~GfGr~g~~v~DlPGV~y~~~~~~ 87 (87)
++... +.--|+.... .++-.+.+.|=|+-..-.....++-..+++|||+
T Consensus 72 d~~~~~~~~s~~~~~~-~l~~~~~lyvGG~p~~~~~~~~~~~~~~f~GCi~ 121 (131)
T PF00054_consen 72 DGEEVVTGESPSGATQ-SLDVDGPLYVGGLPSSSSRPRPLPISPGFKGCIR 121 (131)
T ss_dssp TTSEEEEEEECSSSSS-SCEECSEEEESSSSTTTGCGSSCSCCSB-EEEEE
T ss_pred CCccceeeecCCcccc-ccccccCEEEccCCchhhcccccccCCCeeEEEE
Confidence 33333 4445544441 3677777666443222333445566778999985
No 67
>PF12663 DUF3788: Protein of unknown function (DUF3788); InterPro: IPR024265 This family of functionally uncharacterised proteins is found in bacteria and archaea. Proteins in this family are typically between 137 and 149 amino acids in length and may be distantly related to RelE proteins.
Probab=20.76 E-value=1.7e+02 Score=20.30 Aligned_cols=30 Identities=33% Similarity=0.692 Sum_probs=22.3
Q ss_pred EEEEEecCCcEEEEEeCCCCcccccccCCeEEEeecCC
Q 042342 31 SRVQLIKNGKKIVTFVPSDGCLNYIEENDKVLIAGFGR 68 (87)
Q Consensus 31 ~rV~Likngk~v~A~IPg~G~ln~lqeh~~VLV~GfGr 68 (87)
=-++..+.+|.+....|.+|. | .|+|. ||.
T Consensus 50 W~~Kykk~~K~lc~lyp~~g~--F-----~~~iv-~g~ 79 (133)
T PF12663_consen 50 WNVKYKKKGKTLCTLYPEEGY--F-----TVMIV-IGK 79 (133)
T ss_pred EEEEEEEccceEEEEEecCCc--E-----EEEEE-ECc
Confidence 334544779999999999999 6 56776 665
No 68
>PRK14494 putative molybdopterin-guanine dinucleotide biosynthesis protein MobB/FeS domain-containing protein protein; Provisional
Probab=20.55 E-value=80 Score=24.05 Aligned_cols=12 Identities=42% Similarity=0.736 Sum_probs=10.4
Q ss_pred cCCeEEEeecCC
Q 042342 57 ENDKVLIAGFGR 68 (87)
Q Consensus 57 eh~~VLV~GfGr 68 (87)
+.|.|||+||.+
T Consensus 85 ~~DlvlVEGfk~ 96 (229)
T PRK14494 85 DADFLLIEGFKE 96 (229)
T ss_pred CCCEEEEeCCCC
Confidence 679999999766
No 69
>cd01730 LSm3 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm3 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=20.35 E-value=1.7e+02 Score=18.59 Aligned_cols=29 Identities=21% Similarity=0.324 Sum_probs=19.8
Q ss_pred ccccEEEEEEecCCcEEEEEeCC-CCccccc
Q 042342 26 AIRKCSRVQLIKNGKKIVTFVPS-DGCLNYI 55 (87)
Q Consensus 26 A~RK~~rV~Likngk~v~A~IPg-~G~ln~l 55 (87)
++-|-+.|+| ++|+++...+=+ |.|.|-+
T Consensus 9 ~~~k~V~V~l-~~gr~~~G~L~~fD~~mNlv 38 (82)
T cd01730 9 SLDERVYVKL-RGDRELRGRLHAYDQHLNMI 38 (82)
T ss_pred hCCCEEEEEE-CCCCEEEEEEEEEccceEEe
Confidence 3556788998 899988876443 5565544
No 70
>cd04497 hPOT1_OB1_like hPOT1_OB1_like: A subfamily of OB folds similar to the first OB fold (OB1) of human protection of telomeres 1 protein (hPOT1), the single OB fold of the N-terminal domain of Schizosaccharomyces pombe POT1 (SpPOT1), and the first OB fold of the N-terminal domain of the alpha subunit (OB1Nalpha) of Oxytricha nova telomere end binding protein (OnTEBP). POT1 proteins recognize single-stranded (ss) 3-prime ends of the telomere. A 3-prime ss overhang is conserved in ciliated protozoa, yeast, and mammals. SpPOT1 is essential for telomere maintenance. It binds specifically to the ss G-rich telomeric sequence (GGTTAC) of S. pombe. hPOT1 binds specifically to ss telomeric DNA repeats ending with the sequence GGTTAG. Deletion of the S. pombe pot1+ gene results in a rapid loss of telomere sequences, chromosome mis-segregation and chromosome circularization. hPOT1 is implicated in telomere length regulation. The hPOT1 monomer consists of two closely connected OB folds (OB1-OB
Probab=20.26 E-value=1.5e+02 Score=20.32 Aligned_cols=28 Identities=21% Similarity=0.434 Sum_probs=23.5
Q ss_pred CcEEEEEeCCCCcccccccCCeEEEeec
Q 042342 39 GKKIVTFVPSDGCLNYIEENDKVLIAGF 66 (87)
Q Consensus 39 gk~v~A~IPg~G~ln~lqeh~~VLV~Gf 66 (87)
+-++.-|=|-.-+|-.+++.|+|++++|
T Consensus 53 ~l~v~~F~~~~~~LP~v~~GDVIll~~~ 80 (138)
T cd04497 53 GLTVKLFRPNEESLPIVKVGDIILLRRV 80 (138)
T ss_pred cEEEEEECCChhhCCCCCCCCEEEEEEE
Confidence 4667778888888888899999999994
Done!