Query 038639
Match_columns 229
No_of_seqs 118 out of 1132
Neff 5.8
Searched_HMMs 46136
Date Fri Mar 29 13:07:50 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/038639.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/038639hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG2265 TrmA SAM-dependent met 99.9 3.4E-25 7.3E-30 209.6 12.3 137 80-221 3-200 (432)
2 PRK13168 rumA 23S rRNA m(5)U19 99.9 4.9E-24 1.1E-28 201.5 14.3 125 65-195 2-188 (443)
3 TIGR00479 rumA 23S rRNA (uraci 99.9 6.8E-24 1.5E-28 199.4 12.3 128 89-221 1-191 (431)
4 TIGR02085 meth_trns_rumB 23S r 99.2 2.7E-11 5.8E-16 112.8 6.2 86 131-220 16-130 (374)
5 COG3269 Predicted RNA-binding 99.1 3E-10 6.6E-15 83.0 8.2 57 72-130 9-65 (73)
6 PRK12336 translation initiatio 98.8 2E-08 4.4E-13 86.7 8.8 55 74-130 143-197 (201)
7 PRK03522 rumB 23S rRNA methylu 98.7 3.1E-08 6.7E-13 90.1 7.8 63 154-220 8-70 (315)
8 PF01938 TRAM: TRAM domain; I 98.7 1.2E-07 2.7E-12 66.3 7.9 53 77-130 3-57 (61)
9 PRK05031 tRNA (uracil-5-)-meth 98.6 3.4E-08 7.3E-13 91.8 4.1 64 131-195 7-97 (362)
10 TIGR02143 trmA_only tRNA (urac 98.2 1.3E-06 2.7E-11 81.2 4.8 61 134-195 1-88 (353)
11 PF05958 tRNA_U5-meth_tr: tRNA 98.1 1.2E-06 2.6E-11 81.2 2.4 61 134-195 1-88 (352)
12 KOG2187 tRNA uracil-5-methyltr 97.6 0.00011 2.4E-09 71.2 6.1 139 78-221 62-274 (534)
13 PF08206 OB_RNB: Ribonuclease 94.3 0.19 4.2E-06 34.8 6.1 37 87-123 3-44 (58)
14 smart00357 CSP Cold shock prot 73.2 13 0.00027 24.7 5.3 34 90-123 7-49 (64)
15 COG4956 Integral membrane prot 70.9 13 0.00027 34.8 6.3 47 77-124 292-341 (356)
16 TIGR00358 3_prime_RNase VacB a 68.3 22 0.00048 35.9 8.0 43 81-124 16-64 (654)
17 PF00575 S1: S1 RNA binding do 66.4 33 0.00072 23.6 6.5 49 76-126 2-64 (74)
18 TIGR02062 RNase_B exoribonucle 65.5 13 0.00029 37.5 5.8 42 81-124 18-64 (639)
19 smart00316 S1 Ribosomal protei 63.1 37 0.0008 22.3 6.1 47 78-126 2-62 (72)
20 PRK11642 exoribonuclease R; Pr 61.9 22 0.00047 37.1 6.6 41 82-123 85-130 (813)
21 PRK14332 (dimethylallyl)adenos 61.5 29 0.00063 33.4 7.1 49 78-127 384-441 (449)
22 PRK05054 exoribonuclease II; P 60.6 18 0.00038 36.6 5.6 42 81-124 21-67 (644)
23 PRK10943 cold shock-like prote 60.3 48 0.001 23.6 6.4 46 82-127 4-60 (69)
24 PRK14339 (dimethylallyl)adenos 58.1 46 0.001 31.6 7.7 49 78-127 362-412 (420)
25 PRK14330 (dimethylallyl)adenos 57.9 46 0.001 31.6 7.7 50 78-128 373-424 (434)
26 cd05789 S1_Rrp4 S1_Rrp4: Rrp4 57.9 66 0.0014 23.0 7.0 50 75-126 3-70 (86)
27 PRK09507 cspE cold shock prote 56.1 61 0.0013 23.0 6.4 46 82-127 4-60 (69)
28 PF00313 CSD: 'Cold-shock' DNA 54.6 67 0.0015 22.0 7.2 46 83-128 2-58 (66)
29 cd04465 S1_RPS1_repeat_ec2_hs2 54.4 57 0.0012 22.2 5.9 45 79-126 1-57 (67)
30 PRK14336 (dimethylallyl)adenos 53.5 60 0.0013 30.8 7.7 50 78-129 357-408 (418)
31 TIGR00008 infA translation ini 52.1 88 0.0019 22.6 6.6 41 82-123 7-57 (68)
32 PRK08582 hypothetical protein; 50.2 80 0.0017 25.6 6.9 49 75-125 2-64 (139)
33 PRK14327 (dimethylallyl)adenos 48.5 69 0.0015 31.6 7.4 51 78-129 444-498 (509)
34 PRK14331 (dimethylallyl)adenos 48.3 81 0.0018 30.0 7.7 49 78-127 377-427 (437)
35 PRK14340 (dimethylallyl)adenos 47.3 78 0.0017 30.4 7.5 49 78-127 381-433 (445)
36 PRK05807 hypothetical protein; 47.2 98 0.0021 24.9 7.0 48 75-125 2-63 (136)
37 COG2100 Predicted Fe-S oxidore 47.2 96 0.0021 29.5 7.7 52 75-128 351-408 (414)
38 PRK09937 stationary phase/star 46.6 86 0.0019 22.7 6.0 44 84-127 4-58 (74)
39 cd04458 CSP_CDS Cold-Shock Pro 46.5 87 0.0019 21.3 5.8 44 84-127 3-57 (65)
40 PRK14325 (dimethylallyl)adenos 46.4 85 0.0018 29.9 7.5 49 78-127 381-432 (444)
41 PRK14333 (dimethylallyl)adenos 46.2 87 0.0019 30.0 7.6 49 78-127 387-440 (448)
42 TIGR00089 RNA modification enz 45.7 89 0.0019 29.5 7.5 49 78-127 371-425 (429)
43 PRK12442 translation initiatio 45.0 1.3E+02 0.0029 22.9 6.8 14 110-123 46-59 (87)
44 PRK14335 (dimethylallyl)adenos 44.9 85 0.0018 30.2 7.3 50 78-128 390-445 (455)
45 PRK15463 cold shock-like prote 44.7 1E+02 0.0022 22.1 6.0 45 83-127 6-61 (70)
46 PRK14998 cold shock-like prote 44.2 90 0.002 22.5 5.7 44 84-127 4-58 (73)
47 PRK14338 (dimethylallyl)adenos 43.2 1.1E+02 0.0023 29.6 7.7 48 78-127 391-440 (459)
48 PRK15464 cold shock-like prote 43.1 1.1E+02 0.0025 21.9 6.1 45 83-127 6-61 (70)
49 cd04453 S1_RNase_E S1_RNase_E: 43.1 1.3E+02 0.0029 22.1 6.7 46 77-124 6-70 (88)
50 PRK09890 cold shock protein Cs 42.9 1.2E+02 0.0026 21.5 6.2 45 83-127 6-61 (70)
51 cd05694 S1_Rrp5_repeat_hs2_sc2 42.3 1.2E+02 0.0027 21.5 7.2 50 76-126 2-59 (74)
52 TIGR02063 RNase_R ribonuclease 41.8 81 0.0018 32.1 7.0 42 82-124 69-116 (709)
53 PF13509 S1_2: S1 domain; PDB: 40.5 78 0.0017 21.8 4.8 47 79-127 2-54 (61)
54 TIGR01574 miaB-methiolase tRNA 39.3 1.3E+02 0.0029 28.5 7.7 49 78-127 379-431 (438)
55 PF12988 DUF3872: Domain of un 38.2 70 0.0015 26.3 4.8 41 77-119 45-103 (137)
56 PF07076 DUF1344: Protein of u 38.1 1.5E+02 0.0032 21.1 6.1 44 81-126 4-53 (61)
57 PF12945 YcgR_2: Flagellar pro 36.6 1.5E+02 0.0033 20.9 6.5 54 77-130 2-67 (87)
58 cd05692 S1_RPS1_repeat_hs4 S1_ 36.6 1.2E+02 0.0027 19.8 5.7 45 79-125 1-59 (69)
59 PRK14328 (dimethylallyl)adenos 36.2 1.5E+02 0.0033 28.2 7.6 49 78-127 379-431 (439)
60 PRK08059 general stress protei 34.9 1.7E+02 0.0036 22.9 6.4 48 76-125 5-66 (123)
61 COG2421 Predicted acetamidase/ 34.4 1.2E+02 0.0026 28.1 6.2 53 75-127 22-86 (305)
62 TIGR01125 MiaB-like tRNA modif 32.2 1.7E+02 0.0036 27.8 7.1 49 78-127 367-426 (430)
63 PRK07252 hypothetical protein; 32.1 2E+02 0.0043 22.7 6.4 47 77-125 2-62 (120)
64 PRK14329 (dimethylallyl)adenos 31.8 2E+02 0.0044 27.7 7.7 49 78-127 406-458 (467)
65 PF03069 FmdA_AmdA: Acetamidas 31.5 49 0.0011 31.4 3.3 19 105-123 73-91 (369)
66 cd04473 S1_RecJ_like S1_RecJ_l 30.8 1.9E+02 0.0042 20.3 6.7 47 76-124 14-66 (77)
67 PRK14862 rimO ribosomal protei 29.8 1.6E+02 0.0035 28.1 6.6 48 78-127 378-433 (440)
68 PRK10354 RNA chaperone/anti-te 29.3 2.1E+02 0.0045 20.2 6.3 45 83-127 6-61 (70)
69 TIGR02381 cspD cold shock doma 29.3 1.8E+02 0.0039 20.5 5.2 44 84-127 4-58 (68)
70 cd04454 S1_Rrp4_like S1_Rrp4_l 28.8 2.1E+02 0.0046 20.2 7.5 50 75-126 3-66 (82)
71 COG0621 MiaB 2-methylthioadeni 27.8 2.4E+02 0.0051 27.5 7.3 51 78-129 377-431 (437)
72 cd05698 S1_Rrp5_repeat_hs6_sc5 26.9 2E+02 0.0044 19.3 6.7 46 79-126 1-60 (70)
73 COG1098 VacB Predicted RNA bin 26.8 2.5E+02 0.0055 22.9 6.1 48 75-124 2-63 (129)
74 PRK14337 (dimethylallyl)adenos 24.9 3.2E+02 0.007 26.1 7.7 49 78-127 381-438 (446)
75 COG2996 Predicted RNA-bindinin 22.2 6.3E+02 0.014 23.3 11.4 46 157-207 202-247 (287)
76 cd04461 S1_Rrp5_repeat_hs8_sc7 21.9 3E+02 0.0064 19.4 6.8 48 76-125 12-73 (83)
77 PRK14326 (dimethylallyl)adenos 21.7 3.6E+02 0.0077 26.4 7.4 52 78-130 389-451 (502)
78 PF06453 LT-IIB: Type II heat- 20.2 87 0.0019 24.8 2.2 56 53-111 18-75 (122)
79 cd05705 S1_Rrp5_repeat_hs14 S1 20.1 3.2E+02 0.007 19.2 7.3 48 76-125 1-65 (74)
No 1
>COG2265 TrmA SAM-dependent methyltransferases related to tRNA (uracil-5-)-methyltransferase [Translation, ribosomal structure and biogenesis]
Probab=99.92 E-value=3.4e-25 Score=209.62 Aligned_cols=137 Identities=31% Similarity=0.542 Sum_probs=124.4
Q ss_pred cEEEEEEeeeCCCCcEEEEEcCCCcEEEecCCCCCcEEEEEEEeecCCeee-----------------------------
Q 038639 80 QELELVCESLAYKGKGVCKVADTGFVVLCDRVLPGEKFIGRVTRKKGSYAE----------------------------- 130 (229)
Q Consensus 80 ~~i~l~I~~l~~~G~GVar~~~~G~vVFVpgaLPGE~V~vrI~k~kk~y~~----------------------------- 130 (229)
+.++++|++|+++|.|||+++ |++|||||+||||+|++++++.+++|++
T Consensus 3 ~~~~~~I~~l~~~G~Gva~~~--~~~vfVp~alPge~v~~~~~~~~~~~~~a~~~~i~~~Sp~R~~~~c~~~g~cggC~l 80 (432)
T COG2265 3 QIIEVTIEDLGHNGEGVARHD--GKVVFVPGALPGEEVEVRVTKVKKKYAEAKLVKVLEASPDRVDPPCPHFGRCGGCQL 80 (432)
T ss_pred ceEEEEEEEcCCCCeeEEEec--CceEEeCCCCCCcEEEEEEEeccccceeeEeeeeccCChhhcCCCCccccccccccc
Confidence 678999999999999999997 8899999999999999999999999998
Q ss_pred eeecccccccchhhccCcc----C----------------------------CCCCceeEEEeccCCCCceEeCCCCcCC
Q 038639 131 MEFSFGPKRWFPKESLPKR----G----------------------------DHIENYALGLHAPGFFDKVLNIDKCLLQ 178 (229)
Q Consensus 131 qhlsY~~QL~~K~~~l~~~----~----------------------------~~~g~~~lGf~~rgS~~~IVdie~CpL~ 178 (229)
||++|+.||++|++.|.+. + ..++.+.+||++++|| +||++++|+++
T Consensus 81 qhl~y~~QL~~K~~~l~~~l~~~~~~~~~~~~~~~~~~~~~yR~ka~~~v~~~~~~~l~~Gf~~~~s~-~iv~i~~C~v~ 159 (432)
T COG2265 81 QHLSYEAQLEFKREQLKELLKRIGGSEVEIDPTVGMSPPWGYRNRARFSVRGSGKGQLLAGFFRQGSH-EIVDIDECPVF 159 (432)
T ss_pred cCCCHHHHHHHHHHHHHHHHHHhcCCCcccccccCCCCCcCceeEEEEEEEEcCCCcEEEEeeccCCC-ceecccccCcc
Confidence 8999999999998665431 0 0123577899999997 89999999999
Q ss_pred ChhHHHHHHHHHHHHhcCCCCCCCCcCCCCccceeEEEEEeec
Q 038639 179 SEPANLVLAAVQDYWRDPQLGLSPYDVHSHSGFLKHLMLRTGS 221 (229)
Q Consensus 179 ~~~in~il~~lr~~l~~~~~~l~~Yd~~~~~G~LRhLvVR~s~ 221 (229)
++.++.++..++++++. ..+++||+..+.|.|+++++|.|.
T Consensus 160 ~~~~~~il~~l~~~l~~--~~~~~y~~~~~~g~l~~~~~~~g~ 200 (432)
T COG2265 160 PPRSNEILPLLRELLAK--LGLPPYNEKKKKGILRLIVLREGQ 200 (432)
T ss_pred CHhHHHHHHHHHHHHHH--cCCCccchhhccceEEEEEeccCc
Confidence 99999999999999997 899999999999999999999986
No 2
>PRK13168 rumA 23S rRNA m(5)U1939 methyltransferase; Reviewed
Probab=99.91 E-value=4.9e-24 Score=201.54 Aligned_cols=125 Identities=22% Similarity=0.340 Sum_probs=109.4
Q ss_pred ccccCCCCCCCCCCCcEEEEEEeeeCCCCcEEEEEcCCCcEEEecCCCCCcEEEEEEEeecCCeee--------------
Q 038639 65 TFDSNNNDYFKPIRGQELELVCESLAYKGKGVCKVADTGFVVLCDRVLPGEKFIGRVTRKKGSYAE-------------- 130 (229)
Q Consensus 65 ~~~~~~~~~~~~k~~~~i~l~I~~l~~~G~GVar~~~~G~vVFVpgaLPGE~V~vrI~k~kk~y~~-------------- 130 (229)
+|+||+++. ..-++++++|++++++|+|||+.+ |++|||||++|||+|+++|++.+++|++
T Consensus 2 ~~~~~~~~~---~~~~~~~l~i~~l~~~G~Gv~~~~--~~~vfV~~~lPGe~v~v~i~~~~~~~~~~~~~~vl~~sp~Rv 76 (443)
T PRK13168 2 QFYSPKRRV---TTRQIITVTIESLDHDGRGVARHN--GKTVFIEGALPGERVEVQVTEDKKQYARAKVVRILKPSPERV 76 (443)
T ss_pred CccCCCCCC---CCCcEEEEEEEEcCCCCceEEEEC--CEEEEeCCCCCCCEEEEEEEEecCcEEEEEEEEEecCCcccC
Confidence 789999887 466788999999999999999996 8999999999999999999999998887
Q ss_pred ---------------eeecccccccchhhccCcc----C---------------------------C--CCCceeEEEec
Q 038639 131 ---------------MEFSFGPKRWFPKESLPKR----G---------------------------D--HIENYALGLHA 162 (229)
Q Consensus 131 ---------------qhlsY~~QL~~K~~~l~~~----~---------------------------~--~~g~~~lGf~~ 162 (229)
||++|+.||++|++.+++. + . .++...+|||+
T Consensus 77 ~p~C~~~~~CGGC~~qh~~y~~Ql~~K~~~v~~~l~r~~~~~~~~~~~~i~~~~~~YRnk~~~~~~~~~~~g~~~~G~~~ 156 (443)
T PRK13168 77 TPRCPHFGVCGGCQLQHLSIDAQIASKQRALEDLLKHLAGVEPEEVLPPIAGPPWGYRRRARLSVRYVPKKGQLLVGFRE 156 (443)
T ss_pred CCCCCcCCcCcCchhcCCCHHHHHHHHHHHHHHHHHHhcCCCcccccCCCcCCCCCCCceEEEEeeeecCCCCEEEEEec
Confidence 9999999999998775431 0 0 02335699999
Q ss_pred cCCCCceEeCCCCcCCChhHHHHHHHHHHHHhc
Q 038639 163 PGFFDKVLNIDKCLLQSEPANLVLAAVQDYWRD 195 (229)
Q Consensus 163 rgS~~~IVdie~CpL~~~~in~il~~lr~~l~~ 195 (229)
++|| ++|++++|+|++|.+++++..+++++..
T Consensus 157 ~~s~-~vv~i~~C~l~~~~~~~~~~~~~~~~~~ 188 (443)
T PRK13168 157 KNSS-DIVDIDQCPVLVPPLSALLPPLRALLSS 188 (443)
T ss_pred CCCc-eeEECCCCccCCHhHHHHHHHHHHHHHH
Confidence 9997 8999999999999999999999999874
No 3
>TIGR00479 rumA 23S rRNA (uracil-5-)-methyltransferase RumA. This protein family was first proposed to be RNA methyltransferases by homology to the TrmA family. The member from E. coli has now been shown to act as the 23S RNA methyltransferase for the conserved U1939. The gene is now designated rumA and was previously designated ygcA.
Probab=99.90 E-value=6.8e-24 Score=199.36 Aligned_cols=128 Identities=30% Similarity=0.433 Sum_probs=112.7
Q ss_pred eCCCCcEEEEEcCCCcEEEecCCCCCcEEEEEEEeecCCeee-----------------------------eeecccccc
Q 038639 89 LAYKGKGVCKVADTGFVVLCDRVLPGEKFIGRVTRKKGSYAE-----------------------------MEFSFGPKR 139 (229)
Q Consensus 89 l~~~G~GVar~~~~G~vVFVpgaLPGE~V~vrI~k~kk~y~~-----------------------------qhlsY~~QL 139 (229)
++++|+|||+.+ |+++||||+||||+|+++|++.+++|++ ||++|++|+
T Consensus 1 l~~~G~Gv~~~~--~~~vfV~~~lpGe~v~~~i~~~~~~~~~~~~~~i~~~S~~Rv~p~C~~~~~CGGC~~qh~~y~~Ql 78 (431)
T TIGR00479 1 LDHQGEGVARFN--GKVVFVPNALPGEKVEVRVTKVKRQYALARVKKIREPSPERTRPPCPVFDQCGGCQLQHLDYEFQL 78 (431)
T ss_pred CCCCCcEEEEEC--CEEEEeCCCCCCCEEEEEEEEecCceeEEEeeeecCCCcCcCCCCCCCCCCCCCCcccCCCHHHHH
Confidence 578999999986 8999999999999999999999998877 999999999
Q ss_pred cchhhccCcc----C---------------C-----------C----CCceeEEEeccCCCCceEeCCCCcCCChhHHHH
Q 038639 140 WFPKESLPKR----G---------------D-----------H----IENYALGLHAPGFFDKVLNIDKCLLQSEPANLV 185 (229)
Q Consensus 140 ~~K~~~l~~~----~---------------~-----------~----~g~~~lGf~~rgS~~~IVdie~CpL~~~~in~i 185 (229)
++|+++|.++ + . . +++..+||++++|| ++|++++|+|++|.++++
T Consensus 79 ~~K~~~v~~~l~r~~~~~~~~~~~~~~~~~~~~~YRnr~~~~v~~~~~g~~~~G~~~~~s~-~vv~i~~C~i~~~~i~~~ 157 (431)
T TIGR00479 79 RSKQQQVIALLERIGKFTSEPIEPLPTIGGDPWGYRNKARLSLGRSPSGQIQAGFYQKGSH-DIVPIKQCPVQDPALNLL 157 (431)
T ss_pred HHHHHHHHHHHHHhcCCCcCCceecCCcCCCCCcccceeEEEeeecCCCCEEEeeecCCCc-ceEcCCCCCCCCHHHHHH
Confidence 9997664331 0 0 0 23356899999998 899999999999999999
Q ss_pred HHHHHHHHhcCCCCCCCCcCCCCccceeEEEEEeec
Q 038639 186 LAAVQDYWRDPQLGLSPYDVHSHSGFLKHLMLRTGS 221 (229)
Q Consensus 186 l~~lr~~l~~~~~~l~~Yd~~~~~G~LRhLvVR~s~ 221 (229)
+..+++++.+ .++++|+..+++|+||+++||.+.
T Consensus 158 ~~~~~~~~~~--~~~~~~~~~~~~g~lr~i~ir~~~ 191 (431)
T TIGR00479 158 LPKVKAILEN--FGASIYLEHKELGKARHGVLRIGR 191 (431)
T ss_pred HHHHHHHHHH--cCCCccccccCcccceEEEEEEec
Confidence 9999999996 899999999999999999999863
No 4
>TIGR02085 meth_trns_rumB 23S rRNA (uracil-5-)-methyltransferase RumB. This family consists of RNA methyltransferases designated RumB, formerly YbjF. Members act on 23S rRNA U747 and the equivalent position in other proteobacterial species. This family is homologous to the other 23S rRNA methyltransferase RumA and to the tRNA methyltransferase TrmA.
Probab=99.18 E-value=2.7e-11 Score=112.82 Aligned_cols=86 Identities=21% Similarity=0.352 Sum_probs=72.5
Q ss_pred eeecccccccchhhccCcc---C------------C--------------CCCceeEEEeccCCCCceEeCCCCcCCChh
Q 038639 131 MEFSFGPKRWFPKESLPKR---G------------D--------------HIENYALGLHAPGFFDKVLNIDKCLLQSEP 181 (229)
Q Consensus 131 qhlsY~~QL~~K~~~l~~~---~------------~--------------~~g~~~lGf~~rgS~~~IVdie~CpL~~~~ 181 (229)
||++|++|+++|+++|++. + . .+++..+||+.++ + .+|++++|+|++|.
T Consensus 16 qhl~y~~Ql~~K~~~v~~~l~r~~~~~~~~~~i~~~~~~YRnr~~l~v~~~~~~~~~G~~~~~-~-~~v~i~~C~i~~~~ 93 (374)
T TIGR02085 16 LAQPYSEQLTNKQQHLKELLAPNATVVQWLAPVTSAEQAFRNKAKMVVSGSVERPILGILHRD-G-TPLDLCDCPLYPQS 93 (374)
T ss_pred cCCCHHHHHHHHHHHHHHHHhhcCCCccccCCcCCCCccccceEEEEEEEcCCcEEEeEecCC-C-cEEcCccCCCCCHh
Confidence 9999999999997764331 0 0 0233568987766 5 69999999999999
Q ss_pred HHHHHHHHHHHHhcCCCCCCCCcCCCCccceeEEEEEee
Q 038639 182 ANLVLAAVQDYWRDPQLGLSPYDVHSHSGFLKHLMLRTG 220 (229)
Q Consensus 182 in~il~~lr~~l~~~~~~l~~Yd~~~~~G~LRhLvVR~s 220 (229)
++.++..+++++.. .+++.||+.+++|+|||++||.+
T Consensus 94 ~~~~~~~~~~~~~~--~~~~~~~~~~~~g~lr~i~ir~~ 130 (374)
T TIGR02085 94 FQPVFAYLKNFIAR--AGLTPYNVAKKKGELKFILLTES 130 (374)
T ss_pred HHHHHHHHHHHHHH--cCCCCccccCCCccceEEEEEEe
Confidence 99999999999986 89999999999999999999976
No 5
>COG3269 Predicted RNA-binding protein, contains TRAM domain [General function prediction only]
Probab=99.13 E-value=3e-10 Score=82.99 Aligned_cols=57 Identities=25% Similarity=0.383 Sum_probs=53.3
Q ss_pred CCCCCCCCcEEEEEEeeeCCCCcEEEEEcCCCcEEEecCCCCCcEEEEEEEeecCCeee
Q 038639 72 DYFKPIRGQELELVCESLAYKGKGVCKVADTGFVVLCDRVLPGEKFIGRVTRKKGSYAE 130 (229)
Q Consensus 72 ~~~~~k~~~~i~l~I~~l~~~G~GVar~~~~G~vVFVpgaLPGE~V~vrI~k~kk~y~~ 130 (229)
....+..|+..+++|++++..|.|+|+.+ |.+||||++-+||+|.++|.+.+.+|++
T Consensus 9 ~~~PVeeGe~y~V~I~d~g~~GDGiarve--GfvVFVp~a~~Gd~V~vkI~~v~~~~af 65 (73)
T COG3269 9 RTPPVEEGETYEVEIEDVGDQGDGIARVE--GFVVFVPGAEVGDEVKVKITKVKPNFAF 65 (73)
T ss_pred CCCCcccCCEEEEEEEEeccCCCceEEEE--EEEEEeCCCCCCCeeeEEEEEeecccee
Confidence 44566889999999999999999999998 9999999999999999999999999986
No 6
>PRK12336 translation initiation factor IF-2 subunit beta; Provisional
Probab=98.81 E-value=2e-08 Score=86.69 Aligned_cols=55 Identities=20% Similarity=0.258 Sum_probs=49.4
Q ss_pred CCCCCCcEEEEEEeeeCCCCcEEEEEcCCCcEEEecCCCCCcEEEEEEEeecCCeee
Q 038639 74 FKPIRGQELELVCESLAYKGKGVCKVADTGFVVLCDRVLPGEKFIGRVTRKKGSYAE 130 (229)
Q Consensus 74 ~~~k~~~~i~l~I~~l~~~G~GVar~~~~G~vVFVpgaLPGE~V~vrI~k~kk~y~~ 130 (229)
..++.++.++++|++++++|.|+++.+ |+++||+|++|||+|++++++.+++|++
T Consensus 143 ~~~~~~e~~~v~Ie~l~~~G~GVak~~--g~~vfV~galpGE~V~vri~k~kk~~~~ 197 (201)
T PRK12336 143 EAIEEGKTYEVEITGTGRKGDGVAKKG--KYTIFVPGAKKGEVVKVKIKKISGNLAF 197 (201)
T ss_pred CCCccCCEEEEEEEEccCCCceEEEEC--CEEEEeCCCCCCCEEEEEEEEecCCcee
Confidence 345778889999999999999999996 8999999999999999999999888653
No 7
>PRK03522 rumB 23S rRNA methyluridine methyltransferase; Reviewed
Probab=98.73 E-value=3.1e-08 Score=90.09 Aligned_cols=63 Identities=27% Similarity=0.402 Sum_probs=57.4
Q ss_pred CceeEEEeccCCCCceEeCCCCcCCChhHHHHHHHHHHHHhcCCCCCCCCcCCCCccceeEEEEEee
Q 038639 154 ENYALGLHAPGFFDKVLNIDKCLLQSEPANLVLAAVQDYWRDPQLGLSPYDVHSHSGFLKHLMLRTG 220 (229)
Q Consensus 154 g~~~lGf~~rgS~~~IVdie~CpL~~~~in~il~~lr~~l~~~~~~l~~Yd~~~~~G~LRhLvVR~s 220 (229)
++..+|||++++. +|++++|||++|.+++++..+++++++ .++++|++..++|+|||++||.+
T Consensus 8 ~~~~~G~~~~~~~--~v~i~~C~i~~~~~~~~~~~l~~~~~~--~~~~~~~~~~~~g~lr~~~ir~~ 70 (315)
T PRK03522 8 ERPLLGILHRDGT--PVDLCDCPLYPASFAPVFAALKPFIAR--AGLTPYNVARKRGELKYILLTES 70 (315)
T ss_pred CccEEeEEcCCCc--EEcCCCCcCCCHHHHHHHHHHHHHHHH--cCCCCCcCCCCCceeeEEEEEee
Confidence 4567899998763 699999999999999999999999986 89999999999999999999976
No 8
>PF01938 TRAM: TRAM domain; InterPro: IPR002792 The TRAM (after TRM2 and miaB) domain is a 60-70-residue-long module that is found in: Two distinct classes of tRNA-modifying enzymes, namely uridine methylases of the TRM2 family and enzymes of the miaB family that are involved in 2- methylthioadenine formation In several other proteins associated with the translation machinery In a family of small uncharacterised archaeal proteins that are predicted to have a role in the regulation of tRNA modification and/or translation The TRAM domain can be found alone or in association with other domains, such as the catalytic biotin/lipoate synthetase-like domain, the RNA methylase domain, the ribosomal S2 domain and the eIF2-beta domain. The TRAM domain is predicted to bind tRNA and deliver the RNA-modifying enzymatic domain to their targets []. Secondary structure prediction indicates that the TRAM domain adopts a simple beta-barrel fold. The conservation pattern of the TRAM domain consists primarily of small and hydrophobic residues that correspond to five beta-strands in the predicted secondary structure [].; PDB: 1YEZ_A 2BH2_A 1UWV_A 1YVC_A.
Probab=98.68 E-value=1.2e-07 Score=66.33 Aligned_cols=53 Identities=34% Similarity=0.507 Sum_probs=44.2
Q ss_pred CCCcEEEEEEeeeCCCCcEEEEEcCCCcEEEecCCCC--CcEEEEEEEeecCCeee
Q 038639 77 IRGQELELVCESLAYKGKGVCKVADTGFVVLCDRVLP--GEKFIGRVTRKKGSYAE 130 (229)
Q Consensus 77 k~~~~i~l~I~~l~~~G~GVar~~~~G~vVFVpgaLP--GE~V~vrI~k~kk~y~~ 130 (229)
..|+.+++.|++++++|.++||.+ +++.|||+++.| ||.|.++|++.++.|++
T Consensus 3 ~~G~~~~VlVe~~~~~g~~~gr~~-~~~~V~v~~~~~~iG~~v~v~I~~~~~~~l~ 57 (61)
T PF01938_consen 3 YVGKTLEVLVEELGDEGQGIGRTD-NGKVVFVPGGLPLIGEFVKVRITKAKKNYLF 57 (61)
T ss_dssp -TTEEEEEEEEEE-TTSEEEEEET--TEEEEETT--T--TEEEEEEEEEE-SSEEE
T ss_pred cCCcEEEEEEEEecCCCEEEEEeC-CCeEEEECCCCCCCCCEEEEEEEEeeCCcEE
Confidence 368999999999999999999997 589999999999 99999999999998864
No 9
>PRK05031 tRNA (uracil-5-)-methyltransferase; Validated
Probab=98.60 E-value=3.4e-08 Score=91.81 Aligned_cols=64 Identities=14% Similarity=0.095 Sum_probs=53.9
Q ss_pred eeecccccccchhhccCcc----C---------C-------------CC-CceeEEEeccCCCCceEeCCCCcCCChhHH
Q 038639 131 MEFSFGPKRWFPKESLPKR----G---------D-------------HI-ENYALGLHAPGFFDKVLNIDKCLLQSEPAN 183 (229)
Q Consensus 131 qhlsY~~QL~~K~~~l~~~----~---------~-------------~~-g~~~lGf~~rgS~~~IVdie~CpL~~~~in 183 (229)
||++|+.|+++|+++|++. + . .. ++..+|||+++|| ++|++++|+|++|.++
T Consensus 7 qhl~y~~Ql~~K~~~v~~~l~r~~~~~~~i~~s~~~~YRnr~~~~v~~~~g~~~~G~~~~~s~-~vv~i~~C~i~~~~~~ 85 (362)
T PRK05031 7 PPEQYEAQLAEKVARLKELFAPFSAPEPEVFRSPPSHYRMRAEFRIWHEGDDLYYAMFDQQTK-QRIRIDQFPIASELIN 85 (362)
T ss_pred CCCCHHHHHHHHHHHHHHHHHhcCCCCCCcccCCcccccceEEEEEEEeCCCEEEEEEeCCCC-CeEECccCcCCCHHHH
Confidence 8999999999998886552 1 0 01 4456999999997 8999999999999999
Q ss_pred HHHHHHHHHHhc
Q 038639 184 LVLAAVQDYWRD 195 (229)
Q Consensus 184 ~il~~lr~~l~~ 195 (229)
+++..++++++.
T Consensus 86 ~~~~~~~~~~~~ 97 (362)
T PRK05031 86 ALMPALLAALRA 97 (362)
T ss_pred HHHHHHHHHHHh
Confidence 999999999874
No 10
>TIGR02143 trmA_only tRNA (uracil-5-)-methyltransferase. This family consists exclusively of proteins believed to act as tRNA (uracil-5-)-methyltransferase. All members of far are proteobacterial. The seed alignment was taken directly from pfam05958 in Pfam 12.0, but higher cutoffs are used to select only functionally equivalent proteins. Homologous proteins excluded by the higher cutoff scores of this model include other uracil methyltransferases, such as RumA, active on rRNA.
Probab=98.23 E-value=1.3e-06 Score=81.16 Aligned_cols=61 Identities=13% Similarity=0.064 Sum_probs=49.9
Q ss_pred cccccccchhhccCcc----C----------------------CC-CCceeEEEeccCCCCceEeCCCCcCCChhHHHHH
Q 038639 134 SFGPKRWFPKESLPKR----G----------------------DH-IENYALGLHAPGFFDKVLNIDKCLLQSEPANLVL 186 (229)
Q Consensus 134 sY~~QL~~K~~~l~~~----~----------------------~~-~g~~~lGf~~rgS~~~IVdie~CpL~~~~in~il 186 (229)
+|+.|+++|++.|++. + .. +|++.+||++++|| ++|++++|+|++|.++.++
T Consensus 1 ~y~~Ql~~K~~~v~~~l~r~~~~~~~v~~s~~~~YRnr~~~~~~~~~g~~~~G~~~~~s~-~iv~i~~C~i~~~~i~~~~ 79 (353)
T TIGR02143 1 QYTAQLAEKVSRLKDLFAPFDAPEPEVFESPDKHYRMRAEFRIWHEGDDLYYAMFDQQTK-SKIRVDQFPAASELINRLM 79 (353)
T ss_pred ChHHHHHHHHHHHHHHHHhcCCCcCCCcCCccccccceEEEEEEecCCcEEEEEEeCCCC-CeEECCCCcCCCHHHHHHH
Confidence 5899999998776542 1 01 24456899999998 8999999999999999999
Q ss_pred HHHHHHHhc
Q 038639 187 AAVQDYWRD 195 (229)
Q Consensus 187 ~~lr~~l~~ 195 (229)
..+++++..
T Consensus 80 ~~~~~~l~~ 88 (353)
T TIGR02143 80 PALIAALRQ 88 (353)
T ss_pred HHHHHHHHh
Confidence 999999874
No 11
>PF05958 tRNA_U5-meth_tr: tRNA (Uracil-5-)-methyltransferase; InterPro: IPR010280 This family consists of (uracil-5-)-methyltransferases 2.1.1.35 from EC from bacteria, archaea and eukaryotes. A 5-methyluridine (m(5)U) residue at position 54 is a conserved feature of bacterial and eukaryotic tRNAs. The methylation of U54 is catalysed by the tRNA(m5U54)methyltransferase, which in Saccharomyces cerevisiae is encoded by the nonessential TRM2 gene. It is thought that tRNA modification enzymes might have a role in tRNA maturation not necessarily linked to their known catalytic activity []. This protein family also contains the 23SrRNA methyltransferases, first proposed to be RNA methyltransferases by homology to the TrmA family. The member from Escherichia coli has now been shown to act as the 23S RNA methyltransferase for the conserved U1939. The gene is now designated rumA and was previously designated ygcA [].; GO: 0008173 RNA methyltransferase activity, 0006396 RNA processing; PDB: 2VS1_A 2JJQ_A 2BH2_A 1UWV_A 3BT7_B.
Probab=98.12 E-value=1.2e-06 Score=81.21 Aligned_cols=61 Identities=18% Similarity=0.404 Sum_probs=46.7
Q ss_pred cccccccchhhccCcc----C-----------------------CCCCceeEEEeccCCCCceEeCCCCcCCChhHHHHH
Q 038639 134 SFGPKRWFPKESLPKR----G-----------------------DHIENYALGLHAPGFFDKVLNIDKCLLQSEPANLVL 186 (229)
Q Consensus 134 sY~~QL~~K~~~l~~~----~-----------------------~~~g~~~lGf~~rgS~~~IVdie~CpL~~~~in~il 186 (229)
+|+.||++|+++|.++ + ..+++..+|||+++|| ++|++++|||++|.+++++
T Consensus 1 ~Y~~QL~~K~~~l~~~l~~~~~~~~~i~~s~~~~YRnKa~~~v~~~~~~~~~g~~~~~s~-~iv~i~~C~i~~~~In~~l 79 (352)
T PF05958_consen 1 KYEKQLEFKQQILKELLRRIGKLEIEIIASPPWGYRNKARFPVRKDKGKLILGFFRRGSH-EIVDIEECPIADPEINKLL 79 (352)
T ss_dssp GHHHHHHHHHHHHHHHHTTT-----EEE---SSS-BSEEEEEEEECTTCEEEEEEECTTS--EEE-S--TTB-HHHHHHH
T ss_pred ChHHHHHHHHHHHHHHHHhcCCCCCceecCCChhcccEEEEEEEEcCCcEEEEEEecCCC-ceEECCCCccccHHHHHHH
Confidence 5999999999887653 1 0145677899999998 8999999999999999999
Q ss_pred HHHHHHHhc
Q 038639 187 AAVQDYWRD 195 (229)
Q Consensus 187 ~~lr~~l~~ 195 (229)
..++++++.
T Consensus 80 ~~l~~~l~~ 88 (352)
T PF05958_consen 80 PALRELLKK 88 (352)
T ss_dssp HHHHHHHTT
T ss_pred HHHHHHHhh
Confidence 999999963
No 12
>KOG2187 consensus tRNA uracil-5-methyltransferase and related tRNA-modifying enzymes [Translation, ribosomal structure and biogenesis]
Probab=97.59 E-value=0.00011 Score=71.21 Aligned_cols=139 Identities=29% Similarity=0.362 Sum_probs=100.6
Q ss_pred CCcEEEEEEeeeCCCCcEEEEEcCCCcEEEecCCCCCcEEEEEEEeecCCeee------------------eeecccccc
Q 038639 78 RGQELELVCESLAYKGKGVCKVADTGFVVLCDRVLPGEKFIGRVTRKKGSYAE------------------MEFSFGPKR 139 (229)
Q Consensus 78 ~~~~i~l~I~~l~~~G~GVar~~~~G~vVFVpgaLPGE~V~vrI~k~kk~y~~------------------qhlsY~~QL 139 (229)
......++.+.....|.++-..++..+..+..-+.+|..........+ +.. -.++|.+||
T Consensus 62 ~~~~~~~~~et~~~~~ka~~~v~g~~~k~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~r~~~~~Vtpl~~~Sy~~qL 139 (534)
T KOG2187|consen 62 MPKYAYVTFETPSDAGKAINLVDGLLYKGFILRVQLGATEVGSLRRRK--SQPGPTEPPQQRTARDVVTPLEYLSYGEQL 139 (534)
T ss_pred CCCceEEEEeccchhhhHHHHHhhhhhhcchhhhhhcccccccccccc--cCCCcCccccchhhhhhcceeeeeccccch
Confidence 344567888888888877766653345566777778877766555544 111 467999999
Q ss_pred cchhhc----cCcc---------------C------C------------------------------C-CCceeEEEecc
Q 038639 140 WFPKES----LPKR---------------G------D------------------------------H-IENYALGLHAP 163 (229)
Q Consensus 140 ~~K~~~----l~~~---------------~------~------------------------------~-~g~~~lGf~~r 163 (229)
++|..- |+.. + + . .....+|-+..
T Consensus 140 ~lk~~~~~~vl~kl~~~~~~li~~kv~~~~~~~~~~d~~Le~I~pSp~~~~yrnKceFsvg~~~~g~~~~vgf~lg~~~~ 219 (534)
T KOG2187|consen 140 ELKQLSQEAVLQKLERLIGDLIRAKVAFLGPQYHLHDRVLEVIIPSPIQNGYRNKCEFSVGQLLDGEDDTVGFVLGRFSK 219 (534)
T ss_pred hhhhccHHHHHHHHHHHHHHHHhheeecccccchhhcccccccccCccccCchhcceeeccccccCCcCceeeeeeeeec
Confidence 999422 1110 0 0 0 12345677888
Q ss_pred CCCCceEeCCCCcCCChhHHHHHHHHHHHHhcCCCCCCCCcCCCCccceeEEEEEeec
Q 038639 164 GFFDKVLNIDKCLLQSEPANLVLAAVQDYWRDPQLGLSPYDVHSHSGFLKHLMLRTGS 221 (229)
Q Consensus 164 gS~~~IVdie~CpL~~~~in~il~~lr~~l~~~~~~l~~Yd~~~~~G~LRhLvVR~s~ 221 (229)
|.+ .++.=-+|.+.++..+.++..+++++++ ..+.+||+..+.|++|+|+||...
T Consensus 220 g~~-~~~~pvd~~llp~~~~~V~s~~Q~f~R~--t~l~P~~~~~~~G~wk~LtVRt~~ 274 (534)
T KOG2187|consen 220 GAF-AVVAPVDVKLLPEIMSQVASAVQEFYRE--TKLSPYDDFPKGGFWKQLTVRTEF 274 (534)
T ss_pred Cce-EEeccccccccChHHHHHHHHHHHHHhc--CCCccccccCCCCceeeeEEEecc
Confidence 887 6777678888889999999999999996 899999999999999999999443
No 13
>PF08206 OB_RNB: Ribonuclease B OB domain; InterPro: IPR013223 This domain includes the N-terminal OB domain found in ribonuclease B proteins in one or two copies.; PDB: 2ID0_D 2IX1_A 2IX0_A.
Probab=94.30 E-value=0.19 Score=34.76 Aligned_cols=37 Identities=24% Similarity=0.313 Sum_probs=26.9
Q ss_pred eeeCCCCcEEEEEcCCCcEEEec-----CCCCCcEEEEEEEe
Q 038639 87 ESLAYKGKGVCKVADTGFVVLCD-----RVLPGEKFIGRVTR 123 (229)
Q Consensus 87 ~~l~~~G~GVar~~~~G~vVFVp-----gaLPGE~V~vrI~k 123 (229)
.++..+|+|.+..++.+.-+||| +|+.||+|.|++++
T Consensus 3 ~~~~~~GfGFv~~~~~~~DifIp~~~l~~A~~gD~V~v~i~~ 44 (58)
T PF08206_consen 3 LKIHPKGFGFVIPDDGGEDIFIPPRNLNGAMDGDKVLVRITP 44 (58)
T ss_dssp EEE-SSS-EEEEECT-TEEEEE-HHHHTTS-TT-EEEEEEEE
T ss_pred EEEEcCCCEEEEECCCCCCEEECHHHHCCCCCCCEEEEEEec
Confidence 45678999999987436789998 99999999999998
No 14
>smart00357 CSP Cold shock protein domain. RNA-binding domain that functions as a RNA-chaperone in bacteria and is involved in regulating translation in eukaryotes. Contains sub-family of RNA-binding domains in the Rho transcription termination factor.
Probab=73.18 E-value=13 Score=24.70 Aligned_cols=34 Identities=24% Similarity=0.259 Sum_probs=24.3
Q ss_pred CCCCcEEEEEcCCCcEEEec---------CCCCCcEEEEEEEe
Q 038639 90 AYKGKGVCKVADTGFVVLCD---------RVLPGEKFIGRVTR 123 (229)
Q Consensus 90 ~~~G~GVar~~~~G~vVFVp---------gaLPGE~V~vrI~k 123 (229)
..+|+|....++++.-+||+ ++.+||+|.+++..
T Consensus 7 ~~~g~gfv~~~~~~~~i~v~~~~~~~~~~~~~~Gd~V~~~i~~ 49 (64)
T smart00357 7 FNKGFGFIRPDDGGKDVFVHPSQIQGGLKSLREGDEVEFKVVS 49 (64)
T ss_pred EcCCeeEEecCCCCccEEEEhHHhhcCCCcCCCCCEEEEEEEE
Confidence 33789998876222457763 36789999999976
No 15
>COG4956 Integral membrane protein (PIN domain superfamily) [General function prediction only]
Probab=70.95 E-value=13 Score=34.83 Aligned_cols=47 Identities=23% Similarity=0.306 Sum_probs=40.6
Q ss_pred CCCcEEEEEEeeeCC-CCcEEEEEcCCCcEEEecCC--CCCcEEEEEEEee
Q 038639 77 IRGQELELVCESLAY-KGKGVCKVADTGFVVLCDRV--LPGEKFIGRVTRK 124 (229)
Q Consensus 77 k~~~~i~l~I~~l~~-~G~GVar~~~~G~vVFVpga--LPGE~V~vrI~k~ 124 (229)
-+|+.+++.|.+-+. .|.|||+.+ ||.-|-|+++ +-|+.+++.++..
T Consensus 292 lpGe~l~v~iiK~GkE~~QGVgYLd-DGTMiVVE~gr~~ig~~~~V~Vtsv 341 (356)
T COG4956 292 LPGEELTVQIIKDGKEPGQGVGYLD-DGTMIVVEEGRKLIGKTVQVEVTSV 341 (356)
T ss_pred cCCCeeEEEEeecCcccCCceEEec-CCeEEEEecchhhCCCeeEEEEeeh
Confidence 478999999997765 799999998 7888888876 8999999999875
No 16
>TIGR00358 3_prime_RNase VacB and RNase II family 3'-5' exoribonucleases. This model is defined to identify a pair of paralogous 3-prime exoribonucleases in E. coli, plus the set of proteins apparently orthologous to one or the other in other eubacteria. VacB was characterized originally as required for the expression of virulence genes, but is now recognized as the exoribonuclease RNase R (Rnr). Its paralog in E. coli and H. influenzae is designated exoribonuclease II (Rnb). Both are involved in the degradation of mRNA, and consequently have strong pleiotropic effects that may be difficult to disentangle. Both these proteins share domain-level similarity (RNB, S1) with a considerable number of other proteins, and full-length similarity scoring below the trusted cutoff to proteins associated with various phenotypes but uncertain biochemistry; it may be that these latter proteins are also 3-prime exoribonucleases.
Probab=68.30 E-value=22 Score=35.95 Aligned_cols=43 Identities=16% Similarity=0.116 Sum_probs=32.5
Q ss_pred EEEEEEeeeCCCCcEEEEEcC-CCcEEEec-----CCCCCcEEEEEEEee
Q 038639 81 ELELVCESLAYKGKGVCKVAD-TGFVVLCD-----RVLPGEKFIGRVTRK 124 (229)
Q Consensus 81 ~i~l~I~~l~~~G~GVar~~~-~G~vVFVp-----gaLPGE~V~vrI~k~ 124 (229)
.++.+|. .+.+|+|.+..++ ++.-+||| ++++||+|.++|.+.
T Consensus 16 ~~~G~i~-~~~~gfgFv~~~~~~~~difI~~~~~~~a~~GD~V~v~i~~~ 64 (654)
T TIGR00358 16 LVKGVVK-AHNKGFGFLRPDDDDKKDYFIPPPQMKKVMHGDLVEACPLSQ 64 (654)
T ss_pred eEEEEEE-ECCCccEEEEeCCCCCCcEEEchHHhCcCCCCCEEEEEEeec
Confidence 3454444 6789999998763 13689997 799999999998753
No 17
>PF00575 S1: S1 RNA binding domain; InterPro: IPR003029 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 S1 domain was originally identified in ribosomal protein S1 but is found in a large number of RNA-associated proteins. The structure of the S1 RNA-binding domain from the Escherichia coli polynucleotide phosphorylase has been determined using NMR methods and consists of a five-stranded antiparallel beta barrel. Conserved residues on one face of the barrel and adjacent loops form the putative RNA-binding site []. The structure of the S1 domain is very similar to that of cold shock proteins. This suggests that they may both be derived from an ancient nucleic acid-binding protein []. More information about these proteins can be found at Protein of the Month: RNA Exosomes []. This entry does not include translation initiation factor IF-1 S1 domains.; GO: 0003723 RNA binding; PDB: 3L7Z_F 2JE6_I 2JEA_I 2JEB_I 1E3P_A 2Y0S_E 1WI5_A 2BH8_A 2CQO_A 2EQS_A ....
Probab=66.39 E-value=33 Score=23.65 Aligned_cols=49 Identities=16% Similarity=-0.025 Sum_probs=35.7
Q ss_pred CCCCcEEEEEEeeeCCCCcEEEEEcCCCcEEEecC--------------CCCCcEEEEEEEeecC
Q 038639 76 PIRGQELELVCESLAYKGKGVCKVADTGFVVLCDR--------------VLPGEKFIGRVTRKKG 126 (229)
Q Consensus 76 ~k~~~~i~l~I~~l~~~G~GVar~~~~G~vVFVpg--------------aLPGE~V~vrI~k~kk 126 (229)
++.|++++.+|.++...|.-|--- .+..-|||- -.+||.++++|.+...
T Consensus 2 ~~~G~iv~g~V~~v~~~g~~V~l~--~~~~g~ip~~~l~~~~~~~~~~~~~~G~~v~v~v~~vd~ 64 (74)
T PF00575_consen 2 LKEGDIVEGKVTSVEDFGVFVDLG--NGIEGFIPISELSDDRIDDPSEVYKIGQTVRVKVIKVDK 64 (74)
T ss_dssp SSTTSEEEEEEEEEETTEEEEEES--TSSEEEEEGGGSSSSEESSSHGTCETTCEEEEEEEEEET
T ss_pred CCCCCEEEEEEEEEECCEEEEEEC--CcEEEEEEeehhcCccccccccccCCCCEEEEEEEEEEC
Confidence 578999999999999976655433 255666652 2469999999988644
No 18
>TIGR02062 RNase_B exoribonuclease II. This family consists of exoribonuclease II, the product of the rnb gene, as found in a number of gamma proteobacteria. In Escherichia coli, it is one of eight different exoribonucleases. It is involved in mRNA degradation and tRNA precursor end processing.
Probab=65.48 E-value=13 Score=37.49 Aligned_cols=42 Identities=24% Similarity=0.316 Sum_probs=31.9
Q ss_pred EEEEEEeeeCCCCcEEEEEcCCCcEEEec-----CCCCCcEEEEEEEee
Q 038639 81 ELELVCESLAYKGKGVCKVADTGFVVLCD-----RVLPGEKFIGRVTRK 124 (229)
Q Consensus 81 ~i~l~I~~l~~~G~GVar~~~~G~vVFVp-----gaLPGE~V~vrI~k~ 124 (229)
.++.+| +.+.+|+|.+..+ ++.-+||| ++++||+|.++|++.
T Consensus 18 ~~~G~i-~~~~kGfgFv~~~-~~~difI~~~~l~~A~~GD~V~v~i~~~ 64 (639)
T TIGR02062 18 RVEGVV-KATEKGFGFLEVD-AQKSYFIPPPQMKKVMHGDKIIAVIHSE 64 (639)
T ss_pred eEEEEE-EECCCccEEEEEC-CCCcEEEChHHHccCCCCCEEEEEEecC
Confidence 344444 4778999999755 23379997 899999999998864
No 19
>smart00316 S1 Ribosomal protein S1-like RNA-binding domain.
Probab=63.06 E-value=37 Score=22.31 Aligned_cols=47 Identities=17% Similarity=0.032 Sum_probs=34.1
Q ss_pred CCcEEEEEEeeeCCCCcEEEEEcCCCcEEEecC--------------CCCCcEEEEEEEeecC
Q 038639 78 RGQELELVCESLAYKGKGVCKVADTGFVVLCDR--------------VLPGEKFIGRVTRKKG 126 (229)
Q Consensus 78 ~~~~i~l~I~~l~~~G~GVar~~~~G~vVFVpg--------------aLPGE~V~vrI~k~kk 126 (229)
.|+.++.+|.+....|.-+--.. +...|++. --+||.+++++.+...
T Consensus 2 ~G~~v~g~V~~v~~~g~~v~i~~--~~~g~l~~~~~~~~~~~~~~~~~~~G~~v~~~V~~~~~ 62 (72)
T smart00316 2 VGDVVEGTVTEITPFGAFVDLGN--GVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDE 62 (72)
T ss_pred CCCEEEEEEEEEEccEEEEEeCC--CCEEEEEHHHCCccccCCHHHeecCCCEEEEEEEEEeC
Confidence 58889999999998776664332 45566652 3689999999988643
No 20
>PRK11642 exoribonuclease R; Provisional
Probab=61.88 E-value=22 Score=37.11 Aligned_cols=41 Identities=12% Similarity=0.113 Sum_probs=31.8
Q ss_pred EEEEEeeeCCCCcEEEEEcCCCcEEEec-----CCCCCcEEEEEEEe
Q 038639 82 LELVCESLAYKGKGVCKVADTGFVVLCD-----RVLPGEKFIGRVTR 123 (229)
Q Consensus 82 i~l~I~~l~~~G~GVar~~~~G~vVFVp-----gaLPGE~V~vrI~k 123 (229)
++.++ +.+.+|+|.+..++++.-+||| +++.||+|.|++.+
T Consensus 85 ~~G~v-~~~~~GfgFv~~e~~~~difI~~~~l~~A~~GD~V~v~i~~ 130 (813)
T PRK11642 85 LKGTV-IGHRDGYGFLRVEGRKDDLYLSSEQMKTCIHGDQVLAQPLG 130 (813)
T ss_pred EEEEE-EECCCccEEEEECCCCCCEEEChHHHccCCCCCEEEEEEcc
Confidence 34444 4778999999876334579997 89999999999876
No 21
>PRK14332 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional
Probab=61.52 E-value=29 Score=33.39 Aligned_cols=49 Identities=10% Similarity=0.124 Sum_probs=37.0
Q ss_pred CCcEEEEEEeeeCCCC--cEEEEEcCCCcEEEec---CC----CCCcEEEEEEEeecCC
Q 038639 78 RGQELELVCESLAYKG--KGVCKVADTGFVVLCD---RV----LPGEKFIGRVTRKKGS 127 (229)
Q Consensus 78 ~~~~i~l~I~~l~~~G--~GVar~~~~G~vVFVp---ga----LPGE~V~vrI~k~kk~ 127 (229)
.|..+++-|+..+.+| .-+||.. .+.+|+++ +. .+||.|.|+|+.....
T Consensus 384 vG~~~~vlve~~~~~~~~~~~gr~~-~~~~v~~~~~~~~~~~~~~G~~v~v~I~~~~~~ 441 (449)
T PRK14332 384 IGRVYSILIENTSRKSEKQLCGRTP-CGRMTVFPLPEGQDLSDMIGSTVSVLIESATSA 441 (449)
T ss_pred cCCEEEEEEEeccCCCCCeEEEECC-CCeEEEEecCCCcccccCCCCEEEEEEEecccC
Confidence 6888899999877664 3468876 46778777 22 5999999999986543
No 22
>PRK05054 exoribonuclease II; Provisional
Probab=60.57 E-value=18 Score=36.65 Aligned_cols=42 Identities=21% Similarity=0.312 Sum_probs=31.5
Q ss_pred EEEEEEeeeCCCCcEEEEEcCCCcEEEec-----CCCCCcEEEEEEEee
Q 038639 81 ELELVCESLAYKGKGVCKVADTGFVVLCD-----RVLPGEKFIGRVTRK 124 (229)
Q Consensus 81 ~i~l~I~~l~~~G~GVar~~~~G~vVFVp-----gaLPGE~V~vrI~k~ 124 (229)
.++.++ +.+.+|+|.+..+ ++.-+||| ++++||+|.++|.+.
T Consensus 21 ~~~G~~-~~~~~gfgFv~~~-~~~difI~~~~l~~a~~GD~V~v~i~~~ 67 (644)
T PRK05054 21 RVEGVV-KATEKGFGFLEVD-AQKSYFIPPPQMKKVMHGDRIIAVIHTE 67 (644)
T ss_pred eEEEEE-EECCCccEEEEEC-CCCcEEEChHHHccCCCCCEEEEEEecC
Confidence 344444 4778999999765 22379997 899999999998764
No 23
>PRK10943 cold shock-like protein CspC; Provisional
Probab=60.31 E-value=48 Score=23.60 Aligned_cols=46 Identities=15% Similarity=0.109 Sum_probs=33.6
Q ss_pred EEEEEeeeCC-CCcEEEEEcCCCcEEEec-------C---CCCCcEEEEEEEeecCC
Q 038639 82 LELVCESLAY-KGKGVCKVADTGFVVLCD-------R---VLPGEKFIGRVTRKKGS 127 (229)
Q Consensus 82 i~l~I~~l~~-~G~GVar~~~~G~vVFVp-------g---aLPGE~V~vrI~k~kk~ 127 (229)
++.+|..++. +|+|....++++.-|||. + ..+||+|+..+...+++
T Consensus 4 ~~G~Vk~f~~~kGfGFI~~~~g~~dvFvH~s~l~~~g~~~l~~G~~V~f~~~~~~~g 60 (69)
T PRK10943 4 IKGQVKWFNESKGFGFITPADGSKDVFVHFSAIQGNGFKTLAEGQNVEFEIQDGQKG 60 (69)
T ss_pred cceEEEEEeCCCCcEEEecCCCCeeEEEEhhHccccCCCCCCCCCEEEEEEEECCCC
Confidence 4577777777 999988776345567763 2 46899999999886553
No 24
>PRK14339 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional
Probab=58.10 E-value=46 Score=31.65 Aligned_cols=49 Identities=18% Similarity=0.160 Sum_probs=37.4
Q ss_pred CCcEEEEEEeeeCCCCcEEEEEcCCCcEEEecCC--CCCcEEEEEEEeecCC
Q 038639 78 RGQELELVCESLAYKGKGVCKVADTGFVVLCDRV--LPGEKFIGRVTRKKGS 127 (229)
Q Consensus 78 ~~~~i~l~I~~l~~~G~GVar~~~~G~vVFVpga--LPGE~V~vrI~k~kk~ 127 (229)
.|..+++-|+....+|.-+|+.+ ....|++++. ++|+.|.|+|+.....
T Consensus 362 vG~~~~vlve~~~~~~~~~g~t~-~~~~v~~~~~~~~~G~~~~v~i~~~~~~ 412 (420)
T PRK14339 362 VGKTHVVLFEELRANGGVAGRSD-NNKLVQVKGSEELLGEFVKVKITNASRG 412 (420)
T ss_pred CCCEEEEEEEEecCCCeEEEECC-CCeEEEECCCCCCCCCEEEEEEEeeecC
Confidence 57888899987766777678876 3557777754 5899999999886554
No 25
>PRK14330 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional
Probab=57.89 E-value=46 Score=31.61 Aligned_cols=50 Identities=14% Similarity=0.114 Sum_probs=38.2
Q ss_pred CCcEEEEEEeeeCCCCcEEEEEcCCCcEEEecCC--CCCcEEEEEEEeecCCe
Q 038639 78 RGQELELVCESLAYKGKGVCKVADTGFVVLCDRV--LPGEKFIGRVTRKKGSY 128 (229)
Q Consensus 78 ~~~~i~l~I~~l~~~G~GVar~~~~G~vVFVpga--LPGE~V~vrI~k~kk~y 128 (229)
.|..+++-|+....+|.-+|+.+ ++..|++++. ++|+.|.|+|++.+...
T Consensus 373 ~G~~~~vlve~~~~~~~~~g~t~-~~~~v~~~~~~~~~g~~~~v~i~~~~~~~ 424 (434)
T PRK14330 373 LGKTVEIIVEAKAKNGLFYGRDI-RNKIIAFEGEEELIGRFADVKIEKITAGP 424 (434)
T ss_pred CCCEEEEEEEEccCCCeEEEECC-CCEEEEECCCCCCCCCEEEEEEEEeecCe
Confidence 57788898887666676668876 5777877754 59999999999876543
No 26
>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=57.88 E-value=66 Score=23.00 Aligned_cols=50 Identities=12% Similarity=0.080 Sum_probs=34.0
Q ss_pred CCCCCcEEEEEEeeeCCCCcEEEEEcCCCcEEEec------------------CCCCCcEEEEEEEeecC
Q 038639 75 KPIRGQELELVCESLAYKGKGVCKVADTGFVVLCD------------------RVLPGEKFIGRVTRKKG 126 (229)
Q Consensus 75 ~~k~~~~i~l~I~~l~~~G~GVar~~~~G~vVFVp------------------gaLPGE~V~vrI~k~kk 126 (229)
.+++|+.++.+|.++...|.-+.-.+ +..-|++ ..-+||.++++|.....
T Consensus 3 ~p~~GdiV~g~V~~i~~~g~~v~i~~--~~~G~l~~se~~~~~~~~~~~~~~~~l~vGd~i~~~V~~~~~ 70 (86)
T cd05789 3 IPEVGDVVIGRVTEVGFKRWKVDINS--PYDAVLPLSEVNLPRTDEDELNMRSYLDEGDLIVAEVQSVDS 70 (86)
T ss_pred cCCCCCEEEEEEEEECCCEEEEECCC--CeEEEEEHHHccCCCCccchHHHHhhCCCCCEEEEEEEEECC
Confidence 35789999999999888775553221 2222333 14699999999988643
No 27
>PRK09507 cspE cold shock protein CspE; Reviewed
Probab=56.07 E-value=61 Score=23.04 Aligned_cols=46 Identities=15% Similarity=0.109 Sum_probs=33.3
Q ss_pred EEEEEeeeCC-CCcEEEEEcCCCcEEEec-------C---CCCCcEEEEEEEeecCC
Q 038639 82 LELVCESLAY-KGKGVCKVADTGFVVLCD-------R---VLPGEKFIGRVTRKKGS 127 (229)
Q Consensus 82 i~l~I~~l~~-~G~GVar~~~~G~vVFVp-------g---aLPGE~V~vrI~k~kk~ 127 (229)
++.+|.-++. +|+|....++.+.-|||. + .-+||+|+..+.+..+.
T Consensus 4 ~~G~Vk~f~~~kGyGFI~~~~g~~dvfvH~s~l~~~g~~~l~~G~~V~f~~~~~~~G 60 (69)
T PRK09507 4 IKGNVKWFNESKGFGFITPEDGSKDVFVHFSAIQTNGFKTLAEGQRVEFEITNGAKG 60 (69)
T ss_pred cceEEEEEeCCCCcEEEecCCCCeeEEEEeecccccCCCCCCCCCEEEEEEEECCCC
Confidence 4567777775 999998876334567773 2 47899999999886554
No 28
>PF00313 CSD: 'Cold-shock' DNA-binding domain; InterPro: IPR002059 When Escherichia coli is exposed to a temperature drop from 37 to 10 degrees centigrade, a 4-5 hour lag phase occurs, after which growth is resumed at a reduced rate []. During the lag phase, the expression of around 13 proteins, which contain specific DNA-binding regions [], is increased 2-10 fold. These so-called 'cold shock' proteins are thought to help the cell to survive in temperatures lower than optimum growth temperature, by contrast with heat shock proteins, which help the cell to survive in temperatures greater than the optimum, possibly by condensation of the chromosome and organisation of the prokaryotic nucleoid []. A conserved domain of about 70 amino acids has been found in prokaryotic and eukaryotic DNA-binding proteins [, , ]. This domain is known as the 'cold-shock domain' (CSD), part of which is highly similar [] to the RNP-1 RNA-binding motif.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1HZC_A 1I5F_A 1HZ9_B 1C9O_B 1HZB_B 1HZA_A 2HAX_B 2L15_A 2LSS_A 3I2Z_B ....
Probab=54.65 E-value=67 Score=21.98 Aligned_cols=46 Identities=17% Similarity=0.133 Sum_probs=32.5
Q ss_pred EEEEeeeCC-CCcEEEEEcCCCcEEEec----------CCCCCcEEEEEEEeecCCe
Q 038639 83 ELVCESLAY-KGKGVCKVADTGFVVLCD----------RVLPGEKFIGRVTRKKGSY 128 (229)
Q Consensus 83 ~l~I~~l~~-~G~GVar~~~~G~vVFVp----------gaLPGE~V~vrI~k~kk~y 128 (229)
..+|..++. +|+|....++.+.-+|+. -.-.||.|+..+....++.
T Consensus 2 ~G~V~~~~~~kgyGFI~~~~~~~diFfh~s~~~~~~~~~l~~G~~V~F~~~~~~~g~ 58 (66)
T PF00313_consen 2 TGTVKWFDDEKGYGFITSDDGGEDIFFHISDLSGNGFRSLKEGDRVEFEVEEGKKGP 58 (66)
T ss_dssp EEEEEEEETTTTEEEEEETTSSSEEEEEGGGBCSSSSTS--TTSEEEEEEEECTTSE
T ss_pred eEEEEEEECCCCceEEEEcccceeEEeccccccccccccCCCCCEEEEEEEECCCCC
Confidence 467777776 899999887444467774 2358999999998865543
No 29
>cd04465 S1_RPS1_repeat_ec2_hs2 S1_RPS1_repeat_ec2_hs2: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain.While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 2 of the Escherichia coli and Homo sapiens RPS1 (ec2 and hs2, respectively). Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=54.40 E-value=57 Score=22.23 Aligned_cols=45 Identities=13% Similarity=0.039 Sum_probs=32.9
Q ss_pred CcEEEEEEeeeCCCCcEEEEEcCCCcEEEecC------------CCCCcEEEEEEEeecC
Q 038639 79 GQELELVCESLAYKGKGVCKVADTGFVVLCDR------------VLPGEKFIGRVTRKKG 126 (229)
Q Consensus 79 ~~~i~l~I~~l~~~G~GVar~~~~G~vVFVpg------------aLPGE~V~vrI~k~kk 126 (229)
|+.++.+|.+....|.=+-. + |...|+|. ...||.++++|.+..+
T Consensus 1 G~iv~g~V~~v~~~G~~v~l-~--g~~gfip~s~~~~~~~~~~~~~vG~~i~~~i~~vd~ 57 (67)
T cd04465 1 GEIVEGKVTEKVKGGLIVDI-E--GVRAFLPASQVDLRPVEDLDEYVGKELKFKIIEIDR 57 (67)
T ss_pred CCEEEEEEEEEECCeEEEEE-C--CEEEEEEHHHCCCcccCChHHhCCCEEEEEEEEEeC
Confidence 56788999999887766544 4 66667762 1479999999988654
No 30
>PRK14336 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional
Probab=53.46 E-value=60 Score=30.85 Aligned_cols=50 Identities=16% Similarity=0.052 Sum_probs=37.0
Q ss_pred CCcEEEEEEeeeCCCCcEEEEEcCCCcEEEecCC--CCCcEEEEEEEeecCCee
Q 038639 78 RGQELELVCESLAYKGKGVCKVADTGFVVLCDRV--LPGEKFIGRVTRKKGSYA 129 (229)
Q Consensus 78 ~~~~i~l~I~~l~~~G~GVar~~~~G~vVFVpga--LPGE~V~vrI~k~kk~y~ 129 (229)
.|..+++-|+. ..+|.-+|+.. ++..|++++. ++|+.|.|+|+.......
T Consensus 357 ~G~~~~vlve~-~~~~~~~g~~~-~~~~v~~~~~~~~~G~~~~v~i~~~~~~~l 408 (418)
T PRK14336 357 MDTFAEVLVEG-LQKNKWQGRTL-GGKLVFLESDLPLEGCLVNVKIFKTSPWSL 408 (418)
T ss_pred CCCEEEEEEEE-cCCCeEEEECC-CCeEEEECCCCCCCCCEEEEEEEEeecccE
Confidence 57788888887 34455568876 5677888865 479999999998765543
No 31
>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=52.05 E-value=88 Score=22.62 Aligned_cols=41 Identities=17% Similarity=0.160 Sum_probs=24.4
Q ss_pred EEEEEeeeCCCCcEEEEEcCCCcEE--EecC--------CCCCcEEEEEEEe
Q 038639 82 LELVCESLAYKGKGVCKVADTGFVV--LCDR--------VLPGEKFIGRVTR 123 (229)
Q Consensus 82 i~l~I~~l~~~G~GVar~~~~G~vV--FVpg--------aLPGE~V~vrI~k 123 (229)
++..++.+-.+|.-.++.+ +|..+ +++| .+|||+|.+.+..
T Consensus 7 ~~G~V~e~L~~~~f~V~l~-ng~~vla~i~GKmr~~rI~I~~GD~V~Ve~sp 57 (68)
T TIGR00008 7 MEGKVTESLPNAMFRVELE-NGHEVLAHISGKIRMHYIRILPGDKVKVELSP 57 (68)
T ss_pred EEEEEEEECCCCEEEEEEC-CCCEEEEEecCcchhccEEECCCCEEEEEECc
Confidence 3455555555555555554 23322 4454 6899999998754
No 32
>PRK08582 hypothetical protein; Provisional
Probab=50.22 E-value=80 Score=25.57 Aligned_cols=49 Identities=16% Similarity=0.064 Sum_probs=32.4
Q ss_pred CCCCCcEEEEEEeeeCCCCcEEEEEcCCCcEEEec--------------CCCCCcEEEEEEEeec
Q 038639 75 KPIRGQELELVCESLAYKGKGVCKVADTGFVVLCD--------------RVLPGEKFIGRVTRKK 125 (229)
Q Consensus 75 ~~k~~~~i~l~I~~l~~~G~GVar~~~~G~vVFVp--------------gaLPGE~V~vrI~k~k 125 (229)
.++.|++++.+|..+...|.-|.-.+ +..-+|+ ..-.||.|+|+|....
T Consensus 2 ~~kvG~iv~G~V~~I~~fG~fV~L~~--~~~GlVhiSels~~~v~~~~~~l~vGD~VkvkV~~id 64 (139)
T PRK08582 2 SIEVGSKLQGKVTGITNFGAFVELPE--GKTGLVHISEVADNYVKDINDHLKVGDEVEVKVLNVE 64 (139)
T ss_pred CCcCCCEEEEEEEEEECCeEEEEECC--CCEEEEEeeccCcccccccccccCCCCEEEEEEEEEC
Confidence 45789999999998888776664332 2222221 2356999999988864
No 33
>PRK14327 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional
Probab=48.54 E-value=69 Score=31.57 Aligned_cols=51 Identities=20% Similarity=0.103 Sum_probs=37.7
Q ss_pred CCcEEEEEEeeeCCCCc--EEEEEcCCCcEEEecCC--CCCcEEEEEEEeecCCee
Q 038639 78 RGQELELVCESLAYKGK--GVCKVADTGFVVLCDRV--LPGEKFIGRVTRKKGSYA 129 (229)
Q Consensus 78 ~~~~i~l~I~~l~~~G~--GVar~~~~G~vVFVpga--LPGE~V~vrI~k~kk~y~ 129 (229)
.|..+++-|+..+.++. -.|+.+ ....|++++. ++|+.|.|+|+..+..+.
T Consensus 444 ~G~~~~VLve~~~~~~~~~~~Grt~-~~~~V~~~~~~~~~G~~v~v~I~~~~~~~l 498 (509)
T PRK14327 444 EGQTVEVLVEGESKKNPEVLAGYTR-KNKLVNFKGPKSLIGQLVKVKITEAKTWSL 498 (509)
T ss_pred CCCEEEEEEEecccCCCceEEEECC-CCcEEEECCCCCCCCCEEEEEEEeeecceE
Confidence 68889999998766544 447876 3566777753 589999999998765543
No 34
>PRK14331 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional
Probab=48.29 E-value=81 Score=30.04 Aligned_cols=49 Identities=14% Similarity=0.091 Sum_probs=36.7
Q ss_pred CCcEEEEEEeeeCCCCcEEEEEcCCCcEEEecCC--CCCcEEEEEEEeecCC
Q 038639 78 RGQELELVCESLAYKGKGVCKVADTGFVVLCDRV--LPGEKFIGRVTRKKGS 127 (229)
Q Consensus 78 ~~~~i~l~I~~l~~~G~GVar~~~~G~vVFVpga--LPGE~V~vrI~k~kk~ 127 (229)
.|..+++-|+....+|.-+|+.+ ....|++++. .+|+.|.++|+.....
T Consensus 377 ~g~~~~vlve~~~~~~~~~g~t~-~~~~v~~~~~~~~~g~~~~v~i~~~~~~ 427 (437)
T PRK14331 377 EGTVQEVLVEEEKEGNKLIGRTR-TNKWVSIEGSQEMLGKIVKVKIIKSNPF 427 (437)
T ss_pred CCCEEEEEEEEecCCCcEEEECC-CCCEEEECCCCCCCCCEEEEEEEeeecc
Confidence 57788888887655666678876 3456778754 5899999999987654
No 35
>PRK14340 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional
Probab=47.27 E-value=78 Score=30.40 Aligned_cols=49 Identities=24% Similarity=0.303 Sum_probs=36.6
Q ss_pred CCcEEEEEEeeeCCC--CcEEEEEcCCCcEEEecCC--CCCcEEEEEEEeecCC
Q 038639 78 RGQELELVCESLAYK--GKGVCKVADTGFVVLCDRV--LPGEKFIGRVTRKKGS 127 (229)
Q Consensus 78 ~~~~i~l~I~~l~~~--G~GVar~~~~G~vVFVpga--LPGE~V~vrI~k~kk~ 127 (229)
.|+.+++-|+.-+.+ |.-+||.+ .+..|++++. .+|+.|.|+|+.....
T Consensus 381 vG~~~~vlve~~~~~~~~~~~grt~-~~~~v~~~~~~~~~G~~~~v~i~~~~~~ 433 (445)
T PRK14340 381 VGSVVEVLAESESRRSSEQLMGRTD-GNRVVVFDRGGFQPGDLVRVRITGSTSA 433 (445)
T ss_pred CCCEEEEEEEecccCCCCeEEEECC-CCeEEEECCCCCCCCCEEEEEEEecccc
Confidence 688889999876555 44568876 4667888743 5899999999987654
No 36
>PRK05807 hypothetical protein; Provisional
Probab=47.24 E-value=98 Score=24.92 Aligned_cols=48 Identities=19% Similarity=0.032 Sum_probs=33.8
Q ss_pred CCCCCcEEEEEEeeeCCCCcEEEEEcCCCcEEEecC--------------CCCCcEEEEEEEeec
Q 038639 75 KPIRGQELELVCESLAYKGKGVCKVADTGFVVLCDR--------------VLPGEKFIGRVTRKK 125 (229)
Q Consensus 75 ~~k~~~~i~l~I~~l~~~G~GVar~~~~G~vVFVpg--------------aLPGE~V~vrI~k~k 125 (229)
.++.|+.++.+|..+...|.-|.. + +..-+|+. .-.||.|++.|....
T Consensus 2 ~~~vG~vv~G~Vt~i~~~GafV~L-~--~~~Glvhiseis~~~v~~~~~~~kvGd~V~VkV~~id 63 (136)
T PRK05807 2 TLKAGSILEGTVVNITNFGAFVEV-E--GKTGLVHISEVADTYVKDIREHLKEQDKVKVKVISID 63 (136)
T ss_pred CccCCCEEEEEEEEEECCeEEEEE-C--CEEEEEEhhhcccccccCccccCCCCCEEEEEEEEEC
Confidence 356799999999999888877755 3 33333321 257999999887764
No 37
>COG2100 Predicted Fe-S oxidoreductase [General function prediction only]
Probab=47.16 E-value=96 Score=29.52 Aligned_cols=52 Identities=19% Similarity=0.196 Sum_probs=39.8
Q ss_pred CCCCCcEEEEEEeeeC-CCCcEEEEEcCCCcEEEecC-----CCCCcEEEEEEEeecCCe
Q 038639 75 KPIRGQELELVCESLA-YKGKGVCKVADTGFVVLCDR-----VLPGEKFIGRVTRKKGSY 128 (229)
Q Consensus 75 ~~k~~~~i~l~I~~l~-~~G~GVar~~~~G~vVFVpg-----aLPGE~V~vrI~k~kk~y 128 (229)
..+.|+.+.++|.--+ .+|+=+|..- ++++-|.+ .++|++|+++|++.|-+.
T Consensus 351 PF~rGevv~aevV~~Gr~kGEmlavAr--dRvIav~~~~~~~~~vG~~vkvrIvr~khnI 408 (414)
T COG2100 351 PFKRGEVVKAEVVLPGRLKGEMLAVAR--DRVIAVINSNEGALLVGDRVKVRIVRTKHNI 408 (414)
T ss_pred ccccCcEEEEEEEecceecceEEEEec--ccEEEEecCchhhhccCceEEEEEEEccCce
Confidence 4467999888777443 5888888775 78887763 389999999999987653
No 38
>PRK09937 stationary phase/starvation inducible regulatory protein CspD; Provisional
Probab=46.64 E-value=86 Score=22.75 Aligned_cols=44 Identities=14% Similarity=0.072 Sum_probs=31.4
Q ss_pred EEEeeeCC-CCcEEEEEcCCCcEEEec----------CCCCCcEEEEEEEeecCC
Q 038639 84 LVCESLAY-KGKGVCKVADTGFVVLCD----------RVLPGEKFIGRVTRKKGS 127 (229)
Q Consensus 84 l~I~~l~~-~G~GVar~~~~G~vVFVp----------gaLPGE~V~vrI~k~kk~ 127 (229)
.+|.-++. +|+|....++++.-|||- ..-+||+|+..+.+..+.
T Consensus 4 G~Vkwfn~~KGfGFI~~~~gg~dVFvH~s~i~~~g~~~l~~G~~V~f~~~~~~~G 58 (74)
T PRK09937 4 GTVKWFNNAKGFGFICPEGGGEDIFAHYSTIQMDGYRTLKAGQSVQFDVHQGPKG 58 (74)
T ss_pred eEEEEEeCCCCeEEEeeCCCCccEEEEEeeccccCCCCCCCCCEEEEEEEECCCC
Confidence 45666655 899988765445667764 257899999999887554
No 39
>cd04458 CSP_CDS Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in eukaryotes, prokaryotes, and archaea. CSP's include the major cold-shock proteins CspA and CspB in bacteria and the eukaryotic gene regulatory factor Y-box protein. CSP expression is up-regulated by an abrupt drop in growth temperature. CSP's are also expressed under normal condition at lower level. The function of cold-shock proteins is not fully understood. They preferentially bind poly-pyrimidine region of single-stranded RNA and DNA. CSP's are thought to bind mRNA and regulate ribosomal translation, mRNA degradation, and the rate of transcription termination. The human Y-box protein, which contains a CSD, regulates transcription and translation of genes that contain the Y-box sequence in their promoters. This specific ssDNA-binding properties of CSD are required for the binding of Y-box protein to the promoter's Y-box sequence, thereby regulating transcription.
Probab=46.53 E-value=87 Score=21.33 Aligned_cols=44 Identities=16% Similarity=0.119 Sum_probs=31.5
Q ss_pred EEEeeeCC-CCcEEEEEcCCCcEEEec----------CCCCCcEEEEEEEeecCC
Q 038639 84 LVCESLAY-KGKGVCKVADTGFVVLCD----------RVLPGEKFIGRVTRKKGS 127 (229)
Q Consensus 84 l~I~~l~~-~G~GVar~~~~G~vVFVp----------gaLPGE~V~vrI~k~kk~ 127 (229)
.+|..++. +|+|....++.|.-+|+. -.-+|+.|++.+....++
T Consensus 3 G~Vk~~~~~kGfGFI~~~~~g~diffh~~~~~~~~~~~~~~G~~V~f~~~~~~~g 57 (65)
T cd04458 3 GTVKWFDDEKGFGFITPDDGGEDVFVHISALEGDGFRSLEEGDRVEFELEEGDKG 57 (65)
T ss_pred EEEEEEECCCCeEEEecCCCCcCEEEEhhHhhccCCCcCCCCCEEEEEEEECCCC
Confidence 45666666 899999887435667663 357899999998886443
No 40
>PRK14325 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional
Probab=46.42 E-value=85 Score=29.89 Aligned_cols=49 Identities=18% Similarity=0.146 Sum_probs=35.9
Q ss_pred CCcEEEEEEeeeCCC-CcEEEEEcCCCcEEEecCC--CCCcEEEEEEEeecCC
Q 038639 78 RGQELELVCESLAYK-GKGVCKVADTGFVVLCDRV--LPGEKFIGRVTRKKGS 127 (229)
Q Consensus 78 ~~~~i~l~I~~l~~~-G~GVar~~~~G~vVFVpga--LPGE~V~vrI~k~kk~ 127 (229)
.|+.+++-|+.-..+ |.-+|+.+ ....|+|++. ++|+.|.|+|+.....
T Consensus 381 ~g~~~~vlve~~~~~~~~~~g~t~-~~~~v~~~~~~~~~g~~~~v~i~~~~~~ 432 (444)
T PRK14325 381 VGTVQRVLVEGPSRKDGQLIGRTE-NNRVVNFEGDPDLIGQFVDVKITEAYPN 432 (444)
T ss_pred cCCEEEEEEEEeecCCCeEEEECC-CCcEEEECCCCCCCCCEEEEEEEEcccc
Confidence 578888888865443 66668875 3557888764 5899999999986554
No 41
>PRK14333 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional
Probab=46.23 E-value=87 Score=29.96 Aligned_cols=49 Identities=16% Similarity=0.197 Sum_probs=35.1
Q ss_pred CCcEEEEEEeeeCCC--CcEEEEEcCCCcEEEecCC---CCCcEEEEEEEeecCC
Q 038639 78 RGQELELVCESLAYK--GKGVCKVADTGFVVLCDRV---LPGEKFIGRVTRKKGS 127 (229)
Q Consensus 78 ~~~~i~l~I~~l~~~--G~GVar~~~~G~vVFVpga---LPGE~V~vrI~k~kk~ 127 (229)
.|..+++-|+....+ |.-+||.+ ....|++++. .+|+.|.|+|+.....
T Consensus 387 ~G~~~~vlve~~~~~~~~~~~g~t~-~~~~v~~~~~~~~~~g~~~~v~i~~~~~~ 440 (448)
T PRK14333 387 LGRIEEVLVEGINPKDPSQVMGRTR-TNRLTFFEGDINQLKGDLVKVKITEVRAF 440 (448)
T ss_pred CCCEEEEEEEecccCCCceEEEECC-CCcEEEEcCCCcCCCCCEEEEEEEeeecc
Confidence 578889999865444 55568876 3456777653 5899999999986543
No 42
>TIGR00089 RNA modification enzyme, MiaB family. This subfamily is aparrently a part of a larger superfamily of enzymes utilizing both a 4Fe4S cluster and S-adenosyl methionine (SAM) to initiate radical reactions. MiaB acts on a particular isoprenylated Adenine base of certain tRNAs causing thiolation at an aromatic carbon, and probably also transferring a methyl grouyp from SAM to the thiol. The particular substrate of the three other clades is unknown but may be very closely related.
Probab=45.66 E-value=89 Score=29.51 Aligned_cols=49 Identities=18% Similarity=0.157 Sum_probs=35.7
Q ss_pred CCcEEEEEEeee--CCCCcEEEEEcCCCcEEEecC---C-CCCcEEEEEEEeecCC
Q 038639 78 RGQELELVCESL--AYKGKGVCKVADTGFVVLCDR---V-LPGEKFIGRVTRKKGS 127 (229)
Q Consensus 78 ~~~~i~l~I~~l--~~~G~GVar~~~~G~vVFVpg---a-LPGE~V~vrI~k~kk~ 127 (229)
.|+.+++-|+.. ..+|.-+|+.+ ....|+|++ . .+|+.|.|+|+..+..
T Consensus 371 ~G~~~~vlve~~~~~~~~~~~g~~~-~~~~v~~~~~~~~~~~g~~~~v~i~~~~~~ 425 (429)
T TIGR00089 371 VGKTLEVLVEGEEGKKEGELTGRTE-NYKPVVFEGGVGKNLIGKFVKVKITEAAEY 425 (429)
T ss_pred CCCEEEEEEEecccCCCCeEEEECC-CCeEEEECCCCCcCCCCCEEEEEEEecccc
Confidence 588888888863 34466678876 345788886 2 5899999999886543
No 43
>PRK12442 translation initiation factor IF-1; Reviewed
Probab=45.01 E-value=1.3e+02 Score=22.85 Aligned_cols=14 Identities=21% Similarity=0.525 Sum_probs=11.4
Q ss_pred CCCCCcEEEEEEEe
Q 038639 110 RVLPGEKFIGRVTR 123 (229)
Q Consensus 110 gaLPGE~V~vrI~k 123 (229)
-.+|||+|.|++..
T Consensus 46 rIl~GD~V~VE~sp 59 (87)
T PRK12442 46 RILAGDRVTLELSP 59 (87)
T ss_pred EecCCCEEEEEECc
Confidence 46899999998765
No 44
>PRK14335 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional
Probab=44.90 E-value=85 Score=30.17 Aligned_cols=50 Identities=16% Similarity=0.147 Sum_probs=36.4
Q ss_pred CCcEEEEEEeeeCCC--CcEEEEEcCCCcEEEecCC----CCCcEEEEEEEeecCCe
Q 038639 78 RGQELELVCESLAYK--GKGVCKVADTGFVVLCDRV----LPGEKFIGRVTRKKGSY 128 (229)
Q Consensus 78 ~~~~i~l~I~~l~~~--G~GVar~~~~G~vVFVpga----LPGE~V~vrI~k~kk~y 128 (229)
.|..+++-|+.-..+ |.-+||.+ .+..|++++. ++|+.|.|+|+......
T Consensus 390 ~G~~~~vlve~~~~~~~~~~~g~t~-~~~~v~~~~~~~~~~~G~~~~v~i~~~~~~~ 445 (455)
T PRK14335 390 VGKTLPVLVESRSRNNPEELFGHTE-LGEMTVLEGKVDETLIGRFVDVQLKELRGRT 445 (455)
T ss_pred CCCEEEEEEeccccCCCCeeEEECC-CCeEEEEcCCcccCCCCCEEEEEEEEcccCe
Confidence 578888999865444 45568876 4667877753 48999999999865543
No 45
>PRK15463 cold shock-like protein CspF; Provisional
Probab=44.66 E-value=1e+02 Score=22.08 Aligned_cols=45 Identities=13% Similarity=0.044 Sum_probs=33.7
Q ss_pred EEEEeeeCC-CCcEEEEEcCCCcEEEec----------CCCCCcEEEEEEEeecCC
Q 038639 83 ELVCESLAY-KGKGVCKVADTGFVVLCD----------RVLPGEKFIGRVTRKKGS 127 (229)
Q Consensus 83 ~l~I~~l~~-~G~GVar~~~~G~vVFVp----------gaLPGE~V~vrI~k~kk~ 127 (229)
..+|.-++. +|+|....++++.-|||. ..-+||+|++.+.+.+++
T Consensus 6 ~G~Vk~fn~~kGfGFI~~~~g~~DvFvH~sal~~~g~~~l~~G~~V~f~v~~~~~G 61 (70)
T PRK15463 6 TGIVKTFDGKSGKGLITPSDGRKDVQVHISALNLRDAEELTTGLRVEFCRINGLRG 61 (70)
T ss_pred eEEEEEEeCCCceEEEecCCCCccEEEEehhhhhcCCCCCCCCCEEEEEEEECCCC
Confidence 577777777 899988776445567764 256899999999887655
No 46
>PRK14998 cold shock-like protein CspD; Provisional
Probab=44.24 E-value=90 Score=22.54 Aligned_cols=44 Identities=14% Similarity=0.068 Sum_probs=31.2
Q ss_pred EEEeeeCC-CCcEEEEEcCCCcEEEec----------CCCCCcEEEEEEEeecCC
Q 038639 84 LVCESLAY-KGKGVCKVADTGFVVLCD----------RVLPGEKFIGRVTRKKGS 127 (229)
Q Consensus 84 l~I~~l~~-~G~GVar~~~~G~vVFVp----------gaLPGE~V~vrI~k~kk~ 127 (229)
.+|.-++. +|+|....++++.-|||. ..-+||+|+..+.+..+.
T Consensus 4 G~Vkwfn~~kGfGFI~~~~g~~dVFvH~s~l~~~g~~~l~~G~~V~f~~~~~~~G 58 (73)
T PRK14998 4 GTVKWFNNAKGFGFICPEGGGEDIFAHYSTIQMDGYRTLKAGQSVRFDVHQGPKG 58 (73)
T ss_pred eEEEEEeCCCceEEEecCCCCccEEEEeeeecccCCCCCCCCCEEEEEEEECCCC
Confidence 45666665 899988766344567764 257899999999887554
No 47
>PRK14338 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional
Probab=43.21 E-value=1.1e+02 Score=29.56 Aligned_cols=48 Identities=23% Similarity=0.216 Sum_probs=35.8
Q ss_pred CCcEEEEEEeeeCCCCcEEEEEcCCCcEEEecCC--CCCcEEEEEEEeecCC
Q 038639 78 RGQELELVCESLAYKGKGVCKVADTGFVVLCDRV--LPGEKFIGRVTRKKGS 127 (229)
Q Consensus 78 ~~~~i~l~I~~l~~~G~GVar~~~~G~vVFVpga--LPGE~V~vrI~k~kk~ 127 (229)
.|..+++-|+. ..+|.-+|+.+ ....|+|++. .+|+.+.|+|++....
T Consensus 391 ~G~~~~vlve~-~~~~~~~g~~~-~~~~v~~~~~~~~~G~~~~v~i~~~~~~ 440 (459)
T PRK14338 391 LGQTVEVLVEG-EAKGKWRGRTR-GNKLVFFSAPGDWTGKLVPVRITHTSPW 440 (459)
T ss_pred CCCEEEEEEEE-cCCCeEEEECC-CCeEEEECCCCCCCCCEEEEEEEEeecC
Confidence 57788888887 34455668876 3567888754 5899999999986554
No 48
>PRK15464 cold shock-like protein CspH; Provisional
Probab=43.07 E-value=1.1e+02 Score=21.89 Aligned_cols=45 Identities=16% Similarity=0.111 Sum_probs=32.4
Q ss_pred EEEEeeeCC-CCcEEEEEcCCCcEEEec----------CCCCCcEEEEEEEeecCC
Q 038639 83 ELVCESLAY-KGKGVCKVADTGFVVLCD----------RVLPGEKFIGRVTRKKGS 127 (229)
Q Consensus 83 ~l~I~~l~~-~G~GVar~~~~G~vVFVp----------gaLPGE~V~vrI~k~kk~ 127 (229)
+.+|.-++. +|+|....++.+.-|||. ...+||+|++.+.+..+.
T Consensus 6 ~G~Vk~fn~~KGfGFI~~~~g~~DvFvH~s~l~~~g~~~l~~G~~V~f~v~~~~kG 61 (70)
T PRK15464 6 TGIVKTFDRKSGKGFIIPSDGRKEVQVHISAFTPRDAEVLIPGLRVEFCRVNGLRG 61 (70)
T ss_pred eEEEEEEECCCCeEEEccCCCCccEEEEehhehhcCCCCCCCCCEEEEEEEECCCC
Confidence 567777776 899987765334567764 256899999999886554
No 49
>cd04453 S1_RNase_E S1_RNase_E: RNase E and RNase G, S1-like RNA-binding domain. RNase E is an essential endoribonuclease in the processing and degradation of RNA. In addition to its role in mRNA degradation, RNase E has also been implicated in the processing of rRNA, and the maturation of tRNA, 10Sa RNA and the M1 precursor of RNase P. RNase E associates with PNPase (3' to 5' exonuclease), Rhl B (DEAD-box RNA helicase) and enolase (glycolytic enzyme) to form the RNA degradosome. RNase E tends to cut mRNA within single-stranded regions that are rich in A/U nucleotides. The N-terminal region of RNase E contains the catalytic site. Within the conserved N-terminal domain of RNAse E and RNase G, there is an S1-like subdomain, which is an ancient single-stranded RNA-binding domain. S1 domain is an RNA-binding module originally identified in the ribosomal protein S1. The S1 domain is required for RNA cleavage by RNase E. RNase G is paralogous to RNase E with an N-terminal catalytic domain th
Probab=43.06 E-value=1.3e+02 Score=22.12 Aligned_cols=46 Identities=13% Similarity=0.096 Sum_probs=31.6
Q ss_pred CCCcEEEEEEeeeCCC--CcEEEEEcCCCcEEEec-----------------CCCCCcEEEEEEEee
Q 038639 77 IRGQELELVCESLAYK--GKGVCKVADTGFVVLCD-----------------RVLPGEKFIGRVTRK 124 (229)
Q Consensus 77 k~~~~i~l~I~~l~~~--G~GVar~~~~G~vVFVp-----------------gaLPGE~V~vrI~k~ 124 (229)
..|+++..+|+++... |.-| .++ +|..-|++ ..-.||.|.+++.+.
T Consensus 6 ~~G~iy~g~V~~i~~~~~GaFV-~l~-~g~~Gllh~seis~~~~~~v~~~~~~~~~Gd~v~VqV~~~ 70 (88)
T cd04453 6 IVGNIYLGRVKKIVPGLQAAFV-DIG-LGKNGFLHLSDILPAYFKKHKKIAKLLKEGQEILVQVVKE 70 (88)
T ss_pred CCCCEEEEEEEEeccCCcEEEE-EeC-CCCEEEEEhHHcCchhccccCCHHHcCCCCCEEEEEEEEe
Confidence 6899999999999986 3333 332 24444444 255699999999884
No 50
>PRK09890 cold shock protein CspG; Provisional
Probab=42.89 E-value=1.2e+02 Score=21.55 Aligned_cols=45 Identities=13% Similarity=0.066 Sum_probs=32.6
Q ss_pred EEEEeeeCC-CCcEEEEEcCCCcEEEec------C----CCCCcEEEEEEEeecCC
Q 038639 83 ELVCESLAY-KGKGVCKVADTGFVVLCD------R----VLPGEKFIGRVTRKKGS 127 (229)
Q Consensus 83 ~l~I~~l~~-~G~GVar~~~~G~vVFVp------g----aLPGE~V~vrI~k~kk~ 127 (229)
+.+|..++. +|+|....++.+.-|||. . .-+||+|+..+...++.
T Consensus 6 ~G~Vk~f~~~kGfGFI~~~~g~~dvFvH~s~l~~~~~~~l~~G~~V~f~~~~~~~G 61 (70)
T PRK09890 6 TGLVKWFNADKGFGFITPDDGSKDVFVHFTAIQSNEFRTLNENQKVEFSIEQGQRG 61 (70)
T ss_pred eEEEEEEECCCCcEEEecCCCCceEEEEEeeeccCCCCCCCCCCEEEEEEEECCCC
Confidence 577777775 999988876334567764 2 35999999998876544
No 51
>cd05694 S1_Rrp5_repeat_hs2_sc2 S1_Rrp5_repeat_hs2_sc2: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 2 (hs2) and S. cerevisiae S1 repeat 2 (sc2). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=42.34 E-value=1.2e+02 Score=21.51 Aligned_cols=50 Identities=16% Similarity=0.104 Sum_probs=37.5
Q ss_pred CCCCcEEEEEEeeeCCCCcEEEEEcCCCcEEEec--------CCCCCcEEEEEEEeecC
Q 038639 76 PIRGQELELVCESLAYKGKGVCKVADTGFVVLCD--------RVLPGEKFIGRVTRKKG 126 (229)
Q Consensus 76 ~k~~~~i~l~I~~l~~~G~GVar~~~~G~vVFVp--------gaLPGE~V~vrI~k~kk 126 (229)
++.|+.+..+|.++...|.=|---. +|..-|+| ..-+|+.+.++|++..+
T Consensus 2 l~~G~~v~g~V~si~d~G~~v~~g~-~gv~Gfl~~~~~~~~~~~~~Gq~v~~~V~~vd~ 59 (74)
T cd05694 2 LVEGMVLSGCVSSVEDHGYILDIGI-PGTTGFLPKKDAGNFSKLKVGQLLLCVVEKVKD 59 (74)
T ss_pred CCCCCEEEEEEEEEeCCEEEEEeCC-CCcEEEEEHHHCCcccccCCCCEEEEEEEEEEC
Confidence 4678899999999999888776421 25556776 35799999999987643
No 52
>TIGR02063 RNase_R ribonuclease R. This family consists of an exoribonuclease, ribonuclease R, also called VacB. It is one of the eight exoribonucleases reported in E. coli and is broadly distributed throughout the bacteria. In E. coli, double mutants of this protein and polynucleotide phosphorylase are not viable. Scoring between trusted and noise cutoffs to the model are shorter, divergent forms from the Chlamydiae, and divergent forms from the Campylobacterales (including Helicobacter pylori) and Leptospira interrogans.
Probab=41.79 E-value=81 Score=32.13 Aligned_cols=42 Identities=17% Similarity=0.221 Sum_probs=31.3
Q ss_pred EEEEEeeeCCCCcEEEEEcC-CCcEEEec-----CCCCCcEEEEEEEee
Q 038639 82 LELVCESLAYKGKGVCKVAD-TGFVVLCD-----RVLPGEKFIGRVTRK 124 (229)
Q Consensus 82 i~l~I~~l~~~G~GVar~~~-~G~vVFVp-----gaLPGE~V~vrI~k~ 124 (229)
+..++ ..+.+|+|.+..++ .+.-+||| ++++||+|.|+|.+.
T Consensus 69 ~~G~i-~~~~~g~gFv~~~~~~~~di~I~~~~~~~a~~GD~Vlv~I~~~ 116 (709)
T TIGR02063 69 VKGTV-IAHRDGFGFLRPEDDDEDDIFIPPRQMNGAMHGDRVLVRITGK 116 (709)
T ss_pred EEEEE-EECCCccEEEEECCCCCCcEEEChHHhCcCCCCCEEEEEEecc
Confidence 44444 35688999998752 13579997 899999999998763
No 53
>PF13509 S1_2: S1 domain; PDB: 3GO5_A.
Probab=40.50 E-value=78 Score=21.76 Aligned_cols=47 Identities=21% Similarity=-0.005 Sum_probs=26.6
Q ss_pred CcEEEEEEeeeCCCCcEEEEEcCCCcEEEec------CCCCCcEEEEEEEeecCC
Q 038639 79 GQELELVCESLAYKGKGVCKVADTGFVVLCD------RVLPGEKFIGRVTRKKGS 127 (229)
Q Consensus 79 ~~~i~l~I~~l~~~G~GVar~~~~G~vVFVp------gaLPGE~V~vrI~k~kk~ 127 (229)
|+...++|.+.+..|.=+- .. .+..+|+| ..-+||.|.+-+...+++
T Consensus 2 G~~~~L~V~~~~~~g~fL~-~~-~~~~vlLp~~e~~~~~~~Gd~v~VFvY~D~~~ 54 (61)
T PF13509_consen 2 GQINTLKVVDKNEFGYFLD-DG-EGKEVLLPKSEVPEPLKVGDEVEVFVYLDKEG 54 (61)
T ss_dssp -------EEEE-SSEEEEE-ET-T-EEEEEEGGG------TTSEEEEEEEE-TTS
T ss_pred CCCcceEEEEEeCCEEEEE-CC-CCCEEEechHHcCCCCCCCCEEEEEEEECCCC
Confidence 5667899999998888765 32 34788887 346799999988877655
No 54
>TIGR01574 miaB-methiolase tRNA-N(6)-(isopentenyl)adenosine-37 thiotransferase enzyme MiaB. Hits to this model span all major groups of bacteria and eukaryotes, but not archaea, which are known to lack this particular tRNA modification. The enzyme from Thermotoga maritima has been cloned, expressed, spectroscopically characterized and shown to complement the E. coli MiaB enzyme.
Probab=39.28 E-value=1.3e+02 Score=28.55 Aligned_cols=49 Identities=18% Similarity=0.260 Sum_probs=35.9
Q ss_pred CCcEEEEEEeeeCCCC--cEEEEEcCCCcEEEecCC--CCCcEEEEEEEeecCC
Q 038639 78 RGQELELVCESLAYKG--KGVCKVADTGFVVLCDRV--LPGEKFIGRVTRKKGS 127 (229)
Q Consensus 78 ~~~~i~l~I~~l~~~G--~GVar~~~~G~vVFVpga--LPGE~V~vrI~k~kk~ 127 (229)
.|..+++-|+....+| .-+|+.+ ....|+|++. .+|+.+.|+|++....
T Consensus 379 ~G~~~~vlve~~~~~~~~~~~g~t~-~~~~v~~~~~~~~~g~~~~v~i~~~~~~ 431 (438)
T TIGR01574 379 EGKTFKVLVEGLSRNNPEELAGRTE-NNFLVNFEGSEDLIGKFVDVKITNVKRM 431 (438)
T ss_pred CCCEEEEEEEeccCCCCceEEEECC-CCCEEEECCCCCCCCCEEEEEEEeeecC
Confidence 6788888888765555 4467776 3457888754 4899999999886553
No 55
>PF12988 DUF3872: Domain of unknown function, B. Theta Gene description (DUF3872); InterPro: IPR024355 This entry represents proteins of unknown function found primarily in Bacteroides species. The Bacteroides thetaiotaomicron gene coding for this protein is located in a conjugate transposon and appears to be upregulated in the presence of host or other bacterial species compared to growth in pure culture [, ].; PDB: 2L3B_A 2L7Q_A.
Probab=38.20 E-value=70 Score=26.32 Aligned_cols=41 Identities=29% Similarity=0.394 Sum_probs=23.7
Q ss_pred CCCcEEEEEEe---------------eeCCCCcEEEEEcCCCcEEEecCC---CCCcEEEE
Q 038639 77 IRGQELELVCE---------------SLAYKGKGVCKVADTGFVVLCDRV---LPGEKFIG 119 (229)
Q Consensus 77 k~~~~i~l~I~---------------~l~~~G~GVar~~~~G~vVFVpga---LPGE~V~v 119 (229)
++|+.+|+.|+ -+..+|.|..+.+ +.++|+|+- |+-|+.+.
T Consensus 45 ~~GeTvEIR~~l~reG~y~~t~Y~iRYFQ~dGkG~L~~~--~g~~~~pND~Y~L~~~~FRL 103 (137)
T PF12988_consen 45 KKGETVEIRCELKREGNYADTRYTIRYFQPDGKGTLRMD--DGTVLLPNDRYPLEKEVFRL 103 (137)
T ss_dssp -TTEEEEEEEEEEESS--SS---EEEEE-SSS-EEEEET--TS-EE-TTSEEE-S-SEEEE
T ss_pred CCCCEEEEEEEEecCceecccEEEEEEEeecCCEEEEec--CCcEeccccceecCcCEEEE
Confidence 56777666554 5667999999997 568889863 56565544
No 56
>PF07076 DUF1344: Protein of unknown function (DUF1344); InterPro: IPR009780 This family consists of several short, hypothetical bacterial proteins of around 80 residues in length. Members of this family are found in Rhizobium, Agrobacterium and Brucella species. The function of this family is unknown.
Probab=38.13 E-value=1.5e+02 Score=21.15 Aligned_cols=44 Identities=16% Similarity=0.098 Sum_probs=34.5
Q ss_pred EEEEEEeeeCCCCcEEEEEcCCCcEEEec------CCCCCcEEEEEEEeecC
Q 038639 81 ELELVCESLAYKGKGVCKVADTGFVVLCD------RVLPGEKFIGRVTRKKG 126 (229)
Q Consensus 81 ~i~l~I~~l~~~G~GVar~~~~G~vVFVp------gaLPGE~V~vrI~k~kk 126 (229)
.++.+|.+++...+-|..-+ |+.+-+| +.-||++|.|......+
T Consensus 4 ~veG~I~~id~~~~titLdD--Gksy~lp~ef~~~~L~~G~kV~V~yd~~~g 53 (61)
T PF07076_consen 4 DVEGTIKSIDPETMTITLDD--GKSYKLPEEFDFDGLKPGMKVVVFYDEVDG 53 (61)
T ss_pred cceEEEEEEcCCceEEEecC--CCEEECCCcccccccCCCCEEEEEEEccCC
Confidence 36889999999999998864 7876554 67899999887766543
No 57
>PF12945 YcgR_2: Flagellar protein YcgR; PDB: 2RDE_B 1YLN_A 3KYG_A.
Probab=36.65 E-value=1.5e+02 Score=20.86 Aligned_cols=54 Identities=24% Similarity=0.295 Sum_probs=25.7
Q ss_pred CCCcEEEEEEeeeC-CCCcEEEEEcC--CCcEEEe--c-------CCCCCcEEEEEEEeecCCeee
Q 038639 77 IRGQELELVCESLA-YKGKGVCKVAD--TGFVVLC--D-------RVLPGEKFIGRVTRKKGSYAE 130 (229)
Q Consensus 77 k~~~~i~l~I~~l~-~~G~GVar~~~--~G~vVFV--p-------gaLPGE~V~vrI~k~kk~y~~ 130 (229)
+.|+.+++++.+-+ ..+.--++..+ ++..+.| | ...+|+.|.++......-|++
T Consensus 2 ~iG~~i~i~i~~~~~~~~~y~S~v~g~~~~~~l~i~~P~~~g~~~~l~~g~~v~v~~~~~~~~y~F 67 (87)
T PF12945_consen 2 KIGQKIEIEITNPTGEKGRYKSRVIGIDDDRYLIISMPMEKGRPIPLREGEEVIVRFISEDGVYAF 67 (87)
T ss_dssp -TT-EEEEEEE-TTS-EEEEEEEEEEEETTTEEEEE---CCHHHCCS-TT-EEEEEEEE-SCEEEE
T ss_pred CCCCEEEEEEECCCCceEEEEEEEEEECCCCEEEEEcCccCCcEEeecCCCEEEEEEEECCeEEEE
Confidence 46777777664433 22222333211 1323333 3 345899999999988776665
No 58
>cd05692 S1_RPS1_repeat_hs4 S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 4 (hs4) of the H. sapiens RPS1 homolog. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=36.56 E-value=1.2e+02 Score=19.82 Aligned_cols=45 Identities=22% Similarity=0.106 Sum_probs=28.3
Q ss_pred CcEEEEEEeeeCCCCcEEEEEcCCCcEEEecC--------------CCCCcEEEEEEEeec
Q 038639 79 GQELELVCESLAYKGKGVCKVADTGFVVLCDR--------------VLPGEKFIGRVTRKK 125 (229)
Q Consensus 79 ~~~i~l~I~~l~~~G~GVar~~~~G~vVFVpg--------------aLPGE~V~vrI~k~k 125 (229)
|+.+..+|.++...|.-+--.+ +...|++. .-+||.+++++.+..
T Consensus 1 G~~~~g~V~~i~~~g~~v~i~~--~~~g~l~~~~l~~~~~~~~~~~~~~Gd~v~v~v~~~~ 59 (69)
T cd05692 1 GSVVEGTVTRLKPFGAFVELGG--GISGLVHISQIAHKRVKDVKDVLKEGDKVKVKVLSID 59 (69)
T ss_pred CCEEEEEEEEEEeeeEEEEECC--CCEEEEEhHHcCCcccCCHHHccCCCCEEEEEEEEEC
Confidence 4567777777777666664332 34444441 256999999887754
No 59
>PRK14328 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional
Probab=36.19 E-value=1.5e+02 Score=28.16 Aligned_cols=49 Identities=18% Similarity=0.131 Sum_probs=35.5
Q ss_pred CCcEEEEEEeeeCCC--CcEEEEEcCCCcEEEecCC--CCCcEEEEEEEeecCC
Q 038639 78 RGQELELVCESLAYK--GKGVCKVADTGFVVLCDRV--LPGEKFIGRVTRKKGS 127 (229)
Q Consensus 78 ~~~~i~l~I~~l~~~--G~GVar~~~~G~vVFVpga--LPGE~V~vrI~k~kk~ 127 (229)
.|..+++-|+.-..+ |.-+|+.+ +...|+|++. .+|+.|.|+|+.....
T Consensus 379 ~g~~~~vl~e~~~~~~~~~~~g~~~-~~~~v~~~~~~~~~g~~~~v~i~~~~~~ 431 (439)
T PRK14328 379 EGKIVEVLVEGPSKNDENKLTGRTR-TNKLVNFIGDKELIGKLVNVKITKANSF 431 (439)
T ss_pred CCCEEEEEEEecccCCCceEEEECC-CCeEEEECCCCCCCCCEEEEEEEeeecc
Confidence 577888888875444 44457876 4667888754 4899999999886543
No 60
>PRK08059 general stress protein 13; Validated
Probab=34.91 E-value=1.7e+02 Score=22.91 Aligned_cols=48 Identities=13% Similarity=-0.060 Sum_probs=32.8
Q ss_pred CCCCcEEEEEEeeeCCCCcEEEEEcCCCcEEEecC--------------CCCCcEEEEEEEeec
Q 038639 76 PIRGQELELVCESLAYKGKGVCKVADTGFVVLCDR--------------VLPGEKFIGRVTRKK 125 (229)
Q Consensus 76 ~k~~~~i~l~I~~l~~~G~GVar~~~~G~vVFVpg--------------aLPGE~V~vrI~k~k 125 (229)
++.|+.+..+|.++...|.-|--.+ +..-|++. --.||.|+++|.+..
T Consensus 5 ~k~G~iv~G~V~~i~~~G~fV~i~~--~~~Gli~~sel~~~~~~~~~~~~~vGD~I~vkI~~id 66 (123)
T PRK08059 5 YEVGSVVTGKVTGIQPYGAFVALDE--ETQGLVHISEITHGFVKDIHDFLSVGDEVKVKVLSVD 66 (123)
T ss_pred CCCCCEEEEEEEEEecceEEEEECC--CCEEEEEHHHCCcccccCHHHcCCCCCEEEEEEEEEE
Confidence 4679999999999998877775432 33333321 145999999888753
No 61
>COG2421 Predicted acetamidase/formamidase [Energy production and conversion]
Probab=34.45 E-value=1.2e+02 Score=28.15 Aligned_cols=53 Identities=11% Similarity=0.038 Sum_probs=34.4
Q ss_pred CCCCCcEEEEEEeeeCCC-C------cEEEEEcC-----CCcEEEecCCCCCcEEEEEEEeecCC
Q 038639 75 KPIRGQELELVCESLAYK-G------KGVCKVAD-----TGFVVLCDRVLPGEKFIGRVTRKKGS 127 (229)
Q Consensus 75 ~~k~~~~i~l~I~~l~~~-G------~GVar~~~-----~G~vVFVpgaLPGE~V~vrI~k~kk~ 127 (229)
.++.|+.+++++.+.-.+ + .++...+- --..+||.||-|||..+|+|.+.+-.
T Consensus 22 ~v~~Gd~V~iet~d~~~gq~~~~~~~~~~~~iD~~rv~p~TGPi~v~gA~pGD~L~V~i~~i~~~ 86 (305)
T COG2421 22 TVKPGDTVTIETLDALGGQIKAEETLEDIFKIDFSRVHPLTGPIYVEGAEPGDALEVEIEDIKPS 86 (305)
T ss_pred ecCCCCEEEEEEEeccCccccccchhhhhcccCcccccCCCCCeEEeccCCCceEEEEEEeeccC
Confidence 447898877777665211 0 22322210 12369999999999999999887644
No 62
>TIGR01125 MiaB-like tRNA modifying enzyme YliG, TIGR01125. This clade spans alpha and gamma proteobacteria, cyano bacteria, deinococcus, porphyromonas, aquifex, helicobacter, campylobacter, thermotoga, chlamydia, streptococcus coelicolor and clostridium, but does not include most other gram positive bacteria, archaea or eukaryotes.
Probab=32.23 E-value=1.7e+02 Score=27.78 Aligned_cols=49 Identities=10% Similarity=0.051 Sum_probs=33.4
Q ss_pred CCcEEEEEEeeeCCC--CcEEEEEcCCCcE-----EEecCC----CCCcEEEEEEEeecCC
Q 038639 78 RGQELELVCESLAYK--GKGVCKVADTGFV-----VLCDRV----LPGEKFIGRVTRKKGS 127 (229)
Q Consensus 78 ~~~~i~l~I~~l~~~--G~GVar~~~~G~v-----VFVpga----LPGE~V~vrI~k~kk~ 127 (229)
.|..+++-++....+ |.-+|+.++ ... |++++. .+|+.+.|+|+.....
T Consensus 367 ~g~~~~vl~e~~~~~~~~~~~g~~~~-~~~~~~~~v~~~~~~~~~~~g~~~~v~i~~~~~~ 426 (430)
T TIGR01125 367 VGKKIEVLIDGYEPETNLLLIGRTYG-QAPEVDGVVYVNGAKLNVKIGDILRVVITGTDEY 426 (430)
T ss_pred CCCEEEEEEEeccCCCCCcEEEECcc-CCcccCceEEEcCCcccCCCCCEEEEEEEEcccC
Confidence 577888888876544 455677651 222 677754 4899999999886543
No 63
>PRK07252 hypothetical protein; Provisional
Probab=32.13 E-value=2e+02 Score=22.69 Aligned_cols=47 Identities=19% Similarity=0.108 Sum_probs=31.1
Q ss_pred CCCcEEEEEEeeeCCCCcEEEEEcCCCcEEEec--------------CCCCCcEEEEEEEeec
Q 038639 77 IRGQELELVCESLAYKGKGVCKVADTGFVVLCD--------------RVLPGEKFIGRVTRKK 125 (229)
Q Consensus 77 k~~~~i~l~I~~l~~~G~GVar~~~~G~vVFVp--------------gaLPGE~V~vrI~k~k 125 (229)
+.|+.+..+|.++...|.-|--.+ +..-|++ ..-.||.|+|+|....
T Consensus 2 kvG~iv~G~V~~V~~~G~fVei~~--~~~GllhiseLs~~~~~~~~~~~~vGD~V~VkI~~iD 62 (120)
T PRK07252 2 KIGDKLKGTITGIKPYGAFVALEN--GTTGLIHISEIKTGFIDNIHQLLKVGEEVLVQVVDFD 62 (120)
T ss_pred CCCCEEEEEEEEEeCcEEEEEECC--CCEEEEEHHHcCCccccChhhccCCCCEEEEEEEEEe
Confidence 568888899998888776664322 3333433 1245999999887754
No 64
>PRK14329 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional
Probab=31.81 E-value=2e+02 Score=27.74 Aligned_cols=49 Identities=16% Similarity=0.186 Sum_probs=35.2
Q ss_pred CCcEEEEEEeeeCCC--CcEEEEEcCCCcEEEecC--CCCCcEEEEEEEeecCC
Q 038639 78 RGQELELVCESLAYK--GKGVCKVADTGFVVLCDR--VLPGEKFIGRVTRKKGS 127 (229)
Q Consensus 78 ~~~~i~l~I~~l~~~--G~GVar~~~~G~vVFVpg--aLPGE~V~vrI~k~kk~ 127 (229)
.|..+++-|+.-..+ |.-+||.+ ...+|++++ ..+|+.|.|+|+.....
T Consensus 406 ~G~~~~vlve~~~~~~~~~~~g~t~-~~~~v~~~~~~~~~g~~~~v~i~~~~~~ 458 (467)
T PRK14329 406 IGKTFEVLIEGVSKRSREQLFGRNS-QNKVVVFPKENYKIGDFVNVRITDCTSA 458 (467)
T ss_pred CCCEEEEEEEecccCCCCeEEEECC-CCeEEEECCCCCCCCCEEEEEEEEeecC
Confidence 578888888865544 44467876 355677765 35899999999986554
No 65
>PF03069 FmdA_AmdA: Acetamidase/Formamidase family; InterPro: IPR004304 This family includes amidohydrolases of formamide 3.5.1.49 from EC and acetamide 3.5.1 from EC. The formamidase from Methylophilus methylotrophus (Bacterium W3A1) forms a homotrimer suggesting that this may be a common property of other members of this family.; GO: 0016811 hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides, 0008152 metabolic process; PDB: 3TKK_D 3B9T_D 2II1_C 2F4L_C 2WKN_C.
Probab=31.48 E-value=49 Score=31.36 Aligned_cols=19 Identities=11% Similarity=0.237 Sum_probs=15.2
Q ss_pred EEEecCCCCCcEEEEEEEe
Q 038639 105 VVLCDRVLPGEKFIGRVTR 123 (229)
Q Consensus 105 vVFVpgaLPGE~V~vrI~k 123 (229)
.|||.||-|||.++|+|.+
T Consensus 73 PI~VeGAePGDvL~V~I~~ 91 (369)
T PF03069_consen 73 PIYVEGAEPGDVLEVEILD 91 (369)
T ss_dssp EEEETT--TT-EEEEEEEE
T ss_pred CEEEecCCCCCEEEEEEEe
Confidence 6999999999999999998
No 66
>cd04473 S1_RecJ_like S1_RecJ_like: The S1 domain of the archaea-specific RecJ-like exonuclease. The function of this family is not fully understood. In Escherichia coli, RecJ degrades single-stranded DNA in the 5'-3' direction and participates in homologous recombination and mismatch repair.
Probab=30.85 E-value=1.9e+02 Score=20.35 Aligned_cols=47 Identities=21% Similarity=0.017 Sum_probs=34.2
Q ss_pred CCCCcEEEEEEeeeCCCCcEEEEEcCCCcEEEecC------CCCCcEEEEEEEee
Q 038639 76 PIRGQELELVCESLAYKGKGVCKVADTGFVVLCDR------VLPGEKFIGRVTRK 124 (229)
Q Consensus 76 ~k~~~~i~l~I~~l~~~G~GVar~~~~G~vVFVpg------aLPGE~V~vrI~k~ 124 (229)
++.|+.++.+|.++...|.-+--.+ +..-|++. --.||.+++++.+.
T Consensus 14 ~~~G~~~~g~V~~i~~~G~fV~l~~--~~~Glv~~se~~~~~~iGd~v~v~I~~i 66 (77)
T cd04473 14 LEVGKLYKGKVNGVAKYGVFVDLND--HVRGLIHRSNLLRDYEVGDEVIVQVTDI 66 (77)
T ss_pred CCCCCEEEEEEEeEecceEEEEECC--CcEEEEEchhccCcCCCCCEEEEEEEEE
Confidence 4679999999999988887776542 33344432 26899999998876
No 67
>PRK14862 rimO ribosomal protein S12 methylthiotransferase; Provisional
Probab=29.84 E-value=1.6e+02 Score=28.10 Aligned_cols=48 Identities=13% Similarity=0.187 Sum_probs=33.6
Q ss_pred CCcEEEEEEeeeCCCCcEEEEEcCCCcE-----EEecCC---CCCcEEEEEEEeecCC
Q 038639 78 RGQELELVCESLAYKGKGVCKVADTGFV-----VLCDRV---LPGEKFIGRVTRKKGS 127 (229)
Q Consensus 78 ~~~~i~l~I~~l~~~G~GVar~~~~G~v-----VFVpga---LPGE~V~vrI~k~kk~ 127 (229)
.|..+++-|+....+|. +||.+ .... |++++. .+|+.|.|+|+.....
T Consensus 378 ~G~~~~vlie~~~~~~~-~Gr~~-~~~~~v~~~v~~~~~~~~~~g~~~~v~i~~~~~~ 433 (440)
T PRK14862 378 VGRTLQVLIDEVDEEGA-IGRSK-ADAPEIDGVVYLNGETGLKVGDIVRVKITDADEY 433 (440)
T ss_pred cCCEEEEEEEEcCCCCe-EEECc-ccCccCCCceeccCCCCCCCCCEEEEEEEEeeCC
Confidence 58888999997766663 67765 1222 666532 3899999999886544
No 68
>PRK10354 RNA chaperone/anti-terminator; Provisional
Probab=29.31 E-value=2.1e+02 Score=20.23 Aligned_cols=45 Identities=16% Similarity=0.090 Sum_probs=31.3
Q ss_pred EEEEeeeCC-CCcEEEEEcCCCcEEEec----------CCCCCcEEEEEEEeecCC
Q 038639 83 ELVCESLAY-KGKGVCKVADTGFVVLCD----------RVLPGEKFIGRVTRKKGS 127 (229)
Q Consensus 83 ~l~I~~l~~-~G~GVar~~~~G~vVFVp----------gaLPGE~V~vrI~k~kk~ 127 (229)
..+|..++. +|+|....++.+.-|||. ..-+||+|+..+...++.
T Consensus 6 ~G~Vk~f~~~kGfGFI~~~~g~~dvfvH~s~l~~~g~~~l~~G~~V~f~~~~~~~G 61 (70)
T PRK10354 6 TGIVKWFNADKGFGFITPDDGSKDVFVHFSAIQNDGYKSLDEGQKVSFTIESGAKG 61 (70)
T ss_pred eEEEEEEeCCCCcEEEecCCCCccEEEEEeeccccCCCCCCCCCEEEEEEEECCCC
Confidence 567777664 999988776334556653 247899999998876544
No 69
>TIGR02381 cspD cold shock domain protein CspD. This model represents what appears to be a phylogenetically distinct clade, containing E. coli CspD and related proteobacterial proteins within the larger family of cold shock domain proteins described by pfam model pfam00313. The gene symbol cspD may have been used idependently for other subfamilies of cold shock domain proteins, such as for B. subtilis CspD. These proteins typically are shorter than 70 amino acids. In E. coli, CspD is a stress response protein induced in stationary phase. This homodimer binds single-stranded DNA and appears to inhibit DNA replication.
Probab=29.25 E-value=1.8e+02 Score=20.47 Aligned_cols=44 Identities=14% Similarity=0.064 Sum_probs=30.5
Q ss_pred EEEeeeC-CCCcEEEEEcCCCcEEEec-------C---CCCCcEEEEEEEeecCC
Q 038639 84 LVCESLA-YKGKGVCKVADTGFVVLCD-------R---VLPGEKFIGRVTRKKGS 127 (229)
Q Consensus 84 l~I~~l~-~~G~GVar~~~~G~vVFVp-------g---aLPGE~V~vrI~k~kk~ 127 (229)
.+|.-++ .+|+|....++.+.-|||- + .-+||+|+..+....+.
T Consensus 4 G~Vk~f~~~kGfGFI~~~~g~~dvfvH~s~~~~~g~~~l~~G~~V~f~~~~~~~G 58 (68)
T TIGR02381 4 GIVKWFNNAKGFGFICPEGVDGDIFAHYSTIQMDGYRTLKAGQKVQFEVVQGPKG 58 (68)
T ss_pred eEEEEEeCCCCeEEEecCCCCccEEEEHHHhhhcCCCCCCCCCEEEEEEEECCCC
Confidence 4555555 4899998776334567763 2 47899999998886544
No 70
>cd04454 S1_Rrp4_like S1_Rrp4_like: Rrp4-like, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Rrp4 protein, and Rrp40 and Csl4 proteins, also represented in this group, are subunits 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=28.76 E-value=2.1e+02 Score=20.16 Aligned_cols=50 Identities=12% Similarity=0.070 Sum_probs=32.8
Q ss_pred CCCCCcEEEEEEeeeCCCCcEEEEEcCCCcEEEec--------------CCCCCcEEEEEEEeecC
Q 038639 75 KPIRGQELELVCESLAYKGKGVCKVADTGFVVLCD--------------RVLPGEKFIGRVTRKKG 126 (229)
Q Consensus 75 ~~k~~~~i~l~I~~l~~~G~GVar~~~~G~vVFVp--------------gaLPGE~V~vrI~k~kk 126 (229)
.+++|+.+..+|.++..+|.=|--.. +.--|++ ..-+||.+.+++.+..+
T Consensus 3 ~p~~GdiV~G~V~~v~~~~~~V~i~~--~~~g~l~~~~~~~~~~~~~~~~~~~GD~i~~~V~~~~~ 66 (82)
T cd04454 3 LPDVGDIVIGIVTEVNSRFWKVDILS--RGTARLEDSSATEKDKKEIRKSLQPGDLILAKVISLGD 66 (82)
T ss_pred CCCCCCEEEEEEEEEcCCEEEEEeCC--CceEEeechhccCcchHHHHhcCCCCCEEEEEEEEeCC
Confidence 34789999999998887766553211 1122222 24789999999987644
No 71
>COG0621 MiaB 2-methylthioadenine synthetase [Translation, ribosomal structure and biogenesis]
Probab=27.82 E-value=2.4e+02 Score=27.49 Aligned_cols=51 Identities=22% Similarity=0.152 Sum_probs=37.7
Q ss_pred CCcEEEEEEee-eCCCCcEEEEEcCCCcEEEecCC--C-CCcEEEEEEEeecCCee
Q 038639 78 RGQELELVCES-LAYKGKGVCKVADTGFVVLCDRV--L-PGEKFIGRVTRKKGSYA 129 (229)
Q Consensus 78 ~~~~i~l~I~~-l~~~G~GVar~~~~G~vVFVpga--L-PGE~V~vrI~k~kk~y~ 129 (229)
.|..+++-|+. -..+|.-+||.+ ....+.+++. . +|+.|.|+|+.....+.
T Consensus 377 vG~~~~VLVe~~~~~~~~~~Grt~-~~~~v~~~~~~~~~~G~~v~VkIt~~~~~~L 431 (437)
T COG0621 377 VGKTLEVLVEEGGSKKGELIGRTE-NYRPVVFGGVYTEDIGEFVEVKITEADEYSL 431 (437)
T ss_pred cCCEEEEEEEeccCcCCceEEEcC-CCCEEEecCcccCCCCCEEEEEEEecCCCce
Confidence 68889999994 445555678876 4667777764 3 69999999999766543
No 72
>cd05698 S1_Rrp5_repeat_hs6_sc5 S1_Rrp5_repeat_hs6_sc5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 6 (hs6) and S. cerevisiae S1 repeat 5 (sc5). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=26.93 E-value=2e+02 Score=19.34 Aligned_cols=46 Identities=11% Similarity=-0.060 Sum_probs=28.7
Q ss_pred CcEEEEEEeeeCCCCcEEEEEcCCCcEEEecC--------------CCCCcEEEEEEEeecC
Q 038639 79 GQELELVCESLAYKGKGVCKVADTGFVVLCDR--------------VLPGEKFIGRVTRKKG 126 (229)
Q Consensus 79 ~~~i~l~I~~l~~~G~GVar~~~~G~vVFVpg--------------aLPGE~V~vrI~k~kk 126 (229)
|+.++.+|.++...|.=|--.+ +..-|+|- .-+||.+++++.+...
T Consensus 1 g~~~~g~V~~v~~~G~~V~l~~--~~~gli~~s~l~~~~~~~~~~~~~~G~~i~v~v~~~d~ 60 (70)
T cd05698 1 GLKTHGTIVKVKPNGCIVSFYN--NVKGFLPKSELSEAFIKDPEEHFRVGQVVKVKVLSCDP 60 (70)
T ss_pred CCEEEEEEEEEecCcEEEEECC--CCEEEEEHHHcChhhcCCHHHcccCCCEEEEEEEEEcC
Confidence 4567777777777665554432 33333331 4679999999988644
No 73
>COG1098 VacB Predicted RNA binding protein (contains ribosomal protein S1 domain) [Translation, ribosomal structure and biogenesis]
Probab=26.76 E-value=2.5e+02 Score=22.88 Aligned_cols=48 Identities=17% Similarity=0.074 Sum_probs=33.1
Q ss_pred CCCCCcEEEEEEeeeCCCCcEEEEEcCCCcE--E--------Eec----CCCCCcEEEEEEEee
Q 038639 75 KPIRGQELELVCESLAYKGKGVCKVADTGFV--V--------LCD----RVLPGEKFIGRVTRK 124 (229)
Q Consensus 75 ~~k~~~~i~l~I~~l~~~G~GVar~~~~G~v--V--------FVp----gaLPGE~V~vrI~k~ 124 (229)
.|+.|+.++.+|+.+..=|.-|+... |.. | ||. .+--||.|.|+|...
T Consensus 2 ~~kvG~~l~GkItgI~~yGAFV~l~~--g~tGLVHISEIa~~fVkdI~d~L~vG~eV~vKVl~i 63 (129)
T COG1098 2 SMKVGSKLKGKITGITPYGAFVELEG--GKTGLVHISEIADGFVKDIHDHLKVGQEVKVKVLDI 63 (129)
T ss_pred CccccceEEEEEEeeEecceEEEecC--CCcceEEehHhhhhhHHhHHHHhcCCCEEEEEEEee
Confidence 46889999999999999888887653 222 2 232 445677777766654
No 74
>PRK14337 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional
Probab=24.86 E-value=3.2e+02 Score=26.11 Aligned_cols=49 Identities=22% Similarity=0.154 Sum_probs=32.7
Q ss_pred CCcEEEEEEeeeCCC-----CcEEEEEcCCCcEEEe--cC--CCCCcEEEEEEEeecCC
Q 038639 78 RGQELELVCESLAYK-----GKGVCKVADTGFVVLC--DR--VLPGEKFIGRVTRKKGS 127 (229)
Q Consensus 78 ~~~~i~l~I~~l~~~-----G~GVar~~~~G~vVFV--pg--aLPGE~V~vrI~k~kk~ 127 (229)
.|..+++-|+.-..+ |...|+.+ ++.+|+| ++ .++|+.+.|+|+.....
T Consensus 381 vG~~~~vlve~~~~~~~~~~~~~~g~~~-~~~~v~v~~~~~~~~~g~~~~v~i~~~~~~ 438 (446)
T PRK14337 381 VGRKTTVLLEGPSRKPGEGGDSWQGRDP-GGRVVNVPLPAGADLTGRLVPVRITEAKKH 438 (446)
T ss_pred CCCEEEEEEEeccccCCCCCceEEEECC-CCeEEEEecCCCcCCCCCEEEEEEEeeecc
Confidence 577888888854322 34567775 4565555 43 25899999999886543
No 75
>COG2996 Predicted RNA-bindining protein (contains S1 and HTH domains) [General function prediction only]
Probab=22.23 E-value=6.3e+02 Score=23.33 Aligned_cols=46 Identities=20% Similarity=0.293 Sum_probs=35.4
Q ss_pred eEEEeccCCCCceEeCCCCcCCChhHHHHHHHHHHHHhcCCCCCCCCcCCC
Q 038639 157 ALGLHAPGFFDKVLNIDKCLLQSEPANLVLAAVQDYWRDPQLGLSPYDVHS 207 (229)
Q Consensus 157 ~lGf~~rgS~~~IVdie~CpL~~~~in~il~~lr~~l~~~~~~l~~Yd~~~ 207 (229)
.+|+++.+ =+++.--|+..+.++.--..|-++|.+ ..+.-+|++++
T Consensus 202 Vi~~reDg----~lnLSl~p~~~E~l~~daq~Il~yL~~-~gG~mpf~DKS 247 (287)
T COG2996 202 VIGVREDG----KLNLSLRPRAHEMLDEDAQMILTYLES-NGGFMPFNDKS 247 (287)
T ss_pred EEEEccCC----eeecccccccHHhhhhhHHHHHHHHHH-cCCccccCCCC
Confidence 35666633 378888999999999999999999987 45677777765
No 76
>cd04461 S1_Rrp5_repeat_hs8_sc7 S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 repeat 7 (sc7)-like domains. Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in S. cerevisiae Rrp5 and 14 S1 repeats in H. sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 8 and S. cerevisiae S1 repeat 7. Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=21.92 E-value=3e+02 Score=19.44 Aligned_cols=48 Identities=17% Similarity=0.105 Sum_probs=34.0
Q ss_pred CCCCcEEEEEEeeeCCCCcEEEEEcCCCcEEEec--------------CCCCCcEEEEEEEeec
Q 038639 76 PIRGQELELVCESLAYKGKGVCKVADTGFVVLCD--------------RVLPGEKFIGRVTRKK 125 (229)
Q Consensus 76 ~k~~~~i~l~I~~l~~~G~GVar~~~~G~vVFVp--------------gaLPGE~V~vrI~k~k 125 (229)
++.|+.++.+|.++...|.-+--.+ +..-||| ..-.||.++++|.+..
T Consensus 12 ~~~G~i~~g~V~~v~~~G~fv~l~~--~~~g~v~~~el~~~~~~~~~~~~~~Gd~v~vkV~~id 73 (83)
T cd04461 12 LKPGMVVHGYVRNITPYGVFVEFLG--GLTGLAPKSYISDEFVTDPSFGFKKGQSVTAKVTSVD 73 (83)
T ss_pred CCCCCEEEEEEEEEeeceEEEEcCC--CCEEEEEHHHCCcccccCHHHhcCCCCEEEEEEEEEc
Confidence 4789999999999998887765432 4445554 1245888888887754
No 77
>PRK14326 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional
Probab=21.69 E-value=3.6e+02 Score=26.41 Aligned_cols=52 Identities=17% Similarity=0.108 Sum_probs=34.7
Q ss_pred CCcEEEEEEeee-CC----CCcEEEEEcCCCcEEEecC-----C-CCCcEEEEEEEeecCCeee
Q 038639 78 RGQELELVCESL-AY----KGKGVCKVADTGFVVLCDR-----V-LPGEKFIGRVTRKKGSYAE 130 (229)
Q Consensus 78 ~~~~i~l~I~~l-~~----~G~GVar~~~~G~vVFVpg-----a-LPGE~V~vrI~k~kk~y~~ 130 (229)
.|+.+++-|+.- +. .|+-.|+.+ ++..|+|++ . ++|+.|.|+|++....+..
T Consensus 389 vg~~~~vLve~~~~~~~~~~~~~~g~~~-~~~~V~~~~~~~~~~~~~G~~v~v~I~~~~~~~L~ 451 (502)
T PRK14326 389 VGRTVELLVATGEGRKDAATHRMSGRAR-DGRLVHFTVPEGAPEVRPGDVVTVTVTYAAPHHLI 451 (502)
T ss_pred CCCEEEEEEEecccccCCcCceeEEECC-CCCEEEEccCCccccCCCCCEEEEEEEecccCcEE
Confidence 577778887742 11 234456765 466777764 2 5899999999997666543
No 78
>PF06453 LT-IIB: Type II heat-labile enterotoxin , B subunit (LT-IIB); InterPro: IPR010503 These are B subunits from the type II heat-labile enterotoxin. The B subunits form a pentameric ring, which interacts with one A subunit. Thus, the structural arrangement of type I and type II heat-labile enterotoxins are very similar [].; GO: 0009405 pathogenesis, 0005576 extracellular region; PDB: 1TII_F 1QCB_E 1QB5_D.
Probab=20.16 E-value=87 Score=24.82 Aligned_cols=56 Identities=20% Similarity=0.141 Sum_probs=23.9
Q ss_pred ccccCCCCCcccccccC--CCCCCCCCCCcEEEEEEeeeCCCCcEEEEEcCCCcEEEecCC
Q 038639 53 RTRTHDAKPQFETFDSN--NNDYFKPIRGQELELVCESLAYKGKGVCKVADTGFVVLCDRV 111 (229)
Q Consensus 53 ~~~~~~~~~~~~~~~~~--~~~~~~~k~~~~i~l~I~~l~~~G~GVar~~~~G~vVFVpga 111 (229)
+-.|++.-+ ++|.+ +.+-.++-.+-.+.--|.+...+-.|+--.+..|++.|+||+
T Consensus 18 S~~~yAgvS---~~Fkd~C~~TTA~iV~~V~L~k~~sDvN~~t~GiYv~sstG~~w~Ipgg 75 (122)
T PF06453_consen 18 SLQTYAGVS---KHFKDNCNSTTAKIVQGVQLVKYISDVNKNTKGIYVVSSTGGVWFIPGG 75 (122)
T ss_dssp ------------HHHHHHHTTSSSEEEEEE-EEEEEEE-STTT-EEEEEETTS-EEEE---
T ss_pred cccccccHH---HHHHhhhhhhHHHHHhhhhhhhhhhhccCCCCcEEEEeCCCCeEEccCC
Confidence 344666666 55554 233322223333445577888888998655446999999986
No 79
>cd05705 S1_Rrp5_repeat_hs14 S1_Rrp5_repeat_hs14: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 14 (hs14). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=20.15 E-value=3.2e+02 Score=19.21 Aligned_cols=48 Identities=17% Similarity=0.035 Sum_probs=32.7
Q ss_pred CCCCcEEEEEEeeeCCCCcEEEEEcCCCcEEEec-----------------CCCCCcEEEEEEEeec
Q 038639 76 PIRGQELELVCESLAYKGKGVCKVADTGFVVLCD-----------------RVLPGEKFIGRVTRKK 125 (229)
Q Consensus 76 ~k~~~~i~l~I~~l~~~G~GVar~~~~G~vVFVp-----------------gaLPGE~V~vrI~k~k 125 (229)
++.|+.++.+|.++...|.-|---+ +..-||+ ..=+||.++++|....
T Consensus 1 ~k~G~~V~g~V~~i~~~G~fV~l~~--~v~G~v~~~~ls~~~~~~~~~~~~~~~~G~~v~~kVl~id 65 (74)
T cd05705 1 IKEGQLLRGYVSSVTKQGVFFRLSS--SIVGRVLFQNVTKYFVSDPSLYNKYLPEGKLLTAKVLSVN 65 (74)
T ss_pred CCCCCEEEEEEEEEeCCcEEEEeCC--CCEEEEEHHHccCccccChhhHhcccCCCCEEEEEEEEEE
Confidence 3679999999999988876554322 3333333 1257899999988764
Done!