Query 022231
Match_columns 300
No_of_seqs 177 out of 1259
Neff 4.7
Searched_HMMs 46136
Date Fri Mar 29 09:01:24 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/022231.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/022231hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK14640 hypothetical protein; 100.0 6.5E-40 1.4E-44 283.6 19.5 147 122-300 3-151 (152)
2 PRK14633 hypothetical protein; 100.0 1.1E-39 2.4E-44 281.7 20.1 147 123-300 2-149 (150)
3 PRK14647 hypothetical protein; 100.0 2.8E-39 6E-44 281.4 20.0 150 120-300 3-159 (159)
4 PRK14643 hypothetical protein; 100.0 2.7E-39 5.8E-44 283.3 19.0 157 122-300 6-164 (164)
5 COG0779 Uncharacterized protei 100.0 3.2E-39 6.9E-44 280.2 19.0 149 120-300 3-153 (153)
6 PRK14632 hypothetical protein; 100.0 7.3E-39 1.6E-43 282.3 21.3 157 120-300 3-163 (172)
7 PRK14634 hypothetical protein; 100.0 3.8E-39 8.3E-44 279.8 18.5 146 122-299 4-153 (155)
8 PRK14646 hypothetical protein; 100.0 5.3E-39 1.2E-43 278.9 18.7 147 120-297 2-151 (155)
9 PRK14638 hypothetical protein; 100.0 4.5E-38 9.6E-43 271.9 19.8 145 122-300 5-150 (150)
10 PRK00092 ribosome maturation p 100.0 8.6E-38 1.9E-42 269.9 20.2 149 122-300 4-154 (154)
11 PRK14636 hypothetical protein; 100.0 8.2E-38 1.8E-42 276.7 19.9 148 122-299 2-152 (176)
12 PRK14639 hypothetical protein; 100.0 2.2E-37 4.9E-42 264.8 18.8 138 130-300 2-140 (140)
13 PRK14631 hypothetical protein; 100.0 2.4E-37 5.3E-42 273.3 19.5 151 122-299 5-173 (174)
14 PRK14635 hypothetical protein; 100.0 3.5E-36 7.5E-41 262.8 21.0 159 121-300 2-162 (162)
15 PRK14641 hypothetical protein; 100.0 5.2E-36 1.1E-40 264.7 19.6 156 123-300 5-173 (173)
16 PRK14630 hypothetical protein; 100.0 9.4E-36 2E-40 255.7 18.0 136 124-297 7-143 (143)
17 PF02576 DUF150: Uncharacteris 100.0 8.7E-36 1.9E-40 253.2 15.7 139 130-296 1-141 (141)
18 PRK14637 hypothetical protein; 100.0 7.7E-35 1.7E-39 252.1 18.5 137 128-299 11-148 (151)
19 PRK14645 hypothetical protein; 100.0 9.2E-35 2E-39 252.4 17.4 140 121-294 5-145 (154)
20 PRK02001 hypothetical protein; 100.0 5.9E-34 1.3E-38 247.0 20.0 150 123-298 2-152 (152)
21 PRK14642 hypothetical protein; 100.0 2.4E-33 5.3E-38 252.0 19.9 160 127-299 3-181 (197)
22 PRK14644 hypothetical protein; 100.0 5.6E-33 1.2E-37 236.9 16.3 132 130-293 3-136 (136)
23 cd01734 YlxS_C YxlS is a Bacil 99.9 8.1E-22 1.8E-26 154.5 10.7 82 198-300 1-83 (83)
24 cd06168 LSm9 The eukaryotic Sm 86.4 3.8 8.2E-05 31.9 7.0 72 215-296 3-74 (75)
25 PF01423 LSM: LSM domain ; In 78.6 7.6 0.00017 28.4 5.8 41 216-265 2-42 (67)
26 cd01726 LSm6 The eukaryotic Sm 74.8 5.6 0.00012 29.8 4.2 40 216-264 4-43 (67)
27 cd01729 LSm7 The eukaryotic Sm 71.1 7.9 0.00017 30.4 4.4 42 214-264 4-45 (81)
28 cd01722 Sm_F The eukaryotic Sm 70.8 7.9 0.00017 29.1 4.2 40 216-264 5-44 (68)
29 PRK00737 small nuclear ribonuc 70.3 9.6 0.00021 29.1 4.6 41 215-264 7-47 (72)
30 PF14438 SM-ATX: Ataxin 2 SM d 69.7 9.8 0.00021 29.0 4.6 38 217-260 7-46 (77)
31 cd01731 archaeal_Sm1 The archa 69.1 9.1 0.0002 28.7 4.2 40 216-264 4-43 (68)
32 cd01719 Sm_G The eukaryotic Sm 68.5 8.8 0.00019 29.5 4.0 41 215-264 3-43 (72)
33 cd01721 Sm_D3 The eukaryotic S 67.2 35 0.00075 25.9 7.1 39 217-264 5-43 (70)
34 cd00600 Sm_like The eukaryotic 63.9 11 0.00025 27.0 3.7 38 218-264 2-39 (63)
35 COG1958 LSM1 Small nuclear rib 63.7 12 0.00027 28.8 4.1 41 215-264 10-50 (79)
36 cd01717 Sm_B The eukaryotic Sm 63.2 15 0.00031 28.5 4.4 41 216-265 4-44 (79)
37 smart00651 Sm snRNP Sm protein 60.7 16 0.00035 26.6 4.1 40 216-264 2-41 (67)
38 cd01732 LSm5 The eukaryotic Sm 58.0 31 0.00067 26.8 5.4 38 218-264 9-46 (76)
39 PF10842 DUF2642: Protein of u 56.9 52 0.0011 25.4 6.3 33 214-253 13-45 (66)
40 PF08863 YolD: YolD-like prote 55.7 57 0.0012 25.0 6.6 49 222-293 42-91 (92)
41 cd01728 LSm1 The eukaryotic Sm 54.0 23 0.0005 27.4 4.1 40 215-263 5-44 (74)
42 cd01725 LSm2 The eukaryotic Sm 53.8 24 0.00052 27.6 4.2 38 218-264 7-44 (81)
43 cd01723 LSm4 The eukaryotic Sm 53.7 25 0.00054 27.0 4.3 39 217-264 6-44 (76)
44 cd01724 Sm_D1 The eukaryotic S 51.6 42 0.00091 26.9 5.4 39 217-264 6-44 (90)
45 cd01733 LSm10 The eukaryotic S 50.3 86 0.0019 24.4 6.8 38 218-264 15-52 (78)
46 PF08442 ATP-grasp_2: ATP-gras 49.8 60 0.0013 29.6 6.8 65 107-176 50-137 (202)
47 cd01730 LSm3 The eukaryotic Sm 48.5 34 0.00074 26.6 4.3 41 216-265 4-45 (82)
48 cd01727 LSm8 The eukaryotic Sm 48.2 33 0.00072 26.2 4.2 31 216-252 3-33 (74)
49 PF08608 Wyosine_form: Wyosine 47.9 19 0.00042 27.2 2.7 37 106-144 14-50 (62)
50 COG0045 SucC Succinyl-CoA synt 46.6 80 0.0017 32.1 7.6 69 108-178 52-138 (387)
51 KOG1783 Small nuclear ribonucl 46.6 13 0.00028 29.5 1.6 29 216-250 10-38 (77)
52 PF12701 LSM14: Scd6-like Sm d 45.2 1.1E+02 0.0024 25.0 7.0 67 219-297 5-77 (96)
53 cd02978 KaiB_like KaiB-like fa 43.5 60 0.0013 25.4 4.9 39 153-204 2-40 (72)
54 cd04869 ACT_GcvR_2 ACT domains 41.9 1.4E+02 0.003 22.0 7.8 55 127-185 12-73 (81)
55 cd04870 ACT_PSP_1 CT domains f 38.2 1.6E+02 0.0036 21.7 7.2 54 127-184 12-66 (75)
56 TIGR03793 TOMM_pelo TOMM prope 35.7 1.9E+02 0.0041 22.7 6.7 54 123-178 19-75 (77)
57 PF02237 BPL_C: Biotin protein 35.5 1.5E+02 0.0033 20.6 5.8 32 220-259 1-32 (48)
58 PF06372 Gemin6: Gemin6 protei 32.5 77 0.0017 28.5 4.5 40 211-257 6-45 (166)
59 cd04872 ACT_1ZPV ACT domain pr 29.8 2.1E+02 0.0045 21.8 6.1 46 127-176 14-61 (88)
60 PRK00194 hypothetical protein; 29.6 2E+02 0.0044 21.8 6.0 46 126-175 15-62 (90)
61 PRK09301 circadian clock prote 29.4 1.2E+02 0.0026 25.4 4.8 42 151-205 5-46 (103)
62 PF14472 DUF4429: Domain of un 29.1 68 0.0015 25.6 3.3 39 247-297 2-40 (94)
63 TIGR02654 circ_KaiB circadian 28.6 1.3E+02 0.0029 24.3 4.9 41 152-205 3-43 (87)
64 cd04873 ACT_UUR-ACR-like ACT d 28.4 2.1E+02 0.0045 19.9 8.0 56 127-184 13-69 (70)
65 TIGR02024 FtcD glutamate formi 28.2 1.4E+02 0.003 29.3 5.8 65 114-186 47-116 (298)
66 PLN00180 NDF6 (NDH-dependent f 28.1 35 0.00076 30.7 1.6 19 101-119 123-141 (180)
67 PF05219 DREV: DREV methyltran 27.0 91 0.002 30.1 4.3 41 104-146 193-239 (265)
68 PF06257 DUF1021: Protein of u 26.8 2E+02 0.0043 22.7 5.4 66 214-300 9-76 (76)
69 cd04861 LigD_Pol_like LigD_Pol 26.7 2.2E+02 0.0048 26.9 6.7 84 121-230 111-197 (227)
70 PF00788 RA: Ras association ( 26.1 12 0.00027 28.3 -1.5 20 195-214 46-67 (93)
71 KOG3482 Small nuclear ribonucl 26.0 1.2E+02 0.0027 24.0 4.1 33 213-251 8-41 (79)
72 TIGR01634 tail_P2_I phage tail 25.8 2.8E+02 0.006 24.1 6.7 52 129-183 79-134 (139)
73 PLN02677 mevalonate kinase 25.7 1.1E+02 0.0025 30.6 4.9 39 110-148 335-375 (387)
74 cd01720 Sm_D2 The eukaryotic S 23.1 2E+02 0.0044 23.0 5.0 34 222-264 14-47 (87)
75 TIGR03610 RutC pyrimidine util 23.0 3.3E+02 0.0071 22.7 6.5 57 125-202 53-109 (127)
76 PF13222 DUF4030: Protein of u 22.9 3.7E+02 0.0079 23.8 6.8 86 120-206 51-139 (142)
77 TIGR02778 ligD_pol DNA polymer 22.9 2.1E+02 0.0045 27.3 5.8 80 125-230 133-213 (245)
78 TIGR03341 YhgI_GntY IscR-regul 22.5 2.7E+02 0.0059 25.2 6.3 52 108-161 80-146 (190)
79 cd04865 LigD_Pol_like_2 LigD_P 22.4 2.2E+02 0.0048 26.9 5.8 83 122-230 113-198 (228)
80 PF01106 NifU: NifU-like domai 22.2 1.9E+02 0.0041 21.8 4.4 33 125-161 3-35 (68)
81 cd04905 ACT_CM-PDT C-terminal 22.0 3.4E+02 0.0074 20.2 7.2 53 128-184 15-69 (80)
82 COG5406 Nucleosome binding fac 21.6 65 0.0014 35.1 2.3 55 66-127 923-987 (1001)
83 cd04862 PaeLigD_Pol_like PaeLi 21.3 3.1E+02 0.0067 25.9 6.5 84 121-230 111-197 (227)
84 KOG1781 Small Nuclear ribonucl 21.2 60 0.0013 27.1 1.6 43 202-250 6-49 (108)
85 COG2921 Uncharacterized conser 20.8 2.8E+02 0.0061 22.8 5.3 57 120-183 25-82 (90)
86 TIGR00405 L26e_arch ribosomal 20.6 3.4E+02 0.0074 22.8 6.2 133 123-295 9-141 (145)
87 PF14153 Spore_coat_CotO: Spor 20.3 2.5E+02 0.0054 25.6 5.6 39 237-297 145-183 (185)
88 PTZ00138 small nuclear ribonuc 20.0 1.6E+02 0.0034 23.9 3.8 44 216-264 18-61 (89)
No 1
>PRK14640 hypothetical protein; Provisional
Probab=100.00 E-value=6.5e-40 Score=283.61 Aligned_cols=147 Identities=18% Similarity=0.245 Sum_probs=133.2
Q ss_pred CHHHHHHHHHHHHHhhcCCeEEEEEEE-ecCCcEEEEEEcccCCCCCCCChHHHHHHHHHHHHhhhccccCCCCCCCeEE
Q 022231 122 PWGERALSIAHEVLLQLGDDIKLYAFK-ATPRGYVYVRLDKLSNKYGCPSMEELESYSQEYKKKLDEVGALGEIPDDLAL 200 (300)
Q Consensus 122 ~~~e~I~el~epvl~~~G~eLvdVe~~-~~~~~~LrV~IDk~~~~dggVsLDDCe~vSr~Is~~LD~~e~~d~I~~~Y~L 200 (300)
.+.++++++++|+++++||+||+|+|. .++.++|||+||+ ++|||+|||+.+||+|+++|| ++|+|+++|+|
T Consensus 3 ~~~~~i~~li~p~~~~~G~el~dve~~~~~~~~~lrV~ID~----~~gv~lddC~~vSr~is~~LD---~~d~i~~~Y~L 75 (152)
T PRK14640 3 TLEQRLTDLLEAPVVALGFELWGIEFIRAGKHSTLRVYIDG----ENGVSVENCAEVSHQVGAIMD---VEDPITEEYYL 75 (152)
T ss_pred hHHHHHHHHHHHHHHhcCCEEEEEEEEecCCCcEEEEEEEC----CCCCCHHHHHHHHHHHHHHhc---ccccCCCCeEE
Confidence 367899999999999999999999999 6678999999999 788999999999999999999 57899999999
Q ss_pred EEecCCCCCCCCChHHHhhcCCCeeEEEE-eecCCCeeeEeeeeEEEEEeCCeeEEEEEeccccccCCCCCCCCcccccc
Q 022231 201 EVSTPGAERMLKVPDDLGRFKEMPITVCY-EDQDSDSREKTGVFLLDSIEMDSEICVWKLADVKENRDPQEKGRPLSRKR 279 (300)
Q Consensus 201 EVSSPGieRpLk~~~df~RfiGr~VkV~l-~~ieG~kke~~GVl~L~~vDee~i~l~~~l~dVk~nr~k~~KGk~l~kkq 279 (300)
||||||++|||++++||+||+|++|+|++ .+.+|+ ++++| +|.+++++++++.+ +|+
T Consensus 76 EVSSPGl~RpL~~~~~f~r~~G~~v~V~l~~~~~~~-k~~~G--~L~~v~~~~v~l~~-------------~~~------ 133 (152)
T PRK14640 76 EVSSPGLDRPLFKVAQFEKYVGQEAAVTLRMATNNR-RKFKG--VIKAVQGDMITLTV-------------DGK------ 133 (152)
T ss_pred EEeCCCCCCcCCCHHHHHHhCCCeEEEEEecccCCc-eEEEE--EEEEEeCCEEEEEE-------------CCe------
Confidence 99999999999999999999999999999 777886 78999 78999999875442 243
Q ss_pred cceeEEeeccccceeEEEEeC
Q 022231 280 RDWRLNLPFVMHKRVTLYLEY 300 (300)
Q Consensus 280 ~~~~l~Ipf~dI~KArL~ieF 300 (300)
.+.|||++|+||||.++|
T Consensus 134 ---~~~i~~~~I~ka~l~~~~ 151 (152)
T PRK14640 134 ---DEVLAFTNIQKANIVPNF 151 (152)
T ss_pred ---EEEEEhHHeeeEEEeccc
Confidence 278999999999999987
No 2
>PRK14633 hypothetical protein; Provisional
Probab=100.00 E-value=1.1e-39 Score=281.73 Aligned_cols=147 Identities=16% Similarity=0.199 Sum_probs=132.0
Q ss_pred HHHHHHHHHHHHHhhcCCeEEEEEEEecCCcEEEEEEcccCCCCCCCChHHHHHHHHHHHHhhhccccCCCCCCCeEEEE
Q 022231 123 WGERALSIAHEVLLQLGDDIKLYAFKATPRGYVYVRLDKLSNKYGCPSMEELESYSQEYKKKLDEVGALGEIPDDLALEV 202 (300)
Q Consensus 123 ~~e~I~el~epvl~~~G~eLvdVe~~~~~~~~LrV~IDk~~~~dggVsLDDCe~vSr~Is~~LD~~e~~d~I~~~Y~LEV 202 (300)
+.++++++++|+++++||+||+|+|...++++|||+||+ ++|||+|||+.+||+|+++|| ++++|+++|+|||
T Consensus 2 ~~~~i~~lv~p~~~~~G~eL~dve~~~~~~~~lrV~ID~----~~Gv~lddC~~vSr~i~~~LD---~~d~i~~~Y~LEV 74 (150)
T PRK14633 2 LLDDLYEIVEPITADLGYILWGIEVVGSGKLTIRIFIDH----ENGVSVDDCQIVSKEISAVFD---VEDPVSGKYILEV 74 (150)
T ss_pred hHHHHHHHHHHHHHHCCCEEEEEEEEeCCCcEEEEEEeC----CCCCCHHHHHHHHHHHHHHhc---cCcCCCCCeEEEE
Confidence 467999999999999999999999995455899999999 789999999999999999999 6899999999999
Q ss_pred ecCCCCCCCCChHHHhhcCCCeeEEEE-eecCCCeeeEeeeeEEEEEeCCeeEEEEEeccccccCCCCCCCCcccccccc
Q 022231 203 STPGAERMLKVPDDLGRFKEMPITVCY-EDQDSDSREKTGVFLLDSIEMDSEICVWKLADVKENRDPQEKGRPLSRKRRD 281 (300)
Q Consensus 203 SSPGieRpLk~~~df~RfiGr~VkV~l-~~ieG~kke~~GVl~L~~vDee~i~l~~~l~dVk~nr~k~~KGk~l~kkq~~ 281 (300)
||||++|||++++||.||+|++|+|++ .+.+|+ ++++| +|.+++++++++.+. .|+
T Consensus 75 SSPGldRpL~~~~~f~r~~G~~v~V~~~~~~~~~-~~~~G--~L~~v~~~~i~l~~~------------~~~-------- 131 (150)
T PRK14633 75 SSPGMNRQIFNIIQAQALVGFNVKAVTLAPVGSQ-TKFKG--VLERVEGNNVILNLE------------DGK-------- 131 (150)
T ss_pred eCCCCCCCCCCHHHHHHhCCCeEEEEEecccCCc-EEEEE--EEEEEeCCEEEEEEc------------CCc--------
Confidence 999999999999999999999999999 778887 77999 889999998754321 132
Q ss_pred eeEEeeccccceeEEEEeC
Q 022231 282 WRLNLPFVMHKRVTLYLEY 300 (300)
Q Consensus 282 ~~l~Ipf~dI~KArL~ieF 300 (300)
.++|||++|+||||.++|
T Consensus 132 -~~~i~~~~I~ka~l~~~f 149 (150)
T PRK14633 132 -EISFDFDELKKLRVSPDF 149 (150)
T ss_pred -EEEEEhHHeeeEEEeccc
Confidence 378999999999999987
No 3
>PRK14647 hypothetical protein; Provisional
Probab=100.00 E-value=2.8e-39 Score=281.37 Aligned_cols=150 Identities=25% Similarity=0.329 Sum_probs=133.2
Q ss_pred CCCHHHHHHHHHHHHHhhcCCeEEEEEEE-ecCCcEEEEEEcccCCCCCCCChHHHHHHHHHHHHhhhccccCCCCCCCe
Q 022231 120 GVPWGERALSIAHEVLLQLGDDIKLYAFK-ATPRGYVYVRLDKLSNKYGCPSMEELESYSQEYKKKLDEVGALGEIPDDL 198 (300)
Q Consensus 120 ~~~~~e~I~el~epvl~~~G~eLvdVe~~-~~~~~~LrV~IDk~~~~dggVsLDDCe~vSr~Is~~LD~~e~~d~I~~~Y 198 (300)
..++.++|+++++|+++++||+||+|+|. .++.++|||+||+ ++|||+|||+.+||+|+++|| ++|+|+++|
T Consensus 3 ~~~~~~~i~~~i~~~~~~~G~~L~dv~~~~~~~~~~lrV~ID~----~~gvslddC~~vSr~is~~LD---~~d~i~~~Y 75 (159)
T PRK14647 3 KVDVVDRVTELAEQVLSSLGLELVELEYKREGREMVLRLFIDK----EGGVNLDDCAEVSRELSEILD---VEDFIPERY 75 (159)
T ss_pred cchHHHHHHHHHHHHHHHCCCEEEEEEEEecCCCeEEEEEEeC----CCCCCHHHHHHHHHHHHHHHc---ccccCCCCe
Confidence 34578899999999999999999999999 5667899999999 799999999999999999999 578999999
Q ss_pred EEEEecCCCCCCCCChHHHhhcCCCeeEEEE-eecC-----CCeeeEeeeeEEEEEeCCeeEEEEEeccccccCCCCCCC
Q 022231 199 ALEVSTPGAERMLKVPDDLGRFKEMPITVCY-EDQD-----SDSREKTGVFLLDSIEMDSEICVWKLADVKENRDPQEKG 272 (300)
Q Consensus 199 ~LEVSSPGieRpLk~~~df~RfiGr~VkV~l-~~ie-----G~kke~~GVl~L~~vDee~i~l~~~l~dVk~nr~k~~KG 272 (300)
+|||||||++|||++++||+||+|++|+|++ .+.+ |+ +.++| +|.+++++.+++.+. +|
T Consensus 76 ~LEVSSPG~~RpL~~~~~f~r~~G~~v~V~l~~~~~~~~~~~~-~~~~G--~L~~~~~~~v~l~~~------------~~ 140 (159)
T PRK14647 76 TLEVSSPGLDRPLKKEADYERYAGRLVKVRTFELLADEAGNKR-KTFLG--ELEGLADGVVTIALK------------EG 140 (159)
T ss_pred EEEEcCCCCCCcCCCHHHHHHhCCcEEEEEEeccccccccCCc-eEEEE--EEEeecCCEEEEEEc------------CC
Confidence 9999999999999999999999999999999 6664 44 78999 789999987644321 13
Q ss_pred CcccccccceeEEeeccccceeEEEEeC
Q 022231 273 RPLSRKRRDWRLNLPFVMHKRVTLYLEY 300 (300)
Q Consensus 273 k~l~kkq~~~~l~Ipf~dI~KArL~ieF 300 (300)
+ .++|||++|++|+|.++|
T Consensus 141 ~---------~~~i~~~~I~ka~l~~ef 159 (159)
T PRK14647 141 Q---------QARIPLDKIAKANLEFEF 159 (159)
T ss_pred c---------EEEEEHHHCCEEEEeeeC
Confidence 3 388999999999999998
No 4
>PRK14643 hypothetical protein; Provisional
Probab=100.00 E-value=2.7e-39 Score=283.34 Aligned_cols=157 Identities=11% Similarity=0.155 Sum_probs=134.8
Q ss_pred CHHHHHHHHHHHHHhhcCCeEEEEEEE-ecCCcEEEEEEcccCCCCCCCChHHHHHHHHHHHHhhhccccCCCCCCCeEE
Q 022231 122 PWGERALSIAHEVLLQLGDDIKLYAFK-ATPRGYVYVRLDKLSNKYGCPSMEELESYSQEYKKKLDEVGALGEIPDDLAL 200 (300)
Q Consensus 122 ~~~e~I~el~epvl~~~G~eLvdVe~~-~~~~~~LrV~IDk~~~~dggVsLDDCe~vSr~Is~~LD~~e~~d~I~~~Y~L 200 (300)
.+.++++++++|+++++||+||+|+|. .++.++|||+||+...++||||+|||+.+||+|+++|| ++|+|+++|+|
T Consensus 6 ~~~~~l~~l~~p~~~~~G~eL~die~~~~~~~~~lrV~Id~~~~~~ggvtldDC~~vSr~is~~LD---~~d~i~~~Y~L 82 (164)
T PRK14643 6 SIKFQINELVNKELEVLNLKVYEINNLKEFENDMIQILVEDILQANKPLDFDILIKANDLVSNKID---QFIKTSEKYLL 82 (164)
T ss_pred HHHHHHHHHHHHHHHhcCCEEEEEEEEecCCCcEEEEEEecCCCcCCCcCHHHHHHHHHHHHHHhC---ccCCCCCCeEE
Confidence 367899999999999999999999999 66789999999851112478999999999999999999 68999999999
Q ss_pred EEecCCCCCCCCChHHHhhcCCCeeEEEE-eecCCCeeeEeeeeEEEEEeCCeeEEEEEeccccccCCCCCCCCcccccc
Q 022231 201 EVSTPGAERMLKVPDDLGRFKEMPITVCY-EDQDSDSREKTGVFLLDSIEMDSEICVWKLADVKENRDPQEKGRPLSRKR 279 (300)
Q Consensus 201 EVSSPGieRpLk~~~df~RfiGr~VkV~l-~~ieG~kke~~GVl~L~~vDee~i~l~~~l~dVk~nr~k~~KGk~l~kkq 279 (300)
||||||++|||++++||.||+|++|+|++ .+.+|+ +.++| .|.+++++.+++.+.+. ++ ..|+
T Consensus 83 EVSSPGleRpL~~~~df~r~~G~~V~V~l~~~~~g~-k~~~G--~L~~~~~~~~~l~l~~~-~~------~~~~------ 146 (164)
T PRK14643 83 EISSSGIEKQIRSQEELVKALNQWVYVQLNNEIKKV-KEFEG--YVTKYNVNTNTFRFTFF-IK------GQKK------ 146 (164)
T ss_pred EecCCCCCCCCCCHHHHHHhcCCeEEEEEecccCCc-eEEEE--EEEEEeCCcEEEEEEee-cc------CcCc------
Confidence 99999999999999999999999999999 888887 77999 78999998876554321 10 1123
Q ss_pred cceeEEeeccccceeEEEEeC
Q 022231 280 RDWRLNLPFVMHKRVTLYLEY 300 (300)
Q Consensus 280 ~~~~l~Ipf~dI~KArL~ieF 300 (300)
.++|||++|++|||+++|
T Consensus 147 ---~~~ip~~~I~karl~~~f 164 (164)
T PRK14643 147 ---KLDVKYEQIKFIRYAVRF 164 (164)
T ss_pred ---EEEEeHHHhhheEecccC
Confidence 288999999999999988
No 5
>COG0779 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=100.00 E-value=3.2e-39 Score=280.17 Aligned_cols=149 Identities=21% Similarity=0.314 Sum_probs=135.8
Q ss_pred CCCHHHHHHHHHHHHHhhcCCeEEEEEEE-ecCCcEEEEEEcccCCCCCCCChHHHHHHHHHHHHhhhccccCCCCCCCe
Q 022231 120 GVPWGERALSIAHEVLLQLGDDIKLYAFK-ATPRGYVYVRLDKLSNKYGCPSMEELESYSQEYKKKLDEVGALGEIPDDL 198 (300)
Q Consensus 120 ~~~~~e~I~el~epvl~~~G~eLvdVe~~-~~~~~~LrV~IDk~~~~dggVsLDDCe~vSr~Is~~LD~~e~~d~I~~~Y 198 (300)
..+..+++.++++|+++++||+||+|+|. .++.++|||+||+ ++++|+|||+++||++|++|| ++|||++.|
T Consensus 3 ~~~~~~~v~~liep~~~~lG~ELv~ve~~~~~~~~~lrI~id~----~g~v~lddC~~vSr~is~~LD---~edpi~~~Y 75 (153)
T COG0779 3 ESPITEKVTELIEPVVESLGFELVDVEFVKEGRDSVLRIYIDK----EGGVTLDDCADVSRAISALLD---VEDPIEGAY 75 (153)
T ss_pred ccchHHHHHHHHHHhHhhcCcEEEEEEEEEcCCCcEEEEEeCC----CCCCCHHHHHHHHHHHHHHhc---cCCcccccE
Confidence 45788999999999999999999999999 6668999999999 699999999999999999999 689999999
Q ss_pred EEEEecCCCCCCCCChHHHhhcCCCeeEEEE-eecCCCeeeEeeeeEEEEEeCCeeEEEEEeccccccCCCCCCCCcccc
Q 022231 199 ALEVSTPGAERMLKVPDDLGRFKEMPITVCY-EDQDSDSREKTGVFLLDSIEMDSEICVWKLADVKENRDPQEKGRPLSR 277 (300)
Q Consensus 199 ~LEVSSPGieRpLk~~~df~RfiGr~VkV~l-~~ieG~kke~~GVl~L~~vDee~i~l~~~l~dVk~nr~k~~KGk~l~k 277 (300)
+|||||||+||||++++||.||+|++|+|++ .|.+|+ +.+.| .|.+++++.+++.. .|+
T Consensus 76 ~LEVSSPGldRpL~~~~~f~r~~G~~Vkv~l~~~~~~~-k~~~G--~i~~~d~~~v~~~~-------------~~k---- 135 (153)
T COG0779 76 FLEVSSPGLDRPLKTAEHFARFIGEKVKVKLRLPIEGR-KKFEG--KIVAVDGETVTLEV-------------DGK---- 135 (153)
T ss_pred EEEeeCCCCCCCcCCHHHHHHhcCcEEEEEEecccCCc-eEEEE--EEEEEcCCeEEEEE-------------CCE----
Confidence 9999999999999999999999999999999 889997 67899 88999999864432 244
Q ss_pred cccceeEEeeccccceeEEEEeC
Q 022231 278 KRRDWRLNLPFVMHKRVTLYLEY 300 (300)
Q Consensus 278 kq~~~~l~Ipf~dI~KArL~ieF 300 (300)
.++|||++|+||||.+.|
T Consensus 136 -----~v~Ip~~~i~kArl~~~~ 153 (153)
T COG0779 136 -----EVEIPFSDIAKARLVPEF 153 (153)
T ss_pred -----EEEEEcccchhheecccC
Confidence 289999999999999876
No 6
>PRK14632 hypothetical protein; Provisional
Probab=100.00 E-value=7.3e-39 Score=282.32 Aligned_cols=157 Identities=17% Similarity=0.163 Sum_probs=134.6
Q ss_pred CCCHHHHHHHHHHHHHhhcCCeEEEEEEEecCCcEEEEEEcccCCCCCCCChHHHHHHHHHHHHhhhccccCCCCCCCeE
Q 022231 120 GVPWGERALSIAHEVLLQLGDDIKLYAFKATPRGYVYVRLDKLSNKYGCPSMEELESYSQEYKKKLDEVGALGEIPDDLA 199 (300)
Q Consensus 120 ~~~~~e~I~el~epvl~~~G~eLvdVe~~~~~~~~LrV~IDk~~~~dggVsLDDCe~vSr~Is~~LD~~e~~d~I~~~Y~ 199 (300)
+.++.++|+++++|+++++||+||+|++..++.++|||+||+ ++|||||||+.+||+|+++|| +.++|+++|+
T Consensus 3 ~~~~~~~i~~li~pv~~~~G~eLvdve~~~~~~~~lrV~ID~----~~GV~ldDC~~vSr~is~~LD---~~d~i~~~Y~ 75 (172)
T PRK14632 3 KQALDATIADMAGPFLASLGLELWGIELSYGGRTVVRLFVDG----PEGVTIDQCAEVSRHVGLALE---VEDVISSAYV 75 (172)
T ss_pred cchHHHHHHHHHHHHHHHCCCEEEEEEEEeCCCcEEEEEEEC----CCCCCHHHHHHHHHHHHHHhc---ccccCCCCeE
Confidence 456889999999999999999999999997678999999999 789999999999999999999 5789999999
Q ss_pred EEEecCCCCCCCCChHHHhhcCCCeeEEEE-eecC---CCeeeEeeeeEEEEEeCCeeEEEEEeccccccCCCCCCCCcc
Q 022231 200 LEVSTPGAERMLKVPDDLGRFKEMPITVCY-EDQD---SDSREKTGVFLLDSIEMDSEICVWKLADVKENRDPQEKGRPL 275 (300)
Q Consensus 200 LEVSSPGieRpLk~~~df~RfiGr~VkV~l-~~ie---G~kke~~GVl~L~~vDee~i~l~~~l~dVk~nr~k~~KGk~l 275 (300)
|||||||++|||++++||+||+|++|+|++ .+.+ |+ +.+.| +|.+++++.+++... . +.+|+.
T Consensus 76 LEVSSPGldRpL~~~~~f~r~iG~~V~V~l~~~~~~~~g~-k~~~G--~L~~v~~~~i~l~~~--~------~~~~~~-- 142 (172)
T PRK14632 76 LEVSSPGLERPFFRAEQMSPYVGRQIELTLIDPTPEWPGR-RKFRG--ELLAVEGDTVVLRPE--G------APAPEA-- 142 (172)
T ss_pred EEEeCCCCCCcCCCHHHHHHhCCCEEEEEEeccccccCCc-eEEEE--EEEEEeCCEEEEEEc--C------cccccC--
Confidence 999999999999999999999999999999 6663 65 78999 889999998754421 1 001110
Q ss_pred cccccceeEEeeccccceeEEEEeC
Q 022231 276 SRKRRDWRLNLPFVMHKRVTLYLEY 300 (300)
Q Consensus 276 ~kkq~~~~l~Ipf~dI~KArL~ieF 300 (300)
....++|||++|++|+|.++|
T Consensus 143 ----~~~~~~i~~~~I~ka~l~~~f 163 (172)
T PRK14632 143 ----EEAVLRTSWQGVRKANLIHVF 163 (172)
T ss_pred ----CceeEEEEhHHccEEEEEEEc
Confidence 112489999999999999987
No 7
>PRK14634 hypothetical protein; Provisional
Probab=100.00 E-value=3.8e-39 Score=279.83 Aligned_cols=146 Identities=20% Similarity=0.227 Sum_probs=131.4
Q ss_pred CHHHHHHHHHHHHHhhcCCeEEEEEEE-ecCCcEEEEEEcccCCCCCC--CChHHHHHHHHHHHHhhhccccCCCCCCCe
Q 022231 122 PWGERALSIAHEVLLQLGDDIKLYAFK-ATPRGYVYVRLDKLSNKYGC--PSMEELESYSQEYKKKLDEVGALGEIPDDL 198 (300)
Q Consensus 122 ~~~e~I~el~epvl~~~G~eLvdVe~~-~~~~~~LrV~IDk~~~~dgg--VsLDDCe~vSr~Is~~LD~~e~~d~I~~~Y 198 (300)
+..++++++++|+++++||+||+|+|. .++.++|||+||+ ++| ||+|||+.+||+|+++|| ++|+|+++|
T Consensus 4 ~~~~~i~~l~~~~~~~~G~elvdve~~~~~~~~~lrV~ID~----~~g~~v~lddC~~vSr~is~~LD---~~d~i~~~Y 76 (155)
T PRK14634 4 PLLPDLETLASATAADKGFELCGIQVLTHLQPMTLQVQIRR----SSGSDVSLDDCAGFSGPMGEALE---ASQLLTEAY 76 (155)
T ss_pred hhHHHHHHHHHHHHHHcCCEEEEEEEEeCCCCcEEEEEEEC----CCCCcccHHHHHHHHHHHHHHhc---ccccCCCCe
Confidence 578899999999999999999999999 6678999999999 566 999999999999999999 578999999
Q ss_pred EEEEecCCCCCCCCChHHHhhcCCCeeEEEE-eecCCCeeeEeeeeEEEEEeCCeeEEEEEeccccccCCCCCCCCcccc
Q 022231 199 ALEVSTPGAERMLKVPDDLGRFKEMPITVCY-EDQDSDSREKTGVFLLDSIEMDSEICVWKLADVKENRDPQEKGRPLSR 277 (300)
Q Consensus 199 ~LEVSSPGieRpLk~~~df~RfiGr~VkV~l-~~ieG~kke~~GVl~L~~vDee~i~l~~~l~dVk~nr~k~~KGk~l~k 277 (300)
+|||||||++|||++++||.||+|++|+|++ .+.+|+ ++++| +|.+++++.+++.+ +|+
T Consensus 77 ~LEVSSPGldRpL~~~~~f~r~~G~~V~V~l~~~~~~~-k~~~G--~L~~~~~~~v~l~~-------------~~~---- 136 (155)
T PRK14634 77 VLEISSPGIGDQLSSDRDFQTFRGFPVEVSHRDDDGSE-QRLEG--LLLERNEDHLQINI-------------RGR---- 136 (155)
T ss_pred EEEEeCCCCCCcCCCHHHHHHhCCCeEEEEEecCCCCe-EEEEE--EEEEEeCCEEEEEE-------------CCE----
Confidence 9999999999999999999999999999999 777786 78999 78999999875432 233
Q ss_pred cccceeEEeeccccceeEEEEe
Q 022231 278 KRRDWRLNLPFVMHKRVTLYLE 299 (300)
Q Consensus 278 kq~~~~l~Ipf~dI~KArL~ie 299 (300)
.++|||++|+||||.++
T Consensus 137 -----~~~i~~~~I~ka~l~~~ 153 (155)
T PRK14634 137 -----IKRIPRDSVISVRLTNP 153 (155)
T ss_pred -----EEEEEHHHeeeEEeCCC
Confidence 38899999999999764
No 8
>PRK14646 hypothetical protein; Provisional
Probab=100.00 E-value=5.3e-39 Score=278.93 Aligned_cols=147 Identities=16% Similarity=0.186 Sum_probs=130.9
Q ss_pred CCCHHHHHHHHHHHHHhhcCCeEEEEEEE-ecCCcEEEEEEcccCCCC-CCCChHHHHHHHHHHHHhhhccccCCCCCCC
Q 022231 120 GVPWGERALSIAHEVLLQLGDDIKLYAFK-ATPRGYVYVRLDKLSNKY-GCPSMEELESYSQEYKKKLDEVGALGEIPDD 197 (300)
Q Consensus 120 ~~~~~e~I~el~epvl~~~G~eLvdVe~~-~~~~~~LrV~IDk~~~~d-ggVsLDDCe~vSr~Is~~LD~~e~~d~I~~~ 197 (300)
...+.++|+++++|+++++||+||+|+|. .++.++|||+||++ + +|||+|||+.+||+|+++|| ++|+|+++
T Consensus 2 ~~~~~~~i~~li~p~~~~~G~eLvdve~~~~~~~~~LrV~IDk~---~g~gVtldDC~~vSr~is~~LD---~~D~i~~~ 75 (155)
T PRK14646 2 NKENKSKLEILLEKVANEFDLKICSLNIQTNQNPIVIKIIIKKT---NGDDISLDDCALFNTPASEEIE---NSNLLNCS 75 (155)
T ss_pred CchHHHHHHHHHHHHHHHcCCEEEEEEEEeCCCCeEEEEEEECC---CCCCccHHHHHHHHHHHHHHhC---cCCCCCCC
Confidence 35678899999999999999999999999 66789999999993 3 46999999999999999999 68999999
Q ss_pred eEEEEecCCCCCCCCChHHHhhcCCCeeEEEE-eecCCCeeeEeeeeEEEEEeCCeeEEEEEeccccccCCCCCCCCccc
Q 022231 198 LALEVSTPGAERMLKVPDDLGRFKEMPITVCY-EDQDSDSREKTGVFLLDSIEMDSEICVWKLADVKENRDPQEKGRPLS 276 (300)
Q Consensus 198 Y~LEVSSPGieRpLk~~~df~RfiGr~VkV~l-~~ieG~kke~~GVl~L~~vDee~i~l~~~l~dVk~nr~k~~KGk~l~ 276 (300)
|+|||||||++|||++++||.||+|++|+|++ .+.+|+ +.+.| +|.+++++.+++. + +|+
T Consensus 76 Y~LEVSSPGldRpL~~~~df~r~~G~~v~V~l~~~~~~~-~~~~G--~L~~~~~~~v~l~--~-----------~g~--- 136 (155)
T PRK14646 76 YVLEISSQGVSDELTSERDFKTFKGFPVNVELNQKNSKI-KFLNG--LLYEKSKDYLAIN--I-----------KGK--- 136 (155)
T ss_pred eEEEEcCCCCCCcCCCHHHHHHhCCCEEEEEEecCcCCe-EEEEE--EEEEEeCCEEEEE--E-----------CCE---
Confidence 99999999999999999999999999999999 777776 78999 7899999976443 1 244
Q ss_pred ccccceeEEeeccccceeEEE
Q 022231 277 RKRRDWRLNLPFVMHKRVTLY 297 (300)
Q Consensus 277 kkq~~~~l~Ipf~dI~KArL~ 297 (300)
.+.|||++|+||||.
T Consensus 137 ------~~~i~~~~I~ka~L~ 151 (155)
T PRK14646 137 ------IKKIPFNEVLKISLC 151 (155)
T ss_pred ------EEEEEHHHeeeEEeC
Confidence 288999999999985
No 9
>PRK14638 hypothetical protein; Provisional
Probab=100.00 E-value=4.5e-38 Score=271.87 Aligned_cols=145 Identities=21% Similarity=0.252 Sum_probs=127.8
Q ss_pred CHHHHHHHHHHHHHhhcCCeEEEEEEE-ecCCcEEEEEEcccCCCCCCCChHHHHHHHHHHHHhhhccccCCCCCCCeEE
Q 022231 122 PWGERALSIAHEVLLQLGDDIKLYAFK-ATPRGYVYVRLDKLSNKYGCPSMEELESYSQEYKKKLDEVGALGEIPDDLAL 200 (300)
Q Consensus 122 ~~~e~I~el~epvl~~~G~eLvdVe~~-~~~~~~LrV~IDk~~~~dggVsLDDCe~vSr~Is~~LD~~e~~d~I~~~Y~L 200 (300)
+..++++++++|+++++||+||+|+|. .+++++|||+||+. .|+||+|||+.+||.|+++|| ++++|+++|+|
T Consensus 5 ~~~~~i~~~~~~i~~~~G~elvdve~~~~~~~~~lrV~ID~~---~G~v~lddC~~vSr~is~~LD---~~d~i~~~Y~L 78 (150)
T PRK14638 5 MILEKVRKEAERIAEEQGLEIFDVQYRRESRGWVLRIIIDNP---VGYVSVRDCELFSREIERFLD---REDLIEHSYTL 78 (150)
T ss_pred hHHHHHHHHHHHHHHHcCCEEEEEEEEecCCCcEEEEEEECC---CCCcCHHHHHHHHHHHHHHhc---cccccCCceEE
Confidence 367899999999999999999999999 56789999999993 345999999999999999999 57899999999
Q ss_pred EEecCCCCCCCCChHHHhhcCCCeeEEEEeecCCCeeeEeeeeEEEEEeCCeeEEEEEeccccccCCCCCCCCccccccc
Q 022231 201 EVSTPGAERMLKVPDDLGRFKEMPITVCYEDQDSDSREKTGVFLLDSIEMDSEICVWKLADVKENRDPQEKGRPLSRKRR 280 (300)
Q Consensus 201 EVSSPGieRpLk~~~df~RfiGr~VkV~l~~ieG~kke~~GVl~L~~vDee~i~l~~~l~dVk~nr~k~~KGk~l~kkq~ 280 (300)
||||||++|||++++||.||+|++|+|++. |+ +.++| +|.+++++.+++. . +|+
T Consensus 79 EVSSPGldRpL~~~~~f~r~~G~~v~V~~~---~~-k~~~G--~L~~~~~~~i~l~--~-----------~~~------- 132 (150)
T PRK14638 79 EVSSPGLDRPLRGPKDYVRFTGKLAKIVTK---DG-KTFIG--RIESFVDGTITIS--D-----------EKE------- 132 (150)
T ss_pred EEeCCCCCCCCCCHHHHHHhCCCEEEEEEC---CC-cEEEE--EEEEEeCCEEEEE--E-----------CCc-------
Confidence 999999999999999999999999999994 33 57899 7899999876432 1 123
Q ss_pred ceeEEeeccccceeEEEEeC
Q 022231 281 DWRLNLPFVMHKRVTLYLEY 300 (300)
Q Consensus 281 ~~~l~Ipf~dI~KArL~ieF 300 (300)
.++|||++|++|+|.++|
T Consensus 133 --~~~i~~~~I~~a~l~~ef 150 (150)
T PRK14638 133 --KYEINIDDVKRANLEVEF 150 (150)
T ss_pred --EEEEEhHHcceEEEeeeC
Confidence 288999999999999987
No 10
>PRK00092 ribosome maturation protein RimP; Reviewed
Probab=100.00 E-value=8.6e-38 Score=269.90 Aligned_cols=149 Identities=23% Similarity=0.360 Sum_probs=132.8
Q ss_pred CHHHHHHHHHHHHHhhcCCeEEEEEEE-ecCCcEEEEEEcccCCCCCCCChHHHHHHHHHHHHhhhccccCCCCCCCeEE
Q 022231 122 PWGERALSIAHEVLLQLGDDIKLYAFK-ATPRGYVYVRLDKLSNKYGCPSMEELESYSQEYKKKLDEVGALGEIPDDLAL 200 (300)
Q Consensus 122 ~~~e~I~el~epvl~~~G~eLvdVe~~-~~~~~~LrV~IDk~~~~dggVsLDDCe~vSr~Is~~LD~~e~~d~I~~~Y~L 200 (300)
+..++|+++++|+++++|++||+|++. .+++++|+|+||+ ++|||+|||+++||+|+++|| +.++++++|+|
T Consensus 4 ~~~~~i~~~~~~~~~~~g~~l~dv~~~~~~~~~~l~V~Id~----~~gv~iddc~~~Sr~is~~LD---~~d~i~~~Y~L 76 (154)
T PRK00092 4 PLEEQLTELIEPVVEALGYELVDVEYVKEGRDSTLRIYIDK----EGGIDLDDCEEVSRQISAVLD---VEDPIPGAYTL 76 (154)
T ss_pred hHHHHHHHHHHHHHHHCCCEEEEEEEEecCCCcEEEEEEEC----CCCCCHHHHHHHHHHHHHHhc---cccCCCCCeEE
Confidence 477899999999999999999999999 6678999999999 789999999999999999999 57899999999
Q ss_pred EEecCCCCCCCCChHHHhhcCCCeeEEEE-eecCCCeeeEeeeeEEEEEeCCeeEEEEEeccccccCCCCCCCCcccccc
Q 022231 201 EVSTPGAERMLKVPDDLGRFKEMPITVCY-EDQDSDSREKTGVFLLDSIEMDSEICVWKLADVKENRDPQEKGRPLSRKR 279 (300)
Q Consensus 201 EVSSPGieRpLk~~~df~RfiGr~VkV~l-~~ieG~kke~~GVl~L~~vDee~i~l~~~l~dVk~nr~k~~KGk~l~kkq 279 (300)
||||||++|||++++||+||+|++|+|++ ++.+|+ ++++| +|.+++++++++.+. |++
T Consensus 77 EVSSPGi~RpL~~~~~f~r~~G~~v~V~~~~~~~~~-~~~~G--~L~~~~~~~i~l~~~-------------~~~----- 135 (154)
T PRK00092 77 EVSSPGLDRPLKKARDFRRFIGREVKVKLYEPIDGR-KKFQG--ILLAVDGETVTLEVE-------------GKE----- 135 (154)
T ss_pred EEeCCCCCCcCCCHHHHHHhCCCeEEEEEEcccCCc-eEEEE--EEEEeeCCEEEEEEC-------------CCe-----
Confidence 99999999999999999999999999999 666776 77899 889999998644421 221
Q ss_pred cceeEEeeccccceeEEEEeC
Q 022231 280 RDWRLNLPFVMHKRVTLYLEY 300 (300)
Q Consensus 280 ~~~~l~Ipf~dI~KArL~ieF 300 (300)
..++|||++|++|+|.++|
T Consensus 136 --~~~~i~~~~I~~a~l~~ef 154 (154)
T PRK00092 136 --KEVEIPLDNIAKARLVVEF 154 (154)
T ss_pred --EEEEEEHHHcceEEEeeeC
Confidence 1389999999999999998
No 11
>PRK14636 hypothetical protein; Provisional
Probab=100.00 E-value=8.2e-38 Score=276.67 Aligned_cols=148 Identities=22% Similarity=0.254 Sum_probs=130.7
Q ss_pred CHHHHHHHHHHHHHhhcCCeEEEEEEE-ecCCcEEEEEEcccCCCC-CCCChHHHHHHHHHHHHhhhccccCCCCCCCeE
Q 022231 122 PWGERALSIAHEVLLQLGDDIKLYAFK-ATPRGYVYVRLDKLSNKY-GCPSMEELESYSQEYKKKLDEVGALGEIPDDLA 199 (300)
Q Consensus 122 ~~~e~I~el~epvl~~~G~eLvdVe~~-~~~~~~LrV~IDk~~~~d-ggVsLDDCe~vSr~Is~~LD~~e~~d~I~~~Y~ 199 (300)
...++|+++++|+++++||+||+|+|. .+++++|||+||++ + ++||+|||+.+||+|+++|| +.++|+++|+
T Consensus 2 ~~~~~i~~lvep~~~~~GleLvdve~~~~~~~~~lrV~ID~~---~~ggV~lDDC~~vSr~Is~~LD---~~d~i~~~Y~ 75 (176)
T PRK14636 2 ADIAALTALIEPEAKALGLDLVRVAMFGGKSDPTLQIMAERP---DTRQLVIEDCAALSRRLSDVFD---ELDPIEDAYR 75 (176)
T ss_pred chHHHHHHHHHHHHHHcCCEEEEEEEEcCCCCeEEEEEEECC---CCCCcCHHHHHHHHHHHHHHhc---cCcCCCCCeE
Confidence 357899999999999999999999999 56689999999984 3 46999999999999999999 5789999999
Q ss_pred EEEecCCCCCCCCChHHHhhcCCCeeEEEE-eecCCCeeeEeeeeEEEEEeCCeeEEEEEeccccccCCCCCCCCccccc
Q 022231 200 LEVSTPGAERMLKVPDDLGRFKEMPITVCY-EDQDSDSREKTGVFLLDSIEMDSEICVWKLADVKENRDPQEKGRPLSRK 278 (300)
Q Consensus 200 LEVSSPGieRpLk~~~df~RfiGr~VkV~l-~~ieG~kke~~GVl~L~~vDee~i~l~~~l~dVk~nr~k~~KGk~l~kk 278 (300)
|||||||++|||++++||.||+|++|+|++ .+.+|+ +.++| +|.+++++.+++.+. +++
T Consensus 76 LEVSSPGldRpL~~~~df~r~~G~~V~V~l~~~~~g~-k~~~G--~L~~v~~~~v~l~~~------------~~~----- 135 (176)
T PRK14636 76 LEVSSPGIDRPLTRPKDFADWAGHEARIALSEPLDGR-KQFRG--ELKGIDGDTVTIADN------------KAG----- 135 (176)
T ss_pred EEEeCCCCCCCCCCHHHHHHhCCCeEEEEEecccCCe-EEEEE--EEEEEeCCEEEEEEc------------CCc-----
Confidence 999999999999999999999999999999 778886 77999 789999998654321 122
Q ss_pred ccceeEEeeccccceeEEEEe
Q 022231 279 RRDWRLNLPFVMHKRVTLYLE 299 (300)
Q Consensus 279 q~~~~l~Ipf~dI~KArL~ie 299 (300)
.++|||++|+||||.++
T Consensus 136 ----~~~i~~~~I~kA~l~~~ 152 (176)
T PRK14636 136 ----EVILPFAAIESAKLILT 152 (176)
T ss_pred ----EEEEEhHHcceEEEecc
Confidence 27899999999999874
No 12
>PRK14639 hypothetical protein; Provisional
Probab=100.00 E-value=2.2e-37 Score=264.80 Aligned_cols=138 Identities=17% Similarity=0.194 Sum_probs=121.9
Q ss_pred HHHHHHhhcCCeEEEEEEE-ecCCcEEEEEEcccCCCCCCCChHHHHHHHHHHHHhhhccccCCCCCCCeEEEEecCCCC
Q 022231 130 IAHEVLLQLGDDIKLYAFK-ATPRGYVYVRLDKLSNKYGCPSMEELESYSQEYKKKLDEVGALGEIPDDLALEVSTPGAE 208 (300)
Q Consensus 130 l~epvl~~~G~eLvdVe~~-~~~~~~LrV~IDk~~~~dggVsLDDCe~vSr~Is~~LD~~e~~d~I~~~Y~LEVSSPGie 208 (300)
.++|+++++||+||+|+|. .++.++|||+||+ ++|||+|||+.+||+|++.|| ++|+|+++|+|||||||++
T Consensus 2 ~~ep~~~~~G~eLvdve~~~~~~~~~lrV~Id~----~~gv~iddC~~vSr~is~~LD---~~d~i~~~Y~LEVSSPGl~ 74 (140)
T PRK14639 2 NLEALCKECGVSFYDDELVSENGRKIYRVYITK----EGGVNLDDCERLSELLSPIFD---VEPPVSGEYFLEVSSPGLE 74 (140)
T ss_pred chhHhHHhCCCEEEEEEEEecCCCcEEEEEEeC----CCCCCHHHHHHHHHHHHHHhc---cccccCCCeEEEEeCCCCC
Confidence 3789999999999999999 6678999999999 789999999999999999999 5789999999999999999
Q ss_pred CCCCChHHHhhcCCCeeEEEEeecCCCeeeEeeeeEEEEEeCCeeEEEEEeccccccCCCCCCCCcccccccceeEEeec
Q 022231 209 RMLKVPDDLGRFKEMPITVCYEDQDSDSREKTGVFLLDSIEMDSEICVWKLADVKENRDPQEKGRPLSRKRRDWRLNLPF 288 (300)
Q Consensus 209 RpLk~~~df~RfiGr~VkV~l~~ieG~kke~~GVl~L~~vDee~i~l~~~l~dVk~nr~k~~KGk~l~kkq~~~~l~Ipf 288 (300)
|||++++||+||+|++|+|++. ++ +.+.| +|.+++++++++... .+++ .++|||
T Consensus 75 RpL~~~~~f~r~~G~~v~v~l~---~~-~~~~G--~L~~~~~~~i~l~~~-----------~~~~---------~~~i~~ 128 (140)
T PRK14639 75 RKLSKIEHFAKSIGELVKITTN---EK-EKFEG--KIVSVDDENITLENL-----------ENKE---------KTTINF 128 (140)
T ss_pred CcCCCHHHHHHhCCCEEEEEEC---CC-cEEEE--EEEEEeCCEEEEEEc-----------cCCc---------EEEEEh
Confidence 9999999999999999999984 33 57899 789999998754311 1122 278999
Q ss_pred cccceeEEEEeC
Q 022231 289 VMHKRVTLYLEY 300 (300)
Q Consensus 289 ~dI~KArL~ieF 300 (300)
++|+||+|+++|
T Consensus 129 ~~I~ka~l~~~~ 140 (140)
T PRK14639 129 NDIKKAKTYVEW 140 (140)
T ss_pred HHeeeEEEEEeC
Confidence 999999999998
No 13
>PRK14631 hypothetical protein; Provisional
Probab=100.00 E-value=2.4e-37 Score=273.28 Aligned_cols=151 Identities=17% Similarity=0.186 Sum_probs=130.3
Q ss_pred CHHHHHHHHHHHHHhhcCCeEEEEEEE-ecCCcEEEEEEcccCC--------------CCCCCChHHHHHHHHHHHHhhh
Q 022231 122 PWGERALSIAHEVLLQLGDDIKLYAFK-ATPRGYVYVRLDKLSN--------------KYGCPSMEELESYSQEYKKKLD 186 (300)
Q Consensus 122 ~~~e~I~el~epvl~~~G~eLvdVe~~-~~~~~~LrV~IDk~~~--------------~dggVsLDDCe~vSr~Is~~LD 186 (300)
...++|+++++|+++++||+||+|+|. .++.++|||+||++.. .++|||||||+.+||+|+++||
T Consensus 5 ~~~~~i~~li~p~~~~~G~eLvdve~~~~~~~~~LrV~ID~~~~~~~~~~~~~~~~~~~~~gvtiddC~~vSr~is~~LD 84 (174)
T PRK14631 5 NKSQALTDIIAPAVAACGVDLWGIEFLPQGKRSLLRIYIDRLVEENAEPVINEDGEVEQGRGIGVEDCVRVTQQVGAMLD 84 (174)
T ss_pred hHHHHHHHHHHHHHHHcCCEEEEEEEEeCCCceEEEEEEecCcccccccccccccccccCCCcCHHHHHHHHHHHHHHhc
Confidence 367899999999999999999999999 5678999999997310 1368999999999999999999
Q ss_pred ccccCCCCCCCeEEEEecCCCCCCCCChHHHhhcCCCeeEEEE-eecCCCeeeEeeeeEEEEEe--CCeeEEEEEecccc
Q 022231 187 EVGALGEIPDDLALEVSTPGAERMLKVPDDLGRFKEMPITVCY-EDQDSDSREKTGVFLLDSIE--MDSEICVWKLADVK 263 (300)
Q Consensus 187 ~~e~~d~I~~~Y~LEVSSPGieRpLk~~~df~RfiGr~VkV~l-~~ieG~kke~~GVl~L~~vD--ee~i~l~~~l~dVk 263 (300)
++++|+++|+|||||||++|||++++||.||+|+.|+|++ .+.+|+ +.++| +|.+++ ++.+++ .+.
T Consensus 85 ---~~d~i~~~Y~LEVSSPGldRpL~~~~df~r~~G~~V~V~l~~~~~~~-k~~~G--~L~~v~~~~~~v~l--~~~--- 153 (174)
T PRK14631 85 ---VHDPISGEYALEVSSPGWDRPFFQLEQLQGYIGQQVALRLIAAVENR-RKFQA--KLLAVDLENEEIQV--EVE--- 153 (174)
T ss_pred ---ccccCCCCeEEEEeCCCCCCcCCCHHHHHHhCCCeEEEEEecccCCc-eEEEE--EEEEeecCCCEEEE--EEc---
Confidence 6789999999999999999999999999999999999999 777887 67999 889999 776543 321
Q ss_pred ccCCCCCCCCcccccccceeEEeeccccceeEEEEe
Q 022231 264 ENRDPQEKGRPLSRKRRDWRLNLPFVMHKRVTLYLE 299 (300)
Q Consensus 264 ~nr~k~~KGk~l~kkq~~~~l~Ipf~dI~KArL~ie 299 (300)
.++ .+.|||++|+||||.++
T Consensus 154 -------~~~---------~~~i~~~~I~ka~L~~~ 173 (174)
T PRK14631 154 -------GKH---------VLDIDSNNIDKANLIYQ 173 (174)
T ss_pred -------CCc---------EEEEEhHHcceEEEeec
Confidence 112 27899999999999864
No 14
>PRK14635 hypothetical protein; Provisional
Probab=100.00 E-value=3.5e-36 Score=262.79 Aligned_cols=159 Identities=26% Similarity=0.361 Sum_probs=127.7
Q ss_pred CCHHHHHHHHHHHHHhhcCCeEEEEEEE-ecCCcEEEEEEcccCCCCCCCChHHHHHHHHHHHHhhhccccCCCCCCCeE
Q 022231 121 VPWGERALSIAHEVLLQLGDDIKLYAFK-ATPRGYVYVRLDKLSNKYGCPSMEELESYSQEYKKKLDEVGALGEIPDDLA 199 (300)
Q Consensus 121 ~~~~e~I~el~epvl~~~G~eLvdVe~~-~~~~~~LrV~IDk~~~~dggVsLDDCe~vSr~Is~~LD~~e~~d~I~~~Y~ 199 (300)
++..++|+++++|+++ .|++||+|+|. .+++++|||+||+..++++||+||||+++||.|+++|| +.+++ ++|+
T Consensus 2 ~~~~~~i~~l~~~~~~-~g~el~dve~~~~~~~~~lrV~ID~~~~~~~gv~lddC~~vSr~is~~LD---~~d~~-~~Y~ 76 (162)
T PRK14635 2 TVSEEEISEILDRVLA-LPVKLYSLKVNQRPNHSLIEVVLDNLEHPYGSVSLLECEQVSRKLKEELE---RISPD-LDFT 76 (162)
T ss_pred CCcHHHHHHHHHHHHC-CCCEEEEEEEEecCCCcEEEEEEecCCCCCCCcCHHHHHHHHHHHHHHhC---CCCCC-CCeE
Confidence 4678899999999996 69999999999 66778999999985444689999999999999999999 45665 7999
Q ss_pred EEEecCCCCCCCCChHHHhhcCCCeeEEEEeecCCCeeeEee-eeEEEEEeCCeeEEEEEeccccccCCCCCCCCccccc
Q 022231 200 LEVSTPGAERMLKVPDDLGRFKEMPITVCYEDQDSDSREKTG-VFLLDSIEMDSEICVWKLADVKENRDPQEKGRPLSRK 278 (300)
Q Consensus 200 LEVSSPGieRpLk~~~df~RfiGr~VkV~l~~ieG~kke~~G-Vl~L~~vDee~i~l~~~l~dVk~nr~k~~KGk~l~kk 278 (300)
|||||||++|||++++||.||+|++|+|++.. +|.++ +.| +.+|.+++++++++.+. . |+++ ++
T Consensus 77 LEVSSPGldRpL~~~~~~~r~~G~~v~v~~~~-~~~~~-~~g~~g~L~~~~~~~v~l~~~--~---------k~~~--~~ 141 (162)
T PRK14635 77 LKVSSAGAERKLRLPEDLDRFRGIPVRLVFRS-EESEK-WQEGIFRLVNRDGDQVELEKF--Q---------KGKK--SK 141 (162)
T ss_pred EEEcCCCCCCcCCCHHHHHHhCCCEEEEEEec-CCCcE-EEecceEEEEEcCCEEEEEEe--c---------cccc--cc
Confidence 99999999999999999999999999999832 33323 444 33689999998755432 1 1111 01
Q ss_pred ccceeEEeeccccceeEEEEeC
Q 022231 279 RRDWRLNLPFVMHKRVTLYLEY 300 (300)
Q Consensus 279 q~~~~l~Ipf~dI~KArL~ieF 300 (300)
. ...++|||++|++|+|+++.
T Consensus 142 ~-~~~~~ip~~~I~ka~l~~e~ 162 (162)
T PRK14635 142 V-KKQTTLNLKDILKGNLYVEI 162 (162)
T ss_pred C-CeEEEEEhHHeeeeEEEEeC
Confidence 1 12489999999999999874
No 15
>PRK14641 hypothetical protein; Provisional
Probab=100.00 E-value=5.2e-36 Score=264.66 Aligned_cols=156 Identities=22% Similarity=0.273 Sum_probs=129.1
Q ss_pred HHHHHHHHHHHHH--hhcCCeEEEEEEE-ecCCcEEEEEEcccCCCCCCCChHHHHHHHHHHHHhhhccccCCCCC----
Q 022231 123 WGERALSIAHEVL--LQLGDDIKLYAFK-ATPRGYVYVRLDKLSNKYGCPSMEELESYSQEYKKKLDEVGALGEIP---- 195 (300)
Q Consensus 123 ~~e~I~el~epvl--~~~G~eLvdVe~~-~~~~~~LrV~IDk~~~~dggVsLDDCe~vSr~Is~~LD~~e~~d~I~---- 195 (300)
..+.+.++++|++ +++||+||+|++. .++.++|||+||+ ++||+||||+++||+|++.||+ +++++
T Consensus 5 i~~~~~~~~~~~~~~~~~G~eLvdve~~~~~~~~~lrV~ID~----~~gv~lDdC~~vSr~Is~~LD~---~d~i~~~~~ 77 (173)
T PRK14641 5 INNCVLQVLEASAGTKGEGVYLVSMTVKGSGKGRKIEVLLDA----DTGIRIDQCAFFSRRIRERLEE---DEELLGLVG 77 (173)
T ss_pred HHHHHHHHHHhhhccccCCeEEEEEEEEeCCCCcEEEEEEeC----CCCCCHHHHHHHHHHHHHHhCc---ccccccCCC
Confidence 6788999999988 8999999999999 5678999999998 7899999999999999999994 45554
Q ss_pred CCeEEEEecCCCCCCCCChHHHhhcCCCeeEEEE-eecCCCeeeEeeeeEEEEEe-----CCeeEEEEEeccccccCCCC
Q 022231 196 DDLALEVSTPGAERMLKVPDDLGRFKEMPITVCY-EDQDSDSREKTGVFLLDSIE-----MDSEICVWKLADVKENRDPQ 269 (300)
Q Consensus 196 ~~Y~LEVSSPGieRpLk~~~df~RfiGr~VkV~l-~~ieG~kke~~GVl~L~~vD-----ee~i~l~~~l~dVk~nr~k~ 269 (300)
++|+|||||||++|||++++||+||+|++|+|++ .+.+|+ +.++| +|.+++ ++.+ ++... ++.
T Consensus 78 ~~Y~LEVSSPGldRpL~~~~~f~r~~G~~V~V~l~~~~~~~-~~~~G--~L~~~~~~~~~~~~v--~~~~~------~~~ 146 (173)
T PRK14641 78 EDFDLMVSSPGLGEPIILPRQYGRHVGRLLRVTYRDEEGSE-HEVTG--HLQEVSLTEGEGASI--VLKPE------QKK 146 (173)
T ss_pred CCeEEEEeCCCCCCcCCCHHHHHHhCCCEEEEEEecccCCe-EEEEE--EEEeeecccCCCCcE--EEEec------ccc
Confidence 7999999999999999999999999999999999 667776 67999 789997 4433 43321 111
Q ss_pred CCCCcccccccceeEEeeccccceeEEEEeC
Q 022231 270 EKGRPLSRKRRDWRLNLPFVMHKRVTLYLEY 300 (300)
Q Consensus 270 ~KGk~l~kkq~~~~l~Ipf~dI~KArL~ieF 300 (300)
+|++ +....++++||++|++|++++||
T Consensus 147 ~~~~----~~~~~~~~v~~~~v~~A~vevE~ 173 (173)
T PRK14641 147 KKGK----QEETENITLELDAVIRAVPEAEL 173 (173)
T ss_pred cccc----CCCCceEEEEhHHccceeeeeeC
Confidence 2221 22234689999999999999998
No 16
>PRK14630 hypothetical protein; Provisional
Probab=100.00 E-value=9.4e-36 Score=255.70 Aligned_cols=136 Identities=19% Similarity=0.238 Sum_probs=119.5
Q ss_pred HHHHHHHHHHHHhhcCCeEEEEEEE-ecCCcEEEEEEcccCCCCCCCChHHHHHHHHHHHHhhhccccCCCCCCCeEEEE
Q 022231 124 GERALSIAHEVLLQLGDDIKLYAFK-ATPRGYVYVRLDKLSNKYGCPSMEELESYSQEYKKKLDEVGALGEIPDDLALEV 202 (300)
Q Consensus 124 ~e~I~el~epvl~~~G~eLvdVe~~-~~~~~~LrV~IDk~~~~dggVsLDDCe~vSr~Is~~LD~~e~~d~I~~~Y~LEV 202 (300)
..+++++++|+++++||+||+++|. .++.++|||+||+ ++|||+|||+.+||++++.|| ++|+++|+|||
T Consensus 7 ~~~i~~li~~~~~~~G~eLvdve~~~~~~~~~lrV~Id~----~~gV~idDC~~vSr~i~~~ld-----~~i~~~Y~LEV 77 (143)
T PRK14630 7 NSEVYNLIKNVTDRLGIEIIEINTFRNRNEGKIQIVLYK----KDSFGVDTLCDLHKMILLILE-----AVLKYNFSLEI 77 (143)
T ss_pred HHHHHHHHHHHHHHcCCEEEEEEEEecCCCcEEEEEEEC----CCCCCHHHHHHHHHHHHHHhc-----ccCCCCeEEEE
Confidence 4789999999999999999999999 5678999999999 789999999999999999998 48899999999
Q ss_pred ecCCCCCCCCChHHHhhcCCCeeEEEEeecCCCeeeEeeeeEEEEEeCCeeEEEEEeccccccCCCCCCCCcccccccce
Q 022231 203 STPGAERMLKVPDDLGRFKEMPITVCYEDQDSDSREKTGVFLLDSIEMDSEICVWKLADVKENRDPQEKGRPLSRKRRDW 282 (300)
Q Consensus 203 SSPGieRpLk~~~df~RfiGr~VkV~l~~ieG~kke~~GVl~L~~vDee~i~l~~~l~dVk~nr~k~~KGk~l~kkq~~~ 282 (300)
||||++|||++++||.||+|++|+|++. + ...+| +|.+++++++++. . +|+
T Consensus 78 SSPGldRpL~~~~df~r~~G~~v~V~l~---~--~~~~G--~L~~~~d~~i~l~--~-----------~~~--------- 128 (143)
T PRK14630 78 STPGINRKIKSDREFKIFEGKKIKLMLD---N--DFEEG--FILEAKADSFIFK--T-----------DSK--------- 128 (143)
T ss_pred eCCCCCCcCCCHHHHHHhCCCEEEEEEc---C--cceEE--EEEEEeCCEEEEE--E-----------CCE---------
Confidence 9999999999999999999999999983 1 12479 7899999987433 1 233
Q ss_pred eEEeeccccceeEEE
Q 022231 283 RLNLPFVMHKRVTLY 297 (300)
Q Consensus 283 ~l~Ipf~dI~KArL~ 297 (300)
.+.|||++|+||||.
T Consensus 129 ~~~i~~~~I~ka~lv 143 (143)
T PRK14630 129 EVNVLYSDVKKAKLS 143 (143)
T ss_pred EEEEEhHhcceEEEC
Confidence 389999999999983
No 17
>PF02576 DUF150: Uncharacterised BCR, YhbC family COG0779; InterPro: IPR003728 The RimP protein facilitates maturation of the 30S ribsomal subunit, and is required for the efficient production of translationally competent ribosmomes [].; PDB: 1IB8_A.
Probab=100.00 E-value=8.7e-36 Score=253.20 Aligned_cols=139 Identities=29% Similarity=0.388 Sum_probs=100.6
Q ss_pred HHHHHHhhcCCeEEEEEEE-ecCCcEEEEEEcccCCCCCCCChHHHHHHHHHHHHhhhccccCCCCCCCeEEEEecCCCC
Q 022231 130 IAHEVLLQLGDDIKLYAFK-ATPRGYVYVRLDKLSNKYGCPSMEELESYSQEYKKKLDEVGALGEIPDDLALEVSTPGAE 208 (300)
Q Consensus 130 l~epvl~~~G~eLvdVe~~-~~~~~~LrV~IDk~~~~dggVsLDDCe~vSr~Is~~LD~~e~~d~I~~~Y~LEVSSPGie 208 (300)
|++|+++++|++||+|++. .+++++|+|+||+ ++|||+|||+++||+|++.|| ++++++++|+|||||||++
T Consensus 1 li~~~~~~~g~~l~~v~~~~~~~~~~l~V~id~----~~gv~lddc~~~sr~i~~~LD---~~d~i~~~y~LEVSSPG~~ 73 (141)
T PF02576_consen 1 LIEPLLEELGLELVDVEVVKEGGNRILRVFIDK----DGGVSLDDCEKVSRAISALLD---AEDPIPEDYTLEVSSPGID 73 (141)
T ss_dssp -HHHHH-S-SSEEEEEEEEEETTEEEEEEEEE-----SS---HHHHHHHHHHHGGGTT---TS----S-EEEEEE--SSS
T ss_pred CcccchhhcCCEEEEEEEEECCCCEEEEEEEEe----CCCCCHHHHHHHHHHHHHHHc---cccccCcceEEEEeCCCCC
Confidence 6899999999999999999 6667899999999 788999999999999999999 5789999999999999999
Q ss_pred CCCCChHHHhhcCCCeeEEEE-eecCCCeeeEeeeeEEEEEeCCeeEEEEEeccccccCCCCCCCCcccccccceeEEee
Q 022231 209 RMLKVPDDLGRFKEMPITVCY-EDQDSDSREKTGVFLLDSIEMDSEICVWKLADVKENRDPQEKGRPLSRKRRDWRLNLP 287 (300)
Q Consensus 209 RpLk~~~df~RfiGr~VkV~l-~~ieG~kke~~GVl~L~~vDee~i~l~~~l~dVk~nr~k~~KGk~l~kkq~~~~l~Ip 287 (300)
|||++++||.||+|++|+|++ .+.+|+ +++.| +|.+++++++++.+. .|++. ..++||
T Consensus 74 r~L~~~~~~~~~iG~~v~v~~~~~~~~~-~~~~G--~L~~~~~~~i~l~~~-----------~~~~~-------~~~~I~ 132 (141)
T PF02576_consen 74 RPLKSPRDFERFIGRKVKVKLKQPVNGR-KEFEG--KLLEVDEDEITLEVE-----------GKGKK-------KEVEIP 132 (141)
T ss_dssp S--SSHHHHHHH-SEEEEEE-SS-SSS--SEEEE--EEEEEETTEEEEEEE------------SS-E-------EEEEE-
T ss_pred CcCCCHHHHHHhcCCeEEEEEeccCCCc-EEEEE--EEEEEeCCEEEEEEC-----------Cccce-------EEEEEE
Confidence 999999999999999999999 777776 77999 889999998765543 22221 148999
Q ss_pred ccccceeEE
Q 022231 288 FVMHKRVTL 296 (300)
Q Consensus 288 f~dI~KArL 296 (300)
|++|+||||
T Consensus 133 ~~~I~ka~L 141 (141)
T PF02576_consen 133 FSDIKKARL 141 (141)
T ss_dssp SS--SS-EE
T ss_pred HHHCceEeC
Confidence 999999997
No 18
>PRK14637 hypothetical protein; Provisional
Probab=100.00 E-value=7.7e-35 Score=252.13 Aligned_cols=137 Identities=20% Similarity=0.313 Sum_probs=117.9
Q ss_pred HHHHHHHHhhcCCeEEEEEEE-ecCCcEEEEEEcccCCCCCCCChHHHHHHHHHHHHhhhccccCCCCCCCeEEEEecCC
Q 022231 128 LSIAHEVLLQLGDDIKLYAFK-ATPRGYVYVRLDKLSNKYGCPSMEELESYSQEYKKKLDEVGALGEIPDDLALEVSTPG 206 (300)
Q Consensus 128 ~el~epvl~~~G~eLvdVe~~-~~~~~~LrV~IDk~~~~dggVsLDDCe~vSr~Is~~LD~~e~~d~I~~~Y~LEVSSPG 206 (300)
.++++|+++++||+||+|+|. .++.++|||+||+ ++|||+|||+++||+|+++||. .++ +.+|+|||||||
T Consensus 11 ~~~v~p~~~~~g~eLvdve~~~~~~~~~lrV~ID~----~~gV~iddC~~vSr~Is~~LD~---~~~-~~~y~LEVSSPG 82 (151)
T PRK14637 11 FSECEPVVEGLGCKLVDLSRRVQQAQGRVRAVIYS----AGGVGLDDCARVHRILVPRLEA---LGG-VRDVFLEVSSPG 82 (151)
T ss_pred HHHHHHHHHhcCCEEEEEEEEecCCCcEEEEEEEC----CCCCCHHHHHHHHHHHHHHhcc---ccc-ccCcEEEEeCCC
Confidence 678999999999999999999 6678999999999 7899999999999999999994 222 478999999999
Q ss_pred CCCCCCChHHHhhcCCCeeEEEEeecCCCeeeEeeeeEEEEEeCCeeEEEEEeccccccCCCCCCCCcccccccceeEEe
Q 022231 207 AERMLKVPDDLGRFKEMPITVCYEDQDSDSREKTGVFLLDSIEMDSEICVWKLADVKENRDPQEKGRPLSRKRRDWRLNL 286 (300)
Q Consensus 207 ieRpLk~~~df~RfiGr~VkV~l~~ieG~kke~~GVl~L~~vDee~i~l~~~l~dVk~nr~k~~KGk~l~kkq~~~~l~I 286 (300)
++|||++++||+||+|++|+|++ +|++++++| +|.+++++.+++. . +|+ .+.|
T Consensus 83 ldRpL~~~~~f~r~~G~~V~V~l---~~~~~~~~G--~L~~~~d~~v~l~--~-----------~~~---------~~~i 135 (151)
T PRK14637 83 IERVIKNAAEFSIFVGETVKVWF---ECTGQWQVG--TIAEADETCLVLT--S-----------DGV---------PVTI 135 (151)
T ss_pred CCCCCCCHHHHHHhCCCEEEEEE---CCCCcEEEE--EEEEEeCCEEEEE--E-----------CCE---------EEEE
Confidence 99999999999999999999998 444344489 7899999976433 1 233 3889
Q ss_pred eccccceeEEEEe
Q 022231 287 PFVMHKRVTLYLE 299 (300)
Q Consensus 287 pf~dI~KArL~ie 299 (300)
||++|++|+|.+.
T Consensus 136 ~~~~I~ka~L~~~ 148 (151)
T PRK14637 136 PYVQITKAQLHPA 148 (151)
T ss_pred EHHHeeeEEEEEE
Confidence 9999999999875
No 19
>PRK14645 hypothetical protein; Provisional
Probab=100.00 E-value=9.2e-35 Score=252.44 Aligned_cols=140 Identities=22% Similarity=0.256 Sum_probs=121.2
Q ss_pred CCHHHHHHHHHHHHHhhcCCeEEEEEEE-ecCCcEEEEEEcccCCCCCCCChHHHHHHHHHHHHhhhccccCCCCCCCeE
Q 022231 121 VPWGERALSIAHEVLLQLGDDIKLYAFK-ATPRGYVYVRLDKLSNKYGCPSMEELESYSQEYKKKLDEVGALGEIPDDLA 199 (300)
Q Consensus 121 ~~~~e~I~el~epvl~~~G~eLvdVe~~-~~~~~~LrV~IDk~~~~dggVsLDDCe~vSr~Is~~LD~~e~~d~I~~~Y~ 199 (300)
+.-.++|+++++|+++++||+||+|++. .++.++|||+||+. ..++|+||||+++||+|+++|| ++++|+++|+
T Consensus 5 ~~~~~~i~~li~~~~~~~G~elvdve~~~~~~~~ilrV~ID~~--~~~~v~lddC~~vSr~is~~LD---~~d~i~~~Y~ 79 (154)
T PRK14645 5 TENNPDLQQLAEGALEPLGYEVLEVQVQRSGGKRIVLVRIDRK--DEQPVTVEDLERASRALEAELD---RLDPIEGEYR 79 (154)
T ss_pred cccHHHHHHHHHHHHHHcCCEEEEEEEEeCCCCeEEEEEEECC--CCCCcCHHHHHHHHHHHHHHhc---ccccCCCceE
Confidence 3456889999999999999999999999 66689999999983 0246999999999999999999 5789999999
Q ss_pred EEEecCCCCCCCCChHHHhhcCCCeeEEEEeecCCCeeeEeeeeEEEEEeCCeeEEEEEeccccccCCCCCCCCcccccc
Q 022231 200 LEVSTPGAERMLKVPDDLGRFKEMPITVCYEDQDSDSREKTGVFLLDSIEMDSEICVWKLADVKENRDPQEKGRPLSRKR 279 (300)
Q Consensus 200 LEVSSPGieRpLk~~~df~RfiGr~VkV~l~~ieG~kke~~GVl~L~~vDee~i~l~~~l~dVk~nr~k~~KGk~l~kkq 279 (300)
|||||||++|||++++||.||+|++|+|++ |+ +.+.| +|.+++++.+++.+ +|+
T Consensus 80 LEVSSPGldRpL~~~~df~r~~G~~v~v~~----~~-k~~~G--~L~~~~d~~i~l~~-------------~~~------ 133 (154)
T PRK14645 80 LEVESPGPKRPLFTARHFERFAGLKAKVRG----PG-ENFTG--RIKAVSGDQVTFDV-------------GGE------ 133 (154)
T ss_pred EEEeCCCCCCCCCCHHHHHHhCCCEEEEEc----CC-eEEEE--EEEEEeCCEEEEEE-------------CCe------
Confidence 999999999999999999999999999984 33 57899 78999999764431 244
Q ss_pred cceeEEeecccccee
Q 022231 280 RDWRLNLPFVMHKRV 294 (300)
Q Consensus 280 ~~~~l~Ipf~dI~KA 294 (300)
.++|||++|+++
T Consensus 134 ---~~~i~~~~I~~~ 145 (154)
T PRK14645 134 ---DRTLRIGTFQAN 145 (154)
T ss_pred ---EEEEEHHHhhhh
Confidence 388999999765
No 20
>PRK02001 hypothetical protein; Validated
Probab=100.00 E-value=5.9e-34 Score=247.00 Aligned_cols=150 Identities=17% Similarity=0.187 Sum_probs=120.1
Q ss_pred HHHHHHHH-HHHHHhhcCCeEEEEEEEecCCcEEEEEEcccCCCCCCCChHHHHHHHHHHHHhhhccccCCCCCCCeEEE
Q 022231 123 WGERALSI-AHEVLLQLGDDIKLYAFKATPRGYVYVRLDKLSNKYGCPSMEELESYSQEYKKKLDEVGALGEIPDDLALE 201 (300)
Q Consensus 123 ~~e~I~el-~epvl~~~G~eLvdVe~~~~~~~~LrV~IDk~~~~dggVsLDDCe~vSr~Is~~LD~~e~~d~I~~~Y~LE 201 (300)
+..+|.++ ++|+++++||+||||++.. ++.|||+||+ ++||++|||+++||+|+++||+ .+ ++|+||
T Consensus 2 ~~~~~~~~~~e~~~~~~g~eLvdv~~~~--~~~lrV~ID~----~~Gv~lddC~~vSr~is~~LD~---~d---~~Y~LE 69 (152)
T PRK02001 2 IKKKVVELLVEELLEGPELFLVDLTISP--DNKIVVEIDG----DEGVWIEDCVELSRAIEHNLDR---EE---EDFELE 69 (152)
T ss_pred HHHHHHHHHHHhhhhhcCcEEEEEEEEc--CCEEEEEEEC----CCCCCHHHHHHHHHHHHHHhcC---CC---CCeEEE
Confidence 34566666 9999999999999999983 3569999999 7899999999999999999994 32 799999
Q ss_pred EecCCCCCCCCChHHHhhcCCCeeEEEEeecCCCeeeEeeeeEEEEEeCCeeEEEEEeccccccCCCCCCCCcccccccc
Q 022231 202 VSTPGAERMLKVPDDLGRFKEMPITVCYEDQDSDSREKTGVFLLDSIEMDSEICVWKLADVKENRDPQEKGRPLSRKRRD 281 (300)
Q Consensus 202 VSSPGieRpLk~~~df~RfiGr~VkV~l~~ieG~kke~~GVl~L~~vDee~i~l~~~l~dVk~nr~k~~KGk~l~kkq~~ 281 (300)
|||||++|||++++||.||+|++|+|++. |+ +++.| +|.+++++++++... + +.. ++..||+. ++.
T Consensus 70 VSSPGldRpL~~~~~f~r~~G~~v~V~l~---~~-~~~~G--~L~~~~~~~i~l~~~--~-~~~-~~~~k~~~----~~~ 135 (152)
T PRK02001 70 VGSAGLTSPLKVPRQYKKNIGRELEVLTK---NG-KKIEG--ELKSADENDITLEVK--A-REP-KEGGKGKV----TVE 135 (152)
T ss_pred EeCCCCCCcCCCHHHHHHhCCCEEEEEEC---CC-CEEEE--EEEEEeCCEEEEEEc--c-ccc-cccccccc----ccc
Confidence 99999999999999999999999999994 33 57899 789999998755422 1 000 01122321 222
Q ss_pred eeEEeeccccceeEEEE
Q 022231 282 WRLNLPFVMHKRVTLYL 298 (300)
Q Consensus 282 ~~l~Ipf~dI~KArL~i 298 (300)
..++|||++|++|+|.+
T Consensus 136 ~~~~i~~~~I~ka~l~~ 152 (152)
T PRK02001 136 KEETITYDDIKEAKVII 152 (152)
T ss_pred eeEEEEhHheeeEEEeC
Confidence 35899999999999975
No 21
>PRK14642 hypothetical protein; Provisional
Probab=100.00 E-value=2.4e-33 Score=251.96 Aligned_cols=160 Identities=21% Similarity=0.200 Sum_probs=125.3
Q ss_pred HHHHHHHHHhhcCCeEEEEEEEecCCcEEEEEEcccCC---------CCCCCChHHHHHHHHHHHHhhhccccCCCCCCC
Q 022231 127 ALSIAHEVLLQLGDDIKLYAFKATPRGYVYVRLDKLSN---------KYGCPSMEELESYSQEYKKKLDEVGALGEIPDD 197 (300)
Q Consensus 127 I~el~epvl~~~G~eLvdVe~~~~~~~~LrV~IDk~~~---------~dggVsLDDCe~vSr~Is~~LD~~e~~d~I~~~ 197 (300)
|+++++|+++++||+||+|++.. ++.|||+||++.. +++|||+|||+.+||+|+++||. ++. +.
T Consensus 3 l~~liepvv~~lG~eLvdve~~~--~~~LrV~ID~~~~~~~~~~~~~~~~gVtidDC~~vSR~Is~~LDv---e~~--~y 75 (197)
T PRK14642 3 LQQIVEQTVTGLGYDLVEIERSA--GGLLRVTIDLPWVPPTEGAPVGPEQFVTVEDCEKVTRQLQFALEV---DGV--DY 75 (197)
T ss_pred HHHHHHHHHHHcCCEEEEEEEec--CCEEEEEEecCccccccccccccCCCccHHHHHHHHHHHHHHhcc---cCc--cc
Confidence 78999999999999999999873 3489999998421 24689999999999999999994 332 33
Q ss_pred eEEEEecCCCCCCCCChHHHhhcCCCeeEEEE-eecC---------CCeeeEeeeeEEEEEeCCeeEEEEEeccccccCC
Q 022231 198 LALEVSTPGAERMLKVPDDLGRFKEMPITVCY-EDQD---------SDSREKTGVFLLDSIEMDSEICVWKLADVKENRD 267 (300)
Q Consensus 198 Y~LEVSSPGieRpLk~~~df~RfiGr~VkV~l-~~ie---------G~kke~~GVl~L~~vDee~i~l~~~l~dVk~nr~ 267 (300)
|+||||||||+|||++++||.||+|+.|+|++ .+++ |+ +.|+| +|.++++++++++|.-++...+-+
T Consensus 76 ~~LEVSSPGldRPLk~~~df~rfiG~~V~V~l~~pi~~~~~~~~~~~r-k~f~G--~L~~~~~~~i~l~~~~~~~~k~g~ 152 (197)
T PRK14642 76 KRLEVSSPGIDRPLRHEQDFERFAGEVIDITLKAPIGAAAGGQVSANR-KKFRG--TLERAESGGWQIVWSDEPPVKPGQ 152 (197)
T ss_pred cEEEEeCCCCCCCCCCHHHHHHhCCCeEEEEEeccccccccccccCCc-eEEEE--EEEEEcCCEEEEEEeecccCCCcc
Confidence 47999999999999999999999999999999 7887 54 78999 789999999988887321111100
Q ss_pred CCCCCCcccccccceeEEeeccccceeEEEEe
Q 022231 268 PQEKGRPLSRKRRDWRLNLPFVMHKRVTLYLE 299 (300)
Q Consensus 268 k~~KGk~l~kkq~~~~l~Ipf~dI~KArL~ie 299 (300)
...|||.. .....+.|+|++|++|+|.+.
T Consensus 153 ~~~k~~~~---~~~~~~~~~~~eik~a~l~p~ 181 (197)
T PRK14642 153 RVSKKRVP---APLQALGFTLDELREARLAPI 181 (197)
T ss_pred cccccccc---ccceeEEeehhheeeEEEEEE
Confidence 11233310 112358999999999999974
No 22
>PRK14644 hypothetical protein; Provisional
Probab=100.00 E-value=5.6e-33 Score=236.91 Aligned_cols=132 Identities=19% Similarity=0.233 Sum_probs=115.6
Q ss_pred HHHHHHhhcCCeEEEEEEE-ecCCcEEEEEEcccCCCCCCCChHHHHHHHHHHHHhhhccccCCCCCCCeEEEEecCCCC
Q 022231 130 IAHEVLLQLGDDIKLYAFK-ATPRGYVYVRLDKLSNKYGCPSMEELESYSQEYKKKLDEVGALGEIPDDLALEVSTPGAE 208 (300)
Q Consensus 130 l~epvl~~~G~eLvdVe~~-~~~~~~LrV~IDk~~~~dggVsLDDCe~vSr~Is~~LD~~e~~d~I~~~Y~LEVSSPGie 208 (300)
+.+|+++++|++||+|+|. .++.++|||+||+ . +||||+.+||+|+++|| +.++++++|+|||||||++
T Consensus 3 ~~e~~~~~~g~el~dve~~~~~~~~~LrV~Idk----~---~iddC~~vSr~is~~LD---~~d~i~~~Y~LEVSSPGld 72 (136)
T PRK14644 3 WKEKLLEKFGNKINEIKIVKEDGDLFLEVILNS----R---DLKDIEELTKEISDFID---NLSVEFDFDSLDISSPGFD 72 (136)
T ss_pred chhhhHHhcCCEEEEEEEEeCCCCEEEEEEECC----C---CHHHHHHHHHHHHHHhc---cccCCCCCeEEEEECCCCC
Confidence 4689999999999999999 6778999999998 3 79999999999999999 6799999999999999999
Q ss_pred CCCCChHHHhhcCCCeeEEEE-eecCCCeeeEeeeeEEEEEeCCeeEEEEEeccccccCCCCCCCCcccccccceeEEee
Q 022231 209 RMLKVPDDLGRFKEMPITVCY-EDQDSDSREKTGVFLLDSIEMDSEICVWKLADVKENRDPQEKGRPLSRKRRDWRLNLP 287 (300)
Q Consensus 209 RpLk~~~df~RfiGr~VkV~l-~~ieG~kke~~GVl~L~~vDee~i~l~~~l~dVk~nr~k~~KGk~l~kkq~~~~l~Ip 287 (300)
|||+. +||.||+|++|+|++ .+.+|+ +.++| .|.+++++.+++.+. .||+. ..++|+
T Consensus 73 RpL~~-~~f~r~~G~~v~V~l~~~~~~~-~~~~G--~L~~v~~~~i~l~~~-----------~k~~~-------~~i~~~ 130 (136)
T PRK14644 73 MDYET-DELENHIGEIIDVSLNKEVNKT-DFITG--ELLENNPETITLKWN-----------CKGQF-------RKVEIN 130 (136)
T ss_pred CCCCH-HHHHHhCCCeEEEEEccCcCCe-EEEEE--EEEEEeCCEEEEEEe-----------cCCcE-------EEEEEC
Confidence 99998 599999999999999 878887 78999 789999998766544 24442 138899
Q ss_pred ccccce
Q 022231 288 FVMHKR 293 (300)
Q Consensus 288 f~dI~K 293 (300)
+++|++
T Consensus 131 ~~~i~~ 136 (136)
T PRK14644 131 KENIKK 136 (136)
T ss_pred HHHhcC
Confidence 999874
No 23
>cd01734 YlxS_C YxlS is a Bacillus subtilis gene of unknown function with two domains that each have an alpha/beta fold. The N-terminal domain is composed of two alpha-helices and a three-stranded beta-sheet, while the C-terminal domain is composed of one alpha-helix and a five-stranded beta-sheet. This CD represents the C-terminal domain which has a fold similar to the Sm fold of proteins like Sm-D3.
Probab=99.87 E-value=8.1e-22 Score=154.48 Aligned_cols=82 Identities=29% Similarity=0.321 Sum_probs=69.2
Q ss_pred eEEEEecCCCCCCCCChHHHhhcCCCeeEEEE-eecCCCeeeEeeeeEEEEEeCCeeEEEEEeccccccCCCCCCCCccc
Q 022231 198 LALEVSTPGAERMLKVPDDLGRFKEMPITVCY-EDQDSDSREKTGVFLLDSIEMDSEICVWKLADVKENRDPQEKGRPLS 276 (300)
Q Consensus 198 Y~LEVSSPGieRpLk~~~df~RfiGr~VkV~l-~~ieG~kke~~GVl~L~~vDee~i~l~~~l~dVk~nr~k~~KGk~l~ 276 (300)
|+|||||||++|||++++||.||+|+.|+|++ .+.+|+ +++.| +|.+++++++++... .|++
T Consensus 1 Y~LEVSSPGl~RpL~~~~~~~r~~G~~v~v~~~~~~~~~-~~~~G--~L~~~~~~~v~l~~~-----------~~~~--- 63 (83)
T cd01734 1 YFLEVSSPGAERPLKKEADFERAVGKYVHVKLYQPIDGQ-KEFEG--TLLGVDDDTVTLEVD-----------IKTR--- 63 (83)
T ss_pred CEEEEcCCCCCCcCCCHHHHHHhCCCEEEEEEEcccCCe-EEEEE--EEEeEeCCEEEEEEe-----------cCCC---
Confidence 89999999999999999999999999999999 677776 67899 789999998755422 1121
Q ss_pred ccccceeEEeeccccceeEEEEeC
Q 022231 277 RKRRDWRLNLPFVMHKRVTLYLEY 300 (300)
Q Consensus 277 kkq~~~~l~Ipf~dI~KArL~ieF 300 (300)
...++|||++|++|+|.++|
T Consensus 64 ----~~~~~i~~~~I~ka~l~~~f 83 (83)
T cd01734 64 ----GKTVEIPLDKIAKARLAPEF 83 (83)
T ss_pred ----CeEEEEEhHHeeEEEEEEEC
Confidence 12489999999999999998
No 24
>cd06168 LSm9 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm9 proteins have a single Sm-like domain structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=86.37 E-value=3.8 Score=31.90 Aligned_cols=72 Identities=14% Similarity=0.164 Sum_probs=44.8
Q ss_pred HHHhhcCCCeeEEEEeecCCCeeeEeeeeEEEEEeCCeeEEEEEeccccccCCCCCCCCcccccccceeEEeecccccee
Q 022231 215 DDLGRFKEMPITVCYEDQDSDSREKTGVFLLDSIEMDSEICVWKLADVKENRDPQEKGRPLSRKRRDWRLNLPFVMHKRV 294 (300)
Q Consensus 215 ~df~RfiGr~VkV~l~~ieG~kke~~GVl~L~~vDee~i~l~~~l~dVk~nr~k~~KGk~l~kkq~~~~l~Ipf~dI~KA 294 (300)
..+..++|+.|+|++. +|+ .+.| +|..+|... .+. |.|+.+-+....+.....++. -.-+-+|-+.|.++
T Consensus 3 ~~L~~~l~~~v~V~l~--dgR--~~~G--~l~~~D~~~-Niv--L~~~~E~~~~~~~~~~~~~r~-lGlv~IrG~~Iv~i 72 (75)
T cd06168 3 QKLRSLLGRTMRIHMT--DGR--TLVG--VFLCTDRDC-NII--LGSAQEYRPPPDSFSPTEPRV-LGLVMIPGHHIVSI 72 (75)
T ss_pred hHHHHhcCCeEEEEEc--CCe--EEEE--EEEEEcCCC-cEE--ecCcEEEEcccCccCCccEEE-eeeEEEeCCeEEEE
Confidence 3567889999999996 775 7999 779998876 344 556666542211101001111 12367888888776
Q ss_pred EE
Q 022231 295 TL 296 (300)
Q Consensus 295 rL 296 (300)
.+
T Consensus 73 ~v 74 (75)
T cd06168 73 EV 74 (75)
T ss_pred EE
Confidence 54
No 25
>PF01423 LSM: LSM domain ; InterPro: IPR001163 This family is found in Lsm (like-Sm) proteins and in bacterial Lsm-related Hfq proteins. In each case, the domain adopts a core structure consisting of an open beta-barrel with an SH3-like topology. Lsm (like-Sm) proteins have diverse functions, and are thought to be important modulators of RNA biogenesis and function [, ]. The Sm proteins form part of specific small nuclear ribonucleoproteins (snRNPs) that are involved in the processing of pre-mRNAs to mature mRNAs, and are a major component of the eukaryotic spliceosome. Most snRNPs consist of seven Sm proteins (B/B', D1, D2, D3, E, F and G) arranged in a ring on a uridine-rich sequence (Sm site), plus a small nuclear RNA (snRNA) (either U1, U2, U5 or U4/6) []. All Sm proteins contain a common sequence motif in two segments, Sm1 and Sm2, separated by a short variable linker []. In other snRNPs, certain Sm proteins are replaced with different Lsm proteins, such as with U7 snRNPs, in which the D1 and D2 Sm proteins are replaced with U7-specific Lsm10 and Lsm11 proteins, where Lsm11 plays a role in histone U7-specific RNA processing []. Lsm proteins are also found in archaebacteria, which do not have any splicing apparatus suggesting a more general role for Lsm proteins. The pleiotropic translational regulator Hfq (host factor Q) is a bacterial Lsm-like protein, which modulates the structure of numerous RNA molecules by binding preferentially to A/U-rich sequences in RNA []. Hfq forms an Lsm-like fold, however, unlike the heptameric Sm proteins, Hfq forms a homo-hexameric ring.; PDB: 1D3B_K 2Y9D_D 2Y9A_D 2Y9C_R 3VRI_C 2Y9B_K 3QUI_D 3M4G_H 3INZ_E 1U1S_C ....
Probab=78.64 E-value=7.6 Score=28.44 Aligned_cols=41 Identities=24% Similarity=0.199 Sum_probs=31.0
Q ss_pred HHhhcCCCeeEEEEeecCCCeeeEeeeeEEEEEeCCeeEEEEEecccccc
Q 022231 216 DLGRFKEMPITVCYEDQDSDSREKTGVFLLDSIEMDSEICVWKLADVKEN 265 (300)
Q Consensus 216 df~RfiGr~VkV~l~~ieG~kke~~GVl~L~~vDee~i~l~~~l~dVk~n 265 (300)
.+..++|++|+|.+. +|+ .+.| +|.++|... .+. |.|+++.
T Consensus 2 ~L~~~~g~~V~V~l~--~g~--~~~G--~L~~~D~~~-Nl~--L~~~~~~ 42 (67)
T PF01423_consen 2 FLQKLIGKRVRVELK--NGR--TYRG--TLVSFDQFM-NLV--LSDVTET 42 (67)
T ss_dssp HHHHTTTSEEEEEET--TSE--EEEE--EEEEEETTE-EEE--EEEEEEE
T ss_pred hhHHhCCcEEEEEEe--CCE--EEEE--EEEEeechh-eEE--eeeEEEE
Confidence 467899999999996 664 6899 789999875 344 5566554
No 26
>cd01726 LSm6 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm6 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=74.83 E-value=5.6 Score=29.81 Aligned_cols=40 Identities=18% Similarity=0.183 Sum_probs=29.6
Q ss_pred HHhhcCCCeeEEEEeecCCCeeeEeeeeEEEEEeCCeeEEEEEeccccc
Q 022231 216 DLGRFKEMPITVCYEDQDSDSREKTGVFLLDSIEMDSEICVWKLADVKE 264 (300)
Q Consensus 216 df~RfiGr~VkV~l~~ieG~kke~~GVl~L~~vDee~i~l~~~l~dVk~ 264 (300)
-+..++|+.|.|+++ +|+ ++.| +|.++|.-- .++ |.|+.+
T Consensus 4 ~L~~~~~~~V~V~Lk--~g~--~~~G--~L~~~D~~m-Nlv--L~~~~~ 43 (67)
T cd01726 4 FLKAIIGRPVVVKLN--SGV--DYRG--ILACLDGYM-NIA--LEQTEE 43 (67)
T ss_pred HHHhhCCCeEEEEEC--CCC--EEEE--EEEEEccce-eeE--EeeEEE
Confidence 347889999999996 664 7899 889998653 455 446543
No 27
>cd01729 LSm7 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm7 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=71.08 E-value=7.9 Score=30.35 Aligned_cols=42 Identities=29% Similarity=0.348 Sum_probs=31.5
Q ss_pred hHHHhhcCCCeeEEEEeecCCCeeeEeeeeEEEEEeCCeeEEEEEeccccc
Q 022231 214 PDDLGRFKEMPITVCYEDQDSDSREKTGVFLLDSIEMDSEICVWKLADVKE 264 (300)
Q Consensus 214 ~~df~RfiGr~VkV~l~~ieG~kke~~GVl~L~~vDee~i~l~~~l~dVk~ 264 (300)
.-++.+++|+.|.|+++ +|+ ++.| +|.++|.-. .++ |.++.+
T Consensus 4 ~~~L~~~i~k~V~V~l~--~gr--~~~G--~L~~~D~~m-Nlv--L~~~~E 45 (81)
T cd01729 4 ILDLSKYVDKKIRVKFQ--GGR--EVTG--ILKGYDQLL-NLV--LDDTVE 45 (81)
T ss_pred hhhHHHhcCCeEEEEEC--CCc--EEEE--EEEEEcCcc-cEE--ecCEEE
Confidence 45688999999999996 664 7899 789998865 344 445533
No 28
>cd01722 Sm_F The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit F is capable of forming both homo- and hetero-heptamer ring structures. To form the hetero-heptamer, Sm subunit F initially binds subunits E and G to form a trimer which then assembles onto snRNA along with the D3/B and D1/D2 heterodimers.
Probab=70.77 E-value=7.9 Score=29.13 Aligned_cols=40 Identities=25% Similarity=0.182 Sum_probs=30.0
Q ss_pred HHhhcCCCeeEEEEeecCCCeeeEeeeeEEEEEeCCeeEEEEEeccccc
Q 022231 216 DLGRFKEMPITVCYEDQDSDSREKTGVFLLDSIEMDSEICVWKLADVKE 264 (300)
Q Consensus 216 df~RfiGr~VkV~l~~ieG~kke~~GVl~L~~vDee~i~l~~~l~dVk~ 264 (300)
.+..++|+.|.|.++ +|+ .+.| +|.++|... .++ +.|+.+
T Consensus 5 ~L~~~~g~~V~V~Lk--~g~--~~~G--~L~~~D~~m-Ni~--L~~~~e 44 (68)
T cd01722 5 FLNDLTGKPVIVKLK--WGM--EYKG--TLVSVDSYM-NLQ--LANTEE 44 (68)
T ss_pred HHHHcCCCEEEEEEC--CCc--EEEE--EEEEECCCE-EEE--EeeEEE
Confidence 347789999999996 675 7899 889998764 455 556644
No 29
>PRK00737 small nuclear ribonucleoprotein; Provisional
Probab=70.35 E-value=9.6 Score=29.05 Aligned_cols=41 Identities=24% Similarity=0.296 Sum_probs=30.7
Q ss_pred HHHhhcCCCeeEEEEeecCCCeeeEeeeeEEEEEeCCeeEEEEEeccccc
Q 022231 215 DDLGRFKEMPITVCYEDQDSDSREKTGVFLLDSIEMDSEICVWKLADVKE 264 (300)
Q Consensus 215 ~df~RfiGr~VkV~l~~ieG~kke~~GVl~L~~vDee~i~l~~~l~dVk~ 264 (300)
+-+.+++|++|.|.++ +|+ .+.| +|.++|..- .++ |.|+++
T Consensus 7 ~~L~~~~~k~V~V~lk--~g~--~~~G--~L~~~D~~m-Nlv--L~d~~e 47 (72)
T PRK00737 7 DVLNNALNSPVLVRLK--GGR--EFRG--ELQGYDIHM-NLV--LDNAEE 47 (72)
T ss_pred HHHHHhCCCEEEEEEC--CCC--EEEE--EEEEEcccc-eeE--EeeEEE
Confidence 3457889999999996 675 6899 789998864 455 556644
No 30
>PF14438 SM-ATX: Ataxin 2 SM domain; PDB: 1M5Q_1.
Probab=69.72 E-value=9.8 Score=28.98 Aligned_cols=38 Identities=18% Similarity=0.209 Sum_probs=24.7
Q ss_pred HhhcCCCeeEEEEeecCCCeeeEeeeeEEEEEeCC--eeEEEEEec
Q 022231 217 LGRFKEMPITVCYEDQDSDSREKTGVFLLDSIEMD--SEICVWKLA 260 (300)
Q Consensus 217 f~RfiGr~VkV~l~~ieG~kke~~GVl~L~~vDee--~i~l~~~l~ 260 (300)
+...+|+.|.|++. +|. .|+|+ |.+++.+ ...++++.+
T Consensus 7 ~~~lvG~~V~V~~~--~G~--~yeGi--f~s~s~~~~~~~vvLk~a 46 (77)
T PF14438_consen 7 LTNLVGQTVEVTTK--NGS--VYEGI--FHSASPESNEFDVVLKMA 46 (77)
T ss_dssp HHTTTTSEEEEEET--TS---EEEEE--EEEE-T---T--EEEEEE
T ss_pred HHhCcCCEEEEEEC--CCC--EEEEE--EEeCCCcccceeEEEEee
Confidence 45689999999996 786 58995 5777774 345666654
No 31
>cd01731 archaeal_Sm1 The archaeal sm1 proteins: The Sm proteins are conserved in all three domains of life and are always associated with U-rich RNA sequences. They function to mediate RNA-RNA interactions and RNA biogenesis. All Sm proteins contain a common sequence motif in two segments, Sm1 and Sm2, separated by a short variable linker. Eukaryotic Sm proteins form part of specific small nuclear ribonucleoproteins (snRNPs) that are involved in the processing of pre-mRNAs to mature mRNAs, and are a major component of the eukaryotic spliceosome. Most snRNPs consist of seven Sm proteins (B/B', D1, D2, D3, E, F and G) arranged in a ring on a uridine-rich sequence (Sm site), plus a small nuclear RNA (snRNA) (either U1, U2, U5 or U4/6). Since archaebacteria do not have any splicing apparatus, Sm proteins of archaebacteria may play a more general role. Archaeal Lsm proteins are likely to represent the ancestral Sm domain.
Probab=69.06 E-value=9.1 Score=28.66 Aligned_cols=40 Identities=28% Similarity=0.268 Sum_probs=29.5
Q ss_pred HHhhcCCCeeEEEEeecCCCeeeEeeeeEEEEEeCCeeEEEEEeccccc
Q 022231 216 DLGRFKEMPITVCYEDQDSDSREKTGVFLLDSIEMDSEICVWKLADVKE 264 (300)
Q Consensus 216 df~RfiGr~VkV~l~~ieG~kke~~GVl~L~~vDee~i~l~~~l~dVk~ 264 (300)
-+..++|++|.|.++ +|+ .+.| +|.++|.-. .++ |.++.+
T Consensus 4 ~L~~~~~~~V~V~l~--~g~--~~~G--~L~~~D~~m-Nlv--L~~~~e 43 (68)
T cd01731 4 VLKDSLNKPVLVKLK--GGK--EVRG--RLKSYDQHM-NLV--LEDAEE 43 (68)
T ss_pred HHHHhcCCEEEEEEC--CCC--EEEE--EEEEECCcc-eEE--EeeEEE
Confidence 356789999999996 665 6899 789998864 444 445543
No 32
>cd01719 Sm_G The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit G binds subunits E and F to form a trimer which then assembles onto snRNA along with the D1/D2 and D3/B heterodimers forming a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=68.48 E-value=8.8 Score=29.46 Aligned_cols=41 Identities=17% Similarity=0.297 Sum_probs=30.9
Q ss_pred HHHhhcCCCeeEEEEeecCCCeeeEeeeeEEEEEeCCeeEEEEEeccccc
Q 022231 215 DDLGRFKEMPITVCYEDQDSDSREKTGVFLLDSIEMDSEICVWKLADVKE 264 (300)
Q Consensus 215 ~df~RfiGr~VkV~l~~ieG~kke~~GVl~L~~vDee~i~l~~~l~dVk~ 264 (300)
.++..+++++|.|+++ +|+ .+.| +|.++|.-. .++ |.|+.+
T Consensus 3 ~~L~~~i~k~V~V~L~--~g~--~~~G--~L~~~D~~m-Nlv--L~~~~E 43 (72)
T cd01719 3 PELKKYMDKKLSLKLN--GNR--KVSG--ILRGFDPFM-NLV--LDDAVE 43 (72)
T ss_pred hhhHHhCCCeEEEEEC--CCe--EEEE--EEEEEcccc-cEE--eccEEE
Confidence 4678899999999996 664 7899 889998654 445 556544
No 33
>cd01721 Sm_D3 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit D3 heterodimerizes with subunit B and three such heterodimers form a hexameric ring structure with alternating B and D3 subunits. The D3 - B heterodimer also assembles into a heptameric ring containing D1, D2, E, F, and G subunits. Sm-like proteins exist in archaea as well as prokaryotes which form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=67.25 E-value=35 Score=25.86 Aligned_cols=39 Identities=26% Similarity=0.223 Sum_probs=29.9
Q ss_pred HhhcCCCeeEEEEeecCCCeeeEeeeeEEEEEeCCeeEEEEEeccccc
Q 022231 217 LGRFKEMPITVCYEDQDSDSREKTGVFLLDSIEMDSEICVWKLADVKE 264 (300)
Q Consensus 217 f~RfiGr~VkV~l~~ieG~kke~~GVl~L~~vDee~i~l~~~l~dVk~ 264 (300)
+...+|+.|.|.++ +|. .+.| +|.++|.-. .++ |.++++
T Consensus 5 L~~~~g~~V~VeLk--~g~--~~~G--~L~~~D~~M-Nl~--L~~~~~ 43 (70)
T cd01721 5 LHEAEGHIVTVELK--TGE--VYRG--KLIEAEDNM-NCQ--LKDVTV 43 (70)
T ss_pred HhhCCCCEEEEEEC--CCc--EEEE--EEEEEcCCc-eeE--EEEEEE
Confidence 46789999999997 664 7899 889998864 455 456654
No 34
>cd00600 Sm_like The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=63.94 E-value=11 Score=26.98 Aligned_cols=38 Identities=24% Similarity=0.233 Sum_probs=28.0
Q ss_pred hhcCCCeeEEEEeecCCCeeeEeeeeEEEEEeCCeeEEEEEeccccc
Q 022231 218 GRFKEMPITVCYEDQDSDSREKTGVFLLDSIEMDSEICVWKLADVKE 264 (300)
Q Consensus 218 ~RfiGr~VkV~l~~ieG~kke~~GVl~L~~vDee~i~l~~~l~dVk~ 264 (300)
..++|++|.|.+. +|+ .+.| +|.++|... .++ |.++++
T Consensus 2 ~~~~g~~V~V~l~--~g~--~~~G--~L~~~D~~~-Ni~--L~~~~~ 39 (63)
T cd00600 2 KDLVGKTVRVELK--DGR--VLEG--VLVAFDKYM-NLV--LDDVEE 39 (63)
T ss_pred hHHCCCEEEEEEC--CCc--EEEE--EEEEECCCC-CEE--ECCEEE
Confidence 4578999999996 664 6899 789999875 344 445544
No 35
>COG1958 LSM1 Small nuclear ribonucleoprotein (snRNP) homolog [Transcription]
Probab=63.71 E-value=12 Score=28.77 Aligned_cols=41 Identities=24% Similarity=0.232 Sum_probs=30.5
Q ss_pred HHHhhcCCCeeEEEEeecCCCeeeEeeeeEEEEEeCCeeEEEEEeccccc
Q 022231 215 DDLGRFKEMPITVCYEDQDSDSREKTGVFLLDSIEMDSEICVWKLADVKE 264 (300)
Q Consensus 215 ~df~RfiGr~VkV~l~~ieG~kke~~GVl~L~~vDee~i~l~~~l~dVk~ 264 (300)
.-+.+++|+.|.|+++ +|+ ++.| +|.++|.-- .++ |.|+.+
T Consensus 10 ~~l~~~~~~~V~V~lk--~g~--~~~G--~L~~~D~~m-Nlv--L~d~~e 50 (79)
T COG1958 10 SFLKKLLNKRVLVKLK--NGR--EYRG--TLVGFDQYM-NLV--LDDVEE 50 (79)
T ss_pred HHHHHhhCCEEEEEEC--CCC--EEEE--EEEEEccce-eEE--EeceEE
Confidence 3456788899999996 674 7899 889998874 344 556655
No 36
>cd01717 Sm_B The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit B heterodimerizes with subunit D3 and three such heterodimers form a hexameric ring structure with alternating B and D3 subunits. The D3 - B heterodimer also assembles into a heptameric ring containing D1, D2, E, F, and G subunits. Sm-like proteins exist in archaea as well as prokaryotes which form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=63.19 E-value=15 Score=28.45 Aligned_cols=41 Identities=17% Similarity=0.217 Sum_probs=30.9
Q ss_pred HHhhcCCCeeEEEEeecCCCeeeEeeeeEEEEEeCCeeEEEEEecccccc
Q 022231 216 DLGRFKEMPITVCYEDQDSDSREKTGVFLLDSIEMDSEICVWKLADVKEN 265 (300)
Q Consensus 216 df~RfiGr~VkV~l~~ieG~kke~~GVl~L~~vDee~i~l~~~l~dVk~n 265 (300)
.+..++|+.|.|+++ +|+ .+.| +|.++|... .++ |.|+.+-
T Consensus 4 ~l~~~l~~~V~V~l~--dgR--~~~G--~L~~~D~~~-NlV--L~~~~E~ 44 (79)
T cd01717 4 KMLQLINYRLRVTLQ--DGR--QFVG--QFLAFDKHM-NLV--LSDCEEF 44 (79)
T ss_pred hhHHHcCCEEEEEEC--CCc--EEEE--EEEEEcCcc-CEE--cCCEEEE
Confidence 467889999999996 675 6899 789998875 334 5566553
No 37
>smart00651 Sm snRNP Sm proteins. small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA splicing
Probab=60.66 E-value=16 Score=26.62 Aligned_cols=40 Identities=25% Similarity=0.234 Sum_probs=29.8
Q ss_pred HHhhcCCCeeEEEEeecCCCeeeEeeeeEEEEEeCCeeEEEEEeccccc
Q 022231 216 DLGRFKEMPITVCYEDQDSDSREKTGVFLLDSIEMDSEICVWKLADVKE 264 (300)
Q Consensus 216 df~RfiGr~VkV~l~~ieG~kke~~GVl~L~~vDee~i~l~~~l~dVk~ 264 (300)
.+..++|+.|.|.+. +|+ .+.| +|.++|... .++ |.|+.+
T Consensus 2 ~L~~~~~~~V~V~l~--~g~--~~~G--~L~~~D~~~-Nlv--L~~~~e 41 (67)
T smart00651 2 FLKKLIGKRVLVELK--NGR--EYRG--TLKGFDQFM-NLV--LEDVEE 41 (67)
T ss_pred hhHHhCCcEEEEEEC--CCc--EEEE--EEEEECccc-cEE--EccEEE
Confidence 356789999999996 664 6899 789998864 344 556544
No 38
>cd01732 LSm5 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm4 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=58.00 E-value=31 Score=26.83 Aligned_cols=38 Identities=24% Similarity=0.189 Sum_probs=28.7
Q ss_pred hhcCCCeeEEEEeecCCCeeeEeeeeEEEEEeCCeeEEEEEeccccc
Q 022231 218 GRFKEMPITVCYEDQDSDSREKTGVFLLDSIEMDSEICVWKLADVKE 264 (300)
Q Consensus 218 ~RfiGr~VkV~l~~ieG~kke~~GVl~L~~vDee~i~l~~~l~dVk~ 264 (300)
.++++++|.|+++ +|+ ++.| +|.++|.-. .++ |.|+.+
T Consensus 9 ~~~~~~~V~V~l~--~gr--~~~G--~L~g~D~~m-Nlv--L~da~E 46 (76)
T cd01732 9 DKCIGSRIWIVMK--SDK--EFVG--TLLGFDDYV-NMV--LEDVTE 46 (76)
T ss_pred HHhCCCEEEEEEC--CCe--EEEE--EEEEeccce-EEE--EccEEE
Confidence 7889999999996 664 6899 789998864 344 556544
No 39
>PF10842 DUF2642: Protein of unknown function (DUF2642); InterPro: IPR020139 This entry contains proteins with no known function.
Probab=56.88 E-value=52 Score=25.36 Aligned_cols=33 Identities=15% Similarity=0.136 Sum_probs=27.2
Q ss_pred hHHHhhcCCCeeEEEEeecCCCeeeEeeeeEEEEEeCCee
Q 022231 214 PDDLGRFKEMPITVCYEDQDSDSREKTGVFLLDSIEMDSE 253 (300)
Q Consensus 214 ~~df~RfiGr~VkV~l~~ieG~kke~~GVl~L~~vDee~i 253 (300)
...+...+|+.+.|.+. .|. +.| +|.++..|.+
T Consensus 13 yq~lq~liG~~vvV~T~--~g~---v~G--~L~~V~pDhI 45 (66)
T PF10842_consen 13 YQTLQSLIGQRVVVQTT--RGS---VRG--ILVDVKPDHI 45 (66)
T ss_pred HHHHHHhcCCEEEEEEc--CCc---EEE--EEEeecCCEE
Confidence 36788999999999984 453 689 7899999976
No 40
>PF08863 YolD: YolD-like protein; InterPro: IPR014962 These proteins are functionally uncharacterised. However it has been predicted that these proteins are functionally equivalent to the UmuD subunit of polymerase V from Gram-negative bacteria [].
Probab=55.65 E-value=57 Score=24.98 Aligned_cols=49 Identities=29% Similarity=0.409 Sum_probs=34.9
Q ss_pred CCeeEEEE-eecCCCeeeEeeeeEEEEEeCCeeEEEEEeccccccCCCCCCCCcccccccceeEEeeccccce
Q 022231 222 EMPITVCY-EDQDSDSREKTGVFLLDSIEMDSEICVWKLADVKENRDPQEKGRPLSRKRRDWRLNLPFVMHKR 293 (300)
Q Consensus 222 Gr~VkV~l-~~ieG~kke~~GVl~L~~vDee~i~l~~~l~dVk~nr~k~~KGk~l~kkq~~~~l~Ipf~dI~K 293 (300)
+.+|.|+| . +|.-....| .+..+|...-++.+. + ..+. ...|||++|..
T Consensus 42 ~~~v~ity~~--~g~~~~~~G--~I~~id~~~~~l~~~--~--------~~~~---------~~~I~~~~I~~ 91 (92)
T PF08863_consen 42 NQPVTITYYE--DGYYQSVTG--TIHKIDEINRTLKLK--D--------EDGE---------TEKIPFDDIID 91 (92)
T ss_pred CCEEEEEEEE--CCeeEEEEE--EEEEEcCCCCEEEEE--e--------CCCC---------EEEEEhhhEEE
Confidence 57888988 5 676677899 789999988765543 2 0121 37899999865
No 41
>cd01728 LSm1 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm1 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=54.02 E-value=23 Score=27.42 Aligned_cols=40 Identities=23% Similarity=0.201 Sum_probs=30.2
Q ss_pred HHHhhcCCCeeEEEEeecCCCeeeEeeeeEEEEEeCCeeEEEEEecccc
Q 022231 215 DDLGRFKEMPITVCYEDQDSDSREKTGVFLLDSIEMDSEICVWKLADVK 263 (300)
Q Consensus 215 ~df~RfiGr~VkV~l~~ieG~kke~~GVl~L~~vDee~i~l~~~l~dVk 263 (300)
.++..+++++|.|+++ +|+ .+.| +|.++|.-. .++ |.|+.
T Consensus 5 ~~L~~~l~k~v~V~l~--~gr--~~~G--~L~~fD~~~-Nlv--L~d~~ 44 (74)
T cd01728 5 ASLVDDLDKKVVVLLR--DGR--KLIG--ILRSFDQFA-NLV--LQDTV 44 (74)
T ss_pred HHHHHhcCCEEEEEEc--CCe--EEEE--EEEEECCcc-cEE--ecceE
Confidence 4678899999999996 664 7899 789998764 344 55553
No 42
>cd01725 LSm2 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm2 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=53.82 E-value=24 Score=27.61 Aligned_cols=38 Identities=16% Similarity=0.128 Sum_probs=29.0
Q ss_pred hhcCCCeeEEEEeecCCCeeeEeeeeEEEEEeCCeeEEEEEeccccc
Q 022231 218 GRFKEMPITVCYEDQDSDSREKTGVFLLDSIEMDSEICVWKLADVKE 264 (300)
Q Consensus 218 ~RfiGr~VkV~l~~ieG~kke~~GVl~L~~vDee~i~l~~~l~dVk~ 264 (300)
....|+.|.|.++ +|. .+.| +|.++|.-- .++ +.|++.
T Consensus 7 ~~l~g~~V~VeLK--ng~--~~~G--~L~~vD~~M-Ni~--L~n~~~ 44 (81)
T cd01725 7 KTLVGKEVTVELK--NDL--SIRG--TLHSVDQYL-NIK--LTNISV 44 (81)
T ss_pred HhCCCCEEEEEEC--CCc--EEEE--EEEEECCCc-ccE--EEEEEE
Confidence 7789999999996 664 6899 789998875 455 456643
No 43
>cd01723 LSm4 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm4 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=53.70 E-value=25 Score=27.03 Aligned_cols=39 Identities=18% Similarity=0.118 Sum_probs=29.2
Q ss_pred HhhcCCCeeEEEEeecCCCeeeEeeeeEEEEEeCCeeEEEEEeccccc
Q 022231 217 LGRFKEMPITVCYEDQDSDSREKTGVFLLDSIEMDSEICVWKLADVKE 264 (300)
Q Consensus 217 f~RfiGr~VkV~l~~ieG~kke~~GVl~L~~vDee~i~l~~~l~dVk~ 264 (300)
++...|+.|.|.++ +|. .+.| +|.++|+.- .++ +.++++
T Consensus 6 L~~~~g~~V~VeLk--ng~--~~~G--~L~~~D~~m-Ni~--L~~~~~ 44 (76)
T cd01723 6 LKTAQNHPMLVELK--NGE--TYNG--HLVNCDNWM-NIH--LREVIC 44 (76)
T ss_pred HHhcCCCEEEEEEC--CCC--EEEE--EEEEEcCCC-ceE--EEeEEE
Confidence 46789999999996 564 6899 789998874 445 446544
No 44
>cd01724 Sm_D1 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit D1 heterodimerizes with subunit D2 and three such heterodimers form a hexameric ring structure with alternating D1 and D2 subunits. The D1 - D2 heterodimer also assembles into a heptameric ring containing DB, D3, E, F, and G subunits. Sm-like proteins exist in archaea as well as prokaryotes which form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=51.58 E-value=42 Score=26.92 Aligned_cols=39 Identities=15% Similarity=0.210 Sum_probs=29.5
Q ss_pred HhhcCCCeeEEEEeecCCCeeeEeeeeEEEEEeCCeeEEEEEeccccc
Q 022231 217 LGRFKEMPITVCYEDQDSDSREKTGVFLLDSIEMDSEICVWKLADVKE 264 (300)
Q Consensus 217 f~RfiGr~VkV~l~~ieG~kke~~GVl~L~~vDee~i~l~~~l~dVk~ 264 (300)
++...|+.|.|.++ +|. .+.| +|.++|+-. .++ +.|+++
T Consensus 6 L~~l~g~~V~VeLK--ng~--~~~G--~L~~vD~~M-Nl~--L~~a~~ 44 (90)
T cd01724 6 LMKLTNETVTIELK--NGT--IVHG--TITGVDPSM-NTH--LKNVKL 44 (90)
T ss_pred HHhCCCCEEEEEEC--CCC--EEEE--EEEEEcCce-eEE--EEEEEE
Confidence 46789999999996 564 6899 789998875 455 446544
No 45
>cd01733 LSm10 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm10 is an SmD1-like protein which is thought to bind U7 snRNA along with LSm11 and five other Sm subunits to form a 7-member ring structure. LSm10 and the U7 snRNP of which it is a part are thought to play an important role in histone mRNA 3' processing.
Probab=50.30 E-value=86 Score=24.42 Aligned_cols=38 Identities=21% Similarity=0.152 Sum_probs=29.2
Q ss_pred hhcCCCeeEEEEeecCCCeeeEeeeeEEEEEeCCeeEEEEEeccccc
Q 022231 218 GRFKEMPITVCYEDQDSDSREKTGVFLLDSIEMDSEICVWKLADVKE 264 (300)
Q Consensus 218 ~RfiGr~VkV~l~~ieG~kke~~GVl~L~~vDee~i~l~~~l~dVk~ 264 (300)
....|+.|.|.++ +|. .+.| +|.++|+.. .++ |.|++.
T Consensus 15 ~~l~g~~V~VeLK--ng~--~~~G--~L~~vD~~M-Nl~--L~~~~~ 52 (78)
T cd01733 15 QGLQGKVVTVELR--NET--TVTG--RIASVDAFM-NIR--LAKVTI 52 (78)
T ss_pred HHCCCCEEEEEEC--CCC--EEEE--EEEEEcCCc-eeE--EEEEEE
Confidence 6789999999996 664 7899 889998875 445 556654
No 46
>PF08442 ATP-grasp_2: ATP-grasp domain; InterPro: IPR013650 The ATP-grasp superfamily currently includes 17 groups of enzymes, catalyzing ATP-dependent ligation of a carboxylate containing molecule to an amino or thiol group-containing molecule []. They contribute predominantly to macromolecular synthesis. ATP-hydrolysis is used to activate a substrate. For example, DD-ligase transfers phosphate from ATP to D-alanine on the first step of catalysis. On the second step the resulting acylphosphate is attacked by a second D-alanine to produce a DD dipeptide following phosphate elimination []. The ATP-grasp domain contains three conserved motifs, corresponding to the phosphate binding loop and the Mg(2+) binding site []. The fold is characterised by two alpha-beta subdomains that grasp the ATP molecule between them. Each subdomain provides a variable loop that forms a part of the active site, completed by region of other domains not conserved between the various ATP-grasp enzymes []. The ATP-grasp domain represented by this entry is found primarily in succinyl-CoA synthetases (6.2.1.5 from EC).; PDB: 3PFF_A 3MWD_A 3MWE_A 1CQI_E 1SCU_B 2NU9_G 2NU6_E 1CQJ_E 2NU7_B 1JLL_E ....
Probab=49.78 E-value=60 Score=29.62 Aligned_cols=65 Identities=34% Similarity=0.473 Sum_probs=41.9
Q ss_pred cccCCCCCceEecCCCHHHHHHHHHHHHHhhcCCeEE--------------EEEEE-ec-CCcEEEEEEcccCC------
Q 022231 107 VGDGGDGGGVVFQGVPWGERALSIAHEVLLQLGDDIK--------------LYAFK-AT-PRGYVYVRLDKLSN------ 164 (300)
Q Consensus 107 ~~d~~~g~~i~~~~~~~~e~I~el~epvl~~~G~eLv--------------dVe~~-~~-~~~~LrV~IDk~~~------ 164 (300)
.|-=|-+|||.++..+ +.+.+.+...+ |..|. .|+=. .. ...|+-|.+|+...
T Consensus 50 ~GgRGK~GgVk~~~s~--~ea~~~a~~ml---g~~l~T~Qtg~~G~~v~~vlvee~v~~~~E~Ylsi~~DR~~~~p~ii~ 124 (202)
T PF08442_consen 50 AGGRGKAGGVKIAKSP--EEAKEAAKEML---GKTLKTKQTGPKGEKVNKVLVEEFVDIKREYYLSITLDRESRGPVIIA 124 (202)
T ss_dssp SSTTTTTTCEEEESSH--HHHHHHHHTTT---TSEEE-TTSTTTEEEE--EEEEE---CCEEEEEEEEEETTTTEEEEEE
T ss_pred ecCcccCCceeecCCH--HHHHHHHHHHh---CCceEeeecCCCCCEeeEEEEEecCccCceEEEEEEeccCCCceEEEE
Confidence 3445556999999886 66777777765 33343 22212 22 34789999987542
Q ss_pred -CCCCCChHHHHH
Q 022231 165 -KYGCPSMEELES 176 (300)
Q Consensus 165 -~dggVsLDDCe~ 176 (300)
+.||++|++.++
T Consensus 125 S~~GGvdIEeva~ 137 (202)
T PF08442_consen 125 SKEGGVDIEEVAA 137 (202)
T ss_dssp ESSTSSTHHHHHH
T ss_pred eccCCccHHHHhh
Confidence 378999998764
No 47
>cd01730 LSm3 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm3 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=48.52 E-value=34 Score=26.64 Aligned_cols=41 Identities=24% Similarity=0.251 Sum_probs=29.8
Q ss_pred HH-hhcCCCeeEEEEeecCCCeeeEeeeeEEEEEeCCeeEEEEEecccccc
Q 022231 216 DL-GRFKEMPITVCYEDQDSDSREKTGVFLLDSIEMDSEICVWKLADVKEN 265 (300)
Q Consensus 216 df-~RfiGr~VkV~l~~ieG~kke~~GVl~L~~vDee~i~l~~~l~dVk~n 265 (300)
+| +.+.+++|.|+++ +|+ .+.| +|.++|.-. .++ |.|+.+.
T Consensus 4 ~~l~~~~~k~V~V~l~--~gr--~~~G--~L~~fD~~m-Nlv--L~d~~E~ 45 (82)
T cd01730 4 DLIRLSLDERVYVKLR--GDR--ELRG--RLHAYDQHL-NMI--LGDVEET 45 (82)
T ss_pred HHHHHhCCCEEEEEEC--CCC--EEEE--EEEEEccce-EEe--ccceEEE
Confidence 44 6679999999996 664 6899 789998864 334 5566554
No 48
>cd01727 LSm8 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm8 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=48.25 E-value=33 Score=26.15 Aligned_cols=31 Identities=16% Similarity=0.254 Sum_probs=25.6
Q ss_pred HHhhcCCCeeEEEEeecCCCeeeEeeeeEEEEEeCCe
Q 022231 216 DLGRFKEMPITVCYEDQDSDSREKTGVFLLDSIEMDS 252 (300)
Q Consensus 216 df~RfiGr~VkV~l~~ieG~kke~~GVl~L~~vDee~ 252 (300)
.+..++++.|.|+++ +|+ .+.| +|.++|...
T Consensus 3 ~L~~~l~~~V~V~l~--dgr--~~~G--~L~~~D~~~ 33 (74)
T cd01727 3 TLEDYLNKTVSVITV--DGR--VIVG--TLKGFDQAT 33 (74)
T ss_pred hHHHhcCCEEEEEEC--CCc--EEEE--EEEEEcccc
Confidence 467889999999986 664 6899 789998875
No 49
>PF08608 Wyosine_form: Wyosine base formation; InterPro: IPR013917 The proteins in this entry appear to be important in wyosine base formation in a subset of phenylalanine specific tRNAs. It has been proposed that it participates in converting tRNA(Phe)-m(1)G(37) to tRNA(Phe)-yW []. ; PDB: 2YX0_A 2Z2U_A.
Probab=47.88 E-value=19 Score=27.18 Aligned_cols=37 Identities=30% Similarity=0.495 Sum_probs=22.2
Q ss_pred ccccCCCCCceEecCCCHHHHHHHHHHHHHhhcCCeEEE
Q 022231 106 QVGDGGDGGGVVFQGVPWGERALSIAHEVLLQLGDDIKL 144 (300)
Q Consensus 106 ~~~d~~~g~~i~~~~~~~~e~I~el~epvl~~~G~eLvd 144 (300)
++|.+. ......+|||-++|.+.++.+++..||.+.+
T Consensus 14 ~~G~s~--~rLt~~nmp~h~eV~~F~~~l~~~~~y~i~~ 50 (62)
T PF08608_consen 14 HVGYSR--NRLTMGNMPWHEEVLDFAEELAELLGYEITD 50 (62)
T ss_dssp ------------GGGS--HHHHHHHHHHHHTTSTEEEEE
T ss_pred cccccc--CccccCCCCcHHHHHHHHHHHHhhcCCEEEe
Confidence 345544 7788899999999999999999999965544
No 50
>COG0045 SucC Succinyl-CoA synthetase, beta subunit [Energy production and conversion]
Probab=46.62 E-value=80 Score=32.06 Aligned_cols=69 Identities=28% Similarity=0.391 Sum_probs=43.9
Q ss_pred ccCCCCCceEecCCCHHHHHHHHHHHHHh------hcCCeEEEEEEEe----cC-CcEEEEEEcccCC-------CCCCC
Q 022231 108 GDGGDGGGVVFQGVPWGERALSIAHEVLL------QLGDDIKLYAFKA----TP-RGYVYVRLDKLSN-------KYGCP 169 (300)
Q Consensus 108 ~d~~~g~~i~~~~~~~~e~I~el~epvl~------~~G~eLvdVe~~~----~~-~~~LrV~IDk~~~-------~dggV 169 (300)
|==|-+|||.++-.+ +.+.+.++.++- -.|..+.-+-+.. .. ..|+-|.+|+... ..||+
T Consensus 52 GGRGKaGGVk~~~s~--~ea~~~a~~~lg~~~q~~~~G~~v~~vlvee~~~~~~~E~Ylsiv~DR~~~~p~~~~S~eGGm 129 (387)
T COG0045 52 GGRGKAGGVKLAKSP--EEAKEAAEEILGKNYQTDIKGEPVNKVLVEEAVDIIKKEYYLSIVLDRSSRRPVLMASTEGGM 129 (387)
T ss_pred cCccccCceEEeCCH--HHHHHHHHHHhCcccccCcCCceeeEEEEEecCCCccceEEEEEEEEcCCCcEEEEEecCCCc
Confidence 444444999999886 666777777775 2343333222221 12 4688888888643 27899
Q ss_pred ChHHHHHHH
Q 022231 170 SMEELESYS 178 (300)
Q Consensus 170 sLDDCe~vS 178 (300)
+|++.++=+
T Consensus 130 DIEeVa~~~ 138 (387)
T COG0045 130 DIEEVAEKT 138 (387)
T ss_pred cHHHhhhhC
Confidence 999887643
No 51
>KOG1783 consensus Small nuclear ribonucleoprotein F [RNA processing and modification]
Probab=46.56 E-value=13 Score=29.46 Aligned_cols=29 Identities=14% Similarity=0.069 Sum_probs=22.6
Q ss_pred HHhhcCCCeeEEEEeecCCCeeeEeeeeEEEEEeC
Q 022231 216 DLGRFKEMPITVCYEDQDSDSREKTGVFLLDSIEM 250 (300)
Q Consensus 216 df~RfiGr~VkV~l~~ieG~kke~~GVl~L~~vDe 250 (300)
=+..++|++|.|++. +|. .++| +|..+|.
T Consensus 10 fl~~iiGr~V~VKl~--sgv--dyrG--~l~~lDg 38 (77)
T KOG1783|consen 10 FLKAIIGRTVVVKLN--SGV--DYRG--TLVCLDG 38 (77)
T ss_pred HHHHHhCCeEEEEec--CCc--cccc--eehhhhh
Confidence 356899999999995 553 7899 6777765
No 52
>PF12701 LSM14: Scd6-like Sm domain; PDB: 2RM4_A 2FB7_A 2VC8_A 2VXF_A 2VXE_A.
Probab=45.15 E-value=1.1e+02 Score=24.98 Aligned_cols=67 Identities=19% Similarity=0.232 Sum_probs=43.1
Q ss_pred hcCCCeeEEEEeecCCCeeeEeeeeEEEEEeCCeeEEEEEeccccccCCCCCCCCc------ccccccceeEEeeccccc
Q 022231 219 RFKEMPITVCYEDQDSDSREKTGVFLLDSIEMDSEICVWKLADVKENRDPQEKGRP------LSRKRRDWRLNLPFVMHK 292 (300)
Q Consensus 219 RfiGr~VkV~l~~ieG~kke~~GVl~L~~vDee~i~l~~~l~dVk~nr~k~~KGk~------l~kkq~~~~l~Ipf~dI~ 292 (300)
.|+|..|.+..+ .+ -.++| .|..+|.+.-+++ |.+|+-+- ..||+ .+++..+ -+.+.-+||+
T Consensus 5 ~~IGs~ISlisk--~~--iRYeG--~L~~Id~~~sTIt--L~nVr~~G---tE~R~~~~~ipp~~~v~~-~I~Fr~sDIk 72 (96)
T PF12701_consen 5 PYIGSKISLISK--SD--IRYEG--ILYSIDTEDSTIT--LKNVRSFG---TEGRPTDREIPPSDEVYD-YIVFRGSDIK 72 (96)
T ss_dssp CCTTCEEEEEET--TT--EEEEE--EEEEEETTTTEEE--EEEEEETT---ETTSS-SS---C-CSSSS-EEEEETTTEE
T ss_pred cccCCEEEEEEC--CC--cEEEE--EEEEEcCCCCEEE--eeeeeecC---cCCCCcCcccCCCCceee-EEEEEccccc
Confidence 589999998874 33 24899 7899998766555 55776542 22331 1122223 4788889998
Q ss_pred eeEEE
Q 022231 293 RVTLY 297 (300)
Q Consensus 293 KArL~ 297 (300)
..++.
T Consensus 73 dL~v~ 77 (96)
T PF12701_consen 73 DLKVI 77 (96)
T ss_dssp EEEEC
T ss_pred eEEEE
Confidence 87764
No 53
>cd02978 KaiB_like KaiB-like family; composed of the circadian clock proteins, KaiB and the N-terminal KaiB-like sensory domain of SasA. KaiB is an essential protein in maintaining circadian rhythm. It was originally discovered from the cyanobacterium Synechococcus as part of the circadian clock gene cluster, kaiABC. KaiB attenuates KaiA-enhanced KaiC autokinase activity by interacting with KaiA-KaiC complexes in a circadian fashion. KaiB is membrane-associated as well as cytosolic. The amount of membrane-associated protein peaks in the evening (at circadian time (CT) 12-16) while the cytosolic form peaks later (at CT 20). The rhythmic localization of KaiB may function in regulating the formation of Kai complexes. SasA is a sensory histidine kinase which associates with KaiC. Although it is not an essential oscillator component, it is important in enhancing kaiABC expression and is important in metabolic growth control under day/night cycle conditions. SasA contains an N-terminal sensor
Probab=43.51 E-value=60 Score=25.36 Aligned_cols=39 Identities=15% Similarity=0.054 Sum_probs=27.3
Q ss_pred cEEEEEEcccCCCCCCCChHHHHHHHHHHHHhhhccccCCCCCCCeEEEEec
Q 022231 153 GYVYVRLDKLSNKYGCPSMEELESYSQEYKKKLDEVGALGEIPDDLALEVST 204 (300)
Q Consensus 153 ~~LrV~IDk~~~~dggVsLDDCe~vSr~Is~~LD~~e~~d~I~~~Y~LEVSS 204 (300)
..+++||++ ...-|..+.+.+.+.+...+ ++.|.|||-=
T Consensus 2 ~~L~Lyv~g----~tp~S~~ai~nl~~i~e~~l---------~~~~~LeVID 40 (72)
T cd02978 2 YVLRLYVAG----RTPKSERALQNLKRILEELL---------GGPYELEVID 40 (72)
T ss_pred eEEEEEECC----CCchHHHHHHHHHHHHHHhc---------CCcEEEEEEE
Confidence 468899988 45667777766665555444 3789999963
No 54
>cd04869 ACT_GcvR_2 ACT domains that comprise the Glycine Cleavage System Transcriptional Repressor (GcvR) protein, and other related domains. This CD includes the second of the two ACT domains that comprise the Glycine Cleavage System Transcriptional Repressor (GcvR) protein, and other related domains. The glycine cleavage enzyme system in Escherichia coli provides one-carbon units for cellular methylation reactions. This enzyme system, encoded by the gcvTHP operon and lpd gene, catalyzes the cleavage of glycine into CO2 + NH3 and transfers a one-carbon unit to tetrahydrofolate, producing 5,10-methylenetetrahydrofolate. The gcvTHP operon is activated by the GcvA protein in response to glycine and repressed by a GcvA/GcvR interaction in the absence of glycine. It has been proposed that the co-activator glycine acts through a mechanism of de-repression by binding to GcvR and preventing GcvR from interacting with GcvA to block GcvA's activator function. Evidence also suggests that GcvR in
Probab=41.94 E-value=1.4e+02 Score=21.95 Aligned_cols=55 Identities=15% Similarity=0.058 Sum_probs=34.9
Q ss_pred HHHHHHHHHhhcCCeEEEEEEE-ec------CCcEEEEEEcccCCCCCCCChHHHHHHHHHHHHhh
Q 022231 127 ALSIAHEVLLQLGDDIKLYAFK-AT------PRGYVYVRLDKLSNKYGCPSMEELESYSQEYKKKL 185 (300)
Q Consensus 127 I~el~epvl~~~G~eLvdVe~~-~~------~~~~LrV~IDk~~~~dggVsLDDCe~vSr~Is~~L 185 (300)
+.+-+..++.++|+.+.++... .+ +.-.+++.++- +.+.++.++.+-=+.+...|
T Consensus 12 iv~~it~~l~~~~~nI~~~~~~~~~~~~~~~~~~~~~~~v~~----p~~~~~~~l~~~l~~l~~~~ 73 (81)
T cd04869 12 IVHEVTQFLAQRNINIEDLSTETYSAPMSGTPLFKAQATLAL----PAGTDLDALREELEELCDDL 73 (81)
T ss_pred HHHHHHHHHHHcCCCeEEeEeeeecCCCCCcceEEEEEEEec----CCCCCHHHHHHHHHHHHHHh
Confidence 3455777888999999999987 33 22346777776 44566665554444444333
No 55
>cd04870 ACT_PSP_1 CT domains found N-terminal of phosphoserine phosphatase (PSP, SerB). The ACT_PSP_1 CD includes the first of the two ACT domains found N-terminal of phosphoserine phosphatase (PSP, SerB). PSPs belong to the L-2-haloacid dehalogenase-like protein superfamily. PSP is involved in serine metabolism; serine is synthesized from phosphoglycerate through sequential reactions catalyzed by 3-phosphoglycerate dehydrogenase (SerA), 3-phosphoserine aminotransferase (SerC), and SerB. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=38.19 E-value=1.6e+02 Score=21.74 Aligned_cols=54 Identities=17% Similarity=-0.071 Sum_probs=34.7
Q ss_pred HHHHHHHHHhhcCCeEEEEEEE-ecCCcEEEEEEcccCCCCCCCChHHHHHHHHHHHHh
Q 022231 127 ALSIAHEVLLQLGDDIKLYAFK-ATPRGYVYVRLDKLSNKYGCPSMEELESYSQEYKKK 184 (300)
Q Consensus 127 I~el~epvl~~~G~eLvdVe~~-~~~~~~LrV~IDk~~~~dggVsLDDCe~vSr~Is~~ 184 (300)
|.+.+..++.++|+.+++++.. ..+.-...+.++- +.++++++.++.=+.+.+.
T Consensus 12 iv~~vt~~la~~~~nI~dl~~~~~~~~f~~~~~v~~----p~~~~~~~l~~~l~~l~~~ 66 (75)
T cd04870 12 LTSALTEVLAAHGVRILDVGQAVIHGRLSLGILVQI----PDSADSEALLKDLLFKAHE 66 (75)
T ss_pred HHHHHHHHHHHCCCCEEecccEEEcCeeEEEEEEEc----CCCCCHHHHHHHHHHHHHH
Confidence 3455778889999999999866 4444556666665 3446666655544444433
No 56
>TIGR03793 TOMM_pelo TOMM propeptide domain. This model represents a domain that is conserved among a large number of putative thiazole/oxazole-modified microcins (TOMM). Oddly, most of this seqence region appears homologous to nitrile hydratase subunits. This family is expanded especially in Pelotomaculum thermopropionicum SI.
Probab=35.74 E-value=1.9e+02 Score=22.71 Aligned_cols=54 Identities=15% Similarity=0.084 Sum_probs=37.7
Q ss_pred HHHHHHHHHHHHHhhcCCeE---EEEEEEecCCcEEEEEEcccCCCCCCCChHHHHHHH
Q 022231 123 WGERALSIAHEVLLQLGDDI---KLYAFKATPRGYVYVRLDKLSNKYGCPSMEELESYS 178 (300)
Q Consensus 123 ~~e~I~el~epvl~~~G~eL---vdVe~~~~~~~~LrV~IDk~~~~dggVsLDDCe~vS 178 (300)
+.+++..--..+++++|+.+ +.|.+..+...+..+.|-.. +.+++|-++++.|+
T Consensus 19 Fr~~Ll~DPraaL~e~G~~~P~~~~i~VvE~t~~~~~lVlP~~--P~~~lse~~L~~va 75 (77)
T TIGR03793 19 FKQALLTNPKEALEREGVQVPAEVEVKVVEESPTVLYLVLPVN--PDIELTDEQLDAVA 75 (77)
T ss_pred HHHHHHHCHHHHHHHhCCCCCCceEEEEEEcCCCeEEEEecCC--CCCCCCHHHHHHhh
Confidence 55666666677889999987 56666666666777777542 35588888877764
No 57
>PF02237 BPL_C: Biotin protein ligase C terminal domain; InterPro: IPR003142 This C-terminal domain has an SH3-like barrel fold, the function of which is unknown. It is found associated with prokaryotic bifunctional transcriptional repressors [] and eukaryotic enzymes involved in biotin utilization [, ]. In Escherichia coli the biotin operon repressor (BirA) is a bifunctional protein. BirA acts both as the acetyl-coA carboxylase biotin holoenzyme synthetase (6.3.4.15 from EC) and as the biotin operon repressor. DNA sequence analysis of mutations indicates that the helix-turn-helix DNA binding region is located at the N terminus while mutations affecting enzyme function, although mapping over a large region, are found mainly in the central part of the protein's primary sequence [].; GO: 0006464 protein modification process; PDB: 3RUX_A 2CGH_A 3L1A_B 3L2Z_A 1HXD_A 1BIB_A 2EWN_B 1BIA_A 2EJ9_A 3FJP_A ....
Probab=35.51 E-value=1.5e+02 Score=20.59 Aligned_cols=32 Identities=16% Similarity=0.158 Sum_probs=22.9
Q ss_pred cCCCeeEEEEeecCCCeeeEeeeeEEEEEeCCeeEEEEEe
Q 022231 220 FKEMPITVCYEDQDSDSREKTGVFLLDSIEMDSEICVWKL 259 (300)
Q Consensus 220 fiGr~VkV~l~~ieG~kke~~GVl~L~~vDee~i~l~~~l 259 (300)
++|+.|+|.. ++ ..++| +...+|+++. +.++.
T Consensus 1 ~lG~~V~v~~---~~--~~~~G--~~~gId~~G~-L~v~~ 32 (48)
T PF02237_consen 1 TLGQEVRVET---GD--GEIEG--IAEGIDDDGA-LLVRT 32 (48)
T ss_dssp STTSEEEEEE---TS--CEEEE--EEEEEETTSE-EEEEE
T ss_pred CCCCEEEEEE---CC--eEEEE--EEEEECCCCE-EEEEE
Confidence 4789999987 23 24689 6699999983 55543
No 58
>PF06372 Gemin6: Gemin6 protein; InterPro: IPR009422 This family consists of several mammalian Gemin6 proteins. The exact function of Gemin6 is unknown but it has been found to form part of the Survival of motor neuron complex. The SMN complex plays a key role in the biogenesis of spliceosomal small nuclear ribonucleoproteins (snRNPs) and other ribonucleoprotein particles [].; GO: 0000245 spliceosome assembly, 0005634 nucleus; PDB: 1Y96_A.
Probab=32.48 E-value=77 Score=28.51 Aligned_cols=40 Identities=23% Similarity=0.253 Sum_probs=28.7
Q ss_pred CCChHHHhhcCCCeeEEEEeecCCCeeeEeeeeEEEEEeCCeeEEEE
Q 022231 211 LKVPDDLGRFKEMPITVCYEDQDSDSREKTGVFLLDSIEMDSEICVW 257 (300)
Q Consensus 211 Lk~~~df~RfiGr~VkV~l~~ieG~kke~~GVl~L~~vDee~i~l~~ 257 (300)
.+.|-+|..|+|+.|+|++. + +++.| -|..+|..+-.+++
T Consensus 6 ~~~p~~~~~yv~K~VkV~~~--d---~~~~G--~v~TiDPVS~siVL 45 (166)
T PF06372_consen 6 KKSPLEWQDYVGKEVKVTLS--D---KEYKG--WVYTIDPVSASIVL 45 (166)
T ss_dssp HS-HHHHHCTTT-EEEEEET--T---EEEEE--EEEEE-TTT--EEE
T ss_pred hCCHHHHHHhhCcEEEEEEe--c---cEEEE--EEEEeCCCCCeEEE
Confidence 46789999999999999985 3 46899 67899998876653
No 59
>cd04872 ACT_1ZPV ACT domain proteins similar to the yet uncharacterized Streptococcus pneumoniae ACT domain protein. This CD, ACT_1ZPV, includes those single ACT domain proteins similar to the yet uncharacterized Streptococcus pneumoniae ACT domain protein (pdb structure 1ZPV). Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=29.84 E-value=2.1e+02 Score=21.84 Aligned_cols=46 Identities=13% Similarity=-0.013 Sum_probs=32.5
Q ss_pred HHHHHHHHHhhcCCeEEEEEEE-ecCCcEEEEEEcccCCCCC-CCChHHHHH
Q 022231 127 ALSIAHEVLLQLGDDIKLYAFK-ATPRGYVYVRLDKLSNKYG-CPSMEELES 176 (300)
Q Consensus 127 I~el~epvl~~~G~eLvdVe~~-~~~~~~LrV~IDk~~~~dg-gVsLDDCe~ 176 (300)
+.+.+..++.++|+.+.+++.. .++.-.+++.++. ++ +.++++...
T Consensus 14 iva~vt~~la~~g~nI~~~~~~~~~~~f~~~~~v~~----~~~~~~~~~L~~ 61 (88)
T cd04872 14 IVAGVSTKLAELNVNILDISQTIMDGYFTMIMIVDI----SESNLDFAELQE 61 (88)
T ss_pred HHHHHHHHHHHcCCCEEechhHhhCCccEEEEEEEe----CCCCCCHHHHHH
Confidence 4566788899999999999977 4455667777876 34 455554443
No 60
>PRK00194 hypothetical protein; Validated
Probab=29.57 E-value=2e+02 Score=21.82 Aligned_cols=46 Identities=15% Similarity=0.025 Sum_probs=32.1
Q ss_pred HHHHHHHHHHhhcCCeEEEEEEE-ecCCcEEEEEEcccCCCCC-CCChHHHH
Q 022231 126 RALSIAHEVLLQLGDDIKLYAFK-ATPRGYVYVRLDKLSNKYG-CPSMEELE 175 (300)
Q Consensus 126 ~I~el~epvl~~~G~eLvdVe~~-~~~~~~LrV~IDk~~~~dg-gVsLDDCe 175 (300)
-+.+-+..++.++|+.+.+++-. .++.-++++.++- ++ +.+++++.
T Consensus 15 Giva~vt~~la~~g~nI~~~~~~~~~~~~~~~~~v~~----~~~~~~~~~l~ 62 (90)
T PRK00194 15 GIIAGVSTVLAELNVNILDISQTIMDGYFTMIMLVDI----SESKKDFAELK 62 (90)
T ss_pred CHHHHHHHHHHHcCCCEEehhhHhhCCeeEEEEEEEe----cCCCCCHHHHH
Confidence 35666778889999999999977 4455677778876 33 44554443
No 61
>PRK09301 circadian clock protein KaiB; Provisional
Probab=29.37 E-value=1.2e+02 Score=25.36 Aligned_cols=42 Identities=12% Similarity=0.055 Sum_probs=30.2
Q ss_pred CCcEEEEEEcccCCCCCCCChHHHHHHHHHHHHhhhccccCCCCCCCeEEEEecC
Q 022231 151 PRGYVYVRLDKLSNKYGCPSMEELESYSQEYKKKLDEVGALGEIPDDLALEVSTP 205 (300)
Q Consensus 151 ~~~~LrV~IDk~~~~dggVsLDDCe~vSr~Is~~LD~~e~~d~I~~~Y~LEVSSP 205 (300)
+.+.+|+||-+ ...-|..+.+.+.+.+...|. +.|.|||-=.
T Consensus 5 ~~~~LrLyVag----~tp~S~~ai~nL~~icE~~l~---------g~y~LeVIDv 46 (103)
T PRK09301 5 KTYILKLYVAG----NTPNSVRALKTLKNILETEFK---------GVYALKVIDV 46 (103)
T ss_pred ceEEEEEEEeC----CCchHHHHHHHHHHHHHHhcC---------CceEEEEEEc
Confidence 35789999977 456777777777766665554 4699999743
No 62
>PF14472 DUF4429: Domain of unknown function (DUF4429)
Probab=29.06 E-value=68 Score=25.61 Aligned_cols=39 Identities=18% Similarity=0.261 Sum_probs=23.3
Q ss_pred EEeCCeeEEEEEeccccccCCCCCCCCcccccccceeEEeeccccceeEEE
Q 022231 247 SIEMDSEICVWKLADVKENRDPQEKGRPLSRKRRDWRLNLPFVMHKRVTLY 297 (300)
Q Consensus 247 ~vDee~i~l~~~l~dVk~nr~k~~KGk~l~kkq~~~~l~Ipf~dI~KArL~ 297 (300)
++|++.+.++|. .-+..+.+..+| ..+||+++|.-+.+.
T Consensus 2 sfDg~~V~i~~~--g~~a~~~~~~~G----------~~~ipl~~i~gV~~~ 40 (94)
T PF14472_consen 2 SFDGDTVRIRWG--GWRAPRAKRALG----------EKTIPLSAISGVEWK 40 (94)
T ss_pred EEcCCEEEEEEC--CccchhhhccCC----------CEEEEHHHcceEEEE
Confidence 467787766665 222222122222 378999999988775
No 63
>TIGR02654 circ_KaiB circadian clock protein KaiB. Members of this protein family are the circadian clock protein KaiB of Cyanobacteria, encoded in the circadian clock gene cluster kaiABC. KaiB has homologs of unknown function in some Archaea and Proteobacteria, and has paralogs of unknown function in some Cyanobacteria. KaiB forms homodimers, homotetramers, and multimeric complexes with KaiA and/or KaiC.
Probab=28.63 E-value=1.3e+02 Score=24.31 Aligned_cols=41 Identities=12% Similarity=0.062 Sum_probs=29.5
Q ss_pred CcEEEEEEcccCCCCCCCChHHHHHHHHHHHHhhhccccCCCCCCCeEEEEecC
Q 022231 152 RGYVYVRLDKLSNKYGCPSMEELESYSQEYKKKLDEVGALGEIPDDLALEVSTP 205 (300)
Q Consensus 152 ~~~LrV~IDk~~~~dggVsLDDCe~vSr~Is~~LD~~e~~d~I~~~Y~LEVSSP 205 (300)
.+.++++|-+ ...-|..+.+.+.+.+...|. +.|.|||-=+
T Consensus 3 ~~~LrLyvag----~~p~S~~ai~nl~~i~e~~l~---------g~y~LeVIDv 43 (87)
T TIGR02654 3 TYVLKLYVAG----NTPNSVRALKTLKNILETEFQ---------GVYALKVIDV 43 (87)
T ss_pred eEEEEEEEeC----CCchHHHHHHHHHHHHHHhcC---------CceEEEEEEc
Confidence 4678999977 456777777777766665554 4699999743
No 64
>cd04873 ACT_UUR-ACR-like ACT domains of the bacterial signal-transducing uridylyltransferase /uridylyl-removing (UUR) enzyme, GlnD. This ACT domain family, ACT_UUR_ACR-like, includes the two C-terminal ACT domains of the bacterial signal-transducing uridylyltransferase /uridylyl-removing (UUR) enzyme, GlnD; including those enzymes similar to the GlnD found in enteric Escherichia coli and those found in photosynthetic, nitrogen-fixing bacterium Rhodospirillum rubrum. Also included in this CD are the four ACT domains of a novel protein composed almost entirely of ACT domain repeats (the ACR protein) and like proteins. These ACR proteins, found in Arabidopsis and Oryza, are proposed to function as novel regulatory or sensor proteins in plants. This CD also includes the first of the two ACT domains that comprise the Glycine Cleavage System Transcriptional Repressor (GcvR) protein and related domains, as well as, the N-terminal ACT domain of a yet characterized Arabidopsis/Oryza predicted t
Probab=28.37 E-value=2.1e+02 Score=19.90 Aligned_cols=56 Identities=16% Similarity=0.089 Sum_probs=35.5
Q ss_pred HHHHHHHHHhhcCCeEEEEEEEec-CCcEEEEEEcccCCCCCCCChHHHHHHHHHHHHh
Q 022231 127 ALSIAHEVLLQLGDDIKLYAFKAT-PRGYVYVRLDKLSNKYGCPSMEELESYSQEYKKK 184 (300)
Q Consensus 127 I~el~epvl~~~G~eLvdVe~~~~-~~~~LrV~IDk~~~~dggVsLDDCe~vSr~Is~~ 184 (300)
+..-+..++.++|+.+..+..... ....+.++++.++ ....+-+.++.+.+.+...
T Consensus 13 ~l~~i~~~l~~~~~~I~~~~~~~~~~~~~~~~~v~~~~--~~~~~~~~~~~l~~~l~~~ 69 (70)
T cd04873 13 LLADITRVLADLGLNIHDARISTTGERALDVFYVTDSD--GRPLDPERIARLEEALEDA 69 (70)
T ss_pred HHHHHHHHHHHCCCeEEEEEEeecCCEEEEEEEEECCC--CCcCCHHHHHHHHHHHHhh
Confidence 455566778999999999987743 3445566666531 1225556777666666443
No 65
>TIGR02024 FtcD glutamate formiminotransferase. This model covers enzymes from metazoa as well as gram-positive bacteria and archaea. In humans, deficiency of this enzyme results in a disease phenotype. The crystal structure of the enzyme has been studied in the context of the catalytic mechanism.
Probab=28.15 E-value=1.4e+02 Score=29.32 Aligned_cols=65 Identities=23% Similarity=0.302 Sum_probs=39.0
Q ss_pred CceEecCCCHHHHHHHHHHHHHhhcCCeEEEEEEEec--CC-cEEEE--EEcccCCCCCCCChHHHHHHHHHHHHhhh
Q 022231 114 GGVVFQGVPWGERALSIAHEVLLQLGDDIKLYAFKAT--PR-GYVYV--RLDKLSNKYGCPSMEELESYSQEYKKKLD 186 (300)
Q Consensus 114 ~~i~~~~~~~~e~I~el~epvl~~~G~eLvdVe~~~~--~~-~~LrV--~IDk~~~~dggVsLDDCe~vSr~Is~~LD 186 (300)
-++-+.|.+ +.|.+.+-..++. -+++.|++...+ ++ +.+=+ ++. =+++|+|+|.++++.+.+.+-
T Consensus 47 sv~Tlvg~p--e~v~eaa~~~~~~-A~elIDm~~H~G~HPR~GAvDvipf~P-----l~~~t~eec~~lA~~vg~~i~ 116 (298)
T TIGR02024 47 SVITFVGEP--ECVVNAALKLAKK-AAELIDMRNHKGEHPRMGAADVIPFIP-----VRNVTMEECVELAKEFGKRLG 116 (298)
T ss_pred eEEEEecCh--HHHHHHHHHHHHH-HHHhcCcccccCCCCCCCccceeeeee-----CCCCCHHHHHHHHHHHHHHHH
Confidence 355666664 3333333333322 345778777733 33 22222 232 368999999999999999886
No 66
>PLN00180 NDF6 (NDH-dependent flow 6); Provisional
Probab=28.05 E-value=35 Score=30.75 Aligned_cols=19 Identities=42% Similarity=0.623 Sum_probs=15.5
Q ss_pred ccCCcccccCCCCCceEec
Q 022231 101 DEAEPQVGDGGDGGGVVFQ 119 (300)
Q Consensus 101 ~~~~~~~~d~~~g~~i~~~ 119 (300)
.+.|.|=||||||-|--.=
T Consensus 123 YDSe~YRgdGGDGT~hW~Y 141 (180)
T PLN00180 123 YDSEEYRGDGGDGTGHWVY 141 (180)
T ss_pred cchHHhcccCCCCceeeEe
Confidence 5677899999999887663
No 67
>PF05219 DREV: DREV methyltransferase; InterPro: IPR007884 This family contains DREV protein homologues from several eukaryotes. The function of this protein is unknown []. However, these proteins appear to be related to other methyltransferases.
Probab=27.02 E-value=91 Score=30.10 Aligned_cols=41 Identities=24% Similarity=0.425 Sum_probs=33.2
Q ss_pred CcccccCCCC------CceEecCCCHHHHHHHHHHHHHhhcCCeEEEEE
Q 022231 104 EPQVGDGGDG------GGVVFQGVPWGERALSIAHEVLLQLGDDIKLYA 146 (300)
Q Consensus 104 ~~~~~d~~~g------~~i~~~~~~~~e~I~el~epvl~~~G~eLvdVe 146 (300)
-|||..|+ | --+.+.|..|++.+..++ .+++..|++++-..
T Consensus 193 ~pyVE~~~-g~~~~P~e~l~~~g~~~E~~v~~l~-~v~~p~GF~v~~~t 239 (265)
T PF05219_consen 193 RPYVEFGG-GKSNRPSELLPVKGATFEEQVSSLV-NVFEPAGFEVERWT 239 (265)
T ss_pred cccEEcCC-CCCCCchhhcCCCCCcHHHHHHHHH-HHHHhcCCEEEEEe
Confidence 47777776 2 225567788999999999 99999999998876
No 68
>PF06257 DUF1021: Protein of unknown function (DUF1021); InterPro: IPR009366 This entry consists of several hypothetical bacterial proteins of unknown function.; PDB: 3FB9_A.
Probab=26.75 E-value=2e+02 Score=22.75 Aligned_cols=66 Identities=15% Similarity=0.165 Sum_probs=38.2
Q ss_pred hHHHhhcCCCeeEEEEeecCCCe--eeEeeeeEEEEEeCCeeEEEEEeccccccCCCCCCCCcccccccceeEEeecccc
Q 022231 214 PDDLGRFKEMPITVCYEDQDSDS--REKTGVFLLDSIEMDSEICVWKLADVKENRDPQEKGRPLSRKRRDWRLNLPFVMH 291 (300)
Q Consensus 214 ~~df~RfiGr~VkV~l~~ieG~k--ke~~GVl~L~~vDee~i~l~~~l~dVk~nr~k~~KGk~l~kkq~~~~l~Ipf~dI 291 (300)
.+++..++|+.|.++.+ .|++ .+.+| .|.++=..- .++.+.+ ..+. ..++.+.|+||
T Consensus 9 k~~l~~~vG~~V~l~a~--~GRkK~~~r~G--vL~~tYPsv--FvV~l~~--------~~~~-------~~rvSySYsDv 67 (76)
T PF06257_consen 9 KKELESHVGKRVKLKAN--KGRKKIIEREG--VLEETYPSV--FVVELDQ--------EENQ-------FERVSYSYSDV 67 (76)
T ss_dssp HHHHHHTTTSEEEEEE----SSS--S-EEE--EEEEE-SSE--EEEEES---------S-SS--------EEEEEEHHHH
T ss_pred HHHHHHcCCCEEEEEEc--CCceEEEEEEE--EEEeecCcE--EEEEEcc--------CCCc-------eEEEEEEeehh
Confidence 35788999999999985 5653 35678 566665553 3434322 0111 13689999998
Q ss_pred ceeEEEEeC
Q 022231 292 KRVTLYLEY 300 (300)
Q Consensus 292 ~KArL~ieF 300 (300)
---.+.+.|
T Consensus 68 LT~~Vel~f 76 (76)
T PF06257_consen 68 LTETVELTF 76 (76)
T ss_dssp HTTSCEEEE
T ss_pred ccccEEEeC
Confidence 665555544
No 69
>cd04861 LigD_Pol_like LigD_Pol_like: Polymerase (Pol) domain of bacterial LigD proteins similar to Pseudomonas aeruginosa (Pae) LigD. The LigD Pol domain belongs to the archaeal/eukaryal primase (AEP) superfamily. In prokaryotes, LigD along with Ku is required for non-homologous end joining (NHEJ)-mediated repair of DNA double-strand breaks (DSB). NHEJ-mediated DNA DSB repair is error-prone. PaeLigD is monomeric, containing an N-terminal phosphoesterase module, a central polymerase (Pol) domain, and a C-terminal ATP-dependent ligase domain. Mycobacterium tuberculosis (Mt)LigD, also found in this group, is monomeric and contains the same modules but these are arranged differently: an N-terminal Pol domain, a central phosphoesterase module, and a C-terminal ligase domain. It has been suggested that LigD Pol contributes to NHEJ-mediated DNA DSB repair in vivo, by filling in short 5'-overhangs with ribonucleotides; the filled in termini would then be sealed by the associated LigD ligase do
Probab=26.69 E-value=2.2e+02 Score=26.85 Aligned_cols=84 Identities=20% Similarity=0.216 Sum_probs=60.7
Q ss_pred CCHHHH--HHHHHHHHHhhcCCeEEEEEEEecCCcEEEEEEcccCCCCCCCChHHHHHHHHHHHHhhhccccCCCCCCCe
Q 022231 121 VPWGER--ALSIAHEVLLQLGDDIKLYAFKATPRGYVYVRLDKLSNKYGCPSMEELESYSQEYKKKLDEVGALGEIPDDL 198 (300)
Q Consensus 121 ~~~~e~--I~el~epvl~~~G~eLvdVe~~~~~~~~LrV~IDk~~~~dggVsLDDCe~vSr~Is~~LD~~e~~d~I~~~Y 198 (300)
..|.+- +--++.++++++|+.-+ .+++++.-|.|+|-- ....+-+++-.+++.|...|.+ ..|+-|
T Consensus 111 ~~f~~v~~~A~~vr~~L~~lgL~~f---~KTSG~kGlHV~vPl----~~~~~~~~~r~fa~~iA~~l~~-----~~P~~~ 178 (227)
T cd04861 111 VPFEDVVEAALLLRELLDELGLESF---PKTSGGKGLHVYVPL----APRYTWDEVRAFAKALARELAR-----RLPDLF 178 (227)
T ss_pred CCHHHHHHHHHHHHHHHHHcCCccc---eEccCCCeEEEEEEc----CCCCCHHHHHHHHHHHHHHHHH-----HCchhh
Confidence 345444 46678889999997544 246666667888865 4679999999999999999984 234555
Q ss_pred EEEEecCCCCCCCCChHHHhhcCCCeeEEEE-e
Q 022231 199 ALEVSTPGAERMLKVPDDLGRFKEMPITVCY-E 230 (300)
Q Consensus 199 ~LEVSSPGieRpLk~~~df~RfiGr~VkV~l-~ 230 (300)
+.| -.+...|.+|.|-| +
T Consensus 179 t~~--------------~~k~~R~grvfiDy~q 197 (227)
T cd04861 179 TAE--------------MAKAKRGGKIFVDYLQ 197 (227)
T ss_pred hhH--------------hhHHhCCCCEEEECcc
Confidence 543 45677888899988 5
No 70
>PF00788 RA: Ras association (RalGDS/AF-6) domain; InterPro: IPR000159 Proteins with this domain are mostly RasGTP effectors and include guanine-nucleotide releasing factor in mammals []. This factor stimulates the dissociation of GDP from the Ras-related RALA and RALB GTPases, which allows GTP binding and activation of the GTPases. It interacts and acts as an effector molecule for R-ras, K-Ras and Rap []. The domain is also present in a number of other proteins among them the sexual differentiation protein in yeast that is essential for mating and meiosis and yeast adenylate cyclase. These proteins contain repeated leucine-rich (LRR) segments.; GO: 0007165 signal transduction; PDB: 3EC8_A 2C5L_D 2BYF_A 2CS4_A 3KH0_A 2B3A_A 1RAX_A 2RGF_A 1WGR_A 1WXA_A ....
Probab=26.07 E-value=12 Score=28.29 Aligned_cols=20 Identities=35% Similarity=0.451 Sum_probs=16.7
Q ss_pred CCCeEE--EEecCCCCCCCCCh
Q 022231 195 PDDLAL--EVSTPGAERMLKVP 214 (300)
Q Consensus 195 ~~~Y~L--EVSSPGieRpLk~~ 214 (300)
+..|.| ...++|.+|+|...
T Consensus 46 ~~~y~L~~~~~~~~~er~L~~~ 67 (93)
T PF00788_consen 46 PSDYCLVEVEESGGEERPLDDD 67 (93)
T ss_dssp GGGEEEEEEECTTTEEEEETTT
T ss_pred CCCEEEEEEEcCCCEEEEcCCC
Confidence 478999 89999999988643
No 71
>KOG3482 consensus Small nuclear ribonucleoprotein (snRNP) SMF [RNA processing and modification]
Probab=25.95 E-value=1.2e+02 Score=24.05 Aligned_cols=33 Identities=21% Similarity=0.252 Sum_probs=25.4
Q ss_pred ChHHH-hhcCCCeeEEEEeecCCCeeeEeeeeEEEEEeCC
Q 022231 213 VPDDL-GRFKEMPITVCYEDQDSDSREKTGVFLLDSIEMD 251 (300)
Q Consensus 213 ~~~df-~RfiGr~VkV~l~~ieG~kke~~GVl~L~~vDee 251 (300)
+|+.| .+.+|++|.|+++ =|+ +++| .|.++|.=
T Consensus 8 NPKpFL~~l~gk~V~vkLK--wg~--eYkG--~LvsvD~Y 41 (79)
T KOG3482|consen 8 NPKPFLNGLTGKPVLVKLK--WGQ--EYKG--TLVSVDNY 41 (79)
T ss_pred CchHHHhhccCCeEEEEEe--cCc--EEEE--EEEEecch
Confidence 56666 4789999999995 354 7999 78998764
No 72
>TIGR01634 tail_P2_I phage tail protein, P2 protein I family. This model represents the family of phage P2 protein I and related tail proteins from a number of temperate phage of Gram-negative bacteria. This alignment is built as a fragment model and identifies some phage tail proteins with strong but local similarity to members of the seed alignment.
Probab=25.82 E-value=2.8e+02 Score=24.11 Aligned_cols=52 Identities=12% Similarity=0.087 Sum_probs=37.5
Q ss_pred HHHHHHHhhcCCeEEEEEEE-ec---CCcEEEEEEcccCCCCCCCChHHHHHHHHHHHH
Q 022231 129 SIAHEVLLQLGDDIKLYAFK-AT---PRGYVYVRLDKLSNKYGCPSMEELESYSQEYKK 183 (300)
Q Consensus 129 el~epvl~~~G~eLvdVe~~-~~---~~~~LrV~IDk~~~~dggVsLDDCe~vSr~Is~ 183 (300)
..++.+++.+|+++.-.|.. .+ ...+.+|.|+.. +.|++-.....+-|.|..
T Consensus 79 ~avr~~l~~lg~~~~i~EW~e~~p~g~P~tF~i~~~~~---~~g~~~~~~~~~~~~i~~ 134 (139)
T TIGR01634 79 GAVRRVVEPFGGIVNITEWWQTGPPGPPGTFELTLTVS---GSGGTEETYLEVERLIAD 134 (139)
T ss_pred HHHHHHHHHcCCCeEEeehhccCCCCCCeEEEEEEEcc---CCCCCHHHHHHHHHHHHh
Confidence 34677888899888888765 33 356899998874 567888777777766653
No 73
>PLN02677 mevalonate kinase
Probab=25.73 E-value=1.1e+02 Score=30.60 Aligned_cols=39 Identities=15% Similarity=0.131 Sum_probs=24.3
Q ss_pred CCCCCc--eEecCCCHHHHHHHHHHHHHhhcCCeEEEEEEE
Q 022231 110 GGDGGG--VVFQGVPWGERALSIAHEVLLQLGDDIKLYAFK 148 (300)
Q Consensus 110 ~~~g~~--i~~~~~~~~e~I~el~epvl~~~G~eLvdVe~~ 148 (300)
|++||| |+|......+...+-+...++..|++.+...+-
T Consensus 335 GAGgGGC~IaL~~~~~~~~~~~~l~~~l~~~G~~~~~~~~g 375 (387)
T PLN02677 335 GAGGGGCVLTLLPTLLSGTVVDKVIAELESSGFQCFTAGIG 375 (387)
T ss_pred cCCCCCEEEEEcccccchhHHHHHHHHHHHCCCeEEEEEeC
Confidence 344455 667654444444455666677779999887754
No 74
>cd01720 Sm_D2 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit D2 heterodimerizes with subunit D1 and three such heterodimers form a hexameric ring structure with alternating D1 and D2 subunits. The D1 - D2 heterodimer also assembles into a heptameric ring containing D2, D3, E, F, and G subunits. Sm-like proteins exist in archaea as well as prokaryotes which form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=23.12 E-value=2e+02 Score=22.97 Aligned_cols=34 Identities=18% Similarity=0.304 Sum_probs=24.8
Q ss_pred CCeeEEEEeecCCCeeeEeeeeEEEEEeCCeeEEEEEeccccc
Q 022231 222 EMPITVCYEDQDSDSREKTGVFLLDSIEMDSEICVWKLADVKE 264 (300)
Q Consensus 222 Gr~VkV~l~~ieG~kke~~GVl~L~~vDee~i~l~~~l~dVk~ 264 (300)
|++|.|+++ +|+ .+.| +|.++|.-- .++ |.|+.+
T Consensus 14 ~~~V~V~lr--~~r--~~~G--~L~~fD~hm-Nlv--L~d~~E 47 (87)
T cd01720 14 NTQVLINCR--NNK--KLLG--RVKAFDRHC-NMV--LENVKE 47 (87)
T ss_pred CCEEEEEEc--CCC--EEEE--EEEEecCcc-EEE--EcceEE
Confidence 899999996 564 6899 789998764 333 556544
No 75
>TIGR03610 RutC pyrimidine utilization protein C. This protein is observed in operons extremely similar to that characterized in E. coli K-12 responsible for the import and catabolism of pyrimidines, primarily uracil. This protein is a member of the endoribonuclease L-PSP family defined by pfam01042.
Probab=23.05 E-value=3.3e+02 Score=22.66 Aligned_cols=57 Identities=11% Similarity=0.230 Sum_probs=38.9
Q ss_pred HHHHHHHHHHHhhcCCeEEEEEEEecCCcEEEEEEcccCCCCCCCChHHHHHHHHHHHHhhhccccCCCCCCCeEEEE
Q 022231 125 ERALSIAHEVLLQLGDDIKLYAFKATPRGYVYVRLDKLSNKYGCPSMEELESYSQEYKKKLDEVGALGEIPDDLALEV 202 (300)
Q Consensus 125 e~I~el~epvl~~~G~eLvdVe~~~~~~~~LrV~IDk~~~~dggVsLDDCe~vSr~Is~~LD~~e~~d~I~~~Y~LEV 202 (300)
.++.+-++.+|++.|..+-+|- .++||+.. ++|++.+.+.+.+.+.. +.|..-.++|
T Consensus 53 ~~~l~ni~~iL~~aG~~~~dvv-------~~~iyl~d---------~~~~~~~~~~~~~~f~~-----~~Pa~t~v~v 109 (127)
T TIGR03610 53 RHVLETIKSVIETAGGTMDDVT-------FNHIFIRD---------WADYAAINEVYAEYFPG-----EKPARYCIQC 109 (127)
T ss_pred HHHHHHHHHHHHHcCCCHHHEE-------EEEEEEcC---------HHHHHHHHHHHHHHcCC-----CCCcEEEEEe
Confidence 3456667778888898775554 35566532 68999999999998872 2344555555
No 76
>PF13222 DUF4030: Protein of unknown function (DUF4030)
Probab=22.91 E-value=3.7e+02 Score=23.79 Aligned_cols=86 Identities=17% Similarity=0.102 Sum_probs=51.6
Q ss_pred CCCHHHHHHHHHHHHHhhcCCeEEEEE-EEecCCcEEEEEEcccCCCCCCCChHH-HHHHHHHHHHhhhccccCCCCC-C
Q 022231 120 GVPWGERALSIAHEVLLQLGDDIKLYA-FKATPRGYVYVRLDKLSNKYGCPSMEE-LESYSQEYKKKLDEVGALGEIP-D 196 (300)
Q Consensus 120 ~~~~~e~I~el~epvl~~~G~eLvdVe-~~~~~~~~LrV~IDk~~~~dggVsLDD-Ce~vSr~Is~~LD~~e~~d~I~-~ 196 (300)
.--|..-+..+...+....||....+. +.-.++..+.|.|+..=+ ...++--+ -+++-..+...|-..+...+|. +
T Consensus 51 e~RW~~V~~~I~d~lf~Kn~Y~~~gI~~~n~k~~qp~~v~I~t~in-~~d~~AKE~g~kiEkei~~~lkt~evkkwI~~D 129 (142)
T PF13222_consen 51 ENRWNYVFSSIFDELFGKNGYKGFGIQQINVKSSQPVTVTIKTKIN-SSDPGAKEFGKKIEKEINEVLKTEEVKKWIEND 129 (142)
T ss_pred hhhHHHHHHHHHHHHhhccCccccceeEeeecCCCcEEEEEecccc-ccccchHHHHHHHHHHHHHHHccHHHHHHHhCC
Confidence 334777788889999999999999998 444455667777764100 11222222 2334444555554322233443 5
Q ss_pred CeEEEEecCC
Q 022231 197 DLALEVSTPG 206 (300)
Q Consensus 197 ~Y~LEVSSPG 206 (300)
.|++|+-|-+
T Consensus 130 sYtI~iy~~d 139 (142)
T PF13222_consen 130 SYTIEIYSQD 139 (142)
T ss_pred ceEEEEeccc
Confidence 6999998754
No 77
>TIGR02778 ligD_pol DNA polymerase LigD, polymerase domain. DNA repair of double-stranded breaks by non-homologous end joining (NHEJ) is accomplished by a two-protein system that is present in a minority of prokaryotes. One component is the Ku protein (see TIGR02772), which binds DNA ends. The other is a DNA ligase, a protein that is a multidomain polypeptide in most of those bacteria that have NHEJ, a permuted polypeptide in Mycobacterium tuberculosis and a few other species, and the product of tandem genes in some other bacteria. This model represents the polymerase domain.
Probab=22.91 E-value=2.1e+02 Score=27.35 Aligned_cols=80 Identities=19% Similarity=0.201 Sum_probs=59.1
Q ss_pred HHHHHHHHHHHhhcCCeEEEEEEEecCCcEEEEEEcccCCCCCCCChHHHHHHHHHHHHhhhccccCCCCCCCeEEEEec
Q 022231 125 ERALSIAHEVLLQLGDDIKLYAFKATPRGYVYVRLDKLSNKYGCPSMEELESYSQEYKKKLDEVGALGEIPDDLALEVST 204 (300)
Q Consensus 125 e~I~el~epvl~~~G~eLvdVe~~~~~~~~LrV~IDk~~~~dggVsLDDCe~vSr~Is~~LD~~e~~d~I~~~Y~LEVSS 204 (300)
-++-.++.++++++|+.-+ .+++++.-|.|+|-- ....+-+++-.+++.|-..|.+. .|+-|+.
T Consensus 133 ~~~A~~~r~~L~~lgL~~f---~KTSG~kGlHV~vPl----~~~~~~~~~r~fa~~iA~~l~~~-----~Pd~~t~---- 196 (245)
T TIGR02778 133 VEAAQLIRELLDELGLESF---VKTSGGKGLHVYVPL----RPTLSWDEVKDFAKALAQALAQQ-----MPDRFTA---- 196 (245)
T ss_pred HHHHHHHHHHHHHcCCccc---eEccCCCeEEEEEEC----CCCCCHHHHHHHHHHHHHHHHHH-----Cchhhhh----
Confidence 3456678899999997654 346666668888865 45789999999999999999851 3454544
Q ss_pred CCCCCCCCChHHHhhcCCCeeEEEE-e
Q 022231 205 PGAERMLKVPDDLGRFKEMPITVCY-E 230 (300)
Q Consensus 205 PGieRpLk~~~df~RfiGr~VkV~l-~ 230 (300)
+-....+|.+|.|-| +
T Consensus 197 ----------~~~k~~R~gkvfiDylq 213 (245)
T TIGR02778 197 ----------EMSKKNRVGKIFVDYLR 213 (245)
T ss_pred ----------HhhHHhCCCCEEEECcc
Confidence 445677888999988 5
No 78
>TIGR03341 YhgI_GntY IscR-regulated protein YhgI. IscR (TIGR02010) is an iron-sulfur cluster-binding transcriptional regulator (see Genome Property GenProp0138). Members of this protein family include YhgI, whose expression is under control of IscR, and show sequence similarity to IscA, a known protein of iron-sulfur cluster biosynthesis. These two lines of evidence strongly suggest a role as an iron-sulfur cluster biosynthesis protein. An older study designated this protein GntY and suggested a role for it and for the product of an adjacent gene, based on complementation studies, in gluconate utilization.
Probab=22.50 E-value=2.7e+02 Score=25.22 Aligned_cols=52 Identities=15% Similarity=0.222 Sum_probs=37.1
Q ss_pred ccCCCCCceEecCCC-----------HHHHHHHHHH----HHHhhcCCeEEEEEEEecCCcEEEEEEcc
Q 022231 108 GDGGDGGGVVFQGVP-----------WGERALSIAH----EVLLQLGDDIKLYAFKATPRGYVYVRLDK 161 (300)
Q Consensus 108 ~d~~~g~~i~~~~~~-----------~~e~I~el~e----pvl~~~G~eLvdVe~~~~~~~~LrV~IDk 161 (300)
.+.+-|+|..+.+.. ..++|+++++ |.++..|-++..+.+... ++|+|..-.
T Consensus 80 ve~~~g~gF~f~NPna~~~~~~~~~~~~~~i~~~l~~~irP~l~~dGGdielv~v~~~--~~v~v~l~G 146 (190)
T TIGR03341 80 VTDRMGGQLTLKAPNAKMPKVADDAPLEERINYVLQSEINPQLASHGGKVTLVEITDD--GVAVLQFGG 146 (190)
T ss_pred eecCCCceeEEeCCccCCCcCccchHHHHHHHHHHHhccCHHHHhcCCceEEEEEcCC--CEEEEEEee
Confidence 345566777775432 5677777776 899999999998888733 467777765
No 79
>cd04865 LigD_Pol_like_2 LigD_Pol_like_2: Polymerase (Pol) domain of bacterial LigD proteins similar to Pseudomonas aeruginosa (Pae) LigD, subgroup 2. The LigD Pol domain belongs to the archaeal/eukaryal primase (AEP) superfamily. In prokaryotes, LigD along with Ku is required for non-homologous end joining (NHEJ)-mediated repair of DNA double-strand breaks (DSB). NHEJ-mediated DNA DSB repair is error-prone. It has been suggested that LigD Pol contributes to NHEJ-mediated DNA DSB repair in vivo, by filling in short 5'-overhangs with ribonucleotides; the filled in termini would then be sealed by the associated LigD ligase domain, resulting in short stretches of RNA incorporated into the genomic DNA. The Pol domains of PaeLigD and Mycobacterium tuberculosis (Mt)LigD are stimulated by manganese, are error-prone, and prefer adding rNTPs to dNTPs in vitro; however PaeLigD and MtLigD belong to other subgroups, proteins in this subgroup await functional characterization.
Probab=22.39 E-value=2.2e+02 Score=26.87 Aligned_cols=83 Identities=14% Similarity=0.163 Sum_probs=60.2
Q ss_pred CHHHH--HHHHHHHHHhhcCCeEEEEEEEecCCcEEEEEEcccCCCCCCCChHHHHHHHHHHHHhhhccccCCCCCCCeE
Q 022231 122 PWGER--ALSIAHEVLLQLGDDIKLYAFKATPRGYVYVRLDKLSNKYGCPSMEELESYSQEYKKKLDEVGALGEIPDDLA 199 (300)
Q Consensus 122 ~~~e~--I~el~epvl~~~G~eLvdVe~~~~~~~~LrV~IDk~~~~dggVsLDDCe~vSr~Is~~LD~~e~~d~I~~~Y~ 199 (300)
+|.+- +-.++..+++++|+.-+ .+++++.-|.|+|-- ....+-+++-.+++.|...|.+ ..|+-|+
T Consensus 113 ~f~~v~~~A~~vr~~L~~lgL~sf---~KTSG~kGlHv~vPl----~~~~~~~~~r~fa~~iA~~l~~-----~~P~~~t 180 (228)
T cd04865 113 SFEDVVEVALLVREVLDELGLRGY---PKTSGARGLHIYVPI----APRYTFEEVRRFAELLAREVER-----RLPDLAT 180 (228)
T ss_pred CHHHHHHHHHHHHHHHHHcCCccc---eEccCCCeEEEEEEc----CCCCCHHHHHHHHHHHHHHHHH-----HCchhhh
Confidence 34444 56678889999997644 245666667777765 4578999999999999999985 2345555
Q ss_pred EEEecCCCCCCCCChHHHhhcCCCeeEEEE-e
Q 022231 200 LEVSTPGAERMLKVPDDLGRFKEMPITVCY-E 230 (300)
Q Consensus 200 LEVSSPGieRpLk~~~df~RfiGr~VkV~l-~ 230 (300)
.| -..+..|.+|.|-| +
T Consensus 181 ~~--------------~~k~~R~grvfiDylq 198 (228)
T cd04865 181 TE--------------RWKKERGGRVYLDYLQ 198 (228)
T ss_pred hH--------------hhHHhCCCCEEEECcc
Confidence 44 44567888899988 5
No 80
>PF01106 NifU: NifU-like domain; InterPro: IPR001075 Iron-sulphur (FeS) clusters are important cofactors for numerous proteins involved in electron transfer, in redox and non-redox catalysis, in gene regulation, and as sensors of oxygen and iron. These functions depend on the various FeS cluster prosthetic groups, the most common being [2Fe-2S] and [4Fe-4S] []. FeS cluster assembly is a complex process involving the mobilisation of Fe and S atoms from storage sources, their assembly into [Fe-S] form, their transport to specific cellular locations, and their transfer to recipient apoproteins. So far, three FeS assembly machineries have been identified, which are capable of synthesising all types of [Fe-S] clusters: ISC (iron-sulphur cluster), SUF (sulphur assimilation), and NIF (nitrogen fixation) systems. The ISC system is conserved in eubacteria and eukaryotes (mitochondria), and has broad specificity, targeting general FeS proteins [, ]. It is encoded by the isc operon (iscRSUA-hscBA-fdx-iscX). IscS is a cysteine desulphurase, which obtains S from cysteine (converting it to alanine) and serves as a S donor for FeS cluster assembly. IscU and IscA act as scaffolds to accept S and Fe atoms, assembling clusters and transfering them to recipient apoproteins. HscA is a molecular chaperone and HscB is a co-chaperone. Fdx is a [2Fe-2S]-type ferredoxin. IscR is a transcription factor that regulates expression of the isc operon. IscX (also known as YfhJ) appears to interact with IscS and may function as an Fe donor during cluster assembly []. The SUF system is an alternative pathway to the ISC system that operates under iron starvation and oxidative stress. It is found in eubacteria, archaea and eukaryotes (plastids). The SUF system is encoded by the suf operon (sufABCDSE), and the six encoded proteins are arranged into two complexes (SufSE and SufBCD) and one protein (SufA). SufS is a pyridoxal-phosphate (PLP) protein displaying cysteine desulphurase activity. SufE acts as a scaffold protein that accepts S from SufS and donates it to SufA []. SufC is an ATPase with an unorthodox ATP-binding cassette (ABC)-like component. No specific functions have been assigned to SufB and SufD. SufA is homologous to IscA [], acting as a scaffold protein in which Fe and S atoms are assembled into [FeS] cluster forms, which can then easily be transferred to apoproteins targets. In the NIF system, NifS and NifU are required for the formation of metalloclusters of nitrogenase in Azotobacter vinelandii, and other organisms, as well as in the maturation of other FeS proteins. Nitrogenase catalyses the fixation of nitrogen. It contains a complex cluster, the FeMo cofactor, which contains molybdenum, Fe and S. NifS is a cysteine desulphurase. NifU binds one Fe atom at its N-terminal, assembling an FeS cluster that is transferred to nitrogenase apoproteins []. Nif proteins involved in the formation of FeS clusters can also be found in organisms that do not fix nitrogen []. This entry represents the C-terminal of NifU and homologous proteins. NifU contains two domains: an N-terminal (IPR002871 from INTERPRO) and a C-terminal domain []. These domains exist either together or on different polypeptides, both domains being found in organisms that do not fix nitrogen (e.g. yeast), so they have a broader significance in the cell than nitrogen fixation. ; GO: 0005506 iron ion binding, 0051536 iron-sulfur cluster binding, 0016226 iron-sulfur cluster assembly; PDB: 2JNV_A 2Z51_A 1TH5_A 1VEH_A 1XHJ_A.
Probab=22.20 E-value=1.9e+02 Score=21.82 Aligned_cols=33 Identities=30% Similarity=0.337 Sum_probs=25.5
Q ss_pred HHHHHHHHHHHhhcCCeEEEEEEEecCCcEEEEEEcc
Q 022231 125 ERALSIAHEVLLQLGDDIKLYAFKATPRGYVYVRLDK 161 (300)
Q Consensus 125 e~I~el~epvl~~~G~eLvdVe~~~~~~~~LrV~IDk 161 (300)
+-|.+ +.|.++..|-++..+.+..+ .++|..-.
T Consensus 3 ~~l~~-IrP~L~~dGGdv~lv~v~~~---~V~V~l~G 35 (68)
T PF01106_consen 3 EVLEE-IRPYLQSDGGDVELVDVDDG---VVYVRLTG 35 (68)
T ss_dssp HHHHH-CHHHHHHTTEEEEEEEEETT---EEEEEEES
T ss_pred HHHHH-hChHHHhcCCcEEEEEecCC---EEEEEEEe
Confidence 33445 99999999999998888744 77777755
No 81
>cd04905 ACT_CM-PDT C-terminal ACT domain of the bifunctional chorismate mutase-prephenate dehydratase (CM-PDT) enzyme and the prephenate dehydratase (PDT) enzyme. The C-terminal ACT domain of the bifunctional chorismate mutase-prephenate dehydratase (CM-PDT) enzyme and the prephenate dehydratase (PDT) enzyme, found in plants, fungi, bacteria, and archaea. The P-protein of E. coli (CM-PDT, PheA) catalyzes the conversion of chorismate to prephenate and then the decarboxylation and dehydration to form phenylpyruvate. These are the first two steps in the biosynthesis of L-Phe and L-Tyr via the shikimate pathway in microorganisms and plants. The E. coli P-protein (CM-PDT) has three domains with an N-terminal domain with chorismate mutase activity, a middle domain with prephenate dehydratase activity, and an ACT regulatory C-terminal domain. The prephenate dehydratase enzyme has a PDT and ACT domain. The ACT domain is essential to bring about the negative allosteric regulation by L-Phe bindi
Probab=21.95 E-value=3.4e+02 Score=20.16 Aligned_cols=53 Identities=13% Similarity=-0.015 Sum_probs=37.5
Q ss_pred HHHHHHHHhhcCCeEEEEEEE-e-cCCcEEEEEEcccCCCCCCCChHHHHHHHHHHHHh
Q 022231 128 LSIAHEVLLQLGDDIKLYAFK-A-TPRGYVYVRLDKLSNKYGCPSMEELESYSQEYKKK 184 (300)
Q Consensus 128 ~el~epvl~~~G~eLvdVe~~-~-~~~~~LrV~IDk~~~~dggVsLDDCe~vSr~Is~~ 184 (300)
..-+-.+++++|..+..++.. . ...+.+.++||- ++.++.+++..+-..+...
T Consensus 15 L~~il~~f~~~~ini~~i~s~p~~~~~~~~~f~vd~----~~~~~~~~~~~~l~~l~~~ 69 (80)
T cd04905 15 LYDVLGVFAERGINLTKIESRPSKGGLWEYVFFIDF----EGHIEDPNVAEALEELKRL 69 (80)
T ss_pred HHHHHHHHHHCCcCEEEEEEEEcCCCCceEEEEEEE----ECCCCCHHHHHHHHHHHHh
Confidence 344557778899999999876 3 236778888887 5556677776666666653
No 82
>COG5406 Nucleosome binding factor SPN, SPT16 subunit [Transcription / DNA replication, recombination, and repair / Chromatin structure and dynamics]
Probab=21.55 E-value=65 Score=35.11 Aligned_cols=55 Identities=33% Similarity=0.441 Sum_probs=31.4
Q ss_pred ecccccccCCCCCCCCCCccccccCCc--cCCCCC--------ccccCCcccccCCCCCceEecCCCHHHHH
Q 022231 66 LSSSVTQNKDHYEEHPLQHEETEAGET--TDDGWE--------EEDEAEPQVGDGGDGGGVVFQGVPWGERA 127 (300)
Q Consensus 66 ~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~--------~~~~~~~~~~d~~~g~~i~~~~~~~~e~I 127 (300)
+.++...-++..++..-+||+++|+++ +|++.| +|||.|.+.||--+| -.|.+.=
T Consensus 923 L~~gsddE~deseeEvSEyeaS~dd~sdet~edees~e~seD~sedeSe~~~~DeE~g-------EDwdele 987 (1001)
T COG5406 923 LMVGSDDESDESEEEVSEYEASSDDESDETDEDEESDESSEDLSEDESENDSSDEEDG-------EDWDELE 987 (1001)
T ss_pred eecCCcccccccchhhhhhhccCCCccccccccccccccccccccccccccccccccc-------cchhhHh
Confidence 444444444555556677887777665 222222 126778888887654 4566543
No 83
>cd04862 PaeLigD_Pol_like PaeLigD_Pol_like: Polymerase (Pol) domain of bacterial LigD proteins similar to Pseudomonas aeruginosa (Pae) LigD. The LigD Pol domain belongs to the archaeal/eukaryal primase (AEP) superfamily. In prokaryotes, LigD along with Ku is required for non-homologous end joining (NHEJ)-mediated repair of DNA double-strand breaks (DSB). NHEJ-mediated DNA DSB repair is error-prone. PaeLigD is monomeric, containing an N-terminal phosphoesterase module, a central polymerase (Pol) domain, and a C-terminal ATP-dependent ligase domain. It has been suggested that LigD Pol contributes to NHEJ-mediated DNA DSB repair in vivo, by filling in short 5'-overhangs with ribonucleotides; the filled in termini would then be sealed by the associated LigD ligase domain, resulting in short stretches of RNA incorporated into the genomic DNA. The PaeLigD Pol domain in vitro, in a manganese-dependent fashion, catalyzes templated extensions of 5'-overhang duplex DNA, and nontemplated single-nu
Probab=21.29 E-value=3.1e+02 Score=25.89 Aligned_cols=84 Identities=19% Similarity=0.222 Sum_probs=59.9
Q ss_pred CCHHHH--HHHHHHHHHhhcCCeEEEEEEEecCCcEEEEEEcccCCCCCCCChHHHHHHHHHHHHhhhccccCCCCCCCe
Q 022231 121 VPWGER--ALSIAHEVLLQLGDDIKLYAFKATPRGYVYVRLDKLSNKYGCPSMEELESYSQEYKKKLDEVGALGEIPDDL 198 (300)
Q Consensus 121 ~~~~e~--I~el~epvl~~~G~eLvdVe~~~~~~~~LrV~IDk~~~~dggVsLDDCe~vSr~Is~~LD~~e~~d~I~~~Y 198 (300)
.+|.+- +--++.++++++|+.-+ .+++++.-|.|+|-- ....+-+++-.+++.|-..|.+. .|+-|
T Consensus 111 ~~f~~v~~~A~~~r~~L~~lgL~~~---~KTSG~kGlHV~vPl----~~~~~~~~~r~fa~~lA~~l~~~-----~P~~~ 178 (227)
T cd04862 111 VPWKAVVEAALLVRELLDELGLESF---VKTSGGKGLHVVVPL----APRAGWDEVKAFAKALAQHLART-----NPDRF 178 (227)
T ss_pred CCHHHHHHHHHHHHHHHHHcCCccc---eEccCCCeEEEEEEc----CCCCCHHHHHHHHHHHHHHHHHH-----Cchhh
Confidence 345444 44678889999997654 245666667777765 45789999999999999999851 34445
Q ss_pred EEEEecCCCCCCCCChHHHhhcCCCeeEEEE-e
Q 022231 199 ALEVSTPGAERMLKVPDDLGRFKEMPITVCY-E 230 (300)
Q Consensus 199 ~LEVSSPGieRpLk~~~df~RfiGr~VkV~l-~ 230 (300)
+. +-.++..+.+|.|-| +
T Consensus 179 t~--------------~~~k~~R~gkvfiDylq 197 (227)
T cd04862 179 VA--------------TMGKAKRVGKIFIDYLR 197 (227)
T ss_pred hH--------------HhhHHhCCCcEEEECcc
Confidence 44 345677788898888 5
No 84
>KOG1781 consensus Small Nuclear ribonucleoprotein splicing factor [RNA processing and modification]
Probab=21.19 E-value=60 Score=27.11 Aligned_cols=43 Identities=21% Similarity=0.292 Sum_probs=30.9
Q ss_pred EecCCCCCCCC-ChHHHhhcCCCeeEEEEeecCCCeeeEeeeeEEEEEeC
Q 022231 202 VSTPGAERMLK-VPDDLGRFKEMPITVCYEDQDSDSREKTGVFLLDSIEM 250 (300)
Q Consensus 202 VSSPGieRpLk-~~~df~RfiGr~VkV~l~~ieG~kke~~GVl~L~~vDe 250 (300)
+++-+.++|=| +.=|+.||+.+.|+|++. .|+ +.+| .|.++|.
T Consensus 6 ~~~~~~e~~kkEsilDLsky~Dk~Irvkf~--GGr--~~sG--iLkGyDq 49 (108)
T KOG1781|consen 6 SQRKKFEKPKKESILDLSKYLDKKIRVKFT--GGR--EASG--ILKGYDQ 49 (108)
T ss_pred hccccccccchhHHhhHHHhhccceEEEee--cCc--eeee--ehhhHHH
Confidence 45556665544 345899999999999996 554 7899 5677754
No 85
>COG2921 Uncharacterized conserved protein [Function unknown]
Probab=20.78 E-value=2.8e+02 Score=22.75 Aligned_cols=57 Identities=18% Similarity=0.336 Sum_probs=36.9
Q ss_pred CCCHHHHHHHHHHHHHhhcCCeEEEEEEE-ecCCcEEEEEEcccCCCCCCCChHHHHHHHHHHHH
Q 022231 120 GVPWGERALSIAHEVLLQLGDDIKLYAFK-ATPRGYVYVRLDKLSNKYGCPSMEELESYSQEYKK 183 (300)
Q Consensus 120 ~~~~~e~I~el~epvl~~~G~eLvdVe~~-~~~~~~LrV~IDk~~~~dggVsLDDCe~vSr~Is~ 183 (300)
+..+.+.+-++++.-+. |...--+.++ .+++.++.|.|+- ..-++|+.+.+-+.+.+
T Consensus 25 ~~~l~~~vv~vvqr~ap--~~~~~~~~~k~SSkGnY~svsI~i-----~A~~~EQ~e~ly~eL~~ 82 (90)
T COG2921 25 GPELEDQVVEVVQRHAP--GDYTPRVSWKPSSKGNYLSVSITI-----RATNIEQVEALYRELRK 82 (90)
T ss_pred chhHHHHHHHHHHHHCC--cccCceeeeccCCCCceEEEEEEE-----EECCHHHHHHHHHHHhh
Confidence 33455555555544433 4555666677 5667787777765 34679999999888875
No 86
>TIGR00405 L26e_arch ribosomal protein L24p/L26e, archaeal. This protein contains a KOW domain, shared by bacterial NusG and the L24p/L26e family of ribosomal proteins. Although called archaeal NusG in several publications, it is the only close homolog of eukaryotic L26e in archaeal genomes, shares an operon with L11 in many genomes, and has been sequenced from purified ribosomes. It is here designated as a ribosomal protein for these reasons.
Probab=20.59 E-value=3.4e+02 Score=22.78 Aligned_cols=133 Identities=8% Similarity=0.019 Sum_probs=68.5
Q ss_pred HHHHHHHHHHHHHhhcCCeEEEEEEEecCCcEEEEEEcccCCCCCCCChHHHHHHHHHHHHhhhccccCCCCCCCeEEEE
Q 022231 123 WGERALSIAHEVLLQLGDDIKLYAFKATPRGYVYVRLDKLSNKYGCPSMEELESYSQEYKKKLDEVGALGEIPDDLALEV 202 (300)
Q Consensus 123 ~~e~I~el~epvl~~~G~eLvdVe~~~~~~~~LrV~IDk~~~~dggVsLDDCe~vSr~Is~~LD~~e~~d~I~~~Y~LEV 202 (300)
-++++.+.++.-++..|++++.+-+...=.+||-|..+...+.. -.+..+-.+++.+...+...+.+.. +-.
T Consensus 9 ~E~~v~~~L~~~~~~~~~~~~~~~vp~~fpGYvFV~~~~~~~~~--~~i~~~~gv~~~v~~~i~~~ei~~l------~~~ 80 (145)
T TIGR00405 9 QEKNVARLMARKARKSGLEVYSILAPESLKGYILVEAETKIDMR--NPIIGVPHVRGVVEGEIDFEEIERF------LTP 80 (145)
T ss_pred hHHHHHHHHHHHHhhCCCcEEEEEccCCCCcEEEEEEECcHHHH--HHHhCCCCEEeecCCCCCHHHHHHH------hcc
Confidence 46778888888888889997666555444678877776420000 0000000000000001110000000 000
Q ss_pred ecCCCCCCCCChHHHhhcCCCeeEEEEeecCCCeeeEeeeeEEEEEeCCeeEEEEEeccccccCCCCCCCCcccccccce
Q 022231 203 STPGAERMLKVPDDLGRFKEMPITVCYEDQDSDSREKTGVFLLDSIEMDSEICVWKLADVKENRDPQEKGRPLSRKRRDW 282 (300)
Q Consensus 203 SSPGieRpLk~~~df~RfiGr~VkV~l~~ieG~kke~~GVl~L~~vDee~i~l~~~l~dVk~nr~k~~KGk~l~kkq~~~ 282 (300)
. ++ . .. -..|..|+|.--|..|. .| .+..+|.....+.+.+.+ .+.+ -
T Consensus 81 ~--~~---~---~~--~~~Gd~V~I~~GPf~G~----~g--~v~~~d~~k~~v~v~l~~---------~~~~-------~ 128 (145)
T TIGR00405 81 K--KI---I---ES--IKKGDIVEIISGPFKGE----RA--KVIRVDESKEEVTLELIE---------AAVP-------I 128 (145)
T ss_pred c--cc---c---cc--cCCCCEEEEeecCCCCC----eE--EEEEEcCCCCEEEEEEEE---------cCcc-------c
Confidence 0 00 0 11 33799999987667774 68 668888766556655432 2221 1
Q ss_pred eEEeeccccceeE
Q 022231 283 RLNLPFVMHKRVT 295 (300)
Q Consensus 283 ~l~Ipf~dI~KAr 295 (300)
.+++++++|++++
T Consensus 129 ~v~v~~~~l~~~~ 141 (145)
T TIGR00405 129 PVTVKGDQVRIIQ 141 (145)
T ss_pred eEEEeeeEEEEec
Confidence 3889999998865
No 87
>PF14153 Spore_coat_CotO: Spore coat protein CotO
Probab=20.28 E-value=2.5e+02 Score=25.61 Aligned_cols=39 Identities=10% Similarity=0.195 Sum_probs=27.2
Q ss_pred eeEeeeeEEEEEeCCeeEEEEEeccccccCCCCCCCCcccccccceeEEeeccccceeEEE
Q 022231 237 REKTGVFLLDSIEMDSEICVWKLADVKENRDPQEKGRPLSRKRRDWRLNLPFVMHKRVTLY 297 (300)
Q Consensus 237 ke~~GVl~L~~vDee~i~l~~~l~dVk~nr~k~~KGk~l~kkq~~~~l~Ipf~dI~KArL~ 297 (300)
+.+.| .|.+.+++.+ .+... ..|. .+.|++++|..+++.
T Consensus 145 ~~Y~G--~I~~~~~~~v--~i~~~---------~~~~---------~~~i~~~~I~sI~~i 183 (185)
T PF14153_consen 145 KSYRG--IILSYDEGEV--SIMPF---------NQGE---------EIEIPIDDITSIKMI 183 (185)
T ss_pred ceEEE--EEEeccCCEE--EEecc---------CCCc---------ceEeehhheeeeeec
Confidence 36899 6789988865 43311 1233 389999999998874
No 88
>PTZ00138 small nuclear ribonucleoprotein; Provisional
Probab=20.05 E-value=1.6e+02 Score=23.86 Aligned_cols=44 Identities=20% Similarity=0.068 Sum_probs=28.8
Q ss_pred HHhhcCCCeeEEEEeecCCCeeeEeeeeEEEEEeCCeeEEEEEeccccc
Q 022231 216 DLGRFKEMPITVCYEDQDSDSREKTGVFLLDSIEMDSEICVWKLADVKE 264 (300)
Q Consensus 216 df~RfiGr~VkV~l~~ieG~kke~~GVl~L~~vDee~i~l~~~l~dVk~ 264 (300)
.+.+|.....+|.....++..+++.| +|.++|.-- .++ |.|+++
T Consensus 18 ~~~~~~~~~~~V~i~l~~~~~r~~~G--~L~gfD~~m-NlV--L~d~~E 61 (89)
T PTZ00138 18 QIFRFFTEKTRVQIWLYDHPNLRIEG--KILGFDEYM-NMV--LDDAEE 61 (89)
T ss_pred HHHHHhcCCcEEEEEEEeCCCcEEEE--EEEEEcccc-eEE--EccEEE
Confidence 45567777777766434544468999 789998864 344 556543
Done!