Query 026585
Match_columns 236
No_of_seqs 149 out of 1249
Neff 5.3
Searched_HMMs 46136
Date Fri Mar 29 09:55:54 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/026585.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/026585hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK14633 hypothetical protein; 100.0 2.5E-37 5.4E-42 257.5 19.3 143 58-235 4-148 (150)
2 PRK14640 hypothetical protein; 100.0 4.4E-37 9.6E-42 256.5 19.1 143 57-235 5-150 (152)
3 PRK14634 hypothetical protein; 100.0 7E-37 1.5E-41 256.1 18.2 143 57-235 6-153 (155)
4 PRK14647 hypothetical protein; 100.0 1.2E-36 2.6E-41 255.5 19.0 149 57-235 7-158 (159)
5 PRK14643 hypothetical protein; 100.0 1.4E-36 3.1E-41 256.4 19.3 152 58-235 9-163 (164)
6 PRK14632 hypothetical protein; 100.0 2.1E-36 4.5E-41 257.2 19.8 153 55-235 5-162 (172)
7 COG0779 Uncharacterized protei 100.0 1.3E-36 2.8E-41 254.0 18.0 145 55-235 5-152 (153)
8 PRK14646 hypothetical protein; 100.0 1.1E-36 2.3E-41 255.0 17.2 143 57-233 6-151 (155)
9 PRK14636 hypothetical protein; 100.0 5E-36 1.1E-40 255.7 18.6 145 58-235 5-152 (176)
10 PRK14631 hypothetical protein; 100.0 1.8E-35 4E-40 251.8 19.1 148 57-235 7-173 (174)
11 PRK14638 hypothetical protein; 100.0 2.4E-35 5.2E-40 245.7 18.2 139 58-235 8-149 (150)
12 PRK00092 ribosome maturation p 100.0 4.4E-35 9.4E-40 244.3 19.2 145 57-235 6-153 (154)
13 PRK14639 hypothetical protein; 100.0 6.4E-35 1.4E-39 240.7 17.6 135 63-235 2-139 (140)
14 PRK14635 hypothetical protein; 100.0 3.4E-34 7.4E-39 241.3 19.2 156 57-235 5-161 (162)
15 PRK14641 hypothetical protein; 100.0 4.9E-34 1.1E-38 242.9 18.6 152 58-235 7-172 (173)
16 PF02576 DUF150: Uncharacteris 100.0 1.7E-34 3.7E-39 236.9 14.8 138 63-232 1-141 (141)
17 PRK14630 hypothetical protein; 100.0 2.2E-33 4.7E-38 232.4 17.9 136 57-233 7-143 (143)
18 PRK02001 hypothetical protein; 100.0 5.7E-33 1.2E-37 232.0 18.1 146 58-234 4-152 (152)
19 PRK14642 hypothetical protein; 100.0 1E-32 2.2E-37 238.7 18.2 165 60-234 3-180 (197)
20 PRK14637 hypothetical protein; 100.0 2.3E-32 5E-37 228.1 16.9 135 60-235 10-148 (151)
21 PRK14645 hypothetical protein; 100.0 4.3E-32 9.3E-37 227.1 16.3 136 56-230 7-145 (154)
22 PRK14644 hypothetical protein; 100.0 2.6E-31 5.6E-36 218.4 15.6 131 63-229 3-136 (136)
23 cd01734 YlxS_C YxlS is a Bacil 99.8 6.5E-21 1.4E-25 144.0 9.9 80 131-235 1-82 (83)
24 cd06168 LSm9 The eukaryotic Sm 65.5 35 0.00076 25.3 6.7 71 148-232 3-74 (75)
25 cd04861 LigD_Pol_like LigD_Pol 60.3 37 0.00079 30.6 7.0 83 54-163 111-196 (227)
26 PF01106 NifU: NifU-like domai 59.8 21 0.00045 25.9 4.4 33 59-94 3-35 (68)
27 TIGR02778 ligD_pol DNA polymer 57.7 36 0.00077 31.0 6.5 84 54-163 127-212 (245)
28 cd04865 LigD_Pol_like_2 LigD_P 56.1 36 0.00079 30.6 6.3 83 54-163 112-197 (228)
29 TIGR01634 tail_P2_I phage tail 56.0 55 0.0012 27.2 6.9 50 64-116 81-134 (139)
30 cd04479 RPA3 RPA3: A subfamily 54.3 25 0.00055 27.2 4.4 45 142-193 2-46 (101)
31 cd04864 LigD_Pol_like_1 LigD_P 52.7 37 0.00079 30.6 5.7 81 56-163 114-197 (228)
32 cd04863 MtLigD_Pol_like MtLigD 52.1 52 0.0011 29.7 6.6 83 54-163 115-200 (231)
33 cd04862 PaeLigD_Pol_like PaeLi 51.6 54 0.0012 29.5 6.6 83 54-163 111-196 (227)
34 cd04866 LigD_Pol_like_3 LigD_P 50.5 37 0.0008 30.5 5.4 83 54-163 106-192 (223)
35 PF00788 RA: Ras association ( 46.7 3.3 7.2E-05 30.2 -1.6 20 127-146 45-66 (93)
36 cd01729 LSm7 The eukaryotic Sm 40.6 52 0.0011 24.5 4.1 31 147-187 4-35 (81)
37 cd01726 LSm6 The eukaryotic Sm 40.5 51 0.0011 23.5 3.9 34 149-193 4-38 (67)
38 PF14438 SM-ATX: Ataxin 2 SM d 39.1 44 0.00096 24.2 3.5 37 150-196 7-46 (77)
39 cd01719 Sm_G The eukaryotic Sm 37.4 58 0.0013 23.7 3.9 31 147-187 2-33 (72)
40 PRK05972 ligD ATP-dependent DN 36.9 1.1E+02 0.0025 32.6 7.3 84 54-164 697-783 (860)
41 PF14472 DUF4429: Domain of un 36.6 40 0.00087 25.7 3.0 39 183-233 2-40 (94)
42 PF12701 LSM14: Scd6-like Sm d 36.3 2E+02 0.0044 22.4 6.9 65 152-233 5-77 (96)
43 PRK00737 small nuclear ribonuc 35.6 68 0.0015 23.2 4.0 30 148-187 7-37 (72)
44 COG1958 LSM1 Small nuclear rib 35.5 62 0.0013 23.7 3.8 30 148-187 10-40 (79)
45 TIGR02776 NHEJ_ligase_prk DNA 35.5 1.3E+02 0.0028 30.4 7.1 83 55-164 405-491 (552)
46 PF13222 DUF4030: Protein of u 34.2 2.7E+02 0.0058 23.4 7.6 87 53-139 51-139 (142)
47 COG3285 Predicted eukaryotic-t 34.2 85 0.0019 29.5 5.2 85 53-164 137-224 (299)
48 cd01731 archaeal_Sm1 The archa 33.7 76 0.0016 22.5 3.9 29 149-187 4-33 (68)
49 cd01722 Sm_F The eukaryotic Sm 33.5 77 0.0017 22.6 3.9 34 149-193 5-39 (68)
50 PF01423 LSM: LSM domain ; In 32.4 75 0.0016 22.0 3.7 40 149-201 2-42 (67)
51 TIGR02174 CXXU_selWTH selT/sel 31.3 1.6E+02 0.0035 21.2 5.4 39 55-93 10-48 (72)
52 cd01717 Sm_B The eukaryotic Sm 31.3 81 0.0018 23.1 3.8 31 148-188 3-34 (79)
53 COG3526 Uncharacterized protei 29.9 1.1E+02 0.0023 23.9 4.3 61 55-119 17-83 (99)
54 PRK09633 ligD ATP-dependent DN 29.2 1.9E+02 0.0041 29.6 7.2 85 54-164 445-532 (610)
55 PRK09632 ATP-dependent DNA lig 28.9 1.7E+02 0.0036 31.0 6.8 69 54-135 148-219 (764)
56 smart00651 Sm snRNP Sm protein 28.2 1E+02 0.0023 21.2 3.8 29 149-187 2-31 (67)
57 PRK11190 Fe/S biogenesis prote 28.2 1.3E+02 0.0027 26.2 5.1 50 43-94 83-147 (192)
58 PF10842 DUF2642: Protein of u 28.2 1.5E+02 0.0033 21.6 4.7 33 147-191 13-47 (66)
59 PF09684 Tail_P2_I: Phage tail 26.3 3.2E+02 0.0069 21.8 6.8 56 52-116 75-134 (139)
60 cd00600 Sm_like The eukaryotic 25.6 1.1E+02 0.0023 20.8 3.4 27 151-188 2-30 (63)
61 PF11211 DUF2997: Protein of u 25.3 1.6E+02 0.0035 20.1 4.1 36 79-121 2-37 (48)
62 cd01721 Sm_D3 The eukaryotic S 25.2 1.3E+02 0.0028 21.6 3.9 64 149-232 4-68 (70)
63 TIGR03341 YhgI_GntY IscR-regul 25.1 1.5E+02 0.0033 25.7 5.0 50 43-94 82-146 (190)
64 PF14535 AMP-binding_C_2: AMP- 24.8 3E+02 0.0065 20.6 6.6 68 63-139 8-80 (96)
65 PRK10263 DNA translocase FtsK; 24.7 5.5E+02 0.012 29.1 10.0 91 55-150 885-977 (1355)
66 PHA02595 tk.4 hypothetical pro 24.5 1.2E+02 0.0026 25.1 4.1 35 37-81 118-152 (154)
67 cd01728 LSm1 The eukaryotic Sm 23.8 1.4E+02 0.0031 21.9 4.0 30 148-187 5-35 (74)
68 cd02978 KaiB_like KaiB-like fa 23.7 2E+02 0.0044 21.3 4.8 39 86-137 2-40 (72)
69 cd01723 LSm4 The eukaryotic Sm 23.6 1.5E+02 0.0032 21.7 4.0 28 150-187 6-34 (76)
70 cd07015 Clp_protease_NfeD Nodu 23.6 1.3E+02 0.0027 25.7 4.1 57 100-162 8-65 (172)
71 PF10262 Rdx: Rdx family; Int 22.9 1.6E+02 0.0034 21.3 4.1 40 54-93 11-50 (76)
72 COG1481 Uncharacterized protei 22.1 79 0.0017 29.8 2.8 58 105-163 117-174 (308)
73 COG1094 Predicted RNA-binding 21.8 50 0.0011 29.2 1.3 56 101-158 61-117 (194)
74 PF04931 DNA_pol_phi: DNA poly 21.1 46 0.00099 34.7 1.1 21 100-120 727-747 (784)
75 cd01725 LSm2 The eukaryotic Sm 21.0 1.7E+02 0.0037 21.7 3.9 28 150-187 6-34 (81)
76 TIGR02000 NifU_proper Fe-S clu 20.9 1.5E+02 0.0033 27.4 4.4 33 59-94 226-258 (290)
77 cd01730 LSm3 The eukaryotic Sm 20.4 1.8E+02 0.0039 21.5 4.0 39 150-201 6-45 (82)
78 PF08496 Peptidase_S49_N: Pept 20.2 3.1E+02 0.0068 23.1 5.8 46 85-139 97-142 (155)
No 1
>PRK14633 hypothetical protein; Provisional
Probab=100.00 E-value=2.5e-37 Score=257.54 Aligned_cols=143 Identities=20% Similarity=0.247 Sum_probs=129.3
Q ss_pred HHHHHHHHHHHhhcCCcEEEEEEEEcCCceEEEEEeccCCCCCCCChhHHHHHHHHHHHhhhhhhccCCCCCCeEEEEec
Q 026585 58 KEALAIAEDVCLSFDGDLKIYAFRTLPNSTIKVRIEKMSNKSGSPSMEDIEAFCTTYRARLDEAEIAKSIPENTSLEVSS 137 (236)
Q Consensus 58 ~~v~~lae~vl~~~g~el~lv~~~~~~~~~lrV~IDk~~~~~ggvsldDCe~vSr~i~~~LD~~d~~~~i~~~Y~LEVSS 137 (236)
+++.++++|+++++|++|+.++|...++++|||+||+ ++||||+||+.+||+|+++||+.+ +|+++|+|||||
T Consensus 4 ~~i~~lv~p~~~~~G~eL~dve~~~~~~~~lrV~ID~----~~Gv~lddC~~vSr~i~~~LD~~d---~i~~~Y~LEVSS 76 (150)
T PRK14633 4 DDLYEIVEPITADLGYILWGIEVVGSGKLTIRIFIDH----ENGVSVDDCQIVSKEISAVFDVED---PVSGKYILEVSS 76 (150)
T ss_pred HHHHHHHHHHHHHCCCEEEEEEEEeCCCcEEEEEEeC----CCCCCHHHHHHHHHHHHHHhccCc---CCCCCeEEEEeC
Confidence 6789999999999999999999987766899999998 789999999999999999999988 999999999999
Q ss_pred CCCCCCCCChHHHhhcCCCeEEEEEeeccccCCCCCCCCceE--EEEEEeCCceEEEEeecceehhhcccCCCCCccccc
Q 026585 138 PGVERVVRIPLELERFKDRAMYVKYVGETVTTGSPSESDGVF--RLISFDMETECCTWGLADVRINREKAGKGRPLSKKQ 215 (236)
Q Consensus 138 PGleRpL~~~~df~rf~G~~V~V~~~~~~~~~~~~~eg~k~f--~L~~vd~e~~~~~~~la~vk~nr~~~~KGr~~~kk~ 215 (236)
||++|||++++||+||+|++|+|+++ .++++++.| +|.+++++++++.+. .|+
T Consensus 77 PGldRpL~~~~~f~r~~G~~v~V~~~-------~~~~~~~~~~G~L~~v~~~~i~l~~~------------~~~------ 131 (150)
T PRK14633 77 PGMNRQIFNIIQAQALVGFNVKAVTL-------APVGSQTKFKGVLERVEGNNVILNLE------------DGK------ 131 (150)
T ss_pred CCCCCCCCCHHHHHHhCCCeEEEEEe-------cccCCcEEEEEEEEEEeCCEEEEEEc------------CCc------
Confidence 99999999999999999999999999 677889999 999999987766331 111
Q ss_pred cceeeeeccccccceEEEec
Q 026585 216 REWRLNTTFDSLRLVRLHSD 235 (236)
Q Consensus 216 ~~~~l~ipf~~I~karL~~e 235 (236)
.+.|||++|++|||+++
T Consensus 132 ---~~~i~~~~I~ka~l~~~ 148 (150)
T PRK14633 132 ---EISFDFDELKKLRVSPD 148 (150)
T ss_pred ---EEEEEhHHeeeEEEecc
Confidence 36899999999999875
No 2
>PRK14640 hypothetical protein; Provisional
Probab=100.00 E-value=4.4e-37 Score=256.48 Aligned_cols=143 Identities=19% Similarity=0.245 Sum_probs=128.5
Q ss_pred HHHHHHHHHHHHhhcCCcEEEEEEEEcC-CceEEEEEeccCCCCCCCChhHHHHHHHHHHHhhhhhhccCCCCCCeEEEE
Q 026585 57 DKEALAIAEDVCLSFDGDLKIYAFRTLP-NSTIKVRIEKMSNKSGSPSMEDIEAFCTTYRARLDEAEIAKSIPENTSLEV 135 (236)
Q Consensus 57 ~~~v~~lae~vl~~~g~el~lv~~~~~~-~~~lrV~IDk~~~~~ggvsldDCe~vSr~i~~~LD~~d~~~~i~~~Y~LEV 135 (236)
-+++.++++|+++++|++|+.+++...+ +++|||+||+ ++|||++||+.+||+|+++||+.+ +|+++|+|||
T Consensus 5 ~~~i~~li~p~~~~~G~el~dve~~~~~~~~~lrV~ID~----~~gv~lddC~~vSr~is~~LD~~d---~i~~~Y~LEV 77 (152)
T PRK14640 5 EQRLTDLLEAPVVALGFELWGIEFIRAGKHSTLRVYIDG----ENGVSVENCAEVSHQVGAIMDVED---PITEEYYLEV 77 (152)
T ss_pred HHHHHHHHHHHHHhcCCEEEEEEEEecCCCcEEEEEEEC----CCCCCHHHHHHHHHHHHHHhcccc---cCCCCeEEEE
Confidence 3578899999999999999999987765 7999999998 788999999999999999999988 9999999999
Q ss_pred ecCCCCCCCCChHHHhhcCCCeEEEEEeeccccCCCCCCCCceE--EEEEEeCCceEEEEeecceehhhcccCCCCCccc
Q 026585 136 SSPGVERVVRIPLELERFKDRAMYVKYVGETVTTGSPSESDGVF--RLISFDMETECCTWGLADVRINREKAGKGRPLSK 213 (236)
Q Consensus 136 SSPGleRpL~~~~df~rf~G~~V~V~~~~~~~~~~~~~eg~k~f--~L~~vd~e~~~~~~~la~vk~nr~~~~KGr~~~k 213 (236)
||||++|||++++||+||+|++|+|+++ .++++++.| +|.+++++++++.+ +|+
T Consensus 78 SSPGl~RpL~~~~~f~r~~G~~v~V~l~-------~~~~~~k~~~G~L~~v~~~~v~l~~-------------~~~---- 133 (152)
T PRK14640 78 SSPGLDRPLFKVAQFEKYVGQEAAVTLR-------MATNNRRKFKGVIKAVQGDMITLTV-------------DGK---- 133 (152)
T ss_pred eCCCCCCcCCCHHHHHHhCCCeEEEEEe-------cccCCceEEEEEEEEEeCCEEEEEE-------------CCe----
Confidence 9999999999999999999999999999 677889999 99999998776632 122
Q ss_pred cccceeeeeccccccceEEEec
Q 026585 214 KQREWRLNTTFDSLRLVRLHSD 235 (236)
Q Consensus 214 k~~~~~l~ipf~~I~karL~~e 235 (236)
.+.|||++|++|||.++
T Consensus 134 -----~~~i~~~~I~ka~l~~~ 150 (152)
T PRK14640 134 -----DEVLAFTNIQKANIVPN 150 (152)
T ss_pred -----EEEEEhHHeeeEEEecc
Confidence 25799999999999864
No 3
>PRK14634 hypothetical protein; Provisional
Probab=100.00 E-value=7e-37 Score=256.13 Aligned_cols=143 Identities=20% Similarity=0.213 Sum_probs=128.7
Q ss_pred HHHHHHHHHHHHhhcCCcEEEEEEEEcC-CceEEEEEeccCCCCCC--CChhHHHHHHHHHHHhhhhhhccCCCCCCeEE
Q 026585 57 DKEALAIAEDVCLSFDGDLKIYAFRTLP-NSTIKVRIEKMSNKSGS--PSMEDIEAFCTTYRARLDEAEIAKSIPENTSL 133 (236)
Q Consensus 57 ~~~v~~lae~vl~~~g~el~lv~~~~~~-~~~lrV~IDk~~~~~gg--vsldDCe~vSr~i~~~LD~~d~~~~i~~~Y~L 133 (236)
.+++.++++|+++++|++|+.++|...+ +++|||+||+ ++| ||||||+.+||+|++.||+.+ +|+++|+|
T Consensus 6 ~~~i~~l~~~~~~~~G~elvdve~~~~~~~~~lrV~ID~----~~g~~v~lddC~~vSr~is~~LD~~d---~i~~~Y~L 78 (155)
T PRK14634 6 LPDLETLASATAADKGFELCGIQVLTHLQPMTLQVQIRR----SSGSDVSLDDCAGFSGPMGEALEASQ---LLTEAYVL 78 (155)
T ss_pred HHHHHHHHHHHHHHcCCEEEEEEEEeCCCCcEEEEEEEC----CCCCcccHHHHHHHHHHHHHHhcccc---cCCCCeEE
Confidence 4689999999999999999999998765 7999999999 566 999999999999999999988 99999999
Q ss_pred EEecCCCCCCCCChHHHhhcCCCeEEEEEeeccccCCCCCCCCceE--EEEEEeCCceEEEEeecceehhhcccCCCCCc
Q 026585 134 EVSSPGVERVVRIPLELERFKDRAMYVKYVGETVTTGSPSESDGVF--RLISFDMETECCTWGLADVRINREKAGKGRPL 211 (236)
Q Consensus 134 EVSSPGleRpL~~~~df~rf~G~~V~V~~~~~~~~~~~~~eg~k~f--~L~~vd~e~~~~~~~la~vk~nr~~~~KGr~~ 211 (236)
||||||++|||++++||+||+|++|+|+++ .+.++++.| +|.+++++.+++.+ +|+
T Consensus 79 EVSSPGldRpL~~~~~f~r~~G~~V~V~l~-------~~~~~~k~~~G~L~~~~~~~v~l~~-------------~~~-- 136 (155)
T PRK14634 79 EISSPGIGDQLSSDRDFQTFRGFPVEVSHR-------DDDGSEQRLEGLLLERNEDHLQINI-------------RGR-- 136 (155)
T ss_pred EEeCCCCCCcCCCHHHHHHhCCCeEEEEEe-------cCCCCeEEEEEEEEEEeCCEEEEEE-------------CCE--
Confidence 999999999999999999999999999999 677888999 99999998876632 111
Q ss_pred cccccceeeeeccccccceEEEec
Q 026585 212 SKKQREWRLNTTFDSLRLVRLHSD 235 (236)
Q Consensus 212 ~kk~~~~~l~ipf~~I~karL~~e 235 (236)
.++|||++|++|||..+
T Consensus 137 -------~~~i~~~~I~ka~l~~~ 153 (155)
T PRK14634 137 -------IKRIPRDSVISVRLTNP 153 (155)
T ss_pred -------EEEEEHHHeeeEEeCCC
Confidence 36899999999999875
No 4
>PRK14647 hypothetical protein; Provisional
Probab=100.00 E-value=1.2e-36 Score=255.48 Aligned_cols=149 Identities=21% Similarity=0.313 Sum_probs=127.3
Q ss_pred HHHHHHHHHHHHhhcCCcEEEEEEEEcC-CceEEEEEeccCCCCCCCChhHHHHHHHHHHHhhhhhhccCCCCCCeEEEE
Q 026585 57 DKEALAIAEDVCLSFDGDLKIYAFRTLP-NSTIKVRIEKMSNKSGSPSMEDIEAFCTTYRARLDEAEIAKSIPENTSLEV 135 (236)
Q Consensus 57 ~~~v~~lae~vl~~~g~el~lv~~~~~~-~~~lrV~IDk~~~~~ggvsldDCe~vSr~i~~~LD~~d~~~~i~~~Y~LEV 135 (236)
.+++.++++|+++++|++|+.+.|...+ .++|||+||+ ++||||+||+.+||+|+++||+.+ +|+++|+|||
T Consensus 7 ~~~i~~~i~~~~~~~G~~L~dv~~~~~~~~~~lrV~ID~----~~gvslddC~~vSr~is~~LD~~d---~i~~~Y~LEV 79 (159)
T PRK14647 7 VDRVTELAEQVLSSLGLELVELEYKREGREMVLRLFIDK----EGGVNLDDCAEVSRELSEILDVED---FIPERYTLEV 79 (159)
T ss_pred HHHHHHHHHHHHHHCCCEEEEEEEEecCCCeEEEEEEeC----CCCCCHHHHHHHHHHHHHHHcccc---cCCCCeEEEE
Confidence 4679999999999999999999998766 6899999998 789999999999999999999988 9999999999
Q ss_pred ecCCCCCCCCChHHHhhcCCCeEEEEEeeccccCCCCCCCCceE--EEEEEeCCceEEEEeecceehhhcccCCCCCccc
Q 026585 136 SSPGVERVVRIPLELERFKDRAMYVKYVGETVTTGSPSESDGVF--RLISFDMETECCTWGLADVRINREKAGKGRPLSK 213 (236)
Q Consensus 136 SSPGleRpL~~~~df~rf~G~~V~V~~~~~~~~~~~~~eg~k~f--~L~~vd~e~~~~~~~la~vk~nr~~~~KGr~~~k 213 (236)
||||++|||++++||+||+|++|+|+++.+.... .-++++.| +|.+++++.+++.+. +|+
T Consensus 80 SSPG~~RpL~~~~~f~r~~G~~v~V~l~~~~~~~--~~~~~~~~~G~L~~~~~~~v~l~~~------------~~~---- 141 (159)
T PRK14647 80 SSPGLDRPLKKEADYERYAGRLVKVRTFELLADE--AGNKRKTFLGELEGLADGVVTIALK------------EGQ---- 141 (159)
T ss_pred cCCCCCCcCCCHHHHHHhCCcEEEEEEecccccc--ccCCceEEEEEEEeecCCEEEEEEc------------CCc----
Confidence 9999999999999999999999999999322100 00267888 999999887765321 111
Q ss_pred cccceeeeeccccccceEEEec
Q 026585 214 KQREWRLNTTFDSLRLVRLHSD 235 (236)
Q Consensus 214 k~~~~~l~ipf~~I~karL~~e 235 (236)
.++|||++|++|+|.++
T Consensus 142 -----~~~i~~~~I~ka~l~~e 158 (159)
T PRK14647 142 -----QARIPLDKIAKANLEFE 158 (159)
T ss_pred -----EEEEEHHHCCEEEEeee
Confidence 36899999999999875
No 5
>PRK14643 hypothetical protein; Provisional
Probab=100.00 E-value=1.4e-36 Score=256.44 Aligned_cols=152 Identities=14% Similarity=0.226 Sum_probs=130.3
Q ss_pred HHHHHHHHHHHhhcCCcEEEEEEEEcC-CceEEEEEeccCCCCCCCChhHHHHHHHHHHHhhhhhhccCCCCCCeEEEEe
Q 026585 58 KEALAIAEDVCLSFDGDLKIYAFRTLP-NSTIKVRIEKMSNKSGSPSMEDIEAFCTTYRARLDEAEIAKSIPENTSLEVS 136 (236)
Q Consensus 58 ~~v~~lae~vl~~~g~el~lv~~~~~~-~~~lrV~IDk~~~~~ggvsldDCe~vSr~i~~~LD~~d~~~~i~~~Y~LEVS 136 (236)
+++.++++|+++++|++|+.++|...+ +++|||+||+...+.||||||||+.+||+|+++||+.+ +|++.|+||||
T Consensus 9 ~~l~~l~~p~~~~~G~eL~die~~~~~~~~~lrV~Id~~~~~~ggvtldDC~~vSr~is~~LD~~d---~i~~~Y~LEVS 85 (164)
T PRK14643 9 FQINELVNKELEVLNLKVYEINNLKEFENDMIQILVEDILQANKPLDFDILIKANDLVSNKIDQFI---KTSEKYLLEIS 85 (164)
T ss_pred HHHHHHHHHHHHhcCCEEEEEEEEecCCCcEEEEEEecCCCcCCCcCHHHHHHHHHHHHHHhCccC---CCCCCeEEEec
Confidence 578999999999999999999998776 78999999852112478999999999999999999999 99999999999
Q ss_pred cCCCCCCCCChHHHhhcCCCeEEEEEeeccccCCCCCCCCceE--EEEEEeCCceEEEEeecceehhhcccCCCCCcccc
Q 026585 137 SPGVERVVRIPLELERFKDRAMYVKYVGETVTTGSPSESDGVF--RLISFDMETECCTWGLADVRINREKAGKGRPLSKK 214 (236)
Q Consensus 137 SPGleRpL~~~~df~rf~G~~V~V~~~~~~~~~~~~~eg~k~f--~L~~vd~e~~~~~~~la~vk~nr~~~~KGr~~~kk 214 (236)
|||++|||++++||.||+|++|+|+++ .+++|++.| .|.+++++.++++..+. ++ ..|+
T Consensus 86 SPGleRpL~~~~df~r~~G~~V~V~l~-------~~~~g~k~~~G~L~~~~~~~~~l~l~~~-~~------~~~~----- 146 (164)
T PRK14643 86 SSGIEKQIRSQEELVKALNQWVYVQLN-------NEIKKVKEFEGYVTKYNVNTNTFRFTFF-IK------GQKK----- 146 (164)
T ss_pred CCCCCCCCCCHHHHHHhcCCeEEEEEe-------cccCCceEEEEEEEEEeCCcEEEEEEee-cc------CcCc-----
Confidence 999999999999999999999999999 778899999 99999988776643321 00 1121
Q ss_pred ccceeeeeccccccceEEEec
Q 026585 215 QREWRLNTTFDSLRLVRLHSD 235 (236)
Q Consensus 215 ~~~~~l~ipf~~I~karL~~e 235 (236)
.++|||++|++|||+++
T Consensus 147 ----~~~ip~~~I~karl~~~ 163 (164)
T PRK14643 147 ----KLDVKYEQIKFIRYAVR 163 (164)
T ss_pred ----EEEEeHHHhhheEeccc
Confidence 36899999999999875
No 6
>PRK14632 hypothetical protein; Provisional
Probab=100.00 E-value=2.1e-36 Score=257.16 Aligned_cols=153 Identities=16% Similarity=0.192 Sum_probs=130.2
Q ss_pred cHHHHHHHHHHHHHhhcCCcEEEEEEEEcCCceEEEEEeccCCCCCCCChhHHHHHHHHHHHhhhhhhccCCCCCCeEEE
Q 026585 55 WWDKEALAIAEDVCLSFDGDLKIYAFRTLPNSTIKVRIEKMSNKSGSPSMEDIEAFCTTYRARLDEAEIAKSIPENTSLE 134 (236)
Q Consensus 55 ~w~~~v~~lae~vl~~~g~el~lv~~~~~~~~~lrV~IDk~~~~~ggvsldDCe~vSr~i~~~LD~~d~~~~i~~~Y~LE 134 (236)
.-.+++..+++|+++++|++|+.+++...++++|||+||+ ++||||+||+.+||+|+++||+.+ +|+++|+||
T Consensus 5 ~~~~~i~~li~pv~~~~G~eLvdve~~~~~~~~lrV~ID~----~~GV~ldDC~~vSr~is~~LD~~d---~i~~~Y~LE 77 (172)
T PRK14632 5 ALDATIADMAGPFLASLGLELWGIELSYGGRTVVRLFVDG----PEGVTIDQCAEVSRHVGLALEVED---VISSAYVLE 77 (172)
T ss_pred hHHHHHHHHHHHHHHHCCCEEEEEEEEeCCCcEEEEEEEC----CCCCCHHHHHHHHHHHHHHhcccc---cCCCCeEEE
Confidence 3457899999999999999999999986568999999998 789999999999999999999988 999999999
Q ss_pred EecCCCCCCCCChHHHhhcCCCeEEEEEeeccccCCCCC---CCCceE--EEEEEeCCceEEEEeecceehhhcccCCCC
Q 026585 135 VSSPGVERVVRIPLELERFKDRAMYVKYVGETVTTGSPS---ESDGVF--RLISFDMETECCTWGLADVRINREKAGKGR 209 (236)
Q Consensus 135 VSSPGleRpL~~~~df~rf~G~~V~V~~~~~~~~~~~~~---eg~k~f--~L~~vd~e~~~~~~~la~vk~nr~~~~KGr 209 (236)
|||||++|||++++||+||+|+.|+|+++ .++ +|++.| +|.+++++++++... + .+++
T Consensus 78 VSSPGldRpL~~~~~f~r~iG~~V~V~l~-------~~~~~~~g~k~~~G~L~~v~~~~i~l~~~------~----~~~~ 140 (172)
T PRK14632 78 VSSPGLERPFFRAEQMSPYVGRQIELTLI-------DPTPEWPGRRKFRGELLAVEGDTVVLRPE------G----APAP 140 (172)
T ss_pred EeCCCCCCcCCCHHHHHHhCCCEEEEEEe-------ccccccCCceEEEEEEEEEeCCEEEEEEc------C----cccc
Confidence 99999999999999999999999999999 444 478888 999999987765431 0 1111
Q ss_pred CccccccceeeeeccccccceEEEec
Q 026585 210 PLSKKQREWRLNTTFDSLRLVRLHSD 235 (236)
Q Consensus 210 ~~~kk~~~~~l~ipf~~I~karL~~e 235 (236)
+ .....++|||++|++|||.++
T Consensus 141 ~----~~~~~~~i~~~~I~ka~l~~~ 162 (172)
T PRK14632 141 E----AEEAVLRTSWQGVRKANLIHV 162 (172)
T ss_pred c----CCceeEEEEhHHccEEEEEEE
Confidence 1 011247899999999999874
No 7
>COG0779 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=100.00 E-value=1.3e-36 Score=254.05 Aligned_cols=145 Identities=25% Similarity=0.349 Sum_probs=131.7
Q ss_pred cHHHHHHHHHHHHHhhcCCcEEEEEEEEcC-CceEEEEEeccCCCCCCCChhHHHHHHHHHHHhhhhhhccCCCCCCeEE
Q 026585 55 WWDKEALAIAEDVCLSFDGDLKIYAFRTLP-NSTIKVRIEKMSNKSGSPSMEDIEAFCTTYRARLDEAEIAKSIPENTSL 133 (236)
Q Consensus 55 ~w~~~v~~lae~vl~~~g~el~lv~~~~~~-~~~lrV~IDk~~~~~ggvsldDCe~vSr~i~~~LD~~d~~~~i~~~Y~L 133 (236)
.-.+++..+++|+++++|++|+.++|...+ .++|||+||+ .|++|+|||+++||+|+++||..+ ||++.|+|
T Consensus 5 ~~~~~v~~liep~~~~lG~ELv~ve~~~~~~~~~lrI~id~----~g~v~lddC~~vSr~is~~LD~ed---pi~~~Y~L 77 (153)
T COG0779 5 PITEKVTELIEPVVESLGFELVDVEFVKEGRDSVLRIYIDK----EGGVTLDDCADVSRAISALLDVED---PIEGAYFL 77 (153)
T ss_pred chHHHHHHHHHHhHhhcCcEEEEEEEEEcCCCcEEEEEeCC----CCCCCHHHHHHHHHHHHHHhccCC---cccccEEE
Confidence 345789999999999999999999998877 7999999999 699999999999999999999988 99999999
Q ss_pred EEecCCCCCCCCChHHHhhcCCCeEEEEEeeccccCCCCCCCCceE--EEEEEeCCceEEEEeecceehhhcccCCCCCc
Q 026585 134 EVSSPGVERVVRIPLELERFKDRAMYVKYVGETVTTGSPSESDGVF--RLISFDMETECCTWGLADVRINREKAGKGRPL 211 (236)
Q Consensus 134 EVSSPGleRpL~~~~df~rf~G~~V~V~~~~~~~~~~~~~eg~k~f--~L~~vd~e~~~~~~~la~vk~nr~~~~KGr~~ 211 (236)
||||||++|||++++||.||+|+.|+|+++ .++++++.| .|.+++++++++.. .|+
T Consensus 78 EVSSPGldRpL~~~~~f~r~~G~~Vkv~l~-------~~~~~~k~~~G~i~~~d~~~v~~~~-------------~~k-- 135 (153)
T COG0779 78 EVSSPGLDRPLKTAEHFARFIGEKVKVKLR-------LPIEGRKKFEGKIVAVDGETVTLEV-------------DGK-- 135 (153)
T ss_pred EeeCCCCCCCcCCHHHHHHhcCcEEEEEEe-------cccCCceEEEEEEEEEcCCeEEEEE-------------CCE--
Confidence 999999999999999999999999999999 788999999 99999999866532 122
Q ss_pred cccccceeeeeccccccceEEEec
Q 026585 212 SKKQREWRLNTTFDSLRLVRLHSD 235 (236)
Q Consensus 212 ~kk~~~~~l~ipf~~I~karL~~e 235 (236)
.+.|||++|+||||++.
T Consensus 136 -------~v~Ip~~~i~kArl~~~ 152 (153)
T COG0779 136 -------EVEIPFSDIAKARLVPE 152 (153)
T ss_pred -------EEEEEcccchhheeccc
Confidence 37999999999999863
No 8
>PRK14646 hypothetical protein; Provisional
Probab=100.00 E-value=1.1e-36 Score=255.02 Aligned_cols=143 Identities=19% Similarity=0.213 Sum_probs=126.7
Q ss_pred HHHHHHHHHHHHhhcCCcEEEEEEEEcC-CceEEEEEeccCCCCCCCChhHHHHHHHHHHHhhhhhhccCCCCCCeEEEE
Q 026585 57 DKEALAIAEDVCLSFDGDLKIYAFRTLP-NSTIKVRIEKMSNKSGSPSMEDIEAFCTTYRARLDEAEIAKSIPENTSLEV 135 (236)
Q Consensus 57 ~~~v~~lae~vl~~~g~el~lv~~~~~~-~~~lrV~IDk~~~~~ggvsldDCe~vSr~i~~~LD~~d~~~~i~~~Y~LEV 135 (236)
.+++.++++|+++++|++|+.++|...+ .++|||+||+.. .++||+|||+.+||+|+++||+.+ +|+++|+|||
T Consensus 6 ~~~i~~li~p~~~~~G~eLvdve~~~~~~~~~LrV~IDk~~--g~gVtldDC~~vSr~is~~LD~~D---~i~~~Y~LEV 80 (155)
T PRK14646 6 KSKLEILLEKVANEFDLKICSLNIQTNQNPIVIKIIIKKTN--GDDISLDDCALFNTPASEEIENSN---LLNCSYVLEI 80 (155)
T ss_pred HHHHHHHHHHHHHHcCCEEEEEEEEeCCCCeEEEEEEECCC--CCCccHHHHHHHHHHHHHHhCcCC---CCCCCeEEEE
Confidence 3679999999999999999999998765 789999999831 146999999999999999999999 9999999999
Q ss_pred ecCCCCCCCCChHHHhhcCCCeEEEEEeeccccCCCCCCCCceE--EEEEEeCCceEEEEeecceehhhcccCCCCCccc
Q 026585 136 SSPGVERVVRIPLELERFKDRAMYVKYVGETVTTGSPSESDGVF--RLISFDMETECCTWGLADVRINREKAGKGRPLSK 213 (236)
Q Consensus 136 SSPGleRpL~~~~df~rf~G~~V~V~~~~~~~~~~~~~eg~k~f--~L~~vd~e~~~~~~~la~vk~nr~~~~KGr~~~k 213 (236)
||||++|||++++||+||+|++|+|+++ .+.++++.| +|.+++++.+++.. +|+
T Consensus 81 SSPGldRpL~~~~df~r~~G~~v~V~l~-------~~~~~~~~~~G~L~~~~~~~v~l~~-------------~g~---- 136 (155)
T PRK14646 81 SSQGVSDELTSERDFKTFKGFPVNVELN-------QKNSKIKFLNGLLYEKSKDYLAINI-------------KGK---- 136 (155)
T ss_pred cCCCCCCcCCCHHHHHHhCCCEEEEEEe-------cCcCCeEEEEEEEEEEeCCEEEEEE-------------CCE----
Confidence 9999999999999999999999999999 677888998 99999998776521 222
Q ss_pred cccceeeeeccccccceEEE
Q 026585 214 KQREWRLNTTFDSLRLVRLH 233 (236)
Q Consensus 214 k~~~~~l~ipf~~I~karL~ 233 (236)
.+.|||++|++|||+
T Consensus 137 -----~~~i~~~~I~ka~L~ 151 (155)
T PRK14646 137 -----IKKIPFNEVLKISLC 151 (155)
T ss_pred -----EEEEEHHHeeeEEeC
Confidence 368999999999996
No 9
>PRK14636 hypothetical protein; Provisional
Probab=100.00 E-value=5e-36 Score=255.69 Aligned_cols=145 Identities=21% Similarity=0.266 Sum_probs=128.0
Q ss_pred HHHHHHHHHHHhhcCCcEEEEEEEEcC-CceEEEEEeccCCCCCCCChhHHHHHHHHHHHhhhhhhccCCCCCCeEEEEe
Q 026585 58 KEALAIAEDVCLSFDGDLKIYAFRTLP-NSTIKVRIEKMSNKSGSPSMEDIEAFCTTYRARLDEAEIAKSIPENTSLEVS 136 (236)
Q Consensus 58 ~~v~~lae~vl~~~g~el~lv~~~~~~-~~~lrV~IDk~~~~~ggvsldDCe~vSr~i~~~LD~~d~~~~i~~~Y~LEVS 136 (236)
+++.++++|+++++|++|+.++|...+ +++|||+||+.. .++|||+||+.+||+|++.||+.+ +|+++|+||||
T Consensus 5 ~~i~~lvep~~~~~GleLvdve~~~~~~~~~lrV~ID~~~--~ggV~lDDC~~vSr~Is~~LD~~d---~i~~~Y~LEVS 79 (176)
T PRK14636 5 AALTALIEPEAKALGLDLVRVAMFGGKSDPTLQIMAERPD--TRQLVIEDCAALSRRLSDVFDELD---PIEDAYRLEVS 79 (176)
T ss_pred HHHHHHHHHHHHHcCCEEEEEEEEcCCCCeEEEEEEECCC--CCCcCHHHHHHHHHHHHHHhccCc---CCCCCeEEEEe
Confidence 568999999999999999999998765 789999999841 246999999999999999999988 99999999999
Q ss_pred cCCCCCCCCChHHHhhcCCCeEEEEEeeccccCCCCCCCCceE--EEEEEeCCceEEEEeecceehhhcccCCCCCcccc
Q 026585 137 SPGVERVVRIPLELERFKDRAMYVKYVGETVTTGSPSESDGVF--RLISFDMETECCTWGLADVRINREKAGKGRPLSKK 214 (236)
Q Consensus 137 SPGleRpL~~~~df~rf~G~~V~V~~~~~~~~~~~~~eg~k~f--~L~~vd~e~~~~~~~la~vk~nr~~~~KGr~~~kk 214 (236)
|||++|||++++||+||+|++|+|+++ .+++|++.| +|.+++++.+++.+. +++
T Consensus 80 SPGldRpL~~~~df~r~~G~~V~V~l~-------~~~~g~k~~~G~L~~v~~~~v~l~~~------------~~~----- 135 (176)
T PRK14636 80 SPGIDRPLTRPKDFADWAGHEARIALS-------EPLDGRKQFRGELKGIDGDTVTIADN------------KAG----- 135 (176)
T ss_pred CCCCCCCCCCHHHHHHhCCCeEEEEEe-------cccCCeEEEEEEEEEEeCCEEEEEEc------------CCc-----
Confidence 999999999999999999999999999 777888999 999999987765431 111
Q ss_pred ccceeeeeccccccceEEEec
Q 026585 215 QREWRLNTTFDSLRLVRLHSD 235 (236)
Q Consensus 215 ~~~~~l~ipf~~I~karL~~e 235 (236)
.++|||++|++|||.++
T Consensus 136 ----~~~i~~~~I~kA~l~~~ 152 (176)
T PRK14636 136 ----EVILPFAAIESAKLILT 152 (176)
T ss_pred ----EEEEEhHHcceEEEecc
Confidence 35899999999999874
No 10
>PRK14631 hypothetical protein; Provisional
Probab=100.00 E-value=1.8e-35 Score=251.80 Aligned_cols=148 Identities=20% Similarity=0.246 Sum_probs=127.7
Q ss_pred HHHHHHHHHHHHhhcCCcEEEEEEEEcC-CceEEEEEeccCC--------------CCCCCChhHHHHHHHHHHHhhhhh
Q 026585 57 DKEALAIAEDVCLSFDGDLKIYAFRTLP-NSTIKVRIEKMSN--------------KSGSPSMEDIEAFCTTYRARLDEA 121 (236)
Q Consensus 57 ~~~v~~lae~vl~~~g~el~lv~~~~~~-~~~lrV~IDk~~~--------------~~ggvsldDCe~vSr~i~~~LD~~ 121 (236)
-+++.++++|+++++|++|+.++|...+ +++|||+||+... ..++|||+||+.+||+|+++||..
T Consensus 7 ~~~i~~li~p~~~~~G~eLvdve~~~~~~~~~LrV~ID~~~~~~~~~~~~~~~~~~~~~gvtiddC~~vSr~is~~LD~~ 86 (174)
T PRK14631 7 SQALTDIIAPAVAACGVDLWGIEFLPQGKRSLLRIYIDRLVEENAEPVINEDGEVEQGRGIGVEDCVRVTQQVGAMLDVH 86 (174)
T ss_pred HHHHHHHHHHHHHHcCCEEEEEEEEeCCCceEEEEEEecCcccccccccccccccccCCCcCHHHHHHHHHHHHHHhccc
Confidence 4678899999999999999999998765 7899999997311 136899999999999999999998
Q ss_pred hccCCCCCCeEEEEecCCCCCCCCChHHHhhcCCCeEEEEEeeccccCCCCCCCCceE--EEEEEe--CCceEEEEeecc
Q 026585 122 EIAKSIPENTSLEVSSPGVERVVRIPLELERFKDRAMYVKYVGETVTTGSPSESDGVF--RLISFD--METECCTWGLAD 197 (236)
Q Consensus 122 d~~~~i~~~Y~LEVSSPGleRpL~~~~df~rf~G~~V~V~~~~~~~~~~~~~eg~k~f--~L~~vd--~e~~~~~~~la~ 197 (236)
+ +|++.|+|||||||++|||++++||+||+|+.|+|+++ .+.++++.| +|.+++ ++.+++.+.
T Consensus 87 d---~i~~~Y~LEVSSPGldRpL~~~~df~r~~G~~V~V~l~-------~~~~~~k~~~G~L~~v~~~~~~v~l~~~--- 153 (174)
T PRK14631 87 D---PISGEYALEVSSPGWDRPFFQLEQLQGYIGQQVALRLI-------AAVENRRKFQAKLLAVDLENEEIQVEVE--- 153 (174)
T ss_pred c---cCCCCeEEEEeCCCCCCcCCCHHHHHHhCCCeEEEEEe-------cccCCceEEEEEEEEeecCCCEEEEEEc---
Confidence 8 99999999999999999999999999999999999999 677889999 999999 766554221
Q ss_pred eehhhcccCCCCCccccccceeeeeccccccceEEEec
Q 026585 198 VRINREKAGKGRPLSKKQREWRLNTTFDSLRLVRLHSD 235 (236)
Q Consensus 198 vk~nr~~~~KGr~~~kk~~~~~l~ipf~~I~karL~~e 235 (236)
++ + .+.|||++|+||||...
T Consensus 154 ----------~~----~----~~~i~~~~I~ka~L~~~ 173 (174)
T PRK14631 154 ----------GK----H----VLDIDSNNIDKANLIYQ 173 (174)
T ss_pred ----------CC----c----EEEEEhHHcceEEEeec
Confidence 11 0 36899999999999863
No 11
>PRK14638 hypothetical protein; Provisional
Probab=100.00 E-value=2.4e-35 Score=245.69 Aligned_cols=139 Identities=22% Similarity=0.288 Sum_probs=121.9
Q ss_pred HHHHHHHHHHHhhcCCcEEEEEEEEcC-CceEEEEEeccCCCCCCCChhHHHHHHHHHHHhhhhhhccCCCCCCeEEEEe
Q 026585 58 KEALAIAEDVCLSFDGDLKIYAFRTLP-NSTIKVRIEKMSNKSGSPSMEDIEAFCTTYRARLDEAEIAKSIPENTSLEVS 136 (236)
Q Consensus 58 ~~v~~lae~vl~~~g~el~lv~~~~~~-~~~lrV~IDk~~~~~ggvsldDCe~vSr~i~~~LD~~d~~~~i~~~Y~LEVS 136 (236)
+++.++++|+++++|++|+.++|...+ +++|||+||+. .|+|||+||+.+||+|+++||+.+ +|+++|+||||
T Consensus 8 ~~i~~~~~~i~~~~G~elvdve~~~~~~~~~lrV~ID~~---~G~v~lddC~~vSr~is~~LD~~d---~i~~~Y~LEVS 81 (150)
T PRK14638 8 EKVRKEAERIAEEQGLEIFDVQYRRESRGWVLRIIIDNP---VGYVSVRDCELFSREIERFLDRED---LIEHSYTLEVS 81 (150)
T ss_pred HHHHHHHHHHHHHcCCEEEEEEEEecCCCcEEEEEEECC---CCCcCHHHHHHHHHHHHHHhcccc---ccCCceEEEEe
Confidence 578899999999999999999998865 79999999982 345999999999999999999988 99999999999
Q ss_pred cCCCCCCCCChHHHhhcCCCeEEEEEeeccccCCCCCCCCceE--EEEEEeCCceEEEEeecceehhhcccCCCCCcccc
Q 026585 137 SPGVERVVRIPLELERFKDRAMYVKYVGETVTTGSPSESDGVF--RLISFDMETECCTWGLADVRINREKAGKGRPLSKK 214 (236)
Q Consensus 137 SPGleRpL~~~~df~rf~G~~V~V~~~~~~~~~~~~~eg~k~f--~L~~vd~e~~~~~~~la~vk~nr~~~~KGr~~~kk 214 (236)
|||++|||++++||.||+|++|+|++. +.+.| +|.+++++++++.. +|+
T Consensus 82 SPGldRpL~~~~~f~r~~G~~v~V~~~-----------~~k~~~G~L~~~~~~~i~l~~-------------~~~----- 132 (150)
T PRK14638 82 SPGLDRPLRGPKDYVRFTGKLAKIVTK-----------DGKTFIGRIESFVDGTITISD-------------EKE----- 132 (150)
T ss_pred CCCCCCCCCCHHHHHHhCCCEEEEEEC-----------CCcEEEEEEEEEeCCEEEEEE-------------CCc-----
Confidence 999999999999999999999999997 25667 99999988766520 111
Q ss_pred ccceeeeeccccccceEEEec
Q 026585 215 QREWRLNTTFDSLRLVRLHSD 235 (236)
Q Consensus 215 ~~~~~l~ipf~~I~karL~~e 235 (236)
.+.|||++|++|||.++
T Consensus 133 ----~~~i~~~~I~~a~l~~e 149 (150)
T PRK14638 133 ----KYEINIDDVKRANLEVE 149 (150)
T ss_pred ----EEEEEhHHcceEEEeee
Confidence 36899999999999875
No 12
>PRK00092 ribosome maturation protein RimP; Reviewed
Probab=100.00 E-value=4.4e-35 Score=244.30 Aligned_cols=145 Identities=27% Similarity=0.412 Sum_probs=128.1
Q ss_pred HHHHHHHHHHHHhhcCCcEEEEEEEEcC-CceEEEEEeccCCCCCCCChhHHHHHHHHHHHhhhhhhccCCCCCCeEEEE
Q 026585 57 DKEALAIAEDVCLSFDGDLKIYAFRTLP-NSTIKVRIEKMSNKSGSPSMEDIEAFCTTYRARLDEAEIAKSIPENTSLEV 135 (236)
Q Consensus 57 ~~~v~~lae~vl~~~g~el~lv~~~~~~-~~~lrV~IDk~~~~~ggvsldDCe~vSr~i~~~LD~~d~~~~i~~~Y~LEV 135 (236)
.+++.++++|+++++|++|+.+.+...+ +++|+|+||+ ++|+|+++|+.+||+|+++||+.+ +++++|+|||
T Consensus 6 ~~~i~~~~~~~~~~~g~~l~dv~~~~~~~~~~l~V~Id~----~~gv~iddc~~~Sr~is~~LD~~d---~i~~~Y~LEV 78 (154)
T PRK00092 6 EEQLTELIEPVVEALGYELVDVEYVKEGRDSTLRIYIDK----EGGIDLDDCEEVSRQISAVLDVED---PIPGAYTLEV 78 (154)
T ss_pred HHHHHHHHHHHHHHCCCEEEEEEEEecCCCcEEEEEEEC----CCCCCHHHHHHHHHHHHHHhcccc---CCCCCeEEEE
Confidence 3568999999999999999999988765 7999999998 788999999999999999999888 9999999999
Q ss_pred ecCCCCCCCCChHHHhhcCCCeEEEEEeeccccCCCCCCCCceE--EEEEEeCCceEEEEeecceehhhcccCCCCCccc
Q 026585 136 SSPGVERVVRIPLELERFKDRAMYVKYVGETVTTGSPSESDGVF--RLISFDMETECCTWGLADVRINREKAGKGRPLSK 213 (236)
Q Consensus 136 SSPGleRpL~~~~df~rf~G~~V~V~~~~~~~~~~~~~eg~k~f--~L~~vd~e~~~~~~~la~vk~nr~~~~KGr~~~k 213 (236)
||||++|||++++||+||+|+.|+|+++ .+.++.+.| +|.+++++++++.+. |++
T Consensus 79 SSPGi~RpL~~~~~f~r~~G~~v~V~~~-------~~~~~~~~~~G~L~~~~~~~i~l~~~-------------~~~--- 135 (154)
T PRK00092 79 SSPGLDRPLKKARDFRRFIGREVKVKLY-------EPIDGRKKFQGILLAVDGETVTLEVE-------------GKE--- 135 (154)
T ss_pred eCCCCCCcCCCHHHHHHhCCCeEEEEEE-------cccCCceEEEEEEEEeeCCEEEEEEC-------------CCe---
Confidence 9999999999999999999999999999 666778888 999999987765321 211
Q ss_pred cccceeeeeccccccceEEEec
Q 026585 214 KQREWRLNTTFDSLRLVRLHSD 235 (236)
Q Consensus 214 k~~~~~l~ipf~~I~karL~~e 235 (236)
+ .++|||++|++|||.++
T Consensus 136 ~----~~~i~~~~I~~a~l~~e 153 (154)
T PRK00092 136 K----EVEIPLDNIAKARLVVE 153 (154)
T ss_pred E----EEEEEHHHcceEEEeee
Confidence 1 36899999999999875
No 13
>PRK14639 hypothetical protein; Provisional
Probab=100.00 E-value=6.4e-35 Score=240.65 Aligned_cols=135 Identities=17% Similarity=0.209 Sum_probs=118.2
Q ss_pred HHHHHHhhcCCcEEEEEEEEcC-CceEEEEEeccCCCCCCCChhHHHHHHHHHHHhhhhhhccCCCCCCeEEEEecCCCC
Q 026585 63 IAEDVCLSFDGDLKIYAFRTLP-NSTIKVRIEKMSNKSGSPSMEDIEAFCTTYRARLDEAEIAKSIPENTSLEVSSPGVE 141 (236)
Q Consensus 63 lae~vl~~~g~el~lv~~~~~~-~~~lrV~IDk~~~~~ggvsldDCe~vSr~i~~~LD~~d~~~~i~~~Y~LEVSSPGle 141 (236)
.++|+++++|++|+.+++...+ +++|||+||+ ++||||+||+.+||+|+++||+.+ +|+++|+|||||||++
T Consensus 2 ~~ep~~~~~G~eLvdve~~~~~~~~~lrV~Id~----~~gv~iddC~~vSr~is~~LD~~d---~i~~~Y~LEVSSPGl~ 74 (140)
T PRK14639 2 NLEALCKECGVSFYDDELVSENGRKIYRVYITK----EGGVNLDDCERLSELLSPIFDVEP---PVSGEYFLEVSSPGLE 74 (140)
T ss_pred chhHhHHhCCCEEEEEEEEecCCCcEEEEEEeC----CCCCCHHHHHHHHHHHHHHhcccc---ccCCCeEEEEeCCCCC
Confidence 3689999999999999998765 7899999998 788999999999999999999998 9999999999999999
Q ss_pred CCCCChHHHhhcCCCeEEEEEeeccccCCCCCCCCceE--EEEEEeCCceEEEEeecceehhhcccCCCCCcccccccee
Q 026585 142 RVVRIPLELERFKDRAMYVKYVGETVTTGSPSESDGVF--RLISFDMETECCTWGLADVRINREKAGKGRPLSKKQREWR 219 (236)
Q Consensus 142 RpL~~~~df~rf~G~~V~V~~~~~~~~~~~~~eg~k~f--~L~~vd~e~~~~~~~la~vk~nr~~~~KGr~~~kk~~~~~ 219 (236)
|||++++||+||+|++|+|++. +.+.| +|.++++++++++.. .+++ .
T Consensus 75 RpL~~~~~f~r~~G~~v~v~l~-----------~~~~~~G~L~~~~~~~i~l~~~-----------~~~~---------~ 123 (140)
T PRK14639 75 RKLSKIEHFAKSIGELVKITTN-----------EKEKFEGKIVSVDDENITLENL-----------ENKE---------K 123 (140)
T ss_pred CcCCCHHHHHHhCCCEEEEEEC-----------CCcEEEEEEEEEeCCEEEEEEc-----------cCCc---------E
Confidence 9999999999999999999986 24666 999999987765321 0111 3
Q ss_pred eeeccccccceEEEec
Q 026585 220 LNTTFDSLRLVRLHSD 235 (236)
Q Consensus 220 l~ipf~~I~karL~~e 235 (236)
++|||++|++|||+++
T Consensus 124 ~~i~~~~I~ka~l~~~ 139 (140)
T PRK14639 124 TTINFNDIKKAKTYVE 139 (140)
T ss_pred EEEEhHHeeeEEEEEe
Confidence 6899999999999975
No 14
>PRK14635 hypothetical protein; Provisional
Probab=100.00 E-value=3.4e-34 Score=241.32 Aligned_cols=156 Identities=22% Similarity=0.303 Sum_probs=122.8
Q ss_pred HHHHHHHHHHHHhhcCCcEEEEEEEEcC-CceEEEEEeccCCCCCCCChhHHHHHHHHHHHhhhhhhccCCCCCCeEEEE
Q 026585 57 DKEALAIAEDVCLSFDGDLKIYAFRTLP-NSTIKVRIEKMSNKSGSPSMEDIEAFCTTYRARLDEAEIAKSIPENTSLEV 135 (236)
Q Consensus 57 ~~~v~~lae~vl~~~g~el~lv~~~~~~-~~~lrV~IDk~~~~~ggvsldDCe~vSr~i~~~LD~~d~~~~i~~~Y~LEV 135 (236)
.+++.++++|+++ .|++|+.++|...+ +++|||+||+.+++++||||+||+++||+|+++||+.+ ++ .+|+|||
T Consensus 5 ~~~i~~l~~~~~~-~g~el~dve~~~~~~~~~lrV~ID~~~~~~~gv~lddC~~vSr~is~~LD~~d---~~-~~Y~LEV 79 (162)
T PRK14635 5 EEEISEILDRVLA-LPVKLYSLKVNQRPNHSLIEVVLDNLEHPYGSVSLLECEQVSRKLKEELERIS---PD-LDFTLKV 79 (162)
T ss_pred HHHHHHHHHHHHC-CCCEEEEEEEEecCCCcEEEEEEecCCCCCCCcCHHHHHHHHHHHHHHhCCCC---CC-CCeEEEE
Confidence 4679999999996 69999999997766 68999999986555689999999999999999999877 65 8999999
Q ss_pred ecCCCCCCCCChHHHhhcCCCeEEEEEeeccccCCCCCCCCceEEEEEEeCCceEEEEeecceehhhcccCCCCCccccc
Q 026585 136 SSPGVERVVRIPLELERFKDRAMYVKYVGETVTTGSPSESDGVFRLISFDMETECCTWGLADVRINREKAGKGRPLSKKQ 215 (236)
Q Consensus 136 SSPGleRpL~~~~df~rf~G~~V~V~~~~~~~~~~~~~eg~k~f~L~~vd~e~~~~~~~la~vk~nr~~~~KGr~~~kk~ 215 (236)
||||++|||++++||.||+|++|+|++..+++ ....| .+++|.+++++++++.+.. |+++. +
T Consensus 80 SSPGldRpL~~~~~~~r~~G~~v~v~~~~~~~---~~~~g-~~g~L~~~~~~~v~l~~~~-----------k~~~~--~- 141 (162)
T PRK14635 80 SSAGAERKLRLPEDLDRFRGIPVRLVFRSEES---EKWQE-GIFRLVNRDGDQVELEKFQ-----------KGKKS--K- 141 (162)
T ss_pred cCCCCCCcCCCHHHHHHhCCCEEEEEEecCCC---cEEEe-cceEEEEEcCCEEEEEEec-----------ccccc--c-
Confidence 99999999999999999999999999863211 00000 1126999999887764321 12211 1
Q ss_pred cceeeeeccccccceEEEec
Q 026585 216 REWRLNTTFDSLRLVRLHSD 235 (236)
Q Consensus 216 ~~~~l~ipf~~I~karL~~e 235 (236)
....++|||++|++|||+++
T Consensus 142 ~~~~~~ip~~~I~ka~l~~e 161 (162)
T PRK14635 142 VKKQTTLNLKDILKGNLYVE 161 (162)
T ss_pred CCeEEEEEhHHeeeeEEEEe
Confidence 11247899999999999976
No 15
>PRK14641 hypothetical protein; Provisional
Probab=100.00 E-value=4.9e-34 Score=242.86 Aligned_cols=152 Identities=19% Similarity=0.235 Sum_probs=122.6
Q ss_pred HHHHHHHHHHH--hhcCCcEEEEEEEEcC-CceEEEEEeccCCCCCCCChhHHHHHHHHHHHhhhhhhccCCCC----CC
Q 026585 58 KEALAIAEDVC--LSFDGDLKIYAFRTLP-NSTIKVRIEKMSNKSGSPSMEDIEAFCTTYRARLDEAEIAKSIP----EN 130 (236)
Q Consensus 58 ~~v~~lae~vl--~~~g~el~lv~~~~~~-~~~lrV~IDk~~~~~ggvsldDCe~vSr~i~~~LD~~d~~~~i~----~~ 130 (236)
+.++++++|++ .++|++|+.+.+..++ +++|||+||+ ++|||||||+++||+|++.||+.+ +++ ++
T Consensus 7 ~~~~~~~~~~~~~~~~G~eLvdve~~~~~~~~~lrV~ID~----~~gv~lDdC~~vSr~Is~~LD~~d---~i~~~~~~~ 79 (173)
T PRK14641 7 NCVLQVLEASAGTKGEGVYLVSMTVKGSGKGRKIEVLLDA----DTGIRIDQCAFFSRRIRERLEEDE---ELLGLVGED 79 (173)
T ss_pred HHHHHHHHhhhccccCCeEEEEEEEEeCCCCcEEEEEEeC----CCCCCHHHHHHHHHHHHHHhCccc---ccccCCCCC
Confidence 45778888877 6888888888887765 7899999998 789999999999999999999887 554 79
Q ss_pred eEEEEecCCCCCCCCChHHHhhcCCCeEEEEEeeccccCCCCCCCCceE--EEEEEe-----CCceEEEEeecceehhhc
Q 026585 131 TSLEVSSPGVERVVRIPLELERFKDRAMYVKYVGETVTTGSPSESDGVF--RLISFD-----METECCTWGLADVRINRE 203 (236)
Q Consensus 131 Y~LEVSSPGleRpL~~~~df~rf~G~~V~V~~~~~~~~~~~~~eg~k~f--~L~~vd-----~e~~~~~~~la~vk~nr~ 203 (236)
|+|||||||++|||++++||+||+|+.|+|+++ .+.++++.| +|.+++ +..+++ ... .
T Consensus 80 Y~LEVSSPGldRpL~~~~~f~r~~G~~V~V~l~-------~~~~~~~~~~G~L~~~~~~~~~~~~v~~--~~~------~ 144 (173)
T PRK14641 80 FDLMVSSPGLGEPIILPRQYGRHVGRLLRVTYR-------DEEGSEHEVTGHLQEVSLTEGEGASIVL--KPE------Q 144 (173)
T ss_pred eEEEEeCCCCCCcCCCHHHHHHhCCCEEEEEEe-------cccCCeEEEEEEEEeeecccCCCCcEEE--Eec------c
Confidence 999999999999999999999999999999999 667788888 999996 333333 211 1
Q ss_pred ccCCCCCccccccceeeeeccccccceEEEec
Q 026585 204 KAGKGRPLSKKQREWRLNTTFDSLRLVRLHSD 235 (236)
Q Consensus 204 ~~~KGr~~~kk~~~~~l~ipf~~I~karL~~e 235 (236)
+.+|++ +.....+++||++|++|+++++
T Consensus 145 ~~~~~~----~~~~~~~~v~~~~v~~A~vevE 172 (173)
T PRK14641 145 KKKKGK----QEETENITLELDAVIRAVPEAE 172 (173)
T ss_pred cccccc----CCCCceEEEEhHHccceeeeee
Confidence 112222 2223467999999999999886
No 16
>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=1.7e-34 Score=236.95 Aligned_cols=138 Identities=30% Similarity=0.463 Sum_probs=100.3
Q ss_pred HHHHHHhhcCCcEEEEEEEEcC-CceEEEEEeccCCCCCCCChhHHHHHHHHHHHhhhhhhccCCCCCCeEEEEecCCCC
Q 026585 63 IAEDVCLSFDGDLKIYAFRTLP-NSTIKVRIEKMSNKSGSPSMEDIEAFCTTYRARLDEAEIAKSIPENTSLEVSSPGVE 141 (236)
Q Consensus 63 lae~vl~~~g~el~lv~~~~~~-~~~lrV~IDk~~~~~ggvsldDCe~vSr~i~~~LD~~d~~~~i~~~Y~LEVSSPGle 141 (236)
||+|+++++|++|+.+.+...+ +++|+|+||+ +++||+++|+++||+|++.||..+ +++++|+|||||||++
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----DGGVSLDDCEKVSRAISALLDAED---PIPEDYTLEVSSPGID 73 (141)
T ss_dssp -HHHHH-S-SSEEEEEEEEEETTEEEEEEEEE-----SS---HHHHHHHHHHHGGGTTTS-------S-EEEEEE--SSS
T ss_pred CcccchhhcCCEEEEEEEEECCCCEEEEEEEEe----CCCCCHHHHHHHHHHHHHHHcccc---ccCcceEEEEeCCCCC
Confidence 6899999999999999998877 6799999998 678999999999999999999988 9999999999999999
Q ss_pred CCCCChHHHhhcCCCeEEEEEeeccccCCCCCCCCceE--EEEEEeCCceEEEEeecceehhhcccCCCCCcccccccee
Q 026585 142 RVVRIPLELERFKDRAMYVKYVGETVTTGSPSESDGVF--RLISFDMETECCTWGLADVRINREKAGKGRPLSKKQREWR 219 (236)
Q Consensus 142 RpL~~~~df~rf~G~~V~V~~~~~~~~~~~~~eg~k~f--~L~~vd~e~~~~~~~la~vk~nr~~~~KGr~~~kk~~~~~ 219 (236)
|||++++||.||+|++|+|+++ .+.++++.| .|.+++++++++.+. .|+++ ..
T Consensus 74 r~L~~~~~~~~~iG~~v~v~~~-------~~~~~~~~~~G~L~~~~~~~i~l~~~-----------~~~~~-------~~ 128 (141)
T PF02576_consen 74 RPLKSPRDFERFIGRKVKVKLK-------QPVNGRKEFEGKLLEVDEDEITLEVE-----------GKGKK-------KE 128 (141)
T ss_dssp S--SSHHHHHHH-SEEEEEE-S-------S-SSS-SEEEEEEEEEETTEEEEEEE------------SS-E-------EE
T ss_pred CcCCCHHHHHHhcCCeEEEEEe-------ccCCCcEEEEEEEEEEeCCEEEEEEC-----------Cccce-------EE
Confidence 9999999999999999999998 667788888 999999988777543 23322 14
Q ss_pred eeeccccccceEE
Q 026585 220 LNTTFDSLRLVRL 232 (236)
Q Consensus 220 l~ipf~~I~karL 232 (236)
++|||++|++|||
T Consensus 129 ~~I~~~~I~ka~L 141 (141)
T PF02576_consen 129 VEIPFSDIKKARL 141 (141)
T ss_dssp EEE-SS--SS-EE
T ss_pred EEEEHHHCceEeC
Confidence 7999999999997
No 17
>PRK14630 hypothetical protein; Provisional
Probab=100.00 E-value=2.2e-33 Score=232.36 Aligned_cols=136 Identities=14% Similarity=0.189 Sum_probs=117.2
Q ss_pred HHHHHHHHHHHHhhcCCcEEEEEEEEcC-CceEEEEEeccCCCCCCCChhHHHHHHHHHHHhhhhhhccCCCCCCeEEEE
Q 026585 57 DKEALAIAEDVCLSFDGDLKIYAFRTLP-NSTIKVRIEKMSNKSGSPSMEDIEAFCTTYRARLDEAEIAKSIPENTSLEV 135 (236)
Q Consensus 57 ~~~v~~lae~vl~~~g~el~lv~~~~~~-~~~lrV~IDk~~~~~ggvsldDCe~vSr~i~~~LD~~d~~~~i~~~Y~LEV 135 (236)
..++.++++|+++++|++|+.+++...+ +++|||+||+ ++|||++||+.+||+|+..|| + +|+++|+|||
T Consensus 7 ~~~i~~li~~~~~~~G~eLvdve~~~~~~~~~lrV~Id~----~~gV~idDC~~vSr~i~~~ld--~---~i~~~Y~LEV 77 (143)
T PRK14630 7 NSEVYNLIKNVTDRLGIEIIEINTFRNRNEGKIQIVLYK----KDSFGVDTLCDLHKMILLILE--A---VLKYNFSLEI 77 (143)
T ss_pred HHHHHHHHHHHHHHcCCEEEEEEEEecCCCcEEEEEEEC----CCCCCHHHHHHHHHHHHHHhc--c---cCCCCeEEEE
Confidence 3578999999999999999999998765 7999999998 789999999999999999996 4 8899999999
Q ss_pred ecCCCCCCCCChHHHhhcCCCeEEEEEeeccccCCCCCCCCceEEEEEEeCCceEEEEeecceehhhcccCCCCCccccc
Q 026585 136 SSPGVERVVRIPLELERFKDRAMYVKYVGETVTTGSPSESDGVFRLISFDMETECCTWGLADVRINREKAGKGRPLSKKQ 215 (236)
Q Consensus 136 SSPGleRpL~~~~df~rf~G~~V~V~~~~~~~~~~~~~eg~k~f~L~~vd~e~~~~~~~la~vk~nr~~~~KGr~~~kk~ 215 (236)
||||++|||++++||+||+|++|+|++. .+.. .-.|.+++++++++.. .|+
T Consensus 78 SSPGldRpL~~~~df~r~~G~~v~V~l~-------~~~~---~G~L~~~~d~~i~l~~-------------~~~------ 128 (143)
T PRK14630 78 STPGINRKIKSDREFKIFEGKKIKLMLD-------NDFE---EGFILEAKADSFIFKT-------------DSK------ 128 (143)
T ss_pred eCCCCCCcCCCHHHHHHhCCCEEEEEEc-------Ccce---EEEEEEEeCCEEEEEE-------------CCE------
Confidence 9999999999999999999999999997 3322 2279999998776521 111
Q ss_pred cceeeeeccccccceEEE
Q 026585 216 REWRLNTTFDSLRLVRLH 233 (236)
Q Consensus 216 ~~~~l~ipf~~I~karL~ 233 (236)
.+.|||++|++|||.
T Consensus 129 ---~~~i~~~~I~ka~lv 143 (143)
T PRK14630 129 ---EVNVLYSDVKKAKLS 143 (143)
T ss_pred ---EEEEEhHhcceEEEC
Confidence 368999999999984
No 18
>PRK02001 hypothetical protein; Validated
Probab=100.00 E-value=5.7e-33 Score=232.03 Aligned_cols=146 Identities=21% Similarity=0.249 Sum_probs=117.0
Q ss_pred HHHHHH-HHHHHhhcCCcEEEEEEEEcCCceEEEEEeccCCCCCCCChhHHHHHHHHHHHhhhhhhccCCCCCCeEEEEe
Q 026585 58 KEALAI-AEDVCLSFDGDLKIYAFRTLPNSTIKVRIEKMSNKSGSPSMEDIEAFCTTYRARLDEAEIAKSIPENTSLEVS 136 (236)
Q Consensus 58 ~~v~~l-ae~vl~~~g~el~lv~~~~~~~~~lrV~IDk~~~~~ggvsldDCe~vSr~i~~~LD~~d~~~~i~~~Y~LEVS 136 (236)
++|.+| ++|+++++|++|+.+.+. +++.|||+||+ ++|||++||+.+||+|+++||+.+ ++|+||||
T Consensus 4 ~~~~~~~~e~~~~~~g~eLvdv~~~--~~~~lrV~ID~----~~Gv~lddC~~vSr~is~~LD~~d------~~Y~LEVS 71 (152)
T PRK02001 4 KKVVELLVEELLEGPELFLVDLTIS--PDNKIVVEIDG----DEGVWIEDCVELSRAIEHNLDREE------EDFELEVG 71 (152)
T ss_pred HHHHHHHHHhhhhhcCcEEEEEEEE--cCCEEEEEEEC----CCCCCHHHHHHHHHHHHHHhcCCC------CCeEEEEe
Confidence 455566 999999999888877776 45679999998 789999999999999999999654 79999999
Q ss_pred cCCCCCCCCChHHHhhcCCCeEEEEEeeccccCCCCCCCCceE--EEEEEeCCceEEEEeecceehhhcccCCCCCcccc
Q 026585 137 SPGVERVVRIPLELERFKDRAMYVKYVGETVTTGSPSESDGVF--RLISFDMETECCTWGLADVRINREKAGKGRPLSKK 214 (236)
Q Consensus 137 SPGleRpL~~~~df~rf~G~~V~V~~~~~~~~~~~~~eg~k~f--~L~~vd~e~~~~~~~la~vk~nr~~~~KGr~~~kk 214 (236)
|||++|||++++||+||+|++|+|++. +.+.| +|.+++++++++...-. ...+.+||+..
T Consensus 72 SPGldRpL~~~~~f~r~~G~~v~V~l~-----------~~~~~~G~L~~~~~~~i~l~~~~~----~~~~~~k~~~~--- 133 (152)
T PRK02001 72 SAGLTSPLKVPRQYKKNIGRELEVLTK-----------NGKKIEGELKSADENDITLEVKAR----EPKEGGKGKVT--- 133 (152)
T ss_pred CCCCCCcCCCHHHHHHhCCCEEEEEEC-----------CCCEEEEEEEEEeCCEEEEEEccc----ccccccccccc---
Confidence 999999999999999999999999996 25667 99999998877643210 00112233321
Q ss_pred ccceeeeeccccccceEEEe
Q 026585 215 QREWRLNTTFDSLRLVRLHS 234 (236)
Q Consensus 215 ~~~~~l~ipf~~I~karL~~ 234 (236)
+...++|||++|++|+|.+
T Consensus 134 -~~~~~~i~~~~I~ka~l~~ 152 (152)
T PRK02001 134 -VEKEETITYDDIKEAKVII 152 (152)
T ss_pred -cceeEEEEhHheeeEEEeC
Confidence 2235799999999999975
No 19
>PRK14642 hypothetical protein; Provisional
Probab=100.00 E-value=1e-32 Score=238.73 Aligned_cols=165 Identities=22% Similarity=0.219 Sum_probs=124.4
Q ss_pred HHHHHHHHHhhcCCcEEEEEEEEcCCceEEEEEeccCC---------CCCCCChhHHHHHHHHHHHhhhhhhccCCCCCC
Q 026585 60 ALAIAEDVCLSFDGDLKIYAFRTLPNSTIKVRIEKMSN---------KSGSPSMEDIEAFCTTYRARLDEAEIAKSIPEN 130 (236)
Q Consensus 60 v~~lae~vl~~~g~el~lv~~~~~~~~~lrV~IDk~~~---------~~ggvsldDCe~vSr~i~~~LD~~d~~~~i~~~ 130 (236)
+.++++++++++|++|+.+++. ++++|||+||+.+. +.++|||+||+.+||+|+.+||..+ . ..
T Consensus 3 l~~liepvv~~lG~eLvdve~~--~~~~LrV~ID~~~~~~~~~~~~~~~~gVtidDC~~vSR~Is~~LDve~---~--~y 75 (197)
T PRK14642 3 LQQIVEQTVTGLGYDLVEIERS--AGGLLRVTIDLPWVPPTEGAPVGPEQFVTVEDCEKVTRQLQFALEVDG---V--DY 75 (197)
T ss_pred HHHHHHHHHHHcCCEEEEEEEe--cCCEEEEEEecCccccccccccccCCCccHHHHHHHHHHHHHHhcccC---c--cc
Confidence 5689999999999777777654 45699999998421 1367999999999999999999765 2 33
Q ss_pred eEEEEecCCCCCCCCChHHHhhcCCCeEEEEEeecccc--CCCCCCCCceE--EEEEEeCCceEEEEeecceehhhcccC
Q 026585 131 TSLEVSSPGVERVVRIPLELERFKDRAMYVKYVGETVT--TGSPSESDGVF--RLISFDMETECCTWGLADVRINREKAG 206 (236)
Q Consensus 131 Y~LEVSSPGleRpL~~~~df~rf~G~~V~V~~~~~~~~--~~~~~eg~k~f--~L~~vd~e~~~~~~~la~vk~nr~~~~ 206 (236)
|+||||||||+|||++++||.||+|+.|+|+++.+.+. .+....++++| +|.++++++++++|.-++.+..-+..+
T Consensus 76 ~~LEVSSPGldRPLk~~~df~rfiG~~V~V~l~~pi~~~~~~~~~~~rk~f~G~L~~~~~~~i~l~~~~~~~~k~g~~~~ 155 (197)
T PRK14642 76 KRLEVSSPGIDRPLRHEQDFERFAGEVIDITLKAPIGAAAGGQVSANRKKFRGTLERAESGGWQIVWSDEPPVKPGQRVS 155 (197)
T ss_pred cEEEEeCCCCCCCCCCHHHHHHhCCCeEEEEEeccccccccccccCCceEEEEEEEEEcCCEEEEEEeecccCCCccccc
Confidence 47999999999999999999999999999999943321 01122268888 999999999999997532111101113
Q ss_pred CCCCccccccceeeeeccccccceEEEe
Q 026585 207 KGRPLSKKQREWRLNTTFDSLRLVRLHS 234 (236)
Q Consensus 207 KGr~~~kk~~~~~l~ipf~~I~karL~~ 234 (236)
|||.+.. ...+.|+|++|++|||.+
T Consensus 156 k~~~~~~---~~~~~~~~~eik~a~l~p 180 (197)
T PRK14642 156 KKRVPAP---LQALGFTLDELREARLAP 180 (197)
T ss_pred ccccccc---ceeEEeehhheeeEEEEE
Confidence 4443211 235899999999999986
No 20
>PRK14637 hypothetical protein; Provisional
Probab=100.00 E-value=2.3e-32 Score=228.10 Aligned_cols=135 Identities=21% Similarity=0.281 Sum_probs=114.5
Q ss_pred HHHHHHHHHhhcCCcEEEEEEEEcC-CceEEEEEeccCCCCCCCChhHHHHHHHHHHHhhhhhhccCCCCCCeEEEEecC
Q 026585 60 ALAIAEDVCLSFDGDLKIYAFRTLP-NSTIKVRIEKMSNKSGSPSMEDIEAFCTTYRARLDEAEIAKSIPENTSLEVSSP 138 (236)
Q Consensus 60 v~~lae~vl~~~g~el~lv~~~~~~-~~~lrV~IDk~~~~~ggvsldDCe~vSr~i~~~LD~~d~~~~i~~~Y~LEVSSP 138 (236)
-.++++|+++++|++|+.+.+...+ +++|||+||+ ++||||+||+++||+|+++||... + +.+|+||||||
T Consensus 10 ~~~~v~p~~~~~g~eLvdve~~~~~~~~~lrV~ID~----~~gV~iddC~~vSr~Is~~LD~~~---~-~~~y~LEVSSP 81 (151)
T PRK14637 10 YFSECEPVVEGLGCKLVDLSRRVQQAQGRVRAVIYS----AGGVGLDDCARVHRILVPRLEALG---G-VRDVFLEVSSP 81 (151)
T ss_pred HHHHHHHHHHhcCCEEEEEEEEecCCCcEEEEEEEC----CCCCCHHHHHHHHHHHHHHhcccc---c-ccCcEEEEeCC
Confidence 3489999999999999999998766 7899999998 789999999999999999999643 2 57899999999
Q ss_pred CCCCCCCChHHHhhcCCCeEEEEEeeccccCCCCCCCCceE---EEEEEeCCceEEEEeecceehhhcccCCCCCccccc
Q 026585 139 GVERVVRIPLELERFKDRAMYVKYVGETVTTGSPSESDGVF---RLISFDMETECCTWGLADVRINREKAGKGRPLSKKQ 215 (236)
Q Consensus 139 GleRpL~~~~df~rf~G~~V~V~~~~~~~~~~~~~eg~k~f---~L~~vd~e~~~~~~~la~vk~nr~~~~KGr~~~kk~ 215 (236)
|++|||++++||.||+|++|+|++. +++.| +|.+++++++++.. +|+
T Consensus 82 GldRpL~~~~~f~r~~G~~V~V~l~-----------~~~~~~~G~L~~~~d~~v~l~~-------------~~~------ 131 (151)
T PRK14637 82 GIERVIKNAAEFSIFVGETVKVWFE-----------CTGQWQVGTIAEADETCLVLTS-------------DGV------ 131 (151)
T ss_pred CCCCCCCCHHHHHHhCCCEEEEEEC-----------CCCcEEEEEEEEEeCCEEEEEE-------------CCE------
Confidence 9999999999999999999999983 12222 89999998766521 111
Q ss_pred cceeeeeccccccceEEEec
Q 026585 216 REWRLNTTFDSLRLVRLHSD 235 (236)
Q Consensus 216 ~~~~l~ipf~~I~karL~~e 235 (236)
.+.|||++|++|||++.
T Consensus 132 ---~~~i~~~~I~ka~L~~~ 148 (151)
T PRK14637 132 ---PVTIPYVQITKAQLHPA 148 (151)
T ss_pred ---EEEEEHHHeeeEEEEEE
Confidence 36899999999999875
No 21
>PRK14645 hypothetical protein; Provisional
Probab=100.00 E-value=4.3e-32 Score=227.15 Aligned_cols=136 Identities=19% Similarity=0.231 Sum_probs=116.4
Q ss_pred HHHHHHHHHHHHHhhcCCcEEEEEEEEcC-CceEEEEEeccCCCCCCCChhHHHHHHHHHHHhhhhhhccCCCCCCeEEE
Q 026585 56 WDKEALAIAEDVCLSFDGDLKIYAFRTLP-NSTIKVRIEKMSNKSGSPSMEDIEAFCTTYRARLDEAEIAKSIPENTSLE 134 (236)
Q Consensus 56 w~~~v~~lae~vl~~~g~el~lv~~~~~~-~~~lrV~IDk~~~~~ggvsldDCe~vSr~i~~~LD~~d~~~~i~~~Y~LE 134 (236)
=-+++.++++|+++++|++|+.+.+...+ +++|||+||+.+ .++|+|+||+++||+|+++||+.+ +|+++|+||
T Consensus 7 ~~~~i~~li~~~~~~~G~elvdve~~~~~~~~ilrV~ID~~~--~~~v~lddC~~vSr~is~~LD~~d---~i~~~Y~LE 81 (154)
T PRK14645 7 NNPDLQQLAEGALEPLGYEVLEVQVQRSGGKRIVLVRIDRKD--EQPVTVEDLERASRALEAELDRLD---PIEGEYRLE 81 (154)
T ss_pred cHHHHHHHHHHHHHHcCCEEEEEEEEeCCCCeEEEEEEECCC--CCCcCHHHHHHHHHHHHHHhcccc---cCCCceEEE
Confidence 34678999999999999999999998765 789999999731 246999999999999999999998 999999999
Q ss_pred EecCCCCCCCCChHHHhhcCCCeEEEEEeeccccCCCCCCCCceE--EEEEEeCCceEEEEeecceehhhcccCCCCCcc
Q 026585 135 VSSPGVERVVRIPLELERFKDRAMYVKYVGETVTTGSPSESDGVF--RLISFDMETECCTWGLADVRINREKAGKGRPLS 212 (236)
Q Consensus 135 VSSPGleRpL~~~~df~rf~G~~V~V~~~~~~~~~~~~~eg~k~f--~L~~vd~e~~~~~~~la~vk~nr~~~~KGr~~~ 212 (236)
|||||++|||++++||.||+|++|+|++ +.+.| +|.+++++.+++.+ +|+
T Consensus 82 VSSPGldRpL~~~~df~r~~G~~v~v~~------------~~k~~~G~L~~~~d~~i~l~~-------------~~~--- 133 (154)
T PRK14645 82 VESPGPKRPLFTARHFERFAGLKAKVRG------------PGENFTGRIKAVSGDQVTFDV-------------GGE--- 133 (154)
T ss_pred EeCCCCCCCCCCHHHHHHhCCCEEEEEc------------CCeEEEEEEEEEeCCEEEEEE-------------CCe---
Confidence 9999999999999999999999999974 25666 99999998766532 121
Q ss_pred ccccceeeeeccccccce
Q 026585 213 KKQREWRLNTTFDSLRLV 230 (236)
Q Consensus 213 kk~~~~~l~ipf~~I~ka 230 (236)
.++|||++|+++
T Consensus 134 ------~~~i~~~~I~~~ 145 (154)
T PRK14645 134 ------DRTLRIGTFQAN 145 (154)
T ss_pred ------EEEEEHHHhhhh
Confidence 368999999755
No 22
>PRK14644 hypothetical protein; Provisional
Probab=99.97 E-value=2.6e-31 Score=218.40 Aligned_cols=131 Identities=18% Similarity=0.233 Sum_probs=114.8
Q ss_pred HHHHHHhhcCCcEEEEEEEEcC-CceEEEEEeccCCCCCCCChhHHHHHHHHHHHhhhhhhccCCCCCCeEEEEecCCCC
Q 026585 63 IAEDVCLSFDGDLKIYAFRTLP-NSTIKVRIEKMSNKSGSPSMEDIEAFCTTYRARLDEAEIAKSIPENTSLEVSSPGVE 141 (236)
Q Consensus 63 lae~vl~~~g~el~lv~~~~~~-~~~lrV~IDk~~~~~ggvsldDCe~vSr~i~~~LD~~d~~~~i~~~Y~LEVSSPGle 141 (236)
+.+|+++++|++|+.++|...+ +++|||+||+ . +|+||+.+||+|+++||+.+ +++++|+|||||||++
T Consensus 3 ~~e~~~~~~g~el~dve~~~~~~~~~LrV~Idk----~---~iddC~~vSr~is~~LD~~d---~i~~~Y~LEVSSPGld 72 (136)
T PRK14644 3 WKEKLLEKFGNKINEIKIVKEDGDLFLEVILNS----R---DLKDIEELTKEISDFIDNLS---VEFDFDSLDISSPGFD 72 (136)
T ss_pred chhhhHHhcCCEEEEEEEEeCCCCEEEEEEECC----C---CHHHHHHHHHHHHHHhcccc---CCCCCeEEEEECCCCC
Confidence 4689999999999999987765 7899999997 3 79999999999999999988 9999999999999999
Q ss_pred CCCCChHHHhhcCCCeEEEEEeeccccCCCCCCCCceE--EEEEEeCCceEEEEeecceehhhcccCCCCCcccccccee
Q 026585 142 RVVRIPLELERFKDRAMYVKYVGETVTTGSPSESDGVF--RLISFDMETECCTWGLADVRINREKAGKGRPLSKKQREWR 219 (236)
Q Consensus 142 RpL~~~~df~rf~G~~V~V~~~~~~~~~~~~~eg~k~f--~L~~vd~e~~~~~~~la~vk~nr~~~~KGr~~~kk~~~~~ 219 (236)
|||++ +||.||+|+.|+|+++ .+++|++.| .|.+++++++++.|.. ||+. ..
T Consensus 73 RpL~~-~~f~r~~G~~v~V~l~-------~~~~~~~~~~G~L~~v~~~~i~l~~~~-----------k~~~-------~~ 126 (136)
T PRK14644 73 MDYET-DELENHIGEIIDVSLN-------KEVNKTDFITGELLENNPETITLKWNC-----------KGQF-------RK 126 (136)
T ss_pred CCCCH-HHHHHhCCCeEEEEEc-------cCcCCeEEEEEEEEEEeCCEEEEEEec-----------CCcE-------EE
Confidence 99998 5999999999999999 777889999 9999999988776542 3432 24
Q ss_pred eeeccccccc
Q 026585 220 LNTTFDSLRL 229 (236)
Q Consensus 220 l~ipf~~I~k 229 (236)
+++|+++|++
T Consensus 127 i~~~~~~i~~ 136 (136)
T PRK14644 127 VEINKENIKK 136 (136)
T ss_pred EEECHHHhcC
Confidence 7899999874
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=99.85 E-value=6.5e-21 Score=143.98 Aligned_cols=80 Identities=29% Similarity=0.361 Sum_probs=67.7
Q ss_pred eEEEEecCCCCCCCCChHHHhhcCCCeEEEEEeeccccCCCCCCCCceE--EEEEEeCCceEEEEeecceehhhcccCCC
Q 026585 131 TSLEVSSPGVERVVRIPLELERFKDRAMYVKYVGETVTTGSPSESDGVF--RLISFDMETECCTWGLADVRINREKAGKG 208 (236)
Q Consensus 131 Y~LEVSSPGleRpL~~~~df~rf~G~~V~V~~~~~~~~~~~~~eg~k~f--~L~~vd~e~~~~~~~la~vk~nr~~~~KG 208 (236)
|+|||||||++|||++++||.||+|+.|+|++. .+++|++.| +|.+++++++++.+. .|+
T Consensus 1 Y~LEVSSPGl~RpL~~~~~~~r~~G~~v~v~~~-------~~~~~~~~~~G~L~~~~~~~v~l~~~-----------~~~ 62 (83)
T cd01734 1 YFLEVSSPGAERPLKKEADFERAVGKYVHVKLY-------QPIDGQKEFEGTLLGVDDDTVTLEVD-----------IKT 62 (83)
T ss_pred CEEEEcCCCCCCcCCCHHHHHHhCCCEEEEEEE-------cccCCeEEEEEEEEeEeCCEEEEEEe-----------cCC
Confidence 899999999999999999999999999999999 667788888 999999988766432 122
Q ss_pred CCccccccceeeeeccccccceEEEec
Q 026585 209 RPLSKKQREWRLNTTFDSLRLVRLHSD 235 (236)
Q Consensus 209 r~~~kk~~~~~l~ipf~~I~karL~~e 235 (236)
+ ...++|||++|++|||+++
T Consensus 63 ~-------~~~~~i~~~~I~ka~l~~~ 82 (83)
T cd01734 63 R-------GKTVEIPLDKIAKARLAPE 82 (83)
T ss_pred C-------CeEEEEEhHHeeEEEEEEE
Confidence 1 1257999999999999875
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=65.51 E-value=35 Score=25.25 Aligned_cols=71 Identities=10% Similarity=0.120 Sum_probs=39.9
Q ss_pred HHHhhcCCCeEEEEEeeccccCCCCCCCCceE-EEEEEeCCceEEEEeecceehhhcccCCCCCccccccceeeeecccc
Q 026585 148 LELERFKDRAMYVKYVGETVTTGSPSESDGVF-RLISFDMETECCTWGLADVRINREKAGKGRPLSKKQREWRLNTTFDS 226 (236)
Q Consensus 148 ~df~rf~G~~V~V~~~~~~~~~~~~~eg~k~f-~L~~vd~e~~~~~~~la~vk~nr~~~~KGr~~~kk~~~~~l~ipf~~ 226 (236)
..+..|+|++|+|++. +|+-.. .|..+|.... +. |.++.+.+....+.....++..+ -+-+|-+.
T Consensus 3 ~~L~~~l~~~v~V~l~----------dgR~~~G~l~~~D~~~N-iv--L~~~~E~~~~~~~~~~~~~r~lG-lv~IrG~~ 68 (75)
T cd06168 3 QKLRSLLGRTMRIHMT----------DGRTLVGVFLCTDRDCN-II--LGSAQEYRPPPDSFSPTEPRVLG-LVMIPGHH 68 (75)
T ss_pred hHHHHhcCCeEEEEEc----------CCeEEEEEEEEEcCCCc-EE--ecCcEEEEcccCccCCccEEEee-eEEEeCCe
Confidence 4578899999999998 344433 9999987643 22 33444443211110111111122 35778888
Q ss_pred ccceEE
Q 026585 227 LRLVRL 232 (236)
Q Consensus 227 I~karL 232 (236)
|.++.+
T Consensus 69 Iv~i~v 74 (75)
T cd06168 69 IVSIEV 74 (75)
T ss_pred EEEEEE
Confidence 877653
No 25
>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=60.34 E-value=37 Score=30.60 Aligned_cols=83 Identities=13% Similarity=0.212 Sum_probs=60.9
Q ss_pred CcHHHH--HHHHHHHHHhhcCCcEEEEEE-EEcCCceEEEEEeccCCCCCCCChhHHHHHHHHHHHhhhhhhccCCCCCC
Q 026585 54 TWWDKE--ALAIAEDVCLSFDGDLKIYAF-RTLPNSTIKVRIEKMSNKSGSPSMEDIEAFCTTYRARLDEAEIAKSIPEN 130 (236)
Q Consensus 54 ~~w~~~--v~~lae~vl~~~g~el~lv~~-~~~~~~~lrV~IDk~~~~~ggvsldDCe~vSr~i~~~LD~~d~~~~i~~~ 130 (236)
..|.+- +..+++++|.++|+ ..| |++++.=|+|+|-- ....+-+++..++++|...|.... |+-
T Consensus 111 ~~f~~v~~~A~~vr~~L~~lgL----~~f~KTSG~kGlHV~vPl----~~~~~~~~~r~fa~~iA~~l~~~~-----P~~ 177 (227)
T cd04861 111 VPFEDVVEAALLLRELLDELGL----ESFPKTSGGKGLHVYVPL----APRYTWDEVRAFAKALARELARRL-----PDL 177 (227)
T ss_pred CCHHHHHHHHHHHHHHHHHcCC----ccceEccCCCeEEEEEEc----CCCCCHHHHHHHHHHHHHHHHHHC-----chh
Confidence 447654 45668889998874 343 77777777777765 467999999999999999998653 565
Q ss_pred eEEEEecCCCCCCCCChHHHhhcCCCeEEEEEe
Q 026585 131 TSLEVSSPGVERVVRIPLELERFKDRAMYVKYV 163 (236)
Q Consensus 131 Y~LEVSSPGleRpL~~~~df~rf~G~~V~V~~~ 163 (236)
|+.+ -.+..++-+|.|=|.
T Consensus 178 ~t~~--------------~~k~~R~grvfiDy~ 196 (227)
T cd04861 178 FTAE--------------MAKAKRGGKIFVDYL 196 (227)
T ss_pred hhhH--------------hhHHhCCCCEEEECc
Confidence 5544 456677888888776
No 26
>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=59.78 E-value=21 Score=25.86 Aligned_cols=33 Identities=21% Similarity=0.245 Sum_probs=26.2
Q ss_pred HHHHHHHHHHhhcCCcEEEEEEEEcCCceEEEEEec
Q 026585 59 EALAIAEDVCLSFDGDLKIYAFRTLPNSTIKVRIEK 94 (236)
Q Consensus 59 ~v~~lae~vl~~~g~el~lv~~~~~~~~~lrV~IDk 94 (236)
++++-++|.|+..|.+++++.+.. ..++|.+-.
T Consensus 3 ~~l~~IrP~L~~dGGdv~lv~v~~---~~V~V~l~G 35 (68)
T PF01106_consen 3 EVLEEIRPYLQSDGGDVELVDVDD---GVVYVRLTG 35 (68)
T ss_dssp HHHHHCHHHHHHTTEEEEEEEEET---TEEEEEEES
T ss_pred HHHHHhChHHHhcCCcEEEEEecC---CEEEEEEEe
Confidence 455559999999999999999984 377777654
No 27
>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=57.70 E-value=36 Score=31.02 Aligned_cols=84 Identities=13% Similarity=0.231 Sum_probs=60.9
Q ss_pred CcHHHH--HHHHHHHHHhhcCCcEEEEEEEEcCCceEEEEEeccCCCCCCCChhHHHHHHHHHHHhhhhhhccCCCCCCe
Q 026585 54 TWWDKE--ALAIAEDVCLSFDGDLKIYAFRTLPNSTIKVRIEKMSNKSGSPSMEDIEAFCTTYRARLDEAEIAKSIPENT 131 (236)
Q Consensus 54 ~~w~~~--v~~lae~vl~~~g~el~lv~~~~~~~~~lrV~IDk~~~~~ggvsldDCe~vSr~i~~~LD~~d~~~~i~~~Y 131 (236)
..|.+- +..+++++|+++|+.-+ .|+++..=|+|+|-- ....+-+++..++++|-..|.... |+-|
T Consensus 127 ~~f~~v~~~A~~~r~~L~~lgL~~f---~KTSG~kGlHV~vPl----~~~~~~~~~r~fa~~iA~~l~~~~-----Pd~~ 194 (245)
T TIGR02778 127 VAWKLVVEAAQLIRELLDELGLESF---VKTSGGKGLHVYVPL----RPTLSWDEVKDFAKALAQALAQQM-----PDRF 194 (245)
T ss_pred CCHHHHHHHHHHHHHHHHHcCCccc---eEccCCCeEEEEEEC----CCCCCHHHHHHHHHHHHHHHHHHC-----chhh
Confidence 346554 66678889998884321 377777777777765 457899999999999999997653 5655
Q ss_pred EEEEecCCCCCCCCChHHHhhcCCCeEEEEEe
Q 026585 132 SLEVSSPGVERVVRIPLELERFKDRAMYVKYV 163 (236)
Q Consensus 132 ~LEVSSPGleRpL~~~~df~rf~G~~V~V~~~ 163 (236)
+.+ -.+..++-+|.|=|.
T Consensus 195 t~~--------------~~k~~R~gkvfiDyl 212 (245)
T TIGR02778 195 TAE--------------MSKKNRVGKIFVDYL 212 (245)
T ss_pred hhH--------------hhHHhCCCCEEEECc
Confidence 543 456677788888876
No 28
>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=56.10 E-value=36 Score=30.63 Aligned_cols=83 Identities=11% Similarity=0.249 Sum_probs=60.5
Q ss_pred CcHHHH--HHHHHHHHHhhcCCcEEEEEE-EEcCCceEEEEEeccCCCCCCCChhHHHHHHHHHHHhhhhhhccCCCCCC
Q 026585 54 TWWDKE--ALAIAEDVCLSFDGDLKIYAF-RTLPNSTIKVRIEKMSNKSGSPSMEDIEAFCTTYRARLDEAEIAKSIPEN 130 (236)
Q Consensus 54 ~~w~~~--v~~lae~vl~~~g~el~lv~~-~~~~~~~lrV~IDk~~~~~ggvsldDCe~vSr~i~~~LD~~d~~~~i~~~ 130 (236)
..|.+- +..+++++|+++|+ ..| |+++..=|.|+|-- ....+-+++..++++|...|.... |+-
T Consensus 112 ~~f~~v~~~A~~vr~~L~~lgL----~sf~KTSG~kGlHv~vPl----~~~~~~~~~r~fa~~iA~~l~~~~-----P~~ 178 (228)
T cd04865 112 TSFEDVVEVALLVREVLDELGL----RGYPKTSGARGLHIYVPI----APRYTFEEVRRFAELLAREVERRL-----PDL 178 (228)
T ss_pred CCHHHHHHHHHHHHHHHHHcCC----ccceEccCCCeEEEEEEc----CCCCCHHHHHHHHHHHHHHHHHHC-----chh
Confidence 346554 66678889998884 333 77777677777765 457899999999999999997653 566
Q ss_pred eEEEEecCCCCCCCCChHHHhhcCCCeEEEEEe
Q 026585 131 TSLEVSSPGVERVVRIPLELERFKDRAMYVKYV 163 (236)
Q Consensus 131 Y~LEVSSPGleRpL~~~~df~rf~G~~V~V~~~ 163 (236)
|+++ -.+..++-+|.|=|.
T Consensus 179 ~t~~--------------~~k~~R~grvfiDyl 197 (228)
T cd04865 179 ATTE--------------RWKKERGGRVYLDYL 197 (228)
T ss_pred hhhH--------------hhHHhCCCCEEEECc
Confidence 6554 345677788888776
No 29
>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=56.05 E-value=55 Score=27.17 Aligned_cols=50 Identities=14% Similarity=0.109 Sum_probs=36.8
Q ss_pred HHHHHhhcCCcEEEEEE-EEc--C-CceEEEEEeccCCCCCCCChhHHHHHHHHHHH
Q 026585 64 AEDVCLSFDGDLKIYAF-RTL--P-NSTIKVRIEKMSNKSGSPSMEDIEAFCTTYRA 116 (236)
Q Consensus 64 ae~vl~~~g~el~lv~~-~~~--~-~~~lrV~IDk~~~~~ggvsldDCe~vSr~i~~ 116 (236)
++.++..+|++..+.+. ... + -.+.+|.|+.. ..+++-.....+-|.|..
T Consensus 81 vr~~l~~lg~~~~i~EW~e~~p~g~P~tF~i~~~~~---~~g~~~~~~~~~~~~i~~ 134 (139)
T TIGR01634 81 VRRVVEPFGGIVNITEWWQTGPPGPPGTFELTLTVS---GSGGTEETYLEVERLIAD 134 (139)
T ss_pred HHHHHHHcCCCeEEeehhccCCCCCCeEEEEEEEcc---CCCCCHHHHHHHHHHHHh
Confidence 66678889999998884 555 3 35889988874 457888777777777654
No 30
>cd04479 RPA3 RPA3: A subfamily of OB folds similar to human RPA3 (also called RPA14). RPA3 is the smallest subunit of Replication protein A (RPA). RPA is a nuclear ssDNA binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). RPA3 is believed to have a structural role in assembly of the RPA heterotrimer.
Probab=54.26 E-value=25 Score=27.17 Aligned_cols=45 Identities=18% Similarity=0.056 Sum_probs=31.2
Q ss_pred CCCCChHHHhhcCCCeEEEEEeeccccCCCCCCCCceEEEEEEeCCceEEEE
Q 026585 142 RVVRIPLELERFKDRAMYVKYVGETVTTGSPSESDGVFRLISFDMETECCTW 193 (236)
Q Consensus 142 RpL~~~~df~rf~G~~V~V~~~~~~~~~~~~~eg~k~f~L~~vd~e~~~~~~ 193 (236)
+|.-+.+++.+|+|++|++.-+-. ..++. .+.+.+.|...++|.+
T Consensus 2 ~prVn~~~L~~f~gk~V~ivGkV~------~~~~~-~~~~~~~Dg~~v~v~l 46 (101)
T cd04479 2 TPRINGAMLSQFVGKTVRIVGKVE------KVDGD-SLTLISSDGVNVTVEL 46 (101)
T ss_pred CceeCHHHHHhhCCCEEEEEEEEE------EecCC-eEEEEcCCCCEEEEEe
Confidence 577889999999999999876522 22333 4577777765566544
No 31
>cd04864 LigD_Pol_like_1 LigD_Pol_like_1: Polymerase (Pol) domain of mostly bacterial LigD proteins similar to Pseudomonas aeruginosa (Pae) LigD, subgroup 1. 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=52.66 E-value=37 Score=30.62 Aligned_cols=81 Identities=12% Similarity=0.186 Sum_probs=59.8
Q ss_pred HHH--HHHHHHHHHHhhcCCcEEEEEE-EEcCCceEEEEEeccCCCCCCCChhHHHHHHHHHHHhhhhhhccCCCCCCeE
Q 026585 56 WDK--EALAIAEDVCLSFDGDLKIYAF-RTLPNSTIKVRIEKMSNKSGSPSMEDIEAFCTTYRARLDEAEIAKSIPENTS 132 (236)
Q Consensus 56 w~~--~v~~lae~vl~~~g~el~lv~~-~~~~~~~lrV~IDk~~~~~ggvsldDCe~vSr~i~~~LD~~d~~~~i~~~Y~ 132 (236)
|.+ ++..+++++|+++|+ ..| |+++..=|.|+|-- ....+-+++..++++|...|.... |+-|+
T Consensus 114 f~~v~~~A~~~r~~L~~~gL----~~f~KTSG~kGlHv~vPl----~~~~~~~~~r~fa~~lA~~l~~~~-----P~~~t 180 (228)
T cd04864 114 IEAVRTAALAVRELLDELGL----PSFVKTTGSRGFHVVVPL----DGRGDFDDVRAFAAEAADALAKRD-----PDLLT 180 (228)
T ss_pred HHHHHHHHHHHHHHHHHcCC----ccceEccCCCeEEEEEEc----CCCCCHHHHHHHHHHHHHHHHHHC-----chhhh
Confidence 654 355668889998884 333 77777777777765 457899999999999999998654 56555
Q ss_pred EEEecCCCCCCCCChHHHhhcCCCeEEEEEe
Q 026585 133 LEVSSPGVERVVRIPLELERFKDRAMYVKYV 163 (236)
Q Consensus 133 LEVSSPGleRpL~~~~df~rf~G~~V~V~~~ 163 (236)
. +-.++.++-+|.|=|.
T Consensus 181 ~--------------~~~k~~R~grvfiDyl 197 (228)
T cd04864 181 T--------------EARKAKRGDRVFLDIG 197 (228)
T ss_pred H--------------HhhHHhCCCcEEEECc
Confidence 4 4456677788888877
No 32
>cd04863 MtLigD_Pol_like MtLigD_Pol_like: Polymerase (Pol) domain of bacterial LigD proteins similar to Mycobacterium tuberculosis (Mt)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. MtLigD is monomeric and contains 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 domain, resulting in short stretches of RNA incorporated into the genomic DNA. The MtLigD Pol domain is stimulated by manganese, is error-prone, and prefers adding rNTPs to dNTPs in vitro. The MtLigD Pol domain has been shown to prefer DNA gapped substrates
Probab=52.09 E-value=52 Score=29.68 Aligned_cols=83 Identities=10% Similarity=0.113 Sum_probs=59.0
Q ss_pred CcHHHH--HHHHHHHHHhhcCCcEEEEE-EEEcCCceEEEEEeccCCCCCCCChhHHHHHHHHHHHhhhhhhccCCCCCC
Q 026585 54 TWWDKE--ALAIAEDVCLSFDGDLKIYA-FRTLPNSTIKVRIEKMSNKSGSPSMEDIEAFCTTYRARLDEAEIAKSIPEN 130 (236)
Q Consensus 54 ~~w~~~--v~~lae~vl~~~g~el~lv~-~~~~~~~~lrV~IDk~~~~~ggvsldDCe~vSr~i~~~LD~~d~~~~i~~~ 130 (236)
..|.+. +..+++++|.++|+ .. .|+++..=|.|+|-- ....+-+++-.++++|-..|.... |+-
T Consensus 115 ~~f~~v~~~A~~~r~~L~~lgL----~s~~KTSG~kGlHV~vPl----~~~~~~~~vr~fa~~~A~~l~~~~-----P~~ 181 (231)
T cd04863 115 AGLVECARVALWLRDRLAALGL----ASFPKTSGSKGLHLYVPL----DGPVSSDQTKEFAKALARELEREH-----PDL 181 (231)
T ss_pred CCHHHHHHHHHHHHHHHHHcCC----ccceECCCCCeEEEEEEc----CCCCCHHHHHHHHHHHHHHHHHHC-----chh
Confidence 346544 45567888998884 33 377777777777765 457899999999999999997653 565
Q ss_pred eEEEEecCCCCCCCCChHHHhhcCCCeEEEEEe
Q 026585 131 TSLEVSSPGVERVVRIPLELERFKDRAMYVKYV 163 (236)
Q Consensus 131 Y~LEVSSPGleRpL~~~~df~rf~G~~V~V~~~ 163 (236)
|+. +-.++.++-+|.|=|.
T Consensus 182 ~t~--------------~~~k~~R~grvfiDyl 200 (231)
T cd04863 182 VVS--------------RMTKSLRAGKVFVDWS 200 (231)
T ss_pred hhh--------------HhhHhhCCCcEEEECc
Confidence 543 3345567778888776
No 33
>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=51.63 E-value=54 Score=29.53 Aligned_cols=83 Identities=12% Similarity=0.243 Sum_probs=60.0
Q ss_pred CcHHHH--HHHHHHHHHhhcCCcEEEEEE-EEcCCceEEEEEeccCCCCCCCChhHHHHHHHHHHHhhhhhhccCCCCCC
Q 026585 54 TWWDKE--ALAIAEDVCLSFDGDLKIYAF-RTLPNSTIKVRIEKMSNKSGSPSMEDIEAFCTTYRARLDEAEIAKSIPEN 130 (236)
Q Consensus 54 ~~w~~~--v~~lae~vl~~~g~el~lv~~-~~~~~~~lrV~IDk~~~~~ggvsldDCe~vSr~i~~~LD~~d~~~~i~~~ 130 (236)
..|.+- +..+++++|+++|+ ..| |+++..=|.|+|-- ....+-+++..++++|-..|.... |+-
T Consensus 111 ~~f~~v~~~A~~~r~~L~~lgL----~~~~KTSG~kGlHV~vPl----~~~~~~~~~r~fa~~lA~~l~~~~-----P~~ 177 (227)
T cd04862 111 VPWKAVVEAALLVRELLDELGL----ESFVKTSGGKGLHVVVPL----APRAGWDEVKAFAKALAQHLARTN-----PDR 177 (227)
T ss_pred CCHHHHHHHHHHHHHHHHHcCC----ccceEccCCCeEEEEEEc----CCCCCHHHHHHHHHHHHHHHHHHC-----chh
Confidence 347554 45668889998884 333 77777777777765 457899999999999999998653 565
Q ss_pred eEEEEecCCCCCCCCChHHHhhcCCCeEEEEEe
Q 026585 131 TSLEVSSPGVERVVRIPLELERFKDRAMYVKYV 163 (236)
Q Consensus 131 Y~LEVSSPGleRpL~~~~df~rf~G~~V~V~~~ 163 (236)
|+.+ -.++.++-+|.|=|.
T Consensus 178 ~t~~--------------~~k~~R~gkvfiDyl 196 (227)
T cd04862 178 FVAT--------------MGKAKRVGKIFIDYL 196 (227)
T ss_pred hhHH--------------hhHHhCCCcEEEECc
Confidence 5543 445677778888777
No 34
>cd04866 LigD_Pol_like_3 LigD_Pol_like_3: Polymerase (Pol) domain of bacterial LigD proteins similar to Pseudomonas aeruginosa (Pae) LigD, subgroup 3. 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 repair 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=50.46 E-value=37 Score=30.51 Aligned_cols=83 Identities=18% Similarity=0.265 Sum_probs=59.7
Q ss_pred CcHHHH--HHHHHHHHHhhcCCcEEEEEE-EEcCCceEEEEEeccCCCC-CCCChhHHHHHHHHHHHhhhhhhccCCCCC
Q 026585 54 TWWDKE--ALAIAEDVCLSFDGDLKIYAF-RTLPNSTIKVRIEKMSNKS-GSPSMEDIEAFCTTYRARLDEAEIAKSIPE 129 (236)
Q Consensus 54 ~~w~~~--v~~lae~vl~~~g~el~lv~~-~~~~~~~lrV~IDk~~~~~-ggvsldDCe~vSr~i~~~LD~~d~~~~i~~ 129 (236)
..|.+- +..+++++|+++|+ ..| |+++..=|.|+|-- . ...+-+++..++++|...|.... |+
T Consensus 106 ~~f~~v~~~A~~vr~~L~~lgL----~~f~KTSG~kGlHV~vPl----~~~~~~~~~~r~fa~~iA~~l~~~~-----P~ 172 (223)
T cd04866 106 DHFSLAVEAANLLKEILDALGL----TSFVKTSGNKGLQVYIPL----PDNKFTYDETRLFTEFIAEYLCQQF-----PE 172 (223)
T ss_pred CCHHHHHHHHHHHHHHHHHcCC----ccceEccCCCeEEEEEEc----CCCCCCHHHHHHHHHHHHHHHHHHC-----ch
Confidence 346554 56678889998884 333 77776667777654 3 56899999999999999998653 56
Q ss_pred CeEEEEecCCCCCCCCChHHHhhcCCCeEEEEEe
Q 026585 130 NTSLEVSSPGVERVVRIPLELERFKDRAMYVKYV 163 (236)
Q Consensus 130 ~Y~LEVSSPGleRpL~~~~df~rf~G~~V~V~~~ 163 (236)
-|+++ -.+..++.+|.|=|.
T Consensus 173 ~~t~~--------------~~k~~R~gkVfiDyl 192 (223)
T cd04866 173 LFTTE--------------RLKKNRHNRLYLDYV 192 (223)
T ss_pred hhhHH--------------hhHHhCCCCEEEECc
Confidence 55544 345667778888776
No 35
>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=46.68 E-value=3.3 Score=30.23 Aligned_cols=20 Identities=30% Similarity=0.240 Sum_probs=16.9
Q ss_pred CCCCeEE--EEecCCCCCCCCC
Q 026585 127 IPENTSL--EVSSPGVERVVRI 146 (236)
Q Consensus 127 i~~~Y~L--EVSSPGleRpL~~ 146 (236)
-|.+|.| -..++|.+|+|..
T Consensus 45 ~~~~y~L~~~~~~~~~er~L~~ 66 (93)
T PF00788_consen 45 DPSDYCLVEVEESGGEERPLDD 66 (93)
T ss_dssp SGGGEEEEEEECTTTEEEEETT
T ss_pred CCCCEEEEEEEcCCCEEEEcCC
Confidence 3688999 8999999998864
No 36
>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=40.56 E-value=52 Score=24.55 Aligned_cols=31 Identities=26% Similarity=0.409 Sum_probs=24.3
Q ss_pred hHHHhhcCCCeEEEEEeeccccCCCCCCCCceE-EEEEEeCC
Q 026585 147 PLELERFKDRAMYVKYVGETVTTGSPSESDGVF-RLISFDME 187 (236)
Q Consensus 147 ~~df~rf~G~~V~V~~~~~~~~~~~~~eg~k~f-~L~~vd~e 187 (236)
+-++.++++++|.|+++ +|+... +|.++|.-
T Consensus 4 ~~~L~~~i~k~V~V~l~----------~gr~~~G~L~~~D~~ 35 (81)
T cd01729 4 ILDLSKYVDKKIRVKFQ----------GGREVTGILKGYDQL 35 (81)
T ss_pred hhhHHHhcCCeEEEEEC----------CCcEEEEEEEEEcCc
Confidence 45789999999999998 443333 99999875
No 37
>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=40.46 E-value=51 Score=23.45 Aligned_cols=34 Identities=18% Similarity=-0.002 Sum_probs=24.1
Q ss_pred HHhhcCCCeEEEEEeeccccCCCCCCCCceE-EEEEEeCCceEEEE
Q 026585 149 ELERFKDRAMYVKYVGETVTTGSPSESDGVF-RLISFDMETECCTW 193 (236)
Q Consensus 149 df~rf~G~~V~V~~~~~~~~~~~~~eg~k~f-~L~~vd~e~~~~~~ 193 (236)
-++.++|++|.|+++ +|+... +|.++|.- -.+.+
T Consensus 4 ~L~~~~~~~V~V~Lk----------~g~~~~G~L~~~D~~-mNlvL 38 (67)
T cd01726 4 FLKAIIGRPVVVKLN----------SGVDYRGILACLDGY-MNIAL 38 (67)
T ss_pred HHHhhCCCeEEEEEC----------CCCEEEEEEEEEccc-eeeEE
Confidence 357889999999999 343333 99999853 44443
No 38
>PF14438 SM-ATX: Ataxin 2 SM domain; PDB: 1M5Q_1.
Probab=39.15 E-value=44 Score=24.21 Aligned_cols=37 Identities=14% Similarity=-0.050 Sum_probs=22.7
Q ss_pred HhhcCCCeEEEEEeeccccCCCCCCCCceE-EEEEEeCC--ceEEEEeec
Q 026585 150 LERFKDRAMYVKYVGETVTTGSPSESDGVF-RLISFDME--TECCTWGLA 196 (236)
Q Consensus 150 f~rf~G~~V~V~~~~~~~~~~~~~eg~k~f-~L~~vd~e--~~~~~~~la 196 (236)
+..++|++|.|+++ +|...- .|.+++.+ ...+.++.+
T Consensus 7 ~~~lvG~~V~V~~~----------~G~~yeGif~s~s~~~~~~~vvLk~a 46 (77)
T PF14438_consen 7 LTNLVGQTVEVTTK----------NGSVYEGIFHSASPESNEFDVVLKMA 46 (77)
T ss_dssp HHTTTTSEEEEEET----------TS-EEEEEEEEE-T---T--EEEEEE
T ss_pred HHhCcCCEEEEEEC----------CCCEEEEEEEeCCCcccceeEEEEee
Confidence 45789999999998 444422 78888775 455555554
No 39
>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=37.45 E-value=58 Score=23.73 Aligned_cols=31 Identities=29% Similarity=0.383 Sum_probs=24.0
Q ss_pred hHHHhhcCCCeEEEEEeeccccCCCCCCCCceE-EEEEEeCC
Q 026585 147 PLELERFKDRAMYVKYVGETVTTGSPSESDGVF-RLISFDME 187 (236)
Q Consensus 147 ~~df~rf~G~~V~V~~~~~~~~~~~~~eg~k~f-~L~~vd~e 187 (236)
+.++..|++++|.|+++ +|+... +|.++|.-
T Consensus 2 ~~~L~~~i~k~V~V~L~----------~g~~~~G~L~~~D~~ 33 (72)
T cd01719 2 PPELKKYMDKKLSLKLN----------GNRKVSGILRGFDPF 33 (72)
T ss_pred chhhHHhCCCeEEEEEC----------CCeEEEEEEEEEccc
Confidence 34688999999999998 444434 99999854
No 40
>PRK05972 ligD ATP-dependent DNA ligase; Reviewed
Probab=36.94 E-value=1.1e+02 Score=32.57 Aligned_cols=84 Identities=12% Similarity=0.196 Sum_probs=60.4
Q ss_pred CcHHHH--HHHHHHHHHhhcCCcEEEEEE-EEcCCceEEEEEeccCCCCCCCChhHHHHHHHHHHHhhhhhhccCCCCCC
Q 026585 54 TWWDKE--ALAIAEDVCLSFDGDLKIYAF-RTLPNSTIKVRIEKMSNKSGSPSMEDIEAFCTTYRARLDEAEIAKSIPEN 130 (236)
Q Consensus 54 ~~w~~~--v~~lae~vl~~~g~el~lv~~-~~~~~~~lrV~IDk~~~~~ggvsldDCe~vSr~i~~~LD~~d~~~~i~~~ 130 (236)
..|.+. +..+++++|.++|+ ..| |+++..=|+|+|-- ....+-+++-.|+++|...|.... |+-
T Consensus 697 ~~f~~v~~aA~~~r~~L~~lgL----~sf~KTSG~kGlHv~vPl----~~~~~~~~~~~fa~~ia~~l~~~~-----P~~ 763 (860)
T PRK05972 697 VPWKAVVEAARLMRTRLDELGL----ESFLKTSGGKGLHVVVPL----ARRLDWDEVKAFAQAVCQHMARDL-----PER 763 (860)
T ss_pred CCHHHHHHHHHHHHHHHHHcCC----ceeeECCCCCeEEEEEEc----CCCCCHHHHHHHHHHHHHHHHHHC-----chh
Confidence 457654 55567888998874 343 77777677777765 457899999999999999997653 677
Q ss_pred eEEEEecCCCCCCCCChHHHhhcCCCeEEEEEee
Q 026585 131 TSLEVSSPGVERVVRIPLELERFKDRAMYVKYVG 164 (236)
Q Consensus 131 Y~LEVSSPGleRpL~~~~df~rf~G~~V~V~~~~ 164 (236)
|+.+. .++.++-+|.|=|.+
T Consensus 764 ~t~~~--------------~k~~R~grifiDylq 783 (860)
T PRK05972 764 FLAKM--------------GKKNRVGKIFLDYLR 783 (860)
T ss_pred ehhhh--------------hHhhCCCcEEEEccc
Confidence 76653 356667788887763
No 41
>PF14472 DUF4429: Domain of unknown function (DUF4429)
Probab=36.55 E-value=40 Score=25.73 Aligned_cols=39 Identities=28% Similarity=0.370 Sum_probs=25.0
Q ss_pred EEeCCceEEEEeecceehhhcccCCCCCccccccceeeeeccccccceEEE
Q 026585 183 SFDMETECCTWGLADVRINREKAGKGRPLSKKQREWRLNTTFDSLRLVRLH 233 (236)
Q Consensus 183 ~vd~e~~~~~~~la~vk~nr~~~~KGr~~~kk~~~~~l~ipf~~I~karL~ 233 (236)
++|.+.+.+.|+- .+..+-+..+| ..+||+++|.-|.+.
T Consensus 2 sfDg~~V~i~~~g--~~a~~~~~~~G----------~~~ipl~~i~gV~~~ 40 (94)
T PF14472_consen 2 SFDGDTVRIRWGG--WRAPRAKRALG----------EKTIPLSAISGVEWK 40 (94)
T ss_pred EEcCCEEEEEECC--ccchhhhccCC----------CEEEEHHHcceEEEE
Confidence 6788888888872 22212111222 248999999988876
No 42
>PF12701 LSM14: Scd6-like Sm domain; PDB: 2RM4_A 2FB7_A 2VC8_A 2VXF_A 2VXE_A.
Probab=36.34 E-value=2e+02 Score=22.38 Aligned_cols=65 Identities=18% Similarity=0.187 Sum_probs=41.4
Q ss_pred hcCCCeEEEEEeeccccCCCCCCCCceE--EEEEEeCCceEEEEeecceehhhcccCCCCCc------cccccceeeeec
Q 026585 152 RFKDRAMYVKYVGETVTTGSPSESDGVF--RLISFDMETECCTWGLADVRINREKAGKGRPL------SKKQREWRLNTT 223 (236)
Q Consensus 152 rf~G~~V~V~~~~~~~~~~~~~eg~k~f--~L~~vd~e~~~~~~~la~vk~nr~~~~KGr~~------~kk~~~~~l~ip 223 (236)
.|+|..|.+..+ . ..+| .|..++.+.-++++. +|+-+= ..||+. +++..+ -+.+.
T Consensus 5 ~~IGs~ISlisk----------~-~iRYeG~L~~Id~~~sTItL~--nVr~~G---tE~R~~~~~ipp~~~v~~-~I~Fr 67 (96)
T PF12701_consen 5 PYIGSKISLISK----------S-DIRYEGILYSIDTEDSTITLK--NVRSFG---TEGRPTDREIPPSDEVYD-YIVFR 67 (96)
T ss_dssp CCTTCEEEEEET----------T-TEEEEEEEEEEETTTTEEEEE--EEEETT---ETTSS-SS---C-CSSSS-EEEEE
T ss_pred cccCCEEEEEEC----------C-CcEEEEEEEEEcCCCCEEEee--eeeecC---cCCCCcCcccCCCCceee-EEEEE
Confidence 689999999877 2 2444 999999877776653 555442 244422 122222 36788
Q ss_pred cccccceEEE
Q 026585 224 FDSLRLVRLH 233 (236)
Q Consensus 224 f~~I~karL~ 233 (236)
-.+|+..++.
T Consensus 68 ~sDIkdL~v~ 77 (96)
T PF12701_consen 68 GSDIKDLKVI 77 (96)
T ss_dssp TTTEEEEEEC
T ss_pred ccccceEEEE
Confidence 8888888764
No 43
>PRK00737 small nuclear ribonucleoprotein; Provisional
Probab=35.64 E-value=68 Score=23.23 Aligned_cols=30 Identities=13% Similarity=0.160 Sum_probs=22.9
Q ss_pred HHHhhcCCCeEEEEEeeccccCCCCCCCCceE-EEEEEeCC
Q 026585 148 LELERFKDRAMYVKYVGETVTTGSPSESDGVF-RLISFDME 187 (236)
Q Consensus 148 ~df~rf~G~~V~V~~~~~~~~~~~~~eg~k~f-~L~~vd~e 187 (236)
.-+.+++|++|.|.++ +|+... +|.++|.-
T Consensus 7 ~~L~~~~~k~V~V~lk----------~g~~~~G~L~~~D~~ 37 (72)
T PRK00737 7 DVLNNALNSPVLVRLK----------GGREFRGELQGYDIH 37 (72)
T ss_pred HHHHHhCCCEEEEEEC----------CCCEEEEEEEEEccc
Confidence 4567889999999998 343333 99999874
No 44
>COG1958 LSM1 Small nuclear ribonucleoprotein (snRNP) homolog [Transcription]
Probab=35.47 E-value=62 Score=23.71 Aligned_cols=30 Identities=20% Similarity=0.266 Sum_probs=23.1
Q ss_pred HHHhhcCCCeEEEEEeeccccCCCCCCCCceE-EEEEEeCC
Q 026585 148 LELERFKDRAMYVKYVGETVTTGSPSESDGVF-RLISFDME 187 (236)
Q Consensus 148 ~df~rf~G~~V~V~~~~~~~~~~~~~eg~k~f-~L~~vd~e 187 (236)
.-+.++++++|.|+++ +|+... +|.++|.-
T Consensus 10 ~~l~~~~~~~V~V~lk----------~g~~~~G~L~~~D~~ 40 (79)
T COG1958 10 SFLKKLLNKRVLVKLK----------NGREYRGTLVGFDQY 40 (79)
T ss_pred HHHHHhhCCEEEEEEC----------CCCEEEEEEEEEccc
Confidence 3467788899999999 454444 99999875
No 45
>TIGR02776 NHEJ_ligase_prk DNA ligase D. Members of this protein family are DNA ligases involved in the repair of DNA double-stranded breaks by non-homologous end joining (NHEJ). The system of the bacterial Ku protein (TIGR02772) plus this DNA ligase is seen in about 20 % of bacterial genomes to date and at least one archaeon (Archeoglobus fulgidus). This model describes a central and a C-terminal domain. These two domains may be permuted, as in genus Mycobacterium, or divided into tandem ORFs, and therefore not be identified by this model. An additional N-terminal 3'-phosphoesterase (PE) domain present in some but not all examples of this ligase is not included in the seed alignment for this model; This alignment models only the central ATP-dependent ligase domain and the C-terminal polymerase domain. Most examples of genes for this ligase are adjacent to the gene for Ku.
Probab=35.47 E-value=1.3e+02 Score=30.42 Aligned_cols=83 Identities=12% Similarity=0.208 Sum_probs=60.0
Q ss_pred cHHHH--HHHHHHHHHhhcCCcEEEEEE-EEcCCceEEEEEeccCCCCC-CCChhHHHHHHHHHHHhhhhhhccCCCCCC
Q 026585 55 WWDKE--ALAIAEDVCLSFDGDLKIYAF-RTLPNSTIKVRIEKMSNKSG-SPSMEDIEAFCTTYRARLDEAEIAKSIPEN 130 (236)
Q Consensus 55 ~w~~~--v~~lae~vl~~~g~el~lv~~-~~~~~~~lrV~IDk~~~~~g-gvsldDCe~vSr~i~~~LD~~d~~~~i~~~ 130 (236)
.|.+. +..+++++|.++|+ ..| |++++.=|+|+|-- .. ..+-+++-.+++.|...|... .|+-
T Consensus 405 ~f~~v~~~A~~~r~~L~~~gl----~~~~KtSG~kGlhv~vPl----~~~~~~~~~~~~fa~~~a~~~~~~-----~P~~ 471 (552)
T TIGR02776 405 AFKLAVEAAQLMKQLLDELGL----VSFVKTSGGKGLHVVVPL----RPNTFTWDETKLFAKAIAEYLARQ-----FPER 471 (552)
T ss_pred CHHHHHHHHHHHHHHHHHcCC----ccceEccCCCeEEEEEEc----CCCCCCHHHHHHHHHHHHHHHHHH-----Ccce
Confidence 46554 55668889998874 333 77776667777654 33 689999999999999999765 3677
Q ss_pred eEEEEecCCCCCCCCChHHHhhcCCCeEEEEEee
Q 026585 131 TSLEVSSPGVERVVRIPLELERFKDRAMYVKYVG 164 (236)
Q Consensus 131 Y~LEVSSPGleRpL~~~~df~rf~G~~V~V~~~~ 164 (236)
|+++- .+..++-+|.|=|.+
T Consensus 472 ~t~~~--------------~k~~R~grv~iDy~q 491 (552)
T TIGR02776 472 FTTEM--------------GKKNRVGRIFIDYLR 491 (552)
T ss_pred ehhhh--------------hHhhCCCCEEEEccc
Confidence 76653 456677788888773
No 46
>PF13222 DUF4030: Protein of unknown function (DUF4030)
Probab=34.24 E-value=2.7e+02 Score=23.43 Aligned_cols=87 Identities=15% Similarity=0.092 Sum_probs=54.1
Q ss_pred CCcHHHHHHHHHHHHHhhcCCcEEEEE-EEEcCCceEEEEEeccCCCCCCCChhHHHHHHHHHHHhhhhhhccCCCC-CC
Q 026585 53 GTWWDKEALAIAEDVCLSFDGDLKIYA-FRTLPNSTIKVRIEKMSNKSGSPSMEDIEAFCTTYRARLDEAEIAKSIP-EN 130 (236)
Q Consensus 53 ~~~w~~~v~~lae~vl~~~g~el~lv~-~~~~~~~~lrV~IDk~~~~~ggvsldDCe~vSr~i~~~LD~~d~~~~i~-~~ 130 (236)
..-|..-+-.|...+....|+..+-+. +...++..+.|.|..+-+.+..=.=+=-+++-..+...|-.......|. +.
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~~Ds 130 (142)
T PF13222_consen 51 ENRWNYVFSSIFDELFGKNGYKGFGIQQINVKSSQPVTVTIKTKINSSDPGAKEFGKKIEKEINEVLKTEEVKKWIENDS 130 (142)
T ss_pred hhhHHHHHHHHHHHHhhccCccccceeEeeecCCCcEEEEEeccccccccchHHHHHHHHHHHHHHHccHHHHHHHhCCc
Confidence 446988888999999998898777666 5666677888888752111121222333445555555554433333443 56
Q ss_pred eEEEEecCC
Q 026585 131 TSLEVSSPG 139 (236)
Q Consensus 131 Y~LEVSSPG 139 (236)
|++++-|-+
T Consensus 131 YtI~iy~~d 139 (142)
T PF13222_consen 131 YTIEIYSQD 139 (142)
T ss_pred eEEEEeccc
Confidence 999988754
No 47
>COG3285 Predicted eukaryotic-type DNA primase [DNA replication, recombination, and repair]
Probab=34.20 E-value=85 Score=29.46 Aligned_cols=85 Identities=14% Similarity=0.253 Sum_probs=56.6
Q ss_pred CCcHHHHHHHH--HHHHHhhcCCcEEEEEE-EEcCCceEEEEEeccCCCCCCCChhHHHHHHHHHHHhhhhhhccCCCCC
Q 026585 53 GTWWDKEALAI--AEDVCLSFDGDLKIYAF-RTLPNSTIKVRIEKMSNKSGSPSMEDIEAFCTTYRARLDEAEIAKSIPE 129 (236)
Q Consensus 53 ~~~w~~~v~~l--ae~vl~~~g~el~lv~~-~~~~~~~lrV~IDk~~~~~ggvsldDCe~vSr~i~~~LD~~d~~~~i~~ 129 (236)
|+.|...++.. ++..|+++| ++.| |++++.=|.|++-- .-..+-++.-.+++++...|.... |+
T Consensus 137 gv~~~~vveaA~~lr~~Ld~lG----L~~f~KTSGGKG~Hv~~PL----~~~~~w~e~k~fa~~va~~la~~~-----Pd 203 (299)
T COG3285 137 GVAFAEVVEAALELRDLLDELG----LVSFPKTSGGKGLHVYVPL----APKATWEEVKQFAKAVAQQLARAA-----PD 203 (299)
T ss_pred CCCHHHHHHHHHHHHHHHHHcC----CccceeccCCCeeEEEEec----CCcCCcHHHHHHHHHHHHHHHHhC-----hH
Confidence 45695443322 344556555 5666 66776667776654 347999999999999999998654 56
Q ss_pred CeEEEEecCCCCCCCCChHHHhhcCCCeEEEEEee
Q 026585 130 NTSLEVSSPGVERVVRIPLELERFKDRAMYVKYVG 164 (236)
Q Consensus 130 ~Y~LEVSSPGleRpL~~~~df~rf~G~~V~V~~~~ 164 (236)
.|+- .-.++.++.++.|-|..
T Consensus 204 ~~tt--------------~~~K~~R~grIFlDylr 224 (299)
T COG3285 204 LFTT--------------TMGKENRGGRIFLDYLR 224 (299)
T ss_pred HHHH--------------HhhHhhcCCcEEEEecc
Confidence 6642 33456677777777763
No 48
>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=33.67 E-value=76 Score=22.54 Aligned_cols=29 Identities=28% Similarity=0.315 Sum_probs=22.3
Q ss_pred HHhhcCCCeEEEEEeeccccCCCCCCCCceE-EEEEEeCC
Q 026585 149 ELERFKDRAMYVKYVGETVTTGSPSESDGVF-RLISFDME 187 (236)
Q Consensus 149 df~rf~G~~V~V~~~~~~~~~~~~~eg~k~f-~L~~vd~e 187 (236)
-++.++|++|.|+++ +|+... +|.++|.-
T Consensus 4 ~L~~~~~~~V~V~l~----------~g~~~~G~L~~~D~~ 33 (68)
T cd01731 4 VLKDSLNKPVLVKLK----------GGKEVRGRLKSYDQH 33 (68)
T ss_pred HHHHhcCCEEEEEEC----------CCCEEEEEEEEECCc
Confidence 467789999999998 344433 99999874
No 49
>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=33.54 E-value=77 Score=22.63 Aligned_cols=34 Identities=18% Similarity=0.036 Sum_probs=24.0
Q ss_pred HHhhcCCCeEEEEEeeccccCCCCCCCCceE-EEEEEeCCceEEEE
Q 026585 149 ELERFKDRAMYVKYVGETVTTGSPSESDGVF-RLISFDMETECCTW 193 (236)
Q Consensus 149 df~rf~G~~V~V~~~~~~~~~~~~~eg~k~f-~L~~vd~e~~~~~~ 193 (236)
.+..++|++|.|.++ +|+... +|.++|.- -.+.+
T Consensus 5 ~L~~~~g~~V~V~Lk----------~g~~~~G~L~~~D~~-mNi~L 39 (68)
T cd01722 5 FLNDLTGKPVIVKLK----------WGMEYKGTLVSVDSY-MNLQL 39 (68)
T ss_pred HHHHcCCCEEEEEEC----------CCcEEEEEEEEECCC-EEEEE
Confidence 457889999999999 343333 99999864 34433
No 50
>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=32.35 E-value=75 Score=22.04 Aligned_cols=40 Identities=23% Similarity=0.221 Sum_probs=26.9
Q ss_pred HHhhcCCCeEEEEEeeccccCCCCCCCCceE-EEEEEeCCceEEEEeecceehh
Q 026585 149 ELERFKDRAMYVKYVGETVTTGSPSESDGVF-RLISFDMETECCTWGLADVRIN 201 (236)
Q Consensus 149 df~rf~G~~V~V~~~~~~~~~~~~~eg~k~f-~L~~vd~e~~~~~~~la~vk~n 201 (236)
.++.++|++|+|.++ +|+..- .|.++|.. ..+. +.++...
T Consensus 2 ~L~~~~g~~V~V~l~----------~g~~~~G~L~~~D~~-~Nl~--L~~~~~~ 42 (67)
T PF01423_consen 2 FLQKLIGKRVRVELK----------NGRTYRGTLVSFDQF-MNLV--LSDVTET 42 (67)
T ss_dssp HHHHTTTSEEEEEET----------TSEEEEEEEEEEETT-EEEE--EEEEEEE
T ss_pred hhHHhCCcEEEEEEe----------CCEEEEEEEEEeech-heEE--eeeEEEE
Confidence 467899999999998 343333 99999975 3333 3344443
No 51
>TIGR02174 CXXU_selWTH selT/selW/selH selenoprotein domain. This model represents a domain found in both bacteria and animals, including animal proteins SelT, SelW, and SelH, all of which are selenoproteins. In a CXXC motif near the N-terminus of the domain, selenocysteine may replace the second Cys. Proteins with this domain may include an insert of about 70 amino acids. This model is broader than the current SelW model pfam05169 in Pfam.
Probab=31.32 E-value=1.6e+02 Score=21.23 Aligned_cols=39 Identities=8% Similarity=-0.008 Sum_probs=26.4
Q ss_pred cHHHHHHHHHHHHHhhcCCcEEEEEEEEcCCceEEEEEe
Q 026585 55 WWDKEALAIAEDVCLSFDGDLKIYAFRTLPNSTIKVRIE 93 (236)
Q Consensus 55 ~w~~~v~~lae~vl~~~g~el~lv~~~~~~~~~lrV~ID 93 (236)
-|..++..+++.+++.|......+......++...|+++
T Consensus 10 ~y~~Ra~~l~q~L~~~Fp~~~v~~~~~~~~~G~Fev~~~ 48 (72)
T TIGR02174 10 GYKPRAAWLKQELLEEFPDLEIEGENTPPTTGAFEVTVN 48 (72)
T ss_pred CChHHHHHHHHHHHHHCCCCeeEEeeecCCCcEEEEEEC
Confidence 499999999999999996532222222223678888765
No 52
>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=31.27 E-value=81 Score=23.15 Aligned_cols=31 Identities=10% Similarity=0.247 Sum_probs=24.4
Q ss_pred HHHhhcCCCeEEEEEeeccccCCCCCCCCceE-EEEEEeCCc
Q 026585 148 LELERFKDRAMYVKYVGETVTTGSPSESDGVF-RLISFDMET 188 (236)
Q Consensus 148 ~df~rf~G~~V~V~~~~~~~~~~~~~eg~k~f-~L~~vd~e~ 188 (236)
..+..++|++|.|+++ +|+... .|.++|...
T Consensus 3 ~~l~~~l~~~V~V~l~----------dgR~~~G~L~~~D~~~ 34 (79)
T cd01717 3 SKMLQLINYRLRVTLQ----------DGRQFVGQFLAFDKHM 34 (79)
T ss_pred chhHHHcCCEEEEEEC----------CCcEEEEEEEEEcCcc
Confidence 4577899999999998 455544 999998763
No 53
>COG3526 Uncharacterized protein conserved in bacteria [Posttranslational modification, protein turnover, chaperones]
Probab=29.91 E-value=1.1e+02 Score=23.92 Aligned_cols=61 Identities=16% Similarity=0.279 Sum_probs=44.6
Q ss_pred cHHHHHHHHHHHHHhhcCCcEEEEEEEEcCCceEEEEEe------ccCCCCCCCChhHHHHHHHHHHHhhh
Q 026585 55 WWDKEALAIAEDVCLSFDGDLKIYAFRTLPNSTIKVRIE------KMSNKSGSPSMEDIEAFCTTYRARLD 119 (236)
Q Consensus 55 ~w~~~v~~lae~vl~~~g~el~lv~~~~~~~~~lrV~ID------k~~~~~ggvsldDCe~vSr~i~~~LD 119 (236)
.|-=|+.=+|++.|..|+.+|..|.+..+..+..+|++| ++ ++|| .-+...+-+.+++.+|
T Consensus 17 nWlLRa~WmaQElL~TF~~dlgeV~L~PgTGG~FeI~~dg~~iWeRK--rdGG--FP~ak~LKQrvRD~id 83 (99)
T COG3526 17 NWLLRAAWMAQELLSTFADDLGEVALIPGTGGVFEITCDGVLIWERK--RDGG--FPEAKVLKQRVRDLID 83 (99)
T ss_pred hHHHHHHHHHHHHHHHHHhhhheEEEecCCCceEEEEECCEEEEEee--ccCC--CCchHHHHHHHHhhcC
Confidence 577788889999999999999999988776777777655 21 2455 3345566677777776
No 54
>PRK09633 ligD ATP-dependent DNA ligase; Reviewed
Probab=29.19 E-value=1.9e+02 Score=29.63 Aligned_cols=85 Identities=19% Similarity=0.158 Sum_probs=59.4
Q ss_pred CcHHHH--HHHHHHHHHhhcCCcEEEEEEEEcCCceEEEEEeccCCCCC-CCChhHHHHHHHHHHHhhhhhhccCCCCCC
Q 026585 54 TWWDKE--ALAIAEDVCLSFDGDLKIYAFRTLPNSTIKVRIEKMSNKSG-SPSMEDIEAFCTTYRARLDEAEIAKSIPEN 130 (236)
Q Consensus 54 ~~w~~~--v~~lae~vl~~~g~el~lv~~~~~~~~~lrV~IDk~~~~~g-gvsldDCe~vSr~i~~~LD~~d~~~~i~~~ 130 (236)
..|.+- +..+++++|.++|+.- ..|++++.=|+|+|-- .. ..+-+++-.++++|...|.... |+-
T Consensus 445 ~~~~~v~~~A~~~r~~L~~~gl~~---~~ktSG~kGlhv~vPl----~~~~~~~~~~~~fa~~~a~~~~~~~-----P~~ 512 (610)
T PRK09633 445 DEFPLAVEAALELKRLFDQFGLTS---FVKTSGNKGLQLYIPL----SKNAFTYEETRLFTEFIAEYLCSQF-----PEL 512 (610)
T ss_pred CCHHHHHHHHHHHHHHHHHcCCcc---ceEccCCCeEEEEEEc----CCCCCCHHHHHHHHHHHHHHHHHHC-----cce
Confidence 346543 5566888999888422 1377777777777754 34 4899999999999999997654 676
Q ss_pred eEEEEecCCCCCCCCChHHHhhcCCCeEEEEEee
Q 026585 131 TSLEVSSPGVERVVRIPLELERFKDRAMYVKYVG 164 (236)
Q Consensus 131 Y~LEVSSPGleRpL~~~~df~rf~G~~V~V~~~~ 164 (236)
|+.+- .+..++-.|.|=|.+
T Consensus 513 ~t~~~--------------~k~~R~grvfiDy~q 532 (610)
T PRK09633 513 FTTER--------------LKKNRGNRLYLDYVQ 532 (610)
T ss_pred ehhhh--------------hHhhCCCCEEEEccc
Confidence 66553 355667778887763
No 55
>PRK09632 ATP-dependent DNA ligase; Reviewed
Probab=28.90 E-value=1.7e+02 Score=30.98 Aligned_cols=69 Identities=13% Similarity=0.095 Sum_probs=49.8
Q ss_pred CcHHHH--HHHHHHHHHhhcCCcEEEEEE-EEcCCceEEEEEeccCCCCCCCChhHHHHHHHHHHHhhhhhhccCCCCCC
Q 026585 54 TWWDKE--ALAIAEDVCLSFDGDLKIYAF-RTLPNSTIKVRIEKMSNKSGSPSMEDIEAFCTTYRARLDEAEIAKSIPEN 130 (236)
Q Consensus 54 ~~w~~~--v~~lae~vl~~~g~el~lv~~-~~~~~~~lrV~IDk~~~~~ggvsldDCe~vSr~i~~~LD~~d~~~~i~~~ 130 (236)
..|.+- +..+++++|+++|+ ..| |+++..=|.|+|-- ....+-+++..++++|...|.... |+-
T Consensus 148 ~~f~~v~~~A~~~r~~L~~lgL----~~~~KTSG~kGlHv~vPl----~~~~~~~~~~~fa~~~A~~l~~~~-----P~~ 214 (764)
T PRK09632 148 VGLAECAEVARAVRDLLADIGL----ETFPVTSGSKGIHLYAPL----DGPVSSEGASVVAKEVARALEQDH-----PDL 214 (764)
T ss_pred CCHHHHHHHHHHHHHHHHHcCC----ceeeECCCCCeEEEEEEC----CCCCCHHHHHHHHHHHHHHHHHHC-----cce
Confidence 346544 55668889998884 333 67776677777765 467899999999999999997653 566
Q ss_pred eEEEE
Q 026585 131 TSLEV 135 (236)
Q Consensus 131 Y~LEV 135 (236)
|+.+.
T Consensus 215 ~t~~~ 219 (764)
T PRK09632 215 VTSTM 219 (764)
T ss_pred ehhhh
Confidence 66554
No 56
>smart00651 Sm snRNP Sm proteins. small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA splicing
Probab=28.20 E-value=1e+02 Score=21.24 Aligned_cols=29 Identities=17% Similarity=0.179 Sum_probs=22.3
Q ss_pred HHhhcCCCeEEEEEeeccccCCCCCCCCceE-EEEEEeCC
Q 026585 149 ELERFKDRAMYVKYVGETVTTGSPSESDGVF-RLISFDME 187 (236)
Q Consensus 149 df~rf~G~~V~V~~~~~~~~~~~~~eg~k~f-~L~~vd~e 187 (236)
.+..++|+.|.|.++ +|+... .|.++|..
T Consensus 2 ~L~~~~~~~V~V~l~----------~g~~~~G~L~~~D~~ 31 (67)
T smart00651 2 FLKKLIGKRVLVELK----------NGREYRGTLKGFDQF 31 (67)
T ss_pred hhHHhCCcEEEEEEC----------CCcEEEEEEEEECcc
Confidence 367889999999998 444333 99999875
No 57
>PRK11190 Fe/S biogenesis protein NfuA; Provisional
Probab=28.18 E-value=1.3e+02 Score=26.25 Aligned_cols=50 Identities=6% Similarity=0.087 Sum_probs=35.9
Q ss_pred CCCCCceeccCC--c---------HHHHHHHHHH----HHHhhcCCcEEEEEEEEcCCceEEEEEec
Q 026585 43 GGAGGGISLAGT--W---------WDKEALAIAE----DVCLSFDGDLKIYAFRTLPNSTIKVRIEK 94 (236)
Q Consensus 43 ~~~gg~i~l~~~--~---------w~~~v~~lae----~vl~~~g~el~lv~~~~~~~~~lrV~IDk 94 (236)
.+-|+|..+.++ . =-++|.++++ |.|++.|++++++.+.. +++|+|++-.
T Consensus 83 ~~~g~gF~f~NPNa~~~~~~~~~~~~~~i~~~l~~~irP~l~~dGGdielv~v~~--~~~v~v~l~G 147 (192)
T PRK11190 83 DQLGSQLTLKAPNAKMRKVADDAPLMERVEYVLQSQINPQLAGHGGRVSLMEITE--DGYAILQFGG 147 (192)
T ss_pred cCCCCceEEECCCCCCCCCcccHHHHHHHHHHHHhccChhHHhcCCcEEEEEEcC--CCEEEEEEee
Confidence 555677777655 2 2356777765 88999999999999983 3577777654
No 58
>PF10842 DUF2642: Protein of unknown function (DUF2642); InterPro: IPR020139 This entry contains proteins with no known function.
Probab=28.18 E-value=1.5e+02 Score=21.65 Aligned_cols=33 Identities=12% Similarity=0.124 Sum_probs=26.1
Q ss_pred hHHHhhcCCCeEEEEEeeccccCCCCCCCCceE--EEEEEeCCceEE
Q 026585 147 PLELERFKDRAMYVKYVGETVTTGSPSESDGVF--RLISFDMETECC 191 (236)
Q Consensus 147 ~~df~rf~G~~V~V~~~~~~~~~~~~~eg~k~f--~L~~vd~e~~~~ 191 (236)
-+.++.++|+.+.|.+. ++.+ +|.++..+.+.+
T Consensus 13 yq~lq~liG~~vvV~T~------------~g~v~G~L~~V~pDhIvl 47 (66)
T PF10842_consen 13 YQTLQSLIGQRVVVQTT------------RGSVRGILVDVKPDHIVL 47 (66)
T ss_pred HHHHHHhcCCEEEEEEc------------CCcEEEEEEeecCCEEEE
Confidence 36789999999999987 2222 899999987755
No 59
>PF09684 Tail_P2_I: Phage tail protein (Tail_P2_I); InterPro: IPR006521 These sequences represent a family of phage tail proteins from phage P2 protein and related temperates phage of Gram-negative bacteria.
Probab=26.28 E-value=3.2e+02 Score=21.81 Aligned_cols=56 Identities=13% Similarity=-0.040 Sum_probs=35.6
Q ss_pred cCCcHHHHHHHHHHHHHhhcCCcEEEEEE-EEc--C-CceEEEEEeccCCCCCCCChhHHHHHHHHHHH
Q 026585 52 AGTWWDKEALAIAEDVCLSFDGDLKIYAF-RTL--P-NSTIKVRIEKMSNKSGSPSMEDIEAFCTTYRA 116 (236)
Q Consensus 52 ~~~~w~~~v~~lae~vl~~~g~el~lv~~-~~~--~-~~~lrV~IDk~~~~~ggvsldDCe~vSr~i~~ 116 (236)
.||.|+ ++.++..+|++..+.+. ... + ....++.|... ..+++.++.+.+-+.|..
T Consensus 75 kGT~~a------l~~~l~~lg~~~~i~E~~~~~~~g~p~~f~~~v~~~---~~~~~~~~~~~i~~~i~~ 134 (139)
T PF09684_consen 75 KGTPAA------LRRALEWLGYEAEIIEWFEYDPRGRPYWFEVQVYLS---DPPIDPEDAERIIRLIEE 134 (139)
T ss_pred cCCHHH------HHHHHHHcCCCeeeeeccccCCCCCCceEEEEEEec---CCCCCHHHHHHHHHHHHH
Confidence 466664 56667777888888875 333 2 34555555441 237888888888877764
No 60
>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=25.60 E-value=1.1e+02 Score=20.82 Aligned_cols=27 Identities=19% Similarity=0.347 Sum_probs=20.9
Q ss_pred hhcCCCeEEEEEeeccccCCCCCCCCceE--EEEEEeCCc
Q 026585 151 ERFKDRAMYVKYVGETVTTGSPSESDGVF--RLISFDMET 188 (236)
Q Consensus 151 ~rf~G~~V~V~~~~~~~~~~~~~eg~k~f--~L~~vd~e~ 188 (236)
..++|++|.|.++ +| +.| .|.++|...
T Consensus 2 ~~~~g~~V~V~l~----------~g-~~~~G~L~~~D~~~ 30 (63)
T cd00600 2 KDLVGKTVRVELK----------DG-RVLEGVLVAFDKYM 30 (63)
T ss_pred hHHCCCEEEEEEC----------CC-cEEEEEEEEECCCC
Confidence 4678999999998 33 344 999999763
No 61
>PF11211 DUF2997: Protein of unknown function (DUF2997); InterPro: IPR021375 This family of proteins has no known function.
Probab=25.33 E-value=1.6e+02 Score=20.08 Aligned_cols=36 Identities=11% Similarity=0.169 Sum_probs=26.9
Q ss_pred EEEEcCCceEEEEEeccCCCCCCCChhHHHHHHHHHHHhhhhh
Q 026585 79 AFRTLPNSTIKVRIEKMSNKSGSPSMEDIEAFCTTYRARLDEA 121 (236)
Q Consensus 79 ~~~~~~~~~lrV~IDk~~~~~ggvsldDCe~vSr~i~~~LD~~ 121 (236)
.|...+.+.|++.+. |+.=..|..+++.|.++|-..
T Consensus 2 ~~~I~~dG~V~~~v~-------G~~G~~C~~~t~~lE~~LG~v 37 (48)
T PF11211_consen 2 EFTIYPDGRVEEEVE-------GFKGSSCLEATAALEEALGTV 37 (48)
T ss_pred EEEECCCcEEEEEEE-------eccChhHHHHHHHHHHHhCce
Confidence 455666777777664 466789999999999999643
No 62
>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=25.20 E-value=1.3e+02 Score=21.64 Aligned_cols=64 Identities=17% Similarity=0.181 Sum_probs=36.7
Q ss_pred HHhhcCCCeEEEEEeeccccCCCCCCCCceE-EEEEEeCCceEEEEeecceehhhcccCCCCCccccccceeeeeccccc
Q 026585 149 ELERFKDRAMYVKYVGETVTTGSPSESDGVF-RLISFDMETECCTWGLADVRINREKAGKGRPLSKKQREWRLNTTFDSL 227 (236)
Q Consensus 149 df~rf~G~~V~V~~~~~~~~~~~~~eg~k~f-~L~~vd~e~~~~~~~la~vk~nr~~~~KGr~~~kk~~~~~l~ipf~~I 227 (236)
-+...+|++|.|.++ +|.... +|.++|.- -.+.+. +++... ..|+.. + . ..+-|-=++|
T Consensus 4 ~L~~~~g~~V~VeLk----------~g~~~~G~L~~~D~~-MNl~L~--~~~~~~---~~g~~~-~--~-~~v~IRG~nI 63 (70)
T cd01721 4 LLHEAEGHIVTVELK----------TGEVYRGKLIEAEDN-MNCQLK--DVTVTA---RDGRVS-Q--L-EQVYIRGSKI 63 (70)
T ss_pred HHhhCCCCEEEEEEC----------CCcEEEEEEEEEcCC-ceeEEE--EEEEEC---CCCcEe-E--c-CcEEEeCCEE
Confidence 357889999999999 343333 99999874 444443 444321 223321 1 1 1355666666
Q ss_pred cceEE
Q 026585 228 RLVRL 232 (236)
Q Consensus 228 ~karL 232 (236)
+.++|
T Consensus 64 ~~v~l 68 (70)
T cd01721 64 RFFIL 68 (70)
T ss_pred EEEEe
Confidence 66554
No 63
>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=25.15 E-value=1.5e+02 Score=25.66 Aligned_cols=50 Identities=10% Similarity=0.147 Sum_probs=36.0
Q ss_pred CCCCCceeccCCc-----------HHHHHHHHHH----HHHhhcCCcEEEEEEEEcCCceEEEEEec
Q 026585 43 GGAGGGISLAGTW-----------WDKEALAIAE----DVCLSFDGDLKIYAFRTLPNSTIKVRIEK 94 (236)
Q Consensus 43 ~~~gg~i~l~~~~-----------w~~~v~~lae----~vl~~~g~el~lv~~~~~~~~~lrV~IDk 94 (236)
.+-|+|..+.++. --++|.++++ |.|+++|++++++.+... ++|.|++-.
T Consensus 82 ~~~g~gF~f~NPna~~~~~~~~~~~~~~i~~~l~~~irP~l~~dGGdielv~v~~~--~~v~v~l~G 146 (190)
T TIGR03341 82 DRMGGQLTLKAPNAKMPKVADDAPLEERINYVLQSEINPQLASHGGKVTLVEITDD--GVAVLQFGG 146 (190)
T ss_pred cCCCceeEEeCCccCCCcCccchHHHHHHHHHHHhccCHHHHhcCCceEEEEEcCC--CEEEEEEee
Confidence 5566778776553 2456766665 889999999999999843 467777654
No 64
>PF14535 AMP-binding_C_2: AMP-binding enzyme C-terminal domain; PDB: 2Y27_A 2Y4N_A 3QOV_B 3S89_D 3LAX_A 2Y4O_B.
Probab=24.84 E-value=3e+02 Score=20.56 Aligned_cols=68 Identities=29% Similarity=0.422 Sum_probs=40.5
Q ss_pred HHHHHHhhcCCcEE-EEEE---EEcCCceEEEEEeccCCCCC-CCChhHHHHHHHHHHHhhhhhhccCCCCCCeEEEEec
Q 026585 63 IAEDVCLSFDGDLK-IYAF---RTLPNSTIKVRIEKMSNKSG-SPSMEDIEAFCTTYRARLDEAEIAKSIPENTSLEVSS 137 (236)
Q Consensus 63 lae~vl~~~g~el~-lv~~---~~~~~~~lrV~IDk~~~~~g-gvsldDCe~vSr~i~~~LD~~d~~~~i~~~Y~LEVSS 137 (236)
-++.++.++. ++. .|.+ +......+.|.|... .+ .-++.+..++...|...|-..- - -.-.+++-.
T Consensus 8 ~Ie~vl~~~~-~~~~~y~i~v~~~~~~D~l~v~vE~~---~~~~~~~~~~~~l~~~i~~~lk~~l---g--v~~~V~lv~ 78 (96)
T PF14535_consen 8 QIEEVLREFP-EVSPEYQIVVTREGGLDELTVRVELR---PGFSDDAEDLEALAERIAERLKERL---G--VRPEVELVP 78 (96)
T ss_dssp HHHHHHCTST-TEEEEEEEEEEEETTEEEEEEEEEES---TTCCTTHHHHHHHHHHHHHHHHHHH---S--S-EEEEEE-
T ss_pred HHHHHHHhCc-CCCCcEEEEEEcCCCCcEEEEEEEEC---CccCcchHHHHHHHHHHHHHHHhhc---C--ceEEEEEEC
Confidence 3566666662 332 3333 333356788888773 22 2246788888888888886543 2 234788888
Q ss_pred CC
Q 026585 138 PG 139 (236)
Q Consensus 138 PG 139 (236)
||
T Consensus 79 ~g 80 (96)
T PF14535_consen 79 PG 80 (96)
T ss_dssp TT
T ss_pred CC
Confidence 88
No 65
>PRK10263 DNA translocase FtsK; Provisional
Probab=24.66 E-value=5.5e+02 Score=29.11 Aligned_cols=91 Identities=11% Similarity=0.156 Sum_probs=63.7
Q ss_pred cHHHHHHHHHHHHHhhcCCcEEEEEEEEcCCceEEEEEeccCCCCCCCChhHHHHHHHHHHHhhhhhhc--cCCCCCCeE
Q 026585 55 WWDKEALAIAEDVCLSFDGDLKIYAFRTLPNSTIKVRIEKMSNKSGSPSMEDIEAFCTTYRARLDEAEI--AKSIPENTS 132 (236)
Q Consensus 55 ~w~~~v~~lae~vl~~~g~el~lv~~~~~~~~~lrV~IDk~~~~~ggvsldDCe~vSr~i~~~LD~~d~--~~~i~~~Y~ 132 (236)
.+-++..++++.+|.+||.+-.++.+..++ .+.|+.|+- .-|+.+.++..++..|...|-.... ..+||+.-.
T Consensus 885 ~~l~~~a~~l~~~L~~F~i~~~v~~v~~GP-~vtr~ev~l----~pGvkvs~I~~La~dLA~aL~a~~vRI~apiPGk~~ 959 (1355)
T PRK10263 885 FALEQMARLVEARLADFRIKADVVNYSPGP-VITRFELNL----APGVKAARISNLSRDLARSLSTVAVRVVEVIPGKPY 959 (1355)
T ss_pred HHHHHHHHHHHHHHHHCCcceEEEEEEECC-EEEEEEEEe----CCCCCHHHHHHHHHHHHHHhcCCccceecCCCCCCc
Confidence 455667788999999999999999987754 344555654 5689999999999999988875432 125677655
Q ss_pred EEEecCCCCCCCCChHHH
Q 026585 133 LEVSSPGVERVVRIPLEL 150 (236)
Q Consensus 133 LEVSSPGleRpL~~~~df 150 (236)
+-+.-|--.|.....++.
T Consensus 960 VGiEvPn~~r~~V~lrdl 977 (1355)
T PRK10263 960 VGLELPNKKRQTVYLREV 977 (1355)
T ss_pred eeEECCCCCCceeeHHHh
Confidence 555555555555444444
No 66
>PHA02595 tk.4 hypothetical protein; Provisional
Probab=24.45 E-value=1.2e+02 Score=25.15 Aligned_cols=35 Identities=26% Similarity=0.421 Sum_probs=24.0
Q ss_pred cccccCCCCCCceeccCCcHHHHHHHHHHHHHhhcCCcEEEEEEE
Q 026585 37 EAYVGDGGAGGGISLAGTWWDKEALAIAEDVCLSFDGDLKIYAFR 81 (236)
Q Consensus 37 ~~~~~~~~~gg~i~l~~~~w~~~v~~lae~vl~~~g~el~lv~~~ 81 (236)
=|-+|-|-+| .+| .+|..++++++. +.++.+|.|.
T Consensus 118 ~P~IG~GlgG-------l~W-~~V~~ii~~~~~--~~~i~Vy~~~ 152 (154)
T PHA02595 118 IPRIGAGIAG-------GDW-DKIEAIIDEATP--DIDIVVVEYE 152 (154)
T ss_pred eCCCCccCCC-------CCH-HHHHHHHHHhcC--CCcEEEEEec
Confidence 3677776554 479 688899988865 4556666654
No 67
>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=23.82 E-value=1.4e+02 Score=21.91 Aligned_cols=30 Identities=23% Similarity=0.154 Sum_probs=23.6
Q ss_pred HHHhhcCCCeEEEEEeeccccCCCCCCCCceE-EEEEEeCC
Q 026585 148 LELERFKDRAMYVKYVGETVTTGSPSESDGVF-RLISFDME 187 (236)
Q Consensus 148 ~df~rf~G~~V~V~~~~~~~~~~~~~eg~k~f-~L~~vd~e 187 (236)
..+..+++++|.|+++ +|+... .|.++|.-
T Consensus 5 ~~L~~~l~k~v~V~l~----------~gr~~~G~L~~fD~~ 35 (74)
T cd01728 5 ASLVDDLDKKVVVLLR----------DGRKLIGILRSFDQF 35 (74)
T ss_pred HHHHHhcCCEEEEEEc----------CCeEEEEEEEEECCc
Confidence 5688999999999998 444333 99999865
No 68
>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=23.71 E-value=2e+02 Score=21.30 Aligned_cols=39 Identities=13% Similarity=0.121 Sum_probs=25.6
Q ss_pred ceEEEEEeccCCCCCCCChhHHHHHHHHHHHhhhhhhccCCCCCCeEEEEec
Q 026585 86 STIKVRIEKMSNKSGSPSMEDIEAFCTTYRARLDEAEIAKSIPENTSLEVSS 137 (236)
Q Consensus 86 ~~lrV~IDk~~~~~ggvsldDCe~vSr~i~~~LD~~d~~~~i~~~Y~LEVSS 137 (236)
..++.||+. ...-|...+..+.+.+...+ ++.|.|||.=
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 357888887 34556666666655554433 5789999964
No 69
>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=23.62 E-value=1.5e+02 Score=21.68 Aligned_cols=28 Identities=18% Similarity=0.230 Sum_probs=21.9
Q ss_pred HhhcCCCeEEEEEeeccccCCCCCCCCceE-EEEEEeCC
Q 026585 150 LERFKDRAMYVKYVGETVTTGSPSESDGVF-RLISFDME 187 (236)
Q Consensus 150 f~rf~G~~V~V~~~~~~~~~~~~~eg~k~f-~L~~vd~e 187 (236)
++...|+.|.|.++ +|+... +|.++|.-
T Consensus 6 L~~~~g~~V~VeLk----------ng~~~~G~L~~~D~~ 34 (76)
T cd01723 6 LKTAQNHPMLVELK----------NGETYNGHLVNCDNW 34 (76)
T ss_pred HHhcCCCEEEEEEC----------CCCEEEEEEEEEcCC
Confidence 46789999999999 344444 99999874
No 70
>cd07015 Clp_protease_NfeD Nodulation formation efficiency D (NfeD) is a membrane-bound ClpP-class protease. Nodulation formation efficiency D (NfeD; stomatin operon partner protein, STOPP; DUF107) is a member of membrane-anchored ClpP-class proteases. Currently, more than 300 NfeD homologs have been identified - all of which are bacterial or archaeal in origin. Majority of these genomes have been shown to possess operons containing a homologous NfeD/stomatin gene pair, causing NfeD to be previously named STOPP (stomatin operon partner protein). NfeD homologs can be divided into two groups: long and short forms. Long-form homologs have a putative ClpP-class serine protease domain while the short form homologs do not. Downstream from the ClpP-class domain is the so-called NfeD or DUF107 domain. N-terminal region of the NfeD homolog PH1510 (1510-N or PH1510-N) from Pyrococcus horikoshii has been shown to possess serine protease activity and has a Ser-Lys catalytic dyad, preferentially cle
Probab=23.55 E-value=1.3e+02 Score=25.74 Aligned_cols=57 Identities=11% Similarity=0.105 Sum_probs=32.7
Q ss_pred CCCChhHHHHHHHHHHHhhhhhhccCCCCCCeEEEEecCCCC-CCCCChHHHhhcCCCeEEEEE
Q 026585 100 GSPSMEDIEAFCTTYRARLDEAEIAKSIPENTSLEVSSPGVE-RVVRIPLELERFKDRAMYVKY 162 (236)
Q Consensus 100 ggvsldDCe~vSr~i~~~LD~~d~~~~i~~~Y~LEVSSPGle-RpL~~~~df~rf~G~~V~V~~ 162 (236)
|.|+-.....+.|.|..+-+. . .....|++.|||=. ..-...-+.-++...+|.+..
T Consensus 8 G~I~~~~~~~l~~~l~~A~~~-----~-~~~i~l~inSPGG~v~~~~~I~~~i~~~~~pvv~~v 65 (172)
T cd07015 8 GQITSYTYDQFDRYITIAEQD-----N-AEAIIIELDTPGGRADAAGNIVQRIQQSKIPVIIYV 65 (172)
T ss_pred eEECHhHHHHHHHHHHHHhcC-----C-CCeEEEEEECCCCCHHHHHHHHHHHHhcCcCEEEEE
Confidence 556655666777777765442 2 26789999999832 222222333345555555443
No 71
>PF10262 Rdx: Rdx family; InterPro: IPR011893 This entry represents the Rdx family of selenoproteins, which includes mammalian selenoproteins SelW, SelV, SelT and SelH, bacterial SelW-like proteins and cysteine-containing proteins of unknown function in all three domains of life. Mammalian Rdx12 and its fish selenoprotein orthologues are also members of this family []. These proteins possess a thioredoxin-like fold and a conserved CXXC or CxxU (U is selenocysteine) motif near the N terminus, suggesting a redox function. Rdx proteins can use catalytic cysteine (or selenocysteine) to form transient mixed disulphides with substrate proteins. Selenium (Se) plays an essential role in cell survival and most of the effects of Se are probably mediated by selenoproteins. Selenoprotein W (SelW) plays an important role in protection of neurons from oxidative stress during neuronal development [], []. Selenoprotein T (SelT) is conserved from plants to humans. SelT is localized to the endoplasmic reticulum through a hydrophobic domain. The protein binds to UDP-glucose:glycoprotein glucosyltransferase (UGTR), the endoplasmic reticulum (ER)-resident protein, which is known to be involved in the quality control of protein folding [, ]. The function of SelT is unknown, although it may have a role in PACAP signaling during PC12 cell differentiation [, ]. Selenoprotein H (SelH) protects neurons against UVB-induced damage by inhibiting apoptotic cell death pathways, by preventing mitochondrial depolarization, and by promoting cell survival pathways [].; GO: 0008430 selenium binding, 0045454 cell redox homeostasis; PDB: 2OJL_B 2FA8_A 2P0G_C 2NPB_A 3DEX_C 2OKA_A 2OBK_G.
Probab=22.93 E-value=1.6e+02 Score=21.27 Aligned_cols=40 Identities=13% Similarity=0.242 Sum_probs=29.8
Q ss_pred CcHHHHHHHHHHHHHhhcCCcEEEEEEEEcCCceEEEEEe
Q 026585 54 TWWDKEALAIAEDVCLSFDGDLKIYAFRTLPNSTIKVRIE 93 (236)
Q Consensus 54 ~~w~~~v~~lae~vl~~~g~el~lv~~~~~~~~~lrV~ID 93 (236)
--|..++..+++.++..+...+.-+.......+..+|+++
T Consensus 11 C~~~~~a~~l~~~l~~~fp~~~~~v~~~~~~~G~FEV~v~ 50 (76)
T PF10262_consen 11 CGYRPRALELAQELLQTFPDRIAEVELSPGSTGAFEVTVN 50 (76)
T ss_dssp TTCHHHHHHHHHHHHHHSTTTCSEEEEEEESTT-EEEEET
T ss_pred CCCHHHHHHHHHHHHHHCCCcceEEEEEeccCCEEEEEEc
Confidence 3588899999999999998755555555555778888776
No 72
>COG1481 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=22.08 E-value=79 Score=29.82 Aligned_cols=58 Identities=19% Similarity=0.040 Sum_probs=36.4
Q ss_pred hHHHHHHHHHHHhhhhhhccCCCCCCeEEEEecCCCCCCCCChHHHhhcCCCeEEEEEe
Q 026585 105 EDIEAFCTTYRARLDEAEIAKSIPENTSLEVSSPGVERVVRIPLELERFKDRAMYVKYV 163 (236)
Q Consensus 105 dDCe~vSr~i~~~LD~~d~~~~i~~~Y~LEVSSPGleRpL~~~~df~rf~G~~V~V~~~ 163 (236)
++|..-+=..++.|-.--...|....|+||+|||+-+--+. ...+-++.|...++..+
T Consensus 117 ~~~~~~~ylrGAFLagGSis~Pe~~~YhLEi~s~~ee~a~~-L~~l~~~f~l~ak~~er 174 (308)
T COG1481 117 DDEDFRAYLRGAFLAGGSISDPETSSYHLEISSNYEEHALA-LVKLLRRFGLNAKIIER 174 (308)
T ss_pred cHHHHHHHHHHHHHcCCccCCCCCCceeEEEecCcHHHHHH-HHHHHHHhccchheeee
Confidence 45555555556666432223365578999999999994444 44444566777777655
No 73
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=21.83 E-value=50 Score=29.15 Aligned_cols=56 Identities=18% Similarity=0.197 Sum_probs=38.5
Q ss_pred CCChhHHHHHHHHHHHhhhhhhccCCCCCCeEEEEecCCCCCCCC-ChHHHhhcCCCeE
Q 026585 101 SPSMEDIEAFCTTYRARLDEAEIAKSIPENTSLEVSSPGVERVVR-IPLELERFKDRAM 158 (236)
Q Consensus 101 gvsldDCe~vSr~i~~~LD~~d~~~~i~~~Y~LEVSSPGleRpL~-~~~df~rf~G~~V 158 (236)
...+-....+-++|+.=++-..+..++.++|+|||=. |..-.+ ...||+|.+||-+
T Consensus 61 p~~~~ka~d~VkAIgrGF~pe~A~~LL~d~~~levId--i~~~~~~~~~~l~R~kgRII 117 (194)
T COG1094 61 PLALLKARDVVKAIGRGFPPEKALKLLEDDYYLEVID--LKDVVTLSGDHLRRIKGRII 117 (194)
T ss_pred hHHHHHHHHHHHHHhcCCCHHHHHHHhcCCcEEEEEE--HHHhccCchhhhhHhhceee
Confidence 4556666777788887666555555777899999965 334444 3455999888754
No 74
>PF04931 DNA_pol_phi: DNA polymerase phi; InterPro: IPR007015 Proteins of this family are predominantly nucleolar. The majority are described as transcription factor transactivators. The family also includes the fifth essential DNA polymerase (Pol5p) of Schizosaccharomyces pombe (Fission yeast) and Saccharomyces cerevisiae (Baker's yeast) (2.7.7.7 from EC). Pol5p is localized exclusively to the nucleolus and binds near or at the enhancer region of rRNA-encoding DNA repeating units.; GO: 0003677 DNA binding, 0003887 DNA-directed DNA polymerase activity, 0006351 transcription, DNA-dependent
Probab=21.14 E-value=46 Score=34.67 Aligned_cols=21 Identities=19% Similarity=0.104 Sum_probs=12.8
Q ss_pred CCCChhHHHHHHHHHHHhhhh
Q 026585 100 GSPSMEDIEAFCTTYRARLDE 120 (236)
Q Consensus 100 ggvsldDCe~vSr~i~~~LD~ 120 (236)
..++=+.-.++-.+|.+++-.
T Consensus 727 ~~mdDe~m~~lD~~La~~Fk~ 747 (784)
T PF04931_consen 727 EDMDDEQMMALDEQLAAIFKE 747 (784)
T ss_pred cccCHHHHHHHHHHHHHHHHH
Confidence 346666666666666666643
No 75
>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=20.95 E-value=1.7e+02 Score=21.70 Aligned_cols=28 Identities=14% Similarity=0.137 Sum_probs=21.3
Q ss_pred HhhcCCCeEEEEEeeccccCCCCCCCCceE-EEEEEeCC
Q 026585 150 LERFKDRAMYVKYVGETVTTGSPSESDGVF-RLISFDME 187 (236)
Q Consensus 150 f~rf~G~~V~V~~~~~~~~~~~~~eg~k~f-~L~~vd~e 187 (236)
++...|++|.|.++ +|...- +|.++|.-
T Consensus 6 L~~l~g~~V~VeLK----------ng~~~~G~L~~vD~~ 34 (81)
T cd01725 6 FKTLVGKEVTVELK----------NDLSIRGTLHSVDQY 34 (81)
T ss_pred HHhCCCCEEEEEEC----------CCcEEEEEEEEECCC
Confidence 37889999999999 333333 89999874
No 76
>TIGR02000 NifU_proper Fe-S cluster assembly protein NifU. Three different but partially homologous Fe-S cluster assembly systems have been described: Isc, Suf, and Nif. The latter is associated with donation of an Fe-S cluster to nitrogenase in a number of nitrogen-fixing species. NifU, described here, consists of an N-terminal domain (pfam01592) and a C-terminal domain (pfam01106). Homologs with an equivalent domain archictecture from Helicobacter and Campylobacter, however, are excluded from this model by a high trusted cutoff. The model, therefore, is specific for NifU involved in nitrogenase maturation. The related model TIGR01999 homologous to the N-terminus of this model describes IscU from the Isc system as in E. coli, Saccharomyces cerevisiae, and Homo sapiens.
Probab=20.91 E-value=1.5e+02 Score=27.39 Aligned_cols=33 Identities=18% Similarity=0.266 Sum_probs=25.5
Q ss_pred HHHHHHHHHHhhcCCcEEEEEEEEcCCceEEEEEec
Q 026585 59 EALAIAEDVCLSFDGDLKIYAFRTLPNSTIKVRIEK 94 (236)
Q Consensus 59 ~v~~lae~vl~~~g~el~lv~~~~~~~~~lrV~IDk 94 (236)
++++-++|.|+..|++++++.|+. ++|+|++-.
T Consensus 226 ~~l~~irP~l~~dGGdv~lv~v~~---~~v~v~l~G 258 (290)
T TIGR02000 226 KVLEEVRPVLQADGGDVELYDVDG---KIVYVVLTG 258 (290)
T ss_pred HHHHHhCchHhhcCCcEEEEEEeC---CEEEEEEee
Confidence 344556788999999999999973 578887754
No 77
>cd01730 LSm3 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm3 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=20.38 E-value=1.8e+02 Score=21.50 Aligned_cols=39 Identities=26% Similarity=0.283 Sum_probs=26.6
Q ss_pred HhhcCCCeEEEEEeeccccCCCCCCCCceE-EEEEEeCCceEEEEeecceehh
Q 026585 150 LERFKDRAMYVKYVGETVTTGSPSESDGVF-RLISFDMETECCTWGLADVRIN 201 (236)
Q Consensus 150 f~rf~G~~V~V~~~~~~~~~~~~~eg~k~f-~L~~vd~e~~~~~~~la~vk~n 201 (236)
++.+.+++|.|+++ +|+... +|.++|.- +.+.|.++...
T Consensus 6 l~~~~~k~V~V~l~----------~gr~~~G~L~~fD~~---mNlvL~d~~E~ 45 (82)
T cd01730 6 IRLSLDERVYVKLR----------GDRELRGRLHAYDQH---LNMILGDVEET 45 (82)
T ss_pred HHHhCCCEEEEEEC----------CCCEEEEEEEEEccc---eEEeccceEEE
Confidence 36779999999998 454444 99999864 34445555443
No 78
>PF08496 Peptidase_S49_N: Peptidase family S49 N-terminal; InterPro: IPR013703 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ]. This domain is found to the N terminus of bacterial signal peptidases that belong to the MEROPS peptidase family S49 (protease IV family, clan SK) (see also IPR002142 from INTERPRO) [, ]. ; GO: 0004252 serine-type endopeptidase activity, 0005886 plasma membrane
Probab=20.22 E-value=3.1e+02 Score=23.08 Aligned_cols=46 Identities=20% Similarity=0.338 Sum_probs=36.2
Q ss_pred CceEEEEEeccCCCCCCCChhHHHHHHHHHHHhhhhhhccCCCCCCeEEEEecCC
Q 026585 85 NSTIKVRIEKMSNKSGSPSMEDIEAFCTTYRARLDEAEIAKSIPENTSLEVSSPG 139 (236)
Q Consensus 85 ~~~lrV~IDk~~~~~ggvsldDCe~vSr~i~~~LD~~d~~~~i~~~Y~LEVSSPG 139 (236)
++.|.| +|= .|+|.-..++.+-+.|+++|..+. + .+...|=+-|||
T Consensus 97 ~~r~~V-ldF----~Gdi~A~~v~~LReeisail~~a~---~-~DeV~~rLES~G 142 (155)
T PF08496_consen 97 KPRLFV-LDF----KGDIKASEVESLREEISAILSVAT---P-EDEVLVRLESPG 142 (155)
T ss_pred CCeEEE-Eec----CCCccHHHHHHHHHHHHHHHHhCC---C-CCeEEEEEecCC
Confidence 344444 565 789999999999999999998775 4 366778888998
Done!