Query 036084
Match_columns 126
No_of_seqs 181 out of 1056
Neff 7.6
Searched_HMMs 46136
Date Fri Mar 29 09:17:13 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/036084.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/036084hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK05417 glutathione-dependent 99.9 5.3E-27 1.1E-31 170.9 9.6 108 13-125 17-137 (191)
2 COG3791 Uncharacterized conser 99.9 9.7E-27 2.1E-31 161.4 7.6 102 17-125 4-109 (133)
3 TIGR02820 formald_GSH S-(hydro 99.9 5.9E-26 1.3E-30 164.1 9.7 109 14-125 14-133 (182)
4 PF04828 GFA: Glutathione-depe 99.9 3.1E-22 6.8E-27 129.0 3.7 84 39-125 1-88 (92)
5 KOG4192 Uncharacterized conser 99.8 1.1E-20 2.5E-25 126.8 9.0 110 13-123 4-124 (134)
6 PF13240 zinc_ribbon_2: zinc-r 91.9 0.05 1.1E-06 26.4 0.1 12 82-93 12-23 (23)
7 PF13248 zf-ribbon_3: zinc-rib 91.4 0.064 1.4E-06 26.6 0.2 13 81-93 14-26 (26)
8 PF14803 Nudix_N_2: Nudix N-te 89.4 0.14 3.1E-06 27.2 0.5 15 84-98 1-15 (34)
9 PF09297 zf-NADH-PPase: NADH p 88.0 0.16 3.4E-06 26.4 0.0 16 82-97 2-17 (32)
10 COG1998 RPS31 Ribosomal protei 84.5 1.2 2.6E-05 25.7 2.5 17 82-98 18-34 (51)
11 PRK00432 30S ribosomal protein 84.1 1.3 2.8E-05 25.5 2.6 22 71-92 6-29 (50)
12 smart00661 RPOL9 RNA polymeras 82.3 0.65 1.4E-05 26.3 0.8 13 85-97 2-14 (52)
13 PF02150 RNA_POL_M_15KD: RNA p 81.6 0.59 1.3E-05 24.8 0.5 15 84-98 2-16 (35)
14 PF03119 DNA_ligase_ZBD: NAD-d 78.2 1.1 2.4E-05 22.6 0.8 13 85-97 1-13 (28)
15 PF08772 NOB1_Zn_bind: Nin one 77.9 0.8 1.7E-05 28.5 0.3 16 80-95 21-36 (73)
16 COG1645 Uncharacterized Zn-fin 70.6 1.9 4E-05 29.9 0.6 19 78-96 23-41 (131)
17 PF06677 Auto_anti-p27: Sjogre 68.7 2.3 5E-05 23.5 0.6 13 83-95 17-29 (41)
18 PF04032 Rpr2: RNAse P Rpr2/Rp 68.3 1.8 3.9E-05 26.9 0.2 16 79-94 42-57 (85)
19 TIGR00357 methionine-R-sulfoxi 65.0 11 0.00024 26.2 3.6 20 82-101 88-107 (134)
20 PF07754 DUF1610: Domain of un 63.8 4.6 9.9E-05 19.7 1.1 10 81-90 14-23 (24)
21 COG4469 CoiA Competence protei 62.8 3.2 7E-05 33.1 0.7 15 83-97 25-39 (342)
22 PRK12496 hypothetical protein; 61.0 3.4 7.4E-05 29.5 0.5 16 82-97 142-157 (164)
23 PF12773 DZR: Double zinc ribb 60.5 3 6.6E-05 23.3 0.1 13 82-94 11-23 (50)
24 PRK00398 rpoP DNA-directed RNA 60.3 6.3 0.00014 21.8 1.4 16 83-98 21-36 (46)
25 PRK00420 hypothetical protein; 59.8 4.2 9.1E-05 27.4 0.7 13 84-96 24-36 (112)
26 PRK00222 methionine sulfoxide 58.8 15 0.00032 25.8 3.3 19 83-101 92-110 (142)
27 TIGR01384 TFS_arch transcripti 56.3 4.8 0.00011 26.1 0.6 12 85-96 2-13 (104)
28 TIGR02098 MJ0042_CXXC MJ0042 f 54.2 8.6 0.00019 20.2 1.3 13 83-95 25-37 (38)
29 COG2816 NPY1 NTP pyrophosphohy 52.4 6.9 0.00015 30.5 0.9 15 82-96 110-124 (279)
30 COG1594 RPB9 DNA-directed RNA 50.8 6.8 0.00015 26.3 0.6 13 84-96 3-15 (113)
31 PRK00241 nudC NADH pyrophospha 49.7 6.9 0.00015 29.8 0.6 15 82-96 98-112 (256)
32 COG0229 Conserved domain frequ 49.5 23 0.0005 24.8 3.0 32 70-101 76-109 (140)
33 PF13408 Zn_ribbon_recom: Reco 48.5 8.1 0.00018 21.9 0.6 17 83-99 5-21 (58)
34 COG1439 Predicted nucleic acid 48.0 7.8 0.00017 28.2 0.6 15 82-96 152-166 (177)
35 PF00301 Rubredoxin: Rubredoxi 47.8 5.5 0.00012 22.6 -0.2 18 83-101 1-18 (47)
36 PRK12495 hypothetical protein; 46.4 7.7 0.00017 29.2 0.4 18 78-95 37-54 (226)
37 smart00659 RPOLCX RNA polymera 46.1 10 0.00022 21.1 0.7 17 82-98 18-34 (44)
38 PF13842 Tnp_zf-ribbon_2: DDE_ 46.1 14 0.00031 19.0 1.3 13 82-94 15-27 (32)
39 PF09151 DUF1936: Domain of un 45.4 15 0.00032 19.1 1.2 13 84-96 2-14 (36)
40 PF08882 Acetone_carb_G: Aceto 45.3 14 0.0003 24.9 1.4 17 81-97 72-88 (112)
41 KOG2906 RNA polymerase III sub 45.2 9.4 0.0002 25.2 0.6 15 84-98 2-16 (105)
42 PRK14890 putative Zn-ribbon RN 45.1 15 0.00032 22.0 1.3 16 81-96 23-38 (59)
43 PF09889 DUF2116: Uncharacteri 45.0 9.7 0.00021 22.7 0.6 13 83-95 3-15 (59)
44 PF11062 DUF2863: Protein of u 42.1 13 0.00028 30.3 1.1 15 84-98 365-379 (398)
45 PF08271 TF_Zn_Ribbon: TFIIB z 41.4 13 0.00029 20.2 0.7 11 84-94 20-30 (43)
46 smart00714 LITAF Possible memb 40.3 16 0.00035 21.8 1.1 18 78-95 47-64 (67)
47 PRK11586 napB nitrate reductas 40.1 13 0.00027 26.3 0.6 13 81-93 118-130 (149)
48 PF07191 zinc-ribbons_6: zinc- 39.8 20 0.00043 22.1 1.4 15 80-94 27-41 (70)
49 PF13005 zf-IS66: zinc-finger 39.7 14 0.00029 20.3 0.6 13 85-97 4-16 (47)
50 PF01641 SelR: SelR domain; I 37.7 38 0.00083 23.2 2.7 23 79-101 82-104 (124)
51 PRK06393 rpoE DNA-directed RNA 37.5 29 0.00063 21.0 1.8 11 85-95 19-29 (64)
52 smart00068 GHB Glycoprotein ho 36.9 50 0.0011 22.1 3.1 35 16-50 48-93 (107)
53 cd00069 GHB Glycoprotein hormo 36.7 49 0.0011 21.9 3.0 35 16-50 44-89 (102)
54 PF10571 UPF0547: Uncharacteri 36.7 16 0.00034 18.0 0.5 10 83-92 14-23 (26)
55 PRK05508 methionine sulfoxide 36.4 60 0.0013 22.1 3.4 17 82-98 78-94 (119)
56 KOG3084 NADH pyrophosphatase I 35.8 20 0.00043 28.6 1.1 16 82-97 149-164 (345)
57 PRK08351 DNA-directed RNA poly 34.9 22 0.00047 21.4 1.0 12 85-96 17-28 (61)
58 PF01396 zf-C4_Topoisom: Topoi 34.4 18 0.0004 19.4 0.6 14 85-98 3-16 (39)
59 COG1996 RPC10 DNA-directed RNA 34.4 19 0.0004 20.7 0.6 17 83-99 24-40 (49)
60 COG3043 NapB Nitrate reductase 34.3 17 0.00036 25.8 0.5 13 81-93 124-136 (155)
61 PF05191 ADK_lid: Adenylate ki 34.3 19 0.0004 19.1 0.6 10 83-92 1-10 (36)
62 PF00007 Cys_knot: Cystine-kno 34.0 15 0.00032 24.0 0.2 50 1-50 30-92 (105)
63 PF03811 Zn_Tnp_IS1: InsA N-te 33.9 37 0.00079 18.0 1.7 17 73-89 19-35 (36)
64 COG2023 RPR2 RNase P subunit R 33.7 8.6 0.00019 25.6 -1.0 18 78-95 51-68 (105)
65 PF03604 DNA_RNApol_7kD: DNA d 33.7 19 0.00042 18.6 0.6 13 84-96 18-30 (32)
66 KOG2907 RNA polymerase I trans 33.3 13 0.00029 25.1 -0.1 17 82-98 6-22 (116)
67 PF10601 zf-LITAF-like: LITAF- 32.9 25 0.00053 21.3 1.1 16 80-95 55-70 (73)
68 PRK15103 paraquat-inducible me 32.9 29 0.00062 28.5 1.7 18 82-99 29-46 (419)
69 PHA00626 hypothetical protein 32.7 20 0.00044 21.2 0.6 8 85-92 2-9 (59)
70 PF11682 DUF3279: Protein of u 32.2 26 0.00057 24.1 1.2 17 80-96 25-41 (128)
71 PHA02450 hypothetical protein 32.0 20 0.00043 20.4 0.5 22 12-34 8-29 (53)
72 PF03892 NapB: Nitrate reducta 31.7 16 0.00034 25.4 -0.0 13 81-93 107-119 (133)
73 PF09855 DUF2082: Nucleic-acid 31.6 1.1E+02 0.0023 18.5 3.7 38 58-98 13-51 (64)
74 COG2888 Predicted Zn-ribbon RN 30.8 35 0.00076 20.4 1.4 19 78-96 22-40 (61)
75 PRK00564 hypA hydrogenase nick 30.6 21 0.00046 23.9 0.5 13 84-96 88-101 (117)
76 PF12172 DUF35_N: Rubredoxin-l 30.4 19 0.00042 18.8 0.2 10 83-92 25-34 (37)
77 TIGR03831 YgiT_finger YgiT-typ 30.3 24 0.00051 18.8 0.6 15 81-95 30-44 (46)
78 COG3024 Uncharacterized protei 30.2 31 0.00068 20.9 1.1 13 84-96 8-20 (65)
79 smart00834 CxxC_CXXC_SSSS Puta 29.9 26 0.00056 18.3 0.7 12 82-93 25-36 (41)
80 PF10955 DUF2757: Protein of u 29.7 29 0.00063 21.7 1.0 16 82-97 3-18 (76)
81 PF08792 A2L_zn_ribbon: A2L zi 29.5 32 0.00068 17.9 1.0 11 82-92 20-30 (33)
82 PF02591 DUF164: Putative zinc 29.4 29 0.00063 19.9 0.9 11 81-91 44-54 (56)
83 PF04423 Rad50_zn_hook: Rad50 28.8 22 0.00047 20.3 0.3 11 85-95 22-32 (54)
84 COG1885 Uncharacterized protei 28.8 63 0.0014 21.6 2.5 33 85-117 51-84 (115)
85 PF11781 RRN7: RNA polymerase 28.7 26 0.00057 18.5 0.6 12 82-93 24-35 (36)
86 PF03226 Yippee-Mis18: Yippee 28.6 28 0.00062 22.1 0.8 22 79-100 53-74 (96)
87 PF09862 DUF2089: Protein of u 28.4 41 0.00089 22.7 1.6 20 79-98 8-27 (113)
88 PF14446 Prok-RING_1: Prokaryo 28.2 36 0.00079 19.9 1.2 13 82-94 20-32 (54)
89 TIGR00155 pqiA_fam integral me 28.2 39 0.00085 27.5 1.8 18 82-99 32-49 (403)
90 TIGR03655 anti_R_Lar restricti 27.7 80 0.0017 17.8 2.6 11 85-95 28-38 (53)
91 PF00643 zf-B_box: B-box zinc 27.4 28 0.00061 18.4 0.6 14 81-94 13-26 (42)
92 PRK12380 hydrogenase nickel in 27.4 26 0.00057 23.3 0.5 12 84-95 87-98 (113)
93 PF05207 zf-CSL: CSL zinc fing 27.1 1E+02 0.0022 17.8 2.9 21 13-34 13-33 (55)
94 PF01599 Ribosomal_S27: Riboso 26.9 43 0.00094 19.0 1.3 17 82-98 17-35 (47)
95 COG4306 Uncharacterized protei 25.5 26 0.00056 24.3 0.2 16 82-97 67-82 (160)
96 PRK14018 trifunctional thiored 25.1 80 0.0017 26.8 3.1 18 84-101 468-485 (521)
97 PF10497 zf-4CXXC_R1: Zinc-fin 24.9 39 0.00084 22.3 1.0 13 39-51 69-81 (105)
98 PF04606 Ogr_Delta: Ogr/Delta- 24.4 35 0.00076 18.9 0.6 12 86-97 2-13 (47)
99 COG3058 FdhE Uncharacterized p 24.0 34 0.00074 26.8 0.7 13 82-94 184-196 (308)
100 COG0375 HybF Zn finger protein 23.9 92 0.002 21.1 2.7 18 81-98 84-101 (115)
101 KOG2463 Predicted RNA-binding 23.6 34 0.00074 27.5 0.6 16 78-93 252-267 (376)
102 cd00730 rubredoxin Rubredoxin; 23.6 44 0.00095 19.1 0.9 16 83-99 1-16 (50)
103 PF09538 FYDLN_acid: Protein o 23.1 35 0.00076 22.7 0.5 16 82-97 8-23 (108)
104 PF06054 CoiA: Competence prot 23.0 41 0.00089 27.1 1.0 16 81-96 28-43 (375)
105 PF13824 zf-Mss51: Zinc-finger 22.9 42 0.00091 19.7 0.7 15 82-96 13-27 (55)
106 COG2093 DNA-directed RNA polym 22.7 42 0.00092 20.3 0.7 13 84-96 19-31 (64)
107 PRK13130 H/ACA RNA-protein com 22.5 44 0.00096 19.6 0.8 14 83-96 17-30 (56)
108 TIGR01562 FdhE formate dehydro 22.1 37 0.0008 26.8 0.5 14 81-94 182-195 (305)
109 COG1579 Zn-ribbon protein, pos 22.1 33 0.00072 26.1 0.3 17 81-97 219-235 (239)
110 PRK05550 bifunctional methioni 22.0 1.3E+02 0.0028 23.5 3.5 18 81-98 80-97 (283)
111 TIGR01053 LSD1 zinc finger dom 22.0 45 0.00096 17.1 0.7 13 85-97 3-15 (31)
112 PF10892 DUF2688: Protein of u 21.9 27 0.00059 20.7 -0.2 16 83-98 10-25 (60)
113 smart00673 CARP Domain in CAPs 21.8 1.1E+02 0.0024 15.6 2.3 25 23-48 1-25 (38)
114 COG1545 Predicted nucleic-acid 21.8 1E+02 0.0022 21.2 2.7 11 83-93 43-53 (140)
115 COG2174 RPL34A Ribosomal prote 21.6 56 0.0012 21.2 1.2 23 79-101 30-52 (93)
116 PF14952 zf-tcix: Putative tre 21.5 43 0.00093 18.8 0.6 12 85-96 13-24 (44)
117 PF02943 FeThRed_B: Ferredoxin 21.3 33 0.00071 22.9 0.1 9 17-25 77-85 (108)
118 smart00067 GHA Glycoprotein ho 21.3 44 0.00094 21.2 0.6 34 14-47 47-83 (87)
119 PRK03564 formate dehydrogenase 21.0 40 0.00087 26.7 0.5 12 82-93 186-197 (309)
120 smart00508 PostSET Cysteine-ri 20.9 47 0.001 16.4 0.6 8 20-27 4-11 (26)
121 PF01258 zf-dskA_traR: Prokary 20.6 48 0.001 17.2 0.6 13 84-96 4-16 (36)
122 PF09723 Zn-ribbon_8: Zinc rib 20.4 50 0.0011 17.8 0.7 10 82-91 25-34 (42)
123 TIGR00373 conserved hypothetic 20.3 45 0.00098 23.5 0.6 12 85-96 130-141 (158)
124 PRK03954 ribonuclease P protei 20.1 19 0.00042 24.5 -1.2 17 78-94 59-75 (121)
125 TIGR01206 lysW lysine biosynth 20.0 49 0.0011 19.3 0.6 12 85-96 4-15 (54)
No 1
>PRK05417 glutathione-dependent formaldehyde-activating enzyme; Provisional
Probab=99.94 E-value=5.3e-27 Score=170.85 Aligned_cols=108 Identities=20% Similarity=0.357 Sum_probs=92.5
Q ss_pred CCceeEEe---eeCCC--eEEEEEcCCCCeeeeecChhhhcCCc----eeEEecCCCeEEcCCCCcceeEEecCCCeeee
Q 036084 13 DSGLHKGG---CRCRK--VRWRVRAPRSVEAWKCNCSDCSMRGN----VHFTVAPENFELLGNSEEFLTTHTFGTGTAKH 83 (126)
Q Consensus 13 ~~~~~~Gs---C~CGa--V~~~v~~~p~~~~~~ChC~~Crk~~g----~~~~~~~~~~~i~~g~~~~l~~y~~~~~~~~r 83 (126)
+...++|+ |+||+ |+|+++++|... ..|||++|||.+| .++.+|+++|+|+.+ ++.++.|. +++.++|
T Consensus 17 ~~~~f~Gg~l~ClCG~~aVry~v~g~p~~~-~~CHCs~CrK~sGs~fs~~a~vp~d~~~it~g-~~~l~~y~-ss~~i~R 93 (191)
T PRK05417 17 GAEGFAGGTLVCKCTSNPVEVRVKAQTAHN-HACGCTKCWKPEGALFSVVAVVPRDNVTVTAN-GDKLKVVD-ESATIQR 93 (191)
T ss_pred CcCccCCCCcEEeCCCcEEEEEEecCCCce-eeeChhhhhccccCcceEEEEEEhhheEEEeC-CcceEEEe-CCCCeEe
Confidence 35668999 99996 999999999876 8999999999975 467899999999877 67788887 6788999
Q ss_pred eeCCcCCcccccCCC----CCCCcEEEEEeeeecCCCCcccccccC
Q 036084 84 VFCKVCGITSFYVPR----GTPNGMLLLSDIKHNDGHNWESSLDQL 125 (126)
Q Consensus 84 ~FC~~CGs~l~~~~~----~~p~~~~v~v~~g~~d~~~~~~~~~~~ 125 (126)
+||++||++||.+.+ ..|+. +.|++|+||++.|.+|..++
T Consensus 94 ~FC~~CGS~L~~~~e~~~~~~pgl--~fV~~gllDd~~~~~P~~~i 137 (191)
T PRK05417 94 HACKECGVHMYGRIENKDHPFYGL--DFVHTELSQEQGWSAPGFAA 137 (191)
T ss_pred eeCCCCCCccccccccccCCCCCe--EEEehhhcCCCCCCCceEEe
Confidence 999999999999866 34565 57999999999999997664
No 2
>COG3791 Uncharacterized conserved protein [Function unknown]
Probab=99.94 E-value=9.7e-27 Score=161.39 Aligned_cols=102 Identities=24% Similarity=0.421 Sum_probs=81.8
Q ss_pred eEEeeeCCCeEEEEEcCCCCeeeeecChhhhcCCc-ee---EEecCCCeEEcCCCCcceeEEecCCCeeeeeeCCcCCcc
Q 036084 17 HKGGCRCRKVRWRVRAPRSVEAWKCNCSDCSMRGN-VH---FTVAPENFELLGNSEEFLTTHTFGTGTAKHVFCKVCGIT 92 (126)
Q Consensus 17 ~~GsC~CGaV~~~v~~~p~~~~~~ChC~~Crk~~g-~~---~~~~~~~~~i~~g~~~~l~~y~~~~~~~~r~FC~~CGs~ 92 (126)
+.|+||||+|+|++++++... .+|||++|||.+| ++ ..++.+.|+++.+ . ..|..++..+.|.||++||++
T Consensus 4 ~~G~C~CGaVrf~v~~~~~~~-~~ChCs~Crk~~G~~~~~~~~~~~~~~~~~~g-~---~~~~~~s~~~~r~FC~~CGs~ 78 (133)
T COG3791 4 IEGGCLCGAVRFEVEGDPGHV-SACHCSDCRKASGAAFAAYAVVPRDALRGTRG-L---PTYYFSSGSAGRGFCPTCGSP 78 (133)
T ss_pred cccceeeceEEEEEecCCCCc-eeeCchHhhhhhCCceeeeeecccceeeecCC-C---ceEEeecCCCCCeecccCCCc
Confidence 449999999999999999876 7999999999954 33 4567788888766 2 234446677899999999999
Q ss_pred cccCCCCCCCcEEEEEeeeecCCCCcccccccC
Q 036084 93 SFYVPRGTPNGMLLLSDIKHNDGHNWESSLDQL 125 (126)
Q Consensus 93 l~~~~~~~p~~~~v~v~~g~~d~~~~~~~~~~~ 125 (126)
||+...+.. -.+.|+++.||++++..|..++
T Consensus 79 l~~~~~~~~--~~~~v~~~~ld~p~~~~p~~~~ 109 (133)
T COG3791 79 LFWRGPDED--PFVGVNAGALDDPEFLPPQVQI 109 (133)
T ss_pred eEEecCCCC--ceEEEEEeeecCcccCCCceee
Confidence 999876643 2378999999998888876654
No 3
>TIGR02820 formald_GSH S-(hydroxymethyl)glutathione synthase. The formation of S-(hydroxymethyl)glutathione synthase from glutathione and formaldehyde occurs naturally, but this enzyme speeds its formation in some species as part of a pathway of formaldehyde detoxification.
Probab=99.93 E-value=5.9e-26 Score=164.10 Aligned_cols=109 Identities=21% Similarity=0.349 Sum_probs=89.1
Q ss_pred CceeEEe---eeCC--CeEEEEEcCCCCeeeeecChhhhcCCc----eeEEecCCCeEEcCCCCcceeEEecCCCeeeee
Q 036084 14 SGLHKGG---CRCR--KVRWRVRAPRSVEAWKCNCSDCSMRGN----VHFTVAPENFELLGNSEEFLTTHTFGTGTAKHV 84 (126)
Q Consensus 14 ~~~~~Gs---C~CG--aV~~~v~~~p~~~~~~ChC~~Crk~~g----~~~~~~~~~~~i~~g~~~~l~~y~~~~~~~~r~ 84 (126)
...++|+ |+|| +|+|+++++|... ..|||++|||++| .++.+++++|+|+.| ++.++.|. +++.+.|.
T Consensus 14 ~~~~~GgtasClCGsvaV~y~v~~~p~~v-~~CHCs~CRK~TGsafs~~~~v~~~~~~i~~G-~~~l~~Y~-ss~~~~R~ 90 (182)
T TIGR02820 14 STSFAGGTLKCLCTSNKVTVKIKGQSAHN-HACGCSKCWKPEGAIFSVVAVVPRDNVTVTAN-GDKLKVVD-ASATIQRH 90 (182)
T ss_pred CCCCCCCCcEEccCCCEEEEEEecCCCce-eeeChHHhhccccCcceEEEEEEhhheEEecC-CcceEEEe-CCCCEEee
Confidence 4458899 9999 6999999998766 8999999999975 367899999999877 67788897 67789999
Q ss_pred eCCcCCcccccCCCC-CCCcE-EEEEeeeecCCCCcccccccC
Q 036084 85 FCKVCGITSFYVPRG-TPNGM-LLLSDIKHNDGHNWESSLDQL 125 (126)
Q Consensus 85 FC~~CGs~l~~~~~~-~p~~~-~v~v~~g~~d~~~~~~~~~~~ 125 (126)
||++||++||++... .++.+ .+.|++|+||++.+++|..+|
T Consensus 91 FC~~CGS~L~~~~~~~~~~~~g~v~I~aGtLDd~~~~~P~~hI 133 (182)
T TIGR02820 91 ACKGCGTHMYGRIENKDHPFYGLDFIHTELSAEDGWSAPGFAA 133 (182)
T ss_pred cCCCCCCcccccccccCCCccceeEEEEeecCCCCcCCCeEEE
Confidence 999999999988642 23332 147999999997776777664
No 4
>PF04828 GFA: Glutathione-dependent formaldehyde-activating enzyme; InterPro: IPR006913 The GFA family consists mainly of glutathione-dependent formaldehyde-activating enzymes, but also includes centromere protein V and a fission yeast protein described as uncharacterised lyase. Glutathione-dependent formaldehyde-activating enzyme catalyse the condensation of formaldehyde and glutathione to S-hydroxymethylglutathione. All known members of this family contain 5 strongly conserved cysteine residues.; GO: 0016846 carbon-sulfur lyase activity, 0008152 metabolic process; PDB: 3FAC_B 1XA8_A 1X6M_B.
Probab=99.85 E-value=3.1e-22 Score=128.95 Aligned_cols=84 Identities=20% Similarity=0.372 Sum_probs=64.3
Q ss_pred eeecChhhhcCCc----eeEEecCCCeEEcCCCCcceeEEecCCCeeeeeeCCcCCcccccCCCCCCCcEEEEEeeeecC
Q 036084 39 WKCNCSDCSMRGN----VHFTVAPENFELLGNSEEFLTTHTFGTGTAKHVFCKVCGITSFYVPRGTPNGMLLLSDIKHND 114 (126)
Q Consensus 39 ~~ChC~~Crk~~g----~~~~~~~~~~~i~~g~~~~l~~y~~~~~~~~r~FC~~CGs~l~~~~~~~p~~~~v~v~~g~~d 114 (126)
+.|||++|||.+| .++.+|+++|+|+.| ++.++.|..+++.++|+||++||++||......|+. +.|++|+||
T Consensus 1 ~~ChC~~Cr~~~g~~~~~~~~~~~~~~~~~~g-~~~l~~y~~s~~~~~r~FC~~CGs~l~~~~~~~~~~--~~V~~g~ld 77 (92)
T PF04828_consen 1 YVCHCSDCRKWSGSPFSAWAIVPKDDFRWTSG-SENLKEYQFSGKGVERYFCPTCGSPLFSEDERDPDL--VGVNAGTLD 77 (92)
T ss_dssp EEE-STTCHHHTT-SSEEEEEEEGGGEEEEE--GGGEEEC--TTSSCEEEEETTT--EEEEEESSTTTE--EEEEGGGBT
T ss_pred CEeeChHHhcccCCceeeEEEEcccceEEeec-cccceEEEeCCCcCcCcccCCCCCeeecccCCCCCE--EEEEeEeeC
Confidence 4799999999987 578899999999888 678999986788899999999999999876666775 689999999
Q ss_pred CCCcccccccC
Q 036084 115 GHNWESSLDQL 125 (126)
Q Consensus 115 ~~~~~~~~~~~ 125 (126)
+++.++|..+|
T Consensus 78 ~~~~~~p~~hi 88 (92)
T PF04828_consen 78 DPDEFKPKAHI 88 (92)
T ss_dssp T--S--EEEEE
T ss_pred CCCCCCCEEEE
Confidence 99988887665
No 5
>KOG4192 consensus Uncharacterized conserved protein [Function unknown]
Probab=99.84 E-value=1.1e-20 Score=126.77 Aligned_cols=110 Identities=43% Similarity=0.874 Sum_probs=97.1
Q ss_pred CCceeEEeeeCCCeEEEEEcCCCCeeeeecChhhhcCCceeEEecCCCeEEcCCCCcceeEEecCCCeeeeeeCCcCCcc
Q 036084 13 DSGLHKGGCRCRKVRWRVRAPRSVEAWKCNCSDCSMRGNVHFTVAPENFELLGNSEEFLTTHTFGTGTAKHVFCKVCGIT 92 (126)
Q Consensus 13 ~~~~~~GsC~CGaV~~~v~~~p~~~~~~ChC~~Crk~~g~~~~~~~~~~~i~~g~~~~l~~y~~~~~~~~r~FC~~CGs~ 92 (126)
+.+..+|+||||+|+|++.++....+..|+|++|++....++.+|..+|.+..| .+.+.+|.++...+.+.||+.||..
T Consensus 4 ~lV~H~GgCHCGaVkw~v~ap~~l~~~~Cncrics~k~~~hfivpas~f~ll~g-~efitty~~gth~aqhtfck~cGV~ 82 (134)
T KOG4192|consen 4 GLVQHTGGCHCGAVKWSVWAPADLDGCDCNCRICSKKQNRHFIVPASRFVLLVG-AEFITTYTFGTHQAQHTFCKRCGVQ 82 (134)
T ss_pred cceeecCCcccceEEEEEecccceEEeeccchhhhhccceEEEEeccceEEEeC-cceEEEEEeccchhheeeeccccce
Confidence 467789999999999999999876668899999999999999999999999888 7889999988889999999999999
Q ss_pred cccCCCCCCCcEEE-----------EEeeeecCCCCcccccc
Q 036084 93 SFYVPRGTPNGMLL-----------LSDIKHNDGHNWESSLD 123 (126)
Q Consensus 93 l~~~~~~~p~~~~v-----------~v~~g~~d~~~~~~~~~ 123 (126)
-|+..++.|+.+.| .|.+-.|||.+|+..++
T Consensus 83 sf~~~rs~p~~~~i~phCld~gTlr~v~~~~fnGqdwe~~~e 124 (134)
T KOG4192|consen 83 SFYSPRSNPYGKGIAPHCLDEGTLRSVVWEEFNGQDWEATME 124 (134)
T ss_pred eccccccCCCceeecceeecCCceeEEEEEEecCcchhHhhh
Confidence 99999988887665 57788888888776544
No 6
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=91.92 E-value=0.05 Score=26.36 Aligned_cols=12 Identities=33% Similarity=0.811 Sum_probs=9.5
Q ss_pred eeeeCCcCCccc
Q 036084 82 KHVFCKVCGITS 93 (126)
Q Consensus 82 ~r~FC~~CGs~l 93 (126)
.-.||++||++|
T Consensus 12 ~~~fC~~CG~~l 23 (23)
T PF13240_consen 12 DAKFCPNCGTPL 23 (23)
T ss_pred cCcchhhhCCcC
Confidence 446899999875
No 7
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=91.41 E-value=0.064 Score=26.63 Aligned_cols=13 Identities=31% Similarity=0.751 Sum_probs=10.1
Q ss_pred eeeeeCCcCCccc
Q 036084 81 AKHVFCKVCGITS 93 (126)
Q Consensus 81 ~~r~FC~~CGs~l 93 (126)
....||++||++|
T Consensus 14 ~~~~fC~~CG~~L 26 (26)
T PF13248_consen 14 PDAKFCPNCGAKL 26 (26)
T ss_pred cccccChhhCCCC
Confidence 3457999999875
No 8
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=89.45 E-value=0.14 Score=27.21 Aligned_cols=15 Identities=27% Similarity=0.337 Sum_probs=6.7
Q ss_pred eeCCcCCcccccCCC
Q 036084 84 VFCKVCGITSFYVPR 98 (126)
Q Consensus 84 ~FC~~CGs~l~~~~~ 98 (126)
.||++||.+|-....
T Consensus 1 kfC~~CG~~l~~~ip 15 (34)
T PF14803_consen 1 KFCPQCGGPLERRIP 15 (34)
T ss_dssp -B-TTT--B-EEE--
T ss_pred CccccccChhhhhcC
Confidence 399999999866543
No 9
>PF09297 zf-NADH-PPase: NADH pyrophosphatase zinc ribbon domain; InterPro: IPR015376 This domain has a zinc ribbon structure and is often found between two NUDIX domains.; GO: 0016787 hydrolase activity, 0046872 metal ion binding; PDB: 1VK6_A 2GB5_A.
Probab=87.97 E-value=0.16 Score=26.35 Aligned_cols=16 Identities=38% Similarity=0.841 Sum_probs=9.1
Q ss_pred eeeeCCcCCcccccCC
Q 036084 82 KHVFCKVCGITSFYVP 97 (126)
Q Consensus 82 ~r~FC~~CGs~l~~~~ 97 (126)
++.||+.||+++....
T Consensus 2 ~~rfC~~CG~~t~~~~ 17 (32)
T PF09297_consen 2 NHRFCGRCGAPTKPAP 17 (32)
T ss_dssp TTSB-TTT--BEEE-S
T ss_pred CCcccCcCCccccCCC
Confidence 3569999999986654
No 10
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=84.53 E-value=1.2 Score=25.71 Aligned_cols=17 Identities=35% Similarity=0.755 Sum_probs=11.6
Q ss_pred eeeeCCcCCcccccCCC
Q 036084 82 KHVFCKVCGITSFYVPR 98 (126)
Q Consensus 82 ~r~FC~~CGs~l~~~~~ 98 (126)
.+.|||+||-.+|...+
T Consensus 18 k~~~CPrCG~gvfmA~H 34 (51)
T COG1998 18 KNRFCPRCGPGVFMADH 34 (51)
T ss_pred ccccCCCCCCcchhhhc
Confidence 44589999976665443
No 11
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=84.12 E-value=1.3 Score=25.47 Aligned_cols=22 Identities=27% Similarity=0.504 Sum_probs=13.1
Q ss_pred eeEEecCCCee--eeeeCCcCCcc
Q 036084 71 LTTHTFGTGTA--KHVFCKVCGIT 92 (126)
Q Consensus 71 l~~y~~~~~~~--~r~FC~~CGs~ 92 (126)
+..|.-.+..+ .+.|||+||+.
T Consensus 6 ~~~y~v~~~~v~~~~~fCP~Cg~~ 29 (50)
T PRK00432 6 REYYEVDGGKVKRKNKFCPRCGSG 29 (50)
T ss_pred eeeEEECCCEEEEccCcCcCCCcc
Confidence 34454333333 34589999996
No 12
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=82.26 E-value=0.65 Score=26.27 Aligned_cols=13 Identities=31% Similarity=0.628 Sum_probs=10.9
Q ss_pred eCCcCCcccccCC
Q 036084 85 FCKVCGITSFYVP 97 (126)
Q Consensus 85 FC~~CGs~l~~~~ 97 (126)
||+.||..|+...
T Consensus 2 FCp~Cg~~l~~~~ 14 (52)
T smart00661 2 FCPKCGNMLIPKE 14 (52)
T ss_pred CCCCCCCcccccc
Confidence 9999999887653
No 13
>PF02150 RNA_POL_M_15KD: RNA polymerases M/15 Kd subunit; InterPro: IPR001529 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. In archaebacteria, there is generally a single form of RNA polymerase which also consist of an oligomeric assemblage of 10 to 13 polypeptides. It has recently been shown [], [] that small subunits of about 15 kDa, found in polymerase types I and II, are highly conserved. These proteins contain a probable zinc finger in their N-terminal region and a C-terminal zinc ribbon domain (see IPR001222 from INTERPRO).; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3H0G_I 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I ....
Probab=81.63 E-value=0.59 Score=24.85 Aligned_cols=15 Identities=27% Similarity=0.565 Sum_probs=11.6
Q ss_pred eeCCcCCcccccCCC
Q 036084 84 VFCKVCGITSFYVPR 98 (126)
Q Consensus 84 ~FC~~CGs~l~~~~~ 98 (126)
.||+.||.-|+....
T Consensus 2 ~FCp~C~nlL~p~~~ 16 (35)
T PF02150_consen 2 RFCPECGNLLYPKED 16 (35)
T ss_dssp -BETTTTSBEEEEEE
T ss_pred eeCCCCCccceEcCC
Confidence 599999999976543
No 14
>PF03119 DNA_ligase_ZBD: NAD-dependent DNA ligase C4 zinc finger domain; InterPro: IPR004149 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the zinc finger domain found in NAD-dependent DNA ligases. DNA ligases catalyse the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilizing either ATP or NAD(+) as a cofactor []. This domain is a small zinc binding motif that is presumably DNA binding. It is found only in NAD-dependent DNA ligases. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003911 DNA ligase (NAD+) activity, 0006260 DNA replication, 0006281 DNA repair; PDB: 1DGS_A 1V9P_B 2OWO_A.
Probab=78.16 E-value=1.1 Score=22.60 Aligned_cols=13 Identities=31% Similarity=0.572 Sum_probs=7.2
Q ss_pred eCCcCCcccccCC
Q 036084 85 FCKVCGITSFYVP 97 (126)
Q Consensus 85 FC~~CGs~l~~~~ 97 (126)
+||.||+.|....
T Consensus 1 ~CP~C~s~l~~~~ 13 (28)
T PF03119_consen 1 TCPVCGSKLVREE 13 (28)
T ss_dssp B-TTT--BEEE-C
T ss_pred CcCCCCCEeEcCC
Confidence 6999999998543
No 15
>PF08772 NOB1_Zn_bind: Nin one binding (NOB1) Zn-ribbon like; InterPro: IPR014881 This entry corresponds to a zinc ribbon and is found on the RNA binding protein NOB1. ; PDB: 2CON_A.
Probab=77.95 E-value=0.8 Score=28.54 Aligned_cols=16 Identities=25% Similarity=0.667 Sum_probs=6.6
Q ss_pred eeeeeeCCcCCccccc
Q 036084 80 TAKHVFCKVCGITSFY 95 (126)
Q Consensus 80 ~~~r~FC~~CGs~l~~ 95 (126)
...+.|||.||-....
T Consensus 21 ~~~k~FCp~CGn~TL~ 36 (73)
T PF08772_consen 21 DMTKQFCPKCGNATLK 36 (73)
T ss_dssp -SS--S-SSS--S--E
T ss_pred CCCceeCcccCCCcce
Confidence 4688999999987543
No 16
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=70.56 E-value=1.9 Score=29.90 Aligned_cols=19 Identities=21% Similarity=0.392 Sum_probs=14.4
Q ss_pred CCeeeeeeCCcCCcccccC
Q 036084 78 TGTAKHVFCKVCGITSFYV 96 (126)
Q Consensus 78 ~~~~~r~FC~~CGs~l~~~ 96 (126)
|....-..|+.||+|||-.
T Consensus 23 GAkML~~hCp~Cg~PLF~K 41 (131)
T COG1645 23 GAKMLAKHCPKCGTPLFRK 41 (131)
T ss_pred hhHHHHhhCcccCCcceee
Confidence 4445556799999999983
No 17
>PF06677 Auto_anti-p27: Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27); InterPro: IPR009563 The proteins in this entry are functionally uncharacterised and include several proteins that characterise Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27). It is thought that the potential association of anti-p27 with anti-centromere antibodies suggests that autoantigen p27 might play a role in mitosis [].
Probab=68.70 E-value=2.3 Score=23.49 Aligned_cols=13 Identities=23% Similarity=0.557 Sum_probs=11.0
Q ss_pred eeeCCcCCccccc
Q 036084 83 HVFCKVCGITSFY 95 (126)
Q Consensus 83 r~FC~~CGs~l~~ 95 (126)
-..|+.||+||+.
T Consensus 17 ~~~Cp~C~~PL~~ 29 (41)
T PF06677_consen 17 DEHCPDCGTPLMR 29 (41)
T ss_pred cCccCCCCCeeEE
Confidence 3469999999987
No 18
>PF04032 Rpr2: RNAse P Rpr2/Rpp21/SNM1 subunit domain; InterPro: IPR007175 This family contains a ribonuclease P subunit of human and yeast. Other members of the family include the probable archaeal homologues. This subunit possibly binds the precursor tRNA [].; PDB: 2K3R_A 2KI7_B 2ZAE_B 1X0T_A.
Probab=68.32 E-value=1.8 Score=26.92 Aligned_cols=16 Identities=31% Similarity=0.609 Sum_probs=8.9
Q ss_pred CeeeeeeCCcCCcccc
Q 036084 79 GTAKHVFCKVCGITSF 94 (126)
Q Consensus 79 ~~~~r~FC~~CGs~l~ 94 (126)
+...|.||+.||+.+-
T Consensus 42 ~~~kr~~Ck~C~~~li 57 (85)
T PF04032_consen 42 PEIKRTICKKCGSLLI 57 (85)
T ss_dssp TTCCCTB-TTT--B--
T ss_pred hHHhcccccCCCCEEe
Confidence 3468899999999874
No 19
>TIGR00357 methionine-R-sulfoxide reductase. This model describes a domain found in PilB, a protein important for pilin expression, N-terminal to a domain coextensive to with the known peptide methionine sulfoxide reductase (MsrA), a protein repair enzyme, of E. coli. Among the early completed genomes, this module is found if and only if MsrA is also found, whether N-terminal to MsrA (as for Helicobacter pylori), C-terminal (as for Treponema pallidum), or in a separate polypeptide. Although the function of this region is not clear, an auxiliary function to MsrA is suggested.
Probab=64.97 E-value=11 Score=26.17 Aligned_cols=20 Identities=25% Similarity=0.328 Sum_probs=15.8
Q ss_pred eeeeCCcCCcccccCCCCCC
Q 036084 82 KHVFCKVCGITSFYVPRGTP 101 (126)
Q Consensus 82 ~r~FC~~CGs~l~~~~~~~p 101 (126)
.-.-|.+||++|.+...+.|
T Consensus 88 tEv~C~~Cg~HLGHVF~DGP 107 (134)
T TIGR00357 88 TEVRCRNCDAHLGHVFDDGP 107 (134)
T ss_pred EEEEecCCCCccCcccCCCC
Confidence 33689999999988776655
No 20
>PF07754 DUF1610: Domain of unknown function (DUF1610); InterPro: IPR011668 This domain is found in archaeal species. It is likely to bind zinc via its four well-conserved cysteine residues.
Probab=63.83 E-value=4.6 Score=19.74 Aligned_cols=10 Identities=40% Similarity=0.757 Sum_probs=8.3
Q ss_pred eeeeeCCcCC
Q 036084 81 AKHVFCKVCG 90 (126)
Q Consensus 81 ~~r~FC~~CG 90 (126)
..++-||+||
T Consensus 14 ~v~f~CPnCG 23 (24)
T PF07754_consen 14 AVPFPCPNCG 23 (24)
T ss_pred CceEeCCCCC
Confidence 5677899998
No 21
>COG4469 CoiA Competence protein CoiA-like family, contains a predicted nuclease domain [General function prediction only]
Probab=62.80 E-value=3.2 Score=33.06 Aligned_cols=15 Identities=27% Similarity=0.711 Sum_probs=12.9
Q ss_pred eeeCCcCCcccccCC
Q 036084 83 HVFCKVCGITSFYVP 97 (126)
Q Consensus 83 r~FC~~CGs~l~~~~ 97 (126)
|+|||.||++|.-..
T Consensus 25 ~ffCPaC~~~l~lK~ 39 (342)
T COG4469 25 RFFCPACGSQLILKQ 39 (342)
T ss_pred ccccCCCCCeeeeec
Confidence 799999999997653
No 22
>PRK12496 hypothetical protein; Provisional
Probab=61.00 E-value=3.4 Score=29.49 Aligned_cols=16 Identities=19% Similarity=0.397 Sum_probs=12.4
Q ss_pred eeeeCCcCCcccccCC
Q 036084 82 KHVFCKVCGITSFYVP 97 (126)
Q Consensus 82 ~r~FC~~CGs~l~~~~ 97 (126)
.+.||+.||+++....
T Consensus 142 ~~~~C~~CG~~~~r~~ 157 (164)
T PRK12496 142 PDDVCEICGSPVKRKM 157 (164)
T ss_pred CCCcCCCCCChhhhcc
Confidence 4568999999996544
No 23
>PF12773 DZR: Double zinc ribbon
Probab=60.51 E-value=3 Score=23.30 Aligned_cols=13 Identities=31% Similarity=0.657 Sum_probs=11.4
Q ss_pred eeeeCCcCCcccc
Q 036084 82 KHVFCKVCGITSF 94 (126)
Q Consensus 82 ~r~FC~~CGs~l~ 94 (126)
...||+.||+.|.
T Consensus 11 ~~~fC~~CG~~l~ 23 (50)
T PF12773_consen 11 DAKFCPHCGTPLP 23 (50)
T ss_pred cccCChhhcCChh
Confidence 4679999999998
No 24
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=60.26 E-value=6.3 Score=21.81 Aligned_cols=16 Identities=31% Similarity=0.700 Sum_probs=12.8
Q ss_pred eeeCCcCCcccccCCC
Q 036084 83 HVFCKVCGITSFYVPR 98 (126)
Q Consensus 83 r~FC~~CGs~l~~~~~ 98 (126)
...|+.||+++.....
T Consensus 21 ~~~Cp~CG~~~~~~~~ 36 (46)
T PRK00398 21 GVRCPYCGYRILFKER 36 (46)
T ss_pred ceECCCCCCeEEEccC
Confidence 5679999999987544
No 25
>PRK00420 hypothetical protein; Validated
Probab=59.76 E-value=4.2 Score=27.39 Aligned_cols=13 Identities=38% Similarity=0.961 Sum_probs=11.1
Q ss_pred eeCCcCCcccccC
Q 036084 84 VFCKVCGITSFYV 96 (126)
Q Consensus 84 ~FC~~CGs~l~~~ 96 (126)
..||.||+++|..
T Consensus 24 ~~CP~Cg~pLf~l 36 (112)
T PRK00420 24 KHCPVCGLPLFEL 36 (112)
T ss_pred CCCCCCCCcceec
Confidence 5699999999974
No 26
>PRK00222 methionine sulfoxide reductase B; Provisional
Probab=58.83 E-value=15 Score=25.82 Aligned_cols=19 Identities=26% Similarity=0.261 Sum_probs=15.1
Q ss_pred eeeCCcCCcccccCCCCCC
Q 036084 83 HVFCKVCGITSFYVPRGTP 101 (126)
Q Consensus 83 r~FC~~CGs~l~~~~~~~p 101 (126)
-.-|.+||++|.+...+.|
T Consensus 92 Ev~C~~Cg~HLGHVF~DGP 110 (142)
T PRK00222 92 EVRCANCDSHLGHVFPDGP 110 (142)
T ss_pred EEEeCCCCCccCcccCCCC
Confidence 3689999999988766644
No 27
>TIGR01384 TFS_arch transcription factor S, archaeal. There has been an apparent duplication event in the Halobacteriaceae lineage (Haloarcula, Haloferax, Haloquadratum, Halobacterium and Natromonas). There appears to be a separate duplication in Methanosphaera stadtmanae.
Probab=56.29 E-value=4.8 Score=26.10 Aligned_cols=12 Identities=33% Similarity=0.634 Sum_probs=9.8
Q ss_pred eCCcCCcccccC
Q 036084 85 FCKVCGITSFYV 96 (126)
Q Consensus 85 FC~~CGs~l~~~ 96 (126)
||++||..|...
T Consensus 2 fC~~Cg~~l~~~ 13 (104)
T TIGR01384 2 FCPKCGSLMTPK 13 (104)
T ss_pred CCcccCcccccC
Confidence 899999988653
No 28
>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain. This domain contains a CXXCX(19)CXXC motif suggestive of both zinc fingers and thioredoxin, usually found at the N-terminus of prokaryotic proteins. One partially characterized gene, agmX, is among a large set in Myxococcus whose interruption affects adventurous gliding motility.
Probab=54.18 E-value=8.6 Score=20.17 Aligned_cols=13 Identities=31% Similarity=0.641 Sum_probs=10.5
Q ss_pred eeeCCcCCccccc
Q 036084 83 HVFCKVCGITSFY 95 (126)
Q Consensus 83 r~FC~~CGs~l~~ 95 (126)
...|++||..++.
T Consensus 25 ~v~C~~C~~~~~~ 37 (38)
T TIGR02098 25 KVRCGKCGHVWYA 37 (38)
T ss_pred EEECCCCCCEEEe
Confidence 5779999998754
No 29
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=52.39 E-value=6.9 Score=30.47 Aligned_cols=15 Identities=33% Similarity=0.857 Sum_probs=12.1
Q ss_pred eeeeCCcCCcccccC
Q 036084 82 KHVFCKVCGITSFYV 96 (126)
Q Consensus 82 ~r~FC~~CGs~l~~~ 96 (126)
++.||+.||++++..
T Consensus 110 ~~RFCg~CG~~~~~~ 124 (279)
T COG2816 110 SHRFCGRCGTKTYPR 124 (279)
T ss_pred hCcCCCCCCCcCccc
Confidence 566999999998765
No 30
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=50.83 E-value=6.8 Score=26.30 Aligned_cols=13 Identities=31% Similarity=0.703 Sum_probs=11.3
Q ss_pred eeCCcCCcccccC
Q 036084 84 VFCKVCGITSFYV 96 (126)
Q Consensus 84 ~FC~~CGs~l~~~ 96 (126)
.||+.||+-|+..
T Consensus 3 ~FCp~Cgsll~p~ 15 (113)
T COG1594 3 RFCPKCGSLLYPK 15 (113)
T ss_pred cccCCccCeeEEe
Confidence 5999999999874
No 31
>PRK00241 nudC NADH pyrophosphatase; Reviewed
Probab=49.75 E-value=6.9 Score=29.83 Aligned_cols=15 Identities=33% Similarity=0.685 Sum_probs=11.8
Q ss_pred eeeeCCcCCcccccC
Q 036084 82 KHVFCKVCGITSFYV 96 (126)
Q Consensus 82 ~r~FC~~CGs~l~~~ 96 (126)
++.||+.||+++...
T Consensus 98 ~~~fC~~CG~~~~~~ 112 (256)
T PRK00241 98 SHRFCGYCGHPMHPS 112 (256)
T ss_pred cCccccccCCCCeec
Confidence 567999999997543
No 32
>COG0229 Conserved domain frequently associated with peptide methionine sulfoxide reductase [Posttranslational modification, protein turnover, chaperones]
Probab=49.55 E-value=23 Score=24.77 Aligned_cols=32 Identities=19% Similarity=0.082 Sum_probs=21.0
Q ss_pred ceeEEecCCCeeee--eeCCcCCcccccCCCCCC
Q 036084 70 FLTTHTFGTGTAKH--VFCKVCGITSFYVPRGTP 101 (126)
Q Consensus 70 ~l~~y~~~~~~~~r--~FC~~CGs~l~~~~~~~p 101 (126)
.+....+.+.+..| .-|.+|+++|.+...+.|
T Consensus 76 ~I~~~~D~S~gM~RtEVrc~~c~sHLGHVF~DGP 109 (140)
T COG0229 76 AITYKEDRSHGMVRTEVRCANCDSHLGHVFPDGP 109 (140)
T ss_pred cceEeeccCCCcEEEEEEecCCCCccccccCCCC
Confidence 34444444444444 479999999998877655
No 33
>PF13408 Zn_ribbon_recom: Recombinase zinc beta ribbon domain
Probab=48.54 E-value=8.1 Score=21.86 Aligned_cols=17 Identities=24% Similarity=0.337 Sum_probs=13.3
Q ss_pred eeeCCcCCcccccCCCC
Q 036084 83 HVFCKVCGITSFYVPRG 99 (126)
Q Consensus 83 r~FC~~CGs~l~~~~~~ 99 (126)
..+|+.||.++......
T Consensus 5 ~l~C~~CG~~m~~~~~~ 21 (58)
T PF13408_consen 5 LLRCGHCGSKMTRRKRK 21 (58)
T ss_pred cEEcccCCcEeEEEECC
Confidence 46899999999876543
No 34
>COG1439 Predicted nucleic acid-binding protein, consists of a PIN domain and a Zn-ribbon module [General function prediction only]
Probab=47.97 E-value=7.8 Score=28.21 Aligned_cols=15 Identities=27% Similarity=0.569 Sum_probs=11.9
Q ss_pred eeeeCCcCCcccccC
Q 036084 82 KHVFCKVCGITSFYV 96 (126)
Q Consensus 82 ~r~FC~~CGs~l~~~ 96 (126)
...||+.||+++--.
T Consensus 152 ~~~~Cp~CG~~~~~~ 166 (177)
T COG1439 152 PKDFCPICGSPLKRK 166 (177)
T ss_pred CCCcCCCCCCceEEe
Confidence 467999999997544
No 35
>PF00301 Rubredoxin: Rubredoxin; InterPro: IPR004039 Rubredoxin is a low molecular weight iron-containing bacterial protein involved in electron transfer [, ], sometimes replacing ferredoxin as an electron carrier []. The 3-D structures of a number of rubredoxins have been solved [, ]. The fold belongs to the alpha+beta class, with 2 alpha-helices and 2-3 beta-strands. Its active site contains an iron ion which is co-ordinated by the sulphurs of four conserved cysteine residues forming an almost regular tetrahedron. The conserved cysteines reside on two loops, which are the most conserved regions of the protein. In addition, a ring of acidic residues in the proximity of the [Fe(Cys)4] centre is also well-conserved []. ; GO: 0009055 electron carrier activity, 0046872 metal ion binding; PDB: 2RDV_C 1RDV_A 1S24_A 1T9O_B 1B2J_A 1SMW_A 2PVE_B 1BFY_A 1T9P_C 1C09_C ....
Probab=47.79 E-value=5.5 Score=22.58 Aligned_cols=18 Identities=33% Similarity=0.802 Sum_probs=12.0
Q ss_pred eeeCCcCCcccccCCCCCC
Q 036084 83 HVFCKVCGITSFYVPRGTP 101 (126)
Q Consensus 83 r~FC~~CGs~l~~~~~~~p 101 (126)
|+.|+.|| .+|......|
T Consensus 1 ky~C~~Cg-yvYd~~~Gd~ 18 (47)
T PF00301_consen 1 KYQCPVCG-YVYDPEKGDP 18 (47)
T ss_dssp EEEETTTS-BEEETTTBBG
T ss_pred CcCCCCCC-EEEcCCcCCc
Confidence 57899999 6665544433
No 36
>PRK12495 hypothetical protein; Provisional
Probab=46.37 E-value=7.7 Score=29.21 Aligned_cols=18 Identities=28% Similarity=0.564 Sum_probs=14.3
Q ss_pred CCeeeeeeCCcCCccccc
Q 036084 78 TGTAKHVFCKVCGITSFY 95 (126)
Q Consensus 78 ~~~~~r~FC~~CGs~l~~ 95 (126)
+......+|..||.+||.
T Consensus 37 gatmsa~hC~~CG~PIpa 54 (226)
T PRK12495 37 GATMTNAHCDECGDPIFR 54 (226)
T ss_pred hcccchhhcccccCcccC
Confidence 445677889999999994
No 37
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=46.14 E-value=10 Score=21.14 Aligned_cols=17 Identities=35% Similarity=0.757 Sum_probs=13.5
Q ss_pred eeeeCCcCCcccccCCC
Q 036084 82 KHVFCKVCGITSFYVPR 98 (126)
Q Consensus 82 ~r~FC~~CGs~l~~~~~ 98 (126)
.-..|++||..|.+..+
T Consensus 18 ~~irC~~CG~rIlyK~R 34 (44)
T smart00659 18 DVVRCRECGYRILYKKR 34 (44)
T ss_pred CceECCCCCceEEEEeC
Confidence 33569999999998765
No 38
>PF13842 Tnp_zf-ribbon_2: DDE_Tnp_1-like zinc-ribbon
Probab=46.11 E-value=14 Score=19.04 Aligned_cols=13 Identities=15% Similarity=0.590 Sum_probs=10.8
Q ss_pred eeeeCCcCCcccc
Q 036084 82 KHVFCKVCGITSF 94 (126)
Q Consensus 82 ~r~FC~~CGs~l~ 94 (126)
++++|..|+.+|-
T Consensus 15 T~~~C~~C~v~lC 27 (32)
T PF13842_consen 15 TRYMCSKCDVPLC 27 (32)
T ss_pred eEEEccCCCCccc
Confidence 8899999987664
No 39
>PF09151 DUF1936: Domain of unknown function (DUF1936); InterPro: IPR015234 This domain is found in a set of hypothetical archaeal proteins. Its exact function has not, as yet, been defined. ; PDB: 2QH1_B 1PVM_B.
Probab=45.43 E-value=15 Score=19.15 Aligned_cols=13 Identities=23% Similarity=0.662 Sum_probs=8.2
Q ss_pred eeCCcCCcccccC
Q 036084 84 VFCKVCGITSFYV 96 (126)
Q Consensus 84 ~FC~~CGs~l~~~ 96 (126)
+.|+.||..+...
T Consensus 2 hlcpkcgvgvl~p 14 (36)
T PF09151_consen 2 HLCPKCGVGVLEP 14 (36)
T ss_dssp -B-TTTSSSBEEE
T ss_pred ccCCccCceEEEE
Confidence 5699999877543
No 40
>PF08882 Acetone_carb_G: Acetone carboxylase gamma subunit; InterPro: IPR014979 Acetone carboxylase is the key enzyme of bacterial acetone metabolism, catalysing the condensation of acetone and CO2 to form acetoacetate [] according to the following reaction: CH3COCH3 + CO2 + ATP = CH3COCH2COO- + AMP + 2P(i) + H+ It has the subunit composition: (alpha(2)beta(2)gamma(2) multimers of 85kDa, 78kDa, and 20kDa subunits). It is expressed to high levels (17 to 25% of soluble protein) in cells grown with acetone as the carbon source but are not present at detectable levels in cells grown with other carbon sources []. Acetone carboxylase may enable Helicobacter pylori to survive off acetone in the stomach of humans and other mammals where it is the etiological agent of peptic ulcer disease []. This entry represents the family of gamma subunit-related acetone carboxylase proteins.
Probab=45.35 E-value=14 Score=24.87 Aligned_cols=17 Identities=18% Similarity=0.446 Sum_probs=12.9
Q ss_pred eeeeeCCcCCcccccCC
Q 036084 81 AKHVFCKVCGITSFYVP 97 (126)
Q Consensus 81 ~~r~FC~~CGs~l~~~~ 97 (126)
+.-++|+.||+.+=.+.
T Consensus 72 irEyyCP~Cgt~levE~ 88 (112)
T PF08882_consen 72 IREYYCPGCGTQLEVEA 88 (112)
T ss_pred EEEEECCCCcceeEEcc
Confidence 45578999999986554
No 41
>KOG2906 consensus RNA polymerase III subunit C11 [Transcription]
Probab=45.18 E-value=9.4 Score=25.21 Aligned_cols=15 Identities=27% Similarity=0.660 Sum_probs=12.0
Q ss_pred eeCCcCCcccccCCC
Q 036084 84 VFCKVCGITSFYVPR 98 (126)
Q Consensus 84 ~FC~~CGs~l~~~~~ 98 (126)
.|||.||..|-....
T Consensus 2 ~FCP~Cgn~Live~g 16 (105)
T KOG2906|consen 2 LFCPTCGNMLIVESG 16 (105)
T ss_pred cccCCCCCEEEEecC
Confidence 599999999876543
No 42
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=45.10 E-value=15 Score=21.97 Aligned_cols=16 Identities=31% Similarity=0.677 Sum_probs=12.0
Q ss_pred eeeeeCCcCCcccccC
Q 036084 81 AKHVFCKVCGITSFYV 96 (126)
Q Consensus 81 ~~r~FC~~CGs~l~~~ 96 (126)
..++.|++||..+-++
T Consensus 23 ~~~F~CPnCG~~~I~R 38 (59)
T PRK14890 23 AVKFLCPNCGEVIIYR 38 (59)
T ss_pred cCEeeCCCCCCeeEee
Confidence 5778899999984333
No 43
>PF09889 DUF2116: Uncharacterized protein containing a Zn-ribbon (DUF2116); InterPro: IPR019216 This entry contains various hypothetical prokaryotic proteins whose functions are unknown. They contain a conserved zinc ribbon motif in the N-terminal part and a predicted transmembrane segment in the C-terminal part.
Probab=44.97 E-value=9.7 Score=22.69 Aligned_cols=13 Identities=38% Similarity=0.664 Sum_probs=10.2
Q ss_pred eeeCCcCCccccc
Q 036084 83 HVFCKVCGITSFY 95 (126)
Q Consensus 83 r~FC~~CGs~l~~ 95 (126)
|.-|++||.+|-.
T Consensus 3 HkHC~~CG~~Ip~ 15 (59)
T PF09889_consen 3 HKHCPVCGKPIPP 15 (59)
T ss_pred CCcCCcCCCcCCc
Confidence 4569999999853
No 44
>PF11062 DUF2863: Protein of unknown function (DUF2863); InterPro: IPR021292 This bacterial family of proteins have no known function.
Probab=42.12 E-value=13 Score=30.34 Aligned_cols=15 Identities=33% Similarity=0.813 Sum_probs=12.6
Q ss_pred eeCCcCCcccccCCC
Q 036084 84 VFCKVCGITSFYVPR 98 (126)
Q Consensus 84 ~FC~~CGs~l~~~~~ 98 (126)
.||-.||.|+|-...
T Consensus 365 E~CdDCGaPlypd~~ 379 (398)
T PF11062_consen 365 EFCDDCGAPLYPDPE 379 (398)
T ss_pred hhcccCCCCCCCCCC
Confidence 499999999997654
No 45
>PF08271 TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013137 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIB (TFIIB). In eukaryotes the initiation of transcription of protein encoding genes by the polymerase II complexe (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least seven different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, and -IIH []. TFIIB and TFIID are responsible for promoter recognition and interaction with pol II; together with Pol II, they form a minimal initiation complex capable of transcription under certain conditions. The TATA box of a Pol II promoter is bound in the initiation complex by the TBP subunit of TFIID, which bends the DNA around the C-terminal domain of TFIIB whereas the N-terminal zinc finger of TFIIB interacts with Pol II [, ]. The TFIIB zinc finger adopts a zinc ribbon fold characterised by two beta-hairpins forming two structurally similar zinc-binding sub-sites []. The zinc finger contacts the rbp1 subunit of Pol II through its dock domain, a conserved region of about 70 amino acids located close to the polymerase active site []. In the Pol II complex this surface is located near the RNA exit groove. Interestingly this sequence is best conserved in the three polymerases that utilise a TFIIB-like general transcription factor (Pol II, Pol III, and archaeal RNA polymerase) but not in Pol I []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1VD4_A 1PFT_A 3K1F_M 3K7A_M 1RO4_A 1RLY_A 1DL6_A.
Probab=41.44 E-value=13 Score=20.17 Aligned_cols=11 Identities=27% Similarity=0.772 Sum_probs=6.7
Q ss_pred eeCCcCCcccc
Q 036084 84 VFCKVCGITSF 94 (126)
Q Consensus 84 ~FC~~CGs~l~ 94 (126)
..|++||..|-
T Consensus 20 ~vC~~CG~Vl~ 30 (43)
T PF08271_consen 20 LVCPNCGLVLE 30 (43)
T ss_dssp EEETTT-BBEE
T ss_pred EECCCCCCEee
Confidence 36777777664
No 46
>smart00714 LITAF Possible membrane-associated motif in LPS-induced tumor necrosis factor alpha factor (LITAF), also known as PIG7, and other animal proteins.
Probab=40.33 E-value=16 Score=21.75 Aligned_cols=18 Identities=17% Similarity=0.248 Sum_probs=13.4
Q ss_pred CCeeeeeeCCcCCccccc
Q 036084 78 TGTAKHVFCKVCGITSFY 95 (126)
Q Consensus 78 ~~~~~r~FC~~CGs~l~~ 95 (126)
+-.-..++|++||..|..
T Consensus 47 ~~kd~~H~Cp~C~~~lg~ 64 (67)
T smart00714 47 SFKDVNHYCPNCGAFLGT 64 (67)
T ss_pred cccCccEECCCCCCEeEE
Confidence 334577899999998854
No 47
>PRK11586 napB nitrate reductase cytochrome C550 subunit; Provisional
Probab=40.07 E-value=13 Score=26.30 Aligned_cols=13 Identities=23% Similarity=0.792 Sum_probs=10.9
Q ss_pred eeeeeCCcCCccc
Q 036084 81 AKHVFCKVCGITS 93 (126)
Q Consensus 81 ~~r~FC~~CGs~l 93 (126)
-.||||..|..+=
T Consensus 118 prRYfCtQCHVPQ 130 (149)
T PRK11586 118 PRRYFCLQCHVPQ 130 (149)
T ss_pred ccceeeccccCcc
Confidence 4899999998774
No 48
>PF07191 zinc-ribbons_6: zinc-ribbons; InterPro: IPR010807 This family consists of several short, hypothetical bacterial proteins of around 70 residues in length. Members of this family 8 highly conserved cysteine residues. The function of the family is unknown.; PDB: 2JRP_A 2JNE_A.
Probab=39.78 E-value=20 Score=22.14 Aligned_cols=15 Identities=33% Similarity=0.594 Sum_probs=8.9
Q ss_pred eeeeeeCCcCCcccc
Q 036084 80 TAKHVFCKVCGITSF 94 (126)
Q Consensus 80 ~~~r~FC~~CGs~l~ 94 (126)
-....+||+||.+|-
T Consensus 27 ~~~~a~CPdC~~~Le 41 (70)
T PF07191_consen 27 YKKEAFCPDCGQPLE 41 (70)
T ss_dssp EEEEEE-TTT-SB-E
T ss_pred ceecccCCCcccHHH
Confidence 346679999999874
No 49
>PF13005 zf-IS66: zinc-finger binding domain of transposase IS66 ; InterPro: IPR024474 This entry represents a predicted helix-turn-helix domain from insertion element IS66 transposases [].
Probab=39.65 E-value=14 Score=20.28 Aligned_cols=13 Identities=23% Similarity=0.324 Sum_probs=10.4
Q ss_pred eCCcCCcccccCC
Q 036084 85 FCKVCGITSFYVP 97 (126)
Q Consensus 85 FC~~CGs~l~~~~ 97 (126)
.|+.||..|....
T Consensus 4 ~C~~Cg~~l~~ig 16 (47)
T PF13005_consen 4 ACPDCGGELKEIG 16 (47)
T ss_pred cCCCCCceeeECC
Confidence 6999999987443
No 50
>PF01641 SelR: SelR domain; InterPro: IPR002579 Peptide methionine sulphoxide reductase (Msr) reverses the inactivation of many proteins due to the oxidation of critical methionine residues by reducing methionine sulphoxide, Met(O), to methionine []. It is present in most living organisms, and the cognate structural gene belongs to the so-called minimum gene set [, ]. The domains: MsrA and MsrB, reduce different epimeric forms of methionine sulphoxide. This group represents MsrB, the crystal structure of which has been determined to 1.8A []. The overall structure shows no resemblance to the structures of MsrA (IPR002569 from INTERPRO) from other organisms; though the active sites show approximate mirror symmetry. In each case, conserved amino acid motifs mediate the stereo-specific recognition and reduction of the substrate. Unlike the MsrA domain, the MsrB domain activates the cysteine or selenocysteine nucleophile through a unique Cys-Arg-Asp/Glu catalytic triad. The collapse of the reaction intermediate most likely results in the formation of a sulphenic or selenenic acid moiety. Regeneration of the active site occurs through a series of thiol-disulphide exchange steps involving another active site Cys residue and thioredoxin. In a number of pathogenic bacteria, including Neisseria gonorrhoeae, the MsrA and MsrB domains are fused; the MsrA being N-terminal to MsrB. This arrangement is reversed in Treponema pallidum. In N. gonorrhoeae and Neisseria meningitidis, a thioredoxin domain is fused to the N terminus. This may function to reduce the active sites of the downstream MsrA and MsrB domains. ; GO: 0008113 peptide-methionine-(S)-S-oxide reductase activity, 0055114 oxidation-reduction process; PDB: 1L1D_A 3E0O_D 2KZN_A 3HCG_B 3HCH_A 2L1U_A 3MAO_A 2K8D_A 3HCJ_A 3HCI_A ....
Probab=37.66 E-value=38 Score=23.16 Aligned_cols=23 Identities=26% Similarity=0.264 Sum_probs=16.8
Q ss_pred CeeeeeeCCcCCcccccCCCCCC
Q 036084 79 GTAKHVFCKVCGITSFYVPRGTP 101 (126)
Q Consensus 79 ~~~~r~FC~~CGs~l~~~~~~~p 101 (126)
....-..|.+||++|.+...+.|
T Consensus 82 ~~R~Ev~C~~Cg~HLGHVF~DGp 104 (124)
T PF01641_consen 82 MVRTEVRCARCGSHLGHVFDDGP 104 (124)
T ss_dssp SEEEEEEETTTCCEEEEEESTSS
T ss_pred ceEEEEEecCCCCccccEeCCCC
Confidence 34455689999999987765544
No 51
>PRK06393 rpoE DNA-directed RNA polymerase subunit E''; Validated
Probab=37.46 E-value=29 Score=21.03 Aligned_cols=11 Identities=27% Similarity=0.289 Sum_probs=8.6
Q ss_pred eCCcCCccccc
Q 036084 85 FCKVCGITSFY 95 (126)
Q Consensus 85 FC~~CGs~l~~ 95 (126)
.|+.||+.-+.
T Consensus 19 ~Cp~Cgs~~~S 29 (64)
T PRK06393 19 TCPVHGDEKTT 29 (64)
T ss_pred cCCCCCCCcCC
Confidence 79999997433
No 52
>smart00068 GHB Glycoprotein hormone beta chain homologues. Also called gonadotropins. Glycoprotein hormones consist of two glycosylated chains (alpha and beta) of similar topology.
Probab=36.94 E-value=50 Score=22.08 Aligned_cols=35 Identities=23% Similarity=0.534 Sum_probs=25.4
Q ss_pred eeEEeeeCCCeEEEEEcCCC-----------CeeeeecChhhhcCC
Q 036084 16 LHKGGCRCRKVRWRVRAPRS-----------VEAWKCNCSDCSMRG 50 (126)
Q Consensus 16 ~~~GsC~CGaV~~~v~~~p~-----------~~~~~ChC~~Crk~~ 50 (126)
...--|.-+.++|+...-|. .+|..|||+.|...+
T Consensus 48 ~~Q~vCtY~d~~Y~tv~lpgCp~gvdp~~tYPVAlSC~C~~C~t~~ 93 (107)
T smart00068 48 LPQRVCTYRELRYETVRLPGCPPGVDPVVTYPVALSCHCGKCNTDT 93 (107)
T ss_pred cccCCccCCceEEEEEECCCccCCCCCcEEeeeecccCCCCcCCCC
Confidence 35667999999999875321 135679999998754
No 53
>cd00069 GHB Glycoprotein hormone beta chain homologues. Gonadotropins; reproductive hormones consisting of two glycosylated chains (alpha and beta) of similar topology with Cysteine-knot motifs.
Probab=36.73 E-value=49 Score=21.90 Aligned_cols=35 Identities=20% Similarity=0.488 Sum_probs=25.4
Q ss_pred eeEEeeeCCCeEEEEEcCCC-----------CeeeeecChhhhcCC
Q 036084 16 LHKGGCRCRKVRWRVRAPRS-----------VEAWKCNCSDCSMRG 50 (126)
Q Consensus 16 ~~~GsC~CGaV~~~v~~~p~-----------~~~~~ChC~~Crk~~ 50 (126)
...--|.=+.++|+...-|. .+|..|||+.|...+
T Consensus 44 ~~Q~vCtY~~~~Y~tv~lpgCp~gvdp~~tYPVAlsC~C~~C~t~~ 89 (102)
T cd00069 44 LPQRVCTYRELSYETVRLPGCPPGVDPGVTYPVALSCHCGKCNTDT 89 (102)
T ss_pred cccCcccCCcEEEEEEECCCCcCCCCCCEEeeeecccccCCcCCCC
Confidence 35677999999999865321 135689999998754
No 54
>PF10571 UPF0547: Uncharacterised protein family UPF0547; InterPro: IPR018886 This domain may well be a type of zinc-finger as it carries two pairs of highly conserved cysteine residues though with no accompanying histidines. Several members are annotated as putative helicases.
Probab=36.65 E-value=16 Score=18.01 Aligned_cols=10 Identities=40% Similarity=1.025 Sum_probs=7.0
Q ss_pred eeeCCcCCcc
Q 036084 83 HVFCKVCGIT 92 (126)
Q Consensus 83 r~FC~~CGs~ 92 (126)
-.+|+.||-.
T Consensus 14 ~~~Cp~CG~~ 23 (26)
T PF10571_consen 14 AKFCPHCGYD 23 (26)
T ss_pred cCcCCCCCCC
Confidence 3579999843
No 55
>PRK05508 methionine sulfoxide reductase B; Provisional
Probab=36.43 E-value=60 Score=22.11 Aligned_cols=17 Identities=24% Similarity=0.323 Sum_probs=13.9
Q ss_pred eeeeCCcCCcccccCCC
Q 036084 82 KHVFCKVCGITSFYVPR 98 (126)
Q Consensus 82 ~r~FC~~CGs~l~~~~~ 98 (126)
.-.-|.+||++|.+...
T Consensus 78 tEv~C~~C~~HLGHVF~ 94 (119)
T PRK05508 78 TEIVCANCGGHLGHVFE 94 (119)
T ss_pred EEEEeCCCCCccCcccC
Confidence 44689999999988765
No 56
>KOG3084 consensus NADH pyrophosphatase I of the Nudix family of hydrolases [Replication, recombination and repair]
Probab=35.76 E-value=20 Score=28.63 Aligned_cols=16 Identities=31% Similarity=0.480 Sum_probs=12.9
Q ss_pred eeeeCCcCCcccccCC
Q 036084 82 KHVFCKVCGITSFYVP 97 (126)
Q Consensus 82 ~r~FC~~CGs~l~~~~ 97 (126)
...||+.||++++.+.
T Consensus 149 kykFCp~CG~~tkp~e 164 (345)
T KOG3084|consen 149 KYKFCPGCGSPTKPEE 164 (345)
T ss_pred HhccCcccCCCccccc
Confidence 3459999999998764
No 57
>PRK08351 DNA-directed RNA polymerase subunit E''; Validated
Probab=34.94 E-value=22 Score=21.37 Aligned_cols=12 Identities=33% Similarity=0.692 Sum_probs=9.7
Q ss_pred eCCcCCcccccC
Q 036084 85 FCKVCGITSFYV 96 (126)
Q Consensus 85 FC~~CGs~l~~~ 96 (126)
.||+||+.-+..
T Consensus 17 ~CP~Cgs~~~T~ 28 (61)
T PRK08351 17 RCPVCGSRDLSD 28 (61)
T ss_pred cCCCCcCCcccc
Confidence 599999987654
No 58
>PF01396 zf-C4_Topoisom: Topoisomerase DNA binding C4 zinc finger; InterPro: IPR013498 DNA topoisomerases regulate the number of topological links between two DNA strands (i.e. change the number of superhelical turns) by catalysing transient single- or double-strand breaks, crossing the strands through one another, then resealing the breaks []. These enzymes have several functions: to remove DNA supercoils during transcription and DNA replication; for strand breakage during recombination; for chromosome condensation; and to disentangle intertwined DNA during mitosis [, ]. DNA topoisomerases are divided into two classes: type I enzymes (5.99.1.2 from EC; topoisomerases I, III and V) break single-strand DNA, and type II enzymes (5.99.1.3 from EC; topoisomerases II, IV and VI) break double-strand DNA []. Type I topoisomerases are ATP-independent enzymes (except for reverse gyrase), and can be subdivided according to their structure and reaction mechanisms: type IA (bacterial and archaeal topoisomerase I, topoisomerase III and reverse gyrase) and type IB (eukaryotic topoisomerase I and topoisomerase V). These enzymes are primarily responsible for relaxing positively and/or negatively supercoiled DNA, except for reverse gyrase, which can introduce positive supercoils into DNA. This entry represents the zinc-finger domain found in type IA topoisomerases, including bacterial and archaeal topoisomerase I and III enzymes, and in eukaryotic topoisomerase III enzymes. Escherichia coli topoisomerase I proteins contain five copies of a zinc-ribbon-like domain at their C terminus, two of which have lost their cysteine residues and are therefore probably not able to bind zinc []. This domain is still considered to be a member of the zinc-ribbon superfamily despite not being able to bind zinc. More information about this protein can be found at Protein of the Month: DNA Topoisomerase [].; GO: 0003677 DNA binding, 0003916 DNA topoisomerase activity, 0006265 DNA topological change, 0005694 chromosome
Probab=34.40 E-value=18 Score=19.38 Aligned_cols=14 Identities=21% Similarity=0.327 Sum_probs=10.6
Q ss_pred eCCcCCcccccCCC
Q 036084 85 FCKVCGITSFYVPR 98 (126)
Q Consensus 85 FC~~CGs~l~~~~~ 98 (126)
.|+.||..|..+..
T Consensus 3 ~CP~Cg~~lv~r~~ 16 (39)
T PF01396_consen 3 KCPKCGGPLVLRRG 16 (39)
T ss_pred CCCCCCceeEEEEC
Confidence 59999988866543
No 59
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=34.37 E-value=19 Score=20.70 Aligned_cols=17 Identities=24% Similarity=0.479 Sum_probs=13.4
Q ss_pred eeeCCcCCcccccCCCC
Q 036084 83 HVFCKVCGITSFYVPRG 99 (126)
Q Consensus 83 r~FC~~CGs~l~~~~~~ 99 (126)
..-|+.||+.|+...+.
T Consensus 24 ~irCp~Cg~rIl~K~R~ 40 (49)
T COG1996 24 GIRCPYCGSRILVKERP 40 (49)
T ss_pred ceeCCCCCcEEEEeccC
Confidence 34699999999987653
No 60
>COG3043 NapB Nitrate reductase cytochrome c-type subunit [Energy production and conversion]
Probab=34.33 E-value=17 Score=25.80 Aligned_cols=13 Identities=23% Similarity=0.792 Sum_probs=10.7
Q ss_pred eeeeeCCcCCccc
Q 036084 81 AKHVFCKVCGITS 93 (126)
Q Consensus 81 ~~r~FC~~CGs~l 93 (126)
-+||||-.|..+=
T Consensus 124 PRRYFClQCHVPQ 136 (155)
T COG3043 124 PRRYFCLQCHVPQ 136 (155)
T ss_pred ccceeeeeccccc
Confidence 4899999997763
No 61
>PF05191 ADK_lid: Adenylate kinase, active site lid; InterPro: IPR007862 Adenylate kinases (ADK; 2.7.4.3 from EC) are phosphotransferases that catalyse the Mg-dependent reversible conversion of ATP and AMP to two molecules of ADP, an essential reaction for many processes in living cells. In large variants of adenylate kinase, the AMP and ATP substrates are buried in a domain that undergoes conformational changes from an open to a closed state when bound to substrate; the ligand is then contained within a highly specific environment required for catalysis. Adenylate kinase is a 3-domain protein consisting of a large central CORE domain flanked by a LID domain on one side and the AMP-binding NMPbind domain on the other []. The LID domain binds ATP and covers the phosphates at the active site. The substrates first bind the CORE domain, followed by closure of the active site by the LID and NMPbind domains. Comparisons of adenylate kinases have revealed a particular divergence in the active site lid. In some organisms, particularly the Gram-positive bacteria, residues in the lid domain have been mutated to cysteines and these cysteine residues (two CX(n)C motifs) are responsible for the binding of a zinc ion. The bound zinc ion in the lid domain is clearly structurally homologous to Zinc-finger domains. However, it is unclear whether the adenylate kinase lid is a novel zinc-finger DNA/RNA binding domain, or that the lid bound zinc serves a purely structural function [].; GO: 0004017 adenylate kinase activity; PDB: 3BE4_A 2OSB_B 2ORI_A 2EU8_A 3DL0_A 1P3J_A 2QAJ_A 2OO7_A 2P3S_A 3DKV_A ....
Probab=34.31 E-value=19 Score=19.14 Aligned_cols=10 Identities=30% Similarity=0.796 Sum_probs=8.1
Q ss_pred eeeCCcCCcc
Q 036084 83 HVFCKVCGIT 92 (126)
Q Consensus 83 r~FC~~CGs~ 92 (126)
|..|+.||..
T Consensus 1 Rr~C~~Cg~~ 10 (36)
T PF05191_consen 1 RRICPKCGRI 10 (36)
T ss_dssp EEEETTTTEE
T ss_pred CcCcCCCCCc
Confidence 5789999875
No 62
>PF00007 Cys_knot: Cystine-knot domain; InterPro: IPR006208 This domain is found at the C-terminal of glycoprotein hormones and various extracellular proteins. It is believed to be involved in disulphide-linked dimerisation. ; PDB: 1QFW_B 1HRP_B 1HCN_B 1XWD_B 1FL7_B.
Probab=33.98 E-value=15 Score=23.97 Aligned_cols=50 Identities=24% Similarity=0.483 Sum_probs=25.4
Q ss_pred CcccccccccCCCCceeEEeeeCCC--eEEEEEcCC----C-------CeeeeecChhhhcCC
Q 036084 1 WSYCESLSSMDQDSGLHKGGCRCRK--VRWRVRAPR----S-------VEAWKCNCSDCSMRG 50 (126)
Q Consensus 1 ~~~~~~~~~m~~~~~~~~GsC~CGa--V~~~v~~~p----~-------~~~~~ChC~~Crk~~ 50 (126)
|+||++.+..........-+|.|-. .+++....+ . ..+..|+|..|...+
T Consensus 30 ~G~C~s~~~~~~~~~~~~~~~~Cc~~~~~~~~~v~~~C~~G~~~~~~y~~a~sC~C~~C~~~~ 92 (105)
T PF00007_consen 30 SGYCESSEPYSKDPRKFQSQCVCCYPERTYETVVLLGCPDGVDPTFTYPVATSCSCSNCNTDT 92 (105)
T ss_dssp EEEEEEE--SCTTTTT----EEEEEEEEEEEEEEETTBTTCS-EEEEEEEEEEEEEEEEETTT
T ss_pred EEEecCCeEecccCCcCcccCcCCCcceEEEEEECCCCccCCcceEEeeEeeeeeCCCCCCCc
Confidence 6788887765544444555566654 333333221 1 124679999998765
No 63
>PF03811 Zn_Tnp_IS1: InsA N-terminal domain; InterPro: IPR003220 Insertion elements are mobile elements in DNA, usually encoding proteins required for transposition, for example transposases. Protein InsA is absolutely required for transposition of insertion element 1. This entry represents a short zinc binding domain found in IS1 InsA family protein. It is found at the N terminus of the protein and may be a DNA-binding domain.; GO: 0006313 transposition, DNA-mediated
Probab=33.85 E-value=37 Score=18.04 Aligned_cols=17 Identities=18% Similarity=0.335 Sum_probs=12.2
Q ss_pred EEecCCCeeeeeeCCcC
Q 036084 73 THTFGTGTAKHVFCKVC 89 (126)
Q Consensus 73 ~y~~~~~~~~r~FC~~C 89 (126)
.+..+..+..|+.|..|
T Consensus 19 k~G~~~~G~qryrC~~C 35 (36)
T PF03811_consen 19 KNGKSPSGHQRYRCKDC 35 (36)
T ss_pred eCCCCCCCCEeEecCcC
Confidence 33335566799999998
No 64
>COG2023 RPR2 RNase P subunit RPR2 [Translation, ribosomal structure and biogenesis]
Probab=33.70 E-value=8.6 Score=25.63 Aligned_cols=18 Identities=22% Similarity=0.333 Sum_probs=14.5
Q ss_pred CCeeeeeeCCcCCccccc
Q 036084 78 TGTAKHVFCKVCGITSFY 95 (126)
Q Consensus 78 ~~~~~r~FC~~CGs~l~~ 95 (126)
+....|.||++|.++|.-
T Consensus 51 p~~iKR~~CkkC~t~Lvp 68 (105)
T COG2023 51 PREIKRTICKKCYTPLVP 68 (105)
T ss_pred CHHHHHHhccccCccccc
Confidence 445789999999998753
No 65
>PF03604 DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa subunit; InterPro: IPR006591 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Each class of RNA polymerase is assembled from 9 to 15 different polypeptides. Rbp10 (RNA polymerase CX) is a domain found in RNA polymerase subunit 10; present in RNA polymerase I, II and III.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_Z 3HKZ_X 2NVX_L 3S1Q_L 2JA6_L 3S17_L 3HOW_L 3HOV_L 3PO2_L 3HOZ_L ....
Probab=33.66 E-value=19 Score=18.64 Aligned_cols=13 Identities=31% Similarity=0.792 Sum_probs=9.1
Q ss_pred eeCCcCCcccccC
Q 036084 84 VFCKVCGITSFYV 96 (126)
Q Consensus 84 ~FC~~CGs~l~~~ 96 (126)
.-|+.||-.|.+.
T Consensus 18 irC~~CG~RIlyK 30 (32)
T PF03604_consen 18 IRCPECGHRILYK 30 (32)
T ss_dssp SSBSSSS-SEEBE
T ss_pred EECCcCCCeEEEe
Confidence 3599999888764
No 66
>KOG2907 consensus RNA polymerase I transcription factor TFIIS, subunit A12.2/RPA12 [Transcription]
Probab=33.30 E-value=13 Score=25.07 Aligned_cols=17 Identities=24% Similarity=0.309 Sum_probs=13.2
Q ss_pred eeeeCCcCCcccccCCC
Q 036084 82 KHVFCKVCGITSFYVPR 98 (126)
Q Consensus 82 ~r~FC~~CGs~l~~~~~ 98 (126)
.-.||+.||+-|.....
T Consensus 6 ~~~FC~~CG~ll~~~~~ 22 (116)
T KOG2907|consen 6 DLDFCSDCGSLLEEPSA 22 (116)
T ss_pred Ccchhhhhhhhcccccc
Confidence 45699999999876543
No 67
>PF10601 zf-LITAF-like: LITAF-like zinc ribbon domain; InterPro: IPR006629 Members of this family display a conserved zinc ribbon structure [] with the motif C-XX-C- separated from the more C-terminal HX-C(P)X-C-X4-G-R motif by a variable region of usually 25-30 (hydrophobic) residues. Although it belongs to one of the zinc finger's fold groups (zinc ribbon), this particular domain was first identified in LPS-induced tumour necrosis alpha factor (LITAF) which is produced in mammalian cells after being challenged with lipopolysaccharide (LPS). The hydrophobic region probably inserts into the membrane rather than traversing it. Such an insertion brings together the N- and C-terminal C-XX-C motifs to form a compact Zn2+-binding structure [].
Probab=32.95 E-value=25 Score=21.29 Aligned_cols=16 Identities=19% Similarity=0.285 Sum_probs=12.8
Q ss_pred eeeeeeCCcCCccccc
Q 036084 80 TAKHVFCKVCGITSFY 95 (126)
Q Consensus 80 ~~~r~FC~~CGs~l~~ 95 (126)
.-..++|++||..|..
T Consensus 55 kd~~H~Cp~C~~~lg~ 70 (73)
T PF10601_consen 55 KDVYHYCPNCGAFLGT 70 (73)
T ss_pred cCceEECCCCCCEeEE
Confidence 3577899999998854
No 68
>PRK15103 paraquat-inducible membrane protein A; Provisional
Probab=32.90 E-value=29 Score=28.51 Aligned_cols=18 Identities=22% Similarity=0.285 Sum_probs=14.2
Q ss_pred eeeeCCcCCcccccCCCC
Q 036084 82 KHVFCKVCGITSFYVPRG 99 (126)
Q Consensus 82 ~r~FC~~CGs~l~~~~~~ 99 (126)
++..|++||+.|+.....
T Consensus 29 ~~a~CpRCg~~L~~~~~~ 46 (419)
T PRK15103 29 QKAACPRCGTTLTVRWDE 46 (419)
T ss_pred CeeECCCCCCCCcCCCCC
Confidence 467799999999876544
No 69
>PHA00626 hypothetical protein
Probab=32.74 E-value=20 Score=21.23 Aligned_cols=8 Identities=38% Similarity=0.899 Sum_probs=6.8
Q ss_pred eCCcCCcc
Q 036084 85 FCKVCGIT 92 (126)
Q Consensus 85 FC~~CGs~ 92 (126)
.||+||+.
T Consensus 2 ~CP~CGS~ 9 (59)
T PHA00626 2 SCPKCGSG 9 (59)
T ss_pred CCCCCCCc
Confidence 59999995
No 70
>PF11682 DUF3279: Protein of unknown function (DUF3279); InterPro: IPR021696 This family of proteins with unknown function appears to be restricted to Enterobacteriaceae.
Probab=32.24 E-value=26 Score=24.13 Aligned_cols=17 Identities=24% Similarity=0.485 Sum_probs=14.4
Q ss_pred eeeeeeCCcCCcccccC
Q 036084 80 TAKHVFCKVCGITSFYV 96 (126)
Q Consensus 80 ~~~r~FC~~CGs~l~~~ 96 (126)
...++||..||++|-..
T Consensus 25 ~~~~~tC~~Cg~~L~lh 41 (128)
T PF11682_consen 25 PYDHWTCHSCGCPLILH 41 (128)
T ss_pred CCCeEEEecCCceEEEe
Confidence 46899999999999665
No 71
>PHA02450 hypothetical protein
Probab=32.04 E-value=20 Score=20.36 Aligned_cols=22 Identities=14% Similarity=0.365 Sum_probs=15.2
Q ss_pred CCCceeEEeeeCCCeEEEEEcCC
Q 036084 12 QDSGLHKGGCRCRKVRWRVRAPR 34 (126)
Q Consensus 12 ~~~~~~~GsC~CGaV~~~v~~~p 34 (126)
++...|-|.|-||.| |+..+.+
T Consensus 8 egf~ryggdc~cg~i-yty~g~~ 29 (53)
T PHA02450 8 EGFTRYGGDCTCGPI-YTYGGHA 29 (53)
T ss_pred ccceeeCCcccccce-eeeCCcC
Confidence 345567899999997 5555543
No 72
>PF03892 NapB: Nitrate reductase cytochrome c-type subunit (NapB); InterPro: IPR005591 The napB gene encodes a dihaem cytochrome c, the small subunit of a heterodimeric periplasmic nitrate reductase [].; PDB: 3O5A_B 3ML1_B 1OGY_L 1JNI_A.
Probab=31.70 E-value=16 Score=25.42 Aligned_cols=13 Identities=23% Similarity=0.848 Sum_probs=8.9
Q ss_pred eeeeeCCcCCccc
Q 036084 81 AKHVFCKVCGITS 93 (126)
Q Consensus 81 ~~r~FC~~CGs~l 93 (126)
-.||||..|..+=
T Consensus 107 ~~RyfC~qCHvpQ 119 (133)
T PF03892_consen 107 PRRYFCTQCHVPQ 119 (133)
T ss_dssp CCCCSGGGT--B-
T ss_pred cceeeeccccCcc
Confidence 4899999998764
No 73
>PF09855 DUF2082: Nucleic-acid-binding protein containing Zn-ribbon domain (DUF2082); InterPro: IPR018652 This family of proteins contains various hypothetical prokaryotic proteins as well as some Zn-ribbon nucleic-acid-binding proteins.
Probab=31.64 E-value=1.1e+02 Score=18.46 Aligned_cols=38 Identities=24% Similarity=0.417 Sum_probs=21.9
Q ss_pred CCCeEEcCCCCccee-EEecCCCeeeeeeCCcCCcccccCCC
Q 036084 58 PENFELLGNSEEFLT-THTFGTGTAKHVFCKVCGITSFYVPR 98 (126)
Q Consensus 58 ~~~~~i~~g~~~~l~-~y~~~~~~~~r~FC~~CGs~l~~~~~ 98 (126)
.+.++.+++ .++ .++..-+...-.-|++||=.=|+...
T Consensus 13 ~~~v~~tgg---~~skiFdvq~~~f~~v~C~~CGYTE~Y~~~ 51 (64)
T PF09855_consen 13 SGEVRATGG---GLSKIFDVQNKKFTTVSCTNCGYTEFYKAK 51 (64)
T ss_pred cceEEccCC---eeEEEEEecCcEEEEEECCCCCCEEEEeec
Confidence 345555543 132 34434445566679999977666543
No 74
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=30.77 E-value=35 Score=20.45 Aligned_cols=19 Identities=32% Similarity=0.515 Sum_probs=12.0
Q ss_pred CCeeeeeeCCcCCcccccC
Q 036084 78 TGTAKHVFCKVCGITSFYV 96 (126)
Q Consensus 78 ~~~~~r~FC~~CGs~l~~~ 96 (126)
+.....+-||+||-.+-++
T Consensus 22 ~e~~v~F~CPnCGe~~I~R 40 (61)
T COG2888 22 GETAVKFPCPNCGEVEIYR 40 (61)
T ss_pred CCceeEeeCCCCCceeeeh
Confidence 3345667799999544333
No 75
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=30.56 E-value=21 Score=23.89 Aligned_cols=13 Identities=15% Similarity=0.424 Sum_probs=9.6
Q ss_pred ee-CCcCCcccccC
Q 036084 84 VF-CKVCGITSFYV 96 (126)
Q Consensus 84 ~F-C~~CGs~l~~~ 96 (126)
++ ||.||++-...
T Consensus 88 ~~~CP~Cgs~~~~i 101 (117)
T PRK00564 88 YGVCEKCHSKNVII 101 (117)
T ss_pred CCcCcCCCCCceEE
Confidence 44 99999986443
No 76
>PF12172 DUF35_N: Rubredoxin-like zinc ribbon domain (DUF35_N); InterPro: IPR022002 This domain has no known function and is found in conserved hypothetical archaeal and bacterial proteins. The domain is duplicated in O53566 from SWISSPROT. The structure of a DUF35 representative reveals two long N-terminal helices followed by a rubredoxin-like zinc ribbon domain represented in this family and a C-terminal OB fold domain. Zinc is chelated by the four conserved cysteines in the alignment. ; PDB: 3IRB_A.
Probab=30.42 E-value=19 Score=18.76 Aligned_cols=10 Identities=30% Similarity=0.803 Sum_probs=5.8
Q ss_pred eeeCCcCCcc
Q 036084 83 HVFCKVCGIT 92 (126)
Q Consensus 83 r~FC~~CGs~ 92 (126)
+.+|+.||+.
T Consensus 25 r~~Cp~C~s~ 34 (37)
T PF12172_consen 25 RPVCPHCGSD 34 (37)
T ss_dssp -SEETTTT--
T ss_pred CcCCCCcCcc
Confidence 4578998864
No 77
>TIGR03831 YgiT_finger YgiT-type zinc finger domain. This domain model describes a small domain with two copies of a putative zinc-binding motif CXXC (usually CXXCG). Most member proteins consist largely of this domain or else carry an additional C-terminal helix-turn-helix domain, resembling that of the phage protein Cro and modeled by pfam01381.
Probab=30.32 E-value=24 Score=18.85 Aligned_cols=15 Identities=20% Similarity=0.503 Sum_probs=11.4
Q ss_pred eeeeeCCcCCccccc
Q 036084 81 AKHVFCKVCGITSFY 95 (126)
Q Consensus 81 ~~r~FC~~CGs~l~~ 95 (126)
+.-++|++||-.+|.
T Consensus 30 vp~~~C~~CGE~~~~ 44 (46)
T TIGR03831 30 VPALVCPQCGEEYLD 44 (46)
T ss_pred CCccccccCCCEeeC
Confidence 344579999998875
No 78
>COG3024 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=30.17 E-value=31 Score=20.92 Aligned_cols=13 Identities=31% Similarity=0.680 Sum_probs=10.6
Q ss_pred eeCCcCCcccccC
Q 036084 84 VFCKVCGITSFYV 96 (126)
Q Consensus 84 ~FC~~CGs~l~~~ 96 (126)
.=|+.||.++-+.
T Consensus 8 v~CP~Cgkpv~w~ 20 (65)
T COG3024 8 VPCPTCGKPVVWG 20 (65)
T ss_pred ccCCCCCCccccc
Confidence 4599999999774
No 79
>smart00834 CxxC_CXXC_SSSS Putative regulatory protein. CxxC_CXXC_SSSS represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=29.90 E-value=26 Score=18.32 Aligned_cols=12 Identities=25% Similarity=0.473 Sum_probs=8.4
Q ss_pred eeeeCCcCCccc
Q 036084 82 KHVFCKVCGITS 93 (126)
Q Consensus 82 ~r~FC~~CGs~l 93 (126)
...-|+.||+.+
T Consensus 25 ~~~~CP~Cg~~~ 36 (41)
T smart00834 25 PLATCPECGGDV 36 (41)
T ss_pred CCCCCCCCCCcc
Confidence 334599999854
No 80
>PF10955 DUF2757: Protein of unknown function (DUF2757); InterPro: IPR020115 This entry contains proteins with no known function.
Probab=29.71 E-value=29 Score=21.75 Aligned_cols=16 Identities=25% Similarity=0.650 Sum_probs=13.3
Q ss_pred eeeeCCcCCcccccCC
Q 036084 82 KHVFCKVCGITSFYVP 97 (126)
Q Consensus 82 ~r~FC~~CGs~l~~~~ 97 (126)
-+++|..||+.|....
T Consensus 3 i~Y~CRHCg~~IG~i~ 18 (76)
T PF10955_consen 3 IHYYCRHCGTKIGTID 18 (76)
T ss_pred eEEEecCCCCEEEEee
Confidence 5789999999997654
No 81
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=29.55 E-value=32 Score=17.90 Aligned_cols=11 Identities=27% Similarity=0.721 Sum_probs=8.9
Q ss_pred eeeeCCcCCcc
Q 036084 82 KHVFCKVCGIT 92 (126)
Q Consensus 82 ~r~FC~~CGs~ 92 (126)
...||..||..
T Consensus 20 ~~~~C~~Cg~~ 30 (33)
T PF08792_consen 20 DYEVCIFCGSS 30 (33)
T ss_pred CeEEcccCCcE
Confidence 56799999975
No 82
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=29.43 E-value=29 Score=19.87 Aligned_cols=11 Identities=45% Similarity=1.014 Sum_probs=8.8
Q ss_pred eeeeeCCcCCc
Q 036084 81 AKHVFCKVCGI 91 (126)
Q Consensus 81 ~~r~FC~~CGs 91 (126)
....||++||-
T Consensus 44 ~~i~~Cp~CgR 54 (56)
T PF02591_consen 44 DEIVFCPNCGR 54 (56)
T ss_pred CCeEECcCCCc
Confidence 36689999985
No 83
>PF04423 Rad50_zn_hook: Rad50 zinc hook motif; InterPro: IPR007517 The Mre11 complex (Mre11 Rad50 Nbs1) is central to chromosomal maintenance and functions in homologous recombination, telomere maintenance and sister chromatid association. The Rad50 coiled-coil region contains a dimer interface at the apex of the coiled coils in which pairs of conserved Cys-X-X-Cys motifs form interlocking hooks that bind one Zn ion. This alignment includes the zinc hook motif and a short stretch of coiled-coil on either side.; GO: 0004518 nuclease activity, 0005524 ATP binding, 0008270 zinc ion binding, 0006281 DNA repair; PDB: 1L8D_B.
Probab=28.83 E-value=22 Score=20.26 Aligned_cols=11 Identities=27% Similarity=0.558 Sum_probs=5.6
Q ss_pred eCCcCCccccc
Q 036084 85 FCKVCGITSFY 95 (126)
Q Consensus 85 FC~~CGs~l~~ 95 (126)
-||.||.++-.
T Consensus 22 ~CPlC~r~l~~ 32 (54)
T PF04423_consen 22 CCPLCGRPLDE 32 (54)
T ss_dssp E-TTT--EE-H
T ss_pred cCCCCCCCCCH
Confidence 69999998743
No 84
>COG1885 Uncharacterized protein conserved in archaea [Function unknown]
Probab=28.83 E-value=63 Score=21.62 Aligned_cols=33 Identities=15% Similarity=0.113 Sum_probs=20.1
Q ss_pred eCCcCCcccccCCC-CCCCcEEEEEeeeecCCCC
Q 036084 85 FCKVCGITSFYVPR-GTPNGMLLLSDIKHNDGHN 117 (126)
Q Consensus 85 FC~~CGs~l~~~~~-~~p~~~~v~v~~g~~d~~~ 117 (126)
-||.||.++-...- .+...+.+.+.+..|+-.+
T Consensus 51 ~CP~Cg~~~e~~fvva~~aLVgl~l~mkVFNaes 84 (115)
T COG1885 51 SCPKCGEPFESAFVVANTALVGLILSMKVFNAES 84 (115)
T ss_pred cCCCCCCccceeEEEecceeEEEEEEEEEecCCC
Confidence 49999999744322 2223455667777777443
No 85
>PF11781 RRN7: RNA polymerase I-specific transcription initiation factor Rrn7; InterPro: IPR021752 Rrn7 is a transcription binding factor that associates strongly with both Rrn6 and Rrn11 to form a complex which itself binds the TATA-binding protein and is required for transcription by the core domain of the RNA PolI promoter [],[].
Probab=28.69 E-value=26 Score=18.54 Aligned_cols=12 Identities=33% Similarity=0.858 Sum_probs=8.9
Q ss_pred eeeeCCcCCccc
Q 036084 82 KHVFCKVCGITS 93 (126)
Q Consensus 82 ~r~FC~~CGs~l 93 (126)
-+++|..||+.+
T Consensus 24 G~~yC~~cG~~~ 35 (36)
T PF11781_consen 24 GFYYCDRCGHQS 35 (36)
T ss_pred CEEEhhhCceEc
Confidence 467899998753
No 86
>PF03226 Yippee-Mis18: Yippee zinc-binding/DNA-binding /Mis18, centromere assembly; InterPro: IPR004910 This entry represents the Yippee-like (YPEL) family of putative zinc-binding proteins which is highly conserved among eukaryotes. The first protein in this family to be characterised, the Yippee protein from Drosophila, was identified by yeast interaction trap screen as a protein that physically interacts with moth hemolin []. It was subsequently found to be a member of a highly conserved family of proteins found in diverse eukaryotes including plants, animals and fungi []. Mammals contain five members of this family, YPEL1 to YPEL5, while other organisms tend to contain only two or three members. The mammalian proteins all appear to localise in the nucleus. YPEL1-4 are located in an unknown structure located on or close to the mitotic apparatus in the mitotic phase, whereas in the interphase they are located in the nuclei and nucleoli. In contrast, YPEL5 is localised to the centrosome and nucleus during interphase and at the mitotic spindle during mitosis, suggesting a function distinct from that of YPEL1-4. The localisation of the YPEL proteins suggests a novel, thopugh still unknown, function involved in cell division.
Probab=28.63 E-value=28 Score=22.07 Aligned_cols=22 Identities=18% Similarity=0.387 Sum_probs=16.8
Q ss_pred CeeeeeeCCcCCcccccCCCCC
Q 036084 79 GTAKHVFCKVCGITSFYVPRGT 100 (126)
Q Consensus 79 ~~~~r~FC~~CGs~l~~~~~~~ 100 (126)
......+|..|++.|.+.....
T Consensus 53 ~~~~~l~C~~C~~~lGwkY~~a 74 (96)
T PF03226_consen 53 HTVRDLFCSGCNTILGWKYESA 74 (96)
T ss_pred EEEEEeEcccCChhHCcEEEEc
Confidence 3467779999999998775443
No 87
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=28.36 E-value=41 Score=22.66 Aligned_cols=20 Identities=15% Similarity=0.122 Sum_probs=15.6
Q ss_pred CeeeeeeCCcCCcccccCCC
Q 036084 79 GTAKHVFCKVCGITSFYVPR 98 (126)
Q Consensus 79 ~~~~r~FC~~CGs~l~~~~~ 98 (126)
-.+++..|++||+.|-....
T Consensus 8 l~vt~l~C~~C~t~i~G~F~ 27 (113)
T PF09862_consen 8 LVVTRLKCPSCGTEIEGEFE 27 (113)
T ss_pred eEEEEEEcCCCCCEEEeeec
Confidence 35788899999999866543
No 88
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=28.21 E-value=36 Score=19.89 Aligned_cols=13 Identities=31% Similarity=0.672 Sum_probs=10.7
Q ss_pred eeeeCCcCCcccc
Q 036084 82 KHVFCKVCGITSF 94 (126)
Q Consensus 82 ~r~FC~~CGs~l~ 94 (126)
....|+.||++-.
T Consensus 20 DiVvCp~CgapyH 32 (54)
T PF14446_consen 20 DIVVCPECGAPYH 32 (54)
T ss_pred CEEECCCCCCccc
Confidence 5678999999854
No 89
>TIGR00155 pqiA_fam integral membrane protein, PqiA family. This family consists of uncharacterized predicted integral membrane proteins found, so far, only in the Proteobacteria. Of two members in E. coli, one is induced by paraquat and is designated PqiA, paraquat-inducible protein A.
Probab=28.15 E-value=39 Score=27.54 Aligned_cols=18 Identities=22% Similarity=0.202 Sum_probs=14.0
Q ss_pred eeeeCCcCCcccccCCCC
Q 036084 82 KHVFCKVCGITSFYVPRG 99 (126)
Q Consensus 82 ~r~FC~~CGs~l~~~~~~ 99 (126)
++..|++||+.++.....
T Consensus 32 ~~a~CpRCg~~L~~~~~~ 49 (403)
T TIGR00155 32 QKAACPRCGTTLTVGWDW 49 (403)
T ss_pred CeeECCCCCCCCcCCCCC
Confidence 456799999999876544
No 90
>TIGR03655 anti_R_Lar restriction alleviation protein, Lar family. Restriction alleviation proteins provide a countermeasure to host cell restriction enzyme defense against foreign DNA such as phage or plasmids. This family consists of homologs to the phage antirestriction protein Lar, and most members belong to phage genomes or prophage regions of bacterial genomes.
Probab=27.66 E-value=80 Score=17.83 Aligned_cols=11 Identities=27% Similarity=0.667 Sum_probs=8.2
Q ss_pred eCCcCCccccc
Q 036084 85 FCKVCGITSFY 95 (126)
Q Consensus 85 FC~~CGs~l~~ 95 (126)
.|+.||...-.
T Consensus 28 ~C~~Cga~~~~ 38 (53)
T TIGR03655 28 ECSTCGASGPV 38 (53)
T ss_pred ECCCCCCCccc
Confidence 59999987543
No 91
>PF00643 zf-B_box: B-box zinc finger; InterPro: IPR000315 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents B-box-type zinc finger domains, which are around 40 residues in length. B-box zinc fingers can be divided into two groups, where types 1 and 2 B-box domains differ in their consensus sequence and in the spacing of the 7-8 zinc-binding residues. Several proteins contain both types 1 and 2 B-boxes, suggesting some level of cooperativity between these two domains. B-box domains are found in over 1500 proteins from a variety of organisms. They are found in TRIM (tripartite motif) proteins that consist of an N-terminal RING finger (originally called an A-box), followed by 1-2 B-box domains and a coiled-coil domain (also called RBCC for Ring, B-box, Coiled-Coil). TRIM proteins contain a type 2 B-box domain, and may also contain a type 1 B-box. In proteins that do not contain RING or coiled-coil domains, the B-box domain is primarily type 2. Many type 2 B-box proteins are involved in ubiquitinylation. Proteins containing a B-box zinc finger domain include transcription factors, ribonucleoproteins and proto-oncoproteins; for example, MID1, MID2, TRIM9, TNL, TRIM36, TRIM63, TRIFIC, NCL1 and CONSTANS-like proteins []. The microtubule-associated E3 ligase MID1 (6.3.2 from EC) contains a type 1 B-box zinc finger domain. MID1 specifically binds Alpha-4, which in turn recruits the catalytic subunit of phosphatase 2A (PP2Ac). This complex is required for targeting of PP2Ac for proteasome-mediated degradation. The MID1 B-box coordinates two zinc ions and adopts a beta/beta/alpha cross-brace structure similar to that of ZZ, PHD, RING and FYVE zinc fingers [, ]. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 3DDT_B 2D8U_A 3Q1D_A 2EGM_A 2YVR_B 2DJA_A 2DQ5_A 2JUN_A 2YRG_A 2DID_A ....
Probab=27.39 E-value=28 Score=18.37 Aligned_cols=14 Identities=21% Similarity=0.548 Sum_probs=10.3
Q ss_pred eeeeeCCcCCcccc
Q 036084 81 AKHVFCKVCGITSF 94 (126)
Q Consensus 81 ~~r~FC~~CGs~l~ 94 (126)
...+||.+|+.+|=
T Consensus 13 ~~~~~C~~C~~~~C 26 (42)
T PF00643_consen 13 PLSLFCEDCNEPLC 26 (42)
T ss_dssp BEEEEETTTTEEEE
T ss_pred ceEEEecCCCCccC
Confidence 46788888887763
No 92
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=27.35 E-value=26 Score=23.31 Aligned_cols=12 Identities=17% Similarity=0.332 Sum_probs=8.8
Q ss_pred eeCCcCCccccc
Q 036084 84 VFCKVCGITSFY 95 (126)
Q Consensus 84 ~FC~~CGs~l~~ 95 (126)
+.||+||+.-..
T Consensus 87 ~~CP~Cgs~~~~ 98 (113)
T PRK12380 87 AQCPHCHGERLR 98 (113)
T ss_pred ccCcCCCCCCcE
Confidence 449999987443
No 93
>PF05207 zf-CSL: CSL zinc finger; InterPro: IPR007872 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a probable zinc binding motif that contains four cysteines and may chelate zinc, known as the DPH-type after the diphthamide (DPH) biosynthesis protein in which it was first characterised, including the proteins DPH3 and DPH4. This domain is also found associated with N-terminal domain of heat shock protein DnaJ IPR001623 from INTERPRO domain. Diphthamide is a unique post-translationally modified histidine residue found only in translation elongation factor 2 (eEF-2). It is conserved from archaea to humans and serves as the target for diphteria toxin and Pseudomonas exotoxin A. These two toxins catalyse the transfer of ADP-ribose to diphtamide on eEF-2, thus inactivating eEF-2, halting cellular protein synthesis, and causing cell death []. The biosynthesis of diphtamide is dependent on at least five proteins, DPH1 to -5, and a still unidentified amidating enzyme. DPH3 and DPH4 share a conserved region, which encode a putative zinc finger, the DPH-type or CSL-type (after the conserved motif of the final cysteine) zinc finger [, ]. The function of this motif is unknown. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 2L6L_A 1WGE_A 2JR7_A 1YOP_A 1YWS_A.
Probab=27.12 E-value=1e+02 Score=17.77 Aligned_cols=21 Identities=19% Similarity=0.531 Sum_probs=16.9
Q ss_pred CCceeEEeeeCCCeEEEEEcCC
Q 036084 13 DSGLHKGGCRCRKVRWRVRAPR 34 (126)
Q Consensus 13 ~~~~~~GsC~CGaV~~~v~~~p 34 (126)
+..++.=.|.||.. |.++.+.
T Consensus 13 ~~~~~~y~CRCG~~-f~i~e~~ 33 (55)
T PF05207_consen 13 EEGVYSYPCRCGGE-FEISEED 33 (55)
T ss_dssp TTTEEEEEETTSSE-EEEEHHH
T ss_pred CCCEEEEcCCCCCE-EEEcchh
Confidence 35569999999998 9998653
No 94
>PF01599 Ribosomal_S27: Ribosomal protein S27a; InterPro: IPR002906 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This family of ribosomal proteins consists mainly of the 40S ribosomal protein S27a which is synthesized as a C-terminal extension of ubiquitin (CEP) (IPR000626 from INTERPRO). The S27a domain compromises the C-terminal half of the protein. The synthesis of ribosomal proteins as extensions of ubiquitin promotes their incorporation into nascent ribosomes by a transient metabolic stabilisation and is required for efficient ribosome biogenesis []. The ribosomal extension protein S27a contains a basic region that is proposed to form a zinc finger; its fusion gene is proposed as a mechanism to maintain a fixed ratio between ubiquitin necessary for degrading proteins and ribosomes a source of proteins [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 2K4X_A 3U5C_f 3U5G_f 2XZN_9 2XZM_9.
Probab=26.85 E-value=43 Score=19.00 Aligned_cols=17 Identities=24% Similarity=0.471 Sum_probs=11.4
Q ss_pred eeeeCC--cCCcccccCCC
Q 036084 82 KHVFCK--VCGITSFYVPR 98 (126)
Q Consensus 82 ~r~FC~--~CGs~l~~~~~ 98 (126)
.|..|| +||.-+|.-.+
T Consensus 17 ~rk~CP~~~CG~GvFMA~H 35 (47)
T PF01599_consen 17 LRKECPSPRCGAGVFMAEH 35 (47)
T ss_dssp SSEE-TSTTTTSSSEEEE-
T ss_pred hhhcCCCcccCCceEeeec
Confidence 466899 99998876543
No 95
>COG4306 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=25.52 E-value=26 Score=24.33 Aligned_cols=16 Identities=25% Similarity=0.569 Sum_probs=12.2
Q ss_pred eeeeCCcCCcccccCC
Q 036084 82 KHVFCKVCGITSFYVP 97 (126)
Q Consensus 82 ~r~FC~~CGs~l~~~~ 97 (126)
--.||.+||++.-+..
T Consensus 67 ~psfchncgs~fpwte 82 (160)
T COG4306 67 PPSFCHNCGSRFPWTE 82 (160)
T ss_pred CcchhhcCCCCCCcHH
Confidence 3469999999976653
No 96
>PRK14018 trifunctional thioredoxin/methionine sulfoxide reductase A/B protein; Provisional
Probab=25.10 E-value=80 Score=26.82 Aligned_cols=18 Identities=17% Similarity=-0.046 Sum_probs=15.2
Q ss_pred eeCCcCCcccccCCCCCC
Q 036084 84 VFCKVCGITSFYVPRGTP 101 (126)
Q Consensus 84 ~FC~~CGs~l~~~~~~~p 101 (126)
..|.+||++|.+...++|
T Consensus 468 v~c~~c~~HLGHvf~dgp 485 (521)
T PRK14018 468 VRSRAADSHLGHVFPDGP 485 (521)
T ss_pred EEECCCCCcCCcccCCCC
Confidence 689999999988877655
No 97
>PF10497 zf-4CXXC_R1: Zinc-finger domain of monoamine-oxidase A repressor R1; InterPro: IPR018866 R1 is a transcription factor repressor that inhibits monoamine oxidase A gene expression. This domain is a four-CXXC zinc finger putative DNA-binding domain found at the C-terminal end of R1. The domain carries 12 cysteines of which four pairs are of the CXXC type [].
Probab=24.91 E-value=39 Score=22.30 Aligned_cols=13 Identities=38% Similarity=0.772 Sum_probs=11.1
Q ss_pred eeecChhhhcCCc
Q 036084 39 WKCNCSDCSMRGN 51 (126)
Q Consensus 39 ~~ChC~~Crk~~g 51 (126)
.+|+|+.|||..|
T Consensus 69 giCnCs~Crrk~g 81 (105)
T PF10497_consen 69 GICNCSFCRRKRG 81 (105)
T ss_pred CeeCCHhhhccCC
Confidence 5899999998865
No 98
>PF04606 Ogr_Delta: Ogr/Delta-like zinc finger; InterPro: IPR007684 This entry is represented by Bacteriophage P2, Ogr. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This is a viral family of phage zinc-binding transcriptional activators, which also contains cryptic members in some bacterial genomes []. The P4 phage delta protein contains two such domains attached covalently, while the P2 phage Ogr proteins possess one domain but function as dimers. All the members of this family have the following consensus sequence: C-X(2)-C-X(3)-A-(X)2-R-X(15)-C-X(4)-C-X(3)-F [].; GO: 0006355 regulation of transcription, DNA-dependent
Probab=24.42 E-value=35 Score=18.94 Aligned_cols=12 Identities=25% Similarity=0.573 Sum_probs=9.3
Q ss_pred CCcCCcccccCC
Q 036084 86 CKVCGITSFYVP 97 (126)
Q Consensus 86 C~~CGs~l~~~~ 97 (126)
||.||+..-.+.
T Consensus 2 CP~Cg~~a~ir~ 13 (47)
T PF04606_consen 2 CPHCGSKARIRT 13 (47)
T ss_pred cCCCCCeeEEEE
Confidence 999999875543
No 99
>COG3058 FdhE Uncharacterized protein involved in formate dehydrogenase formation [Posttranslational modification, protein turnover, chaperones]
Probab=24.01 E-value=34 Score=26.84 Aligned_cols=13 Identities=31% Similarity=0.892 Sum_probs=10.7
Q ss_pred eeeeCCcCCcccc
Q 036084 82 KHVFCKVCGITSF 94 (126)
Q Consensus 82 ~r~FC~~CGs~l~ 94 (126)
.|.+||.||+...
T Consensus 184 ~~~~CPvCGS~Pv 196 (308)
T COG3058 184 SRQYCPVCGSMPV 196 (308)
T ss_pred ccccCCCcCCCCc
Confidence 6789999999753
No 100
>COG0375 HybF Zn finger protein HypA/HybF (possibly regulating hydrogenase expression) [General function prediction only]
Probab=23.90 E-value=92 Score=21.05 Aligned_cols=18 Identities=17% Similarity=0.362 Sum_probs=12.7
Q ss_pred eeeeeCCcCCcccccCCC
Q 036084 81 AKHVFCKVCGITSFYVPR 98 (126)
Q Consensus 81 ~~r~FC~~CGs~l~~~~~ 98 (126)
..++.||.||+.-+....
T Consensus 84 ~~~~~CP~C~s~~~~i~~ 101 (115)
T COG0375 84 ELDYRCPKCGSINLRIIG 101 (115)
T ss_pred hheeECCCCCCCceEEec
Confidence 345559999998765543
No 101
>KOG2463 consensus Predicted RNA-binding protein Nob1p involved in 26S proteasome assembly [Posttranslational modification, protein turnover, chaperones]
Probab=23.64 E-value=34 Score=27.50 Aligned_cols=16 Identities=31% Similarity=0.700 Sum_probs=12.3
Q ss_pred CCeeeeeeCCcCCccc
Q 036084 78 TGTAKHVFCKVCGITS 93 (126)
Q Consensus 78 ~~~~~r~FC~~CGs~l 93 (126)
.....+.||+.||-..
T Consensus 252 t~~m~k~FCp~CG~~T 267 (376)
T KOG2463|consen 252 TSEMPKDFCPSCGHKT 267 (376)
T ss_pred cCccchhcccccCCCe
Confidence 3456799999999763
No 102
>cd00730 rubredoxin Rubredoxin; nonheme iron binding domains containing a [Fe(SCys)4] center. Rubredoxins are small nonheme iron proteins. The iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc. They are believed to be involved in electron transfer.
Probab=23.57 E-value=44 Score=19.08 Aligned_cols=16 Identities=25% Similarity=0.731 Sum_probs=10.1
Q ss_pred eeeCCcCCcccccCCCC
Q 036084 83 HVFCKVCGITSFYVPRG 99 (126)
Q Consensus 83 r~FC~~CGs~l~~~~~~ 99 (126)
++-|..|| .+|.....
T Consensus 1 ~y~C~~Cg-yiYd~~~G 16 (50)
T cd00730 1 KYECRICG-YIYDPAEG 16 (50)
T ss_pred CcCCCCCC-eEECCCCC
Confidence 35689998 56654433
No 103
>PF09538 FYDLN_acid: Protein of unknown function (FYDLN_acid); InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=23.07 E-value=35 Score=22.73 Aligned_cols=16 Identities=19% Similarity=0.505 Sum_probs=9.2
Q ss_pred eeeeCCcCCcccccCC
Q 036084 82 KHVFCKVCGITSFYVP 97 (126)
Q Consensus 82 ~r~FC~~CGs~l~~~~ 97 (126)
+...|++||+..|-.+
T Consensus 8 tKR~Cp~CG~kFYDLn 23 (108)
T PF09538_consen 8 TKRTCPSCGAKFYDLN 23 (108)
T ss_pred CcccCCCCcchhccCC
Confidence 4455777776655443
No 104
>PF06054 CoiA: Competence protein CoiA-like family; InterPro: IPR010330 Competence is the ability of a cell to take up exogenous DNA from its environment, resulting in transformation. It is widespread among bacteria and is probably an important mechanism for the horizontal transfer of genes. Cells that take up DNA inevitably acquire the nucleotides the DNA consists of, and, because nucleotides are needed for DNA and RNA synthesis and are expensive to synthesise, these may make a significant contribution to the cell's energy budget []. The lateral gene transfer caused by competence also contributes to the genetic diversity that makes evolution possible. DNA usually becomes available by the death and lysis of other cells. Competent bacteria use components of extracellular filaments called type 4 pili to create pores in their membranes and pull DNA through the pores into the cytoplasm. This process, including the development of competence and the expression of the uptake machinery, is regulated in response to cell-cell signalling and/or nutritional conditions []. Many of the members of this family are described as transcription factors. CoiA falls within a competence-specific operon in Streptococcus. CoiA is an uncharacterised protein.
Probab=23.01 E-value=41 Score=27.09 Aligned_cols=16 Identities=25% Similarity=0.551 Sum_probs=13.6
Q ss_pred eeeeeCCcCCcccccC
Q 036084 81 AKHVFCKVCGITSFYV 96 (126)
Q Consensus 81 ~~r~FC~~CGs~l~~~ 96 (126)
...+|||.||.+|...
T Consensus 28 ~~~~~CP~C~~~v~lk 43 (375)
T PF06054_consen 28 KGKYFCPGCGEPVILK 43 (375)
T ss_pred CCcEECCCCCCeeEEE
Confidence 5678999999999765
No 105
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=22.87 E-value=42 Score=19.71 Aligned_cols=15 Identities=27% Similarity=0.574 Sum_probs=11.7
Q ss_pred eeeeCCcCCcccccC
Q 036084 82 KHVFCKVCGITSFYV 96 (126)
Q Consensus 82 ~r~FC~~CGs~l~~~ 96 (126)
..+-|+.||.+.+..
T Consensus 13 v~~~Cp~cGipthcS 27 (55)
T PF13824_consen 13 VNFECPDCGIPTHCS 27 (55)
T ss_pred cCCcCCCCCCcCccC
Confidence 445699999998764
No 106
>COG2093 DNA-directed RNA polymerase, subunit E'' [Transcription]
Probab=22.69 E-value=42 Score=20.29 Aligned_cols=13 Identities=38% Similarity=0.792 Sum_probs=10.0
Q ss_pred eeCCcCCcccccC
Q 036084 84 VFCKVCGITSFYV 96 (126)
Q Consensus 84 ~FC~~CGs~l~~~ 96 (126)
..||.||++=|.+
T Consensus 19 e~CP~Cgs~~~te 31 (64)
T COG2093 19 EICPVCGSTDLTE 31 (64)
T ss_pred ccCCCCCCcccch
Confidence 4599999996554
No 107
>PRK13130 H/ACA RNA-protein complex component Nop10p; Reviewed
Probab=22.48 E-value=44 Score=19.63 Aligned_cols=14 Identities=29% Similarity=0.541 Sum_probs=11.0
Q ss_pred eeeCCcCCcccccC
Q 036084 83 HVFCKVCGITSFYV 96 (126)
Q Consensus 83 r~FC~~CGs~l~~~ 96 (126)
...|+.||+++...
T Consensus 17 k~~CP~CG~~t~~~ 30 (56)
T PRK13130 17 KEICPVCGGKTKNP 30 (56)
T ss_pred cccCcCCCCCCCCC
Confidence 45699999998654
No 108
>TIGR01562 FdhE formate dehydrogenase accessory protein FdhE. The only sequence scoring between trusted and noise is that from Aquifex aeolicus, which shows certain structural differences from the proteobacterial forms in the alignment. However it is notable that A. aeolicus also has a sequence scoring above trusted to the alpha subunit of formate dehydrogenase (TIGR01553).
Probab=22.11 E-value=37 Score=26.77 Aligned_cols=14 Identities=21% Similarity=0.729 Sum_probs=11.2
Q ss_pred eeeeeCCcCCcccc
Q 036084 81 AKHVFCKVCGITSF 94 (126)
Q Consensus 81 ~~r~FC~~CGs~l~ 94 (126)
-.|.+||.||+.-.
T Consensus 182 ~~~~~CPvCGs~P~ 195 (305)
T TIGR01562 182 ESRTLCPACGSPPV 195 (305)
T ss_pred CCCCcCCCCCChhh
Confidence 35779999999853
No 109
>COG1579 Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only]
Probab=22.07 E-value=33 Score=26.12 Aligned_cols=17 Identities=35% Similarity=0.811 Sum_probs=13.6
Q ss_pred eeeeeCCcCCcccccCC
Q 036084 81 AKHVFCKVCGITSFYVP 97 (126)
Q Consensus 81 ~~r~FC~~CGs~l~~~~ 97 (126)
-.-.|||.||.=||+..
T Consensus 219 d~iv~CP~CgRILy~~e 235 (239)
T COG1579 219 DEIVFCPYCGRILYYDE 235 (239)
T ss_pred CCCccCCccchHHHhhh
Confidence 35679999999988754
No 110
>PRK05550 bifunctional methionine sulfoxide reductase B/A protein; Provisional
Probab=22.03 E-value=1.3e+02 Score=23.51 Aligned_cols=18 Identities=22% Similarity=0.362 Sum_probs=14.4
Q ss_pred eeeeeCCcCCcccccCCC
Q 036084 81 AKHVFCKVCGITSFYVPR 98 (126)
Q Consensus 81 ~~r~FC~~CGs~l~~~~~ 98 (126)
..-.-|.+||++|.+...
T Consensus 80 R~Ev~c~~c~~HLGHvF~ 97 (283)
T PRK05550 80 RTEIVCANCGAHLGHVFE 97 (283)
T ss_pred eEEEEecCCCCccCcccC
Confidence 355689999999988765
No 111
>TIGR01053 LSD1 zinc finger domain, LSD1 subclass. This model describes a putative zinc finger domain found in three closely spaced copies in Arabidopsis protein LSD1 and in two copies in other proteins from the same species. The motif resembles CxxCRxxLMYxxGASxVxCxxC
Probab=22.01 E-value=45 Score=17.12 Aligned_cols=13 Identities=23% Similarity=0.524 Sum_probs=10.5
Q ss_pred eCCcCCcccccCC
Q 036084 85 FCKVCGITSFYVP 97 (126)
Q Consensus 85 FC~~CGs~l~~~~ 97 (126)
-|+.|++.|.+-.
T Consensus 3 ~C~~C~t~L~yP~ 15 (31)
T TIGR01053 3 VCGGCRTLLMYPR 15 (31)
T ss_pred CcCCCCcEeecCC
Confidence 4999999997753
No 112
>PF10892 DUF2688: Protein of unknown function (DUF2688); InterPro: IPR024392 Members of this protein family are annotated as KleB, and may play a role in the regulation of transcription in plasmids.
Probab=21.85 E-value=27 Score=20.66 Aligned_cols=16 Identities=25% Similarity=0.549 Sum_probs=11.7
Q ss_pred eeeCCcCCcccccCCC
Q 036084 83 HVFCKVCGITSFYVPR 98 (126)
Q Consensus 83 r~FC~~CGs~l~~~~~ 98 (126)
..-|.+||.+|-...+
T Consensus 10 ~t~CrRCGk~i~tl~~ 25 (60)
T PF10892_consen 10 ETPCRRCGKSIRTLSR 25 (60)
T ss_pred eehhhhhCccHHHHHH
Confidence 3459999999865544
No 113
>smart00673 CARP Domain in CAPs (cyclase-associated proteins) and X-linked retinitis pigmentosa 2 gene product.
Probab=21.83 E-value=1.1e+02 Score=15.62 Aligned_cols=25 Identities=20% Similarity=0.418 Sum_probs=15.3
Q ss_pred CCCeEEEEEcCCCCeeeeecChhhhc
Q 036084 23 CRKVRWRVRAPRSVEAWKCNCSDCSM 48 (126)
Q Consensus 23 CGaV~~~v~~~p~~~~~~ChC~~Crk 48 (126)
|-..++.+.+..... ..-.|..|+-
T Consensus 1 C~~~~i~v~g~~~~v-~id~~~~~~i 25 (38)
T smart00673 1 CESCTIQVSGKVNTI-SIDKCKKCSI 25 (38)
T ss_pred CCcEEEEEeCccCEE-EEECCCCeEE
Confidence 455666777666554 5666666653
No 114
>COG1545 Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]
Probab=21.80 E-value=1e+02 Score=21.22 Aligned_cols=11 Identities=27% Similarity=0.990 Sum_probs=7.7
Q ss_pred eeeCCcCCccc
Q 036084 83 HVFCKVCGITS 93 (126)
Q Consensus 83 r~FC~~CGs~l 93 (126)
|.+|+.||+..
T Consensus 43 r~~Cp~C~~~~ 53 (140)
T COG1545 43 RAYCPKCGSET 53 (140)
T ss_pred cccCCCCCCCC
Confidence 45688888773
No 115
>COG2174 RPL34A Ribosomal protein L34E [Translation, ribosomal structure and biogenesis]
Probab=21.64 E-value=56 Score=21.24 Aligned_cols=23 Identities=30% Similarity=0.583 Sum_probs=17.1
Q ss_pred CeeeeeeCCcCCcccccCCCCCC
Q 036084 79 GTAKHVFCKVCGITSFYVPRGTP 101 (126)
Q Consensus 79 ~~~~r~FC~~CGs~l~~~~~~~p 101 (126)
+.....-|..||.+|.......|
T Consensus 30 K~~~~p~C~~cg~pL~Gi~r~RP 52 (93)
T COG2174 30 KKPTIPKCAICGRPLGGIPRGRP 52 (93)
T ss_pred ccCCCCcccccCCccCCccCCCc
Confidence 33455679999999988776544
No 116
>PF14952 zf-tcix: Putative treble-clef, zinc-finger, Zn-binding
Probab=21.49 E-value=43 Score=18.76 Aligned_cols=12 Identities=25% Similarity=0.371 Sum_probs=8.5
Q ss_pred eCCcCCcccccC
Q 036084 85 FCKVCGITSFYV 96 (126)
Q Consensus 85 FC~~CGs~l~~~ 96 (126)
-|+.||+-=..+
T Consensus 13 kCp~CGt~NG~R 24 (44)
T PF14952_consen 13 KCPKCGTYNGTR 24 (44)
T ss_pred cCCcCcCccCcc
Confidence 499999865433
No 117
>PF02943 FeThRed_B: Ferredoxin thioredoxin reductase catalytic beta chain; InterPro: IPR004209 Ferredoxin thioredoxin reductase is a [4FE-4S] protein present in organisms performing oxygenic photosynthesis, and plays an important role in the ferredoxin/thioredoxin regulatory chain. It converts an electron signal (photoreduced ferredoxin) to a thiol signal (reduced thioredoxin), regulating enzymes by reduction of specific disulphide groups. It catalyses the light-dependent activation of several photosynthetis enzymes. Ferredoxin thioredoxin reductase is a heterodimer of subunit alpha and subunit beta. Subunit alpha is the variable subunit, and beta is the catalytic chain []. The structure of the beta subunit has been determined and found to fold around the FeS cluster [].; GO: 0008937 ferredoxin-NAD(P) reductase activity, 0055114 oxidation-reduction process; PDB: 2PUK_E 2PVD_A 2PVG_A 2PUO_A 2PU9_A 1DJ7_A 2PVO_A.
Probab=21.33 E-value=33 Score=22.92 Aligned_cols=9 Identities=33% Similarity=0.888 Sum_probs=3.2
Q ss_pred eEEeeeCCC
Q 036084 17 HKGGCRCRK 25 (126)
Q Consensus 17 ~~GsC~CGa 25 (126)
..|+||||-
T Consensus 77 ~~G~ChC~L 85 (108)
T PF02943_consen 77 EYGHCHCGL 85 (108)
T ss_dssp -----TTSS
T ss_pred ccccceEee
Confidence 679999984
No 118
>smart00067 GHA Glycoprotein hormone alpha chain homologues. Also called gonadotropins. Glycoprotein hormones consist of two glycosylated chains (alpha and beta) of similar topology.
Probab=21.28 E-value=44 Score=21.25 Aligned_cols=34 Identities=24% Similarity=0.446 Sum_probs=17.9
Q ss_pred CceeEEeeeCCCeEEEEEc---CCCCeeeeecChhhh
Q 036084 14 SGLHKGGCRCRKVRWRVRA---PRSVEAWKCNCSDCS 47 (126)
Q Consensus 14 ~~~~~GsC~CGaV~~~v~~---~p~~~~~~ChC~~Cr 47 (126)
.++-++.|-=..--+++.. -.......|||+.|.
T Consensus 47 NITSEAtCCVAk~~~~v~v~~~~~v~NHT~ChCsTCy 83 (87)
T smart00067 47 NITSEATCCVAKEFYRVTVMDNIKVENHTECHCSTCY 83 (87)
T ss_pred cccCceeEEEecccEEEEEeCCcEEeeccccccccee
Confidence 3444566644443344433 122223679999985
No 119
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=21.05 E-value=40 Score=26.66 Aligned_cols=12 Identities=42% Similarity=1.054 Sum_probs=10.5
Q ss_pred eeeeCCcCCccc
Q 036084 82 KHVFCKVCGITS 93 (126)
Q Consensus 82 ~r~FC~~CGs~l 93 (126)
.+.+||.||+.-
T Consensus 186 ~~~~CPvCGs~P 197 (309)
T PRK03564 186 QRQFCPVCGSMP 197 (309)
T ss_pred CCCCCCCCCCcc
Confidence 678999999985
No 120
>smart00508 PostSET Cysteine-rich motif following a subset of SET domains.
Probab=20.94 E-value=47 Score=16.45 Aligned_cols=8 Identities=25% Similarity=0.679 Sum_probs=5.4
Q ss_pred eeeCCCeE
Q 036084 20 GCRCRKVR 27 (126)
Q Consensus 20 sC~CGaV~ 27 (126)
.|+||+..
T Consensus 4 ~C~CGs~~ 11 (26)
T smart00508 4 PCLCGAPN 11 (26)
T ss_pred eeeCCCcc
Confidence 57787754
No 121
>PF01258 zf-dskA_traR: Prokaryotic dksA/traR C4-type zinc finger; InterPro: IPR000962 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents domains identified in zinc finger-containing members of the DksA/TraR family. DksA is a critical component of the rRNA transcription initiation machinery that potentiates the regulation of rRNA promoters by ppGpp and the initiating NTP. In delta-dksA mutants, rRNA promoters are unresponsive to changes in amino acid availability, growth rate, or growth phase. In vitro, DksA binds to RNAP, reduces open complex lifetime, inhibits rRNA promoter activity, and amplifies effects of ppGpp and the initiating NTP on rRNA transcription [, ]. The dksA gene product suppresses the temperature-sensitive growth and filamentation of a dnaK deletion mutant of Escherichia coli. Gene knockout [] and deletion [] experiments have shown the gene to be non-essential, mutations causing a mild sensitivity to UV light, but not affecting DNA recombination []. In Pseudomonas aeruginosa, dksA is a novel regulator involved in the post-transcriptional control of extracellular virulence factor production []. The proteins contain a C-terminal region thought to fold into a 4-cysteine zinc finger. Other proteins found to contain a similar zinc finger domain include: the traR gene products encoded on the E. coli F and R100 plasmids [, ] the traR gene products encoded on Salmonella spp. plasmids pED208 and pSLT the dnaK suppressor hypothetical proteins from bacteria and bacteriophage FHL4, LIM proteins from Homo sapiens (Human) and Mus musculus (Mouse) [] More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2GVI_A 2KQ9_A 2KGO_A 1TJL_I.
Probab=20.56 E-value=48 Score=17.16 Aligned_cols=13 Identities=23% Similarity=0.330 Sum_probs=9.4
Q ss_pred eeCCcCCcccccC
Q 036084 84 VFCKVCGITSFYV 96 (126)
Q Consensus 84 ~FC~~CGs~l~~~ 96 (126)
.+|..||-+|...
T Consensus 4 g~C~~CGe~I~~~ 16 (36)
T PF01258_consen 4 GICEDCGEPIPEE 16 (36)
T ss_dssp SB-TTTSSBEEHH
T ss_pred CCccccCChHHHH
Confidence 3599999998754
No 122
>PF09723 Zn-ribbon_8: Zinc ribbon domain; InterPro: IPR013429 This entry represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB []. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=20.41 E-value=50 Score=17.83 Aligned_cols=10 Identities=40% Similarity=0.810 Sum_probs=8.0
Q ss_pred eeeeCCcCCc
Q 036084 82 KHVFCKVCGI 91 (126)
Q Consensus 82 ~r~FC~~CGs 91 (126)
...-|+.||+
T Consensus 25 ~~~~CP~Cg~ 34 (42)
T PF09723_consen 25 DPVPCPECGS 34 (42)
T ss_pred CCCcCCCCCC
Confidence 4556999998
No 123
>TIGR00373 conserved hypothetical protein TIGR00373. This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.
Probab=20.26 E-value=45 Score=23.48 Aligned_cols=12 Identities=33% Similarity=0.733 Sum_probs=9.5
Q ss_pred eCCcCCcccccC
Q 036084 85 FCKVCGITSFYV 96 (126)
Q Consensus 85 FC~~CGs~l~~~ 96 (126)
-||.||..|-..
T Consensus 130 ~Cp~Cg~~L~~~ 141 (158)
T TIGR00373 130 TCPRCGAMLDYL 141 (158)
T ss_pred cCCCCCCEeeec
Confidence 499999998654
No 124
>PRK03954 ribonuclease P protein component 4; Validated
Probab=20.14 E-value=19 Score=24.54 Aligned_cols=17 Identities=24% Similarity=0.380 Sum_probs=14.1
Q ss_pred CCeeeeeeCCcCCcccc
Q 036084 78 TGTAKHVFCKVCGITSF 94 (126)
Q Consensus 78 ~~~~~r~FC~~CGs~l~ 94 (126)
++...|.||..|.+.|-
T Consensus 59 p~~~KR~~CK~C~t~Li 75 (121)
T PRK03954 59 PRKWKRRYCKRCHSFLV 75 (121)
T ss_pred CHHHHHHHhhcCCCeee
Confidence 44578999999999984
No 125
>TIGR01206 lysW lysine biosynthesis protein LysW. This very small, poorly characterized protein has been shown essential in Thermus thermophilus for an unusual pathway of Lys biosynthesis from aspartate by way of alpha-aminoadipate (AAA) rather than diaminopimelate. It is found also in Deinococcus radiodurans and Pyrococcus horikoshii, which appear to share the AAA pathway.
Probab=20.00 E-value=49 Score=19.25 Aligned_cols=12 Identities=25% Similarity=0.382 Sum_probs=9.4
Q ss_pred eCCcCCcccccC
Q 036084 85 FCKVCGITSFYV 96 (126)
Q Consensus 85 FC~~CGs~l~~~ 96 (126)
-|+.||..|-..
T Consensus 4 ~CP~CG~~iev~ 15 (54)
T TIGR01206 4 ECPDCGAEIELE 15 (54)
T ss_pred CCCCCCCEEecC
Confidence 499999988543
Done!