Query 033418
Match_columns 119
No_of_seqs 166 out of 817
Neff 5.5
Searched_HMMs 46136
Date Fri Mar 29 13:40:00 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/033418.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/033418hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1088 Uncharacterized conser 100.0 7E-52 1.5E-56 295.7 9.8 118 1-119 1-124 (124)
2 PF03966 Trm112p: Trm112p-like 99.8 3.8E-21 8.2E-26 125.2 1.5 68 2-108 1-68 (68)
3 COG2835 Uncharacterized conser 99.1 1.4E-11 3.1E-16 79.1 1.5 31 88-118 21-51 (60)
4 PRK11827 hypothetical protein; 99.1 4.1E-11 8.8E-16 77.1 0.7 31 88-118 21-51 (60)
5 PF13717 zinc_ribbon_4: zinc-r 89.3 0.18 3.9E-06 28.9 0.9 18 93-110 2-20 (36)
6 PF08792 A2L_zn_ribbon: A2L zi 82.7 0.78 1.7E-05 25.9 1.2 17 89-105 17-33 (33)
7 PF12760 Zn_Tnp_IS1595: Transp 81.8 1.5 3.3E-05 25.9 2.4 30 77-107 3-34 (46)
8 PF08271 TF_Zn_Ribbon: TFIIB z 79.5 1.2 2.6E-05 26.0 1.3 15 88-102 14-28 (43)
9 PF13719 zinc_ribbon_5: zinc-r 78.8 1.1 2.4E-05 25.6 1.0 15 94-108 3-17 (37)
10 PF08274 PhnA_Zn_Ribbon: PhnA 78.0 1.2 2.5E-05 24.8 0.9 16 89-104 15-30 (30)
11 PF05191 ADK_lid: Adenylate ki 76.4 1.3 2.8E-05 25.4 0.9 14 94-107 2-15 (36)
12 PRK00420 hypothetical protein; 76.0 1.4 3.1E-05 31.5 1.1 21 88-108 35-55 (112)
13 TIGR02098 MJ0042_CXXC MJ0042 f 74.2 1.3 2.8E-05 24.9 0.5 15 94-108 3-17 (38)
14 PF10571 UPF0547: Uncharacteri 74.0 1.6 3.4E-05 23.5 0.7 17 88-104 9-25 (26)
15 PF14353 CpXC: CpXC protein 72.2 1.7 3.7E-05 30.6 0.8 19 88-106 30-51 (128)
16 PF13913 zf-C2HC_2: zinc-finge 71.5 1.8 3.9E-05 22.8 0.6 11 94-104 3-13 (25)
17 COG4391 Uncharacterized protei 71.1 2.2 4.8E-05 27.6 1.0 17 89-105 44-60 (62)
18 PF13408 Zn_ribbon_recom: Reco 69.3 2.7 5.9E-05 25.0 1.1 17 90-106 2-18 (58)
19 PF00096 zf-C2H2: Zinc finger, 68.9 2.3 5E-05 20.9 0.6 12 95-106 2-13 (23)
20 smart00834 CxxC_CXXC_SSSS Puta 67.2 3.1 6.8E-05 23.3 1.0 18 93-110 5-22 (41)
21 PF07295 DUF1451: Protein of u 66.4 6.8 0.00015 29.0 2.9 30 78-107 90-126 (146)
22 TIGR00686 phnA alkylphosphonat 66.2 3.1 6.8E-05 29.7 1.1 18 90-107 16-33 (109)
23 PRK10220 hypothetical protein; 63.6 4.2 9.1E-05 29.2 1.3 18 90-107 17-34 (111)
24 smart00661 RPOL9 RNA polymeras 60.5 5.6 0.00012 23.4 1.3 16 93-108 20-35 (52)
25 PRK11032 hypothetical protein; 60.2 7.5 0.00016 29.4 2.2 30 78-107 102-138 (160)
26 PF14569 zf-UDP: Zinc-binding 59.5 5.5 0.00012 27.0 1.2 33 86-118 44-76 (80)
27 TIGR00515 accD acetyl-CoA carb 58.8 2.4 5.1E-05 34.6 -0.7 33 74-106 26-58 (285)
28 PF09538 FYDLN_acid: Protein o 58.6 6 0.00013 28.0 1.4 19 88-106 21-39 (108)
29 COG1645 Uncharacterized Zn-fin 58.5 5.4 0.00012 29.3 1.2 38 51-104 18-55 (131)
30 PF13878 zf-C2H2_3: zinc-finge 53.6 6.3 0.00014 23.0 0.7 15 92-106 12-26 (41)
31 PRK00398 rpoP DNA-directed RNA 53.5 9.5 0.0002 22.4 1.5 15 94-108 4-18 (46)
32 PF13894 zf-C2H2_4: C2H2-type 52.9 6.9 0.00015 18.6 0.7 12 95-106 2-13 (24)
33 COG1594 RPB9 DNA-directed RNA 52.8 9.1 0.0002 27.1 1.6 20 88-107 17-36 (113)
34 smart00531 TFIIE Transcription 52.3 11 0.00024 27.4 2.0 24 80-104 111-134 (147)
35 TIGR02605 CxxC_CxxC_SSSS putat 51.2 8.8 0.00019 22.7 1.1 15 93-107 5-19 (52)
36 PRK05654 acetyl-CoA carboxylas 50.6 4.1 8.9E-05 33.3 -0.6 33 74-106 27-59 (292)
37 PF09723 Zn-ribbon_8: Zinc rib 50.1 8.6 0.00019 22.3 0.9 18 93-110 5-22 (42)
38 PF04423 Rad50_zn_hook: Rad50 49.1 16 0.00035 22.0 2.0 17 86-104 15-31 (54)
39 PF13248 zf-ribbon_3: zinc-rib 48.7 8.5 0.00018 20.2 0.7 7 95-101 4-10 (26)
40 PRK11088 rrmA 23S rRNA methylt 47.8 14 0.0003 28.9 2.1 25 90-115 15-40 (272)
41 COG0068 HypF Hydrogenase matur 47.0 14 0.0003 34.2 2.1 42 70-111 97-141 (750)
42 PF02591 DUF164: Putative zinc 46.9 12 0.00025 22.9 1.2 12 91-102 44-55 (56)
43 PF13912 zf-C2H2_6: C2H2-type 46.6 10 0.00023 19.2 0.8 11 94-104 2-12 (27)
44 PRK12380 hydrogenase nickel in 46.3 12 0.00025 26.3 1.2 20 88-107 65-84 (113)
45 TIGR00100 hypA hydrogenase nic 46.1 12 0.00026 26.3 1.3 20 88-107 65-84 (115)
46 PF02150 RNA_POL_M_15KD: RNA p 45.4 11 0.00023 21.3 0.8 13 95-107 22-34 (35)
47 PF08671 SinI: Anti-repressor 44.0 20 0.00044 19.9 1.7 16 48-63 3-18 (30)
48 PRK03681 hypA hydrogenase nick 43.7 13 0.00029 26.1 1.2 19 88-106 65-83 (114)
49 cd00924 Cyt_c_Oxidase_Vb Cytoc 41.9 12 0.00026 26.0 0.7 19 88-106 73-92 (97)
50 PF13240 zinc_ribbon_2: zinc-r 41.8 11 0.00024 19.4 0.4 15 88-102 8-22 (23)
51 CHL00174 accD acetyl-CoA carbo 41.4 8.6 0.00019 31.7 -0.1 33 74-106 38-70 (296)
52 PF01927 Mut7-C: Mut7-C RNAse 41.2 13 0.00027 27.0 0.8 12 92-103 123-134 (147)
53 PF13451 zf-trcl: Probable zin 40.8 15 0.00032 22.6 1.0 18 91-108 2-19 (49)
54 COG2824 PhnA Uncharacterized Z 40.8 14 0.0003 26.5 0.9 15 90-104 17-31 (112)
55 smart00659 RPOLCX RNA polymera 40.5 21 0.00046 21.2 1.6 21 91-111 17-37 (44)
56 PF11781 RRN7: RNA polymerase 40.2 15 0.00032 21.0 0.8 15 88-102 20-34 (36)
57 cd07153 Fur_like Ferric uptake 39.6 16 0.00034 24.6 1.1 16 93-108 73-88 (116)
58 PF01155 HypA: Hydrogenase exp 39.5 11 0.00025 26.3 0.3 21 88-108 65-85 (113)
59 PF13465 zf-H2C2_2: Zinc-finge 39.2 22 0.00047 18.4 1.3 17 88-104 9-25 (26)
60 PRK07591 threonine synthase; V 38.7 17 0.00038 30.7 1.4 14 93-106 18-31 (421)
61 PF01475 FUR: Ferric uptake re 38.7 15 0.00032 25.1 0.8 17 92-108 79-95 (120)
62 PRK12496 hypothetical protein; 38.5 17 0.00036 27.2 1.1 13 94-106 128-140 (164)
63 PF04475 DUF555: Protein of un 38.5 14 0.00031 26.1 0.7 18 87-104 41-58 (102)
64 COG4493 Uncharacterized protei 38.5 25 0.00055 27.6 2.1 38 66-107 141-179 (209)
65 PRK03824 hypA hydrogenase nick 37.7 14 0.0003 26.7 0.6 21 88-108 102-123 (135)
66 PF10080 DUF2318: Predicted me 37.6 16 0.00035 25.6 0.9 19 88-106 47-65 (102)
67 PF14446 Prok-RING_1: Prokaryo 37.4 22 0.00049 22.3 1.4 15 90-104 18-32 (54)
68 PF09297 zf-NADH-PPase: NADH p 36.7 20 0.00044 19.4 1.0 13 91-103 19-31 (32)
69 PRK00564 hypA hydrogenase nick 36.7 19 0.00042 25.4 1.1 19 88-106 66-84 (117)
70 PF10122 Mu-like_Com: Mu-like 36.7 38 0.00082 21.1 2.3 33 81-113 11-44 (51)
71 TIGR01384 TFS_arch transcripti 36.4 22 0.00048 23.9 1.4 18 89-106 12-29 (104)
72 PF05488 PAAR_motif: PAAR moti 36.2 26 0.00056 22.3 1.6 27 90-116 31-57 (76)
73 PRK00423 tfb transcription ini 36.0 19 0.00041 29.3 1.1 16 88-103 25-40 (310)
74 PLN02569 threonine synthase 35.8 18 0.00039 31.5 1.0 16 93-108 49-64 (484)
75 KOG3352 Cytochrome c oxidase, 35.0 16 0.00034 27.6 0.5 19 89-107 128-147 (153)
76 PF07754 DUF1610: Domain of un 33.3 24 0.00052 18.6 0.9 9 93-101 16-24 (24)
77 PRK06266 transcription initiat 33.1 46 0.001 25.2 2.8 16 91-106 115-130 (178)
78 PLN02459 probable adenylate ki 33.0 25 0.00055 28.3 1.4 18 89-106 149-166 (261)
79 TIGR00143 hypF [NiFe] hydrogen 32.9 31 0.00068 31.5 2.1 41 70-110 64-107 (711)
80 COG4049 Uncharacterized protei 32.7 17 0.00038 23.4 0.3 14 93-106 17-30 (65)
81 COG0375 HybF Zn finger protein 32.7 25 0.00054 25.3 1.2 21 88-108 81-102 (115)
82 PF10609 ParA: ParA/MinD ATPas 31.9 24 0.00052 23.7 0.9 14 92-105 64-77 (81)
83 smart00355 ZnF_C2H2 zinc finge 31.9 20 0.00044 16.9 0.5 11 95-105 2-12 (26)
84 PRK03922 hypothetical protein; 31.8 22 0.00047 25.6 0.8 18 87-104 43-60 (113)
85 PF01215 COX5B: Cytochrome c o 31.7 16 0.00035 26.9 0.1 20 88-107 106-126 (136)
86 PF03604 DNA_RNApol_7kD: DNA d 31.3 31 0.00067 19.3 1.2 9 93-101 17-25 (32)
87 TIGR02300 FYDLN_acid conserved 30.9 26 0.00056 25.8 1.0 19 88-106 21-39 (129)
88 PLN02189 cellulose synthase 30.9 28 0.00061 33.5 1.5 32 87-118 70-101 (1040)
89 PF12171 zf-C2H2_jaz: Zinc-fin 30.5 29 0.00064 17.8 1.0 11 94-104 2-12 (27)
90 PF14311 DUF4379: Domain of un 30.4 25 0.00055 21.2 0.8 11 94-104 29-39 (55)
91 PRK09462 fur ferric uptake reg 29.9 28 0.00061 24.9 1.1 16 93-108 90-105 (148)
92 PHA02768 hypothetical protein; 29.7 18 0.0004 22.7 0.1 14 94-107 6-19 (55)
93 COG1656 Uncharacterized conser 29.5 24 0.00053 26.9 0.7 11 93-103 130-140 (165)
94 PF05129 Elf1: Transcription e 29.3 27 0.00058 23.3 0.8 22 89-112 42-63 (81)
95 PHA00616 hypothetical protein 29.1 16 0.00035 22.0 -0.2 10 95-104 3-12 (44)
96 COG0777 AccD Acetyl-CoA carbox 28.7 8.8 0.00019 31.7 -1.9 33 74-106 28-60 (294)
97 PF10013 DUF2256: Uncharacteri 28.0 27 0.00059 20.9 0.6 10 95-104 10-19 (42)
98 TIGR00373 conserved hypothetic 27.8 66 0.0014 23.7 2.8 16 91-106 107-122 (158)
99 PTZ00088 adenylate kinase 1; P 27.8 26 0.00056 27.3 0.6 17 90-106 127-143 (229)
100 TIGR03829 YokU_near_AblA uncha 27.5 26 0.00057 24.1 0.6 12 93-104 35-46 (89)
101 PLN02294 cytochrome c oxidase 27.4 28 0.0006 26.8 0.7 19 88-106 135-154 (174)
102 PRK11639 zinc uptake transcrip 27.1 33 0.00072 25.4 1.1 16 93-108 100-115 (169)
103 cd03467 Rieske Rieske domain; 27.0 50 0.0011 21.5 1.8 23 89-111 54-76 (98)
104 TIGR03831 YgiT_finger YgiT-typ 26.9 28 0.0006 19.5 0.5 11 93-103 32-42 (46)
105 PF15541 Toxin_63: Putative to 26.7 64 0.0014 22.7 2.3 35 78-112 39-74 (104)
106 PLN02638 cellulose synthase A 26.4 35 0.00076 32.9 1.3 33 86-118 52-84 (1079)
107 cd03478 Rieske_AIFL_N AIFL (ap 26.0 47 0.001 21.6 1.6 24 88-111 51-74 (95)
108 PF10276 zf-CHCC: Zinc-finger 25.8 41 0.00089 19.7 1.1 12 92-103 28-39 (40)
109 PLN02436 cellulose synthase A 25.8 40 0.00086 32.6 1.5 32 87-118 72-103 (1094)
110 cd00350 rubredoxin_like Rubred 25.6 36 0.00079 18.6 0.8 13 94-106 2-14 (33)
111 PF08209 Sgf11: Sgf11 (transcr 25.3 43 0.00092 18.9 1.1 12 92-103 3-14 (33)
112 PHA00626 hypothetical protein 25.0 33 0.00072 21.9 0.7 18 94-111 1-18 (59)
113 KOG2593 Transcription initiati 25.0 38 0.00082 29.5 1.2 13 92-104 127-139 (436)
114 PRK00432 30S ribosomal protein 24.9 45 0.00098 20.2 1.2 16 88-103 32-47 (50)
115 PF06750 DiS_P_DiS: Bacterial 24.9 33 0.00071 23.3 0.6 25 88-112 28-52 (92)
116 cd03528 Rieske_RO_ferredoxin R 24.3 51 0.0011 21.4 1.5 23 89-111 53-75 (98)
117 TIGR01206 lysW lysine biosynth 24.1 58 0.0012 20.3 1.6 20 91-110 20-39 (54)
118 PTZ00043 cytochrome c oxidase 24.0 31 0.00068 28.0 0.5 19 88-106 175-194 (268)
119 PF00628 PHD: PHD-finger; Int 24.0 59 0.0013 18.7 1.6 17 90-106 11-27 (51)
120 PF13926 DUF4211: Domain of un 23.9 1.2E+02 0.0026 21.9 3.6 66 34-102 50-125 (153)
121 PRK09521 exosome complex RNA-b 23.6 46 0.00099 25.0 1.3 13 92-104 165-177 (189)
122 PF11238 DUF3039: Protein of u 23.0 18 0.00039 23.1 -0.9 11 94-104 45-55 (58)
123 COG0821 gcpE 1-hydroxy-2-methy 23.0 48 0.001 28.2 1.4 26 77-102 245-270 (361)
124 COG4888 Uncharacterized Zn rib 22.8 42 0.00091 23.8 0.9 18 88-105 41-58 (104)
125 PF10426 zf-RAG1: Recombinatio 22.8 30 0.00065 19.3 0.1 10 8-17 2-11 (30)
126 PLN02915 cellulose synthase A 22.7 47 0.001 32.0 1.5 30 86-115 50-79 (1044)
127 PLN02400 cellulose synthase 22.7 53 0.0011 31.8 1.8 32 87-118 72-103 (1085)
128 COG1545 Predicted nucleic-acid 22.5 39 0.00084 24.6 0.7 24 78-103 16-39 (140)
129 PF11023 DUF2614: Protein of u 22.5 46 0.00099 24.0 1.0 12 92-103 68-79 (114)
130 COG4530 Uncharacterized protei 22.4 48 0.001 24.1 1.1 19 88-106 21-39 (129)
131 PRK00762 hypA hydrogenase nick 22.4 45 0.00098 23.7 1.0 18 88-106 65-82 (124)
132 COG1990 pth2 Peptidyl-tRNA hyd 21.7 69 0.0015 23.3 1.8 18 80-97 85-102 (122)
133 PF08996 zf-DNA_Pol: DNA Polym 21.5 48 0.001 25.0 1.0 20 88-107 13-32 (188)
134 COG1326 Uncharacterized archae 21.2 79 0.0017 24.9 2.2 17 89-105 26-42 (201)
135 PRK14526 adenylate kinase; Pro 20.9 44 0.00095 25.6 0.7 19 89-107 118-136 (211)
136 PF13959 DUF4217: Domain of un 20.6 93 0.002 19.5 2.1 21 45-68 43-63 (65)
137 PLN02674 adenylate kinase 20.5 49 0.0011 26.3 0.9 23 88-110 153-175 (244)
138 PF02954 HTH_8: Bacterial regu 20.3 24 0.00052 20.2 -0.7 27 36-63 5-31 (42)
139 smart00249 PHD PHD zinc finger 20.3 63 0.0014 17.4 1.2 16 91-106 12-27 (47)
140 PF14205 Cys_rich_KTR: Cystein 20.3 60 0.0013 20.5 1.1 11 91-101 2-12 (55)
141 PF11336 DUF3138: Protein of u 20.1 35 0.00077 30.1 0.1 12 1-12 232-243 (514)
142 PF10083 DUF2321: Uncharacteri 20.1 34 0.00073 26.0 -0.1 13 94-106 69-81 (158)
143 COG4338 Uncharacterized protei 20.1 33 0.00071 21.4 -0.1 11 94-104 13-23 (54)
144 PF10884 DUF2683: Protein of u 20.0 42 0.00092 22.7 0.4 16 31-46 43-58 (80)
No 1
>KOG1088 consensus Uncharacterized conserved protein [Function unknown]
Probab=100.00 E-value=7e-52 Score=295.67 Aligned_cols=118 Identities=58% Similarity=1.068 Sum_probs=114.1
Q ss_pred CccccchhhccCcCCccC-CCCeeEEEeEEEEecccCCHHHHhcccchhcHHHHHHHHHhCCCCCCCCCCCCCCCCC-cH
Q 033418 1 MRLLTHNMLSSNIKGVAN-GFPLLIEVEKVIEKQVDFNPDFLKNIFPKIEWQALVQASRSMGYSELPEESPESSMLD-SD 78 (119)
Q Consensus 1 MrllthN~L~c~~k~c~~-~fPL~l~~~~~~~~e~efn~~fi~~~l~kldw~al~~~a~~lg~~~lP~~~~p~~~~~-~e 78 (119)
|||+|||||+|++|+|.+ ||||++++.++++.++||||+|+.+|++|+||+||+.+|+++|..+||+. .|+++.+ ||
T Consensus 1 MKLlthNfLsc~~k~~~s~gFPL~l~~~k~~~~~vEFnPdFl~~m~~kidW~All~~A~~l~~~~lP~~-kPe~~~e~de 79 (124)
T KOG1088|consen 1 MKLLTHNFLSCSVKKVVSVGFPLRLVAKKVVEKEVEFNPDFLIRMLPKIDWSALLEAARSLGNTELPDE-KPEKLVEDDE 79 (124)
T ss_pred CceeeeehhhheeecccccCCceEEEeeEEEEEeeecChHHHHHhhhhccHHHHHHHHHHhccccCCCC-CccccccccH
Confidence 999999999999999985 99999999999999999999999999999999999999999999999999 8988777 88
Q ss_pred HHHHHHHhc----ccccceeecCCCCccccccCCccccCCCCCCC
Q 033418 79 DFLMKFHHL----HLEEGALVCPETGRKFPVNKGIPNMLLHEDEV 119 (119)
Q Consensus 79 e~L~~lH~~----~i~~g~L~C~~c~~~ypI~~GIP~mL~~e~~v 119 (119)
+|||++||+ +|.||+|+||+|||.|||++||||||+.++|+
T Consensus 80 ~~Lr~lHhlLle~~v~EG~l~CpetG~vfpI~~GIPNMLL~e~Ev 124 (124)
T KOG1088|consen 80 EFLRKLHHLLLEIDVIEGELVCPETGRVFPISDGIPNMLLSEDEV 124 (124)
T ss_pred HHHHHHHHHHhhhhhccceEecCCCCcEeecccCCcccccCcccC
Confidence 899999999 99999999999999999999999999999986
No 2
>PF03966 Trm112p: Trm112p-like protein; InterPro: IPR005651 This family of short proteins have no known function. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. The function of this family is uncertain. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. The entry contains 2 families: Trm112, which is required for tRNA methylation in Saccharomyces cerevisiae (Baker's yeast) and is found in complexes with 2 tRNA methylases (TRM9 and TRM11) also with putative methyltransferase YDR140W []. The zinc-finger protein Ynr046w is plurifunctional and a component of the eRF1 methyltransferase in yeast []. The crystal structure of Ynr046w has been determined to 1.7 A resolution. It comprises a zinc-binding domain built from both the N- and C-terminal sequences and an inserted domain, absent from bacterial and archaeal orthologs of the protein, composed of three alpha-helices []. UPF0434, which are proteins that are functionally uncharacterised. ; PDB: 3Q87_A 2KPI_A 2K5R_A 2HF1_A 2JS4_A 2J6A_A 2JR6_A 2PK7_A 2JNY_A.
Probab=99.81 E-value=3.8e-21 Score=125.21 Aligned_cols=68 Identities=40% Similarity=0.838 Sum_probs=57.0
Q ss_pred ccccchhhccCcCCccCCCCeeEEEeEEEEecccCCHHHHhcccchhcHHHHHHHHHhCCCCCCCCCCCCCCCCCcHHHH
Q 033418 2 RLLTHNMLSSNIKGVANGFPLLIEVEKVIEKQVDFNPDFLKNIFPKIEWQALVQASRSMGYSELPEESPESSMLDSDDFL 81 (119)
Q Consensus 2 rllthN~L~c~~k~c~~~fPL~l~~~~~~~~e~efn~~fi~~~l~kldw~al~~~a~~lg~~~lP~~~~p~~~~~~ee~L 81 (119)
|++|||||+|+ .|+ | || ||.+|+++|+ +|+.++|+. .++++
T Consensus 1 k~~llniL~Cp--~ck-~-pL--------------------------~~~~l~~~~~-~~~~~lp~~-~~~~~------- 41 (68)
T PF03966_consen 1 KLLLLNILACP--VCK-G-PL--------------------------DWEALVETAQ-LGLSELPKE-LPEDY------- 41 (68)
T ss_dssp BGGGCGTBB-T--TTS-S-BE--------------------------HHHHHHHHHH-CCCCHCHHC-HHCHC-------
T ss_pred ChhHHhhhcCC--CCC-C-cc--------------------------hHHHHHHHHH-hCcccCCCC-Cccch-------
Confidence 68999999999 687 5 88 9999999999 998778877 66444
Q ss_pred HHHHhcccccceeecCCCCccccccCC
Q 033418 82 MKFHHLHLEEGALVCPETGRKFPVNKG 108 (119)
Q Consensus 82 ~~lH~~~i~~g~L~C~~c~~~ypI~~G 108 (119)
+.+...++++|.|+||+|||+|||+||
T Consensus 42 ~~l~~~~i~eg~L~Cp~c~r~YPI~dG 68 (68)
T PF03966_consen 42 HVLLEVEIVEGELICPECGREYPIRDG 68 (68)
T ss_dssp EHHCTEETTTTEEEETTTTEEEEEETT
T ss_pred hhhhcccccCCEEEcCCCCCEEeCCCC
Confidence 233346999999999999999999998
No 3
>COG2835 Uncharacterized conserved protein [Function unknown]
Probab=99.14 E-value=1.4e-11 Score=79.09 Aligned_cols=31 Identities=32% Similarity=0.699 Sum_probs=27.6
Q ss_pred ccccceeecCCCCccccccCCccccCCCCCC
Q 033418 88 HLEEGALVCPETGRKFPVNKGIPNMLLHEDE 118 (119)
Q Consensus 88 ~i~~g~L~C~~c~~~ypI~~GIP~mL~~e~~ 118 (119)
+-..++|+|+.|+++|||+||||+||++|+.
T Consensus 21 ~~~~~~L~c~~~~~aYpI~dGIPvlL~~eaR 51 (60)
T COG2835 21 DEEKQELICPRCKLAYPIRDGIPVLLPDEAR 51 (60)
T ss_pred eccCCEEEecccCceeecccCccccCchhhc
Confidence 4556699999999999999999999999864
No 4
>PRK11827 hypothetical protein; Provisional
Probab=99.05 E-value=4.1e-11 Score=77.12 Aligned_cols=31 Identities=32% Similarity=0.613 Sum_probs=27.3
Q ss_pred ccccceeecCCCCccccccCCccccCCCCCC
Q 033418 88 HLEEGALVCPETGRKFPVNKGIPNMLLHEDE 118 (119)
Q Consensus 88 ~i~~g~L~C~~c~~~ypI~~GIP~mL~~e~~ 118 (119)
+..+++|+|+.||++|||+||||+||.++++
T Consensus 21 ~~~~~~Lic~~~~laYPI~dgIPVlL~deAr 51 (60)
T PRK11827 21 NQEKQELICKLDNLAFPLRDGIPVLLETEAR 51 (60)
T ss_pred cCCCCeEECCccCeeccccCCccccCHHHhc
Confidence 3445789999999999999999999999874
No 5
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=89.35 E-value=0.18 Score=28.89 Aligned_cols=18 Identities=28% Similarity=0.820 Sum_probs=15.1
Q ss_pred eeecCCCCccccccCC-cc
Q 033418 93 ALVCPETGRKFPVNKG-IP 110 (119)
Q Consensus 93 ~L~C~~c~~~ypI~~G-IP 110 (119)
.++||+|+..|.|.|. ||
T Consensus 2 ~i~Cp~C~~~y~i~d~~ip 20 (36)
T PF13717_consen 2 IITCPNCQAKYEIDDEKIP 20 (36)
T ss_pred EEECCCCCCEEeCCHHHCC
Confidence 3689999999999987 54
No 6
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=82.70 E-value=0.78 Score=25.94 Aligned_cols=17 Identities=35% Similarity=0.534 Sum_probs=14.5
Q ss_pred cccceeecCCCCccccc
Q 033418 89 LEEGALVCPETGRKFPV 105 (119)
Q Consensus 89 i~~g~L~C~~c~~~ypI 105 (119)
-..+.++|+.||..||+
T Consensus 17 ~~~~~~~C~~Cg~~~~~ 33 (33)
T PF08792_consen 17 KEDDYEVCIFCGSSFPY 33 (33)
T ss_pred ecCCeEEcccCCcEeeC
Confidence 35788999999999985
No 7
>PF12760 Zn_Tnp_IS1595: Transposase zinc-ribbon domain; InterPro: IPR024442 This zinc binding domain is found in a range of transposase proteins such as ISSPO8, ISSOD11, ISRSSP2 etc. It may be a zinc-binding beta ribbon domain that could bind DNA.
Probab=81.82 E-value=1.5 Score=25.92 Aligned_cols=30 Identities=17% Similarity=0.535 Sum_probs=20.0
Q ss_pred cHHHHHHHHhcccccceeecCCCCc--cccccC
Q 033418 77 SDDFLMKFHHLHLEEGALVCPETGR--KFPVNK 107 (119)
Q Consensus 77 ~ee~L~~lH~~~i~~g~L~C~~c~~--~ypI~~ 107 (119)
++++++-|...---+| .+||.||. .|.|++
T Consensus 3 e~~c~~~l~~~RW~~g-~~CP~Cg~~~~~~~~~ 34 (46)
T PF12760_consen 3 EEACREYLEEIRWPDG-FVCPHCGSTKHYRLKT 34 (46)
T ss_pred HHHHHHHHHHhcCCCC-CCCCCCCCeeeEEeCC
Confidence 3556665555544555 88999994 677766
No 8
>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=79.47 E-value=1.2 Score=26.01 Aligned_cols=15 Identities=47% Similarity=0.851 Sum_probs=12.1
Q ss_pred ccccceeecCCCCcc
Q 033418 88 HLEEGALVCPETGRK 102 (119)
Q Consensus 88 ~i~~g~L~C~~c~~~ 102 (119)
|-..|+++|++||..
T Consensus 14 D~~~g~~vC~~CG~V 28 (43)
T PF08271_consen 14 DPERGELVCPNCGLV 28 (43)
T ss_dssp ETTTTEEEETTT-BB
T ss_pred cCCCCeEECCCCCCE
Confidence 567899999999975
No 9
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=78.78 E-value=1.1 Score=25.61 Aligned_cols=15 Identities=27% Similarity=0.733 Sum_probs=12.8
Q ss_pred eecCCCCccccccCC
Q 033418 94 LVCPETGRKFPVNKG 108 (119)
Q Consensus 94 L~C~~c~~~ypI~~G 108 (119)
..||+|+..|.|.+.
T Consensus 3 i~CP~C~~~f~v~~~ 17 (37)
T PF13719_consen 3 ITCPNCQTRFRVPDD 17 (37)
T ss_pred EECCCCCceEEcCHH
Confidence 579999999998875
No 10
>PF08274 PhnA_Zn_Ribbon: PhnA Zinc-Ribbon ; InterPro: IPR013987 The PhnA protein family includes the uncharacterised Escherichia coli protein PhnA and its homologues. The E. coli phnA gene is part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage []. The protein is not related to the characterised phosphonoacetate hydrolase designated PhnA []. This entry represents the N-terminal domain of PhnA, which is predicted to form a zinc-ribbon.; PDB: 2AKL_A.
Probab=78.00 E-value=1.2 Score=24.84 Aligned_cols=16 Identities=38% Similarity=0.787 Sum_probs=11.6
Q ss_pred cccceeecCCCCcccc
Q 033418 89 LEEGALVCPETGRKFP 104 (119)
Q Consensus 89 i~~g~L~C~~c~~~yp 104 (119)
..+..++||.|++.++
T Consensus 15 ~D~~~~vCp~C~~ew~ 30 (30)
T PF08274_consen 15 EDGELLVCPECGHEWN 30 (30)
T ss_dssp E-SSSEEETTTTEEE-
T ss_pred ccCCEEeCCcccccCC
Confidence 4566789999998763
No 11
>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=76.44 E-value=1.3 Score=25.42 Aligned_cols=14 Identities=29% Similarity=0.823 Sum_probs=11.9
Q ss_pred eecCCCCccccccC
Q 033418 94 LVCPETGRKFPVNK 107 (119)
Q Consensus 94 L~C~~c~~~ypI~~ 107 (119)
.+|+.||+.|-|.-
T Consensus 2 r~C~~Cg~~Yh~~~ 15 (36)
T PF05191_consen 2 RICPKCGRIYHIEF 15 (36)
T ss_dssp EEETTTTEEEETTT
T ss_pred cCcCCCCCcccccc
Confidence 68999999998753
No 12
>PRK00420 hypothetical protein; Validated
Probab=76.02 E-value=1.4 Score=31.48 Aligned_cols=21 Identities=33% Similarity=0.817 Sum_probs=18.2
Q ss_pred ccccceeecCCCCccccccCC
Q 033418 88 HLEEGALVCPETGRKFPVNKG 108 (119)
Q Consensus 88 ~i~~g~L~C~~c~~~ypI~~G 108 (119)
...+|..+||.||..+-+++|
T Consensus 35 ~lk~g~~~Cp~Cg~~~~v~~~ 55 (112)
T PRK00420 35 ELKDGEVVCPVHGKVYIVKSD 55 (112)
T ss_pred ecCCCceECCCCCCeeeeccH
Confidence 457999999999999988765
No 13
>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=74.17 E-value=1.3 Score=24.90 Aligned_cols=15 Identities=27% Similarity=0.618 Sum_probs=12.4
Q ss_pred eecCCCCccccccCC
Q 033418 94 LVCPETGRKFPVNKG 108 (119)
Q Consensus 94 L~C~~c~~~ypI~~G 108 (119)
+.||+|+..|.|.++
T Consensus 3 ~~CP~C~~~~~v~~~ 17 (38)
T TIGR02098 3 IQCPNCKTSFRVVDS 17 (38)
T ss_pred EECCCCCCEEEeCHH
Confidence 679999999988753
No 14
>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=74.03 E-value=1.6 Score=23.46 Aligned_cols=17 Identities=35% Similarity=0.724 Sum_probs=12.6
Q ss_pred ccccceeecCCCCcccc
Q 033418 88 HLEEGALVCPETGRKFP 104 (119)
Q Consensus 88 ~i~~g~L~C~~c~~~yp 104 (119)
.|-...-.||.||+.|.
T Consensus 9 ~V~~~~~~Cp~CG~~F~ 25 (26)
T PF10571_consen 9 EVPESAKFCPHCGYDFE 25 (26)
T ss_pred CchhhcCcCCCCCCCCc
Confidence 45566778999998874
No 15
>PF14353 CpXC: CpXC protein
Probab=72.23 E-value=1.7 Score=30.60 Aligned_cols=19 Identities=32% Similarity=0.894 Sum_probs=14.2
Q ss_pred ccccce---eecCCCCcccccc
Q 033418 88 HLEEGA---LVCPETGRKFPVN 106 (119)
Q Consensus 88 ~i~~g~---L~C~~c~~~ypI~ 106 (119)
.|.+|+ .+||+||+.+.+.
T Consensus 30 ~il~g~l~~~~CP~Cg~~~~~~ 51 (128)
T PF14353_consen 30 KILDGSLFSFTCPSCGHKFRLE 51 (128)
T ss_pred HHHcCCcCEEECCCCCCceecC
Confidence 344554 4999999999873
No 16
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=71.46 E-value=1.8 Score=22.75 Aligned_cols=11 Identities=55% Similarity=1.105 Sum_probs=9.5
Q ss_pred eecCCCCcccc
Q 033418 94 LVCPETGRKFP 104 (119)
Q Consensus 94 L~C~~c~~~yp 104 (119)
..||.|||.|.
T Consensus 3 ~~C~~CgR~F~ 13 (25)
T PF13913_consen 3 VPCPICGRKFN 13 (25)
T ss_pred CcCCCCCCEEC
Confidence 47999999995
No 17
>COG4391 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=71.13 E-value=2.2 Score=27.62 Aligned_cols=17 Identities=29% Similarity=0.755 Sum_probs=14.7
Q ss_pred cccceeecCCCCccccc
Q 033418 89 LEEGALVCPETGRKFPV 105 (119)
Q Consensus 89 i~~g~L~C~~c~~~ypI 105 (119)
-.+|+.+||-|++.|..
T Consensus 44 g~~gev~CPYC~t~y~l 60 (62)
T COG4391 44 GDEGEVVCPYCSTRYRL 60 (62)
T ss_pred CCCCcEecCccccEEEe
Confidence 46789999999999974
No 18
>PF13408 Zn_ribbon_recom: Recombinase zinc beta ribbon domain
Probab=69.30 E-value=2.7 Score=25.04 Aligned_cols=17 Identities=29% Similarity=0.475 Sum_probs=14.4
Q ss_pred ccceeecCCCCcccccc
Q 033418 90 EEGALVCPETGRKFPVN 106 (119)
Q Consensus 90 ~~g~L~C~~c~~~ypI~ 106 (119)
..|.++|+.||+.+-.+
T Consensus 2 l~g~l~C~~CG~~m~~~ 18 (58)
T PF13408_consen 2 LSGLLRCGHCGSKMTRR 18 (58)
T ss_pred CCCcEEcccCCcEeEEE
Confidence 57899999999988764
No 19
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 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. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=68.93 E-value=2.3 Score=20.94 Aligned_cols=12 Identities=33% Similarity=0.855 Sum_probs=10.2
Q ss_pred ecCCCCcccccc
Q 033418 95 VCPETGRKFPVN 106 (119)
Q Consensus 95 ~C~~c~~~ypI~ 106 (119)
.|+.|++.|+-.
T Consensus 2 ~C~~C~~~f~~~ 13 (23)
T PF00096_consen 2 KCPICGKSFSSK 13 (23)
T ss_dssp EETTTTEEESSH
T ss_pred CCCCCCCccCCH
Confidence 699999999754
No 20
>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=67.16 E-value=3.1 Score=23.30 Aligned_cols=18 Identities=28% Similarity=0.560 Sum_probs=14.0
Q ss_pred eeecCCCCccccccCCcc
Q 033418 93 ALVCPETGRKFPVNKGIP 110 (119)
Q Consensus 93 ~L~C~~c~~~ypI~~GIP 110 (119)
+..|++||+.|.+..++.
T Consensus 5 ~y~C~~Cg~~fe~~~~~~ 22 (41)
T smart00834 5 EYRCEDCGHTFEVLQKIS 22 (41)
T ss_pred EEEcCCCCCEEEEEEecC
Confidence 357999999998777654
No 21
>PF07295 DUF1451: Protein of unknown function (DUF1451); InterPro: IPR009912 This family consists of several hypothetical bacterial proteins of around 160 residues in length. Members of this family contain four highly conserved cysteine resides toward the C-terminal region of the protein. The function of this family is unknown.
Probab=66.35 E-value=6.8 Score=29.04 Aligned_cols=30 Identities=20% Similarity=0.496 Sum_probs=23.2
Q ss_pred HHHHHHHHhc-------ccccceeecCCCCccccccC
Q 033418 78 DDFLMKFHHL-------HLEEGALVCPETGRKFPVNK 107 (119)
Q Consensus 78 ee~L~~lH~~-------~i~~g~L~C~~c~~~ypI~~ 107 (119)
.++.+.+.|. -+--|.|+|.+||+.-.+..
T Consensus 90 ~el~~d~~h~g~Y~sGE~~g~G~l~C~~Cg~~~~~~~ 126 (146)
T PF07295_consen 90 AELAQDLEHHGVYHSGEVVGPGTLVCENCGHEVELTH 126 (146)
T ss_pred HHHHHHHHhcCCeecCcEecCceEecccCCCEEEecC
Confidence 4567777554 56678999999999988876
No 22
>TIGR00686 phnA alkylphosphonate utilization operon protein PhnA. The protein family includes an uncharacterized member designated phnA in Escherichia coli, part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage. This protein is not related to the characterized phosphonoacetate hydrolase designated PhnA by Kulakova, et al. (2001, 1997).
Probab=66.23 E-value=3.1 Score=29.72 Aligned_cols=18 Identities=22% Similarity=0.506 Sum_probs=13.9
Q ss_pred ccceeecCCCCccccccC
Q 033418 90 EEGALVCPETGRKFPVNK 107 (119)
Q Consensus 90 ~~g~L~C~~c~~~ypI~~ 107 (119)
....++||+|++.|.=.+
T Consensus 16 dg~~~iCpeC~~EW~~~~ 33 (109)
T TIGR00686 16 DGTQLICPSCLYEWNENE 33 (109)
T ss_pred cCCeeECccccccccccc
Confidence 445689999999997543
No 23
>PRK10220 hypothetical protein; Provisional
Probab=63.64 E-value=4.2 Score=29.15 Aligned_cols=18 Identities=22% Similarity=0.700 Sum_probs=14.6
Q ss_pred ccceeecCCCCccccccC
Q 033418 90 EEGALVCPETGRKFPVNK 107 (119)
Q Consensus 90 ~~g~L~C~~c~~~ypI~~ 107 (119)
....++||+|++.|+-.+
T Consensus 17 d~~~~vCpeC~hEW~~~~ 34 (111)
T PRK10220 17 DNGMYICPECAHEWNDAE 34 (111)
T ss_pred CCCeEECCcccCcCCccc
Confidence 445689999999998665
No 24
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=60.52 E-value=5.6 Score=23.41 Aligned_cols=16 Identities=25% Similarity=0.630 Sum_probs=14.2
Q ss_pred eeecCCCCccccccCC
Q 033418 93 ALVCPETGRKFPVNKG 108 (119)
Q Consensus 93 ~L~C~~c~~~ypI~~G 108 (119)
.++|+.||..++|..-
T Consensus 20 ~~vC~~Cg~~~~~~~~ 35 (52)
T smart00661 20 RFVCRKCGYEEPIEQK 35 (52)
T ss_pred EEECCcCCCeEECCCc
Confidence 7899999999998755
No 25
>PRK11032 hypothetical protein; Provisional
Probab=60.15 E-value=7.5 Score=29.37 Aligned_cols=30 Identities=17% Similarity=0.377 Sum_probs=22.1
Q ss_pred HHHHHHHHhc-------ccccceeecCCCCccccccC
Q 033418 78 DDFLMKFHHL-------HLEEGALVCPETGRKFPVNK 107 (119)
Q Consensus 78 ee~L~~lH~~-------~i~~g~L~C~~c~~~ypI~~ 107 (119)
-++.+++.|. -+--|.|+|.+||+...|..
T Consensus 102 ~el~~dl~h~g~Y~sGEvvg~G~LvC~~Cg~~~~~~~ 138 (160)
T PRK11032 102 REVFQDLNHHGVYHSGEVVGLGNLVCEKCHHHLAFYT 138 (160)
T ss_pred HHHHHHhhhcCeeecceeeecceEEecCCCCEEEecC
Confidence 4577777443 45568999999999887754
No 26
>PF14569 zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.
Probab=59.48 E-value=5.5 Score=27.00 Aligned_cols=33 Identities=30% Similarity=0.581 Sum_probs=16.0
Q ss_pred hcccccceeecCCCCccccccCCccccCCCCCC
Q 033418 86 HLHLEEGALVCPETGRKFPVNKGIPNMLLHEDE 118 (119)
Q Consensus 86 ~~~i~~g~L~C~~c~~~ypI~~GIP~mL~~e~~ 118 (119)
..+..+|.-+||+|+..|.=..|-|.+--+++|
T Consensus 44 EYErkeg~q~CpqCkt~ykr~kgsp~V~gDeee 76 (80)
T PF14569_consen 44 EYERKEGNQVCPQCKTRYKRHKGSPRVEGDEEE 76 (80)
T ss_dssp HHHHHTS-SB-TTT--B----TT----TTS---
T ss_pred HHHhhcCcccccccCCCcccccCCCCCCCCccc
Confidence 448999999999999999999999998887754
No 27
>TIGR00515 accD acetyl-CoA carboxylase, carboxyl transferase, beta subunit. The enzyme acetyl-CoA carboxylase contains a biotin carboxyl carrier protein or domain, a biotin carboxylase, and a carboxyl transferase. This model represents the beta chain of the carboxyl transferase for cases in which the architecture of the protein is as in E. coli, in which the carboxyltransferase portion consists of two non-identical subnits, alpha and beta.
Probab=58.80 E-value=2.4 Score=34.63 Aligned_cols=33 Identities=15% Similarity=0.218 Sum_probs=25.6
Q ss_pred CCCcHHHHHHHHhcccccceeecCCCCcccccc
Q 033418 74 MLDSDDFLMKFHHLHLEEGALVCPETGRKFPVN 106 (119)
Q Consensus 74 ~~~~ee~L~~lH~~~i~~g~L~C~~c~~~ypI~ 106 (119)
|..+++|=+.+++-++.+..-+||.||+.|+++
T Consensus 26 ~~~c~~c~~~~~~~~l~~~~~vc~~c~~h~rl~ 58 (285)
T TIGR00515 26 WTKCPKCGQVLYTKELERNLEVCPKCDHHMRMD 58 (285)
T ss_pred eeECCCCcchhhHHHHHhhCCCCCCCCCcCcCC
Confidence 555666666666668888888999999999873
No 28
>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=58.60 E-value=6 Score=27.95 Aligned_cols=19 Identities=37% Similarity=0.950 Sum_probs=17.4
Q ss_pred ccccceeecCCCCcccccc
Q 033418 88 HLEEGALVCPETGRKFPVN 106 (119)
Q Consensus 88 ~i~~g~L~C~~c~~~ypI~ 106 (119)
+....-.+||.||..|++.
T Consensus 21 DLnk~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 21 DLNKDPIVCPKCGTEFPPE 39 (108)
T ss_pred cCCCCCccCCCCCCccCcc
Confidence 7777889999999999998
No 29
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=58.47 E-value=5.4 Score=29.34 Aligned_cols=38 Identities=18% Similarity=0.463 Sum_probs=23.7
Q ss_pred HHHHHHHHhCCCCCCCCCCCCCCCCCcHHHHHHHHhcccccceeecCCCCcccc
Q 033418 51 QALVQASRSMGYSELPEESPESSMLDSDDFLMKFHHLHLEEGALVCPETGRKFP 104 (119)
Q Consensus 51 ~al~~~a~~lg~~~lP~~~~p~~~~~~ee~L~~lH~~~i~~g~L~C~~c~~~yp 104 (119)
.-|++.|+-|+.. =|.|..| .. . .+|+++||.||+..-
T Consensus 18 ~lLl~GAkML~~h-Cp~Cg~P--------LF------~-KdG~v~CPvC~~~~~ 55 (131)
T COG1645 18 ELLLQGAKMLAKH-CPKCGTP--------LF------R-KDGEVFCPVCGYREV 55 (131)
T ss_pred HHHHhhhHHHHhh-CcccCCc--------ce------e-eCCeEECCCCCceEE
Confidence 3466777766532 4555222 11 3 899999999995443
No 30
>PF13878 zf-C2H2_3: zinc-finger of acetyl-transferase ESCO
Probab=53.56 E-value=6.3 Score=23.00 Aligned_cols=15 Identities=33% Similarity=0.736 Sum_probs=12.0
Q ss_pred ceeecCCCCcccccc
Q 033418 92 GALVCPETGRKFPVN 106 (119)
Q Consensus 92 g~L~C~~c~~~ypI~ 106 (119)
|.-.|+.||..|-..
T Consensus 12 ~~~~C~~CgM~Y~~~ 26 (41)
T PF13878_consen 12 GATTCPTCGMLYSPG 26 (41)
T ss_pred CCcCCCCCCCEECCC
Confidence 456999999999653
No 31
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=53.55 E-value=9.5 Score=22.36 Aligned_cols=15 Identities=20% Similarity=0.519 Sum_probs=7.1
Q ss_pred eecCCCCccccccCC
Q 033418 94 LVCPETGRKFPVNKG 108 (119)
Q Consensus 94 L~C~~c~~~ypI~~G 108 (119)
..|++||..+.+.++
T Consensus 4 y~C~~CG~~~~~~~~ 18 (46)
T PRK00398 4 YKCARCGREVELDEY 18 (46)
T ss_pred EECCCCCCEEEECCC
Confidence 345555555544433
No 32
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=52.87 E-value=6.9 Score=18.64 Aligned_cols=12 Identities=33% Similarity=0.825 Sum_probs=7.9
Q ss_pred ecCCCCcccccc
Q 033418 95 VCPETGRKFPVN 106 (119)
Q Consensus 95 ~C~~c~~~ypI~ 106 (119)
.|+.|+..|+=.
T Consensus 2 ~C~~C~~~~~~~ 13 (24)
T PF13894_consen 2 QCPICGKSFRSK 13 (24)
T ss_dssp E-SSTS-EESSH
T ss_pred CCcCCCCcCCcH
Confidence 699999998743
No 33
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=52.85 E-value=9.1 Score=27.07 Aligned_cols=20 Identities=30% Similarity=0.459 Sum_probs=17.2
Q ss_pred ccccceeecCCCCccccccC
Q 033418 88 HLEEGALVCPETGRKFPVNK 107 (119)
Q Consensus 88 ~i~~g~L~C~~c~~~ypI~~ 107 (119)
+..++.|+|+.||..+++++
T Consensus 17 ~~~~~~l~C~kCgye~~~~~ 36 (113)
T COG1594 17 DDEGGKLVCRKCGYEEEASN 36 (113)
T ss_pred cCCCcEEECCCCCcchhccc
Confidence 44677999999999999985
No 34
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=52.28 E-value=11 Score=27.36 Aligned_cols=24 Identities=29% Similarity=0.731 Sum_probs=16.7
Q ss_pred HHHHHHhcccccceeecCCCCcccc
Q 033418 80 FLMKFHHLHLEEGALVCPETGRKFP 104 (119)
Q Consensus 80 ~L~~lH~~~i~~g~L~C~~c~~~yp 104 (119)
|+.++...+. +|.++||.||..-.
T Consensus 111 ~~ea~~~~d~-~~~f~Cp~Cg~~l~ 134 (147)
T smart00531 111 FLEANQLLDM-DGTFTCPRCGEELE 134 (147)
T ss_pred HHHHHHhcCC-CCcEECCCCCCEEE
Confidence 4545545453 88999999997643
No 35
>TIGR02605 CxxC_CxxC_SSSS putative regulatory protein, FmdB family. This model represents a region of about 50 amino acids found in a number of small proteins in a wide range of bacteria. The region begins usually with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One member of this family is has been noted as a putative regulatory protein, designated FmdB (PubMed:8841393). Most members of this family have a C-terminal region containing highly degenerate sequence, such as SSTSESTKSSGSSGSSGSSESKASGSTEKSTSSTTAAAAV in Mycobacterium tuberculosis and VAVGGSAPAPSPAPRAGGGGGGCCGGGCCG in Streptomyces avermitilis. These low complexity regions, which are not included in the model, resemble low-complexity C-terminal regions of some heterocycle-containing bacteriocin precursors.
Probab=51.18 E-value=8.8 Score=22.75 Aligned_cols=15 Identities=27% Similarity=0.609 Sum_probs=11.1
Q ss_pred eeecCCCCccccccC
Q 033418 93 ALVCPETGRKFPVNK 107 (119)
Q Consensus 93 ~L~C~~c~~~ypI~~ 107 (119)
+..|++||+.|.+..
T Consensus 5 ey~C~~Cg~~fe~~~ 19 (52)
T TIGR02605 5 EYRCTACGHRFEVLQ 19 (52)
T ss_pred EEEeCCCCCEeEEEE
Confidence 467888888887753
No 36
>PRK05654 acetyl-CoA carboxylase subunit beta; Validated
Probab=50.63 E-value=4.1 Score=33.31 Aligned_cols=33 Identities=18% Similarity=0.288 Sum_probs=25.4
Q ss_pred CCCcHHHHHHHHhcccccceeecCCCCcccccc
Q 033418 74 MLDSDDFLMKFHHLHLEEGALVCPETGRKFPVN 106 (119)
Q Consensus 74 ~~~~ee~L~~lH~~~i~~g~L~C~~c~~~ypI~ 106 (119)
|..+++|=+.+++-++.+..-+||.||+-|+++
T Consensus 27 ~~~c~~c~~~~~~~~l~~~~~vc~~c~~h~rl~ 59 (292)
T PRK05654 27 WTKCPSCGQVLYRKELEANLNVCPKCGHHMRIS 59 (292)
T ss_pred eeECCCccchhhHHHHHhcCCCCCCCCCCeeCC
Confidence 555666666666768777777999999999875
No 37
>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=50.08 E-value=8.6 Score=22.35 Aligned_cols=18 Identities=33% Similarity=0.624 Sum_probs=13.5
Q ss_pred eeecCCCCccccccCCcc
Q 033418 93 ALVCPETGRKFPVNKGIP 110 (119)
Q Consensus 93 ~L~C~~c~~~ypI~~GIP 110 (119)
+..|++||+.|.+.-.|-
T Consensus 5 ey~C~~Cg~~fe~~~~~~ 22 (42)
T PF09723_consen 5 EYRCEECGHEFEVLQSIS 22 (42)
T ss_pred EEEeCCCCCEEEEEEEcC
Confidence 467999999998765543
No 38
>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=49.06 E-value=16 Score=22.05 Aligned_cols=17 Identities=35% Similarity=0.741 Sum_probs=7.8
Q ss_pred hcccccceeecCCCCcccc
Q 033418 86 HLHLEEGALVCPETGRKFP 104 (119)
Q Consensus 86 ~~~i~~g~L~C~~c~~~yp 104 (119)
.+.-.+| .||-|||.|.
T Consensus 15 ~l~~~~~--~CPlC~r~l~ 31 (54)
T PF04423_consen 15 ELKEAKG--CCPLCGRPLD 31 (54)
T ss_dssp HHTT-SE--E-TTT--EE-
T ss_pred HHhcCCC--cCCCCCCCCC
Confidence 3344444 9999999774
No 39
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=48.68 E-value=8.5 Score=20.15 Aligned_cols=7 Identities=43% Similarity=1.217 Sum_probs=3.9
Q ss_pred ecCCCCc
Q 033418 95 VCPETGR 101 (119)
Q Consensus 95 ~C~~c~~ 101 (119)
+||+||.
T Consensus 4 ~Cp~Cg~ 10 (26)
T PF13248_consen 4 FCPNCGA 10 (26)
T ss_pred CCcccCC
Confidence 4555555
No 40
>PRK11088 rrmA 23S rRNA methyltransferase A; Provisional
Probab=47.78 E-value=14 Score=28.88 Aligned_cols=25 Identities=32% Similarity=0.708 Sum_probs=20.5
Q ss_pred ccceeecCCCCccccc-cCCccccCCC
Q 033418 90 EEGALVCPETGRKFPV-NKGIPNMLLH 115 (119)
Q Consensus 90 ~~g~L~C~~c~~~ypI-~~GIP~mL~~ 115 (119)
.++.++|++ ||.|.+ ++|+.||++.
T Consensus 15 ~~~~~~C~~-~h~fd~a~~Gy~~ll~~ 40 (272)
T PRK11088 15 EENSWICPQ-NHQFDCAKEGYVNLLPV 40 (272)
T ss_pred CCCEEEcCC-CCCCccccCceEEeccc
Confidence 467899987 999955 5899999984
No 41
>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=46.95 E-value=14 Score=34.16 Aligned_cols=42 Identities=14% Similarity=0.280 Sum_probs=30.9
Q ss_pred CCCCCCCcHHHHHHHHhc---ccccceeecCCCCccccccCCccc
Q 033418 70 PESSMLDSDDFLMKFHHL---HLEEGALVCPETGRKFPVNKGIPN 111 (119)
Q Consensus 70 ~p~~~~~~ee~L~~lH~~---~i~~g~L~C~~c~~~ypI~~GIP~ 111 (119)
.|+|...+++||+.+..- .-.=---.|.+||=.|.|.+.+|-
T Consensus 97 I~pD~a~C~~Cl~Ei~dp~~rrY~YPF~~CT~CGPRfTIi~alPY 141 (750)
T COG0068 97 IPPDAATCEDCLEEIFDPNSRRYLYPFINCTNCGPRFTIIEALPY 141 (750)
T ss_pred cCCchhhhHHHHHHhcCCCCcceeccccccCCCCcceeeeccCCC
Confidence 467778899999865432 111223579999999999999993
No 42
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=46.85 E-value=12 Score=22.86 Aligned_cols=12 Identities=33% Similarity=0.880 Sum_probs=10.3
Q ss_pred cceeecCCCCcc
Q 033418 91 EGALVCPETGRK 102 (119)
Q Consensus 91 ~g~L~C~~c~~~ 102 (119)
++...||+|||.
T Consensus 44 ~~i~~Cp~CgRi 55 (56)
T PF02591_consen 44 DEIVFCPNCGRI 55 (56)
T ss_pred CCeEECcCCCcc
Confidence 678899999984
No 43
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=46.65 E-value=10 Score=19.20 Aligned_cols=11 Identities=36% Similarity=0.933 Sum_probs=9.7
Q ss_pred eecCCCCcccc
Q 033418 94 LVCPETGRKFP 104 (119)
Q Consensus 94 L~C~~c~~~yp 104 (119)
+.|..|+..|.
T Consensus 2 ~~C~~C~~~F~ 12 (27)
T PF13912_consen 2 FECDECGKTFS 12 (27)
T ss_dssp EEETTTTEEES
T ss_pred CCCCccCCccC
Confidence 57999999996
No 44
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=46.25 E-value=12 Score=26.34 Aligned_cols=20 Identities=5% Similarity=0.160 Sum_probs=15.0
Q ss_pred ccccceeecCCCCccccccC
Q 033418 88 HLEEGALVCPETGRKFPVNK 107 (119)
Q Consensus 88 ~i~~g~L~C~~c~~~ypI~~ 107 (119)
+...+...|+.||..|++.+
T Consensus 65 ~~vp~~~~C~~Cg~~~~~~~ 84 (113)
T PRK12380 65 VYKPAQAWCWDCSQVVEIHQ 84 (113)
T ss_pred EeeCcEEEcccCCCEEecCC
Confidence 66667788888888887754
No 45
>TIGR00100 hypA hydrogenase nickel insertion protein HypA. In Hpylori, hypA mutant abolished hydrogenase activity and decrease in urease activity. Nickel supplementation in media restored urease activity and partial hydrogenase activity. HypA probably involved in inserting Ni in enzymes.
Probab=46.08 E-value=12 Score=26.32 Aligned_cols=20 Identities=10% Similarity=0.094 Sum_probs=15.5
Q ss_pred ccccceeecCCCCccccccC
Q 033418 88 HLEEGALVCPETGRKFPVNK 107 (119)
Q Consensus 88 ~i~~g~L~C~~c~~~ypI~~ 107 (119)
+...+...|+.||+.|++.+
T Consensus 65 ~~~p~~~~C~~Cg~~~~~~~ 84 (115)
T TIGR00100 65 EDEPVECECEDCSEEVSPEI 84 (115)
T ss_pred EeeCcEEEcccCCCEEecCC
Confidence 66677788888888888764
No 46
>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=45.44 E-value=11 Score=21.32 Aligned_cols=13 Identities=23% Similarity=0.649 Sum_probs=9.9
Q ss_pred ecCCCCccccccC
Q 033418 95 VCPETGRKFPVNK 107 (119)
Q Consensus 95 ~C~~c~~~ypI~~ 107 (119)
.|+.|+..|||.+
T Consensus 22 ~C~~C~Y~~~~~~ 34 (35)
T PF02150_consen 22 ACRTCGYEEPISQ 34 (35)
T ss_dssp EESSSS-EEE-SS
T ss_pred CCCCCCCccCCCC
Confidence 7999999999975
No 47
>PF08671 SinI: Anti-repressor SinI; InterPro: IPR010981 The SinR repressor is part of a group of Sin (sporulation inhibition) proteins in Bacillus subtilis that regulate the commitment to sporulation in response to extreme adversity []. SinR is a tetrameric repressor protein that binds to the promoters of genes essential for entry into sporulation and prevents their transcription. This repression is overcome through the activity of SinI, which disrupts the SinR tetramer through the formation of a SinI-SinR heterodimer, thereby allowing sporulation to proceed. The SinR structure consists of two domains: a dimerisation domain stabilised by a hydrophobic core, and a DNA-binding domain that is identical to domains of the bacteriophage 434 CI and Cro proteins that regulate prophage induction. The dimerisation domain is a four-helical bundle formed from two helices from the C-terminal residues of SinR and two helices from the central residues of SinI. These regions in SinR and SinI are similar in both structure and sequence. The interaction of SinR monomers to form tetramers is weaker than between SinR and SinI, since SinI can effectively disrupt SinR tetramers. This entry represents the dimerisation domain in both SinI and SinR proteins.; GO: 0005488 binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1B0N_A 2YAL_A.
Probab=44.03 E-value=20 Score=19.85 Aligned_cols=16 Identities=31% Similarity=0.700 Sum_probs=13.0
Q ss_pred hcHHHHHHHHHhCCCC
Q 033418 48 IEWQALVQASRSMGYS 63 (119)
Q Consensus 48 ldw~al~~~a~~lg~~ 63 (119)
-+|-.|...|++.|++
T Consensus 3 ~EW~~Li~eA~~~Gls 18 (30)
T PF08671_consen 3 EEWVELIKEAKESGLS 18 (30)
T ss_dssp HHHHHHHHHHHHTT--
T ss_pred HHHHHHHHHHHHcCCC
Confidence 3899999999999974
No 48
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=43.70 E-value=13 Score=26.09 Aligned_cols=19 Identities=11% Similarity=0.127 Sum_probs=14.3
Q ss_pred ccccceeecCCCCcccccc
Q 033418 88 HLEEGALVCPETGRKFPVN 106 (119)
Q Consensus 88 ~i~~g~L~C~~c~~~ypI~ 106 (119)
+...+...|+.||..|++.
T Consensus 65 ~~~p~~~~C~~Cg~~~~~~ 83 (114)
T PRK03681 65 EEQEAECWCETCQQYVTLL 83 (114)
T ss_pred EeeCcEEEcccCCCeeecC
Confidence 6667777888888888775
No 49
>cd00924 Cyt_c_Oxidase_Vb Cytochrome c oxidase subunit Vb. Cytochrome c oxidase (CcO), the terminal oxidase in the respiratory chains of eukaryotes and most bacteria, is a multi-chain transmembrane protein located in the inner membrane of mitochondria and the cell membrane of prokaryotes. It catalyzes the reduction of O2 and simultaneously pumps protons across the membrane. The number of subunits varies from three to five in bacteria and up to 13 in mammalian mitochondria. Subunits I, II, and III of mammalian CcO are encoded within the mitochondrial genome and the remaining 10 subunits are encoded within the nuclear genome. Found only in eukaryotes, subunit Vb is one of three mammalian subunits that lacks a transmembrane region. Subunit Vb is located on the matrix side of the membrane and binds the regulatory subunit of protein kinase A. The abnormally extended conformation is stable only in the CcO assembly.
Probab=41.94 E-value=12 Score=26.03 Aligned_cols=19 Identities=42% Similarity=0.765 Sum_probs=15.0
Q ss_pred cccccee-ecCCCCcccccc
Q 033418 88 HLEEGAL-VCPETGRKFPVN 106 (119)
Q Consensus 88 ~i~~g~L-~C~~c~~~ypI~ 106 (119)
.+.+|.. .|++||++|-..
T Consensus 73 ~l~~g~~~rC~eCG~~fkL~ 92 (97)
T cd00924 73 WLEKGKPKRCPECGHVFKLV 92 (97)
T ss_pred EEeCCCceeCCCCCcEEEEE
Confidence 5666655 899999999765
No 50
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=41.83 E-value=11 Score=19.39 Aligned_cols=15 Identities=33% Similarity=0.784 Sum_probs=9.5
Q ss_pred ccccceeecCCCCcc
Q 033418 88 HLEEGALVCPETGRK 102 (119)
Q Consensus 88 ~i~~g~L~C~~c~~~ 102 (119)
++.++.-.|+.||..
T Consensus 8 ~~~~~~~fC~~CG~~ 22 (23)
T PF13240_consen 8 EIEDDAKFCPNCGTP 22 (23)
T ss_pred CCCCcCcchhhhCCc
Confidence 455566667777753
No 51
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=41.37 E-value=8.6 Score=31.74 Aligned_cols=33 Identities=9% Similarity=0.190 Sum_probs=26.0
Q ss_pred CCCcHHHHHHHHhcccccceeecCCCCcccccc
Q 033418 74 MLDSDDFLMKFHHLHLEEGALVCPETGRKFPVN 106 (119)
Q Consensus 74 ~~~~ee~L~~lH~~~i~~g~L~C~~c~~~ypI~ 106 (119)
|..+++|=+.+++-++.+..-+||.||+.|+++
T Consensus 38 w~kc~~C~~~~~~~~l~~~~~vcp~c~~h~rlt 70 (296)
T CHL00174 38 WVQCENCYGLNYKKFLKSKMNICEQCGYHLKMS 70 (296)
T ss_pred eeECCCccchhhHHHHHHcCCCCCCCCCCcCCC
Confidence 555666666666668888889999999999876
No 52
>PF01927 Mut7-C: Mut7-C RNAse domain; InterPro: IPR002782 This prokaryotic family of proteins have no known function. The proteins contain four conserved cysteines that may be involved in metal binding or disulphide bridges.
Probab=41.16 E-value=13 Score=27.00 Aligned_cols=12 Identities=25% Similarity=0.675 Sum_probs=10.1
Q ss_pred ceeecCCCCccc
Q 033418 92 GALVCPETGRKF 103 (119)
Q Consensus 92 g~L~C~~c~~~y 103 (119)
---+||.||+.|
T Consensus 123 ~f~~C~~C~kiy 134 (147)
T PF01927_consen 123 EFWRCPGCGKIY 134 (147)
T ss_pred eEEECCCCCCEe
Confidence 356999999998
No 53
>PF13451 zf-trcl: Probable zinc-binding domain
Probab=40.79 E-value=15 Score=22.63 Aligned_cols=18 Identities=28% Similarity=0.713 Sum_probs=14.4
Q ss_pred cceeecCCCCccccccCC
Q 033418 91 EGALVCPETGRKFPVNKG 108 (119)
Q Consensus 91 ~g~L~C~~c~~~ypI~~G 108 (119)
+-.|+|..||..|-++-|
T Consensus 2 Dk~l~C~dCg~~FvfTa~ 19 (49)
T PF13451_consen 2 DKTLTCKDCGAEFVFTAG 19 (49)
T ss_pred CeeEEcccCCCeEEEehh
Confidence 457999999999977644
No 54
>COG2824 PhnA Uncharacterized Zn-ribbon-containing protein involved in phosphonate metabolism [Inorganic ion transport and metabolism]
Probab=40.77 E-value=14 Score=26.51 Aligned_cols=15 Identities=33% Similarity=0.946 Sum_probs=12.4
Q ss_pred ccceeecCCCCcccc
Q 033418 90 EEGALVCPETGRKFP 104 (119)
Q Consensus 90 ~~g~L~C~~c~~~yp 104 (119)
..+.|+||+|++.|-
T Consensus 17 d~~~~~cpec~~ew~ 31 (112)
T COG2824 17 DGGQLICPECAHEWN 31 (112)
T ss_pred cCceEeCchhccccc
Confidence 345899999999886
No 55
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=40.53 E-value=21 Score=21.20 Aligned_cols=21 Identities=19% Similarity=0.352 Sum_probs=11.8
Q ss_pred cceeecCCCCccccccCCccc
Q 033418 91 EGALVCPETGRKFPVNKGIPN 111 (119)
Q Consensus 91 ~g~L~C~~c~~~ypI~~GIP~ 111 (119)
.+.+.||+||+.=-.+...+.
T Consensus 17 ~~~irC~~CG~rIlyK~R~~~ 37 (44)
T smart00659 17 KDVVRCRECGYRILYKKRTKR 37 (44)
T ss_pred CCceECCCCCceEEEEeCCCc
Confidence 456677777765444444433
No 56
>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=40.24 E-value=15 Score=20.98 Aligned_cols=15 Identities=20% Similarity=0.527 Sum_probs=13.1
Q ss_pred ccccceeecCCCCcc
Q 033418 88 HLEEGALVCPETGRK 102 (119)
Q Consensus 88 ~i~~g~L~C~~c~~~ 102 (119)
...+|..+|.+||+.
T Consensus 20 ~~~dG~~yC~~cG~~ 34 (36)
T PF11781_consen 20 YSDDGFYYCDRCGHQ 34 (36)
T ss_pred EccCCEEEhhhCceE
Confidence 678999999999985
No 57
>cd07153 Fur_like Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators. Ferric uptake regulator (Fur) and related metalloregulatory proteins are iron-dependent, DNA-binding repressors and activators mainly involved in iron metabolism. A general model for Fur repression under iron-rich conditions is that activated Fur (a dimer having one Fe2+ coordinated per monomer) binds to specific DNA sequences (Fur boxes) in the promoter region of iron-responsive genes, hindering access of RNA polymerase, and repressing transcription. Positive regulation by Fur can be direct or indirect, as in the Fur repression of an anti-sense regulatory small RNA. Some members sense metal ions other than Fe2+. For example, the zinc uptake regulator (Zur) responds to Zn2+, the manganese uptake regulator (Mur) responds to Mn2+, and the nickel uptake regulator (Nur) responds to Ni2+. Other members sense signals other than metal ions.
Probab=39.65 E-value=16 Score=24.64 Aligned_cols=16 Identities=19% Similarity=0.542 Sum_probs=13.9
Q ss_pred eeecCCCCccccccCC
Q 033418 93 ALVCPETGRKFPVNKG 108 (119)
Q Consensus 93 ~L~C~~c~~~ypI~~G 108 (119)
-++|..||+.+.+.+.
T Consensus 73 H~~C~~Cg~i~~~~~~ 88 (116)
T cd07153 73 HLICTKCGKVIDFEDC 88 (116)
T ss_pred ceEeCCCCCEEEecCc
Confidence 4999999999998654
No 58
>PF01155 HypA: Hydrogenase expression/synthesis hypA family; InterPro: IPR000688 Bacterial membrane-bound nickel-dependent hydrogenases requires a number of accessory proteins which are involved in their maturation. The exact role of these proteins is not yet clear, but some seem to be required for the incorporation of the nickel ions []. One of these proteins is generally known as hypA. It is a protein of about 12 to 14 kDa that contains, in its C-terminal region, four conserved cysteines that form a zinc-finger like motif. Escherichia coli has two proteins that belong to this family, hypA and hybF. A homologue, MJ0214, has also been found in a number of archaeal species, including the genome of Methanocaldococcus jannaschii (Methanococcus jannaschii).; GO: 0016151 nickel ion binding, 0006464 protein modification process; PDB: 2KDX_A 3A44_D 3A43_B.
Probab=39.48 E-value=11 Score=26.27 Aligned_cols=21 Identities=14% Similarity=0.256 Sum_probs=13.7
Q ss_pred ccccceeecCCCCccccccCC
Q 033418 88 HLEEGALVCPETGRKFPVNKG 108 (119)
Q Consensus 88 ~i~~g~L~C~~c~~~ypI~~G 108 (119)
+.......|..||+.|++.+.
T Consensus 65 e~~p~~~~C~~Cg~~~~~~~~ 85 (113)
T PF01155_consen 65 EEVPARARCRDCGHEFEPDEF 85 (113)
T ss_dssp EEE--EEEETTTS-EEECHHC
T ss_pred EecCCcEECCCCCCEEecCCC
Confidence 666778888888888887653
No 59
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=39.21 E-value=22 Score=18.37 Aligned_cols=17 Identities=35% Similarity=0.739 Sum_probs=13.2
Q ss_pred ccccceeecCCCCcccc
Q 033418 88 HLEEGALVCPETGRKFP 104 (119)
Q Consensus 88 ~i~~g~L~C~~c~~~yp 104 (119)
+..+-...|+.|++.|.
T Consensus 9 H~~~k~~~C~~C~k~F~ 25 (26)
T PF13465_consen 9 HTGEKPYKCPYCGKSFS 25 (26)
T ss_dssp HSSSSSEEESSSSEEES
T ss_pred cCCCCCCCCCCCcCeeC
Confidence 44556689999999884
No 60
>PRK07591 threonine synthase; Validated
Probab=38.74 E-value=17 Score=30.68 Aligned_cols=14 Identities=43% Similarity=0.964 Sum_probs=12.1
Q ss_pred eeecCCCCcccccc
Q 033418 93 ALVCPETGRKFPVN 106 (119)
Q Consensus 93 ~L~C~~c~~~ypI~ 106 (119)
.|+|..||+.||+.
T Consensus 18 ~l~C~~Cg~~~~~~ 31 (421)
T PRK07591 18 ALKCRECGAEYPLG 31 (421)
T ss_pred EEEeCCCCCcCCCC
Confidence 58999999999975
No 61
>PF01475 FUR: Ferric uptake regulator family; InterPro: IPR002481 The Ferric uptake regulator (FUR) family includes metal ion uptake regulator proteins. These are responsible for controlling the intracellular concentration of iron in many bacteria. Although iron is essential for most organisms, high concentrations can be toxic because of the formation of hydroxyl radicals []. FURs can also control zinc homeostasis [] and is the subject of research on the pathogenesis of mycobacteria.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1MZB_A 2RGV_B 2FE3_B 3F8N_B 3EYY_B 2W57_A 2FU4_A 2O03_A 3MWM_B 2XIG_B ....
Probab=38.66 E-value=15 Score=25.15 Aligned_cols=17 Identities=12% Similarity=0.520 Sum_probs=12.5
Q ss_pred ceeecCCCCccccccCC
Q 033418 92 GALVCPETGRKFPVNKG 108 (119)
Q Consensus 92 g~L~C~~c~~~ypI~~G 108 (119)
.-++|..||+.+++.+.
T Consensus 79 ~h~iC~~Cg~v~~~~~~ 95 (120)
T PF01475_consen 79 HHFICTQCGKVIDLDDP 95 (120)
T ss_dssp EEEEETTTS-EEEE-GH
T ss_pred eEEEECCCCCEEEecch
Confidence 35999999999998763
No 62
>PRK12496 hypothetical protein; Provisional
Probab=38.53 E-value=17 Score=27.17 Aligned_cols=13 Identities=31% Similarity=0.736 Sum_probs=11.3
Q ss_pred eecCCCCcccccc
Q 033418 94 LVCPETGRKFPVN 106 (119)
Q Consensus 94 L~C~~c~~~ypI~ 106 (119)
.+|+.||+.|+..
T Consensus 128 ~~C~gC~~~~~~~ 140 (164)
T PRK12496 128 KVCKGCKKKYPED 140 (164)
T ss_pred EECCCCCccccCC
Confidence 7899999999853
No 63
>PF04475 DUF555: Protein of unknown function (DUF555); InterPro: IPR007564 This is a family of uncharacterised, hypothetical archaeal proteins.
Probab=38.52 E-value=14 Score=26.05 Aligned_cols=18 Identities=28% Similarity=0.816 Sum_probs=15.6
Q ss_pred cccccceeecCCCCcccc
Q 033418 87 LHLEEGALVCPETGRKFP 104 (119)
Q Consensus 87 ~~i~~g~L~C~~c~~~yp 104 (119)
++|.-|...||.||..++
T Consensus 41 VeIevG~~~cP~Cge~~~ 58 (102)
T PF04475_consen 41 VEIEVGDTICPKCGEELD 58 (102)
T ss_pred EEEecCcccCCCCCCccC
Confidence 399999999999998664
No 64
>COG4493 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=38.51 E-value=25 Score=27.56 Aligned_cols=38 Identities=26% Similarity=0.434 Sum_probs=27.7
Q ss_pred CCCCCCCCCCCcHHHHHHHHhc-ccccceeecCCCCccccccC
Q 033418 66 PEESPESSMLDSDDFLMKFHHL-HLEEGALVCPETGRKFPVNK 107 (119)
Q Consensus 66 P~~~~p~~~~~~ee~L~~lH~~-~i~~g~L~C~~c~~~ypI~~ 107 (119)
|++ +|....+++.+=.++-|+ +|..|+|. ||+.|+=.|
T Consensus 141 p~t-~~~sel~~~~l~~~~eRl~~VKK~Ell---ig~~~~~ed 179 (209)
T COG4493 141 PDT-YPISELTDDALKEAAERLRDVKKGELL---IGRVLPPED 179 (209)
T ss_pred CCC-CCcccccHHHHHHHHHHHHhcchhheE---eeeecCchh
Confidence 444 565666677777777888 99999998 677776443
No 65
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=37.69 E-value=14 Score=26.72 Aligned_cols=21 Identities=33% Similarity=0.716 Sum_probs=11.5
Q ss_pred ccccceeecCCCCc-cccccCC
Q 033418 88 HLEEGALVCPETGR-KFPVNKG 108 (119)
Q Consensus 88 ~i~~g~L~C~~c~~-~ypI~~G 108 (119)
++....+.||.||- .+.|..|
T Consensus 102 ~~~~~~~~CP~Cgs~~~~i~~G 123 (135)
T PRK03824 102 EVVHAFLKCPKCGSRDFEIVKG 123 (135)
T ss_pred cccccCcCCcCCCCCCcEEecC
Confidence 44455566777763 3555554
No 66
>PF10080 DUF2318: Predicted membrane protein (DUF2318); InterPro: IPR018758 This domain of unknown function is found in hypothetical bacterial membrane proteins with no known function.
Probab=37.58 E-value=16 Score=25.55 Aligned_cols=19 Identities=32% Similarity=0.560 Sum_probs=16.6
Q ss_pred ccccceeecCCCCcccccc
Q 033418 88 HLEEGALVCPETGRKFPVN 106 (119)
Q Consensus 88 ~i~~g~L~C~~c~~~ypI~ 106 (119)
...++.|+|..|+..|.+.
T Consensus 47 ~q~g~~lvC~~C~~~~~~~ 65 (102)
T PF10080_consen 47 YQEGDQLVCKNCGVRFNLP 65 (102)
T ss_pred EEECCEEEEecCCCEEehh
Confidence 5778899999999999874
No 67
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=37.41 E-value=22 Score=22.31 Aligned_cols=15 Identities=33% Similarity=0.844 Sum_probs=12.4
Q ss_pred ccceeecCCCCcccc
Q 033418 90 EEGALVCPETGRKFP 104 (119)
Q Consensus 90 ~~g~L~C~~c~~~yp 104 (119)
.+..++||.||..|-
T Consensus 18 ~dDiVvCp~CgapyH 32 (54)
T PF14446_consen 18 GDDIVVCPECGAPYH 32 (54)
T ss_pred CCCEEECCCCCCccc
Confidence 567899999998774
No 68
>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=36.73 E-value=20 Score=19.42 Aligned_cols=13 Identities=31% Similarity=0.526 Sum_probs=8.6
Q ss_pred cceeecCCCCccc
Q 033418 91 EGALVCPETGRKF 103 (119)
Q Consensus 91 ~g~L~C~~c~~~y 103 (119)
+-.++||.||+.+
T Consensus 19 g~~r~C~~Cg~~~ 31 (32)
T PF09297_consen 19 GWARRCPSCGHEH 31 (32)
T ss_dssp SS-EEESSSS-EE
T ss_pred cCEeECCCCcCEe
Confidence 4478999999865
No 69
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=36.72 E-value=19 Score=25.37 Aligned_cols=19 Identities=26% Similarity=0.324 Sum_probs=12.7
Q ss_pred ccccceeecCCCCcccccc
Q 033418 88 HLEEGALVCPETGRKFPVN 106 (119)
Q Consensus 88 ~i~~g~L~C~~c~~~ypI~ 106 (119)
+...+...|+.||..|++.
T Consensus 66 e~vp~~~~C~~Cg~~~~~~ 84 (117)
T PRK00564 66 VDEKVELECKDCSHVFKPN 84 (117)
T ss_pred EecCCEEEhhhCCCccccC
Confidence 4555666777777777765
No 70
>PF10122 Mu-like_Com: Mu-like prophage protein Com; InterPro: IPR019294 Members of this entry belong to the Com family of proteins that act as translational regulators of mom [, ].
Probab=36.66 E-value=38 Score=21.12 Aligned_cols=33 Identities=15% Similarity=0.093 Sum_probs=25.1
Q ss_pred HHHHHhc-ccccceeecCCCCccccccCCccccC
Q 033418 81 LMKFHHL-HLEEGALVCPETGRKFPVNKGIPNML 113 (119)
Q Consensus 81 L~~lH~~-~i~~g~L~C~~c~~~ypI~~GIP~mL 113 (119)
=|.|-++ ++.+.+..||.||...-|+.-.|.--
T Consensus 11 nklLa~~g~~~~leIKCpRC~tiN~~~a~~~~~~ 44 (51)
T PF10122_consen 11 NKLLAKAGEVIELEIKCPRCKTINHVRATSPEPE 44 (51)
T ss_pred hHHHhhhcCccEEEEECCCCCccceEeccCCCCC
Confidence 3444565 77788999999999999988776543
No 71
>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=36.35 E-value=22 Score=23.94 Aligned_cols=18 Identities=28% Similarity=0.556 Sum_probs=15.1
Q ss_pred cccceeecCCCCcccccc
Q 033418 89 LEEGALVCPETGRKFPVN 106 (119)
Q Consensus 89 i~~g~L~C~~c~~~ypI~ 106 (119)
+.++.+.|+.||..+.++
T Consensus 12 ~~~~~~~C~~C~~~~~~~ 29 (104)
T TIGR01384 12 PKNGVYVCPSCGYEKEKK 29 (104)
T ss_pred cCCCeEECcCCCCccccc
Confidence 456899999999998874
No 72
>PF05488 PAAR_motif: PAAR motif; InterPro: IPR008727 The PAAR motif is usually found in pairs in a family of bacterial membrane proteins. It is also found as a triplet of tandem repeats comprising the entire length in a another family of hypothetical proteins.
Probab=36.23 E-value=26 Score=22.33 Aligned_cols=27 Identities=19% Similarity=0.498 Sum_probs=22.2
Q ss_pred ccceeecCCCCccccccCCccccCCCC
Q 033418 90 EEGALVCPETGRKFPVNKGIPNMLLHE 116 (119)
Q Consensus 90 ~~g~L~C~~c~~~ypI~~GIP~mL~~e 116 (119)
....-.||.|+..++|..|-|.+..+.
T Consensus 31 ~Gd~~~C~~~~~~~~I~~G~~~v~i~G 57 (76)
T PF05488_consen 31 VGDQVTCPKCKGPGPIVEGSPTVFING 57 (76)
T ss_pred CcCcccCCCccccceeccCCCCccCCc
Confidence 344779999999999999999887653
No 73
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=36.04 E-value=19 Score=29.28 Aligned_cols=16 Identities=31% Similarity=0.727 Sum_probs=13.7
Q ss_pred ccccceeecCCCCccc
Q 033418 88 HLEEGALVCPETGRKF 103 (119)
Q Consensus 88 ~i~~g~L~C~~c~~~y 103 (119)
|-..|+++|.+||.+-
T Consensus 25 d~~~Ge~vC~~CG~Vl 40 (310)
T PRK00423 25 DYERGEIVCADCGLVI 40 (310)
T ss_pred ECCCCeEeecccCCcc
Confidence 5678999999999864
No 74
>PLN02569 threonine synthase
Probab=35.83 E-value=18 Score=31.51 Aligned_cols=16 Identities=38% Similarity=0.754 Sum_probs=13.9
Q ss_pred eeecCCCCccccccCC
Q 033418 93 ALVCPETGRKFPVNKG 108 (119)
Q Consensus 93 ~L~C~~c~~~ypI~~G 108 (119)
.|.|+.||+.|++.+-
T Consensus 49 ~l~C~~Cg~~y~~~~~ 64 (484)
T PLN02569 49 FLECPLTGEKYSLDEV 64 (484)
T ss_pred ccEeCCCCCcCCCccc
Confidence 4899999999998755
No 75
>KOG3352 consensus Cytochrome c oxidase, subunit Vb/COX4 [Energy production and conversion]
Probab=35.02 E-value=16 Score=27.60 Aligned_cols=19 Identities=42% Similarity=0.781 Sum_probs=13.1
Q ss_pred cccce-eecCCCCccccccC
Q 033418 89 LEEGA-LVCPETGRKFPVNK 107 (119)
Q Consensus 89 i~~g~-L~C~~c~~~ypI~~ 107 (119)
+..|+ -.|++||++|-..+
T Consensus 128 l~Kge~~rc~eCG~~fkL~~ 147 (153)
T KOG3352|consen 128 LEKGETQRCPECGHYFKLVP 147 (153)
T ss_pred EEcCCcccCCcccceEEeee
Confidence 33443 36999999997653
No 76
>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=33.29 E-value=24 Score=18.65 Aligned_cols=9 Identities=33% Similarity=0.866 Sum_probs=7.1
Q ss_pred eeecCCCCc
Q 033418 93 ALVCPETGR 101 (119)
Q Consensus 93 ~L~C~~c~~ 101 (119)
...||+||.
T Consensus 16 ~f~CPnCG~ 24 (24)
T PF07754_consen 16 PFPCPNCGF 24 (24)
T ss_pred eEeCCCCCC
Confidence 578999983
No 77
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=33.14 E-value=46 Score=25.16 Aligned_cols=16 Identities=19% Similarity=0.521 Sum_probs=11.3
Q ss_pred cceeecCCCCcccccc
Q 033418 91 EGALVCPETGRKFPVN 106 (119)
Q Consensus 91 ~g~L~C~~c~~~ypI~ 106 (119)
....+||.|++.|.--
T Consensus 115 ~~~Y~Cp~C~~rytf~ 130 (178)
T PRK06266 115 NMFFFCPNCHIRFTFD 130 (178)
T ss_pred CCEEECCCCCcEEeHH
Confidence 3466788888888644
No 78
>PLN02459 probable adenylate kinase
Probab=32.95 E-value=25 Score=28.34 Aligned_cols=18 Identities=33% Similarity=0.617 Sum_probs=15.6
Q ss_pred cccceeecCCCCcccccc
Q 033418 89 LEEGALVCPETGRKFPVN 106 (119)
Q Consensus 89 i~~g~L~C~~c~~~ypI~ 106 (119)
-..|..+||.||+.|.+.
T Consensus 149 Rl~gR~~~~~~g~~Yn~~ 166 (261)
T PLN02459 149 KCLGRRICSECGKNFNVA 166 (261)
T ss_pred HhhccccccccCcccccc
Confidence 457888999999999985
No 79
>TIGR00143 hypF [NiFe] hydrogenase maturation protein HypF. A previously described regulatory effect of HypF mutatation is attributable to loss of activity of a regulatory hydrogenase. A zinc finger-like region CXXCX(18)CXXCX(24)CXXCX(18)CXXC region further supported the regulatory hypothesis. However, more recent work (PUBMED:11375153) shows the direct effect is on the activity of expressed hydrogenases with nickel/iron centers, rather than on expression.
Probab=32.92 E-value=31 Score=31.52 Aligned_cols=41 Identities=15% Similarity=0.302 Sum_probs=30.7
Q ss_pred CCCCCCCcHHHHHHHHhc---ccccceeecCCCCccccccCCcc
Q 033418 70 PESSMLDSDDFLMKFHHL---HLEEGALVCPETGRKFPVNKGIP 110 (119)
Q Consensus 70 ~p~~~~~~ee~L~~lH~~---~i~~g~L~C~~c~~~ypI~~GIP 110 (119)
.|.|...+++|++.++.- .-.=--..|.+||=.|.|...+|
T Consensus 64 ippD~a~C~~Cl~E~~dp~~Rry~YpF~nCt~CGPr~~i~~~lp 107 (711)
T TIGR00143 64 IPADVATCSDCLEEMLDKNDRRYLYPFISCTHCGPRFTIIEALP 107 (711)
T ss_pred cCCchhhHHHHHHHhcCCCcccccCCcccccCCCCCeEEeecCC
Confidence 455667799999988643 22223458999999999999988
No 80
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=32.69 E-value=17 Score=23.38 Aligned_cols=14 Identities=36% Similarity=0.627 Sum_probs=10.9
Q ss_pred eeecCCCCcccccc
Q 033418 93 ALVCPETGRKFPVN 106 (119)
Q Consensus 93 ~L~C~~c~~~ypI~ 106 (119)
-|.||.||..|.=+
T Consensus 17 ~lrCPRC~~~FR~~ 30 (65)
T COG4049 17 FLRCPRCGMVFRRR 30 (65)
T ss_pred eeeCCchhHHHHHh
Confidence 36899999988643
No 81
>COG0375 HybF Zn finger protein HypA/HybF (possibly regulating hydrogenase expression) [General function prediction only]
Probab=32.68 E-value=25 Score=25.29 Aligned_cols=21 Identities=33% Similarity=0.582 Sum_probs=15.9
Q ss_pred ccccceeecCCCC-ccccccCC
Q 033418 88 HLEEGALVCPETG-RKFPVNKG 108 (119)
Q Consensus 88 ~i~~g~L~C~~c~-~~ypI~~G 108 (119)
...+....||.|| ..+.|..|
T Consensus 81 ~~e~~~~~CP~C~s~~~~i~~G 102 (115)
T COG0375 81 ELEELDYRCPKCGSINLRIIGG 102 (115)
T ss_pred cchhheeECCCCCCCceEEecC
Confidence 4455556699999 88888887
No 82
>PF10609 ParA: ParA/MinD ATPase like; InterPro: IPR019591 This entry represents ATPases involved in plasmid partitioning []. It also contains cytosolic Fe-S cluster assembling factors, NBP35 and CFD1 which are required for biogenesis and export of both ribosomal subunits probably through assembling the ISCs in RLI1, a protein which performs rRNA processing and ribosome export [, , ].; PDB: 2PH1_A 3KB1_B.
Probab=31.89 E-value=24 Score=23.75 Aligned_cols=14 Identities=29% Similarity=0.793 Sum_probs=8.5
Q ss_pred ceeecCCCCccccc
Q 033418 92 GALVCPETGRKFPV 105 (119)
Q Consensus 92 g~L~C~~c~~~ypI 105 (119)
+.++||.||+.+.|
T Consensus 64 s~~~Cp~Cg~~~~i 77 (81)
T PF10609_consen 64 SYFVCPHCGERIYI 77 (81)
T ss_dssp -EEE-TTT--EEET
T ss_pred CccCCCCCCCeecC
Confidence 48899999998765
No 83
>smart00355 ZnF_C2H2 zinc finger.
Probab=31.86 E-value=20 Score=16.89 Aligned_cols=11 Identities=45% Similarity=1.005 Sum_probs=8.9
Q ss_pred ecCCCCccccc
Q 033418 95 VCPETGRKFPV 105 (119)
Q Consensus 95 ~C~~c~~~ypI 105 (119)
.|+.|+..|.-
T Consensus 2 ~C~~C~~~f~~ 12 (26)
T smart00355 2 RCPECGKVFKS 12 (26)
T ss_pred CCCCCcchhCC
Confidence 68999988864
No 84
>PRK03922 hypothetical protein; Provisional
Probab=31.75 E-value=22 Score=25.58 Aligned_cols=18 Identities=33% Similarity=0.840 Sum_probs=15.8
Q ss_pred cccccceeecCCCCcccc
Q 033418 87 LHLEEGALVCPETGRKFP 104 (119)
Q Consensus 87 ~~i~~g~L~C~~c~~~yp 104 (119)
++|.-|...||.||..|+
T Consensus 43 VeievG~~~cP~cge~~~ 60 (113)
T PRK03922 43 VEVEVGLTICPKCGEPFD 60 (113)
T ss_pred EEEecCcccCCCCCCcCC
Confidence 499999999999998764
No 85
>PF01215 COX5B: Cytochrome c oxidase subunit Vb This family consists of chains F and S ; InterPro: IPR002124 Cytochrome c oxidase (1.9.3.1 from EC) is an oligomeric enzymatic complex which is a component of the respiratory chain complex and is involved in the transfer of electrons from cytochrome c to oxygen []. In eukaryotes this enzyme complex is located in the mitochondrial inner membrane; in aerobic prokaryotes it is found in the plasma membrane. In eukaryotes, in addition to the three large subunits, I, II and III, that form the catalytic centre of the enzyme complex, there are a variable number of small polypeptidic subunits. One of these subunits, which is known as Vb in mammals, V in Dictyostelium discoideum (Slime mold) and IV in yeast, binds a zinc atom. The sequence of subunit Vb is well conserved and includes three conserved cysteines that coordinate the zinc ion [, ]. Two of these cysteines are clustered in the C-terminal section of the subunit.; GO: 0004129 cytochrome-c oxidase activity, 0005740 mitochondrial envelope; PDB: 2EIL_S 2ZXW_S 3ASN_S 1OCO_S 3AG4_S 3ABK_S 1OCZ_S 1OCC_F 3ASO_S 3ABL_S ....
Probab=31.70 E-value=16 Score=26.92 Aligned_cols=20 Identities=35% Similarity=0.703 Sum_probs=14.8
Q ss_pred cccccee-ecCCCCccccccC
Q 033418 88 HLEEGAL-VCPETGRKFPVNK 107 (119)
Q Consensus 88 ~i~~g~L-~C~~c~~~ypI~~ 107 (119)
.+.+|.. .|++||.+|-...
T Consensus 106 ~l~~g~~~RCpeCG~~fkL~~ 126 (136)
T PF01215_consen 106 WLHKGKPQRCPECGQVFKLKY 126 (136)
T ss_dssp EEETTSEEEETTTEEEEEEEE
T ss_pred EEeCCCccCCCCCCeEEEEEE
Confidence 4555544 8999999998754
No 86
>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=31.29 E-value=31 Score=19.26 Aligned_cols=9 Identities=44% Similarity=1.128 Sum_probs=4.4
Q ss_pred eeecCCCCc
Q 033418 93 ALVCPETGR 101 (119)
Q Consensus 93 ~L~C~~c~~ 101 (119)
.+.|+.||+
T Consensus 17 ~irC~~CG~ 25 (32)
T PF03604_consen 17 PIRCPECGH 25 (32)
T ss_dssp TSSBSSSS-
T ss_pred cEECCcCCC
Confidence 345555554
No 87
>TIGR02300 FYDLN_acid conserved hypothetical protein TIGR02300. 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=30.93 E-value=26 Score=25.79 Aligned_cols=19 Identities=37% Similarity=0.648 Sum_probs=17.1
Q ss_pred ccccceeecCCCCcccccc
Q 033418 88 HLEEGALVCPETGRKFPVN 106 (119)
Q Consensus 88 ~i~~g~L~C~~c~~~ypI~ 106 (119)
++...-.+||.||..|++.
T Consensus 21 DLnk~p~vcP~cg~~~~~~ 39 (129)
T TIGR02300 21 DLNRRPAVSPYTGEQFPPE 39 (129)
T ss_pred ccCCCCccCCCcCCccCcc
Confidence 7777889999999999987
No 88
>PLN02189 cellulose synthase
Probab=30.91 E-value=28 Score=33.46 Aligned_cols=32 Identities=28% Similarity=0.506 Sum_probs=28.5
Q ss_pred cccccceeecCCCCccccccCCccccCCCCCC
Q 033418 87 LHLEEGALVCPETGRKFPVNKGIPNMLLHEDE 118 (119)
Q Consensus 87 ~~i~~g~L~C~~c~~~ypI~~GIP~mL~~e~~ 118 (119)
.+..||.=.||+|+..|.-..|.|.+-.+++|
T Consensus 70 yer~eg~q~CpqCkt~Y~r~kgs~~v~gd~ee 101 (1040)
T PLN02189 70 YERREGTQNCPQCKTRYKRLKGSPRVEGDDDE 101 (1040)
T ss_pred hhhhcCCccCcccCCchhhccCCCCcCCcccc
Confidence 38899999999999999999999999887544
No 89
>PF12171 zf-C2H2_jaz: Zinc-finger double-stranded RNA-binding; InterPro: IPR022755 This zinc finger is found in archaea and eukaryotes, and is approximately 30 amino acids in length. The mammalian members of this group occur multiple times along the protein, joined by flexible linkers, and are referred to as JAZ - dsRNA-binding ZF protein - zinc-fingers. The JAZ proteins are expressed in all tissues tested and localise in the nucleus, particularly the nucleolus []. JAZ preferentially binds to double-stranded (ds) RNA or RNA/DNA hybrids rather than DNA. In addition to binding double-stranded RNA, these zinc-fingers are required for nucleolar localisation. This entry represents the multiple-adjacent-C2H2 zinc finger, JAZ. ; PDB: 4DGW_A 1ZR9_A.
Probab=30.50 E-value=29 Score=17.76 Aligned_cols=11 Identities=18% Similarity=0.585 Sum_probs=9.3
Q ss_pred eecCCCCcccc
Q 033418 94 LVCPETGRKFP 104 (119)
Q Consensus 94 L~C~~c~~~yp 104 (119)
..|..|++.|.
T Consensus 2 ~~C~~C~k~f~ 12 (27)
T PF12171_consen 2 FYCDACDKYFS 12 (27)
T ss_dssp CBBTTTTBBBS
T ss_pred CCcccCCCCcC
Confidence 57999999885
No 90
>PF14311 DUF4379: Domain of unknown function (DUF4379)
Probab=30.45 E-value=25 Score=21.17 Aligned_cols=11 Identities=27% Similarity=0.872 Sum_probs=9.5
Q ss_pred eecCCCCcccc
Q 033418 94 LVCPETGRKFP 104 (119)
Q Consensus 94 L~C~~c~~~yp 104 (119)
-.|+.||+.|.
T Consensus 29 W~C~~Cgh~w~ 39 (55)
T PF14311_consen 29 WKCPKCGHEWK 39 (55)
T ss_pred EECCCCCCeeE
Confidence 48999999985
No 91
>PRK09462 fur ferric uptake regulator; Provisional
Probab=29.94 E-value=28 Score=24.92 Aligned_cols=16 Identities=19% Similarity=0.571 Sum_probs=13.6
Q ss_pred eeecCCCCccccccCC
Q 033418 93 ALVCPETGRKFPVNKG 108 (119)
Q Consensus 93 ~L~C~~c~~~ypI~~G 108 (119)
-++|..||+.+.|.+.
T Consensus 90 H~iC~~Cg~i~~i~~~ 105 (148)
T PRK09462 90 HLICLDCGKVIEFSDD 105 (148)
T ss_pred ceEECCCCCEEEeCCc
Confidence 3999999999998653
No 92
>PHA02768 hypothetical protein; Provisional
Probab=29.71 E-value=18 Score=22.73 Aligned_cols=14 Identities=29% Similarity=0.553 Sum_probs=11.1
Q ss_pred eecCCCCccccccC
Q 033418 94 LVCPETGRKFPVNK 107 (119)
Q Consensus 94 L~C~~c~~~ypI~~ 107 (119)
..|+.||+.|..++
T Consensus 6 y~C~~CGK~Fs~~~ 19 (55)
T PHA02768 6 YECPICGEIYIKRK 19 (55)
T ss_pred cCcchhCCeeccHH
Confidence 37999999997654
No 93
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=29.54 E-value=24 Score=26.88 Aligned_cols=11 Identities=27% Similarity=0.842 Sum_probs=8.5
Q ss_pred eeecCCCCccc
Q 033418 93 ALVCPETGRKF 103 (119)
Q Consensus 93 ~L~C~~c~~~y 103 (119)
-.+||.||+.|
T Consensus 130 f~~C~~CgkiY 140 (165)
T COG1656 130 FYRCPKCGKIY 140 (165)
T ss_pred eeECCCCcccc
Confidence 34699999887
No 94
>PF05129 Elf1: Transcription elongation factor Elf1 like; InterPro: IPR007808 This family of uncharacterised, mostly short, proteins contain a putative zinc binding domain with four conserved cysteines.; PDB: 1WII_A.
Probab=29.34 E-value=27 Score=23.28 Aligned_cols=22 Identities=27% Similarity=0.462 Sum_probs=13.9
Q ss_pred cccceeecCCCCccccccCCcccc
Q 033418 89 LEEGALVCPETGRKFPVNKGIPNM 112 (119)
Q Consensus 89 i~~g~L~C~~c~~~ypI~~GIP~m 112 (119)
-.-|.+.|..||..|... |+.+
T Consensus 42 ~~~~~~~C~~Cg~~~~~~--i~~L 63 (81)
T PF05129_consen 42 EGIGILSCRVCGESFQTK--INPL 63 (81)
T ss_dssp TTEEEEEESSS--EEEEE----SS
T ss_pred CCEEEEEecCCCCeEEEc--cCcc
Confidence 356799999999999776 6543
No 95
>PHA00616 hypothetical protein
Probab=29.07 E-value=16 Score=21.98 Aligned_cols=10 Identities=30% Similarity=0.574 Sum_probs=8.5
Q ss_pred ecCCCCcccc
Q 033418 95 VCPETGRKFP 104 (119)
Q Consensus 95 ~C~~c~~~yp 104 (119)
.|+.||..|.
T Consensus 3 qC~~CG~~F~ 12 (44)
T PHA00616 3 QCLRCGGIFR 12 (44)
T ss_pred ccchhhHHHh
Confidence 6999999874
No 96
>COG0777 AccD Acetyl-CoA carboxylase beta subunit [Lipid metabolism]
Probab=28.69 E-value=8.8 Score=31.73 Aligned_cols=33 Identities=18% Similarity=0.292 Sum_probs=26.5
Q ss_pred CCCcHHHHHHHHhcccccceeecCCCCcccccc
Q 033418 74 MLDSDDFLMKFHHLHLEEGALVCPETGRKFPVN 106 (119)
Q Consensus 74 ~~~~ee~L~~lH~~~i~~g~L~C~~c~~~ypI~ 106 (119)
|..+.+|=.-+|+-|+....-+||.|++-++|.
T Consensus 28 w~KCp~c~~~~y~~eL~~n~~vcp~c~~h~ri~ 60 (294)
T COG0777 28 WTKCPSCGEMLYRKELESNLKVCPKCGHHMRIS 60 (294)
T ss_pred eeECCCccceeeHHHHHhhhhcccccCcccccC
Confidence 444566666667779999999999999999985
No 97
>PF10013 DUF2256: Uncharacterized protein conserved in bacteria (DUF2256); InterPro: IPR017136 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=27.99 E-value=27 Score=20.93 Aligned_cols=10 Identities=50% Similarity=1.251 Sum_probs=8.7
Q ss_pred ecCCCCcccc
Q 033418 95 VCPETGRKFP 104 (119)
Q Consensus 95 ~C~~c~~~yp 104 (119)
+|+.|||.|.
T Consensus 10 ~C~~C~rpf~ 19 (42)
T PF10013_consen 10 ICPVCGRPFT 19 (42)
T ss_pred cCcccCCcch
Confidence 7999999885
No 98
>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=27.85 E-value=66 Score=23.74 Aligned_cols=16 Identities=25% Similarity=0.611 Sum_probs=10.5
Q ss_pred cceeecCCCCcccccc
Q 033418 91 EGALVCPETGRKFPVN 106 (119)
Q Consensus 91 ~g~L~C~~c~~~ypI~ 106 (119)
....+||.|++.|.-.
T Consensus 107 ~~~Y~Cp~c~~r~tf~ 122 (158)
T TIGR00373 107 NMFFICPNMCVRFTFN 122 (158)
T ss_pred CCeEECCCCCcEeeHH
Confidence 3455788888777543
No 99
>PTZ00088 adenylate kinase 1; Provisional
Probab=27.81 E-value=26 Score=27.32 Aligned_cols=17 Identities=24% Similarity=0.513 Sum_probs=14.4
Q ss_pred ccceeecCCCCcccccc
Q 033418 90 EEGALVCPETGRKFPVN 106 (119)
Q Consensus 90 ~~g~L~C~~c~~~ypI~ 106 (119)
.-|..+||.||+.|.+.
T Consensus 127 l~~Rr~~~~~g~~y~~~ 143 (229)
T PTZ00088 127 LLGRRICNTCNRNFNIA 143 (229)
T ss_pred HHcCcCCCccCCcceec
Confidence 35678999999999885
No 100
>TIGR03829 YokU_near_AblA uncharacterized protein, YokU family. Members of this protein family occur in various species of the genus Bacillus, always next to the gene (kamA or ablA) for lysine 2,3-aminomutase. Members have a pair of CXXC motifs, and share homology to the amino-terminal region of a family of putative transcription factors for which the C-terminal is modeled by pfam01381, a helix-turn-helix domain model. This family, however, is shorter and lacks the helix-turn-helix region. The function of this protein family is unknown, but a regulatory role in compatible solute biosynthesis is suggested by local genome context.
Probab=27.50 E-value=26 Score=24.08 Aligned_cols=12 Identities=17% Similarity=0.714 Sum_probs=10.0
Q ss_pred eeecCCCCcccc
Q 033418 93 ALVCPETGRKFP 104 (119)
Q Consensus 93 ~L~C~~c~~~yp 104 (119)
.++|++||-.|-
T Consensus 35 a~~C~~CGe~y~ 46 (89)
T TIGR03829 35 SISCSHCGMEYQ 46 (89)
T ss_pred cccccCCCcEee
Confidence 578999999883
No 101
>PLN02294 cytochrome c oxidase subunit Vb
Probab=27.38 E-value=28 Score=26.84 Aligned_cols=19 Identities=32% Similarity=0.604 Sum_probs=15.0
Q ss_pred cccccee-ecCCCCcccccc
Q 033418 88 HLEEGAL-VCPETGRKFPVN 106 (119)
Q Consensus 88 ~i~~g~L-~C~~c~~~ypI~ 106 (119)
-+.+|.. .||+||.+|-.+
T Consensus 135 ~L~kGkp~RCpeCG~~fkL~ 154 (174)
T PLN02294 135 WLEKGKSFECPVCTQYFELE 154 (174)
T ss_pred EecCCCceeCCCCCCEEEEE
Confidence 5556655 799999999876
No 102
>PRK11639 zinc uptake transcriptional repressor; Provisional
Probab=27.11 E-value=33 Score=25.39 Aligned_cols=16 Identities=13% Similarity=0.225 Sum_probs=14.0
Q ss_pred eeecCCCCccccccCC
Q 033418 93 ALVCPETGRKFPVNKG 108 (119)
Q Consensus 93 ~L~C~~c~~~ypI~~G 108 (119)
-++|..||+.+.|.+.
T Consensus 100 H~iC~~CGki~~i~~~ 115 (169)
T PRK11639 100 MFICDRCGAVKEECAE 115 (169)
T ss_pred eEEeCCCCCEEEeccc
Confidence 4999999999999755
No 103
>cd03467 Rieske Rieske domain; a [2Fe-2S] cluster binding domain commonly found in Rieske non-heme iron oxygenase (RO) systems such as naphthalene and biphenyl dioxygenases, as well as in plant/cyanobacterial chloroplast b6f and mitochondrial cytochrome bc(1) complexes. The Rieske domain can be divided into two subdomains, with an incomplete six-stranded, antiparallel beta-barrel at one end, and an iron-sulfur cluster binding subdomain at the other. The Rieske iron-sulfur center contains a [2Fe-2S] cluster, which is involved in electron transfer, and is liganded to two histidine and two cysteine residues present in conserved sequences called Rieske motifs. In RO systems, the N-terminal Rieske domain of the alpha subunit acts as an electron shuttle that accepts electrons from a reductase or ferredoxin component and transfers them to the mononuclear iron in the alpha subunit C-terminal domain to be used for catalysis.
Probab=27.04 E-value=50 Score=21.49 Aligned_cols=23 Identities=35% Similarity=0.703 Sum_probs=20.5
Q ss_pred cccceeecCCCCccccccCCccc
Q 033418 89 LEEGALVCPETGRKFPVNKGIPN 111 (119)
Q Consensus 89 i~~g~L~C~~c~~~ypI~~GIP~ 111 (119)
+.++.++||--|-.|-+++|.+.
T Consensus 54 ~~~~~i~Cp~H~~~f~~~~G~~~ 76 (98)
T cd03467 54 GEDGCIVCPCHGSRFDLRTGEVV 76 (98)
T ss_pred cCCCEEEeCCCCCEEeCCCccCc
Confidence 56889999999999999999874
No 104
>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=26.90 E-value=28 Score=19.54 Aligned_cols=11 Identities=55% Similarity=1.313 Sum_probs=8.5
Q ss_pred eeecCCCCccc
Q 033418 93 ALVCPETGRKF 103 (119)
Q Consensus 93 ~L~C~~c~~~y 103 (119)
..+|+.||..|
T Consensus 32 ~~~C~~CGE~~ 42 (46)
T TIGR03831 32 ALVCPQCGEEY 42 (46)
T ss_pred ccccccCCCEe
Confidence 45789998776
No 105
>PF15541 Toxin_63: Putative toxin 63
Probab=26.66 E-value=64 Score=22.67 Aligned_cols=35 Identities=17% Similarity=0.259 Sum_probs=26.8
Q ss_pred HHHHHHHHhc-ccccceeecCCCCccccccCCcccc
Q 033418 78 DDFLMKFHHL-HLEEGALVCPETGRKFPVNKGIPNM 112 (119)
Q Consensus 78 ee~L~~lH~~-~i~~g~L~C~~c~~~ypI~~GIP~m 112 (119)
|++||.+|-+ .-..-++.|..-..+||.++|--+.
T Consensus 39 Ek~iRel~~l~~~~~~k~f~~~~~~a~P~~~~~~~~ 74 (104)
T PF15541_consen 39 EKFIRELQVLSQQEPRKVFCRCRRFAHPPKGKSLNA 74 (104)
T ss_pred HHHHHHHHhcCCCCCeeEEEeeceeecCCCCCcccc
Confidence 6899999988 4455577888777899988886543
No 106
>PLN02638 cellulose synthase A (UDP-forming), catalytic subunit
Probab=26.42 E-value=35 Score=32.95 Aligned_cols=33 Identities=30% Similarity=0.605 Sum_probs=29.0
Q ss_pred hcccccceeecCCCCccccccCCccccCCCCCC
Q 033418 86 HLHLEEGALVCPETGRKFPVNKGIPNMLLHEDE 118 (119)
Q Consensus 86 ~~~i~~g~L~C~~c~~~ypI~~GIP~mL~~e~~ 118 (119)
..+..||.=.||+|+..|.-..|.|..-.+|+|
T Consensus 52 EYEr~eG~q~CPqCktrYkr~kgsprv~gDeee 84 (1079)
T PLN02638 52 EYERKDGNQSCPQCKTKYKRHKGSPAILGDEEE 84 (1079)
T ss_pred hhhhhcCCccCCccCCchhhhcCCCCcCccccc
Confidence 448899999999999999999999999887644
No 107
>cd03478 Rieske_AIFL_N AIFL (apoptosis-inducing factor like) family, N-terminal Rieske domain; members of this family show similarity to human AIFL, containing an N-terminal Rieske domain and a C-terminal pyridine nucleotide-disulfide oxidoreductase domain (Pyr_redox). The Rieske domain is a [2Fe-2S] cluster binding domain involved in electron transfer. AIFL shares 35% homology with human AIF (apoptosis-inducing factor), mainly in the Pyr_redox domain. AIFL is predominantly localized to the mitochondria. AIFL induces apoptosis in a caspase-dependent manner.
Probab=25.99 E-value=47 Score=21.64 Aligned_cols=24 Identities=29% Similarity=0.536 Sum_probs=19.8
Q ss_pred ccccceeecCCCCccccccCCccc
Q 033418 88 HLEEGALVCPETGRKFPVNKGIPN 111 (119)
Q Consensus 88 ~i~~g~L~C~~c~~~ypI~~GIP~ 111 (119)
.+.++.++||--|-.|.+++|-..
T Consensus 51 ~~~~~~i~CP~Hg~~Fdl~tG~~~ 74 (95)
T cd03478 51 VLTDGRIRCPWHGACFNLRTGDIE 74 (95)
T ss_pred eEeCCEEEcCCCCCEEECCCCcCc
Confidence 345789999999999999999653
No 108
>PF10276 zf-CHCC: Zinc-finger domain; InterPro: IPR019401 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 short conserved zinc-finger domain. It contains the sequence motif Cx8Hx14Cx2C. ; PDB: 2JVM_A 2JRR_A 2JZ8_A.
Probab=25.83 E-value=41 Score=19.72 Aligned_cols=12 Identities=42% Similarity=1.171 Sum_probs=10.6
Q ss_pred ceeecCCCCccc
Q 033418 92 GALVCPETGRKF 103 (119)
Q Consensus 92 g~L~C~~c~~~y 103 (119)
+.-.||=||+.|
T Consensus 28 ~~~~CpYCg~~y 39 (40)
T PF10276_consen 28 GPVVCPYCGTRY 39 (40)
T ss_dssp CEEEETTTTEEE
T ss_pred CeEECCCCCCEE
Confidence 568999999988
No 109
>PLN02436 cellulose synthase A
Probab=25.76 E-value=40 Score=32.65 Aligned_cols=32 Identities=28% Similarity=0.511 Sum_probs=28.4
Q ss_pred cccccceeecCCCCccccccCCccccCCCCCC
Q 033418 87 LHLEEGALVCPETGRKFPVNKGIPNMLLHEDE 118 (119)
Q Consensus 87 ~~i~~g~L~C~~c~~~ypI~~GIP~mL~~e~~ 118 (119)
.+..||.=.||+|+..|.-..|.|.+-.+|+|
T Consensus 72 yer~eg~~~Cpqckt~Y~r~kgs~~~~~d~ee 103 (1094)
T PLN02436 72 YERREGNQACPQCKTRYKRIKGSPRVEGDEEE 103 (1094)
T ss_pred hhhhcCCccCcccCCchhhccCCCCcCCcccc
Confidence 38899999999999999999999999887544
No 110
>cd00350 rubredoxin_like Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center. The family includes rubredoxins, a small electron transfer protein, and a slightly smaller modular rubredoxin domain present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=25.56 E-value=36 Score=18.62 Aligned_cols=13 Identities=31% Similarity=0.636 Sum_probs=9.6
Q ss_pred eecCCCCcccccc
Q 033418 94 LVCPETGRKFPVN 106 (119)
Q Consensus 94 L~C~~c~~~ypI~ 106 (119)
-+|+.||..|.-.
T Consensus 2 ~~C~~CGy~y~~~ 14 (33)
T cd00350 2 YVCPVCGYIYDGE 14 (33)
T ss_pred EECCCCCCEECCC
Confidence 4789999888643
No 111
>PF08209 Sgf11: Sgf11 (transcriptional regulation protein); InterPro: IPR013246 The Sgf11 family is a SAGA complex subunit in Saccharomyces cerevisiae (Baker's yeast). The SAGA complex is a multisubunit protein complex involved in transcriptional regulation. SAGA combines proteins involved in interactions with DNA-bound activators and TATA-binding protein (TBP), as well as enzymes for histone acetylation and deubiquitylation [].; PDB: 3M99_B 2LO2_A 3MHH_C 3MHS_C.
Probab=25.34 E-value=43 Score=18.89 Aligned_cols=12 Identities=33% Similarity=0.733 Sum_probs=8.1
Q ss_pred ceeecCCCCccc
Q 033418 92 GALVCPETGRKF 103 (119)
Q Consensus 92 g~L~C~~c~~~y 103 (119)
....||+|+|..
T Consensus 3 ~~~~C~nC~R~v 14 (33)
T PF08209_consen 3 PYVECPNCGRPV 14 (33)
T ss_dssp -EEE-TTTSSEE
T ss_pred CeEECCCCcCCc
Confidence 457899999954
No 112
>PHA00626 hypothetical protein
Probab=25.02 E-value=33 Score=21.93 Aligned_cols=18 Identities=17% Similarity=0.362 Sum_probs=12.0
Q ss_pred eecCCCCccccccCCccc
Q 033418 94 LVCPETGRKFPVNKGIPN 111 (119)
Q Consensus 94 L~C~~c~~~ypI~~GIP~ 111 (119)
+.||.||..=-|+.||-+
T Consensus 1 m~CP~CGS~~Ivrcg~cr 18 (59)
T PHA00626 1 MSCPKCGSGNIAKEKTMR 18 (59)
T ss_pred CCCCCCCCceeeeeceec
Confidence 358888886556766643
No 113
>KOG2593 consensus Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=24.98 E-value=38 Score=29.55 Aligned_cols=13 Identities=31% Similarity=0.871 Sum_probs=9.7
Q ss_pred ceeecCCCCcccc
Q 033418 92 GALVCPETGRKFP 104 (119)
Q Consensus 92 g~L~C~~c~~~yp 104 (119)
....||.|++.|-
T Consensus 127 ~~Y~Cp~C~kkyt 139 (436)
T KOG2593|consen 127 AGYVCPNCQKKYT 139 (436)
T ss_pred ccccCCccccchh
Confidence 3568888888874
No 114
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=24.90 E-value=45 Score=20.25 Aligned_cols=16 Identities=13% Similarity=0.052 Sum_probs=12.7
Q ss_pred ccccceeecCCCCccc
Q 033418 88 HLEEGALVCPETGRKF 103 (119)
Q Consensus 88 ~i~~g~L~C~~c~~~y 103 (119)
...++.+.|+.||..|
T Consensus 32 ~~~~~r~~C~~Cgyt~ 47 (50)
T PRK00432 32 AEHLDRWHCGKCGYTE 47 (50)
T ss_pred eccCCcEECCCcCCEE
Confidence 4455899999999876
No 115
>PF06750 DiS_P_DiS: Bacterial Peptidase A24 N-terminal domain; InterPro: IPR010627 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Aspartic endopeptidases 3.4.23. from EC of vertebrate, fungal and retroviral origin have been characterised []. More recently, aspartic endopeptidases associated with the processing of bacterial type 4 prepilin [] and archaean preflagellin have been described [, ]. Structurally, aspartic endopeptidases are bilobal enzymes, each lobe contributing a catalytic Asp residue, with an extended active site cleft localised between the two lobes of the molecule. One lobe has probably evolved from the other through a gene duplication event in the distant past. In modern-day enzymes, although the three-dimensional structures are very similar, the amino acid sequences are more divergent, except for the catalytic site motif, which is very conserved. The presence and position of disulphide bridges are other conserved features of aspartic peptidases. All or most aspartate peptidases are endopeptidases. These enzymes have been assigned into clans (proteins which are evolutionary related), and further sub-divided into families, largely on the basis of their tertiary structure. This domain is found at the N terminus of bacterial aspartic peptidases belonging to MEROPS peptidase family A24 (clan AD), subfamily A24A (type IV prepilin peptidase, IPR000045 from INTERPRO). It's function has not been specifically determined; however some of the family have been characterised as bifunctional [], and this domain may contain the N-methylation activity. The domain consists of an intracellular region between a pair of transmembrane domains. This intracellular region contains an invariant proline and four conserved cysteines. These Cys residues are arranged in a two-pair motif, with the Cys residues of a pair separated (usually) by 2 aa and with each pair separated by 21 largely hydrophilic residues (C-X-X-C...X21...C-X-X-C); they have been shown to be essential to the overall function of the enzyme [, ]. The bifunctional enzyme prepilin peptidase (PilD) from Pseudomonas aeruginosa is a key determinant in both type-IV pilus biogenesis and extracellular protein secretion, in its roles as a leader peptidase and methyl transferase (MTase). It is responsible for endopeptidic cleavage of the unique leader peptides that characterise type-IV pilin precursors, as well as proteins with homologous leader sequences that are essential components of the general secretion pathway found in a variety of Gram-negative pathogens. Following removal of the leader peptides, the same enzyme is responsible for the second posttranslational modification that characterises the type-IV pilins and their homologues, namely N-methylation of the newly exposed N-terminal amino acid residue [].
Probab=24.88 E-value=33 Score=23.28 Aligned_cols=25 Identities=20% Similarity=0.258 Sum_probs=21.0
Q ss_pred ccccceeecCCCCccccccCCcccc
Q 033418 88 HLEEGALVCPETGRKFPVNKGIPNM 112 (119)
Q Consensus 88 ~i~~g~L~C~~c~~~ypI~~GIP~m 112 (119)
.+..+.=.|+.|++.-+..|=||++
T Consensus 28 ~i~~~rS~C~~C~~~L~~~~lIPi~ 52 (92)
T PF06750_consen 28 SIIFPRSHCPHCGHPLSWWDLIPIL 52 (92)
T ss_pred CccCCCCcCcCCCCcCcccccchHH
Confidence 4556677899999999999999974
No 116
>cd03528 Rieske_RO_ferredoxin Rieske non-heme iron oxygenase (RO) family, Rieske ferredoxin component; composed of the Rieske ferredoxin component of some three-component RO systems including biphenyl dioxygenase (BPDO) and carbazole 1,9a-dioxygenase (CARDO). The RO family comprise a large class of aromatic ring-hydroxylating dioxygenases found predominantly in microorganisms. These enzymes enable microorganisms to tolerate and even exclusively utilize aromatic compounds for growth. ROs consist of two or three components: reductase, oxygenase, and ferredoxin (in some cases) components. The ferredoxin component contains either a plant-type or Rieske-type [2Fe-2S] cluster. The Rieske ferredoxin component in this family carries an electron from the RO reductase component to the terminal RO oxygenase component. BPDO degrades biphenyls and polychlorinated biphenyls. BPDO ferredoxin (BphF) has structural features consistent with a minimal and perhaps archetypical Rieske protein in that the in
Probab=24.32 E-value=51 Score=21.36 Aligned_cols=23 Identities=30% Similarity=0.678 Sum_probs=19.4
Q ss_pred cccceeecCCCCccccccCCccc
Q 033418 89 LEEGALVCPETGRKFPVNKGIPN 111 (119)
Q Consensus 89 i~~g~L~C~~c~~~ypI~~GIP~ 111 (119)
+.++.++||--|-.|-+++|-+.
T Consensus 53 ~~~~~i~Cp~Hg~~fd~~~G~~~ 75 (98)
T cd03528 53 VEGGVIECPLHGGRFDLRTGKAL 75 (98)
T ss_pred EeCCEEEeCCcCCEEECCCCccc
Confidence 45679999999999999999654
No 117
>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=24.07 E-value=58 Score=20.27 Aligned_cols=20 Identities=25% Similarity=0.424 Sum_probs=16.0
Q ss_pred cceeecCCCCccccccCCcc
Q 033418 91 EGALVCPETGRKFPVNKGIP 110 (119)
Q Consensus 91 ~g~L~C~~c~~~ypI~~GIP 110 (119)
...+.||.||..|.|..-=|
T Consensus 20 GeiV~Cp~CGaeleVv~~~p 39 (54)
T TIGR01206 20 GELVICDECGAELEVVSLDP 39 (54)
T ss_pred CCEEeCCCCCCEEEEEeCCC
Confidence 34669999999999977666
No 118
>PTZ00043 cytochrome c oxidase subunit; Provisional
Probab=24.02 E-value=31 Score=27.98 Aligned_cols=19 Identities=32% Similarity=0.459 Sum_probs=14.6
Q ss_pred cccccee-ecCCCCcccccc
Q 033418 88 HLEEGAL-VCPETGRKFPVN 106 (119)
Q Consensus 88 ~i~~g~L-~C~~c~~~ypI~ 106 (119)
-+.+|.. .|++||.+|-..
T Consensus 175 wLrEGkpqRCpECGqVFKLV 194 (268)
T PTZ00043 175 RCREGFLYRCGECDQIFMLV 194 (268)
T ss_pred EecCCCCccCCCCCcEEEEE
Confidence 4556665 899999999763
No 119
>PF00628 PHD: PHD-finger; InterPro: IPR019787 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 PHD (homeodomain) zinc finger domain [,], which is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in chromatin-mediated transcriptional regulation. The PHD finger motif is reminiscent of, but distinct from the C3HC4 type RING finger. The function of this domain is not yet known but in analogy with the LIM domain it could be involved in protein-protein interaction and be important for the assembly or activity of multicomponent complexes involved in transcriptional activation or repression. Alternatively, the interactions could be intra-molecular and be important in maintaining the structural integrity of the protein. In similarity to the RING finger and the LIM domain, the PHD finger is thought to bind two zinc ions. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0005515 protein binding; PDB: 3ZVY_A 2LGG_A 3SOW_A 3SOU_B 3ASL_A 3ASK_A 3ZVZ_B 3T6R_A 2LGK_A 3SOX_B ....
Probab=23.98 E-value=59 Score=18.72 Aligned_cols=17 Identities=12% Similarity=0.357 Sum_probs=13.8
Q ss_pred ccceeecCCCCcccccc
Q 033418 90 EEGALVCPETGRKFPVN 106 (119)
Q Consensus 90 ~~g~L~C~~c~~~ypI~ 106 (119)
.+..+.|..|+++|-+.
T Consensus 11 ~~~~i~C~~C~~~~H~~ 27 (51)
T PF00628_consen 11 DGDMIQCDSCNRWYHQE 27 (51)
T ss_dssp TSSEEEBSTTSCEEETT
T ss_pred CCCeEEcCCCChhhCcc
Confidence 45678999999999764
No 120
>PF13926 DUF4211: Domain of unknown function (DUF4211)
Probab=23.93 E-value=1.2e+02 Score=21.88 Aligned_cols=66 Identities=17% Similarity=0.288 Sum_probs=36.1
Q ss_pred ccCCHHHHhcccchhcHHHHHHHHHhCC--CCCCCCCC-CCCCCCCcHHHHHHHHhc---cccc----ceeecCCCCcc
Q 033418 34 VDFNPDFLKNIFPKIEWQALVQASRSMG--YSELPEES-PESSMLDSDDFLMKFHHL---HLEE----GALVCPETGRK 102 (119)
Q Consensus 34 ~efn~~fi~~~l~kldw~al~~~a~~lg--~~~lP~~~-~p~~~~~~ee~L~~lH~~---~i~~----g~L~C~~c~~~ 102 (119)
.-+||+|++.+..+-||- |..+.+.+. +.+.-... ....| ..+|.++|+.. .+.+ +.-.|..|++.
T Consensus 50 ~aldp~f~~~l~~~~de~-fl~a~~~id~~~~~~~~~l~~ss~W--~~~f~~aL~~~P~l~v~~~~~~~~~~C~AC~~~ 125 (153)
T PF13926_consen 50 NALDPDFLQELEDERDEY-FLPALKKIDDELQGRKDSLLSSSAW--KPDFKKALETYPELSVTEISYHTGPSCDACNRS 125 (153)
T ss_pred HHcCHHHHHHHhhhhHHH-HHHHHHHHHHHHHHHHhceeeeccC--CHHHHHHHHHCCCeEEEecCCCCCCcCcccCCC
Confidence 457888998887766654 333333321 00000000 00122 47799999888 2222 55689889875
No 121
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=23.61 E-value=46 Score=24.98 Aligned_cols=13 Identities=31% Similarity=0.595 Sum_probs=11.6
Q ss_pred ceeecCCCCcccc
Q 033418 92 GALVCPETGRKFP 104 (119)
Q Consensus 92 g~L~C~~c~~~yp 104 (119)
++|.|++||..++
T Consensus 165 ~~~~c~~~~~~e~ 177 (189)
T PRK09521 165 NELKCPNCGNIET 177 (189)
T ss_pred CEEECCCCCCEEe
Confidence 8899999998776
No 122
>PF11238 DUF3039: Protein of unknown function (DUF3039); InterPro: IPR021400 This family of proteins with unknown function appears to be restricted to Actinobacteria.
Probab=23.03 E-value=18 Score=23.13 Aligned_cols=11 Identities=36% Similarity=0.760 Sum_probs=8.0
Q ss_pred eecCCCCcccc
Q 033418 94 LVCPETGRKFP 104 (119)
Q Consensus 94 L~C~~c~~~yp 104 (119)
=+||.|.+.|.
T Consensus 45 PVCP~Ck~iye 55 (58)
T PF11238_consen 45 PVCPECKEIYE 55 (58)
T ss_pred CCCcCHHHHHH
Confidence 37888887773
No 123
>COG0821 gcpE 1-hydroxy-2-methyl-2-(e)-butenyl 4-diphosphate synthase [Lipid metabolism]
Probab=23.03 E-value=48 Score=28.22 Aligned_cols=26 Identities=19% Similarity=0.415 Sum_probs=18.5
Q ss_pred cHHHHHHHHhcccccceeecCCCCcc
Q 033418 77 SDDFLMKFHHLHLEEGALVCPETGRK 102 (119)
Q Consensus 77 ~ee~L~~lH~~~i~~g~L~C~~c~~~ 102 (119)
..+.|+.+....-.-....||.|||.
T Consensus 245 ~~eILqslglR~~~v~~iaCP~CGR~ 270 (361)
T COG0821 245 AQEILQSLGLRSRGVEVIACPTCGRT 270 (361)
T ss_pred HHHHHHHhCccccCceEEECCCCCce
Confidence 45678777655444456789999995
No 124
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=22.79 E-value=42 Score=23.80 Aligned_cols=18 Identities=28% Similarity=0.564 Sum_probs=14.8
Q ss_pred ccccceeecCCCCccccc
Q 033418 88 HLEEGALVCPETGRKFPV 105 (119)
Q Consensus 88 ~i~~g~L~C~~c~~~ypI 105 (119)
...-|.++|..||..|..
T Consensus 41 ~~~~g~~~Cg~CGls~e~ 58 (104)
T COG4888 41 TVNIGTAVCGNCGLSFEC 58 (104)
T ss_pred cCceeEEEcccCcceEEE
Confidence 556789999999998864
No 125
>PF10426 zf-RAG1: Recombination-activating protein 1 zinc-finger domain; InterPro: IPR019485 During lymphocyte development, the genes encoding immunoglobulins and T-cell receptors are assembled from variable (V), diversity (D), and joining (J) gene segments. This combinatorial process, known as V(D)J recombination, allows the generation of an enormous range of binding specificities from a limited amount of genetic information. The V(D)J recombination-activating proteins 1 and 2 (RAG1 and RAG2) form a complex that initiates this process by binding to the conserved recombination signal sequences (RSS) and introducing a double-strand break between the RSS and the adjacent coding segment. These breaks are generated in two steps, nicking of one strand (hydrolysis), followed by hairpin formation (transesterification). RAG1/2 has also been shown to function as a transposase in vitro, and to possess RSS-independent endonuclease activity (end processing) and hairpin opening. RAG1 alone can bind to RSS but stable, efficient binding requires RAG2. All known catalytic activities require the presence of both proteins. For more information see []. 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. C2H2-type (classical) zinc fingers (Znf) were the first class to be characterised. They contain a short beta hairpin and an alpha helix (beta/beta/alpha structure), where a single zinc atom is held in place by Cys(2)His(2) (C2H2) residues in a tetrahedral array. C2H2 Znf's can be divided into three groups based on the number and pattern of fingers: triple-C2H2 (binds single ligand), multiple-adjacent-C2H2 (binds multiple ligands), and separated paired-C2H2 []. C2H2 Znf's are the most common DNA-binding motifs found in eukaryotic transcription factors, and have also been identified in prokaryotes []. Transcription factors usually contain several Znf's (each with a conserved beta/beta/alpha structure) capable of making multiple contacts along the DNA, where the C2H2 Znf motifs recognise DNA sequences by binding to the major groove of DNA via a short alpha-helix in the Znf, the Znf spanning 3-4 bases of the DNA []. C2H2 Znf's can also bind to RNA and protein targets []. This entry represents a C2H2-type zinc-finger domain found in the RAG1 protein. The structure contains the characteristic two-stranded beta-sheet and alpha-helix of a classical zinc-finger. The domain binds one zinc and, in complex with an adjacent RING-type zinc finger domain, helps to stabilise the whole of the dimerisation region of recombination activating protein 1 (RAG1) []. The function of the whole is to bind double-stranded DNA. ; GO: 0016788 hydrolase activity, acting on ester bonds, 0016881 acid-amino acid ligase activity; PDB: 1RMD_A.
Probab=22.78 E-value=30 Score=19.32 Aligned_cols=10 Identities=10% Similarity=0.285 Sum_probs=4.7
Q ss_pred hhccCcCCcc
Q 033418 8 MLSSNIKGVA 17 (119)
Q Consensus 8 ~L~c~~k~c~ 17 (119)
.+.|++|.|.
T Consensus 2 ~vrCPvkdC~ 11 (30)
T PF10426_consen 2 VVRCPVKDCD 11 (30)
T ss_dssp EEE--STT--
T ss_pred ccccccccCc
Confidence 3689999996
No 126
>PLN02915 cellulose synthase A [UDP-forming], catalytic subunit
Probab=22.75 E-value=47 Score=32.00 Aligned_cols=30 Identities=23% Similarity=0.505 Sum_probs=27.3
Q ss_pred hcccccceeecCCCCccccccCCccccCCC
Q 033418 86 HLHLEEGALVCPETGRKFPVNKGIPNMLLH 115 (119)
Q Consensus 86 ~~~i~~g~L~C~~c~~~ypI~~GIP~mL~~ 115 (119)
..+..||.=.||+|+..|.-..|.|.+-.+
T Consensus 50 eye~~~g~~~cp~c~t~y~~~~~~~~~~~d 79 (1044)
T PLN02915 50 EYERSEGNQCCPQCNTRYKRHKGCPRVEGD 79 (1044)
T ss_pred hhhhhcCCccCCccCCchhhhcCCCCccCC
Confidence 348899999999999999999999999887
No 127
>PLN02400 cellulose synthase
Probab=22.73 E-value=53 Score=31.81 Aligned_cols=32 Identities=28% Similarity=0.578 Sum_probs=28.6
Q ss_pred cccccceeecCCCCccccccCCccccCCCCCC
Q 033418 87 LHLEEGALVCPETGRKFPVNKGIPNMLLHEDE 118 (119)
Q Consensus 87 ~~i~~g~L~C~~c~~~ypI~~GIP~mL~~e~~ 118 (119)
.+..||.=.||+|+..|.=..|.|.+--+|+|
T Consensus 72 YERkeGnq~CPQCkTrYkR~KgsprV~GDeee 103 (1085)
T PLN02400 72 YERKDGTQCCPQCKTRYRRHKGSPRVEGDEDE 103 (1085)
T ss_pred eecccCCccCcccCCccccccCCCCCCccccc
Confidence 38999999999999999999999999887654
No 128
>COG1545 Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]
Probab=22.52 E-value=39 Score=24.56 Aligned_cols=24 Identities=21% Similarity=0.441 Sum_probs=14.1
Q ss_pred HHHHHHHHhcccccceeecCCCCccc
Q 033418 78 DDFLMKFHHLHLEEGALVCPETGRKF 103 (119)
Q Consensus 78 ee~L~~lH~~~i~~g~L~C~~c~~~y 103 (119)
..|.+.+..-.+. .-.|++||+.|
T Consensus 16 ~~f~~~l~~~kl~--g~kC~~CG~v~ 39 (140)
T COG1545 16 SKFFKGLKEGKLL--GTKCKKCGRVY 39 (140)
T ss_pred hHHhhhhhhCcEE--EEEcCCCCeEE
Confidence 4566544332222 22799999986
No 129
>PF11023 DUF2614: Protein of unknown function (DUF2614); InterPro: IPR020912 This entry describes proteins of unknown function, which are thought to be membrane proteins.; GO: 0005887 integral to plasma membrane
Probab=22.48 E-value=46 Score=23.99 Aligned_cols=12 Identities=25% Similarity=0.681 Sum_probs=9.4
Q ss_pred ceeecCCCCccc
Q 033418 92 GALVCPETGRKF 103 (119)
Q Consensus 92 g~L~C~~c~~~y 103 (119)
-..+||+|++.-
T Consensus 68 v~V~CP~C~K~T 79 (114)
T PF11023_consen 68 VQVECPNCGKQT 79 (114)
T ss_pred eeeECCCCCChH
Confidence 356799999865
No 130
>COG4530 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=22.44 E-value=48 Score=24.12 Aligned_cols=19 Identities=32% Similarity=0.716 Sum_probs=16.1
Q ss_pred ccccceeecCCCCcccccc
Q 033418 88 HLEEGALVCPETGRKFPVN 106 (119)
Q Consensus 88 ~i~~g~L~C~~c~~~ypI~ 106 (119)
++...-.+||-||..||-+
T Consensus 21 DLNrdPiVsPytG~s~P~s 39 (129)
T COG4530 21 DLNRDPIVSPYTGKSYPRS 39 (129)
T ss_pred ccCCCccccCcccccchHH
Confidence 7777888999999999853
No 131
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=22.43 E-value=45 Score=23.70 Aligned_cols=18 Identities=22% Similarity=0.313 Sum_probs=13.8
Q ss_pred ccccceeecCCCCcccccc
Q 033418 88 HLEEGALVCPETGRKFPVN 106 (119)
Q Consensus 88 ~i~~g~L~C~~c~~~ypI~ 106 (119)
+...+...| .||+.|++.
T Consensus 65 ~~vp~~~~C-~Cg~~~~~~ 82 (124)
T PRK00762 65 EMIPVEIEC-ECGYEGVVD 82 (124)
T ss_pred EecCeeEEe-eCcCccccc
Confidence 566777888 888887775
No 132
>COG1990 pth2 Peptidyl-tRNA hydrolase [Translation, ribosomal structure and biogenesis]
Probab=21.72 E-value=69 Score=23.32 Aligned_cols=18 Identities=6% Similarity=0.185 Sum_probs=12.2
Q ss_pred HHHHHHhcccccceeecC
Q 033418 80 FLMKFHHLHLEEGALVCP 97 (119)
Q Consensus 80 ~L~~lH~~~i~~g~L~C~ 97 (119)
.+++.|+.+|-.|+.+|=
T Consensus 85 ~i~DaG~TqippGt~T~L 102 (122)
T COG1990 85 LIRDAGRTQIPPGTITVL 102 (122)
T ss_pred HHHhcCccccCCCCeEEE
Confidence 666666667777777663
No 133
>PF08996 zf-DNA_Pol: DNA Polymerase alpha zinc finger; InterPro: IPR015088 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. The DNA Polymerase alpha zinc finger domain adopts an alpha-helix-like structure, followed by three turns, all of which involve proline. The resulting motif is a helix-turn-helix motif, in contrast to other zinc finger domains, which show anti-parallel sheet and helix conformation. Zinc binding occurs due to the presence of four cysteine residues positioned to bind the metal centre in a tetrahedral coordination geometry. The function of this domain is uncertain: it has been proposed that the zinc finger motif may be an essential part of the DNA binding domain []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0001882 nucleoside binding, 0003887 DNA-directed DNA polymerase activity, 0006260 DNA replication; PDB: 3FLO_D 1N5G_A 1K0P_A 1K18_A.
Probab=21.46 E-value=48 Score=25.04 Aligned_cols=20 Identities=30% Similarity=0.537 Sum_probs=10.7
Q ss_pred ccccceeecCCCCccccccC
Q 033418 88 HLEEGALVCPETGRKFPVNK 107 (119)
Q Consensus 88 ~i~~g~L~C~~c~~~ypI~~ 107 (119)
+...=.+.||.|+..|++..
T Consensus 13 ~c~~l~~~C~~C~~~~~f~g 32 (188)
T PF08996_consen 13 DCEPLKLTCPSCGTEFEFPG 32 (188)
T ss_dssp T---EEEE-TTT--EEEE-S
T ss_pred CCCceEeECCCCCCCccccc
Confidence 44555799999999998854
No 134
>COG1326 Uncharacterized archaeal Zn-finger protein [General function prediction only]
Probab=21.21 E-value=79 Score=24.88 Aligned_cols=17 Identities=29% Similarity=0.452 Sum_probs=13.1
Q ss_pred cccceeecCCCCccccc
Q 033418 89 LEEGALVCPETGRKFPV 105 (119)
Q Consensus 89 i~~g~L~C~~c~~~ypI 105 (119)
..+-.+.|++||..||-
T Consensus 26 g~~~lvrC~eCG~V~~~ 42 (201)
T COG1326 26 GREPLVRCEECGTVHPA 42 (201)
T ss_pred CCceEEEccCCCcEeec
Confidence 33347899999999954
No 135
>PRK14526 adenylate kinase; Provisional
Probab=20.89 E-value=44 Score=25.62 Aligned_cols=19 Identities=16% Similarity=0.338 Sum_probs=15.3
Q ss_pred cccceeecCCCCccccccC
Q 033418 89 LEEGALVCPETGRKFPVNK 107 (119)
Q Consensus 89 i~~g~L~C~~c~~~ypI~~ 107 (119)
-..|..+||.||+.|.+.-
T Consensus 118 Rl~~R~~~~~~g~~y~~~~ 136 (211)
T PRK14526 118 RLSGRRICKSCNNIFNIYT 136 (211)
T ss_pred HHHCCCcccccCCcccccc
Confidence 3467889999999997754
No 136
>PF13959 DUF4217: Domain of unknown function (DUF4217)
Probab=20.63 E-value=93 Score=19.49 Aligned_cols=21 Identities=29% Similarity=0.495 Sum_probs=15.8
Q ss_pred cchhcHHHHHHHHHhCCCCCCCCC
Q 033418 45 FPKIEWQALVQASRSMGYSELPEE 68 (119)
Q Consensus 45 l~kldw~al~~~a~~lg~~~lP~~ 68 (119)
+.++||..+ |++.|+.+.|.-
T Consensus 43 ~~~L~l~~~---A~sfGL~~~P~v 63 (65)
T PF13959_consen 43 VKKLDLGHL---AKSFGLLEAPKV 63 (65)
T ss_pred cccCCHHHH---HHHcCCCCCCCC
Confidence 356888887 799998766653
No 137
>PLN02674 adenylate kinase
Probab=20.49 E-value=49 Score=26.28 Aligned_cols=23 Identities=22% Similarity=0.439 Sum_probs=18.2
Q ss_pred ccccceeecCCCCccccccCCcc
Q 033418 88 HLEEGALVCPETGRKFPVNKGIP 110 (119)
Q Consensus 88 ~i~~g~L~C~~c~~~ypI~~GIP 110 (119)
+-..|..+||.||+.|.+.-.=|
T Consensus 153 ~Rl~gR~~~~~~g~~yn~~~~pp 175 (244)
T PLN02674 153 ERITGRWIHPSSGRTYHTKFAPP 175 (244)
T ss_pred HHHhccccccccCCccccccCCC
Confidence 34578899999999998876555
No 138
>PF02954 HTH_8: Bacterial regulatory protein, Fis family; InterPro: IPR002197 The Factor for Inversion Stimulation (FIS) protein is a regulator of bacterial functions, and binds specifically to weakly related DNA sequences [,]. It activates ribosomal RNA transcription, and is involved in upstream activation of rRNA promoters. The protein has been shown to play a role in the regulation of virulence factors in both Salmonella typhimurium and Escherichia coli []. Some of its functions include inhibition of the initiation of DNA replication from the OriC site, and promotion of Hin-mediated DNA inversion. In its C-terminal extremity, FIS encodes a helix-turn-helix (HTH) DNA- binding motif, which shares a high degree of similarity with other HTH motifs of more primitive bacterial transcriptional regulators, such as the nitrogen assimilation regulatory proteins (NtrC) from species like Azobacter, Rhodobacter and Rhizobium. This has led to speculation that both evolved from a single common ancestor []. The 3-dimensional structure of the E. coli FIS DNA-binding protein has been determined by means of X-ray diffraction to 2.0A resolution [,]. FIS is composed of four alpha-helices tightly intertwined to form a globular dimer with two protruding HTH motifs. The 24 N-terminal amino acids are poorly defined, indicating that they might act as `feelers' suitable for DNA or protein (invertase) recognition []. Other proteins belonging to this subfamily include: E. coli: atoC, hydG, ntrC, fhlA, tyrR, Rhizobium spp.: ntrC, nifA, dctD ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1NTC_A 3JRH_A 3JRB_A 3IV5_A 3JRI_A 1ETQ_A 1ETW_B 1ETY_A 3JRF_A 3JRA_A ....
Probab=20.30 E-value=24 Score=20.17 Aligned_cols=27 Identities=19% Similarity=0.420 Sum_probs=20.1
Q ss_pred CCHHHHhcccchhcHHHHHHHHHhCCCC
Q 033418 36 FNPDFLKNIFPKIEWQALVQASRSMGYS 63 (119)
Q Consensus 36 fn~~fi~~~l~kldw~al~~~a~~lg~~ 63 (119)
|..++|...|.+-.|. ...||+.||++
T Consensus 5 ~E~~~i~~aL~~~~gn-~~~aA~~Lgis 31 (42)
T PF02954_consen 5 FEKQLIRQALERCGGN-VSKAARLLGIS 31 (42)
T ss_dssp HHHHHHHHHHHHTTT--HHHHHHHHTS-
T ss_pred HHHHHHHHHHHHhCCC-HHHHHHHHCCC
Confidence 4567888888888888 57899999974
No 139
>smart00249 PHD PHD zinc finger. The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the PF14205 Cys_rich_KTR: Cysteine-rich KTR
Probab=20.28 E-value=60 Score=20.53 Aligned_cols=11 Identities=27% Similarity=0.703 Sum_probs=6.8
Q ss_pred cceeecCCCCc
Q 033418 91 EGALVCPETGR 101 (119)
Q Consensus 91 ~g~L~C~~c~~ 101 (119)
++.+.||.||.
T Consensus 2 ~~Wi~CP~Cgn 12 (55)
T PF14205_consen 2 SEWILCPICGN 12 (55)
T ss_pred CeEEECCCCCC
Confidence 35566777763
No 141
>PF11336 DUF3138: Protein of unknown function (DUF3138); InterPro: IPR021485 This family of proteins with unknown function appear to be restricted to Proteobacteria.
Probab=20.13 E-value=35 Score=30.08 Aligned_cols=12 Identities=50% Similarity=0.540 Sum_probs=10.2
Q ss_pred CccccchhhccC
Q 033418 1 MRLLTHNMLSSN 12 (119)
Q Consensus 1 MrllthN~L~c~ 12 (119)
|+++|||+|---
T Consensus 232 ~~~lTHNLLyDF 243 (514)
T PF11336_consen 232 MLTLTHNLLYDF 243 (514)
T ss_pred cceeeeceeeec
Confidence 889999999654
No 142
>PF10083 DUF2321: Uncharacterized protein conserved in bacteria (DUF2321); InterPro: IPR016891 This entry is represented by Bacteriophage 'Lactobacillus prophage Lj928', Orf-Ljo1454. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=20.10 E-value=34 Score=25.97 Aligned_cols=13 Identities=23% Similarity=0.690 Sum_probs=10.9
Q ss_pred eecCCCCcccccc
Q 033418 94 LVCPETGRKFPVN 106 (119)
Q Consensus 94 L~C~~c~~~ypI~ 106 (119)
=.|.+||..||=.
T Consensus 69 sYC~~CGkpyPWt 81 (158)
T PF10083_consen 69 SYCHNCGKPYPWT 81 (158)
T ss_pred hhHHhCCCCCchH
Confidence 3799999999954
No 143
>COG4338 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=20.07 E-value=33 Score=21.42 Aligned_cols=11 Identities=36% Similarity=0.854 Sum_probs=8.9
Q ss_pred eecCCCCcccc
Q 033418 94 LVCPETGRKFP 104 (119)
Q Consensus 94 L~C~~c~~~yp 104 (119)
-+||.|+|-|.
T Consensus 13 KICpvCqRPFs 23 (54)
T COG4338 13 KICPVCQRPFS 23 (54)
T ss_pred hhhhhhcCchH
Confidence 37999999875
No 144
>PF10884 DUF2683: Protein of unknown function (DUF2683); InterPro: IPR020271 This entry contains proteins with no known function.
Probab=20.02 E-value=42 Score=22.74 Aligned_cols=16 Identities=19% Similarity=0.455 Sum_probs=13.0
Q ss_pred EecccCCHHHHhcccc
Q 033418 31 EKQVDFNPDFLKNIFP 46 (119)
Q Consensus 31 ~~e~efn~~fi~~~l~ 46 (119)
..|.+++||||+++..
T Consensus 43 ~lEpElkPEfVeki~~ 58 (80)
T PF10884_consen 43 ILEPELKPEFVEKIKK 58 (80)
T ss_pred hcccccCHHHHHHHHH
Confidence 4467999999999855
Done!