Query 036116
Match_columns 53
No_of_seqs 124 out of 804
Neff 4.6
Searched_HMMs 46136
Date Fri Mar 29 09:34:46 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/036116.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/036116hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG2835 Uncharacterized conser 99.7 8.9E-18 1.9E-22 95.7 1.9 39 1-39 20-58 (60)
2 PRK11827 hypothetical protein; 99.7 1E-17 2.2E-22 95.1 1.6 40 1-40 20-59 (60)
3 KOG1088 Uncharacterized conser 99.2 1.2E-11 2.7E-16 78.5 2.4 31 2-32 93-123 (124)
4 PF03966 Trm112p: Trm112p-like 98.7 7.1E-09 1.5E-13 58.4 2.1 21 2-22 48-68 (68)
5 PF13717 zinc_ribbon_4: zinc-r 92.2 0.086 1.9E-06 26.6 1.2 16 7-22 2-17 (36)
6 PF08271 TF_Zn_Ribbon: TFIIB z 89.5 0.19 4.1E-06 25.7 1.0 15 2-16 14-28 (43)
7 PF08792 A2L_zn_ribbon: A2L zi 87.4 0.48 1E-05 23.7 1.6 17 3-19 17-33 (33)
8 PF09538 FYDLN_acid: Protein o 85.5 0.41 9E-06 29.5 1.0 20 1-20 20-39 (108)
9 PF13719 zinc_ribbon_5: zinc-r 83.5 0.79 1.7E-05 23.0 1.3 16 7-22 2-17 (37)
10 COG4391 Uncharacterized protei 81.5 1 2.2E-05 25.9 1.4 16 4-19 45-60 (62)
11 TIGR02098 MJ0042_CXXC MJ0042 f 81.0 1.1 2.5E-05 21.9 1.4 16 7-22 2-17 (38)
12 PF05191 ADK_lid: Adenylate ki 79.7 1.4 3E-05 22.3 1.5 15 7-21 1-15 (36)
13 PRK00420 hypothetical protein; 79.4 1.3 2.7E-05 27.7 1.4 19 4-22 37-55 (112)
14 PF08274 PhnA_Zn_Ribbon: PhnA 77.7 1.8 3.9E-05 21.4 1.4 15 4-18 16-30 (30)
15 smart00661 RPOL9 RNA polymeras 77.4 2.4 5.2E-05 21.7 2.0 17 6-22 19-35 (52)
16 smart00834 CxxC_CXXC_SSSS Puta 77.0 2.2 4.8E-05 20.8 1.7 18 7-24 5-22 (41)
17 PF10080 DUF2318: Predicted me 76.2 1.5 3.3E-05 26.8 1.1 20 1-20 46-65 (102)
18 PF00096 zf-C2H2: Zinc finger, 76.0 1.8 3.9E-05 18.7 1.1 12 9-20 2-13 (23)
19 PF14353 CpXC: CpXC protein 73.9 2.3 5E-05 25.6 1.5 25 7-33 38-62 (128)
20 PF13913 zf-C2HC_2: zinc-finge 72.5 1.8 3.8E-05 20.1 0.6 11 8-18 3-13 (25)
21 TIGR00686 phnA alkylphosphonat 70.8 2.4 5.3E-05 26.6 1.1 18 4-21 16-33 (109)
22 PF13912 zf-C2H2_6: C2H2-type 70.6 3.4 7.3E-05 18.5 1.3 11 8-18 2-12 (27)
23 TIGR02300 FYDLN_acid conserved 70.2 2.2 4.8E-05 27.5 0.9 20 1-20 20-39 (129)
24 PF01475 FUR: Ferric uptake re 69.5 3.2 7E-05 24.4 1.4 17 6-22 79-95 (120)
25 PF13408 Zn_ribbon_recom: Reco 67.9 4.4 9.5E-05 20.7 1.6 16 5-20 3-18 (58)
26 PF13878 zf-C2H2_3: zinc-finge 67.1 3 6.4E-05 21.4 0.8 14 6-19 12-25 (41)
27 PF13894 zf-C2H2_4: C2H2-type 66.2 3.7 7.9E-05 17.1 0.9 11 9-19 2-12 (24)
28 cd07153 Fur_like Ferric uptake 66.1 4.3 9.4E-05 23.5 1.5 17 6-22 72-88 (116)
29 PRK10220 hypothetical protein; 65.4 4.1 8.9E-05 25.7 1.4 18 4-21 17-34 (111)
30 COG1594 RPB9 DNA-directed RNA 64.6 4.9 0.00011 24.7 1.6 18 4-21 19-36 (113)
31 TIGR02605 CxxC_CxxC_SSSS putat 64.6 5.8 0.00012 20.4 1.7 15 7-21 5-19 (52)
32 smart00531 TFIIE Transcription 63.8 5.9 0.00013 24.7 1.9 18 4-21 96-113 (147)
33 COG1645 Uncharacterized Zn-fin 63.4 6 0.00013 25.4 1.9 16 4-19 41-56 (131)
34 PRK00423 tfb transcription ini 62.2 4.1 8.9E-05 28.3 1.0 15 2-16 25-39 (310)
35 PF10276 zf-CHCC: Zinc-finger 62.0 8.7 0.00019 19.9 2.0 13 5-17 27-39 (40)
36 COG4530 Uncharacterized protei 61.2 3.9 8.4E-05 26.3 0.7 13 6-18 25-37 (129)
37 PF00628 PHD: PHD-finger; Int 60.1 10 0.00022 19.1 2.1 18 3-20 10-27 (51)
38 PF06750 DiS_P_DiS: Bacterial 59.9 4 8.7E-05 24.1 0.6 21 6-26 32-52 (92)
39 PRK09462 fur ferric uptake reg 59.8 6.5 0.00014 24.2 1.5 17 6-22 89-105 (148)
40 PRK08197 threonine synthase; V 59.0 5.3 0.00012 28.3 1.2 16 7-22 7-22 (394)
41 PF09723 Zn-ribbon_8: Zinc rib 58.5 8.3 0.00018 19.6 1.6 17 7-23 5-21 (42)
42 PRK00398 rpoP DNA-directed RNA 58.4 11 0.00025 19.1 2.1 14 7-20 21-34 (46)
43 PF10571 UPF0547: Uncharacteri 58.3 4.4 9.5E-05 19.2 0.5 13 6-18 13-25 (26)
44 PF02150 RNA_POL_M_15KD: RNA p 57.8 6.8 0.00015 19.5 1.1 13 9-21 22-34 (35)
45 PF13465 zf-H2C2_2: Zinc-finge 56.4 8.3 0.00018 17.6 1.2 13 6-18 13-25 (26)
46 PRK07591 threonine synthase; V 56.3 6.4 0.00014 28.4 1.2 14 7-20 18-31 (421)
47 PF01927 Mut7-C: Mut7-C RNAse 56.3 6.3 0.00014 24.6 1.1 11 7-17 124-134 (147)
48 PRK11088 rrmA 23S rRNA methylt 56.3 9.6 0.00021 25.4 2.0 27 5-32 16-43 (272)
49 PF12760 Zn_Tnp_IS1595: Transp 55.8 7.1 0.00015 20.0 1.0 15 7-21 18-34 (46)
50 COG0375 HybF Zn finger protein 55.6 8.5 0.00018 24.2 1.5 18 5-22 84-102 (115)
51 PRK06260 threonine synthase; V 55.2 6.8 0.00015 27.8 1.2 15 7-21 3-17 (397)
52 PF05129 Elf1: Transcription e 54.7 8.4 0.00018 22.4 1.4 20 5-26 44-63 (81)
53 TIGR00100 hypA hydrogenase nic 54.5 8.1 0.00017 23.5 1.3 18 4-21 67-84 (115)
54 PLN02569 threonine synthase 54.4 5.7 0.00012 29.6 0.7 16 7-22 49-64 (484)
55 PRK06266 transcription initiat 53.5 11 0.00023 24.7 1.8 18 4-21 114-131 (178)
56 PRK03681 hypA hydrogenase nick 52.9 9.8 0.00021 23.1 1.5 18 4-21 67-84 (114)
57 PF13445 zf-RING_UBOX: RING-ty 52.6 6.4 0.00014 20.4 0.5 18 10-28 1-18 (43)
58 PF07295 DUF1451: Protein of u 52.5 13 0.00028 23.9 2.1 18 4-21 109-126 (146)
59 PRK11032 hypothetical protein; 52.2 10 0.00022 24.9 1.6 16 5-20 122-137 (160)
60 PRK11639 zinc uptake transcrip 52.2 10 0.00022 24.2 1.5 17 7-23 100-116 (169)
61 PRK12380 hydrogenase nickel in 52.2 11 0.00023 23.0 1.5 17 5-21 68-84 (113)
62 PF01430 HSP33: Hsp33 protein; 52.1 11 0.00023 25.9 1.7 15 6-20 265-279 (280)
63 PRK12496 hypothetical protein; 52.1 8.3 0.00018 24.8 1.1 13 8-20 128-140 (164)
64 PF11781 RRN7: RNA polymerase 52.0 8.7 0.00019 19.3 1.0 15 2-16 20-34 (36)
65 cd03467 Rieske Rieske domain; 52.0 15 0.00033 20.5 2.1 25 4-28 55-79 (98)
66 PF12171 zf-C2H2_jaz: Zinc-fin 51.4 7.5 0.00016 17.6 0.6 11 8-18 2-12 (27)
67 COG4049 Uncharacterized protei 50.6 5.1 0.00011 23.0 -0.0 13 6-18 16-28 (65)
68 PRK09521 exosome complex RNA-b 50.6 12 0.00027 24.1 1.8 14 5-18 164-177 (189)
69 TIGR03844 cysteate_syn cysteat 50.3 8.6 0.00019 27.8 1.1 12 7-18 2-13 (398)
70 cd06232 Peptidase_M14-like_5 P 50.2 6.5 0.00014 27.5 0.4 20 14-33 217-236 (240)
71 TIGR01206 lysW lysine biosynth 49.8 18 0.00039 19.8 2.1 20 5-24 20-39 (54)
72 smart00659 RPOLCX RNA polymera 49.4 17 0.00037 18.9 1.9 13 8-20 3-15 (44)
73 PF14205 Cys_rich_KTR: Cystein 49.3 11 0.00025 21.1 1.3 9 6-14 3-11 (55)
74 TIGR01384 TFS_arch transcripti 49.2 13 0.00028 21.6 1.6 17 4-20 13-29 (104)
75 PF13451 zf-trcl: Probable zin 48.9 14 0.00029 20.1 1.5 17 6-22 3-19 (49)
76 PF14803 Nudix_N_2: Nudix N-te 47.9 15 0.00032 18.4 1.4 13 4-16 19-31 (34)
77 PF09297 zf-NADH-PPase: NADH p 47.2 17 0.00038 17.2 1.6 13 5-17 19-31 (32)
78 PRK00432 30S ribosomal protein 46.8 16 0.00035 19.5 1.6 13 5-17 35-47 (50)
79 TIGR00373 conserved hypothetic 46.3 16 0.00034 23.3 1.8 18 4-21 106-123 (158)
80 PF01155 HypA: Hydrogenase exp 46.2 11 0.00024 22.7 1.0 18 5-22 68-85 (113)
81 PRK03824 hypA hydrogenase nick 45.7 14 0.00031 23.0 1.4 16 5-20 68-83 (135)
82 COG0735 Fur Fe2+/Zn2+ uptake r 44.8 15 0.00033 22.9 1.5 17 6-22 92-108 (145)
83 COG2824 PhnA Uncharacterized Z 44.6 18 0.00038 22.9 1.7 29 9-37 5-33 (112)
84 COG4888 Uncharacterized Zn rib 44.5 16 0.00034 22.9 1.5 16 5-20 44-59 (104)
85 PF12874 zf-met: Zinc-finger o 44.3 18 0.0004 15.6 1.4 11 8-18 1-11 (25)
86 PRK00114 hslO Hsp33-like chape 43.7 15 0.00032 25.6 1.4 14 7-20 268-281 (293)
87 PRK00564 hypA hydrogenase nick 42.9 14 0.0003 22.6 1.0 17 5-21 69-85 (117)
88 PF11238 DUF3039: Protein of u 42.3 4.2 9.1E-05 23.0 -1.2 12 7-18 44-55 (58)
89 cd03528 Rieske_RO_ferredoxin R 42.2 25 0.00055 19.6 2.0 25 4-28 54-78 (98)
90 PF10609 ParA: ParA/MinD ATPas 41.9 17 0.00038 21.3 1.3 14 6-19 64-77 (81)
91 smart00355 ZnF_C2H2 zinc finge 41.5 9 0.0002 15.8 0.0 11 9-19 2-12 (26)
92 PF09986 DUF2225: Uncharacteri 41.3 19 0.00042 23.9 1.6 15 6-20 4-18 (214)
93 cd09020 D-hex-6-P-epi_like D-h 41.2 10 0.00022 25.5 0.3 17 16-32 43-59 (269)
94 cd00498 Hsp33 Heat shock prote 40.7 17 0.00036 25.0 1.3 13 7-19 262-274 (275)
95 KOG2907 RNA polymerase I trans 40.3 11 0.00024 23.9 0.3 19 6-24 24-42 (116)
96 PRK05638 threonine synthase; V 40.3 13 0.00029 26.8 0.8 13 7-19 1-13 (442)
97 TIGR03829 YokU_near_AblA uncha 40.2 14 0.0003 22.3 0.7 13 6-18 34-46 (89)
98 PF08996 zf-DNA_Pol: DNA Polym 40.0 22 0.00048 23.1 1.7 15 7-21 18-32 (188)
99 PF13248 zf-ribbon_3: zinc-rib 39.7 12 0.00025 17.3 0.3 8 8-15 3-10 (26)
100 TIGR03831 YgiT_finger YgiT-typ 39.6 15 0.00031 17.9 0.7 11 7-17 32-42 (46)
101 PF05495 zf-CHY: CHY zinc fing 39.0 23 0.00051 19.8 1.5 12 7-18 10-21 (71)
102 PRK08329 threonine synthase; V 38.9 12 0.00026 26.1 0.4 12 8-19 2-13 (347)
103 PRK14811 formamidopyrimidine-D 38.6 17 0.00037 24.9 1.1 16 5-20 253-268 (269)
104 PF01190 Pollen_Ole_e_I: Polle 38.3 17 0.00037 20.8 0.9 12 5-16 2-13 (97)
105 PLN02436 cellulose synthase A 38.3 16 0.00035 30.5 1.1 32 1-32 72-103 (1094)
106 smart00249 PHD PHD zinc finger 38.1 25 0.00055 16.4 1.4 17 4-20 11-27 (47)
107 PLN02189 cellulose synthase 37.8 17 0.00038 30.2 1.1 31 1-31 70-100 (1040)
108 cd03478 Rieske_AIFL_N AIFL (ap 36.8 37 0.0008 19.0 2.2 24 5-28 54-77 (95)
109 KOG1594 Uncharacterized enzyme 36.7 14 0.0003 26.8 0.4 16 16-31 68-83 (305)
110 cd06918 ChtBD1_like Domain obs 36.5 16 0.00035 19.8 0.6 13 12-24 6-18 (51)
111 PF05488 PAAR_motif: PAAR moti 36.4 26 0.00055 19.3 1.4 25 6-30 33-57 (76)
112 smart00451 ZnF_U1 U1-like zinc 35.2 21 0.00044 16.5 0.8 13 6-18 2-14 (35)
113 PRK14892 putative transcriptio 34.8 25 0.00055 21.3 1.3 15 5-19 40-54 (99)
114 COG1439 Predicted nucleic acid 34.1 25 0.00054 23.6 1.3 14 7-20 139-152 (177)
115 COG1656 Uncharacterized conser 34.1 24 0.00053 23.5 1.2 11 7-17 130-140 (165)
116 PF04475 DUF555: Protein of un 33.8 17 0.00037 22.6 0.4 16 3-18 43-58 (102)
117 PHA00616 hypothetical protein 33.7 10 0.00022 20.2 -0.5 10 9-18 3-12 (44)
118 KOG3352 Cytochrome c oxidase, 33.5 23 0.00049 23.4 1.0 16 6-21 132-147 (153)
119 PF07754 DUF1610: Domain of un 33.4 27 0.00059 16.4 1.0 11 5-15 14-24 (24)
120 PF14446 Prok-RING_1: Prokaryo 33.4 34 0.00073 18.9 1.5 14 4-17 18-31 (54)
121 cd00924 Cyt_c_Oxidase_Vb Cytoc 33.2 28 0.00061 21.0 1.3 14 7-20 79-92 (97)
122 PF04423 Rad50_zn_hook: Rad50 33.2 24 0.00052 18.4 0.9 10 9-18 22-31 (54)
123 PF14787 zf-CCHC_5: GAG-polypr 33.2 18 0.00039 18.7 0.4 11 9-19 4-14 (36)
124 PF01214 CK_II_beta: Casein ki 33.1 30 0.00065 22.9 1.5 15 5-19 125-139 (184)
125 PRK06450 threonine synthase; V 32.9 21 0.00046 25.1 0.8 13 7-19 3-15 (338)
126 PF12013 DUF3505: Protein of u 32.7 30 0.00064 20.3 1.3 18 1-18 5-22 (109)
127 cd00350 rubredoxin_like Rubred 32.6 29 0.00062 16.7 1.1 13 8-20 2-14 (33)
128 PRK01402 hslO Hsp33-like chape 32.2 30 0.00065 24.8 1.5 14 7-20 308-321 (328)
129 PHA02768 hypothetical protein; 32.1 19 0.00041 19.9 0.4 16 8-23 6-21 (55)
130 PF10083 DUF2321: Uncharacteri 32.0 13 0.00028 24.7 -0.4 13 9-21 70-82 (158)
131 KOG2906 RNA polymerase III sub 31.9 32 0.00069 21.5 1.4 18 6-23 20-37 (105)
132 PF14122 YokU: YokU-like prote 31.2 36 0.00079 20.6 1.6 15 4-18 32-46 (87)
133 PF07282 OrfB_Zn_ribbon: Putat 30.7 38 0.00082 18.1 1.5 13 5-17 44-56 (69)
134 COG3677 Transposase and inacti 30.5 28 0.00061 21.7 1.0 19 6-24 52-70 (129)
135 PF10013 DUF2256: Uncharacteri 30.4 22 0.00047 18.9 0.4 11 8-18 9-19 (42)
136 PF05605 zf-Di19: Drought indu 30.1 22 0.00048 18.5 0.4 11 7-17 2-12 (54)
137 smart00647 IBR In Between Ring 30.1 49 0.0011 16.8 1.8 13 5-17 38-50 (64)
138 COG1405 SUA7 Transcription ini 30.0 33 0.00071 24.2 1.4 15 2-16 15-29 (285)
139 PTZ00088 adenylate kinase 1; P 30.0 22 0.00048 23.8 0.5 15 6-20 129-143 (229)
140 PF14311 DUF4379: Domain of un 29.8 32 0.00069 18.0 1.0 12 7-18 28-39 (55)
141 KOG1407 WD40 repeat protein [F 29.6 14 0.0003 26.9 -0.5 15 6-20 219-235 (313)
142 PF07503 zf-HYPF: HypF finger; 28.7 33 0.00072 17.2 0.9 15 7-21 21-35 (35)
143 PF01428 zf-AN1: AN1-like Zinc 28.3 40 0.00087 17.0 1.2 15 7-21 13-27 (43)
144 PF06170 DUF983: Protein of un 28.3 22 0.00049 20.9 0.3 12 9-20 10-21 (86)
145 PF05443 ROS_MUCR: ROS/MUCR tr 28.2 37 0.0008 21.6 1.3 16 4-19 69-84 (132)
146 PLN02459 probable adenylate ki 28.0 29 0.00063 24.2 0.8 16 5-20 151-166 (261)
147 PF08209 Sgf11: Sgf11 (transcr 27.7 46 0.00099 16.6 1.3 13 5-17 2-14 (33)
148 PF10122 Mu-like_Com: Mu-like 27.5 64 0.0014 17.7 2.0 22 5-26 22-43 (51)
149 PF01215 COX5B: Cytochrome c o 27.5 34 0.00073 22.0 1.0 15 7-21 112-126 (136)
150 PF03711 OKR_DC_1_C: Orn/Lys/A 27.3 24 0.00051 22.3 0.3 16 17-32 83-98 (136)
151 PF14570 zf-RING_4: RING/Ubox 27.2 27 0.00057 18.8 0.4 12 6-17 36-47 (48)
152 KOG0978 E3 ubiquitin ligase in 26.9 30 0.00065 27.6 0.8 18 9-26 680-697 (698)
153 PF14569 zf-UDP: Zinc-binding 26.8 16 0.00036 21.8 -0.5 28 3-30 47-74 (80)
154 PF03604 DNA_RNApol_7kD: DNA d 26.4 35 0.00077 16.8 0.8 14 9-22 2-15 (32)
155 COG1096 Predicted RNA-binding 26.3 46 0.001 22.6 1.5 13 4-16 162-174 (188)
156 COG0267 RpmG Ribosomal protein 26.2 43 0.00093 18.2 1.1 14 7-20 7-21 (50)
157 PF09845 DUF2072: Zn-ribbon co 26.1 27 0.00059 22.5 0.4 10 9-18 3-12 (131)
158 PF03811 Zn_Tnp_IS1: InsA N-te 25.8 54 0.0012 16.4 1.4 16 7-22 5-21 (36)
159 COG1743 Adenine-specific DNA m 25.5 37 0.0008 27.9 1.1 15 7-21 178-192 (875)
160 COG4338 Uncharacterized protei 25.3 19 0.00042 20.0 -0.3 11 8-18 13-23 (54)
161 TIGR02378 nirD_assim_sml nitri 25.2 59 0.0013 18.5 1.7 19 7-25 64-82 (105)
162 PLN02294 cytochrome c oxidase 25.0 42 0.00092 22.6 1.2 14 7-20 141-154 (174)
163 PRK09965 3-phenylpropionate di 25.0 74 0.0016 18.3 2.1 20 6-25 58-77 (106)
164 TIGR00515 accD acetyl-CoA carb 24.9 29 0.00064 24.4 0.4 22 6-27 44-67 (285)
165 PRK03922 hypothetical protein; 24.6 32 0.00069 21.8 0.5 15 4-18 46-60 (113)
166 PTZ00396 Casein kinase II subu 24.4 34 0.00074 23.9 0.7 17 5-21 146-162 (251)
167 PF10601 zf-LITAF-like: LITAF- 24.3 66 0.0014 17.6 1.7 14 2-15 2-15 (73)
168 PF05864 Chordopox_RPO7: Chord 24.3 38 0.00081 19.4 0.7 10 7-16 4-13 (63)
169 cd03529 Rieske_NirD Assimilato 24.2 70 0.0015 18.2 1.9 22 6-27 62-83 (103)
170 PHA00626 hypothetical protein 24.0 39 0.00084 19.2 0.7 16 9-24 2-17 (59)
171 COG1545 Predicted nucleic-acid 23.7 46 0.001 20.8 1.1 10 8-17 30-39 (140)
172 PLN02674 adenylate kinase 23.3 42 0.00091 22.9 0.9 20 5-24 156-175 (244)
173 TIGR00311 aIF-2beta translatio 23.2 41 0.00089 21.3 0.8 14 7-20 118-131 (133)
174 PRK08116 hypothetical protein; 23.1 36 0.00077 23.1 0.5 16 3-18 12-27 (268)
175 TIGR02377 MocE_fam_FeS Rieske 23.0 79 0.0017 18.1 2.0 22 4-25 56-77 (101)
176 CHL00037 petA cytochrome f 23.0 37 0.0008 24.9 0.6 26 3-28 49-75 (320)
177 TIGR00595 priA primosomal prot 23.0 46 0.00099 24.8 1.1 17 4-20 237-253 (505)
178 PHA03082 DNA-dependent RNA pol 23.0 40 0.00088 19.3 0.7 10 7-16 4-13 (63)
179 PRK00762 hypA hydrogenase nick 22.9 45 0.00099 20.5 1.0 15 5-20 68-82 (124)
180 PF06676 DUF1178: Protein of u 22.7 38 0.00081 22.0 0.6 12 4-15 29-40 (148)
181 PF00301 Rubredoxin: Rubredoxi 22.6 72 0.0016 16.9 1.6 18 8-25 2-19 (47)
182 COG3364 Zn-ribbon containing p 22.6 36 0.00077 21.5 0.4 10 9-18 4-13 (112)
183 PLN02915 cellulose synthase A 22.5 41 0.00089 28.1 0.9 29 1-29 51-79 (1044)
184 PF10405 BHD_3: Rad4 beta-hair 22.4 37 0.0008 19.5 0.4 18 11-28 50-67 (76)
185 cd00730 rubredoxin Rubredoxin; 22.3 55 0.0012 17.5 1.1 17 8-24 2-18 (50)
186 PRK14526 adenylate kinase; Pro 22.2 37 0.00079 22.3 0.5 17 5-21 120-136 (211)
187 PF10058 DUF2296: Predicted in 22.2 44 0.00095 18.1 0.7 10 6-15 21-30 (54)
188 PF05454 DAG1: Dystroglycan (D 21.9 30 0.00065 24.6 0.0 15 19-33 187-201 (290)
189 PF11822 DUF3342: Domain of un 21.9 45 0.00097 24.2 0.9 16 6-21 260-275 (317)
190 COG1281 Disulfide bond chapero 21.4 52 0.0011 23.5 1.1 16 5-20 264-279 (286)
191 PRK09919 anti-adapter protein 21.4 52 0.0011 20.8 1.0 18 5-22 6-23 (114)
192 cd00729 rubredoxin_SM Rubredox 21.2 60 0.0013 15.8 1.0 13 7-19 2-14 (34)
193 PLN02400 cellulose synthase 21.2 58 0.0013 27.4 1.5 30 1-30 72-101 (1085)
194 COG0068 HypF Hydrogenase matur 20.8 51 0.0011 26.7 1.1 18 8-25 124-141 (750)
195 PRK05654 acetyl-CoA carboxylas 20.7 43 0.00092 23.6 0.6 23 6-28 45-69 (292)
196 PF02146 SIR2: Sir2 family; I 20.7 55 0.0012 20.5 1.0 15 7-21 105-119 (178)
197 PF11023 DUF2614: Protein of u 20.4 60 0.0013 20.5 1.1 13 7-19 69-81 (114)
198 TIGR03830 CxxCG_CxxCG_HTH puta 20.2 65 0.0014 18.7 1.2 16 6-21 30-45 (127)
199 PF06677 Auto_anti-p27: Sjogre 20.0 69 0.0015 16.5 1.1 11 4-14 31-41 (41)
200 PF01783 Ribosomal_L32p: Ribos 20.0 50 0.0011 17.7 0.6 6 9-14 41-46 (56)
No 1
>COG2835 Uncharacterized conserved protein [Function unknown]
Probab=99.69 E-value=8.9e-18 Score=95.70 Aligned_cols=39 Identities=36% Similarity=0.680 Sum_probs=35.7
Q ss_pred CcccCCeEEcCCCCeeeeeeCCccccCCCCCccCCCCcc
Q 036116 1 VCEETNSLISDSIGVSFPIKDGIPSLVPKDGKILGVDDD 39 (53)
Q Consensus 1 ~~~~~g~LiC~~c~~~YPI~dGIPvLL~~ear~l~~~e~ 39 (53)
|+.++++|+|+.|+++|||+|||||||+++||.++.++.
T Consensus 20 ~~~~~~~L~c~~~~~aYpI~dGIPvlL~~eaR~~~~d~~ 58 (60)
T COG2835 20 YDEEKQELICPRCKLAYPIRDGIPVLLPDEARDLSEDES 58 (60)
T ss_pred EeccCCEEEecccCceeecccCccccCchhhcccchhhc
Confidence 467789999999999999999999999999999988764
No 2
>PRK11827 hypothetical protein; Provisional
Probab=99.68 E-value=1e-17 Score=95.11 Aligned_cols=40 Identities=30% Similarity=0.652 Sum_probs=35.2
Q ss_pred CcccCCeEEcCCCCeeeeeeCCccccCCCCCccCCCCccc
Q 036116 1 VCEETNSLISDSIGVSFPIKDGIPSLVPKDGKILGVDDDQ 40 (53)
Q Consensus 1 ~~~~~g~LiC~~c~~~YPI~dGIPvLL~~ear~l~~~e~~ 40 (53)
|+..+++|+|+.|+++|||+|||||||+++||.++.++..
T Consensus 20 ~~~~~~~Lic~~~~laYPI~dgIPVlL~deAr~~~~~~~~ 59 (60)
T PRK11827 20 YNQEKQELICKLDNLAFPLRDGIPVLLETEARVLTADESK 59 (60)
T ss_pred EcCCCCeEECCccCeeccccCCccccCHHHhccCCccccc
Confidence 3556789999999999999999999999999999876543
No 3
>KOG1088 consensus Uncharacterized conserved protein [Function unknown]
Probab=99.17 E-value=1.2e-11 Score=78.52 Aligned_cols=31 Identities=29% Similarity=0.552 Sum_probs=27.8
Q ss_pred cccCCeEEcCCCCeeeeeeCCccccCCCCCc
Q 036116 2 CEETNSLISDSIGVSFPIKDGIPSLVPKDGK 32 (53)
Q Consensus 2 ~~~~g~LiC~~c~~~YPI~dGIPvLL~~ear 32 (53)
+..+|+|+||.||+.|||++|||+||..++.
T Consensus 93 ~v~EG~l~CpetG~vfpI~~GIPNMLL~e~E 123 (124)
T KOG1088|consen 93 DVIEGELVCPETGRVFPISDGIPNMLLSEDE 123 (124)
T ss_pred hhccceEecCCCCcEeecccCCcccccCccc
Confidence 4578999999999999999999999998753
No 4
>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=98.72 E-value=7.1e-09 Score=58.41 Aligned_cols=21 Identities=33% Similarity=0.555 Sum_probs=19.4
Q ss_pred cccCCeEEcCCCCeeeeeeCC
Q 036116 2 CEETNSLISDSIGVSFPIKDG 22 (53)
Q Consensus 2 ~~~~g~LiC~~c~~~YPI~dG 22 (53)
++.+|.|+|+.|+++|||+||
T Consensus 48 ~i~eg~L~Cp~c~r~YPI~dG 68 (68)
T PF03966_consen 48 EIVEGELICPECGREYPIRDG 68 (68)
T ss_dssp ETTTTEEEETTTTEEEEEETT
T ss_pred cccCCEEEcCCCCCEEeCCCC
Confidence 467899999999999999998
No 5
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=92.23 E-value=0.086 Score=26.62 Aligned_cols=16 Identities=13% Similarity=0.248 Sum_probs=14.4
Q ss_pred eEEcCCCCeeeeeeCC
Q 036116 7 SLISDSIGVSFPIKDG 22 (53)
Q Consensus 7 ~LiC~~c~~~YPI~dG 22 (53)
.+.|+.|+..|.|.|.
T Consensus 2 ~i~Cp~C~~~y~i~d~ 17 (36)
T PF13717_consen 2 IITCPNCQAKYEIDDE 17 (36)
T ss_pred EEECCCCCCEEeCCHH
Confidence 4789999999999987
No 6
>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=89.48 E-value=0.19 Score=25.72 Aligned_cols=15 Identities=20% Similarity=0.313 Sum_probs=11.5
Q ss_pred cccCCeEEcCCCCee
Q 036116 2 CEETNSLISDSIGVS 16 (53)
Q Consensus 2 ~~~~g~LiC~~c~~~ 16 (53)
|..+|.++|+.||..
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 557899999999853
No 7
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=87.41 E-value=0.48 Score=23.68 Aligned_cols=17 Identities=29% Similarity=0.384 Sum_probs=14.3
Q ss_pred ccCCeEEcCCCCeeeee
Q 036116 3 EETNSLISDSIGVSFPI 19 (53)
Q Consensus 3 ~~~g~LiC~~c~~~YPI 19 (53)
.+.+.++|..|+..||+
T Consensus 17 ~~~~~~~C~~Cg~~~~~ 33 (33)
T PF08792_consen 17 KEDDYEVCIFCGSSFPY 33 (33)
T ss_pred ecCCeEEcccCCcEeeC
Confidence 35678999999999985
No 8
>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=85.54 E-value=0.41 Score=29.47 Aligned_cols=20 Identities=15% Similarity=0.348 Sum_probs=16.4
Q ss_pred CcccCCeEEcCCCCeeeeee
Q 036116 1 VCEETNSLISDSIGVSFPIK 20 (53)
Q Consensus 1 ~~~~~g~LiC~~c~~~YPI~ 20 (53)
|+-.+.-.+||.||..|++.
T Consensus 20 YDLnk~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 20 YDLNKDPIVCPKCGTEFPPE 39 (108)
T ss_pred ccCCCCCccCCCCCCccCcc
Confidence 45556678999999999998
No 9
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=83.52 E-value=0.79 Score=23.01 Aligned_cols=16 Identities=13% Similarity=0.248 Sum_probs=13.5
Q ss_pred eEEcCCCCeeeeeeCC
Q 036116 7 SLISDSIGVSFPIKDG 22 (53)
Q Consensus 7 ~LiC~~c~~~YPI~dG 22 (53)
.+.||.|+..|.|.+.
T Consensus 2 ~i~CP~C~~~f~v~~~ 17 (37)
T PF13719_consen 2 IITCPNCQTRFRVPDD 17 (37)
T ss_pred EEECCCCCceEEcCHH
Confidence 3689999999999875
No 10
>COG4391 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=81.53 E-value=1 Score=25.87 Aligned_cols=16 Identities=0% Similarity=0.246 Sum_probs=14.1
Q ss_pred cCCeEEcCCCCeeeee
Q 036116 4 ETNSLISDSIGVSFPI 19 (53)
Q Consensus 4 ~~g~LiC~~c~~~YPI 19 (53)
.+|+.+||-|+..|..
T Consensus 45 ~~gev~CPYC~t~y~l 60 (62)
T COG4391 45 DEGEVVCPYCSTRYRL 60 (62)
T ss_pred CCCcEecCccccEEEe
Confidence 5789999999999975
No 11
>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=81.05 E-value=1.1 Score=21.90 Aligned_cols=16 Identities=19% Similarity=0.285 Sum_probs=13.2
Q ss_pred eEEcCCCCeeeeeeCC
Q 036116 7 SLISDSIGVSFPIKDG 22 (53)
Q Consensus 7 ~LiC~~c~~~YPI~dG 22 (53)
.+.||.|+..|.|.+.
T Consensus 2 ~~~CP~C~~~~~v~~~ 17 (38)
T TIGR02098 2 RIQCPNCKTSFRVVDS 17 (38)
T ss_pred EEECCCCCCEEEeCHH
Confidence 3789999999998753
No 12
>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=79.73 E-value=1.4 Score=22.28 Aligned_cols=15 Identities=20% Similarity=0.169 Sum_probs=12.2
Q ss_pred eEEcCCCCeeeeeeC
Q 036116 7 SLISDSIGVSFPIKD 21 (53)
Q Consensus 7 ~LiC~~c~~~YPI~d 21 (53)
..+|+.||..|-|.-
T Consensus 1 Rr~C~~Cg~~Yh~~~ 15 (36)
T PF05191_consen 1 RRICPKCGRIYHIEF 15 (36)
T ss_dssp EEEETTTTEEEETTT
T ss_pred CcCcCCCCCcccccc
Confidence 368999999998643
No 13
>PRK00420 hypothetical protein; Validated
Probab=79.39 E-value=1.3 Score=27.71 Aligned_cols=19 Identities=11% Similarity=0.286 Sum_probs=15.9
Q ss_pred cCCeEEcCCCCeeeeeeCC
Q 036116 4 ETNSLISDSIGVSFPIKDG 22 (53)
Q Consensus 4 ~~g~LiC~~c~~~YPI~dG 22 (53)
..|..+||.||..+-|.+|
T Consensus 37 k~g~~~Cp~Cg~~~~v~~~ 55 (112)
T PRK00420 37 KDGEVVCPVHGKVYIVKSD 55 (112)
T ss_pred CCCceECCCCCCeeeeccH
Confidence 4688999999998888765
No 14
>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=77.71 E-value=1.8 Score=21.36 Aligned_cols=15 Identities=13% Similarity=0.302 Sum_probs=11.0
Q ss_pred cCCeEEcCCCCeeee
Q 036116 4 ETNSLISDSIGVSFP 18 (53)
Q Consensus 4 ~~g~LiC~~c~~~YP 18 (53)
+...|+|+.|+..++
T Consensus 16 D~~~~vCp~C~~ew~ 30 (30)
T PF08274_consen 16 DGELLVCPECGHEWN 30 (30)
T ss_dssp -SSSEEETTTTEEE-
T ss_pred cCCEEeCCcccccCC
Confidence 456899999998763
No 15
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=77.36 E-value=2.4 Score=21.65 Aligned_cols=17 Identities=18% Similarity=0.362 Sum_probs=14.3
Q ss_pred CeEEcCCCCeeeeeeCC
Q 036116 6 NSLISDSIGVSFPIKDG 22 (53)
Q Consensus 6 g~LiC~~c~~~YPI~dG 22 (53)
..++|+.|+..++|..-
T Consensus 19 ~~~vC~~Cg~~~~~~~~ 35 (52)
T smart00661 19 RRFVCRKCGYEEPIEQK 35 (52)
T ss_pred CEEECCcCCCeEECCCc
Confidence 48999999999988744
No 16
>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=77.00 E-value=2.2 Score=20.76 Aligned_cols=18 Identities=17% Similarity=0.331 Sum_probs=14.9
Q ss_pred eEEcCCCCeeeeeeCCcc
Q 036116 7 SLISDSIGVSFPIKDGIP 24 (53)
Q Consensus 7 ~LiC~~c~~~YPI~dGIP 24 (53)
...|+.||..|.+..++-
T Consensus 5 ~y~C~~Cg~~fe~~~~~~ 22 (41)
T smart00834 5 EYRCEDCGHTFEVLQKIS 22 (41)
T ss_pred EEEcCCCCCEEEEEEecC
Confidence 468999999999887763
No 17
>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=76.23 E-value=1.5 Score=26.79 Aligned_cols=20 Identities=25% Similarity=0.511 Sum_probs=16.4
Q ss_pred CcccCCeEEcCCCCeeeeee
Q 036116 1 VCEETNSLISDSIGVSFPIK 20 (53)
Q Consensus 1 ~~~~~g~LiC~~c~~~YPI~ 20 (53)
|-+..+.|+|..|+..|.+.
T Consensus 46 Y~q~g~~lvC~~C~~~~~~~ 65 (102)
T PF10080_consen 46 YYQEGDQLVCKNCGVRFNLP 65 (102)
T ss_pred eEEECCEEEEecCCCEEehh
Confidence 34567899999999999874
No 18
>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=76.04 E-value=1.8 Score=18.67 Aligned_cols=12 Identities=33% Similarity=0.288 Sum_probs=10.0
Q ss_pred EcCCCCeeeeee
Q 036116 9 ISDSIGVSFPIK 20 (53)
Q Consensus 9 iC~~c~~~YPI~ 20 (53)
.|+.|++.|+-.
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 19
>PF14353 CpXC: CpXC protein
Probab=73.93 E-value=2.3 Score=25.63 Aligned_cols=25 Identities=28% Similarity=0.316 Sum_probs=18.1
Q ss_pred eEEcCCCCeeeeeeCCccccCCCCCcc
Q 036116 7 SLISDSIGVSFPIKDGIPSLVPKDGKI 33 (53)
Q Consensus 7 ~LiC~~c~~~YPI~dGIPvLL~~ear~ 33 (53)
..+||.||..+.+ ..|.|..+..+.
T Consensus 38 ~~~CP~Cg~~~~~--~~p~lY~D~~~~ 62 (128)
T PF14353_consen 38 SFTCPSCGHKFRL--EYPLLYHDPEKK 62 (128)
T ss_pred EEECCCCCCceec--CCCEEEEcCCCC
Confidence 6799999999988 556666555443
No 20
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=72.53 E-value=1.8 Score=20.10 Aligned_cols=11 Identities=18% Similarity=0.199 Sum_probs=9.5
Q ss_pred EEcCCCCeeee
Q 036116 8 LISDSIGVSFP 18 (53)
Q Consensus 8 LiC~~c~~~YP 18 (53)
..|+.||+.|.
T Consensus 3 ~~C~~CgR~F~ 13 (25)
T PF13913_consen 3 VPCPICGRKFN 13 (25)
T ss_pred CcCCCCCCEEC
Confidence 57999999994
No 21
>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=70.76 E-value=2.4 Score=26.62 Aligned_cols=18 Identities=17% Similarity=0.169 Sum_probs=14.4
Q ss_pred cCCeEEcCCCCeeeeeeC
Q 036116 4 ETNSLISDSIGVSFPIKD 21 (53)
Q Consensus 4 ~~g~LiC~~c~~~YPI~d 21 (53)
+...|+||.|++.|.=.+
T Consensus 16 dg~~~iCpeC~~EW~~~~ 33 (109)
T TIGR00686 16 DGTQLICPSCLYEWNENE 33 (109)
T ss_pred cCCeeECccccccccccc
Confidence 456799999999997554
No 22
>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=70.59 E-value=3.4 Score=18.46 Aligned_cols=11 Identities=27% Similarity=0.516 Sum_probs=9.6
Q ss_pred EEcCCCCeeee
Q 036116 8 LISDSIGVSFP 18 (53)
Q Consensus 8 LiC~~c~~~YP 18 (53)
+.|..|+..|.
T Consensus 2 ~~C~~C~~~F~ 12 (27)
T PF13912_consen 2 FECDECGKTFS 12 (27)
T ss_dssp EEETTTTEEES
T ss_pred CCCCccCCccC
Confidence 67999999995
No 23
>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=70.18 E-value=2.2 Score=27.46 Aligned_cols=20 Identities=20% Similarity=0.223 Sum_probs=15.4
Q ss_pred CcccCCeEEcCCCCeeeeee
Q 036116 1 VCEETNSLISDSIGVSFPIK 20 (53)
Q Consensus 1 ~~~~~g~LiC~~c~~~YPI~ 20 (53)
|+-.+.-.+||.||..|++.
T Consensus 20 YDLnk~p~vcP~cg~~~~~~ 39 (129)
T TIGR02300 20 YDLNRRPAVSPYTGEQFPPE 39 (129)
T ss_pred cccCCCCccCCCcCCccCcc
Confidence 44455678899999999887
No 24
>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=69.50 E-value=3.2 Score=24.41 Aligned_cols=17 Identities=18% Similarity=0.331 Sum_probs=12.9
Q ss_pred CeEEcCCCCeeeeeeCC
Q 036116 6 NSLISDSIGVSFPIKDG 22 (53)
Q Consensus 6 g~LiC~~c~~~YPI~dG 22 (53)
.-|+|..||+.+++.+.
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 46999999999999763
No 25
>PF13408 Zn_ribbon_recom: Recombinase zinc beta ribbon domain
Probab=67.86 E-value=4.4 Score=20.73 Aligned_cols=16 Identities=13% Similarity=0.169 Sum_probs=13.6
Q ss_pred CCeEEcCCCCeeeeee
Q 036116 5 TNSLISDSIGVSFPIK 20 (53)
Q Consensus 5 ~g~LiC~~c~~~YPI~ 20 (53)
.|.|+|..||..+-..
T Consensus 3 ~g~l~C~~CG~~m~~~ 18 (58)
T PF13408_consen 3 SGLLRCGHCGSKMTRR 18 (58)
T ss_pred CCcEEcccCCcEeEEE
Confidence 5889999999888764
No 26
>PF13878 zf-C2H2_3: zinc-finger of acetyl-transferase ESCO
Probab=67.05 E-value=3 Score=21.43 Aligned_cols=14 Identities=7% Similarity=0.202 Sum_probs=11.5
Q ss_pred CeEEcCCCCeeeee
Q 036116 6 NSLISDSIGVSFPI 19 (53)
Q Consensus 6 g~LiC~~c~~~YPI 19 (53)
+.-.|+.||..|-.
T Consensus 12 ~~~~C~~CgM~Y~~ 25 (41)
T PF13878_consen 12 GATTCPTCGMLYSP 25 (41)
T ss_pred CCcCCCCCCCEECC
Confidence 45799999999964
No 27
>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=66.18 E-value=3.7 Score=17.09 Aligned_cols=11 Identities=27% Similarity=0.184 Sum_probs=7.2
Q ss_pred EcCCCCeeeee
Q 036116 9 ISDSIGVSFPI 19 (53)
Q Consensus 9 iC~~c~~~YPI 19 (53)
.|+.|+..|+=
T Consensus 2 ~C~~C~~~~~~ 12 (24)
T PF13894_consen 2 QCPICGKSFRS 12 (24)
T ss_dssp E-SSTS-EESS
T ss_pred CCcCCCCcCCc
Confidence 69999998863
No 28
>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=66.13 E-value=4.3 Score=23.47 Aligned_cols=17 Identities=24% Similarity=0.339 Sum_probs=14.4
Q ss_pred CeEEcCCCCeeeeeeCC
Q 036116 6 NSLISDSIGVSFPIKDG 22 (53)
Q Consensus 6 g~LiC~~c~~~YPI~dG 22 (53)
.-|+|..||+.+.+.+.
T Consensus 72 ~H~~C~~Cg~i~~~~~~ 88 (116)
T cd07153 72 HHLICTKCGKVIDFEDC 88 (116)
T ss_pred CceEeCCCCCEEEecCc
Confidence 36999999999998754
No 29
>PRK10220 hypothetical protein; Provisional
Probab=65.40 E-value=4.1 Score=25.69 Aligned_cols=18 Identities=6% Similarity=0.088 Sum_probs=15.0
Q ss_pred cCCeEEcCCCCeeeeeeC
Q 036116 4 ETNSLISDSIGVSFPIKD 21 (53)
Q Consensus 4 ~~g~LiC~~c~~~YPI~d 21 (53)
+...|+||.|++.|+-.+
T Consensus 17 d~~~~vCpeC~hEW~~~~ 34 (111)
T PRK10220 17 DNGMYICPECAHEWNDAE 34 (111)
T ss_pred CCCeEECCcccCcCCccc
Confidence 456799999999998665
No 30
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=64.59 E-value=4.9 Score=24.68 Aligned_cols=18 Identities=17% Similarity=0.219 Sum_probs=15.5
Q ss_pred cCCeEEcCCCCeeeeeeC
Q 036116 4 ETNSLISDSIGVSFPIKD 21 (53)
Q Consensus 4 ~~g~LiC~~c~~~YPI~d 21 (53)
..+.|+|+.|+..+++..
T Consensus 19 ~~~~l~C~kCgye~~~~~ 36 (113)
T COG1594 19 EGGKLVCRKCGYEEEASN 36 (113)
T ss_pred CCcEEECCCCCcchhccc
Confidence 467899999999999885
No 31
>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=64.57 E-value=5.8 Score=20.42 Aligned_cols=15 Identities=13% Similarity=0.239 Sum_probs=12.5
Q ss_pred eEEcCCCCeeeeeeC
Q 036116 7 SLISDSIGVSFPIKD 21 (53)
Q Consensus 7 ~LiC~~c~~~YPI~d 21 (53)
++.|..|+..|.+.-
T Consensus 5 ey~C~~Cg~~fe~~~ 19 (52)
T TIGR02605 5 EYRCTACGHRFEVLQ 19 (52)
T ss_pred EEEeCCCCCEeEEEE
Confidence 578999999998764
No 32
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=63.76 E-value=5.9 Score=24.75 Aligned_cols=18 Identities=0% Similarity=0.025 Sum_probs=13.7
Q ss_pred cCCeEEcCCCCeeeeeeC
Q 036116 4 ETNSLISDSIGVSFPIKD 21 (53)
Q Consensus 4 ~~g~LiC~~c~~~YPI~d 21 (53)
.....+||.|+..|...+
T Consensus 96 ~~~~Y~Cp~C~~~y~~~e 113 (147)
T smart00531 96 NNAYYKCPNCQSKYTFLE 113 (147)
T ss_pred CCcEEECcCCCCEeeHHH
Confidence 456788999998888644
No 33
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=63.45 E-value=6 Score=25.44 Aligned_cols=16 Identities=6% Similarity=0.098 Sum_probs=12.2
Q ss_pred cCCeEEcCCCCeeeee
Q 036116 4 ETNSLISDSIGVSFPI 19 (53)
Q Consensus 4 ~~g~LiC~~c~~~YPI 19 (53)
..|.++||.|++.+-+
T Consensus 41 KdG~v~CPvC~~~~~~ 56 (131)
T COG1645 41 KDGEVFCPVCGYREVV 56 (131)
T ss_pred eCCeEECCCCCceEEE
Confidence 5699999999954433
No 34
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=62.24 E-value=4.1 Score=28.33 Aligned_cols=15 Identities=13% Similarity=0.237 Sum_probs=12.5
Q ss_pred cccCCeEEcCCCCee
Q 036116 2 CEETNSLISDSIGVS 16 (53)
Q Consensus 2 ~~~~g~LiC~~c~~~ 16 (53)
|...|.++|..||..
T Consensus 25 d~~~Ge~vC~~CG~V 39 (310)
T PRK00423 25 DYERGEIVCADCGLV 39 (310)
T ss_pred ECCCCeEeecccCCc
Confidence 456899999999974
No 35
>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=61.97 E-value=8.7 Score=19.95 Aligned_cols=13 Identities=8% Similarity=0.353 Sum_probs=11.1
Q ss_pred CCeEEcCCCCeee
Q 036116 5 TNSLISDSIGVSF 17 (53)
Q Consensus 5 ~g~LiC~~c~~~Y 17 (53)
.+...|+-|++.|
T Consensus 27 ~~~~~CpYCg~~y 39 (40)
T PF10276_consen 27 PGPVVCPYCGTRY 39 (40)
T ss_dssp TCEEEETTTTEEE
T ss_pred CCeEECCCCCCEE
Confidence 3569999999998
No 36
>COG4530 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=61.22 E-value=3.9 Score=26.29 Aligned_cols=13 Identities=31% Similarity=0.700 Sum_probs=6.7
Q ss_pred CeEEcCCCCeeee
Q 036116 6 NSLISDSIGVSFP 18 (53)
Q Consensus 6 g~LiC~~c~~~YP 18 (53)
.-.+||.||..||
T Consensus 25 dPiVsPytG~s~P 37 (129)
T COG4530 25 DPIVSPYTGKSYP 37 (129)
T ss_pred CccccCcccccch
Confidence 3445555555554
No 37
>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=60.09 E-value=10 Score=19.12 Aligned_cols=18 Identities=11% Similarity=0.193 Sum_probs=14.8
Q ss_pred ccCCeEEcCCCCeeeeee
Q 036116 3 EETNSLISDSIGVSFPIK 20 (53)
Q Consensus 3 ~~~g~LiC~~c~~~YPI~ 20 (53)
..+..|.|..|+++|=+.
T Consensus 10 ~~~~~i~C~~C~~~~H~~ 27 (51)
T PF00628_consen 10 DDGDMIQCDSCNRWYHQE 27 (51)
T ss_dssp TTSSEEEBSTTSCEEETT
T ss_pred CCCCeEEcCCCChhhCcc
Confidence 356789999999999765
No 38
>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=59.90 E-value=4 Score=24.12 Aligned_cols=21 Identities=24% Similarity=0.143 Sum_probs=18.2
Q ss_pred CeEEcCCCCeeeeeeCCcccc
Q 036116 6 NSLISDSIGVSFPIKDGIPSL 26 (53)
Q Consensus 6 g~LiC~~c~~~YPI~dGIPvL 26 (53)
..=.|+.|++.-+..|-||++
T Consensus 32 ~rS~C~~C~~~L~~~~lIPi~ 52 (92)
T PF06750_consen 32 PRSHCPHCGHPLSWWDLIPIL 52 (92)
T ss_pred CCCcCcCCCCcCcccccchHH
Confidence 345799999999999999986
No 39
>PRK09462 fur ferric uptake regulator; Provisional
Probab=59.83 E-value=6.5 Score=24.22 Aligned_cols=17 Identities=24% Similarity=0.311 Sum_probs=14.3
Q ss_pred CeEEcCCCCeeeeeeCC
Q 036116 6 NSLISDSIGVSFPIKDG 22 (53)
Q Consensus 6 g~LiC~~c~~~YPI~dG 22 (53)
.-|+|..||+.+.|.+.
T Consensus 89 ~H~iC~~Cg~i~~i~~~ 105 (148)
T PRK09462 89 DHLICLDCGKVIEFSDD 105 (148)
T ss_pred CceEECCCCCEEEeCCc
Confidence 35999999999999754
No 40
>PRK08197 threonine synthase; Validated
Probab=58.98 E-value=5.3 Score=28.34 Aligned_cols=16 Identities=13% Similarity=0.181 Sum_probs=13.7
Q ss_pred eEEcCCCCeeeeeeCC
Q 036116 7 SLISDSIGVSFPIKDG 22 (53)
Q Consensus 7 ~LiC~~c~~~YPI~dG 22 (53)
.|.|..||+.|++.+.
T Consensus 7 ~~~C~~Cg~~~~~~~~ 22 (394)
T PRK08197 7 HLECSKCGETYDADQV 22 (394)
T ss_pred EEEECCCCCCCCCCCc
Confidence 6999999999998653
No 41
>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=58.52 E-value=8.3 Score=19.59 Aligned_cols=17 Identities=18% Similarity=0.341 Sum_probs=13.4
Q ss_pred eEEcCCCCeeeeeeCCc
Q 036116 7 SLISDSIGVSFPIKDGI 23 (53)
Q Consensus 7 ~LiC~~c~~~YPI~dGI 23 (53)
+..|..||..|.+.-.|
T Consensus 5 ey~C~~Cg~~fe~~~~~ 21 (42)
T PF09723_consen 5 EYRCEECGHEFEVLQSI 21 (42)
T ss_pred EEEeCCCCCEEEEEEEc
Confidence 47899999999876543
No 42
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=58.43 E-value=11 Score=19.13 Aligned_cols=14 Identities=14% Similarity=0.107 Sum_probs=6.7
Q ss_pred eEEcCCCCeeeeee
Q 036116 7 SLISDSIGVSFPIK 20 (53)
Q Consensus 7 ~LiC~~c~~~YPI~ 20 (53)
.+.||.||-.+-+.
T Consensus 21 ~~~Cp~CG~~~~~~ 34 (46)
T PRK00398 21 GVRCPYCGYRILFK 34 (46)
T ss_pred ceECCCCCCeEEEc
Confidence 45555555444433
No 43
>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=58.25 E-value=4.4 Score=19.19 Aligned_cols=13 Identities=15% Similarity=0.296 Sum_probs=9.9
Q ss_pred CeEEcCCCCeeee
Q 036116 6 NSLISDSIGVSFP 18 (53)
Q Consensus 6 g~LiC~~c~~~YP 18 (53)
..-.|+.||..|.
T Consensus 13 ~~~~Cp~CG~~F~ 25 (26)
T PF10571_consen 13 SAKFCPHCGYDFE 25 (26)
T ss_pred hcCcCCCCCCCCc
Confidence 4567999998874
No 44
>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=57.81 E-value=6.8 Score=19.48 Aligned_cols=13 Identities=23% Similarity=0.355 Sum_probs=9.7
Q ss_pred EcCCCCeeeeeeC
Q 036116 9 ISDSIGVSFPIKD 21 (53)
Q Consensus 9 iC~~c~~~YPI~d 21 (53)
.|+.|+..|||.+
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 7999999999875
No 45
>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=56.44 E-value=8.3 Score=17.60 Aligned_cols=13 Identities=23% Similarity=0.258 Sum_probs=10.6
Q ss_pred CeEEcCCCCeeee
Q 036116 6 NSLISDSIGVSFP 18 (53)
Q Consensus 6 g~LiC~~c~~~YP 18 (53)
....|+.|++.|.
T Consensus 13 k~~~C~~C~k~F~ 25 (26)
T PF13465_consen 13 KPYKCPYCGKSFS 25 (26)
T ss_dssp SSEEESSSSEEES
T ss_pred CCCCCCCCcCeeC
Confidence 4588999999883
No 46
>PRK07591 threonine synthase; Validated
Probab=56.31 E-value=6.4 Score=28.41 Aligned_cols=14 Identities=21% Similarity=0.553 Sum_probs=12.3
Q ss_pred eEEcCCCCeeeeee
Q 036116 7 SLISDSIGVSFPIK 20 (53)
Q Consensus 7 ~LiC~~c~~~YPI~ 20 (53)
.|.|..|++.||+.
T Consensus 18 ~l~C~~Cg~~~~~~ 31 (421)
T PRK07591 18 ALKCRECGAEYPLG 31 (421)
T ss_pred EEEeCCCCCcCCCC
Confidence 59999999999974
No 47
>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=56.31 E-value=6.3 Score=24.58 Aligned_cols=11 Identities=9% Similarity=0.033 Sum_probs=9.6
Q ss_pred eEEcCCCCeee
Q 036116 7 SLISDSIGVSF 17 (53)
Q Consensus 7 ~LiC~~c~~~Y 17 (53)
--.|+.||+.|
T Consensus 124 f~~C~~C~kiy 134 (147)
T PF01927_consen 124 FWRCPGCGKIY 134 (147)
T ss_pred EEECCCCCCEe
Confidence 56899999988
No 48
>PRK11088 rrmA 23S rRNA methyltransferase A; Provisional
Probab=56.27 E-value=9.6 Score=25.37 Aligned_cols=27 Identities=33% Similarity=0.443 Sum_probs=20.4
Q ss_pred CCeEEcCCCCeee-eeeCCccccCCCCCc
Q 036116 5 TNSLISDSIGVSF-PIKDGIPSLVPKDGK 32 (53)
Q Consensus 5 ~g~LiC~~c~~~Y-PI~dGIPvLL~~ear 32 (53)
.+.|+|.. ++.| .-++|+-+||+...+
T Consensus 16 ~~~~~C~~-~h~fd~a~~Gy~~ll~~~~~ 43 (272)
T PRK11088 16 ENSWICPQ-NHQFDCAKEGYVNLLPVQHK 43 (272)
T ss_pred CCEEEcCC-CCCCccccCceEEecccccc
Confidence 46788887 6778 556899999986543
No 49
>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=55.79 E-value=7.1 Score=20.03 Aligned_cols=15 Identities=13% Similarity=0.412 Sum_probs=12.0
Q ss_pred eEEcCCCC--eeeeeeC
Q 036116 7 SLISDSIG--VSFPIKD 21 (53)
Q Consensus 7 ~LiC~~c~--~~YPI~d 21 (53)
..+||.|+ ..|.|++
T Consensus 18 g~~CP~Cg~~~~~~~~~ 34 (46)
T PF12760_consen 18 GFVCPHCGSTKHYRLKT 34 (46)
T ss_pred CCCCCCCCCeeeEEeCC
Confidence 47899998 5787776
No 50
>COG0375 HybF Zn finger protein HypA/HybF (possibly regulating hydrogenase expression) [General function prediction only]
Probab=55.62 E-value=8.5 Score=24.17 Aligned_cols=18 Identities=17% Similarity=0.255 Sum_probs=13.3
Q ss_pred CCeEEcCCCC-eeeeeeCC
Q 036116 5 TNSLISDSIG-VSFPIKDG 22 (53)
Q Consensus 5 ~g~LiC~~c~-~~YPI~dG 22 (53)
.....||.|+ ..+.|..|
T Consensus 84 ~~~~~CP~C~s~~~~i~~G 102 (115)
T COG0375 84 ELDYRCPKCGSINLRIIGG 102 (115)
T ss_pred hheeECCCCCCCceEEecC
Confidence 3455688887 88888777
No 51
>PRK06260 threonine synthase; Validated
Probab=55.17 E-value=6.8 Score=27.84 Aligned_cols=15 Identities=13% Similarity=0.093 Sum_probs=12.0
Q ss_pred eEEcCCCCeeeeeeC
Q 036116 7 SLISDSIGVSFPIKD 21 (53)
Q Consensus 7 ~LiC~~c~~~YPI~d 21 (53)
.|.|..||+.|++..
T Consensus 3 ~~~C~~cg~~~~~~~ 17 (397)
T PRK06260 3 WLKCIECGKEYDPDE 17 (397)
T ss_pred EEEECCCCCCCCCCC
Confidence 588999999998653
No 52
>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=54.74 E-value=8.4 Score=22.40 Aligned_cols=20 Identities=35% Similarity=0.363 Sum_probs=12.5
Q ss_pred CCeEEcCCCCeeeeeeCCcccc
Q 036116 5 TNSLISDSIGVSFPIKDGIPSL 26 (53)
Q Consensus 5 ~g~LiC~~c~~~YPI~dGIPvL 26 (53)
.+.|.|..|+..|-.. |+-|
T Consensus 44 ~~~~~C~~Cg~~~~~~--i~~L 63 (81)
T PF05129_consen 44 IGILSCRVCGESFQTK--INPL 63 (81)
T ss_dssp EEEEEESSS--EEEEE----SS
T ss_pred EEEEEecCCCCeEEEc--cCcc
Confidence 4689999999999776 6544
No 53
>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=54.52 E-value=8.1 Score=23.50 Aligned_cols=18 Identities=6% Similarity=-0.114 Sum_probs=14.2
Q ss_pred cCCeEEcCCCCeeeeeeC
Q 036116 4 ETNSLISDSIGVSFPIKD 21 (53)
Q Consensus 4 ~~g~LiC~~c~~~YPI~d 21 (53)
....+.|+.|+..|++.+
T Consensus 67 ~p~~~~C~~Cg~~~~~~~ 84 (115)
T TIGR00100 67 EPVECECEDCSEEVSPEI 84 (115)
T ss_pred eCcEEEcccCCCEEecCC
Confidence 346788999999998865
No 54
>PLN02569 threonine synthase
Probab=54.41 E-value=5.7 Score=29.58 Aligned_cols=16 Identities=13% Similarity=0.173 Sum_probs=13.7
Q ss_pred eEEcCCCCeeeeeeCC
Q 036116 7 SLISDSIGVSFPIKDG 22 (53)
Q Consensus 7 ~LiC~~c~~~YPI~dG 22 (53)
.|.|..|++.|++..-
T Consensus 49 ~l~C~~Cg~~y~~~~~ 64 (484)
T PLN02569 49 FLECPLTGEKYSLDEV 64 (484)
T ss_pred ccEeCCCCCcCCCccc
Confidence 4999999999998654
No 55
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=53.53 E-value=11 Score=24.68 Aligned_cols=18 Identities=6% Similarity=0.213 Sum_probs=13.9
Q ss_pred cCCeEEcCCCCeeeeeeC
Q 036116 4 ETNSLISDSIGVSFPIKD 21 (53)
Q Consensus 4 ~~g~LiC~~c~~~YPI~d 21 (53)
.....+||.|+..|.-.|
T Consensus 114 ~~~~Y~Cp~C~~rytf~e 131 (178)
T PRK06266 114 NNMFFFCPNCHIRFTFDE 131 (178)
T ss_pred CCCEEECCCCCcEEeHHH
Confidence 446788999999997655
No 56
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=52.95 E-value=9.8 Score=23.14 Aligned_cols=18 Identities=0% Similarity=-0.036 Sum_probs=13.8
Q ss_pred cCCeEEcCCCCeeeeeeC
Q 036116 4 ETNSLISDSIGVSFPIKD 21 (53)
Q Consensus 4 ~~g~LiC~~c~~~YPI~d 21 (53)
....+.|..|+..|++.+
T Consensus 67 ~p~~~~C~~Cg~~~~~~~ 84 (114)
T PRK03681 67 QEAECWCETCQQYVTLLT 84 (114)
T ss_pred eCcEEEcccCCCeeecCC
Confidence 346788999998888853
No 57
>PF13445 zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.
Probab=52.60 E-value=6.4 Score=20.43 Aligned_cols=18 Identities=17% Similarity=0.361 Sum_probs=8.9
Q ss_pred cCCCCeeeeeeCCccccCC
Q 036116 10 SDSIGVSFPIKDGIPSLVP 28 (53)
Q Consensus 10 C~~c~~~YPI~dGIPvLL~ 28 (53)
|+.|+. |--.+..|++|+
T Consensus 1 CpIc~e-~~~~~n~P~~L~ 18 (43)
T PF13445_consen 1 CPICKE-FSTEENPPMVLP 18 (43)
T ss_dssp -TTT-----TTSS-EEE-S
T ss_pred CCcccc-ccCCCCCCEEEe
Confidence 777887 877788888887
No 58
>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=52.53 E-value=13 Score=23.88 Aligned_cols=18 Identities=11% Similarity=0.346 Sum_probs=14.8
Q ss_pred cCCeEEcCCCCeeeeeeC
Q 036116 4 ETNSLISDSIGVSFPIKD 21 (53)
Q Consensus 4 ~~g~LiC~~c~~~YPI~d 21 (53)
.-|.|+|..||..--+..
T Consensus 109 g~G~l~C~~Cg~~~~~~~ 126 (146)
T PF07295_consen 109 GPGTLVCENCGHEVELTH 126 (146)
T ss_pred cCceEecccCCCEEEecC
Confidence 358999999998887765
No 59
>PRK11032 hypothetical protein; Provisional
Probab=52.23 E-value=10 Score=24.87 Aligned_cols=16 Identities=6% Similarity=0.137 Sum_probs=13.4
Q ss_pred CCeEEcCCCCeeeeee
Q 036116 5 TNSLISDSIGVSFPIK 20 (53)
Q Consensus 5 ~g~LiC~~c~~~YPI~ 20 (53)
-|.|+|..||+..-|.
T Consensus 122 ~G~LvC~~Cg~~~~~~ 137 (160)
T PRK11032 122 LGNLVCEKCHHHLAFY 137 (160)
T ss_pred cceEEecCCCCEEEec
Confidence 4899999999887665
No 60
>PRK11639 zinc uptake transcriptional repressor; Provisional
Probab=52.22 E-value=10 Score=24.22 Aligned_cols=17 Identities=18% Similarity=-0.019 Sum_probs=14.5
Q ss_pred eEEcCCCCeeeeeeCCc
Q 036116 7 SLISDSIGVSFPIKDGI 23 (53)
Q Consensus 7 ~LiC~~c~~~YPI~dGI 23 (53)
-|+|..||+.+.|.+.-
T Consensus 100 H~iC~~CGki~~i~~~~ 116 (169)
T PRK11639 100 MFICDRCGAVKEECAEG 116 (169)
T ss_pred eEEeCCCCCEEEecccH
Confidence 49999999999997653
No 61
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=52.17 E-value=11 Score=22.95 Aligned_cols=17 Identities=6% Similarity=-0.109 Sum_probs=13.6
Q ss_pred CCeEEcCCCCeeeeeeC
Q 036116 5 TNSLISDSIGVSFPIKD 21 (53)
Q Consensus 5 ~g~LiC~~c~~~YPI~d 21 (53)
...+.|+.|+..|++.+
T Consensus 68 p~~~~C~~Cg~~~~~~~ 84 (113)
T PRK12380 68 PAQAWCWDCSQVVEIHQ 84 (113)
T ss_pred CcEEEcccCCCEEecCC
Confidence 46788999998888864
No 62
>PF01430 HSP33: Hsp33 protein; InterPro: IPR000397 Hsp33 is a molecular chaperone, distinguished from all other known chaperones by its mode of functional regulation. Its activity is redox regulated. Hsp33 is a cytoplasmically localized protein with highly reactive cysteines that respond quickly to changes in the redox environment. Oxidizing conditions like H2O2 cause disulphide bonds to form in Hsp33, a process that leads to the activation of its chaperone function [].; GO: 0051082 unfolded protein binding, 0006457 protein folding, 0005737 cytoplasm; PDB: 1VZY_B 1VQ0_A 1I7F_A 3M7M_X 1XJH_A 1HW7_A.
Probab=52.11 E-value=11 Score=25.88 Aligned_cols=15 Identities=7% Similarity=0.175 Sum_probs=9.9
Q ss_pred CeEEcCCCCeeeeee
Q 036116 6 NSLISDSIGVSFPIK 20 (53)
Q Consensus 6 g~LiC~~c~~~YPI~ 20 (53)
-++.|.+|+..|-+.
T Consensus 265 iev~C~fC~~~Y~f~ 279 (280)
T PF01430_consen 265 IEVTCEFCGKKYRFT 279 (280)
T ss_dssp EEEE-TTT--EEEEE
T ss_pred EEEEeeCCCCEEEeC
Confidence 479999999999764
No 63
>PRK12496 hypothetical protein; Provisional
Probab=52.06 E-value=8.3 Score=24.85 Aligned_cols=13 Identities=8% Similarity=0.225 Sum_probs=11.2
Q ss_pred EEcCCCCeeeeee
Q 036116 8 LISDSIGVSFPIK 20 (53)
Q Consensus 8 LiC~~c~~~YPI~ 20 (53)
.+|+.|++.|+..
T Consensus 128 ~~C~gC~~~~~~~ 140 (164)
T PRK12496 128 KVCKGCKKKYPED 140 (164)
T ss_pred EECCCCCccccCC
Confidence 6799999999864
No 64
>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=52.03 E-value=8.7 Score=19.30 Aligned_cols=15 Identities=13% Similarity=0.171 Sum_probs=11.1
Q ss_pred cccCCeEEcCCCCee
Q 036116 2 CEETNSLISDSIGVS 16 (53)
Q Consensus 2 ~~~~g~LiC~~c~~~ 16 (53)
....|.++|.+||..
T Consensus 20 ~~~dG~~yC~~cG~~ 34 (36)
T PF11781_consen 20 YSDDGFYYCDRCGHQ 34 (36)
T ss_pred EccCCEEEhhhCceE
Confidence 346788899888863
No 65
>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=52.00 E-value=15 Score=20.54 Aligned_cols=25 Identities=20% Similarity=0.372 Sum_probs=21.5
Q ss_pred cCCeEEcCCCCeeeeeeCCccccCC
Q 036116 4 ETNSLISDSIGVSFPIKDGIPSLVP 28 (53)
Q Consensus 4 ~~g~LiC~~c~~~YPI~dGIPvLL~ 28 (53)
.++.++||.-+-.|-+++|.++--|
T Consensus 55 ~~~~i~Cp~H~~~f~~~~G~~~~~p 79 (98)
T cd03467 55 EDGCIVCPCHGSRFDLRTGEVVSGP 79 (98)
T ss_pred CCCEEEeCCCCCEEeCCCccCcCCC
Confidence 4678999999999999999986544
No 66
>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=51.36 E-value=7.5 Score=17.60 Aligned_cols=11 Identities=18% Similarity=0.304 Sum_probs=8.9
Q ss_pred EEcCCCCeeee
Q 036116 8 LISDSIGVSFP 18 (53)
Q Consensus 8 LiC~~c~~~YP 18 (53)
++|..|++.|.
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 57999998874
No 67
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=50.65 E-value=5.1 Score=23.03 Aligned_cols=13 Identities=23% Similarity=0.286 Sum_probs=10.6
Q ss_pred CeEEcCCCCeeee
Q 036116 6 NSLISDSIGVSFP 18 (53)
Q Consensus 6 g~LiC~~c~~~YP 18 (53)
.-|.||+|+..|.
T Consensus 16 ~~lrCPRC~~~FR 28 (65)
T COG4049 16 EFLRCPRCGMVFR 28 (65)
T ss_pred eeeeCCchhHHHH
Confidence 3589999998775
No 68
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=50.56 E-value=12 Score=24.05 Aligned_cols=14 Identities=21% Similarity=0.093 Sum_probs=11.9
Q ss_pred CCeEEcCCCCeeee
Q 036116 5 TNSLISDSIGVSFP 18 (53)
Q Consensus 5 ~g~LiC~~c~~~YP 18 (53)
+++|.|+.|+..++
T Consensus 164 ~~~~~c~~~~~~e~ 177 (189)
T PRK09521 164 ENELKCPNCGNIET 177 (189)
T ss_pred CCEEECCCCCCEEe
Confidence 47899999998775
No 69
>TIGR03844 cysteate_syn cysteate synthase. Members of this family are cysteate synthase, an enzyme of alternate pathway to sulfopyruvate, a precursor of coenzyme M.
Probab=50.27 E-value=8.6 Score=27.78 Aligned_cols=12 Identities=25% Similarity=0.421 Sum_probs=10.9
Q ss_pred eEEcCCCCeeee
Q 036116 7 SLISDSIGVSFP 18 (53)
Q Consensus 7 ~LiC~~c~~~YP 18 (53)
.|+|..||+.||
T Consensus 2 ~l~C~~Cg~~~~ 13 (398)
T TIGR03844 2 TLRCPGCGEVLP 13 (398)
T ss_pred EEEeCCCCCccC
Confidence 589999999998
No 70
>cd06232 Peptidase_M14-like_5 Peptidase M14-like domain of a functionally uncharacterized subgroup of the M14 family of metallocarboxypeptidases (MCPs). The M14 family are zinc-binding carboxypeptidases (CPs) which hydrolyze single, C-terminal amino acids from polypeptide chains, and have a recognition site for the free C-terminal carboxyl group, which is a key determinant of specificity. Two major subfamilies of the M14 family, defined based on sequence and structural homology, are the A/B and N/E subfamilies. Enzymes belonging to the A/B subfamily are normally synthesized as inactive precursors containing preceding signal peptide, followed by an N-terminal pro-region linked to the enzyme; these proenzymes are called procarboxypeptidases. The A/B enzymes can be further divided based on their substrate specificity; Carboxypeptidase A-like (CPA-like) enzymes favor hydrophobic residues while carboxypeptidase B-like (CPB-like) enzymes only cleave the basic residues lysine or arginine. The
Probab=50.21 E-value=6.5 Score=27.53 Aligned_cols=20 Identities=35% Similarity=0.657 Sum_probs=17.1
Q ss_pred CeeeeeeCCccccCCCCCcc
Q 036116 14 GVSFPIKDGIPSLVPKDGKI 33 (53)
Q Consensus 14 ~~~YPI~dGIPvLL~~ear~ 33 (53)
...||+.+|||+++.+..+.
T Consensus 217 ~~~~~~~~g~~~~~~e~~~~ 236 (240)
T cd06232 217 TLWFPDINGIPCPIEEDGRE 236 (240)
T ss_pred CCCcccccCeeeEEeecCcC
Confidence 46799999999999987765
No 71
>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=49.82 E-value=18 Score=19.82 Aligned_cols=20 Identities=20% Similarity=0.287 Sum_probs=15.2
Q ss_pred CCeEEcCCCCeeeeeeCCcc
Q 036116 5 TNSLISDSIGVSFPIKDGIP 24 (53)
Q Consensus 5 ~g~LiC~~c~~~YPI~dGIP 24 (53)
...+.|+.||..|.|..-=|
T Consensus 20 GeiV~Cp~CGaeleVv~~~p 39 (54)
T TIGR01206 20 GELVICDECGAELEVVSLDP 39 (54)
T ss_pred CCEEeCCCCCCEEEEEeCCC
Confidence 34678999999998876555
No 72
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=49.35 E-value=17 Score=18.94 Aligned_cols=13 Identities=31% Similarity=0.302 Sum_probs=6.3
Q ss_pred EEcCCCCeeeeee
Q 036116 8 LISDSIGVSFPIK 20 (53)
Q Consensus 8 LiC~~c~~~YPI~ 20 (53)
.+|..||..+.+.
T Consensus 3 Y~C~~Cg~~~~~~ 15 (44)
T smart00659 3 YICGECGRENEIK 15 (44)
T ss_pred EECCCCCCEeecC
Confidence 3455555555444
No 73
>PF14205 Cys_rich_KTR: Cysteine-rich KTR
Probab=49.27 E-value=11 Score=21.07 Aligned_cols=9 Identities=11% Similarity=0.235 Sum_probs=5.8
Q ss_pred CeEEcCCCC
Q 036116 6 NSLISDSIG 14 (53)
Q Consensus 6 g~LiC~~c~ 14 (53)
+++.||.||
T Consensus 3 ~Wi~CP~Cg 11 (55)
T PF14205_consen 3 EWILCPICG 11 (55)
T ss_pred eEEECCCCC
Confidence 466666665
No 74
>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=49.24 E-value=13 Score=21.59 Aligned_cols=17 Identities=18% Similarity=0.153 Sum_probs=14.2
Q ss_pred cCCeEEcCCCCeeeeee
Q 036116 4 ETNSLISDSIGVSFPIK 20 (53)
Q Consensus 4 ~~g~LiC~~c~~~YPI~ 20 (53)
.++.|+|+.|+..+.+.
T Consensus 13 ~~~~~~C~~C~~~~~~~ 29 (104)
T TIGR01384 13 KNGVYVCPSCGYEKEKK 29 (104)
T ss_pred CCCeEECcCCCCccccc
Confidence 45789999999888874
No 75
>PF13451 zf-trcl: Probable zinc-binding domain
Probab=48.90 E-value=14 Score=20.10 Aligned_cols=17 Identities=24% Similarity=0.495 Sum_probs=13.7
Q ss_pred CeEEcCCCCeeeeeeCC
Q 036116 6 NSLISDSIGVSFPIKDG 22 (53)
Q Consensus 6 g~LiC~~c~~~YPI~dG 22 (53)
..|+|..||..|-+.-|
T Consensus 3 k~l~C~dCg~~FvfTa~ 19 (49)
T PF13451_consen 3 KTLTCKDCGAEFVFTAG 19 (49)
T ss_pred eeEEcccCCCeEEEehh
Confidence 57999999999876543
No 76
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=47.87 E-value=15 Score=18.36 Aligned_cols=13 Identities=15% Similarity=0.376 Sum_probs=9.7
Q ss_pred cCCeEEcCCCCee
Q 036116 4 ETNSLISDSIGVS 16 (53)
Q Consensus 4 ~~g~LiC~~c~~~ 16 (53)
.+..++|+.|+..
T Consensus 19 ~r~R~vC~~Cg~I 31 (34)
T PF14803_consen 19 DRERLVCPACGFI 31 (34)
T ss_dssp SS-EEEETTTTEE
T ss_pred CccceECCCCCCE
Confidence 4578999999864
No 77
>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=47.16 E-value=17 Score=17.23 Aligned_cols=13 Identities=15% Similarity=-0.074 Sum_probs=8.6
Q ss_pred CCeEEcCCCCeee
Q 036116 5 TNSLISDSIGVSF 17 (53)
Q Consensus 5 ~g~LiC~~c~~~Y 17 (53)
+-.++|+.|++.+
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 4578999998764
No 78
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=46.78 E-value=16 Score=19.50 Aligned_cols=13 Identities=8% Similarity=0.005 Sum_probs=9.4
Q ss_pred CCeEEcCCCCeee
Q 036116 5 TNSLISDSIGVSF 17 (53)
Q Consensus 5 ~g~LiC~~c~~~Y 17 (53)
.+.+.|..|+..|
T Consensus 35 ~~r~~C~~Cgyt~ 47 (50)
T PRK00432 35 LDRWHCGKCGYTE 47 (50)
T ss_pred CCcEECCCcCCEE
Confidence 4677888887665
No 79
>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=46.34 E-value=16 Score=23.30 Aligned_cols=18 Identities=17% Similarity=0.335 Sum_probs=13.1
Q ss_pred cCCeEEcCCCCeeeeeeC
Q 036116 4 ETNSLISDSIGVSFPIKD 21 (53)
Q Consensus 4 ~~g~LiC~~c~~~YPI~d 21 (53)
.....+||.|+..|...+
T Consensus 106 ~~~~Y~Cp~c~~r~tf~e 123 (158)
T TIGR00373 106 NNMFFICPNMCVRFTFNE 123 (158)
T ss_pred CCCeEECCCCCcEeeHHH
Confidence 345678999998886544
No 80
>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=46.16 E-value=11 Score=22.73 Aligned_cols=18 Identities=11% Similarity=0.038 Sum_probs=12.5
Q ss_pred CCeEEcCCCCeeeeeeCC
Q 036116 5 TNSLISDSIGVSFPIKDG 22 (53)
Q Consensus 5 ~g~LiC~~c~~~YPI~dG 22 (53)
.....|..|+..|++.+.
T Consensus 68 p~~~~C~~Cg~~~~~~~~ 85 (113)
T PF01155_consen 68 PARARCRDCGHEFEPDEF 85 (113)
T ss_dssp --EEEETTTS-EEECHHC
T ss_pred CCcEECCCCCCEEecCCC
Confidence 457889999999988654
No 81
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=45.74 E-value=14 Score=23.04 Aligned_cols=16 Identities=19% Similarity=0.308 Sum_probs=13.6
Q ss_pred CCeEEcCCCCeeeeee
Q 036116 5 TNSLISDSIGVSFPIK 20 (53)
Q Consensus 5 ~g~LiC~~c~~~YPI~ 20 (53)
.....|+.||..|++.
T Consensus 68 p~~~~C~~CG~~~~~~ 83 (135)
T PRK03824 68 EAVLKCRNCGNEWSLK 83 (135)
T ss_pred ceEEECCCCCCEEecc
Confidence 3678999999999987
No 82
>COG0735 Fur Fe2+/Zn2+ uptake regulation proteins [Inorganic ion transport and metabolism]
Probab=44.84 E-value=15 Score=22.91 Aligned_cols=17 Identities=24% Similarity=0.313 Sum_probs=15.4
Q ss_pred CeEEcCCCCeeeeeeCC
Q 036116 6 NSLISDSIGVSFPIKDG 22 (53)
Q Consensus 6 g~LiC~~c~~~YPI~dG 22 (53)
.-|+|..||+...|.+.
T Consensus 92 ~HliC~~CG~v~e~~~~ 108 (145)
T COG0735 92 HHLICLDCGKVIEFEDD 108 (145)
T ss_pred cEEEecCCCCEEEecch
Confidence 46999999999999986
No 83
>COG2824 PhnA Uncharacterized Zn-ribbon-containing protein involved in phosphonate metabolism [Inorganic ion transport and metabolism]
Probab=44.61 E-value=18 Score=22.93 Aligned_cols=29 Identities=10% Similarity=0.145 Sum_probs=19.4
Q ss_pred EcCCCCeeeeeeCCccccCCCCCccCCCC
Q 036116 9 ISDSIGVSFPIKDGIPSLVPKDGKILGVD 37 (53)
Q Consensus 9 iC~~c~~~YPI~dGIPvLL~~ear~l~~~ 37 (53)
-||.|+-.|--+||.-...|+.+...+..
T Consensus 5 ~cp~c~sEytYed~~~~~cpec~~ew~~~ 33 (112)
T COG2824 5 PCPKCNSEYTYEDGGQLICPECAHEWNEN 33 (112)
T ss_pred CCCccCCceEEecCceEeCchhccccccc
Confidence 37777777777777755566666666643
No 84
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=44.47 E-value=16 Score=22.88 Aligned_cols=16 Identities=19% Similarity=0.426 Sum_probs=13.3
Q ss_pred CCeEEcCCCCeeeeee
Q 036116 5 TNSLISDSIGVSFPIK 20 (53)
Q Consensus 5 ~g~LiC~~c~~~YPI~ 20 (53)
.+.++|..||+.|..+
T Consensus 44 ~g~~~Cg~CGls~e~e 59 (104)
T COG4888 44 IGTAVCGNCGLSFECE 59 (104)
T ss_pred eeEEEcccCcceEEEe
Confidence 4679999999999764
No 85
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=44.26 E-value=18 Score=15.57 Aligned_cols=11 Identities=27% Similarity=0.350 Sum_probs=8.7
Q ss_pred EEcCCCCeeee
Q 036116 8 LISDSIGVSFP 18 (53)
Q Consensus 8 LiC~~c~~~YP 18 (53)
+.|..|++.|.
T Consensus 1 ~~C~~C~~~f~ 11 (25)
T PF12874_consen 1 FYCDICNKSFS 11 (25)
T ss_dssp EEETTTTEEES
T ss_pred CCCCCCCCCcC
Confidence 47999998874
No 86
>PRK00114 hslO Hsp33-like chaperonin; Reviewed
Probab=43.68 E-value=15 Score=25.56 Aligned_cols=14 Identities=7% Similarity=0.287 Sum_probs=12.8
Q ss_pred eEEcCCCCeeeeee
Q 036116 7 SLISDSIGVSFPIK 20 (53)
Q Consensus 7 ~LiC~~c~~~YPI~ 20 (53)
+++|.+|+..|.+.
T Consensus 268 ev~C~FC~~~Y~f~ 281 (293)
T PRK00114 268 EMVCQFCGNKYLFD 281 (293)
T ss_pred EEEEeCCCCEEEeC
Confidence 79999999999875
No 87
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=42.87 E-value=14 Score=22.58 Aligned_cols=17 Identities=12% Similarity=0.024 Sum_probs=12.5
Q ss_pred CCeEEcCCCCeeeeeeC
Q 036116 5 TNSLISDSIGVSFPIKD 21 (53)
Q Consensus 5 ~g~LiC~~c~~~YPI~d 21 (53)
...+.|..|+..|++.+
T Consensus 69 p~~~~C~~Cg~~~~~~~ 85 (117)
T PRK00564 69 KVELECKDCSHVFKPNA 85 (117)
T ss_pred CCEEEhhhCCCccccCC
Confidence 45678888888887753
No 88
>PF11238 DUF3039: Protein of unknown function (DUF3039); InterPro: IPR021400 This family of proteins with unknown function appears to be restricted to Actinobacteria.
Probab=42.33 E-value=4.2 Score=23.02 Aligned_cols=12 Identities=0% Similarity=-0.100 Sum_probs=9.3
Q ss_pred eEEcCCCCeeee
Q 036116 7 SLISDSIGVSFP 18 (53)
Q Consensus 7 ~LiC~~c~~~YP 18 (53)
.=+||.|+..|.
T Consensus 44 ~PVCP~Ck~iye 55 (58)
T PF11238_consen 44 FPVCPECKEIYE 55 (58)
T ss_pred CCCCcCHHHHHH
Confidence 458999998873
No 89
>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=42.18 E-value=25 Score=19.56 Aligned_cols=25 Identities=20% Similarity=0.295 Sum_probs=20.4
Q ss_pred cCCeEEcCCCCeeeeeeCCccccCC
Q 036116 4 ETNSLISDSIGVSFPIKDGIPSLVP 28 (53)
Q Consensus 4 ~~g~LiC~~c~~~YPI~dGIPvLL~ 28 (53)
.++.|+||--+-.|-+++|-.+--|
T Consensus 54 ~~~~i~Cp~Hg~~fd~~~G~~~~~p 78 (98)
T cd03528 54 EGGVIECPLHGGRFDLRTGKALSLP 78 (98)
T ss_pred eCCEEEeCCcCCEEECCCCcccCCC
Confidence 3568999999999999999775433
No 90
>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=41.93 E-value=17 Score=21.31 Aligned_cols=14 Identities=14% Similarity=0.206 Sum_probs=8.4
Q ss_pred CeEEcCCCCeeeee
Q 036116 6 NSLISDSIGVSFPI 19 (53)
Q Consensus 6 g~LiC~~c~~~YPI 19 (53)
..++|+.|+..+.|
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 57999999988765
No 91
>smart00355 ZnF_C2H2 zinc finger.
Probab=41.47 E-value=9 Score=15.78 Aligned_cols=11 Identities=18% Similarity=0.141 Sum_probs=8.3
Q ss_pred EcCCCCeeeee
Q 036116 9 ISDSIGVSFPI 19 (53)
Q Consensus 9 iC~~c~~~YPI 19 (53)
.|+.|+..|.-
T Consensus 2 ~C~~C~~~f~~ 12 (26)
T smart00355 2 RCPECGKVFKS 12 (26)
T ss_pred CCCCCcchhCC
Confidence 58888888753
No 92
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=41.32 E-value=19 Score=23.91 Aligned_cols=15 Identities=20% Similarity=0.324 Sum_probs=13.0
Q ss_pred CeEEcCCCCeeeeee
Q 036116 6 NSLISDSIGVSFPIK 20 (53)
Q Consensus 6 g~LiC~~c~~~YPI~ 20 (53)
..+.||.|+..|..+
T Consensus 4 k~~~CPvC~~~F~~~ 18 (214)
T PF09986_consen 4 KKITCPVCGKEFKTK 18 (214)
T ss_pred CceECCCCCCeeeee
Confidence 578999999999875
No 93
>cd09020 D-hex-6-P-epi_like D-hexose-6-phosphate epimerase-like. D-Hexose-6-phosphate epimerase Ymr099c from Saccharomyces cerevisiae belongs to the large superfamily of aldose-1-epimerases. Its active site is very similar to the catalytic site of galactose mutarotase, the best studied member of the superfamily. It also contains the conserved glutamate and histidine residues that have been shown in galactose mutarotase to be critical for catalysis, the glutamate serving as the active site base to initiate the reaction by removing the proton from the C-1 hydroxyl group of the sugar substrate, and the histidine as the active site acid to protonate the C-5 ring oxygen. In addition Ymr099c contains 2 conserved arginine residues which are involved in phosphate binding, and exhibits hexose-6-phosphate mutarotase activity on glucose-6-P, galactose-6-P and mannose-6-P.
Probab=41.25 E-value=10 Score=25.50 Aligned_cols=17 Identities=35% Similarity=0.450 Sum_probs=12.9
Q ss_pred eeeeeCCccccCCCCCc
Q 036116 16 SFPIKDGIPSLVPKDGK 32 (53)
Q Consensus 16 ~YPI~dGIPvLL~~ear 32 (53)
.=+|+.|||+|.|--.+
T Consensus 43 ~~~irgGiPvlfP~~g~ 59 (269)
T cd09020 43 GKAIRGGIPVCWPWFGP 59 (269)
T ss_pred CCcccCCCeEeeeccCC
Confidence 34689999999995443
No 94
>cd00498 Hsp33 Heat shock protein 33 (Hsp33): Cytosolic protein that acts as a molecular chaperone under oxidative conditions. In normal (reducing) cytosolic conditions, four conserved Cys residues are coordinated by a Zn ion. Under oxidative stress (such as heat shock), the Cys are reversibly oxidized to disulfide bonds, which causes the chaperone activity to be turned on. Hsp33 is homodimeric in its functional form.
Probab=40.69 E-value=17 Score=25.01 Aligned_cols=13 Identities=8% Similarity=0.261 Sum_probs=11.8
Q ss_pred eEEcCCCCeeeee
Q 036116 7 SLISDSIGVSFPI 19 (53)
Q Consensus 7 ~LiC~~c~~~YPI 19 (53)
++.|.+|+..|.+
T Consensus 262 ev~C~FC~~~Y~f 274 (275)
T cd00498 262 EVTCEFCGEKYHF 274 (275)
T ss_pred EEEEeCCCCEEec
Confidence 7999999999975
No 95
>KOG2907 consensus RNA polymerase I transcription factor TFIIS, subunit A12.2/RPA12 [Transcription]
Probab=40.28 E-value=11 Score=23.94 Aligned_cols=19 Identities=5% Similarity=0.219 Sum_probs=15.0
Q ss_pred CeEEcCCCCeeeeeeCCcc
Q 036116 6 NSLISDSIGVSFPIKDGIP 24 (53)
Q Consensus 6 g~LiC~~c~~~YPI~dGIP 24 (53)
...+|..|+..||++.--+
T Consensus 24 ~~~~C~~Ck~~~~v~~~~~ 42 (116)
T KOG2907|consen 24 STVLCIRCKIEYPVSQFSG 42 (116)
T ss_pred CceEeccccccCCHHHhCC
Confidence 4567999999999986444
No 96
>PRK05638 threonine synthase; Validated
Probab=40.27 E-value=13 Score=26.80 Aligned_cols=13 Identities=8% Similarity=0.166 Sum_probs=11.0
Q ss_pred eEEcCCCCeeeee
Q 036116 7 SLISDSIGVSFPI 19 (53)
Q Consensus 7 ~LiC~~c~~~YPI 19 (53)
.|.|..||+.|+.
T Consensus 1 ~l~C~~Cg~~~~~ 13 (442)
T PRK05638 1 KMKCPKCGREYNS 13 (442)
T ss_pred CeEeCCCCCCCCC
Confidence 3789999999983
No 97
>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=40.22 E-value=14 Score=22.33 Aligned_cols=13 Identities=15% Similarity=0.383 Sum_probs=10.6
Q ss_pred CeEEcCCCCeeee
Q 036116 6 NSLISDSIGVSFP 18 (53)
Q Consensus 6 g~LiC~~c~~~YP 18 (53)
-.++|+.||-.|-
T Consensus 34 Pa~~C~~CGe~y~ 46 (89)
T TIGR03829 34 PSISCSHCGMEYQ 46 (89)
T ss_pred CcccccCCCcEee
Confidence 3589999998883
No 98
>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=39.95 E-value=22 Score=23.08 Aligned_cols=15 Identities=27% Similarity=0.397 Sum_probs=9.9
Q ss_pred eEEcCCCCeeeeeeC
Q 036116 7 SLISDSIGVSFPIKD 21 (53)
Q Consensus 7 ~LiC~~c~~~YPI~d 21 (53)
.|.|+.|+..|++..
T Consensus 18 ~~~C~~C~~~~~f~g 32 (188)
T PF08996_consen 18 KLTCPSCGTEFEFPG 32 (188)
T ss_dssp EEE-TTT--EEEE-S
T ss_pred EeECCCCCCCccccc
Confidence 699999999999876
No 99
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=39.73 E-value=12 Score=17.26 Aligned_cols=8 Identities=13% Similarity=0.405 Sum_probs=5.1
Q ss_pred EEcCCCCe
Q 036116 8 LISDSIGV 15 (53)
Q Consensus 8 LiC~~c~~ 15 (53)
.+|+.||.
T Consensus 3 ~~Cp~Cg~ 10 (26)
T PF13248_consen 3 MFCPNCGA 10 (26)
T ss_pred CCCcccCC
Confidence 45677766
No 100
>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=39.59 E-value=15 Score=17.93 Aligned_cols=11 Identities=18% Similarity=0.507 Sum_probs=8.9
Q ss_pred eEEcCCCCeee
Q 036116 7 SLISDSIGVSF 17 (53)
Q Consensus 7 ~LiC~~c~~~Y 17 (53)
.++|+.||..|
T Consensus 32 ~~~C~~CGE~~ 42 (46)
T TIGR03831 32 ALVCPQCGEEY 42 (46)
T ss_pred ccccccCCCEe
Confidence 46899999776
No 101
>PF05495 zf-CHY: CHY zinc finger; InterPro: IPR008913 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. Pirh2 is an eukaryotic ubiquitin protein ligase, which has been shown to promote p53 degradation in mammals. Pirh2 physically interacts with p53 and promotes ubiquitination of p53 independently of MDM2. Like MDM2, Pirh2 is thought to participate in an autoregulatory feedback loop that controls p53 function. Pirh2 proteins contain three distinct zinc fingers, the CHY-type, the CTCHY-type which is C-terminal to the CHY-type zinc finger and a RING finger. The CHY-type zinc finger has no currently known function []. As well as Pirh2, the CHY-type zinc finger is also found in the following proteins: Yeast helper of Tim protein 13. Hot13 may have a role in the assembly and recycling of the small Tims, a complex of the mitochondrial intermembrane space that participates in the TIM22 import pathway for assembly of the inner membrane [] Several plant hypothetical proteins that also contain haemerythrin cation binding domains Several protozoan hypothetical proteins that also contain a Myb domain The solution structure of this zinc finger has been solved and binds 3 zinc atoms as shown in the following schematic representation: ++---------+-----+ || | | CXHYxxxxxxxxxCCxxxxxCxxCHxxxxxHxxxxxxxxxxxCxxCxxxxxxxxxCxxC | | | | | | | | +-+-----------------+--+ +--+---------+--+ 'C': conserved cysteine involved in the binding of one zinc atom. 'H': conserved histidine involved in the binding of one zinc atom. More information about these proteins can be found at Protein of the Month: Zinc Fingers []; GO: 0008270 zinc ion binding; PDB: 2DKT_A 2K2C_A.
Probab=38.99 E-value=23 Score=19.77 Aligned_cols=12 Identities=17% Similarity=0.354 Sum_probs=8.7
Q ss_pred eEEcCCCCeeee
Q 036116 7 SLISDSIGVSFP 18 (53)
Q Consensus 7 ~LiC~~c~~~YP 18 (53)
.|.|+-|+++||
T Consensus 10 ~~~~~cC~~~y~ 21 (71)
T PF05495_consen 10 AIRFPCCGKYYP 21 (71)
T ss_dssp EEEETTTTEEES
T ss_pred EEECCcccCeec
Confidence 567777777776
No 102
>PRK08329 threonine synthase; Validated
Probab=38.87 E-value=12 Score=26.14 Aligned_cols=12 Identities=17% Similarity=0.243 Sum_probs=10.9
Q ss_pred EEcCCCCeeeee
Q 036116 8 LISDSIGVSFPI 19 (53)
Q Consensus 8 LiC~~c~~~YPI 19 (53)
|.|..|++.|+.
T Consensus 2 l~C~~Cg~~~~~ 13 (347)
T PRK08329 2 LRCTKCGRTYEE 13 (347)
T ss_pred cCcCCCCCCcCC
Confidence 789999999985
No 103
>PRK14811 formamidopyrimidine-DNA glycosylase; Provisional
Probab=38.59 E-value=17 Score=24.93 Aligned_cols=16 Identities=6% Similarity=0.092 Sum_probs=13.4
Q ss_pred CCeEEcCCCCeeeeee
Q 036116 5 TNSLISDSIGVSFPIK 20 (53)
Q Consensus 5 ~g~LiC~~c~~~YPI~ 20 (53)
++...||.|+..+|++
T Consensus 253 R~ty~Cp~CQ~~~~~~ 268 (269)
T PRK14811 253 RGTHFCPQCQPLRPLR 268 (269)
T ss_pred CCcEECCCCcCCCCCC
Confidence 5678999999998875
No 104
>PF01190 Pollen_Ole_e_I: Pollen proteins Ole e I like; InterPro: IPR006041 Allergies are hypersensitivity reactions of the immune system to specific substances called allergens (such as pollen, stings, drugs, or food) that, in most people, result in no symptoms. A nomenclature system has been established for antigens (allergens) that cause IgE-mediated atopic allergies in humans [WHO/IUIS Allergen Nomenclature Subcommittee King T.P., Hoffmann D., Loewenstein H., Marsh D.G., Platts-Mills T.A.E., Thomas W. Bull. World Health Organ. 72:797-806(1994)]. This nomenclature system is defined by a designation that is composed of the first three letters of the genus; a space; the first letter of the species name; a space and an arabic number. In the event that two species names have identical designations, they are discriminated from one another by adding one or more letters (as necessary) to each species designation. The allergens in this family include allergens with the following designations: Ole e 1. A number of plant pollen proteins, whose biological function is not yet known, are structurally related []. These proteins are most probably secreted and consist of about 145 residues. There are six cysteines which are conserved in the sequence of these proteins. They seem to be involved in disulphide bonds.
Probab=38.31 E-value=17 Score=20.83 Aligned_cols=12 Identities=8% Similarity=0.124 Sum_probs=10.0
Q ss_pred CCeEEcCCCCee
Q 036116 5 TNSLISDSIGVS 16 (53)
Q Consensus 5 ~g~LiC~~c~~~ 16 (53)
+|..+|..|...
T Consensus 2 ~G~V~C~~C~~~ 13 (97)
T PF01190_consen 2 EGVVYCDDCSSG 13 (97)
T ss_pred EEEEEeCCCCCC
Confidence 578999999983
No 105
>PLN02436 cellulose synthase A
Probab=38.31 E-value=16 Score=30.49 Aligned_cols=32 Identities=6% Similarity=0.078 Sum_probs=26.8
Q ss_pred CcccCCeEEcCCCCeeeeeeCCccccCCCCCc
Q 036116 1 VCEETNSLISDSIGVSFPIKDGIPSLVPKDGK 32 (53)
Q Consensus 1 ~~~~~g~LiC~~c~~~YPI~dGIPvLL~~ear 32 (53)
|...+|.=.||.|+..|.-..|.|.+--|+..
T Consensus 72 yer~eg~~~Cpqckt~Y~r~kgs~~~~~d~ee 103 (1094)
T PLN02436 72 YERREGNQACPQCKTRYKRIKGSPRVEGDEEE 103 (1094)
T ss_pred hhhhcCCccCcccCCchhhccCCCCcCCcccc
Confidence 45678889999999999999999988876543
No 106
>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 PLN02189 cellulose synthase
Probab=37.79 E-value=17 Score=30.16 Aligned_cols=31 Identities=10% Similarity=0.084 Sum_probs=26.4
Q ss_pred CcccCCeEEcCCCCeeeeeeCCccccCCCCC
Q 036116 1 VCEETNSLISDSIGVSFPIKDGIPSLVPKDG 31 (53)
Q Consensus 1 ~~~~~g~LiC~~c~~~YPI~dGIPvLL~~ea 31 (53)
|...+|.=.||.|+..|.-..|.|.+--|+.
T Consensus 70 yer~eg~q~CpqCkt~Y~r~kgs~~v~gd~e 100 (1040)
T PLN02189 70 YERREGTQNCPQCKTRYKRLKGSPRVEGDDD 100 (1040)
T ss_pred hhhhcCCccCcccCCchhhccCCCCcCCccc
Confidence 4567888999999999999999998887644
No 108
>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=36.81 E-value=37 Score=18.98 Aligned_cols=24 Identities=17% Similarity=0.238 Sum_probs=20.0
Q ss_pred CCeEEcCCCCeeeeeeCCccccCC
Q 036116 5 TNSLISDSIGVSFPIKDGIPSLVP 28 (53)
Q Consensus 5 ~g~LiC~~c~~~YPI~dGIPvLL~ 28 (53)
.+.|+||.-+-.|-+++|-.+=-|
T Consensus 54 ~~~i~CP~Hg~~Fdl~tG~~~~~p 77 (95)
T cd03478 54 DGRIRCPWHGACFNLRTGDIEDAP 77 (95)
T ss_pred CCEEEcCCCCCEEECCCCcCcCCC
Confidence 578999999999999999765434
No 109
>KOG1594 consensus Uncharacterized enzymes related to aldose 1-epimerase [Carbohydrate transport and metabolism]
Probab=36.69 E-value=14 Score=26.83 Aligned_cols=16 Identities=44% Similarity=0.785 Sum_probs=13.0
Q ss_pred eeeeeCCccccCCCCC
Q 036116 16 SFPIKDGIPSLVPKDG 31 (53)
Q Consensus 16 ~YPI~dGIPvLL~~ea 31 (53)
-=||+.|||+..|.=.
T Consensus 68 pKpIRGGIP~~FPQFG 83 (305)
T KOG1594|consen 68 PKPIRGGIPICFPQFG 83 (305)
T ss_pred CCcccCCcceEeeccC
Confidence 3489999999998654
No 110
>cd06918 ChtBD1_like Domain observed in several metazoan proteins. The pattern of conserved cysteine residues resembles that of chitin binding domains found in plants and fungi.
Probab=36.51 E-value=16 Score=19.84 Aligned_cols=13 Identities=38% Similarity=0.836 Sum_probs=11.1
Q ss_pred CCCeeeeeeCCcc
Q 036116 12 SIGVSFPIKDGIP 24 (53)
Q Consensus 12 ~c~~~YPI~dGIP 24 (53)
+|+..||..+|-|
T Consensus 6 rCG~~~p~~~g~~ 18 (51)
T cd06918 6 RCGPKFPLPGGKP 18 (51)
T ss_pred ccCCCccCCCCCc
Confidence 6999999999954
No 111
>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=36.36 E-value=26 Score=19.29 Aligned_cols=25 Identities=16% Similarity=0.262 Sum_probs=20.7
Q ss_pred CeEEcCCCCeeeeeeCCccccCCCC
Q 036116 6 NSLISDSIGVSFPIKDGIPSLVPKD 30 (53)
Q Consensus 6 g~LiC~~c~~~YPI~dGIPvLL~~e 30 (53)
....|+.|+-.++|..|-|.+..+.
T Consensus 33 d~~~C~~~~~~~~I~~G~~~v~i~G 57 (76)
T PF05488_consen 33 DQVTCPKCKGPGPIVEGSPTVFING 57 (76)
T ss_pred CcccCCCccccceeccCCCCccCCc
Confidence 3678999999999999999776654
No 112
>smart00451 ZnF_U1 U1-like zinc finger. Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins.
Probab=35.22 E-value=21 Score=16.49 Aligned_cols=13 Identities=15% Similarity=0.307 Sum_probs=10.3
Q ss_pred CeEEcCCCCeeee
Q 036116 6 NSLISDSIGVSFP 18 (53)
Q Consensus 6 g~LiC~~c~~~YP 18 (53)
+.+.|.-|+..|-
T Consensus 2 ~~~~C~~C~~~~~ 14 (35)
T smart00451 2 GGFYCKLCNVTFT 14 (35)
T ss_pred cCeEccccCCccC
Confidence 4578999998775
No 113
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=34.84 E-value=25 Score=21.35 Aligned_cols=15 Identities=7% Similarity=0.098 Sum_probs=11.9
Q ss_pred CCeEEcCCCCeeeee
Q 036116 5 TNSLISDSIGVSFPI 19 (53)
Q Consensus 5 ~g~LiC~~c~~~YPI 19 (53)
.+.++|+.||..|--
T Consensus 40 ~~h~~C~~CG~y~~~ 54 (99)
T PRK14892 40 IAIITCGNCGLYTEF 54 (99)
T ss_pred cceEECCCCCCccCE
Confidence 467899999988765
No 114
>COG1439 Predicted nucleic acid-binding protein, consists of a PIN domain and a Zn-ribbon module [General function prediction only]
Probab=34.13 E-value=25 Score=23.63 Aligned_cols=14 Identities=21% Similarity=0.183 Sum_probs=12.0
Q ss_pred eEEcCCCCeeeeee
Q 036116 7 SLISDSIGVSFPIK 20 (53)
Q Consensus 7 ~LiC~~c~~~YPI~ 20 (53)
.++|..|++.||..
T Consensus 139 ~~rC~GC~~~f~~~ 152 (177)
T COG1439 139 RLRCHGCKRIFPEP 152 (177)
T ss_pred eEEEecCceecCCC
Confidence 68999999999943
No 115
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=34.05 E-value=24 Score=23.47 Aligned_cols=11 Identities=9% Similarity=0.045 Sum_probs=9.1
Q ss_pred eEEcCCCCeee
Q 036116 7 SLISDSIGVSF 17 (53)
Q Consensus 7 ~LiC~~c~~~Y 17 (53)
-..|+.||+.|
T Consensus 130 f~~C~~CgkiY 140 (165)
T COG1656 130 FYRCPKCGKIY 140 (165)
T ss_pred eeECCCCcccc
Confidence 45699999988
No 116
>PF04475 DUF555: Protein of unknown function (DUF555); InterPro: IPR007564 This is a family of uncharacterised, hypothetical archaeal proteins.
Probab=33.78 E-value=17 Score=22.61 Aligned_cols=16 Identities=19% Similarity=0.192 Sum_probs=12.1
Q ss_pred ccCCeEEcCCCCeeee
Q 036116 3 EETNSLISDSIGVSFP 18 (53)
Q Consensus 3 ~~~g~LiC~~c~~~YP 18 (53)
++-|...||.|+..+.
T Consensus 43 IevG~~~cP~Cge~~~ 58 (102)
T PF04475_consen 43 IEVGDTICPKCGEELD 58 (102)
T ss_pred EecCcccCCCCCCccC
Confidence 3558899999986553
No 117
>PHA00616 hypothetical protein
Probab=33.71 E-value=10 Score=20.16 Aligned_cols=10 Identities=20% Similarity=0.019 Sum_probs=7.8
Q ss_pred EcCCCCeeee
Q 036116 9 ISDSIGVSFP 18 (53)
Q Consensus 9 iC~~c~~~YP 18 (53)
.|+.||..|-
T Consensus 3 qC~~CG~~F~ 12 (44)
T PHA00616 3 QCLRCGGIFR 12 (44)
T ss_pred ccchhhHHHh
Confidence 5899988774
No 118
>KOG3352 consensus Cytochrome c oxidase, subunit Vb/COX4 [Energy production and conversion]
Probab=33.54 E-value=23 Score=23.45 Aligned_cols=16 Identities=13% Similarity=0.135 Sum_probs=12.3
Q ss_pred CeEEcCCCCeeeeeeC
Q 036116 6 NSLISDSIGVSFPIKD 21 (53)
Q Consensus 6 g~LiC~~c~~~YPI~d 21 (53)
..-.|+.||.+|-..+
T Consensus 132 e~~rc~eCG~~fkL~~ 147 (153)
T KOG3352|consen 132 ETQRCPECGHYFKLVP 147 (153)
T ss_pred CcccCCcccceEEeee
Confidence 3456999999998753
No 119
>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=33.45 E-value=27 Score=16.39 Aligned_cols=11 Identities=9% Similarity=0.126 Sum_probs=8.4
Q ss_pred CCeEEcCCCCe
Q 036116 5 TNSLISDSIGV 15 (53)
Q Consensus 5 ~g~LiC~~c~~ 15 (53)
.-...||.||.
T Consensus 14 ~v~f~CPnCG~ 24 (24)
T PF07754_consen 14 AVPFPCPNCGF 24 (24)
T ss_pred CceEeCCCCCC
Confidence 34789999983
No 120
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=33.44 E-value=34 Score=18.94 Aligned_cols=14 Identities=7% Similarity=0.363 Sum_probs=10.7
Q ss_pred cCCeEEcCCCCeee
Q 036116 4 ETNSLISDSIGVSF 17 (53)
Q Consensus 4 ~~g~LiC~~c~~~Y 17 (53)
....++|+.|+.-|
T Consensus 18 ~dDiVvCp~Cgapy 31 (54)
T PF14446_consen 18 GDDIVVCPECGAPY 31 (54)
T ss_pred CCCEEECCCCCCcc
Confidence 45678999998765
No 121
>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=33.24 E-value=28 Score=21.05 Aligned_cols=14 Identities=14% Similarity=0.133 Sum_probs=11.6
Q ss_pred eEEcCCCCeeeeee
Q 036116 7 SLISDSIGVSFPIK 20 (53)
Q Consensus 7 ~LiC~~c~~~YPI~ 20 (53)
--.|+.||.+|-..
T Consensus 79 ~~rC~eCG~~fkL~ 92 (97)
T cd00924 79 PKRCPECGHVFKLV 92 (97)
T ss_pred ceeCCCCCcEEEEE
Confidence 45799999999875
No 122
>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=33.23 E-value=24 Score=18.45 Aligned_cols=10 Identities=10% Similarity=0.049 Sum_probs=5.3
Q ss_pred EcCCCCeeee
Q 036116 9 ISDSIGVSFP 18 (53)
Q Consensus 9 iC~~c~~~YP 18 (53)
.||-|++-|.
T Consensus 22 ~CPlC~r~l~ 31 (54)
T PF04423_consen 22 CCPLCGRPLD 31 (54)
T ss_dssp E-TTT--EE-
T ss_pred cCCCCCCCCC
Confidence 8999998763
No 123
>PF14787 zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB: 1CL4_A 1DSV_A.
Probab=33.22 E-value=18 Score=18.68 Aligned_cols=11 Identities=18% Similarity=0.314 Sum_probs=6.8
Q ss_pred EcCCCCeeeee
Q 036116 9 ISDSIGVSFPI 19 (53)
Q Consensus 9 iC~~c~~~YPI 19 (53)
.|++|++-|-.
T Consensus 4 ~CprC~kg~Hw 14 (36)
T PF14787_consen 4 LCPRCGKGFHW 14 (36)
T ss_dssp C-TTTSSSCS-
T ss_pred cCcccCCCcch
Confidence 58999887643
No 124
>PF01214 CK_II_beta: Casein kinase II regulatory subunit; InterPro: IPR000704 Protein phosphorylation, which plays a key role in most cellular activities, is a reversible process mediated by protein kinases and phosphoprotein phosphatases. Protein kinases catalyse the transfer of the gamma phosphate from nucleotide triphosphates (often ATP) to one or more amino acid residues in a protein substrate side chain, resulting in a conformational change affecting protein function. Phosphoprotein phosphatases catalyse the reverse process. Protein kinases fall into three broad classes, characterised with respect to substrate specificity []: Serine/threonine-protein kinases Tyrosine-protein kinases Dual specific protein kinases (e.g. MEK - phosphorylates both Thr and Tyr on target proteins) Protein kinase function has been evolutionarily conserved from Escherichia coli to human []. Protein kinases play a role in a multitude of cellular processes, including division, proliferation, apoptosis, and differentiation []. Phosphorylation usually results in a functional change of the target protein by changing enzyme activity, cellular location, or association with other proteins. The catalytic subunits of protein kinases are highly conserved, and several structures have been solved [], leading to large screens to develop kinase-specific inhibitors for the treatments of a number of diseases []. Casein kinase, a ubiquitous, well-conserved protein kinase involved in cell metabolism and differentiation, is characterised by its preference for Ser or Thr in acidic stretches of amino acids. The enzyme is a tetramer of 2 alpha- and 2 beta-subunits [, ]. However, some species (e.g., mammals) possess 2 related forms of the alpha-subunit (alpha and alpha'), while others (e.g., fungi) possess 2 related beta-subunits (beta and beta') []. The alpha-subunit is the catalytic unit and contains regions characteristic of serine/threonine protein kinases. The beta-subunit is believed to be regulatory, possessing an N-terminal auto-phosphorylation site, an internal acidic domain, and a potential metal-binding motif []. The beta subunit is a highly conserved protein of about 25kDa that contains, in its central section, a cysteine-rich motif, CX(n)C, that could be involved in binding a metal such as zinc []. The mammalian beta-subunit gene promoter shares common features with those of other mammalian protein kinases and is closely related to the promoter of the regulatory subunit of cAMP-dependent protein kinase [].; GO: 0019887 protein kinase regulator activity, 0005956 protein kinase CK2 complex; PDB: 2R6M_B 1RQF_K 1DS5_G 1QF8_B 3EED_A 4DGL_A 1JWH_D.
Probab=33.07 E-value=30 Score=22.88 Aligned_cols=15 Identities=13% Similarity=-0.037 Sum_probs=11.1
Q ss_pred CCeEEcCCCCeeeee
Q 036116 5 TNSLISDSIGVSFPI 19 (53)
Q Consensus 5 ~g~LiC~~c~~~YPI 19 (53)
.=.|.||+|+-.|-.
T Consensus 125 ~vKlyCP~C~dvY~p 139 (184)
T PF01214_consen 125 TVKLYCPRCKDVYHP 139 (184)
T ss_dssp BBEEEETTTTEEE--
T ss_pred ceeEECCCCccccCC
Confidence 347999999998876
No 125
>PRK06450 threonine synthase; Validated
Probab=32.90 E-value=21 Score=25.09 Aligned_cols=13 Identities=8% Similarity=-0.097 Sum_probs=10.8
Q ss_pred eEEcCCCCeeeee
Q 036116 7 SLISDSIGVSFPI 19 (53)
Q Consensus 7 ~LiC~~c~~~YPI 19 (53)
.|.|..|++.|+.
T Consensus 3 ~~~C~~Cg~~~~~ 15 (338)
T PRK06450 3 KEVCMKCGKERES 15 (338)
T ss_pred eeEECCcCCcCCC
Confidence 4899999999974
No 126
>PF12013 DUF3505: Protein of unknown function (DUF3505); InterPro: IPR022698 This family of proteins is functionally uncharacterised. This protein is found in eukaryotes. Proteins in this family are typically between 247 to 1018 amino acids in length. This region contains two segments that are likely to be C2H2 zinc binding domains.
Probab=32.67 E-value=30 Score=20.27 Aligned_cols=18 Identities=17% Similarity=0.065 Sum_probs=13.2
Q ss_pred CcccCCeEEcCCCCeeee
Q 036116 1 VCEETNSLISDSIGVSFP 18 (53)
Q Consensus 1 ~~~~~g~LiC~~c~~~YP 18 (53)
|...-..|||..|+.+-.
T Consensus 5 y~~~~~vlIC~~C~~av~ 22 (109)
T PF12013_consen 5 YNPEYRVLICRQCQYAVQ 22 (109)
T ss_pred EcCcCCEEEeCCCCcccC
Confidence 455667899999986543
No 127
>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=32.62 E-value=29 Score=16.67 Aligned_cols=13 Identities=8% Similarity=0.135 Sum_probs=9.8
Q ss_pred EEcCCCCeeeeee
Q 036116 8 LISDSIGVSFPIK 20 (53)
Q Consensus 8 LiC~~c~~~YPI~ 20 (53)
.+|+.||..|.-.
T Consensus 2 ~~C~~CGy~y~~~ 14 (33)
T cd00350 2 YVCPVCGYIYDGE 14 (33)
T ss_pred EECCCCCCEECCC
Confidence 4799999887543
No 128
>PRK01402 hslO Hsp33-like chaperonin; Reviewed
Probab=32.19 E-value=30 Score=24.78 Aligned_cols=14 Identities=7% Similarity=0.131 Sum_probs=12.4
Q ss_pred eEEcCCCCeeeeee
Q 036116 7 SLISDSIGVSFPIK 20 (53)
Q Consensus 7 ~LiC~~c~~~YPI~ 20 (53)
++.|.+|+..|-+.
T Consensus 308 ev~CeFC~~~Y~f~ 321 (328)
T PRK01402 308 SVTCEFCSRVYRFD 321 (328)
T ss_pred EEEeeCCCCEEEeC
Confidence 79999999999764
No 129
>PHA02768 hypothetical protein; Provisional
Probab=32.06 E-value=19 Score=19.93 Aligned_cols=16 Identities=6% Similarity=0.069 Sum_probs=12.2
Q ss_pred EEcCCCCeeeeeeCCc
Q 036116 8 LISDSIGVSFPIKDGI 23 (53)
Q Consensus 8 LiC~~c~~~YPI~dGI 23 (53)
..|+.||+.|-..+..
T Consensus 6 y~C~~CGK~Fs~~~~L 21 (55)
T PHA02768 6 YECPICGEIYIKRKSM 21 (55)
T ss_pred cCcchhCCeeccHHHH
Confidence 4799999999876543
No 130
>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=31.99 E-value=13 Score=24.72 Aligned_cols=13 Identities=15% Similarity=0.478 Sum_probs=10.7
Q ss_pred EcCCCCeeeeeeC
Q 036116 9 ISDSIGVSFPIKD 21 (53)
Q Consensus 9 iC~~c~~~YPI~d 21 (53)
+|..||..||-..
T Consensus 70 YC~~CGkpyPWt~ 82 (158)
T PF10083_consen 70 YCHNCGKPYPWTE 82 (158)
T ss_pred hHHhCCCCCchHH
Confidence 6999999999643
No 131
>KOG2906 consensus RNA polymerase III subunit C11 [Transcription]
Probab=31.90 E-value=32 Score=21.54 Aligned_cols=18 Identities=28% Similarity=0.407 Sum_probs=15.5
Q ss_pred CeEEcCCCCeeeeeeCCc
Q 036116 6 NSLISDSIGVSFPIKDGI 23 (53)
Q Consensus 6 g~LiC~~c~~~YPI~dGI 23 (53)
..|.|+.|...|||+.-|
T Consensus 20 ~rf~C~tCpY~~~I~~ei 37 (105)
T KOG2906|consen 20 NRFSCRTCPYVFPISREI 37 (105)
T ss_pred eeEEcCCCCceeeEeeee
Confidence 579999999999998555
No 132
>PF14122 YokU: YokU-like protein
Probab=31.25 E-value=36 Score=20.61 Aligned_cols=15 Identities=20% Similarity=0.550 Sum_probs=12.1
Q ss_pred cCCeEEcCCCCeeee
Q 036116 4 ETNSLISDSIGVSFP 18 (53)
Q Consensus 4 ~~g~LiC~~c~~~YP 18 (53)
+.-.++|..||..|-
T Consensus 32 ~tP~i~C~~CgmvYq 46 (87)
T PF14122_consen 32 DTPAIICSNCGMVYQ 46 (87)
T ss_pred CCceeeecCCCcEEe
Confidence 345799999999984
No 133
>PF07282 OrfB_Zn_ribbon: Putative transposase DNA-binding domain; InterPro: IPR010095 This entry represents a region of a sequence similarity between a family of putative transposases of Thermoanaerobacter tengcongensis, smaller related proteins from Bacillus anthracis, putative transposes described by IPR001959 from INTERPRO, and other proteins. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=30.71 E-value=38 Score=18.08 Aligned_cols=13 Identities=8% Similarity=0.189 Sum_probs=9.7
Q ss_pred CCeEEcCCCCeee
Q 036116 5 TNSLISDSIGVSF 17 (53)
Q Consensus 5 ~g~LiC~~c~~~Y 17 (53)
...+.|+.||..+
T Consensus 44 ~r~~~C~~Cg~~~ 56 (69)
T PF07282_consen 44 GRVFTCPNCGFEM 56 (69)
T ss_pred cceEEcCCCCCEE
Confidence 4578899998764
No 134
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=30.47 E-value=28 Score=21.69 Aligned_cols=19 Identities=26% Similarity=0.545 Sum_probs=13.1
Q ss_pred CeEEcCCCCeeeeeeCCcc
Q 036116 6 NSLISDSIGVSFPIKDGIP 24 (53)
Q Consensus 6 g~LiC~~c~~~YPI~dGIP 24 (53)
+...|+.|++.|-+..|=|
T Consensus 52 qRyrC~~C~~tf~~~~~~~ 70 (129)
T COG3677 52 QRYKCKSCGSTFTVETGSP 70 (129)
T ss_pred cccccCCcCcceeeeccCc
Confidence 4566777777777776655
No 135
>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=30.40 E-value=22 Score=18.91 Aligned_cols=11 Identities=27% Similarity=0.344 Sum_probs=8.8
Q ss_pred EEcCCCCeeee
Q 036116 8 LISDSIGVSFP 18 (53)
Q Consensus 8 LiC~~c~~~YP 18 (53)
=+|+.|++-|-
T Consensus 9 K~C~~C~rpf~ 19 (42)
T PF10013_consen 9 KICPVCGRPFT 19 (42)
T ss_pred CcCcccCCcch
Confidence 47999998874
No 136
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=30.08 E-value=22 Score=18.53 Aligned_cols=11 Identities=27% Similarity=0.374 Sum_probs=7.2
Q ss_pred eEEcCCCCeee
Q 036116 7 SLISDSIGVSF 17 (53)
Q Consensus 7 ~LiC~~c~~~Y 17 (53)
.+.||.|+..|
T Consensus 2 ~f~CP~C~~~~ 12 (54)
T PF05605_consen 2 SFTCPYCGKGF 12 (54)
T ss_pred CcCCCCCCCcc
Confidence 46677777743
No 137
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=30.05 E-value=49 Score=16.82 Aligned_cols=13 Identities=31% Similarity=0.478 Sum_probs=9.3
Q ss_pred CCeEEcCCCCeee
Q 036116 5 TNSLISDSIGVSF 17 (53)
Q Consensus 5 ~g~LiC~~c~~~Y 17 (53)
...+.|+.|+..|
T Consensus 38 ~~~v~C~~C~~~f 50 (64)
T smart00647 38 CNRVTCPKCGFSF 50 (64)
T ss_pred CCeeECCCCCCeE
Confidence 3567788887776
No 138
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]
Probab=29.99 E-value=33 Score=24.20 Aligned_cols=15 Identities=13% Similarity=0.237 Sum_probs=12.1
Q ss_pred cccCCeEEcCCCCee
Q 036116 2 CEETNSLISDSIGVS 16 (53)
Q Consensus 2 ~~~~g~LiC~~c~~~ 16 (53)
|.+.|+++|..||..
T Consensus 15 d~~~ge~VC~~CG~V 29 (285)
T COG1405 15 DYERGEIVCADCGLV 29 (285)
T ss_pred eccCCeEEeccCCEE
Confidence 345799999999974
No 139
>PTZ00088 adenylate kinase 1; Provisional
Probab=29.98 E-value=22 Score=23.76 Aligned_cols=15 Identities=20% Similarity=0.306 Sum_probs=13.3
Q ss_pred CeEEcCCCCeeeeee
Q 036116 6 NSLISDSIGVSFPIK 20 (53)
Q Consensus 6 g~LiC~~c~~~YPI~ 20 (53)
+..+|+.||+.|-+.
T Consensus 129 ~Rr~~~~~g~~y~~~ 143 (229)
T PTZ00088 129 GRRICNTCNRNFNIA 143 (229)
T ss_pred cCcCCCccCCcceec
Confidence 568999999999986
No 140
>PF14311 DUF4379: Domain of unknown function (DUF4379)
Probab=29.81 E-value=32 Score=17.97 Aligned_cols=12 Identities=8% Similarity=0.005 Sum_probs=9.7
Q ss_pred eEEcCCCCeeee
Q 036116 7 SLISDSIGVSFP 18 (53)
Q Consensus 7 ~LiC~~c~~~YP 18 (53)
.-.|+.|++.|.
T Consensus 28 ~W~C~~Cgh~w~ 39 (55)
T PF14311_consen 28 WWKCPKCGHEWK 39 (55)
T ss_pred EEECCCCCCeeE
Confidence 357999999885
No 141
>KOG1407 consensus WD40 repeat protein [Function unknown]
Probab=29.63 E-value=14 Score=26.93 Aligned_cols=15 Identities=20% Similarity=0.671 Sum_probs=13.3
Q ss_pred CeEEcCCC--Ceeeeee
Q 036116 6 NSLISDSI--GVSFPIK 20 (53)
Q Consensus 6 g~LiC~~c--~~~YPI~ 20 (53)
.+|+|.+| ++.||||
T Consensus 219 ~ELiC~R~isRldwpVR 235 (313)
T KOG1407|consen 219 DELICERCISRLDWPVR 235 (313)
T ss_pred hHhhhheeeccccCceE
Confidence 57999998 8999997
No 142
>PF07503 zf-HYPF: HypF finger; InterPro: IPR011125 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. Proteins of the HypF family are involved in the maturation and regulation of hydrogenase []. In the N terminus they appear to have two zinc finger domains that are similar to those found in the DnaJ chaperone []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3TTD_A 3TSQ_A 3TTC_A 3TSP_A 3TTF_A 3TSU_A.
Probab=28.70 E-value=33 Score=17.17 Aligned_cols=15 Identities=20% Similarity=0.330 Sum_probs=9.4
Q ss_pred eEEcCCCCeeeeeeC
Q 036116 7 SLISDSIGVSFPIKD 21 (53)
Q Consensus 7 ~LiC~~c~~~YPI~d 21 (53)
...|+.||-.|-|.|
T Consensus 21 ~isC~~CGPr~~i~~ 35 (35)
T PF07503_consen 21 FISCTNCGPRYSIID 35 (35)
T ss_dssp T--BTTCC-SCCCES
T ss_pred CccCCCCCCCEEEeC
Confidence 467999998887754
No 143
>PF01428 zf-AN1: AN1-like Zinc finger; InterPro: IPR000058 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 AN1-type zinc finger domain, which has a dimetal (zinc)-bound alpha/beta fold. This domain was first identified as a zinc finger at the C terminus of AN1 Q91889 from SWISSPROT, a ubiquitin-like protein in Xenopus laevis []. The AN1-type zinc finger contains six conserved cysteines and two histidines that could potentially coordinate 2 zinc atoms. Certain stress-associated proteins (SAP) contain AN1 domain, often in combination with A20 zinc finger domains (SAP8) or C2H2 domains (SAP16) []. For example, the human protein Znf216 has an A20 zinc-finger at the N terminus and an AN1 zinc-finger at the C terminus, acting to negatively regulate the NFkappaB activation pathway and to interact with components of the immune response like RIP, IKKgamma and TRAF6. The interact of Znf216 with IKK-gamma and RIP is mediated by the A20 zinc-finger domain, while its interaction with TRAF6 is mediated by the AN1 zinc-finger domain; therefore, both zinc-finger domains are involved in regulating the immune response []. The AN1 zinc finger domain is also found in proteins containing a ubiquitin-like domain, which are involved in the ubiquitination pathway []. Proteins containing an AN1-type zinc finger include: Ascidian posterior end mark 6 (pem-6) protein []. Human AWP1 protein (associated with PRK1), which is expressed during early embryogenesis []. Human immunoglobulin mu binding protein 2 (SMUBP-2), mutations in which cause muscular atrophy with respiratory distress type 1 []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 1WFP_A 1WYS_A 1WG2_A 1WFH_A 1X4W_A 1WFE_A 1WFL_A 1X4V_A.
Probab=28.28 E-value=40 Score=16.96 Aligned_cols=15 Identities=27% Similarity=0.379 Sum_probs=9.0
Q ss_pred eEEcCCCCeeeeeeC
Q 036116 7 SLISDSIGVSFPIKD 21 (53)
Q Consensus 7 ~LiC~~c~~~YPI~d 21 (53)
.+.|+.|+..|=++.
T Consensus 13 ~~~C~~C~~~FC~~H 27 (43)
T PF01428_consen 13 PFKCKHCGKSFCLKH 27 (43)
T ss_dssp HEE-TTTS-EE-TTT
T ss_pred CeECCCCCcccCccc
Confidence 478999998885543
No 144
>PF06170 DUF983: Protein of unknown function (DUF983); InterPro: IPR009325 This family consists of several bacterial proteins of unknown function.
Probab=28.28 E-value=22 Score=20.89 Aligned_cols=12 Identities=8% Similarity=0.210 Sum_probs=9.5
Q ss_pred EcCCCCeeeeee
Q 036116 9 ISDSIGVSFPIK 20 (53)
Q Consensus 9 iC~~c~~~YPI~ 20 (53)
.|+.||..|--.
T Consensus 10 ~C~~CG~d~~~~ 21 (86)
T PF06170_consen 10 RCPHCGLDYSHA 21 (86)
T ss_pred cccccCCccccC
Confidence 599999888654
No 145
>PF05443 ROS_MUCR: ROS/MUCR transcriptional regulator protein; InterPro: IPR008807 This family consists of several ROS/MUCR transcriptional regulator proteins. The ros chromosomal gene is present in octopine and nopaline strains of Agrobacterium tumefaciens as well as in Rhizobium meliloti (Sinorhizobium meliloti). This gene encodes a 15.5 kDa protein that specifically represses the virC and virD operons in the virulence region of the Ti plasmid [] and is necessary for succinoglycan production []. S. meliloti can produce two types of acidic exopolysaccharides, succinoglycan and galactoglucan, that are interchangeable for infection of Medicago sativa (Alfalfa) nodules. MucR from S. meliloti acts as a transcriptional repressor that blocks the expression of the exp genes responsible for galactoglucan production therefore allowing the exclusive production of succinoglycan [].; GO: 0003677 DNA binding, 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2JSP_A.
Probab=28.22 E-value=37 Score=21.60 Aligned_cols=16 Identities=19% Similarity=0.274 Sum_probs=9.0
Q ss_pred cCCeEEcCCCCeeeee
Q 036116 4 ETNSLISDSIGVSFPI 19 (53)
Q Consensus 4 ~~g~LiC~~c~~~YPI 19 (53)
....++|-.||+.|..
T Consensus 69 ~~d~i~clecGk~~k~ 84 (132)
T PF05443_consen 69 TPDYIICLECGKKFKT 84 (132)
T ss_dssp -SS-EE-TBT--EESB
T ss_pred ccCeeEEccCCcccch
Confidence 4578999999998864
No 146
>PLN02459 probable adenylate kinase
Probab=28.03 E-value=29 Score=24.16 Aligned_cols=16 Identities=19% Similarity=0.314 Sum_probs=14.0
Q ss_pred CCeEEcCCCCeeeeee
Q 036116 5 TNSLISDSIGVSFPIK 20 (53)
Q Consensus 5 ~g~LiC~~c~~~YPI~ 20 (53)
.|..+|+.||+.|-+.
T Consensus 151 ~gR~~~~~~g~~Yn~~ 166 (261)
T PLN02459 151 LGRRICSECGKNFNVA 166 (261)
T ss_pred hccccccccCcccccc
Confidence 4678999999999985
No 147
>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=27.71 E-value=46 Score=16.56 Aligned_cols=13 Identities=8% Similarity=0.056 Sum_probs=8.4
Q ss_pred CCeEEcCCCCeee
Q 036116 5 TNSLISDSIGVSF 17 (53)
Q Consensus 5 ~g~LiC~~c~~~Y 17 (53)
...+.|+.|++..
T Consensus 2 ~~~~~C~nC~R~v 14 (33)
T PF08209_consen 2 SPYVECPNCGRPV 14 (33)
T ss_dssp S-EEE-TTTSSEE
T ss_pred CCeEECCCCcCCc
Confidence 3568999999853
No 148
>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=27.49 E-value=64 Score=17.74 Aligned_cols=22 Identities=5% Similarity=-0.044 Sum_probs=17.1
Q ss_pred CCeEEcCCCCeeeeeeCCcccc
Q 036116 5 TNSLISDSIGVSFPIKDGIPSL 26 (53)
Q Consensus 5 ~g~LiC~~c~~~YPI~dGIPvL 26 (53)
.-++-||+|+..+-|+--.|-.
T Consensus 22 ~leIKCpRC~tiN~~~a~~~~~ 43 (51)
T PF10122_consen 22 ELEIKCPRCKTINHVRATSPEP 43 (51)
T ss_pred EEEEECCCCCccceEeccCCCC
Confidence 3578899999999888766643
No 149
>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=27.49 E-value=34 Score=21.98 Aligned_cols=15 Identities=20% Similarity=0.193 Sum_probs=12.2
Q ss_pred eEEcCCCCeeeeeeC
Q 036116 7 SLISDSIGVSFPIKD 21 (53)
Q Consensus 7 ~LiC~~c~~~YPI~d 21 (53)
.-.|+.||.+|-+..
T Consensus 112 ~~RCpeCG~~fkL~~ 126 (136)
T PF01215_consen 112 PQRCPECGQVFKLKY 126 (136)
T ss_dssp EEEETTTEEEEEEEE
T ss_pred ccCCCCCCeEEEEEE
Confidence 458999999998753
No 150
>PF03711 OKR_DC_1_C: Orn/Lys/Arg decarboxylase, C-terminal domain; InterPro: IPR008286 Pyridoxal-dependent decarboxylases are bacterial proteins acting on ornithine, lysine, arginine and related substrates []. One of the regions of sequence similarity contains a conserved lysine residue, which is the site of attachment of the pyridoxal-phosphate group.; GO: 0003824 catalytic activity; PDB: 1C4K_A 1ORD_A 3Q16_C 3N75_A 2X3L_A 2VYC_D.
Probab=27.34 E-value=24 Score=22.31 Aligned_cols=16 Identities=44% Similarity=0.735 Sum_probs=9.6
Q ss_pred eeeeCCccccCCCCCc
Q 036116 17 FPIKDGIPSLVPKDGK 32 (53)
Q Consensus 17 YPI~dGIPvLL~~ear 32 (53)
+|===|||+|+|.|-.
T Consensus 83 ~pYPPGIPll~pGE~i 98 (136)
T PF03711_consen 83 VPYPPGIPLLVPGERI 98 (136)
T ss_dssp EECTTTS-SB-TTEEB
T ss_pred eecCCCCcEECCcccc
Confidence 3444699999998744
No 151
>PF14570 zf-RING_4: RING/Ubox like zinc-binding domain; PDB: 1E4U_A 1UR6_B.
Probab=27.24 E-value=27 Score=18.85 Aligned_cols=12 Identities=0% Similarity=-0.114 Sum_probs=5.8
Q ss_pred CeEEcCCCCeee
Q 036116 6 NSLISDSIGVSF 17 (53)
Q Consensus 6 g~LiC~~c~~~Y 17 (53)
+.=.||.|++.|
T Consensus 36 ~~g~CPgCr~~Y 47 (48)
T PF14570_consen 36 EGGRCPGCREPY 47 (48)
T ss_dssp S-SB-TTT--B-
T ss_pred cCCCCCCCCCCC
Confidence 566899999988
No 152
>KOG0978 consensus E3 ubiquitin ligase involved in syntaxin degradation [Posttranslational modification, protein turnover, chaperones]
Probab=26.87 E-value=30 Score=27.62 Aligned_cols=18 Identities=11% Similarity=-0.036 Sum_probs=13.4
Q ss_pred EcCCCCeeeeeeCCcccc
Q 036116 9 ISDSIGVSFPIKDGIPSL 26 (53)
Q Consensus 9 iC~~c~~~YPI~dGIPvL 26 (53)
-||.|+.+|-..|=.||-
T Consensus 680 KCP~Cn~aFganDv~~I~ 697 (698)
T KOG0978|consen 680 KCPKCNAAFGANDVHRIH 697 (698)
T ss_pred CCCCCCCCCCcccccccC
Confidence 488888888777766654
No 153
>PF14569 zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.
Probab=26.77 E-value=16 Score=21.82 Aligned_cols=28 Identities=7% Similarity=0.221 Sum_probs=11.3
Q ss_pred ccCCeEEcCCCCeeeeeeCCccccCCCC
Q 036116 3 EETNSLISDSIGVSFPIKDGIPSLVPKD 30 (53)
Q Consensus 3 ~~~g~LiC~~c~~~YPI~dGIPvLL~~e 30 (53)
..+|.-.|++|+-.|-=..|-|-+.-++
T Consensus 47 rkeg~q~CpqCkt~ykr~kgsp~V~gDe 74 (80)
T PF14569_consen 47 RKEGNQVCPQCKTRYKRHKGSPRVEGDE 74 (80)
T ss_dssp HHTS-SB-TTT--B----TT----TTS-
T ss_pred hhcCcccccccCCCcccccCCCCCCCCc
Confidence 4567789999999999888888665544
No 154
>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=26.44 E-value=35 Score=16.76 Aligned_cols=14 Identities=29% Similarity=0.518 Sum_probs=6.7
Q ss_pred EcCCCCeeeeeeCC
Q 036116 9 ISDSIGVSFPIKDG 22 (53)
Q Consensus 9 iC~~c~~~YPI~dG 22 (53)
+|..|+..+.|+.+
T Consensus 2 ~C~~Cg~~~~~~~~ 15 (32)
T PF03604_consen 2 ICGECGAEVELKPG 15 (32)
T ss_dssp BESSSSSSE-BSTS
T ss_pred CCCcCCCeeEcCCC
Confidence 35555555554433
No 155
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=26.30 E-value=46 Score=22.62 Aligned_cols=13 Identities=23% Similarity=0.245 Sum_probs=10.3
Q ss_pred cCCeEEcCCCCee
Q 036116 4 ETNSLISDSIGVS 16 (53)
Q Consensus 4 ~~g~LiC~~c~~~ 16 (53)
.+..|.||.|+..
T Consensus 162 ~~~~l~Cp~Cg~t 174 (188)
T COG1096 162 KGNMLKCPNCGNT 174 (188)
T ss_pred cCcEEECCCCCCE
Confidence 4678999999853
No 156
>COG0267 RpmG Ribosomal protein L33 [Translation, ribosomal structure and biogenesis]
Probab=26.22 E-value=43 Score=18.24 Aligned_cols=14 Identities=7% Similarity=0.143 Sum_probs=11.3
Q ss_pred eEEcCCCC-eeeeee
Q 036116 7 SLISDSIG-VSFPIK 20 (53)
Q Consensus 7 ~LiC~~c~-~~YPI~ 20 (53)
.|.|..|+ +.|--.
T Consensus 7 ~L~ct~c~g~nY~t~ 21 (50)
T COG0267 7 KLACTACTSRNYTTT 21 (50)
T ss_pred EEEEeccCCeeEEEe
Confidence 69999999 888653
No 157
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=26.13 E-value=27 Score=22.48 Aligned_cols=10 Identities=20% Similarity=0.245 Sum_probs=8.3
Q ss_pred EcCCCCeeee
Q 036116 9 ISDSIGVSFP 18 (53)
Q Consensus 9 iC~~c~~~YP 18 (53)
.|..||+.|+
T Consensus 3 ~Ct~Cg~~f~ 12 (131)
T PF09845_consen 3 QCTKCGRVFE 12 (131)
T ss_pred ccCcCCCCcC
Confidence 4888998887
No 158
>PF03811 Zn_Tnp_IS1: InsA N-terminal domain; InterPro: IPR003220 Insertion elements are mobile elements in DNA, usually encoding proteins required for transposition, for example transposases. Protein InsA is absolutely required for transposition of insertion element 1. This entry represents a short zinc binding domain found in IS1 InsA family protein. It is found at the N terminus of the protein and may be a DNA-binding domain.; GO: 0006313 transposition, DNA-mediated
Probab=25.81 E-value=54 Score=16.42 Aligned_cols=16 Identities=13% Similarity=0.042 Sum_probs=11.8
Q ss_pred eEEcCCCCeee-eeeCC
Q 036116 7 SLISDSIGVSF-PIKDG 22 (53)
Q Consensus 7 ~LiC~~c~~~Y-PI~dG 22 (53)
.+.||+|+..= -+++|
T Consensus 5 ~v~CP~C~s~~~v~k~G 21 (36)
T PF03811_consen 5 DVHCPRCQSTEGVKKNG 21 (36)
T ss_pred eeeCCCCCCCCcceeCC
Confidence 57899998766 55555
No 159
>COG1743 Adenine-specific DNA methylase containing a Zn-ribbon [DNA replication, recombination, and repair]
Probab=25.52 E-value=37 Score=27.90 Aligned_cols=15 Identities=13% Similarity=0.160 Sum_probs=12.5
Q ss_pred eEEcCCCCeeeeeeC
Q 036116 7 SLISDSIGVSFPIKD 21 (53)
Q Consensus 7 ~LiC~~c~~~YPI~d 21 (53)
+.-||.||+.+|...
T Consensus 178 ~VkCP~CG~~tP~vg 192 (875)
T COG1743 178 EVKCPRCGRLTPLVG 192 (875)
T ss_pred EEecCCcCccccCcc
Confidence 578999999999643
No 160
>COG4338 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=25.31 E-value=19 Score=20.01 Aligned_cols=11 Identities=18% Similarity=0.123 Sum_probs=8.7
Q ss_pred EEcCCCCeeee
Q 036116 8 LISDSIGVSFP 18 (53)
Q Consensus 8 LiC~~c~~~YP 18 (53)
-||+.|++-|-
T Consensus 13 KICpvCqRPFs 23 (54)
T COG4338 13 KICPVCQRPFS 23 (54)
T ss_pred hhhhhhcCchH
Confidence 48999998764
No 161
>TIGR02378 nirD_assim_sml nitrite reductase [NAD(P)H], small subunit. This model describes NirD, the small subunit of nitrite reductase [NAD(P)H] (the assimilatory nitrite reductase), which associates with NirB, the large subunit (TIGR02374). In a few bacteria such as Klebsiella pneumoniae and in Fungi, the two regions are fused.
Probab=25.20 E-value=59 Score=18.54 Aligned_cols=19 Identities=16% Similarity=0.079 Sum_probs=16.8
Q ss_pred eEEcCCCCeeeeeeCCccc
Q 036116 7 SLISDSIGVSFPIKDGIPS 25 (53)
Q Consensus 7 ~LiC~~c~~~YPI~dGIPv 25 (53)
.|+||..+-.|-+++|-++
T Consensus 64 ~i~Cp~Hg~~Fdl~tG~~~ 82 (105)
T TIGR02378 64 WVACPLHKRNFRLEDGRCL 82 (105)
T ss_pred EEECCcCCCEEEcCCcccc
Confidence 3999999999999999654
No 162
>PLN02294 cytochrome c oxidase subunit Vb
Probab=25.00 E-value=42 Score=22.60 Aligned_cols=14 Identities=14% Similarity=0.116 Sum_probs=11.7
Q ss_pred eEEcCCCCeeeeee
Q 036116 7 SLISDSIGVSFPIK 20 (53)
Q Consensus 7 ~LiC~~c~~~YPI~ 20 (53)
--.|+.||..|-.+
T Consensus 141 p~RCpeCG~~fkL~ 154 (174)
T PLN02294 141 SFECPVCTQYFELE 154 (174)
T ss_pred ceeCCCCCCEEEEE
Confidence 34699999999887
No 163
>PRK09965 3-phenylpropionate dioxygenase ferredoxin subunit; Provisional
Probab=24.96 E-value=74 Score=18.34 Aligned_cols=20 Identities=15% Similarity=0.174 Sum_probs=18.0
Q ss_pred CeEEcCCCCeeeeeeCCccc
Q 036116 6 NSLISDSIGVSFPIKDGIPS 25 (53)
Q Consensus 6 g~LiC~~c~~~YPI~dGIPv 25 (53)
+.++||--+-.|-+++|-++
T Consensus 58 ~~i~Cp~Hg~~Fd~~tG~~~ 77 (106)
T PRK09965 58 ATVECPLHAASFCLRTGKAL 77 (106)
T ss_pred CEEEcCCCCCEEEcCCCCee
Confidence 57999999999999999875
No 164
>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=24.90 E-value=29 Score=24.37 Aligned_cols=22 Identities=18% Similarity=0.265 Sum_probs=15.2
Q ss_pred CeEEcCCCCeeeee--eCCccccC
Q 036116 6 NSLISDSIGVSFPI--KDGIPSLV 27 (53)
Q Consensus 6 g~LiC~~c~~~YPI--~dGIPvLL 27 (53)
+.-+||.|++.|++ ++-|-.|+
T Consensus 44 ~~~vc~~c~~h~rl~areRi~~L~ 67 (285)
T TIGR00515 44 NLEVCPKCDHHMRMDARERIESLL 67 (285)
T ss_pred hCCCCCCCCCcCcCCHHHHHHHce
Confidence 45699999999987 34444433
No 165
>PRK03922 hypothetical protein; Provisional
Probab=24.65 E-value=32 Score=21.80 Aligned_cols=15 Identities=27% Similarity=0.322 Sum_probs=11.6
Q ss_pred cCCeEEcCCCCeeee
Q 036116 4 ETNSLISDSIGVSFP 18 (53)
Q Consensus 4 ~~g~LiC~~c~~~YP 18 (53)
+-|...||.|+..|.
T Consensus 46 evG~~~cP~cge~~~ 60 (113)
T PRK03922 46 EVGLTICPKCGEPFD 60 (113)
T ss_pred ecCcccCCCCCCcCC
Confidence 457889999987654
No 166
>PTZ00396 Casein kinase II subunit beta; Provisional
Probab=24.37 E-value=34 Score=23.95 Aligned_cols=17 Identities=6% Similarity=-0.035 Sum_probs=13.0
Q ss_pred CCeEEcCCCCeeeeeeC
Q 036116 5 TNSLISDSIGVSFPIKD 21 (53)
Q Consensus 5 ~g~LiC~~c~~~YPI~d 21 (53)
.=.|+||+|+-.|--+.
T Consensus 146 ~VKlyCP~C~DvY~p~s 162 (251)
T PTZ00396 146 RVKVYCPRCQEVYHPKK 162 (251)
T ss_pred ceeEeCCCchhhcCCCC
Confidence 34699999999996544
No 167
>PF10601 zf-LITAF-like: LITAF-like zinc ribbon domain; InterPro: IPR006629 Members of this family display a conserved zinc ribbon structure [] with the motif C-XX-C- separated from the more C-terminal HX-C(P)X-C-X4-G-R motif by a variable region of usually 25-30 (hydrophobic) residues. Although it belongs to one of the zinc finger's fold groups (zinc ribbon), this particular domain was first identified in LPS-induced tumour necrosis alpha factor (LITAF) which is produced in mammalian cells after being challenged with lipopolysaccharide (LPS). The hydrophobic region probably inserts into the membrane rather than traversing it. Such an insertion brings together the N- and C-terminal C-XX-C motifs to form a compact Zn2+-binding structure [].
Probab=24.28 E-value=66 Score=17.60 Aligned_cols=14 Identities=7% Similarity=-0.121 Sum_probs=10.4
Q ss_pred cccCCeEEcCCCCe
Q 036116 2 CEETNSLISDSIGV 15 (53)
Q Consensus 2 ~~~~g~LiC~~c~~ 15 (53)
......+.||.|+.
T Consensus 2 ~~~p~~~~CP~C~~ 15 (73)
T PF10601_consen 2 GPEPVRIYCPYCQQ 15 (73)
T ss_pred CCCceeeECCCCCC
Confidence 34556799999975
No 168
>PF05864 Chordopox_RPO7: Chordopoxvirus DNA-directed RNA polymerase 7 kDa polypeptide (RPO7); InterPro: IPR008448 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. This family consists of several Chordopoxvirus DNA-directed RNA polymerase 7 kDa polypeptide sequences. DNA-dependent RNA polymerase catalyses the transcription of DNA into RNA [].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent
Probab=24.27 E-value=38 Score=19.43 Aligned_cols=10 Identities=20% Similarity=0.448 Sum_probs=8.1
Q ss_pred eEEcCCCCee
Q 036116 7 SLISDSIGVS 16 (53)
Q Consensus 7 ~LiC~~c~~~ 16 (53)
.|+|..||+-
T Consensus 4 ~lvCSTCGrD 13 (63)
T PF05864_consen 4 QLVCSTCGRD 13 (63)
T ss_pred eeeecccCCc
Confidence 5899999864
No 169
>cd03529 Rieske_NirD Assimilatory nitrite reductase (NirD) family, Rieske domain; Assimilatory nitrate and nitrite reductases convert nitrate through nitrite to ammonium. Members include bacterial and fungal proteins. The bacterial NirD contains a single Rieske domain while fungal proteins have a C-terminal Rieske domain in addition to several other domains. The fungal NirD is involved in nutrient acquisition, functioning at the soil/fungus interface to control nutrient exchange between the fungus and the host plant. The Rieske domain is a [2Fe-2S] cluster binding domain involved in electron transfer. The Rieske [2Fe-2S] cluster is liganded to two histidine and two cysteine residues present in conserved sequences called Rieske motifs. In this family, only a few members contain these residues. Other members may have lost the ability to bind the Rieske [2Fe-2S] cluster.
Probab=24.18 E-value=70 Score=18.24 Aligned_cols=22 Identities=18% Similarity=0.028 Sum_probs=18.8
Q ss_pred CeEEcCCCCeeeeeeCCccccC
Q 036116 6 NSLISDSIGVSFPIKDGIPSLV 27 (53)
Q Consensus 6 g~LiC~~c~~~YPI~dGIPvLL 27 (53)
+.|+||.-+-.|-+++|-.+--
T Consensus 62 ~~i~Cp~Hg~~Fdl~tG~~~~~ 83 (103)
T cd03529 62 PVVASPLYKQHFSLKTGRCLED 83 (103)
T ss_pred eEEECCCCCCEEEcCCCCccCC
Confidence 4799999999999999987543
No 170
>PHA00626 hypothetical protein
Probab=23.96 E-value=39 Score=19.21 Aligned_cols=16 Identities=13% Similarity=-0.041 Sum_probs=10.2
Q ss_pred EcCCCCeeeeeeCCcc
Q 036116 9 ISDSIGVSFPIKDGIP 24 (53)
Q Consensus 9 iC~~c~~~YPI~dGIP 24 (53)
.||.||..=-|+.||=
T Consensus 2 ~CP~CGS~~Ivrcg~c 17 (59)
T PHA00626 2 SCPKCGSGNIAKEKTM 17 (59)
T ss_pred CCCCCCCceeeeecee
Confidence 5777777555566653
No 171
>COG1545 Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]
Probab=23.70 E-value=46 Score=20.84 Aligned_cols=10 Identities=10% Similarity=0.165 Sum_probs=7.0
Q ss_pred EEcCCCCeee
Q 036116 8 LISDSIGVSF 17 (53)
Q Consensus 8 LiC~~c~~~Y 17 (53)
-.|+.||+.|
T Consensus 30 ~kC~~CG~v~ 39 (140)
T COG1545 30 TKCKKCGRVY 39 (140)
T ss_pred EEcCCCCeEE
Confidence 4688888654
No 172
>PLN02674 adenylate kinase
Probab=23.25 E-value=42 Score=22.93 Aligned_cols=20 Identities=30% Similarity=0.322 Sum_probs=16.6
Q ss_pred CCeEEcCCCCeeeeeeCCcc
Q 036116 5 TNSLISDSIGVSFPIKDGIP 24 (53)
Q Consensus 5 ~g~LiC~~c~~~YPI~dGIP 24 (53)
.+..+|+.||+.|.+...=|
T Consensus 156 ~gR~~~~~~g~~yn~~~~pp 175 (244)
T PLN02674 156 TGRWIHPSSGRTYHTKFAPP 175 (244)
T ss_pred hccccccccCCccccccCCC
Confidence 47889999999999876555
No 173
>TIGR00311 aIF-2beta translation initiation factor aIF-2, beta subunit, putative.
Probab=23.25 E-value=41 Score=21.25 Aligned_cols=14 Identities=21% Similarity=0.482 Sum_probs=11.8
Q ss_pred eEEcCCCCeeeeee
Q 036116 7 SLISDSIGVSFPIK 20 (53)
Q Consensus 7 ~LiC~~c~~~YPI~ 20 (53)
.|.|..||...||.
T Consensus 118 ~l~C~ACGa~~~v~ 131 (133)
T TIGR00311 118 LLKCEACGAKAPLR 131 (133)
T ss_pred EEecccCCCCCccC
Confidence 47899999998884
No 174
>PRK08116 hypothetical protein; Validated
Probab=23.10 E-value=36 Score=23.11 Aligned_cols=16 Identities=19% Similarity=0.219 Sum_probs=12.1
Q ss_pred ccCCeEEcCCCCeeee
Q 036116 3 EETNSLISDSIGVSFP 18 (53)
Q Consensus 3 ~~~g~LiC~~c~~~YP 18 (53)
.+.+.+.|+.||..+.
T Consensus 12 ~~~~~~~C~~Cg~~~~ 27 (268)
T PRK08116 12 EEDGGEYCEVCGKRIE 27 (268)
T ss_pred ccccCccCcCCCCcce
Confidence 3568899999997543
No 175
>TIGR02377 MocE_fam_FeS Rieske [2Fe-2S] domain protein, MocE subfamily. This model describes a subfamily of the Rieske-like [2Fe-2S] family of ferredoxins that includes MocE, part of the rhizopine (3-O-methyl-scyllo-inosamine) catabolic cluster in Rhizobium. Members of this family are related to, yet distinct from, the small subunit of nitrite reductase [NAD(P)H].
Probab=23.00 E-value=79 Score=18.10 Aligned_cols=22 Identities=9% Similarity=0.064 Sum_probs=18.4
Q ss_pred cCCeEEcCCCCeeeeeeCCccc
Q 036116 4 ETNSLISDSIGVSFPIKDGIPS 25 (53)
Q Consensus 4 ~~g~LiC~~c~~~YPI~dGIPv 25 (53)
..+.+.||-=+-.|-+++|=+.
T Consensus 56 ~~~~i~CP~Hg~~Fdl~tG~~~ 77 (101)
T TIGR02377 56 MDTTVECPKHAGCFDYRTGEAL 77 (101)
T ss_pred cCCEEECCccCCEEECCCCccc
Confidence 3468999999999999999553
No 176
>CHL00037 petA cytochrome f
Probab=22.99 E-value=37 Score=24.88 Aligned_cols=26 Identities=19% Similarity=0.353 Sum_probs=19.3
Q ss_pred ccCCeEEcCCCCee-eeeeCCccccCC
Q 036116 3 EETNSLISDSIGVS-FPIKDGIPSLVP 28 (53)
Q Consensus 3 ~~~g~LiC~~c~~~-YPI~dGIPvLL~ 28 (53)
+.+|.++|-.|+++ .||+=-+|.=+.
T Consensus 49 EAtGrIVCANCHLA~KpveiEvPQaVl 75 (320)
T CHL00037 49 EATGRIVCANCHLANKPVDIEVPQAVL 75 (320)
T ss_pred hhcCcEEeeccccccCceeeecccccC
Confidence 46799999999875 677766765433
No 177
>TIGR00595 priA primosomal protein N'. All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=22.97 E-value=46 Score=24.77 Aligned_cols=17 Identities=24% Similarity=0.266 Sum_probs=12.8
Q ss_pred cCCeEEcCCCCeeeeee
Q 036116 4 ETNSLISDSIGVSFPIK 20 (53)
Q Consensus 4 ~~g~LiC~~c~~~YPI~ 20 (53)
..+.|.|..||..+++-
T Consensus 237 ~~~~l~Ch~Cg~~~~~~ 253 (505)
T TIGR00595 237 KEGKLRCHYCGYQEPIP 253 (505)
T ss_pred CCCeEEcCCCcCcCCCC
Confidence 46788888888887753
No 178
>PHA03082 DNA-dependent RNA polymerase subunit; Provisional
Probab=22.97 E-value=40 Score=19.30 Aligned_cols=10 Identities=20% Similarity=0.448 Sum_probs=8.0
Q ss_pred eEEcCCCCee
Q 036116 7 SLISDSIGVS 16 (53)
Q Consensus 7 ~LiC~~c~~~ 16 (53)
.|+|..||+-
T Consensus 4 ~lVCsTCGrD 13 (63)
T PHA03082 4 QLVCSTCGRD 13 (63)
T ss_pred eeeecccCcc
Confidence 5899999874
No 179
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=22.95 E-value=45 Score=20.46 Aligned_cols=15 Identities=7% Similarity=-0.004 Sum_probs=10.2
Q ss_pred CCeEEcCCCCeeeeee
Q 036116 5 TNSLISDSIGVSFPIK 20 (53)
Q Consensus 5 ~g~LiC~~c~~~YPI~ 20 (53)
.....| .|+..|++.
T Consensus 68 p~~~~C-~Cg~~~~~~ 82 (124)
T PRK00762 68 PVEIEC-ECGYEGVVD 82 (124)
T ss_pred CeeEEe-eCcCccccc
Confidence 456677 777777665
No 180
>PF06676 DUF1178: Protein of unknown function (DUF1178); InterPro: IPR009562 This family consists of several hypothetical bacterial proteins of around 150 residues in length. The function of this family is unknown.
Probab=22.71 E-value=38 Score=22.00 Aligned_cols=12 Identities=8% Similarity=0.030 Sum_probs=9.6
Q ss_pred cCCeEEcCCCCe
Q 036116 4 ETNSLISDSIGV 15 (53)
Q Consensus 4 ~~g~LiC~~c~~ 15 (53)
..|.|.||.||-
T Consensus 29 ~~glv~CP~Cgs 40 (148)
T PF06676_consen 29 ARGLVSCPVCGS 40 (148)
T ss_pred HcCCccCCCCCC
Confidence 357899999984
No 181
>PF00301 Rubredoxin: Rubredoxin; InterPro: IPR004039 Rubredoxin is a low molecular weight iron-containing bacterial protein involved in electron transfer [, ], sometimes replacing ferredoxin as an electron carrier []. The 3-D structures of a number of rubredoxins have been solved [, ]. The fold belongs to the alpha+beta class, with 2 alpha-helices and 2-3 beta-strands. Its active site contains an iron ion which is co-ordinated by the sulphurs of four conserved cysteine residues forming an almost regular tetrahedron. The conserved cysteines reside on two loops, which are the most conserved regions of the protein. In addition, a ring of acidic residues in the proximity of the [Fe(Cys)4] centre is also well-conserved []. ; GO: 0009055 electron carrier activity, 0046872 metal ion binding; PDB: 2RDV_C 1RDV_A 1S24_A 1T9O_B 1B2J_A 1SMW_A 2PVE_B 1BFY_A 1T9P_C 1C09_C ....
Probab=22.58 E-value=72 Score=16.85 Aligned_cols=18 Identities=17% Similarity=0.261 Sum_probs=14.6
Q ss_pred EEcCCCCeeeeeeCCccc
Q 036116 8 LISDSIGVSFPIKDGIPS 25 (53)
Q Consensus 8 LiC~~c~~~YPI~dGIPv 25 (53)
.+|..|+-.|-=..|-|.
T Consensus 2 y~C~~CgyvYd~~~Gd~~ 19 (47)
T PF00301_consen 2 YQCPVCGYVYDPEKGDPE 19 (47)
T ss_dssp EEETTTSBEEETTTBBGG
T ss_pred cCCCCCCEEEcCCcCCcc
Confidence 579999999988877653
No 182
>COG3364 Zn-ribbon containing protein [General function prediction only]
Probab=22.57 E-value=36 Score=21.52 Aligned_cols=10 Identities=20% Similarity=0.232 Sum_probs=7.6
Q ss_pred EcCCCCeeee
Q 036116 9 ISDSIGVSFP 18 (53)
Q Consensus 9 iC~~c~~~YP 18 (53)
.|.+||..|+
T Consensus 4 ~CtrCG~vf~ 13 (112)
T COG3364 4 QCTRCGEVFD 13 (112)
T ss_pred eecccccccc
Confidence 5788888776
No 183
>PLN02915 cellulose synthase A [UDP-forming], catalytic subunit
Probab=22.50 E-value=41 Score=28.10 Aligned_cols=29 Identities=7% Similarity=0.101 Sum_probs=25.1
Q ss_pred CcccCCeEEcCCCCeeeeeeCCccccCCC
Q 036116 1 VCEETNSLISDSIGVSFPIKDGIPSLVPK 29 (53)
Q Consensus 1 ~~~~~g~LiC~~c~~~YPI~dGIPvLL~~ 29 (53)
|...+|.=.||+|+..|.-..|.|-+--+
T Consensus 51 ye~~~g~~~cp~c~t~y~~~~~~~~~~~d 79 (1044)
T PLN02915 51 YERSEGNQCCPQCNTRYKRHKGCPRVEGD 79 (1044)
T ss_pred hhhhcCCccCCccCCchhhhcCCCCccCC
Confidence 45678899999999999988899988776
No 184
>PF10405 BHD_3: Rad4 beta-hairpin domain 3; InterPro: IPR018328 Mutations in the nucleotide excision repair (NER) pathway can cause the xeroderma pigmentosum skin cancer predisposition syndrome. NER lesions are limited to one DNA strand, but otherwise they are chemically and structurally diverse, being caused by a wide variety of genotoxic chemicals and ultraviolet radiation. The xeroderma pigmentosum C (XPC) protein has a central role in initiating global-genome NER by recognising the lesion and recruiting downstream factors. In NER in eukaryotes, DNA is incised on both sides of the lesion, resulting in the removal of a fragment ~25-30 nucleotides long. This is followed by repair synthesis and ligation. This reaction, in yeast, requires the damage binding factors Rad14, RPA, and the Rad4-Rad23 complex, the transcription factor TFIIH which contains the two DNA helicases Rad3 and Rad25, essential for creating a bubble structure, and the two endonucleases, the Rad1-Rad10 complex and Rad2, which incise the damaged DNA strand on the 5'- and 3'-side of the lesion, respectively []. The crystal structure of the yeast XPC orthologue Rad4 bound to DNA containing a cyclobutane pyrimidine dimer lesion has been determined. The structure shows that Rad4 inserts a beta-hairpin through the DNA duplex, causing the two damaged base pairs to flip out of the double helix. The expelled nucleotides of the undamaged strand are recognised by Rad4, whereas the two cyclobutane pyrimidine dimer-linked nucleotides become disordered. This indicates that the lesions recognised by Rad4/XPC thermodynamically destabilise the double helix in a manner that facilitates the flipping-out of two base pairs []. Homologues of all the above mentioned yeast genes, except for RAD7, RAD16, and MMS19, have been identified in humans, and mutations in these human genes affect NER in a similar fashion as they do in yeast, with the exception of XPC, the human counterpart of yeast RAD4. Deletion of RAD4 causes the same high level of UV sensitivity as do mutations in the other class 1 genes, and rad4 mutants are completely defective in incision. By contrast, XPC is required for the repair of nontranscribed regions of the genome but not for the repair of the transcribed DNA strand. This entry represents the DNA-binding domain of Rad4, which has a beta-hairpin structure []. Rad4 inserts a beta-hairpin through the DNA duplex, causing the two damaged base pairs to flip out of the double helix. ; GO: 0003684 damaged DNA binding, 0006289 nucleotide-excision repair, 0005634 nucleus; PDB: 2QSG_A 2QSF_A 2QSH_A.
Probab=22.35 E-value=37 Score=19.51 Aligned_cols=18 Identities=28% Similarity=0.368 Sum_probs=12.7
Q ss_pred CCCCeeeeeeCCccccCC
Q 036116 11 DSIGVSFPIKDGIPSLVP 28 (53)
Q Consensus 11 ~~c~~~YPI~dGIPvLL~ 28 (53)
...++++|+.|||=|.-.
T Consensus 50 ~~~g~~~Pv~~GiVV~~e 67 (76)
T PF10405_consen 50 QKGGRAVPVIDGIVVAEE 67 (76)
T ss_dssp -STT-EEEEEEEEEEEGG
T ss_pred ccCCCCeEEECeEEEEhh
Confidence 356899999999976543
No 185
>cd00730 rubredoxin Rubredoxin; nonheme iron binding domains containing a [Fe(SCys)4] center. Rubredoxins are small nonheme iron proteins. The iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc. They are believed to be involved in electron transfer.
Probab=22.27 E-value=55 Score=17.49 Aligned_cols=17 Identities=18% Similarity=0.245 Sum_probs=13.4
Q ss_pred EEcCCCCeeeeeeCCcc
Q 036116 8 LISDSIGVSFPIKDGIP 24 (53)
Q Consensus 8 LiC~~c~~~YPI~dGIP 24 (53)
.+|..|+..|.=..|-|
T Consensus 2 y~C~~CgyiYd~~~Gd~ 18 (50)
T cd00730 2 YECRICGYIYDPAEGDP 18 (50)
T ss_pred cCCCCCCeEECCCCCCc
Confidence 47999999998776654
No 186
>PRK14526 adenylate kinase; Provisional
Probab=22.22 E-value=37 Score=22.34 Aligned_cols=17 Identities=24% Similarity=0.190 Sum_probs=14.1
Q ss_pred CCeEEcCCCCeeeeeeC
Q 036116 5 TNSLISDSIGVSFPIKD 21 (53)
Q Consensus 5 ~g~LiC~~c~~~YPI~d 21 (53)
.+..+|+.||..|-+.-
T Consensus 120 ~~R~~~~~~g~~y~~~~ 136 (211)
T PRK14526 120 SGRRICKSCNNIFNIYT 136 (211)
T ss_pred HCCCcccccCCcccccc
Confidence 46789999999998763
No 187
>PF10058 DUF2296: Predicted integral membrane metal-binding protein (DUF2296); InterPro: IPR019273 This domain, found mainly in the eukaryotic lunapark proteins, has no known function [].
Probab=22.16 E-value=44 Score=18.08 Aligned_cols=10 Identities=20% Similarity=0.039 Sum_probs=8.2
Q ss_pred CeEEcCCCCe
Q 036116 6 NSLISDSIGV 15 (53)
Q Consensus 6 g~LiC~~c~~ 15 (53)
-.|||+.|..
T Consensus 21 ~aLIC~~C~~ 30 (54)
T PF10058_consen 21 YALICSKCFS 30 (54)
T ss_pred eeEECcccch
Confidence 4799999964
No 188
>PF05454 DAG1: Dystroglycan (Dystrophin-associated glycoprotein 1); InterPro: IPR008465 Dystroglycan is one of the dystrophin-associated glycoproteins, which is encoded by a 5.5 kb transcript in Homo sapiens. The protein product is cleaved into two non-covalently associated subunits, [alpha] (N-terminal) and [beta] (C-terminal). In skeletal muscle the dystroglycan complex works as a transmembrane linkage between the extracellular matrix and the cytoskeleton [alpha]-dystroglycan is extracellular and binds to merosin ([alpha]-2 laminin) in the basement membrane, while [beta]-dystroglycan is a transmembrane protein and binds to dystrophin, which is a large rod-like cytoskeletal protein, absent in Duchenne muscular dystrophy patients. Dystrophin binds to intracellular actin cables. In this way, the dystroglycan complex, which links the extracellular matrix to the intracellular actin cables, is thought to provide structural integrity in muscle tissues. The dystroglycan complex is also known to serve as an agrin receptor in muscle, where it may regulate agrin-induced acetylcholine receptor clustering at the neuromuscular junction. There is also evidence which suggests the function of dystroglycan as a part of the signal transduction pathway because it is shown that Grb2, a mediator of the Ras-related signal pathway, can interact with the cytoplasmic domain of dystroglycan. In general, aberrant expression of dystrophin-associated protein complex underlies the pathogenesis of Duchenne muscular dystrophy, Becker muscular dystrophy and severe childhood autosomal recessive muscular dystrophy. Interestingly, no genetic disease has been described for either [alpha]- or [beta]-dystroglycan. Dystroglycan is widely distributed in non-muscle tissues as well as in muscle tissues. During epithelial morphogenesis of kidney, the dystroglycan complex is shown to act as a receptor for the basement membrane. Dystroglycan expression in Mus musculus brain and neural retina has also been reported. However, the physiological role of dystroglycan in non-muscle tissues has remained unclear [].; PDB: 1EG4_P.
Probab=21.90 E-value=30 Score=24.63 Aligned_cols=15 Identities=27% Similarity=0.485 Sum_probs=0.0
Q ss_pred eeCCccccCCCCCcc
Q 036116 19 IKDGIPSLVPKDGKI 33 (53)
Q Consensus 19 I~dGIPvLL~~ear~ 33 (53)
|..||||...||-..
T Consensus 187 ~~KGiPvIF~dElee 201 (290)
T PF05454_consen 187 ISKGIPVIFQDELEE 201 (290)
T ss_dssp ---------------
T ss_pred HhcCCceeccccccc
Confidence 789999999987544
No 189
>PF11822 DUF3342: Domain of unknown function (DUF3342); InterPro: IPR021777 This family of proteins are functionally uncharacterised. This family is found in bacteria. This presumed domain is typically between 170 to 303 amino acids in length. The N-terminal half of this family is a BTB-like domain.
Probab=21.86 E-value=45 Score=24.22 Aligned_cols=16 Identities=19% Similarity=0.318 Sum_probs=14.2
Q ss_pred CeEEcCCCCeeeeeeC
Q 036116 6 NSLISDSIGVSFPIKD 21 (53)
Q Consensus 6 g~LiC~~c~~~YPI~d 21 (53)
..|.|..|+..||+.|
T Consensus 260 ~~l~CsrC~q~F~~~e 275 (317)
T PF11822_consen 260 HFLYCSRCNQVFPCSE 275 (317)
T ss_pred eEEECccCCcEeeHHH
Confidence 4699999999999876
No 190
>COG1281 Disulfide bond chaperones of the HSP33 family [Posttranslational modification, protein turnover, chaperones]
Probab=21.45 E-value=52 Score=23.55 Aligned_cols=16 Identities=6% Similarity=0.156 Sum_probs=13.1
Q ss_pred CCeEEcCCCCeeeeee
Q 036116 5 TNSLISDSIGVSFPIK 20 (53)
Q Consensus 5 ~g~LiC~~c~~~YPI~ 20 (53)
.-+..|.+|+..|-..
T Consensus 264 ~iev~C~FC~~~Y~f~ 279 (286)
T COG1281 264 GIEVTCEFCGTKYLFD 279 (286)
T ss_pred CeEEEeeccCCEEecC
Confidence 4579999999999754
No 191
>PRK09919 anti-adapter protein IraM; Provisional
Probab=21.41 E-value=52 Score=20.76 Aligned_cols=18 Identities=33% Similarity=0.543 Sum_probs=14.0
Q ss_pred CCeEEcCCCCeeeeeeCC
Q 036116 5 TNSLISDSIGVSFPIKDG 22 (53)
Q Consensus 5 ~g~LiC~~c~~~YPI~dG 22 (53)
.+.++||.||..|-..-|
T Consensus 6 ~dtvi~P~tG~~FS~i~~ 23 (114)
T PRK09919 6 IDTVISPSTGISFSAISS 23 (114)
T ss_pred eeeEEcCCCCcchhhhhh
Confidence 468999999998865544
No 192
>cd00729 rubredoxin_SM Rubredoxin, Small Modular nonheme iron binding domain containing a [Fe(SCys)4] center, 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), 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=21.23 E-value=60 Score=15.79 Aligned_cols=13 Identities=8% Similarity=-0.066 Sum_probs=9.6
Q ss_pred eEEcCCCCeeeee
Q 036116 7 SLISDSIGVSFPI 19 (53)
Q Consensus 7 ~LiC~~c~~~YPI 19 (53)
..+|..||..|.-
T Consensus 2 ~~~C~~CG~i~~g 14 (34)
T cd00729 2 VWVCPVCGYIHEG 14 (34)
T ss_pred eEECCCCCCEeEC
Confidence 3589999977753
No 193
>PLN02400 cellulose synthase
Probab=21.23 E-value=58 Score=27.38 Aligned_cols=30 Identities=7% Similarity=0.119 Sum_probs=25.1
Q ss_pred CcccCCeEEcCCCCeeeeeeCCccccCCCC
Q 036116 1 VCEETNSLISDSIGVSFPIKDGIPSLVPKD 30 (53)
Q Consensus 1 ~~~~~g~LiC~~c~~~YPI~dGIPvLL~~e 30 (53)
|...+|.=.||.|+..|.=..|-|-+--|+
T Consensus 72 YERkeGnq~CPQCkTrYkR~KgsprV~GDe 101 (1085)
T PLN02400 72 YERKDGTQCCPQCKTRYRRHKGSPRVEGDE 101 (1085)
T ss_pred eecccCCccCcccCCccccccCCCCCCccc
Confidence 456778899999999999889999876654
No 194
>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=20.82 E-value=51 Score=26.68 Aligned_cols=18 Identities=22% Similarity=0.467 Sum_probs=16.3
Q ss_pred EEcCCCCeeeeeeCCccc
Q 036116 8 LISDSIGVSFPIKDGIPS 25 (53)
Q Consensus 8 LiC~~c~~~YPI~dGIPv 25 (53)
..|..||-+|-|...||-
T Consensus 124 ~~CT~CGPRfTIi~alPY 141 (750)
T COG0068 124 INCTNCGPRFTIIEALPY 141 (750)
T ss_pred cccCCCCcceeeeccCCC
Confidence 469999999999999995
No 195
>PRK05654 acetyl-CoA carboxylase subunit beta; Validated
Probab=20.74 E-value=43 Score=23.62 Aligned_cols=23 Identities=17% Similarity=0.237 Sum_probs=15.9
Q ss_pred CeEEcCCCCeeeeee--CCccccCC
Q 036116 6 NSLISDSIGVSFPIK--DGIPSLVP 28 (53)
Q Consensus 6 g~LiC~~c~~~YPI~--dGIPvLL~ 28 (53)
+.-+||.|+..|++. +-|-.|+-
T Consensus 45 ~~~vc~~c~~h~rl~areRi~~L~D 69 (292)
T PRK05654 45 NLNVCPKCGHHMRISARERLDLLLD 69 (292)
T ss_pred cCCCCCCCCCCeeCCHHHHHHHHcc
Confidence 345999999999874 55554443
No 196
>PF02146 SIR2: Sir2 family; InterPro: IPR003000 These sequences represent the Sirtuin (Sir2-related) family of NAD+-dependent deacetylases. This family of enzymes is broadly conserved from bacteria to humans. In yeast, Sir2 proteins form complexes with other proteins to silence chromatin by accessing histones and deacetylating them. Sir2 proteins have been proposed to play a role in silencing, chromosome stability and ageing []. The bacterial enzyme CobB, an homologue of Sir2, is a phosphoribosyltransferase []. An in vitro ADP ribosyltransferase activity has also been associated with human members of this family []. Sir2-like enzymes employ NAD+ as a cosubstrate in deacetylation reactions [] and catalyse a reaction in which the cleavage of NAD(+)and histone and/or protein deacetylation are coupled to the formation of O-acetyl-ADP-ribose, a novel metabolite. The dependence of the reaction on both NAD(+) and the generation of this potential second messenger offers new clues to understanding the function and regulation of nuclear, cytoplasmic and mitochondrial Sir2-like enzymes []. Silent Information Regulator protein of Saccharomyces cerevisiae (Sir2) is one of several factors critical for silencing at least three loci. Among them, it is unique because it silences the rDNA as well as the mating type loci and telomeres []. Sir2 interacts in a complex with itself and with Sir3 and Sir4, two proteins that are able to interact with nucleosomes. In addition Sir2 also interacts with ubiquitination factors and/or complexes []. Homologues of Sir2 share a core domain including the GAG and NID motifs and a putative C4 Zinc finger. The regions containing these three conserved motifs are individually essential for Sir2 silencing function, as are the four cysteins []. In addition, the conserved residues HG next to the putative Zn finger have been shown to be essential for the ADP ribosyltransferase activity []. ; GO: 0008270 zinc ion binding, 0070403 NAD+ binding, 0006476 protein deacetylation; PDB: 1S5P_A 3PKI_E 3PKJ_F 3K35_A 1ICI_A 1M2K_A 1M2G_A 1M2N_B 1M2H_A 1M2J_A ....
Probab=20.67 E-value=55 Score=20.50 Aligned_cols=15 Identities=20% Similarity=0.313 Sum_probs=12.7
Q ss_pred eEEcCCCCeeeeeeC
Q 036116 7 SLISDSIGVSFPIKD 21 (53)
Q Consensus 7 ~LiC~~c~~~YPI~d 21 (53)
.+.|..|+..|+..+
T Consensus 105 ~~~C~~C~~~~~~~~ 119 (178)
T PF02146_consen 105 RLRCSKCGKEYDRED 119 (178)
T ss_dssp EEEETTTSBEEEGHH
T ss_pred eeeecCCCccccchh
Confidence 589999999998765
No 197
>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=20.39 E-value=60 Score=20.55 Aligned_cols=13 Identities=8% Similarity=0.087 Sum_probs=9.6
Q ss_pred eEEcCCCCeeeee
Q 036116 7 SLISDSIGVSFPI 19 (53)
Q Consensus 7 ~LiC~~c~~~YPI 19 (53)
.+.||+|++.--+
T Consensus 69 ~V~CP~C~K~TKm 81 (114)
T PF11023_consen 69 QVECPNCGKQTKM 81 (114)
T ss_pred eeECCCCCChHhh
Confidence 5789999876543
No 198
>TIGR03830 CxxCG_CxxCG_HTH putative zinc finger/helix-turn-helix protein, YgiT family. This model describes a family of predicted regulatory proteins with a conserved zinc finger/HTH architecture. The amino-terminal region contains a novel domain, featuring two CXXC motifs and occuring in a number of small bacterial proteins as well as in the present family. The carboxyl-terminal region consists of a helix-turn-helix domain, modeled by pfam01381. The predicted function is DNA binding and transcriptional regulation.
Probab=20.16 E-value=65 Score=18.65 Aligned_cols=16 Identities=6% Similarity=0.011 Sum_probs=11.9
Q ss_pred CeEEcCCCCeeeeeeC
Q 036116 6 NSLISDSIGVSFPIKD 21 (53)
Q Consensus 6 g~LiC~~c~~~YPI~d 21 (53)
...+|+.||-.|-..+
T Consensus 30 ~~~~C~~CGe~~~~~e 45 (127)
T TIGR03830 30 PGWYCPACGEELLDPE 45 (127)
T ss_pred eeeECCCCCCEEEcHH
Confidence 4578999998776544
No 199
>PF06677 Auto_anti-p27: Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27); InterPro: IPR009563 The proteins in this entry are functionally uncharacterised and include several proteins that characterise Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27). It is thought that the potential association of anti-p27 with anti-centromere antibodies suggests that autoantigen p27 might play a role in mitosis [].
Probab=20.02 E-value=69 Score=16.52 Aligned_cols=11 Identities=18% Similarity=0.265 Sum_probs=8.0
Q ss_pred cCCeEEcCCCC
Q 036116 4 ETNSLISDSIG 14 (53)
Q Consensus 4 ~~g~LiC~~c~ 14 (53)
..|..+|+.|+
T Consensus 31 k~g~~~Cv~C~ 41 (41)
T PF06677_consen 31 KDGKIYCVSCG 41 (41)
T ss_pred cCCCEECCCCC
Confidence 45778888875
No 200
>PF01783 Ribosomal_L32p: Ribosomal L32p protein family; InterPro: IPR002677 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein L32p is part of the 50S ribosomal subunit. This family is found in both prokaryotes and eukaryotes. Ribosomal protein L32 of yeast binds to and regulates the splicing and the translation of the transcript of its own gene [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0015934 large ribosomal subunit; PDB: 3PYT_2 3F1F_5 3PYV_2 3D5B_5 3MRZ_2 3D5D_5 3F1H_5 1VSP_Y 3PYR_2 3MS1_2 ....
Probab=20.01 E-value=50 Score=17.70 Aligned_cols=6 Identities=33% Similarity=0.567 Sum_probs=3.1
Q ss_pred EcCCCC
Q 036116 9 ISDSIG 14 (53)
Q Consensus 9 iC~~c~ 14 (53)
+|+.||
T Consensus 41 vc~~cG 46 (56)
T PF01783_consen 41 VCPSCG 46 (56)
T ss_dssp BCTTTB
T ss_pred eeCCCC
Confidence 455554
Done!