Query psy15340
Match_columns 81
No_of_seqs 108 out of 745
Neff 5.2
Searched_HMMs 46136
Date Fri Aug 16 18:27:25 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy15340.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/15340hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1088|consensus 100.0 3.5E-34 7.5E-39 192.9 5.6 79 1-81 45-124 (124)
2 PF03966 Trm112p: Trm112p-like 99.6 7.6E-17 1.6E-21 98.1 0.8 53 4-70 16-68 (68)
3 COG2835 Uncharacterized conser 99.3 8.6E-13 1.9E-17 80.0 2.1 34 47-80 18-51 (60)
4 PRK11827 hypothetical protein; 99.3 9.7E-13 2.1E-17 79.7 0.9 46 35-80 2-51 (60)
5 PF13717 zinc_ribbon_4: zinc-r 92.0 0.079 1.7E-06 28.6 1.0 18 55-72 2-20 (36)
6 PF14569 zf-UDP: Zinc-binding 90.0 0.069 1.5E-06 34.1 -0.5 39 42-80 38-76 (80)
7 PF08271 TF_Zn_Ribbon: TFIIB z 89.6 0.32 6.9E-06 26.7 2.0 18 47-64 11-28 (43)
8 PF13719 zinc_ribbon_5: zinc-r 85.8 0.43 9.3E-06 25.7 1.0 15 56-70 3-17 (37)
9 COG4391 Uncharacterized protei 85.4 0.42 9.1E-06 29.2 0.9 22 45-67 39-60 (62)
10 PF08792 A2L_zn_ribbon: A2L zi 85.2 0.56 1.2E-05 25.0 1.3 17 51-67 17-33 (33)
11 PF05191 ADK_lid: Adenylate ki 85.1 0.56 1.2E-05 25.4 1.2 15 55-69 1-15 (36)
12 COG1645 Uncharacterized Zn-fin 83.7 0.66 1.4E-05 32.0 1.4 20 45-67 37-56 (131)
13 PRK00420 hypothetical protein; 83.3 0.69 1.5E-05 31.0 1.4 19 52-70 37-55 (112)
14 TIGR02098 MJ0042_CXXC MJ0042 f 82.5 0.67 1.4E-05 24.5 0.9 15 56-70 3-17 (38)
15 PF00096 zf-C2H2: Zinc finger, 81.0 0.82 1.8E-05 21.2 0.8 12 57-68 2-13 (23)
16 PF08274 PhnA_Zn_Ribbon: PhnA 80.3 1.1 2.4E-05 23.5 1.2 16 51-66 15-30 (30)
17 PRK12380 hydrogenase nickel in 80.0 1.6 3.4E-05 28.7 2.1 28 42-69 57-84 (113)
18 PF10609 ParA: ParA/MinD ATPas 79.8 1.7 3.7E-05 27.5 2.2 33 35-67 45-77 (81)
19 PLN02189 cellulose synthase 79.7 0.77 1.7E-05 40.6 0.8 37 44-80 65-101 (1040)
20 PF13913 zf-C2HC_2: zinc-finge 79.4 0.84 1.8E-05 22.6 0.5 11 56-66 3-13 (25)
21 TIGR00100 hypA hydrogenase nic 79.2 1.7 3.8E-05 28.6 2.2 26 44-69 59-84 (115)
22 PLN02400 cellulose synthase 79.2 1.1 2.4E-05 39.8 1.6 39 42-80 65-103 (1085)
23 PRK03681 hypA hydrogenase nick 79.2 1.6 3.4E-05 28.8 2.0 28 42-69 57-84 (114)
24 smart00834 CxxC_CXXC_SSSS Puta 79.2 1.1 2.4E-05 23.6 1.0 18 55-72 5-22 (41)
25 PF01155 HypA: Hydrogenase exp 79.1 1.3 2.9E-05 28.9 1.6 29 42-70 57-85 (113)
26 PLN02638 cellulose synthase A 78.6 0.78 1.7E-05 40.7 0.5 39 42-80 46-84 (1079)
27 smart00661 RPOL9 RNA polymeras 76.4 1.9 4E-05 23.8 1.5 16 55-70 20-35 (52)
28 PLN02436 cellulose synthase A 76.1 1.2 2.5E-05 39.7 0.8 38 43-80 66-103 (1094)
29 PF10571 UPF0547: Uncharacteri 75.3 1.2 2.6E-05 22.5 0.4 17 50-66 9-25 (26)
30 PF14353 CpXC: CpXC protein 74.5 1.2 2.7E-05 29.1 0.5 12 56-67 39-50 (128)
31 PF09538 FYDLN_acid: Protein o 74.1 1.5 3.4E-05 28.9 0.9 19 50-68 21-39 (108)
32 PF13408 Zn_ribbon_recom: Reco 73.9 1.8 3.9E-05 24.1 1.0 17 52-68 2-18 (58)
33 PRK00564 hypA hydrogenase nick 73.8 2.7 5.9E-05 27.7 2.0 27 43-69 59-85 (117)
34 TIGR00686 phnA alkylphosphonat 73.1 1.8 4E-05 29.0 1.0 18 52-69 16-33 (109)
35 PF13878 zf-C2H2_3: zinc-finge 72.1 1.6 3.6E-05 24.0 0.5 15 54-68 12-26 (41)
36 PLN02915 cellulose synthase A 71.6 1.6 3.5E-05 38.7 0.7 36 42-77 44-79 (1044)
37 PF02150 RNA_POL_M_15KD: RNA p 71.1 4.2 9.1E-05 21.6 2.0 18 52-69 17-34 (35)
38 PRK10220 hypothetical protein; 70.9 2.5 5.4E-05 28.5 1.3 18 52-69 17-34 (111)
39 PRK03824 hypA hydrogenase nick 70.0 3.8 8.1E-05 27.7 2.0 22 47-68 62-83 (135)
40 PF13894 zf-C2H2_4: C2H2-type 69.4 2.4 5.3E-05 19.0 0.7 12 57-68 2-13 (24)
41 PRK00398 rpoP DNA-directed RNA 69.3 4.2 9E-05 22.4 1.8 25 48-72 14-38 (46)
42 TIGR02605 CxxC_CxxC_SSSS putat 68.3 3.2 6.9E-05 23.1 1.2 15 55-69 5-19 (52)
43 PF04475 DUF555: Protein of un 67.2 5.6 0.00012 26.4 2.3 30 37-66 29-58 (102)
44 PF10276 zf-CHCC: Zinc-finger 66.5 3.2 7E-05 23.0 0.9 13 53-65 27-39 (40)
45 PF09723 Zn-ribbon_8: Zinc rib 65.5 3.5 7.7E-05 22.5 1.0 17 55-71 5-21 (42)
46 PF13912 zf-C2H2_6: C2H2-type 65.4 3.8 8.3E-05 19.6 1.0 12 56-67 2-13 (27)
47 PF10122 Mu-like_Com: Mu-like 64.1 4.7 0.0001 23.7 1.4 33 43-75 11-44 (51)
48 PF10080 DUF2318: Predicted me 63.6 4.9 0.00011 26.4 1.5 20 49-68 46-65 (102)
49 PRK11032 hypothetical protein; 63.4 4.2 9.1E-05 28.7 1.3 32 38-69 104-138 (160)
50 COG4049 Uncharacterized protei 63.4 2.6 5.6E-05 25.7 0.2 15 54-68 16-30 (65)
51 PRK11088 rrmA 23S rRNA methylt 62.6 5.7 0.00012 28.8 1.9 25 52-77 15-40 (272)
52 PF07295 DUF1451: Protein of u 62.4 5.5 0.00012 27.6 1.7 33 37-69 91-126 (146)
53 PRK00762 hypA hydrogenase nick 61.1 7.1 0.00015 26.0 2.0 24 44-68 59-82 (124)
54 COG1594 RPB9 DNA-directed RNA 60.8 5.4 0.00012 26.4 1.4 18 52-69 19-36 (113)
55 KOG3352|consensus 60.0 4.9 0.00011 28.4 1.1 27 43-69 121-147 (153)
56 PRK08197 threonine synthase; V 59.4 5.9 0.00013 30.6 1.6 16 55-70 7-22 (394)
57 COG0375 HybF Zn finger protein 58.0 6.5 0.00014 26.5 1.4 17 54-70 85-102 (115)
58 PRK07591 threonine synthase; V 56.8 6.9 0.00015 30.7 1.6 14 55-68 18-31 (421)
59 PRK06260 threonine synthase; V 56.6 7.1 0.00015 30.2 1.6 15 55-69 3-17 (397)
60 TIGR00515 accD acetyl-CoA carb 56.4 2.6 5.6E-05 32.0 -0.8 19 49-67 39-57 (285)
61 PF13465 zf-H2C2_2: Zinc-finge 56.1 7.2 0.00016 19.0 1.1 16 51-66 10-25 (26)
62 PF08671 SinI: Anti-repressor 56.0 10 0.00022 19.8 1.7 15 6-20 4-18 (30)
63 PRK00423 tfb transcription ini 55.4 8.2 0.00018 29.1 1.7 18 48-65 23-40 (310)
64 PF01475 FUR: Ferric uptake re 55.1 6.4 0.00014 25.1 1.0 16 54-69 79-94 (120)
65 PF09297 zf-NADH-PPase: NADH p 54.9 11 0.00025 19.1 1.8 15 51-65 17-31 (32)
66 smart00659 RPOLCX RNA polymera 54.9 9.9 0.00021 21.2 1.6 21 53-73 17-37 (44)
67 TIGR02300 FYDLN_acid conserved 54.3 6 0.00013 27.3 0.8 19 50-68 21-39 (129)
68 cd07153 Fur_like Ferric uptake 54.0 7.7 0.00017 24.3 1.2 16 55-70 73-88 (116)
69 PLN02569 threonine synthase 53.1 7.1 0.00015 31.6 1.1 16 55-70 49-64 (484)
70 smart00531 TFIIE Transcription 52.9 7.1 0.00015 26.4 1.0 22 48-69 92-113 (147)
71 PRK03922 hypothetical protein; 52.7 13 0.00029 25.1 2.2 29 38-66 31-60 (113)
72 PF01927 Mut7-C: Mut7-C RNAse 52.5 6.7 0.00015 26.5 0.8 11 55-65 124-134 (147)
73 TIGR03844 cysteate_syn cysteat 52.5 8 0.00017 30.3 1.3 12 55-66 2-13 (398)
74 cd03478 Rieske_AIFL_N AIFL (ap 51.0 13 0.00029 22.6 1.9 25 49-73 50-74 (95)
75 cd03467 Rieske Rieske domain; 51.0 13 0.00028 22.6 1.9 25 50-74 53-77 (98)
76 PF13248 zf-ribbon_3: zinc-rib 50.7 7 0.00015 19.3 0.5 7 57-63 4-10 (26)
77 smart00355 ZnF_C2H2 zinc finge 49.1 6.7 0.00014 17.5 0.3 12 57-68 2-13 (26)
78 PF11781 RRN7: RNA polymerase 48.9 10 0.00022 20.3 1.0 17 48-64 18-34 (36)
79 cd03528 Rieske_RO_ferredoxin R 48.5 17 0.00037 22.0 2.1 23 51-73 53-75 (98)
80 TIGR01384 TFS_arch transcripti 48.1 11 0.00025 23.6 1.3 17 52-68 13-29 (104)
81 PRK05654 acetyl-CoA carboxylas 48.0 4.2 9.1E-05 31.0 -0.9 19 50-68 41-59 (292)
82 PF05488 PAAR_motif: PAAR moti 48.0 12 0.00026 22.3 1.3 25 54-78 33-57 (76)
83 PF12760 Zn_Tnp_IS1595: Transp 47.9 7.8 0.00017 21.3 0.4 14 56-69 19-34 (46)
84 PF13451 zf-trcl: Probable zin 47.4 10 0.00022 21.9 0.9 18 53-70 2-19 (49)
85 CHL00174 accD acetyl-CoA carbo 47.2 4.3 9.4E-05 31.2 -0.9 19 50-68 52-70 (296)
86 cd00924 Cyt_c_Oxidase_Vb Cytoc 47.0 8.4 0.00018 25.0 0.6 15 54-68 78-92 (97)
87 PHA00616 hypothetical protein 47.0 5.5 0.00012 22.6 -0.3 10 57-66 3-12 (44)
88 PRK09521 exosome complex RNA-b 46.8 12 0.00025 26.2 1.3 15 52-66 163-177 (189)
89 PHA02768 hypothetical protein; 46.6 6.7 0.00015 23.2 0.0 14 56-69 6-19 (55)
90 PF04423 Rad50_zn_hook: Rad50 46.5 9.1 0.0002 21.6 0.6 10 57-66 22-31 (54)
91 PRK05638 threonine synthase; V 46.3 10 0.00022 29.7 1.1 13 55-67 1-13 (442)
92 PF09986 DUF2225: Uncharacteri 46.3 11 0.00023 27.2 1.0 16 53-68 3-18 (214)
93 PLN02459 probable adenylate ki 45.6 10 0.00023 28.4 1.0 17 52-68 150-166 (261)
94 PF01215 COX5B: Cytochrome c o 45.5 13 0.00029 25.6 1.4 27 43-69 100-126 (136)
95 PRK00114 hslO Hsp33-like chape 45.4 45 0.00097 25.1 4.3 15 55-69 268-282 (293)
96 TIGR01206 lysW lysine biosynth 45.3 14 0.00029 21.7 1.2 20 53-72 20-39 (54)
97 PRK09462 fur ferric uptake reg 44.8 13 0.00028 24.8 1.3 16 55-70 90-105 (148)
98 PF03604 DNA_RNApol_7kD: DNA d 44.6 16 0.00034 19.3 1.3 9 55-63 17-25 (32)
99 PF02591 DUF164: Putative zinc 44.0 14 0.0003 21.0 1.1 12 53-64 44-55 (56)
100 PRK12496 hypothetical protein; 43.1 14 0.00029 25.8 1.2 36 32-68 94-140 (164)
101 PF07754 DUF1610: Domain of un 43.0 14 0.0003 18.4 0.9 10 54-63 15-24 (24)
102 PF12171 zf-C2H2_jaz: Zinc-fin 42.6 14 0.00029 17.9 0.8 11 56-66 2-12 (27)
103 PF05129 Elf1: Transcription e 42.5 14 0.00031 23.0 1.1 21 52-74 43-63 (81)
104 COG0777 AccD Acetyl-CoA carbox 41.9 7 0.00015 30.3 -0.5 26 43-68 35-60 (294)
105 PF13240 zinc_ribbon_2: zinc-r 41.5 9.3 0.0002 18.5 0.1 15 50-64 8-22 (23)
106 PF06750 DiS_P_DiS: Bacterial 41.5 12 0.00025 23.8 0.6 25 50-74 28-52 (92)
107 PF14311 DUF4379: Domain of un 41.4 13 0.00029 20.9 0.8 12 55-66 28-39 (55)
108 COG1656 Uncharacterized conser 41.4 12 0.00027 26.7 0.7 11 55-65 130-140 (165)
109 TIGR03829 YokU_near_AblA uncha 40.5 12 0.00026 24.2 0.5 12 55-66 35-46 (89)
110 PRK00432 30S ribosomal protein 40.1 18 0.00039 20.6 1.2 12 54-65 36-47 (50)
111 PTZ00088 adenylate kinase 1; P 39.9 12 0.00026 27.2 0.5 17 52-68 127-143 (229)
112 PF14446 Prok-RING_1: Prokaryo 39.6 20 0.00043 21.2 1.3 15 52-66 18-32 (54)
113 PF10013 DUF2256: Uncharacteri 39.4 13 0.00029 21.0 0.5 11 56-66 9-19 (42)
114 PF14787 zf-CCHC_5: GAG-polypr 39.4 14 0.00031 20.2 0.6 11 57-67 4-14 (36)
115 PRK06266 transcription initiat 39.3 16 0.00035 25.7 1.1 22 48-69 110-131 (178)
116 PHA02825 LAP/PHD finger-like p 39.2 6.7 0.00014 28.0 -0.9 32 39-70 31-63 (162)
117 PRK08329 threonine synthase; V 38.6 14 0.0003 28.1 0.7 13 56-68 2-14 (347)
118 COG4530 Uncharacterized protei 38.5 14 0.0003 25.3 0.6 17 51-67 22-38 (129)
119 PRK11639 zinc uptake transcrip 38.2 18 0.0004 24.9 1.2 16 55-70 100-115 (169)
120 TIGR03831 YgiT_finger YgiT-typ 38.1 14 0.0003 19.4 0.5 12 55-66 32-43 (46)
121 PF11881 DUF3401: Domain of un 38.0 22 0.00048 26.8 1.7 15 4-18 165-179 (239)
122 KOG2907|consensus 38.0 14 0.0003 25.1 0.6 19 53-71 23-41 (116)
123 TIGR02378 nirD_assim_sml nitri 37.6 27 0.00058 21.7 1.8 18 56-73 65-82 (105)
124 PF11238 DUF3039: Protein of u 36.9 6.8 0.00015 23.6 -1.0 12 55-66 44-55 (58)
125 PF13959 DUF4217: Domain of un 36.8 38 0.00082 19.9 2.3 20 2-26 43-62 (65)
126 PF14577 SEO_C: Sieve element 36.7 30 0.00066 25.9 2.2 13 53-65 212-224 (235)
127 PF14205 Cys_rich_KTR: Cystein 36.4 21 0.00045 21.3 1.1 11 53-63 2-12 (55)
128 COG1273 Ku-homolog [Replicatio 36.2 7.1 0.00015 30.0 -1.2 68 1-76 1-77 (278)
129 PF15392 Joubert: Joubert synd 36.2 21 0.00047 28.0 1.4 18 1-18 303-320 (329)
130 PRK06450 threonine synthase; V 35.9 20 0.00044 27.3 1.2 13 55-67 3-15 (338)
131 PF08996 zf-DNA_Pol: DNA Polym 35.9 20 0.00042 25.2 1.1 15 55-69 18-32 (188)
132 COG4888 Uncharacterized Zn rib 35.5 25 0.00053 23.5 1.4 21 47-67 38-58 (104)
133 PF00301 Rubredoxin: Rubredoxi 34.9 31 0.00066 19.6 1.6 17 56-72 2-18 (47)
134 PF07572 BCNT: Bucentaur or cr 34.6 8.2 0.00018 24.5 -0.9 39 4-46 29-69 (81)
135 cd00350 rubredoxin_like Rubred 34.5 21 0.00045 18.4 0.8 13 56-68 2-14 (33)
136 PF05443 ROS_MUCR: ROS/MUCR tr 34.5 21 0.00045 24.4 1.0 21 47-67 64-84 (132)
137 PF14122 YokU: YokU-like prote 34.3 22 0.00049 23.0 1.0 13 54-66 34-46 (87)
138 COG4338 Uncharacterized protei 34.1 12 0.00026 22.1 -0.2 12 56-67 13-24 (54)
139 COG1545 Predicted nucleic-acid 33.8 19 0.00041 24.4 0.7 10 56-65 30-39 (140)
140 PRK14526 adenylate kinase; Pro 33.5 18 0.0004 25.8 0.6 19 52-70 119-137 (211)
141 PLN02674 adenylate kinase 32.9 22 0.00048 26.3 1.0 21 52-72 155-175 (244)
142 TIGR02377 MocE_fam_FeS Rieske 32.4 37 0.00079 21.1 1.8 23 50-72 54-76 (101)
143 PF08772 NOB1_Zn_bind: Nin one 32.1 20 0.00043 22.3 0.5 20 45-64 14-33 (73)
144 COG1996 RPC10 DNA-directed RNA 31.7 27 0.00059 20.2 1.0 23 48-70 17-39 (49)
145 PHA00626 hypothetical protein 31.6 20 0.00043 21.6 0.4 18 56-73 1-18 (59)
146 TIGR00373 conserved hypothetic 31.6 23 0.00049 24.4 0.8 20 49-68 103-122 (158)
147 PF00681 Plectin: Plectin repe 31.4 5.2 0.00011 22.0 -2.0 26 46-71 3-28 (45)
148 COG3677 Transposase and inacti 31.3 23 0.0005 23.8 0.8 20 53-72 51-70 (129)
149 PF08209 Sgf11: Sgf11 (transcr 31.0 32 0.00069 18.3 1.2 12 54-65 3-14 (33)
150 PF14030 DUF4245: Protein of u 30.9 55 0.0012 22.8 2.7 33 2-36 38-71 (169)
151 PF13806 Rieske_2: Rieske-like 30.8 37 0.0008 21.7 1.7 19 54-72 63-81 (104)
152 cd06918 ChtBD1_like Domain obs 30.4 27 0.00059 20.2 0.9 13 60-72 6-18 (51)
153 PF01430 HSP33: Hsp33 protein; 30.3 25 0.00054 26.1 0.9 15 54-68 265-279 (280)
154 PF09845 DUF2072: Zn-ribbon co 30.0 23 0.0005 24.4 0.6 11 57-67 3-13 (131)
155 PF09237 GAGA: GAGA factor; I 29.8 25 0.00054 20.9 0.6 14 53-66 22-35 (54)
156 COG0735 Fur Fe2+/Zn2+ uptake r 29.8 30 0.00065 23.3 1.2 16 55-70 93-108 (145)
157 PF10083 DUF2321: Uncharacteri 29.7 18 0.00039 25.7 0.0 13 56-68 69-81 (158)
158 PF14803 Nudix_N_2: Nudix N-te 29.7 36 0.00077 18.1 1.2 11 54-64 21-31 (34)
159 PF06420 Mgm101p: Mitochondria 29.7 59 0.0013 23.4 2.7 29 7-45 112-140 (171)
160 PF07282 OrfB_Zn_ribbon: Putat 29.5 33 0.00072 19.8 1.2 49 10-65 8-56 (69)
161 KOG1597|consensus 29.5 31 0.00068 26.9 1.3 19 47-65 13-31 (308)
162 COG1326 Uncharacterized archae 29.3 27 0.00059 25.7 0.9 14 54-67 29-42 (201)
163 COG3880 Modulator of heat shoc 29.3 9.3 0.0002 27.6 -1.5 12 55-66 74-85 (176)
164 PLN02294 cytochrome c oxidase 29.1 32 0.00069 24.8 1.2 14 55-68 141-154 (174)
165 COG3364 Zn-ribbon containing p 29.0 25 0.00054 23.6 0.6 11 57-67 4-14 (112)
166 PHA02776 E7 protein; Provision 28.9 53 0.0011 21.6 2.1 26 35-64 75-100 (101)
167 cd03531 Rieske_RO_Alpha_KSH Th 28.8 59 0.0013 20.8 2.4 30 46-76 50-79 (115)
168 PRK14892 putative transcriptio 28.6 34 0.00073 22.3 1.2 15 53-67 40-54 (99)
169 PRK09919 anti-adapter protein 28.5 30 0.00065 23.3 1.0 19 52-70 5-23 (114)
170 COG4640 Predicted membrane pro 28.5 23 0.00051 28.9 0.5 24 45-68 5-28 (465)
171 cd00730 rubredoxin Rubredoxin; 28.4 31 0.00066 19.8 0.9 17 56-72 2-18 (50)
172 COG1405 SUA7 Transcription ini 28.3 36 0.00079 25.9 1.5 18 47-64 12-29 (285)
173 PLN02195 cellulose synthase A 28.1 20 0.00044 31.9 0.1 28 43-70 36-63 (977)
174 PF11023 DUF2614: Protein of u 28.0 32 0.0007 23.2 1.0 12 55-66 69-80 (114)
175 KOG0978|consensus 28.0 30 0.00065 29.7 1.1 20 55-74 678-697 (698)
176 PF01190 Pollen_Ole_e_I: Polle 28.0 41 0.00089 20.8 1.5 13 52-64 1-13 (97)
177 PF12874 zf-met: Zinc-finger o 28.0 37 0.00081 15.6 1.0 11 56-66 1-11 (25)
178 PF13445 zf-RING_UBOX: RING-ty 27.8 31 0.00068 19.0 0.8 18 58-76 1-18 (43)
179 COG4493 Uncharacterized protei 27.3 44 0.00096 24.7 1.7 38 25-68 141-178 (209)
180 PF07503 zf-HYPF: HypF finger; 27.3 35 0.00075 18.2 0.9 15 55-69 21-35 (35)
181 PF15135 UPF0515: Uncharacteri 27.1 30 0.00064 26.6 0.8 13 54-66 154-166 (278)
182 smart00647 IBR In Between Ring 26.9 40 0.00086 18.6 1.2 18 51-68 36-53 (64)
183 PF03884 DUF329: Domain of unk 26.5 42 0.00092 19.9 1.3 16 55-70 2-17 (57)
184 PRK09965 3-phenylpropionate di 26.4 64 0.0014 20.1 2.2 20 54-73 58-77 (106)
185 cd03529 Rieske_NirD Assimilato 26.1 48 0.001 20.5 1.5 20 54-73 62-81 (103)
186 PF06677 Auto_anti-p27: Sjogre 26.1 47 0.001 18.3 1.3 12 51-62 30-41 (41)
187 COG1096 Predicted RNA-binding 26.0 39 0.00085 24.6 1.3 13 52-64 162-174 (188)
188 PF06170 DUF983: Protein of un 26.0 31 0.00068 21.8 0.7 13 57-69 10-22 (86)
189 cd01413 SIR2_Af2 SIR2_Af2: Arc 25.5 40 0.00087 24.1 1.2 23 46-68 104-126 (222)
190 PF02146 SIR2: Sir2 family; I 25.4 33 0.00072 23.3 0.8 25 45-69 95-119 (178)
191 cd01409 SIRT4 SIRT4: Eukaryoti 25.1 59 0.0013 24.0 2.1 23 45-67 108-130 (260)
192 PF05605 zf-Di19: Drought indu 25.1 23 0.00051 19.8 -0.0 11 55-65 2-12 (54)
193 PF07582 AP_endonuc_2_N: AP en 25.0 66 0.0014 18.8 1.9 15 6-20 1-15 (55)
194 COG2824 PhnA Uncharacterized Z 24.9 37 0.0008 22.9 0.9 14 53-66 18-31 (112)
195 smart00451 ZnF_U1 U1-like zinc 24.9 40 0.00087 16.6 0.9 13 54-66 2-14 (35)
196 PF04438 zf-HIT: HIT zinc fing 24.6 36 0.00078 17.4 0.6 13 53-65 11-23 (30)
197 cd00498 Hsp33 Heat shock prote 24.4 41 0.0009 25.0 1.2 13 55-67 262-274 (275)
198 PRK14811 formamidopyrimidine-D 24.1 45 0.00098 24.8 1.3 16 53-68 253-268 (269)
199 PF13935 Ead_Ea22: Ead/Ea22-li 23.9 60 0.0013 21.8 1.8 17 3-19 1-17 (139)
200 PF05495 zf-CHY: CHY zinc fing 23.9 48 0.001 19.9 1.2 12 55-66 10-21 (71)
201 PF09665 RE_Alw26IDE: Type II 23.9 60 0.0013 27.0 2.0 42 12-69 55-96 (511)
202 COG1439 Predicted nucleic acid 23.7 48 0.001 23.9 1.3 17 53-69 137-153 (177)
203 TIGR00595 priA primosomal prot 23.4 69 0.0015 25.9 2.3 19 51-69 236-254 (505)
204 smart00504 Ubox Modified RING 23.2 36 0.00078 18.8 0.5 20 56-75 36-55 (63)
205 COG4647 AcxC Acetone carboxyla 23.1 41 0.00089 23.7 0.9 33 35-67 97-132 (165)
206 KOG2462|consensus 23.0 34 0.00075 26.3 0.5 22 40-65 150-171 (279)
207 PF01096 TFIIS_C: Transcriptio 22.7 49 0.0011 17.7 1.0 12 54-65 27-38 (39)
208 TIGR01351 adk adenylate kinase 22.7 44 0.00096 23.1 1.0 21 52-72 121-141 (210)
209 PRK12267 methionyl-tRNA synthe 22.7 2E+02 0.0044 23.7 4.9 63 7-69 76-139 (648)
210 COG1743 Adenine-specific DNA m 22.4 45 0.00098 29.4 1.1 16 54-69 177-192 (875)
211 cd00729 rubredoxin_SM Rubredox 22.2 47 0.001 17.3 0.8 12 56-67 3-14 (34)
212 PF14570 zf-RING_4: RING/Ubox 22.0 38 0.00083 19.4 0.5 14 53-66 35-48 (48)
213 PRK02935 hypothetical protein; 21.5 52 0.0011 22.1 1.1 11 55-65 70-80 (110)
214 PRK05580 primosome assembly pr 21.5 69 0.0015 26.8 2.0 18 51-68 404-421 (679)
215 PRK04309 DNA-directed RNA poly 21.4 39 0.00085 26.8 0.5 11 35-45 75-85 (383)
216 PF06676 DUF1178: Protein of u 21.1 23 0.00049 24.8 -0.8 12 52-63 29-40 (148)
217 PF00628 PHD: PHD-finger; Int 21.0 76 0.0016 17.0 1.5 18 51-68 10-27 (51)
218 COG0068 HypF Hydrogenase matur 21.0 44 0.00095 29.1 0.8 18 56-73 124-141 (750)
219 PRK00279 adk adenylate kinase; 20.8 52 0.0011 22.8 1.0 22 52-73 124-145 (215)
220 cd03532 Rieske_RO_Alpha_VanA_D 20.8 74 0.0016 20.2 1.7 24 48-72 55-78 (116)
221 cd00814 MetRS_core catalytic c 20.7 2.3E+02 0.005 21.1 4.5 55 8-66 73-132 (319)
222 PF13695 zf-3CxxC: Zinc-bindin 20.7 59 0.0013 20.5 1.2 16 53-68 3-18 (98)
223 PRK00481 NAD-dependent deacety 20.7 55 0.0012 23.6 1.2 24 46-69 113-136 (242)
224 PRK05978 hypothetical protein; 20.7 46 0.001 23.2 0.7 13 57-69 54-66 (148)
225 PF14907 NTP_transf_5: Unchara 20.6 84 0.0018 21.8 2.1 17 3-19 217-233 (249)
226 PF12013 DUF3505: Protein of u 20.5 76 0.0016 20.0 1.7 21 46-66 2-22 (109)
227 COG1176 PotB ABC-type spermidi 20.5 54 0.0012 24.9 1.1 17 2-19 176-192 (287)
228 COG1856 Uncharacterized homolo 20.4 26 0.00056 26.8 -0.6 12 55-66 22-33 (275)
229 PF14375 Cys_rich_CWC: Cystein 20.4 47 0.001 18.6 0.6 11 58-68 1-11 (50)
230 PF01197 Ribosomal_L31: Riboso 20.4 70 0.0015 19.3 1.4 19 55-73 13-31 (69)
231 COG1779 C4-type Zn-finger prot 20.2 54 0.0012 24.1 1.0 24 42-65 30-53 (201)
232 KOG2906|consensus 20.2 53 0.0011 21.9 0.9 18 54-71 20-37 (105)
233 PTZ00043 cytochrome c oxidase 20.2 53 0.0011 25.1 1.0 25 43-68 169-194 (268)
234 COG2331 Uncharacterized protei 20.1 29 0.00063 22.2 -0.3 17 55-71 12-28 (82)
235 smart00249 PHD PHD zinc finger 20.1 67 0.0014 16.0 1.1 16 52-67 11-26 (47)
No 1
>KOG1088|consensus
Probab=100.00 E-value=3.5e-34 Score=192.94 Aligned_cols=79 Identities=56% Similarity=1.063 Sum_probs=75.6
Q ss_pred CCccccHHHHHHHHHHhCCCCCCCCCCccCcccc-cHHHHHHhhhhceeeeeccceeEeCCCCccccccCCccccCCCCc
Q psy15340 1 MIPKLDWSAFYKATLMLGDAEISIPEKLIDSYEK-DSEFLKKVHHALLEVEVVEGDLECPESGRKFPISSGIPNMLLKED 79 (81)
Q Consensus 1 ml~kldw~al~~aa~~lg~~~~~lP~~~~~~~~~-~e~~l~~lh~~ll~~~v~eg~L~C~~c~~~ypI~dGIP~ml~~e~ 79 (81)
|++||||+||+.||+++|. .+||+..|+++.+ |++|||.+||+|+++++.+|+|+||+|||.|||++||||||..++
T Consensus 45 m~~kidW~All~~A~~l~~--~~lP~~kPe~~~e~de~~Lr~lHhlLle~~v~EG~l~CpetG~vfpI~~GIPNMLL~e~ 122 (124)
T KOG1088|consen 45 MLPKIDWSALLEAARSLGN--TELPDEKPEKLVEDDEEFLRKLHHLLLEIDVIEGELVCPETGRVFPISDGIPNMLLSED 122 (124)
T ss_pred hhhhccHHHHHHHHHHhcc--ccCCCCCccccccccHHHHHHHHHHHhhhhhccceEecCCCCcEeecccCCcccccCcc
Confidence 7999999999999999999 6799999988766 999999999999999999999999999999999999999999999
Q ss_pred CC
Q psy15340 80 EI 81 (81)
Q Consensus 80 ev 81 (81)
|+
T Consensus 123 Ev 124 (124)
T KOG1088|consen 123 EV 124 (124)
T ss_pred cC
Confidence 86
No 2
>PF03966 Trm112p: Trm112p-like protein; InterPro: IPR005651 This family of short proteins have no known function. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. The function of this family is uncertain. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. The entry contains 2 families: Trm112, which is required for tRNA methylation in Saccharomyces cerevisiae (Baker's yeast) and is found in complexes with 2 tRNA methylases (TRM9 and TRM11) also with putative methyltransferase YDR140W []. The zinc-finger protein Ynr046w is plurifunctional and a component of the eRF1 methyltransferase in yeast []. The crystal structure of Ynr046w has been determined to 1.7 A resolution. It comprises a zinc-binding domain built from both the N- and C-terminal sequences and an inserted domain, absent from bacterial and archaeal orthologs of the protein, composed of three alpha-helices []. UPF0434, which are proteins that are functionally uncharacterised. ; PDB: 3Q87_A 2KPI_A 2K5R_A 2HF1_A 2JS4_A 2J6A_A 2JR6_A 2PK7_A 2JNY_A.
Probab=99.62 E-value=7.6e-17 Score=98.13 Aligned_cols=53 Identities=51% Similarity=1.012 Sum_probs=48.0
Q ss_pred cccHHHHHHHHHHhCCCCCCCCCCccCcccccHHHHHHhhhhceeeeeccceeEeCCCCccccccCC
Q psy15340 4 KLDWSAFYKATLMLGDAEISIPEKLIDSYEKDSEFLKKVHHALLEVEVVEGDLECPESGRKFPISSG 70 (81)
Q Consensus 4 kldw~al~~aa~~lg~~~~~lP~~~~~~~~~~e~~l~~lh~~ll~~~v~eg~L~C~~c~~~ypI~dG 70 (81)
.+||++|+++|+ +|. .++|+..++++ ++++++++++|.|+||+|||+|||+||
T Consensus 16 pL~~~~l~~~~~-~~~--~~lp~~~~~~~-----------~~l~~~~i~eg~L~Cp~c~r~YPI~dG 68 (68)
T PF03966_consen 16 PLDWEALVETAQ-LGL--SELPKELPEDY-----------HVLLEVEIVEGELICPECGREYPIRDG 68 (68)
T ss_dssp BEHHHHHHHHHH-CCC--CHCHHCHHCHC-----------EHHCTEETTTTEEEETTTTEEEEEETT
T ss_pred cchHHHHHHHHH-hCc--ccCCCCCccch-----------hhhhcccccCCEEEcCCCCCEEeCCCC
Confidence 469999999999 998 44888877766 899999999999999999999999998
No 3
>COG2835 Uncharacterized conserved protein [Function unknown]
Probab=99.31 E-value=8.6e-13 Score=79.97 Aligned_cols=34 Identities=32% Similarity=0.605 Sum_probs=30.6
Q ss_pred eeeeeccceeEeCCCCccccccCCccccCCCCcC
Q psy15340 47 LEVEVVEGDLECPESGRKFPISSGIPNMLLKEDE 80 (81)
Q Consensus 47 l~~~v~eg~L~C~~c~~~ypI~dGIP~ml~~e~e 80 (81)
+..+-.+++|+|+.|+++|||+||||+||+++++
T Consensus 18 L~~~~~~~~L~c~~~~~aYpI~dGIPvlL~~eaR 51 (60)
T COG2835 18 LVYDEEKQELICPRCKLAYPIRDGIPVLLPDEAR 51 (60)
T ss_pred ceEeccCCEEEecccCceeecccCccccCchhhc
Confidence 4566778899999999999999999999999875
No 4
>PRK11827 hypothetical protein; Provisional
Probab=99.27 E-value=9.7e-13 Score=79.69 Aligned_cols=46 Identities=24% Similarity=0.427 Sum_probs=35.8
Q ss_pred cHHHHHHhhhhceee----eeccceeEeCCCCccccccCCccccCCCCcC
Q psy15340 35 DSEFLKKVHHALLEV----EVVEGDLECPESGRKFPISSGIPNMLLKEDE 80 (81)
Q Consensus 35 ~e~~l~~lh~~ll~~----~v~eg~L~C~~c~~~ypI~dGIP~ml~~e~e 80 (81)
|.++|.-+.+.+... +..+++|+|+.|+++|||+||||+||.++|+
T Consensus 2 d~~LLeILaCP~ckg~L~~~~~~~~Lic~~~~laYPI~dgIPVlL~deAr 51 (60)
T PRK11827 2 DHRLLEIIACPVCNGKLWYNQEKQELICKLDNLAFPLRDGIPVLLETEAR 51 (60)
T ss_pred ChHHHhheECCCCCCcCeEcCCCCeEECCccCeeccccCCccccCHHHhc
Confidence 345666666655543 3456789999999999999999999999875
No 5
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=91.97 E-value=0.079 Score=28.57 Aligned_cols=18 Identities=33% Similarity=0.759 Sum_probs=15.0
Q ss_pred eeEeCCCCccccccCC-cc
Q psy15340 55 DLECPESGRKFPISSG-IP 72 (81)
Q Consensus 55 ~L~C~~c~~~ypI~dG-IP 72 (81)
.++||+|+..|.|.|. ||
T Consensus 2 ~i~Cp~C~~~y~i~d~~ip 20 (36)
T PF13717_consen 2 IITCPNCQAKYEIDDEKIP 20 (36)
T ss_pred EEECCCCCCEEeCCHHHCC
Confidence 3689999999999887 44
No 6
>PF14569 zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.
Probab=90.01 E-value=0.069 Score=34.07 Aligned_cols=39 Identities=28% Similarity=0.468 Sum_probs=19.9
Q ss_pred hhhhceeeeeccceeEeCCCCccccccCCccccCCCCcC
Q psy15340 42 VHHALLEVEVVEGDLECPESGRKFPISSGIPNMLLKEDE 80 (81)
Q Consensus 42 lh~~ll~~~v~eg~L~C~~c~~~ypI~dGIP~ml~~e~e 80 (81)
+=+..++++..+|.-.||+|+..|.=..|-|.+--+++|
T Consensus 38 vCr~CyEYErkeg~q~CpqCkt~ykr~kgsp~V~gDeee 76 (80)
T PF14569_consen 38 VCRPCYEYERKEGNQVCPQCKTRYKRHKGSPRVEGDEEE 76 (80)
T ss_dssp --HHHHHHHHHTS-SB-TTT--B----TT----TTS---
T ss_pred cchhHHHHHhhcCcccccccCCCcccccCCCCCCCCccc
Confidence 346778899999999999999999999999998877654
No 7
>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=89.58 E-value=0.32 Score=26.69 Aligned_cols=18 Identities=28% Similarity=0.641 Sum_probs=14.2
Q ss_pred eeeeeccceeEeCCCCcc
Q psy15340 47 LEVEVVEGDLECPESGRK 64 (81)
Q Consensus 47 l~~~v~eg~L~C~~c~~~ 64 (81)
+..|..+|+++|+.||..
T Consensus 11 ~~~D~~~g~~vC~~CG~V 28 (43)
T PF08271_consen 11 IVFDPERGELVCPNCGLV 28 (43)
T ss_dssp EEEETTTTEEEETTT-BB
T ss_pred eEEcCCCCeEECCCCCCE
Confidence 456778999999999865
No 8
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=85.85 E-value=0.43 Score=25.66 Aligned_cols=15 Identities=20% Similarity=0.767 Sum_probs=12.7
Q ss_pred eEeCCCCccccccCC
Q psy15340 56 LECPESGRKFPISSG 70 (81)
Q Consensus 56 L~C~~c~~~ypI~dG 70 (81)
.+||+|+..|.|.+.
T Consensus 3 i~CP~C~~~f~v~~~ 17 (37)
T PF13719_consen 3 ITCPNCQTRFRVPDD 17 (37)
T ss_pred EECCCCCceEEcCHH
Confidence 579999999998774
No 9
>COG4391 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=85.45 E-value=0.42 Score=29.20 Aligned_cols=22 Identities=23% Similarity=0.658 Sum_probs=17.4
Q ss_pred hceeeeeccceeEeCCCCccccc
Q psy15340 45 ALLEVEVVEGDLECPESGRKFPI 67 (81)
Q Consensus 45 ~ll~~~v~eg~L~C~~c~~~ypI 67 (81)
+-|+. -.+|+.+||-|+++|..
T Consensus 39 V~L~m-g~~gev~CPYC~t~y~l 60 (62)
T COG4391 39 VFLDM-GDEGEVVCPYCSTRYRL 60 (62)
T ss_pred EEEEc-CCCCcEecCccccEEEe
Confidence 34444 67899999999999975
No 10
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=85.16 E-value=0.56 Score=24.98 Aligned_cols=17 Identities=24% Similarity=0.339 Sum_probs=14.7
Q ss_pred eccceeEeCCCCccccc
Q psy15340 51 VVEGDLECPESGRKFPI 67 (81)
Q Consensus 51 v~eg~L~C~~c~~~ypI 67 (81)
-..+.++|+.||..||+
T Consensus 17 ~~~~~~~C~~Cg~~~~~ 33 (33)
T PF08792_consen 17 KEDDYEVCIFCGSSFPY 33 (33)
T ss_pred ecCCeEEcccCCcEeeC
Confidence 46789999999999985
No 11
>PF05191 ADK_lid: Adenylate kinase, active site lid; InterPro: IPR007862 Adenylate kinases (ADK; 2.7.4.3 from EC) are phosphotransferases that catalyse the Mg-dependent reversible conversion of ATP and AMP to two molecules of ADP, an essential reaction for many processes in living cells. In large variants of adenylate kinase, the AMP and ATP substrates are buried in a domain that undergoes conformational changes from an open to a closed state when bound to substrate; the ligand is then contained within a highly specific environment required for catalysis. Adenylate kinase is a 3-domain protein consisting of a large central CORE domain flanked by a LID domain on one side and the AMP-binding NMPbind domain on the other []. The LID domain binds ATP and covers the phosphates at the active site. The substrates first bind the CORE domain, followed by closure of the active site by the LID and NMPbind domains. Comparisons of adenylate kinases have revealed a particular divergence in the active site lid. In some organisms, particularly the Gram-positive bacteria, residues in the lid domain have been mutated to cysteines and these cysteine residues (two CX(n)C motifs) are responsible for the binding of a zinc ion. The bound zinc ion in the lid domain is clearly structurally homologous to Zinc-finger domains. However, it is unclear whether the adenylate kinase lid is a novel zinc-finger DNA/RNA binding domain, or that the lid bound zinc serves a purely structural function [].; GO: 0004017 adenylate kinase activity; PDB: 3BE4_A 2OSB_B 2ORI_A 2EU8_A 3DL0_A 1P3J_A 2QAJ_A 2OO7_A 2P3S_A 3DKV_A ....
Probab=85.08 E-value=0.56 Score=25.38 Aligned_cols=15 Identities=33% Similarity=0.662 Sum_probs=12.3
Q ss_pred eeEeCCCCccccccC
Q psy15340 55 DLECPESGRKFPISS 69 (81)
Q Consensus 55 ~L~C~~c~~~ypI~d 69 (81)
..+|+.||+.|.+.-
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 368999999998753
No 12
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=83.67 E-value=0.66 Score=31.98 Aligned_cols=20 Identities=25% Similarity=0.619 Sum_probs=15.1
Q ss_pred hceeeeeccceeEeCCCCccccc
Q psy15340 45 ALLEVEVVEGDLECPESGRKFPI 67 (81)
Q Consensus 45 ~ll~~~v~eg~L~C~~c~~~ypI 67 (81)
.||+ .+|+.+||.|++.+-+
T Consensus 37 PLF~---KdG~v~CPvC~~~~~~ 56 (131)
T COG1645 37 PLFR---KDGEVFCPVCGYREVV 56 (131)
T ss_pred ccee---eCCeEECCCCCceEEE
Confidence 3555 8999999999965443
No 13
>PRK00420 hypothetical protein; Validated
Probab=83.30 E-value=0.69 Score=30.98 Aligned_cols=19 Identities=26% Similarity=0.751 Sum_probs=16.7
Q ss_pred ccceeEeCCCCccccccCC
Q psy15340 52 VEGDLECPESGRKFPISSG 70 (81)
Q Consensus 52 ~eg~L~C~~c~~~ypI~dG 70 (81)
.+|..+||.||..+-+.+|
T Consensus 37 k~g~~~Cp~Cg~~~~v~~~ 55 (112)
T PRK00420 37 KDGEVVCPVHGKVYIVKSD 55 (112)
T ss_pred CCCceECCCCCCeeeeccH
Confidence 6899999999999988765
No 14
>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=82.54 E-value=0.67 Score=24.46 Aligned_cols=15 Identities=20% Similarity=0.722 Sum_probs=12.5
Q ss_pred eEeCCCCccccccCC
Q psy15340 56 LECPESGRKFPISSG 70 (81)
Q Consensus 56 L~C~~c~~~ypI~dG 70 (81)
+.||+|+..|.|.+.
T Consensus 3 ~~CP~C~~~~~v~~~ 17 (38)
T TIGR02098 3 IQCPNCKTSFRVVDS 17 (38)
T ss_pred EECCCCCCEEEeCHH
Confidence 689999999988753
No 15
>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=80.97 E-value=0.82 Score=21.24 Aligned_cols=12 Identities=33% Similarity=0.911 Sum_probs=10.3
Q ss_pred EeCCCCcccccc
Q psy15340 57 ECPESGRKFPIS 68 (81)
Q Consensus 57 ~C~~c~~~ypI~ 68 (81)
.|+.|++.|+-+
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 16
>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=80.30 E-value=1.1 Score=23.49 Aligned_cols=16 Identities=31% Similarity=0.534 Sum_probs=11.8
Q ss_pred eccceeEeCCCCcccc
Q psy15340 51 VVEGDLECPESGRKFP 66 (81)
Q Consensus 51 v~eg~L~C~~c~~~yp 66 (81)
..+..++||.|++.++
T Consensus 15 ~D~~~~vCp~C~~ew~ 30 (30)
T PF08274_consen 15 EDGELLVCPECGHEWN 30 (30)
T ss_dssp E-SSSEEETTTTEEE-
T ss_pred ccCCEEeCCcccccCC
Confidence 4567899999998763
No 17
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=79.97 E-value=1.6 Score=28.74 Aligned_cols=28 Identities=11% Similarity=0.094 Sum_probs=22.7
Q ss_pred hhhhceeeeeccceeEeCCCCccccccC
Q psy15340 42 VHHALLEVEVVEGDLECPESGRKFPISS 69 (81)
Q Consensus 42 lh~~ll~~~v~eg~L~C~~c~~~ypI~d 69 (81)
+..+-|+++...+...|+.||..|++.+
T Consensus 57 ~egA~L~I~~vp~~~~C~~Cg~~~~~~~ 84 (113)
T PRK12380 57 AQGCDLHIVYKPAQAWCWDCSQVVEIHQ 84 (113)
T ss_pred cCCCEEEEEeeCcEEEcccCCCEEecCC
Confidence 3455677788889999999999999864
No 18
>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=79.77 E-value=1.7 Score=27.50 Aligned_cols=33 Identities=21% Similarity=0.422 Sum_probs=21.0
Q ss_pred cHHHHHHhhhhceeeeeccceeEeCCCCccccc
Q psy15340 35 DSEFLKKVHHALLEVEVVEGDLECPESGRKFPI 67 (81)
Q Consensus 35 ~e~~l~~lh~~ll~~~v~eg~L~C~~c~~~ypI 67 (81)
.=+++++++-.++..-.-=+.++||.||..+.|
T Consensus 45 ~~~~~~~~~vpilGvVENMs~~~Cp~Cg~~~~i 77 (81)
T PF10609_consen 45 AIDMFRKLNVPILGVVENMSYFVCPHCGERIYI 77 (81)
T ss_dssp HHHHHHCTT-EEEEEEECT-EEE-TTT--EEET
T ss_pred HHHHHHhcCCCcEEEEECCCccCCCCCCCeecC
Confidence 345777777777776666689999999998765
No 19
>PLN02189 cellulose synthase
Probab=79.73 E-value=0.77 Score=40.60 Aligned_cols=37 Identities=27% Similarity=0.469 Sum_probs=32.7
Q ss_pred hhceeeeeccceeEeCCCCccccccCCccccCCCCcC
Q psy15340 44 HALLEVEVVEGDLECPESGRKFPISSGIPNMLLKEDE 80 (81)
Q Consensus 44 ~~ll~~~v~eg~L~C~~c~~~ypI~dGIP~ml~~e~e 80 (81)
+..++++..+|.=.||+|+..|.-.+|.|.+-.+++|
T Consensus 65 r~Cyeyer~eg~q~CpqCkt~Y~r~kgs~~v~gd~ee 101 (1040)
T PLN02189 65 RPCYEYERREGTQNCPQCKTRYKRLKGSPRVEGDDDE 101 (1040)
T ss_pred cchhhhhhhcCCccCcccCCchhhccCCCCcCCcccc
Confidence 5677899999999999999999999999999887543
No 20
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=79.37 E-value=0.84 Score=22.61 Aligned_cols=11 Identities=55% Similarity=1.162 Sum_probs=9.5
Q ss_pred eEeCCCCcccc
Q psy15340 56 LECPESGRKFP 66 (81)
Q Consensus 56 L~C~~c~~~yp 66 (81)
..||.|||.|.
T Consensus 3 ~~C~~CgR~F~ 13 (25)
T PF13913_consen 3 VPCPICGRKFN 13 (25)
T ss_pred CcCCCCCCEEC
Confidence 47999999995
No 21
>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=79.23 E-value=1.7 Score=28.55 Aligned_cols=26 Identities=19% Similarity=0.243 Sum_probs=21.3
Q ss_pred hhceeeeeccceeEeCCCCccccccC
Q psy15340 44 HALLEVEVVEGDLECPESGRKFPISS 69 (81)
Q Consensus 44 ~~ll~~~v~eg~L~C~~c~~~ypI~d 69 (81)
.+-|+++...+...|+.||+.|++.+
T Consensus 59 ga~L~I~~~p~~~~C~~Cg~~~~~~~ 84 (115)
T TIGR00100 59 GAKLNIEDEPVECECEDCSEEVSPEI 84 (115)
T ss_pred CCEEEEEeeCcEEEcccCCCEEecCC
Confidence 35567777888999999999999865
No 22
>PLN02400 cellulose synthase
Probab=79.20 E-value=1.1 Score=39.78 Aligned_cols=39 Identities=28% Similarity=0.446 Sum_probs=33.7
Q ss_pred hhhhceeeeeccceeEeCCCCccccccCCccccCCCCcC
Q psy15340 42 VHHALLEVEVVEGDLECPESGRKFPISSGIPNMLLKEDE 80 (81)
Q Consensus 42 lh~~ll~~~v~eg~L~C~~c~~~ypI~dGIP~ml~~e~e 80 (81)
+=|.+++++..||.=.||+|+..|.=..|.|.+-.+++|
T Consensus 65 VCRpCYEYERkeGnq~CPQCkTrYkR~KgsprV~GDeee 103 (1085)
T PLN02400 65 VCRPCYEYERKDGTQCCPQCKTRYRRHKGSPRVEGDEDE 103 (1085)
T ss_pred cccchhheecccCCccCcccCCccccccCCCCCCccccc
Confidence 345678999999999999999999999999999877544
No 23
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=79.19 E-value=1.6 Score=28.78 Aligned_cols=28 Identities=14% Similarity=0.201 Sum_probs=23.0
Q ss_pred hhhhceeeeeccceeEeCCCCccccccC
Q psy15340 42 VHHALLEVEVVEGDLECPESGRKFPISS 69 (81)
Q Consensus 42 lh~~ll~~~v~eg~L~C~~c~~~ypI~d 69 (81)
+..+-|+++...+...|+.||..|++.+
T Consensus 57 ~egA~L~i~~~p~~~~C~~Cg~~~~~~~ 84 (114)
T PRK03681 57 AEGCKLHLEEQEAECWCETCQQYVTLLT 84 (114)
T ss_pred cCCCEEEEEeeCcEEEcccCCCeeecCC
Confidence 4456677888889999999999999863
No 24
>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=79.19 E-value=1.1 Score=23.58 Aligned_cols=18 Identities=22% Similarity=0.652 Sum_probs=14.2
Q ss_pred eeEeCCCCccccccCCcc
Q psy15340 55 DLECPESGRKFPISSGIP 72 (81)
Q Consensus 55 ~L~C~~c~~~ypI~dGIP 72 (81)
+..|++||+.|.+..++.
T Consensus 5 ~y~C~~Cg~~fe~~~~~~ 22 (41)
T smart00834 5 EYRCEDCGHTFEVLQKIS 22 (41)
T ss_pred EEEcCCCCCEEEEEEecC
Confidence 358999999998877654
No 25
>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=79.09 E-value=1.3 Score=28.91 Aligned_cols=29 Identities=28% Similarity=0.418 Sum_probs=20.1
Q ss_pred hhhhceeeeeccceeEeCCCCccccccCC
Q psy15340 42 VHHALLEVEVVEGDLECPESGRKFPISSG 70 (81)
Q Consensus 42 lh~~ll~~~v~eg~L~C~~c~~~ypI~dG 70 (81)
+..+-|+++.......|..||+.|++.+.
T Consensus 57 ~e~a~L~Ie~~p~~~~C~~Cg~~~~~~~~ 85 (113)
T PF01155_consen 57 LEGAELEIEEVPARARCRDCGHEFEPDEF 85 (113)
T ss_dssp TTT-EEEEEEE--EEEETTTS-EEECHHC
T ss_pred ccCCEEEEEecCCcEECCCCCCEEecCCC
Confidence 44566778888899999999999998654
No 26
>PLN02638 cellulose synthase A (UDP-forming), catalytic subunit
Probab=78.61 E-value=0.78 Score=40.69 Aligned_cols=39 Identities=31% Similarity=0.543 Sum_probs=33.6
Q ss_pred hhhhceeeeeccceeEeCCCCccccccCCccccCCCCcC
Q psy15340 42 VHHALLEVEVVEGDLECPESGRKFPISSGIPNMLLKEDE 80 (81)
Q Consensus 42 lh~~ll~~~v~eg~L~C~~c~~~ypI~dGIP~ml~~e~e 80 (81)
+=+.+++++..||.=.||+|+..|.-..|.|..-.+++|
T Consensus 46 VCrpCYEYEr~eG~q~CPqCktrYkr~kgsprv~gDeee 84 (1079)
T PLN02638 46 VCRPCYEYERKDGNQSCPQCKTKYKRHKGSPAILGDEEE 84 (1079)
T ss_pred cccchhhhhhhcCCccCCccCCchhhhcCCCCcCccccc
Confidence 345677899999999999999999999999999887543
No 27
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=76.45 E-value=1.9 Score=23.84 Aligned_cols=16 Identities=25% Similarity=0.515 Sum_probs=14.2
Q ss_pred eeEeCCCCccccccCC
Q psy15340 55 DLECPESGRKFPISSG 70 (81)
Q Consensus 55 ~L~C~~c~~~ypI~dG 70 (81)
.++|+.||..++|..-
T Consensus 20 ~~vC~~Cg~~~~~~~~ 35 (52)
T smart00661 20 RFVCRKCGYEEPIEQK 35 (52)
T ss_pred EEECCcCCCeEECCCc
Confidence 8999999999998754
No 28
>PLN02436 cellulose synthase A
Probab=76.14 E-value=1.2 Score=39.71 Aligned_cols=38 Identities=26% Similarity=0.450 Sum_probs=33.0
Q ss_pred hhhceeeeeccceeEeCCCCccccccCCccccCCCCcC
Q psy15340 43 HHALLEVEVVEGDLECPESGRKFPISSGIPNMLLKEDE 80 (81)
Q Consensus 43 h~~ll~~~v~eg~L~C~~c~~~ypI~dGIP~ml~~e~e 80 (81)
=+..++++..+|.=.||+|+..|.-..|.|.+-.+++|
T Consensus 66 Cr~Cyeyer~eg~~~Cpqckt~Y~r~kgs~~~~~d~ee 103 (1094)
T PLN02436 66 CRPCYEYERREGNQACPQCKTRYKRIKGSPRVEGDEEE 103 (1094)
T ss_pred ccchhhhhhhcCCccCcccCCchhhccCCCCcCCcccc
Confidence 35677899999999999999999999999998886543
No 29
>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=75.32 E-value=1.2 Score=22.53 Aligned_cols=17 Identities=41% Similarity=0.673 Sum_probs=12.0
Q ss_pred eeccceeEeCCCCcccc
Q psy15340 50 EVVEGDLECPESGRKFP 66 (81)
Q Consensus 50 ~v~eg~L~C~~c~~~yp 66 (81)
.|-...-.||.||+.|.
T Consensus 9 ~V~~~~~~Cp~CG~~F~ 25 (26)
T PF10571_consen 9 EVPESAKFCPHCGYDFE 25 (26)
T ss_pred CchhhcCcCCCCCCCCc
Confidence 34556678888888874
No 30
>PF14353 CpXC: CpXC protein
Probab=74.45 E-value=1.2 Score=29.10 Aligned_cols=12 Identities=42% Similarity=1.126 Sum_probs=8.9
Q ss_pred eEeCCCCccccc
Q psy15340 56 LECPESGRKFPI 67 (81)
Q Consensus 56 L~C~~c~~~ypI 67 (81)
.+||+||+.|.+
T Consensus 39 ~~CP~Cg~~~~~ 50 (128)
T PF14353_consen 39 FTCPSCGHKFRL 50 (128)
T ss_pred EECCCCCCceec
Confidence 467888877776
No 31
>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=74.14 E-value=1.5 Score=28.93 Aligned_cols=19 Identities=26% Similarity=0.772 Sum_probs=15.1
Q ss_pred eeccceeEeCCCCcccccc
Q psy15340 50 EVVEGDLECPESGRKFPIS 68 (81)
Q Consensus 50 ~v~eg~L~C~~c~~~ypI~ 68 (81)
+....-.+||.||..|++.
T Consensus 21 DLnk~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 21 DLNKDPIVCPKCGTEFPPE 39 (108)
T ss_pred cCCCCCccCCCCCCccCcc
Confidence 3444667899999999998
No 32
>PF13408 Zn_ribbon_recom: Recombinase zinc beta ribbon domain
Probab=73.94 E-value=1.8 Score=24.08 Aligned_cols=17 Identities=29% Similarity=0.552 Sum_probs=14.3
Q ss_pred ccceeEeCCCCcccccc
Q psy15340 52 VEGDLECPESGRKFPIS 68 (81)
Q Consensus 52 ~eg~L~C~~c~~~ypI~ 68 (81)
..|.+.|+.||..+-.+
T Consensus 2 l~g~l~C~~CG~~m~~~ 18 (58)
T PF13408_consen 2 LSGLLRCGHCGSKMTRR 18 (58)
T ss_pred CCCcEEcccCCcEeEEE
Confidence 46899999999988764
No 33
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=73.78 E-value=2.7 Score=27.75 Aligned_cols=27 Identities=22% Similarity=0.449 Sum_probs=21.5
Q ss_pred hhhceeeeeccceeEeCCCCccccccC
Q psy15340 43 HHALLEVEVVEGDLECPESGRKFPISS 69 (81)
Q Consensus 43 h~~ll~~~v~eg~L~C~~c~~~ypI~d 69 (81)
..+-|+++.......|+.||..|++.+
T Consensus 59 ega~L~Ie~vp~~~~C~~Cg~~~~~~~ 85 (117)
T PRK00564 59 KDAILDIVDEKVELECKDCSHVFKPNA 85 (117)
T ss_pred CCCEEEEEecCCEEEhhhCCCccccCC
Confidence 345567777888999999999999864
No 34
>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=73.08 E-value=1.8 Score=29.02 Aligned_cols=18 Identities=17% Similarity=0.241 Sum_probs=14.2
Q ss_pred ccceeEeCCCCccccccC
Q psy15340 52 VEGDLECPESGRKFPISS 69 (81)
Q Consensus 52 ~eg~L~C~~c~~~ypI~d 69 (81)
....++||+|++.|.=.+
T Consensus 16 dg~~~iCpeC~~EW~~~~ 33 (109)
T TIGR00686 16 DGTQLICPSCLYEWNENE 33 (109)
T ss_pred cCCeeECccccccccccc
Confidence 445799999999997553
No 35
>PF13878 zf-C2H2_3: zinc-finger of acetyl-transferase ESCO
Probab=72.11 E-value=1.6 Score=23.96 Aligned_cols=15 Identities=27% Similarity=0.669 Sum_probs=12.2
Q ss_pred ceeEeCCCCcccccc
Q psy15340 54 GDLECPESGRKFPIS 68 (81)
Q Consensus 54 g~L~C~~c~~~ypI~ 68 (81)
|.-.|+.||..|-..
T Consensus 12 ~~~~C~~CgM~Y~~~ 26 (41)
T PF13878_consen 12 GATTCPTCGMLYSPG 26 (41)
T ss_pred CCcCCCCCCCEECCC
Confidence 567999999999653
No 36
>PLN02915 cellulose synthase A [UDP-forming], catalytic subunit
Probab=71.64 E-value=1.6 Score=38.66 Aligned_cols=36 Identities=25% Similarity=0.432 Sum_probs=32.0
Q ss_pred hhhhceeeeeccceeEeCCCCccccccCCccccCCC
Q psy15340 42 VHHALLEVEVVEGDLECPESGRKFPISSGIPNMLLK 77 (81)
Q Consensus 42 lh~~ll~~~v~eg~L~C~~c~~~ypI~dGIP~ml~~ 77 (81)
+=+..++++..+|.=.||+|+..|.-..|.|.+-.+
T Consensus 44 vCr~cyeye~~~g~~~cp~c~t~y~~~~~~~~~~~d 79 (1044)
T PLN02915 44 VCKPCYEYERSEGNQCCPQCNTRYKRHKGCPRVEGD 79 (1044)
T ss_pred cccchhhhhhhcCCccCCccCCchhhhcCCCCccCC
Confidence 345677899999999999999999999999999886
No 37
>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=71.15 E-value=4.2 Score=21.63 Aligned_cols=18 Identities=33% Similarity=0.538 Sum_probs=11.8
Q ss_pred ccceeEeCCCCccccccC
Q psy15340 52 VEGDLECPESGRKFPISS 69 (81)
Q Consensus 52 ~eg~L~C~~c~~~ypI~d 69 (81)
.++...|+.|+..|||.+
T Consensus 17 ~~~~~~C~~C~Y~~~~~~ 34 (35)
T PF02150_consen 17 KEKRVACRTCGYEEPISQ 34 (35)
T ss_dssp TTTTEEESSSS-EEE-SS
T ss_pred CccCcCCCCCCCccCCCC
Confidence 333338999999999975
No 38
>PRK10220 hypothetical protein; Provisional
Probab=70.85 E-value=2.5 Score=28.48 Aligned_cols=18 Identities=22% Similarity=0.449 Sum_probs=14.7
Q ss_pred ccceeEeCCCCccccccC
Q psy15340 52 VEGDLECPESGRKFPISS 69 (81)
Q Consensus 52 ~eg~L~C~~c~~~ypI~d 69 (81)
....++||+|++.|+-.+
T Consensus 17 d~~~~vCpeC~hEW~~~~ 34 (111)
T PRK10220 17 DNGMYICPECAHEWNDAE 34 (111)
T ss_pred CCCeEECCcccCcCCccc
Confidence 345799999999998665
No 39
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=70.01 E-value=3.8 Score=27.71 Aligned_cols=22 Identities=23% Similarity=0.501 Sum_probs=17.5
Q ss_pred eeeeeccceeEeCCCCcccccc
Q psy15340 47 LEVEVVEGDLECPESGRKFPIS 68 (81)
Q Consensus 47 l~~~v~eg~L~C~~c~~~ypI~ 68 (81)
|+++.......|+.||..|++.
T Consensus 62 L~i~~~p~~~~C~~CG~~~~~~ 83 (135)
T PRK03824 62 IIFEEEEAVLKCRNCGNEWSLK 83 (135)
T ss_pred EEEEecceEEECCCCCCEEecc
Confidence 3444555789999999999997
No 40
>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=69.38 E-value=2.4 Score=19.02 Aligned_cols=12 Identities=33% Similarity=0.888 Sum_probs=7.9
Q ss_pred EeCCCCcccccc
Q psy15340 57 ECPESGRKFPIS 68 (81)
Q Consensus 57 ~C~~c~~~ypI~ 68 (81)
.|+.|+..|+=.
T Consensus 2 ~C~~C~~~~~~~ 13 (24)
T PF13894_consen 2 QCPICGKSFRSK 13 (24)
T ss_dssp E-SSTS-EESSH
T ss_pred CCcCCCCcCCcH
Confidence 699999998743
No 41
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=69.29 E-value=4.2 Score=22.38 Aligned_cols=25 Identities=20% Similarity=0.448 Sum_probs=16.3
Q ss_pred eeeeccceeEeCCCCccccccCCcc
Q psy15340 48 EVEVVEGDLECPESGRKFPISSGIP 72 (81)
Q Consensus 48 ~~~v~eg~L~C~~c~~~ypI~dGIP 72 (81)
+++...+.+.||.||..+.+.+.=+
T Consensus 14 ~~~~~~~~~~Cp~CG~~~~~~~~~~ 38 (46)
T PRK00398 14 ELDEYGTGVRCPYCGYRILFKERPP 38 (46)
T ss_pred EECCCCCceECCCCCCeEEEccCCC
Confidence 3444444788898988777665543
No 42
>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=68.34 E-value=3.2 Score=23.09 Aligned_cols=15 Identities=20% Similarity=0.720 Sum_probs=11.4
Q ss_pred eeEeCCCCccccccC
Q psy15340 55 DLECPESGRKFPISS 69 (81)
Q Consensus 55 ~L~C~~c~~~ypI~d 69 (81)
++.|++||+.|.+..
T Consensus 5 ey~C~~Cg~~fe~~~ 19 (52)
T TIGR02605 5 EYRCTACGHRFEVLQ 19 (52)
T ss_pred EEEeCCCCCEeEEEE
Confidence 467888998888753
No 43
>PF04475 DUF555: Protein of unknown function (DUF555); InterPro: IPR007564 This is a family of uncharacterised, hypothetical archaeal proteins.
Probab=67.25 E-value=5.6 Score=26.45 Aligned_cols=30 Identities=33% Similarity=0.503 Sum_probs=23.7
Q ss_pred HHHHHhhhhceeeeeccceeEeCCCCcccc
Q psy15340 37 EFLKKVHHALLEVEVVEGDLECPESGRKFP 66 (81)
Q Consensus 37 ~~l~~lh~~ll~~~v~eg~L~C~~c~~~yp 66 (81)
+.-+.++.-+=-.+|.-|...||.||..++
T Consensus 29 eaGkrLn~~~~~VeIevG~~~cP~Cge~~~ 58 (102)
T PF04475_consen 29 EAGKRLNPDLDYVEIEVGDTICPKCGEELD 58 (102)
T ss_pred HHHHhhCCCCCeEEEecCcccCCCCCCccC
Confidence 455677776666788889999999998764
No 44
>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=66.46 E-value=3.2 Score=23.02 Aligned_cols=13 Identities=31% Similarity=0.922 Sum_probs=11.2
Q ss_pred cceeEeCCCCccc
Q psy15340 53 EGDLECPESGRKF 65 (81)
Q Consensus 53 eg~L~C~~c~~~y 65 (81)
.+.-.||=||+.|
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 45
>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=65.50 E-value=3.5 Score=22.51 Aligned_cols=17 Identities=29% Similarity=0.751 Sum_probs=13.3
Q ss_pred eeEeCCCCccccccCCc
Q psy15340 55 DLECPESGRKFPISSGI 71 (81)
Q Consensus 55 ~L~C~~c~~~ypI~dGI 71 (81)
+..|+.||+.|.+.-.+
T Consensus 5 ey~C~~Cg~~fe~~~~~ 21 (42)
T PF09723_consen 5 EYRCEECGHEFEVLQSI 21 (42)
T ss_pred EEEeCCCCCEEEEEEEc
Confidence 46899999999876554
No 46
>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=65.44 E-value=3.8 Score=19.60 Aligned_cols=12 Identities=42% Similarity=0.974 Sum_probs=10.1
Q ss_pred eEeCCCCccccc
Q psy15340 56 LECPESGRKFPI 67 (81)
Q Consensus 56 L~C~~c~~~ypI 67 (81)
+.|..|++.|.=
T Consensus 2 ~~C~~C~~~F~~ 13 (27)
T PF13912_consen 2 FECDECGKTFSS 13 (27)
T ss_dssp EEETTTTEEESS
T ss_pred CCCCccCCccCC
Confidence 579999999963
No 47
>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=64.06 E-value=4.7 Score=23.68 Aligned_cols=33 Identities=21% Similarity=0.342 Sum_probs=25.4
Q ss_pred hhhcee-eeeccceeEeCCCCccccccCCccccC
Q psy15340 43 HHALLE-VEVVEGDLECPESGRKFPISSGIPNML 75 (81)
Q Consensus 43 h~~ll~-~~v~eg~L~C~~c~~~ypI~dGIP~ml 75 (81)
++.|+. .++.+.+.-||.|+..+.|+.-.|.--
T Consensus 11 nklLa~~g~~~~leIKCpRC~tiN~~~a~~~~~~ 44 (51)
T PF10122_consen 11 NKLLAKAGEVIELEIKCPRCKTINHVRATSPEPE 44 (51)
T ss_pred hHHHhhhcCccEEEEECCCCCccceEeccCCCCC
Confidence 345666 477788999999999999987776543
No 48
>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=63.60 E-value=4.9 Score=26.37 Aligned_cols=20 Identities=20% Similarity=0.395 Sum_probs=16.9
Q ss_pred eeeccceeEeCCCCcccccc
Q psy15340 49 VEVVEGDLECPESGRKFPIS 68 (81)
Q Consensus 49 ~~v~eg~L~C~~c~~~ypI~ 68 (81)
+...++.|+|..|+.+|.+.
T Consensus 46 Y~q~g~~lvC~~C~~~~~~~ 65 (102)
T PF10080_consen 46 YYQEGDQLVCKNCGVRFNLP 65 (102)
T ss_pred eEEECCEEEEecCCCEEehh
Confidence 45678899999999999874
No 49
>PRK11032 hypothetical protein; Provisional
Probab=63.45 E-value=4.2 Score=28.73 Aligned_cols=32 Identities=25% Similarity=0.530 Sum_probs=20.1
Q ss_pred HHHHh-hhhcee-eeec-cceeEeCCCCccccccC
Q psy15340 38 FLKKV-HHALLE-VEVV-EGDLECPESGRKFPISS 69 (81)
Q Consensus 38 ~l~~l-h~~ll~-~~v~-eg~L~C~~c~~~ypI~d 69 (81)
+.+++ |+-... .++. =|.|+|.+||+...|..
T Consensus 104 l~~dl~h~g~Y~sGEvvg~G~LvC~~Cg~~~~~~~ 138 (160)
T PRK11032 104 VFQDLNHHGVYHSGEVVGLGNLVCEKCHHHLAFYT 138 (160)
T ss_pred HHHHhhhcCeeecceeeecceEEecCCCCEEEecC
Confidence 44555 333322 3333 38999999999887754
No 50
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=63.44 E-value=2.6 Score=25.67 Aligned_cols=15 Identities=33% Similarity=0.565 Sum_probs=11.8
Q ss_pred ceeEeCCCCcccccc
Q psy15340 54 GDLECPESGRKFPIS 68 (81)
Q Consensus 54 g~L~C~~c~~~ypI~ 68 (81)
--|.||.||..|.=+
T Consensus 16 ~~lrCPRC~~~FR~~ 30 (65)
T COG4049 16 EFLRCPRCGMVFRRR 30 (65)
T ss_pred eeeeCCchhHHHHHh
Confidence 358999999988643
No 51
>PRK11088 rrmA 23S rRNA methyltransferase A; Provisional
Probab=62.55 E-value=5.7 Score=28.79 Aligned_cols=25 Identities=28% Similarity=0.517 Sum_probs=20.1
Q ss_pred ccceeEeCCCCccccc-cCCccccCCC
Q psy15340 52 VEGDLECPESGRKFPI-SSGIPNMLLK 77 (81)
Q Consensus 52 ~eg~L~C~~c~~~ypI-~dGIP~ml~~ 77 (81)
.++.++|++ +|.|.+ ++|+.||++.
T Consensus 15 ~~~~~~C~~-~h~fd~a~~Gy~~ll~~ 40 (272)
T PRK11088 15 EENSWICPQ-NHQFDCAKEGYVNLLPV 40 (272)
T ss_pred CCCEEEcCC-CCCCccccCceEEeccc
Confidence 357899976 999955 5899999984
No 52
>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=62.36 E-value=5.5 Score=27.59 Aligned_cols=33 Identities=24% Similarity=0.493 Sum_probs=21.4
Q ss_pred HHHHHhhhh-cee-ee-eccceeEeCCCCccccccC
Q psy15340 37 EFLKKVHHA-LLE-VE-VVEGDLECPESGRKFPISS 69 (81)
Q Consensus 37 ~~l~~lh~~-ll~-~~-v~eg~L~C~~c~~~ypI~d 69 (81)
++.+.+.|. ... .+ +--|.|+|.+||+.-.+..
T Consensus 91 el~~d~~h~g~Y~sGE~~g~G~l~C~~Cg~~~~~~~ 126 (146)
T PF07295_consen 91 ELAQDLEHHGVYHSGEVVGPGTLVCENCGHEVELTH 126 (146)
T ss_pred HHHHHHHhcCCeecCcEecCceEecccCCCEEEecC
Confidence 344555444 222 22 3458999999999988876
No 53
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=61.06 E-value=7.1 Score=26.00 Aligned_cols=24 Identities=33% Similarity=0.486 Sum_probs=19.9
Q ss_pred hhceeeeeccceeEeCCCCcccccc
Q psy15340 44 HALLEVEVVEGDLECPESGRKFPIS 68 (81)
Q Consensus 44 ~~ll~~~v~eg~L~C~~c~~~ypI~ 68 (81)
.+-|.++...+...| .||..|++.
T Consensus 59 gA~L~I~~vp~~~~C-~Cg~~~~~~ 82 (124)
T PRK00762 59 DADLIVEMIPVEIEC-ECGYEGVVD 82 (124)
T ss_pred CCEEEEEecCeeEEe-eCcCccccc
Confidence 455677778889999 999998886
No 54
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=60.82 E-value=5.4 Score=26.37 Aligned_cols=18 Identities=28% Similarity=0.414 Sum_probs=15.9
Q ss_pred ccceeEeCCCCccccccC
Q psy15340 52 VEGDLECPESGRKFPISS 69 (81)
Q Consensus 52 ~eg~L~C~~c~~~ypI~d 69 (81)
.++.|+|+.||..++++.
T Consensus 19 ~~~~l~C~kCgye~~~~~ 36 (113)
T COG1594 19 EGGKLVCRKCGYEEEASN 36 (113)
T ss_pred CCcEEECCCCCcchhccc
Confidence 566999999999999985
No 55
>KOG3352|consensus
Probab=59.99 E-value=4.9 Score=28.42 Aligned_cols=27 Identities=22% Similarity=0.361 Sum_probs=17.5
Q ss_pred hhhceeeeeccceeEeCCCCccccccC
Q psy15340 43 HHALLEVEVVEGDLECPESGRKFPISS 69 (81)
Q Consensus 43 h~~ll~~~v~eg~L~C~~c~~~ypI~d 69 (81)
|++..-+--++..-.|++||+.|....
T Consensus 121 ~~V~Wmwl~Kge~~rc~eCG~~fkL~~ 147 (153)
T KOG3352|consen 121 HAVVWMWLEKGETQRCPECGHYFKLVP 147 (153)
T ss_pred cceEEEEEEcCCcccCCcccceEEeee
Confidence 444433333455667999999998653
No 56
>PRK08197 threonine synthase; Validated
Probab=59.40 E-value=5.9 Score=30.58 Aligned_cols=16 Identities=25% Similarity=0.611 Sum_probs=13.7
Q ss_pred eeEeCCCCccccccCC
Q psy15340 55 DLECPESGRKFPISSG 70 (81)
Q Consensus 55 ~L~C~~c~~~ypI~dG 70 (81)
.|+|..||+.|++.+.
T Consensus 7 ~~~C~~Cg~~~~~~~~ 22 (394)
T PRK08197 7 HLECSKCGETYDADQV 22 (394)
T ss_pred EEEECCCCCCCCCCCc
Confidence 5999999999998754
No 57
>COG0375 HybF Zn finger protein HypA/HybF (possibly regulating hydrogenase expression) [General function prediction only]
Probab=57.99 E-value=6.5 Score=26.47 Aligned_cols=17 Identities=35% Similarity=0.714 Sum_probs=10.4
Q ss_pred ceeEeCCCC-ccccccCC
Q psy15340 54 GDLECPESG-RKFPISSG 70 (81)
Q Consensus 54 g~L~C~~c~-~~ypI~dG 70 (81)
....||.|| ..+.|..|
T Consensus 85 ~~~~CP~C~s~~~~i~~G 102 (115)
T COG0375 85 LDYRCPKCGSINLRIIGG 102 (115)
T ss_pred heeECCCCCCCceEEecC
Confidence 344477776 66666665
No 58
>PRK07591 threonine synthase; Validated
Probab=56.84 E-value=6.9 Score=30.70 Aligned_cols=14 Identities=36% Similarity=1.006 Sum_probs=12.3
Q ss_pred eeEeCCCCcccccc
Q psy15340 55 DLECPESGRKFPIS 68 (81)
Q Consensus 55 ~L~C~~c~~~ypI~ 68 (81)
.|+|..||+.|++.
T Consensus 18 ~l~C~~Cg~~~~~~ 31 (421)
T PRK07591 18 ALKCRECGAEYPLG 31 (421)
T ss_pred EEEeCCCCCcCCCC
Confidence 49999999999975
No 59
>PRK06260 threonine synthase; Validated
Probab=56.64 E-value=7.1 Score=30.18 Aligned_cols=15 Identities=27% Similarity=0.570 Sum_probs=12.4
Q ss_pred eeEeCCCCccccccC
Q psy15340 55 DLECPESGRKFPISS 69 (81)
Q Consensus 55 ~L~C~~c~~~ypI~d 69 (81)
.|+|..||+.|++..
T Consensus 3 ~~~C~~cg~~~~~~~ 17 (397)
T PRK06260 3 WLKCIECGKEYDPDE 17 (397)
T ss_pred EEEECCCCCCCCCCC
Confidence 489999999998754
No 60
>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=56.38 E-value=2.6 Score=32.04 Aligned_cols=19 Identities=16% Similarity=0.331 Sum_probs=14.6
Q ss_pred eeeccceeEeCCCCccccc
Q psy15340 49 VEVVEGDLECPESGRKFPI 67 (81)
Q Consensus 49 ~~v~eg~L~C~~c~~~ypI 67 (81)
-+..+..-+||.|++.|++
T Consensus 39 ~~l~~~~~vc~~c~~h~rl 57 (285)
T TIGR00515 39 KELERNLEVCPKCDHHMRM 57 (285)
T ss_pred HHHHhhCCCCCCCCCcCcC
Confidence 3445556799999999987
No 61
>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=56.07 E-value=7.2 Score=19.03 Aligned_cols=16 Identities=31% Similarity=0.688 Sum_probs=12.5
Q ss_pred eccceeEeCCCCcccc
Q psy15340 51 VVEGDLECPESGRKFP 66 (81)
Q Consensus 51 v~eg~L~C~~c~~~yp 66 (81)
..+-...|+.|++.|.
T Consensus 10 ~~~k~~~C~~C~k~F~ 25 (26)
T PF13465_consen 10 TGEKPYKCPYCGKSFS 25 (26)
T ss_dssp SSSSSEEESSSSEEES
T ss_pred CCCCCCCCCCCcCeeC
Confidence 3455689999999984
No 62
>PF08671 SinI: Anti-repressor SinI; InterPro: IPR010981 The SinR repressor is part of a group of Sin (sporulation inhibition) proteins in Bacillus subtilis that regulate the commitment to sporulation in response to extreme adversity []. SinR is a tetrameric repressor protein that binds to the promoters of genes essential for entry into sporulation and prevents their transcription. This repression is overcome through the activity of SinI, which disrupts the SinR tetramer through the formation of a SinI-SinR heterodimer, thereby allowing sporulation to proceed. The SinR structure consists of two domains: a dimerisation domain stabilised by a hydrophobic core, and a DNA-binding domain that is identical to domains of the bacteriophage 434 CI and Cro proteins that regulate prophage induction. The dimerisation domain is a four-helical bundle formed from two helices from the C-terminal residues of SinR and two helices from the central residues of SinI. These regions in SinR and SinI are similar in both structure and sequence. The interaction of SinR monomers to form tetramers is weaker than between SinR and SinI, since SinI can effectively disrupt SinR tetramers. This entry represents the dimerisation domain in both SinI and SinR proteins.; GO: 0005488 binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1B0N_A 2YAL_A.
Probab=55.97 E-value=10 Score=19.82 Aligned_cols=15 Identities=20% Similarity=0.412 Sum_probs=12.5
Q ss_pred cHHHHHHHHHHhCCC
Q psy15340 6 DWSAFYKATLMLGDA 20 (81)
Q Consensus 6 dw~al~~aa~~lg~~ 20 (81)
+|-.|..-|+++|++
T Consensus 4 EW~~Li~eA~~~Gls 18 (30)
T PF08671_consen 4 EWVELIKEAKESGLS 18 (30)
T ss_dssp HHHHHHHHHHHTT--
T ss_pred HHHHHHHHHHHcCCC
Confidence 799999999999983
No 63
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=55.38 E-value=8.2 Score=29.13 Aligned_cols=18 Identities=17% Similarity=0.460 Sum_probs=14.3
Q ss_pred eeeeccceeEeCCCCccc
Q psy15340 48 EVEVVEGDLECPESGRKF 65 (81)
Q Consensus 48 ~~~v~eg~L~C~~c~~~y 65 (81)
..|-..|+++|..||..-
T Consensus 23 v~d~~~Ge~vC~~CG~Vl 40 (310)
T PRK00423 23 IYDYERGEIVCADCGLVI 40 (310)
T ss_pred eEECCCCeEeecccCCcc
Confidence 345678999999999853
No 64
>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=55.15 E-value=6.4 Score=25.09 Aligned_cols=16 Identities=13% Similarity=0.488 Sum_probs=12.2
Q ss_pred ceeEeCCCCccccccC
Q psy15340 54 GDLECPESGRKFPISS 69 (81)
Q Consensus 54 g~L~C~~c~~~ypI~d 69 (81)
.-++|..||+.+++.+
T Consensus 79 ~h~iC~~Cg~v~~~~~ 94 (120)
T PF01475_consen 79 HHFICTQCGKVIDLDD 94 (120)
T ss_dssp EEEEETTTS-EEEE-G
T ss_pred eEEEECCCCCEEEecc
Confidence 3699999999999875
No 65
>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=54.92 E-value=11 Score=19.14 Aligned_cols=15 Identities=20% Similarity=0.350 Sum_probs=9.6
Q ss_pred eccceeEeCCCCccc
Q psy15340 51 VVEGDLECPESGRKF 65 (81)
Q Consensus 51 v~eg~L~C~~c~~~y 65 (81)
..+-.++||.|++.+
T Consensus 17 ~~g~~r~C~~Cg~~~ 31 (32)
T PF09297_consen 17 PGGWARRCPSCGHEH 31 (32)
T ss_dssp SSSS-EEESSSS-EE
T ss_pred CCcCEeECCCCcCEe
Confidence 345588999999864
No 66
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=54.88 E-value=9.9 Score=21.24 Aligned_cols=21 Identities=14% Similarity=0.298 Sum_probs=12.5
Q ss_pred cceeEeCCCCccccccCCccc
Q psy15340 53 EGDLECPESGRKFPISSGIPN 73 (81)
Q Consensus 53 eg~L~C~~c~~~ypI~dGIP~ 73 (81)
.+.+.||+||..=-.+..-+.
T Consensus 17 ~~~irC~~CG~rIlyK~R~~~ 37 (44)
T smart00659 17 KDVVRCRECGYRILYKKRTKR 37 (44)
T ss_pred CCceECCCCCceEEEEeCCCc
Confidence 456777777766544444443
No 67
>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=54.32 E-value=6 Score=27.26 Aligned_cols=19 Identities=21% Similarity=0.441 Sum_probs=14.8
Q ss_pred eeccceeEeCCCCcccccc
Q psy15340 50 EVVEGDLECPESGRKFPIS 68 (81)
Q Consensus 50 ~v~eg~L~C~~c~~~ypI~ 68 (81)
+....-.+||.||..|++.
T Consensus 21 DLnk~p~vcP~cg~~~~~~ 39 (129)
T TIGR02300 21 DLNRRPAVSPYTGEQFPPE 39 (129)
T ss_pred ccCCCCccCCCcCCccCcc
Confidence 3445667899999999887
No 68
>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=54.04 E-value=7.7 Score=24.33 Aligned_cols=16 Identities=19% Similarity=0.463 Sum_probs=13.8
Q ss_pred eeEeCCCCccccccCC
Q psy15340 55 DLECPESGRKFPISSG 70 (81)
Q Consensus 55 ~L~C~~c~~~ypI~dG 70 (81)
-++|..||+.+.+.+-
T Consensus 73 H~~C~~Cg~i~~~~~~ 88 (116)
T cd07153 73 HLICTKCGKVIDFEDC 88 (116)
T ss_pred ceEeCCCCCEEEecCc
Confidence 5999999999998654
No 69
>PLN02569 threonine synthase
Probab=53.13 E-value=7.1 Score=31.56 Aligned_cols=16 Identities=38% Similarity=0.767 Sum_probs=13.8
Q ss_pred eeEeCCCCccccccCC
Q psy15340 55 DLECPESGRKFPISSG 70 (81)
Q Consensus 55 ~L~C~~c~~~ypI~dG 70 (81)
.|.|+.||+.|++.+-
T Consensus 49 ~l~C~~Cg~~y~~~~~ 64 (484)
T PLN02569 49 FLECPLTGEKYSLDEV 64 (484)
T ss_pred ccEeCCCCCcCCCccc
Confidence 4999999999998654
No 70
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=52.87 E-value=7.1 Score=26.40 Aligned_cols=22 Identities=23% Similarity=0.430 Sum_probs=16.6
Q ss_pred eeeeccceeEeCCCCccccccC
Q psy15340 48 EVEVVEGDLECPESGRKFPISS 69 (81)
Q Consensus 48 ~~~v~eg~L~C~~c~~~ypI~d 69 (81)
+.+......+||.|+..|...+
T Consensus 92 ~~e~~~~~Y~Cp~C~~~y~~~e 113 (147)
T smart00531 92 EDETNNAYYKCPNCQSKYTFLE 113 (147)
T ss_pred hcccCCcEEECcCCCCEeeHHH
Confidence 4445567899999999998644
No 71
>PRK03922 hypothetical protein; Provisional
Probab=52.74 E-value=13 Score=25.07 Aligned_cols=29 Identities=34% Similarity=0.419 Sum_probs=21.3
Q ss_pred HHHHhhh-hceeeeeccceeEeCCCCcccc
Q psy15340 38 FLKKVHH-ALLEVEVVEGDLECPESGRKFP 66 (81)
Q Consensus 38 ~l~~lh~-~ll~~~v~eg~L~C~~c~~~yp 66 (81)
.-+.++. -+=-.+|.=|...||.||..|+
T Consensus 31 aGkrLn~~~l~yVeievG~~~cP~cge~~~ 60 (113)
T PRK03922 31 AGKRLNPEDLDYVEVEVGLTICPKCGEPFD 60 (113)
T ss_pred HHhhcCcccCCeEEEecCcccCCCCCCcCC
Confidence 4455666 4444677889999999998775
No 72
>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=52.49 E-value=6.7 Score=26.47 Aligned_cols=11 Identities=27% Similarity=0.785 Sum_probs=8.7
Q ss_pred eeEeCCCCccc
Q psy15340 55 DLECPESGRKF 65 (81)
Q Consensus 55 ~L~C~~c~~~y 65 (81)
--+||.||+.|
T Consensus 124 f~~C~~C~kiy 134 (147)
T PF01927_consen 124 FWRCPGCGKIY 134 (147)
T ss_pred EEECCCCCCEe
Confidence 56788888887
No 73
>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=52.48 E-value=8 Score=30.32 Aligned_cols=12 Identities=42% Similarity=1.046 Sum_probs=10.9
Q ss_pred eeEeCCCCcccc
Q psy15340 55 DLECPESGRKFP 66 (81)
Q Consensus 55 ~L~C~~c~~~yp 66 (81)
.|+|+.||+.||
T Consensus 2 ~l~C~~Cg~~~~ 13 (398)
T TIGR03844 2 TLRCPGCGEVLP 13 (398)
T ss_pred EEEeCCCCCccC
Confidence 589999999998
No 74
>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=51.01 E-value=13 Score=22.59 Aligned_cols=25 Identities=24% Similarity=0.506 Sum_probs=20.5
Q ss_pred eeeccceeEeCCCCccccccCCccc
Q psy15340 49 VEVVEGDLECPESGRKFPISSGIPN 73 (81)
Q Consensus 49 ~~v~eg~L~C~~c~~~ypI~dGIP~ 73 (81)
..+.++.++||--+-.|-+++|-..
T Consensus 50 g~~~~~~i~CP~Hg~~Fdl~tG~~~ 74 (95)
T cd03478 50 GVLTDGRIRCPWHGACFNLRTGDIE 74 (95)
T ss_pred CeEeCCEEEcCCCCCEEECCCCcCc
Confidence 3445789999999999999999654
No 75
>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=50.95 E-value=13 Score=22.61 Aligned_cols=25 Identities=28% Similarity=0.525 Sum_probs=21.5
Q ss_pred eeccceeEeCCCCccccccCCcccc
Q psy15340 50 EVVEGDLECPESGRKFPISSGIPNM 74 (81)
Q Consensus 50 ~v~eg~L~C~~c~~~ypI~dGIP~m 74 (81)
...++.++||--+-.|-+++|.+.=
T Consensus 53 ~~~~~~i~Cp~H~~~f~~~~G~~~~ 77 (98)
T cd03467 53 EGEDGCIVCPCHGSRFDLRTGEVVS 77 (98)
T ss_pred ccCCCEEEeCCCCCEEeCCCccCcC
Confidence 3578899999999999999998753
No 76
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=50.74 E-value=7 Score=19.25 Aligned_cols=7 Identities=43% Similarity=1.056 Sum_probs=3.9
Q ss_pred EeCCCCc
Q psy15340 57 ECPESGR 63 (81)
Q Consensus 57 ~C~~c~~ 63 (81)
.||+||.
T Consensus 4 ~Cp~Cg~ 10 (26)
T PF13248_consen 4 FCPNCGA 10 (26)
T ss_pred CCcccCC
Confidence 4555555
No 77
>smart00355 ZnF_C2H2 zinc finger.
Probab=49.09 E-value=6.7 Score=17.50 Aligned_cols=12 Identities=42% Similarity=0.985 Sum_probs=9.4
Q ss_pred EeCCCCcccccc
Q psy15340 57 ECPESGRKFPIS 68 (81)
Q Consensus 57 ~C~~c~~~ypI~ 68 (81)
.|+.|+..|.-+
T Consensus 2 ~C~~C~~~f~~~ 13 (26)
T smart00355 2 RCPECGKVFKSK 13 (26)
T ss_pred CCCCCcchhCCH
Confidence 589999988643
No 78
>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=48.89 E-value=10 Score=20.33 Aligned_cols=17 Identities=18% Similarity=0.223 Sum_probs=13.0
Q ss_pred eeeeccceeEeCCCCcc
Q psy15340 48 EVEVVEGDLECPESGRK 64 (81)
Q Consensus 48 ~~~v~eg~L~C~~c~~~ 64 (81)
.+...+|..+|.+||+.
T Consensus 18 ~~~~~dG~~yC~~cG~~ 34 (36)
T PF11781_consen 18 WFYSDDGFYYCDRCGHQ 34 (36)
T ss_pred EeEccCCEEEhhhCceE
Confidence 35567889999888875
No 79
>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=48.54 E-value=17 Score=22.01 Aligned_cols=23 Identities=35% Similarity=0.687 Sum_probs=19.8
Q ss_pred eccceeEeCCCCccccccCCccc
Q psy15340 51 VVEGDLECPESGRKFPISSGIPN 73 (81)
Q Consensus 51 v~eg~L~C~~c~~~ypI~dGIP~ 73 (81)
+.++.++||--|-.|-+++|-+.
T Consensus 53 ~~~~~i~Cp~Hg~~fd~~~G~~~ 75 (98)
T cd03528 53 VEGGVIECPLHGGRFDLRTGKAL 75 (98)
T ss_pred EeCCEEEeCCcCCEEECCCCccc
Confidence 45679999999999999999664
No 80
>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=48.12 E-value=11 Score=23.62 Aligned_cols=17 Identities=24% Similarity=0.405 Sum_probs=14.5
Q ss_pred ccceeEeCCCCcccccc
Q psy15340 52 VEGDLECPESGRKFPIS 68 (81)
Q Consensus 52 ~eg~L~C~~c~~~ypI~ 68 (81)
.++.+.|+.|+..+.++
T Consensus 13 ~~~~~~C~~C~~~~~~~ 29 (104)
T TIGR01384 13 KNGVYVCPSCGYEKEKK 29 (104)
T ss_pred CCCeEECcCCCCccccc
Confidence 46799999999998874
No 81
>PRK05654 acetyl-CoA carboxylase subunit beta; Validated
Probab=48.01 E-value=4.2 Score=30.97 Aligned_cols=19 Identities=32% Similarity=0.529 Sum_probs=14.2
Q ss_pred eeccceeEeCCCCcccccc
Q psy15340 50 EVVEGDLECPESGRKFPIS 68 (81)
Q Consensus 50 ~v~eg~L~C~~c~~~ypI~ 68 (81)
+..+..-+||+|++.|++.
T Consensus 41 ~l~~~~~vc~~c~~h~rl~ 59 (292)
T PRK05654 41 ELEANLNVCPKCGHHMRIS 59 (292)
T ss_pred HHHhcCCCCCCCCCCeeCC
Confidence 3444456999999999874
No 82
>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=47.96 E-value=12 Score=22.30 Aligned_cols=25 Identities=24% Similarity=0.604 Sum_probs=21.1
Q ss_pred ceeEeCCCCccccccCCccccCCCC
Q psy15340 54 GDLECPESGRKFPISSGIPNMLLKE 78 (81)
Q Consensus 54 g~L~C~~c~~~ypI~dGIP~ml~~e 78 (81)
..-.||.|+..++|..|-|.+..+.
T Consensus 33 d~~~C~~~~~~~~I~~G~~~v~i~G 57 (76)
T PF05488_consen 33 DQVTCPKCKGPGPIVEGSPTVFING 57 (76)
T ss_pred CcccCCCccccceeccCCCCccCCc
Confidence 4778999999999999999877643
No 83
>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=47.90 E-value=7.8 Score=21.35 Aligned_cols=14 Identities=21% Similarity=0.909 Sum_probs=11.2
Q ss_pred eEeCCCC--ccccccC
Q psy15340 56 LECPESG--RKFPISS 69 (81)
Q Consensus 56 L~C~~c~--~~ypI~d 69 (81)
.+||.|| ..|.|++
T Consensus 19 ~~CP~Cg~~~~~~~~~ 34 (46)
T PF12760_consen 19 FVCPHCGSTKHYRLKT 34 (46)
T ss_pred CCCCCCCCeeeEEeCC
Confidence 8899999 4677765
No 84
>PF13451 zf-trcl: Probable zinc-binding domain
Probab=47.38 E-value=10 Score=21.94 Aligned_cols=18 Identities=28% Similarity=0.774 Sum_probs=14.2
Q ss_pred cceeEeCCCCccccccCC
Q psy15340 53 EGDLECPESGRKFPISSG 70 (81)
Q Consensus 53 eg~L~C~~c~~~ypI~dG 70 (81)
+-.|+|..||..|-++-|
T Consensus 2 Dk~l~C~dCg~~FvfTa~ 19 (49)
T PF13451_consen 2 DKTLTCKDCGAEFVFTAG 19 (49)
T ss_pred CeeEEcccCCCeEEEehh
Confidence 357999999999977643
No 85
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=47.18 E-value=4.3 Score=31.21 Aligned_cols=19 Identities=16% Similarity=0.193 Sum_probs=14.6
Q ss_pred eeccceeEeCCCCcccccc
Q psy15340 50 EVVEGDLECPESGRKFPIS 68 (81)
Q Consensus 50 ~v~eg~L~C~~c~~~ypI~ 68 (81)
+..+..-+||+|++.|++.
T Consensus 52 ~l~~~~~vcp~c~~h~rlt 70 (296)
T CHL00174 52 FLKSKMNICEQCGYHLKMS 70 (296)
T ss_pred HHHHcCCCCCCCCCCcCCC
Confidence 3445567999999999875
No 86
>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=46.97 E-value=8.4 Score=25.05 Aligned_cols=15 Identities=33% Similarity=0.733 Sum_probs=12.2
Q ss_pred ceeEeCCCCcccccc
Q psy15340 54 GDLECPESGRKFPIS 68 (81)
Q Consensus 54 g~L~C~~c~~~ypI~ 68 (81)
.--+|++||+.|...
T Consensus 78 ~~~rC~eCG~~fkL~ 92 (97)
T cd00924 78 KPKRCPECGHVFKLV 92 (97)
T ss_pred CceeCCCCCcEEEEE
Confidence 356899999999765
No 87
>PHA00616 hypothetical protein
Probab=46.95 E-value=5.5 Score=22.60 Aligned_cols=10 Identities=30% Similarity=0.700 Sum_probs=8.6
Q ss_pred EeCCCCcccc
Q psy15340 57 ECPESGRKFP 66 (81)
Q Consensus 57 ~C~~c~~~yp 66 (81)
.|+.||..|-
T Consensus 3 qC~~CG~~F~ 12 (44)
T PHA00616 3 QCLRCGGIFR 12 (44)
T ss_pred ccchhhHHHh
Confidence 6999999884
No 88
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=46.76 E-value=12 Score=26.23 Aligned_cols=15 Identities=33% Similarity=0.660 Sum_probs=12.4
Q ss_pred ccceeEeCCCCcccc
Q psy15340 52 VEGDLECPESGRKFP 66 (81)
Q Consensus 52 ~eg~L~C~~c~~~yp 66 (81)
.+.+|.|++||..++
T Consensus 163 ~~~~~~c~~~~~~e~ 177 (189)
T PRK09521 163 GENELKCPNCGNIET 177 (189)
T ss_pred CCCEEECCCCCCEEe
Confidence 348999999998876
No 89
>PHA02768 hypothetical protein; Provisional
Probab=46.59 E-value=6.7 Score=23.23 Aligned_cols=14 Identities=29% Similarity=0.603 Sum_probs=11.2
Q ss_pred eEeCCCCccccccC
Q psy15340 56 LECPESGRKFPISS 69 (81)
Q Consensus 56 L~C~~c~~~ypI~d 69 (81)
..|+.||+.|..++
T Consensus 6 y~C~~CGK~Fs~~~ 19 (55)
T PHA02768 6 YECPICGEIYIKRK 19 (55)
T ss_pred cCcchhCCeeccHH
Confidence 37999999997654
No 90
>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=46.45 E-value=9.1 Score=21.64 Aligned_cols=10 Identities=40% Similarity=0.846 Sum_probs=5.5
Q ss_pred EeCCCCcccc
Q psy15340 57 ECPESGRKFP 66 (81)
Q Consensus 57 ~C~~c~~~yp 66 (81)
.||-|+|.|.
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 9999999874
No 91
>PRK05638 threonine synthase; Validated
Probab=46.32 E-value=10 Score=29.74 Aligned_cols=13 Identities=31% Similarity=1.020 Sum_probs=11.2
Q ss_pred eeEeCCCCccccc
Q psy15340 55 DLECPESGRKFPI 67 (81)
Q Consensus 55 ~L~C~~c~~~ypI 67 (81)
+|+|..||+.|+.
T Consensus 1 ~l~C~~Cg~~~~~ 13 (442)
T PRK05638 1 KMKCPKCGREYNS 13 (442)
T ss_pred CeEeCCCCCCCCC
Confidence 4799999999985
No 92
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=46.26 E-value=11 Score=27.24 Aligned_cols=16 Identities=25% Similarity=0.802 Sum_probs=13.2
Q ss_pred cceeEeCCCCcccccc
Q psy15340 53 EGDLECPESGRKFPIS 68 (81)
Q Consensus 53 eg~L~C~~c~~~ypI~ 68 (81)
+-+.+||.|+..|..+
T Consensus 3 ~k~~~CPvC~~~F~~~ 18 (214)
T PF09986_consen 3 DKKITCPVCGKEFKTK 18 (214)
T ss_pred CCceECCCCCCeeeee
Confidence 3468999999999865
No 93
>PLN02459 probable adenylate kinase
Probab=45.62 E-value=10 Score=28.45 Aligned_cols=17 Identities=29% Similarity=0.679 Sum_probs=15.1
Q ss_pred ccceeEeCCCCcccccc
Q psy15340 52 VEGDLECPESGRKFPIS 68 (81)
Q Consensus 52 ~eg~L~C~~c~~~ypI~ 68 (81)
..|..+||.||+.|.+.
T Consensus 150 l~gR~~~~~~g~~Yn~~ 166 (261)
T PLN02459 150 CLGRRICSECGKNFNVA 166 (261)
T ss_pred hhccccccccCcccccc
Confidence 56889999999999986
No 94
>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=45.46 E-value=13 Score=25.59 Aligned_cols=27 Identities=22% Similarity=0.352 Sum_probs=16.8
Q ss_pred hhhceeeeeccceeEeCCCCccccccC
Q psy15340 43 HHALLEVEVVEGDLECPESGRKFPISS 69 (81)
Q Consensus 43 h~~ll~~~v~eg~L~C~~c~~~ypI~d 69 (81)
|.++.-.--.+.--+|++||..|....
T Consensus 100 H~v~W~~l~~g~~~RCpeCG~~fkL~~ 126 (136)
T PF01215_consen 100 HDVIWFWLHKGKPQRCPECGQVFKLKY 126 (136)
T ss_dssp SS-EEEEEETTSEEEETTTEEEEEEEE
T ss_pred ceeEEEEEeCCCccCCCCCCeEEEEEE
Confidence 444433333344568999999998754
No 95
>PRK00114 hslO Hsp33-like chaperonin; Reviewed
Probab=45.41 E-value=45 Score=25.07 Aligned_cols=15 Identities=20% Similarity=0.572 Sum_probs=12.8
Q ss_pred eeEeCCCCccccccC
Q psy15340 55 DLECPESGRKFPISS 69 (81)
Q Consensus 55 ~L~C~~c~~~ypI~d 69 (81)
+++|.-|+..|.++.
T Consensus 268 ev~C~FC~~~Y~f~~ 282 (293)
T PRK00114 268 EMVCQFCGNKYLFDE 282 (293)
T ss_pred EEEEeCCCCEEEeCH
Confidence 799999999998753
No 96
>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=45.34 E-value=14 Score=21.70 Aligned_cols=20 Identities=25% Similarity=0.341 Sum_probs=16.2
Q ss_pred cceeEeCCCCccccccCCcc
Q psy15340 53 EGDLECPESGRKFPISSGIP 72 (81)
Q Consensus 53 eg~L~C~~c~~~ypI~dGIP 72 (81)
...+.||.||..|.|..-=|
T Consensus 20 GeiV~Cp~CGaeleVv~~~p 39 (54)
T TIGR01206 20 GELVICDECGAELEVVSLDP 39 (54)
T ss_pred CCEEeCCCCCCEEEEEeCCC
Confidence 44678999999999987666
No 97
>PRK09462 fur ferric uptake regulator; Provisional
Probab=44.77 E-value=13 Score=24.77 Aligned_cols=16 Identities=25% Similarity=0.534 Sum_probs=13.7
Q ss_pred eeEeCCCCccccccCC
Q psy15340 55 DLECPESGRKFPISSG 70 (81)
Q Consensus 55 ~L~C~~c~~~ypI~dG 70 (81)
-++|..||+.+.|.+.
T Consensus 90 H~iC~~Cg~i~~i~~~ 105 (148)
T PRK09462 90 HLICLDCGKVIEFSDD 105 (148)
T ss_pred ceEECCCCCEEEeCCc
Confidence 4999999999998653
No 98
>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=44.64 E-value=16 Score=19.26 Aligned_cols=9 Identities=44% Similarity=1.202 Sum_probs=4.1
Q ss_pred eeEeCCCCc
Q psy15340 55 DLECPESGR 63 (81)
Q Consensus 55 ~L~C~~c~~ 63 (81)
.+.|+.||.
T Consensus 17 ~irC~~CG~ 25 (32)
T PF03604_consen 17 PIRCPECGH 25 (32)
T ss_dssp TSSBSSSS-
T ss_pred cEECCcCCC
Confidence 345555554
No 99
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=43.96 E-value=14 Score=20.99 Aligned_cols=12 Identities=33% Similarity=0.703 Sum_probs=10.1
Q ss_pred cceeEeCCCCcc
Q psy15340 53 EGDLECPESGRK 64 (81)
Q Consensus 53 eg~L~C~~c~~~ 64 (81)
++-..||+|||.
T Consensus 44 ~~i~~Cp~CgRi 55 (56)
T PF02591_consen 44 DEIVFCPNCGRI 55 (56)
T ss_pred CCeEECcCCCcc
Confidence 678899999984
No 100
>PRK12496 hypothetical protein; Provisional
Probab=43.08 E-value=14 Score=25.77 Aligned_cols=36 Identities=17% Similarity=0.257 Sum_probs=22.2
Q ss_pred ccccHHHHHHhhhhceeeeeccc-----------eeEeCCCCcccccc
Q psy15340 32 YEKDSEFLKKVHHALLEVEVVEG-----------DLECPESGRKFPIS 68 (81)
Q Consensus 32 ~~~~e~~l~~lh~~ll~~~v~eg-----------~L~C~~c~~~ypI~ 68 (81)
...|+--++.+...+ .+.+..- ..+|+.||+.|+..
T Consensus 94 lvtDD~~~~~vA~~l-gi~v~~~~~~~i~~~~~w~~~C~gC~~~~~~~ 140 (164)
T PRK12496 94 LYTDDYGIQNVAKKL-NIKFENIKTKGIKKVIKWRKVCKGCKKKYPED 140 (164)
T ss_pred EECcHHHHHHHHHHc-CCeEeccccccchhheeeeEECCCCCccccCC
Confidence 444666666666543 3333221 37899999999853
No 101
>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=42.96 E-value=14 Score=18.44 Aligned_cols=10 Identities=30% Similarity=0.700 Sum_probs=7.9
Q ss_pred ceeEeCCCCc
Q psy15340 54 GDLECPESGR 63 (81)
Q Consensus 54 g~L~C~~c~~ 63 (81)
-...||+||.
T Consensus 15 v~f~CPnCG~ 24 (24)
T PF07754_consen 15 VPFPCPNCGF 24 (24)
T ss_pred ceEeCCCCCC
Confidence 4689999983
No 102
>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=42.59 E-value=14 Score=17.90 Aligned_cols=11 Identities=18% Similarity=0.555 Sum_probs=9.3
Q ss_pred eEeCCCCcccc
Q psy15340 56 LECPESGRKFP 66 (81)
Q Consensus 56 L~C~~c~~~yp 66 (81)
..|..|++.|.
T Consensus 2 ~~C~~C~k~f~ 12 (27)
T PF12171_consen 2 FYCDACDKYFS 12 (27)
T ss_dssp CBBTTTTBBBS
T ss_pred CCcccCCCCcC
Confidence 57999999885
No 103
>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=42.47 E-value=14 Score=23.03 Aligned_cols=21 Identities=29% Similarity=0.449 Sum_probs=13.4
Q ss_pred ccceeEeCCCCccccccCCcccc
Q psy15340 52 VEGDLECPESGRKFPISSGIPNM 74 (81)
Q Consensus 52 ~eg~L~C~~c~~~ypI~dGIP~m 74 (81)
.-|.+.|..||..|... |+-+
T Consensus 43 ~~~~~~C~~Cg~~~~~~--i~~L 63 (81)
T PF05129_consen 43 GIGILSCRVCGESFQTK--INPL 63 (81)
T ss_dssp TEEEEEESSS--EEEEE----SS
T ss_pred CEEEEEecCCCCeEEEc--cCcc
Confidence 45799999999999776 5543
No 104
>COG0777 AccD Acetyl-CoA carboxylase beta subunit [Lipid metabolism]
Probab=41.94 E-value=7 Score=30.27 Aligned_cols=26 Identities=27% Similarity=0.414 Sum_probs=20.5
Q ss_pred hhhceeeeeccceeEeCCCCcccccc
Q psy15340 43 HHALLEVEVVEGDLECPESGRKFPIS 68 (81)
Q Consensus 43 h~~ll~~~v~eg~L~C~~c~~~ypI~ 68 (81)
++.++.-++....-+||.|++-|+|.
T Consensus 35 ~~~~y~~eL~~n~~vcp~c~~h~ri~ 60 (294)
T COG0777 35 GEMLYRKELESNLKVCPKCGHHMRIS 60 (294)
T ss_pred cceeeHHHHHhhhhcccccCcccccC
Confidence 44556667778888999999999885
No 105
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=41.54 E-value=9.3 Score=18.54 Aligned_cols=15 Identities=27% Similarity=0.605 Sum_probs=9.0
Q ss_pred eeccceeEeCCCCcc
Q psy15340 50 EVVEGDLECPESGRK 64 (81)
Q Consensus 50 ~v~eg~L~C~~c~~~ 64 (81)
.+.++.-.|+.||..
T Consensus 8 ~~~~~~~fC~~CG~~ 22 (23)
T PF13240_consen 8 EIEDDAKFCPNCGTP 22 (23)
T ss_pred CCCCcCcchhhhCCc
Confidence 344556667777754
No 106
>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=41.53 E-value=12 Score=23.81 Aligned_cols=25 Identities=20% Similarity=0.402 Sum_probs=21.7
Q ss_pred eeccceeEeCCCCccccccCCcccc
Q psy15340 50 EVVEGDLECPESGRKFPISSGIPNM 74 (81)
Q Consensus 50 ~v~eg~L~C~~c~~~ypI~dGIP~m 74 (81)
.+..+.=.|+.|++.-+..|-||++
T Consensus 28 ~i~~~rS~C~~C~~~L~~~~lIPi~ 52 (92)
T PF06750_consen 28 SIIFPRSHCPHCGHPLSWWDLIPIL 52 (92)
T ss_pred CccCCCCcCcCCCCcCcccccchHH
Confidence 5666778999999999999999974
No 107
>PF14311 DUF4379: Domain of unknown function (DUF4379)
Probab=41.44 E-value=13 Score=20.94 Aligned_cols=12 Identities=25% Similarity=0.753 Sum_probs=10.1
Q ss_pred eeEeCCCCcccc
Q psy15340 55 DLECPESGRKFP 66 (81)
Q Consensus 55 ~L~C~~c~~~yp 66 (81)
.-.|+.||+.|.
T Consensus 28 ~W~C~~Cgh~w~ 39 (55)
T PF14311_consen 28 WWKCPKCGHEWK 39 (55)
T ss_pred EEECCCCCCeeE
Confidence 468999999985
No 108
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=41.40 E-value=12 Score=26.68 Aligned_cols=11 Identities=27% Similarity=0.866 Sum_probs=8.2
Q ss_pred eeEeCCCCccc
Q psy15340 55 DLECPESGRKF 65 (81)
Q Consensus 55 ~L~C~~c~~~y 65 (81)
-.+||.||+.|
T Consensus 130 f~~C~~CgkiY 140 (165)
T COG1656 130 FYRCPKCGKIY 140 (165)
T ss_pred eeECCCCcccc
Confidence 34588888887
No 109
>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=40.46 E-value=12 Score=24.18 Aligned_cols=12 Identities=17% Similarity=0.747 Sum_probs=10.3
Q ss_pred eeEeCCCCcccc
Q psy15340 55 DLECPESGRKFP 66 (81)
Q Consensus 55 ~L~C~~c~~~yp 66 (81)
.++|++||-.|-
T Consensus 35 a~~C~~CGe~y~ 46 (89)
T TIGR03829 35 SISCSHCGMEYQ 46 (89)
T ss_pred cccccCCCcEee
Confidence 679999999883
No 110
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=40.10 E-value=18 Score=20.64 Aligned_cols=12 Identities=17% Similarity=0.326 Sum_probs=8.2
Q ss_pred ceeEeCCCCccc
Q psy15340 54 GDLECPESGRKF 65 (81)
Q Consensus 54 g~L~C~~c~~~y 65 (81)
+.+.|+.||..|
T Consensus 36 ~r~~C~~Cgyt~ 47 (50)
T PRK00432 36 DRWHCGKCGYTE 47 (50)
T ss_pred CcEECCCcCCEE
Confidence 677777777654
No 111
>PTZ00088 adenylate kinase 1; Provisional
Probab=39.87 E-value=12 Score=27.17 Aligned_cols=17 Identities=29% Similarity=0.552 Sum_probs=14.5
Q ss_pred ccceeEeCCCCcccccc
Q psy15340 52 VEGDLECPESGRKFPIS 68 (81)
Q Consensus 52 ~eg~L~C~~c~~~ypI~ 68 (81)
.-|..+||.||+.|.+.
T Consensus 127 l~~Rr~~~~~g~~y~~~ 143 (229)
T PTZ00088 127 LLGRRICNTCNRNFNIA 143 (229)
T ss_pred HHcCcCCCccCCcceec
Confidence 34788999999999886
No 112
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=39.56 E-value=20 Score=21.19 Aligned_cols=15 Identities=27% Similarity=0.618 Sum_probs=12.2
Q ss_pred ccceeEeCCCCcccc
Q psy15340 52 VEGDLECPESGRKFP 66 (81)
Q Consensus 52 ~eg~L~C~~c~~~yp 66 (81)
.+..++||.||..|.
T Consensus 18 ~dDiVvCp~CgapyH 32 (54)
T PF14446_consen 18 GDDIVVCPECGAPYH 32 (54)
T ss_pred CCCEEECCCCCCccc
Confidence 566889999998874
No 113
>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=39.45 E-value=13 Score=20.99 Aligned_cols=11 Identities=45% Similarity=0.917 Sum_probs=9.1
Q ss_pred eEeCCCCcccc
Q psy15340 56 LECPESGRKFP 66 (81)
Q Consensus 56 L~C~~c~~~yp 66 (81)
=+|+.||+.|.
T Consensus 9 K~C~~C~rpf~ 19 (42)
T PF10013_consen 9 KICPVCGRPFT 19 (42)
T ss_pred CcCcccCCcch
Confidence 37999999885
No 114
>PF14787 zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB: 1CL4_A 1DSV_A.
Probab=39.37 E-value=14 Score=20.24 Aligned_cols=11 Identities=36% Similarity=0.881 Sum_probs=7.6
Q ss_pred EeCCCCccccc
Q psy15340 57 ECPESGRKFPI 67 (81)
Q Consensus 57 ~C~~c~~~ypI 67 (81)
.||.|++.|.-
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 59999998864
No 115
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=39.27 E-value=16 Score=25.74 Aligned_cols=22 Identities=23% Similarity=0.304 Sum_probs=15.7
Q ss_pred eeeeccceeEeCCCCccccccC
Q psy15340 48 EVEVVEGDLECPESGRKFPISS 69 (81)
Q Consensus 48 ~~~v~eg~L~C~~c~~~ypI~d 69 (81)
+.+-.....+||.|++.|.--+
T Consensus 110 ~~e~~~~~Y~Cp~C~~rytf~e 131 (178)
T PRK06266 110 EEEENNMFFFCPNCHIRFTFDE 131 (178)
T ss_pred hhccCCCEEECCCCCcEEeHHH
Confidence 3444556889999999997543
No 116
>PHA02825 LAP/PHD finger-like protein; Provisional
Probab=39.22 E-value=6.7 Score=28.00 Aligned_cols=32 Identities=22% Similarity=0.277 Sum_probs=24.5
Q ss_pred HHHhhhhceeeee-ccceeEeCCCCccccccCC
Q psy15340 39 LKKVHHALLEVEV-VEGDLECPESGRKFPISSG 70 (81)
Q Consensus 39 l~~lh~~ll~~~v-~eg~L~C~~c~~~ypI~dG 70 (81)
++-+|+..++.-+ ..+...|+.|+..|.|+.+
T Consensus 31 ~k~VH~sCL~rWi~~s~~~~CeiC~~~Y~i~~~ 63 (162)
T PHA02825 31 NKIVHKECLEEWINTSKNKSCKICNGPYNIKKN 63 (162)
T ss_pred chHHHHHHHHHHHhcCCCCcccccCCeEEEEEe
Confidence 4567777776444 4579999999999999864
No 117
>PRK08329 threonine synthase; Validated
Probab=38.58 E-value=14 Score=28.14 Aligned_cols=13 Identities=31% Similarity=0.787 Sum_probs=11.3
Q ss_pred eEeCCCCcccccc
Q psy15340 56 LECPESGRKFPIS 68 (81)
Q Consensus 56 L~C~~c~~~ypI~ 68 (81)
|.|..||+.|+..
T Consensus 2 l~C~~Cg~~~~~~ 14 (347)
T PRK08329 2 LRCTKCGRTYEEK 14 (347)
T ss_pred cCcCCCCCCcCCC
Confidence 7899999999864
No 118
>COG4530 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=38.46 E-value=14 Score=25.30 Aligned_cols=17 Identities=18% Similarity=0.520 Sum_probs=12.4
Q ss_pred eccceeEeCCCCccccc
Q psy15340 51 VVEGDLECPESGRKFPI 67 (81)
Q Consensus 51 v~eg~L~C~~c~~~ypI 67 (81)
....-.+||.||..||-
T Consensus 22 LNrdPiVsPytG~s~P~ 38 (129)
T COG4530 22 LNRDPIVSPYTGKSYPR 38 (129)
T ss_pred cCCCccccCcccccchH
Confidence 34456788888888875
No 119
>PRK11639 zinc uptake transcriptional repressor; Provisional
Probab=38.19 E-value=18 Score=24.92 Aligned_cols=16 Identities=13% Similarity=0.123 Sum_probs=14.0
Q ss_pred eeEeCCCCccccccCC
Q psy15340 55 DLECPESGRKFPISSG 70 (81)
Q Consensus 55 ~L~C~~c~~~ypI~dG 70 (81)
-++|..||+.+.|.+.
T Consensus 100 H~iC~~CGki~~i~~~ 115 (169)
T PRK11639 100 MFICDRCGAVKEECAE 115 (169)
T ss_pred eEEeCCCCCEEEeccc
Confidence 4999999999999754
No 120
>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=38.13 E-value=14 Score=19.43 Aligned_cols=12 Identities=33% Similarity=0.935 Sum_probs=9.5
Q ss_pred eeEeCCCCcccc
Q psy15340 55 DLECPESGRKFP 66 (81)
Q Consensus 55 ~L~C~~c~~~yp 66 (81)
..+|++||..|-
T Consensus 32 ~~~C~~CGE~~~ 43 (46)
T TIGR03831 32 ALVCPQCGEEYL 43 (46)
T ss_pred ccccccCCCEee
Confidence 567999998773
No 121
>PF11881 DUF3401: Domain of unknown function (DUF3401); InterPro: IPR021818 This domain is functionally uncharacterised. This domain is found in eukaryotes. This presumed domain is typically between 231 to 250 amino acids in length. This domain is found associated with PF02145 from PFAM, PF00595 from PFAM.
Probab=38.01 E-value=22 Score=26.80 Aligned_cols=15 Identities=33% Similarity=0.578 Sum_probs=13.5
Q ss_pred cccHHHHHHHHHHhC
Q psy15340 4 KLDWSAFYKATLMLG 18 (81)
Q Consensus 4 kldw~al~~aa~~lg 18 (81)
-|||.-|+.|||++-
T Consensus 165 gLdWShLVdAAkAfE 179 (239)
T PF11881_consen 165 GLDWSHLVDAAKAFE 179 (239)
T ss_pred cccHHHHHHHHHHhh
Confidence 489999999999875
No 122
>KOG2907|consensus
Probab=37.99 E-value=14 Score=25.06 Aligned_cols=19 Identities=16% Similarity=0.342 Sum_probs=14.5
Q ss_pred cceeEeCCCCccccccCCc
Q psy15340 53 EGDLECPESGRKFPISSGI 71 (81)
Q Consensus 53 eg~L~C~~c~~~ypI~dGI 71 (81)
.+..+|.+|+..||++.--
T Consensus 23 ~~~~~C~~Ck~~~~v~~~~ 41 (116)
T KOG2907|consen 23 QSTVLCIRCKIEYPVSQFS 41 (116)
T ss_pred cCceEeccccccCCHHHhC
Confidence 3455599999999997643
No 123
>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=37.58 E-value=27 Score=21.66 Aligned_cols=18 Identities=28% Similarity=0.556 Sum_probs=16.1
Q ss_pred eEeCCCCccccccCCccc
Q psy15340 56 LECPESGRKFPISSGIPN 73 (81)
Q Consensus 56 L~C~~c~~~ypI~dGIP~ 73 (81)
++||-.+-.|.+++|-+.
T Consensus 65 i~Cp~Hg~~Fdl~tG~~~ 82 (105)
T TIGR02378 65 VACPLHKRNFRLEDGRCL 82 (105)
T ss_pred EECCcCCCEEEcCCcccc
Confidence 999999999999999653
No 124
>PF11238 DUF3039: Protein of unknown function (DUF3039); InterPro: IPR021400 This family of proteins with unknown function appears to be restricted to Actinobacteria.
Probab=36.95 E-value=6.8 Score=23.58 Aligned_cols=12 Identities=25% Similarity=0.442 Sum_probs=8.7
Q ss_pred eeEeCCCCcccc
Q psy15340 55 DLECPESGRKFP 66 (81)
Q Consensus 55 ~L~C~~c~~~yp 66 (81)
.=+||.|.+.|.
T Consensus 44 ~PVCP~Ck~iye 55 (58)
T PF11238_consen 44 FPVCPECKEIYE 55 (58)
T ss_pred CCCCcCHHHHHH
Confidence 457888888773
No 125
>PF13959 DUF4217: Domain of unknown function (DUF4217)
Probab=36.82 E-value=38 Score=19.91 Aligned_cols=20 Identities=25% Similarity=0.468 Sum_probs=14.3
Q ss_pred CccccHHHHHHHHHHhCCCCCCCCC
Q psy15340 2 IPKLDWSAFYKATLMLGDAEISIPE 26 (81)
Q Consensus 2 l~kldw~al~~aa~~lg~~~~~lP~ 26 (81)
+.+||+..+ |+++|+ .+.|.
T Consensus 43 ~~~L~l~~~---A~sfGL--~~~P~ 62 (65)
T PF13959_consen 43 VKKLDLGHL---AKSFGL--LEAPK 62 (65)
T ss_pred cccCCHHHH---HHHcCC--CCCCC
Confidence 457888877 679998 55564
No 126
>PF14577 SEO_C: Sieve element occlusion C-terminus
Probab=36.75 E-value=30 Score=25.91 Aligned_cols=13 Identities=38% Similarity=0.889 Sum_probs=10.3
Q ss_pred cceeEeCCCCccc
Q psy15340 53 EGDLECPESGRKF 65 (81)
Q Consensus 53 eg~L~C~~c~~~y 65 (81)
-....||+|+|.-
T Consensus 212 pe~i~CpeC~R~M 224 (235)
T PF14577_consen 212 PETIVCPECGRPM 224 (235)
T ss_pred CceeECCCCCCch
Confidence 3589999999853
No 127
>PF14205 Cys_rich_KTR: Cysteine-rich KTR
Probab=36.37 E-value=21 Score=21.29 Aligned_cols=11 Identities=27% Similarity=0.534 Sum_probs=7.4
Q ss_pred cceeEeCCCCc
Q psy15340 53 EGDLECPESGR 63 (81)
Q Consensus 53 eg~L~C~~c~~ 63 (81)
++++.||.||.
T Consensus 2 ~~Wi~CP~Cgn 12 (55)
T PF14205_consen 2 SEWILCPICGN 12 (55)
T ss_pred CeEEECCCCCC
Confidence 45677777774
No 128
>COG1273 Ku-homolog [Replication, recombination, and repair]
Probab=36.22 E-value=7.1 Score=30.00 Aligned_cols=68 Identities=16% Similarity=0.228 Sum_probs=47.7
Q ss_pred CCccccHHHHHHHHHHhCCCCCCCCCCccCcccccHHHHHHhhhhceeeeeccceeEeCCCC---------ccccccCCc
Q psy15340 1 MIPKLDWSAFYKATLMLGDAEISIPEKLIDSYEKDSEFLKKVHHALLEVEVVEGDLECPESG---------RKFPISSGI 71 (81)
Q Consensus 1 ml~kldw~al~~aa~~lg~~~~~lP~~~~~~~~~~e~~l~~lh~~ll~~~v~eg~L~C~~c~---------~~ypI~dGI 71 (81)
|++|--|..-. ++|+ -..|-.+-..-.+++--++.||+- ..+-+.-.-+|+.|| +.|.+.+|=
T Consensus 1 m~~Ra~WKG~i----kfgL--V~~PV~ly~ATs~seI~F~~L~r~--t~nrV~~~~Vd~~tGk~Ve~~d~VKGYE~~~~~ 72 (278)
T COG1273 1 MAMRAIWKGYI----KFGL--VNCPVKLYPATSESEIRFHTLHRK--TGNRVRYKYVDSVTGKEVERDDIVKGYEYGKGD 72 (278)
T ss_pred CCcccccccee----Eeee--EecceEeeecccccccchhhhhhh--hCCceeeEEeccccCCccCccceeeeeEecCCc
Confidence 56777887655 5676 556777655555555778888888 666777899999999 567776665
Q ss_pred cccCC
Q psy15340 72 PNMLL 76 (81)
Q Consensus 72 P~ml~ 76 (81)
=+.|.
T Consensus 73 yVile 77 (278)
T COG1273 73 YVILE 77 (278)
T ss_pred EEEec
Confidence 44443
No 129
>PF15392 Joubert: Joubert syndrome-associated
Probab=36.18 E-value=21 Score=28.03 Aligned_cols=18 Identities=28% Similarity=0.586 Sum_probs=14.8
Q ss_pred CCccccHHHHHHHHHHhC
Q psy15340 1 MIPKLDWSAFYKATLMLG 18 (81)
Q Consensus 1 ml~kldw~al~~aa~~lg 18 (81)
+|.||||.|+-....++-
T Consensus 303 ILSKlDW~AiedMvA~Ve 320 (329)
T PF15392_consen 303 ILSKLDWNAIEDMVASVE 320 (329)
T ss_pred hhhhcchHHHHHHHhhhh
Confidence 588999999988776664
No 130
>PRK06450 threonine synthase; Validated
Probab=35.94 E-value=20 Score=27.33 Aligned_cols=13 Identities=15% Similarity=0.289 Sum_probs=11.1
Q ss_pred eeEeCCCCccccc
Q psy15340 55 DLECPESGRKFPI 67 (81)
Q Consensus 55 ~L~C~~c~~~ypI 67 (81)
.|.|..||+.|+.
T Consensus 3 ~~~C~~Cg~~~~~ 15 (338)
T PRK06450 3 KEVCMKCGKERES 15 (338)
T ss_pred eeEECCcCCcCCC
Confidence 3899999999975
No 131
>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=35.86 E-value=20 Score=25.25 Aligned_cols=15 Identities=33% Similarity=0.882 Sum_probs=9.6
Q ss_pred eeEeCCCCccccccC
Q psy15340 55 DLECPESGRKFPISS 69 (81)
Q Consensus 55 ~L~C~~c~~~ypI~d 69 (81)
.+.||.|+..|++..
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 689999999998865
No 132
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=35.47 E-value=25 Score=23.48 Aligned_cols=21 Identities=24% Similarity=0.382 Sum_probs=15.9
Q ss_pred eeeeeccceeEeCCCCccccc
Q psy15340 47 LEVEVVEGDLECPESGRKFPI 67 (81)
Q Consensus 47 l~~~v~eg~L~C~~c~~~ypI 67 (81)
++--..-|.++|..||..|..
T Consensus 38 vkk~~~~g~~~Cg~CGls~e~ 58 (104)
T COG4888 38 VKKTVNIGTAVCGNCGLSFEC 58 (104)
T ss_pred EEecCceeEEEcccCcceEEE
Confidence 344456689999999999864
No 133
>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=34.86 E-value=31 Score=19.57 Aligned_cols=17 Identities=29% Similarity=0.679 Sum_probs=14.2
Q ss_pred eEeCCCCccccccCCcc
Q psy15340 56 LECPESGRKFPISSGIP 72 (81)
Q Consensus 56 L~C~~c~~~ypI~dGIP 72 (81)
-+|+.||..|.=..|-|
T Consensus 2 y~C~~CgyvYd~~~Gd~ 18 (47)
T PF00301_consen 2 YQCPVCGYVYDPEKGDP 18 (47)
T ss_dssp EEETTTSBEEETTTBBG
T ss_pred cCCCCCCEEEcCCcCCc
Confidence 57999999998887755
No 134
>PF07572 BCNT: Bucentaur or craniofacial development; InterPro: IPR011421 Vertebrate BCNT (named after Bucentaur) or human craniofacial development protein 1 (CFDP1) are characterised by an N-terminal acidic region, a central and single IR element (inverted repeat) from the retrotransposable element-1 family (RTE-1) and a highly conserved 82-amino acid region at the C terminus. This entry represents the BCNT C-terminal domain that is also found in Drosophila YETI, a protein that binds to a microtubule-based motor kinesin-1, and the yeast SWR1-complex protein 5 (SWC5), a component of the SWR1 chromatin remodeling complex [, ]. In the bovine genome recombination of BCNT through the IR element with a member of the retrotransposable element-1 family, leads to gene duplications, the insertion of the RTE-1 apurinic/apyrimidinic endonuclease (APE)-like domain (see IPR005135 from INTERPRO) with the concomitant loss of the conserved C-terminal domain of BCNT and with the additional recruitment of either 2 (p97bcnt) or 3 (p97bcnt-2) C-terminal IR-elements [].
Probab=34.58 E-value=8.2 Score=24.45 Aligned_cols=39 Identities=28% Similarity=0.532 Sum_probs=26.6
Q ss_pred cccHHHHHHHHHHhCCCCCCCCCCc--cCcccccHHHHHHhhhhc
Q psy15340 4 KLDWSAFYKATLMLGDAEISIPEKL--IDSYEKDSEFLKKVHHAL 46 (81)
Q Consensus 4 kldw~al~~aa~~lg~~~~~lP~~~--~~~~~~~e~~l~~lh~~l 46 (81)
++||..+...- |+. .+|-... -.+|.+.++||..+..--
T Consensus 29 ~lDW~~fk~~e---gi~-deL~~~~k~k~gYLekq~FL~R~d~r~ 69 (81)
T PF07572_consen 29 KLDWASFKDKE---GIE-DELEKHNKGKDGYLEKQDFLQRVDWRQ 69 (81)
T ss_pred HHhHHHHHHhc---chH-HHHHHHhhcchhhhHHHHHHHHHHHHH
Confidence 78999999754 553 3344433 357888899998876543
No 135
>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=34.52 E-value=21 Score=18.39 Aligned_cols=13 Identities=23% Similarity=0.467 Sum_probs=9.6
Q ss_pred eEeCCCCcccccc
Q psy15340 56 LECPESGRKFPIS 68 (81)
Q Consensus 56 L~C~~c~~~ypI~ 68 (81)
-+|+.||..|.-.
T Consensus 2 ~~C~~CGy~y~~~ 14 (33)
T cd00350 2 YVCPVCGYIYDGE 14 (33)
T ss_pred EECCCCCCEECCC
Confidence 4788999887643
No 136
>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=34.50 E-value=21 Score=24.44 Aligned_cols=21 Identities=24% Similarity=0.523 Sum_probs=12.2
Q ss_pred eeeeeccceeEeCCCCccccc
Q psy15340 47 LEVEVVEGDLECPESGRKFPI 67 (81)
Q Consensus 47 l~~~v~eg~L~C~~c~~~ypI 67 (81)
.+-.|.+..++|=+||+.|..
T Consensus 64 i~kSI~~d~i~clecGk~~k~ 84 (132)
T PF05443_consen 64 IRKSITPDYIICLECGKKFKT 84 (132)
T ss_dssp SSTTB-SS-EE-TBT--EESB
T ss_pred HhhccccCeeEEccCCcccch
Confidence 344567889999999999964
No 137
>PF14122 YokU: YokU-like protein
Probab=34.27 E-value=22 Score=22.96 Aligned_cols=13 Identities=15% Similarity=0.493 Sum_probs=11.1
Q ss_pred ceeEeCCCCcccc
Q psy15340 54 GDLECPESGRKFP 66 (81)
Q Consensus 54 g~L~C~~c~~~yp 66 (81)
-.++|.+||..|-
T Consensus 34 P~i~C~~CgmvYq 46 (87)
T PF14122_consen 34 PAIICSNCGMVYQ 46 (87)
T ss_pred ceeeecCCCcEEe
Confidence 3799999999984
No 138
>COG4338 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=34.10 E-value=12 Score=22.05 Aligned_cols=12 Identities=33% Similarity=0.589 Sum_probs=9.5
Q ss_pred eEeCCCCccccc
Q psy15340 56 LECPESGRKFPI 67 (81)
Q Consensus 56 L~C~~c~~~ypI 67 (81)
-+||.|+|-|.-
T Consensus 13 KICpvCqRPFsW 24 (54)
T COG4338 13 KICPVCQRPFSW 24 (54)
T ss_pred hhhhhhcCchHH
Confidence 479999998853
No 139
>COG1545 Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]
Probab=33.77 E-value=19 Score=24.42 Aligned_cols=10 Identities=30% Similarity=0.893 Sum_probs=8.2
Q ss_pred eEeCCCCccc
Q psy15340 56 LECPESGRKF 65 (81)
Q Consensus 56 L~C~~c~~~y 65 (81)
-.|++||+.|
T Consensus 30 ~kC~~CG~v~ 39 (140)
T COG1545 30 TKCKKCGRVY 39 (140)
T ss_pred EEcCCCCeEE
Confidence 3699999976
No 140
>PRK14526 adenylate kinase; Provisional
Probab=33.55 E-value=18 Score=25.75 Aligned_cols=19 Identities=21% Similarity=0.326 Sum_probs=15.3
Q ss_pred ccceeEeCCCCccccccCC
Q psy15340 52 VEGDLECPESGRKFPISSG 70 (81)
Q Consensus 52 ~eg~L~C~~c~~~ypI~dG 70 (81)
..|..+||.||+.|.+.-.
T Consensus 119 l~~R~~~~~~g~~y~~~~~ 137 (211)
T PRK14526 119 LSGRRICKSCNNIFNIYTL 137 (211)
T ss_pred HHCCCcccccCCccccccC
Confidence 4578999999999987643
No 141
>PLN02674 adenylate kinase
Probab=32.92 E-value=22 Score=26.28 Aligned_cols=21 Identities=29% Similarity=0.512 Sum_probs=17.4
Q ss_pred ccceeEeCCCCccccccCCcc
Q psy15340 52 VEGDLECPESGRKFPISSGIP 72 (81)
Q Consensus 52 ~eg~L~C~~c~~~ypI~dGIP 72 (81)
..|..+||.||+.|.+.-.=|
T Consensus 155 l~gR~~~~~~g~~yn~~~~pp 175 (244)
T PLN02674 155 ITGRWIHPSSGRTYHTKFAPP 175 (244)
T ss_pred HhccccccccCCccccccCCC
Confidence 568999999999998876555
No 142
>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=32.42 E-value=37 Score=21.15 Aligned_cols=23 Identities=26% Similarity=0.538 Sum_probs=18.8
Q ss_pred eeccceeEeCCCCccccccCCcc
Q psy15340 50 EVVEGDLECPESGRKFPISSGIP 72 (81)
Q Consensus 50 ~v~eg~L~C~~c~~~ypI~dGIP 72 (81)
.+.++.++||-=+-.|.+++|=+
T Consensus 54 ~~~~~~i~CP~Hg~~Fdl~tG~~ 76 (101)
T TIGR02377 54 LVMDTTVECPKHAGCFDYRTGEA 76 (101)
T ss_pred EEcCCEEECCccCCEEECCCCcc
Confidence 44567899999999999998854
No 143
>PF08772 NOB1_Zn_bind: Nin one binding (NOB1) Zn-ribbon like; InterPro: IPR014881 This entry corresponds to a zinc ribbon and is found on the RNA binding protein NOB1. ; PDB: 2CON_A.
Probab=32.13 E-value=20 Score=22.25 Aligned_cols=20 Identities=20% Similarity=0.356 Sum_probs=8.5
Q ss_pred hceeeeeccceeEeCCCCcc
Q psy15340 45 ALLEVEVVEGDLECPESGRK 64 (81)
Q Consensus 45 ~ll~~~v~eg~L~C~~c~~~ 64 (81)
+.+.+-...+..-||.||..
T Consensus 14 aCf~~t~~~~k~FCp~CGn~ 33 (73)
T PF08772_consen 14 ACFKITKDMTKQFCPKCGNA 33 (73)
T ss_dssp SS--EES-SS--S-SSS--S
T ss_pred ccccCcCCCCceeCcccCCC
Confidence 44555556788899999865
No 144
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=31.71 E-value=27 Score=20.21 Aligned_cols=23 Identities=17% Similarity=0.488 Sum_probs=14.9
Q ss_pred eeeeccceeEeCCCCccccccCC
Q psy15340 48 EVEVVEGDLECPESGRKFPISSG 70 (81)
Q Consensus 48 ~~~v~eg~L~C~~c~~~ypI~dG 70 (81)
+.+.......||.||..--++.-
T Consensus 17 ~~~~~~~~irCp~Cg~rIl~K~R 39 (49)
T COG1996 17 ELDQETRGIRCPYCGSRILVKER 39 (49)
T ss_pred ehhhccCceeCCCCCcEEEEecc
Confidence 33445667889999877555443
No 145
>PHA00626 hypothetical protein
Probab=31.63 E-value=20 Score=21.65 Aligned_cols=18 Identities=17% Similarity=0.348 Sum_probs=11.4
Q ss_pred eEeCCCCccccccCCccc
Q psy15340 56 LECPESGRKFPISSGIPN 73 (81)
Q Consensus 56 L~C~~c~~~ypI~dGIP~ 73 (81)
+.||.||..=-++.||-+
T Consensus 1 m~CP~CGS~~Ivrcg~cr 18 (59)
T PHA00626 1 MSCPKCGSGNIAKEKTMR 18 (59)
T ss_pred CCCCCCCCceeeeeceec
Confidence 357888776555666643
No 146
>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=31.60 E-value=23 Score=24.41 Aligned_cols=20 Identities=20% Similarity=0.335 Sum_probs=14.6
Q ss_pred eeeccceeEeCCCCcccccc
Q psy15340 49 VEVVEGDLECPESGRKFPIS 68 (81)
Q Consensus 49 ~~v~eg~L~C~~c~~~ypI~ 68 (81)
.+-.....+||.|+++|.--
T Consensus 103 ~e~~~~~Y~Cp~c~~r~tf~ 122 (158)
T TIGR00373 103 FETNNMFFICPNMCVRFTFN 122 (158)
T ss_pred hccCCCeEECCCCCcEeeHH
Confidence 44455678899999998654
No 147
>PF00681 Plectin: Plectin repeat; InterPro: IPR001101 Plectin may have a role in cross-linking intermediate filaments, in inter-linking intermediate filaments with microtubules and microfilaments and in anchoring intermediate filaments to the plasma and nuclear membranes. Plectin is recruited into hemidesmosomes, multiprotein complexes that facilitate adhesion of epithelia to the basement membrane, thereby providing linkage between the intracellular keratin filaments to the laminins of the extracellular matrix. Plectin binds to hemidesmosomes through association of its actin-binding domain with the first pair of fibronectin type III repeats and a small part of the connecting segment of the integrin-beta4 subunit, the latter (integrin-alpha6,beta4) acting as a receptor for the extracellular matrix component laminin-5. The plectin repeat is also seen in the cell adhesion junction plaque proteins, desmoplakin, envoplakin, and bullous pemphigoid antigen. The domains in plakins show considerable sequence homology. The N terminus consists of a plakin domain containing a number of subdomains with high alpha-helical content, while the central coiled-coil domain is composed of heptad repeats involved in the dimerisation of plakin, and the C terminus contains one or more homologous repeat sequences referred to plectin repeats []. This entry represents the plectin repeats found in the C terminus of plakin proteins.; GO: 0005856 cytoskeleton; PDB: 1LM7_A 1LM5_A.
Probab=31.40 E-value=5.2 Score=22.01 Aligned_cols=26 Identities=31% Similarity=0.662 Sum_probs=20.5
Q ss_pred ceeeeeccceeEeCCCCccccccCCc
Q psy15340 46 LLEVEVVEGDLECPESGRKFPISSGI 71 (81)
Q Consensus 46 ll~~~v~eg~L~C~~c~~~ypI~dGI 71 (81)
+++.....|.++.|..|..++|.+.+
T Consensus 3 lLe~Q~~~gGiidp~tg~~lsv~~A~ 28 (45)
T PF00681_consen 3 LLEAQLATGGIIDPETGERLSVEEAI 28 (45)
T ss_dssp HHHHHHTTTSEEETTTTEEEEHHHHH
T ss_pred eeeeeeeeeeEEeCCCCeEEcHHHHH
Confidence 34556678899999999999987654
No 148
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=31.25 E-value=23 Score=23.81 Aligned_cols=20 Identities=25% Similarity=0.705 Sum_probs=16.1
Q ss_pred cceeEeCCCCccccccCCcc
Q psy15340 53 EGDLECPESGRKFPISSGIP 72 (81)
Q Consensus 53 eg~L~C~~c~~~ypI~dGIP 72 (81)
.....|+.|++.|-+..|-|
T Consensus 51 ~qRyrC~~C~~tf~~~~~~~ 70 (129)
T COG3677 51 HQRYKCKSCGSTFTVETGSP 70 (129)
T ss_pred ccccccCCcCcceeeeccCc
Confidence 45778999999888888765
No 149
>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=31.04 E-value=32 Score=18.25 Aligned_cols=12 Identities=42% Similarity=0.886 Sum_probs=8.2
Q ss_pred ceeEeCCCCccc
Q psy15340 54 GDLECPESGRKF 65 (81)
Q Consensus 54 g~L~C~~c~~~y 65 (81)
....||.|+|..
T Consensus 3 ~~~~C~nC~R~v 14 (33)
T PF08209_consen 3 PYVECPNCGRPV 14 (33)
T ss_dssp -EEE-TTTSSEE
T ss_pred CeEECCCCcCCc
Confidence 467899999964
No 150
>PF14030 DUF4245: Protein of unknown function (DUF4245)
Probab=30.85 E-value=55 Score=22.77 Aligned_cols=33 Identities=24% Similarity=0.463 Sum_probs=21.3
Q ss_pred CccccHHHHHHHHH-HhCCCCCCCCCCccCcccccH
Q psy15340 2 IPKLDWSAFYKATL-MLGDAEISIPEKLIDSYEKDS 36 (81)
Q Consensus 2 l~kldw~al~~aa~-~lg~~~~~lP~~~~~~~~~~e 36 (81)
.+.+||.+.+.+++ +++++ .-.|+ +|+++.-|.
T Consensus 38 v~~VD~~~~l~~aar~a~~p-v~~P~-lP~gW~~nS 71 (169)
T PF14030_consen 38 VPEVDYSAALQTAARAAPFP-VRAPE-LPEGWKANS 71 (169)
T ss_pred CcccchhHHHHHHHHhCCCC-eeCCC-CCCCceeee
Confidence 46889988666554 47775 44566 777765543
No 151
>PF13806 Rieske_2: Rieske-like [2Fe-2S] domain; PDB: 2JO6_A 3C0D_A 3D89_A 2JZA_A.
Probab=30.81 E-value=37 Score=21.67 Aligned_cols=19 Identities=21% Similarity=0.427 Sum_probs=16.7
Q ss_pred ceeEeCCCCccccccCCcc
Q psy15340 54 GDLECPESGRKFPISSGIP 72 (81)
Q Consensus 54 g~L~C~~c~~~ypI~dGIP 72 (81)
+.++||-.+..|-++.|-.
T Consensus 63 ~~V~CPlH~~~f~L~tG~~ 81 (104)
T PF13806_consen 63 PCVACPLHKWRFDLRTGEC 81 (104)
T ss_dssp EEEEETTTTEEEETTTTEE
T ss_pred EEEECCCCCCeEECCCcCc
Confidence 3899999999999999953
No 152
>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=30.37 E-value=27 Score=20.21 Aligned_cols=13 Identities=46% Similarity=1.017 Sum_probs=11.3
Q ss_pred CCCccccccCCcc
Q psy15340 60 ESGRKFPISSGIP 72 (81)
Q Consensus 60 ~c~~~ypI~dGIP 72 (81)
+||..||..+|-|
T Consensus 6 rCG~~~p~~~g~~ 18 (51)
T cd06918 6 RCGPKFPLPGGKP 18 (51)
T ss_pred ccCCCccCCCCCc
Confidence 6999999999965
No 153
>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=30.28 E-value=25 Score=26.08 Aligned_cols=15 Identities=20% Similarity=0.585 Sum_probs=9.8
Q ss_pred ceeEeCCCCcccccc
Q psy15340 54 GDLECPESGRKFPIS 68 (81)
Q Consensus 54 g~L~C~~c~~~ypI~ 68 (81)
=+++|.-||+.|.++
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 388999999999764
No 154
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=29.96 E-value=23 Score=24.42 Aligned_cols=11 Identities=36% Similarity=0.815 Sum_probs=9.0
Q ss_pred EeCCCCccccc
Q psy15340 57 ECPESGRKFPI 67 (81)
Q Consensus 57 ~C~~c~~~ypI 67 (81)
.|.+||+.|+-
T Consensus 3 ~Ct~Cg~~f~d 13 (131)
T PF09845_consen 3 QCTKCGRVFED 13 (131)
T ss_pred ccCcCCCCcCC
Confidence 58999999963
No 155
>PF09237 GAGA: GAGA factor; InterPro: IPR015318 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. Members of this entry bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognises the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognises the A in the fourth position of the consensus sequence []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1YUI_A 1YUJ_A.
Probab=29.81 E-value=25 Score=20.89 Aligned_cols=14 Identities=29% Similarity=0.513 Sum_probs=6.8
Q ss_pred cceeEeCCCCcccc
Q psy15340 53 EGDLECPESGRKFP 66 (81)
Q Consensus 53 eg~L~C~~c~~~yp 66 (81)
+.-=+||.|++..+
T Consensus 22 ~~PatCP~C~a~~~ 35 (54)
T PF09237_consen 22 EQPATCPICGAVIR 35 (54)
T ss_dssp S--EE-TTT--EES
T ss_pred CCCCCCCcchhhcc
Confidence 34568999998765
No 156
>COG0735 Fur Fe2+/Zn2+ uptake regulation proteins [Inorganic ion transport and metabolism]
Probab=29.80 E-value=30 Score=23.33 Aligned_cols=16 Identities=19% Similarity=0.493 Sum_probs=14.6
Q ss_pred eeEeCCCCccccccCC
Q psy15340 55 DLECPESGRKFPISSG 70 (81)
Q Consensus 55 ~L~C~~c~~~ypI~dG 70 (81)
-|+|..||+...|.+.
T Consensus 93 HliC~~CG~v~e~~~~ 108 (145)
T COG0735 93 HLICLDCGKVIEFEDD 108 (145)
T ss_pred EEEecCCCCEEEecch
Confidence 6899999999999886
No 157
>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=29.74 E-value=18 Score=25.75 Aligned_cols=13 Identities=23% Similarity=0.710 Sum_probs=10.4
Q ss_pred eEeCCCCcccccc
Q psy15340 56 LECPESGRKFPIS 68 (81)
Q Consensus 56 L~C~~c~~~ypI~ 68 (81)
=.|.+||..||=.
T Consensus 69 sYC~~CGkpyPWt 81 (158)
T PF10083_consen 69 SYCHNCGKPYPWT 81 (158)
T ss_pred hhHHhCCCCCchH
Confidence 3699999999954
No 158
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=29.71 E-value=36 Score=18.06 Aligned_cols=11 Identities=36% Similarity=0.652 Sum_probs=8.6
Q ss_pred ceeEeCCCCcc
Q psy15340 54 GDLECPESGRK 64 (81)
Q Consensus 54 g~L~C~~c~~~ 64 (81)
-.++|+.||..
T Consensus 21 ~R~vC~~Cg~I 31 (34)
T PF14803_consen 21 ERLVCPACGFI 31 (34)
T ss_dssp -EEEETTTTEE
T ss_pred cceECCCCCCE
Confidence 37999999964
No 159
>PF06420 Mgm101p: Mitochondrial genome maintenance MGM101; InterPro: IPR009446 The mgm101 gene was identified as essential for maintenance of the mitochondrial genome in Saccharomyces cerevisiae []. Based on its DNA-binding activity, and experimental work with a temperature-sensitive mgm101 mutant, it has been proposed that the mgm101 gene product performs an essential function in the repair of oxidatively damaged mitochondrial DNA [].; GO: 0000002 mitochondrial genome maintenance, 0000262 mitochondrial chromosome
Probab=29.70 E-value=59 Score=23.42 Aligned_cols=29 Identities=24% Similarity=0.264 Sum_probs=20.6
Q ss_pred HHHHHHHHHHhCCCCCCCCCCccCcccccHHHHHHhhhh
Q psy15340 7 WSAFYKATLMLGDAEISIPEKLIDSYEKDSEFLKKVHHA 45 (81)
Q Consensus 7 w~al~~aa~~lg~~~~~lP~~~~~~~~~~e~~l~~lh~~ 45 (81)
-+||...||+||++ .+ +=|+.|+|.+-.-
T Consensus 112 SNALmRCCKDLGIa-SE---------LWDP~FIr~~k~~ 140 (171)
T PF06420_consen 112 SNALMRCCKDLGIA-SE---------LWDPRFIRKFKKK 140 (171)
T ss_pred HHHHHHHHHHcCcc-hh---------hcChHHHHHHHHH
Confidence 47999999999994 22 2367787776543
No 160
>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=29.53 E-value=33 Score=19.80 Aligned_cols=49 Identities=10% Similarity=0.047 Sum_probs=25.7
Q ss_pred HHHHHHHhCCCCCCCCCCccCcccccHHHHHHhhhhceeeeeccceeEeCCCCccc
Q psy15340 10 FYKATLMLGDAEISIPEKLIDSYEKDSEFLKKVHHALLEVEVVEGDLECPESGRKF 65 (81)
Q Consensus 10 l~~aa~~lg~~~~~lP~~~~~~~~~~e~~l~~lh~~ll~~~v~eg~L~C~~c~~~y 65 (81)
|...|..-|.....+++.+++..=. ..............+.|+.||..+
T Consensus 8 L~yka~~~G~~v~~v~~~~TSq~C~-------~CG~~~~~~~~~r~~~C~~Cg~~~ 56 (69)
T PF07282_consen 8 LEYKAEEYGIQVVEVDEAYTSQTCP-------RCGHRNKKRRSGRVFTCPNCGFEM 56 (69)
T ss_pred HHHHHHHhCCEEEEECCCCCccCcc-------CcccccccccccceEEcCCCCCEE
Confidence 4445555675434456655433211 011111114566789999999875
No 161
>KOG1597|consensus
Probab=29.52 E-value=31 Score=26.91 Aligned_cols=19 Identities=32% Similarity=0.497 Sum_probs=15.8
Q ss_pred eeeeeccceeEeCCCCccc
Q psy15340 47 LEVEVVEGDLECPESGRKF 65 (81)
Q Consensus 47 l~~~v~eg~L~C~~c~~~y 65 (81)
+-.+-..|..+|++||+.+
T Consensus 13 ~V~d~~~gdtvC~~CGlVl 31 (308)
T KOG1597|consen 13 LVEDHSAGDTVCSECGLVL 31 (308)
T ss_pred eeeeccCCceecccCCeee
Confidence 4566678999999999975
No 162
>COG1326 Uncharacterized archaeal Zn-finger protein [General function prediction only]
Probab=29.34 E-value=27 Score=25.71 Aligned_cols=14 Identities=29% Similarity=0.541 Sum_probs=11.9
Q ss_pred ceeEeCCCCccccc
Q psy15340 54 GDLECPESGRKFPI 67 (81)
Q Consensus 54 g~L~C~~c~~~ypI 67 (81)
-.+.|++||..||-
T Consensus 29 ~lvrC~eCG~V~~~ 42 (201)
T COG1326 29 PLVRCEECGTVHPA 42 (201)
T ss_pred eEEEccCCCcEeec
Confidence 47899999999964
No 163
>COG3880 Modulator of heat shock repressor CtsR, McsA [Signal transduction mechanisms]
Probab=29.30 E-value=9.3 Score=27.60 Aligned_cols=12 Identities=33% Similarity=0.612 Sum_probs=10.7
Q ss_pred eeEeCCCCcccc
Q psy15340 55 DLECPESGRKFP 66 (81)
Q Consensus 55 ~L~C~~c~~~yp 66 (81)
.|+|+.|++.|.
T Consensus 74 ~l~C~~C~~Tfk 85 (176)
T COG3880 74 LLGCHNCGMTFK 85 (176)
T ss_pred HhcCccccccHH
Confidence 699999999884
No 164
>PLN02294 cytochrome c oxidase subunit Vb
Probab=29.13 E-value=32 Score=24.83 Aligned_cols=14 Identities=29% Similarity=0.743 Sum_probs=11.9
Q ss_pred eeEeCCCCcccccc
Q psy15340 55 DLECPESGRKFPIS 68 (81)
Q Consensus 55 ~L~C~~c~~~ypI~ 68 (81)
--.||+||..|..+
T Consensus 141 p~RCpeCG~~fkL~ 154 (174)
T PLN02294 141 SFECPVCTQYFELE 154 (174)
T ss_pred ceeCCCCCCEEEEE
Confidence 45699999999876
No 165
>COG3364 Zn-ribbon containing protein [General function prediction only]
Probab=28.97 E-value=25 Score=23.65 Aligned_cols=11 Identities=27% Similarity=0.655 Sum_probs=8.9
Q ss_pred EeCCCCccccc
Q psy15340 57 ECPESGRKFPI 67 (81)
Q Consensus 57 ~C~~c~~~ypI 67 (81)
+|..||..|+=
T Consensus 4 ~CtrCG~vf~~ 14 (112)
T COG3364 4 QCTRCGEVFDD 14 (112)
T ss_pred eeccccccccc
Confidence 58889998873
No 166
>PHA02776 E7 protein; Provisional
Probab=28.85 E-value=53 Score=21.60 Aligned_cols=26 Identities=23% Similarity=0.436 Sum_probs=18.7
Q ss_pred cHHHHHHhhhhceeeeeccceeEeCCCCcc
Q psy15340 35 DSEFLKKVHHALLEVEVVEGDLECPESGRK 64 (81)
Q Consensus 35 ~e~~l~~lh~~ll~~~v~eg~L~C~~c~~~ 64 (81)
+..-+|.|+..|+. +=.++||.|.+.
T Consensus 75 t~~~IR~lqqLLl~----~L~ivCp~Ca~~ 100 (101)
T PHA02776 75 TEPDIQELHNLLLG----SLNIVCPICAPK 100 (101)
T ss_pred ChhhHHHHHHHhcC----CeEEECCCCCCC
Confidence 45667888777773 347899999864
No 167
>cd03531 Rieske_RO_Alpha_KSH The alignment model represents the N-terminal rieske iron-sulfur domain of KshA, the oxygenase component of 3-ketosteroid 9-alpha-hydroxylase (KSH). The terminal oxygenase component of KSH is a key enzyme in the microbial steroid degradation pathway, catalyzing the 9 alpha-hydroxylation of 4-androstene-3,17-dione (AD) and 1,4-androstadiene-3,17-dione (ADD). KSH is a two-component class IA monooxygenase, with terminal oxygenase (KshA) and oxygenase reductase (KshB) components. KSH activity has been found in many actino- and proteo- bacterial genera including Rhodococcus, Nocardia, Arthrobacter, Mycobacterium, and Burkholderia.
Probab=28.76 E-value=59 Score=20.77 Aligned_cols=30 Identities=17% Similarity=0.253 Sum_probs=22.6
Q ss_pred ceeeeeccceeEeCCCCccccccCCccccCC
Q psy15340 46 LLEVEVVEGDLECPESGRKFPISSGIPNMLL 76 (81)
Q Consensus 46 ll~~~v~eg~L~C~~c~~~ypI~dGIP~ml~ 76 (81)
|....+..+.++||--+-.|-+ +|-+.-++
T Consensus 50 L~~G~~~~~~i~CP~Hg~~fd~-~G~~~~~p 79 (115)
T cd03531 50 LSQGTVKGDEIACPFHDWRWGG-DGRCKAIP 79 (115)
T ss_pred CccCcccCCEEECCCCCCEECC-CCCEEECC
Confidence 3344566789999999999999 88665543
No 168
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=28.64 E-value=34 Score=22.31 Aligned_cols=15 Identities=13% Similarity=0.184 Sum_probs=12.6
Q ss_pred cceeEeCCCCccccc
Q psy15340 53 EGDLECPESGRKFPI 67 (81)
Q Consensus 53 eg~L~C~~c~~~ypI 67 (81)
.+..+|+.||..|.-
T Consensus 40 ~~h~~C~~CG~y~~~ 54 (99)
T PRK14892 40 IAIITCGNCGLYTEF 54 (99)
T ss_pred cceEECCCCCCccCE
Confidence 578999999998765
No 169
>PRK09919 anti-adapter protein IraM; Provisional
Probab=28.54 E-value=30 Score=23.35 Aligned_cols=19 Identities=26% Similarity=0.370 Sum_probs=15.8
Q ss_pred ccceeEeCCCCccccccCC
Q psy15340 52 VEGDLECPESGRKFPISSG 70 (81)
Q Consensus 52 ~eg~L~C~~c~~~ypI~dG 70 (81)
+.++++||.||..|-..-|
T Consensus 5 v~dtvi~P~tG~~FS~i~~ 23 (114)
T PRK09919 5 VIDTVISPSTGISFSAISS 23 (114)
T ss_pred EeeeEEcCCCCcchhhhhh
Confidence 4578999999999987655
No 170
>COG4640 Predicted membrane protein [Function unknown]
Probab=28.51 E-value=23 Score=28.90 Aligned_cols=24 Identities=25% Similarity=0.498 Sum_probs=17.2
Q ss_pred hceeeeeccceeEeCCCCcccccc
Q psy15340 45 ALLEVEVVEGDLECPESGRKFPIS 68 (81)
Q Consensus 45 ~ll~~~v~eg~L~C~~c~~~ypI~ 68 (81)
..+.-+-.++...|++||+.|-=+
T Consensus 5 ~kcG~qk~Ed~~qC~qCG~~~t~~ 28 (465)
T COG4640 5 PKCGSQKAEDDVQCTQCGHKFTSR 28 (465)
T ss_pred cccccccccccccccccCCcCCch
Confidence 344446678888899999987533
No 171
>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=28.39 E-value=31 Score=19.79 Aligned_cols=17 Identities=29% Similarity=0.546 Sum_probs=13.1
Q ss_pred eEeCCCCccccccCCcc
Q psy15340 56 LECPESGRKFPISSGIP 72 (81)
Q Consensus 56 L~C~~c~~~ypI~dGIP 72 (81)
.+|..||..|.=..|-|
T Consensus 2 y~C~~CgyiYd~~~Gd~ 18 (50)
T cd00730 2 YECRICGYIYDPAEGDP 18 (50)
T ss_pred cCCCCCCeEECCCCCCc
Confidence 47999999998766643
No 172
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]
Probab=28.32 E-value=36 Score=25.88 Aligned_cols=18 Identities=17% Similarity=0.514 Sum_probs=14.7
Q ss_pred eeeeeccceeEeCCCCcc
Q psy15340 47 LEVEVVEGDLECPESGRK 64 (81)
Q Consensus 47 l~~~v~eg~L~C~~c~~~ 64 (81)
+..|...|+.+|..||..
T Consensus 12 ~~~d~~~ge~VC~~CG~V 29 (285)
T COG1405 12 IITDYERGEIVCADCGLV 29 (285)
T ss_pred ceeeccCCeEEeccCCEE
Confidence 456667899999999975
No 173
>PLN02195 cellulose synthase A
Probab=28.11 E-value=20 Score=31.86 Aligned_cols=28 Identities=29% Similarity=0.402 Sum_probs=23.0
Q ss_pred hhhceeeeeccceeEeCCCCccccccCC
Q psy15340 43 HHALLEVEVVEGDLECPESGRKFPISSG 70 (81)
Q Consensus 43 h~~ll~~~v~eg~L~C~~c~~~ypI~dG 70 (81)
=+..++++..||.=.||+|+..|.=.++
T Consensus 36 CrpCyeyer~eg~q~CpqCkt~Yk~~~~ 63 (977)
T PLN02195 36 CKACLEYEIKEGRKVCLRCGGPYDAENV 63 (977)
T ss_pred ccchhhhhhhcCCccCCccCCccccccc
Confidence 4567788999999999999999993333
No 174
>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=28.01 E-value=32 Score=23.24 Aligned_cols=12 Identities=33% Similarity=0.955 Sum_probs=9.5
Q ss_pred eeEeCCCCcccc
Q psy15340 55 DLECPESGRKFP 66 (81)
Q Consensus 55 ~L~C~~c~~~yp 66 (81)
..+||+|++.-.
T Consensus 69 ~V~CP~C~K~TK 80 (114)
T PF11023_consen 69 QVECPNCGKQTK 80 (114)
T ss_pred eeECCCCCChHh
Confidence 567999998754
No 175
>KOG0978|consensus
Probab=28.01 E-value=30 Score=29.74 Aligned_cols=20 Identities=15% Similarity=0.255 Sum_probs=15.0
Q ss_pred eeEeCCCCccccccCCcccc
Q psy15340 55 DLECPESGRKFPISSGIPNM 74 (81)
Q Consensus 55 ~L~C~~c~~~ypI~dGIP~m 74 (81)
.=.||.|+.+|--.|=.|+.
T Consensus 678 qRKCP~Cn~aFganDv~~I~ 697 (698)
T KOG0978|consen 678 QRKCPKCNAAFGANDVHRIH 697 (698)
T ss_pred cCCCCCCCCCCCcccccccC
Confidence 45688888888877766654
No 176
>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=28.00 E-value=41 Score=20.77 Aligned_cols=13 Identities=31% Similarity=0.578 Sum_probs=10.8
Q ss_pred ccceeEeCCCCcc
Q psy15340 52 VEGDLECPESGRK 64 (81)
Q Consensus 52 ~eg~L~C~~c~~~ 64 (81)
++|...|..|...
T Consensus 1 V~G~V~C~~C~~~ 13 (97)
T PF01190_consen 1 VEGVVYCDDCSSG 13 (97)
T ss_pred CEEEEEeCCCCCC
Confidence 4688999999993
No 177
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=27.97 E-value=37 Score=15.59 Aligned_cols=11 Identities=18% Similarity=0.549 Sum_probs=8.8
Q ss_pred eEeCCCCcccc
Q psy15340 56 LECPESGRKFP 66 (81)
Q Consensus 56 L~C~~c~~~yp 66 (81)
+.|..|++.|.
T Consensus 1 ~~C~~C~~~f~ 11 (25)
T PF12874_consen 1 FYCDICNKSFS 11 (25)
T ss_dssp EEETTTTEEES
T ss_pred CCCCCCCCCcC
Confidence 47999998875
No 178
>PF13445 zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.
Probab=27.79 E-value=31 Score=19.01 Aligned_cols=18 Identities=28% Similarity=0.547 Sum_probs=7.4
Q ss_pred eCCCCccccccCCccccCC
Q psy15340 58 CPESGRKFPISSGIPNMLL 76 (81)
Q Consensus 58 C~~c~~~ypI~dGIP~ml~ 76 (81)
||.|.. |--.+..|.+|+
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 666766 766666777665
No 179
>COG4493 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=27.33 E-value=44 Score=24.66 Aligned_cols=38 Identities=24% Similarity=0.321 Sum_probs=26.4
Q ss_pred CCCccCcccccHHHHHHhhhhceeeeeccceeEeCCCCcccccc
Q psy15340 25 PEKLIDSYEKDSEFLKKVHHALLEVEVVEGDLECPESGRKFPIS 68 (81)
Q Consensus 25 P~~~~~~~~~~e~~l~~lh~~ll~~~v~eg~L~C~~c~~~ypI~ 68 (81)
|++++....+++.|-.++-+. .+|..|+|.| |+.|+=.
T Consensus 141 p~t~~~sel~~~~l~~~~eRl---~~VKK~Elli---g~~~~~e 178 (209)
T COG4493 141 PDTYPISELTDDALKEAAERL---RDVKKGELLI---GRVLPPE 178 (209)
T ss_pred CCCCCcccccHHHHHHHHHHH---HhcchhheEe---eeecCch
Confidence 445666666777777777666 6889999985 6666543
No 180
>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=27.30 E-value=35 Score=18.23 Aligned_cols=15 Identities=20% Similarity=0.616 Sum_probs=9.4
Q ss_pred eeEeCCCCccccccC
Q psy15340 55 DLECPESGRKFPISS 69 (81)
Q Consensus 55 ~L~C~~c~~~ypI~d 69 (81)
...|+.||=.|.|.+
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 457999998887754
No 181
>PF15135 UPF0515: Uncharacterised protein UPF0515
Probab=27.09 E-value=30 Score=26.62 Aligned_cols=13 Identities=23% Similarity=0.833 Sum_probs=11.3
Q ss_pred ceeEeCCCCcccc
Q psy15340 54 GDLECPESGRKFP 66 (81)
Q Consensus 54 g~L~C~~c~~~yp 66 (81)
+++.|++|+|.|.
T Consensus 154 aef~C~~C~h~F~ 166 (278)
T PF15135_consen 154 AEFHCPKCRHNFR 166 (278)
T ss_pred eeeecccccccch
Confidence 4899999999986
No 182
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=26.87 E-value=40 Score=18.61 Aligned_cols=18 Identities=22% Similarity=0.412 Sum_probs=12.5
Q ss_pred eccceeEeCCCCcccccc
Q psy15340 51 VVEGDLECPESGRKFPIS 68 (81)
Q Consensus 51 v~eg~L~C~~c~~~ypI~ 68 (81)
.......|+.|++.|=.+
T Consensus 36 ~~~~~v~C~~C~~~fC~~ 53 (64)
T smart00647 36 EGCNRVTCPKCGFSFCFR 53 (64)
T ss_pred CCCCeeECCCCCCeECCC
Confidence 345678888888887443
No 183
>PF03884 DUF329: Domain of unknown function (DUF329); InterPro: IPR005584 The biological function of these short proteins is unknown, but they contain four conserved cysteines, suggesting that they all bind zinc. YacG (Q5X8H6 from SWISSPROT) from Escherichia coli has been shown to bind zinc and contains the structural motifs typical of zinc-binding proteins []. The conserved four cysteine motif in these proteins (-C-X(2)-C-X(15)-C-X(3)-C-) is not found in other zinc-binding proteins with known structures.; GO: 0008270 zinc ion binding; PDB: 1LV3_A.
Probab=26.52 E-value=42 Score=19.87 Aligned_cols=16 Identities=25% Similarity=0.580 Sum_probs=8.4
Q ss_pred eeEeCCCCccccccCC
Q psy15340 55 DLECPESGRKFPISSG 70 (81)
Q Consensus 55 ~L~C~~c~~~ypI~dG 70 (81)
+..||.||+....+.+
T Consensus 2 ~v~CP~C~k~~~~~~~ 17 (57)
T PF03884_consen 2 TVKCPICGKPVEWSPE 17 (57)
T ss_dssp EEE-TTT--EEE-SSS
T ss_pred cccCCCCCCeecccCC
Confidence 3579999998877443
No 184
>PRK09965 3-phenylpropionate dioxygenase ferredoxin subunit; Provisional
Probab=26.37 E-value=64 Score=20.15 Aligned_cols=20 Identities=25% Similarity=0.531 Sum_probs=17.1
Q ss_pred ceeEeCCCCccccccCCccc
Q psy15340 54 GDLECPESGRKFPISSGIPN 73 (81)
Q Consensus 54 g~L~C~~c~~~ypI~dGIP~ 73 (81)
+.++||--+-.|.+++|-+.
T Consensus 58 ~~i~Cp~Hg~~Fd~~tG~~~ 77 (106)
T PRK09965 58 ATVECPLHAASFCLRTGKAL 77 (106)
T ss_pred CEEEcCCCCCEEEcCCCCee
Confidence 57999999999999999753
No 185
>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=26.07 E-value=48 Score=20.53 Aligned_cols=20 Identities=15% Similarity=0.188 Sum_probs=17.4
Q ss_pred ceeEeCCCCccccccCCccc
Q psy15340 54 GDLECPESGRKFPISSGIPN 73 (81)
Q Consensus 54 g~L~C~~c~~~ypI~dGIP~ 73 (81)
+.++||--+-.|.+++|-..
T Consensus 62 ~~i~Cp~Hg~~Fdl~tG~~~ 81 (103)
T cd03529 62 PVVASPLYKQHFSLKTGRCL 81 (103)
T ss_pred eEEECCCCCCEEEcCCCCcc
Confidence 47999999999999999753
No 186
>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=26.05 E-value=47 Score=18.30 Aligned_cols=12 Identities=25% Similarity=0.609 Sum_probs=9.5
Q ss_pred eccceeEeCCCC
Q psy15340 51 VVEGDLECPESG 62 (81)
Q Consensus 51 v~eg~L~C~~c~ 62 (81)
..+|+.+|+.|+
T Consensus 30 ~k~g~~~Cv~C~ 41 (41)
T PF06677_consen 30 DKDGKIYCVSCG 41 (41)
T ss_pred ecCCCEECCCCC
Confidence 467888999885
No 187
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=26.04 E-value=39 Score=24.61 Aligned_cols=13 Identities=31% Similarity=0.698 Sum_probs=11.1
Q ss_pred ccceeEeCCCCcc
Q psy15340 52 VEGDLECPESGRK 64 (81)
Q Consensus 52 ~eg~L~C~~c~~~ 64 (81)
.+..|.||.||+.
T Consensus 162 ~~~~l~Cp~Cg~t 174 (188)
T COG1096 162 KGNMLKCPNCGNT 174 (188)
T ss_pred cCcEEECCCCCCE
Confidence 6779999999974
No 188
>PF06170 DUF983: Protein of unknown function (DUF983); InterPro: IPR009325 This family consists of several bacterial proteins of unknown function.
Probab=25.95 E-value=31 Score=21.76 Aligned_cols=13 Identities=23% Similarity=0.746 Sum_probs=10.2
Q ss_pred EeCCCCccccccC
Q psy15340 57 ECPESGRKFPISS 69 (81)
Q Consensus 57 ~C~~c~~~ypI~d 69 (81)
.|+.||..|--.+
T Consensus 10 ~C~~CG~d~~~~~ 22 (86)
T PF06170_consen 10 RCPHCGLDYSHAR 22 (86)
T ss_pred cccccCCccccCC
Confidence 6999999886543
No 189
>cd01413 SIR2_Af2 SIR2_Af2: Archaeal and prokaryotic group which includes Archaeoglobus fulgidus Sir2-Af2, Sulfolobus solfataricus ssSir2, and several bacterial homologs; and are members of the SIR2 family of proteins, silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation. Sir2 proteins have been shown to regulate gene silencing, DNA repair, metabolic enzymes, and life span. The Sir2 homolog from the archaea Sulfolobus solftaricus deacetylates the non-specific DNA protein Alba to mediate transcription repression.
Probab=25.52 E-value=40 Score=24.10 Aligned_cols=23 Identities=17% Similarity=0.394 Sum_probs=18.1
Q ss_pred ceeeeeccceeEeCCCCcccccc
Q psy15340 46 LLEVEVVEGDLECPESGRKFPIS 68 (81)
Q Consensus 46 ll~~~v~eg~L~C~~c~~~ypI~ 68 (81)
+++.+-.-..++|..|+..|+..
T Consensus 104 v~elHG~l~~~~C~~C~~~~~~~ 126 (222)
T cd01413 104 VIELHGTLQTAYCVNCGSKYDLE 126 (222)
T ss_pred EEEccCCcCcceECCCCCCcchh
Confidence 45555566789999999999876
No 190
>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=25.41 E-value=33 Score=23.33 Aligned_cols=25 Identities=16% Similarity=0.377 Sum_probs=17.9
Q ss_pred hceeeeeccceeEeCCCCccccccC
Q psy15340 45 ALLEVEVVEGDLECPESGRKFPISS 69 (81)
Q Consensus 45 ~ll~~~v~eg~L~C~~c~~~ypI~d 69 (81)
-+++.+-.=..++|..|++.|+..+
T Consensus 95 ~vielHG~l~~~~C~~C~~~~~~~~ 119 (178)
T PF02146_consen 95 KVIELHGSLFRLRCSKCGKEYDRED 119 (178)
T ss_dssp CEEETTEEEEEEEETTTSBEEEGHH
T ss_pred hhHHHHhhhceeeecCCCccccchh
Confidence 3444444556799999999998754
No 191
>cd01409 SIRT4 SIRT4: Eukaryotic and prokaryotic group (class2) which includes human sirtuin SIRT4 and several bacterial homologs; and are members of the SIR2 family of proteins, silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation. Sir2 proteins have been shown to regulate gene silencing, DNA repair, metabolic enzymes, and life span.
Probab=25.12 E-value=59 Score=23.97 Aligned_cols=23 Identities=17% Similarity=0.274 Sum_probs=17.7
Q ss_pred hceeeeeccceeEeCCCCccccc
Q psy15340 45 ALLEVEVVEGDLECPESGRKFPI 67 (81)
Q Consensus 45 ~ll~~~v~eg~L~C~~c~~~ypI 67 (81)
-+++.+-.=..+.|..|++.|++
T Consensus 108 ~vielHG~~~~~~C~~C~~~~~~ 130 (260)
T cd01409 108 NVVELHGSLHRVVCLSCGFRTPR 130 (260)
T ss_pred CEEEEeeecCEEEeCCCcCccCH
Confidence 35566656668999999999984
No 192
>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=25.10 E-value=23 Score=19.84 Aligned_cols=11 Identities=36% Similarity=1.032 Sum_probs=6.3
Q ss_pred eeEeCCCCccc
Q psy15340 55 DLECPESGRKF 65 (81)
Q Consensus 55 ~L~C~~c~~~y 65 (81)
++.||-|++.|
T Consensus 2 ~f~CP~C~~~~ 12 (54)
T PF05605_consen 2 SFTCPYCGKGF 12 (54)
T ss_pred CcCCCCCCCcc
Confidence 35566666633
No 193
>PF07582 AP_endonuc_2_N: AP endonuclease family 2 C terminus; InterPro: IPR011418 DNA damaging agents such as the anti-tumour drugs bleomycin and neocarzinostatin or those that generate oxygen radicals produce a variety of lesions in DNA. Amongst these is base-loss which forms apurinic/apyrimidinic (AP) sites or strand breaks with atypical 3' termini. DNA repair at the AP sites is initiated by specific endonuclease cleavage of the phosphodiester backbone. Such endonucleases are also generally capable of removing blocking groups from the 3' terminus of DNA strand breaks. AP endonucleases can be classified into two families based on sequence similarity []. This entry represents a highly-conserved sequence found at the C terminus of several apurinic/apyrimidinic (AP) endonucleases in a range of Gram-positive and Gram-negative bacteria. ; PDB: 3LMZ_A 2ZDS_D.
Probab=25.00 E-value=66 Score=18.80 Aligned_cols=15 Identities=27% Similarity=0.618 Sum_probs=11.8
Q ss_pred cHHHHHHHHHHhCCC
Q psy15340 6 DWSAFYKATLMLGDA 20 (81)
Q Consensus 6 dw~al~~aa~~lg~~ 20 (81)
||+.+.++-+++|+.
T Consensus 1 dw~~i~~~L~~~GYd 15 (55)
T PF07582_consen 1 DWKRIFSALREIGYD 15 (55)
T ss_dssp -HHHHHHHHHHTT--
T ss_pred CHHHHHHHHHHcCCC
Confidence 799999999999974
No 194
>COG2824 PhnA Uncharacterized Zn-ribbon-containing protein involved in phosphonate metabolism [Inorganic ion transport and metabolism]
Probab=24.94 E-value=37 Score=22.91 Aligned_cols=14 Identities=36% Similarity=0.852 Sum_probs=11.5
Q ss_pred cceeEeCCCCcccc
Q psy15340 53 EGDLECPESGRKFP 66 (81)
Q Consensus 53 eg~L~C~~c~~~yp 66 (81)
.+.|+||+|++.|-
T Consensus 18 ~~~~~cpec~~ew~ 31 (112)
T COG2824 18 GGQLICPECAHEWN 31 (112)
T ss_pred CceEeCchhccccc
Confidence 45799999999886
No 195
>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=24.92 E-value=40 Score=16.62 Aligned_cols=13 Identities=23% Similarity=0.508 Sum_probs=10.7
Q ss_pred ceeEeCCCCcccc
Q psy15340 54 GDLECPESGRKFP 66 (81)
Q Consensus 54 g~L~C~~c~~~yp 66 (81)
|...|.-|+..|.
T Consensus 2 ~~~~C~~C~~~~~ 14 (35)
T smart00451 2 GGFYCKLCNVTFT 14 (35)
T ss_pred cCeEccccCCccC
Confidence 5678999999875
No 196
>PF04438 zf-HIT: HIT zinc finger; InterPro: IPR007529 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 HIT-type zinc finger, which contains 7 conserved cysteines and one histidine that can potentially coordinate two zinc atoms. It has been named after the first protein that originally defined the domain: the yeast HIT1 protein (P46973 from SWISSPROT) []. The HIT-type zinc finger displays some sequence similarities to the MYND-type zinc finger. The function of this domain is unknown but it is mainly found in nuclear proteins involved in gene regulation and chromatin remodeling. This domain is also found in the thyroid receptor interacting protein 3 (TRIP-3) Q15649 from SWISSPROT, that specifically interacts with the ligand binding domain of the thyroid receptor. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 2YQP_A 2YQQ_A 1X4S_A.
Probab=24.56 E-value=36 Score=17.45 Aligned_cols=13 Identities=23% Similarity=0.879 Sum_probs=7.6
Q ss_pred cceeEeCCCCccc
Q psy15340 53 EGDLECPESGRKF 65 (81)
Q Consensus 53 eg~L~C~~c~~~y 65 (81)
.+.-.||.|+..|
T Consensus 11 ~~kY~Cp~C~~~~ 23 (30)
T PF04438_consen 11 PAKYRCPRCGARY 23 (30)
T ss_dssp EESEE-TTT--EE
T ss_pred CCEEECCCcCCce
Confidence 5677899998765
No 197
>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=24.43 E-value=41 Score=25.00 Aligned_cols=13 Identities=23% Similarity=0.687 Sum_probs=11.6
Q ss_pred eeEeCCCCccccc
Q psy15340 55 DLECPESGRKFPI 67 (81)
Q Consensus 55 ~L~C~~c~~~ypI 67 (81)
+++|.-|+..|.+
T Consensus 262 ev~C~FC~~~Y~f 274 (275)
T cd00498 262 EVTCEFCGEKYHF 274 (275)
T ss_pred EEEEeCCCCEEec
Confidence 7999999999975
No 198
>PRK14811 formamidopyrimidine-DNA glycosylase; Provisional
Probab=24.07 E-value=45 Score=24.75 Aligned_cols=16 Identities=25% Similarity=0.524 Sum_probs=13.3
Q ss_pred cceeEeCCCCcccccc
Q psy15340 53 EGDLECPESGRKFPIS 68 (81)
Q Consensus 53 eg~L~C~~c~~~ypI~ 68 (81)
.++-.||.|++.+|.+
T Consensus 253 R~ty~Cp~CQ~~~~~~ 268 (269)
T PRK14811 253 RGTHFCPQCQPLRPLR 268 (269)
T ss_pred CCcEECCCCcCCCCCC
Confidence 4578899999999876
No 199
>PF13935 Ead_Ea22: Ead/Ea22-like protein
Probab=23.94 E-value=60 Score=21.77 Aligned_cols=17 Identities=18% Similarity=0.249 Sum_probs=14.1
Q ss_pred ccccHHHHHHHHHHhCC
Q psy15340 3 PKLDWSAFYKATLMLGD 19 (81)
Q Consensus 3 ~kldw~al~~aa~~lg~ 19 (81)
.+|||.+|+++|+..-.
T Consensus 1 S~Id~QaLREaAEkAt~ 17 (139)
T PF13935_consen 1 SNIDYQALREAAEKATP 17 (139)
T ss_pred CcccHHHHHHHHHHhcc
Confidence 47999999999988753
No 200
>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=23.90 E-value=48 Score=19.89 Aligned_cols=12 Identities=25% Similarity=0.742 Sum_probs=8.1
Q ss_pred eeEeCCCCcccc
Q psy15340 55 DLECPESGRKFP 66 (81)
Q Consensus 55 ~L~C~~c~~~yp 66 (81)
.+.|+-|++.||
T Consensus 10 ~~~~~cC~~~y~ 21 (71)
T PF05495_consen 10 AIRFPCCGKYYP 21 (71)
T ss_dssp EEEETTTTEEES
T ss_pred EEECCcccCeec
Confidence 466777777766
No 201
>PF09665 RE_Alw26IDE: Type II restriction endonuclease (RE_Alw26IDE); InterPro: IPR014328 There are four classes of restriction endonucleases: types I, II,III and IV. All types of enzymes recognise specific short DNA sequences and carry out the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. They differ in their recognition sequence, subunit composition, cleavage position, and cofactor requirements [, ], as summarised below: Type I enzymes (3.1.21.3 from EC) cleave at sites remote from recognition site; require both ATP and S-adenosyl-L-methionine to function; multifunctional protein with both restriction and methylase (2.1.1.72 from EC) activities. Type II enzymes (3.1.21.4 from EC) cleave within or at short specific distances from recognition site; most require magnesium; single function (restriction) enzymes independent of methylase. Type III enzymes (3.1.21.5 from EC) cleave at sites a short distance from recognition site; require ATP (but doesn't hydrolyse it); S-adenosyl-L-methionine stimulates reaction but is not required; exists as part of a complex with a modification methylase methylase (2.1.1.72 from EC). Type IV enzymes target methylated DNA. Type II restriction endonucleases (3.1.21.4 from EC) are components of prokaryotic DNA restriction-modification mechanisms that protect the organism against invading foreign DNA. These site-specific deoxyribonucleases catalyse the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. Of the 3000 restriction endonucleases that have been characterised, most are homodimeric or tetrameric enzymes that cleave target DNA at sequence-specific sites close to the recognition site. For homodimeric enzymes, the recognition site is usually a palindromic sequence 4-8 bp in length. Most enzymes require magnesium ions as a cofactor for catalysis. Although they can vary in their mode of recognition, many restriction endonucleases share a similar structural core comprising four beta-strands and one alpha-helix, as well as a similar mechanism of cleavage, suggesting a common ancestral origin []. However, there is still considerable diversity amongst restriction endonucleases [, ]. The target site recognition process triggers large conformational changes of the enzyme and the target DNA, leading to the activation of the catalytic centres. Like other DNA binding proteins, restriction enzymes are capable of non-specific DNA binding as well, which is the prerequisite for efficient target site location by facilitated diffusion. Non-specific binding usually does not involve interactions with the bases but only with the DNA backbone []. This entry represents type II restriction endonucleases of the Alw26I/Eco31I/Esp3I family [], whose recognition sequences are 5'-GTCTC-3' (Alw26I), 5'-GGTCTC-3' (Eco31I) and 5'-CGTCTC-3' (Esp3I).
Probab=23.86 E-value=60 Score=27.02 Aligned_cols=42 Identities=21% Similarity=0.233 Sum_probs=29.1
Q ss_pred HHHHHhCCCCCCCCCCccCcccccHHHHHHhhhhceeeeeccceeEeCCCCccccccC
Q psy15340 12 KATLMLGDAEISIPEKLIDSYEKDSEFLKKVHHALLEVEVVEGDLECPESGRKFPISS 69 (81)
Q Consensus 12 ~aa~~lg~~~~~lP~~~~~~~~~~e~~l~~lh~~ll~~~v~eg~L~C~~c~~~ypI~d 69 (81)
+-|.+||+ |+ .+..--....|.+|.+ |.=.|..||+..-|.=
T Consensus 55 ~Ka~elGi-----p~---~~~~~~s~~ar~IHPT--------~~kpCk~CG~~m~i~Y 96 (511)
T PF09665_consen 55 KKADELGI-----PP---SENGWISKAARLIHPT--------KQKPCKTCGKIMSIYY 96 (511)
T ss_pred HHHHHhCC-----CC---CcccHHHHHHHHhCCC--------CCcchHhcCCeeeeee
Confidence 56889996 42 2222245677888876 6778999999877653
No 202
>COG1439 Predicted nucleic acid-binding protein, consists of a PIN domain and a Zn-ribbon module [General function prediction only]
Probab=23.70 E-value=48 Score=23.90 Aligned_cols=17 Identities=29% Similarity=0.489 Sum_probs=13.5
Q ss_pred cceeEeCCCCccccccC
Q psy15340 53 EGDLECPESGRKFPISS 69 (81)
Q Consensus 53 eg~L~C~~c~~~ypI~d 69 (81)
.=.++|..|++.||...
T Consensus 137 ~w~~rC~GC~~~f~~~~ 153 (177)
T COG1439 137 KWRLRCHGCKRIFPEPK 153 (177)
T ss_pred eeeEEEecCceecCCCC
Confidence 34799999999999433
No 203
>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=23.43 E-value=69 Score=25.88 Aligned_cols=19 Identities=37% Similarity=0.597 Sum_probs=13.8
Q ss_pred eccceeEeCCCCccccccC
Q psy15340 51 VVEGDLECPESGRKFPISS 69 (81)
Q Consensus 51 v~eg~L~C~~c~~~ypI~d 69 (81)
-.++.|.|..||..+++.+
T Consensus 236 ~~~~~l~Ch~Cg~~~~~~~ 254 (505)
T TIGR00595 236 KKEGKLRCHYCGYQEPIPK 254 (505)
T ss_pred cCCCeEEcCCCcCcCCCCC
Confidence 3567888888888877643
No 204
>smart00504 Ubox Modified RING finger domain. Modified RING finger domain, without the full complement of Zn2+-binding ligands. Probable involvement in E2-dependent ubiquitination.
Probab=23.18 E-value=36 Score=18.85 Aligned_cols=20 Identities=25% Similarity=0.338 Sum_probs=16.3
Q ss_pred eEeCCCCccccccCCccccC
Q psy15340 56 LECPESGRKFPISSGIPNML 75 (81)
Q Consensus 56 L~C~~c~~~ypI~dGIP~ml 75 (81)
..||.|+..+..++=||+..
T Consensus 36 ~~cP~~~~~~~~~~l~~~~~ 55 (63)
T smart00504 36 GTDPVTGQPLTHEDLIPNLA 55 (63)
T ss_pred CCCCCCcCCCChhhceeCHH
Confidence 48999999998888777643
No 205
>COG4647 AcxC Acetone carboxylase, gamma subunit [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=23.15 E-value=41 Score=23.72 Aligned_cols=33 Identities=18% Similarity=0.211 Sum_probs=23.3
Q ss_pred cHHHHHHhhhhceeeeecc---ceeEeCCCCccccc
Q psy15340 35 DSEFLKKVHHALLEVEVVE---GDLECPESGRKFPI 67 (81)
Q Consensus 35 ~e~~l~~lh~~ll~~~v~e---g~L~C~~c~~~ypI 67 (81)
.+|-|+.+...+.--+... .+.+||+||.--.+
T Consensus 97 tee~lreiyp~s~ipdp~wme~reficpecg~l~ev 132 (165)
T COG4647 97 TEEKLREIYPKSDIPDPQWMEIREFICPECGILHEV 132 (165)
T ss_pred hHHHHHHhCcccCCCCchHHHHHHhhCccccceeee
Confidence 4677888877766655544 47899999985433
No 206
>KOG2462|consensus
Probab=23.03 E-value=34 Score=26.34 Aligned_cols=22 Identities=23% Similarity=0.540 Sum_probs=11.7
Q ss_pred HHhhhhceeeeeccceeEeCCCCccc
Q psy15340 40 KKVHHALLEVEVVEGDLECPESGRKF 65 (81)
Q Consensus 40 ~~lh~~ll~~~v~eg~L~C~~c~~~y 65 (81)
|++|+.+-+ .-...|+.|+++|
T Consensus 150 kQ~H~~~~s----~ka~~C~~C~K~Y 171 (279)
T KOG2462|consen 150 KQTHRSLDS----KKAFSCKYCGKVY 171 (279)
T ss_pred hcccccccc----cccccCCCCCcee
Confidence 455555544 3345555565555
No 207
>PF01096 TFIIS_C: Transcription factor S-II (TFIIS); InterPro: IPR001222 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 IIs (TFIIS). In eukaryotes the initiation of transcription of protein encoding genes by polymerase II (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 eight different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, -IIH and -IIS []. During mRNA elongation, Pol II can encounter DNA sequences that cause reverse movement of the enzyme. Such backtracking involves extrusion of the RNA 3'-end into the pore, and can lead to transcriptional arrest. Escape from arrest requires cleavage of the extruded RNA with the help of TFIIS, which induces mRNA cleavage by enhancing the intrinsic nuclease activity of RNA polymerase (Pol) II, past template-encoded pause sites []. TFIIS extends from the polymerase surface via a pore to the internal active site. Two essential and invariant acidic residues in a TFIIS loop complement the Pol II active site and could position a metal ion and a water molecule for hydrolytic RNA cleavage. TFIIS also induces extensive structural changes in Pol II that would realign nucleic acids in the active centre. TFIIS is a protein of about 300 amino acids. It contains three regions: a variable N-terminal domain not required for TFIIS activity; a conserved central domain required for Pol II binding; and a conserved C-terminal C4-type zinc finger essential for RNA cleavage. The zinc finger folds in a conformation termed a zinc ribbon [] characterised by a three-stranded antiparallel beta-sheet and two beta-hairpins. A backbone model for Pol II-TFIIS complex was obtained from X-ray analysis. It shows that a beta hairpin protrudes from the zinc finger and complements the pol II active site []. Some viral proteins also contain the TFIIS zinc ribbon C-terminal domain. The Vaccinia virus protein, unlike its eukaryotic homologue, is an integral RNA polymerase subunit rather than a readily separable transcription factor []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding, 0006351 transcription, DNA-dependent; PDB: 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I 3I4M_I ....
Probab=22.75 E-value=49 Score=17.66 Aligned_cols=12 Identities=17% Similarity=0.337 Sum_probs=9.2
Q ss_pred ceeEeCCCCccc
Q psy15340 54 GDLECPESGRKF 65 (81)
Q Consensus 54 g~L~C~~c~~~y 65 (81)
--.+|..||+.|
T Consensus 27 ~fy~C~~C~~~w 38 (39)
T PF01096_consen 27 LFYVCCNCGHRW 38 (39)
T ss_dssp EEEEESSSTEEE
T ss_pred EEEEeCCCCCee
Confidence 356788898877
No 208
>TIGR01351 adk adenylate kinases. Adenylate kinase (EC 2.7.4.3) converts ATP + AMP to ADP + ADP, that is, uses ATP as a phosphate donor for AMP. Most members of this family are known or believed to be adenylate kinase. However, some members accept other nucleotide triphosphates as donors, may be unable to use ATP, and may fail to complement adenylate kinase mutants. An example of a nucleoside-triphosphate--adenylate kinase (EC 2.7.4.10) is a GTP:AMP phosphotransferase. This family is designated subfamily rather than equivalog for this reason.
Probab=22.71 E-value=44 Score=23.07 Aligned_cols=21 Identities=29% Similarity=0.665 Sum_probs=17.3
Q ss_pred ccceeEeCCCCccccccCCcc
Q psy15340 52 VEGDLECPESGRKFPISSGIP 72 (81)
Q Consensus 52 ~eg~L~C~~c~~~ypI~dGIP 72 (81)
..+..+||.||+.|.+...-|
T Consensus 121 l~~R~~~~~~g~~y~~~~~~p 141 (210)
T TIGR01351 121 LSGRRICPSCGRVYHLKFNPP 141 (210)
T ss_pred HHCCCccCCcCCccccccCCC
Confidence 456889999999999886655
No 209
>PRK12267 methionyl-tRNA synthetase; Reviewed
Probab=22.67 E-value=2e+02 Score=23.73 Aligned_cols=63 Identities=10% Similarity=-0.102 Sum_probs=35.5
Q ss_pred HHHHHHHHHHhCCCCCCCCCCccC-cccccHHHHHHhhhhceeeeeccceeEeCCCCccccccC
Q psy15340 7 WSAFYKATLMLGDAEISIPEKLID-SYEKDSEFLKKVHHALLEVEVVEGDLECPESGRKFPISS 69 (81)
Q Consensus 7 w~al~~aa~~lg~~~~~lP~~~~~-~~~~~e~~l~~lh~~ll~~~v~eg~L~C~~c~~~ypI~d 69 (81)
.+.+.+..+.+|++-...+.+-.+ ....-+++++.|+..=.-.......+.|+.|++.++=++
T Consensus 76 ~~~fk~~l~~lgI~~D~f~rTt~~~h~~~v~~~~~~L~~kG~IY~~~~~~~yc~~~~~~l~~~~ 139 (648)
T PRK12267 76 SAGFKELWKKLDISYDKFIRTTDERHKKVVQKIFEKLYEQGDIYKGEYEGWYCVSCETFFTESQ 139 (648)
T ss_pred HHHHHHHHHHcCCCCCCCeeCCCHHHHHHHHHHHHHHHHCCCEEEeeEEEeecCCCCccCChHH
Confidence 456778888888741222222111 111234566666554333444446789999999988754
No 210
>COG1743 Adenine-specific DNA methylase containing a Zn-ribbon [DNA replication, recombination, and repair]
Probab=22.41 E-value=45 Score=29.41 Aligned_cols=16 Identities=31% Similarity=0.794 Sum_probs=13.1
Q ss_pred ceeEeCCCCccccccC
Q psy15340 54 GDLECPESGRKFPISS 69 (81)
Q Consensus 54 g~L~C~~c~~~ypI~d 69 (81)
-+..||.||+.+|...
T Consensus 177 w~VkCP~CG~~tP~vg 192 (875)
T COG1743 177 WEVKCPRCGRLTPLVG 192 (875)
T ss_pred EEEecCCcCccccCcc
Confidence 3678999999999653
No 211
>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=22.16 E-value=47 Score=17.33 Aligned_cols=12 Identities=25% Similarity=0.343 Sum_probs=9.2
Q ss_pred eEeCCCCccccc
Q psy15340 56 LECPESGRKFPI 67 (81)
Q Consensus 56 L~C~~c~~~ypI 67 (81)
-+|+.||..|.-
T Consensus 3 ~~C~~CG~i~~g 14 (34)
T cd00729 3 WVCPVCGYIHEG 14 (34)
T ss_pred EECCCCCCEeEC
Confidence 579999987753
No 212
>PF14570 zf-RING_4: RING/Ubox like zinc-binding domain; PDB: 1E4U_A 1UR6_B.
Probab=22.00 E-value=38 Score=19.43 Aligned_cols=14 Identities=14% Similarity=0.427 Sum_probs=6.6
Q ss_pred cceeEeCCCCcccc
Q psy15340 53 EGDLECPESGRKFP 66 (81)
Q Consensus 53 eg~L~C~~c~~~yp 66 (81)
++.=.||.|++.|.
T Consensus 35 ~~~g~CPgCr~~Y~ 48 (48)
T PF14570_consen 35 NEGGRCPGCREPYK 48 (48)
T ss_dssp SS-SB-TTT--B--
T ss_pred ccCCCCCCCCCCCC
Confidence 46778999999883
No 213
>PRK02935 hypothetical protein; Provisional
Probab=21.50 E-value=52 Score=22.14 Aligned_cols=11 Identities=18% Similarity=0.561 Sum_probs=8.7
Q ss_pred eeEeCCCCccc
Q psy15340 55 DLECPESGRKF 65 (81)
Q Consensus 55 ~L~C~~c~~~y 65 (81)
..+||+|++.=
T Consensus 70 qV~CP~C~K~T 80 (110)
T PRK02935 70 QVICPSCEKPT 80 (110)
T ss_pred eeECCCCCchh
Confidence 56999999853
No 214
>PRK05580 primosome assembly protein PriA; Validated
Probab=21.46 E-value=69 Score=26.84 Aligned_cols=18 Identities=28% Similarity=0.523 Sum_probs=13.0
Q ss_pred eccceeEeCCCCcccccc
Q psy15340 51 VVEGDLECPESGRKFPIS 68 (81)
Q Consensus 51 v~eg~L~C~~c~~~ypI~ 68 (81)
...+.|.|..||..+++.
T Consensus 404 ~~~~~l~Ch~Cg~~~~~~ 421 (679)
T PRK05580 404 RFQRRLRCHHCGYQEPIP 421 (679)
T ss_pred CCCCeEECCCCcCCCCCC
Confidence 356778888888877653
No 215
>PRK04309 DNA-directed RNA polymerase subunit A''; Validated
Probab=21.35 E-value=39 Score=26.76 Aligned_cols=11 Identities=18% Similarity=0.241 Sum_probs=8.6
Q ss_pred cHHHHHHhhhh
Q psy15340 35 DSEFLKKVHHA 45 (81)
Q Consensus 35 ~e~~l~~lh~~ 45 (81)
.|--|+.+|.+
T Consensus 75 TQMTL~TFH~A 85 (383)
T PRK04309 75 TQMTMRTFHYA 85 (383)
T ss_pred hhccccccccc
Confidence 45588899988
No 216
>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=21.05 E-value=23 Score=24.76 Aligned_cols=12 Identities=33% Similarity=0.800 Sum_probs=9.9
Q ss_pred ccceeEeCCCCc
Q psy15340 52 VEGDLECPESGR 63 (81)
Q Consensus 52 ~eg~L~C~~c~~ 63 (81)
..|-+.||.||-
T Consensus 29 ~~glv~CP~Cgs 40 (148)
T PF06676_consen 29 ARGLVSCPVCGS 40 (148)
T ss_pred HcCCccCCCCCC
Confidence 468899999984
No 217
>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=20.99 E-value=76 Score=16.97 Aligned_cols=18 Identities=11% Similarity=0.187 Sum_probs=14.2
Q ss_pred eccceeEeCCCCcccccc
Q psy15340 51 VVEGDLECPESGRKFPIS 68 (81)
Q Consensus 51 v~eg~L~C~~c~~~ypI~ 68 (81)
-.+..+.|..|++.|...
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 345688999999999764
No 218
>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=20.98 E-value=44 Score=29.05 Aligned_cols=18 Identities=28% Similarity=0.809 Sum_probs=15.9
Q ss_pred eEeCCCCccccccCCccc
Q psy15340 56 LECPESGRKFPISSGIPN 73 (81)
Q Consensus 56 L~C~~c~~~ypI~dGIP~ 73 (81)
-.|..||=+|.|.+.+|-
T Consensus 124 ~~CT~CGPRfTIi~alPY 141 (750)
T COG0068 124 INCTNCGPRFTIIEALPY 141 (750)
T ss_pred cccCCCCcceeeeccCCC
Confidence 369999999999999983
No 219
>PRK00279 adk adenylate kinase; Reviewed
Probab=20.83 E-value=52 Score=22.79 Aligned_cols=22 Identities=27% Similarity=0.676 Sum_probs=18.2
Q ss_pred ccceeEeCCCCccccccCCccc
Q psy15340 52 VEGDLECPESGRKFPISSGIPN 73 (81)
Q Consensus 52 ~eg~L~C~~c~~~ypI~dGIP~ 73 (81)
..+..+||.||..|++.-.-|.
T Consensus 124 l~~R~~~~~~g~~~~~~~~~p~ 145 (215)
T PRK00279 124 LSGRRICPACGRTYHVKFNPPK 145 (215)
T ss_pred HhCCcccCccCCcccccCCCCC
Confidence 4578899999999999876664
No 220
>cd03532 Rieske_RO_Alpha_VanA_DdmC Rieske non-heme iron oxygenase (RO) family, Vanillate-O-demethylase oxygenase (VanA) and dicamba O-demethylase oxygenase (DdmC) subfamily, N-terminal Rieske domain of the oxygenase alpha subunit; ROs comprise a large class of aromatic ring-hydroxylating dioxygenases that enable microorganisms to tolerate and utilize aromatic compounds for growth. The oxygenase alpha subunit contains an N-terminal Rieske domain with an [2Fe-2S] cluster and a C-terminal catalytic domain with a mononuclear Fe(II) binding site. The Rieske [2Fe-2S] cluster accepts electrons from a reductase or ferredoxin component and transfers them to the mononuclear iron for catalysis. Vanillate-O-demethylase is a heterodimeric enzyme consisting of a terminal oxygenase (VanA) and reductase (VanB) components. This enzyme reductively catalyzes the conversion of vanillate into protocatechuate and formaldehyde. Protocatechuate and vanillate are important intermediate metabolites in the degrad
Probab=20.80 E-value=74 Score=20.18 Aligned_cols=24 Identities=33% Similarity=0.422 Sum_probs=18.5
Q ss_pred eeeeccceeEeCCCCccccccCCcc
Q psy15340 48 EVEVVEGDLECPESGRKFPISSGIP 72 (81)
Q Consensus 48 ~~~v~eg~L~C~~c~~~ypI~dGIP 72 (81)
...+.++.++||-.+-.|- .+|-.
T Consensus 55 ~G~~~~~~i~Cp~Hg~~fd-~~G~~ 78 (116)
T cd03532 55 KGSVEGGGLVCGYHGLEFD-SDGRC 78 (116)
T ss_pred CCcccCCEEEeCCCCcEEc-CCCCE
Confidence 3345678899999999999 68843
No 221
>cd00814 MetRS_core catalytic core domain of methioninyl-tRNA synthetases. Methionine tRNA synthetase (MetRS) catalytic core domain. This class I enzyme aminoacylates the 2'-OH of the nucleotide at the 3' of the appropriate tRNA. MetRS, which consists of the core domain and an anti-codon binding domain, functions as a monomer. However, in some species the anti-codon binding domain is followed by an EMAP domain. In this case, MetRS functions as a homodimer. The core domain is based on the Rossman fold and is responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate. It contains the characteristic class I HIGH and KMSKS motifs, which are involved in ATP binding. As a result of a deletion event, MetRS has a significantly shorter core domain insertion than IleRS, ValRS, and LeuR. Consequently, the MetRS insertion lacks the editing function.
Probab=20.72 E-value=2.3e+02 Score=21.06 Aligned_cols=55 Identities=24% Similarity=0.167 Sum_probs=32.3
Q ss_pred HHHHHHHHHhCCCCCCCCCCcc--Ccccc---cHHHHHHhhhhceeeeeccceeEeCCCCcccc
Q psy15340 8 SAFYKATLMLGDAEISIPEKLI--DSYEK---DSEFLKKVHHALLEVEVVEGDLECPESGRKFP 66 (81)
Q Consensus 8 ~al~~aa~~lg~~~~~lP~~~~--~~~~~---~e~~l~~lh~~ll~~~v~eg~L~C~~c~~~yp 66 (81)
+.+.+..+.||+. ++... .+... -+++++.|+..=+-.........|+.|++.++
T Consensus 73 ~~~~~~l~~LgI~----~D~~~~tt~~~~~~~v~~i~~~L~ekG~iY~~~~~~~yc~~~~~~l~ 132 (319)
T cd00814 73 EIFKDLFKWLNIS----FDYFIRTTSPRHKEIVQEFFKKLYENGYIYEGEYEGLYCVSCERFLP 132 (319)
T ss_pred HHHHHHHHHcCCc----CCCCeeCCCHHHHHHHHHHHHHHHHCCCEEeeeeeeeECCCCCcEee
Confidence 4567778888873 22221 12111 23455555554333445667889999998876
No 222
>PF13695 zf-3CxxC: Zinc-binding domain
Probab=20.69 E-value=59 Score=20.53 Aligned_cols=16 Identities=19% Similarity=0.549 Sum_probs=12.3
Q ss_pred cceeEeCCCCcccccc
Q psy15340 53 EGDLECPESGRKFPIS 68 (81)
Q Consensus 53 eg~L~C~~c~~~ypI~ 68 (81)
-|.+.|+.|++.+.=.
T Consensus 3 ~grF~C~~C~~~W~S~ 18 (98)
T PF13695_consen 3 FGRFQCSKCSRGWTSA 18 (98)
T ss_pred EEEEECCCCCCCCccC
Confidence 3789999999887533
No 223
>PRK00481 NAD-dependent deacetylase; Provisional
Probab=20.67 E-value=55 Score=23.55 Aligned_cols=24 Identities=13% Similarity=0.373 Sum_probs=18.0
Q ss_pred ceeeeeccceeEeCCCCccccccC
Q psy15340 46 LLEVEVVEGDLECPESGRKFPISS 69 (81)
Q Consensus 46 ll~~~v~eg~L~C~~c~~~ypI~d 69 (81)
+++.+-.-..+.|..|+..|+..+
T Consensus 113 v~elHG~~~~~~C~~C~~~~~~~~ 136 (242)
T PRK00481 113 VIELHGSLLRARCTKCGQTYDLDE 136 (242)
T ss_pred eeeccCCcCceeeCCCCCCcChhh
Confidence 555555667899999999997653
No 224
>PRK05978 hypothetical protein; Provisional
Probab=20.65 E-value=46 Score=23.17 Aligned_cols=13 Identities=23% Similarity=0.623 Sum_probs=10.3
Q ss_pred EeCCCCccccccC
Q psy15340 57 ECPESGRKFPISS 69 (81)
Q Consensus 57 ~C~~c~~~ypI~d 69 (81)
.|+.||..|...+
T Consensus 54 ~C~~CG~~~~~~~ 66 (148)
T PRK05978 54 HCAACGEDFTHHR 66 (148)
T ss_pred CccccCCccccCC
Confidence 6888888887763
No 225
>PF14907 NTP_transf_5: Uncharacterised nucleotidyltransferase
Probab=20.58 E-value=84 Score=21.81 Aligned_cols=17 Identities=24% Similarity=0.542 Sum_probs=15.3
Q ss_pred ccccHHHHHHHHHHhCC
Q psy15340 3 PKLDWSAFYKATLMLGD 19 (81)
Q Consensus 3 ~kldw~al~~aa~~lg~ 19 (81)
+.+||+.+.+.|+.+|+
T Consensus 217 ~~~dw~~l~~~~~~~~~ 233 (249)
T PF14907_consen 217 SQIDWEYLLERAKRLGL 233 (249)
T ss_pred CcccHHHHHHHHHHcCC
Confidence 36899999999999997
No 226
>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=20.54 E-value=76 Score=20.01 Aligned_cols=21 Identities=14% Similarity=0.102 Sum_probs=16.4
Q ss_pred ceeeeeccceeEeCCCCcccc
Q psy15340 46 LLEVEVVEGDLECPESGRKFP 66 (81)
Q Consensus 46 ll~~~v~eg~L~C~~c~~~yp 66 (81)
||..+..-..|+|..|+.+-.
T Consensus 2 lf~y~~~~~vlIC~~C~~av~ 22 (109)
T PF12013_consen 2 LFHYNPEYRVLICRQCQYAVQ 22 (109)
T ss_pred CceEcCcCCEEEeCCCCcccC
Confidence 566777788999999997643
No 227
>COG1176 PotB ABC-type spermidine/putrescine transport system, permease component I [Amino acid transport and metabolism]
Probab=20.46 E-value=54 Score=24.94 Aligned_cols=17 Identities=35% Similarity=0.423 Sum_probs=14.3
Q ss_pred CccccHHHHHHHHHHhCC
Q psy15340 2 IPKLDWSAFYKATLMLGD 19 (81)
Q Consensus 2 l~kldw~al~~aa~~lg~ 19 (81)
+.|+|.+ +.+||++||-
T Consensus 176 l~~id~~-L~eAA~dLGA 192 (287)
T COG1176 176 LEKIDPS-LLEAARDLGA 192 (287)
T ss_pred HHhCCHH-HHHHHHHcCC
Confidence 4588887 9999999994
No 228
>COG1856 Uncharacterized homolog of biotin synthetase [Function unknown]
Probab=20.42 E-value=26 Score=26.84 Aligned_cols=12 Identities=42% Similarity=1.101 Sum_probs=10.6
Q ss_pred eeEeCCCCcccc
Q psy15340 55 DLECPESGRKFP 66 (81)
Q Consensus 55 ~L~C~~c~~~yp 66 (81)
.|-|+.||+.|-
T Consensus 22 ~lnC~HCg~~~L 33 (275)
T COG1856 22 SLNCPHCGRHYL 33 (275)
T ss_pred EecChHHHHHHH
Confidence 799999999883
No 229
>PF14375 Cys_rich_CWC: Cysteine-rich CWC
Probab=20.42 E-value=47 Score=18.59 Aligned_cols=11 Identities=36% Similarity=0.933 Sum_probs=8.3
Q ss_pred eCCCCcccccc
Q psy15340 58 CPESGRKFPIS 68 (81)
Q Consensus 58 C~~c~~~ypI~ 68 (81)
||.||..|.=.
T Consensus 1 CP~Cg~~f~C~ 11 (50)
T PF14375_consen 1 CPRCGAPFECG 11 (50)
T ss_pred CCCCCCcCCCC
Confidence 78888888654
No 230
>PF01197 Ribosomal_L31: Ribosomal protein L31; InterPro: IPR002150 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 L31 is one of the proteins from the large ribosomal subunit. L31 is a protein of 66 to 97 amino-acid residues which has only been found so far in bacteria and in some plant and algal chloroplasts.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3D5D_4 3PYO_1 3D5B_4 3PYV_1 3PYT_1 3MRZ_1 3MS1_1 3PYR_1 3F1F_4 3F1H_4 ....
Probab=20.36 E-value=70 Score=19.28 Aligned_cols=19 Identities=21% Similarity=0.426 Sum_probs=15.7
Q ss_pred eeEeCCCCccccccCCccc
Q psy15340 55 DLECPESGRKFPISSGIPN 73 (81)
Q Consensus 55 ~L~C~~c~~~ypI~dGIP~ 73 (81)
...|..||..|.+...++.
T Consensus 13 ~v~c~s~g~~~~~~St~~~ 31 (69)
T PF01197_consen 13 KVTCSSCGNTFETRSTKEY 31 (69)
T ss_dssp EEEES-SSSCECECSSSSE
T ss_pred EEEEcCCCCEEEEEECCcc
Confidence 6789999999999998875
No 231
>COG1779 C4-type Zn-finger protein [General function prediction only]
Probab=20.23 E-value=54 Score=24.14 Aligned_cols=24 Identities=17% Similarity=0.087 Sum_probs=16.9
Q ss_pred hhhhceeeeeccceeEeCCCCccc
Q psy15340 42 VHHALLEVEVVEGDLECPESGRKF 65 (81)
Q Consensus 42 lh~~ll~~~v~eg~L~C~~c~~~y 65 (81)
++.......|+....+|.+||-++
T Consensus 30 ~~~IPyFG~V~i~t~~C~~CgYR~ 53 (201)
T COG1779 30 LYDIPYFGEVLISTGVCERCGYRS 53 (201)
T ss_pred eecCCccceEEEEEEEccccCCcc
Confidence 344555667788888888888654
No 232
>KOG2906|consensus
Probab=20.18 E-value=53 Score=21.90 Aligned_cols=18 Identities=33% Similarity=0.586 Sum_probs=15.5
Q ss_pred ceeEeCCCCccccccCCc
Q psy15340 54 GDLECPESGRKFPISSGI 71 (81)
Q Consensus 54 g~L~C~~c~~~ypI~dGI 71 (81)
.++.|+.|.-.|||+.-|
T Consensus 20 ~rf~C~tCpY~~~I~~ei 37 (105)
T KOG2906|consen 20 NRFSCRTCPYVFPISREI 37 (105)
T ss_pred eeEEcCCCCceeeEeeee
Confidence 589999999999998554
No 233
>PTZ00043 cytochrome c oxidase subunit; Provisional
Probab=20.15 E-value=53 Score=25.08 Aligned_cols=25 Identities=28% Similarity=0.377 Sum_probs=16.0
Q ss_pred hhhceeeeeccc-eeEeCCCCcccccc
Q psy15340 43 HHALLEVEVVEG-DLECPESGRKFPIS 68 (81)
Q Consensus 43 h~~ll~~~v~eg-~L~C~~c~~~ypI~ 68 (81)
|.++.- -..+| -=+|++||..|...
T Consensus 169 H~VvWF-wLrEGkpqRCpECGqVFKLV 194 (268)
T PTZ00043 169 HVPLWF-RCREGFLYRCGECDQIFMLV 194 (268)
T ss_pred ceeEEE-EecCCCCccCCCCCcEEEEE
Confidence 444432 33444 55899999999763
No 234
>COG2331 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=20.10 E-value=29 Score=22.18 Aligned_cols=17 Identities=29% Similarity=0.796 Sum_probs=13.6
Q ss_pred eeEeCCCCccccccCCc
Q psy15340 55 DLECPESGRKFPISSGI 71 (81)
Q Consensus 55 ~L~C~~c~~~ypI~dGI 71 (81)
.-.|.+||.+|.+-.++
T Consensus 12 ~Y~c~~cg~~~dvvq~~ 28 (82)
T COG2331 12 SYECTECGNRFDVVQAM 28 (82)
T ss_pred EEeecccchHHHHHHhc
Confidence 35799999999887765
No 235
>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