Query psy5308
Match_columns 137
No_of_seqs 131 out of 185
Neff 4.8
Searched_HMMs 46136
Date Fri Aug 16 23:13:45 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy5308.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/5308hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3799|consensus 100.0 1.8E-35 3.8E-40 226.6 8.4 114 16-129 1-114 (169)
2 PF02318 FYVE_2: FYVE-type zin 100.0 3.2E-30 7E-35 189.6 6.6 99 23-130 1-102 (118)
3 cd00065 FYVE FYVE domain; Zinc 94.7 0.021 4.5E-07 36.0 1.7 50 80-129 2-55 (57)
4 PF09297 zf-NADH-PPase: NADH p 93.5 0.043 9.3E-07 31.7 1.3 29 103-131 2-30 (32)
5 PF01363 FYVE: FYVE zinc finge 92.4 0.047 1E-06 35.8 0.4 50 80-129 9-64 (69)
6 smart00064 FYVE Protein presen 90.9 0.15 3.2E-06 33.3 1.7 50 80-129 10-63 (68)
7 PF05715 zf-piccolo: Piccolo Z 90.8 0.16 3.4E-06 34.3 1.7 46 81-128 3-55 (61)
8 PF04810 zf-Sec23_Sec24: Sec23 90.7 0.08 1.7E-06 32.2 0.2 13 120-132 22-34 (40)
9 PF03604 DNA_RNApol_7kD: DNA d 87.3 0.27 5.8E-06 29.0 0.8 24 106-130 2-25 (32)
10 PRK12495 hypothetical protein; 86.1 2 4.2E-05 35.7 5.4 65 24-106 4-68 (226)
11 PF10235 Cript: Microtubule-as 85.1 0.57 1.2E-05 33.8 1.6 34 80-114 44-79 (90)
12 KOG1013|consensus 84.4 0.64 1.4E-05 40.8 2.0 100 20-130 82-193 (362)
13 smart00661 RPOL9 RNA polymeras 83.2 0.68 1.5E-05 28.5 1.2 9 122-130 20-28 (52)
14 PF04545 Sigma70_r4: Sigma-70, 82.0 4 8.8E-05 24.8 4.4 26 22-47 2-27 (50)
15 PF14803 Nudix_N_2: Nudix N-te 81.2 0.54 1.2E-05 28.0 0.2 27 105-131 1-31 (34)
16 cd00729 rubredoxin_SM Rubredox 79.7 0.58 1.3E-05 27.6 0.0 12 122-133 2-13 (34)
17 PF04880 NUDE_C: NUDE protein, 78.7 2.3 5E-05 33.6 3.1 32 29-65 14-47 (166)
18 PF07282 OrfB_Zn_ribbon: Putat 75.9 1.5 3.2E-05 28.6 1.1 27 105-131 29-55 (69)
19 PRK00398 rpoP DNA-directed RNA 75.0 2.2 4.7E-05 26.2 1.7 24 106-129 5-28 (46)
20 PF05400 FliT: Flagellar prote 74.1 10 0.00022 24.7 4.9 40 24-63 37-76 (84)
21 PRK00432 30S ribosomal protein 73.8 1.7 3.7E-05 27.8 1.0 27 104-131 20-46 (50)
22 smart00154 ZnF_AN1 AN1-like Zi 73.7 1.7 3.7E-05 26.3 0.9 27 83-111 1-27 (39)
23 COG1998 RPS31 Ribosomal protei 72.0 2.3 5.1E-05 27.7 1.3 25 105-129 20-44 (51)
24 COG2816 NPY1 NTP pyrophosphohy 71.1 2.1 4.5E-05 36.5 1.1 25 80-104 111-137 (279)
25 PF01485 IBR: IBR domain; Int 71.0 3.3 7.2E-05 25.8 1.8 35 80-114 18-58 (64)
26 cd00350 rubredoxin_like Rubred 70.9 2.5 5.4E-05 24.5 1.1 25 105-131 2-26 (33)
27 PF07754 DUF1610: Domain of un 70.9 2.3 5E-05 23.7 0.9 24 107-130 1-24 (24)
28 smart00659 RPOLCX RNA polymera 70.4 3 6.5E-05 26.0 1.5 24 106-130 4-27 (44)
29 PF14156 AbbA_antirepres: Anti 68.6 4.8 0.0001 27.2 2.3 33 23-62 7-39 (63)
30 COG1996 RPC10 DNA-directed RNA 67.0 2.8 6.1E-05 27.1 0.9 23 81-103 7-31 (49)
31 PF10367 Vps39_2: Vacuolar sor 65.3 30 0.00065 23.5 5.9 12 80-91 78-89 (109)
32 smart00249 PHD PHD zinc finger 64.6 4.7 0.0001 23.0 1.5 46 82-128 1-47 (47)
33 PF07295 DUF1451: Protein of u 64.5 27 0.00059 26.9 6.1 25 19-43 27-51 (146)
34 PF09776 Mitoc_L55: Mitochondr 63.4 6 0.00013 29.7 2.2 17 19-35 71-87 (116)
35 PHA03158 hypothetical protein; 61.9 19 0.00041 30.0 5.0 41 24-64 229-269 (273)
36 KOG1985|consensus 61.6 3.6 7.8E-05 39.9 0.9 39 95-133 207-251 (887)
37 PTZ00303 phosphatidylinositol 60.4 5.2 0.00011 39.3 1.7 33 81-113 461-498 (1374)
38 PRK00241 nudC NADH pyrophospha 60.3 4.1 8.9E-05 33.6 0.9 32 80-117 99-130 (256)
39 PLN00162 transport protein sec 59.3 5.8 0.00013 37.7 1.8 33 97-133 54-86 (761)
40 PF04201 TPD52: Tumour protein 59.1 72 0.0016 25.3 7.6 17 21-37 22-38 (162)
41 COG2023 RPR2 RNase P subunit R 58.8 5.8 0.00013 29.4 1.4 38 80-133 56-93 (105)
42 TIGR01053 LSD1 zinc finger dom 58.3 7.9 0.00017 22.5 1.6 25 105-129 2-26 (31)
43 PF13639 zf-RING_2: Ring finge 57.6 1.7 3.7E-05 25.9 -1.3 32 82-114 2-33 (44)
44 COG1997 RPL43A Ribosomal prote 56.6 6.3 0.00014 28.4 1.2 10 122-131 53-62 (89)
45 PRK11595 DNA utilization prote 56.6 5.9 0.00013 31.7 1.2 33 80-113 5-43 (227)
46 PF12760 Zn_Tnp_IS1595: Transp 55.9 8.1 0.00017 23.7 1.5 9 122-130 37-45 (46)
47 KOG3507|consensus 55.7 6 0.00013 26.7 0.9 26 104-130 20-45 (62)
48 TIGR00269 conserved hypothetic 55.1 21 0.00045 25.4 3.7 21 80-104 80-100 (104)
49 PF12773 DZR: Double zinc ribb 55.0 4.3 9.3E-05 24.8 0.1 10 122-131 29-38 (50)
50 PRK11546 zraP zinc resistance 54.8 53 0.0011 25.4 6.2 45 21-65 40-105 (143)
51 PF06943 zf-LSD1: LSD1 zinc fi 54.4 10 0.00023 21.2 1.6 23 107-129 1-23 (25)
52 PF13801 Metal_resist: Heavy-m 53.5 66 0.0014 21.6 6.0 39 20-58 37-75 (125)
53 PF09849 DUF2076: Uncharacteri 52.9 49 0.0011 27.6 6.1 19 25-43 1-19 (247)
54 PF03754 DUF313: Domain of unk 52.6 6.2 0.00013 29.3 0.7 16 18-33 46-61 (114)
55 COG5028 Vesicle coat complex C 52.2 6.1 0.00013 38.2 0.7 28 105-132 200-231 (861)
56 PF11781 RRN7: RNA polymerase 52.1 9.4 0.0002 22.8 1.3 23 107-130 11-33 (36)
57 PF14723 SSFA2_C: Sperm-specif 51.5 42 0.00091 27.1 5.2 11 55-65 158-168 (179)
58 KOG1818|consensus 51.3 7 0.00015 36.8 1.0 49 80-128 165-217 (634)
59 PF04981 NMD3: NMD3 family ; 50.9 12 0.00026 30.3 2.1 19 102-124 33-51 (236)
60 KOG0804|consensus 50.8 8.9 0.00019 35.1 1.5 34 93-132 211-250 (493)
61 KOG1729|consensus 50.8 3.8 8.2E-05 35.0 -0.8 50 80-129 168-221 (288)
62 PF11290 DUF3090: Protein of u 50.4 20 0.00043 28.7 3.2 27 68-99 145-171 (171)
63 COG0675 Transposase and inacti 50.2 7.3 0.00016 31.0 0.8 22 105-131 310-331 (364)
64 PF08274 PhnA_Zn_Ribbon: PhnA 49.0 6 0.00013 23.0 0.1 24 107-131 5-28 (30)
65 PRK11032 hypothetical protein; 46.0 61 0.0013 25.5 5.3 23 21-43 39-61 (160)
66 PF01195 Pept_tRNA_hydro: Pept 45.9 19 0.00041 28.3 2.5 23 17-40 142-164 (184)
67 PF13442 Cytochrome_CBB3: Cyto 45.8 29 0.00063 21.9 3.0 21 15-37 47-67 (67)
68 cd02406 CRS2 Chloroplast RNA s 44.2 32 0.0007 27.6 3.6 26 15-41 143-168 (191)
69 KOG0860|consensus 44.0 83 0.0018 23.7 5.5 33 30-63 46-78 (116)
70 COG2888 Predicted Zn-ribbon RN 43.4 13 0.00028 25.1 1.1 47 80-132 9-60 (61)
71 cd00162 RING RING-finger (Real 43.3 6.1 0.00013 22.1 -0.5 42 82-129 1-42 (45)
72 PF13864 Enkurin: Calmodulin-b 43.1 1.1E+02 0.0025 21.3 6.9 32 19-50 31-62 (98)
73 PF04829 PT-VENN: Pre-toxin do 43.0 17 0.00038 23.7 1.6 16 21-36 1-16 (55)
74 PF03119 DNA_ligase_ZBD: NAD-d 42.7 22 0.00049 20.0 1.8 20 107-126 2-21 (28)
75 PF13936 HTH_38: Helix-turn-he 42.0 17 0.00036 22.0 1.3 16 23-38 3-18 (44)
76 PF13274 DUF4065: Protein of u 41.3 28 0.00061 23.6 2.6 24 20-43 66-89 (108)
77 smart00647 IBR In Between Ring 41.2 15 0.00033 22.7 1.1 35 80-114 18-58 (64)
78 KOG3088|consensus 41.0 1.1E+02 0.0024 26.7 6.5 19 32-50 65-83 (313)
79 PF06906 DUF1272: Protein of u 40.9 19 0.00041 24.0 1.5 39 80-118 5-55 (57)
80 PF14319 Zn_Tnp_IS91: Transpos 40.7 14 0.00031 26.9 1.0 28 80-113 42-69 (111)
81 PF04032 Rpr2: RNAse P Rpr2/Rp 40.5 13 0.00028 24.8 0.7 40 80-130 46-85 (85)
82 PHA02078 hypothetical protein 40.5 14 0.0003 24.4 0.8 28 21-48 26-53 (54)
83 PRK10548 flagellar biosynthesi 40.4 1.2E+02 0.0025 22.6 5.9 37 27-63 62-98 (121)
84 KOG2041|consensus 40.3 34 0.00073 33.7 3.6 46 81-131 1118-1165(1189)
85 PHA02942 putative transposase; 40.3 14 0.0003 32.3 1.1 30 103-133 324-353 (383)
86 PF04236 Transp_Tc5_C: Tc5 tra 40.1 16 0.00034 24.5 1.1 28 79-111 26-55 (63)
87 COG1592 Rubrerythrin [Energy p 39.8 12 0.00027 29.5 0.6 12 122-133 134-145 (166)
88 KOG4010|consensus 39.4 1.5E+02 0.0032 24.4 6.7 30 8-37 19-53 (208)
89 PRK14890 putative Zn-ribbon RN 39.0 16 0.00035 24.4 1.0 47 80-132 7-58 (59)
90 TIGR03847 conserved hypothetic 38.9 38 0.00082 27.3 3.2 26 70-100 149-174 (177)
91 PF01086 Clathrin_lg_ch: Clath 38.4 53 0.0011 26.6 4.1 41 22-62 111-151 (225)
92 KOG3476|consensus 37.7 4.4 9.5E-05 29.5 -2.0 34 80-114 54-89 (100)
93 PF02150 RNA_POL_M_15KD: RNA p 37.6 12 0.00025 22.1 0.1 27 105-132 2-30 (35)
94 PF11304 DUF3106: Protein of u 37.5 50 0.0011 23.9 3.4 20 23-42 39-58 (107)
95 PF10910 DUF2744: Protein of u 37.2 27 0.00058 26.6 2.0 27 14-40 91-117 (125)
96 PF04423 Rad50_zn_hook: Rad50 36.6 37 0.00081 21.2 2.4 10 81-90 21-30 (54)
97 PF14471 DUF4428: Domain of un 36.6 14 0.00029 23.6 0.3 25 82-106 1-30 (51)
98 COG1571 Predicted DNA-binding 36.5 19 0.0004 32.5 1.3 27 106-133 352-378 (421)
99 PF00643 zf-B_box: B-box zinc 36.4 8.3 0.00018 22.6 -0.7 30 80-113 3-32 (42)
100 PF14311 DUF4379: Domain of un 36.4 15 0.00032 23.1 0.5 13 121-133 27-39 (55)
101 PF01780 Ribosomal_L37ae: Ribo 36.3 13 0.00028 26.8 0.2 11 80-90 35-45 (90)
102 PF10335 DUF294_C: Putative nu 35.5 51 0.0011 24.5 3.4 29 17-45 111-139 (145)
103 TIGR00447 pth peptidyl-tRNA hy 35.3 60 0.0013 25.8 3.9 26 15-41 142-167 (188)
104 KOG2114|consensus 34.4 68 0.0015 31.7 4.7 88 18-112 785-880 (933)
105 PF01428 zf-AN1: AN1-like Zinc 33.3 12 0.00026 22.7 -0.3 23 86-111 6-28 (43)
106 PHA02565 49 recombination endo 32.8 55 0.0012 25.9 3.2 10 81-90 21-30 (157)
107 PRK14714 DNA polymerase II lar 32.8 28 0.0006 35.6 1.9 47 80-131 667-718 (1337)
108 PRK09458 pspB phage shock prot 32.8 80 0.0017 22.1 3.7 22 23-44 34-55 (75)
109 PF07227 DUF1423: Protein of u 32.6 30 0.00065 31.5 1.9 31 97-131 124-155 (446)
110 TIGR00280 L37a ribosomal prote 32.6 19 0.00041 26.0 0.5 11 80-90 35-45 (91)
111 TIGR03045 PS_II_C550 cytochrom 32.6 50 0.0011 25.8 3.0 26 17-42 124-149 (159)
112 PF04120 Iron_permease: Low af 32.4 63 0.0014 24.6 3.4 21 17-37 87-107 (132)
113 COG5582 Uncharacterized conser 32.2 72 0.0016 25.7 3.8 35 27-63 145-179 (182)
114 cd00462 PTH Peptidyl-tRNA hydr 32.2 70 0.0015 25.1 3.8 26 16-42 140-165 (171)
115 PF10217 DUF2039: Uncharacteri 32.1 11 0.00023 27.3 -0.8 33 80-112 55-89 (92)
116 PF09098 Dehyd-heme_bind: Quin 31.7 2.6 5.7E-05 33.5 -4.3 55 24-88 50-105 (167)
117 KOG0955|consensus 31.3 30 0.00064 34.6 1.8 57 75-133 214-271 (1051)
118 PF07051 OCIA: Ovarian carcino 31.2 92 0.002 23.2 4.0 20 17-36 18-37 (111)
119 TIGR02890 spore_yteA sporulati 31.1 1.1E+02 0.0024 23.7 4.7 29 75-105 83-116 (159)
120 KOG1814|consensus 30.9 1.1E+02 0.0023 28.0 5.0 35 80-114 368-404 (445)
121 COG0732 HsdS Restriction endon 30.7 1.8E+02 0.004 23.3 6.1 40 26-65 141-180 (391)
122 PF11686 DUF3283: Protein of u 30.6 39 0.00084 22.8 1.8 14 21-34 1-14 (61)
123 PRK04136 rpl40e 50S ribosomal 30.5 31 0.00066 22.3 1.2 11 103-113 13-23 (48)
124 PF12875 DUF3826: Protein of u 30.5 79 0.0017 25.7 3.8 44 23-67 123-166 (188)
125 PF10571 UPF0547: Uncharacteri 30.4 23 0.00049 19.7 0.5 22 106-131 2-23 (26)
126 KOG1842|consensus 30.2 12 0.00026 34.2 -0.9 37 79-115 179-215 (505)
127 PRK03636 hypothetical protein; 29.8 91 0.002 24.8 4.1 16 23-38 124-139 (179)
128 cd07177 terB_like tellurium re 29.6 1.2E+02 0.0025 19.9 4.1 24 23-46 14-37 (104)
129 PRK05426 peptidyl-tRNA hydrola 29.5 88 0.0019 24.9 4.0 25 16-41 143-167 (189)
130 PF07191 zinc-ribbons_6: zinc- 29.4 14 0.0003 25.5 -0.6 33 81-113 2-39 (70)
131 PF13376 OmdA: Bacteriocin-pro 29.2 66 0.0014 20.7 2.7 37 21-61 23-59 (63)
132 TIGR00570 cdk7 CDK-activating 29.1 16 0.00035 31.6 -0.3 48 80-130 3-51 (309)
133 PF06698 DUF1192: Protein of u 29.0 1.5E+02 0.0031 19.7 4.3 18 19-36 15-32 (59)
134 PRK10778 dksA RNA polymerase-b 28.9 1.4E+02 0.0031 22.9 4.9 26 80-105 111-141 (151)
135 PF10960 DUF2762: Protein of u 28.6 1.9E+02 0.0042 19.7 5.1 33 33-65 23-55 (71)
136 PF07820 TraC: TraC-like prote 28.6 2.2E+02 0.0047 20.7 5.5 26 30-55 8-33 (92)
137 smart00109 C1 Protein kinase C 28.5 39 0.00084 19.6 1.4 34 80-113 11-44 (49)
138 PF10955 DUF2757: Protein of u 28.4 30 0.00064 24.2 0.9 19 18-36 25-43 (76)
139 KOG1451|consensus 28.4 1.4E+02 0.0031 28.8 5.6 63 23-85 74-144 (812)
140 PF11672 DUF3268: Protein of u 28.3 36 0.00079 24.9 1.4 7 122-128 31-37 (102)
141 PTZ00255 60S ribosomal protein 28.1 27 0.00059 25.1 0.8 12 80-91 36-47 (90)
142 PRK03057 hypothetical protein; 27.9 66 0.0014 25.7 3.0 23 40-62 154-176 (180)
143 KOG0954|consensus 27.9 70 0.0015 31.3 3.6 50 80-131 271-321 (893)
144 PF06667 PspB: Phage shock pro 27.8 1.1E+02 0.0024 21.2 3.7 22 23-44 34-55 (75)
145 TIGR02420 dksA RNA polymerase- 27.6 2.3E+02 0.005 20.2 6.1 28 75-104 77-109 (110)
146 PF13923 zf-C3HC4_2: Zinc fing 27.4 10 0.00022 22.1 -1.3 28 83-113 1-28 (39)
147 PRK09737 EcoKI restriction-mod 27.3 2.1E+02 0.0045 24.2 6.1 40 26-65 371-410 (461)
148 PRK14892 putative transcriptio 27.2 29 0.00064 25.2 0.8 11 104-114 42-52 (99)
149 PF05191 ADK_lid: Adenylate ki 27.1 20 0.00043 21.4 -0.1 6 106-111 3-8 (36)
150 PLN02492 ribonucleoside-diphos 27.1 1.2E+02 0.0026 25.6 4.6 34 18-51 43-76 (324)
151 KOG2874|consensus 26.9 1.1E+02 0.0025 26.7 4.4 46 9-61 265-316 (356)
152 PF00416 Ribosomal_S13: Riboso 26.8 2.4E+02 0.0052 20.1 5.8 22 18-39 39-60 (107)
153 COG1107 Archaea-specific RecJ- 26.5 49 0.0011 31.6 2.2 46 80-131 18-89 (715)
154 TIGR03831 YgiT_finger YgiT-typ 26.5 33 0.00071 20.0 0.8 14 119-132 29-42 (46)
155 PF04216 FdhE: Protein involve 26.4 31 0.00068 28.6 0.9 48 80-133 172-222 (290)
156 cd07313 terB_like_2 tellurium 26.3 1.5E+02 0.0033 20.0 4.3 28 23-50 14-41 (104)
157 PRK03976 rpl37ae 50S ribosomal 26.1 27 0.0006 25.1 0.5 12 80-91 36-47 (90)
158 smart00290 ZnF_UBP Ubiquitin C 26.1 40 0.00087 20.2 1.2 21 107-133 2-22 (50)
159 PF00097 zf-C3HC4: Zinc finger 26.0 12 0.00026 21.6 -1.2 28 83-113 1-28 (41)
160 COG3416 Uncharacterized protei 26.0 2.5E+02 0.0055 23.5 6.1 18 25-42 1-18 (233)
161 COG1096 Predicted RNA-binding 25.9 36 0.00079 27.6 1.2 16 81-96 150-165 (188)
162 cd01278 aprataxin_related apra 25.4 1.1E+02 0.0023 20.9 3.4 25 17-41 45-69 (104)
163 PF07225 NDUF_B4: NADH-ubiquin 25.2 1E+02 0.0022 23.3 3.4 19 24-42 20-38 (125)
164 PF09862 DUF2089: Protein of u 25.0 77 0.0017 23.6 2.7 32 18-49 27-58 (113)
165 TIGR03629 arch_S13P archaeal r 24.9 1.9E+02 0.0042 22.1 5.0 22 18-39 45-66 (144)
166 PRK12286 rpmF 50S ribosomal pr 24.8 39 0.00085 22.1 1.0 22 81-113 28-49 (57)
167 cd01277 HINT_subgroup HINT (hi 24.8 66 0.0014 21.6 2.2 24 17-40 43-66 (103)
168 KOG3313|consensus 24.7 2.6E+02 0.0057 22.7 5.8 46 20-67 31-76 (187)
169 COG4014 Uncharacterized protei 24.4 51 0.0011 24.1 1.6 33 18-61 54-86 (97)
170 PF10497 zf-4CXXC_R1: Zinc-fin 24.4 21 0.00045 25.9 -0.4 47 81-128 8-67 (105)
171 PF13920 zf-C3HC4_3: Zinc fing 24.1 22 0.00047 21.6 -0.3 43 80-130 2-45 (50)
172 KOG4005|consensus 24.0 2.6E+02 0.0056 24.0 5.9 10 21-30 60-69 (292)
173 PF15554 FSIP1: FSIP1 family 23.9 1.2E+02 0.0025 27.5 4.1 45 18-63 380-424 (425)
174 PF11023 DUF2614: Protein of u 23.9 29 0.00063 26.1 0.2 25 80-104 69-93 (114)
175 PF13945 NST1: Salt tolerance 23.9 1E+02 0.0022 24.9 3.4 13 26-38 100-112 (190)
176 PRK06418 transcription elongat 23.8 29 0.00063 27.4 0.3 21 80-106 3-23 (166)
177 PF00645 zf-PARP: Poly(ADP-rib 23.7 59 0.0013 21.7 1.7 24 14-37 58-81 (82)
178 PF10058 DUF2296: Predicted in 23.7 40 0.00087 21.8 0.9 11 121-131 43-53 (54)
179 CHL00183 petJ cytochrome c553; 23.6 1.1E+02 0.0023 21.3 3.1 22 19-40 81-103 (108)
180 PF05823 Gp-FAR-1: Nematode fa 23.6 61 0.0013 24.9 2.0 39 22-61 18-56 (154)
181 KOG1356|consensus 23.6 29 0.00063 34.0 0.2 37 75-113 224-260 (889)
182 PF00130 C1_1: Phorbol esters/ 23.5 27 0.00058 21.3 0.0 34 80-113 11-45 (53)
183 PRK13920 putative anti-sigmaE 23.4 1.9E+02 0.004 22.6 4.8 27 22-48 6-32 (206)
184 PTZ00074 60S ribosomal protein 23.2 60 0.0013 25.0 1.9 20 22-42 91-110 (135)
185 cd00029 C1 Protein kinase C co 23.2 34 0.00074 20.1 0.4 34 80-113 11-45 (50)
186 PF13811 DUF4186: Domain of un 23.2 76 0.0016 23.8 2.3 21 19-39 87-107 (111)
187 PF04568 IATP: Mitochondrial A 23.1 2.1E+02 0.0045 20.9 4.6 21 40-60 63-83 (100)
188 PF00569 ZZ: Zinc finger, ZZ t 22.8 34 0.00073 21.0 0.4 22 105-129 5-26 (46)
189 smart00184 RING Ring finger. E 22.7 25 0.00055 18.6 -0.2 26 83-112 1-26 (39)
190 PHA02929 N1R/p28-like protein; 22.6 37 0.00079 28.2 0.6 48 80-131 174-225 (238)
191 PF07047 OPA3: Optic atrophy 3 22.5 2.8E+02 0.006 20.6 5.4 17 49-65 112-128 (134)
192 COG1734 DksA DnaK suppressor p 22.2 1.6E+02 0.0034 22.0 3.9 29 75-105 77-110 (120)
193 PRK05179 rpsM 30S ribosomal pr 22.1 2.5E+02 0.0054 20.9 5.0 48 19-70 42-89 (122)
194 smart00547 ZnF_RBZ Zinc finger 22.1 28 0.0006 18.4 -0.1 12 122-133 2-13 (26)
195 COG5141 PHD zinc finger-contai 22.1 1.3E+02 0.0028 28.4 4.0 54 80-135 193-247 (669)
196 PF02132 RecR: RecR protein; 22.1 74 0.0016 19.0 1.8 19 81-103 18-36 (41)
197 KOG1571|consensus 21.9 42 0.0009 29.7 0.9 21 80-100 305-328 (355)
198 TIGR03631 bact_S13 30S ribosom 21.8 2.5E+02 0.0054 20.6 4.9 21 19-39 40-60 (113)
199 PRK14161 heat shock protein Gr 21.8 3.1E+02 0.0066 21.7 5.7 19 49-67 40-58 (178)
200 PF08216 CTNNBL: Catenin-beta- 21.7 79 0.0017 23.4 2.2 35 26-60 1-37 (108)
201 KOG0930|consensus 21.7 2.6E+02 0.0056 24.7 5.6 39 23-65 9-47 (395)
202 PF14446 Prok-RING_1: Prokaryo 21.6 47 0.001 21.8 0.9 25 80-104 5-29 (54)
203 TIGR00721 tfx DNA-binding prot 21.6 2.7E+02 0.0059 21.1 5.2 17 19-35 1-17 (137)
204 cd07321 Extradiol_Dioxygenase_ 21.5 58 0.0013 22.2 1.4 14 22-35 32-45 (77)
205 cd00730 rubredoxin Rubredoxin; 21.5 44 0.00096 21.3 0.7 11 121-131 33-43 (50)
206 COG5325 t-SNARE complex subuni 21.5 2.3E+02 0.0051 24.4 5.2 28 19-46 149-182 (283)
207 PF13035 DUF3896: Protein of u 21.5 99 0.0022 20.6 2.4 19 24-42 29-47 (61)
208 KOG2689|consensus 21.4 88 0.0019 27.0 2.7 28 28-55 139-166 (290)
209 PF00641 zf-RanBP: Zn-finger i 21.4 25 0.00055 19.5 -0.4 12 122-133 4-15 (30)
210 PF02148 zf-UBP: Zn-finger in 21.3 39 0.00084 21.8 0.4 12 120-131 9-20 (63)
211 KOG1819|consensus 21.1 26 0.00057 33.1 -0.5 33 80-112 901-933 (990)
212 PRK06835 DNA replication prote 21.1 3E+02 0.0065 23.5 5.9 15 80-94 98-112 (329)
213 PRK00420 hypothetical protein; 21.1 92 0.002 23.1 2.5 28 80-114 23-50 (112)
214 KOG2177|consensus 21.1 27 0.00058 26.3 -0.4 30 80-113 13-42 (386)
215 KOG4538|consensus 21.1 3.8E+02 0.0083 20.4 5.8 34 29-65 56-90 (130)
216 COG1579 Zn-ribbon protein, pos 21.1 3.9E+02 0.0083 22.3 6.4 30 33-62 112-144 (239)
217 COG0333 RpmF Ribosomal protein 21.0 52 0.0011 21.8 1.0 23 80-113 27-49 (57)
218 PF11471 Sugarporin_N: Maltopo 20.9 2.2E+02 0.0048 18.7 4.0 11 24-34 27-37 (60)
219 PF08776 VASP_tetra: VASP tetr 20.9 2.2E+02 0.0048 17.7 4.5 18 41-58 18-35 (40)
220 PF07975 C1_4: TFIIH C1-like d 20.9 11 0.00023 24.5 -2.3 20 95-114 20-39 (51)
221 COG1645 Uncharacterized Zn-fin 20.9 39 0.00084 25.9 0.4 25 80-104 28-52 (131)
222 KOG2807|consensus 20.9 36 0.00078 30.2 0.3 46 80-130 330-375 (378)
223 TIGR00622 ssl1 transcription f 20.9 55 0.0012 24.4 1.2 34 80-114 55-99 (112)
224 COG5347 GTPase-activating prot 20.9 61 0.0013 28.1 1.6 10 80-89 20-29 (319)
225 cd07178 terB_like_YebE telluri 20.8 1E+02 0.0022 21.6 2.6 18 23-40 14-31 (95)
226 cd02342 ZZ_UBA_plant Zinc fing 20.7 58 0.0013 20.5 1.1 21 106-129 2-22 (43)
227 PF12563 Hemolysin_N: Hemolyti 20.7 58 0.0012 26.4 1.4 22 19-40 80-101 (187)
228 cd01275 FHIT FHIT (fragile his 20.6 1.1E+02 0.0024 21.8 2.7 23 17-39 43-65 (126)
229 PF11727 ISG65-75: Invariant s 20.6 5E+02 0.011 21.6 7.4 44 22-65 90-133 (286)
230 PF13894 zf-C2H2_4: C2H2-type 20.5 35 0.00077 16.6 0.1 10 123-132 1-10 (24)
231 COG2960 Uncharacterized protei 20.4 2.8E+02 0.006 20.5 4.8 39 21-59 52-90 (103)
232 COG2126 RPL37A Ribosomal prote 20.3 43 0.00094 22.6 0.5 35 80-123 16-50 (61)
233 TIGR02161 napC_nirT periplasmi 20.3 1.1E+02 0.0023 24.4 2.8 9 80-88 135-143 (185)
234 PTZ00211 ribonucleoside-diphos 20.2 1.6E+02 0.0035 24.9 4.1 33 19-51 55-87 (330)
235 cd07176 terB tellurite resista 20.2 1.3E+02 0.0028 20.3 2.9 21 23-43 17-37 (111)
236 PTZ00134 40S ribosomal protein 20.0 2.6E+02 0.0057 21.7 4.9 22 18-39 54-75 (154)
237 PF09548 Spore_III_AB: Stage I 20.0 4E+02 0.0088 20.3 6.4 44 20-63 97-145 (170)
238 PF01230 HIT: HIT domain; Int 20.0 67 0.0014 21.7 1.4 23 17-39 35-57 (98)
No 1
>KOG3799|consensus
Probab=100.00 E-value=1.8e-35 Score=226.64 Aligned_cols=114 Identities=56% Similarity=0.875 Sum_probs=110.6
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHhhhCccccccccccccccccCCC
Q psy5308 16 ADIIPDLSHLTLEERQIIESVMMRQKQEEERELEIMRRKQDEVHLLEQSIRQRSEQQKKAGVELDATCHICLKTKFADGV 95 (137)
Q Consensus 16 ~~~~~dLS~LteeEr~~Il~VL~R~~~le~~E~~RirkL~~el~~lk~~~~~~~~~~r~~G~~~~~~C~~C~ktkf~~g~ 95 (137)
|.++|||||||+.||=.|..|+.|++.++.++-+..++..+++-+|.++|..++++.+++|.+++++|+||+|||||||+
T Consensus 1 ~~~~~d~sh~T~he~~qik~vf~rqk~ee~kq~ei~~~~~~e~~el~~Qi~erkEqqKKaGv~ddatC~IC~KTKFADG~ 80 (169)
T KOG3799|consen 1 MDEMPDLSHLTPHERMQIKEVFIRQKIEEHKQFEIYKEQVKEMGELSQQIQERKEQQKKAGVGDDATCGICHKTKFADGC 80 (169)
T ss_pred CccccchhhcCccchHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccccCcCcchhhhhhccccccc
Confidence 57899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCccccccccccCCceeecCCCCcceEEeeec
Q psy5308 96 GHMCNYCNIRCCARCGGKVTLRSNKVSVEVTTRG 129 (137)
Q Consensus 96 G~~C~~C~~rvC~rCg~~v~lr~n~~~W~Ctvc~ 129 (137)
||.|.||+.|+|+|||++|++++|+++|+|..|-
T Consensus 81 GH~C~YCq~r~CARCGGrv~lrsNKv~wvcnlc~ 114 (169)
T KOG3799|consen 81 GHNCSYCQTRFCARCGGRVSLRSNKVMWVCNLCR 114 (169)
T ss_pred CcccchhhhhHHHhcCCeeeeccCceEEeccCCc
Confidence 9999999999999999999999999999999974
No 2
>PF02318 FYVE_2: FYVE-type zinc finger; InterPro: IPR003315 This entry represents the zinc-binding domain found in rabphilin Rab3A. The small G protein Rab3A plays an important role in the regulation of neurotransmitter release. The crystal structure of the small G protein Rab3A complexed with the effector domain of rabphilin-3A shows that the effector domain of rabphilin-3A contacts Rab3A in two distinct areas. The first interface involves the Rab3A switch I and switch II regions, which are sensitive to the nucleotide-binding state of Rab3A. The second interface consists of a deep pocket in Rab3A that interacts with a SGAWFF structural element of rabphilin-3A. Sequence and structure analysis, and biochemical data suggest that this pocket, or Rab complementarity-determining region (RabCDR), establishes a specific interaction between each Rab protein and its effectors. It has been suggested that RabCDRs could be major determinants of effector specificity during vesicle trafficking and fusion [].; GO: 0008270 zinc ion binding, 0017137 Rab GTPase binding, 0006886 intracellular protein transport; PDB: 2CSZ_A 2ZET_C 1ZBD_B 3BC1_B 2CJS_C 2A20_A.
Probab=99.96 E-value=3.2e-30 Score=189.58 Aligned_cols=99 Identities=26% Similarity=0.404 Sum_probs=79.8
Q ss_pred CCCCHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHH--HHHHHHHHhHHHHhhhCcccccccccccccc-ccCCCCCCC
Q psy5308 23 SHLTLEERQIIESVMMRQKQEEERELEIMRRKQDEVH--LLEQSIRQRSEQQKKAGVELDATCHICLKTK-FADGVGHMC 99 (137)
Q Consensus 23 S~LteeEr~~Il~VL~R~~~le~~E~~RirkL~~el~--~lk~~~~~~~~~~r~~G~~~~~~C~~C~ktk-f~~g~G~~C 99 (137)
||||++||++|++||+||++++++|++||++|+++|+ .+++.+. ...+.+++++|++|++++ |++++|++|
T Consensus 1 s~Lt~eE~~~I~~Vl~R~~~l~~~E~~Ri~kLk~~L~~e~~r~~~~------~~~~~~~~~~C~~C~~~fg~l~~~~~~C 74 (118)
T PF02318_consen 1 SHLTEEEREIILQVLQRDEELRKKEEERIRKLKQELQKEKMRREAL------GNSQKYGERHCARCGKPFGFLFNRGRVC 74 (118)
T ss_dssp TTS-CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC------SCSTTHCCSB-TTTS-BCSCTSTTCEEE
T ss_pred CCCCHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHhhcc------ccccccCCcchhhhCCcccccCCCCCcC
Confidence 8999999999999999999999999999999999994 3443321 112233479999999865 999999999
Q ss_pred ccccccccccCCceeecCCCCcceEEeeecc
Q psy5308 100 NYCNIRCCARCGGKVTLRSNKVSVEVTTRGH 130 (137)
Q Consensus 100 ~~C~~rvC~rCg~~v~lr~n~~~W~Ctvc~~ 130 (137)
.+|+++||++||++ .++...|+|+||..
T Consensus 75 ~~C~~~VC~~C~~~---~~~~~~WlC~vC~k 102 (118)
T PF02318_consen 75 VDCKHRVCKKCGVY---SKKEPIWLCKVCQK 102 (118)
T ss_dssp TTTTEEEETTSEEE---TSSSCCEEEHHHHH
T ss_pred CcCCccccCccCCc---CCCCCCEEChhhHH
Confidence 99999999999987 33467999999764
No 3
>cd00065 FYVE FYVE domain; Zinc-binding domain; targets proteins to membrane lipids via interaction with phosphatidylinositol-3-phosphate, PI3P; present in Fab1, YOTB, Vac1, and EEA1;
Probab=94.65 E-value=0.021 Score=36.01 Aligned_cols=50 Identities=18% Similarity=0.288 Sum_probs=38.4
Q ss_pred cccccccccccccCCCCCCCccccccccccCCceeecC----CCCcceEEeeec
Q psy5308 80 DATCHICLKTKFADGVGHMCNYCNIRCCARCGGKVTLR----SNKVSVEVTTRG 129 (137)
Q Consensus 80 ~~~C~~C~ktkf~~g~G~~C~~C~~rvC~rCg~~v~lr----~n~~~W~Ctvc~ 129 (137)
...|..|.+.+....+.|.|..|...||..|-.+.... .+.++.+|..|.
T Consensus 2 ~~~C~~C~~~F~~~~rk~~Cr~Cg~~~C~~C~~~~~~~~~~~~~~~~rvC~~C~ 55 (57)
T cd00065 2 ASSCMGCGKPFTLTRRRHHCRNCGRIFCSKCSSNRIPLPSMGGGKPVRVCDSCY 55 (57)
T ss_pred cCcCcccCccccCCccccccCcCcCCcChHHcCCeeecCcccCCCccEeChHHh
Confidence 36799999776556799999999999999998765432 234678888764
No 4
>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=93.48 E-value=0.043 Score=31.68 Aligned_cols=29 Identities=28% Similarity=0.540 Sum_probs=15.7
Q ss_pred cccccccCCceeecCCCCcceEEeeeccC
Q psy5308 103 NIRCCARCGGKVTLRSNKVSVEVTTRGHN 131 (137)
Q Consensus 103 ~~rvC~rCg~~v~lr~n~~~W~Ctvc~~~ 131 (137)
++++|++||..+.....+..=+|.-|++.
T Consensus 2 ~~rfC~~CG~~t~~~~~g~~r~C~~Cg~~ 30 (32)
T PF09297_consen 2 NHRFCGRCGAPTKPAPGGWARRCPSCGHE 30 (32)
T ss_dssp TTSB-TTT--BEEE-SSSS-EEESSSS-E
T ss_pred CCcccCcCCccccCCCCcCEeECCCCcCE
Confidence 46788888888766655555567777654
No 5
>PF01363 FYVE: FYVE zinc finger; InterPro: IPR000306 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 FYVE zinc finger is named after four proteins that it has been found in: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two zinc ions []. The FYVE finger has eight potential zinc coordinating cysteine positions. Many members of this family also include two histidines in a motif R+HHC+XCG, where + represents a charged residue and X any residue. FYVE-type domains are divided into two known classes: FYVE domains that specifically bind to phosphatidylinositol 3-phosphate in lipid bilayers and FYVE-related domains of undetermined function []. Those that bind to phosphatidylinositol 3-phosphate are often found in proteins targeted to lipid membranes that are involved in regulating membrane traffic [, , ]. Most FYVE domains target proteins to endosomes by binding specifically to phosphatidylinositol-3-phosphate at the membrane surface. By contrast, the CARP2 FYVE-like domain is not optimized to bind to phosphoinositides or insert into lipid bilayers. FYVE domains are distinguished from other zinc fingers by three signature sequences: an N-terminal WxxD motif, a basic R(R/K)HHCR patch, and a C-terminal RVC motif. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0046872 metal ion binding; PDB: 1HYI_A 1JOC_B 1HYJ_A 1DVP_A 3ZYQ_A 4AVX_A 1VFY_A 3T7L_A 1X4U_A 1WFK_A ....
Probab=92.36 E-value=0.047 Score=35.79 Aligned_cols=50 Identities=18% Similarity=0.284 Sum_probs=27.8
Q ss_pred cccccccccccccCCCCCCCccccccccccCCceeecCC------CCcceEEeeec
Q psy5308 80 DATCHICLKTKFADGVGHMCNYCNIRCCARCGGKVTLRS------NKVSVEVTTRG 129 (137)
Q Consensus 80 ~~~C~~C~ktkf~~g~G~~C~~C~~rvC~rCg~~v~lr~------n~~~W~Ctvc~ 129 (137)
...|.+|.+.+.++.+-|.|..|-..||+.|-......+ ..+.-+|..|.
T Consensus 9 ~~~C~~C~~~F~~~~rrhhCr~CG~~vC~~Cs~~~~~~~~~~~~~~~~~RvC~~C~ 64 (69)
T PF01363_consen 9 ASNCMICGKKFSLFRRRHHCRNCGRVVCSSCSSQRIPLPTPSSGSGEPVRVCDSCY 64 (69)
T ss_dssp -SB-TTT--B-BSSS-EEE-TTT--EEECCCS-EEEEET--GGTESEEEEE-HHHH
T ss_pred CCcCcCcCCcCCCceeeEccCCCCCEECCchhCCEEcccccccCCCCcCEECHHHH
Confidence 588999998865557999999999999999987654221 22456666653
No 6
>smart00064 FYVE Protein present in Fab1, YOTB, Vac1, and EEA1. The FYVE zinc finger is named after four proteins where it was first found: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two Zn2+ ions. The FYVE finger has eight potential zinc coordinating cysteine positions. The FYVE finger is structurally related to the PF05715 zf-piccolo: Piccolo Zn-finger; InterPro: IPR008899 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 (predicted) zinc finger is found in the bassoon and piccolo proteins, both of which are components of the presynaptic cytoskeletal matrix (PCM) assembled at the active zone of neurotransmitter release, where Piccolo plays a role in the trafficking of synaptic vesicles (SVs) [, , ]. The Piccolo zinc fingers were found to interact with the dual prenylated rab3A and VAMP2/Synaptobrevin II receptor PRA1. There are eight conserved cysteines in Piccolo-type zinc fingers, suggesting that they coordinates two zinc ligands. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0046872 metal ion binding, 0045202 synapse
Probab=90.78 E-value=0.16 Score=34.26 Aligned_cols=46 Identities=17% Similarity=0.322 Sum_probs=32.0
Q ss_pred ccccccccccccC----CCCCCCccccccccccCCceeecCCC---CcceEEeee
Q psy5308 81 ATCHICLKTKFAD----GVGHMCNYCNIRCCARCGGKVTLRSN---KVSVEVTTR 128 (137)
Q Consensus 81 ~~C~~C~ktkf~~----g~G~~C~~C~~rvC~rCg~~v~lr~n---~~~W~Ctvc 128 (137)
..|.+|..++... .--+.|..|+..||+-||.- -.+| ..-|+|--|
T Consensus 3 ~~CPlCkt~~n~gsk~~pNyntCT~Ck~~VCnlCGFN--P~Phl~E~~eWLCLnC 55 (61)
T PF05715_consen 3 SLCPLCKTTLNVGSKDPPNYNTCTECKSQVCNLCGFN--PTPHLTEVKEWLCLNC 55 (61)
T ss_pred ccCCcccchhhcCCCCCCCccHHHHHhhhhhcccCCC--CCccccccceeeeecc
Confidence 6799998665332 13468999999999999943 2222 257999765
No 8
>PF04810 zf-Sec23_Sec24: Sec23/Sec24 zinc finger; InterPro: IPR006895 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. COPII (coat protein complex II)-coated vesicles carry proteins from the endoplasmic reticulum (ER) to the Golgi complex []. COPII-coated vesicles form on the ER by the stepwise recruitment of three cytosolic components: Sar1-GTP to initiate coat formation, Sec23/24 heterodimer to select SNARE and cargo molecules, and Sec13/31 to induce coat polymerisation and membrane deformation []. Sec23 p and Sec24p are structurally related, folding into five distinct domains: a beta-barrel, a zinc-finger, an alpha/beta trunk domain (IPR006896 from INTERPRO), an all-helical region (IPR006900 from INTERPRO), and a C-terminal gelsolin-like domain (IPR007123 from INTERPRO). This entry describes an approximately 55-residue Sec23/24 zinc-binding domain, which lies against the beta-barrel at the periphery of the complex. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006886 intracellular protein transport, 0006888 ER to Golgi vesicle-mediated transport, 0030127 COPII vesicle coat; PDB: 3EFO_B 3EG9_B 3EGD_A 2YRC_A 2NUP_A 2YRD_A 3EGX_A 2NUT_A 3EH1_A 1PD0_A ....
Probab=90.72 E-value=0.08 Score=32.17 Aligned_cols=13 Identities=15% Similarity=0.013 Sum_probs=8.8
Q ss_pred CcceEEeeeccCC
Q psy5308 120 KVSVEVTTRGHNN 132 (137)
Q Consensus 120 ~~~W~Ctvc~~~~ 132 (137)
+..|+|.+|.+.|
T Consensus 22 ~~~w~C~~C~~~N 34 (40)
T PF04810_consen 22 GKTWICNFCGTKN 34 (40)
T ss_dssp TTEEEETTT--EE
T ss_pred CCEEECcCCCCcC
Confidence 3589999998865
No 9
>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=87.33 E-value=0.27 Score=29.01 Aligned_cols=24 Identities=29% Similarity=0.787 Sum_probs=15.9
Q ss_pred ccccCCceeecCCCCcceEEeeecc
Q psy5308 106 CCARCGGKVTLRSNKVSVEVTTRGH 130 (137)
Q Consensus 106 vC~rCg~~v~lr~n~~~W~Ctvc~~ 130 (137)
+|.+||..+.+.++. .-.|.-|+|
T Consensus 2 ~C~~Cg~~~~~~~~~-~irC~~CG~ 25 (32)
T PF03604_consen 2 ICGECGAEVELKPGD-PIRCPECGH 25 (32)
T ss_dssp BESSSSSSE-BSTSS-TSSBSSSS-
T ss_pred CCCcCCCeeEcCCCC-cEECCcCCC
Confidence 678888888777655 457877776
No 10
>PRK12495 hypothetical protein; Provisional
Probab=86.05 E-value=2 Score=35.71 Aligned_cols=65 Identities=17% Similarity=0.276 Sum_probs=35.2
Q ss_pred CCCHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHhhhCccccccccccccccccCCCCCCCcccc
Q psy5308 24 HLTLEERQIIESVMMRQKQEEERELEIMRRKQDEVHLLEQSIRQRSEQQKKAGVELDATCHICLKTKFADGVGHMCNYCN 103 (137)
Q Consensus 24 ~LteeEr~~Il~VL~R~~~le~~E~~RirkL~~el~~lk~~~~~~~~~~r~~G~~~~~~C~~C~ktkf~~g~G~~C~~C~ 103 (137)
|=.|.||+.+-+-..+|++-++.- +++-+.|. ++ ..-+...|..|+.++|...--..|..|+
T Consensus 4 FDkEaEREkLREKye~d~~~R~~~----~~ma~lL~---------~g-----atmsa~hC~~CG~PIpa~pG~~~Cp~CQ 65 (226)
T PRK12495 4 FDKEAEREKLREKYEQDEQKREAT----ERMSELLL---------QG-----ATMTNAHCDECGDPIFRHDGQEFCPTCQ 65 (226)
T ss_pred hhHHHHHHHHHHHHhhhHHHHHHH----HHHHHHHH---------hh-----cccchhhcccccCcccCCCCeeECCCCC
Confidence 445778888776555555433222 22222121 11 1223688999999999753333466666
Q ss_pred ccc
Q psy5308 104 IRC 106 (137)
Q Consensus 104 ~rv 106 (137)
..|
T Consensus 66 ~~~ 68 (226)
T PRK12495 66 QPV 68 (226)
T ss_pred Ccc
Confidence 443
No 11
>PF10235 Cript: Microtubule-associated protein CRIPT; InterPro: IPR019367 The CRIPT protein is a cytoskeletal protein involved in microtubule production. This C-terminal domain is essential for binding to the PDZ3 domain of the SAP90 protein, one of a super-family of PDZ-containing proteins that play an important role in coupling the membrane ion channels with their signalling partners [].
Probab=85.07 E-value=0.57 Score=33.75 Aligned_cols=34 Identities=35% Similarity=0.813 Sum_probs=27.2
Q ss_pred cccccccccccccCCCCCCCccc--cccccccCCcee
Q psy5308 80 DATCHICLKTKFADGVGHMCNYC--NIRCCARCGGKV 114 (137)
Q Consensus 80 ~~~C~~C~ktkf~~g~G~~C~~C--~~rvC~rCg~~v 114 (137)
...|.+|. ++....-++.|+.| ++-+|+-||..+
T Consensus 44 ~~~C~~CK-~~v~q~g~~YCq~CAYkkGiCamCGKki 79 (90)
T PF10235_consen 44 SSKCKICK-TKVHQPGAKYCQTCAYKKGICAMCGKKI 79 (90)
T ss_pred Cccccccc-cccccCCCccChhhhcccCcccccCCee
Confidence 36899995 66555466899999 578999999887
No 12
>KOG1013|consensus
Probab=84.37 E-value=0.64 Score=40.78 Aligned_cols=100 Identities=5% Similarity=-0.177 Sum_probs=72.1
Q ss_pred CCCCCCCHHHHHH---------HHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHhhhCcccccccccccccc
Q psy5308 20 PDLSHLTLEERQI---------IESVMMRQKQEEERELEIMRRKQDEVHLLEQSIRQRSEQQKKAGVELDATCHICLKTK 90 (137)
Q Consensus 20 ~dLS~LteeEr~~---------Il~VL~R~~~le~~E~~RirkL~~el~~lk~~~~~~~~~~r~~G~~~~~~C~~C~ktk 90 (137)
++|++|-..|... -|.||++.......+..++..+..++..|+... ++. ..+.|-.|-.+.
T Consensus 82 ~~~~~~y~~~~~~~~~tl~~a~~lk~~~~~~~~d~~~~~~llpga~kl~slr~~t---------~~n-~lN~~w~etev~ 151 (362)
T KOG1013|consen 82 LEFELLYDSESRMLDTTLDRAKGLKPMDINGLADPYVKLHLLPGAGKLNSLRTKT---------TRN-TLNPEWNETEVY 151 (362)
T ss_pred hhhhhhhhhhhhhcceeechhcccchhhhhhhcchHHhhhcccchhhhhhhhHHh---------hcc-CcCcceecccee
Confidence 4455555555443 367788888888888888888888888887532 121 157789998885
Q ss_pred -ccCCCCCCCccccccccccCCce--eecCCCCcceEEeeecc
Q psy5308 91 -FADGVGHMCNYCNIRCCARCGGK--VTLRSNKVSVEVTTRGH 130 (137)
Q Consensus 91 -f~~g~G~~C~~C~~rvC~rCg~~--v~lr~n~~~W~Ctvc~~ 130 (137)
|+......|..|.+.||..|+.. .+... ...|+|++|..
T Consensus 152 ~~i~~~~~~~K~~Rk~vcdn~~~~~~~sqGq-~r~~lkKl~p~ 193 (362)
T KOG1013|consen 152 EGITDDDTHLKVLRKVVCDNDKKTHNESQGQ-SRVSLKKLKPL 193 (362)
T ss_pred cccccchhhhhhhheeeccCcccccccCccc-chhhhhccChh
Confidence 88788999999999999999977 33332 23699999754
No 13
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=83.16 E-value=0.68 Score=28.53 Aligned_cols=9 Identities=11% Similarity=0.006 Sum_probs=4.3
Q ss_pred ceEEeeecc
Q psy5308 122 SVEVTTRGH 130 (137)
Q Consensus 122 ~W~Ctvc~~ 130 (137)
.|+|..|++
T Consensus 20 ~~vC~~Cg~ 28 (52)
T smart00661 20 RFVCRKCGY 28 (52)
T ss_pred EEECCcCCC
Confidence 344544444
No 14
>PF04545 Sigma70_r4: Sigma-70, region 4; InterPro: IPR007630 The bacterial core RNA polymerase complex, which consists of five subunits, 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 []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors is involved in binding to the -35 promoter element via a helix-turn-helix motif []. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2P7V_B 3IYD_F 1TLH_B 1KU7_A 1RIO_H 3N97_A 1KU3_A 1RP3_C 1SC5_A 1NR3_A ....
Probab=81.98 E-value=4 Score=24.82 Aligned_cols=26 Identities=27% Similarity=0.284 Sum_probs=19.5
Q ss_pred CCCCCHHHHHHHHHHHHhhHHHHHHH
Q psy5308 22 LSHLTLEERQIIESVMMRQKQEEERE 47 (137)
Q Consensus 22 LS~LteeEr~~Il~VL~R~~~le~~E 47 (137)
|+.|+++||++|.-....+.-++++-
T Consensus 2 l~~L~~~er~vi~~~y~~~~t~~eIa 27 (50)
T PF04545_consen 2 LDQLPPREREVIRLRYFEGLTLEEIA 27 (50)
T ss_dssp HCTS-HHHHHHHHHHHTST-SHHHHH
T ss_pred hhhCCHHHHHHHHHHhcCCCCHHHHH
Confidence 57899999999999887776666663
No 15
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=81.19 E-value=0.54 Score=28.03 Aligned_cols=27 Identities=22% Similarity=0.604 Sum_probs=14.2
Q ss_pred cccccCCceeecC----CCCcceEEeeeccC
Q psy5308 105 RCCARCGGKVTLR----SNKVSVEVTTRGHN 131 (137)
Q Consensus 105 rvC~rCg~~v~lr----~n~~~W~Ctvc~~~ 131 (137)
++|..||..+..+ -+..-|+|+-|++-
T Consensus 1 kfC~~CG~~l~~~ip~gd~r~R~vC~~Cg~I 31 (34)
T PF14803_consen 1 KFCPQCGGPLERRIPEGDDRERLVCPACGFI 31 (34)
T ss_dssp -B-TTT--B-EEE--TT-SS-EEEETTTTEE
T ss_pred CccccccChhhhhcCCCCCccceECCCCCCE
Confidence 5889999887543 22357889888764
No 16
>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=79.68 E-value=0.58 Score=27.59 Aligned_cols=12 Identities=8% Similarity=-0.105 Sum_probs=8.4
Q ss_pred ceEEeeeccCCC
Q psy5308 122 SVEVTTRGHNNN 133 (137)
Q Consensus 122 ~W~Ctvc~~~~~ 133 (137)
.|+|.+||+.+.
T Consensus 2 ~~~C~~CG~i~~ 13 (34)
T cd00729 2 VWVCPVCGYIHE 13 (34)
T ss_pred eEECCCCCCEeE
Confidence 577777777644
No 17
>PF04880 NUDE_C: NUDE protein, C-terminal conserved region; InterPro: IPR006964 This domain represents the C-terminal conserved region of NUDE proteins. Emericella nidulans (Aspergillus nidulans) NUDE, acts in the cytoplasmic dynein/dynactin pathway and is required for distribution of nuclei []. It is a homologue of the nuclear distribution protein RO11 of Neurospora crassa. NUDE interacts with the NUDF via an N-terminal coiled coil domain; this is the only domain which is absolutely required for NUDE function.; PDB: 2V66_B 2V71_B.
Probab=78.65 E-value=2.3 Score=33.62 Aligned_cols=32 Identities=28% Similarity=0.383 Sum_probs=10.3
Q ss_pred HHHHHHHHHHhhHHHHHHHHHH--HHHHHHHHHHHHHHH
Q psy5308 29 ERQIIESVMMRQKQEEERELEI--MRRKQDEVHLLEQSI 65 (137)
Q Consensus 29 Er~~Il~VL~R~~~le~~E~~R--irkL~~el~~lk~~~ 65 (137)
||.++|+ .+|+++|.-| ++||++|+.+||+-+
T Consensus 14 ERnalLE-----~ELdEKE~L~~~~QRLkDE~RDLKqEl 47 (166)
T PF04880_consen 14 ERNALLE-----SELDEKENLREEVQRLKDELRDLKQEL 47 (166)
T ss_dssp HHHHHHH-----HHHHHHHHHHHCH--------------
T ss_pred HHhHHHH-----HHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 5555554 4556677655 679999999998744
No 18
>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=75.90 E-value=1.5 Score=28.59 Aligned_cols=27 Identities=22% Similarity=0.492 Sum_probs=13.7
Q ss_pred cccccCCceeecCCCCcceEEeeeccC
Q psy5308 105 RCCARCGGKVTLRSNKVSVEVTTRGHN 131 (137)
Q Consensus 105 rvC~rCg~~v~lr~n~~~W~Ctvc~~~ 131 (137)
+.|+.||.....+.+...|.|..|++.
T Consensus 29 q~C~~CG~~~~~~~~~r~~~C~~Cg~~ 55 (69)
T PF07282_consen 29 QTCPRCGHRNKKRRSGRVFTCPNCGFE 55 (69)
T ss_pred cCccCcccccccccccceEEcCCCCCE
Confidence 344555544432223446777776653
No 19
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=75.04 E-value=2.2 Score=26.19 Aligned_cols=24 Identities=38% Similarity=0.634 Sum_probs=10.0
Q ss_pred ccccCCceeecCCCCcceEEeeec
Q psy5308 106 CCARCGGKVTLRSNKVSVEVTTRG 129 (137)
Q Consensus 106 vC~rCg~~v~lr~n~~~W~Ctvc~ 129 (137)
.|..||..+...+....+.|..|+
T Consensus 5 ~C~~CG~~~~~~~~~~~~~Cp~CG 28 (46)
T PRK00398 5 KCARCGREVELDEYGTGVRCPYCG 28 (46)
T ss_pred ECCCCCCEEEECCCCCceECCCCC
Confidence 344444444333322244444444
No 20
>PF05400 FliT: Flagellar protein FliT; InterPro: IPR008622 This entry represents the bacterial flagellar FliT family of dual-function proteins. Together with FlgN, FliT has been proposed to act as a substrate-specific export chaperone, facilitating the incorporation of the enterobacterial hook-associated axial proteins (HAPs) FlgK/FlgL and FliD into the growing flagellum []. FliT has also been shown to act as a transcriptional regulator in Salmonella typhimurium [].; GO: 0019861 flagellum; PDB: 3A7M_A 3H3M_B 3NKZ_C 2G42_A 2FZT_B.
Probab=74.12 E-value=10 Score=24.73 Aligned_cols=40 Identities=10% Similarity=0.084 Sum_probs=32.8
Q ss_pred CCCHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHH
Q psy5308 24 HLTLEERQIIESVMMRQKQEEERELEIMRRKQDEVHLLEQ 63 (137)
Q Consensus 24 ~LteeEr~~Il~VL~R~~~le~~E~~RirkL~~el~~lk~ 63 (137)
.++++.++.|..+|..|+++...=+.|...|..++..+++
T Consensus 37 ~~~~~~~~~l~~Il~~d~~i~~ll~~~~~~l~~~l~~~~~ 76 (84)
T PF05400_consen 37 PEQEELRELLRRILELDQEIRALLQARRDELKQELRQLRK 76 (84)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHH
T ss_pred hhHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3467778888889999999988888888888888887765
No 21
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=73.80 E-value=1.7 Score=27.79 Aligned_cols=27 Identities=19% Similarity=0.356 Sum_probs=13.7
Q ss_pred ccccccCCceeecCCCCcceEEeeeccC
Q psy5308 104 IRCCARCGGKVTLRSNKVSVEVTTRGHN 131 (137)
Q Consensus 104 ~rvC~rCg~~v~lr~n~~~W~Ctvc~~~ 131 (137)
.++|.+||.. .+..+...|.|.-|++.
T Consensus 20 ~~fCP~Cg~~-~m~~~~~r~~C~~Cgyt 46 (50)
T PRK00432 20 NKFCPRCGSG-FMAEHLDRWHCGKCGYT 46 (50)
T ss_pred cCcCcCCCcc-hheccCCcEECCCcCCE
Confidence 4456666652 22333445666666543
No 22
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=73.67 E-value=1.7 Score=26.34 Aligned_cols=27 Identities=30% Similarity=0.666 Sum_probs=19.9
Q ss_pred ccccccccccCCCCCCCccccccccccCC
Q psy5308 83 CHICLKTKFADGVGHMCNYCNIRCCARCG 111 (137)
Q Consensus 83 C~~C~ktkf~~g~G~~C~~C~~rvC~rCg 111 (137)
|..|.+-.|+. +..|.+|+..||++=+
T Consensus 1 C~~C~~~~~l~--~f~C~~C~~~FC~~HR 27 (39)
T smart00154 1 CHFCRKKVGLT--GFKCRHCGNLFCGEHR 27 (39)
T ss_pred CcccCCccccc--CeECCccCCccccccC
Confidence 66787554543 6789999999998643
No 23
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=72.00 E-value=2.3 Score=27.72 Aligned_cols=25 Identities=32% Similarity=0.558 Sum_probs=10.4
Q ss_pred cccccCCceeecCCCCcceEEeeec
Q psy5308 105 RCCARCGGKVTLRSNKVSVEVTTRG 129 (137)
Q Consensus 105 rvC~rCg~~v~lr~n~~~W~Ctvc~ 129 (137)
++|.|||--+.+-.|+--|.|--|+
T Consensus 20 ~~CPrCG~gvfmA~H~dR~~CGkCg 44 (51)
T COG1998 20 RFCPRCGPGVFMADHKDRWACGKCG 44 (51)
T ss_pred ccCCCCCCcchhhhcCceeEecccc
Confidence 4444444323333333344444443
No 24
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=71.14 E-value=2.1 Score=36.54 Aligned_cols=25 Identities=20% Similarity=0.575 Sum_probs=15.1
Q ss_pred ccccccccccccc--CCCCCCCccccc
Q psy5308 80 DATCHICLKTKFA--DGVGHMCNYCNI 104 (137)
Q Consensus 80 ~~~C~~C~ktkf~--~g~G~~C~~C~~ 104 (137)
.+-|+.|+..... .+...+|+.|.+
T Consensus 111 ~RFCg~CG~~~~~~~~g~~~~C~~cg~ 137 (279)
T COG2816 111 HRFCGRCGTKTYPREGGWARVCPKCGH 137 (279)
T ss_pred CcCCCCCCCcCccccCceeeeCCCCCC
Confidence 6899999954433 345555555433
No 25
>PF01485 IBR: IBR domain; InterPro: IPR002867 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 cysteine-rich (C6HC) zinc finger domain that is present in Triad1, and which is conserved in other proteins encoded by various eukaryotes. The C6HC consensus pattern is: C-x(4)-C-x(14-30)-C-x(1-4)-C-x(4)-C-x(2)-C-x(4)-H-x(4)-C The C6HC zinc finger motif is the fourth family member of the zinc-binding RING, LIM, and LAP/PHD fingers. Strikingly, in most of the proteins the C6HC domain is flanked by two RING finger structures IPR001841 from INTERPRO. The novel C6HC motif has been called DRIL (double RING finger linked). The strong conservation of the larger tripartite TRIAD (twoRING fingers and DRIL) structure indicates that the three subdomains are functionally linked and identifies a novel class of proteins []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CT7_A 1WD2_A 2JMO_A 1WIM_A.
Probab=71.01 E-value=3.3 Score=25.78 Aligned_cols=35 Identities=26% Similarity=0.515 Sum_probs=21.8
Q ss_pred cccccc--ccccccc-CCCC---CCCccccccccccCCcee
Q psy5308 80 DATCHI--CLKTKFA-DGVG---HMCNYCNIRCCARCGGKV 114 (137)
Q Consensus 80 ~~~C~~--C~ktkf~-~g~G---~~C~~C~~rvC~rCg~~v 114 (137)
-+.|.. |...... ++.. ..|..|.+.+|..|+...
T Consensus 18 ~~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~fC~~C~~~~ 58 (64)
T PF01485_consen 18 IRWCPNPDCEYIIEKDDGCNSPIVTCPSCGTEFCFKCGEPW 58 (64)
T ss_dssp CC--TTSST---ECS-SSTTS--CCTTSCCSEECSSSTSES
T ss_pred ccCCCCCCCcccEEecCCCCCCeeECCCCCCcCccccCccc
Confidence 367977 9866533 3322 689999999999998663
No 26
>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=70.89 E-value=2.5 Score=24.47 Aligned_cols=25 Identities=16% Similarity=0.271 Sum_probs=17.2
Q ss_pred cccccCCceeecCCCCcceEEeeeccC
Q psy5308 105 RCCARCGGKVTLRSNKVSVEVTTRGHN 131 (137)
Q Consensus 105 rvC~rCg~~v~lr~n~~~W~Ctvc~~~ 131 (137)
-+|.-||-... ....-|+|.+|+..
T Consensus 2 ~~C~~CGy~y~--~~~~~~~CP~Cg~~ 26 (33)
T cd00350 2 YVCPVCGYIYD--GEEAPWVCPVCGAP 26 (33)
T ss_pred EECCCCCCEEC--CCcCCCcCcCCCCc
Confidence 47888984432 23457999999764
No 27
>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=70.88 E-value=2.3 Score=23.68 Aligned_cols=24 Identities=25% Similarity=0.602 Sum_probs=17.6
Q ss_pred cccCCceeecCCCCcceEEeeecc
Q psy5308 107 CARCGGKVTLRSNKVSVEVTTRGH 130 (137)
Q Consensus 107 C~rCg~~v~lr~n~~~W~Ctvc~~ 130 (137)
|..||..+.-+...+...|.-|++
T Consensus 1 C~sC~~~i~~r~~~v~f~CPnCG~ 24 (24)
T PF07754_consen 1 CTSCGRPIAPREQAVPFPCPNCGF 24 (24)
T ss_pred CccCCCcccCcccCceEeCCCCCC
Confidence 678887776665567888888764
No 28
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=70.40 E-value=3 Score=25.98 Aligned_cols=24 Identities=29% Similarity=0.556 Sum_probs=12.2
Q ss_pred ccccCCceeecCCCCcceEEeeecc
Q psy5308 106 CCARCGGKVTLRSNKVSVEVTTRGH 130 (137)
Q Consensus 106 vC~rCg~~v~lr~n~~~W~Ctvc~~ 130 (137)
+|.+||..+++.. ...-.|.-|+|
T Consensus 4 ~C~~Cg~~~~~~~-~~~irC~~CG~ 27 (44)
T smart00659 4 ICGECGRENEIKS-KDVVRCRECGY 27 (44)
T ss_pred ECCCCCCEeecCC-CCceECCCCCc
Confidence 4555655555443 22455555554
No 29
>PF14156 AbbA_antirepres: Antirepressor AbbA
Probab=68.59 E-value=4.8 Score=27.25 Aligned_cols=33 Identities=21% Similarity=0.365 Sum_probs=24.3
Q ss_pred CCCCHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHH
Q psy5308 23 SHLTLEERQIIESVMMRQKQEEERELEIMRRKQDEVHLLE 62 (137)
Q Consensus 23 S~LteeEr~~Il~VL~R~~~le~~E~~RirkL~~el~~lk 62 (137)
..||+||++.+|.||.+|..-= .-|..||.+++
T Consensus 7 ~rlt~EE~~LLLdiLf~q~YA~-------Ells~El~DIE 39 (63)
T PF14156_consen 7 ERLTEEEKKLLLDILFQQNYAS-------ELLSSELNDIE 39 (63)
T ss_pred HHhhHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHh
Confidence 4689999999999999998732 23455565554
No 30
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=66.96 E-value=2.8 Score=27.07 Aligned_cols=23 Identities=26% Similarity=0.618 Sum_probs=12.9
Q ss_pred ccccccccccc-c-CCCCCCCcccc
Q psy5308 81 ATCHICLKTKF-A-DGVGHMCNYCN 103 (137)
Q Consensus 81 ~~C~~C~ktkf-~-~g~G~~C~~C~ 103 (137)
-.|++|.+..- . ...+..|.||.
T Consensus 7 Y~C~~Cg~~~~~~~~~~~irCp~Cg 31 (49)
T COG1996 7 YKCARCGREVELDQETRGIRCPYCG 31 (49)
T ss_pred EEhhhcCCeeehhhccCceeCCCCC
Confidence 34788876542 2 24666666553
No 31
>PF10367 Vps39_2: Vacuolar sorting protein 39 domain 2; InterPro: IPR019453 This entry represents a domain found in the vacuolar sorting protein Vps39 and transforming growth factor beta receptor-associated protein Trap1. Vps39, a component of the C-Vps complex, is thought to be required for the fusion of endosomes and other types of transport intermediates with the vacuole [, ]. In Saccharomyces cerevisiae (Baker's yeast), Vps39 has been shown to stimulate nucleotide exchange []. Trap1 plays a role in the TGF-beta/activin signaling pathway. It associates with inactive heteromeric TGF-beta and activin receptor complexes, mainly through the type II receptor, and is released upon activation of signaling [, ]. The precise function of this domain has not been characterised In Vps39 this domain is involved in localisation and in mediating the interactions with Vps11 [].
Probab=65.30 E-value=30 Score=23.46 Aligned_cols=12 Identities=25% Similarity=0.520 Sum_probs=9.8
Q ss_pred cccccccccccc
Q psy5308 80 DATCHICLKTKF 91 (137)
Q Consensus 80 ~~~C~~C~ktkf 91 (137)
...|.+|+|.++
T Consensus 78 ~~~C~vC~k~l~ 89 (109)
T PF10367_consen 78 STKCSVCGKPLG 89 (109)
T ss_pred CCCccCcCCcCC
Confidence 578999998853
No 32
>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 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=64.54 E-value=27 Score=26.86 Aligned_cols=25 Identities=24% Similarity=0.344 Sum_probs=20.9
Q ss_pred CCCCCCCCHHHHHHHHHHHHhhHHH
Q psy5308 19 IPDLSHLTLEERQIIESVMMRQKQE 43 (137)
Q Consensus 19 ~~dLS~LteeEr~~Il~VL~R~~~l 43 (137)
+..++.||.+|-+.|.+.|+||=+.
T Consensus 27 ~~~~~elT~eEl~lv~~ylkRDl~~ 51 (146)
T PF07295_consen 27 LVAAGELTREELALVSAYLKRDLEE 51 (146)
T ss_pred HHHHhhcCHHHHHHHHHHHHHHHHH
Confidence 3457889999999999999998553
No 34
>PF09776 Mitoc_L55: Mitochondrial ribosomal protein L55; InterPro: IPR018615 Members of this family are involved in mitochondrial biogenesis and G2/M phase cell cycle progression. They form a component of the mitochondrial ribosome large subunit (39S) which comprises a 16S rRNA and about 50 distinct proteins.
Probab=63.44 E-value=6 Score=29.74 Aligned_cols=17 Identities=35% Similarity=0.274 Sum_probs=15.1
Q ss_pred CCCCCCCCHHHHHHHHH
Q psy5308 19 IPDLSHLTLEERQIIES 35 (137)
Q Consensus 19 ~~dLS~LteeEr~~Il~ 35 (137)
-+||+-||||||...+.
T Consensus 71 PlDl~~LSeeERk~rl~ 87 (116)
T PF09776_consen 71 PLDLDTLSEEERKARLR 87 (116)
T ss_pred ccCcccCCHHHHHHHHH
Confidence 58999999999988776
No 35
>PHA03158 hypothetical protein; Provisional
Probab=61.93 E-value=19 Score=29.99 Aligned_cols=41 Identities=20% Similarity=0.242 Sum_probs=32.6
Q ss_pred CCCHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHH
Q psy5308 24 HLTLEERQIIESVMMRQKQEEERELEIMRRKQDEVHLLEQS 64 (137)
Q Consensus 24 ~LteeEr~~Il~VL~R~~~le~~E~~RirkL~~el~~lk~~ 64 (137)
-+|.+|+..|++-|-+.+.-=-+..+++.+|++++++|+++
T Consensus 229 v~t~~EK~~~~kQllka~kkc~~~s~~~~~leeei~eleks 269 (273)
T PHA03158 229 IKTAKEKAAILKQLLKAAKKCCKNSEHEKELEEEIEELEKS 269 (273)
T ss_pred eecHHHhHHHHHHHHHHHHHHhcchHHHHHHHHHHHHHHHh
Confidence 37899998888766666665566778999999999999864
No 36
>KOG1985|consensus
Probab=61.55 E-value=3.6 Score=39.91 Aligned_cols=39 Identities=13% Similarity=0.212 Sum_probs=23.8
Q ss_pred CCCCCccccccc--cccCCcee----ecCCCCcceEEeeeccCCC
Q psy5308 95 VGHMCNYCNIRC--CARCGGKV----TLRSNKVSVEVTTRGHNNN 133 (137)
Q Consensus 95 ~G~~C~~C~~rv--C~rCg~~v----~lr~n~~~W~Ctvc~~~~~ 133 (137)
.+-+|..+.+.+ |.+|+.++ +.-.++..|+|.+|...|.
T Consensus 207 ~~~~p~~~~~~IvRCr~CRtYiNPFV~fid~gr~WrCNlC~~~Nd 251 (887)
T KOG1985|consen 207 IDPLPVITSTLIVRCRRCRTYINPFVEFIDQGRRWRCNLCGRVND 251 (887)
T ss_pred cCCCCcccCCceeeehhhhhhcCCeEEecCCCceeeechhhhhcC
Confidence 344444444433 77777665 2233446899999887764
No 37
>PTZ00303 phosphatidylinositol kinase; Provisional
Probab=60.41 E-value=5.2 Score=39.34 Aligned_cols=33 Identities=30% Similarity=0.684 Sum_probs=27.6
Q ss_pred cccccccccccc-----CCCCCCCccccccccccCCce
Q psy5308 81 ATCHICLKTKFA-----DGVGHMCNYCNIRCCARCGGK 113 (137)
Q Consensus 81 ~~C~~C~ktkf~-----~g~G~~C~~C~~rvC~rCg~~ 113 (137)
.+|.+|.+.+|. ..+-|.|..|-..||..|-..
T Consensus 461 dtC~~C~kkFfSlsK~L~~RKHHCRkCGrVFC~~CSSn 498 (1374)
T PTZ00303 461 DSCPSCGRAFISLSRPLGTRAHHCRSCGIRLCVFCITK 498 (1374)
T ss_pred CcccCcCCcccccccccccccccccCCccccCccccCC
Confidence 679999988653 358999999999999999754
No 38
>PRK00241 nudC NADH pyrophosphatase; Reviewed
Probab=60.30 E-value=4.1 Score=33.63 Aligned_cols=32 Identities=16% Similarity=0.301 Sum_probs=18.4
Q ss_pred cccccccccccccCCCCCCCccccccccccCCceeecC
Q psy5308 80 DATCHICLKTKFADGVGHMCNYCNIRCCARCGGKVTLR 117 (137)
Q Consensus 80 ~~~C~~C~ktkf~~g~G~~C~~C~~rvC~rCg~~v~lr 117 (137)
.+-|+.|+........+ ..++|..||.....+
T Consensus 99 ~~fC~~CG~~~~~~~~~------~~~~C~~c~~~~yp~ 130 (256)
T PRK00241 99 HRFCGYCGHPMHPSKTE------WAMLCPHCRERYYPR 130 (256)
T ss_pred CccccccCCCCeecCCc------eeEECCCCCCEECCC
Confidence 58899999664322111 135566676555444
No 39
>PLN00162 transport protein sec23; Provisional
Probab=59.32 E-value=5.8 Score=37.65 Aligned_cols=33 Identities=12% Similarity=0.038 Sum_probs=20.0
Q ss_pred CCCccccccccccCCceeecCCCCcceEEeeeccCCC
Q psy5308 97 HMCNYCNIRCCARCGGKVTLRSNKVSVEVTTRGHNNN 133 (137)
Q Consensus 97 ~~C~~C~~rvC~rCg~~v~lr~n~~~W~Ctvc~~~~~ 133 (137)
..|..|+-.+..-|.+. . ++..|.|.+|...|.
T Consensus 54 vRC~~CraylNPf~~~d---~-~~~~W~C~~C~~~N~ 86 (761)
T PLN00162 54 LRCRTCRAVLNPYCRVD---F-QAKIWICPFCFQRNH 86 (761)
T ss_pred CccCCCcCEECCceEEe---c-CCCEEEccCCCCCCC
Confidence 45555555555555322 1 235899999987763
No 40
>PF04201 TPD52: Tumour protein D52 family; InterPro: IPR007327 The hD52 gene was originally identified through its elevated expression level in human breast carcinoma. Cloning of D52 homologues from other species has indicated that D52 may play roles in calcium-mediated signal transduction and cell proliferation. Two human homologues of hD52, hD53 and hD54, have also been identified, demonstrating the existence of a novel gene/protein family []. These proteins have an N-terminal coiled-coil that allows members to form homo- and heterodimers with each other [].
Probab=59.06 E-value=72 Score=25.30 Aligned_cols=17 Identities=29% Similarity=0.323 Sum_probs=13.0
Q ss_pred CCCCCCHHHHHHHHHHH
Q psy5308 21 DLSHLTLEERQIIESVM 37 (137)
Q Consensus 21 dLS~LteeEr~~Il~VL 37 (137)
+...|||+||+.+..-|
T Consensus 22 ~~~~LsEeE~eeLr~EL 38 (162)
T PF04201_consen 22 SEEGLSEEEREELRSEL 38 (162)
T ss_pred CcccCCHHHHHHHHHHH
Confidence 34699999999876644
No 41
>COG2023 RPR2 RNase P subunit RPR2 [Translation, ribosomal structure and biogenesis]
Probab=58.78 E-value=5.8 Score=29.38 Aligned_cols=38 Identities=24% Similarity=0.411 Sum_probs=25.1
Q ss_pred cccccccccccccCCCCCCCccccccccccCCceeecCCCCcceEEeeeccCCC
Q psy5308 80 DATCHICLKTKFADGVGHMCNYCNIRCCARCGGKVTLRSNKVSVEVTTRGHNNN 133 (137)
Q Consensus 80 ~~~C~~C~ktkf~~g~G~~C~~C~~rvC~rCg~~v~lr~n~~~W~Ctvc~~~~~ 133 (137)
...|-.|+ +.+.-|. .|+++ ++++.+.|.|..||+..+
T Consensus 56 R~~CkkC~-t~Lvpg~-------------n~rvR--~~~~~v~vtC~~CG~~~R 93 (105)
T COG2023 56 RTICKKCY-TPLVPGK-------------NARVR--LRKGRVVVTCLECGTIRR 93 (105)
T ss_pred HHhccccC-cccccCc-------------ceEEE--EcCCeEEEEecCCCcEEE
Confidence 46799998 4333232 35544 476669999999998643
No 42
>TIGR01053 LSD1 zinc finger domain, LSD1 subclass. This model describes a putative zinc finger domain found in three closely spaced copies in Arabidopsis protein LSD1 and in two copies in other proteins from the same species. The motif resembles CxxCRxxLMYxxGASxVxCxxC
Probab=58.26 E-value=7.9 Score=22.54 Aligned_cols=25 Identities=16% Similarity=0.235 Sum_probs=18.4
Q ss_pred cccccCCceeecCCCCcceEEeeec
Q psy5308 105 RCCARCGGKVTLRSNKVSVEVTTRG 129 (137)
Q Consensus 105 rvC~rCg~~v~lr~n~~~W~Ctvc~ 129 (137)
-+|..||..+...+.-..++|.+|.
T Consensus 2 ~~C~~C~t~L~yP~gA~~vrCs~C~ 26 (31)
T TIGR01053 2 VVCGGCRTLLMYPRGASSVRCALCQ 26 (31)
T ss_pred cCcCCCCcEeecCCCCCeEECCCCC
Confidence 3688888777666656788888864
No 43
>PF13639 zf-RING_2: Ring finger domain; PDB: 2KIZ_A 4EPO_C 1IYM_A 2EP4_A 2ECT_A 2JRJ_A 2ECN_A 2ECM_A 3NG2_A 2EA6_A ....
Probab=57.62 E-value=1.7 Score=25.93 Aligned_cols=32 Identities=19% Similarity=0.223 Sum_probs=21.8
Q ss_pred cccccccccccCCCCCCCccccccccccCCcee
Q psy5308 82 TCHICLKTKFADGVGHMCNYCNIRCCARCGGKV 114 (137)
Q Consensus 82 ~C~~C~ktkf~~g~G~~C~~C~~rvC~rCg~~v 114 (137)
.|+||+.....+..-.... |.|.||..|-...
T Consensus 2 ~C~IC~~~~~~~~~~~~l~-C~H~fh~~Ci~~~ 33 (44)
T PF13639_consen 2 ECPICLEEFEDGEKVVKLP-CGHVFHRSCIKEW 33 (44)
T ss_dssp CETTTTCBHHTTSCEEEET-TSEEEEHHHHHHH
T ss_pred CCcCCChhhcCCCeEEEcc-CCCeeCHHHHHHH
Confidence 5999997653433333444 9999999995443
No 44
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=56.61 E-value=6.3 Score=28.43 Aligned_cols=10 Identities=10% Similarity=0.039 Sum_probs=6.4
Q ss_pred ceEEeeeccC
Q psy5308 122 SVEVTTRGHN 131 (137)
Q Consensus 122 ~W~Ctvc~~~ 131 (137)
+|.|.-|++.
T Consensus 53 IW~C~kCg~~ 62 (89)
T COG1997 53 IWKCRKCGAK 62 (89)
T ss_pred eEEcCCCCCe
Confidence 6777766653
No 45
>PRK11595 DNA utilization protein GntX; Provisional
Probab=56.57 E-value=5.9 Score=31.68 Aligned_cols=33 Identities=24% Similarity=0.692 Sum_probs=21.4
Q ss_pred cccccccccccccCCCCCCCcccccc------ccccCCce
Q psy5308 80 DATCHICLKTKFADGVGHMCNYCNIR------CCARCGGK 113 (137)
Q Consensus 80 ~~~C~~C~ktkf~~g~G~~C~~C~~r------vC~rCg~~ 113 (137)
++.|..|++.... +...+|..|... .|.+||..
T Consensus 5 P~~C~~C~~~~~~-~~~~lC~~C~~~l~~~~~~C~~Cg~~ 43 (227)
T PRK11595 5 PGLCWLCRMPLAL-SHWGICSVCSRALRTLKTCCPQCGLP 43 (227)
T ss_pred CCcCccCCCccCC-CCCcccHHHHhhCCcccCcCccCCCc
Confidence 4679999866432 222378888654 48888854
No 46
>PF12760 Zn_Tnp_IS1595: Transposase zinc-ribbon domain; InterPro: IPR024442 This zinc binding domain is found in a range of transposase proteins such as ISSPO8, ISSOD11, ISRSSP2 etc. It may be a zinc-binding beta ribbon domain that could bind DNA.
Probab=55.85 E-value=8.1 Score=23.69 Aligned_cols=9 Identities=0% Similarity=-0.101 Sum_probs=5.3
Q ss_pred ceEEeeecc
Q psy5308 122 SVEVTTRGH 130 (137)
Q Consensus 122 ~W~Ctvc~~ 130 (137)
.|.|+-|.+
T Consensus 37 ~~~C~~C~~ 45 (46)
T PF12760_consen 37 RYRCKACRK 45 (46)
T ss_pred eEECCCCCC
Confidence 566666543
No 47
>KOG3507|consensus
Probab=55.72 E-value=6 Score=26.73 Aligned_cols=26 Identities=27% Similarity=0.554 Sum_probs=17.2
Q ss_pred ccccccCCceeecCCCCcceEEeeecc
Q psy5308 104 IRCCARCGGKVTLRSNKVSVEVTTRGH 130 (137)
Q Consensus 104 ~rvC~rCg~~v~lr~n~~~W~Ctvc~~ 130 (137)
..+|..||.+-++.+.. ...|.-|||
T Consensus 20 iYiCgdC~~en~lk~~D-~irCReCG~ 45 (62)
T KOG3507|consen 20 IYICGDCGQENTLKRGD-VIRCRECGY 45 (62)
T ss_pred EEEeccccccccccCCC-cEehhhcch
Confidence 35777777776666533 677777776
No 48
>TIGR00269 conserved hypothetical protein TIGR00269.
Probab=55.10 E-value=21 Score=25.44 Aligned_cols=21 Identities=24% Similarity=0.700 Sum_probs=15.8
Q ss_pred cccccccccccccCCCCCCCccccc
Q psy5308 80 DATCHICLKTKFADGVGHMCNYCNI 104 (137)
Q Consensus 80 ~~~C~~C~ktkf~~g~G~~C~~C~~ 104 (137)
-..|.+|+-+ .+|.+|+.|+.
T Consensus 80 ~~~C~~CG~p----ss~~iC~~C~l 100 (104)
T TIGR00269 80 LRRCERCGEP----TSGRICKACKF 100 (104)
T ss_pred CCcCCcCcCc----CCccccHhhhh
Confidence 4779999944 46778888865
No 49
>PF12773 DZR: Double zinc ribbon
Probab=54.97 E-value=4.3 Score=24.83 Aligned_cols=10 Identities=10% Similarity=0.029 Sum_probs=4.9
Q ss_pred ceEEeeeccC
Q psy5308 122 SVEVTTRGHN 131 (137)
Q Consensus 122 ~W~Ctvc~~~ 131 (137)
.+.|..|++.
T Consensus 29 ~~~C~~Cg~~ 38 (50)
T PF12773_consen 29 KKICPNCGAE 38 (50)
T ss_pred CCCCcCCcCC
Confidence 4555555444
No 50
>PRK11546 zraP zinc resistance protein; Provisional
Probab=54.78 E-value=53 Score=25.42 Aligned_cols=45 Identities=16% Similarity=0.169 Sum_probs=29.5
Q ss_pred CCCCCCHHHHHHHHHHHHh---------------hHHHHHH------HHHHHHHHHHHHHHHHHHH
Q psy5308 21 DLSHLTLEERQIIESVMMR---------------QKQEEER------ELEIMRRKQDEVHLLEQSI 65 (137)
Q Consensus 21 dLS~LteeEr~~Il~VL~R---------------~~~le~~------E~~RirkL~~el~~lk~~~ 65 (137)
--+-||+|.+..+..+.+. ..+|+.. +++.|+.|..|+.+|+.++
T Consensus 40 ~~~~LT~EQQa~~q~I~~~f~~~t~~LRqqL~aKr~ELnALl~~~~pD~~kI~aL~kEI~~Lr~kL 105 (143)
T PRK11546 40 NAAPLTTEQQAAWQKIHNDFYAQTSALRQQLVSKRYEYNALLTANPPDSSKINAVAKEMENLRQSL 105 (143)
T ss_pred ccccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHH
Confidence 3567999999988655432 1222221 2367888999998888755
No 51
>PF06943 zf-LSD1: LSD1 zinc finger; InterPro: IPR005735 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 model describes a putative zinc finger domain found in three closely spaced copies in Arabidopsis protein LSD1 and in two copies in other proteins from the same species. The motif resembles CxxCRxxLMYxxGASxVxCxxC []. This domain may play a role in the regulation of transcription, via either repression of a prodeath pathway or activation of an antideath pathway, in response to signals emanating from cells undergoing pathogen-induced hypersensitive cell death. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].
Probab=54.45 E-value=10 Score=21.23 Aligned_cols=23 Identities=17% Similarity=0.278 Sum_probs=15.1
Q ss_pred cccCCceeecCCCCcceEEeeec
Q psy5308 107 CARCGGKVTLRSNKVSVEVTTRG 129 (137)
Q Consensus 107 C~rCg~~v~lr~n~~~W~Ctvc~ 129 (137)
|..|+.-+.....-+.|.|.+|.
T Consensus 1 C~~Cr~~L~yp~GA~sVrCa~C~ 23 (25)
T PF06943_consen 1 CGGCRTLLMYPRGAPSVRCACCH 23 (25)
T ss_pred CCCCCceEEcCCCCCCeECCccC
Confidence 56777666555545678887764
No 52
>PF13801 Metal_resist: Heavy-metal resistance; PDB: 3EPV_C 2Y3D_A 2Y3H_D 2Y3G_B 2Y3B_A 2Y39_A 3LAY_H.
Probab=53.53 E-value=66 Score=21.63 Aligned_cols=39 Identities=23% Similarity=0.308 Sum_probs=22.1
Q ss_pred CCCCCCCHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHH
Q psy5308 20 PDLSHLTLEERQIIESVMMRQKQEEERELEIMRRKQDEV 58 (137)
Q Consensus 20 ~dLS~LteeEr~~Il~VL~R~~~le~~E~~RirkL~~el 58 (137)
.+-..||++.++.|..++......-.....-++.+..+|
T Consensus 37 ~~~l~Lt~eQ~~~l~~~~~~~~~~~~~~r~~~~~~r~~l 75 (125)
T PF13801_consen 37 ADMLNLTPEQQAKLRALMDEFRQEMRALRQELRAARQEL 75 (125)
T ss_dssp HHHS-TTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred hhhcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 345689999999999987544432222222244444444
No 53
>PF09849 DUF2076: Uncharacterized protein conserved in bacteria (DUF2076); InterPro: IPR018648 This family of hypothetical prokaryotic proteins has no known function but includes putative perimplasmic ligand-binding sensor proteins.
Probab=52.93 E-value=49 Score=27.63 Aligned_cols=19 Identities=47% Similarity=0.678 Sum_probs=15.1
Q ss_pred CCHHHHHHHHHHHHhhHHH
Q psy5308 25 LTLEERQIIESVMMRQKQE 43 (137)
Q Consensus 25 LteeEr~~Il~VL~R~~~l 43 (137)
+|++||.+|-.++.|=++.
T Consensus 1 M~~eE~qLI~~lf~RL~~a 19 (247)
T PF09849_consen 1 MTPEERQLIDDLFSRLKQA 19 (247)
T ss_pred CchHHHHHHHHHHHHHHhc
Confidence 4789999999999875544
No 54
>PF03754 DUF313: Domain of unknown function (DUF313) ; InterPro: IPR005508 This is a family of proteins from Arabidopsis thaliana (Mouse-ear cress) with uncharacterised function.
Probab=52.65 E-value=6.2 Score=29.31 Aligned_cols=16 Identities=50% Similarity=0.515 Sum_probs=14.2
Q ss_pred CCCCCCCCCHHHHHHH
Q psy5308 18 IIPDLSHLTLEERQII 33 (137)
Q Consensus 18 ~~~dLS~LteeEr~~I 33 (137)
+.+|..|||++|.++|
T Consensus 46 qi~~~dFLt~eE~~~i 61 (114)
T PF03754_consen 46 QIIDNDFLTEEEKRII 61 (114)
T ss_pred HhcccccCCHHHHHHH
Confidence 4568899999999999
No 55
>COG5028 Vesicle coat complex COPII, subunit SEC24/subunit SFB2/subunit SFB3 [Intracellular trafficking and secretion]
Probab=52.20 E-value=6.1 Score=38.23 Aligned_cols=28 Identities=14% Similarity=0.242 Sum_probs=19.5
Q ss_pred cccccCCceee----cCCCCcceEEeeeccCC
Q psy5308 105 RCCARCGGKVT----LRSNKVSVEVTTRGHNN 132 (137)
Q Consensus 105 rvC~rCg~~v~----lr~n~~~W~Ctvc~~~~ 132 (137)
--|.||+.+++ --.++..|.|.||.-.|
T Consensus 200 vRCrrCrsYiNPfv~fi~~g~kw~CNiC~~kN 231 (861)
T COG5028 200 VRCRRCRSYINPFVQFIEQGRKWRCNICRSKN 231 (861)
T ss_pred hhhhhhHhhcCceEEEecCCcEEEEeeccccc
Confidence 55889998874 11124589999987665
No 56
>PF11781 RRN7: RNA polymerase I-specific transcription initiation factor Rrn7; InterPro: IPR021752 Rrn7 is a transcription binding factor that associates strongly with both Rrn6 and Rrn11 to form a complex which itself binds the TATA-binding protein and is required for transcription by the core domain of the RNA PolI promoter [],[].
Probab=52.08 E-value=9.4 Score=22.77 Aligned_cols=23 Identities=22% Similarity=0.453 Sum_probs=9.8
Q ss_pred cccCCceeecCCCCcceEEeeecc
Q psy5308 107 CARCGGKVTLRSNKVSVEVTTRGH 130 (137)
Q Consensus 107 C~rCg~~v~lr~n~~~W~Ctvc~~ 130 (137)
|..||.+.....++ .|.|.-|+|
T Consensus 11 C~~C~~~~~~~~dG-~~yC~~cG~ 33 (36)
T PF11781_consen 11 CPVCGSRWFYSDDG-FYYCDRCGH 33 (36)
T ss_pred CCCCCCeEeEccCC-EEEhhhCce
Confidence 33444443333333 455555444
No 57
>PF14723 SSFA2_C: Sperm-specific antigen 2 C-terminus
Probab=51.54 E-value=42 Score=27.07 Aligned_cols=11 Identities=27% Similarity=0.431 Sum_probs=5.6
Q ss_pred HHHHHHHHHHH
Q psy5308 55 QDEVHLLEQSI 65 (137)
Q Consensus 55 ~~el~~lk~~~ 65 (137)
.+||++|+.++
T Consensus 158 RqElqELE~QL 168 (179)
T PF14723_consen 158 RQELQELEFQL 168 (179)
T ss_pred HHHHHHHHHHH
Confidence 44555555544
No 58
>KOG1818|consensus
Probab=51.32 E-value=7 Score=36.85 Aligned_cols=49 Identities=18% Similarity=0.311 Sum_probs=34.2
Q ss_pred cccccccccccccCCCCCCCccccccccccCCceeecCC----CCcceEEeee
Q psy5308 80 DATCHICLKTKFADGVGHMCNYCNIRCCARCGGKVTLRS----NKVSVEVTTR 128 (137)
Q Consensus 80 ~~~C~~C~ktkf~~g~G~~C~~C~~rvC~rCg~~v~lr~----n~~~W~Ctvc 128 (137)
...|.+|...+..+++.|.|..|...||..|-...-..+ .++.=||..|
T Consensus 165 ~~~C~rCr~~F~~~~rkHHCr~CG~vFC~qcss~s~~lP~~Gi~~~VRVCd~C 217 (634)
T KOG1818|consen 165 SEECLRCRVKFGLTNRKHHCRNCGQVFCGQCSSKSLTLPKLGIEKPVRVCDSC 217 (634)
T ss_pred ccccceeeeeeeeccccccccccchhhccCccccccCcccccccccceehhhh
Confidence 477999984443457999999999999999975532121 1234567765
No 59
>PF04981 NMD3: NMD3 family ; InterPro: IPR007064 The NMD3 protein is involved in nonsense mediated mRNA decay. This N-terminal region contains four conserved CXXC motifs that could be metal binding. NMD3 is involved in export of the 60S ribosomal subunit is mediated by the adapter protein Nmd3p in a Crm1p-dependent pathway [].
Probab=50.90 E-value=12 Score=30.27 Aligned_cols=19 Identities=16% Similarity=0.375 Sum_probs=13.1
Q ss_pred ccccccccCCceeecCCCCcceE
Q psy5308 102 CNIRCCARCGGKVTLRSNKVSVE 124 (137)
Q Consensus 102 C~~rvC~rCg~~v~lr~n~~~W~ 124 (137)
-...+|..||.+. .+ + .|.
T Consensus 33 i~v~~C~~Cg~~~--~~-~-~W~ 51 (236)
T PF04981_consen 33 IEVTICPKCGRYR--IG-G-RWV 51 (236)
T ss_pred cCceECCCCCCEE--CC-C-Eee
Confidence 3678999999773 22 3 686
No 60
>KOG0804|consensus
Probab=50.78 E-value=8.9 Score=35.05 Aligned_cols=34 Identities=24% Similarity=0.517 Sum_probs=27.0
Q ss_pred CCCCCCCccccc------cccccCCceeecCCCCcceEEeeeccCC
Q psy5308 93 DGVGHMCNYCNI------RCCARCGGKVTLRSNKVSVEVTTRGHNN 132 (137)
Q Consensus 93 ~g~G~~C~~C~~------rvC~rCg~~v~lr~n~~~W~Ctvc~~~~ 132 (137)
+.+.-+|.||+. ..|..||.- +. .|.|-|||+-+
T Consensus 211 ~~scpvcR~~q~p~~ve~~~c~~c~~~-----~~-LwicliCg~vg 250 (493)
T KOG0804|consen 211 DSSCPVCRYCQSPSVVESSLCLACGCT-----ED-LWICLICGNVG 250 (493)
T ss_pred cCcChhhhhhcCcchhhhhhhhhhccc-----cc-EEEEEEcccee
Confidence 457778999987 589999844 23 89999999865
No 61
>KOG1729|consensus
Probab=50.75 E-value=3.8 Score=34.97 Aligned_cols=50 Identities=24% Similarity=0.320 Sum_probs=37.0
Q ss_pred cccccccccccccC-CCCCCCccccccccccCCceee---cCCCCcceEEeeec
Q psy5308 80 DATCHICLKTKFAD-GVGHMCNYCNIRCCARCGGKVT---LRSNKVSVEVTTRG 129 (137)
Q Consensus 80 ~~~C~~C~ktkf~~-g~G~~C~~C~~rvC~rCg~~v~---lr~n~~~W~Ctvc~ 129 (137)
...|..|.++.|.. .+-|.|..|-.-||+-|..... .-++++.-+|-+|=
T Consensus 168 a~~C~~C~~~~Ftl~~RRHHCR~CG~ivC~~Cs~n~~~l~~~~~k~~rvC~~CF 221 (288)
T KOG1729|consen 168 ATECMVCGCTEFTLSERRHHCRNCGDIVCAPCSRNRFLLPNLSTKPIRVCDICF 221 (288)
T ss_pred ceecccCCCccccHHHHHHHHHhcchHhhhhhhcCcccccccCCCCceecHHHH
Confidence 67899999987654 5889999999999999976621 12234556777753
No 62
>PF11290 DUF3090: Protein of unknown function (DUF3090); InterPro: IPR021441 This family of proteins with unknown function appears to be restricted to Actinobacteria.
Probab=50.38 E-value=20 Score=28.69 Aligned_cols=27 Identities=33% Similarity=0.760 Sum_probs=19.6
Q ss_pred hHHHHhhhCccccccccccccccccCCCCCCC
Q psy5308 68 RSEQQKKAGVELDATCHICLKTKFADGVGHMC 99 (137)
Q Consensus 68 ~~~~~r~~G~~~~~~C~~C~ktkf~~g~G~~C 99 (137)
+...+-.+| .+.|.+|+.+ +|..||+|
T Consensus 145 ra~~VVaAG---RP~CPlCg~P--lDP~GH~C 171 (171)
T PF11290_consen 145 RAREVVAAG---RPPCPLCGEP--LDPEGHIC 171 (171)
T ss_pred HHHHHHhCC---CCCCCCCCCC--CCCCCCcC
Confidence 334444466 7899999977 56679998
No 63
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=50.23 E-value=7.3 Score=31.01 Aligned_cols=22 Identities=23% Similarity=0.462 Sum_probs=12.7
Q ss_pred cccccCCceeecCCCCcceEEeeeccC
Q psy5308 105 RCCARCGGKVTLRSNKVSVEVTTRGHN 131 (137)
Q Consensus 105 rvC~rCg~~v~lr~n~~~W~Ctvc~~~ 131 (137)
+.|+.||. +. ...|.|..|++.
T Consensus 310 ~~C~~cg~---~~--~r~~~C~~cg~~ 331 (364)
T COG0675 310 KTCPCCGH---LS--GRLFKCPRCGFV 331 (364)
T ss_pred ccccccCC---cc--ceeEECCCCCCe
Confidence 45555554 11 336888888763
No 64
>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=48.98 E-value=6 Score=22.96 Aligned_cols=24 Identities=25% Similarity=0.548 Sum_probs=9.0
Q ss_pred cccCCceeecCCCCcceEEeeeccC
Q psy5308 107 CARCGGKVTLRSNKVSVEVTTRGHN 131 (137)
Q Consensus 107 C~rCg~~v~lr~n~~~W~Ctvc~~~ 131 (137)
|-.|+...++. ++.+++|..|+|+
T Consensus 5 Cp~C~se~~y~-D~~~~vCp~C~~e 28 (30)
T PF08274_consen 5 CPLCGSEYTYE-DGELLVCPECGHE 28 (30)
T ss_dssp -TTT-----EE--SSSEEETTTTEE
T ss_pred CCCCCCcceec-cCCEEeCCccccc
Confidence 44455444432 3446666666553
No 65
>PRK11032 hypothetical protein; Provisional
Probab=46.01 E-value=61 Score=25.48 Aligned_cols=23 Identities=26% Similarity=0.351 Sum_probs=19.8
Q ss_pred CCCCCCHHHHHHHHHHHHhhHHH
Q psy5308 21 DLSHLTLEERQIIESVMMRQKQE 43 (137)
Q Consensus 21 dLS~LteeEr~~Il~VL~R~~~l 43 (137)
-++.||.+|-+.|.+.|+||=+.
T Consensus 39 ~~~elT~dEl~lv~~ylkRDL~e 61 (160)
T PRK11032 39 AAGELTRDEVDLITRAVRRDLEE 61 (160)
T ss_pred HHHhcCHHHHHHHHHHHHHHHHH
Confidence 36789999999999999998654
No 66
>PF01195 Pept_tRNA_hydro: Peptidyl-tRNA hydrolase; InterPro: IPR001328 Peptidyl-tRNA hydrolase (3.1.1.29 from EC) (PTH) is a bacterial enzyme that cleaves peptidyl-tRNA or N-acyl-aminoacyl-tRNA to yield free peptides or N-acyl-amino acids and tRNA. The natural substrate for this enzyme may be peptidyl-tRNA which drop off the ribosome during protein synthesis [, ]. Bacterial PTH has been found to be evolutionary related to a yeast protein [].; GO: 0004045 aminoacyl-tRNA hydrolase activity; PDB: 3KJZ_A 3KK0_A 3P2J_A 3V2I_A 3TCN_A 3TD6_A 2Z2K_A 3TD2_A 2Z2J_B 2JRC_A ....
Probab=45.87 E-value=19 Score=28.29 Aligned_cols=23 Identities=26% Similarity=0.410 Sum_probs=17.7
Q ss_pred CCCCCCCCCCHHHHHHHHHHHHhh
Q psy5308 17 DIIPDLSHLTLEERQIIESVMMRQ 40 (137)
Q Consensus 17 ~~~~dLS~LteeEr~~Il~VL~R~ 40 (137)
.+.+ ||.++++|++.|..++...
T Consensus 142 ~~yV-L~~f~~~E~~~l~~~~~~a 164 (184)
T PF01195_consen 142 ADYV-LSKFSPEERELLDKVIPQA 164 (184)
T ss_dssp HHHH-TSB-HHHHHHHHHHHHHHH
T ss_pred HHHH-hcCCCHHHHHHHHHHHHHH
Confidence 3444 8999999999999988663
No 67
>PF13442 Cytochrome_CBB3: Cytochrome C oxidase, cbb3-type, subunit III ; PDB: 1KB0_A 2DGE_D 2CE1_A 2CE0_A 2V07_A 1W2L_A 2ZOO_A 2ZBO_G 1DVV_A 2EXV_A ....
Probab=45.83 E-value=29 Score=21.87 Aligned_cols=21 Identities=14% Similarity=0.154 Sum_probs=15.1
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHH
Q psy5308 15 NADIIPDLSHLTLEERQIIESVM 37 (137)
Q Consensus 15 ~~~~~~dLS~LteeEr~~Il~VL 37 (137)
.|+...+ .||++|.+.|...|
T Consensus 47 ~Mp~~~~--~ls~~e~~~l~~yi 67 (67)
T PF13442_consen 47 GMPPFGG--QLSDEEIEALAAYI 67 (67)
T ss_dssp TBSCTTT--TSTHHHHHHHHHHH
T ss_pred CCCCCCC--CCCHHHHHHHHHHC
Confidence 4444444 89999999988754
No 68
>cd02406 CRS2 Chloroplast RNA splicing 2 (CRS2) is a nuclear-encoded protein required for the splicing of group II introns in the chloroplast. CRS2 forms stable complexes with two CRS2-associated factors, CAF1 and CAF2, which are required for the splicing of distinct subsets of CRS2-dependent introns. CRS2 is closely related to bacterial peptidyl-tRNA hydrolases (PTH).
Probab=44.18 E-value=32 Score=27.58 Aligned_cols=26 Identities=19% Similarity=0.333 Sum_probs=20.8
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHHhhH
Q psy5308 15 NADIIPDLSHLTLEERQIIESVMMRQK 41 (137)
Q Consensus 15 ~~~~~~dLS~LteeEr~~Il~VL~R~~ 41 (137)
+..+-+ ||.++++|++.|..++.+..
T Consensus 143 ~v~~yV-L~~f~~~E~~~l~~~~~~a~ 168 (191)
T cd02406 143 DPRAFL-LQKFSSEEREQIDTALEQGV 168 (191)
T ss_pred chhhhh-cCCCCHHHHHHHHHHHHHHH
Confidence 445566 99999999999999886654
No 69
>KOG0860|consensus
Probab=44.02 E-value=83 Score=23.70 Aligned_cols=33 Identities=21% Similarity=0.244 Sum_probs=19.8
Q ss_pred HHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHH
Q psy5308 30 RQIIESVMMRQKQEEERELEIMRRKQDEVHLLEQ 63 (137)
Q Consensus 30 r~~Il~VL~R~~~le~~E~~RirkL~~el~~lk~ 63 (137)
|+-|-.||+|++.|.+.++ |-..|.+--...++
T Consensus 46 r~NV~KVlER~ekL~~L~d-rad~L~~~as~F~~ 78 (116)
T KOG0860|consen 46 RENVEKVLERGEKLDELDD-RADQLQAGASQFEK 78 (116)
T ss_pred HHhHHHHHHhcchHHHHHH-HHHHHHHHHHHHHH
Confidence 4556778999988887764 33344443334433
No 70
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=43.42 E-value=13 Score=25.10 Aligned_cols=47 Identities=19% Similarity=0.381 Sum_probs=27.5
Q ss_pred ccccccccccccc--CCCCCCCccccccc---cccCCceeecCCCCcceEEeeeccCC
Q psy5308 80 DATCHICLKTKFA--DGVGHMCNYCNIRC---CARCGGKVTLRSNKVSVEVTTRGHNN 132 (137)
Q Consensus 80 ~~~C~~C~ktkf~--~g~G~~C~~C~~rv---C~rCg~~v~lr~n~~~W~Ctvc~~~~ 132 (137)
...|--|+..+-. ...-..|..|-.-+ |++|+. .+..++|.-|++.+
T Consensus 9 ~~~CtSCg~~i~p~e~~v~F~CPnCGe~~I~Rc~~CRk------~g~~Y~Cp~CGF~G 60 (61)
T COG2888 9 PPVCTSCGREIAPGETAVKFPCPNCGEVEIYRCAKCRK------LGNPYRCPKCGFEG 60 (61)
T ss_pred CceeccCCCEeccCCceeEeeCCCCCceeeehhhhHHH------cCCceECCCcCccC
Confidence 4678888866522 23556677766555 444432 23457777777653
No 71
>cd00162 RING RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)
Probab=43.26 E-value=6.1 Score=22.07 Aligned_cols=42 Identities=19% Similarity=0.215 Sum_probs=22.9
Q ss_pred cccccccccccCCCCCCCccccccccccCCceeecCCCCcceEEeeec
Q psy5308 82 TCHICLKTKFADGVGHMCNYCNIRCCARCGGKVTLRSNKVSVEVTTRG 129 (137)
Q Consensus 82 ~C~~C~ktkf~~g~G~~C~~C~~rvC~rCg~~v~lr~n~~~W~Ctvc~ 129 (137)
.|.+|.... .....-..|.|.+|..|-...... ....|.+|.
T Consensus 1 ~C~iC~~~~---~~~~~~~~C~H~~c~~C~~~~~~~---~~~~Cp~C~ 42 (45)
T cd00162 1 ECPICLEEF---REPVVLLPCGHVFCRSCIDKWLKS---GKNTCPLCR 42 (45)
T ss_pred CCCcCchhh---hCceEecCCCChhcHHHHHHHHHh---CcCCCCCCC
Confidence 488888553 122223348888888885432111 135566653
No 72
>PF13864 Enkurin: Calmodulin-binding
Probab=43.14 E-value=1.1e+02 Score=21.33 Aligned_cols=32 Identities=25% Similarity=0.284 Sum_probs=24.0
Q ss_pred CCCCCCCCHHHHHHHHHHHHhhHHHHHHHHHH
Q psy5308 19 IPDLSHLTLEERQIIESVMMRQKQEEERELEI 50 (137)
Q Consensus 19 ~~dLS~LteeEr~~Il~VL~R~~~le~~E~~R 50 (137)
.+-...|+++||..+|.-|...-..=..|.++
T Consensus 31 ~~~~~~l~eeER~~lL~~Lk~~~~el~~ey~~ 62 (98)
T PF13864_consen 31 PPGMRLLSEEERQELLEGLKKNWDELNKEYQK 62 (98)
T ss_pred ccccccCCHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 35578899999999999997666655555543
No 73
>PF04829 PT-VENN: Pre-toxin domain with VENN motif; InterPro: IPR006914 This group of proteins, mainly from Neisseria meningitidis, may have haemagglutinin or haemolysin activity. A number of them have a second conserved domain, IPR006915 from INTERPRO, which is found in possible Pseudomonas aeruginosa haemagglutinins []. Filamentous haemagglutinin (FHA) is a major virulence attachment factor produced by certain bacterial species that functions as both a primary adhesin and an immunomodulator. Haemolysin is pore-forming toxin.
Probab=42.99 E-value=17 Score=23.67 Aligned_cols=16 Identities=44% Similarity=0.530 Sum_probs=13.0
Q ss_pred CCCCCCHHHHHHHHHH
Q psy5308 21 DLSHLTLEERQIIESV 36 (137)
Q Consensus 21 dLS~LteeEr~~Il~V 36 (137)
|-+.|||+|++.|..+
T Consensus 1 d~~~Lte~eK~~v~~l 16 (55)
T PF04829_consen 1 DPSELTEEEKQKVSAL 16 (55)
T ss_pred ChHhcCHHHHHHHHHH
Confidence 5578999999988764
No 74
>PF03119 DNA_ligase_ZBD: NAD-dependent DNA ligase C4 zinc finger domain; InterPro: IPR004149 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the zinc finger domain found in NAD-dependent DNA ligases. DNA ligases catalyse the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilizing either ATP or NAD(+) as a cofactor []. This domain is a small zinc binding motif that is presumably DNA binding. It is found only in NAD-dependent DNA ligases. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003911 DNA ligase (NAD+) activity, 0006260 DNA replication, 0006281 DNA repair; PDB: 1DGS_A 1V9P_B 2OWO_A.
Probab=42.67 E-value=22 Score=19.96 Aligned_cols=20 Identities=25% Similarity=0.680 Sum_probs=11.7
Q ss_pred cccCCceeecCCCCcceEEe
Q psy5308 107 CARCGGKVTLRSNKVSVEVT 126 (137)
Q Consensus 107 C~rCg~~v~lr~n~~~W~Ct 126 (137)
|-.||..+.-..+.+.|+|+
T Consensus 2 CP~C~s~l~~~~~ev~~~C~ 21 (28)
T PF03119_consen 2 CPVCGSKLVREEGEVDIRCP 21 (28)
T ss_dssp -TTT--BEEE-CCTTCEEE-
T ss_pred cCCCCCEeEcCCCCEeEECC
Confidence 67788887655667899986
No 75
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=41.97 E-value=17 Score=22.03 Aligned_cols=16 Identities=50% Similarity=0.673 Sum_probs=5.2
Q ss_pred CCCCHHHHHHHHHHHH
Q psy5308 23 SHLTLEERQIIESVMM 38 (137)
Q Consensus 23 S~LteeEr~~Il~VL~ 38 (137)
.|||++||..|...+.
T Consensus 3 ~~Lt~~eR~~I~~l~~ 18 (44)
T PF13936_consen 3 KHLTPEERNQIEALLE 18 (44)
T ss_dssp ---------HHHHHHC
T ss_pred cchhhhHHHHHHHHHH
Confidence 6899999999997654
No 76
>PF13274 DUF4065: Protein of unknown function (DUF4065)
Probab=41.32 E-value=28 Score=23.56 Aligned_cols=24 Identities=33% Similarity=0.506 Sum_probs=20.9
Q ss_pred CCCCCCCHHHHHHHHHHHHhhHHH
Q psy5308 20 PDLSHLTLEERQIIESVMMRQKQE 43 (137)
Q Consensus 20 ~dLS~LteeEr~~Il~VL~R~~~l 43 (137)
.++..|+++|+++|-.|+.+-..+
T Consensus 66 ~~~~~l~~~~~~~i~~V~~~~~~~ 89 (108)
T PF13274_consen 66 FDLEELSEEEKEIIDEVINKYGDK 89 (108)
T ss_pred cccccCCHHHHHHHHHHHHHHcCC
Confidence 688999999999999999776654
No 77
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=41.15 E-value=15 Score=22.75 Aligned_cols=35 Identities=20% Similarity=0.361 Sum_probs=25.6
Q ss_pred ccccc--cccccccc----CCCCCCCccccccccccCCcee
Q psy5308 80 DATCH--ICLKTKFA----DGVGHMCNYCNIRCCARCGGKV 114 (137)
Q Consensus 80 ~~~C~--~C~ktkf~----~g~G~~C~~C~~rvC~rCg~~v 114 (137)
-.-|. .|...... ......|..|.+.||-+|+...
T Consensus 18 ~~~CP~~~C~~~~~~~~~~~~~~v~C~~C~~~fC~~C~~~~ 58 (64)
T smart00647 18 LKWCPAPDCSAAIIVTEEEGCNRVTCPKCGFSFCFRCKVPW 58 (64)
T ss_pred ccCCCCCCCcceEEecCCCCCCeeECCCCCCeECCCCCCcC
Confidence 35688 88755433 2466789999999999998653
No 78
>KOG3088|consensus
Probab=40.96 E-value=1.1e+02 Score=26.69 Aligned_cols=19 Identities=16% Similarity=0.296 Sum_probs=9.3
Q ss_pred HHHHHHHhhHHHHHHHHHH
Q psy5308 32 IIESVMMRQKQEEERELEI 50 (137)
Q Consensus 32 ~Il~VL~R~~~le~~E~~R 50 (137)
.-.+.++|++||+.+|++.
T Consensus 65 kq~eL~~rqeEL~Rke~EL 83 (313)
T KOG3088|consen 65 KQAELLKKQEELRRKEQEL 83 (313)
T ss_pred HHHHHHHHHHHHHHHHHHH
Confidence 3344445555555555443
No 79
>PF06906 DUF1272: Protein of unknown function (DUF1272); InterPro: IPR010696 This family consists of several hypothetical bacterial proteins of around 80 residues in length. This family contains a number of conserved cysteine residues and its function is unknown.
Probab=40.92 E-value=19 Score=24.02 Aligned_cols=39 Identities=28% Similarity=0.744 Sum_probs=25.5
Q ss_pred cccccccccccccCC-----CCCCCcccc-------ccccccCCceeecCC
Q psy5308 80 DATCHICLKTKFADG-----VGHMCNYCN-------IRCCARCGGKVTLRS 118 (137)
Q Consensus 80 ~~~C~~C~ktkf~~g-----~G~~C~~C~-------~rvC~rCg~~v~lr~ 118 (137)
.+.|..|.+.+-.+. +..-|.+|. ..+|..|||.+.-|+
T Consensus 5 rpnCE~C~~dLp~~s~~A~ICSfECTFC~~C~e~~l~~~CPNCgGelv~RP 55 (57)
T PF06906_consen 5 RPNCECCDKDLPPDSPEAYICSFECTFCADCAETMLNGVCPNCGGELVRRP 55 (57)
T ss_pred CCCccccCCCCCCCCCcceEEeEeCcccHHHHHHHhcCcCcCCCCccccCC
Confidence 467999998875543 334455553 477888888865443
No 80
>PF14319 Zn_Tnp_IS91: Transposase zinc-binding domain
Probab=40.72 E-value=14 Score=26.88 Aligned_cols=28 Identities=32% Similarity=0.701 Sum_probs=21.9
Q ss_pred cccccccccccccCCCCCCCccccccccccCCce
Q psy5308 80 DATCHICLKTKFADGVGHMCNYCNIRCCARCGGK 113 (137)
Q Consensus 80 ~~~C~~C~ktkf~~g~G~~C~~C~~rvC~rCg~~ 113 (137)
.-.|.-|+...+ +...|+.|+|..||..
T Consensus 42 ~~~C~~Cg~~~~------~~~SCk~R~CP~C~~~ 69 (111)
T PF14319_consen 42 RYRCEDCGHEKI------VYNSCKNRHCPSCQAK 69 (111)
T ss_pred eeecCCCCceEE------ecCcccCcCCCCCCCh
Confidence 567888986653 4567999999999976
No 81
>PF04032 Rpr2: RNAse P Rpr2/Rpp21/SNM1 subunit domain; InterPro: IPR007175 This family contains a ribonuclease P subunit of human and yeast. Other members of the family include the probable archaeal homologues. This subunit possibly binds the precursor tRNA [].; PDB: 2K3R_A 2KI7_B 2ZAE_B 1X0T_A.
Probab=40.51 E-value=13 Score=24.83 Aligned_cols=40 Identities=23% Similarity=0.435 Sum_probs=18.4
Q ss_pred cccccccccccccCCCCCCCccccccccccCCceeecCCCCcceEEeeecc
Q psy5308 80 DATCHICLKTKFADGVGHMCNYCNIRCCARCGGKVTLRSNKVSVEVTTRGH 130 (137)
Q Consensus 80 ~~~C~~C~ktkf~~g~G~~C~~C~~rvC~rCg~~v~lr~n~~~W~Ctvc~~ 130 (137)
...|..|+ +.|+.|. .|..++-.+- ...+...|.|..|+|
T Consensus 46 r~~Ck~C~-~~liPG~-----~~~vri~~~~-----~~~~~l~~~C~~C~~ 85 (85)
T PF04032_consen 46 RTICKKCG-SLLIPGV-----NCSVRIRKKK-----KKKNFLVYTCLNCGH 85 (85)
T ss_dssp CTB-TTT---B--CTT-----TEEEEEE--------SSS-EEEEEETTTTE
T ss_pred cccccCCC-CEEeCCC-----ccEEEEEecC-----CCCCEEEEEccccCC
Confidence 57788887 5555443 2344544221 112346788888875
No 82
>PHA02078 hypothetical protein
Probab=40.48 E-value=14 Score=24.41 Aligned_cols=28 Identities=21% Similarity=0.401 Sum_probs=20.6
Q ss_pred CCCCCCHHHHHHHHHHHHhhHHHHHHHH
Q psy5308 21 DLSHLTLEERQIIESVMMRQKQEEEREL 48 (137)
Q Consensus 21 dLS~LteeEr~~Il~VL~R~~~le~~E~ 48 (137)
|+-.+-++||+|-+..|..+-+++.+++
T Consensus 26 ~ienMmP~ER~Iylsll~k~lkE~n~~q 53 (54)
T PHA02078 26 ELENMMPWEREIYAALLIQYIQEKNKKQ 53 (54)
T ss_pred HHHHHhHHHHHHHHHHHHHHHHHHHHhc
Confidence 3445678999999999987776665543
No 83
>PRK10548 flagellar biosynthesis protein FliT; Provisional
Probab=40.42 E-value=1.2e+02 Score=22.63 Aligned_cols=37 Identities=5% Similarity=0.048 Sum_probs=30.9
Q ss_pred HHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHH
Q psy5308 27 LEERQIIESVMMRQKQEEERELEIMRRKQDEVHLLEQ 63 (137)
Q Consensus 27 eeEr~~Il~VL~R~~~le~~E~~RirkL~~el~~lk~ 63 (137)
+.-+.+|-.+|..|.+.+..=+.|+.+|..-+....+
T Consensus 62 ~~~~~lL~~IL~nda~Ir~Llq~rl~eL~~li~~~~r 98 (121)
T PRK10548 62 EQLRPMLRQILDNEAELKQLLQQRMDELSSLIGQSTR 98 (121)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHH
Confidence 4557788899999999999999999998888877754
No 84
>KOG2041|consensus
Probab=40.29 E-value=34 Score=33.70 Aligned_cols=46 Identities=20% Similarity=0.429 Sum_probs=32.5
Q ss_pred ccccccccccccCCCCCCCcccccc--ccccCCceeecCCCCcceEEeeeccC
Q psy5308 81 ATCHICLKTKFADGVGHMCNYCNIR--CCARCGGKVTLRSNKVSVEVTTRGHN 131 (137)
Q Consensus 81 ~~C~~C~ktkf~~g~G~~C~~C~~r--vC~rCg~~v~lr~n~~~W~Ctvc~~~ 131 (137)
--|..|+-. ++...-.|+.|+.+ +|-.=|..++. ...|.|++|-|-
T Consensus 1118 vdc~~cg~~--i~~~~~~c~ec~~kfP~CiasG~pIt~---~~fWlC~~CkH~ 1165 (1189)
T KOG2041|consen 1118 VDCSVCGAK--IDPYDLQCSECQTKFPVCIASGRPITD---NIFWLCPRCKHR 1165 (1189)
T ss_pred eeeeecCCc--CCccCCCChhhcCcCceeeccCCcccc---ceEEEccccccc
Confidence 458888732 34577789999876 58777766542 249999998763
No 85
>PHA02942 putative transposase; Provisional
Probab=40.29 E-value=14 Score=32.27 Aligned_cols=30 Identities=20% Similarity=0.439 Sum_probs=19.0
Q ss_pred cccccccCCceeecCCCCcceEEeeeccCCC
Q psy5308 103 NIRCCARCGGKVTLRSNKVSVEVTTRGHNNN 133 (137)
Q Consensus 103 ~~rvC~rCg~~v~lr~n~~~W~Ctvc~~~~~ 133 (137)
....|+.||.... +.+...|.|.-||+.++
T Consensus 324 TSq~Cs~CG~~~~-~l~~r~f~C~~CG~~~d 353 (383)
T PHA02942 324 SSVSCPKCGHKMV-EIAHRYFHCPSCGYEND 353 (383)
T ss_pred CCccCCCCCCccC-cCCCCEEECCCCCCEeC
Confidence 3466777775542 22234799999998643
No 86
>PF04236 Transp_Tc5_C: Tc5 transposase C-terminal domain; InterPro: IPR007350 This domain corresponds to a C-terminal cysteine rich region that probably binds to a metal ion and could be DNA-binding. It is found in association with the DDE superfamily (IPR004875 from INTERPRO) and the Tc5 transposase family (IPR004906 from INTERPRO). More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=40.12 E-value=16 Score=24.51 Aligned_cols=28 Identities=32% Similarity=0.771 Sum_probs=23.1
Q ss_pred ccccccc--cccccccCCCCCCCccccccccccCC
Q psy5308 79 LDATCHI--CLKTKFADGVGHMCNYCNIRCCARCG 111 (137)
Q Consensus 79 ~~~~C~~--C~ktkf~~g~G~~C~~C~~rvC~rCg 111 (137)
....|.+ |..+-|+ .|.+|++.+|-..-
T Consensus 26 ~~~~C~~~gC~~~s~I-----~C~~Ckk~~Cf~Hf 55 (63)
T PF04236_consen 26 VAGDCDITGCNNTSFI-----RCAYCKKSLCFNHF 55 (63)
T ss_pred CcCcCCCCCCCCcCEE-----EccccCCcccccce
Confidence 3678999 9988787 79999999997764
No 87
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=39.76 E-value=12 Score=29.54 Aligned_cols=12 Identities=8% Similarity=-0.014 Sum_probs=7.6
Q ss_pred ceEEeeeccCCC
Q psy5308 122 SVEVTTRGHNNN 133 (137)
Q Consensus 122 ~W~Ctvc~~~~~ 133 (137)
.|+|.||||-.-
T Consensus 134 ~~vC~vCGy~~~ 145 (166)
T COG1592 134 VWVCPVCGYTHE 145 (166)
T ss_pred EEEcCCCCCccc
Confidence 577777766543
No 88
>KOG4010|consensus
Probab=39.45 E-value=1.5e+02 Score=24.41 Aligned_cols=30 Identities=13% Similarity=0.233 Sum_probs=19.1
Q ss_pred cccCCCCCC-----CCCCCCCCCCHHHHHHHHHHH
Q psy5308 8 VTSMAQTNA-----DIIPDLSHLTLEERQIIESVM 37 (137)
Q Consensus 8 ~~~~~~~~~-----~~~~dLS~LteeEr~~Il~VL 37 (137)
.+.|++++- +....+.-|+++|++-+-.=|
T Consensus 19 ~~~pt~~~~~~~~a~s~s~~~~LSe~Ekeelr~EL 53 (208)
T KOG4010|consen 19 LTEPTSEPVGTDVAASASEFEALSEEEKEELRTEL 53 (208)
T ss_pred ccCCCCCCCccchhhhhhHHhhhcHHHHHHHHHHH
Confidence 344666533 336677889999999554444
No 89
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=39.05 E-value=16 Score=24.44 Aligned_cols=47 Identities=17% Similarity=0.430 Sum_probs=34.6
Q ss_pred ccccccccccccc-C-CCCCCCccccc---cccccCCceeecCCCCcceEEeeeccCC
Q psy5308 80 DATCHICLKTKFA-D-GVGHMCNYCNI---RCCARCGGKVTLRSNKVSVEVTTRGHNN 132 (137)
Q Consensus 80 ~~~C~~C~ktkf~-~-g~G~~C~~C~~---rvC~rCg~~v~lr~n~~~W~Ctvc~~~~ 132 (137)
...|.-|+..+.. + +.-..|..|-. .-|.+||.. ++.++|.-|++.+
T Consensus 7 ~~~CtSCg~~i~~~~~~~~F~CPnCG~~~I~RC~~CRk~------~~~Y~CP~CGF~G 58 (59)
T PRK14890 7 PPKCTSCGIEIAPREKAVKFLCPNCGEVIIYRCEKCRKQ------SNPYTCPKCGFEG 58 (59)
T ss_pred CccccCCCCcccCCCccCEeeCCCCCCeeEeechhHHhc------CCceECCCCCCcC
Confidence 4679999988632 2 46778999964 359999755 3469999998864
No 90
>TIGR03847 conserved hypothetical protein. The conserved hypothetical protein described here occurs as part of the trio of uncharacterized proteins common in the Actinobacteria.
Probab=38.86 E-value=38 Score=27.27 Aligned_cols=26 Identities=31% Similarity=0.696 Sum_probs=19.0
Q ss_pred HHHhhhCccccccccccccccccCCCCCCCc
Q psy5308 70 EQQKKAGVELDATCHICLKTKFADGVGHMCN 100 (137)
Q Consensus 70 ~~~r~~G~~~~~~C~~C~ktkf~~g~G~~C~ 100 (137)
..+-.+| .+.|.+|+.+. |..||+|.
T Consensus 149 ~~VVaAG---RP~CPlCg~Pl--dP~GH~Cp 174 (177)
T TIGR03847 149 RRVVAAG---RPPCPLCGRPI--DPDGHICP 174 (177)
T ss_pred HHHHhCC---CCCCCCCCCCC--CCCCccCC
Confidence 3344466 78999999775 55799996
No 91
>PF01086 Clathrin_lg_ch: Clathrin light chain; InterPro: IPR000996 Proteins synthesized on the ribosome and processed in the endoplasmic reticulum are transported from the Golgi apparatus to the trans-Golgi network (TGN), and from there via small carrier vesicles to their final destination compartment. These vesicles have specific coat proteins (such as clathrin or coatomer) that are important for cargo selection and direction of transport []. Clathrin coats contain both clathrin (acts as a scaffold) and adaptor complexes that link clathrin to receptors in coated vesicles. Clathrin-associated protein complexes are believed to interact with the cytoplasmic tails of membrane proteins, leading to their selection and concentration. The two major types of clathrin adaptor complexes are the heterotetrameric adaptor protein (AP) complexes, and the monomeric GGA (Golgi-localising, Gamma-adaptin ear domain homology, ARF-binding proteins) adaptors [, ]. Clathrin is a trimer composed of three heavy chains and three light chains, each monomer projecting outwards like a leg; this three-legged structure is known as a triskelion [, ]. The heavy chains form the legs, their N-terminal beta-propeller regions extending outwards, while their C-terminal alpha-alpha-superhelical regions form the central hub of the triskelion. Peptide motifs can bind between the beta-propeller blades. The light chains appear to have a regulatory role, and may help orient the assembly and disassembly of clathrin coats as they interact with hsc70 uncoating ATPase []. Clathrin triskelia self-polymerise into a curved lattice by twisting individual legs together. The clathrin lattice forms around a vesicle as it buds from the TGN, plasma membrane or endosomes, acting to stabilise the vesicle and facilitate the budding process []. The multiple blades created when the triskelia polymerise are involved in multiple protein interactions, enabling the recruitment of different cargo adaptors and membrane attachment proteins []. This entry represents clathrin light chains, which are more divergent in sequence than the heavy chains []. In higher eukaryotes, two genes encode distinct but related light chains, each of which can yield two separate forms via alternative splicing. In yeast there is a single light chain whose sequence is only distantly related to that of higher eukaryotes. Clathrin light chains have a conserved acidic N-terminal domain, a central coiled-coil domain and a conserved C-terminal domain. More information about these proteins can be found at Protein of the Month: Clathrin [].; GO: 0005198 structural molecule activity, 0006886 intracellular protein transport, 0016192 vesicle-mediated transport, 0030130 clathrin coat of trans-Golgi network vesicle, 0030132 clathrin coat of coated pit; PDB: 3LVG_E 3LVH_D.
Probab=38.43 E-value=53 Score=26.64 Aligned_cols=41 Identities=15% Similarity=0.147 Sum_probs=33.4
Q ss_pred CCCCCHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHH
Q psy5308 22 LSHLTLEERQIIESVMMRQKQEEERELEIMRRKQDEVHLLE 62 (137)
Q Consensus 22 LS~LteeEr~~Il~VL~R~~~le~~E~~RirkL~~el~~lk 62 (137)
-..|.+|..+.-..+-.||++.+++.++.+.+.+..|+++-
T Consensus 111 ~e~ireWre~~~~~i~ekD~~e~~kk~e~~~~A~k~lddfY 151 (225)
T PF01086_consen 111 PEAIREWREERDKRIEEKDAEEEEKKEEIKEKAKKELDDFY 151 (225)
T ss_dssp TTHHHHHHHHHTTTSTHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 45667777777777778999999999999999999998773
No 92
>KOG3476|consensus
Probab=37.74 E-value=4.4 Score=29.50 Aligned_cols=34 Identities=35% Similarity=0.758 Sum_probs=25.8
Q ss_pred cccccccccccccCCCCCCCccc--cccccccCCcee
Q psy5308 80 DATCHICLKTKFADGVGHMCNYC--NIRCCARCGGKV 114 (137)
Q Consensus 80 ~~~C~~C~ktkf~~g~G~~C~~C--~~rvC~rCg~~v 114 (137)
-..|.||. .+.-..-.|.|+.| ++-+|+=||..|
T Consensus 54 ~~kC~iCk-~~vHQ~GshYC~tCAY~KgiCAMCGKki 89 (100)
T KOG3476|consen 54 LAKCRICK-QLVHQPGSHYCQTCAYKKGICAMCGKKI 89 (100)
T ss_pred cchhHHHH-HHhcCCcchhHhHhhhhhhHHHHhhhHh
Confidence 47899996 44443445899998 577999999886
No 93
>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=37.57 E-value=12 Score=22.12 Aligned_cols=27 Identities=26% Similarity=0.516 Sum_probs=13.5
Q ss_pred cccccCCceeecCCCC--cceEEeeeccCC
Q psy5308 105 RCCARCGGKVTLRSNK--VSVEVTTRGHNN 132 (137)
Q Consensus 105 rvC~rCg~~v~lr~n~--~~W~Ctvc~~~~ 132 (137)
+||.+||.-.....++ .. .|..|++..
T Consensus 2 ~FCp~C~nlL~p~~~~~~~~-~C~~C~Y~~ 30 (35)
T PF02150_consen 2 RFCPECGNLLYPKEDKEKRV-ACRTCGYEE 30 (35)
T ss_dssp -BETTTTSBEEEEEETTTTE-EESSSS-EE
T ss_pred eeCCCCCccceEcCCCccCc-CCCCCCCcc
Confidence 5777887655333222 12 477777643
No 94
>PF11304 DUF3106: Protein of unknown function (DUF3106); InterPro: IPR021455 Some members in this family of proteins are annotated as transmembrane proteins however this cannot be confirmed. Currently no function is known.
Probab=37.48 E-value=50 Score=23.88 Aligned_cols=20 Identities=20% Similarity=0.247 Sum_probs=9.0
Q ss_pred CCCCHHHHHHHHHHHHhhHH
Q psy5308 23 SHLTLEERQIIESVMMRQKQ 42 (137)
Q Consensus 23 S~LteeEr~~Il~VL~R~~~ 42 (137)
++||++||+.|..-|.+=..
T Consensus 39 ~~mspeqq~r~~~rm~~W~~ 58 (107)
T PF11304_consen 39 PSMSPEQQQRLRERMRRWAA 58 (107)
T ss_pred hcCCHHHHHHHHHHHHHHHh
Confidence 44444444444444443333
No 95
>PF10910 DUF2744: Protein of unknown function (DUF2744); InterPro: IPR021226 This entry is represented by Mycobacteriophage D29, Gp29. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=37.15 E-value=27 Score=26.63 Aligned_cols=27 Identities=26% Similarity=0.342 Sum_probs=21.3
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHHHhh
Q psy5308 14 TNADIIPDLSHLTLEERQIIESVMMRQ 40 (137)
Q Consensus 14 ~~~~~~~dLS~LteeEr~~Il~VL~R~ 40 (137)
|+....+|.+.||..|+..+++-|++.
T Consensus 91 p~p~~~~d~~~lt~~E~~a~l~ql~~~ 117 (125)
T PF10910_consen 91 PEPVRIPDVSKLTQQEQRAMLEQLREL 117 (125)
T ss_pred CCCCCCcCHHHHhHHHHHHHHHHHHHc
Confidence 333468999999999999998866554
No 96
>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=36.62 E-value=37 Score=21.22 Aligned_cols=10 Identities=20% Similarity=0.700 Sum_probs=5.2
Q ss_pred cccccccccc
Q psy5308 81 ATCHICLKTK 90 (137)
Q Consensus 81 ~~C~~C~ktk 90 (137)
..|++|++++
T Consensus 21 ~~CPlC~r~l 30 (54)
T PF04423_consen 21 GCCPLCGRPL 30 (54)
T ss_dssp EE-TTT--EE
T ss_pred CcCCCCCCCC
Confidence 3899999763
No 97
>PF14471 DUF4428: Domain of unknown function (DUF4428)
Probab=36.60 E-value=14 Score=23.64 Aligned_cols=25 Identities=32% Similarity=0.612 Sum_probs=18.1
Q ss_pred ccccccccc--cc---CCCCCCCccccccc
Q psy5308 82 TCHICLKTK--FA---DGVGHMCNYCNIRC 106 (137)
Q Consensus 82 ~C~~C~ktk--f~---~g~G~~C~~C~~rv 106 (137)
.|++|++-. |. ..-|.+|.+|-.+.
T Consensus 1 ~C~iCg~kigl~~~~k~~DG~iC~~C~~Kl 30 (51)
T PF14471_consen 1 KCAICGKKIGLFKRFKIKDGYICKDCLKKL 30 (51)
T ss_pred CCCccccccccccceeccCccchHHHHHHh
Confidence 489999653 33 34568999999887
No 98
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=36.55 E-value=19 Score=32.51 Aligned_cols=27 Identities=22% Similarity=0.617 Sum_probs=13.3
Q ss_pred ccccCCceeecCCCCcceEEeeeccCCC
Q psy5308 106 CCARCGGKVTLRSNKVSVEVTTRGHNNN 133 (137)
Q Consensus 106 vC~rCg~~v~lr~n~~~W~Ctvc~~~~~ 133 (137)
+|.+||++..+...+ -|+|+-|+...+
T Consensus 352 ~Cp~Cg~~m~S~G~~-g~rC~kCg~~~~ 378 (421)
T COG1571 352 VCPRCGGRMKSAGRN-GFRCKKCGTRAR 378 (421)
T ss_pred CCCccCCchhhcCCC-CcccccccccCC
Confidence 555666555222222 466666655443
No 99
>PF00643 zf-B_box: B-box zinc finger; InterPro: IPR000315 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents B-box-type zinc finger domains, which are around 40 residues in length. B-box zinc fingers can be divided into two groups, where types 1 and 2 B-box domains differ in their consensus sequence and in the spacing of the 7-8 zinc-binding residues. Several proteins contain both types 1 and 2 B-boxes, suggesting some level of cooperativity between these two domains. B-box domains are found in over 1500 proteins from a variety of organisms. They are found in TRIM (tripartite motif) proteins that consist of an N-terminal RING finger (originally called an A-box), followed by 1-2 B-box domains and a coiled-coil domain (also called RBCC for Ring, B-box, Coiled-Coil). TRIM proteins contain a type 2 B-box domain, and may also contain a type 1 B-box. In proteins that do not contain RING or coiled-coil domains, the B-box domain is primarily type 2. Many type 2 B-box proteins are involved in ubiquitinylation. Proteins containing a B-box zinc finger domain include transcription factors, ribonucleoproteins and proto-oncoproteins; for example, MID1, MID2, TRIM9, TNL, TRIM36, TRIM63, TRIFIC, NCL1 and CONSTANS-like proteins []. The microtubule-associated E3 ligase MID1 (6.3.2 from EC) contains a type 1 B-box zinc finger domain. MID1 specifically binds Alpha-4, which in turn recruits the catalytic subunit of phosphatase 2A (PP2Ac). This complex is required for targeting of PP2Ac for proteasome-mediated degradation. The MID1 B-box coordinates two zinc ions and adopts a beta/beta/alpha cross-brace structure similar to that of ZZ, PHD, RING and FYVE zinc fingers [, ]. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 3DDT_B 2D8U_A 3Q1D_A 2EGM_A 2YVR_B 2DJA_A 2DQ5_A 2JUN_A 2YRG_A 2DID_A ....
Probab=36.44 E-value=8.3 Score=22.58 Aligned_cols=30 Identities=20% Similarity=0.562 Sum_probs=21.2
Q ss_pred cccccccccccccCCCCCCCccccccccccCCce
Q psy5308 80 DATCHICLKTKFADGVGHMCNYCNIRCCARCGGK 113 (137)
Q Consensus 80 ~~~C~~C~ktkf~~g~G~~C~~C~~rvC~rCg~~ 113 (137)
...|..+.+.... ..|..|+..+|..|...
T Consensus 3 ~~~C~~H~~~~~~----~~C~~C~~~~C~~C~~~ 32 (42)
T PF00643_consen 3 EPKCPEHPEEPLS----LFCEDCNEPLCSECTVS 32 (42)
T ss_dssp SSB-SSTTTSBEE----EEETTTTEEEEHHHHHT
T ss_pred CccCccCCccceE----EEecCCCCccCccCCCC
Confidence 4678888765322 27999999999999644
No 100
>PF14311 DUF4379: Domain of unknown function (DUF4379)
Probab=36.39 E-value=15 Score=23.12 Aligned_cols=13 Identities=23% Similarity=0.192 Sum_probs=10.1
Q ss_pred cceEEeeeccCCC
Q psy5308 121 VSVEVTTRGHNNN 133 (137)
Q Consensus 121 ~~W~Ctvc~~~~~ 133 (137)
+-|+|..|+|...
T Consensus 27 v~W~C~~Cgh~w~ 39 (55)
T PF14311_consen 27 VWWKCPKCGHEWK 39 (55)
T ss_pred EEEECCCCCCeeE
Confidence 6799999888654
No 101
>PF01780 Ribosomal_L37ae: Ribosomal L37ae protein family; InterPro: IPR002674 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This ribosomal protein is found in archaebacteria and eukaryotes []. Ribosomal protein L37 has a single zinc finger-like motif of the C2-C2 type [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 4A1E_Y 4A17_Y 4A1C_Y 4A1A_Y 3O58_g 3IZS_m 3O5H_g 1S1I_9 3IZR_m 1YSH_D ....
Probab=36.33 E-value=13 Score=26.79 Aligned_cols=11 Identities=45% Similarity=0.761 Sum_probs=8.0
Q ss_pred ccccccccccc
Q psy5308 80 DATCHICLKTK 90 (137)
Q Consensus 80 ~~~C~~C~ktk 90 (137)
..+|..|.++.
T Consensus 35 ky~Cp~Cgk~~ 45 (90)
T PF01780_consen 35 KYTCPFCGKTS 45 (90)
T ss_dssp -BEESSSSSSE
T ss_pred CCcCCCCCCce
Confidence 46799998875
No 102
>PF10335 DUF294_C: Putative nucleotidyltransferase substrate binding domain; InterPro: IPR018821 This entry is found associated with presumed nucleotidyltransferase domains and seems to be distantly related to other helical substrate binding domains.
Probab=35.47 E-value=51 Score=24.54 Aligned_cols=29 Identities=21% Similarity=0.179 Sum_probs=23.3
Q ss_pred CCCCCCCCCCHHHHHHHHHHHHhhHHHHH
Q psy5308 17 DIIPDLSHLTLEERQIIESVMMRQKQEEE 45 (137)
Q Consensus 17 ~~~~dLS~LteeEr~~Il~VL~R~~~le~ 45 (137)
...+|++.|+..||+.+-..+..-+.+++
T Consensus 111 ~n~i~~~~Ls~~er~~Lk~al~~i~~lq~ 139 (145)
T PF10335_consen 111 DNYIDPDELSKLERRRLKEALRVIKRLQR 139 (145)
T ss_pred CCccCHHHCCHHHHHHHHHHHHHHHHHHH
Confidence 46899999999999999998866555444
No 103
>TIGR00447 pth peptidyl-tRNA hydrolase. The natural substrate for this enzyme may be peptidyl-tRNAs that drop off the ribosome during protein synthesis. Peptidyl-tRNA hydrolase is a bacterial protein; YHR189W from Saccharomyces cerevisiae appears to be orthologous and likely has the same function.
Probab=35.28 E-value=60 Score=25.82 Aligned_cols=26 Identities=19% Similarity=0.195 Sum_probs=20.5
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHHhhH
Q psy5308 15 NADIIPDLSHLTLEERQIIESVMMRQK 41 (137)
Q Consensus 15 ~~~~~~dLS~LteeEr~~Il~VL~R~~ 41 (137)
+.++.+ ||.++++|++.|..++.+..
T Consensus 142 ~v~~yV-L~~f~~~e~~~l~~~i~~~~ 167 (188)
T TIGR00447 142 KVVEFV-LSKFTKSELPLLEKALDKAV 167 (188)
T ss_pred chhhhc-cCCCCHHHHHHHHHHHHHHH
Confidence 344555 99999999999999886644
No 104
>KOG2114|consensus
Probab=34.42 E-value=68 Score=31.69 Aligned_cols=88 Identities=15% Similarity=0.175 Sum_probs=56.5
Q ss_pred CCCCCCCCCHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHhhhCcccccccccccccc-cc---C
Q psy5308 18 IIPDLSHLTLEERQIIESVMMRQKQEEERELEIMRRKQDEVHLLEQSIRQRSEQQKKAGVELDATCHICLKTK-FA---D 93 (137)
Q Consensus 18 ~~~dLS~LteeEr~~Il~VL~R~~~le~~E~~RirkL~~el~~lk~~~~~~~~~~r~~G~~~~~~C~~C~ktk-f~---~ 93 (137)
..+.||++ +..|+.+|+.+...=+..+.+|+.-++++.++++.+..-+-.++-.+ ...|-.|.-++ .. +
T Consensus 785 ~~ltls~I----kD~ii~~l~~~~~~I~qd~~~Ie~yk~~i~e~r~~l~~lr~sa~i~q---~skCs~C~~~LdlP~VhF 857 (933)
T KOG2114|consen 785 GTLTLSVI----KDYIIKWLNKYSTIIEQDEDAIEVYKKDIEEKRQELETLRTSAQIFQ---VSKCSACEGTLDLPFVHF 857 (933)
T ss_pred CceEEehh----HHHHHHHHHhhhHHHHhhHHHHHHHHHHHHHHHHHHHHhhcccceee---eeeecccCCccccceeee
Confidence 34566766 56899999888777777778899999999998887754333222233 46799998775 32 2
Q ss_pred CCCCC----CccccccccccCCc
Q psy5308 94 GVGHM----CNYCNIRCCARCGG 112 (137)
Q Consensus 94 g~G~~----C~~C~~rvC~rCg~ 112 (137)
-+||. |-.=+...|.+|..
T Consensus 858 ~CgHsyHqhC~e~~~~~CP~C~~ 880 (933)
T KOG2114|consen 858 LCGHSYHQHCLEDKEDKCPKCLP 880 (933)
T ss_pred ecccHHHHHhhccCcccCCccch
Confidence 35543 22222256666653
No 105
>PF01428 zf-AN1: AN1-like Zinc finger; InterPro: IPR000058 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the AN1-type zinc finger domain, which has a dimetal (zinc)-bound alpha/beta fold. This domain was first identified as a zinc finger at the C terminus of AN1 Q91889 from SWISSPROT, a ubiquitin-like protein in Xenopus laevis []. The AN1-type zinc finger contains six conserved cysteines and two histidines that could potentially coordinate 2 zinc atoms. Certain stress-associated proteins (SAP) contain AN1 domain, often in combination with A20 zinc finger domains (SAP8) or C2H2 domains (SAP16) []. For example, the human protein Znf216 has an A20 zinc-finger at the N terminus and an AN1 zinc-finger at the C terminus, acting to negatively regulate the NFkappaB activation pathway and to interact with components of the immune response like RIP, IKKgamma and TRAF6. The interact of Znf216 with IKK-gamma and RIP is mediated by the A20 zinc-finger domain, while its interaction with TRAF6 is mediated by the AN1 zinc-finger domain; therefore, both zinc-finger domains are involved in regulating the immune response []. The AN1 zinc finger domain is also found in proteins containing a ubiquitin-like domain, which are involved in the ubiquitination pathway []. Proteins containing an AN1-type zinc finger include: Ascidian posterior end mark 6 (pem-6) protein []. Human AWP1 protein (associated with PRK1), which is expressed during early embryogenesis []. Human immunoglobulin mu binding protein 2 (SMUBP-2), mutations in which cause muscular atrophy with respiratory distress type 1 []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 1WFP_A 1WYS_A 1WG2_A 1WFH_A 1X4W_A 1WFE_A 1WFL_A 1X4V_A.
Probab=33.33 E-value=12 Score=22.67 Aligned_cols=23 Identities=26% Similarity=0.703 Sum_probs=13.5
Q ss_pred cccccccCCCCCCCccccccccccCC
Q psy5308 86 CLKTKFADGVGHMCNYCNIRCCARCG 111 (137)
Q Consensus 86 C~ktkf~~g~G~~C~~C~~rvC~rCg 111 (137)
|.+..| .+..|.+|...||.+=+
T Consensus 6 C~~~~~---~~~~C~~C~~~FC~~Hr 28 (43)
T PF01428_consen 6 CKKKDF---LPFKCKHCGKSFCLKHR 28 (43)
T ss_dssp T--BCT---SHEE-TTTS-EE-TTTH
T ss_pred CcCccC---CCeECCCCCcccCcccc
Confidence 664444 46689999999999875
No 106
>PHA02565 49 recombination endonuclease VII; Provisional
Probab=32.85 E-value=55 Score=25.85 Aligned_cols=10 Identities=20% Similarity=0.767 Sum_probs=7.8
Q ss_pred cccccccccc
Q psy5308 81 ATCHICLKTK 90 (137)
Q Consensus 81 ~~C~~C~ktk 90 (137)
-.|+||++.+
T Consensus 21 G~CaiC~~~l 30 (157)
T PHA02565 21 GICPLCKREL 30 (157)
T ss_pred CcCCCCCCcc
Confidence 5699999764
No 107
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=32.80 E-value=28 Score=35.59 Aligned_cols=47 Identities=21% Similarity=0.527 Sum_probs=29.7
Q ss_pred cccccccccccccCCCCCCCccccccc-----cccCCceeecCCCCcceEEeeeccC
Q psy5308 80 DATCHICLKTKFADGVGHMCNYCNIRC-----CARCGGKVTLRSNKVSVEVTTRGHN 131 (137)
Q Consensus 80 ~~~C~~C~ktkf~~g~G~~C~~C~~rv-----C~rCg~~v~lr~n~~~W~Ctvc~~~ 131 (137)
.+.|..|+...+. ..|..|-.+. |..||..+....++ .=.|.-|+..
T Consensus 667 ~rkCPkCG~~t~~----~fCP~CGs~te~vy~CPsCGaev~~des~-a~~CP~CGtp 718 (1337)
T PRK14714 667 RRRCPSCGTETYE----NRCPDCGTHTEPVYVCPDCGAEVPPDESG-RVECPRCDVE 718 (1337)
T ss_pred EEECCCCCCcccc----ccCcccCCcCCCceeCccCCCccCCCccc-cccCCCCCCc
Confidence 4889999965443 2788887664 88888776433333 2346666544
No 108
>PRK09458 pspB phage shock protein B; Provisional
Probab=32.78 E-value=80 Score=22.07 Aligned_cols=22 Identities=18% Similarity=0.267 Sum_probs=17.0
Q ss_pred CCCCHHHHHHHHHHHHhhHHHH
Q psy5308 23 SHLTLEERQIIESVMMRQKQEE 44 (137)
Q Consensus 23 S~LteeEr~~Il~VL~R~~~le 44 (137)
+.||++|++.+.+...+.+.++
T Consensus 34 ~~Ls~~d~~~L~~L~~~A~rm~ 55 (75)
T PRK09458 34 QGLSQEEQQRLAQLTEKAERMR 55 (75)
T ss_pred CCCCHHHHHHHHHHHHHHHHHH
Confidence 4689999999888877666554
No 109
>PF07227 DUF1423: Protein of unknown function (DUF1423); InterPro: IPR004082 A total of 715 potential protein-coding genes have been identified in the nucleotide sequence of Arabidopsis thaliana chromosome 5, with an average gene density of 1 gene per 4001 bp []. Amongst the gene products is a well-conserved family of 130.7kDa proteins that share no sequence similarity with any other known proteins, other than in plants. The sequences are characterised by an N-terminal domain of variable length, a central cysteine-rich region and a relatively acidic C-terminal domain. The sequences may possess a PHD finger.
Probab=32.62 E-value=30 Score=31.46 Aligned_cols=31 Identities=23% Similarity=0.336 Sum_probs=17.5
Q ss_pred CCCccccccccccCCceeecCCCCcceE-EeeeccC
Q psy5308 97 HMCNYCNIRCCARCGGKVTLRSNKVSVE-VTTRGHN 131 (137)
Q Consensus 97 ~~C~~C~~rvC~rCg~~v~lr~n~~~W~-Ctvc~~~ 131 (137)
..|..|.=-+|.+ + -...|+..|+ |-+|+|-
T Consensus 124 gFC~~C~C~iC~k---f-D~~~n~~~Wi~Cd~CgH~ 155 (446)
T PF07227_consen 124 GFCRRCMCCICSK---F-DDNKNTCSWIGCDVCGHW 155 (446)
T ss_pred CccccCCccccCC---c-ccCCCCeeEEeccCCCce
Confidence 4555665444432 2 2344567786 8888773
No 110
>TIGR00280 L37a ribosomal protein L37a. This model finds eukaryotic ribosomal protein L37a and its archaeal orthologs. The nomeclature is tricky because eukaryotes have proteins called both L37 and L37a.
Probab=32.59 E-value=19 Score=26.04 Aligned_cols=11 Identities=27% Similarity=0.613 Sum_probs=8.0
Q ss_pred ccccccccccc
Q psy5308 80 DATCHICLKTK 90 (137)
Q Consensus 80 ~~~C~~C~ktk 90 (137)
..+|..|.++.
T Consensus 35 ~y~CpfCgk~~ 45 (91)
T TIGR00280 35 KYVCPFCGKKT 45 (91)
T ss_pred CccCCCCCCCc
Confidence 46788887764
No 111
>TIGR03045 PS_II_C550 cytochrome c-550. Members of this protein family are cytochrome c-550, the PsbV extrinsic protein of photosystem II, from both Cyanobacteria and chloroplasts. A paralog to this protein, PsbV2, is found in some species in addition to PsbV itself.
Probab=32.55 E-value=50 Score=25.84 Aligned_cols=26 Identities=31% Similarity=0.537 Sum_probs=21.6
Q ss_pred CCCCCCCCCCHHHHHHHHHHHHhhHH
Q psy5308 17 DIIPDLSHLTLEERQIIESVMMRQKQ 42 (137)
Q Consensus 17 ~~~~dLS~LteeEr~~Il~VL~R~~~ 42 (137)
..||.+.+||++|.+.|..-|-.+..
T Consensus 124 ~~mP~~~~LsdeEL~avAaYIl~q~~ 149 (159)
T TIGR03045 124 DIFPKMRNLTDEDLRLIAGHILVQPK 149 (159)
T ss_pred cccCCcCCCCHHHHHHHHHHHHHhcc
Confidence 45888899999999999998866543
No 112
>PF04120 Iron_permease: Low affinity iron permease ; InterPro: IPR007251 Although originally identified as a low-affinity iron(II) permease [, ], Fet4 has since been shown to import several other transition metal ions, including copper [, ] and zinc []. Copper, cobalt, and cadmium inhibit Fet4 [, ]. Fet4 is an integral protein of the plasma membrane [, ]. FET4 is not essential, not even in fet3 fet4 double mutants []. Over expression of FET4 improves growth under alkaline conditions []. Transcription of FET4 is induced by Aft1 in response to low levels of iron [, , ] or by Zap1 in response to low zinc [, ], but not in response to low copper []. When the high-affinity iron permease component Fet3 is deleted, FET4 is induced by the addition of copper, zinc, cobalt, or manganese []. It is also induced under anaerobic conditions [, , ] and repressed by Rox1 in aerobic conditions [, ]. Rox1 attenuates the activation of FET4 by Aft1 or Zap1 []. ; GO: 0055085 transmembrane transport
Probab=32.37 E-value=63 Score=24.59 Aligned_cols=21 Identities=29% Similarity=0.284 Sum_probs=15.7
Q ss_pred CCCCCCCCCCHHHHHHHHHHH
Q psy5308 17 DIIPDLSHLTLEERQIIESVM 37 (137)
Q Consensus 17 ~~~~dLS~LteeEr~~Il~VL 37 (137)
.+++|+.+|+|+|.+.|..-+
T Consensus 87 n~li~iE~l~~~el~~~~~~~ 107 (132)
T PF04120_consen 87 NELIDIEDLTEEELEEIRKRY 107 (132)
T ss_pred HHhCCcccCCHHHHHHHHHHH
Confidence 357888888888887776644
No 113
>COG5582 Uncharacterized conserved protein [Function unknown]
Probab=32.23 E-value=72 Score=25.75 Aligned_cols=35 Identities=14% Similarity=0.121 Sum_probs=24.0
Q ss_pred HHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHH
Q psy5308 27 LEERQIIESVMMRQKQEEERELEIMRRKQDEVHLLEQ 63 (137)
Q Consensus 27 eeEr~~Il~VL~R~~~le~~E~~RirkL~~el~~lk~ 63 (137)
.-|++.+|.=+ |+.|...+.+|...|.+.|++|++
T Consensus 145 ~f~~~~LL~~I--DeALd~~Dk~~F~~L~q~Lq~L~~ 179 (182)
T COG5582 145 AFERKKLLQQI--DEALDMRDKERFYQLVQILQQLDL 179 (182)
T ss_pred HHHHHHHHHHH--HHHHhhhhHHHHHHHHHHHHHHHh
Confidence 33555555533 667777777888888888888864
No 114
>cd00462 PTH Peptidyl-tRNA hydrolase (PTH) is a monomeric protein that cleaves the ester bond linking the nascent peptide and tRNA when peptidyl-tRNA is released prematurely from the ribosome. This ensures the recycling of peptidyl-tRNAs into tRNAs produced through abortion of translation and is essential for cell viability.This group also contains chloroplast RNA splicing 2 (CRS2), which is closely related nuclear-encoded protein required for the splicing of nine group II introns in chloroplasts.
Probab=32.22 E-value=70 Score=25.07 Aligned_cols=26 Identities=23% Similarity=0.364 Sum_probs=20.5
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHHhhHH
Q psy5308 16 ADIIPDLSHLTLEERQIIESVMMRQKQ 42 (137)
Q Consensus 16 ~~~~~dLS~LteeEr~~Il~VL~R~~~ 42 (137)
..+.+ ||.++++|++.|..++.+..+
T Consensus 140 v~~yV-L~~f~~~E~~~l~~~~~~~~~ 165 (171)
T cd00462 140 VADYV-LSKFSKEERELLEEAIEKAAD 165 (171)
T ss_pred hhhhh-cCCCCHHHHHHHHHHHHHHHH
Confidence 34555 899999999999998866543
No 115
>PF10217 DUF2039: Uncharacterized conserved protein (DUF2039); InterPro: IPR019351 This entry is a region of approximately 100 residues containing three pairs of cysteine residues. The region is conserved from plants to humans but its function is unknown.
Probab=32.15 E-value=11 Score=27.32 Aligned_cols=33 Identities=24% Similarity=0.815 Sum_probs=22.9
Q ss_pred cccccccccccccCCCCCCCcccc--ccccccCCc
Q psy5308 80 DATCHICLKTKFADGVGHMCNYCN--IRCCARCGG 112 (137)
Q Consensus 80 ~~~C~~C~ktkf~~g~G~~C~~C~--~rvC~rCg~ 112 (137)
+..|..|++-..-+.--++|..|. +.+|++|+.
T Consensus 55 p~kC~~C~qktVk~AYh~iC~~Ca~~~~vCaKC~k 89 (92)
T PF10217_consen 55 PKKCNKCQQKTVKHAYHVICDPCAKELKVCAKCGK 89 (92)
T ss_pred CccccccccchHHHHHHHHHHHHHHhhccCcccCC
Confidence 678999993322223455888884 689999974
No 116
>PF09098 Dehyd-heme_bind: Quinohemoprotein amine dehydrogenase A, alpha subunit, haem binding; InterPro: IPR015182 Quinohemoprotein amine dehydrogenases (QHNDH) 1.4.99 from EC) are enzymes produced in the periplasmic space of certain Gram-negative bacteria, such as Paracoccus denitrificans and Pseudomonas putida, in response to primary amines, including n-butylamine and benzylamine. QHNDH catalyses the oxidative deamination of a wide range of aliphatic and aromatic amines through formation of a Schiff-base intermediate involving one of the quinone O atoms []. Catalysis requires the presence of a novel redox cofactor, cysteine tryptophylquinone (CTQ). CTQ is derived from the post-translational modification of specific residues, which involves the oxidation of the indole ring of a tryptophan residue to form tryptophylquinone, followed by covalent cross-linking with a cysteine residue []. There is one CTQ per subunit in QHNDH. In addition to CTQ, two haem c cofactors are present in QHNDH that mediate the transfer of the substrate-derived electrons from CTQ to an external electron acceptor, cytochrome c-550 [, ]. QHNDH is a heterotrimer of alpha, beta and gamma subunits. The alpha and beta subunits contain signal peptides necessary for the translocation of QHNDH to the periplasm. The alpha subunit is composed of four domains - domain 1 forming a dihaem cytochrome, and domains 2-4 forming antiparallel beta-barrel structures; the beta subunit is a 7-bladed beta-propeller that provides part of the active site; and the small, catalytic gamma subunit contains the novel cross-linked CTQ cofactor, in addition to additional thioester cross-links between Cys and Asp/Glu residues that encage CTQ. The gamma subunit assumes a globular secondary structure with two short alpha-helices having many turns and bends []. This entry represents the dihaem cytochrome c domain of the QHNDH alpha subunit. The domain contain two cysteine residues that are involved in thioether linkages to haem []. ; PDB: 1PBY_A 1JJU_A 1JMZ_A 1JMX_A.
Probab=31.70 E-value=2.6 Score=33.51 Aligned_cols=55 Identities=15% Similarity=0.191 Sum_probs=24.9
Q ss_pred CCCHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHhhhCc-ccccccccccc
Q psy5308 24 HLTLEERQIIESVMMRQKQEEERELEIMRRKQDEVHLLEQSIRQRSEQQKKAGV-ELDATCHICLK 88 (137)
Q Consensus 24 ~LteeEr~~Il~VL~R~~~le~~E~~RirkL~~el~~lk~~~~~~~~~~r~~G~-~~~~~C~~C~k 88 (137)
.||++||..|..-|....=|.-.|.+.++.+-+.-.+...++ +. ....+|++||-
T Consensus 50 ~Is~eer~avVkYLAd~~GLap~Et~~~ry~~er~~~~~e~~----------~~e~~~~~C~rCHs 105 (167)
T PF09098_consen 50 PISPEERRAVVKYLADTQGLAPSETAPVRYALERRPNTVEQF----------PNEEITQMCARCHS 105 (167)
T ss_dssp ---HHHHHHHHHHHHHHT---CGGCTT-CCCCCT-TT---------------SCHHHHHHHSSSS-
T ss_pred CCCHHHHHHHHHHHHHccCCCchhhcchhhhhhcCcchhhcc----------cchHHHHHHHHhhh
Confidence 477888888888777666665555554444332222221111 11 12467999994
No 117
>KOG0955|consensus
Probab=31.34 E-value=30 Score=34.60 Aligned_cols=57 Identities=25% Similarity=0.341 Sum_probs=42.2
Q ss_pred hCcccccccccccccc-ccCCCCCCCccccccccccCCceeecCCCCcceEEeeeccCCC
Q psy5308 75 AGVELDATCHICLKTK-FADGVGHMCNYCNIRCCARCGGKVTLRSNKVSVEVTTRGHNNN 133 (137)
Q Consensus 75 ~G~~~~~~C~~C~ktk-f~~g~G~~C~~C~~rvC~rCg~~v~lr~n~~~W~Ctvc~~~~~ 133 (137)
++.+.+..|.+|.++- +-.+.-..|.+|+.-|=..|=|.-... ...|.|.-|...-.
T Consensus 214 ~~~~~D~~C~iC~~~~~~n~n~ivfCD~Cnl~VHq~Cygi~~ip--eg~WlCr~Cl~s~~ 271 (1051)
T KOG0955|consen 214 ALLEEDAVCCICLDGECQNSNVIVFCDGCNLAVHQECYGIPFIP--EGQWLCRRCLQSPQ 271 (1051)
T ss_pred cccCCCccceeecccccCCCceEEEcCCCcchhhhhccCCCCCC--CCcEeehhhccCcC
Confidence 3444579999999774 544677899999999999997743333 34899999876544
No 118
>PF07051 OCIA: Ovarian carcinoma immunoreactive antigen (OCIA); InterPro: IPR009764 This family consists of several ovarian carcinoma immunoreactive antigen (OCIA) and related eukaryotic sequences. The function of this family is unknown [,].
Probab=31.20 E-value=92 Score=23.24 Aligned_cols=20 Identities=25% Similarity=0.177 Sum_probs=15.5
Q ss_pred CCCCCCCCCCHHHHHHHHHH
Q psy5308 17 DIIPDLSHLTLEERQIIESV 36 (137)
Q Consensus 17 ~~~~dLS~LteeEr~~Il~V 36 (137)
+...+-=.|||||++++.+=
T Consensus 18 ~~~~~~~~~T~EE~kvlrEC 37 (111)
T PF07051_consen 18 PHPGMPYQLTEEERKVLREC 37 (111)
T ss_pred CCCCcCccCCHHHHHHHHHH
Confidence 45666778999999988763
No 119
>TIGR02890 spore_yteA sporulation protein, yteA family. Members of this predicted regulatory protein are found only in endospore-forming members of the Firmicutes group of bacteria, and in nearly every such species; Clostridium perfringens seems to be an exception. The member from Bacillus subtilis, the model system for the study of the sporulation program, has been designated both yteA and yzwB. Some (but not all) members of this family show a strong sequence match to PFAM family pfam01258 the C4-type zinc finger protein, DksA/TraR family, but only one of the four key Cys residues is conserved. All members of this protein family share an additional C-terminal domain. The function of proteins in this family is unknown. YteA was detected in mature spores of Bacillus subtilis by Kuwana, et al., and appears to be expressed under control of sigma-K.
Probab=31.10 E-value=1.1e+02 Score=23.72 Aligned_cols=29 Identities=28% Similarity=0.463 Sum_probs=20.6
Q ss_pred hCcccccccccccccc-----ccCCCCCCCcccccc
Q psy5308 75 AGVELDATCHICLKTK-----FADGVGHMCNYCNIR 105 (137)
Q Consensus 75 ~G~~~~~~C~~C~ktk-----f~~g~G~~C~~C~~r 105 (137)
.|.| -.|..|+... -+......|..|+.+
T Consensus 83 ~G~Y--G~Ce~CGe~I~~~RL~a~P~a~~Ci~Cq~~ 116 (159)
T TIGR02890 83 NGTY--GICEVCGKPIPYERLEAIPTATTCVECQNR 116 (159)
T ss_pred CCCC--CeecccCCcccHHHHhhCCCcchhHHHHHH
Confidence 3554 4799999773 345678889999763
No 120
>KOG1814|consensus
Probab=30.93 E-value=1.1e+02 Score=27.99 Aligned_cols=35 Identities=20% Similarity=0.478 Sum_probs=26.2
Q ss_pred ccccccccccc-ccCC-CCCCCccccccccccCCcee
Q psy5308 80 DATCHICLKTK-FADG-VGHMCNYCNIRCCARCGGKV 114 (137)
Q Consensus 80 ~~~C~~C~ktk-f~~g-~G~~C~~C~~rvC~rCg~~v 114 (137)
...|.-|.... ..+| .-..|..|-+.+|-.|++-+
T Consensus 368 ~krCP~C~v~IEr~eGCnKM~C~~c~~~fc~~c~~~l 404 (445)
T KOG1814|consen 368 SKRCPKCKVVIERSEGCNKMHCTKCGTYFCWICAELL 404 (445)
T ss_pred CCCCCcccceeecCCCccceeeccccccceeehhhhc
Confidence 47799998664 6666 45678888888888887554
No 121
>COG0732 HsdS Restriction endonuclease S subunits [Defense mechanisms]
Probab=30.71 E-value=1.8e+02 Score=23.28 Aligned_cols=40 Identities=18% Similarity=0.140 Sum_probs=29.8
Q ss_pred CHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy5308 26 TLEERQIIESVMMRQKQEEERELEIMRRKQDEVHLLEQSI 65 (137)
Q Consensus 26 teeEr~~Il~VL~R~~~le~~E~~RirkL~~el~~lk~~~ 65 (137)
+-+|++.|..+|....++-+..++.+..|+...+.+.+.+
T Consensus 141 pl~eQ~~I~~iL~~~d~~i~~~~~~i~~l~~~~~~~~~~~ 180 (391)
T COG0732 141 PLEEQQAIAKILSTLDDLIELLEKLIELLEAIKQKLFKEL 180 (391)
T ss_pred ChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3689999999998888887777777777766666555443
No 122
>PF11686 DUF3283: Protein of unknown function (DUF3283); InterPro: IPR021700 This family of proteins with unknown function appears to be restricted to Proteobacteria.
Probab=30.62 E-value=39 Score=22.84 Aligned_cols=14 Identities=50% Similarity=0.581 Sum_probs=12.5
Q ss_pred CCCCCCHHHHHHHH
Q psy5308 21 DLSHLTLEERQIIE 34 (137)
Q Consensus 21 dLS~LteeEr~~Il 34 (137)
|||.|+++|++.|.
T Consensus 1 NLslLp~~EKnkIE 14 (61)
T PF11686_consen 1 NLSLLPPEEKNKIE 14 (61)
T ss_pred CcccCCHHHHhHHH
Confidence 69999999999885
No 123
>PRK04136 rpl40e 50S ribosomal protein L40e; Provisional
Probab=30.50 E-value=31 Score=22.28 Aligned_cols=11 Identities=36% Similarity=1.026 Sum_probs=5.0
Q ss_pred cccccccCCce
Q psy5308 103 NIRCCARCGGK 113 (137)
Q Consensus 103 ~~rvC~rCg~~ 113 (137)
...||-+|+.+
T Consensus 13 ~k~ICrkC~AR 23 (48)
T PRK04136 13 NKKICMRCNAR 23 (48)
T ss_pred cccchhcccCC
Confidence 34445555433
No 124
>PF12875 DUF3826: Protein of unknown function (DUF3826); InterPro: IPR024284 This is a putative sugar-binding family.; PDB: 3KDW_A 3G6I_A.
Probab=30.49 E-value=79 Score=25.70 Aligned_cols=44 Identities=16% Similarity=0.142 Sum_probs=24.4
Q ss_pred CCCCHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy5308 23 SHLTLEERQIIESVMMRQKQEEERELEIMRRKQDEVHLLEQSIRQ 67 (137)
Q Consensus 23 S~LteeEr~~Il~VL~R~~~le~~E~~RirkL~~el~~lk~~~~~ 67 (137)
..||++|+..|+.-|.-+++ ..++.+=..+.+.=|...+-+|.+
T Consensus 123 P~Lteeek~~I~~~L~eARE-~A~D~~~~~~kha~F~kYKgrinn 166 (188)
T PF12875_consen 123 PSLTEEEKAQILTWLKEARE-FAMDAKSSKKKHAWFGKYKGRINN 166 (188)
T ss_dssp TT--HHHHHHHHHHHHHHHH-HHTTSSSHHHHHHHHHHHHHHHHH
T ss_pred CcccHHHHHHHHHHHHHHHH-HhccccchHHHHHHHHHHHHHHHH
Confidence 46899999999998854433 233333344445555555544433
No 125
>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=30.37 E-value=23 Score=19.75 Aligned_cols=22 Identities=23% Similarity=0.481 Sum_probs=10.7
Q ss_pred ccccCCceeecCCCCcceEEeeeccC
Q psy5308 106 CCARCGGKVTLRSNKVSVEVTTRGHN 131 (137)
Q Consensus 106 vC~rCg~~v~lr~n~~~W~Ctvc~~~ 131 (137)
.|..|+..|.+. .=.|..|||.
T Consensus 2 ~CP~C~~~V~~~----~~~Cp~CG~~ 23 (26)
T PF10571_consen 2 TCPECGAEVPES----AKFCPHCGYD 23 (26)
T ss_pred cCCCCcCCchhh----cCcCCCCCCC
Confidence 455565554322 2345555553
No 126
>KOG1842|consensus
Probab=30.19 E-value=12 Score=34.24 Aligned_cols=37 Identities=19% Similarity=0.406 Sum_probs=32.0
Q ss_pred ccccccccccccccCCCCCCCccccccccccCCceee
Q psy5308 79 LDATCHICLKTKFADGVGHMCNYCNIRCCARCGGKVT 115 (137)
Q Consensus 79 ~~~~C~~C~ktkf~~g~G~~C~~C~~rvC~rCg~~v~ 115 (137)
+...|..|.+.+.+..+-|.|.-|-.-+|..|-..++
T Consensus 179 ~V~~CP~Ca~~F~l~rRrHHCRLCG~VmC~~C~k~iS 215 (505)
T KOG1842|consen 179 SVQFCPECANSFGLTRRRHHCRLCGRVMCRDCSKFIS 215 (505)
T ss_pred cccccccccchhhhHHHhhhhhhcchHHHHHHHHhcC
Confidence 4689999997766667999999999999999987765
No 127
>PRK03636 hypothetical protein; Provisional
Probab=29.76 E-value=91 Score=24.84 Aligned_cols=16 Identities=13% Similarity=0.289 Sum_probs=10.7
Q ss_pred CCCCHHHHHHHHHHHH
Q psy5308 23 SHLTLEERQIIESVMM 38 (137)
Q Consensus 23 S~LteeEr~~Il~VL~ 38 (137)
.++.++....+..||.
T Consensus 124 ~~~~~~~~~~ae~~L~ 139 (179)
T PRK03636 124 EEVNEKDRLLAEQFLE 139 (179)
T ss_pred hhhhhhhHHHHHHHHH
Confidence 4566777777777764
No 128
>cd07177 terB_like tellurium resistance terB-like protein. This family consists of tellurium resistance terB proteins, N-terminal domain of heat shock DnaJ-like proteins, N-terminal domain of Mo-dependent nitrogenase-like proteins, C-terminal domain of ABC transporter ATP-binding proteins, C-terminal domain of serine/threonine protein kinase, and many hypothetical bacterial proteins. The function of this family is unknown.
Probab=29.60 E-value=1.2e+02 Score=19.91 Aligned_cols=24 Identities=21% Similarity=0.232 Sum_probs=18.2
Q ss_pred CCCCHHHHHHHHHHHHhhHHHHHH
Q psy5308 23 SHLTLEERQIIESVMMRQKQEEER 46 (137)
Q Consensus 23 S~LteeEr~~Il~VL~R~~~le~~ 46 (137)
..++++|++.|...+.+...+...
T Consensus 14 G~i~~~E~~~i~~~~~~~~~~~~~ 37 (104)
T cd07177 14 GRVDEEEIAAIEALLRRLPLLDAE 37 (104)
T ss_pred CCCCHHHHHHHHHHHHHHhCCCHH
Confidence 468899999999999887643333
No 129
>PRK05426 peptidyl-tRNA hydrolase; Provisional
Probab=29.52 E-value=88 Score=24.86 Aligned_cols=25 Identities=12% Similarity=0.239 Sum_probs=19.5
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHHhhH
Q psy5308 16 ADIIPDLSHLTLEERQIIESVMMRQK 41 (137)
Q Consensus 16 ~~~~~dLS~LteeEr~~Il~VL~R~~ 41 (137)
.++.+ ||.++++|++.|-.++.+..
T Consensus 143 v~~yV-L~~f~~~E~~~l~~~~~~a~ 167 (189)
T PRK05426 143 VVDYV-LGKFSKEEQELLDKAIDKAA 167 (189)
T ss_pred cchhh-cCCCCHHHHHHHHHHHHHHH
Confidence 34555 89999999999998886543
No 130
>PF07191 zinc-ribbons_6: zinc-ribbons; InterPro: IPR010807 This family consists of several short, hypothetical bacterial proteins of around 70 residues in length. Members of this family 8 highly conserved cysteine residues. The function of the family is unknown.; PDB: 2JRP_A 2JNE_A.
Probab=29.39 E-value=14 Score=25.54 Aligned_cols=33 Identities=27% Similarity=0.593 Sum_probs=16.0
Q ss_pred ccccccccccccCCCCCCCcccccc-----ccccCCce
Q psy5308 81 ATCHICLKTKFADGVGHMCNYCNIR-----CCARCGGK 113 (137)
Q Consensus 81 ~~C~~C~ktkf~~g~G~~C~~C~~r-----vC~rCg~~ 113 (137)
.+|..|+..+-+.+....|..|... +|..|+-.
T Consensus 2 ~~CP~C~~~L~~~~~~~~C~~C~~~~~~~a~CPdC~~~ 39 (70)
T PF07191_consen 2 NTCPKCQQELEWQGGHYHCEACQKDYKKEAFCPDCGQP 39 (70)
T ss_dssp -B-SSS-SBEEEETTEEEETTT--EEEEEEE-TTT-SB
T ss_pred CcCCCCCCccEEeCCEEECccccccceecccCCCcccH
Confidence 4677777666555555666666544 36666544
No 131
>PF13376 OmdA: Bacteriocin-protection, YdeI or OmpD-Associated
Probab=29.17 E-value=66 Score=20.72 Aligned_cols=37 Identities=19% Similarity=0.095 Sum_probs=24.7
Q ss_pred CCCCCCHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHH
Q psy5308 21 DLSHLTLEERQIIESVMMRQKQEEERELEIMRRKQDEVHLL 61 (137)
Q Consensus 21 dLS~LteeEr~~Il~VL~R~~~le~~E~~RirkL~~el~~l 61 (137)
.+..||+..|..|+.-+.-.+. ++.|.+|+..-++.|
T Consensus 23 ~f~~l~~~~rr~~i~wi~~AK~----~etR~kRi~~~i~~l 59 (63)
T PF13376_consen 23 FFESLTPSYRREYIRWINSAKT----EETRAKRIAKLIEML 59 (63)
T ss_pred HHHHCCHHHHHHHHHHHHHcCC----HHHHHHHHHHHHHHH
Confidence 3578999999999988875543 455555555544444
No 132
>TIGR00570 cdk7 CDK-activating kinase assembly factor MAT1. All proteins in this family for which functions are known are cyclin dependent protein kinases that are components of TFIIH, a complex that is involved in nucleotide excision repair and transcription initiation. Also known as MAT1 (menage a trois 1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=29.14 E-value=16 Score=31.60 Aligned_cols=48 Identities=23% Similarity=0.404 Sum_probs=27.6
Q ss_pred cccccccccccccCCCC-CCCccccccccccCCceeecCCCCcceEEeeecc
Q psy5308 80 DATCHICLKTKFADGVG-HMCNYCNIRCCARCGGKVTLRSNKVSVEVTTRGH 130 (137)
Q Consensus 80 ~~~C~~C~ktkf~~g~G-~~C~~C~~rvC~rCg~~v~lr~n~~~W~Ctvc~~ 130 (137)
+..|.+|..+......- ..=..|-|++|..|=-.+.... . =.|.+|..
T Consensus 3 ~~~CP~Ck~~~y~np~~kl~i~~CGH~~C~sCv~~l~~~~-~--~~CP~C~~ 51 (309)
T TIGR00570 3 DQGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVRG-S--GSCPECDT 51 (309)
T ss_pred CCCCCcCCCCCccCcccccccCCCCCcccHHHHHHHhcCC-C--CCCCCCCC
Confidence 35799998765332211 1111688899999965543221 1 26888754
No 133
>PF06698 DUF1192: Protein of unknown function (DUF1192); InterPro: IPR009579 This family consists of several short, hypothetical, bacterial proteins of around 60 residues in length. The function of this family is unknown.
Probab=28.96 E-value=1.5e+02 Score=19.73 Aligned_cols=18 Identities=33% Similarity=0.244 Sum_probs=12.5
Q ss_pred CCCCCCCCHHHHHHHHHH
Q psy5308 19 IPDLSHLTLEERQIIESV 36 (137)
Q Consensus 19 ~~dLS~LteeEr~~Il~V 36 (137)
--|||.|+.+|-+-=+..
T Consensus 15 g~dLs~lSv~EL~~RIa~ 32 (59)
T PF06698_consen 15 GEDLSLLSVEELEERIAL 32 (59)
T ss_pred CCCchhcCHHHHHHHHHH
Confidence 358999999886544333
No 134
>PRK10778 dksA RNA polymerase-binding transcription factor; Provisional
Probab=28.87 E-value=1.4e+02 Score=22.89 Aligned_cols=26 Identities=19% Similarity=0.298 Sum_probs=18.2
Q ss_pred ccccccccccc-----ccCCCCCCCcccccc
Q psy5308 80 DATCHICLKTK-----FADGVGHMCNYCNIR 105 (137)
Q Consensus 80 ~~~C~~C~ktk-----f~~g~G~~C~~C~~r 105 (137)
--.|..|+..- -+......|..|+.+
T Consensus 111 YG~Ce~CGe~I~~~RL~A~P~A~~CI~CQe~ 141 (151)
T PRK10778 111 FGYCESCGVEIGIRRLEARPTADLCIDCKTL 141 (151)
T ss_pred CceeccCCCcccHHHHhcCCCccccHHHHHH
Confidence 36799999772 334567788888753
No 135
>PF10960 DUF2762: Protein of unknown function (DUF2762); InterPro: IPR024405 BhlA is a SP-beta prophage-derived protein found in Bacillus subtilis [, ] and other Bacilli. A related protein, UviB, has also been described in Clostridia, where it is believed to be involved in bacteriocin secretion or immunity [, ].
Probab=28.64 E-value=1.9e+02 Score=19.67 Aligned_cols=33 Identities=21% Similarity=0.345 Sum_probs=25.1
Q ss_pred HHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy5308 33 IESVMMRQKQEEERELEIMRRKQDEVHLLEQSI 65 (137)
Q Consensus 33 Il~VL~R~~~le~~E~~RirkL~~el~~lk~~~ 65 (137)
+.-||...++++++.++|-.++++.++++-..+
T Consensus 23 l~yvlK~~~~re~~~~~RE~kyq~~I~~lte~~ 55 (71)
T PF10960_consen 23 LFYVLKENKKREEKQEEREEKYQEQIEKLTEKL 55 (71)
T ss_pred HHHHHHHhHHhHHHHHHHHHHHHHHHHHHHHHH
Confidence 456778888888888888888888887775543
No 136
>PF07820 TraC: TraC-like protein; InterPro: IPR012930 The members of this family are sequences that are similar to TraC (Q84HT8 from SWISSPROT) from Rhizobium etli. The gene encoding this protein is one of a group of genes found on plasmid p42a of Rhizobium etli (strain CFN 42/ATCC 51251) that are thought to be involved in the process of plasmid self-transmission. Mobilisation of plasmid p42a is of importance as it is required for transfer of plasmid p42d, the symbiotic plasmid which carries most of the genes required for nodulation and nitrogen fixation by this symbiotic bacterium. The predicted protein products of p42a are similar to known transfer proteins of Agrobacterium tumefaciens plasmid pTiC58 []. ; GO: 0000746 conjugation
Probab=28.62 E-value=2.2e+02 Score=20.67 Aligned_cols=26 Identities=35% Similarity=0.382 Sum_probs=19.9
Q ss_pred HHHHHHHHHhhHHHHHHHHHHHHHHH
Q psy5308 30 RQIIESVMMRQKQEEERELEIMRRKQ 55 (137)
Q Consensus 30 r~~Il~VL~R~~~le~~E~~RirkL~ 55 (137)
++-|.....+=++++.++.+||+++-
T Consensus 8 ~~eIekLqe~lk~~e~keaERigr~A 33 (92)
T PF07820_consen 8 REEIEKLQEQLKQAETKEAERIGRIA 33 (92)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 44566666678888999999999763
No 137
>smart00109 C1 Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains). Some bind phorbol esters and diacylglycerol. Some bind RasGTP. Zinc-binding domains.
Probab=28.47 E-value=39 Score=19.57 Aligned_cols=34 Identities=26% Similarity=0.858 Sum_probs=21.8
Q ss_pred cccccccccccccCCCCCCCccccccccccCCce
Q psy5308 80 DATCHICLKTKFADGVGHMCNYCNIRCCARCGGK 113 (137)
Q Consensus 80 ~~~C~~C~ktkf~~g~G~~C~~C~~rvC~rCg~~ 113 (137)
...|..|++.......|..|.+|+..+=.+|-..
T Consensus 11 ~~~C~~C~~~i~~~~~~~~C~~C~~~~H~~C~~~ 44 (49)
T smart00109 11 PTKCCVCRKSIWGSFQGLRCSWCKVKCHKKCAEK 44 (49)
T ss_pred CCCccccccccCcCCCCcCCCCCCchHHHHHHhh
Confidence 4669999977522114788888876655555433
No 138
>PF10955 DUF2757: Protein of unknown function (DUF2757); InterPro: IPR020115 This entry contains proteins with no known function.
Probab=28.40 E-value=30 Score=24.20 Aligned_cols=19 Identities=42% Similarity=0.298 Sum_probs=15.5
Q ss_pred CCCCCCCCCHHHHHHHHHH
Q psy5308 18 IIPDLSHLTLEERQIIESV 36 (137)
Q Consensus 18 ~~~dLS~LteeEr~~Il~V 36 (137)
+.+=|.+||++||+-|+.+
T Consensus 25 ~~LGf~~Lt~eEr~dmI~~ 43 (76)
T PF10955_consen 25 EQLGFHHLTPEERQDMISY 43 (76)
T ss_pred hhcCcccCCHHHHhhheEE
Confidence 4566899999999988764
No 139
>KOG1451|consensus
Probab=28.35 E-value=1.4e+02 Score=28.78 Aligned_cols=63 Identities=21% Similarity=0.088 Sum_probs=40.9
Q ss_pred CCCCHHHHHHHHHHHHhhHHHHHHHHHHHHHH-------HHHHHHHHH-HHHHhHHHHhhhCccccccccc
Q psy5308 23 SHLTLEERQIIESVMMRQKQEEERELEIMRRK-------QDEVHLLEQ-SIRQRSEQQKKAGVELDATCHI 85 (137)
Q Consensus 23 S~LteeEr~~Il~VL~R~~~le~~E~~RirkL-------~~el~~lk~-~~~~~~~~~r~~G~~~~~~C~~ 85 (137)
..+|+.|+-|-...-+=..-+.+.|++|++-. ...|++.++ +|--.++.+++.-.++++-|.+
T Consensus 74 d~~tdde~~ia~slkefa~ll~~ve~er~~~v~~Ase~li~PlekFRkEqIG~~KE~KkKydKe~ekfy~~ 144 (812)
T KOG1451|consen 74 DAETDDEIFIATSLKEFASLLNQVEDERMRMVGNASESLIEPLEKFRKEQIGTLKEEKKKYDKESEKFYQT 144 (812)
T ss_pred ccccchHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHhHHHHHHHHHhhhhHHHHhhhhhhhHHHHHH
Confidence 35799999988777777888899999998743 344555543 4433455555555444555543
No 140
>PF11672 DUF3268: Protein of unknown function (DUF3268); InterPro: IPR021686 This entry is represented by Listeria phage P100, Gp150. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=28.25 E-value=36 Score=24.87 Aligned_cols=7 Identities=14% Similarity=-0.221 Sum_probs=4.3
Q ss_pred ceEEeee
Q psy5308 122 SVEVTTR 128 (137)
Q Consensus 122 ~W~Ctvc 128 (137)
.|+|+-|
T Consensus 31 ~y~C~~C 37 (102)
T PF11672_consen 31 LYVCTPC 37 (102)
T ss_pred eEECCCC
Confidence 3777763
No 141
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=28.14 E-value=27 Score=25.12 Aligned_cols=12 Identities=25% Similarity=0.479 Sum_probs=8.6
Q ss_pred cccccccccccc
Q psy5308 80 DATCHICLKTKF 91 (137)
Q Consensus 80 ~~~C~~C~ktkf 91 (137)
..+|.-|.++.+
T Consensus 36 ~y~CpfCgk~~v 47 (90)
T PTZ00255 36 KYFCPFCGKHAV 47 (90)
T ss_pred CccCCCCCCCce
Confidence 467888887653
No 142
>PRK03057 hypothetical protein; Provisional
Probab=27.93 E-value=66 Score=25.67 Aligned_cols=23 Identities=17% Similarity=0.423 Sum_probs=16.4
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHH
Q psy5308 40 QKQEEERELEIMRRKQDEVHLLE 62 (137)
Q Consensus 40 ~~~le~~E~~RirkL~~el~~lk 62 (137)
|..|+..++++..+|-++|..|+
T Consensus 154 D~ALd~~D~e~F~~Lt~~L~~l~ 176 (180)
T PRK03057 154 DQALDRKDMEEFQRLTEKLKKLE 176 (180)
T ss_pred HHHHHCCCHHHHHHHHHHHHHHH
Confidence 56666666677777777777774
No 143
>KOG0954|consensus
Probab=27.90 E-value=70 Score=31.29 Aligned_cols=50 Identities=20% Similarity=0.373 Sum_probs=31.2
Q ss_pred ccccccccccccc-CCCCCCCccccccccccCCceeecCCCCcceEEeeeccC
Q psy5308 80 DATCHICLKTKFA-DGVGHMCNYCNIRCCARCGGKVTLRSNKVSVEVTTRGHN 131 (137)
Q Consensus 80 ~~~C~~C~ktkf~-~g~G~~C~~C~~rvC~rCg~~v~lr~n~~~W~Ctvc~~~ 131 (137)
+-.|-.|+-+--- .+-..+|..|+.-|=..|-|-.-+. .+ .|+|..|++.
T Consensus 271 dviCDvCrspD~e~~neMVfCd~Cn~cVHqaCyGIle~p-~g-pWlCr~Calg 321 (893)
T KOG0954|consen 271 DVICDVCRSPDSEEANEMVFCDKCNICVHQACYGILEVP-EG-PWLCRTCALG 321 (893)
T ss_pred cceeceecCCCccccceeEEeccchhHHHHhhhceeecC-CC-Ceeehhcccc
Confidence 5789999844211 1344556666655555665544433 35 7999999875
No 144
>PF06667 PspB: Phage shock protein B; InterPro: IPR009554 This family consists of several bacterial phage shock protein B (PspB) sequences. The phage shock protein (psp) operon is induced in response to heat, ethanol, osmotic shock and infection by filamentous bacteriophages []. Expression of the operon requires the alternative sigma factor sigma54 and the transcriptional activator PspF. In addition, PspA plays a negative regulatory role, and the integral-membrane proteins PspB and PspC play a positive one [].; GO: 0006355 regulation of transcription, DNA-dependent, 0009271 phage shock
Probab=27.76 E-value=1.1e+02 Score=21.18 Aligned_cols=22 Identities=18% Similarity=0.280 Sum_probs=16.1
Q ss_pred CCCCHHHHHHHHHHHHhhHHHH
Q psy5308 23 SHLTLEERQIIESVMMRQKQEE 44 (137)
Q Consensus 23 S~LteeEr~~Il~VL~R~~~le 44 (137)
+.||++|++.+.+...+.+.++
T Consensus 34 ~gLs~~d~~~L~~L~~~a~rm~ 55 (75)
T PF06667_consen 34 QGLSEEDEQRLQELYEQAERME 55 (75)
T ss_pred CCCCHHHHHHHHHHHHHHHHHH
Confidence 5688999888888776655543
No 145
>TIGR02420 dksA RNA polymerase-binding protein DksA. The model that is the basis for this family describes a small, pleiotropic protein, DksA (DnaK suppressor A), originally named as a multicopy suppressor of temperature sensitivity of dnaKJ mutants. DksA mutants are defective in quorum sensing, virulence, etc. DksA is now understood to bind RNA polymerase directly and modulate its response to small molecules to control the level of transcription of rRNA. Nearly all members of this family are in the Proteobacteria. Whether the closest homologs outside the Proteobacteria function equivalently is unknown. The low value set for the noise cutoff allows identification of possible DksA proteins from outside the proteobacteria. TIGR02419 describes a closely related family of short sequences usually found in prophage regions of proteobacterial genomes or in known phage.
Probab=27.63 E-value=2.3e+02 Score=20.18 Aligned_cols=28 Identities=21% Similarity=0.392 Sum_probs=19.8
Q ss_pred hCcccccccccccccc-----ccCCCCCCCccccc
Q psy5308 75 AGVELDATCHICLKTK-----FADGVGHMCNYCNI 104 (137)
Q Consensus 75 ~G~~~~~~C~~C~ktk-----f~~g~G~~C~~C~~ 104 (137)
.|.| -.|.-|++.- .+......|..|+.
T Consensus 77 ~g~y--G~C~~Cge~I~~~RL~a~P~a~~Cv~Cq~ 109 (110)
T TIGR02420 77 DGEY--GYCEECGEEIGLRRLEARPTATLCIDCKT 109 (110)
T ss_pred CCCC--CchhccCCcccHHHHhhCCCccccHHhHc
Confidence 3544 5899999872 34567778988875
No 146
>PF13923 zf-C3HC4_2: Zinc finger, C3HC4 type (RING finger); PDB: 3HCU_A 2ECI_A 2JMD_A 3HCS_B 3HCT_A 3ZTG_A 2YUR_A 3L11_A.
Probab=27.40 E-value=10 Score=22.05 Aligned_cols=28 Identities=32% Similarity=0.682 Sum_probs=18.3
Q ss_pred ccccccccccCCCCCCCccccccccccCCce
Q psy5308 83 CHICLKTKFADGVGHMCNYCNIRCCARCGGK 113 (137)
Q Consensus 83 C~~C~ktkf~~g~G~~C~~C~~rvC~rCg~~ 113 (137)
|.||.+.. .+ ..+-..|.|.+|..|-..
T Consensus 1 C~iC~~~~-~~--~~~~~~CGH~fC~~C~~~ 28 (39)
T PF13923_consen 1 CPICLDEL-RD--PVVVTPCGHSFCKECIEK 28 (39)
T ss_dssp ETTTTSB--SS--EEEECTTSEEEEHHHHHH
T ss_pred CCCCCCcc-cC--cCEECCCCCchhHHHHHH
Confidence 77887542 22 335667888899999544
No 147
>PRK09737 EcoKI restriction-modification system protein HsdS; Provisional
Probab=27.32 E-value=2.1e+02 Score=24.20 Aligned_cols=40 Identities=23% Similarity=0.120 Sum_probs=21.6
Q ss_pred CHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy5308 26 TLEERQIIESVMMRQKQEEERELEIMRRKQDEVHLLEQSI 65 (137)
Q Consensus 26 teeEr~~Il~VL~R~~~le~~E~~RirkL~~el~~lk~~~ 65 (137)
.-+||+.|-.+|..-....+.-++.+.+..+.|+++++.+
T Consensus 371 pl~EQ~kI~~~l~~l~~~~d~i~~~~~~~l~~L~~lKqsl 410 (461)
T PRK09737 371 PLEEQAEIVRRVEQLFAYADTIEKQVNNALARVNNLTQSI 410 (461)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3588999988884422221222222334445566676655
No 148
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=27.15 E-value=29 Score=25.17 Aligned_cols=11 Identities=36% Similarity=0.757 Sum_probs=8.7
Q ss_pred ccccccCCcee
Q psy5308 104 IRCCARCGGKV 114 (137)
Q Consensus 104 ~rvC~rCg~~v 114 (137)
|.+|..||.+.
T Consensus 42 h~~C~~CG~y~ 52 (99)
T PRK14892 42 IITCGNCGLYT 52 (99)
T ss_pred eEECCCCCCcc
Confidence 68899998764
No 149
>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=27.13 E-value=20 Score=21.35 Aligned_cols=6 Identities=50% Similarity=1.747 Sum_probs=2.7
Q ss_pred ccccCC
Q psy5308 106 CCARCG 111 (137)
Q Consensus 106 vC~rCg 111 (137)
+|..||
T Consensus 3 ~C~~Cg 8 (36)
T PF05191_consen 3 ICPKCG 8 (36)
T ss_dssp EETTTT
T ss_pred CcCCCC
Confidence 444444
No 150
>PLN02492 ribonucleoside-diphosphate reductase
Probab=27.12 E-value=1.2e+02 Score=25.60 Aligned_cols=34 Identities=26% Similarity=0.270 Sum_probs=26.0
Q ss_pred CCCCCCCCCHHHHHHHHHHHHhhHHHHHHHHHHH
Q psy5308 18 IIPDLSHLTLEERQIIESVMMRQKQEEERELEIM 51 (137)
Q Consensus 18 ~~~dLS~LteeEr~~Il~VL~R~~~le~~E~~Ri 51 (137)
+..|...||+.||..|..||.-...++..-...+
T Consensus 43 D~~dw~~Lt~~Er~~~~~il~~~~~~D~~v~~~~ 76 (324)
T PLN02492 43 DLKDWEKLTDDERHFISHVLAFFAASDGIVLENL 76 (324)
T ss_pred hHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3444557999999999999998888777655444
No 151
>KOG2874|consensus
Probab=26.94 E-value=1.1e+02 Score=26.75 Aligned_cols=46 Identities=22% Similarity=0.258 Sum_probs=25.5
Q ss_pred ccCCCCCCCCCCCCC------CCCHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHH
Q psy5308 9 TSMAQTNADIIPDLS------HLTLEERQIIESVMMRQKQEEERELEIMRRKQDEVHLL 61 (137)
Q Consensus 9 ~~~~~~~~~~~~dLS------~LteeEr~~Il~VL~R~~~le~~E~~RirkL~~el~~l 61 (137)
||++|++.+..+|+. ||.+++++. .+..+++|.+++++...+-+.+
T Consensus 265 tpfPp~q~~sKiD~eleSGEYFl~~~~k~~-------kK~~e~~Ekq~e~~~er~~~r~ 316 (356)
T KOG2874|consen 265 TPFPPAQPPSKIDKELESGEYFLRDEEKSR-------KKMQEKKEKQAEKRKERQEERM 316 (356)
T ss_pred CCCCCCcCcchhhhhhhcchhhhhhhHHHH-------HHHHHHHHHHHHHHHHHHHHHh
Confidence 555555555666663 677777653 3444555656655554444444
No 152
>PF00416 Ribosomal_S13: Ribosomal protein S13/S18; InterPro: IPR001892 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 S13 is one of the proteins from the small ribosomal subunit. In Escherichia coli, S13 is known to be involved in binding fMet-tRNA and, hence, in the initiation of translation. It is a basic protein of 115 to 177 amino-acid residues that contains thee helices and a beta-hairpin in the core of the protein, forming a helix-two turns-helix (H2TH) motif, and a non-globular C-terminal extension. This family of ribosomal proteins is present in prokaryotes, eukaryotes and archaea [, ].; GO: 0003723 RNA binding, 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3BBN_M 2QBB_M 3I1M_M 3OFP_M 3OFX_M 3OFO_M 1VS5_M 3OAQ_M 2QAL_M 3J18_M ....
Probab=26.83 E-value=2.4e+02 Score=20.09 Aligned_cols=22 Identities=9% Similarity=0.152 Sum_probs=18.6
Q ss_pred CCCCCCCCCHHHHHHHHHHHHh
Q psy5308 18 IIPDLSHLTLEERQIIESVMMR 39 (137)
Q Consensus 18 ~~~dLS~LteeEr~~Il~VL~R 39 (137)
+..-+..||++|-+.|..+|..
T Consensus 39 ~~~~~~~Ls~~~i~~l~~~i~~ 60 (107)
T PF00416_consen 39 PNKKVGDLSDEQIDKLRKIIEK 60 (107)
T ss_dssp SSSBTTTSTHHHHHHHHHHHHT
T ss_pred hhhhcccCCHHHHHHHHHHHHH
Confidence 3455889999999999999877
No 153
>COG1107 Archaea-specific RecJ-like exonuclease, contains DnaJ-type Zn finger domain [DNA replication, recombination, and repair]
Probab=26.46 E-value=49 Score=31.60 Aligned_cols=46 Identities=26% Similarity=0.602 Sum_probs=32.0
Q ss_pred cccccccccccccC-------------------CCCCCCccccc-------cccccCCceeecCCCCcceEEeeeccC
Q psy5308 80 DATCHICLKTKFAD-------------------GVGHMCNYCNI-------RCCARCGGKVTLRSNKVSVEVTTRGHN 131 (137)
Q Consensus 80 ~~~C~~C~ktkf~~-------------------g~G~~C~~C~~-------rvC~rCg~~v~lr~n~~~W~Ctvc~~~ 131 (137)
...|.+|+-|.|.+ ..+.+|..|+- ..|..||+.. .+-.|.+|+..
T Consensus 18 ~e~c~vc~gtG~~~~~d~k~~~~~~~~~~D~~~~~~~pc~~c~gkG~V~v~~~c~~c~G~g------kv~~c~~cG~~ 89 (715)
T COG1107 18 EEECPVCHGTGFSDDFDPKGVANLSRETVDLFASFEIPCPKCRGKGTVTVYDTCPECGGTG------KVLTCDICGDI 89 (715)
T ss_pred eeecccccccccccccChhhhhhhhhccccccccCCCCCCeeccceeEEEEeecccCCCce------eEEeeccccce
Confidence 46688888654431 23678999974 5799998772 36788888754
No 154
>TIGR03831 YgiT_finger YgiT-type zinc finger domain. This domain model describes a small domain with two copies of a putative zinc-binding motif CXXC (usually CXXCG). Most member proteins consist largely of this domain or else carry an additional C-terminal helix-turn-helix domain, resembling that of the phage protein Cro and modeled by pfam01381.
Probab=26.45 E-value=33 Score=20.00 Aligned_cols=14 Identities=14% Similarity=0.138 Sum_probs=10.0
Q ss_pred CCcceEEeeeccCC
Q psy5308 119 NKVSVEVTTRGHNN 132 (137)
Q Consensus 119 n~~~W~Ctvc~~~~ 132 (137)
|-+.|+|..|++..
T Consensus 29 ~vp~~~C~~CGE~~ 42 (46)
T TIGR03831 29 NVPALVCPQCGEEY 42 (46)
T ss_pred CCCccccccCCCEe
Confidence 44788888888653
No 155
>PF04216 FdhE: Protein involved in formate dehydrogenase formation; InterPro: IPR006452 This family of sequences describe an accessory protein required for the assembly of formate dehydrogenase of certain proteobacteria although not present in the final complex []. The exact nature of the function of FdhE in the assembly of the complex is unknown, but considering the presence of selenocysteine, molybdopterin, iron-sulphur clusters and cytochrome b556, it is likely to be involved in the insertion of cofactors. ; GO: 0005737 cytoplasm; PDB: 2FIY_B.
Probab=26.36 E-value=31 Score=28.56 Aligned_cols=48 Identities=15% Similarity=0.335 Sum_probs=20.8
Q ss_pred ccccccccccc---ccCCCCCCCccccccccccCCceeecCCCCcceEEeeeccCCC
Q psy5308 80 DATCHICLKTK---FADGVGHMCNYCNIRCCARCGGKVTLRSNKVSVEVTTRGHNNN 133 (137)
Q Consensus 80 ~~~C~~C~ktk---f~~g~G~~C~~C~~rvC~rCg~~v~lr~n~~~W~Ctvc~~~~~ 133 (137)
...|.+|+-.- .+.+.+. .+=++.+|+.|+...... -..|..|++.+.
T Consensus 172 ~g~CPvCGs~P~~s~l~~~~~--~G~R~L~Cs~C~t~W~~~----R~~Cp~Cg~~~~ 222 (290)
T PF04216_consen 172 RGYCPVCGSPPVLSVLRGGER--EGKRYLHCSLCGTEWRFV----RIKCPYCGNTDH 222 (290)
T ss_dssp -SS-TTT---EEEEEEE--------EEEEEETTT--EEE------TTS-TTT---SS
T ss_pred CCcCCCCCCcCceEEEecCCC--CccEEEEcCCCCCeeeec----CCCCcCCCCCCC
Confidence 47999999552 3333332 455888999999776322 246999888765
No 156
>cd07313 terB_like_2 tellurium resistance terB-like protein, subgroup 2. This family includes several uncharacterized bacterial proteins. Protein sequence homology analysis shows they are similar to tellurium resistance protein terB, but the function of this family is unknown.
Probab=26.26 E-value=1.5e+02 Score=20.02 Aligned_cols=28 Identities=18% Similarity=0.203 Sum_probs=19.3
Q ss_pred CCCCHHHHHHHHHHHHhhHHHHHHHHHH
Q psy5308 23 SHLTLEERQIIESVMMRQKQEEERELEI 50 (137)
Q Consensus 23 S~LteeEr~~Il~VL~R~~~le~~E~~R 50 (137)
..+++.|++.|..+|.+.-.+...+..+
T Consensus 14 G~v~~~E~~~i~~~l~~~~~l~~~~~~~ 41 (104)
T cd07313 14 GEYDEEERAAIDRLLAERFGLDAEEAAE 41 (104)
T ss_pred CCCCHHHHHHHHHHHHHHhCcCHHHHHH
Confidence 3578999999999987764444444333
No 157
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=26.08 E-value=27 Score=25.11 Aligned_cols=12 Identities=25% Similarity=0.733 Sum_probs=8.6
Q ss_pred cccccccccccc
Q psy5308 80 DATCHICLKTKF 91 (137)
Q Consensus 80 ~~~C~~C~ktkf 91 (137)
..+|..|.++.+
T Consensus 36 ~y~CpfCgk~~v 47 (90)
T PRK03976 36 KHVCPVCGRPKV 47 (90)
T ss_pred CccCCCCCCCce
Confidence 467999977753
No 158
>smart00290 ZnF_UBP Ubiquitin Carboxyl-terminal Hydrolase-like zinc finger.
Probab=26.05 E-value=40 Score=20.25 Aligned_cols=21 Identities=24% Similarity=0.365 Sum_probs=14.1
Q ss_pred cccCCceeecCCCCcceEEeeeccCCC
Q psy5308 107 CARCGGKVTLRSNKVSVEVTTRGHNNN 133 (137)
Q Consensus 107 C~rCg~~v~lr~n~~~W~Ctvc~~~~~ 133 (137)
|..|+.. +. .|+|-.|++..-
T Consensus 2 C~~C~~~-----~~-l~~CL~C~~~~c 22 (50)
T smart00290 2 CSVCGTI-----EN-LWLCLTCGQVGC 22 (50)
T ss_pred cccCCCc-----CC-eEEecCCCCccc
Confidence 6777632 23 899999886543
No 159
>PF00097 zf-C3HC4: Zinc finger, C3HC4 type (RING finger); InterPro: IPR018957 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 C3HC4 type zinc-finger (RING finger) is a cysteine-rich domain of 40 to 60 residues that coordinates two zinc ions, and has the consensus sequence: C-X2-C-X(9-39)-C-X(1-3)-H-X(2-3)-C-X2-C-X(4-48)-C-X2-C where X is any amino acid []. Many proteins containing a RING finger play a key role in the ubiquitination pathway []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1CHC_A 2ECW_A 2Y43_B 1V87_A 2DJB_A 2H0D_B 3RPG_C 3KNV_A 2CKL_B 1JM7_A ....
Probab=25.99 E-value=12 Score=21.57 Aligned_cols=28 Identities=36% Similarity=0.689 Sum_probs=16.9
Q ss_pred ccccccccccCCCCCCCccccccccccCCce
Q psy5308 83 CHICLKTKFADGVGHMCNYCNIRCCARCGGK 113 (137)
Q Consensus 83 C~~C~ktkf~~g~G~~C~~C~~rvC~rCg~~ 113 (137)
|.+|.... .+.. .=..|.|.||..|=..
T Consensus 1 C~iC~~~~-~~~~--~~~~C~H~fC~~C~~~ 28 (41)
T PF00097_consen 1 CPICLEPF-EDPV--ILLPCGHSFCRDCLRK 28 (41)
T ss_dssp ETTTSSBC-SSEE--EETTTSEEEEHHHHHH
T ss_pred CCcCCccc-cCCC--EEecCCCcchHHHHHH
Confidence 67777542 2111 3457888899988433
No 160
>COG3416 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=25.97 E-value=2.5e+02 Score=23.47 Aligned_cols=18 Identities=39% Similarity=0.659 Sum_probs=13.6
Q ss_pred CCHHHHHHHHHHHHhhHH
Q psy5308 25 LTLEERQIIESVMMRQKQ 42 (137)
Q Consensus 25 LteeEr~~Il~VL~R~~~ 42 (137)
+|++|.+.|...+.|=+.
T Consensus 1 MtpeE~qlle~lf~rlk~ 18 (233)
T COG3416 1 MTPEEKQLLENLFHRLKK 18 (233)
T ss_pred CCHHHHHHHHHHHHHHhh
Confidence 478888888888876443
No 161
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=25.92 E-value=36 Score=27.58 Aligned_cols=16 Identities=25% Similarity=0.399 Sum_probs=7.9
Q ss_pred ccccccccccccCCCC
Q psy5308 81 ATCHICLKTKFADGVG 96 (137)
Q Consensus 81 ~~C~~C~ktkf~~g~G 96 (137)
+.|.+|+..++-++.-
T Consensus 150 A~CsrC~~~L~~~~~~ 165 (188)
T COG1096 150 ARCSRCRAPLVKKGNM 165 (188)
T ss_pred EEccCCCcceEEcCcE
Confidence 4566665444334443
No 162
>cd01278 aprataxin_related aprataxin related: Aprataxin, a HINT family hydrolase is mutated in ataxia oculomotor apraxia syndrome. All the members of this subgroup have the conserved HxHxHxx (where x is a hydrophobic residue) signature motif. Members of this subgroup are predominantly eukaryotic in origin.
Probab=25.43 E-value=1.1e+02 Score=20.91 Aligned_cols=25 Identities=24% Similarity=0.332 Sum_probs=20.0
Q ss_pred CCCCCCCCCCHHHHHHHHHHHHhhH
Q psy5308 17 DIIPDLSHLTLEERQIIESVMMRQK 41 (137)
Q Consensus 17 ~~~~dLS~LteeEr~~Il~VL~R~~ 41 (137)
....+++.|+++|.+.+..+++...
T Consensus 45 ~h~~~~~~l~~~~~~~l~~~~~~~~ 69 (104)
T cd01278 45 EHIASLKALTKEDVPLLEHMETVGR 69 (104)
T ss_pred CCCCChHHCCHhHHHHHHHHHHHHH
Confidence 4677999999999999988875433
No 163
>PF07225 NDUF_B4: NADH-ubiquinone oxidoreductase B15 subunit (NDUFB4); InterPro: IPR009866 NADH:ubiquinone oxidoreductase (complex I) (1.6.5.3 from EC) is a respiratory-chain enzyme that catalyses the transfer of two electrons from NADH to ubiquinone in a reaction that is associated with proton translocation across the membrane (NADH + ubiquinone = NAD+ + ubiquinol) []. Complex I is a major source of reactive oxygen species (ROS) that are predominantly formed by electron transfer from FMNH(2). Complex I is found in bacteria, cyanobacteria (as a NADH-plastoquinone oxidoreductase), archaea [], mitochondira, and in the hydrogenosome, a mitochondria-derived organelle. In general, the bacterial complex consists of 14 different subunits, while the mitochondrial complex contains homologues to these subunits in addition to approximately 31 additional proteins []. Mitochondrial complex I, which is located in the inner mitochondrial membrane, is the largest multimeric respiratory enzyme in the mitochondria, consisting of more than 40 subunits, one FMN co-factor and eight FeS clusters []. The assembly of mitochondrial complex I is an intricate process that requires the cooperation of the nuclear and mitochondrial genomes [, ]. Mitochondrial complex I can cycle between active and deactive forms that can be distinguished by the reactivity towards divalent cations and thiol-reactive agents. All redox prosthetic groups reside in the peripheral arm of the L-shaped structure. The NADH oxidation domain harbouring the FMN cofactor is connected via a chain of iron-sulphur clusters to the ubiquinone reduction site that is located in a large pocket formed by the PSST and 49kDa subunits of complex I []. This family contains human NADH-ubiquinone oxidoreductase subunit NDUFB4 and related sequences.; GO: 0008137 NADH dehydrogenase (ubiquinone) activity, 0005739 mitochondrion
Probab=25.23 E-value=1e+02 Score=23.33 Aligned_cols=19 Identities=16% Similarity=0.191 Sum_probs=14.1
Q ss_pred CCCHHHHHHHHHHHHhhHH
Q psy5308 24 HLTLEERQIIESVMMRQKQ 42 (137)
Q Consensus 24 ~LteeEr~~Il~VL~R~~~ 42 (137)
++|+|||++|+.=+.+-.+
T Consensus 20 ~~SpE~r~a~~eR~a~Ra~ 38 (125)
T PF07225_consen 20 DVSPEERRAQQERAAIRAR 38 (125)
T ss_pred CCCHHHHHHHHHHHHHHHH
Confidence 7899999999885544333
No 164
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=24.97 E-value=77 Score=23.60 Aligned_cols=32 Identities=22% Similarity=0.276 Sum_probs=28.6
Q ss_pred CCCCCCCCCHHHHHHHHHHHHhhHHHHHHHHH
Q psy5308 18 IIPDLSHLTLEERQIIESVMMRQKQEEERELE 49 (137)
Q Consensus 18 ~~~dLS~LteeEr~~Il~VL~R~~~le~~E~~ 49 (137)
+.+.|..|++|+++-|..++.-...++++|.+
T Consensus 27 ~l~~~~~L~~E~~~Fi~~Fi~~rGnlKe~e~~ 58 (113)
T PF09862_consen 27 ELPWFARLSPEQLEFIKLFIKNRGNLKEMEKE 58 (113)
T ss_pred ccchhhcCCHHHHHHHHHHHHhcCCHHHHHHH
Confidence 46779999999999999999999999988764
No 165
>TIGR03629 arch_S13P archaeal ribosomal protein S13P. This model describes exclusively the archaeal ribosomal protein S13P. It excludes the homologous eukaryotic 40S ribosomal protein S18 and bacterial 30S ribosomal protein S13.
Probab=24.86 E-value=1.9e+02 Score=22.12 Aligned_cols=22 Identities=23% Similarity=0.132 Sum_probs=18.3
Q ss_pred CCCCCCCCCHHHHHHHHHHHHh
Q psy5308 18 IIPDLSHLTLEERQIIESVMMR 39 (137)
Q Consensus 18 ~~~dLS~LteeEr~~Il~VL~R 39 (137)
+..-++.||+++-+.|..+|..
T Consensus 45 ~~~~~~~Lt~~qi~~l~~~i~~ 66 (144)
T TIGR03629 45 PNAKLGYLDDEEIEKLEEAVEN 66 (144)
T ss_pred CCCCcccCCHHHHHHHHHHHHh
Confidence 3455789999999999999964
No 166
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=24.78 E-value=39 Score=22.07 Aligned_cols=22 Identities=32% Similarity=0.721 Sum_probs=15.5
Q ss_pred ccccccccccccCCCCCCCccccccccccCCce
Q psy5308 81 ATCHICLKTKFADGVGHMCNYCNIRCCARCGGK 113 (137)
Q Consensus 81 ~~C~~C~ktkf~~g~G~~C~~C~~rvC~rCg~~ 113 (137)
..|..|+..+.. |++|..||.+
T Consensus 28 ~~C~~CG~~~~~-----------H~vC~~CG~Y 49 (57)
T PRK12286 28 VECPNCGEPKLP-----------HRVCPSCGYY 49 (57)
T ss_pred eECCCCCCccCC-----------eEECCCCCcC
Confidence 457777765554 7888888865
No 167
>cd01277 HINT_subgroup HINT (histidine triad nucleotide-binding protein) subgroup: Members of this CD belong to the superfamily of histidine triad hydrolases that act on alpha-phosphate of ribonucleotides. This subgroup includes members from all three forms of cellular life. Although the biochemical function has not been characterised for many of the members of this subgroup, the proteins from Yeast have been shown to be involved in secretion, peroxisome formation and gene expression.
Probab=24.77 E-value=66 Score=21.60 Aligned_cols=24 Identities=17% Similarity=0.039 Sum_probs=19.2
Q ss_pred CCCCCCCCCCHHHHHHHHHHHHhh
Q psy5308 17 DIIPDLSHLTLEERQIIESVMMRQ 40 (137)
Q Consensus 17 ~~~~dLS~LteeEr~~Il~VL~R~ 40 (137)
....+|+.|+++|+..+..++.+-
T Consensus 43 ~H~~~~~~l~~~e~~~l~~~~~~v 66 (103)
T cd01277 43 KHYENLLDLDPEELAELILAAKKV 66 (103)
T ss_pred cccCChhhCCHHHHHHHHHHHHHH
Confidence 346689999999999999887543
No 168
>KOG3313|consensus
Probab=24.68 E-value=2.6e+02 Score=22.70 Aligned_cols=46 Identities=20% Similarity=0.234 Sum_probs=34.7
Q ss_pred CCCCCCCHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy5308 20 PDLSHLTLEERQIIESVMMRQKQEEERELEIMRRKQDEVHLLEQSIRQ 67 (137)
Q Consensus 20 ~dLS~LteeEr~~Il~VL~R~~~le~~E~~RirkL~~el~~lk~~~~~ 67 (137)
|-++++.. -+...+-+..++.++..=..++++|+.++.++++++..
T Consensus 31 p~~~~~~~--l~~~~E~~~kYkfme~~l~a~~~~l~~kIPd~entLei 76 (187)
T KOG3313|consen 31 PELESLEA--LKKLQERYGKYKFMEASLLAQKRRLKTKIPDIENTLEI 76 (187)
T ss_pred cccccchH--HHHHHHHHHHHHHHHHHHHHHHHHHHhhchHHHHHHHH
Confidence 44555544 44555667788889998889999999999999987643
No 169
>COG4014 Uncharacterized protein conserved in archaea [Function unknown]
Probab=24.45 E-value=51 Score=24.06 Aligned_cols=33 Identities=27% Similarity=0.451 Sum_probs=18.8
Q ss_pred CCCCCCCCCHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHH
Q psy5308 18 IIPDLSHLTLEERQIIESVMMRQKQEEERELEIMRRKQDEVHLL 61 (137)
Q Consensus 18 ~~~dLS~LteeEr~~Il~VL~R~~~le~~E~~RirkL~~el~~l 61 (137)
+.+|-|.+++++..-|-+|. +|||+++.+++.+
T Consensus 54 e~vdKse~ke~re~~~~evv-----------erirk~kE~~e~v 86 (97)
T COG4014 54 EVVDKSEIKEEREEDIDEVV-----------ERIRKEKEEFELV 86 (97)
T ss_pred eeecchhhHHHhhccHHHHH-----------HHHHHHHHhhhhc
Confidence 34566666644444444443 5677777666654
No 170
>PF10497 zf-4CXXC_R1: Zinc-finger domain of monoamine-oxidase A repressor R1; InterPro: IPR018866 R1 is a transcription factor repressor that inhibits monoamine oxidase A gene expression. This domain is a four-CXXC zinc finger putative DNA-binding domain found at the C-terminal end of R1. The domain carries 12 cysteines of which four pairs are of the CXXC type [].
Probab=24.38 E-value=21 Score=25.90 Aligned_cols=47 Identities=23% Similarity=0.443 Sum_probs=26.2
Q ss_pred cccccccc-cc-ccCC-----CCCCCccccccccccCCce-----e-ecCCCCcceEEeee
Q psy5308 81 ATCHICLK-TK-FADG-----VGHMCNYCNIRCCARCGGK-----V-TLRSNKVSVEVTTR 128 (137)
Q Consensus 81 ~~C~~C~k-tk-f~~g-----~G~~C~~C~~rvC~rCg~~-----v-~lr~n~~~W~Ctvc 128 (137)
.+|.-|++ |. +... ....|..|..++|..|=.. + .... ...|+|..|
T Consensus 8 ~~CHqCrqKt~~~~~~C~~~~~~~~C~~~~~~fC~~CL~~ryge~~~ev~~-~~~W~CP~C 67 (105)
T PF10497_consen 8 KTCHQCRQKTLDFKTICTGHWKNSSCRGCRGKFCGGCLRNRYGENVEEVLE-DPNWKCPKC 67 (105)
T ss_pred CCchhhcCCCCCCceEcCCCCCCCCCccCcceehHhHHHHHHhhhHHHHhc-CCceECCCC
Confidence 67999983 32 2211 1234444499999999211 1 0011 247999875
No 171
>PF13920 zf-C3HC4_3: Zinc finger, C3HC4 type (RING finger); PDB: 2YHN_B 2YHO_G 3T6P_A 2CSY_A 2VJE_B 2VJF_B 2HDP_B 2EA5_A 2ECG_A 3EB5_A ....
Probab=24.13 E-value=22 Score=21.64 Aligned_cols=43 Identities=19% Similarity=0.433 Sum_probs=24.0
Q ss_pred cccccccccccccCCCCCCCcccccc-ccccCCceeecCCCCcceEEeeecc
Q psy5308 80 DATCHICLKTKFADGVGHMCNYCNIR-CCARCGGKVTLRSNKVSVEVTTRGH 130 (137)
Q Consensus 80 ~~~C~~C~ktkf~~g~G~~C~~C~~r-vC~rCg~~v~lr~n~~~W~Ctvc~~ 130 (137)
+..|.+|.... .+ .+-.-|.|. +|..|...+.. ....|.+|-.
T Consensus 2 ~~~C~iC~~~~-~~---~~~~pCgH~~~C~~C~~~~~~----~~~~CP~Cr~ 45 (50)
T PF13920_consen 2 DEECPICFENP-RD---VVLLPCGHLCFCEECAERLLK----RKKKCPICRQ 45 (50)
T ss_dssp HSB-TTTSSSB-SS---EEEETTCEEEEEHHHHHHHHH----TTSBBTTTTB
T ss_pred cCCCccCCccC-Cc---eEEeCCCChHHHHHHhHHhcc----cCCCCCcCCh
Confidence 36799998652 21 233346677 88888655422 2356666543
No 172
>KOG4005|consensus
Probab=23.97 E-value=2.6e+02 Score=24.00 Aligned_cols=10 Identities=50% Similarity=0.830 Sum_probs=8.6
Q ss_pred CCCCCCHHHH
Q psy5308 21 DLSHLTLEER 30 (137)
Q Consensus 21 dLS~LteeEr 30 (137)
-|.|||.||+
T Consensus 60 RL~HLS~EEK 69 (292)
T KOG4005|consen 60 RLDHLSWEEK 69 (292)
T ss_pred hhcccCHHHH
Confidence 5899999995
No 173
>PF15554 FSIP1: FSIP1 family
Probab=23.89 E-value=1.2e+02 Score=27.53 Aligned_cols=45 Identities=22% Similarity=0.268 Sum_probs=31.9
Q ss_pred CCCCCCCCCHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHH
Q psy5308 18 IIPDLSHLTLEERQIIESVMMRQKQEEERELEIMRRKQDEVHLLEQ 63 (137)
Q Consensus 18 ~~~dLS~LteeEr~~Il~VL~R~~~le~~E~~RirkL~~el~~lk~ 63 (137)
..+||..=...+......||+--++.+ ..++|++...++|+.|++
T Consensus 380 ~~~~~~~~~~~~~~pGEkVlr~tKe~R-~q~~RL~eIdq~L~~L~e 424 (425)
T PF15554_consen 380 QEPDLEDSRNDEITPGEKVLRNTKEER-DQQNRLREIDQQLRKLKE 424 (425)
T ss_pred cccccccccccccChHHHHHHHHHHHH-HHHHHHHHHHHHHHHHhc
Confidence 456665556677777788885444444 477899999999988864
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=23.87 E-value=29 Score=26.10 Aligned_cols=25 Identities=24% Similarity=0.383 Sum_probs=18.3
Q ss_pred cccccccccccccCCCCCCCccccc
Q psy5308 80 DATCHICLKTKFADGVGHMCNYCNI 104 (137)
Q Consensus 80 ~~~C~~C~ktkf~~g~G~~C~~C~~ 104 (137)
.-.|+-|+|.--..|+-+.|.+|++
T Consensus 69 ~V~CP~C~K~TKmLGr~D~CM~C~~ 93 (114)
T PF11023_consen 69 QVECPNCGKQTKMLGRVDACMHCKE 93 (114)
T ss_pred eeECCCCCChHhhhchhhccCcCCC
Confidence 3569999987544467778888875
No 175
>PF13945 NST1: Salt tolerance down-regulator
Probab=23.86 E-value=1e+02 Score=24.94 Aligned_cols=13 Identities=23% Similarity=0.327 Sum_probs=9.4
Q ss_pred CHHHHHHHHHHHH
Q psy5308 26 TLEERQIIESVMM 38 (137)
Q Consensus 26 teeEr~~Il~VL~ 38 (137)
+.+||+.|-.++.
T Consensus 100 s~eEre~LkeFW~ 112 (190)
T PF13945_consen 100 SQEEREKLKEFWE 112 (190)
T ss_pred hHHHHHHHHHHHH
Confidence 5677887777763
No 176
>PRK06418 transcription elongation factor NusA-like protein; Validated
Probab=23.79 E-value=29 Score=27.38 Aligned_cols=21 Identities=33% Similarity=0.839 Sum_probs=16.7
Q ss_pred cccccccccccccCCCCCCCccccccc
Q psy5308 80 DATCHICLKTKFADGVGHMCNYCNIRC 106 (137)
Q Consensus 80 ~~~C~~C~ktkf~~g~G~~C~~C~~rv 106 (137)
-+.|.+|-|| |-+|+.|+.++
T Consensus 3 ~p~~~~c~kt------~ilC~~c~~~~ 23 (166)
T PRK06418 3 IPICEVCVKT------GLLCPRCQSLL 23 (166)
T ss_pred CceeeEEecc------CccChhHHhHh
Confidence 3789999987 55899998775
No 177
>PF00645 zf-PARP: Poly(ADP-ribose) polymerase and DNA-Ligase Zn-finger region; InterPro: IPR001510 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 PARP (Poly(ADP) polymerase) type zinc finger domains. NAD(+) ADP-ribosyltransferase(2.4.2.30 from EC) [, ] is a eukaryotic enzyme that catalyses the covalent attachment of ADP-ribose units from NAD(+) to various nuclear acceptor proteins. This post-translational modification of nuclear proteins is dependent on DNA. It appears to be involved in the regulation of various important cellular processes such as differentiation, proliferation and tumour transformation as well as in the regulation of the molecular events involved in the recovery of the cell from DNA damage. Structurally, NAD(+) ADP-ribosyltransferase consists of three distinct domains: an N-terminal zinc-dependent DNA-binding domain, a central automodification domain and a C-terminal NAD-binding domain. The DNA-binding region contains a pair of PARP-type zinc finger domains which have been shown to bind DNA in a zinc-dependent manner. The PARP-type zinc finger domains seem to bind specifically to single-stranded DNA and to act as a DNA nick sensor. DNA ligase III [] contains, in its N-terminal section, a single copy of a zinc finger highly similar to those of PARP. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding, 0008270 zinc ion binding; PDB: 1UW0_A 3OD8_D 3ODA_A 4AV1_A 2DMJ_A 4DQY_D 2L30_A 2CS2_A 2L31_A 3ODE_B ....
Probab=23.74 E-value=59 Score=21.67 Aligned_cols=24 Identities=17% Similarity=0.344 Sum_probs=19.1
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHH
Q psy5308 14 TNADIIPDLSHLTLEERQIIESVM 37 (137)
Q Consensus 14 ~~~~~~~dLS~LteeEr~~Il~VL 37 (137)
.+..++..++.|+++.|+.|...|
T Consensus 58 ~~~~~i~G~~~L~~~Dq~~i~~~i 81 (82)
T PF00645_consen 58 GDIEEIKGFDELKPEDQEKIRKLI 81 (82)
T ss_dssp SCGGGCETCCCS-HHHHHHHHHHH
T ss_pred CCHHHCCChHHCCHHHHHHHHHHh
Confidence 445678899999999999998865
No 178
>PF10058 DUF2296: Predicted integral membrane metal-binding protein (DUF2296); InterPro: IPR019273 This domain, found mainly in the eukaryotic lunapark proteins, has no known function [].
Probab=23.70 E-value=40 Score=21.76 Aligned_cols=11 Identities=9% Similarity=0.045 Sum_probs=7.3
Q ss_pred cceEEeeeccC
Q psy5308 121 VSVEVTTRGHN 131 (137)
Q Consensus 121 ~~W~Ctvc~~~ 131 (137)
..|+|--|++-
T Consensus 43 i~y~C~~Cg~~ 53 (54)
T PF10058_consen 43 IQYRCPYCGAL 53 (54)
T ss_pred eEEEcCCCCCc
Confidence 56777777654
No 179
>CHL00183 petJ cytochrome c553; Provisional
Probab=23.65 E-value=1.1e+02 Score=21.34 Aligned_cols=22 Identities=18% Similarity=0.394 Sum_probs=17.0
Q ss_pred CCCC-CCCCHHHHHHHHHHHHhh
Q psy5308 19 IPDL-SHLTLEERQIIESVMMRQ 40 (137)
Q Consensus 19 ~~dL-S~LteeEr~~Il~VL~R~ 40 (137)
||-+ +.||++|++.|...|.-+
T Consensus 81 MP~f~~~Ls~~ei~~i~aYi~~~ 103 (108)
T CHL00183 81 MPAFGGRLSDEDIEDVANYVLSQ 103 (108)
T ss_pred cccccCCCCHHHHHHHHHHHHHh
Confidence 4544 689999999999987543
No 180
>PF05823 Gp-FAR-1: Nematode fatty acid retinoid binding protein (Gp-FAR-1); InterPro: IPR008632 Parasitic nematodes produce at least two structurally novel classes of small helix-rich retinol- and fatty-acid-binding proteins that have no counterparts in their plant or animal hosts and thus represent potential targets for new nematicides. Gp-FAR-1 is a member of the nematode-specific fatty-acid- and retinol-binding (FAR) family of proteins but localises to the surface of the organism, placing it in a strategic position for interaction with the host. Gp-FAR-1 functions as a broad-spectrum retinol- and fatty-acid-binding protein, and it is thought that it is involved in the evasion of primary host plant defence systems [].; GO: 0008289 lipid binding; PDB: 2W9Y_A.
Probab=23.62 E-value=61 Score=24.85 Aligned_cols=39 Identities=21% Similarity=0.219 Sum_probs=21.6
Q ss_pred CCCCCHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHH
Q psy5308 22 LSHLTLEERQIIESVMMRQKQEEERELEIMRRKQDEVHLL 61 (137)
Q Consensus 22 LS~LteeEr~~Il~VL~R~~~le~~E~~RirkL~~el~~l 61 (137)
++.||++|+.++.+|........ -+++.+.-|+.....|
T Consensus 18 ~~~Lt~eeK~~lkev~~~~~~~~-~~de~i~~LK~ksP~L 56 (154)
T PF05823_consen 18 YKNLTPEEKAELKEVAKNYAKFK-NEDEMIAALKEKSPSL 56 (154)
T ss_dssp HHH--TTTHHHHHHHHTT--------TTHHHHHHHH-HHH
T ss_pred HHcCCHHHHHHHHHHHHHccccC-CHHHHHHHHHHhCHHH
Confidence 46799999999999998886553 4555666666554433
No 181
>KOG1356|consensus
Probab=23.59 E-value=29 Score=34.02 Aligned_cols=37 Identities=27% Similarity=0.573 Sum_probs=28.7
Q ss_pred hCccccccccccccccccCCCCCCCccccccccccCCce
Q psy5308 75 AGVELDATCHICLKTKFADGVGHMCNYCNIRCCARCGGK 113 (137)
Q Consensus 75 ~G~~~~~~C~~C~ktkf~~g~G~~C~~C~~rvC~rCg~~ 113 (137)
+..+....|.+|.+|.|- .--.|.-|.++||-.|.-.
T Consensus 224 a~~g~~~mC~~C~~tlfn--~hw~C~~C~~~~Cl~C~r~ 260 (889)
T KOG1356|consen 224 AVKGIREMCDRCETTLFN--IHWRCPRCGFGVCLDCYRK 260 (889)
T ss_pred cccCcchhhhhhcccccc--eeEEccccCCeeeecchhh
Confidence 344456899999998774 4558999999999999643
No 182
>PF00130 C1_1: Phorbol esters/diacylglycerol binding domain (C1 domain); InterPro: IPR002219 Diacylglycerol (DAG) is an important second messenger. Phorbol esters (PE) are analogues of DAG and potent tumour promoters that cause a variety of physiological changes when administered to both cells and tissues. DAG activates a family of serine/threonine protein kinases, collectively known as protein kinase C (PKC) []. Phorbol esters can directly stimulate PKC. The N-terminal region of PKC, known as C1, has been shown [] to bind PE and DAG in a phospholipid and zinc-dependent fashion. The C1 region contains one or two copies (depending on the isozyme of PKC) of a cysteine-rich domain, which is about 50 amino-acid residues long, and which is essential for DAG/PE-binding. The DAG/PE-binding domain binds two zinc ions; the ligands of these metal ions are probably the six cysteines and two histidines that are conserved in this domain.; GO: 0035556 intracellular signal transduction; PDB: 1RFH_A 2FNF_X 3PFQ_A 1PTQ_A 1PTR_A 2VRW_B 1XA6_A 2ENN_A 1TBN_A 1TBO_A ....
Probab=23.50 E-value=27 Score=21.27 Aligned_cols=34 Identities=26% Similarity=0.639 Sum_probs=23.3
Q ss_pred ccccccccccc-ccCCCCCCCccccccccccCCce
Q psy5308 80 DATCHICLKTK-FADGVGHMCNYCNIRCCARCGGK 113 (137)
Q Consensus 80 ~~~C~~C~ktk-f~~g~G~~C~~C~~rvC~rCg~~ 113 (137)
...|..|.+.. .....|-.|..|+..+=.+|-..
T Consensus 11 ~~~C~~C~~~i~g~~~~g~~C~~C~~~~H~~C~~~ 45 (53)
T PF00130_consen 11 PTYCDVCGKFIWGLGKQGYRCSWCGLVCHKKCLSK 45 (53)
T ss_dssp TEB-TTSSSBECSSSSCEEEETTTT-EEETTGGCT
T ss_pred CCCCcccCcccCCCCCCeEEECCCCChHhhhhhhh
Confidence 56799998776 33458888998888777777544
No 183
>PRK13920 putative anti-sigmaE protein; Provisional
Probab=23.44 E-value=1.9e+02 Score=22.65 Aligned_cols=27 Identities=22% Similarity=0.149 Sum_probs=22.3
Q ss_pred CCCCCHHHHHHHHHHHHhhHHHHHHHH
Q psy5308 22 LSHLTLEERQIIESVMMRQKQEEEREL 48 (137)
Q Consensus 22 LS~LteeEr~~Il~VL~R~~~le~~E~ 48 (137)
+..|+++|++.+..-|..+.+.++..+
T Consensus 6 lG~Ls~eE~~~ve~~L~~dp~~~~~v~ 32 (206)
T PRK13920 6 LGALSPEERARVEAALEAYPELWAELR 32 (206)
T ss_pred cCCCCHHHHHHHHHHHHHCHHHHHHHH
Confidence 578999999999999998877766543
No 184
>PTZ00074 60S ribosomal protein L34; Provisional
Probab=23.23 E-value=60 Score=25.00 Aligned_cols=20 Identities=25% Similarity=0.489 Sum_probs=13.5
Q ss_pred CCCCCHHHHHHHHHHHHhhHH
Q psy5308 22 LSHLTLEERQIIESVMMRQKQ 42 (137)
Q Consensus 22 LS~LteeEr~~Il~VL~R~~~ 42 (137)
-.||. ||++|+..||.-++.
T Consensus 91 rAFLi-EEqKivkkv~k~~~~ 110 (135)
T PTZ00074 91 RAFLV-EEQKIVKQVLKEKAK 110 (135)
T ss_pred HHHHH-HHHHHHHHHHHHHHH
Confidence 45555 677888888766555
No 185
>cd00029 C1 Protein kinase C conserved region 1 (C1) . Cysteine-rich zinc binding domain. Some members of this domain family bind phorbol esters and diacylglycerol, some are reported to bind RasGTP. May occur in tandem arrangement. Diacylglycerol (DAG) is a second messenger, released by activation of Phospholipase D. Phorbol Esters (PE) can act as analogues of DAG and mimic its downstream effects in, for example, tumor promotion. Protein Kinases C are activated by DAG/PE, this activation is mediated by their N-terminal conserved region (C1). DAG/PE binding may be phospholipid dependent. C1 domains may also mediate DAG/PE signals in chimaerins (a family of Rac GTPase activating proteins), RasGRPs (exchange factors for Ras/Rap1), and Munc13 isoforms (scaffolding proteins involved in exocytosis).
Probab=23.22 E-value=34 Score=20.11 Aligned_cols=34 Identities=26% Similarity=0.750 Sum_probs=22.1
Q ss_pred ccccccccccc-ccCCCCCCCccccccccccCCce
Q psy5308 80 DATCHICLKTK-FADGVGHMCNYCNIRCCARCGGK 113 (137)
Q Consensus 80 ~~~C~~C~ktk-f~~g~G~~C~~C~~rvC~rCg~~ 113 (137)
...|..|++.. +....|..|..|+..+=.+|-..
T Consensus 11 ~~~C~~C~~~i~~~~~~~~~C~~C~~~~H~~C~~~ 45 (50)
T cd00029 11 PTFCDVCRKSIWGLFKQGLRCSWCKVKCHKKCADK 45 (50)
T ss_pred CCChhhcchhhhccccceeEcCCCCCchhhhhhcc
Confidence 45699998765 22247777888876665666443
No 186
>PF13811 DUF4186: Domain of unknown function (DUF4186)
Probab=23.15 E-value=76 Score=23.76 Aligned_cols=21 Identities=48% Similarity=0.586 Sum_probs=17.1
Q ss_pred CCCCCCCCHHHHHHHHHHHHh
Q psy5308 19 IPDLSHLTLEERQIIESVMMR 39 (137)
Q Consensus 19 ~~dLS~LteeEr~~Il~VL~R 39 (137)
.|-=-.||++|++-|..||.+
T Consensus 87 Ip~gr~Lt~~eq~yiv~vi~~ 107 (111)
T PF13811_consen 87 IPKGRELTEEEQAYIVDVIMR 107 (111)
T ss_pred CCCCCCCCHHHHHHHHHHHHH
Confidence 444567999999999999865
No 187
>PF04568 IATP: Mitochondrial ATPase inhibitor, IATP; InterPro: IPR007648 ATP synthase inhibitor prevents the enzyme from switching to ATP hydrolysis during collapse of the electrochemical gradient, for example during oxygen deprivation [] ATP synthase inhibitor forms a one to one complex with the F1 ATPase, possibly by binding at the alpha-beta interface. It is thought to inhibit ATP synthesis by preventing the release of ATP []. The minimum inhibitory region for bovine inhibitor (P01096 from SWISSPROT) is from residues 39 to 72 []. The inhibitor has two oligomeric states, dimer (the active state) and tetramer. At low pH , the inhibitor forms a dimer via antiparallel coiled coil interactions between the C-terminal regions of two monomers. At high pH, the inhibitor forms tetramers and higher oligomers by coiled coil interactions involving the N terminus and inhibitory region, thus preventing the inhibitory activity []. ; GO: 0004857 enzyme inhibitor activity, 0045980 negative regulation of nucleotide metabolic process, 0005739 mitochondrion; PDB: 1GMJ_B 1OHH_H 1HF9_B 2V7Q_J.
Probab=23.14 E-value=2.1e+02 Score=20.85 Aligned_cols=21 Identities=10% Similarity=0.259 Sum_probs=13.0
Q ss_pred hHHHHHHHHHHHHHHHHHHHH
Q psy5308 40 QKQEEERELEIMRRKQDEVHL 60 (137)
Q Consensus 40 ~~~le~~E~~RirkL~~el~~ 60 (137)
+.+.+++|.+.+.+|+.+|.+
T Consensus 63 ~~Y~r~~EkEqL~~Lk~kl~~ 83 (100)
T PF04568_consen 63 EQYFRKKEKEQLKKLKEKLKE 83 (100)
T ss_dssp HHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHH
Confidence 445555666666677766655
No 188
>PF00569 ZZ: Zinc finger, ZZ type; InterPro: IPR000433 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 ZZ-type zinc finger domains, named because of their ability to bind two zinc ions []. These domains contain 4-6 Cys residues that participate in zinc binding (plus additional Ser/His residues), including a Cys-X2-Cys motif found in other zinc finger domains. These zinc fingers are thought to be involved in protein-protein interactions. The structure of the ZZ domain shows that it belongs to the family of cross-brace zinc finger motifs that include the PHD, RING, and FYVE domains []. ZZ-type zinc finger domains are found in: Transcription factors P300 and CBP. Plant proteins involved in light responses, such as Hrb1. E3 ubiquitin ligases MEX and MIB2 (6.3.2 from EC). Dystrophin and its homologues. Single copies of the ZZ zinc finger occur in the transcriptional adaptor/coactivator proteins P300, in cAMP response element-binding protein (CREB)-binding protein (CBP) and ADA2. CBP provides several binding sites for transcriptional coactivators. The site of interaction with the tumour suppressor protein p53 and the oncoprotein E1A with CBP/P300 is a Cys-rich region that incorporates two zinc-binding motifs: ZZ-type and TAZ2-type. The ZZ-type zinc finger of CBP contains two twisted anti-parallel beta-sheets and a short alpha-helix, and binds two zinc ions []. One zinc ion is coordinated by four cysteine residues via 2 Cys-X2-Cys motifs, and the third zinc ion via a third Cys-X-Cys motif and a His-X-His motif. The first zinc cluster is strictly conserved, whereas the second zinc cluster displays variability in the position of the two His residues. In Arabidopsis thaliana (Mouse-ear cress), the hypersensitive to red and blue 1 (Hrb1) protein, which regulating both red and blue light responses, contains a ZZ-type zinc finger domain []. ZZ-type zinc finger domains have also been identified in the testis-specific E3 ubiquitin ligase MEX that promotes death receptor-induced apoptosis []. MEX has four putative zinc finger domains: one ZZ-type, one SWIM-type and two RING-type. The region containing the ZZ-type and RING-type zinc fingers is required for interaction with UbcH5a and MEX self-association, whereas the SWIM domain was critical for MEX ubiquitination. In addition, the Cys-rich domains of dystrophin, utrophin and an 87kDa post-synaptic protein contain a ZZ-type zinc finger with high sequence identity to P300/CBP ZZ-type zinc fingers. In dystrophin and utrophin, the ZZ-type zinc finger lies between a WW domain (flanked by and EF hand) and the C-terminal coiled-coil domain. Dystrophin is thought to act as a link between the actin cytoskeleton and the extracellular matrix, and perturbations of the dystrophin-associated complex, for example, between dystrophin and the transmembrane glycoprotein beta-dystroglycan, may lead to muscular dystrophy. Dystrophin and its autosomal homologue utrophin interact with beta-dystroglycan via their C-terminal regions, which are comprised of a WW domain, an EF hand domain and a ZZ-type zinc finger domain []. The WW domain is the primary site of interaction between dystrophin or utrophin and dystroglycan, while the EF hand and ZZ-type zinc finger domains stabilise and strengthen this interaction. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 1TOT_A 2DIP_A 2FC7_A 2E5R_A.
Probab=22.82 E-value=34 Score=20.96 Aligned_cols=22 Identities=18% Similarity=0.252 Sum_probs=12.4
Q ss_pred cccccCCceeecCCCCcceEEeeec
Q psy5308 105 RCCARCGGKVTLRSNKVSVEVTTRG 129 (137)
Q Consensus 105 rvC~rCg~~v~lr~n~~~W~Ctvc~ 129 (137)
..|..|+.... .+.-|.|.+|.
T Consensus 5 ~~C~~C~~~~i---~g~Ry~C~~C~ 26 (46)
T PF00569_consen 5 YTCDGCGTDPI---IGVRYHCLVCP 26 (46)
T ss_dssp CE-SSS-SSSE---ESSEEEESSSS
T ss_pred eECcCCCCCcC---cCCeEECCCCC
Confidence 35777775311 14579999975
No 189
>smart00184 RING Ring finger. E3 ubiquitin-protein ligase activity is intrinsic to the RING domain of c-Cbl and is likely to be a general function of this domain; Various RING fingers exhibit binding activity towards E2 ubiquitin-conjugating enzymes (Ubc' s)
Probab=22.74 E-value=25 Score=18.60 Aligned_cols=26 Identities=27% Similarity=0.604 Sum_probs=15.2
Q ss_pred ccccccccccCCCCCCCccccccccccCCc
Q psy5308 83 CHICLKTKFADGVGHMCNYCNIRCCARCGG 112 (137)
Q Consensus 83 C~~C~ktkf~~g~G~~C~~C~~rvC~rCg~ 112 (137)
|.+|.... ....-..|.|.+|..|-.
T Consensus 1 C~iC~~~~----~~~~~~~C~H~~c~~C~~ 26 (39)
T smart00184 1 CPICLEEL----KDPVVLPCGHTFCRSCIR 26 (39)
T ss_pred CCcCccCC----CCcEEecCCChHHHHHHH
Confidence 56776441 122233588888888843
No 190
>PHA02929 N1R/p28-like protein; Provisional
Probab=22.58 E-value=37 Score=28.23 Aligned_cols=48 Identities=17% Similarity=0.434 Sum_probs=27.7
Q ss_pred cccccccccccccCCCC----CCCccccccccccCCceeecCCCCcceEEeeeccC
Q psy5308 80 DATCHICLKTKFADGVG----HMCNYCNIRCCARCGGKVTLRSNKVSVEVTTRGHN 131 (137)
Q Consensus 80 ~~~C~~C~ktkf~~g~G----~~C~~C~~rvC~rCg~~v~lr~n~~~W~Ctvc~~~ 131 (137)
+..|++|....+..... .+=..|.|.||..|=.... ..+. .|.+|-..
T Consensus 174 ~~eC~ICle~~~~~~~~~~~~~vl~~C~H~FC~~CI~~Wl-~~~~---tCPlCR~~ 225 (238)
T PHA02929 174 DKECAICMEKVYDKEIKNMYFGILSNCNHVFCIECIDIWK-KEKN---TCPVCRTP 225 (238)
T ss_pred CCCCccCCcccccCccccccceecCCCCCcccHHHHHHHH-hcCC---CCCCCCCE
Confidence 57899999764432211 1224788999999954331 2111 47776443
No 191
>PF07047 OPA3: Optic atrophy 3 protein (OPA3); InterPro: IPR010754 OPA3 deficiency causes type III 3-methylglutaconic aciduria (MGA) in humans. This disease manifests with early bilateral optic atrophy, spasticity, extrapyramidal dysfunction, ataxia, and cognitive deficits, but normal longevity []. This family consists of several optic atrophy 3 (OPA3) proteins and related proteins from other eukaryotic species, the function is unknown.
Probab=22.48 E-value=2.8e+02 Score=20.62 Aligned_cols=17 Identities=18% Similarity=0.409 Sum_probs=10.8
Q ss_pred HHHHHHHHHHHHHHHHH
Q psy5308 49 EIMRRKQDEVHLLEQSI 65 (137)
Q Consensus 49 ~RirkL~~el~~lk~~~ 65 (137)
+++..|..++.+|...+
T Consensus 112 ~~l~~L~~~i~~L~~~~ 128 (134)
T PF07047_consen 112 ERLEELEERIEELEEQV 128 (134)
T ss_pred HHHHHHHHHHHHHHHHH
Confidence 55666677777776544
No 192
>COG1734 DksA DnaK suppressor protein [Signal transduction mechanisms]
Probab=22.19 E-value=1.6e+02 Score=22.03 Aligned_cols=29 Identities=24% Similarity=0.461 Sum_probs=19.7
Q ss_pred hCcccccccccccccc-----ccCCCCCCCcccccc
Q psy5308 75 AGVELDATCHICLKTK-----FADGVGHMCNYCNIR 105 (137)
Q Consensus 75 ~G~~~~~~C~~C~ktk-----f~~g~G~~C~~C~~r 105 (137)
.|.| -.|..|+.+- .|......|..|+..
T Consensus 77 ~gtY--G~Ce~cG~~Ip~~RL~A~P~A~~Ci~cQ~~ 110 (120)
T COG1734 77 EGTY--GICEECGEPIPEARLEARPTARLCIECQER 110 (120)
T ss_pred cCCc--cchhccCCcCCHHHHhhCcchHHHHHHHHH
Confidence 3544 5699999872 334677788888754
No 193
>PRK05179 rpsM 30S ribosomal protein S13; Validated
Probab=22.14 E-value=2.5e+02 Score=20.87 Aligned_cols=48 Identities=19% Similarity=0.099 Sum_probs=28.9
Q ss_pred CCCCCCCCHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhHH
Q psy5308 19 IPDLSHLTLEERQIIESVMMRQKQEEERELEIMRRKQDEVHLLEQSIRQRSE 70 (137)
Q Consensus 19 ~~dLS~LteeEr~~Il~VL~R~~~le~~E~~RirkL~~el~~lk~~~~~~~~ 70 (137)
..-+..||++|-+.|..+|... . ..|.+..+...+.++.|+ .+.+|++
T Consensus 42 ~~~~~~L~~~qi~~l~~~i~~~-~--~i~~dL~~~~~~dI~rl~-~I~sYRG 89 (122)
T PRK05179 42 DTRVKDLTDEELDKIREEIDKN-Y--KVEGDLRREVSMNIKRLM-DIGCYRG 89 (122)
T ss_pred ccccccCCHHHHHHHHHHHHhh-c--cchHHHHHHHHHHHHHHH-Hhcceee
Confidence 3447899999999999999642 1 234444444444444443 2334444
No 194
>smart00547 ZnF_RBZ Zinc finger domain. Zinc finger domain in Ran-binding proteins (RanBPs), and other proteins. In RanBPs, this domain binds RanGDP.
Probab=22.12 E-value=28 Score=18.43 Aligned_cols=12 Identities=17% Similarity=-0.094 Sum_probs=9.4
Q ss_pred ceEEeeeccCCC
Q psy5308 122 SVEVTTRGHNNN 133 (137)
Q Consensus 122 ~W~Ctvc~~~~~ 133 (137)
.|.|..|.+.|-
T Consensus 2 ~W~C~~C~~~N~ 13 (26)
T smart00547 2 DWECPACTFLNF 13 (26)
T ss_pred cccCCCCCCcCh
Confidence 599999887764
No 195
>COG5141 PHD zinc finger-containing protein [General function prediction only]
Probab=22.09 E-value=1.3e+02 Score=28.40 Aligned_cols=54 Identities=19% Similarity=0.222 Sum_probs=37.6
Q ss_pred ccccccccccc-ccCCCCCCCccccccccccCCceeecCCCCcceEEeeeccCCCCC
Q psy5308 80 DATCHICLKTK-FADGVGHMCNYCNIRCCARCGGKVTLRSNKVSVEVTTRGHNNNGV 135 (137)
Q Consensus 80 ~~~C~~C~ktk-f~~g~G~~C~~C~~rvC~rCg~~v~lr~n~~~W~Ctvc~~~~~~~ 135 (137)
+-.|.+|..|- --.+.-..|.+|..-|=..|-|-..+.. + .|+|.-|-.+..+|
T Consensus 193 d~~C~~c~~t~~eN~naiVfCdgC~i~VHq~CYGI~f~pe-G-~WlCrkCi~~~~~i 247 (669)
T COG5141 193 DDICTKCTSTHNENSNAIVFCDGCEICVHQSCYGIQFLPE-G-FWLCRKCIYGEYQI 247 (669)
T ss_pred hhhhHhccccccCCcceEEEecCcchhhhhhcccceecCc-c-hhhhhhhcccccce
Confidence 45666776553 1124567899999999999977766664 4 69999887765543
No 196
>PF02132 RecR: RecR protein; InterPro: IPR023628 The bacterial protein RecR seems to play a role in a recombinational process of DNA repair []. It may act with RecF and RecO. RecR's structure consists of a N-terminal helix-hairpin-helix (HhH) motif, followed by a Cys4 zinc-finger motif, a Toprim domain and a Walker B motif []. This entry represents the C4-type zinc finger.; PDB: 1VDD_D 2V1C_B.
Probab=22.07 E-value=74 Score=19.03 Aligned_cols=19 Identities=26% Similarity=0.751 Sum_probs=7.9
Q ss_pred ccccccccccccCCCCCCCcccc
Q psy5308 81 ATCHICLKTKFADGVGHMCNYCN 103 (137)
Q Consensus 81 ~~C~~C~ktkf~~g~G~~C~~C~ 103 (137)
..|.+|+ . |. ...+|..|.
T Consensus 18 ~~C~~C~-n-ls--e~~~C~IC~ 36 (41)
T PF02132_consen 18 KFCSICG-N-LS--EEDPCEICS 36 (41)
T ss_dssp EE-SSS----EE--SSSS-HHHH
T ss_pred CccCCCC-C-cC--CCCcCcCCC
Confidence 5577776 2 22 344666554
No 197
>KOG1571|consensus
Probab=21.95 E-value=42 Score=29.72 Aligned_cols=21 Identities=29% Similarity=0.654 Sum_probs=15.1
Q ss_pred ccccccccccc--ccC-CCCCCCc
Q psy5308 80 DATCHICLKTK--FAD-GVGHMCN 100 (137)
Q Consensus 80 ~~~C~~C~ktk--f~~-g~G~~C~ 100 (137)
...|.+|...+ +.+ .+||+|.
T Consensus 305 p~lcVVcl~e~~~~~fvpcGh~cc 328 (355)
T KOG1571|consen 305 PDLCVVCLDEPKSAVFVPCGHVCC 328 (355)
T ss_pred CCceEEecCCccceeeecCCcEEE
Confidence 57899999553 333 5999975
No 198
>TIGR03631 bact_S13 30S ribosomal protein S13. This model describes bacterial ribosomal protein S13, to the exclusion of the homologous archaeal S13P and eukaryotic ribosomal protein S18. This model identifies some (but not all) instances of chloroplast and mitochondrial S13, which is of bacterial type.
Probab=21.81 E-value=2.5e+02 Score=20.55 Aligned_cols=21 Identities=24% Similarity=0.142 Sum_probs=17.6
Q ss_pred CCCCCCCCHHHHHHHHHHHHh
Q psy5308 19 IPDLSHLTLEERQIIESVMMR 39 (137)
Q Consensus 19 ~~dLS~LteeEr~~Il~VL~R 39 (137)
..-+..||++|-+.|..+|..
T Consensus 40 ~~~~~~L~~~qi~~l~~~l~~ 60 (113)
T TIGR03631 40 DKRVKDLTEEELNAIREEIEA 60 (113)
T ss_pred ccccccCCHHHHHHHHHHHHh
Confidence 344789999999999999954
No 199
>PRK14161 heat shock protein GrpE; Provisional
Probab=21.75 E-value=3.1e+02 Score=21.70 Aligned_cols=19 Identities=11% Similarity=0.260 Sum_probs=13.1
Q ss_pred HHHHHHHHHHHHHHHHHHH
Q psy5308 49 EIMRRKQDEVHLLEQSIRQ 67 (137)
Q Consensus 49 ~RirkL~~el~~lk~~~~~ 67 (137)
.+..|++.++++++++...
T Consensus 40 d~~lR~~AefeN~rkR~~k 58 (178)
T PRK14161 40 DKLIRTTAEIDNTRKRLEK 58 (178)
T ss_pred HHHHHHHHHHHHHHHHHHH
Confidence 4555778888888876643
No 200
>PF08216 CTNNBL: Catenin-beta-like, Arm-motif containing nuclear; InterPro: IPR013180 This domain is found in eukaryotic proteins. A human nuclear protein with this domain (Q8WYA6 from SWISSPROT) is thought to have a role in apoptosis [].
Probab=21.66 E-value=79 Score=23.42 Aligned_cols=35 Identities=14% Similarity=0.103 Sum_probs=27.1
Q ss_pred CHHHHHHHHHHHHhhHH--HHHHHHHHHHHHHHHHHH
Q psy5308 26 TLEERQIIESVMMRQKQ--EEERELEIMRRKQDEVHL 60 (137)
Q Consensus 26 teeEr~~Il~VL~R~~~--le~~E~~RirkL~~el~~ 60 (137)
||+|++-|+..+..+.. .+.....-++||...|+.
T Consensus 1 ~e~~~~~il~~~e~~~~~~~e~lD~~~lkklvl~fek 37 (108)
T PF08216_consen 1 SEEEREDILEIVEEAEEEEVEVLDEAWLKKLVLSFEK 37 (108)
T ss_pred CchHHHHHHHHHHhcccccccccCHHHHHHHHHHHHH
Confidence 68899999999988877 456777778888776653
No 201
>KOG0930|consensus
Probab=21.66 E-value=2.6e+02 Score=24.73 Aligned_cols=39 Identities=26% Similarity=0.383 Sum_probs=25.3
Q ss_pred CCCCHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy5308 23 SHLTLEERQIIESVMMRQKQEEERELEIMRRKQDEVHLLEQSI 65 (137)
Q Consensus 23 S~LteeEr~~Il~VL~R~~~le~~E~~RirkL~~el~~lk~~~ 65 (137)
..|+++|+.-+..|=.|-++|=. -|.+|++|+.+.-..+
T Consensus 9 ~~Ls~~E~~eL~~ir~rk~qL~d----eIq~Lk~Ei~ev~~ei 47 (395)
T KOG0930|consen 9 NDLSEEERMELENIRRRKQELLD----EIQRLKDEIAEVMEEI 47 (395)
T ss_pred CCCCHHHHHhHHHHHHHHHHHHH----HHHHHHHHHHHHHHHh
Confidence 35789999999988655544321 2557787776654433
No 202
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=21.62 E-value=47 Score=21.81 Aligned_cols=25 Identities=20% Similarity=0.389 Sum_probs=17.6
Q ss_pred cccccccccccccCCCCCCCccccc
Q psy5308 80 DATCHICLKTKFADGVGHMCNYCNI 104 (137)
Q Consensus 80 ~~~C~~C~ktkf~~g~G~~C~~C~~ 104 (137)
...|..|++++...+-..+|..|..
T Consensus 5 ~~~C~~Cg~~~~~~dDiVvCp~Cga 29 (54)
T PF14446_consen 5 GCKCPVCGKKFKDGDDIVVCPECGA 29 (54)
T ss_pred CccChhhCCcccCCCCEEECCCCCC
Confidence 4679999988655556667777763
No 203
>TIGR00721 tfx DNA-binding protein, Tfx family. Tfx from Methanobacterium thermoautotrophicum is associated with the operon for molybdenum formyl-methanofuran dehydrogenase and binds a DNA sequence near its promoter.
Probab=21.55 E-value=2.7e+02 Score=21.14 Aligned_cols=17 Identities=18% Similarity=0.296 Sum_probs=14.7
Q ss_pred CCCCCCCCHHHHHHHHH
Q psy5308 19 IPDLSHLTLEERQIIES 35 (137)
Q Consensus 19 ~~dLS~LteeEr~~Il~ 35 (137)
|++-|+||+.|+++|.-
T Consensus 1 ~~~~~~Lte~qr~VL~L 17 (137)
T TIGR00721 1 MSKKTFLTERQIKVLEL 17 (137)
T ss_pred CCccCCCCHHHHHHHHH
Confidence 46789999999999976
No 204
>cd07321 Extradiol_Dioxygenase_3A_like Subunit A of Class III extradiol dioxygenases. Extradiol dioxygenases catalyze the incorporation of both atoms of molecular oxygen into substrates using a variety of reaction mechanisms, resulting in the cleavage of aromatic rings. There are two major groups of dioxygenases according to the cleavage site of the aromatic ring. Intradiol enzymes cleave the aromatic ring between two hydroxyl groups, whereas extradiol enzymes cleave the aromatic ring between a hydroxylated carbon and an adjacent non-hydroxylated carbon. Extradiol dioxygenases can be divided into three classes. Class I and II enzymes are evolutionary related and show sequence similarity, with the two domain class II enzymes evolving from the class I enzyme through gene duplication. Class III enzymes are different in sequence and structure and usually have two subunits, designated A and B, which form a tetramer composed of two copies of each subunit. This model represents subunit A of c
Probab=21.50 E-value=58 Score=22.23 Aligned_cols=14 Identities=29% Similarity=0.195 Sum_probs=11.2
Q ss_pred CCCCCHHHHHHHHH
Q psy5308 22 LSHLTLEERQIIES 35 (137)
Q Consensus 22 LS~LteeEr~~Il~ 35 (137)
-=.||+||++.|+.
T Consensus 32 ~~~Lt~eE~~al~~ 45 (77)
T cd07321 32 EYGLTPEEKAALLA 45 (77)
T ss_pred HcCCCHHHHHHHHc
Confidence 34799999998876
No 205
>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=21.47 E-value=44 Score=21.28 Aligned_cols=11 Identities=9% Similarity=-0.082 Sum_probs=8.1
Q ss_pred cceEEeeeccC
Q psy5308 121 VSVEVTTRGHN 131 (137)
Q Consensus 121 ~~W~Ctvc~~~ 131 (137)
..|+|.+|+..
T Consensus 33 ~~w~CP~C~a~ 43 (50)
T cd00730 33 DDWVCPVCGAG 43 (50)
T ss_pred CCCCCCCCCCc
Confidence 36999998643
No 206
>COG5325 t-SNARE complex subunit, syntaxin [Intracellular trafficking and secretion]
Probab=21.46 E-value=2.3e+02 Score=24.39 Aligned_cols=28 Identities=25% Similarity=0.134 Sum_probs=19.9
Q ss_pred CCCCCCCCHHHHHHHHH------HHHhhHHHHHH
Q psy5308 19 IPDLSHLTLEERQIIES------VMMRQKQEEER 46 (137)
Q Consensus 19 ~~dLS~LteeEr~~Il~------VL~R~~~le~~ 46 (137)
-.|-++|-++|++.-+. +|+|+...++.
T Consensus 149 ~~~~~~l~eee~e~~~~~~~sq~~lqq~~l~~ee 182 (283)
T COG5325 149 NNDQHPLEEEEDEESLSSLGSQQTLQQQGLSNEE 182 (283)
T ss_pred ccccCchhhhhhhhhhhccchhhHHHHhhhhhhh
Confidence 46778899999998887 56666554443
No 207
>PF13035 DUF3896: Protein of unknown function (DUF3896)
Probab=21.46 E-value=99 Score=20.60 Aligned_cols=19 Identities=26% Similarity=0.296 Sum_probs=14.1
Q ss_pred CCCHHHHHHHHHHHHhhHH
Q psy5308 24 HLTLEERQIIESVMMRQKQ 42 (137)
Q Consensus 24 ~LteeEr~~Il~VL~R~~~ 42 (137)
+|+++||+.|.--+...+.
T Consensus 29 ~ls~~er~qi~~eidnyey 47 (61)
T PF13035_consen 29 HLSEKEREQIKLEIDNYEY 47 (61)
T ss_pred ccCHHHHHHHHhhhhhHHH
Confidence 6899999988766655544
No 208
>KOG2689|consensus
Probab=21.43 E-value=88 Score=27.02 Aligned_cols=28 Identities=21% Similarity=0.222 Sum_probs=14.2
Q ss_pred HHHHHHHHHHHhhHHHHHHHHHHHHHHH
Q psy5308 28 EERQIIESVMMRQKQEEERELEIMRRKQ 55 (137)
Q Consensus 28 eEr~~Il~VL~R~~~le~~E~~RirkL~ 55 (137)
.|...+.+=-.|.+.+++.+.+||.++.
T Consensus 139 ~e~~~~~qkRrreK~e~~eaRqRV~~~I 166 (290)
T KOG2689|consen 139 DEMRRAAQKRRREKAEDEEARQRVLRQI 166 (290)
T ss_pred HHHHHHHHHHHHHhhhhHHHHHHHHHHH
Confidence 3444444434444545555666766644
No 209
>PF00641 zf-RanBP: Zn-finger in Ran binding protein and others; InterPro: IPR001876 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the zinc finger domain found in RanBP2 proteins. Ran is an evolutionary conserved member of the Ras superfamily that regulates all receptor-mediated transport between the nucleus and the cytoplasm. Ran binding protein 2 (RanBP2) is a 358kDa nucleoporin located on the cytoplasmic side of the nuclear pore complex which plays a role in nuclear protein import []. RanBP2 contains multiple zinc fingers which mediate binding to RanGDP []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9G_A 2EBR_A 2WX0_C 2WX1_C 2WWZ_C 3GJ6_B 2LK0_A 2LK1_A 3GJ5_B 3GJ8_B ....
Probab=21.41 E-value=25 Score=19.46 Aligned_cols=12 Identities=8% Similarity=-0.053 Sum_probs=10.0
Q ss_pred ceEEeeeccCCC
Q psy5308 122 SVEVTTRGHNNN 133 (137)
Q Consensus 122 ~W~Ctvc~~~~~ 133 (137)
.|.|.+|.+.|.
T Consensus 4 ~W~C~~C~~~N~ 15 (30)
T PF00641_consen 4 DWKCPSCTFMNP 15 (30)
T ss_dssp SEEETTTTEEEE
T ss_pred CccCCCCcCCch
Confidence 699999987764
No 210
>PF02148 zf-UBP: Zn-finger in ubiquitin-hydrolases and other protein; InterPro: IPR001607 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 UBP-type zinc finger domains, which display some similarity with the Zn-binding domain of the insulinase family. The UBP-type zinc finger domain is found only in a small subfamily of ubiquitin C-terminal hydrolases (deubiquitinases or UBP) [, ], All members of this subfamily are isopeptidase-T, which are known to cleave isopeptide bonds between ubiquitin moieties. Some of the proteins containing an UBP zinc finger include: Homo sapiens (Human) deubiquitinating enzyme 13 (UBPD) Human deubiquitinating enzyme 5 (UBP5) Dictyostelium discoideum (Slime mold) deubiquitinating enzyme A (UBPA) Saccharomyces cerevisiae (Baker's yeast) deubiquitinating enzyme 8 (UBP8) Yeast deubiquitinating enzyme 14 (UBP14) More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3GV4_A 3PHD_B 3C5K_A 2UZG_A 3IHP_B 2G43_B 2G45_D 2I50_A 3MHH_A 3MHS_A ....
Probab=21.33 E-value=39 Score=21.79 Aligned_cols=12 Identities=17% Similarity=-0.230 Sum_probs=8.6
Q ss_pred CcceEEeeeccC
Q psy5308 120 KVSVEVTTRGHN 131 (137)
Q Consensus 120 ~~~W~Ctvc~~~ 131 (137)
+.+|+|-+|++-
T Consensus 9 ~~lw~CL~Cg~~ 20 (63)
T PF02148_consen 9 SNLWLCLTCGYV 20 (63)
T ss_dssp SSEEEETTTS-E
T ss_pred CceEEeCCCCcc
Confidence 358999998864
No 211
>KOG1819|consensus
Probab=21.12 E-value=26 Score=33.09 Aligned_cols=33 Identities=24% Similarity=0.497 Sum_probs=28.1
Q ss_pred cccccccccccccCCCCCCCccccccccccCCc
Q psy5308 80 DATCHICLKTKFADGVGHMCNYCNIRCCARCGG 112 (137)
Q Consensus 80 ~~~C~~C~ktkf~~g~G~~C~~C~~rvC~rCg~ 112 (137)
...|.-|+-++-++-+-|.|..|-.-||..|.-
T Consensus 901 a~~cmacq~pf~afrrrhhcrncggifcg~cs~ 933 (990)
T KOG1819|consen 901 AEQCMACQMPFNAFRRRHHCRNCGGIFCGKCSC 933 (990)
T ss_pred chhhhhccCcHHHHHHhhhhcccCceeeccccc
Confidence 578999997766667999999999999999963
No 212
>PRK06835 DNA replication protein DnaC; Validated
Probab=21.11 E-value=3e+02 Score=23.51 Aligned_cols=15 Identities=40% Similarity=0.787 Sum_probs=11.9
Q ss_pred cccccccccccccCC
Q psy5308 80 DATCHICLKTKFADG 94 (137)
Q Consensus 80 ~~~C~~C~ktkf~~g 94 (137)
.-.|..|+-|.|++|
T Consensus 98 ~y~Cp~C~dtG~i~~ 112 (329)
T PRK06835 98 KYTCPKCKDTGFING 112 (329)
T ss_pred CCCCCCCCCCCCcCC
Confidence 356999999988853
No 213
>PRK00420 hypothetical protein; Validated
Probab=21.11 E-value=92 Score=23.11 Aligned_cols=28 Identities=21% Similarity=0.376 Sum_probs=18.7
Q ss_pred cccccccccccccCCCCCCCccccccccccCCcee
Q psy5308 80 DATCHICLKTKFADGVGHMCNYCNIRCCARCGGKV 114 (137)
Q Consensus 80 ~~~C~~C~ktkf~~g~G~~C~~C~~rvC~rCg~~v 114 (137)
..+|..|+-++|-+..|. .+|..||..+
T Consensus 23 ~~~CP~Cg~pLf~lk~g~-------~~Cp~Cg~~~ 50 (112)
T PRK00420 23 SKHCPVCGLPLFELKDGE-------VVCPVHGKVY 50 (112)
T ss_pred cCCCCCCCCcceecCCCc-------eECCCCCCee
Confidence 588999997777743332 4666676544
No 214
>KOG2177|consensus
Probab=21.10 E-value=27 Score=26.28 Aligned_cols=30 Identities=30% Similarity=0.682 Sum_probs=22.4
Q ss_pred cccccccccccccCCCCCCCccccccccccCCce
Q psy5308 80 DATCHICLKTKFADGVGHMCNYCNIRCCARCGGK 113 (137)
Q Consensus 80 ~~~C~~C~ktkf~~g~G~~C~~C~~rvC~rCg~~ 113 (137)
.-+|.||. ..|.+. .--.|.|.||..|-..
T Consensus 13 ~~~C~iC~-~~~~~p---~~l~C~H~~c~~C~~~ 42 (386)
T KOG2177|consen 13 ELTCPICL-EYFREP---VLLPCGHNFCRACLTR 42 (386)
T ss_pred cccChhhH-HHhhcC---ccccccchHhHHHHHH
Confidence 68899998 445544 6777889999999533
No 215
>KOG4538|consensus
Probab=21.09 E-value=3.8e+02 Score=20.41 Aligned_cols=34 Identities=24% Similarity=0.337 Sum_probs=16.5
Q ss_pred HHHHHHHHHHhhHHHHHH-HHHHHHHHHHHHHHHHHHH
Q psy5308 29 ERQIIESVMMRQKQEEER-ELEIMRRKQDEVHLLEQSI 65 (137)
Q Consensus 29 Er~~Il~VL~R~~~le~~-E~~RirkL~~el~~lk~~~ 65 (137)
|+..|-.| +..++++ +++|..+-+-.++++++++
T Consensus 56 e~~~vK~~---~~~i~ek~~~~rqeKkqRrvEn~kRRL 90 (130)
T KOG4538|consen 56 EKDMVKRV---QDNIREKQVQERQEKKQRRVENEKRRL 90 (130)
T ss_pred HHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 44444444 4444433 5555555555555555544
No 216
>COG1579 Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only]
Probab=21.07 E-value=3.9e+02 Score=22.33 Aligned_cols=30 Identities=17% Similarity=0.185 Sum_probs=13.5
Q ss_pred HHHHHHhhHHHHHH---HHHHHHHHHHHHHHHH
Q psy5308 33 IESVMMRQKQEEER---ELEIMRRKQDEVHLLE 62 (137)
Q Consensus 33 Il~VL~R~~~le~~---E~~RirkL~~el~~lk 62 (137)
|..|+.+.+.+++. ...++.++.+.|.+++
T Consensus 112 l~~l~~~~~~l~~~i~~l~~~~~~~e~~~~e~~ 144 (239)
T COG1579 112 LAELMEEIEKLEKEIEDLKERLERLEKNLAEAE 144 (239)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 44455555544433 2244444544444433
No 217
>COG0333 RpmF Ribosomal protein L32 [Translation, ribosomal structure and biogenesis]
Probab=21.00 E-value=52 Score=21.79 Aligned_cols=23 Identities=30% Similarity=0.639 Sum_probs=16.9
Q ss_pred cccccccccccccCCCCCCCccccccccccCCce
Q psy5308 80 DATCHICLKTKFADGVGHMCNYCNIRCCARCGGK 113 (137)
Q Consensus 80 ~~~C~~C~ktkf~~g~G~~C~~C~~rvC~rCg~~ 113 (137)
-..|..|++.++. |+||..||.+
T Consensus 27 ~~~c~~cG~~~l~-----------Hrvc~~cg~Y 49 (57)
T COG0333 27 LSVCPNCGEYKLP-----------HRVCLKCGYY 49 (57)
T ss_pred ceeccCCCCcccC-----------ceEcCCCCCc
Confidence 4668888877665 5888888855
No 218
>PF11471 Sugarporin_N: Maltoporin periplasmic N-terminal extension; InterPro: IPR021570 This N-terminal domain is found in members of the sugar porin family 1.B.3 from TC, They are related to LamB - the well characterised maltoporin of Escherichia coli for which the three-dimensional structures with and without its substrate have been obtained by X-ray diffraction. The protein consists of an 18 beta-stranded beta-barrel in contrast to proteins of the general bacterial porin family (GBP) and the Rhodobacter PorCa Porin (RPP) family which consist of 16 beta-stranded beta-barrels. Although maltoporin contains a wider beta-barrel than the porins of the GBP and RPP families (1.B.1 from TC and 1.B.7 from TC), it exhibits a narrower channel, showing only 5% of the ionic conductance of the latter porins.
Probab=20.94 E-value=2.2e+02 Score=18.69 Aligned_cols=11 Identities=36% Similarity=0.371 Sum_probs=5.4
Q ss_pred CCCHHHHHHHH
Q psy5308 24 HLTLEERQIIE 34 (137)
Q Consensus 24 ~LteeEr~~Il 34 (137)
.||-|+|=..|
T Consensus 27 ~ltiEqRLa~L 37 (60)
T PF11471_consen 27 PLTIEQRLAAL 37 (60)
T ss_pred cCCHHHHHHHH
Confidence 45655554433
No 219
>PF08776 VASP_tetra: VASP tetramerisation domain; InterPro: IPR014885 Vasodilator-stimulated phosphoprotein (VASP) is an actin cytoskeletal regulatory protein. This region corresponds to the tetramerisation domain which forms a right handed alpha helical coiled coil structure []. ; PDB: 1USE_A 1USD_A.
Probab=20.92 E-value=2.2e+02 Score=17.65 Aligned_cols=18 Identities=22% Similarity=0.316 Sum_probs=8.6
Q ss_pred HHHHHHHHHHHHHHHHHH
Q psy5308 41 KQEEERELEIMRRKQDEV 58 (137)
Q Consensus 41 ~~le~~E~~RirkL~~el 58 (137)
+++.+..++.|.-+.++|
T Consensus 18 kEl~K~K~EIIeA~~~eL 35 (40)
T PF08776_consen 18 KELQKVKEEIIEAIRQEL 35 (40)
T ss_dssp HHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHH
Confidence 444444445554444444
No 220
>PF07975 C1_4: TFIIH C1-like domain; InterPro: IPR004595 All proteins in this domain for which functions are known are components of the TFIIH complex which is involved in the initiation of transcription and nucleotide excision repair. It includes the yeast transcription factor Ssl1 (Suppressor of stem-loop protein 1) that is essential for translation initiation and affects UV resistance. The C-terminal region is essential for transcription activity. This regions binds three zinc atoms through two independent domain. The first contains a C4 zinc finger motif, whereas the second is characterised by a CX(2)CX(2-4)FCADCD motif. The solution structure of the second C-terminal domain revealed homology with the regulatory domain of protein kinase C [].; GO: 0006281 DNA repair, 0005634 nucleus; PDB: 1Z60_A.
Probab=20.91 E-value=11 Score=24.46 Aligned_cols=20 Identities=20% Similarity=0.507 Sum_probs=10.9
Q ss_pred CCCCCccccccccccCCcee
Q psy5308 95 VGHMCNYCNIRCCARCGGKV 114 (137)
Q Consensus 95 ~G~~C~~C~~rvC~rCg~~v 114 (137)
..-.|..|+..||-.|-+++
T Consensus 20 ~~y~C~~C~~~FC~dCD~fi 39 (51)
T PF07975_consen 20 SRYRCPKCKNHFCIDCDVFI 39 (51)
T ss_dssp EEE--TTTT--B-HHHHHTT
T ss_pred CeEECCCCCCccccCcChhh
Confidence 34678888888888887664
No 221
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=20.90 E-value=39 Score=25.91 Aligned_cols=25 Identities=20% Similarity=0.477 Sum_probs=16.9
Q ss_pred cccccccccccccCCCCCCCccccc
Q psy5308 80 DATCHICLKTKFADGVGHMCNYCNI 104 (137)
Q Consensus 80 ~~~C~~C~ktkf~~g~G~~C~~C~~ 104 (137)
+.+|..|+-++|--+--.+|..|.+
T Consensus 28 ~~hCp~Cg~PLF~KdG~v~CPvC~~ 52 (131)
T COG1645 28 AKHCPKCGTPLFRKDGEVFCPVCGY 52 (131)
T ss_pred HhhCcccCCcceeeCCeEECCCCCc
Confidence 6789999988888433344555543
No 222
>KOG2807|consensus
Probab=20.88 E-value=36 Score=30.17 Aligned_cols=46 Identities=15% Similarity=0.324 Sum_probs=32.6
Q ss_pred cccccccccccccCCCCCCCccccccccccCCceeecCCCCcceEEeeecc
Q psy5308 80 DATCHICLKTKFADGVGHMCNYCNIRCCARCGGKVTLRSNKVSVEVTTRGH 130 (137)
Q Consensus 80 ~~~C~~C~ktkf~~g~G~~C~~C~~rvC~rCg~~v~lr~n~~~W~Ctvc~~ 130 (137)
.+.|--|+.+ ..++.+-.|..|+..||..|-+.+. ...-.|--|-|
T Consensus 330 ~~~Cf~C~~~-~~~~~~y~C~~Ck~~FCldCDv~iH----esLh~CpgCeh 375 (378)
T KOG2807|consen 330 SRFCFACQGE-LLSSGRYRCESCKNVFCLDCDVFIH----ESLHNCPGCEH 375 (378)
T ss_pred Ccceeeeccc-cCCCCcEEchhccceeeccchHHHH----hhhhcCCCcCC
Confidence 4569999644 4456788999999999999987752 23445555543
No 223
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=20.87 E-value=55 Score=24.40 Aligned_cols=34 Identities=24% Similarity=0.536 Sum_probs=25.7
Q ss_pred cccccccccccccC-----------CCCCCCccccccccccCCcee
Q psy5308 80 DATCHICLKTKFAD-----------GVGHMCNYCNIRCCARCGGKV 114 (137)
Q Consensus 80 ~~~C~~C~ktkf~~-----------g~G~~C~~C~~rvC~rCg~~v 114 (137)
...|--|++. |.. ...-.|..|+..||..|-+++
T Consensus 55 ~~~C~~C~~~-f~~~~~~~~~~~~~~~~y~C~~C~~~FC~dCD~fi 99 (112)
T TIGR00622 55 SRFCFGCQGP-FPKPPVSPFDELKDSHRYVCAVCKNVFCVDCDVFV 99 (112)
T ss_pred CCcccCcCCC-CCCcccccccccccccceeCCCCCCccccccchhh
Confidence 3569999965 332 234569999999999998876
No 224
>COG5347 GTPase-activating protein that regulates ARFs (ADP-ribosylation factors), involved in ARF-mediated vesicular transport [Intracellular trafficking and secretion]
Probab=20.85 E-value=61 Score=28.07 Aligned_cols=10 Identities=20% Similarity=0.521 Sum_probs=5.4
Q ss_pred cccccccccc
Q psy5308 80 DATCHICLKT 89 (137)
Q Consensus 80 ~~~C~~C~kt 89 (137)
...|+-|.-+
T Consensus 20 Nk~CaDCga~ 29 (319)
T COG5347 20 NKKCADCGAP 29 (319)
T ss_pred cCccccCCCC
Confidence 3556666543
No 225
>cd07178 terB_like_YebE tellurium resistance terB-like protein, subgroup 3. This family includes several uncharacterized bacterial proteins including an Escherichia coli protein called YebE. Protein sequence homology analysis shows they are similar to tellurium resistance protein terB, but the function of this family is unknown.
Probab=20.79 E-value=1e+02 Score=21.57 Aligned_cols=18 Identities=22% Similarity=0.211 Sum_probs=15.6
Q ss_pred CCCCHHHHHHHHHHHHhh
Q psy5308 23 SHLTLEERQIIESVMMRQ 40 (137)
Q Consensus 23 S~LteeEr~~Il~VL~R~ 40 (137)
.|+.++||+.|.+++.+.
T Consensus 14 G~id~~E~~~I~~~~~~~ 31 (95)
T cd07178 14 GHIDEAERARILGELGEA 31 (95)
T ss_pred CCCCHHHHHHHHHHHHHh
Confidence 578999999999999764
No 226
>cd02342 ZZ_UBA_plant Zinc finger, ZZ type. Zinc finger present in plant ubiquitin-associated (UBA) proteins. The ZZ motif coordinates a zinc ion and most likely participates in ligand binding or molecular scaffolding.
Probab=20.72 E-value=58 Score=20.48 Aligned_cols=21 Identities=14% Similarity=0.260 Sum_probs=14.1
Q ss_pred ccccCCceeecCCCCcceEEeeec
Q psy5308 106 CCARCGGKVTLRSNKVSVEVTTRG 129 (137)
Q Consensus 106 vC~rCg~~v~lr~n~~~W~Ctvc~ 129 (137)
.|..||.. .--+.-|+|.+|.
T Consensus 2 ~CDgCg~~---PI~G~RykC~~C~ 22 (43)
T cd02342 2 QCDGCGVL---PITGPRYKSKVKE 22 (43)
T ss_pred CCCCCCCC---cccccceEeCCCC
Confidence 47788854 2224679999975
No 227
>PF12563 Hemolysin_N: Hemolytic toxin N terminal; InterPro: IPR022220 This domain family is found in bacteria, and is approximately 190 amino acids in length. The family is found in association with PF07968 from PFAM, PF00652 from PFAM. This family is a bacterial virulence factor - hemolysin - which forms pores in erythrocytes and causes them to lyse. ; PDB: 1XEZ_A 3O44_I.
Probab=20.70 E-value=58 Score=26.45 Aligned_cols=22 Identities=23% Similarity=0.348 Sum_probs=13.4
Q ss_pred CCCCCCCCHHHHHHHHHHHHhh
Q psy5308 19 IPDLSHLTLEERQIIESVMMRQ 40 (137)
Q Consensus 19 ~~dLS~LteeEr~~Il~VL~R~ 40 (137)
++|||.++++|++..++.+.|+
T Consensus 80 lvDFS~iede~~k~~aq~~~r~ 101 (187)
T PF12563_consen 80 LVDFSQIEDEEEKAQAQAKFRK 101 (187)
T ss_dssp EEE-TT--SHHHHHHHHHHHHH
T ss_pred EEEccccCChHHHHHHHHHHHH
Confidence 7899999988777666655443
No 228
>cd01275 FHIT FHIT (fragile histidine family): FHIT proteins, related to the HIT family carry a motif HxHxH/Qxx (x, is a hydrophobic amino acid), On the basis of sequence, substrate specificity, structure, evolution and mechanism, HIT proteins are classified into three branches: the Hint branch, which consists of adenosine 5' -monophosphoramide hydrolases, the Fhit branch, that consists of diadenosine polyphosphate hydrolases, and the GalT branch consisting of specific nucloside monophosphate transferases. Fhit plays a very important role in the development of tumours. Infact, Fhit deletions are among the earliest and most frequent genetic alterations in the development of tumours.
Probab=20.62 E-value=1.1e+02 Score=21.78 Aligned_cols=23 Identities=26% Similarity=0.244 Sum_probs=19.2
Q ss_pred CCCCCCCCCCHHHHHHHHHHHHh
Q psy5308 17 DIIPDLSHLTLEERQIIESVMMR 39 (137)
Q Consensus 17 ~~~~dLS~LteeEr~~Il~VL~R 39 (137)
....+++.|+++|+..++.++.+
T Consensus 43 ~H~~~~~~L~~~e~~~l~~~~~~ 65 (126)
T cd01275 43 RHVPRLEDLTPEEIADLFKLVQL 65 (126)
T ss_pred cccCChhhCCHHHHHHHHHHHHH
Confidence 35778999999999999988743
No 229
>PF11727 ISG65-75: Invariant surface glycoprotein; InterPro: IPR021057 This family is found in Trypanosome species, and appears to be one of two invariant surface glycoproteins, ISG65 and ISG75, that are found in the mammalian stage of the parasitic protozoan. The sequence suggests the two families are polypeptides with N-terminal signal sequences, hydrophilic extracellular domains, single trans-membrane alpha-helices and short cytoplasmic domains. They are both expressed in the bloodstream form but not in the midgut stage. Both polypeptides are distributed over the entire surface of the parasite [, ].
Probab=20.61 E-value=5e+02 Score=21.56 Aligned_cols=44 Identities=14% Similarity=0.210 Sum_probs=33.3
Q ss_pred CCCCCHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy5308 22 LSHLTLEERQIIESVMMRQKQEEERELEIMRRKQDEVHLLEQSI 65 (137)
Q Consensus 22 LS~LteeEr~~Il~VL~R~~~le~~E~~RirkL~~el~~lk~~~ 65 (137)
.+.||+.+.+.|..++.+.+........++.+......+....+
T Consensus 90 ~~~l~~~~~~kl~~~~~~a~~~~~~~~~~a~~~~~~~~~~~~~a 133 (286)
T PF11727_consen 90 KGKLTDSDVKKLKEICEEAKKKNTEQLEEAKKAMEEAEETHEEA 133 (286)
T ss_pred hcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 78999999999999998888776666666666666665554444
No 230
>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=20.46 E-value=35 Score=16.60 Aligned_cols=10 Identities=10% Similarity=0.139 Sum_probs=5.3
Q ss_pred eEEeeeccCC
Q psy5308 123 VEVTTRGHNN 132 (137)
Q Consensus 123 W~Ctvc~~~~ 132 (137)
|.|.+|+...
T Consensus 1 ~~C~~C~~~~ 10 (24)
T PF13894_consen 1 FQCPICGKSF 10 (24)
T ss_dssp EE-SSTS-EE
T ss_pred CCCcCCCCcC
Confidence 6777776543
No 231
>COG2960 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=20.44 E-value=2.8e+02 Score=20.53 Aligned_cols=39 Identities=13% Similarity=0.197 Sum_probs=28.0
Q ss_pred CCCCCCHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHH
Q psy5308 21 DLSHLTLEERQIIESVMMRQKQEEERELEIMRRKQDEVH 59 (137)
Q Consensus 21 dLS~LteeEr~~Il~VL~R~~~le~~E~~RirkL~~el~ 59 (137)
-|.-.|-||=++-.+||-|..+.-+.=++||..|...|.
T Consensus 52 kLDlVsREEFdvq~qvl~rtR~kl~~Leari~~LEarl~ 90 (103)
T COG2960 52 KLDLVSREEFDVQRQVLLRTREKLAALEARIEELEARLA 90 (103)
T ss_pred hhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 355578888888888888877766666677776666654
No 232
>COG2126 RPL37A Ribosomal protein L37E [Translation, ribosomal structure and biogenesis]
Probab=20.34 E-value=43 Score=22.57 Aligned_cols=35 Identities=20% Similarity=0.429 Sum_probs=21.7
Q ss_pred cccccccccccccCCCCCCCccccccccccCCceeecCCCCcce
Q psy5308 80 DATCHICLKTKFADGVGHMCNYCNIRCCARCGGKVTLRSNKVSV 123 (137)
Q Consensus 80 ~~~C~~C~ktkf~~g~G~~C~~C~~rvC~rCg~~v~lr~n~~~W 123 (137)
.-.|.+|++--|-. ++..|+-||..-+-+--.+.|
T Consensus 16 H~~CRRCGr~syhv---------~k~~CaaCGfgrs~r~R~y~W 50 (61)
T COG2126 16 HIRCRRCGRRSYHV---------RKKYCAACGFGRSARMRSYNW 50 (61)
T ss_pred eehhhhccchheee---------ccceecccCCCCccccccchh
Confidence 56789998665442 568899998652323223556
No 233
>TIGR02161 napC_nirT periplasmic nitrate (or nitrite) reductase c-type cytochrome, NapC/NirT family. Nearly every member of this subfamily is NapC, a predicted membrane-anchored four-heme c-type cytochrome that forms one component of the periplasmic nitrate reductase along with NapA, NapB, NapD, NapE, and NapF subunits. A single known exception at this time is NirT, which is instead a component of a nitrite reductase. This family excludes TorC subunits of trimethylamine N-oxide (TMAO) reductases.
Probab=20.31 E-value=1.1e+02 Score=24.40 Aligned_cols=9 Identities=22% Similarity=0.700 Sum_probs=7.1
Q ss_pred ccccccccc
Q psy5308 80 DATCHICLK 88 (137)
Q Consensus 80 ~~~C~~C~k 88 (137)
.+.|..|+.
T Consensus 135 s~~C~~CH~ 143 (185)
T TIGR02161 135 SLECRNCHN 143 (185)
T ss_pred chhchhhcC
Confidence 567999986
No 234
>PTZ00211 ribonucleoside-diphosphate reductase small subunit; Provisional
Probab=20.23 E-value=1.6e+02 Score=24.92 Aligned_cols=33 Identities=24% Similarity=0.271 Sum_probs=25.2
Q ss_pred CCCCCCCCHHHHHHHHHHHHhhHHHHHHHHHHH
Q psy5308 19 IPDLSHLTLEERQIIESVMMRQKQEEERELEIM 51 (137)
Q Consensus 19 ~~dLS~LteeEr~~Il~VL~R~~~le~~E~~Ri 51 (137)
..|...||+.||..|..+|.-...++..--..+
T Consensus 55 ~~dw~~Lt~~Er~~~~~~l~~~~~~D~~v~~~~ 87 (330)
T PTZ00211 55 LKDWEKLNDGERHFIKHVLAFFAASDGIVLENL 87 (330)
T ss_pred HHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344458999999999999988887777654443
No 235
>cd07176 terB tellurite resistance protein terB. This family contains uncharacterized bacterial proteins involved in tellurium resistance. The prototype of this CD is the Kp-terB protein from Klebsiella pneumoniae, whose 3D structure was recently determined. The biological function of terB and the mechanism responsible for tellurium resistance are unknown.
Probab=20.17 E-value=1.3e+02 Score=20.27 Aligned_cols=21 Identities=19% Similarity=0.126 Sum_probs=15.8
Q ss_pred CCCCHHHHHHHHHHHHhhHHH
Q psy5308 23 SHLTLEERQIIESVMMRQKQE 43 (137)
Q Consensus 23 S~LteeEr~~Il~VL~R~~~l 43 (137)
.+++++|++.|.+.|...-.+
T Consensus 17 G~v~~~E~~~i~~~l~~~~~l 37 (111)
T cd07176 17 GDIDDAELQAIEALLRSLPVL 37 (111)
T ss_pred cCCCHHHHHHHHHHHHcCccc
Confidence 467899999999998754443
No 236
>PTZ00134 40S ribosomal protein S18; Provisional
Probab=20.04 E-value=2.6e+02 Score=21.74 Aligned_cols=22 Identities=23% Similarity=0.280 Sum_probs=18.4
Q ss_pred CCCCCCCCCHHHHHHHHHHHHh
Q psy5308 18 IIPDLSHLTLEERQIIESVMMR 39 (137)
Q Consensus 18 ~~~dLS~LteeEr~~Il~VL~R 39 (137)
+..-+..||++|-+.|..+|..
T Consensus 54 ~~~~~~~Lt~~qi~~l~~~i~~ 75 (154)
T PTZ00134 54 VTKRAGELTAEEIEKIVEIIAN 75 (154)
T ss_pred cCCCcccCCHHHHHHHHHHHhc
Confidence 3455789999999999999964
No 237
>PF09548 Spore_III_AB: Stage III sporulation protein AB (spore_III_AB); InterPro: IPR014198 This entry represents the stage III sporulation protein AB, which is encoded in a spore formation operon: spoIIIAABCDEFGH that is under sigma G regulation []. A comparative genome analysis of all sequenced genomes of Firmicutes shows that the proteins are strictly conserved among the sub-set of endospore-forming species.
Probab=20.03 E-value=4e+02 Score=20.28 Aligned_cols=44 Identities=14% Similarity=0.293 Sum_probs=25.3
Q ss_pred CCCCCCCHHHHHHHHHHHHh----hHHHHHHHHHH-HHHHHHHHHHHHH
Q psy5308 20 PDLSHLTLEERQIIESVMMR----QKQEEERELEI-MRRKQDEVHLLEQ 63 (137)
Q Consensus 20 ~dLS~LteeEr~~Il~VL~R----~~~le~~E~~R-irkL~~el~~lk~ 63 (137)
..-+.|++++++++.++-.- |.+.+.+--+. +..|+.++++.+.
T Consensus 97 ~~~~~L~~~d~e~L~~lg~~LG~~D~~~Q~k~i~l~~~~L~~~~~~a~~ 145 (170)
T PF09548_consen 97 LKESALKKEDKEILLELGKSLGYSDREMQEKHIELYLEQLEQQLEEARE 145 (170)
T ss_pred hhcCCCCHHHHHHHHHHHHHHccCCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 44688999999999886432 23322222222 3455555555554
No 238
>PF01230 HIT: HIT domain; InterPro: IPR001310 The Histidine Triad (HIT) motif, His-x-His-x-His-x-x (x, a hydrophobic amino acid) was identified as being highly conserved in a variety of organisms []. Crystal structure of rabbit Hint, purified as an adenosine and AMP-binding protein, showed that proteins in the HIT superfamily are conserved as nucleotide-binding proteins and that Hint homologues, which are found in all forms of life, are structurally related to Fhit homologues and GalT-related enzymes, which have more restricted phylogenetic profiles []. Hint homologues including rabbit Hint and yeast Hnt1 hydrolyse adenosine 5' monophosphoramide substrates such as AMP-NH2 and AMP-lysine to AMP plus the amine product and function as positive regulators of Cdk7/Kin28 in vivo []. Fhit homologues are diadenosine polyphosphate hydrolases [] and function as tumour suppressors in human and mouse [] though the tumour suppressing function of Fhit does not depend on ApppA hydrolysis []. The third branch of the HIT superfamily, which includes GalT homologues, contains a related His-X-His-X-Gln motif and transfers nucleoside monophosphate moieties to phosphorylated second substrates rather than hydrolysing them [].; PDB: 3LB5_B 1EMS_A 1Y23_A 3ANO_B 1KPE_B 1KPC_A 4EQE_B 1KPA_A 1KPB_B 4EQG_B ....
Probab=20.03 E-value=67 Score=21.74 Aligned_cols=23 Identities=26% Similarity=0.351 Sum_probs=19.3
Q ss_pred CCCCCCCCCCHHHHHHHHHHHHh
Q psy5308 17 DIIPDLSHLTLEERQIIESVMMR 39 (137)
Q Consensus 17 ~~~~dLS~LteeEr~~Il~VL~R 39 (137)
....+|+.|+++|+..++.++++
T Consensus 35 ~H~~~l~dl~~~~~~~l~~~~~~ 57 (98)
T PF01230_consen 35 RHVESLSDLPPEERAELMQLVQK 57 (98)
T ss_dssp STGSSGGGSHHHHHHHHHHHHHH
T ss_pred ccccchhcCCHHHHHHHHHHHHH
Confidence 46788999999999999998744
Done!