Query psy517
Match_columns 138
No_of_seqs 132 out of 1776
Neff 10.7
Searched_HMMs 46136
Date Fri Aug 16 19:08:31 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy517.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/517hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2462|consensus 99.9 1.3E-26 2.9E-31 150.6 4.8 117 16-138 133-249 (279)
2 KOG2462|consensus 99.9 6.6E-24 1.4E-28 138.1 3.3 102 16-126 164-265 (279)
3 KOG3576|consensus 99.7 2.3E-18 5E-23 108.0 -1.9 95 43-138 113-218 (267)
4 KOG1074|consensus 99.6 8.8E-17 1.9E-21 118.0 3.5 58 78-136 608-669 (958)
5 KOG3623|consensus 99.6 1.9E-17 4.1E-22 120.1 -0.7 82 43-125 890-971 (1007)
6 KOG1074|consensus 99.5 1.6E-14 3.5E-19 106.4 3.8 54 78-132 882-935 (958)
7 KOG3576|consensus 99.4 1.3E-14 2.8E-19 91.3 -0.2 107 19-132 123-240 (267)
8 KOG3623|consensus 99.4 4.4E-14 9.6E-19 102.9 1.1 65 73-138 892-956 (1007)
9 KOG3608|consensus 99.4 3E-14 6.5E-19 96.3 -0.3 107 23-137 189-324 (467)
10 KOG3608|consensus 99.2 4.3E-13 9.4E-18 90.8 -2.2 110 19-138 243-358 (467)
11 PHA00733 hypothetical protein 99.2 8.8E-12 1.9E-16 74.9 3.2 84 43-129 36-124 (128)
12 PLN03086 PRLI-interacting fact 99.1 6.1E-11 1.3E-15 86.1 3.8 87 45-138 451-547 (567)
13 PHA02768 hypothetical protein; 99.0 1.3E-10 2.9E-15 58.6 2.3 43 75-120 5-47 (55)
14 PHA02768 hypothetical protein; 98.9 1.8E-10 3.8E-15 58.2 -1.5 43 47-91 5-47 (55)
15 PHA00616 hypothetical protein 98.8 1.5E-09 3.3E-14 52.2 1.3 32 105-136 2-33 (44)
16 PHA00733 hypothetical protein 98.8 8.1E-09 1.8E-13 62.1 3.8 55 44-100 70-124 (128)
17 PF13465 zf-H2C2_2: Zinc-finge 98.7 9.3E-09 2E-13 44.5 2.3 26 90-116 1-26 (26)
18 KOG3993|consensus 98.6 1.3E-09 2.9E-14 75.6 -2.7 84 45-128 265-380 (500)
19 PLN03086 PRLI-interacting fact 98.6 6E-08 1.3E-12 70.9 5.1 59 74-138 452-510 (567)
20 PF13465 zf-H2C2_2: Zinc-finge 98.6 1.8E-08 3.9E-13 43.6 1.1 20 119-138 1-20 (26)
21 PHA00616 hypothetical protein 98.5 1E-07 2.2E-12 45.9 1.7 34 75-109 1-34 (44)
22 PHA00732 hypothetical protein 98.4 3.4E-07 7.4E-12 50.3 2.8 46 47-98 1-47 (79)
23 PF00096 zf-C2H2: Zinc finger, 98.0 3.3E-06 7.1E-11 35.2 1.6 22 105-126 1-22 (23)
24 PHA00732 hypothetical protein 98.0 1.5E-06 3.2E-11 47.8 0.5 47 75-128 1-48 (79)
25 PF05605 zf-Di19: Drought indu 97.9 3.6E-05 7.8E-10 39.3 4.5 52 75-129 2-54 (54)
26 PF00096 zf-C2H2: Zinc finger, 97.8 1.8E-05 3.9E-10 32.9 2.2 23 76-98 1-23 (23)
27 PF13894 zf-C2H2_4: C2H2-type 97.8 2E-05 4.2E-10 32.9 1.9 24 105-128 1-24 (24)
28 PF13912 zf-C2H2_6: C2H2-type 97.6 2.1E-05 4.7E-10 34.0 1.0 24 105-128 2-25 (27)
29 KOG3993|consensus 97.6 2.4E-05 5.3E-10 55.0 1.3 84 11-100 265-381 (500)
30 PF09237 GAGA: GAGA factor; I 97.5 6.3E-05 1.4E-09 37.2 1.3 28 74-101 23-50 (54)
31 PF12756 zf-C2H2_2: C2H2 type 97.4 0.00014 3E-09 41.6 2.5 73 49-128 1-74 (100)
32 PF13912 zf-C2H2_6: C2H2-type 97.4 0.00012 2.6E-09 31.6 1.7 25 75-99 1-25 (27)
33 PF09237 GAGA: GAGA factor; I 97.3 0.00067 1.5E-08 33.6 3.7 35 98-132 18-52 (54)
34 PF13894 zf-C2H2_4: C2H2-type 97.3 0.00036 7.7E-09 28.9 2.3 23 76-98 1-23 (24)
35 COG5189 SFP1 Putative transcri 97.2 6.4E-05 1.4E-09 51.2 -0.2 70 45-125 347-419 (423)
36 smart00355 ZnF_C2H2 zinc finge 97.2 0.00035 7.7E-09 29.4 2.2 23 106-128 2-24 (26)
37 PRK04860 hypothetical protein; 97.2 0.00024 5.3E-09 44.4 2.2 23 116-138 127-149 (160)
38 PF05605 zf-Di19: Drought indu 97.1 0.00093 2E-08 34.0 3.2 33 105-138 3-37 (54)
39 smart00355 ZnF_C2H2 zinc finge 96.8 0.0018 3.8E-08 27.1 2.3 24 76-99 1-24 (26)
40 PRK04860 hypothetical protein; 96.6 0.0014 3E-08 41.0 2.1 38 75-117 119-156 (160)
41 PF13909 zf-H2C2_5: C2H2-type 96.6 0.0013 2.8E-08 27.5 1.2 23 105-128 1-23 (24)
42 PF12874 zf-met: Zinc-finger o 96.3 0.0019 4.1E-08 27.2 0.9 22 105-126 1-22 (25)
43 COG5189 SFP1 Putative transcri 95.9 0.0056 1.2E-07 42.1 1.9 37 101-138 347-404 (423)
44 PF12874 zf-met: Zinc-finger o 95.8 0.0083 1.8E-07 25.1 1.7 23 76-98 1-23 (25)
45 PF13909 zf-H2C2_5: C2H2-type 95.6 0.017 3.8E-07 23.9 2.3 23 76-99 1-23 (24)
46 PF13913 zf-C2HC_2: zinc-finge 95.4 0.016 3.6E-07 24.4 1.8 20 105-125 3-22 (25)
47 PF12171 zf-C2H2_jaz: Zinc-fin 94.5 0.015 3.3E-07 24.9 0.5 19 77-95 3-21 (27)
48 COG5048 FOG: Zn-finger [Genera 93.7 0.015 3.3E-07 41.5 -0.5 57 76-133 290-352 (467)
49 COG5048 FOG: Zn-finger [Genera 93.3 0.058 1.3E-06 38.5 1.9 62 46-108 288-355 (467)
50 KOG1146|consensus 93.1 0.088 1.9E-06 42.9 2.8 76 50-126 439-540 (1406)
51 smart00451 ZnF_U1 U1-like zinc 92.9 0.066 1.4E-06 24.2 1.2 21 105-125 4-24 (35)
52 KOG1146|consensus 92.3 0.069 1.5E-06 43.5 1.3 55 43-97 461-540 (1406)
53 cd00350 rubredoxin_like Rubred 91.8 0.1 2.2E-06 23.5 1.1 9 48-56 2-10 (33)
54 PF09986 DUF2225: Uncharacteri 88.7 0.23 4.9E-06 32.8 1.1 44 45-88 3-61 (214)
55 PRK00464 nrdR transcriptional 88.4 0.38 8.2E-06 30.1 1.9 13 48-60 29-41 (154)
56 COG4049 Uncharacterized protei 88.3 0.21 4.5E-06 25.3 0.6 30 71-100 13-42 (65)
57 KOG2893|consensus 87.5 0.21 4.5E-06 33.3 0.4 45 73-123 9-53 (341)
58 TIGR02605 CxxC_CxxC_SSSS putat 86.9 0.27 5.7E-06 24.5 0.5 12 48-59 6-17 (52)
59 PF09538 FYDLN_acid: Protein o 86.8 0.56 1.2E-05 27.5 1.9 11 105-115 27-37 (108)
60 KOG2186|consensus 86.7 0.52 1.1E-05 31.7 1.9 47 48-97 4-50 (276)
61 PF12756 zf-C2H2_2: C2H2 type 86.6 0.77 1.7E-05 25.8 2.4 25 75-99 50-74 (100)
62 PF09723 Zn-ribbon_8: Zinc rib 85.7 0.26 5.7E-06 23.5 0.1 29 48-83 6-34 (42)
63 PF13719 zinc_ribbon_5: zinc-r 85.5 0.75 1.6E-05 21.3 1.6 34 76-115 3-36 (37)
64 PRK00398 rpoP DNA-directed RNA 85.3 0.55 1.2E-05 22.8 1.2 11 48-58 4-14 (46)
65 smart00834 CxxC_CXXC_SSSS Puta 84.7 0.42 9.1E-06 22.4 0.6 12 48-59 6-17 (41)
66 PHA00626 hypothetical protein 83.8 1.2 2.6E-05 22.6 2.0 12 75-86 23-34 (59)
67 COG1592 Rubrerythrin [Energy p 83.6 0.95 2E-05 28.7 1.9 7 105-111 150-156 (166)
68 TIGR00622 ssl1 transcription f 82.8 1.2 2.6E-05 26.2 2.0 81 45-128 13-105 (112)
69 PF13717 zinc_ribbon_4: zinc-r 82.7 1.2 2.6E-05 20.5 1.6 33 76-114 3-35 (36)
70 TIGR02098 MJ0042_CXXC MJ0042 f 82.6 0.97 2.1E-05 20.8 1.4 14 76-89 3-16 (38)
71 cd00729 rubredoxin_SM Rubredox 81.6 0.89 1.9E-05 20.6 1.0 9 48-56 3-11 (34)
72 COG2888 Predicted Zn-ribbon RN 80.8 0.84 1.8E-05 23.5 0.8 32 75-112 27-58 (61)
73 smart00659 RPOLCX RNA polymera 79.9 1.3 2.9E-05 21.4 1.3 11 48-58 3-13 (44)
74 smart00614 ZnF_BED BED zinc fi 78.4 2.3 4.9E-05 21.0 1.9 21 105-125 19-44 (50)
75 KOG2186|consensus 77.5 0.92 2E-05 30.6 0.4 21 46-67 28-48 (276)
76 COG1997 RPL43A Ribosomal prote 76.8 0.93 2E-05 25.3 0.3 11 105-115 54-64 (89)
77 PRK14890 putative Zn-ribbon RN 74.9 1.8 3.9E-05 22.3 1.0 32 75-112 25-56 (59)
78 TIGR00373 conserved hypothetic 74.6 4.1 9E-05 25.6 2.8 32 73-114 107-138 (158)
79 TIGR02300 FYDLN_acid conserved 74.6 2.2 4.8E-05 25.7 1.5 12 75-86 26-37 (129)
80 smart00734 ZnF_Rad18 Rad18-lik 74.4 3.4 7.4E-05 17.4 1.7 20 105-125 2-21 (26)
81 PF12013 DUF3505: Protein of u 73.9 2.9 6.3E-05 24.3 1.9 25 105-129 81-109 (109)
82 PRK03824 hypA hydrogenase nick 71.9 2.5 5.4E-05 25.8 1.3 15 46-60 69-83 (135)
83 smart00531 TFIIE Transcription 71.8 3.2 6.9E-05 25.7 1.8 37 73-114 97-133 (147)
84 PRK06266 transcription initiat 70.8 4.5 9.7E-05 26.0 2.3 33 73-115 115-147 (178)
85 PF15135 UPF0515: Uncharacteri 70.7 1.9 4.1E-05 29.1 0.6 20 40-59 105-124 (278)
86 PF02892 zf-BED: BED zinc fing 70.0 5.1 0.00011 19.0 2.0 21 105-125 17-41 (45)
87 cd00730 rubredoxin Rubredoxin; 68.0 8.4 0.00018 19.2 2.5 13 48-60 2-14 (50)
88 PF05443 ROS_MUCR: ROS/MUCR tr 66.4 3.6 7.7E-05 25.1 1.2 24 105-131 73-96 (132)
89 PF13453 zf-TFIIB: Transcripti 65.8 7.8 0.00017 18.1 2.1 20 74-93 18-37 (41)
90 COG1773 Rubredoxin [Energy pro 64.3 7.7 0.00017 19.8 2.0 16 47-62 3-18 (55)
91 PF04959 ARS2: Arsenite-resist 62.6 2.2 4.8E-05 28.2 -0.2 24 105-128 78-101 (214)
92 PF03604 DNA_RNApol_7kD: DNA d 62.5 4 8.6E-05 18.3 0.7 7 77-83 19-25 (32)
93 PF10571 UPF0547: Uncharacteri 61.8 5.6 0.00012 16.8 1.0 11 48-58 15-25 (26)
94 PF12760 Zn_Tnp_IS1595: Transp 60.9 3 6.6E-05 20.2 0.1 9 105-113 19-27 (46)
95 PRK04023 DNA polymerase II lar 59.8 16 0.00035 30.1 3.8 11 46-56 625-635 (1121)
96 COG1996 RPC10 DNA-directed RNA 59.6 6.5 0.00014 19.5 1.2 10 76-85 7-16 (49)
97 PRK09678 DNA-binding transcrip 58.8 6.8 0.00015 21.2 1.3 14 75-88 27-42 (72)
98 COG1198 PriA Primosomal protei 58.1 4 8.6E-05 32.2 0.4 9 105-113 476-484 (730)
99 COG3091 SprT Zn-dependent meta 57.6 3.4 7.4E-05 25.7 0.0 29 105-138 118-146 (156)
100 COG3357 Predicted transcriptio 56.1 11 0.00025 21.3 1.9 27 74-111 57-83 (97)
101 KOG4173|consensus 55.8 6.2 0.00013 26.0 0.9 77 48-128 80-170 (253)
102 smart00440 ZnF_C2C2 C2C2 Zinc 55.7 7.8 0.00017 18.2 1.1 10 76-85 29-38 (40)
103 PF07754 DUF1610: Domain of un 55.5 6.1 0.00013 16.4 0.6 8 75-82 16-23 (24)
104 PF14311 DUF4379: Domain of un 55.1 12 0.00026 18.7 1.8 10 105-114 29-38 (55)
105 PF06524 NOA36: NOA36 protein; 54.6 6.2 0.00013 27.0 0.8 81 44-127 139-232 (314)
106 PF12013 DUF3505: Protein of u 54.2 14 0.0003 21.4 2.2 26 75-100 80-109 (109)
107 TIGR00100 hypA hydrogenase nic 53.6 6.5 0.00014 23.3 0.7 11 48-58 71-81 (115)
108 PF08274 PhnA_Zn_Ribbon: PhnA 52.6 7.9 0.00017 17.0 0.8 7 76-82 20-26 (30)
109 PF13824 zf-Mss51: Zinc-finger 52.4 15 0.00034 18.7 1.9 15 73-87 12-26 (55)
110 TIGR01206 lysW lysine biosynth 52.1 14 0.00031 18.7 1.7 10 48-57 3-12 (54)
111 PF00301 Rubredoxin: Rubredoxi 52.0 7.9 0.00017 19.0 0.8 12 48-59 2-13 (47)
112 COG4530 Uncharacterized protei 50.8 9.2 0.0002 22.4 1.0 10 105-114 27-36 (129)
113 smart00154 ZnF_AN1 AN1-like Zi 48.8 13 0.00028 17.3 1.2 15 47-61 12-26 (39)
114 PF10013 DUF2256: Uncharacteri 48.8 15 0.00032 17.6 1.4 11 78-88 11-21 (42)
115 KOG2807|consensus 48.4 35 0.00076 24.3 3.6 22 75-96 290-311 (378)
116 PRK12380 hydrogenase nickel in 47.7 8.7 0.00019 22.7 0.6 9 48-56 71-79 (113)
117 KOG2785|consensus 47.3 22 0.00048 25.8 2.6 22 105-126 69-90 (390)
118 PF13878 zf-C2H2_3: zinc-finge 46.9 24 0.00052 16.6 2.0 24 76-99 14-39 (41)
119 PRK00564 hypA hydrogenase nick 46.3 10 0.00023 22.5 0.8 11 48-58 72-82 (117)
120 PF03811 Zn_Tnp_IS1: InsA N-te 45.8 29 0.00062 15.9 2.1 19 63-81 17-35 (36)
121 PRK14714 DNA polymerase II lar 45.7 32 0.00069 29.2 3.5 8 48-55 668-675 (1337)
122 PF01096 TFIIS_C: Transcriptio 44.8 6.2 0.00013 18.4 -0.2 10 76-85 29-38 (39)
123 KOG4167|consensus 44.6 5.6 0.00012 31.2 -0.6 25 75-99 792-816 (907)
124 KOG4167|consensus 44.0 4.3 9.3E-05 31.8 -1.3 24 105-128 793-816 (907)
125 KOG2593|consensus 43.8 13 0.00027 27.4 1.1 15 45-59 126-140 (436)
126 PF15269 zf-C2H2_7: Zinc-finge 43.4 9.5 0.00021 18.5 0.3 21 76-96 21-41 (54)
127 KOG2593|consensus 42.9 14 0.00029 27.2 1.1 39 70-112 123-161 (436)
128 smart00661 RPOL9 RNA polymeras 42.7 32 0.00069 16.7 2.2 12 75-86 20-31 (52)
129 COG0068 HypF Hydrogenase matur 42.2 15 0.00033 28.9 1.3 56 49-112 125-181 (750)
130 TIGR00595 priA primosomal prot 41.5 36 0.00078 25.8 3.2 10 49-58 215-224 (505)
131 PRK03681 hypA hydrogenase nick 41.4 13 0.00029 21.9 0.8 10 48-57 71-80 (114)
132 PRK03564 formate dehydrogenase 41.2 18 0.00038 25.6 1.4 38 44-84 184-221 (309)
133 COG4957 Predicted transcriptio 40.7 15 0.00033 22.5 0.9 24 75-101 76-99 (148)
134 PRK05978 hypothetical protein; 40.6 27 0.00059 21.8 2.0 31 48-87 34-64 (148)
135 KOG0320|consensus 40.1 18 0.0004 23.3 1.2 51 44-115 128-178 (187)
136 COG3364 Zn-ribbon containing p 39.8 25 0.00054 20.4 1.6 13 47-59 2-14 (112)
137 COG1571 Predicted DNA-binding 39.5 24 0.00051 26.1 1.9 12 105-116 368-379 (421)
138 PF01927 Mut7-C: Mut7-C RNAse 39.4 37 0.00081 20.9 2.6 10 48-57 92-101 (147)
139 PF04810 zf-Sec23_Sec24: Sec23 38.7 27 0.00058 16.3 1.4 12 72-83 21-32 (40)
140 PF07282 OrfB_Zn_ribbon: Putat 38.4 29 0.00062 18.1 1.7 10 75-84 46-55 (69)
141 PF01155 HypA: Hydrogenase exp 38.4 20 0.00043 21.1 1.2 11 76-86 71-81 (113)
142 KOG3408|consensus 38.0 21 0.00045 21.4 1.2 24 74-97 56-79 (129)
143 COG1198 PriA Primosomal protei 38.0 25 0.00054 28.0 1.9 16 69-84 469-484 (730)
144 COG1655 Uncharacterized protei 37.2 17 0.00036 24.5 0.8 28 45-72 17-44 (267)
145 COG5151 SSL1 RNA polymerase II 37.1 3.8 8.2E-05 28.7 -2.2 23 105-127 389-411 (421)
146 TIGR00244 transcriptional regu 37.1 27 0.00059 21.8 1.6 16 48-63 29-44 (147)
147 COG1327 Predicted transcriptio 36.8 28 0.00062 21.8 1.7 14 48-61 29-42 (156)
148 KOG0978|consensus 36.4 20 0.00043 28.3 1.2 21 102-123 677-697 (698)
149 KOG1842|consensus 34.9 20 0.00042 26.6 0.9 23 75-97 15-37 (505)
150 PF14787 zf-CCHC_5: GAG-polypr 34.6 25 0.00054 16.2 0.9 15 105-119 3-17 (36)
151 COG4888 Uncharacterized Zn rib 34.6 24 0.00053 20.4 1.1 39 44-86 19-57 (104)
152 PF01428 zf-AN1: AN1-like Zinc 33.9 15 0.00032 17.4 0.1 13 105-117 14-26 (43)
153 PF08209 Sgf11: Sgf11 (transcr 33.6 53 0.0012 14.7 2.0 23 105-128 5-27 (33)
154 PF02176 zf-TRAF: TRAF-type zi 33.6 11 0.00023 19.0 -0.4 39 75-115 9-53 (60)
155 PF01363 FYVE: FYVE zinc finge 33.6 27 0.00059 18.2 1.1 11 48-58 10-20 (69)
156 PRK05452 anaerobic nitric oxid 33.0 39 0.00084 25.4 2.2 17 44-60 422-438 (479)
157 TIGR00310 ZPR1_znf ZPR1 zinc f 32.6 25 0.00054 23.0 1.0 9 76-84 31-39 (192)
158 PF08271 TF_Zn_Ribbon: TFIIB z 32.5 28 0.00061 16.4 1.0 10 75-84 19-28 (43)
159 PF08790 zf-LYAR: LYAR-type C2 32.3 10 0.00023 16.4 -0.5 9 106-114 2-10 (28)
160 COG4391 Uncharacterized protei 32.1 12 0.00027 19.4 -0.3 45 66-115 15-59 (62)
161 PRK00762 hypA hydrogenase nick 31.7 26 0.00056 21.0 1.0 10 48-58 71-80 (124)
162 PF07295 DUF1451: Protein of u 31.2 17 0.00037 22.6 0.1 30 45-84 110-139 (146)
163 cd00924 Cyt_c_Oxidase_Vb Cytoc 30.9 22 0.00047 20.5 0.5 21 65-86 70-90 (97)
164 PRK00432 30S ribosomal protein 30.8 47 0.001 16.4 1.6 9 76-84 38-46 (50)
165 PLN02294 cytochrome c oxidase 30.6 35 0.00075 21.9 1.4 10 105-114 142-151 (174)
166 smart00064 FYVE Protein presen 29.0 45 0.00097 17.3 1.5 29 48-88 11-39 (68)
167 COG4306 Uncharacterized protei 28.7 19 0.00042 21.7 0.0 17 73-89 66-82 (160)
168 COG2331 Uncharacterized protei 28.4 6.3 0.00014 21.5 -1.8 31 48-85 13-43 (82)
169 PTZ00255 60S ribosomal protein 28.2 44 0.00095 19.0 1.4 10 76-85 55-64 (90)
170 PRK04351 hypothetical protein; 28.2 36 0.00078 21.2 1.2 32 75-115 112-143 (149)
171 KOG2231|consensus 27.7 74 0.0016 25.2 2.9 50 77-128 184-236 (669)
172 PF13451 zf-trcl: Probable zin 27.7 32 0.00068 17.1 0.7 17 73-89 2-18 (49)
173 cd00065 FYVE FYVE domain; Zinc 27.6 53 0.0012 16.2 1.6 11 49-59 4-14 (57)
174 PF05191 ADK_lid: Adenylate ki 27.3 39 0.00085 15.4 0.9 31 76-115 2-32 (36)
175 TIGR00416 sms DNA repair prote 27.2 40 0.00088 25.2 1.5 23 47-83 7-29 (454)
176 TIGR00280 L37a ribosomal prote 27.2 39 0.00084 19.2 1.1 8 48-55 36-43 (91)
177 PF14369 zf-RING_3: zinc-finge 27.0 54 0.0012 14.8 1.4 9 77-85 23-31 (35)
178 PF14353 CpXC: CpXC protein 26.8 31 0.00066 20.6 0.7 23 47-69 38-60 (128)
179 COG5533 UBP5 Ubiquitin C-termi 26.7 8.9 0.00019 27.1 -1.8 13 100-113 281-293 (415)
180 PF04423 Rad50_zn_hook: Rad50 26.6 26 0.00056 17.4 0.3 11 106-116 22-32 (54)
181 PRK11823 DNA repair protein Ra 26.6 42 0.00091 25.0 1.5 24 46-83 6-29 (446)
182 PF10083 DUF2321: Uncharacteri 26.5 1.2E+02 0.0025 19.2 3.1 20 73-92 66-85 (158)
183 PHA02998 RNA polymerase subuni 25.8 44 0.00095 21.6 1.2 10 76-85 172-181 (195)
184 PRK12496 hypothetical protein; 25.4 52 0.0011 20.9 1.5 12 76-87 128-139 (164)
185 PF09845 DUF2072: Zn-ribbon co 24.9 38 0.00083 20.7 0.8 15 75-89 1-15 (131)
186 PRK14892 putative transcriptio 24.9 58 0.0013 18.8 1.5 35 46-87 20-54 (99)
187 PF10263 SprT-like: SprT-like 23.7 37 0.00081 20.9 0.7 31 75-114 123-153 (157)
188 PF09963 DUF2197: Uncharacteri 23.7 40 0.00086 17.3 0.6 36 77-113 4-40 (56)
189 KOG3002|consensus 23.4 91 0.002 22.0 2.5 86 47-137 48-141 (299)
190 PF14803 Nudix_N_2: Nudix N-te 23.2 46 0.00099 15.0 0.7 8 76-83 23-30 (34)
191 TIGR00340 zpr1_rel ZPR1-relate 23.1 49 0.0011 21.0 1.1 11 48-58 29-39 (163)
192 smart00132 LIM Zinc-binding do 23.1 80 0.0017 13.6 1.6 7 77-83 29-35 (39)
193 PF11789 zf-Nse: Zinc-finger o 22.9 1E+02 0.0022 15.7 2.1 30 75-109 24-53 (57)
194 PF07975 C1_4: TFIIH C1-like d 22.8 12 0.00025 18.8 -1.4 26 45-70 19-44 (51)
195 KOG0782|consensus 22.5 15 0.00032 28.3 -1.5 29 90-119 240-268 (1004)
196 COG1594 RPB9 DNA-directed RNA 22.4 51 0.0011 19.5 1.0 10 76-85 101-110 (113)
197 cd02341 ZZ_ZZZ3 Zinc finger, Z 22.3 56 0.0012 16.0 1.0 7 105-111 16-22 (48)
198 cd02335 ZZ_ADA2 Zinc finger, Z 22.3 55 0.0012 15.9 1.0 7 105-111 16-22 (49)
199 KOG2071|consensus 22.1 71 0.0015 24.8 1.9 27 101-128 416-442 (579)
200 KOG2482|consensus 21.6 55 0.0012 23.6 1.2 23 105-127 196-218 (423)
201 COG3809 Uncharacterized protei 21.4 1.1E+02 0.0023 17.0 2.0 42 49-98 3-44 (88)
202 KOG0717|consensus 21.3 49 0.0011 24.9 0.9 19 106-124 294-312 (508)
203 KOG3507|consensus 21.3 55 0.0012 16.9 0.8 11 75-85 37-47 (62)
204 KOG2231|consensus 21.2 58 0.0012 25.7 1.3 79 48-135 183-274 (669)
205 COG2956 Predicted N-acetylgluc 21.2 1E+02 0.0022 22.4 2.4 10 102-111 352-361 (389)
206 KOG2461|consensus 21.2 73 0.0016 23.5 1.8 39 64-102 320-358 (396)
207 PF05502 Dynactin_p62: Dynacti 21.0 59 0.0013 24.6 1.3 10 76-85 53-62 (483)
208 PF06397 Desulfoferrod_N: Desu 20.8 31 0.00068 15.9 -0.1 11 47-57 6-16 (36)
209 PF10276 zf-CHCC: Zinc-finger 20.8 38 0.00083 16.0 0.2 10 105-114 30-39 (40)
210 PF12907 zf-met2: Zinc-binding 20.7 17 0.00037 17.2 -0.9 9 106-114 3-11 (40)
211 PF01286 XPA_N: XPA protein N- 20.6 58 0.0013 14.8 0.8 13 49-61 5-17 (34)
212 PF11672 DUF3268: Protein of u 20.3 1.4E+02 0.003 17.4 2.5 10 47-56 2-11 (102)
213 PRK08222 hydrogenase 4 subunit 20.1 71 0.0015 20.5 1.4 13 105-117 115-127 (181)
214 COG4896 Uncharacterized protei 20.1 41 0.00088 17.5 0.3 39 77-116 4-43 (68)
No 1
>KOG2462|consensus
Probab=99.93 E-value=1.3e-26 Score=150.55 Aligned_cols=117 Identities=21% Similarity=0.309 Sum_probs=105.3
Q ss_pred hcccccccccccccccccccccccCCCCCCCCCCCCCCCCCCcCCCCCcccccccCCCCceeccccccccCChHHHHHHH
Q psy517 16 NHKHQVFSSWKEDINIDDMSHFITSSPSNAKPFHNNNNVDSASEFQGSGTNRRTRSEDARWECPQCGKRYKYSRGLAMHR 95 (138)
Q Consensus 16 ~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~c~~c~~~f~~~~~l~~h~~~h~~~~~~~c~~c~~~~~~~~~l~~h~ 95 (138)
..++++.....++|..|.++| .+-...+.+.|..|++.+.....|.-|+++|. -+++|+.||+.|..+=-|+-|+
T Consensus 133 c~eCgk~ysT~snLsrHkQ~H---~~~~s~ka~~C~~C~K~YvSmpALkMHirTH~--l~c~C~iCGKaFSRPWLLQGHi 207 (279)
T KOG2462|consen 133 CPECGKSYSTSSNLSRHKQTH---RSLDSKKAFSCKYCGKVYVSMPALKMHIRTHT--LPCECGICGKAFSRPWLLQGHI 207 (279)
T ss_pred ccccccccccccccchhhccc---ccccccccccCCCCCceeeehHHHhhHhhccC--CCcccccccccccchHHhhccc
Confidence 344666677778999999998 33345778999999999999999999999998 5799999999999999999999
Q ss_pred HHhcCCCCCccCCCCCccccCccHHHHHHHhhCCCCCCCCCCC
Q psy517 96 RLECGKEPMFHCPYCPQKCHQKGNMVIHIKKKHPEKANPHDEA 138 (138)
Q Consensus 96 ~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~k~~~C~~C 138 (138)
|+|+|+|| |.|..|+|.|.-.++|+.|+++|.+.|.|+|..|
T Consensus 208 RTHTGEKP-F~C~hC~kAFADRSNLRAHmQTHS~~K~~qC~~C 249 (279)
T KOG2462|consen 208 RTHTGEKP-FSCPHCGKAFADRSNLRAHMQTHSDVKKHQCPRC 249 (279)
T ss_pred ccccCCCC-ccCCcccchhcchHHHHHHHHhhcCCccccCcch
Confidence 99999999 9999999999999999999999999999999987
No 2
>KOG2462|consensus
Probab=99.89 E-value=6.6e-24 Score=138.09 Aligned_cols=102 Identities=17% Similarity=0.237 Sum_probs=93.0
Q ss_pred hcccccccccccccccccccccccCCCCCCCCCCCCCCCCCCcCCCCCcccccccCCCCceeccccccccCChHHHHHHH
Q psy517 16 NHKHQVFSSWKEDINIDDMSHFITSSPSNAKPFHNNNNVDSASEFQGSGTNRRTRSEDARWECPQCGKRYKYSRGLAMHR 95 (138)
Q Consensus 16 ~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~c~~c~~~f~~~~~l~~h~~~h~~~~~~~c~~c~~~~~~~~~l~~h~ 95 (138)
...+++.+.....|+.|+++| + .+++|.+|||.|+..=.|+.|+|+|+|+|||.|+.|+++|...++|..|+
T Consensus 164 C~~C~K~YvSmpALkMHirTH------~--l~c~C~iCGKaFSRPWLLQGHiRTHTGEKPF~C~hC~kAFADRSNLRAHm 235 (279)
T KOG2462|consen 164 CKYCGKVYVSMPALKMHIRTH------T--LPCECGICGKAFSRPWLLQGHIRTHTGEKPFSCPHCGKAFADRSNLRAHM 235 (279)
T ss_pred CCCCCceeeehHHHhhHhhcc------C--CCcccccccccccchHHhhcccccccCCCCccCCcccchhcchHHHHHHH
Confidence 344566677777899999999 2 67999999999999999999999999999999999999999999999999
Q ss_pred HHhcCCCCCccCCCCCccccCccHHHHHHHh
Q psy517 96 RLECGKEPMFHCPYCPQKCHQKGNMVIHIKK 126 (138)
Q Consensus 96 ~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~ 126 (138)
.+|.+.|+ |.|..|+|+|...+-|++|...
T Consensus 236 QTHS~~K~-~qC~~C~KsFsl~SyLnKH~ES 265 (279)
T KOG2462|consen 236 QTHSDVKK-HQCPRCGKSFALKSYLNKHSES 265 (279)
T ss_pred HhhcCCcc-ccCcchhhHHHHHHHHHHhhhh
Confidence 99999998 9999999999999999999754
No 3
>KOG3576|consensus
Probab=99.67 E-value=2.3e-18 Score=107.96 Aligned_cols=95 Identities=22% Similarity=0.363 Sum_probs=87.4
Q ss_pred CCCCCCCCCCCCCCCcCCCCCcccccccCCCCceeccccccccCChHHHHHHHHHhcCCCCCccCCCCCccccCccHHHH
Q psy517 43 SNAKPFHNNNNVDSASEFQGSGTNRRTRSEDARWECPQCGKRYKYSRGLAMHRRLECGKEPMFHCPYCPQKCHQKGNMVI 122 (138)
Q Consensus 43 ~~~~~~~c~~c~~~f~~~~~l~~h~~~h~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~C~~C~~~f~~~~~l~~ 122 (138)
++...|.|.+|++.|.....|..|++.|...+.+.|.-||+.|...-+|.+|.|+|+|.+| |.|..|+++|.+.-+|..
T Consensus 113 sd~d~ftCrvCgK~F~lQRmlnrh~kch~~vkr~lct~cgkgfndtfdlkrh~rthtgvrp-ykc~~c~kaftqrcsles 191 (267)
T KOG3576|consen 113 SDQDSFTCRVCGKKFGLQRMLNRHLKCHSDVKRHLCTFCGKGFNDTFDLKRHTRTHTGVRP-YKCSLCEKAFTQRCSLES 191 (267)
T ss_pred CCCCeeeeehhhhhhhHHHHHHHHhhhccHHHHHHHhhccCcccchhhhhhhhccccCccc-cchhhhhHHHHhhccHHH
Confidence 3556799999999999999999999999999999999999999999999999999999999 999999999999999999
Q ss_pred HHHhhCCC-----------CCCCCCCC
Q psy517 123 HIKKKHPE-----------KANPHDEA 138 (138)
Q Consensus 123 H~~~h~~~-----------k~~~C~~C 138 (138)
|++.-+|. |.|.|++|
T Consensus 192 hl~kvhgv~~~yaykerr~kl~vcedc 218 (267)
T KOG3576|consen 192 HLKKVHGVQHQYAYKERRAKLYVCEDC 218 (267)
T ss_pred HHHHHcCchHHHHHHHhhhheeeeccc
Confidence 98876654 56888887
No 4
>KOG1074|consensus
Probab=99.64 E-value=8.8e-17 Score=117.97 Aligned_cols=58 Identities=26% Similarity=0.524 Sum_probs=52.6
Q ss_pred ccccccccCChHHHHHHHHHhcCCCCCccCCCCCccccCccHHHHHHHhhCCC----CCCCCC
Q psy517 78 CPQCGKRYKYSRGLAMHRRLECGKEPMFHCPYCPQKCHQKGNMVIHIKKKHPE----KANPHD 136 (138)
Q Consensus 78 c~~c~~~~~~~~~l~~h~~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~----k~~~C~ 136 (138)
|..|-+...-++.|+.|.|+|+|++| |+|++||+.|..+++|+.|+.+|--. ..+.|+
T Consensus 608 CiiC~rVlSC~saLqmHyrtHtGERP-FkCKiCgRAFtTkGNLkaH~~vHka~p~~R~q~ScP 669 (958)
T KOG1074|consen 608 CIICLRVLSCPSALQMHYRTHTGERP-FKCKICGRAFTTKGNLKAHMSVHKAKPPARVQFSCP 669 (958)
T ss_pred eeeeeecccchhhhhhhhhcccCcCc-cccccccchhccccchhhcccccccCccccccccCC
Confidence 88899999999999999999999999 99999999999999999999888743 347777
No 5
>KOG3623|consensus
Probab=99.64 E-value=1.9e-17 Score=120.07 Aligned_cols=82 Identities=20% Similarity=0.457 Sum_probs=78.3
Q ss_pred CCCCCCCCCCCCCCCcCCCCCcccccccCCCCceeccccccccCChHHHHHHHHHhcCCCCCccCCCCCccccCccHHHH
Q psy517 43 SNAKPFHNNNNVDSASEFQGSGTNRRTRSEDARWECPQCGKRYKYSRGLAMHRRLECGKEPMFHCPYCPQKCHQKGNMVI 122 (138)
Q Consensus 43 ~~~~~~~c~~c~~~f~~~~~l~~h~~~h~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~C~~C~~~f~~~~~l~~ 122 (138)
+.+..|.|..|.|+|...+.|.+|.--|+|.+||+|.+|.++|..+-.|..|.|.|.|++| |.|+.|+|+|+..+++..
T Consensus 890 te~gmyaCDqCDK~FqKqSSLaRHKYEHsGqRPyqC~iCkKAFKHKHHLtEHkRLHSGEKP-fQCdKClKRFSHSGSYSQ 968 (1007)
T KOG3623|consen 890 TEDGMYACDQCDKAFQKQSSLARHKYEHSGQRPYQCIICKKAFKHKHHLTEHKRLHSGEKP-FQCDKCLKRFSHSGSYSQ 968 (1007)
T ss_pred CccccchHHHHHHHHHhhHHHHHhhhhhcCCCCcccchhhHhhhhhhhhhhhhhhccCCCc-chhhhhhhhcccccchHh
Confidence 4567899999999999999999999999999999999999999999999999999999999 999999999999999999
Q ss_pred HHH
Q psy517 123 HIK 125 (138)
Q Consensus 123 H~~ 125 (138)
|+.
T Consensus 969 HMN 971 (1007)
T KOG3623|consen 969 HMN 971 (1007)
T ss_pred hhc
Confidence 873
No 6
>KOG1074|consensus
Probab=99.50 E-value=1.6e-14 Score=106.37 Aligned_cols=54 Identities=30% Similarity=0.733 Sum_probs=44.3
Q ss_pred ccccccccCChHHHHHHHHHhcCCCCCccCCCCCccccCccHHHHHHHhhCCCCC
Q psy517 78 CPQCGKRYKYSRGLAMHRRLECGKEPMFHCPYCPQKCHQKGNMVIHIKKKHPEKA 132 (138)
Q Consensus 78 c~~c~~~~~~~~~l~~h~~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~k~ 132 (138)
|..||+.|.+.+.|..|+++|+|++| |.|..|++.|...++|+.|+.+|+...+
T Consensus 882 C~vCgk~FsSSsALqiH~rTHtg~KP-F~C~fC~~aFttrgnLKvHMgtH~w~q~ 935 (958)
T KOG1074|consen 882 CNVCGKQFSSSAALEIHMRTHTGPKP-FFCHFCEEAFTTRGNLKVHMGTHMWVQP 935 (958)
T ss_pred hccchhcccchHHHHHhhhcCCCCCC-ccchhhhhhhhhhhhhhhhhccccccCC
Confidence 77788888888888888888888888 8888888888888888888888776544
No 7
>KOG3576|consensus
Probab=99.44 E-value=1.3e-14 Score=91.26 Aligned_cols=107 Identities=17% Similarity=0.213 Sum_probs=92.8
Q ss_pred cccccccccccccccccccccCCCCCCCCCCCCCCCCCCcCCCCCcccccccCCCCceeccccccccCChHHHHHHHHHh
Q psy517 19 HQVFSSWKEDINIDDMSHFITSSPSNAKPFHNNNNVDSASEFQGSGTNRRTRSEDARWECPQCGKRYKYSRGLAMHRRLE 98 (138)
Q Consensus 19 ~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~c~~c~~~f~~~~~l~~h~~~h~~~~~~~c~~c~~~~~~~~~l~~h~~~~ 98 (138)
+++.|..-.-|++|++-| +..+.+.|..||+.|....+|+.|.|+|+|.+||.|..|+++|.....|..|.+.-
T Consensus 123 CgK~F~lQRmlnrh~kch------~~vkr~lct~cgkgfndtfdlkrh~rthtgvrpykc~~c~kaftqrcsleshl~kv 196 (267)
T KOG3576|consen 123 CGKKFGLQRMLNRHLKCH------SDVKRHLCTFCGKGFNDTFDLKRHTRTHTGVRPYKCSLCEKAFTQRCSLESHLKKV 196 (267)
T ss_pred hhhhhhHHHHHHHHhhhc------cHHHHHHHhhccCcccchhhhhhhhccccCccccchhhhhHHHHhhccHHHHHHHH
Confidence 455566666689999988 68888999999999999999999999999999999999999999999999998765
Q ss_pred cC-----------CCCCccCCCCCccccCccHHHHHHHhhCCCCC
Q psy517 99 CG-----------KEPMFHCPYCPQKCHQKGNMVIHIKKKHPEKA 132 (138)
Q Consensus 99 ~~-----------~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~k~ 132 (138)
.| .+- |.|..||........+..|+..|+...|
T Consensus 197 hgv~~~yaykerr~kl-~vcedcg~t~~~~e~~~~h~~~~hp~Sp 240 (267)
T KOG3576|consen 197 HGVQHQYAYKERRAKL-YVCEDCGYTSERPEVYYLHLKLHHPFSP 240 (267)
T ss_pred cCchHHHHHHHhhhhe-eeecccCCCCCChhHHHHHHHhcCCCCH
Confidence 44 344 8999999999999999999998886543
No 8
>KOG3623|consensus
Probab=99.41 E-value=4.4e-14 Score=102.95 Aligned_cols=65 Identities=26% Similarity=0.557 Sum_probs=62.5
Q ss_pred CCceeccccccccCChHHHHHHHHHhcCCCCCccCCCCCccccCccHHHHHHHhhCCCCCCCCCCC
Q psy517 73 DARWECPQCGKRYKYSRGLAMHRRLECGKEPMFHCPYCPQKCHQKGNMVIHIKKKHPEKANPHDEA 138 (138)
Q Consensus 73 ~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~k~~~C~~C 138 (138)
.-+|.|+.|++.|...+.|.+|.--|+|.+| |.|.+|.|.|..+-.|..|.|.|.|||||+|..|
T Consensus 892 ~gmyaCDqCDK~FqKqSSLaRHKYEHsGqRP-yqC~iCkKAFKHKHHLtEHkRLHSGEKPfQCdKC 956 (1007)
T KOG3623|consen 892 DGMYACDQCDKAFQKQSSLARHKYEHSGQRP-YQCIICKKAFKHKHHLTEHKRLHSGEKPFQCDKC 956 (1007)
T ss_pred cccchHHHHHHHHHhhHHHHHhhhhhcCCCC-cccchhhHhhhhhhhhhhhhhhccCCCcchhhhh
Confidence 3479999999999999999999999999999 9999999999999999999999999999999987
No 9
>KOG3608|consensus
Probab=99.40 E-value=3e-14 Score=96.27 Aligned_cols=107 Identities=17% Similarity=0.301 Sum_probs=80.7
Q ss_pred cccccccccccccccccCCCCCCCCCCCCCCCCCCcCCCCCccccccc--CCCCce------------------------
Q psy517 23 SSWKEDINIDDMSHFITSSPSNAKPFHNNNNVDSASEFQGSGTNRRTR--SEDARW------------------------ 76 (138)
Q Consensus 23 ~~~~~~l~~~~~~~~~~~~~~~~~~~~c~~c~~~f~~~~~l~~h~~~h--~~~~~~------------------------ 76 (138)
+..++.|..|.++| ++++...|+.||..|.....|-.|.+.. ....+|
T Consensus 189 ~~~k~~LreH~r~H------s~eKvvACp~Cg~~F~~~tkl~DH~rRqt~l~~n~fqC~~C~KrFaTeklL~~Hv~rHvn 262 (467)
T KOG3608|consen 189 MGNKYRLREHIRTH------SNEKVVACPHCGELFRTKTKLFDHLRRQTELNTNSFQCAQCFKRFATEKLLKSHVVRHVN 262 (467)
T ss_pred hccHHHHHHHHHhc------CCCeEEecchHHHHhccccHHHHHHHhhhhhcCCchHHHHHHHHHhHHHHHHHHHHHhhh
Confidence 67788899999999 8999999999999999998888776543 233444
Q ss_pred --eccccccccCChHHHHHHHHH-hcCCCCCccCCCCCccccCccHHHHHHHhhCCCCCCCCCC
Q psy517 77 --ECPQCGKRYKYSRGLAMHRRL-ECGKEPMFHCPYCPQKCHQKGNMVIHIKKKHPEKANPHDE 137 (138)
Q Consensus 77 --~c~~c~~~~~~~~~l~~h~~~-~~~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~k~~~C~~ 137 (138)
+|+.|..+....+.|..|++. |...+| |+|+.|.+++...+.|.+|..+|. +..|+|+.
T Consensus 263 ~ykCplCdmtc~~~ssL~~H~r~rHs~dkp-fKCd~Cd~~c~~esdL~kH~~~HS-~~~y~C~h 324 (467)
T KOG3608|consen 263 CYKCPLCDMTCSSASSLTTHIRYRHSKDKP-FKCDECDTRCVRESDLAKHVQVHS-KTVYQCEH 324 (467)
T ss_pred cccccccccCCCChHHHHHHHHhhhccCCC-ccccchhhhhccHHHHHHHHHhcc-ccceecCC
Confidence 566666666677777777664 445556 888888888888888888888777 66677764
No 10
>KOG3608|consensus
Probab=99.23 E-value=4.3e-13 Score=90.77 Aligned_cols=110 Identities=15% Similarity=0.190 Sum_probs=91.8
Q ss_pred cccccccccccccccccccccCCCCCCCCCCCCCCCCCCcCCCCCcccccc-cCCCCceeccccccccCChHHHHHHHHH
Q psy517 19 HQVFSSWKEDINIDDMSHFITSSPSNAKPFHNNNNVDSASEFQGSGTNRRT-RSEDARWECPQCGKRYKYSRGLAMHRRL 97 (138)
Q Consensus 19 ~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~c~~c~~~f~~~~~l~~h~~~-h~~~~~~~c~~c~~~~~~~~~l~~h~~~ 97 (138)
+.+.|..+--|+.|...|+ .-|+|+.|.......+.|..|++. |+..+||+|+.|...+...+.|..|...
T Consensus 243 C~KrFaTeklL~~Hv~rHv--------n~ykCplCdmtc~~~ssL~~H~r~rHs~dkpfKCd~Cd~~c~~esdL~kH~~~ 314 (467)
T KOG3608|consen 243 CFKRFATEKLLKSHVVRHV--------NCYKCPLCDMTCSSASSLTTHIRYRHSKDKPFKCDECDTRCVRESDLAKHVQV 314 (467)
T ss_pred HHHHHhHHHHHHHHHHHhh--------hcccccccccCCCChHHHHHHHHhhhccCCCccccchhhhhccHHHHHHHHHh
Confidence 3455666667788887763 348999999999999999999885 8889999999999999999999999999
Q ss_pred hcCCCCCccCCC--CCccccCccHHHHHHHhhC-CCC--CCCCCCC
Q psy517 98 ECGKEPMFHCPY--CPQKCHQKGNMVIHIKKKH-PEK--ANPHDEA 138 (138)
Q Consensus 98 ~~~~~~~~~C~~--C~~~f~~~~~l~~H~~~h~-~~k--~~~C~~C 138 (138)
|.. +.|.|.. |..++.+...+.+|.+-++ |.. +|.|-.|
T Consensus 315 HS~--~~y~C~h~~C~~s~r~~~q~~~H~~evhEg~np~~Y~CH~C 358 (467)
T KOG3608|consen 315 HSK--TVYQCEHPDCHYSVRTYTQMRRHFLEVHEGNNPILYACHCC 358 (467)
T ss_pred ccc--cceecCCCCCcHHHHHHHHHHHHHHHhccCCCCCceeeecc
Confidence 983 4499977 9999999999999987766 554 4888765
No 11
>PHA00733 hypothetical protein
Probab=99.22 E-value=8.8e-12 Score=74.87 Aligned_cols=84 Identities=20% Similarity=0.243 Sum_probs=69.8
Q ss_pred CCCCCCCCCCCCCCCcCCCCCccc--c---cccCCCCceeccccccccCChHHHHHHHHHhcCCCCCccCCCCCccccCc
Q psy517 43 SNAKPFHNNNNVDSASEFQGSGTN--R---RTRSEDARWECPQCGKRYKYSRGLAMHRRLECGKEPMFHCPYCPQKCHQK 117 (138)
Q Consensus 43 ~~~~~~~c~~c~~~f~~~~~l~~h--~---~~h~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~C~~C~~~f~~~ 117 (138)
..++++.|.+|...|.....|..+ . ..+.+.+||.|+.||+.|.....|..|++.+. .+ |.|..|++.|...
T Consensus 36 ~~~~~~~~~~~~~~~~~~~~l~~~~~l~~~~~~~~~kPy~C~~Cgk~Fss~s~L~~H~r~h~--~~-~~C~~CgK~F~~~ 112 (128)
T PHA00733 36 PEQKRLIRAVVKTLIYNPQLLDESSYLYKLLTSKAVSPYVCPLCLMPFSSSVSLKQHIRYTE--HS-KVCPVCGKEFRNT 112 (128)
T ss_pred hhhhhHHHHHHhhhccChhhhcchHHHHhhcccCCCCCccCCCCCCcCCCHHHHHHHHhcCC--cC-ccCCCCCCccCCH
Confidence 367889999999988877666654 1 12344789999999999999999999999763 46 9999999999999
Q ss_pred cHHHHHHHhhCC
Q psy517 118 GNMVIHIKKKHP 129 (138)
Q Consensus 118 ~~l~~H~~~h~~ 129 (138)
..|..|+...++
T Consensus 113 ~sL~~H~~~~h~ 124 (128)
T PHA00733 113 DSTLDHVCKKHN 124 (128)
T ss_pred HHHHHHHHHhcC
Confidence 999999988775
No 12
>PLN03086 PRLI-interacting factor K; Provisional
Probab=99.11 E-value=6.1e-11 Score=86.09 Aligned_cols=87 Identities=15% Similarity=0.277 Sum_probs=73.4
Q ss_pred CCCCCCCCCCCCCcCCCCCcccccccCCCCceeccccccccCChHHHHHHHHHhcCCCCCccCCCCCccccC--------
Q psy517 45 AKPFHNNNNVDSASEFQGSGTNRRTRSEDARWECPQCGKRYKYSRGLAMHRRLECGKEPMFHCPYCPQKCHQ-------- 116 (138)
Q Consensus 45 ~~~~~c~~c~~~f~~~~~l~~h~~~h~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~C~~C~~~f~~-------- 116 (138)
++.+.|+.|++.|. ...|..|+.+++ .++.|+ ||..+ ....|..|+.+|.+.++ +.|..|++.+..
T Consensus 451 ~~H~~C~~Cgk~f~-~s~LekH~~~~H--kpv~Cp-Cg~~~-~R~~L~~H~~thCp~Kp-i~C~fC~~~v~~g~~~~d~~ 524 (567)
T PLN03086 451 KNHVHCEKCGQAFQ-QGEMEKHMKVFH--EPLQCP-CGVVL-EKEQMVQHQASTCPLRL-ITCRFCGDMVQAGGSAMDVR 524 (567)
T ss_pred ccCccCCCCCCccc-hHHHHHHHHhcC--CCccCC-CCCCc-chhHHHhhhhccCCCCc-eeCCCCCCccccCccccchh
Confidence 45578999999996 577899988874 789999 99765 56889999999999888 999999998852
Q ss_pred --ccHHHHHHHhhCCCCCCCCCCC
Q psy517 117 --KGNMVIHIKKKHPEKANPHDEA 138 (138)
Q Consensus 117 --~~~l~~H~~~h~~~k~~~C~~C 138 (138)
.+.|..|..+. |.+++.|..|
T Consensus 525 d~~s~Lt~HE~~C-G~rt~~C~~C 547 (567)
T PLN03086 525 DRLRGMSEHESIC-GSRTAPCDSC 547 (567)
T ss_pred hhhhhHHHHHHhc-CCcceEcccc
Confidence 34789999885 9999999887
No 13
>PHA02768 hypothetical protein; Provisional
Probab=99.04 E-value=1.3e-10 Score=58.61 Aligned_cols=43 Identities=23% Similarity=0.545 Sum_probs=36.5
Q ss_pred ceeccccccccCChHHHHHHHHHhcCCCCCccCCCCCccccCccHH
Q psy517 75 RWECPQCGKRYKYSRGLAMHRRLECGKEPMFHCPYCPQKCHQKGNM 120 (138)
Q Consensus 75 ~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~C~~C~~~f~~~~~l 120 (138)
.|.|+.||+.|...++|..|+++|+ ++ +.|..|++.|.+.+.|
T Consensus 5 ~y~C~~CGK~Fs~~~~L~~H~r~H~--k~-~kc~~C~k~f~~~s~l 47 (55)
T PHA02768 5 GYECPICGEIYIKRKSMITHLRKHN--TN-LKLSNCKRISLRTGEY 47 (55)
T ss_pred ccCcchhCCeeccHHHHHHHHHhcC--Cc-ccCCcccceeccccee
Confidence 4789999999999999999999988 46 8899999988877665
No 14
>PHA02768 hypothetical protein; Provisional
Probab=98.85 E-value=1.8e-10 Score=58.18 Aligned_cols=43 Identities=7% Similarity=-0.016 Sum_probs=38.8
Q ss_pred CCCCCCCCCCCcCCCCCcccccccCCCCceeccccccccCChHHH
Q psy517 47 PFHNNNNVDSASEFQGSGTNRRTRSEDARWECPQCGKRYKYSRGL 91 (138)
Q Consensus 47 ~~~c~~c~~~f~~~~~l~~h~~~h~~~~~~~c~~c~~~~~~~~~l 91 (138)
-|.|+.||+.|...+.|..|+++|. +++.|..|++.|...+.|
T Consensus 5 ~y~C~~CGK~Fs~~~~L~~H~r~H~--k~~kc~~C~k~f~~~s~l 47 (55)
T PHA02768 5 GYECPICGEIYIKRKSMITHLRKHN--TNLKLSNCKRISLRTGEY 47 (55)
T ss_pred ccCcchhCCeeccHHHHHHHHHhcC--CcccCCcccceeccccee
Confidence 3899999999999999999999998 689999999999877655
No 15
>PHA00616 hypothetical protein
Probab=98.83 E-value=1.5e-09 Score=52.25 Aligned_cols=32 Identities=16% Similarity=0.390 Sum_probs=23.0
Q ss_pred ccCCCCCccccCccHHHHHHHhhCCCCCCCCC
Q psy517 105 FHCPYCPQKCHQKGNMVIHIKKKHPEKANPHD 136 (138)
Q Consensus 105 ~~C~~C~~~f~~~~~l~~H~~~h~~~k~~~C~ 136 (138)
|.|+.||+.|.+.+.+..|++.|+|++++.|+
T Consensus 2 YqC~~CG~~F~~~s~l~~H~r~~hg~~~~~~~ 33 (44)
T PHA00616 2 YQCLRCGGIFRKKKEVIEHLLSVHKQNKLTLE 33 (44)
T ss_pred CccchhhHHHhhHHHHHHHHHHhcCCCcccee
Confidence 67777777777777777777777777776664
No 16
>PHA00733 hypothetical protein
Probab=98.78 E-value=8.1e-09 Score=62.10 Aligned_cols=55 Identities=16% Similarity=0.213 Sum_probs=49.4
Q ss_pred CCCCCCCCCCCCCCcCCCCCcccccccCCCCceeccccccccCChHHHHHHHHHhcC
Q psy517 44 NAKPFHNNNNVDSASEFQGSGTNRRTRSEDARWECPQCGKRYKYSRGLAMHRRLECG 100 (138)
Q Consensus 44 ~~~~~~c~~c~~~f~~~~~l~~h~~~h~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~ 100 (138)
+.+||.|..|++.|.....|..|++.+ ..++.|+.|++.|.....|..|+....+
T Consensus 70 ~~kPy~C~~Cgk~Fss~s~L~~H~r~h--~~~~~C~~CgK~F~~~~sL~~H~~~~h~ 124 (128)
T PHA00733 70 AVSPYVCPLCLMPFSSSVSLKQHIRYT--EHSKVCPVCGKEFRNTDSTLDHVCKKHN 124 (128)
T ss_pred CCCCccCCCCCCcCCCHHHHHHHHhcC--CcCccCCCCCCccCCHHHHHHHHHHhcC
Confidence 588999999999999999999999876 3579999999999999999999987665
No 17
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=98.74 E-value=9.3e-09 Score=44.53 Aligned_cols=26 Identities=35% Similarity=0.898 Sum_probs=20.8
Q ss_pred HHHHHHHHhcCCCCCccCCCCCccccC
Q psy517 90 GLAMHRRLECGKEPMFHCPYCPQKCHQ 116 (138)
Q Consensus 90 ~l~~h~~~~~~~~~~~~C~~C~~~f~~ 116 (138)
+|..|+++|+|++| |.|+.|++.|.+
T Consensus 1 ~l~~H~~~H~~~k~-~~C~~C~k~F~~ 26 (26)
T PF13465_consen 1 NLRRHMRTHTGEKP-YKCPYCGKSFSN 26 (26)
T ss_dssp HHHHHHHHHSSSSS-EEESSSSEEESS
T ss_pred CHHHHhhhcCCCCC-CCCCCCcCeeCc
Confidence 46788888888888 888888888753
No 18
>KOG3993|consensus
Probab=98.65 E-value=1.3e-09 Score=75.60 Aligned_cols=84 Identities=19% Similarity=0.357 Sum_probs=70.0
Q ss_pred CCCCCCCCCCCCCcCCCCCcccccccCCCCceeccccccccCChHHHHHHHHHhcC--------CC--------------
Q psy517 45 AKPFHNNNNVDSASEFQGSGTNRRTRSEDARWECPQCGKRYKYSRGLAMHRRLECG--------KE-------------- 102 (138)
Q Consensus 45 ~~~~~c~~c~~~f~~~~~l~~h~~~h~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~--------~~-------------- 102 (138)
-..|.|+.|...|.....|.+|.-.......|.|++|++.|.-+.+|..|+|+|.- ..
T Consensus 265 iGdyiCqLCK~kYeD~F~LAQHrC~RIV~vEYrCPEC~KVFsCPANLASHRRWHKPR~eaa~a~~~P~k~~~~~rae~~e 344 (500)
T KOG3993|consen 265 IGDYICQLCKEKYEDAFALAQHRCPRIVHVEYRCPECDKVFSCPANLASHRRWHKPRPEAAKAGSPPPKQAVETRAEVQE 344 (500)
T ss_pred HHHHHHHHHHHhhhhHHHHhhccCCeeEEeeecCCcccccccCchhhhhhhcccCCchhhhhcCCCChhhhhhhhhhhhh
Confidence 34588999999988888899998776666789999999999999999999998731 11
Q ss_pred ----------CCccCCCCCccccCccHHHHHHHhhC
Q psy517 103 ----------PMFHCPYCPQKCHQKGNMVIHIKKKH 128 (138)
Q Consensus 103 ----------~~~~C~~C~~~f~~~~~l~~H~~~h~ 128 (138)
..|.|..|+|.|.....|+.|+.+|+
T Consensus 345 a~rsg~dss~gi~~C~~C~KkFrRqAYLrKHqlthq 380 (500)
T KOG3993|consen 345 AERSGDDSSSGIFSCHTCGKKFRRQAYLRKHQLTHQ 380 (500)
T ss_pred ccccCCcccCceeecHHhhhhhHHHHHHHHhHHhhh
Confidence 13889999999999999999988876
No 19
>PLN03086 PRLI-interacting factor K; Provisional
Probab=98.63 E-value=6e-08 Score=70.87 Aligned_cols=59 Identities=24% Similarity=0.510 Sum_probs=50.9
Q ss_pred CceeccccccccCChHHHHHHHHHhcCCCCCccCCCCCccccCccHHHHHHHhhCCCCCCCCCCC
Q psy517 74 ARWECPQCGKRYKYSRGLAMHRRLECGKEPMFHCPYCPQKCHQKGNMVIHIKKKHPEKANPHDEA 138 (138)
Q Consensus 74 ~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~k~~~C~~C 138 (138)
+++.|+.|+..|. ...|..|+..++ .+ +.|+ |++.+ ....|..|+.+|.+++++.|..|
T Consensus 452 ~H~~C~~Cgk~f~-~s~LekH~~~~H--kp-v~Cp-Cg~~~-~R~~L~~H~~thCp~Kpi~C~fC 510 (567)
T PLN03086 452 NHVHCEKCGQAFQ-QGEMEKHMKVFH--EP-LQCP-CGVVL-EKEQMVQHQASTCPLRLITCRFC 510 (567)
T ss_pred cCccCCCCCCccc-hHHHHHHHHhcC--CC-ccCC-CCCCc-chhHHHhhhhccCCCCceeCCCC
Confidence 4568999999996 577999999975 56 9999 99765 56899999999999999999987
No 20
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=98.59 E-value=1.8e-08 Score=43.63 Aligned_cols=20 Identities=20% Similarity=0.220 Sum_probs=18.8
Q ss_pred HHHHHHHhhCCCCCCCCCCC
Q psy517 119 NMVIHIKKKHPEKANPHDEA 138 (138)
Q Consensus 119 ~l~~H~~~h~~~k~~~C~~C 138 (138)
+|..|+++|+|++||.|+.|
T Consensus 1 ~l~~H~~~H~~~k~~~C~~C 20 (26)
T PF13465_consen 1 NLRRHMRTHTGEKPYKCPYC 20 (26)
T ss_dssp HHHHHHHHHSSSSSEEESSS
T ss_pred CHHHHhhhcCCCCCCCCCCC
Confidence 58899999999999999998
No 21
>PHA00616 hypothetical protein
Probab=98.45 E-value=1e-07 Score=45.94 Aligned_cols=34 Identities=15% Similarity=0.399 Sum_probs=30.4
Q ss_pred ceeccccccccCChHHHHHHHHHhcCCCCCccCCC
Q psy517 75 RWECPQCGKRYKYSRGLAMHRRLECGKEPMFHCPY 109 (138)
Q Consensus 75 ~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~C~~ 109 (138)
||.|+.||+.|...+++..|++.|+|+++ +.|+.
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~~hg~~~-~~~~~ 34 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLSVHKQNK-LTLEY 34 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHHhcCCCc-cceeE
Confidence 58899999999999999999999999888 88764
No 22
>PHA00732 hypothetical protein
Probab=98.37 E-value=3.4e-07 Score=50.34 Aligned_cols=46 Identities=20% Similarity=0.255 Sum_probs=29.3
Q ss_pred CCCCCCCCCCCcCCCCCcccccc-cCCCCceeccccccccCChHHHHHHHHHh
Q psy517 47 PFHNNNNVDSASEFQGSGTNRRT-RSEDARWECPQCGKRYKYSRGLAMHRRLE 98 (138)
Q Consensus 47 ~~~c~~c~~~f~~~~~l~~h~~~-h~~~~~~~c~~c~~~~~~~~~l~~h~~~~ 98 (138)
||.|..|++.|.....|..|++. |. ++.|+.||+.|.. +..|..+.
T Consensus 1 py~C~~Cgk~F~s~s~Lk~H~r~~H~---~~~C~~CgKsF~~---l~~H~~~~ 47 (79)
T PHA00732 1 MFKCPICGFTTVTLFALKQHARRNHT---LTKCPVCNKSYRR---LNQHFYSQ 47 (79)
T ss_pred CccCCCCCCccCCHHHHHHHhhcccC---CCccCCCCCEeCC---hhhhhccc
Confidence 46677777777777777777663 44 2467777777763 45566443
No 23
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=98.03 E-value=3.3e-06 Score=35.24 Aligned_cols=22 Identities=27% Similarity=0.830 Sum_probs=13.1
Q ss_pred ccCCCCCccccCccHHHHHHHh
Q psy517 105 FHCPYCPQKCHQKGNMVIHIKK 126 (138)
Q Consensus 105 ~~C~~C~~~f~~~~~l~~H~~~ 126 (138)
|.|+.|++.|.....|..|++.
T Consensus 1 y~C~~C~~~f~~~~~l~~H~~~ 22 (23)
T PF00096_consen 1 YKCPICGKSFSSKSNLKRHMRR 22 (23)
T ss_dssp EEETTTTEEESSHHHHHHHHHH
T ss_pred CCCCCCCCccCCHHHHHHHHhH
Confidence 3556666666666666666554
No 24
>PHA00732 hypothetical protein
Probab=98.01 E-value=1.5e-06 Score=47.81 Aligned_cols=47 Identities=23% Similarity=0.460 Sum_probs=38.6
Q ss_pred ceeccccccccCChHHHHHHHHH-hcCCCCCccCCCCCccccCccHHHHHHHhhC
Q psy517 75 RWECPQCGKRYKYSRGLAMHRRL-ECGKEPMFHCPYCPQKCHQKGNMVIHIKKKH 128 (138)
Q Consensus 75 ~~~c~~c~~~~~~~~~l~~h~~~-~~~~~~~~~C~~C~~~f~~~~~l~~H~~~h~ 128 (138)
||.|+.||+.|...+.|..|++. |. + +.|+.|++.|. .+..|.++..
T Consensus 1 py~C~~Cgk~F~s~s~Lk~H~r~~H~---~-~~C~~CgKsF~---~l~~H~~~~~ 48 (79)
T PHA00732 1 MFKCPICGFTTVTLFALKQHARRNHT---L-TKCPVCNKSYR---RLNQHFYSQY 48 (79)
T ss_pred CccCCCCCCccCCHHHHHHHhhcccC---C-CccCCCCCEeC---ChhhhhcccC
Confidence 57899999999999999999984 54 3 78999999998 4677875543
No 25
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=97.92 E-value=3.6e-05 Score=39.26 Aligned_cols=52 Identities=25% Similarity=0.561 Sum_probs=35.7
Q ss_pred ceeccccccccCChHHHHHHHHH-hcCCCCCccCCCCCccccCccHHHHHHHhhCC
Q psy517 75 RWECPQCGKRYKYSRGLAMHRRL-ECGKEPMFHCPYCPQKCHQKGNMVIHIKKKHP 129 (138)
Q Consensus 75 ~~~c~~c~~~~~~~~~l~~h~~~-~~~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~ 129 (138)
.|.|+.|++ ..+...|..|... |..+...+.|++|...+. .+|..|+...++
T Consensus 2 ~f~CP~C~~-~~~~~~L~~H~~~~H~~~~~~v~CPiC~~~~~--~~l~~Hl~~~H~ 54 (54)
T PF05605_consen 2 SFTCPYCGK-GFSESSLVEHCEDEHRSESKNVVCPICSSRVT--DNLIRHLNSQHR 54 (54)
T ss_pred CcCCCCCCC-ccCHHHHHHHHHhHCcCCCCCccCCCchhhhh--hHHHHHHHHhcC
Confidence 477888888 4556678888665 444332388999987544 378888887664
No 26
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=97.83 E-value=1.8e-05 Score=32.92 Aligned_cols=23 Identities=35% Similarity=0.816 Sum_probs=20.6
Q ss_pred eeccccccccCChHHHHHHHHHh
Q psy517 76 WECPQCGKRYKYSRGLAMHRRLE 98 (138)
Q Consensus 76 ~~c~~c~~~~~~~~~l~~h~~~~ 98 (138)
|.|+.|++.|...+.|..|++.|
T Consensus 1 y~C~~C~~~f~~~~~l~~H~~~H 23 (23)
T PF00096_consen 1 YKCPICGKSFSSKSNLKRHMRRH 23 (23)
T ss_dssp EEETTTTEEESSHHHHHHHHHHH
T ss_pred CCCCCCCCccCCHHHHHHHHhHC
Confidence 67999999999999999999864
No 27
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=97.78 E-value=2e-05 Score=32.93 Aligned_cols=24 Identities=29% Similarity=0.825 Sum_probs=14.8
Q ss_pred ccCCCCCccccCccHHHHHHHhhC
Q psy517 105 FHCPYCPQKCHQKGNMVIHIKKKH 128 (138)
Q Consensus 105 ~~C~~C~~~f~~~~~l~~H~~~h~ 128 (138)
|.|+.|++.|.....|..|+.+++
T Consensus 1 ~~C~~C~~~~~~~~~l~~H~~~~H 24 (24)
T PF13894_consen 1 FQCPICGKSFRSKSELRQHMRTHH 24 (24)
T ss_dssp EE-SSTS-EESSHHHHHHHHHHHS
T ss_pred CCCcCCCCcCCcHHHHHHHHHhhC
Confidence 456777777777777777766653
No 28
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=97.65 E-value=2.1e-05 Score=34.05 Aligned_cols=24 Identities=17% Similarity=0.394 Sum_probs=16.7
Q ss_pred ccCCCCCccccCccHHHHHHHhhC
Q psy517 105 FHCPYCPQKCHQKGNMVIHIKKKH 128 (138)
Q Consensus 105 ~~C~~C~~~f~~~~~l~~H~~~h~ 128 (138)
|.|..|++.|.....|..|++.|.
T Consensus 2 ~~C~~C~~~F~~~~~l~~H~~~h~ 25 (27)
T PF13912_consen 2 FECDECGKTFSSLSALREHKRSHC 25 (27)
T ss_dssp EEETTTTEEESSHHHHHHHHCTTT
T ss_pred CCCCccCCccCChhHHHHHhHHhc
Confidence 667777777777777777776654
No 29
>KOG3993|consensus
Probab=97.61 E-value=2.4e-05 Score=55.04 Aligned_cols=84 Identities=11% Similarity=0.115 Sum_probs=60.7
Q ss_pred HHHHHhcccccccccccccccccccccccCCCCCCCCCCCCCCCCCCcCCCCCcccccccCC--------C---------
Q psy517 11 VSQFFNHKHQVFSSWKEDINIDDMSHFITSSPSNAKPFHNNNNVDSASEFQGSGTNRRTRSE--------D--------- 73 (138)
Q Consensus 11 ~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~c~~c~~~f~~~~~l~~h~~~h~~--------~--------- 73 (138)
+.+++..-+-..+....-|..|.-..+ --..|+|++|+|.|+--.+|..|.|=|.. .
T Consensus 265 iGdyiCqLCK~kYeD~F~LAQHrC~RI------V~vEYrCPEC~KVFsCPANLASHRRWHKPR~eaa~a~~~P~k~~~~~ 338 (500)
T KOG3993|consen 265 IGDYICQLCKEKYEDAFALAQHRCPRI------VHVEYRCPECDKVFSCPANLASHRRWHKPRPEAAKAGSPPPKQAVET 338 (500)
T ss_pred HHHHHHHHHHHhhhhHHHHhhccCCee------EEeeecCCcccccccCchhhhhhhcccCCchhhhhcCCCChhhhhhh
Confidence 344444444444444555777776553 34469999999999999999999876631 1
Q ss_pred ----------------CceeccccccccCChHHHHHHHHHhcC
Q psy517 74 ----------------ARWECPQCGKRYKYSRGLAMHRRLECG 100 (138)
Q Consensus 74 ----------------~~~~c~~c~~~~~~~~~l~~h~~~~~~ 100 (138)
-.|.|..|++.|....-|..|+.+|..
T Consensus 339 rae~~ea~rsg~dss~gi~~C~~C~KkFrRqAYLrKHqlthq~ 381 (500)
T KOG3993|consen 339 RAEVQEAERSGDDSSSGIFSCHTCGKKFRRQAYLRKHQLTHQR 381 (500)
T ss_pred hhhhhhccccCCcccCceeecHHhhhhhHHHHHHHHhHHhhhc
Confidence 137899999999999999999887653
No 30
>PF09237 GAGA: GAGA factor; InterPro: IPR015318 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Members of this entry bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognises the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognises the A in the fourth position of the consensus sequence []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1YUI_A 1YUJ_A.
Probab=97.46 E-value=6.3e-05 Score=37.17 Aligned_cols=28 Identities=32% Similarity=0.495 Sum_probs=11.3
Q ss_pred CceeccccccccCChHHHHHHHHHhcCC
Q psy517 74 ARWECPQCGKRYKYSRGLAMHRRLECGK 101 (138)
Q Consensus 74 ~~~~c~~c~~~~~~~~~l~~h~~~~~~~ 101 (138)
.|-.|++|+..+....+|.+|+....+.
T Consensus 23 ~PatCP~C~a~~~~srnLrRHle~~H~~ 50 (54)
T PF09237_consen 23 QPATCPICGAVIRQSRNLRRHLEIRHFK 50 (54)
T ss_dssp --EE-TTT--EESSHHHHHHHHHHHTTT
T ss_pred CCCCCCcchhhccchhhHHHHHHHHhcc
Confidence 3445555555555555555555444443
No 31
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=97.41 E-value=0.00014 Score=41.62 Aligned_cols=73 Identities=21% Similarity=0.285 Sum_probs=20.7
Q ss_pred CCCCCCCCCcCCCCCcccccccCC-CCceeccccccccCChHHHHHHHHHhcCCCCCccCCCCCccccCccHHHHHHHhh
Q psy517 49 HNNNNVDSASEFQGSGTNRRTRSE-DARWECPQCGKRYKYSRGLAMHRRLECGKEPMFHCPYCPQKCHQKGNMVIHIKKK 127 (138)
Q Consensus 49 ~c~~c~~~f~~~~~l~~h~~~h~~-~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~h 127 (138)
.|..|+..|.....|..|+....+ ..+ . ...+.....+....+.... .. +.|..|++.|.....|..|++.+
T Consensus 1 ~C~~C~~~f~~~~~l~~H~~~~H~~~~~----~-~~~l~~~~~~~~~~~~~~~-~~-~~C~~C~~~f~s~~~l~~Hm~~~ 73 (100)
T PF12756_consen 1 QCLFCDESFSSVDDLLQHMKKKHGFDIP----D-QKYLVDPNRLLNYLRKKVK-ES-FRCPYCNKTFRSREALQEHMRSK 73 (100)
T ss_dssp ------------------------------------------------------SS-EEBSSSS-EESSHHHHHHHHHHT
T ss_pred Cccccccccccccccccccccccccccc----c-ccccccccccccccccccC-CC-CCCCccCCCCcCHHHHHHHHcCc
Confidence 478899999998888888754332 212 1 1111222333333333322 24 88999999999999999998865
Q ss_pred C
Q psy517 128 H 128 (138)
Q Consensus 128 ~ 128 (138)
.
T Consensus 74 ~ 74 (100)
T PF12756_consen 74 H 74 (100)
T ss_dssp T
T ss_pred c
Confidence 3
No 32
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=97.40 E-value=0.00012 Score=31.61 Aligned_cols=25 Identities=36% Similarity=0.880 Sum_probs=21.4
Q ss_pred ceeccccccccCChHHHHHHHHHhc
Q psy517 75 RWECPQCGKRYKYSRGLAMHRRLEC 99 (138)
Q Consensus 75 ~~~c~~c~~~~~~~~~l~~h~~~~~ 99 (138)
+|.|..|+..|.....|..|++.|.
T Consensus 1 ~~~C~~C~~~F~~~~~l~~H~~~h~ 25 (27)
T PF13912_consen 1 PFECDECGKTFSSLSALREHKRSHC 25 (27)
T ss_dssp SEEETTTTEEESSHHHHHHHHCTTT
T ss_pred CCCCCccCCccCChhHHHHHhHHhc
Confidence 5789999999999999999988764
No 33
>PF09237 GAGA: GAGA factor; InterPro: IPR015318 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Members of this entry bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognises the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognises the A in the fourth position of the consensus sequence []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1YUI_A 1YUJ_A.
Probab=97.28 E-value=0.00067 Score=33.59 Aligned_cols=35 Identities=26% Similarity=0.441 Sum_probs=24.9
Q ss_pred hcCCCCCccCCCCCccccCccHHHHHHHhhCCCCC
Q psy517 98 ECGKEPMFHCPYCPQKCHQKGNMVIHIKKKHPEKA 132 (138)
Q Consensus 98 ~~~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~k~ 132 (138)
+....+|-.|+.|+..+.+..+|.+|+.+.++.||
T Consensus 18 ~~~S~~PatCP~C~a~~~~srnLrRHle~~H~~k~ 52 (54)
T PF09237_consen 18 KSQSEQPATCPICGAVIRQSRNLRRHLEIRHFKKP 52 (54)
T ss_dssp CCTTS--EE-TTT--EESSHHHHHHHHHHHTTTS-
T ss_pred hhccCCCCCCCcchhhccchhhHHHHHHHHhcccC
Confidence 33333349999999999999999999999999887
No 34
>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=97.25 E-value=0.00036 Score=28.88 Aligned_cols=23 Identities=35% Similarity=0.856 Sum_probs=18.5
Q ss_pred eeccccccccCChHHHHHHHHHh
Q psy517 76 WECPQCGKRYKYSRGLAMHRRLE 98 (138)
Q Consensus 76 ~~c~~c~~~~~~~~~l~~h~~~~ 98 (138)
|.|+.|+..|.....|..|+..+
T Consensus 1 ~~C~~C~~~~~~~~~l~~H~~~~ 23 (24)
T PF13894_consen 1 FQCPICGKSFRSKSELRQHMRTH 23 (24)
T ss_dssp EE-SSTS-EESSHHHHHHHHHHH
T ss_pred CCCcCCCCcCCcHHHHHHHHHhh
Confidence 57999999999999999998875
No 35
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=97.23 E-value=6.4e-05 Score=51.20 Aligned_cols=70 Identities=14% Similarity=0.257 Sum_probs=43.4
Q ss_pred CCCCCCCC--CCCCCcCCCCCcccccc-cCCCCceeccccccccCChHHHHHHHHHhcCCCCCccCCCCCccccCccHHH
Q psy517 45 AKPFHNNN--NVDSASEFQGSGTNRRT-RSEDARWECPQCGKRYKYSRGLAMHRRLECGKEPMFHCPYCPQKCHQKGNMV 121 (138)
Q Consensus 45 ~~~~~c~~--c~~~f~~~~~l~~h~~~-h~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~C~~C~~~f~~~~~l~ 121 (138)
++||+|++ |.|.+.....|+.|+.- |-..+...-+ + -..+..+....+| |.|..|+|.+.....|+
T Consensus 347 ~KpykCpV~gC~K~YknqnGLKYH~lhGH~~~~~~~~p---------~-p~~~~~F~~~~KP-YrCevC~KRYKNlNGLK 415 (423)
T COG5189 347 GKPYKCPVEGCNKKYKNQNGLKYHMLHGHQNQKLHENP---------S-PEKMNIFSAKDKP-YRCEVCDKRYKNLNGLK 415 (423)
T ss_pred CceecCCCCCchhhhccccchhhhhhccccCcccCCCC---------C-ccccccccccCCc-eeccccchhhccCccce
Confidence 47888876 88888888888877642 2222211111 0 1112222345577 99999999999888887
Q ss_pred HHHH
Q psy517 122 IHIK 125 (138)
Q Consensus 122 ~H~~ 125 (138)
-|..
T Consensus 416 YHr~ 419 (423)
T COG5189 416 YHRK 419 (423)
T ss_pred eccc
Confidence 6653
No 36
>smart00355 ZnF_C2H2 zinc finger.
Probab=97.22 E-value=0.00035 Score=29.37 Aligned_cols=23 Identities=22% Similarity=0.573 Sum_probs=14.0
Q ss_pred cCCCCCccccCccHHHHHHHhhC
Q psy517 106 HCPYCPQKCHQKGNMVIHIKKKH 128 (138)
Q Consensus 106 ~C~~C~~~f~~~~~l~~H~~~h~ 128 (138)
.|..|++.|.....|..|++.|.
T Consensus 2 ~C~~C~~~f~~~~~l~~H~~~H~ 24 (26)
T smart00355 2 RCPECGKVFKSKSALKEHMRTHX 24 (26)
T ss_pred CCCCCcchhCCHHHHHHHHHHhc
Confidence 46666666666666666665443
No 37
>PRK04860 hypothetical protein; Provisional
Probab=97.22 E-value=0.00024 Score=44.40 Aligned_cols=23 Identities=9% Similarity=-0.029 Sum_probs=11.1
Q ss_pred CccHHHHHHHhhCCCCCCCCCCC
Q psy517 116 QKGNMVIHIKKKHPEKANPHDEA 138 (138)
Q Consensus 116 ~~~~l~~H~~~h~~~k~~~C~~C 138 (138)
...++.+|.++++|+++|.|..|
T Consensus 127 ~~~~~rrH~ri~~g~~~YrC~~C 149 (160)
T PRK04860 127 HQLTVRRHNRVVRGEAVYRCRRC 149 (160)
T ss_pred eeCHHHHHHHHhcCCccEECCCC
Confidence 33344455555555555555444
No 38
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=97.07 E-value=0.00093 Score=34.00 Aligned_cols=33 Identities=30% Similarity=0.619 Sum_probs=26.2
Q ss_pred ccCCCCCccccCccHHHHHHHhhCC-C-CCCCCCCC
Q psy517 105 FHCPYCPQKCHQKGNMVIHIKKKHP-E-KANPHDEA 138 (138)
Q Consensus 105 ~~C~~C~~~f~~~~~l~~H~~~h~~-~-k~~~C~~C 138 (138)
|.|+.|++. .....|..|....+. + +.+.|++|
T Consensus 3 f~CP~C~~~-~~~~~L~~H~~~~H~~~~~~v~CPiC 37 (54)
T PF05605_consen 3 FTCPYCGKG-FSESSLVEHCEDEHRSESKNVVCPIC 37 (54)
T ss_pred cCCCCCCCc-cCHHHHHHHHHhHCcCCCCCccCCCc
Confidence 899999995 556789999776553 3 57999998
No 39
>smart00355 ZnF_C2H2 zinc finger.
Probab=96.76 E-value=0.0018 Score=27.10 Aligned_cols=24 Identities=38% Similarity=0.845 Sum_probs=19.5
Q ss_pred eeccccccccCChHHHHHHHHHhc
Q psy517 76 WECPQCGKRYKYSRGLAMHRRLEC 99 (138)
Q Consensus 76 ~~c~~c~~~~~~~~~l~~h~~~~~ 99 (138)
+.|+.|++.|.....+..|++.|.
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~~H~ 24 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMRTHX 24 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHHHhc
Confidence 468888899988888888888654
No 40
>PRK04860 hypothetical protein; Provisional
Probab=96.64 E-value=0.0014 Score=41.03 Aligned_cols=38 Identities=21% Similarity=0.513 Sum_probs=32.0
Q ss_pred ceeccccccccCChHHHHHHHHHhcCCCCCccCCCCCccccCc
Q psy517 75 RWECPQCGKRYKYSRGLAMHRRLECGKEPMFHCPYCPQKCHQK 117 (138)
Q Consensus 75 ~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~C~~C~~~f~~~ 117 (138)
+|.|. |+. ....+..|.+++.++++ |.|..|+..|...
T Consensus 119 ~Y~C~-C~~---~~~~~rrH~ri~~g~~~-YrC~~C~~~l~~~ 156 (160)
T PRK04860 119 PYRCK-CQE---HQLTVRRHNRVVRGEAV-YRCRRCGETLVFK 156 (160)
T ss_pred EEEcC-CCC---eeCHHHHHHHHhcCCcc-EECCCCCceeEEe
Confidence 68998 987 55667899999999988 9999999887654
No 41
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=96.57 E-value=0.0013 Score=27.45 Aligned_cols=23 Identities=35% Similarity=0.863 Sum_probs=12.0
Q ss_pred ccCCCCCccccCccHHHHHHHhhC
Q psy517 105 FHCPYCPQKCHQKGNMVIHIKKKH 128 (138)
Q Consensus 105 ~~C~~C~~~f~~~~~l~~H~~~h~ 128 (138)
|.|+.|..... ...|..|++.++
T Consensus 1 y~C~~C~y~t~-~~~l~~H~~~~H 23 (24)
T PF13909_consen 1 YKCPHCSYSTS-KSNLKRHLKRHH 23 (24)
T ss_dssp EE-SSSS-EES-HHHHHHHHHHHH
T ss_pred CCCCCCCCcCC-HHHHHHHHHhhC
Confidence 45666665555 556666665544
No 42
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=96.32 E-value=0.0019 Score=27.16 Aligned_cols=22 Identities=18% Similarity=0.596 Sum_probs=13.5
Q ss_pred ccCCCCCccccCccHHHHHHHh
Q psy517 105 FHCPYCPQKCHQKGNMVIHIKK 126 (138)
Q Consensus 105 ~~C~~C~~~f~~~~~l~~H~~~ 126 (138)
|.|..|++.|.....+..|++.
T Consensus 1 ~~C~~C~~~f~s~~~~~~H~~s 22 (25)
T PF12874_consen 1 FYCDICNKSFSSENSLRQHLRS 22 (25)
T ss_dssp EEETTTTEEESSHHHHHHHHTT
T ss_pred CCCCCCCCCcCCHHHHHHHHCc
Confidence 3466666666666666666543
No 43
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=95.88 E-value=0.0056 Score=42.11 Aligned_cols=37 Identities=22% Similarity=0.590 Sum_probs=26.6
Q ss_pred CCCCccCCC--CCccccCccHHHHHHHhhC-------------------CCCCCCCCCC
Q psy517 101 KEPMFHCPY--CPQKCHQKGNMVIHIKKKH-------------------PEKANPHDEA 138 (138)
Q Consensus 101 ~~~~~~C~~--C~~~f~~~~~l~~H~~~h~-------------------~~k~~~C~~C 138 (138)
++| |+|++ |.|.+.....|+-|+.-.+ ..|||.|++|
T Consensus 347 ~Kp-ykCpV~gC~K~YknqnGLKYH~lhGH~~~~~~~~p~p~~~~~F~~~~KPYrCevC 404 (423)
T COG5189 347 GKP-YKCPVEGCNKKYKNQNGLKYHMLHGHQNQKLHENPSPEKMNIFSAKDKPYRCEVC 404 (423)
T ss_pred Cce-ecCCCCCchhhhccccchhhhhhccccCcccCCCCCccccccccccCCceecccc
Confidence 366 88865 8888887777777754222 3489999998
No 44
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=95.81 E-value=0.0083 Score=25.08 Aligned_cols=23 Identities=26% Similarity=0.564 Sum_probs=19.7
Q ss_pred eeccccccccCChHHHHHHHHHh
Q psy517 76 WECPQCGKRYKYSRGLAMHRRLE 98 (138)
Q Consensus 76 ~~c~~c~~~~~~~~~l~~h~~~~ 98 (138)
|.|..|+..|.+...+..|++.+
T Consensus 1 ~~C~~C~~~f~s~~~~~~H~~s~ 23 (25)
T PF12874_consen 1 FYCDICNKSFSSENSLRQHLRSK 23 (25)
T ss_dssp EEETTTTEEESSHHHHHHHHTTH
T ss_pred CCCCCCCCCcCCHHHHHHHHCcC
Confidence 57899999999999999998754
No 45
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=95.60 E-value=0.017 Score=23.88 Aligned_cols=23 Identities=22% Similarity=0.566 Sum_probs=17.5
Q ss_pred eeccccccccCChHHHHHHHHHhc
Q psy517 76 WECPQCGKRYKYSRGLAMHRRLEC 99 (138)
Q Consensus 76 ~~c~~c~~~~~~~~~l~~h~~~~~ 99 (138)
|.|+.|+.... ...|..|+..+.
T Consensus 1 y~C~~C~y~t~-~~~l~~H~~~~H 23 (24)
T PF13909_consen 1 YKCPHCSYSTS-KSNLKRHLKRHH 23 (24)
T ss_dssp EE-SSSS-EES-HHHHHHHHHHHH
T ss_pred CCCCCCCCcCC-HHHHHHHHHhhC
Confidence 67999998887 888999988764
No 46
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=95.39 E-value=0.016 Score=24.43 Aligned_cols=20 Identities=30% Similarity=0.617 Sum_probs=12.0
Q ss_pred ccCCCCCccccCccHHHHHHH
Q psy517 105 FHCPYCPQKCHQKGNMVIHIK 125 (138)
Q Consensus 105 ~~C~~C~~~f~~~~~l~~H~~ 125 (138)
..|+.||+.| ....|..|+.
T Consensus 3 ~~C~~CgR~F-~~~~l~~H~~ 22 (25)
T PF13913_consen 3 VPCPICGRKF-NPDRLEKHEK 22 (25)
T ss_pred CcCCCCCCEE-CHHHHHHHHH
Confidence 4566777777 4445666654
No 47
>PF12171 zf-C2H2_jaz: Zinc-finger double-stranded RNA-binding; InterPro: IPR022755 This zinc finger is found in archaea and eukaryotes, and is approximately 30 amino acids in length. The mammalian members of this group occur multiple times along the protein, joined by flexible linkers, and are referred to as JAZ - dsRNA-binding ZF protein - zinc-fingers. The JAZ proteins are expressed in all tissues tested and localise in the nucleus, particularly the nucleolus []. JAZ preferentially binds to double-stranded (ds) RNA or RNA/DNA hybrids rather than DNA. In addition to binding double-stranded RNA, these zinc-fingers are required for nucleolar localisation. This entry represents the multiple-adjacent-C2H2 zinc finger, JAZ. ; PDB: 4DGW_A 1ZR9_A.
Probab=94.45 E-value=0.015 Score=24.89 Aligned_cols=19 Identities=26% Similarity=0.537 Sum_probs=8.9
Q ss_pred eccccccccCChHHHHHHH
Q psy517 77 ECPQCGKRYKYSRGLAMHR 95 (138)
Q Consensus 77 ~c~~c~~~~~~~~~l~~h~ 95 (138)
.|..|++.|.+...+..|+
T Consensus 3 ~C~~C~k~f~~~~~~~~H~ 21 (27)
T PF12171_consen 3 YCDACDKYFSSENQLKQHM 21 (27)
T ss_dssp BBTTTTBBBSSHHHHHCCT
T ss_pred CcccCCCCcCCHHHHHHHH
Confidence 3444444444444444443
No 48
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=93.67 E-value=0.015 Score=41.54 Aligned_cols=57 Identities=25% Similarity=0.465 Sum_probs=28.1
Q ss_pred eeccccccccCChHHHHHHHH--HhcCC--CCCccCC--CCCccccCccHHHHHHHhhCCCCCC
Q psy517 76 WECPQCGKRYKYSRGLAMHRR--LECGK--EPMFHCP--YCPQKCHQKGNMVIHIKKKHPEKAN 133 (138)
Q Consensus 76 ~~c~~c~~~~~~~~~l~~h~~--~~~~~--~~~~~C~--~C~~~f~~~~~l~~H~~~h~~~k~~ 133 (138)
+.|..|...|.....+..|.+ .|.++ ++ +.|+ .|++.|.+...+..|..+|++-.+.
T Consensus 290 ~~~~~~~~~~s~~~~l~~~~~~~~h~~~~~~~-~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~ 352 (467)
T COG5048 290 IKSKQCNISFSRSSPLTRHLRSVNHSGESLKP-FSCPYSLCGKLFSRNDALKRHILLHTSISPA 352 (467)
T ss_pred CCCccccCCccccccccccccccccccccCCc-eeeeccCCCccccccccccCCcccccCCCcc
Confidence 444445555555555555555 44444 44 5554 4555555555555555555544433
No 49
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=93.25 E-value=0.058 Score=38.53 Aligned_cols=62 Identities=23% Similarity=0.308 Sum_probs=53.6
Q ss_pred CCCCCCCCCCCCcCCCCCccccc--ccCCC--Cceecc--ccccccCChHHHHHHHHHhcCCCCCccCC
Q psy517 46 KPFHNNNNVDSASEFQGSGTNRR--TRSED--ARWECP--QCGKRYKYSRGLAMHRRLECGKEPMFHCP 108 (138)
Q Consensus 46 ~~~~c~~c~~~f~~~~~l~~h~~--~h~~~--~~~~c~--~c~~~~~~~~~l~~h~~~~~~~~~~~~C~ 108 (138)
.++.|..|...|.....|..|.+ .|.++ +++.|+ .|+..|.....+..|...|.+..+ +.+.
T Consensus 288 ~~~~~~~~~~~~s~~~~l~~~~~~~~h~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~ 355 (467)
T COG5048 288 LPIKSKQCNISFSRSSPLTRHLRSVNHSGESLKPFSCPYSLCGKLFSRNDALKRHILLHTSISP-AKEK 355 (467)
T ss_pred cCCCCccccCCccccccccccccccccccccCCceeeeccCCCccccccccccCCcccccCCCc-cccc
Confidence 46888899999999999999999 79999 899999 799999999999999999888665 5554
No 50
>KOG1146|consensus
Probab=93.12 E-value=0.088 Score=42.90 Aligned_cols=76 Identities=22% Similarity=0.442 Sum_probs=55.8
Q ss_pred CCCCCCCCcCCCCCccccc-ccCCCCceeccccccccCChHHHHHHHHHh-------------------------cCCCC
Q psy517 50 NNNNVDSASEFQGSGTNRR-TRSEDARWECPQCGKRYKYSRGLAMHRRLE-------------------------CGKEP 103 (138)
Q Consensus 50 c~~c~~~f~~~~~l~~h~~-~h~~~~~~~c~~c~~~~~~~~~l~~h~~~~-------------------------~~~~~ 103 (138)
+.-++..+.+...+..+.+ .++..+.+.|+.|+..+.....|-.|+|.- .+.++
T Consensus 439 ~~~~e~~~~s~r~~~~~t~~L~S~~kt~~cpkc~~~yk~a~~L~vhmRskhp~~~~~~c~~gq~~~~~arg~~~~~~~~p 518 (1406)
T KOG1146|consen 439 LTKAEPLLESKRSLEGQTVVLHSFFKTLKCPKCNWHYKLAQTLGVHMRSKHPESQSAYCKAGQNHPRLARGEVYRCPGKP 518 (1406)
T ss_pred ccchhhhhhhhcccccceeeeecccccccCCccchhhhhHHHhhhcccccccccchhHhHhccccccccccccccCCCCc
Confidence 3345555555555555543 466668899999999999999999999871 11244
Q ss_pred CccCCCCCccccCccHHHHHHHh
Q psy517 104 MFHCPYCPQKCHQKGNMVIHIKK 126 (138)
Q Consensus 104 ~~~C~~C~~~f~~~~~l~~H~~~ 126 (138)
|.|..|..++..+.+|.+|++.
T Consensus 519 -~~C~~C~~stttng~LsihlqS 540 (1406)
T KOG1146|consen 519 -YPCRACNYSTTTNGNLSIHLQS 540 (1406)
T ss_pred -ccceeeeeeeecchHHHHHHHH
Confidence 8888999999999999999763
No 51
>smart00451 ZnF_U1 U1-like zinc finger. Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins.
Probab=92.88 E-value=0.066 Score=24.21 Aligned_cols=21 Identities=24% Similarity=0.528 Sum_probs=16.5
Q ss_pred ccCCCCCccccCccHHHHHHH
Q psy517 105 FHCPYCPQKCHQKGNMVIHIK 125 (138)
Q Consensus 105 ~~C~~C~~~f~~~~~l~~H~~ 125 (138)
|.|..|+..|.....+..|+.
T Consensus 4 ~~C~~C~~~~~~~~~~~~H~~ 24 (35)
T smart00451 4 FYCKLCNVTFTDEISVEAHLK 24 (35)
T ss_pred eEccccCCccCCHHHHHHHHC
Confidence 778888888887777777764
No 52
>KOG1146|consensus
Probab=92.31 E-value=0.069 Score=43.46 Aligned_cols=55 Identities=16% Similarity=0.160 Sum_probs=44.4
Q ss_pred CCCCCCCCCCCCCCCcCCCCCcccccc-c------------------------CCCCceeccccccccCChHHHHHHHHH
Q psy517 43 SNAKPFHNNNNVDSASEFQGSGTNRRT-R------------------------SEDARWECPQCGKRYKYSRGLAMHRRL 97 (138)
Q Consensus 43 ~~~~~~~c~~c~~~f~~~~~l~~h~~~-h------------------------~~~~~~~c~~c~~~~~~~~~l~~h~~~ 97 (138)
+-.+.+.|+.|++.|.....|..|+|. | -+.++|.|..|...+..+.+|.+|+..
T Consensus 461 S~~kt~~cpkc~~~yk~a~~L~vhmRskhp~~~~~~c~~gq~~~~~arg~~~~~~~~p~~C~~C~~stttng~LsihlqS 540 (1406)
T KOG1146|consen 461 SFFKTLKCPKCNWHYKLAQTLGVHMRSKHPESQSAYCKAGQNHPRLARGEVYRCPGKPYPCRACNYSTTTNGNLSIHLQS 540 (1406)
T ss_pred cccccccCCccchhhhhHHHhhhcccccccccchhHhHhccccccccccccccCCCCcccceeeeeeeecchHHHHHHHH
Confidence 345778999999999999999999887 1 123577899999999999999988753
No 53
>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=91.78 E-value=0.1 Score=23.52 Aligned_cols=9 Identities=0% Similarity=-0.422 Sum_probs=4.3
Q ss_pred CCCCCCCCC
Q psy517 48 FHNNNNVDS 56 (138)
Q Consensus 48 ~~c~~c~~~ 56 (138)
|.|..||..
T Consensus 2 ~~C~~CGy~ 10 (33)
T cd00350 2 YVCPVCGYI 10 (33)
T ss_pred EECCCCCCE
Confidence 345555543
No 54
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=88.67 E-value=0.23 Score=32.80 Aligned_cols=44 Identities=16% Similarity=0.179 Sum_probs=27.4
Q ss_pred CCCCCCCCCCCCCcCCCCCcccccc---c-------CCCCc-----eeccccccccCCh
Q psy517 45 AKPFHNNNNVDSASEFQGSGTNRRT---R-------SEDAR-----WECPQCGKRYKYS 88 (138)
Q Consensus 45 ~~~~~c~~c~~~f~~~~~l~~h~~~---h-------~~~~~-----~~c~~c~~~~~~~ 88 (138)
++...|+.|++.|..+.-.....+. . .+..| ..|+.||.++...
T Consensus 3 ~k~~~CPvC~~~F~~~~vrs~~~r~~~~d~D~~~~Y~~vnP~~Y~V~vCP~CgyA~~~~ 61 (214)
T PF09986_consen 3 DKKITCPVCGKEFKTKKVRSGKIRVIRRDSDFCPRYKGVNPLFYEVWVCPHCGYAAFEE 61 (214)
T ss_pred CCceECCCCCCeeeeeEEEcCCceEeeecCCCccccCCCCCeeeeEEECCCCCCccccc
Confidence 3567899999999876444433322 1 12223 2688888877654
No 55
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=88.37 E-value=0.38 Score=30.08 Aligned_cols=13 Identities=8% Similarity=-0.166 Sum_probs=6.4
Q ss_pred CCCCCCCCCCcCC
Q psy517 48 FHNNNNVDSASEF 60 (138)
Q Consensus 48 ~~c~~c~~~f~~~ 60 (138)
+.|+.||.+|...
T Consensus 29 ~~c~~c~~~f~~~ 41 (154)
T PRK00464 29 RECLACGKRFTTF 41 (154)
T ss_pred eeccccCCcceEe
Confidence 4455555555443
No 56
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=88.34 E-value=0.21 Score=25.31 Aligned_cols=30 Identities=20% Similarity=0.532 Sum_probs=17.7
Q ss_pred CCCCceeccccccccCChHHHHHHHHHhcC
Q psy517 71 SEDARWECPQCGKRYKYSRGLAMHRRLECG 100 (138)
Q Consensus 71 ~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~ 100 (138)
-++.-+.|+.||..|....+..+|....++
T Consensus 13 DGE~~lrCPRC~~~FR~~K~Y~RHVNKaH~ 42 (65)
T COG4049 13 DGEEFLRCPRCGMVFRRRKDYIRHVNKAHG 42 (65)
T ss_pred CCceeeeCCchhHHHHHhHHHHHHhhHHhh
Confidence 345556666666666666666666554444
No 57
>KOG2893|consensus
Probab=87.46 E-value=0.21 Score=33.31 Aligned_cols=45 Identities=27% Similarity=0.670 Sum_probs=29.9
Q ss_pred CCceeccccccccCChHHHHHHHHHhcCCCCCccCCCCCccccCccHHHHH
Q psy517 73 DARWECPQCGKRYKYSRGLAMHRRLECGKEPMFHCPYCPQKCHQKGNMVIH 123 (138)
Q Consensus 73 ~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~C~~C~~~f~~~~~l~~H 123 (138)
.++| |=.|.+.|.....|.+|+.. +- |+|.+|.+.+.+...|..|
T Consensus 9 ~kpw-cwycnrefddekiliqhqka----kh-fkchichkkl~sgpglsih 53 (341)
T KOG2893|consen 9 DKPW-CWYCNREFDDEKILIQHQKA----KH-FKCHICHKKLFSGPGLSIH 53 (341)
T ss_pred CCce-eeecccccchhhhhhhhhhh----cc-ceeeeehhhhccCCCceee
Confidence 3455 45577788777777777653 33 7888887766666666666
No 58
>TIGR02605 CxxC_CxxC_SSSS putative regulatory protein, FmdB family. This model represents a region of about 50 amino acids found in a number of small proteins in a wide range of bacteria. The region begins usually with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One member of this family is has been noted as a putative regulatory protein, designated FmdB (PubMed:8841393). Most members of this family have a C-terminal region containing highly degenerate sequence, such as SSTSESTKSSGSSGSSGSSESKASGSTEKSTSSTTAAAAV in Mycobacterium tuberculosis and VAVGGSAPAPSPAPRAGGGGGGCCGGGCCG in Streptomyces avermitilis. These low complexity regions, which are not included in the model, resemble low-complexity C-terminal regions of some heterocycle-containing bacteriocin precursors.
Probab=86.89 E-value=0.27 Score=24.53 Aligned_cols=12 Identities=0% Similarity=-0.130 Sum_probs=7.8
Q ss_pred CCCCCCCCCCcC
Q psy517 48 FHNNNNVDSASE 59 (138)
Q Consensus 48 ~~c~~c~~~f~~ 59 (138)
|+|..|+..|..
T Consensus 6 y~C~~Cg~~fe~ 17 (52)
T TIGR02605 6 YRCTACGHRFEV 17 (52)
T ss_pred EEeCCCCCEeEE
Confidence 567777766654
No 59
>PF09538 FYDLN_acid: Protein of unknown function (FYDLN_acid); InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=86.78 E-value=0.56 Score=27.49 Aligned_cols=11 Identities=27% Similarity=0.763 Sum_probs=5.5
Q ss_pred ccCCCCCcccc
Q psy517 105 FHCPYCPQKCH 115 (138)
Q Consensus 105 ~~C~~C~~~f~ 115 (138)
..|+.||..|.
T Consensus 27 ivCP~CG~~~~ 37 (108)
T PF09538_consen 27 IVCPKCGTEFP 37 (108)
T ss_pred ccCCCCCCccC
Confidence 45555554443
No 60
>KOG2186|consensus
Probab=86.70 E-value=0.52 Score=31.71 Aligned_cols=47 Identities=19% Similarity=0.289 Sum_probs=29.2
Q ss_pred CCCCCCCCCCcCCCCCcccccccCCCCceeccccccccCChHHHHHHHHH
Q psy517 48 FHNNNNVDSASEFQGSGTNRRTRSEDARWECPQCGKRYKYSRGLAMHRRL 97 (138)
Q Consensus 48 ~~c~~c~~~f~~~~~l~~h~~~h~~~~~~~c~~c~~~~~~~~~l~~h~~~ 97 (138)
|.|..||.... +..+..|+...++ .-|.|..|+..|.. -....|..-
T Consensus 4 FtCnvCgEsvK-Kp~vekH~srCrn-~~fSCIDC~k~F~~-~sYknH~kC 50 (276)
T KOG2186|consen 4 FTCNVCGESVK-KPQVEKHMSRCRN-AYFSCIDCGKTFER-VSYKNHTKC 50 (276)
T ss_pred Eehhhhhhhcc-ccchHHHHHhccC-CeeEEeeccccccc-chhhhhhhh
Confidence 56777777644 4556667655555 46777777777776 335555543
No 61
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=86.61 E-value=0.77 Score=25.79 Aligned_cols=25 Identities=28% Similarity=0.684 Sum_probs=21.8
Q ss_pred ceeccccccccCChHHHHHHHHHhc
Q psy517 75 RWECPQCGKRYKYSRGLAMHRRLEC 99 (138)
Q Consensus 75 ~~~c~~c~~~~~~~~~l~~h~~~~~ 99 (138)
.+.|..|+..|.+...|..|++.+.
T Consensus 50 ~~~C~~C~~~f~s~~~l~~Hm~~~~ 74 (100)
T PF12756_consen 50 SFRCPYCNKTFRSREALQEHMRSKH 74 (100)
T ss_dssp SEEBSSSS-EESSHHHHHHHHHHTT
T ss_pred CCCCCccCCCCcCHHHHHHHHcCcc
Confidence 6899999999999999999999753
No 62
>PF09723 Zn-ribbon_8: Zinc ribbon domain; InterPro: IPR013429 This entry represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB []. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=85.75 E-value=0.26 Score=23.52 Aligned_cols=29 Identities=21% Similarity=0.463 Sum_probs=15.0
Q ss_pred CCCCCCCCCCcCCCCCcccccccCCCCceecccccc
Q psy517 48 FHNNNNVDSASEFQGSGTNRRTRSEDARWECPQCGK 83 (138)
Q Consensus 48 ~~c~~c~~~f~~~~~l~~h~~~h~~~~~~~c~~c~~ 83 (138)
|+|..||..|.....+.. ..+..|+.||.
T Consensus 6 y~C~~Cg~~fe~~~~~~~-------~~~~~CP~Cg~ 34 (42)
T PF09723_consen 6 YRCEECGHEFEVLQSISE-------DDPVPCPECGS 34 (42)
T ss_pred EEeCCCCCEEEEEEEcCC-------CCCCcCCCCCC
Confidence 566667766654332222 22345666655
No 63
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=85.50 E-value=0.75 Score=21.26 Aligned_cols=34 Identities=26% Similarity=0.727 Sum_probs=19.3
Q ss_pred eeccccccccCChHHHHHHHHHhcCCCCCccCCCCCcccc
Q psy517 76 WECPQCGKRYKYSRGLAMHRRLECGKEPMFHCPYCPQKCH 115 (138)
Q Consensus 76 ~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~C~~C~~~f~ 115 (138)
..|+.|+..|.-...- ...+... ..|+.|+..|.
T Consensus 3 i~CP~C~~~f~v~~~~-----l~~~~~~-vrC~~C~~~f~ 36 (37)
T PF13719_consen 3 ITCPNCQTRFRVPDDK-----LPAGGRK-VRCPKCGHVFR 36 (37)
T ss_pred EECCCCCceEEcCHHH-----cccCCcE-EECCCCCcEee
Confidence 3577777777665531 1122234 67777776653
No 64
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=85.30 E-value=0.55 Score=22.81 Aligned_cols=11 Identities=0% Similarity=-0.027 Sum_probs=6.1
Q ss_pred CCCCCCCCCCc
Q psy517 48 FHNNNNVDSAS 58 (138)
Q Consensus 48 ~~c~~c~~~f~ 58 (138)
|.|+.||..|.
T Consensus 4 y~C~~CG~~~~ 14 (46)
T PRK00398 4 YKCARCGREVE 14 (46)
T ss_pred EECCCCCCEEE
Confidence 55666665444
No 65
>smart00834 CxxC_CXXC_SSSS Putative regulatory protein. CxxC_CXXC_SSSS represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=84.70 E-value=0.42 Score=22.35 Aligned_cols=12 Identities=0% Similarity=-0.003 Sum_probs=7.1
Q ss_pred CCCCCCCCCCcC
Q psy517 48 FHNNNNVDSASE 59 (138)
Q Consensus 48 ~~c~~c~~~f~~ 59 (138)
|+|..||..|..
T Consensus 6 y~C~~Cg~~fe~ 17 (41)
T smart00834 6 YRCEDCGHTFEV 17 (41)
T ss_pred EEcCCCCCEEEE
Confidence 566666665553
No 66
>PHA00626 hypothetical protein
Probab=83.84 E-value=1.2 Score=22.64 Aligned_cols=12 Identities=25% Similarity=0.689 Sum_probs=7.2
Q ss_pred ceeccccccccC
Q psy517 75 RWECPQCGKRYK 86 (138)
Q Consensus 75 ~~~c~~c~~~~~ 86 (138)
.|.|+.||..|.
T Consensus 23 rYkCkdCGY~ft 34 (59)
T PHA00626 23 DYVCCDCGYNDS 34 (59)
T ss_pred ceEcCCCCCeec
Confidence 466666666554
No 67
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=83.64 E-value=0.95 Score=28.66 Aligned_cols=7 Identities=43% Similarity=1.065 Sum_probs=3.7
Q ss_pred ccCCCCC
Q psy517 105 FHCPYCP 111 (138)
Q Consensus 105 ~~C~~C~ 111 (138)
..||.||
T Consensus 150 ~~CPiCg 156 (166)
T COG1592 150 EVCPICG 156 (166)
T ss_pred CcCCCCC
Confidence 5555554
No 68
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=82.81 E-value=1.2 Score=26.21 Aligned_cols=81 Identities=7% Similarity=0.039 Sum_probs=43.6
Q ss_pred CCCCCCCCCCCCCcCCCCCcccc---cccC--CC-------CceeccccccccCChHHHHHHHHHhcCCCCCccCCCCCc
Q psy517 45 AKPFHNNNNVDSASEFQGSGTNR---RTRS--ED-------ARWECPQCGKRYKYSRGLAMHRRLECGKEPMFHCPYCPQ 112 (138)
Q Consensus 45 ~~~~~c~~c~~~f~~~~~l~~h~---~~h~--~~-------~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~C~~C~~ 112 (138)
+.|-.|+.|+-.......|.+.- ..-. .+ ..-.|-.|...|........-. -..... |.|+.|.+
T Consensus 13 ~LP~~CpiCgLtLVss~HLARSyHHLfPl~~f~ev~~~~~~~~~~C~~C~~~f~~~~~~~~~~--~~~~~~-y~C~~C~~ 89 (112)
T TIGR00622 13 ELPVECPICGLTLILSTHLARSYHHLFPLKAFQEIPLEEYNGSRFCFGCQGPFPKPPVSPFDE--LKDSHR-YVCAVCKN 89 (112)
T ss_pred CCCCcCCcCCCEEeccchHHHhhhccCCCcccccccccccCCCCcccCcCCCCCCcccccccc--cccccc-eeCCCCCC
Confidence 35677888887776665554321 0000 00 1113666777776542111000 111223 88988988
Q ss_pred cccCccHHHHHHHhhC
Q psy517 113 KCHQKGNMVIHIKKKH 128 (138)
Q Consensus 113 ~f~~~~~l~~H~~~h~ 128 (138)
.|...-..-.|...|.
T Consensus 90 ~FC~dCD~fiHe~Lh~ 105 (112)
T TIGR00622 90 VFCVDCDVFVHESLHC 105 (112)
T ss_pred ccccccchhhhhhccC
Confidence 8887777667766654
No 69
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=82.66 E-value=1.2 Score=20.49 Aligned_cols=33 Identities=18% Similarity=0.492 Sum_probs=17.4
Q ss_pred eeccccccccCChHHHHHHHHHhcCCCCCccCCCCCccc
Q psy517 76 WECPQCGKRYKYSRGLAMHRRLECGKEPMFHCPYCPQKC 114 (138)
Q Consensus 76 ~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~C~~C~~~f 114 (138)
..|+.|+..|.-..... ..+... ..|+.|+..|
T Consensus 3 i~Cp~C~~~y~i~d~~i-----p~~g~~-v~C~~C~~~f 35 (36)
T PF13717_consen 3 ITCPNCQAKYEIDDEKI-----PPKGRK-VRCSKCGHVF 35 (36)
T ss_pred EECCCCCCEEeCCHHHC-----CCCCcE-EECCCCCCEe
Confidence 35677766666554321 111123 6677776654
No 70
>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain. This domain contains a CXXCX(19)CXXC motif suggestive of both zinc fingers and thioredoxin, usually found at the N-terminus of prokaryotic proteins. One partially characterized gene, agmX, is among a large set in Myxococcus whose interruption affects adventurous gliding motility.
Probab=82.63 E-value=0.97 Score=20.81 Aligned_cols=14 Identities=21% Similarity=0.842 Sum_probs=7.8
Q ss_pred eeccccccccCChH
Q psy517 76 WECPQCGKRYKYSR 89 (138)
Q Consensus 76 ~~c~~c~~~~~~~~ 89 (138)
+.|+.|+..|....
T Consensus 3 ~~CP~C~~~~~v~~ 16 (38)
T TIGR02098 3 IQCPNCKTSFRVVD 16 (38)
T ss_pred EECCCCCCEEEeCH
Confidence 35666666655443
No 71
>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=81.64 E-value=0.89 Score=20.62 Aligned_cols=9 Identities=0% Similarity=-0.477 Sum_probs=5.0
Q ss_pred CCCCCCCCC
Q psy517 48 FHNNNNVDS 56 (138)
Q Consensus 48 ~~c~~c~~~ 56 (138)
|.|..||..
T Consensus 3 ~~C~~CG~i 11 (34)
T cd00729 3 WVCPVCGYI 11 (34)
T ss_pred EECCCCCCE
Confidence 456666644
No 72
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=80.84 E-value=0.84 Score=23.52 Aligned_cols=32 Identities=34% Similarity=0.894 Sum_probs=16.4
Q ss_pred ceeccccccccCChHHHHHHHHHhcCCCCCccCCCCCc
Q psy517 75 RWECPQCGKRYKYSRGLAMHRRLECGKEPMFHCPYCPQ 112 (138)
Q Consensus 75 ~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~C~~C~~ 112 (138)
.|.|+.||........- -|. .+ .+ |.|+.||.
T Consensus 27 ~F~CPnCGe~~I~Rc~~---CRk-~g-~~-Y~Cp~CGF 58 (61)
T COG2888 27 KFPCPNCGEVEIYRCAK---CRK-LG-NP-YRCPKCGF 58 (61)
T ss_pred EeeCCCCCceeeehhhh---HHH-cC-Cc-eECCCcCc
Confidence 46677777544433321 111 12 35 77777764
No 73
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=79.92 E-value=1.3 Score=21.36 Aligned_cols=11 Identities=0% Similarity=-0.085 Sum_probs=5.2
Q ss_pred CCCCCCCCCCc
Q psy517 48 FHNNNNVDSAS 58 (138)
Q Consensus 48 ~~c~~c~~~f~ 58 (138)
|.|..||..|.
T Consensus 3 Y~C~~Cg~~~~ 13 (44)
T smart00659 3 YICGECGRENE 13 (44)
T ss_pred EECCCCCCEee
Confidence 44555554433
No 74
>smart00614 ZnF_BED BED zinc finger. DNA-binding domain in chromatin-boundary-element-binding proteins and transposases
Probab=78.36 E-value=2.3 Score=20.99 Aligned_cols=21 Identities=29% Similarity=0.724 Sum_probs=11.4
Q ss_pred ccCCCCCccccCc-----cHHHHHHH
Q psy517 105 FHCPYCPQKCHQK-----GNMVIHIK 125 (138)
Q Consensus 105 ~~C~~C~~~f~~~-----~~l~~H~~ 125 (138)
-.|..|++.+... ++|.+|++
T Consensus 19 a~C~~C~~~l~~~~~~gTs~L~rHl~ 44 (50)
T smart00614 19 AKCKYCGKKLSRSSKGGTSNLRRHLR 44 (50)
T ss_pred EEecCCCCEeeeCCCCCcHHHHHHHH
Confidence 3555666555433 35666665
No 75
>KOG2186|consensus
Probab=77.48 E-value=0.92 Score=30.58 Aligned_cols=21 Identities=5% Similarity=-0.100 Sum_probs=10.9
Q ss_pred CCCCCCCCCCCCcCCCCCcccc
Q psy517 46 KPFHNNNNVDSASEFQGSGTNR 67 (138)
Q Consensus 46 ~~~~c~~c~~~f~~~~~l~~h~ 67 (138)
.-|.|..|++.|.. ..+..|.
T Consensus 28 ~~fSCIDC~k~F~~-~sYknH~ 48 (276)
T KOG2186|consen 28 AYFSCIDCGKTFER-VSYKNHT 48 (276)
T ss_pred CeeEEeeccccccc-chhhhhh
Confidence 34556666666665 3334443
No 76
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=76.76 E-value=0.93 Score=25.30 Aligned_cols=11 Identities=27% Similarity=0.727 Sum_probs=5.8
Q ss_pred ccCCCCCcccc
Q psy517 105 FHCPYCPQKCH 115 (138)
Q Consensus 105 ~~C~~C~~~f~ 115 (138)
|.|..|+..|.
T Consensus 54 W~C~kCg~~fA 64 (89)
T COG1997 54 WKCRKCGAKFA 64 (89)
T ss_pred EEcCCCCCeec
Confidence 55555555543
No 77
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=74.87 E-value=1.8 Score=22.32 Aligned_cols=32 Identities=31% Similarity=0.862 Sum_probs=15.2
Q ss_pred ceeccccccccCChHHHHHHHHHhcCCCCCccCCCCCc
Q psy517 75 RWECPQCGKRYKYSRGLAMHRRLECGKEPMFHCPYCPQ 112 (138)
Q Consensus 75 ~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~C~~C~~ 112 (138)
.|.|+.||........ .-|... .+ |.|+.||.
T Consensus 25 ~F~CPnCG~~~I~RC~---~CRk~~--~~-Y~CP~CGF 56 (59)
T PRK14890 25 KFLCPNCGEVIIYRCE---KCRKQS--NP-YTCPKCGF 56 (59)
T ss_pred EeeCCCCCCeeEeech---hHHhcC--Cc-eECCCCCC
Confidence 4667777665222221 111111 34 77777764
No 78
>TIGR00373 conserved hypothetical protein TIGR00373. This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.
Probab=74.57 E-value=4.1 Score=25.57 Aligned_cols=32 Identities=22% Similarity=0.637 Sum_probs=17.9
Q ss_pred CCceeccccccccCChHHHHHHHHHhcCCCCCccCCCCCccc
Q psy517 73 DARWECPQCGKRYKYSRGLAMHRRLECGKEPMFHCPYCPQKC 114 (138)
Q Consensus 73 ~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~C~~C~~~f 114 (138)
..-|.|+.|+..|..-..+. .. |.|+.||...
T Consensus 107 ~~~Y~Cp~c~~r~tf~eA~~---------~~-F~Cp~Cg~~L 138 (158)
T TIGR00373 107 NMFFICPNMCVRFTFNEAME---------LN-FTCPRCGAML 138 (158)
T ss_pred CCeEECCCCCcEeeHHHHHH---------cC-CcCCCCCCEe
Confidence 34566777766665544432 12 6777776543
No 79
>TIGR02300 FYDLN_acid conserved hypothetical protein TIGR02300. Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=74.56 E-value=2.2 Score=25.68 Aligned_cols=12 Identities=17% Similarity=0.360 Sum_probs=5.9
Q ss_pred ceeccccccccC
Q psy517 75 RWECPQCGKRYK 86 (138)
Q Consensus 75 ~~~c~~c~~~~~ 86 (138)
|..|+.||..|.
T Consensus 26 p~vcP~cg~~~~ 37 (129)
T TIGR02300 26 PAVSPYTGEQFP 37 (129)
T ss_pred CccCCCcCCccC
Confidence 444555555443
No 80
>smart00734 ZnF_Rad18 Rad18-like CCHC zinc finger. Yeast Rad18p functions with Rad5p in error-free post-replicative DNA repair. This zinc finger is likely to bind nucleic-acids.
Probab=74.38 E-value=3.4 Score=17.42 Aligned_cols=20 Identities=20% Similarity=0.599 Sum_probs=12.7
Q ss_pred ccCCCCCccccCccHHHHHHH
Q psy517 105 FHCPYCPQKCHQKGNMVIHIK 125 (138)
Q Consensus 105 ~~C~~C~~~f~~~~~l~~H~~ 125 (138)
..|+.|++.+ ....++.|+.
T Consensus 2 v~CPiC~~~v-~~~~in~HLD 21 (26)
T smart00734 2 VQCPVCFREV-PENLINSHLD 21 (26)
T ss_pred CcCCCCcCcc-cHHHHHHHHH
Confidence 4577887776 4455666654
No 81
>PF12013 DUF3505: Protein of unknown function (DUF3505); InterPro: IPR022698 This family of proteins is functionally uncharacterised. This protein is found in eukaryotes. Proteins in this family are typically between 247 to 1018 amino acids in length. This region contains two segments that are likely to be C2H2 zinc binding domains.
Probab=73.95 E-value=2.9 Score=24.33 Aligned_cols=25 Identities=32% Similarity=0.634 Sum_probs=21.9
Q ss_pred ccC----CCCCccccCccHHHHHHHhhCC
Q psy517 105 FHC----PYCPQKCHQKGNMVIHIKKKHP 129 (138)
Q Consensus 105 ~~C----~~C~~~f~~~~~l~~H~~~h~~ 129 (138)
|.| ..|+....+...+..|.+.+||
T Consensus 81 ~~C~~~~~~C~y~~~~~~~m~~H~~~~Hg 109 (109)
T PF12013_consen 81 YRCQCDPPHCGYITRSKKTMRKHWRKEHG 109 (109)
T ss_pred eeeecCCCCCCcEeccHHHHHHHHHHhcC
Confidence 888 8899999999999999988875
No 82
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=71.89 E-value=2.5 Score=25.83 Aligned_cols=15 Identities=13% Similarity=-0.163 Sum_probs=10.6
Q ss_pred CCCCCCCCCCCCcCC
Q psy517 46 KPFHNNNNVDSASEF 60 (138)
Q Consensus 46 ~~~~c~~c~~~f~~~ 60 (138)
..+.|..||..|...
T Consensus 69 ~~~~C~~CG~~~~~~ 83 (135)
T PRK03824 69 AVLKCRNCGNEWSLK 83 (135)
T ss_pred eEEECCCCCCEEecc
Confidence 447888888776653
No 83
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=71.77 E-value=3.2 Score=25.67 Aligned_cols=37 Identities=27% Similarity=0.842 Sum_probs=19.5
Q ss_pred CCceeccccccccCChHHHHHHHHHhcCCCCCccCCCCCccc
Q psy517 73 DARWECPQCGKRYKYSRGLAMHRRLECGKEPMFHCPYCPQKC 114 (138)
Q Consensus 73 ~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~C~~C~~~f 114 (138)
..-|.|+.|+..|.....+.. ... ... |.|+.||...
T Consensus 97 ~~~Y~Cp~C~~~y~~~ea~~~---~d~-~~~-f~Cp~Cg~~l 133 (147)
T smart00531 97 NAYYKCPNCQSKYTFLEANQL---LDM-DGT-FTCPRCGEEL 133 (147)
T ss_pred CcEEECcCCCCEeeHHHHHHh---cCC-CCc-EECCCCCCEE
Confidence 345677777776664332211 011 223 7777777654
No 84
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=70.75 E-value=4.5 Score=25.99 Aligned_cols=33 Identities=24% Similarity=0.755 Sum_probs=20.3
Q ss_pred CCceeccccccccCChHHHHHHHHHhcCCCCCccCCCCCcccc
Q psy517 73 DARWECPQCGKRYKYSRGLAMHRRLECGKEPMFHCPYCPQKCH 115 (138)
Q Consensus 73 ~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~C~~C~~~f~ 115 (138)
..-|.|+.|+..|..-..+. .. |.|+.||....
T Consensus 115 ~~~Y~Cp~C~~rytf~eA~~---------~~-F~Cp~Cg~~L~ 147 (178)
T PRK06266 115 NMFFFCPNCHIRFTFDEAME---------YG-FRCPQCGEMLE 147 (178)
T ss_pred CCEEECCCCCcEEeHHHHhh---------cC-CcCCCCCCCCe
Confidence 34577877777766554431 23 77888876543
No 85
>PF15135 UPF0515: Uncharacterised protein UPF0515
Probab=70.70 E-value=1.9 Score=29.09 Aligned_cols=20 Identities=15% Similarity=0.001 Sum_probs=14.4
Q ss_pred CCCCCCCCCCCCCCCCCCcC
Q psy517 40 SSPSNAKPFHNNNNVDSASE 59 (138)
Q Consensus 40 ~~~~~~~~~~c~~c~~~f~~ 59 (138)
.+|+..+.|.|..|...+..
T Consensus 105 ~ip~~drqFaC~~Cd~~WwR 124 (278)
T PF15135_consen 105 LIPSVDRQFACSSCDHMWWR 124 (278)
T ss_pred cccccceeeeccccchHHHh
Confidence 34566678899998877665
No 86
>PF02892 zf-BED: BED zinc finger; InterPro: IPR003656 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 predicted BED-type zinc finger domains. The BED finger which was named after the Drosophila proteins BEAF and DREF, is found in one or more copies in cellular regulatory factors and transposases from plants, animals and fungi. The BED finger is an about 50 to 60 amino acid residues domain that contains a characteristic motif with two highly conserved aromatic positions, as well as a shared pattern of cysteines and histidines that is predicted to form a zinc finger. As diverse BED fingers are able to bind DNA, it has been suggested that DNA-binding is the general function of this domain []. Some proteins known to contain a BED domain include animal, plant and fungi AC1 and Hobo-like transposases; Caenorhabditis elegans Dpy-20 protein, a predicted cuticular gene transcriptional regulator; Drosophila BEAF (boundary element-associated factor), thought to be involved in chromatin insulation; Drosophila DREF, a transcriptional regulator for S-phase genes; and tobacco 3AF1 and tomato E4/E8-BP1, light- and ethylene-regulated DNA binding proteins that contain two BED fingers. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding; PDB: 2DJR_A 2CT5_A.
Probab=70.04 E-value=5.1 Score=18.99 Aligned_cols=21 Identities=29% Similarity=0.627 Sum_probs=11.3
Q ss_pred ccCCCCCccccC----ccHHHHHHH
Q psy517 105 FHCPYCPQKCHQ----KGNMVIHIK 125 (138)
Q Consensus 105 ~~C~~C~~~f~~----~~~l~~H~~ 125 (138)
..|..|++.+.. -++|..|++
T Consensus 17 a~C~~C~~~~~~~~~~ts~l~~HL~ 41 (45)
T PF02892_consen 17 AKCKYCGKVIKYSSGGTSNLKRHLK 41 (45)
T ss_dssp EEETTTTEE-----SSTHHHHHHHH
T ss_pred EEeCCCCeEEeeCCCcHHHHHHhhh
Confidence 567777766544 356666663
No 87
>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=68.01 E-value=8.4 Score=19.17 Aligned_cols=13 Identities=0% Similarity=-0.330 Sum_probs=8.6
Q ss_pred CCCCCCCCCCcCC
Q psy517 48 FHNNNNVDSASEF 60 (138)
Q Consensus 48 ~~c~~c~~~f~~~ 60 (138)
|.|..||..+...
T Consensus 2 y~C~~CgyiYd~~ 14 (50)
T cd00730 2 YECRICGYIYDPA 14 (50)
T ss_pred cCCCCCCeEECCC
Confidence 6677777766543
No 88
>PF05443 ROS_MUCR: ROS/MUCR transcriptional regulator protein; InterPro: IPR008807 This family consists of several ROS/MUCR transcriptional regulator proteins. The ros chromosomal gene is present in octopine and nopaline strains of Agrobacterium tumefaciens as well as in Rhizobium meliloti (Sinorhizobium meliloti). This gene encodes a 15.5 kDa protein that specifically represses the virC and virD operons in the virulence region of the Ti plasmid [] and is necessary for succinoglycan production []. S. meliloti can produce two types of acidic exopolysaccharides, succinoglycan and galactoglucan, that are interchangeable for infection of Medicago sativa (Alfalfa) nodules. MucR from S. meliloti acts as a transcriptional repressor that blocks the expression of the exp genes responsible for galactoglucan production therefore allowing the exclusive production of succinoglycan [].; GO: 0003677 DNA binding, 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2JSP_A.
Probab=66.37 E-value=3.6 Score=25.09 Aligned_cols=24 Identities=21% Similarity=0.382 Sum_probs=12.7
Q ss_pred ccCCCCCccccCccHHHHHHHhhCCCC
Q psy517 105 FHCPYCPQKCHQKGNMVIHIKKKHPEK 131 (138)
Q Consensus 105 ~~C~~C~~~f~~~~~l~~H~~~h~~~k 131 (138)
..|-.||+.|... .+|++.|+|-.
T Consensus 73 i~clecGk~~k~L---krHL~~~~glt 96 (132)
T PF05443_consen 73 IICLECGKKFKTL---KRHLRTHHGLT 96 (132)
T ss_dssp EE-TBT--EESBH---HHHHHHTT-S-
T ss_pred eEEccCCcccchH---HHHHHHccCCC
Confidence 5677777766543 67777776643
No 89
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=65.77 E-value=7.8 Score=18.14 Aligned_cols=20 Identities=25% Similarity=0.406 Sum_probs=14.4
Q ss_pred CceeccccccccCChHHHHH
Q psy517 74 ARWECPQCGKRYKYSRGLAM 93 (138)
Q Consensus 74 ~~~~c~~c~~~~~~~~~l~~ 93 (138)
.-..|+.|+..+.....|.+
T Consensus 18 ~id~C~~C~G~W~d~~el~~ 37 (41)
T PF13453_consen 18 EIDVCPSCGGIWFDAGELEK 37 (41)
T ss_pred EEEECCCCCeEEccHHHHHH
Confidence 34678888888877776654
No 90
>COG1773 Rubredoxin [Energy production and conversion]
Probab=64.34 E-value=7.7 Score=19.75 Aligned_cols=16 Identities=6% Similarity=-0.137 Sum_probs=11.2
Q ss_pred CCCCCCCCCCCcCCCC
Q psy517 47 PFHNNNNVDSASEFQG 62 (138)
Q Consensus 47 ~~~c~~c~~~f~~~~~ 62 (138)
.|+|..||..|.....
T Consensus 3 ~~~C~~CG~vYd~e~G 18 (55)
T COG1773 3 RWRCSVCGYVYDPEKG 18 (55)
T ss_pred ceEecCCceEeccccC
Confidence 4788888887775443
No 91
>PF04959 ARS2: Arsenite-resistance protein 2; InterPro: IPR007042 This entry represents Arsenite-resistance protein 2 (also known as Serrate RNA effector molecule homolog) which is thought to play a role in arsenite resistance [], although does not directly confer arsenite resistance but rather modulates arsenic sensitivity []. Arsenite is a carcinogenic compound which can act as a comutagen by inhibiting DNA repair. It is also involved in cell cycle progression at S phase. ; PDB: 3AX1_A.
Probab=62.59 E-value=2.2 Score=28.24 Aligned_cols=24 Identities=29% Similarity=0.571 Sum_probs=10.5
Q ss_pred ccCCCCCccccCccHHHHHHHhhC
Q psy517 105 FHCPYCPQKCHQKGNMVIHIKKKH 128 (138)
Q Consensus 105 ~~C~~C~~~f~~~~~l~~H~~~h~ 128 (138)
|.|+.|+|.|.-..-...|+..-|
T Consensus 78 ~~C~lc~KlFkg~eFV~KHI~nKH 101 (214)
T PF04959_consen 78 WRCPLCGKLFKGPEFVRKHIFNKH 101 (214)
T ss_dssp EEE-SSS-EESSHHHHHHHHHHH-
T ss_pred ECCCCCCcccCChHHHHHHHhhcC
Confidence 555555555555444455544433
No 92
>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=62.55 E-value=4 Score=18.26 Aligned_cols=7 Identities=57% Similarity=1.896 Sum_probs=2.9
Q ss_pred ecccccc
Q psy517 77 ECPQCGK 83 (138)
Q Consensus 77 ~c~~c~~ 83 (138)
.|+.||.
T Consensus 19 rC~~CG~ 25 (32)
T PF03604_consen 19 RCPECGH 25 (32)
T ss_dssp SBSSSS-
T ss_pred ECCcCCC
Confidence 4555543
No 93
>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=61.85 E-value=5.6 Score=16.82 Aligned_cols=11 Identities=0% Similarity=-0.432 Sum_probs=8.2
Q ss_pred CCCCCCCCCCc
Q psy517 48 FHNNNNVDSAS 58 (138)
Q Consensus 48 ~~c~~c~~~f~ 58 (138)
-.|+.||..|.
T Consensus 15 ~~Cp~CG~~F~ 25 (26)
T PF10571_consen 15 KFCPHCGYDFE 25 (26)
T ss_pred CcCCCCCCCCc
Confidence 36888888875
No 94
>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=60.90 E-value=3 Score=20.16 Aligned_cols=9 Identities=44% Similarity=1.187 Sum_probs=5.4
Q ss_pred ccCCCCCcc
Q psy517 105 FHCPYCPQK 113 (138)
Q Consensus 105 ~~C~~C~~~ 113 (138)
+.|+.|+..
T Consensus 19 ~~CP~Cg~~ 27 (46)
T PF12760_consen 19 FVCPHCGST 27 (46)
T ss_pred CCCCCCCCe
Confidence 556666643
No 95
>PRK04023 DNA polymerase II large subunit; Validated
Probab=59.84 E-value=16 Score=30.08 Aligned_cols=11 Identities=0% Similarity=-0.323 Sum_probs=7.3
Q ss_pred CCCCCCCCCCC
Q psy517 46 KPFHNNNNVDS 56 (138)
Q Consensus 46 ~~~~c~~c~~~ 56 (138)
....|+.||..
T Consensus 625 g~RfCpsCG~~ 635 (1121)
T PRK04023 625 GRRKCPSCGKE 635 (1121)
T ss_pred cCccCCCCCCc
Confidence 34577777765
No 96
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=59.59 E-value=6.5 Score=19.50 Aligned_cols=10 Identities=30% Similarity=1.288 Sum_probs=4.9
Q ss_pred eecccccccc
Q psy517 76 WECPQCGKRY 85 (138)
Q Consensus 76 ~~c~~c~~~~ 85 (138)
|.|..||+.+
T Consensus 7 Y~C~~Cg~~~ 16 (49)
T COG1996 7 YKCARCGREV 16 (49)
T ss_pred EEhhhcCCee
Confidence 4455555544
No 97
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=58.76 E-value=6.8 Score=21.18 Aligned_cols=14 Identities=14% Similarity=0.515 Sum_probs=6.7
Q ss_pred ceecc--ccccccCCh
Q psy517 75 RWECP--QCGKRYKYS 88 (138)
Q Consensus 75 ~~~c~--~c~~~~~~~ 88 (138)
-+.|. +||.+|...
T Consensus 27 Y~qC~N~eCg~tF~t~ 42 (72)
T PRK09678 27 YHQCQNVNCSATFITY 42 (72)
T ss_pred eeecCCCCCCCEEEEE
Confidence 34454 455555443
No 98
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=58.14 E-value=4 Score=32.18 Aligned_cols=9 Identities=33% Similarity=0.922 Sum_probs=6.3
Q ss_pred ccCCCCCcc
Q psy517 105 FHCPYCPQK 113 (138)
Q Consensus 105 ~~C~~C~~~ 113 (138)
..|+.||..
T Consensus 476 ~~Cp~Cgs~ 484 (730)
T COG1198 476 QSCPECGSE 484 (730)
T ss_pred CCCCCCCCC
Confidence 777777753
No 99
>COG3091 SprT Zn-dependent metalloprotease, SprT family [General function prediction only]
Probab=57.63 E-value=3.4 Score=25.72 Aligned_cols=29 Identities=17% Similarity=0.339 Sum_probs=15.0
Q ss_pred ccCCCCCccccCccHHHHHHHhhCCCCCCCCCCC
Q psy517 105 FHCPYCPQKCHQKGNMVIHIKKKHPEKANPHDEA 138 (138)
Q Consensus 105 ~~C~~C~~~f~~~~~l~~H~~~h~~~k~~~C~~C 138 (138)
|.|. |+..+... ++|-.+-.|+ .|.|..|
T Consensus 118 Y~C~-C~q~~l~~---RRhn~~~~g~-~YrC~~C 146 (156)
T COG3091 118 YRCQ-CQQHYLRI---RRHNTVRRGE-VYRCGKC 146 (156)
T ss_pred EEee-cCCccchh---hhcccccccc-eEEeccC
Confidence 6666 66554333 3444444455 5666555
No 100
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=56.08 E-value=11 Score=21.27 Aligned_cols=27 Identities=30% Similarity=0.794 Sum_probs=16.4
Q ss_pred CceeccccccccCChHHHHHHHHHhcCCCCCccCCCCC
Q psy517 74 ARWECPQCGKRYKYSRGLAMHRRLECGKEPMFHCPYCP 111 (138)
Q Consensus 74 ~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~C~~C~ 111 (138)
+|-.|..||..|..-. -.+| ..|+.|.
T Consensus 57 ~Pa~CkkCGfef~~~~----------ik~p-SRCP~CK 83 (97)
T COG3357 57 RPARCKKCGFEFRDDK----------IKKP-SRCPKCK 83 (97)
T ss_pred cChhhcccCccccccc----------cCCc-ccCCcch
Confidence 4567888888776411 1134 7777775
No 101
>KOG4173|consensus
Probab=55.81 E-value=6.2 Score=25.97 Aligned_cols=77 Identities=18% Similarity=0.290 Sum_probs=50.7
Q ss_pred CCCCC--CCCCCcCCCCCcccccccCCCCceeccccccccCChHHHHHHHHH----------hcCCCCCccCC--CCCcc
Q psy517 48 FHNNN--NVDSASEFQGSGTNRRTRSEDARWECPQCGKRYKYSRGLAMHRRL----------ECGKEPMFHCP--YCPQK 113 (138)
Q Consensus 48 ~~c~~--c~~~f~~~~~l~~h~~~h~~~~~~~c~~c~~~~~~~~~l~~h~~~----------~~~~~~~~~C~--~C~~~ 113 (138)
+.|++ |-..|.....+..|-.+-.+ -.|..|.+.|...--|..|+.- ..| +++|.|- .|+..
T Consensus 80 ~~cqvagc~~~~d~lD~~E~hY~~~h~---~sCs~C~r~~Pt~hLLd~HI~E~HDs~Fqa~veRG-~dMy~ClvEgCt~K 155 (253)
T KOG4173|consen 80 FACQVAGCCQVFDALDDYEHHYHTLHG---NSCSFCKRAFPTGHLLDAHILEWHDSLFQALVERG-QDMYQCLVEGCTEK 155 (253)
T ss_pred ccccccchHHHHhhhhhHHHhhhhccc---chhHHHHHhCCchhhhhHHHHHHHHHHHHHHHHcC-ccHHHHHHHhhhhh
Confidence 66776 66666666656666543222 2588888888888777777542 234 4558884 48888
Q ss_pred ccCccHHHHHHHhhC
Q psy517 114 CHQKGNMVIHIKKKH 128 (138)
Q Consensus 114 f~~~~~l~~H~~~h~ 128 (138)
|........|+-..|
T Consensus 156 FkT~r~RkdH~I~~H 170 (253)
T KOG4173|consen 156 FKTSRDRKDHMIRMH 170 (253)
T ss_pred hhhhhhhhhHHHHhc
Confidence 888877777776544
No 102
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=55.74 E-value=7.8 Score=18.17 Aligned_cols=10 Identities=40% Similarity=1.424 Sum_probs=5.7
Q ss_pred eecccccccc
Q psy517 76 WECPQCGKRY 85 (138)
Q Consensus 76 ~~c~~c~~~~ 85 (138)
|.|..|+..+
T Consensus 29 y~C~~C~~~w 38 (40)
T smart00440 29 YVCTKCGHRW 38 (40)
T ss_pred EEeCCCCCEe
Confidence 5666666544
No 103
>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=55.49 E-value=6.1 Score=16.42 Aligned_cols=8 Identities=50% Similarity=1.668 Sum_probs=3.6
Q ss_pred ceeccccc
Q psy517 75 RWECPQCG 82 (138)
Q Consensus 75 ~~~c~~c~ 82 (138)
.|.|+.||
T Consensus 16 ~f~CPnCG 23 (24)
T PF07754_consen 16 PFPCPNCG 23 (24)
T ss_pred eEeCCCCC
Confidence 34444444
No 104
>PF14311 DUF4379: Domain of unknown function (DUF4379)
Probab=55.11 E-value=12 Score=18.72 Aligned_cols=10 Identities=30% Similarity=1.082 Sum_probs=4.5
Q ss_pred ccCCCCCccc
Q psy517 105 FHCPYCPQKC 114 (138)
Q Consensus 105 ~~C~~C~~~f 114 (138)
+.|+.|+..|
T Consensus 29 W~C~~Cgh~w 38 (55)
T PF14311_consen 29 WKCPKCGHEW 38 (55)
T ss_pred EECCCCCCee
Confidence 4444444433
No 105
>PF06524 NOA36: NOA36 protein; InterPro: IPR010531 This family consists of several NOA36 proteins which contain 29 highly conserved cysteine residues. The function of this protein is unknown.; GO: 0008270 zinc ion binding, 0005634 nucleus
Probab=54.61 E-value=6.2 Score=26.95 Aligned_cols=81 Identities=17% Similarity=0.313 Sum_probs=40.2
Q ss_pred CCCCCCCCCCCCCCcCCCCCcccccc--cCCCCceeccccccccCChHHHH-------HHHHH----hcCCCCCccCCCC
Q psy517 44 NAKPFHNNNNVDSASEFQGSGTNRRT--RSEDARWECPQCGKRYKYSRGLA-------MHRRL----ECGKEPMFHCPYC 110 (138)
Q Consensus 44 ~~~~~~c~~c~~~f~~~~~l~~h~~~--h~~~~~~~c~~c~~~~~~~~~l~-------~h~~~----~~~~~~~~~C~~C 110 (138)
|-+.|+|+.|...+.....+. |+.. -.....|+|..|.+.-..+. |. .|.+. ....++ +.|+.|
T Consensus 139 GGrif~CsfC~~flCEDDQFE-HQAsCQvLe~E~~KC~SCNrlGq~sC-LRCK~cfCddHvrrKg~ky~k~k~-~PCPKC 215 (314)
T PF06524_consen 139 GGRIFKCSFCDNFLCEDDQFE-HQASCQVLESETFKCQSCNRLGQYSC-LRCKICFCDDHVRRKGFKYEKGKP-IPCPKC 215 (314)
T ss_pred CCeEEEeecCCCeeeccchhh-hhhhhhhhhcccccccccccccchhh-hheeeeehhhhhhhcccccccCCC-CCCCCC
Confidence 556677887777665544443 2221 22334677777655433221 21 23322 112245 788888
Q ss_pred CccccCccHHHHHHHhh
Q psy517 111 PQKCHQKGNMVIHIKKK 127 (138)
Q Consensus 111 ~~~f~~~~~l~~H~~~h 127 (138)
+.-......|..-.|+|
T Consensus 216 g~et~eTkdLSmStR~h 232 (314)
T PF06524_consen 216 GYETQETKDLSMSTRSH 232 (314)
T ss_pred CCcccccccceeeeecc
Confidence 76555444444333333
No 106
>PF12013 DUF3505: Protein of unknown function (DUF3505); InterPro: IPR022698 This family of proteins is functionally uncharacterised. This protein is found in eukaryotes. Proteins in this family are typically between 247 to 1018 amino acids in length. This region contains two segments that are likely to be C2H2 zinc binding domains.
Probab=54.24 E-value=14 Score=21.43 Aligned_cols=26 Identities=31% Similarity=0.701 Sum_probs=22.0
Q ss_pred ceec----cccccccCChHHHHHHHHHhcC
Q psy517 75 RWEC----PQCGKRYKYSRGLAMHRRLECG 100 (138)
Q Consensus 75 ~~~c----~~c~~~~~~~~~l~~h~~~~~~ 100 (138)
-|.| ..|+....+...+..|.+.+.|
T Consensus 80 G~~C~~~~~~C~y~~~~~~~m~~H~~~~Hg 109 (109)
T PF12013_consen 80 GYRCQCDPPHCGYITRSKKTMRKHWRKEHG 109 (109)
T ss_pred CeeeecCCCCCCcEeccHHHHHHHHHHhcC
Confidence 4789 8999999999999999887654
No 107
>TIGR00100 hypA hydrogenase nickel insertion protein HypA. In Hpylori, hypA mutant abolished hydrogenase activity and decrease in urease activity. Nickel supplementation in media restored urease activity and partial hydrogenase activity. HypA probably involved in inserting Ni in enzymes.
Probab=53.61 E-value=6.5 Score=23.26 Aligned_cols=11 Identities=9% Similarity=0.102 Sum_probs=5.5
Q ss_pred CCCCCCCCCCc
Q psy517 48 FHNNNNVDSAS 58 (138)
Q Consensus 48 ~~c~~c~~~f~ 58 (138)
..|..|+..|.
T Consensus 71 ~~C~~Cg~~~~ 81 (115)
T TIGR00100 71 CECEDCSEEVS 81 (115)
T ss_pred EEcccCCCEEe
Confidence 45555554443
No 108
>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=52.56 E-value=7.9 Score=17.02 Aligned_cols=7 Identities=57% Similarity=1.725 Sum_probs=3.2
Q ss_pred eeccccc
Q psy517 76 WECPQCG 82 (138)
Q Consensus 76 ~~c~~c~ 82 (138)
+.|+.|+
T Consensus 20 ~vCp~C~ 26 (30)
T PF08274_consen 20 LVCPECG 26 (30)
T ss_dssp EEETTTT
T ss_pred EeCCccc
Confidence 4444444
No 109
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=52.38 E-value=15 Score=18.67 Aligned_cols=15 Identities=33% Similarity=0.917 Sum_probs=8.6
Q ss_pred CCceeccccccccCC
Q psy517 73 DARWECPQCGKRYKY 87 (138)
Q Consensus 73 ~~~~~c~~c~~~~~~ 87 (138)
...|.|+.||..+--
T Consensus 12 ~v~~~Cp~cGipthc 26 (55)
T PF13824_consen 12 HVNFECPDCGIPTHC 26 (55)
T ss_pred ccCCcCCCCCCcCcc
Confidence 345667777665433
No 110
>TIGR01206 lysW lysine biosynthesis protein LysW. This very small, poorly characterized protein has been shown essential in Thermus thermophilus for an unusual pathway of Lys biosynthesis from aspartate by way of alpha-aminoadipate (AAA) rather than diaminopimelate. It is found also in Deinococcus radiodurans and Pyrococcus horikoshii, which appear to share the AAA pathway.
Probab=52.11 E-value=14 Score=18.69 Aligned_cols=10 Identities=10% Similarity=0.033 Sum_probs=6.2
Q ss_pred CCCCCCCCCC
Q psy517 48 FHNNNNVDSA 57 (138)
Q Consensus 48 ~~c~~c~~~f 57 (138)
+.|+.|+..+
T Consensus 3 ~~CP~CG~~i 12 (54)
T TIGR01206 3 FECPDCGAEI 12 (54)
T ss_pred cCCCCCCCEE
Confidence 4666676644
No 111
>PF00301 Rubredoxin: Rubredoxin; InterPro: IPR004039 Rubredoxin is a low molecular weight iron-containing bacterial protein involved in electron transfer [, ], sometimes replacing ferredoxin as an electron carrier []. The 3-D structures of a number of rubredoxins have been solved [, ]. The fold belongs to the alpha+beta class, with 2 alpha-helices and 2-3 beta-strands. Its active site contains an iron ion which is co-ordinated by the sulphurs of four conserved cysteine residues forming an almost regular tetrahedron. The conserved cysteines reside on two loops, which are the most conserved regions of the protein. In addition, a ring of acidic residues in the proximity of the [Fe(Cys)4] centre is also well-conserved []. ; GO: 0009055 electron carrier activity, 0046872 metal ion binding; PDB: 2RDV_C 1RDV_A 1S24_A 1T9O_B 1B2J_A 1SMW_A 2PVE_B 1BFY_A 1T9P_C 1C09_C ....
Probab=52.00 E-value=7.9 Score=18.99 Aligned_cols=12 Identities=0% Similarity=-0.266 Sum_probs=6.3
Q ss_pred CCCCCCCCCCcC
Q psy517 48 FHNNNNVDSASE 59 (138)
Q Consensus 48 ~~c~~c~~~f~~ 59 (138)
|.|..|+..+..
T Consensus 2 y~C~~CgyvYd~ 13 (47)
T PF00301_consen 2 YQCPVCGYVYDP 13 (47)
T ss_dssp EEETTTSBEEET
T ss_pred cCCCCCCEEEcC
Confidence 455666655443
No 112
>COG4530 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=50.81 E-value=9.2 Score=22.44 Aligned_cols=10 Identities=20% Similarity=0.451 Sum_probs=5.4
Q ss_pred ccCCCCCccc
Q psy517 105 FHCPYCPQKC 114 (138)
Q Consensus 105 ~~C~~C~~~f 114 (138)
..|++||++|
T Consensus 27 iVsPytG~s~ 36 (129)
T COG4530 27 IVSPYTGKSY 36 (129)
T ss_pred cccCcccccc
Confidence 5555555555
No 113
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=48.81 E-value=13 Score=17.33 Aligned_cols=15 Identities=7% Similarity=-0.108 Sum_probs=12.6
Q ss_pred CCCCCCCCCCCcCCC
Q psy517 47 PFHNNNNVDSASEFQ 61 (138)
Q Consensus 47 ~~~c~~c~~~f~~~~ 61 (138)
|+.|..|++.|...-
T Consensus 12 ~f~C~~C~~~FC~~H 26 (39)
T smart00154 12 GFKCRHCGNLFCGEH 26 (39)
T ss_pred CeECCccCCcccccc
Confidence 788999999998654
No 114
>PF10013 DUF2256: Uncharacterized protein conserved in bacteria (DUF2256); InterPro: IPR017136 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=48.80 E-value=15 Score=17.60 Aligned_cols=11 Identities=36% Similarity=1.410 Sum_probs=6.5
Q ss_pred ccccccccCCh
Q psy517 78 CPQCGKRYKYS 88 (138)
Q Consensus 78 c~~c~~~~~~~ 88 (138)
|..||+.|...
T Consensus 11 C~~C~rpf~WR 21 (42)
T PF10013_consen 11 CPVCGRPFTWR 21 (42)
T ss_pred CcccCCcchHH
Confidence 66666666544
No 115
>KOG2807|consensus
Probab=48.38 E-value=35 Score=24.33 Aligned_cols=22 Identities=32% Similarity=0.415 Sum_probs=15.5
Q ss_pred ceeccccccccCChHHHHHHHH
Q psy517 75 RWECPQCGKRYKYSRGLAMHRR 96 (138)
Q Consensus 75 ~~~c~~c~~~~~~~~~l~~h~~ 96 (138)
|..|+.|+-......+|.+..+
T Consensus 290 P~eCpiC~ltLVss~hLARSyh 311 (378)
T KOG2807|consen 290 PIECPICSLTLVSSPHLARSYH 311 (378)
T ss_pred CccCCccceeEecchHHHHHHH
Confidence 5677888887777777765544
No 116
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=47.70 E-value=8.7 Score=22.67 Aligned_cols=9 Identities=0% Similarity=-0.337 Sum_probs=4.2
Q ss_pred CCCCCCCCC
Q psy517 48 FHNNNNVDS 56 (138)
Q Consensus 48 ~~c~~c~~~ 56 (138)
.+|..|+..
T Consensus 71 ~~C~~Cg~~ 79 (113)
T PRK12380 71 AWCWDCSQV 79 (113)
T ss_pred EEcccCCCE
Confidence 445555543
No 117
>KOG2785|consensus
Probab=47.25 E-value=22 Score=25.76 Aligned_cols=22 Identities=18% Similarity=0.329 Sum_probs=18.6
Q ss_pred ccCCCCCccccCccHHHHHHHh
Q psy517 105 FHCPYCPQKCHQKGNMVIHIKK 126 (138)
Q Consensus 105 ~~C~~C~~~f~~~~~l~~H~~~ 126 (138)
+.|..|.++|........|+..
T Consensus 69 ~~c~~c~k~~~s~~a~~~hl~S 90 (390)
T KOG2785|consen 69 VYCEACNKSFASPKAHENHLKS 90 (390)
T ss_pred eehHHhhccccChhhHHHHHHH
Confidence 8899999999988888888754
No 118
>PF13878 zf-C2H2_3: zinc-finger of acetyl-transferase ESCO
Probab=46.86 E-value=24 Score=16.62 Aligned_cols=24 Identities=25% Similarity=0.610 Sum_probs=13.4
Q ss_pred eeccccccccCCh--HHHHHHHHHhc
Q psy517 76 WECPQCGKRYKYS--RGLAMHRRLEC 99 (138)
Q Consensus 76 ~~c~~c~~~~~~~--~~l~~h~~~~~ 99 (138)
-.|+.||..+... ..-..|.+.|.
T Consensus 14 ~~C~~CgM~Y~~~~~eD~~~H~~yH~ 39 (41)
T PF13878_consen 14 TTCPTCGMLYSPGSPEDEKLHKKYHD 39 (41)
T ss_pred cCCCCCCCEECCCCHHHHHHHHHHHh
Confidence 4677777655433 44555655553
No 119
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=46.29 E-value=10 Score=22.49 Aligned_cols=11 Identities=0% Similarity=-0.058 Sum_probs=5.9
Q ss_pred CCCCCCCCCCc
Q psy517 48 FHNNNNVDSAS 58 (138)
Q Consensus 48 ~~c~~c~~~f~ 58 (138)
+.|..|+..|.
T Consensus 72 ~~C~~Cg~~~~ 82 (117)
T PRK00564 72 LECKDCSHVFK 82 (117)
T ss_pred EEhhhCCCccc
Confidence 45666655443
No 120
>PF03811 Zn_Tnp_IS1: InsA N-terminal domain; InterPro: IPR003220 Insertion elements are mobile elements in DNA, usually encoding proteins required for transposition, for example transposases. Protein InsA is absolutely required for transposition of insertion element 1. This entry represents a short zinc binding domain found in IS1 InsA family protein. It is found at the N terminus of the protein and may be a DNA-binding domain.; GO: 0006313 transposition, DNA-mediated
Probab=45.75 E-value=29 Score=15.92 Aligned_cols=19 Identities=26% Similarity=0.670 Sum_probs=9.9
Q ss_pred CcccccccCCCCceecccc
Q psy517 63 SGTNRRTRSEDARWECPQC 81 (138)
Q Consensus 63 l~~h~~~h~~~~~~~c~~c 81 (138)
+..|-....+...|.|..|
T Consensus 17 v~k~G~~~~G~qryrC~~C 35 (36)
T PF03811_consen 17 VKKNGKSPSGHQRYRCKDC 35 (36)
T ss_pred ceeCCCCCCCCEeEecCcC
Confidence 3444444455555666555
No 121
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=45.66 E-value=32 Score=29.21 Aligned_cols=8 Identities=0% Similarity=-0.392 Sum_probs=5.4
Q ss_pred CCCCCCCC
Q psy517 48 FHNNNNVD 55 (138)
Q Consensus 48 ~~c~~c~~ 55 (138)
++|+.||.
T Consensus 668 rkCPkCG~ 675 (1337)
T PRK14714 668 RRCPSCGT 675 (1337)
T ss_pred EECCCCCC
Confidence 56777775
No 122
>PF01096 TFIIS_C: Transcription factor S-II (TFIIS); InterPro: IPR001222 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIs (TFIIS). In eukaryotes the initiation of transcription of protein encoding genes by polymerase II (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least eight different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, -IIH and -IIS []. During mRNA elongation, Pol II can encounter DNA sequences that cause reverse movement of the enzyme. Such backtracking involves extrusion of the RNA 3'-end into the pore, and can lead to transcriptional arrest. Escape from arrest requires cleavage of the extruded RNA with the help of TFIIS, which induces mRNA cleavage by enhancing the intrinsic nuclease activity of RNA polymerase (Pol) II, past template-encoded pause sites []. TFIIS extends from the polymerase surface via a pore to the internal active site. Two essential and invariant acidic residues in a TFIIS loop complement the Pol II active site and could position a metal ion and a water molecule for hydrolytic RNA cleavage. TFIIS also induces extensive structural changes in Pol II that would realign nucleic acids in the active centre. TFIIS is a protein of about 300 amino acids. It contains three regions: a variable N-terminal domain not required for TFIIS activity; a conserved central domain required for Pol II binding; and a conserved C-terminal C4-type zinc finger essential for RNA cleavage. The zinc finger folds in a conformation termed a zinc ribbon [] characterised by a three-stranded antiparallel beta-sheet and two beta-hairpins. A backbone model for Pol II-TFIIS complex was obtained from X-ray analysis. It shows that a beta hairpin protrudes from the zinc finger and complements the pol II active site []. Some viral proteins also contain the TFIIS zinc ribbon C-terminal domain. The Vaccinia virus protein, unlike its eukaryotic homologue, is an integral RNA polymerase subunit rather than a readily separable transcription factor []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding, 0006351 transcription, DNA-dependent; PDB: 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I 3I4M_I ....
Probab=44.78 E-value=6.2 Score=18.39 Aligned_cols=10 Identities=40% Similarity=1.291 Sum_probs=5.9
Q ss_pred eecccccccc
Q psy517 76 WECPQCGKRY 85 (138)
Q Consensus 76 ~~c~~c~~~~ 85 (138)
|.|..||..|
T Consensus 29 y~C~~C~~~w 38 (39)
T PF01096_consen 29 YVCCNCGHRW 38 (39)
T ss_dssp EEESSSTEEE
T ss_pred EEeCCCCCee
Confidence 5666666543
No 123
>KOG4167|consensus
Probab=44.61 E-value=5.6 Score=31.22 Aligned_cols=25 Identities=20% Similarity=0.454 Sum_probs=22.2
Q ss_pred ceeccccccccCChHHHHHHHHHhc
Q psy517 75 RWECPQCGKRYKYSRGLAMHRRLEC 99 (138)
Q Consensus 75 ~~~c~~c~~~~~~~~~l~~h~~~~~ 99 (138)
-|-|.+|++.|.....+..||.+|.
T Consensus 792 iFpCreC~kvF~KiKSrNAHMK~Hr 816 (907)
T KOG4167|consen 792 IFPCRECGKVFFKIKSRNAHMKTHR 816 (907)
T ss_pred eeehHHHHHHHHHHhhhhHHHHHHH
Confidence 4789999999999999999999875
No 124
>KOG4167|consensus
Probab=43.96 E-value=4.3 Score=31.82 Aligned_cols=24 Identities=21% Similarity=0.419 Sum_probs=21.9
Q ss_pred ccCCCCCccccCccHHHHHHHhhC
Q psy517 105 FHCPYCPQKCHQKGNMVIHIKKKH 128 (138)
Q Consensus 105 ~~C~~C~~~f~~~~~l~~H~~~h~ 128 (138)
|.|..|++.|-..-+++.|+++|.
T Consensus 793 FpCreC~kvF~KiKSrNAHMK~Hr 816 (907)
T KOG4167|consen 793 FPCRECGKVFFKIKSRNAHMKTHR 816 (907)
T ss_pred eehHHHHHHHHHHhhhhHHHHHHH
Confidence 899999999998888999999885
No 125
>KOG2593|consensus
Probab=43.78 E-value=13 Score=27.38 Aligned_cols=15 Identities=7% Similarity=-0.017 Sum_probs=8.0
Q ss_pred CCCCCCCCCCCCCcC
Q psy517 45 AKPFHNNNNVDSASE 59 (138)
Q Consensus 45 ~~~~~c~~c~~~f~~ 59 (138)
...|.|+.|.+.|..
T Consensus 126 ~~~Y~Cp~C~kkyt~ 140 (436)
T KOG2593|consen 126 VAGYVCPNCQKKYTS 140 (436)
T ss_pred cccccCCccccchhh
Confidence 344555555555554
No 126
>PF15269 zf-C2H2_7: Zinc-finger
Probab=43.44 E-value=9.5 Score=18.45 Aligned_cols=21 Identities=24% Similarity=0.393 Sum_probs=11.8
Q ss_pred eeccccccccCChHHHHHHHH
Q psy517 76 WECPQCGKRYKYSRGLAMHRR 96 (138)
Q Consensus 76 ~~c~~c~~~~~~~~~l~~h~~ 96 (138)
|.|-+|..+...++.|-+|+.
T Consensus 21 ykcfqcpftc~~kshl~nhmk 41 (54)
T PF15269_consen 21 YKCFQCPFTCNEKSHLFNHMK 41 (54)
T ss_pred ceeecCCcccchHHHHHHHHH
Confidence 345555555555666666655
No 127
>KOG2593|consensus
Probab=42.91 E-value=14 Score=27.24 Aligned_cols=39 Identities=31% Similarity=0.697 Sum_probs=25.7
Q ss_pred cCCCCceeccccccccCChHHHHHHHHHhcCCCCCccCCCCCc
Q psy517 70 RSEDARWECPQCGKRYKYSRGLAMHRRLECGKEPMFHCPYCPQ 112 (138)
Q Consensus 70 h~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~C~~C~~ 112 (138)
......|.|+.|.+.|.....+ +......-. |.|..|+-
T Consensus 123 ~t~~~~Y~Cp~C~kkyt~Lea~---~L~~~~~~~-F~C~~C~g 161 (436)
T KOG2593|consen 123 DTNVAGYVCPNCQKKYTSLEAL---QLLDNETGE-FHCENCGG 161 (436)
T ss_pred ccccccccCCccccchhhhHHH---HhhcccCce-EEEecCCC
Confidence 3445679999999998765543 333332234 89988875
No 128
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=42.68 E-value=32 Score=16.69 Aligned_cols=12 Identities=33% Similarity=0.877 Sum_probs=6.3
Q ss_pred ceeccccccccC
Q psy517 75 RWECPQCGKRYK 86 (138)
Q Consensus 75 ~~~c~~c~~~~~ 86 (138)
.+.|+.||..+.
T Consensus 20 ~~vC~~Cg~~~~ 31 (52)
T smart00661 20 RFVCRKCGYEEP 31 (52)
T ss_pred EEECCcCCCeEE
Confidence 355666655443
No 129
>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=42.16 E-value=15 Score=28.90 Aligned_cols=56 Identities=29% Similarity=0.470 Sum_probs=37.1
Q ss_pred CCCCCCCCCcCCCCCcccc-cccCCCCceeccccccccCChHHHHHHHHHhcCCCCCccCCCCCc
Q psy517 49 HNNNNVDSASEFQGSGTNR-RTRSEDARWECPQCGKRYKYSRGLAMHRRLECGKEPMFHCPYCPQ 112 (138)
Q Consensus 49 ~c~~c~~~f~~~~~l~~h~-~~h~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~C~~C~~ 112 (138)
.|-.||-.|+-...|-.-+ .+-...- -.|+.|.+-+..+.+ +|.|.. | ..|+.||-
T Consensus 125 ~CT~CGPRfTIi~alPYDR~nTsM~~F-~lC~~C~~EY~dP~n----RRfHAQ--p-~aCp~CGP 181 (750)
T COG0068 125 NCTNCGPRFTIIEALPYDRENTSMADF-PLCPFCDKEYKDPLN----RRFHAQ--P-IACPKCGP 181 (750)
T ss_pred ccCCCCcceeeeccCCCCcccCccccC-cCCHHHHHHhcCccc----cccccc--c-ccCcccCC
Confidence 5888999888766554432 2222222 258999887777653 566753 5 88999995
No 130
>TIGR00595 priA primosomal protein N'. All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=41.51 E-value=36 Score=25.79 Aligned_cols=10 Identities=0% Similarity=-0.439 Sum_probs=5.0
Q ss_pred CCCCCCCCCc
Q psy517 49 HNNNNVDSAS 58 (138)
Q Consensus 49 ~c~~c~~~f~ 58 (138)
.|..||....
T Consensus 215 ~C~~Cg~~~~ 224 (505)
T TIGR00595 215 LCRSCGYILC 224 (505)
T ss_pred EhhhCcCccC
Confidence 4555555433
No 131
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=41.39 E-value=13 Score=21.91 Aligned_cols=10 Identities=0% Similarity=-0.203 Sum_probs=5.6
Q ss_pred CCCCCCCCCC
Q psy517 48 FHNNNNVDSA 57 (138)
Q Consensus 48 ~~c~~c~~~f 57 (138)
++|..|+..|
T Consensus 71 ~~C~~Cg~~~ 80 (114)
T PRK03681 71 CWCETCQQYV 80 (114)
T ss_pred EEcccCCCee
Confidence 5566666543
No 132
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=41.19 E-value=18 Score=25.56 Aligned_cols=38 Identities=8% Similarity=-0.038 Sum_probs=19.7
Q ss_pred CCCCCCCCCCCCCCcCCCCCcccccccCCCCceeccccccc
Q psy517 44 NAKPFHNNNNVDSASEFQGSGTNRRTRSEDARWECPQCGKR 84 (138)
Q Consensus 44 ~~~~~~c~~c~~~f~~~~~l~~h~~~h~~~~~~~c~~c~~~ 84 (138)
++..-.|+.||..-.. +.+ +.....|.+-..|..|+..
T Consensus 184 ~~~~~~CPvCGs~P~~-s~v--~~~~~~G~RyL~CslC~te 221 (309)
T PRK03564 184 GEQRQFCPVCGSMPVS-SVV--QIGTTQGLRYLHCNLCESE 221 (309)
T ss_pred ccCCCCCCCCCCcchh-hee--eccCCCCceEEEcCCCCCc
Confidence 4445679999975321 111 1122345555566666543
No 133
>COG4957 Predicted transcriptional regulator [Transcription]
Probab=40.73 E-value=15 Score=22.47 Aligned_cols=24 Identities=29% Similarity=0.402 Sum_probs=19.3
Q ss_pred ceeccccccccCChHHHHHHHHHhcCC
Q psy517 75 RWECPQCGKRYKYSRGLAMHRRLECGK 101 (138)
Q Consensus 75 ~~~c~~c~~~~~~~~~l~~h~~~~~~~ 101 (138)
-..|-++|+.|.+ |.+|..+|.|-
T Consensus 76 ~IicLEDGkkfKS---LKRHL~t~~gm 99 (148)
T COG4957 76 YIICLEDGKKFKS---LKRHLTTHYGL 99 (148)
T ss_pred eEEEeccCcchHH---HHHHHhcccCC
Confidence 3579999999864 78999998773
No 134
>PRK05978 hypothetical protein; Provisional
Probab=40.63 E-value=27 Score=21.79 Aligned_cols=31 Identities=10% Similarity=-0.009 Sum_probs=15.9
Q ss_pred CCCCCCCCCCcCCCCCcccccccCCCCceeccccccccCC
Q psy517 48 FHNNNNVDSASEFQGSGTNRRTRSEDARWECPQCGKRYKY 87 (138)
Q Consensus 48 ~~c~~c~~~f~~~~~l~~h~~~h~~~~~~~c~~c~~~~~~ 87 (138)
-+|+.|++.=-....|+.+ -.|+.||..|..
T Consensus 34 grCP~CG~G~LF~g~Lkv~---------~~C~~CG~~~~~ 64 (148)
T PRK05978 34 GRCPACGEGKLFRAFLKPV---------DHCAACGEDFTH 64 (148)
T ss_pred CcCCCCCCCcccccccccC---------CCccccCCcccc
Confidence 4788887743322222222 247777665543
No 135
>KOG0320|consensus
Probab=40.11 E-value=18 Score=23.28 Aligned_cols=51 Identities=20% Similarity=0.328 Sum_probs=27.6
Q ss_pred CCCCCCCCCCCCCCcCCCCCcccccccCCCCceeccccccccCChHHHHHHHHHhcCCCCCccCCCCCcccc
Q psy517 44 NAKPFHNNNNVDSASEFQGSGTNRRTRSEDARWECPQCGKRYKYSRGLAMHRRLECGKEPMFHCPYCPQKCH 115 (138)
Q Consensus 44 ~~~~~~c~~c~~~f~~~~~l~~h~~~h~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~C~~C~~~f~ 115 (138)
.+..|+|++|-..+..+.. ..-.||-.|.... +..-+. .. ..|+.|++...
T Consensus 128 ~~~~~~CPiCl~~~sek~~--------------vsTkCGHvFC~~C-ik~alk-----~~-~~CP~C~kkIt 178 (187)
T KOG0320|consen 128 KEGTYKCPICLDSVSEKVP--------------VSTKCGHVFCSQC-IKDALK-----NT-NKCPTCRKKIT 178 (187)
T ss_pred cccccCCCceecchhhccc--------------cccccchhHHHHH-HHHHHH-----hC-CCCCCcccccc
Confidence 3445888888877765442 1234555555433 111111 23 67888886443
No 136
>COG3364 Zn-ribbon containing protein [General function prediction only]
Probab=39.76 E-value=25 Score=20.40 Aligned_cols=13 Identities=8% Similarity=0.135 Sum_probs=6.4
Q ss_pred CCCCCCCCCCCcC
Q psy517 47 PFHNNNNVDSASE 59 (138)
Q Consensus 47 ~~~c~~c~~~f~~ 59 (138)
|+.|..||..|..
T Consensus 2 pH~CtrCG~vf~~ 14 (112)
T COG3364 2 PHQCTRCGEVFDD 14 (112)
T ss_pred Cceeccccccccc
Confidence 3445555555543
No 137
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=39.48 E-value=24 Score=26.06 Aligned_cols=12 Identities=25% Similarity=0.883 Sum_probs=6.6
Q ss_pred ccCCCCCccccC
Q psy517 105 FHCPYCPQKCHQ 116 (138)
Q Consensus 105 ~~C~~C~~~f~~ 116 (138)
|.|+.|+..+..
T Consensus 368 ~rC~kCg~~~~~ 379 (421)
T COG1571 368 FRCKKCGTRARE 379 (421)
T ss_pred cccccccccCCc
Confidence 666666655443
No 138
>PF01927 Mut7-C: Mut7-C RNAse domain; InterPro: IPR002782 This prokaryotic family of proteins have no known function. The proteins contain four conserved cysteines that may be involved in metal binding or disulphide bridges.
Probab=39.37 E-value=37 Score=20.93 Aligned_cols=10 Identities=0% Similarity=-0.290 Sum_probs=5.3
Q ss_pred CCCCCCCCCC
Q psy517 48 FHNNNNVDSA 57 (138)
Q Consensus 48 ~~c~~c~~~f 57 (138)
-+|..|+..+
T Consensus 92 sRC~~CN~~L 101 (147)
T PF01927_consen 92 SRCPKCNGPL 101 (147)
T ss_pred CccCCCCcEe
Confidence 3566665543
No 139
>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=38.69 E-value=27 Score=16.27 Aligned_cols=12 Identities=33% Similarity=1.010 Sum_probs=5.7
Q ss_pred CCCceecccccc
Q psy517 72 EDARWECPQCGK 83 (138)
Q Consensus 72 ~~~~~~c~~c~~ 83 (138)
+.+.+.|+.|+.
T Consensus 21 ~~~~w~C~~C~~ 32 (40)
T PF04810_consen 21 GGKTWICNFCGT 32 (40)
T ss_dssp TTTEEEETTT--
T ss_pred CCCEEECcCCCC
Confidence 334566666654
No 140
>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=38.44 E-value=29 Score=18.12 Aligned_cols=10 Identities=40% Similarity=1.215 Sum_probs=5.7
Q ss_pred ceeccccccc
Q psy517 75 RWECPQCGKR 84 (138)
Q Consensus 75 ~~~c~~c~~~ 84 (138)
.|.|+.||..
T Consensus 46 ~~~C~~Cg~~ 55 (69)
T PF07282_consen 46 VFTCPNCGFE 55 (69)
T ss_pred eEEcCCCCCE
Confidence 4556666554
No 141
>PF01155 HypA: Hydrogenase expression/synthesis hypA family; InterPro: IPR000688 Bacterial membrane-bound nickel-dependent hydrogenases requires a number of accessory proteins which are involved in their maturation. The exact role of these proteins is not yet clear, but some seem to be required for the incorporation of the nickel ions []. One of these proteins is generally known as hypA. It is a protein of about 12 to 14 kDa that contains, in its C-terminal region, four conserved cysteines that form a zinc-finger like motif. Escherichia coli has two proteins that belong to this family, hypA and hybF. A homologue, MJ0214, has also been found in a number of archaeal species, including the genome of Methanocaldococcus jannaschii (Methanococcus jannaschii).; GO: 0016151 nickel ion binding, 0006464 protein modification process; PDB: 2KDX_A 3A44_D 3A43_B.
Probab=38.38 E-value=20 Score=21.09 Aligned_cols=11 Identities=27% Similarity=1.020 Sum_probs=5.0
Q ss_pred eeccccccccC
Q psy517 76 WECPQCGKRYK 86 (138)
Q Consensus 76 ~~c~~c~~~~~ 86 (138)
..|..||..|.
T Consensus 71 ~~C~~Cg~~~~ 81 (113)
T PF01155_consen 71 ARCRDCGHEFE 81 (113)
T ss_dssp EEETTTS-EEE
T ss_pred EECCCCCCEEe
Confidence 34555555544
No 142
>KOG3408|consensus
Probab=38.05 E-value=21 Score=21.45 Aligned_cols=24 Identities=17% Similarity=0.530 Sum_probs=20.8
Q ss_pred CceeccccccccCChHHHHHHHHH
Q psy517 74 ARWECPQCGKRYKYSRGLAMHRRL 97 (138)
Q Consensus 74 ~~~~c~~c~~~~~~~~~l~~h~~~ 97 (138)
-.|.|..|.+.|.....|..|.++
T Consensus 56 GqfyCi~CaRyFi~~~~l~~H~kt 79 (129)
T KOG3408|consen 56 GQFYCIECARYFIDAKALKTHFKT 79 (129)
T ss_pred ceeehhhhhhhhcchHHHHHHHhc
Confidence 357899999999999999988775
No 143
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=38.00 E-value=25 Score=28.00 Aligned_cols=16 Identities=31% Similarity=0.738 Sum_probs=11.5
Q ss_pred ccCCCCceeccccccc
Q psy517 69 TRSEDARWECPQCGKR 84 (138)
Q Consensus 69 ~h~~~~~~~c~~c~~~ 84 (138)
.+....|..|+.||..
T Consensus 469 g~~~~~p~~Cp~Cgs~ 484 (730)
T COG1198 469 GYQEPIPQSCPECGSE 484 (730)
T ss_pred CCCCCCCCCCCCCCCC
Confidence 3344678899999875
No 144
>COG1655 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=37.16 E-value=17 Score=24.53 Aligned_cols=28 Identities=7% Similarity=-0.147 Sum_probs=19.7
Q ss_pred CCCCCCCCCCCCCcCCCCCcccccccCC
Q psy517 45 AKPFHNNNNVDSASEFQGSGTNRRTRSE 72 (138)
Q Consensus 45 ~~~~~c~~c~~~f~~~~~l~~h~~~h~~ 72 (138)
++...|+.|+-.|.....+....|+-.+
T Consensus 17 kk~ieCPvC~tkFkkeev~tgsiRiiag 44 (267)
T COG1655 17 KKTIECPVCNTKFKKEEVKTGSIRIIAG 44 (267)
T ss_pred hceeccCcccchhhhhheeccceeEecc
Confidence 4557899999998877666655555443
No 145
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=37.12 E-value=3.8 Score=28.70 Aligned_cols=23 Identities=17% Similarity=0.507 Sum_probs=14.9
Q ss_pred ccCCCCCccccCccHHHHHHHhh
Q psy517 105 FHCPYCPQKCHQKGNMVIHIKKK 127 (138)
Q Consensus 105 ~~C~~C~~~f~~~~~l~~H~~~h 127 (138)
|.|..|...|...-..-.|...|
T Consensus 389 Y~Ce~CK~~FC~dCdvfiHe~Lh 411 (421)
T COG5151 389 YQCELCKSTFCSDCDVFIHETLH 411 (421)
T ss_pred eechhhhhhhhhhhHHHHHHHHh
Confidence 67777777776666655665554
No 146
>TIGR00244 transcriptional regulator NrdR. Members of this almost entirely bacterial family contain an ATP cone domain (PFAM:PF03477). There is never more than one member per genome. Common gene symbols given include nrdR, ybaD, ribX and ytcG. The member from Streptomyces coelicolor is found upstream in the operon of the class II oxygen-independent ribonucleotide reductase gene nrdJ and was shown to repress nrdJ expression. Many members of this family are found near genes for riboflavin biosynthesis in Gram-negative bacteria, suggesting a role in that pathway. However, a phylogenetic profiling study associates members of this family with the presence of a palindromic signal with consensus acaCwAtATaTwGtgt, termed the NrdR-box, an upstream element for most operons for ribonucleotide reductase of all three classes in bacterial genomes.
Probab=37.11 E-value=27 Score=21.76 Aligned_cols=16 Identities=6% Similarity=0.000 Sum_probs=10.7
Q ss_pred CCCCCCCCCCcCCCCC
Q psy517 48 FHNNNNVDSASEFQGS 63 (138)
Q Consensus 48 ~~c~~c~~~f~~~~~l 63 (138)
=.|..|++.|.....+
T Consensus 29 ReC~~C~~RFTTyErv 44 (147)
T TIGR00244 29 RECLECHERFTTFERA 44 (147)
T ss_pred ccCCccCCccceeeec
Confidence 4677788777765544
No 147
>COG1327 Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains [Transcription]
Probab=36.80 E-value=28 Score=21.78 Aligned_cols=14 Identities=7% Similarity=-0.033 Sum_probs=9.6
Q ss_pred CCCCCCCCCCcCCC
Q psy517 48 FHNNNNVDSASEFQ 61 (138)
Q Consensus 48 ~~c~~c~~~f~~~~ 61 (138)
=.|..|+..|....
T Consensus 29 ReC~~C~~RFTTfE 42 (156)
T COG1327 29 RECLECGERFTTFE 42 (156)
T ss_pred hcccccccccchhh
Confidence 46777777777654
No 148
>KOG0978|consensus
Probab=36.39 E-value=20 Score=28.28 Aligned_cols=21 Identities=24% Similarity=0.439 Sum_probs=15.2
Q ss_pred CCCccCCCCCccccCccHHHHH
Q psy517 102 EPMFHCPYCPQKCHQKGNMVIH 123 (138)
Q Consensus 102 ~~~~~C~~C~~~f~~~~~l~~H 123 (138)
+. -.||.|+..|.....+..|
T Consensus 677 Rq-RKCP~Cn~aFganDv~~I~ 697 (698)
T KOG0978|consen 677 RQ-RKCPKCNAAFGANDVHRIH 697 (698)
T ss_pred hc-CCCCCCCCCCCcccccccC
Confidence 44 6799999999887655443
No 149
>KOG1842|consensus
Probab=34.92 E-value=20 Score=26.65 Aligned_cols=23 Identities=22% Similarity=0.348 Sum_probs=11.7
Q ss_pred ceeccccccccCChHHHHHHHHH
Q psy517 75 RWECPQCGKRYKYSRGLAMHRRL 97 (138)
Q Consensus 75 ~~~c~~c~~~~~~~~~l~~h~~~ 97 (138)
.|.|+.|...|...+.|..|...
T Consensus 15 gflCPiC~~dl~~~~~L~~H~d~ 37 (505)
T KOG1842|consen 15 GFLCPICLLDLPNLSALNDHLDV 37 (505)
T ss_pred cccCchHhhhhhhHHHHHHHHhh
Confidence 34555555555555555544443
No 150
>PF14787 zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB: 1CL4_A 1DSV_A.
Probab=34.64 E-value=25 Score=16.19 Aligned_cols=15 Identities=27% Similarity=0.532 Sum_probs=8.2
Q ss_pred ccCCCCCccccCccH
Q psy517 105 FHCPYCPQKCHQKGN 119 (138)
Q Consensus 105 ~~C~~C~~~f~~~~~ 119 (138)
-.|+.|++.|.+.+.
T Consensus 3 ~~CprC~kg~Hwa~~ 17 (36)
T PF14787_consen 3 GLCPRCGKGFHWASE 17 (36)
T ss_dssp -C-TTTSSSCS-TTT
T ss_pred ccCcccCCCcchhhh
Confidence 457788887766543
No 151
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=34.56 E-value=24 Score=20.40 Aligned_cols=39 Identities=13% Similarity=0.144 Sum_probs=20.1
Q ss_pred CCCCCCCCCCCCCCcCCCCCcccccccCCCCceeccccccccC
Q psy517 44 NAKPFHNNNNVDSASEFQGSGTNRRTRSEDARWECPQCGKRYK 86 (138)
Q Consensus 44 ~~~~~~c~~c~~~f~~~~~l~~h~~~h~~~~~~~c~~c~~~~~ 86 (138)
-.+.|.|+.|+..-.....++.-... -...|..||.+|.
T Consensus 19 L~k~FtCp~Cghe~vs~ctvkk~~~~----g~~~Cg~CGls~e 57 (104)
T COG4888 19 LPKTFTCPRCGHEKVSSCTVKKTVNI----GTAVCGNCGLSFE 57 (104)
T ss_pred CCceEecCccCCeeeeEEEEEecCce----eEEEcccCcceEE
Confidence 45668888888754432222211111 1245777776654
No 152
>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=33.88 E-value=15 Score=17.44 Aligned_cols=13 Identities=31% Similarity=0.700 Sum_probs=8.0
Q ss_pred ccCCCCCccccCc
Q psy517 105 FHCPYCPQKCHQK 117 (138)
Q Consensus 105 ~~C~~C~~~f~~~ 117 (138)
+.|..|++.|-..
T Consensus 14 ~~C~~C~~~FC~~ 26 (43)
T PF01428_consen 14 FKCKHCGKSFCLK 26 (43)
T ss_dssp EE-TTTS-EE-TT
T ss_pred eECCCCCcccCcc
Confidence 8888888888655
No 153
>PF08209 Sgf11: Sgf11 (transcriptional regulation protein); InterPro: IPR013246 The Sgf11 family is a SAGA complex subunit in Saccharomyces cerevisiae (Baker's yeast). The SAGA complex is a multisubunit protein complex involved in transcriptional regulation. SAGA combines proteins involved in interactions with DNA-bound activators and TATA-binding protein (TBP), as well as enzymes for histone acetylation and deubiquitylation [].; PDB: 3M99_B 2LO2_A 3MHH_C 3MHS_C.
Probab=33.64 E-value=53 Score=14.75 Aligned_cols=23 Identities=22% Similarity=0.535 Sum_probs=11.7
Q ss_pred ccCCCCCccccCccHHHHHHHhhC
Q psy517 105 FHCPYCPQKCHQKGNMVIHIKKKH 128 (138)
Q Consensus 105 ~~C~~C~~~f~~~~~l~~H~~~h~ 128 (138)
+.|+.|++.... +.+..|+..-.
T Consensus 5 ~~C~nC~R~v~a-~RfA~HLekCm 27 (33)
T PF08209_consen 5 VECPNCGRPVAA-SRFAPHLEKCM 27 (33)
T ss_dssp EE-TTTSSEEEG-GGHHHHHHHHT
T ss_pred EECCCCcCCcch-hhhHHHHHHHH
Confidence 566667654432 35566655433
No 154
>PF02176 zf-TRAF: TRAF-type zinc finger; PDB: 2EOD_A 2YUC_A 3HCU_A 3HCS_B 3HCT_A.
Probab=33.58 E-value=11 Score=19.05 Aligned_cols=39 Identities=33% Similarity=0.806 Sum_probs=16.7
Q ss_pred ceeccc--cccccCChHHHHHHHHHhcCCCCCccCCC----CCcccc
Q psy517 75 RWECPQ--CGKRYKYSRGLAMHRRLECGKEPMFHCPY----CPQKCH 115 (138)
Q Consensus 75 ~~~c~~--c~~~~~~~~~l~~h~~~~~~~~~~~~C~~----C~~~f~ 115 (138)
+..|+. |...+. ...|..|....-...+ ..|+. |+..+.
T Consensus 9 ~v~C~~~cc~~~i~-r~~l~~H~~~~C~~~~-v~C~~~~~GC~~~~~ 53 (60)
T PF02176_consen 9 PVPCPNGCCNEMIP-RKELDDHLENECPKRP-VPCPYSPYGCKERVP 53 (60)
T ss_dssp EEE-TT--S-BEEE-CCCHHHHHHTTSTTSE-EE-SS----S--EEE
T ss_pred EeeCCCCCccccee-HHHHHHHHHccCCCCc-EECCCCCCCCCCccc
Confidence 345555 333333 3346666665444444 56665 655443
No 155
>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=33.56 E-value=27 Score=18.18 Aligned_cols=11 Identities=9% Similarity=-0.390 Sum_probs=4.7
Q ss_pred CCCCCCCCCCc
Q psy517 48 FHNNNNVDSAS 58 (138)
Q Consensus 48 ~~c~~c~~~f~ 58 (138)
-.|..|++.|.
T Consensus 10 ~~C~~C~~~F~ 20 (69)
T PF01363_consen 10 SNCMICGKKFS 20 (69)
T ss_dssp SB-TTT--B-B
T ss_pred CcCcCcCCcCC
Confidence 45777888875
No 156
>PRK05452 anaerobic nitric oxide reductase flavorubredoxin; Provisional
Probab=33.04 E-value=39 Score=25.43 Aligned_cols=17 Identities=0% Similarity=-0.371 Sum_probs=11.0
Q ss_pred CCCCCCCCCCCCCCcCC
Q psy517 44 NAKPFHNNNNVDSASEF 60 (138)
Q Consensus 44 ~~~~~~c~~c~~~f~~~ 60 (138)
....|+|..|+..+...
T Consensus 422 ~~~~~~c~~c~~~yd~~ 438 (479)
T PRK05452 422 LGPRMQCSVCQWIYDPA 438 (479)
T ss_pred CCCeEEECCCCeEECCC
Confidence 44557788888766643
No 157
>TIGR00310 ZPR1_znf ZPR1 zinc finger domain.
Probab=32.63 E-value=25 Score=22.97 Aligned_cols=9 Identities=44% Similarity=0.988 Sum_probs=4.5
Q ss_pred eeccccccc
Q psy517 76 WECPQCGKR 84 (138)
Q Consensus 76 ~~c~~c~~~ 84 (138)
|.|+.||..
T Consensus 31 f~C~~CGyr 39 (192)
T TIGR00310 31 TICEHCGYR 39 (192)
T ss_pred EECCCCCCc
Confidence 455555543
No 158
>PF08271 TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013137 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIB (TFIIB). In eukaryotes the initiation of transcription of protein encoding genes by the polymerase II complexe (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least seven different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, and -IIH []. TFIIB and TFIID are responsible for promoter recognition and interaction with pol II; together with Pol II, they form a minimal initiation complex capable of transcription under certain conditions. The TATA box of a Pol II promoter is bound in the initiation complex by the TBP subunit of TFIID, which bends the DNA around the C-terminal domain of TFIIB whereas the N-terminal zinc finger of TFIIB interacts with Pol II [, ]. The TFIIB zinc finger adopts a zinc ribbon fold characterised by two beta-hairpins forming two structurally similar zinc-binding sub-sites []. The zinc finger contacts the rbp1 subunit of Pol II through its dock domain, a conserved region of about 70 amino acids located close to the polymerase active site []. In the Pol II complex this surface is located near the RNA exit groove. Interestingly this sequence is best conserved in the three polymerases that utilise a TFIIB-like general transcription factor (Pol II, Pol III, and archaeal RNA polymerase) but not in Pol I []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1VD4_A 1PFT_A 3K1F_M 3K7A_M 1RO4_A 1RLY_A 1DL6_A.
Probab=32.51 E-value=28 Score=16.36 Aligned_cols=10 Identities=40% Similarity=1.052 Sum_probs=4.9
Q ss_pred ceeccccccc
Q psy517 75 RWECPQCGKR 84 (138)
Q Consensus 75 ~~~c~~c~~~ 84 (138)
.+.|..||..
T Consensus 19 ~~vC~~CG~V 28 (43)
T PF08271_consen 19 ELVCPNCGLV 28 (43)
T ss_dssp EEEETTT-BB
T ss_pred eEECCCCCCE
Confidence 3456666544
No 159
>PF08790 zf-LYAR: LYAR-type C2HC zinc finger ; InterPro: IPR014898 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 C2HC zinc finger domain is found in LYAR proteins such as Q08288 from SWISSPROT, which are involved in cell growth regulation. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1WJV_A.
Probab=32.26 E-value=10 Score=16.37 Aligned_cols=9 Identities=22% Similarity=0.704 Sum_probs=4.3
Q ss_pred cCCCCCccc
Q psy517 106 HCPYCPQKC 114 (138)
Q Consensus 106 ~C~~C~~~f 114 (138)
.|-.|++.|
T Consensus 2 sCiDC~~~F 10 (28)
T PF08790_consen 2 SCIDCSKDF 10 (28)
T ss_dssp EETTTTEEE
T ss_pred eeecCCCCc
Confidence 344455555
No 160
>COG4391 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=32.07 E-value=12 Score=19.43 Aligned_cols=45 Identities=24% Similarity=0.479 Sum_probs=22.5
Q ss_pred cccccCCCCceeccccccccCChHHHHHHHHHhcCCCCCccCCCCCcccc
Q psy517 66 NRRTRSEDARWECPQCGKRYKYSRGLAMHRRLECGKEPMFHCPYCPQKCH 115 (138)
Q Consensus 66 h~~~h~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~C~~C~~~f~ 115 (138)
+..++.+..++.|+--+..+..+.-+ ...|......|+.|+..|.
T Consensus 15 ~~~I~~~~~~l~C~g~~~p~~HPrV~-----L~mg~~gev~CPYC~t~y~ 59 (62)
T COG4391 15 HETIEIGDLPLMCPGPEPPNDHPRVF-----LDMGDEGEVVCPYCSTRYR 59 (62)
T ss_pred ceEEEeCCeeEEcCCCCCCCCCCEEE-----EEcCCCCcEecCccccEEE
Confidence 44455666667776554444333211 1113222256777776664
No 161
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=31.73 E-value=26 Score=21.04 Aligned_cols=10 Identities=0% Similarity=-0.253 Sum_probs=5.1
Q ss_pred CCCCCCCCCCc
Q psy517 48 FHNNNNVDSAS 58 (138)
Q Consensus 48 ~~c~~c~~~f~ 58 (138)
+.| .|+..|.
T Consensus 71 ~~C-~Cg~~~~ 80 (124)
T PRK00762 71 IEC-ECGYEGV 80 (124)
T ss_pred EEe-eCcCccc
Confidence 455 5555443
No 162
>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=31.19 E-value=17 Score=22.61 Aligned_cols=30 Identities=23% Similarity=0.372 Sum_probs=16.8
Q ss_pred CCCCCCCCCCCCCcCCCCCcccccccCCCCceeccccccc
Q psy517 45 AKPFHNNNNVDSASEFQGSGTNRRTRSEDARWECPQCGKR 84 (138)
Q Consensus 45 ~~~~~c~~c~~~f~~~~~l~~h~~~h~~~~~~~c~~c~~~ 84 (138)
...|.|..||..... .+.+. .-.|+.||..
T Consensus 110 ~G~l~C~~Cg~~~~~---------~~~~~-l~~Cp~C~~~ 139 (146)
T PF07295_consen 110 PGTLVCENCGHEVEL---------THPER-LPPCPKCGHT 139 (146)
T ss_pred CceEecccCCCEEEe---------cCCCc-CCCCCCCCCC
Confidence 345888888874321 12222 2358888654
No 163
>cd00924 Cyt_c_Oxidase_Vb Cytochrome c oxidase subunit Vb. Cytochrome c oxidase (CcO), the terminal oxidase in the respiratory chains of eukaryotes and most bacteria, is a multi-chain transmembrane protein located in the inner membrane of mitochondria and the cell membrane of prokaryotes. It catalyzes the reduction of O2 and simultaneously pumps protons across the membrane. The number of subunits varies from three to five in bacteria and up to 13 in mammalian mitochondria. Subunits I, II, and III of mammalian CcO are encoded within the mitochondrial genome and the remaining 10 subunits are encoded within the nuclear genome. Found only in eukaryotes, subunit Vb is one of three mammalian subunits that lacks a transmembrane region. Subunit Vb is located on the matrix side of the membrane and binds the regulatory subunit of protein kinase A. The abnormally extended conformation is stable only in the CcO assembly.
Probab=30.90 E-value=22 Score=20.46 Aligned_cols=21 Identities=24% Similarity=0.514 Sum_probs=12.9
Q ss_pred ccccccCCCCceeccccccccC
Q psy517 65 TNRRTRSEDARWECPQCGKRYK 86 (138)
Q Consensus 65 ~h~~~h~~~~~~~c~~c~~~~~ 86 (138)
..+..+.+ ++..|.+||..|.
T Consensus 70 ~W~~l~~g-~~~rC~eCG~~fk 90 (97)
T cd00924 70 IWMWLEKG-KPKRCPECGHVFK 90 (97)
T ss_pred EEEEEeCC-CceeCCCCCcEEE
Confidence 33444445 5777777777665
No 164
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=30.76 E-value=47 Score=16.44 Aligned_cols=9 Identities=44% Similarity=1.545 Sum_probs=4.5
Q ss_pred eeccccccc
Q psy517 76 WECPQCGKR 84 (138)
Q Consensus 76 ~~c~~c~~~ 84 (138)
+.|..||..
T Consensus 38 ~~C~~Cgyt 46 (50)
T PRK00432 38 WHCGKCGYT 46 (50)
T ss_pred EECCCcCCE
Confidence 445555543
No 165
>PLN02294 cytochrome c oxidase subunit Vb
Probab=30.63 E-value=35 Score=21.87 Aligned_cols=10 Identities=50% Similarity=1.225 Sum_probs=5.3
Q ss_pred ccCCCCCccc
Q psy517 105 FHCPYCPQKC 114 (138)
Q Consensus 105 ~~C~~C~~~f 114 (138)
..|+.||..|
T Consensus 142 ~RCpeCG~~f 151 (174)
T PLN02294 142 FECPVCTQYF 151 (174)
T ss_pred eeCCCCCCEE
Confidence 5555555544
No 166
>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 COG4306 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=28.70 E-value=19 Score=21.70 Aligned_cols=17 Identities=24% Similarity=0.772 Sum_probs=11.7
Q ss_pred CCceeccccccccCChH
Q psy517 73 DARWECPQCGKRYKYSR 89 (138)
Q Consensus 73 ~~~~~c~~c~~~~~~~~ 89 (138)
+.|.-|..||..|++..
T Consensus 66 e~psfchncgs~fpwte 82 (160)
T COG4306 66 EPPSFCHNCGSRFPWTE 82 (160)
T ss_pred CCcchhhcCCCCCCcHH
Confidence 45666777888777664
No 168
>COG2331 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=28.39 E-value=6.3 Score=21.46 Aligned_cols=31 Identities=16% Similarity=0.322 Sum_probs=17.3
Q ss_pred CCCCCCCCCCcCCCCCcccccccCCCCceecccccccc
Q psy517 48 FHNNNNVDSASEFQGSGTNRRTRSEDARWECPQCGKRY 85 (138)
Q Consensus 48 ~~c~~c~~~f~~~~~l~~h~~~h~~~~~~~c~~c~~~~ 85 (138)
|+|..|+..|.- .+++. ....-.|++|+..+
T Consensus 13 Y~c~~cg~~~dv----vq~~~---ddplt~ce~c~a~~ 43 (82)
T COG2331 13 YECTECGNRFDV----VQAMT---DDPLTTCEECGARL 43 (82)
T ss_pred EeecccchHHHH----HHhcc---cCccccChhhChHH
Confidence 788888877653 22221 11234677777644
No 169
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=28.20 E-value=44 Score=18.97 Aligned_cols=10 Identities=40% Similarity=1.225 Sum_probs=4.8
Q ss_pred eecccccccc
Q psy517 76 WECPQCGKRY 85 (138)
Q Consensus 76 ~~c~~c~~~~ 85 (138)
+.|..|++.|
T Consensus 55 W~C~~C~~~~ 64 (90)
T PTZ00255 55 WRCKGCKKTV 64 (90)
T ss_pred EEcCCCCCEE
Confidence 4455554443
No 170
>PRK04351 hypothetical protein; Provisional
Probab=28.20 E-value=36 Score=21.23 Aligned_cols=32 Identities=31% Similarity=0.838 Sum_probs=16.6
Q ss_pred ceeccccccccCChHHHHHHHHHhcCCCCCccCCCCCcccc
Q psy517 75 RWECPQCGKRYKYSRGLAMHRRLECGKEPMFHCPYCPQKCH 115 (138)
Q Consensus 75 ~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~C~~C~~~f~ 115 (138)
.|.|..||..+... ++. .... |.|..|+..+.
T Consensus 112 ~Y~C~~Cg~~~~r~------Rr~--n~~~-yrCg~C~g~L~ 143 (149)
T PRK04351 112 LYECQSCGQQYLRK------RRI--NTKR-YRCGKCRGKLK 143 (149)
T ss_pred EEECCCCCCEeeee------eec--CCCc-EEeCCCCcEee
Confidence 46777776554321 111 1234 77777765543
No 171
>KOG2231|consensus
Probab=27.72 E-value=74 Score=25.18 Aligned_cols=50 Identities=20% Similarity=0.318 Sum_probs=27.6
Q ss_pred eccccccccCChHHHHHHHHHhcCCCCCccC---CCCCccccCccHHHHHHHhhC
Q psy517 77 ECPQCGKRYKYSRGLAMHRRLECGKEPMFHC---PYCPQKCHQKGNMVIHIKKKH 128 (138)
Q Consensus 77 ~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~C---~~C~~~f~~~~~l~~H~~~h~ 128 (138)
.|..|...|.....|..|++.+.-.. ..| ..++..|.....|..|-+..|
T Consensus 184 ~C~~C~~~fld~~el~rH~~~~h~~c--hfC~~~~~~neyy~~~~dLe~HfR~~H 236 (669)
T KOG2231|consen 184 LCKFCHERFLDDDELYRHLRFDHEFC--HFCDYKTGQNEYYNDYDDLEEHFRKGH 236 (669)
T ss_pred cchhhhhhhccHHHHHHhhccceehe--eecCcccccchhcccchHHHHHhhhcC
Confidence 46666666666666666666554321 112 123345566666666666555
No 172
>PF13451 zf-trcl: Probable zinc-binding domain
Probab=27.69 E-value=32 Score=17.10 Aligned_cols=17 Identities=24% Similarity=0.835 Sum_probs=11.9
Q ss_pred CCceeccccccccCChH
Q psy517 73 DARWECPQCGKRYKYSR 89 (138)
Q Consensus 73 ~~~~~c~~c~~~~~~~~ 89 (138)
.+.+.|..||..|....
T Consensus 2 Dk~l~C~dCg~~FvfTa 18 (49)
T PF13451_consen 2 DKTLTCKDCGAEFVFTA 18 (49)
T ss_pred CeeEEcccCCCeEEEeh
Confidence 35677888887776654
No 173
>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=27.58 E-value=53 Score=16.18 Aligned_cols=11 Identities=0% Similarity=-0.348 Sum_probs=6.2
Q ss_pred CCCCCCCCCcC
Q psy517 49 HNNNNVDSASE 59 (138)
Q Consensus 49 ~c~~c~~~f~~ 59 (138)
.|..|++.|..
T Consensus 4 ~C~~C~~~F~~ 14 (57)
T cd00065 4 SCMGCGKPFTL 14 (57)
T ss_pred cCcccCccccC
Confidence 35566666553
No 174
>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=27.30 E-value=39 Score=15.43 Aligned_cols=31 Identities=26% Similarity=0.481 Sum_probs=16.8
Q ss_pred eeccccccccCChHHHHHHHHHhcCCCCCccCCCCCcccc
Q psy517 76 WECPQCGKRYKYSRGLAMHRRLECGKEPMFHCPYCPQKCH 115 (138)
Q Consensus 76 ~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~C~~C~~~f~ 115 (138)
..|+.||..|..... ..... -.|..||..+.
T Consensus 2 r~C~~Cg~~Yh~~~~--------pP~~~-~~Cd~cg~~L~ 32 (36)
T PF05191_consen 2 RICPKCGRIYHIEFN--------PPKVE-GVCDNCGGELV 32 (36)
T ss_dssp EEETTTTEEEETTTB----------SST-TBCTTTTEBEB
T ss_pred cCcCCCCCccccccC--------CCCCC-CccCCCCCeeE
Confidence 357778877654322 12223 57777775443
No 175
>TIGR00416 sms DNA repair protein RadA. The gene protuct codes for a probable ATP-dependent protease involved in both DNA repair and degradation of proteins, peptides, glycopeptides. Also known as sms. Residues 11-28 of the SEED alignment contain a putative Zn binding domain. Residues 110-117 of the seed contain a putative ATP binding site both documented in Haemophilus and in Listeria monocytogenes. for E.coli see ( J. BACTERIOL. 178:5045-5048(1996)).
Probab=27.21 E-value=40 Score=25.16 Aligned_cols=23 Identities=17% Similarity=0.378 Sum_probs=15.6
Q ss_pred CCCCCCCCCCCcCCCCCcccccccCCCCceecccccc
Q psy517 47 PFHNNNNVDSASEFQGSGTNRRTRSEDARWECPQCGK 83 (138)
Q Consensus 47 ~~~c~~c~~~f~~~~~l~~h~~~h~~~~~~~c~~c~~ 83 (138)
.|.|..||..... ....|+.|+.
T Consensus 7 ~y~C~~Cg~~~~~--------------~~g~Cp~C~~ 29 (454)
T TIGR00416 7 KFVCQHCGADSPK--------------WQGKCPACHA 29 (454)
T ss_pred eEECCcCCCCCcc--------------ccEECcCCCC
Confidence 4889999965332 2367888864
No 176
>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=27.20 E-value=39 Score=19.21 Aligned_cols=8 Identities=0% Similarity=-0.300 Sum_probs=4.0
Q ss_pred CCCCCCCC
Q psy517 48 FHNNNNVD 55 (138)
Q Consensus 48 ~~c~~c~~ 55 (138)
|.|+.|++
T Consensus 36 y~CpfCgk 43 (91)
T TIGR00280 36 YVCPFCGK 43 (91)
T ss_pred ccCCCCCC
Confidence 45555543
No 177
>PF14369 zf-RING_3: zinc-finger
Probab=27.00 E-value=54 Score=14.83 Aligned_cols=9 Identities=33% Similarity=1.246 Sum_probs=4.7
Q ss_pred ecccccccc
Q psy517 77 ECPQCGKRY 85 (138)
Q Consensus 77 ~c~~c~~~~ 85 (138)
.|+.|+..|
T Consensus 23 ~CP~C~~gF 31 (35)
T PF14369_consen 23 ACPRCHGGF 31 (35)
T ss_pred CCcCCCCcE
Confidence 355555544
No 178
>PF14353 CpXC: CpXC protein
Probab=26.82 E-value=31 Score=20.62 Aligned_cols=23 Identities=4% Similarity=-0.291 Sum_probs=17.9
Q ss_pred CCCCCCCCCCCcCCCCCcccccc
Q psy517 47 PFHNNNNVDSASEFQGSGTNRRT 69 (138)
Q Consensus 47 ~~~c~~c~~~f~~~~~l~~h~~~ 69 (138)
.+.|+.||..|.-...+..|-..
T Consensus 38 ~~~CP~Cg~~~~~~~p~lY~D~~ 60 (128)
T PF14353_consen 38 SFTCPSCGHKFRLEYPLLYHDPE 60 (128)
T ss_pred EEECCCCCCceecCCCEEEEcCC
Confidence 47899999999877777666544
No 179
>COG5533 UBP5 Ubiquitin C-terminal hydrolase [Posttranslational modification, protein turnover, chaperones]
Probab=26.67 E-value=8.9 Score=27.09 Aligned_cols=13 Identities=46% Similarity=1.244 Sum_probs=9.2
Q ss_pred CCCCCccCCCCCcc
Q psy517 100 GKEPMFHCPYCPQK 113 (138)
Q Consensus 100 ~~~~~~~C~~C~~~ 113 (138)
|... |.|+.|++.
T Consensus 281 g~d~-W~CpkC~~k 293 (415)
T COG5533 281 GKDA-WRCPKCGRK 293 (415)
T ss_pred Cccc-ccCchhccc
Confidence 4445 889998864
No 180
>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=26.63 E-value=26 Score=17.43 Aligned_cols=11 Identities=27% Similarity=0.884 Sum_probs=5.7
Q ss_pred cCCCCCccccC
Q psy517 106 HCPYCPQKCHQ 116 (138)
Q Consensus 106 ~C~~C~~~f~~ 116 (138)
.|+.|++.|..
T Consensus 22 ~CPlC~r~l~~ 32 (54)
T PF04423_consen 22 CCPLCGRPLDE 32 (54)
T ss_dssp E-TTT--EE-H
T ss_pred cCCCCCCCCCH
Confidence 79999988763
No 181
>PRK11823 DNA repair protein RadA; Provisional
Probab=26.62 E-value=42 Score=24.99 Aligned_cols=24 Identities=17% Similarity=0.416 Sum_probs=15.6
Q ss_pred CCCCCCCCCCCCcCCCCCcccccccCCCCceecccccc
Q psy517 46 KPFHNNNNVDSASEFQGSGTNRRTRSEDARWECPQCGK 83 (138)
Q Consensus 46 ~~~~c~~c~~~f~~~~~l~~h~~~h~~~~~~~c~~c~~ 83 (138)
..|.|..||..... ....|+.|+.
T Consensus 6 ~~y~C~~Cg~~~~~--------------~~g~Cp~C~~ 29 (446)
T PRK11823 6 TAYVCQECGAESPK--------------WLGRCPECGA 29 (446)
T ss_pred CeEECCcCCCCCcc--------------cCeeCcCCCC
Confidence 35889999865332 2367888854
No 182
>PF10083 DUF2321: Uncharacterized protein conserved in bacteria (DUF2321); InterPro: IPR016891 This entry is represented by Bacteriophage 'Lactobacillus prophage Lj928', Orf-Ljo1454. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=26.50 E-value=1.2e+02 Score=19.25 Aligned_cols=20 Identities=30% Similarity=0.682 Sum_probs=15.3
Q ss_pred CCceeccccccccCChHHHH
Q psy517 73 DARWECPQCGKRYKYSRGLA 92 (138)
Q Consensus 73 ~~~~~c~~c~~~~~~~~~l~ 92 (138)
+.|.-|..||+.|++.....
T Consensus 66 ~~PsYC~~CGkpyPWt~~~L 85 (158)
T PF10083_consen 66 EAPSYCHNCGKPYPWTENAL 85 (158)
T ss_pred CCChhHHhCCCCCchHHHHH
Confidence 46778999999998875533
No 183
>PHA02998 RNA polymerase subunit; Provisional
Probab=25.78 E-value=44 Score=21.62 Aligned_cols=10 Identities=30% Similarity=0.999 Sum_probs=4.7
Q ss_pred eecccccccc
Q psy517 76 WECPQCGKRY 85 (138)
Q Consensus 76 ~~c~~c~~~~ 85 (138)
|.|..||..|
T Consensus 172 YkC~~CG~~w 181 (195)
T PHA02998 172 HACRDCKKHF 181 (195)
T ss_pred EEcCCCCCcc
Confidence 3455554444
No 184
>PRK12496 hypothetical protein; Provisional
Probab=25.44 E-value=52 Score=20.86 Aligned_cols=12 Identities=33% Similarity=0.703 Sum_probs=7.8
Q ss_pred eeccccccccCC
Q psy517 76 WECPQCGKRYKY 87 (138)
Q Consensus 76 ~~c~~c~~~~~~ 87 (138)
+.|.-|++.|..
T Consensus 128 ~~C~gC~~~~~~ 139 (164)
T PRK12496 128 KVCKGCKKKYPE 139 (164)
T ss_pred EECCCCCccccC
Confidence 567777776643
No 185
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=24.93 E-value=38 Score=20.66 Aligned_cols=15 Identities=20% Similarity=0.791 Sum_probs=12.3
Q ss_pred ceeccccccccCChH
Q psy517 75 RWECPQCGKRYKYSR 89 (138)
Q Consensus 75 ~~~c~~c~~~~~~~~ 89 (138)
|++|..||+.|..-+
T Consensus 1 PH~Ct~Cg~~f~dgs 15 (131)
T PF09845_consen 1 PHQCTKCGRVFEDGS 15 (131)
T ss_pred CcccCcCCCCcCCCc
Confidence 568999999998765
No 186
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=24.87 E-value=58 Score=18.82 Aligned_cols=35 Identities=20% Similarity=0.162 Sum_probs=18.2
Q ss_pred CCCCCCCCCCCCcCCCCCcccccccCCCCceeccccccccCC
Q psy517 46 KPFHNNNNVDSASEFQGSGTNRRTRSEDARWECPQCGKRYKY 87 (138)
Q Consensus 46 ~~~~c~~c~~~f~~~~~l~~h~~~h~~~~~~~c~~c~~~~~~ 87 (138)
..|.|+.|+. ......+.. +.-...|+.||..+..
T Consensus 20 t~f~CP~Cge-~~v~v~~~k------~~~h~~C~~CG~y~~~ 54 (99)
T PRK14892 20 KIFECPRCGK-VSISVKIKK------NIAIITCGNCGLYTEF 54 (99)
T ss_pred cEeECCCCCC-eEeeeecCC------CcceEECCCCCCccCE
Confidence 4577888883 221111211 2233568888766544
No 187
>PF10263 SprT-like: SprT-like family; InterPro: IPR006640 This is a family of uncharacterised bacterial proteins which includes Escherichia coli SprT (P39902 from SWISSPROT). SprT is described as a regulator of bolA gene in stationary phase []. The majority of members contain the metallopeptidase zinc binding signature which has a HExxH motif, however there is no evidence for them being metallopeptidases.
Probab=23.74 E-value=37 Score=20.87 Aligned_cols=31 Identities=35% Similarity=0.945 Sum_probs=15.5
Q ss_pred ceeccccccccCChHHHHHHHHHhcCCCCCccCCCCCccc
Q psy517 75 RWECPQCGKRYKYSRGLAMHRRLECGKEPMFHCPYCPQKC 114 (138)
Q Consensus 75 ~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~C~~C~~~f 114 (138)
.|.|..|+..+.. +.+. .... |.|..|+..+
T Consensus 123 ~~~C~~C~~~~~r------~~~~--~~~~-~~C~~C~~~l 153 (157)
T PF10263_consen 123 VYRCPSCGREYKR------HRRS--KRKR-YRCGRCGGPL 153 (157)
T ss_pred EEEcCCCCCEeee------eccc--chhh-EECCCCCCEE
Confidence 4667777655422 2222 1123 6677776444
No 188
>PF09963 DUF2197: Uncharacterized protein conserved in bacteria (DUF2197); InterPro: IPR019241 This family represents various hypothetical bacterial proteins with no known function.
Probab=23.68 E-value=40 Score=17.27 Aligned_cols=36 Identities=19% Similarity=0.510 Sum_probs=16.7
Q ss_pred eccccccccCChHHHHHHHHHhc-CCCCCccCCCCCcc
Q psy517 77 ECPQCGKRYKYSRGLAMHRRLEC-GKEPMFHCPYCPQK 113 (138)
Q Consensus 77 ~c~~c~~~~~~~~~l~~h~~~~~-~~~~~~~C~~C~~~ 113 (138)
.|..|++.+..-.......+.-. .... |-|..|...
T Consensus 4 kC~lCdk~~~Id~~~~~aKrLrnrPi~t-YmC~eC~~R 40 (56)
T PF09963_consen 4 KCILCDKKEEIDEDTPEAKRLRNRPIHT-YMCDECKER 40 (56)
T ss_pred EEEecCCEEEeccCCHHHHHhhcCCCcc-eeChhHHHH
Confidence 56667665443322222222211 1233 888888543
No 189
>KOG3002|consensus
Probab=23.36 E-value=91 Score=22.02 Aligned_cols=86 Identities=13% Similarity=0.059 Sum_probs=47.2
Q ss_pred CCCCCCCCCCCcCCC--CCcccccc--cCCCCceeccccccccCChHHHHHHHHHhcCCCCCccCC----CCCccccCcc
Q psy517 47 PFHNNNNVDSASEFQ--GSGTNRRT--RSEDARWECPQCGKRYKYSRGLAMHRRLECGKEPMFHCP----YCPQKCHQKG 118 (138)
Q Consensus 47 ~~~c~~c~~~f~~~~--~l~~h~~~--h~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~C~----~C~~~f~~~~ 118 (138)
.+.|++|.....-.. .-..|+.- ...+....|+.|...+.....+..-.- ..... +.|+ .|.++|....
T Consensus 48 lleCPvC~~~l~~Pi~QC~nGHlaCssC~~~~~~~CP~Cr~~~g~~R~~amEkV--~e~~~-vpC~~~~~GC~~~~~Y~~ 124 (299)
T KOG3002|consen 48 LLDCPVCFNPLSPPIFQCDNGHLACSSCRTKVSNKCPTCRLPIGNIRCRAMEKV--AEAVL-VPCKNAKLGCTKSFPYGE 124 (299)
T ss_pred hccCchhhccCcccceecCCCcEehhhhhhhhcccCCccccccccHHHHHHHHH--HHhce-ecccccccCCceeecccc
Confidence 468888887544211 11112211 112456688888877775554433222 22223 5665 4777887765
Q ss_pred HHHHHHHhhCCCCCCCCCC
Q psy517 119 NMVIHIKKKHPEKANPHDE 137 (138)
Q Consensus 119 ~l~~H~~~h~~~k~~~C~~ 137 (138)
. ..|.+.-.. .||.|+.
T Consensus 125 ~-~~HE~~C~f-~~~~CP~ 141 (299)
T KOG3002|consen 125 K-SKHEKVCEF-RPCSCPV 141 (299)
T ss_pred c-ccccccccc-CCcCCCC
Confidence 5 567666665 7777763
No 190
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=23.17 E-value=46 Score=15.03 Aligned_cols=8 Identities=50% Similarity=1.294 Sum_probs=3.5
Q ss_pred eecccccc
Q psy517 76 WECPQCGK 83 (138)
Q Consensus 76 ~~c~~c~~ 83 (138)
+.|+.||.
T Consensus 23 ~vC~~Cg~ 30 (34)
T PF14803_consen 23 LVCPACGF 30 (34)
T ss_dssp EEETTTTE
T ss_pred eECCCCCC
Confidence 34444443
No 191
>TIGR00340 zpr1_rel ZPR1-related zinc finger protein. A model ZPR1_znf (TIGR00310) has been created to describe the domain shared by this protein and ZPR1.
Probab=23.15 E-value=49 Score=21.01 Aligned_cols=11 Identities=0% Similarity=-0.079 Sum_probs=5.9
Q ss_pred CCCCCCCCCCc
Q psy517 48 FHNNNNVDSAS 58 (138)
Q Consensus 48 ~~c~~c~~~f~ 58 (138)
|.|+.||....
T Consensus 29 f~C~~CGyr~~ 39 (163)
T TIGR00340 29 YICEKCGYRST 39 (163)
T ss_pred EECCCCCCchh
Confidence 45666665433
No 192
>smart00132 LIM Zinc-binding domain present in Lin-11, Isl-1, Mec-3. Zinc-binding domain family. Some LIM domains bind protein partners via tyrosine-containing motifs. LIM domains are found in many key regulators of developmental pathways.
Probab=23.09 E-value=80 Score=13.61 Aligned_cols=7 Identities=57% Similarity=1.706 Sum_probs=2.7
Q ss_pred ecccccc
Q psy517 77 ECPQCGK 83 (138)
Q Consensus 77 ~c~~c~~ 83 (138)
.|..|+.
T Consensus 29 ~C~~C~~ 35 (39)
T smart00132 29 KCSKCGK 35 (39)
T ss_pred CCcccCC
Confidence 3444433
No 193
>PF11789 zf-Nse: Zinc-finger of the MIZ type in Nse subunit; PDB: 2YU4_A 3HTK_C.
Probab=22.93 E-value=1e+02 Score=15.66 Aligned_cols=30 Identities=13% Similarity=0.327 Sum_probs=14.2
Q ss_pred ceeccccccccCChHHHHHHHHHhcCCCCCccCCC
Q psy517 75 RWECPQCGKRYKYSRGLAMHRRLECGKEPMFHCPY 109 (138)
Q Consensus 75 ~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~C~~ 109 (138)
|.....||-.|...+ +...+ ..... ..|+.
T Consensus 24 PV~s~~C~H~fek~a-I~~~i---~~~~~-~~CPv 53 (57)
T PF11789_consen 24 PVKSKKCGHTFEKEA-ILQYI---QRNGS-KRCPV 53 (57)
T ss_dssp EEEESSS--EEEHHH-HHHHC---TTTS--EE-SC
T ss_pred CcCcCCCCCeecHHH-HHHHH---HhcCC-CCCCC
Confidence 666677877776554 33333 12233 67776
No 194
>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=22.83 E-value=12 Score=18.77 Aligned_cols=26 Identities=0% Similarity=-0.192 Sum_probs=13.7
Q ss_pred CCCCCCCCCCCCCcCCCCCccccccc
Q psy517 45 AKPFHNNNNVDSASEFQGSGTNRRTR 70 (138)
Q Consensus 45 ~~~~~c~~c~~~f~~~~~l~~h~~~h 70 (138)
...|+|+.|.+.|...-++-.|...|
T Consensus 19 ~~~y~C~~C~~~FC~dCD~fiHE~LH 44 (51)
T PF07975_consen 19 SSRYRCPKCKNHFCIDCDVFIHETLH 44 (51)
T ss_dssp -EEE--TTTT--B-HHHHHTTTTTS-
T ss_pred CCeEECCCCCCccccCcChhhhcccc
Confidence 35699999999998776666665444
No 195
>KOG0782|consensus
Probab=22.51 E-value=15 Score=28.33 Aligned_cols=29 Identities=21% Similarity=0.315 Sum_probs=14.8
Q ss_pred HHHHHHHHhcCCCCCccCCCCCccccCccH
Q psy517 90 GLAMHRRLECGKEPMFHCPYCPQKCHQKGN 119 (138)
Q Consensus 90 ~l~~h~~~~~~~~~~~~C~~C~~~f~~~~~ 119 (138)
.+.+|.=.|..... -+|..|++.|.++..
T Consensus 240 ~fvrHHWVHrrRqe-GkC~~CgKgFQQKf~ 268 (1004)
T KOG0782|consen 240 GFVRHHWVHRRRQE-GKCNTCGKGFQQKFF 268 (1004)
T ss_pred cchHHhHhhHhhhc-cccchhhhhhhhhee
Confidence 44444444443333 456667766665543
No 196
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=22.35 E-value=51 Score=19.48 Aligned_cols=10 Identities=40% Similarity=1.438 Sum_probs=5.0
Q ss_pred eecccccccc
Q psy517 76 WECPQCGKRY 85 (138)
Q Consensus 76 ~~c~~c~~~~ 85 (138)
|.|..||..|
T Consensus 101 y~C~~Cg~~w 110 (113)
T COG1594 101 YKCTRCGYRW 110 (113)
T ss_pred EEecccCCEe
Confidence 4555555443
No 197
>cd02341 ZZ_ZZZ3 Zinc finger, ZZ type. Zinc finger present in ZZZ3 (ZZ finger containing 3) and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
Probab=22.34 E-value=56 Score=16.02 Aligned_cols=7 Identities=43% Similarity=1.478 Sum_probs=4.8
Q ss_pred ccCCCCC
Q psy517 105 FHCPYCP 111 (138)
Q Consensus 105 ~~C~~C~ 111 (138)
|.|..|.
T Consensus 16 ~~C~~C~ 22 (48)
T cd02341 16 YHCSECD 22 (48)
T ss_pred EECCCCC
Confidence 7777665
No 198
>cd02335 ZZ_ADA2 Zinc finger, ZZ type. Zinc finger present in ADA2, a putative transcriptional adaptor, and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
Probab=22.32 E-value=55 Score=15.93 Aligned_cols=7 Identities=43% Similarity=1.417 Sum_probs=4.3
Q ss_pred ccCCCCC
Q psy517 105 FHCPYCP 111 (138)
Q Consensus 105 ~~C~~C~ 111 (138)
|.|..|.
T Consensus 16 ~~C~~C~ 22 (49)
T cd02335 16 IKCAECP 22 (49)
T ss_pred EECCCCC
Confidence 6776653
No 199
>KOG2071|consensus
Probab=22.12 E-value=71 Score=24.75 Aligned_cols=27 Identities=15% Similarity=0.374 Sum_probs=21.5
Q ss_pred CCCCccCCCCCccccCccHHHHHHHhhC
Q psy517 101 KEPMFHCPYCPQKCHQKGNMVIHIKKKH 128 (138)
Q Consensus 101 ~~~~~~C~~C~~~f~~~~~l~~H~~~h~ 128 (138)
..+ -.|..||.+|........|+..|.
T Consensus 416 ~~p-nqC~~CG~R~~~~ee~sk~md~H~ 442 (579)
T KOG2071|consen 416 DSP-NQCKSCGLRFDDSEERSKHMDIHD 442 (579)
T ss_pred CCc-chhcccccccccchhhhhHhhhhh
Confidence 345 889999999998888887776665
No 200
>KOG2482|consensus
Probab=21.64 E-value=55 Score=23.60 Aligned_cols=23 Identities=30% Similarity=0.736 Sum_probs=20.7
Q ss_pred ccCCCCCccccCccHHHHHHHhh
Q psy517 105 FHCPYCPQKCHQKGNMVIHIKKK 127 (138)
Q Consensus 105 ~~C~~C~~~f~~~~~l~~H~~~h 127 (138)
+.|-.|.+.|..+..|..|++.-
T Consensus 196 ~~CLyCekifrdkntLkeHMrkK 218 (423)
T KOG2482|consen 196 LRCLYCEKIFRDKNTLKEHMRKK 218 (423)
T ss_pred heeeeeccccCCcHHHHHHHHhc
Confidence 78999999999999999998753
No 201
>COG3809 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=21.40 E-value=1.1e+02 Score=16.98 Aligned_cols=42 Identities=14% Similarity=-0.038 Sum_probs=26.3
Q ss_pred CCCCCCCCCcCCCCCcccccccCCCCceeccccccccCChHHHHHHHHHh
Q psy517 49 HNNNNVDSASEFQGSGTNRRTRSEDARWECPQCGKRYKYSRGLAMHRRLE 98 (138)
Q Consensus 49 ~c~~c~~~f~~~~~l~~h~~~h~~~~~~~c~~c~~~~~~~~~l~~h~~~~ 98 (138)
.|+.|+..... ....+..--.|+.|+..+.....|..-+...
T Consensus 3 lCP~C~v~l~~--------~~rs~vEiD~CPrCrGVWLDrGELdKli~r~ 44 (88)
T COG3809 3 LCPICGVELVM--------SVRSGVEIDYCPRCRGVWLDRGELDKLIERS 44 (88)
T ss_pred ccCcCCceeee--------eeecCceeeeCCccccEeecchhHHHHHHHh
Confidence 47778765433 1222333446999999888888777655443
No 202
>KOG0717|consensus
Probab=21.34 E-value=49 Score=24.87 Aligned_cols=19 Identities=16% Similarity=0.370 Sum_probs=10.6
Q ss_pred cCCCCCccccCccHHHHHH
Q psy517 106 HCPYCPQKCHQKGNMVIHI 124 (138)
Q Consensus 106 ~C~~C~~~f~~~~~l~~H~ 124 (138)
-|..|.++|.+--.+..|.
T Consensus 294 yC~vCnKsFKseKq~kNHE 312 (508)
T KOG0717|consen 294 YCVVCNKSFKSEKQLKNHE 312 (508)
T ss_pred EEeeccccccchHHHHhhH
Confidence 4555666665555555554
No 203
>KOG3507|consensus
Probab=21.26 E-value=55 Score=16.93 Aligned_cols=11 Identities=36% Similarity=0.875 Sum_probs=6.2
Q ss_pred ceecccccccc
Q psy517 75 RWECPQCGKRY 85 (138)
Q Consensus 75 ~~~c~~c~~~~ 85 (138)
.+.|.+||...
T Consensus 37 ~irCReCG~RI 47 (62)
T KOG3507|consen 37 VIRCRECGYRI 47 (62)
T ss_pred cEehhhcchHH
Confidence 45566666544
No 204
>KOG2231|consensus
Probab=21.23 E-value=58 Score=25.74 Aligned_cols=79 Identities=19% Similarity=0.140 Sum_probs=47.4
Q ss_pred CCCCCCCCCCcCCCCCcccccccCCCCceecccc------ccccCChHHHHHHHHHhcCCCCCccCC--CCC-ccccCcc
Q psy517 48 FHNNNNVDSASEFQGSGTNRRTRSEDARWECPQC------GKRYKYSRGLAMHRRLECGKEPMFHCP--YCP-QKCHQKG 118 (138)
Q Consensus 48 ~~c~~c~~~f~~~~~l~~h~~~h~~~~~~~c~~c------~~~~~~~~~l~~h~~~~~~~~~~~~C~--~C~-~~f~~~~ 118 (138)
-.|..|...|.....|..|++.+. +.|..| +..|..-..|..|-+.++ |.|. .|. +.|....
T Consensus 183 p~C~~C~~~fld~~el~rH~~~~h----~~chfC~~~~~~neyy~~~~dLe~HfR~~H-----flCE~~~C~~~~f~~~~ 253 (669)
T KOG2231|consen 183 PLCKFCHERFLDDDELYRHLRFDH----EFCHFCDYKTGQNEYYNDYDDLEEHFRKGH-----FLCEEEFCRTKKFYVAF 253 (669)
T ss_pred ccchhhhhhhccHHHHHHhhccce----eheeecCcccccchhcccchHHHHHhhhcC-----ccccccccccceeeehh
Confidence 358889998888888888887654 334444 456666678888888655 6665 343 3343333
Q ss_pred HHHHHHH----hhCCCCCCCC
Q psy517 119 NMVIHIK----KKHPEKANPH 135 (138)
Q Consensus 119 ~l~~H~~----~h~~~k~~~C 135 (138)
.+..+++ .+.-|+.|.|
T Consensus 254 ~~ei~lk~~~~~~~~e~~~~~ 274 (669)
T KOG2231|consen 254 ELEIELKAHNRFIQHEKCYIC 274 (669)
T ss_pred HHHHHHHhhccccchheeccC
Confidence 3344444 3333455554
No 205
>COG2956 Predicted N-acetylglucosaminyl transferase [Carbohydrate transport and metabolism]
Probab=21.21 E-value=1e+02 Score=22.38 Aligned_cols=10 Identities=30% Similarity=1.085 Sum_probs=4.9
Q ss_pred CCCccCCCCC
Q psy517 102 EPMFHCPYCP 111 (138)
Q Consensus 102 ~~~~~C~~C~ 111 (138)
+|+|.|..||
T Consensus 352 ~~~YRC~~CG 361 (389)
T COG2956 352 KPRYRCQNCG 361 (389)
T ss_pred cCCceecccC
Confidence 3345555554
No 206
>KOG2461|consensus
Probab=21.19 E-value=73 Score=23.46 Aligned_cols=39 Identities=3% Similarity=-0.186 Sum_probs=16.4
Q ss_pred cccccccCCCCceeccccccccCChHHHHHHHHHhcCCC
Q psy517 64 GTNRRTRSEDARWECPQCGKRYKYSRGLAMHRRLECGKE 102 (138)
Q Consensus 64 ~~h~~~h~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~ 102 (138)
..+...+.+..+..++.+.+.......+..+...+.+..
T Consensus 320 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 358 (396)
T KOG2461|consen 320 DQSEVPATVSVWTGETIPVRTPAGQLIYTQSHSMEVAEP 358 (396)
T ss_pred ccccccccccccCcCcccccccccccchhhhhhcccCCC
Confidence 333344444433334444444444444444444444433
No 207
>PF05502 Dynactin_p62: Dynactin p62 family; InterPro: IPR008603 Dynactin is a multi-subunit complex and a required cofactor for most, or all, o f the cellular processes powered by the microtubule-based motor cytoplasmic dyn ein. p62 binds directly to the Arp1 subunit of dynactin [, ].
Probab=20.97 E-value=59 Score=24.62 Aligned_cols=10 Identities=30% Similarity=0.966 Sum_probs=5.1
Q ss_pred eecccccccc
Q psy517 76 WECPQCGKRY 85 (138)
Q Consensus 76 ~~c~~c~~~~ 85 (138)
|.|+.|....
T Consensus 53 f~CP~C~~~L 62 (483)
T PF05502_consen 53 FDCPICFSPL 62 (483)
T ss_pred ccCCCCCCcc
Confidence 5555555433
No 208
>PF06397 Desulfoferrod_N: Desulfoferrodoxin, N-terminal domain; InterPro: IPR004462 This domain is found as essentially the full length of desulforedoxin, a 37-residue homodimeric non-haem iron protein. It is also found as the N-terminal domain of desulfoferrodoxin (rbo), a homodimeric non-haem iron protein with 2 Fe atoms per monomer in different oxidation states. This domain binds the ferric rather than the ferrous Fe of desulfoferrodoxin. Neelaredoxin, a monomeric blue non-haem iron protein, lacks this domain.; GO: 0005506 iron ion binding; PDB: 1DFX_A 1VZI_B 2JI2_D 1VZH_B 2JI3_C 2JI1_C 1VZG_A 1CFW_A 2LK5_B 1DHG_B ....
Probab=20.82 E-value=31 Score=15.86 Aligned_cols=11 Identities=0% Similarity=-0.070 Sum_probs=5.7
Q ss_pred CCCCCCCCCCC
Q psy517 47 PFHNNNNVDSA 57 (138)
Q Consensus 47 ~~~c~~c~~~f 57 (138)
.|+|..||...
T Consensus 6 ~YkC~~CGniV 16 (36)
T PF06397_consen 6 FYKCEHCGNIV 16 (36)
T ss_dssp EEE-TTT--EE
T ss_pred EEEccCCCCEE
Confidence 48888888753
No 209
>PF10276 zf-CHCC: Zinc-finger domain; InterPro: IPR019401 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a short conserved zinc-finger domain. It contains the sequence motif Cx8Hx14Cx2C. ; PDB: 2JVM_A 2JRR_A 2JZ8_A.
Probab=20.77 E-value=38 Score=15.97 Aligned_cols=10 Identities=40% Similarity=1.235 Sum_probs=5.1
Q ss_pred ccCCCCCccc
Q psy517 105 FHCPYCPQKC 114 (138)
Q Consensus 105 ~~C~~C~~~f 114 (138)
-.|+.|+..|
T Consensus 30 ~~CpYCg~~y 39 (40)
T PF10276_consen 30 VVCPYCGTRY 39 (40)
T ss_dssp EEETTTTEEE
T ss_pred EECCCCCCEE
Confidence 4555555443
No 210
>PF12907 zf-met2: Zinc-binding
Probab=20.74 E-value=17 Score=17.16 Aligned_cols=9 Identities=33% Similarity=0.763 Sum_probs=4.1
Q ss_pred cCCCCCccc
Q psy517 106 HCPYCPQKC 114 (138)
Q Consensus 106 ~C~~C~~~f 114 (138)
.|.+|...|
T Consensus 3 ~C~iC~qtF 11 (40)
T PF12907_consen 3 ICKICRQTF 11 (40)
T ss_pred CcHHhhHHH
Confidence 455554433
No 211
>PF01286 XPA_N: XPA protein N-terminal; InterPro: IPR022652 Xeroderma pigmentosum (XP) [] is a human autosomal recessive disease, characterised by a high incidence of sunlight-induced skin cancer. Skin cells of individual's with this condition are hypersensitive to ultraviolet light, due to defects in the incision step of DNA excision repair. There are a minimum of seven genetic complementation groups involved in this pathway: XP-A to XP-G. XP-A is the most severe form of the disease and is due to defects in a 30 kDa nuclear protein called XPA (or XPAC) []. The sequence of the XPA protein is conserved from higher eukaryotes [] to yeast (gene RAD14) []. XPA is a hydrophilic protein of 247 to 296 amino-acid residues which has a C4-type zinc finger motif in its central section. This entry contains the zinc-finger containing region in the XPA protein. It is found N-terminal to PF05181 from PFAM ; PDB: 1D4U_A 1XPA_A.
Probab=20.60 E-value=58 Score=14.77 Aligned_cols=13 Identities=0% Similarity=-0.197 Sum_probs=6.2
Q ss_pred CCCCCCCCCcCCC
Q psy517 49 HNNNNVDSASEFQ 61 (138)
Q Consensus 49 ~c~~c~~~f~~~~ 61 (138)
.|..|++.|....
T Consensus 5 ~C~eC~~~f~dSy 17 (34)
T PF01286_consen 5 KCDECGKPFMDSY 17 (34)
T ss_dssp E-TTT--EES-SS
T ss_pred hHhHhCCHHHHHH
Confidence 5788888877533
No 212
>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=20.29 E-value=1.4e+02 Score=17.41 Aligned_cols=10 Identities=10% Similarity=-0.074 Sum_probs=5.9
Q ss_pred CCCCCCCCCC
Q psy517 47 PFHNNNNVDS 56 (138)
Q Consensus 47 ~~~c~~c~~~ 56 (138)
|-.|+.||..
T Consensus 2 p~~CpYCg~~ 11 (102)
T PF11672_consen 2 PIICPYCGGP 11 (102)
T ss_pred CcccCCCCCe
Confidence 4456666663
No 213
>PRK08222 hydrogenase 4 subunit H; Validated
Probab=20.09 E-value=71 Score=20.54 Aligned_cols=13 Identities=15% Similarity=0.506 Sum_probs=7.2
Q ss_pred ccCCCCCccccCc
Q psy517 105 FHCPYCPQKCHQK 117 (138)
Q Consensus 105 ~~C~~C~~~f~~~ 117 (138)
..|..||+.|...
T Consensus 115 ~~C~~Cg~~f~~~ 127 (181)
T PRK08222 115 QRCSRCERPFAPQ 127 (181)
T ss_pred CcCcccCCccCcH
Confidence 5566666655533
No 214
>COG4896 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=20.08 E-value=41 Score=17.55 Aligned_cols=39 Identities=18% Similarity=0.414 Sum_probs=18.8
Q ss_pred ecccccc-ccCChHHHHHHHHHhcCCCCCccCCCCCccccC
Q psy517 77 ECPQCGK-RYKYSRGLAMHRRLECGKEPMFHCPYCPQKCHQ 116 (138)
Q Consensus 77 ~c~~c~~-~~~~~~~l~~h~~~~~~~~~~~~C~~C~~~f~~ 116 (138)
+|..|.+ .+.....+..-+..-.-.+. |.|+.|.-...-
T Consensus 4 kCiiCd~v~~iD~rt~~tKrLrN~PIrt-ymC~eC~~Rva~ 43 (68)
T COG4896 4 KCIICDRVDEIDNRTFKTKRLRNKPIRT-YMCPECEHRVAI 43 (68)
T ss_pred eEEEecceeeecchhHHHHHhhCCCcee-EechhhHhhhch
Confidence 4666643 23333333322222222344 899999755443
Done!