Query psy553
Match_columns 129
No_of_seqs 114 out of 1251
Neff 9.9
Searched_HMMs 46136
Date Fri Aug 16 19:53:53 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy553.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/553hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2462|consensus 99.8 7.1E-21 1.5E-25 128.8 2.1 75 31-105 187-262 (279)
2 KOG2462|consensus 99.8 2.3E-20 4.9E-25 126.4 -0.1 96 28-125 158-263 (279)
3 KOG3623|consensus 99.6 7.2E-17 1.6E-21 121.2 3.4 81 27-107 890-971 (1007)
4 KOG3576|consensus 99.6 2.2E-16 4.7E-21 103.1 0.8 77 29-105 115-192 (267)
5 KOG3623|consensus 99.4 8.2E-14 1.8E-18 105.1 3.3 81 30-110 239-333 (1007)
6 KOG3608|consensus 99.1 1.9E-11 4.1E-16 86.1 1.1 84 30-115 236-324 (467)
7 PHA00733 hypothetical protein 99.0 2.5E-11 5.4E-16 75.6 -1.1 83 28-112 37-125 (128)
8 KOG3576|consensus 99.0 3.2E-11 7E-16 79.2 -1.3 73 29-101 143-226 (267)
9 KOG3608|consensus 99.0 1.5E-10 3.2E-15 81.6 0.7 95 30-125 262-372 (467)
10 PHA02768 hypothetical protein; 98.9 3.1E-10 6.7E-15 59.7 1.1 40 60-101 6-45 (55)
11 PF13465 zf-H2C2_2: Zinc-finge 98.9 3.2E-10 6.9E-15 51.3 0.3 25 74-98 1-25 (26)
12 KOG1074|consensus 98.9 7.9E-10 1.7E-14 85.0 2.6 77 29-105 603-687 (958)
13 PHA02768 hypothetical protein; 98.8 1.3E-09 2.8E-14 57.4 1.4 43 32-76 6-48 (55)
14 KOG1074|consensus 98.8 6.7E-09 1.5E-13 80.1 4.3 60 30-89 878-937 (958)
15 PLN03086 PRLI-interacting fact 98.6 2.7E-08 5.8E-13 75.0 3.7 85 28-117 450-548 (567)
16 PLN03086 PRLI-interacting fact 98.6 3E-08 6.5E-13 74.8 2.2 74 30-106 477-560 (567)
17 PF13465 zf-H2C2_2: Zinc-finge 98.4 1.5E-07 3.3E-12 42.4 2.1 25 46-70 1-25 (26)
18 PHA00733 hypothetical protein 98.4 6.1E-07 1.3E-11 55.9 4.1 55 28-84 70-124 (128)
19 PHA00616 hypothetical protein 98.3 2.3E-07 5E-12 46.6 1.3 33 31-63 1-33 (44)
20 PHA00616 hypothetical protein 98.3 4.8E-07 1E-11 45.5 2.1 34 59-92 1-34 (44)
21 PHA00732 hypothetical protein 98.1 8.6E-07 1.9E-11 50.6 0.9 37 31-70 1-38 (79)
22 PHA00732 hypothetical protein 98.0 7.3E-06 1.6E-10 46.8 2.6 43 59-106 1-44 (79)
23 KOG3993|consensus 97.9 3E-06 6.6E-11 61.4 -0.0 74 32-105 268-375 (500)
24 KOG3993|consensus 97.9 6.6E-06 1.4E-10 59.7 1.7 54 30-83 294-380 (500)
25 PF05605 zf-Di19: Drought indu 97.6 0.00018 3.8E-09 38.0 4.0 50 31-83 2-53 (54)
26 PF00096 zf-C2H2: Zinc finger, 97.6 4.6E-05 9.9E-10 32.9 1.4 22 32-53 1-22 (23)
27 COG5189 SFP1 Putative transcri 97.4 7.1E-05 1.5E-09 52.8 1.6 24 83-106 394-418 (423)
28 PF00096 zf-C2H2: Zinc finger, 97.4 8.9E-05 1.9E-09 32.0 1.4 23 60-82 1-23 (23)
29 PF13912 zf-C2H2_6: C2H2-type 97.2 0.00021 4.5E-09 32.1 1.4 23 32-54 2-24 (27)
30 PF13912 zf-C2H2_6: C2H2-type 97.1 0.00032 6.9E-09 31.4 1.4 25 59-83 1-25 (27)
31 PF05605 zf-Di19: Drought indu 97.0 0.00015 3.3E-09 38.3 -0.4 46 59-106 2-49 (54)
32 PRK04860 hypothetical protein; 96.9 0.00034 7.4E-09 45.2 1.0 38 59-100 119-156 (160)
33 PF13894 zf-C2H2_4: C2H2-type 96.9 0.00068 1.5E-08 29.1 1.6 21 33-53 2-22 (24)
34 PF13894 zf-C2H2_4: C2H2-type 96.9 0.00071 1.5E-08 29.0 1.6 23 60-82 1-23 (24)
35 PF09237 GAGA: GAGA factor; I 96.6 0.0012 2.6E-08 34.1 1.2 32 56-87 21-52 (54)
36 PF12756 zf-C2H2_2: C2H2 type 96.6 0.0019 4.1E-08 37.9 2.3 75 33-112 1-76 (100)
37 smart00355 ZnF_C2H2 zinc finge 96.3 0.0045 9.8E-08 26.7 2.2 22 33-54 2-23 (26)
38 PF09237 GAGA: GAGA factor; I 96.2 0.006 1.3E-07 31.5 2.4 34 26-59 19-52 (54)
39 smart00355 ZnF_C2H2 zinc finge 96.1 0.0044 9.6E-08 26.7 1.7 24 60-83 1-24 (26)
40 PF12756 zf-C2H2_2: C2H2 type 96.0 0.00024 5.1E-09 41.8 -3.9 24 59-82 50-73 (100)
41 PRK04860 hypothetical protein; 95.7 0.0095 2.1E-07 38.6 2.3 39 30-72 118-156 (160)
42 PF12171 zf-C2H2_jaz: Zinc-fin 95.2 0.0016 3.4E-08 29.2 -1.8 20 88-107 2-22 (27)
43 PF12874 zf-met: Zinc-finger o 95.2 0.012 2.5E-07 25.6 1.1 20 33-52 2-21 (25)
44 PF12874 zf-met: Zinc-finger o 94.9 0.017 3.8E-07 25.0 1.3 22 60-81 1-22 (25)
45 PF13909 zf-H2C2_5: C2H2-type 94.3 0.032 7E-07 24.0 1.4 20 33-53 2-21 (24)
46 KOG2231|consensus 92.8 0.088 1.9E-06 41.3 2.4 72 43-117 126-213 (669)
47 cd00350 rubredoxin_like Rubred 92.2 0.063 1.4E-06 25.2 0.6 9 86-94 16-24 (33)
48 COG5236 Uncharacterized conser 92.0 0.05 1.1E-06 39.3 0.2 54 61-118 222-283 (493)
49 COG5048 FOG: Zn-finger [Genera 91.7 0.048 1E-06 39.7 -0.1 62 31-92 289-356 (467)
50 PF13913 zf-C2HC_2: zinc-finge 91.6 0.19 4.2E-06 22.0 1.9 19 33-52 4-22 (25)
51 COG5236 Uncharacterized conser 89.4 0.079 1.7E-06 38.3 -0.7 83 32-116 152-250 (493)
52 smart00451 ZnF_U1 U1-like zinc 88.3 0.35 7.6E-06 22.5 1.4 22 59-80 3-24 (35)
53 COG1592 Rubrerythrin [Energy p 87.3 0.24 5.3E-06 32.3 0.6 23 59-94 134-156 (166)
54 COG5048 FOG: Zn-finger [Genera 86.5 0.24 5.1E-06 36.1 0.3 49 58-106 288-343 (467)
55 cd00729 rubredoxin_SM Rubredox 86.1 0.31 6.8E-06 23.0 0.5 9 87-95 18-26 (34)
56 KOG2186|consensus 86.0 0.39 8.4E-06 33.3 1.1 50 31-83 3-52 (276)
57 KOG2893|consensus 84.7 0.36 7.7E-06 33.3 0.4 41 30-75 10-50 (341)
58 PF09986 DUF2225: Uncharacteri 84.6 0.17 3.6E-06 34.4 -1.2 14 88-101 49-62 (214)
59 PRK00464 nrdR transcriptional 83.8 0.19 4.2E-06 32.3 -1.1 13 88-100 29-41 (154)
60 COG4049 Uncharacterized protei 82.2 0.89 1.9E-05 24.0 1.2 27 27-53 13-39 (65)
61 PF13719 zinc_ribbon_5: zinc-r 81.1 0.6 1.3E-05 22.4 0.3 11 59-69 25-35 (37)
62 KOG2186|consensus 80.5 0.68 1.5E-05 32.2 0.5 45 59-105 3-47 (276)
63 KOG1146|consensus 80.2 1.2 2.6E-05 37.7 1.9 51 30-80 464-539 (1406)
64 KOG2893|consensus 80.0 0.78 1.7E-05 31.7 0.7 43 58-105 10-53 (341)
65 PF02176 zf-TRAF: TRAF-type zi 79.7 0.39 8.4E-06 25.4 -0.7 47 58-105 8-60 (60)
66 PF13717 zinc_ribbon_4: zinc-r 78.8 0.82 1.8E-05 21.8 0.4 9 34-42 5-13 (36)
67 PF09538 FYDLN_acid: Protein o 78.3 1.4 3E-05 26.7 1.3 15 58-72 25-39 (108)
68 COG2888 Predicted Zn-ribbon RN 78.1 1 2.2E-05 24.1 0.7 33 58-95 26-58 (61)
69 KOG4167|consensus 76.0 1.6 3.5E-05 34.9 1.4 32 24-55 785-816 (907)
70 COG5189 SFP1 Putative transcri 75.3 0.76 1.7E-05 33.1 -0.4 24 28-51 395-418 (423)
71 KOG4173|consensus 74.6 3.2 7E-05 28.1 2.4 73 30-105 78-165 (253)
72 smart00659 RPOLCX RNA polymera 74.2 1.3 2.8E-05 22.2 0.4 11 32-42 3-13 (44)
73 KOG1146|consensus 72.3 0.68 1.5E-05 39.1 -1.3 53 59-112 1284-1354(1406)
74 PRK06266 transcription initiat 71.6 1.7 3.7E-05 28.7 0.6 32 58-98 116-147 (178)
75 TIGR02098 MJ0042_CXXC MJ0042 f 70.8 1.4 3E-05 21.0 0.0 11 33-43 4-14 (38)
76 TIGR00373 conserved hypothetic 69.9 3.4 7.3E-05 26.7 1.7 35 56-99 106-140 (158)
77 TIGR02605 CxxC_CxxC_SSSS putat 69.7 0.95 2.1E-05 23.2 -0.7 11 60-70 6-16 (52)
78 TIGR00622 ssl1 transcription f 67.9 3.3 7.1E-05 25.2 1.2 72 30-105 14-100 (112)
79 smart00531 TFIIE Transcription 67.5 6.8 0.00015 24.9 2.7 41 56-100 96-136 (147)
80 COG1198 PriA Primosomal protei 67.0 1.4 3.1E-05 35.4 -0.6 48 33-96 437-484 (730)
81 TIGR02300 FYDLN_acid conserved 65.0 2.7 5.8E-05 26.2 0.5 14 58-71 25-38 (129)
82 PF10571 UPF0547: Uncharacteri 63.7 1.6 3.6E-05 19.2 -0.5 8 90-97 17-24 (26)
83 PRK14890 putative Zn-ribbon RN 63.6 3 6.5E-05 22.3 0.4 33 58-95 24-56 (59)
84 PRK00398 rpoP DNA-directed RNA 62.7 1.3 2.8E-05 22.3 -1.1 10 88-97 22-31 (46)
85 KOG2785|consensus 61.8 12 0.00026 27.7 3.3 27 30-56 165-191 (390)
86 PF08790 zf-LYAR: LYAR-type C2 60.7 2.2 4.7E-05 19.2 -0.4 18 88-105 1-18 (28)
87 PF14353 CpXC: CpXC protein 60.6 2.4 5.1E-05 26.2 -0.4 27 87-113 38-65 (128)
88 PRK09678 DNA-binding transcrip 60.4 1.5 3.2E-05 24.5 -1.1 16 85-100 25-42 (72)
89 PF15135 UPF0515: Uncharacteri 59.2 5 0.00011 28.0 1.0 12 29-40 110-121 (278)
90 PHA00626 hypothetical protein 58.2 2.3 4.9E-05 22.5 -0.6 16 85-100 21-36 (59)
91 PF07754 DUF1610: Domain of un 56.8 2.5 5.4E-05 18.3 -0.5 8 87-94 16-23 (24)
92 KOG0978|consensus 56.1 3.1 6.8E-05 33.2 -0.4 18 84-101 675-692 (698)
93 smart00440 ZnF_C2C2 C2C2 Zinc 55.5 0.84 1.8E-05 22.3 -2.4 10 88-97 29-38 (40)
94 KOG2482|consensus 54.9 1.4 3.1E-05 32.0 -2.2 26 88-113 196-222 (423)
95 KOG4124|consensus 54.8 3.6 7.8E-05 30.1 -0.3 69 28-105 346-417 (442)
96 COG4896 Uncharacterized protei 54.6 10 0.00022 20.5 1.5 18 83-100 27-44 (68)
97 COG1997 RPL43A Ribosomal prote 54.2 4.3 9.3E-05 23.5 0.0 13 87-99 53-65 (89)
98 PF04959 ARS2: Arsenite-resist 54.0 8.1 0.00018 26.4 1.3 27 28-54 74-100 (214)
99 COG1996 RPC10 DNA-directed RNA 54.0 4.2 9.2E-05 20.9 -0.0 11 31-41 6-16 (49)
100 COG1773 Rubredoxin [Energy pro 54.0 2.8 6.2E-05 22.1 -0.7 15 86-100 2-16 (55)
101 KOG4173|consensus 53.9 7.5 0.00016 26.4 1.1 44 59-105 79-125 (253)
102 PF05290 Baculo_IE-1: Baculovi 53.3 4.5 9.7E-05 25.4 0.0 13 89-101 123-135 (140)
103 PF03604 DNA_RNApol_7kD: DNA d 52.8 2.7 5.9E-05 19.5 -0.8 8 60-67 18-25 (32)
104 smart00834 CxxC_CXXC_SSSS Puta 51.9 3 6.5E-05 20.0 -0.8 14 87-100 5-18 (41)
105 KOG2231|consensus 51.8 5 0.00011 32.0 0.1 73 43-119 161-245 (669)
106 PF08274 PhnA_Zn_Ribbon: PhnA 51.8 3.2 6.9E-05 19.0 -0.6 9 87-95 19-27 (30)
107 COG5152 Uncharacterized conser 49.9 12 0.00026 25.3 1.6 20 25-44 190-209 (259)
108 PF05443 ROS_MUCR: ROS/MUCR tr 49.7 11 0.00023 23.8 1.3 25 60-87 73-97 (132)
109 KOG3408|consensus 49.0 13 0.00028 23.0 1.5 24 58-81 56-79 (129)
110 smart00154 ZnF_AN1 AN1-like Zi 48.3 4.6 0.0001 19.6 -0.4 15 87-101 12-26 (39)
111 PRK03824 hypA hydrogenase nick 48.0 5.9 0.00013 24.9 -0.0 13 59-71 70-82 (135)
112 PF09723 Zn-ribbon_8: Zinc rib 48.0 3.3 7.1E-05 20.4 -1.0 14 88-101 6-19 (42)
113 smart00614 ZnF_BED BED zinc fi 46.0 16 0.00035 18.5 1.4 9 33-41 20-28 (50)
114 smart00734 ZnF_Rad18 Rad18-lik 45.7 15 0.00033 16.0 1.1 9 61-69 3-11 (26)
115 KOG4167|consensus 45.6 5.7 0.00012 32.0 -0.4 25 59-83 792-816 (907)
116 PF13451 zf-trcl: Probable zin 45.2 4.8 0.0001 20.7 -0.6 16 85-100 2-17 (49)
117 COG3357 Predicted transcriptio 45.1 10 0.00022 22.2 0.6 32 58-99 57-88 (97)
118 COG5188 PRP9 Splicing factor 3 43.1 5.7 0.00012 29.2 -0.7 32 81-112 368-401 (470)
119 PF10013 DUF2256: Uncharacteri 42.5 5.3 0.00012 19.8 -0.7 13 89-101 10-22 (42)
120 PF02892 zf-BED: BED zinc fing 42.1 20 0.00043 17.4 1.4 13 30-42 15-27 (45)
121 PF05191 ADK_lid: Adenylate ki 41.9 8.1 0.00018 18.4 -0.1 8 88-95 22-29 (36)
122 PF01428 zf-AN1: AN1-like Zinc 41.3 5.7 0.00012 19.6 -0.7 16 86-101 12-27 (43)
123 PF11931 DUF3449: Domain of un 41.1 9 0.00019 25.8 0.0 32 81-112 95-128 (196)
124 TIGR00595 priA primosomal prot 40.9 6.7 0.00014 30.3 -0.7 10 86-95 252-261 (505)
125 PF01096 TFIIS_C: Transcriptio 40.1 0.68 1.5E-05 22.5 -4.1 10 88-97 29-38 (39)
126 PRK14873 primosome assembly pr 39.8 5.9 0.00013 31.7 -1.1 10 87-96 422-431 (665)
127 COG5151 SSL1 RNA polymerase II 39.8 21 0.00045 26.0 1.6 10 88-97 389-398 (421)
128 cd00730 rubredoxin Rubredoxin; 39.4 6.3 0.00014 20.3 -0.7 13 88-100 2-14 (50)
129 KOG2593|consensus 39.2 20 0.00044 27.1 1.5 32 86-117 127-160 (436)
130 TIGR00100 hypA hydrogenase nic 39.0 11 0.00024 22.9 0.2 25 60-96 71-95 (115)
131 KOG2807|consensus 38.9 22 0.00047 26.0 1.6 20 58-77 289-308 (378)
132 cd00924 Cyt_c_Oxidase_Vb Cytoc 38.6 5.1 0.00011 23.8 -1.3 27 73-100 66-92 (97)
133 PF00301 Rubredoxin: Rubredoxi 38.5 6.4 0.00014 20.0 -0.8 13 88-100 2-14 (47)
134 COG1571 Predicted DNA-binding 38.4 13 0.00029 28.0 0.6 15 87-101 367-381 (421)
135 PF04423 Rad50_zn_hook: Rad50 37.4 18 0.00039 18.6 0.8 11 89-99 22-32 (54)
136 PF01363 FYVE: FYVE zinc finge 37.3 12 0.00026 20.2 0.1 29 32-72 10-38 (69)
137 PF01286 XPA_N: XPA protein N- 36.9 13 0.00029 17.5 0.2 17 89-105 5-21 (34)
138 PF07282 OrfB_Zn_ribbon: Putat 36.6 10 0.00022 20.5 -0.2 11 58-68 45-55 (69)
139 PF12013 DUF3505: Protein of u 36.5 26 0.00056 20.9 1.5 20 63-82 88-107 (109)
140 PRK12380 hydrogenase nickel in 36.3 14 0.0003 22.5 0.3 24 60-95 71-94 (113)
141 PTZ00255 60S ribosomal protein 36.2 8.9 0.00019 22.4 -0.5 13 87-99 54-66 (90)
142 KOG0801|consensus 35.6 7 0.00015 25.5 -1.1 18 88-105 139-156 (205)
143 KOG2785|consensus 35.4 8.5 0.00018 28.5 -0.8 55 59-113 166-247 (390)
144 PF04810 zf-Sec23_Sec24: Sec23 35.2 8.3 0.00018 18.7 -0.7 12 84-95 21-32 (40)
145 COG3091 SprT Zn-dependent meta 35.2 13 0.00029 23.9 0.1 14 86-100 116-129 (156)
146 PLN02294 cytochrome c oxidase 34.7 10 0.00022 24.9 -0.5 27 73-100 128-154 (174)
147 COG4338 Uncharacterized protei 34.3 11 0.00024 19.2 -0.3 12 89-100 14-25 (54)
148 KOG2071|consensus 34.1 23 0.00049 27.9 1.2 27 28-54 415-441 (579)
149 COG1594 RPB9 DNA-directed RNA 33.9 6.2 0.00013 24.1 -1.5 13 86-98 99-111 (113)
150 smart00064 FYVE Protein presen 33.7 16 0.00034 19.7 0.2 11 32-42 11-21 (68)
151 PHA02998 RNA polymerase subuni 33.5 5.1 0.00011 26.5 -2.0 15 87-101 171-185 (195)
152 KOG2636|consensus 32.9 5.2 0.00011 30.2 -2.2 33 80-112 394-428 (497)
153 PF12760 Zn_Tnp_IS1595: Transp 32.6 25 0.00054 17.4 0.9 11 85-95 35-45 (46)
154 TIGR00280 L37a ribosomal prote 32.6 8.6 0.00019 22.5 -1.0 13 87-99 53-65 (91)
155 PF09963 DUF2197: Uncharacteri 32.1 33 0.00072 18.2 1.3 12 86-97 30-41 (56)
156 COG1655 Uncharacterized protei 31.9 11 0.00024 26.0 -0.6 29 29-57 17-45 (267)
157 PF11672 DUF3268: Protein of u 31.5 14 0.00031 22.1 -0.2 9 31-39 2-10 (102)
158 PRK00564 hypA hydrogenase nick 30.9 18 0.00039 22.1 0.2 11 60-70 72-82 (117)
159 PF14311 DUF4379: Domain of un 30.9 25 0.00055 18.1 0.7 8 60-67 29-36 (55)
160 PF06397 Desulfoferrod_N: Desu 30.8 16 0.00034 17.5 -0.1 13 86-98 5-17 (36)
161 COG4530 Uncharacterized protei 29.3 17 0.00037 22.1 -0.1 29 61-100 11-39 (129)
162 PRK05580 primosome assembly pr 29.0 13 0.00028 29.9 -0.9 11 86-96 420-430 (679)
163 PRK00432 30S ribosomal protein 28.3 15 0.00032 18.9 -0.5 8 60-67 38-45 (50)
164 PF02318 FYVE_2: FYVE-type zin 28.1 15 0.00033 22.4 -0.5 49 32-96 55-103 (118)
165 PF13453 zf-TFIIB: Transcripti 28.1 22 0.00047 17.2 0.2 18 59-76 19-36 (41)
166 PF14445 Prok-RING_2: Prokaryo 27.6 13 0.00028 19.3 -0.7 16 88-103 8-23 (57)
167 KOG2482|consensus 27.3 36 0.00077 25.2 1.2 52 30-81 143-217 (423)
168 KOG2907|consensus 27.3 16 0.00035 22.3 -0.4 13 86-98 101-113 (116)
169 PF11789 zf-Nse: Zinc-finger o 27.0 20 0.00044 18.9 -0.1 16 58-73 23-38 (57)
170 PF09845 DUF2072: Zn-ribbon co 26.9 20 0.00043 22.5 -0.1 13 88-100 2-14 (131)
171 cd00065 FYVE FYVE domain; Zinc 26.8 26 0.00057 17.9 0.3 10 33-42 4-13 (57)
172 PF12230 PRP21_like_P: Pre-mRN 26.5 22 0.00047 24.3 0.0 24 84-107 165-188 (229)
173 KOG3507|consensus 26.4 32 0.0007 18.4 0.6 13 58-70 36-48 (62)
174 PRK04023 DNA polymerase II lar 26.3 25 0.00055 29.7 0.3 11 30-40 625-635 (1121)
175 PF13824 zf-Mss51: Zinc-finger 26.2 27 0.00058 18.4 0.3 11 57-67 12-22 (55)
176 PRK03681 hypA hydrogenase nick 25.9 19 0.00041 21.9 -0.3 10 60-69 71-80 (114)
177 COG1675 TFA1 Transcription ini 25.8 48 0.001 22.0 1.5 36 54-98 108-143 (176)
178 PF13878 zf-C2H2_3: zinc-finge 25.7 65 0.0014 15.6 1.6 25 31-55 13-39 (41)
179 PF15269 zf-C2H2_7: Zinc-finge 25.7 99 0.0021 15.6 2.3 21 32-52 21-41 (54)
180 COG4957 Predicted transcriptio 25.5 36 0.00077 21.6 0.8 24 61-87 78-101 (148)
181 PF01155 HypA: Hydrogenase exp 25.4 17 0.00036 22.1 -0.6 12 60-71 71-82 (113)
182 COG1326 Uncharacterized archae 25.0 38 0.00081 22.9 0.9 14 86-99 29-42 (201)
183 COG0068 HypF Hydrogenase matur 24.5 34 0.00074 27.8 0.7 43 61-104 125-168 (750)
184 PF02891 zf-MIZ: MIZ/SP-RING z 24.0 32 0.0007 17.5 0.4 9 87-95 41-49 (50)
185 COG3677 Transposase and inacti 24.0 21 0.00047 22.2 -0.4 17 85-101 51-67 (129)
186 KOG0717|consensus 22.3 89 0.0019 24.2 2.5 22 32-53 293-314 (508)
187 COG5112 UFD2 U1-like Zn-finger 21.4 91 0.002 18.9 1.9 24 29-52 53-76 (126)
188 COG3364 Zn-ribbon containing p 21.2 56 0.0012 19.6 1.0 14 59-72 2-15 (112)
189 PF08792 A2L_zn_ribbon: A2L zi 20.6 21 0.00045 16.6 -0.7 13 86-98 20-32 (33)
190 PF10263 SprT-like: SprT-like 20.2 18 0.00038 22.9 -1.4 7 88-94 144-150 (157)
191 PF14787 zf-CCHC_5: GAG-polypr 20.0 29 0.00063 16.6 -0.3 14 88-101 3-16 (36)
No 1
>KOG2462|consensus
Probab=99.81 E-value=7.1e-21 Score=128.83 Aligned_cols=75 Identities=32% Similarity=0.596 Sum_probs=39.4
Q ss_pred CcccccchhhccChHHHHHHHhhcCCCCceecccchhhcCCchhHHHhhhhhcCCCccchhhhhhhhhccc-cCcC
Q psy553 31 PHQCQQCLKSFSSNHQLVQHIRVHTGEKPYKCTYCERRFKQLSHVQQHTRLHTVEGVNSCLQILSLWIQLD-LKDE 105 (129)
Q Consensus 31 ~~~C~~C~~~f~~~~~l~~h~~~h~~~~~~~C~~c~~~f~~~~~l~~H~~~h~~~~~y~C~~C~~~f~~~~-l~~h 105 (129)
++.|.+||+.|...=.|+.|+|+|+|++||.|..|++.|.+.++|..||+||++.|+|.|..|+|+|...+ |.+|
T Consensus 187 ~c~C~iCGKaFSRPWLLQGHiRTHTGEKPF~C~hC~kAFADRSNLRAHmQTHS~~K~~qC~~C~KsFsl~SyLnKH 262 (279)
T KOG2462|consen 187 PCECGICGKAFSRPWLLQGHIRTHTGEKPFSCPHCGKAFADRSNLRAHMQTHSDVKKHQCPRCGKSFALKSYLNKH 262 (279)
T ss_pred CcccccccccccchHHhhcccccccCCCCccCCcccchhcchHHHHHHHHhhcCCccccCcchhhHHHHHHHHHHh
Confidence 34455555555544455555555555555555555555555555555555555555555555555555554 4444
No 2
>KOG2462|consensus
Probab=99.78 E-value=2.3e-20 Score=126.40 Aligned_cols=96 Identities=27% Similarity=0.380 Sum_probs=78.5
Q ss_pred CCCCcccccchhhccChHHHHHHHhhcCCCCceecccchhhcCCchhHHHhhhhhcCCCccchhhhhhhhhccc-cCcCC
Q psy553 28 ANKPHQCQQCLKSFSSNHQLVQHIRVHTGEKPYKCTYCERRFKQLSHVQQHTRLHTVEGVNSCLQILSLWIQLD-LKDEP 106 (129)
Q Consensus 28 ~~~~~~C~~C~~~f~~~~~l~~h~~~h~~~~~~~C~~c~~~f~~~~~l~~H~~~h~~~~~y~C~~C~~~f~~~~-l~~h~ 106 (129)
+.+.+.|+.|++.|.....|..|+++|+ -+.+|.+||+.|...=.|+.|+++|+|||||.|..|+|.|+.++ |+.|+
T Consensus 158 s~ka~~C~~C~K~YvSmpALkMHirTH~--l~c~C~iCGKaFSRPWLLQGHiRTHTGEKPF~C~hC~kAFADRSNLRAHm 235 (279)
T KOG2462|consen 158 SKKAFSCKYCGKVYVSMPALKMHIRTHT--LPCECGICGKAFSRPWLLQGHIRTHTGEKPFSCPHCGKAFADRSNLRAHM 235 (279)
T ss_pred ccccccCCCCCceeeehHHHhhHhhccC--CCcccccccccccchHHhhcccccccCCCCccCCcccchhcchHHHHHHH
Confidence 3566788888888888888888888887 57899999999999999999999999999999999999999996 88774
Q ss_pred ----CCCCeeE-----eeccccccchhh
Q psy553 107 ----RNRNYVV-----RFSWWDDLRPLL 125 (129)
Q Consensus 107 ----~~~~~~~-----~~~~~~~l~~~~ 125 (129)
..++|.| .|+-.+=|.+|.
T Consensus 236 QTHS~~K~~qC~~C~KsFsl~SyLnKH~ 263 (279)
T KOG2462|consen 236 QTHSDVKKHQCPRCGKSFALKSYLNKHS 263 (279)
T ss_pred HhhcCCccccCcchhhHHHHHHHHHHhh
Confidence 3667764 566666666653
No 3
>KOG3623|consensus
Probab=99.65 E-value=7.2e-17 Score=121.24 Aligned_cols=81 Identities=28% Similarity=0.588 Sum_probs=76.5
Q ss_pred CCCCCcccccchhhccChHHHHHHHhhcCCCCceecccchhhcCCchhHHHhhhhhcCCCccchhhhhhhhhccc-cCcC
Q psy553 27 EANKPHQCQQCLKSFSSNHQLVQHIRVHTGEKPYKCTYCERRFKQLSHVQQHTRLHTVEGVNSCLQILSLWIQLD-LKDE 105 (129)
Q Consensus 27 ~~~~~~~C~~C~~~f~~~~~l~~h~~~h~~~~~~~C~~c~~~f~~~~~l~~H~~~h~~~~~y~C~~C~~~f~~~~-l~~h 105 (129)
.+...|.|..|.+.|...+.|.+|...|+|.+||+|.+|.+.|....+|..|+++|+|||||.|..|+|.|.++. .-.|
T Consensus 890 te~gmyaCDqCDK~FqKqSSLaRHKYEHsGqRPyqC~iCkKAFKHKHHLtEHkRLHSGEKPfQCdKClKRFSHSGSYSQH 969 (1007)
T KOG3623|consen 890 TEDGMYACDQCDKAFQKQSSLARHKYEHSGQRPYQCIICKKAFKHKHHLTEHKRLHSGEKPFQCDKCLKRFSHSGSYSQH 969 (1007)
T ss_pred CccccchHHHHHHHHHhhHHHHHhhhhhcCCCCcccchhhHhhhhhhhhhhhhhhccCCCcchhhhhhhhcccccchHhh
Confidence 345689999999999999999999999999999999999999999999999999999999999999999999995 8888
Q ss_pred CC
Q psy553 106 PR 107 (129)
Q Consensus 106 ~~ 107 (129)
|.
T Consensus 970 MN 971 (1007)
T KOG3623|consen 970 MN 971 (1007)
T ss_pred hc
Confidence 83
No 4
>KOG3576|consensus
Probab=99.59 E-value=2.2e-16 Score=103.12 Aligned_cols=77 Identities=26% Similarity=0.489 Sum_probs=72.9
Q ss_pred CCCcccccchhhccChHHHHHHHhhcCCCCceecccchhhcCCchhHHHhhhhhcCCCccchhhhhhhhhcc-ccCcC
Q psy553 29 NKPHQCQQCLKSFSSNHQLVQHIRVHTGEKPYKCTYCERRFKQLSHVQQHTRLHTVEGVNSCLQILSLWIQL-DLKDE 105 (129)
Q Consensus 29 ~~~~~C~~C~~~f~~~~~l~~h~~~h~~~~~~~C~~c~~~f~~~~~l~~H~~~h~~~~~y~C~~C~~~f~~~-~l~~h 105 (129)
...|.|.+|++.|.....|.+|+..|...+.+.|..||+.|...-.|.+|+++|+|.+||+|..|++.|.++ +|..|
T Consensus 115 ~d~ftCrvCgK~F~lQRmlnrh~kch~~vkr~lct~cgkgfndtfdlkrh~rthtgvrpykc~~c~kaftqrcslesh 192 (267)
T KOG3576|consen 115 QDSFTCRVCGKKFGLQRMLNRHLKCHSDVKRHLCTFCGKGFNDTFDLKRHTRTHTGVRPYKCSLCEKAFTQRCSLESH 192 (267)
T ss_pred CCeeeeehhhhhhhHHHHHHHHhhhccHHHHHHHhhccCcccchhhhhhhhccccCccccchhhhhHHHHhhccHHHH
Confidence 567999999999999999999999999999999999999999999999999999999999999999999998 57766
No 5
>KOG3623|consensus
Probab=99.42 E-value=8.2e-14 Score=105.13 Aligned_cols=81 Identities=23% Similarity=0.485 Sum_probs=69.5
Q ss_pred CCcccccchhhccChHHHHHHHhhcCCC-------------CceecccchhhcCCchhHHHhhhhhcCCCccchhhhhhh
Q psy553 30 KPHQCQQCLKSFSSNHQLVQHIRVHTGE-------------KPYKCTYCERRFKQLSHVQQHTRLHTVEGVNSCLQILSL 96 (129)
Q Consensus 30 ~~~~C~~C~~~f~~~~~l~~h~~~h~~~-------------~~~~C~~c~~~f~~~~~l~~H~~~h~~~~~y~C~~C~~~ 96 (129)
..|.|..|...|..+..|-+||..|... +-|+|..|++.|.+..+|..|+++|+|||||.|+.|.|.
T Consensus 239 ~nfsC~lCsytFAyRtQLErhm~~hkpg~dqa~sltqsa~lRKFKCtECgKAFKfKHHLKEHlRIHSGEKPfeCpnCkKR 318 (1007)
T KOG3623|consen 239 PNFSCMLCSYTFAYRTQLERHMQLHKPGGDQAISLTQSALLRKFKCTECGKAFKFKHHLKEHLRIHSGEKPFECPNCKKR 318 (1007)
T ss_pred CCCcchhhhhhhhhHHHHHHHHHhhcCCCcccccccchhhhccccccccchhhhhHHHHHhhheeecCCCCcCCcccccc
Confidence 4578999999999999999999887532 458999999999999999999999999999999999999
Q ss_pred hhccc-cCcCCCCCC
Q psy553 97 WIQLD-LKDEPRNRN 110 (129)
Q Consensus 97 f~~~~-l~~h~~~~~ 110 (129)
|.++. .-.||..+.
T Consensus 319 FSHSGSySSHmSSKK 333 (1007)
T KOG3623|consen 319 FSHSGSYSSHMSSKK 333 (1007)
T ss_pred cccCCcccccccccc
Confidence 99984 888876554
No 6
>KOG3608|consensus
Probab=99.11 E-value=1.9e-11 Score=86.06 Aligned_cols=84 Identities=24% Similarity=0.459 Sum_probs=64.6
Q ss_pred CCcccccchhhccChHHHHHHHhhcCCCCceecccchhhcCCchhHHHhhh-hhcCCCccchhhhhhhhhccc-cCcC--
Q psy553 30 KPHQCQQCLKSFSSNHQLVQHIRVHTGEKPYKCTYCERRFKQLSHVQQHTR-LHTVEGVNSCLQILSLWIQLD-LKDE-- 105 (129)
Q Consensus 30 ~~~~C~~C~~~f~~~~~l~~h~~~h~~~~~~~C~~c~~~f~~~~~l~~H~~-~h~~~~~y~C~~C~~~f~~~~-l~~h-- 105 (129)
++|.|..|.+.|.+...|..|++.|. +-|+|++|..+....+.|..|++ .|+..|||+|..|++.|.+.+ |.+|
T Consensus 236 n~fqC~~C~KrFaTeklL~~Hv~rHv--n~ykCplCdmtc~~~ssL~~H~r~rHs~dkpfKCd~Cd~~c~~esdL~kH~~ 313 (467)
T KOG3608|consen 236 NSFQCAQCFKRFATEKLLKSHVVRHV--NCYKCPLCDMTCSSASSLTTHIRYRHSKDKPFKCDECDTRCVRESDLAKHVQ 313 (467)
T ss_pred CchHHHHHHHHHhHHHHHHHHHHHhh--hcccccccccCCCChHHHHHHHHhhhccCCCccccchhhhhccHHHHHHHHH
Confidence 57888888888888888888888776 34788888888888888888877 456778888888888888874 7777
Q ss_pred -CCCCCeeEee
Q psy553 106 -PRNRNYVVRF 115 (129)
Q Consensus 106 -~~~~~~~~~~ 115 (129)
+.+..|.|.+
T Consensus 314 ~HS~~~y~C~h 324 (467)
T KOG3608|consen 314 VHSKTVYQCEH 324 (467)
T ss_pred hccccceecCC
Confidence 4466666644
No 7
>PHA00733 hypothetical protein
Probab=99.02 E-value=2.5e-11 Score=75.57 Aligned_cols=83 Identities=17% Similarity=0.215 Sum_probs=67.0
Q ss_pred CCCCcccccchhhccChHHHHHH--Hh---hcCCCCceecccchhhcCCchhHHHhhhhhcCCCccchhhhhhhhhccc-
Q psy553 28 ANKPHQCQQCLKSFSSNHQLVQH--IR---VHTGEKPYKCTYCERRFKQLSHVQQHTRLHTVEGVNSCLQILSLWIQLD- 101 (129)
Q Consensus 28 ~~~~~~C~~C~~~f~~~~~l~~h--~~---~h~~~~~~~C~~c~~~f~~~~~l~~H~~~h~~~~~y~C~~C~~~f~~~~- 101 (129)
+++++.|.+|.+.|.....|..+ .. .+.+.+||.|..|++.|.....|..|++.+ +.+|.|.+|++.|...+
T Consensus 37 ~~~~~~~~~~~~~~~~~~~l~~~~~l~~~~~~~~~kPy~C~~Cgk~Fss~s~L~~H~r~h--~~~~~C~~CgK~F~~~~s 114 (128)
T PHA00733 37 EQKRLIRAVVKTLIYNPQLLDESSYLYKLLTSKAVSPYVCPLCLMPFSSSVSLKQHIRYT--EHSKVCPVCGKEFRNTDS 114 (128)
T ss_pred hhhhHHHHHHhhhccChhhhcchHHHHhhcccCCCCCccCCCCCCcCCCHHHHHHHHhcC--CcCccCCCCCCccCCHHH
Confidence 36789999999888887777655 11 233478999999999999999999999976 46799999999999996
Q ss_pred cCcCCCCCCee
Q psy553 102 LKDEPRNRNYV 112 (129)
Q Consensus 102 l~~h~~~~~~~ 112 (129)
|..|..+++-.
T Consensus 115 L~~H~~~~h~~ 125 (128)
T PHA00733 115 TLDHVCKKHNI 125 (128)
T ss_pred HHHHHHHhcCc
Confidence 98887665543
No 8
>KOG3576|consensus
Probab=99.00 E-value=3.2e-11 Score=79.16 Aligned_cols=73 Identities=30% Similarity=0.547 Sum_probs=64.3
Q ss_pred CCCcccccchhhccChHHHHHHHhhcCCCCceecccchhhcCCchhHHHhhhhhc-----------CCCccchhhhhhhh
Q psy553 29 NKPHQCQQCLKSFSSNHQLVQHIRVHTGEKPYKCTYCERRFKQLSHVQQHTRLHT-----------VEGVNSCLQILSLW 97 (129)
Q Consensus 29 ~~~~~C~~C~~~f~~~~~l~~h~~~h~~~~~~~C~~c~~~f~~~~~l~~H~~~h~-----------~~~~y~C~~C~~~f 97 (129)
.+.|.|..||++|..-..|.+|+++|+|.+||+|..|++.|.+.-+|..|.+.-. +++-|+|..||.+-
T Consensus 143 vkr~lct~cgkgfndtfdlkrh~rthtgvrpykc~~c~kaftqrcsleshl~kvhgv~~~yaykerr~kl~vcedcg~t~ 222 (267)
T KOG3576|consen 143 VKRHLCTFCGKGFNDTFDLKRHTRTHTGVRPYKCSLCEKAFTQRCSLESHLKKVHGVQHQYAYKERRAKLYVCEDCGYTS 222 (267)
T ss_pred HHHHHHhhccCcccchhhhhhhhccccCccccchhhhhHHHHhhccHHHHHHHHcCchHHHHHHHhhhheeeecccCCCC
Confidence 3678999999999999999999999999999999999999999999998876432 35779999999887
Q ss_pred hccc
Q psy553 98 IQLD 101 (129)
Q Consensus 98 ~~~~ 101 (129)
...+
T Consensus 223 ~~~e 226 (267)
T KOG3576|consen 223 ERPE 226 (267)
T ss_pred CChh
Confidence 7764
No 9
>KOG3608|consensus
Probab=98.96 E-value=1.5e-10 Score=81.60 Aligned_cols=95 Identities=25% Similarity=0.416 Sum_probs=75.0
Q ss_pred CCcccccchhhccChHHHHHHHhh-cCCCCceecccchhhcCCchhHHHhhhhhcCCCccchhh--hhhhhhccc-cCcC
Q psy553 30 KPHQCQQCLKSFSSNHQLVQHIRV-HTGEKPYKCTYCERRFKQLSHVQQHTRLHTVEGVNSCLQ--ILSLWIQLD-LKDE 105 (129)
Q Consensus 30 ~~~~C~~C~~~f~~~~~l~~h~~~-h~~~~~~~C~~c~~~f~~~~~l~~H~~~h~~~~~y~C~~--C~~~f~~~~-l~~h 105 (129)
+-|+|+.|.++....+.|..|++. |..++||+|..|..+|...+.|++|..+|+ +..|.|+. |...|.+.. +.+|
T Consensus 262 n~ykCplCdmtc~~~ssL~~H~r~rHs~dkpfKCd~Cd~~c~~esdL~kH~~~HS-~~~y~C~h~~C~~s~r~~~q~~~H 340 (467)
T KOG3608|consen 262 NCYKCPLCDMTCSSASSLTTHIRYRHSKDKPFKCDECDTRCVRESDLAKHVQVHS-KTVYQCEHPDCHYSVRTYTQMRRH 340 (467)
T ss_pred hcccccccccCCCChHHHHHHHHhhhccCCCccccchhhhhccHHHHHHHHHhcc-ccceecCCCCCcHHHHHHHHHHHH
Confidence 458899999999999999999875 888899999999999999999999999887 66788887 888888873 7666
Q ss_pred CCCC-------CeeE-----eeccccccchhh
Q psy553 106 PRNR-------NYVV-----RFSWWDDLRPLL 125 (129)
Q Consensus 106 ~~~~-------~~~~-----~~~~~~~l~~~~ 125 (129)
+++. .|+| .|....+|..|+
T Consensus 341 ~~evhEg~np~~Y~CH~Cdr~ft~G~~L~~HL 372 (467)
T KOG3608|consen 341 FLEVHEGNNPILYACHCCDRFFTSGKSLSAHL 372 (467)
T ss_pred HHHhccCCCCCceeeecchhhhccchhHHHHH
Confidence 4433 3554 566666676665
No 10
>PHA02768 hypothetical protein; Provisional
Probab=98.93 E-value=3.1e-10 Score=59.71 Aligned_cols=40 Identities=15% Similarity=0.288 Sum_probs=27.8
Q ss_pred eecccchhhcCCchhHHHhhhhhcCCCccchhhhhhhhhccc
Q psy553 60 YKCTYCERRFKQLSHVQQHTRLHTVEGVNSCLQILSLWIQLD 101 (129)
Q Consensus 60 ~~C~~c~~~f~~~~~l~~H~~~h~~~~~y~C~~C~~~f~~~~ 101 (129)
|.|+.|++.|...++|..|+++|+ ++|+|..|++.|.+.+
T Consensus 6 y~C~~CGK~Fs~~~~L~~H~r~H~--k~~kc~~C~k~f~~~s 45 (55)
T PHA02768 6 YECPICGEIYIKRKSMITHLRKHN--TNLKLSNCKRISLRTG 45 (55)
T ss_pred cCcchhCCeeccHHHHHHHHHhcC--CcccCCcccceecccc
Confidence 567777777777777777777766 5677777777776654
No 11
>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=98.89 E-value=3.2e-10 Score=51.27 Aligned_cols=25 Identities=24% Similarity=0.284 Sum_probs=20.2
Q ss_pred hHHHhhhhhcCCCccchhhhhhhhh
Q psy553 74 HVQQHTRLHTVEGVNSCLQILSLWI 98 (129)
Q Consensus 74 ~l~~H~~~h~~~~~y~C~~C~~~f~ 98 (129)
+|..|+++|++++||.|++|++.|.
T Consensus 1 ~l~~H~~~H~~~k~~~C~~C~k~F~ 25 (26)
T PF13465_consen 1 NLRRHMRTHTGEKPYKCPYCGKSFS 25 (26)
T ss_dssp HHHHHHHHHSSSSSEEESSSSEEES
T ss_pred CHHHHhhhcCCCCCCCCCCCcCeeC
Confidence 4677888888888888888888875
No 12
>KOG1074|consensus
Probab=98.89 E-value=7.9e-10 Score=85.01 Aligned_cols=77 Identities=31% Similarity=0.604 Sum_probs=68.2
Q ss_pred CCCcccccchhhccChHHHHHHHhhcCCCCceecccchhhcCCchhHHHhhhhhcC----CCccchh---hhhhhhhccc
Q psy553 29 NKPHQCQQCLKSFSSNHQLVQHIRVHTGEKPYKCTYCERRFKQLSHVQQHTRLHTV----EGVNSCL---QILSLWIQLD 101 (129)
Q Consensus 29 ~~~~~C~~C~~~f~~~~~l~~h~~~h~~~~~~~C~~c~~~f~~~~~l~~H~~~h~~----~~~y~C~---~C~~~f~~~~ 101 (129)
..|..|.+|.++...+..|+.|.++|+|++||+|.+|++.|..+.+|+.|+..|-- ..++.|+ +|.+-|.+.=
T Consensus 603 TdPNqCiiC~rVlSC~saLqmHyrtHtGERPFkCKiCgRAFtTkGNLkaH~~vHka~p~~R~q~ScP~~~ic~~kftn~V 682 (958)
T KOG1074|consen 603 TDPNQCIICLRVLSCPSALQMHYRTHTGERPFKCKICGRAFTTKGNLKAHMSVHKAKPPARVQFSCPSTFICQKKFTNAV 682 (958)
T ss_pred CCccceeeeeecccchhhhhhhhhcccCcCccccccccchhccccchhhcccccccCccccccccCCchhhhcccccccc
Confidence 35789999999999999999999999999999999999999999999999998843 2458899 9999999883
Q ss_pred -cCcC
Q psy553 102 -LKDE 105 (129)
Q Consensus 102 -l~~h 105 (129)
|..|
T Consensus 683 ~lpQh 687 (958)
T KOG1074|consen 683 TLPQH 687 (958)
T ss_pred cccce
Confidence 6665
No 13
>PHA02768 hypothetical protein; Provisional
Probab=98.84 E-value=1.3e-09 Score=57.37 Aligned_cols=43 Identities=19% Similarity=0.413 Sum_probs=39.4
Q ss_pred cccccchhhccChHHHHHHHhhcCCCCceecccchhhcCCchhHH
Q psy553 32 HQCQQCLKSFSSNHQLVQHIRVHTGEKPYKCTYCERRFKQLSHVQ 76 (129)
Q Consensus 32 ~~C~~C~~~f~~~~~l~~h~~~h~~~~~~~C~~c~~~f~~~~~l~ 76 (129)
|.|+.||+.|.....|..|++.|. ++++|..|++.|...+.|+
T Consensus 6 y~C~~CGK~Fs~~~~L~~H~r~H~--k~~kc~~C~k~f~~~s~l~ 48 (55)
T PHA02768 6 YECPICGEIYIKRKSMITHLRKHN--TNLKLSNCKRISLRTGEYI 48 (55)
T ss_pred cCcchhCCeeccHHHHHHHHHhcC--CcccCCcccceecccceeE
Confidence 799999999999999999999998 6899999999998777664
No 14
>KOG1074|consensus
Probab=98.78 E-value=6.7e-09 Score=80.07 Aligned_cols=60 Identities=37% Similarity=0.671 Sum_probs=44.4
Q ss_pred CCcccccchhhccChHHHHHHHhhcCCCCceecccchhhcCCchhHHHhhhhhcCCCccc
Q psy553 30 KPHQCQQCLKSFSSNHQLVQHIRVHTGEKPYKCTYCERRFKQLSHVQQHTRLHTVEGVNS 89 (129)
Q Consensus 30 ~~~~C~~C~~~f~~~~~l~~h~~~h~~~~~~~C~~c~~~f~~~~~l~~H~~~h~~~~~y~ 89 (129)
..+.|..|++.|.....|..|+++|++++||.|.+|++.|....+|+.||.+|.+..|..
T Consensus 878 n~h~C~vCgk~FsSSsALqiH~rTHtg~KPF~C~fC~~aFttrgnLKvHMgtH~w~q~~s 937 (958)
T KOG1074|consen 878 NAHVCNVCGKQFSSSAALEIHMRTHTGPKPFFCHFCEEAFTTRGNLKVHMGTHMWVQPPS 937 (958)
T ss_pred chhhhccchhcccchHHHHHhhhcCCCCCCccchhhhhhhhhhhhhhhhhccccccCCCc
Confidence 346777777777777777777777777777777777777777777777777776655543
No 15
>PLN03086 PRLI-interacting factor K; Provisional
Probab=98.64 E-value=2.7e-08 Score=75.04 Aligned_cols=85 Identities=15% Similarity=0.307 Sum_probs=67.6
Q ss_pred CCCCcccccchhhccChHHHHHHHhhcCCCCceecccchhhcCCchhHHHhhhhhcCCCccchhhhhhhhhc--------
Q psy553 28 ANKPHQCQQCLKSFSSNHQLVQHIRVHTGEKPYKCTYCERRFKQLSHVQQHTRLHTVEGVNSCLQILSLWIQ-------- 99 (129)
Q Consensus 28 ~~~~~~C~~C~~~f~~~~~l~~h~~~h~~~~~~~C~~c~~~f~~~~~l~~H~~~h~~~~~y~C~~C~~~f~~-------- 99 (129)
-++.+.|..|++.|. ...|..|+..+. .++.|+ |+..+ ....|..|+.+|.+.+++.|..|++.|..
T Consensus 450 l~~H~~C~~Cgk~f~-~s~LekH~~~~H--kpv~Cp-Cg~~~-~R~~L~~H~~thCp~Kpi~C~fC~~~v~~g~~~~d~~ 524 (567)
T PLN03086 450 AKNHVHCEKCGQAFQ-QGEMEKHMKVFH--EPLQCP-CGVVL-EKEQMVQHQASTCPLRLITCRFCGDMVQAGGSAMDVR 524 (567)
T ss_pred cccCccCCCCCCccc-hHHHHHHHHhcC--CCccCC-CCCCc-chhHHHhhhhccCCCCceeCCCCCCccccCccccchh
Confidence 356788999999886 677899999874 789999 99654 66889999999999999999999999852
Q ss_pred ---cccCcC---CCCCCeeEeecc
Q psy553 100 ---LDLKDE---PRNRNYVVRFSW 117 (129)
Q Consensus 100 ---~~l~~h---~~~~~~~~~~~~ 117 (129)
..|..| .+.+++.|..+.
T Consensus 525 d~~s~Lt~HE~~CG~rt~~C~~Cg 548 (567)
T PLN03086 525 DRLRGMSEHESICGSRTAPCDSCG 548 (567)
T ss_pred hhhhhHHHHHHhcCCcceEccccC
Confidence 136666 457777775554
No 16
>PLN03086 PRLI-interacting factor K; Provisional
Probab=98.56 E-value=3e-08 Score=74.77 Aligned_cols=74 Identities=18% Similarity=0.324 Sum_probs=63.6
Q ss_pred CCcccccchhhccChHHHHHHHhhcCCCCceecccchhhcCC----------chhHHHhhhhhcCCCccchhhhhhhhhc
Q psy553 30 KPHQCQQCLKSFSSNHQLVQHIRVHTGEKPYKCTYCERRFKQ----------LSHVQQHTRLHTVEGVNSCLQILSLWIQ 99 (129)
Q Consensus 30 ~~~~C~~C~~~f~~~~~l~~h~~~h~~~~~~~C~~c~~~f~~----------~~~l~~H~~~h~~~~~y~C~~C~~~f~~ 99 (129)
+++.|+ |++.+ .+..|..|+..|...+++.|..|+..|.. ...|..|.... |.+++.|..|++.+..
T Consensus 477 kpv~Cp-Cg~~~-~R~~L~~H~~thCp~Kpi~C~fC~~~v~~g~~~~d~~d~~s~Lt~HE~~C-G~rt~~C~~Cgk~Vrl 553 (567)
T PLN03086 477 EPLQCP-CGVVL-EKEQMVQHQASTCPLRLITCRFCGDMVQAGGSAMDVRDRLRGMSEHESIC-GSRTAPCDSCGRSVML 553 (567)
T ss_pred CCccCC-CCCCc-chhHHHhhhhccCCCCceeCCCCCCccccCccccchhhhhhhHHHHHHhc-CCcceEccccCCeeee
Confidence 678999 99754 67889999999999999999999998842 24788998875 9999999999999999
Q ss_pred cccCcCC
Q psy553 100 LDLKDEP 106 (129)
Q Consensus 100 ~~l~~h~ 106 (129)
+++..|.
T Consensus 554 rdm~~H~ 560 (567)
T PLN03086 554 KEMDIHQ 560 (567)
T ss_pred hhHHHHH
Confidence 9888773
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=98.44 E-value=1.5e-07 Score=42.35 Aligned_cols=25 Identities=60% Similarity=1.299 Sum_probs=23.0
Q ss_pred HHHHHHhhcCCCCceecccchhhcC
Q psy553 46 QLVQHIRVHTGEKPYKCTYCERRFK 70 (129)
Q Consensus 46 ~l~~h~~~h~~~~~~~C~~c~~~f~ 70 (129)
+|..|+++|.+++||.|..|++.|.
T Consensus 1 ~l~~H~~~H~~~k~~~C~~C~k~F~ 25 (26)
T PF13465_consen 1 NLRRHMRTHTGEKPYKCPYCGKSFS 25 (26)
T ss_dssp HHHHHHHHHSSSSSEEESSSSEEES
T ss_pred CHHHHhhhcCCCCCCCCCCCcCeeC
Confidence 4789999999999999999999885
No 18
>PHA00733 hypothetical protein
Probab=98.36 E-value=6.1e-07 Score=55.91 Aligned_cols=55 Identities=33% Similarity=0.551 Sum_probs=48.5
Q ss_pred CCCCcccccchhhccChHHHHHHHhhcCCCCceecccchhhcCCchhHHHhhhhhcC
Q psy553 28 ANKPHQCQQCLKSFSSNHQLVQHIRVHTGEKPYKCTYCERRFKQLSHVQQHTRLHTV 84 (129)
Q Consensus 28 ~~~~~~C~~C~~~f~~~~~l~~h~~~h~~~~~~~C~~c~~~f~~~~~l~~H~~~h~~ 84 (129)
+.+||.|..|++.|.....|..|++.+ ..++.|..|++.|.....|..|+....+
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 367899999999999999999999876 3579999999999999999999886544
No 19
>PHA00616 hypothetical protein
Probab=98.33 E-value=2.3e-07 Score=46.59 Aligned_cols=33 Identities=15% Similarity=0.334 Sum_probs=18.4
Q ss_pred CcccccchhhccChHHHHHHHhhcCCCCceecc
Q psy553 31 PHQCQQCLKSFSSNHQLVQHIRVHTGEKPYKCT 63 (129)
Q Consensus 31 ~~~C~~C~~~f~~~~~l~~h~~~h~~~~~~~C~ 63 (129)
||.|..||+.|..+..|..|++.|++.+++.|.
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~~hg~~~~~~~ 33 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLSVHKQNKLTLE 33 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHHhcCCCcccee
Confidence 355555555555555555555555555555544
No 20
>PHA00616 hypothetical protein
Probab=98.30 E-value=4.8e-07 Score=45.45 Aligned_cols=34 Identities=18% Similarity=0.244 Sum_probs=32.0
Q ss_pred ceecccchhhcCCchhHHHhhhhhcCCCccchhh
Q psy553 59 PYKCTYCERRFKQLSHVQQHTRLHTVEGVNSCLQ 92 (129)
Q Consensus 59 ~~~C~~c~~~f~~~~~l~~H~~~h~~~~~y~C~~ 92 (129)
||+|..||..|...+.+..|++.|++++++.|..
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~~hg~~~~~~~~ 34 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLSVHKQNKLTLEY 34 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHHhcCCCccceeE
Confidence 6899999999999999999999999999998865
No 21
>PHA00732 hypothetical protein
Probab=98.13 E-value=8.6e-07 Score=50.60 Aligned_cols=37 Identities=30% Similarity=0.543 Sum_probs=20.6
Q ss_pred CcccccchhhccChHHHHHHHhh-cCCCCceecccchhhcC
Q psy553 31 PHQCQQCLKSFSSNHQLVQHIRV-HTGEKPYKCTYCERRFK 70 (129)
Q Consensus 31 ~~~C~~C~~~f~~~~~l~~h~~~-h~~~~~~~C~~c~~~f~ 70 (129)
||.|..|++.|.....|..|++. |.+ +.|..|++.|.
T Consensus 1 py~C~~Cgk~F~s~s~Lk~H~r~~H~~---~~C~~CgKsF~ 38 (79)
T PHA00732 1 MFKCPICGFTTVTLFALKQHARRNHTL---TKCPVCNKSYR 38 (79)
T ss_pred CccCCCCCCccCCHHHHHHHhhcccCC---CccCCCCCEeC
Confidence 35566666666666666666553 332 35556665554
No 22
>PHA00732 hypothetical protein
Probab=97.95 E-value=7.3e-06 Score=46.78 Aligned_cols=43 Identities=26% Similarity=0.417 Sum_probs=36.2
Q ss_pred ceecccchhhcCCchhHHHhhhh-hcCCCccchhhhhhhhhccccCcCC
Q psy553 59 PYKCTYCERRFKQLSHVQQHTRL-HTVEGVNSCLQILSLWIQLDLKDEP 106 (129)
Q Consensus 59 ~~~C~~c~~~f~~~~~l~~H~~~-h~~~~~y~C~~C~~~f~~~~l~~h~ 106 (129)
||.|..|++.|.....|..|++. |. ++.|++|++.|.+ |..|.
T Consensus 1 py~C~~Cgk~F~s~s~Lk~H~r~~H~---~~~C~~CgKsF~~--l~~H~ 44 (79)
T PHA00732 1 MFKCPICGFTTVTLFALKQHARRNHT---LTKCPVCNKSYRR--LNQHF 44 (79)
T ss_pred CccCCCCCCccCCHHHHHHHhhcccC---CCccCCCCCEeCC--hhhhh
Confidence 58899999999999999999984 54 3689999999985 45554
No 23
>KOG3993|consensus
Probab=97.86 E-value=3e-06 Score=61.44 Aligned_cols=74 Identities=23% Similarity=0.445 Sum_probs=57.5
Q ss_pred cccccchhhccChHHHHHHHhhcCCCCceecccchhhcCCchhHHHhhhhhc--------C-------------------
Q psy553 32 HQCQQCLKSFSSNHQLVQHIRVHTGEKPYKCTYCERRFKQLSHVQQHTRLHT--------V------------------- 84 (129)
Q Consensus 32 ~~C~~C~~~f~~~~~l~~h~~~h~~~~~~~C~~c~~~f~~~~~l~~H~~~h~--------~------------------- 84 (129)
|.|..|...|.....|..|.-.--....|+|+.|++.|....+|..|.+-|- +
T Consensus 268 yiCqLCK~kYeD~F~LAQHrC~RIV~vEYrCPEC~KVFsCPANLASHRRWHKPR~eaa~a~~~P~k~~~~~rae~~ea~r 347 (500)
T KOG3993|consen 268 YICQLCKEKYEDAFALAQHRCPRIVHVEYRCPECDKVFSCPANLASHRRWHKPRPEAAKAGSPPPKQAVETRAEVQEAER 347 (500)
T ss_pred HHHHHHHHhhhhHHHHhhccCCeeEEeeecCCcccccccCchhhhhhhcccCCchhhhhcCCCChhhhhhhhhhhhhccc
Confidence 7888898888888888888654333356899999999999999988887551 1
Q ss_pred ------CCccchhhhhhhhhccc-cCcC
Q psy553 85 ------EGVNSCLQILSLWIQLD-LKDE 105 (129)
Q Consensus 85 ------~~~y~C~~C~~~f~~~~-l~~h 105 (129)
+..|+|..|+|.|.+.- |++|
T Consensus 348 sg~dss~gi~~C~~C~KkFrRqAYLrKH 375 (500)
T KOG3993|consen 348 SGDDSSSGIFSCHTCGKKFRRQAYLRKH 375 (500)
T ss_pred cCCcccCceeecHHhhhhhHHHHHHHHh
Confidence 12399999999999986 7766
No 24
>KOG3993|consensus
Probab=97.86 E-value=6.6e-06 Score=59.75 Aligned_cols=54 Identities=26% Similarity=0.565 Sum_probs=47.6
Q ss_pred CCcccccchhhccChHHHHHHHhhcCC---------------------------------CCceecccchhhcCCchhHH
Q psy553 30 KPHQCQQCLKSFSSNHQLVQHIRVHTG---------------------------------EKPYKCTYCERRFKQLSHVQ 76 (129)
Q Consensus 30 ~~~~C~~C~~~f~~~~~l~~h~~~h~~---------------------------------~~~~~C~~c~~~f~~~~~l~ 76 (129)
..|+|++|++.|....+|.-|+++|.. +.+|.|..|++.|.....|.
T Consensus 294 vEYrCPEC~KVFsCPANLASHRRWHKPR~eaa~a~~~P~k~~~~~rae~~ea~rsg~dss~gi~~C~~C~KkFrRqAYLr 373 (500)
T KOG3993|consen 294 VEYRCPECDKVFSCPANLASHRRWHKPRPEAAKAGSPPPKQAVETRAEVQEAERSGDDSSSGIFSCHTCGKKFRRQAYLR 373 (500)
T ss_pred eeecCCcccccccCchhhhhhhcccCCchhhhhcCCCChhhhhhhhhhhhhccccCCcccCceeecHHhhhhhHHHHHHH
Confidence 459999999999999999999999832 13588999999999999999
Q ss_pred Hhhhhhc
Q psy553 77 QHTRLHT 83 (129)
Q Consensus 77 ~H~~~h~ 83 (129)
.|+.+|.
T Consensus 374 KHqlthq 380 (500)
T KOG3993|consen 374 KHQLTHQ 380 (500)
T ss_pred HhHHhhh
Confidence 9988874
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=97.57 E-value=0.00018 Score=38.05 Aligned_cols=50 Identities=28% Similarity=0.470 Sum_probs=34.7
Q ss_pred CcccccchhhccChHHHHHHHhh-cCCC-CceecccchhhcCCchhHHHhhhhhc
Q psy553 31 PHQCQQCLKSFSSNHQLVQHIRV-HTGE-KPYKCTYCERRFKQLSHVQQHTRLHT 83 (129)
Q Consensus 31 ~~~C~~C~~~f~~~~~l~~h~~~-h~~~-~~~~C~~c~~~f~~~~~l~~H~~~h~ 83 (129)
.|.|+.|++ ......|..|... |..+ +.+.|++|...+. .+|..|+....
T Consensus 2 ~f~CP~C~~-~~~~~~L~~H~~~~H~~~~~~v~CPiC~~~~~--~~l~~Hl~~~H 53 (54)
T PF05605_consen 2 SFTCPYCGK-GFSESSLVEHCEDEHRSESKNVVCPICSSRVT--DNLIRHLNSQH 53 (54)
T ss_pred CcCCCCCCC-ccCHHHHHHHHHhHCcCCCCCccCCCchhhhh--hHHHHHHHHhc
Confidence 478999998 4556778888554 5543 5688888887543 47778876543
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=97.55 E-value=4.6e-05 Score=32.91 Aligned_cols=22 Identities=45% Similarity=0.741 Sum_probs=12.5
Q ss_pred cccccchhhccChHHHHHHHhh
Q psy553 32 HQCQQCLKSFSSNHQLVQHIRV 53 (129)
Q Consensus 32 ~~C~~C~~~f~~~~~l~~h~~~ 53 (129)
|.|+.|++.|.....|..|++.
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 3455566666666666555544
No 27
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=97.41 E-value=7.1e-05 Score=52.78 Aligned_cols=24 Identities=17% Similarity=0.140 Sum_probs=20.1
Q ss_pred cCCCccchhhhhhhhhccc-cCcCC
Q psy553 83 TVEGVNSCLQILSLWIQLD-LKDEP 106 (129)
Q Consensus 83 ~~~~~y~C~~C~~~f~~~~-l~~h~ 106 (129)
...|||.|++|+|.|.... |+-|.
T Consensus 394 ~~~KPYrCevC~KRYKNlNGLKYHr 418 (423)
T COG5189 394 AKDKPYRCEVCDKRYKNLNGLKYHR 418 (423)
T ss_pred ccCCceeccccchhhccCccceecc
Confidence 3469999999999999996 77663
No 28
>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=97.41 E-value=8.9e-05 Score=31.97 Aligned_cols=23 Identities=39% Similarity=0.904 Sum_probs=18.7
Q ss_pred eecccchhhcCCchhHHHhhhhh
Q psy553 60 YKCTYCERRFKQLSHVQQHTRLH 82 (129)
Q Consensus 60 ~~C~~c~~~f~~~~~l~~H~~~h 82 (129)
|.|..|++.|.....|..|++.|
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 57888888888888888888764
No 29
>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=97.21 E-value=0.00021 Score=32.05 Aligned_cols=23 Identities=43% Similarity=0.765 Sum_probs=12.5
Q ss_pred cccccchhhccChHHHHHHHhhc
Q psy553 32 HQCQQCLKSFSSNHQLVQHIRVH 54 (129)
Q Consensus 32 ~~C~~C~~~f~~~~~l~~h~~~h 54 (129)
|.|..|++.|.....|..|++.|
T Consensus 2 ~~C~~C~~~F~~~~~l~~H~~~h 24 (27)
T PF13912_consen 2 FECDECGKTFSSLSALREHKRSH 24 (27)
T ss_dssp EEETTTTEEESSHHHHHHHHCTT
T ss_pred CCCCccCCccCChhHHHHHhHHh
Confidence 45555555555555555555444
No 30
>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=97.09 E-value=0.00032 Score=31.42 Aligned_cols=25 Identities=36% Similarity=0.903 Sum_probs=20.7
Q ss_pred ceecccchhhcCCchhHHHhhhhhc
Q psy553 59 PYKCTYCERRFKQLSHVQQHTRLHT 83 (129)
Q Consensus 59 ~~~C~~c~~~f~~~~~l~~H~~~h~ 83 (129)
||.|..|+..|.....|..|++.|.
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 5788888888888888888888764
No 31
>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=96.96 E-value=0.00015 Score=38.28 Aligned_cols=46 Identities=20% Similarity=0.258 Sum_probs=33.2
Q ss_pred ceecccchhhcCCchhHHHhhhh-hcC-CCccchhhhhhhhhccccCcCC
Q psy553 59 PYKCTYCERRFKQLSHVQQHTRL-HTV-EGVNSCLQILSLWIQLDLKDEP 106 (129)
Q Consensus 59 ~~~C~~c~~~f~~~~~l~~H~~~-h~~-~~~y~C~~C~~~f~~~~l~~h~ 106 (129)
-|.|+.|++ -.+...|..|... |.. .+.+.|++|...+.. +|..|+
T Consensus 2 ~f~CP~C~~-~~~~~~L~~H~~~~H~~~~~~v~CPiC~~~~~~-~l~~Hl 49 (54)
T PF05605_consen 2 SFTCPYCGK-GFSESSLVEHCEDEHRSESKNVVCPICSSRVTD-NLIRHL 49 (54)
T ss_pred CcCCCCCCC-ccCHHHHHHHHHhHCcCCCCCccCCCchhhhhh-HHHHHH
Confidence 478999999 4567889999665 443 357999999986543 455554
No 32
>PRK04860 hypothetical protein; Provisional
Probab=96.94 E-value=0.00034 Score=45.23 Aligned_cols=38 Identities=26% Similarity=0.546 Sum_probs=31.6
Q ss_pred ceecccchhhcCCchhHHHhhhhhcCCCccchhhhhhhhhcc
Q psy553 59 PYKCTYCERRFKQLSHVQQHTRLHTVEGVNSCLQILSLWIQL 100 (129)
Q Consensus 59 ~~~C~~c~~~f~~~~~l~~H~~~h~~~~~y~C~~C~~~f~~~ 100 (129)
+|.|. |+. ....+..|.+++.++++|.|..|+..|...
T Consensus 119 ~Y~C~-C~~---~~~~~rrH~ri~~g~~~YrC~~C~~~l~~~ 156 (160)
T PRK04860 119 PYRCK-CQE---HQLTVRRHNRVVRGEAVYRCRRCGETLVFK 156 (160)
T ss_pred EEEcC-CCC---eeCHHHHHHHHhcCCccEECCCCCceeEEe
Confidence 58887 876 667788999999999999999999888765
No 33
>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=96.91 E-value=0.00068 Score=29.07 Aligned_cols=21 Identities=52% Similarity=0.854 Sum_probs=9.4
Q ss_pred ccccchhhccChHHHHHHHhh
Q psy553 33 QCQQCLKSFSSNHQLVQHIRV 53 (129)
Q Consensus 33 ~C~~C~~~f~~~~~l~~h~~~ 53 (129)
.|..|+..|.....|..|+..
T Consensus 2 ~C~~C~~~~~~~~~l~~H~~~ 22 (24)
T PF13894_consen 2 QCPICGKSFRSKSELRQHMRT 22 (24)
T ss_dssp E-SSTS-EESSHHHHHHHHHH
T ss_pred CCcCCCCcCCcHHHHHHHHHh
Confidence 445555555555555555443
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=96.88 E-value=0.00071 Score=28.99 Aligned_cols=23 Identities=35% Similarity=0.896 Sum_probs=19.3
Q ss_pred eecccchhhcCCchhHHHhhhhh
Q psy553 60 YKCTYCERRFKQLSHVQQHTRLH 82 (129)
Q Consensus 60 ~~C~~c~~~f~~~~~l~~H~~~h 82 (129)
|.|++|+..|.....+..|+..+
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 68999999999999999999876
No 35
>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=96.57 E-value=0.0012 Score=34.07 Aligned_cols=32 Identities=19% Similarity=0.487 Sum_probs=15.8
Q ss_pred CCCceecccchhhcCCchhHHHhhhhhcCCCc
Q psy553 56 GEKPYKCTYCERRFKQLSHVQQHTRLHTVEGV 87 (129)
Q Consensus 56 ~~~~~~C~~c~~~f~~~~~l~~H~~~h~~~~~ 87 (129)
+..|..|++|+..+.+..+|.+|+...++.+|
T Consensus 21 S~~PatCP~C~a~~~~srnLrRHle~~H~~k~ 52 (54)
T PF09237_consen 21 SEQPATCPICGAVIRQSRNLRRHLEIRHFKKP 52 (54)
T ss_dssp TS--EE-TTT--EESSHHHHHHHHHHHTTTS-
T ss_pred cCCCCCCCcchhhccchhhHHHHHHHHhcccC
Confidence 34556666666666666666666665555444
No 36
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=96.57 E-value=0.0019 Score=37.86 Aligned_cols=75 Identities=21% Similarity=0.280 Sum_probs=17.7
Q ss_pred ccccchhhccChHHHHHHHhhcCCCCceecccchhhcCCchhHHHhhhhhcCCCccchhhhhhhhhccc-cCcCCCCCCe
Q psy553 33 QCQQCLKSFSSNHQLVQHIRVHTGEKPYKCTYCERRFKQLSHVQQHTRLHTVEGVNSCLQILSLWIQLD-LKDEPRNRNY 111 (129)
Q Consensus 33 ~C~~C~~~f~~~~~l~~h~~~h~~~~~~~C~~c~~~f~~~~~l~~H~~~h~~~~~y~C~~C~~~f~~~~-l~~h~~~~~~ 111 (129)
.|..|+..|.....|..|+....+...-.. ..+.....+..+...- -...+.|..|++.|.... |..|++.+.|
T Consensus 1 ~C~~C~~~f~~~~~l~~H~~~~H~~~~~~~----~~l~~~~~~~~~~~~~-~~~~~~C~~C~~~f~s~~~l~~Hm~~~~H 75 (100)
T PF12756_consen 1 QCLFCDESFSSVDDLLQHMKKKHGFDIPDQ----KYLVDPNRLLNYLRKK-VKESFRCPYCNKTFRSREALQEHMRSKHH 75 (100)
T ss_dssp -----------------------------------------------------SSEEBSSSS-EESSHHHHHHHHHHTTT
T ss_pred Cccccccccccccccccccccccccccccc----cccccccccccccccc-cCCCCCCCccCCCCcCHHHHHHHHcCccC
Confidence 488899999999999999865433211110 1111222222222211 122577888888887775 7777665444
Q ss_pred e
Q psy553 112 V 112 (129)
Q Consensus 112 ~ 112 (129)
.
T Consensus 76 ~ 76 (100)
T PF12756_consen 76 K 76 (100)
T ss_dssp T
T ss_pred C
Confidence 3
No 37
>smart00355 ZnF_C2H2 zinc finger.
Probab=96.31 E-value=0.0045 Score=26.72 Aligned_cols=22 Identities=41% Similarity=0.859 Sum_probs=11.8
Q ss_pred ccccchhhccChHHHHHHHhhc
Q psy553 33 QCQQCLKSFSSNHQLVQHIRVH 54 (129)
Q Consensus 33 ~C~~C~~~f~~~~~l~~h~~~h 54 (129)
.|..|++.|.....+..|+..|
T Consensus 2 ~C~~C~~~f~~~~~l~~H~~~H 23 (26)
T smart00355 2 RCPECGKVFKSKSALKEHMRTH 23 (26)
T ss_pred CCCCCcchhCCHHHHHHHHHHh
Confidence 4555555555555555555433
No 38
>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=96.18 E-value=0.006 Score=31.54 Aligned_cols=34 Identities=21% Similarity=0.502 Sum_probs=23.7
Q ss_pred CCCCCCcccccchhhccChHHHHHHHhhcCCCCc
Q psy553 26 LEANKPHQCQQCLKSFSSNHQLVQHIRVHTGEKP 59 (129)
Q Consensus 26 ~~~~~~~~C~~C~~~f~~~~~l~~h~~~h~~~~~ 59 (129)
..++.|..|++|+..+....+|.+|+....+.+|
T Consensus 19 ~~S~~PatCP~C~a~~~~srnLrRHle~~H~~k~ 52 (54)
T PF09237_consen 19 SQSEQPATCPICGAVIRQSRNLRRHLEIRHFKKP 52 (54)
T ss_dssp CTTS--EE-TTT--EESSHHHHHHHHHHHTTTS-
T ss_pred hccCCCCCCCcchhhccchhhHHHHHHHHhcccC
Confidence 3456789999999999999999999988776665
No 39
>smart00355 ZnF_C2H2 zinc finger.
Probab=96.13 E-value=0.0044 Score=26.74 Aligned_cols=24 Identities=38% Similarity=0.787 Sum_probs=19.3
Q ss_pred eecccchhhcCCchhHHHhhhhhc
Q psy553 60 YKCTYCERRFKQLSHVQQHTRLHT 83 (129)
Q Consensus 60 ~~C~~c~~~f~~~~~l~~H~~~h~ 83 (129)
+.|..|+..|.....+..|++.|.
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~~H~ 24 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMRTHX 24 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHHHhc
Confidence 468888888888888888887653
No 40
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=95.98 E-value=0.00024 Score=41.82 Aligned_cols=24 Identities=29% Similarity=0.894 Sum_probs=17.2
Q ss_pred ceecccchhhcCCchhHHHhhhhh
Q psy553 59 PYKCTYCERRFKQLSHVQQHTRLH 82 (129)
Q Consensus 59 ~~~C~~c~~~f~~~~~l~~H~~~h 82 (129)
.+.|.+|+..|.....|..|++.+
T Consensus 50 ~~~C~~C~~~f~s~~~l~~Hm~~~ 73 (100)
T PF12756_consen 50 SFRCPYCNKTFRSREALQEHMRSK 73 (100)
T ss_dssp SEEBSSSS-EESSHHHHHHHHHHT
T ss_pred CCCCCccCCCCcCHHHHHHHHcCc
Confidence 467777777777777777777765
No 41
>PRK04860 hypothetical protein; Provisional
Probab=95.66 E-value=0.0095 Score=38.59 Aligned_cols=39 Identities=28% Similarity=0.609 Sum_probs=33.0
Q ss_pred CCcccccchhhccChHHHHHHHhhcCCCCceecccchhhcCCc
Q psy553 30 KPHQCQQCLKSFSSNHQLVQHIRVHTGEKPYKCTYCERRFKQL 72 (129)
Q Consensus 30 ~~~~C~~C~~~f~~~~~l~~h~~~h~~~~~~~C~~c~~~f~~~ 72 (129)
-+|.|. |+. ....+..|.+++.+.++|.|..|+..|...
T Consensus 118 ~~Y~C~-C~~---~~~~~rrH~ri~~g~~~YrC~~C~~~l~~~ 156 (160)
T PRK04860 118 FPYRCK-CQE---HQLTVRRHNRVVRGEAVYRCRRCGETLVFK 156 (160)
T ss_pred EEEEcC-CCC---eeCHHHHHHHHhcCCccEECCCCCceeEEe
Confidence 479997 987 566788999999999999999999877643
No 42
>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=95.19 E-value=0.0016 Score=29.22 Aligned_cols=20 Identities=15% Similarity=0.127 Sum_probs=9.7
Q ss_pred cchhhhhhhhhccc-cCcCCC
Q psy553 88 NSCLQILSLWIQLD-LKDEPR 107 (129)
Q Consensus 88 y~C~~C~~~f~~~~-l~~h~~ 107 (129)
|.|..|++.|.... |..|+.
T Consensus 2 ~~C~~C~k~f~~~~~~~~H~~ 22 (27)
T PF12171_consen 2 FYCDACDKYFSSENQLKQHMK 22 (27)
T ss_dssp CBBTTTTBBBSSHHHHHCCTT
T ss_pred CCcccCCCCcCCHHHHHHHHc
Confidence 34555555555553 444443
No 43
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=95.17 E-value=0.012 Score=25.61 Aligned_cols=20 Identities=55% Similarity=0.909 Sum_probs=10.4
Q ss_pred ccccchhhccChHHHHHHHh
Q psy553 33 QCQQCLKSFSSNHQLVQHIR 52 (129)
Q Consensus 33 ~C~~C~~~f~~~~~l~~h~~ 52 (129)
.|..|+..|.....+..|++
T Consensus 2 ~C~~C~~~f~s~~~~~~H~~ 21 (25)
T PF12874_consen 2 YCDICNKSFSSENSLRQHLR 21 (25)
T ss_dssp EETTTTEEESSHHHHHHHHT
T ss_pred CCCCCCCCcCCHHHHHHHHC
Confidence 45555555555555555543
No 44
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=94.89 E-value=0.017 Score=25.02 Aligned_cols=22 Identities=27% Similarity=0.715 Sum_probs=17.2
Q ss_pred eecccchhhcCCchhHHHhhhh
Q psy553 60 YKCTYCERRFKQLSHVQQHTRL 81 (129)
Q Consensus 60 ~~C~~c~~~f~~~~~l~~H~~~ 81 (129)
|.|.+|...|.....+..|++.
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 5678888888888888888764
No 45
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=94.31 E-value=0.032 Score=23.97 Aligned_cols=20 Identities=30% Similarity=0.635 Sum_probs=8.4
Q ss_pred ccccchhhccChHHHHHHHhh
Q psy553 33 QCQQCLKSFSSNHQLVQHIRV 53 (129)
Q Consensus 33 ~C~~C~~~f~~~~~l~~h~~~ 53 (129)
.|..|..... ...|..|+..
T Consensus 2 ~C~~C~y~t~-~~~l~~H~~~ 21 (24)
T PF13909_consen 2 KCPHCSYSTS-KSNLKRHLKR 21 (24)
T ss_dssp E-SSSS-EES-HHHHHHHHHH
T ss_pred CCCCCCCcCC-HHHHHHHHHh
Confidence 4555554444 4445555443
No 46
>KOG2231|consensus
Probab=92.79 E-value=0.088 Score=41.29 Aligned_cols=72 Identities=19% Similarity=0.240 Sum_probs=47.4
Q ss_pred ChHHHHHHHh-hcCCCCceecccch---------hhcCCchhHHHhhhhhcC-C---Cc-cchhhhhhhhhccc-cCcCC
Q psy553 43 SNHQLVQHIR-VHTGEKPYKCTYCE---------RRFKQLSHVQQHTRLHTV-E---GV-NSCLQILSLWIQLD-LKDEP 106 (129)
Q Consensus 43 ~~~~l~~h~~-~h~~~~~~~C~~c~---------~~f~~~~~l~~H~~~h~~-~---~~-y~C~~C~~~f~~~~-l~~h~ 106 (129)
....|..|++ .|.. +.|.+|. ........|+.|++.-.. + +. -.|..|...|...+ |.+|+
T Consensus 126 s~~~Lk~H~~~~H~~---~~c~lC~~~~kif~~e~k~Yt~~el~~h~~~gd~d~~s~rGhp~C~~C~~~fld~~el~rH~ 202 (669)
T KOG2231|consen 126 SVENLKNHMRDQHKL---HLCSLCLQNLKIFINERKLYTRAELNLHLMFGDPDDESCRGHPLCKFCHERFLDDDELYRHL 202 (669)
T ss_pred HHHHHHHHHHHhhhh---hccccccccceeeeeeeehehHHHHHHHHhcCCCccccccCCccchhhhhhhccHHHHHHhh
Confidence 6677888985 4533 3333322 222355667777664321 1 11 34899999999997 99999
Q ss_pred CCCCeeEeecc
Q psy553 107 RNRNYVVRFSW 117 (129)
Q Consensus 107 ~~~~~~~~~~~ 117 (129)
+..++.|.|+.
T Consensus 203 ~~~h~~chfC~ 213 (669)
T KOG2231|consen 203 RFDHEFCHFCD 213 (669)
T ss_pred ccceeheeecC
Confidence 99999998884
No 47
>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=92.16 E-value=0.063 Score=25.20 Aligned_cols=9 Identities=11% Similarity=-0.134 Sum_probs=5.0
Q ss_pred Cccchhhhh
Q psy553 86 GVNSCLQIL 94 (129)
Q Consensus 86 ~~y~C~~C~ 94 (129)
.++.|++|+
T Consensus 16 ~~~~CP~Cg 24 (33)
T cd00350 16 APWVCPVCG 24 (33)
T ss_pred CCCcCcCCC
Confidence 455565555
No 48
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=91.96 E-value=0.05 Score=39.30 Aligned_cols=54 Identities=22% Similarity=0.440 Sum_probs=39.4
Q ss_pred ecccchhhcCCchhHHHhhhhhcCCCccchhhhhh-------hhhccc-cCcCCCCCCeeEeeccc
Q psy553 61 KCTYCERRFKQLSHVQQHTRLHTVEGVNSCLQILS-------LWIQLD-LKDEPRNRNYVVRFSWW 118 (129)
Q Consensus 61 ~C~~c~~~f~~~~~l~~H~~~h~~~~~y~C~~C~~-------~f~~~~-l~~h~~~~~~~~~~~~~ 118 (129)
.|..|...|-....|..|++.- --.|-+|++ .|...+ |.+|.+..+|.|+|+.+
T Consensus 222 ~C~FC~~~FYdDDEL~~HcR~~----HE~ChICD~v~p~~~QYFK~Y~~Le~HF~~~hy~ct~qtc 283 (493)
T COG5236 222 LCIFCKIYFYDDDELRRHCRLR----HEACHICDMVGPIRYQYFKSYEDLEAHFRNAHYCCTFQTC 283 (493)
T ss_pred hhhhccceecChHHHHHHHHhh----hhhhhhhhccCccchhhhhCHHHHHHHhhcCceEEEEEEE
Confidence 4777888888888888888743 335666664 355554 88999999999877654
No 49
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=91.72 E-value=0.048 Score=39.73 Aligned_cols=62 Identities=34% Similarity=0.626 Sum_probs=42.4
Q ss_pred CcccccchhhccChHHHHHHHh--hcCCC--Cceecc--cchhhcCCchhHHHhhhhhcCCCccchhh
Q psy553 31 PHQCQQCLKSFSSNHQLVQHIR--VHTGE--KPYKCT--YCERRFKQLSHVQQHTRLHTVEGVNSCLQ 92 (129)
Q Consensus 31 ~~~C~~C~~~f~~~~~l~~h~~--~h~~~--~~~~C~--~c~~~f~~~~~l~~H~~~h~~~~~y~C~~ 92 (129)
++.|..|...|.....+..|.+ .|.++ +++.|+ .|+..|.....+..|..+|.+.+++.|..
T Consensus 289 ~~~~~~~~~~~s~~~~l~~~~~~~~h~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 356 (467)
T COG5048 289 PIKSKQCNISFSRSSPLTRHLRSVNHSGESLKPFSCPYSLCGKLFSRNDALKRHILLHTSISPAKEKL 356 (467)
T ss_pred CCCCccccCCccccccccccccccccccccCCceeeeccCCCccccccccccCCcccccCCCcccccc
Confidence 5666677777777777777777 57666 677776 57777777777777777776666655543
No 50
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=91.64 E-value=0.19 Score=21.96 Aligned_cols=19 Identities=26% Similarity=0.660 Sum_probs=9.5
Q ss_pred ccccchhhccChHHHHHHHh
Q psy553 33 QCQQCLKSFSSNHQLVQHIR 52 (129)
Q Consensus 33 ~C~~C~~~f~~~~~l~~h~~ 52 (129)
.|+.||+.| ....|..|+.
T Consensus 4 ~C~~CgR~F-~~~~l~~H~~ 22 (25)
T PF13913_consen 4 PCPICGRKF-NPDRLEKHEK 22 (25)
T ss_pred cCCCCCCEE-CHHHHHHHHH
Confidence 455555555 3444455543
No 51
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=89.35 E-value=0.079 Score=38.33 Aligned_cols=83 Identities=20% Similarity=0.331 Sum_probs=51.9
Q ss_pred ccccc--chhhccChHHHHHHHhhcCCCCceecccchh---------hcCCchhHHHhhhhhcCCCc----cchhhhhhh
Q psy553 32 HQCQQ--CLKSFSSNHQLVQHIRVHTGEKPYKCTYCER---------RFKQLSHVQQHTRLHTVEGV----NSCLQILSL 96 (129)
Q Consensus 32 ~~C~~--C~~~f~~~~~l~~h~~~h~~~~~~~C~~c~~---------~f~~~~~l~~H~~~h~~~~~----y~C~~C~~~ 96 (129)
|.|+. |......-..|..|..+..+. +.|.+|.. .......|..|...-..+.. -.|..|...
T Consensus 152 F~CP~skc~~~C~~~k~lk~H~K~~H~~--~~C~~C~~nKk~F~~E~~lF~~~~Lr~H~~~G~~e~GFKGHP~C~FC~~~ 229 (493)
T COG5236 152 FKCPKSKCHRRCGSLKELKKHYKAQHGF--VLCSECIGNKKDFWNEIRLFRSSTLRDHKNGGLEEEGFKGHPLCIFCKIY 229 (493)
T ss_pred hcCCchhhhhhhhhHHHHHHHHHhhcCc--EEhHhhhcCcccCccceeeeecccccccccCCccccCcCCCchhhhccce
Confidence 66765 554444445577776654433 45555542 23345567777664433322 349999988
Q ss_pred hhccc-cCcCCCCCCeeEeec
Q psy553 97 WIQLD-LKDEPRNRNYVVRFS 116 (129)
Q Consensus 97 f~~~~-l~~h~~~~~~~~~~~ 116 (129)
|-..| |..|++.++-.|..+
T Consensus 230 FYdDDEL~~HcR~~HE~ChIC 250 (493)
T COG5236 230 FYDDDELRRHCRLRHEACHIC 250 (493)
T ss_pred ecChHHHHHHHHhhhhhhhhh
Confidence 88887 999999888876443
No 52
>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=88.30 E-value=0.35 Score=22.50 Aligned_cols=22 Identities=23% Similarity=0.587 Sum_probs=12.4
Q ss_pred ceecccchhhcCCchhHHHhhh
Q psy553 59 PYKCTYCERRFKQLSHVQQHTR 80 (129)
Q Consensus 59 ~~~C~~c~~~f~~~~~l~~H~~ 80 (129)
+|.|.+|...|.....+..|+.
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~ 24 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLK 24 (35)
T ss_pred CeEccccCCccCCHHHHHHHHC
Confidence 3556666666665555555544
No 53
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=87.34 E-value=0.24 Score=32.26 Aligned_cols=23 Identities=22% Similarity=0.368 Sum_probs=18.6
Q ss_pred ceecccchhhcCCchhHHHhhhhhcCCCccchhhhh
Q psy553 59 PYKCTYCERRFKQLSHVQQHTRLHTVEGVNSCLQIL 94 (129)
Q Consensus 59 ~~~C~~c~~~f~~~~~l~~H~~~h~~~~~y~C~~C~ 94 (129)
.|.|.+||. ++-|+-|-+|++|+
T Consensus 134 ~~vC~vCGy-------------~~~ge~P~~CPiCg 156 (166)
T COG1592 134 VWVCPVCGY-------------THEGEAPEVCPICG 156 (166)
T ss_pred EEEcCCCCC-------------cccCCCCCcCCCCC
Confidence 699999986 34557789999998
No 54
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=86.47 E-value=0.24 Score=36.09 Aligned_cols=49 Identities=31% Similarity=0.365 Sum_probs=43.6
Q ss_pred CceecccchhhcCCchhHHHhhh--hhcCC--Cccchh--hhhhhhhccc-cCcCC
Q psy553 58 KPYKCTYCERRFKQLSHVQQHTR--LHTVE--GVNSCL--QILSLWIQLD-LKDEP 106 (129)
Q Consensus 58 ~~~~C~~c~~~f~~~~~l~~H~~--~h~~~--~~y~C~--~C~~~f~~~~-l~~h~ 106 (129)
.++.|..|...|.....+..|.+ .|.++ +|+.|+ .|++.|.+.+ +..|.
T Consensus 288 ~~~~~~~~~~~~s~~~~l~~~~~~~~h~~~~~~~~~~p~~~~~~~~~~~~~~~~~~ 343 (467)
T COG5048 288 LPIKSKQCNISFSRSSPLTRHLRSVNHSGESLKPFSCPYSLCGKLFSRNDALKRHI 343 (467)
T ss_pred cCCCCccccCCccccccccccccccccccccCCceeeeccCCCccccccccccCCc
Confidence 36788889999999999999999 89999 999999 7999999997 77664
No 55
>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=86.06 E-value=0.31 Score=23.01 Aligned_cols=9 Identities=11% Similarity=0.080 Sum_probs=5.0
Q ss_pred ccchhhhhh
Q psy553 87 VNSCLQILS 95 (129)
Q Consensus 87 ~y~C~~C~~ 95 (129)
|..|++|+.
T Consensus 18 p~~CP~Cg~ 26 (34)
T cd00729 18 PEKCPICGA 26 (34)
T ss_pred CCcCcCCCC
Confidence 455666653
No 56
>KOG2186|consensus
Probab=85.99 E-value=0.39 Score=33.32 Aligned_cols=50 Identities=22% Similarity=0.462 Sum_probs=37.6
Q ss_pred CcccccchhhccChHHHHHHHhhcCCCCceecccchhhcCCchhHHHhhhhhc
Q psy553 31 PHQCQQCLKSFSSNHQLVQHIRVHTGEKPYKCTYCERRFKQLSHVQQHTRLHT 83 (129)
Q Consensus 31 ~~~C~~C~~~f~~~~~l~~h~~~h~~~~~~~C~~c~~~f~~~~~l~~H~~~h~ 83 (129)
.|.|..||.... +..+-+|+....+ .-|.|.-|+..|.. ..+..|...-+
T Consensus 3 ~FtCnvCgEsvK-Kp~vekH~srCrn-~~fSCIDC~k~F~~-~sYknH~kCIT 52 (276)
T KOG2186|consen 3 FFTCNVCGESVK-KPQVEKHMSRCRN-AYFSCIDCGKTFER-VSYKNHTKCIT 52 (276)
T ss_pred EEehhhhhhhcc-ccchHHHHHhccC-CeeEEeeccccccc-chhhhhhhhcc
Confidence 367999997766 4556679888887 56899999999987 56777766443
No 57
>KOG2893|consensus
Probab=84.67 E-value=0.36 Score=33.31 Aligned_cols=41 Identities=29% Similarity=0.702 Sum_probs=25.6
Q ss_pred CCcccccchhhccChHHHHHHHhhcCCCCceecccchhhcCCchhH
Q psy553 30 KPHQCQQCLKSFSSNHQLVQHIRVHTGEKPYKCTYCERRFKQLSHV 75 (129)
Q Consensus 30 ~~~~C~~C~~~f~~~~~l~~h~~~h~~~~~~~C~~c~~~f~~~~~l 75 (129)
++| |=.|.+.|.....|..|+.. +-|+|.+|-+.+.+..-|
T Consensus 10 kpw-cwycnrefddekiliqhqka----khfkchichkkl~sgpgl 50 (341)
T KOG2893|consen 10 KPW-CWYCNREFDDEKILIQHQKA----KHFKCHICHKKLFSGPGL 50 (341)
T ss_pred Cce-eeecccccchhhhhhhhhhh----ccceeeeehhhhccCCCc
Confidence 444 33677888877777777653 457888876544444333
No 58
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=84.55 E-value=0.17 Score=34.42 Aligned_cols=14 Identities=14% Similarity=-0.040 Sum_probs=11.1
Q ss_pred cchhhhhhhhhccc
Q psy553 88 NSCLQILSLWIQLD 101 (129)
Q Consensus 88 y~C~~C~~~f~~~~ 101 (129)
.+|+.||.++...+
T Consensus 49 ~vCP~CgyA~~~~~ 62 (214)
T PF09986_consen 49 WVCPHCGYAAFEED 62 (214)
T ss_pred EECCCCCCcccccc
Confidence 57999998888764
No 59
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=83.83 E-value=0.19 Score=32.35 Aligned_cols=13 Identities=15% Similarity=0.340 Sum_probs=8.3
Q ss_pred cchhhhhhhhhcc
Q psy553 88 NSCLQILSLWIQL 100 (129)
Q Consensus 88 y~C~~C~~~f~~~ 100 (129)
|.|+.||++|...
T Consensus 29 ~~c~~c~~~f~~~ 41 (154)
T PRK00464 29 RECLACGKRFTTF 41 (154)
T ss_pred eeccccCCcceEe
Confidence 6666666666654
No 60
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=82.22 E-value=0.89 Score=24.00 Aligned_cols=27 Identities=15% Similarity=0.486 Sum_probs=20.2
Q ss_pred CCCCCcccccchhhccChHHHHHHHhh
Q psy553 27 EANKPHQCQQCLKSFSSNHQLVQHIRV 53 (129)
Q Consensus 27 ~~~~~~~C~~C~~~f~~~~~l~~h~~~ 53 (129)
.++..+.|+.|++.|.....+.+|...
T Consensus 13 DGE~~lrCPRC~~~FR~~K~Y~RHVNK 39 (65)
T COG4049 13 DGEEFLRCPRCGMVFRRRKDYIRHVNK 39 (65)
T ss_pred CCceeeeCCchhHHHHHhHHHHHHhhH
Confidence 456677888888888888877777653
No 61
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=81.05 E-value=0.6 Score=22.43 Aligned_cols=11 Identities=27% Similarity=0.812 Sum_probs=5.3
Q ss_pred ceecccchhhc
Q psy553 59 PYKCTYCERRF 69 (129)
Q Consensus 59 ~~~C~~c~~~f 69 (129)
..+|..|+..|
T Consensus 25 ~vrC~~C~~~f 35 (37)
T PF13719_consen 25 KVRCPKCGHVF 35 (37)
T ss_pred EEECCCCCcEe
Confidence 34555555444
No 62
>KOG2186|consensus
Probab=80.45 E-value=0.68 Score=32.16 Aligned_cols=45 Identities=18% Similarity=0.394 Sum_probs=36.0
Q ss_pred ceecccchhhcCCchhHHHhhhhhcCCCccchhhhhhhhhccccCcC
Q psy553 59 PYKCTYCERRFKQLSHVQQHTRLHTVEGVNSCLQILSLWIQLDLKDE 105 (129)
Q Consensus 59 ~~~C~~c~~~f~~~~~l~~H~~~h~~~~~y~C~~C~~~f~~~~l~~h 105 (129)
-|.|.+||....- ..+-+|+....+ ..|.|-.|++.|..-+...|
T Consensus 3 ~FtCnvCgEsvKK-p~vekH~srCrn-~~fSCIDC~k~F~~~sYknH 47 (276)
T KOG2186|consen 3 FFTCNVCGESVKK-PQVEKHMSRCRN-AYFSCIDCGKTFERVSYKNH 47 (276)
T ss_pred EEehhhhhhhccc-cchHHHHHhccC-CeeEEeecccccccchhhhh
Confidence 3789999987644 456678887766 68999999999999777777
No 63
>KOG1146|consensus
Probab=80.16 E-value=1.2 Score=37.75 Aligned_cols=51 Identities=25% Similarity=0.523 Sum_probs=36.5
Q ss_pred CCcccccchhhccChHHHHHHHhh-cC------------------------CCCceecccchhhcCCchhHHHhhh
Q psy553 30 KPHQCQQCLKSFSSNHQLVQHIRV-HT------------------------GEKPYKCTYCERRFKQLSHVQQHTR 80 (129)
Q Consensus 30 ~~~~C~~C~~~f~~~~~l~~h~~~-h~------------------------~~~~~~C~~c~~~f~~~~~l~~H~~ 80 (129)
+.+.|+.|+..|+....|..||++ |. +-++|.|..|...+.....|.+|+.
T Consensus 464 kt~~cpkc~~~yk~a~~L~vhmRskhp~~~~~~c~~gq~~~~~arg~~~~~~~~p~~C~~C~~stttng~Lsihlq 539 (1406)
T KOG1146|consen 464 KTLKCPKCNWHYKLAQTLGVHMRSKHPESQSAYCKAGQNHPRLARGEVYRCPGKPYPCRACNYSTTTNGNLSIHLQ 539 (1406)
T ss_pred ccccCCccchhhhhHHHhhhcccccccccchhHhHhccccccccccccccCCCCcccceeeeeeeecchHHHHHHH
Confidence 667888888888888888888876 11 1246677777777777777776655
No 64
>KOG2893|consensus
Probab=80.01 E-value=0.78 Score=31.70 Aligned_cols=43 Identities=26% Similarity=0.424 Sum_probs=31.3
Q ss_pred CceecccchhhcCCchhHHHhhhhhcCCCccchhhhhhhh-hccccCcC
Q psy553 58 KPYKCTYCERRFKQLSHVQQHTRLHTVEGVNSCLQILSLW-IQLDLKDE 105 (129)
Q Consensus 58 ~~~~C~~c~~~f~~~~~l~~H~~~h~~~~~y~C~~C~~~f-~~~~l~~h 105 (129)
++| |=+|.+-|.....|++|++ .+-|+|-+|.|-. .-..|.-|
T Consensus 10 kpw-cwycnrefddekiliqhqk----akhfkchichkkl~sgpglsih 53 (341)
T KOG2893|consen 10 KPW-CWYCNREFDDEKILIQHQK----AKHFKCHICHKKLFSGPGLSIH 53 (341)
T ss_pred Cce-eeecccccchhhhhhhhhh----hccceeeeehhhhccCCCceee
Confidence 454 4569999999999999988 5679999998543 33334444
No 65
>PF02176 zf-TRAF: TRAF-type zinc finger; PDB: 2EOD_A 2YUC_A 3HCU_A 3HCS_B 3HCT_A.
Probab=79.71 E-value=0.39 Score=25.40 Aligned_cols=47 Identities=15% Similarity=0.273 Sum_probs=22.7
Q ss_pred Cceeccc--chhhcCCchhHHHhhhhhcCCCccchhh----hhhhhhccccCcC
Q psy553 58 KPYKCTY--CERRFKQLSHVQQHTRLHTVEGVNSCLQ----ILSLWIQLDLKDE 105 (129)
Q Consensus 58 ~~~~C~~--c~~~f~~~~~l~~H~~~h~~~~~y~C~~----C~~~f~~~~l~~h 105 (129)
.+..|+. |...+ ....|..|...-=..++-.|.. |...+...+|..|
T Consensus 8 ~~v~C~~~cc~~~i-~r~~l~~H~~~~C~~~~v~C~~~~~GC~~~~~~~~l~~H 60 (60)
T PF02176_consen 8 RPVPCPNGCCNEMI-PRKELDDHLENECPKRPVPCPYSPYGCKERVPREDLEEH 60 (60)
T ss_dssp SEEE-TT--S-BEE-ECCCHHHHHHTTSTTSEEE-SS----S--EEEHHHHHHC
T ss_pred CEeeCCCCCcccce-eHHHHHHHHHccCCCCcEECCCCCCCCCCccchhHHhCC
Confidence 3456655 33323 3445666666444555666777 7666666555443
No 66
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=78.77 E-value=0.82 Score=21.83 Aligned_cols=9 Identities=22% Similarity=0.995 Sum_probs=4.0
Q ss_pred cccchhhcc
Q psy553 34 CQQCLKSFS 42 (129)
Q Consensus 34 C~~C~~~f~ 42 (129)
|+.|+..|.
T Consensus 5 Cp~C~~~y~ 13 (36)
T PF13717_consen 5 CPNCQAKYE 13 (36)
T ss_pred CCCCCCEEe
Confidence 444444443
No 67
>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=78.27 E-value=1.4 Score=26.71 Aligned_cols=15 Identities=27% Similarity=0.656 Sum_probs=8.5
Q ss_pred CceecccchhhcCCc
Q psy553 58 KPYKCTYCERRFKQL 72 (129)
Q Consensus 58 ~~~~C~~c~~~f~~~ 72 (129)
.|..|+.||..|...
T Consensus 25 ~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 25 DPIVCPKCGTEFPPE 39 (108)
T ss_pred CCccCCCCCCccCcc
Confidence 455666666555443
No 68
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=78.12 E-value=1 Score=24.08 Aligned_cols=33 Identities=9% Similarity=0.149 Sum_probs=17.3
Q ss_pred CceecccchhhcCCchhHHHhhhhhcCCCccchhhhhh
Q psy553 58 KPYKCTYCERRFKQLSHVQQHTRLHTVEGVNSCLQILS 95 (129)
Q Consensus 58 ~~~~C~~c~~~f~~~~~l~~H~~~h~~~~~y~C~~C~~ 95 (129)
..|.|+.||......- .+.-....+|.|+.||.
T Consensus 26 v~F~CPnCGe~~I~Rc-----~~CRk~g~~Y~Cp~CGF 58 (61)
T COG2888 26 VKFPCPNCGEVEIYRC-----AKCRKLGNPYRCPKCGF 58 (61)
T ss_pred eEeeCCCCCceeeehh-----hhHHHcCCceECCCcCc
Confidence 3467777774333221 12222345778877764
No 69
>KOG4167|consensus
Probab=76.01 E-value=1.6 Score=34.90 Aligned_cols=32 Identities=22% Similarity=0.446 Sum_probs=24.9
Q ss_pred CCCCCCCCcccccchhhccChHHHHHHHhhcC
Q psy553 24 GGLEANKPHQCQQCLKSFSSNHQLVQHIRVHT 55 (129)
Q Consensus 24 ~~~~~~~~~~C~~C~~~f~~~~~l~~h~~~h~ 55 (129)
+..+....|.|.+|++.|.....+..||..|.
T Consensus 785 ~~~~~~giFpCreC~kvF~KiKSrNAHMK~Hr 816 (907)
T KOG4167|consen 785 GETDPTGIFPCRECGKVFFKIKSRNAHMKTHR 816 (907)
T ss_pred CCCCCCceeehHHHHHHHHHHhhhhHHHHHHH
Confidence 33444567899999999888888888888875
No 70
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=75.31 E-value=0.76 Score=33.08 Aligned_cols=24 Identities=29% Similarity=0.578 Sum_probs=16.6
Q ss_pred CCCCcccccchhhccChHHHHHHH
Q psy553 28 ANKPHQCQQCLKSFSSNHQLVQHI 51 (129)
Q Consensus 28 ~~~~~~C~~C~~~f~~~~~l~~h~ 51 (129)
+.+||+|.+|++.++....|..|+
T Consensus 395 ~~KPYrCevC~KRYKNlNGLKYHr 418 (423)
T COG5189 395 KDKPYRCEVCDKRYKNLNGLKYHR 418 (423)
T ss_pred cCCceeccccchhhccCccceecc
Confidence 357788888887777666665553
No 71
>KOG4173|consensus
Probab=74.58 E-value=3.2 Score=28.09 Aligned_cols=73 Identities=21% Similarity=0.404 Sum_probs=49.5
Q ss_pred CCccccc--chhhccChHHHHHHHhhcCCCCceecccchhhcCCchhHHHhhhhhc----------CCCccchhh--hhh
Q psy553 30 KPHQCQQ--CLKSFSSNHQLVQHIRVHTGEKPYKCTYCERRFKQLSHVQQHTRLHT----------VEGVNSCLQ--ILS 95 (129)
Q Consensus 30 ~~~~C~~--C~~~f~~~~~l~~h~~~h~~~~~~~C~~c~~~f~~~~~l~~H~~~h~----------~~~~y~C~~--C~~ 95 (129)
..+.|+. |.+.|......-.|-..-.+ ..|..|.+.|.....|..|+...+ |..-|.|-+ |+.
T Consensus 78 ~~~~cqvagc~~~~d~lD~~E~hY~~~h~---~sCs~C~r~~Pt~hLLd~HI~E~HDs~Fqa~veRG~dMy~ClvEgCt~ 154 (253)
T KOG4173|consen 78 PAFACQVAGCCQVFDALDDYEHHYHTLHG---NSCSFCKRAFPTGHLLDAHILEWHDSLFQALVERGQDMYQCLVEGCTE 154 (253)
T ss_pred ccccccccchHHHHhhhhhHHHhhhhccc---chhHHHHHhCCchhhhhHHHHHHHHHHHHHHHHcCccHHHHHHHhhhh
Confidence 4467877 66777766655555433222 379999999999999988877442 344588865 998
Q ss_pred hhhccc-cCcC
Q psy553 96 LWIQLD-LKDE 105 (129)
Q Consensus 96 ~f~~~~-l~~h 105 (129)
-|.+.. -..|
T Consensus 155 KFkT~r~RkdH 165 (253)
T KOG4173|consen 155 KFKTSRDRKDH 165 (253)
T ss_pred hhhhhhhhhhH
Confidence 888763 4444
No 72
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=74.19 E-value=1.3 Score=22.25 Aligned_cols=11 Identities=18% Similarity=0.462 Sum_probs=6.2
Q ss_pred cccccchhhcc
Q psy553 32 HQCQQCLKSFS 42 (129)
Q Consensus 32 ~~C~~C~~~f~ 42 (129)
|.|..||..+.
T Consensus 3 Y~C~~Cg~~~~ 13 (44)
T smart00659 3 YICGECGRENE 13 (44)
T ss_pred EECCCCCCEee
Confidence 55666665544
No 73
>KOG1146|consensus
Probab=72.35 E-value=0.68 Score=39.15 Aligned_cols=53 Identities=21% Similarity=0.265 Sum_probs=31.1
Q ss_pred ceecccchhhcCCchhHHHhhhh-----------------hcCCCccchhhhhhhhhccc-cCcCCCCCCee
Q psy553 59 PYKCTYCERRFKQLSHVQQHTRL-----------------HTVEGVNSCLQILSLWIQLD-LKDEPRNRNYV 112 (129)
Q Consensus 59 ~~~C~~c~~~f~~~~~l~~H~~~-----------------h~~~~~y~C~~C~~~f~~~~-l~~h~~~~~~~ 112 (129)
+|.|..|...|.....+..|.+. +....+| |..|...|.... |..||+...|.
T Consensus 1284 ~~~~~~~~~~~~~~~~l~~~~~k~~~~~~~~~~~~~~~l~~~d~~~~-c~~c~~~~~~~~alqihm~~~~~~ 1354 (1406)
T KOG1146|consen 1284 RYLCRQCKMAFDGEAPLTAHQRKFCFAGRGSGGSMPPPLRVPDCTYH-CLACEVLLSGREALQIHMRSSAHR 1354 (1406)
T ss_pred hHHHHHHHhhhcchhHHHHHHHHHHhccCccccCCCCcccCcccccc-chHHHhhcchhHHHHHHHHHhhhc
Confidence 45565566556555555555431 2233446 777777777775 77776655444
No 74
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=71.58 E-value=1.7 Score=28.71 Aligned_cols=32 Identities=19% Similarity=0.206 Sum_probs=18.9
Q ss_pred CceecccchhhcCCchhHHHhhhhhcCCCccchhhhhhhhh
Q psy553 58 KPYKCTYCERRFKQLSHVQQHTRLHTVEGVNSCLQILSLWI 98 (129)
Q Consensus 58 ~~~~C~~c~~~f~~~~~l~~H~~~h~~~~~y~C~~C~~~f~ 98 (129)
.-|.|+.|+..|.....+. ..|.|+.||....
T Consensus 116 ~~Y~Cp~C~~rytf~eA~~---------~~F~Cp~Cg~~L~ 147 (178)
T PRK06266 116 MFFFCPNCHIRFTFDEAME---------YGFRCPQCGEMLE 147 (178)
T ss_pred CEEECCCCCcEEeHHHHhh---------cCCcCCCCCCCCe
Confidence 4467777776666554431 2477777775443
No 75
>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=70.77 E-value=1.4 Score=21.03 Aligned_cols=11 Identities=45% Similarity=0.975 Sum_probs=5.4
Q ss_pred ccccchhhccC
Q psy553 33 QCQQCLKSFSS 43 (129)
Q Consensus 33 ~C~~C~~~f~~ 43 (129)
.|+.|+..|..
T Consensus 4 ~CP~C~~~~~v 14 (38)
T TIGR02098 4 QCPNCKTSFRV 14 (38)
T ss_pred ECCCCCCEEEe
Confidence 45555554443
No 76
>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=69.89 E-value=3.4 Score=26.73 Aligned_cols=35 Identities=11% Similarity=0.069 Sum_probs=22.6
Q ss_pred CCCceecccchhhcCCchhHHHhhhhhcCCCccchhhhhhhhhc
Q psy553 56 GEKPYKCTYCERRFKQLSHVQQHTRLHTVEGVNSCLQILSLWIQ 99 (129)
Q Consensus 56 ~~~~~~C~~c~~~f~~~~~l~~H~~~h~~~~~y~C~~C~~~f~~ 99 (129)
...-|.|+.|+..|.....+. .-|.|+.||.....
T Consensus 106 ~~~~Y~Cp~c~~r~tf~eA~~---------~~F~Cp~Cg~~L~~ 140 (158)
T TIGR00373 106 NNMFFICPNMCVRFTFNEAME---------LNFTCPRCGAMLDY 140 (158)
T ss_pred CCCeEECCCCCcEeeHHHHHH---------cCCcCCCCCCEeee
Confidence 344577888887776666553 24888888865443
No 77
>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=69.75 E-value=0.95 Score=23.25 Aligned_cols=11 Identities=55% Similarity=1.407 Sum_probs=5.3
Q ss_pred eecccchhhcC
Q psy553 60 YKCTYCERRFK 70 (129)
Q Consensus 60 ~~C~~c~~~f~ 70 (129)
|+|..|+..|.
T Consensus 6 y~C~~Cg~~fe 16 (52)
T TIGR02605 6 YRCTACGHRFE 16 (52)
T ss_pred EEeCCCCCEeE
Confidence 44555554444
No 78
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=67.95 E-value=3.3 Score=25.24 Aligned_cols=72 Identities=17% Similarity=0.190 Sum_probs=37.8
Q ss_pred CCcccccchhhccChHHHHHHHhhcCC-------CCc-------eecccchhhcCCchhHHHhhhhhcCCCccchhhhhh
Q psy553 30 KPHQCQQCLKSFSSNHQLVQHIRVHTG-------EKP-------YKCTYCERRFKQLSHVQQHTRLHTVEGVNSCLQILS 95 (129)
Q Consensus 30 ~~~~C~~C~~~f~~~~~l~~h~~~h~~-------~~~-------~~C~~c~~~f~~~~~l~~H~~~h~~~~~y~C~~C~~ 95 (129)
-|-.|+.|+-.......|.+. .|.- +.+ -.|..|...|........- .......|.|..|..
T Consensus 14 LP~~CpiCgLtLVss~HLARS--yHHLfPl~~f~ev~~~~~~~~~~C~~C~~~f~~~~~~~~~--~~~~~~~y~C~~C~~ 89 (112)
T TIGR00622 14 LPVECPICGLTLILSTHLARS--YHHLFPLKAFQEIPLEEYNGSRFCFGCQGPFPKPPVSPFD--ELKDSHRYVCAVCKN 89 (112)
T ss_pred CCCcCCcCCCEEeccchHHHh--hhccCCCcccccccccccCCCCcccCcCCCCCCccccccc--ccccccceeCCCCCC
Confidence 466788888766666666532 1110 011 1266676666543211110 022344688888888
Q ss_pred hhhcc-ccCcC
Q psy553 96 LWIQL-DLKDE 105 (129)
Q Consensus 96 ~f~~~-~l~~h 105 (129)
.|=.. |...|
T Consensus 90 ~FC~dCD~fiH 100 (112)
T TIGR00622 90 VFCVDCDVFVH 100 (112)
T ss_pred ccccccchhhh
Confidence 77655 55554
No 79
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=67.52 E-value=6.8 Score=24.90 Aligned_cols=41 Identities=20% Similarity=0.358 Sum_probs=26.0
Q ss_pred CCCceecccchhhcCCchhHHHhhhhhcCCCccchhhhhhhhhcc
Q psy553 56 GEKPYKCTYCERRFKQLSHVQQHTRLHTVEGVNSCLQILSLWIQL 100 (129)
Q Consensus 56 ~~~~~~C~~c~~~f~~~~~l~~H~~~h~~~~~y~C~~C~~~f~~~ 100 (129)
+..-|.|+.|+..|.....+.. ...+..|.|+.||......
T Consensus 96 ~~~~Y~Cp~C~~~y~~~ea~~~----~d~~~~f~Cp~Cg~~l~~~ 136 (147)
T smart00531 96 NNAYYKCPNCQSKYTFLEANQL----LDMDGTFTCPRCGEELEED 136 (147)
T ss_pred CCcEEECcCCCCEeeHHHHHHh----cCCCCcEECCCCCCEEEEc
Confidence 4456889999988875443322 1113349999999766544
No 80
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=67.00 E-value=1.4 Score=35.39 Aligned_cols=48 Identities=19% Similarity=0.326 Sum_probs=25.2
Q ss_pred ccccchhhccChHHHHHHHhhcCCCCceecccchhhcCCchhHHHhhhhhcCCCccchhhhhhh
Q psy553 33 QCQQCLKSFSSNHQLVQHIRVHTGEKPYKCTYCERRFKQLSHVQQHTRLHTVEGVNSCLQILSL 96 (129)
Q Consensus 33 ~C~~C~~~f~~~~~l~~h~~~h~~~~~~~C~~c~~~f~~~~~l~~H~~~h~~~~~y~C~~C~~~ 96 (129)
.|..||..+..+.. ...+..|...+...|..|++ ....|..|+.||..
T Consensus 437 ~C~~Cg~v~~Cp~C-d~~lt~H~~~~~L~CH~Cg~---------------~~~~p~~Cp~Cgs~ 484 (730)
T COG1198 437 LCRDCGYIAECPNC-DSPLTLHKATGQLRCHYCGY---------------QEPIPQSCPECGSE 484 (730)
T ss_pred ecccCCCcccCCCC-CcceEEecCCCeeEeCCCCC---------------CCCCCCCCCCCCCC
Confidence 46666655443321 11233334445566666653 23557888888865
No 81
>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=64.99 E-value=2.7 Score=26.17 Aligned_cols=14 Identities=21% Similarity=0.505 Sum_probs=7.5
Q ss_pred CceecccchhhcCC
Q psy553 58 KPYKCTYCERRFKQ 71 (129)
Q Consensus 58 ~~~~C~~c~~~f~~ 71 (129)
.|..|+.||..|..
T Consensus 25 ~p~vcP~cg~~~~~ 38 (129)
T TIGR02300 25 RPAVSPYTGEQFPP 38 (129)
T ss_pred CCccCCCcCCccCc
Confidence 45556666655433
No 82
>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=63.71 E-value=1.6 Score=19.23 Aligned_cols=8 Identities=13% Similarity=0.110 Sum_probs=3.8
Q ss_pred hhhhhhhh
Q psy553 90 CLQILSLW 97 (129)
Q Consensus 90 C~~C~~~f 97 (129)
|+.||+.|
T Consensus 17 Cp~CG~~F 24 (26)
T PF10571_consen 17 CPHCGYDF 24 (26)
T ss_pred CCCCCCCC
Confidence 44444444
No 83
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=63.56 E-value=3 Score=22.30 Aligned_cols=33 Identities=9% Similarity=0.171 Sum_probs=17.4
Q ss_pred CceecccchhhcCCchhHHHhhhhhcCCCccchhhhhh
Q psy553 58 KPYKCTYCERRFKQLSHVQQHTRLHTVEGVNSCLQILS 95 (129)
Q Consensus 58 ~~~~C~~c~~~f~~~~~l~~H~~~h~~~~~y~C~~C~~ 95 (129)
..|.|+.||......- .+.-....+|.|+.||.
T Consensus 24 ~~F~CPnCG~~~I~RC-----~~CRk~~~~Y~CP~CGF 56 (59)
T PRK14890 24 VKFLCPNCGEVIIYRC-----EKCRKQSNPYTCPKCGF 56 (59)
T ss_pred CEeeCCCCCCeeEeec-----hhHHhcCCceECCCCCC
Confidence 3477777775422211 11222345788888874
No 84
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=62.73 E-value=1.3 Score=22.25 Aligned_cols=10 Identities=10% Similarity=-0.207 Sum_probs=4.7
Q ss_pred cchhhhhhhh
Q psy553 88 NSCLQILSLW 97 (129)
Q Consensus 88 y~C~~C~~~f 97 (129)
..|+.||..+
T Consensus 22 ~~Cp~CG~~~ 31 (46)
T PRK00398 22 VRCPYCGYRI 31 (46)
T ss_pred eECCCCCCeE
Confidence 4455555433
No 85
>KOG2785|consensus
Probab=61.77 E-value=12 Score=27.74 Aligned_cols=27 Identities=26% Similarity=0.413 Sum_probs=21.8
Q ss_pred CCcccccchhhccChHHHHHHHhhcCC
Q psy553 30 KPHQCQQCLKSFSSNHQLVQHIRVHTG 56 (129)
Q Consensus 30 ~~~~C~~C~~~f~~~~~l~~h~~~h~~ 56 (129)
.|-.|-.|+..+.....-..||..+.+
T Consensus 165 ~Pt~CLfC~~~~k~~e~~~~HM~~~Hg 191 (390)
T KOG2785|consen 165 IPTDCLFCDKKSKSLEENLKHMFKEHG 191 (390)
T ss_pred CCcceeecCCCcccHHHHHHHHhhccC
Confidence 455688899988888888889988765
No 86
>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=60.69 E-value=2.2 Score=19.25 Aligned_cols=18 Identities=17% Similarity=0.124 Sum_probs=12.4
Q ss_pred cchhhhhhhhhccccCcC
Q psy553 88 NSCLQILSLWIQLDLKDE 105 (129)
Q Consensus 88 y~C~~C~~~f~~~~l~~h 105 (129)
|.|-.|++.|...+...|
T Consensus 1 ~sCiDC~~~F~~~~y~~H 18 (28)
T PF08790_consen 1 FSCIDCSKDFDGDSYKSH 18 (28)
T ss_dssp EEETTTTEEEEGGGTTT-
T ss_pred CeeecCCCCcCcCCcCCC
Confidence 467888888865566666
No 87
>PF14353 CpXC: CpXC protein
Probab=60.57 E-value=2.4 Score=26.21 Aligned_cols=27 Identities=7% Similarity=0.065 Sum_probs=15.9
Q ss_pred ccchhhhhhhhhccc-cCcCCCCCCeeE
Q psy553 87 VNSCLQILSLWIQLD-LKDEPRNRNYVV 113 (129)
Q Consensus 87 ~y~C~~C~~~f~~~~-l~~h~~~~~~~~ 113 (129)
.|.|+.||..|.-.- +.-|..++.+..
T Consensus 38 ~~~CP~Cg~~~~~~~p~lY~D~~~~~~i 65 (128)
T PF14353_consen 38 SFTCPSCGHKFRLEYPLLYHDPEKKFMI 65 (128)
T ss_pred EEECCCCCCceecCCCEEEEcCCCCEEE
Confidence 367777777776553 555544555544
No 88
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=60.35 E-value=1.5 Score=24.53 Aligned_cols=16 Identities=19% Similarity=0.370 Sum_probs=8.4
Q ss_pred CCccchh--hhhhhhhcc
Q psy553 85 EGVNSCL--QILSLWIQL 100 (129)
Q Consensus 85 ~~~y~C~--~C~~~f~~~ 100 (129)
++-+.|. .||.+|..-
T Consensus 25 ~~Y~qC~N~eCg~tF~t~ 42 (72)
T PRK09678 25 ERYHQCQNVNCSATFITY 42 (72)
T ss_pred eeeeecCCCCCCCEEEEE
Confidence 4445555 555555543
No 89
>PF15135 UPF0515: Uncharacterised protein UPF0515
Probab=59.17 E-value=5 Score=27.97 Aligned_cols=12 Identities=17% Similarity=0.639 Sum_probs=8.4
Q ss_pred CCCcccccchhh
Q psy553 29 NKPHQCQQCLKS 40 (129)
Q Consensus 29 ~~~~~C~~C~~~ 40 (129)
.+.|.|..|...
T Consensus 110 drqFaC~~Cd~~ 121 (278)
T PF15135_consen 110 DRQFACSSCDHM 121 (278)
T ss_pred ceeeeccccchH
Confidence 466888888654
No 90
>PHA00626 hypothetical protein
Probab=58.16 E-value=2.3 Score=22.51 Aligned_cols=16 Identities=6% Similarity=-0.288 Sum_probs=13.0
Q ss_pred CCccchhhhhhhhhcc
Q psy553 85 EGVNSCLQILSLWIQL 100 (129)
Q Consensus 85 ~~~y~C~~C~~~f~~~ 100 (129)
...|+|+.|++.|...
T Consensus 21 snrYkCkdCGY~ft~~ 36 (59)
T PHA00626 21 SDDYVCCDCGYNDSKD 36 (59)
T ss_pred CcceEcCCCCCeechh
Confidence 3469999999998765
No 91
>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=56.83 E-value=2.5 Score=18.31 Aligned_cols=8 Identities=13% Similarity=-0.002 Sum_probs=4.3
Q ss_pred ccchhhhh
Q psy553 87 VNSCLQIL 94 (129)
Q Consensus 87 ~y~C~~C~ 94 (129)
+|.|+.||
T Consensus 16 ~f~CPnCG 23 (24)
T PF07754_consen 16 PFPCPNCG 23 (24)
T ss_pred eEeCCCCC
Confidence 45555554
No 92
>KOG0978|consensus
Probab=56.07 E-value=3.1 Score=33.21 Aligned_cols=18 Identities=11% Similarity=0.058 Sum_probs=14.6
Q ss_pred CCCccchhhhhhhhhccc
Q psy553 84 VEGVNSCLQILSLWIQLD 101 (129)
Q Consensus 84 ~~~~y~C~~C~~~f~~~~ 101 (129)
..|.-+||.|+..|...|
T Consensus 675 etRqRKCP~Cn~aFganD 692 (698)
T KOG0978|consen 675 ETRQRKCPKCNAAFGAND 692 (698)
T ss_pred HHhcCCCCCCCCCCCccc
Confidence 445568999999999887
No 93
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=55.52 E-value=0.84 Score=22.35 Aligned_cols=10 Identities=20% Similarity=0.521 Sum_probs=6.3
Q ss_pred cchhhhhhhh
Q psy553 88 NSCLQILSLW 97 (129)
Q Consensus 88 y~C~~C~~~f 97 (129)
|.|..|++.|
T Consensus 29 y~C~~C~~~w 38 (40)
T smart00440 29 YVCTKCGHRW 38 (40)
T ss_pred EEeCCCCCEe
Confidence 6666666554
No 94
>KOG2482|consensus
Probab=54.87 E-value=1.4 Score=32.01 Aligned_cols=26 Identities=19% Similarity=0.284 Sum_probs=23.3
Q ss_pred cchhhhhhhhhccc-cCcCCCCCCeeE
Q psy553 88 NSCLQILSLWIQLD-LKDEPRNRNYVV 113 (129)
Q Consensus 88 y~C~~C~~~f~~~~-l~~h~~~~~~~~ 113 (129)
+.|-.|.+.|..+. |..||+.++|.+
T Consensus 196 ~~CLyCekifrdkntLkeHMrkK~Hrr 222 (423)
T KOG2482|consen 196 LRCLYCEKIFRDKNTLKEHMRKKRHRR 222 (423)
T ss_pred heeeeeccccCCcHHHHHHHHhccCcc
Confidence 78999999999996 999999998874
No 95
>KOG4124|consensus
Probab=54.77 E-value=3.6 Score=30.14 Aligned_cols=69 Identities=19% Similarity=0.268 Sum_probs=38.1
Q ss_pred CCCCccccc--chhhccChHHHHHHHhhcCCCCceecccchhhcCCchhHHHhhhhhcCCCccchhhhhhhhhccc-cCc
Q psy553 28 ANKPHQCQQ--CLKSFSSNHQLVQHIRVHTGEKPYKCTYCERRFKQLSHVQQHTRLHTVEGVNSCLQILSLWIQLD-LKD 104 (129)
Q Consensus 28 ~~~~~~C~~--C~~~f~~~~~l~~h~~~h~~~~~~~C~~c~~~f~~~~~l~~H~~~h~~~~~y~C~~C~~~f~~~~-l~~ 104 (129)
..++|.|.+ |.+.++....+..|..... |...-.....-+.|+-.....|||.|++|.+.+.... |.-
T Consensus 346 ~~~~~~~~vp~~~~~~~n~ng~~~~~~~~h---------~s~i~~~s~~~~ph~~~~~~nk~~r~~i~~~~~k~~~~l~~ 416 (442)
T KOG4124|consen 346 VDKPYKCPVPNCDKAYKNQNGLKYHKLHGH---------CSPITTPTPAPIPHQGFVVENKPYRCEVCSKRYKNLNGLKY 416 (442)
T ss_pred ecCCCCCCCCcchhhcccCcceeeccccCc---------CCCCCCCCCCCCCcceeeeccCcccChhhhhhhccCCCCCc
Confidence 457777765 6666655444433322110 1111111223344555556689999999999998773 544
Q ss_pred C
Q psy553 105 E 105 (129)
Q Consensus 105 h 105 (129)
|
T Consensus 417 ~ 417 (442)
T KOG4124|consen 417 H 417 (442)
T ss_pred e
Confidence 3
No 96
>COG4896 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=54.64 E-value=10 Score=20.48 Aligned_cols=18 Identities=6% Similarity=-0.200 Sum_probs=10.4
Q ss_pred cCCCccchhhhhhhhhcc
Q psy553 83 TVEGVNSCLQILSLWIQL 100 (129)
Q Consensus 83 ~~~~~y~C~~C~~~f~~~ 100 (129)
-.-+.|.|+.|......+
T Consensus 27 ~PIrtymC~eC~~Rva~k 44 (68)
T COG4896 27 KPIRTYMCPECEHRVAIK 44 (68)
T ss_pred CCceeEechhhHhhhchh
Confidence 344557777776555554
No 97
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=54.21 E-value=4.3 Score=23.53 Aligned_cols=13 Identities=8% Similarity=0.148 Sum_probs=7.5
Q ss_pred ccchhhhhhhhhc
Q psy553 87 VNSCLQILSLWIQ 99 (129)
Q Consensus 87 ~y~C~~C~~~f~~ 99 (129)
-|.|+.|+..|+=
T Consensus 53 IW~C~kCg~~fAG 65 (89)
T COG1997 53 IWKCRKCGAKFAG 65 (89)
T ss_pred eEEcCCCCCeecc
Confidence 4666666665543
No 98
>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=54.01 E-value=8.1 Score=26.38 Aligned_cols=27 Identities=22% Similarity=0.372 Sum_probs=21.0
Q ss_pred CCCCcccccchhhccChHHHHHHHhhc
Q psy553 28 ANKPHQCQQCLKSFSSNHQLVQHIRVH 54 (129)
Q Consensus 28 ~~~~~~C~~C~~~f~~~~~l~~h~~~h 54 (129)
.+..|.|..|++.|+-.....+|+..-
T Consensus 74 ~~~K~~C~lc~KlFkg~eFV~KHI~nK 100 (214)
T PF04959_consen 74 DEDKWRCPLCGKLFKGPEFVRKHIFNK 100 (214)
T ss_dssp SSEEEEE-SSS-EESSHHHHHHHHHHH
T ss_pred cCCEECCCCCCcccCChHHHHHHHhhc
Confidence 345699999999999999999998753
No 99
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=54.01 E-value=4.2 Score=20.91 Aligned_cols=11 Identities=18% Similarity=0.658 Sum_probs=5.9
Q ss_pred Ccccccchhhc
Q psy553 31 PHQCQQCLKSF 41 (129)
Q Consensus 31 ~~~C~~C~~~f 41 (129)
.|.|..||+.+
T Consensus 6 ~Y~C~~Cg~~~ 16 (49)
T COG1996 6 EYKCARCGREV 16 (49)
T ss_pred EEEhhhcCCee
Confidence 35555555554
No 100
>COG1773 Rubredoxin [Energy production and conversion]
Probab=53.95 E-value=2.8 Score=22.09 Aligned_cols=15 Identities=7% Similarity=-0.159 Sum_probs=11.5
Q ss_pred Cccchhhhhhhhhcc
Q psy553 86 GVNSCLQILSLWIQL 100 (129)
Q Consensus 86 ~~y~C~~C~~~f~~~ 100 (129)
+.|+|.+||..|.=.
T Consensus 2 ~~~~C~~CG~vYd~e 16 (55)
T COG1773 2 KRWRCSVCGYVYDPE 16 (55)
T ss_pred CceEecCCceEeccc
Confidence 358899999888654
No 101
>KOG4173|consensus
Probab=53.91 E-value=7.5 Score=26.40 Aligned_cols=44 Identities=20% Similarity=0.343 Sum_probs=32.0
Q ss_pred ceeccc--chhhcCCchhHHHhhhhhcCCCccchhhhhhhhhccc-cCcC
Q psy553 59 PYKCTY--CERRFKQLSHVQQHTRLHTVEGVNSCLQILSLWIQLD-LKDE 105 (129)
Q Consensus 59 ~~~C~~--c~~~f~~~~~l~~H~~~h~~~~~y~C~~C~~~f~~~~-l~~h 105 (129)
.|.|.+ |...|.....+..|-.+.++ -.|.+|.+.|++.+ |-.|
T Consensus 79 ~~~cqvagc~~~~d~lD~~E~hY~~~h~---~sCs~C~r~~Pt~hLLd~H 125 (253)
T KOG4173|consen 79 AFACQVAGCCQVFDALDDYEHHYHTLHG---NSCSFCKRAFPTGHLLDAH 125 (253)
T ss_pred cccccccchHHHHhhhhhHHHhhhhccc---chhHHHHHhCCchhhhhHH
Confidence 366875 77888777766666555444 48999999999997 4445
No 102
>PF05290 Baculo_IE-1: Baculovirus immediate-early protein (IE-0); InterPro: IPR007954 This entry contains the Baculovirus immediate-early protein IE-0.
Probab=53.32 E-value=4.5 Score=25.44 Aligned_cols=13 Identities=8% Similarity=0.079 Sum_probs=9.6
Q ss_pred chhhhhhhhhccc
Q psy553 89 SCLQILSLWIQLD 101 (129)
Q Consensus 89 ~C~~C~~~f~~~~ 101 (129)
+|++|.-+|..+.
T Consensus 123 vCPvCkTSFKss~ 135 (140)
T PF05290_consen 123 VCPVCKTSFKSSS 135 (140)
T ss_pred CCCcccccccccc
Confidence 4888888887763
No 103
>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=52.85 E-value=2.7 Score=19.54 Aligned_cols=8 Identities=25% Similarity=0.924 Sum_probs=3.6
Q ss_pred eecccchh
Q psy553 60 YKCTYCER 67 (129)
Q Consensus 60 ~~C~~c~~ 67 (129)
.+|..||.
T Consensus 18 irC~~CG~ 25 (32)
T PF03604_consen 18 IRCPECGH 25 (32)
T ss_dssp SSBSSSS-
T ss_pred EECCcCCC
Confidence 45555554
No 104
>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=51.88 E-value=3 Score=19.98 Aligned_cols=14 Identities=14% Similarity=0.062 Sum_probs=11.3
Q ss_pred ccchhhhhhhhhcc
Q psy553 87 VNSCLQILSLWIQL 100 (129)
Q Consensus 87 ~y~C~~C~~~f~~~ 100 (129)
.|.|..|+..|...
T Consensus 5 ~y~C~~Cg~~fe~~ 18 (41)
T smart00834 5 EYRCEDCGHTFEVL 18 (41)
T ss_pred EEEcCCCCCEEEEE
Confidence 37899999988765
No 105
>KOG2231|consensus
Probab=51.85 E-value=5 Score=31.98 Aligned_cols=73 Identities=16% Similarity=0.354 Sum_probs=46.9
Q ss_pred ChHHHHHHHhhcCC-CCc----eecccchhhcCCchhHHHhhhhhcCCCccchhhhh------hhhhcc-ccCcCCCCCC
Q psy553 43 SNHQLVQHIRVHTG-EKP----YKCTYCERRFKQLSHVQQHTRLHTVEGVNSCLQIL------SLWIQL-DLKDEPRNRN 110 (129)
Q Consensus 43 ~~~~l~~h~~~h~~-~~~----~~C~~c~~~f~~~~~l~~H~~~h~~~~~y~C~~C~------~~f~~~-~l~~h~~~~~ 110 (129)
+...|..|+..... ++- -.|..|...|.....+..|++.. -|-|..|. ..|..- +|..|-++.+
T Consensus 161 t~~el~~h~~~gd~d~~s~rGhp~C~~C~~~fld~~el~rH~~~~----h~~chfC~~~~~~neyy~~~~dLe~HfR~~H 236 (669)
T KOG2231|consen 161 TRAELNLHLMFGDPDDESCRGHPLCKFCHERFLDDDELYRHLRFD----HEFCHFCDYKTGQNEYYNDYDDLEEHFRKGH 236 (669)
T ss_pred hHHHHHHHHhcCCCccccccCCccchhhhhhhccHHHHHHhhccc----eeheeecCcccccchhcccchHHHHHhhhcC
Confidence 34556666554322 211 35777888888888888888854 35677773 334444 4899999999
Q ss_pred eeEeecccc
Q psy553 111 YVVRFSWWD 119 (129)
Q Consensus 111 ~~~~~~~~~ 119 (129)
|.|.+..+.
T Consensus 237 flCE~~~C~ 245 (669)
T KOG2231|consen 237 FLCEEEFCR 245 (669)
T ss_pred ccccccccc
Confidence 998754443
No 106
>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=51.76 E-value=3.2 Score=19.01 Aligned_cols=9 Identities=11% Similarity=0.113 Sum_probs=4.2
Q ss_pred ccchhhhhh
Q psy553 87 VNSCLQILS 95 (129)
Q Consensus 87 ~y~C~~C~~ 95 (129)
-|.|+.|+.
T Consensus 19 ~~vCp~C~~ 27 (30)
T PF08274_consen 19 LLVCPECGH 27 (30)
T ss_dssp SEEETTTTE
T ss_pred EEeCCcccc
Confidence 344554443
No 107
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=49.88 E-value=12 Score=25.33 Aligned_cols=20 Identities=30% Similarity=0.607 Sum_probs=13.5
Q ss_pred CCCCCCCcccccchhhccCh
Q psy553 25 GLEANKPHQCQQCLKSFSSN 44 (129)
Q Consensus 25 ~~~~~~~~~C~~C~~~f~~~ 44 (129)
++.+.-||.|.+|.+.|..+
T Consensus 190 ~~~e~IPF~C~iCKkdy~sp 209 (259)
T COG5152 190 GPGEKIPFLCGICKKDYESP 209 (259)
T ss_pred CCCCCCceeehhchhhccch
Confidence 34456688888888776543
No 108
>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=49.70 E-value=11 Score=23.75 Aligned_cols=25 Identities=28% Similarity=0.542 Sum_probs=13.1
Q ss_pred eecccchhhcCCchhHHHhhhhhcCCCc
Q psy553 60 YKCTYCERRFKQLSHVQQHTRLHTVEGV 87 (129)
Q Consensus 60 ~~C~~c~~~f~~~~~l~~H~~~h~~~~~ 87 (129)
..|-+||+.|.. |.+|+..|.|..|
T Consensus 73 i~clecGk~~k~---LkrHL~~~~gltp 97 (132)
T PF05443_consen 73 IICLECGKKFKT---LKRHLRTHHGLTP 97 (132)
T ss_dssp EE-TBT--EESB---HHHHHHHTT-S-H
T ss_pred eEEccCCcccch---HHHHHHHccCCCH
Confidence 467777776644 4777777766555
No 109
>KOG3408|consensus
Probab=48.97 E-value=13 Score=23.04 Aligned_cols=24 Identities=21% Similarity=0.510 Sum_probs=16.9
Q ss_pred CceecccchhhcCCchhHHHhhhh
Q psy553 58 KPYKCTYCERRFKQLSHVQQHTRL 81 (129)
Q Consensus 58 ~~~~C~~c~~~f~~~~~l~~H~~~ 81 (129)
..|-|..|.+-|.....|..|.++
T Consensus 56 GqfyCi~CaRyFi~~~~l~~H~kt 79 (129)
T KOG3408|consen 56 GQFYCIECARYFIDAKALKTHFKT 79 (129)
T ss_pred ceeehhhhhhhhcchHHHHHHHhc
Confidence 446777777777777777777664
No 110
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=48.32 E-value=4.6 Score=19.57 Aligned_cols=15 Identities=13% Similarity=0.062 Sum_probs=12.7
Q ss_pred ccchhhhhhhhhccc
Q psy553 87 VNSCLQILSLWIQLD 101 (129)
Q Consensus 87 ~y~C~~C~~~f~~~~ 101 (129)
|+.|+.|++.|=..+
T Consensus 12 ~f~C~~C~~~FC~~H 26 (39)
T smart00154 12 GFKCRHCGNLFCGEH 26 (39)
T ss_pred CeECCccCCcccccc
Confidence 789999999987764
No 111
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=47.98 E-value=5.9 Score=24.91 Aligned_cols=13 Identities=23% Similarity=0.636 Sum_probs=8.3
Q ss_pred ceecccchhhcCC
Q psy553 59 PYKCTYCERRFKQ 71 (129)
Q Consensus 59 ~~~C~~c~~~f~~ 71 (129)
.+.|..|+..|..
T Consensus 70 ~~~C~~CG~~~~~ 82 (135)
T PRK03824 70 VLKCRNCGNEWSL 82 (135)
T ss_pred EEECCCCCCEEec
Confidence 3667777766554
No 112
>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=47.95 E-value=3.3 Score=20.39 Aligned_cols=14 Identities=14% Similarity=0.112 Sum_probs=11.8
Q ss_pred cchhhhhhhhhccc
Q psy553 88 NSCLQILSLWIQLD 101 (129)
Q Consensus 88 y~C~~C~~~f~~~~ 101 (129)
|.|..||..|....
T Consensus 6 y~C~~Cg~~fe~~~ 19 (42)
T PF09723_consen 6 YRCEECGHEFEVLQ 19 (42)
T ss_pred EEeCCCCCEEEEEE
Confidence 88999999988763
No 113
>smart00614 ZnF_BED BED zinc finger. DNA-binding domain in chromatin-boundary-element-binding proteins and transposases
Probab=46.02 E-value=16 Score=18.48 Aligned_cols=9 Identities=33% Similarity=0.932 Sum_probs=4.3
Q ss_pred ccccchhhc
Q psy553 33 QCQQCLKSF 41 (129)
Q Consensus 33 ~C~~C~~~f 41 (129)
.|..|++.+
T Consensus 20 ~C~~C~~~l 28 (50)
T smart00614 20 KCKYCGKKL 28 (50)
T ss_pred EecCCCCEe
Confidence 355555443
No 114
>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=45.75 E-value=15 Score=15.99 Aligned_cols=9 Identities=33% Similarity=0.918 Sum_probs=4.5
Q ss_pred ecccchhhc
Q psy553 61 KCTYCERRF 69 (129)
Q Consensus 61 ~C~~c~~~f 69 (129)
.|++|.+.+
T Consensus 3 ~CPiC~~~v 11 (26)
T smart00734 3 QCPVCFREV 11 (26)
T ss_pred cCCCCcCcc
Confidence 355555544
No 115
>KOG4167|consensus
Probab=45.59 E-value=5.7 Score=32.00 Aligned_cols=25 Identities=20% Similarity=0.546 Sum_probs=18.9
Q ss_pred ceecccchhhcCCchhHHHhhhhhc
Q psy553 59 PYKCTYCERRFKQLSHVQQHTRLHT 83 (129)
Q Consensus 59 ~~~C~~c~~~f~~~~~l~~H~~~h~ 83 (129)
.|.|.+|++.|.-..++..||++|.
T Consensus 792 iFpCreC~kvF~KiKSrNAHMK~Hr 816 (907)
T KOG4167|consen 792 IFPCRECGKVFFKIKSRNAHMKTHR 816 (907)
T ss_pred eeehHHHHHHHHHHhhhhHHHHHHH
Confidence 5778888888877777777777773
No 116
>PF13451 zf-trcl: Probable zinc-binding domain
Probab=45.17 E-value=4.8 Score=20.70 Aligned_cols=16 Identities=6% Similarity=0.127 Sum_probs=12.2
Q ss_pred CCccchhhhhhhhhcc
Q psy553 85 EGVNSCLQILSLWIQL 100 (129)
Q Consensus 85 ~~~y~C~~C~~~f~~~ 100 (129)
++++.|..||..|+.-
T Consensus 2 Dk~l~C~dCg~~FvfT 17 (49)
T PF13451_consen 2 DKTLTCKDCGAEFVFT 17 (49)
T ss_pred CeeEEcccCCCeEEEe
Confidence 4567899999888764
No 117
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=45.09 E-value=10 Score=22.21 Aligned_cols=32 Identities=25% Similarity=0.665 Sum_probs=19.2
Q ss_pred CceecccchhhcCCchhHHHhhhhhcCCCccchhhhhhhhhc
Q psy553 58 KPYKCTYCERRFKQLSHVQQHTRLHTVEGVNSCLQILSLWIQ 99 (129)
Q Consensus 58 ~~~~C~~c~~~f~~~~~l~~H~~~h~~~~~y~C~~C~~~f~~ 99 (129)
+|-.|..||..|.... -.+|-.|+.|-.-++-
T Consensus 57 ~Pa~CkkCGfef~~~~----------ik~pSRCP~CKSE~Ie 88 (97)
T COG3357 57 RPARCKKCGFEFRDDK----------IKKPSRCPKCKSEWIE 88 (97)
T ss_pred cChhhcccCccccccc----------cCCcccCCcchhhccc
Confidence 4667777877765521 1345667777655544
No 118
>COG5188 PRP9 Splicing factor 3a, subunit 3 [RNA processing and modification]
Probab=43.06 E-value=5.7 Score=29.19 Aligned_cols=32 Identities=13% Similarity=0.119 Sum_probs=25.4
Q ss_pred hhcCCCccchhhhh-hhhhccc-cCcCCCCCCee
Q psy553 81 LHTVEGVNSCLQIL-SLWIQLD-LKDEPRNRNYV 112 (129)
Q Consensus 81 ~h~~~~~y~C~~C~-~~f~~~~-l~~h~~~~~~~ 112 (129)
.|.-.+.|.|.+|| +++.-++ .-+|..+.+|.
T Consensus 368 lhgLd~ef~CEICgNyvy~GR~~FdrHF~E~rHi 401 (470)
T COG5188 368 LHGLDIEFECEICGNYVYYGRDRFDRHFEEDRHI 401 (470)
T ss_pred hcCCCcceeeeecccccccchHHHHhhhhhhhhh
Confidence 45556779999999 8887776 88888777776
No 119
>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=42.51 E-value=5.3 Score=19.79 Aligned_cols=13 Identities=8% Similarity=-0.087 Sum_probs=10.4
Q ss_pred chhhhhhhhhccc
Q psy553 89 SCLQILSLWIQLD 101 (129)
Q Consensus 89 ~C~~C~~~f~~~~ 101 (129)
.|.+|++.|.++.
T Consensus 10 ~C~~C~rpf~WRK 22 (42)
T PF10013_consen 10 ICPVCGRPFTWRK 22 (42)
T ss_pred cCcccCCcchHHH
Confidence 4888999998873
No 120
>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=42.12 E-value=20 Score=17.43 Aligned_cols=13 Identities=31% Similarity=0.641 Sum_probs=5.3
Q ss_pred CCcccccchhhcc
Q psy553 30 KPHQCQQCLKSFS 42 (129)
Q Consensus 30 ~~~~C~~C~~~f~ 42 (129)
....|..|++.+.
T Consensus 15 ~~a~C~~C~~~~~ 27 (45)
T PF02892_consen 15 KKAKCKYCGKVIK 27 (45)
T ss_dssp S-EEETTTTEE--
T ss_pred CeEEeCCCCeEEe
Confidence 3345555555443
No 121
>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=41.86 E-value=8.1 Score=18.39 Aligned_cols=8 Identities=13% Similarity=0.106 Sum_probs=3.5
Q ss_pred cchhhhhh
Q psy553 88 NSCLQILS 95 (129)
Q Consensus 88 y~C~~C~~ 95 (129)
-.|..||-
T Consensus 22 ~~Cd~cg~ 29 (36)
T PF05191_consen 22 GVCDNCGG 29 (36)
T ss_dssp TBCTTTTE
T ss_pred CccCCCCC
Confidence 34444443
No 122
>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=41.30 E-value=5.7 Score=19.59 Aligned_cols=16 Identities=6% Similarity=-0.141 Sum_probs=10.7
Q ss_pred Cccchhhhhhhhhccc
Q psy553 86 GVNSCLQILSLWIQLD 101 (129)
Q Consensus 86 ~~y~C~~C~~~f~~~~ 101 (129)
.|+.|+.|++.|=..+
T Consensus 12 ~~~~C~~C~~~FC~~H 27 (43)
T PF01428_consen 12 LPFKCKHCGKSFCLKH 27 (43)
T ss_dssp SHEE-TTTS-EE-TTT
T ss_pred CCeECCCCCcccCccc
Confidence 4789999999998775
No 123
>PF11931 DUF3449: Domain of unknown function (DUF3449); InterPro: IPR024598 This presumed domain is functionally uncharacterised. It has two conserved sequence motifs: PIP and CEICG and contains a zinc-finger of the C2H2-type.; PDB: 4DGW_A.
Probab=41.07 E-value=9 Score=25.80 Aligned_cols=32 Identities=9% Similarity=-0.033 Sum_probs=0.0
Q ss_pred hhcCCCccchhhhhhhhh-ccc-cCcCCCCCCee
Q psy553 81 LHTVEGVNSCLQILSLWI-QLD-LKDEPRNRNYV 112 (129)
Q Consensus 81 ~h~~~~~y~C~~C~~~f~-~~~-l~~h~~~~~~~ 112 (129)
.|.-.+.|.|.+||...= =+. ..+|..+.+|+
T Consensus 95 LhGL~~ey~CEICGN~~Y~GrkaFekHF~E~rH~ 128 (196)
T PF11931_consen 95 LHGLGVEYKCEICGNQSYKGRKAFEKHFQEWRHA 128 (196)
T ss_dssp ----------------------------------
T ss_pred HhCCCCeeeeEeCCCcceecHHHHHHhcChhHHH
Confidence 444456688888884332 223 67776666666
No 124
>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=40.88 E-value=6.7 Score=30.26 Aligned_cols=10 Identities=30% Similarity=0.155 Sum_probs=6.2
Q ss_pred Cccchhhhhh
Q psy553 86 GVNSCLQILS 95 (129)
Q Consensus 86 ~~y~C~~C~~ 95 (129)
.|..|+.|+.
T Consensus 252 ~~~~Cp~C~s 261 (505)
T TIGR00595 252 IPKTCPQCGS 261 (505)
T ss_pred CCCCCCCCCC
Confidence 3556777764
No 125
>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=40.07 E-value=0.68 Score=22.54 Aligned_cols=10 Identities=20% Similarity=0.488 Sum_probs=6.0
Q ss_pred cchhhhhhhh
Q psy553 88 NSCLQILSLW 97 (129)
Q Consensus 88 y~C~~C~~~f 97 (129)
|.|..|++.|
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 6666666544
No 126
>PRK14873 primosome assembly protein PriA; Provisional
Probab=39.84 E-value=5.9 Score=31.68 Aligned_cols=10 Identities=20% Similarity=-0.107 Sum_probs=6.8
Q ss_pred ccchhhhhhh
Q psy553 87 VNSCLQILSL 96 (129)
Q Consensus 87 ~y~C~~C~~~ 96 (129)
|+.|+.|+..
T Consensus 422 p~~Cp~Cgs~ 431 (665)
T PRK14873 422 DWRCPRCGSD 431 (665)
T ss_pred CccCCCCcCC
Confidence 5677777754
No 127
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=39.79 E-value=21 Score=25.95 Aligned_cols=10 Identities=20% Similarity=0.242 Sum_probs=4.5
Q ss_pred cchhhhhhhh
Q psy553 88 NSCLQILSLW 97 (129)
Q Consensus 88 y~C~~C~~~f 97 (129)
|.|+.|-..|
T Consensus 389 Y~Ce~CK~~F 398 (421)
T COG5151 389 YQCELCKSTF 398 (421)
T ss_pred eechhhhhhh
Confidence 4444444433
No 128
>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=39.45 E-value=6.3 Score=20.31 Aligned_cols=13 Identities=8% Similarity=0.015 Sum_probs=10.3
Q ss_pred cchhhhhhhhhcc
Q psy553 88 NSCLQILSLWIQL 100 (129)
Q Consensus 88 y~C~~C~~~f~~~ 100 (129)
|.|..|++.|.-.
T Consensus 2 y~C~~CgyiYd~~ 14 (50)
T cd00730 2 YECRICGYIYDPA 14 (50)
T ss_pred cCCCCCCeEECCC
Confidence 7899999888743
No 129
>KOG2593|consensus
Probab=39.15 E-value=20 Score=27.10 Aligned_cols=32 Identities=9% Similarity=0.117 Sum_probs=16.8
Q ss_pred Cccchhhhhhhhhccc-cCc-CCCCCCeeEeecc
Q psy553 86 GVNSCLQILSLWIQLD-LKD-EPRNRNYVVRFSW 117 (129)
Q Consensus 86 ~~y~C~~C~~~f~~~~-l~~-h~~~~~~~~~~~~ 117 (129)
.-|.|+.|.+.|...+ +.. -+..-.|.|.++.
T Consensus 127 ~~Y~Cp~C~kkyt~Lea~~L~~~~~~~F~C~~C~ 160 (436)
T KOG2593|consen 127 AGYVCPNCQKKYTSLEALQLLDNETGEFHCENCG 160 (436)
T ss_pred ccccCCccccchhhhHHHHhhcccCceEEEecCC
Confidence 4466666666666664 111 2334555565554
No 130
>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=39.02 E-value=11 Score=22.93 Aligned_cols=25 Identities=12% Similarity=0.384 Sum_probs=14.5
Q ss_pred eecccchhhcCCchhHHHhhhhhcCCCccchhhhhhh
Q psy553 60 YKCTYCERRFKQLSHVQQHTRLHTVEGVNSCLQILSL 96 (129)
Q Consensus 60 ~~C~~c~~~f~~~~~l~~H~~~h~~~~~y~C~~C~~~ 96 (129)
+.|..|+..|..... .+.|+.|+..
T Consensus 71 ~~C~~Cg~~~~~~~~------------~~~CP~Cgs~ 95 (115)
T TIGR00100 71 CECEDCSEEVSPEID------------LYRCPKCHGI 95 (115)
T ss_pred EEcccCCCEEecCCc------------CccCcCCcCC
Confidence 567777765544321 3567777743
No 131
>KOG2807|consensus
Probab=38.92 E-value=22 Score=26.02 Aligned_cols=20 Identities=20% Similarity=0.569 Sum_probs=12.9
Q ss_pred CceecccchhhcCCchhHHH
Q psy553 58 KPYKCTYCERRFKQLSHVQQ 77 (129)
Q Consensus 58 ~~~~C~~c~~~f~~~~~l~~ 77 (129)
-|..|++|+-+.....+|.+
T Consensus 289 LP~eCpiC~ltLVss~hLAR 308 (378)
T KOG2807|consen 289 LPIECPICSLTLVSSPHLAR 308 (378)
T ss_pred CCccCCccceeEecchHHHH
Confidence 36677777776666666644
No 132
>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=38.64 E-value=5.1 Score=23.78 Aligned_cols=27 Identities=15% Similarity=0.083 Sum_probs=19.6
Q ss_pred hhHHHhhhhhcCCCccchhhhhhhhhcc
Q psy553 73 SHVQQHTRLHTVEGVNSCLQILSLWIQL 100 (129)
Q Consensus 73 ~~l~~H~~~h~~~~~y~C~~C~~~f~~~ 100 (129)
++...++..+-+ +|+.|..||..|.-.
T Consensus 66 ~h~v~W~~l~~g-~~~rC~eCG~~fkL~ 92 (97)
T cd00924 66 SHDVIWMWLEKG-KPKRCPECGHVFKLV 92 (97)
T ss_pred CceEEEEEEeCC-CceeCCCCCcEEEEE
Confidence 344455666666 699999999998765
No 133
>PF00301 Rubredoxin: Rubredoxin; InterPro: IPR004039 Rubredoxin is a low molecular weight iron-containing bacterial protein involved in electron transfer [, ], sometimes replacing ferredoxin as an electron carrier []. The 3-D structures of a number of rubredoxins have been solved [, ]. The fold belongs to the alpha+beta class, with 2 alpha-helices and 2-3 beta-strands. Its active site contains an iron ion which is co-ordinated by the sulphurs of four conserved cysteine residues forming an almost regular tetrahedron. The conserved cysteines reside on two loops, which are the most conserved regions of the protein. In addition, a ring of acidic residues in the proximity of the [Fe(Cys)4] centre is also well-conserved []. ; GO: 0009055 electron carrier activity, 0046872 metal ion binding; PDB: 2RDV_C 1RDV_A 1S24_A 1T9O_B 1B2J_A 1SMW_A 2PVE_B 1BFY_A 1T9P_C 1C09_C ....
Probab=38.46 E-value=6.4 Score=20.03 Aligned_cols=13 Identities=8% Similarity=-0.043 Sum_probs=9.7
Q ss_pred cchhhhhhhhhcc
Q psy553 88 NSCLQILSLWIQL 100 (129)
Q Consensus 88 y~C~~C~~~f~~~ 100 (129)
|.|.+|+..|.-.
T Consensus 2 y~C~~CgyvYd~~ 14 (47)
T PF00301_consen 2 YQCPVCGYVYDPE 14 (47)
T ss_dssp EEETTTSBEEETT
T ss_pred cCCCCCCEEEcCC
Confidence 7788888777554
No 134
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=38.42 E-value=13 Score=27.97 Aligned_cols=15 Identities=7% Similarity=-0.252 Sum_probs=10.5
Q ss_pred ccchhhhhhhhhccc
Q psy553 87 VNSCLQILSLWIQLD 101 (129)
Q Consensus 87 ~y~C~~C~~~f~~~~ 101 (129)
-|+|+.|+..+....
T Consensus 367 g~rC~kCg~~~~~~~ 381 (421)
T COG1571 367 GFRCKKCGTRARETL 381 (421)
T ss_pred CcccccccccCCccc
Confidence 677777777776653
No 135
>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=37.38 E-value=18 Score=18.65 Aligned_cols=11 Identities=9% Similarity=-0.091 Sum_probs=4.5
Q ss_pred chhhhhhhhhc
Q psy553 89 SCLQILSLWIQ 99 (129)
Q Consensus 89 ~C~~C~~~f~~ 99 (129)
.|++|++.|..
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 67777766654
No 136
>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=37.26 E-value=12 Score=20.17 Aligned_cols=29 Identities=28% Similarity=0.469 Sum_probs=11.2
Q ss_pred cccccchhhccChHHHHHHHhhcCCCCceecccchhhcCCc
Q psy553 32 HQCQQCLKSFSSNHQLVQHIRVHTGEKPYKCTYCERRFKQL 72 (129)
Q Consensus 32 ~~C~~C~~~f~~~~~l~~h~~~h~~~~~~~C~~c~~~f~~~ 72 (129)
-.|..|++.|.. ..+.+.|..||..|-..
T Consensus 10 ~~C~~C~~~F~~------------~~rrhhCr~CG~~vC~~ 38 (69)
T PF01363_consen 10 SNCMICGKKFSL------------FRRRHHCRNCGRVVCSS 38 (69)
T ss_dssp SB-TTT--B-BS------------SS-EEE-TTT--EEECC
T ss_pred CcCcCcCCcCCC------------ceeeEccCCCCCEECCc
Confidence 467777777742 12345666666655533
No 137
>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=36.92 E-value=13 Score=17.48 Aligned_cols=17 Identities=12% Similarity=0.173 Sum_probs=9.6
Q ss_pred chhhhhhhhhccccCcC
Q psy553 89 SCLQILSLWIQLDLKDE 105 (129)
Q Consensus 89 ~C~~C~~~f~~~~l~~h 105 (129)
.|..|++.|..+-|..+
T Consensus 5 ~C~eC~~~f~dSyL~~~ 21 (34)
T PF01286_consen 5 KCDECGKPFMDSYLLNN 21 (34)
T ss_dssp E-TTT--EES-SSCCCC
T ss_pred hHhHhCCHHHHHHHHHh
Confidence 58889998888866555
No 138
>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=36.63 E-value=10 Score=20.49 Aligned_cols=11 Identities=18% Similarity=0.733 Sum_probs=5.4
Q ss_pred Cceecccchhh
Q psy553 58 KPYKCTYCERR 68 (129)
Q Consensus 58 ~~~~C~~c~~~ 68 (129)
+.|.|+.|+..
T Consensus 45 r~~~C~~Cg~~ 55 (69)
T PF07282_consen 45 RVFTCPNCGFE 55 (69)
T ss_pred ceEEcCCCCCE
Confidence 34555555543
No 139
>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=36.49 E-value=26 Score=20.89 Aligned_cols=20 Identities=15% Similarity=0.217 Sum_probs=11.1
Q ss_pred ccchhhcCCchhHHHhhhhh
Q psy553 63 TYCERRFKQLSHVQQHTRLH 82 (129)
Q Consensus 63 ~~c~~~f~~~~~l~~H~~~h 82 (129)
..|+..+.....+.+|.+..
T Consensus 88 ~~C~y~~~~~~~m~~H~~~~ 107 (109)
T PF12013_consen 88 PHCGYITRSKKTMRKHWRKE 107 (109)
T ss_pred CCCCcEeccHHHHHHHHHHh
Confidence 55555555555555555543
No 140
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=36.34 E-value=14 Score=22.48 Aligned_cols=24 Identities=13% Similarity=0.166 Sum_probs=13.7
Q ss_pred eecccchhhcCCchhHHHhhhhhcCCCccchhhhhh
Q psy553 60 YKCTYCERRFKQLSHVQQHTRLHTVEGVNSCLQILS 95 (129)
Q Consensus 60 ~~C~~c~~~f~~~~~l~~H~~~h~~~~~y~C~~C~~ 95 (129)
+.|..|+..|.... ..+.|+.||.
T Consensus 71 ~~C~~Cg~~~~~~~------------~~~~CP~Cgs 94 (113)
T PRK12380 71 AWCWDCSQVVEIHQ------------HDAQCPHCHG 94 (113)
T ss_pred EEcccCCCEEecCC------------cCccCcCCCC
Confidence 56777775543321 2355777773
No 141
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=36.17 E-value=8.9 Score=22.43 Aligned_cols=13 Identities=8% Similarity=-0.025 Sum_probs=7.6
Q ss_pred ccchhhhhhhhhc
Q psy553 87 VNSCLQILSLWIQ 99 (129)
Q Consensus 87 ~y~C~~C~~~f~~ 99 (129)
.|.|..|++.|+=
T Consensus 54 IW~C~~C~~~~AG 66 (90)
T PTZ00255 54 IWRCKGCKKTVAG 66 (90)
T ss_pred EEEcCCCCCEEeC
Confidence 4666666665543
No 142
>KOG0801|consensus
Probab=35.64 E-value=7 Score=25.49 Aligned_cols=18 Identities=11% Similarity=-0.056 Sum_probs=12.9
Q ss_pred cchhhhhhhhhccccCcC
Q psy553 88 NSCLQILSLWIQLDLKDE 105 (129)
Q Consensus 88 y~C~~C~~~f~~~~l~~h 105 (129)
++|++|.|+....+..-|
T Consensus 139 ~KCPvC~K~V~sDd~e~H 156 (205)
T KOG0801|consen 139 MKCPVCHKVVPSDDAEIH 156 (205)
T ss_pred ccCCccccccCCCcceEE
Confidence 788888887777655544
No 143
>KOG2785|consensus
Probab=35.43 E-value=8.5 Score=28.51 Aligned_cols=55 Identities=18% Similarity=0.290 Sum_probs=42.3
Q ss_pred ceecccchhhcCCchhHHHhhhhhcCC-----------------------Cccchhhhh---hhhhccc-cCcCCCCCCe
Q psy553 59 PYKCTYCERRFKQLSHVQQHTRLHTVE-----------------------GVNSCLQIL---SLWIQLD-LKDEPRNRNY 111 (129)
Q Consensus 59 ~~~C~~c~~~f~~~~~l~~H~~~h~~~-----------------------~~y~C~~C~---~~f~~~~-l~~h~~~~~~ 111 (129)
|-.|..|.+.+.....-..||..++|- .-+.|-.|. +.|.... .+.||..+.|
T Consensus 166 Pt~CLfC~~~~k~~e~~~~HM~~~HgffIPdreYL~D~~GLl~YLgeKV~~~~~CL~CN~~~~~f~sleavr~HM~~K~H 245 (390)
T KOG2785|consen 166 PTDCLFCDKKSKSLEENLKHMFKEHGFFIPDREYLTDEKGLLKYLGEKVGIGFICLFCNELGRPFSSLEAVRAHMRDKGH 245 (390)
T ss_pred CcceeecCCCcccHHHHHHHHhhccCCcCCchHhhhchhHHHHHHHHHhccCceEEEeccccCcccccHHHHHHHhhccC
Confidence 467888999988888888898876541 237788888 8887776 8889988777
Q ss_pred eE
Q psy553 112 VV 113 (129)
Q Consensus 112 ~~ 113 (129)
-+
T Consensus 246 Ck 247 (390)
T KOG2785|consen 246 CK 247 (390)
T ss_pred cc
Confidence 53
No 144
>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=35.25 E-value=8.3 Score=18.70 Aligned_cols=12 Identities=8% Similarity=-0.238 Sum_probs=5.1
Q ss_pred CCCccchhhhhh
Q psy553 84 VEGVNSCLQILS 95 (129)
Q Consensus 84 ~~~~y~C~~C~~ 95 (129)
+.+.|.|..|+.
T Consensus 21 ~~~~w~C~~C~~ 32 (40)
T PF04810_consen 21 GGKTWICNFCGT 32 (40)
T ss_dssp TTTEEEETTT--
T ss_pred CCCEEECcCCCC
Confidence 344455555553
No 145
>COG3091 SprT Zn-dependent metalloprotease, SprT family [General function prediction only]
Probab=35.22 E-value=13 Score=23.94 Aligned_cols=14 Identities=7% Similarity=0.223 Sum_probs=8.0
Q ss_pred Cccchhhhhhhhhcc
Q psy553 86 GVNSCLQILSLWIQL 100 (129)
Q Consensus 86 ~~y~C~~C~~~f~~~ 100 (129)
-+|.|. |+..|.+.
T Consensus 116 ~~Y~C~-C~q~~l~~ 129 (156)
T COG3091 116 YPYRCQ-CQQHYLRI 129 (156)
T ss_pred eeEEee-cCCccchh
Confidence 346666 66655554
No 146
>PLN02294 cytochrome c oxidase subunit Vb
Probab=34.71 E-value=10 Score=24.91 Aligned_cols=27 Identities=11% Similarity=-0.072 Sum_probs=19.6
Q ss_pred hhHHHhhhhhcCCCccchhhhhhhhhcc
Q psy553 73 SHVQQHTRLHTVEGVNSCLQILSLWIQL 100 (129)
Q Consensus 73 ~~l~~H~~~h~~~~~y~C~~C~~~f~~~ 100 (129)
.....++..+-| +|+.|.+||..|.-.
T Consensus 128 sh~v~Wf~L~kG-kp~RCpeCG~~fkL~ 154 (174)
T PLN02294 128 EHDVVWFWLEKG-KSFECPVCTQYFELE 154 (174)
T ss_pred CceeEEEEecCC-CceeCCCCCCEEEEE
Confidence 344445555555 689999999999886
No 147
>COG4338 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=34.34 E-value=11 Score=19.24 Aligned_cols=12 Identities=8% Similarity=-0.064 Sum_probs=9.6
Q ss_pred chhhhhhhhhcc
Q psy553 89 SCLQILSLWIQL 100 (129)
Q Consensus 89 ~C~~C~~~f~~~ 100 (129)
-|++|++-|.++
T Consensus 14 ICpvCqRPFsWR 25 (54)
T COG4338 14 ICPVCQRPFSWR 25 (54)
T ss_pred hhhhhcCchHHH
Confidence 488888888876
No 148
>KOG2071|consensus
Probab=34.12 E-value=23 Score=27.92 Aligned_cols=27 Identities=26% Similarity=0.716 Sum_probs=21.5
Q ss_pred CCCCcccccchhhccChHHHHHHHhhc
Q psy553 28 ANKPHQCQQCLKSFSSNHQLVQHIRVH 54 (129)
Q Consensus 28 ~~~~~~C~~C~~~f~~~~~l~~h~~~h 54 (129)
...+..|..||.+|........||..|
T Consensus 415 ~~~pnqC~~CG~R~~~~ee~sk~md~H 441 (579)
T KOG2071|consen 415 KDSPNQCKSCGLRFDDSEERSKHMDIH 441 (579)
T ss_pred cCCcchhcccccccccchhhhhHhhhh
Confidence 356789999999999888777776665
No 149
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=33.94 E-value=6.2 Score=24.07 Aligned_cols=13 Identities=15% Similarity=0.302 Sum_probs=10.0
Q ss_pred Cccchhhhhhhhh
Q psy553 86 GVNSCLQILSLWI 98 (129)
Q Consensus 86 ~~y~C~~C~~~f~ 98 (129)
+-|.|..||+.|.
T Consensus 99 ~Fy~C~~Cg~~wr 111 (113)
T COG1594 99 RFYKCTRCGYRWR 111 (113)
T ss_pred EEEEecccCCEee
Confidence 3488999998774
No 150
>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 PHA02998 RNA polymerase subunit; Provisional
Probab=33.47 E-value=5.1 Score=26.49 Aligned_cols=15 Identities=7% Similarity=0.113 Sum_probs=12.0
Q ss_pred ccchhhhhhhhhccc
Q psy553 87 VNSCLQILSLWIQLD 101 (129)
Q Consensus 87 ~y~C~~C~~~f~~~~ 101 (129)
-|.|..|++.|.-+.
T Consensus 171 FYkC~~CG~~wkppk 185 (195)
T PHA02998 171 RHACRDCKKHFKPPK 185 (195)
T ss_pred EEEcCCCCCccCCcc
Confidence 389999999887664
No 152
>KOG2636|consensus
Probab=32.95 E-value=5.2 Score=30.24 Aligned_cols=33 Identities=9% Similarity=0.066 Sum_probs=20.5
Q ss_pred hhhcCCCccchhhhh-hhhhccc-cCcCCCCCCee
Q psy553 80 RLHTVEGVNSCLQIL-SLWIQLD-LKDEPRNRNYV 112 (129)
Q Consensus 80 ~~h~~~~~y~C~~C~-~~f~~~~-l~~h~~~~~~~ 112 (129)
+.|.-...|.|.+|| +++.=+. ..+|..+-+|.
T Consensus 394 KLHGL~~ey~CEICGNy~Y~GrkaF~RHF~EwRH~ 428 (497)
T KOG2636|consen 394 KLHGLDIEYNCEICGNYVYKGRKAFDRHFNEWRHA 428 (497)
T ss_pred hhcCCCcccceeeccCccccCcHHHHHHhHHHHHh
Confidence 345555668888887 6666554 66665555554
No 153
>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=32.64 E-value=25 Score=17.45 Aligned_cols=11 Identities=18% Similarity=0.286 Sum_probs=7.1
Q ss_pred CCccchhhhhh
Q psy553 85 EGVNSCLQILS 95 (129)
Q Consensus 85 ~~~y~C~~C~~ 95 (129)
...|.|..|.+
T Consensus 35 ~~~~~C~~C~~ 45 (46)
T PF12760_consen 35 RGRYRCKACRK 45 (46)
T ss_pred CCeEECCCCCC
Confidence 45577777754
No 154
>TIGR00280 L37a ribosomal protein L37a. This model finds eukaryotic ribosomal protein L37a and its archaeal orthologs. The nomeclature is tricky because eukaryotes have proteins called both L37 and L37a.
Probab=32.60 E-value=8.6 Score=22.52 Aligned_cols=13 Identities=8% Similarity=0.184 Sum_probs=7.3
Q ss_pred ccchhhhhhhhhc
Q psy553 87 VNSCLQILSLWIQ 99 (129)
Q Consensus 87 ~y~C~~C~~~f~~ 99 (129)
.|.|..|++.|+=
T Consensus 53 IW~C~~C~~~~AG 65 (91)
T TIGR00280 53 IWTCRKCGAKFAG 65 (91)
T ss_pred EEEcCCCCCEEeC
Confidence 4566666655543
No 155
>PF09963 DUF2197: Uncharacterized protein conserved in bacteria (DUF2197); InterPro: IPR019241 This family represents various hypothetical bacterial proteins with no known function.
Probab=32.11 E-value=33 Score=18.16 Aligned_cols=12 Identities=8% Similarity=-0.053 Sum_probs=6.1
Q ss_pred Cccchhhhhhhh
Q psy553 86 GVNSCLQILSLW 97 (129)
Q Consensus 86 ~~y~C~~C~~~f 97 (129)
..|-|..|...-
T Consensus 30 ~tYmC~eC~~RI 41 (56)
T PF09963_consen 30 HTYMCDECKERI 41 (56)
T ss_pred cceeChhHHHHH
Confidence 345566655433
No 156
>COG1655 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=31.94 E-value=11 Score=26.05 Aligned_cols=29 Identities=24% Similarity=0.522 Sum_probs=20.3
Q ss_pred CCCcccccchhhccChHHHHHHHhhcCCC
Q psy553 29 NKPHQCQQCLKSFSSNHQLVQHIRVHTGE 57 (129)
Q Consensus 29 ~~~~~C~~C~~~f~~~~~l~~h~~~h~~~ 57 (129)
.+...|++|+..|........-.+.-.++
T Consensus 17 kk~ieCPvC~tkFkkeev~tgsiRiiagD 45 (267)
T COG1655 17 KKTIECPVCNTKFKKEEVKTGSIRIIAGD 45 (267)
T ss_pred hceeccCcccchhhhhheeccceeEeccc
Confidence 46688999998887766665555555544
No 157
>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=31.46 E-value=14 Score=22.13 Aligned_cols=9 Identities=33% Similarity=0.707 Sum_probs=4.9
Q ss_pred Ccccccchh
Q psy553 31 PHQCQQCLK 39 (129)
Q Consensus 31 ~~~C~~C~~ 39 (129)
|-.|+.||.
T Consensus 2 p~~CpYCg~ 10 (102)
T PF11672_consen 2 PIICPYCGG 10 (102)
T ss_pred CcccCCCCC
Confidence 445666664
No 158
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=30.92 E-value=18 Score=22.11 Aligned_cols=11 Identities=36% Similarity=0.924 Sum_probs=6.4
Q ss_pred eecccchhhcC
Q psy553 60 YKCTYCERRFK 70 (129)
Q Consensus 60 ~~C~~c~~~f~ 70 (129)
+.|..|+..|.
T Consensus 72 ~~C~~Cg~~~~ 82 (117)
T PRK00564 72 LECKDCSHVFK 82 (117)
T ss_pred EEhhhCCCccc
Confidence 56666765443
No 159
>PF14311 DUF4379: Domain of unknown function (DUF4379)
Probab=30.90 E-value=25 Score=18.11 Aligned_cols=8 Identities=38% Similarity=1.169 Sum_probs=3.4
Q ss_pred eecccchh
Q psy553 60 YKCTYCER 67 (129)
Q Consensus 60 ~~C~~c~~ 67 (129)
++|..|+.
T Consensus 29 W~C~~Cgh 36 (55)
T PF14311_consen 29 WKCPKCGH 36 (55)
T ss_pred EECCCCCC
Confidence 34444443
No 160
>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=30.78 E-value=16 Score=17.48 Aligned_cols=13 Identities=8% Similarity=0.023 Sum_probs=7.1
Q ss_pred Cccchhhhhhhhh
Q psy553 86 GVNSCLQILSLWI 98 (129)
Q Consensus 86 ~~y~C~~C~~~f~ 98 (129)
.-|+|.+||....
T Consensus 5 ~~YkC~~CGniVe 17 (36)
T PF06397_consen 5 EFYKCEHCGNIVE 17 (36)
T ss_dssp EEEE-TTT--EEE
T ss_pred cEEEccCCCCEEE
Confidence 3589999997654
No 161
>COG4530 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=29.26 E-value=17 Score=22.10 Aligned_cols=29 Identities=3% Similarity=-0.188 Sum_probs=19.8
Q ss_pred ecccchhhcCCchhHHHhhhhhcCCCccchhhhhhhhhcc
Q psy553 61 KCTYCERRFKQLSHVQQHTRLHTVEGVNSCLQILSLWIQL 100 (129)
Q Consensus 61 ~C~~c~~~f~~~~~l~~H~~~h~~~~~y~C~~C~~~f~~~ 100 (129)
.|+.|++.|.. ....|-.|+.||++|+.+
T Consensus 11 idPetg~KFYD-----------LNrdPiVsPytG~s~P~s 39 (129)
T COG4530 11 IDPETGKKFYD-----------LNRDPIVSPYTGKSYPRS 39 (129)
T ss_pred cCccccchhhc-----------cCCCccccCcccccchHH
Confidence 46667666543 235678888899888765
No 162
>PRK05580 primosome assembly protein PriA; Validated
Probab=28.97 E-value=13 Score=29.86 Aligned_cols=11 Identities=18% Similarity=0.060 Sum_probs=6.5
Q ss_pred Cccchhhhhhh
Q psy553 86 GVNSCLQILSL 96 (129)
Q Consensus 86 ~~y~C~~C~~~ 96 (129)
.|..|+.|+..
T Consensus 420 ~~~~Cp~Cg~~ 430 (679)
T PRK05580 420 IPKACPECGST 430 (679)
T ss_pred CCCCCCCCcCC
Confidence 35567777643
No 163
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=28.27 E-value=15 Score=18.92 Aligned_cols=8 Identities=25% Similarity=0.912 Sum_probs=3.8
Q ss_pred eecccchh
Q psy553 60 YKCTYCER 67 (129)
Q Consensus 60 ~~C~~c~~ 67 (129)
+.|..|+.
T Consensus 38 ~~C~~Cgy 45 (50)
T PRK00432 38 WHCGKCGY 45 (50)
T ss_pred EECCCcCC
Confidence 44544443
No 164
>PF02318 FYVE_2: FYVE-type zinc finger; InterPro: IPR003315 This entry represents the zinc-binding domain found in rabphilin Rab3A. The small G protein Rab3A plays an important role in the regulation of neurotransmitter release. The crystal structure of the small G protein Rab3A complexed with the effector domain of rabphilin-3A shows that the effector domain of rabphilin-3A contacts Rab3A in two distinct areas. The first interface involves the Rab3A switch I and switch II regions, which are sensitive to the nucleotide-binding state of Rab3A. The second interface consists of a deep pocket in Rab3A that interacts with a SGAWFF structural element of rabphilin-3A. Sequence and structure analysis, and biochemical data suggest that this pocket, or Rab complementarity-determining region (RabCDR), establishes a specific interaction between each Rab protein and its effectors. It has been suggested that RabCDRs could be major determinants of effector specificity during vesicle trafficking and fusion [].; GO: 0008270 zinc ion binding, 0017137 Rab GTPase binding, 0006886 intracellular protein transport; PDB: 2CSZ_A 2ZET_C 1ZBD_B 3BC1_B 2CJS_C 2A20_A.
Probab=28.11 E-value=15 Score=22.38 Aligned_cols=49 Identities=20% Similarity=0.343 Sum_probs=25.9
Q ss_pred cccccchhhccChHHHHHHHhhcCCCCceecccchhhcCCchhHHHhhhhhcCCCccchhhhhhh
Q psy553 32 HQCQQCLKSFSSNHQLVQHIRVHTGEKPYKCTYCERRFKQLSHVQQHTRLHTVEGVNSCLQILSL 96 (129)
Q Consensus 32 ~~C~~C~~~f~~~~~l~~h~~~h~~~~~~~C~~c~~~f~~~~~l~~H~~~h~~~~~y~C~~C~~~ 96 (129)
..|..|+..|....+ ....|..|...+...=... ..++..|.|.+|.+.
T Consensus 55 ~~C~~C~~~fg~l~~-----------~~~~C~~C~~~VC~~C~~~-----~~~~~~WlC~vC~k~ 103 (118)
T PF02318_consen 55 RHCARCGKPFGFLFN-----------RGRVCVDCKHRVCKKCGVY-----SKKEPIWLCKVCQKQ 103 (118)
T ss_dssp SB-TTTS-BCSCTST-----------TCEEETTTTEEEETTSEEE-----TSSSCCEEEHHHHHH
T ss_pred cchhhhCCcccccCC-----------CCCcCCcCCccccCccCCc-----CCCCCCEEChhhHHH
Confidence 478889887653211 2245555554443321111 345677999999864
No 165
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=28.07 E-value=22 Score=17.17 Aligned_cols=18 Identities=11% Similarity=0.265 Sum_probs=9.7
Q ss_pred ceecccchhhcCCchhHH
Q psy553 59 PYKCTYCERRFKQLSHVQ 76 (129)
Q Consensus 59 ~~~C~~c~~~f~~~~~l~ 76 (129)
...|..|+..+.....|.
T Consensus 19 id~C~~C~G~W~d~~el~ 36 (41)
T PF13453_consen 19 IDVCPSCGGIWFDAGELE 36 (41)
T ss_pred EEECCCCCeEEccHHHHH
Confidence 345666666555555443
No 166
>PF14445 Prok-RING_2: Prokaryotic RING finger family 2
Probab=27.58 E-value=13 Score=19.25 Aligned_cols=16 Identities=25% Similarity=0.100 Sum_probs=8.7
Q ss_pred cchhhhhhhhhccccC
Q psy553 88 NSCLQILSLWIQLDLK 103 (129)
Q Consensus 88 y~C~~C~~~f~~~~l~ 103 (129)
|.|..|.-+|+-++|+
T Consensus 8 y~CDLCn~~~p~~~LR 23 (57)
T PF14445_consen 8 YSCDLCNSSHPISELR 23 (57)
T ss_pred HhHHhhcccCcHHHHH
Confidence 5555555555555444
No 167
>KOG2482|consensus
Probab=27.33 E-value=36 Score=25.16 Aligned_cols=52 Identities=23% Similarity=0.604 Sum_probs=35.4
Q ss_pred CCcccccchhh-ccChHHHHHHHhh-cC-----CC----------------CceecccchhhcCCchhHHHhhhh
Q psy553 30 KPHQCQQCLKS-FSSNHQLVQHIRV-HT-----GE----------------KPYKCTYCERRFKQLSHVQQHTRL 81 (129)
Q Consensus 30 ~~~~C~~C~~~-f~~~~~l~~h~~~-h~-----~~----------------~~~~C~~c~~~f~~~~~l~~H~~~ 81 (129)
....|-.|... ...++....|+.. |. .+ ..+.|-.|.+.|.....|..||+-
T Consensus 143 fslqClFCn~e~lgnRs~~l~Hlf~~H~lniGlpDniVyvnelLehLkekL~r~~CLyCekifrdkntLkeHMrk 217 (423)
T KOG2482|consen 143 FSLQCLFCNNEGLGNRSEILEHLFHVHGLNIGLPDNIVYVNELLEHLKEKLERLRCLYCEKIFRDKNTLKEHMRK 217 (423)
T ss_pred eeeEEEEecchhcccHHHHHHHHHHHhhhccCCCcceeeHHHHHHHHHHHHhhheeeeeccccCCcHHHHHHHHh
Confidence 44578888754 3444555566542 21 11 246899999999999999999984
No 168
>KOG2907|consensus
Probab=27.28 E-value=16 Score=22.26 Aligned_cols=13 Identities=8% Similarity=0.089 Sum_probs=9.2
Q ss_pred Cccchhhhhhhhh
Q psy553 86 GVNSCLQILSLWI 98 (129)
Q Consensus 86 ~~y~C~~C~~~f~ 98 (129)
.-|-|..|++.|.
T Consensus 101 VFYTC~kC~~k~~ 113 (116)
T KOG2907|consen 101 VFYTCPKCKYKFT 113 (116)
T ss_pred EEEEcCccceeee
Confidence 4478888887665
No 169
>PF11789 zf-Nse: Zinc-finger of the MIZ type in Nse subunit; PDB: 2YU4_A 3HTK_C.
Probab=26.98 E-value=20 Score=18.88 Aligned_cols=16 Identities=25% Similarity=0.571 Sum_probs=7.7
Q ss_pred CceecccchhhcCCch
Q psy553 58 KPYKCTYCERRFKQLS 73 (129)
Q Consensus 58 ~~~~C~~c~~~f~~~~ 73 (129)
.|+....|++.|....
T Consensus 23 ~PV~s~~C~H~fek~a 38 (57)
T PF11789_consen 23 DPVKSKKCGHTFEKEA 38 (57)
T ss_dssp SEEEESSS--EEEHHH
T ss_pred CCcCcCCCCCeecHHH
Confidence 4555556666665443
No 170
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=26.88 E-value=20 Score=22.51 Aligned_cols=13 Identities=8% Similarity=0.171 Sum_probs=6.6
Q ss_pred cchhhhhhhhhcc
Q psy553 88 NSCLQILSLWIQL 100 (129)
Q Consensus 88 y~C~~C~~~f~~~ 100 (129)
..|..||+.|...
T Consensus 2 H~Ct~Cg~~f~dg 14 (131)
T PF09845_consen 2 HQCTKCGRVFEDG 14 (131)
T ss_pred cccCcCCCCcCCC
Confidence 4455555555543
No 171
>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=26.79 E-value=26 Score=17.91 Aligned_cols=10 Identities=40% Similarity=0.962 Sum_probs=5.5
Q ss_pred ccccchhhcc
Q psy553 33 QCQQCLKSFS 42 (129)
Q Consensus 33 ~C~~C~~~f~ 42 (129)
.|..|++.|.
T Consensus 4 ~C~~C~~~F~ 13 (57)
T cd00065 4 SCMGCGKPFT 13 (57)
T ss_pred cCcccCcccc
Confidence 3555665554
No 172
>PF12230 PRP21_like_P: Pre-mRNA splicing factor PRP21 like protein; InterPro: IPR022030 This domain family is found in eukaryotes, and is typically between 212 and 238 amino acids in length. The family is found in association with PF01805 from PFAM. There are two completely conserved residues (W and H) that may be functionally important. PRP21 is required for assembly of the prespliceosome and it interacts with U2 snRNP and/or pre-mRNA in the prespliceosome. This family also contains proteins similar to PRP21, such as the mammalian SF3a. SF3a also interacts with U2 snRNP from the prespliceosome, converting it to its active form. ; PDB: 4DGW_B.
Probab=26.52 E-value=22 Score=24.34 Aligned_cols=24 Identities=13% Similarity=0.084 Sum_probs=0.0
Q ss_pred CCCccchhhhhhhhhccccCcCCC
Q psy553 84 VEGVNSCLQILSLWIQLDLKDEPR 107 (129)
Q Consensus 84 ~~~~y~C~~C~~~f~~~~l~~h~~ 107 (129)
+.....|++||...+-..+..||+
T Consensus 165 ~~~~~~cPitGe~IP~~e~~eHmR 188 (229)
T PF12230_consen 165 KEKMIICPITGEMIPADEMDEHMR 188 (229)
T ss_dssp ------------------------
T ss_pred cccccccccccccccccccccccc
Confidence 445578999999999988888865
No 173
>KOG3507|consensus
Probab=26.43 E-value=32 Score=18.40 Aligned_cols=13 Identities=23% Similarity=0.559 Sum_probs=7.6
Q ss_pred CceecccchhhcC
Q psy553 58 KPYKCTYCERRFK 70 (129)
Q Consensus 58 ~~~~C~~c~~~f~ 70 (129)
..+.|..||....
T Consensus 36 D~irCReCG~RIl 48 (62)
T KOG3507|consen 36 DVIRCRECGYRIL 48 (62)
T ss_pred CcEehhhcchHHH
Confidence 3566777765443
No 174
>PRK04023 DNA polymerase II large subunit; Validated
Probab=26.26 E-value=25 Score=29.70 Aligned_cols=11 Identities=27% Similarity=0.670 Sum_probs=7.0
Q ss_pred CCcccccchhh
Q psy553 30 KPHQCQQCLKS 40 (129)
Q Consensus 30 ~~~~C~~C~~~ 40 (129)
....|+.||..
T Consensus 625 g~RfCpsCG~~ 635 (1121)
T PRK04023 625 GRRKCPSCGKE 635 (1121)
T ss_pred cCccCCCCCCc
Confidence 34567777754
No 175
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=26.17 E-value=27 Score=18.43 Aligned_cols=11 Identities=18% Similarity=0.643 Sum_probs=6.5
Q ss_pred CCceecccchh
Q psy553 57 EKPYKCTYCER 67 (129)
Q Consensus 57 ~~~~~C~~c~~ 67 (129)
...|.|+.||-
T Consensus 12 ~v~~~Cp~cGi 22 (55)
T PF13824_consen 12 HVNFECPDCGI 22 (55)
T ss_pred ccCCcCCCCCC
Confidence 34566666664
No 176
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=25.93 E-value=19 Score=21.90 Aligned_cols=10 Identities=20% Similarity=0.617 Sum_probs=6.2
Q ss_pred eecccchhhc
Q psy553 60 YKCTYCERRF 69 (129)
Q Consensus 60 ~~C~~c~~~f 69 (129)
+.|..|+..|
T Consensus 71 ~~C~~Cg~~~ 80 (114)
T PRK03681 71 CWCETCQQYV 80 (114)
T ss_pred EEcccCCCee
Confidence 5677777544
No 177
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=25.78 E-value=48 Score=21.97 Aligned_cols=36 Identities=14% Similarity=0.211 Sum_probs=19.6
Q ss_pred cCCCCceecccchhhcCCchhHHHhhhhhcCCCccchhhhhhhhh
Q psy553 54 HTGEKPYKCTYCERRFKQLSHVQQHTRLHTVEGVNSCLQILSLWI 98 (129)
Q Consensus 54 h~~~~~~~C~~c~~~f~~~~~l~~H~~~h~~~~~y~C~~C~~~f~ 98 (129)
-.+..-|.|+.|.-.+....+ ...+ |.|+.||....
T Consensus 108 ~~~~~~y~C~~~~~r~sfdeA------~~~~---F~Cp~Cg~~L~ 143 (176)
T COG1675 108 ETENNYYVCPNCHVKYSFDEA------MELG---FTCPKCGEDLE 143 (176)
T ss_pred hccCCceeCCCCCCcccHHHH------HHhC---CCCCCCCchhh
Confidence 344556788766554433322 1122 88888885443
No 178
>PF13878 zf-C2H2_3: zinc-finger of acetyl-transferase ESCO
Probab=25.73 E-value=65 Score=15.64 Aligned_cols=25 Identities=20% Similarity=0.397 Sum_probs=16.0
Q ss_pred CcccccchhhccCh--HHHHHHHhhcC
Q psy553 31 PHQCQQCLKSFSSN--HQLVQHIRVHT 55 (129)
Q Consensus 31 ~~~C~~C~~~f~~~--~~l~~h~~~h~ 55 (129)
.-.|+.||+.|... .....|.+.|.
T Consensus 13 ~~~C~~CgM~Y~~~~~eD~~~H~~yH~ 39 (41)
T PF13878_consen 13 ATTCPTCGMLYSPGSPEDEKLHKKYHD 39 (41)
T ss_pred CcCCCCCCCEECCCCHHHHHHHHHHHh
Confidence 35899999876543 44556666553
No 179
>PF15269 zf-C2H2_7: Zinc-finger
Probab=25.67 E-value=99 Score=15.58 Aligned_cols=21 Identities=24% Similarity=0.578 Sum_probs=11.2
Q ss_pred cccccchhhccChHHHHHHHh
Q psy553 32 HQCQQCLKSFSSNHQLVQHIR 52 (129)
Q Consensus 32 ~~C~~C~~~f~~~~~l~~h~~ 52 (129)
|.|-.|......++.|..||.
T Consensus 21 ykcfqcpftc~~kshl~nhmk 41 (54)
T PF15269_consen 21 YKCFQCPFTCNEKSHLFNHMK 41 (54)
T ss_pred ceeecCCcccchHHHHHHHHH
Confidence 445555555555555555554
No 180
>COG4957 Predicted transcriptional regulator [Transcription]
Probab=25.48 E-value=36 Score=21.57 Aligned_cols=24 Identities=21% Similarity=0.278 Sum_probs=13.1
Q ss_pred ecccchhhcCCchhHHHhhhhhcCCCc
Q psy553 61 KCTYCERRFKQLSHVQQHTRLHTVEGV 87 (129)
Q Consensus 61 ~C~~c~~~f~~~~~l~~H~~~h~~~~~ 87 (129)
.|-++|+.|. +|.+|+.+|.|..|
T Consensus 78 icLEDGkkfK---SLKRHL~t~~gmTP 101 (148)
T COG4957 78 ICLEDGKKFK---SLKRHLTTHYGLTP 101 (148)
T ss_pred EEeccCcchH---HHHHHHhcccCCCH
Confidence 4555555443 36666666655444
No 181
>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=25.43 E-value=17 Score=22.05 Aligned_cols=12 Identities=25% Similarity=0.797 Sum_probs=6.7
Q ss_pred eecccchhhcCC
Q psy553 60 YKCTYCERRFKQ 71 (129)
Q Consensus 60 ~~C~~c~~~f~~ 71 (129)
+.|..|+..|..
T Consensus 71 ~~C~~Cg~~~~~ 82 (113)
T PF01155_consen 71 ARCRDCGHEFEP 82 (113)
T ss_dssp EEETTTS-EEEC
T ss_pred EECCCCCCEEec
Confidence 566677766544
No 182
>COG1326 Uncharacterized archaeal Zn-finger protein [General function prediction only]
Probab=25.03 E-value=38 Score=22.85 Aligned_cols=14 Identities=7% Similarity=0.060 Sum_probs=9.2
Q ss_pred Cccchhhhhhhhhc
Q psy553 86 GVNSCLQILSLWIQ 99 (129)
Q Consensus 86 ~~y~C~~C~~~f~~ 99 (129)
-.+.|..||.+++.
T Consensus 29 ~lvrC~eCG~V~~~ 42 (201)
T COG1326 29 PLVRCEECGTVHPA 42 (201)
T ss_pred eEEEccCCCcEeec
Confidence 34667777777744
No 183
>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=24.51 E-value=34 Score=27.76 Aligned_cols=43 Identities=19% Similarity=0.218 Sum_probs=26.7
Q ss_pred ecccchhhcCCchhHHHhhhhhcCCCccc-hhhhhhhhhccccCc
Q psy553 61 KCTYCERRFKQLSHVQQHTRLHTVEGVNS-CLQILSLWIQLDLKD 104 (129)
Q Consensus 61 ~C~~c~~~f~~~~~l~~H~~~h~~~~~y~-C~~C~~~f~~~~l~~ 104 (129)
.|..||.+|+-...|..- +.++..+.|+ |+.|.+-|....-++
T Consensus 125 ~CT~CGPRfTIi~alPYD-R~nTsM~~F~lC~~C~~EY~dP~nRR 168 (750)
T COG0068 125 NCTNCGPRFTIIEALPYD-RENTSMADFPLCPFCDKEYKDPLNRR 168 (750)
T ss_pred ccCCCCcceeeeccCCCC-cccCccccCcCCHHHHHHhcCccccc
Confidence 477788777655544332 3455566666 888888777664333
No 184
>PF02891 zf-MIZ: MIZ/SP-RING zinc finger; InterPro: IPR004181 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 MIZ-type zinc finger domains. Miz1 (Msx-interacting-zinc finger) is a zinc finger-containing protein with homology to the yeast protein, Nfi-1. Miz1 is a sequence specific DNA binding protein that can function as a positive-acting transcription factor. Miz1 binds to the homeobox protein Msx2, enhancing the specific DNA-binding ability of Msx2 []. Other proteins containing this domain include the human pias family (protein inhibitor of activated STAT protein). More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3I2D_A.
Probab=24.05 E-value=32 Score=17.53 Aligned_cols=9 Identities=11% Similarity=-0.067 Sum_probs=3.1
Q ss_pred ccchhhhhh
Q psy553 87 VNSCLQILS 95 (129)
Q Consensus 87 ~y~C~~C~~ 95 (129)
.|.|++|++
T Consensus 41 ~W~CPiC~~ 49 (50)
T PF02891_consen 41 KWKCPICNK 49 (50)
T ss_dssp --B-TTT--
T ss_pred CeECcCCcC
Confidence 377777764
No 185
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=24.02 E-value=21 Score=22.24 Aligned_cols=17 Identities=12% Similarity=-0.001 Sum_probs=14.1
Q ss_pred CCccchhhhhhhhhccc
Q psy553 85 EGVNSCLQILSLWIQLD 101 (129)
Q Consensus 85 ~~~y~C~~C~~~f~~~~ 101 (129)
.--|.|..|++.|....
T Consensus 51 ~qRyrC~~C~~tf~~~~ 67 (129)
T COG3677 51 HQRYKCKSCGSTFTVET 67 (129)
T ss_pred ccccccCCcCcceeeec
Confidence 44599999999998873
No 186
>KOG0717|consensus
Probab=22.30 E-value=89 Score=24.18 Aligned_cols=22 Identities=41% Similarity=0.575 Sum_probs=19.4
Q ss_pred cccccchhhccChHHHHHHHhh
Q psy553 32 HQCQQCLKSFSSNHQLVQHIRV 53 (129)
Q Consensus 32 ~~C~~C~~~f~~~~~l~~h~~~ 53 (129)
+.|.+|.+.|.+...+..|..+
T Consensus 293 lyC~vCnKsFKseKq~kNHEnS 314 (508)
T KOG0717|consen 293 LYCVVCNKSFKSEKQLKNHENS 314 (508)
T ss_pred eEEeeccccccchHHHHhhHHH
Confidence 8899999999999999888654
No 187
>COG5112 UFD2 U1-like Zn-finger-containing protein [General function prediction only]
Probab=21.35 E-value=91 Score=18.91 Aligned_cols=24 Identities=25% Similarity=0.616 Sum_probs=16.7
Q ss_pred CCCcccccchhhccChHHHHHHHh
Q psy553 29 NKPHQCQQCLKSFSSNHQLVQHIR 52 (129)
Q Consensus 29 ~~~~~C~~C~~~f~~~~~l~~h~~ 52 (129)
-..|.|.+|.+-|.+...|..|.+
T Consensus 53 lGqhYCieCaryf~t~~aL~~Hkk 76 (126)
T COG5112 53 LGQHYCIECARYFITEKALMEHKK 76 (126)
T ss_pred CceeeeehhHHHHHHHHHHHHHhc
Confidence 345777778877777777766654
No 188
>COG3364 Zn-ribbon containing protein [General function prediction only]
Probab=21.22 E-value=56 Score=19.63 Aligned_cols=14 Identities=36% Similarity=0.766 Sum_probs=6.9
Q ss_pred ceecccchhhcCCc
Q psy553 59 PYKCTYCERRFKQL 72 (129)
Q Consensus 59 ~~~C~~c~~~f~~~ 72 (129)
|.+|..||..|...
T Consensus 2 pH~CtrCG~vf~~g 15 (112)
T COG3364 2 PHQCTRCGEVFDDG 15 (112)
T ss_pred Cceecccccccccc
Confidence 34455555555443
No 189
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=20.55 E-value=21 Score=16.61 Aligned_cols=13 Identities=15% Similarity=0.161 Sum_probs=8.1
Q ss_pred Cccchhhhhhhhh
Q psy553 86 GVNSCLQILSLWI 98 (129)
Q Consensus 86 ~~y~C~~C~~~f~ 98 (129)
.-+.|..|+.+|.
T Consensus 20 ~~~~C~~Cg~~~~ 32 (33)
T PF08792_consen 20 DYEVCIFCGSSFP 32 (33)
T ss_pred CeEEcccCCcEee
Confidence 3456777776654
No 190
>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=20.24 E-value=18 Score=22.92 Aligned_cols=7 Identities=14% Similarity=0.074 Sum_probs=3.6
Q ss_pred cchhhhh
Q psy553 88 NSCLQIL 94 (129)
Q Consensus 88 y~C~~C~ 94 (129)
|.|..|+
T Consensus 144 ~~C~~C~ 150 (157)
T PF10263_consen 144 YRCGRCG 150 (157)
T ss_pred EECCCCC
Confidence 5555554
No 191
>PF14787 zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB: 1CL4_A 1DSV_A.
Probab=20.03 E-value=29 Score=16.58 Aligned_cols=14 Identities=7% Similarity=-0.064 Sum_probs=9.0
Q ss_pred cchhhhhhhhhccc
Q psy553 88 NSCLQILSLWIQLD 101 (129)
Q Consensus 88 y~C~~C~~~f~~~~ 101 (129)
-.|..|++.|-+.+
T Consensus 3 ~~CprC~kg~Hwa~ 16 (36)
T PF14787_consen 3 GLCPRCGKGFHWAS 16 (36)
T ss_dssp -C-TTTSSSCS-TT
T ss_pred ccCcccCCCcchhh
Confidence 46888999988874
Done!