Query psy2643
Match_columns 134
No_of_seqs 129 out of 2261
Neff 11.0
Searched_HMMs 46136
Date Fri Aug 16 21:28:22 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy2643.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/2643hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2462|consensus 100.0 2.4E-29 5.1E-34 159.0 5.5 116 1-118 133-251 (279)
2 KOG2462|consensus 99.9 2.2E-28 4.8E-33 154.7 5.5 104 1-106 164-267 (279)
3 KOG1074|consensus 99.8 1.3E-20 2.8E-25 134.1 2.7 58 55-112 606-663 (958)
4 KOG3576|consensus 99.8 2.4E-19 5.1E-24 109.5 1.6 112 1-112 120-242 (267)
5 KOG3623|consensus 99.7 3.1E-18 6.7E-23 120.9 2.1 105 1-105 213-332 (1007)
6 KOG1074|consensus 99.7 1.3E-17 2.9E-22 119.1 4.9 59 56-114 881-939 (958)
7 KOG3623|consensus 99.6 6E-17 1.3E-21 114.6 2.6 80 24-103 892-971 (1007)
8 KOG3576|consensus 99.6 6.2E-17 1.4E-21 99.0 1.4 86 24-109 115-200 (267)
9 KOG3608|consensus 99.6 2.5E-15 5.5E-20 98.8 5.3 115 3-118 184-327 (467)
10 KOG3608|consensus 99.6 2.2E-14 4.8E-19 94.5 7.6 110 1-111 266-381 (467)
11 PLN03086 PRLI-interacting fact 99.4 7.7E-13 1.7E-17 93.3 8.0 101 1-108 456-566 (567)
12 PHA00733 hypothetical protein 99.4 2.7E-13 5.8E-18 79.3 4.6 84 23-108 37-125 (128)
13 PHA02768 hypothetical protein; 99.1 2.9E-11 6.3E-16 59.5 1.9 44 54-99 5-48 (55)
14 KOG3993|consensus 99.1 4.1E-11 8.9E-16 80.9 1.1 50 1-50 270-319 (500)
15 PHA00733 hypothetical protein 99.1 2.8E-10 6E-15 66.7 4.4 77 1-79 43-124 (128)
16 PLN03086 PRLI-interacting fact 99.0 7E-10 1.5E-14 78.7 5.2 84 25-114 452-545 (567)
17 PF13465 zf-H2C2_2: Zinc-finge 99.0 3.2E-10 7E-15 48.0 1.9 26 69-94 1-26 (26)
18 PHA02768 hypothetical protein; 98.9 8.8E-10 1.9E-14 54.3 2.1 42 26-69 5-46 (55)
19 PHA00616 hypothetical protein 98.8 5.6E-09 1.2E-13 49.0 2.2 31 82-112 1-31 (44)
20 PF13465 zf-H2C2_2: Zinc-finge 98.8 5.8E-09 1.3E-13 44.0 1.9 24 14-37 2-25 (26)
21 KOG3993|consensus 98.7 2.9E-09 6.3E-14 72.2 0.8 86 27-112 268-386 (500)
22 PHA00732 hypothetical protein 98.6 5.1E-08 1.1E-12 52.3 2.5 37 27-65 2-38 (79)
23 PHA00616 hypothetical protein 98.5 9.5E-08 2.1E-12 44.9 1.9 32 27-58 2-33 (44)
24 PF00096 zf-C2H2: Zinc finger, 98.4 1.8E-07 3.9E-12 38.2 1.7 22 83-104 1-22 (23)
25 PF05605 zf-Di19: Drought indu 98.4 8.8E-07 1.9E-11 44.1 4.3 50 55-107 3-54 (54)
26 PF13894 zf-C2H2_4: C2H2-type 98.3 6.1E-07 1.3E-11 36.8 2.0 24 83-106 1-24 (24)
27 PF05605 zf-Di19: Drought indu 98.2 4E-06 8.6E-11 41.8 4.3 50 26-78 2-53 (54)
28 PHA00732 hypothetical protein 98.2 1.9E-06 4.1E-11 46.2 2.8 36 55-93 2-38 (79)
29 PF13912 zf-C2H2_6: C2H2-type 98.1 1.4E-06 3.1E-11 37.0 1.6 26 82-107 1-26 (27)
30 PF12756 zf-C2H2_2: C2H2 type 98.1 3.8E-06 8.1E-11 47.0 2.8 73 29-106 2-74 (100)
31 COG5189 SFP1 Putative transcri 98.0 1.3E-06 2.8E-11 57.7 -0.3 26 78-103 394-419 (423)
32 PF00096 zf-C2H2: Zinc finger, 97.9 8.3E-06 1.8E-10 33.1 2.0 22 55-76 1-22 (23)
33 PF12756 zf-C2H2_2: C2H2 type 97.8 2.6E-05 5.7E-10 43.6 2.7 72 1-77 2-73 (100)
34 PF09237 GAGA: GAGA factor; I 97.7 4.1E-05 8.9E-10 36.9 2.4 33 78-110 20-52 (54)
35 PF13894 zf-C2H2_4: C2H2-type 97.7 4.1E-05 8.9E-10 31.1 2.2 23 55-77 1-23 (24)
36 smart00355 ZnF_C2H2 zinc finge 97.6 5.9E-05 1.3E-09 31.1 2.4 23 83-105 1-23 (26)
37 PF13912 zf-C2H2_6: C2H2-type 97.6 5.2E-05 1.1E-09 32.0 1.9 24 54-77 1-24 (27)
38 PF13909 zf-H2C2_5: C2H2-type 97.5 6.9E-05 1.5E-09 30.7 1.3 24 83-107 1-24 (24)
39 PF12874 zf-met: Zinc-finger o 97.5 7.9E-05 1.7E-09 30.8 1.4 22 83-104 1-22 (25)
40 PF12171 zf-C2H2_jaz: Zinc-fin 97.2 0.00012 2.6E-09 30.9 0.5 22 83-104 2-23 (27)
41 PF09237 GAGA: GAGA factor; I 97.2 0.00055 1.2E-08 33.1 2.5 29 53-81 23-51 (54)
42 PRK04860 hypothetical protein; 97.1 0.00041 8.9E-09 42.3 2.1 38 54-95 119-156 (160)
43 smart00355 ZnF_C2H2 zinc finge 97.0 0.00089 1.9E-08 27.4 2.3 21 56-76 2-22 (26)
44 PF12874 zf-met: Zinc-finger o 97.0 0.0006 1.3E-08 28.0 1.6 22 55-76 1-22 (25)
45 COG4049 Uncharacterized protei 96.8 0.00061 1.3E-08 33.4 1.2 32 77-108 12-43 (65)
46 PF13909 zf-H2C2_5: C2H2-type 96.5 0.0024 5.2E-08 25.9 1.7 22 55-77 1-22 (24)
47 KOG1146|consensus 96.4 0.00096 2.1E-08 52.1 0.2 87 24-110 463-617 (1406)
48 smart00451 ZnF_U1 U1-like zinc 96.2 0.004 8.6E-08 27.7 1.6 24 82-105 3-26 (35)
49 PF13913 zf-C2HC_2: zinc-finge 96.1 0.005 1.1E-07 25.4 1.7 19 84-103 4-22 (25)
50 PF12171 zf-C2H2_jaz: Zinc-fin 95.9 0.0019 4.1E-08 27.1 -0.1 21 55-75 2-22 (27)
51 KOG2231|consensus 95.9 0.025 5.5E-07 41.9 5.4 96 7-108 123-238 (669)
52 cd00350 rubredoxin_like Rubred 95.9 0.0056 1.2E-07 27.1 1.3 24 55-90 2-25 (33)
53 PRK04860 hypothetical protein; 95.7 0.0083 1.8E-07 36.7 2.1 38 26-67 119-156 (160)
54 KOG1146|consensus 95.2 0.007 1.5E-07 47.7 0.6 105 1-105 468-641 (1406)
55 KOG2785|consensus 95.0 0.15 3.3E-06 35.3 6.3 51 55-105 167-243 (390)
56 KOG4173|consensus 94.9 0.012 2.7E-07 37.1 1.0 71 32-105 87-169 (253)
57 PF12013 DUF3505: Protein of u 94.8 0.087 1.9E-06 30.1 4.3 26 82-107 80-109 (109)
58 KOG2231|consensus 94.8 0.073 1.6E-06 39.7 4.7 77 28-107 117-207 (669)
59 TIGR00622 ssl1 transcription f 94.4 0.055 1.2E-06 31.0 2.7 81 24-106 13-105 (112)
60 PF09538 FYDLN_acid: Protein o 93.9 0.039 8.4E-07 31.5 1.6 30 27-67 10-39 (108)
61 KOG2186|consensus 93.8 0.046 1E-06 35.6 1.9 47 26-75 3-49 (276)
62 KOG4173|consensus 93.4 0.065 1.4E-06 33.9 2.0 72 4-78 87-171 (253)
63 cd00729 rubredoxin_SM Rubredox 92.9 0.066 1.4E-06 23.8 1.1 25 54-90 2-26 (34)
64 COG5236 Uncharacterized conser 92.8 0.092 2E-06 36.0 2.2 24 27-50 152-177 (493)
65 COG5189 SFP1 Putative transcri 92.7 0.035 7.5E-07 37.5 0.1 63 3-75 356-419 (423)
66 PF12013 DUF3505: Protein of u 92.6 0.31 6.8E-06 27.8 4.0 26 54-79 80-109 (109)
67 KOG2893|consensus 92.4 0.037 7.9E-07 35.9 -0.0 41 57-101 13-53 (341)
68 PF13719 zinc_ribbon_5: zinc-r 92.4 0.088 1.9E-06 23.9 1.2 32 28-64 4-35 (37)
69 PF13717 zinc_ribbon_4: zinc-r 92.2 0.12 2.6E-06 23.3 1.5 33 55-92 3-35 (36)
70 COG5048 FOG: Zn-finger [Genera 92.0 0.05 1.1E-06 38.0 0.2 61 54-114 289-355 (467)
71 PF02892 zf-BED: BED zinc fing 91.9 0.11 2.4E-06 24.4 1.3 27 80-106 14-44 (45)
72 PF10571 UPF0547: Uncharacteri 91.8 0.098 2.1E-06 21.7 0.9 9 28-36 16-24 (26)
73 COG4049 Uncharacterized protei 91.6 0.095 2E-06 25.9 0.9 31 21-51 12-42 (65)
74 COG1592 Rubrerythrin [Energy p 91.6 0.13 2.8E-06 31.7 1.7 24 53-89 133-156 (166)
75 TIGR02098 MJ0042_CXXC MJ0042 f 91.4 0.11 2.4E-06 23.5 1.0 33 27-64 3-35 (38)
76 PF09986 DUF2225: Uncharacteri 91.1 0.028 6.1E-07 36.2 -1.6 14 82-95 48-61 (214)
77 TIGR00373 conserved hypothetic 91.1 0.25 5.4E-06 30.3 2.6 29 53-90 108-136 (158)
78 smart00614 ZnF_BED BED zinc fi 90.5 0.24 5.3E-06 24.0 1.8 25 83-107 19-48 (50)
79 PF04959 ARS2: Arsenite-resist 90.2 0.097 2.1E-06 33.6 0.2 23 55-77 78-100 (214)
80 COG5236 Uncharacterized conser 90.2 0.36 7.9E-06 33.2 2.9 76 29-109 223-308 (493)
81 KOG2893|consensus 90.1 0.092 2E-06 34.1 0.0 41 29-73 13-53 (341)
82 PF09986 DUF2225: Uncharacteri 90.0 0.059 1.3E-06 34.7 -0.8 43 25-67 4-61 (214)
83 TIGR00373 conserved hypothetic 89.5 0.43 9.3E-06 29.2 2.6 38 20-66 103-140 (158)
84 TIGR02300 FYDLN_acid conserved 89.3 0.28 6.2E-06 28.7 1.7 30 27-67 10-39 (129)
85 PRK06266 transcription initiat 89.2 0.37 8E-06 30.2 2.2 16 54-69 117-132 (178)
86 KOG2807|consensus 88.8 0.67 1.5E-05 31.7 3.3 27 80-106 343-369 (378)
87 PRK00398 rpoP DNA-directed RNA 88.6 0.19 4.2E-06 23.8 0.6 29 54-92 3-31 (46)
88 smart00531 TFIIE Transcription 88.5 0.69 1.5E-05 28.0 3.0 37 52-92 97-133 (147)
89 KOG2482|consensus 88.5 0.73 1.6E-05 31.7 3.3 51 55-105 280-357 (423)
90 PF09723 Zn-ribbon_8: Zinc rib 88.0 0.15 3.3E-06 23.8 -0.0 29 55-90 6-34 (42)
91 smart00659 RPOLCX RNA polymera 87.8 0.4 8.7E-06 22.6 1.4 25 55-90 3-27 (44)
92 smart00734 ZnF_Rad18 Rad18-lik 87.7 0.5 1.1E-05 19.6 1.5 19 84-103 3-21 (26)
93 TIGR02605 CxxC_CxxC_SSSS putat 87.6 0.14 3E-06 25.0 -0.3 29 55-90 6-34 (52)
94 COG2888 Predicted Zn-ribbon RN 87.3 0.44 9.5E-06 24.0 1.4 34 25-63 26-59 (61)
95 PRK00464 nrdR transcriptional 87.2 0.081 1.8E-06 32.2 -1.5 16 54-69 28-43 (154)
96 PRK06266 transcription initiat 87.1 0.64 1.4E-05 29.1 2.4 36 22-66 113-148 (178)
97 smart00531 TFIIE Transcription 86.7 1.4 3E-05 26.6 3.6 41 22-66 95-135 (147)
98 smart00834 CxxC_CXXC_SSSS Puta 86.3 0.17 3.7E-06 23.2 -0.4 29 55-90 6-34 (41)
99 PHA00626 hypothetical protein 86.1 0.35 7.5E-06 24.0 0.6 15 53-67 22-36 (59)
100 KOG2186|consensus 86.0 0.65 1.4E-05 30.6 2.0 44 1-47 6-49 (276)
101 KOG2482|consensus 85.8 1.2 2.6E-05 30.7 3.2 25 83-107 280-304 (423)
102 COG5048 FOG: Zn-finger [Genera 85.0 0.24 5.2E-06 34.6 -0.3 60 26-85 289-354 (467)
103 PF12907 zf-met2: Zinc-binding 83.8 1 2.3E-05 20.8 1.6 29 83-111 2-33 (40)
104 COG1198 PriA Primosomal protei 83.8 0.41 8.8E-06 36.5 0.4 49 27-91 436-484 (730)
105 COG1996 RPC10 DNA-directed RNA 83.7 0.63 1.4E-05 22.5 0.9 27 54-90 6-32 (49)
106 KOG2785|consensus 83.0 2.3 5.1E-05 29.8 3.7 50 27-76 167-242 (390)
107 PF05443 ROS_MUCR: ROS/MUCR tr 82.9 0.59 1.3E-05 27.8 0.8 28 81-111 71-98 (132)
108 PRK04023 DNA polymerase II lar 82.2 1.6 3.5E-05 34.5 3.0 9 82-90 663-671 (1121)
109 COG5151 SSL1 RNA polymerase II 82.0 0.93 2E-05 30.8 1.5 48 57-106 365-412 (421)
110 COG3357 Predicted transcriptio 80.6 0.94 2E-05 24.9 1.0 27 54-90 58-84 (97)
111 PF15135 UPF0515: Uncharacteri 79.9 1.7 3.7E-05 28.6 2.1 71 12-95 93-168 (278)
112 PF07754 DUF1610: Domain of un 79.5 0.71 1.5E-05 18.8 0.2 8 82-89 16-23 (24)
113 PF13878 zf-C2H2_3: zinc-finge 79.4 2.2 4.8E-05 19.7 1.9 21 1-21 16-38 (41)
114 PF08274 PhnA_Zn_Ribbon: PhnA 79.3 0.56 1.2E-05 20.2 -0.1 10 53-62 18-27 (30)
115 PF13240 zinc_ribbon_2: zinc-r 79.0 0.87 1.9E-05 18.2 0.4 8 1-8 2-9 (23)
116 COG1997 RPL43A Ribosomal prote 78.5 0.91 2E-05 24.8 0.5 13 81-93 52-64 (89)
117 PRK14890 putative Zn-ribbon RN 78.4 1.3 2.9E-05 22.3 1.0 34 25-63 24-57 (59)
118 PRK03824 hypA hydrogenase nick 78.1 0.79 1.7E-05 27.3 0.2 15 53-67 69-83 (135)
119 PF02176 zf-TRAF: TRAF-type zi 77.2 1.5 3.3E-05 21.8 1.1 19 69-87 25-43 (60)
120 PF03604 DNA_RNApol_7kD: DNA d 76.2 1.5 3.2E-05 19.2 0.8 10 82-91 17-26 (32)
121 PF04780 DUF629: Protein of un 76.1 2 4.3E-05 31.1 1.8 30 81-110 56-85 (466)
122 PF15269 zf-C2H2_7: Zinc-finge 74.9 2.6 5.7E-05 19.9 1.5 22 55-76 21-42 (54)
123 PF07800 DUF1644: Protein of u 74.7 17 0.00037 22.4 5.7 61 54-116 80-142 (162)
124 PF04959 ARS2: Arsenite-resist 73.9 1.4 3.1E-05 28.5 0.6 34 78-111 73-106 (214)
125 COG4957 Predicted transcriptio 73.7 1.5 3.3E-05 26.0 0.6 26 83-111 77-102 (148)
126 PF14353 CpXC: CpXC protein 73.0 0.13 2.8E-06 30.2 -4.0 14 27-40 39-52 (128)
127 KOG3408|consensus 72.8 2.8 6E-05 24.4 1.5 24 82-105 57-80 (129)
128 PRK09678 DNA-binding transcrip 72.4 0.77 1.7E-05 24.2 -0.7 41 55-97 2-44 (72)
129 COG4530 Uncharacterized protei 72.0 2.5 5.4E-05 24.2 1.2 12 53-64 25-36 (129)
130 TIGR00686 phnA alkylphosphonat 72.0 2.2 4.8E-05 24.3 1.0 12 26-37 19-30 (109)
131 KOG4377|consensus 71.5 3.4 7.3E-05 29.4 2.0 104 2-108 277-429 (480)
132 KOG4167|consensus 70.8 0.81 1.8E-05 34.7 -1.1 23 1-23 795-817 (907)
133 PTZ00255 60S ribosomal protein 70.8 1.2 2.7E-05 24.5 -0.2 31 54-94 36-66 (90)
134 PF08790 zf-LYAR: LYAR-type C2 69.7 0.7 1.5E-05 19.5 -1.0 19 83-102 1-19 (28)
135 PRK10220 hypothetical protein; 69.6 3 6.5E-05 23.8 1.2 11 27-37 21-31 (111)
136 KOG1280|consensus 68.9 5.6 0.00012 27.7 2.5 32 80-111 77-108 (381)
137 PF01780 Ribosomal_L37ae: Ribo 68.2 0.97 2.1E-05 24.9 -0.9 30 54-93 35-64 (90)
138 KOG0717|consensus 67.9 3.1 6.6E-05 30.1 1.2 22 83-104 293-314 (508)
139 PF13451 zf-trcl: Probable zin 67.6 5.1 0.00011 19.4 1.6 38 53-90 3-41 (49)
140 PRK14873 primosome assembly pr 67.5 1.5 3.3E-05 33.3 -0.3 47 28-91 385-431 (665)
141 KOG4167|consensus 67.1 1.9 4.1E-05 32.9 0.1 29 81-109 791-819 (907)
142 KOG2593|consensus 66.4 7.9 0.00017 27.8 2.9 39 22-63 124-162 (436)
143 PF07282 OrfB_Zn_ribbon: Putat 66.2 9.9 0.00021 19.5 2.7 13 54-66 46-58 (69)
144 COG2879 Uncharacterized small 65.7 8.6 0.00019 19.6 2.2 21 93-113 23-43 (65)
145 PRK14714 DNA polymerase II lar 65.4 7.1 0.00015 32.0 2.8 50 27-90 668-717 (1337)
146 TIGR00280 L37a ribosomal prote 65.4 1.5 3.3E-05 24.2 -0.5 31 54-94 35-65 (91)
147 KOG3408|consensus 64.5 4.9 0.00011 23.5 1.4 27 50-76 53-79 (129)
148 TIGR00100 hypA hydrogenase nic 63.4 3.6 7.8E-05 23.8 0.8 24 55-90 71-94 (115)
149 TIGR00595 priA primosomal prot 62.2 2.4 5.3E-05 31.1 -0.1 47 28-90 215-261 (505)
150 PRK00432 30S ribosomal protein 62.2 3.6 7.8E-05 20.0 0.5 10 82-91 37-46 (50)
151 COG1655 Uncharacterized protei 61.7 1.5 3.4E-05 28.5 -1.0 8 83-90 63-70 (267)
152 PRK12380 hydrogenase nickel in 61.4 4.5 9.8E-05 23.3 0.9 24 55-90 71-94 (113)
153 PRK03976 rpl37ae 50S ribosomal 60.2 2 4.4E-05 23.7 -0.6 31 54-94 36-66 (90)
154 TIGR01206 lysW lysine biosynth 60.1 4.2 9.1E-05 20.1 0.6 10 55-64 3-12 (54)
155 COG1773 Rubredoxin [Energy pro 59.2 3.5 7.7E-05 20.5 0.2 12 82-93 3-14 (55)
156 PF02891 zf-MIZ: MIZ/SP-RING z 59.2 3.5 7.5E-05 20.0 0.2 8 83-90 42-49 (50)
157 COG1656 Uncharacterized conser 58.9 6.3 0.00014 24.4 1.3 43 55-99 98-147 (165)
158 PF13453 zf-TFIIB: Transcripti 58.8 4.1 8.8E-05 18.7 0.4 17 55-71 20-36 (41)
159 PF10013 DUF2256: Uncharacteri 58.3 3 6.4E-05 19.5 -0.1 13 84-96 10-22 (42)
160 PF14311 DUF4379: Domain of un 57.4 9.1 0.0002 18.7 1.5 12 55-66 29-40 (55)
161 KOG2636|consensus 57.1 8.3 0.00018 27.8 1.8 37 74-110 393-433 (497)
162 smart00154 ZnF_AN1 AN1-like Zi 56.4 4.9 0.00011 18.3 0.4 12 82-93 12-23 (39)
163 PRK00564 hypA hydrogenase nick 56.1 5.6 0.00012 23.1 0.7 25 55-90 72-96 (117)
164 COG1675 TFA1 Transcription ini 55.9 16 0.00034 23.0 2.6 31 51-90 110-140 (176)
165 smart00661 RPOL9 RNA polymeras 55.9 6.7 0.00015 18.7 0.9 10 82-91 20-29 (52)
166 PLN02294 cytochrome c oxidase 55.2 5.6 0.00012 24.7 0.7 16 79-94 138-153 (174)
167 PF01363 FYVE: FYVE zinc finge 53.8 5.9 0.00013 20.3 0.5 9 28-36 11-19 (69)
168 PF13824 zf-Mss51: Zinc-finger 53.3 13 0.00028 18.5 1.6 14 24-37 12-25 (55)
169 PF10276 zf-CHCC: Zinc-finger 53.1 4.1 8.9E-05 18.8 -0.1 11 82-92 29-39 (40)
170 PF04423 Rad50_zn_hook: Rad50 52.7 5 0.00011 19.6 0.1 11 84-94 22-32 (54)
171 PRK03681 hypA hydrogenase nick 52.4 5.1 0.00011 23.1 0.2 25 55-90 71-95 (114)
172 cd00924 Cyt_c_Oxidase_Vb Cytoc 52.2 6.6 0.00014 22.0 0.6 14 80-93 77-90 (97)
173 PF14446 Prok-RING_1: Prokaryo 50.9 6.1 0.00013 19.6 0.3 10 28-37 7-16 (54)
174 KOG2857|consensus 50.4 16 0.00034 22.1 1.9 21 83-103 18-38 (157)
175 COG1571 Predicted DNA-binding 50.3 11 0.00024 27.1 1.6 29 28-67 352-380 (421)
176 KOG1842|consensus 49.4 13 0.00028 27.0 1.7 29 82-110 15-43 (505)
177 PF01428 zf-AN1: AN1-like Zinc 49.2 4.5 9.7E-05 18.8 -0.3 13 81-93 12-24 (43)
178 COG3091 SprT Zn-dependent meta 49.1 8.1 0.00017 23.6 0.6 32 54-90 117-148 (156)
179 KOG4118|consensus 49.1 14 0.0003 19.1 1.4 30 82-111 38-67 (74)
180 COG1998 RPS31 Ribosomal protei 48.9 9.3 0.0002 18.5 0.7 8 83-90 38-45 (51)
181 smart00440 ZnF_C2C2 C2C2 Zinc 48.5 2.1 4.5E-05 19.7 -1.5 9 83-91 29-37 (40)
182 PF01155 HypA: Hydrogenase exp 48.3 7 0.00015 22.5 0.3 25 55-91 71-95 (113)
183 PF00301 Rubredoxin: Rubredoxi 48.1 6.1 0.00013 18.9 0.0 12 83-94 2-13 (47)
184 KOG1994|consensus 48.0 15 0.00033 24.1 1.7 21 53-73 238-258 (268)
185 COG4888 Uncharacterized Zn rib 47.8 3 6.5E-05 23.4 -1.2 8 27-34 23-30 (104)
186 PF07975 C1_4: TFIIH C1-like d 47.8 3.9 8.4E-05 20.0 -0.7 22 82-103 21-42 (51)
187 PF12760 Zn_Tnp_IS1595: Transp 47.1 32 0.00069 16.1 2.5 8 83-90 19-26 (46)
188 KOG2907|consensus 46.9 7.9 0.00017 22.3 0.4 38 27-66 75-114 (116)
189 cd00730 rubredoxin Rubredoxin; 46.5 7.5 0.00016 18.9 0.2 11 83-93 2-12 (50)
190 KOG1280|consensus 45.3 23 0.00049 24.9 2.3 24 55-78 80-103 (381)
191 cd00065 FYVE FYVE domain; Zinc 45.1 15 0.00032 17.9 1.2 9 29-37 5-13 (57)
192 COG1326 Uncharacterized archae 44.8 22 0.00048 22.7 2.1 10 55-64 31-40 (201)
193 smart00064 FYVE Protein presen 44.7 13 0.00027 19.0 0.9 10 28-37 12-21 (68)
194 COG1327 Predicted transcriptio 44.3 5 0.00011 24.4 -0.7 14 27-40 29-42 (156)
195 PRK00420 hypothetical protein; 43.4 16 0.00035 21.1 1.2 9 83-91 41-49 (112)
196 KOG4727|consensus 43.2 12 0.00027 23.3 0.8 23 82-104 75-97 (193)
197 PF14787 zf-CCHC_5: GAG-polypr 42.8 9.2 0.0002 17.2 0.2 10 84-93 4-13 (36)
198 KOG2593|consensus 42.5 21 0.00046 25.7 2.0 35 52-89 126-160 (436)
199 PF05191 ADK_lid: Adenylate ki 42.4 8.4 0.00018 17.3 0.0 11 83-93 2-12 (36)
200 PF04780 DUF629: Protein of un 42.1 22 0.00048 26.0 2.0 22 55-76 58-79 (466)
201 COG5188 PRP9 Splicing factor 3 40.8 21 0.00046 25.1 1.7 30 74-103 366-396 (470)
202 COG3677 Transposase and inacti 40.8 12 0.00026 22.2 0.5 16 80-95 51-66 (129)
203 PRK00762 hypA hydrogenase nick 40.6 11 0.00023 22.2 0.3 30 55-90 71-100 (124)
204 PF06524 NOA36: NOA36 protein; 40.4 8.4 0.00018 25.8 -0.2 21 78-98 205-225 (314)
205 COG1594 RPB9 DNA-directed RNA 40.1 4.9 0.00011 23.2 -1.2 12 82-93 100-111 (113)
206 COG4391 Uncharacterized protei 39.7 13 0.00028 18.9 0.5 14 81-94 47-60 (62)
207 PF05495 zf-CHY: CHY zinc fing 39.4 5.4 0.00012 20.9 -1.0 57 27-91 11-70 (71)
208 PRK05580 primosome assembly pr 39.3 9 0.0002 29.4 -0.2 9 82-90 421-429 (679)
209 COG0675 Transposase and inacti 39.1 30 0.00065 23.6 2.3 10 81-90 321-330 (364)
210 TIGR01562 FdhE formate dehydro 39.0 18 0.00039 24.9 1.2 9 28-36 186-194 (305)
211 KOG0978|consensus 38.8 12 0.00026 28.8 0.4 17 81-97 677-693 (698)
212 PF01927 Mut7-C: Mut7-C RNAse 38.7 12 0.00025 22.7 0.2 44 55-98 92-140 (147)
213 PF04810 zf-Sec23_Sec24: Sec23 37.6 5.9 0.00013 18.1 -0.9 11 52-62 22-32 (40)
214 PF10263 SprT-like: SprT-like 37.2 8.2 0.00018 23.3 -0.6 32 54-93 123-154 (157)
215 COG0068 HypF Hydrogenase matur 36.6 5.3 0.00011 30.6 -1.7 29 28-62 153-181 (750)
216 PF08209 Sgf11: Sgf11 (transcr 36.3 21 0.00045 15.7 0.8 19 27-46 5-23 (33)
217 PF15616 TerY-C: TerY-C metal 36.1 4.6 9.9E-05 24.0 -1.7 37 28-64 79-115 (131)
218 PF12773 DZR: Double zinc ribb 35.6 23 0.00049 16.7 0.9 26 27-63 13-38 (50)
219 PF06220 zf-U1: U1 zinc finger 34.9 34 0.00074 15.4 1.4 10 83-92 4-13 (38)
220 PF11931 DUF3449: Domain of un 34.7 13 0.00028 23.8 0.0 26 77-102 96-122 (196)
221 PF04438 zf-HIT: HIT zinc fing 34.4 16 0.00035 15.5 0.3 12 82-93 13-24 (30)
222 KOG1842|consensus 33.8 26 0.00057 25.5 1.3 23 1-23 18-40 (505)
223 PLN02748 tRNA dimethylallyltra 33.7 30 0.00065 25.5 1.6 25 81-105 417-442 (468)
224 PHA02998 RNA polymerase subuni 33.5 5.1 0.00011 25.1 -1.8 36 55-94 144-183 (195)
225 PF02591 DUF164: Putative zinc 33.2 36 0.00078 16.7 1.5 11 80-90 44-54 (56)
226 PF12230 PRP21_like_P: Pre-mRN 33.2 14 0.00031 24.1 0.0 24 55-79 169-192 (229)
227 PF09963 DUF2197: Uncharacteri 32.8 19 0.00042 18.0 0.4 11 54-64 31-41 (56)
228 PRK12496 hypothetical protein; 32.7 34 0.00075 21.2 1.6 25 55-91 128-152 (164)
229 PF01215 COX5B: Cytochrome c o 32.5 12 0.00026 22.4 -0.4 15 80-94 110-124 (136)
230 TIGR01384 TFS_arch transcripti 32.0 21 0.00046 20.0 0.6 26 1-38 3-28 (104)
231 COG3364 Zn-ribbon containing p 31.9 25 0.00054 20.0 0.8 27 54-90 2-28 (112)
232 PF11789 zf-Nse: Zinc-finger o 31.9 23 0.00049 17.7 0.6 31 53-87 23-53 (57)
233 PF08792 A2L_zn_ribbon: A2L zi 31.8 19 0.00041 15.8 0.3 10 83-92 22-31 (33)
234 COG5112 UFD2 U1-like Zn-finger 31.7 29 0.00064 19.8 1.1 21 83-103 56-76 (126)
235 PF14369 zf-RING_3: zinc-finge 31.6 22 0.00048 15.7 0.5 8 1-8 24-31 (35)
236 PTZ00448 hypothetical protein; 31.6 36 0.00077 24.2 1.7 24 82-105 314-337 (373)
237 KOG0717|consensus 31.4 34 0.00073 25.1 1.5 22 55-76 293-314 (508)
238 PTZ00043 cytochrome c oxidase 31.4 24 0.00052 23.2 0.8 16 79-94 178-193 (268)
239 PRK05452 anaerobic nitric oxid 31.3 12 0.00027 27.4 -0.6 38 52-90 423-466 (479)
240 PRK12860 transcriptional activ 31.1 32 0.00068 22.0 1.3 27 27-61 135-161 (189)
241 PF11672 DUF3268: Protein of u 30.9 18 0.00039 20.5 0.2 10 26-35 2-11 (102)
242 PRK12722 transcriptional activ 30.5 33 0.00072 21.8 1.3 28 27-62 135-162 (187)
243 PF07295 DUF1451: Protein of u 29.9 22 0.00047 21.7 0.4 30 53-92 111-140 (146)
244 PF08271 TF_Zn_Ribbon: TFIIB z 29.8 22 0.00048 16.3 0.3 9 83-91 1-9 (43)
245 PF10122 Mu-like_Com: Mu-like 29.4 14 0.0003 18.0 -0.4 30 54-91 4-33 (51)
246 KOG3214|consensus 29.3 15 0.00032 20.7 -0.3 13 82-94 47-59 (109)
247 COG4896 Uncharacterized protei 29.1 28 0.00061 17.7 0.7 8 27-34 32-39 (68)
248 PRK14559 putative protein seri 28.8 70 0.0015 24.7 2.9 12 84-95 43-54 (645)
249 PF11023 DUF2614: Protein of u 28.6 36 0.00077 19.7 1.1 12 24-35 67-78 (114)
250 PF02748 PyrI_C: Aspartate car 28.5 22 0.00048 17.4 0.2 17 78-94 31-47 (52)
251 PF09855 DUF2082: Nucleic-acid 28.3 24 0.00053 18.1 0.4 8 83-90 1-8 (64)
252 KOG1088|consensus 28.2 25 0.00054 20.5 0.4 21 76-96 92-112 (124)
253 COG3880 Modulator of heat shoc 27.7 13 0.00029 23.1 -0.8 32 26-67 74-105 (176)
254 PF06397 Desulfoferrod_N: Desu 27.6 28 0.0006 15.7 0.5 11 54-64 6-16 (36)
255 smart00731 SprT SprT homologue 27.6 24 0.00053 21.2 0.3 32 54-92 112-143 (146)
256 PF11494 Ta0938: Ta0938; Inte 27.3 28 0.0006 19.5 0.5 37 25-67 13-50 (105)
257 KOG0402|consensus 27.2 18 0.00038 19.7 -0.3 13 81-93 53-65 (92)
258 PF03811 Zn_Tnp_IS1: InsA N-te 27.1 9.6 0.00021 17.1 -1.1 7 82-88 29-35 (36)
259 PRK04351 hypothetical protein; 26.5 34 0.00075 20.9 0.9 31 55-93 113-143 (149)
260 COG4338 Uncharacterized protei 26.4 23 0.0005 17.0 0.1 15 28-42 14-28 (54)
261 PF01286 XPA_N: XPA protein N- 26.1 25 0.00055 15.6 0.2 12 84-95 5-16 (34)
262 TIGR03826 YvyF flagellar opero 26.0 24 0.00052 21.2 0.1 11 84-94 5-15 (137)
263 PF03966 Trm112p: Trm112p-like 25.9 21 0.00046 18.3 -0.1 17 77-93 48-64 (68)
264 PF14255 Cys_rich_CPXG: Cystei 25.5 28 0.00061 17.1 0.3 9 84-92 2-10 (52)
265 PLN03238 probable histone acet 25.4 85 0.0018 21.6 2.6 25 80-104 46-70 (290)
266 KOG2071|consensus 25.1 53 0.0012 24.9 1.7 28 78-105 414-441 (579)
267 PF11238 DUF3039: Protein of u 24.9 30 0.00064 17.4 0.3 7 31-37 30-36 (58)
268 TIGR03829 YokU_near_AblA uncha 24.5 51 0.0011 18.3 1.2 13 1-13 38-50 (89)
269 PF04606 Ogr_Delta: Ogr/Delta- 24.4 10 0.00022 18.0 -1.4 12 82-93 25-38 (47)
270 COG3809 Uncharacterized protei 24.0 67 0.0015 17.3 1.5 21 1-21 24-44 (88)
271 PRK01343 zinc-binding protein; 23.2 36 0.00078 17.1 0.4 12 82-93 9-20 (57)
272 TIGR00244 transcriptional regu 23.2 32 0.00069 21.0 0.3 14 82-95 28-41 (147)
273 PRK06260 threonine synthase; V 23.1 57 0.0012 23.3 1.5 11 27-37 4-14 (397)
274 PF01096 TFIIS_C: Transcriptio 22.9 27 0.00058 15.8 -0.1 10 83-92 29-38 (39)
275 PF09082 DUF1922: Domain of un 22.7 18 0.00039 18.9 -0.7 11 80-91 18-28 (68)
276 KOG0562|consensus 22.7 58 0.0013 20.4 1.3 29 80-108 151-179 (184)
277 KOG2932|consensus 22.7 1.6E+02 0.0034 20.7 3.4 31 77-107 139-172 (389)
278 COG1439 Predicted nucleic acid 22.7 41 0.00089 21.2 0.7 24 54-91 139-162 (177)
279 PF04216 FdhE: Protein involve 22.6 17 0.00037 24.7 -1.1 53 23-90 194-246 (290)
280 PF13821 DUF4187: Domain of un 22.5 43 0.00094 16.6 0.6 17 83-99 28-44 (55)
281 PF14375 Cys_rich_CWC: Cystein 22.3 49 0.0011 15.9 0.8 10 1-10 1-10 (50)
282 KOG3352|consensus 22.2 40 0.00086 20.7 0.5 15 79-93 130-144 (153)
283 PRK05978 hypothetical protein; 21.9 34 0.00074 20.9 0.2 12 56-67 54-65 (148)
284 PF14690 zf-ISL3: zinc-finger 21.9 44 0.00095 15.4 0.6 9 82-90 2-10 (47)
285 COG3478 Predicted nucleic-acid 21.7 46 0.001 17.2 0.6 9 82-90 4-12 (68)
286 PF04328 DUF466: Protein of un 21.5 96 0.0021 16.0 1.8 17 97-113 27-43 (65)
287 TIGR03831 YgiT_finger YgiT-typ 21.4 39 0.00084 15.3 0.3 10 55-64 33-42 (46)
288 KOG4124|consensus 21.2 28 0.0006 24.5 -0.3 33 78-111 209-241 (442)
289 TIGR00515 accD acetyl-CoA carb 20.2 44 0.00096 22.8 0.5 32 27-67 27-58 (285)
No 1
>KOG2462|consensus
Probab=99.96 E-value=2.4e-29 Score=159.02 Aligned_cols=116 Identities=40% Similarity=0.760 Sum_probs=93.3
Q ss_pred CCcCccccCChHHHHHHHHHcCC---CCCccCcccccccCChhhHHHHHHhhcCCCceeccccccccCChhHHHHHHHHc
Q psy2643 1 CKQCGKTFKRSSTLSTHLLIHSD---TRPYPCQYCGKRFHQKSDMKKHTYIHTGEKPHKCVVCGKAFSQSSNLITHLRKH 77 (134)
Q Consensus 1 C~~C~~~f~~~~~l~~h~~~~~~---~~~~~c~~C~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~~~~~~~l~~h~~~~ 77 (134)
|++||+.+.+.++|..|.++|-. .+.+.|++|++.+.+...|.+|+++|. -+.+|.+||+.|.+++.|+.|+++|
T Consensus 133 c~eCgk~ysT~snLsrHkQ~H~~~~s~ka~~C~~C~K~YvSmpALkMHirTH~--l~c~C~iCGKaFSRPWLLQGHiRTH 210 (279)
T KOG2462|consen 133 CPECGKSYSTSSNLSRHKQTHRSLDSKKAFSCKYCGKVYVSMPALKMHIRTHT--LPCECGICGKAFSRPWLLQGHIRTH 210 (279)
T ss_pred ccccccccccccccchhhcccccccccccccCCCCCceeeehHHHhhHhhccC--CCcccccccccccchHHhhcccccc
Confidence 67888888888888888887743 455788888888888888888888776 4678888888888888888888888
Q ss_pred CCCCCcccCcchhhccChHHHHHHHHhhCCCCCCcccccCC
Q psy2643 78 TGYKPFSCGLCDKAFQRKVDLRRHRESQHPGSPAQQHHISS 118 (134)
Q Consensus 78 ~~~~~~~C~~C~~~f~~~~~l~~H~~~~h~~~~~~~~~~~~ 118 (134)
+|||||.|+.|+|+|+++++|+.||++|...+.+++.....
T Consensus 211 TGEKPF~C~hC~kAFADRSNLRAHmQTHS~~K~~qC~~C~K 251 (279)
T KOG2462|consen 211 TGEKPFSCPHCGKAFADRSNLRAHMQTHSDVKKHQCPRCGK 251 (279)
T ss_pred cCCCCccCCcccchhcchHHHHHHHHhhcCCccccCcchhh
Confidence 88888888888888888888888888888888877665443
No 2
>KOG2462|consensus
Probab=99.95 E-value=2.2e-28 Score=154.65 Aligned_cols=104 Identities=40% Similarity=0.762 Sum_probs=99.7
Q ss_pred CCcCccccCChHHHHHHHHHcCCCCCccCcccccccCChhhHHHHHHhhcCCCceeccccccccCChhHHHHHHHHcCCC
Q psy2643 1 CKQCGKTFKRSSTLSTHLLIHSDTRPYPCQYCGKRFHQKSDMKKHTYIHTGEKPHKCVVCGKAFSQSSNLITHLRKHTGY 80 (134)
Q Consensus 1 C~~C~~~f~~~~~l~~h~~~~~~~~~~~c~~C~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~~~~~~~l~~h~~~~~~~ 80 (134)
|..||++|.....|..|+++|+ .+..|.+||+.|...+-|+.|+++|+|++||.|+.|++.|.+.++|+.|+++|.+.
T Consensus 164 C~~C~K~YvSmpALkMHirTH~--l~c~C~iCGKaFSRPWLLQGHiRTHTGEKPF~C~hC~kAFADRSNLRAHmQTHS~~ 241 (279)
T KOG2462|consen 164 CKYCGKVYVSMPALKMHIRTHT--LPCECGICGKAFSRPWLLQGHIRTHTGEKPFSCPHCGKAFADRSNLRAHMQTHSDV 241 (279)
T ss_pred CCCCCceeeehHHHhhHhhccC--CCcccccccccccchHHhhcccccccCCCCccCCcccchhcchHHHHHHHHhhcCC
Confidence 8899999999999999999997 57999999999999999999999999999999999999999999999999999999
Q ss_pred CCcccCcchhhccChHHHHHHHHhhC
Q psy2643 81 KPFSCGLCDKAFQRKVDLRRHRESQH 106 (134)
Q Consensus 81 ~~~~C~~C~~~f~~~~~l~~H~~~~h 106 (134)
|.|+|..|+|.|+..+.|.+|.....
T Consensus 242 K~~qC~~C~KsFsl~SyLnKH~ES~C 267 (279)
T KOG2462|consen 242 KKHQCPRCGKSFALKSYLNKHSESAC 267 (279)
T ss_pred ccccCcchhhHHHHHHHHHHhhhhcc
Confidence 99999999999999999999986543
No 3
>KOG1074|consensus
Probab=99.80 E-value=1.3e-20 Score=134.11 Aligned_cols=58 Identities=36% Similarity=0.792 Sum_probs=52.6
Q ss_pred eeccccccccCChhHHHHHHHHcCCCCCcccCcchhhccChHHHHHHHHhhCCCCCCc
Q psy2643 55 HKCVVCGKAFSQSSNLITHLRKHTGYKPFSCGLCDKAFQRKVDLRRHRESQHPGSPAQ 112 (134)
Q Consensus 55 ~~C~~C~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~~h~~~~~~ 112 (134)
-.|.+|.++..-...|+.|.++|+||+||+|.+||++|+++.+|+.|+..|-...+..
T Consensus 606 NqCiiC~rVlSC~saLqmHyrtHtGERPFkCKiCgRAFtTkGNLkaH~~vHka~p~~R 663 (958)
T KOG1074|consen 606 NQCIICLRVLSCPSALQMHYRTHTGERPFKCKICGRAFTTKGNLKAHMSVHKAKPPAR 663 (958)
T ss_pred cceeeeeecccchhhhhhhhhcccCcCccccccccchhccccchhhcccccccCcccc
Confidence 3799999999999999999999999999999999999999999999998776655443
No 4
>KOG3576|consensus
Probab=99.75 E-value=2.4e-19 Score=109.47 Aligned_cols=112 Identities=40% Similarity=0.712 Sum_probs=98.6
Q ss_pred CCcCccccCChHHHHHHHHHcCCCCCccCcccccccCChhhHHHHHHhhcCCCceeccccccccCChhHHHHHHHHcC--
Q psy2643 1 CKQCGKTFKRSSTLSTHLLIHSDTRPYPCQYCGKRFHQKSDMKKHTYIHTGEKPHKCVVCGKAFSQSSNLITHLRKHT-- 78 (134)
Q Consensus 1 C~~C~~~f~~~~~l~~h~~~~~~~~~~~c~~C~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~~~~~~~l~~h~~~~~-- 78 (134)
|..|++.|.....|..|++.|...+.+.|-.||+.|.....|.+|.+.|++-+||+|..|++.|...-.|..|++.-+
T Consensus 120 CrvCgK~F~lQRmlnrh~kch~~vkr~lct~cgkgfndtfdlkrh~rthtgvrpykc~~c~kaftqrcsleshl~kvhgv 199 (267)
T KOG3576|consen 120 CRVCGKKFGLQRMLNRHLKCHSDVKRHLCTFCGKGFNDTFDLKRHTRTHTGVRPYKCSLCEKAFTQRCSLESHLKKVHGV 199 (267)
T ss_pred eehhhhhhhHHHHHHHHhhhccHHHHHHHhhccCcccchhhhhhhhccccCccccchhhhhHHHHhhccHHHHHHHHcCc
Confidence 788999999999999999999999999999999999999999999999999999999999999999999999987433
Q ss_pred ---------CCCCcccCcchhhccChHHHHHHHHhhCCCCCCc
Q psy2643 79 ---------GYKPFSCGLCDKAFQRKVDLRRHRESQHPGSPAQ 112 (134)
Q Consensus 79 ---------~~~~~~C~~C~~~f~~~~~l~~H~~~~h~~~~~~ 112 (134)
.++.|.|..||.+-.....+..|++.+|+..++-
T Consensus 200 ~~~yaykerr~kl~vcedcg~t~~~~e~~~~h~~~~hp~Spal 242 (267)
T KOG3576|consen 200 QHQYAYKERRAKLYVCEDCGYTSERPEVYYLHLKLHHPFSPAL 242 (267)
T ss_pred hHHHHHHHhhhheeeecccCCCCCChhHHHHHHHhcCCCCHHH
Confidence 3567999999988888888889999999887663
No 5
>KOG3623|consensus
Probab=99.71 E-value=3.1e-18 Score=120.94 Aligned_cols=105 Identities=31% Similarity=0.698 Sum_probs=93.7
Q ss_pred CCcCccccCChHHHHHHHHHcCC--CCCccCcccccccCChhhHHHHHHhhcC-------------CCceeccccccccC
Q psy2643 1 CKQCGKTFKRSSTLSTHLLIHSD--TRPYPCQYCGKRFHQKSDMKKHTYIHTG-------------EKPHKCVVCGKAFS 65 (134)
Q Consensus 1 C~~C~~~f~~~~~l~~h~~~~~~--~~~~~c~~C~~~~~~~~~l~~h~~~~~~-------------~~~~~C~~C~~~~~ 65 (134)
|++|.+.+.....|+.|++..+. +..|.|+.|..+|.....|.+|+..|.. -+.|+|..|++.|.
T Consensus 213 cpycdrgykrltslkeHikyrhekne~nfsC~lCsytFAyRtQLErhm~~hkpg~dqa~sltqsa~lRKFKCtECgKAFK 292 (1007)
T KOG3623|consen 213 CPYCDRGYKRLTSLKEHIKYRHEKNEPNFSCMLCSYTFAYRTQLERHMQLHKPGGDQAISLTQSALLRKFKCTECGKAFK 292 (1007)
T ss_pred chhHHHHHHHHHHHHHHHHHHHhhCCCCCcchhhhhhhhhHHHHHHHHHhhcCCCcccccccchhhhccccccccchhhh
Confidence 78999999999999999977543 3458999999999999999999988753 34599999999999
Q ss_pred ChhHHHHHHHHcCCCCCcccCcchhhccChHHHHHHHHhh
Q psy2643 66 QSSNLITHLRKHTGYKPFSCGLCDKAFQRKVDLRRHRESQ 105 (134)
Q Consensus 66 ~~~~l~~h~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~~ 105 (134)
.+-.|+.|+++|.|||||.|+.|+|.|+...++..||..+
T Consensus 293 fKHHLKEHlRIHSGEKPfeCpnCkKRFSHSGSySSHmSSK 332 (1007)
T KOG3623|consen 293 FKHHLKEHLRIHSGEKPFECPNCKKRFSHSGSYSSHMSSK 332 (1007)
T ss_pred hHHHHHhhheeecCCCCcCCcccccccccCCccccccccc
Confidence 9999999999999999999999999999999999998544
No 6
>KOG1074|consensus
Probab=99.70 E-value=1.3e-17 Score=119.09 Aligned_cols=59 Identities=41% Similarity=0.767 Sum_probs=55.7
Q ss_pred eccccccccCChhHHHHHHHHcCCCCCcccCcchhhccChHHHHHHHHhhCCCCCCccc
Q psy2643 56 KCVVCGKAFSQSSNLITHLRKHTGYKPFSCGLCDKAFQRKVDLRRHRESQHPGSPAQQH 114 (134)
Q Consensus 56 ~C~~C~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~~h~~~~~~~~ 114 (134)
.|.+|++.|...+.|..|+++|+++|+|.|..|++.|..+..|+.||.+|+-..+....
T Consensus 881 ~C~vCgk~FsSSsALqiH~rTHtg~KPF~C~fC~~aFttrgnLKvHMgtH~w~q~~srr 939 (958)
T KOG1074|consen 881 VCNVCGKQFSSSAALEIHMRTHTGPKPFFCHFCEEAFTTRGNLKVHMGTHMWVQPPSRR 939 (958)
T ss_pred hhccchhcccchHHHHHhhhcCCCCCCccchhhhhhhhhhhhhhhhhccccccCCCccC
Confidence 69999999999999999999999999999999999999999999999999888877654
No 7
>KOG3623|consensus
Probab=99.65 E-value=6e-17 Score=114.55 Aligned_cols=80 Identities=36% Similarity=0.828 Sum_probs=76.6
Q ss_pred CCCccCcccccccCChhhHHHHHHhhcCCCceeccccccccCChhHHHHHHHHcCCCCCcccCcchhhccChHHHHHHHH
Q psy2643 24 TRPYPCQYCGKRFHQKSDMKKHTYIHTGEKPHKCVVCGKAFSQSSNLITHLRKHTGYKPFSCGLCDKAFQRKVDLRRHRE 103 (134)
Q Consensus 24 ~~~~~c~~C~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~ 103 (134)
...|.|..|+++|.-.+.|.+|...|.|++||.|.+|.+.|..+-.|..|.+.|.|||||+|..|+|.|+...++..||.
T Consensus 892 ~gmyaCDqCDK~FqKqSSLaRHKYEHsGqRPyqC~iCkKAFKHKHHLtEHkRLHSGEKPfQCdKClKRFSHSGSYSQHMN 971 (1007)
T KOG3623|consen 892 DGMYACDQCDKAFQKQSSLARHKYEHSGQRPYQCIICKKAFKHKHHLTEHKRLHSGEKPFQCDKCLKRFSHSGSYSQHMN 971 (1007)
T ss_pred cccchHHHHHHHHHhhHHHHHhhhhhcCCCCcccchhhHhhhhhhhhhhhhhhccCCCcchhhhhhhhcccccchHhhhc
Confidence 34599999999999999999999999999999999999999999999999999999999999999999999999999985
No 8
>KOG3576|consensus
Probab=99.63 E-value=6.2e-17 Score=98.99 Aligned_cols=86 Identities=35% Similarity=0.789 Sum_probs=80.9
Q ss_pred CCCccCcccccccCChhhHHHHHHhhcCCCceeccccccccCChhHHHHHHHHcCCCCCcccCcchhhccChHHHHHHHH
Q psy2643 24 TRPYPCQYCGKRFHQKSDMKKHTYIHTGEKPHKCVVCGKAFSQSSNLITHLRKHTGYKPFSCGLCDKAFQRKVDLRRHRE 103 (134)
Q Consensus 24 ~~~~~c~~C~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~ 103 (134)
...+.|.+|++.|....-|.+|+.-|...+.+-|..||+.|.+--+|++|+++|+|.+||+|..|+|+|+.+-+|..|.+
T Consensus 115 ~d~ftCrvCgK~F~lQRmlnrh~kch~~vkr~lct~cgkgfndtfdlkrh~rthtgvrpykc~~c~kaftqrcsleshl~ 194 (267)
T KOG3576|consen 115 QDSFTCRVCGKKFGLQRMLNRHLKCHSDVKRHLCTFCGKGFNDTFDLKRHTRTHTGVRPYKCSLCEKAFTQRCSLESHLK 194 (267)
T ss_pred CCeeeeehhhhhhhHHHHHHHHhhhccHHHHHHHhhccCcccchhhhhhhhccccCccccchhhhhHHHHhhccHHHHHH
Confidence 44589999999999999999999999998999999999999999999999999999999999999999999999999998
Q ss_pred hhCCCC
Q psy2643 104 SQHPGS 109 (134)
Q Consensus 104 ~~h~~~ 109 (134)
..|+..
T Consensus 195 kvhgv~ 200 (267)
T KOG3576|consen 195 KVHGVQ 200 (267)
T ss_pred HHcCch
Confidence 888765
No 9
>KOG3608|consensus
Probab=99.58 E-value=2.5e-15 Score=98.81 Aligned_cols=115 Identities=30% Similarity=0.535 Sum_probs=77.3
Q ss_pred cCccccCChHHHHHHHHHcCCCCCccCcccccccCChhhHHHHHHhhcC--C--------------------------Cc
Q psy2643 3 QCGKTFKRSSTLSTHLLIHSDTRPYPCQYCGKRFHQKSDMKKHTYIHTG--E--------------------------KP 54 (134)
Q Consensus 3 ~C~~~f~~~~~l~~h~~~~~~~~~~~c~~C~~~~~~~~~l~~h~~~~~~--~--------------------------~~ 54 (134)
.|-+.|.++..|+.|+++|++++-..|+.||.-|.....|--|++-.+. . .-
T Consensus 184 ~Ct~~~~~k~~LreH~r~Hs~eKvvACp~Cg~~F~~~tkl~DH~rRqt~l~~n~fqC~~C~KrFaTeklL~~Hv~rHvn~ 263 (467)
T KOG3608|consen 184 MCTKHMGNKYRLREHIRTHSNEKVVACPHCGELFRTKTKLFDHLRRQTELNTNSFQCAQCFKRFATEKLLKSHVVRHVNC 263 (467)
T ss_pred hhhhhhccHHHHHHHHHhcCCCeEEecchHHHHhccccHHHHHHHhhhhhcCCchHHHHHHHHHhHHHHHHHHHHHhhhc
Confidence 3556777777788888777777776677776666666555555543221 1 23
Q ss_pred eeccccccccCChhHHHHHHHH-cCCCCCcccCcchhhccChHHHHHHHHhhCCCCCCcccccCC
Q psy2643 55 HKCVVCGKAFSQSSNLITHLRK-HTGYKPFSCGLCDKAFQRKVDLRRHRESQHPGSPAQQHHISS 118 (134)
Q Consensus 55 ~~C~~C~~~~~~~~~l~~h~~~-~~~~~~~~C~~C~~~f~~~~~l~~H~~~~h~~~~~~~~~~~~ 118 (134)
|+|++|.-+....+.|..|++. |..++||+|..|.+.|...++|.+|...| ++.-+++.....
T Consensus 264 ykCplCdmtc~~~ssL~~H~r~rHs~dkpfKCd~Cd~~c~~esdL~kH~~~H-S~~~y~C~h~~C 327 (467)
T KOG3608|consen 264 YKCPLCDMTCSSASSLTTHIRYRHSKDKPFKCDECDTRCVRESDLAKHVQVH-SKTVYQCEHPDC 327 (467)
T ss_pred ccccccccCCCChHHHHHHHHhhhccCCCccccchhhhhccHHHHHHHHHhc-cccceecCCCCC
Confidence 6777777777777777777764 66778888888888888888888887744 455555544433
No 10
>KOG3608|consensus
Probab=99.55 E-value=2.2e-14 Score=94.45 Aligned_cols=110 Identities=26% Similarity=0.534 Sum_probs=78.6
Q ss_pred CCcCccccCChHHHHHHHHH-cCCCCCccCcccccccCChhhHHHHHHhhcCCCceeccc--cccccCChhHHHHHHHHc
Q psy2643 1 CKQCGKTFKRSSTLSTHLLI-HSDTRPYPCQYCGKRFHQKSDMKKHTYIHTGEKPHKCVV--CGKAFSQSSNLITHLRKH 77 (134)
Q Consensus 1 C~~C~~~f~~~~~l~~h~~~-~~~~~~~~c~~C~~~~~~~~~l~~h~~~~~~~~~~~C~~--C~~~~~~~~~l~~h~~~~ 77 (134)
|+.|+.+.+..+.|..|++. |...+||.|..|+..+...+.|++|...|. +..|.|.. |...+.....+.+|.+.+
T Consensus 266 CplCdmtc~~~ssL~~H~r~rHs~dkpfKCd~Cd~~c~~esdL~kH~~~HS-~~~y~C~h~~C~~s~r~~~q~~~H~~ev 344 (467)
T KOG3608|consen 266 CPLCDMTCSSASSLTTHIRYRHSKDKPFKCDECDTRCVRESDLAKHVQVHS-KTVYQCEHPDCHYSVRTYTQMRRHFLEV 344 (467)
T ss_pred ccccccCCCChHHHHHHHHhhhccCCCccccchhhhhccHHHHHHHHHhcc-ccceecCCCCCcHHHHHHHHHHHHHHHh
Confidence 66777777777777777765 455667777777777777777777776544 55677766 777777777777776653
Q ss_pred C-C--CCCcccCcchhhccChHHHHHHHHhhCCCCCC
Q psy2643 78 T-G--YKPFSCGLCDKAFQRKVDLRRHRESQHPGSPA 111 (134)
Q Consensus 78 ~-~--~~~~~C~~C~~~f~~~~~l~~H~~~~h~~~~~ 111 (134)
+ | +.+|.|..|.+.|++-.+|.+|.+..|+-+.+
T Consensus 345 hEg~np~~Y~CH~Cdr~ft~G~~L~~HL~kkH~f~~P 381 (467)
T KOG3608|consen 345 HEGNNPILYACHCCDRFFTSGKSLSAHLMKKHGFRLP 381 (467)
T ss_pred ccCCCCCceeeecchhhhccchhHHHHHHHhhcccCC
Confidence 3 3 34588888888888888888888777766544
No 11
>PLN03086 PRLI-interacting factor K; Provisional
Probab=99.43 E-value=7.7e-13 Score=93.28 Aligned_cols=101 Identities=22% Similarity=0.547 Sum_probs=82.1
Q ss_pred CCcCccccCChHHHHHHHHHcCCCCCccCcccccccCChhhHHHHHHhhcCCCceeccccccccCC----------hhHH
Q psy2643 1 CKQCGKTFKRSSTLSTHLLIHSDTRPYPCQYCGKRFHQKSDMKKHTYIHTGEKPHKCVVCGKAFSQ----------SSNL 70 (134)
Q Consensus 1 C~~C~~~f~~~~~l~~h~~~~~~~~~~~c~~C~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~~~~----------~~~l 70 (134)
|+.|++.|. ...|..|+..++ +++.|+ |+..+ ....|..|+..+...+++.|..|+..+.. ...|
T Consensus 456 C~~Cgk~f~-~s~LekH~~~~H--kpv~Cp-Cg~~~-~R~~L~~H~~thCp~Kpi~C~fC~~~v~~g~~~~d~~d~~s~L 530 (567)
T PLN03086 456 CEKCGQAFQ-QGEMEKHMKVFH--EPLQCP-CGVVL-EKEQMVQHQASTCPLRLITCRFCGDMVQAGGSAMDVRDRLRGM 530 (567)
T ss_pred CCCCCCccc-hHHHHHHHHhcC--CCccCC-CCCCc-chhHHHhhhhccCCCCceeCCCCCCccccCccccchhhhhhhH
Confidence 789999886 577999999875 688999 99755 55779999999999999999999988842 3478
Q ss_pred HHHHHHcCCCCCcccCcchhhccChHHHHHHHHhhCCC
Q psy2643 71 ITHLRKHTGYKPFSCGLCDKAFQRKVDLRRHRESQHPG 108 (134)
Q Consensus 71 ~~h~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~~h~~ 108 (134)
..|.... +.+++.|..||+.+..+ .+..|+...|..
T Consensus 531 t~HE~~C-G~rt~~C~~Cgk~Vrlr-dm~~H~~~~h~~ 566 (567)
T PLN03086 531 SEHESIC-GSRTAPCDSCGRSVMLK-EMDIHQIAVHQK 566 (567)
T ss_pred HHHHHhc-CCcceEccccCCeeeeh-hHHHHHHHhhcC
Confidence 8888874 88999999999887654 678898777653
No 12
>PHA00733 hypothetical protein
Probab=99.42 E-value=2.7e-13 Score=79.35 Aligned_cols=84 Identities=18% Similarity=0.253 Sum_probs=70.5
Q ss_pred CCCCccCcccccccCChhhHHHH--H---HhhcCCCceeccccccccCChhHHHHHHHHcCCCCCcccCcchhhccChHH
Q psy2643 23 DTRPYPCQYCGKRFHQKSDMKKH--T---YIHTGEKPHKCVVCGKAFSQSSNLITHLRKHTGYKPFSCGLCDKAFQRKVD 97 (134)
Q Consensus 23 ~~~~~~c~~C~~~~~~~~~l~~h--~---~~~~~~~~~~C~~C~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~f~~~~~ 97 (134)
.++++.|.+|+..|.....|..+ + ...++.++|.|..|+..|.....|..|++.+ +.+|.|+.|++.|.....
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 35678999999888887666555 1 1334578999999999999999999999976 457999999999999999
Q ss_pred HHHHHHhhCCC
Q psy2643 98 LRRHRESQHPG 108 (134)
Q Consensus 98 l~~H~~~~h~~ 108 (134)
|.+|+...|+.
T Consensus 115 L~~H~~~~h~~ 125 (128)
T PHA00733 115 TLDHVCKKHNI 125 (128)
T ss_pred HHHHHHHhcCc
Confidence 99999998874
No 13
>PHA02768 hypothetical protein; Provisional
Probab=99.12 E-value=2.9e-11 Score=59.45 Aligned_cols=44 Identities=27% Similarity=0.580 Sum_probs=36.2
Q ss_pred ceeccccccccCChhHHHHHHHHcCCCCCcccCcchhhccChHHHH
Q psy2643 54 PHKCVVCGKAFSQSSNLITHLRKHTGYKPFSCGLCDKAFQRKVDLR 99 (134)
Q Consensus 54 ~~~C~~C~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~f~~~~~l~ 99 (134)
.|.|+.||+.|.....|..|+++|+ ++|+|..|++.|...+.|.
T Consensus 5 ~y~C~~CGK~Fs~~~~L~~H~r~H~--k~~kc~~C~k~f~~~s~l~ 48 (55)
T PHA02768 5 GYECPICGEIYIKRKSMITHLRKHN--TNLKLSNCKRISLRTGEYI 48 (55)
T ss_pred ccCcchhCCeeccHHHHHHHHHhcC--CcccCCcccceecccceeE
Confidence 3788888888888888888888887 6788888998888776653
No 14
>KOG3993|consensus
Probab=99.06 E-value=4.1e-11 Score=80.86 Aligned_cols=50 Identities=22% Similarity=0.482 Sum_probs=38.3
Q ss_pred CCcCccccCChHHHHHHHHHcCCCCCccCcccccccCChhhHHHHHHhhc
Q psy2643 1 CKQCGKTFKRSSTLSTHLLIHSDTRPYPCQYCGKRFHQKSDMKKHTYIHT 50 (134)
Q Consensus 1 C~~C~~~f~~~~~l~~h~~~~~~~~~~~c~~C~~~~~~~~~l~~h~~~~~ 50 (134)
|..|...|.+.-.|.+|....+....|.|++|++.|.-..+|..|++.|.
T Consensus 270 CqLCK~kYeD~F~LAQHrC~RIV~vEYrCPEC~KVFsCPANLASHRRWHK 319 (500)
T KOG3993|consen 270 CQLCKEKYEDAFALAQHRCPRIVHVEYRCPECDKVFSCPANLASHRRWHK 319 (500)
T ss_pred HHHHHHhhhhHHHHhhccCCeeEEeeecCCcccccccCchhhhhhhcccC
Confidence 56777777777778888776666677888888888888888888877664
No 15
>PHA00733 hypothetical protein
Probab=99.06 E-value=2.8e-10 Score=66.68 Aligned_cols=77 Identities=25% Similarity=0.472 Sum_probs=60.0
Q ss_pred CCcCccccCChHHHHHH--H---HHcCCCCCccCcccccccCChhhHHHHHHhhcCCCceeccccccccCChhHHHHHHH
Q psy2643 1 CKQCGKTFKRSSTLSTH--L---LIHSDTRPYPCQYCGKRFHQKSDMKKHTYIHTGEKPHKCVVCGKAFSQSSNLITHLR 75 (134)
Q Consensus 1 C~~C~~~f~~~~~l~~h--~---~~~~~~~~~~c~~C~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~~~~~~~l~~h~~ 75 (134)
|.+|++.|.....|..+ + ..+.+.++|.|+.|++.|.....|..|++.+ ..+|.|..|++.|.....|..|+.
T Consensus 43 ~~~~~~~~~~~~~l~~~~~l~~~~~~~~~kPy~C~~Cgk~Fss~s~L~~H~r~h--~~~~~C~~CgK~F~~~~sL~~H~~ 120 (128)
T PHA00733 43 RAVVKTLIYNPQLLDESSYLYKLLTSKAVSPYVCPLCLMPFSSSVSLKQHIRYT--EHSKVCPVCGKEFRNTDSTLDHVC 120 (128)
T ss_pred HHHHhhhccChhhhcchHHHHhhcccCCCCCccCCCCCCcCCCHHHHHHHHhcC--CcCccCCCCCCccCCHHHHHHHHH
Confidence 45566666666555544 1 2334578999999999999999999998865 357999999999999999999988
Q ss_pred HcCC
Q psy2643 76 KHTG 79 (134)
Q Consensus 76 ~~~~ 79 (134)
..++
T Consensus 121 ~~h~ 124 (128)
T PHA00733 121 KKHN 124 (128)
T ss_pred HhcC
Confidence 6543
No 16
>PLN03086 PRLI-interacting factor K; Provisional
Probab=99.00 E-value=7e-10 Score=78.66 Aligned_cols=84 Identities=20% Similarity=0.523 Sum_probs=68.0
Q ss_pred CCccCcccccccCChhhHHHHHHhhcCCCceeccccccccCChhHHHHHHHHcCCCCCcccCcchhhccC----------
Q psy2643 25 RPYPCQYCGKRFHQKSDMKKHTYIHTGEKPHKCVVCGKAFSQSSNLITHLRKHTGYKPFSCGLCDKAFQR---------- 94 (134)
Q Consensus 25 ~~~~c~~C~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~f~~---------- 94 (134)
+.+.|+.|+..|. ...|..|+..++ .++.|+ |+..+ ....|..|+..|...+++.|+.|++.|..
T Consensus 452 ~H~~C~~Cgk~f~-~s~LekH~~~~H--kpv~Cp-Cg~~~-~R~~L~~H~~thCp~Kpi~C~fC~~~v~~g~~~~d~~d~ 526 (567)
T PLN03086 452 NHVHCEKCGQAFQ-QGEMEKHMKVFH--EPLQCP-CGVVL-EKEQMVQHQASTCPLRLITCRFCGDMVQAGGSAMDVRDR 526 (567)
T ss_pred cCccCCCCCCccc-hHHHHHHHHhcC--CCccCC-CCCCc-chhHHHhhhhccCCCCceeCCCCCCccccCccccchhhh
Confidence 3468999999996 567999999875 789999 99765 56899999999999999999999998852
Q ss_pred hHHHHHHHHhhCCCCCCccc
Q psy2643 95 KVDLRRHRESQHPGSPAQQH 114 (134)
Q Consensus 95 ~~~l~~H~~~~h~~~~~~~~ 114 (134)
.+.|..|... .+..+..+.
T Consensus 527 ~s~Lt~HE~~-CG~rt~~C~ 545 (567)
T PLN03086 527 LRGMSEHESI-CGSRTAPCD 545 (567)
T ss_pred hhhHHHHHHh-cCCcceEcc
Confidence 4589999887 477666653
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=98.98 E-value=3.2e-10 Score=47.96 Aligned_cols=26 Identities=50% Similarity=1.031 Sum_probs=21.0
Q ss_pred HHHHHHHHcCCCCCcccCcchhhccC
Q psy2643 69 NLITHLRKHTGYKPFSCGLCDKAFQR 94 (134)
Q Consensus 69 ~l~~h~~~~~~~~~~~C~~C~~~f~~ 94 (134)
+|..|++.|.++++|.|+.|++.|++
T Consensus 1 ~l~~H~~~H~~~k~~~C~~C~k~F~~ 26 (26)
T PF13465_consen 1 NLRRHMRTHTGEKPYKCPYCGKSFSN 26 (26)
T ss_dssp HHHHHHHHHSSSSSEEESSSSEEESS
T ss_pred CHHHHhhhcCCCCCCCCCCCcCeeCc
Confidence 46788888888888888888888863
No 18
>PHA02768 hypothetical protein; Provisional
Probab=98.90 E-value=8.8e-10 Score=54.27 Aligned_cols=42 Identities=21% Similarity=0.461 Sum_probs=29.4
Q ss_pred CccCcccccccCChhhHHHHHHhhcCCCceeccccccccCChhH
Q psy2643 26 PYPCQYCGKRFHQKSDMKKHTYIHTGEKPHKCVVCGKAFSQSSN 69 (134)
Q Consensus 26 ~~~c~~C~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~~~~~~~ 69 (134)
.|.|+.||+.|.....|..|++.|. ++++|..|++.|...+.
T Consensus 5 ~y~C~~CGK~Fs~~~~L~~H~r~H~--k~~kc~~C~k~f~~~s~ 46 (55)
T PHA02768 5 GYECPICGEIYIKRKSMITHLRKHN--TNLKLSNCKRISLRTGE 46 (55)
T ss_pred ccCcchhCCeeccHHHHHHHHHhcC--CcccCCcccceecccce
Confidence 3677777777777777777777766 56777777777665544
No 19
>PHA00616 hypothetical protein
Probab=98.77 E-value=5.6e-09 Score=49.03 Aligned_cols=31 Identities=23% Similarity=0.409 Sum_probs=24.7
Q ss_pred CcccCcchhhccChHHHHHHHHhhCCCCCCc
Q psy2643 82 PFSCGLCDKAFQRKVDLRRHRESQHPGSPAQ 112 (134)
Q Consensus 82 ~~~C~~C~~~f~~~~~l~~H~~~~h~~~~~~ 112 (134)
||+|+.||+.|.+.++|.+|++.+|++++..
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~~hg~~~~~ 31 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLSVHKQNKLT 31 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHHhcCCCccc
Confidence 5788888888888888888888888887653
No 20
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=98.76 E-value=5.8e-09 Score=44.05 Aligned_cols=24 Identities=46% Similarity=1.132 Sum_probs=15.4
Q ss_pred HHHHHHHcCCCCCccCcccccccC
Q psy2643 14 LSTHLLIHSDTRPYPCQYCGKRFH 37 (134)
Q Consensus 14 l~~h~~~~~~~~~~~c~~C~~~~~ 37 (134)
|..|+++|+++++|.|+.|++.|.
T Consensus 2 l~~H~~~H~~~k~~~C~~C~k~F~ 25 (26)
T PF13465_consen 2 LRRHMRTHTGEKPYKCPYCGKSFS 25 (26)
T ss_dssp HHHHHHHHSSSSSEEESSSSEEES
T ss_pred HHHHhhhcCCCCCCCCCCCcCeeC
Confidence 556666666666666666666654
No 21
>KOG3993|consensus
Probab=98.73 E-value=2.9e-09 Score=72.17 Aligned_cols=86 Identities=30% Similarity=0.582 Sum_probs=72.1
Q ss_pred ccCcccccccCChhhHHHHHHhhcCCCceeccccccccCChhHHHHHHHHcC----------------------------
Q psy2643 27 YPCQYCGKRFHQKSDMKKHTYIHTGEKPHKCVVCGKAFSQSSNLITHLRKHT---------------------------- 78 (134)
Q Consensus 27 ~~c~~C~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~~~~~~~l~~h~~~~~---------------------------- 78 (134)
|+|..|...|.....|.+|.-.-.....|+|+.|+++|.-..+|..|.+=|.
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 8999999999999999999765555567999999999999999999987442
Q ss_pred -----CCCCcccCcchhhccChHHHHHHHHhhCCCCCCc
Q psy2643 79 -----GYKPFSCGLCDKAFQRKVDLRRHRESQHPGSPAQ 112 (134)
Q Consensus 79 -----~~~~~~C~~C~~~f~~~~~l~~H~~~~h~~~~~~ 112 (134)
.+..|.|..|+|.|.....|+.|+.+|+......
T Consensus 348 sg~dss~gi~~C~~C~KkFrRqAYLrKHqlthq~~~~~k 386 (500)
T KOG3993|consen 348 SGDDSSSGIFSCHTCGKKFRRQAYLRKHQLTHQRAPLAK 386 (500)
T ss_pred cCCcccCceeecHHhhhhhHHHHHHHHhHHhhhccccch
Confidence 1225999999999999999999998887655443
No 22
>PHA00732 hypothetical protein
Probab=98.56 E-value=5.1e-08 Score=52.26 Aligned_cols=37 Identities=27% Similarity=0.584 Sum_probs=18.7
Q ss_pred ccCcccccccCChhhHHHHHHhhcCCCceeccccccccC
Q psy2643 27 YPCQYCGKRFHQKSDMKKHTYIHTGEKPHKCVVCGKAFS 65 (134)
Q Consensus 27 ~~c~~C~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~~~ 65 (134)
|.|..|++.|.....|..|++.++. ++.|..|++.|.
T Consensus 2 y~C~~Cgk~F~s~s~Lk~H~r~~H~--~~~C~~CgKsF~ 38 (79)
T PHA00732 2 FKCPICGFTTVTLFALKQHARRNHT--LTKCPVCNKSYR 38 (79)
T ss_pred ccCCCCCCccCCHHHHHHHhhcccC--CCccCCCCCEeC
Confidence 4555555555555555555542211 234555555554
No 23
>PHA00616 hypothetical protein
Probab=98.48 E-value=9.5e-08 Score=44.90 Aligned_cols=32 Identities=22% Similarity=0.442 Sum_probs=15.9
Q ss_pred ccCcccccccCChhhHHHHHHhhcCCCceecc
Q psy2643 27 YPCQYCGKRFHQKSDMKKHTYIHTGEKPHKCV 58 (134)
Q Consensus 27 ~~c~~C~~~~~~~~~l~~h~~~~~~~~~~~C~ 58 (134)
+.|+.||+.|...++|..|++.+++++++.|+
T Consensus 2 YqC~~CG~~F~~~s~l~~H~r~~hg~~~~~~~ 33 (44)
T PHA00616 2 YQCLRCGGIFRKKKEVIEHLLSVHKQNKLTLE 33 (44)
T ss_pred CccchhhHHHhhHHHHHHHHHHhcCCCcccee
Confidence 44555555555555555555555555444443
No 24
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=98.41 E-value=1.8e-07 Score=38.22 Aligned_cols=22 Identities=36% Similarity=0.925 Sum_probs=18.0
Q ss_pred cccCcchhhccChHHHHHHHHh
Q psy2643 83 FSCGLCDKAFQRKVDLRRHRES 104 (134)
Q Consensus 83 ~~C~~C~~~f~~~~~l~~H~~~ 104 (134)
|.|+.|++.|.....|.+|++.
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 5788888888888888888876
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=98.39 E-value=8.8e-07 Score=44.15 Aligned_cols=50 Identities=34% Similarity=0.582 Sum_probs=32.7
Q ss_pred eeccccccccCChhHHHHHHHH-cCCC-CCcccCcchhhccChHHHHHHHHhhCC
Q psy2643 55 HKCVVCGKAFSQSSNLITHLRK-HTGY-KPFSCGLCDKAFQRKVDLRRHRESQHP 107 (134)
Q Consensus 55 ~~C~~C~~~~~~~~~l~~h~~~-~~~~-~~~~C~~C~~~f~~~~~l~~H~~~~h~ 107 (134)
|.|+.|++ ..+...|..|... |..+ +.+.||.|...+. .+|.+|+...|+
T Consensus 3 f~CP~C~~-~~~~~~L~~H~~~~H~~~~~~v~CPiC~~~~~--~~l~~Hl~~~H~ 54 (54)
T PF05605_consen 3 FTCPYCGK-GFSESSLVEHCEDEHRSESKNVVCPICSSRVT--DNLIRHLNSQHR 54 (54)
T ss_pred cCCCCCCC-ccCHHHHHHHHHhHCcCCCCCccCCCchhhhh--hHHHHHHHHhcC
Confidence 67777777 4556677777664 4332 4577888876543 477788877663
No 26
>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=98.29 E-value=6.1e-07 Score=36.83 Aligned_cols=24 Identities=42% Similarity=1.007 Sum_probs=17.7
Q ss_pred cccCcchhhccChHHHHHHHHhhC
Q psy2643 83 FSCGLCDKAFQRKVDLRRHRESQH 106 (134)
Q Consensus 83 ~~C~~C~~~f~~~~~l~~H~~~~h 106 (134)
|.|+.|++.|.+...|..|++.+|
T Consensus 1 ~~C~~C~~~~~~~~~l~~H~~~~H 24 (24)
T PF13894_consen 1 FQCPICGKSFRSKSELRQHMRTHH 24 (24)
T ss_dssp EE-SSTS-EESSHHHHHHHHHHHS
T ss_pred CCCcCCCCcCCcHHHHHHHHHhhC
Confidence 578888888888888888887765
No 27
>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=98.21 E-value=4e-06 Score=41.78 Aligned_cols=50 Identities=30% Similarity=0.622 Sum_probs=33.3
Q ss_pred CccCcccccccCChhhHHHHHHhhcC--CCceeccccccccCChhHHHHHHHHcC
Q psy2643 26 PYPCQYCGKRFHQKSDMKKHTYIHTG--EKPHKCVVCGKAFSQSSNLITHLRKHT 78 (134)
Q Consensus 26 ~~~c~~C~~~~~~~~~l~~h~~~~~~--~~~~~C~~C~~~~~~~~~l~~h~~~~~ 78 (134)
.|.||+|++ ..+...|..|....+. .+.+.|++|...+. .+|..|+..++
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 467888888 4455668888766543 24577888887544 37777877644
No 28
>PHA00732 hypothetical protein
Probab=98.17 E-value=1.9e-06 Score=46.23 Aligned_cols=36 Identities=33% Similarity=0.717 Sum_probs=17.0
Q ss_pred eeccccccccCChhHHHHHHHH-cCCCCCcccCcchhhcc
Q psy2643 55 HKCVVCGKAFSQSSNLITHLRK-HTGYKPFSCGLCDKAFQ 93 (134)
Q Consensus 55 ~~C~~C~~~~~~~~~l~~h~~~-~~~~~~~~C~~C~~~f~ 93 (134)
|.|..|++.|.....|..|++. |. ++.|+.|++.|.
T Consensus 2 y~C~~Cgk~F~s~s~Lk~H~r~~H~---~~~C~~CgKsF~ 38 (79)
T PHA00732 2 FKCPICGFTTVTLFALKQHARRNHT---LTKCPVCNKSYR 38 (79)
T ss_pred ccCCCCCCccCCHHHHHHHhhcccC---CCccCCCCCEeC
Confidence 4455555555555555555442 22 134555555554
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=98.14 E-value=1.4e-06 Score=36.96 Aligned_cols=26 Identities=38% Similarity=0.811 Sum_probs=19.5
Q ss_pred CcccCcchhhccChHHHHHHHHhhCC
Q psy2643 82 PFSCGLCDKAFQRKVDLRRHRESQHP 107 (134)
Q Consensus 82 ~~~C~~C~~~f~~~~~l~~H~~~~h~ 107 (134)
+|.|..|++.|.+...|..|++.+++
T Consensus 1 ~~~C~~C~~~F~~~~~l~~H~~~h~~ 26 (27)
T PF13912_consen 1 PFECDECGKTFSSLSALREHKRSHCS 26 (27)
T ss_dssp SEEETTTTEEESSHHHHHHHHCTTTT
T ss_pred CCCCCccCCccCChhHHHHHhHHhcC
Confidence 46788888888888888888776653
No 30
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=98.07 E-value=3.8e-06 Score=47.05 Aligned_cols=73 Identities=27% Similarity=0.539 Sum_probs=19.1
Q ss_pred CcccccccCChhhHHHHHHhhcCCCceeccccccccCChhHHHHHHHHcCCCCCcccCcchhhccChHHHHHHHHhhC
Q psy2643 29 CQYCGKRFHQKSDMKKHTYIHTGEKPHKCVVCGKAFSQSSNLITHLRKHTGYKPFSCGLCDKAFQRKVDLRRHRESQH 106 (134)
Q Consensus 29 c~~C~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~~h 106 (134)
|..|+..|.+...+..|+...++-.. . ....+.....+..+++.. ....+.|..|++.|.+...|..|++.++
T Consensus 2 C~~C~~~f~~~~~l~~H~~~~H~~~~---~-~~~~l~~~~~~~~~~~~~-~~~~~~C~~C~~~f~s~~~l~~Hm~~~~ 74 (100)
T PF12756_consen 2 CLFCDESFSSVDDLLQHMKKKHGFDI---P-DQKYLVDPNRLLNYLRKK-VKESFRCPYCNKTFRSREALQEHMRSKH 74 (100)
T ss_dssp ----------------------------------------------------SSEEBSSSS-EESSHHHHHHHHHHTT
T ss_pred cccccccccccccccccccccccccc---c-cccccccccccccccccc-cCCCCCCCccCCCCcCHHHHHHHHcCcc
Confidence 56666666666666666655443211 0 001111222232333221 1225788888888888888888887653
No 31
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=97.98 E-value=1.3e-06 Score=57.75 Aligned_cols=26 Identities=35% Similarity=0.810 Sum_probs=22.8
Q ss_pred CCCCCcccCcchhhccChHHHHHHHH
Q psy2643 78 TGYKPFSCGLCDKAFQRKVDLRRHRE 103 (134)
Q Consensus 78 ~~~~~~~C~~C~~~f~~~~~l~~H~~ 103 (134)
..+|||+|++|+|.|.....|+-|+.
T Consensus 394 ~~~KPYrCevC~KRYKNlNGLKYHr~ 419 (423)
T COG5189 394 AKDKPYRCEVCDKRYKNLNGLKYHRK 419 (423)
T ss_pred ccCCceeccccchhhccCccceeccc
Confidence 34689999999999999999988864
No 32
>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=97.94 E-value=8.3e-06 Score=33.12 Aligned_cols=22 Identities=55% Similarity=1.053 Sum_probs=12.7
Q ss_pred eeccccccccCChhHHHHHHHH
Q psy2643 55 HKCVVCGKAFSQSSNLITHLRK 76 (134)
Q Consensus 55 ~~C~~C~~~~~~~~~l~~h~~~ 76 (134)
|.|+.|++.|.....|..|++.
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 4555666666666666666554
No 33
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=97.76 E-value=2.6e-05 Score=43.57 Aligned_cols=72 Identities=18% Similarity=0.333 Sum_probs=21.6
Q ss_pred CCcCccccCChHHHHHHHHHcCCCCCccCcccccccCChhhHHHHHHhhcCCCceeccccccccCChhHHHHHHHHc
Q psy2643 1 CKQCGKTFKRSSTLSTHLLIHSDTRPYPCQYCGKRFHQKSDMKKHTYIHTGEKPHKCVVCGKAFSQSSNLITHLRKH 77 (134)
Q Consensus 1 C~~C~~~f~~~~~l~~h~~~~~~~~~~~c~~C~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~~~~~~~l~~h~~~~ 77 (134)
|..|+..|.....|..|+...++... +. ...+.....+....... ....+.|..|+..|.+...|..|++.+
T Consensus 2 C~~C~~~f~~~~~l~~H~~~~H~~~~---~~-~~~l~~~~~~~~~~~~~-~~~~~~C~~C~~~f~s~~~l~~Hm~~~ 73 (100)
T PF12756_consen 2 CLFCDESFSSVDDLLQHMKKKHGFDI---PD-QKYLVDPNRLLNYLRKK-VKESFRCPYCNKTFRSREALQEHMRSK 73 (100)
T ss_dssp ----------------------------------------------------SSEEBSSSS-EESSHHHHHHHHHHT
T ss_pred cccccccccccccccccccccccccc---cc-ccccccccccccccccc-cCCCCCCCccCCCCcCHHHHHHHHcCc
Confidence 78999999999999999976554321 11 11111222233333222 223699999999999999999999964
No 34
>PF09237 GAGA: GAGA factor; InterPro: IPR015318 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Members of this entry bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognises the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognises the A in the fourth position of the consensus sequence []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1YUI_A 1YUJ_A.
Probab=97.70 E-value=4.1e-05 Score=36.90 Aligned_cols=33 Identities=30% Similarity=0.643 Sum_probs=21.4
Q ss_pred CCCCCcccCcchhhccChHHHHHHHHhhCCCCC
Q psy2643 78 TGYKPFSCGLCDKAFQRKVDLRRHRESQHPGSP 110 (134)
Q Consensus 78 ~~~~~~~C~~C~~~f~~~~~l~~H~~~~h~~~~ 110 (134)
..+.|-.||.|+..+.+..+|++|+...|..++
T Consensus 20 ~S~~PatCP~C~a~~~~srnLrRHle~~H~~k~ 52 (54)
T PF09237_consen 20 QSEQPATCPICGAVIRQSRNLRRHLEIRHFKKP 52 (54)
T ss_dssp TTS--EE-TTT--EESSHHHHHHHHHHHTTTS-
T ss_pred ccCCCCCCCcchhhccchhhHHHHHHHHhcccC
Confidence 345678888888888888888888888887765
No 35
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=97.70 E-value=4.1e-05 Score=31.10 Aligned_cols=23 Identities=43% Similarity=0.985 Sum_probs=12.3
Q ss_pred eeccccccccCChhHHHHHHHHc
Q psy2643 55 HKCVVCGKAFSQSSNLITHLRKH 77 (134)
Q Consensus 55 ~~C~~C~~~~~~~~~l~~h~~~~ 77 (134)
|.|+.|+..|.....|..|+..+
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 45666666666666666665543
No 36
>smart00355 ZnF_C2H2 zinc finger.
Probab=97.65 E-value=5.9e-05 Score=31.14 Aligned_cols=23 Identities=30% Similarity=0.748 Sum_probs=17.8
Q ss_pred cccCcchhhccChHHHHHHHHhh
Q psy2643 83 FSCGLCDKAFQRKVDLRRHRESQ 105 (134)
Q Consensus 83 ~~C~~C~~~f~~~~~l~~H~~~~ 105 (134)
|.|..|++.|.....|..|++.|
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~~H 23 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMRTH 23 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHHHh
Confidence 46888888888888888887743
No 37
>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=97.61 E-value=5.2e-05 Score=31.98 Aligned_cols=24 Identities=50% Similarity=0.870 Sum_probs=16.3
Q ss_pred ceeccccccccCChhHHHHHHHHc
Q psy2643 54 PHKCVVCGKAFSQSSNLITHLRKH 77 (134)
Q Consensus 54 ~~~C~~C~~~~~~~~~l~~h~~~~ 77 (134)
+|.|..|+..|.+...|..|++.|
T Consensus 1 ~~~C~~C~~~F~~~~~l~~H~~~h 24 (27)
T PF13912_consen 1 PFECDECGKTFSSLSALREHKRSH 24 (27)
T ss_dssp SEEETTTTEEESSHHHHHHHHCTT
T ss_pred CCCCCccCCccCChhHHHHHhHHh
Confidence 356777777777777777776654
No 38
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=97.47 E-value=6.9e-05 Score=30.69 Aligned_cols=24 Identities=33% Similarity=0.800 Sum_probs=15.5
Q ss_pred cccCcchhhccChHHHHHHHHhhCC
Q psy2643 83 FSCGLCDKAFQRKVDLRRHRESQHP 107 (134)
Q Consensus 83 ~~C~~C~~~f~~~~~l~~H~~~~h~ 107 (134)
|+|+.|+.... ...|.+|++.+|+
T Consensus 1 y~C~~C~y~t~-~~~l~~H~~~~H~ 24 (24)
T PF13909_consen 1 YKCPHCSYSTS-KSNLKRHLKRHHP 24 (24)
T ss_dssp EE-SSSS-EES-HHHHHHHHHHHHS
T ss_pred CCCCCCCCcCC-HHHHHHHHHhhCc
Confidence 56777777666 7777777776653
No 39
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=97.45 E-value=7.9e-05 Score=30.79 Aligned_cols=22 Identities=41% Similarity=0.917 Sum_probs=15.6
Q ss_pred cccCcchhhccChHHHHHHHHh
Q psy2643 83 FSCGLCDKAFQRKVDLRRHRES 104 (134)
Q Consensus 83 ~~C~~C~~~f~~~~~l~~H~~~ 104 (134)
|.|..|++.|.+...|..|++.
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 4577777777777777777654
No 40
>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=97.19 E-value=0.00012 Score=30.88 Aligned_cols=22 Identities=41% Similarity=0.841 Sum_probs=17.3
Q ss_pred cccCcchhhccChHHHHHHHHh
Q psy2643 83 FSCGLCDKAFQRKVDLRRHRES 104 (134)
Q Consensus 83 ~~C~~C~~~f~~~~~l~~H~~~ 104 (134)
|.|..|++.|.+...|..|++.
T Consensus 2 ~~C~~C~k~f~~~~~~~~H~~s 23 (27)
T PF12171_consen 2 FYCDACDKYFSSENQLKQHMKS 23 (27)
T ss_dssp CBBTTTTBBBSSHHHHHCCTTS
T ss_pred CCcccCCCCcCCHHHHHHHHcc
Confidence 6788888888888888888754
No 41
>PF09237 GAGA: GAGA factor; InterPro: IPR015318 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Members of this entry bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognises the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognises the A in the fourth position of the consensus sequence []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1YUI_A 1YUJ_A.
Probab=97.15 E-value=0.00055 Score=33.08 Aligned_cols=29 Identities=38% Similarity=0.623 Sum_probs=12.3
Q ss_pred CceeccccccccCChhHHHHHHHHcCCCC
Q psy2643 53 KPHKCVVCGKAFSQSSNLITHLRKHTGYK 81 (134)
Q Consensus 53 ~~~~C~~C~~~~~~~~~l~~h~~~~~~~~ 81 (134)
.|-.|++|+..+....+|.+|+...++.+
T Consensus 23 ~PatCP~C~a~~~~srnLrRHle~~H~~k 51 (54)
T PF09237_consen 23 QPATCPICGAVIRQSRNLRRHLEIRHFKK 51 (54)
T ss_dssp --EE-TTT--EESSHHHHHHHHHHHTTTS
T ss_pred CCCCCCcchhhccchhhHHHHHHHHhccc
Confidence 34455555555555555555555444433
No 42
>PRK04860 hypothetical protein; Provisional
Probab=97.07 E-value=0.00041 Score=42.34 Aligned_cols=38 Identities=24% Similarity=0.537 Sum_probs=32.0
Q ss_pred ceeccccccccCChhHHHHHHHHcCCCCCcccCcchhhccCh
Q psy2643 54 PHKCVVCGKAFSQSSNLITHLRKHTGYKPFSCGLCDKAFQRK 95 (134)
Q Consensus 54 ~~~C~~C~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~f~~~ 95 (134)
+|.|. |+. ....+..|.+++.++++|.|..|+..|...
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 58898 887 455788999999999999999999988654
No 43
>smart00355 ZnF_C2H2 zinc finger.
Probab=96.99 E-value=0.00089 Score=27.36 Aligned_cols=21 Identities=43% Similarity=0.898 Sum_probs=11.3
Q ss_pred eccccccccCChhHHHHHHHH
Q psy2643 56 KCVVCGKAFSQSSNLITHLRK 76 (134)
Q Consensus 56 ~C~~C~~~~~~~~~l~~h~~~ 76 (134)
.|..|+..|.....+..|++.
T Consensus 2 ~C~~C~~~f~~~~~l~~H~~~ 22 (26)
T smart00355 2 RCPECGKVFKSKSALKEHMRT 22 (26)
T ss_pred CCCCCcchhCCHHHHHHHHHH
Confidence 455555555555555555553
No 44
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=96.96 E-value=0.0006 Score=28.03 Aligned_cols=22 Identities=41% Similarity=0.810 Sum_probs=15.9
Q ss_pred eeccccccccCChhHHHHHHHH
Q psy2643 55 HKCVVCGKAFSQSSNLITHLRK 76 (134)
Q Consensus 55 ~~C~~C~~~~~~~~~l~~h~~~ 76 (134)
|.|.+|+..|.+...+..|++.
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 5677777777777777777664
No 45
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=96.83 E-value=0.00061 Score=33.43 Aligned_cols=32 Identities=28% Similarity=0.502 Sum_probs=27.0
Q ss_pred cCCCCCcccCcchhhccChHHHHHHHHhhCCC
Q psy2643 77 HTGYKPFSCGLCDKAFQRKVDLRRHRESQHPG 108 (134)
Q Consensus 77 ~~~~~~~~C~~C~~~f~~~~~l~~H~~~~h~~ 108 (134)
-.||.-+.||.|+..|.+..++.+|+...|+-
T Consensus 12 RDGE~~lrCPRC~~~FR~~K~Y~RHVNKaH~~ 43 (65)
T COG4049 12 RDGEEFLRCPRCGMVFRRRKDYIRHVNKAHGW 43 (65)
T ss_pred cCCceeeeCCchhHHHHHhHHHHHHhhHHhhh
Confidence 45677899999999999999999999777653
No 46
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=96.51 E-value=0.0024 Score=25.95 Aligned_cols=22 Identities=45% Similarity=0.739 Sum_probs=12.6
Q ss_pred eeccccccccCChhHHHHHHHHc
Q psy2643 55 HKCVVCGKAFSQSSNLITHLRKH 77 (134)
Q Consensus 55 ~~C~~C~~~~~~~~~l~~h~~~~ 77 (134)
|.|+.|+.... ...|..|++.+
T Consensus 1 y~C~~C~y~t~-~~~l~~H~~~~ 22 (24)
T PF13909_consen 1 YKCPHCSYSTS-KSNLKRHLKRH 22 (24)
T ss_dssp EE-SSSS-EES-HHHHHHHHHHH
T ss_pred CCCCCCCCcCC-HHHHHHHHHhh
Confidence 45666666665 66666666654
No 47
>KOG1146|consensus
Probab=96.38 E-value=0.00096 Score=52.11 Aligned_cols=87 Identities=23% Similarity=0.465 Sum_probs=60.9
Q ss_pred CCCccCcccccccCChhhHHHHHHhhc-------------------------CCCceeccccccccCChhHHHHHHHH--
Q psy2643 24 TRPYPCQYCGKRFHQKSDMKKHTYIHT-------------------------GEKPHKCVVCGKAFSQSSNLITHLRK-- 76 (134)
Q Consensus 24 ~~~~~c~~C~~~~~~~~~l~~h~~~~~-------------------------~~~~~~C~~C~~~~~~~~~l~~h~~~-- 76 (134)
.+.+.|+.|++.|+....|..|++..+ +.++|.|..|...+....+|..|++.
T Consensus 463 ~kt~~cpkc~~~yk~a~~L~vhmRskhp~~~~~~c~~gq~~~~~arg~~~~~~~~p~~C~~C~~stttng~LsihlqS~~ 542 (1406)
T KOG1146|consen 463 FKTLKCPKCNWHYKLAQTLGVHMRSKHPESQSAYCKAGQNHPRLARGEVYRCPGKPYPCRACNYSTTTNGNLSIHLQSDL 542 (1406)
T ss_pred cccccCCccchhhhhHHHhhhcccccccccchhHhHhccccccccccccccCCCCcccceeeeeeeecchHHHHHHHHHh
Confidence 355777777777777777777777622 24467888888888888888888753
Q ss_pred cC----------C-------------------------------CCCcccCcchhhccChHHHHHHHHhhCCCCC
Q psy2643 77 HT----------G-------------------------------YKPFSCGLCDKAFQRKVDLRRHRESQHPGSP 110 (134)
Q Consensus 77 ~~----------~-------------------------------~~~~~C~~C~~~f~~~~~l~~H~~~~h~~~~ 110 (134)
|. + .-.|.|..|++--.-..+|+.|+..-+...+
T Consensus 543 h~~~lee~~~~~g~~v~~~~~~v~s~~P~~ag~~~~ags~~pktkP~~~C~vc~yetniarnlrihmtss~~s~~ 617 (1406)
T KOG1146|consen 543 HRNELEEAEENAGEQVRLLPASVTSAVPEEAGLGPSAGSSGPKTKPSWRCEVCSYETNIARNLRIHMTASPSSSP 617 (1406)
T ss_pred hHHHHHHHHhccccchhhhhhhhcccCcccccCCCCCCCCCCCCCCCcchhhhcchhhhhhccccccccCCCCCC
Confidence 11 0 0148999999877777788888866655555
No 48
>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=96.17 E-value=0.004 Score=27.72 Aligned_cols=24 Identities=25% Similarity=0.701 Sum_probs=18.0
Q ss_pred CcccCcchhhccChHHHHHHHHhh
Q psy2643 82 PFSCGLCDKAFQRKVDLRRHRESQ 105 (134)
Q Consensus 82 ~~~C~~C~~~f~~~~~l~~H~~~~ 105 (134)
+|.|..|++.|.+...+..|+...
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~gk 26 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLKGK 26 (35)
T ss_pred CeEccccCCccCCHHHHHHHHChH
Confidence 467888888888888888887543
No 49
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=96.12 E-value=0.005 Score=25.40 Aligned_cols=19 Identities=26% Similarity=0.793 Sum_probs=11.6
Q ss_pred ccCcchhhccChHHHHHHHH
Q psy2643 84 SCGLCDKAFQRKVDLRRHRE 103 (134)
Q Consensus 84 ~C~~C~~~f~~~~~l~~H~~ 103 (134)
.|+.||+.| ....|.+|++
T Consensus 4 ~C~~CgR~F-~~~~l~~H~~ 22 (25)
T PF13913_consen 4 PCPICGRKF-NPDRLEKHEK 22 (25)
T ss_pred cCCCCCCEE-CHHHHHHHHH
Confidence 566666666 4555666654
No 50
>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=95.91 E-value=0.0019 Score=27.12 Aligned_cols=21 Identities=33% Similarity=0.694 Sum_probs=13.4
Q ss_pred eeccccccccCChhHHHHHHH
Q psy2643 55 HKCVVCGKAFSQSSNLITHLR 75 (134)
Q Consensus 55 ~~C~~C~~~~~~~~~l~~h~~ 75 (134)
|.|..|++.|.+...+..|++
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 556667766766666665554
No 51
>KOG2231|consensus
Probab=95.89 E-value=0.025 Score=41.93 Aligned_cols=96 Identities=21% Similarity=0.407 Sum_probs=45.5
Q ss_pred ccCChHHHHHHHHHcCCCCCccCcccc---------cccCChhhHHHHHHhhcC-CC----ceeccccccccCChhHHHH
Q psy2643 7 TFKRSSTLSTHLLIHSDTRPYPCQYCG---------KRFHQKSDMKKHTYIHTG-EK----PHKCVVCGKAFSQSSNLIT 72 (134)
Q Consensus 7 ~f~~~~~l~~h~~~~~~~~~~~c~~C~---------~~~~~~~~l~~h~~~~~~-~~----~~~C~~C~~~~~~~~~l~~ 72 (134)
.|.....|+.|+...+. .+.|..|- ...-....|+.|++.-.. ++ .-.|..|...|.....+..
T Consensus 123 ~~~s~~~Lk~H~~~~H~--~~~c~lC~~~~kif~~e~k~Yt~~el~~h~~~gd~d~~s~rGhp~C~~C~~~fld~~el~r 200 (669)
T KOG2231|consen 123 EFKSVENLKNHMRDQHK--LHLCSLCLQNLKIFINERKLYTRAELNLHLMFGDPDDESCRGHPLCKFCHERFLDDDELYR 200 (669)
T ss_pred chhHHHHHHHHHHHhhh--hhccccccccceeeeeeeehehHHHHHHHHhcCCCccccccCCccchhhhhhhccHHHHHH
Confidence 33466788888854332 12333331 111223345555543221 11 1245666666666666666
Q ss_pred HHHHcCCCCCcccCcc------hhhccChHHHHHHHHhhCCC
Q psy2643 73 HLRKHTGYKPFSCGLC------DKAFQRKVDLRRHRESQHPG 108 (134)
Q Consensus 73 h~~~~~~~~~~~C~~C------~~~f~~~~~l~~H~~~~h~~ 108 (134)
|++.++ |.|..| +..|.....|..|.+..|-.
T Consensus 201 H~~~~h----~~chfC~~~~~~neyy~~~~dLe~HfR~~Hfl 238 (669)
T KOG2231|consen 201 HLRFDH----EFCHFCDYKTGQNEYYNDYDDLEEHFRKGHFL 238 (669)
T ss_pred hhccce----eheeecCcccccchhcccchHHHHHhhhcCcc
Confidence 666432 222222 23444455555555555443
No 52
>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=95.85 E-value=0.0056 Score=27.06 Aligned_cols=24 Identities=29% Similarity=0.862 Sum_probs=15.5
Q ss_pred eeccccccccCChhHHHHHHHHcCCCCCcccCcchh
Q psy2643 55 HKCVVCGKAFSQSSNLITHLRKHTGYKPFSCGLCDK 90 (134)
Q Consensus 55 ~~C~~C~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~ 90 (134)
|.|..||..+.... .++.||.||.
T Consensus 2 ~~C~~CGy~y~~~~------------~~~~CP~Cg~ 25 (33)
T cd00350 2 YVCPVCGYIYDGEE------------APWVCPVCGA 25 (33)
T ss_pred EECCCCCCEECCCc------------CCCcCcCCCC
Confidence 66777777654432 5577777774
No 53
>PRK04860 hypothetical protein; Provisional
Probab=95.70 E-value=0.0083 Score=36.70 Aligned_cols=38 Identities=26% Similarity=0.761 Sum_probs=31.5
Q ss_pred CccCcccccccCChhhHHHHHHhhcCCCceeccccccccCCh
Q psy2643 26 PYPCQYCGKRFHQKSDMKKHTYIHTGEKPHKCVVCGKAFSQS 67 (134)
Q Consensus 26 ~~~c~~C~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~~~~~ 67 (134)
+|.|. |+. ....+..|.+.+.++++|.|..|+..|...
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 37887 877 455688999999999999999999887654
No 54
>KOG1146|consensus
Probab=95.19 E-value=0.007 Score=47.65 Aligned_cols=105 Identities=19% Similarity=0.338 Sum_probs=78.3
Q ss_pred CCcCccccCChHHHHHHHHHc-------------------------CCCCCccCcccccccCChhhHHHHHHhhcC----
Q psy2643 1 CKQCGKTFKRSSTLSTHLLIH-------------------------SDTRPYPCQYCGKRFHQKSDMKKHTYIHTG---- 51 (134)
Q Consensus 1 C~~C~~~f~~~~~l~~h~~~~-------------------------~~~~~~~c~~C~~~~~~~~~l~~h~~~~~~---- 51 (134)
|+.|+..|.....|..||++- .+.++|.|..|...+....+|..|+.+...
T Consensus 468 cpkc~~~yk~a~~L~vhmRskhp~~~~~~c~~gq~~~~~arg~~~~~~~~p~~C~~C~~stttng~LsihlqS~~h~~~l 547 (1406)
T KOG1146|consen 468 CPKCNWHYKLAQTLGVHMRSKHPESQSAYCKAGQNHPRLARGEVYRCPGKPYPCRACNYSTTTNGNLSIHLQSDLHRNEL 547 (1406)
T ss_pred CCccchhhhhHHHhhhcccccccccchhHhHhccccccccccccccCCCCcccceeeeeeeecchHHHHHHHHHhhHHHH
Confidence 899999999999999999982 224668999999999999899999864320
Q ss_pred ---------------------------------------CCceeccccccccCChhHHHHHHHHc-CCCCCcccCcchhh
Q psy2643 52 ---------------------------------------EKPHKCVVCGKAFSQSSNLITHLRKH-TGYKPFSCGLCDKA 91 (134)
Q Consensus 52 ---------------------------------------~~~~~C~~C~~~~~~~~~l~~h~~~~-~~~~~~~C~~C~~~ 91 (134)
+..|.|.+|+.--.-..+|+.|+..- +-..+..+..++-.
T Consensus 548 ee~~~~~g~~v~~~~~~v~s~~P~~ag~~~~ags~~pktkP~~~C~vc~yetniarnlrihmtss~~s~~p~~~Lq~~it 627 (1406)
T KOG1146|consen 548 EEAEENAGEQVRLLPASVTSAVPEEAGLGPSAGSSGPKTKPSWRCEVCSYETNIARNLRIHMTASPSSSPPSLVLQQNIT 627 (1406)
T ss_pred HHHHhccccchhhhhhhhcccCcccccCCCCCCCCCCCCCCCcchhhhcchhhhhhccccccccCCCCCChHHHhhhcch
Confidence 11389999998877778888888753 33334677777777
Q ss_pred ccChHHHHHHHHhh
Q psy2643 92 FQRKVDLRRHRESQ 105 (134)
Q Consensus 92 f~~~~~l~~H~~~~ 105 (134)
+.....+..+.+..
T Consensus 628 ~~l~~~~~~~~~lp 641 (1406)
T KOG1146|consen 628 SSLASLLGGQGRLP 641 (1406)
T ss_pred hhccccccCcCCCC
Confidence 66666665555555
No 55
>KOG2785|consensus
Probab=94.98 E-value=0.15 Score=35.32 Aligned_cols=51 Identities=24% Similarity=0.573 Sum_probs=42.4
Q ss_pred eeccccccccCChhHHHHHHHHcCCC-----------------------CCcccCcch---hhccChHHHHHHHHhh
Q psy2643 55 HKCVVCGKAFSQSSNLITHLRKHTGY-----------------------KPFSCGLCD---KAFQRKVDLRRHRESQ 105 (134)
Q Consensus 55 ~~C~~C~~~~~~~~~l~~h~~~~~~~-----------------------~~~~C~~C~---~~f~~~~~l~~H~~~~ 105 (134)
-.|..|+..+.+......||..+++- .-+.|-.|+ +.|.+....+.||..+
T Consensus 167 t~CLfC~~~~k~~e~~~~HM~~~HgffIPdreYL~D~~GLl~YLgeKV~~~~~CL~CN~~~~~f~sleavr~HM~~K 243 (390)
T KOG2785|consen 167 TDCLFCDKKSKSLEENLKHMFKEHGFFIPDREYLTDEKGLLKYLGEKVGIGFICLFCNELGRPFSSLEAVRAHMRDK 243 (390)
T ss_pred cceeecCCCcccHHHHHHHHhhccCCcCCchHhhhchhHHHHHHHHHhccCceEEEeccccCcccccHHHHHHHhhc
Confidence 46889999999999999999887652 247888888 9999999999999665
No 56
>KOG4173|consensus
Probab=94.90 E-value=0.012 Score=37.06 Aligned_cols=71 Identities=24% Similarity=0.492 Sum_probs=32.5
Q ss_pred cccccCChhhHHHHHHhhcCCCceeccccccccCChhHHHHHHHHcC----------CCCCccc--CcchhhccChHHHH
Q psy2643 32 CGKRFHQKSDMKKHTYIHTGEKPHKCVVCGKAFSQSSNLITHLRKHT----------GYKPFSC--GLCDKAFQRKVDLR 99 (134)
Q Consensus 32 C~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~~~~~~~l~~h~~~~~----------~~~~~~C--~~C~~~f~~~~~l~ 99 (134)
|-..|.+...+..|....++ -.|..|.+.|.+...|..|+...+ |.-.|.| ..|+--|.+..+.+
T Consensus 87 c~~~~d~lD~~E~hY~~~h~---~sCs~C~r~~Pt~hLLd~HI~E~HDs~Fqa~veRG~dMy~ClvEgCt~KFkT~r~Rk 163 (253)
T KOG4173|consen 87 CCQVFDALDDYEHHYHTLHG---NSCSFCKRAFPTGHLLDAHILEWHDSLFQALVERGQDMYQCLVEGCTEKFKTSRDRK 163 (253)
T ss_pred hHHHHhhhhhHHHhhhhccc---chhHHHHHhCCchhhhhHHHHHHHHHHHHHHHHcCccHHHHHHHhhhhhhhhhhhhh
Confidence 33444444434444333222 135555555555555555543221 2334555 23555555555555
Q ss_pred HHHHhh
Q psy2643 100 RHRESQ 105 (134)
Q Consensus 100 ~H~~~~ 105 (134)
+|+-..
T Consensus 164 dH~I~~ 169 (253)
T KOG4173|consen 164 DHMIRM 169 (253)
T ss_pred hHHHHh
Confidence 555333
No 57
>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=94.82 E-value=0.087 Score=30.07 Aligned_cols=26 Identities=23% Similarity=0.537 Sum_probs=23.8
Q ss_pred Cccc----CcchhhccChHHHHHHHHhhCC
Q psy2643 82 PFSC----GLCDKAFQRKVDLRRHRESQHP 107 (134)
Q Consensus 82 ~~~C----~~C~~~f~~~~~l~~H~~~~h~ 107 (134)
.|.| +.|+....+...+++|.+.+|+
T Consensus 80 G~~C~~~~~~C~y~~~~~~~m~~H~~~~Hg 109 (109)
T PF12013_consen 80 GYRCQCDPPHCGYITRSKKTMRKHWRKEHG 109 (109)
T ss_pred CeeeecCCCCCCcEeccHHHHHHHHHHhcC
Confidence 3999 9999999999999999999885
No 58
>KOG2231|consensus
Probab=94.76 E-value=0.073 Score=39.66 Aligned_cols=77 Identities=23% Similarity=0.424 Sum_probs=49.9
Q ss_pred cCcccccccCChhhHHHHHHhhcCCCceeccccc---------cccCChhHHHHHHHHcCC-CC----CcccCcchhhcc
Q psy2643 28 PCQYCGKRFHQKSDMKKHTYIHTGEKPHKCVVCG---------KAFSQSSNLITHLRKHTG-YK----PFSCGLCDKAFQ 93 (134)
Q Consensus 28 ~c~~C~~~~~~~~~l~~h~~~~~~~~~~~C~~C~---------~~~~~~~~l~~h~~~~~~-~~----~~~C~~C~~~f~ 93 (134)
.|..| ..|.+...|..|+...|. .+.|..|- ....+.+.|..|+....- ++ .-.|..|...|.
T Consensus 117 ~~~~c-~~~~s~~~Lk~H~~~~H~--~~~c~lC~~~~kif~~e~k~Yt~~el~~h~~~gd~d~~s~rGhp~C~~C~~~fl 193 (669)
T KOG2231|consen 117 ECLHC-TEFKSVENLKNHMRDQHK--LHLCSLCLQNLKIFINERKLYTRAELNLHLMFGDPDDESCRGHPLCKFCHERFL 193 (669)
T ss_pred CCccc-cchhHHHHHHHHHHHhhh--hhccccccccceeeeeeeehehHHHHHHHHhcCCCccccccCCccchhhhhhhc
Confidence 34444 445577889999976553 23443332 233445677788775322 22 256888999999
Q ss_pred ChHHHHHHHHhhCC
Q psy2643 94 RKVDLRRHRESQHP 107 (134)
Q Consensus 94 ~~~~l~~H~~~~h~ 107 (134)
....|.+|++..|-
T Consensus 194 d~~el~rH~~~~h~ 207 (669)
T KOG2231|consen 194 DDDELYRHLRFDHE 207 (669)
T ss_pred cHHHHHHhhcccee
Confidence 99999999987654
No 59
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=94.36 E-value=0.055 Score=30.97 Aligned_cols=81 Identities=16% Similarity=0.316 Sum_probs=51.2
Q ss_pred CCCccCcccccccCChhhHHHHHHhhcCCCc------------eeccccccccCChhHHHHHHHHcCCCCCcccCcchhh
Q psy2643 24 TRPYPCQYCGKRFHQKSDMKKHTYIHTGEKP------------HKCVVCGKAFSQSSNLITHLRKHTGYKPFSCGLCDKA 91 (134)
Q Consensus 24 ~~~~~c~~C~~~~~~~~~l~~h~~~~~~~~~------------~~C~~C~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~ 91 (134)
+.|..|+.|+-...+...|.+..-....-++ ..|..|...|........ ..-.....|.|+.|...
T Consensus 13 ~LP~~CpiCgLtLVss~HLARSyHHLfPl~~f~ev~~~~~~~~~~C~~C~~~f~~~~~~~~--~~~~~~~~y~C~~C~~~ 90 (112)
T TIGR00622 13 ELPVECPICGLTLILSTHLARSYHHLFPLKAFQEIPLEEYNGSRFCFGCQGPFPKPPVSPF--DELKDSHRYVCAVCKNV 90 (112)
T ss_pred CCCCcCCcCCCEEeccchHHHhhhccCCCcccccccccccCCCCcccCcCCCCCCcccccc--cccccccceeCCCCCCc
Confidence 3578899999888877777664221111111 138888888876431110 00122346999999999
Q ss_pred ccChHHHHHHHHhhC
Q psy2643 92 FQRKVDLRRHRESQH 106 (134)
Q Consensus 92 f~~~~~l~~H~~~~h 106 (134)
|-..-+.-.|..+|.
T Consensus 91 FC~dCD~fiHe~Lh~ 105 (112)
T TIGR00622 91 FCVDCDVFVHESLHC 105 (112)
T ss_pred cccccchhhhhhccC
Confidence 998888888877764
No 60
>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=93.94 E-value=0.039 Score=31.52 Aligned_cols=30 Identities=30% Similarity=0.790 Sum_probs=20.2
Q ss_pred ccCcccccccCChhhHHHHHHhhcCCCceeccccccccCCh
Q psy2643 27 YPCQYCGKRFHQKSDMKKHTYIHTGEKPHKCVVCGKAFSQS 67 (134)
Q Consensus 27 ~~c~~C~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~~~~~ 67 (134)
..|+.||..|--. +..|..|+.||..|...
T Consensus 10 R~Cp~CG~kFYDL-----------nk~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 10 RTCPSCGAKFYDL-----------NKDPIVCPKCGTEFPPE 39 (108)
T ss_pred ccCCCCcchhccC-----------CCCCccCCCCCCccCcc
Confidence 3688888776542 23567788888777665
No 61
>KOG2186|consensus
Probab=93.83 E-value=0.046 Score=35.64 Aligned_cols=47 Identities=23% Similarity=0.595 Sum_probs=30.8
Q ss_pred CccCcccccccCChhhHHHHHHhhcCCCceeccccccccCChhHHHHHHH
Q psy2643 26 PYPCQYCGKRFHQKSDMKKHTYIHTGEKPHKCVVCGKAFSQSSNLITHLR 75 (134)
Q Consensus 26 ~~~c~~C~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~~~~~~~l~~h~~ 75 (134)
.|.|..||.+..-.. +..|+..-++ .-|.|.-|+..|.. .+...|..
T Consensus 3 ~FtCnvCgEsvKKp~-vekH~srCrn-~~fSCIDC~k~F~~-~sYknH~k 49 (276)
T KOG2186|consen 3 FFTCNVCGESVKKPQ-VEKHMSRCRN-AYFSCIDCGKTFER-VSYKNHTK 49 (276)
T ss_pred EEehhhhhhhccccc-hHHHHHhccC-CeeEEeeccccccc-chhhhhhh
Confidence 366777777766554 6667655444 45777778877777 45666665
No 62
>KOG4173|consensus
Probab=93.37 E-value=0.065 Score=33.93 Aligned_cols=72 Identities=21% Similarity=0.486 Sum_probs=54.4
Q ss_pred CccccCChHHHHHHHHHcCCCCCccCcccccccCChhhHHHHHHhhc----------CCCceeccc--cccccCChhHHH
Q psy2643 4 CGKTFKRSSTLSTHLLIHSDTRPYPCQYCGKRFHQKSDMKKHTYIHT----------GEKPHKCVV--CGKAFSQSSNLI 71 (134)
Q Consensus 4 C~~~f~~~~~l~~h~~~~~~~~~~~c~~C~~~~~~~~~l~~h~~~~~----------~~~~~~C~~--C~~~~~~~~~l~ 71 (134)
|-..|.....+..|..+.++. .|..|.+.|++...|..|+...| |+..|.|.+ |+..|.+...-.
T Consensus 87 c~~~~d~lD~~E~hY~~~h~~---sCs~C~r~~Pt~hLLd~HI~E~HDs~Fqa~veRG~dMy~ClvEgCt~KFkT~r~Rk 163 (253)
T KOG4173|consen 87 CCQVFDALDDYEHHYHTLHGN---SCSFCKRAFPTGHLLDAHILEWHDSLFQALVERGQDMYQCLVEGCTEKFKTSRDRK 163 (253)
T ss_pred hHHHHhhhhhHHHhhhhcccc---hhHHHHHhCCchhhhhHHHHHHHHHHHHHHHHcCccHHHHHHHhhhhhhhhhhhhh
Confidence 445666667777777665553 79999999999988888876443 456688876 999999998888
Q ss_pred HHHH-HcC
Q psy2643 72 THLR-KHT 78 (134)
Q Consensus 72 ~h~~-~~~ 78 (134)
.|+- .|.
T Consensus 164 dH~I~~Hk 171 (253)
T KOG4173|consen 164 DHMIRMHK 171 (253)
T ss_pred hHHHHhcc
Confidence 8865 454
No 63
>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=92.88 E-value=0.066 Score=23.79 Aligned_cols=25 Identities=28% Similarity=0.639 Sum_probs=15.7
Q ss_pred ceeccccccccCChhHHHHHHHHcCCCCCcccCcchh
Q psy2643 54 PHKCVVCGKAFSQSSNLITHLRKHTGYKPFSCGLCDK 90 (134)
Q Consensus 54 ~~~C~~C~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~ 90 (134)
.|.|..||..+... +.|..||.||.
T Consensus 2 ~~~C~~CG~i~~g~------------~~p~~CP~Cg~ 26 (34)
T cd00729 2 VWVCPVCGYIHEGE------------EAPEKCPICGA 26 (34)
T ss_pred eEECCCCCCEeECC------------cCCCcCcCCCC
Confidence 36788888765432 13457888874
No 64
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=92.78 E-value=0.092 Score=35.97 Aligned_cols=24 Identities=25% Similarity=0.573 Sum_probs=12.1
Q ss_pred ccCcc--cccccCChhhHHHHHHhhc
Q psy2643 27 YPCQY--CGKRFHQKSDMKKHTYIHT 50 (134)
Q Consensus 27 ~~c~~--C~~~~~~~~~l~~h~~~~~ 50 (134)
|.||. |.........|..|....+
T Consensus 152 F~CP~skc~~~C~~~k~lk~H~K~~H 177 (493)
T COG5236 152 FKCPKSKCHRRCGSLKELKKHYKAQH 177 (493)
T ss_pred hcCCchhhhhhhhhHHHHHHHHHhhc
Confidence 44543 4444444555555655544
No 65
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=92.71 E-value=0.035 Score=37.49 Aligned_cols=63 Identities=24% Similarity=0.456 Sum_probs=37.3
Q ss_pred cCccccCChHHHHHHHHHcC-CCCCccCcccccccCChhhHHHHHHhhcCCCceeccccccccCChhHHHHHHH
Q psy2643 3 QCGKTFKRSSTLSTHLLIHS-DTRPYPCQYCGKRFHQKSDMKKHTYIHTGEKPHKCVVCGKAFSQSSNLITHLR 75 (134)
Q Consensus 3 ~C~~~f~~~~~l~~h~~~~~-~~~~~~c~~C~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~~~~~~~l~~h~~ 75 (134)
-|.+.+.....|+-|+.--+ ..+..+=| .-..+.......+||+|.+|++.+...-.|+-|+.
T Consensus 356 gC~K~YknqnGLKYH~lhGH~~~~~~~~p----------~p~~~~~F~~~~KPYrCevC~KRYKNlNGLKYHr~ 419 (423)
T COG5189 356 GCNKKYKNQNGLKYHMLHGHQNQKLHENP----------SPEKMNIFSAKDKPYRCEVCDKRYKNLNGLKYHRK 419 (423)
T ss_pred CchhhhccccchhhhhhccccCcccCCCC----------CccccccccccCCceeccccchhhccCccceeccc
Confidence 47888998888998875422 22111111 00111112344678888888888888777776654
No 66
>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=92.58 E-value=0.31 Score=27.76 Aligned_cols=26 Identities=27% Similarity=0.522 Sum_probs=22.8
Q ss_pred ceec----cccccccCChhHHHHHHHHcCC
Q psy2643 54 PHKC----VVCGKAFSQSSNLITHLRKHTG 79 (134)
Q Consensus 54 ~~~C----~~C~~~~~~~~~l~~h~~~~~~ 79 (134)
.|.| ..|+..+.+...+..|++.+++
T Consensus 80 G~~C~~~~~~C~y~~~~~~~m~~H~~~~Hg 109 (109)
T PF12013_consen 80 GYRCQCDPPHCGYITRSKKTMRKHWRKEHG 109 (109)
T ss_pred CeeeecCCCCCCcEeccHHHHHHHHHHhcC
Confidence 3889 9999999999999999987654
No 67
>KOG2893|consensus
Probab=92.45 E-value=0.037 Score=35.87 Aligned_cols=41 Identities=32% Similarity=0.665 Sum_probs=20.3
Q ss_pred ccccccccCChhHHHHHHHHcCCCCCcccCcchhhccChHHHHHH
Q psy2643 57 CVVCGKAFSQSSNLITHLRKHTGYKPFSCGLCDKAFQRKVDLRRH 101 (134)
Q Consensus 57 C~~C~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~f~~~~~l~~H 101 (134)
|=.|++.|.++..|..|++ .+.|+|..|-|...+-..|..|
T Consensus 13 cwycnrefddekiliqhqk----akhfkchichkkl~sgpglsih 53 (341)
T KOG2893|consen 13 CWYCNREFDDEKILIQHQK----AKHFKCHICHKKLFSGPGLSIH 53 (341)
T ss_pred eeecccccchhhhhhhhhh----hccceeeeehhhhccCCCceee
Confidence 3345555555555554444 2345555555544444444444
No 68
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=92.42 E-value=0.088 Score=23.85 Aligned_cols=32 Identities=31% Similarity=0.818 Sum_probs=17.2
Q ss_pred cCcccccccCChhhHHHHHHhhcCCCceecccccccc
Q psy2643 28 PCQYCGKRFHQKSDMKKHTYIHTGEKPHKCVVCGKAF 64 (134)
Q Consensus 28 ~c~~C~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~~ 64 (134)
.||.|+..|.-... ....+....+|..|+..|
T Consensus 4 ~CP~C~~~f~v~~~-----~l~~~~~~vrC~~C~~~f 35 (37)
T PF13719_consen 4 TCPNCQTRFRVPDD-----KLPAGGRKVRCPKCGHVF 35 (37)
T ss_pred ECCCCCceEEcCHH-----HcccCCcEEECCCCCcEe
Confidence 56667666655432 111233456677776665
No 69
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=92.21 E-value=0.12 Score=23.28 Aligned_cols=33 Identities=15% Similarity=0.417 Sum_probs=17.3
Q ss_pred eeccccccccCChhHHHHHHHHcCCCCCcccCcchhhc
Q psy2643 55 HKCVVCGKAFSQSSNLITHLRKHTGYKPFSCGLCDKAF 92 (134)
Q Consensus 55 ~~C~~C~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~f 92 (134)
..|+.|+..|.-.... .-.+....+|+.|+..|
T Consensus 3 i~Cp~C~~~y~i~d~~-----ip~~g~~v~C~~C~~~f 35 (36)
T PF13717_consen 3 ITCPNCQAKYEIDDEK-----IPPKGRKVRCSKCGHVF 35 (36)
T ss_pred EECCCCCCEEeCCHHH-----CCCCCcEEECCCCCCEe
Confidence 3566666666555432 12233346666666554
No 70
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=91.98 E-value=0.05 Score=37.98 Aligned_cols=61 Identities=48% Similarity=0.768 Sum_probs=51.9
Q ss_pred ceeccccccccCChhHHHHHHH--HcCCC--CCcccC--cchhhccChHHHHHHHHhhCCCCCCccc
Q psy2643 54 PHKCVVCGKAFSQSSNLITHLR--KHTGY--KPFSCG--LCDKAFQRKVDLRRHRESQHPGSPAQQH 114 (134)
Q Consensus 54 ~~~C~~C~~~~~~~~~l~~h~~--~~~~~--~~~~C~--~C~~~f~~~~~l~~H~~~~h~~~~~~~~ 114 (134)
.+.|..|...|.....+..|.+ .|.++ +++.|+ .|++.|.....+.+|...+....+....
T Consensus 289 ~~~~~~~~~~~s~~~~l~~~~~~~~h~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 355 (467)
T COG5048 289 PIKSKQCNISFSRSSPLTRHLRSVNHSGESLKPFSCPYSLCGKLFSRNDALKRHILLHTSISPAKEK 355 (467)
T ss_pred CCCCccccCCccccccccccccccccccccCCceeeeccCCCccccccccccCCcccccCCCccccc
Confidence 5778889999999999999999 78888 899999 7999999999999998888777755433
No 71
>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=91.85 E-value=0.11 Score=24.42 Aligned_cols=27 Identities=30% Similarity=0.613 Sum_probs=14.6
Q ss_pred CCCcccCcchhhccCh----HHHHHHHHhhC
Q psy2643 80 YKPFSCGLCDKAFQRK----VDLRRHRESQH 106 (134)
Q Consensus 80 ~~~~~C~~C~~~f~~~----~~l~~H~~~~h 106 (134)
.....|..|++.+... +.|.+|++..|
T Consensus 14 ~~~a~C~~C~~~~~~~~~~ts~l~~HL~~~h 44 (45)
T PF02892_consen 14 KKKAKCKYCGKVIKYSSGGTSNLKRHLKKKH 44 (45)
T ss_dssp SS-EEETTTTEE-----SSTHHHHHHHHHTT
T ss_pred cCeEEeCCCCeEEeeCCCcHHHHHHhhhhhC
Confidence 3446777777766653 67777775544
No 72
>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=91.81 E-value=0.098 Score=21.75 Aligned_cols=9 Identities=44% Similarity=1.036 Sum_probs=5.2
Q ss_pred cCccccccc
Q psy2643 28 PCQYCGKRF 36 (134)
Q Consensus 28 ~c~~C~~~~ 36 (134)
.|+.||..|
T Consensus 16 ~Cp~CG~~F 24 (26)
T PF10571_consen 16 FCPHCGYDF 24 (26)
T ss_pred cCCCCCCCC
Confidence 456666555
No 73
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=91.59 E-value=0.095 Score=25.88 Aligned_cols=31 Identities=23% Similarity=0.495 Sum_probs=21.0
Q ss_pred cCCCCCccCcccccccCChhhHHHHHHhhcC
Q psy2643 21 HSDTRPYPCQYCGKRFHQKSDMKKHTYIHTG 51 (134)
Q Consensus 21 ~~~~~~~~c~~C~~~~~~~~~l~~h~~~~~~ 51 (134)
..++..+.||-|+..|.....+.+|.+..++
T Consensus 12 RDGE~~lrCPRC~~~FR~~K~Y~RHVNKaH~ 42 (65)
T COG4049 12 RDGEEFLRCPRCGMVFRRRKDYIRHVNKAHG 42 (65)
T ss_pred cCCceeeeCCchhHHHHHhHHHHHHhhHHhh
Confidence 3456667777777777777777777665443
No 74
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=91.57 E-value=0.13 Score=31.68 Aligned_cols=24 Identities=38% Similarity=0.818 Sum_probs=18.8
Q ss_pred CceeccccccccCChhHHHHHHHHcCCCCCcccCcch
Q psy2643 53 KPHKCVVCGKAFSQSSNLITHLRKHTGYKPFSCGLCD 89 (134)
Q Consensus 53 ~~~~C~~C~~~~~~~~~l~~h~~~~~~~~~~~C~~C~ 89 (134)
+.|.|++||..+ .++-|..||.||
T Consensus 133 ~~~vC~vCGy~~-------------~ge~P~~CPiCg 156 (166)
T COG1592 133 KVWVCPVCGYTH-------------EGEAPEVCPICG 156 (166)
T ss_pred CEEEcCCCCCcc-------------cCCCCCcCCCCC
Confidence 369999998764 335678999998
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=91.44 E-value=0.11 Score=23.52 Aligned_cols=33 Identities=18% Similarity=0.489 Sum_probs=16.4
Q ss_pred ccCcccccccCChhhHHHHHHhhcCCCceecccccccc
Q psy2643 27 YPCQYCGKRFHQKSDMKKHTYIHTGEKPHKCVVCGKAF 64 (134)
Q Consensus 27 ~~c~~C~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~~ 64 (134)
+.||.|+..|....... ........|..|+..|
T Consensus 3 ~~CP~C~~~~~v~~~~~-----~~~~~~v~C~~C~~~~ 35 (38)
T TIGR02098 3 IQCPNCKTSFRVVDSQL-----GANGGKVRCGKCGHVW 35 (38)
T ss_pred EECCCCCCEEEeCHHHc-----CCCCCEEECCCCCCEE
Confidence 35666666655443211 1112245677776655
No 76
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=91.15 E-value=0.028 Score=36.15 Aligned_cols=14 Identities=21% Similarity=0.415 Sum_probs=10.4
Q ss_pred CcccCcchhhccCh
Q psy2643 82 PFSCGLCDKAFQRK 95 (134)
Q Consensus 82 ~~~C~~C~~~f~~~ 95 (134)
...||.||.++...
T Consensus 48 V~vCP~CgyA~~~~ 61 (214)
T PF09986_consen 48 VWVCPHCGYAAFEE 61 (214)
T ss_pred EEECCCCCCccccc
Confidence 37899999876643
No 77
>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=91.12 E-value=0.25 Score=30.29 Aligned_cols=29 Identities=17% Similarity=0.301 Sum_probs=15.0
Q ss_pred CceeccccccccCChhHHHHHHHHcCCCCCcccCcchh
Q psy2643 53 KPHKCVVCGKAFSQSSNLITHLRKHTGYKPFSCGLCDK 90 (134)
Q Consensus 53 ~~~~C~~C~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~ 90 (134)
.-|.|+.|+..|.....+. .-|.||.||.
T Consensus 108 ~~Y~Cp~c~~r~tf~eA~~---------~~F~Cp~Cg~ 136 (158)
T TIGR00373 108 MFFICPNMCVRFTFNEAME---------LNFTCPRCGA 136 (158)
T ss_pred CeEECCCCCcEeeHHHHHH---------cCCcCCCCCC
Confidence 3455655655555554442 1356666654
No 78
>smart00614 ZnF_BED BED zinc finger. DNA-binding domain in chromatin-boundary-element-binding proteins and transposases
Probab=90.50 E-value=0.24 Score=23.95 Aligned_cols=25 Identities=40% Similarity=0.844 Sum_probs=16.0
Q ss_pred cccCcchhhccCh-----HHHHHHHHhhCC
Q psy2643 83 FSCGLCDKAFQRK-----VDLRRHRESQHP 107 (134)
Q Consensus 83 ~~C~~C~~~f~~~-----~~l~~H~~~~h~ 107 (134)
-.|..|++.++.. +.|.+|++..|+
T Consensus 19 a~C~~C~~~l~~~~~~gTs~L~rHl~~~h~ 48 (50)
T smart00614 19 AKCKYCGKKLSRSSKGGTSNLRRHLRRKHP 48 (50)
T ss_pred EEecCCCCEeeeCCCCCcHHHHHHHHhHCc
Confidence 4567777766554 577888775443
No 79
>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=90.19 E-value=0.097 Score=33.64 Aligned_cols=23 Identities=26% Similarity=0.632 Sum_probs=10.7
Q ss_pred eeccccccccCChhHHHHHHHHc
Q psy2643 55 HKCVVCGKAFSQSSNLITHLRKH 77 (134)
Q Consensus 55 ~~C~~C~~~~~~~~~l~~h~~~~ 77 (134)
|.|..|++.|....-..+|+..-
T Consensus 78 ~~C~lc~KlFkg~eFV~KHI~nK 100 (214)
T PF04959_consen 78 WRCPLCGKLFKGPEFVRKHIFNK 100 (214)
T ss_dssp EEE-SSS-EESSHHHHHHHHHHH
T ss_pred ECCCCCCcccCChHHHHHHHhhc
Confidence 45555555555555555555443
No 80
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=90.15 E-value=0.36 Score=33.21 Aligned_cols=76 Identities=22% Similarity=0.527 Sum_probs=38.9
Q ss_pred CcccccccCChhhHHHHHHhhcCCCceecccccc----ccCChhHHHHHHHHcCCCCCcccCc--ch----hhccChHHH
Q psy2643 29 CQYCGKRFHQKSDMKKHTYIHTGEKPHKCVVCGK----AFSQSSNLITHLRKHTGYKPFSCGL--CD----KAFQRKVDL 98 (134)
Q Consensus 29 c~~C~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~----~~~~~~~l~~h~~~~~~~~~~~C~~--C~----~~f~~~~~l 98 (134)
|..|...|-...+|-.|++..+. +-+.|++-+. .|.+-.+|..|.+ .-.|.|.. |. .+|.+...|
T Consensus 223 C~FC~~~FYdDDEL~~HcR~~HE-~ChICD~v~p~~~QYFK~Y~~Le~HF~----~~hy~ct~qtc~~~k~~vf~~~~el 297 (493)
T COG5236 223 CIFCKIYFYDDDELRRHCRLRHE-ACHICDMVGPIRYQYFKSYEDLEAHFR----NAHYCCTFQTCRVGKCYVFPYHTEL 297 (493)
T ss_pred hhhccceecChHHHHHHHHhhhh-hhhhhhccCccchhhhhCHHHHHHHhh----cCceEEEEEEEecCcEEEeccHHHH
Confidence 55555555555555555554432 2222322211 2333334444333 22355532 22 478899999
Q ss_pred HHHHHhhCCCC
Q psy2643 99 RRHRESQHPGS 109 (134)
Q Consensus 99 ~~H~~~~h~~~ 109 (134)
+.|+..-|+..
T Consensus 298 ~~h~~~~h~~~ 308 (493)
T COG5236 298 LEHLTRFHKVN 308 (493)
T ss_pred HHHHHHHhhcc
Confidence 99987776643
No 81
>KOG2893|consensus
Probab=90.06 E-value=0.092 Score=34.10 Aligned_cols=41 Identities=29% Similarity=0.664 Sum_probs=20.3
Q ss_pred CcccccccCChhhHHHHHHhhcCCCceeccccccccCChhHHHHH
Q psy2643 29 CQYCGKRFHQKSDMKKHTYIHTGEKPHKCVVCGKAFSQSSNLITH 73 (134)
Q Consensus 29 c~~C~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~~~~~~~l~~h 73 (134)
|=+|++.|....-|..|+.. +.|+|.+|.+.+.+...|..|
T Consensus 13 cwycnrefddekiliqhqka----khfkchichkkl~sgpglsih 53 (341)
T KOG2893|consen 13 CWYCNREFDDEKILIQHQKA----KHFKCHICHKKLFSGPGLSIH 53 (341)
T ss_pred eeecccccchhhhhhhhhhh----ccceeeeehhhhccCCCceee
Confidence 44555555555555555442 235555555544444444444
No 82
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=90.05 E-value=0.059 Score=34.68 Aligned_cols=43 Identities=28% Similarity=0.554 Sum_probs=25.9
Q ss_pred CCccCcccccccCChhhHHHHHHhh----------cCCCc-----eeccccccccCCh
Q psy2643 25 RPYPCQYCGKRFHQKSDMKKHTYIH----------TGEKP-----HKCVVCGKAFSQS 67 (134)
Q Consensus 25 ~~~~c~~C~~~~~~~~~l~~h~~~~----------~~~~~-----~~C~~C~~~~~~~ 67 (134)
+...||+|+..|....-.....+.. .+-.| +.|+.||.++...
T Consensus 4 k~~~CPvC~~~F~~~~vrs~~~r~~~~d~D~~~~Y~~vnP~~Y~V~vCP~CgyA~~~~ 61 (214)
T PF09986_consen 4 KKITCPVCGKEFKTKKVRSGKIRVIRRDSDFCPRYKGVNPLFYEVWVCPHCGYAAFEE 61 (214)
T ss_pred CceECCCCCCeeeeeEEEcCCceEeeecCCCccccCCCCCeeeeEEECCCCCCccccc
Confidence 4567888888887765433333211 11122 5899999876643
No 83
>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=89.48 E-value=0.43 Score=29.25 Aligned_cols=38 Identities=18% Similarity=0.399 Sum_probs=27.7
Q ss_pred HcCCCCCccCcccccccCChhhHHHHHHhhcCCCceeccccccccCC
Q psy2643 20 IHSDTRPYPCQYCGKRFHQKSDMKKHTYIHTGEKPHKCVVCGKAFSQ 66 (134)
Q Consensus 20 ~~~~~~~~~c~~C~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~~~~ 66 (134)
.......|.|+.|+..|+....+. ..|.|+.||.....
T Consensus 103 ~e~~~~~Y~Cp~c~~r~tf~eA~~---------~~F~Cp~Cg~~L~~ 140 (158)
T TIGR00373 103 FETNNMFFICPNMCVRFTFNEAME---------LNFTCPRCGAMLDY 140 (158)
T ss_pred hccCCCeEECCCCCcEeeHHHHHH---------cCCcCCCCCCEeee
Confidence 345566789999998888776554 25899999986443
No 84
>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=89.32 E-value=0.28 Score=28.69 Aligned_cols=30 Identities=20% Similarity=0.427 Sum_probs=20.2
Q ss_pred ccCcccccccCChhhHHHHHHhhcCCCceeccccccccCCh
Q psy2643 27 YPCQYCGKRFHQKSDMKKHTYIHTGEKPHKCVVCGKAFSQS 67 (134)
Q Consensus 27 ~~c~~C~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~~~~~ 67 (134)
..|+.||..|--. +..|..|+.||..|...
T Consensus 10 r~Cp~cg~kFYDL-----------nk~p~vcP~cg~~~~~~ 39 (129)
T TIGR02300 10 RICPNTGSKFYDL-----------NRRPAVSPYTGEQFPPE 39 (129)
T ss_pred ccCCCcCcccccc-----------CCCCccCCCcCCccCcc
Confidence 4688888776532 23567788888877655
No 85
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=89.19 E-value=0.37 Score=30.15 Aligned_cols=16 Identities=19% Similarity=0.293 Sum_probs=8.2
Q ss_pred ceeccccccccCChhH
Q psy2643 54 PHKCVVCGKAFSQSSN 69 (134)
Q Consensus 54 ~~~C~~C~~~~~~~~~ 69 (134)
-|.|+.|+..|.....
T Consensus 117 ~Y~Cp~C~~rytf~eA 132 (178)
T PRK06266 117 FFFCPNCHIRFTFDEA 132 (178)
T ss_pred EEECCCCCcEEeHHHH
Confidence 3555555555554443
No 86
>KOG2807|consensus
Probab=88.82 E-value=0.67 Score=31.66 Aligned_cols=27 Identities=19% Similarity=0.411 Sum_probs=20.9
Q ss_pred CCCcccCcchhhccChHHHHHHHHhhC
Q psy2643 80 YKPFSCGLCDKAFQRKVDLRRHRESQH 106 (134)
Q Consensus 80 ~~~~~C~~C~~~f~~~~~l~~H~~~~h 106 (134)
...|.|+.|...|-..-+.-.|-.+|-
T Consensus 343 ~~~y~C~~Ck~~FCldCDv~iHesLh~ 369 (378)
T KOG2807|consen 343 SGRYRCESCKNVFCLDCDVFIHESLHN 369 (378)
T ss_pred CCcEEchhccceeeccchHHHHhhhhc
Confidence 345899999988888777778877763
No 87
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=88.57 E-value=0.19 Score=23.84 Aligned_cols=29 Identities=21% Similarity=0.496 Sum_probs=16.4
Q ss_pred ceeccccccccCChhHHHHHHHHcCCCCCcccCcchhhc
Q psy2643 54 PHKCVVCGKAFSQSSNLITHLRKHTGYKPFSCGLCDKAF 92 (134)
Q Consensus 54 ~~~C~~C~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~f 92 (134)
.|.|..||..+..... .....|+.||..+
T Consensus 3 ~y~C~~CG~~~~~~~~----------~~~~~Cp~CG~~~ 31 (46)
T PRK00398 3 EYKCARCGREVELDEY----------GTGVRCPYCGYRI 31 (46)
T ss_pred EEECCCCCCEEEECCC----------CCceECCCCCCeE
Confidence 4667777766544321 1146777777543
No 88
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=88.52 E-value=0.69 Score=27.95 Aligned_cols=37 Identities=16% Similarity=0.305 Sum_probs=23.6
Q ss_pred CCceeccccccccCChhHHHHHHHHcCCCCCcccCcchhhc
Q psy2643 52 EKPHKCVVCGKAFSQSSNLITHLRKHTGYKPFSCGLCDKAF 92 (134)
Q Consensus 52 ~~~~~C~~C~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~f 92 (134)
..-|.|+.|+..|.....+.. .. .+..|.||.||...
T Consensus 97 ~~~Y~Cp~C~~~y~~~ea~~~---~d-~~~~f~Cp~Cg~~l 133 (147)
T smart00531 97 NAYYKCPNCQSKYTFLEANQL---LD-MDGTFTCPRCGEEL 133 (147)
T ss_pred CcEEECcCCCCEeeHHHHHHh---cC-CCCcEECCCCCCEE
Confidence 345889999988876544321 11 24448999998654
No 89
>KOG2482|consensus
Probab=88.48 E-value=0.73 Score=31.73 Aligned_cols=51 Identities=24% Similarity=0.440 Sum_probs=39.3
Q ss_pred eeccccccccCChhHHHHHHHH-cCC--------------------------CCCcccCcchhhccChHHHHHHHHhh
Q psy2643 55 HKCVVCGKAFSQSSNLITHLRK-HTG--------------------------YKPFSCGLCDKAFQRKVDLRRHRESQ 105 (134)
Q Consensus 55 ~~C~~C~~~~~~~~~l~~h~~~-~~~--------------------------~~~~~C~~C~~~f~~~~~l~~H~~~~ 105 (134)
.+|..|.........|..|++. |.- .+.-.|-.|.-.|-....|..|+..+
T Consensus 280 v~CLfC~~~~en~~~l~eHmk~vHe~Dl~Ki~sd~~Ln~YqrvrviNyiRkq~~~~~c~~cd~~F~~e~~l~~hm~e~ 357 (423)
T KOG2482|consen 280 VVCLFCTNFYENPVFLFEHMKIVHEFDLLKIQSDYSLNFYQRVRVINYIRKQKKKSRCAECDLSFWKEPGLLIHMVED 357 (423)
T ss_pred eEEEeeccchhhHHHHHHHHHHHHHhhHHhhccccccchhhhhhHHHHHHHHhhccccccccccccCcchhhhhcccc
Confidence 4899999998889999999975 321 11356777888999999999998543
No 90
>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=87.98 E-value=0.15 Score=23.76 Aligned_cols=29 Identities=24% Similarity=0.675 Sum_probs=16.8
Q ss_pred eeccccccccCChhHHHHHHHHcCCCCCcccCcchh
Q psy2643 55 HKCVVCGKAFSQSSNLITHLRKHTGYKPFSCGLCDK 90 (134)
Q Consensus 55 ~~C~~C~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~ 90 (134)
|.|..||..|...... .. +..-.||.||.
T Consensus 6 y~C~~Cg~~fe~~~~~------~~-~~~~~CP~Cg~ 34 (42)
T PF09723_consen 6 YRCEECGHEFEVLQSI------SE-DDPVPCPECGS 34 (42)
T ss_pred EEeCCCCCEEEEEEEc------CC-CCCCcCCCCCC
Confidence 6677777666554321 12 34567777775
No 91
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=87.79 E-value=0.4 Score=22.64 Aligned_cols=25 Identities=20% Similarity=0.430 Sum_probs=14.4
Q ss_pred eeccccccccCChhHHHHHHHHcCCCCCcccCcchh
Q psy2643 55 HKCVVCGKAFSQSSNLITHLRKHTGYKPFSCGLCDK 90 (134)
Q Consensus 55 ~~C~~C~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~ 90 (134)
|.|..||..|... ...+.+|+.||.
T Consensus 3 Y~C~~Cg~~~~~~-----------~~~~irC~~CG~ 27 (44)
T smart00659 3 YICGECGRENEIK-----------SKDVVRCRECGY 27 (44)
T ss_pred EECCCCCCEeecC-----------CCCceECCCCCc
Confidence 6667777655432 123467777764
No 92
>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=87.72 E-value=0.5 Score=19.55 Aligned_cols=19 Identities=16% Similarity=0.443 Sum_probs=14.2
Q ss_pred ccCcchhhccChHHHHHHHH
Q psy2643 84 SCGLCDKAFQRKVDLRRHRE 103 (134)
Q Consensus 84 ~C~~C~~~f~~~~~l~~H~~ 103 (134)
.||.|++.+ ....+.+|..
T Consensus 3 ~CPiC~~~v-~~~~in~HLD 21 (26)
T smart00734 3 QCPVCFREV-PENLINSHLD 21 (26)
T ss_pred cCCCCcCcc-cHHHHHHHHH
Confidence 688888887 5567777765
No 93
>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=87.61 E-value=0.14 Score=24.97 Aligned_cols=29 Identities=21% Similarity=0.558 Sum_probs=15.6
Q ss_pred eeccccccccCChhHHHHHHHHcCCCCCcccCcchh
Q psy2643 55 HKCVVCGKAFSQSSNLITHLRKHTGYKPFSCGLCDK 90 (134)
Q Consensus 55 ~~C~~C~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~ 90 (134)
|.|..|+..|.....+ .. +..-.||.||.
T Consensus 6 y~C~~Cg~~fe~~~~~------~~-~~~~~CP~Cg~ 34 (52)
T TIGR02605 6 YRCTACGHRFEVLQKM------SD-DPLATCPECGG 34 (52)
T ss_pred EEeCCCCCEeEEEEec------CC-CCCCCCCCCCC
Confidence 6677777766543211 11 33456777774
No 94
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=87.31 E-value=0.44 Score=23.95 Aligned_cols=34 Identities=24% Similarity=0.540 Sum_probs=22.5
Q ss_pred CCccCcccccccCChhhHHHHHHhhcCCCceeccccccc
Q psy2643 25 RPYPCQYCGKRFHQKSDMKKHTYIHTGEKPHKCVVCGKA 63 (134)
Q Consensus 25 ~~~~c~~C~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~ 63 (134)
..|.||.||......-.-. -....+|.|+.||..
T Consensus 26 v~F~CPnCGe~~I~Rc~~C-----Rk~g~~Y~Cp~CGF~ 59 (61)
T COG2888 26 VKFPCPNCGEVEIYRCAKC-----RKLGNPYRCPKCGFE 59 (61)
T ss_pred eEeeCCCCCceeeehhhhH-----HHcCCceECCCcCcc
Confidence 3589999997655543222 122468999999853
No 95
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=87.23 E-value=0.081 Score=32.21 Aligned_cols=16 Identities=31% Similarity=0.858 Sum_probs=10.9
Q ss_pred ceeccccccccCChhH
Q psy2643 54 PHKCVVCGKAFSQSSN 69 (134)
Q Consensus 54 ~~~C~~C~~~~~~~~~ 69 (134)
.+.|+.||..|..-..
T Consensus 28 ~~~c~~c~~~f~~~e~ 43 (154)
T PRK00464 28 RRECLACGKRFTTFER 43 (154)
T ss_pred eeeccccCCcceEeEe
Confidence 3778888887766443
No 96
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=87.15 E-value=0.64 Score=29.13 Aligned_cols=36 Identities=22% Similarity=0.564 Sum_probs=26.0
Q ss_pred CCCCCccCcccccccCChhhHHHHHHhhcCCCceeccccccccCC
Q psy2643 22 SDTRPYPCQYCGKRFHQKSDMKKHTYIHTGEKPHKCVVCGKAFSQ 66 (134)
Q Consensus 22 ~~~~~~~c~~C~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~~~~ 66 (134)
.....|.|+.|+..|.....+. ..|.|+.||.....
T Consensus 113 ~~~~~Y~Cp~C~~rytf~eA~~---------~~F~Cp~Cg~~L~~ 148 (178)
T PRK06266 113 ENNMFFFCPNCHIRFTFDEAME---------YGFRCPQCGEMLEE 148 (178)
T ss_pred cCCCEEECCCCCcEEeHHHHhh---------cCCcCCCCCCCCee
Confidence 4456689999998888765442 25899999976544
No 97
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=86.68 E-value=1.4 Score=26.64 Aligned_cols=41 Identities=15% Similarity=0.515 Sum_probs=27.1
Q ss_pred CCCCCccCcccccccCChhhHHHHHHhhcCCCceeccccccccCC
Q psy2643 22 SDTRPYPCQYCGKRFHQKSDMKKHTYIHTGEKPHKCVVCGKAFSQ 66 (134)
Q Consensus 22 ~~~~~~~c~~C~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~~~~ 66 (134)
.....|.||.|+..|.....+.. ... ...|.|+.||.....
T Consensus 95 ~~~~~Y~Cp~C~~~y~~~ea~~~---~d~-~~~f~Cp~Cg~~l~~ 135 (147)
T smart00531 95 TNNAYYKCPNCQSKYTFLEANQL---LDM-DGTFTCPRCGEELEE 135 (147)
T ss_pred cCCcEEECcCCCCEeeHHHHHHh---cCC-CCcEECCCCCCEEEE
Confidence 44566999999999886433221 112 344999999986533
No 98
>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=86.25 E-value=0.17 Score=23.18 Aligned_cols=29 Identities=21% Similarity=0.516 Sum_probs=15.0
Q ss_pred eeccccccccCChhHHHHHHHHcCCCCCcccCcchh
Q psy2643 55 HKCVVCGKAFSQSSNLITHLRKHTGYKPFSCGLCDK 90 (134)
Q Consensus 55 ~~C~~C~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~ 90 (134)
|.|..||..|...... .. .....||.||.
T Consensus 6 y~C~~Cg~~fe~~~~~------~~-~~~~~CP~Cg~ 34 (41)
T smart00834 6 YRCEDCGHTFEVLQKI------SD-DPLATCPECGG 34 (41)
T ss_pred EEcCCCCCEEEEEEec------CC-CCCCCCCCCCC
Confidence 5666677665543221 11 33456777764
No 99
>PHA00626 hypothetical protein
Probab=86.09 E-value=0.35 Score=23.98 Aligned_cols=15 Identities=27% Similarity=0.443 Sum_probs=9.3
Q ss_pred CceeccccccccCCh
Q psy2643 53 KPHKCVVCGKAFSQS 67 (134)
Q Consensus 53 ~~~~C~~C~~~~~~~ 67 (134)
..|+|..||..|...
T Consensus 22 nrYkCkdCGY~ft~~ 36 (59)
T PHA00626 22 DDYVCCDCGYNDSKD 36 (59)
T ss_pred cceEcCCCCCeechh
Confidence 356777777666543
No 100
>KOG2186|consensus
Probab=85.97 E-value=0.65 Score=30.56 Aligned_cols=44 Identities=30% Similarity=0.702 Sum_probs=21.6
Q ss_pred CCcCccccCChHHHHHHHHHcCCCCCccCcccccccCChhhHHHHHH
Q psy2643 1 CKQCGKTFKRSSTLSTHLLIHSDTRPYPCQYCGKRFHQKSDMKKHTY 47 (134)
Q Consensus 1 C~~C~~~f~~~~~l~~h~~~~~~~~~~~c~~C~~~~~~~~~l~~h~~ 47 (134)
|..||....- ..+..|+-.-.+ ..|.|-.|+..|... .+..|..
T Consensus 6 CnvCgEsvKK-p~vekH~srCrn-~~fSCIDC~k~F~~~-sYknH~k 49 (276)
T KOG2186|consen 6 CNVCGESVKK-PQVEKHMSRCRN-AYFSCIDCGKTFERV-SYKNHTK 49 (276)
T ss_pred hhhhhhhccc-cchHHHHHhccC-CeeEEeecccccccc-hhhhhhh
Confidence 4455554433 234445543333 345666666666653 3455544
No 101
>KOG2482|consensus
Probab=85.83 E-value=1.2 Score=30.74 Aligned_cols=25 Identities=24% Similarity=0.434 Sum_probs=21.3
Q ss_pred cccCcchhhccChHHHHHHHHhhCC
Q psy2643 83 FSCGLCDKAFQRKVDLRRHRESQHP 107 (134)
Q Consensus 83 ~~C~~C~~~f~~~~~l~~H~~~~h~ 107 (134)
..|--|...+-....|..|+...|.
T Consensus 280 v~CLfC~~~~en~~~l~eHmk~vHe 304 (423)
T KOG2482|consen 280 VVCLFCTNFYENPVFLFEHMKIVHE 304 (423)
T ss_pred eEEEeeccchhhHHHHHHHHHHHHH
Confidence 5888899888888999999988765
No 102
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=84.98 E-value=0.24 Score=34.63 Aligned_cols=60 Identities=35% Similarity=0.668 Sum_probs=43.4
Q ss_pred CccCcccccccCChhhHHHHHH--hhcCC--Cceecc--ccccccCChhHHHHHHHHcCCCCCccc
Q psy2643 26 PYPCQYCGKRFHQKSDMKKHTY--IHTGE--KPHKCV--VCGKAFSQSSNLITHLRKHTGYKPFSC 85 (134)
Q Consensus 26 ~~~c~~C~~~~~~~~~l~~h~~--~~~~~--~~~~C~--~C~~~~~~~~~l~~h~~~~~~~~~~~C 85 (134)
++.|..|...|.....+..|.+ .|.++ +++.|+ .|+..|.....+..|...|.+..+..+
T Consensus 289 ~~~~~~~~~~~s~~~~l~~~~~~~~h~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 354 (467)
T COG5048 289 PIKSKQCNISFSRSSPLTRHLRSVNHSGESLKPFSCPYSLCGKLFSRNDALKRHILLHTSISPAKE 354 (467)
T ss_pred CCCCccccCCccccccccccccccccccccCCceeeeccCCCccccccccccCCcccccCCCcccc
Confidence 4667777777777777777777 67777 777777 677777777777777777766655544
No 103
>PF12907 zf-met2: Zinc-binding
Probab=83.83 E-value=1 Score=20.78 Aligned_cols=29 Identities=28% Similarity=0.713 Sum_probs=20.4
Q ss_pred cccCcchhhcc---ChHHHHHHHHhhCCCCCC
Q psy2643 83 FSCGLCDKAFQ---RKVDLRRHRESQHPGSPA 111 (134)
Q Consensus 83 ~~C~~C~~~f~---~~~~l~~H~~~~h~~~~~ 111 (134)
+.|.+|..+|. ....|..|....|+....
T Consensus 2 i~C~iC~qtF~~t~~~~~L~eH~enKHpK~~~ 33 (40)
T PF12907_consen 2 IICKICRQTFMQTTNEPQLKEHAENKHPKNTF 33 (40)
T ss_pred cCcHHhhHHHHhcCCHHHHHHHHHccCCCCCH
Confidence 56888885554 456788888888877533
No 104
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=83.75 E-value=0.41 Score=36.50 Aligned_cols=49 Identities=22% Similarity=0.449 Sum_probs=30.8
Q ss_pred ccCcccccccCChhhHHHHHHhhcCCCceeccccccccCChhHHHHHHHHcCCCCCcccCcchhh
Q psy2643 27 YPCQYCGKRFHQKSDMKKHTYIHTGEKPHKCVVCGKAFSQSSNLITHLRKHTGYKPFSCGLCDKA 91 (134)
Q Consensus 27 ~~c~~C~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~ 91 (134)
..|..||..+.... ....+..|...+...|..||.. ...|..|+.||..
T Consensus 436 l~C~~Cg~v~~Cp~-Cd~~lt~H~~~~~L~CH~Cg~~---------------~~~p~~Cp~Cgs~ 484 (730)
T COG1198 436 LLCRDCGYIAECPN-CDSPLTLHKATGQLRCHYCGYQ---------------EPIPQSCPECGSE 484 (730)
T ss_pred eecccCCCcccCCC-CCcceEEecCCCeeEeCCCCCC---------------CCCCCCCCCCCCC
Confidence 35777877765542 2222344455566788888744 2467899999954
No 105
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=83.67 E-value=0.63 Score=22.53 Aligned_cols=27 Identities=22% Similarity=0.629 Sum_probs=15.7
Q ss_pred ceeccccccccCChhHHHHHHHHcCCCCCcccCcchh
Q psy2643 54 PHKCVVCGKAFSQSSNLITHLRKHTGYKPFSCGLCDK 90 (134)
Q Consensus 54 ~~~C~~C~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~ 90 (134)
.|.|..|+..|... .......|+.||.
T Consensus 6 ~Y~C~~Cg~~~~~~----------~~~~~irCp~Cg~ 32 (49)
T COG1996 6 EYKCARCGREVELD----------QETRGIRCPYCGS 32 (49)
T ss_pred EEEhhhcCCeeehh----------hccCceeCCCCCc
Confidence 46777777776221 1234467777774
No 106
>KOG2785|consensus
Probab=82.99 E-value=2.3 Score=29.76 Aligned_cols=50 Identities=24% Similarity=0.571 Sum_probs=36.2
Q ss_pred ccCcccccccCChhhHHHHHHhhcC-----------------------CCceeccccc---cccCChhHHHHHHHH
Q psy2643 27 YPCQYCGKRFHQKSDMKKHTYIHTG-----------------------EKPHKCVVCG---KAFSQSSNLITHLRK 76 (134)
Q Consensus 27 ~~c~~C~~~~~~~~~l~~h~~~~~~-----------------------~~~~~C~~C~---~~~~~~~~l~~h~~~ 76 (134)
-.|-.|+..+.+......||..+|+ ...+.|..|+ +.|.+....+.||..
T Consensus 167 t~CLfC~~~~k~~e~~~~HM~~~HgffIPdreYL~D~~GLl~YLgeKV~~~~~CL~CN~~~~~f~sleavr~HM~~ 242 (390)
T KOG2785|consen 167 TDCLFCDKKSKSLEENLKHMFKEHGFFIPDREYLTDEKGLLKYLGEKVGIGFICLFCNELGRPFSSLEAVRAHMRD 242 (390)
T ss_pred cceeecCCCcccHHHHHHHHhhccCCcCCchHhhhchhHHHHHHHHHhccCceEEEeccccCcccccHHHHHHHhh
Confidence 4566677666666666666665554 3347899999 889999999999874
No 107
>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=82.90 E-value=0.59 Score=27.76 Aligned_cols=28 Identities=32% Similarity=0.608 Sum_probs=16.1
Q ss_pred CCcccCcchhhccChHHHHHHHHhhCCCCCC
Q psy2643 81 KPFSCGLCDKAFQRKVDLRRHRESQHPGSPA 111 (134)
Q Consensus 81 ~~~~C~~C~~~f~~~~~l~~H~~~~h~~~~~ 111 (134)
....|-.||+.|.. |++|++.||+..+.
T Consensus 71 d~i~clecGk~~k~---LkrHL~~~~gltp~ 98 (132)
T PF05443_consen 71 DYIICLECGKKFKT---LKRHLRTHHGLTPE 98 (132)
T ss_dssp S-EE-TBT--EESB---HHHHHHHTT-S-HH
T ss_pred CeeEEccCCcccch---HHHHHHHccCCCHH
Confidence 34678888888764 47888888877654
No 108
>PRK04023 DNA polymerase II large subunit; Validated
Probab=82.24 E-value=1.6 Score=34.50 Aligned_cols=9 Identities=22% Similarity=0.671 Sum_probs=6.3
Q ss_pred CcccCcchh
Q psy2643 82 PFSCGLCDK 90 (134)
Q Consensus 82 ~~~C~~C~~ 90 (134)
++.|+.||.
T Consensus 663 ~y~CPKCG~ 671 (1121)
T PRK04023 663 EDECEKCGR 671 (1121)
T ss_pred CCcCCCCCC
Confidence 367888874
No 109
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=81.97 E-value=0.93 Score=30.85 Aligned_cols=48 Identities=23% Similarity=0.479 Sum_probs=31.7
Q ss_pred ccccccccCChhHHHHHHHHcCCCCCcccCcchhhccChHHHHHHHHhhC
Q psy2643 57 CVVCGKAFSQSSNLITHLRKHTGYKPFSCGLCDKAFQRKVDLRRHRESQH 106 (134)
Q Consensus 57 C~~C~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~~h 106 (134)
|..|...|..+..-.. -.-+....|.|+.|...|-..-+.-.|..+|.
T Consensus 365 Cf~CQ~~fp~~~~~~~--~~~~ss~rY~Ce~CK~~FC~dCdvfiHe~Lh~ 412 (421)
T COG5151 365 CFVCQGPFPKPPVSPF--DESTSSGRYQCELCKSTFCSDCDVFIHETLHF 412 (421)
T ss_pred ceeccCCCCCCCCCcc--cccccccceechhhhhhhhhhhHHHHHHHHhh
Confidence 7777777766533110 01122346999999999998888888877763
No 110
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=80.56 E-value=0.94 Score=24.87 Aligned_cols=27 Identities=33% Similarity=0.763 Sum_probs=18.0
Q ss_pred ceeccccccccCChhHHHHHHHHcCCCCCcccCcchh
Q psy2643 54 PHKCVVCGKAFSQSSNLITHLRKHTGYKPFSCGLCDK 90 (134)
Q Consensus 54 ~~~C~~C~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~ 90 (134)
|-.|..||+.|.+.. -.+|-+||.|..
T Consensus 58 Pa~CkkCGfef~~~~----------ik~pSRCP~CKS 84 (97)
T COG3357 58 PARCKKCGFEFRDDK----------IKKPSRCPKCKS 84 (97)
T ss_pred ChhhcccCccccccc----------cCCcccCCcchh
Confidence 457888888887631 135677888863
No 111
>PF15135 UPF0515: Uncharacterised protein UPF0515
Probab=79.87 E-value=1.7 Score=28.62 Aligned_cols=71 Identities=18% Similarity=0.405 Sum_probs=32.5
Q ss_pred HHHHHHHHHcCCC-----CCccCcccccccCChhhHHHHHHhhcCCCceeccccccccCChhHHHHHHHHcCCCCCcccC
Q psy2643 12 STLSTHLLIHSDT-----RPYPCQYCGKRFHQKSDMKKHTYIHTGEKPHKCVVCGKAFSQSSNLITHLRKHTGYKPFSCG 86 (134)
Q Consensus 12 ~~l~~h~~~~~~~-----~~~~c~~C~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~~~~~~~l~~h~~~~~~~~~~~C~ 86 (134)
.+|+......... +.|.|..|+..+ +.+.-.....-.|..|...|.-...- .-.|-.-|.|+
T Consensus 93 ~Nlrm~d~a~~~~ip~~drqFaC~~Cd~~W--------wRrvp~rKeVSRCr~C~~rYDPVP~d-----kmwG~aef~C~ 159 (278)
T PF15135_consen 93 ENLRMFDDAQENLIPSVDRQFACSSCDHMW--------WRRVPQRKEVSRCRKCRKRYDPVPCD-----KMWGIAEFHCP 159 (278)
T ss_pred HHHHHhhhhhhccccccceeeeccccchHH--------HhccCcccccccccccccccCCCccc-----cccceeeeecc
Confidence 3444444444333 557888886431 11222222223466666555432210 01222336676
Q ss_pred cchhhccCh
Q psy2643 87 LCDKAFQRK 95 (134)
Q Consensus 87 ~C~~~f~~~ 95 (134)
.|+..|...
T Consensus 160 ~C~h~F~G~ 168 (278)
T PF15135_consen 160 KCRHNFRGF 168 (278)
T ss_pred cccccchhh
Confidence 676666533
No 112
>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=79.52 E-value=0.71 Score=18.77 Aligned_cols=8 Identities=50% Similarity=1.393 Sum_probs=5.2
Q ss_pred CcccCcch
Q psy2643 82 PFSCGLCD 89 (134)
Q Consensus 82 ~~~C~~C~ 89 (134)
.|.||.||
T Consensus 16 ~f~CPnCG 23 (24)
T PF07754_consen 16 PFPCPNCG 23 (24)
T ss_pred eEeCCCCC
Confidence 46666666
No 113
>PF13878 zf-C2H2_3: zinc-finger of acetyl-transferase ESCO
Probab=79.40 E-value=2.2 Score=19.73 Aligned_cols=21 Identities=24% Similarity=0.545 Sum_probs=11.3
Q ss_pred CCcCccccCCh--HHHHHHHHHc
Q psy2643 1 CKQCGKTFKRS--STLSTHLLIH 21 (134)
Q Consensus 1 C~~C~~~f~~~--~~l~~h~~~~ 21 (134)
|+.||..|... .+-..|.+.|
T Consensus 16 C~~CgM~Y~~~~~eD~~~H~~yH 38 (41)
T PF13878_consen 16 CPTCGMLYSPGSPEDEKLHKKYH 38 (41)
T ss_pred CCCCCCEECCCCHHHHHHHHHHH
Confidence 66677665544 3445555444
No 114
>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=79.35 E-value=0.56 Score=20.19 Aligned_cols=10 Identities=30% Similarity=0.727 Sum_probs=5.3
Q ss_pred Cceecccccc
Q psy2643 53 KPHKCVVCGK 62 (134)
Q Consensus 53 ~~~~C~~C~~ 62 (134)
..|.|+.|+.
T Consensus 18 ~~~vCp~C~~ 27 (30)
T PF08274_consen 18 ELLVCPECGH 27 (30)
T ss_dssp SSEEETTTTE
T ss_pred CEEeCCcccc
Confidence 3455655553
No 115
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=78.96 E-value=0.87 Score=18.22 Aligned_cols=8 Identities=38% Similarity=1.257 Sum_probs=4.0
Q ss_pred CCcCcccc
Q psy2643 1 CKQCGKTF 8 (134)
Q Consensus 1 C~~C~~~f 8 (134)
|+.||...
T Consensus 2 Cp~CG~~~ 9 (23)
T PF13240_consen 2 CPNCGAEI 9 (23)
T ss_pred CcccCCCC
Confidence 45555443
No 116
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=78.46 E-value=0.91 Score=24.76 Aligned_cols=13 Identities=23% Similarity=0.667 Sum_probs=8.0
Q ss_pred CCcccCcchhhcc
Q psy2643 81 KPFSCGLCDKAFQ 93 (134)
Q Consensus 81 ~~~~C~~C~~~f~ 93 (134)
.-|.|..||..|+
T Consensus 52 GIW~C~kCg~~fA 64 (89)
T COG1997 52 GIWKCRKCGAKFA 64 (89)
T ss_pred CeEEcCCCCCeec
Confidence 4466666666655
No 117
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=78.41 E-value=1.3 Score=22.27 Aligned_cols=34 Identities=21% Similarity=0.537 Sum_probs=21.4
Q ss_pred CCccCcccccccCChhhHHHHHHhhcCCCceeccccccc
Q psy2643 25 RPYPCQYCGKRFHQKSDMKKHTYIHTGEKPHKCVVCGKA 63 (134)
Q Consensus 25 ~~~~c~~C~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~ 63 (134)
..|.||.||......-.- .+ ....+|.|+.||..
T Consensus 24 ~~F~CPnCG~~~I~RC~~---CR--k~~~~Y~CP~CGF~ 57 (59)
T PRK14890 24 VKFLCPNCGEVIIYRCEK---CR--KQSNPYTCPKCGFE 57 (59)
T ss_pred CEeeCCCCCCeeEeechh---HH--hcCCceECCCCCCc
Confidence 458999999873333211 12 12367999999864
No 118
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=78.10 E-value=0.79 Score=27.34 Aligned_cols=15 Identities=33% Similarity=0.658 Sum_probs=11.0
Q ss_pred CceeccccccccCCh
Q psy2643 53 KPHKCVVCGKAFSQS 67 (134)
Q Consensus 53 ~~~~C~~C~~~~~~~ 67 (134)
..|.|..||..|...
T Consensus 69 ~~~~C~~CG~~~~~~ 83 (135)
T PRK03824 69 AVLKCRNCGNEWSLK 83 (135)
T ss_pred eEEECCCCCCEEecc
Confidence 347899999877654
No 119
>PF02176 zf-TRAF: TRAF-type zinc finger; PDB: 2EOD_A 2YUC_A 3HCU_A 3HCS_B 3HCT_A.
Probab=77.20 E-value=1.5 Score=21.77 Aligned_cols=19 Identities=26% Similarity=0.513 Sum_probs=7.4
Q ss_pred HHHHHHHHcCCCCCcccCc
Q psy2643 69 NLITHLRKHTGYKPFSCGL 87 (134)
Q Consensus 69 ~l~~h~~~~~~~~~~~C~~ 87 (134)
.|..|+...-..++..|+.
T Consensus 25 ~l~~H~~~~C~~~~v~C~~ 43 (60)
T PF02176_consen 25 ELDDHLENECPKRPVPCPY 43 (60)
T ss_dssp CHHHHHHTTSTTSEEE-SS
T ss_pred HHHHHHHccCCCCcEECCC
Confidence 3444444333333444444
No 120
>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=76.22 E-value=1.5 Score=19.18 Aligned_cols=10 Identities=30% Similarity=0.903 Sum_probs=5.7
Q ss_pred CcccCcchhh
Q psy2643 82 PFSCGLCDKA 91 (134)
Q Consensus 82 ~~~C~~C~~~ 91 (134)
+.+|+.||..
T Consensus 17 ~irC~~CG~R 26 (32)
T PF03604_consen 17 PIRCPECGHR 26 (32)
T ss_dssp TSSBSSSS-S
T ss_pred cEECCcCCCe
Confidence 4577777643
No 121
>PF04780 DUF629: Protein of unknown function (DUF629); InterPro: IPR006865 This domain represents a region of several plant proteins of unknown function. A C2H2 zinc finger is predicted in this region in some family members, but the spacing between the cysteine residues is not conserved throughout the family.
Probab=76.11 E-value=2 Score=31.14 Aligned_cols=30 Identities=27% Similarity=0.516 Sum_probs=24.9
Q ss_pred CCcccCcchhhccChHHHHHHHHhhCCCCC
Q psy2643 81 KPFSCGLCDKAFQRKVDLRRHRESQHPGSP 110 (134)
Q Consensus 81 ~~~~C~~C~~~f~~~~~l~~H~~~~h~~~~ 110 (134)
+-+.|+.|.+.|.+...+..|+...|....
T Consensus 56 rFWiCp~CskkF~d~~~~~~H~~~eH~~~l 85 (466)
T PF04780_consen 56 RFWICPRCSKKFSDAESCLSHMEQEHPAGL 85 (466)
T ss_pred eEeeCCcccceeCCHHHHHHHHHHhhhhhc
Confidence 458889999999999999999987777654
No 122
>PF15269 zf-C2H2_7: Zinc-finger
Probab=74.92 E-value=2.6 Score=19.87 Aligned_cols=22 Identities=27% Similarity=0.584 Sum_probs=18.0
Q ss_pred eeccccccccCChhHHHHHHHH
Q psy2643 55 HKCVVCGKAFSQSSNLITHLRK 76 (134)
Q Consensus 55 ~~C~~C~~~~~~~~~l~~h~~~ 76 (134)
|.|-.|+......+.|..|++-
T Consensus 21 ykcfqcpftc~~kshl~nhmky 42 (54)
T PF15269_consen 21 YKCFQCPFTCNEKSHLFNHMKY 42 (54)
T ss_pred ceeecCCcccchHHHHHHHHHH
Confidence 6788888888888888888873
No 123
>PF07800 DUF1644: Protein of unknown function (DUF1644); InterPro: IPR012866 This family consists of sequences found in a number of hypothetical plant proteins of unknown function. The region of interest contains nine highly conserved cysteine residues and is approximately 160 amino acids in length, which probably represent a zinc-binding domain.
Probab=74.72 E-value=17 Score=22.40 Aligned_cols=61 Identities=21% Similarity=0.394 Sum_probs=37.8
Q ss_pred ceeccccccccCChhHHHHHHHHcCCCCCcccCc--chhhccChHHHHHHHHhhCCCCCCccccc
Q psy2643 54 PHKCVVCGKAFSQSSNLITHLRKHTGYKPFSCGL--CDKAFQRKVDLRRHRESQHPGSPAQQHHI 116 (134)
Q Consensus 54 ~~~C~~C~~~~~~~~~l~~h~~~~~~~~~~~C~~--C~~~f~~~~~l~~H~~~~h~~~~~~~~~~ 116 (134)
...|+.|..... .+......+.+-+.|+-.|.. |...- +..+|+.|.+..|+...+..+++
T Consensus 80 ~L~CPLCRG~V~-GWtvve~AR~~LN~K~RsC~~e~C~F~G-tY~eLrKHar~~HP~~rP~~vDP 142 (162)
T PF07800_consen 80 ELACPLCRGEVK-GWTVVEPARRFLNAKKRSCSQESCSFSG-TYSELRKHARSEHPSARPSEVDP 142 (162)
T ss_pred cccCccccCcee-ceEEchHHHHHhccCCccCccccccccc-CHHHHHHHHHhhCCCCCCccCCH
Confidence 467888875321 122223345555566666654 65442 56799999999999876665443
No 124
>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=73.88 E-value=1.4 Score=28.45 Aligned_cols=34 Identities=26% Similarity=0.501 Sum_probs=24.2
Q ss_pred CCCCCcccCcchhhccChHHHHHHHHhhCCCCCC
Q psy2643 78 TGYKPFSCGLCDKAFQRKVDLRRHRESQHPGSPA 111 (134)
Q Consensus 78 ~~~~~~~C~~C~~~f~~~~~l~~H~~~~h~~~~~ 111 (134)
..+..|.|+.|+|.|.-..-++.|+..+|++...
T Consensus 73 ~~~~K~~C~lc~KlFkg~eFV~KHI~nKH~e~ve 106 (214)
T PF04959_consen 73 EDEDKWRCPLCGKLFKGPEFVRKHIFNKHPEKVE 106 (214)
T ss_dssp SSSEEEEE-SSS-EESSHHHHHHHHHHH-HHHHH
T ss_pred HcCCEECCCCCCcccCChHHHHHHHhhcCHHHHH
Confidence 3455688988999998888888888888877643
No 125
>COG4957 Predicted transcriptional regulator [Transcription]
Probab=73.67 E-value=1.5 Score=25.99 Aligned_cols=26 Identities=27% Similarity=0.393 Sum_probs=18.7
Q ss_pred cccCcchhhccChHHHHHHHHhhCCCCCC
Q psy2643 83 FSCGLCDKAFQRKVDLRRHRESQHPGSPA 111 (134)
Q Consensus 83 ~~C~~C~~~f~~~~~l~~H~~~~h~~~~~ 111 (134)
..|-.+||.|. +|++|..+|++..|.
T Consensus 77 IicLEDGkkfK---SLKRHL~t~~gmTPd 102 (148)
T COG4957 77 IICLEDGKKFK---SLKRHLTTHYGLTPD 102 (148)
T ss_pred EEEeccCcchH---HHHHHHhcccCCCHH
Confidence 56777787774 578888887776654
No 126
>PF14353 CpXC: CpXC protein
Probab=72.97 E-value=0.13 Score=30.22 Aligned_cols=14 Identities=29% Similarity=0.982 Sum_probs=7.8
Q ss_pred ccCcccccccCChh
Q psy2643 27 YPCQYCGKRFHQKS 40 (134)
Q Consensus 27 ~~c~~C~~~~~~~~ 40 (134)
+.||.||..|.-..
T Consensus 39 ~~CP~Cg~~~~~~~ 52 (128)
T PF14353_consen 39 FTCPSCGHKFRLEY 52 (128)
T ss_pred EECCCCCCceecCC
Confidence 55666666554433
No 127
>KOG3408|consensus
Probab=72.76 E-value=2.8 Score=24.44 Aligned_cols=24 Identities=25% Similarity=0.510 Sum_probs=14.7
Q ss_pred CcccCcchhhccChHHHHHHHHhh
Q psy2643 82 PFSCGLCDKAFQRKVDLRRHRESQ 105 (134)
Q Consensus 82 ~~~C~~C~~~f~~~~~l~~H~~~~ 105 (134)
.|.|-.|.+-|.+...|..|.++.
T Consensus 57 qfyCi~CaRyFi~~~~l~~H~ktK 80 (129)
T KOG3408|consen 57 QFYCIECARYFIDAKALKTHFKTK 80 (129)
T ss_pred eeehhhhhhhhcchHHHHHHHhcc
Confidence 366666666666666666665443
No 128
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=72.36 E-value=0.77 Score=24.21 Aligned_cols=41 Identities=17% Similarity=0.362 Sum_probs=21.1
Q ss_pred eeccccccccCChhHHHHHHHHcCCCCCcccC--cchhhccChHH
Q psy2643 55 HKCVVCGKAFSQSSNLITHLRKHTGYKPFSCG--LCDKAFQRKVD 97 (134)
Q Consensus 55 ~~C~~C~~~~~~~~~l~~h~~~~~~~~~~~C~--~C~~~f~~~~~ 97 (134)
+.|+.||..-...+.-. +.....+.-+.|. .||..|+..-.
T Consensus 2 m~CP~Cg~~a~irtSr~--~s~~~~~~Y~qC~N~eCg~tF~t~es 44 (72)
T PRK09678 2 FHCPLCQHAAHARTSRY--ITDTTKERYHQCQNVNCSATFITYES 44 (72)
T ss_pred ccCCCCCCccEEEEChh--cChhhheeeeecCCCCCCCEEEEEEE
Confidence 35666765432222211 1112445567776 78888875543
No 129
>COG4530 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=72.03 E-value=2.5 Score=24.15 Aligned_cols=12 Identities=25% Similarity=0.470 Sum_probs=6.9
Q ss_pred Cceecccccccc
Q psy2643 53 KPHKCVVCGKAF 64 (134)
Q Consensus 53 ~~~~C~~C~~~~ 64 (134)
.|..|+.||..|
T Consensus 25 dPiVsPytG~s~ 36 (129)
T COG4530 25 DPIVSPYTGKSY 36 (129)
T ss_pred CccccCcccccc
Confidence 455566666655
No 130
>TIGR00686 phnA alkylphosphonate utilization operon protein PhnA. The protein family includes an uncharacterized member designated phnA in Escherichia coli, part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage. This protein is not related to the characterized phosphonoacetate hydrolase designated PhnA by Kulakova, et al. (2001, 1997).
Probab=71.97 E-value=2.2 Score=24.29 Aligned_cols=12 Identities=17% Similarity=0.468 Sum_probs=6.0
Q ss_pred CccCcccccccC
Q psy2643 26 PYPCQYCGKRFH 37 (134)
Q Consensus 26 ~~~c~~C~~~~~ 37 (134)
.+.||+|+..+.
T Consensus 19 ~~iCpeC~~EW~ 30 (109)
T TIGR00686 19 QLICPSCLYEWN 30 (109)
T ss_pred eeECcccccccc
Confidence 355555554443
No 131
>KOG4377|consensus
Probab=71.48 E-value=3.4 Score=29.37 Aligned_cols=104 Identities=23% Similarity=0.428 Sum_probs=58.9
Q ss_pred CcCccccCChHHHHHHHHHcCCCCC------------ccC--cccccccCChhhHHHHHHhhcCC-------Cceecccc
Q psy2643 2 KQCGKTFKRSSTLSTHLLIHSDTRP------------YPC--QYCGKRFHQKSDMKKHTYIHTGE-------KPHKCVVC 60 (134)
Q Consensus 2 ~~C~~~f~~~~~l~~h~~~~~~~~~------------~~c--~~C~~~~~~~~~l~~h~~~~~~~-------~~~~C~~C 60 (134)
+.|++.+..+.++..|...|...+. |.| ..|.+ +.+.+..|-..|... ..|.|..+
T Consensus 277 e~C~ykr~~k~DvirH~~~hkkrdnsL~dgf~rfs~syhC~~~~C~k---sTsdV~~h~nFht~~~n~GfrrthfhC~r~ 353 (480)
T KOG4377|consen 277 EYCFYKRGQKNDVIRHVEIHKKRDNSLIDGFHRFSNSYHCTGQICEK---STSDVLLHDNFHTDKRNNGFRRTHFHCQRI 353 (480)
T ss_pred ccccccccchhhhHHHHHHHhhcccccccchhhcCccchhhhcccCc---ccccccccCccccccccCceecceeEEecc
Confidence 3578777778888888877743221 344 24555 334455665555321 23678887
Q ss_pred c--cccCChhHHHHHHHHcCCCC------------------------Cccc--CcchhhccChHHHHHHHHhhCCC
Q psy2643 61 G--KAFSQSSNLITHLRKHTGYK------------------------PFSC--GLCDKAFQRKVDLRRHRESQHPG 108 (134)
Q Consensus 61 ~--~~~~~~~~l~~h~~~~~~~~------------------------~~~C--~~C~~~f~~~~~l~~H~~~~h~~ 108 (134)
+ ..|.....-..|.+.+.++. .+.| +-|+..+...+++..|.+.|-..
T Consensus 354 gCTdtfK~~khk~yh~kdda~~~dGfkkf~k~e~cay~gCkys~~cnhfhc~r~Gc~~tl~s~sqm~shkrkheRq 429 (480)
T KOG4377|consen 354 GCTDTFKDSKHKPYHYKDDAGEIDGFKKFFKDENCAYTGCKYSGICNHFHCDRLGCEATLYSVSQMASHKRKHERQ 429 (480)
T ss_pred CCccccccccccccccCcchhhhhhhhhhhccccCCccCcccccceeeeeecccCCceEEEehhhhhhhhhhhhhh
Confidence 7 45543333222332222111 2334 23889999999999998777433
No 132
>KOG4167|consensus
Probab=70.85 E-value=0.81 Score=34.72 Aligned_cols=23 Identities=30% Similarity=0.804 Sum_probs=19.0
Q ss_pred CCcCccccCChHHHHHHHHHcCC
Q psy2643 1 CKQCGKTFKRSSTLSTHLLIHSD 23 (134)
Q Consensus 1 C~~C~~~f~~~~~l~~h~~~~~~ 23 (134)
|.+|++.|.....+++||++|..
T Consensus 795 CreC~kvF~KiKSrNAHMK~Hr~ 817 (907)
T KOG4167|consen 795 CRECGKVFFKIKSRNAHMKTHRQ 817 (907)
T ss_pred hHHHHHHHHHHhhhhHHHHHHHH
Confidence 77889999888888889888743
No 133
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=70.78 E-value=1.2 Score=24.49 Aligned_cols=31 Identities=23% Similarity=0.461 Sum_probs=18.1
Q ss_pred ceeccccccccCChhHHHHHHHHcCCCCCcccCcchhhccC
Q psy2643 54 PHKCVVCGKAFSQSSNLITHLRKHTGYKPFSCGLCDKAFQR 94 (134)
Q Consensus 54 ~~~C~~C~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~f~~ 94 (134)
.|.|+.|+..-.. -.+...|.|..|++.|+-
T Consensus 36 ~y~CpfCgk~~vk----------R~a~GIW~C~~C~~~~AG 66 (90)
T PTZ00255 36 KYFCPFCGKHAVK----------RQAVGIWRCKGCKKTVAG 66 (90)
T ss_pred CccCCCCCCCcee----------eeeeEEEEcCCCCCEEeC
Confidence 5777777643111 122355778888877764
No 134
>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=69.73 E-value=0.7 Score=19.53 Aligned_cols=19 Identities=37% Similarity=0.677 Sum_probs=10.3
Q ss_pred cccCcchhhccChHHHHHHH
Q psy2643 83 FSCGLCDKAFQRKVDLRRHR 102 (134)
Q Consensus 83 ~~C~~C~~~f~~~~~l~~H~ 102 (134)
|.|-.|++.| ....++.|.
T Consensus 1 ~sCiDC~~~F-~~~~y~~Ht 19 (28)
T PF08790_consen 1 FSCIDCSKDF-DGDSYKSHT 19 (28)
T ss_dssp EEETTTTEEE-EGGGTTT--
T ss_pred CeeecCCCCc-CcCCcCCCC
Confidence 3567777777 444455553
No 135
>PRK10220 hypothetical protein; Provisional
Probab=69.60 E-value=3 Score=23.81 Aligned_cols=11 Identities=27% Similarity=0.957 Sum_probs=5.2
Q ss_pred ccCcccccccC
Q psy2643 27 YPCQYCGKRFH 37 (134)
Q Consensus 27 ~~c~~C~~~~~ 37 (134)
+.||+|+..+.
T Consensus 21 ~vCpeC~hEW~ 31 (111)
T PRK10220 21 YICPECAHEWN 31 (111)
T ss_pred EECCcccCcCC
Confidence 45555544433
No 136
>KOG1280|consensus
Probab=68.94 E-value=5.6 Score=27.66 Aligned_cols=32 Identities=25% Similarity=0.417 Sum_probs=21.8
Q ss_pred CCCcccCcchhhccChHHHHHHHHhhCCCCCC
Q psy2643 80 YKPFSCGLCDKAFQRKVDLRRHRESQHPGSPA 111 (134)
Q Consensus 80 ~~~~~C~~C~~~f~~~~~l~~H~~~~h~~~~~ 111 (134)
+..|.|++|+..-.+...|+.|....|++-..
T Consensus 77 ~qSftCPyC~~~Gfte~~f~~Hv~s~Hpda~~ 108 (381)
T KOG1280|consen 77 PQSFTCPYCGIMGFTERQFGTHVLSQHPEAST 108 (381)
T ss_pred cccccCCcccccccchhHHHHHhhhcCcccCc
Confidence 34577777777666666777777777776654
No 137
>PF01780 Ribosomal_L37ae: Ribosomal L37ae protein family; InterPro: IPR002674 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This ribosomal protein is found in archaebacteria and eukaryotes []. Ribosomal protein L37 has a single zinc finger-like motif of the C2-C2 type [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 4A1E_Y 4A17_Y 4A1C_Y 4A1A_Y 3O58_g 3IZS_m 3O5H_g 1S1I_9 3IZR_m 1YSH_D ....
Probab=68.21 E-value=0.97 Score=24.91 Aligned_cols=30 Identities=27% Similarity=0.607 Sum_probs=17.3
Q ss_pred ceeccccccccCChhHHHHHHHHcCCCCCcccCcchhhcc
Q psy2643 54 PHKCVVCGKAFSQSSNLITHLRKHTGYKPFSCGLCDKAFQ 93 (134)
Q Consensus 54 ~~~C~~C~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~f~ 93 (134)
.|.|+.|+..-... ....-|.|..|++.|+
T Consensus 35 ky~Cp~Cgk~~vkR----------~a~GIW~C~~C~~~~A 64 (90)
T PF01780_consen 35 KYTCPFCGKTSVKR----------VATGIWKCKKCGKKFA 64 (90)
T ss_dssp -BEESSSSSSEEEE----------EETTEEEETTTTEEEE
T ss_pred CCcCCCCCCceeEE----------eeeEEeecCCCCCEEe
Confidence 47777777542111 2234577888877665
No 138
>KOG0717|consensus
Probab=67.92 E-value=3.1 Score=30.08 Aligned_cols=22 Identities=32% Similarity=0.807 Sum_probs=19.3
Q ss_pred cccCcchhhccChHHHHHHHHh
Q psy2643 83 FSCGLCDKAFQRKVDLRRHRES 104 (134)
Q Consensus 83 ~~C~~C~~~f~~~~~l~~H~~~ 104 (134)
+.|.+|+|.|.+..+|.+|...
T Consensus 293 lyC~vCnKsFKseKq~kNHEnS 314 (508)
T KOG0717|consen 293 LYCVVCNKSFKSEKQLKNHENS 314 (508)
T ss_pred eEEeeccccccchHHHHhhHHH
Confidence 7899999999999999999743
No 139
>PF13451 zf-trcl: Probable zinc-binding domain
Probab=67.60 E-value=5.1 Score=19.41 Aligned_cols=38 Identities=21% Similarity=0.433 Sum_probs=16.8
Q ss_pred CceeccccccccCChhHHHHHHHH-cCCCCCcccCcchh
Q psy2643 53 KPHKCVVCGKAFSQSSNLITHLRK-HTGYKPFSCGLCDK 90 (134)
Q Consensus 53 ~~~~C~~C~~~~~~~~~l~~h~~~-~~~~~~~~C~~C~~ 90 (134)
+.+.|..||..|..-..=+..... .....|-.|+.|.+
T Consensus 3 k~l~C~dCg~~FvfTa~EQ~fy~eKgf~n~p~RC~~CR~ 41 (49)
T PF13451_consen 3 KTLTCKDCGAEFVFTAGEQKFYAEKGFDNEPKRCPSCRQ 41 (49)
T ss_pred eeEEcccCCCeEEEehhHHHHHHhcCCcCCCccCHHHHH
Confidence 345566666554443332222221 11123456666653
No 140
>PRK14873 primosome assembly protein PriA; Provisional
Probab=67.49 E-value=1.5 Score=33.30 Aligned_cols=47 Identities=17% Similarity=0.442 Sum_probs=24.2
Q ss_pred cCcccccccCChhhHHHHHHhhcCCCceeccccccccCChhHHHHHHHHcCCCCCcccCcchhh
Q psy2643 28 PCQYCGKRFHQKSDMKKHTYIHTGEKPHKCVVCGKAFSQSSNLITHLRKHTGYKPFSCGLCDKA 91 (134)
Q Consensus 28 ~c~~C~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~ 91 (134)
.|..||..+.-.. ....+..|...+...|..||.. ..++.|+.||..
T Consensus 385 ~C~~Cg~~~~C~~-C~~~L~~h~~~~~l~Ch~CG~~----------------~~p~~Cp~Cgs~ 431 (665)
T PRK14873 385 ACARCRTPARCRH-CTGPLGLPSAGGTPRCRWCGRA----------------APDWRCPRCGSD 431 (665)
T ss_pred EhhhCcCeeECCC-CCCceeEecCCCeeECCCCcCC----------------CcCccCCCCcCC
Confidence 5666665544331 1112222334445677777642 135688888853
No 141
>KOG4167|consensus
Probab=67.12 E-value=1.9 Score=32.89 Aligned_cols=29 Identities=21% Similarity=0.408 Sum_probs=24.5
Q ss_pred CCcccCcchhhccChHHHHHHHHhhCCCC
Q psy2643 81 KPFSCGLCDKAFQRKVDLRRHRESQHPGS 109 (134)
Q Consensus 81 ~~~~C~~C~~~f~~~~~l~~H~~~~h~~~ 109 (134)
..|.|..|+|.|-...++..||+.|.-..
T Consensus 791 giFpCreC~kvF~KiKSrNAHMK~Hr~q~ 819 (907)
T KOG4167|consen 791 GIFPCRECGKVFFKIKSRNAHMKTHRQQE 819 (907)
T ss_pred ceeehHHHHHHHHHHhhhhHHHHHHHHHH
Confidence 45999999999999999999998885443
No 142
>KOG2593|consensus
Probab=66.39 E-value=7.9 Score=27.79 Aligned_cols=39 Identities=18% Similarity=0.560 Sum_probs=25.3
Q ss_pred CCCCCccCcccccccCChhhHHHHHHhhcCCCceeccccccc
Q psy2643 22 SDTRPYPCQYCGKRFHQKSDMKKHTYIHTGEKPHKCVVCGKA 63 (134)
Q Consensus 22 ~~~~~~~c~~C~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~ 63 (134)
+....|.||.|.+.|.....+ +........|.|..|+.-
T Consensus 124 t~~~~Y~Cp~C~kkyt~Lea~---~L~~~~~~~F~C~~C~ge 162 (436)
T KOG2593|consen 124 TNVAGYVCPNCQKKYTSLEAL---QLLDNETGEFHCENCGGE 162 (436)
T ss_pred cccccccCCccccchhhhHHH---HhhcccCceEEEecCCCc
Confidence 445568999999888765432 233333456888888864
No 143
>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=66.21 E-value=9.9 Score=19.47 Aligned_cols=13 Identities=23% Similarity=0.618 Sum_probs=6.0
Q ss_pred ceeccccccccCC
Q psy2643 54 PHKCVVCGKAFSQ 66 (134)
Q Consensus 54 ~~~C~~C~~~~~~ 66 (134)
.|.|+.||..+..
T Consensus 46 ~~~C~~Cg~~~~r 58 (69)
T PF07282_consen 46 VFTCPNCGFEMDR 58 (69)
T ss_pred eEEcCCCCCEECc
Confidence 3455555544433
No 144
>COG2879 Uncharacterized small protein [Function unknown]
Probab=65.69 E-value=8.6 Score=19.63 Aligned_cols=21 Identities=19% Similarity=0.352 Sum_probs=16.8
Q ss_pred cChHHHHHHHHhhCCCCCCcc
Q psy2643 93 QRKVDLRRHRESQHPGSPAQQ 113 (134)
Q Consensus 93 ~~~~~l~~H~~~~h~~~~~~~ 113 (134)
.+...+-+|++.+|+++|+..
T Consensus 23 pdYdnYVehmr~~hPd~p~mT 43 (65)
T COG2879 23 PDYDNYVEHMRKKHPDKPPMT 43 (65)
T ss_pred CcHHHHHHHHHHhCcCCCccc
Confidence 456678899999999998754
No 145
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=65.41 E-value=7.1 Score=32.00 Aligned_cols=50 Identities=26% Similarity=0.498 Sum_probs=25.5
Q ss_pred ccCcccccccCChhhHHHHHHhhcCCCceeccccccccCChhHHHHHHHHcCCCCCcccCcchh
Q psy2643 27 YPCQYCGKRFHQKSDMKKHTYIHTGEKPHKCVVCGKAFSQSSNLITHLRKHTGYKPFSCGLCDK 90 (134)
Q Consensus 27 ~~c~~C~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~ 90 (134)
+.|+.||...... +....-.+. ...|.|+.||....... ++ ...|+.|+.
T Consensus 668 rkCPkCG~~t~~~--fCP~CGs~t-e~vy~CPsCGaev~~de---------s~--a~~CP~CGt 717 (1337)
T PRK14714 668 RRCPSCGTETYEN--RCPDCGTHT-EPVYVCPDCGAEVPPDE---------SG--RVECPRCDV 717 (1337)
T ss_pred EECCCCCCccccc--cCcccCCcC-CCceeCccCCCccCCCc---------cc--cccCCCCCC
Confidence 5788888643221 111111111 23578888887543321 11 457999984
No 146
>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=65.37 E-value=1.5 Score=24.17 Aligned_cols=31 Identities=23% Similarity=0.527 Sum_probs=17.5
Q ss_pred ceeccccccccCChhHHHHHHHHcCCCCCcccCcchhhccC
Q psy2643 54 PHKCVVCGKAFSQSSNLITHLRKHTGYKPFSCGLCDKAFQR 94 (134)
Q Consensus 54 ~~~C~~C~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~f~~ 94 (134)
.|.|+.|+..-.. -.+...|.|..|++.|+-
T Consensus 35 ~y~CpfCgk~~vk----------R~a~GIW~C~~C~~~~AG 65 (91)
T TIGR00280 35 KYVCPFCGKKTVK----------RGSTGIWTCRKCGAKFAG 65 (91)
T ss_pred CccCCCCCCCceE----------EEeeEEEEcCCCCCEEeC
Confidence 4677777643111 122345777777777653
No 147
>KOG3408|consensus
Probab=64.54 E-value=4.9 Score=23.47 Aligned_cols=27 Identities=26% Similarity=0.615 Sum_probs=23.1
Q ss_pred cCCCceeccccccccCChhHHHHHHHH
Q psy2643 50 TGEKPHKCVVCGKAFSQSSNLITHLRK 76 (134)
Q Consensus 50 ~~~~~~~C~~C~~~~~~~~~l~~h~~~ 76 (134)
.|...|.|..|.+.|.+...|..|.++
T Consensus 53 PG~GqfyCi~CaRyFi~~~~l~~H~kt 79 (129)
T KOG3408|consen 53 PGGGQFYCIECARYFIDAKALKTHFKT 79 (129)
T ss_pred CCCceeehhhhhhhhcchHHHHHHHhc
Confidence 455568999999999999999999874
No 148
>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=63.41 E-value=3.6 Score=23.79 Aligned_cols=24 Identities=21% Similarity=0.606 Sum_probs=16.5
Q ss_pred eeccccccccCChhHHHHHHHHcCCCCCcccCcchh
Q psy2643 55 HKCVVCGKAFSQSSNLITHLRKHTGYKPFSCGLCDK 90 (134)
Q Consensus 55 ~~C~~C~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~ 90 (134)
..|..|+..|..... .+.||.||.
T Consensus 71 ~~C~~Cg~~~~~~~~------------~~~CP~Cgs 94 (115)
T TIGR00100 71 CECEDCSEEVSPEID------------LYRCPKCHG 94 (115)
T ss_pred EEcccCCCEEecCCc------------CccCcCCcC
Confidence 678888877655421 367888884
No 149
>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=62.18 E-value=2.4 Score=31.11 Aligned_cols=47 Identities=23% Similarity=0.451 Sum_probs=23.6
Q ss_pred cCcccccccCChhhHHHHHHhhcCCCceeccccccccCChhHHHHHHHHcCCCCCcccCcchh
Q psy2643 28 PCQYCGKRFHQKSDMKKHTYIHTGEKPHKCVVCGKAFSQSSNLITHLRKHTGYKPFSCGLCDK 90 (134)
Q Consensus 28 ~c~~C~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~ 90 (134)
.|..||....-.. ....+..|...+...|..||... ..+..||.|+.
T Consensus 215 ~C~~Cg~~~~C~~-C~~~l~~h~~~~~l~Ch~Cg~~~---------------~~~~~Cp~C~s 261 (505)
T TIGR00595 215 LCRSCGYILCCPN-CDVSLTYHKKEGKLRCHYCGYQE---------------PIPKTCPQCGS 261 (505)
T ss_pred EhhhCcCccCCCC-CCCceEEecCCCeEEcCCCcCcC---------------CCCCCCCCCCC
Confidence 4666665544331 12223333444556677776432 23457777774
No 150
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=62.18 E-value=3.6 Score=19.97 Aligned_cols=10 Identities=30% Similarity=0.953 Sum_probs=5.1
Q ss_pred CcccCcchhh
Q psy2643 82 PFSCGLCDKA 91 (134)
Q Consensus 82 ~~~C~~C~~~ 91 (134)
.+.|..||..
T Consensus 37 r~~C~~Cgyt 46 (50)
T PRK00432 37 RWHCGKCGYT 46 (50)
T ss_pred cEECCCcCCE
Confidence 3555555543
No 151
>COG1655 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=61.73 E-value=1.5 Score=28.51 Aligned_cols=8 Identities=25% Similarity=0.766 Sum_probs=6.0
Q ss_pred cccCcchh
Q psy2643 83 FSCGLCDK 90 (134)
Q Consensus 83 ~~C~~C~~ 90 (134)
+.||.|..
T Consensus 63 vvCP~C~y 70 (267)
T COG1655 63 VVCPICYY 70 (267)
T ss_pred EEcchhhH
Confidence 67888875
No 152
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=61.45 E-value=4.5 Score=23.32 Aligned_cols=24 Identities=17% Similarity=0.421 Sum_probs=16.3
Q ss_pred eeccccccccCChhHHHHHHHHcCCCCCcccCcchh
Q psy2643 55 HKCVVCGKAFSQSSNLITHLRKHTGYKPFSCGLCDK 90 (134)
Q Consensus 55 ~~C~~C~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~ 90 (134)
+.|..|+..|.... ..+.||.||.
T Consensus 71 ~~C~~Cg~~~~~~~------------~~~~CP~Cgs 94 (113)
T PRK12380 71 AWCWDCSQVVEIHQ------------HDAQCPHCHG 94 (113)
T ss_pred EEcccCCCEEecCC------------cCccCcCCCC
Confidence 67888887665532 3356888884
No 153
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=60.16 E-value=2 Score=23.67 Aligned_cols=31 Identities=29% Similarity=0.704 Sum_probs=17.8
Q ss_pred ceeccccccccCChhHHHHHHHHcCCCCCcccCcchhhccC
Q psy2643 54 PHKCVVCGKAFSQSSNLITHLRKHTGYKPFSCGLCDKAFQR 94 (134)
Q Consensus 54 ~~~C~~C~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~f~~ 94 (134)
.|.|+.|+..-.. -.+...|.|..|++.|+-
T Consensus 36 ~y~CpfCgk~~vk----------R~a~GIW~C~~C~~~~AG 66 (90)
T PRK03976 36 KHVCPVCGRPKVK----------RVGTGIWECRKCGAKFAG 66 (90)
T ss_pred CccCCCCCCCceE----------EEEEEEEEcCCCCCEEeC
Confidence 4777777643111 122345778888877664
No 154
>TIGR01206 lysW lysine biosynthesis protein LysW. This very small, poorly characterized protein has been shown essential in Thermus thermophilus for an unusual pathway of Lys biosynthesis from aspartate by way of alpha-aminoadipate (AAA) rather than diaminopimelate. It is found also in Deinococcus radiodurans and Pyrococcus horikoshii, which appear to share the AAA pathway.
Probab=60.08 E-value=4.2 Score=20.14 Aligned_cols=10 Identities=30% Similarity=0.886 Sum_probs=4.7
Q ss_pred eecccccccc
Q psy2643 55 HKCVVCGKAF 64 (134)
Q Consensus 55 ~~C~~C~~~~ 64 (134)
++|+.|+..+
T Consensus 3 ~~CP~CG~~i 12 (54)
T TIGR01206 3 FECPDCGAEI 12 (54)
T ss_pred cCCCCCCCEE
Confidence 3455555443
No 155
>COG1773 Rubredoxin [Energy production and conversion]
Probab=59.24 E-value=3.5 Score=20.47 Aligned_cols=12 Identities=17% Similarity=0.883 Sum_probs=9.1
Q ss_pred CcccCcchhhcc
Q psy2643 82 PFSCGLCDKAFQ 93 (134)
Q Consensus 82 ~~~C~~C~~~f~ 93 (134)
.|+|..||..|-
T Consensus 3 ~~~C~~CG~vYd 14 (55)
T COG1773 3 RWRCSVCGYVYD 14 (55)
T ss_pred ceEecCCceEec
Confidence 578888887764
No 156
>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=59.19 E-value=3.5 Score=19.98 Aligned_cols=8 Identities=38% Similarity=1.385 Sum_probs=3.0
Q ss_pred cccCcchh
Q psy2643 83 FSCGLCDK 90 (134)
Q Consensus 83 ~~C~~C~~ 90 (134)
|.||.|++
T Consensus 42 W~CPiC~~ 49 (50)
T PF02891_consen 42 WKCPICNK 49 (50)
T ss_dssp -B-TTT--
T ss_pred eECcCCcC
Confidence 77777764
No 157
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=58.93 E-value=6.3 Score=24.39 Aligned_cols=43 Identities=19% Similarity=0.379 Sum_probs=23.4
Q ss_pred eeccccccccCChhHHH--H-----HHHHcCCCCCcccCcchhhccChHHHH
Q psy2643 55 HKCVVCGKAFSQSSNLI--T-----HLRKHTGYKPFSCGLCDKAFQRKVDLR 99 (134)
Q Consensus 55 ~~C~~C~~~~~~~~~l~--~-----h~~~~~~~~~~~C~~C~~~f~~~~~l~ 99 (134)
-.|+.|+......+.-. . +.. .-+.-|.|+.||+.|=.-+.+.
T Consensus 98 ~RCp~CN~~L~~vs~eev~~~Vp~~~~~--~~~~f~~C~~CgkiYW~GsHw~ 147 (165)
T COG1656 98 SRCPECNGELEKVSREEVKEKVPEKVYR--NYEEFYRCPKCGKIYWKGSHWR 147 (165)
T ss_pred ccCcccCCEeccCcHHHHhhccchhhhh--cccceeECCCCcccccCchHHH
Confidence 36888887544332211 0 111 1234578999998876555543
No 158
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=58.84 E-value=4.1 Score=18.68 Aligned_cols=17 Identities=24% Similarity=0.569 Sum_probs=9.3
Q ss_pred eeccccccccCChhHHH
Q psy2643 55 HKCVVCGKAFSQSSNLI 71 (134)
Q Consensus 55 ~~C~~C~~~~~~~~~l~ 71 (134)
+.|+.|+..+.+...+.
T Consensus 20 d~C~~C~G~W~d~~el~ 36 (41)
T PF13453_consen 20 DVCPSCGGIWFDAGELE 36 (41)
T ss_pred EECCCCCeEEccHHHHH
Confidence 44666666655555443
No 159
>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=58.30 E-value=3 Score=19.46 Aligned_cols=13 Identities=23% Similarity=0.792 Sum_probs=9.2
Q ss_pred ccCcchhhccChH
Q psy2643 84 SCGLCDKAFQRKV 96 (134)
Q Consensus 84 ~C~~C~~~f~~~~ 96 (134)
.|+.|++.|+-+.
T Consensus 10 ~C~~C~rpf~WRK 22 (42)
T PF10013_consen 10 ICPVCGRPFTWRK 22 (42)
T ss_pred cCcccCCcchHHH
Confidence 6788888776544
No 160
>PF14311 DUF4379: Domain of unknown function (DUF4379)
Probab=57.37 E-value=9.1 Score=18.75 Aligned_cols=12 Identities=33% Similarity=0.905 Sum_probs=6.5
Q ss_pred eeccccccccCC
Q psy2643 55 HKCVVCGKAFSQ 66 (134)
Q Consensus 55 ~~C~~C~~~~~~ 66 (134)
|+|..|+..|..
T Consensus 29 W~C~~Cgh~w~~ 40 (55)
T PF14311_consen 29 WKCPKCGHEWKA 40 (55)
T ss_pred EECCCCCCeeEc
Confidence 456666555444
No 161
>KOG2636|consensus
Probab=57.13 E-value=8.3 Score=27.84 Aligned_cols=37 Identities=16% Similarity=0.343 Sum_probs=28.5
Q ss_pred HHHcCCCCCcccCcch-hhccChHHHHHHH---HhhCCCCC
Q psy2643 74 LRKHTGYKPFSCGLCD-KAFQRKVDLRRHR---ESQHPGSP 110 (134)
Q Consensus 74 ~~~~~~~~~~~C~~C~-~~f~~~~~l~~H~---~~~h~~~~ 110 (134)
.+.|.-...|.|..|| ++|.-+..+.+|. +-.|+...
T Consensus 393 yKLHGL~~ey~CEICGNy~Y~GrkaF~RHF~EwRH~hGmrC 433 (497)
T KOG2636|consen 393 YKLHGLDIEYNCEICGNYVYKGRKAFDRHFNEWRHAHGMRC 433 (497)
T ss_pred HhhcCCCcccceeeccCccccCcHHHHHHhHHHHHhhccee
Confidence 4567777889999999 8998899999996 44455443
No 162
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=56.35 E-value=4.9 Score=18.33 Aligned_cols=12 Identities=33% Similarity=0.830 Sum_probs=9.8
Q ss_pred CcccCcchhhcc
Q psy2643 82 PFSCGLCDKAFQ 93 (134)
Q Consensus 82 ~~~C~~C~~~f~ 93 (134)
++.|..|++.|=
T Consensus 12 ~f~C~~C~~~FC 23 (39)
T smart00154 12 GFKCRHCGNLFC 23 (39)
T ss_pred CeECCccCCccc
Confidence 688988988775
No 163
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=56.06 E-value=5.6 Score=23.09 Aligned_cols=25 Identities=20% Similarity=0.487 Sum_probs=15.6
Q ss_pred eeccccccccCChhHHHHHHHHcCCCCCcccCcchh
Q psy2643 55 HKCVVCGKAFSQSSNLITHLRKHTGYKPFSCGLCDK 90 (134)
Q Consensus 55 ~~C~~C~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~ 90 (134)
+.|..|+..|..... ..+.||.||.
T Consensus 72 ~~C~~Cg~~~~~~~~-----------~~~~CP~Cgs 96 (117)
T PRK00564 72 LECKDCSHVFKPNAL-----------DYGVCEKCHS 96 (117)
T ss_pred EEhhhCCCccccCCc-----------cCCcCcCCCC
Confidence 678888876655321 1134888884
No 164
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=55.95 E-value=16 Score=23.04 Aligned_cols=31 Identities=19% Similarity=0.440 Sum_probs=18.5
Q ss_pred CCCceeccccccccCChhHHHHHHHHcCCCCCcccCcchh
Q psy2643 51 GEKPHKCVVCGKAFSQSSNLITHLRKHTGYKPFSCGLCDK 90 (134)
Q Consensus 51 ~~~~~~C~~C~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~ 90 (134)
...-|.|+.|...+....++.. -|.||.||-
T Consensus 110 ~~~~y~C~~~~~r~sfdeA~~~---------~F~Cp~Cg~ 140 (176)
T COG1675 110 ENNYYVCPNCHVKYSFDEAMEL---------GFTCPKCGE 140 (176)
T ss_pred cCCceeCCCCCCcccHHHHHHh---------CCCCCCCCc
Confidence 4455777777666655544321 177888874
No 165
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=55.90 E-value=6.7 Score=18.74 Aligned_cols=10 Identities=30% Similarity=0.767 Sum_probs=5.3
Q ss_pred CcccCcchhh
Q psy2643 82 PFSCGLCDKA 91 (134)
Q Consensus 82 ~~~C~~C~~~ 91 (134)
.+.|+.||..
T Consensus 20 ~~vC~~Cg~~ 29 (52)
T smart00661 20 RFVCRKCGYE 29 (52)
T ss_pred EEECCcCCCe
Confidence 3556666543
No 166
>PLN02294 cytochrome c oxidase subunit Vb
Probab=55.21 E-value=5.6 Score=24.72 Aligned_cols=16 Identities=31% Similarity=0.723 Sum_probs=12.8
Q ss_pred CCCCcccCcchhhccC
Q psy2643 79 GYKPFSCGLCDKAFQR 94 (134)
Q Consensus 79 ~~~~~~C~~C~~~f~~ 94 (134)
..++.+|+.||..|.-
T Consensus 138 kGkp~RCpeCG~~fkL 153 (174)
T PLN02294 138 KGKSFECPVCTQYFEL 153 (174)
T ss_pred CCCceeCCCCCCEEEE
Confidence 3568999999998863
No 167
>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=53.78 E-value=5.9 Score=20.30 Aligned_cols=9 Identities=56% Similarity=1.475 Sum_probs=2.7
Q ss_pred cCccccccc
Q psy2643 28 PCQYCGKRF 36 (134)
Q Consensus 28 ~c~~C~~~~ 36 (134)
.|..|++.|
T Consensus 11 ~C~~C~~~F 19 (69)
T PF01363_consen 11 NCMICGKKF 19 (69)
T ss_dssp B-TTT--B-
T ss_pred cCcCcCCcC
Confidence 455555555
No 168
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=53.26 E-value=13 Score=18.53 Aligned_cols=14 Identities=29% Similarity=0.686 Sum_probs=8.2
Q ss_pred CCCccCcccccccC
Q psy2643 24 TRPYPCQYCGKRFH 37 (134)
Q Consensus 24 ~~~~~c~~C~~~~~ 37 (134)
...|.|+.||....
T Consensus 12 ~v~~~Cp~cGipth 25 (55)
T PF13824_consen 12 HVNFECPDCGIPTH 25 (55)
T ss_pred ccCCcCCCCCCcCc
Confidence 34567777765443
No 169
>PF10276 zf-CHCC: Zinc-finger domain; InterPro: IPR019401 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a short conserved zinc-finger domain. It contains the sequence motif Cx8Hx14Cx2C. ; PDB: 2JVM_A 2JRR_A 2JZ8_A.
Probab=53.07 E-value=4.1 Score=18.81 Aligned_cols=11 Identities=27% Similarity=0.993 Sum_probs=7.5
Q ss_pred CcccCcchhhc
Q psy2643 82 PFSCGLCDKAF 92 (134)
Q Consensus 82 ~~~C~~C~~~f 92 (134)
+-.|++|+..|
T Consensus 29 ~~~CpYCg~~y 39 (40)
T PF10276_consen 29 PVVCPYCGTRY 39 (40)
T ss_dssp EEEETTTTEEE
T ss_pred eEECCCCCCEE
Confidence 46777777665
No 170
>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=52.69 E-value=5 Score=19.62 Aligned_cols=11 Identities=27% Similarity=0.966 Sum_probs=5.9
Q ss_pred ccCcchhhccC
Q psy2643 84 SCGLCDKAFQR 94 (134)
Q Consensus 84 ~C~~C~~~f~~ 94 (134)
.||+|++.|..
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 89999998864
No 171
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=52.40 E-value=5.1 Score=23.15 Aligned_cols=25 Identities=16% Similarity=0.418 Sum_probs=15.9
Q ss_pred eeccccccccCChhHHHHHHHHcCCCCCcccCcchh
Q psy2643 55 HKCVVCGKAFSQSSNLITHLRKHTGYKPFSCGLCDK 90 (134)
Q Consensus 55 ~~C~~C~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~ 90 (134)
+.|..|+..|..... ..+.||.||.
T Consensus 71 ~~C~~Cg~~~~~~~~-----------~~~~CP~Cgs 95 (114)
T PRK03681 71 CWCETCQQYVTLLTQ-----------RVRRCPQCHG 95 (114)
T ss_pred EEcccCCCeeecCCc-----------cCCcCcCcCC
Confidence 678888876544311 1156898984
No 172
>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=52.18 E-value=6.6 Score=22.05 Aligned_cols=14 Identities=36% Similarity=0.743 Sum_probs=11.7
Q ss_pred CCCcccCcchhhcc
Q psy2643 80 YKPFSCGLCDKAFQ 93 (134)
Q Consensus 80 ~~~~~C~~C~~~f~ 93 (134)
.++.+|+.||..|.
T Consensus 77 g~~~rC~eCG~~fk 90 (97)
T cd00924 77 GKPKRCPECGHVFK 90 (97)
T ss_pred CCceeCCCCCcEEE
Confidence 37899999998875
No 173
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=50.93 E-value=6.1 Score=19.57 Aligned_cols=10 Identities=50% Similarity=1.371 Sum_probs=5.5
Q ss_pred cCcccccccC
Q psy2643 28 PCQYCGKRFH 37 (134)
Q Consensus 28 ~c~~C~~~~~ 37 (134)
.|+.|+..|.
T Consensus 7 ~C~~Cg~~~~ 16 (54)
T PF14446_consen 7 KCPVCGKKFK 16 (54)
T ss_pred cChhhCCccc
Confidence 4555555554
No 174
>KOG2857|consensus
Probab=50.43 E-value=16 Score=22.06 Aligned_cols=21 Identities=14% Similarity=0.480 Sum_probs=10.3
Q ss_pred cccCcchhhccChHHHHHHHH
Q psy2643 83 FSCGLCDKAFQRKVDLRRHRE 103 (134)
Q Consensus 83 ~~C~~C~~~f~~~~~l~~H~~ 103 (134)
|+|+.|.--|-+-.-++.|+.
T Consensus 18 YKCpkC~vPYCSl~CfKiHk~ 38 (157)
T KOG2857|consen 18 YKCPKCSVPYCSLPCFKIHKS 38 (157)
T ss_pred ccCCCCCCccccchhhhhccC
Confidence 555555544444444544443
No 175
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=50.25 E-value=11 Score=27.05 Aligned_cols=29 Identities=28% Similarity=0.765 Sum_probs=21.6
Q ss_pred cCcccccccCChhhHHHHHHhhcCCCceeccccccccCCh
Q psy2643 28 PCQYCGKRFHQKSDMKKHTYIHTGEKPHKCVVCGKAFSQS 67 (134)
Q Consensus 28 ~c~~C~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~~~~~ 67 (134)
.||.||.+..+. +.+-|+|..|+..+...
T Consensus 352 ~Cp~Cg~~m~S~-----------G~~g~rC~kCg~~~~~~ 380 (421)
T COG1571 352 VCPRCGGRMKSA-----------GRNGFRCKKCGTRARET 380 (421)
T ss_pred CCCccCCchhhc-----------CCCCcccccccccCCcc
Confidence 799999876554 33378999999887665
No 176
>KOG1842|consensus
Probab=49.44 E-value=13 Score=26.96 Aligned_cols=29 Identities=21% Similarity=0.368 Sum_probs=17.9
Q ss_pred CcccCcchhhccChHHHHHHHHhhCCCCC
Q psy2643 82 PFSCGLCDKAFQRKVDLRRHRESQHPGSP 110 (134)
Q Consensus 82 ~~~C~~C~~~f~~~~~l~~H~~~~h~~~~ 110 (134)
.|.||.|.+.|.....|..|....|++..
T Consensus 15 gflCPiC~~dl~~~~~L~~H~d~eH~~ed 43 (505)
T KOG1842|consen 15 GFLCPICLLDLPNLSALNDHLDVEHFEED 43 (505)
T ss_pred cccCchHhhhhhhHHHHHHHHhhhccccc
Confidence 36666666666666666666655555543
No 177
>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=49.23 E-value=4.5 Score=18.81 Aligned_cols=13 Identities=46% Similarity=1.066 Sum_probs=7.9
Q ss_pred CCcccCcchhhcc
Q psy2643 81 KPFSCGLCDKAFQ 93 (134)
Q Consensus 81 ~~~~C~~C~~~f~ 93 (134)
.++.|+.|++.|=
T Consensus 12 ~~~~C~~C~~~FC 24 (43)
T PF01428_consen 12 LPFKCKHCGKSFC 24 (43)
T ss_dssp SHEE-TTTS-EE-
T ss_pred CCeECCCCCcccC
Confidence 4688888988875
No 178
>COG3091 SprT Zn-dependent metalloprotease, SprT family [General function prediction only]
Probab=49.11 E-value=8.1 Score=23.59 Aligned_cols=32 Identities=25% Similarity=0.671 Sum_probs=18.1
Q ss_pred ceeccccccccCChhHHHHHHHHcCCCCCcccCcchh
Q psy2643 54 PHKCVVCGKAFSQSSNLITHLRKHTGYKPFSCGLCDK 90 (134)
Q Consensus 54 ~~~C~~C~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~ 90 (134)
+|.|. |+..+.+. .+|-..-.|+ .|.|..|+-
T Consensus 117 ~Y~C~-C~q~~l~~---RRhn~~~~g~-~YrC~~C~g 148 (156)
T COG3091 117 PYRCQ-CQQHYLRI---RRHNTVRRGE-VYRCGKCGG 148 (156)
T ss_pred eEEee-cCCccchh---hhcccccccc-eEEeccCCc
Confidence 47777 77765543 2222223344 588877763
No 179
>KOG4118|consensus
Probab=49.06 E-value=14 Score=19.06 Aligned_cols=30 Identities=23% Similarity=0.563 Sum_probs=22.9
Q ss_pred CcccCcchhhccChHHHHHHHHhhCCCCCC
Q psy2643 82 PFSCGLCDKAFQRKVDLRRHRESQHPGSPA 111 (134)
Q Consensus 82 ~~~C~~C~~~f~~~~~l~~H~~~~h~~~~~ 111 (134)
.|.|.+|.-.....-.+..|....|+..+.
T Consensus 38 ~~kCtVC~~~mpdpktfkqhfe~kHpk~~~ 67 (74)
T KOG4118|consen 38 HHKCTVCMVQMPDPKTFKQHFENKHPKEPL 67 (74)
T ss_pred HhhhHhhHhhCCCCchHHHHHhhcCCCCCC
Confidence 378888888777888888888777776643
No 180
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=48.92 E-value=9.3 Score=18.53 Aligned_cols=8 Identities=38% Similarity=1.257 Sum_probs=4.5
Q ss_pred cccCcchh
Q psy2643 83 FSCGLCDK 90 (134)
Q Consensus 83 ~~C~~C~~ 90 (134)
|.|..||.
T Consensus 38 ~~CGkCgy 45 (51)
T COG1998 38 WACGKCGY 45 (51)
T ss_pred eEeccccc
Confidence 55555554
No 181
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=48.52 E-value=2.1 Score=19.69 Aligned_cols=9 Identities=22% Similarity=0.888 Sum_probs=4.2
Q ss_pred cccCcchhh
Q psy2643 83 FSCGLCDKA 91 (134)
Q Consensus 83 ~~C~~C~~~ 91 (134)
|.|..|+..
T Consensus 29 y~C~~C~~~ 37 (40)
T smart00440 29 YVCTKCGHR 37 (40)
T ss_pred EEeCCCCCE
Confidence 444444443
No 182
>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=48.34 E-value=7 Score=22.50 Aligned_cols=25 Identities=32% Similarity=0.800 Sum_probs=15.7
Q ss_pred eeccccccccCChhHHHHHHHHcCCCCCcccCcchhh
Q psy2643 55 HKCVVCGKAFSQSSNLITHLRKHTGYKPFSCGLCDKA 91 (134)
Q Consensus 55 ~~C~~C~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~ 91 (134)
+.|..|+..|..... .+.||.||..
T Consensus 71 ~~C~~Cg~~~~~~~~------------~~~CP~Cgs~ 95 (113)
T PF01155_consen 71 ARCRDCGHEFEPDEF------------DFSCPRCGSP 95 (113)
T ss_dssp EEETTTS-EEECHHC------------CHH-SSSSSS
T ss_pred EECCCCCCEEecCCC------------CCCCcCCcCC
Confidence 678888888866532 1568888854
No 183
>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=48.14 E-value=6.1 Score=18.92 Aligned_cols=12 Identities=17% Similarity=0.880 Sum_probs=8.7
Q ss_pred cccCcchhhccC
Q psy2643 83 FSCGLCDKAFQR 94 (134)
Q Consensus 83 ~~C~~C~~~f~~ 94 (134)
|+|..|+..|--
T Consensus 2 y~C~~CgyvYd~ 13 (47)
T PF00301_consen 2 YQCPVCGYVYDP 13 (47)
T ss_dssp EEETTTSBEEET
T ss_pred cCCCCCCEEEcC
Confidence 678888876643
No 184
>KOG1994|consensus
Probab=48.04 E-value=15 Score=24.07 Aligned_cols=21 Identities=24% Similarity=0.651 Sum_probs=12.9
Q ss_pred CceeccccccccCChhHHHHH
Q psy2643 53 KPHKCVVCGKAFSQSSNLITH 73 (134)
Q Consensus 53 ~~~~C~~C~~~~~~~~~l~~h 73 (134)
..|.|..||..|.+..+|..|
T Consensus 238 eh~YC~fCG~~y~~~edl~eh 258 (268)
T KOG1994|consen 238 EHYYCFFCGIKYKDEEDLYEH 258 (268)
T ss_pred cceEEEEeccccCCHHHHHHh
Confidence 346666666666666666554
No 185
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=47.84 E-value=3 Score=23.43 Aligned_cols=8 Identities=38% Similarity=1.389 Sum_probs=3.9
Q ss_pred ccCccccc
Q psy2643 27 YPCQYCGK 34 (134)
Q Consensus 27 ~~c~~C~~ 34 (134)
|.|+.|+.
T Consensus 23 FtCp~Cgh 30 (104)
T COG4888 23 FTCPRCGH 30 (104)
T ss_pred EecCccCC
Confidence 45555543
No 186
>PF07975 C1_4: TFIIH C1-like domain; InterPro: IPR004595 All proteins in this domain for which functions are known are components of the TFIIH complex which is involved in the initiation of transcription and nucleotide excision repair. It includes the yeast transcription factor Ssl1 (Suppressor of stem-loop protein 1) that is essential for translation initiation and affects UV resistance. The C-terminal region is essential for transcription activity. This regions binds three zinc atoms through two independent domain. The first contains a C4 zinc finger motif, whereas the second is characterised by a CX(2)CX(2-4)FCADCD motif. The solution structure of the second C-terminal domain revealed homology with the regulatory domain of protein kinase C [].; GO: 0006281 DNA repair, 0005634 nucleus; PDB: 1Z60_A.
Probab=47.83 E-value=3.9 Score=20.00 Aligned_cols=22 Identities=23% Similarity=0.511 Sum_probs=7.8
Q ss_pred CcccCcchhhccChHHHHHHHH
Q psy2643 82 PFSCGLCDKAFQRKVDLRRHRE 103 (134)
Q Consensus 82 ~~~C~~C~~~f~~~~~l~~H~~ 103 (134)
.|+|+.|+..|=..=++-.|..
T Consensus 21 ~y~C~~C~~~FC~dCD~fiHE~ 42 (51)
T PF07975_consen 21 RYRCPKCKNHFCIDCDVFIHET 42 (51)
T ss_dssp EE--TTTT--B-HHHHHTTTTT
T ss_pred eEECCCCCCccccCcChhhhcc
Confidence 3555555555544444434433
No 187
>PF12760 Zn_Tnp_IS1595: Transposase zinc-ribbon domain; InterPro: IPR024442 This zinc binding domain is found in a range of transposase proteins such as ISSPO8, ISSOD11, ISRSSP2 etc. It may be a zinc-binding beta ribbon domain that could bind DNA.
Probab=47.14 E-value=32 Score=16.09 Aligned_cols=8 Identities=38% Similarity=1.070 Sum_probs=4.9
Q ss_pred cccCcchh
Q psy2643 83 FSCGLCDK 90 (134)
Q Consensus 83 ~~C~~C~~ 90 (134)
+.||.||.
T Consensus 19 ~~CP~Cg~ 26 (46)
T PF12760_consen 19 FVCPHCGS 26 (46)
T ss_pred CCCCCCCC
Confidence 55666664
No 188
>KOG2907|consensus
Probab=46.88 E-value=7.9 Score=22.30 Aligned_cols=38 Identities=18% Similarity=0.384 Sum_probs=19.8
Q ss_pred ccCcccccccCChhhHHHHHHhhc-CC-CceeccccccccCC
Q psy2643 27 YPCQYCGKRFHQKSDMKKHTYIHT-GE-KPHKCVVCGKAFSQ 66 (134)
Q Consensus 27 ~~c~~C~~~~~~~~~l~~h~~~~~-~~-~~~~C~~C~~~~~~ 66 (134)
..||.||..=-...-++ +++-. |+ .-|.|..|+..|..
T Consensus 75 ~kCpkCghe~m~Y~T~Q--lRSADEGQTVFYTC~kC~~k~~e 114 (116)
T KOG2907|consen 75 HKCPKCGHEEMSYHTLQ--LRSADEGQTVFYTCPKCKYKFTE 114 (116)
T ss_pred ccCcccCCchhhhhhhh--cccccCCceEEEEcCccceeeec
Confidence 57888875322222122 22221 21 12789999887753
No 189
>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=46.52 E-value=7.5 Score=18.90 Aligned_cols=11 Identities=18% Similarity=1.008 Sum_probs=8.9
Q ss_pred cccCcchhhcc
Q psy2643 83 FSCGLCDKAFQ 93 (134)
Q Consensus 83 ~~C~~C~~~f~ 93 (134)
|.|..||..|-
T Consensus 2 y~C~~CgyiYd 12 (50)
T cd00730 2 YECRICGYIYD 12 (50)
T ss_pred cCCCCCCeEEC
Confidence 78999997765
No 190
>KOG1280|consensus
Probab=45.26 E-value=23 Score=24.85 Aligned_cols=24 Identities=21% Similarity=0.324 Sum_probs=15.9
Q ss_pred eeccccccccCChhHHHHHHHHcC
Q psy2643 55 HKCVVCGKAFSQSSNLITHLRKHT 78 (134)
Q Consensus 55 ~~C~~C~~~~~~~~~l~~h~~~~~ 78 (134)
|.|+.|+..-.++..|..|....+
T Consensus 80 ftCPyC~~~Gfte~~f~~Hv~s~H 103 (381)
T KOG1280|consen 80 FTCPYCGIMGFTERQFGTHVLSQH 103 (381)
T ss_pred ccCCcccccccchhHHHHHhhhcC
Confidence 677777776666677777765433
No 191
>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=45.05 E-value=15 Score=17.88 Aligned_cols=9 Identities=56% Similarity=1.243 Sum_probs=3.8
Q ss_pred CcccccccC
Q psy2643 29 CQYCGKRFH 37 (134)
Q Consensus 29 c~~C~~~~~ 37 (134)
|..|++.|.
T Consensus 5 C~~C~~~F~ 13 (57)
T cd00065 5 CMGCGKPFT 13 (57)
T ss_pred CcccCcccc
Confidence 344444443
No 192
>COG1326 Uncharacterized archaeal Zn-finger protein [General function prediction only]
Probab=44.78 E-value=22 Score=22.73 Aligned_cols=10 Identities=30% Similarity=0.886 Sum_probs=4.6
Q ss_pred eecccccccc
Q psy2643 55 HKCVVCGKAF 64 (134)
Q Consensus 55 ~~C~~C~~~~ 64 (134)
+.|..||..+
T Consensus 31 vrC~eCG~V~ 40 (201)
T COG1326 31 VRCEECGTVH 40 (201)
T ss_pred EEccCCCcEe
Confidence 3444444443
No 193
>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 COG1327 Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains [Transcription]
Probab=44.32 E-value=5 Score=24.42 Aligned_cols=14 Identities=36% Similarity=0.774 Sum_probs=10.0
Q ss_pred ccCcccccccCChh
Q psy2643 27 YPCQYCGKRFHQKS 40 (134)
Q Consensus 27 ~~c~~C~~~~~~~~ 40 (134)
-.|+.|+..|++..
T Consensus 29 ReC~~C~~RFTTfE 42 (156)
T COG1327 29 RECLECGERFTTFE 42 (156)
T ss_pred hcccccccccchhh
Confidence 46888888877653
No 195
>PRK00420 hypothetical protein; Validated
Probab=43.36 E-value=16 Score=21.15 Aligned_cols=9 Identities=22% Similarity=0.479 Sum_probs=4.3
Q ss_pred cccCcchhh
Q psy2643 83 FSCGLCDKA 91 (134)
Q Consensus 83 ~~C~~C~~~ 91 (134)
..||.||..
T Consensus 41 ~~Cp~Cg~~ 49 (112)
T PRK00420 41 VVCPVHGKV 49 (112)
T ss_pred eECCCCCCe
Confidence 345555543
No 196
>KOG4727|consensus
Probab=43.19 E-value=12 Score=23.30 Aligned_cols=23 Identities=17% Similarity=0.574 Sum_probs=19.0
Q ss_pred CcccCcchhhccChHHHHHHHHh
Q psy2643 82 PFSCGLCDKAFQRKVDLRRHRES 104 (134)
Q Consensus 82 ~~~C~~C~~~f~~~~~l~~H~~~ 104 (134)
.|.|.+|.-+|...-++..|+..
T Consensus 75 GyyCdVCdcvvKDSinflDHiNg 97 (193)
T KOG4727|consen 75 GYYCDVCDCVVKDSINFLDHING 97 (193)
T ss_pred ceeeeecceeehhhHHHHHHhcc
Confidence 48899999888888888888754
No 197
>PF14787 zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB: 1CL4_A 1DSV_A.
Probab=42.77 E-value=9.2 Score=17.17 Aligned_cols=10 Identities=40% Similarity=0.969 Sum_probs=6.8
Q ss_pred ccCcchhhcc
Q psy2643 84 SCGLCDKAFQ 93 (134)
Q Consensus 84 ~C~~C~~~f~ 93 (134)
.|+.|++.|-
T Consensus 4 ~CprC~kg~H 13 (36)
T PF14787_consen 4 LCPRCGKGFH 13 (36)
T ss_dssp C-TTTSSSCS
T ss_pred cCcccCCCcc
Confidence 5888888764
No 198
>KOG2593|consensus
Probab=42.49 E-value=21 Score=25.72 Aligned_cols=35 Identities=20% Similarity=0.364 Sum_probs=24.3
Q ss_pred CCceeccccccccCChhHHHHHHHHcCCCCCcccCcch
Q psy2643 52 EKPHKCVVCGKAFSQSSNLITHLRKHTGYKPFSCGLCD 89 (134)
Q Consensus 52 ~~~~~C~~C~~~~~~~~~l~~h~~~~~~~~~~~C~~C~ 89 (134)
...|.|+.|.+.|.....+. -.......|.|..|+
T Consensus 126 ~~~Y~Cp~C~kkyt~Lea~~---L~~~~~~~F~C~~C~ 160 (436)
T KOG2593|consen 126 VAGYVCPNCQKKYTSLEALQ---LLDNETGEFHCENCG 160 (436)
T ss_pred cccccCCccccchhhhHHHH---hhcccCceEEEecCC
Confidence 44589999999988876643 223334568898887
No 199
>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=42.40 E-value=8.4 Score=17.26 Aligned_cols=11 Identities=18% Similarity=0.685 Sum_probs=8.1
Q ss_pred cccCcchhhcc
Q psy2643 83 FSCGLCDKAFQ 93 (134)
Q Consensus 83 ~~C~~C~~~f~ 93 (134)
+.|+.||+.|-
T Consensus 2 r~C~~Cg~~Yh 12 (36)
T PF05191_consen 2 RICPKCGRIYH 12 (36)
T ss_dssp EEETTTTEEEE
T ss_pred cCcCCCCCccc
Confidence 35888888775
No 200
>PF04780 DUF629: Protein of unknown function (DUF629); InterPro: IPR006865 This domain represents a region of several plant proteins of unknown function. A C2H2 zinc finger is predicted in this region in some family members, but the spacing between the cysteine residues is not conserved throughout the family.
Probab=42.05 E-value=22 Score=26.04 Aligned_cols=22 Identities=27% Similarity=0.687 Sum_probs=17.2
Q ss_pred eeccccccccCChhHHHHHHHH
Q psy2643 55 HKCVVCGKAFSQSSNLITHLRK 76 (134)
Q Consensus 55 ~~C~~C~~~~~~~~~l~~h~~~ 76 (134)
|.|+.|.+.|.....+..|+..
T Consensus 58 WiCp~CskkF~d~~~~~~H~~~ 79 (466)
T PF04780_consen 58 WICPRCSKKFSDAESCLSHMEQ 79 (466)
T ss_pred eeCCcccceeCCHHHHHHHHHH
Confidence 5678888888888888888764
No 201
>COG5188 PRP9 Splicing factor 3a, subunit 3 [RNA processing and modification]
Probab=40.81 E-value=21 Score=25.09 Aligned_cols=30 Identities=23% Similarity=0.436 Sum_probs=23.6
Q ss_pred HHHcCCCCCcccCcch-hhccChHHHHHHHH
Q psy2643 74 LRKHTGYKPFSCGLCD-KAFQRKVDLRRHRE 103 (134)
Q Consensus 74 ~~~~~~~~~~~C~~C~-~~f~~~~~l~~H~~ 103 (134)
.+.|.-++.|.|..|| ++|.-+..+.+|..
T Consensus 366 ~klhgLd~ef~CEICgNyvy~GR~~FdrHF~ 396 (470)
T COG5188 366 CKLHGLDIEFECEICGNYVYYGRDRFDRHFE 396 (470)
T ss_pred HHhcCCCcceeeeecccccccchHHHHhhhh
Confidence 4567778889999999 78877888888763
No 202
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=40.78 E-value=12 Score=22.17 Aligned_cols=16 Identities=19% Similarity=0.634 Sum_probs=12.0
Q ss_pred CCCcccCcchhhccCh
Q psy2643 80 YKPFSCGLCDKAFQRK 95 (134)
Q Consensus 80 ~~~~~C~~C~~~f~~~ 95 (134)
...|.|+.|++.|...
T Consensus 51 ~qRyrC~~C~~tf~~~ 66 (129)
T COG3677 51 HQRYKCKSCGSTFTVE 66 (129)
T ss_pred ccccccCCcCcceeee
Confidence 4458888888888754
No 203
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=40.61 E-value=11 Score=22.17 Aligned_cols=30 Identities=23% Similarity=0.512 Sum_probs=16.2
Q ss_pred eeccccccccCChhHHHHHHHHcCCCCCcccCcchh
Q psy2643 55 HKCVVCGKAFSQSSNLITHLRKHTGYKPFSCGLCDK 90 (134)
Q Consensus 55 ~~C~~C~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~ 90 (134)
+.| .|+..|.....-.. +. .-.+.||.||.
T Consensus 71 ~~C-~Cg~~~~~~~~~~~----~~-~~~~~CP~Cgs 100 (124)
T PRK00762 71 IEC-ECGYEGVVDEDEID----HY-AAVIECPVCGN 100 (124)
T ss_pred EEe-eCcCcccccccchh----cc-ccCCcCcCCCC
Confidence 678 89877655421000 00 01257999984
No 204
>PF06524 NOA36: NOA36 protein; InterPro: IPR010531 This family consists of several NOA36 proteins which contain 29 highly conserved cysteine residues. The function of this protein is unknown.; GO: 0008270 zinc ion binding, 0005634 nucleus
Probab=40.44 E-value=8.4 Score=25.78 Aligned_cols=21 Identities=33% Similarity=0.513 Sum_probs=13.8
Q ss_pred CCCCCcccCcchhhccChHHH
Q psy2643 78 TGYKPFSCGLCDKAFQRKVDL 98 (134)
Q Consensus 78 ~~~~~~~C~~C~~~f~~~~~l 98 (134)
...+++.||.||........|
T Consensus 205 ~k~k~~PCPKCg~et~eTkdL 225 (314)
T PF06524_consen 205 EKGKPIPCPKCGYETQETKDL 225 (314)
T ss_pred ccCCCCCCCCCCCcccccccc
Confidence 345789999999655544444
No 205
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=40.13 E-value=4.9 Score=23.22 Aligned_cols=12 Identities=17% Similarity=0.656 Sum_probs=9.4
Q ss_pred CcccCcchhhcc
Q psy2643 82 PFSCGLCDKAFQ 93 (134)
Q Consensus 82 ~~~C~~C~~~f~ 93 (134)
-|.|..||..|.
T Consensus 100 Fy~C~~Cg~~wr 111 (113)
T COG1594 100 FYKCTRCGYRWR 111 (113)
T ss_pred EEEecccCCEee
Confidence 488988987764
No 206
>COG4391 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=39.73 E-value=13 Score=18.90 Aligned_cols=14 Identities=14% Similarity=0.555 Sum_probs=9.9
Q ss_pred CCcccCcchhhccC
Q psy2643 81 KPFSCGLCDKAFQR 94 (134)
Q Consensus 81 ~~~~C~~C~~~f~~ 94 (134)
+--.|++|+..|..
T Consensus 47 gev~CPYC~t~y~l 60 (62)
T COG4391 47 GEVVCPYCSTRYRL 60 (62)
T ss_pred CcEecCccccEEEe
Confidence 33588888887753
No 207
>PF05495 zf-CHY: CHY zinc finger; InterPro: IPR008913 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Pirh2 is an eukaryotic ubiquitin protein ligase, which has been shown to promote p53 degradation in mammals. Pirh2 physically interacts with p53 and promotes ubiquitination of p53 independently of MDM2. Like MDM2, Pirh2 is thought to participate in an autoregulatory feedback loop that controls p53 function. Pirh2 proteins contain three distinct zinc fingers, the CHY-type, the CTCHY-type which is C-terminal to the CHY-type zinc finger and a RING finger. The CHY-type zinc finger has no currently known function []. As well as Pirh2, the CHY-type zinc finger is also found in the following proteins: Yeast helper of Tim protein 13. Hot13 may have a role in the assembly and recycling of the small Tims, a complex of the mitochondrial intermembrane space that participates in the TIM22 import pathway for assembly of the inner membrane [] Several plant hypothetical proteins that also contain haemerythrin cation binding domains Several protozoan hypothetical proteins that also contain a Myb domain The solution structure of this zinc finger has been solved and binds 3 zinc atoms as shown in the following schematic representation: ++---------+-----+ || | | CXHYxxxxxxxxxCCxxxxxCxxCHxxxxxHxxxxxxxxxxxCxxCxxxxxxxxxCxxC | | | | | | | | +-+-----------------+--+ +--+---------+--+ 'C': conserved cysteine involved in the binding of one zinc atom. 'H': conserved histidine involved in the binding of one zinc atom. More information about these proteins can be found at Protein of the Month: Zinc Fingers []; GO: 0008270 zinc ion binding; PDB: 2DKT_A 2K2C_A.
Probab=39.40 E-value=5.4 Score=20.87 Aligned_cols=57 Identities=18% Similarity=0.339 Sum_probs=23.4
Q ss_pred ccCcccccccCChhh---HHHHHHhhcCCCceeccccccccCChhHHHHHHHHcCCCCCcccCcchhh
Q psy2643 27 YPCQYCGKRFHQKSD---MKKHTYIHTGEKPHKCVVCGKAFSQSSNLITHLRKHTGYKPFSCGLCDKA 91 (134)
Q Consensus 27 ~~c~~C~~~~~~~~~---l~~h~~~~~~~~~~~C~~C~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~ 91 (134)
+.++-|++.|.-..- +..|...........|..|+..+..... ..+ ..+.|+.|+..
T Consensus 11 ~~~~cC~~~y~C~~CHde~~~H~~~~~~~~~v~Cg~C~~~~~~~~~-------~c~-~~~~C~~C~~~ 70 (71)
T PF05495_consen 11 IRFPCCGKYYPCRFCHDELEDHPFDRWPVKRVICGKCRTEQPIDEY-------SCG-ADYFCPICGLY 70 (71)
T ss_dssp EEETTTTEEESSHHHHHHCSSS---TTT--EEEETTT--EEES-SB-------TT---SEEETTTTEE
T ss_pred EECCcccCeecHHHHHHHhccCccccccccCeECCCCCCccChhhh-------hcC-CCccCcCcCCC
Confidence 445556555544311 1122222222334567777766544332 111 45778888754
No 208
>PRK05580 primosome assembly protein PriA; Validated
Probab=39.31 E-value=9 Score=29.38 Aligned_cols=9 Identities=33% Similarity=0.896 Sum_probs=5.4
Q ss_pred CcccCcchh
Q psy2643 82 PFSCGLCDK 90 (134)
Q Consensus 82 ~~~C~~C~~ 90 (134)
+..|+.||.
T Consensus 421 ~~~Cp~Cg~ 429 (679)
T PRK05580 421 PKACPECGS 429 (679)
T ss_pred CCCCCCCcC
Confidence 446777764
No 209
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=39.08 E-value=30 Score=23.55 Aligned_cols=10 Identities=30% Similarity=0.783 Sum_probs=5.4
Q ss_pred CCcccCcchh
Q psy2643 81 KPFSCGLCDK 90 (134)
Q Consensus 81 ~~~~C~~C~~ 90 (134)
+.|.|+.||.
T Consensus 321 r~~~C~~cg~ 330 (364)
T COG0675 321 RLFKCPRCGF 330 (364)
T ss_pred eeEECCCCCC
Confidence 3455666654
No 210
>TIGR01562 FdhE formate dehydrogenase accessory protein FdhE. The only sequence scoring between trusted and noise is that from Aquifex aeolicus, which shows certain structural differences from the proteobacterial forms in the alignment. However it is notable that A. aeolicus also has a sequence scoring above trusted to the alpha subunit of formate dehydrogenase (TIGR01553).
Probab=38.96 E-value=18 Score=24.92 Aligned_cols=9 Identities=33% Similarity=0.752 Sum_probs=6.3
Q ss_pred cCccccccc
Q psy2643 28 PCQYCGKRF 36 (134)
Q Consensus 28 ~c~~C~~~~ 36 (134)
.||+||..-
T Consensus 186 ~CPvCGs~P 194 (305)
T TIGR01562 186 LCPACGSPP 194 (305)
T ss_pred cCCCCCChh
Confidence 688887653
No 211
>KOG0978|consensus
Probab=38.83 E-value=12 Score=28.76 Aligned_cols=17 Identities=24% Similarity=0.458 Sum_probs=11.3
Q ss_pred CCcccCcchhhccChHH
Q psy2643 81 KPFSCGLCDKAFQRKVD 97 (134)
Q Consensus 81 ~~~~C~~C~~~f~~~~~ 97 (134)
+.-+||.|+.+|..-.-
T Consensus 677 RqRKCP~Cn~aFganDv 693 (698)
T KOG0978|consen 677 RQRKCPKCNAAFGANDV 693 (698)
T ss_pred hcCCCCCCCCCCCcccc
Confidence 33488888888865433
No 212
>PF01927 Mut7-C: Mut7-C RNAse domain; InterPro: IPR002782 This prokaryotic family of proteins have no known function. The proteins contain four conserved cysteines that may be involved in metal binding or disulphide bridges.
Probab=38.72 E-value=12 Score=22.66 Aligned_cols=44 Identities=16% Similarity=0.274 Sum_probs=24.4
Q ss_pred eeccccccccCChhHHHH--HHH---HcCCCCCcccCcchhhccChHHH
Q psy2643 55 HKCVVCGKAFSQSSNLIT--HLR---KHTGYKPFSCGLCDKAFQRKVDL 98 (134)
Q Consensus 55 ~~C~~C~~~~~~~~~l~~--h~~---~~~~~~~~~C~~C~~~f~~~~~l 98 (134)
-.|..|+..+.....-.. -+. ....+.-+.|+.||+.|=.-+.+
T Consensus 92 sRC~~CN~~L~~v~~~~v~~~vp~~v~~~~~~f~~C~~C~kiyW~GsH~ 140 (147)
T PF01927_consen 92 SRCPKCNGPLRPVSKEEVKDRVPPYVYETYDEFWRCPGCGKIYWEGSHW 140 (147)
T ss_pred CccCCCCcEeeechhhccccccCccccccCCeEEECCCCCCEecccccH
Confidence 479999986544322100 000 11234469999999988544433
No 213
>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=37.62 E-value=5.9 Score=18.12 Aligned_cols=11 Identities=36% Similarity=0.824 Sum_probs=4.7
Q ss_pred CCceecccccc
Q psy2643 52 EKPHKCVVCGK 62 (134)
Q Consensus 52 ~~~~~C~~C~~ 62 (134)
.+.|.|.+|+.
T Consensus 22 ~~~w~C~~C~~ 32 (40)
T PF04810_consen 22 GKTWICNFCGT 32 (40)
T ss_dssp TTEEEETTT--
T ss_pred CCEEECcCCCC
Confidence 34455555554
No 214
>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=37.20 E-value=8.2 Score=23.30 Aligned_cols=32 Identities=25% Similarity=0.737 Sum_probs=18.0
Q ss_pred ceeccccccccCChhHHHHHHHHcCCCCCcccCcchhhcc
Q psy2643 54 PHKCVVCGKAFSQSSNLITHLRKHTGYKPFSCGLCDKAFQ 93 (134)
Q Consensus 54 ~~~C~~C~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~f~ 93 (134)
.|.|..|+..+.... +. +...|.|+.|+..+.
T Consensus 123 ~~~C~~C~~~~~r~~------~~--~~~~~~C~~C~~~l~ 154 (157)
T PF10263_consen 123 VYRCPSCGREYKRHR------RS--KRKRYRCGRCGGPLV 154 (157)
T ss_pred EEEcCCCCCEeeeec------cc--chhhEECCCCCCEEE
Confidence 467877876653322 22 223378888875543
No 215
>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=36.60 E-value=5.3 Score=30.59 Aligned_cols=29 Identities=28% Similarity=0.839 Sum_probs=13.6
Q ss_pred cCcccccccCChhhHHHHHHhhcCCCceecccccc
Q psy2643 28 PCQYCGKRFHQKSDMKKHTYIHTGEKPHKCVVCGK 62 (134)
Q Consensus 28 ~c~~C~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~ 62 (134)
.|+.|.+.+....+ ++.|. .+.-|+.||-
T Consensus 153 lC~~C~~EY~dP~n----RRfHA--Qp~aCp~CGP 181 (750)
T COG0068 153 LCPFCDKEYKDPLN----RRFHA--QPIACPKCGP 181 (750)
T ss_pred CCHHHHHHhcCccc----ccccc--ccccCcccCC
Confidence 45556555554433 12121 2345666664
No 216
>PF08209 Sgf11: Sgf11 (transcriptional regulation protein); InterPro: IPR013246 The Sgf11 family is a SAGA complex subunit in Saccharomyces cerevisiae (Baker's yeast). The SAGA complex is a multisubunit protein complex involved in transcriptional regulation. SAGA combines proteins involved in interactions with DNA-bound activators and TATA-binding protein (TBP), as well as enzymes for histone acetylation and deubiquitylation [].; PDB: 3M99_B 2LO2_A 3MHH_C 3MHS_C.
Probab=36.25 E-value=21 Score=15.69 Aligned_cols=19 Identities=21% Similarity=0.571 Sum_probs=9.1
Q ss_pred ccCcccccccCChhhHHHHH
Q psy2643 27 YPCQYCGKRFHQKSDMKKHT 46 (134)
Q Consensus 27 ~~c~~C~~~~~~~~~l~~h~ 46 (134)
+.|+.|++.+.... +..|+
T Consensus 5 ~~C~nC~R~v~a~R-fA~HL 23 (33)
T PF08209_consen 5 VECPNCGRPVAASR-FAPHL 23 (33)
T ss_dssp EE-TTTSSEEEGGG-HHHHH
T ss_pred EECCCCcCCcchhh-hHHHH
Confidence 45666666554432 44444
No 217
>PF15616 TerY-C: TerY-C metal binding domain
Probab=36.12 E-value=4.6 Score=24.02 Aligned_cols=37 Identities=22% Similarity=0.417 Sum_probs=20.5
Q ss_pred cCcccccccCChhhHHHHHHhhcCCCceecccccccc
Q psy2643 28 PCQYCGKRFHQKSDMKKHTYIHTGEKPHKCVVCGKAF 64 (134)
Q Consensus 28 ~c~~C~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~~ 64 (134)
.||.||..+....--...+.-..++....|+.|+..-
T Consensus 79 gCP~CGn~~~fa~C~CGkl~Ci~g~~~~~CPwCg~~g 115 (131)
T PF15616_consen 79 GCPHCGNQYAFAVCGCGKLFCIDGEGEVTCPWCGNEG 115 (131)
T ss_pred CCCCCcChhcEEEecCCCEEEeCCCCCEECCCCCCee
Confidence 6888887644332111112222345567899999753
No 218
>PF12773 DZR: Double zinc ribbon
Probab=35.56 E-value=23 Score=16.74 Aligned_cols=26 Identities=23% Similarity=0.583 Sum_probs=14.3
Q ss_pred ccCcccccccCChhhHHHHHHhhcCCCceeccccccc
Q psy2643 27 YPCQYCGKRFHQKSDMKKHTYIHTGEKPHKCVVCGKA 63 (134)
Q Consensus 27 ~~c~~C~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~ 63 (134)
-.|+.||..+. ........|..|+..
T Consensus 13 ~fC~~CG~~l~-----------~~~~~~~~C~~Cg~~ 38 (50)
T PF12773_consen 13 KFCPHCGTPLP-----------PPDQSKKICPNCGAE 38 (50)
T ss_pred cCChhhcCChh-----------hccCCCCCCcCCcCC
Confidence 35777776555 112223567777765
No 219
>PF06220 zf-U1: U1 zinc finger; InterPro: IPR013085 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. C2H2-type (classical) zinc fingers (Znf) were the first class to be characterised. They contain a short beta hairpin and an alpha helix (beta/beta/alpha structure), where a single zinc atom is held in place by Cys(2)His(2) (C2H2) residues in a tetrahedral array. C2H2 Znf's can be divided into three groups based on the number and pattern of fingers: triple-C2H2 (binds single ligand), multiple-adjacent-C2H2 (binds multiple ligands), and separated paired-C2H2 []. C2H2 Znf's are the most common DNA-binding motifs found in eukaryotic transcription factors, and have also been identified in prokaryotes []. Transcription factors usually contain several Znf's (each with a conserved beta/beta/alpha structure) capable of making multiple contacts along the DNA, where the C2H2 Znf motifs recognise DNA sequences by binding to the major groove of DNA via a short alpha-helix in the Znf, the Znf spanning 3-4 bases of the DNA []. C2H2 Znf's can also bind to RNA and protein targets []. This entry represents a C2H2-type zinc finger motif found in several U1 small nuclear ribonucleoprotein C (U1-C) proteins. Some proteins contain multiple copies of this motif. The U1 small nuclear ribonucleoprotein (U1 snRNP) binds to the pre-mRNA 5' splice site at early stages of spliceosome assembly. Recruitment of U1 to a class of weak 5' splice site is promoted by binding of the protein TIA-1 to uridine-rich sequences immediately downstream from the 5' splice site. Binding of TIA-1 in the vicinity of a 5' splice site helps to stabilise U1 snRNP recruitment, at least in part, via a direct interaction with U1-C, thus providing one molecular mechanism for the function of this splicing regulator []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2VRD_A.
Probab=34.92 E-value=34 Score=15.43 Aligned_cols=10 Identities=30% Similarity=0.992 Sum_probs=3.5
Q ss_pred cccCcchhhc
Q psy2643 83 FSCGLCDKAF 92 (134)
Q Consensus 83 ~~C~~C~~~f 92 (134)
|-|..|...+
T Consensus 4 yyCdyC~~~~ 13 (38)
T PF06220_consen 4 YYCDYCKKYL 13 (38)
T ss_dssp -B-TTT--B-
T ss_pred eeccccccee
Confidence 5677777666
No 220
>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=34.70 E-value=13 Score=23.81 Aligned_cols=26 Identities=15% Similarity=0.522 Sum_probs=0.0
Q ss_pred cCCCCCcccCcchh-hccChHHHHHHH
Q psy2643 77 HTGYKPFSCGLCDK-AFQRKVDLRRHR 102 (134)
Q Consensus 77 ~~~~~~~~C~~C~~-~f~~~~~l~~H~ 102 (134)
|.-.+.|.|..||- +|.-+..+.+|.
T Consensus 96 hGL~~ey~CEICGN~~Y~GrkaFekHF 122 (196)
T PF11931_consen 96 HGLGVEYKCEICGNQSYKGRKAFEKHF 122 (196)
T ss_dssp ---------------------------
T ss_pred hCCCCeeeeEeCCCcceecHHHHHHhc
Confidence 33344566666663 444455555554
No 221
>PF04438 zf-HIT: HIT zinc finger; InterPro: IPR007529 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the HIT-type zinc finger, which contains 7 conserved cysteines and one histidine that can potentially coordinate two zinc atoms. It has been named after the first protein that originally defined the domain: the yeast HIT1 protein (P46973 from SWISSPROT) []. The HIT-type zinc finger displays some sequence similarities to the MYND-type zinc finger. The function of this domain is unknown but it is mainly found in nuclear proteins involved in gene regulation and chromatin remodeling. This domain is also found in the thyroid receptor interacting protein 3 (TRIP-3) Q15649 from SWISSPROT, that specifically interacts with the ligand binding domain of the thyroid receptor. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 2YQP_A 2YQQ_A 1X4S_A.
Probab=34.40 E-value=16 Score=15.55 Aligned_cols=12 Identities=17% Similarity=0.703 Sum_probs=5.9
Q ss_pred CcccCcchhhcc
Q psy2643 82 PFSCGLCDKAFQ 93 (134)
Q Consensus 82 ~~~C~~C~~~f~ 93 (134)
.|.|+.|+..|=
T Consensus 13 kY~Cp~C~~~~C 24 (30)
T PF04438_consen 13 KYRCPRCGARYC 24 (30)
T ss_dssp SEE-TTT--EES
T ss_pred EEECCCcCCcee
Confidence 477888776553
No 222
>KOG1842|consensus
Probab=33.79 E-value=26 Score=25.49 Aligned_cols=23 Identities=26% Similarity=0.379 Sum_probs=20.2
Q ss_pred CCcCccccCChHHHHHHHHHcCC
Q psy2643 1 CKQCGKTFKRSSTLSTHLLIHSD 23 (134)
Q Consensus 1 C~~C~~~f~~~~~l~~h~~~~~~ 23 (134)
||+|...|.+...|..|....+.
T Consensus 18 CPiC~~dl~~~~~L~~H~d~eH~ 40 (505)
T KOG1842|consen 18 CPICLLDLPNLSALNDHLDVEHF 40 (505)
T ss_pred CchHhhhhhhHHHHHHHHhhhcc
Confidence 89999999999999999976544
No 223
>PLN02748 tRNA dimethylallyltransferase
Probab=33.66 E-value=30 Score=25.46 Aligned_cols=25 Identities=12% Similarity=0.565 Sum_probs=20.8
Q ss_pred CCcccCcchh-hccChHHHHHHHHhh
Q psy2643 81 KPFSCGLCDK-AFQRKVDLRRHRESQ 105 (134)
Q Consensus 81 ~~~~C~~C~~-~f~~~~~l~~H~~~~ 105 (134)
+.|.|..|++ ++....++..|++..
T Consensus 417 ~~~~Ce~C~~~~~~G~~eW~~Hlksr 442 (468)
T PLN02748 417 TQYVCEACGNKVLRGAHEWEQHKQGR 442 (468)
T ss_pred ccccccCCCCcccCCHHHHHHHhcch
Confidence 5588999997 899999999998544
No 224
>PHA02998 RNA polymerase subunit; Provisional
Probab=33.53 E-value=5.1 Score=25.09 Aligned_cols=36 Identities=19% Similarity=0.496 Sum_probs=19.2
Q ss_pred eeccccccccCChhHHHHHHHHcCCCCC----cccCcchhhccC
Q psy2643 55 HKCVVCGKAFSQSSNLITHLRKHTGYKP----FSCGLCDKAFQR 94 (134)
Q Consensus 55 ~~C~~C~~~~~~~~~l~~h~~~~~~~~~----~~C~~C~~~f~~ 94 (134)
..|+.|+..-..... +++-.++.| |.|..||+.|.-
T Consensus 144 v~CPkCg~~~A~f~q----lQTRSADEPmT~FYkC~~CG~~wkp 183 (195)
T PHA02998 144 TPCPNCKSKNTTPMM----IQTRAADEPPLVRHACRDCKKHFKP 183 (195)
T ss_pred CCCCCCCCCceEEEE----EeeccCCCCceEEEEcCCCCCccCC
Confidence 467778754222211 222233333 888888887753
No 225
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=33.19 E-value=36 Score=16.65 Aligned_cols=11 Identities=18% Similarity=0.434 Sum_probs=6.5
Q ss_pred CCCcccCcchh
Q psy2643 80 YKPFSCGLCDK 90 (134)
Q Consensus 80 ~~~~~C~~C~~ 90 (134)
+....|+.||+
T Consensus 44 ~~i~~Cp~CgR 54 (56)
T PF02591_consen 44 DEIVFCPNCGR 54 (56)
T ss_pred CCeEECcCCCc
Confidence 44566666664
No 226
>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=33.15 E-value=14 Score=24.06 Aligned_cols=24 Identities=17% Similarity=0.317 Sum_probs=0.0
Q ss_pred eeccccccccCChhHHHHHHHHcCC
Q psy2643 55 HKCVVCGKAFSQSSNLITHLRKHTG 79 (134)
Q Consensus 55 ~~C~~C~~~~~~~~~l~~h~~~~~~ 79 (134)
..|++||..... ..+..|+++...
T Consensus 169 ~~cPitGe~IP~-~e~~eHmRi~Ll 192 (229)
T PF12230_consen 169 IICPITGEMIPA-DEMDEHMRIELL 192 (229)
T ss_dssp -------------------------
T ss_pred cccccccccccc-cccccccccccc
Confidence 445555544333 244555554433
No 227
>PF09963 DUF2197: Uncharacterized protein conserved in bacteria (DUF2197); InterPro: IPR019241 This family represents various hypothetical bacterial proteins with no known function.
Probab=32.80 E-value=19 Score=17.98 Aligned_cols=11 Identities=18% Similarity=0.461 Sum_probs=6.4
Q ss_pred ceecccccccc
Q psy2643 54 PHKCVVCGKAF 64 (134)
Q Consensus 54 ~~~C~~C~~~~ 64 (134)
.|-|+.|....
T Consensus 31 tYmC~eC~~RI 41 (56)
T PF09963_consen 31 TYMCDECKERI 41 (56)
T ss_pred ceeChhHHHHH
Confidence 46666665443
No 228
>PRK12496 hypothetical protein; Provisional
Probab=32.73 E-value=34 Score=21.17 Aligned_cols=25 Identities=20% Similarity=0.571 Sum_probs=16.3
Q ss_pred eeccccccccCChhHHHHHHHHcCCCCCcccCcchhh
Q psy2643 55 HKCVVCGKAFSQSSNLITHLRKHTGYKPFSCGLCDKA 91 (134)
Q Consensus 55 ~~C~~C~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~ 91 (134)
|.|..|++.|..... .-.||.||..
T Consensus 128 ~~C~gC~~~~~~~~~------------~~~C~~CG~~ 152 (164)
T PRK12496 128 KVCKGCKKKYPEDYP------------DDVCEICGSP 152 (164)
T ss_pred EECCCCCccccCCCC------------CCcCCCCCCh
Confidence 679999988754210 1259999854
No 229
>PF01215 COX5B: Cytochrome c oxidase subunit Vb This family consists of chains F and S ; InterPro: IPR002124 Cytochrome c oxidase (1.9.3.1 from EC) is an oligomeric enzymatic complex which is a component of the respiratory chain complex and is involved in the transfer of electrons from cytochrome c to oxygen []. In eukaryotes this enzyme complex is located in the mitochondrial inner membrane; in aerobic prokaryotes it is found in the plasma membrane. In eukaryotes, in addition to the three large subunits, I, II and III, that form the catalytic centre of the enzyme complex, there are a variable number of small polypeptidic subunits. One of these subunits, which is known as Vb in mammals, V in Dictyostelium discoideum (Slime mold) and IV in yeast, binds a zinc atom. The sequence of subunit Vb is well conserved and includes three conserved cysteines that coordinate the zinc ion [, ]. Two of these cysteines are clustered in the C-terminal section of the subunit.; GO: 0004129 cytochrome-c oxidase activity, 0005740 mitochondrial envelope; PDB: 2EIL_S 2ZXW_S 3ASN_S 1OCO_S 3AG4_S 3ABK_S 1OCZ_S 1OCC_F 3ASO_S 3ABL_S ....
Probab=32.47 E-value=12 Score=22.43 Aligned_cols=15 Identities=33% Similarity=0.680 Sum_probs=12.1
Q ss_pred CCCcccCcchhhccC
Q psy2643 80 YKPFSCGLCDKAFQR 94 (134)
Q Consensus 80 ~~~~~C~~C~~~f~~ 94 (134)
.++.+|+.||..|.-
T Consensus 110 g~~~RCpeCG~~fkL 124 (136)
T PF01215_consen 110 GKPQRCPECGQVFKL 124 (136)
T ss_dssp TSEEEETTTEEEEEE
T ss_pred CCccCCCCCCeEEEE
Confidence 458999999988863
No 230
>TIGR01384 TFS_arch transcription factor S, archaeal. There has been an apparent duplication event in the Halobacteriaceae lineage (Haloarcula, Haloferax, Haloquadratum, Halobacterium and Natromonas). There appears to be a separate duplication in Methanosphaera stadtmanae.
Probab=32.04 E-value=21 Score=20.00 Aligned_cols=26 Identities=27% Similarity=0.747 Sum_probs=16.6
Q ss_pred CCcCccccCChHHHHHHHHHcCCCCCccCcccccccCC
Q psy2643 1 CKQCGKTFKRSSTLSTHLLIHSDTRPYPCQYCGKRFHQ 38 (134)
Q Consensus 1 C~~C~~~f~~~~~l~~h~~~~~~~~~~~c~~C~~~~~~ 38 (134)
|+.||..+... ...+.|+.|+..+..
T Consensus 3 C~~Cg~~l~~~------------~~~~~C~~C~~~~~~ 28 (104)
T TIGR01384 3 CPKCGSLMTPK------------NGVYVCPSCGYEKEK 28 (104)
T ss_pred CcccCcccccC------------CCeEECcCCCCcccc
Confidence 77888766321 125788888866553
No 231
>COG3364 Zn-ribbon containing protein [General function prediction only]
Probab=31.88 E-value=25 Score=19.97 Aligned_cols=27 Identities=33% Similarity=0.778 Sum_probs=16.9
Q ss_pred ceeccccccccCChhHHHHHHHHcCCCCCcccCcchh
Q psy2643 54 PHKCVVCGKAFSQSSNLITHLRKHTGYKPFSCGLCDK 90 (134)
Q Consensus 54 ~~~C~~C~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~ 90 (134)
+..|..||..|.+.+. +-.--|+.||-
T Consensus 2 pH~CtrCG~vf~~g~~----------~il~GCp~CG~ 28 (112)
T COG3364 2 PHQCTRCGEVFDDGSE----------EILSGCPKCGC 28 (112)
T ss_pred CceecccccccccccH----------HHHccCccccc
Confidence 3467778877766422 24566778773
No 232
>PF11789 zf-Nse: Zinc-finger of the MIZ type in Nse subunit; PDB: 2YU4_A 3HTK_C.
Probab=31.86 E-value=23 Score=17.67 Aligned_cols=31 Identities=23% Similarity=0.455 Sum_probs=14.0
Q ss_pred CceeccccccccCChhHHHHHHHHcCCCCCcccCc
Q psy2643 53 KPHKCVVCGKAFSQSSNLITHLRKHTGYKPFSCGL 87 (134)
Q Consensus 53 ~~~~C~~C~~~~~~~~~l~~h~~~~~~~~~~~C~~ 87 (134)
.|+....|+-.|...+-+ ..+ .+.+...||+
T Consensus 23 ~PV~s~~C~H~fek~aI~-~~i---~~~~~~~CPv 53 (57)
T PF11789_consen 23 DPVKSKKCGHTFEKEAIL-QYI---QRNGSKRCPV 53 (57)
T ss_dssp SEEEESSS--EEEHHHHH-HHC---TTTS-EE-SC
T ss_pred CCcCcCCCCCeecHHHHH-HHH---HhcCCCCCCC
Confidence 355566677777655332 233 2344567766
No 233
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=31.81 E-value=19 Score=15.76 Aligned_cols=10 Identities=30% Similarity=0.796 Sum_probs=5.6
Q ss_pred cccCcchhhc
Q psy2643 83 FSCGLCDKAF 92 (134)
Q Consensus 83 ~~C~~C~~~f 92 (134)
+.|..|+.+|
T Consensus 22 ~~C~~Cg~~~ 31 (33)
T PF08792_consen 22 EVCIFCGSSF 31 (33)
T ss_pred EEcccCCcEe
Confidence 4566666554
No 234
>COG5112 UFD2 U1-like Zn-finger-containing protein [General function prediction only]
Probab=31.69 E-value=29 Score=19.80 Aligned_cols=21 Identities=24% Similarity=0.487 Sum_probs=11.7
Q ss_pred cccCcchhhccChHHHHHHHH
Q psy2643 83 FSCGLCDKAFQRKVDLRRHRE 103 (134)
Q Consensus 83 ~~C~~C~~~f~~~~~l~~H~~ 103 (134)
+.|-.|.+-|-+...|..|.+
T Consensus 56 hYCieCaryf~t~~aL~~Hkk 76 (126)
T COG5112 56 HYCIECARYFITEKALMEHKK 76 (126)
T ss_pred eeeehhHHHHHHHHHHHHHhc
Confidence 455555555555555555554
No 235
>PF14369 zf-RING_3: zinc-finger
Probab=31.63 E-value=22 Score=15.73 Aligned_cols=8 Identities=38% Similarity=1.136 Sum_probs=4.2
Q ss_pred CCcCcccc
Q psy2643 1 CKQCGKTF 8 (134)
Q Consensus 1 C~~C~~~f 8 (134)
|+.|+..|
T Consensus 24 CP~C~~gF 31 (35)
T PF14369_consen 24 CPRCHGGF 31 (35)
T ss_pred CcCCCCcE
Confidence 45555544
No 236
>PTZ00448 hypothetical protein; Provisional
Probab=31.63 E-value=36 Score=24.17 Aligned_cols=24 Identities=17% Similarity=0.429 Sum_probs=19.9
Q ss_pred CcccCcchhhccChHHHHHHHHhh
Q psy2643 82 PFSCGLCDKAFQRKVDLRRHRESQ 105 (134)
Q Consensus 82 ~~~C~~C~~~f~~~~~l~~H~~~~ 105 (134)
.|.|..|+-.|.+....+.|.+.-
T Consensus 314 ~~tC~~C~v~F~~~~~qR~H~KSD 337 (373)
T PTZ00448 314 MLLCRKCNIQLMDHNAFKQHYRSE 337 (373)
T ss_pred CccccccccccCCHHHHHHHhhhh
Confidence 588999999998888888887654
No 237
>KOG0717|consensus
Probab=31.39 E-value=34 Score=25.14 Aligned_cols=22 Identities=36% Similarity=0.679 Sum_probs=18.5
Q ss_pred eeccccccccCChhHHHHHHHH
Q psy2643 55 HKCVVCGKAFSQSSNLITHLRK 76 (134)
Q Consensus 55 ~~C~~C~~~~~~~~~l~~h~~~ 76 (134)
+.|.+|.+.|.+...+..|...
T Consensus 293 lyC~vCnKsFKseKq~kNHEnS 314 (508)
T KOG0717|consen 293 LYCVVCNKSFKSEKQLKNHENS 314 (508)
T ss_pred eEEeeccccccchHHHHhhHHH
Confidence 7799999999999888888753
No 238
>PTZ00043 cytochrome c oxidase subunit; Provisional
Probab=31.35 E-value=24 Score=23.19 Aligned_cols=16 Identities=31% Similarity=0.636 Sum_probs=12.9
Q ss_pred CCCCcccCcchhhccC
Q psy2643 79 GYKPFSCGLCDKAFQR 94 (134)
Q Consensus 79 ~~~~~~C~~C~~~f~~ 94 (134)
..++.+|+.||..|.-
T Consensus 178 EGkpqRCpECGqVFKL 193 (268)
T PTZ00043 178 EGFLYRCGECDQIFML 193 (268)
T ss_pred CCCCccCCCCCcEEEE
Confidence 4558999999998873
No 239
>PRK05452 anaerobic nitric oxide reductase flavorubredoxin; Provisional
Probab=31.30 E-value=12 Score=27.37 Aligned_cols=38 Identities=18% Similarity=0.350 Sum_probs=21.4
Q ss_pred CCceeccccccccCChhHHHHHHHHcCC------CCCcccCcchh
Q psy2643 52 EKPHKCVVCGKAFSQSSNLITHLRKHTG------YKPFSCGLCDK 90 (134)
Q Consensus 52 ~~~~~C~~C~~~~~~~~~l~~h~~~~~~------~~~~~C~~C~~ 90 (134)
...|.|..|+..+.....-.. ..+-.| ...|.||.|+.
T Consensus 423 ~~~~~c~~c~~~yd~~~g~~~-~~~~~gt~~~~lp~~~~cp~c~~ 466 (479)
T PRK05452 423 GPRMQCSVCQWIYDPAKGEPM-QDVAPGTPWSEVPDNFLCPECSL 466 (479)
T ss_pred CCeEEECCCCeEECCCCCCcc-cCCCCCCChhhCCCCCcCcCCCC
Confidence 345899999988765422110 001111 12489999984
No 240
>PRK12860 transcriptional activator FlhC; Provisional
Probab=31.06 E-value=32 Score=21.98 Aligned_cols=27 Identities=22% Similarity=0.561 Sum_probs=18.5
Q ss_pred ccCcccccccCChhhHHHHHHhhcCCCceeccccc
Q psy2643 27 YPCQYCGKRFHQKSDMKKHTYIHTGEKPHKCVVCG 61 (134)
Q Consensus 27 ~~c~~C~~~~~~~~~l~~h~~~~~~~~~~~C~~C~ 61 (134)
..|..|+..|..... .....|.|+.|.
T Consensus 135 ~~C~~Cgg~fv~~~~--------e~~~~f~CplC~ 161 (189)
T PRK12860 135 ARCCRCGGKFVTHAH--------DLRHNFVCGLCQ 161 (189)
T ss_pred ccCCCCCCCeecccc--------ccCCCCcCCCCC
Confidence 578899988774421 223468899987
No 241
>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=30.94 E-value=18 Score=20.53 Aligned_cols=10 Identities=50% Similarity=1.315 Sum_probs=6.1
Q ss_pred CccCcccccc
Q psy2643 26 PYPCQYCGKR 35 (134)
Q Consensus 26 ~~~c~~C~~~ 35 (134)
|..|+.||..
T Consensus 2 p~~CpYCg~~ 11 (102)
T PF11672_consen 2 PIICPYCGGP 11 (102)
T ss_pred CcccCCCCCe
Confidence 5567777643
No 242
>PRK12722 transcriptional activator FlhC; Provisional
Probab=30.46 E-value=33 Score=21.84 Aligned_cols=28 Identities=21% Similarity=0.581 Sum_probs=19.0
Q ss_pred ccCcccccccCChhhHHHHHHhhcCCCceecccccc
Q psy2643 27 YPCQYCGKRFHQKSDMKKHTYIHTGEKPHKCVVCGK 62 (134)
Q Consensus 27 ~~c~~C~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~ 62 (134)
..|..|+..|..... .....|.|+.|..
T Consensus 135 ~~C~~Cgg~fv~~~~--------e~~~~f~CplC~~ 162 (187)
T PRK12722 135 SSCNCCGGHFVTHAH--------DPVGSFVCGLCQP 162 (187)
T ss_pred ccCCCCCCCeecccc--------ccCCCCcCCCCCC
Confidence 468999988774431 2234688999976
No 243
>PF07295 DUF1451: Protein of unknown function (DUF1451); InterPro: IPR009912 This family consists of several hypothetical bacterial proteins of around 160 residues in length. Members of this family contain four highly conserved cysteine resides toward the C-terminal region of the protein. The function of this family is unknown.
Probab=29.87 E-value=22 Score=21.67 Aligned_cols=30 Identities=20% Similarity=0.413 Sum_probs=17.7
Q ss_pred CceeccccccccCChhHHHHHHHHcCCCCCcccCcchhhc
Q psy2643 53 KPHKCVVCGKAFSQSSNLITHLRKHTGYKPFSCGLCDKAF 92 (134)
Q Consensus 53 ~~~~C~~C~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~f 92 (134)
..|.|..||...... + .+.--.||.|+...
T Consensus 111 G~l~C~~Cg~~~~~~---------~-~~~l~~Cp~C~~~~ 140 (146)
T PF07295_consen 111 GTLVCENCGHEVELT---------H-PERLPPCPKCGHTE 140 (146)
T ss_pred ceEecccCCCEEEec---------C-CCcCCCCCCCCCCe
Confidence 347888888653221 1 23345788888643
No 244
>PF08271 TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013137 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIB (TFIIB). In eukaryotes the initiation of transcription of protein encoding genes by the polymerase II complexe (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least seven different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, and -IIH []. TFIIB and TFIID are responsible for promoter recognition and interaction with pol II; together with Pol II, they form a minimal initiation complex capable of transcription under certain conditions. The TATA box of a Pol II promoter is bound in the initiation complex by the TBP subunit of TFIID, which bends the DNA around the C-terminal domain of TFIIB whereas the N-terminal zinc finger of TFIIB interacts with Pol II [, ]. The TFIIB zinc finger adopts a zinc ribbon fold characterised by two beta-hairpins forming two structurally similar zinc-binding sub-sites []. The zinc finger contacts the rbp1 subunit of Pol II through its dock domain, a conserved region of about 70 amino acids located close to the polymerase active site []. In the Pol II complex this surface is located near the RNA exit groove. Interestingly this sequence is best conserved in the three polymerases that utilise a TFIIB-like general transcription factor (Pol II, Pol III, and archaeal RNA polymerase) but not in Pol I []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1VD4_A 1PFT_A 3K1F_M 3K7A_M 1RO4_A 1RLY_A 1DL6_A.
Probab=29.75 E-value=22 Score=16.35 Aligned_cols=9 Identities=22% Similarity=0.737 Sum_probs=6.0
Q ss_pred cccCcchhh
Q psy2643 83 FSCGLCDKA 91 (134)
Q Consensus 83 ~~C~~C~~~ 91 (134)
|.||.|+..
T Consensus 1 m~Cp~Cg~~ 9 (43)
T PF08271_consen 1 MKCPNCGSK 9 (43)
T ss_dssp ESBTTTSSS
T ss_pred CCCcCCcCC
Confidence 467777754
No 245
>PF10122 Mu-like_Com: Mu-like prophage protein Com; InterPro: IPR019294 Members of this entry belong to the Com family of proteins that act as translational regulators of mom [, ].
Probab=29.37 E-value=14 Score=18.05 Aligned_cols=30 Identities=17% Similarity=0.417 Sum_probs=15.2
Q ss_pred ceeccccccccCChhHHHHHHHHcCCCCCcccCcchhh
Q psy2643 54 PHKCVVCGKAFSQSSNLITHLRKHTGYKPFSCGLCDKA 91 (134)
Q Consensus 54 ~~~C~~C~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~ 91 (134)
.+.|..|++.+...+. ..+.-.+|+.|+..
T Consensus 4 eiRC~~CnklLa~~g~--------~~~leIKCpRC~ti 33 (51)
T PF10122_consen 4 EIRCGHCNKLLAKAGE--------VIELEIKCPRCKTI 33 (51)
T ss_pred ceeccchhHHHhhhcC--------ccEEEEECCCCCcc
Confidence 3566667655433211 11233677777754
No 246
>KOG3214|consensus
Probab=29.34 E-value=15 Score=20.72 Aligned_cols=13 Identities=38% Similarity=0.989 Sum_probs=7.1
Q ss_pred CcccCcchhhccC
Q psy2643 82 PFSCGLCDKAFQR 94 (134)
Q Consensus 82 ~~~C~~C~~~f~~ 94 (134)
...|.+|+.+|..
T Consensus 47 ~~sC~iC~esFqt 59 (109)
T KOG3214|consen 47 KASCRICEESFQT 59 (109)
T ss_pred eeeeeehhhhhcc
Confidence 3456666655553
No 247
>COG4896 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=29.08 E-value=28 Score=17.71 Aligned_cols=8 Identities=38% Similarity=1.053 Sum_probs=3.6
Q ss_pred ccCccccc
Q psy2643 27 YPCQYCGK 34 (134)
Q Consensus 27 ~~c~~C~~ 34 (134)
|.|++|..
T Consensus 32 ymC~eC~~ 39 (68)
T COG4896 32 YMCPECEH 39 (68)
T ss_pred EechhhHh
Confidence 44444443
No 248
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=28.82 E-value=70 Score=24.74 Aligned_cols=12 Identities=17% Similarity=0.346 Sum_probs=8.5
Q ss_pred ccCcchhhccCh
Q psy2643 84 SCGLCDKAFQRK 95 (134)
Q Consensus 84 ~C~~C~~~f~~~ 95 (134)
.|+.||......
T Consensus 43 fC~~CG~~~~~~ 54 (645)
T PRK14559 43 HCPNCGAETGTI 54 (645)
T ss_pred cccccCCcccch
Confidence 688898765544
No 249
>PF11023 DUF2614: Protein of unknown function (DUF2614); InterPro: IPR020912 This entry describes proteins of unknown function, which are thought to be membrane proteins.; GO: 0005887 integral to plasma membrane
Probab=28.63 E-value=36 Score=19.72 Aligned_cols=12 Identities=33% Similarity=0.819 Sum_probs=7.2
Q ss_pred CCCccCcccccc
Q psy2643 24 TRPYPCQYCGKR 35 (134)
Q Consensus 24 ~~~~~c~~C~~~ 35 (134)
.....||.|++.
T Consensus 67 av~V~CP~C~K~ 78 (114)
T PF11023_consen 67 AVQVECPNCGKQ 78 (114)
T ss_pred ceeeECCCCCCh
Confidence 345567777663
No 250
>PF02748 PyrI_C: Aspartate carbamoyltransferase regulatory chain, metal binding domain; InterPro: IPR020542 Aspartate carbamoyltransferase (aspartate transcarbamylase, ATCase) 2.1.3.2 from EC is an allosteric enzyme that plays a central role in the regulation of the pyrimidine pathway in bacteria. The holoenzyme is a dodecamer composed of six catalytic chains, each with an active site, and six regulatory chains lacking catalytic activity []. The catalytic subunits exist as a dimer of catalytic trimers, (c3)2, while the regulatory subunits exist as a trimer of regulatory dimers, (r2)3, therefore the complete holoenzyme can be represented as (c3)2(r2)3. The association of the catalytic subunits c3 with the regulatory subunits r2 is responsible for the establishment of positive co-operativity between catalytic sites for the binding of aspartate and it dictates the pattern of allosteric response toward nucleotide effectors. ATCase from Escherichia coli is the most extensively studied allosteric enzyme []. The crystal structure of the T-state, the T-state with CTP bound, the R-state with N-phosphonacetyl-L-aspartate (PALA) bound, and the R-state with phosphonoacetamide plus malonate bound have been used in interpreting kinetic and mutational studies. A high-resolution structure of E. coli ATCase in the presence of PALA (a bisubstrate analog) allows a detailed description of the binding at the active site of the enzyme and allows a detailed model of the tetrahedral intermediate to be constructed. The entire regulatory chain has been traced showing that the N-terminal regions of the regulatory chains R1 and R6 are located in close proximity to each other and to the regulatory site. This portion of the molecule may be involved in the observed asymmetry between the regulatory binding sites as well as in the heterotropic response of the enzyme []. The C-terminal domain of the regulatory chains have a rubredoxin-like zinc-bound fold. ATCase from Enterobacter agglomerans (Erwinia herbicola) (Pantoea agglomerans) differs from the other investigated enterobacterial ATCases by its absence of homotropic co-operativity toward the substrate aspartate and its lack of response to ATP which is an allosteric effector (activator) of this family of enzymes. Nevertheless, the E. herbicola ATCase has the same quaternary structure, two trimers of catalytic chains with three dimers of regulatory chains, (c3)2(r2)3, as other enterobacterial ATCases and shows extensive primary structure conservation []. This entry represents the C-terminal domain.; PDB: 2YWW_B 1SKU_D 1Q95_L 8ATC_B 3AT1_D 1RAI_D 4E2F_D 1NBE_B 6AT1_B 2FZC_D ....
Probab=28.52 E-value=22 Score=17.39 Aligned_cols=17 Identities=12% Similarity=0.450 Sum_probs=10.0
Q ss_pred CCCCCcccCcchhhccC
Q psy2643 78 TGYKPFSCGLCDKAFQR 94 (134)
Q Consensus 78 ~~~~~~~C~~C~~~f~~ 94 (134)
.....|+|.+|++.+..
T Consensus 31 ~~~~~~rC~YCe~~~~~ 47 (52)
T PF02748_consen 31 KEPIKLRCHYCERIITE 47 (52)
T ss_dssp TTTCEEEETTT--EEEH
T ss_pred CCCCEEEeeCCCCEecc
Confidence 34556888888877653
No 251
>PF09855 DUF2082: Nucleic-acid-binding protein containing Zn-ribbon domain (DUF2082); InterPro: IPR018652 This family of proteins contains various hypothetical prokaryotic proteins as well as some Zn-ribbon nucleic-acid-binding proteins.
Probab=28.33 E-value=24 Score=18.13 Aligned_cols=8 Identities=25% Similarity=1.057 Sum_probs=5.6
Q ss_pred cccCcchh
Q psy2643 83 FSCGLCDK 90 (134)
Q Consensus 83 ~~C~~C~~ 90 (134)
|.|+.||.
T Consensus 1 y~C~KCg~ 8 (64)
T PF09855_consen 1 YKCPKCGN 8 (64)
T ss_pred CCCCCCCC
Confidence 56777774
No 252
>KOG1088|consensus
Probab=28.23 E-value=25 Score=20.49 Aligned_cols=21 Identities=10% Similarity=0.028 Sum_probs=16.3
Q ss_pred HcCCCCCcccCcchhhccChH
Q psy2643 76 KHTGYKPFSCGLCDKAFQRKV 96 (134)
Q Consensus 76 ~~~~~~~~~C~~C~~~f~~~~ 96 (134)
++-.++...|+.||+.|.-+.
T Consensus 92 ~~v~EG~l~CpetG~vfpI~~ 112 (124)
T KOG1088|consen 92 IDVIEGELVCPETGRVFPISD 112 (124)
T ss_pred hhhccceEecCCCCcEeeccc
Confidence 455677899999999987553
No 253
>COG3880 Modulator of heat shock repressor CtsR, McsA [Signal transduction mechanisms]
Probab=27.67 E-value=13 Score=23.10 Aligned_cols=32 Identities=25% Similarity=0.555 Sum_probs=21.5
Q ss_pred CccCcccccccCChhhHHHHHHhhcCCCceeccccccccCCh
Q psy2643 26 PYPCQYCGKRFHQKSDMKKHTYIHTGEKPHKCVVCGKAFSQS 67 (134)
Q Consensus 26 ~~~c~~C~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~~~~~ 67 (134)
...|+.|+.+|..... .+.|.|..|..+|.+.
T Consensus 74 ~l~C~~C~~Tfk~f~~----------~g~fGCaeCY~tf~~~ 105 (176)
T COG3880 74 LLGCHNCGMTFKEFIQ----------SGLFGCAECYKTFESQ 105 (176)
T ss_pred HhcCccccccHHHHHH----------hcccchHHHHHHHHHH
Confidence 3678889888765421 1357788888877653
No 254
>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=27.64 E-value=28 Score=15.65 Aligned_cols=11 Identities=36% Similarity=0.697 Sum_probs=5.7
Q ss_pred ceecccccccc
Q psy2643 54 PHKCVVCGKAF 64 (134)
Q Consensus 54 ~~~C~~C~~~~ 64 (134)
-|+|..||...
T Consensus 6 ~YkC~~CGniV 16 (36)
T PF06397_consen 6 FYKCEHCGNIV 16 (36)
T ss_dssp EEE-TTT--EE
T ss_pred EEEccCCCCEE
Confidence 47888888764
No 255
>smart00731 SprT SprT homologues. Predicted to have roles in transcription elongation. Contains a conserved HExxH motif, indicating a metalloprotease function.
Probab=27.62 E-value=24 Score=21.20 Aligned_cols=32 Identities=25% Similarity=0.751 Sum_probs=16.7
Q ss_pred ceeccccccccCChhHHHHHHHHcCCCCCcccCcchhhc
Q psy2643 54 PHKCVVCGKAFSQSSNLITHLRKHTGYKPFSCGLCDKAF 92 (134)
Q Consensus 54 ~~~C~~C~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~f 92 (134)
.|.|..|+..+.. +.+ +.....|.|..|+-.+
T Consensus 112 ~y~C~~C~~~~~~------~rr-~~~~~~y~C~~C~g~l 143 (146)
T smart00731 112 PYRCTGCGQRYLR------VRR-SNNVSRYRCGKCGGKL 143 (146)
T ss_pred EEECCCCCCCCce------Ecc-ccCcceEEcCCCCCEE
Confidence 4677777765432 111 2222447777777544
No 256
>PF11494 Ta0938: Ta0938; InterPro: IPR021585 Ta0938 is a protein of unknown function however the structure has been determined. The protein has a novel fold and a putative Zn-binding motif. The structure has two different parts, one region contains a beta sheet flanked by two alpha helices and the other contains a bundle of loops which contain all cysteines in the protein. ; PDB: 2FQH_A.
Probab=27.25 E-value=28 Score=19.54 Aligned_cols=37 Identities=24% Similarity=0.514 Sum_probs=10.3
Q ss_pred CCccCcccccccCChhhHHHHHHhhcCCC-ceeccccccccCCh
Q psy2643 25 RPYPCQYCGKRFHQKSDMKKHTYIHTGEK-PHKCVVCGKAFSQS 67 (134)
Q Consensus 25 ~~~~c~~C~~~~~~~~~l~~h~~~~~~~~-~~~C~~C~~~~~~~ 67 (134)
+.-.|..|+.++.... .. ..+++ -|-|+.|..-|..-
T Consensus 13 ke~~CalCG~tWg~~y-----~E-v~G~rLfFCCd~ca~EF~nm 50 (105)
T PF11494_consen 13 KEMGCALCGATWGDYY-----EE-VDGERLFFCCDDCAKEFKNM 50 (105)
T ss_dssp GGGS-SS---S---SS------B--TT--BSSS--SSSS-TTS-
T ss_pred ccccccccCCcHHHHH-----Hh-hcCCEEEEEcHHHHHHHHHH
Confidence 3445666666554321 11 12222 24556666655553
No 257
>KOG0402|consensus
Probab=27.20 E-value=18 Score=19.69 Aligned_cols=13 Identities=31% Similarity=0.800 Sum_probs=7.6
Q ss_pred CCcccCcchhhcc
Q psy2643 81 KPFSCGLCDKAFQ 93 (134)
Q Consensus 81 ~~~~C~~C~~~f~ 93 (134)
..|.|..|.+.+.
T Consensus 53 GiW~C~~C~kv~a 65 (92)
T KOG0402|consen 53 GIWKCGSCKKVVA 65 (92)
T ss_pred eEEecCCccceec
Confidence 3466666666554
No 258
>PF03811 Zn_Tnp_IS1: InsA N-terminal domain; InterPro: IPR003220 Insertion elements are mobile elements in DNA, usually encoding proteins required for transposition, for example transposases. Protein InsA is absolutely required for transposition of insertion element 1. This entry represents a short zinc binding domain found in IS1 InsA family protein. It is found at the N terminus of the protein and may be a DNA-binding domain.; GO: 0006313 transposition, DNA-mediated
Probab=27.15 E-value=9.6 Score=17.09 Aligned_cols=7 Identities=29% Similarity=1.042 Sum_probs=3.0
Q ss_pred CcccCcc
Q psy2643 82 PFSCGLC 88 (134)
Q Consensus 82 ~~~C~~C 88 (134)
.|.|..|
T Consensus 29 ryrC~~C 35 (36)
T PF03811_consen 29 RYRCKDC 35 (36)
T ss_pred eEecCcC
Confidence 3444443
No 259
>PRK04351 hypothetical protein; Provisional
Probab=26.54 E-value=34 Score=20.85 Aligned_cols=31 Identities=26% Similarity=0.775 Sum_probs=16.8
Q ss_pred eeccccccccCChhHHHHHHHHcCCCCCcccCcchhhcc
Q psy2643 55 HKCVVCGKAFSQSSNLITHLRKHTGYKPFSCGLCDKAFQ 93 (134)
Q Consensus 55 ~~C~~C~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~f~ 93 (134)
|.|..|+..+... +.+ +...|.|..|+-.+.
T Consensus 113 Y~C~~Cg~~~~r~-------Rr~-n~~~yrCg~C~g~L~ 143 (149)
T PRK04351 113 YECQSCGQQYLRK-------RRI-NTKRYRCGKCRGKLK 143 (149)
T ss_pred EECCCCCCEeeee-------eec-CCCcEEeCCCCcEee
Confidence 6777777555332 112 234577777775443
No 260
>COG4338 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=26.44 E-value=23 Score=17.04 Aligned_cols=15 Identities=20% Similarity=0.585 Sum_probs=11.0
Q ss_pred cCcccccccCChhhH
Q psy2643 28 PCQYCGKRFHQKSDM 42 (134)
Q Consensus 28 ~c~~C~~~~~~~~~l 42 (134)
+|+.|+..|......
T Consensus 14 ICpvCqRPFsWRkKW 28 (54)
T COG4338 14 ICPVCQRPFSWRKKW 28 (54)
T ss_pred hhhhhcCchHHHHHH
Confidence 688888888765433
No 261
>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=26.14 E-value=25 Score=15.56 Aligned_cols=12 Identities=33% Similarity=0.827 Sum_probs=5.3
Q ss_pred ccCcchhhccCh
Q psy2643 84 SCGLCDKAFQRK 95 (134)
Q Consensus 84 ~C~~C~~~f~~~ 95 (134)
.|..|++.|..+
T Consensus 5 ~C~eC~~~f~dS 16 (34)
T PF01286_consen 5 KCDECGKPFMDS 16 (34)
T ss_dssp E-TTT--EES-S
T ss_pred hHhHhCCHHHHH
Confidence 567777777654
No 262
>TIGR03826 YvyF flagellar operon protein TIGR03826. This gene is found in flagellar operons of Bacillus-related organisms. Its function has not been determined and an official gene symbol has not been assigned, although the gene is designated yvyF in B. subtilus. A tentative assignment as a regulator is suggested in the NCBI record GI:16080597.
Probab=26.01 E-value=24 Score=21.23 Aligned_cols=11 Identities=27% Similarity=0.908 Sum_probs=9.1
Q ss_pred ccCcchhhccC
Q psy2643 84 SCGLCDKAFQR 94 (134)
Q Consensus 84 ~C~~C~~~f~~ 94 (134)
.|+.||+.|.+
T Consensus 5 nC~~CgklF~~ 15 (137)
T TIGR03826 5 NCPKCGRLFVK 15 (137)
T ss_pred cccccchhhhh
Confidence 58889988886
No 263
>PF03966 Trm112p: Trm112p-like protein; InterPro: IPR005651 This family of short proteins have no known function. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. The function of this family is uncertain. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. The entry contains 2 families: Trm112, which is required for tRNA methylation in Saccharomyces cerevisiae (Baker's yeast) and is found in complexes with 2 tRNA methylases (TRM9 and TRM11) also with putative methyltransferase YDR140W []. The zinc-finger protein Ynr046w is plurifunctional and a component of the eRF1 methyltransferase in yeast []. The crystal structure of Ynr046w has been determined to 1.7 A resolution. It comprises a zinc-binding domain built from both the N- and C-terminal sequences and an inserted domain, absent from bacterial and archaeal orthologs of the protein, composed of three alpha-helices []. UPF0434, which are proteins that are functionally uncharacterised. ; PDB: 3Q87_A 2KPI_A 2K5R_A 2HF1_A 2JS4_A 2J6A_A 2JR6_A 2PK7_A 2JNY_A.
Probab=25.93 E-value=21 Score=18.35 Aligned_cols=17 Identities=12% Similarity=0.368 Sum_probs=12.1
Q ss_pred cCCCCCcccCcchhhcc
Q psy2643 77 HTGYKPFSCGLCDKAFQ 93 (134)
Q Consensus 77 ~~~~~~~~C~~C~~~f~ 93 (134)
+-.+....|+.|++.|.
T Consensus 48 ~i~eg~L~Cp~c~r~YP 64 (68)
T PF03966_consen 48 EIVEGELICPECGREYP 64 (68)
T ss_dssp ETTTTEEEETTTTEEEE
T ss_pred cccCCEEEcCCCCCEEe
Confidence 44556688888888775
No 264
>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG
Probab=25.50 E-value=28 Score=17.08 Aligned_cols=9 Identities=22% Similarity=0.896 Sum_probs=6.0
Q ss_pred ccCcchhhc
Q psy2643 84 SCGLCDKAF 92 (134)
Q Consensus 84 ~C~~C~~~f 92 (134)
.||.||..+
T Consensus 2 ~CPyCge~~ 10 (52)
T PF14255_consen 2 QCPYCGEPI 10 (52)
T ss_pred CCCCCCCee
Confidence 577777654
No 265
>PLN03238 probable histone acetyltransferase MYST; Provisional
Probab=25.44 E-value=85 Score=21.58 Aligned_cols=25 Identities=32% Similarity=0.530 Sum_probs=16.7
Q ss_pred CCCcccCcchhhccChHHHHHHHHh
Q psy2643 80 YKPFSCGLCDKAFQRKVDLRRHRES 104 (134)
Q Consensus 80 ~~~~~C~~C~~~f~~~~~l~~H~~~ 104 (134)
+.-|.|..|-+-|.+...|.+|+..
T Consensus 46 ~~lyiCe~Clky~~~~~~l~~H~~~ 70 (290)
T PLN03238 46 TKLYICEYCLKYMRKKKSLLRHLAK 70 (290)
T ss_pred CeEEEcCCCcchhCCHHHHHHHHHh
Confidence 4456777777777777777777653
No 266
>KOG2071|consensus
Probab=25.12 E-value=53 Score=24.86 Aligned_cols=28 Identities=18% Similarity=0.375 Sum_probs=21.5
Q ss_pred CCCCCcccCcchhhccChHHHHHHHHhh
Q psy2643 78 TGYKPFSCGLCDKAFQRKVDLRRHRESQ 105 (134)
Q Consensus 78 ~~~~~~~C~~C~~~f~~~~~l~~H~~~~ 105 (134)
....+-.|..||..|-.......||..|
T Consensus 414 y~~~pnqC~~CG~R~~~~ee~sk~md~H 441 (579)
T KOG2071|consen 414 YKDSPNQCKSCGLRFDDSEERSKHMDIH 441 (579)
T ss_pred ccCCcchhcccccccccchhhhhHhhhh
Confidence 3456788999999998888777777655
No 267
>PF11238 DUF3039: Protein of unknown function (DUF3039); InterPro: IPR021400 This family of proteins with unknown function appears to be restricted to Actinobacteria.
Probab=24.86 E-value=30 Score=17.43 Aligned_cols=7 Identities=43% Similarity=0.994 Sum_probs=3.4
Q ss_pred ccccccC
Q psy2643 31 YCGKRFH 37 (134)
Q Consensus 31 ~C~~~~~ 37 (134)
.||+.|.
T Consensus 30 LCGk~wv 36 (58)
T PF11238_consen 30 LCGKVWV 36 (58)
T ss_pred eeCceeC
Confidence 4555544
No 268
>TIGR03829 YokU_near_AblA uncharacterized protein, YokU family. Members of this protein family occur in various species of the genus Bacillus, always next to the gene (kamA or ablA) for lysine 2,3-aminomutase. Members have a pair of CXXC motifs, and share homology to the amino-terminal region of a family of putative transcription factors for which the C-terminal is modeled by pfam01381, a helix-turn-helix domain model. This family, however, is shorter and lacks the helix-turn-helix region. The function of this protein family is unknown, but a regulatory role in compatible solute biosynthesis is suggested by local genome context.
Probab=24.50 E-value=51 Score=18.26 Aligned_cols=13 Identities=31% Similarity=1.030 Sum_probs=8.8
Q ss_pred CCcCccccCChHH
Q psy2643 1 CKQCGKTFKRSST 13 (134)
Q Consensus 1 C~~C~~~f~~~~~ 13 (134)
|++||..|-+..-
T Consensus 38 C~~CGe~y~~dev 50 (89)
T TIGR03829 38 CSHCGMEYQDDTT 50 (89)
T ss_pred ccCCCcEeecHHH
Confidence 6777777766543
No 269
>PF04606 Ogr_Delta: Ogr/Delta-like zinc finger; InterPro: IPR007684 This entry is represented by Bacteriophage P2, Ogr. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This is a viral family of phage zinc-binding transcriptional activators, which also contains cryptic members in some bacterial genomes []. The P4 phage delta protein contains two such domains attached covalently, while the P2 phage Ogr proteins possess one domain but function as dimers. All the members of this family have the following consensus sequence: C-X(2)-C-X(3)-A-(X)2-R-X(15)-C-X(4)-C-X(3)-F [].; GO: 0006355 regulation of transcription, DNA-dependent
Probab=24.39 E-value=10 Score=17.97 Aligned_cols=12 Identities=25% Similarity=0.611 Sum_probs=5.8
Q ss_pred CcccCc--chhhcc
Q psy2643 82 PFSCGL--CDKAFQ 93 (134)
Q Consensus 82 ~~~C~~--C~~~f~ 93 (134)
-+.|.. ||..|.
T Consensus 25 Y~qC~N~~Cg~tfv 38 (47)
T PF04606_consen 25 YCQCTNPECGHTFV 38 (47)
T ss_pred EEEECCCcCCCEEE
Confidence 345533 555554
No 270
>COG3809 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=24.01 E-value=67 Score=17.32 Aligned_cols=21 Identities=14% Similarity=0.370 Sum_probs=15.6
Q ss_pred CCcCccccCChHHHHHHHHHc
Q psy2643 1 CKQCGKTFKRSSTLSTHLLIH 21 (134)
Q Consensus 1 C~~C~~~f~~~~~l~~h~~~~ 21 (134)
|+.|+.++.....|..-+...
T Consensus 24 CPrCrGVWLDrGELdKli~r~ 44 (88)
T COG3809 24 CPRCRGVWLDRGELDKLIERS 44 (88)
T ss_pred CCccccEeecchhHHHHHHHh
Confidence 788888888888877665443
No 271
>PRK01343 zinc-binding protein; Provisional
Probab=23.18 E-value=36 Score=17.10 Aligned_cols=12 Identities=25% Similarity=0.465 Sum_probs=9.2
Q ss_pred CcccCcchhhcc
Q psy2643 82 PFSCGLCDKAFQ 93 (134)
Q Consensus 82 ~~~C~~C~~~f~ 93 (134)
...|+.|++.+.
T Consensus 9 ~~~CP~C~k~~~ 20 (57)
T PRK01343 9 TRPCPECGKPST 20 (57)
T ss_pred CCcCCCCCCcCc
Confidence 467999998765
No 272
>TIGR00244 transcriptional regulator NrdR. Members of this almost entirely bacterial family contain an ATP cone domain (PFAM:PF03477). There is never more than one member per genome. Common gene symbols given include nrdR, ybaD, ribX and ytcG. The member from Streptomyces coelicolor is found upstream in the operon of the class II oxygen-independent ribonucleotide reductase gene nrdJ and was shown to repress nrdJ expression. Many members of this family are found near genes for riboflavin biosynthesis in Gram-negative bacteria, suggesting a role in that pathway. However, a phylogenetic profiling study associates members of this family with the presence of a palindromic signal with consensus acaCwAtATaTwGtgt, termed the NrdR-box, an upstream element for most operons for ribonucleotide reductase of all three classes in bacterial genomes.
Probab=23.16 E-value=32 Score=20.99 Aligned_cols=14 Identities=21% Similarity=0.392 Sum_probs=11.1
Q ss_pred CcccCcchhhccCh
Q psy2643 82 PFSCGLCDKAFQRK 95 (134)
Q Consensus 82 ~~~C~~C~~~f~~~ 95 (134)
--.|..|++.|++.
T Consensus 28 RReC~~C~~RFTTy 41 (147)
T TIGR00244 28 RRECLECHERFTTF 41 (147)
T ss_pred cccCCccCCcccee
Confidence 36899999998864
No 273
>PRK06260 threonine synthase; Validated
Probab=23.11 E-value=57 Score=23.31 Aligned_cols=11 Identities=36% Similarity=1.014 Sum_probs=5.4
Q ss_pred ccCcccccccC
Q psy2643 27 YPCQYCGKRFH 37 (134)
Q Consensus 27 ~~c~~C~~~~~ 37 (134)
+.|..|+..+.
T Consensus 4 ~~C~~cg~~~~ 14 (397)
T PRK06260 4 LKCIECGKEYD 14 (397)
T ss_pred EEECCCCCCCC
Confidence 34555555443
No 274
>PF01096 TFIIS_C: Transcription factor S-II (TFIIS); InterPro: IPR001222 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIs (TFIIS). In eukaryotes the initiation of transcription of protein encoding genes by polymerase II (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least eight different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, -IIH and -IIS []. During mRNA elongation, Pol II can encounter DNA sequences that cause reverse movement of the enzyme. Such backtracking involves extrusion of the RNA 3'-end into the pore, and can lead to transcriptional arrest. Escape from arrest requires cleavage of the extruded RNA with the help of TFIIS, which induces mRNA cleavage by enhancing the intrinsic nuclease activity of RNA polymerase (Pol) II, past template-encoded pause sites []. TFIIS extends from the polymerase surface via a pore to the internal active site. Two essential and invariant acidic residues in a TFIIS loop complement the Pol II active site and could position a metal ion and a water molecule for hydrolytic RNA cleavage. TFIIS also induces extensive structural changes in Pol II that would realign nucleic acids in the active centre. TFIIS is a protein of about 300 amino acids. It contains three regions: a variable N-terminal domain not required for TFIIS activity; a conserved central domain required for Pol II binding; and a conserved C-terminal C4-type zinc finger essential for RNA cleavage. The zinc finger folds in a conformation termed a zinc ribbon [] characterised by a three-stranded antiparallel beta-sheet and two beta-hairpins. A backbone model for Pol II-TFIIS complex was obtained from X-ray analysis. It shows that a beta hairpin protrudes from the zinc finger and complements the pol II active site []. Some viral proteins also contain the TFIIS zinc ribbon C-terminal domain. The Vaccinia virus protein, unlike its eukaryotic homologue, is an integral RNA polymerase subunit rather than a readily separable transcription factor []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding, 0006351 transcription, DNA-dependent; PDB: 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I 3I4M_I ....
Probab=22.91 E-value=27 Score=15.81 Aligned_cols=10 Identities=20% Similarity=0.860 Sum_probs=5.1
Q ss_pred cccCcchhhc
Q psy2643 83 FSCGLCDKAF 92 (134)
Q Consensus 83 ~~C~~C~~~f 92 (134)
|.|..|+..|
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 5555555443
No 275
>PF09082 DUF1922: Domain of unknown function (DUF1922); InterPro: IPR015166 Members of this family consist of a beta-sheet region followed by an alpha-helix and an unstructured C terminus. The beta-sheet region contains a CXCX...XCXC sequence with Cys residues located in two proximal loops and pointing towards each other. This precise function of this set of bacterial proteins is, as yet, unknown []. ; PDB: 1GH9_A.
Probab=22.73 E-value=18 Score=18.88 Aligned_cols=11 Identities=36% Similarity=0.806 Sum_probs=5.6
Q ss_pred CCCcccCcchhh
Q psy2643 80 YKPFSCGLCDKA 91 (134)
Q Consensus 80 ~~~~~C~~C~~~ 91 (134)
.+.-+| .||+.
T Consensus 18 ~kTkkC-~CG~~ 28 (68)
T PF09082_consen 18 AKTKKC-VCGKT 28 (68)
T ss_dssp -SEEEE-TTTEE
T ss_pred cceeEe-cCCCe
Confidence 344566 66654
No 276
>KOG0562|consensus
Probab=22.72 E-value=58 Score=20.40 Aligned_cols=29 Identities=14% Similarity=0.170 Sum_probs=22.6
Q ss_pred CCCcccCcchhhccChHHHHHHHHhhCCC
Q psy2643 80 YKPFSCGLCDKAFQRKVDLRRHRESQHPG 108 (134)
Q Consensus 80 ~~~~~C~~C~~~f~~~~~l~~H~~~~h~~ 108 (134)
+....|-.|+..-...+.|+.|.+.++.+
T Consensus 151 k~dLrC~~Cq~~~~~~~kLK~Hl~~~~~q 179 (184)
T KOG0562|consen 151 KEDLRCWRCQTFGPHFPKLKAHLREEYDQ 179 (184)
T ss_pred ccceeehhhhhcccccHHHHHHHHHHHhh
Confidence 34688999996666788999999887654
No 277
>KOG2932|consensus
Probab=22.70 E-value=1.6e+02 Score=20.70 Aligned_cols=31 Identities=23% Similarity=0.386 Sum_probs=25.0
Q ss_pred cCCCCCcccCc---chhhccChHHHHHHHHhhCC
Q psy2643 77 HTGYKPFSCGL---CDKAFQRKVDLRRHRESQHP 107 (134)
Q Consensus 77 ~~~~~~~~C~~---C~~~f~~~~~l~~H~~~~h~ 107 (134)
-..+..|.|.. |.++|.+..+|+.|+.-.|.
T Consensus 139 ~~~g~iFmC~~~~GC~RTyLsqrDlqAHInhrH~ 172 (389)
T KOG2932|consen 139 IMMGGIFMCAAPHGCLRTYLSQRDLQAHINHRHG 172 (389)
T ss_pred hcccceEEeecchhHHHHHhhHHHHHHHhhhhhc
Confidence 35566788843 99999999999999977776
No 278
>COG1439 Predicted nucleic acid-binding protein, consists of a PIN domain and a Zn-ribbon module [General function prediction only]
Probab=22.68 E-value=41 Score=21.22 Aligned_cols=24 Identities=21% Similarity=0.621 Sum_probs=16.5
Q ss_pred ceeccccccccCChhHHHHHHHHcCCCCCcccCcchhh
Q psy2643 54 PHKCVVCGKAFSQSSNLITHLRKHTGYKPFSCGLCDKA 91 (134)
Q Consensus 54 ~~~C~~C~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~ 91 (134)
.+.|..|.+.|..+ .-.|+.||-.
T Consensus 139 ~~rC~GC~~~f~~~--------------~~~Cp~CG~~ 162 (177)
T COG1439 139 RLRCHGCKRIFPEP--------------KDFCPICGSP 162 (177)
T ss_pred eEEEecCceecCCC--------------CCcCCCCCCc
Confidence 36788899888721 1268889843
No 279
>PF04216 FdhE: Protein involved in formate dehydrogenase formation; InterPro: IPR006452 This family of sequences describe an accessory protein required for the assembly of formate dehydrogenase of certain proteobacteria although not present in the final complex []. The exact nature of the function of FdhE in the assembly of the complex is unknown, but considering the presence of selenocysteine, molybdopterin, iron-sulphur clusters and cytochrome b556, it is likely to be involved in the insertion of cofactors. ; GO: 0005737 cytoplasm; PDB: 2FIY_B.
Probab=22.59 E-value=17 Score=24.66 Aligned_cols=53 Identities=21% Similarity=0.516 Sum_probs=20.8
Q ss_pred CCCCccCcccccccCChhhHHHHHHhhcCCCceeccccccccCChhHHHHHHHHcCCCCCcccCcchh
Q psy2643 23 DTRPYPCQYCGKRFHQKSDMKKHTYIHTGEKPHKCVVCGKAFSQSSNLITHLRKHTGYKPFSCGLCDK 90 (134)
Q Consensus 23 ~~~~~~c~~C~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~ 90 (134)
|.+...|+.|+..+.. ....|..||..-...-... ......+.+.+.|..|+.
T Consensus 194 G~R~L~Cs~C~t~W~~--------------~R~~Cp~Cg~~~~~~l~~~-~~e~~~~~rve~C~~C~~ 246 (290)
T PF04216_consen 194 GKRYLHCSLCGTEWRF--------------VRIKCPYCGNTDHEKLEYF-TVEGEPAYRVEVCESCGS 246 (290)
T ss_dssp -EEEEEETTT--EEE----------------TTS-TTT---SS-EEE---------SEEEEEETTTTE
T ss_pred ccEEEEcCCCCCeeee--------------cCCCCcCCCCCCCcceeeE-ecCCCCcEEEEECCcccc
Confidence 4455667777654332 1346888887633322211 012223455678888873
No 280
>PF13821 DUF4187: Domain of unknown function (DUF4187)
Probab=22.54 E-value=43 Score=16.58 Aligned_cols=17 Identities=24% Similarity=0.511 Sum_probs=8.5
Q ss_pred cccCcchhhccChHHHH
Q psy2643 83 FSCGLCDKAFQRKVDLR 99 (134)
Q Consensus 83 ~~C~~C~~~f~~~~~l~ 99 (134)
+-|-.||..|.+...|.
T Consensus 28 ~YC~~Cg~~Y~d~~dL~ 44 (55)
T PF13821_consen 28 NYCFWCGTKYDDEEDLE 44 (55)
T ss_pred ceeeeeCCccCCHHHHH
Confidence 44555555555554443
No 281
>PF14375 Cys_rich_CWC: Cysteine-rich CWC
Probab=22.31 E-value=49 Score=15.86 Aligned_cols=10 Identities=40% Similarity=1.205 Sum_probs=5.0
Q ss_pred CCcCccccCC
Q psy2643 1 CKQCGKTFKR 10 (134)
Q Consensus 1 C~~C~~~f~~ 10 (134)
|+.||..|.-
T Consensus 1 CP~Cg~~f~C 10 (50)
T PF14375_consen 1 CPRCGAPFEC 10 (50)
T ss_pred CCCCCCcCCC
Confidence 4555555543
No 282
>KOG3352|consensus
Probab=22.24 E-value=40 Score=20.65 Aligned_cols=15 Identities=20% Similarity=0.423 Sum_probs=11.5
Q ss_pred CCCCcccCcchhhcc
Q psy2643 79 GYKPFSCGLCDKAFQ 93 (134)
Q Consensus 79 ~~~~~~C~~C~~~f~ 93 (134)
..+..+|+.||.-|.
T Consensus 130 Kge~~rc~eCG~~fk 144 (153)
T KOG3352|consen 130 KGETQRCPECGHYFK 144 (153)
T ss_pred cCCcccCCcccceEE
Confidence 345688999998775
No 283
>PRK05978 hypothetical protein; Provisional
Probab=21.87 E-value=34 Score=20.90 Aligned_cols=12 Identities=33% Similarity=1.132 Sum_probs=8.1
Q ss_pred eccccccccCCh
Q psy2643 56 KCVVCGKAFSQS 67 (134)
Q Consensus 56 ~C~~C~~~~~~~ 67 (134)
.|..||..|...
T Consensus 54 ~C~~CG~~~~~~ 65 (148)
T PRK05978 54 HCAACGEDFTHH 65 (148)
T ss_pred CccccCCccccC
Confidence 577888766553
No 284
>PF14690 zf-ISL3: zinc-finger of transposase IS204/IS1001/IS1096/IS1165
Probab=21.87 E-value=44 Score=15.40 Aligned_cols=9 Identities=33% Similarity=0.862 Sum_probs=6.8
Q ss_pred CcccCcchh
Q psy2643 82 PFSCGLCDK 90 (134)
Q Consensus 82 ~~~C~~C~~ 90 (134)
+..|+.||.
T Consensus 2 ~~~Cp~Cg~ 10 (47)
T PF14690_consen 2 PPRCPHCGS 10 (47)
T ss_pred CccCCCcCC
Confidence 567899984
No 285
>COG3478 Predicted nucleic-acid-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=21.70 E-value=46 Score=17.17 Aligned_cols=9 Identities=33% Similarity=1.021 Sum_probs=6.2
Q ss_pred CcccCcchh
Q psy2643 82 PFSCGLCDK 90 (134)
Q Consensus 82 ~~~C~~C~~ 90 (134)
.++|+.||-
T Consensus 4 ~~kCpKCgn 12 (68)
T COG3478 4 AFKCPKCGN 12 (68)
T ss_pred cccCCCcCC
Confidence 456888874
No 286
>PF04328 DUF466: Protein of unknown function (DUF466); InterPro: IPR007423 This is a small bacterial protein of unknown function.
Probab=21.55 E-value=96 Score=15.96 Aligned_cols=17 Identities=24% Similarity=0.487 Sum_probs=12.4
Q ss_pred HHHHHHHhhCCCCCCcc
Q psy2643 97 DLRRHRESQHPGSPAQQ 113 (134)
Q Consensus 97 ~l~~H~~~~h~~~~~~~ 113 (134)
.+-.|++.+|++.++.+
T Consensus 27 ~Yv~H~~~~HP~~p~ms 43 (65)
T PF04328_consen 27 RYVEHMRRHHPDEPPMS 43 (65)
T ss_pred HHHHHHHHHCcCCCCCC
Confidence 34578899998887643
No 287
>TIGR03831 YgiT_finger YgiT-type zinc finger domain. This domain model describes a small domain with two copies of a putative zinc-binding motif CXXC (usually CXXCG). Most member proteins consist largely of this domain or else carry an additional C-terminal helix-turn-helix domain, resembling that of the phage protein Cro and modeled by pfam01381.
Probab=21.42 E-value=39 Score=15.35 Aligned_cols=10 Identities=30% Similarity=0.966 Sum_probs=5.7
Q ss_pred eecccccccc
Q psy2643 55 HKCVVCGKAF 64 (134)
Q Consensus 55 ~~C~~C~~~~ 64 (134)
+.|+.||..+
T Consensus 33 ~~C~~CGE~~ 42 (46)
T TIGR03831 33 LVCPQCGEEY 42 (46)
T ss_pred cccccCCCEe
Confidence 4566666554
No 288
>KOG4124|consensus
Probab=21.24 E-value=28 Score=24.54 Aligned_cols=33 Identities=18% Similarity=0.104 Sum_probs=24.4
Q ss_pred CCCCCcccCcchhhccChHHHHHHHHhhCCCCCC
Q psy2643 78 TGYKPFSCGLCDKAFQRKVDLRRHRESQHPGSPA 111 (134)
Q Consensus 78 ~~~~~~~C~~C~~~f~~~~~l~~H~~~~h~~~~~ 111 (134)
+..++|+|+ |++++...+.|+.|-.-.+.....
T Consensus 209 t~~~p~k~~-~~~~~~T~~~l~~HS~N~~~~~Sa 241 (442)
T KOG4124|consen 209 TTGTPKKMP-ESLVMDTSSPLSDHSMNIDVGESA 241 (442)
T ss_pred cccCCccCc-ccccccccchhhhccccCCCCccH
Confidence 345689987 999999999998886555554443
No 289
>TIGR00515 accD acetyl-CoA carboxylase, carboxyl transferase, beta subunit. The enzyme acetyl-CoA carboxylase contains a biotin carboxyl carrier protein or domain, a biotin carboxylase, and a carboxyl transferase. This model represents the beta chain of the carboxyl transferase for cases in which the architecture of the protein is as in E. coli, in which the carboxyltransferase portion consists of two non-identical subnits, alpha and beta.
Probab=20.20 E-value=44 Score=22.84 Aligned_cols=32 Identities=19% Similarity=0.539 Sum_probs=19.6
Q ss_pred ccCcccccccCChhhHHHHHHhhcCCCceeccccccccCCh
Q psy2643 27 YPCQYCGKRFHQKSDMKKHTYIHTGEKPHKCVVCGKAFSQS 67 (134)
Q Consensus 27 ~~c~~C~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~~~~~ 67 (134)
..|+.|+.....+. |.. +-+.|+.|+..|.-.
T Consensus 27 ~~c~~c~~~~~~~~-l~~--------~~~vc~~c~~h~rl~ 58 (285)
T TIGR00515 27 TKCPKCGQVLYTKE-LER--------NLEVCPKCDHHMRMD 58 (285)
T ss_pred eECCCCcchhhHHH-HHh--------hCCCCCCCCCcCcCC
Confidence 46888877654432 221 236788888877653
Done!