Query psy11352
Match_columns 107
No_of_seqs 222 out of 1181
Neff 10.7
Searched_HMMs 46136
Date Fri Aug 16 16:12:31 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy11352.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/11352hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2462|consensus 99.9 1.3E-23 2.9E-28 128.0 3.8 77 12-99 187-264 (279)
2 KOG2462|consensus 99.9 2.5E-23 5.4E-28 126.8 2.9 87 7-107 156-243 (279)
3 KOG3623|consensus 99.7 2.5E-18 5.5E-23 116.4 -1.0 84 5-99 887-971 (1007)
4 KOG3576|consensus 99.6 1.9E-17 4.1E-22 97.7 -3.8 82 11-103 116-198 (267)
5 PHA00733 hypothetical protein 99.5 3.7E-15 8E-20 83.8 2.5 93 2-103 30-124 (128)
6 KOG3623|consensus 99.5 9E-16 1.9E-20 104.3 -2.7 84 10-99 238-330 (1007)
7 KOG3576|consensus 99.5 9.5E-15 2.1E-19 86.4 1.1 93 1-104 133-238 (267)
8 PHA02768 hypothetical protein; 99.4 1.1E-13 2.4E-18 65.9 1.8 44 51-95 5-48 (55)
9 KOG1074|consensus 99.3 9E-13 2E-17 91.0 0.4 82 10-103 603-692 (958)
10 KOG3608|consensus 99.2 4.9E-12 1.1E-16 80.4 1.5 83 12-105 263-348 (467)
11 KOG1074|consensus 99.1 2E-11 4.3E-16 84.6 2.2 55 50-104 878-933 (958)
12 KOG3608|consensus 99.1 6.1E-12 1.3E-16 80.0 -2.3 78 12-103 237-316 (467)
13 PF13465 zf-H2C2_2: Zinc-finge 99.0 1.1E-10 2.3E-15 48.0 1.6 25 66-90 1-26 (26)
14 KOG3993|consensus 98.9 1.8E-10 3.9E-15 74.8 -0.9 84 11-105 266-383 (500)
15 PHA00732 hypothetical protein 98.8 4.1E-09 8.9E-14 54.5 2.5 45 51-100 1-46 (79)
16 PHA00733 hypothetical protein 98.8 2.6E-09 5.5E-14 60.2 1.6 59 5-76 66-124 (128)
17 PHA00616 hypothetical protein 98.8 3E-09 6.5E-14 48.5 1.3 33 51-83 1-34 (44)
18 PHA00616 hypothetical protein 98.7 4.4E-09 9.5E-14 47.9 1.1 29 78-107 1-29 (44)
19 PLN03086 PRLI-interacting fact 98.7 8E-09 1.7E-13 70.2 2.6 64 10-89 451-515 (567)
20 PLN03086 PRLI-interacting fact 98.7 1.4E-08 3.1E-13 69.1 3.2 80 11-104 477-566 (567)
21 PHA02768 hypothetical protein; 98.6 3.4E-09 7.4E-14 50.6 -1.9 44 12-68 5-48 (55)
22 PF05605 zf-Di19: Drought indu 98.5 1.7E-07 3.7E-12 45.1 3.8 49 51-102 2-53 (54)
23 PF00096 zf-C2H2: Zinc finger, 98.4 1.7E-07 3.8E-12 37.1 2.0 21 79-99 1-21 (23)
24 PF13894 zf-C2H2_4: C2H2-type 98.3 3.2E-07 7E-12 36.5 1.8 24 79-102 1-24 (24)
25 PF00096 zf-C2H2: Zinc finger, 98.3 2.1E-07 4.5E-12 36.9 0.9 23 52-74 1-23 (23)
26 PF13912 zf-C2H2_6: C2H2-type 98.3 4.4E-07 9.5E-12 37.4 1.4 23 78-100 1-23 (27)
27 PHA00732 hypothetical protein 98.2 3.9E-07 8.4E-12 47.2 0.3 48 12-76 1-49 (79)
28 PF13912 zf-C2H2_6: C2H2-type 98.1 2.7E-06 5.8E-11 35.0 1.8 25 51-75 1-25 (27)
29 KOG3993|consensus 98.1 2.1E-06 4.6E-11 56.4 1.9 59 11-75 294-380 (500)
30 PF13894 zf-C2H2_4: C2H2-type 98.0 6E-06 1.3E-10 32.6 2.4 23 52-74 1-23 (24)
31 PF13465 zf-H2C2_2: Zinc-finge 98.0 9.8E-08 2.1E-12 39.1 -3.3 20 38-62 6-25 (26)
32 COG5189 SFP1 Putative transcri 97.8 5E-06 1.1E-10 53.0 0.6 51 49-99 347-419 (423)
33 PF09237 GAGA: GAGA factor; I 97.8 4.6E-05 9.9E-10 35.7 3.1 29 50-78 23-52 (54)
34 PF12756 zf-C2H2_2: C2H2 type 97.7 2.3E-05 5E-10 41.9 2.1 72 14-100 1-72 (100)
35 smart00355 ZnF_C2H2 zinc finge 97.7 4.1E-05 8.9E-10 30.6 2.3 21 79-99 1-21 (26)
36 COG5189 SFP1 Putative transcri 97.7 1.4E-05 3E-10 51.1 1.2 59 10-71 347-418 (423)
37 smart00355 ZnF_C2H2 zinc finge 97.7 3.2E-05 7E-10 30.9 1.9 24 52-75 1-24 (26)
38 PRK04860 hypothetical protein; 97.7 2.6E-05 5.7E-10 45.6 2.1 38 50-91 118-156 (160)
39 PF09237 GAGA: GAGA factor; I 97.6 3.4E-05 7.5E-10 36.1 1.3 27 77-103 23-49 (54)
40 PF13909 zf-H2C2_5: C2H2-type 97.5 5.4E-05 1.2E-09 30.1 1.2 23 79-102 1-23 (24)
41 PF05605 zf-Di19: Drought indu 97.5 2E-05 4.3E-10 37.9 -0.5 52 12-75 2-53 (54)
42 PF12874 zf-met: Zinc-finger o 97.4 0.00015 3.3E-09 29.0 1.7 20 53-72 2-21 (25)
43 PF12874 zf-met: Zinc-finger o 97.3 0.00016 3.5E-09 28.9 1.2 22 79-100 1-22 (25)
44 PF12171 zf-C2H2_jaz: Zinc-fin 97.2 0.00016 3.5E-09 29.6 1.0 22 79-100 2-23 (27)
45 PF13909 zf-H2C2_5: C2H2-type 96.8 0.0012 2.6E-08 26.0 2.0 23 52-75 1-23 (24)
46 PF12171 zf-C2H2_jaz: Zinc-fin 96.8 0.00045 9.8E-09 28.2 0.4 22 52-73 2-23 (27)
47 PF13913 zf-C2HC_2: zinc-finge 96.6 0.0024 5.2E-08 25.6 1.9 19 80-99 4-22 (25)
48 smart00451 ZnF_U1 U1-like zinc 96.4 0.0032 7E-08 27.1 1.9 22 78-99 3-24 (35)
49 smart00451 ZnF_U1 U1-like zinc 95.8 0.0085 1.8E-07 25.7 1.9 22 51-72 3-24 (35)
50 PRK04860 hypothetical protein; 95.6 0.0021 4.5E-08 37.7 -0.7 40 10-64 117-156 (160)
51 cd00350 rubredoxin_like Rubred 95.6 0.012 2.7E-07 25.1 1.8 24 52-86 2-25 (33)
52 KOG2186|consensus 95.1 0.017 3.7E-07 36.2 2.0 25 51-76 29-53 (276)
53 COG2888 Predicted Zn-ribbon RN 94.7 0.05 1.1E-06 26.4 2.6 33 50-86 26-58 (61)
54 KOG1146|consensus 94.6 0.023 5.1E-07 43.0 1.9 51 50-100 464-540 (1406)
55 PF12756 zf-C2H2_2: C2H2 type 94.6 0.041 8.9E-07 29.1 2.5 25 51-75 50-74 (100)
56 KOG2893|consensus 94.6 0.0071 1.5E-07 37.6 -0.6 41 54-97 13-53 (341)
57 COG4049 Uncharacterized protei 94.0 0.037 8.1E-07 26.5 1.4 25 50-74 16-40 (65)
58 PF09538 FYDLN_acid: Protein o 94.0 0.066 1.4E-06 29.5 2.5 31 51-91 9-39 (108)
59 cd00729 rubredoxin_SM Rubredox 94.0 0.064 1.4E-06 23.1 2.0 25 51-86 2-26 (34)
60 KOG4173|consensus 93.8 0.011 2.4E-07 35.9 -0.8 80 10-103 77-171 (253)
61 PRK00464 nrdR transcriptional 93.7 0.058 1.3E-06 31.6 2.0 17 51-67 28-44 (154)
62 PF09986 DUF2225: Uncharacteri 93.2 0.028 6E-07 34.7 0.2 13 79-91 49-61 (214)
63 COG5048 FOG: Zn-finger [Genera 93.2 0.025 5.3E-07 37.5 -0.1 53 51-104 289-348 (467)
64 COG5048 FOG: Zn-finger [Genera 93.0 0.11 2.3E-06 34.5 2.7 64 11-83 288-356 (467)
65 COG5236 Uncharacterized conser 92.0 0.21 4.6E-06 33.0 3.0 92 2-99 170-272 (493)
66 TIGR02605 CxxC_CxxC_SSSS putat 91.9 0.078 1.7E-06 24.9 0.8 12 52-63 6-17 (52)
67 smart00614 ZnF_BED BED zinc fi 91.8 0.18 3.8E-06 23.6 1.9 8 92-99 37-44 (50)
68 TIGR02098 MJ0042_CXXC MJ0042 f 91.7 0.19 4.1E-06 21.9 1.9 33 52-88 3-35 (38)
69 smart00834 CxxC_CXXC_SSSS Puta 91.7 0.09 1.9E-06 23.3 0.8 30 51-86 5-34 (41)
70 smart00659 RPOLCX RNA polymera 91.5 0.2 4.4E-06 22.9 1.9 27 51-87 2-28 (44)
71 PHA00626 hypothetical protein 91.5 0.22 4.7E-06 23.9 2.0 14 50-63 22-35 (59)
72 TIGR00622 ssl1 transcription f 91.5 0.23 4.9E-06 27.5 2.4 85 11-100 14-103 (112)
73 PF13719 zinc_ribbon_5: zinc-r 91.3 0.14 3.1E-06 22.4 1.3 10 52-61 26-35 (37)
74 COG1592 Rubrerythrin [Energy p 90.7 0.22 4.7E-06 29.6 2.0 25 50-86 133-157 (166)
75 PRK00398 rpoP DNA-directed RNA 90.4 0.18 4E-06 23.1 1.2 11 51-61 3-13 (46)
76 smart00531 TFIIE Transcription 90.1 0.38 8.2E-06 27.9 2.6 37 50-89 98-134 (147)
77 PF13717 zinc_ribbon_4: zinc-r 90.1 0.28 6.1E-06 21.3 1.6 13 53-65 4-16 (36)
78 TIGR00373 conserved hypothetic 89.7 0.4 8.7E-06 28.2 2.5 32 49-88 107-138 (158)
79 PF02892 zf-BED: BED zinc fing 89.5 0.25 5.5E-06 22.3 1.3 22 78-99 16-41 (45)
80 PRK06266 transcription initiat 89.5 0.41 8.8E-06 28.8 2.5 32 50-89 116-147 (178)
81 PF09723 Zn-ribbon_8: Zinc rib 89.4 0.14 3E-06 23.1 0.3 12 13-27 6-17 (42)
82 TIGR02300 FYDLN_acid conserved 89.2 0.28 6.1E-06 27.7 1.5 30 52-91 10-39 (129)
83 PRK14890 putative Zn-ribbon RN 89.2 0.62 1.3E-05 22.7 2.5 32 50-86 24-56 (59)
84 smart00734 ZnF_Rad18 Rad18-lik 89.1 0.55 1.2E-05 18.8 2.0 19 80-99 3-21 (26)
85 smart00440 ZnF_C2C2 C2C2 Zinc 89.1 0.27 5.8E-06 21.9 1.2 13 50-62 27-39 (40)
86 PF03604 DNA_RNApol_7kD: DNA d 89.1 0.31 6.6E-06 20.7 1.3 11 77-87 16-26 (32)
87 PF04959 ARS2: Arsenite-resist 88.2 0.29 6.3E-06 30.3 1.3 26 78-103 77-102 (214)
88 COG1997 RPL43A Ribosomal prote 87.7 0.52 1.1E-05 24.8 1.8 11 78-88 53-63 (89)
89 KOG1146|consensus 87.5 0.33 7.2E-06 37.3 1.4 59 8-72 461-539 (1406)
90 COG1996 RPC10 DNA-directed RNA 86.8 0.48 1E-05 22.2 1.3 29 50-87 5-33 (49)
91 PF05290 Baculo_IE-1: Baculovi 86.3 0.7 1.5E-05 26.4 2.0 13 80-92 123-135 (140)
92 PF01096 TFIIS_C: Transcriptio 86.2 0.2 4.2E-06 22.2 -0.2 12 50-61 27-38 (39)
93 COG3357 Predicted transcriptio 86.2 0.32 6.9E-06 25.8 0.6 27 50-85 57-83 (97)
94 PF12013 DUF3505: Protein of u 85.8 0.73 1.6E-05 25.2 1.9 24 79-102 81-108 (109)
95 TIGR01206 lysW lysine biosynth 85.7 1.2 2.5E-05 21.4 2.3 13 50-62 21-33 (54)
96 KOG2186|consensus 85.3 0.29 6.3E-06 30.9 0.2 48 50-99 2-49 (276)
97 PF01927 Mut7-C: Mut7-C RNAse 84.8 1.9 4.1E-05 25.0 3.4 18 78-95 124-141 (147)
98 PF10571 UPF0547: Uncharacteri 84.1 0.65 1.4E-05 18.7 0.9 10 80-89 16-25 (26)
99 PRK09678 DNA-binding transcrip 83.4 0.73 1.6E-05 23.5 1.1 18 50-67 26-45 (72)
100 KOG4167|consensus 83.2 0.88 1.9E-05 33.2 1.8 26 50-75 791-816 (907)
101 PF14353 CpXC: CpXC protein 83.2 0.38 8.2E-06 27.1 0.1 55 13-70 2-57 (128)
102 PF05443 ROS_MUCR: ROS/MUCR tr 82.9 0.86 1.9E-05 26.1 1.4 24 50-76 71-94 (132)
103 PF12013 DUF3505: Protein of u 82.8 1.4 3E-05 24.1 2.2 27 50-76 79-109 (109)
104 cd00730 rubredoxin Rubredoxin; 82.3 2 4.4E-05 20.2 2.3 6 13-18 2-7 (50)
105 TIGR00244 transcriptional regu 81.5 1.2 2.6E-05 25.9 1.7 18 50-67 27-44 (147)
106 PF08790 zf-LYAR: LYAR-type C2 81.3 0.75 1.6E-05 18.9 0.6 19 52-71 1-19 (28)
107 PF07754 DUF1610: Domain of un 81.1 1.6 3.4E-05 17.3 1.5 10 50-59 15-24 (24)
108 COG3677 Transposase and inacti 80.9 1.3 2.8E-05 25.2 1.7 15 50-64 52-66 (129)
109 COG1327 Predicted transcriptio 80.8 1.3 2.9E-05 25.8 1.7 16 50-65 27-42 (156)
110 PF12907 zf-met2: Zinc-binding 79.0 1.4 3.1E-05 19.7 1.2 27 79-105 2-31 (40)
111 PF04959 ARS2: Arsenite-resist 77.8 2.4 5.1E-05 26.4 2.2 24 50-73 76-99 (214)
112 PF02176 zf-TRAF: TRAF-type zi 77.5 2.1 4.5E-05 20.4 1.6 40 50-90 8-54 (60)
113 PRK03824 hypA hydrogenase nick 76.9 1.5 3.4E-05 25.1 1.2 15 50-64 69-83 (135)
114 PF13451 zf-trcl: Probable zin 76.6 1.7 3.7E-05 20.4 1.1 35 50-85 3-40 (49)
115 COG4888 Uncharacterized Zn rib 76.0 1.5 3.2E-05 23.8 0.9 9 10-18 20-28 (104)
116 COG0068 HypF Hydrogenase matur 75.9 1.4 3E-05 32.1 1.0 57 14-87 125-182 (750)
117 KOG2893|consensus 75.7 0.5 1.1E-05 29.7 -1.1 50 10-75 9-59 (341)
118 KOG2785|consensus 75.6 3.8 8.2E-05 27.6 2.8 51 50-100 165-242 (390)
119 KOG2907|consensus 75.6 2.3 4.9E-05 23.6 1.5 12 78-89 102-113 (116)
120 PF15269 zf-C2H2_7: Zinc-finge 74.9 2.6 5.6E-05 19.3 1.4 21 79-99 21-41 (54)
121 PF08274 PhnA_Zn_Ribbon: PhnA 74.7 1.5 3.3E-05 18.3 0.6 9 77-85 18-26 (30)
122 PHA02998 RNA polymerase subuni 74.7 2 4.4E-05 25.8 1.3 10 79-88 172-181 (195)
123 COG1198 PriA Primosomal protei 74.4 4.8 0.0001 29.7 3.3 11 77-87 474-484 (730)
124 PF12760 Zn_Tnp_IS1595: Transp 74.3 3.5 7.6E-05 18.8 1.9 10 50-59 36-45 (46)
125 COG4530 Uncharacterized protei 73.8 2 4.3E-05 23.7 1.1 27 53-89 11-37 (129)
126 KOG3408|consensus 73.1 2 4.4E-05 24.1 1.0 22 78-99 57-78 (129)
127 smart00154 ZnF_AN1 AN1-like Zi 72.8 2.1 4.5E-05 18.9 0.8 14 78-91 12-25 (39)
128 KOG2482|consensus 72.7 2.3 4.9E-05 28.4 1.3 23 78-100 195-217 (423)
129 PF03811 Zn_Tnp_IS1: InsA N-te 72.6 6.3 0.00014 17.1 2.3 8 50-57 28-35 (36)
130 KOG2593|consensus 72.2 2.8 6E-05 28.7 1.6 14 50-63 127-140 (436)
131 COG1594 RPB9 DNA-directed RNA 72.1 2.7 5.8E-05 23.3 1.4 36 52-89 73-111 (113)
132 COG1198 PriA Primosomal protei 71.9 3.4 7.4E-05 30.4 2.1 11 50-60 474-484 (730)
133 cd00924 Cyt_c_Oxidase_Vb Cytoc 71.8 1.9 4.1E-05 23.3 0.7 18 72-89 73-90 (97)
134 KOG4167|consensus 71.8 0.52 1.1E-05 34.2 -1.8 24 78-101 792-815 (907)
135 PF01155 HypA: Hydrogenase exp 71.5 2.7 5.9E-05 23.2 1.3 27 50-87 69-95 (113)
136 PRK14873 primosome assembly pr 71.3 4.8 0.0001 29.4 2.7 23 50-87 409-431 (665)
137 PF11672 DUF3268: Protein of u 71.2 7.1 0.00015 21.3 2.8 8 11-18 1-8 (102)
138 PLN02294 cytochrome c oxidase 71.1 1.5 3.2E-05 26.2 0.2 21 71-91 134-154 (174)
139 PF00301 Rubredoxin: Rubredoxi 70.8 1.8 3.9E-05 20.1 0.4 12 52-63 2-13 (47)
140 KOG2785|consensus 70.0 4.7 0.0001 27.2 2.3 24 77-100 67-90 (390)
141 PRK05978 hypothetical protein; 69.4 4 8.6E-05 23.9 1.7 10 53-62 54-63 (148)
142 KOG2593|consensus 69.2 2.1 4.6E-05 29.2 0.6 39 8-60 124-162 (436)
143 PF04810 zf-Sec23_Sec24: Sec23 69.0 2.9 6.4E-05 18.5 0.9 11 50-60 23-33 (40)
144 PF13878 zf-C2H2_3: zinc-finge 68.8 5.2 0.00011 17.8 1.7 24 52-75 14-39 (41)
145 TIGR01562 FdhE formate dehydro 68.8 8.3 0.00018 25.4 3.2 8 12-19 184-191 (305)
146 PF07800 DUF1644: Protein of u 68.3 16 0.00035 21.7 4.0 56 50-107 79-137 (162)
147 PF13453 zf-TFIIB: Transcripti 68.2 6 0.00013 17.5 1.8 21 50-70 18-38 (41)
148 KOG1842|consensus 68.0 3 6.5E-05 28.8 1.1 22 51-72 15-36 (505)
149 PRK12380 hydrogenase nickel in 67.7 4.4 9.5E-05 22.5 1.6 26 50-86 69-94 (113)
150 PF01363 FYVE: FYVE zinc finge 66.9 2.5 5.5E-05 20.9 0.5 9 53-61 11-19 (69)
151 cd00065 FYVE FYVE domain; Zinc 66.1 4.9 0.00011 18.9 1.4 10 52-61 19-28 (57)
152 PF01780 Ribosomal_L37ae: Ribo 65.9 1.6 3.6E-05 23.2 -0.3 11 78-88 53-63 (90)
153 TIGR00100 hypA hydrogenase nic 65.8 5.1 0.00011 22.2 1.6 26 50-86 69-94 (115)
154 PF04780 DUF629: Protein of un 65.8 4.9 0.00011 28.0 1.8 28 77-104 56-83 (466)
155 PF01428 zf-AN1: AN1-like Zinc 65.7 2 4.3E-05 19.3 -0.0 15 77-91 12-26 (43)
156 PRK12496 hypothetical protein; 65.0 6.1 0.00013 23.4 1.9 27 51-88 127-153 (164)
157 PF09963 DUF2197: Uncharacteri 64.6 3.3 7.1E-05 20.0 0.6 36 52-87 3-40 (56)
158 COG3364 Zn-ribbon containing p 64.2 4.4 9.6E-05 22.1 1.1 14 51-64 2-15 (112)
159 PTZ00255 60S ribosomal protein 63.1 5.5 0.00012 21.2 1.4 11 78-88 54-64 (90)
160 PRK00564 hypA hydrogenase nick 61.8 6.4 0.00014 22.0 1.5 27 50-86 70-96 (117)
161 PRK03564 formate dehydrogenase 61.6 14 0.00029 24.5 3.2 9 11-19 186-194 (309)
162 COG4957 Predicted transcriptio 60.4 9 0.00019 22.1 1.9 26 50-78 75-101 (148)
163 smart00064 FYVE Protein presen 59.6 9.1 0.0002 18.8 1.8 10 53-62 12-21 (68)
164 PRK03681 hypA hydrogenase nick 58.6 8.2 0.00018 21.4 1.6 27 50-86 69-95 (114)
165 TIGR00686 phnA alkylphosphonat 58.5 5.8 0.00013 21.9 1.0 14 51-64 19-32 (109)
166 smart00661 RPOL9 RNA polymeras 58.2 18 0.00039 16.5 2.6 15 50-64 19-33 (52)
167 TIGR00280 L37a ribosomal prote 57.9 6.1 0.00013 21.1 1.0 11 78-88 53-63 (91)
168 TIGR01384 TFS_arch transcripti 57.2 7.4 0.00016 21.0 1.3 37 51-89 62-101 (104)
169 PF07975 C1_4: TFIIH C1-like d 57.0 4.3 9.2E-05 19.2 0.3 26 50-75 20-45 (51)
170 KOG0717|consensus 56.5 6.4 0.00014 27.4 1.1 22 79-100 293-314 (508)
171 COG3091 SprT Zn-dependent meta 56.2 7.6 0.00016 22.8 1.2 34 50-87 116-149 (156)
172 PF04423 Rad50_zn_hook: Rad50 56.1 4.2 9.1E-05 19.2 0.2 12 80-91 22-33 (54)
173 PRK10220 hypothetical protein; 55.9 8.3 0.00018 21.3 1.3 15 50-64 19-33 (111)
174 PF07503 zf-HYPF: HypF finger; 55.5 1.5 3.4E-05 18.9 -1.3 11 78-88 21-31 (35)
175 KOG2482|consensus 55.5 7.3 0.00016 26.1 1.2 23 51-73 195-217 (423)
176 TIGR01385 TFSII transcription 55.0 10 0.00022 24.9 1.8 10 52-61 287-296 (299)
177 KOG2636|consensus 54.8 9.1 0.0002 26.6 1.6 23 50-72 400-423 (497)
178 PRK14714 DNA polymerase II lar 54.6 24 0.00051 28.1 3.7 28 50-87 691-718 (1337)
179 KOG0978|consensus 54.5 8.5 0.00018 28.3 1.5 46 51-96 643-696 (698)
180 TIGR00595 priA primosomal prot 54.4 12 0.00027 26.3 2.3 9 51-59 240-248 (505)
181 PF13824 zf-Mss51: Zinc-finger 53.2 14 0.0003 17.8 1.7 12 50-61 13-24 (55)
182 PF15135 UPF0515: Uncharacteri 53.1 16 0.00034 23.4 2.3 14 50-63 154-167 (278)
183 COG1773 Rubredoxin [Energy pro 53.0 7.4 0.00016 18.7 0.7 36 50-86 2-44 (55)
184 PRK00432 30S ribosomal protein 52.5 17 0.00037 17.0 1.9 9 52-60 38-46 (50)
185 PF14311 DUF4379: Domain of un 51.5 21 0.00046 16.7 2.3 16 50-65 27-42 (55)
186 PRK03976 rpl37ae 50S ribosomal 51.0 8.7 0.00019 20.5 0.9 11 78-88 54-64 (90)
187 PF09855 DUF2082: Nucleic-acid 50.9 7.6 0.00017 19.3 0.6 6 13-18 1-6 (64)
188 PF07282 OrfB_Zn_ribbon: Putat 50.8 12 0.00025 18.4 1.3 13 77-89 45-57 (69)
189 KOG3507|consensus 50.4 10 0.00022 18.5 1.0 30 50-89 19-48 (62)
190 KOG2071|consensus 50.0 9.3 0.0002 27.4 1.1 24 77-100 417-440 (579)
191 PF09845 DUF2072: Zn-ribbon co 49.7 8.2 0.00018 22.1 0.7 15 51-65 1-15 (131)
192 TIGR00416 sms DNA repair prote 49.6 19 0.00041 25.1 2.5 9 51-59 21-29 (454)
193 PRK05452 anaerobic nitric oxid 49.5 22 0.00047 25.0 2.8 36 50-86 424-466 (479)
194 PRK11823 DNA repair protein Ra 49.3 20 0.00043 24.9 2.6 7 12-18 7-13 (446)
195 PRK04023 DNA polymerase II lar 49.2 40 0.00086 26.3 4.1 10 78-87 663-672 (1121)
196 PF04606 Ogr_Delta: Ogr/Delta- 49.1 4.4 9.5E-05 18.6 -0.4 15 50-64 24-40 (47)
197 PRK05580 primosome assembly pr 48.6 16 0.00035 26.8 2.2 9 51-59 421-429 (679)
198 PF10083 DUF2321: Uncharacteri 48.5 15 0.00032 21.8 1.6 17 50-66 67-83 (158)
199 PF10263 SprT-like: SprT-like 47.8 12 0.00027 21.5 1.3 32 50-88 122-153 (157)
200 COG1571 Predicted DNA-binding 47.7 15 0.00031 25.4 1.7 15 51-65 367-381 (421)
201 TIGR00515 accD acetyl-CoA carb 47.0 20 0.00043 23.4 2.2 32 51-90 26-57 (285)
202 KOG2071|consensus 46.9 15 0.00031 26.5 1.7 27 49-75 416-442 (579)
203 PRK04351 hypothetical protein; 46.3 15 0.00033 21.5 1.5 34 50-90 111-144 (149)
204 PTZ00448 hypothetical protein; 46.1 18 0.00039 24.6 1.9 23 78-100 314-336 (373)
205 CHL00174 accD acetyl-CoA carbo 45.7 22 0.00047 23.4 2.2 34 50-91 37-70 (296)
206 COG1066 Sms Predicted ATP-depe 45.7 19 0.00041 25.1 2.0 6 13-18 8-13 (456)
207 COG1656 Uncharacterized conser 45.5 16 0.00036 21.8 1.5 20 77-96 129-148 (165)
208 PF04780 DUF629: Protein of un 45.3 18 0.00039 25.4 1.9 27 50-76 56-83 (466)
209 PTZ00043 cytochrome c oxidase 44.7 11 0.00024 23.7 0.8 18 73-90 176-193 (268)
210 PRK09710 lar restriction allev 44.5 25 0.00054 17.5 1.8 11 50-60 26-36 (64)
211 KOG3362|consensus 44.4 8.4 0.00018 22.4 0.2 23 78-100 129-151 (156)
212 PF01215 COX5B: Cytochrome c o 44.3 4.8 0.0001 23.2 -0.8 18 73-90 107-124 (136)
213 PF10058 DUF2296: Predicted in 43.9 35 0.00076 16.3 2.3 8 51-58 44-51 (54)
214 PF06397 Desulfoferrod_N: Desu 43.8 9.8 0.00021 16.6 0.3 10 51-60 6-15 (36)
215 smart00731 SprT SprT homologue 43.5 26 0.00057 20.1 2.2 12 51-62 112-123 (146)
216 COG4338 Uncharacterized protei 43.4 10 0.00022 17.7 0.4 12 80-91 14-25 (54)
217 KOG2231|consensus 42.7 27 0.00058 25.8 2.4 21 80-100 184-204 (669)
218 COG1326 Uncharacterized archae 42.2 33 0.00071 21.2 2.5 11 78-88 30-40 (201)
219 PF08209 Sgf11: Sgf11 (transcr 41.5 33 0.00071 14.6 2.7 24 50-74 3-26 (33)
220 PRK14892 putative transcriptio 41.4 41 0.0009 18.3 2.6 12 52-63 43-54 (99)
221 PF06220 zf-U1: U1 zinc finger 41.3 28 0.00062 15.2 1.6 10 79-88 4-13 (38)
222 KOG0782|consensus 41.1 8.9 0.00019 27.7 -0.0 26 66-91 240-266 (1004)
223 COG1675 TFA1 Transcription ini 40.8 32 0.0007 20.8 2.3 30 50-87 112-141 (176)
224 COG4896 Uncharacterized protei 40.6 15 0.00033 18.1 0.7 12 77-88 30-41 (68)
225 PF10537 WAC_Acf1_DNA_bd: ATP- 40.6 59 0.0013 17.8 3.1 38 50-87 2-39 (102)
226 PLN02748 tRNA dimethylallyltra 40.4 21 0.00046 25.1 1.7 24 50-73 417-441 (468)
227 PF05129 Elf1: Transcription e 40.4 6.5 0.00014 20.5 -0.6 12 52-63 47-58 (81)
228 TIGR03830 CxxCG_CxxCG_HTH puta 40.4 17 0.00037 20.1 1.1 21 50-70 30-50 (127)
229 TIGR00143 hypF [NiFe] hydrogen 40.2 11 0.00023 27.9 0.3 59 14-88 92-150 (711)
230 PF07295 DUF1451: Protein of u 39.9 12 0.00026 21.9 0.4 28 50-86 111-138 (146)
231 PRK06260 threonine synthase; V 39.3 24 0.00052 24.0 1.8 15 50-64 18-32 (397)
232 PF14787 zf-CCHC_5: GAG-polypr 39.2 18 0.00038 15.8 0.8 14 53-66 4-17 (36)
233 PF11931 DUF3449: Domain of un 39.1 10 0.00022 23.3 0.0 23 10-34 99-121 (196)
234 COG2331 Uncharacterized protei 38.9 4.1 8.9E-05 21.0 -1.4 13 12-27 12-24 (82)
235 cd01121 Sms Sms (bacterial rad 38.4 18 0.00039 24.5 1.1 10 51-60 14-23 (372)
236 PRK05654 acetyl-CoA carboxylas 38.2 27 0.00059 22.9 1.8 31 51-89 27-57 (292)
237 PF15616 TerY-C: TerY-C metal 38.1 20 0.00044 20.6 1.1 11 77-87 104-114 (131)
238 PRK00762 hypA hydrogenase nick 37.9 21 0.00046 20.1 1.2 32 50-86 69-100 (124)
239 PF10276 zf-CHCC: Zinc-finger 37.7 24 0.00051 15.7 1.1 12 50-61 28-39 (40)
240 TIGR00627 tfb4 transcription f 37.7 36 0.00077 22.2 2.3 26 50-88 254-279 (279)
241 COG5188 PRP9 Splicing factor 3 37.7 22 0.00047 24.1 1.3 22 50-71 373-395 (470)
242 PF01286 XPA_N: XPA protein N- 37.6 29 0.00062 14.9 1.3 13 14-29 5-17 (34)
243 KOG3214|consensus 37.3 19 0.00041 19.6 0.9 13 52-64 48-60 (109)
244 PF07649 C1_3: C1-like domain; 37.1 31 0.00067 13.9 1.4 9 51-59 15-23 (30)
245 PF05180 zf-DNL: DNL zinc fing 36.3 4.1 8.9E-05 20.4 -1.6 34 51-87 4-38 (66)
246 PF05191 ADK_lid: Adenylate ki 36.3 17 0.00037 15.7 0.5 30 52-89 2-32 (36)
247 COG0675 Transposase and inacti 36.1 21 0.00045 23.1 1.1 14 77-90 321-334 (364)
248 TIGR00310 ZPR1_znf ZPR1 zinc f 35.4 9.3 0.0002 23.4 -0.5 12 51-62 30-41 (192)
249 cd02341 ZZ_ZZZ3 Zinc finger, Z 34.6 55 0.0012 15.1 2.2 8 51-58 15-22 (48)
250 PLN03238 probable histone acet 33.5 60 0.0013 21.4 2.8 23 50-72 47-69 (290)
251 KOG3352|consensus 33.4 19 0.00042 21.1 0.6 18 73-90 128-145 (153)
252 PF02591 DUF164: Putative zinc 33.2 45 0.00098 15.7 1.8 31 53-87 24-55 (56)
253 PRK00420 hypothetical protein; 33.0 33 0.00072 19.1 1.4 9 52-60 41-49 (112)
254 PRK08222 hydrogenase 4 subunit 32.6 38 0.00083 20.4 1.8 19 77-95 113-131 (181)
255 smart00132 LIM Zinc-binding do 32.2 35 0.00077 13.9 1.2 9 52-60 28-36 (39)
256 COG4306 Uncharacterized protei 32.0 20 0.00042 20.5 0.4 16 50-65 67-82 (160)
257 COG5151 SSL1 RNA polymerase II 31.8 70 0.0015 21.5 2.9 23 77-99 387-409 (421)
258 PRK07591 threonine synthase; V 31.1 37 0.00081 23.4 1.7 9 52-60 34-42 (421)
259 PF10071 DUF2310: Zn-ribbon-co 31.0 26 0.00057 22.6 0.9 32 50-87 219-250 (258)
260 TIGR00319 desulf_FeS4 desulfof 30.9 35 0.00075 14.2 1.1 12 50-61 6-17 (34)
261 PF10013 DUF2256: Uncharacteri 30.8 48 0.001 15.0 1.5 16 53-68 10-25 (42)
262 COG4391 Uncharacterized protei 30.7 21 0.00045 17.6 0.3 37 50-89 23-59 (62)
263 PF14599 zinc_ribbon_6: Zinc-r 30.6 17 0.00037 17.9 0.1 14 52-65 31-44 (61)
264 cd00974 DSRD Desulforedoxin (D 30.3 37 0.0008 14.2 1.1 12 50-61 3-14 (34)
265 KOG1994|consensus 30.3 24 0.00052 22.4 0.6 21 77-97 238-258 (268)
266 PRK06450 threonine synthase; V 30.1 38 0.00082 22.6 1.6 10 52-61 19-28 (338)
267 PF11023 DUF2614: Protein of u 30.1 45 0.00097 18.7 1.6 31 50-91 68-98 (114)
268 KOG4118|consensus 29.7 27 0.0006 17.4 0.7 28 78-105 38-65 (74)
269 PRK01343 zinc-binding protein; 29.3 37 0.00081 16.5 1.1 10 79-88 10-19 (57)
270 KOG1280|consensus 29.3 67 0.0014 21.8 2.5 37 49-85 77-116 (381)
271 PF14255 Cys_rich_CPXG: Cystei 29.2 29 0.00062 16.5 0.7 9 80-88 2-10 (52)
272 PF11789 zf-Nse: Zinc-finger o 29.2 61 0.0013 15.5 1.8 31 50-83 23-53 (57)
273 TIGR03831 YgiT_finger YgiT-typ 29.2 26 0.00056 15.4 0.5 13 51-63 32-44 (46)
274 COG2995 PqiA Uncharacterized p 28.9 84 0.0018 21.8 2.9 34 10-62 16-49 (418)
275 PRK14138 NAD-dependent deacety 28.3 1E+02 0.0022 19.6 3.2 34 50-86 118-151 (244)
276 KOG4727|consensus 28.3 49 0.0011 20.0 1.6 23 50-72 74-96 (193)
277 PF14690 zf-ISL3: zinc-finger 28.2 33 0.00071 15.2 0.8 10 77-86 1-10 (47)
278 PF05876 Terminase_GpA: Phage 28.2 80 0.0017 22.8 2.9 14 50-63 228-241 (557)
279 PF06524 NOA36: NOA36 protein; 27.9 16 0.00034 23.6 -0.4 20 77-96 208-227 (314)
280 PF14447 Prok-RING_4: Prokaryo 27.9 32 0.00069 16.6 0.7 11 80-90 41-51 (55)
281 COG5112 UFD2 U1-like Zn-finger 27.8 20 0.00044 19.7 0.0 21 79-99 56-76 (126)
282 PF03833 PolC_DP2: DNA polymer 27.6 20 0.00044 27.1 0.0 7 80-86 694-700 (900)
283 PF08792 A2L_zn_ribbon: A2L zi 27.1 32 0.00069 14.6 0.6 10 52-61 22-31 (33)
284 COG4332 Uncharacterized protei 27.0 24 0.00052 21.5 0.2 44 13-63 18-61 (203)
285 PF04032 Rpr2: RNAse P Rpr2/Rp 26.8 31 0.00066 17.6 0.6 9 10-18 44-52 (85)
286 PF03145 Sina: Seven in absent 26.8 62 0.0014 19.6 2.0 53 50-104 13-73 (198)
287 PF02150 RNA_POL_M_15KD: RNA p 26.6 13 0.00029 15.9 -0.7 10 53-62 22-31 (35)
288 TIGR03829 YokU_near_AblA uncha 26.2 46 0.00099 17.8 1.2 22 51-72 35-56 (89)
289 PF09332 Mcm10: Mcm10 replicat 26.1 19 0.00041 24.2 -0.3 14 51-64 252-265 (344)
290 COG1779 C4-type Zn-finger prot 26.1 15 0.00032 22.7 -0.7 11 52-62 44-54 (201)
291 PLN03239 histone acetyltransfe 25.8 47 0.001 22.5 1.4 23 77-99 105-127 (351)
292 COG1998 RPS31 Ribosomal protei 25.3 66 0.0014 15.2 1.5 8 52-59 38-45 (51)
293 PF13901 DUF4206: Domain of un 25.2 1.1E+02 0.0024 18.8 2.9 14 50-63 171-184 (202)
294 PRK12387 formate hydrogenlyase 25.1 52 0.0011 19.7 1.4 18 77-94 113-130 (180)
295 PLN00104 MYST -like histone ac 25.1 68 0.0015 22.6 2.1 23 77-99 197-219 (450)
296 cd01327 KAZAL_PSTI Kazal-type 24.9 41 0.00089 15.1 0.8 16 16-31 11-26 (45)
297 PF06170 DUF983: Protein of un 24.1 41 0.00089 17.7 0.8 12 79-90 9-20 (86)
298 PF02146 SIR2: Sir2 family; I 23.7 1.1E+02 0.0023 18.2 2.6 35 50-87 104-138 (178)
299 PF02891 zf-MIZ: MIZ/SP-RING z 23.7 34 0.00074 15.9 0.4 10 77-86 40-49 (50)
300 PF14446 Prok-RING_1: Prokaryo 23.6 35 0.00076 16.4 0.4 12 79-90 6-17 (54)
301 PF03107 C1_2: C1 domain; Int 23.3 55 0.0012 13.2 1.0 9 79-87 1-9 (30)
302 KOG2807|consensus 23.2 85 0.0018 21.2 2.2 19 78-96 290-308 (378)
303 PF08271 TF_Zn_Ribbon: TFIIB z 23.0 48 0.001 14.6 0.8 10 52-61 20-29 (43)
304 PF14375 Cys_rich_CWC: Cystein 22.6 50 0.0011 15.2 0.8 9 81-89 1-9 (50)
305 cd01410 SIRT7 SIRT7: Eukaryoti 22.4 1.4E+02 0.0029 18.5 2.9 34 50-86 94-128 (206)
306 PTZ00064 histone acetyltransfe 22.2 95 0.002 22.4 2.3 24 77-100 279-302 (552)
307 PRK08270 anaerobic ribonucleos 22.2 65 0.0014 23.9 1.6 10 77-86 638-647 (656)
308 PF14369 zf-RING_3: zinc-finge 21.7 49 0.0011 14.1 0.7 8 81-88 24-31 (35)
309 KOG2857|consensus 21.7 50 0.0011 19.3 0.8 21 12-35 17-37 (157)
310 PF12230 PRP21_like_P: Pre-mRN 21.5 31 0.00067 21.5 0.0 26 50-76 167-192 (229)
311 cd01413 SIR2_Af2 SIR2_Af2: Arc 21.5 1.4E+02 0.0029 18.6 2.8 33 50-86 112-144 (222)
312 PF03966 Trm112p: Trm112p-like 21.0 43 0.00093 16.5 0.4 14 50-63 52-65 (68)
313 COG2879 Uncharacterized small 20.8 1.1E+02 0.0024 15.2 1.8 16 90-105 24-39 (65)
314 PF02748 PyrI_C: Aspartate car 20.7 70 0.0015 15.1 1.1 15 50-64 34-48 (52)
315 COG1439 Predicted nucleic acid 20.7 61 0.0013 19.7 1.1 25 50-87 138-162 (177)
316 PF04328 DUF466: Protein of un 20.4 1E+02 0.0022 15.3 1.7 15 93-107 27-41 (65)
317 PF12773 DZR: Double zinc ribb 20.3 65 0.0014 14.5 1.0 10 78-87 29-38 (50)
318 KOG4477|consensus 20.1 57 0.0012 20.0 0.9 23 50-85 23-45 (228)
319 PF01844 HNH: HNH endonuclease 20.0 19 0.00041 15.9 -0.9 11 54-64 1-11 (47)
320 PRK11032 hypothetical protein; 20.0 41 0.00089 20.0 0.3 28 51-87 124-151 (160)
No 1
>KOG2462|consensus
Probab=99.88 E-value=1.3e-23 Score=128.00 Aligned_cols=77 Identities=27% Similarity=0.379 Sum_probs=40.3
Q ss_pred cccCCCCCCCCCccCCCCCCCCCCCCCCCCCCCCCCCCCeeeCCCCcccccchhhHHHHHhhhCC-CcccCCCCCCcccC
Q psy11352 12 FLISDHCLTSPLSSSIPGSSKTKASGSGTTGGSSNHSKLFATCFVCGKQLSNQYNLRVHMETHQN-AFYACSSCSHVSRS 90 (107)
Q Consensus 12 ~~~C~~C~~~~~~~~~~~~l~~h~~~~~~~~~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~-k~~~C~~C~~~f~~ 90 (107)
+++|.+| ++.|..+..|.-| .++|+|+ +||.|+.|++.|...++|+.|+++|.+ |+|+|..|+|.|+.
T Consensus 187 ~c~C~iC---GKaFSRPWLLQGH---iRTHTGE-----KPF~C~hC~kAFADRSNLRAHmQTHS~~K~~qC~~C~KsFsl 255 (279)
T KOG2462|consen 187 PCECGIC---GKAFSRPWLLQGH---IRTHTGE-----KPFSCPHCGKAFADRSNLRAHMQTHSDVKKHQCPRCGKSFAL 255 (279)
T ss_pred Ccccccc---cccccchHHhhcc---cccccCC-----CCccCCcccchhcchHHHHHHHHhhcCCccccCcchhhHHHH
Confidence 4455555 5555555555555 5555555 555555555555555555555555555 55555555555555
Q ss_pred hHHHHHHHH
Q psy11352 91 RDALRKHVS 99 (107)
Q Consensus 91 ~~~l~~H~~ 99 (107)
.+.|.+|..
T Consensus 256 ~SyLnKH~E 264 (279)
T KOG2462|consen 256 KSYLNKHSE 264 (279)
T ss_pred HHHHHHhhh
Confidence 555555543
No 2
>KOG2462|consensus
Probab=99.87 E-value=2.5e-23 Score=126.85 Aligned_cols=87 Identities=22% Similarity=0.374 Sum_probs=80.3
Q ss_pred CCCcccccCCCCCCCCCccCCCCCCCCCCCCCCCCCCCCCCCCCeeeCCCCcccccchhhHHHHHhhhCC-CcccCCCCC
Q psy11352 7 PSTLHFLISDHCLTSPLSSSIPGSSKTKASGSGTTGGSSNHSKLFATCFVCGKQLSNQYNLRVHMETHQN-AFYACSSCS 85 (107)
Q Consensus 7 ~~~~~~~~C~~C~~~~~~~~~~~~l~~h~~~~~~~~~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~-k~~~C~~C~ 85 (107)
-...+.+.|++| ++.+.+...|+.| .++|+.. ++|.+|||.|...=-|+.|+|+|+| |||.|+.|+
T Consensus 156 ~~s~ka~~C~~C---~K~YvSmpALkMH---irTH~l~-------c~C~iCGKaFSRPWLLQGHiRTHTGEKPF~C~hC~ 222 (279)
T KOG2462|consen 156 LDSKKAFSCKYC---GKVYVSMPALKMH---IRTHTLP-------CECGICGKAFSRPWLLQGHIRTHTGEKPFSCPHCG 222 (279)
T ss_pred ccccccccCCCC---CceeeehHHHhhH---hhccCCC-------cccccccccccchHHhhcccccccCCCCccCCccc
Confidence 344788999999 9999999999999 8888854 9999999999999999999999999 999999999
Q ss_pred CcccChHHHHHHHHccCCCCCC
Q psy11352 86 HVSRSRDALRKHVSYRHPHISP 107 (107)
Q Consensus 86 ~~f~~~~~l~~H~~~~H~~ekp 107 (107)
++|...++|+.||+| |.+.|+
T Consensus 223 kAFADRSNLRAHmQT-HS~~K~ 243 (279)
T KOG2462|consen 223 KAFADRSNLRAHMQT-HSDVKK 243 (279)
T ss_pred chhcchHHHHHHHHh-hcCCcc
Confidence 999999999999998 887764
No 3
>KOG3623|consensus
Probab=99.68 E-value=2.5e-18 Score=116.39 Aligned_cols=84 Identities=15% Similarity=0.292 Sum_probs=78.6
Q ss_pred cCCCCcccccCCCCCCCCCccCCCCCCCCCCCCCCCCCCCCCCCCCeeeCCCCcccccchhhHHHHHhhhCC-CcccCCC
Q psy11352 5 YKPSTLHFLISDHCLTSPLSSSIPGSSKTKASGSGTTGGSSNHSKLFATCFVCGKQLSNQYNLRVHMETHQN-AFYACSS 83 (107)
Q Consensus 5 ~~~~~~~~~~C~~C~~~~~~~~~~~~l~~h~~~~~~~~~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~-k~~~C~~ 83 (107)
++....-.|.|+.| .+.|...++|.+| .-.|+|. +||.|.+|.|.|..+..|..|+|.|.| |||+|+.
T Consensus 887 ~~kte~gmyaCDqC---DK~FqKqSSLaRH---KYEHsGq-----RPyqC~iCkKAFKHKHHLtEHkRLHSGEKPfQCdK 955 (1007)
T KOG3623|consen 887 HAKTEDGMYACDQC---DKAFQKQSSLARH---KYEHSGQ-----RPYQCIICKKAFKHKHHLTEHKRLHSGEKPFQCDK 955 (1007)
T ss_pred cccCccccchHHHH---HHHHHhhHHHHHh---hhhhcCC-----CCcccchhhHhhhhhhhhhhhhhhccCCCcchhhh
Confidence 33444668999999 9999999999999 8899999 999999999999999999999999999 9999999
Q ss_pred CCCcccChHHHHHHHH
Q psy11352 84 CSHVSRSRDALRKHVS 99 (107)
Q Consensus 84 C~~~f~~~~~l~~H~~ 99 (107)
|+|.|+..+...+||.
T Consensus 956 ClKRFSHSGSYSQHMN 971 (1007)
T KOG3623|consen 956 CLKRFSHSGSYSQHMN 971 (1007)
T ss_pred hhhhcccccchHhhhc
Confidence 9999999999999996
No 4
>KOG3576|consensus
Probab=99.59 E-value=1.9e-17 Score=97.69 Aligned_cols=82 Identities=21% Similarity=0.370 Sum_probs=52.9
Q ss_pred ccccCCCCCCCCCccCCCCCCCCCCCCCCCCCCCCCCCCCeeeCCCCcccccchhhHHHHHhhhCC-CcccCCCCCCccc
Q psy11352 11 HFLISDHCLTSPLSSSIPGSSKTKASGSGTTGGSSNHSKLFATCFVCGKQLSNQYNLRVHMETHQN-AFYACSSCSHVSR 89 (107)
Q Consensus 11 ~~~~C~~C~~~~~~~~~~~~l~~h~~~~~~~~~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~-k~~~C~~C~~~f~ 89 (107)
..|.|..| ++.|....-|.+| +.-|... +.+.|..||+.|.....|++|+++|+| +||+|..|+++|.
T Consensus 116 d~ftCrvC---gK~F~lQRmlnrh---~kch~~v-----kr~lct~cgkgfndtfdlkrh~rthtgvrpykc~~c~kaft 184 (267)
T KOG3576|consen 116 DSFTCRVC---GKKFGLQRMLNRH---LKCHSDV-----KRHLCTFCGKGFNDTFDLKRHTRTHTGVRPYKCSLCEKAFT 184 (267)
T ss_pred Ceeeeehh---hhhhhHHHHHHHH---hhhccHH-----HHHHHhhccCcccchhhhhhhhccccCccccchhhhhHHHH
Confidence 34666666 6666666666666 6666655 666666666666666666666666666 6666666666666
Q ss_pred ChHHHHHHHHccCC
Q psy11352 90 SRDALRKHVSYRHP 103 (107)
Q Consensus 90 ~~~~l~~H~~~~H~ 103 (107)
+.-.|..|.+.+|.
T Consensus 185 qrcsleshl~kvhg 198 (267)
T KOG3576|consen 185 QRCSLESHLKKVHG 198 (267)
T ss_pred hhccHHHHHHHHcC
Confidence 66666666665453
No 5
>PHA00733 hypothetical protein
Probab=99.53 E-value=3.7e-15 Score=83.77 Aligned_cols=93 Identities=18% Similarity=0.208 Sum_probs=72.5
Q ss_pred ccccCCCCcccccCCCCCCCCCccCCCCCCCCCCC--CCCCCCCCCCCCCCeeeCCCCcccccchhhHHHHHhhhCCCcc
Q psy11352 2 NFHYKPSTLHFLISDHCLTSPLSSSIPGSSKTKAS--GSGTTGGSSNHSKLFATCFVCGKQLSNQYNLRVHMETHQNAFY 79 (107)
Q Consensus 2 ~~h~~~~~~~~~~C~~C~~~~~~~~~~~~l~~h~~--~~~~~~~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~k~~ 79 (107)
.+|.=+...+++.|..| ...|..+..|..+.. ......+. .+|.|+.|++.|.....|..|++.+. .+|
T Consensus 30 ~~~~~~~~~~~~~~~~~---~~~~~~~~~l~~~~~l~~~~~~~~~-----kPy~C~~Cgk~Fss~s~L~~H~r~h~-~~~ 100 (128)
T PHA00733 30 RYHSLTPEQKRLIRAVV---KTLIYNPQLLDESSYLYKLLTSKAV-----SPYVCPLCLMPFSSSVSLKQHIRYTE-HSK 100 (128)
T ss_pred hhhcCChhhhhHHHHHH---hhhccChhhhcchHHHHhhcccCCC-----CCccCCCCCCcCCCHHHHHHHHhcCC-cCc
Confidence 34555667889999999 888887776665411 01112224 78999999999999999999998763 579
Q ss_pred cCCCCCCcccChHHHHHHHHccCC
Q psy11352 80 ACSSCSHVSRSRDALRKHVSYRHP 103 (107)
Q Consensus 80 ~C~~C~~~f~~~~~l~~H~~~~H~ 103 (107)
.|..|++.|.....|..|+...|.
T Consensus 101 ~C~~CgK~F~~~~sL~~H~~~~h~ 124 (128)
T PHA00733 101 VCPVCGKEFRNTDSTLDHVCKKHN 124 (128)
T ss_pred cCCCCCCccCCHHHHHHHHHHhcC
Confidence 999999999999999999986553
No 6
>KOG3623|consensus
Probab=99.49 E-value=9e-16 Score=104.31 Aligned_cols=84 Identities=14% Similarity=0.234 Sum_probs=72.1
Q ss_pred cccccCCCCCCCCCccCCCCCCCCCCCCCCCCCCC--------CCCCCCeeeCCCCcccccchhhHHHHHhhhCC-Cccc
Q psy11352 10 LHFLISDHCLTSPLSSSIPGSSKTKASGSGTTGGS--------SNHSKLFATCFVCGKQLSNQYNLRVHMETHQN-AFYA 80 (107)
Q Consensus 10 ~~~~~C~~C~~~~~~~~~~~~l~~h~~~~~~~~~~--------~~~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~-k~~~ 80 (107)
+.-|.|..| ..+|..+..|.+| +..|... .....+.|+|.+|||.|..+..|+.|+|+|.| |||.
T Consensus 238 e~nfsC~lC---sytFAyRtQLErh---m~~hkpg~dqa~sltqsa~lRKFKCtECgKAFKfKHHLKEHlRIHSGEKPfe 311 (1007)
T KOG3623|consen 238 EPNFSCMLC---SYTFAYRTQLERH---MQLHKPGGDQAISLTQSALLRKFKCTECGKAFKFKHHLKEHLRIHSGEKPFE 311 (1007)
T ss_pred CCCCcchhh---hhhhhhHHHHHHH---HHhhcCCCcccccccchhhhccccccccchhhhhHHHHHhhheeecCCCCcC
Confidence 456889999 9999999999988 6655432 11224679999999999999999999999999 9999
Q ss_pred CCCCCCcccChHHHHHHHH
Q psy11352 81 CSSCSHVSRSRDALRKHVS 99 (107)
Q Consensus 81 C~~C~~~f~~~~~l~~H~~ 99 (107)
|+.|+|.|+..+.+..||.
T Consensus 312 CpnCkKRFSHSGSySSHmS 330 (1007)
T KOG3623|consen 312 CPNCKKRFSHSGSYSSHMS 330 (1007)
T ss_pred CcccccccccCCccccccc
Confidence 9999999999999988875
No 7
>KOG3576|consensus
Probab=99.48 E-value=9.5e-15 Score=86.41 Aligned_cols=93 Identities=22% Similarity=0.403 Sum_probs=81.8
Q ss_pred CccccCCCC-cccccCCCCCCCCCccCCCCCCCCCCCCCCCCCCCCCCCCCeeeCCCCcccccchhhHHHHHh-hhC---
Q psy11352 1 MNFHYKPST-LHFLISDHCLTSPLSSSIPGSSKTKASGSGTTGGSSNHSKLFATCFVCGKQLSNQYNLRVHME-THQ--- 75 (107)
Q Consensus 1 ~~~h~~~~~-~~~~~C~~C~~~~~~~~~~~~l~~h~~~~~~~~~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~-~h~--- 75 (107)
||.|+|-.. ++.|.|..| ++.|...-.|++| .++|++. +||+|..|++.|...-+|..|.+ +|.
T Consensus 133 lnrh~kch~~vkr~lct~c---gkgfndtfdlkrh---~rthtgv-----rpykc~~c~kaftqrcsleshl~kvhgv~~ 201 (267)
T KOG3576|consen 133 LNRHLKCHSDVKRHLCTFC---GKGFNDTFDLKRH---TRTHTGV-----RPYKCSLCEKAFTQRCSLESHLKKVHGVQH 201 (267)
T ss_pred HHHHhhhccHHHHHHHhhc---cCcccchhhhhhh---hccccCc-----cccchhhhhHHHHhhccHHHHHHHHcCchH
Confidence 467888554 899999999 9999999999999 9999999 99999999999999999999976 342
Q ss_pred -------C-CcccCCCCCCcccChHHHHHHHHccCCC
Q psy11352 76 -------N-AFYACSSCSHVSRSRDALRKHVSYRHPH 104 (107)
Q Consensus 76 -------~-k~~~C~~C~~~f~~~~~l~~H~~~~H~~ 104 (107)
. |-|.|+.||.+-.....+..|++.+|..
T Consensus 202 ~yaykerr~kl~vcedcg~t~~~~e~~~~h~~~~hp~ 238 (267)
T KOG3576|consen 202 QYAYKERRAKLYVCEDCGYTSERPEVYYLHLKLHHPF 238 (267)
T ss_pred HHHHHHhhhheeeecccCCCCCChhHHHHHHHhcCCC
Confidence 2 5799999999988999999999987754
No 8
>PHA02768 hypothetical protein; Provisional
Probab=99.40 E-value=1.1e-13 Score=65.94 Aligned_cols=44 Identities=18% Similarity=0.363 Sum_probs=40.6
Q ss_pred eeeCCCCcccccchhhHHHHHhhhCCCcccCCCCCCcccChHHHH
Q psy11352 51 FATCFVCGKQLSNQYNLRVHMETHQNAFYACSSCSHVSRSRDALR 95 (107)
Q Consensus 51 ~~~C~~C~~~f~~~~~l~~H~~~h~~k~~~C~~C~~~f~~~~~l~ 95 (107)
.|+|+.||+.|.....|..|+++|+ ++|+|..|++.|.+.+.|.
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 4899999999999999999999999 7999999999999887764
No 9
>KOG1074|consensus
Probab=99.26 E-value=9e-13 Score=90.96 Aligned_cols=82 Identities=22% Similarity=0.375 Sum_probs=75.9
Q ss_pred cccccCCCCCCCCCccCCCCCCCCCCCCCCCCCCCCCCCCCeeeCCCCcccccchhhHHHHHhhhCCC-----cccCC--
Q psy11352 10 LHFLISDHCLTSPLSSSIPGSSKTKASGSGTTGGSSNHSKLFATCFVCGKQLSNQYNLRVHMETHQNA-----FYACS-- 82 (107)
Q Consensus 10 ~~~~~C~~C~~~~~~~~~~~~l~~h~~~~~~~~~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~k-----~~~C~-- 82 (107)
..|-.|-.| .+....++.|+.| .+.|+++ +||+|.+||+.|.++.+|+.|+.+|..+ ++.|+
T Consensus 603 TdPNqCiiC---~rVlSC~saLqmH---yrtHtGE-----RPFkCKiCgRAFtTkGNLkaH~~vHka~p~~R~q~ScP~~ 671 (958)
T KOG1074|consen 603 TDPNQCIIC---LRVLSCPSALQMH---YRTHTGE-----RPFKCKICGRAFTTKGNLKAHMSVHKAKPPARVQFSCPST 671 (958)
T ss_pred CCccceeee---eecccchhhhhhh---hhcccCc-----CccccccccchhccccchhhcccccccCccccccccCCch
Confidence 457889999 9999999999999 9999999 9999999999999999999999999852 68899
Q ss_pred -CCCCcccChHHHHHHHHccCC
Q psy11352 83 -SCSHVSRSRDALRKHVSYRHP 103 (107)
Q Consensus 83 -~C~~~f~~~~~l~~H~~~~H~ 103 (107)
+|-+.|...-.|..|+++ |.
T Consensus 672 ~ic~~kftn~V~lpQhIri-H~ 692 (958)
T KOG1074|consen 672 FICQKKFTNAVTLPQHIRI-HL 692 (958)
T ss_pred hhhcccccccccccceEEe-ec
Confidence 999999999999999997 66
No 10
>KOG3608|consensus
Probab=99.20 E-value=4.9e-12 Score=80.44 Aligned_cols=83 Identities=19% Similarity=0.318 Sum_probs=40.0
Q ss_pred cccCCCCCCCCCccCCCCCCCCCCCCCCC-CCCCCCCCCCeeeCCCCcccccchhhHHHHHhhhCCCcccCCC--CCCcc
Q psy11352 12 FLISDHCLTSPLSSSIPGSSKTKASGSGT-TGGSSNHSKLFATCFVCGKQLSNQYNLRVHMETHQNAFYACSS--CSHVS 88 (107)
Q Consensus 12 ~~~C~~C~~~~~~~~~~~~l~~h~~~~~~-~~~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~k~~~C~~--C~~~f 88 (107)
-|+|+-| .+.....++|..| ++. |..+ ++|+|+.|++.|.+.+.|.+|..+|....|+|+. |...|
T Consensus 263 ~ykCplC---dmtc~~~ssL~~H---~r~rHs~d-----kpfKCd~Cd~~c~~esdL~kH~~~HS~~~y~C~h~~C~~s~ 331 (467)
T KOG3608|consen 263 CYKCPLC---DMTCSSASSLTTH---IRYRHSKD-----KPFKCDECDTRCVRESDLAKHVQVHSKTVYQCEHPDCHYSV 331 (467)
T ss_pred ccccccc---ccCCCChHHHHHH---HHhhhccC-----CCccccchhhhhccHHHHHHHHHhccccceecCCCCCcHHH
Confidence 3455555 5555555555544 322 2333 4555555555555555555555555443444544 44444
Q ss_pred cChHHHHHHHHccCCCC
Q psy11352 89 RSRDALRKHVSYRHPHI 105 (107)
Q Consensus 89 ~~~~~l~~H~~~~H~~e 105 (107)
.+...+.+|++.+|.|.
T Consensus 332 r~~~q~~~H~~evhEg~ 348 (467)
T KOG3608|consen 332 RTYTQMRRHFLEVHEGN 348 (467)
T ss_pred HHHHHHHHHHHHhccCC
Confidence 44445555555444443
No 11
>KOG1074|consensus
Probab=99.14 E-value=2e-11 Score=84.55 Aligned_cols=55 Identities=31% Similarity=0.518 Sum_probs=50.8
Q ss_pred CeeeCCCCcccccchhhHHHHHhhhCC-CcccCCCCCCcccChHHHHHHHHccCCC
Q psy11352 50 LFATCFVCGKQLSNQYNLRVHMETHQN-AFYACSSCSHVSRSRDALRKHVSYRHPH 104 (107)
Q Consensus 50 ~~~~C~~C~~~f~~~~~l~~H~~~h~~-k~~~C~~C~~~f~~~~~l~~H~~~~H~~ 104 (107)
..+.|.+||+.|.....|..|+++|++ |||.|..|++.|....+|+.||.+|+..
T Consensus 878 n~h~C~vCgk~FsSSsALqiH~rTHtg~KPF~C~fC~~aFttrgnLKvHMgtH~w~ 933 (958)
T KOG1074|consen 878 NAHVCNVCGKQFSSSAALEIHMRTHTGPKPFFCHFCEEAFTTRGNLKVHMGTHMWV 933 (958)
T ss_pred chhhhccchhcccchHHHHHhhhcCCCCCCccchhhhhhhhhhhhhhhhhcccccc
Confidence 347899999999999999999999999 9999999999999999999999985543
No 12
>KOG3608|consensus
Probab=99.07 E-value=6.1e-12 Score=80.02 Aligned_cols=78 Identities=19% Similarity=0.289 Sum_probs=54.8
Q ss_pred cccCCCCCCCCCccCCCCCCCCCCCCCCCCCCCCCCCCCeeeCCCCcccccchhhHHHHHhh-hCC-CcccCCCCCCccc
Q psy11352 12 FLISDHCLTSPLSSSIPGSSKTKASGSGTTGGSSNHSKLFATCFVCGKQLSNQYNLRVHMET-HQN-AFYACSSCSHVSR 89 (107)
Q Consensus 12 ~~~C~~C~~~~~~~~~~~~l~~h~~~~~~~~~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~-h~~-k~~~C~~C~~~f~ 89 (107)
+|.|..| .+.|.+...|..| +..|. ..|+|+.|+.+....++|..|++. |.. +||+|+.|.+.|.
T Consensus 237 ~fqC~~C---~KrFaTeklL~~H---v~rHv-------n~ykCplCdmtc~~~ssL~~H~r~rHs~dkpfKCd~Cd~~c~ 303 (467)
T KOG3608|consen 237 SFQCAQC---FKRFATEKLLKSH---VVRHV-------NCYKCPLCDMTCSSASSLTTHIRYRHSKDKPFKCDECDTRCV 303 (467)
T ss_pred chHHHHH---HHHHhHHHHHHHH---HHHhh-------hcccccccccCCCChHHHHHHHHhhhccCCCccccchhhhhc
Confidence 4444444 4444444444444 33333 347888888888888888888875 666 8999999999888
Q ss_pred ChHHHHHHHHccCC
Q psy11352 90 SRDALRKHVSYRHP 103 (107)
Q Consensus 90 ~~~~l~~H~~~~H~ 103 (107)
+.+.|.+|..+ |.
T Consensus 304 ~esdL~kH~~~-HS 316 (467)
T KOG3608|consen 304 RESDLAKHVQV-HS 316 (467)
T ss_pred cHHHHHHHHHh-cc
Confidence 88899998885 65
No 13
>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=99.04 E-value=1.1e-10 Score=48.04 Aligned_cols=25 Identities=40% Similarity=0.703 Sum_probs=22.6
Q ss_pred hHHHHHhhhCC-CcccCCCCCCcccC
Q psy11352 66 NLRVHMETHQN-AFYACSSCSHVSRS 90 (107)
Q Consensus 66 ~l~~H~~~h~~-k~~~C~~C~~~f~~ 90 (107)
+|..|+++|++ +||.|+.|++.|.+
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 47899999999 99999999999864
No 14
>KOG3993|consensus
Probab=98.89 E-value=1.8e-10 Score=74.78 Aligned_cols=84 Identities=20% Similarity=0.222 Sum_probs=59.2
Q ss_pred ccccCCCCCCCCCccCCCCCCCCCCCCCCCCCCCCCCCCCeeeCCCCcccccchhhHHHHHhhhC--------C-C----
Q psy11352 11 HFLISDHCLTSPLSSSIPGSSKTKASGSGTTGGSSNHSKLFATCFVCGKQLSNQYNLRVHMETHQ--------N-A---- 77 (107)
Q Consensus 11 ~~~~C~~C~~~~~~~~~~~~l~~h~~~~~~~~~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~h~--------~-k---- 77 (107)
.-|+|.-| -..|...-.|.+| .-...-. ..|.|++|+|+|+-..+|..|.++|. + .
T Consensus 266 GdyiCqLC---K~kYeD~F~LAQH---rC~RIV~-----vEYrCPEC~KVFsCPANLASHRRWHKPR~eaa~a~~~P~k~ 334 (500)
T KOG3993|consen 266 GDYICQLC---KEKYEDAFALAQH---RCPRIVH-----VEYRCPECDKVFSCPANLASHRRWHKPRPEAAKAGSPPPKQ 334 (500)
T ss_pred HHHHHHHH---HHhhhhHHHHhhc---cCCeeEE-----eeecCCcccccccCchhhhhhhcccCCchhhhhcCCCChhh
Confidence 34777777 7777777777777 3333333 45778888888887777877777763 1 1
Q ss_pred ---------------------cccCCCCCCcccChHHHHHHHHccCCCC
Q psy11352 78 ---------------------FYACSSCSHVSRSRDALRKHVSYRHPHI 105 (107)
Q Consensus 78 ---------------------~~~C~~C~~~f~~~~~l~~H~~~~H~~e 105 (107)
-|.|..|++.|.+...|+.|+.+||..+
T Consensus 335 ~~~~rae~~ea~rsg~dss~gi~~C~~C~KkFrRqAYLrKHqlthq~~~ 383 (500)
T KOG3993|consen 335 AVETRAEVQEAERSGDDSSSGIFSCHTCGKKFRRQAYLRKHQLTHQRAP 383 (500)
T ss_pred hhhhhhhhhhccccCCcccCceeecHHhhhhhHHHHHHHHhHHhhhccc
Confidence 2778899999999989999988766543
No 15
>PHA00732 hypothetical protein
Probab=98.80 E-value=4.1e-09 Score=54.50 Aligned_cols=45 Identities=24% Similarity=0.563 Sum_probs=28.0
Q ss_pred eeeCCCCcccccchhhHHHHHhh-hCCCcccCCCCCCcccChHHHHHHHHc
Q psy11352 51 FATCFVCGKQLSNQYNLRVHMET-HQNAFYACSSCSHVSRSRDALRKHVSY 100 (107)
Q Consensus 51 ~~~C~~C~~~f~~~~~l~~H~~~-h~~k~~~C~~C~~~f~~~~~l~~H~~~ 100 (107)
+|.|+.|++.|.....|..|++. |. ++.|+.|++.|. .+..|.++
T Consensus 1 py~C~~Cgk~F~s~s~Lk~H~r~~H~--~~~C~~CgKsF~---~l~~H~~~ 46 (79)
T PHA00732 1 MFKCPICGFTTVTLFALKQHARRNHT--LTKCPVCNKSYR---RLNQHFYS 46 (79)
T ss_pred CccCCCCCCccCCHHHHHHHhhcccC--CCccCCCCCEeC---Chhhhhcc
Confidence 35677777777777777777663 43 346777777766 35556543
No 16
>PHA00733 hypothetical protein
Probab=98.78 E-value=2.6e-09 Score=60.23 Aligned_cols=59 Identities=22% Similarity=0.257 Sum_probs=49.0
Q ss_pred cCCCCcccccCCCCCCCCCccCCCCCCCCCCCCCCCCCCCCCCCCCeeeCCCCcccccchhhHHHHHhhhCC
Q psy11352 5 YKPSTLHFLISDHCLTSPLSSSIPGSSKTKASGSGTTGGSSNHSKLFATCFVCGKQLSNQYNLRVHMETHQN 76 (107)
Q Consensus 5 ~~~~~~~~~~C~~C~~~~~~~~~~~~l~~h~~~~~~~~~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~ 76 (107)
+.....+||.|+.| ++.|.....|..| +..+ . .++.|+.|++.|.....|..|+....+
T Consensus 66 ~~~~~~kPy~C~~C---gk~Fss~s~L~~H---~r~h--~-----~~~~C~~CgK~F~~~~sL~~H~~~~h~ 124 (128)
T PHA00733 66 LTSKAVSPYVCPLC---LMPFSSSVSLKQH---IRYT--E-----HSKVCPVCGKEFRNTDSTLDHVCKKHN 124 (128)
T ss_pred cccCCCCCccCCCC---CCcCCCHHHHHHH---HhcC--C-----cCccCCCCCCccCCHHHHHHHHHHhcC
Confidence 33445789999999 9999999999999 6654 2 458999999999999999999876543
No 17
>PHA00616 hypothetical protein
Probab=98.77 E-value=3e-09 Score=48.50 Aligned_cols=33 Identities=12% Similarity=0.281 Sum_probs=24.0
Q ss_pred eeeCCCCcccccchhhHHHHHhhhCC-CcccCCC
Q psy11352 51 FATCFVCGKQLSNQYNLRVHMETHQN-AFYACSS 83 (107)
Q Consensus 51 ~~~C~~C~~~f~~~~~l~~H~~~h~~-k~~~C~~ 83 (107)
+|.|..||+.|...+.|..|++.|++ +++.|+.
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~~hg~~~~~~~~ 34 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLSVHKQNKLTLEY 34 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHHhcCCCccceeE
Confidence 46777777777777777777777777 7776653
No 18
>PHA00616 hypothetical protein
Probab=98.72 E-value=4.4e-09 Score=47.95 Aligned_cols=29 Identities=17% Similarity=0.432 Sum_probs=25.6
Q ss_pred cccCCCCCCcccChHHHHHHHHccCCCCCC
Q psy11352 78 FYACSSCSHVSRSRDALRKHVSYRHPHISP 107 (107)
Q Consensus 78 ~~~C~~C~~~f~~~~~l~~H~~~~H~~ekp 107 (107)
||+|+.||+.|...++|..|++. |.|++|
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~-~hg~~~ 29 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLS-VHKQNK 29 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHH-hcCCCc
Confidence 68999999999999999999996 667664
No 19
>PLN03086 PRLI-interacting factor K; Provisional
Probab=98.72 E-value=8e-09 Score=70.25 Aligned_cols=64 Identities=14% Similarity=0.290 Sum_probs=37.4
Q ss_pred cccccCCCCCCCCCccCCCCCCCCCCCCCCCCCCCCCCCCCeeeCCCCcccccchhhHHHHHhhhCC-CcccCCCCCCcc
Q psy11352 10 LHFLISDHCLTSPLSSSIPGSSKTKASGSGTTGGSSNHSKLFATCFVCGKQLSNQYNLRVHMETHQN-AFYACSSCSHVS 88 (107)
Q Consensus 10 ~~~~~C~~C~~~~~~~~~~~~l~~h~~~~~~~~~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~-k~~~C~~C~~~f 88 (107)
.+.+.|+.| +..|. ...+..| +..+. +++.|+ ||+.+ ....|..|+.+|.. +++.|+.|++.|
T Consensus 451 ~~H~~C~~C---gk~f~-~s~LekH---~~~~H-------kpv~Cp-Cg~~~-~R~~L~~H~~thCp~Kpi~C~fC~~~v 514 (567)
T PLN03086 451 KNHVHCEKC---GQAFQ-QGEMEKH---MKVFH-------EPLQCP-CGVVL-EKEQMVQHQASTCPLRLITCRFCGDMV 514 (567)
T ss_pred ccCccCCCC---CCccc-hHHHHHH---HHhcC-------CCccCC-CCCCc-chhHHHhhhhccCCCCceeCCCCCCcc
Confidence 445667777 66664 3445666 44432 346666 66544 44566666666666 666666666666
Q ss_pred c
Q psy11352 89 R 89 (107)
Q Consensus 89 ~ 89 (107)
.
T Consensus 515 ~ 515 (567)
T PLN03086 515 Q 515 (567)
T ss_pred c
Confidence 3
No 20
>PLN03086 PRLI-interacting factor K; Provisional
Probab=98.69 E-value=1.4e-08 Score=69.08 Aligned_cols=80 Identities=16% Similarity=0.221 Sum_probs=64.0
Q ss_pred ccccCCCCCCCCCccCCCCCCCCCCCCCCCCCCCCCCCCCeeeCCCCcccccc----------hhhHHHHHhhhCCCccc
Q psy11352 11 HFLISDHCLTSPLSSSIPGSSKTKASGSGTTGGSSNHSKLFATCFVCGKQLSN----------QYNLRVHMETHQNAFYA 80 (107)
Q Consensus 11 ~~~~C~~C~~~~~~~~~~~~l~~h~~~~~~~~~~~~~~~~~~~C~~C~~~f~~----------~~~l~~H~~~h~~k~~~ 80 (107)
+++.|+ | +..+ ....|..| ...+-+. +++.|..|++.+.. ...|..|..+...+++.
T Consensus 477 kpv~Cp-C---g~~~-~R~~L~~H---~~thCp~-----Kpi~C~fC~~~v~~g~~~~d~~d~~s~Lt~HE~~CG~rt~~ 543 (567)
T PLN03086 477 EPLQCP-C---GVVL-EKEQMVQH---QASTCPL-----RLITCRFCGDMVQAGGSAMDVRDRLRGMSEHESICGSRTAP 543 (567)
T ss_pred CCccCC-C---CCCc-chhHHHhh---hhccCCC-----CceeCCCCCCccccCccccchhhhhhhHHHHHHhcCCcceE
Confidence 789999 9 7654 56888889 7778888 99999999998852 34788998886339999
Q ss_pred CCCCCCcccChHHHHHHHHccCCC
Q psy11352 81 CSSCSHVSRSRDALRKHVSYRHPH 104 (107)
Q Consensus 81 C~~C~~~f~~~~~l~~H~~~~H~~ 104 (107)
|..||+.|... .|..|+..+|..
T Consensus 544 C~~Cgk~Vrlr-dm~~H~~~~h~~ 566 (567)
T PLN03086 544 CDSCGRSVMLK-EMDIHQIAVHQK 566 (567)
T ss_pred ccccCCeeeeh-hHHHHHHHhhcC
Confidence 99999988765 578888877753
No 21
>PHA02768 hypothetical protein; Provisional
Probab=98.56 E-value=3.4e-09 Score=50.61 Aligned_cols=44 Identities=9% Similarity=-0.182 Sum_probs=38.8
Q ss_pred cccCCCCCCCCCccCCCCCCCCCCCCCCCCCCCCCCCCCeeeCCCCcccccchhhHH
Q psy11352 12 FLISDHCLTSPLSSSIPGSSKTKASGSGTTGGSSNHSKLFATCFVCGKQLSNQYNLR 68 (107)
Q Consensus 12 ~~~C~~C~~~~~~~~~~~~l~~h~~~~~~~~~~~~~~~~~~~C~~C~~~f~~~~~l~ 68 (107)
-|.|+.| ++.|.....|..| ++.|. ++++|..|++.|...+.|.
T Consensus 5 ~y~C~~C---GK~Fs~~~~L~~H---~r~H~-------k~~kc~~C~k~f~~~s~l~ 48 (55)
T PHA02768 5 GYECPIC---GEIYIKRKSMITH---LRKHN-------TNLKLSNCKRISLRTGEYI 48 (55)
T ss_pred ccCcchh---CCeeccHHHHHHH---HHhcC-------CcccCCcccceecccceeE
Confidence 5899999 9999999999999 98887 3589999999998877654
No 22
>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=98.54 E-value=1.7e-07 Score=45.14 Aligned_cols=49 Identities=33% Similarity=0.539 Sum_probs=38.9
Q ss_pred eeeCCCCcccccchhhHHHHHhh-hCC--CcccCCCCCCcccChHHHHHHHHccC
Q psy11352 51 FATCFVCGKQLSNQYNLRVHMET-HQN--AFYACSSCSHVSRSRDALRKHVSYRH 102 (107)
Q Consensus 51 ~~~C~~C~~~f~~~~~l~~H~~~-h~~--k~~~C~~C~~~f~~~~~l~~H~~~~H 102 (107)
.|.|+.|++. .+...|..|... |.. +.+.|++|...+. .+|..|+...|
T Consensus 2 ~f~CP~C~~~-~~~~~L~~H~~~~H~~~~~~v~CPiC~~~~~--~~l~~Hl~~~H 53 (54)
T PF05605_consen 2 SFTCPYCGKG-FSESSLVEHCEDEHRSESKNVVCPICSSRVT--DNLIRHLNSQH 53 (54)
T ss_pred CcCCCCCCCc-cCHHHHHHHHHhHCcCCCCCccCCCchhhhh--hHHHHHHHHhc
Confidence 4899999994 556789999765 554 6899999998654 48999998766
No 23
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=98.44 E-value=1.7e-07 Score=37.13 Aligned_cols=21 Identities=29% Similarity=0.760 Sum_probs=11.3
Q ss_pred ccCCCCCCcccChHHHHHHHH
Q psy11352 79 YACSSCSHVSRSRDALRKHVS 99 (107)
Q Consensus 79 ~~C~~C~~~f~~~~~l~~H~~ 99 (107)
|.|+.|++.|.....|..|++
T Consensus 1 y~C~~C~~~f~~~~~l~~H~~ 21 (23)
T PF00096_consen 1 YKCPICGKSFSSKSNLKRHMR 21 (23)
T ss_dssp EEETTTTEEESSHHHHHHHHH
T ss_pred CCCCCCCCccCCHHHHHHHHh
Confidence 345555555555555555554
No 24
>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=98.35 E-value=3.2e-07 Score=36.47 Aligned_cols=24 Identities=33% Similarity=0.779 Sum_probs=13.8
Q ss_pred ccCCCCCCcccChHHHHHHHHccC
Q psy11352 79 YACSSCSHVSRSRDALRKHVSYRH 102 (107)
Q Consensus 79 ~~C~~C~~~f~~~~~l~~H~~~~H 102 (107)
|.|+.|++.|.....|..|+.++|
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 456666666666666666666543
No 25
>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=98.32 E-value=2.1e-07 Score=36.90 Aligned_cols=23 Identities=43% Similarity=0.868 Sum_probs=21.4
Q ss_pred eeCCCCcccccchhhHHHHHhhh
Q psy11352 52 ATCFVCGKQLSNQYNLRVHMETH 74 (107)
Q Consensus 52 ~~C~~C~~~f~~~~~l~~H~~~h 74 (107)
|.|+.|++.|.+...|..|++.|
T Consensus 1 y~C~~C~~~f~~~~~l~~H~~~H 23 (23)
T PF00096_consen 1 YKCPICGKSFSSKSNLKRHMRRH 23 (23)
T ss_dssp EEETTTTEEESSHHHHHHHHHHH
T ss_pred CCCCCCCCccCCHHHHHHHHhHC
Confidence 68999999999999999999875
No 26
>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=98.28 E-value=4.4e-07 Score=37.37 Aligned_cols=23 Identities=30% Similarity=0.551 Sum_probs=15.0
Q ss_pred cccCCCCCCcccChHHHHHHHHc
Q psy11352 78 FYACSSCSHVSRSRDALRKHVSY 100 (107)
Q Consensus 78 ~~~C~~C~~~f~~~~~l~~H~~~ 100 (107)
||.|..|++.|....+|..|++.
T Consensus 1 ~~~C~~C~~~F~~~~~l~~H~~~ 23 (27)
T PF13912_consen 1 PFECDECGKTFSSLSALREHKRS 23 (27)
T ss_dssp SEEETTTTEEESSHHHHHHHHCT
T ss_pred CCCCCccCCccCChhHHHHHhHH
Confidence 45666666666666666666664
No 27
>PHA00732 hypothetical protein
Probab=98.18 E-value=3.9e-07 Score=47.17 Aligned_cols=48 Identities=17% Similarity=0.276 Sum_probs=38.8
Q ss_pred cccCCCCCCCCCccCCCCCCCCCCCCCCC-CCCCCCCCCCeeeCCCCcccccchhhHHHHHhhhCC
Q psy11352 12 FLISDHCLTSPLSSSIPGSSKTKASGSGT-TGGSSNHSKLFATCFVCGKQLSNQYNLRVHMETHQN 76 (107)
Q Consensus 12 ~~~C~~C~~~~~~~~~~~~l~~h~~~~~~-~~~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~ 76 (107)
||.|+.| ++.|.....|..| +.. +.+ +.|+.|++.|. .+..|......
T Consensus 1 py~C~~C---gk~F~s~s~Lk~H---~r~~H~~--------~~C~~CgKsF~---~l~~H~~~~~~ 49 (79)
T PHA00732 1 MFKCPIC---GFTTVTLFALKQH---ARRNHTL--------TKCPVCNKSYR---RLNQHFYSQYD 49 (79)
T ss_pred CccCCCC---CCccCCHHHHHHH---hhcccCC--------CccCCCCCEeC---ChhhhhcccCC
Confidence 6899999 9999999999999 763 432 47999999998 47788865554
No 28
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=98.08 E-value=2.7e-06 Score=34.95 Aligned_cols=25 Identities=36% Similarity=0.513 Sum_probs=22.8
Q ss_pred eeeCCCCcccccchhhHHHHHhhhC
Q psy11352 51 FATCFVCGKQLSNQYNLRVHMETHQ 75 (107)
Q Consensus 51 ~~~C~~C~~~f~~~~~l~~H~~~h~ 75 (107)
+|.|+.|++.|.+...|..|++.|.
T Consensus 1 ~~~C~~C~~~F~~~~~l~~H~~~h~ 25 (27)
T PF13912_consen 1 PFECDECGKTFSSLSALREHKRSHC 25 (27)
T ss_dssp SEEETTTTEEESSHHHHHHHHCTTT
T ss_pred CCCCCccCCccCChhHHHHHhHHhc
Confidence 5899999999999999999998765
No 29
>KOG3993|consensus
Probab=98.07 E-value=2.1e-06 Score=56.40 Aligned_cols=59 Identities=25% Similarity=0.295 Sum_probs=47.3
Q ss_pred ccccCCCCCCCCCccCCCCCCCCCCCCCCCCCCCC------------C----------------CCCCeeeCCCCccccc
Q psy11352 11 HFLISDHCLTSPLSSSIPGSSKTKASGSGTTGGSS------------N----------------HSKLFATCFVCGKQLS 62 (107)
Q Consensus 11 ~~~~C~~C~~~~~~~~~~~~l~~h~~~~~~~~~~~------------~----------------~~~~~~~C~~C~~~f~ 62 (107)
--|+|++| ++.|..+.+|..| .+.|...+ . ...-.|.|..|++.|.
T Consensus 294 vEYrCPEC---~KVFsCPANLASH---RRWHKPR~eaa~a~~~P~k~~~~~rae~~ea~rsg~dss~gi~~C~~C~KkFr 367 (500)
T KOG3993|consen 294 VEYRCPEC---DKVFSCPANLASH---RRWHKPRPEAAKAGSPPPKQAVETRAEVQEAERSGDDSSSGIFSCHTCGKKFR 367 (500)
T ss_pred eeecCCcc---cccccCchhhhhh---hcccCCchhhhhcCCCChhhhhhhhhhhhhccccCCcccCceeecHHhhhhhH
Confidence 36999999 9999999999998 66653210 0 1123699999999999
Q ss_pred chhhHHHHHhhhC
Q psy11352 63 NQYNLRVHMETHQ 75 (107)
Q Consensus 63 ~~~~l~~H~~~h~ 75 (107)
+...|+.|+.+|.
T Consensus 368 RqAYLrKHqlthq 380 (500)
T KOG3993|consen 368 RQAYLRKHQLTHQ 380 (500)
T ss_pred HHHHHHHhHHhhh
Confidence 9999999988775
No 30
>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=98.04 E-value=6e-06 Score=32.63 Aligned_cols=23 Identities=43% Similarity=0.863 Sum_probs=19.4
Q ss_pred eeCCCCcccccchhhHHHHHhhh
Q psy11352 52 ATCFVCGKQLSNQYNLRVHMETH 74 (107)
Q Consensus 52 ~~C~~C~~~f~~~~~l~~H~~~h 74 (107)
|.|+.|++.|.+...|..|+..|
T Consensus 1 ~~C~~C~~~~~~~~~l~~H~~~~ 23 (24)
T PF13894_consen 1 FQCPICGKSFRSKSELRQHMRTH 23 (24)
T ss_dssp EE-SSTS-EESSHHHHHHHHHHH
T ss_pred CCCcCCCCcCCcHHHHHHHHHhh
Confidence 68999999999999999999876
No 31
>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=98.00 E-value=9.8e-08 Score=39.07 Aligned_cols=20 Identities=35% Similarity=0.497 Sum_probs=15.3
Q ss_pred CCCCCCCCCCCCCeeeCCCCccccc
Q psy11352 38 SGTTGGSSNHSKLFATCFVCGKQLS 62 (107)
Q Consensus 38 ~~~~~~~~~~~~~~~~C~~C~~~f~ 62 (107)
++.|.++ ++|.|+.|++.|.
T Consensus 6 ~~~H~~~-----k~~~C~~C~k~F~ 25 (26)
T PF13465_consen 6 MRTHTGE-----KPYKCPYCGKSFS 25 (26)
T ss_dssp HHHHSSS-----SSEEESSSSEEES
T ss_pred hhhcCCC-----CCCCCCCCcCeeC
Confidence 5667777 8888888888775
No 32
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=97.83 E-value=5e-06 Score=52.99 Aligned_cols=51 Identities=27% Similarity=0.472 Sum_probs=41.9
Q ss_pred CCeeeCC--CCcccccchhhHHHHHhh-h------------------CC-CcccCCCCCCcccChHHHHHHHH
Q psy11352 49 KLFATCF--VCGKQLSNQYNLRVHMET-H------------------QN-AFYACSSCSHVSRSRDALRKHVS 99 (107)
Q Consensus 49 ~~~~~C~--~C~~~f~~~~~l~~H~~~-h------------------~~-k~~~C~~C~~~f~~~~~l~~H~~ 99 (107)
.+||+|+ .|.|.|.+...|+.|+.- | .. |||.|++|+|.+.....|+-|..
T Consensus 347 ~KpykCpV~gC~K~YknqnGLKYH~lhGH~~~~~~~~p~p~~~~~F~~~~KPYrCevC~KRYKNlNGLKYHr~ 419 (423)
T COG5189 347 GKPYKCPVEGCNKKYKNQNGLKYHMLHGHQNQKLHENPSPEKMNIFSAKDKPYRCEVCDKRYKNLNGLKYHRK 419 (423)
T ss_pred CceecCCCCCchhhhccccchhhhhhccccCcccCCCCCccccccccccCCceeccccchhhccCccceeccc
Confidence 4899995 499999999889888752 2 13 79999999999999999988875
No 33
>PF09237 GAGA: GAGA factor; InterPro: IPR015318 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Members of this entry bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognises the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognises the A in the fourth position of the consensus sequence []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1YUI_A 1YUJ_A.
Probab=97.78 E-value=4.6e-05 Score=35.69 Aligned_cols=29 Identities=34% Similarity=0.518 Sum_probs=15.3
Q ss_pred CeeeCCCCcccccchhhHHHHHhhhCC-Cc
Q psy11352 50 LFATCFVCGKQLSNQYNLRVHMETHQN-AF 78 (107)
Q Consensus 50 ~~~~C~~C~~~f~~~~~l~~H~~~h~~-k~ 78 (107)
.|..|++|+..+..+.+|.+|+.+..+ ||
T Consensus 23 ~PatCP~C~a~~~~srnLrRHle~~H~~k~ 52 (54)
T PF09237_consen 23 QPATCPICGAVIRQSRNLRRHLEIRHFKKP 52 (54)
T ss_dssp --EE-TTT--EESSHHHHHHHHHHHTTTS-
T ss_pred CCCCCCcchhhccchhhHHHHHHHHhcccC
Confidence 566677777777777777777665554 44
No 34
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=97.73 E-value=2.3e-05 Score=41.94 Aligned_cols=72 Identities=21% Similarity=0.230 Sum_probs=16.4
Q ss_pred cCCCCCCCCCccCCCCCCCCCCCCCCCCCCCCCCCCCeeeCCCCcccccchhhHHHHHhhhCCCcccCCCCCCcccChHH
Q psy11352 14 ISDHCLTSPLSSSIPGSSKTKASGSGTTGGSSNHSKLFATCFVCGKQLSNQYNLRVHMETHQNAFYACSSCSHVSRSRDA 93 (107)
Q Consensus 14 ~C~~C~~~~~~~~~~~~l~~h~~~~~~~~~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~k~~~C~~C~~~f~~~~~ 93 (107)
+|..| +..|.....+..| +....+.. .+ ....+.....+..+...-....+.|..|++.|.....
T Consensus 1 ~C~~C---~~~f~~~~~l~~H---~~~~H~~~----~~-----~~~~l~~~~~~~~~~~~~~~~~~~C~~C~~~f~s~~~ 65 (100)
T PF12756_consen 1 QCLFC---DESFSSVDDLLQH---MKKKHGFD----IP-----DQKYLVDPNRLLNYLRKKVKESFRCPYCNKTFRSREA 65 (100)
T ss_dssp ---------------------------------------------------------------SSEEBSSSS-EESSHHH
T ss_pred Ccccc---ccccccccccccc---cccccccc----cc-----cccccccccccccccccccCCCCCCCccCCCCcCHHH
Confidence 48889 9999999999888 53322210 00 0001111222222222211235777777777777777
Q ss_pred HHHHHHc
Q psy11352 94 LRKHVSY 100 (107)
Q Consensus 94 l~~H~~~ 100 (107)
|..|++.
T Consensus 66 l~~Hm~~ 72 (100)
T PF12756_consen 66 LQEHMRS 72 (100)
T ss_dssp HHHHHHH
T ss_pred HHHHHcC
Confidence 7777774
No 35
>smart00355 ZnF_C2H2 zinc finger.
Probab=97.72 E-value=4.1e-05 Score=30.56 Aligned_cols=21 Identities=38% Similarity=0.923 Sum_probs=13.9
Q ss_pred ccCCCCCCcccChHHHHHHHH
Q psy11352 79 YACSSCSHVSRSRDALRKHVS 99 (107)
Q Consensus 79 ~~C~~C~~~f~~~~~l~~H~~ 99 (107)
|.|..|++.|.....|..|++
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~ 21 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMR 21 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHH
Confidence 456666666666666666666
No 36
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=97.72 E-value=1.4e-05 Score=51.08 Aligned_cols=59 Identities=15% Similarity=0.067 Sum_probs=42.7
Q ss_pred cccccCCC--CCCCCCccCCCCCCCCCCCCC----CCCC---CC----CCCCCCeeeCCCCcccccchhhHHHHH
Q psy11352 10 LHFLISDH--CLTSPLSSSIPGSSKTKASGS----GTTG---GS----SNHSKLFATCFVCGKQLSNQYNLRVHM 71 (107)
Q Consensus 10 ~~~~~C~~--C~~~~~~~~~~~~l~~h~~~~----~~~~---~~----~~~~~~~~~C~~C~~~f~~~~~l~~H~ 71 (107)
.|||+|++ | .+.++....|+.|.... ..+. .+ =+...+||.|++|+|.|.+...|+.|.
T Consensus 347 ~KpykCpV~gC---~K~YknqnGLKYH~lhGH~~~~~~~~p~p~~~~~F~~~~KPYrCevC~KRYKNlNGLKYHr 418 (423)
T COG5189 347 GKPYKCPVEGC---NKKYKNQNGLKYHMLHGHQNQKLHENPSPEKMNIFSAKDKPYRCEVCDKRYKNLNGLKYHR 418 (423)
T ss_pred CceecCCCCCc---hhhhccccchhhhhhccccCcccCCCCCccccccccccCCceeccccchhhccCccceecc
Confidence 48999976 9 99999999999883110 0111 01 113358999999999999988888775
No 37
>smart00355 ZnF_C2H2 zinc finger.
Probab=97.70 E-value=3.2e-05 Score=30.89 Aligned_cols=24 Identities=38% Similarity=0.688 Sum_probs=21.3
Q ss_pred eeCCCCcccccchhhHHHHHhhhC
Q psy11352 52 ATCFVCGKQLSNQYNLRVHMETHQ 75 (107)
Q Consensus 52 ~~C~~C~~~f~~~~~l~~H~~~h~ 75 (107)
|.|+.|++.|.....|..|++.|.
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~~H~ 24 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMRTHX 24 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHHHhc
Confidence 579999999999999999998764
No 38
>PRK04860 hypothetical protein; Provisional
Probab=97.70 E-value=2.6e-05 Score=45.62 Aligned_cols=38 Identities=24% Similarity=0.506 Sum_probs=32.9
Q ss_pred CeeeCCCCcccccchhhHHHHHhhhCC-CcccCCCCCCcccCh
Q psy11352 50 LFATCFVCGKQLSNQYNLRVHMETHQN-AFYACSSCSHVSRSR 91 (107)
Q Consensus 50 ~~~~C~~C~~~f~~~~~l~~H~~~h~~-k~~~C~~C~~~f~~~ 91 (107)
-+|.|. |+. ....+.+|.++|++ ++|.|..|+..|...
T Consensus 118 ~~Y~C~-C~~---~~~~~rrH~ri~~g~~~YrC~~C~~~l~~~ 156 (160)
T PRK04860 118 FPYRCK-CQE---HQLTVRRHNRVVRGEAVYRCRRCGETLVFK 156 (160)
T ss_pred EEEEcC-CCC---eeCHHHHHHHHhcCCccEECCCCCceeEEe
Confidence 569998 987 56778999999999 999999999988654
No 39
>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=97.60 E-value=3.4e-05 Score=36.10 Aligned_cols=27 Identities=33% Similarity=0.580 Sum_probs=20.0
Q ss_pred CcccCCCCCCcccChHHHHHHHHccCC
Q psy11352 77 AFYACSSCSHVSRSRDALRKHVSYRHP 103 (107)
Q Consensus 77 k~~~C~~C~~~f~~~~~l~~H~~~~H~ 103 (107)
.|-.|++|+..+.+..+|.+|+.+.|.
T Consensus 23 ~PatCP~C~a~~~~srnLrRHle~~H~ 49 (54)
T PF09237_consen 23 QPATCPICGAVIRQSRNLRRHLEIRHF 49 (54)
T ss_dssp --EE-TTT--EESSHHHHHHHHHHHTT
T ss_pred CCCCCCcchhhccchhhHHHHHHHHhc
Confidence 799999999999999999999987553
No 40
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=97.50 E-value=5.4e-05 Score=30.08 Aligned_cols=23 Identities=30% Similarity=0.810 Sum_probs=12.6
Q ss_pred ccCCCCCCcccChHHHHHHHHccC
Q psy11352 79 YACSSCSHVSRSRDALRKHVSYRH 102 (107)
Q Consensus 79 ~~C~~C~~~f~~~~~l~~H~~~~H 102 (107)
|+|+.|+.... ...|.+|++++|
T Consensus 1 y~C~~C~y~t~-~~~l~~H~~~~H 23 (24)
T PF13909_consen 1 YKCPHCSYSTS-KSNLKRHLKRHH 23 (24)
T ss_dssp EE-SSSS-EES-HHHHHHHHHHHH
T ss_pred CCCCCCCCcCC-HHHHHHHHHhhC
Confidence 45666666555 666666666544
No 41
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=97.45 E-value=2e-05 Score=37.87 Aligned_cols=52 Identities=13% Similarity=0.226 Sum_probs=35.0
Q ss_pred cccCCCCCCCCCccCCCCCCCCCCCCCCCCCCCCCCCCCeeeCCCCcccccchhhHHHHHhhhC
Q psy11352 12 FLISDHCLTSPLSSSIPGSSKTKASGSGTTGGSSNHSKLFATCFVCGKQLSNQYNLRVHMETHQ 75 (107)
Q Consensus 12 ~~~C~~C~~~~~~~~~~~~l~~h~~~~~~~~~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~h~ 75 (107)
.|.||.| ++. .+...|..|... .|..+ .+.+.|++|...+. ..|..|+..+.
T Consensus 2 ~f~CP~C---~~~-~~~~~L~~H~~~--~H~~~----~~~v~CPiC~~~~~--~~l~~Hl~~~H 53 (54)
T PF05605_consen 2 SFTCPYC---GKG-FSESSLVEHCED--EHRSE----SKNVVCPICSSRVT--DNLIRHLNSQH 53 (54)
T ss_pred CcCCCCC---CCc-cCHHHHHHHHHh--HCcCC----CCCccCCCchhhhh--hHHHHHHHHhc
Confidence 4899999 884 445678888322 23322 14689999998654 48889987643
No 42
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=97.37 E-value=0.00015 Score=28.97 Aligned_cols=20 Identities=35% Similarity=0.770 Sum_probs=9.7
Q ss_pred eCCCCcccccchhhHHHHHh
Q psy11352 53 TCFVCGKQLSNQYNLRVHME 72 (107)
Q Consensus 53 ~C~~C~~~f~~~~~l~~H~~ 72 (107)
.|+.|++.|.+...|..|++
T Consensus 2 ~C~~C~~~f~s~~~~~~H~~ 21 (25)
T PF12874_consen 2 YCDICNKSFSSENSLRQHLR 21 (25)
T ss_dssp EETTTTEEESSHHHHHHHHT
T ss_pred CCCCCCCCcCCHHHHHHHHC
Confidence 44445555555444444443
No 43
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=97.26 E-value=0.00016 Score=28.89 Aligned_cols=22 Identities=27% Similarity=0.665 Sum_probs=20.2
Q ss_pred ccCCCCCCcccChHHHHHHHHc
Q psy11352 79 YACSSCSHVSRSRDALRKHVSY 100 (107)
Q Consensus 79 ~~C~~C~~~f~~~~~l~~H~~~ 100 (107)
|.|.+|++.|.....+..|++.
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 6799999999999999999874
No 44
>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=97.22 E-value=0.00016 Score=29.58 Aligned_cols=22 Identities=23% Similarity=0.653 Sum_probs=16.2
Q ss_pred ccCCCCCCcccChHHHHHHHHc
Q psy11352 79 YACSSCSHVSRSRDALRKHVSY 100 (107)
Q Consensus 79 ~~C~~C~~~f~~~~~l~~H~~~ 100 (107)
|.|..|++.|.....+..|+++
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 5677788778777777777653
No 45
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=96.85 E-value=0.0012 Score=26.01 Aligned_cols=23 Identities=30% Similarity=0.574 Sum_probs=17.8
Q ss_pred eeCCCCcccccchhhHHHHHhhhC
Q psy11352 52 ATCFVCGKQLSNQYNLRVHMETHQ 75 (107)
Q Consensus 52 ~~C~~C~~~f~~~~~l~~H~~~h~ 75 (107)
|.|+.|+.... ...|..|++.+.
T Consensus 1 y~C~~C~y~t~-~~~l~~H~~~~H 23 (24)
T PF13909_consen 1 YKCPHCSYSTS-KSNLKRHLKRHH 23 (24)
T ss_dssp EE-SSSS-EES-HHHHHHHHHHHH
T ss_pred CCCCCCCCcCC-HHHHHHHHHhhC
Confidence 68999999888 889999998753
No 46
>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=96.78 E-value=0.00045 Score=28.20 Aligned_cols=22 Identities=32% Similarity=0.611 Sum_probs=18.9
Q ss_pred eeCCCCcccccchhhHHHHHhh
Q psy11352 52 ATCFVCGKQLSNQYNLRVHMET 73 (107)
Q Consensus 52 ~~C~~C~~~f~~~~~l~~H~~~ 73 (107)
|.|..|++.|.+...+..|++.
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 6799999999999999888764
No 47
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=96.59 E-value=0.0024 Score=25.61 Aligned_cols=19 Identities=32% Similarity=0.602 Sum_probs=10.3
Q ss_pred cCCCCCCcccChHHHHHHHH
Q psy11352 80 ACSSCSHVSRSRDALRKHVS 99 (107)
Q Consensus 80 ~C~~C~~~f~~~~~l~~H~~ 99 (107)
.|+.||+.| ..+.|..|+.
T Consensus 4 ~C~~CgR~F-~~~~l~~H~~ 22 (25)
T PF13913_consen 4 PCPICGRKF-NPDRLEKHEK 22 (25)
T ss_pred cCCCCCCEE-CHHHHHHHHH
Confidence 455666666 3444555554
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=96.38 E-value=0.0032 Score=27.06 Aligned_cols=22 Identities=14% Similarity=0.342 Sum_probs=14.2
Q ss_pred cccCCCCCCcccChHHHHHHHH
Q psy11352 78 FYACSSCSHVSRSRDALRKHVS 99 (107)
Q Consensus 78 ~~~C~~C~~~f~~~~~l~~H~~ 99 (107)
+|.|++|++.|.....+..|+.
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~ 24 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLK 24 (35)
T ss_pred CeEccccCCccCCHHHHHHHHC
Confidence 4567777777766666666654
No 49
>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=95.84 E-value=0.0085 Score=25.70 Aligned_cols=22 Identities=14% Similarity=0.466 Sum_probs=19.5
Q ss_pred eeeCCCCcccccchhhHHHHHh
Q psy11352 51 FATCFVCGKQLSNQYNLRVHME 72 (107)
Q Consensus 51 ~~~C~~C~~~f~~~~~l~~H~~ 72 (107)
+|.|+.|+..|.....+..|+.
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~ 24 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLK 24 (35)
T ss_pred CeEccccCCccCCHHHHHHHHC
Confidence 4889999999999999988875
No 50
>PRK04860 hypothetical protein; Provisional
Probab=95.61 E-value=0.0021 Score=37.75 Aligned_cols=40 Identities=15% Similarity=0.231 Sum_probs=32.5
Q ss_pred cccccCCCCCCCCCccCCCCCCCCCCCCCCCCCCCCCCCCCeeeCCCCcccccch
Q psy11352 10 LHFLISDHCLTSPLSSSIPGSSKTKASGSGTTGGSSNHSKLFATCFVCGKQLSNQ 64 (107)
Q Consensus 10 ~~~~~C~~C~~~~~~~~~~~~l~~h~~~~~~~~~~~~~~~~~~~C~~C~~~f~~~ 64 (107)
.-+|.|. | +. ....+..| .+++.+. ++|.|..|+..|...
T Consensus 117 ~~~Y~C~-C---~~---~~~~~rrH---~ri~~g~-----~~YrC~~C~~~l~~~ 156 (160)
T PRK04860 117 TFPYRCK-C---QE---HQLTVRRH---NRVVRGE-----AVYRCRRCGETLVFK 156 (160)
T ss_pred EEEEEcC-C---CC---eeCHHHHH---HHHhcCC-----ccEECCCCCceeEEe
Confidence 3579998 9 65 56667888 8888888 999999999988654
No 51
>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=95.55 E-value=0.012 Score=25.13 Aligned_cols=24 Identities=29% Similarity=0.663 Sum_probs=15.8
Q ss_pred eeCCCCcccccchhhHHHHHhhhCCCcccCCCCCC
Q psy11352 52 ATCFVCGKQLSNQYNLRVHMETHQNAFYACSSCSH 86 (107)
Q Consensus 52 ~~C~~C~~~f~~~~~l~~H~~~h~~k~~~C~~C~~ 86 (107)
|.|..||..+.... .++.|+.||.
T Consensus 2 ~~C~~CGy~y~~~~-----------~~~~CP~Cg~ 25 (33)
T cd00350 2 YVCPVCGYIYDGEE-----------APWVCPVCGA 25 (33)
T ss_pred EECCCCCCEECCCc-----------CCCcCcCCCC
Confidence 67777876654322 4778888874
No 52
>KOG2186|consensus
Probab=95.11 E-value=0.017 Score=36.17 Aligned_cols=25 Identities=20% Similarity=0.571 Sum_probs=13.8
Q ss_pred eeeCCCCcccccchhhHHHHHhhhCC
Q psy11352 51 FATCFVCGKQLSNQYNLRVHMETHQN 76 (107)
Q Consensus 51 ~~~C~~C~~~f~~~~~l~~H~~~h~~ 76 (107)
.|.|..|++.|.. .++..|...-++
T Consensus 29 ~fSCIDC~k~F~~-~sYknH~kCITE 53 (276)
T KOG2186|consen 29 YFSCIDCGKTFER-VSYKNHTKCITE 53 (276)
T ss_pred eeEEeeccccccc-chhhhhhhhcch
Confidence 4666666666665 445555544443
No 53
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=94.68 E-value=0.05 Score=26.41 Aligned_cols=33 Identities=18% Similarity=0.365 Sum_probs=22.3
Q ss_pred CeeeCCCCcccccchhhHHHHHhhhCCCcccCCCCCC
Q psy11352 50 LFATCFVCGKQLSNQYNLRVHMETHQNAFYACSSCSH 86 (107)
Q Consensus 50 ~~~~C~~C~~~f~~~~~l~~H~~~h~~k~~~C~~C~~ 86 (107)
..|.|+.||..-..... .-.-.+.+|.|+.||.
T Consensus 26 v~F~CPnCGe~~I~Rc~----~CRk~g~~Y~Cp~CGF 58 (61)
T COG2888 26 VKFPCPNCGEVEIYRCA----KCRKLGNPYRCPKCGF 58 (61)
T ss_pred eEeeCCCCCceeeehhh----hHHHcCCceECCCcCc
Confidence 67999999976544322 1122347999999984
No 54
>KOG1146|consensus
Probab=94.59 E-value=0.023 Score=43.01 Aligned_cols=51 Identities=24% Similarity=0.415 Sum_probs=43.9
Q ss_pred CeeeCCCCcccccchhhHHHHHhh-h------------------------CC-CcccCCCCCCcccChHHHHHHHHc
Q psy11352 50 LFATCFVCGKQLSNQYNLRVHMET-H------------------------QN-AFYACSSCSHVSRSRDALRKHVSY 100 (107)
Q Consensus 50 ~~~~C~~C~~~f~~~~~l~~H~~~-h------------------------~~-k~~~C~~C~~~f~~~~~l~~H~~~ 100 (107)
+.+.|+.|+..|.....|-.|++. | .+ +||.|..|...++...+|..|+..
T Consensus 464 kt~~cpkc~~~yk~a~~L~vhmRskhp~~~~~~c~~gq~~~~~arg~~~~~~~~p~~C~~C~~stttng~LsihlqS 540 (1406)
T KOG1146|consen 464 KTLKCPKCNWHYKLAQTLGVHMRSKHPESQSAYCKAGQNHPRLARGEVYRCPGKPYPCRACNYSTTTNGNLSIHLQS 540 (1406)
T ss_pred ccccCCccchhhhhHHHhhhcccccccccchhHhHhccccccccccccccCCCCcccceeeeeeeecchHHHHHHHH
Confidence 678999999999999999999887 1 12 589999999999999999999874
No 55
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=94.58 E-value=0.041 Score=29.11 Aligned_cols=25 Identities=24% Similarity=0.470 Sum_probs=21.7
Q ss_pred eeeCCCCcccccchhhHHHHHhhhC
Q psy11352 51 FATCFVCGKQLSNQYNLRVHMETHQ 75 (107)
Q Consensus 51 ~~~C~~C~~~f~~~~~l~~H~~~h~ 75 (107)
.+.|..|++.|.+...|..|++.+.
T Consensus 50 ~~~C~~C~~~f~s~~~l~~Hm~~~~ 74 (100)
T PF12756_consen 50 SFRCPYCNKTFRSREALQEHMRSKH 74 (100)
T ss_dssp SEEBSSSS-EESSHHHHHHHHHHTT
T ss_pred CCCCCccCCCCcCHHHHHHHHcCcc
Confidence 5999999999999999999998643
No 56
>KOG2893|consensus
Probab=94.58 E-value=0.0071 Score=37.63 Aligned_cols=41 Identities=22% Similarity=0.537 Sum_probs=27.6
Q ss_pred CCCCcccccchhhHHHHHhhhCCCcccCCCCCCcccChHHHHHH
Q psy11352 54 CFVCGKQLSNQYNLRVHMETHQNAFYACSSCSHVSRSRDALRKH 97 (107)
Q Consensus 54 C~~C~~~f~~~~~l~~H~~~h~~k~~~C~~C~~~f~~~~~l~~H 97 (107)
|..|++.|.....|.+|++. |-|+|.+|.+...+...|..|
T Consensus 13 cwycnrefddekiliqhqka---khfkchichkkl~sgpglsih 53 (341)
T KOG2893|consen 13 CWYCNREFDDEKILIQHQKA---KHFKCHICHKKLFSGPGLSIH 53 (341)
T ss_pred eeecccccchhhhhhhhhhh---ccceeeeehhhhccCCCceee
Confidence 77788888888888777642 667888887654444444333
No 57
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=94.03 E-value=0.037 Score=26.48 Aligned_cols=25 Identities=20% Similarity=0.412 Sum_probs=22.0
Q ss_pred CeeeCCCCcccccchhhHHHHHhhh
Q psy11352 50 LFATCFVCGKQLSNQYNLRVHMETH 74 (107)
Q Consensus 50 ~~~~C~~C~~~f~~~~~l~~H~~~h 74 (107)
.-+.|+.||..|.....+.+|+..-
T Consensus 16 ~~lrCPRC~~~FR~~K~Y~RHVNKa 40 (65)
T COG4049 16 EFLRCPRCGMVFRRRKDYIRHVNKA 40 (65)
T ss_pred eeeeCCchhHHHHHhHHHHHHhhHH
Confidence 7889999999999999999998643
No 58
>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=94.01 E-value=0.066 Score=29.45 Aligned_cols=31 Identities=19% Similarity=0.417 Sum_probs=21.6
Q ss_pred eeeCCCCcccccchhhHHHHHhhhCCCcccCCCCCCcccCh
Q psy11352 51 FATCFVCGKQLSNQYNLRVHMETHQNAFYACSSCSHVSRSR 91 (107)
Q Consensus 51 ~~~C~~C~~~f~~~~~l~~H~~~h~~k~~~C~~C~~~f~~~ 91 (107)
...|+.||..|.... ..|..|+.||..|.-.
T Consensus 9 KR~Cp~CG~kFYDLn----------k~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 9 KRTCPSCGAKFYDLN----------KDPIVCPKCGTEFPPE 39 (108)
T ss_pred cccCCCCcchhccCC----------CCCccCCCCCCccCcc
Confidence 357888888876521 1588888888877655
No 59
>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=93.97 E-value=0.064 Score=23.09 Aligned_cols=25 Identities=28% Similarity=0.482 Sum_probs=15.8
Q ss_pred eeeCCCCcccccchhhHHHHHhhhCCCcccCCCCCC
Q psy11352 51 FATCFVCGKQLSNQYNLRVHMETHQNAFYACSSCSH 86 (107)
Q Consensus 51 ~~~C~~C~~~f~~~~~l~~H~~~h~~k~~~C~~C~~ 86 (107)
.|.|..||..+.... .|..|+.||.
T Consensus 2 ~~~C~~CG~i~~g~~-----------~p~~CP~Cg~ 26 (34)
T cd00729 2 VWVCPVCGYIHEGEE-----------APEKCPICGA 26 (34)
T ss_pred eEECCCCCCEeECCc-----------CCCcCcCCCC
Confidence 467888876643321 4677888874
No 60
>KOG4173|consensus
Probab=93.84 E-value=0.011 Score=35.93 Aligned_cols=80 Identities=16% Similarity=0.326 Sum_probs=55.9
Q ss_pred cccccCCC--CCCCCCccCCCCCCCCCCCCCCCCCCCCCCCCCeeeCCCCcccccchhhHHHHHh-hh---------CC-
Q psy11352 10 LHFLISDH--CLTSPLSSSIPGSSKTKASGSGTTGGSSNHSKLFATCFVCGKQLSNQYNLRVHME-TH---------QN- 76 (107)
Q Consensus 10 ~~~~~C~~--C~~~~~~~~~~~~l~~h~~~~~~~~~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~-~h---------~~- 76 (107)
+..|.|+. | ...|........| .....+ ..|..|.+.|.+...|..|+. .| .|
T Consensus 77 ~~~~~cqvagc---~~~~d~lD~~E~h---Y~~~h~--------~sCs~C~r~~Pt~hLLd~HI~E~HDs~Fqa~veRG~ 142 (253)
T KOG4173|consen 77 VPAFACQVAGC---CQVFDALDDYEHH---YHTLHG--------NSCSFCKRAFPTGHLLDAHILEWHDSLFQALVERGQ 142 (253)
T ss_pred cccccccccch---HHHHhhhhhHHHh---hhhccc--------chhHHHHHhCCchhhhhHHHHHHHHHHHHHHHHcCc
Confidence 44567766 5 5556655555555 322222 279999999999999998874 33 34
Q ss_pred CcccC--CCCCCcccChHHHHHHHHccCC
Q psy11352 77 AFYAC--SSCSHVSRSRDALRKHVSYRHP 103 (107)
Q Consensus 77 k~~~C--~~C~~~f~~~~~l~~H~~~~H~ 103 (107)
--|+| +.|+..|........|+-..|.
T Consensus 143 dMy~ClvEgCt~KFkT~r~RkdH~I~~Hk 171 (253)
T KOG4173|consen 143 DMYQCLVEGCTEKFKTSRDRKDHMIRMHK 171 (253)
T ss_pred cHHHHHHHhhhhhhhhhhhhhhHHHHhcc
Confidence 35888 5699999999888999876563
No 61
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=93.66 E-value=0.058 Score=31.56 Aligned_cols=17 Identities=24% Similarity=0.653 Sum_probs=13.2
Q ss_pred eeeCCCCcccccchhhH
Q psy11352 51 FATCFVCGKQLSNQYNL 67 (107)
Q Consensus 51 ~~~C~~C~~~f~~~~~l 67 (107)
.+.|+.||++|..-..+
T Consensus 28 ~~~c~~c~~~f~~~e~~ 44 (154)
T PRK00464 28 RRECLACGKRFTTFERV 44 (154)
T ss_pred eeeccccCCcceEeEec
Confidence 48999999999875443
No 62
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=93.25 E-value=0.028 Score=34.66 Aligned_cols=13 Identities=15% Similarity=0.621 Sum_probs=9.0
Q ss_pred ccCCCCCCcccCh
Q psy11352 79 YACSSCSHVSRSR 91 (107)
Q Consensus 79 ~~C~~C~~~f~~~ 91 (107)
..|+.||.+|...
T Consensus 49 ~vCP~CgyA~~~~ 61 (214)
T PF09986_consen 49 WVCPHCGYAAFEE 61 (214)
T ss_pred EECCCCCCccccc
Confidence 5788888776543
No 63
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=93.16 E-value=0.025 Score=37.46 Aligned_cols=53 Identities=23% Similarity=0.462 Sum_probs=32.8
Q ss_pred eeeCCCCcccccchhhHHHHHh--hhCC---CcccCC--CCCCcccChHHHHHHHHccCCC
Q psy11352 51 FATCFVCGKQLSNQYNLRVHME--THQN---AFYACS--SCSHVSRSRDALRKHVSYRHPH 104 (107)
Q Consensus 51 ~~~C~~C~~~f~~~~~l~~H~~--~h~~---k~~~C~--~C~~~f~~~~~l~~H~~~~H~~ 104 (107)
++.|..|...|.....|..|.+ .|.+ +++.|+ .|++.|.+...+..|..+ |.+
T Consensus 289 ~~~~~~~~~~~s~~~~l~~~~~~~~h~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~-~~~ 348 (467)
T COG5048 289 PIKSKQCNISFSRSSPLTRHLRSVNHSGESLKPFSCPYSLCGKLFSRNDALKRHILL-HTS 348 (467)
T ss_pred CCCCccccCCccccccccccccccccccccCCceeeeccCCCccccccccccCCccc-ccC
Confidence 4566666666666666666666 5553 366666 566666666666666664 444
No 64
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=93.02 E-value=0.11 Score=34.47 Aligned_cols=64 Identities=22% Similarity=0.240 Sum_probs=52.4
Q ss_pred ccccCCCCCCCCCccCCCCCCCCCCCCCC--CCCCCCCCCCCeeeCC--CCcccccchhhHHHHHhhhCC-CcccCCC
Q psy11352 11 HFLISDHCLTSPLSSSIPGSSKTKASGSG--TTGGSSNHSKLFATCF--VCGKQLSNQYNLRVHMETHQN-AFYACSS 83 (107)
Q Consensus 11 ~~~~C~~C~~~~~~~~~~~~l~~h~~~~~--~~~~~~~~~~~~~~C~--~C~~~f~~~~~l~~H~~~h~~-k~~~C~~ 83 (107)
.++.|..| ...|.....+..| .. .+.++. .+++.|+ .|++.|.+...+..|...|.+ .++.+..
T Consensus 288 ~~~~~~~~---~~~~s~~~~l~~~---~~~~~h~~~~---~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 356 (467)
T COG5048 288 LPIKSKQC---NISFSRSSPLTRH---LRSVNHSGES---LKPFSCPYSLCGKLFSRNDALKRHILLHTSISPAKEKL 356 (467)
T ss_pred cCCCCccc---cCCcccccccccc---cccccccccc---CCceeeeccCCCccccccccccCCcccccCCCcccccc
Confidence 47899999 9999999999999 66 454442 3689998 899999999999999999998 6666643
No 65
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=92.03 E-value=0.21 Score=33.01 Aligned_cols=92 Identities=16% Similarity=0.261 Sum_probs=52.4
Q ss_pred ccccCCCCcccccCCCCCCCCCccC------CCCCCCCCCCCCCCCCCCCCCCCC-eeeCCCCcccccchhhHHHHHhhh
Q psy11352 2 NFHYKPSTLHFLISDHCLTSPLSSS------IPGSSKTKASGSGTTGGSSNHSKL-FATCFVCGKQLSNQYNLRVHMETH 74 (107)
Q Consensus 2 ~~h~~~~~~~~~~C~~C~~~~~~~~------~~~~l~~h~~~~~~~~~~~~~~~~-~~~C~~C~~~f~~~~~l~~H~~~h 74 (107)
+.|+|.... .+.|..|-+.-+.|. ....|..| ......+ .+=+ .-.|..|..-|..-..|..|++.-
T Consensus 170 k~H~K~~H~-~~~C~~C~~nKk~F~~E~~lF~~~~Lr~H---~~~G~~e--~GFKGHP~C~FC~~~FYdDDEL~~HcR~~ 243 (493)
T COG5236 170 KKHYKAQHG-FVLCSECIGNKKDFWNEIRLFRSSTLRDH---KNGGLEE--EGFKGHPLCIFCKIYFYDDDELRRHCRLR 243 (493)
T ss_pred HHHHHhhcC-cEEhHhhhcCcccCccceeeeeccccccc---ccCCccc--cCcCCCchhhhccceecChHHHHHHHHhh
Confidence 445554443 456777744344443 33445555 2222111 1102 235999999999999999999875
Q ss_pred CCCcccCCCCCC----cccChHHHHHHHH
Q psy11352 75 QNAFYACSSCSH----VSRSRDALRKHVS 99 (107)
Q Consensus 75 ~~k~~~C~~C~~----~f~~~~~l~~H~~ 99 (107)
.++-+.|+.-+. -|..-.+|-+|.+
T Consensus 244 HE~ChICD~v~p~~~QYFK~Y~~Le~HF~ 272 (493)
T COG5236 244 HEACHICDMVGPIRYQYFKSYEDLEAHFR 272 (493)
T ss_pred hhhhhhhhccCccchhhhhCHHHHHHHhh
Confidence 555555544332 2556666777765
No 66
>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=91.89 E-value=0.078 Score=24.93 Aligned_cols=12 Identities=25% Similarity=0.755 Sum_probs=6.9
Q ss_pred eeCCCCcccccc
Q psy11352 52 ATCFVCGKQLSN 63 (107)
Q Consensus 52 ~~C~~C~~~f~~ 63 (107)
|.|..||..|..
T Consensus 6 y~C~~Cg~~fe~ 17 (52)
T TIGR02605 6 YRCTACGHRFEV 17 (52)
T ss_pred EEeCCCCCEeEE
Confidence 556666665553
No 67
>smart00614 ZnF_BED BED zinc finger. DNA-binding domain in chromatin-boundary-element-binding proteins and transposases
Probab=91.76 E-value=0.18 Score=23.60 Aligned_cols=8 Identities=38% Similarity=0.800 Sum_probs=4.1
Q ss_pred HHHHHHHH
Q psy11352 92 DALRKHVS 99 (107)
Q Consensus 92 ~~l~~H~~ 99 (107)
++|.+|++
T Consensus 37 s~L~rHl~ 44 (50)
T smart00614 37 SNLRRHLR 44 (50)
T ss_pred HHHHHHHH
Confidence 34555555
No 68
>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=91.74 E-value=0.19 Score=21.95 Aligned_cols=33 Identities=18% Similarity=0.307 Sum_probs=15.7
Q ss_pred eeCCCCcccccchhhHHHHHhhhCCCcccCCCCCCcc
Q psy11352 52 ATCFVCGKQLSNQYNLRVHMETHQNAFYACSSCSHVS 88 (107)
Q Consensus 52 ~~C~~C~~~f~~~~~l~~H~~~h~~k~~~C~~C~~~f 88 (107)
..|+.|+..|.-...... ..+....|+.|+..|
T Consensus 3 ~~CP~C~~~~~v~~~~~~----~~~~~v~C~~C~~~~ 35 (38)
T TIGR02098 3 IQCPNCKTSFRVVDSQLG----ANGGKVRCGKCGHVW 35 (38)
T ss_pred EECCCCCCEEEeCHHHcC----CCCCEEECCCCCCEE
Confidence 456666666554432210 011245666666554
No 69
>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=91.68 E-value=0.09 Score=23.27 Aligned_cols=30 Identities=17% Similarity=0.485 Sum_probs=15.4
Q ss_pred eeeCCCCcccccchhhHHHHHhhhCCCcccCCCCCC
Q psy11352 51 FATCFVCGKQLSNQYNLRVHMETHQNAFYACSSCSH 86 (107)
Q Consensus 51 ~~~C~~C~~~f~~~~~l~~H~~~h~~k~~~C~~C~~ 86 (107)
.|.|..||..|....... .+....|+.||.
T Consensus 5 ~y~C~~Cg~~fe~~~~~~------~~~~~~CP~Cg~ 34 (41)
T smart00834 5 EYRCEDCGHTFEVLQKIS------DDPLATCPECGG 34 (41)
T ss_pred EEEcCCCCCEEEEEEecC------CCCCCCCCCCCC
Confidence 366777776665433221 123445666664
No 70
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=91.47 E-value=0.2 Score=22.88 Aligned_cols=27 Identities=19% Similarity=0.486 Sum_probs=16.5
Q ss_pred eeeCCCCcccccchhhHHHHHhhhCCCcccCCCCCCc
Q psy11352 51 FATCFVCGKQLSNQYNLRVHMETHQNAFYACSSCSHV 87 (107)
Q Consensus 51 ~~~C~~C~~~f~~~~~l~~H~~~h~~k~~~C~~C~~~ 87 (107)
.|.|..||..|... .+.+..|+.||..
T Consensus 2 ~Y~C~~Cg~~~~~~----------~~~~irC~~CG~r 28 (44)
T smart00659 2 IYICGECGRENEIK----------SKDVVRCRECGYR 28 (44)
T ss_pred EEECCCCCCEeecC----------CCCceECCCCCce
Confidence 36777777766543 1146677777743
No 71
>PHA00626 hypothetical protein
Probab=91.47 E-value=0.22 Score=23.92 Aligned_cols=14 Identities=29% Similarity=0.306 Sum_probs=10.4
Q ss_pred CeeeCCCCcccccc
Q psy11352 50 LFATCFVCGKQLSN 63 (107)
Q Consensus 50 ~~~~C~~C~~~f~~ 63 (107)
..|.|..||..|..
T Consensus 22 nrYkCkdCGY~ft~ 35 (59)
T PHA00626 22 DDYVCCDCGYNDSK 35 (59)
T ss_pred cceEcCCCCCeech
Confidence 55888888877764
No 72
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=91.47 E-value=0.23 Score=27.50 Aligned_cols=85 Identities=13% Similarity=0.106 Sum_probs=47.6
Q ss_pred ccccCCCCCCCCCccCCCCCCCCCCCCCCCCC--CC-C-CCCCCeeeCCCCcccccchhhHHHHHhhhCC-CcccCCCCC
Q psy11352 11 HFLISDHCLTSPLSSSIPGSSKTKASGSGTTG--GS-S-NHSKLFATCFVCGKQLSNQYNLRVHMETHQN-AFYACSSCS 85 (107)
Q Consensus 11 ~~~~C~~C~~~~~~~~~~~~l~~h~~~~~~~~--~~-~-~~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~-k~~~C~~C~ 85 (107)
-|-.|+.| +.....+..|.+...-.-.-. .+ + ......-.|-.|...|........ ..-.. ..|+|+.|.
T Consensus 14 LP~~CpiC---gLtLVss~HLARSyHHLfPl~~f~ev~~~~~~~~~~C~~C~~~f~~~~~~~~--~~~~~~~~y~C~~C~ 88 (112)
T TIGR00622 14 LPVECPIC---GLTLILSTHLARSYHHLFPLKAFQEIPLEEYNGSRFCFGCQGPFPKPPVSPF--DELKDSHRYVCAVCK 88 (112)
T ss_pred CCCcCCcC---CCEEeccchHHHhhhccCCCcccccccccccCCCCcccCcCCCCCCcccccc--cccccccceeCCCCC
Confidence 47789999 777666665553310000000 00 0 001112348889888876431110 00112 589999999
Q ss_pred CcccChHHHHHHHHc
Q psy11352 86 HVSRSRDALRKHVSY 100 (107)
Q Consensus 86 ~~f~~~~~l~~H~~~ 100 (107)
..|-..-++-.|...
T Consensus 89 ~~FC~dCD~fiHe~L 103 (112)
T TIGR00622 89 NVFCVDCDVFVHESL 103 (112)
T ss_pred Cccccccchhhhhhc
Confidence 999888888788774
No 73
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=91.33 E-value=0.14 Score=22.40 Aligned_cols=10 Identities=30% Similarity=0.836 Sum_probs=4.8
Q ss_pred eeCCCCcccc
Q psy11352 52 ATCFVCGKQL 61 (107)
Q Consensus 52 ~~C~~C~~~f 61 (107)
..|..|+-.|
T Consensus 26 vrC~~C~~~f 35 (37)
T PF13719_consen 26 VRCPKCGHVF 35 (37)
T ss_pred EECCCCCcEe
Confidence 4455554444
No 74
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=90.71 E-value=0.22 Score=29.56 Aligned_cols=25 Identities=28% Similarity=0.511 Sum_probs=17.7
Q ss_pred CeeeCCCCcccccchhhHHHHHhhhCCCcccCCCCCC
Q psy11352 50 LFATCFVCGKQLSNQYNLRVHMETHQNAFYACSSCSH 86 (107)
Q Consensus 50 ~~~~C~~C~~~f~~~~~l~~H~~~h~~k~~~C~~C~~ 86 (107)
+.|.|++||.++.. ..|-+|++||-
T Consensus 133 ~~~vC~vCGy~~~g------------e~P~~CPiCga 157 (166)
T COG1592 133 KVWVCPVCGYTHEG------------EAPEVCPICGA 157 (166)
T ss_pred CEEEcCCCCCcccC------------CCCCcCCCCCC
Confidence 36889999865432 16888999983
No 75
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=90.39 E-value=0.18 Score=23.09 Aligned_cols=11 Identities=27% Similarity=0.773 Sum_probs=5.5
Q ss_pred eeeCCCCcccc
Q psy11352 51 FATCFVCGKQL 61 (107)
Q Consensus 51 ~~~C~~C~~~f 61 (107)
.|.|+.||..|
T Consensus 3 ~y~C~~CG~~~ 13 (46)
T PRK00398 3 EYKCARCGREV 13 (46)
T ss_pred EEECCCCCCEE
Confidence 34555555544
No 76
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=90.09 E-value=0.38 Score=27.88 Aligned_cols=37 Identities=11% Similarity=0.382 Sum_probs=23.6
Q ss_pred CeeeCCCCcccccchhhHHHHHhhhCCCcccCCCCCCccc
Q psy11352 50 LFATCFVCGKQLSNQYNLRVHMETHQNAFYACSSCSHVSR 89 (107)
Q Consensus 50 ~~~~C~~C~~~f~~~~~l~~H~~~h~~k~~~C~~C~~~f~ 89 (107)
..|.|+.|+..|.....+.. . .....|.|+.||....
T Consensus 98 ~~Y~Cp~C~~~y~~~ea~~~-~--d~~~~f~Cp~Cg~~l~ 134 (147)
T smart00531 98 AYYKCPNCQSKYTFLEANQL-L--DMDGTFTCPRCGEELE 134 (147)
T ss_pred cEEECcCCCCEeeHHHHHHh-c--CCCCcEECCCCCCEEE
Confidence 67899999988875443221 0 1123489999987643
No 77
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=90.05 E-value=0.28 Score=21.33 Aligned_cols=13 Identities=23% Similarity=0.388 Sum_probs=6.0
Q ss_pred eCCCCcccccchh
Q psy11352 53 TCFVCGKQLSNQY 65 (107)
Q Consensus 53 ~C~~C~~~f~~~~ 65 (107)
.|+.|+..|.-..
T Consensus 4 ~Cp~C~~~y~i~d 16 (36)
T PF13717_consen 4 TCPNCQAKYEIDD 16 (36)
T ss_pred ECCCCCCEEeCCH
Confidence 4445554444443
No 78
>TIGR00373 conserved hypothetical protein TIGR00373. This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.
Probab=89.69 E-value=0.4 Score=28.19 Aligned_cols=32 Identities=13% Similarity=0.367 Sum_probs=24.3
Q ss_pred CCeeeCCCCcccccchhhHHHHHhhhCCCcccCCCCCCcc
Q psy11352 49 KLFATCFVCGKQLSNQYNLRVHMETHQNAFYACSSCSHVS 88 (107)
Q Consensus 49 ~~~~~C~~C~~~f~~~~~l~~H~~~h~~k~~~C~~C~~~f 88 (107)
..-|.|+.|+..|+....+. --|.|+.||...
T Consensus 107 ~~~Y~Cp~c~~r~tf~eA~~--------~~F~Cp~Cg~~L 138 (158)
T TIGR00373 107 NMFFICPNMCVRFTFNEAME--------LNFTCPRCGAML 138 (158)
T ss_pred CCeEECCCCCcEeeHHHHHH--------cCCcCCCCCCEe
Confidence 36788999998887766654 368999998654
No 79
>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=89.52 E-value=0.25 Score=22.31 Aligned_cols=22 Identities=23% Similarity=0.546 Sum_probs=9.0
Q ss_pred cccCCCCCCcccCh----HHHHHHHH
Q psy11352 78 FYACSSCSHVSRSR----DALRKHVS 99 (107)
Q Consensus 78 ~~~C~~C~~~f~~~----~~l~~H~~ 99 (107)
-..|..|++.+... ++|.+|++
T Consensus 16 ~a~C~~C~~~~~~~~~~ts~l~~HL~ 41 (45)
T PF02892_consen 16 KAKCKYCGKVIKYSSGGTSNLKRHLK 41 (45)
T ss_dssp -EEETTTTEE-----SSTHHHHHHHH
T ss_pred eEEeCCCCeEEeeCCCcHHHHHHhhh
Confidence 34555555544432 45555553
No 80
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=89.51 E-value=0.41 Score=28.76 Aligned_cols=32 Identities=16% Similarity=0.451 Sum_probs=23.6
Q ss_pred CeeeCCCCcccccchhhHHHHHhhhCCCcccCCCCCCccc
Q psy11352 50 LFATCFVCGKQLSNQYNLRVHMETHQNAFYACSSCSHVSR 89 (107)
Q Consensus 50 ~~~~C~~C~~~f~~~~~l~~H~~~h~~k~~~C~~C~~~f~ 89 (107)
.-|.|+.|+..|.....+. --|.|+.||....
T Consensus 116 ~~Y~Cp~C~~rytf~eA~~--------~~F~Cp~Cg~~L~ 147 (178)
T PRK06266 116 MFFFCPNCHIRFTFDEAME--------YGFRCPQCGEMLE 147 (178)
T ss_pred CEEECCCCCcEEeHHHHhh--------cCCcCCCCCCCCe
Confidence 6788999998887765542 3688999986543
No 81
>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=89.36 E-value=0.14 Score=23.12 Aligned_cols=12 Identities=8% Similarity=0.265 Sum_probs=7.0
Q ss_pred ccCCCCCCCCCccCC
Q psy11352 13 LISDHCLTSPLSSSI 27 (107)
Q Consensus 13 ~~C~~C~~~~~~~~~ 27 (107)
|.|+.| +..|..
T Consensus 6 y~C~~C---g~~fe~ 17 (42)
T PF09723_consen 6 YRCEEC---GHEFEV 17 (42)
T ss_pred EEeCCC---CCEEEE
Confidence 566666 655544
No 82
>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=89.22 E-value=0.28 Score=27.70 Aligned_cols=30 Identities=7% Similarity=-0.002 Sum_probs=17.7
Q ss_pred eeCCCCcccccchhhHHHHHhhhCCCcccCCCCCCcccCh
Q psy11352 52 ATCFVCGKQLSNQYNLRVHMETHQNAFYACSSCSHVSRSR 91 (107)
Q Consensus 52 ~~C~~C~~~f~~~~~l~~H~~~h~~k~~~C~~C~~~f~~~ 91 (107)
..|+.||+.|.... ..|..|+.||..|...
T Consensus 10 r~Cp~cg~kFYDLn----------k~p~vcP~cg~~~~~~ 39 (129)
T TIGR02300 10 RICPNTGSKFYDLN----------RRPAVSPYTGEQFPPE 39 (129)
T ss_pred ccCCCcCccccccC----------CCCccCCCcCCccCcc
Confidence 46777777664411 0467777777666444
No 83
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=89.18 E-value=0.62 Score=22.68 Aligned_cols=32 Identities=22% Similarity=0.550 Sum_probs=20.8
Q ss_pred CeeeCCCCcccccchhhHHHHHhh-hCCCcccCCCCCC
Q psy11352 50 LFATCFVCGKQLSNQYNLRVHMET-HQNAFYACSSCSH 86 (107)
Q Consensus 50 ~~~~C~~C~~~f~~~~~l~~H~~~-h~~k~~~C~~C~~ 86 (107)
..|.|+.||......-. +- -.+.+|.|+.||.
T Consensus 24 ~~F~CPnCG~~~I~RC~-----~CRk~~~~Y~CP~CGF 56 (59)
T PRK14890 24 VKFLCPNCGEVIIYRCE-----KCRKQSNPYTCPKCGF 56 (59)
T ss_pred CEeeCCCCCCeeEeech-----hHHhcCCceECCCCCC
Confidence 56999999986333211 11 1226999999984
No 84
>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=89.09 E-value=0.55 Score=18.84 Aligned_cols=19 Identities=16% Similarity=0.534 Sum_probs=12.0
Q ss_pred cCCCCCCcccChHHHHHHHH
Q psy11352 80 ACSSCSHVSRSRDALRKHVS 99 (107)
Q Consensus 80 ~C~~C~~~f~~~~~l~~H~~ 99 (107)
.|++|++.+ ....+..|..
T Consensus 3 ~CPiC~~~v-~~~~in~HLD 21 (26)
T smart00734 3 QCPVCFREV-PENLINSHLD 21 (26)
T ss_pred cCCCCcCcc-cHHHHHHHHH
Confidence 577777766 4456666655
No 85
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=89.06 E-value=0.27 Score=21.95 Aligned_cols=13 Identities=31% Similarity=0.859 Sum_probs=8.7
Q ss_pred CeeeCCCCccccc
Q psy11352 50 LFATCFVCGKQLS 62 (107)
Q Consensus 50 ~~~~C~~C~~~f~ 62 (107)
.-|.|..|+..|.
T Consensus 27 ~fy~C~~C~~~w~ 39 (40)
T smart00440 27 VFYVCTKCGHRWR 39 (40)
T ss_pred EEEEeCCCCCEeC
Confidence 4577877876653
No 86
>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=89.05 E-value=0.31 Score=20.71 Aligned_cols=11 Identities=27% Similarity=0.685 Sum_probs=5.9
Q ss_pred CcccCCCCCCc
Q psy11352 77 AFYACSSCSHV 87 (107)
Q Consensus 77 k~~~C~~C~~~ 87 (107)
.+..|+.||..
T Consensus 16 ~~irC~~CG~R 26 (32)
T PF03604_consen 16 DPIRCPECGHR 26 (32)
T ss_dssp STSSBSSSS-S
T ss_pred CcEECCcCCCe
Confidence 35566666643
No 87
>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=88.17 E-value=0.29 Score=30.26 Aligned_cols=26 Identities=27% Similarity=0.705 Sum_probs=19.8
Q ss_pred cccCCCCCCcccChHHHHHHHHccCC
Q psy11352 78 FYACSSCSHVSRSRDALRKHVSYRHP 103 (107)
Q Consensus 78 ~~~C~~C~~~f~~~~~l~~H~~~~H~ 103 (107)
.|.|.+|+|.|.-...+..|+...|.
T Consensus 77 K~~C~lc~KlFkg~eFV~KHI~nKH~ 102 (214)
T PF04959_consen 77 KWRCPLCGKLFKGPEFVRKHIFNKHP 102 (214)
T ss_dssp EEEE-SSS-EESSHHHHHHHHHHH-H
T ss_pred EECCCCCCcccCChHHHHHHHhhcCH
Confidence 58899999999998889999887775
No 88
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=87.66 E-value=0.52 Score=24.83 Aligned_cols=11 Identities=18% Similarity=0.688 Sum_probs=5.5
Q ss_pred cccCCCCCCcc
Q psy11352 78 FYACSSCSHVS 88 (107)
Q Consensus 78 ~~~C~~C~~~f 88 (107)
-+.|..||..|
T Consensus 53 IW~C~kCg~~f 63 (89)
T COG1997 53 IWKCRKCGAKF 63 (89)
T ss_pred eEEcCCCCCee
Confidence 44555555544
No 89
>KOG1146|consensus
Probab=87.49 E-value=0.33 Score=37.31 Aligned_cols=59 Identities=14% Similarity=0.188 Sum_probs=46.0
Q ss_pred CCcccccCCCCCCCCCccCCCCCCCCCCCCCCCCCCC--------------------CCCCCCeeeCCCCcccccchhhH
Q psy11352 8 STLHFLISDHCLTSPLSSSIPGSSKTKASGSGTTGGS--------------------SNHSKLFATCFVCGKQLSNQYNL 67 (107)
Q Consensus 8 ~~~~~~~C~~C~~~~~~~~~~~~l~~h~~~~~~~~~~--------------------~~~~~~~~~C~~C~~~f~~~~~l 67 (107)
+..+-|+|+.| +..|.....|..| ++....+ .....++|.|..|...+.....|
T Consensus 461 S~~kt~~cpkc---~~~yk~a~~L~vh---mRskhp~~~~~~c~~gq~~~~~arg~~~~~~~~p~~C~~C~~stttng~L 534 (1406)
T KOG1146|consen 461 SFFKTLKCPKC---NWHYKLAQTLGVH---MRSKHPESQSAYCKAGQNHPRLARGEVYRCPGKPYPCRACNYSTTTNGNL 534 (1406)
T ss_pred cccccccCCcc---chhhhhHHHhhhc---ccccccccchhHhHhccccccccccccccCCCCcccceeeeeeeecchHH
Confidence 33478999999 9999999999999 7662110 11335789999999999999999
Q ss_pred HHHHh
Q psy11352 68 RVHME 72 (107)
Q Consensus 68 ~~H~~ 72 (107)
..|+.
T Consensus 535 sihlq 539 (1406)
T KOG1146|consen 535 SIHLQ 539 (1406)
T ss_pred HHHHH
Confidence 88875
No 90
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=86.83 E-value=0.48 Score=22.21 Aligned_cols=29 Identities=17% Similarity=0.455 Sum_probs=19.5
Q ss_pred CeeeCCCCcccccchhhHHHHHhhhCCCcccCCCCCCc
Q psy11352 50 LFATCFVCGKQLSNQYNLRVHMETHQNAFYACSSCSHV 87 (107)
Q Consensus 50 ~~~~C~~C~~~f~~~~~l~~H~~~h~~k~~~C~~C~~~ 87 (107)
..|.|..||+.|.... ......|+.||..
T Consensus 5 ~~Y~C~~Cg~~~~~~~---------~~~~irCp~Cg~r 33 (49)
T COG1996 5 MEYKCARCGREVELDQ---------ETRGIRCPYCGSR 33 (49)
T ss_pred EEEEhhhcCCeeehhh---------ccCceeCCCCCcE
Confidence 5689999998882111 1157789999853
No 91
>PF05290 Baculo_IE-1: Baculovirus immediate-early protein (IE-0); InterPro: IPR007954 This entry contains the Baculovirus immediate-early protein IE-0.
Probab=86.29 E-value=0.7 Score=26.39 Aligned_cols=13 Identities=23% Similarity=0.608 Sum_probs=10.4
Q ss_pred cCCCCCCcccChH
Q psy11352 80 ACSSCSHVSRSRD 92 (107)
Q Consensus 80 ~C~~C~~~f~~~~ 92 (107)
.|+.|.-+|.+.+
T Consensus 123 vCPvCkTSFKss~ 135 (140)
T PF05290_consen 123 VCPVCKTSFKSSS 135 (140)
T ss_pred CCCcccccccccc
Confidence 6899988887664
No 92
>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=86.22 E-value=0.2 Score=22.25 Aligned_cols=12 Identities=42% Similarity=1.021 Sum_probs=8.5
Q ss_pred CeeeCCCCcccc
Q psy11352 50 LFATCFVCGKQL 61 (107)
Q Consensus 50 ~~~~C~~C~~~f 61 (107)
.-|.|..|+..|
T Consensus 27 ~fy~C~~C~~~w 38 (39)
T PF01096_consen 27 LFYVCCNCGHRW 38 (39)
T ss_dssp EEEEESSSTEEE
T ss_pred EEEEeCCCCCee
Confidence 457788888765
No 93
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=86.21 E-value=0.32 Score=25.79 Aligned_cols=27 Identities=22% Similarity=0.525 Sum_probs=16.9
Q ss_pred CeeeCCCCcccccchhhHHHHHhhhCCCcccCCCCC
Q psy11352 50 LFATCFVCGKQLSNQYNLRVHMETHQNAFYACSSCS 85 (107)
Q Consensus 50 ~~~~C~~C~~~f~~~~~l~~H~~~h~~k~~~C~~C~ 85 (107)
+|-.|..||..|.... + .+|-.|+.|.
T Consensus 57 ~Pa~CkkCGfef~~~~-i--------k~pSRCP~CK 83 (97)
T COG3357 57 RPARCKKCGFEFRDDK-I--------KKPSRCPKCK 83 (97)
T ss_pred cChhhcccCccccccc-c--------CCcccCCcch
Confidence 4567888888776511 1 1477777774
No 94
>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=85.80 E-value=0.73 Score=25.18 Aligned_cols=24 Identities=38% Similarity=0.862 Sum_probs=20.3
Q ss_pred ccC----CCCCCcccChHHHHHHHHccC
Q psy11352 79 YAC----SSCSHVSRSRDALRKHVSYRH 102 (107)
Q Consensus 79 ~~C----~~C~~~f~~~~~l~~H~~~~H 102 (107)
|.| ..|+..+.+...+.+|.+..|
T Consensus 81 ~~C~~~~~~C~y~~~~~~~m~~H~~~~H 108 (109)
T PF12013_consen 81 YRCQCDPPHCGYITRSKKTMRKHWRKEH 108 (109)
T ss_pred eeeecCCCCCCcEeccHHHHHHHHHHhc
Confidence 778 889888888889999988755
No 95
>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=85.71 E-value=1.2 Score=21.38 Aligned_cols=13 Identities=31% Similarity=0.703 Sum_probs=9.4
Q ss_pred CeeeCCCCccccc
Q psy11352 50 LFATCFVCGKQLS 62 (107)
Q Consensus 50 ~~~~C~~C~~~f~ 62 (107)
....|+.||..+.
T Consensus 21 eiV~Cp~CGaele 33 (54)
T TIGR01206 21 ELVICDECGAELE 33 (54)
T ss_pred CEEeCCCCCCEEE
Confidence 3568999987654
No 96
>KOG2186|consensus
Probab=85.30 E-value=0.29 Score=30.91 Aligned_cols=48 Identities=27% Similarity=0.674 Sum_probs=37.7
Q ss_pred CeeeCCCCcccccchhhHHHHHhhhCCCcccCCCCCCcccChHHHHHHHH
Q psy11352 50 LFATCFVCGKQLSNQYNLRVHMETHQNAFYACSSCSHVSRSRDALRKHVS 99 (107)
Q Consensus 50 ~~~~C~~C~~~f~~~~~l~~H~~~h~~k~~~C~~C~~~f~~~~~l~~H~~ 99 (107)
..|.|+.||....- ..+.+|+....+.-|.|.-|++.|.. .....|..
T Consensus 2 V~FtCnvCgEsvKK-p~vekH~srCrn~~fSCIDC~k~F~~-~sYknH~k 49 (276)
T KOG2186|consen 2 VFFTCNVCGESVKK-PQVEKHMSRCRNAYFSCIDCGKTFER-VSYKNHTK 49 (276)
T ss_pred eEEehhhhhhhccc-cchHHHHHhccCCeeEEeeccccccc-chhhhhhh
Confidence 35899999987654 45777988888888999999999988 45566654
No 97
>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=84.78 E-value=1.9 Score=24.97 Aligned_cols=18 Identities=22% Similarity=0.700 Sum_probs=10.4
Q ss_pred cccCCCCCCcccChHHHH
Q psy11352 78 FYACSSCSHVSRSRDALR 95 (107)
Q Consensus 78 ~~~C~~C~~~f~~~~~l~ 95 (107)
-+.|+.||+.|...+...
T Consensus 124 f~~C~~C~kiyW~GsH~~ 141 (147)
T PF01927_consen 124 FWRCPGCGKIYWEGSHWR 141 (147)
T ss_pred EEECCCCCCEecccccHH
Confidence 456666666666554443
No 98
>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=84.14 E-value=0.65 Score=18.67 Aligned_cols=10 Identities=20% Similarity=0.461 Sum_probs=6.0
Q ss_pred cCCCCCCccc
Q psy11352 80 ACSSCSHVSR 89 (107)
Q Consensus 80 ~C~~C~~~f~ 89 (107)
.|+.||..|.
T Consensus 16 ~Cp~CG~~F~ 25 (26)
T PF10571_consen 16 FCPHCGYDFE 25 (26)
T ss_pred cCCCCCCCCc
Confidence 4666666653
No 99
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=83.42 E-value=0.73 Score=23.46 Aligned_cols=18 Identities=11% Similarity=0.359 Sum_probs=13.7
Q ss_pred CeeeCC--CCcccccchhhH
Q psy11352 50 LFATCF--VCGKQLSNQYNL 67 (107)
Q Consensus 50 ~~~~C~--~C~~~f~~~~~l 67 (107)
..+.|. .||.+|.....+
T Consensus 26 ~Y~qC~N~eCg~tF~t~es~ 45 (72)
T PRK09678 26 RYHQCQNVNCSATFITYESV 45 (72)
T ss_pred eeeecCCCCCCCEEEEEEEE
Confidence 668897 899998876554
No 100
>KOG4167|consensus
Probab=83.20 E-value=0.88 Score=33.17 Aligned_cols=26 Identities=31% Similarity=0.478 Sum_probs=22.2
Q ss_pred CeeeCCCCcccccchhhHHHHHhhhC
Q psy11352 50 LFATCFVCGKQLSNQYNLRVHMETHQ 75 (107)
Q Consensus 50 ~~~~C~~C~~~f~~~~~l~~H~~~h~ 75 (107)
-.|.|..|++.|..-.++..||++|.
T Consensus 791 giFpCreC~kvF~KiKSrNAHMK~Hr 816 (907)
T KOG4167|consen 791 GIFPCRECGKVFFKIKSRNAHMKTHR 816 (907)
T ss_pred ceeehHHHHHHHHHHhhhhHHHHHHH
Confidence 46889999999988888888988875
No 101
>PF14353 CpXC: CpXC protein
Probab=83.19 E-value=0.38 Score=27.09 Aligned_cols=55 Identities=20% Similarity=0.280 Sum_probs=28.0
Q ss_pred ccCCCCCCCCCccCCCCCCCCCCCCCCCCCCC-CCCCCCeeeCCCCcccccchhhHHHH
Q psy11352 13 LISDHCLTSPLSSSIPGSSKTKASGSGTTGGS-SNHSKLFATCFVCGKQLSNQYNLRVH 70 (107)
Q Consensus 13 ~~C~~C~~~~~~~~~~~~l~~h~~~~~~~~~~-~~~~~~~~~C~~C~~~f~~~~~l~~H 70 (107)
..||.| +..|.........++....-... -...=..+.|+.||..|.-...+..|
T Consensus 2 itCP~C---~~~~~~~v~~~I~~~~~p~l~e~il~g~l~~~~CP~Cg~~~~~~~p~lY~ 57 (128)
T PF14353_consen 2 ITCPHC---GHEFEFEVWTSINADEDPELKEKILDGSLFSFTCPSCGHKFRLEYPLLYH 57 (128)
T ss_pred cCCCCC---CCeeEEEEEeEEcCcCCHHHHHHHHcCCcCEEECCCCCCceecCCCEEEE
Confidence 368888 77776655544431111000000 00111457888888887666555444
No 102
>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=82.92 E-value=0.86 Score=26.05 Aligned_cols=24 Identities=33% Similarity=0.843 Sum_probs=15.8
Q ss_pred CeeeCCCCcccccchhhHHHHHhhhCC
Q psy11352 50 LFATCFVCGKQLSNQYNLRVHMETHQN 76 (107)
Q Consensus 50 ~~~~C~~C~~~f~~~~~l~~H~~~h~~ 76 (107)
..-.|-+||+.|.. |.+|+..|.|
T Consensus 71 d~i~clecGk~~k~---LkrHL~~~~g 94 (132)
T PF05443_consen 71 DYIICLECGKKFKT---LKRHLRTHHG 94 (132)
T ss_dssp S-EE-TBT--EESB---HHHHHHHTT-
T ss_pred CeeEEccCCcccch---HHHHHHHccC
Confidence 45679999999876 6899999865
No 103
>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=82.83 E-value=1.4 Score=24.10 Aligned_cols=27 Identities=19% Similarity=0.258 Sum_probs=23.2
Q ss_pred CeeeC----CCCcccccchhhHHHHHhhhCC
Q psy11352 50 LFATC----FVCGKQLSNQYNLRVHMETHQN 76 (107)
Q Consensus 50 ~~~~C----~~C~~~f~~~~~l~~H~~~h~~ 76 (107)
.-|.| ..|+....+...+..|.+.+.|
T Consensus 79 ~G~~C~~~~~~C~y~~~~~~~m~~H~~~~Hg 109 (109)
T PF12013_consen 79 DGYRCQCDPPHCGYITRSKKTMRKHWRKEHG 109 (109)
T ss_pred CCeeeecCCCCCCcEeccHHHHHHHHHHhcC
Confidence 45889 9999999999999999987543
No 104
>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=82.26 E-value=2 Score=20.19 Aligned_cols=6 Identities=17% Similarity=0.357 Sum_probs=3.7
Q ss_pred ccCCCC
Q psy11352 13 LISDHC 18 (107)
Q Consensus 13 ~~C~~C 18 (107)
|+|..|
T Consensus 2 y~C~~C 7 (50)
T cd00730 2 YECRIC 7 (50)
T ss_pred cCCCCC
Confidence 556666
No 105
>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=81.54 E-value=1.2 Score=25.88 Aligned_cols=18 Identities=11% Similarity=0.300 Sum_probs=13.1
Q ss_pred CeeeCCCCcccccchhhH
Q psy11352 50 LFATCFVCGKQLSNQYNL 67 (107)
Q Consensus 50 ~~~~C~~C~~~f~~~~~l 67 (107)
..-+|..||+.|.+-..+
T Consensus 27 RRReC~~C~~RFTTyErv 44 (147)
T TIGR00244 27 RRRECLECHERFTTFERA 44 (147)
T ss_pred ecccCCccCCccceeeec
Confidence 345899999999875443
No 106
>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=81.30 E-value=0.75 Score=18.89 Aligned_cols=19 Identities=21% Similarity=0.553 Sum_probs=9.7
Q ss_pred eeCCCCcccccchhhHHHHH
Q psy11352 52 ATCFVCGKQLSNQYNLRVHM 71 (107)
Q Consensus 52 ~~C~~C~~~f~~~~~l~~H~ 71 (107)
|.|-.|++.|. ....+.|.
T Consensus 1 ~sCiDC~~~F~-~~~y~~Ht 19 (28)
T PF08790_consen 1 FSCIDCSKDFD-GDSYKSHT 19 (28)
T ss_dssp EEETTTTEEEE-GGGTTT--
T ss_pred CeeecCCCCcC-cCCcCCCC
Confidence 45677777773 33444443
No 107
>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=81.12 E-value=1.6 Score=17.26 Aligned_cols=10 Identities=30% Similarity=0.537 Sum_probs=6.5
Q ss_pred CeeeCCCCcc
Q psy11352 50 LFATCFVCGK 59 (107)
Q Consensus 50 ~~~~C~~C~~ 59 (107)
..|.|+.||+
T Consensus 15 v~f~CPnCG~ 24 (24)
T PF07754_consen 15 VPFPCPNCGF 24 (24)
T ss_pred ceEeCCCCCC
Confidence 4577777763
No 108
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=80.93 E-value=1.3 Score=25.22 Aligned_cols=15 Identities=20% Similarity=0.479 Sum_probs=12.7
Q ss_pred CeeeCCCCcccccch
Q psy11352 50 LFATCFVCGKQLSNQ 64 (107)
Q Consensus 50 ~~~~C~~C~~~f~~~ 64 (107)
..|.|..|+++|...
T Consensus 52 qRyrC~~C~~tf~~~ 66 (129)
T COG3677 52 QRYKCKSCGSTFTVE 66 (129)
T ss_pred cccccCCcCcceeee
Confidence 679999999998764
No 109
>COG1327 Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains [Transcription]
Probab=80.80 E-value=1.3 Score=25.84 Aligned_cols=16 Identities=19% Similarity=0.522 Sum_probs=12.3
Q ss_pred CeeeCCCCcccccchh
Q psy11352 50 LFATCFVCGKQLSNQY 65 (107)
Q Consensus 50 ~~~~C~~C~~~f~~~~ 65 (107)
..-.|..|+..|.+-.
T Consensus 27 RRReC~~C~~RFTTfE 42 (156)
T COG1327 27 RRRECLECGERFTTFE 42 (156)
T ss_pred hhhcccccccccchhh
Confidence 4468999999987743
No 110
>PF12907 zf-met2: Zinc-binding
Probab=78.96 E-value=1.4 Score=19.67 Aligned_cols=27 Identities=22% Similarity=0.557 Sum_probs=13.3
Q ss_pred ccCCCCCCcc---cChHHHHHHHHccCCCC
Q psy11352 79 YACSSCSHVS---RSRDALRKHVSYRHPHI 105 (107)
Q Consensus 79 ~~C~~C~~~f---~~~~~l~~H~~~~H~~e 105 (107)
+.|.+|-..| .....|..|....|..+
T Consensus 2 i~C~iC~qtF~~t~~~~~L~eH~enKHpK~ 31 (40)
T PF12907_consen 2 IICKICRQTFMQTTNEPQLKEHAENKHPKN 31 (40)
T ss_pred cCcHHhhHHHHhcCCHHHHHHHHHccCCCC
Confidence 3455555333 23345666665555543
No 111
>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=77.75 E-value=2.4 Score=26.36 Aligned_cols=24 Identities=25% Similarity=0.342 Sum_probs=19.8
Q ss_pred CeeeCCCCcccccchhhHHHHHhh
Q psy11352 50 LFATCFVCGKQLSNQYNLRVHMET 73 (107)
Q Consensus 50 ~~~~C~~C~~~f~~~~~l~~H~~~ 73 (107)
..|.|..|+|.|.-...+..|+..
T Consensus 76 ~K~~C~lc~KlFkg~eFV~KHI~n 99 (214)
T PF04959_consen 76 DKWRCPLCGKLFKGPEFVRKHIFN 99 (214)
T ss_dssp EEEEE-SSS-EESSHHHHHHHHHH
T ss_pred CEECCCCCCcccCChHHHHHHHhh
Confidence 569999999999999999999874
No 112
>PF02176 zf-TRAF: TRAF-type zinc finger; PDB: 2EOD_A 2YUC_A 3HCU_A 3HCS_B 3HCT_A.
Probab=77.49 E-value=2.1 Score=20.43 Aligned_cols=40 Identities=18% Similarity=0.325 Sum_probs=23.6
Q ss_pred CeeeCCC--CcccccchhhHHHHHhhhCC-CcccCCC----CCCcccC
Q psy11352 50 LFATCFV--CGKQLSNQYNLRVHMETHQN-AFYACSS----CSHVSRS 90 (107)
Q Consensus 50 ~~~~C~~--C~~~f~~~~~l~~H~~~h~~-k~~~C~~----C~~~f~~ 90 (107)
.+-.|+. |...+. ...|..|....-. .+..|+. |...+..
T Consensus 8 ~~v~C~~~cc~~~i~-r~~l~~H~~~~C~~~~v~C~~~~~GC~~~~~~ 54 (60)
T PF02176_consen 8 RPVPCPNGCCNEMIP-RKELDDHLENECPKRPVPCPYSPYGCKERVPR 54 (60)
T ss_dssp SEEE-TT--S-BEEE-CCCHHHHHHTTSTTSEEE-SS----S--EEEH
T ss_pred CEeeCCCCCccccee-HHHHHHHHHccCCCCcEECCCCCCCCCCccch
Confidence 4567877 444444 5678899886555 7788888 8776643
No 113
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=76.86 E-value=1.5 Score=25.06 Aligned_cols=15 Identities=27% Similarity=0.545 Sum_probs=11.3
Q ss_pred CeeeCCCCcccccch
Q psy11352 50 LFATCFVCGKQLSNQ 64 (107)
Q Consensus 50 ~~~~C~~C~~~f~~~ 64 (107)
..+.|..||..|...
T Consensus 69 ~~~~C~~CG~~~~~~ 83 (135)
T PRK03824 69 AVLKCRNCGNEWSLK 83 (135)
T ss_pred eEEECCCCCCEEecc
Confidence 558899999877654
No 114
>PF13451 zf-trcl: Probable zinc-binding domain
Probab=76.58 E-value=1.7 Score=20.35 Aligned_cols=35 Identities=20% Similarity=0.337 Sum_probs=21.8
Q ss_pred CeeeCCCCcccccchhhHHHHHhhhCC---CcccCCCCC
Q psy11352 50 LFATCFVCGKQLSNQYNLRVHMETHQN---AFYACSSCS 85 (107)
Q Consensus 50 ~~~~C~~C~~~f~~~~~l~~H~~~h~~---k~~~C~~C~ 85 (107)
+.+.|..||..|.....=+....- .| .|-.|..|-
T Consensus 3 k~l~C~dCg~~FvfTa~EQ~fy~e-Kgf~n~p~RC~~CR 40 (49)
T PF13451_consen 3 KTLTCKDCGAEFVFTAGEQKFYAE-KGFDNEPKRCPSCR 40 (49)
T ss_pred eeEEcccCCCeEEEehhHHHHHHh-cCCcCCCccCHHHH
Confidence 678899999988776543333221 22 366777663
No 115
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=75.95 E-value=1.5 Score=23.81 Aligned_cols=9 Identities=11% Similarity=0.335 Sum_probs=6.1
Q ss_pred cccccCCCC
Q psy11352 10 LHFLISDHC 18 (107)
Q Consensus 10 ~~~~~C~~C 18 (107)
.+.|.|+.|
T Consensus 20 ~k~FtCp~C 28 (104)
T COG4888 20 PKTFTCPRC 28 (104)
T ss_pred CceEecCcc
Confidence 455777777
No 116
>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=75.91 E-value=1.4 Score=32.10 Aligned_cols=57 Identities=18% Similarity=0.240 Sum_probs=37.7
Q ss_pred cCCCCCCCCCccCCCCCCCCCCCCCCCCCCCCCCCCCee-eCCCCcccccchhhHHHHHhhhCCCcccCCCCCCc
Q psy11352 14 ISDHCLTSPLSSSIPGSSKTKASGSGTTGGSSNHSKLFA-TCFVCGKQLSNQYNLRVHMETHQNAFYACSSCSHV 87 (107)
Q Consensus 14 ~C~~C~~~~~~~~~~~~l~~h~~~~~~~~~~~~~~~~~~-~C~~C~~~f~~~~~l~~H~~~h~~k~~~C~~C~~~ 87 (107)
.|..| +-.|+-...+-.- +..+.- ..| .|+.|.+.|.+..+- |.|. .|..|+.||..
T Consensus 125 ~CT~C---GPRfTIi~alPYD----R~nTsM-----~~F~lC~~C~~EY~dP~nR----RfHA-Qp~aCp~CGP~ 182 (750)
T COG0068 125 NCTNC---GPRFTIIEALPYD----RENTSM-----ADFPLCPFCDKEYKDPLNR----RFHA-QPIACPKCGPH 182 (750)
T ss_pred ccCCC---CcceeeeccCCCC----cccCcc-----ccCcCCHHHHHHhcCcccc----cccc-ccccCcccCCC
Confidence 68889 8888776665433 222222 334 499999888877653 2333 58899999964
No 117
>KOG2893|consensus
Probab=75.70 E-value=0.5 Score=29.74 Aligned_cols=50 Identities=18% Similarity=0.196 Sum_probs=37.0
Q ss_pred cccccCCCCCCCCCccCCCCCCCCCCCCCCCCCCCCCCCCCeeeCCCCcccccchhhHHHH-HhhhC
Q psy11352 10 LHFLISDHCLTSPLSSSIPGSSKTKASGSGTTGGSSNHSKLFATCFVCGKQLSNQYNLRVH-METHQ 75 (107)
Q Consensus 10 ~~~~~C~~C~~~~~~~~~~~~l~~h~~~~~~~~~~~~~~~~~~~C~~C~~~f~~~~~l~~H-~~~h~ 75 (107)
.|+ .|=.| ++.|.....|..| +. . +.|+|.+|.+.+.+-..|..| +.+|.
T Consensus 9 ~kp-wcwyc---nrefddekiliqh---qk----a-----khfkchichkkl~sgpglsihcmqvhk 59 (341)
T KOG2893|consen 9 DKP-WCWYC---NREFDDEKILIQH---QK----A-----KHFKCHICHKKLFSGPGLSIHCMQVHK 59 (341)
T ss_pred CCc-eeeec---ccccchhhhhhhh---hh----h-----ccceeeeehhhhccCCCceeehhhhhh
Confidence 344 57789 9999999888888 32 2 679999999987777667666 44554
No 118
>KOG2785|consensus
Probab=75.65 E-value=3.8 Score=27.64 Aligned_cols=51 Identities=22% Similarity=0.364 Sum_probs=40.7
Q ss_pred CeeeCCCCcccccchhhHHHHHhhhCC--C----------------------cccCCCCC---CcccChHHHHHHHHc
Q psy11352 50 LFATCFVCGKQLSNQYNLRVHMETHQN--A----------------------FYACSSCS---HVSRSRDALRKHVSY 100 (107)
Q Consensus 50 ~~~~C~~C~~~f~~~~~l~~H~~~h~~--k----------------------~~~C~~C~---~~f~~~~~l~~H~~~ 100 (107)
.|-.|-.|++.+.+-..-..||..+.| . -+.|..|. +.|.+..+.+.||..
T Consensus 165 ~Pt~CLfC~~~~k~~e~~~~HM~~~HgffIPdreYL~D~~GLl~YLgeKV~~~~~CL~CN~~~~~f~sleavr~HM~~ 242 (390)
T KOG2785|consen 165 IPTDCLFCDKKSKSLEENLKHMFKEHGFFIPDREYLTDEKGLLKYLGEKVGIGFICLFCNELGRPFSSLEAVRAHMRD 242 (390)
T ss_pred CCcceeecCCCcccHHHHHHHHhhccCCcCCchHhhhchhHHHHHHHHHhccCceEEEeccccCcccccHHHHHHHhh
Confidence 456689999999998888889876543 2 35677787 899999999999973
No 119
>KOG2907|consensus
Probab=75.59 E-value=2.3 Score=23.60 Aligned_cols=12 Identities=33% Similarity=0.891 Sum_probs=7.7
Q ss_pred cccCCCCCCccc
Q psy11352 78 FYACSSCSHVSR 89 (107)
Q Consensus 78 ~~~C~~C~~~f~ 89 (107)
-|.|+.|++.|.
T Consensus 102 FYTC~kC~~k~~ 113 (116)
T KOG2907|consen 102 FYTCPKCKYKFT 113 (116)
T ss_pred EEEcCccceeee
Confidence 466777766654
No 120
>PF15269 zf-C2H2_7: Zinc-finger
Probab=74.95 E-value=2.6 Score=19.31 Aligned_cols=21 Identities=24% Similarity=0.641 Sum_probs=10.6
Q ss_pred ccCCCCCCcccChHHHHHHHH
Q psy11352 79 YACSSCSHVSRSRDALRKHVS 99 (107)
Q Consensus 79 ~~C~~C~~~f~~~~~l~~H~~ 99 (107)
|+|-+|..+...++.|-.||+
T Consensus 21 ykcfqcpftc~~kshl~nhmk 41 (54)
T PF15269_consen 21 YKCFQCPFTCNEKSHLFNHMK 41 (54)
T ss_pred ceeecCCcccchHHHHHHHHH
Confidence 344445444445555555554
No 121
>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=74.67 E-value=1.5 Score=18.26 Aligned_cols=9 Identities=22% Similarity=0.966 Sum_probs=4.8
Q ss_pred CcccCCCCC
Q psy11352 77 AFYACSSCS 85 (107)
Q Consensus 77 k~~~C~~C~ 85 (107)
..|.|+.|+
T Consensus 18 ~~~vCp~C~ 26 (30)
T PF08274_consen 18 ELLVCPECG 26 (30)
T ss_dssp SSEEETTTT
T ss_pred CEEeCCccc
Confidence 445555554
No 122
>PHA02998 RNA polymerase subunit; Provisional
Probab=74.65 E-value=2 Score=25.82 Aligned_cols=10 Identities=30% Similarity=0.647 Sum_probs=4.8
Q ss_pred ccCCCCCCcc
Q psy11352 79 YACSSCSHVS 88 (107)
Q Consensus 79 ~~C~~C~~~f 88 (107)
|.|..||+.|
T Consensus 172 YkC~~CG~~w 181 (195)
T PHA02998 172 HACRDCKKHF 181 (195)
T ss_pred EEcCCCCCcc
Confidence 4455555444
No 123
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=74.39 E-value=4.8 Score=29.69 Aligned_cols=11 Identities=18% Similarity=0.507 Sum_probs=7.5
Q ss_pred CcccCCCCCCc
Q psy11352 77 AFYACSSCSHV 87 (107)
Q Consensus 77 k~~~C~~C~~~ 87 (107)
.|..|+.||-.
T Consensus 474 ~p~~Cp~Cgs~ 484 (730)
T COG1198 474 IPQSCPECGSE 484 (730)
T ss_pred CCCCCCCCCCC
Confidence 57778777743
No 124
>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=74.32 E-value=3.5 Score=18.77 Aligned_cols=10 Identities=30% Similarity=0.401 Sum_probs=7.3
Q ss_pred CeeeCCCCcc
Q psy11352 50 LFATCFVCGK 59 (107)
Q Consensus 50 ~~~~C~~C~~ 59 (107)
..|.|..|++
T Consensus 36 ~~~~C~~C~~ 45 (46)
T PF12760_consen 36 GRYRCKACRK 45 (46)
T ss_pred CeEECCCCCC
Confidence 5688888764
No 125
>COG4530 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=73.77 E-value=2 Score=23.71 Aligned_cols=27 Identities=7% Similarity=-0.102 Sum_probs=16.2
Q ss_pred eCCCCcccccchhhHHHHHhhhCCCcccCCCCCCccc
Q psy11352 53 TCFVCGKQLSNQYNLRVHMETHQNAFYACSSCSHVSR 89 (107)
Q Consensus 53 ~C~~C~~~f~~~~~l~~H~~~h~~k~~~C~~C~~~f~ 89 (107)
.|+.||+.|.... ..|..|+.||+.|.
T Consensus 11 idPetg~KFYDLN----------rdPiVsPytG~s~P 37 (129)
T COG4530 11 IDPETGKKFYDLN----------RDPIVSPYTGKSYP 37 (129)
T ss_pred cCccccchhhccC----------CCccccCcccccch
Confidence 5666776664311 14777777777763
No 126
>KOG3408|consensus
Probab=73.12 E-value=2 Score=24.12 Aligned_cols=22 Identities=23% Similarity=0.499 Sum_probs=13.5
Q ss_pred cccCCCCCCcccChHHHHHHHH
Q psy11352 78 FYACSSCSHVSRSRDALRKHVS 99 (107)
Q Consensus 78 ~~~C~~C~~~f~~~~~l~~H~~ 99 (107)
.|.|-+|.+-|.....|..|.+
T Consensus 57 qfyCi~CaRyFi~~~~l~~H~k 78 (129)
T KOG3408|consen 57 QFYCIECARYFIDAKALKTHFK 78 (129)
T ss_pred eeehhhhhhhhcchHHHHHHHh
Confidence 4566666666666666666655
No 127
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=72.78 E-value=2.1 Score=18.94 Aligned_cols=14 Identities=14% Similarity=0.508 Sum_probs=10.6
Q ss_pred cccCCCCCCcccCh
Q psy11352 78 FYACSSCSHVSRSR 91 (107)
Q Consensus 78 ~~~C~~C~~~f~~~ 91 (107)
||.|..|++.|-..
T Consensus 12 ~f~C~~C~~~FC~~ 25 (39)
T smart00154 12 GFKCRHCGNLFCGE 25 (39)
T ss_pred CeECCccCCccccc
Confidence 78888888877543
No 128
>KOG2482|consensus
Probab=72.68 E-value=2.3 Score=28.36 Aligned_cols=23 Identities=22% Similarity=0.583 Sum_probs=21.1
Q ss_pred cccCCCCCCcccChHHHHHHHHc
Q psy11352 78 FYACSSCSHVSRSRDALRKHVSY 100 (107)
Q Consensus 78 ~~~C~~C~~~f~~~~~l~~H~~~ 100 (107)
.++|-.|.+.|..+..|..||+.
T Consensus 195 r~~CLyCekifrdkntLkeHMrk 217 (423)
T KOG2482|consen 195 RLRCLYCEKIFRDKNTLKEHMRK 217 (423)
T ss_pred hheeeeeccccCCcHHHHHHHHh
Confidence 47899999999999999999984
No 129
>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=72.63 E-value=6.3 Score=17.12 Aligned_cols=8 Identities=25% Similarity=0.401 Sum_probs=4.9
Q ss_pred CeeeCCCC
Q psy11352 50 LFATCFVC 57 (107)
Q Consensus 50 ~~~~C~~C 57 (107)
..|.|..|
T Consensus 28 qryrC~~C 35 (36)
T PF03811_consen 28 QRYRCKDC 35 (36)
T ss_pred EeEecCcC
Confidence 55666655
No 130
>KOG2593|consensus
Probab=72.17 E-value=2.8 Score=28.74 Aligned_cols=14 Identities=21% Similarity=0.346 Sum_probs=7.8
Q ss_pred CeeeCCCCcccccc
Q psy11352 50 LFATCFVCGKQLSN 63 (107)
Q Consensus 50 ~~~~C~~C~~~f~~ 63 (107)
..|.|+.|.+.|..
T Consensus 127 ~~Y~Cp~C~kkyt~ 140 (436)
T KOG2593|consen 127 AGYVCPNCQKKYTS 140 (436)
T ss_pred ccccCCccccchhh
Confidence 44556666655544
No 131
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=72.12 E-value=2.7 Score=23.35 Aligned_cols=36 Identities=25% Similarity=0.676 Sum_probs=17.3
Q ss_pred eeCCCCcccccchhhHHHHHhhhCC---CcccCCCCCCccc
Q psy11352 52 ATCFVCGKQLSNQYNLRVHMETHQN---AFYACSSCSHVSR 89 (107)
Q Consensus 52 ~~C~~C~~~f~~~~~l~~H~~~h~~---k~~~C~~C~~~f~ 89 (107)
..|+.||..=. ..++.+.+.-.+ .-|.|..||..|.
T Consensus 73 ~~CpkCg~~ea--~y~~~QtRsaDEp~T~Fy~C~~Cg~~wr 111 (113)
T COG1594 73 EKCPKCGNKEA--YYWQLQTRSADEPETRFYKCTRCGYRWR 111 (113)
T ss_pred ccCCCCCCcee--EEEeeehhccCCCceEEEEecccCCEee
Confidence 45666664321 122223333222 3477777776653
No 132
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=71.87 E-value=3.4 Score=30.42 Aligned_cols=11 Identities=27% Similarity=0.788 Sum_probs=9.3
Q ss_pred CeeeCCCCccc
Q psy11352 50 LFATCFVCGKQ 60 (107)
Q Consensus 50 ~~~~C~~C~~~ 60 (107)
.|..|+.||..
T Consensus 474 ~p~~Cp~Cgs~ 484 (730)
T COG1198 474 IPQSCPECGSE 484 (730)
T ss_pred CCCCCCCCCCC
Confidence 78899999875
No 133
>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=71.84 E-value=1.9 Score=23.33 Aligned_cols=18 Identities=22% Similarity=0.429 Sum_probs=14.4
Q ss_pred hhhCCCcccCCCCCCccc
Q psy11352 72 ETHQNAFYACSSCSHVSR 89 (107)
Q Consensus 72 ~~h~~k~~~C~~C~~~f~ 89 (107)
..+.++|.+|..||..|.
T Consensus 73 ~l~~g~~~rC~eCG~~fk 90 (97)
T cd00924 73 WLEKGKPKRCPECGHVFK 90 (97)
T ss_pred EEeCCCceeCCCCCcEEE
Confidence 345568999999999885
No 134
>KOG4167|consensus
Probab=71.76 E-value=0.52 Score=34.24 Aligned_cols=24 Identities=17% Similarity=0.434 Sum_probs=21.4
Q ss_pred cccCCCCCCcccChHHHHHHHHcc
Q psy11352 78 FYACSSCSHVSRSRDALRKHVSYR 101 (107)
Q Consensus 78 ~~~C~~C~~~f~~~~~l~~H~~~~ 101 (107)
-|-|.+|++.|-.--.+..||++|
T Consensus 792 iFpCreC~kvF~KiKSrNAHMK~H 815 (907)
T KOG4167|consen 792 IFPCRECGKVFFKIKSRNAHMKTH 815 (907)
T ss_pred eeehHHHHHHHHHHhhhhHHHHHH
Confidence 489999999999888999999973
No 135
>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=71.45 E-value=2.7 Score=23.25 Aligned_cols=27 Identities=22% Similarity=0.535 Sum_probs=17.5
Q ss_pred CeeeCCCCcccccchhhHHHHHhhhCCCcccCCCCCCc
Q psy11352 50 LFATCFVCGKQLSNQYNLRVHMETHQNAFYACSSCSHV 87 (107)
Q Consensus 50 ~~~~C~~C~~~f~~~~~l~~H~~~h~~k~~~C~~C~~~ 87 (107)
-...|..||..|..... .+.|+.||..
T Consensus 69 ~~~~C~~Cg~~~~~~~~-----------~~~CP~Cgs~ 95 (113)
T PF01155_consen 69 ARARCRDCGHEFEPDEF-----------DFSCPRCGSP 95 (113)
T ss_dssp -EEEETTTS-EEECHHC-----------CHH-SSSSSS
T ss_pred CcEECCCCCCEEecCCC-----------CCCCcCCcCC
Confidence 45789999998876442 3669999864
No 136
>PRK14873 primosome assembly protein PriA; Provisional
Probab=71.27 E-value=4.8 Score=29.38 Aligned_cols=23 Identities=22% Similarity=0.557 Sum_probs=14.3
Q ss_pred CeeeCCCCcccccchhhHHHHHhhhCCCcccCCCCCCc
Q psy11352 50 LFATCFVCGKQLSNQYNLRVHMETHQNAFYACSSCSHV 87 (107)
Q Consensus 50 ~~~~C~~C~~~f~~~~~l~~H~~~h~~k~~~C~~C~~~ 87 (107)
....|..||... .|+.|+.||..
T Consensus 409 ~~l~Ch~CG~~~---------------~p~~Cp~Cgs~ 431 (665)
T PRK14873 409 GTPRCRWCGRAA---------------PDWRCPRCGSD 431 (665)
T ss_pred CeeECCCCcCCC---------------cCccCCCCcCC
Confidence 456777777421 36678888753
No 137
>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=71.21 E-value=7.1 Score=21.33 Aligned_cols=8 Identities=25% Similarity=0.513 Sum_probs=6.6
Q ss_pred ccccCCCC
Q psy11352 11 HFLISDHC 18 (107)
Q Consensus 11 ~~~~C~~C 18 (107)
||-.|+.|
T Consensus 1 ~p~~CpYC 8 (102)
T PF11672_consen 1 KPIICPYC 8 (102)
T ss_pred CCcccCCC
Confidence 57789999
No 138
>PLN02294 cytochrome c oxidase subunit Vb
Probab=71.06 E-value=1.5 Score=26.19 Aligned_cols=21 Identities=10% Similarity=0.321 Sum_probs=15.7
Q ss_pred HhhhCCCcccCCCCCCcccCh
Q psy11352 71 METHQNAFYACSSCSHVSRSR 91 (107)
Q Consensus 71 ~~~h~~k~~~C~~C~~~f~~~ 91 (107)
+..+.|+|..|++||..|.-.
T Consensus 134 f~L~kGkp~RCpeCG~~fkL~ 154 (174)
T PLN02294 134 FWLEKGKSFECPVCTQYFELE 154 (174)
T ss_pred EEecCCCceeCCCCCCEEEEE
Confidence 344556899999999988643
No 139
>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=70.79 E-value=1.8 Score=20.06 Aligned_cols=12 Identities=33% Similarity=0.639 Sum_probs=5.8
Q ss_pred eeCCCCcccccc
Q psy11352 52 ATCFVCGKQLSN 63 (107)
Q Consensus 52 ~~C~~C~~~f~~ 63 (107)
|.|..|+..|.-
T Consensus 2 y~C~~CgyvYd~ 13 (47)
T PF00301_consen 2 YQCPVCGYVYDP 13 (47)
T ss_dssp EEETTTSBEEET
T ss_pred cCCCCCCEEEcC
Confidence 445555554433
No 140
>KOG2785|consensus
Probab=70.04 E-value=4.7 Score=27.22 Aligned_cols=24 Identities=21% Similarity=0.401 Sum_probs=19.5
Q ss_pred CcccCCCCCCcccChHHHHHHHHc
Q psy11352 77 AFYACSSCSHVSRSRDALRKHVSY 100 (107)
Q Consensus 77 k~~~C~~C~~~f~~~~~l~~H~~~ 100 (107)
-++.|..|.+.|....+...|+..
T Consensus 67 ~~~~c~~c~k~~~s~~a~~~hl~S 90 (390)
T KOG2785|consen 67 SVVYCEACNKSFASPKAHENHLKS 90 (390)
T ss_pred cceehHHhhccccChhhHHHHHHH
Confidence 368899999999988888888763
No 141
>PRK05978 hypothetical protein; Provisional
Probab=69.43 E-value=4 Score=23.88 Aligned_cols=10 Identities=30% Similarity=1.089 Sum_probs=5.3
Q ss_pred eCCCCccccc
Q psy11352 53 TCFVCGKQLS 62 (107)
Q Consensus 53 ~C~~C~~~f~ 62 (107)
.|+.||..|.
T Consensus 54 ~C~~CG~~~~ 63 (148)
T PRK05978 54 HCAACGEDFT 63 (148)
T ss_pred CccccCCccc
Confidence 4555555443
No 142
>KOG2593|consensus
Probab=69.21 E-value=2.1 Score=29.24 Aligned_cols=39 Identities=10% Similarity=0.132 Sum_probs=27.1
Q ss_pred CCcccccCCCCCCCCCccCCCCCCCCCCCCCCCCCCCCCCCCCeeeCCCCccc
Q psy11352 8 STLHFLISDHCLTSPLSSSIPGSSKTKASGSGTTGGSSNHSKLFATCFVCGKQ 60 (107)
Q Consensus 8 ~~~~~~~C~~C~~~~~~~~~~~~l~~h~~~~~~~~~~~~~~~~~~~C~~C~~~ 60 (107)
....-|.|+.| .+.|+....+..- ..-. -.|.|..|+-.
T Consensus 124 t~~~~Y~Cp~C---~kkyt~Lea~~L~----~~~~-------~~F~C~~C~ge 162 (436)
T KOG2593|consen 124 TNVAGYVCPNC---QKKYTSLEALQLL----DNET-------GEFHCENCGGE 162 (436)
T ss_pred cccccccCCcc---ccchhhhHHHHhh----cccC-------ceEEEecCCCc
Confidence 34678999999 9998887665432 1122 34999999864
No 143
>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=69.05 E-value=2.9 Score=18.48 Aligned_cols=11 Identities=27% Similarity=0.597 Sum_probs=5.8
Q ss_pred CeeeCCCCccc
Q psy11352 50 LFATCFVCGKQ 60 (107)
Q Consensus 50 ~~~~C~~C~~~ 60 (107)
+.+.|..|+..
T Consensus 23 ~~w~C~~C~~~ 33 (40)
T PF04810_consen 23 KTWICNFCGTK 33 (40)
T ss_dssp TEEEETTT--E
T ss_pred CEEECcCCCCc
Confidence 55777777653
No 144
>PF13878 zf-C2H2_3: zinc-finger of acetyl-transferase ESCO
Probab=68.78 E-value=5.2 Score=17.84 Aligned_cols=24 Identities=29% Similarity=0.531 Sum_probs=14.9
Q ss_pred eeCCCCcccccch--hhHHHHHhhhC
Q psy11352 52 ATCFVCGKQLSNQ--YNLRVHMETHQ 75 (107)
Q Consensus 52 ~~C~~C~~~f~~~--~~l~~H~~~h~ 75 (107)
-.|+.||..|... ..-..|.+.|.
T Consensus 14 ~~C~~CgM~Y~~~~~eD~~~H~~yH~ 39 (41)
T PF13878_consen 14 TTCPTCGMLYSPGSPEDEKLHKKYHD 39 (41)
T ss_pred cCCCCCCCEECCCCHHHHHHHHHHHh
Confidence 4788888776543 44555665553
No 145
>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=68.76 E-value=8.3 Score=25.39 Aligned_cols=8 Identities=13% Similarity=0.168 Sum_probs=5.9
Q ss_pred cccCCCCC
Q psy11352 12 FLISDHCL 19 (107)
Q Consensus 12 ~~~C~~C~ 19 (107)
.-.||.||
T Consensus 184 ~~~CPvCG 191 (305)
T TIGR01562 184 RTLCPACG 191 (305)
T ss_pred CCcCCCCC
Confidence 44899994
No 146
>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=68.26 E-value=16 Score=21.69 Aligned_cols=56 Identities=25% Similarity=0.411 Sum_probs=36.9
Q ss_pred CeeeCCCCcccccchhhHHHHHhhhCC-CcccCCC--CCCcccChHHHHHHHHccCCCCCC
Q psy11352 50 LFATCFVCGKQLSNQYNLRVHMETHQN-AFYACSS--CSHVSRSRDALRKHVSYRHPHISP 107 (107)
Q Consensus 50 ~~~~C~~C~~~f~~~~~l~~H~~~h~~-k~~~C~~--C~~~f~~~~~l~~H~~~~H~~ekp 107 (107)
....|+.|-..-.-+..+.. .+.+.. |+-.|.. |... .....|.+|.+..|+..+|
T Consensus 79 ~~L~CPLCRG~V~GWtvve~-AR~~LN~K~RsC~~e~C~F~-GtY~eLrKHar~~HP~~rP 137 (162)
T PF07800_consen 79 PELACPLCRGEVKGWTVVEP-ARRFLNAKKRSCSQESCSFS-GTYSELRKHARSEHPSARP 137 (162)
T ss_pred ccccCccccCceeceEEchH-HHHHhccCCccCcccccccc-cCHHHHHHHHHhhCCCCCC
Confidence 45789998654433333333 455665 7777754 6433 3566899999999998877
No 147
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=68.18 E-value=6 Score=17.48 Aligned_cols=21 Identities=19% Similarity=0.254 Sum_probs=16.0
Q ss_pred CeeeCCCCcccccchhhHHHH
Q psy11352 50 LFATCFVCGKQLSNQYNLRVH 70 (107)
Q Consensus 50 ~~~~C~~C~~~f~~~~~l~~H 70 (107)
....|+.|+-.|.....|.+-
T Consensus 18 ~id~C~~C~G~W~d~~el~~~ 38 (41)
T PF13453_consen 18 EIDVCPSCGGIWFDAGELEKL 38 (41)
T ss_pred EEEECCCCCeEEccHHHHHHH
Confidence 557899999888887776543
No 148
>KOG1842|consensus
Probab=67.95 E-value=3 Score=28.77 Aligned_cols=22 Identities=27% Similarity=0.383 Sum_probs=11.4
Q ss_pred eeeCCCCcccccchhhHHHHHh
Q psy11352 51 FATCFVCGKQLSNQYNLRVHME 72 (107)
Q Consensus 51 ~~~C~~C~~~f~~~~~l~~H~~ 72 (107)
-|.|++|...|.+-..|..|..
T Consensus 15 gflCPiC~~dl~~~~~L~~H~d 36 (505)
T KOG1842|consen 15 GFLCPICLLDLPNLSALNDHLD 36 (505)
T ss_pred cccCchHhhhhhhHHHHHHHHh
Confidence 3555555555555555555544
No 149
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=67.72 E-value=4.4 Score=22.46 Aligned_cols=26 Identities=19% Similarity=0.409 Sum_probs=18.0
Q ss_pred CeeeCCCCcccccchhhHHHHHhhhCCCcccCCCCCC
Q psy11352 50 LFATCFVCGKQLSNQYNLRVHMETHQNAFYACSSCSH 86 (107)
Q Consensus 50 ~~~~C~~C~~~f~~~~~l~~H~~~h~~k~~~C~~C~~ 86 (107)
-...|..||..|.... ..+.|+.||.
T Consensus 69 ~~~~C~~Cg~~~~~~~-----------~~~~CP~Cgs 94 (113)
T PRK12380 69 AQAWCWDCSQVVEIHQ-----------HDAQCPHCHG 94 (113)
T ss_pred cEEEcccCCCEEecCC-----------cCccCcCCCC
Confidence 4578999997775532 2456999984
No 150
>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=66.90 E-value=2.5 Score=20.86 Aligned_cols=9 Identities=44% Similarity=1.534 Sum_probs=2.5
Q ss_pred eCCCCcccc
Q psy11352 53 TCFVCGKQL 61 (107)
Q Consensus 53 ~C~~C~~~f 61 (107)
.|..|++.|
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 355555555
No 151
>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=66.15 E-value=4.9 Score=18.89 Aligned_cols=10 Identities=30% Similarity=0.863 Sum_probs=4.7
Q ss_pred eeCCCCcccc
Q psy11352 52 ATCFVCGKQL 61 (107)
Q Consensus 52 ~~C~~C~~~f 61 (107)
+.|..||+.|
T Consensus 19 ~~Cr~Cg~~~ 28 (57)
T cd00065 19 HHCRNCGRIF 28 (57)
T ss_pred cccCcCcCCc
Confidence 4444444443
No 152
>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=65.85 E-value=1.6 Score=23.18 Aligned_cols=11 Identities=18% Similarity=0.739 Sum_probs=6.2
Q ss_pred cccCCCCCCcc
Q psy11352 78 FYACSSCSHVS 88 (107)
Q Consensus 78 ~~~C~~C~~~f 88 (107)
-+.|..|++.|
T Consensus 53 IW~C~~C~~~~ 63 (90)
T PF01780_consen 53 IWKCKKCGKKF 63 (90)
T ss_dssp EEEETTTTEEE
T ss_pred EeecCCCCCEE
Confidence 35666666554
No 153
>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=65.76 E-value=5.1 Score=22.25 Aligned_cols=26 Identities=23% Similarity=0.708 Sum_probs=18.4
Q ss_pred CeeeCCCCcccccchhhHHHHHhhhCCCcccCCCCCC
Q psy11352 50 LFATCFVCGKQLSNQYNLRVHMETHQNAFYACSSCSH 86 (107)
Q Consensus 50 ~~~~C~~C~~~f~~~~~l~~H~~~h~~k~~~C~~C~~ 86 (107)
-...|..|+..|..... .+.|+.||.
T Consensus 69 ~~~~C~~Cg~~~~~~~~-----------~~~CP~Cgs 94 (115)
T TIGR00100 69 VECECEDCSEEVSPEID-----------LYRCPKCHG 94 (115)
T ss_pred cEEEcccCCCEEecCCc-----------CccCcCCcC
Confidence 45789999987765321 467999985
No 154
>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=65.75 E-value=4.9 Score=28.01 Aligned_cols=28 Identities=25% Similarity=0.600 Sum_probs=20.1
Q ss_pred CcccCCCCCCcccChHHHHHHHHccCCC
Q psy11352 77 AFYACSSCSHVSRSRDALRKHVSYRHPH 104 (107)
Q Consensus 77 k~~~C~~C~~~f~~~~~l~~H~~~~H~~ 104 (107)
+-+.|+.|.+.|.....+..|+...|.+
T Consensus 56 rFWiCp~CskkF~d~~~~~~H~~~eH~~ 83 (466)
T PF04780_consen 56 RFWICPRCSKKFSDAESCLSHMEQEHPA 83 (466)
T ss_pred eEeeCCcccceeCCHHHHHHHHHHhhhh
Confidence 4567777887787777777777755654
No 155
>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=65.73 E-value=2 Score=19.33 Aligned_cols=15 Identities=13% Similarity=0.406 Sum_probs=8.2
Q ss_pred CcccCCCCCCcccCh
Q psy11352 77 AFYACSSCSHVSRSR 91 (107)
Q Consensus 77 k~~~C~~C~~~f~~~ 91 (107)
-|+.|+.|++.|-..
T Consensus 12 ~~~~C~~C~~~FC~~ 26 (43)
T PF01428_consen 12 LPFKCKHCGKSFCLK 26 (43)
T ss_dssp SHEE-TTTS-EE-TT
T ss_pred CCeECCCCCcccCcc
Confidence 377888888777543
No 156
>PRK12496 hypothetical protein; Provisional
Probab=64.98 E-value=6.1 Score=23.45 Aligned_cols=27 Identities=22% Similarity=0.474 Sum_probs=17.8
Q ss_pred eeeCCCCcccccchhhHHHHHhhhCCCcccCCCCCCcc
Q psy11352 51 FATCFVCGKQLSNQYNLRVHMETHQNAFYACSSCSHVS 88 (107)
Q Consensus 51 ~~~C~~C~~~f~~~~~l~~H~~~h~~k~~~C~~C~~~f 88 (107)
.+.|..|++.|.... ..-.|+.||...
T Consensus 127 ~~~C~gC~~~~~~~~-----------~~~~C~~CG~~~ 153 (164)
T PRK12496 127 RKVCKGCKKKYPEDY-----------PDDVCEICGSPV 153 (164)
T ss_pred eEECCCCCccccCCC-----------CCCcCCCCCChh
Confidence 477999998885421 123589998653
No 157
>PF09963 DUF2197: Uncharacterized protein conserved in bacteria (DUF2197); InterPro: IPR019241 This family represents various hypothetical bacterial proteins with no known function.
Probab=64.56 E-value=3.3 Score=20.01 Aligned_cols=36 Identities=17% Similarity=0.421 Sum_probs=18.8
Q ss_pred eeCCCCcccccchhhHHHHHhhhC-C-CcccCCCCCCc
Q psy11352 52 ATCFVCGKQLSNQYNLRVHMETHQ-N-AFYACSSCSHV 87 (107)
Q Consensus 52 ~~C~~C~~~f~~~~~l~~H~~~h~-~-k~~~C~~C~~~ 87 (107)
-.|..|++.+.-...-..-.+.-. . ..|.|+.|.-.
T Consensus 3 vkC~lCdk~~~Id~~~~~aKrLrnrPi~tYmC~eC~~R 40 (56)
T PF09963_consen 3 VKCILCDKKEEIDEDTPEAKRLRNRPIHTYMCDECKER 40 (56)
T ss_pred eEEEecCCEEEeccCCHHHHHhhcCCCcceeChhHHHH
Confidence 357777776554433222222222 2 46888888543
No 158
>COG3364 Zn-ribbon containing protein [General function prediction only]
Probab=64.23 E-value=4.4 Score=22.09 Aligned_cols=14 Identities=21% Similarity=0.577 Sum_probs=9.4
Q ss_pred eeeCCCCcccccch
Q psy11352 51 FATCFVCGKQLSNQ 64 (107)
Q Consensus 51 ~~~C~~C~~~f~~~ 64 (107)
++.|..||..|..-
T Consensus 2 pH~CtrCG~vf~~g 15 (112)
T COG3364 2 PHQCTRCGEVFDDG 15 (112)
T ss_pred Cceecccccccccc
Confidence 46677777777663
No 159
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=63.14 E-value=5.5 Score=21.23 Aligned_cols=11 Identities=18% Similarity=0.839 Sum_probs=5.4
Q ss_pred cccCCCCCCcc
Q psy11352 78 FYACSSCSHVS 88 (107)
Q Consensus 78 ~~~C~~C~~~f 88 (107)
.+.|..|++.|
T Consensus 54 IW~C~~C~~~~ 64 (90)
T PTZ00255 54 IWRCKGCKKTV 64 (90)
T ss_pred EEEcCCCCCEE
Confidence 44555555444
No 160
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=61.83 E-value=6.4 Score=21.97 Aligned_cols=27 Identities=15% Similarity=0.413 Sum_probs=17.3
Q ss_pred CeeeCCCCcccccchhhHHHHHhhhCCCcccCCCCCC
Q psy11352 50 LFATCFVCGKQLSNQYNLRVHMETHQNAFYACSSCSH 86 (107)
Q Consensus 50 ~~~~C~~C~~~f~~~~~l~~H~~~h~~k~~~C~~C~~ 86 (107)
-.+.|..||..|..... .-+.|+.||.
T Consensus 70 ~~~~C~~Cg~~~~~~~~----------~~~~CP~Cgs 96 (117)
T PRK00564 70 VELECKDCSHVFKPNAL----------DYGVCEKCHS 96 (117)
T ss_pred CEEEhhhCCCccccCCc----------cCCcCcCCCC
Confidence 45789999977654321 1224888885
No 161
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=61.61 E-value=14 Score=24.49 Aligned_cols=9 Identities=11% Similarity=0.072 Sum_probs=6.7
Q ss_pred ccccCCCCC
Q psy11352 11 HFLISDHCL 19 (107)
Q Consensus 11 ~~~~C~~C~ 19 (107)
..-.||.||
T Consensus 186 ~~~~CPvCG 194 (309)
T PRK03564 186 QRQFCPVCG 194 (309)
T ss_pred CCCCCCCCC
Confidence 456899994
No 162
>COG4957 Predicted transcriptional regulator [Transcription]
Probab=60.38 E-value=9 Score=22.08 Aligned_cols=26 Identities=27% Similarity=0.511 Sum_probs=20.3
Q ss_pred CeeeCCCCcccccchhhHHHHHhhhCC-Cc
Q psy11352 50 LFATCFVCGKQLSNQYNLRVHMETHQN-AF 78 (107)
Q Consensus 50 ~~~~C~~C~~~f~~~~~l~~H~~~h~~-k~ 78 (107)
..-.|-++|+.|. +|++|+.+|.+ .|
T Consensus 75 D~IicLEDGkkfK---SLKRHL~t~~gmTP 101 (148)
T COG4957 75 DYIICLEDGKKFK---SLKRHLTTHYGLTP 101 (148)
T ss_pred CeEEEeccCcchH---HHHHHHhcccCCCH
Confidence 3456999999985 58999999876 44
No 163
>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 PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=58.61 E-value=8.2 Score=21.42 Aligned_cols=27 Identities=15% Similarity=0.327 Sum_probs=17.7
Q ss_pred CeeeCCCCcccccchhhHHHHHhhhCCCcccCCCCCC
Q psy11352 50 LFATCFVCGKQLSNQYNLRVHMETHQNAFYACSSCSH 86 (107)
Q Consensus 50 ~~~~C~~C~~~f~~~~~l~~H~~~h~~k~~~C~~C~~ 86 (107)
-...|..|+..|..... ..+.|+.||.
T Consensus 69 ~~~~C~~Cg~~~~~~~~----------~~~~CP~Cgs 95 (114)
T PRK03681 69 AECWCETCQQYVTLLTQ----------RVRRCPQCHG 95 (114)
T ss_pred cEEEcccCCCeeecCCc----------cCCcCcCcCC
Confidence 45789999976654211 1256999984
No 165
>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=58.53 E-value=5.8 Score=21.87 Aligned_cols=14 Identities=14% Similarity=0.259 Sum_probs=8.2
Q ss_pred eeeCCCCcccccch
Q psy11352 51 FATCFVCGKQLSNQ 64 (107)
Q Consensus 51 ~~~C~~C~~~f~~~ 64 (107)
.|.|+.|+..+...
T Consensus 19 ~~iCpeC~~EW~~~ 32 (109)
T TIGR00686 19 QLICPSCLYEWNEN 32 (109)
T ss_pred eeECcccccccccc
Confidence 46666666655443
No 166
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=58.19 E-value=18 Score=16.53 Aligned_cols=15 Identities=20% Similarity=0.293 Sum_probs=10.8
Q ss_pred CeeeCCCCcccccch
Q psy11352 50 LFATCFVCGKQLSNQ 64 (107)
Q Consensus 50 ~~~~C~~C~~~f~~~ 64 (107)
..+.|+.||..+...
T Consensus 19 ~~~vC~~Cg~~~~~~ 33 (52)
T smart00661 19 RRFVCRKCGYEEPIE 33 (52)
T ss_pred CEEECCcCCCeEECC
Confidence 368899998776554
No 167
>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=57.95 E-value=6.1 Score=21.11 Aligned_cols=11 Identities=18% Similarity=0.718 Sum_probs=5.6
Q ss_pred cccCCCCCCcc
Q psy11352 78 FYACSSCSHVS 88 (107)
Q Consensus 78 ~~~C~~C~~~f 88 (107)
.+.|..|++.|
T Consensus 53 IW~C~~C~~~~ 63 (91)
T TIGR00280 53 IWTCRKCGAKF 63 (91)
T ss_pred EEEcCCCCCEE
Confidence 45555555544
No 168
>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=57.22 E-value=7.4 Score=20.97 Aligned_cols=37 Identities=24% Similarity=0.547 Sum_probs=19.5
Q ss_pred eeeCCCCcccccchhhHHHHHhhhCC---CcccCCCCCCccc
Q psy11352 51 FATCFVCGKQLSNQYNLRVHMETHQN---AFYACSSCSHVSR 89 (107)
Q Consensus 51 ~~~C~~C~~~f~~~~~l~~H~~~h~~---k~~~C~~C~~~f~ 89 (107)
...|+.||..-.. .++..++.-.+ .-|.|..|+..+.
T Consensus 62 ~~~Cp~Cg~~~a~--f~~~Q~RsadE~~T~fy~C~~C~~~w~ 101 (104)
T TIGR01384 62 RVECPKCGHKEAY--YWLLQTRRADEPETRFYKCTKCGYVWR 101 (104)
T ss_pred cCCCCCCCCCeeE--EEEeccCCCCCCcEEEEEeCCCCCeeE
Confidence 3578888754221 22222333222 3588888887653
No 169
>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=56.95 E-value=4.3 Score=19.22 Aligned_cols=26 Identities=15% Similarity=0.304 Sum_probs=14.3
Q ss_pred CeeeCCCCcccccchhhHHHHHhhhC
Q psy11352 50 LFATCFVCGKQLSNQYNLRVHMETHQ 75 (107)
Q Consensus 50 ~~~~C~~C~~~f~~~~~l~~H~~~h~ 75 (107)
..|.|+.|...|-..-.+-.|...|.
T Consensus 20 ~~y~C~~C~~~FC~dCD~fiHE~LH~ 45 (51)
T PF07975_consen 20 SRYRCPKCKNHFCIDCDVFIHETLHN 45 (51)
T ss_dssp EEE--TTTT--B-HHHHHTTTTTS-S
T ss_pred CeEECCCCCCccccCcChhhhccccC
Confidence 56999999998887776666655443
No 170
>KOG0717|consensus
Probab=56.46 E-value=6.4 Score=27.43 Aligned_cols=22 Identities=23% Similarity=0.496 Sum_probs=17.0
Q ss_pred ccCCCCCCcccChHHHHHHHHc
Q psy11352 79 YACSSCSHVSRSRDALRKHVSY 100 (107)
Q Consensus 79 ~~C~~C~~~f~~~~~l~~H~~~ 100 (107)
+.|.+|.+.|.+..+|..|..+
T Consensus 293 lyC~vCnKsFKseKq~kNHEnS 314 (508)
T KOG0717|consen 293 LYCVVCNKSFKSEKQLKNHENS 314 (508)
T ss_pred eEEeeccccccchHHHHhhHHH
Confidence 6788888888888888777653
No 171
>COG3091 SprT Zn-dependent metalloprotease, SprT family [General function prediction only]
Probab=56.24 E-value=7.6 Score=22.84 Aligned_cols=34 Identities=21% Similarity=0.529 Sum_probs=21.3
Q ss_pred CeeeCCCCcccccchhhHHHHHhhhCCCcccCCCCCCc
Q psy11352 50 LFATCFVCGKQLSNQYNLRVHMETHQNAFYACSSCSHV 87 (107)
Q Consensus 50 ~~~~C~~C~~~f~~~~~l~~H~~~h~~k~~~C~~C~~~ 87 (107)
-+|.|. |+..|.+ .++|-.+-.|..|.|..|+-.
T Consensus 116 ~~Y~C~-C~q~~l~---~RRhn~~~~g~~YrC~~C~gk 149 (156)
T COG3091 116 YPYRCQ-CQQHYLR---IRRHNTVRRGEVYRCGKCGGK 149 (156)
T ss_pred eeEEee-cCCccch---hhhcccccccceEEeccCCce
Confidence 578888 8887654 233433333456888888743
No 172
>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=56.12 E-value=4.2 Score=19.17 Aligned_cols=12 Identities=17% Similarity=0.534 Sum_probs=6.4
Q ss_pred cCCCCCCcccCh
Q psy11352 80 ACSSCSHVSRSR 91 (107)
Q Consensus 80 ~C~~C~~~f~~~ 91 (107)
.|++|++.|...
T Consensus 22 ~CPlC~r~l~~e 33 (54)
T PF04423_consen 22 CCPLCGRPLDEE 33 (54)
T ss_dssp E-TTT--EE-HH
T ss_pred cCCCCCCCCCHH
Confidence 899999988644
No 173
>PRK10220 hypothetical protein; Provisional
Probab=55.93 E-value=8.3 Score=21.32 Aligned_cols=15 Identities=13% Similarity=0.372 Sum_probs=9.0
Q ss_pred CeeeCCCCcccccch
Q psy11352 50 LFATCFVCGKQLSNQ 64 (107)
Q Consensus 50 ~~~~C~~C~~~f~~~ 64 (107)
..|.|+.|+..|...
T Consensus 19 ~~~vCpeC~hEW~~~ 33 (111)
T PRK10220 19 GMYICPECAHEWNDA 33 (111)
T ss_pred CeEECCcccCcCCcc
Confidence 346777776665543
No 174
>PF07503 zf-HYPF: HypF finger; InterPro: IPR011125 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Proteins of the HypF family are involved in the maturation and regulation of hydrogenase []. In the N terminus they appear to have two zinc finger domains that are similar to those found in the DnaJ chaperone []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3TTD_A 3TSQ_A 3TTC_A 3TSP_A 3TTF_A 3TSU_A.
Probab=55.49 E-value=1.5 Score=18.94 Aligned_cols=11 Identities=27% Similarity=0.854 Sum_probs=4.6
Q ss_pred cccCCCCCCcc
Q psy11352 78 FYACSSCSHVS 88 (107)
Q Consensus 78 ~~~C~~C~~~f 88 (107)
+..|..||-.+
T Consensus 21 ~isC~~CGPr~ 31 (35)
T PF07503_consen 21 FISCTNCGPRY 31 (35)
T ss_dssp T--BTTCC-SC
T ss_pred CccCCCCCCCE
Confidence 45566666544
No 175
>KOG2482|consensus
Probab=55.48 E-value=7.3 Score=26.12 Aligned_cols=23 Identities=26% Similarity=0.580 Sum_probs=21.1
Q ss_pred eeeCCCCcccccchhhHHHHHhh
Q psy11352 51 FATCFVCGKQLSNQYNLRVHMET 73 (107)
Q Consensus 51 ~~~C~~C~~~f~~~~~l~~H~~~ 73 (107)
.+.|-.|.+.|..+..|..||+.
T Consensus 195 r~~CLyCekifrdkntLkeHMrk 217 (423)
T KOG2482|consen 195 RLRCLYCEKIFRDKNTLKEHMRK 217 (423)
T ss_pred hheeeeeccccCCcHHHHHHHHh
Confidence 47899999999999999999985
No 176
>TIGR01385 TFSII transcription elongation factor S-II. This model represents eukaryotic transcription elongation factor S-II. This protein allows stalled RNA transcription complexes to perform a cleavage of the nascent RNA and restart at the newly generated 3-prime end.
Probab=55.01 E-value=10 Score=24.92 Aligned_cols=10 Identities=40% Similarity=0.933 Sum_probs=5.0
Q ss_pred eeCCCCcccc
Q psy11352 52 ATCFVCGKQL 61 (107)
Q Consensus 52 ~~C~~C~~~f 61 (107)
|.|..||..|
T Consensus 287 ~~C~~Cg~~w 296 (299)
T TIGR01385 287 VTCEECGNRW 296 (299)
T ss_pred EEcCCCCCee
Confidence 4555555443
No 177
>KOG2636|consensus
Probab=54.81 E-value=9.1 Score=26.57 Aligned_cols=23 Identities=17% Similarity=0.439 Sum_probs=18.9
Q ss_pred CeeeCCCCc-ccccchhhHHHHHh
Q psy11352 50 LFATCFVCG-KQLSNQYNLRVHME 72 (107)
Q Consensus 50 ~~~~C~~C~-~~f~~~~~l~~H~~ 72 (107)
..|.|.+|| +++.-...+.+|-.
T Consensus 400 ~ey~CEICGNy~Y~GrkaF~RHF~ 423 (497)
T KOG2636|consen 400 IEYNCEICGNYVYKGRKAFDRHFN 423 (497)
T ss_pred cccceeeccCccccCcHHHHHHhH
Confidence 679999999 78888888888853
No 178
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=54.59 E-value=24 Score=28.09 Aligned_cols=28 Identities=18% Similarity=0.422 Sum_probs=16.5
Q ss_pred CeeeCCCCcccccchhhHHHHHhhhCCCcccCCCCCCc
Q psy11352 50 LFATCFVCGKQLSNQYNLRVHMETHQNAFYACSSCSHV 87 (107)
Q Consensus 50 ~~~~C~~C~~~f~~~~~l~~H~~~h~~k~~~C~~C~~~ 87 (107)
..+.|+.||....... ++ ...|+.|+..
T Consensus 691 ~vy~CPsCGaev~~de---------s~-a~~CP~CGtp 718 (1337)
T PRK14714 691 PVYVCPDCGAEVPPDE---------SG-RVECPRCDVE 718 (1337)
T ss_pred CceeCccCCCccCCCc---------cc-cccCCCCCCc
Confidence 3578888887543211 11 3468888843
No 179
>KOG0978|consensus
Probab=54.54 E-value=8.5 Score=28.28 Aligned_cols=46 Identities=20% Similarity=0.365 Sum_probs=26.0
Q ss_pred eeeCCCCcccccchhhH-HHHH------hhhCC-CcccCCCCCCcccChHHHHH
Q psy11352 51 FATCFVCGKQLSNQYNL-RVHM------ETHQN-AFYACSSCSHVSRSRDALRK 96 (107)
Q Consensus 51 ~~~C~~C~~~f~~~~~l-~~H~------~~h~~-k~~~C~~C~~~f~~~~~l~~ 96 (107)
..+|+.|...+...... --|. +.-.+ +.-+||.|+..|...+-+..
T Consensus 643 ~LkCs~Cn~R~Kd~vI~kC~H~FC~~Cvq~r~etRqRKCP~Cn~aFganDv~~I 696 (698)
T KOG0978|consen 643 LLKCSVCNTRWKDAVITKCGHVFCEECVQTRYETRQRKCPKCNAAFGANDVHRI 696 (698)
T ss_pred ceeCCCccCchhhHHHHhcchHHHHHHHHHHHHHhcCCCCCCCCCCCccccccc
Confidence 46788887544332111 1121 11123 56689999999987765543
No 180
>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=54.38 E-value=12 Score=26.32 Aligned_cols=9 Identities=33% Similarity=0.800 Sum_probs=4.5
Q ss_pred eeeCCCCcc
Q psy11352 51 FATCFVCGK 59 (107)
Q Consensus 51 ~~~C~~C~~ 59 (107)
...|..||.
T Consensus 240 ~l~Ch~Cg~ 248 (505)
T TIGR00595 240 KLRCHYCGY 248 (505)
T ss_pred eEEcCCCcC
Confidence 345555553
No 181
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=53.20 E-value=14 Score=17.79 Aligned_cols=12 Identities=25% Similarity=0.434 Sum_probs=7.9
Q ss_pred CeeeCCCCcccc
Q psy11352 50 LFATCFVCGKQL 61 (107)
Q Consensus 50 ~~~~C~~C~~~f 61 (107)
..|.|+.||..+
T Consensus 13 v~~~Cp~cGipt 24 (55)
T PF13824_consen 13 VNFECPDCGIPT 24 (55)
T ss_pred cCCcCCCCCCcC
Confidence 557777777644
No 182
>PF15135 UPF0515: Uncharacterised protein UPF0515
Probab=53.14 E-value=16 Score=23.43 Aligned_cols=14 Identities=14% Similarity=0.294 Sum_probs=10.2
Q ss_pred CeeeCCCCcccccc
Q psy11352 50 LFATCFVCGKQLSN 63 (107)
Q Consensus 50 ~~~~C~~C~~~f~~ 63 (107)
-.|.|..|+..|.-
T Consensus 154 aef~C~~C~h~F~G 167 (278)
T PF15135_consen 154 AEFHCPKCRHNFRG 167 (278)
T ss_pred eeeecccccccchh
Confidence 35788888887763
No 183
>COG1773 Rubredoxin [Energy production and conversion]
Probab=53.01 E-value=7.4 Score=18.73 Aligned_cols=36 Identities=17% Similarity=0.239 Sum_probs=22.0
Q ss_pred CeeeCCCCcccccchhhHHHHHhhhCC-------CcccCCCCCC
Q psy11352 50 LFATCFVCGKQLSNQYNLRVHMETHQN-------AFYACSSCSH 86 (107)
Q Consensus 50 ~~~~C~~C~~~f~~~~~l~~H~~~h~~-------k~~~C~~C~~ 86 (107)
+.|.|..||..|.-..--...- +--| ..+.|+.||-
T Consensus 2 ~~~~C~~CG~vYd~e~Gdp~~g-i~pgT~fedlPd~w~CP~Cg~ 44 (55)
T COG1773 2 KRWRCSVCGYVYDPEKGDPRCG-IAPGTPFEDLPDDWVCPECGV 44 (55)
T ss_pred CceEecCCceEeccccCCccCC-CCCCCchhhCCCccCCCCCCC
Confidence 3589999999887654332221 1111 1478999984
No 184
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=52.53 E-value=17 Score=17.00 Aligned_cols=9 Identities=33% Similarity=0.619 Sum_probs=4.4
Q ss_pred eeCCCCccc
Q psy11352 52 ATCFVCGKQ 60 (107)
Q Consensus 52 ~~C~~C~~~ 60 (107)
+.|..||.+
T Consensus 38 ~~C~~Cgyt 46 (50)
T PRK00432 38 WHCGKCGYT 46 (50)
T ss_pred EECCCcCCE
Confidence 445555543
No 185
>PF14311 DUF4379: Domain of unknown function (DUF4379)
Probab=51.50 E-value=21 Score=16.74 Aligned_cols=16 Identities=19% Similarity=0.553 Sum_probs=10.7
Q ss_pred CeeeCCCCcccccchh
Q psy11352 50 LFATCFVCGKQLSNQY 65 (107)
Q Consensus 50 ~~~~C~~C~~~f~~~~ 65 (107)
..+.|+.||-.|...-
T Consensus 27 v~W~C~~Cgh~w~~~v 42 (55)
T PF14311_consen 27 VWWKCPKCGHEWKASV 42 (55)
T ss_pred EEEECCCCCCeeEccH
Confidence 4577888877665543
No 186
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=51.05 E-value=8.7 Score=20.49 Aligned_cols=11 Identities=18% Similarity=0.700 Sum_probs=6.0
Q ss_pred cccCCCCCCcc
Q psy11352 78 FYACSSCSHVS 88 (107)
Q Consensus 78 ~~~C~~C~~~f 88 (107)
.+.|..|++.|
T Consensus 54 IW~C~~C~~~~ 64 (90)
T PRK03976 54 IWECRKCGAKF 64 (90)
T ss_pred EEEcCCCCCEE
Confidence 45555555544
No 187
>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=50.94 E-value=7.6 Score=19.28 Aligned_cols=6 Identities=17% Similarity=0.523 Sum_probs=4.9
Q ss_pred ccCCCC
Q psy11352 13 LISDHC 18 (107)
Q Consensus 13 ~~C~~C 18 (107)
|.|+.|
T Consensus 1 y~C~KC 6 (64)
T PF09855_consen 1 YKCPKC 6 (64)
T ss_pred CCCCCC
Confidence 678888
No 188
>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=50.83 E-value=12 Score=18.44 Aligned_cols=13 Identities=15% Similarity=0.672 Sum_probs=7.7
Q ss_pred CcccCCCCCCccc
Q psy11352 77 AFYACSSCSHVSR 89 (107)
Q Consensus 77 k~~~C~~C~~~f~ 89 (107)
.-|.|+.||..+.
T Consensus 45 r~~~C~~Cg~~~~ 57 (69)
T PF07282_consen 45 RVFTCPNCGFEMD 57 (69)
T ss_pred ceEEcCCCCCEEC
Confidence 4566666665543
No 189
>KOG3507|consensus
Probab=50.44 E-value=10 Score=18.49 Aligned_cols=30 Identities=17% Similarity=0.417 Sum_probs=18.0
Q ss_pred CeeeCCCCcccccchhhHHHHHhhhCCCcccCCCCCCccc
Q psy11352 50 LFATCFVCGKQLSNQYNLRVHMETHQNAFYACSSCSHVSR 89 (107)
Q Consensus 50 ~~~~C~~C~~~f~~~~~l~~H~~~h~~k~~~C~~C~~~f~ 89 (107)
..|.|..|+..-.. ..+..++|..||....
T Consensus 19 miYiCgdC~~en~l----------k~~D~irCReCG~RIl 48 (62)
T KOG3507|consen 19 MIYICGDCGQENTL----------KRGDVIRCRECGYRIL 48 (62)
T ss_pred EEEEeccccccccc----------cCCCcEehhhcchHHH
Confidence 56788888753211 1125788888886543
No 190
>KOG2071|consensus
Probab=50.03 E-value=9.3 Score=27.39 Aligned_cols=24 Identities=21% Similarity=0.357 Sum_probs=18.3
Q ss_pred CcccCCCCCCcccChHHHHHHHHc
Q psy11352 77 AFYACSSCSHVSRSRDALRKHVSY 100 (107)
Q Consensus 77 k~~~C~~C~~~f~~~~~l~~H~~~ 100 (107)
.|-+|..||..|........||.+
T Consensus 417 ~pnqC~~CG~R~~~~ee~sk~md~ 440 (579)
T KOG2071|consen 417 SPNQCKSCGLRFDDSEERSKHMDI 440 (579)
T ss_pred CcchhcccccccccchhhhhHhhh
Confidence 467888888888887777777765
No 191
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=49.73 E-value=8.2 Score=22.08 Aligned_cols=15 Identities=20% Similarity=0.530 Sum_probs=12.6
Q ss_pred eeeCCCCcccccchh
Q psy11352 51 FATCFVCGKQLSNQY 65 (107)
Q Consensus 51 ~~~C~~C~~~f~~~~ 65 (107)
|+.|..||+.|..-+
T Consensus 1 PH~Ct~Cg~~f~dgs 15 (131)
T PF09845_consen 1 PHQCTKCGRVFEDGS 15 (131)
T ss_pred CcccCcCCCCcCCCc
Confidence 578999999998755
No 192
>TIGR00416 sms DNA repair protein RadA. The gene protuct codes for a probable ATP-dependent protease involved in both DNA repair and degradation of proteins, peptides, glycopeptides. Also known as sms. Residues 11-28 of the SEED alignment contain a putative Zn binding domain. Residues 110-117 of the seed contain a putative ATP binding site both documented in Haemophilus and in Listeria monocytogenes. for E.coli see ( J. BACTERIOL. 178:5045-5048(1996)).
Probab=49.61 E-value=19 Score=25.11 Aligned_cols=9 Identities=22% Similarity=0.575 Sum_probs=5.1
Q ss_pred eeeCCCCcc
Q psy11352 51 FATCFVCGK 59 (107)
Q Consensus 51 ~~~C~~C~~ 59 (107)
...|+.|+.
T Consensus 21 ~g~Cp~C~~ 29 (454)
T TIGR00416 21 QGKCPACHA 29 (454)
T ss_pred cEECcCCCC
Confidence 356666653
No 193
>PRK05452 anaerobic nitric oxide reductase flavorubredoxin; Provisional
Probab=49.48 E-value=22 Score=24.98 Aligned_cols=36 Identities=17% Similarity=0.319 Sum_probs=19.8
Q ss_pred CeeeCCCCcccccchhhHHHHHhhhCC-------CcccCCCCCC
Q psy11352 50 LFATCFVCGKQLSNQYNLRVHMETHQN-------AFYACSSCSH 86 (107)
Q Consensus 50 ~~~~C~~C~~~f~~~~~l~~H~~~h~~-------k~~~C~~C~~ 86 (107)
..|.|..||..|.-...-... .+--| ..|.|+.|+-
T Consensus 424 ~~~~c~~c~~~yd~~~g~~~~-~~~~gt~~~~lp~~~~cp~c~~ 466 (479)
T PRK05452 424 PRMQCSVCQWIYDPAKGEPMQ-DVAPGTPWSEVPDNFLCPECSL 466 (479)
T ss_pred CeEEECCCCeEECCCCCCccc-CCCCCCChhhCCCCCcCcCCCC
Confidence 668888888777654221111 11111 2478888874
No 194
>PRK11823 DNA repair protein RadA; Provisional
Probab=49.31 E-value=20 Score=24.89 Aligned_cols=7 Identities=14% Similarity=0.652 Sum_probs=4.1
Q ss_pred cccCCCC
Q psy11352 12 FLISDHC 18 (107)
Q Consensus 12 ~~~C~~C 18 (107)
.|.|..|
T Consensus 7 ~y~C~~C 13 (446)
T PRK11823 7 AYVCQEC 13 (446)
T ss_pred eEECCcC
Confidence 4566666
No 195
>PRK04023 DNA polymerase II large subunit; Validated
Probab=49.19 E-value=40 Score=26.32 Aligned_cols=10 Identities=20% Similarity=0.524 Sum_probs=6.8
Q ss_pred cccCCCCCCc
Q psy11352 78 FYACSSCSHV 87 (107)
Q Consensus 78 ~~~C~~C~~~ 87 (107)
++.|+.||..
T Consensus 663 ~y~CPKCG~E 672 (1121)
T PRK04023 663 EDECEKCGRE 672 (1121)
T ss_pred CCcCCCCCCC
Confidence 5668888753
No 196
>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=49.08 E-value=4.4 Score=18.60 Aligned_cols=15 Identities=27% Similarity=0.817 Sum_probs=9.1
Q ss_pred CeeeCCC--Ccccccch
Q psy11352 50 LFATCFV--CGKQLSNQ 64 (107)
Q Consensus 50 ~~~~C~~--C~~~f~~~ 64 (107)
..+.|.. ||-.|...
T Consensus 24 ~Y~qC~N~~Cg~tfv~~ 40 (47)
T PF04606_consen 24 LYCQCTNPECGHTFVAN 40 (47)
T ss_pred EEEEECCCcCCCEEEEE
Confidence 4566744 77777543
No 197
>PRK05580 primosome assembly protein PriA; Validated
Probab=48.65 E-value=16 Score=26.77 Aligned_cols=9 Identities=33% Similarity=0.755 Sum_probs=4.4
Q ss_pred eeeCCCCcc
Q psy11352 51 FATCFVCGK 59 (107)
Q Consensus 51 ~~~C~~C~~ 59 (107)
+..|+.||.
T Consensus 421 ~~~Cp~Cg~ 429 (679)
T PRK05580 421 PKACPECGS 429 (679)
T ss_pred CCCCCCCcC
Confidence 344555543
No 198
>PF10083 DUF2321: Uncharacterized protein conserved in bacteria (DUF2321); InterPro: IPR016891 This entry is represented by Bacteriophage 'Lactobacillus prophage Lj928', Orf-Ljo1454. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=48.54 E-value=15 Score=21.77 Aligned_cols=17 Identities=29% Similarity=0.440 Sum_probs=12.2
Q ss_pred CeeeCCCCcccccchhh
Q psy11352 50 LFATCFVCGKQLSNQYN 66 (107)
Q Consensus 50 ~~~~C~~C~~~f~~~~~ 66 (107)
.|.-|..||+.|++...
T Consensus 67 ~PsYC~~CGkpyPWt~~ 83 (158)
T PF10083_consen 67 APSYCHNCGKPYPWTEN 83 (158)
T ss_pred CChhHHhCCCCCchHHH
Confidence 56678888888877644
No 199
>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=47.78 E-value=12 Score=21.51 Aligned_cols=32 Identities=19% Similarity=0.477 Sum_probs=17.7
Q ss_pred CeeeCCCCcccccchhhHHHHHhhhCCCcccCCCCCCcc
Q psy11352 50 LFATCFVCGKQLSNQYNLRVHMETHQNAFYACSSCSHVS 88 (107)
Q Consensus 50 ~~~~C~~C~~~f~~~~~l~~H~~~h~~k~~~C~~C~~~f 88 (107)
-.|.|..|+..+.....+ .- ..|.|..|+..|
T Consensus 122 ~~~~C~~C~~~~~r~~~~-~~------~~~~C~~C~~~l 153 (157)
T PF10263_consen 122 YVYRCPSCGREYKRHRRS-KR------KRYRCGRCGGPL 153 (157)
T ss_pred eEEEcCCCCCEeeeeccc-ch------hhEECCCCCCEE
Confidence 457777777665554443 11 126677776544
No 200
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=47.68 E-value=15 Score=25.44 Aligned_cols=15 Identities=20% Similarity=0.401 Sum_probs=11.8
Q ss_pred eeeCCCCcccccchh
Q psy11352 51 FATCFVCGKQLSNQY 65 (107)
Q Consensus 51 ~~~C~~C~~~f~~~~ 65 (107)
-|.|..||..+....
T Consensus 367 g~rC~kCg~~~~~~~ 381 (421)
T COG1571 367 GFRCKKCGTRARETL 381 (421)
T ss_pred CcccccccccCCccc
Confidence 489999998877654
No 201
>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=46.97 E-value=20 Score=23.43 Aligned_cols=32 Identities=28% Similarity=0.638 Sum_probs=19.2
Q ss_pred eeeCCCCcccccchhhHHHHHhhhCCCcccCCCCCCcccC
Q psy11352 51 FATCFVCGKQLSNQYNLRVHMETHQNAFYACSSCSHVSRS 90 (107)
Q Consensus 51 ~~~C~~C~~~f~~~~~l~~H~~~h~~k~~~C~~C~~~f~~ 90 (107)
..+|+.|+.....+. |.. .-+.|+.|+..|.-
T Consensus 26 ~~~c~~c~~~~~~~~-l~~-------~~~vc~~c~~h~rl 57 (285)
T TIGR00515 26 WTKCPKCGQVLYTKE-LER-------NLEVCPKCDHHMRM 57 (285)
T ss_pred eeECCCCcchhhHHH-HHh-------hCCCCCCCCCcCcC
Confidence 567888887644332 111 24678888876653
No 202
>KOG2071|consensus
Probab=46.91 E-value=15 Score=26.48 Aligned_cols=27 Identities=22% Similarity=0.461 Sum_probs=22.5
Q ss_pred CCeeeCCCCcccccchhhHHHHHhhhC
Q psy11352 49 KLFATCFVCGKQLSNQYNLRVHMETHQ 75 (107)
Q Consensus 49 ~~~~~C~~C~~~f~~~~~l~~H~~~h~ 75 (107)
..+..|..||..|........||..|.
T Consensus 416 ~~pnqC~~CG~R~~~~ee~sk~md~H~ 442 (579)
T KOG2071|consen 416 DSPNQCKSCGLRFDDSEERSKHMDIHD 442 (579)
T ss_pred CCcchhcccccccccchhhhhHhhhhh
Confidence 367899999999999988888877664
No 203
>PRK04351 hypothetical protein; Provisional
Probab=46.25 E-value=15 Score=21.46 Aligned_cols=34 Identities=21% Similarity=0.502 Sum_probs=22.6
Q ss_pred CeeeCCCCcccccchhhHHHHHhhhCCCcccCCCCCCcccC
Q psy11352 50 LFATCFVCGKQLSNQYNLRVHMETHQNAFYACSSCSHVSRS 90 (107)
Q Consensus 50 ~~~~C~~C~~~f~~~~~l~~H~~~h~~k~~~C~~C~~~f~~ 90 (107)
-.|.|..||..+... +.+....|.|..|+-.+..
T Consensus 111 y~Y~C~~Cg~~~~r~-------Rr~n~~~yrCg~C~g~L~~ 144 (149)
T PRK04351 111 YLYECQSCGQQYLRK-------RRINTKRYRCGKCRGKLKL 144 (149)
T ss_pred EEEECCCCCCEeeee-------eecCCCcEEeCCCCcEeee
Confidence 458899999766432 2233368999999866543
No 204
>PTZ00448 hypothetical protein; Provisional
Probab=46.06 E-value=18 Score=24.56 Aligned_cols=23 Identities=17% Similarity=0.456 Sum_probs=18.3
Q ss_pred cccCCCCCCcccChHHHHHHHHc
Q psy11352 78 FYACSSCSHVSRSRDALRKHVSY 100 (107)
Q Consensus 78 ~~~C~~C~~~f~~~~~l~~H~~~ 100 (107)
.|.|..|+..|......+.|.++
T Consensus 314 ~~tC~~C~v~F~~~~~qR~H~KS 336 (373)
T PTZ00448 314 MLLCRKCNIQLMDHNAFKQHYRS 336 (373)
T ss_pred CccccccccccCCHHHHHHHhhh
Confidence 57799999888877777788764
No 205
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=45.74 E-value=22 Score=23.42 Aligned_cols=34 Identities=18% Similarity=0.429 Sum_probs=20.9
Q ss_pred CeeeCCCCcccccchhhHHHHHhhhCCCcccCCCCCCcccCh
Q psy11352 50 LFATCFVCGKQLSNQYNLRVHMETHQNAFYACSSCSHVSRSR 91 (107)
Q Consensus 50 ~~~~C~~C~~~f~~~~~l~~H~~~h~~k~~~C~~C~~~f~~~ 91 (107)
-..+|+.|+.....+. |.. .-+.|+.|+..|.-.
T Consensus 37 lw~kc~~C~~~~~~~~-l~~-------~~~vcp~c~~h~rlt 70 (296)
T CHL00174 37 LWVQCENCYGLNYKKF-LKS-------KMNICEQCGYHLKMS 70 (296)
T ss_pred CeeECCCccchhhHHH-HHH-------cCCCCCCCCCCcCCC
Confidence 3567999987654332 111 356888888876533
No 206
>COG1066 Sms Predicted ATP-dependent serine protease [Posttranslational modification, protein turnover, chaperones]
Probab=45.74 E-value=19 Score=25.05 Aligned_cols=6 Identities=17% Similarity=0.999 Sum_probs=3.1
Q ss_pred ccCCCC
Q psy11352 13 LISDHC 18 (107)
Q Consensus 13 ~~C~~C 18 (107)
|.|..|
T Consensus 8 f~C~~C 13 (456)
T COG1066 8 FVCQEC 13 (456)
T ss_pred EEcccC
Confidence 455555
No 207
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=45.46 E-value=16 Score=21.78 Aligned_cols=20 Identities=25% Similarity=0.730 Sum_probs=15.2
Q ss_pred CcccCCCCCCcccChHHHHH
Q psy11352 77 AFYACSSCSHVSRSRDALRK 96 (107)
Q Consensus 77 k~~~C~~C~~~f~~~~~l~~ 96 (107)
.-+.|+.||+.|...+...+
T Consensus 129 ~f~~C~~CgkiYW~GsHw~~ 148 (165)
T COG1656 129 EFYRCPKCGKIYWKGSHWRR 148 (165)
T ss_pred ceeECCCCcccccCchHHHH
Confidence 35779999999987776544
No 208
>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=45.29 E-value=18 Score=25.37 Aligned_cols=27 Identities=33% Similarity=0.518 Sum_probs=23.0
Q ss_pred CeeeCCCCcccccchhhHHHHHh-hhCC
Q psy11352 50 LFATCFVCGKQLSNQYNLRVHME-THQN 76 (107)
Q Consensus 50 ~~~~C~~C~~~f~~~~~l~~H~~-~h~~ 76 (107)
+-+.|+.|.+.|.....+..|+. .|.+
T Consensus 56 rFWiCp~CskkF~d~~~~~~H~~~eH~~ 83 (466)
T PF04780_consen 56 RFWICPRCSKKFSDAESCLSHMEQEHPA 83 (466)
T ss_pred eEeeCCcccceeCCHHHHHHHHHHhhhh
Confidence 45789999999999999999987 4655
No 209
>PTZ00043 cytochrome c oxidase subunit; Provisional
Probab=44.74 E-value=11 Score=23.73 Aligned_cols=18 Identities=17% Similarity=0.573 Sum_probs=14.1
Q ss_pred hhCCCcccCCCCCCcccC
Q psy11352 73 THQNAFYACSSCSHVSRS 90 (107)
Q Consensus 73 ~h~~k~~~C~~C~~~f~~ 90 (107)
.+.|++.+|..||..|.-
T Consensus 176 LrEGkpqRCpECGqVFKL 193 (268)
T PTZ00043 176 CREGFLYRCGECDQIFML 193 (268)
T ss_pred ecCCCCccCCCCCcEEEE
Confidence 345589999999988864
No 210
>PRK09710 lar restriction alleviation and modification protein; Reviewed
Probab=44.46 E-value=25 Score=17.51 Aligned_cols=11 Identities=27% Similarity=0.507 Sum_probs=7.8
Q ss_pred CeeeCCCCccc
Q psy11352 50 LFATCFVCGKQ 60 (107)
Q Consensus 50 ~~~~C~~C~~~ 60 (107)
..+.|..|+..
T Consensus 26 ~~v~C~~CgA~ 36 (64)
T PRK09710 26 YRAKCNGCESR 36 (64)
T ss_pred EEEEcCCCCcC
Confidence 34778888864
No 211
>KOG3362|consensus
Probab=44.36 E-value=8.4 Score=22.43 Aligned_cols=23 Identities=26% Similarity=0.466 Sum_probs=16.1
Q ss_pred cccCCCCCCcccChHHHHHHHHc
Q psy11352 78 FYACSSCSHVSRSRDALRKHVSY 100 (107)
Q Consensus 78 ~~~C~~C~~~f~~~~~l~~H~~~ 100 (107)
+|.|.-||-.+-...-+..|..|
T Consensus 129 ~ysC~~CG~kyCsv~C~~~HneT 151 (156)
T KOG3362|consen 129 KYSCVNCGTKYCSVRCLKTHNET 151 (156)
T ss_pred hhHHHhcCCceeechhhhhcccc
Confidence 66777888777777767666543
No 212
>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=44.33 E-value=4.8 Score=23.21 Aligned_cols=18 Identities=22% Similarity=0.492 Sum_probs=14.2
Q ss_pred hhCCCcccCCCCCCcccC
Q psy11352 73 THQNAFYACSSCSHVSRS 90 (107)
Q Consensus 73 ~h~~k~~~C~~C~~~f~~ 90 (107)
.+.++|.+|..||..|.-
T Consensus 107 l~~g~~~RCpeCG~~fkL 124 (136)
T PF01215_consen 107 LHKGKPQRCPECGQVFKL 124 (136)
T ss_dssp EETTSEEEETTTEEEEEE
T ss_pred EeCCCccCCCCCCeEEEE
Confidence 455689999999988864
No 213
>PF10058 DUF2296: Predicted integral membrane metal-binding protein (DUF2296); InterPro: IPR019273 This domain, found mainly in the eukaryotic lunapark proteins, has no known function [].
Probab=43.90 E-value=35 Score=16.25 Aligned_cols=8 Identities=38% Similarity=0.821 Sum_probs=4.0
Q ss_pred eeeCCCCc
Q psy11352 51 FATCFVCG 58 (107)
Q Consensus 51 ~~~C~~C~ 58 (107)
.|.|..|+
T Consensus 44 ~y~C~~Cg 51 (54)
T PF10058_consen 44 QYRCPYCG 51 (54)
T ss_pred EEEcCCCC
Confidence 35555554
No 214
>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=43.83 E-value=9.8 Score=16.58 Aligned_cols=10 Identities=40% Similarity=0.916 Sum_probs=3.6
Q ss_pred eeeCCCCccc
Q psy11352 51 FATCFVCGKQ 60 (107)
Q Consensus 51 ~~~C~~C~~~ 60 (107)
.|.|+.||..
T Consensus 6 ~YkC~~CGni 15 (36)
T PF06397_consen 6 FYKCEHCGNI 15 (36)
T ss_dssp EEE-TTT--E
T ss_pred EEEccCCCCE
Confidence 4555555543
No 215
>smart00731 SprT SprT homologues. Predicted to have roles in transcription elongation. Contains a conserved HExxH motif, indicating a metalloprotease function.
Probab=43.46 E-value=26 Score=20.15 Aligned_cols=12 Identities=25% Similarity=0.523 Sum_probs=6.4
Q ss_pred eeeCCCCccccc
Q psy11352 51 FATCFVCGKQLS 62 (107)
Q Consensus 51 ~~~C~~C~~~f~ 62 (107)
.|.|..|+..+.
T Consensus 112 ~y~C~~C~~~~~ 123 (146)
T smart00731 112 PYRCTGCGQRYL 123 (146)
T ss_pred EEECCCCCCCCc
Confidence 455655655443
No 216
>COG4338 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=43.37 E-value=10 Score=17.70 Aligned_cols=12 Identities=25% Similarity=0.528 Sum_probs=6.6
Q ss_pred cCCCCCCcccCh
Q psy11352 80 ACSSCSHVSRSR 91 (107)
Q Consensus 80 ~C~~C~~~f~~~ 91 (107)
.|+.|++.|+..
T Consensus 14 ICpvCqRPFsWR 25 (54)
T COG4338 14 ICPVCQRPFSWR 25 (54)
T ss_pred hhhhhcCchHHH
Confidence 455666655543
No 217
>KOG2231|consensus
Probab=42.66 E-value=27 Score=25.77 Aligned_cols=21 Identities=24% Similarity=0.553 Sum_probs=10.9
Q ss_pred cCCCCCCcccChHHHHHHHHc
Q psy11352 80 ACSSCSHVSRSRDALRKHVSY 100 (107)
Q Consensus 80 ~C~~C~~~f~~~~~l~~H~~~ 100 (107)
.|..|...|.....|.+|++.
T Consensus 184 ~C~~C~~~fld~~el~rH~~~ 204 (669)
T KOG2231|consen 184 LCKFCHERFLDDDELYRHLRF 204 (669)
T ss_pred cchhhhhhhccHHHHHHhhcc
Confidence 445555555555555555553
No 218
>COG1326 Uncharacterized archaeal Zn-finger protein [General function prediction only]
Probab=42.24 E-value=33 Score=21.16 Aligned_cols=11 Identities=27% Similarity=0.818 Sum_probs=5.3
Q ss_pred cccCCCCCCcc
Q psy11352 78 FYACSSCSHVS 88 (107)
Q Consensus 78 ~~~C~~C~~~f 88 (107)
.+.|..||..+
T Consensus 30 lvrC~eCG~V~ 40 (201)
T COG1326 30 LVRCEECGTVH 40 (201)
T ss_pred EEEccCCCcEe
Confidence 34555555443
No 219
>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=41.47 E-value=33 Score=14.59 Aligned_cols=24 Identities=21% Similarity=0.566 Sum_probs=13.9
Q ss_pred CeeeCCCCcccccchhhHHHHHhhh
Q psy11352 50 LFATCFVCGKQLSNQYNLRVHMETH 74 (107)
Q Consensus 50 ~~~~C~~C~~~f~~~~~l~~H~~~h 74 (107)
..+.|+.|++.... ..+..|+..-
T Consensus 3 ~~~~C~nC~R~v~a-~RfA~HLekC 26 (33)
T PF08209_consen 3 PYVECPNCGRPVAA-SRFAPHLEKC 26 (33)
T ss_dssp -EEE-TTTSSEEEG-GGHHHHHHHH
T ss_pred CeEECCCCcCCcch-hhhHHHHHHH
Confidence 45778888876543 4566676543
No 220
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=41.40 E-value=41 Score=18.29 Aligned_cols=12 Identities=33% Similarity=0.443 Sum_probs=6.4
Q ss_pred eeCCCCcccccc
Q psy11352 52 ATCFVCGKQLSN 63 (107)
Q Consensus 52 ~~C~~C~~~f~~ 63 (107)
..|..||..+..
T Consensus 43 ~~C~~CG~y~~~ 54 (99)
T PRK14892 43 ITCGNCGLYTEF 54 (99)
T ss_pred EECCCCCCccCE
Confidence 456666654433
No 221
>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=41.30 E-value=28 Score=15.17 Aligned_cols=10 Identities=30% Similarity=0.823 Sum_probs=2.9
Q ss_pred ccCCCCCCcc
Q psy11352 79 YACSSCSHVS 88 (107)
Q Consensus 79 ~~C~~C~~~f 88 (107)
|-|+.|...|
T Consensus 4 yyCdyC~~~~ 13 (38)
T PF06220_consen 4 YYCDYCKKYL 13 (38)
T ss_dssp -B-TTT--B-
T ss_pred eeccccccee
Confidence 4566666555
No 222
>KOG0782|consensus
Probab=41.11 E-value=8.9 Score=27.71 Aligned_cols=26 Identities=15% Similarity=0.294 Sum_probs=12.4
Q ss_pred hHHHHHhhhCC-CcccCCCCCCcccCh
Q psy11352 66 NLRVHMETHQN-AFYACSSCSHVSRSR 91 (107)
Q Consensus 66 ~l~~H~~~h~~-k~~~C~~C~~~f~~~ 91 (107)
.|.+|--+|.. ..-+|..|||.|.++
T Consensus 240 ~fvrHHWVHrrRqeGkC~~CgKgFQQK 266 (1004)
T KOG0782|consen 240 GFVRHHWVHRRRQEGKCNTCGKGFQQK 266 (1004)
T ss_pred cchHHhHhhHhhhccccchhhhhhhhh
Confidence 34444444443 334455555555443
No 223
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=40.75 E-value=32 Score=20.83 Aligned_cols=30 Identities=17% Similarity=0.403 Sum_probs=17.9
Q ss_pred CeeeCCCCcccccchhhHHHHHhhhCCCcccCCCCCCc
Q psy11352 50 LFATCFVCGKQLSNQYNLRVHMETHQNAFYACSSCSHV 87 (107)
Q Consensus 50 ~~~~C~~C~~~f~~~~~l~~H~~~h~~k~~~C~~C~~~ 87 (107)
.-|.|+.|...|+.-..+. .-|.|+.||-.
T Consensus 112 ~~y~C~~~~~r~sfdeA~~--------~~F~Cp~Cg~~ 141 (176)
T COG1675 112 NYYVCPNCHVKYSFDEAME--------LGFTCPKCGED 141 (176)
T ss_pred CceeCCCCCCcccHHHHHH--------hCCCCCCCCch
Confidence 5678877766554432221 24788888854
No 224
>COG4896 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=40.62 E-value=15 Score=18.07 Aligned_cols=12 Identities=33% Similarity=0.863 Sum_probs=6.8
Q ss_pred CcccCCCCCCcc
Q psy11352 77 AFYACSSCSHVS 88 (107)
Q Consensus 77 k~~~C~~C~~~f 88 (107)
..|.|+.|....
T Consensus 30 rtymC~eC~~Rv 41 (68)
T COG4896 30 RTYMCPECEHRV 41 (68)
T ss_pred eeEechhhHhhh
Confidence 346677665433
No 225
>PF10537 WAC_Acf1_DNA_bd: ATP-utilising chromatin assembly and remodelling N-terminal; InterPro: IPR013136 ACF (for ATP-utilising chromatin assembly and remodeling factor) is a chromatin-remodeling complex that catalyzes the ATP-dependent assembly of periodic nucleosome arrays. This reaction utilises the energy of ATP hydrolysis by ISWI, the smaller of the two subunits of ACF. Acf1, the large subunit of ACF, is essential for the full activity of the complex. The WAC (WSTF/Acf1/cbp146) domain is an ~110-residue module present at the N-termini of Acf1-related proteins in a variety of organisms. It is found in association with other domains such as the bromodomain, the PHD-type zinc finger, DDT or WAKS. The DNA-binding region of Acf1 includes the WAC domain, which is necessary for the efficient binding of ACF complex to DNA. It seems probable that the WAC domain will be involved in DNA binding in other related factors [, ]. Some proteins known to contain a WAC domain are the Drosophila melanogaster (Fruit fly) ATP-dependent chromatin assembly factor large subunit Acf1, human WSTF (Williams syndrome transcription factor), mouse cbp146, yeast imitation switch two complex protein 1 (ITC1 or YGL133w), and yeast protein YPL216w.
Probab=40.58 E-value=59 Score=17.77 Aligned_cols=38 Identities=8% Similarity=0.037 Sum_probs=25.7
Q ss_pred CeeeCCCCcccccchhhHHHHHhhhCCCcccCCCCCCc
Q psy11352 50 LFATCFVCGKQLSNQYNLRVHMETHQNAFYACSSCSHV 87 (107)
Q Consensus 50 ~~~~C~~C~~~f~~~~~l~~H~~~h~~k~~~C~~C~~~ 87 (107)
..|.|+.-|..|.+-..+...+.....+-|.|...|+.
T Consensus 2 eVf~i~~T~EiF~dYe~Y~~R~~~y~~~vwtC~~TGk~ 39 (102)
T PF10537_consen 2 EVFYIPFTGEIFRDYEEYLKRMILYNQRVWTCEITGKS 39 (102)
T ss_pred ceEEeCCCCcccCCHHHHHHHHHHHhCCeeEEecCCCC
Confidence 34677777777777666666655555567788877764
No 226
>PLN02748 tRNA dimethylallyltransferase
Probab=40.45 E-value=21 Score=25.05 Aligned_cols=24 Identities=21% Similarity=0.350 Sum_probs=20.0
Q ss_pred CeeeCCCCcc-cccchhhHHHHHhh
Q psy11352 50 LFATCFVCGK-QLSNQYNLRVHMET 73 (107)
Q Consensus 50 ~~~~C~~C~~-~f~~~~~l~~H~~~ 73 (107)
+.|.|+.|++ ++.-...+..|+..
T Consensus 417 ~~~~Ce~C~~~~~~G~~eW~~Hlks 441 (468)
T PLN02748 417 TQYVCEACGNKVLRGAHEWEQHKQG 441 (468)
T ss_pred ccccccCCCCcccCCHHHHHHHhcc
Confidence 6788999997 78888888888753
No 227
>PF05129 Elf1: Transcription elongation factor Elf1 like; InterPro: IPR007808 This family of uncharacterised, mostly short, proteins contain a putative zinc binding domain with four conserved cysteines.; PDB: 1WII_A.
Probab=40.37 E-value=6.5 Score=20.47 Aligned_cols=12 Identities=33% Similarity=0.949 Sum_probs=5.3
Q ss_pred eeCCCCcccccc
Q psy11352 52 ATCFVCGKQLSN 63 (107)
Q Consensus 52 ~~C~~C~~~f~~ 63 (107)
..|..|+..|..
T Consensus 47 ~~C~~Cg~~~~~ 58 (81)
T PF05129_consen 47 LSCRVCGESFQT 58 (81)
T ss_dssp EEESSS--EEEE
T ss_pred EEecCCCCeEEE
Confidence 456666555543
No 228
>TIGR03830 CxxCG_CxxCG_HTH putative zinc finger/helix-turn-helix protein, YgiT family. This model describes a family of predicted regulatory proteins with a conserved zinc finger/HTH architecture. The amino-terminal region contains a novel domain, featuring two CXXC motifs and occuring in a number of small bacterial proteins as well as in the present family. The carboxyl-terminal region consists of a helix-turn-helix domain, modeled by pfam01381. The predicted function is DNA binding and transcriptional regulation.
Probab=40.37 E-value=17 Score=20.07 Aligned_cols=21 Identities=19% Similarity=0.283 Sum_probs=14.7
Q ss_pred CeeeCCCCcccccchhhHHHH
Q psy11352 50 LFATCFVCGKQLSNQYNLRVH 70 (107)
Q Consensus 50 ~~~~C~~C~~~f~~~~~l~~H 70 (107)
.-+.|+.||..+........-
T Consensus 30 ~~~~C~~CGe~~~~~e~~~~~ 50 (127)
T TIGR03830 30 PGWYCPACGEELLDPEESKRN 50 (127)
T ss_pred eeeECCCCCCEEEcHHHHHHH
Confidence 447899999888776655433
No 229
>TIGR00143 hypF [NiFe] hydrogenase maturation protein HypF. A previously described regulatory effect of HypF mutatation is attributable to loss of activity of a regulatory hydrogenase. A zinc finger-like region CXXCX(18)CXXCX(24)CXXCX(18)CXXC region further supported the regulatory hypothesis. However, more recent work (PUBMED:11375153) shows the direct effect is on the activity of expressed hydrogenases with nickel/iron centers, rather than on expression.
Probab=40.19 E-value=11 Score=27.90 Aligned_cols=59 Identities=19% Similarity=0.291 Sum_probs=34.1
Q ss_pred cCCCCCCCCCccCCCCCCCCCCCCCCCCCCCCCCCCCeeeCCCCcccccchhhHHHHHhhhCCCcccCCCCCCcc
Q psy11352 14 ISDHCLTSPLSSSIPGSSKTKASGSGTTGGSSNHSKLFATCFVCGKQLSNQYNLRVHMETHQNAFYACSSCSHVS 88 (107)
Q Consensus 14 ~C~~C~~~~~~~~~~~~l~~h~~~~~~~~~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~k~~~C~~C~~~f 88 (107)
.|..| +-.|+-...+-.- +..+.- +.--.|+.|-+.+.+...- +.|. .+..|..||-..
T Consensus 92 nCt~C---GPr~~i~~~lpyd----r~~t~m----~~f~~C~~C~~ey~~p~~r----r~h~-~~~~C~~Cgp~l 150 (711)
T TIGR00143 92 SCTHC---GPRFTIIEALPYD----RENTSM----ADFPLCPDCAKEYKDPLDR----RFHA-QPIACPRCGPQL 150 (711)
T ss_pred cccCC---CCCeEEeecCCCC----CCCcCC----CCCcCCHHHHHHhcCCccc----cCCC-CCccCCCCCcEE
Confidence 68889 7777666554432 111111 0233589998887665432 2222 577899998643
No 230
>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=39.92 E-value=12 Score=21.85 Aligned_cols=28 Identities=29% Similarity=0.651 Sum_probs=15.9
Q ss_pred CeeeCCCCcccccchhhHHHHHhhhCCCcccCCCCCC
Q psy11352 50 LFATCFVCGKQLSNQYNLRVHMETHQNAFYACSSCSH 86 (107)
Q Consensus 50 ~~~~C~~C~~~f~~~~~l~~H~~~h~~k~~~C~~C~~ 86 (107)
-.+.|..||..... .+.+.--.|+.||.
T Consensus 111 G~l~C~~Cg~~~~~---------~~~~~l~~Cp~C~~ 138 (146)
T PF07295_consen 111 GTLVCENCGHEVEL---------THPERLPPCPKCGH 138 (146)
T ss_pred ceEecccCCCEEEe---------cCCCcCCCCCCCCC
Confidence 34888888865322 12232335888874
No 231
>PRK06260 threonine synthase; Validated
Probab=39.33 E-value=24 Score=24.00 Aligned_cols=15 Identities=33% Similarity=0.565 Sum_probs=9.1
Q ss_pred CeeeCCCCcccccch
Q psy11352 50 LFATCFVCGKQLSNQ 64 (107)
Q Consensus 50 ~~~~C~~C~~~f~~~ 64 (107)
..+.|+.|+..+...
T Consensus 18 ~~~~Cp~cg~~l~~~ 32 (397)
T PRK06260 18 IIYTCPECGGLLEVI 32 (397)
T ss_pred ccccCCCCCCeEEEE
Confidence 346787787654444
No 232
>PF14787 zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB: 1CL4_A 1DSV_A.
Probab=39.16 E-value=18 Score=15.79 Aligned_cols=14 Identities=29% Similarity=0.517 Sum_probs=8.4
Q ss_pred eCCCCcccccchhh
Q psy11352 53 TCFVCGKQLSNQYN 66 (107)
Q Consensus 53 ~C~~C~~~f~~~~~ 66 (107)
.|..|++.|-+.+.
T Consensus 4 ~CprC~kg~Hwa~~ 17 (36)
T PF14787_consen 4 LCPRCGKGFHWASE 17 (36)
T ss_dssp C-TTTSSSCS-TTT
T ss_pred cCcccCCCcchhhh
Confidence 57778887776654
No 233
>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=39.06 E-value=10 Score=23.35 Aligned_cols=23 Identities=9% Similarity=-0.187 Sum_probs=0.0
Q ss_pred cccccCCCCCCCCCccCCCCCCCCC
Q psy11352 10 LHFLISDHCLTSPLSSSIPGSSKTK 34 (107)
Q Consensus 10 ~~~~~C~~C~~~~~~~~~~~~l~~h 34 (107)
.+.|.|++|| +.++.-+..+..|
T Consensus 99 ~~ey~CEICG--N~~Y~GrkaFekH 121 (196)
T PF11931_consen 99 GVEYKCEICG--NQSYKGRKAFEKH 121 (196)
T ss_dssp -------------------------
T ss_pred CCeeeeEeCC--CcceecHHHHHHh
Confidence 3469999994 4455555555555
No 234
>COG2331 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=38.94 E-value=4.1 Score=20.95 Aligned_cols=13 Identities=8% Similarity=0.066 Sum_probs=8.0
Q ss_pred cccCCCCCCCCCccCC
Q psy11352 12 FLISDHCLTSPLSSSI 27 (107)
Q Consensus 12 ~~~C~~C~~~~~~~~~ 27 (107)
.|+|..| +..|..
T Consensus 12 ~Y~c~~c---g~~~dv 24 (82)
T COG2331 12 SYECTEC---GNRFDV 24 (82)
T ss_pred EEeeccc---chHHHH
Confidence 4677777 665543
No 235
>cd01121 Sms Sms (bacterial radA) DNA repair protein. This protein is not related to archael radA any more than is to other RecA-like NTPases. Sms has a role in recombination and recombinational repair and is responsible for the stabilization or processing of branched DNA molecules.
Probab=38.40 E-value=18 Score=24.51 Aligned_cols=10 Identities=30% Similarity=0.833 Sum_probs=7.2
Q ss_pred eeeCCCCccc
Q psy11352 51 FATCFVCGKQ 60 (107)
Q Consensus 51 ~~~C~~C~~~ 60 (107)
...|+.|+..
T Consensus 14 ~g~cp~c~~w 23 (372)
T cd01121 14 LGKCPECGEW 23 (372)
T ss_pred cEECcCCCCc
Confidence 3679998753
No 236
>PRK05654 acetyl-CoA carboxylase subunit beta; Validated
Probab=38.19 E-value=27 Score=22.91 Aligned_cols=31 Identities=29% Similarity=0.714 Sum_probs=18.1
Q ss_pred eeeCCCCcccccchhhHHHHHhhhCCCcccCCCCCCccc
Q psy11352 51 FATCFVCGKQLSNQYNLRVHMETHQNAFYACSSCSHVSR 89 (107)
Q Consensus 51 ~~~C~~C~~~f~~~~~l~~H~~~h~~k~~~C~~C~~~f~ 89 (107)
..+|+.|+.....+. |.. .-+.|+.|+..|.
T Consensus 27 ~~~c~~c~~~~~~~~-l~~-------~~~vc~~c~~h~r 57 (292)
T PRK05654 27 WTKCPSCGQVLYRKE-LEA-------NLNVCPKCGHHMR 57 (292)
T ss_pred eeECCCccchhhHHH-HHh-------cCCCCCCCCCCee
Confidence 567888876543322 111 2457888887665
No 237
>PF15616 TerY-C: TerY-C metal binding domain
Probab=38.08 E-value=20 Score=20.57 Aligned_cols=11 Identities=18% Similarity=0.482 Sum_probs=7.1
Q ss_pred CcccCCCCCCc
Q psy11352 77 AFYACSSCSHV 87 (107)
Q Consensus 77 k~~~C~~C~~~ 87 (107)
....|+.|+..
T Consensus 104 ~~~~CPwCg~~ 114 (131)
T PF15616_consen 104 GEVTCPWCGNE 114 (131)
T ss_pred CCEECCCCCCe
Confidence 45667777754
No 238
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=37.86 E-value=21 Score=20.11 Aligned_cols=32 Identities=22% Similarity=0.405 Sum_probs=16.3
Q ss_pred CeeeCCCCcccccchhhHHHHHhhhCCCcccCCCCCC
Q psy11352 50 LFATCFVCGKQLSNQYNLRVHMETHQNAFYACSSCSH 86 (107)
Q Consensus 50 ~~~~C~~C~~~f~~~~~l~~H~~~h~~k~~~C~~C~~ 86 (107)
-.+.| .||..|.....-..| ..-.+.|+.||.
T Consensus 69 ~~~~C-~Cg~~~~~~~~~~~~----~~~~~~CP~Cgs 100 (124)
T PRK00762 69 VEIEC-ECGYEGVVDEDEIDH----YAAVIECPVCGN 100 (124)
T ss_pred eeEEe-eCcCcccccccchhc----cccCCcCcCCCC
Confidence 34678 888776543211111 111346788873
No 239
>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=37.71 E-value=24 Score=15.75 Aligned_cols=12 Identities=25% Similarity=0.506 Sum_probs=8.9
Q ss_pred CeeeCCCCcccc
Q psy11352 50 LFATCFVCGKQL 61 (107)
Q Consensus 50 ~~~~C~~C~~~f 61 (107)
.+-.|+.|+..|
T Consensus 28 ~~~~CpYCg~~y 39 (40)
T PF10276_consen 28 GPVVCPYCGTRY 39 (40)
T ss_dssp CEEEETTTTEEE
T ss_pred CeEECCCCCCEE
Confidence 457788888766
No 240
>TIGR00627 tfb4 transcription factor tfb4. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=37.69 E-value=36 Score=22.23 Aligned_cols=26 Identities=23% Similarity=0.402 Sum_probs=16.4
Q ss_pred CeeeCCCCcccccchhhHHHHHhhhCCCcccCCCCCCcc
Q psy11352 50 LFATCFVCGKQLSNQYNLRVHMETHQNAFYACSSCSHVS 88 (107)
Q Consensus 50 ~~~~C~~C~~~f~~~~~l~~H~~~h~~k~~~C~~C~~~f 88 (107)
.-|.|+.|.-.|-. .|-.|+.||-.|
T Consensus 254 ~GyvCs~Clsi~C~-------------~p~~C~~Cgt~f 279 (279)
T TIGR00627 254 IGFVCSVCLSVLCQ-------------YTPICKTCKTAF 279 (279)
T ss_pred ceEECCCccCCcCC-------------CCCCCCCCCCCC
Confidence 34788887655542 244788887655
No 241
>COG5188 PRP9 Splicing factor 3a, subunit 3 [RNA processing and modification]
Probab=37.66 E-value=22 Score=24.12 Aligned_cols=22 Identities=18% Similarity=0.403 Sum_probs=16.3
Q ss_pred CeeeCCCCc-ccccchhhHHHHH
Q psy11352 50 LFATCFVCG-KQLSNQYNLRVHM 71 (107)
Q Consensus 50 ~~~~C~~C~-~~f~~~~~l~~H~ 71 (107)
+.|.|++|| +++.-...+.+|-
T Consensus 373 ~ef~CEICgNyvy~GR~~FdrHF 395 (470)
T COG5188 373 IEFECEICGNYVYYGRDRFDRHF 395 (470)
T ss_pred cceeeeecccccccchHHHHhhh
Confidence 678999998 6666666676664
No 242
>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=37.58 E-value=29 Score=14.92 Aligned_cols=13 Identities=15% Similarity=-0.005 Sum_probs=5.1
Q ss_pred cCCCCCCCCCccCCCC
Q psy11352 14 ISDHCLTSPLSSSIPG 29 (107)
Q Consensus 14 ~C~~C~~~~~~~~~~~ 29 (107)
.|.+| ++.|..+.
T Consensus 5 ~C~eC---~~~f~dSy 17 (34)
T PF01286_consen 5 KCDEC---GKPFMDSY 17 (34)
T ss_dssp E-TTT-----EES-SS
T ss_pred hHhHh---CCHHHHHH
Confidence 46666 66665544
No 243
>KOG3214|consensus
Probab=37.29 E-value=19 Score=19.63 Aligned_cols=13 Identities=23% Similarity=0.772 Sum_probs=8.0
Q ss_pred eeCCCCcccccch
Q psy11352 52 ATCFVCGKQLSNQ 64 (107)
Q Consensus 52 ~~C~~C~~~f~~~ 64 (107)
..|.+|+..|...
T Consensus 48 ~sC~iC~esFqt~ 60 (109)
T KOG3214|consen 48 ASCRICEESFQTT 60 (109)
T ss_pred eeeeehhhhhccc
Confidence 4567777666553
No 244
>PF07649 C1_3: C1-like domain; InterPro: IPR011424 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in IPR002219 from INTERPRO. C1 domains are protein kinase C-like zinc finger structures. Diacylglycerol (DAG) kinases (DGKs) have a two or three commonly conserved cysteine-rich C1 domains []. DGKs modulate the balance between the two signaling lipids, DAG and phosphatidic acid (PA), by phosphorylating DAG to yield PA []. The PKD (protein kinase D) family are novel DAG receptors. They have twin C1 domains, designated C1a and C1b, which bind DAG or phorbol esters. Individual C1 domains differ in ligand-binding activity and selectivity []. ; GO: 0047134 protein-disulfide reductase activity, 0055114 oxidation-reduction process; PDB: 1V5N_A.
Probab=37.10 E-value=31 Score=13.89 Aligned_cols=9 Identities=33% Similarity=0.729 Sum_probs=3.3
Q ss_pred eeeCCCCcc
Q psy11352 51 FATCFVCGK 59 (107)
Q Consensus 51 ~~~C~~C~~ 59 (107)
.|.|.+|+.
T Consensus 15 ~Y~C~~Cdf 23 (30)
T PF07649_consen 15 FYRCSECDF 23 (30)
T ss_dssp EEE-TTT--
T ss_pred eEECccCCC
Confidence 455555543
No 245
>PF05180 zf-DNL: DNL zinc finger; InterPro: IPR007853 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 DNL-type zinc finger is found in Tim15, a zinc finger protein essential for protein import into mitochondria. Mitochondrial functions rely on the correct transport of resident proteins synthesized in the cytosol to mitochondria. Protein import into mitochondria is mediated by membrane protein complexes, protein translocators, in the outer and inner mitochondrial membranes, in cooperation with their assistant proteins in the cytosol, intermembrane space and matrix. Proteins destined to the mitochondrial matrix cross the outer membrane with the aid of the outer membrane translocator, the tOM40 complex, and then the inner membrane with the aid of the inner membrane translocator, the TIM23 complex, and mitochondrial motor and chaperone (MMC) proteins including mitochondrial heat- shock protein 70 (mtHsp70), and translocase in the inner mitochondrial membrane (Tim)15. Tim15 is also known as zinc finger motif (Zim)17 or mtHsp70 escort protein (Hep)1. Tim15 contains a zinc-finger motif (CXXC and CXXC) of ~100 residues, which has been named DNL after a short C-terminal motif of D(N/H)L [, , ]. The DNL-type zinc finger is an L-shaped molecule. The two CXXC motifs are located at the end of the L, and are sandwiched by two- stranded antiparallel beta-sheets. Two short alpha-helices constitute another leg of the L. The outer (convex) face of the L has a large acidic groove, which is lined with five acidic residues, whereas the inner (concave) face of the L has two positively charged residues, next to the CXXC motifs []. This entry represents the DNL-type zinc finger.; GO: 0008270 zinc ion binding; PDB: 2E2Z_A.
Probab=36.30 E-value=4.1 Score=20.39 Aligned_cols=34 Identities=21% Similarity=0.463 Sum_probs=18.6
Q ss_pred eeeCCCCcccccchhhHHHHHhhhCC-CcccCCCCCCc
Q psy11352 51 FATCFVCGKQLSNQYNLRVHMETHQN-AFYACSSCSHV 87 (107)
Q Consensus 51 ~~~C~~C~~~f~~~~~l~~H~~~h~~-k~~~C~~C~~~ 87 (107)
.|+|..|+..-. ..+.. ...+.| --.+|+.|...
T Consensus 4 ~FTC~~C~~Rs~--~~~sk-~aY~~GvViv~C~gC~~~ 38 (66)
T PF05180_consen 4 TFTCNKCGTRSA--KMFSK-QAYHKGVVIVQCPGCKNR 38 (66)
T ss_dssp EEEETTTTEEEE--EEEEH-HHHHTSEEEEE-TTS--E
T ss_pred EEEcCCCCCccc--eeeCH-HHHhCCeEEEECCCCcce
Confidence 588988874322 22222 245667 67788888643
No 246
>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=36.30 E-value=17 Score=15.72 Aligned_cols=30 Identities=20% Similarity=0.444 Sum_probs=18.9
Q ss_pred eeCCCCcccccchhhHHHHHhhhCC-CcccCCCCCCccc
Q psy11352 52 ATCFVCGKQLSNQYNLRVHMETHQN-AFYACSSCSHVSR 89 (107)
Q Consensus 52 ~~C~~C~~~f~~~~~l~~H~~~h~~-k~~~C~~C~~~f~ 89 (107)
..|+.||..|..... -. .+-.|..||-.+.
T Consensus 2 r~C~~Cg~~Yh~~~~--------pP~~~~~Cd~cg~~L~ 32 (36)
T PF05191_consen 2 RICPKCGRIYHIEFN--------PPKVEGVCDNCGGELV 32 (36)
T ss_dssp EEETTTTEEEETTTB----------SSTTBCTTTTEBEB
T ss_pred cCcCCCCCccccccC--------CCCCCCccCCCCCeeE
Confidence 578899988764322 11 3567888886544
No 247
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=36.07 E-value=21 Score=23.12 Aligned_cols=14 Identities=21% Similarity=0.769 Sum_probs=8.9
Q ss_pred CcccCCCCCCcccC
Q psy11352 77 AFYACSSCSHVSRS 90 (107)
Q Consensus 77 k~~~C~~C~~~f~~ 90 (107)
+-|.|+.||..+-.
T Consensus 321 r~~~C~~cg~~~~r 334 (364)
T COG0675 321 RLFKCPRCGFVHDR 334 (364)
T ss_pred eeEECCCCCCeehh
Confidence 56777777765443
No 248
>TIGR00310 ZPR1_znf ZPR1 zinc finger domain.
Probab=35.36 E-value=9.3 Score=23.37 Aligned_cols=12 Identities=25% Similarity=0.531 Sum_probs=7.7
Q ss_pred eeeCCCCccccc
Q psy11352 51 FATCFVCGKQLS 62 (107)
Q Consensus 51 ~~~C~~C~~~f~ 62 (107)
.|.|+.||....
T Consensus 30 sf~C~~CGyr~~ 41 (192)
T TIGR00310 30 STICEHCGYRSN 41 (192)
T ss_pred EEECCCCCCccc
Confidence 467777776543
No 249
>cd02341 ZZ_ZZZ3 Zinc finger, ZZ type. Zinc finger present in ZZZ3 (ZZ finger containing 3) and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
Probab=34.59 E-value=55 Score=15.15 Aligned_cols=8 Identities=25% Similarity=0.530 Sum_probs=4.2
Q ss_pred eeeCCCCc
Q psy11352 51 FATCFVCG 58 (107)
Q Consensus 51 ~~~C~~C~ 58 (107)
.|.|..|.
T Consensus 15 R~~C~~C~ 22 (48)
T cd02341 15 RYHCSECD 22 (48)
T ss_pred eEECCCCC
Confidence 35555554
No 250
>PLN03238 probable histone acetyltransferase MYST; Provisional
Probab=33.49 E-value=60 Score=21.41 Aligned_cols=23 Identities=22% Similarity=0.356 Sum_probs=14.7
Q ss_pred CeeeCCCCcccccchhhHHHHHh
Q psy11352 50 LFATCFVCGKQLSNQYNLRVHME 72 (107)
Q Consensus 50 ~~~~C~~C~~~f~~~~~l~~H~~ 72 (107)
..|.|+.|-+-|.....|.+|+.
T Consensus 47 ~lyiCe~Clky~~~~~~l~~H~~ 69 (290)
T PLN03238 47 KLYICEYCLKYMRKKKSLLRHLA 69 (290)
T ss_pred eEEEcCCCcchhCCHHHHHHHHH
Confidence 45666666666666666666655
No 251
>KOG3352|consensus
Probab=33.42 E-value=19 Score=21.14 Aligned_cols=18 Identities=17% Similarity=0.431 Sum_probs=13.9
Q ss_pred hhCCCcccCCCCCCcccC
Q psy11352 73 THQNAFYACSSCSHVSRS 90 (107)
Q Consensus 73 ~h~~k~~~C~~C~~~f~~ 90 (107)
.+-++.++|.+||..|.-
T Consensus 128 l~Kge~~rc~eCG~~fkL 145 (153)
T KOG3352|consen 128 LEKGETQRCPECGHYFKL 145 (153)
T ss_pred EEcCCcccCCcccceEEe
Confidence 455678889999988753
No 252
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=33.21 E-value=45 Score=15.68 Aligned_cols=31 Identities=26% Similarity=0.518 Sum_probs=18.2
Q ss_pred eCCCCcccccchhhHHHHHhhhCC-CcccCCCCCCc
Q psy11352 53 TCFVCGKQLSNQYNLRVHMETHQN-AFYACSSCSHV 87 (107)
Q Consensus 53 ~C~~C~~~f~~~~~l~~H~~~h~~-k~~~C~~C~~~ 87 (107)
.|..|+-..+.... ..+..+ ....|+.||+.
T Consensus 24 ~C~gC~~~l~~~~~----~~i~~~~~i~~Cp~CgRi 55 (56)
T PF02591_consen 24 TCSGCHMELPPQEL----NEIRKGDEIVFCPNCGRI 55 (56)
T ss_pred ccCCCCEEcCHHHH----HHHHcCCCeEECcCCCcc
Confidence 67777766544322 223344 56788988863
No 253
>PRK00420 hypothetical protein; Validated
Probab=32.96 E-value=33 Score=19.13 Aligned_cols=9 Identities=44% Similarity=0.674 Sum_probs=4.4
Q ss_pred eeCCCCccc
Q psy11352 52 ATCFVCGKQ 60 (107)
Q Consensus 52 ~~C~~C~~~ 60 (107)
..|+.||..
T Consensus 41 ~~Cp~Cg~~ 49 (112)
T PRK00420 41 VVCPVHGKV 49 (112)
T ss_pred eECCCCCCe
Confidence 445555543
No 254
>PRK08222 hydrogenase 4 subunit H; Validated
Probab=32.60 E-value=38 Score=20.39 Aligned_cols=19 Identities=16% Similarity=0.417 Sum_probs=14.9
Q ss_pred CcccCCCCCCcccChHHHH
Q psy11352 77 AFYACSSCSHVSRSRDALR 95 (107)
Q Consensus 77 k~~~C~~C~~~f~~~~~l~ 95 (107)
....|..||+.|.....+.
T Consensus 113 ~~~~C~~Cg~~f~~~k~i~ 131 (181)
T PRK08222 113 HLQRCSRCERPFAPQKTVA 131 (181)
T ss_pred ccCcCcccCCccCcHhHHH
Confidence 5788999999998665443
No 255
>smart00132 LIM Zinc-binding domain present in Lin-11, Isl-1, Mec-3. Zinc-binding domain family. Some LIM domains bind protein partners via tyrosine-containing motifs. LIM domains are found in many key regulators of developmental pathways.
Probab=32.23 E-value=35 Score=13.94 Aligned_cols=9 Identities=44% Similarity=0.958 Sum_probs=4.6
Q ss_pred eeCCCCccc
Q psy11352 52 ATCFVCGKQ 60 (107)
Q Consensus 52 ~~C~~C~~~ 60 (107)
|.|..|+..
T Consensus 28 f~C~~C~~~ 36 (39)
T smart00132 28 FKCSKCGKP 36 (39)
T ss_pred CCCcccCCc
Confidence 455555544
No 256
>COG4306 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=32.02 E-value=20 Score=20.47 Aligned_cols=16 Identities=19% Similarity=0.372 Sum_probs=10.5
Q ss_pred CeeeCCCCcccccchh
Q psy11352 50 LFATCFVCGKQLSNQY 65 (107)
Q Consensus 50 ~~~~C~~C~~~f~~~~ 65 (107)
.|--|..||..|++..
T Consensus 67 ~psfchncgs~fpwte 82 (160)
T COG4306 67 PPSFCHNCGSRFPWTE 82 (160)
T ss_pred CcchhhcCCCCCCcHH
Confidence 4455777777777653
No 257
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=31.84 E-value=70 Score=21.46 Aligned_cols=23 Identities=22% Similarity=0.311 Sum_probs=14.4
Q ss_pred CcccCCCCCCcccChHHHHHHHH
Q psy11352 77 AFYACSSCSHVSRSRDALRKHVS 99 (107)
Q Consensus 77 k~~~C~~C~~~f~~~~~l~~H~~ 99 (107)
-.|+|+.|...|...-+.-.|..
T Consensus 387 ~rY~Ce~CK~~FC~dCdvfiHe~ 409 (421)
T COG5151 387 GRYQCELCKSTFCSDCDVFIHET 409 (421)
T ss_pred cceechhhhhhhhhhhHHHHHHH
Confidence 46777777666666655555554
No 258
>PRK07591 threonine synthase; Validated
Probab=31.12 E-value=37 Score=23.36 Aligned_cols=9 Identities=22% Similarity=0.368 Sum_probs=4.5
Q ss_pred eeCCCCccc
Q psy11352 52 ATCFVCGKQ 60 (107)
Q Consensus 52 ~~C~~C~~~ 60 (107)
+.|+.|+-.
T Consensus 34 ~~C~~cg~~ 42 (421)
T PRK07591 34 HVCEECFGP 42 (421)
T ss_pred ccCCCCCCe
Confidence 455555543
No 259
>PF10071 DUF2310: Zn-ribbon-containing, possibly nucleic-acid-binding protein (DUF2310); InterPro: IPR016908 This group represents uncharacterised conserved proteins.
Probab=31.02 E-value=26 Score=22.59 Aligned_cols=32 Identities=25% Similarity=0.474 Sum_probs=21.7
Q ss_pred CeeeCCCCcccccchhhHHHHHhhhCCCcccCCCCCCc
Q psy11352 50 LFATCFVCGKQLSNQYNLRVHMETHQNAFYACSSCSHV 87 (107)
Q Consensus 50 ~~~~C~~C~~~f~~~~~l~~H~~~h~~k~~~C~~C~~~ 87 (107)
..-.|+.||..+.....| |.--.|+|+.|--.
T Consensus 219 ~~r~CP~Cg~~W~L~~pl------h~iFdFKCD~CRLV 250 (258)
T PF10071_consen 219 QARKCPSCGGDWRLKEPL------HDIFDFKCDPCRLV 250 (258)
T ss_pred hCCCCCCCCCccccCCch------hhceeccCCcceee
Confidence 445799999887766655 12157889988543
No 260
>TIGR00319 desulf_FeS4 desulfoferrodoxin FeS4 iron-binding domain. Neelaredoxin, a monomeric blue non-heme iron protein, lacks this domain.
Probab=30.92 E-value=35 Score=14.22 Aligned_cols=12 Identities=33% Similarity=0.728 Sum_probs=8.5
Q ss_pred CeeeCCCCcccc
Q psy11352 50 LFATCFVCGKQL 61 (107)
Q Consensus 50 ~~~~C~~C~~~f 61 (107)
+.|+|+.||...
T Consensus 6 ~~ykC~~Cgniv 17 (34)
T TIGR00319 6 QVYKCEVCGNIV 17 (34)
T ss_pred cEEEcCCCCcEE
Confidence 467888887654
No 261
>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=30.77 E-value=48 Score=15.00 Aligned_cols=16 Identities=25% Similarity=0.623 Sum_probs=11.2
Q ss_pred eCCCCcccccchhhHH
Q psy11352 53 TCFVCGKQLSNQYNLR 68 (107)
Q Consensus 53 ~C~~C~~~f~~~~~l~ 68 (107)
.|..|++.|.......
T Consensus 10 ~C~~C~rpf~WRKKW~ 25 (42)
T PF10013_consen 10 ICPVCGRPFTWRKKWA 25 (42)
T ss_pred cCcccCCcchHHHHHH
Confidence 5888888887765443
No 262
>COG4391 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=30.68 E-value=21 Score=17.60 Aligned_cols=37 Identities=16% Similarity=0.134 Sum_probs=19.8
Q ss_pred CeeeCCCCcccccchhhHHHHHhhhCCCcccCCCCCCccc
Q psy11352 50 LFATCFVCGKQLSNQYNLRVHMETHQNAFYACSSCSHVSR 89 (107)
Q Consensus 50 ~~~~C~~C~~~f~~~~~l~~H~~~h~~k~~~C~~C~~~f~ 89 (107)
.++.|+.-+-.|.....+. .+-...-..|+.|+..|.
T Consensus 23 ~~l~C~g~~~p~~HPrV~L---~mg~~gev~CPYC~t~y~ 59 (62)
T COG4391 23 LPLMCPGPEPPNDHPRVFL---DMGDEGEVVCPYCSTRYR 59 (62)
T ss_pred eeEEcCCCCCCCCCCEEEE---EcCCCCcEecCccccEEE
Confidence 6778876554443332211 110114567888888775
No 263
>PF14599 zinc_ribbon_6: Zinc-ribbon; PDB: 2K2D_A.
Probab=30.64 E-value=17 Score=17.85 Aligned_cols=14 Identities=14% Similarity=0.411 Sum_probs=7.2
Q ss_pred eeCCCCcccccchh
Q psy11352 52 ATCFVCGKQLSNQY 65 (107)
Q Consensus 52 ~~C~~C~~~f~~~~ 65 (107)
-.|+.|+.......
T Consensus 31 IlCNDC~~~s~v~f 44 (61)
T PF14599_consen 31 ILCNDCNAKSEVPF 44 (61)
T ss_dssp EEESSS--EEEEE-
T ss_pred EECCCCCCccceee
Confidence 45899988654433
No 264
>cd00974 DSRD Desulforedoxin (DSRD) domain; a small non-heme iron domain present in the desulforedoxin (rubredoxin oxidoreductase) and desulfoferrodoxin proteins of some archeael and bacterial methanogens and sulfate/sulfur reducers. Desulforedoxin is a small, single-domain homodimeric protein; each subunit contains an iron atom bound to four cysteinyl sulfur atoms, Fe(S-Cys)4, in a distorted tetrahedral coordination. Its metal center is similar to that found in rubredoxin type proteins. Desulforedoxin is regarded as a potential redox partner for rubredoxin. Desulfoferrodoxin forms a homodimeric protein, with each protomer comprised of two domains, the N-terminal DSRD domain and C-terminal superoxide reductase-like (SORL) domain. Each domain has a distinct iron center: the DSRD iron center I, Fe(S-Cys)4; and the SORL iron center II, Fe[His4Cys(Glu)].
Probab=30.31 E-value=37 Score=14.16 Aligned_cols=12 Identities=25% Similarity=0.686 Sum_probs=8.1
Q ss_pred CeeeCCCCcccc
Q psy11352 50 LFATCFVCGKQL 61 (107)
Q Consensus 50 ~~~~C~~C~~~f 61 (107)
+.|+|+.||...
T Consensus 3 ~~ykC~~CGniv 14 (34)
T cd00974 3 EVYKCEICGNIV 14 (34)
T ss_pred cEEEcCCCCcEE
Confidence 457777777654
No 265
>KOG1994|consensus
Probab=30.27 E-value=24 Score=22.36 Aligned_cols=21 Identities=24% Similarity=0.523 Sum_probs=18.5
Q ss_pred CcccCCCCCCcccChHHHHHH
Q psy11352 77 AFYACSSCSHVSRSRDALRKH 97 (107)
Q Consensus 77 k~~~C~~C~~~f~~~~~l~~H 97 (107)
.-|.|-.||-.|.....|..|
T Consensus 238 eh~YC~fCG~~y~~~edl~eh 258 (268)
T KOG1994|consen 238 EHYYCFFCGIKYKDEEDLYEH 258 (268)
T ss_pred cceEEEEeccccCCHHHHHHh
Confidence 578899999999999998877
No 266
>PRK06450 threonine synthase; Validated
Probab=30.12 E-value=38 Score=22.62 Aligned_cols=10 Identities=30% Similarity=0.810 Sum_probs=5.5
Q ss_pred eeCCCCcccc
Q psy11352 52 ATCFVCGKQL 61 (107)
Q Consensus 52 ~~C~~C~~~f 61 (107)
+.|+.|+..+
T Consensus 19 ~~C~~cg~~l 28 (338)
T PRK06450 19 IRCKKCGGPF 28 (338)
T ss_pred ccCCcCCCEe
Confidence 5666665433
No 267
>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=30.08 E-value=45 Score=18.65 Aligned_cols=31 Identities=26% Similarity=0.416 Sum_probs=17.7
Q ss_pred CeeeCCCCcccccchhhHHHHHhhhCCCcccCCCCCCcccCh
Q psy11352 50 LFATCFVCGKQLSNQYNLRVHMETHQNAFYACSSCSHVSRSR 91 (107)
Q Consensus 50 ~~~~C~~C~~~f~~~~~l~~H~~~h~~k~~~C~~C~~~f~~~ 91 (107)
...+|+.|++.... .|+...|..|+....-.
T Consensus 68 v~V~CP~C~K~TKm-----------LGr~D~CM~C~~pLTLd 98 (114)
T PF11023_consen 68 VQVECPNCGKQTKM-----------LGRVDACMHCKEPLTLD 98 (114)
T ss_pred eeeECCCCCChHhh-----------hchhhccCcCCCcCccC
Confidence 45678888765321 23445677776554433
No 268
>KOG4118|consensus
Probab=29.69 E-value=27 Score=17.43 Aligned_cols=28 Identities=18% Similarity=0.472 Sum_probs=16.9
Q ss_pred cccCCCCCCcccChHHHHHHHHccCCCC
Q psy11352 78 FYACSSCSHVSRSRDALRKHVSYRHPHI 105 (107)
Q Consensus 78 ~~~C~~C~~~f~~~~~l~~H~~~~H~~e 105 (107)
.|.|.+|-..-.....+..|..+.|+.+
T Consensus 38 ~~kCtVC~~~mpdpktfkqhfe~kHpk~ 65 (74)
T KOG4118|consen 38 HHKCTVCMVQMPDPKTFKQHFENKHPKE 65 (74)
T ss_pred HhhhHhhHhhCCCCchHHHHHhhcCCCC
Confidence 3667777655555555666666656543
No 269
>PRK01343 zinc-binding protein; Provisional
Probab=29.34 E-value=37 Score=16.48 Aligned_cols=10 Identities=30% Similarity=0.783 Sum_probs=5.2
Q ss_pred ccCCCCCCcc
Q psy11352 79 YACSSCSHVS 88 (107)
Q Consensus 79 ~~C~~C~~~f 88 (107)
..|+.|++.|
T Consensus 10 ~~CP~C~k~~ 19 (57)
T PRK01343 10 RPCPECGKPS 19 (57)
T ss_pred CcCCCCCCcC
Confidence 3455555544
No 270
>KOG1280|consensus
Probab=29.33 E-value=67 Score=21.83 Aligned_cols=37 Identities=24% Similarity=0.415 Sum_probs=25.8
Q ss_pred CCeeeCCCCcccccchhhHHHHHhh-hCCCccc--CCCCC
Q psy11352 49 KLFATCFVCGKQLSNQYNLRVHMET-HQNAFYA--CSSCS 85 (107)
Q Consensus 49 ~~~~~C~~C~~~f~~~~~l~~H~~~-h~~k~~~--C~~C~ 85 (107)
...|+|+.|+..-.+...|..|+.. |-..++. |++|+
T Consensus 77 ~qSftCPyC~~~Gfte~~f~~Hv~s~Hpda~~~~icp~c~ 116 (381)
T KOG1280|consen 77 PQSFTCPYCGIMGFTERQFGTHVLSQHPEASTSVICPLCA 116 (381)
T ss_pred cccccCCcccccccchhHHHHHhhhcCcccCcceeeeccc
Confidence 4578899999887788888888764 4444443 45664
No 271
>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG
Probab=29.19 E-value=29 Score=16.46 Aligned_cols=9 Identities=22% Similarity=0.685 Sum_probs=5.9
Q ss_pred cCCCCCCcc
Q psy11352 80 ACSSCSHVS 88 (107)
Q Consensus 80 ~C~~C~~~f 88 (107)
.|+.||..+
T Consensus 2 ~CPyCge~~ 10 (52)
T PF14255_consen 2 QCPYCGEPI 10 (52)
T ss_pred CCCCCCCee
Confidence 577777654
No 272
>PF11789 zf-Nse: Zinc-finger of the MIZ type in Nse subunit; PDB: 2YU4_A 3HTK_C.
Probab=29.15 E-value=61 Score=15.54 Aligned_cols=31 Identities=16% Similarity=0.229 Sum_probs=14.6
Q ss_pred CeeeCCCCcccccchhhHHHHHhhhCCCcccCCC
Q psy11352 50 LFATCFVCGKQLSNQYNLRVHMETHQNAFYACSS 83 (107)
Q Consensus 50 ~~~~C~~C~~~f~~~~~l~~H~~~h~~k~~~C~~ 83 (107)
.|.....|+-.|.....+ ..+ .......|+.
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 566667777777665433 232 1125667776
No 273
>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=29.15 E-value=26 Score=15.37 Aligned_cols=13 Identities=23% Similarity=0.611 Sum_probs=9.3
Q ss_pred eeeCCCCcccccc
Q psy11352 51 FATCFVCGKQLSN 63 (107)
Q Consensus 51 ~~~C~~C~~~f~~ 63 (107)
-+.|+.||..+..
T Consensus 32 ~~~C~~CGE~~~~ 44 (46)
T TIGR03831 32 ALVCPQCGEEYLD 44 (46)
T ss_pred ccccccCCCEeeC
Confidence 3678999877654
No 274
>COG2995 PqiA Uncharacterized paraquat-inducible protein A [Function unknown]
Probab=28.94 E-value=84 Score=21.82 Aligned_cols=34 Identities=26% Similarity=0.556 Sum_probs=19.8
Q ss_pred cccccCCCCCCCCCccCCCCCCCCCCCCCCCCCCCCCCCCCeeeCCCCccccc
Q psy11352 10 LHFLISDHCLTSPLSSSIPGSSKTKASGSGTTGGSSNHSKLFATCFVCGKQLS 62 (107)
Q Consensus 10 ~~~~~C~~C~~~~~~~~~~~~l~~h~~~~~~~~~~~~~~~~~~~C~~C~~~f~ 62 (107)
.+...|++| +..+.-+ .+..+ ..-.|+.||-...
T Consensus 16 ~~~~~C~eC---d~~~~~P-~l~~~---------------q~A~CPRC~~~l~ 49 (418)
T COG2995 16 GHLILCPEC---DMLVSLP-RLDSG---------------QSAYCPRCGHTLT 49 (418)
T ss_pred cceecCCCC---Cceeccc-cCCCC---------------CcccCCCCCCccc
Confidence 445678888 7766555 33333 3346777775443
No 275
>PRK14138 NAD-dependent deacetylase; Provisional
Probab=28.34 E-value=1e+02 Score=19.61 Aligned_cols=34 Identities=21% Similarity=0.436 Sum_probs=20.3
Q ss_pred CeeeCCCCcccccchhhHHHHHhhhCCCcccCCCCCC
Q psy11352 50 LFATCFVCGKQLSNQYNLRVHMETHQNAFYACSSCSH 86 (107)
Q Consensus 50 ~~~~C~~C~~~f~~~~~l~~H~~~h~~k~~~C~~C~~ 86 (107)
....|..|++.|.....+. .......-.|+.|+-
T Consensus 118 ~~~~C~~C~~~~~~~~~~~---~~~~~~~p~Cp~Cgg 151 (244)
T PRK14138 118 EEYYCVRCGKRYTVEDVIE---KLEKSDVPRCDDCSG 151 (244)
T ss_pred CeeEECCCCCcccHHHHHH---HHhcCCCCCCCCCCC
Confidence 4567999998877644332 111223346888873
No 276
>KOG4727|consensus
Probab=28.25 E-value=49 Score=20.03 Aligned_cols=23 Identities=22% Similarity=0.258 Sum_probs=19.4
Q ss_pred CeeeCCCCcccccchhhHHHHHh
Q psy11352 50 LFATCFVCGKQLSNQYNLRVHME 72 (107)
Q Consensus 50 ~~~~C~~C~~~f~~~~~l~~H~~ 72 (107)
--|-|++|+-++..+-++..|+.
T Consensus 74 ~GyyCdVCdcvvKDSinflDHiN 96 (193)
T KOG4727|consen 74 GGYYCDVCDCVVKDSINFLDHIN 96 (193)
T ss_pred CceeeeecceeehhhHHHHHHhc
Confidence 45889999999999988888864
No 277
>PF14690 zf-ISL3: zinc-finger of transposase IS204/IS1001/IS1096/IS1165
Probab=28.24 E-value=33 Score=15.24 Aligned_cols=10 Identities=20% Similarity=0.517 Sum_probs=7.4
Q ss_pred CcccCCCCCC
Q psy11352 77 AFYACSSCSH 86 (107)
Q Consensus 77 k~~~C~~C~~ 86 (107)
+|..|+.||.
T Consensus 1 ~~~~Cp~Cg~ 10 (47)
T PF14690_consen 1 KPPRCPHCGS 10 (47)
T ss_pred CCccCCCcCC
Confidence 3667899984
No 278
>PF05876 Terminase_GpA: Phage terminase large subunit (GpA); InterPro: IPR008866 This entry is represented by Bacteriophage lambda, GpA. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry consists of several phage terminase large subunit proteins as well as related sequences from several bacterial species. The DNA packaging enzyme of bacteriophage lambda, terminase, is a heteromultimer composed of a small subunit, gpNu1, and a large subunit, gpA, products of the Nu1 and A genes, respectively. Terminase is involved in the site-specific binding and cutting of the DNA in the initial stages of packaging. It is now known that gpA is actively involved in late stages of packaging, including DNA translocation, and that this enzyme contains separate functional domains for its early and late packaging activities [].
Probab=28.15 E-value=80 Score=22.82 Aligned_cols=14 Identities=21% Similarity=0.477 Sum_probs=9.2
Q ss_pred CeeeCCCCcccccc
Q psy11352 50 LFATCFVCGKQLSN 63 (107)
Q Consensus 50 ~~~~C~~C~~~f~~ 63 (107)
-.|.|+.||.....
T Consensus 228 a~y~C~~Cg~~i~e 241 (557)
T PF05876_consen 228 ARYVCPHCGCEIEE 241 (557)
T ss_pred eEEECCCCcCCCCH
Confidence 45778777766544
No 279
>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=27.92 E-value=16 Score=23.64 Aligned_cols=20 Identities=15% Similarity=0.348 Sum_probs=13.7
Q ss_pred CcccCCCCCCcccChHHHHH
Q psy11352 77 AFYACSSCSHVSRSRDALRK 96 (107)
Q Consensus 77 k~~~C~~C~~~f~~~~~l~~ 96 (107)
+++.|+.||.....-..|..
T Consensus 208 k~~PCPKCg~et~eTkdLSm 227 (314)
T PF06524_consen 208 KPIPCPKCGYETQETKDLSM 227 (314)
T ss_pred CCCCCCCCCCccccccccee
Confidence 68899999876555444443
No 280
>PF14447 Prok-RING_4: Prokaryotic RING finger family 4
Probab=27.88 E-value=32 Score=16.58 Aligned_cols=11 Identities=18% Similarity=0.431 Sum_probs=6.8
Q ss_pred cCCCCCCcccC
Q psy11352 80 ACSSCSHVSRS 90 (107)
Q Consensus 80 ~C~~C~~~f~~ 90 (107)
.|+.|++.|..
T Consensus 41 gCPfC~~~~~~ 51 (55)
T PF14447_consen 41 GCPFCGTPFEF 51 (55)
T ss_pred CCCCCCCcccC
Confidence 46677766643
No 281
>COG5112 UFD2 U1-like Zn-finger-containing protein [General function prediction only]
Probab=27.81 E-value=20 Score=19.75 Aligned_cols=21 Identities=24% Similarity=0.400 Sum_probs=11.0
Q ss_pred ccCCCCCCcccChHHHHHHHH
Q psy11352 79 YACSSCSHVSRSRDALRKHVS 99 (107)
Q Consensus 79 ~~C~~C~~~f~~~~~l~~H~~ 99 (107)
+.|.+|.+-|...-.|..|.+
T Consensus 56 hYCieCaryf~t~~aL~~Hkk 76 (126)
T COG5112 56 HYCIECARYFITEKALMEHKK 76 (126)
T ss_pred eeeehhHHHHHHHHHHHHHhc
Confidence 445555555555555555543
No 282
>PF03833 PolC_DP2: DNA polymerase II large subunit DP2; InterPro: IPR016033 DP2 is the large subunit of a two-subunit novel archaebacterial replicative DNA polymerase first characterised for Pyrococcus furiosus. The structure of DP2 appears to be organised as a ~950 residue component separated from a ~300 residue component by a ~150 residue intein. The other subunit, DP1, has sequence similarity to the eukaryotic DNA polymerase delta small subunit. This entry represents the N-terminal ~950 residue component of DP2.; GO: 0003887 DNA-directed DNA polymerase activity; PDB: 3O59_X.
Probab=27.62 E-value=20 Score=27.14 Aligned_cols=7 Identities=29% Similarity=1.165 Sum_probs=0.0
Q ss_pred cCCCCCC
Q psy11352 80 ACSSCSH 86 (107)
Q Consensus 80 ~C~~C~~ 86 (107)
.|+.|+.
T Consensus 694 ~C~~C~~ 700 (900)
T PF03833_consen 694 ECPKCGR 700 (900)
T ss_dssp -------
T ss_pred ccccccc
Confidence 4455543
No 283
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=27.06 E-value=32 Score=14.55 Aligned_cols=10 Identities=30% Similarity=1.099 Sum_probs=5.1
Q ss_pred eeCCCCcccc
Q psy11352 52 ATCFVCGKQL 61 (107)
Q Consensus 52 ~~C~~C~~~f 61 (107)
+.|..|+..|
T Consensus 22 ~~C~~Cg~~~ 31 (33)
T PF08792_consen 22 EVCIFCGSSF 31 (33)
T ss_pred EEcccCCcEe
Confidence 4455555544
No 284
>COG4332 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=27.03 E-value=24 Score=21.51 Aligned_cols=44 Identities=16% Similarity=0.175 Sum_probs=22.7
Q ss_pred ccCCCCCCCCCccCCCCCCCCCCCCCCCCCCCCCCCCCeeeCCCCcccccc
Q psy11352 13 LISDHCLTSPLSSSIPGSSKTKASGSGTTGGSSNHSKLFATCFVCGKQLSN 63 (107)
Q Consensus 13 ~~C~~C~~~~~~~~~~~~l~~h~~~~~~~~~~~~~~~~~~~C~~C~~~f~~ 63 (107)
-.|+.||. -+.|..++-+...+.+...... -.|+|..|++++..
T Consensus 18 k~C~~Cg~-kr~f~cSg~fRvNAq~K~LDvW------lIYkC~~Cd~tWN~ 61 (203)
T COG4332 18 KRCNSCGV-KRAFTCSGKFRVNAQGKVLDVW------LIYKCTHCDYTWNI 61 (203)
T ss_pred hhCcccCC-cceeeecCcEEEcCCCcEEEEE------EEEEeeccCCccch
Confidence 46888821 1335555544444211111111 25889999987654
No 285
>PF04032 Rpr2: RNAse P Rpr2/Rpp21/SNM1 subunit domain; InterPro: IPR007175 This family contains a ribonuclease P subunit of human and yeast. Other members of the family include the probable archaeal homologues. This subunit possibly binds the precursor tRNA [].; PDB: 2K3R_A 2KI7_B 2ZAE_B 1X0T_A.
Probab=26.82 E-value=31 Score=17.61 Aligned_cols=9 Identities=22% Similarity=0.578 Sum_probs=4.5
Q ss_pred cccccCCCC
Q psy11352 10 LHFLISDHC 18 (107)
Q Consensus 10 ~~~~~C~~C 18 (107)
.+...|..|
T Consensus 44 ~kr~~Ck~C 52 (85)
T PF04032_consen 44 IKRTICKKC 52 (85)
T ss_dssp CCCTB-TTT
T ss_pred HhcccccCC
Confidence 455556666
No 286
>PF03145 Sina: Seven in absentia protein family; InterPro: IPR018121 The seven in absentia (sina) gene was first identified in Drosophila. The Drosophila Sina protein is essential for the determination of the R7 pathway in photoreceptor cell development: the loss of functional Sina results in the transformation of the R7 precursor cell to a non-neuronal cell type. The Sina protein contains an N-terminal RING finger domain C3HC4-type. Through this domain, Sina binds E2 ubiquitin-conjugating enzymes (UbcD1) Sina also interacts with Tramtrack (TTK88) via PHYL. Tramtrack is a transcriptional repressor that blocks photoreceptor determination, while PHYL down-regulates the activity of TTK88. In turn, the activity of PHYL requires the activation of the Sevenless receptor tyrosine kinase, a process essential for R7 determination. It is thought that Sina targets TTK88 for degradation, therefore promoting the R7 pathway. Murine and human homologues of Sina have also been identified. The human homologue Siah-1 [] also binds E2 enzymes (UbcH5) and through a series of physical interactions, targets beta-catenin for ubiquitin degradation. Siah-1 expression is enhanced by p53, itself promoted by DNA damage. Thus this pathway links DNA damage to beta-catenin degradation [, ]. Sina proteins, therefore, physically interact with a variety of proteins. The N-terminal RING finger domain that binds ubiquitin conjugating enzymes is a C3HC4-type, and does not form part of the alignment for this family. The remainder C-terminal part is involved in interactions with other proteins, and is included in this alignment. In addition to the Drosophila protein and mammalian homologues, whose similarity was noted previously, this family also includes putative homologues from Caenorhabditis elegans, Arabidopsis thaliana.; GO: 0006511 ubiquitin-dependent protein catabolic process, 0007275 multicellular organismal development, 0005634 nucleus; PDB: 2A25_A 1K2F_B 2AN6_C.
Probab=26.81 E-value=62 Score=19.61 Aligned_cols=53 Identities=21% Similarity=0.317 Sum_probs=27.1
Q ss_pred CeeeCCC----CcccccchhhHHHHHhhhCCCcccCCC----CCCcccChHHHHHHHHccCCC
Q psy11352 50 LFATCFV----CGKQLSNQYNLRVHMETHQNAFYACSS----CSHVSRSRDALRKHVSYRHPH 104 (107)
Q Consensus 50 ~~~~C~~----C~~~f~~~~~l~~H~~~h~~k~~~C~~----C~~~f~~~~~l~~H~~~~H~~ 104 (107)
..+.|.. |...+.. .....|.....-+|+.|+. |+..= ....|..|....|..
T Consensus 13 ~~~pC~~~~~GC~~~~~~-~~~~~HE~~C~~~p~~CP~~~~~C~~~G-~~~~l~~Hl~~~H~~ 73 (198)
T PF03145_consen 13 IKFPCKNAKYGCTETFPY-SEKREHEEECPFRPCSCPFPGSGCDWQG-SYKELLDHLRDKHSW 73 (198)
T ss_dssp --EE-CCGGGT---EE-G-GGHHHHHHT-TTSEEE-SSSSTT---EE-ECCCHHHHHHHHTTT
T ss_pred ceecCCCCCCCCcccccc-cChhhHhccCCCcCCcCCCCCCCccccC-CHHHHHHHHHHHCCC
Confidence 4567744 7777554 3566777655558999987 65432 344688898877754
No 287
>PF02150 RNA_POL_M_15KD: RNA polymerases M/15 Kd subunit; InterPro: IPR001529 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. In archaebacteria, there is generally a single form of RNA polymerase which also consist of an oligomeric assemblage of 10 to 13 polypeptides. It has recently been shown [], [] that small subunits of about 15 kDa, found in polymerase types I and II, are highly conserved. These proteins contain a probable zinc finger in their N-terminal region and a C-terminal zinc ribbon domain (see IPR001222 from INTERPRO).; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3H0G_I 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I ....
Probab=26.63 E-value=13 Score=15.89 Aligned_cols=10 Identities=30% Similarity=0.806 Sum_probs=6.2
Q ss_pred eCCCCccccc
Q psy11352 53 TCFVCGKQLS 62 (107)
Q Consensus 53 ~C~~C~~~f~ 62 (107)
.|..|+..+.
T Consensus 22 ~C~~C~Y~~~ 31 (35)
T PF02150_consen 22 ACRTCGYEEP 31 (35)
T ss_dssp EESSSS-EEE
T ss_pred CCCCCCCccC
Confidence 6777776654
No 288
>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=26.17 E-value=46 Score=17.77 Aligned_cols=22 Identities=14% Similarity=0.395 Sum_probs=17.0
Q ss_pred eeeCCCCcccccchhhHHHHHh
Q psy11352 51 FATCFVCGKQLSNQYNLRVHME 72 (107)
Q Consensus 51 ~~~C~~C~~~f~~~~~l~~H~~ 72 (107)
...|+.||..|.....+..-.+
T Consensus 35 a~~C~~CGe~y~~dev~~eIE~ 56 (89)
T TIGR03829 35 SISCSHCGMEYQDDTTVKEIED 56 (89)
T ss_pred cccccCCCcEeecHHHHHHHHh
Confidence 3679999999998877665544
No 289
>PF09332 Mcm10: Mcm10 replication factor; InterPro: IPR015411 Mcm10 is a eukaryotic DNA replication factor that regulates the stability and chromatin association of DNA polymerase alpha []. ; PDB: 2KWQ_A.
Probab=26.11 E-value=19 Score=24.23 Aligned_cols=14 Identities=21% Similarity=0.285 Sum_probs=6.2
Q ss_pred eeeCCCCcccccch
Q psy11352 51 FATCFVCGKQLSNQ 64 (107)
Q Consensus 51 ~~~C~~C~~~f~~~ 64 (107)
.+.|..|.+++...
T Consensus 252 av~C~~C~yt~~~~ 265 (344)
T PF09332_consen 252 AVTCKQCKYTAFKP 265 (344)
T ss_dssp EEEETTT--EESS-
T ss_pred EEEcCCCCCcccCc
Confidence 45566666554443
No 290
>COG1779 C4-type Zn-finger protein [General function prediction only]
Probab=26.05 E-value=15 Score=22.66 Aligned_cols=11 Identities=27% Similarity=0.697 Sum_probs=5.3
Q ss_pred eeCCCCccccc
Q psy11352 52 ATCFVCGKQLS 62 (107)
Q Consensus 52 ~~C~~C~~~f~ 62 (107)
..|..||+.+.
T Consensus 44 ~~C~~CgYR~~ 54 (201)
T COG1779 44 GVCERCGYRST 54 (201)
T ss_pred EEccccCCccc
Confidence 34555555443
No 291
>PLN03239 histone acetyltransferase; Provisional
Probab=25.77 E-value=47 Score=22.50 Aligned_cols=23 Identities=13% Similarity=0.270 Sum_probs=20.3
Q ss_pred CcccCCCCCCcccChHHHHHHHH
Q psy11352 77 AFYACSSCSHVSRSRDALRKHVS 99 (107)
Q Consensus 77 k~~~C~~C~~~f~~~~~l~~H~~ 99 (107)
.-|.|+.|-+-|.....|.+|+.
T Consensus 105 ~lYiCE~Clky~~~~~~l~~H~~ 127 (351)
T PLN03239 105 VLYVCEFSFGFFARKSELLRFQA 127 (351)
T ss_pred eEEEeccchhhhcCHHHHHHHHH
Confidence 57999999999999999999975
No 292
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=25.35 E-value=66 Score=15.15 Aligned_cols=8 Identities=38% Similarity=0.733 Sum_probs=4.0
Q ss_pred eeCCCCcc
Q psy11352 52 ATCFVCGK 59 (107)
Q Consensus 52 ~~C~~C~~ 59 (107)
+.|..||.
T Consensus 38 ~~CGkCgy 45 (51)
T COG1998 38 WACGKCGY 45 (51)
T ss_pred eEeccccc
Confidence 45555554
No 293
>PF13901 DUF4206: Domain of unknown function (DUF4206)
Probab=25.19 E-value=1.1e+02 Score=18.80 Aligned_cols=14 Identities=14% Similarity=0.335 Sum_probs=10.3
Q ss_pred CeeeCCCCcccccc
Q psy11352 50 LFATCFVCGKQLSN 63 (107)
Q Consensus 50 ~~~~C~~C~~~f~~ 63 (107)
....|+.|+..|-.
T Consensus 171 ~~~~C~~C~~v~H~ 184 (202)
T PF13901_consen 171 TTVRCPKCKSVFHK 184 (202)
T ss_pred CeeeCCcCccccch
Confidence 45789999877644
No 294
>PRK12387 formate hydrogenlyase complex iron-sulfur subunit; Provisional
Probab=25.06 E-value=52 Score=19.69 Aligned_cols=18 Identities=17% Similarity=0.464 Sum_probs=14.3
Q ss_pred CcccCCCCCCcccChHHH
Q psy11352 77 AFYACSSCSHVSRSRDAL 94 (107)
Q Consensus 77 k~~~C~~C~~~f~~~~~l 94 (107)
.++.|..||+.|.....+
T Consensus 113 ~~~~C~~CG~~f~~~~~i 130 (180)
T PRK12387 113 ALCNCRVCGRPFAVQKEI 130 (180)
T ss_pred CcccchhhCCccccHHHH
Confidence 578999999999866543
No 295
>PLN00104 MYST -like histone acetyltransferase; Provisional
Probab=25.05 E-value=68 Score=22.59 Aligned_cols=23 Identities=22% Similarity=0.700 Sum_probs=18.2
Q ss_pred CcccCCCCCCcccChHHHHHHHH
Q psy11352 77 AFYACSSCSHVSRSRDALRKHVS 99 (107)
Q Consensus 77 k~~~C~~C~~~f~~~~~l~~H~~ 99 (107)
.-|.|+.|-+-|.....|.+|+.
T Consensus 197 ~lyiCe~Cl~y~~~~~~~~~H~~ 219 (450)
T PLN00104 197 KLYFCEFCLKFMKRKEQLQRHMK 219 (450)
T ss_pred eEEEchhhhhhhcCHHHHHHHHh
Confidence 46788888888888888888876
No 296
>cd01327 KAZAL_PSTI Kazal-type pancreatic secretory trypsin inhibitors (PSTI) and related proteins, including the second domain of the ovomucoid turkey inhibitor and the C-terminal domain of the esophagus cancer-related gene-2 protein (ECRG-2), are members of the superfamily of kazal-type proteinase inhibitors and follistatin-like proteins.
Probab=24.91 E-value=41 Score=15.15 Aligned_cols=16 Identities=19% Similarity=0.000 Sum_probs=11.0
Q ss_pred CCCCCCCCccCCCCCC
Q psy11352 16 DHCLTSPLSSSIPGSS 31 (107)
Q Consensus 16 ~~C~~~~~~~~~~~~l 31 (107)
++||+++.+|.+.-.|
T Consensus 11 PVCGsDg~TY~N~C~l 26 (45)
T cd01327 11 PVCGTDGVTYSNECLL 26 (45)
T ss_pred ceeCCCCCEeCCHhHH
Confidence 5687777777666555
No 297
>PF06170 DUF983: Protein of unknown function (DUF983); InterPro: IPR009325 This family consists of several bacterial proteins of unknown function.
Probab=24.08 E-value=41 Score=17.72 Aligned_cols=12 Identities=17% Similarity=0.357 Sum_probs=7.6
Q ss_pred ccCCCCCCcccC
Q psy11352 79 YACSSCSHVSRS 90 (107)
Q Consensus 79 ~~C~~C~~~f~~ 90 (107)
-.|+.||..|..
T Consensus 9 ~~C~~CG~d~~~ 20 (86)
T PF06170_consen 9 PRCPHCGLDYSH 20 (86)
T ss_pred CcccccCCcccc
Confidence 357777766654
No 298
>PF02146 SIR2: Sir2 family; InterPro: IPR003000 These sequences represent the Sirtuin (Sir2-related) family of NAD+-dependent deacetylases. This family of enzymes is broadly conserved from bacteria to humans. In yeast, Sir2 proteins form complexes with other proteins to silence chromatin by accessing histones and deacetylating them. Sir2 proteins have been proposed to play a role in silencing, chromosome stability and ageing []. The bacterial enzyme CobB, an homologue of Sir2, is a phosphoribosyltransferase []. An in vitro ADP ribosyltransferase activity has also been associated with human members of this family []. Sir2-like enzymes employ NAD+ as a cosubstrate in deacetylation reactions [] and catalyse a reaction in which the cleavage of NAD(+)and histone and/or protein deacetylation are coupled to the formation of O-acetyl-ADP-ribose, a novel metabolite. The dependence of the reaction on both NAD(+) and the generation of this potential second messenger offers new clues to understanding the function and regulation of nuclear, cytoplasmic and mitochondrial Sir2-like enzymes []. Silent Information Regulator protein of Saccharomyces cerevisiae (Sir2) is one of several factors critical for silencing at least three loci. Among them, it is unique because it silences the rDNA as well as the mating type loci and telomeres []. Sir2 interacts in a complex with itself and with Sir3 and Sir4, two proteins that are able to interact with nucleosomes. In addition Sir2 also interacts with ubiquitination factors and/or complexes []. Homologues of Sir2 share a core domain including the GAG and NID motifs and a putative C4 Zinc finger. The regions containing these three conserved motifs are individually essential for Sir2 silencing function, as are the four cysteins []. In addition, the conserved residues HG next to the putative Zn finger have been shown to be essential for the ADP ribosyltransferase activity []. ; GO: 0008270 zinc ion binding, 0070403 NAD+ binding, 0006476 protein deacetylation; PDB: 1S5P_A 3PKI_E 3PKJ_F 3K35_A 1ICI_A 1M2K_A 1M2G_A 1M2N_B 1M2H_A 1M2J_A ....
Probab=23.72 E-value=1.1e+02 Score=18.21 Aligned_cols=35 Identities=17% Similarity=0.431 Sum_probs=21.9
Q ss_pred CeeeCCCCcccccchhhHHHHHhhhCCCcccCCCCCCc
Q psy11352 50 LFATCFVCGKQLSNQYNLRVHMETHQNAFYACSSCSHV 87 (107)
Q Consensus 50 ~~~~C~~C~~~f~~~~~l~~H~~~h~~k~~~C~~C~~~ 87 (107)
....|..|++.+....... ....+.+-.|+.|+..
T Consensus 104 ~~~~C~~C~~~~~~~~~~~---~~~~~~~~~C~~C~~~ 138 (178)
T PF02146_consen 104 FRLRCSKCGKEYDREDIVD---SIDEEEPPRCPKCGGL 138 (178)
T ss_dssp EEEEETTTSBEEEGHHHHH---HHHTTSSCBCTTTSCB
T ss_pred ceeeecCCCccccchhhcc---cccccccccccccCcc
Confidence 4578999999887644321 1222334489999863
No 299
>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=23.66 E-value=34 Score=15.88 Aligned_cols=10 Identities=20% Similarity=0.793 Sum_probs=3.7
Q ss_pred CcccCCCCCC
Q psy11352 77 AFYACSSCSH 86 (107)
Q Consensus 77 k~~~C~~C~~ 86 (107)
..|.|++|++
T Consensus 40 ~~W~CPiC~~ 49 (50)
T PF02891_consen 40 PKWKCPICNK 49 (50)
T ss_dssp ---B-TTT--
T ss_pred CCeECcCCcC
Confidence 4589999975
No 300
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=23.59 E-value=35 Score=16.37 Aligned_cols=12 Identities=17% Similarity=0.589 Sum_probs=7.6
Q ss_pred ccCCCCCCcccC
Q psy11352 79 YACSSCSHVSRS 90 (107)
Q Consensus 79 ~~C~~C~~~f~~ 90 (107)
..|..||+.|..
T Consensus 6 ~~C~~Cg~~~~~ 17 (54)
T PF14446_consen 6 CKCPVCGKKFKD 17 (54)
T ss_pred ccChhhCCcccC
Confidence 357777777753
No 301
>PF03107 C1_2: C1 domain; InterPro: IPR004146 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in DAG_PE-bind (IPR002219 from INTERPRO), therefore we have termed this domain DC1 for divergent C1 domain. This domain probably also binds to two zinc ions. The function of proteins with this domain is uncertain, however this domain may bind to molecules such as diacylglycerol. This family are found in plant proteins.
Probab=23.26 E-value=55 Score=13.21 Aligned_cols=9 Identities=22% Similarity=0.840 Sum_probs=4.7
Q ss_pred ccCCCCCCc
Q psy11352 79 YACSSCSHV 87 (107)
Q Consensus 79 ~~C~~C~~~ 87 (107)
|.|..|++.
T Consensus 1 ~~C~~C~~~ 9 (30)
T PF03107_consen 1 FWCDVCRRK 9 (30)
T ss_pred CCCCCCCCC
Confidence 345666544
No 302
>KOG2807|consensus
Probab=23.21 E-value=85 Score=21.22 Aligned_cols=19 Identities=26% Similarity=0.350 Sum_probs=10.8
Q ss_pred cccCCCCCCcccChHHHHH
Q psy11352 78 FYACSSCSHVSRSRDALRK 96 (107)
Q Consensus 78 ~~~C~~C~~~f~~~~~l~~ 96 (107)
|..|+.|+-.......|.+
T Consensus 290 P~eCpiC~ltLVss~hLAR 308 (378)
T KOG2807|consen 290 PIECPICSLTLVSSPHLAR 308 (378)
T ss_pred CccCCccceeEecchHHHH
Confidence 5566666655555555543
No 303
>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=22.98 E-value=48 Score=14.63 Aligned_cols=10 Identities=40% Similarity=0.760 Sum_probs=6.1
Q ss_pred eeCCCCcccc
Q psy11352 52 ATCFVCGKQL 61 (107)
Q Consensus 52 ~~C~~C~~~f 61 (107)
+.|..||...
T Consensus 20 ~vC~~CG~Vl 29 (43)
T PF08271_consen 20 LVCPNCGLVL 29 (43)
T ss_dssp EEETTT-BBE
T ss_pred EECCCCCCEe
Confidence 6777777654
No 304
>PF14375 Cys_rich_CWC: Cysteine-rich CWC
Probab=22.57 E-value=50 Score=15.25 Aligned_cols=9 Identities=22% Similarity=0.689 Sum_probs=4.6
Q ss_pred CCCCCCccc
Q psy11352 81 CSSCSHVSR 89 (107)
Q Consensus 81 C~~C~~~f~ 89 (107)
|+.||..|.
T Consensus 1 CP~Cg~~f~ 9 (50)
T PF14375_consen 1 CPRCGAPFE 9 (50)
T ss_pred CCCCCCcCC
Confidence 455555553
No 305
>cd01410 SIRT7 SIRT7: Eukaryotic and prokaryotic group (class4) which includes human sirtuin SIRT6, SIRT7, and several bacterial homologs; and are members of the SIR2 family of proteins, silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation. Sir2 proteins have been shown to regulate gene silencing, DNA repair, metabolic enzymes, and life span.
Probab=22.40 E-value=1.4e+02 Score=18.45 Aligned_cols=34 Identities=15% Similarity=0.420 Sum_probs=19.1
Q ss_pred CeeeCCCCcccccchhhHHHHHhhhCC-CcccCCCCCC
Q psy11352 50 LFATCFVCGKQLSNQYNLRVHMETHQN-AFYACSSCSH 86 (107)
Q Consensus 50 ~~~~C~~C~~~f~~~~~l~~H~~~h~~-k~~~C~~C~~ 86 (107)
....|..|+..+.....+. ..... ....|+.||.
T Consensus 94 ~~~~C~~C~~~~~~~~~~~---~~~~~~~~p~C~~Cgg 128 (206)
T cd01410 94 FIEVCKSCGPEYVRDDVVE---TRGDKETGRRCHACGG 128 (206)
T ss_pred CcccCCCCCCccchHHHHH---HhhcCCCCCcCCCCcC
Confidence 4466888987766543321 11122 3456888874
No 306
>PTZ00064 histone acetyltransferase; Provisional
Probab=22.19 E-value=95 Score=22.37 Aligned_cols=24 Identities=25% Similarity=0.384 Sum_probs=19.7
Q ss_pred CcccCCCCCCcccChHHHHHHHHc
Q psy11352 77 AFYACSSCSHVSRSRDALRKHVSY 100 (107)
Q Consensus 77 k~~~C~~C~~~f~~~~~l~~H~~~ 100 (107)
.-|.|+.|-+-|.....|.+|+..
T Consensus 279 ~LYICEfCLkY~~s~~~l~rH~~~ 302 (552)
T PTZ00064 279 TLHFCEYCLDFFCFEDELIRHLSR 302 (552)
T ss_pred eEEEccchhhhhCCHHHHHHHHhc
Confidence 468888888888888888888873
No 307
>PRK08270 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=22.16 E-value=65 Score=23.85 Aligned_cols=10 Identities=20% Similarity=0.640 Sum_probs=6.5
Q ss_pred CcccCCCCCC
Q psy11352 77 AFYACSSCSH 86 (107)
Q Consensus 77 k~~~C~~C~~ 86 (107)
.-+.|+.||.
T Consensus 638 ~~~~CP~CG~ 647 (656)
T PRK08270 638 EHEFCPKCGE 647 (656)
T ss_pred CCCCCcCCcC
Confidence 3467777774
No 308
>PF14369 zf-RING_3: zinc-finger
Probab=21.74 E-value=49 Score=14.11 Aligned_cols=8 Identities=25% Similarity=0.646 Sum_probs=4.2
Q ss_pred CCCCCCcc
Q psy11352 81 CSSCSHVS 88 (107)
Q Consensus 81 C~~C~~~f 88 (107)
|+.|+-.|
T Consensus 24 CP~C~~gF 31 (35)
T PF14369_consen 24 CPRCHGGF 31 (35)
T ss_pred CcCCCCcE
Confidence 55555444
No 309
>KOG2857|consensus
Probab=21.72 E-value=50 Score=19.33 Aligned_cols=21 Identities=10% Similarity=0.023 Sum_probs=18.1
Q ss_pred cccCCCCCCCCCccCCCCCCCCCC
Q psy11352 12 FLISDHCLTSPLSSSIPGSSKTKA 35 (107)
Q Consensus 12 ~~~C~~C~~~~~~~~~~~~l~~h~ 35 (107)
.|+|+.| ...+-+...++.|.
T Consensus 17 KYKCpkC---~vPYCSl~CfKiHk 37 (157)
T KOG2857|consen 17 KYKCPKC---SVPYCSLPCFKIHK 37 (157)
T ss_pred hccCCCC---CCccccchhhhhcc
Confidence 6999999 88888888888883
No 310
>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=21.53 E-value=31 Score=21.53 Aligned_cols=26 Identities=15% Similarity=0.293 Sum_probs=0.0
Q ss_pred CeeeCCCCcccccchhhHHHHHhhhCC
Q psy11352 50 LFATCFVCGKQLSNQYNLRVHMETHQN 76 (107)
Q Consensus 50 ~~~~C~~C~~~f~~~~~l~~H~~~h~~ 76 (107)
....|++||..... ..|..||++.+-
T Consensus 167 ~~~~cPitGe~IP~-~e~~eHmRi~Ll 192 (229)
T PF12230_consen 167 KMIICPITGEMIPA-DEMDEHMRIELL 192 (229)
T ss_dssp ---------------------------
T ss_pred cccccccccccccc-cccccccccccc
Confidence 34678888877654 557888887764
No 311
>cd01413 SIR2_Af2 SIR2_Af2: Archaeal and prokaryotic group which includes Archaeoglobus fulgidus Sir2-Af2, Sulfolobus solfataricus ssSir2, and several bacterial homologs; and are members of the SIR2 family of proteins, silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation. Sir2 proteins have been shown to regulate gene silencing, DNA repair, metabolic enzymes, and life span. The Sir2 homolog from the archaea Sulfolobus solftaricus deacetylates the non-specific DNA protein Alba to mediate transcription repression.
Probab=21.46 E-value=1.4e+02 Score=18.64 Aligned_cols=33 Identities=18% Similarity=0.434 Sum_probs=18.4
Q ss_pred CeeeCCCCcccccchhhHHHHHhhhCCCcccCCCCCC
Q psy11352 50 LFATCFVCGKQLSNQYNLRVHMETHQNAFYACSSCSH 86 (107)
Q Consensus 50 ~~~~C~~C~~~f~~~~~l~~H~~~h~~k~~~C~~C~~ 86 (107)
....|..|+..+..... . ....+..-.|+.|+.
T Consensus 112 ~~~~C~~C~~~~~~~~~-~---~~~~~~~p~C~~Cgg 144 (222)
T cd01413 112 QTAYCVNCGSKYDLEEV-K---YAKKHEVPRCPKCGG 144 (222)
T ss_pred CcceECCCCCCcchhHH-H---HhccCCCCcCCCCCC
Confidence 44678888887765432 1 111123346888864
No 312
>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=20.97 E-value=43 Score=16.52 Aligned_cols=14 Identities=21% Similarity=0.377 Sum_probs=11.2
Q ss_pred CeeeCCCCcccccc
Q psy11352 50 LFATCFVCGKQLSN 63 (107)
Q Consensus 50 ~~~~C~~C~~~f~~ 63 (107)
-...|+.|+..|.-
T Consensus 52 g~L~Cp~c~r~YPI 65 (68)
T PF03966_consen 52 GELICPECGREYPI 65 (68)
T ss_dssp TEEEETTTTEEEEE
T ss_pred CEEEcCCCCCEEeC
Confidence 45889999998864
No 313
>COG2879 Uncharacterized small protein [Function unknown]
Probab=20.81 E-value=1.1e+02 Score=15.21 Aligned_cols=16 Identities=25% Similarity=0.463 Sum_probs=11.1
Q ss_pred ChHHHHHHHHccCCCC
Q psy11352 90 SRDALRKHVSYRHPHI 105 (107)
Q Consensus 90 ~~~~l~~H~~~~H~~e 105 (107)
.-++...||+.+|++.
T Consensus 24 dYdnYVehmr~~hPd~ 39 (65)
T COG2879 24 DYDNYVEHMRKKHPDK 39 (65)
T ss_pred cHHHHHHHHHHhCcCC
Confidence 4566778888767654
No 314
>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=20.68 E-value=70 Score=15.08 Aligned_cols=15 Identities=13% Similarity=0.578 Sum_probs=9.6
Q ss_pred CeeeCCCCcccccch
Q psy11352 50 LFATCFVCGKQLSNQ 64 (107)
Q Consensus 50 ~~~~C~~C~~~f~~~ 64 (107)
..+.|..|++.+...
T Consensus 34 ~~~rC~YCe~~~~~~ 48 (52)
T PF02748_consen 34 IKLRCHYCERIITED 48 (52)
T ss_dssp CEEEETTT--EEEHH
T ss_pred CEEEeeCCCCEeccc
Confidence 668899998877543
No 315
>COG1439 Predicted nucleic acid-binding protein, consists of a PIN domain and a Zn-ribbon module [General function prediction only]
Probab=20.66 E-value=61 Score=19.71 Aligned_cols=25 Identities=16% Similarity=0.390 Sum_probs=16.7
Q ss_pred CeeeCCCCcccccchhhHHHHHhhhCCCcccCCCCCCc
Q psy11352 50 LFATCFVCGKQLSNQYNLRVHMETHQNAFYACSSCSHV 87 (107)
Q Consensus 50 ~~~~C~~C~~~f~~~~~l~~H~~~h~~k~~~C~~C~~~ 87 (107)
-.+.|..|++.|.. .--.|+.||-.
T Consensus 138 w~~rC~GC~~~f~~-------------~~~~Cp~CG~~ 162 (177)
T COG1439 138 WRLRCHGCKRIFPE-------------PKDFCPICGSP 162 (177)
T ss_pred eeEEEecCceecCC-------------CCCcCCCCCCc
Confidence 34778889888872 12358888854
No 316
>PF04328 DUF466: Protein of unknown function (DUF466); InterPro: IPR007423 This is a small bacterial protein of unknown function.
Probab=20.41 E-value=1e+02 Score=15.28 Aligned_cols=15 Identities=27% Similarity=0.536 Sum_probs=9.5
Q ss_pred HHHHHHHccCCCCCC
Q psy11352 93 ALRKHVSYRHPHISP 107 (107)
Q Consensus 93 ~l~~H~~~~H~~ekp 107 (107)
....|++.+|+++.|
T Consensus 27 ~Yv~H~~~~HP~~p~ 41 (65)
T PF04328_consen 27 RYVEHMRRHHPDEPP 41 (65)
T ss_pred HHHHHHHHHCcCCCC
Confidence 344677777877654
No 317
>PF12773 DZR: Double zinc ribbon
Probab=20.34 E-value=65 Score=14.52 Aligned_cols=10 Identities=20% Similarity=0.527 Sum_probs=5.6
Q ss_pred cccCCCCCCc
Q psy11352 78 FYACSSCSHV 87 (107)
Q Consensus 78 ~~~C~~C~~~ 87 (107)
...|+.|+..
T Consensus 29 ~~~C~~Cg~~ 38 (50)
T PF12773_consen 29 KKICPNCGAE 38 (50)
T ss_pred CCCCcCCcCC
Confidence 4556666654
No 318
>KOG4477|consensus
Probab=20.06 E-value=57 Score=19.99 Aligned_cols=23 Identities=26% Similarity=0.535 Sum_probs=13.8
Q ss_pred CeeeCCCCcccccchhhHHHHHhhhCCCcccCCCCC
Q psy11352 50 LFATCFVCGKQLSNQYNLRVHMETHQNAFYACSSCS 85 (107)
Q Consensus 50 ~~~~C~~C~~~f~~~~~l~~H~~~h~~k~~~C~~C~ 85 (107)
..|.|..|. |.+.. ..|.|.+|+
T Consensus 23 g~WdCsvCT--FrNsA-----------eAfkC~vCd 45 (228)
T KOG4477|consen 23 GKWDCSVCT--FRNSA-----------EAFKCFVCD 45 (228)
T ss_pred Cceeeeeee--ecchh-----------hhhheeeec
Confidence 557777773 43322 367777776
No 319
>PF01844 HNH: HNH endonuclease; InterPro: IPR002711 HNH endonuclease is found in bacteria and viruses [, , ]. This family includes pyocins, colicins and anaredoxins.; GO: 0003676 nucleic acid binding, 0004519 endonuclease activity; PDB: 2QGP_C.
Probab=20.02 E-value=19 Score=15.90 Aligned_cols=11 Identities=45% Similarity=0.896 Sum_probs=3.5
Q ss_pred CCCCcccccch
Q psy11352 54 CFVCGKQLSNQ 64 (107)
Q Consensus 54 C~~C~~~f~~~ 64 (107)
|..|++.+...
T Consensus 1 C~~C~~~~~~~ 11 (47)
T PF01844_consen 1 CQYCGKPGSDN 11 (47)
T ss_dssp -TTT--B--GG
T ss_pred CCCCCCcCccC
Confidence 56666665554
No 320
>PRK11032 hypothetical protein; Provisional
Probab=20.01 E-value=41 Score=20.04 Aligned_cols=28 Identities=21% Similarity=0.463 Sum_probs=16.1
Q ss_pred eeeCCCCcccccchhhHHHHHhhhCCCcccCCCCCCc
Q psy11352 51 FATCFVCGKQLSNQYNLRVHMETHQNAFYACSSCSHV 87 (107)
Q Consensus 51 ~~~C~~C~~~f~~~~~l~~H~~~h~~k~~~C~~C~~~ 87 (107)
.+.|..||..... .+.+.--.|+.||..
T Consensus 124 ~LvC~~Cg~~~~~---------~~p~~i~pCp~C~~~ 151 (160)
T PRK11032 124 NLVCEKCHHHLAF---------YTPEVLPLCPKCGHD 151 (160)
T ss_pred eEEecCCCCEEEe---------cCCCcCCCCCCCCCC
Confidence 4788888865321 233333368888753
Done!