Query psy10762
Match_columns 126
No_of_seqs 123 out of 2490
Neff 11.6
Searched_HMMs 46136
Date Fri Aug 16 17:52:39 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy10762.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/10762hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2462|consensus 100.0 1.2E-30 2.5E-35 156.1 6.1 107 6-114 159-265 (279)
2 KOG2462|consensus 100.0 2.3E-30 5E-35 154.9 6.2 117 6-124 128-247 (279)
3 KOG3576|consensus 99.8 1.2E-21 2.6E-26 113.2 3.0 113 5-117 114-237 (267)
4 KOG1074|consensus 99.8 9.5E-22 2.1E-26 132.5 1.1 51 66-116 607-657 (958)
5 KOG1074|consensus 99.8 1.4E-19 3.1E-24 122.2 2.0 52 66-117 881-932 (958)
6 KOG3623|consensus 99.7 1.2E-18 2.6E-23 116.6 2.3 106 9-114 211-331 (1007)
7 KOG3608|consensus 99.7 2.2E-17 4.8E-22 102.8 5.5 79 37-116 264-345 (467)
8 KOG3623|consensus 99.7 3.4E-18 7.3E-23 114.5 1.5 80 34-113 892-971 (1007)
9 KOG3576|consensus 99.7 6.2E-18 1.3E-22 98.0 0.9 81 34-114 115-195 (267)
10 KOG3608|consensus 99.6 2.4E-16 5.2E-21 98.2 5.3 113 2-116 201-316 (467)
11 PLN03086 PRLI-interacting fact 99.5 7E-14 1.5E-18 93.3 8.0 103 6-115 451-563 (567)
12 PHA00733 hypothetical protein 99.5 5.9E-14 1.3E-18 77.9 5.0 112 4-117 7-124 (128)
13 PHA02768 hypothetical protein; 99.3 2.2E-12 4.9E-17 60.2 1.7 44 64-109 5-48 (55)
14 PHA00733 hypothetical protein 99.3 1E-11 2.3E-16 68.9 4.3 82 6-89 38-124 (128)
15 PLN03086 PRLI-interacting fact 99.1 1.7E-10 3.6E-15 77.5 5.3 101 9-115 408-537 (567)
16 PHA02768 hypothetical protein; 99.1 1.1E-10 2.3E-15 54.6 2.1 39 9-49 6-44 (55)
17 PF13465 zf-H2C2_2: Zinc-finge 99.1 1.3E-10 2.9E-15 46.7 2.1 25 79-103 1-25 (26)
18 PF13465 zf-H2C2_2: Zinc-finge 98.9 1.3E-09 2.9E-14 43.7 1.9 24 52-75 2-25 (26)
19 KOG3993|consensus 98.8 1E-09 2.2E-14 70.5 1.4 114 8-121 295-487 (500)
20 KOG3993|consensus 98.8 8.9E-10 1.9E-14 70.8 0.5 27 91-117 355-381 (500)
21 PHA00616 hypothetical protein 98.8 2.5E-09 5.3E-14 47.7 1.7 29 92-120 1-29 (44)
22 PHA00616 hypothetical protein 98.7 1.4E-08 3E-13 45.3 1.7 33 8-40 1-33 (44)
23 PHA00732 hypothetical protein 98.7 2.3E-08 4.9E-13 50.9 2.6 45 36-86 1-46 (79)
24 PF05605 zf-Di19: Drought indu 98.7 8.6E-08 1.9E-12 45.4 4.4 50 64-116 2-53 (54)
25 PF00096 zf-C2H2: Zinc finger, 98.6 2.9E-08 6.2E-13 38.7 2.0 23 93-115 1-23 (23)
26 PF13894 zf-C2H2_4: C2H2-type 98.4 3.1E-07 6.8E-12 35.9 2.2 24 93-116 1-24 (24)
27 PHA00732 hypothetical protein 98.4 3.4E-07 7.3E-12 46.6 2.7 46 8-59 1-47 (79)
28 PF12756 zf-C2H2_2: C2H2 type 98.3 5.6E-07 1.2E-11 47.9 2.5 23 92-114 50-72 (100)
29 PF00096 zf-C2H2: Zinc finger, 98.3 7.8E-07 1.7E-11 34.5 2.2 23 9-31 1-23 (23)
30 PF13912 zf-C2H2_6: C2H2-type 98.3 4.7E-07 1E-11 36.5 1.5 25 92-116 1-25 (27)
31 PF05605 zf-Di19: Drought indu 98.3 3E-06 6.5E-11 40.1 4.2 48 9-59 3-52 (54)
32 PF09237 GAGA: GAGA factor; I 98.0 3.7E-06 8E-11 38.4 1.8 33 88-120 20-52 (54)
33 PF13912 zf-C2H2_6: C2H2-type 98.0 5.1E-06 1.1E-10 33.4 1.9 25 8-32 1-25 (27)
34 COG5189 SFP1 Putative transcri 98.0 1.4E-06 3.1E-11 54.7 0.1 52 62-113 347-419 (423)
35 smart00355 ZnF_C2H2 zinc finge 98.0 8.3E-06 1.8E-10 32.2 2.3 24 93-116 1-24 (26)
36 PF13894 zf-C2H2_4: C2H2-type 98.0 9.7E-06 2.1E-10 31.4 2.4 23 9-31 1-23 (24)
37 PF12756 zf-C2H2_2: C2H2 type 97.7 3.6E-05 7.7E-10 40.9 2.7 74 10-88 1-74 (100)
38 PF12874 zf-met: Zinc-finger o 97.7 2.3E-05 5E-10 30.8 1.5 23 93-115 1-23 (25)
39 COG5189 SFP1 Putative transcri 97.7 1.1E-05 2.4E-10 50.9 0.1 69 6-84 347-418 (423)
40 PF13909 zf-H2C2_5: C2H2-type 97.6 7.3E-05 1.6E-09 29.1 2.0 23 93-116 1-23 (24)
41 PRK04860 hypothetical protein; 97.6 5.6E-05 1.2E-09 43.8 2.1 38 64-105 119-156 (160)
42 PF09237 GAGA: GAGA factor; I 97.5 0.00021 4.5E-09 32.8 3.2 32 33-64 21-52 (54)
43 smart00355 ZnF_C2H2 zinc finge 97.5 0.00012 2.7E-09 28.6 2.0 23 9-31 1-23 (26)
44 PF12874 zf-met: Zinc-finger o 97.3 0.0002 4.3E-09 28.1 1.8 22 9-30 1-22 (25)
45 PF12171 zf-C2H2_jaz: Zinc-fin 97.2 8.9E-05 1.9E-09 29.7 0.0 22 93-114 2-23 (27)
46 PRK04860 hypothetical protein; 97.0 0.00067 1.4E-08 39.4 2.5 38 36-77 119-156 (160)
47 PF13913 zf-C2HC_2: zinc-finge 96.9 0.0012 2.6E-08 25.9 2.1 21 93-114 3-23 (25)
48 PF13909 zf-H2C2_5: C2H2-type 96.7 0.0022 4.8E-08 24.7 2.1 21 9-30 1-21 (24)
49 PF12171 zf-C2H2_jaz: Zinc-fin 96.5 0.0008 1.7E-08 26.9 0.1 22 9-30 2-23 (27)
50 smart00451 ZnF_U1 U1-like zinc 96.2 0.0046 9.9E-08 26.1 1.7 23 92-114 3-25 (35)
51 COG4049 Uncharacterized protei 96.1 0.0038 8.2E-08 29.2 1.4 28 89-116 14-41 (65)
52 KOG4173|consensus 96.0 0.0031 6.7E-08 37.7 1.1 76 36-114 79-168 (253)
53 cd00350 rubredoxin_like Rubred 95.8 0.0063 1.4E-07 25.6 1.2 8 92-99 17-24 (33)
54 smart00451 ZnF_U1 U1-like zinc 95.6 0.015 3.2E-07 24.5 2.1 22 8-29 3-24 (35)
55 KOG2231|consensus 95.5 0.052 1.1E-06 38.5 5.4 97 17-116 123-236 (669)
56 KOG2893|consensus 95.0 0.0048 1E-07 37.9 -0.5 46 67-116 13-59 (341)
57 KOG2785|consensus 94.9 0.16 3.5E-06 33.5 6.0 50 65-114 167-242 (390)
58 TIGR00622 ssl1 transcription f 94.9 0.064 1.4E-06 29.2 3.5 48 67-116 58-105 (112)
59 COG5048 FOG: Zn-finger [Genera 94.5 0.0062 1.3E-07 40.5 -1.1 58 64-121 289-352 (467)
60 PF10571 UPF0547: Uncharacteri 94.5 0.027 5.8E-07 22.3 1.2 10 94-103 16-25 (26)
61 KOG1146|consensus 94.5 0.01 2.3E-07 44.6 -0.0 75 31-114 460-540 (1406)
62 COG4049 Uncharacterized protei 94.2 0.034 7.3E-07 26.1 1.4 27 4-30 13-39 (65)
63 KOG1146|consensus 94.2 0.0076 1.7E-07 45.3 -1.2 103 9-116 1229-1352(1406)
64 COG2888 Predicted Zn-ribbon RN 93.9 0.056 1.2E-06 25.8 1.8 11 90-100 48-58 (61)
65 PF13719 zinc_ribbon_5: zinc-r 93.7 0.05 1.1E-06 23.5 1.4 32 66-102 4-35 (37)
66 PF13717 zinc_ribbon_4: zinc-r 93.5 0.061 1.3E-06 23.0 1.5 32 66-102 4-35 (36)
67 KOG2186|consensus 93.5 0.052 1.1E-06 33.8 1.6 48 36-86 3-50 (276)
68 COG5236 Uncharacterized conser 93.4 0.11 2.4E-06 34.0 3.1 74 38-116 222-305 (493)
69 PF06524 NOA36: NOA36 protein; 93.4 0.034 7.4E-07 34.7 0.7 42 2-44 136-179 (314)
70 PF09538 FYDLN_acid: Protein o 93.0 0.062 1.3E-06 29.2 1.3 12 9-20 10-21 (108)
71 TIGR02098 MJ0042_CXXC MJ0042 f 92.7 0.073 1.6E-06 22.9 1.1 10 93-102 26-35 (38)
72 PF09986 DUF2225: Uncharacteri 92.6 0.019 4E-07 35.2 -1.1 44 6-49 3-61 (214)
73 PF12013 DUF3505: Protein of u 92.6 0.42 9.1E-06 25.9 4.2 26 92-117 80-109 (109)
74 cd00729 rubredoxin_SM Rubredox 92.4 0.091 2E-06 22.2 1.2 9 65-73 3-11 (34)
75 TIGR00622 ssl1 transcription f 92.2 0.32 7E-06 26.6 3.4 86 6-99 13-110 (112)
76 COG5048 FOG: Zn-finger [Genera 92.1 0.043 9.2E-07 36.6 0.0 57 37-93 290-352 (467)
77 KOG2231|consensus 92.1 0.22 4.7E-06 35.6 3.3 74 39-116 118-206 (669)
78 smart00659 RPOLCX RNA polymera 92.0 0.14 3.1E-06 23.0 1.6 29 8-47 2-30 (44)
79 TIGR00373 conserved hypothetic 92.0 0.17 3.6E-06 29.6 2.3 33 61-102 106-138 (158)
80 TIGR02605 CxxC_CxxC_SSSS putat 91.8 0.05 1.1E-06 25.3 0.0 12 9-20 6-17 (52)
81 TIGR00373 conserved hypothetic 91.8 0.21 4.5E-06 29.2 2.6 37 30-75 103-139 (158)
82 PRK14890 putative Zn-ribbon RN 91.6 0.18 3.9E-06 24.1 1.8 10 91-100 47-56 (59)
83 PF12013 DUF3505: Protein of u 91.5 0.18 3.9E-06 27.4 2.0 26 64-89 80-109 (109)
84 COG5236 Uncharacterized conser 90.7 0.61 1.3E-05 30.7 4.1 48 66-114 222-273 (493)
85 PRK06266 transcription initiat 90.6 0.21 4.6E-06 29.7 1.9 33 62-103 115-147 (178)
86 PRK00464 nrdR transcriptional 90.4 0.059 1.3E-06 31.2 -0.5 13 65-77 29-41 (154)
87 smart00531 TFIIE Transcription 90.2 0.55 1.2E-05 27.0 3.3 38 61-102 96-133 (147)
88 COG1592 Rubrerythrin [Energy p 90.1 0.23 5E-06 29.2 1.7 23 64-99 134-156 (166)
89 KOG4173|consensus 90.1 0.14 3.1E-06 30.9 0.9 75 8-85 79-167 (253)
90 PRK00398 rpoP DNA-directed RNA 90.1 0.14 2.9E-06 23.2 0.6 11 64-74 3-13 (46)
91 KOG2186|consensus 90.0 0.29 6.2E-06 30.6 2.1 48 8-58 3-50 (276)
92 PRK06266 transcription initiat 89.8 0.37 8.1E-06 28.7 2.5 35 33-76 114-148 (178)
93 smart00834 CxxC_CXXC_SSSS Puta 89.7 0.097 2.1E-06 22.8 -0.0 11 9-19 6-16 (41)
94 PF05443 ROS_MUCR: ROS/MUCR tr 89.5 0.27 5.9E-06 27.8 1.6 26 90-118 70-95 (132)
95 PF02892 zf-BED: BED zinc fing 89.5 0.43 9.4E-06 21.2 2.1 24 90-113 14-41 (45)
96 PF02176 zf-TRAF: TRAF-type zi 88.9 0.26 5.6E-06 23.5 1.1 26 79-104 25-54 (60)
97 TIGR02300 FYDLN_acid conserved 88.4 0.31 6.8E-06 27.2 1.4 31 8-49 9-39 (129)
98 smart00614 ZnF_BED BED zinc fi 87.8 0.41 8.8E-06 22.0 1.4 20 94-113 20-44 (50)
99 smart00734 ZnF_Rad18 Rad18-lik 87.2 0.73 1.6E-05 18.1 1.8 19 94-113 3-21 (26)
100 PRK04023 DNA polymerase II lar 87.0 0.83 1.8E-05 34.4 3.1 10 92-101 663-672 (1121)
101 PF07800 DUF1644: Protein of u 86.4 4.8 0.00011 23.6 5.5 104 14-122 32-139 (162)
102 KOG3408|consensus 86.0 0.5 1.1E-05 26.1 1.2 26 89-114 54-79 (129)
103 smart00440 ZnF_C2C2 C2C2 Zinc 85.6 0.077 1.7E-06 23.3 -1.6 12 92-103 28-39 (40)
104 PF14353 CpXC: CpXC protein 85.6 0.73 1.6E-05 25.8 1.9 16 65-80 39-54 (128)
105 PF03604 DNA_RNApol_7kD: DNA d 84.8 0.41 8.9E-06 19.9 0.5 27 9-46 1-27 (32)
106 COG4957 Predicted transcriptio 84.2 0.52 1.1E-05 26.6 0.8 23 93-118 77-99 (148)
107 COG1997 RPL43A Ribosomal prote 83.5 0.81 1.7E-05 23.8 1.3 12 92-103 53-64 (89)
108 PF04959 ARS2: Arsenite-resist 83.3 0.82 1.8E-05 28.1 1.5 29 90-118 75-103 (214)
109 COG1198 PriA Primosomal protei 83.2 0.5 1.1E-05 34.4 0.6 12 62-73 473-484 (730)
110 PHA00626 hypothetical protein 82.1 0.71 1.5E-05 21.8 0.7 16 90-105 21-36 (59)
111 PF08790 zf-LYAR: LYAR-type C2 81.6 0.41 8.8E-06 19.3 -0.1 19 9-28 1-19 (28)
112 PTZ00448 hypothetical protein; 81.4 1.6 3.5E-05 29.1 2.4 34 92-125 314-352 (373)
113 PF08274 PhnA_Zn_Ribbon: PhnA 81.1 0.55 1.2E-05 19.2 0.2 8 36-43 19-26 (30)
114 PRK03824 hypA hydrogenase nick 80.9 0.71 1.5E-05 26.2 0.6 13 8-20 70-82 (135)
115 KOG2482|consensus 80.9 2.4 5.2E-05 28.1 2.9 50 65-114 280-356 (423)
116 PF15135 UPF0515: Uncharacteri 80.3 1.8 3.9E-05 27.2 2.2 13 6-18 110-122 (278)
117 PF12907 zf-met2: Zinc-binding 80.3 1.5 3.3E-05 19.3 1.4 33 93-125 2-38 (40)
118 PF15269 zf-C2H2_7: Zinc-finge 79.5 1.7 3.6E-05 19.5 1.4 22 93-114 21-42 (54)
119 PF13451 zf-trcl: Probable zin 79.4 1.6 3.5E-05 20.1 1.4 17 7-23 3-19 (49)
120 PRK09678 DNA-binding transcrip 79.4 0.62 1.3E-05 23.4 0.1 8 38-45 3-10 (72)
121 smart00661 RPOL9 RNA polymeras 79.2 1.5 3.3E-05 20.1 1.4 11 92-102 20-30 (52)
122 KOG2785|consensus 78.6 3.2 6.9E-05 27.9 3.0 27 7-33 165-191 (390)
123 PF07754 DUF1610: Domain of un 78.6 0.86 1.9E-05 17.6 0.3 8 92-99 16-23 (24)
124 COG3357 Predicted transcriptio 78.0 1.7 3.6E-05 22.8 1.4 13 64-76 58-70 (97)
125 PRK00432 30S ribosomal protein 77.4 1.4 3.1E-05 20.4 0.9 11 91-101 36-46 (50)
126 KOG2893|consensus 77.2 0.69 1.5E-05 28.8 -0.2 43 9-55 11-53 (341)
127 COG3677 Transposase and inacti 77.2 0.72 1.6E-05 26.0 -0.1 13 64-76 53-65 (129)
128 PF12760 Zn_Tnp_IS1595: Transp 77.1 2.7 5.9E-05 18.9 1.8 11 90-100 35-45 (46)
129 PF13453 zf-TFIIB: Transcripti 76.8 1.1 2.3E-05 19.7 0.4 15 38-52 21-35 (41)
130 KOG2907|consensus 76.5 1.2 2.6E-05 24.3 0.6 39 65-104 75-114 (116)
131 COG1996 RPC10 DNA-directed RNA 76.4 1.8 3.8E-05 20.0 1.1 12 7-18 5-16 (49)
132 PF09723 Zn-ribbon_8: Zinc rib 76.3 1.3 2.8E-05 19.6 0.6 29 9-44 6-34 (42)
133 PF13878 zf-C2H2_3: zinc-finge 75.1 3.9 8.4E-05 18.0 2.0 24 9-32 14-39 (41)
134 COG4888 Uncharacterized Zn rib 74.1 0.61 1.3E-05 24.9 -0.8 10 93-102 47-56 (104)
135 COG1571 Predicted DNA-binding 74.0 2.5 5.4E-05 28.8 1.7 14 92-105 367-380 (421)
136 PF04959 ARS2: Arsenite-resist 73.6 1.3 2.9E-05 27.3 0.4 27 36-62 77-103 (214)
137 PF04423 Rad50_zn_hook: Rad50 73.5 3.2 6.9E-05 19.4 1.6 12 94-105 22-33 (54)
138 KOG2807|consensus 73.3 8.8 0.00019 25.4 3.9 26 91-116 344-369 (378)
139 COG3091 SprT Zn-dependent meta 73.2 1.5 3.2E-05 25.4 0.5 33 64-101 117-149 (156)
140 KOG2071|consensus 73.2 2.2 4.7E-05 30.3 1.3 32 90-121 416-447 (579)
141 PF03811 Zn_Tnp_IS1: InsA N-te 73.0 0.72 1.6E-05 19.8 -0.6 18 81-98 18-35 (36)
142 PF01096 TFIIS_C: Transcriptio 72.8 0.046 1E-06 23.9 -4.5 10 93-102 29-38 (39)
143 KOG2482|consensus 72.5 3.8 8.2E-05 27.2 2.2 23 92-114 195-217 (423)
144 PF09845 DUF2072: Zn-ribbon co 72.4 1.9 4.2E-05 24.3 0.8 13 65-77 2-14 (131)
145 KOG4167|consensus 72.2 1 2.2E-05 32.7 -0.3 27 7-33 791-817 (907)
146 PRK03564 formate dehydrogenase 72.2 1 2.2E-05 29.4 -0.3 75 8-104 187-264 (309)
147 COG2331 Uncharacterized protei 72.1 2.3 5E-05 21.5 1.0 31 8-45 12-42 (82)
148 TIGR00686 phnA alkylphosphonat 71.6 1.9 4.2E-05 23.4 0.7 12 92-103 19-30 (109)
149 KOG1842|consensus 71.3 2.8 6E-05 28.8 1.4 25 92-116 15-39 (505)
150 PHA02998 RNA polymerase subuni 71.0 0.69 1.5E-05 27.5 -1.2 41 65-105 144-184 (195)
151 KOG3408|consensus 70.7 3.5 7.7E-05 22.9 1.6 26 5-30 54-79 (129)
152 PTZ00255 60S ribosomal protein 70.5 1.8 3.9E-05 22.8 0.4 11 64-74 54-64 (90)
153 PF10013 DUF2256: Uncharacteri 70.4 3.2 7E-05 18.4 1.1 16 94-109 10-25 (42)
154 TIGR00100 hypA hydrogenase nic 70.2 2.5 5.5E-05 23.3 1.0 12 37-48 71-82 (115)
155 COG1656 Uncharacterized conser 69.9 8 0.00017 22.9 2.9 43 66-110 99-148 (165)
156 PRK10220 hypothetical protein; 69.9 2.6 5.7E-05 22.9 0.9 11 93-103 21-31 (111)
157 PRK14714 DNA polymerase II lar 69.7 6.8 0.00015 30.8 3.2 12 64-75 692-703 (1337)
158 COG1594 RPB9 DNA-directed RNA 69.7 0.96 2.1E-05 24.9 -0.7 13 91-103 99-111 (113)
159 KOG2636|consensus 69.0 7.2 0.00016 26.9 3.0 29 84-112 393-422 (497)
160 TIGR01206 lysW lysine biosynth 68.5 2.1 4.6E-05 20.2 0.4 9 38-46 4-12 (54)
161 PF07282 OrfB_Zn_ribbon: Putat 68.5 3.8 8.2E-05 20.1 1.3 12 91-102 45-56 (69)
162 PRK12380 hydrogenase nickel in 68.4 3.2 7E-05 22.8 1.1 11 37-47 71-81 (113)
163 PRK14873 primosome assembly pr 68.0 1.7 3.7E-05 31.5 0.0 47 10-73 385-431 (665)
164 KOG0717|consensus 67.8 3.4 7.3E-05 28.6 1.3 22 93-114 293-314 (508)
165 COG1655 Uncharacterized protei 66.9 0.94 2E-05 28.1 -1.2 23 6-28 17-39 (267)
166 PF05290 Baculo_IE-1: Baculovi 66.6 5.6 0.00012 22.6 1.8 13 94-106 123-135 (140)
167 PF05191 ADK_lid: Adenylate ki 66.0 1.9 4.1E-05 18.4 -0.0 10 10-19 3-12 (36)
168 TIGR00280 L37a ribosomal prote 65.3 2 4.3E-05 22.6 -0.1 11 64-74 53-63 (91)
169 PF01780 Ribosomal_L37ae: Ribo 65.0 1.5 3.3E-05 23.0 -0.5 10 93-102 54-63 (90)
170 TIGR00595 priA primosomal prot 64.7 2.5 5.4E-05 29.7 0.3 34 10-44 215-248 (505)
171 smart00154 ZnF_AN1 AN1-like Zi 64.5 3.7 8E-05 17.8 0.7 14 8-21 12-25 (39)
172 KOG2593|consensus 64.3 6.3 0.00014 27.0 2.0 12 9-20 129-140 (436)
173 COG4338 Uncharacterized protei 64.0 2.8 6.2E-05 19.1 0.3 17 94-110 14-30 (54)
174 PF04780 DUF629: Protein of un 63.5 6.8 0.00015 27.3 2.1 23 92-114 57-79 (466)
175 KOG1280|consensus 62.4 11 0.00023 25.2 2.7 38 6-43 77-116 (381)
176 KOG1280|consensus 62.1 9.5 0.00021 25.4 2.5 37 64-100 79-117 (381)
177 COG1326 Uncharacterized archae 61.9 8.4 0.00018 23.4 2.1 11 92-102 30-40 (201)
178 COG1675 TFA1 Transcription ini 61.2 12 0.00026 22.5 2.6 33 61-102 110-142 (176)
179 PRK03976 rpl37ae 50S ribosomal 60.1 2.6 5.7E-05 22.2 -0.2 11 64-74 54-64 (90)
180 KOG2593|consensus 60.0 8.7 0.00019 26.4 2.1 38 60-101 124-162 (436)
181 COG4530 Uncharacterized protei 59.9 6.3 0.00014 21.5 1.2 11 64-74 26-36 (129)
182 COG1773 Rubredoxin [Energy pro 59.7 3.9 8.4E-05 19.4 0.4 12 92-103 3-14 (55)
183 COG3364 Zn-ribbon containing p 59.6 3.6 7.8E-05 22.1 0.3 13 64-76 2-14 (112)
184 PRK04351 hypothetical protein; 59.6 3.1 6.7E-05 24.2 0.0 32 64-103 112-143 (149)
185 COG5188 PRP9 Splicing factor 3 59.2 20 0.00043 24.2 3.5 30 84-113 366-396 (470)
186 PRK00564 hypA hydrogenase nick 58.7 6 0.00013 21.9 1.1 11 37-47 72-82 (117)
187 COG1998 RPS31 Ribosomal protei 58.5 4.7 0.0001 18.6 0.5 10 92-101 37-46 (51)
188 PF06397 Desulfoferrod_N: Desu 58.4 5 0.00011 17.2 0.6 12 7-18 5-16 (36)
189 PF10263 SprT-like: SprT-like 58.4 2.6 5.6E-05 24.3 -0.4 32 64-103 123-154 (157)
190 PF01428 zf-AN1: AN1-like Zinc 58.3 4.6 0.0001 17.9 0.5 15 7-21 12-26 (43)
191 PF01155 HypA: Hydrogenase exp 57.6 4.7 0.0001 22.2 0.5 11 37-47 71-81 (113)
192 TIGR01562 FdhE formate dehydro 55.9 3.4 7.3E-05 27.0 -0.2 13 91-103 251-263 (305)
193 PRK03681 hypA hydrogenase nick 55.6 4.7 0.0001 22.2 0.3 11 37-47 71-81 (114)
194 PLN02294 cytochrome c oxidase 55.3 5.8 0.00013 23.5 0.7 16 89-104 138-153 (174)
195 KOG4167|consensus 55.0 3.3 7.2E-05 30.3 -0.4 26 92-117 792-817 (907)
196 COG1327 Predicted transcriptio 54.4 3.4 7.4E-05 24.0 -0.3 13 65-77 29-41 (156)
197 cd00924 Cyt_c_Oxidase_Vb Cytoc 54.3 6.1 0.00013 21.2 0.6 15 90-104 77-91 (97)
198 KOG0978|consensus 53.0 7.5 0.00016 28.5 1.0 17 91-107 677-693 (698)
199 PF13824 zf-Mss51: Zinc-finger 52.6 14 0.0003 17.5 1.6 8 64-71 14-21 (55)
200 KOG4124|consensus 52.0 1.4 3.1E-05 29.1 -2.3 49 63-111 348-417 (442)
201 cd00065 FYVE FYVE domain; Zinc 52.0 12 0.00027 17.3 1.4 13 64-76 18-30 (57)
202 PRK12496 hypothetical protein; 51.7 13 0.00027 22.0 1.7 27 65-103 128-154 (164)
203 PF14311 DUF4379: Domain of un 51.6 13 0.00027 17.4 1.4 9 65-73 29-37 (55)
204 PF04810 zf-Sec23_Sec24: Sec23 51.5 6 0.00013 17.2 0.3 12 89-100 21-32 (40)
205 KOG3002|consensus 50.7 25 0.00054 23.1 3.0 76 35-115 79-162 (299)
206 smart00731 SprT SprT homologue 49.7 9.1 0.0002 22.0 0.9 33 64-103 112-144 (146)
207 PF01363 FYVE: FYVE zinc finge 49.5 8.8 0.00019 18.7 0.7 27 38-76 11-37 (69)
208 PF08209 Sgf11: Sgf11 (transcr 49.4 20 0.00044 15.0 1.7 22 65-87 5-26 (33)
209 PLN03238 probable histone acet 49.4 19 0.00042 23.4 2.3 27 90-116 46-72 (290)
210 TIGR01384 TFS_arch transcripti 49.3 1.9 4E-05 23.2 -1.9 40 65-104 63-102 (104)
211 smart00064 FYVE Protein presen 48.6 14 0.0003 17.9 1.4 28 37-76 11-38 (68)
212 KOG3507|consensus 48.6 9.9 0.00021 18.2 0.8 12 36-47 37-48 (62)
213 cd00730 rubredoxin Rubredoxin; 48.3 8 0.00017 17.9 0.4 12 93-104 2-13 (50)
214 PF04780 DUF629: Protein of un 47.6 16 0.00034 25.6 1.9 25 36-60 57-81 (466)
215 COG0068 HypF Hydrogenase matur 47.3 3.5 7.5E-05 30.1 -1.2 79 9-100 102-181 (750)
216 KOG4727|consensus 46.7 12 0.00027 22.2 1.1 23 7-29 74-96 (193)
217 PF07975 C1_4: TFIIH C1-like d 45.7 4 8.6E-05 19.0 -0.8 14 64-77 21-34 (51)
218 PF12230 PRP21_like_P: Pre-mRN 45.7 6.9 0.00015 24.4 0.0 26 90-116 166-191 (229)
219 PRK00762 hypA hydrogenase nick 45.6 8.8 0.00019 21.5 0.4 7 65-71 93-99 (124)
220 PF00301 Rubredoxin: Rubredoxi 45.4 11 0.00023 17.3 0.6 12 9-20 2-13 (47)
221 PRK05978 hypothetical protein; 45.2 16 0.00035 21.3 1.4 10 94-103 54-63 (148)
222 KOG3214|consensus 43.8 5.9 0.00013 21.2 -0.4 11 94-104 49-59 (109)
223 TIGR00319 desulf_FeS4 desulfof 43.5 13 0.00029 15.3 0.7 12 7-18 6-17 (34)
224 TIGR03829 YokU_near_AblA uncha 43.3 30 0.00066 18.3 2.1 15 65-79 36-50 (89)
225 PF10537 WAC_Acf1_DNA_bd: ATP- 43.2 56 0.0012 17.7 3.3 39 8-47 3-41 (102)
226 PF02891 zf-MIZ: MIZ/SP-RING z 43.0 11 0.00023 17.4 0.4 8 93-100 42-49 (50)
227 cd00974 DSRD Desulforedoxin (D 43.0 14 0.00029 15.3 0.7 12 7-18 3-14 (34)
228 COG5216 Uncharacterized conser 42.5 15 0.00033 17.6 0.9 10 61-70 41-50 (67)
229 PF15616 TerY-C: TerY-C metal 42.5 3.4 7.5E-05 23.4 -1.5 14 61-74 102-115 (131)
230 COG5151 SSL1 RNA polymerase II 41.8 24 0.00052 23.3 1.9 27 90-116 386-412 (421)
231 PF11672 DUF3268: Protein of u 41.6 12 0.00026 20.3 0.5 10 36-45 2-11 (102)
232 PRK11823 DNA repair protein Ra 41.5 18 0.00039 25.1 1.5 24 6-43 5-28 (446)
233 PF02591 DUF164: Putative zinc 41.2 30 0.00065 16.1 1.8 7 65-71 47-53 (56)
234 PF11931 DUF3449: Domain of un 40.7 9.1 0.0002 23.4 0.0 23 89-111 98-121 (196)
235 PF14787 zf-CCHC_5: GAG-polypr 40.6 13 0.00029 15.9 0.5 14 94-107 4-17 (36)
236 PRK00420 hypothetical protein; 40.3 18 0.0004 20.0 1.1 10 65-74 41-50 (112)
237 PF01286 XPA_N: XPA protein N- 39.9 14 0.00031 15.6 0.5 13 9-21 4-16 (34)
238 PF14634 zf-RING_5: zinc-RING 39.7 32 0.00068 15.0 1.7 7 65-71 37-43 (44)
239 COG0675 Transposase and inacti 39.5 16 0.00036 23.7 1.0 14 90-103 320-333 (364)
240 PF11781 RRN7: RNA polymerase 39.1 14 0.00031 15.7 0.5 9 9-17 9-17 (36)
241 TIGR00416 sms DNA repair prote 38.9 21 0.00046 24.9 1.5 12 7-18 6-17 (454)
242 KOG0317|consensus 38.9 16 0.00035 23.7 0.9 32 66-103 253-284 (293)
243 PRK14892 putative transcriptio 38.8 11 0.00023 20.4 0.0 8 36-43 21-28 (99)
244 PF08792 A2L_zn_ribbon: A2L zi 38.7 14 0.0003 15.4 0.4 11 93-103 22-32 (33)
245 PF06676 DUF1178: Protein of u 38.5 24 0.00052 20.6 1.5 30 17-50 17-46 (148)
246 TIGR03831 YgiT_finger YgiT-typ 38.0 13 0.00029 16.2 0.3 12 9-20 33-44 (46)
247 TIGR00515 accD acetyl-CoA carb 37.7 22 0.00047 23.2 1.3 11 65-75 46-56 (285)
248 KOG1994|consensus 37.7 24 0.00052 22.2 1.4 26 87-112 234-259 (268)
249 PTZ00043 cytochrome c oxidase 37.6 16 0.00034 22.9 0.7 17 5-21 178-194 (268)
250 TIGR01385 TFSII transcription 37.4 6.4 0.00014 25.7 -1.1 38 64-103 258-297 (299)
251 PF07503 zf-HYPF: HypF finger; 37.3 3.9 8.5E-05 17.4 -1.4 10 37-46 22-31 (35)
252 COG5112 UFD2 U1-like Zn-finger 37.3 19 0.0004 19.7 0.8 24 91-114 54-77 (126)
253 cd01121 Sms Sms (bacterial rad 36.9 21 0.00045 24.2 1.2 11 9-19 1-11 (372)
254 KOG1842|consensus 36.8 24 0.00051 24.6 1.4 26 7-32 14-39 (505)
255 KOG0717|consensus 36.7 22 0.00047 24.9 1.2 22 65-86 293-314 (508)
256 PLN00104 MYST -like histone ac 36.6 28 0.0006 24.4 1.7 27 90-116 196-222 (450)
257 KOG2272|consensus 35.8 12 0.00026 23.9 -0.0 16 36-51 99-114 (332)
258 PLN03239 histone acetyltransfe 35.7 30 0.00065 23.3 1.7 25 90-114 104-128 (351)
259 smart00132 LIM Zinc-binding do 35.6 6.3 0.00014 16.3 -1.0 10 93-102 28-37 (39)
260 PTZ00064 histone acetyltransfe 35.4 33 0.00072 24.4 1.9 27 90-116 278-304 (552)
261 PF04438 zf-HIT: HIT zinc fing 35.0 39 0.00086 13.7 1.5 15 7-21 12-26 (30)
262 PF12773 DZR: Double zinc ribb 34.9 31 0.00067 15.5 1.3 9 65-73 30-38 (50)
263 PRK12722 transcriptional activ 34.5 31 0.00068 21.0 1.6 28 65-100 135-162 (187)
264 smart00647 IBR In Between Ring 34.3 23 0.0005 16.6 0.9 9 66-74 42-50 (64)
265 PF01215 COX5B: Cytochrome c o 33.7 12 0.00026 21.4 -0.2 15 90-104 110-124 (136)
266 COG1379 PHP family phosphoeste 33.7 46 0.00099 22.4 2.3 32 66-106 248-279 (403)
267 PRK12860 transcriptional activ 33.5 33 0.00072 20.9 1.5 27 65-99 135-161 (189)
268 PF08882 Acetone_carb_G: Aceto 33.3 12 0.00026 20.6 -0.2 12 64-75 74-85 (112)
269 PF10083 DUF2321: Uncharacteri 33.0 20 0.00043 21.1 0.6 14 91-104 67-80 (158)
270 PF08271 TF_Zn_Ribbon: TFIIB z 32.9 19 0.00041 15.8 0.4 7 94-100 2-8 (43)
271 PRK06260 threonine synthase; V 32.8 32 0.00069 23.5 1.6 26 37-74 4-29 (397)
272 TIGR03830 CxxCG_CxxCG_HTH puta 32.7 47 0.001 18.2 2.0 23 7-29 30-52 (127)
273 PF10276 zf-CHCC: Zinc-finger 32.3 34 0.00073 15.0 1.1 11 8-18 29-39 (40)
274 PRK14559 putative protein seri 32.1 33 0.00071 25.3 1.6 8 10-17 3-10 (645)
275 TIGR00627 tfb4 transcription f 31.8 40 0.00087 22.0 1.8 11 65-75 256-266 (279)
276 PLN02748 tRNA dimethylallyltra 31.6 41 0.00089 23.7 1.9 24 91-114 417-441 (468)
277 CHL00174 accD acetyl-CoA carbo 31.6 32 0.0007 22.6 1.4 11 93-103 58-68 (296)
278 COG4391 Uncharacterized protei 31.4 7.9 0.00017 18.8 -1.0 45 55-103 15-59 (62)
279 PF05495 zf-CHY: CHY zinc fing 31.4 7.2 0.00016 19.4 -1.2 12 9-20 11-22 (71)
280 KOG0782|consensus 31.2 9.2 0.0002 27.5 -1.1 51 50-106 239-290 (1004)
281 PRK01343 zinc-binding protein; 30.5 27 0.00059 16.7 0.7 11 93-103 10-20 (57)
282 PRK14138 NAD-dependent deacety 28.7 89 0.0019 19.8 2.9 11 9-19 120-130 (244)
283 TIGR00310 ZPR1_znf ZPR1 zinc f 28.7 6.1 0.00013 24.0 -2.0 38 10-48 2-42 (192)
284 PF01927 Mut7-C: Mut7-C RNAse 28.6 40 0.00087 19.4 1.3 46 65-110 92-142 (147)
285 PRK05654 acetyl-CoA carboxylas 28.5 31 0.00067 22.6 0.9 10 65-74 47-56 (292)
286 PF14369 zf-RING_3: zinc-finge 28.3 27 0.00058 14.7 0.4 10 94-103 23-32 (35)
287 KOG2906|consensus 28.3 6.1 0.00013 21.1 -1.8 38 66-103 67-104 (105)
288 KOG2747|consensus 28.1 39 0.00085 23.2 1.4 29 90-118 156-184 (396)
289 KOG2857|consensus 28.1 28 0.0006 20.1 0.6 23 7-29 16-38 (157)
290 PF07295 DUF1451: Protein of u 26.9 21 0.00046 20.7 -0.0 27 36-72 112-138 (146)
291 PF09855 DUF2082: Nucleic-acid 26.7 29 0.00063 17.0 0.5 8 93-100 1-8 (64)
292 PRK07218 replication factor A; 26.7 41 0.0009 23.4 1.3 10 65-74 298-307 (423)
293 cd04476 RPA1_DBD_C RPA1_DBD_C: 26.7 29 0.00063 20.3 0.6 12 63-74 50-61 (166)
294 COG1066 Sms Predicted ATP-depe 26.5 39 0.00084 23.6 1.1 13 7-19 6-18 (456)
295 PF03107 C1_2: C1 domain; Int 26.3 36 0.00078 13.6 0.7 8 94-101 2-9 (30)
296 KOG1729|consensus 26.2 17 0.00037 23.7 -0.5 9 9-17 169-177 (288)
297 COG5432 RAD18 RING-finger-cont 26.2 44 0.00095 22.0 1.3 14 57-71 53-66 (391)
298 PF14205 Cys_rich_KTR: Cystein 26.1 21 0.00045 16.9 -0.1 9 92-100 28-36 (55)
299 PF02748 PyrI_C: Aspartate car 26.0 30 0.00066 16.1 0.4 16 5-20 32-47 (52)
300 KOG2932|consensus 25.8 80 0.0017 21.1 2.4 29 88-116 140-171 (389)
301 PF04606 Ogr_Delta: Ogr/Delta- 25.8 13 0.00028 16.8 -0.8 6 98-103 33-38 (47)
302 cd01410 SIRT7 SIRT7: Eukaryoti 25.3 1.2E+02 0.0027 18.6 3.1 11 36-46 95-105 (206)
303 PF05741 zf-nanos: Nanos RNA b 25.2 24 0.00052 16.8 0.0 11 91-101 32-42 (55)
304 PF14446 Prok-RING_1: Prokaryo 24.9 29 0.00062 16.4 0.2 12 93-104 6-17 (54)
305 PTZ00409 Sir2 (Silent Informat 24.7 1.1E+02 0.0023 19.9 2.8 14 7-20 136-149 (271)
306 COG4896 Uncharacterized protei 24.7 39 0.00085 16.4 0.7 8 64-71 31-38 (68)
307 PRK14811 formamidopyrimidine-D 24.3 28 0.0006 22.4 0.2 30 66-103 237-266 (269)
308 PF03145 Sina: Seven in absent 24.0 56 0.0012 19.8 1.4 8 79-86 62-69 (198)
309 KOG1088|consensus 23.8 39 0.00083 18.9 0.6 20 58-77 92-111 (124)
310 KOG4118|consensus 23.8 54 0.0012 16.2 1.1 28 37-64 39-66 (74)
311 PF04216 FdhE: Protein involve 23.5 19 0.00042 23.3 -0.7 76 9-102 173-248 (290)
312 TIGR00244 transcriptional regu 23.1 34 0.00075 19.9 0.4 15 91-105 27-41 (147)
313 PF04988 AKAP95: A-kinase anch 23.0 57 0.0012 19.4 1.3 21 37-57 1-21 (165)
314 PRK07591 threonine synthase; V 22.9 59 0.0013 22.5 1.5 25 37-74 19-43 (421)
315 PRK08222 hydrogenase 4 subunit 22.6 1E+02 0.0022 18.6 2.3 21 91-111 113-133 (181)
316 COG4847 Uncharacterized protei 22.5 32 0.00068 18.4 0.1 13 89-101 3-15 (103)
317 cd00122 MBD MeCP2, MBD1, MBD2, 22.5 98 0.0021 14.8 1.9 21 96-116 31-51 (62)
318 PRK11827 hypothetical protein; 22.2 59 0.0013 15.8 1.0 11 93-103 27-37 (60)
319 PF15227 zf-C3HC4_4: zinc fing 22.1 90 0.002 13.6 1.9 6 93-98 37-42 (42)
320 PF00649 Copper-fist: Copper f 22.0 27 0.00058 15.4 -0.1 17 3-19 3-19 (40)
321 PRK06450 threonine synthase; V 22.0 64 0.0014 21.6 1.5 10 37-46 4-13 (338)
322 PF13248 zf-ribbon_3: zinc-rib 21.9 50 0.0011 12.6 0.7 7 66-72 4-10 (26)
323 COG2879 Uncharacterized small 21.9 1.2E+02 0.0026 14.9 2.0 19 46-64 22-40 (65)
324 PF13821 DUF4187: Domain of un 21.7 60 0.0013 15.3 1.0 21 90-110 25-45 (55)
325 smart00586 ZnF_DBF Zinc finger 21.7 63 0.0014 15.0 1.0 21 6-29 3-23 (49)
326 PF09963 DUF2197: Uncharacteri 21.7 43 0.00094 16.0 0.5 6 65-70 32-37 (56)
327 KOG3352|consensus 21.5 44 0.00096 19.6 0.6 15 90-104 131-145 (153)
328 PF10164 DUF2367: Uncharacteri 21.0 50 0.0011 17.8 0.7 13 90-102 86-98 (98)
329 PF02146 SIR2: Sir2 family; I 20.8 67 0.0015 19.0 1.3 9 38-46 107-115 (178)
330 PF11494 Ta0938: Ta0938; Inte 20.7 55 0.0012 17.6 0.8 11 8-18 14-24 (105)
331 PHA02942 putative transposase; 20.6 83 0.0018 21.6 1.8 14 90-103 340-353 (383)
332 PF03884 DUF329: Domain of unk 20.3 38 0.00082 16.2 0.2 12 93-104 3-14 (57)
333 PF03966 Trm112p: Trm112p-like 20.3 41 0.00089 16.4 0.3 13 7-19 52-64 (68)
334 smart00109 C1 Protein kinase C 20.2 68 0.0015 13.8 1.0 9 38-46 13-21 (49)
No 1
>KOG2462|consensus
Probab=99.97 E-value=1.2e-30 Score=156.14 Aligned_cols=107 Identities=37% Similarity=0.739 Sum_probs=74.7
Q ss_pred CcceeccccccccCChhHHHHHHHhhcCCCCcccCCcccccCCchHHHHHHhhhcCCCCcccCCCCCcCCChhhHHHHHH
Q psy10762 6 ETPHRCDYCAKTFTRKEHLVNHVRQHTGESPHHCNYCAKSFTRKDHMVYHERQHTGETPFPCQYCPKAFTRKDHLVNHVR 85 (126)
Q Consensus 6 ~~~~~C~~C~~~f~~~~~l~~h~~~h~~~~~~~c~~C~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~~~~~~~l~~h~~ 85 (126)
++.+.|..|+++|-+...|..|+++|. .+++|.+||+.|...+.|+.|+++|+|||||.|+.|+++|...++|..|++
T Consensus 159 ~ka~~C~~C~K~YvSmpALkMHirTH~--l~c~C~iCGKaFSRPWLLQGHiRTHTGEKPF~C~hC~kAFADRSNLRAHmQ 236 (279)
T KOG2462|consen 159 KKAFSCKYCGKVYVSMPALKMHIRTHT--LPCECGICGKAFSRPWLLQGHIRTHTGEKPFSCPHCGKAFADRSNLRAHMQ 236 (279)
T ss_pred cccccCCCCCceeeehHHHhhHhhccC--CCcccccccccccchHHhhcccccccCCCCccCCcccchhcchHHHHHHHH
Confidence 455666666666666666666666665 356677777777777777777777777777777777777777777777777
Q ss_pred hhcCCCCccCcccccccCCHHHHHHHHHH
Q psy10762 86 RHTGESPHKCTYCMKSFTRKEHLTNHIRQ 114 (126)
Q Consensus 86 ~~~~~~~~~C~~C~~~f~~~~~l~~H~~~ 114 (126)
+|.+.+.|.|..|+|+|+..+.|.+|...
T Consensus 237 THS~~K~~qC~~C~KsFsl~SyLnKH~ES 265 (279)
T KOG2462|consen 237 THSDVKKHQCPRCGKSFALKSYLNKHSES 265 (279)
T ss_pred hhcCCccccCcchhhHHHHHHHHHHhhhh
Confidence 77777777777777777777777777544
No 2
>KOG2462|consensus
Probab=99.96 E-value=2.3e-30 Score=154.88 Aligned_cols=117 Identities=32% Similarity=0.676 Sum_probs=108.4
Q ss_pred CcceeccccccccCChhHHHHHHHhhcC---CCCcccCCcccccCCchHHHHHHhhhcCCCCcccCCCCCcCCChhhHHH
Q psy10762 6 ETPHRCDYCAKTFTRKEHLVNHVRQHTG---ESPHHCNYCAKSFTRKDHMVYHERQHTGETPFPCQYCPKAFTRKDHLVN 82 (126)
Q Consensus 6 ~~~~~C~~C~~~f~~~~~l~~h~~~h~~---~~~~~c~~C~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~~~~~~~l~~ 82 (126)
...|.|.+||+.+...++|..|++.|.. .+.+.|..|++.+.+...|..|+++|.- +.+|..||+.|.+...|+.
T Consensus 128 ~~r~~c~eCgk~ysT~snLsrHkQ~H~~~~s~ka~~C~~C~K~YvSmpALkMHirTH~l--~c~C~iCGKaFSRPWLLQG 205 (279)
T KOG2462|consen 128 HPRYKCPECGKSYSTSSNLSRHKQTHRSLDSKKAFSCKYCGKVYVSMPALKMHIRTHTL--PCECGICGKAFSRPWLLQG 205 (279)
T ss_pred CCceeccccccccccccccchhhcccccccccccccCCCCCceeeehHHHhhHhhccCC--CcccccccccccchHHhhc
Confidence 3459999999999999999999999853 5678999999999999999999999984 6899999999999999999
Q ss_pred HHHhhcCCCCccCcccccccCCHHHHHHHHHHhhhccccCCC
Q psy10762 83 HVRRHTGESPHKCTYCMKSFTRKEHLTNHIRQHTVRRVNDLP 124 (126)
Q Consensus 83 h~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~~~ 124 (126)
|+++|+|||||.|+.|+|.|..+++|+.|+.+|.+.+..+++
T Consensus 206 HiRTHTGEKPF~C~hC~kAFADRSNLRAHmQTHS~~K~~qC~ 247 (279)
T KOG2462|consen 206 HIRTHTGEKPFSCPHCGKAFADRSNLRAHMQTHSDVKKHQCP 247 (279)
T ss_pred ccccccCCCCccCCcccchhcchHHHHHHHHhhcCCccccCc
Confidence 999999999999999999999999999999999998876654
No 3
>KOG3576|consensus
Probab=99.84 E-value=1.2e-21 Score=113.19 Aligned_cols=113 Identities=29% Similarity=0.597 Sum_probs=103.5
Q ss_pred CCcceeccccccccCChhHHHHHHHhhcCCCCcccCCcccccCCchHHHHHHhhhcCCCCcccCCCCCcCCChhhHHHHH
Q psy10762 5 GETPHRCDYCAKTFTRKEHLVNHVRQHTGESPHHCNYCAKSFTRKDHMVYHERQHTGETPFPCQYCPKAFTRKDHLVNHV 84 (126)
Q Consensus 5 ~~~~~~C~~C~~~f~~~~~l~~h~~~h~~~~~~~c~~C~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~~~~~~~l~~h~ 84 (126)
+...|.|.+|++.|.....|..|+..|...+.+.|..||+.|.+.-.|.+|+++|+|.+||.|..|+++|.+.-+|..|.
T Consensus 114 d~d~ftCrvCgK~F~lQRmlnrh~kch~~vkr~lct~cgkgfndtfdlkrh~rthtgvrpykc~~c~kaftqrcsleshl 193 (267)
T KOG3576|consen 114 DQDSFTCRVCGKKFGLQRMLNRHLKCHSDVKRHLCTFCGKGFNDTFDLKRHTRTHTGVRPYKCSLCEKAFTQRCSLESHL 193 (267)
T ss_pred CCCeeeeehhhhhhhHHHHHHHHhhhccHHHHHHHhhccCcccchhhhhhhhccccCccccchhhhhHHHHhhccHHHHH
Confidence 45679999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HhhcC-----------CCCccCcccccccCCHHHHHHHHHHhhh
Q psy10762 85 RRHTG-----------ESPHKCTYCMKSFTRKEHLTNHIRQHTV 117 (126)
Q Consensus 85 ~~~~~-----------~~~~~C~~C~~~f~~~~~l~~H~~~h~~ 117 (126)
+.-+| ++.|+|..||.+-.....+..|+..|+.
T Consensus 194 ~kvhgv~~~yaykerr~kl~vcedcg~t~~~~e~~~~h~~~~hp 237 (267)
T KOG3576|consen 194 KKVHGVQHQYAYKERRAKLYVCEDCGYTSERPEVYYLHLKLHHP 237 (267)
T ss_pred HHHcCchHHHHHHHhhhheeeecccCCCCCChhHHHHHHHhcCC
Confidence 75432 5679999999998888899999888764
No 4
>KOG1074|consensus
Probab=99.83 E-value=9.5e-22 Score=132.49 Aligned_cols=51 Identities=37% Similarity=0.734 Sum_probs=49.4
Q ss_pred ccCCCCCcCCChhhHHHHHHhhcCCCCccCcccccccCCHHHHHHHHHHhh
Q psy10762 66 PCQYCPKAFTRKDHLVNHVRRHTGESPHKCTYCMKSFTRKEHLTNHIRQHT 116 (126)
Q Consensus 66 ~C~~C~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~h~ 116 (126)
+|..|.++++-...|+.|.++|+||+||+|++||+.|..+-+|+.|+-+|.
T Consensus 607 qCiiC~rVlSC~saLqmHyrtHtGERPFkCKiCgRAFtTkGNLkaH~~vHk 657 (958)
T KOG1074|consen 607 QCIICLRVLSCPSALQMHYRTHTGERPFKCKICGRAFTTKGNLKAHMSVHK 657 (958)
T ss_pred ceeeeeecccchhhhhhhhhcccCcCccccccccchhccccchhhcccccc
Confidence 799999999999999999999999999999999999999999999999886
No 5
>KOG1074|consensus
Probab=99.76 E-value=1.4e-19 Score=122.23 Aligned_cols=52 Identities=35% Similarity=0.721 Sum_probs=49.8
Q ss_pred ccCCCCCcCCChhhHHHHHHhhcCCCCccCcccccccCCHHHHHHHHHHhhh
Q psy10762 66 PCQYCPKAFTRKDHLVNHVRRHTGESPHKCTYCMKSFTRKEHLTNHIRQHTV 117 (126)
Q Consensus 66 ~C~~C~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~ 117 (126)
.|..|++.|...+.|+.|+++|+++++|.|..|++.|..+.+|+.||.+|.-
T Consensus 881 ~C~vCgk~FsSSsALqiH~rTHtg~KPF~C~fC~~aFttrgnLKvHMgtH~w 932 (958)
T KOG1074|consen 881 VCNVCGKQFSSSAALEIHMRTHTGPKPFFCHFCEEAFTTRGNLKVHMGTHMW 932 (958)
T ss_pred hhccchhcccchHHHHHhhhcCCCCCCccchhhhhhhhhhhhhhhhhccccc
Confidence 5899999999999999999999999999999999999999999999998873
No 6
>KOG3623|consensus
Probab=99.73 E-value=1.2e-18 Score=116.60 Aligned_cols=106 Identities=30% Similarity=0.682 Sum_probs=94.5
Q ss_pred eeccccccccCChhHHHHHHHhhc--CCCCcccCCcccccCCchHHHHHHhhhcCC-------------CCcccCCCCCc
Q psy10762 9 HRCDYCAKTFTRKEHLVNHVRQHT--GESPHHCNYCAKSFTRKDHMVYHERQHTGE-------------TPFPCQYCPKA 73 (126)
Q Consensus 9 ~~C~~C~~~f~~~~~l~~h~~~h~--~~~~~~c~~C~~~~~~~~~l~~h~~~~~~~-------------~~~~C~~C~~~ 73 (126)
..|+.|...+.....++.|+...+ .+..|.|.+|..+|.+...|.+|+.+|... +.|.|..|+++
T Consensus 211 ltcpycdrgykrltslkeHikyrhekne~nfsC~lCsytFAyRtQLErhm~~hkpg~dqa~sltqsa~lRKFKCtECgKA 290 (1007)
T KOG3623|consen 211 LTCPYCDRGYKRLTSLKEHIKYRHEKNEPNFSCMLCSYTFAYRTQLERHMQLHKPGGDQAISLTQSALLRKFKCTECGKA 290 (1007)
T ss_pred hcchhHHHHHHHHHHHHHHHHHHHhhCCCCCcchhhhhhhhhHHHHHHHHHhhcCCCcccccccchhhhccccccccchh
Confidence 579999999999999999998654 355689999999999999999999877432 45999999999
Q ss_pred CCChhhHHHHHHhhcCCCCccCcccccccCCHHHHHHHHHH
Q psy10762 74 FTRKDHLVNHVRRHTGESPHKCTYCMKSFTRKEHLTNHIRQ 114 (126)
Q Consensus 74 ~~~~~~l~~h~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~ 114 (126)
|...-.|..|+++|.||+||.|+.|+|+|+.+..+..|+-.
T Consensus 291 FKfKHHLKEHlRIHSGEKPfeCpnCkKRFSHSGSySSHmSS 331 (1007)
T KOG3623|consen 291 FKFKHHLKEHLRIHSGEKPFECPNCKKRFSHSGSYSSHMSS 331 (1007)
T ss_pred hhhHHHHHhhheeecCCCCcCCcccccccccCCcccccccc
Confidence 99999999999999999999999999999998888888754
No 7
>KOG3608|consensus
Probab=99.71 E-value=2.2e-17 Score=102.76 Aligned_cols=79 Identities=23% Similarity=0.537 Sum_probs=40.4
Q ss_pred cccCCcccccCCchHHHHHHh-hhcCCCCcccCCCCCcCCChhhHHHHHHhhcCCCCccCcc--cccccCCHHHHHHHHH
Q psy10762 37 HHCNYCAKSFTRKDHMVYHER-QHTGETPFPCQYCPKAFTRKDHLVNHVRRHTGESPHKCTY--CMKSFTRKEHLTNHIR 113 (126)
Q Consensus 37 ~~c~~C~~~~~~~~~l~~h~~-~~~~~~~~~C~~C~~~~~~~~~l~~h~~~~~~~~~~~C~~--C~~~f~~~~~l~~H~~ 113 (126)
|+|+.|..+....++|..|++ .|...+||.|+.|...+.+...|.+|...|. +..|+|.. |..+|.+...|++|++
T Consensus 264 ykCplCdmtc~~~ssL~~H~r~rHs~dkpfKCd~Cd~~c~~esdL~kH~~~HS-~~~y~C~h~~C~~s~r~~~q~~~H~~ 342 (467)
T KOG3608|consen 264 YKCPLCDMTCSSASSLTTHIRYRHSKDKPFKCDECDTRCVRESDLAKHVQVHS-KTVYQCEHPDCHYSVRTYTQMRRHFL 342 (467)
T ss_pred ccccccccCCCChHHHHHHHHhhhccCCCccccchhhhhccHHHHHHHHHhcc-ccceecCCCCCcHHHHHHHHHHHHHH
Confidence 445555555555555555544 2334455555555555555555555555444 34455543 5555555555555554
Q ss_pred Hhh
Q psy10762 114 QHT 116 (126)
Q Consensus 114 ~h~ 116 (126)
.++
T Consensus 343 evh 345 (467)
T KOG3608|consen 343 EVH 345 (467)
T ss_pred Hhc
Confidence 433
No 8
>KOG3623|consensus
Probab=99.70 E-value=3.4e-18 Score=114.54 Aligned_cols=80 Identities=34% Similarity=0.833 Sum_probs=72.1
Q ss_pred CCCcccCCcccccCCchHHHHHHhhhcCCCCcccCCCCCcCCChhhHHHHHHhhcCCCCccCcccccccCCHHHHHHHHH
Q psy10762 34 ESPHHCNYCAKSFTRKDHMVYHERQHTGETPFPCQYCPKAFTRKDHLVNHVRRHTGESPHKCTYCMKSFTRKEHLTNHIR 113 (126)
Q Consensus 34 ~~~~~c~~C~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~ 113 (126)
+..|.|++|.++|.-.++|.+|.-.|.|.+||+|..|.++|...-.|..|.+.|.||+||.|..|+|+|+.+..+..||.
T Consensus 892 ~gmyaCDqCDK~FqKqSSLaRHKYEHsGqRPyqC~iCkKAFKHKHHLtEHkRLHSGEKPfQCdKClKRFSHSGSYSQHMN 971 (1007)
T KOG3623|consen 892 DGMYACDQCDKAFQKQSSLARHKYEHSGQRPYQCIICKKAFKHKHHLTEHKRLHSGEKPFQCDKCLKRFSHSGSYSQHMN 971 (1007)
T ss_pred cccchHHHHHHHHHhhHHHHHhhhhhcCCCCcccchhhHhhhhhhhhhhhhhhccCCCcchhhhhhhhcccccchHhhhc
Confidence 34689999999999999999999999999999999999999999999999999999999999999999998877777764
No 9
>KOG3576|consensus
Probab=99.68 E-value=6.2e-18 Score=98.01 Aligned_cols=81 Identities=31% Similarity=0.658 Sum_probs=76.9
Q ss_pred CCCcccCCcccccCCchHHHHHHhhhcCCCCcccCCCCCcCCChhhHHHHHHhhcCCCCccCcccccccCCHHHHHHHHH
Q psy10762 34 ESPHHCNYCAKSFTRKDHMVYHERQHTGETPFPCQYCPKAFTRKDHLVNHVRRHTGESPHKCTYCMKSFTRKEHLTNHIR 113 (126)
Q Consensus 34 ~~~~~c~~C~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~ 113 (126)
...|.|.+|++.|.....|.+|++.|...+.+-|..||++|...-.|.+|.++|+|.+||+|..|++.|.++-.|..|++
T Consensus 115 ~d~ftCrvCgK~F~lQRmlnrh~kch~~vkr~lct~cgkgfndtfdlkrh~rthtgvrpykc~~c~kaftqrcsleshl~ 194 (267)
T KOG3576|consen 115 QDSFTCRVCGKKFGLQRMLNRHLKCHSDVKRHLCTFCGKGFNDTFDLKRHTRTHTGVRPYKCSLCEKAFTQRCSLESHLK 194 (267)
T ss_pred CCeeeeehhhhhhhHHHHHHHHhhhccHHHHHHHhhccCcccchhhhhhhhccccCccccchhhhhHHHHhhccHHHHHH
Confidence 44689999999999999999999999999999999999999999999999999999999999999999999999999976
Q ss_pred H
Q psy10762 114 Q 114 (126)
Q Consensus 114 ~ 114 (126)
.
T Consensus 195 k 195 (267)
T KOG3576|consen 195 K 195 (267)
T ss_pred H
Confidence 5
No 10
>KOG3608|consensus
Probab=99.65 E-value=2.4e-16 Score=98.21 Aligned_cols=113 Identities=26% Similarity=0.590 Sum_probs=86.0
Q ss_pred CCCCCcceeccccccccCChhHHHHHHHhh--cCCCCcccCCcccccCCchHHHHHHhhhcCCCCcccCCCCCcCCChhh
Q psy10762 2 WHTGETPHRCDYCAKTFTRKEHLVNHVRQH--TGESPHHCNYCAKSFTRKDHMVYHERQHTGETPFPCQYCPKAFTRKDH 79 (126)
Q Consensus 2 ~~~~~~~~~C~~C~~~f~~~~~l~~h~~~h--~~~~~~~c~~C~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~~~~~~~ 79 (126)
.|+++|...|+.||..|.....|-.|.+.- ....+|.|..|.+.|.....|..|+..|.. -|.||.|..+....++
T Consensus 201 ~Hs~eKvvACp~Cg~~F~~~tkl~DH~rRqt~l~~n~fqC~~C~KrFaTeklL~~Hv~rHvn--~ykCplCdmtc~~~ss 278 (467)
T KOG3608|consen 201 THSNEKVVACPHCGELFRTKTKLFDHLRRQTELNTNSFQCAQCFKRFATEKLLKSHVVRHVN--CYKCPLCDMTCSSASS 278 (467)
T ss_pred hcCCCeEEecchHHHHhccccHHHHHHHhhhhhcCCchHHHHHHHHHhHHHHHHHHHHHhhh--cccccccccCCCChHH
Confidence 577788888888888888887777776532 344577888888888888888888777766 4788888888888888
Q ss_pred HHHHHHh-hcCCCCccCcccccccCCHHHHHHHHHHhh
Q psy10762 80 LVNHVRR-HTGESPHKCTYCMKSFTRKEHLTNHIRQHT 116 (126)
Q Consensus 80 l~~h~~~-~~~~~~~~C~~C~~~f~~~~~l~~H~~~h~ 116 (126)
|..|++. |...+||+|..|.+.|...++|.+|..+|.
T Consensus 279 L~~H~r~rHs~dkpfKCd~Cd~~c~~esdL~kH~~~HS 316 (467)
T KOG3608|consen 279 LTTHIRYRHSKDKPFKCDECDTRCVRESDLAKHVQVHS 316 (467)
T ss_pred HHHHHHhhhccCCCccccchhhhhccHHHHHHHHHhcc
Confidence 8888875 666778888888888888888888877766
No 11
>PLN03086 PRLI-interacting factor K; Provisional
Probab=99.52 E-value=7e-14 Score=93.28 Aligned_cols=103 Identities=19% Similarity=0.459 Sum_probs=87.1
Q ss_pred CcceeccccccccCChhHHHHHHHhhcCCCCcccCCcccccCCchHHHHHHhhhcCCCCcccCCCCCcCCC---------
Q psy10762 6 ETPHRCDYCAKTFTRKEHLVNHVRQHTGESPHHCNYCAKSFTRKDHMVYHERQHTGETPFPCQYCPKAFTR--------- 76 (126)
Q Consensus 6 ~~~~~C~~C~~~f~~~~~l~~h~~~h~~~~~~~c~~C~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~~~~--------- 76 (126)
+..+.|+.|++.|. ...|..|+..++ .++.|+ |+..+ ....|..|+..+.+.+++.|+.|+..+..
T Consensus 451 ~~H~~C~~Cgk~f~-~s~LekH~~~~H--kpv~Cp-Cg~~~-~R~~L~~H~~thCp~Kpi~C~fC~~~v~~g~~~~d~~d 525 (567)
T PLN03086 451 KNHVHCEKCGQAFQ-QGEMEKHMKVFH--EPLQCP-CGVVL-EKEQMVQHQASTCPLRLITCRFCGDMVQAGGSAMDVRD 525 (567)
T ss_pred ccCccCCCCCCccc-hHHHHHHHHhcC--CCccCC-CCCCc-chhHHHhhhhccCCCCceeCCCCCCccccCccccchhh
Confidence 45678999999996 578999999975 679999 99654 66889999999999999999999998852
Q ss_pred -hhhHHHHHHhhcCCCCccCcccccccCCHHHHHHHHHHh
Q psy10762 77 -KDHLVNHVRRHTGESPHKCTYCMKSFTRKEHLTNHIRQH 115 (126)
Q Consensus 77 -~~~l~~h~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~h 115 (126)
...|..|...+ +.+++.|..||+.+..+ .|..|+-.-
T Consensus 526 ~~s~Lt~HE~~C-G~rt~~C~~Cgk~Vrlr-dm~~H~~~~ 563 (567)
T PLN03086 526 RLRGMSEHESIC-GSRTAPCDSCGRSVMLK-EMDIHQIAV 563 (567)
T ss_pred hhhhHHHHHHhc-CCcceEccccCCeeeeh-hHHHHHHHh
Confidence 34788898885 88999999999999988 788886553
No 12
>PHA00733 hypothetical protein
Probab=99.49 E-value=5.9e-14 Score=77.85 Aligned_cols=112 Identities=14% Similarity=0.199 Sum_probs=78.8
Q ss_pred CCCcceeccccccccC-ChhHHHHHHHhhcCCCCcccCCcccccCCchHHHHH--H---hhhcCCCCcccCCCCCcCCCh
Q psy10762 4 TGETPHRCDYCAKTFT-RKEHLVNHVRQHTGESPHHCNYCAKSFTRKDHMVYH--E---RQHTGETPFPCQYCPKAFTRK 77 (126)
Q Consensus 4 ~~~~~~~C~~C~~~f~-~~~~l~~h~~~h~~~~~~~c~~C~~~~~~~~~l~~h--~---~~~~~~~~~~C~~C~~~~~~~ 77 (126)
+|.+.|.-+.=|..|- +.+.|..+-......+++.|.+|...+.....|..+ + ....+.+||.|+.|++.|.+.
T Consensus 7 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~l~~~~~~~~~kPy~C~~Cgk~Fss~ 86 (128)
T PHA00733 7 SGSKKYLSNHKGIFIHVTLEELKRYHSLTPEQKRLIRAVVKTLIYNPQLLDESSYLYKLLTSKAVSPYVCPLCLMPFSSS 86 (128)
T ss_pred cchHhhcccCCCeEEecCHHHhhhhhcCChhhhhHHHHHHhhhccChhhhcchHHHHhhcccCCCCCccCCCCCCcCCCH
Confidence 3444444333333322 223344333333345678899998887776666554 1 133457899999999999999
Q ss_pred hhHHHHHHhhcCCCCccCcccccccCCHHHHHHHHHHhhh
Q psy10762 78 DHLVNHVRRHTGESPHKCTYCMKSFTRKEHLTNHIRQHTV 117 (126)
Q Consensus 78 ~~l~~h~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~ 117 (126)
..|..|++.+ +.+|.|.+|++.|.....|.+|+...++
T Consensus 87 s~L~~H~r~h--~~~~~C~~CgK~F~~~~sL~~H~~~~h~ 124 (128)
T PHA00733 87 VSLKQHIRYT--EHSKVCPVCGKEFRNTDSTLDHVCKKHN 124 (128)
T ss_pred HHHHHHHhcC--CcCccCCCCCCccCCHHHHHHHHHHhcC
Confidence 9999999876 4679999999999999999999887664
No 13
>PHA02768 hypothetical protein; Provisional
Probab=99.26 E-value=2.2e-12 Score=60.17 Aligned_cols=44 Identities=18% Similarity=0.557 Sum_probs=35.3
Q ss_pred CcccCCCCCcCCChhhHHHHHHhhcCCCCccCcccccccCCHHHHH
Q psy10762 64 PFPCQYCPKAFTRKDHLVNHVRRHTGESPHKCTYCMKSFTRKEHLT 109 (126)
Q Consensus 64 ~~~C~~C~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~f~~~~~l~ 109 (126)
.|+|+.||+.|...+.|..|+++|+ ++|.|..|++.|...+.|.
T Consensus 5 ~y~C~~CGK~Fs~~~~L~~H~r~H~--k~~kc~~C~k~f~~~s~l~ 48 (55)
T PHA02768 5 GYECPICGEIYIKRKSMITHLRKHN--TNLKLSNCKRISLRTGEYI 48 (55)
T ss_pred ccCcchhCCeeccHHHHHHHHHhcC--CcccCCcccceecccceeE
Confidence 3788888888888888888888887 6888888888888766553
No 14
>PHA00733 hypothetical protein
Probab=99.25 E-value=1e-11 Score=68.92 Aligned_cols=82 Identities=20% Similarity=0.300 Sum_probs=67.2
Q ss_pred CcceeccccccccCChhHHHHH--HH---hhcCCCCcccCCcccccCCchHHHHHHhhhcCCCCcccCCCCCcCCChhhH
Q psy10762 6 ETPHRCDYCAKTFTRKEHLVNH--VR---QHTGESPHHCNYCAKSFTRKDHMVYHERQHTGETPFPCQYCPKAFTRKDHL 80 (126)
Q Consensus 6 ~~~~~C~~C~~~f~~~~~l~~h--~~---~h~~~~~~~c~~C~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~~~~~~~l 80 (126)
++.+.|.+|...|.....+..+ +. .+.+..+|.|+.|+..|.....|..|+..+ ..+|.|+.|++.|.....|
T Consensus 38 ~~~~~~~~~~~~~~~~~~l~~~~~l~~~~~~~~~kPy~C~~Cgk~Fss~s~L~~H~r~h--~~~~~C~~CgK~F~~~~sL 115 (128)
T PHA00733 38 QKRLIRAVVKTLIYNPQLLDESSYLYKLLTSKAVSPYVCPLCLMPFSSSVSLKQHIRYT--EHSKVCPVCGKEFRNTDST 115 (128)
T ss_pred hhhHHHHHHhhhccChhhhcchHHHHhhcccCCCCCccCCCCCCcCCCHHHHHHHHhcC--CcCccCCCCCCccCCHHHH
Confidence 4678899999988887776665 11 233467899999999999999999999875 4579999999999999999
Q ss_pred HHHHHhhcC
Q psy10762 81 VNHVRRHTG 89 (126)
Q Consensus 81 ~~h~~~~~~ 89 (126)
..|+...++
T Consensus 116 ~~H~~~~h~ 124 (128)
T PHA00733 116 LDHVCKKHN 124 (128)
T ss_pred HHHHHHhcC
Confidence 999876543
No 15
>PLN03086 PRLI-interacting factor K; Provisional
Probab=99.10 E-value=1.7e-10 Score=77.51 Aligned_cols=101 Identities=18% Similarity=0.424 Sum_probs=76.0
Q ss_pred eeccccccccCChhHHHHHHHhhcC-------------------CCCcccCCcccccCCchHHHHHHhhhcCCCCcccCC
Q psy10762 9 HRCDYCAKTFTRKEHLVNHVRQHTG-------------------ESPHHCNYCAKSFTRKDHMVYHERQHTGETPFPCQY 69 (126)
Q Consensus 9 ~~C~~C~~~f~~~~~l~~h~~~h~~-------------------~~~~~c~~C~~~~~~~~~l~~h~~~~~~~~~~~C~~ 69 (126)
-.|.-|...... .+|..|...... +..+.|+.|+..|. ...|..|+..++ +++.|+
T Consensus 408 V~C~NC~~~i~l-~~l~lHe~~C~r~~V~Cp~~~Cg~v~~r~el~~H~~C~~Cgk~f~-~s~LekH~~~~H--kpv~Cp- 482 (567)
T PLN03086 408 VECRNCKHYIPS-RSIALHEAYCSRHNVVCPHDGCGIVLRVEEAKNHVHCEKCGQAFQ-QGEMEKHMKVFH--EPLQCP- 482 (567)
T ss_pred EECCCCCCccch-hHHHHHHhhCCCcceeCCcccccceeeccccccCccCCCCCCccc-hHHHHHHHHhcC--CCccCC-
Confidence 356667665544 345566543221 23467899999885 677999999875 789999
Q ss_pred CCCcCCChhhHHHHHHhhcCCCCccCcccccccCC----------HHHHHHHHHHh
Q psy10762 70 CPKAFTRKDHLVNHVRRHTGESPHKCTYCMKSFTR----------KEHLTNHIRQH 115 (126)
Q Consensus 70 C~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~f~~----------~~~l~~H~~~h 115 (126)
|+..+ ....|..|+.++...+++.|..|++.|.. .+.|..|..+.
T Consensus 483 Cg~~~-~R~~L~~H~~thCp~Kpi~C~fC~~~v~~g~~~~d~~d~~s~Lt~HE~~C 537 (567)
T PLN03086 483 CGVVL-EKEQMVQHQASTCPLRLITCRFCGDMVQAGGSAMDVRDRLRGMSEHESIC 537 (567)
T ss_pred CCCCc-chhHHHhhhhccCCCCceeCCCCCCccccCccccchhhhhhhHHHHHHhc
Confidence 99765 56899999999999999999999999852 45788998875
No 16
>PHA02768 hypothetical protein; Provisional
Probab=99.06 E-value=1.1e-10 Score=54.59 Aligned_cols=39 Identities=18% Similarity=0.588 Sum_probs=21.5
Q ss_pred eeccccccccCChhHHHHHHHhhcCCCCcccCCcccccCCc
Q psy10762 9 HRCDYCAKTFTRKEHLVNHVRQHTGESPHHCNYCAKSFTRK 49 (126)
Q Consensus 9 ~~C~~C~~~f~~~~~l~~h~~~h~~~~~~~c~~C~~~~~~~ 49 (126)
|.|+.||+.|....+|..|++.|+ ++++|..|++.|...
T Consensus 6 y~C~~CGK~Fs~~~~L~~H~r~H~--k~~kc~~C~k~f~~~ 44 (55)
T PHA02768 6 YECPICGEIYIKRKSMITHLRKHN--TNLKLSNCKRISLRT 44 (55)
T ss_pred cCcchhCCeeccHHHHHHHHHhcC--CcccCCcccceeccc
Confidence 555555555555555555555555 345555555555443
No 17
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=99.05 E-value=1.3e-10 Score=46.69 Aligned_cols=25 Identities=60% Similarity=1.123 Sum_probs=18.1
Q ss_pred hHHHHHHhhcCCCCccCcccccccC
Q psy10762 79 HLVNHVRRHTGESPHKCTYCMKSFT 103 (126)
Q Consensus 79 ~l~~h~~~~~~~~~~~C~~C~~~f~ 103 (126)
+|.+|+++|+++++|.|+.|++.|.
T Consensus 1 ~l~~H~~~H~~~k~~~C~~C~k~F~ 25 (26)
T PF13465_consen 1 NLRRHMRTHTGEKPYKCPYCGKSFS 25 (26)
T ss_dssp HHHHHHHHHSSSSSEEESSSSEEES
T ss_pred CHHHHhhhcCCCCCCCCCCCcCeeC
Confidence 3567777777777777777777775
No 18
>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=98.88 E-value=1.3e-09 Score=43.75 Aligned_cols=24 Identities=50% Similarity=1.115 Sum_probs=16.1
Q ss_pred HHHHHhhhcCCCCcccCCCCCcCC
Q psy10762 52 MVYHERQHTGETPFPCQYCPKAFT 75 (126)
Q Consensus 52 l~~h~~~~~~~~~~~C~~C~~~~~ 75 (126)
|..|+++|.|++||.|+.|++.|.
T Consensus 2 l~~H~~~H~~~k~~~C~~C~k~F~ 25 (26)
T PF13465_consen 2 LRRHMRTHTGEKPYKCPYCGKSFS 25 (26)
T ss_dssp HHHHHHHHSSSSSEEESSSSEEES
T ss_pred HHHHhhhcCCCCCCCCCCCcCeeC
Confidence 566666777777777777766654
No 19
>KOG3993|consensus
Probab=98.84 E-value=1e-09 Score=70.54 Aligned_cols=114 Identities=25% Similarity=0.388 Sum_probs=82.1
Q ss_pred ceeccccccccCChhHHHHHHHhhcC---------------------------------CCCcccCCcccccCCchHHHH
Q psy10762 8 PHRCDYCAKTFTRKEHLVNHVRQHTG---------------------------------ESPHHCNYCAKSFTRKDHMVY 54 (126)
Q Consensus 8 ~~~C~~C~~~f~~~~~l~~h~~~h~~---------------------------------~~~~~c~~C~~~~~~~~~l~~ 54 (126)
-|+|++|+++|....||.+|.+.|-. +..|.|..|++.|.....|.+
T Consensus 295 EYrCPEC~KVFsCPANLASHRRWHKPR~eaa~a~~~P~k~~~~~rae~~ea~rsg~dss~gi~~C~~C~KkFrRqAYLrK 374 (500)
T KOG3993|consen 295 EYRCPECDKVFSCPANLASHRRWHKPRPEAAKAGSPPPKQAVETRAEVQEAERSGDDSSSGIFSCHTCGKKFRRQAYLRK 374 (500)
T ss_pred eecCCcccccccCchhhhhhhcccCCchhhhhcCCCChhhhhhhhhhhhhccccCCcccCceeecHHhhhhhHHHHHHHH
Confidence 59999999999999999999987732 123789999999999999999
Q ss_pred HHhhhcCCC------C----------------------------------------cccCCCCCcCCChhhHHHHHHhhc
Q psy10762 55 HERQHTGET------P----------------------------------------FPCQYCPKAFTRKDHLVNHVRRHT 88 (126)
Q Consensus 55 h~~~~~~~~------~----------------------------------------~~C~~C~~~~~~~~~l~~h~~~~~ 88 (126)
|+..|.... + -.++.++..+.++..--.+.+...
T Consensus 375 Hqlthq~~~~~k~~a~~f~~s~~~~l~~~~~~~a~h~~a~~~~g~~vl~~a~sael~~pp~~~~ppsss~~sgg~~rlg~ 454 (500)
T KOG3993|consen 375 HQLTHQRAPLAKEKAPKFLLSRVIPLMHFNQAVATHSSASDSHGDEVLYVAGSAELELPPYDGSPPSSSGSSGGYGRLGI 454 (500)
T ss_pred hHHhhhccccchhcccCcchhhcccccccccccccccccccccccceeeeeccccccCCCCCCCCcccCCCCCccccccc
Confidence 987664220 0 123445544444433333334444
Q ss_pred CCCCccCcccccccCCHHHHHHHHHHhhhcccc
Q psy10762 89 GESPHKCTYCMKSFTRKEHLTNHIRQHTVRRVN 121 (126)
Q Consensus 89 ~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~ 121 (126)
.+.-|.|..|.-.|-++..|.+|+..-|....+
T Consensus 455 ~~q~f~~ky~~atfyss~~ltrhin~~Hpse~r 487 (500)
T KOG3993|consen 455 AEQGFTCKYCPATFYSSPGLTRHINKCHPSELR 487 (500)
T ss_pred hhhccccccchHhhhcCcchHhHhhhcChHHhh
Confidence 456789999999999999999998886655444
No 20
>KOG3993|consensus
Probab=98.81 E-value=8.9e-10 Score=70.80 Aligned_cols=27 Identities=30% Similarity=0.491 Sum_probs=23.8
Q ss_pred CCccCcccccccCCHHHHHHHHHHhhh
Q psy10762 91 SPHKCTYCMKSFTRKEHLTNHIRQHTV 117 (126)
Q Consensus 91 ~~~~C~~C~~~f~~~~~l~~H~~~h~~ 117 (126)
..|.|..|+|.|.....|++|+-.|..
T Consensus 355 gi~~C~~C~KkFrRqAYLrKHqlthq~ 381 (500)
T KOG3993|consen 355 GIFSCHTCGKKFRRQAYLRKHQLTHQR 381 (500)
T ss_pred ceeecHHhhhhhHHHHHHHHhHHhhhc
Confidence 359999999999999999999888763
No 21
>PHA00616 hypothetical protein
Probab=98.81 E-value=2.5e-09 Score=47.71 Aligned_cols=29 Identities=17% Similarity=0.343 Sum_probs=17.0
Q ss_pred CccCcccccccCCHHHHHHHHHHhhhccc
Q psy10762 92 PHKCTYCMKSFTRKEHLTNHIRQHTVRRV 120 (126)
Q Consensus 92 ~~~C~~C~~~f~~~~~l~~H~~~h~~~~~ 120 (126)
+|.|+.||+.|...+.|.+|++.|++++.
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~~hg~~~ 29 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLSVHKQNK 29 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHHhcCCCc
Confidence 35566666666666666666666655543
No 22
>PHA00616 hypothetical protein
Probab=98.66 E-value=1.4e-08 Score=45.30 Aligned_cols=33 Identities=15% Similarity=0.351 Sum_probs=19.1
Q ss_pred ceeccccccccCChhHHHHHHHhhcCCCCcccC
Q psy10762 8 PHRCDYCAKTFTRKEHLVNHVRQHTGESPHHCN 40 (126)
Q Consensus 8 ~~~C~~C~~~f~~~~~l~~h~~~h~~~~~~~c~ 40 (126)
||.|..||+.|....+|..|++.|++++++.|+
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~~hg~~~~~~~ 33 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLSVHKQNKLTLE 33 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHHhcCCCcccee
Confidence 355666666666666666666665555555443
No 23
>PHA00732 hypothetical protein
Probab=98.66 E-value=2.3e-08 Score=50.90 Aligned_cols=45 Identities=24% Similarity=0.450 Sum_probs=29.0
Q ss_pred CcccCCcccccCCchHHHHHHhh-hcCCCCcccCCCCCcCCChhhHHHHHHh
Q psy10762 36 PHHCNYCAKSFTRKDHMVYHERQ-HTGETPFPCQYCPKAFTRKDHLVNHVRR 86 (126)
Q Consensus 36 ~~~c~~C~~~~~~~~~l~~h~~~-~~~~~~~~C~~C~~~~~~~~~l~~h~~~ 86 (126)
+|.|+.|++.|.....|..|++. |. ++.|+.|++.|. .+..|..+
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 35677777777777777777764 33 246777777775 34555543
No 24
>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=98.65 E-value=8.6e-08 Score=45.42 Aligned_cols=50 Identities=28% Similarity=0.584 Sum_probs=37.2
Q ss_pred CcccCCCCCcCCChhhHHHHHHhhcC-C-CCccCcccccccCCHHHHHHHHHHhh
Q psy10762 64 PFPCQYCPKAFTRKDHLVNHVRRHTG-E-SPHKCTYCMKSFTRKEHLTNHIRQHT 116 (126)
Q Consensus 64 ~~~C~~C~~~~~~~~~l~~h~~~~~~-~-~~~~C~~C~~~f~~~~~l~~H~~~h~ 116 (126)
.|.||.|++ ..+...|..|...... + +.+.|++|...+. .+|..|+..++
T Consensus 2 ~f~CP~C~~-~~~~~~L~~H~~~~H~~~~~~v~CPiC~~~~~--~~l~~Hl~~~H 53 (54)
T PF05605_consen 2 SFTCPYCGK-GFSESSLVEHCEDEHRSESKNVVCPICSSRVT--DNLIRHLNSQH 53 (54)
T ss_pred CcCCCCCCC-ccCHHHHHHHHHhHCcCCCCCccCCCchhhhh--hHHHHHHHHhc
Confidence 378999998 4566788889876443 2 4588999988655 48889988765
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=98.63 E-value=2.9e-08 Score=38.66 Aligned_cols=23 Identities=48% Similarity=0.917 Sum_probs=19.6
Q ss_pred ccCcccccccCCHHHHHHHHHHh
Q psy10762 93 HKCTYCMKSFTRKEHLTNHIRQH 115 (126)
Q Consensus 93 ~~C~~C~~~f~~~~~l~~H~~~h 115 (126)
|.|+.|++.|.....|..|++.|
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 67888999999999999998774
No 26
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=98.39 E-value=3.1e-07 Score=35.86 Aligned_cols=24 Identities=42% Similarity=0.826 Sum_probs=18.2
Q ss_pred ccCcccccccCCHHHHHHHHHHhh
Q psy10762 93 HKCTYCMKSFTRKEHLTNHIRQHT 116 (126)
Q Consensus 93 ~~C~~C~~~f~~~~~l~~H~~~h~ 116 (126)
|.|+.|++.|.+...|..|++.|+
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 578889999999889998888764
No 27
>PHA00732 hypothetical protein
Probab=98.38 E-value=3.4e-07 Score=46.65 Aligned_cols=46 Identities=28% Similarity=0.466 Sum_probs=37.9
Q ss_pred ceeccccccccCChhHHHHHHHh-hcCCCCcccCCcccccCCchHHHHHHhhh
Q psy10762 8 PHRCDYCAKTFTRKEHLVNHVRQ-HTGESPHHCNYCAKSFTRKDHMVYHERQH 59 (126)
Q Consensus 8 ~~~C~~C~~~f~~~~~l~~h~~~-h~~~~~~~c~~C~~~~~~~~~l~~h~~~~ 59 (126)
||.|..|++.|....+|..|+.. |.+ +.|+.|++.|. .+..|+...
T Consensus 1 py~C~~Cgk~F~s~s~Lk~H~r~~H~~---~~C~~CgKsF~---~l~~H~~~~ 47 (79)
T PHA00732 1 MFKCPICGFTTVTLFALKQHARRNHTL---TKCPVCNKSYR---RLNQHFYSQ 47 (79)
T ss_pred CccCCCCCCccCCHHHHHHHhhcccCC---CccCCCCCEeC---Chhhhhccc
Confidence 58899999999999999999984 553 58999999997 467777443
No 28
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=98.30 E-value=5.6e-07 Score=47.94 Aligned_cols=23 Identities=39% Similarity=0.967 Sum_probs=15.3
Q ss_pred CccCcccccccCCHHHHHHHHHH
Q psy10762 92 PHKCTYCMKSFTRKEHLTNHIRQ 114 (126)
Q Consensus 92 ~~~C~~C~~~f~~~~~l~~H~~~ 114 (126)
.+.|..|++.|.+...|..|++.
T Consensus 50 ~~~C~~C~~~f~s~~~l~~Hm~~ 72 (100)
T PF12756_consen 50 SFRCPYCNKTFRSREALQEHMRS 72 (100)
T ss_dssp SEEBSSSS-EESSHHHHHHHHHH
T ss_pred CCCCCccCCCCcCHHHHHHHHcC
Confidence 46677777777777777777665
No 29
>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=98.29 E-value=7.8e-07 Score=34.47 Aligned_cols=23 Identities=39% Similarity=0.907 Sum_probs=16.9
Q ss_pred eeccccccccCChhHHHHHHHhh
Q psy10762 9 HRCDYCAKTFTRKEHLVNHVRQH 31 (126)
Q Consensus 9 ~~C~~C~~~f~~~~~l~~h~~~h 31 (126)
|.|+.|++.|.....|..|++.|
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 56777777777777777777653
No 30
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=98.28 E-value=4.7e-07 Score=36.55 Aligned_cols=25 Identities=36% Similarity=0.731 Sum_probs=20.3
Q ss_pred CccCcccccccCCHHHHHHHHHHhh
Q psy10762 92 PHKCTYCMKSFTRKEHLTNHIRQHT 116 (126)
Q Consensus 92 ~~~C~~C~~~f~~~~~l~~H~~~h~ 116 (126)
+|.|..|++.|.+...|..|++.|.
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 4778888888888888888887764
No 31
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=98.25 E-value=3e-06 Score=40.11 Aligned_cols=48 Identities=25% Similarity=0.546 Sum_probs=24.3
Q ss_pred eeccccccccCChhHHHHHHHhh-cC-CCCcccCCcccccCCchHHHHHHhhh
Q psy10762 9 HRCDYCAKTFTRKEHLVNHVRQH-TG-ESPHHCNYCAKSFTRKDHMVYHERQH 59 (126)
Q Consensus 9 ~~C~~C~~~f~~~~~l~~h~~~h-~~-~~~~~c~~C~~~~~~~~~l~~h~~~~ 59 (126)
|.|+.|++ ..+...|..|.... .. .+.+.|++|...+. ..|..|+...
T Consensus 3 f~CP~C~~-~~~~~~L~~H~~~~H~~~~~~v~CPiC~~~~~--~~l~~Hl~~~ 52 (54)
T PF05605_consen 3 FTCPYCGK-GFSESSLVEHCEDEHRSESKNVVCPICSSRVT--DNLIRHLNSQ 52 (54)
T ss_pred cCCCCCCC-ccCHHHHHHHHHhHCcCCCCCccCCCchhhhh--hHHHHHHHHh
Confidence 56666666 44455566665442 22 23455666654322 2455555443
No 32
>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=98.03 E-value=3.7e-06 Score=38.44 Aligned_cols=33 Identities=18% Similarity=0.486 Sum_probs=21.9
Q ss_pred cCCCCccCcccccccCCHHHHHHHHHHhhhccc
Q psy10762 88 TGESPHKCTYCMKSFTRKEHLTNHIRQHTVRRV 120 (126)
Q Consensus 88 ~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~ 120 (126)
..+.|..|++|+..+++..+|++|+++++..+.
T Consensus 20 ~S~~PatCP~C~a~~~~srnLrRHle~~H~~k~ 52 (54)
T PF09237_consen 20 QSEQPATCPICGAVIRQSRNLRRHLEIRHFKKP 52 (54)
T ss_dssp TTS--EE-TTT--EESSHHHHHHHHHHHTTTS-
T ss_pred ccCCCCCCCcchhhccchhhHHHHHHHHhcccC
Confidence 346778899999999999999999988776553
No 33
>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=98.00 E-value=5.1e-06 Score=33.42 Aligned_cols=25 Identities=44% Similarity=0.830 Sum_probs=18.0
Q ss_pred ceeccccccccCChhHHHHHHHhhc
Q psy10762 8 PHRCDYCAKTFTRKEHLVNHVRQHT 32 (126)
Q Consensus 8 ~~~C~~C~~~f~~~~~l~~h~~~h~ 32 (126)
+|.|..|++.|.+...|..|++.|.
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 4677777777777777777776553
No 34
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=97.99 E-value=1.4e-06 Score=54.70 Aligned_cols=52 Identities=23% Similarity=0.593 Sum_probs=38.3
Q ss_pred CCCcccCC--CCCcCCChhhHHHHHHhh-------------------cCCCCccCcccccccCCHHHHHHHHH
Q psy10762 62 ETPFPCQY--CPKAFTRKDHLVNHVRRH-------------------TGESPHKCTYCMKSFTRKEHLTNHIR 113 (126)
Q Consensus 62 ~~~~~C~~--C~~~~~~~~~l~~h~~~~-------------------~~~~~~~C~~C~~~f~~~~~l~~H~~ 113 (126)
++||.|++ |.+.|....-|.-|+.-. ...+||+|++|+|+++....|.-|..
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 46777765 777777776666665321 12589999999999999988888743
No 35
>smart00355 ZnF_C2H2 zinc finger.
Probab=97.98 E-value=8.3e-06 Score=32.16 Aligned_cols=24 Identities=38% Similarity=0.690 Sum_probs=20.6
Q ss_pred ccCcccccccCCHHHHHHHHHHhh
Q psy10762 93 HKCTYCMKSFTRKEHLTNHIRQHT 116 (126)
Q Consensus 93 ~~C~~C~~~f~~~~~l~~H~~~h~ 116 (126)
|.|..|++.|...+.|..|++.|.
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~~H~ 24 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMRTHX 24 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHHHhc
Confidence 578899999999999999988664
No 36
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=97.98 E-value=9.7e-06 Score=31.42 Aligned_cols=23 Identities=39% Similarity=0.863 Sum_probs=14.0
Q ss_pred eeccccccccCChhHHHHHHHhh
Q psy10762 9 HRCDYCAKTFTRKEHLVNHVRQH 31 (126)
Q Consensus 9 ~~C~~C~~~f~~~~~l~~h~~~h 31 (126)
|.|+.|+..|.+...|..|+..+
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 46677777777777777776654
No 37
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=97.72 E-value=3.6e-05 Score=40.90 Aligned_cols=74 Identities=23% Similarity=0.588 Sum_probs=22.1
Q ss_pred eccccccccCChhHHHHHHHhhcCCCCcccCCcccccCCchHHHHHHhhhcCCCCcccCCCCCcCCChhhHHHHHHhhc
Q psy10762 10 RCDYCAKTFTRKEHLVNHVRQHTGESPHHCNYCAKSFTRKDHMVYHERQHTGETPFPCQYCPKAFTRKDHLVNHVRRHT 88 (126)
Q Consensus 10 ~C~~C~~~f~~~~~l~~h~~~h~~~~~~~c~~C~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~~~~~~~l~~h~~~~~ 88 (126)
.|..|+..|.....+..|+...++-. .+. ...+.....+..+...... ..+.|..|++.|.+...|..|++.+.
T Consensus 1 ~C~~C~~~f~~~~~l~~H~~~~H~~~---~~~-~~~l~~~~~~~~~~~~~~~-~~~~C~~C~~~f~s~~~l~~Hm~~~~ 74 (100)
T PF12756_consen 1 QCLFCDESFSSVDDLLQHMKKKHGFD---IPD-QKYLVDPNRLLNYLRKKVK-ESFRCPYCNKTFRSREALQEHMRSKH 74 (100)
T ss_dssp -----------------------------------------------------SSEEBSSSS-EESSHHHHHHHHHHTT
T ss_pred Cccccccccccccccccccccccccc---ccc-ccccccccccccccccccC-CCCCCCccCCCCcCHHHHHHHHcCcc
Confidence 48899999999999999986554421 111 1112233333334332222 26899999999999999999999754
No 38
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=97.72 E-value=2.3e-05 Score=30.84 Aligned_cols=23 Identities=35% Similarity=0.758 Sum_probs=18.7
Q ss_pred ccCcccccccCCHHHHHHHHHHh
Q psy10762 93 HKCTYCMKSFTRKEHLTNHIRQH 115 (126)
Q Consensus 93 ~~C~~C~~~f~~~~~l~~H~~~h 115 (126)
|.|.+|++.|.+...|..|++.+
T Consensus 1 ~~C~~C~~~f~s~~~~~~H~~s~ 23 (25)
T PF12874_consen 1 FYCDICNKSFSSENSLRQHLRSK 23 (25)
T ss_dssp EEETTTTEEESSHHHHHHHHTTH
T ss_pred CCCCCCCCCcCCHHHHHHHHCcC
Confidence 56888888888888888887653
No 39
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=97.66 E-value=1.1e-05 Score=50.88 Aligned_cols=69 Identities=20% Similarity=0.444 Sum_probs=41.8
Q ss_pred Ccceeccc--cccccCChhHHHHHHHh-hcCCCCcccCCcccccCCchHHHHHHhhhcCCCCcccCCCCCcCCChhhHHH
Q psy10762 6 ETPHRCDY--CAKTFTRKEHLVNHVRQ-HTGESPHHCNYCAKSFTRKDHMVYHERQHTGETPFPCQYCPKAFTRKDHLVN 82 (126)
Q Consensus 6 ~~~~~C~~--C~~~f~~~~~l~~h~~~-h~~~~~~~c~~C~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~~~~~~~l~~ 82 (126)
++||+|++ |.+.|.....|+.|+.. |...+...-+ .-..+.......|||.|.+|++.|....-|.-
T Consensus 347 ~KpykCpV~gC~K~YknqnGLKYH~lhGH~~~~~~~~p----------~p~~~~~F~~~~KPYrCevC~KRYKNlNGLKY 416 (423)
T COG5189 347 GKPYKCPVEGCNKKYKNQNGLKYHMLHGHQNQKLHENP----------SPEKMNIFSAKDKPYRCEVCDKRYKNLNGLKY 416 (423)
T ss_pred CceecCCCCCchhhhccccchhhhhhccccCcccCCCC----------CccccccccccCCceeccccchhhccCcccee
Confidence 57888865 88888888778877643 2222211111 01111122345689999999999988877765
Q ss_pred HH
Q psy10762 83 HV 84 (126)
Q Consensus 83 h~ 84 (126)
|.
T Consensus 417 Hr 418 (423)
T COG5189 417 HR 418 (423)
T ss_pred cc
Confidence 54
No 40
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=97.58 E-value=7.3e-05 Score=29.08 Aligned_cols=23 Identities=35% Similarity=0.690 Sum_probs=16.5
Q ss_pred ccCcccccccCCHHHHHHHHHHhh
Q psy10762 93 HKCTYCMKSFTRKEHLTNHIRQHT 116 (126)
Q Consensus 93 ~~C~~C~~~f~~~~~l~~H~~~h~ 116 (126)
|+|+.|+.... ...|.+|+++++
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 57888888777 778888887765
No 41
>PRK04860 hypothetical protein; Provisional
Probab=97.56 E-value=5.6e-05 Score=43.78 Aligned_cols=38 Identities=26% Similarity=0.629 Sum_probs=32.4
Q ss_pred CcccCCCCCcCCChhhHHHHHHhhcCCCCccCcccccccCCH
Q psy10762 64 PFPCQYCPKAFTRKDHLVNHVRRHTGESPHKCTYCMKSFTRK 105 (126)
Q Consensus 64 ~~~C~~C~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~f~~~ 105 (126)
+|.|. |+. ....+.+|.+++.++++|.|..|+..|...
T Consensus 119 ~Y~C~-C~~---~~~~~rrH~ri~~g~~~YrC~~C~~~l~~~ 156 (160)
T PRK04860 119 PYRCK-CQE---HQLTVRRHNRVVRGEAVYRCRRCGETLVFK 156 (160)
T ss_pred EEEcC-CCC---eeCHHHHHHHHhcCCccEECCCCCceeEEe
Confidence 58998 986 666788999999999999999999988653
No 42
>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=97.51 E-value=0.00021 Score=32.81 Aligned_cols=32 Identities=19% Similarity=0.409 Sum_probs=19.1
Q ss_pred CCCCcccCCcccccCCchHHHHHHhhhcCCCC
Q psy10762 33 GESPHHCNYCAKSFTRKDHMVYHERQHTGETP 64 (126)
Q Consensus 33 ~~~~~~c~~C~~~~~~~~~l~~h~~~~~~~~~ 64 (126)
.+.|..|++|+..+.+..+|.+|+...++.+|
T Consensus 21 S~~PatCP~C~a~~~~srnLrRHle~~H~~k~ 52 (54)
T PF09237_consen 21 SEQPATCPICGAVIRQSRNLRRHLEIRHFKKP 52 (54)
T ss_dssp TS--EE-TTT--EESSHHHHHHHHHHHTTTS-
T ss_pred cCCCCCCCcchhhccchhhHHHHHHHHhcccC
Confidence 44566778888777777778888777776655
No 43
>smart00355 ZnF_C2H2 zinc finger.
Probab=97.46 E-value=0.00012 Score=28.61 Aligned_cols=23 Identities=43% Similarity=0.823 Sum_probs=14.5
Q ss_pred eeccccccccCChhHHHHHHHhh
Q psy10762 9 HRCDYCAKTFTRKEHLVNHVRQH 31 (126)
Q Consensus 9 ~~C~~C~~~f~~~~~l~~h~~~h 31 (126)
|.|..|++.|.....+..|+..|
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~~H 23 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMRTH 23 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHHHh
Confidence 35666666666666666666544
No 44
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=97.33 E-value=0.0002 Score=28.06 Aligned_cols=22 Identities=36% Similarity=0.834 Sum_probs=16.0
Q ss_pred eeccccccccCChhHHHHHHHh
Q psy10762 9 HRCDYCAKTFTRKEHLVNHVRQ 30 (126)
Q Consensus 9 ~~C~~C~~~f~~~~~l~~h~~~ 30 (126)
|.|..|+..|.+...+..|++.
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 5677777777777777777654
No 45
>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=97.18 E-value=8.9e-05 Score=29.75 Aligned_cols=22 Identities=27% Similarity=0.677 Sum_probs=16.7
Q ss_pred ccCcccccccCCHHHHHHHHHH
Q psy10762 93 HKCTYCMKSFTRKEHLTNHIRQ 114 (126)
Q Consensus 93 ~~C~~C~~~f~~~~~l~~H~~~ 114 (126)
|.|..|++.|.+...|..|++.
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 5688888888888888777654
No 46
>PRK04860 hypothetical protein; Provisional
Probab=97.00 E-value=0.00067 Score=39.39 Aligned_cols=38 Identities=26% Similarity=0.635 Sum_probs=31.4
Q ss_pred CcccCCcccccCCchHHHHHHhhhcCCCCcccCCCCCcCCCh
Q psy10762 36 PHHCNYCAKSFTRKDHMVYHERQHTGETPFPCQYCPKAFTRK 77 (126)
Q Consensus 36 ~~~c~~C~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~~~~~ 77 (126)
+|.|. |+. ....+..|.+++.++++|.|..|+..|...
T Consensus 119 ~Y~C~-C~~---~~~~~rrH~ri~~g~~~YrC~~C~~~l~~~ 156 (160)
T PRK04860 119 PYRCK-CQE---HQLTVRRHNRVVRGEAVYRCRRCGETLVFK 156 (160)
T ss_pred EEEcC-CCC---eeCHHHHHHHHhcCCccEECCCCCceeEEe
Confidence 47887 876 677788999999999999999999877543
No 47
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=96.89 E-value=0.0012 Score=25.92 Aligned_cols=21 Identities=24% Similarity=0.602 Sum_probs=13.5
Q ss_pred ccCcccccccCCHHHHHHHHHH
Q psy10762 93 HKCTYCMKSFTRKEHLTNHIRQ 114 (126)
Q Consensus 93 ~~C~~C~~~f~~~~~l~~H~~~ 114 (126)
..|+.||+.| ..+.|.+|+.+
T Consensus 3 ~~C~~CgR~F-~~~~l~~H~~~ 23 (25)
T PF13913_consen 3 VPCPICGRKF-NPDRLEKHEKI 23 (25)
T ss_pred CcCCCCCCEE-CHHHHHHHHHh
Confidence 3577777777 44466777654
No 48
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=96.67 E-value=0.0022 Score=24.72 Aligned_cols=21 Identities=24% Similarity=0.629 Sum_probs=9.5
Q ss_pred eeccccccccCChhHHHHHHHh
Q psy10762 9 HRCDYCAKTFTRKEHLVNHVRQ 30 (126)
Q Consensus 9 ~~C~~C~~~f~~~~~l~~h~~~ 30 (126)
|.|+.|+.... ..+|..|+..
T Consensus 1 y~C~~C~y~t~-~~~l~~H~~~ 21 (24)
T PF13909_consen 1 YKCPHCSYSTS-KSNLKRHLKR 21 (24)
T ss_dssp EE-SSSS-EES-HHHHHHHHHH
T ss_pred CCCCCCCCcCC-HHHHHHHHHh
Confidence 34555555444 4455555544
No 49
>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=96.46 E-value=0.0008 Score=26.89 Aligned_cols=22 Identities=32% Similarity=0.753 Sum_probs=16.1
Q ss_pred eeccccccccCChhHHHHHHHh
Q psy10762 9 HRCDYCAKTFTRKEHLVNHVRQ 30 (126)
Q Consensus 9 ~~C~~C~~~f~~~~~l~~h~~~ 30 (126)
|.|..|++.|.+...+..|+..
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 5677888888887777777643
No 50
>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=96.15 E-value=0.0046 Score=26.15 Aligned_cols=23 Identities=22% Similarity=0.527 Sum_probs=19.2
Q ss_pred CccCcccccccCCHHHHHHHHHH
Q psy10762 92 PHKCTYCMKSFTRKEHLTNHIRQ 114 (126)
Q Consensus 92 ~~~C~~C~~~f~~~~~l~~H~~~ 114 (126)
+|.|..|+..|.+...+..|+..
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~g 25 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLKG 25 (35)
T ss_pred CeEccccCCccCCHHHHHHHHCh
Confidence 57799999999988888888754
No 51
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=96.12 E-value=0.0038 Score=29.20 Aligned_cols=28 Identities=25% Similarity=0.573 Sum_probs=19.2
Q ss_pred CCCCccCcccccccCCHHHHHHHHHHhh
Q psy10762 89 GESPHKCTYCMKSFTRKEHLTNHIRQHT 116 (126)
Q Consensus 89 ~~~~~~C~~C~~~f~~~~~l~~H~~~h~ 116 (126)
||..+.|+.|+..|....++.+|....+
T Consensus 14 GE~~lrCPRC~~~FR~~K~Y~RHVNKaH 41 (65)
T COG4049 14 GEEFLRCPRCGMVFRRRKDYIRHVNKAH 41 (65)
T ss_pred CceeeeCCchhHHHHHhHHHHHHhhHHh
Confidence 4556677777777777777777765543
No 52
>KOG4173|consensus
Probab=96.03 E-value=0.0031 Score=37.75 Aligned_cols=76 Identities=22% Similarity=0.546 Sum_probs=56.1
Q ss_pred CcccCC--cccccCCchHHHHHHhhhcCCCCcccCCCCCcCCChhhHHHHHHhhc----------CCCCccCcc--cccc
Q psy10762 36 PHHCNY--CAKSFTRKDHMVYHERQHTGETPFPCQYCPKAFTRKDHLVNHVRRHT----------GESPHKCTY--CMKS 101 (126)
Q Consensus 36 ~~~c~~--C~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~~~~~~~l~~h~~~~~----------~~~~~~C~~--C~~~ 101 (126)
.+.|+. |...+.....+..|...-++. .|..|.++|.+...|..|+...+ |.-.|.|.+ |+..
T Consensus 79 ~~~cqvagc~~~~d~lD~~E~hY~~~h~~---sCs~C~r~~Pt~hLLd~HI~E~HDs~Fqa~veRG~dMy~ClvEgCt~K 155 (253)
T KOG4173|consen 79 AFACQVAGCCQVFDALDDYEHHYHTLHGN---SCSFCKRAFPTGHLLDAHILEWHDSLFQALVERGQDMYQCLVEGCTEK 155 (253)
T ss_pred cccccccchHHHHhhhhhHHHhhhhcccc---hhHHHHHhCCchhhhhHHHHHHHHHHHHHHHHcCccHHHHHHHhhhhh
Confidence 456766 667777777777776655554 89999999999888888886533 334588955 9999
Q ss_pred cCCHHHHHHHHHH
Q psy10762 102 FTRKEHLTNHIRQ 114 (126)
Q Consensus 102 f~~~~~l~~H~~~ 114 (126)
|.....-..|+-.
T Consensus 156 FkT~r~RkdH~I~ 168 (253)
T KOG4173|consen 156 FKTSRDRKDHMIR 168 (253)
T ss_pred hhhhhhhhhHHHH
Confidence 9998888888544
No 53
>cd00350 rubredoxin_like Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center. The family includes rubredoxins, a small electron transfer protein, and a slightly smaller modular rubredoxin domain present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=95.76 E-value=0.0063 Score=25.56 Aligned_cols=8 Identities=38% Similarity=0.982 Sum_probs=3.7
Q ss_pred CccCcccc
Q psy10762 92 PHKCTYCM 99 (126)
Q Consensus 92 ~~~C~~C~ 99 (126)
++.|++|+
T Consensus 17 ~~~CP~Cg 24 (33)
T cd00350 17 PWVCPVCG 24 (33)
T ss_pred CCcCcCCC
Confidence 34444443
No 54
>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=95.57 E-value=0.015 Score=24.52 Aligned_cols=22 Identities=27% Similarity=0.578 Sum_probs=15.3
Q ss_pred ceeccccccccCChhHHHHHHH
Q psy10762 8 PHRCDYCAKTFTRKEHLVNHVR 29 (126)
Q Consensus 8 ~~~C~~C~~~f~~~~~l~~h~~ 29 (126)
+|.|..|+..|.....+..|+.
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~ 24 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLK 24 (35)
T ss_pred CeEccccCCccCCHHHHHHHHC
Confidence 4667777777777666766664
No 55
>KOG2231|consensus
Probab=95.48 E-value=0.052 Score=38.52 Aligned_cols=97 Identities=23% Similarity=0.431 Sum_probs=57.7
Q ss_pred ccCChhHHHHHHHhhcCCCCcccCCcc---------cccCCchHHHHHHhhhcC-CC----CcccCCCCCcCCChhhHHH
Q psy10762 17 TFTRKEHLVNHVRQHTGESPHHCNYCA---------KSFTRKDHMVYHERQHTG-ET----PFPCQYCPKAFTRKDHLVN 82 (126)
Q Consensus 17 ~f~~~~~l~~h~~~h~~~~~~~c~~C~---------~~~~~~~~l~~h~~~~~~-~~----~~~C~~C~~~~~~~~~l~~ 82 (126)
.|.....|+.|+..-+. .+.|.+|- ........|..|+..... ++ .-.|..|...|.....+.+
T Consensus 123 ~~~s~~~Lk~H~~~~H~--~~~c~lC~~~~kif~~e~k~Yt~~el~~h~~~gd~d~~s~rGhp~C~~C~~~fld~~el~r 200 (669)
T KOG2231|consen 123 EFKSVENLKNHMRDQHK--LHLCSLCLQNLKIFINERKLYTRAELNLHLMFGDPDDESCRGHPLCKFCHERFLDDDELYR 200 (669)
T ss_pred chhHHHHHHHHHHHhhh--hhccccccccceeeeeeeehehHHHHHHHHhcCCCccccccCCccchhhhhhhccHHHHHH
Confidence 33477889999854332 23444432 223345567777654322 11 1368889888888888888
Q ss_pred HHHhhcCCCCccC---cccccccCCHHHHHHHHHHhh
Q psy10762 83 HVRRHTGESPHKC---TYCMKSFTRKEHLTNHIRQHT 116 (126)
Q Consensus 83 h~~~~~~~~~~~C---~~C~~~f~~~~~l~~H~~~h~ 116 (126)
|++..+-...| | ..++..|.....|..|.|..|
T Consensus 201 H~~~~h~~chf-C~~~~~~neyy~~~~dLe~HfR~~H 236 (669)
T KOG2231|consen 201 HLRFDHEFCHF-CDYKTGQNEYYNDYDDLEEHFRKGH 236 (669)
T ss_pred hhccceeheee-cCcccccchhcccchHHHHHhhhcC
Confidence 88754322211 2 223456777888888887755
No 56
>KOG2893|consensus
Probab=95.02 E-value=0.0048 Score=37.86 Aligned_cols=46 Identities=28% Similarity=0.660 Sum_probs=34.8
Q ss_pred cCCCCCcCCChhhHHHHHHhhcCCCCccCcccccccCCHHHHHHH-HHHhh
Q psy10762 67 CQYCPKAFTRKDHLVNHVRRHTGESPHKCTYCMKSFTRKEHLTNH-IRQHT 116 (126)
Q Consensus 67 C~~C~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~f~~~~~l~~H-~~~h~ 116 (126)
|..|.+.|..+..|..|++ .+.|+|.+|.|..-+.-.|..| +.+|.
T Consensus 13 cwycnrefddekiliqhqk----akhfkchichkkl~sgpglsihcmqvhk 59 (341)
T KOG2893|consen 13 CWYCNREFDDEKILIQHQK----AKHFKCHICHKKLFSGPGLSIHCMQVHK 59 (341)
T ss_pred eeecccccchhhhhhhhhh----hccceeeeehhhhccCCCceeehhhhhh
Confidence 6779999999988888866 5778999998876555577777 44443
No 57
>KOG2785|consensus
Probab=94.91 E-value=0.16 Score=33.54 Aligned_cols=50 Identities=22% Similarity=0.553 Sum_probs=34.9
Q ss_pred cccCCCCCcCCChhhHHHHHHhhcC-----------------------CCCccCcccc---cccCCHHHHHHHHHH
Q psy10762 65 FPCQYCPKAFTRKDHLVNHVRRHTG-----------------------ESPHKCTYCM---KSFTRKEHLTNHIRQ 114 (126)
Q Consensus 65 ~~C~~C~~~~~~~~~l~~h~~~~~~-----------------------~~~~~C~~C~---~~f~~~~~l~~H~~~ 114 (126)
-.|-.|++.+.+...-..|+..+++ ..-+.|..|+ +.|.+....+.||..
T Consensus 167 t~CLfC~~~~k~~e~~~~HM~~~HgffIPdreYL~D~~GLl~YLgeKV~~~~~CL~CN~~~~~f~sleavr~HM~~ 242 (390)
T KOG2785|consen 167 TDCLFCDKKSKSLEENLKHMFKEHGFFIPDREYLTDEKGLLKYLGEKVGIGFICLFCNELGRPFSSLEAVRAHMRD 242 (390)
T ss_pred cceeecCCCcccHHHHHHHHhhccCCcCCchHhhhchhHHHHHHHHHhccCceEEEeccccCcccccHHHHHHHhh
Confidence 4577787777777777777765543 1346777787 788887777888754
No 58
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=94.85 E-value=0.064 Score=29.24 Aligned_cols=48 Identities=17% Similarity=0.275 Sum_probs=24.0
Q ss_pred cCCCCCcCCChhhHHHHHHhhcCCCCccCcccccccCCHHHHHHHHHHhh
Q psy10762 67 CQYCPKAFTRKDHLVNHVRRHTGESPHKCTYCMKSFTRKEHLTNHIRQHT 116 (126)
Q Consensus 67 C~~C~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~h~ 116 (126)
|-.|...|....... ...-.....|.|+.|...|=..-+.-.|...|.
T Consensus 58 C~~C~~~f~~~~~~~--~~~~~~~~~y~C~~C~~~FC~dCD~fiHe~Lh~ 105 (112)
T TIGR00622 58 CFGCQGPFPKPPVSP--FDELKDSHRYVCAVCKNVFCVDCDVFVHESLHC 105 (112)
T ss_pred ccCcCCCCCCccccc--ccccccccceeCCCCCCccccccchhhhhhccC
Confidence 666666665432100 000122345777777777765555555555443
No 59
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=94.48 E-value=0.0062 Score=40.50 Aligned_cols=58 Identities=36% Similarity=0.705 Sum_probs=45.8
Q ss_pred CcccCCCCCcCCChhhHHHHHH--hhcCC--CCccCc--ccccccCCHHHHHHHHHHhhhcccc
Q psy10762 64 PFPCQYCPKAFTRKDHLVNHVR--RHTGE--SPHKCT--YCMKSFTRKEHLTNHIRQHTVRRVN 121 (126)
Q Consensus 64 ~~~C~~C~~~~~~~~~l~~h~~--~~~~~--~~~~C~--~C~~~f~~~~~l~~H~~~h~~~~~~ 121 (126)
++.|..|...|.....+..|.+ .|.++ +++.|+ .|++.|.+...+..|..+|+.....
T Consensus 289 ~~~~~~~~~~~s~~~~l~~~~~~~~h~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~ 352 (467)
T COG5048 289 PIKSKQCNISFSRSSPLTRHLRSVNHSGESLKPFSCPYSLCGKLFSRNDALKRHILLHTSISPA 352 (467)
T ss_pred CCCCccccCCccccccccccccccccccccCCceeeeccCCCccccccccccCCcccccCCCcc
Confidence 5677778888888888888888 78888 888888 6888888888888888777765543
No 60
>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=94.48 E-value=0.027 Score=22.30 Aligned_cols=10 Identities=30% Similarity=0.647 Sum_probs=5.9
Q ss_pred cCcccccccC
Q psy10762 94 KCTYCMKSFT 103 (126)
Q Consensus 94 ~C~~C~~~f~ 103 (126)
.|+.||..|.
T Consensus 16 ~Cp~CG~~F~ 25 (26)
T PF10571_consen 16 FCPHCGYDFE 25 (26)
T ss_pred cCCCCCCCCc
Confidence 4666666653
No 61
>KOG1146|consensus
Probab=94.46 E-value=0.01 Score=44.58 Aligned_cols=75 Identities=24% Similarity=0.368 Sum_probs=49.2
Q ss_pred hcCCCCcccCCcccccCCchHHHHHHhhhcCCCCcccCCCCCcCCChhhHHHHHHh------hcCCCCccCcccccccCC
Q psy10762 31 HTGESPHHCNYCAKSFTRKDHMVYHERQHTGETPFPCQYCPKAFTRKDHLVNHVRR------HTGESPHKCTYCMKSFTR 104 (126)
Q Consensus 31 h~~~~~~~c~~C~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~~~~~~~l~~h~~~------~~~~~~~~C~~C~~~f~~ 104 (126)
++..+.+.|+.|++.+.....|..|++..+.+-.- ..|. ..+.|.+. -.+.++|.|..|..++..
T Consensus 460 ~S~~kt~~cpkc~~~yk~a~~L~vhmRskhp~~~~--~~c~-------~gq~~~~~arg~~~~~~~~p~~C~~C~~sttt 530 (1406)
T KOG1146|consen 460 HSFFKTLKCPKCNWHYKLAQTLGVHMRSKHPESQS--AYCK-------AGQNHPRLARGEVYRCPGKPYPCRACNYSTTT 530 (1406)
T ss_pred ecccccccCCccchhhhhHHHhhhcccccccccch--hHhH-------hccccccccccccccCCCCcccceeeeeeeec
Confidence 34446678888998888888888888864443211 1121 11111111 123578999999999999
Q ss_pred HHHHHHHHHH
Q psy10762 105 KEHLTNHIRQ 114 (126)
Q Consensus 105 ~~~l~~H~~~ 114 (126)
...|.+|+..
T Consensus 531 ng~LsihlqS 540 (1406)
T KOG1146|consen 531 NGNLSIHLQS 540 (1406)
T ss_pred chHHHHHHHH
Confidence 9999999755
No 62
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=94.23 E-value=0.034 Score=26.09 Aligned_cols=27 Identities=33% Similarity=0.730 Sum_probs=17.1
Q ss_pred CCCcceeccccccccCChhHHHHHHHh
Q psy10762 4 TGETPHRCDYCAKTFTRKEHLVNHVRQ 30 (126)
Q Consensus 4 ~~~~~~~C~~C~~~f~~~~~l~~h~~~ 30 (126)
.|+.-+.|+-|+..|....++..|...
T Consensus 13 DGE~~lrCPRC~~~FR~~K~Y~RHVNK 39 (65)
T COG4049 13 DGEEFLRCPRCGMVFRRRKDYIRHVNK 39 (65)
T ss_pred CCceeeeCCchhHHHHHhHHHHHHhhH
Confidence 345556677777777666666666543
No 63
>KOG1146|consensus
Probab=94.16 E-value=0.0076 Score=45.26 Aligned_cols=103 Identities=17% Similarity=0.275 Sum_probs=58.4
Q ss_pred eeccccccccCChhHHHHHHHhhc----CCCCcccCCcccccCCchHHHHHHhhhcCCCCcccCCCCCcCCChhhHHHHH
Q psy10762 9 HRCDYCAKTFTRKEHLVNHVRQHT----GESPHHCNYCAKSFTRKDHMVYHERQHTGETPFPCQYCPKAFTRKDHLVNHV 84 (126)
Q Consensus 9 ~~C~~C~~~f~~~~~l~~h~~~h~----~~~~~~c~~C~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~~~~~~~l~~h~ 84 (126)
..|.+|...|........+-.-.. ....+.|..|.+.+.....+. ++. ....|.|..|...|.....+..|.
T Consensus 1229 l~~~~~e~~f~~~~~~~~~a~~~~~~~~~sGe~~c~~~~~~~~~~~~~~-~l~---~~~~~~~~~~~~~~~~~~~l~~~~ 1304 (1406)
T KOG1146|consen 1229 LLPNALEQPFPQEPEPTATAPPKPPELPASGEGECGAVDELLTPSFGIS-TLD---VTHRYLCRQCKMAFDGEAPLTAHQ 1304 (1406)
T ss_pred ccHHhhhcCccCcccccccCCCCCCcCcCCCcchhhhccccccCcccee-ecc---cchhHHHHHHHhhhcchhHHHHHH
Confidence 345556666665554433321110 011244555555555544433 221 223466777777777766666666
Q ss_pred Hhh-----------------cCCCCccCcccccccCCHHHHHHHHHHhh
Q psy10762 85 RRH-----------------TGESPHKCTYCMKSFTRKEHLTNHIRQHT 116 (126)
Q Consensus 85 ~~~-----------------~~~~~~~C~~C~~~f~~~~~l~~H~~~h~ 116 (126)
+.. ..-..| |..|...|+....|..|+++..
T Consensus 1305 ~k~~~~~~~~~~~~~~~l~~~d~~~~-c~~c~~~~~~~~alqihm~~~~ 1352 (1406)
T KOG1146|consen 1305 RKFCFAGRGSGGSMPPPLRVPDCTYH-CLACEVLLSGREALQIHMRSSA 1352 (1406)
T ss_pred HHHHhccCccccCCCCcccCcccccc-chHHHhhcchhHHHHHHHHHhh
Confidence 421 112345 9999999999999999999843
No 64
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=93.91 E-value=0.056 Score=25.78 Aligned_cols=11 Identities=27% Similarity=0.679 Sum_probs=6.0
Q ss_pred CCCccCccccc
Q psy10762 90 ESPHKCTYCMK 100 (126)
Q Consensus 90 ~~~~~C~~C~~ 100 (126)
..+|.|+.||.
T Consensus 48 g~~Y~Cp~CGF 58 (61)
T COG2888 48 GNPYRCPKCGF 58 (61)
T ss_pred CCceECCCcCc
Confidence 34566666653
No 65
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=93.73 E-value=0.05 Score=23.46 Aligned_cols=32 Identities=25% Similarity=0.624 Sum_probs=15.3
Q ss_pred ccCCCCCcCCChhhHHHHHHhhcCCCCccCccccccc
Q psy10762 66 PCQYCPKAFTRKDHLVNHVRRHTGESPHKCTYCMKSF 102 (126)
Q Consensus 66 ~C~~C~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~f 102 (126)
.||.|+..|.-... ++-.+....+|+.|+-.|
T Consensus 4 ~CP~C~~~f~v~~~-----~l~~~~~~vrC~~C~~~f 35 (37)
T PF13719_consen 4 TCPNCQTRFRVPDD-----KLPAGGRKVRCPKCGHVF 35 (37)
T ss_pred ECCCCCceEEcCHH-----HcccCCcEEECCCCCcEe
Confidence 46666655544322 111223445666666555
No 66
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=93.53 E-value=0.061 Score=23.04 Aligned_cols=32 Identities=19% Similarity=0.487 Sum_probs=16.6
Q ss_pred ccCCCCCcCCChhhHHHHHHhhcCCCCccCccccccc
Q psy10762 66 PCQYCPKAFTRKDHLVNHVRRHTGESPHKCTYCMKSF 102 (126)
Q Consensus 66 ~C~~C~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~f 102 (126)
.|+.|+..|.-.... +-......+|+.|+..|
T Consensus 4 ~Cp~C~~~y~i~d~~-----ip~~g~~v~C~~C~~~f 35 (36)
T PF13717_consen 4 TCPNCQAKYEIDDEK-----IPPKGRKVRCSKCGHVF 35 (36)
T ss_pred ECCCCCCEEeCCHHH-----CCCCCcEEECCCCCCEe
Confidence 566666665444331 22233445676676655
No 67
>KOG2186|consensus
Probab=93.50 E-value=0.052 Score=33.75 Aligned_cols=48 Identities=27% Similarity=0.509 Sum_probs=31.8
Q ss_pred CcccCCcccccCCchHHHHHHhhhcCCCCcccCCCCCcCCChhhHHHHHHh
Q psy10762 36 PHHCNYCAKSFTRKDHMVYHERQHTGETPFPCQYCPKAFTRKDHLVNHVRR 86 (126)
Q Consensus 36 ~~~c~~C~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~~~~~~~l~~h~~~ 86 (126)
.|.|..||.+..-. .+.+|+..-.+ .-|.|..|+..|-. .+...|..-
T Consensus 3 ~FtCnvCgEsvKKp-~vekH~srCrn-~~fSCIDC~k~F~~-~sYknH~kC 50 (276)
T KOG2186|consen 3 FFTCNVCGESVKKP-QVEKHMSRCRN-AYFSCIDCGKTFER-VSYKNHTKC 50 (276)
T ss_pred EEehhhhhhhcccc-chHHHHHhccC-CeeEEeeccccccc-chhhhhhhh
Confidence 36788888766543 35667766656 46788888888876 455566543
No 68
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=93.45 E-value=0.11 Score=33.98 Aligned_cols=74 Identities=23% Similarity=0.450 Sum_probs=43.8
Q ss_pred ccCCcccccCCchHHHHHHhhhcCCCCcccCCCC----CcCCChhhHHHHHHhhcCCCCccCcc--cc----cccCCHHH
Q psy10762 38 HCNYCAKSFTRKDHMVYHERQHTGETPFPCQYCP----KAFTRKDHLVNHVRRHTGESPHKCTY--CM----KSFTRKEH 107 (126)
Q Consensus 38 ~c~~C~~~~~~~~~l~~h~~~~~~~~~~~C~~C~----~~~~~~~~l~~h~~~~~~~~~~~C~~--C~----~~f~~~~~ 107 (126)
.|.+|...|.+...|..|++..+.. -|.|..-+ +-|.+-.+|..|.+ ...|.|.+ |. .+|.....
T Consensus 222 ~C~FC~~~FYdDDEL~~HcR~~HE~-ChICD~v~p~~~QYFK~Y~~Le~HF~----~~hy~ct~qtc~~~k~~vf~~~~e 296 (493)
T COG5236 222 LCIFCKIYFYDDDELRRHCRLRHEA-CHICDMVGPIRYQYFKSYEDLEAHFR----NAHYCCTFQTCRVGKCYVFPYHTE 296 (493)
T ss_pred hhhhccceecChHHHHHHHHhhhhh-hhhhhccCccchhhhhCHHHHHHHhh----cCceEEEEEEEecCcEEEeccHHH
Confidence 4777887788888888887765542 23443322 23444455555544 23466643 42 46888888
Q ss_pred HHHHHHHhh
Q psy10762 108 LTNHIRQHT 116 (126)
Q Consensus 108 l~~H~~~h~ 116 (126)
|..|+..-+
T Consensus 297 l~~h~~~~h 305 (493)
T COG5236 297 LLEHLTRFH 305 (493)
T ss_pred HHHHHHHHh
Confidence 888865533
No 69
>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=93.36 E-value=0.034 Score=34.70 Aligned_cols=42 Identities=17% Similarity=0.612 Sum_probs=22.7
Q ss_pred CCCCCcceeccccccccCChhHHHHHHHhh--cCCCCcccCCccc
Q psy10762 2 WHTGETPHRCDYCAKTFTRKEHLVNHVRQH--TGESPHHCNYCAK 44 (126)
Q Consensus 2 ~~~~~~~~~C~~C~~~f~~~~~l~~h~~~h--~~~~~~~c~~C~~ 44 (126)
|..|++.|.|..|...... ..--.|+..- .....|+|.-|+.
T Consensus 136 w~hGGrif~CsfC~~flCE-DDQFEHQAsCQvLe~E~~KC~SCNr 179 (314)
T PF06524_consen 136 WDHGGRIFKCSFCDNFLCE-DDQFEHQASCQVLESETFKCQSCNR 179 (314)
T ss_pred ccCCCeEEEeecCCCeeec-cchhhhhhhhhhhhccccccccccc
Confidence 5677888888888774433 2333344322 1223466666653
No 70
>PF09538 FYDLN_acid: Protein of unknown function (FYDLN_acid); InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=93.01 E-value=0.062 Score=29.21 Aligned_cols=12 Identities=25% Similarity=0.717 Sum_probs=6.1
Q ss_pred eeccccccccCC
Q psy10762 9 HRCDYCAKTFTR 20 (126)
Q Consensus 9 ~~C~~C~~~f~~ 20 (126)
..|+.||..|..
T Consensus 10 R~Cp~CG~kFYD 21 (108)
T PF09538_consen 10 RTCPSCGAKFYD 21 (108)
T ss_pred ccCCCCcchhcc
Confidence 445555555544
No 71
>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=92.67 E-value=0.073 Score=22.94 Aligned_cols=10 Identities=20% Similarity=0.673 Sum_probs=5.6
Q ss_pred ccCccccccc
Q psy10762 93 HKCTYCMKSF 102 (126)
Q Consensus 93 ~~C~~C~~~f 102 (126)
..|+.|+..|
T Consensus 26 v~C~~C~~~~ 35 (38)
T TIGR02098 26 VRCGKCGHVW 35 (38)
T ss_pred EECCCCCCEE
Confidence 4566665554
No 72
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=92.60 E-value=0.019 Score=35.17 Aligned_cols=44 Identities=20% Similarity=0.416 Sum_probs=26.6
Q ss_pred CcceeccccccccCChhHHHHHHHhh---c-------CCC-----CcccCCcccccCCc
Q psy10762 6 ETPHRCDYCAKTFTRKEHLVNHVRQH---T-------GES-----PHHCNYCAKSFTRK 49 (126)
Q Consensus 6 ~~~~~C~~C~~~f~~~~~l~~h~~~h---~-------~~~-----~~~c~~C~~~~~~~ 49 (126)
++...|+.|+..|..........+.- . +.. .+.|+.||.++...
T Consensus 3 ~k~~~CPvC~~~F~~~~vrs~~~r~~~~d~D~~~~Y~~vnP~~Y~V~vCP~CgyA~~~~ 61 (214)
T PF09986_consen 3 DKKITCPVCGKEFKTKKVRSGKIRVIRRDSDFCPRYKGVNPLFYEVWVCPHCGYAAFEE 61 (214)
T ss_pred CCceECCCCCCeeeeeEEEcCCceEeeecCCCccccCCCCCeeeeEEECCCCCCccccc
Confidence 46788999999998875544443221 1 111 24677787776544
No 73
>PF12013 DUF3505: Protein of unknown function (DUF3505); InterPro: IPR022698 This family of proteins is functionally uncharacterised. This protein is found in eukaryotes. Proteins in this family are typically between 247 to 1018 amino acids in length. This region contains two segments that are likely to be C2H2 zinc binding domains.
Probab=92.57 E-value=0.42 Score=25.94 Aligned_cols=26 Identities=19% Similarity=0.315 Sum_probs=22.6
Q ss_pred CccC----cccccccCCHHHHHHHHHHhhh
Q psy10762 92 PHKC----TYCMKSFTRKEHLTNHIRQHTV 117 (126)
Q Consensus 92 ~~~C----~~C~~~f~~~~~l~~H~~~h~~ 117 (126)
-|.| ..|+....+...|++|++.+++
T Consensus 80 G~~C~~~~~~C~y~~~~~~~m~~H~~~~Hg 109 (109)
T PF12013_consen 80 GYRCQCDPPHCGYITRSKKTMRKHWRKEHG 109 (109)
T ss_pred CeeeecCCCCCCcEeccHHHHHHHHHHhcC
Confidence 4789 8999999999999999988764
No 74
>cd00729 rubredoxin_SM Rubredoxin, Small Modular nonheme iron binding domain containing a [Fe(SCys)4] center, present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=92.38 E-value=0.091 Score=22.20 Aligned_cols=9 Identities=22% Similarity=0.704 Sum_probs=4.3
Q ss_pred cccCCCCCc
Q psy10762 65 FPCQYCPKA 73 (126)
Q Consensus 65 ~~C~~C~~~ 73 (126)
|.|..||..
T Consensus 3 ~~C~~CG~i 11 (34)
T cd00729 3 WVCPVCGYI 11 (34)
T ss_pred EECCCCCCE
Confidence 445555443
No 75
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=92.20 E-value=0.32 Score=26.59 Aligned_cols=86 Identities=20% Similarity=0.430 Sum_probs=52.3
Q ss_pred CcceeccccccccCChhHHHHHHHhhcCCCCc------------ccCCcccccCCchHHHHHHhhhcCCCCcccCCCCCc
Q psy10762 6 ETPHRCDYCAKTFTRKEHLVNHVRQHTGESPH------------HCNYCAKSFTRKDHMVYHERQHTGETPFPCQYCPKA 73 (126)
Q Consensus 6 ~~~~~C~~C~~~f~~~~~l~~h~~~h~~~~~~------------~c~~C~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~ 73 (126)
+.|..|+.|+.+.-+...|......-...++| .|--|...|........ ........|+|+.|...
T Consensus 13 ~LP~~CpiCgLtLVss~HLARSyHHLfPl~~f~ev~~~~~~~~~~C~~C~~~f~~~~~~~~--~~~~~~~~y~C~~C~~~ 90 (112)
T TIGR00622 13 ELPVECPICGLTLILSTHLARSYHHLFPLKAFQEIPLEEYNGSRFCFGCQGPFPKPPVSPF--DELKDSHRYVCAVCKNV 90 (112)
T ss_pred CCCCcCCcCCCEEeccchHHHhhhccCCCcccccccccccCCCCcccCcCCCCCCcccccc--cccccccceeCCCCCCc
Confidence 46788999999887777766553211111111 26667777765421100 00123346999999999
Q ss_pred CCChhhHHHHHHhhcCCCCccCcccc
Q psy10762 74 FTRKDHLVNHVRRHTGESPHKCTYCM 99 (126)
Q Consensus 74 ~~~~~~l~~h~~~~~~~~~~~C~~C~ 99 (126)
|-..-+...|...|. |+-|.
T Consensus 91 FC~dCD~fiHe~Lh~------CPGC~ 110 (112)
T TIGR00622 91 FCVDCDVFVHESLHC------CPGCI 110 (112)
T ss_pred cccccchhhhhhccC------CcCCC
Confidence 988877777766663 66554
No 76
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=92.15 E-value=0.043 Score=36.56 Aligned_cols=57 Identities=40% Similarity=0.746 Sum_probs=28.1
Q ss_pred cccCCcccccCCchHHHHHHh--hhcCC--CCcccC--CCCCcCCChhhHHHHHHhhcCCCCc
Q psy10762 37 HHCNYCAKSFTRKDHMVYHER--QHTGE--TPFPCQ--YCPKAFTRKDHLVNHVRRHTGESPH 93 (126)
Q Consensus 37 ~~c~~C~~~~~~~~~l~~h~~--~~~~~--~~~~C~--~C~~~~~~~~~l~~h~~~~~~~~~~ 93 (126)
+.|..|...+.....+..|.. .|.++ +++.|+ .|++.|.+...+..|...+.+..++
T Consensus 290 ~~~~~~~~~~s~~~~l~~~~~~~~h~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~ 352 (467)
T COG5048 290 IKSKQCNISFSRSSPLTRHLRSVNHSGESLKPFSCPYSLCGKLFSRNDALKRHILLHTSISPA 352 (467)
T ss_pred CCCccccCCccccccccccccccccccccCCceeeeccCCCccccccccccCCcccccCCCcc
Confidence 344445555555555555554 45555 455555 4555555555555555554444433
No 77
>KOG2231|consensus
Probab=92.14 E-value=0.22 Score=35.61 Aligned_cols=74 Identities=22% Similarity=0.495 Sum_probs=46.8
Q ss_pred cCCcccccCCchHHHHHHhhhcCCCCcccCCC----------CCcCCChhhHHHHHHhhcC-C---CC-ccCcccccccC
Q psy10762 39 CNYCAKSFTRKDHMVYHERQHTGETPFPCQYC----------PKAFTRKDHLVNHVRRHTG-E---SP-HKCTYCMKSFT 103 (126)
Q Consensus 39 c~~C~~~~~~~~~l~~h~~~~~~~~~~~C~~C----------~~~~~~~~~l~~h~~~~~~-~---~~-~~C~~C~~~f~ 103 (126)
|..| -.|.....|..|+...+.. +.|..| .+.| +...|+.|++..-- + +. -.|+.|...|-
T Consensus 118 ~~~c-~~~~s~~~Lk~H~~~~H~~--~~c~lC~~~~kif~~e~k~Y-t~~el~~h~~~gd~d~~s~rGhp~C~~C~~~fl 193 (669)
T KOG2231|consen 118 CLHC-TEFKSVENLKNHMRDQHKL--HLCSLCLQNLKIFINERKLY-TRAELNLHLMFGDPDDESCRGHPLCKFCHERFL 193 (669)
T ss_pred Cccc-cchhHHHHHHHHHHHhhhh--hccccccccceeeeeeeehe-hHHHHHHHHhcCCCccccccCCccchhhhhhhc
Confidence 3344 3444778899998655442 344443 2333 34567777765321 2 11 35889999999
Q ss_pred CHHHHHHHHHHhh
Q psy10762 104 RKEHLTNHIRQHT 116 (126)
Q Consensus 104 ~~~~l~~H~~~h~ 116 (126)
....|.+|++.++
T Consensus 194 d~~el~rH~~~~h 206 (669)
T KOG2231|consen 194 DDDELYRHLRFDH 206 (669)
T ss_pred cHHHHHHhhccce
Confidence 9999999998654
No 78
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=92.00 E-value=0.14 Score=23.00 Aligned_cols=29 Identities=17% Similarity=0.361 Sum_probs=17.5
Q ss_pred ceeccccccccCChhHHHHHHHhhcCCCCcccCCcccccC
Q psy10762 8 PHRCDYCAKTFTRKEHLVNHVRQHTGESPHHCNYCAKSFT 47 (126)
Q Consensus 8 ~~~C~~C~~~f~~~~~l~~h~~~h~~~~~~~c~~C~~~~~ 47 (126)
.|.|..||..|... ...+..|+.||....
T Consensus 2 ~Y~C~~Cg~~~~~~-----------~~~~irC~~CG~rIl 30 (44)
T smart00659 2 IYICGECGRENEIK-----------SKDVVRCRECGYRIL 30 (44)
T ss_pred EEECCCCCCEeecC-----------CCCceECCCCCceEE
Confidence 36777787766432 223467777776543
No 79
>TIGR00373 conserved hypothetical protein TIGR00373. This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.
Probab=91.97 E-value=0.17 Score=29.56 Aligned_cols=33 Identities=18% Similarity=0.302 Sum_probs=23.6
Q ss_pred CCCCcccCCCCCcCCChhhHHHHHHhhcCCCCccCccccccc
Q psy10762 61 GETPFPCQYCPKAFTRKDHLVNHVRRHTGESPHKCTYCMKSF 102 (126)
Q Consensus 61 ~~~~~~C~~C~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~f 102 (126)
...-|.||.|+..|+...++. ..|.|+.||...
T Consensus 106 ~~~~Y~Cp~c~~r~tf~eA~~---------~~F~Cp~Cg~~L 138 (158)
T TIGR00373 106 NNMFFICPNMCVRFTFNEAME---------LNFTCPRCGAML 138 (158)
T ss_pred CCCeEECCCCCcEeeHHHHHH---------cCCcCCCCCCEe
Confidence 344588888888887776653 368888888754
No 80
>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=91.80 E-value=0.05 Score=25.26 Aligned_cols=12 Identities=33% Similarity=0.808 Sum_probs=7.6
Q ss_pred eeccccccccCC
Q psy10762 9 HRCDYCAKTFTR 20 (126)
Q Consensus 9 ~~C~~C~~~f~~ 20 (126)
|.|..|+..|..
T Consensus 6 y~C~~Cg~~fe~ 17 (52)
T TIGR02605 6 YRCTACGHRFEV 17 (52)
T ss_pred EEeCCCCCEeEE
Confidence 667777766643
No 81
>TIGR00373 conserved hypothetical protein TIGR00373. This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.
Probab=91.76 E-value=0.21 Score=29.15 Aligned_cols=37 Identities=22% Similarity=0.340 Sum_probs=25.0
Q ss_pred hhcCCCCcccCCcccccCCchHHHHHHhhhcCCCCcccCCCCCcCC
Q psy10762 30 QHTGESPHHCNYCAKSFTRKDHMVYHERQHTGETPFPCQYCPKAFT 75 (126)
Q Consensus 30 ~h~~~~~~~c~~C~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~~~ 75 (126)
...+..-|.|+.|+..|.....+. ..|.||.||..+.
T Consensus 103 ~e~~~~~Y~Cp~c~~r~tf~eA~~---------~~F~Cp~Cg~~L~ 139 (158)
T TIGR00373 103 FETNNMFFICPNMCVRFTFNEAME---------LNFTCPRCGAMLD 139 (158)
T ss_pred hccCCCeEECCCCCcEeeHHHHHH---------cCCcCCCCCCEee
Confidence 334455688988887777665553 2589999987543
No 82
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=91.63 E-value=0.18 Score=24.11 Aligned_cols=10 Identities=30% Similarity=0.687 Sum_probs=5.1
Q ss_pred CCccCccccc
Q psy10762 91 SPHKCTYCMK 100 (126)
Q Consensus 91 ~~~~C~~C~~ 100 (126)
.+|.|+.||.
T Consensus 47 ~~Y~CP~CGF 56 (59)
T PRK14890 47 NPYTCPKCGF 56 (59)
T ss_pred CceECCCCCC
Confidence 4455555543
No 83
>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=91.48 E-value=0.18 Score=27.39 Aligned_cols=26 Identities=23% Similarity=0.496 Sum_probs=22.4
Q ss_pred Cccc----CCCCCcCCChhhHHHHHHhhcC
Q psy10762 64 PFPC----QYCPKAFTRKDHLVNHVRRHTG 89 (126)
Q Consensus 64 ~~~C----~~C~~~~~~~~~l~~h~~~~~~ 89 (126)
.|.| ..|+....+...+.+|++.++|
T Consensus 80 G~~C~~~~~~C~y~~~~~~~m~~H~~~~Hg 109 (109)
T PF12013_consen 80 GYRCQCDPPHCGYITRSKKTMRKHWRKEHG 109 (109)
T ss_pred CeeeecCCCCCCcEeccHHHHHHHHHHhcC
Confidence 3789 8999999999999999987653
No 84
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=90.75 E-value=0.61 Score=30.72 Aligned_cols=48 Identities=31% Similarity=0.566 Sum_probs=25.9
Q ss_pred ccCCCCCcCCChhhHHHHHHhhcCCCCccCccc----ccccCCHHHHHHHHHH
Q psy10762 66 PCQYCPKAFTRKDHLVNHVRRHTGESPHKCTYC----MKSFTRKEHLTNHIRQ 114 (126)
Q Consensus 66 ~C~~C~~~~~~~~~l~~h~~~~~~~~~~~C~~C----~~~f~~~~~l~~H~~~ 114 (126)
.|-.|..-|-....|..|.+.-+ ++=|.|..- ..-|.+..+|.+|.+.
T Consensus 222 ~C~FC~~~FYdDDEL~~HcR~~H-E~ChICD~v~p~~~QYFK~Y~~Le~HF~~ 273 (493)
T COG5236 222 LCIFCKIYFYDDDELRRHCRLRH-EACHICDMVGPIRYQYFKSYEDLEAHFRN 273 (493)
T ss_pred hhhhccceecChHHHHHHHHhhh-hhhhhhhccCccchhhhhCHHHHHHHhhc
Confidence 46666666666667767666432 222333221 1336666666666554
No 85
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=90.64 E-value=0.21 Score=29.74 Aligned_cols=33 Identities=21% Similarity=0.461 Sum_probs=23.2
Q ss_pred CCCcccCCCCCcCCChhhHHHHHHhhcCCCCccCcccccccC
Q psy10762 62 ETPFPCQYCPKAFTRKDHLVNHVRRHTGESPHKCTYCMKSFT 103 (126)
Q Consensus 62 ~~~~~C~~C~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~f~ 103 (126)
..-|.|+.|+..|+...++. ..|.|+.||....
T Consensus 115 ~~~Y~Cp~C~~rytf~eA~~---------~~F~Cp~Cg~~L~ 147 (178)
T PRK06266 115 NMFFFCPNCHIRFTFDEAME---------YGFRCPQCGEMLE 147 (178)
T ss_pred CCEEECCCCCcEEeHHHHhh---------cCCcCCCCCCCCe
Confidence 34588888888887766542 3688988887643
No 86
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=90.42 E-value=0.059 Score=31.24 Aligned_cols=13 Identities=38% Similarity=0.577 Sum_probs=8.7
Q ss_pred cccCCCCCcCCCh
Q psy10762 65 FPCQYCPKAFTRK 77 (126)
Q Consensus 65 ~~C~~C~~~~~~~ 77 (126)
++|+.||..|...
T Consensus 29 ~~c~~c~~~f~~~ 41 (154)
T PRK00464 29 RECLACGKRFTTF 41 (154)
T ss_pred eeccccCCcceEe
Confidence 6677777766554
No 87
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=90.17 E-value=0.55 Score=27.05 Aligned_cols=38 Identities=13% Similarity=0.387 Sum_probs=23.5
Q ss_pred CCCCcccCCCCCcCCChhhHHHHHHhhcCCCCccCccccccc
Q psy10762 61 GETPFPCQYCPKAFTRKDHLVNHVRRHTGESPHKCTYCMKSF 102 (126)
Q Consensus 61 ~~~~~~C~~C~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~f 102 (126)
...-|.||.|+..|.....+.. . . ....|.|+.||...
T Consensus 96 ~~~~Y~Cp~C~~~y~~~ea~~~-~--d-~~~~f~Cp~Cg~~l 133 (147)
T smart00531 96 NNAYYKCPNCQSKYTFLEANQL-L--D-MDGTFTCPRCGEEL 133 (147)
T ss_pred CCcEEECcCCCCEeeHHHHHHh-c--C-CCCcEECCCCCCEE
Confidence 3346889999888875443321 0 1 13348899998765
No 88
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=90.14 E-value=0.23 Score=29.18 Aligned_cols=23 Identities=30% Similarity=0.795 Sum_probs=17.2
Q ss_pred CcccCCCCCcCCChhhHHHHHHhhcCCCCccCcccc
Q psy10762 64 PFPCQYCPKAFTRKDHLVNHVRRHTGESPHKCTYCM 99 (126)
Q Consensus 64 ~~~C~~C~~~~~~~~~l~~h~~~~~~~~~~~C~~C~ 99 (126)
.|.|++||..+ .++-|-+||+||
T Consensus 134 ~~vC~vCGy~~-------------~ge~P~~CPiCg 156 (166)
T COG1592 134 VWVCPVCGYTH-------------EGEAPEVCPICG 156 (166)
T ss_pred EEEcCCCCCcc-------------cCCCCCcCCCCC
Confidence 68999997543 346678899997
No 89
>KOG4173|consensus
Probab=90.13 E-value=0.14 Score=30.95 Aligned_cols=75 Identities=19% Similarity=0.538 Sum_probs=53.3
Q ss_pred ceeccc--cccccCChhHHHHHHHhhcCCCCcccCCcccccCCchHHHHHHhhh----------cCCCCcccCC--CCCc
Q psy10762 8 PHRCDY--CAKTFTRKEHLVNHVRQHTGESPHHCNYCAKSFTRKDHMVYHERQH----------TGETPFPCQY--CPKA 73 (126)
Q Consensus 8 ~~~C~~--C~~~f~~~~~l~~h~~~h~~~~~~~c~~C~~~~~~~~~l~~h~~~~----------~~~~~~~C~~--C~~~ 73 (126)
.|.|++ |-..|.....+..|..+-++ -.|.+|...|+....|..|+... .|..-|+|-+ |+.-
T Consensus 79 ~~~cqvagc~~~~d~lD~~E~hY~~~h~---~sCs~C~r~~Pt~hLLd~HI~E~HDs~Fqa~veRG~dMy~ClvEgCt~K 155 (253)
T KOG4173|consen 79 AFACQVAGCCQVFDALDDYEHHYHTLHG---NSCSFCKRAFPTGHLLDAHILEWHDSLFQALVERGQDMYQCLVEGCTEK 155 (253)
T ss_pred cccccccchHHHHhhhhhHHHhhhhccc---chhHHHHHhCCchhhhhHHHHHHHHHHHHHHHHcCccHHHHHHHhhhhh
Confidence 366765 66777777777777655443 36899999999988888886532 3445588864 8888
Q ss_pred CCChhhHHHHHH
Q psy10762 74 FTRKDHLVNHVR 85 (126)
Q Consensus 74 ~~~~~~l~~h~~ 85 (126)
|.+......|+-
T Consensus 156 FkT~r~RkdH~I 167 (253)
T KOG4173|consen 156 FKTSRDRKDHMI 167 (253)
T ss_pred hhhhhhhhhHHH
Confidence 888777777764
No 90
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=90.05 E-value=0.14 Score=23.20 Aligned_cols=11 Identities=18% Similarity=0.794 Sum_probs=5.9
Q ss_pred CcccCCCCCcC
Q psy10762 64 PFPCQYCPKAF 74 (126)
Q Consensus 64 ~~~C~~C~~~~ 74 (126)
.|.|+.||..+
T Consensus 3 ~y~C~~CG~~~ 13 (46)
T PRK00398 3 EYKCARCGREV 13 (46)
T ss_pred EEECCCCCCEE
Confidence 35566665544
No 91
>KOG2186|consensus
Probab=90.04 E-value=0.29 Score=30.64 Aligned_cols=48 Identities=19% Similarity=0.465 Sum_probs=36.4
Q ss_pred ceeccccccccCChhHHHHHHHhhcCCCCcccCCcccccCCchHHHHHHhh
Q psy10762 8 PHRCDYCAKTFTRKEHLVNHVRQHTGESPHHCNYCAKSFTRKDHMVYHERQ 58 (126)
Q Consensus 8 ~~~C~~C~~~f~~~~~l~~h~~~h~~~~~~~c~~C~~~~~~~~~l~~h~~~ 58 (126)
-|.|..||....-. .+..|+....+ .-|.|-.|+..|.. .++..|...
T Consensus 3 ~FtCnvCgEsvKKp-~vekH~srCrn-~~fSCIDC~k~F~~-~sYknH~kC 50 (276)
T KOG2186|consen 3 FFTCNVCGESVKKP-QVEKHMSRCRN-AYFSCIDCGKTFER-VSYKNHTKC 50 (276)
T ss_pred EEehhhhhhhcccc-chHHHHHhccC-CeeEEeeccccccc-chhhhhhhh
Confidence 37899999887664 56678877766 56889999999887 667777653
No 92
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=89.84 E-value=0.37 Score=28.72 Aligned_cols=35 Identities=23% Similarity=0.472 Sum_probs=23.5
Q ss_pred CCCCcccCCcccccCCchHHHHHHhhhcCCCCcccCCCCCcCCC
Q psy10762 33 GESPHHCNYCAKSFTRKDHMVYHERQHTGETPFPCQYCPKAFTR 76 (126)
Q Consensus 33 ~~~~~~c~~C~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~~~~ 76 (126)
+..-|.|+.|+..|.....+. ..|.||.||..+..
T Consensus 114 ~~~~Y~Cp~C~~rytf~eA~~---------~~F~Cp~Cg~~L~~ 148 (178)
T PRK06266 114 NNMFFFCPNCHIRFTFDEAME---------YGFRCPQCGEMLEE 148 (178)
T ss_pred CCCEEECCCCCcEEeHHHHhh---------cCCcCCCCCCCCee
Confidence 345688888887776655432 25889999876543
No 93
>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=89.75 E-value=0.097 Score=22.83 Aligned_cols=11 Identities=45% Similarity=1.087 Sum_probs=6.7
Q ss_pred eeccccccccC
Q psy10762 9 HRCDYCAKTFT 19 (126)
Q Consensus 9 ~~C~~C~~~f~ 19 (126)
|.|..||..|.
T Consensus 6 y~C~~Cg~~fe 16 (41)
T smart00834 6 YRCEDCGHTFE 16 (41)
T ss_pred EEcCCCCCEEE
Confidence 56666666554
No 94
>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=89.50 E-value=0.27 Score=27.77 Aligned_cols=26 Identities=27% Similarity=0.390 Sum_probs=16.6
Q ss_pred CCCccCcccccccCCHHHHHHHHHHhhhc
Q psy10762 90 ESPHKCTYCMKSFTRKEHLTNHIRQHTVR 118 (126)
Q Consensus 90 ~~~~~C~~C~~~f~~~~~l~~H~~~h~~~ 118 (126)
.....|.+||+.|... .+|++.|++-
T Consensus 70 ~d~i~clecGk~~k~L---krHL~~~~gl 95 (132)
T PF05443_consen 70 PDYIICLECGKKFKTL---KRHLRTHHGL 95 (132)
T ss_dssp SS-EE-TBT--EESBH---HHHHHHTT-S
T ss_pred cCeeEEccCCcccchH---HHHHHHccCC
Confidence 3456899999999965 8999998643
No 95
>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=89.47 E-value=0.43 Score=21.23 Aligned_cols=24 Identities=29% Similarity=0.686 Sum_probs=13.3
Q ss_pred CCCccCcccccccCCH----HHHHHHHH
Q psy10762 90 ESPHKCTYCMKSFTRK----EHLTNHIR 113 (126)
Q Consensus 90 ~~~~~C~~C~~~f~~~----~~l~~H~~ 113 (126)
.....|..|++.+... +.|.+|++
T Consensus 14 ~~~a~C~~C~~~~~~~~~~ts~l~~HL~ 41 (45)
T PF02892_consen 14 KKKAKCKYCGKVIKYSSGGTSNLKRHLK 41 (45)
T ss_dssp SS-EEETTTTEE-----SSTHHHHHHHH
T ss_pred cCeEEeCCCCeEEeeCCCcHHHHHHhhh
Confidence 3445677787777654 67777773
No 96
>PF02176 zf-TRAF: TRAF-type zinc finger; PDB: 2EOD_A 2YUC_A 3HCU_A 3HCS_B 3HCT_A.
Probab=88.86 E-value=0.26 Score=23.46 Aligned_cols=26 Identities=27% Similarity=0.666 Sum_probs=12.0
Q ss_pred hHHHHHHhhcCCCCccCcc----cccccCC
Q psy10762 79 HLVNHVRRHTGESPHKCTY----CMKSFTR 104 (126)
Q Consensus 79 ~l~~h~~~~~~~~~~~C~~----C~~~f~~ 104 (126)
.|..|+...-..++..|+. |+..+..
T Consensus 25 ~l~~H~~~~C~~~~v~C~~~~~GC~~~~~~ 54 (60)
T PF02176_consen 25 ELDDHLENECPKRPVPCPYSPYGCKERVPR 54 (60)
T ss_dssp CHHHHHHTTSTTSEEE-SS----S--EEEH
T ss_pred HHHHHHHccCCCCcEECCCCCCCCCCccch
Confidence 5556666443444555655 6555543
No 97
>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=88.45 E-value=0.31 Score=27.17 Aligned_cols=31 Identities=16% Similarity=0.341 Sum_probs=16.0
Q ss_pred ceeccccccccCChhHHHHHHHhhcCCCCcccCCcccccCCc
Q psy10762 8 PHRCDYCAKTFTRKEHLVNHVRQHTGESPHHCNYCAKSFTRK 49 (126)
Q Consensus 8 ~~~C~~C~~~f~~~~~l~~h~~~h~~~~~~~c~~C~~~~~~~ 49 (126)
...|+.||..|.... ..|..|+.||..|...
T Consensus 9 Kr~Cp~cg~kFYDLn-----------k~p~vcP~cg~~~~~~ 39 (129)
T TIGR02300 9 KRICPNTGSKFYDLN-----------RRPAVSPYTGEQFPPE 39 (129)
T ss_pred cccCCCcCccccccC-----------CCCccCCCcCCccCcc
Confidence 345666666664432 2345566666555443
No 98
>smart00614 ZnF_BED BED zinc finger. DNA-binding domain in chromatin-boundary-element-binding proteins and transposases
Probab=87.80 E-value=0.41 Score=22.03 Aligned_cols=20 Identities=45% Similarity=1.019 Sum_probs=12.1
Q ss_pred cCcccccccCCH-----HHHHHHHH
Q psy10762 94 KCTYCMKSFTRK-----EHLTNHIR 113 (126)
Q Consensus 94 ~C~~C~~~f~~~-----~~l~~H~~ 113 (126)
.|..|++.++.. +.|.+|+.
T Consensus 20 ~C~~C~~~l~~~~~~gTs~L~rHl~ 44 (50)
T smart00614 20 KCKYCGKKLSRSSKGGTSNLRRHLR 44 (50)
T ss_pred EecCCCCEeeeCCCCCcHHHHHHHH
Confidence 466666665443 46777765
No 99
>smart00734 ZnF_Rad18 Rad18-like CCHC zinc finger. Yeast Rad18p functions with Rad5p in error-free post-replicative DNA repair. This zinc finger is likely to bind nucleic-acids.
Probab=87.23 E-value=0.73 Score=18.11 Aligned_cols=19 Identities=16% Similarity=0.704 Sum_probs=11.6
Q ss_pred cCcccccccCCHHHHHHHHH
Q psy10762 94 KCTYCMKSFTRKEHLTNHIR 113 (126)
Q Consensus 94 ~C~~C~~~f~~~~~l~~H~~ 113 (126)
.|++|++.+ ....+..|+.
T Consensus 3 ~CPiC~~~v-~~~~in~HLD 21 (26)
T smart00734 3 QCPVCFREV-PENLINSHLD 21 (26)
T ss_pred cCCCCcCcc-cHHHHHHHHH
Confidence 577777776 3345556653
No 100
>PRK04023 DNA polymerase II large subunit; Validated
Probab=87.03 E-value=0.83 Score=34.42 Aligned_cols=10 Identities=20% Similarity=0.710 Sum_probs=6.0
Q ss_pred CccCcccccc
Q psy10762 92 PHKCTYCMKS 101 (126)
Q Consensus 92 ~~~C~~C~~~ 101 (126)
++.|+.|+..
T Consensus 663 ~y~CPKCG~E 672 (1121)
T PRK04023 663 EDECEKCGRE 672 (1121)
T ss_pred CCcCCCCCCC
Confidence 3557777654
No 101
>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=86.37 E-value=4.8 Score=23.58 Aligned_cols=104 Identities=14% Similarity=0.244 Sum_probs=50.5
Q ss_pred cccccCChhHHHHHHHhhcCCCCcccCCcccccCCchHHHHHHhhhcCCCCcccCCCCC-cCCChhhHHHHHHhhcCCCC
Q psy10762 14 CAKTFTRKEHLVNHVRQHTGESPHHCNYCAKSFTRKDHMVYHERQHTGETPFPCQYCPK-AFTRKDHLVNHVRRHTGESP 92 (126)
Q Consensus 14 C~~~f~~~~~l~~h~~~h~~~~~~~c~~C~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~-~~~~~~~l~~h~~~~~~~~~ 92 (126)
|+..+....-|.+-...+.......-..-.......... . ...........||.|.. ++.+... ...+.+...|+
T Consensus 32 c~Ts~rhSNCLdqfkka~~~~~~~~~~~~~~~~~~~~~~-~-~~~~~~~~~L~CPLCRG~V~GWtvv--e~AR~~LN~K~ 107 (162)
T PF07800_consen 32 CDTSYRHSNCLDQFKKAYGKSSSSSSQSSSSAPSDSSSS-E-SSESQEQPELACPLCRGEVKGWTVV--EPARRFLNAKK 107 (162)
T ss_pred cCCccchhHHHHHHHHHhcCCCCccccccccCcCCCccc-c-cccccccccccCccccCceeceEEc--hHHHHHhccCC
Confidence 666777777777777666543321111000000000000 0 01111222457898853 3333211 23455666777
Q ss_pred ccCcc--cccccCCHHHHHHHHHH-hhhccccC
Q psy10762 93 HKCTY--CMKSFTRKEHLTNHIRQ-HTVRRVND 122 (126)
Q Consensus 93 ~~C~~--C~~~f~~~~~l~~H~~~-h~~~~~~~ 122 (126)
-.|.. |..+- +...|++|.+. |-..++.+
T Consensus 108 RsC~~e~C~F~G-tY~eLrKHar~~HP~~rP~~ 139 (162)
T PF07800_consen 108 RSCSQESCSFSG-TYSELRKHARSEHPSARPSE 139 (162)
T ss_pred ccCccccccccc-CHHHHHHHHHhhCCCCCCcc
Confidence 77865 55443 35589999777 44444443
No 102
>KOG3408|consensus
Probab=85.97 E-value=0.5 Score=26.13 Aligned_cols=26 Identities=23% Similarity=0.565 Sum_probs=18.3
Q ss_pred CCCCccCcccccccCCHHHHHHHHHH
Q psy10762 89 GESPHKCTYCMKSFTRKEHLTNHIRQ 114 (126)
Q Consensus 89 ~~~~~~C~~C~~~f~~~~~l~~H~~~ 114 (126)
|...|.|-.|.+-|.....|..|.+.
T Consensus 54 G~GqfyCi~CaRyFi~~~~l~~H~kt 79 (129)
T KOG3408|consen 54 GGGQFYCIECARYFIDAKALKTHFKT 79 (129)
T ss_pred CCceeehhhhhhhhcchHHHHHHHhc
Confidence 33446677788888877777777665
No 103
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=85.65 E-value=0.077 Score=23.32 Aligned_cols=12 Identities=25% Similarity=0.445 Sum_probs=8.4
Q ss_pred CccCcccccccC
Q psy10762 92 PHKCTYCMKSFT 103 (126)
Q Consensus 92 ~~~C~~C~~~f~ 103 (126)
.|.|..|+..|.
T Consensus 28 fy~C~~C~~~w~ 39 (40)
T smart00440 28 FYVCTKCGHRWR 39 (40)
T ss_pred EEEeCCCCCEeC
Confidence 377877877664
No 104
>PF14353 CpXC: CpXC protein
Probab=85.56 E-value=0.73 Score=25.76 Aligned_cols=16 Identities=31% Similarity=0.677 Sum_probs=9.4
Q ss_pred cccCCCCCcCCChhhH
Q psy10762 65 FPCQYCPKAFTRKDHL 80 (126)
Q Consensus 65 ~~C~~C~~~~~~~~~l 80 (126)
+.||.||..+.-...+
T Consensus 39 ~~CP~Cg~~~~~~~p~ 54 (128)
T PF14353_consen 39 FTCPSCGHKFRLEYPL 54 (128)
T ss_pred EECCCCCCceecCCCE
Confidence 5677777666544443
No 105
>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=84.84 E-value=0.41 Score=19.93 Aligned_cols=27 Identities=22% Similarity=0.522 Sum_probs=13.5
Q ss_pred eeccccccccCChhHHHHHHHhhcCCCCcccCCccccc
Q psy10762 9 HRCDYCAKTFTRKEHLVNHVRQHTGESPHHCNYCAKSF 46 (126)
Q Consensus 9 ~~C~~C~~~f~~~~~l~~h~~~h~~~~~~~c~~C~~~~ 46 (126)
|.|..|+..+... ...+..|+.||...
T Consensus 1 Y~C~~Cg~~~~~~-----------~~~~irC~~CG~RI 27 (32)
T PF03604_consen 1 YICGECGAEVELK-----------PGDPIRCPECGHRI 27 (32)
T ss_dssp EBESSSSSSE-BS-----------TSSTSSBSSSS-SE
T ss_pred CCCCcCCCeeEcC-----------CCCcEECCcCCCeE
Confidence 5566777665421 12245677776543
No 106
>COG4957 Predicted transcriptional regulator [Transcription]
Probab=84.16 E-value=0.52 Score=26.59 Aligned_cols=23 Identities=26% Similarity=0.267 Sum_probs=18.7
Q ss_pred ccCcccccccCCHHHHHHHHHHhhhc
Q psy10762 93 HKCTYCMKSFTRKEHLTNHIRQHTVR 118 (126)
Q Consensus 93 ~~C~~C~~~f~~~~~l~~H~~~h~~~ 118 (126)
..|.++|+.|. .|.+|+.+|.+-
T Consensus 77 IicLEDGkkfK---SLKRHL~t~~gm 99 (148)
T COG4957 77 IICLEDGKKFK---SLKRHLTTHYGL 99 (148)
T ss_pred EEEeccCcchH---HHHHHHhcccCC
Confidence 57999999998 578999987753
No 107
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=83.53 E-value=0.81 Score=23.79 Aligned_cols=12 Identities=33% Similarity=0.675 Sum_probs=6.6
Q ss_pred CccCcccccccC
Q psy10762 92 PHKCTYCMKSFT 103 (126)
Q Consensus 92 ~~~C~~C~~~f~ 103 (126)
-|.|..|+..|.
T Consensus 53 IW~C~kCg~~fA 64 (89)
T COG1997 53 IWKCRKCGAKFA 64 (89)
T ss_pred eEEcCCCCCeec
Confidence 455655655553
No 108
>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=83.31 E-value=0.82 Score=28.15 Aligned_cols=29 Identities=28% Similarity=0.505 Sum_probs=19.3
Q ss_pred CCCccCcccccccCCHHHHHHHHHHhhhc
Q psy10762 90 ESPHKCTYCMKSFTRKEHLTNHIRQHTVR 118 (126)
Q Consensus 90 ~~~~~C~~C~~~f~~~~~l~~H~~~h~~~ 118 (126)
+..|.|+.|+|.|.-..=.++|+..-|.+
T Consensus 75 ~~K~~C~lc~KlFkg~eFV~KHI~nKH~e 103 (214)
T PF04959_consen 75 EDKWRCPLCGKLFKGPEFVRKHIFNKHPE 103 (214)
T ss_dssp SEEEEE-SSS-EESSHHHHHHHHHHH-HH
T ss_pred CCEECCCCCCcccCChHHHHHHHhhcCHH
Confidence 44588888888888887788887764443
No 109
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=83.17 E-value=0.5 Score=34.41 Aligned_cols=12 Identities=25% Similarity=0.637 Sum_probs=7.2
Q ss_pred CCCcccCCCCCc
Q psy10762 62 ETPFPCQYCPKA 73 (126)
Q Consensus 62 ~~~~~C~~C~~~ 73 (126)
..|..||.||..
T Consensus 473 ~~p~~Cp~Cgs~ 484 (730)
T COG1198 473 PIPQSCPECGSE 484 (730)
T ss_pred CCCCCCCCCCCC
Confidence 345677777643
No 110
>PHA00626 hypothetical protein
Probab=82.10 E-value=0.71 Score=21.83 Aligned_cols=16 Identities=13% Similarity=0.237 Sum_probs=13.0
Q ss_pred CCCccCcccccccCCH
Q psy10762 90 ESPHKCTYCMKSFTRK 105 (126)
Q Consensus 90 ~~~~~C~~C~~~f~~~ 105 (126)
...|.|+.||..|+..
T Consensus 21 snrYkCkdCGY~ft~~ 36 (59)
T PHA00626 21 SDDYVCCDCGYNDSKD 36 (59)
T ss_pred CcceEcCCCCCeechh
Confidence 4679999999998754
No 111
>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=81.57 E-value=0.41 Score=19.27 Aligned_cols=19 Identities=26% Similarity=0.592 Sum_probs=11.6
Q ss_pred eeccccccccCChhHHHHHH
Q psy10762 9 HRCDYCAKTFTRKEHLVNHV 28 (126)
Q Consensus 9 ~~C~~C~~~f~~~~~l~~h~ 28 (126)
|.|-+|++.| ....++.|.
T Consensus 1 ~sCiDC~~~F-~~~~y~~Ht 19 (28)
T PF08790_consen 1 FSCIDCSKDF-DGDSYKSHT 19 (28)
T ss_dssp EEETTTTEEE-EGGGTTT--
T ss_pred CeeecCCCCc-CcCCcCCCC
Confidence 5688888888 334555554
No 112
>PTZ00448 hypothetical protein; Provisional
Probab=81.44 E-value=1.6 Score=29.06 Aligned_cols=34 Identities=21% Similarity=0.437 Sum_probs=27.1
Q ss_pred CccCcccccccCCHHHHHHHHHH--hh---hccccCCCC
Q psy10762 92 PHKCTYCMKSFTRKEHLTNHIRQ--HT---VRRVNDLPP 125 (126)
Q Consensus 92 ~~~C~~C~~~f~~~~~l~~H~~~--h~---~~~~~~~~p 125 (126)
.|.|..|+-.|......+.|++. |. .++...+||
T Consensus 314 ~~tC~~C~v~F~~~~~qR~H~KSDwHrYNLKRkl~gLpp 352 (373)
T PTZ00448 314 MLLCRKCNIQLMDHNAFKQHYRSEWHIFNTKRNARKMEP 352 (373)
T ss_pred CccccccccccCCHHHHHHHhhhhHHHHHHHHHhcCCCC
Confidence 58899999999988888999876 33 566667776
No 113
>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=81.08 E-value=0.55 Score=19.24 Aligned_cols=8 Identities=25% Similarity=0.571 Sum_probs=3.9
Q ss_pred CcccCCcc
Q psy10762 36 PHHCNYCA 43 (126)
Q Consensus 36 ~~~c~~C~ 43 (126)
.+.|+.|+
T Consensus 19 ~~vCp~C~ 26 (30)
T PF08274_consen 19 LLVCPECG 26 (30)
T ss_dssp SEEETTTT
T ss_pred EEeCCccc
Confidence 34555554
No 114
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=80.87 E-value=0.71 Score=26.23 Aligned_cols=13 Identities=15% Similarity=0.626 Sum_probs=7.5
Q ss_pred ceeccccccccCC
Q psy10762 8 PHRCDYCAKTFTR 20 (126)
Q Consensus 8 ~~~C~~C~~~f~~ 20 (126)
.+.|..||..|..
T Consensus 70 ~~~C~~CG~~~~~ 82 (135)
T PRK03824 70 VLKCRNCGNEWSL 82 (135)
T ss_pred EEECCCCCCEEec
Confidence 4566666655544
No 115
>KOG2482|consensus
Probab=80.86 E-value=2.4 Score=28.06 Aligned_cols=50 Identities=20% Similarity=0.464 Sum_probs=36.7
Q ss_pred cccCCCCCcCCChhhHHHHHHhhc---------------------------CCCCccCcccccccCCHHHHHHHHHH
Q psy10762 65 FPCQYCPKAFTRKDHLVNHVRRHT---------------------------GESPHKCTYCMKSFTRKEHLTNHIRQ 114 (126)
Q Consensus 65 ~~C~~C~~~~~~~~~l~~h~~~~~---------------------------~~~~~~C~~C~~~f~~~~~l~~H~~~ 114 (126)
..|-.|...+.+...+..|+++-+ +.+.-.|-.|.-.|-....|..|+.-
T Consensus 280 v~CLfC~~~~en~~~l~eHmk~vHe~Dl~Ki~sd~~Ln~YqrvrviNyiRkq~~~~~c~~cd~~F~~e~~l~~hm~e 356 (423)
T KOG2482|consen 280 VVCLFCTNFYENPVFLFEHMKIVHEFDLLKIQSDYSLNFYQRVRVINYIRKQKKKSRCAECDLSFWKEPGLLIHMVE 356 (423)
T ss_pred eEEEeeccchhhHHHHHHHHHHHHHhhHHhhccccccchhhhhhHHHHHHHHhhccccccccccccCcchhhhhccc
Confidence 367888888888888888886532 01223577788889999999999755
No 116
>PF15135 UPF0515: Uncharacterised protein UPF0515
Probab=80.29 E-value=1.8 Score=27.22 Aligned_cols=13 Identities=15% Similarity=0.680 Sum_probs=7.8
Q ss_pred Ccceecccccccc
Q psy10762 6 ETPHRCDYCAKTF 18 (126)
Q Consensus 6 ~~~~~C~~C~~~f 18 (126)
.+.|.|..|....
T Consensus 110 drqFaC~~Cd~~W 122 (278)
T PF15135_consen 110 DRQFACSSCDHMW 122 (278)
T ss_pred ceeeeccccchHH
Confidence 3567777776543
No 117
>PF12907 zf-met2: Zinc-binding
Probab=80.27 E-value=1.5 Score=19.26 Aligned_cols=33 Identities=21% Similarity=0.504 Sum_probs=20.0
Q ss_pred ccCcccccccC---CHHHHHHHHHH-hhhccccCCCC
Q psy10762 93 HKCTYCMKSFT---RKEHLTNHIRQ-HTVRRVNDLPP 125 (126)
Q Consensus 93 ~~C~~C~~~f~---~~~~l~~H~~~-h~~~~~~~~~p 125 (126)
+.|.+|...|. +...|..|... |......++.|
T Consensus 2 i~C~iC~qtF~~t~~~~~L~eH~enKHpK~~~~~CFP 38 (40)
T PF12907_consen 2 IICKICRQTFMQTTNEPQLKEHAENKHPKNTFEECFP 38 (40)
T ss_pred cCcHHhhHHHHhcCCHHHHHHHHHccCCCCCHHHcCC
Confidence 56888886664 45667777654 44433555554
No 118
>PF15269 zf-C2H2_7: Zinc-finger
Probab=79.52 E-value=1.7 Score=19.54 Aligned_cols=22 Identities=36% Similarity=0.614 Sum_probs=16.4
Q ss_pred ccCcccccccCCHHHHHHHHHH
Q psy10762 93 HKCTYCMKSFTRKEHLTNHIRQ 114 (126)
Q Consensus 93 ~~C~~C~~~f~~~~~l~~H~~~ 114 (126)
|.|-.|..+...++.|-+|+.-
T Consensus 21 ykcfqcpftc~~kshl~nhmky 42 (54)
T PF15269_consen 21 YKCFQCPFTCNEKSHLFNHMKY 42 (54)
T ss_pred ceeecCCcccchHHHHHHHHHH
Confidence 5677787777777888887754
No 119
>PF13451 zf-trcl: Probable zinc-binding domain
Probab=79.41 E-value=1.6 Score=20.13 Aligned_cols=17 Identities=18% Similarity=0.419 Sum_probs=10.5
Q ss_pred cceeccccccccCChhH
Q psy10762 7 TPHRCDYCAKTFTRKEH 23 (126)
Q Consensus 7 ~~~~C~~C~~~f~~~~~ 23 (126)
+.+.|.+||..|.....
T Consensus 3 k~l~C~dCg~~FvfTa~ 19 (49)
T PF13451_consen 3 KTLTCKDCGAEFVFTAG 19 (49)
T ss_pred eeEEcccCCCeEEEehh
Confidence 45667777776655544
No 120
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=79.38 E-value=0.62 Score=23.40 Aligned_cols=8 Identities=38% Similarity=1.232 Sum_probs=3.6
Q ss_pred ccCCcccc
Q psy10762 38 HCNYCAKS 45 (126)
Q Consensus 38 ~c~~C~~~ 45 (126)
.|+.||..
T Consensus 3 ~CP~Cg~~ 10 (72)
T PRK09678 3 HCPLCQHA 10 (72)
T ss_pred cCCCCCCc
Confidence 34445443
No 121
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=79.17 E-value=1.5 Score=20.06 Aligned_cols=11 Identities=18% Similarity=0.265 Sum_probs=5.7
Q ss_pred CccCccccccc
Q psy10762 92 PHKCTYCMKSF 102 (126)
Q Consensus 92 ~~~C~~C~~~f 102 (126)
.+.|+.|+..+
T Consensus 20 ~~vC~~Cg~~~ 30 (52)
T smart00661 20 RFVCRKCGYEE 30 (52)
T ss_pred EEECCcCCCeE
Confidence 45555555443
No 122
>KOG2785|consensus
Probab=78.61 E-value=3.2 Score=27.86 Aligned_cols=27 Identities=26% Similarity=0.552 Sum_probs=22.6
Q ss_pred cceeccccccccCChhHHHHHHHhhcC
Q psy10762 7 TPHRCDYCAKTFTRKEHLVNHVRQHTG 33 (126)
Q Consensus 7 ~~~~C~~C~~~f~~~~~l~~h~~~h~~ 33 (126)
.|-.|-.|+..+.....-..||..+++
T Consensus 165 ~Pt~CLfC~~~~k~~e~~~~HM~~~Hg 191 (390)
T KOG2785|consen 165 IPTDCLFCDKKSKSLEENLKHMFKEHG 191 (390)
T ss_pred CCcceeecCCCcccHHHHHHHHhhccC
Confidence 346688999999999999999987765
No 123
>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=78.60 E-value=0.86 Score=17.62 Aligned_cols=8 Identities=38% Similarity=1.044 Sum_probs=4.1
Q ss_pred CccCcccc
Q psy10762 92 PHKCTYCM 99 (126)
Q Consensus 92 ~~~C~~C~ 99 (126)
.|.|+.||
T Consensus 16 ~f~CPnCG 23 (24)
T PF07754_consen 16 PFPCPNCG 23 (24)
T ss_pred eEeCCCCC
Confidence 35555554
No 124
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=78.05 E-value=1.7 Score=22.82 Aligned_cols=13 Identities=31% Similarity=0.728 Sum_probs=7.8
Q ss_pred CcccCCCCCcCCC
Q psy10762 64 PFPCQYCPKAFTR 76 (126)
Q Consensus 64 ~~~C~~C~~~~~~ 76 (126)
|-.|..||..|..
T Consensus 58 Pa~CkkCGfef~~ 70 (97)
T COG3357 58 PARCKKCGFEFRD 70 (97)
T ss_pred ChhhcccCccccc
Confidence 4466666666654
No 125
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=77.42 E-value=1.4 Score=20.38 Aligned_cols=11 Identities=18% Similarity=0.459 Sum_probs=6.2
Q ss_pred CCccCcccccc
Q psy10762 91 SPHKCTYCMKS 101 (126)
Q Consensus 91 ~~~~C~~C~~~ 101 (126)
..+.|..|+..
T Consensus 36 ~r~~C~~Cgyt 46 (50)
T PRK00432 36 DRWHCGKCGYT 46 (50)
T ss_pred CcEECCCcCCE
Confidence 34556666654
No 126
>KOG2893|consensus
Probab=77.17 E-value=0.69 Score=28.82 Aligned_cols=43 Identities=23% Similarity=0.599 Sum_probs=31.7
Q ss_pred eeccccccccCChhHHHHHHHhhcCCCCcccCCcccccCCchHHHHH
Q psy10762 9 HRCDYCAKTFTRKEHLVNHVRQHTGESPHHCNYCAKSFTRKDHMVYH 55 (126)
Q Consensus 9 ~~C~~C~~~f~~~~~l~~h~~~h~~~~~~~c~~C~~~~~~~~~l~~h 55 (126)
-.|=.|...|-...-|.+|++..+ |+|.+|-+...+-..|..|
T Consensus 11 pwcwycnrefddekiliqhqkakh----fkchichkkl~sgpglsih 53 (341)
T KOG2893|consen 11 PWCWYCNREFDDEKILIQHQKAKH----FKCHICHKKLFSGPGLSIH 53 (341)
T ss_pred ceeeecccccchhhhhhhhhhhcc----ceeeeehhhhccCCCceee
Confidence 347779999988888888887654 7888887776665555555
No 127
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=77.17 E-value=0.72 Score=26.01 Aligned_cols=13 Identities=31% Similarity=0.841 Sum_probs=6.8
Q ss_pred CcccCCCCCcCCC
Q psy10762 64 PFPCQYCPKAFTR 76 (126)
Q Consensus 64 ~~~C~~C~~~~~~ 76 (126)
-|.|+.|++.|..
T Consensus 53 RyrC~~C~~tf~~ 65 (129)
T COG3677 53 RYKCKSCGSTFTV 65 (129)
T ss_pred ccccCCcCcceee
Confidence 3555555555533
No 128
>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=77.06 E-value=2.7 Score=18.88 Aligned_cols=11 Identities=27% Similarity=0.691 Sum_probs=6.3
Q ss_pred CCCccCccccc
Q psy10762 90 ESPHKCTYCMK 100 (126)
Q Consensus 90 ~~~~~C~~C~~ 100 (126)
...|.|..|++
T Consensus 35 ~~~~~C~~C~~ 45 (46)
T PF12760_consen 35 RGRYRCKACRK 45 (46)
T ss_pred CCeEECCCCCC
Confidence 34566666654
No 129
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=76.84 E-value=1.1 Score=19.66 Aligned_cols=15 Identities=13% Similarity=0.441 Sum_probs=6.9
Q ss_pred ccCCcccccCCchHH
Q psy10762 38 HCNYCAKSFTRKDHM 52 (126)
Q Consensus 38 ~c~~C~~~~~~~~~l 52 (126)
.|+.|+..|.+...|
T Consensus 21 ~C~~C~G~W~d~~el 35 (41)
T PF13453_consen 21 VCPSCGGIWFDAGEL 35 (41)
T ss_pred ECCCCCeEEccHHHH
Confidence 344444444444443
No 130
>KOG2907|consensus
Probab=76.52 E-value=1.2 Score=24.34 Aligned_cols=39 Identities=21% Similarity=0.312 Sum_probs=20.6
Q ss_pred cccCCCCCcCCChhhHHHHHHhhcC-CCCccCcccccccCC
Q psy10762 65 FPCQYCPKAFTRKDHLVNHVRRHTG-ESPHKCTYCMKSFTR 104 (126)
Q Consensus 65 ~~C~~C~~~~~~~~~l~~h~~~~~~-~~~~~C~~C~~~f~~ 104 (126)
..||.||-.=..-..++- ...-.| .-.|.|+.|++.|..
T Consensus 75 ~kCpkCghe~m~Y~T~Ql-RSADEGQTVFYTC~kC~~k~~e 114 (116)
T KOG2907|consen 75 HKCPKCGHEEMSYHTLQL-RSADEGQTVFYTCPKCKYKFTE 114 (116)
T ss_pred ccCcccCCchhhhhhhhc-ccccCCceEEEEcCccceeeec
Confidence 479999743222212111 011112 234899999998864
No 131
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=76.44 E-value=1.8 Score=19.99 Aligned_cols=12 Identities=17% Similarity=0.653 Sum_probs=8.2
Q ss_pred cceecccccccc
Q psy10762 7 TPHRCDYCAKTF 18 (126)
Q Consensus 7 ~~~~C~~C~~~f 18 (126)
..|.|..||..|
T Consensus 5 ~~Y~C~~Cg~~~ 16 (49)
T COG1996 5 MEYKCARCGREV 16 (49)
T ss_pred EEEEhhhcCCee
Confidence 357777777766
No 132
>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=76.33 E-value=1.3 Score=19.57 Aligned_cols=29 Identities=24% Similarity=0.701 Sum_probs=17.8
Q ss_pred eeccccccccCChhHHHHHHHhhcCCCCcccCCccc
Q psy10762 9 HRCDYCAKTFTRKEHLVNHVRQHTGESPHHCNYCAK 44 (126)
Q Consensus 9 ~~C~~C~~~f~~~~~l~~h~~~h~~~~~~~c~~C~~ 44 (126)
|.|..||..|-....+ .. .....|+.||.
T Consensus 6 y~C~~Cg~~fe~~~~~------~~-~~~~~CP~Cg~ 34 (42)
T PF09723_consen 6 YRCEECGHEFEVLQSI------SE-DDPVPCPECGS 34 (42)
T ss_pred EEeCCCCCEEEEEEEc------CC-CCCCcCCCCCC
Confidence 7788888777544321 11 33457888875
No 133
>PF13878 zf-C2H2_3: zinc-finger of acetyl-transferase ESCO
Probab=75.12 E-value=3.9 Score=17.99 Aligned_cols=24 Identities=21% Similarity=0.419 Sum_probs=16.2
Q ss_pred eeccccccccCCh--hHHHHHHHhhc
Q psy10762 9 HRCDYCAKTFTRK--EHLVNHVRQHT 32 (126)
Q Consensus 9 ~~C~~C~~~f~~~--~~l~~h~~~h~ 32 (126)
-.|+.||..|... .+-..|.+.|.
T Consensus 14 ~~C~~CgM~Y~~~~~eD~~~H~~yH~ 39 (41)
T PF13878_consen 14 TTCPTCGMLYSPGSPEDEKLHKKYHD 39 (41)
T ss_pred cCCCCCCCEECCCCHHHHHHHHHHHh
Confidence 5799999987655 44556665553
No 134
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=74.12 E-value=0.61 Score=24.89 Aligned_cols=10 Identities=40% Similarity=0.720 Sum_probs=6.3
Q ss_pred ccCccccccc
Q psy10762 93 HKCTYCMKSF 102 (126)
Q Consensus 93 ~~C~~C~~~f 102 (126)
..|..||.+|
T Consensus 47 ~~Cg~CGls~ 56 (104)
T COG4888 47 AVCGNCGLSF 56 (104)
T ss_pred EEcccCcceE
Confidence 4566676665
No 135
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=73.98 E-value=2.5 Score=28.82 Aligned_cols=14 Identities=14% Similarity=0.392 Sum_probs=9.1
Q ss_pred CccCcccccccCCH
Q psy10762 92 PHKCTYCMKSFTRK 105 (126)
Q Consensus 92 ~~~C~~C~~~f~~~ 105 (126)
-|+|+.|+..+...
T Consensus 367 g~rC~kCg~~~~~~ 380 (421)
T COG1571 367 GFRCKKCGTRARET 380 (421)
T ss_pred CcccccccccCCcc
Confidence 56777777666544
No 136
>PF04959 ARS2: Arsenite-resistance protein 2; InterPro: IPR007042 This entry represents Arsenite-resistance protein 2 (also known as Serrate RNA effector molecule homolog) which is thought to play a role in arsenite resistance [], although does not directly confer arsenite resistance but rather modulates arsenic sensitivity []. Arsenite is a carcinogenic compound which can act as a comutagen by inhibiting DNA repair. It is also involved in cell cycle progression at S phase. ; PDB: 3AX1_A.
Probab=73.63 E-value=1.3 Score=27.26 Aligned_cols=27 Identities=22% Similarity=0.391 Sum_probs=19.5
Q ss_pred CcccCCcccccCCchHHHHHHhhhcCC
Q psy10762 36 PHHCNYCAKSFTRKDHMVYHERQHTGE 62 (126)
Q Consensus 36 ~~~c~~C~~~~~~~~~l~~h~~~~~~~ 62 (126)
-|.|++|++.|.....+.+|+..-+.+
T Consensus 77 K~~C~lc~KlFkg~eFV~KHI~nKH~e 103 (214)
T PF04959_consen 77 KWRCPLCGKLFKGPEFVRKHIFNKHPE 103 (214)
T ss_dssp EEEE-SSS-EESSHHHHHHHHHHH-HH
T ss_pred EECCCCCCcccCChHHHHHHHhhcCHH
Confidence 478999999999999999998765544
No 137
>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=73.48 E-value=3.2 Score=19.36 Aligned_cols=12 Identities=17% Similarity=0.653 Sum_probs=6.4
Q ss_pred cCcccccccCCH
Q psy10762 94 KCTYCMKSFTRK 105 (126)
Q Consensus 94 ~C~~C~~~f~~~ 105 (126)
.||+|++.|...
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 899999998753
No 138
>KOG2807|consensus
Probab=73.26 E-value=8.8 Score=25.40 Aligned_cols=26 Identities=19% Similarity=0.340 Sum_probs=17.2
Q ss_pred CCccCcccccccCCHHHHHHHHHHhh
Q psy10762 91 SPHKCTYCMKSFTRKEHLTNHIRQHT 116 (126)
Q Consensus 91 ~~~~C~~C~~~f~~~~~l~~H~~~h~ 116 (126)
..|.|..|...|=..-+.-.|...|.
T Consensus 344 ~~y~C~~Ck~~FCldCDv~iHesLh~ 369 (378)
T KOG2807|consen 344 GRYRCESCKNVFCLDCDVFIHESLHN 369 (378)
T ss_pred CcEEchhccceeeccchHHHHhhhhc
Confidence 45788888888766555566655543
No 139
>COG3091 SprT Zn-dependent metalloprotease, SprT family [General function prediction only]
Probab=73.23 E-value=1.5 Score=25.42 Aligned_cols=33 Identities=30% Similarity=0.696 Sum_probs=20.9
Q ss_pred CcccCCCCCcCCChhhHHHHHHhhcCCCCccCcccccc
Q psy10762 64 PFPCQYCPKAFTRKDHLVNHVRRHTGESPHKCTYCMKS 101 (126)
Q Consensus 64 ~~~C~~C~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~ 101 (126)
+|.|. |+..|.+. .+|-..-.|+ .|.|..|+-.
T Consensus 117 ~Y~C~-C~q~~l~~---RRhn~~~~g~-~YrC~~C~gk 149 (156)
T COG3091 117 PYRCQ-CQQHYLRI---RRHNTVRRGE-VYRCGKCGGK 149 (156)
T ss_pred eEEee-cCCccchh---hhcccccccc-eEEeccCCce
Confidence 58888 88776553 2333333344 7889888754
No 140
>KOG2071|consensus
Probab=73.17 E-value=2.2 Score=30.25 Aligned_cols=32 Identities=25% Similarity=0.503 Sum_probs=25.8
Q ss_pred CCCccCcccccccCCHHHHHHHHHHhhhcccc
Q psy10762 90 ESPHKCTYCMKSFTRKEHLTNHIRQHTVRRVN 121 (126)
Q Consensus 90 ~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~ 121 (126)
..+..|..||.+|.......+||-+|.+.+.+
T Consensus 416 ~~pnqC~~CG~R~~~~ee~sk~md~H~dwh~r 447 (579)
T KOG2071|consen 416 DSPNQCKSCGLRFDDSEERSKHMDIHDDWHRR 447 (579)
T ss_pred CCcchhcccccccccchhhhhHhhhhhhhhhh
Confidence 46688999999999988888888888765543
No 141
>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=72.98 E-value=0.72 Score=19.77 Aligned_cols=18 Identities=17% Similarity=0.501 Sum_probs=10.1
Q ss_pred HHHHHhhcCCCCccCccc
Q psy10762 81 VNHVRRHTGESPHKCTYC 98 (126)
Q Consensus 81 ~~h~~~~~~~~~~~C~~C 98 (126)
.+|-....|...|.|..|
T Consensus 18 ~k~G~~~~G~qryrC~~C 35 (36)
T PF03811_consen 18 KKNGKSPSGHQRYRCKDC 35 (36)
T ss_pred eeCCCCCCCCEeEecCcC
Confidence 344444455566777666
No 142
>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=72.76 E-value=0.046 Score=23.88 Aligned_cols=10 Identities=20% Similarity=0.590 Sum_probs=7.2
Q ss_pred ccCccccccc
Q psy10762 93 HKCTYCMKSF 102 (126)
Q Consensus 93 ~~C~~C~~~f 102 (126)
|.|..|+..|
T Consensus 29 y~C~~C~~~w 38 (39)
T PF01096_consen 29 YVCCNCGHRW 38 (39)
T ss_dssp EEESSSTEEE
T ss_pred EEeCCCCCee
Confidence 6777777665
No 143
>KOG2482|consensus
Probab=72.46 E-value=3.8 Score=27.20 Aligned_cols=23 Identities=39% Similarity=0.852 Sum_probs=21.1
Q ss_pred CccCcccccccCCHHHHHHHHHH
Q psy10762 92 PHKCTYCMKSFTRKEHLTNHIRQ 114 (126)
Q Consensus 92 ~~~C~~C~~~f~~~~~l~~H~~~ 114 (126)
.+.|.-|.+.|+.+..|+.|||.
T Consensus 195 r~~CLyCekifrdkntLkeHMrk 217 (423)
T KOG2482|consen 195 RLRCLYCEKIFRDKNTLKEHMRK 217 (423)
T ss_pred hheeeeeccccCCcHHHHHHHHh
Confidence 46899999999999999999987
No 144
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=72.37 E-value=1.9 Score=24.30 Aligned_cols=13 Identities=23% Similarity=0.700 Sum_probs=6.5
Q ss_pred cccCCCCCcCCCh
Q psy10762 65 FPCQYCPKAFTRK 77 (126)
Q Consensus 65 ~~C~~C~~~~~~~ 77 (126)
++|-.||+.|...
T Consensus 2 H~Ct~Cg~~f~dg 14 (131)
T PF09845_consen 2 HQCTKCGRVFEDG 14 (131)
T ss_pred cccCcCCCCcCCC
Confidence 3455555555443
No 145
>KOG4167|consensus
Probab=72.25 E-value=1 Score=32.73 Aligned_cols=27 Identities=22% Similarity=0.443 Sum_probs=23.8
Q ss_pred cceeccccccccCChhHHHHHHHhhcC
Q psy10762 7 TPHRCDYCAKTFTRKEHLVNHVRQHTG 33 (126)
Q Consensus 7 ~~~~C~~C~~~f~~~~~l~~h~~~h~~ 33 (126)
..|.|.+|++.|.....+..||+.|.-
T Consensus 791 giFpCreC~kvF~KiKSrNAHMK~Hr~ 817 (907)
T KOG4167|consen 791 GIFPCRECGKVFFKIKSRNAHMKTHRQ 817 (907)
T ss_pred ceeehHHHHHHHHHHhhhhHHHHHHHH
Confidence 458999999999999999999998853
No 146
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=72.20 E-value=1 Score=29.39 Aligned_cols=75 Identities=16% Similarity=0.374 Sum_probs=35.6
Q ss_pred ceeccccccccCChhHHHHHHHhhcCCCCcccCCcccccCCchHHHHHHhhhcCCCCcccCCCCCcCCChhhHHHHHHhh
Q psy10762 8 PHRCDYCAKTFTRKEHLVNHVRQHTGESPHHCNYCAKSFTRKDHMVYHERQHTGETPFPCQYCPKAFTRKDHLVNHVRRH 87 (126)
Q Consensus 8 ~~~C~~C~~~f~~~~~l~~h~~~h~~~~~~~c~~C~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~~~~~~~l~~h~~~~ 87 (126)
.-.|++||..-. .+ + .+.....+.+-+.|..|+-.+... ...|+.|+.. ..+ ..+...
T Consensus 187 ~~~CPvCGs~P~-~s-~-v~~~~~~G~RyL~CslC~teW~~~--------------R~~C~~Cg~~----~~l-~y~~~~ 244 (309)
T PRK03564 187 RQFCPVCGSMPV-SS-V-VQIGTTQGLRYLHCNLCESEWHVV--------------RVKCSNCEQS----GKL-HYWSLD 244 (309)
T ss_pred CCCCCCCCCcch-hh-e-eeccCCCCceEEEcCCCCCccccc--------------CccCCCCCCC----Cce-eeeeec
Confidence 355777776421 11 1 111223344455677776433221 2378888852 111 111111
Q ss_pred ---cCCCCccCcccccccCC
Q psy10762 88 ---TGESPHKCTYCMKSFTR 104 (126)
Q Consensus 88 ---~~~~~~~C~~C~~~f~~ 104 (126)
.+.+...|..|+.-.+.
T Consensus 245 ~~~~~~r~e~C~~C~~YlK~ 264 (309)
T PRK03564 245 SEQAAVKAESCGDCGTYLKI 264 (309)
T ss_pred CCCcceEeeeccccccccee
Confidence 23355789889765443
No 147
>COG2331 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=72.11 E-value=2.3 Score=21.50 Aligned_cols=31 Identities=23% Similarity=0.624 Sum_probs=17.4
Q ss_pred ceeccccccccCChhHHHHHHHhhcCCCCcccCCcccc
Q psy10762 8 PHRCDYCAKTFTRKEHLVNHVRQHTGESPHHCNYCAKS 45 (126)
Q Consensus 8 ~~~C~~C~~~f~~~~~l~~h~~~h~~~~~~~c~~C~~~ 45 (126)
.|.|..|+..| .+.+++ .++..-.|+.|+..
T Consensus 12 ~Y~c~~cg~~~----dvvq~~---~ddplt~ce~c~a~ 42 (82)
T COG2331 12 SYECTECGNRF----DVVQAM---TDDPLTTCEECGAR 42 (82)
T ss_pred EEeecccchHH----HHHHhc---ccCccccChhhChH
Confidence 37788888765 333333 23333457777653
No 148
>TIGR00686 phnA alkylphosphonate utilization operon protein PhnA. The protein family includes an uncharacterized member designated phnA in Escherichia coli, part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage. This protein is not related to the characterized phosphonoacetate hydrolase designated PhnA by Kulakova, et al. (2001, 1997).
Probab=71.63 E-value=1.9 Score=23.41 Aligned_cols=12 Identities=17% Similarity=0.611 Sum_probs=6.3
Q ss_pred CccCcccccccC
Q psy10762 92 PHKCTYCMKSFT 103 (126)
Q Consensus 92 ~~~C~~C~~~f~ 103 (126)
.|.|+.|+..+.
T Consensus 19 ~~iCpeC~~EW~ 30 (109)
T TIGR00686 19 QLICPSCLYEWN 30 (109)
T ss_pred eeECcccccccc
Confidence 355555555544
No 149
>KOG1842|consensus
Probab=71.28 E-value=2.8 Score=28.79 Aligned_cols=25 Identities=16% Similarity=0.445 Sum_probs=15.9
Q ss_pred CccCcccccccCCHHHHHHHHHHhh
Q psy10762 92 PHKCTYCMKSFTRKEHLTNHIRQHT 116 (126)
Q Consensus 92 ~~~C~~C~~~f~~~~~l~~H~~~h~ 116 (126)
.|.|++|...|.+.+.|..|..+-|
T Consensus 15 gflCPiC~~dl~~~~~L~~H~d~eH 39 (505)
T KOG1842|consen 15 GFLCPICLLDLPNLSALNDHLDVEH 39 (505)
T ss_pred cccCchHhhhhhhHHHHHHHHhhhc
Confidence 3666666666666666666655533
No 150
>PHA02998 RNA polymerase subunit; Provisional
Probab=70.98 E-value=0.69 Score=27.45 Aligned_cols=41 Identities=22% Similarity=0.398 Sum_probs=21.0
Q ss_pred cccCCCCCcCCChhhHHHHHHhhcCCCCccCcccccccCCH
Q psy10762 65 FPCQYCPKAFTRKDHLVNHVRRHTGESPHKCTYCMKSFTRK 105 (126)
Q Consensus 65 ~~C~~C~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~f~~~ 105 (126)
-.|+.|+..=.....++..-.-......|.|..|+..|.-.
T Consensus 144 v~CPkCg~~~A~f~qlQTRSADEPmT~FYkC~~CG~~wkpp 184 (195)
T PHA02998 144 TPCPNCKSKNTTPMMIQTRAADEPPLVRHACRDCKKHFKPP 184 (195)
T ss_pred CCCCCCCCCceEEEEEeeccCCCCceEEEEcCCCCCccCCc
Confidence 47888874322222221100001112348999999988653
No 151
>KOG3408|consensus
Probab=70.75 E-value=3.5 Score=22.93 Aligned_cols=26 Identities=27% Similarity=0.514 Sum_probs=20.2
Q ss_pred CCcceeccccccccCChhHHHHHHHh
Q psy10762 5 GETPHRCDYCAKTFTRKEHLVNHVRQ 30 (126)
Q Consensus 5 ~~~~~~C~~C~~~f~~~~~l~~h~~~ 30 (126)
|...|-|-.|.+-|.....|+.|.++
T Consensus 54 G~GqfyCi~CaRyFi~~~~l~~H~kt 79 (129)
T KOG3408|consen 54 GGGQFYCIECARYFIDAKALKTHFKT 79 (129)
T ss_pred CCceeehhhhhhhhcchHHHHHHHhc
Confidence 45568888888888888888888754
No 152
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=70.45 E-value=1.8 Score=22.77 Aligned_cols=11 Identities=27% Similarity=0.724 Sum_probs=5.3
Q ss_pred CcccCCCCCcC
Q psy10762 64 PFPCQYCPKAF 74 (126)
Q Consensus 64 ~~~C~~C~~~~ 74 (126)
.|.|..|++.|
T Consensus 54 IW~C~~C~~~~ 64 (90)
T PTZ00255 54 IWRCKGCKKTV 64 (90)
T ss_pred EEEcCCCCCEE
Confidence 44555554443
No 153
>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=70.42 E-value=3.2 Score=18.42 Aligned_cols=16 Identities=25% Similarity=0.663 Sum_probs=10.7
Q ss_pred cCcccccccCCHHHHH
Q psy10762 94 KCTYCMKSFTRKEHLT 109 (126)
Q Consensus 94 ~C~~C~~~f~~~~~l~ 109 (126)
.|.+|++.|+.+-...
T Consensus 10 ~C~~C~rpf~WRKKW~ 25 (42)
T PF10013_consen 10 ICPVCGRPFTWRKKWA 25 (42)
T ss_pred cCcccCCcchHHHHHH
Confidence 5778888887664443
No 154
>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=70.22 E-value=2.5 Score=23.30 Aligned_cols=12 Identities=17% Similarity=0.650 Sum_probs=6.6
Q ss_pred cccCCcccccCC
Q psy10762 37 HHCNYCAKSFTR 48 (126)
Q Consensus 37 ~~c~~C~~~~~~ 48 (126)
..|..|+..|..
T Consensus 71 ~~C~~Cg~~~~~ 82 (115)
T TIGR00100 71 CECEDCSEEVSP 82 (115)
T ss_pred EEcccCCCEEec
Confidence 456666655543
No 155
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=69.92 E-value=8 Score=22.88 Aligned_cols=43 Identities=19% Similarity=0.339 Sum_probs=25.2
Q ss_pred ccCCCCCcCCChhhHH-------HHHHhhcCCCCccCcccccccCCHHHHHH
Q psy10762 66 PCQYCPKAFTRKDHLV-------NHVRRHTGESPHKCTYCMKSFTRKEHLTN 110 (126)
Q Consensus 66 ~C~~C~~~~~~~~~l~-------~h~~~~~~~~~~~C~~C~~~f~~~~~l~~ 110 (126)
.|+.|+....--+.-. .+.. ..+..|.|+.||+.|=..+.+.+
T Consensus 99 RCp~CN~~L~~vs~eev~~~Vp~~~~~--~~~~f~~C~~CgkiYW~GsHw~~ 148 (165)
T COG1656 99 RCPECNGELEKVSREEVKEKVPEKVYR--NYEEFYRCPKCGKIYWKGSHWRR 148 (165)
T ss_pred cCcccCCEeccCcHHHHhhccchhhhh--cccceeECCCCcccccCchHHHH
Confidence 6999976543322111 0111 12456789999999877666555
No 156
>PRK10220 hypothetical protein; Provisional
Probab=69.90 E-value=2.6 Score=22.93 Aligned_cols=11 Identities=18% Similarity=0.615 Sum_probs=5.4
Q ss_pred ccCcccccccC
Q psy10762 93 HKCTYCMKSFT 103 (126)
Q Consensus 93 ~~C~~C~~~f~ 103 (126)
|.|+.|+..+.
T Consensus 21 ~vCpeC~hEW~ 31 (111)
T PRK10220 21 YICPECAHEWN 31 (111)
T ss_pred EECCcccCcCC
Confidence 45555554443
No 157
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=69.71 E-value=6.8 Score=30.75 Aligned_cols=12 Identities=17% Similarity=0.548 Sum_probs=8.0
Q ss_pred CcccCCCCCcCC
Q psy10762 64 PFPCQYCPKAFT 75 (126)
Q Consensus 64 ~~~C~~C~~~~~ 75 (126)
+|.|+.||....
T Consensus 692 vy~CPsCGaev~ 703 (1337)
T PRK14714 692 VYVCPDCGAEVP 703 (1337)
T ss_pred ceeCccCCCccC
Confidence 467888876543
No 158
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=69.65 E-value=0.96 Score=24.88 Aligned_cols=13 Identities=31% Similarity=0.470 Sum_probs=10.7
Q ss_pred CCccCcccccccC
Q psy10762 91 SPHKCTYCMKSFT 103 (126)
Q Consensus 91 ~~~~C~~C~~~f~ 103 (126)
..|.|..||..|.
T Consensus 99 ~Fy~C~~Cg~~wr 111 (113)
T COG1594 99 RFYKCTRCGYRWR 111 (113)
T ss_pred EEEEecccCCEee
Confidence 4589999998875
No 159
>KOG2636|consensus
Probab=69.04 E-value=7.2 Score=26.92 Aligned_cols=29 Identities=14% Similarity=0.359 Sum_probs=22.7
Q ss_pred HHhhcCCCCccCcccc-cccCCHHHHHHHH
Q psy10762 84 VRRHTGESPHKCTYCM-KSFTRKEHLTNHI 112 (126)
Q Consensus 84 ~~~~~~~~~~~C~~C~-~~f~~~~~l~~H~ 112 (126)
.+.|.-...|.|.+|| +++.-+..+.+|.
T Consensus 393 yKLHGL~~ey~CEICGNy~Y~GrkaF~RHF 422 (497)
T KOG2636|consen 393 YKLHGLDIEYNCEICGNYVYKGRKAFDRHF 422 (497)
T ss_pred HhhcCCCcccceeeccCccccCcHHHHHHh
Confidence 4667777888888888 7787788888884
No 160
>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=68.53 E-value=2.1 Score=20.19 Aligned_cols=9 Identities=22% Similarity=0.778 Sum_probs=4.3
Q ss_pred ccCCccccc
Q psy10762 38 HCNYCAKSF 46 (126)
Q Consensus 38 ~c~~C~~~~ 46 (126)
+|+.||..+
T Consensus 4 ~CP~CG~~i 12 (54)
T TIGR01206 4 ECPDCGAEI 12 (54)
T ss_pred CCCCCCCEE
Confidence 455555433
No 161
>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=68.47 E-value=3.8 Score=20.05 Aligned_cols=12 Identities=17% Similarity=0.409 Sum_probs=5.6
Q ss_pred CCccCccccccc
Q psy10762 91 SPHKCTYCMKSF 102 (126)
Q Consensus 91 ~~~~C~~C~~~f 102 (126)
+.|.|+.||..+
T Consensus 45 r~~~C~~Cg~~~ 56 (69)
T PF07282_consen 45 RVFTCPNCGFEM 56 (69)
T ss_pred ceEEcCCCCCEE
Confidence 344455554443
No 162
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=68.37 E-value=3.2 Score=22.81 Aligned_cols=11 Identities=18% Similarity=0.504 Sum_probs=6.0
Q ss_pred cccCCcccccC
Q psy10762 37 HHCNYCAKSFT 47 (126)
Q Consensus 37 ~~c~~C~~~~~ 47 (126)
+.|..|+..|.
T Consensus 71 ~~C~~Cg~~~~ 81 (113)
T PRK12380 71 AWCWDCSQVVE 81 (113)
T ss_pred EEcccCCCEEe
Confidence 45666665444
No 163
>PRK14873 primosome assembly protein PriA; Provisional
Probab=68.02 E-value=1.7 Score=31.53 Aligned_cols=47 Identities=13% Similarity=0.471 Sum_probs=23.4
Q ss_pred eccccccccCChhHHHHHHHhhcCCCCcccCCcccccCCchHHHHHHhhhcCCCCcccCCCCCc
Q psy10762 10 RCDYCAKTFTRKEHLVNHVRQHTGESPHHCNYCAKSFTRKDHMVYHERQHTGETPFPCQYCPKA 73 (126)
Q Consensus 10 ~C~~C~~~f~~~~~l~~h~~~h~~~~~~~c~~C~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~ 73 (126)
.|..||..+....- ...+..|.......|..||... .++.|+.|+..
T Consensus 385 ~C~~Cg~~~~C~~C-~~~L~~h~~~~~l~Ch~CG~~~----------------~p~~Cp~Cgs~ 431 (665)
T PRK14873 385 ACARCRTPARCRHC-TGPLGLPSAGGTPRCRWCGRAA----------------PDWRCPRCGSD 431 (665)
T ss_pred EhhhCcCeeECCCC-CCceeEecCCCeeECCCCcCCC----------------cCccCCCCcCC
Confidence 46666655544311 1112233334456677777321 25678888753
No 164
>KOG0717|consensus
Probab=67.78 E-value=3.4 Score=28.56 Aligned_cols=22 Identities=36% Similarity=0.656 Sum_probs=19.4
Q ss_pred ccCcccccccCCHHHHHHHHHH
Q psy10762 93 HKCTYCMKSFTRKEHLTNHIRQ 114 (126)
Q Consensus 93 ~~C~~C~~~f~~~~~l~~H~~~ 114 (126)
+-|.+|+++|.+.-.|.+|...
T Consensus 293 lyC~vCnKsFKseKq~kNHEnS 314 (508)
T KOG0717|consen 293 LYCVVCNKSFKSEKQLKNHENS 314 (508)
T ss_pred eEEeeccccccchHHHHhhHHH
Confidence 6699999999999999999654
No 165
>COG1655 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=66.93 E-value=0.94 Score=28.12 Aligned_cols=23 Identities=17% Similarity=0.501 Sum_probs=14.8
Q ss_pred CcceeccccccccCChhHHHHHH
Q psy10762 6 ETPHRCDYCAKTFTRKEHLVNHV 28 (126)
Q Consensus 6 ~~~~~C~~C~~~f~~~~~l~~h~ 28 (126)
++.+.|++|+..|........-.
T Consensus 17 kk~ieCPvC~tkFkkeev~tgsi 39 (267)
T COG1655 17 KKTIECPVCNTKFKKEEVKTGSI 39 (267)
T ss_pred hceeccCcccchhhhhheeccce
Confidence 45678888888886655433333
No 166
>PF05290 Baculo_IE-1: Baculovirus immediate-early protein (IE-0); InterPro: IPR007954 This entry contains the Baculovirus immediate-early protein IE-0.
Probab=66.56 E-value=5.6 Score=22.62 Aligned_cols=13 Identities=31% Similarity=0.728 Sum_probs=10.5
Q ss_pred cCcccccccCCHH
Q psy10762 94 KCTYCMKSFTRKE 106 (126)
Q Consensus 94 ~C~~C~~~f~~~~ 106 (126)
+||+|.-+|++++
T Consensus 123 vCPvCkTSFKss~ 135 (140)
T PF05290_consen 123 VCPVCKTSFKSSS 135 (140)
T ss_pred CCCcccccccccc
Confidence 6999988888764
No 167
>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=66.02 E-value=1.9 Score=18.44 Aligned_cols=10 Identities=20% Similarity=0.840 Sum_probs=5.9
Q ss_pred eccccccccC
Q psy10762 10 RCDYCAKTFT 19 (126)
Q Consensus 10 ~C~~C~~~f~ 19 (126)
.|+.||.+|-
T Consensus 3 ~C~~Cg~~Yh 12 (36)
T PF05191_consen 3 ICPKCGRIYH 12 (36)
T ss_dssp EETTTTEEEE
T ss_pred CcCCCCCccc
Confidence 4666666653
No 168
>TIGR00280 L37a ribosomal protein L37a. This model finds eukaryotic ribosomal protein L37a and its archaeal orthologs. The nomeclature is tricky because eukaryotes have proteins called both L37 and L37a.
Probab=65.26 E-value=2 Score=22.64 Aligned_cols=11 Identities=27% Similarity=0.851 Sum_probs=5.3
Q ss_pred CcccCCCCCcC
Q psy10762 64 PFPCQYCPKAF 74 (126)
Q Consensus 64 ~~~C~~C~~~~ 74 (126)
.|.|..|+..|
T Consensus 53 IW~C~~C~~~~ 63 (91)
T TIGR00280 53 IWTCRKCGAKF 63 (91)
T ss_pred EEEcCCCCCEE
Confidence 34555554443
No 169
>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=64.99 E-value=1.5 Score=23.02 Aligned_cols=10 Identities=50% Similarity=1.006 Sum_probs=5.2
Q ss_pred ccCccccccc
Q psy10762 93 HKCTYCMKSF 102 (126)
Q Consensus 93 ~~C~~C~~~f 102 (126)
|.|..|++.|
T Consensus 54 W~C~~C~~~~ 63 (90)
T PF01780_consen 54 WKCKKCGKKF 63 (90)
T ss_dssp EEETTTTEEE
T ss_pred eecCCCCCEE
Confidence 4555555544
No 170
>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=64.69 E-value=2.5 Score=29.66 Aligned_cols=34 Identities=21% Similarity=0.460 Sum_probs=14.7
Q ss_pred eccccccccCChhHHHHHHHhhcCCCCcccCCccc
Q psy10762 10 RCDYCAKTFTRKEHLVNHVRQHTGESPHHCNYCAK 44 (126)
Q Consensus 10 ~C~~C~~~f~~~~~l~~h~~~h~~~~~~~c~~C~~ 44 (126)
.|..||.......- ...+..|.......|..||.
T Consensus 215 ~C~~Cg~~~~C~~C-~~~l~~h~~~~~l~Ch~Cg~ 248 (505)
T TIGR00595 215 LCRSCGYILCCPNC-DVSLTYHKKEGKLRCHYCGY 248 (505)
T ss_pred EhhhCcCccCCCCC-CCceEEecCCCeEEcCCCcC
Confidence 45556555443311 11223333334455555553
No 171
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=64.52 E-value=3.7 Score=17.85 Aligned_cols=14 Identities=21% Similarity=0.672 Sum_probs=11.6
Q ss_pred ceeccccccccCCh
Q psy10762 8 PHRCDYCAKTFTRK 21 (126)
Q Consensus 8 ~~~C~~C~~~f~~~ 21 (126)
++.|..|+..|...
T Consensus 12 ~f~C~~C~~~FC~~ 25 (39)
T smart00154 12 GFKCRHCGNLFCGE 25 (39)
T ss_pred CeECCccCCccccc
Confidence 78899999888765
No 172
>KOG2593|consensus
Probab=64.33 E-value=6.3 Score=27.02 Aligned_cols=12 Identities=33% Similarity=0.755 Sum_probs=5.5
Q ss_pred eeccccccccCC
Q psy10762 9 HRCDYCAKTFTR 20 (126)
Q Consensus 9 ~~C~~C~~~f~~ 20 (126)
|.|+.|++.|..
T Consensus 129 Y~Cp~C~kkyt~ 140 (436)
T KOG2593|consen 129 YVCPNCQKKYTS 140 (436)
T ss_pred ccCCccccchhh
Confidence 444444444433
No 173
>COG4338 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=63.99 E-value=2.8 Score=19.12 Aligned_cols=17 Identities=18% Similarity=0.659 Sum_probs=12.3
Q ss_pred cCcccccccCCHHHHHH
Q psy10762 94 KCTYCMKSFTRKEHLTN 110 (126)
Q Consensus 94 ~C~~C~~~f~~~~~l~~ 110 (126)
.|++|++-|+.+....+
T Consensus 14 ICpvCqRPFsWRkKW~~ 30 (54)
T COG4338 14 ICPVCQRPFSWRKKWAR 30 (54)
T ss_pred hhhhhcCchHHHHHHHH
Confidence 68889888887655443
No 174
>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=63.49 E-value=6.8 Score=27.28 Aligned_cols=23 Identities=30% Similarity=0.543 Sum_probs=14.9
Q ss_pred CccCcccccccCCHHHHHHHHHH
Q psy10762 92 PHKCTYCMKSFTRKEHLTNHIRQ 114 (126)
Q Consensus 92 ~~~C~~C~~~f~~~~~l~~H~~~ 114 (126)
.+.|+.|.+.|.....+..|+..
T Consensus 57 FWiCp~CskkF~d~~~~~~H~~~ 79 (466)
T PF04780_consen 57 FWICPRCSKKFSDAESCLSHMEQ 79 (466)
T ss_pred EeeCCcccceeCCHHHHHHHHHH
Confidence 35666666667666666666654
No 175
>KOG1280|consensus
Probab=62.37 E-value=11 Score=25.22 Aligned_cols=38 Identities=24% Similarity=0.474 Sum_probs=26.2
Q ss_pred CcceeccccccccCChhHHHHHHHhhcCCCC--cccCCcc
Q psy10762 6 ETPHRCDYCAKTFTRKEHLVNHVRQHTGESP--HHCNYCA 43 (126)
Q Consensus 6 ~~~~~C~~C~~~f~~~~~l~~h~~~h~~~~~--~~c~~C~ 43 (126)
...|.|+.|+..-.....+..|...-+.+.. ..|+.|+
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 4468899999888888888888876544322 3455554
No 176
>KOG1280|consensus
Probab=62.09 E-value=9.5 Score=25.45 Aligned_cols=37 Identities=24% Similarity=0.511 Sum_probs=27.0
Q ss_pred CcccCCCCCcCCChhhHHHHHHhhcCCCC--ccCccccc
Q psy10762 64 PFPCQYCPKAFTRKDHLVNHVRRHTGESP--HKCTYCMK 100 (126)
Q Consensus 64 ~~~C~~C~~~~~~~~~l~~h~~~~~~~~~--~~C~~C~~ 100 (126)
-|.|+.|+..-.+...|..|....+-+-. ..|++|+-
T Consensus 79 SftCPyC~~~Gfte~~f~~Hv~s~Hpda~~~~icp~c~~ 117 (381)
T KOG1280|consen 79 SFTCPYCGIMGFTERQFGTHVLSQHPEASTSVICPLCAA 117 (381)
T ss_pred cccCCcccccccchhHHHHHhhhcCcccCcceeeecccc
Confidence 58899999877788899999876554433 35777753
No 177
>COG1326 Uncharacterized archaeal Zn-finger protein [General function prediction only]
Probab=61.91 E-value=8.4 Score=23.44 Aligned_cols=11 Identities=18% Similarity=0.428 Sum_probs=5.7
Q ss_pred CccCccccccc
Q psy10762 92 PHKCTYCMKSF 102 (126)
Q Consensus 92 ~~~C~~C~~~f 102 (126)
.+.|..||..+
T Consensus 30 lvrC~eCG~V~ 40 (201)
T COG1326 30 LVRCEECGTVH 40 (201)
T ss_pred EEEccCCCcEe
Confidence 34555555554
No 178
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=61.19 E-value=12 Score=22.47 Aligned_cols=33 Identities=12% Similarity=0.437 Sum_probs=19.5
Q ss_pred CCCCcccCCCCCcCCChhhHHHHHHhhcCCCCccCccccccc
Q psy10762 61 GETPFPCQYCPKAFTRKDHLVNHVRRHTGESPHKCTYCMKSF 102 (126)
Q Consensus 61 ~~~~~~C~~C~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~f 102 (126)
...-|.|+.|..-++...++. ..|.|+.||...
T Consensus 110 ~~~~y~C~~~~~r~sfdeA~~---------~~F~Cp~Cg~~L 142 (176)
T COG1675 110 ENNYYVCPNCHVKYSFDEAME---------LGFTCPKCGEDL 142 (176)
T ss_pred cCCceeCCCCCCcccHHHHHH---------hCCCCCCCCchh
Confidence 344578877765555443332 227888887643
No 179
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=60.07 E-value=2.6 Score=22.16 Aligned_cols=11 Identities=27% Similarity=0.833 Sum_probs=5.2
Q ss_pred CcccCCCCCcC
Q psy10762 64 PFPCQYCPKAF 74 (126)
Q Consensus 64 ~~~C~~C~~~~ 74 (126)
.|.|..|+..|
T Consensus 54 IW~C~~C~~~~ 64 (90)
T PRK03976 54 IWECRKCGAKF 64 (90)
T ss_pred EEEcCCCCCEE
Confidence 34555554443
No 180
>KOG2593|consensus
Probab=59.98 E-value=8.7 Score=26.38 Aligned_cols=38 Identities=21% Similarity=0.446 Sum_probs=23.9
Q ss_pred cCCCCcccCCCCCcCCChhhHHHHHHhhcC-CCCccCcccccc
Q psy10762 60 TGETPFPCQYCPKAFTRKDHLVNHVRRHTG-ESPHKCTYCMKS 101 (126)
Q Consensus 60 ~~~~~~~C~~C~~~~~~~~~l~~h~~~~~~-~~~~~C~~C~~~ 101 (126)
.....|.||.|.+.|.....++ .-.. .-.|.|..|+-.
T Consensus 124 t~~~~Y~Cp~C~kkyt~Lea~~----L~~~~~~~F~C~~C~ge 162 (436)
T KOG2593|consen 124 TNVAGYVCPNCQKKYTSLEALQ----LLDNETGEFHCENCGGE 162 (436)
T ss_pred cccccccCCccccchhhhHHHH----hhcccCceEEEecCCCc
Confidence 3445688999988887765532 2222 346888888743
No 181
>COG4530 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=59.90 E-value=6.3 Score=21.53 Aligned_cols=11 Identities=27% Similarity=0.661 Sum_probs=5.4
Q ss_pred CcccCCCCCcC
Q psy10762 64 PFPCQYCPKAF 74 (126)
Q Consensus 64 ~~~C~~C~~~~ 74 (126)
|..||.||++|
T Consensus 26 PiVsPytG~s~ 36 (129)
T COG4530 26 PIVSPYTGKSY 36 (129)
T ss_pred ccccCcccccc
Confidence 44455555544
No 182
>COG1773 Rubredoxin [Energy production and conversion]
Probab=59.73 E-value=3.9 Score=19.39 Aligned_cols=12 Identities=17% Similarity=0.636 Sum_probs=8.2
Q ss_pred CccCcccccccC
Q psy10762 92 PHKCTYCMKSFT 103 (126)
Q Consensus 92 ~~~C~~C~~~f~ 103 (126)
.|+|.+||..|.
T Consensus 3 ~~~C~~CG~vYd 14 (55)
T COG1773 3 RWRCSVCGYVYD 14 (55)
T ss_pred ceEecCCceEec
Confidence 467777777664
No 183
>COG3364 Zn-ribbon containing protein [General function prediction only]
Probab=59.60 E-value=3.6 Score=22.14 Aligned_cols=13 Identities=31% Similarity=0.894 Sum_probs=7.2
Q ss_pred CcccCCCCCcCCC
Q psy10762 64 PFPCQYCPKAFTR 76 (126)
Q Consensus 64 ~~~C~~C~~~~~~ 76 (126)
|++|..||..|..
T Consensus 2 pH~CtrCG~vf~~ 14 (112)
T COG3364 2 PHQCTRCGEVFDD 14 (112)
T ss_pred Cceeccccccccc
Confidence 3455556655555
No 184
>PRK04351 hypothetical protein; Provisional
Probab=59.58 E-value=3.1 Score=24.16 Aligned_cols=32 Identities=25% Similarity=0.614 Sum_probs=20.8
Q ss_pred CcccCCCCCcCCChhhHHHHHHhhcCCCCccCcccccccC
Q psy10762 64 PFPCQYCPKAFTRKDHLVNHVRRHTGESPHKCTYCMKSFT 103 (126)
Q Consensus 64 ~~~C~~C~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~f~ 103 (126)
.|.|..|+..+.+.- .+ ....|.|..|+..+.
T Consensus 112 ~Y~C~~Cg~~~~r~R-------r~-n~~~yrCg~C~g~L~ 143 (149)
T PRK04351 112 LYECQSCGQQYLRKR-------RI-NTKRYRCGKCRGKLK 143 (149)
T ss_pred EEECCCCCCEeeeee-------ec-CCCcEEeCCCCcEee
Confidence 378988987664421 11 236689999987654
No 185
>COG5188 PRP9 Splicing factor 3a, subunit 3 [RNA processing and modification]
Probab=59.21 E-value=20 Score=24.15 Aligned_cols=30 Identities=13% Similarity=0.401 Sum_probs=23.6
Q ss_pred HHhhcCCCCccCcccc-cccCCHHHHHHHHH
Q psy10762 84 VRRHTGESPHKCTYCM-KSFTRKEHLTNHIR 113 (126)
Q Consensus 84 ~~~~~~~~~~~C~~C~-~~f~~~~~l~~H~~ 113 (126)
++.|.-.+.|.|.+|| +++.-+..+.+|..
T Consensus 366 ~klhgLd~ef~CEICgNyvy~GR~~FdrHF~ 396 (470)
T COG5188 366 CKLHGLDIEFECEICGNYVYYGRDRFDRHFE 396 (470)
T ss_pred HHhcCCCcceeeeecccccccchHHHHhhhh
Confidence 4677778889999998 77777778888753
No 186
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=58.67 E-value=6 Score=21.92 Aligned_cols=11 Identities=27% Similarity=0.827 Sum_probs=5.6
Q ss_pred cccCCcccccC
Q psy10762 37 HHCNYCAKSFT 47 (126)
Q Consensus 37 ~~c~~C~~~~~ 47 (126)
+.|..|+..|.
T Consensus 72 ~~C~~Cg~~~~ 82 (117)
T PRK00564 72 LECKDCSHVFK 82 (117)
T ss_pred EEhhhCCCccc
Confidence 44555654443
No 187
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=58.46 E-value=4.7 Score=18.60 Aligned_cols=10 Identities=20% Similarity=0.454 Sum_probs=6.9
Q ss_pred CccCcccccc
Q psy10762 92 PHKCTYCMKS 101 (126)
Q Consensus 92 ~~~C~~C~~~ 101 (126)
.+.|..||.+
T Consensus 37 R~~CGkCgyT 46 (51)
T COG1998 37 RWACGKCGYT 46 (51)
T ss_pred eeEeccccce
Confidence 5677777764
No 188
>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=58.41 E-value=5 Score=17.20 Aligned_cols=12 Identities=17% Similarity=0.581 Sum_probs=6.6
Q ss_pred cceecccccccc
Q psy10762 7 TPHRCDYCAKTF 18 (126)
Q Consensus 7 ~~~~C~~C~~~f 18 (126)
+-|+|..||...
T Consensus 5 ~~YkC~~CGniV 16 (36)
T PF06397_consen 5 EFYKCEHCGNIV 16 (36)
T ss_dssp EEEE-TTT--EE
T ss_pred cEEEccCCCCEE
Confidence 458899998864
No 189
>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=58.40 E-value=2.6 Score=24.32 Aligned_cols=32 Identities=19% Similarity=0.566 Sum_probs=19.3
Q ss_pred CcccCCCCCcCCChhhHHHHHHhhcCCCCccCcccccccC
Q psy10762 64 PFPCQYCPKAFTRKDHLVNHVRRHTGESPHKCTYCMKSFT 103 (126)
Q Consensus 64 ~~~C~~C~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~f~ 103 (126)
.|.|+.|+..+... .+. ....|.|..|+..+.
T Consensus 123 ~~~C~~C~~~~~r~------~~~--~~~~~~C~~C~~~l~ 154 (157)
T PF10263_consen 123 VYRCPSCGREYKRH------RRS--KRKRYRCGRCGGPLV 154 (157)
T ss_pred EEEcCCCCCEeeee------ccc--chhhEECCCCCCEEE
Confidence 46788888665332 222 234488888886653
No 190
>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=58.28 E-value=4.6 Score=17.85 Aligned_cols=15 Identities=40% Similarity=0.952 Sum_probs=9.7
Q ss_pred cceeccccccccCCh
Q psy10762 7 TPHRCDYCAKTFTRK 21 (126)
Q Consensus 7 ~~~~C~~C~~~f~~~ 21 (126)
.++.|..|+..|-..
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 578899999988765
No 191
>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=57.60 E-value=4.7 Score=22.15 Aligned_cols=11 Identities=27% Similarity=0.863 Sum_probs=4.9
Q ss_pred cccCCcccccC
Q psy10762 37 HHCNYCAKSFT 47 (126)
Q Consensus 37 ~~c~~C~~~~~ 47 (126)
+.|..|+..|.
T Consensus 71 ~~C~~Cg~~~~ 81 (113)
T PF01155_consen 71 ARCRDCGHEFE 81 (113)
T ss_dssp EEETTTS-EEE
T ss_pred EECCCCCCEEe
Confidence 34555555443
No 192
>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=55.86 E-value=3.4 Score=27.04 Aligned_cols=13 Identities=15% Similarity=0.516 Sum_probs=8.6
Q ss_pred CCccCcccccccC
Q psy10762 91 SPHKCTYCMKSFT 103 (126)
Q Consensus 91 ~~~~C~~C~~~f~ 103 (126)
+...|..|+.-.+
T Consensus 251 r~e~C~~C~~YlK 263 (305)
T TIGR01562 251 KAETCDSCQGYLK 263 (305)
T ss_pred EEeeccccccchh
Confidence 5567888875443
No 193
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=55.64 E-value=4.7 Score=22.22 Aligned_cols=11 Identities=27% Similarity=0.664 Sum_probs=5.9
Q ss_pred cccCCcccccC
Q psy10762 37 HHCNYCAKSFT 47 (126)
Q Consensus 37 ~~c~~C~~~~~ 47 (126)
+.|..|+..|.
T Consensus 71 ~~C~~Cg~~~~ 81 (114)
T PRK03681 71 CWCETCQQYVT 81 (114)
T ss_pred EEcccCCCeee
Confidence 45666665443
No 194
>PLN02294 cytochrome c oxidase subunit Vb
Probab=55.28 E-value=5.8 Score=23.55 Aligned_cols=16 Identities=19% Similarity=0.530 Sum_probs=13.0
Q ss_pred CCCCccCcccccccCC
Q psy10762 89 GESPHKCTYCMKSFTR 104 (126)
Q Consensus 89 ~~~~~~C~~C~~~f~~ 104 (126)
..++.+|++||..|.-
T Consensus 138 kGkp~RCpeCG~~fkL 153 (174)
T PLN02294 138 KGKSFECPVCTQYFEL 153 (174)
T ss_pred CCCceeCCCCCCEEEE
Confidence 3578899999999864
No 195
>KOG4167|consensus
Probab=54.98 E-value=3.3 Score=30.34 Aligned_cols=26 Identities=23% Similarity=0.455 Sum_probs=21.3
Q ss_pred CccCcccccccCCHHHHHHHHHHhhh
Q psy10762 92 PHKCTYCMKSFTRKEHLTNHIRQHTV 117 (126)
Q Consensus 92 ~~~C~~C~~~f~~~~~l~~H~~~h~~ 117 (126)
.|-|..|+|.|-.-..+..||+.|.-
T Consensus 792 iFpCreC~kvF~KiKSrNAHMK~Hr~ 817 (907)
T KOG4167|consen 792 IFPCRECGKVFFKIKSRNAHMKTHRQ 817 (907)
T ss_pred eeehHHHHHHHHHHhhhhHHHHHHHH
Confidence 48999999999877777888888763
No 196
>COG1327 Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains [Transcription]
Probab=54.39 E-value=3.4 Score=23.98 Aligned_cols=13 Identities=31% Similarity=0.513 Sum_probs=8.9
Q ss_pred cccCCCCCcCCCh
Q psy10762 65 FPCQYCPKAFTRK 77 (126)
Q Consensus 65 ~~C~~C~~~~~~~ 77 (126)
-.|+.|+..|.+.
T Consensus 29 ReC~~C~~RFTTf 41 (156)
T COG1327 29 RECLECGERFTTF 41 (156)
T ss_pred hcccccccccchh
Confidence 4677777777664
No 197
>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=54.33 E-value=6.1 Score=21.18 Aligned_cols=15 Identities=27% Similarity=0.702 Sum_probs=11.8
Q ss_pred CCCccCcccccccCC
Q psy10762 90 ESPHKCTYCMKSFTR 104 (126)
Q Consensus 90 ~~~~~C~~C~~~f~~ 104 (126)
.++++|..||..|.-
T Consensus 77 g~~~rC~eCG~~fkL 91 (97)
T cd00924 77 GKPKRCPECGHVFKL 91 (97)
T ss_pred CCceeCCCCCcEEEE
Confidence 378889999988863
No 198
>KOG0978|consensus
Probab=52.97 E-value=7.5 Score=28.52 Aligned_cols=17 Identities=24% Similarity=0.583 Sum_probs=11.1
Q ss_pred CCccCcccccccCCHHH
Q psy10762 91 SPHKCTYCMKSFTRKEH 107 (126)
Q Consensus 91 ~~~~C~~C~~~f~~~~~ 107 (126)
+.-+||.|+..|....-
T Consensus 677 RqRKCP~Cn~aFganDv 693 (698)
T KOG0978|consen 677 RQRKCPKCNAAFGANDV 693 (698)
T ss_pred hcCCCCCCCCCCCcccc
Confidence 44467777777776543
No 199
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=52.59 E-value=14 Score=17.54 Aligned_cols=8 Identities=38% Similarity=0.999 Sum_probs=4.1
Q ss_pred CcccCCCC
Q psy10762 64 PFPCQYCP 71 (126)
Q Consensus 64 ~~~C~~C~ 71 (126)
.|.|+.||
T Consensus 14 ~~~Cp~cG 21 (55)
T PF13824_consen 14 NFECPDCG 21 (55)
T ss_pred CCcCCCCC
Confidence 45555554
No 200
>KOG4124|consensus
Probab=52.02 E-value=1.4 Score=29.11 Aligned_cols=49 Identities=29% Similarity=0.677 Sum_probs=32.8
Q ss_pred CCcccCC--CCCcCCChhhHHHHHHh---------------hc----CCCCccCcccccccCCHHHHHHH
Q psy10762 63 TPFPCQY--CPKAFTRKDHLVNHVRR---------------HT----GESPHKCTYCMKSFTRKEHLTNH 111 (126)
Q Consensus 63 ~~~~C~~--C~~~~~~~~~l~~h~~~---------------~~----~~~~~~C~~C~~~f~~~~~l~~H 111 (126)
++|.|++ |.+.+.....+.-|... |+ -.|+|+|++|.++++....|.-|
T Consensus 348 ~~~~~~vp~~~~~~~n~ng~~~~~~~~h~s~i~~~s~~~~ph~~~~~~nk~~r~~i~~~~~k~~~~l~~~ 417 (442)
T KOG4124|consen 348 KPYKCPVPNCDKAYKNQNGLKYHKLHGHCSPITTPTPAPIPHQGFVVENKPYRCEVCSKRYKNLNGLKYH 417 (442)
T ss_pred CCCCCCCCcchhhcccCcceeeccccCcCCCCCCCCCCCCCcceeeeccCcccChhhhhhhccCCCCCce
Confidence 5678865 88888776655544422 11 25889999999998766555444
No 201
>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=52.01 E-value=12 Score=17.30 Aligned_cols=13 Identities=23% Similarity=0.708 Sum_probs=7.9
Q ss_pred CcccCCCCCcCCC
Q psy10762 64 PFPCQYCPKAFTR 76 (126)
Q Consensus 64 ~~~C~~C~~~~~~ 76 (126)
.+.|..||.+|-.
T Consensus 18 k~~Cr~Cg~~~C~ 30 (57)
T cd00065 18 RHHCRNCGRIFCS 30 (57)
T ss_pred ccccCcCcCCcCh
Confidence 3566667666654
No 202
>PRK12496 hypothetical protein; Provisional
Probab=51.71 E-value=13 Score=22.04 Aligned_cols=27 Identities=19% Similarity=0.460 Sum_probs=17.8
Q ss_pred cccCCCCCcCCChhhHHHHHHhhcCCCCccCcccccccC
Q psy10762 65 FPCQYCPKAFTRKDHLVNHVRRHTGESPHKCTYCMKSFT 103 (126)
Q Consensus 65 ~~C~~C~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~f~ 103 (126)
|.|+.|++.|..... .-.|++||....
T Consensus 128 ~~C~gC~~~~~~~~~------------~~~C~~CG~~~~ 154 (164)
T PRK12496 128 KVCKGCKKKYPEDYP------------DDVCEICGSPVK 154 (164)
T ss_pred EECCCCCccccCCCC------------CCcCCCCCChhh
Confidence 679999988854211 125999986543
No 203
>PF14311 DUF4379: Domain of unknown function (DUF4379)
Probab=51.58 E-value=13 Score=17.35 Aligned_cols=9 Identities=22% Similarity=0.840 Sum_probs=3.7
Q ss_pred cccCCCCCc
Q psy10762 65 FPCQYCPKA 73 (126)
Q Consensus 65 ~~C~~C~~~ 73 (126)
+.|+.|+..
T Consensus 29 W~C~~Cgh~ 37 (55)
T PF14311_consen 29 WKCPKCGHE 37 (55)
T ss_pred EECCCCCCe
Confidence 344444433
No 204
>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=51.46 E-value=6 Score=17.20 Aligned_cols=12 Identities=25% Similarity=0.786 Sum_probs=5.7
Q ss_pred CCCCccCccccc
Q psy10762 89 GESPHKCTYCMK 100 (126)
Q Consensus 89 ~~~~~~C~~C~~ 100 (126)
+.+.+.|..|+.
T Consensus 21 ~~~~w~C~~C~~ 32 (40)
T PF04810_consen 21 GGKTWICNFCGT 32 (40)
T ss_dssp TTTEEEETTT--
T ss_pred CCCEEECcCCCC
Confidence 345566666654
No 205
>KOG3002|consensus
Probab=50.74 E-value=25 Score=23.13 Aligned_cols=76 Identities=17% Similarity=0.356 Sum_probs=46.0
Q ss_pred CCcccCCcccccCCchHHHHHHhhhcCCCCcccC----CCCCcCCChhhHHHHHHhhcCCCCccCcc----cccccCCHH
Q psy10762 35 SPHHCNYCAKSFTRKDHMVYHERQHTGETPFPCQ----YCPKAFTRKDHLVNHVRRHTGESPHKCTY----CMKSFTRKE 106 (126)
Q Consensus 35 ~~~~c~~C~~~~~~~~~l~~h~~~~~~~~~~~C~----~C~~~~~~~~~l~~h~~~~~~~~~~~C~~----C~~~f~~~~ 106 (126)
..-.|+.|...+.....+..-.. .......|+ .|.+.|.+... ..|.+.... .+|.|+. |...- ...
T Consensus 79 ~~~~CP~Cr~~~g~~R~~amEkV--~e~~~vpC~~~~~GC~~~~~Y~~~-~~HE~~C~f-~~~~CP~p~~~C~~~G-~~~ 153 (299)
T KOG3002|consen 79 VSNKCPTCRLPIGNIRCRAMEKV--AEAVLVPCKNAKLGCTKSFPYGEK-SKHEKVCEF-RPCSCPVPGAECKYTG-SYK 153 (299)
T ss_pred hcccCCccccccccHHHHHHHHH--HHhceecccccccCCceeeccccc-ccccccccc-CCcCCCCCcccCCccC-cHH
Confidence 34568888777775544433322 333345666 38888877766 567777665 7788865 43333 344
Q ss_pred HHHHHHHHh
Q psy10762 107 HLTNHIRQH 115 (126)
Q Consensus 107 ~l~~H~~~h 115 (126)
.|..|.+.-
T Consensus 154 ~l~~H~~~~ 162 (299)
T KOG3002|consen 154 DLYAHLNDT 162 (299)
T ss_pred HHHHHHHhh
Confidence 777786553
No 206
>smart00731 SprT SprT homologues. Predicted to have roles in transcription elongation. Contains a conserved HExxH motif, indicating a metalloprotease function.
Probab=49.70 E-value=9.1 Score=21.97 Aligned_cols=33 Identities=24% Similarity=0.575 Sum_probs=18.7
Q ss_pred CcccCCCCCcCCChhhHHHHHHhhcCCCCccCcccccccC
Q psy10762 64 PFPCQYCPKAFTRKDHLVNHVRRHTGESPHKCTYCMKSFT 103 (126)
Q Consensus 64 ~~~C~~C~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~f~ 103 (126)
.|.|..|+..+.+. . .+.....|.|..|+..+.
T Consensus 112 ~y~C~~C~~~~~~~------r-r~~~~~~y~C~~C~g~l~ 144 (146)
T smart00731 112 PYRCTGCGQRYLRV------R-RSNNVSRYRCGKCGGKLI 144 (146)
T ss_pred EEECCCCCCCCceE------c-cccCcceEEcCCCCCEEE
Confidence 57787787665421 1 111125578888876653
No 207
>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=49.52 E-value=8.8 Score=18.70 Aligned_cols=27 Identities=22% Similarity=0.593 Sum_probs=9.8
Q ss_pred ccCCcccccCCchHHHHHHhhhcCCCCcccCCCCCcCCC
Q psy10762 38 HCNYCAKSFTRKDHMVYHERQHTGETPFPCQYCPKAFTR 76 (126)
Q Consensus 38 ~c~~C~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~~~~ 76 (126)
.|..|+..|.. ..+.+.|..||.+|-.
T Consensus 11 ~C~~C~~~F~~------------~~rrhhCr~CG~~vC~ 37 (69)
T PF01363_consen 11 NCMICGKKFSL------------FRRRHHCRNCGRVVCS 37 (69)
T ss_dssp B-TTT--B-BS------------SS-EEE-TTT--EEEC
T ss_pred cCcCcCCcCCC------------ceeeEccCCCCCEECC
Confidence 56667766632 1234566666665544
No 208
>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=49.45 E-value=20 Score=14.99 Aligned_cols=22 Identities=14% Similarity=0.525 Sum_probs=10.8
Q ss_pred cccCCCCCcCCChhhHHHHHHhh
Q psy10762 65 FPCQYCPKAFTRKDHLVNHVRRH 87 (126)
Q Consensus 65 ~~C~~C~~~~~~~~~l~~h~~~~ 87 (126)
+.|+.|++.+. .+.+..|+...
T Consensus 5 ~~C~nC~R~v~-a~RfA~HLekC 26 (33)
T PF08209_consen 5 VECPNCGRPVA-ASRFAPHLEKC 26 (33)
T ss_dssp EE-TTTSSEEE-GGGHHHHHHHH
T ss_pred EECCCCcCCcc-hhhhHHHHHHH
Confidence 45666665442 33455555543
No 209
>PLN03238 probable histone acetyltransferase MYST; Provisional
Probab=49.41 E-value=19 Score=23.45 Aligned_cols=27 Identities=26% Similarity=0.592 Sum_probs=20.4
Q ss_pred CCCccCcccccccCCHHHHHHHHHHhh
Q psy10762 90 ESPHKCTYCMKSFTRKEHLTNHIRQHT 116 (126)
Q Consensus 90 ~~~~~C~~C~~~f~~~~~l~~H~~~h~ 116 (126)
...|.|..|-+-|.+...|.+|+..-.
T Consensus 46 ~~lyiCe~Clky~~~~~~l~~H~~~C~ 72 (290)
T PLN03238 46 TKLYICEYCLKYMRKKKSLLRHLAKCD 72 (290)
T ss_pred CeEEEcCCCcchhCCHHHHHHHHHhCC
Confidence 456888888888888888888876543
No 210
>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=49.33 E-value=1.9 Score=23.18 Aligned_cols=40 Identities=18% Similarity=0.189 Sum_probs=19.8
Q ss_pred cccCCCCCcCCChhhHHHHHHhhcCCCCccCcccccccCC
Q psy10762 65 FPCQYCPKAFTRKDHLVNHVRRHTGESPHKCTYCMKSFTR 104 (126)
Q Consensus 65 ~~C~~C~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~f~~ 104 (126)
..|+.||..-.....++..-.-......|.|..|+..+..
T Consensus 63 ~~Cp~Cg~~~a~f~~~Q~RsadE~~T~fy~C~~C~~~w~~ 102 (104)
T TIGR01384 63 VECPKCGHKEAYYWLLQTRRADEPETRFYKCTKCGYVWRE 102 (104)
T ss_pred CCCCCCCCCeeEEEEeccCCCCCCcEEEEEeCCCCCeeEe
Confidence 5788887432221111110011112244899989887653
No 211
>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 KOG3507|consensus
Probab=48.59 E-value=9.9 Score=18.24 Aligned_cols=12 Identities=17% Similarity=0.421 Sum_probs=6.9
Q ss_pred CcccCCcccccC
Q psy10762 36 PHHCNYCAKSFT 47 (126)
Q Consensus 36 ~~~c~~C~~~~~ 47 (126)
++.|..||....
T Consensus 37 ~irCReCG~RIl 48 (62)
T KOG3507|consen 37 VIRCRECGYRIL 48 (62)
T ss_pred cEehhhcchHHH
Confidence 456666665443
No 213
>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=48.30 E-value=8 Score=17.90 Aligned_cols=12 Identities=17% Similarity=0.498 Sum_probs=8.4
Q ss_pred ccCcccccccCC
Q psy10762 93 HKCTYCMKSFTR 104 (126)
Q Consensus 93 ~~C~~C~~~f~~ 104 (126)
|+|.+||..+..
T Consensus 2 y~C~~CgyiYd~ 13 (50)
T cd00730 2 YECRICGYIYDP 13 (50)
T ss_pred cCCCCCCeEECC
Confidence 677788777653
No 214
>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=47.57 E-value=16 Score=25.62 Aligned_cols=25 Identities=24% Similarity=0.460 Sum_probs=21.4
Q ss_pred CcccCCcccccCCchHHHHHHhhhc
Q psy10762 36 PHHCNYCAKSFTRKDHMVYHERQHT 60 (126)
Q Consensus 36 ~~~c~~C~~~~~~~~~l~~h~~~~~ 60 (126)
.|.|+.|.+.|.+...+..|+...+
T Consensus 57 FWiCp~CskkF~d~~~~~~H~~~eH 81 (466)
T PF04780_consen 57 FWICPRCSKKFSDAESCLSHMEQEH 81 (466)
T ss_pred EeeCCcccceeCCHHHHHHHHHHhh
Confidence 4789999999999999999987443
No 215
>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=47.34 E-value=3.5 Score=30.14 Aligned_cols=79 Identities=23% Similarity=0.495 Sum_probs=36.8
Q ss_pred eeccccccccCChhHHHHHHHhhcCCCCcccCCcccccCCchHHHHHHhhhcCCCCc-ccCCCCCcCCChhhHHHHHHhh
Q psy10762 9 HRCDYCAKTFTRKEHLVNHVRQHTGESPHHCNYCAKSFTRKDHMVYHERQHTGETPF-PCQYCPKAFTRKDHLVNHVRRH 87 (126)
Q Consensus 9 ~~C~~C~~~f~~~~~l~~h~~~h~~~~~~~c~~C~~~~~~~~~l~~h~~~~~~~~~~-~C~~C~~~~~~~~~l~~h~~~~ 87 (126)
..|++|-+.+....+-.-+ - ....|..||..|.-...|--- +.++.-..| .|+.|.+.|..... .+-|
T Consensus 102 a~C~~Cl~Ei~dp~~rrY~----Y--PF~~CT~CGPRfTIi~alPYD-R~nTsM~~F~lC~~C~~EY~dP~n----RRfH 170 (750)
T COG0068 102 ATCEDCLEEIFDPNSRRYL----Y--PFINCTNCGPRFTIIEALPYD-RENTSMADFPLCPFCDKEYKDPLN----RRFH 170 (750)
T ss_pred hhhHHHHHHhcCCCCccee----c--cccccCCCCcceeeeccCCCC-cccCccccCcCCHHHHHHhcCccc----cccc
Confidence 4577777666555431111 0 123477777776544332100 111111122 46666666655533 2223
Q ss_pred cCCCCccCccccc
Q psy10762 88 TGESPHKCTYCMK 100 (126)
Q Consensus 88 ~~~~~~~C~~C~~ 100 (126)
..+..|+.||-
T Consensus 171 --AQp~aCp~CGP 181 (750)
T COG0068 171 --AQPIACPKCGP 181 (750)
T ss_pred --cccccCcccCC
Confidence 24556777764
No 216
>KOG4727|consensus
Probab=46.67 E-value=12 Score=22.25 Aligned_cols=23 Identities=17% Similarity=0.446 Sum_probs=20.4
Q ss_pred cceeccccccccCChhHHHHHHH
Q psy10762 7 TPHRCDYCAKTFTRKEHLVNHVR 29 (126)
Q Consensus 7 ~~~~C~~C~~~f~~~~~l~~h~~ 29 (126)
..|-|.+|.-++...-++..|+.
T Consensus 74 ~GyyCdVCdcvvKDSinflDHiN 96 (193)
T KOG4727|consen 74 GGYYCDVCDCVVKDSINFLDHIN 96 (193)
T ss_pred CceeeeecceeehhhHHHHHHhc
Confidence 34889999999999999999985
No 217
>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=45.75 E-value=4 Score=19.03 Aligned_cols=14 Identities=21% Similarity=0.667 Sum_probs=4.6
Q ss_pred CcccCCCCCcCCCh
Q psy10762 64 PFPCQYCPKAFTRK 77 (126)
Q Consensus 64 ~~~C~~C~~~~~~~ 77 (126)
.|.|+.|...|--.
T Consensus 21 ~y~C~~C~~~FC~d 34 (51)
T PF07975_consen 21 RYRCPKCKNHFCID 34 (51)
T ss_dssp EE--TTTT--B-HH
T ss_pred eEECCCCCCccccC
Confidence 35555555555443
No 218
>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=45.75 E-value=6.9 Score=24.37 Aligned_cols=26 Identities=15% Similarity=0.248 Sum_probs=0.0
Q ss_pred CCCccCcccccccCCHHHHHHHHHHhh
Q psy10762 90 ESPHKCTYCMKSFTRKEHLTNHIRQHT 116 (126)
Q Consensus 90 ~~~~~C~~C~~~f~~~~~l~~H~~~h~ 116 (126)
.....|++||....-. .|..|+|+..
T Consensus 166 ~~~~~cPitGe~IP~~-e~~eHmRi~L 191 (229)
T PF12230_consen 166 EKMIICPITGEMIPAD-EMDEHMRIEL 191 (229)
T ss_dssp ---------------------------
T ss_pred cccccccccccccccc-cccccccccc
Confidence 3457899999988765 7899998854
No 219
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=45.63 E-value=8.8 Score=21.50 Aligned_cols=7 Identities=29% Similarity=0.980 Sum_probs=4.0
Q ss_pred cccCCCC
Q psy10762 65 FPCQYCP 71 (126)
Q Consensus 65 ~~C~~C~ 71 (126)
+.||.|+
T Consensus 93 ~~CP~Cg 99 (124)
T PRK00762 93 IECPVCG 99 (124)
T ss_pred CcCcCCC
Confidence 3566665
No 220
>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=45.42 E-value=11 Score=17.25 Aligned_cols=12 Identities=17% Similarity=0.642 Sum_probs=6.7
Q ss_pred eeccccccccCC
Q psy10762 9 HRCDYCAKTFTR 20 (126)
Q Consensus 9 ~~C~~C~~~f~~ 20 (126)
|.|..|+..+--
T Consensus 2 y~C~~CgyvYd~ 13 (47)
T PF00301_consen 2 YQCPVCGYVYDP 13 (47)
T ss_dssp EEETTTSBEEET
T ss_pred cCCCCCCEEEcC
Confidence 556666655533
No 221
>PRK05978 hypothetical protein; Provisional
Probab=45.22 E-value=16 Score=21.29 Aligned_cols=10 Identities=40% Similarity=0.989 Sum_probs=6.2
Q ss_pred cCcccccccC
Q psy10762 94 KCTYCMKSFT 103 (126)
Q Consensus 94 ~C~~C~~~f~ 103 (126)
.|+.||..|.
T Consensus 54 ~C~~CG~~~~ 63 (148)
T PRK05978 54 HCAACGEDFT 63 (148)
T ss_pred CccccCCccc
Confidence 4777766654
No 222
>KOG3214|consensus
Probab=43.83 E-value=5.9 Score=21.24 Aligned_cols=11 Identities=36% Similarity=0.921 Sum_probs=6.1
Q ss_pred cCcccccccCC
Q psy10762 94 KCTYCMKSFTR 104 (126)
Q Consensus 94 ~C~~C~~~f~~ 104 (126)
.|.+|+.+|..
T Consensus 49 sC~iC~esFqt 59 (109)
T KOG3214|consen 49 SCRICEESFQT 59 (109)
T ss_pred eeeehhhhhcc
Confidence 45556555543
No 223
>TIGR00319 desulf_FeS4 desulfoferrodoxin FeS4 iron-binding domain. Neelaredoxin, a monomeric blue non-heme iron protein, lacks this domain.
Probab=43.52 E-value=13 Score=15.33 Aligned_cols=12 Identities=17% Similarity=0.670 Sum_probs=9.4
Q ss_pred cceecccccccc
Q psy10762 7 TPHRCDYCAKTF 18 (126)
Q Consensus 7 ~~~~C~~C~~~f 18 (126)
+-|+|..|+...
T Consensus 6 ~~ykC~~Cgniv 17 (34)
T TIGR00319 6 QVYKCEVCGNIV 17 (34)
T ss_pred cEEEcCCCCcEE
Confidence 468899998875
No 224
>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=43.26 E-value=30 Score=18.27 Aligned_cols=15 Identities=13% Similarity=0.543 Sum_probs=8.3
Q ss_pred cccCCCCCcCCChhh
Q psy10762 65 FPCQYCPKAFTRKDH 79 (126)
Q Consensus 65 ~~C~~C~~~~~~~~~ 79 (126)
..|+.||..|.....
T Consensus 36 ~~C~~CGe~y~~dev 50 (89)
T TIGR03829 36 ISCSHCGMEYQDDTT 50 (89)
T ss_pred ccccCCCcEeecHHH
Confidence 356666666655443
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=43.20 E-value=56 Score=17.74 Aligned_cols=39 Identities=13% Similarity=0.164 Sum_probs=19.7
Q ss_pred ceeccccccccCChhHHHHHHHhhcCCCCcccCCcccccC
Q psy10762 8 PHRCDYCAKTFTRKEHLVNHVRQHTGESPHHCNYCAKSFT 47 (126)
Q Consensus 8 ~~~C~~C~~~f~~~~~l~~h~~~h~~~~~~~c~~C~~~~~ 47 (126)
.|.|+.-+..|.+...+..-+.... .+.|.|...|+.-.
T Consensus 3 Vf~i~~T~EiF~dYe~Y~~R~~~y~-~~vwtC~~TGk~~L 41 (102)
T PF10537_consen 3 VFYIPFTGEIFRDYEEYLKRMILYN-QRVWTCEITGKSNL 41 (102)
T ss_pred eEEeCCCCcccCCHHHHHHHHHHHh-CCeeEEecCCCCCC
Confidence 3455555556665555555544332 23455555554433
No 226
>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=43.00 E-value=11 Score=17.37 Aligned_cols=8 Identities=50% Similarity=1.074 Sum_probs=2.5
Q ss_pred ccCccccc
Q psy10762 93 HKCTYCMK 100 (126)
Q Consensus 93 ~~C~~C~~ 100 (126)
|.|++|++
T Consensus 42 W~CPiC~~ 49 (50)
T PF02891_consen 42 WKCPICNK 49 (50)
T ss_dssp -B-TTT--
T ss_pred eECcCCcC
Confidence 66666653
No 227
>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=42.96 E-value=14 Score=15.32 Aligned_cols=12 Identities=17% Similarity=0.678 Sum_probs=8.8
Q ss_pred cceecccccccc
Q psy10762 7 TPHRCDYCAKTF 18 (126)
Q Consensus 7 ~~~~C~~C~~~f 18 (126)
+-|+|..|+...
T Consensus 3 ~~ykC~~CGniv 14 (34)
T cd00974 3 EVYKCEICGNIV 14 (34)
T ss_pred cEEEcCCCCcEE
Confidence 357888888765
No 228
>COG5216 Uncharacterized conserved protein [Function unknown]
Probab=42.54 E-value=15 Score=17.63 Aligned_cols=10 Identities=40% Similarity=0.869 Sum_probs=4.5
Q ss_pred CCCCcccCCC
Q psy10762 61 GETPFPCQYC 70 (126)
Q Consensus 61 ~~~~~~C~~C 70 (126)
|++.-.||.|
T Consensus 41 GE~VArCPSC 50 (67)
T COG5216 41 GEVVARCPSC 50 (67)
T ss_pred CceEEEcCCc
Confidence 4444444444
No 229
>PF15616 TerY-C: TerY-C metal binding domain
Probab=42.48 E-value=3.4 Score=23.41 Aligned_cols=14 Identities=29% Similarity=0.707 Sum_probs=9.1
Q ss_pred CCCCcccCCCCCcC
Q psy10762 61 GETPFPCQYCPKAF 74 (126)
Q Consensus 61 ~~~~~~C~~C~~~~ 74 (126)
++....||.|++.-
T Consensus 102 g~~~~~CPwCg~~g 115 (131)
T PF15616_consen 102 GEGEVTCPWCGNEG 115 (131)
T ss_pred CCCCEECCCCCCee
Confidence 34456888888643
No 230
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=41.77 E-value=24 Score=23.34 Aligned_cols=27 Identities=19% Similarity=0.352 Sum_probs=20.3
Q ss_pred CCCccCcccccccCCHHHHHHHHHHhh
Q psy10762 90 ESPHKCTYCMKSFTRKEHLTNHIRQHT 116 (126)
Q Consensus 90 ~~~~~C~~C~~~f~~~~~l~~H~~~h~ 116 (126)
...|.|+.|...|-..-+.-.|...|.
T Consensus 386 s~rY~Ce~CK~~FC~dCdvfiHe~Lh~ 412 (421)
T COG5151 386 SGRYQCELCKSTFCSDCDVFIHETLHF 412 (421)
T ss_pred ccceechhhhhhhhhhhHHHHHHHHhh
Confidence 456899999888887777777766554
No 231
>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=41.60 E-value=12 Score=20.30 Aligned_cols=10 Identities=40% Similarity=1.095 Sum_probs=5.2
Q ss_pred CcccCCcccc
Q psy10762 36 PHHCNYCAKS 45 (126)
Q Consensus 36 ~~~c~~C~~~ 45 (126)
|..|+-||..
T Consensus 2 p~~CpYCg~~ 11 (102)
T PF11672_consen 2 PIICPYCGGP 11 (102)
T ss_pred CcccCCCCCe
Confidence 3456666543
No 232
>PRK11823 DNA repair protein RadA; Provisional
Probab=41.47 E-value=18 Score=25.13 Aligned_cols=24 Identities=21% Similarity=0.477 Sum_probs=16.3
Q ss_pred CcceeccccccccCChhHHHHHHHhhcCCCCcccCCcc
Q psy10762 6 ETPHRCDYCAKTFTRKEHLVNHVRQHTGESPHHCNYCA 43 (126)
Q Consensus 6 ~~~~~C~~C~~~f~~~~~l~~h~~~h~~~~~~~c~~C~ 43 (126)
+..|.|..||...... .++|+.|+
T Consensus 5 ~~~y~C~~Cg~~~~~~--------------~g~Cp~C~ 28 (446)
T PRK11823 5 KTAYVCQECGAESPKW--------------LGRCPECG 28 (446)
T ss_pred CCeEECCcCCCCCccc--------------CeeCcCCC
Confidence 4568999999765332 26788885
No 233
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=41.18 E-value=30 Score=16.14 Aligned_cols=7 Identities=29% Similarity=0.766 Sum_probs=3.1
Q ss_pred cccCCCC
Q psy10762 65 FPCQYCP 71 (126)
Q Consensus 65 ~~C~~C~ 71 (126)
..|+.|+
T Consensus 47 ~~Cp~Cg 53 (56)
T PF02591_consen 47 VFCPNCG 53 (56)
T ss_pred EECcCCC
Confidence 3444444
No 234
>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=40.69 E-value=9.1 Score=23.38 Aligned_cols=23 Identities=22% Similarity=0.465 Sum_probs=0.0
Q ss_pred CCCCccCccccc-ccCCHHHHHHH
Q psy10762 89 GESPHKCTYCMK-SFTRKEHLTNH 111 (126)
Q Consensus 89 ~~~~~~C~~C~~-~f~~~~~l~~H 111 (126)
-...|.|.+||. +|.-+..+.+|
T Consensus 98 L~~ey~CEICGN~~Y~GrkaFekH 121 (196)
T PF11931_consen 98 LGVEYKCEICGNQSYKGRKAFEKH 121 (196)
T ss_dssp ------------------------
T ss_pred CCCeeeeEeCCCcceecHHHHHHh
Confidence 344455555543 23334444444
No 235
>PF14787 zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB: 1CL4_A 1DSV_A.
Probab=40.61 E-value=13 Score=15.90 Aligned_cols=14 Identities=29% Similarity=0.586 Sum_probs=8.6
Q ss_pred cCcccccccCCHHH
Q psy10762 94 KCTYCMKSFTRKEH 107 (126)
Q Consensus 94 ~C~~C~~~f~~~~~ 107 (126)
.|+.|++.|...+.
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 58888888876543
No 236
>PRK00420 hypothetical protein; Validated
Probab=40.27 E-value=18 Score=19.96 Aligned_cols=10 Identities=20% Similarity=0.468 Sum_probs=5.1
Q ss_pred cccCCCCCcC
Q psy10762 65 FPCQYCPKAF 74 (126)
Q Consensus 65 ~~C~~C~~~~ 74 (126)
..||.|+...
T Consensus 41 ~~Cp~Cg~~~ 50 (112)
T PRK00420 41 VVCPVHGKVY 50 (112)
T ss_pred eECCCCCCee
Confidence 3555555433
No 237
>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=39.90 E-value=14 Score=15.57 Aligned_cols=13 Identities=38% Similarity=0.938 Sum_probs=5.8
Q ss_pred eeccccccccCCh
Q psy10762 9 HRCDYCAKTFTRK 21 (126)
Q Consensus 9 ~~C~~C~~~f~~~ 21 (126)
-.|.+|++.|...
T Consensus 4 ~~C~eC~~~f~dS 16 (34)
T PF01286_consen 4 PKCDECGKPFMDS 16 (34)
T ss_dssp EE-TTT--EES-S
T ss_pred chHhHhCCHHHHH
Confidence 3577777777554
No 238
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=39.75 E-value=32 Score=15.05 Aligned_cols=7 Identities=29% Similarity=0.985 Sum_probs=3.2
Q ss_pred cccCCCC
Q psy10762 65 FPCQYCP 71 (126)
Q Consensus 65 ~~C~~C~ 71 (126)
..||.|+
T Consensus 37 ~~CP~C~ 43 (44)
T PF14634_consen 37 VKCPICR 43 (44)
T ss_pred CCCcCCC
Confidence 3455443
No 239
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=39.53 E-value=16 Score=23.75 Aligned_cols=14 Identities=21% Similarity=0.315 Sum_probs=9.0
Q ss_pred CCCccCcccccccC
Q psy10762 90 ESPHKCTYCMKSFT 103 (126)
Q Consensus 90 ~~~~~C~~C~~~f~ 103 (126)
.+.|.|+.||..+.
T Consensus 320 ~r~~~C~~cg~~~~ 333 (364)
T COG0675 320 GRLFKCPRCGFVHD 333 (364)
T ss_pred ceeEECCCCCCeeh
Confidence 35567777776654
No 240
>PF11781 RRN7: RNA polymerase I-specific transcription initiation factor Rrn7; InterPro: IPR021752 Rrn7 is a transcription binding factor that associates strongly with both Rrn6 and Rrn11 to form a complex which itself binds the TATA-binding protein and is required for transcription by the core domain of the RNA PolI promoter [],[].
Probab=39.07 E-value=14 Score=15.71 Aligned_cols=9 Identities=22% Similarity=0.781 Sum_probs=4.6
Q ss_pred eeccccccc
Q psy10762 9 HRCDYCAKT 17 (126)
Q Consensus 9 ~~C~~C~~~ 17 (126)
..|.+|+..
T Consensus 9 ~~C~~C~~~ 17 (36)
T PF11781_consen 9 EPCPVCGSR 17 (36)
T ss_pred CcCCCCCCe
Confidence 345555554
No 241
>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=38.90 E-value=21 Score=24.87 Aligned_cols=12 Identities=17% Similarity=0.495 Sum_probs=8.6
Q ss_pred cceecccccccc
Q psy10762 7 TPHRCDYCAKTF 18 (126)
Q Consensus 7 ~~~~C~~C~~~f 18 (126)
..|.|..||...
T Consensus 6 ~~y~C~~Cg~~~ 17 (454)
T TIGR00416 6 SKFVCQHCGADS 17 (454)
T ss_pred CeEECCcCCCCC
Confidence 458888888654
No 242
>KOG0317|consensus
Probab=38.88 E-value=16 Score=23.72 Aligned_cols=32 Identities=22% Similarity=0.475 Sum_probs=15.1
Q ss_pred ccCCCCCcCCChhhHHHHHHhhcCCCCccCcccccccC
Q psy10762 66 PCQYCPKAFTRKDHLVNHVRRHTGESPHKCTYCMKSFT 103 (126)
Q Consensus 66 ~C~~C~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~f~ 103 (126)
.|-.||..|.++-.+ .+.++++ .|+.|...|.
T Consensus 253 SaTpCGHiFCWsCI~-----~w~~ek~-eCPlCR~~~~ 284 (293)
T KOG0317|consen 253 SATPCGHIFCWSCIL-----EWCSEKA-ECPLCREKFQ 284 (293)
T ss_pred CcCcCcchHHHHHHH-----HHHcccc-CCCcccccCC
Confidence 344466666554222 2223333 2666665554
No 243
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=38.78 E-value=11 Score=20.37 Aligned_cols=8 Identities=25% Similarity=0.771 Sum_probs=4.6
Q ss_pred CcccCCcc
Q psy10762 36 PHHCNYCA 43 (126)
Q Consensus 36 ~~~c~~C~ 43 (126)
.|.|+.|+
T Consensus 21 ~f~CP~Cg 28 (99)
T PRK14892 21 IFECPRCG 28 (99)
T ss_pred EeECCCCC
Confidence 35566665
No 244
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=38.68 E-value=14 Score=15.44 Aligned_cols=11 Identities=36% Similarity=0.972 Sum_probs=6.4
Q ss_pred ccCcccccccC
Q psy10762 93 HKCTYCMKSFT 103 (126)
Q Consensus 93 ~~C~~C~~~f~ 103 (126)
+.|..|+.+|.
T Consensus 22 ~~C~~Cg~~~~ 32 (33)
T PF08792_consen 22 EVCIFCGSSFP 32 (33)
T ss_pred EEcccCCcEee
Confidence 45666666553
No 245
>PF06676 DUF1178: Protein of unknown function (DUF1178); InterPro: IPR009562 This family consists of several hypothetical bacterial proteins of around 150 residues in length. The function of this family is unknown.
Probab=38.54 E-value=24 Score=20.59 Aligned_cols=30 Identities=13% Similarity=0.214 Sum_probs=15.8
Q ss_pred ccCChhHHHHHHHhhcCCCCcccCCcccccCCch
Q psy10762 17 TFTRKEHLVNHVRQHTGESPHHCNYCAKSFTRKD 50 (126)
Q Consensus 17 ~f~~~~~l~~h~~~h~~~~~~~c~~C~~~~~~~~ 50 (126)
+|.+...+..... .....|+.||..-..+.
T Consensus 17 WF~ss~~fd~Q~~----~glv~CP~Cgs~~V~K~ 46 (148)
T PF06676_consen 17 WFRSSAAFDRQQA----RGLVSCPVCGSTEVSKA 46 (148)
T ss_pred ecCCHHHHHHHHH----cCCccCCCCCCCeEeee
Confidence 4555555554432 23466777776544443
No 246
>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=38.03 E-value=13 Score=16.17 Aligned_cols=12 Identities=17% Similarity=0.606 Sum_probs=8.5
Q ss_pred eeccccccccCC
Q psy10762 9 HRCDYCAKTFTR 20 (126)
Q Consensus 9 ~~C~~C~~~f~~ 20 (126)
+.|+.||..+.+
T Consensus 33 ~~C~~CGE~~~~ 44 (46)
T TIGR03831 33 LVCPQCGEEYLD 44 (46)
T ss_pred cccccCCCEeeC
Confidence 568888877654
No 247
>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=37.75 E-value=22 Score=23.21 Aligned_cols=11 Identities=18% Similarity=0.471 Sum_probs=5.8
Q ss_pred cccCCCCCcCC
Q psy10762 65 FPCQYCPKAFT 75 (126)
Q Consensus 65 ~~C~~C~~~~~ 75 (126)
+.|+.|+.-|.
T Consensus 46 ~vc~~c~~h~r 56 (285)
T TIGR00515 46 EVCPKCDHHMR 56 (285)
T ss_pred CCCCCCCCcCc
Confidence 35666655443
No 248
>KOG1994|consensus
Probab=37.65 E-value=24 Score=22.18 Aligned_cols=26 Identities=19% Similarity=0.399 Sum_probs=20.7
Q ss_pred hcCCCCccCcccccccCCHHHHHHHH
Q psy10762 87 HTGESPHKCTYCMKSFTRKEHLTNHI 112 (126)
Q Consensus 87 ~~~~~~~~C~~C~~~f~~~~~l~~H~ 112 (126)
......|-|-.||..|....+|..|-
T Consensus 234 ~LR~eh~YC~fCG~~y~~~edl~ehC 259 (268)
T KOG1994|consen 234 FLRSEHYYCFFCGIKYKDEEDLYEHC 259 (268)
T ss_pred HHhccceEEEEeccccCCHHHHHHhC
Confidence 34456688999999999998988873
No 249
>PTZ00043 cytochrome c oxidase subunit; Provisional
Probab=37.64 E-value=16 Score=22.93 Aligned_cols=17 Identities=24% Similarity=0.391 Sum_probs=13.0
Q ss_pred CCcceeccccccccCCh
Q psy10762 5 GETPHRCDYCAKTFTRK 21 (126)
Q Consensus 5 ~~~~~~C~~C~~~f~~~ 21 (126)
.+++.+|.+||..|.-.
T Consensus 178 EGkpqRCpECGqVFKLV 194 (268)
T PTZ00043 178 EGFLYRCGECDQIFMLV 194 (268)
T ss_pred CCCCccCCCCCcEEEEE
Confidence 35688899999988654
No 250
>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=37.41 E-value=6.4 Score=25.74 Aligned_cols=38 Identities=18% Similarity=0.336 Sum_probs=19.6
Q ss_pred CcccCCCCCcCCChhhHHHHHHh--hcCCCCccCcccccccC
Q psy10762 64 PFPCQYCPKAFTRKDHLVNHVRR--HTGESPHKCTYCMKSFT 103 (126)
Q Consensus 64 ~~~C~~C~~~~~~~~~l~~h~~~--~~~~~~~~C~~C~~~f~ 103 (126)
.+.|+.|+..=.....++ .+. ......|.|..||..|.
T Consensus 258 ~~~C~~C~~~~~~~~q~Q--trsaDEpmT~f~~C~~Cg~~w~ 297 (299)
T TIGR01385 258 LFTCGKCKQKKCTYYQLQ--TRSADEPMTTFVTCEECGNRWK 297 (299)
T ss_pred cccCCCCCCccceEEEec--ccCCCCCCeEEEEcCCCCCeee
Confidence 478999974322211211 111 11123478999997754
No 251
>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=37.32 E-value=3.9 Score=17.37 Aligned_cols=10 Identities=20% Similarity=0.816 Sum_probs=3.9
Q ss_pred cccCCccccc
Q psy10762 37 HHCNYCAKSF 46 (126)
Q Consensus 37 ~~c~~C~~~~ 46 (126)
..|..||..+
T Consensus 22 isC~~CGPr~ 31 (35)
T PF07503_consen 22 ISCTNCGPRY 31 (35)
T ss_dssp --BTTCC-SC
T ss_pred ccCCCCCCCE
Confidence 4466666443
No 252
>COG5112 UFD2 U1-like Zn-finger-containing protein [General function prediction only]
Probab=37.31 E-value=19 Score=19.66 Aligned_cols=24 Identities=25% Similarity=0.578 Sum_probs=18.1
Q ss_pred CCccCcccccccCCHHHHHHHHHH
Q psy10762 91 SPHKCTYCMKSFTRKEHLTNHIRQ 114 (126)
Q Consensus 91 ~~~~C~~C~~~f~~~~~l~~H~~~ 114 (126)
..+-|-.|.+-|.....|..|.+.
T Consensus 54 GqhYCieCaryf~t~~aL~~Hkkg 77 (126)
T COG5112 54 GQHYCIECARYFITEKALMEHKKG 77 (126)
T ss_pred ceeeeehhHHHHHHHHHHHHHhcc
Confidence 345677888888888888888654
No 253
>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=36.92 E-value=21 Score=24.21 Aligned_cols=11 Identities=18% Similarity=0.374 Sum_probs=7.5
Q ss_pred eeccccccccC
Q psy10762 9 HRCDYCAKTFT 19 (126)
Q Consensus 9 ~~C~~C~~~f~ 19 (126)
|.|..||....
T Consensus 1 ~~c~~cg~~~~ 11 (372)
T cd01121 1 YVCSECGYVSP 11 (372)
T ss_pred CCCCCCCCCCC
Confidence 56888886543
No 254
>KOG1842|consensus
Probab=36.83 E-value=24 Score=24.63 Aligned_cols=26 Identities=15% Similarity=0.310 Sum_probs=22.5
Q ss_pred cceeccccccccCChhHHHHHHHhhc
Q psy10762 7 TPHRCDYCAKTFTRKEHLVNHVRQHT 32 (126)
Q Consensus 7 ~~~~C~~C~~~f~~~~~l~~h~~~h~ 32 (126)
..|.|+.|...|.....|..|...-+
T Consensus 14 egflCPiC~~dl~~~~~L~~H~d~eH 39 (505)
T KOG1842|consen 14 EGFLCPICLLDLPNLSALNDHLDVEH 39 (505)
T ss_pred hcccCchHhhhhhhHHHHHHHHhhhc
Confidence 45999999999999999999987543
No 255
>KOG0717|consensus
Probab=36.74 E-value=22 Score=24.93 Aligned_cols=22 Identities=32% Similarity=0.649 Sum_probs=19.3
Q ss_pred cccCCCCCcCCChhhHHHHHHh
Q psy10762 65 FPCQYCPKAFTRKDHLVNHVRR 86 (126)
Q Consensus 65 ~~C~~C~~~~~~~~~l~~h~~~ 86 (126)
+-|+.|.+.|.+..++..|...
T Consensus 293 lyC~vCnKsFKseKq~kNHEnS 314 (508)
T KOG0717|consen 293 LYCVVCNKSFKSEKQLKNHENS 314 (508)
T ss_pred eEEeeccccccchHHHHhhHHH
Confidence 6899999999999998888764
No 256
>PLN00104 MYST -like histone acetyltransferase; Provisional
Probab=36.60 E-value=28 Score=24.37 Aligned_cols=27 Identities=30% Similarity=0.664 Sum_probs=23.0
Q ss_pred CCCccCcccccccCCHHHHHHHHHHhh
Q psy10762 90 ESPHKCTYCMKSFTRKEHLTNHIRQHT 116 (126)
Q Consensus 90 ~~~~~C~~C~~~f~~~~~l~~H~~~h~ 116 (126)
...|.|..|-+-|.+...|.+|+..-.
T Consensus 196 ~~lyiCe~Cl~y~~~~~~~~~H~~~C~ 222 (450)
T PLN00104 196 SKLYFCEFCLKFMKRKEQLQRHMKKCD 222 (450)
T ss_pred CeEEEchhhhhhhcCHHHHHHHHhcCC
Confidence 456999999999999999999986544
No 257
>KOG2272|consensus
Probab=35.75 E-value=12 Score=23.85 Aligned_cols=16 Identities=19% Similarity=0.606 Sum_probs=8.4
Q ss_pred CcccCCcccccCCchH
Q psy10762 36 PHHCNYCAKSFTRKDH 51 (126)
Q Consensus 36 ~~~c~~C~~~~~~~~~ 51 (126)
-|.|++|.+...+...
T Consensus 99 CF~Cd~Cn~~Lad~gf 114 (332)
T KOG2272|consen 99 CFRCDLCNKHLADQGF 114 (332)
T ss_pred cchhHHHHHHHhhhhh
Confidence 4566666655444433
No 258
>PLN03239 histone acetyltransferase; Provisional
Probab=35.68 E-value=30 Score=23.30 Aligned_cols=25 Identities=20% Similarity=0.372 Sum_probs=21.6
Q ss_pred CCCccCcccccccCCHHHHHHHHHH
Q psy10762 90 ESPHKCTYCMKSFTRKEHLTNHIRQ 114 (126)
Q Consensus 90 ~~~~~C~~C~~~f~~~~~l~~H~~~ 114 (126)
...|.|..|-+-|.+...|.+|+..
T Consensus 104 ~~lYiCE~Clky~~~~~~l~~H~~~ 128 (351)
T PLN03239 104 DVLYVCEFSFGFFARKSELLRFQAK 128 (351)
T ss_pred ceEEEeccchhhhcCHHHHHHHHHh
Confidence 4679999999999999999999653
No 259
>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=35.63 E-value=6.3 Score=16.25 Aligned_cols=10 Identities=40% Similarity=0.919 Sum_probs=4.9
Q ss_pred ccCccccccc
Q psy10762 93 HKCTYCMKSF 102 (126)
Q Consensus 93 ~~C~~C~~~f 102 (126)
|.|..|+..+
T Consensus 28 f~C~~C~~~L 37 (39)
T smart00132 28 FKCSKCGKPL 37 (39)
T ss_pred CCCcccCCcC
Confidence 4455555443
No 260
>PTZ00064 histone acetyltransferase; Provisional
Probab=35.45 E-value=33 Score=24.41 Aligned_cols=27 Identities=26% Similarity=0.690 Sum_probs=23.1
Q ss_pred CCCccCcccccccCCHHHHHHHHHHhh
Q psy10762 90 ESPHKCTYCMKSFTRKEHLTNHIRQHT 116 (126)
Q Consensus 90 ~~~~~C~~C~~~f~~~~~l~~H~~~h~ 116 (126)
...|.|..|-+-|.+...|.+|+..-.
T Consensus 278 d~LYICEfCLkY~~s~~~l~rH~~~C~ 304 (552)
T PTZ00064 278 DTLHFCEYCLDFFCFEDELIRHLSRCQ 304 (552)
T ss_pred CeEEEccchhhhhCCHHHHHHHHhcCC
Confidence 456999999999999999999987644
No 261
>PF04438 zf-HIT: HIT zinc finger; InterPro: IPR007529 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the HIT-type zinc finger, which contains 7 conserved cysteines and one histidine that can potentially coordinate two zinc atoms. It has been named after the first protein that originally defined the domain: the yeast HIT1 protein (P46973 from SWISSPROT) []. The HIT-type zinc finger displays some sequence similarities to the MYND-type zinc finger. The function of this domain is unknown but it is mainly found in nuclear proteins involved in gene regulation and chromatin remodeling. This domain is also found in the thyroid receptor interacting protein 3 (TRIP-3) Q15649 from SWISSPROT, that specifically interacts with the ligand binding domain of the thyroid receptor. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 2YQP_A 2YQQ_A 1X4S_A.
Probab=34.98 E-value=39 Score=13.65 Aligned_cols=15 Identities=20% Similarity=0.560 Sum_probs=7.1
Q ss_pred cceeccccccccCCh
Q psy10762 7 TPHRCDYCAKTFTRK 21 (126)
Q Consensus 7 ~~~~C~~C~~~f~~~ 21 (126)
..|.|+.|+..+-+.
T Consensus 12 ~kY~Cp~C~~~~CSl 26 (30)
T PF04438_consen 12 AKYRCPRCGARYCSL 26 (30)
T ss_dssp ESEE-TTT--EESSH
T ss_pred CEEECCCcCCceeCc
Confidence 346777777665544
No 262
>PF12773 DZR: Double zinc ribbon
Probab=34.94 E-value=31 Score=15.48 Aligned_cols=9 Identities=22% Similarity=0.501 Sum_probs=4.9
Q ss_pred cccCCCCCc
Q psy10762 65 FPCQYCPKA 73 (126)
Q Consensus 65 ~~C~~C~~~ 73 (126)
..|+.|+..
T Consensus 30 ~~C~~Cg~~ 38 (50)
T PF12773_consen 30 KICPNCGAE 38 (50)
T ss_pred CCCcCCcCC
Confidence 456666543
No 263
>PRK12722 transcriptional activator FlhC; Provisional
Probab=34.51 E-value=31 Score=21.00 Aligned_cols=28 Identities=21% Similarity=0.551 Sum_probs=18.9
Q ss_pred cccCCCCCcCCChhhHHHHHHhhcCCCCccCccccc
Q psy10762 65 FPCQYCPKAFTRKDHLVNHVRRHTGESPHKCTYCMK 100 (126)
Q Consensus 65 ~~C~~C~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~ 100 (126)
..|..|+..|..... .....|.|+.|.-
T Consensus 135 ~~C~~Cgg~fv~~~~--------e~~~~f~CplC~~ 162 (187)
T PRK12722 135 SSCNCCGGHFVTHAH--------DPVGSFVCGLCQP 162 (187)
T ss_pred ccCCCCCCCeecccc--------ccCCCCcCCCCCC
Confidence 478899888765432 2235689999964
No 264
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=34.32 E-value=23 Score=16.62 Aligned_cols=9 Identities=33% Similarity=0.888 Sum_probs=3.8
Q ss_pred ccCCCCCcC
Q psy10762 66 PCQYCPKAF 74 (126)
Q Consensus 66 ~C~~C~~~~ 74 (126)
.|+.|+..|
T Consensus 42 ~C~~C~~~f 50 (64)
T smart00647 42 TCPKCGFSF 50 (64)
T ss_pred ECCCCCCeE
Confidence 444444333
No 265
>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=33.72 E-value=12 Score=21.42 Aligned_cols=15 Identities=27% Similarity=0.735 Sum_probs=12.4
Q ss_pred CCCccCcccccccCC
Q psy10762 90 ESPHKCTYCMKSFTR 104 (126)
Q Consensus 90 ~~~~~C~~C~~~f~~ 104 (126)
.++.+|+.||..|..
T Consensus 110 g~~~RCpeCG~~fkL 124 (136)
T PF01215_consen 110 GKPQRCPECGQVFKL 124 (136)
T ss_dssp TSEEEETTTEEEEEE
T ss_pred CCccCCCCCCeEEEE
Confidence 468899999998864
No 266
>COG1379 PHP family phosphoesterase with a Zn ribbon [General function prediction only]
Probab=33.69 E-value=46 Score=22.40 Aligned_cols=32 Identities=13% Similarity=0.417 Sum_probs=19.8
Q ss_pred ccCCCCCcCCChhhHHHHHHhhcCCCCccCcccccccCCHH
Q psy10762 66 PCQYCPKAFTRKDHLVNHVRRHTGESPHKCTYCMKSFTRKE 106 (126)
Q Consensus 66 ~C~~C~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~f~~~~ 106 (126)
.|..|...|.-.... .-.++|+.||..+....
T Consensus 248 AC~rC~t~y~le~A~---------~~~wrCpkCGg~ikKGV 279 (403)
T COG1379 248 ACSRCYTRYSLEEAK---------SLRWRCPKCGGKIKKGV 279 (403)
T ss_pred HHHHhhhccCcchhh---------hhcccCcccccchhhhH
Confidence 366666655443221 23478999999877653
No 267
>PRK12860 transcriptional activator FlhC; Provisional
Probab=33.47 E-value=33 Score=20.94 Aligned_cols=27 Identities=22% Similarity=0.490 Sum_probs=18.3
Q ss_pred cccCCCCCcCCChhhHHHHHHhhcCCCCccCcccc
Q psy10762 65 FPCQYCPKAFTRKDHLVNHVRRHTGESPHKCTYCM 99 (126)
Q Consensus 65 ~~C~~C~~~~~~~~~l~~h~~~~~~~~~~~C~~C~ 99 (126)
..|..|+..|..... .....|.|+.|.
T Consensus 135 ~~C~~Cgg~fv~~~~--------e~~~~f~CplC~ 161 (189)
T PRK12860 135 ARCCRCGGKFVTHAH--------DLRHNFVCGLCQ 161 (189)
T ss_pred ccCCCCCCCeecccc--------ccCCCCcCCCCC
Confidence 478889887765322 223568899986
No 268
>PF08882 Acetone_carb_G: Acetone carboxylase gamma subunit; InterPro: IPR014979 Acetone carboxylase is the key enzyme of bacterial acetone metabolism, catalysing the condensation of acetone and CO2 to form acetoacetate [] according to the following reaction: CH3COCH3 + CO2 + ATP = CH3COCH2COO- + AMP + 2P(i) + H+ It has the subunit composition: (alpha(2)beta(2)gamma(2) multimers of 85kDa, 78kDa, and 20kDa subunits). It is expressed to high levels (17 to 25% of soluble protein) in cells grown with acetone as the carbon source but are not present at detectable levels in cells grown with other carbon sources []. Acetone carboxylase may enable Helicobacter pylori to survive off acetone in the stomach of humans and other mammals where it is the etiological agent of peptic ulcer disease []. This entry represents the family of gamma subunit-related acetone carboxylase proteins.
Probab=33.30 E-value=12 Score=20.55 Aligned_cols=12 Identities=17% Similarity=0.570 Sum_probs=8.2
Q ss_pred CcccCCCCCcCC
Q psy10762 64 PFPCQYCPKAFT 75 (126)
Q Consensus 64 ~~~C~~C~~~~~ 75 (126)
.|-||.||....
T Consensus 74 EyyCP~Cgt~le 85 (112)
T PF08882_consen 74 EYYCPGCGTQLE 85 (112)
T ss_pred EEECCCCcceeE
Confidence 477888886543
No 269
>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=33.03 E-value=20 Score=21.07 Aligned_cols=14 Identities=29% Similarity=0.748 Sum_probs=6.9
Q ss_pred CCccCcccccccCC
Q psy10762 91 SPHKCTYCMKSFTR 104 (126)
Q Consensus 91 ~~~~C~~C~~~f~~ 104 (126)
.|.-|..||+.|.+
T Consensus 67 ~PsYC~~CGkpyPW 80 (158)
T PF10083_consen 67 APSYCHNCGKPYPW 80 (158)
T ss_pred CChhHHhCCCCCch
Confidence 34445555555554
No 270
>PF08271 TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013137 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIB (TFIIB). In eukaryotes the initiation of transcription of protein encoding genes by the polymerase II complexe (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least seven different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, and -IIH []. TFIIB and TFIID are responsible for promoter recognition and interaction with pol II; together with Pol II, they form a minimal initiation complex capable of transcription under certain conditions. The TATA box of a Pol II promoter is bound in the initiation complex by the TBP subunit of TFIID, which bends the DNA around the C-terminal domain of TFIIB whereas the N-terminal zinc finger of TFIIB interacts with Pol II [, ]. The TFIIB zinc finger adopts a zinc ribbon fold characterised by two beta-hairpins forming two structurally similar zinc-binding sub-sites []. The zinc finger contacts the rbp1 subunit of Pol II through its dock domain, a conserved region of about 70 amino acids located close to the polymerase active site []. In the Pol II complex this surface is located near the RNA exit groove. Interestingly this sequence is best conserved in the three polymerases that utilise a TFIIB-like general transcription factor (Pol II, Pol III, and archaeal RNA polymerase) but not in Pol I []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1VD4_A 1PFT_A 3K1F_M 3K7A_M 1RO4_A 1RLY_A 1DL6_A.
Probab=32.88 E-value=19 Score=15.77 Aligned_cols=7 Identities=43% Similarity=1.023 Sum_probs=3.8
Q ss_pred cCccccc
Q psy10762 94 KCTYCMK 100 (126)
Q Consensus 94 ~C~~C~~ 100 (126)
.|+.|+.
T Consensus 2 ~Cp~Cg~ 8 (43)
T PF08271_consen 2 KCPNCGS 8 (43)
T ss_dssp SBTTTSS
T ss_pred CCcCCcC
Confidence 4555554
No 271
>PRK06260 threonine synthase; Validated
Probab=32.80 E-value=32 Score=23.46 Aligned_cols=26 Identities=23% Similarity=0.623 Sum_probs=16.2
Q ss_pred cccCCcccccCCchHHHHHHhhhcCCCCcccCCCCCcC
Q psy10762 37 HHCNYCAKSFTRKDHMVYHERQHTGETPFPCQYCPKAF 74 (126)
Q Consensus 37 ~~c~~C~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~~ 74 (126)
+.|..||..+... ...+.|+.|+..+
T Consensus 4 ~~C~~cg~~~~~~------------~~~~~Cp~cg~~l 29 (397)
T PRK06260 4 LKCIECGKEYDPD------------EIIYTCPECGGLL 29 (397)
T ss_pred EEECCCCCCCCCC------------CccccCCCCCCeE
Confidence 5777888666422 2246788887543
No 272
>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=32.73 E-value=47 Score=18.23 Aligned_cols=23 Identities=13% Similarity=0.255 Sum_probs=16.7
Q ss_pred cceeccccccccCChhHHHHHHH
Q psy10762 7 TPHRCDYCAKTFTRKEHLVNHVR 29 (126)
Q Consensus 7 ~~~~C~~C~~~f~~~~~l~~h~~ 29 (126)
..+.|+.||..+...........
T Consensus 30 ~~~~C~~CGe~~~~~e~~~~~~~ 52 (127)
T TIGR03830 30 PGWYCPACGEELLDPEESKRNSA 52 (127)
T ss_pred eeeECCCCCCEEEcHHHHHHHHH
Confidence 34779999999888876555443
No 273
>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=32.32 E-value=34 Score=15.04 Aligned_cols=11 Identities=36% Similarity=1.186 Sum_probs=7.7
Q ss_pred ceecccccccc
Q psy10762 8 PHRCDYCAKTF 18 (126)
Q Consensus 8 ~~~C~~C~~~f 18 (126)
+..|+.|+..|
T Consensus 29 ~~~CpYCg~~y 39 (40)
T PF10276_consen 29 PVVCPYCGTRY 39 (40)
T ss_dssp EEEETTTTEEE
T ss_pred eEECCCCCCEE
Confidence 56777777665
No 274
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=32.08 E-value=33 Score=25.30 Aligned_cols=8 Identities=25% Similarity=0.609 Sum_probs=5.7
Q ss_pred eccccccc
Q psy10762 10 RCDYCAKT 17 (126)
Q Consensus 10 ~C~~C~~~ 17 (126)
.|+.||..
T Consensus 3 ~Cp~Cg~~ 10 (645)
T PRK14559 3 ICPQCQFE 10 (645)
T ss_pred cCCCCCCc
Confidence 57788765
No 275
>TIGR00627 tfb4 transcription factor tfb4. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=31.81 E-value=40 Score=21.98 Aligned_cols=11 Identities=27% Similarity=0.809 Sum_probs=5.9
Q ss_pred cccCCCCCcCC
Q psy10762 65 FPCQYCPKAFT 75 (126)
Q Consensus 65 ~~C~~C~~~~~ 75 (126)
|.|+.|.-.|.
T Consensus 256 yvCs~Clsi~C 266 (279)
T TIGR00627 256 FVCSVCLSVLC 266 (279)
T ss_pred EECCCccCCcC
Confidence 55666654443
No 276
>PLN02748 tRNA dimethylallyltransferase
Probab=31.60 E-value=41 Score=23.75 Aligned_cols=24 Identities=13% Similarity=0.278 Sum_probs=19.6
Q ss_pred CCccCccccc-ccCCHHHHHHHHHH
Q psy10762 91 SPHKCTYCMK-SFTRKEHLTNHIRQ 114 (126)
Q Consensus 91 ~~~~C~~C~~-~f~~~~~l~~H~~~ 114 (126)
+.|.|.+|++ .+.-...+..|+..
T Consensus 417 ~~~~Ce~C~~~~~~G~~eW~~Hlks 441 (468)
T PLN02748 417 TQYVCEACGNKVLRGAHEWEQHKQG 441 (468)
T ss_pred ccccccCCCCcccCCHHHHHHHhcc
Confidence 5688999997 79888888888754
No 277
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=31.55 E-value=32 Score=22.62 Aligned_cols=11 Identities=18% Similarity=0.504 Sum_probs=5.1
Q ss_pred ccCcccccccC
Q psy10762 93 HKCTYCMKSFT 103 (126)
Q Consensus 93 ~~C~~C~~~f~ 103 (126)
+.|+.|+.-|.
T Consensus 58 ~vcp~c~~h~r 68 (296)
T CHL00174 58 NICEQCGYHLK 68 (296)
T ss_pred CCCCCCCCCcC
Confidence 34555544443
No 278
>COG4391 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=31.43 E-value=7.9 Score=18.76 Aligned_cols=45 Identities=20% Similarity=0.430 Sum_probs=21.5
Q ss_pred HHhhhcCCCCcccCCCCCcCCChhhHHHHHHhhcCCCCccCcccccccC
Q psy10762 55 HERQHTGETPFPCQYCPKAFTRKDHLVNHVRRHTGESPHKCTYCMKSFT 103 (126)
Q Consensus 55 h~~~~~~~~~~~C~~C~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~f~ 103 (126)
+..+..+..++.|+.-+..+....-++. . ..+....|+-|+..|.
T Consensus 15 ~~~I~~~~~~l~C~g~~~p~~HPrV~L~---m-g~~gev~CPYC~t~y~ 59 (62)
T COG4391 15 HETIEIGDLPLMCPGPEPPNDHPRVFLD---M-GDEGEVVCPYCSTRYR 59 (62)
T ss_pred ceEEEeCCeeEEcCCCCCCCCCCEEEEE---c-CCCCcEecCccccEEE
Confidence 3344555566666654433333222111 1 1233346777877765
No 279
>PF05495 zf-CHY: CHY zinc finger; InterPro: IPR008913 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Pirh2 is an eukaryotic ubiquitin protein ligase, which has been shown to promote p53 degradation in mammals. Pirh2 physically interacts with p53 and promotes ubiquitination of p53 independently of MDM2. Like MDM2, Pirh2 is thought to participate in an autoregulatory feedback loop that controls p53 function. Pirh2 proteins contain three distinct zinc fingers, the CHY-type, the CTCHY-type which is C-terminal to the CHY-type zinc finger and a RING finger. The CHY-type zinc finger has no currently known function []. As well as Pirh2, the CHY-type zinc finger is also found in the following proteins: Yeast helper of Tim protein 13. Hot13 may have a role in the assembly and recycling of the small Tims, a complex of the mitochondrial intermembrane space that participates in the TIM22 import pathway for assembly of the inner membrane [] Several plant hypothetical proteins that also contain haemerythrin cation binding domains Several protozoan hypothetical proteins that also contain a Myb domain The solution structure of this zinc finger has been solved and binds 3 zinc atoms as shown in the following schematic representation: ++---------+-----+ || | | CXHYxxxxxxxxxCCxxxxxCxxCHxxxxxHxxxxxxxxxxxCxxCxxxxxxxxxCxxC | | | | | | | | +-+-----------------+--+ +--+---------+--+ 'C': conserved cysteine involved in the binding of one zinc atom. 'H': conserved histidine involved in the binding of one zinc atom. More information about these proteins can be found at Protein of the Month: Zinc Fingers []; GO: 0008270 zinc ion binding; PDB: 2DKT_A 2K2C_A.
Probab=31.42 E-value=7.2 Score=19.44 Aligned_cols=12 Identities=25% Similarity=0.468 Sum_probs=5.7
Q ss_pred eeccccccccCC
Q psy10762 9 HRCDYCAKTFTR 20 (126)
Q Consensus 9 ~~C~~C~~~f~~ 20 (126)
++++-|++.|.-
T Consensus 11 ~~~~cC~~~y~C 22 (71)
T PF05495_consen 11 IRFPCCGKYYPC 22 (71)
T ss_dssp EEETTTTEEESS
T ss_pred EECCcccCeecH
Confidence 344455555443
No 280
>KOG0782|consensus
Probab=31.17 E-value=9.2 Score=27.49 Aligned_cols=51 Identities=24% Similarity=0.461 Sum_probs=32.4
Q ss_pred hHHHHHHhhhcCCCCcccCCCCCcCCChhhHHHHHHhhcCC-CCccCcccccccCCHH
Q psy10762 50 DHMVYHERQHTGETPFPCQYCPKAFTRKDHLVNHVRRHTGE-SPHKCTYCMKSFTRKE 106 (126)
Q Consensus 50 ~~l~~h~~~~~~~~~~~C~~C~~~~~~~~~l~~h~~~~~~~-~~~~C~~C~~~f~~~~ 106 (126)
..+..|-.+|.....-.|..|+++|.+.-.|. ..| -...|.+|...|..+.
T Consensus 239 ~~fvrHHWVHrrRqeGkC~~CgKgFQQKf~Fh------sKEivAisCSWCKqayH~Kv 290 (1004)
T KOG0782|consen 239 SGFVRHHWVHRRRQEGKCNTCGKGFQQKFFFH------SKEIVAISCSWCKQAYHLKV 290 (1004)
T ss_pred ccchHHhHhhHhhhccccchhhhhhhhheeec------cccEEEEEehHHHHHhhcch
Confidence 34666656665544568999998887654432 222 2357888888877654
No 281
>PRK01343 zinc-binding protein; Provisional
Probab=30.52 E-value=27 Score=16.73 Aligned_cols=11 Identities=36% Similarity=0.612 Sum_probs=6.9
Q ss_pred ccCcccccccC
Q psy10762 93 HKCTYCMKSFT 103 (126)
Q Consensus 93 ~~C~~C~~~f~ 103 (126)
..|++|++.+.
T Consensus 10 ~~CP~C~k~~~ 20 (57)
T PRK01343 10 RPCPECGKPST 20 (57)
T ss_pred CcCCCCCCcCc
Confidence 45777776654
No 282
>PRK14138 NAD-dependent deacetylase; Provisional
Probab=28.69 E-value=89 Score=19.84 Aligned_cols=11 Identities=36% Similarity=0.769 Sum_probs=5.3
Q ss_pred eeccccccccC
Q psy10762 9 HRCDYCAKTFT 19 (126)
Q Consensus 9 ~~C~~C~~~f~ 19 (126)
..|..|+..+.
T Consensus 120 ~~C~~C~~~~~ 130 (244)
T PRK14138 120 YYCVRCGKRYT 130 (244)
T ss_pred eEECCCCCccc
Confidence 44555555443
No 283
>TIGR00310 ZPR1_znf ZPR1 zinc finger domain.
Probab=28.67 E-value=6.1 Score=24.03 Aligned_cols=38 Identities=21% Similarity=0.343 Sum_probs=19.0
Q ss_pred eccccccccCChhHHHHHHHhhcCCC---CcccCCcccccCC
Q psy10762 10 RCDYCAKTFTRKEHLVNHVRQHTGES---PHHCNYCAKSFTR 48 (126)
Q Consensus 10 ~C~~C~~~f~~~~~l~~h~~~h~~~~---~~~c~~C~~~~~~ 48 (126)
.|+.|+........+..+ ..+.++. .+.|+.||+....
T Consensus 2 ~Cp~C~~~~~~~~~~~~~-IP~F~evii~sf~C~~CGyr~~e 42 (192)
T TIGR00310 2 DCPSCGGECETVMKTVND-IPYFGEVLETSTICEHCGYRSND 42 (192)
T ss_pred cCCCCCCCCEEEEEEEcC-CCCcceEEEEEEECCCCCCccce
Confidence 477777543322222221 3333332 4678888866543
No 284
>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=28.62 E-value=40 Score=19.42 Aligned_cols=46 Identities=17% Similarity=0.244 Sum_probs=25.1
Q ss_pred cccCCCCCcCCChhhHHH--HHH---hhcCCCCccCcccccccCCHHHHHH
Q psy10762 65 FPCQYCPKAFTRKDHLVN--HVR---RHTGESPHKCTYCMKSFTRKEHLTN 110 (126)
Q Consensus 65 ~~C~~C~~~~~~~~~l~~--h~~---~~~~~~~~~C~~C~~~f~~~~~l~~ 110 (126)
-.|+.|+..+.....-.. -+. ....+..+.|+.|++.|=..+.+.+
T Consensus 92 sRC~~CN~~L~~v~~~~v~~~vp~~v~~~~~~f~~C~~C~kiyW~GsH~~~ 142 (147)
T PF01927_consen 92 SRCPKCNGPLRPVSKEEVKDRVPPYVYETYDEFWRCPGCGKIYWEGSHWRR 142 (147)
T ss_pred CccCCCCcEeeechhhccccccCccccccCCeEEECCCCCCEecccccHHH
Confidence 478888765433211100 000 1122456889999998866655544
No 285
>PRK05654 acetyl-CoA carboxylase subunit beta; Validated
Probab=28.51 E-value=31 Score=22.61 Aligned_cols=10 Identities=20% Similarity=0.521 Sum_probs=5.7
Q ss_pred cccCCCCCcC
Q psy10762 65 FPCQYCPKAF 74 (126)
Q Consensus 65 ~~C~~C~~~~ 74 (126)
+.|+.|+.-|
T Consensus 47 ~vc~~c~~h~ 56 (292)
T PRK05654 47 NVCPKCGHHM 56 (292)
T ss_pred CCCCCCCCCe
Confidence 3566666544
No 286
>PF14369 zf-RING_3: zinc-finger
Probab=28.35 E-value=27 Score=14.74 Aligned_cols=10 Identities=30% Similarity=0.863 Sum_probs=6.4
Q ss_pred cCcccccccC
Q psy10762 94 KCTYCMKSFT 103 (126)
Q Consensus 94 ~C~~C~~~f~ 103 (126)
.|+.|+..|.
T Consensus 23 ~CP~C~~gFv 32 (35)
T PF14369_consen 23 ACPRCHGGFV 32 (35)
T ss_pred CCcCCCCcEe
Confidence 4777776664
No 287
>KOG2906|consensus
Probab=28.29 E-value=6.1 Score=21.12 Aligned_cols=38 Identities=16% Similarity=0.270 Sum_probs=18.5
Q ss_pred ccCCCCCcCCChhhHHHHHHhhcCCCCccCcccccccC
Q psy10762 66 PCQYCPKAFTRKDHLVNHVRRHTGESPHKCTYCMKSFT 103 (126)
Q Consensus 66 ~C~~C~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~f~ 103 (126)
.|+.||..-.+..+|+..-.-......|+|-.|+.+.+
T Consensus 67 ~Cp~Cgh~rayF~qlQtRSADEPmT~FYkC~~C~~~Wr 104 (105)
T KOG2906|consen 67 TCPTCGHERAYFMQLQTRSADEPMTTFYKCCKCKHRWR 104 (105)
T ss_pred cCCCCCCCceEEEEeeeccCCCcHhHhhhhhccccccc
Confidence 68888743333333321111111224488988877643
No 288
>KOG2747|consensus
Probab=28.15 E-value=39 Score=23.21 Aligned_cols=29 Identities=21% Similarity=0.630 Sum_probs=24.5
Q ss_pred CCCccCcccccccCCHHHHHHHHHHhhhc
Q psy10762 90 ESPHKCTYCMKSFTRKEHLTNHIRQHTVR 118 (126)
Q Consensus 90 ~~~~~C~~C~~~f~~~~~l~~H~~~h~~~ 118 (126)
...|.|..|-+-+.+...|.+|+..-...
T Consensus 156 ~~lYiCEfCLkY~~s~~~l~rH~~kC~~r 184 (396)
T KOG2747|consen 156 DKLYICEFCLKYMKSRTSLQRHLKKCKLR 184 (396)
T ss_pred CeEEEehHHHhHhchHHHHHHHHHhcCCC
Confidence 45699999999999999999999876544
No 289
>KOG2857|consensus
Probab=28.06 E-value=28 Score=20.14 Aligned_cols=23 Identities=13% Similarity=0.307 Sum_probs=20.0
Q ss_pred cceeccccccccCChhHHHHHHH
Q psy10762 7 TPHRCDYCAKTFTRKEHLVNHVR 29 (126)
Q Consensus 7 ~~~~C~~C~~~f~~~~~l~~h~~ 29 (126)
..|+|+.|..-|.+..-++.|+.
T Consensus 16 ~KYKCpkC~vPYCSl~CfKiHk~ 38 (157)
T KOG2857|consen 16 IKYKCPKCSVPYCSLPCFKIHKS 38 (157)
T ss_pred hhccCCCCCCccccchhhhhccC
Confidence 36999999999999999888875
No 290
>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=26.87 E-value=21 Score=20.73 Aligned_cols=27 Identities=26% Similarity=0.580 Sum_probs=14.6
Q ss_pred CcccCCcccccCCchHHHHHHhhhcCCCCcccCCCCC
Q psy10762 36 PHHCNYCAKSFTRKDHMVYHERQHTGETPFPCQYCPK 72 (126)
Q Consensus 36 ~~~c~~C~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~ 72 (126)
.+.|..||...... + ....-.||.|+.
T Consensus 112 ~l~C~~Cg~~~~~~---------~-~~~l~~Cp~C~~ 138 (146)
T PF07295_consen 112 TLVCENCGHEVELT---------H-PERLPPCPKCGH 138 (146)
T ss_pred eEecccCCCEEEec---------C-CCcCCCCCCCCC
Confidence 46777777544221 1 222347777764
No 291
>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=26.71 E-value=29 Score=17.05 Aligned_cols=8 Identities=38% Similarity=0.804 Sum_probs=4.5
Q ss_pred ccCccccc
Q psy10762 93 HKCTYCMK 100 (126)
Q Consensus 93 ~~C~~C~~ 100 (126)
|.|+.|+.
T Consensus 1 y~C~KCg~ 8 (64)
T PF09855_consen 1 YKCPKCGN 8 (64)
T ss_pred CCCCCCCC
Confidence 45666654
No 292
>PRK07218 replication factor A; Provisional
Probab=26.71 E-value=41 Score=23.38 Aligned_cols=10 Identities=20% Similarity=0.584 Sum_probs=6.9
Q ss_pred cccCCCCCcC
Q psy10762 65 FPCQYCPKAF 74 (126)
Q Consensus 65 ~~C~~C~~~~ 74 (126)
..||.|++..
T Consensus 298 ~rCP~C~r~v 307 (423)
T PRK07218 298 ERCPECGRVI 307 (423)
T ss_pred ecCcCccccc
Confidence 4678887665
No 293
>cd04476 RPA1_DBD_C RPA1_DBD_C: A subfamily of OB folds corresponding to the C-terminal OB fold, the ssDNA-binding domain (DBD)-C, of human RPA1 (also called RPA70). RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). In addition to DBD-C, RPA1 contains three other OB folds: DBD-A, DBD-B, and RPA1N. The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B. RPA1 DBD-C is involved in DNA binding and trimerization. It contains two structural insertions not found to date in other OB-folds: a zinc ribbon and a three-helix bundle. RPA1 DBD-C also contains a Cys4-type zinc-binding motif, which plays a role in the ssDNA binding fun
Probab=26.67 E-value=29 Score=20.30 Aligned_cols=12 Identities=25% Similarity=0.814 Sum_probs=6.6
Q ss_pred CCcccCCCCCcC
Q psy10762 63 TPFPCQYCPKAF 74 (126)
Q Consensus 63 ~~~~C~~C~~~~ 74 (126)
..|.|..|+...
T Consensus 50 ~~~~C~~C~~~~ 61 (166)
T cd04476 50 GTYRCEKCNKSV 61 (166)
T ss_pred CcEECCCCCCcC
Confidence 346666665543
No 294
>COG1066 Sms Predicted ATP-dependent serine protease [Posttranslational modification, protein turnover, chaperones]
Probab=26.54 E-value=39 Score=23.58 Aligned_cols=13 Identities=23% Similarity=0.452 Sum_probs=8.3
Q ss_pred cceeccccccccC
Q psy10762 7 TPHRCDYCAKTFT 19 (126)
Q Consensus 7 ~~~~C~~C~~~f~ 19 (126)
..|.|..||....
T Consensus 6 t~f~C~~CG~~s~ 18 (456)
T COG1066 6 TAFVCQECGYVSP 18 (456)
T ss_pred cEEEcccCCCCCc
Confidence 4577777776543
No 295
>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=26.30 E-value=36 Score=13.56 Aligned_cols=8 Identities=25% Similarity=0.812 Sum_probs=4.2
Q ss_pred cCcccccc
Q psy10762 94 KCTYCMKS 101 (126)
Q Consensus 94 ~C~~C~~~ 101 (126)
.|.+|++.
T Consensus 2 ~C~~C~~~ 9 (30)
T PF03107_consen 2 WCDVCRRK 9 (30)
T ss_pred CCCCCCCC
Confidence 45555544
No 296
>KOG1729|consensus
Probab=26.21 E-value=17 Score=23.72 Aligned_cols=9 Identities=33% Similarity=0.711 Sum_probs=4.5
Q ss_pred eeccccccc
Q psy10762 9 HRCDYCAKT 17 (126)
Q Consensus 9 ~~C~~C~~~ 17 (126)
-.|..|+.+
T Consensus 169 ~~C~~C~~~ 177 (288)
T KOG1729|consen 169 TECMVCGCT 177 (288)
T ss_pred eecccCCCc
Confidence 345555553
No 297
>COG5432 RAD18 RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms]
Probab=26.17 E-value=44 Score=21.99 Aligned_cols=14 Identities=43% Similarity=0.999 Sum_probs=6.2
Q ss_pred hhhcCCCCcccCCCC
Q psy10762 57 RQHTGETPFPCQYCP 71 (126)
Q Consensus 57 ~~~~~~~~~~C~~C~ 71 (126)
+.|.+..| -||.|.
T Consensus 53 R~hL~~qp-~CP~Cr 66 (391)
T COG5432 53 RRHLGTQP-FCPVCR 66 (391)
T ss_pred HHHhcCCC-CCcccc
Confidence 34444444 355553
No 298
>PF14205 Cys_rich_KTR: Cysteine-rich KTR
Probab=26.13 E-value=21 Score=16.93 Aligned_cols=9 Identities=33% Similarity=0.914 Sum_probs=4.3
Q ss_pred CccCccccc
Q psy10762 92 PHKCTYCMK 100 (126)
Q Consensus 92 ~~~C~~C~~ 100 (126)
|.-|+.|.+
T Consensus 28 PlyCpKCK~ 36 (55)
T PF14205_consen 28 PLYCPKCKQ 36 (55)
T ss_pred cccCCCCCc
Confidence 344555543
No 299
>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=26.05 E-value=30 Score=16.13 Aligned_cols=16 Identities=31% Similarity=0.781 Sum_probs=10.0
Q ss_pred CCcceeccccccccCC
Q psy10762 5 GETPHRCDYCAKTFTR 20 (126)
Q Consensus 5 ~~~~~~C~~C~~~f~~ 20 (126)
++..++|..|++.+..
T Consensus 32 ~~~~~rC~YCe~~~~~ 47 (52)
T PF02748_consen 32 EPIKLRCHYCERIITE 47 (52)
T ss_dssp TTCEEEETTT--EEEH
T ss_pred CCCEEEeeCCCCEecc
Confidence 4567889888887643
No 300
>KOG2932|consensus
Probab=25.82 E-value=80 Score=21.10 Aligned_cols=29 Identities=17% Similarity=0.474 Sum_probs=22.5
Q ss_pred cCCCCccCcc---cccccCCHHHHHHHHHHhh
Q psy10762 88 TGESPHKCTY---CMKSFTRKEHLTNHIRQHT 116 (126)
Q Consensus 88 ~~~~~~~C~~---C~~~f~~~~~l~~H~~~h~ 116 (126)
..+..|.|.. |.++|.+..+|+.|+..-+
T Consensus 140 ~~g~iFmC~~~~GC~RTyLsqrDlqAHInhrH 171 (389)
T KOG2932|consen 140 MMGGIFMCAAPHGCLRTYLSQRDLQAHINHRH 171 (389)
T ss_pred cccceEEeecchhHHHHHhhHHHHHHHhhhhh
Confidence 4456688854 9999999999999976633
No 301
>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=25.76 E-value=13 Score=16.81 Aligned_cols=6 Identities=33% Similarity=0.949 Sum_probs=3.1
Q ss_pred cccccC
Q psy10762 98 CMKSFT 103 (126)
Q Consensus 98 C~~~f~ 103 (126)
||-.|.
T Consensus 33 Cg~tfv 38 (47)
T PF04606_consen 33 CGHTFV 38 (47)
T ss_pred CCCEEE
Confidence 555553
No 302
>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=25.27 E-value=1.2e+02 Score=18.61 Aligned_cols=11 Identities=18% Similarity=0.694 Sum_probs=5.4
Q ss_pred CcccCCccccc
Q psy10762 36 PHHCNYCAKSF 46 (126)
Q Consensus 36 ~~~c~~C~~~~ 46 (126)
...|..|+..+
T Consensus 95 ~~~C~~C~~~~ 105 (206)
T cd01410 95 IEVCKSCGPEY 105 (206)
T ss_pred cccCCCCCCcc
Confidence 34455555443
No 303
>PF05741 zf-nanos: Nanos RNA binding domain; InterPro: IPR024161 Nanos is a highly conserved RNA-binding protein in higher eukaryotes and functions as a key regulatory protein in translational control using a 3' untranslated region during the development and maintenance of germ cells. Nanos comprises a non-conserved amino-terminus and highly conserved carboxy- terminal regions. The C-terminal region has two conserved Cys-Cys-His-Cys (CCHC)-type zinc-finger motifs that are indispensable for nanos function [, , ]. The structure of the nanos-type zinc finger is composed of two independent zinc-finger (ZF) lobes, the N-terminal ZF1 and the C-terminal ZF2, which are connected by a linker helix []. These lobes create a large cleft. Zinc ions in ZF1 and ZF2 are bound to the CCHC motif by tetrahedral coordination.; PDB: 3ALR_B.
Probab=25.21 E-value=24 Score=16.77 Aligned_cols=11 Identities=18% Similarity=0.464 Sum_probs=3.4
Q ss_pred CCccCcccccc
Q psy10762 91 SPHKCTYCMKS 101 (126)
Q Consensus 91 ~~~~C~~C~~~ 101 (126)
+.|.|+.||.+
T Consensus 32 r~y~Cp~CgAt 42 (55)
T PF05741_consen 32 RKYVCPICGAT 42 (55)
T ss_dssp GG---TTT---
T ss_pred hcCcCCCCcCc
Confidence 45778888765
No 304
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=24.86 E-value=29 Score=16.45 Aligned_cols=12 Identities=42% Similarity=0.847 Sum_probs=8.6
Q ss_pred ccCcccccccCC
Q psy10762 93 HKCTYCMKSFTR 104 (126)
Q Consensus 93 ~~C~~C~~~f~~ 104 (126)
.+|.+|++.|..
T Consensus 6 ~~C~~Cg~~~~~ 17 (54)
T PF14446_consen 6 CKCPVCGKKFKD 17 (54)
T ss_pred ccChhhCCcccC
Confidence 368888888853
No 305
>PTZ00409 Sir2 (Silent Information Regulator) protein; Provisional
Probab=24.75 E-value=1.1e+02 Score=19.93 Aligned_cols=14 Identities=36% Similarity=0.548 Sum_probs=7.9
Q ss_pred cceeccccccccCC
Q psy10762 7 TPHRCDYCAKTFTR 20 (126)
Q Consensus 7 ~~~~C~~C~~~f~~ 20 (126)
....|..|+..+..
T Consensus 136 ~~~~C~~C~~~~~~ 149 (271)
T PTZ00409 136 FEARCCTCRKTIQL 149 (271)
T ss_pred CcceeCCCCCCccc
Confidence 34556667665543
No 306
>COG4896 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=24.71 E-value=39 Score=16.42 Aligned_cols=8 Identities=25% Similarity=0.932 Sum_probs=3.7
Q ss_pred CcccCCCC
Q psy10762 64 PFPCQYCP 71 (126)
Q Consensus 64 ~~~C~~C~ 71 (126)
.|.|+.|.
T Consensus 31 tymC~eC~ 38 (68)
T COG4896 31 TYMCPECE 38 (68)
T ss_pred eEechhhH
Confidence 34455543
No 307
>PRK14811 formamidopyrimidine-DNA glycosylase; Provisional
Probab=24.28 E-value=28 Score=22.45 Aligned_cols=30 Identities=23% Similarity=0.541 Sum_probs=18.9
Q ss_pred ccCCCCCcCCChhhHHHHHHhhcCCCCccCcccccccC
Q psy10762 66 PCQYCPKAFTRKDHLVNHVRRHTGESPHKCTYCMKSFT 103 (126)
Q Consensus 66 ~C~~C~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~f~ 103 (126)
.|+.|+...... ...+...|-|+.|.+.+.
T Consensus 237 pC~~Cg~~I~~~--------~~~gR~ty~Cp~CQ~~~~ 266 (269)
T PRK14811 237 PCPRCGTPIEKI--------VVGGRGTHFCPQCQPLRP 266 (269)
T ss_pred CCCcCCCeeEEE--------EECCCCcEECCCCcCCCC
Confidence 688887543221 223566788999977654
No 308
>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=23.96 E-value=56 Score=19.81 Aligned_cols=8 Identities=38% Similarity=0.858 Sum_probs=3.5
Q ss_pred hHHHHHHh
Q psy10762 79 HLVNHVRR 86 (126)
Q Consensus 79 ~l~~h~~~ 86 (126)
.|..|...
T Consensus 62 ~l~~Hl~~ 69 (198)
T PF03145_consen 62 ELLDHLRD 69 (198)
T ss_dssp CHHHHHHH
T ss_pred HHHHHHHH
Confidence 34444443
No 309
>KOG1088|consensus
Probab=23.83 E-value=39 Score=18.89 Aligned_cols=20 Identities=15% Similarity=0.174 Sum_probs=14.7
Q ss_pred hhcCCCCcccCCCCCcCCCh
Q psy10762 58 QHTGETPFPCQYCPKAFTRK 77 (126)
Q Consensus 58 ~~~~~~~~~C~~C~~~~~~~ 77 (126)
++..+....|+.||+.|.-+
T Consensus 92 ~~v~EG~l~CpetG~vfpI~ 111 (124)
T KOG1088|consen 92 IDVIEGELVCPETGRVFPIS 111 (124)
T ss_pred hhhccceEecCCCCcEeecc
Confidence 45556677899999988654
No 310
>KOG4118|consensus
Probab=23.78 E-value=54 Score=16.18 Aligned_cols=28 Identities=18% Similarity=0.437 Sum_probs=18.3
Q ss_pred cccCCcccccCCchHHHHHHhhhcCCCC
Q psy10762 37 HHCNYCAKSFTRKDHMVYHERQHTGETP 64 (126)
Q Consensus 37 ~~c~~C~~~~~~~~~l~~h~~~~~~~~~ 64 (126)
+.|..|....+..-.+..|..+.+...+
T Consensus 39 ~kCtVC~~~mpdpktfkqhfe~kHpk~~ 66 (74)
T KOG4118|consen 39 HKCTVCMVQMPDPKTFKQHFENKHPKEP 66 (74)
T ss_pred hhhHhhHhhCCCCchHHHHHhhcCCCCC
Confidence 5677777777777777777665554433
No 311
>PF04216 FdhE: Protein involved in formate dehydrogenase formation; InterPro: IPR006452 This family of sequences describe an accessory protein required for the assembly of formate dehydrogenase of certain proteobacteria although not present in the final complex []. The exact nature of the function of FdhE in the assembly of the complex is unknown, but considering the presence of selenocysteine, molybdopterin, iron-sulphur clusters and cytochrome b556, it is likely to be involved in the insertion of cofactors. ; GO: 0005737 cytoplasm; PDB: 2FIY_B.
Probab=23.45 E-value=19 Score=23.34 Aligned_cols=76 Identities=20% Similarity=0.385 Sum_probs=28.2
Q ss_pred eeccccccccCChhHHHHHHHhhcCCCCcccCCcccccCCchHHHHHHhhhcCCCCcccCCCCCcCCChhhHHHHHHhhc
Q psy10762 9 HRCDYCAKTFTRKEHLVNHVRQHTGESPHHCNYCAKSFTRKDHMVYHERQHTGETPFPCQYCPKAFTRKDHLVNHVRRHT 88 (126)
Q Consensus 9 ~~C~~C~~~f~~~~~l~~h~~~h~~~~~~~c~~C~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~~~~~~~l~~h~~~~~ 88 (126)
-.|++||..-.- +.+..--. .+.+-+.|+.|+..+... ...|+.||..-...-.... .....
T Consensus 173 g~CPvCGs~P~~-s~l~~~~~--~G~R~L~Cs~C~t~W~~~--------------R~~Cp~Cg~~~~~~l~~~~-~e~~~ 234 (290)
T PF04216_consen 173 GYCPVCGSPPVL-SVLRGGER--EGKRYLHCSLCGTEWRFV--------------RIKCPYCGNTDHEKLEYFT-VEGEP 234 (290)
T ss_dssp SS-TTT---EEE-EEEE--------EEEEEETTT--EEE----------------TTS-TTT---SS-EEE---------
T ss_pred CcCCCCCCcCce-EEEecCCC--CccEEEEcCCCCCeeeec--------------CCCCcCCCCCCCcceeeEe-cCCCC
Confidence 469999874222 21111111 244567788888655332 2378888854333222110 12223
Q ss_pred CCCCccCccccccc
Q psy10762 89 GESPHKCTYCMKSF 102 (126)
Q Consensus 89 ~~~~~~C~~C~~~f 102 (126)
+.+.+.|..|+.-+
T Consensus 235 ~~rve~C~~C~~Yl 248 (290)
T PF04216_consen 235 AYRVEVCESCGSYL 248 (290)
T ss_dssp SEEEEEETTTTEEE
T ss_pred cEEEEECCcccchH
Confidence 44567888887543
No 312
>TIGR00244 transcriptional regulator NrdR. Members of this almost entirely bacterial family contain an ATP cone domain (PFAM:PF03477). There is never more than one member per genome. Common gene symbols given include nrdR, ybaD, ribX and ytcG. The member from Streptomyces coelicolor is found upstream in the operon of the class II oxygen-independent ribonucleotide reductase gene nrdJ and was shown to repress nrdJ expression. Many members of this family are found near genes for riboflavin biosynthesis in Gram-negative bacteria, suggesting a role in that pathway. However, a phylogenetic profiling study associates members of this family with the presence of a palindromic signal with consensus acaCwAtATaTwGtgt, termed the NrdR-box, an upstream element for most operons for ribonucleotide reductase of all three classes in bacterial genomes.
Probab=23.13 E-value=34 Score=19.93 Aligned_cols=15 Identities=27% Similarity=0.565 Sum_probs=11.5
Q ss_pred CCccCcccccccCCH
Q psy10762 91 SPHKCTYCMKSFTRK 105 (126)
Q Consensus 91 ~~~~C~~C~~~f~~~ 105 (126)
+.-.|..|++.|...
T Consensus 27 RRReC~~C~~RFTTy 41 (147)
T TIGR00244 27 RRRECLECHERFTTF 41 (147)
T ss_pred ecccCCccCCcccee
Confidence 335799999999865
No 313
>PF04988 AKAP95: A-kinase anchoring protein 95 (AKAP95); InterPro: IPR007071 A-kinase (or PKA)-anchoring protein AKAP95 is implicated in mitotic chromosome condensation by acting as a targeting molecule for the condensin complex. The protein contains two zinc fingers which are thought to mediate the binding of AKAP95 to DNA [].; GO: 0003677 DNA binding, 0005634 nucleus
Probab=23.04 E-value=57 Score=19.40 Aligned_cols=21 Identities=14% Similarity=0.396 Sum_probs=14.3
Q ss_pred cccCCcccccCCchHHHHHHh
Q psy10762 37 HHCNYCAKSFTRKDHMVYHER 57 (126)
Q Consensus 37 ~~c~~C~~~~~~~~~l~~h~~ 57 (126)
|.|++|.........+..|+.
T Consensus 1 F~Cs~CKfrtf~~~ei~~Hle 21 (165)
T PF04988_consen 1 FTCSFCKFRTFEEKEIEKHLE 21 (165)
T ss_pred CccceeeeecccHHHHHHHHc
Confidence 457777776666677777754
No 314
>PRK07591 threonine synthase; Validated
Probab=22.90 E-value=59 Score=22.49 Aligned_cols=25 Identities=16% Similarity=0.479 Sum_probs=15.8
Q ss_pred cccCCcccccCCchHHHHHHhhhcCCCCcccCCCCCcC
Q psy10762 37 HHCNYCAKSFTRKDHMVYHERQHTGETPFPCQYCPKAF 74 (126)
Q Consensus 37 ~~c~~C~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~~ 74 (126)
+.|..||..|... . .|.|+.|+..+
T Consensus 19 l~C~~Cg~~~~~~------------~-~~~C~~cg~~l 43 (421)
T PRK07591 19 LKCRECGAEYPLG------------P-IHVCEECFGPL 43 (421)
T ss_pred EEeCCCCCcCCCC------------C-CccCCCCCCeE
Confidence 6788888766422 1 26788887544
No 315
>PRK08222 hydrogenase 4 subunit H; Validated
Probab=22.63 E-value=1e+02 Score=18.59 Aligned_cols=21 Identities=14% Similarity=0.523 Sum_probs=15.0
Q ss_pred CCccCcccccccCCHHHHHHH
Q psy10762 91 SPHKCTYCMKSFTRKEHLTNH 111 (126)
Q Consensus 91 ~~~~C~~C~~~f~~~~~l~~H 111 (126)
....|..||+.|.....+..-
T Consensus 113 ~~~~C~~Cg~~f~~~k~i~~~ 133 (181)
T PRK08222 113 HLQRCSRCERPFAPQKTVALA 133 (181)
T ss_pred ccCcCcccCCccCcHhHHHHH
Confidence 457899999999866554433
No 316
>COG4847 Uncharacterized protein conserved in archaea [Function unknown]
Probab=22.51 E-value=32 Score=18.40 Aligned_cols=13 Identities=31% Similarity=0.583 Sum_probs=8.9
Q ss_pred CCCCccCcccccc
Q psy10762 89 GESPHKCTYCMKS 101 (126)
Q Consensus 89 ~~~~~~C~~C~~~ 101 (126)
+.+.|+|.+|+..
T Consensus 3 ~lkewkC~VCg~~ 15 (103)
T COG4847 3 GLKEWKCYVCGGT 15 (103)
T ss_pred ccceeeEeeeCCE
Confidence 3466888888754
No 317
>cd00122 MBD MeCP2, MBD1, MBD2, MBD3, MBD4, CLLD8-like, and BAZ2A-like proteins constitute a family of proteins that share the methyl-CpG-binding domain (MBD). The MBD consists of about 70 residues and is defined as the minimal region required for binding to methylated DNA by a methyl-CpG-binding protein which binds specifically to methylated DNA. The MBD can recognize a single symmetrically methylated CpG either as naked DNA or within chromatin. MeCP2, MBD1 and MBD2 (and likely MBD3) form complexes with histone deacetylase and are involved in histone deacetylase-dependent repression of transcription. MBD4 is an endonuclease that forms a complex with the DNA mismatch-repair protein MLH1. The MBDs present in putative chromatin remodelling subunit, BAZ2A, and putative histone methyltransferase, CLLD8, represent two phylogenetically distinct groups within the MBD protein family.
Probab=22.50 E-value=98 Score=14.80 Aligned_cols=21 Identities=14% Similarity=0.290 Sum_probs=16.6
Q ss_pred cccccccCCHHHHHHHHHHhh
Q psy10762 96 TYCMKSFTRKEHLTNHIRQHT 116 (126)
Q Consensus 96 ~~C~~~f~~~~~l~~H~~~h~ 116 (126)
.-||+.|.+...+.+.+..+.
T Consensus 31 sP~Gk~~Rs~~ev~~yL~~~~ 51 (62)
T cd00122 31 SPCGKKLRSKPEVARYLEKTG 51 (62)
T ss_pred CCCCceecCHHHHHHHHHhCC
Confidence 348899999999988877653
No 318
>PRK11827 hypothetical protein; Provisional
Probab=22.16 E-value=59 Score=15.77 Aligned_cols=11 Identities=18% Similarity=0.253 Sum_probs=5.7
Q ss_pred ccCcccccccC
Q psy10762 93 HKCTYCMKSFT 103 (126)
Q Consensus 93 ~~C~~C~~~f~ 103 (126)
..|..|+..|.
T Consensus 27 Lic~~~~laYP 37 (60)
T PRK11827 27 LICKLDNLAFP 37 (60)
T ss_pred EECCccCeecc
Confidence 44555555554
No 319
>PF15227 zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB: 2EGP_A 2ECV_A 2ECJ_A 2YSL_A 2YSJ_A.
Probab=22.07 E-value=90 Score=13.56 Aligned_cols=6 Identities=33% Similarity=1.132 Sum_probs=1.3
Q ss_pred ccCccc
Q psy10762 93 HKCTYC 98 (126)
Q Consensus 93 ~~C~~C 98 (126)
+.|+.|
T Consensus 37 ~~CP~C 42 (42)
T PF15227_consen 37 FSCPEC 42 (42)
T ss_dssp ---SSS
T ss_pred CCCcCC
Confidence 445443
No 320
>PF00649 Copper-fist: Copper fist DNA binding domain; InterPro: IPR001083 Some fungal transcription factors contain an N-terminal domain, the copper fist, which seems to be involved in copper-dependent DNA-binding [, ]. These proteins activate the transcription of the metallothionein gene in response to copper. Metallothionein maintains copper levels in yeast [, ]. The copper fist domain, which is similar in structure to metallothionein itself, undergoes a large conformational change on copper-binding that allows DNA-binding. The domain contains a conserved array of zinc-binding residues (Cys-X2-Cys-X8-Cys-X-His) and forms a three-stranded antiparallel beta-sheet with two short helical segments that project from one end of the beta-sheet []. Conserved residues form a basic patch that may be important for DNA binding. ; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0005507 copper ion binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 1CO4_A.
Probab=22.04 E-value=27 Score=15.37 Aligned_cols=17 Identities=12% Similarity=0.346 Sum_probs=11.2
Q ss_pred CCCCcceeccccccccC
Q psy10762 3 HTGETPHRCDYCAKTFT 19 (126)
Q Consensus 3 ~~~~~~~~C~~C~~~f~ 19 (126)
-.++..|.|..|-+.-.
T Consensus 3 li~g~KyAC~~CirGHR 19 (40)
T PF00649_consen 3 LIDGEKYACESCIRGHR 19 (40)
T ss_dssp EETTEEEEETTTTTTSG
T ss_pred eECCeEEEhhhhhCccc
Confidence 34566788888876543
No 321
>PRK06450 threonine synthase; Validated
Probab=21.99 E-value=64 Score=21.60 Aligned_cols=10 Identities=30% Similarity=0.594 Sum_probs=6.3
Q ss_pred cccCCccccc
Q psy10762 37 HHCNYCAKSF 46 (126)
Q Consensus 37 ~~c~~C~~~~ 46 (126)
+.|..||..+
T Consensus 4 ~~C~~Cg~~~ 13 (338)
T PRK06450 4 EVCMKCGKER 13 (338)
T ss_pred eEECCcCCcC
Confidence 5677777554
No 322
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=21.93 E-value=50 Score=12.63 Aligned_cols=7 Identities=29% Similarity=0.743 Sum_probs=3.8
Q ss_pred ccCCCCC
Q psy10762 66 PCQYCPK 72 (126)
Q Consensus 66 ~C~~C~~ 72 (126)
.|+.|+.
T Consensus 4 ~Cp~Cg~ 10 (26)
T PF13248_consen 4 FCPNCGA 10 (26)
T ss_pred CCcccCC
Confidence 4555554
No 323
>COG2879 Uncharacterized small protein [Function unknown]
Probab=21.87 E-value=1.2e+02 Score=14.91 Aligned_cols=19 Identities=26% Similarity=0.413 Sum_probs=14.8
Q ss_pred cCCchHHHHHHhhhcCCCC
Q psy10762 46 FTRKDHMVYHERQHTGETP 64 (126)
Q Consensus 46 ~~~~~~l~~h~~~~~~~~~ 64 (126)
.++.+.+..|++.++..+|
T Consensus 22 vpdYdnYVehmr~~hPd~p 40 (65)
T COG2879 22 VPDYDNYVEHMRKKHPDKP 40 (65)
T ss_pred CCcHHHHHHHHHHhCcCCC
Confidence 5677788888888887776
No 324
>PF13821 DUF4187: Domain of unknown function (DUF4187)
Probab=21.74 E-value=60 Score=15.35 Aligned_cols=21 Identities=24% Similarity=0.597 Sum_probs=12.6
Q ss_pred CCCccCcccccccCCHHHHHH
Q psy10762 90 ESPHKCTYCMKSFTRKEHLTN 110 (126)
Q Consensus 90 ~~~~~C~~C~~~f~~~~~l~~ 110 (126)
..-+-|-.||-.|.+...|.+
T Consensus 25 ~~~~YC~~Cg~~Y~d~~dL~~ 45 (55)
T PF13821_consen 25 EEHNYCFWCGTKYDDEEDLER 45 (55)
T ss_pred hhCceeeeeCCccCCHHHHHh
Confidence 334456667777766666544
No 325
>smart00586 ZnF_DBF Zinc finger in DBF-like proteins.
Probab=21.67 E-value=63 Score=14.96 Aligned_cols=21 Identities=24% Similarity=0.705 Sum_probs=13.9
Q ss_pred CcceeccccccccCChhHHHHHHH
Q psy10762 6 ETPHRCDYCAKTFTRKEHLVNHVR 29 (126)
Q Consensus 6 ~~~~~C~~C~~~f~~~~~l~~h~~ 29 (126)
.++--|+.|...|. .+..|+.
T Consensus 3 ~k~GYCE~Cr~kfd---~l~~Hi~ 23 (49)
T smart00586 3 KKPGYCENCREKYD---DLETHLL 23 (49)
T ss_pred CCCcccccHhHHHh---hHHHHhc
Confidence 45666888888773 4556654
No 326
>PF09963 DUF2197: Uncharacterized protein conserved in bacteria (DUF2197); InterPro: IPR019241 This family represents various hypothetical bacterial proteins with no known function.
Probab=21.65 E-value=43 Score=15.99 Aligned_cols=6 Identities=33% Similarity=1.325 Sum_probs=2.4
Q ss_pred cccCCC
Q psy10762 65 FPCQYC 70 (126)
Q Consensus 65 ~~C~~C 70 (126)
|.|+.|
T Consensus 32 YmC~eC 37 (56)
T PF09963_consen 32 YMCDEC 37 (56)
T ss_pred eeChhH
Confidence 334333
No 327
>KOG3352|consensus
Probab=21.51 E-value=44 Score=19.57 Aligned_cols=15 Identities=20% Similarity=0.532 Sum_probs=11.5
Q ss_pred CCCccCcccccccCC
Q psy10762 90 ESPHKCTYCMKSFTR 104 (126)
Q Consensus 90 ~~~~~C~~C~~~f~~ 104 (126)
.+..+|++||..|.-
T Consensus 131 ge~~rc~eCG~~fkL 145 (153)
T KOG3352|consen 131 GETQRCPECGHYFKL 145 (153)
T ss_pred CCcccCCcccceEEe
Confidence 456779999988863
No 328
>PF10164 DUF2367: Uncharacterized conserved protein (DUF2367); InterPro: IPR019317 This is a highly conserved set of proteins which contains three pairs of cysteine residues within a length of 42 amino acids and is rich in proline residues towards the N terminus. It includes a membrane protein that has been found to be highly expressed in the mouse brain and consequently, several members have been assigned as brain protein i3 (Bri3). Their function is unknown.
Probab=20.98 E-value=50 Score=17.77 Aligned_cols=13 Identities=23% Similarity=0.726 Sum_probs=9.2
Q ss_pred CCCccCccccccc
Q psy10762 90 ESPHKCTYCMKSF 102 (126)
Q Consensus 90 ~~~~~C~~C~~~f 102 (126)
.+..+|..||..|
T Consensus 86 ~r~~rC~nCG~~f 98 (98)
T PF10164_consen 86 MRERRCSNCGATF 98 (98)
T ss_pred cCccccCCCCccC
Confidence 4666788887765
No 329
>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=20.78 E-value=67 Score=19.04 Aligned_cols=9 Identities=33% Similarity=1.161 Sum_probs=4.1
Q ss_pred ccCCccccc
Q psy10762 38 HCNYCAKSF 46 (126)
Q Consensus 38 ~c~~C~~~~ 46 (126)
.|..|+..+
T Consensus 107 ~C~~C~~~~ 115 (178)
T PF02146_consen 107 RCSKCGKEY 115 (178)
T ss_dssp EETTTSBEE
T ss_pred eecCCCccc
Confidence 444444443
No 330
>PF11494 Ta0938: Ta0938; InterPro: IPR021585 Ta0938 is a protein of unknown function however the structure has been determined. The protein has a novel fold and a putative Zn-binding motif. The structure has two different parts, one region contains a beta sheet flanked by two alpha helices and the other contains a bundle of loops which contain all cysteines in the protein. ; PDB: 2FQH_A.
Probab=20.69 E-value=55 Score=17.60 Aligned_cols=11 Identities=27% Similarity=0.791 Sum_probs=2.6
Q ss_pred ceecccccccc
Q psy10762 8 PHRCDYCAKTF 18 (126)
Q Consensus 8 ~~~C~~C~~~f 18 (126)
.-.|..||.+.
T Consensus 14 e~~CalCG~tW 24 (105)
T PF11494_consen 14 EMGCALCGATW 24 (105)
T ss_dssp GGS-SS---S-
T ss_pred cccccccCCcH
Confidence 33444444443
No 331
>PHA02942 putative transposase; Provisional
Probab=20.57 E-value=83 Score=21.58 Aligned_cols=14 Identities=14% Similarity=0.247 Sum_probs=9.3
Q ss_pred CCCccCcccccccC
Q psy10762 90 ESPHKCTYCMKSFT 103 (126)
Q Consensus 90 ~~~~~C~~C~~~f~ 103 (126)
.+.|.|+.||....
T Consensus 340 ~r~f~C~~CG~~~d 353 (383)
T PHA02942 340 HRYFHCPSCGYEND 353 (383)
T ss_pred CCEEECCCCCCEeC
Confidence 35677877777654
No 332
>PF03884 DUF329: Domain of unknown function (DUF329); InterPro: IPR005584 The biological function of these short proteins is unknown, but they contain four conserved cysteines, suggesting that they all bind zinc. YacG (Q5X8H6 from SWISSPROT) from Escherichia coli has been shown to bind zinc and contains the structural motifs typical of zinc-binding proteins []. The conserved four cysteine motif in these proteins (-C-X(2)-C-X(15)-C-X(3)-C-) is not found in other zinc-binding proteins with known structures.; GO: 0008270 zinc ion binding; PDB: 1LV3_A.
Probab=20.28 E-value=38 Score=16.23 Aligned_cols=12 Identities=33% Similarity=0.614 Sum_probs=5.2
Q ss_pred ccCcccccccCC
Q psy10762 93 HKCTYCMKSFTR 104 (126)
Q Consensus 93 ~~C~~C~~~f~~ 104 (126)
..|++|++.+..
T Consensus 3 v~CP~C~k~~~~ 14 (57)
T PF03884_consen 3 VKCPICGKPVEW 14 (57)
T ss_dssp EE-TTT--EEE-
T ss_pred ccCCCCCCeecc
Confidence 468888876543
No 333
>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=20.26 E-value=41 Score=16.44 Aligned_cols=13 Identities=15% Similarity=0.565 Sum_probs=6.7
Q ss_pred cceeccccccccC
Q psy10762 7 TPHRCDYCAKTFT 19 (126)
Q Consensus 7 ~~~~C~~C~~~f~ 19 (126)
....|+.|+..|+
T Consensus 52 g~L~Cp~c~r~YP 64 (68)
T PF03966_consen 52 GELICPECGREYP 64 (68)
T ss_dssp TEEEETTTTEEEE
T ss_pred CEEEcCCCCCEEe
Confidence 3345555655553
No 334
>smart00109 C1 Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains). Some bind phorbol esters and diacylglycerol. Some bind RasGTP. Zinc-binding domains.
Probab=20.22 E-value=68 Score=13.83 Aligned_cols=9 Identities=44% Similarity=0.981 Sum_probs=4.4
Q ss_pred ccCCccccc
Q psy10762 38 HCNYCAKSF 46 (126)
Q Consensus 38 ~c~~C~~~~ 46 (126)
.|..|+..+
T Consensus 13 ~C~~C~~~i 21 (49)
T smart00109 13 KCCVCRKSI 21 (49)
T ss_pred Ccccccccc
Confidence 455555443
Done!