Query psy12028
Match_columns 118
No_of_seqs 129 out of 1137
Neff 11.6
Searched_HMMs 46136
Date Fri Aug 16 16:48:02 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy12028.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/12028hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2462|consensus 100.0 6.5E-33 1.4E-37 161.8 5.1 110 2-118 131-242 (279)
2 KOG2462|consensus 100.0 1.3E-30 2.9E-35 152.2 5.0 104 2-113 162-265 (279)
3 KOG1074|consensus 99.9 3.7E-24 7.9E-29 140.4 1.4 53 62-115 605-657 (958)
4 KOG3576|consensus 99.8 1.2E-21 2.6E-26 110.7 3.4 110 2-116 118-237 (267)
5 KOG1074|consensus 99.8 8.1E-21 1.8E-25 125.0 3.5 53 63-116 880-932 (958)
6 KOG3623|consensus 99.7 2E-18 4.3E-23 112.8 2.9 110 2-112 211-330 (1007)
7 KOG3608|consensus 99.7 5.1E-18 1.1E-22 103.1 3.6 108 2-115 238-376 (467)
8 KOG3576|consensus 99.7 1.9E-18 4.1E-23 97.9 0.5 85 28-117 115-199 (267)
9 KOG3608|consensus 99.7 3.2E-17 7E-22 99.7 5.1 108 4-114 182-315 (467)
10 KOG3623|consensus 99.7 1.8E-17 3.9E-22 108.5 1.6 80 28-112 892-971 (1007)
11 PHA00733 hypothetical protein 99.5 2.6E-14 5.6E-19 77.4 4.0 85 28-116 38-124 (128)
12 PLN03086 PRLI-interacting fact 99.4 5.7E-13 1.2E-17 86.8 7.1 102 2-116 454-565 (567)
13 PHA02768 hypothetical protein; 99.3 1.2E-12 2.6E-17 59.8 1.6 44 62-108 5-48 (55)
14 PHA00733 hypothetical protein 99.3 2.9E-12 6.2E-17 69.5 3.2 80 2-87 41-124 (128)
15 PHA02768 hypothetical protein; 99.2 4.8E-12 1.1E-16 57.8 2.0 42 2-46 6-47 (55)
16 KOG3993|consensus 99.2 4E-12 8.6E-17 79.4 0.9 52 2-54 268-319 (500)
17 PF13465 zf-H2C2_2: Zinc-finge 99.1 2.8E-11 6.1E-16 47.7 1.3 26 77-103 1-26 (26)
18 PLN03086 PRLI-interacting fact 99.1 5.2E-10 1.1E-14 73.4 6.0 77 28-114 451-537 (567)
19 KOG3993|consensus 99.1 2.1E-11 4.6E-16 76.2 -0.4 82 31-116 268-381 (500)
20 PHA00616 hypothetical protein 99.0 1.9E-10 4E-15 50.2 1.2 33 62-95 1-33 (44)
21 PF13465 zf-H2C2_2: Zinc-finge 98.9 6.4E-10 1.4E-14 43.8 1.8 26 16-42 1-26 (26)
22 PHA00616 hypothetical protein 98.9 5.5E-10 1.2E-14 48.8 1.5 34 1-35 1-34 (44)
23 PHA00732 hypothetical protein 98.9 2.8E-09 6E-14 53.0 3.1 45 1-51 1-45 (79)
24 PHA00732 hypothetical protein 98.8 2.2E-09 4.8E-14 53.4 2.1 48 30-86 1-48 (79)
25 PF05605 zf-Di19: Drought indu 98.8 1.5E-08 3.3E-13 46.9 3.6 51 63-116 3-54 (54)
26 PF05605 zf-Di19: Drought indu 98.6 1.2E-07 2.6E-12 43.9 4.1 46 2-50 3-49 (54)
27 PF00096 zf-C2H2: Zinc finger, 98.6 2.5E-08 5.3E-13 38.0 1.1 22 92-113 1-22 (23)
28 PF13894 zf-C2H2_4: C2H2-type 98.5 6.3E-08 1.4E-12 37.1 1.7 24 92-115 1-24 (24)
29 PF00096 zf-C2H2: Zinc finger, 98.5 7.3E-08 1.6E-12 36.7 1.1 22 2-23 1-22 (23)
30 PF13912 zf-C2H2_6: C2H2-type 98.4 1.2E-07 2.7E-12 37.5 1.1 26 91-116 1-26 (27)
31 PF13912 zf-C2H2_6: C2H2-type 98.3 1.8E-07 3.9E-12 37.0 0.9 25 1-25 1-25 (27)
32 PF12756 zf-C2H2_2: C2H2 type 98.3 6.2E-07 1.4E-11 46.6 2.0 73 32-114 1-73 (100)
33 PF13894 zf-C2H2_4: C2H2-type 98.2 8.6E-07 1.9E-11 33.8 1.5 23 2-24 1-23 (24)
34 COG5189 SFP1 Putative transcri 98.1 3.2E-07 7E-12 56.2 -0.6 70 28-112 347-419 (423)
35 PF09237 GAGA: GAGA factor; I 98.1 3E-06 6.6E-11 37.9 1.9 29 89-117 22-50 (54)
36 smart00355 ZnF_C2H2 zinc finge 98.0 8E-06 1.7E-10 31.5 2.5 23 92-114 1-23 (26)
37 PF13909 zf-H2C2_5: C2H2-type 98.0 4.7E-06 1E-10 31.9 1.5 24 92-116 1-24 (24)
38 PF12756 zf-C2H2_2: C2H2 type 98.0 4E-06 8.7E-11 43.6 1.6 74 3-86 1-74 (100)
39 COG5189 SFP1 Putative transcri 97.9 2.4E-06 5.2E-11 52.5 0.6 25 1-25 349-375 (423)
40 smart00355 ZnF_C2H2 zinc finge 97.8 2.4E-05 5.3E-10 30.1 2.1 23 2-24 1-23 (26)
41 PF09237 GAGA: GAGA factor; I 97.7 2.8E-05 6E-10 34.9 1.8 32 59-91 21-52 (54)
42 PF12874 zf-met: Zinc-finger o 97.6 2.4E-05 5.2E-10 30.1 1.0 23 92-114 1-23 (25)
43 PRK04860 hypothetical protein; 97.6 2.7E-05 5.8E-10 44.0 1.2 40 61-105 118-157 (160)
44 PF12874 zf-met: Zinc-finger o 97.5 4.7E-05 1E-09 29.3 0.8 20 3-22 2-21 (25)
45 KOG2785|consensus 97.4 0.0003 6.5E-09 44.6 4.3 112 2-113 4-242 (390)
46 PRK04860 hypothetical protein; 97.4 0.00011 2.3E-09 41.6 1.9 37 30-74 119-155 (160)
47 PF12171 zf-C2H2_jaz: Zinc-fin 97.4 0.00013 2.8E-09 28.6 1.4 21 2-22 2-22 (27)
48 KOG2231|consensus 97.3 0.00095 2.1E-08 45.6 5.8 97 11-115 124-236 (669)
49 PF12171 zf-C2H2_jaz: Zinc-fin 97.3 8.9E-05 1.9E-09 29.1 0.6 22 92-113 2-23 (27)
50 PF13909 zf-H2C2_5: C2H2-type 97.2 0.0002 4.4E-09 27.2 1.3 22 2-24 1-22 (24)
51 PF13913 zf-C2HC_2: zinc-finge 97.0 0.00087 1.9E-08 25.8 2.0 20 92-112 3-22 (25)
52 KOG4173|consensus 96.8 0.00044 9.6E-09 40.3 0.8 80 29-115 78-170 (253)
53 KOG1146|consensus 96.7 0.00044 9.5E-09 50.1 0.3 23 90-112 588-610 (1406)
54 smart00451 ZnF_U1 U1-like zinc 96.5 0.0028 6E-08 26.2 2.0 23 91-113 3-25 (35)
55 KOG1146|consensus 96.4 0.0018 3.9E-08 47.2 1.6 53 61-113 464-540 (1406)
56 smart00451 ZnF_U1 U1-like zinc 96.2 0.004 8.7E-08 25.8 1.5 20 2-21 4-23 (35)
57 cd00350 rubredoxin_like Rubred 96.1 0.0038 8.2E-08 25.7 1.3 25 2-39 2-26 (33)
58 COG2888 Predicted Zn-ribbon RN 95.8 0.0094 2E-07 27.8 2.0 33 29-70 26-58 (61)
59 COG4049 Uncharacterized protei 95.7 0.0038 8.3E-08 28.6 0.5 28 60-87 15-42 (65)
60 COG5048 FOG: Zn-finger [Genera 95.7 0.0028 6E-08 41.1 -0.0 50 1-51 289-344 (467)
61 COG5236 Uncharacterized conser 95.3 0.026 5.6E-07 35.9 3.1 102 2-112 152-272 (493)
62 COG5048 FOG: Zn-finger [Genera 94.9 0.0044 9.5E-08 40.2 -0.9 55 61-116 288-348 (467)
63 PF09538 FYDLN_acid: Protein o 94.5 0.026 5.7E-07 30.0 1.5 11 31-41 10-20 (108)
64 PRK14890 putative Zn-ribbon RN 94.2 0.041 8.9E-07 25.7 1.7 33 29-70 24-56 (59)
65 KOG2482|consensus 94.1 0.068 1.5E-06 34.0 2.9 49 63-111 280-354 (423)
66 KOG2482|consensus 94.1 0.14 3.1E-06 32.7 4.3 24 92-115 280-303 (423)
67 cd00729 rubredoxin_SM Rubredox 94.0 0.038 8.2E-07 22.9 1.2 25 2-39 3-27 (34)
68 PF13719 zinc_ribbon_5: zinc-r 93.9 0.029 6.3E-07 23.7 0.8 32 64-101 4-35 (37)
69 KOG4173|consensus 93.8 0.022 4.9E-07 33.5 0.4 78 3-84 81-168 (253)
70 PF09986 DUF2225: Uncharacteri 93.4 0.017 3.7E-07 34.5 -0.5 41 2-42 6-60 (214)
71 KOG2231|consensus 93.4 0.12 2.6E-06 36.0 3.3 82 32-115 117-206 (669)
72 smart00834 CxxC_CXXC_SSSS Puta 93.2 0.031 6.7E-07 23.9 0.3 12 2-13 6-17 (41)
73 PF12013 DUF3505: Protein of u 93.1 0.085 1.8E-06 28.0 1.9 26 91-116 80-109 (109)
74 KOG2186|consensus 93.1 0.052 1.1E-06 33.0 1.2 46 2-51 4-49 (276)
75 TIGR00622 ssl1 transcription f 93.0 0.26 5.7E-06 26.4 3.6 84 28-114 13-104 (112)
76 PF09723 Zn-ribbon_8: Zinc rib 93.0 0.027 5.8E-07 24.5 -0.1 12 2-13 6-17 (42)
77 COG4049 Uncharacterized protei 92.9 0.11 2.4E-06 23.9 1.9 23 28-50 15-37 (65)
78 TIGR02605 CxxC_CxxC_SSSS putat 92.8 0.032 7E-07 25.3 0.1 12 2-13 6-17 (52)
79 PF13717 zinc_ribbon_4: zinc-r 92.8 0.056 1.2E-06 22.7 0.8 32 64-101 4-35 (36)
80 TIGR02098 MJ0042_CXXC MJ0042 f 92.6 0.057 1.2E-06 22.8 0.7 10 92-101 26-35 (38)
81 TIGR00373 conserved hypothetic 92.4 0.12 2.7E-06 29.4 2.1 32 28-72 107-138 (158)
82 PF12013 DUF3505: Protein of u 92.3 0.25 5.5E-06 26.2 3.1 25 63-87 81-109 (109)
83 PRK00464 nrdR transcriptional 92.2 0.042 9.2E-07 31.1 0.0 48 2-50 1-48 (154)
84 COG1592 Rubrerythrin [Energy p 92.0 0.096 2.1E-06 30.0 1.3 24 62-99 134-157 (166)
85 TIGR00373 conserved hypothetic 91.9 0.11 2.4E-06 29.6 1.5 30 2-41 110-139 (158)
86 COG1997 RPL43A Ribosomal prote 91.8 0.055 1.2E-06 27.4 0.2 29 63-102 36-64 (89)
87 smart00531 TFIIE Transcription 91.8 0.11 2.4E-06 29.2 1.4 38 28-73 97-134 (147)
88 smart00614 ZnF_BED BED zinc fi 91.7 0.18 3.9E-06 22.7 1.8 24 92-115 19-47 (50)
89 PRK00398 rpoP DNA-directed RNA 91.7 0.074 1.6E-06 23.6 0.5 11 2-12 4-14 (46)
90 KOG2186|consensus 91.3 0.13 2.9E-06 31.3 1.5 47 30-83 3-49 (276)
91 PRK06266 transcription initiat 91.3 0.14 3E-06 29.8 1.5 33 28-73 115-147 (178)
92 TIGR02300 FYDLN_acid conserved 91.1 0.18 4E-06 27.5 1.7 13 29-41 25-37 (129)
93 PF02892 zf-BED: BED zinc fing 91.0 0.14 3E-06 22.4 1.0 27 89-115 14-44 (45)
94 PRK06266 transcription initiat 90.9 0.19 4E-06 29.3 1.8 30 61-100 116-145 (178)
95 smart00659 RPOLCX RNA polymera 90.6 0.19 4.1E-06 22.1 1.3 26 2-39 3-28 (44)
96 PF09845 DUF2072: Zn-ribbon co 90.6 0.13 2.8E-06 28.2 0.9 28 1-39 1-28 (131)
97 PF05443 ROS_MUCR: ROS/MUCR tr 90.6 0.12 2.7E-06 28.5 0.8 25 89-116 70-94 (132)
98 smart00734 ZnF_Rad18 Rad18-lik 89.5 0.48 1E-05 18.3 1.9 19 93-112 3-21 (26)
99 COG3357 Predicted transcriptio 88.9 0.26 5.5E-06 25.2 1.1 14 29-42 57-70 (97)
100 KOG4167|consensus 88.7 0.069 1.5E-06 37.3 -1.2 25 2-26 793-817 (907)
101 PF14353 CpXC: CpXC protein 88.7 0.38 8.3E-06 26.3 1.8 48 2-49 2-57 (128)
102 KOG2893|consensus 88.6 0.09 1.9E-06 31.8 -0.7 41 65-110 13-53 (341)
103 PF03604 DNA_RNApol_7kD: DNA d 88.6 0.34 7.5E-06 19.7 1.2 26 2-39 1-26 (32)
104 PF10571 UPF0547: Uncharacteri 88.5 0.31 6.8E-06 18.8 1.0 10 93-102 16-25 (26)
105 PF04959 ARS2: Arsenite-resist 88.0 0.2 4.3E-06 30.1 0.4 29 89-117 75-103 (214)
106 PF06524 NOA36: NOA36 protein; 87.2 0.27 5.8E-06 30.3 0.7 26 89-114 207-232 (314)
107 COG5188 PRP9 Splicing factor 3 86.3 0.54 1.2E-05 30.3 1.7 23 89-111 372-395 (470)
108 PF08274 PhnA_Zn_Ribbon: PhnA 86.2 0.32 7E-06 19.5 0.5 26 3-40 4-29 (30)
109 TIGR01206 lysW lysine biosynth 86.2 0.33 7.2E-06 22.4 0.6 31 2-41 3-33 (54)
110 smart00440 ZnF_C2C2 C2C2 Zinc 86.1 0.1 2.3E-06 22.4 -1.1 11 30-40 28-38 (40)
111 COG1996 RPC10 DNA-directed RNA 86.0 0.36 7.9E-06 21.8 0.6 10 2-11 7-16 (49)
112 PF13878 zf-C2H2_3: zinc-finge 85.5 1.1 2.3E-05 19.4 2.0 22 3-24 15-38 (41)
113 PHA00626 hypothetical protein 85.4 0.5 1.1E-05 21.9 0.9 15 89-103 21-35 (59)
114 COG4957 Predicted transcriptio 84.9 0.66 1.4E-05 25.6 1.4 22 92-116 77-98 (148)
115 PF07754 DUF1610: Domain of un 84.3 0.51 1.1E-05 17.9 0.6 11 28-38 14-24 (24)
116 COG5236 Uncharacterized conser 84.2 1.8 3.9E-05 28.1 3.2 21 4-24 223-243 (493)
117 KOG2893|consensus 84.2 0.28 6E-06 29.8 -0.2 41 4-49 13-53 (341)
118 PF09963 DUF2197: Uncharacteri 84.0 0.27 5.8E-06 22.9 -0.3 9 4-12 5-13 (56)
119 KOG2785|consensus 83.7 1.6 3.4E-05 28.6 2.9 49 3-51 168-241 (390)
120 TIGR00686 phnA alkylphosphonat 83.6 0.7 1.5E-05 24.5 1.1 30 3-44 4-33 (109)
121 PF15269 zf-C2H2_7: Zinc-finge 83.4 0.88 1.9E-05 20.0 1.2 19 3-21 22-40 (54)
122 COG3364 Zn-ribbon containing p 83.1 0.86 1.9E-05 23.9 1.3 14 1-14 2-15 (112)
123 PF13453 zf-TFIIB: Transcripti 82.9 0.63 1.4E-05 20.0 0.7 21 28-48 17-37 (41)
124 PRK09678 DNA-binding transcrip 82.3 0.7 1.5E-05 22.7 0.8 40 2-44 2-43 (72)
125 PF07975 C1_4: TFIIH C1-like d 81.8 1.4 2.9E-05 20.1 1.6 21 29-49 20-40 (51)
126 KOG2593|consensus 81.8 0.98 2.1E-05 30.0 1.5 18 30-47 128-145 (436)
127 PF06524 NOA36: NOA36 protein; 81.2 0.72 1.6E-05 28.5 0.7 82 2-85 143-232 (314)
128 KOG2907|consensus 80.6 0.95 2.1E-05 24.2 1.0 40 30-73 74-113 (116)
129 PRK10220 hypothetical protein; 80.4 1.3 2.8E-05 23.6 1.4 30 3-44 5-34 (111)
130 PF01927 Mut7-C: Mut7-C RNAse 79.8 1.3 2.7E-05 25.0 1.4 11 62-72 124-134 (147)
131 COG4338 Uncharacterized protei 78.6 0.86 1.9E-05 20.4 0.4 18 31-48 13-30 (54)
132 COG1656 Uncharacterized conser 78.5 2.5 5.5E-05 24.4 2.3 18 30-47 130-147 (165)
133 PRK03824 hypA hydrogenase nick 78.3 0.91 2E-05 25.2 0.5 15 29-43 69-83 (135)
134 PF01096 TFIIS_C: Transcriptio 78.1 0.083 1.8E-06 22.6 -2.9 10 31-40 29-38 (39)
135 PRK04023 DNA polymerase II lar 78.0 4.2 9E-05 30.4 3.6 10 30-39 626-635 (1121)
136 PF07503 zf-HYPF: HypF finger; 77.9 1.1 2.4E-05 18.7 0.6 31 65-102 2-32 (35)
137 PF14446 Prok-RING_1: Prokaryo 77.8 0.75 1.6E-05 21.2 0.1 10 31-40 22-31 (54)
138 smart00154 ZnF_AN1 AN1-like Zi 77.4 1.2 2.6E-05 19.0 0.7 12 1-12 12-23 (39)
139 COG0068 HypF Hydrogenase matur 76.7 0.46 9.9E-06 33.5 -1.1 58 31-100 124-182 (750)
140 PF12907 zf-met2: Zinc-binding 76.0 2 4.3E-05 18.5 1.1 22 63-84 2-26 (40)
141 COG1675 TFA1 Transcription ini 75.2 4.4 9.5E-05 23.7 2.7 33 28-73 111-143 (176)
142 PF02176 zf-TRAF: TRAF-type zi 75.2 0.88 1.9E-05 21.1 -0.1 41 29-74 8-54 (60)
143 KOG0978|consensus 74.9 1.4 2.9E-05 31.3 0.7 20 91-110 678-697 (698)
144 TIGR00280 L37a ribosomal prote 74.8 0.76 1.6E-05 23.7 -0.4 11 91-101 53-63 (91)
145 PF10013 DUF2256: Uncharacteri 74.2 2.8 6E-05 18.3 1.3 16 93-108 10-25 (42)
146 PF04780 DUF629: Protein of un 74.0 2.8 6.1E-05 28.4 1.9 25 91-115 57-81 (466)
147 PRK12380 hydrogenase nickel in 73.8 1.6 3.4E-05 23.5 0.7 13 31-43 71-83 (113)
148 KOG4167|consensus 73.7 1.7 3.6E-05 31.1 0.9 28 60-87 790-817 (907)
149 PF04959 ARS2: Arsenite-resist 73.5 2.2 4.7E-05 25.8 1.2 27 28-54 75-101 (214)
150 PF05191 ADK_lid: Adenylate ki 72.9 0.74 1.6E-05 19.3 -0.6 9 64-72 3-11 (36)
151 KOG2636|consensus 72.5 3.3 7.1E-05 27.9 1.9 28 83-111 394-422 (497)
152 COG1594 RPB9 DNA-directed RNA 72.5 0.87 1.9E-05 24.5 -0.5 39 31-73 73-111 (113)
153 PF13240 zinc_ribbon_2: zinc-r 71.5 2.2 4.8E-05 15.8 0.7 6 33-38 16-21 (23)
154 TIGR00100 hypA hydrogenase nic 71.4 1.7 3.7E-05 23.4 0.5 13 31-43 71-83 (115)
155 KOG1842|consensus 71.4 2.3 5E-05 28.5 1.1 25 63-87 16-40 (505)
156 PF13824 zf-Mss51: Zinc-finger 71.3 5.7 0.00012 18.4 2.1 15 28-42 12-26 (55)
157 PF08790 zf-LYAR: LYAR-type C2 71.2 0.9 2E-05 17.9 -0.5 9 32-40 2-10 (28)
158 PRK03976 rpl37ae 50S ribosomal 71.1 1 2.2E-05 23.2 -0.4 11 91-101 54-64 (90)
159 PF07282 OrfB_Zn_ribbon: Putat 69.8 3.8 8.3E-05 19.6 1.5 29 31-73 29-57 (69)
160 KOG1280|consensus 69.8 5.3 0.00011 26.0 2.3 24 2-25 80-103 (381)
161 COG1655 Uncharacterized protei 69.6 1 2.2E-05 27.4 -0.7 20 3-22 21-40 (267)
162 COG2331 Uncharacterized protei 68.9 1.1 2.3E-05 22.2 -0.6 10 31-40 13-22 (82)
163 COG4896 Uncharacterized protei 68.6 1.8 4E-05 20.4 0.2 38 3-41 4-42 (68)
164 smart00661 RPOL9 RNA polymeras 67.9 2.8 6.1E-05 18.7 0.7 13 30-42 20-32 (52)
165 KOG3408|consensus 66.1 4.7 0.0001 22.0 1.4 24 61-84 56-79 (129)
166 PF13451 zf-trcl: Probable zin 65.6 3 6.4E-05 18.9 0.5 41 28-71 2-42 (49)
167 PHA02998 RNA polymerase subuni 65.5 1.5 3.2E-05 25.6 -0.5 42 30-75 143-184 (195)
168 KOG2071|consensus 65.2 5.7 0.00012 27.7 2.0 27 89-115 416-442 (579)
169 COG1571 Predicted DNA-binding 64.3 4.6 0.0001 27.0 1.4 29 64-104 352-380 (421)
170 PRK00564 hypA hydrogenase nick 64.3 3 6.5E-05 22.6 0.5 13 31-43 72-84 (117)
171 PRK03681 hypA hydrogenase nick 64.0 3.5 7.5E-05 22.2 0.7 12 31-42 71-82 (114)
172 PF04423 Rad50_zn_hook: Rad50 63.9 2.7 5.9E-05 19.2 0.3 12 32-43 22-33 (54)
173 KOG4124|consensus 63.0 1.3 2.8E-05 28.7 -1.1 22 1-22 349-372 (442)
174 PF01428 zf-AN1: AN1-like Zinc 62.0 2.2 4.7E-05 18.5 -0.2 12 90-101 12-23 (43)
175 PTZ00255 60S ribosomal protein 61.0 3.9 8.4E-05 21.1 0.5 33 28-74 34-66 (90)
176 PF15135 UPF0515: Uncharacteri 60.5 8.1 0.00018 24.0 1.9 14 29-42 111-124 (278)
177 PTZ00448 hypothetical protein; 59.8 8.5 0.00018 25.3 2.0 23 91-113 314-336 (373)
178 cd00730 rubredoxin Rubredoxin; 59.5 4.7 0.0001 18.3 0.6 12 2-13 2-13 (50)
179 PF01155 HypA: Hydrogenase exp 58.9 3.2 6.9E-05 22.3 0.0 12 31-42 71-82 (113)
180 PTZ00448 hypothetical protein; 57.4 9.2 0.0002 25.2 1.8 21 31-51 315-335 (373)
181 COG1773 Rubredoxin [Energy pro 57.3 3.8 8.2E-05 19.0 0.1 12 2-13 4-15 (55)
182 PRK00762 hypA hydrogenase nick 57.3 5.1 0.00011 21.9 0.6 11 31-42 71-81 (124)
183 PRK05978 hypothetical protein; 57.3 3.7 8.1E-05 23.3 0.1 9 31-39 34-42 (148)
184 PF06397 Desulfoferrod_N: Desu 56.8 3.2 6.8E-05 17.5 -0.2 10 2-11 7-16 (36)
185 PF01780 Ribosomal_L37ae: Ribo 56.6 2 4.3E-05 22.1 -0.9 32 29-74 34-65 (90)
186 PF04780 DUF629: Protein of un 56.6 8.1 0.00017 26.4 1.5 23 29-51 56-78 (466)
187 TIGR01384 TFS_arch transcripti 56.3 2.1 4.5E-05 22.5 -0.9 40 30-73 62-101 (104)
188 COG1198 PriA Primosomal protei 55.8 4.9 0.00011 29.0 0.5 12 28-39 473-484 (730)
189 PLN02294 cytochrome c oxidase 55.0 7.2 0.00016 22.7 1.0 16 28-43 139-154 (174)
190 PRK14714 DNA polymerase II lar 54.9 14 0.0003 28.7 2.5 32 31-71 668-701 (1337)
191 PF05290 Baculo_IE-1: Baculovi 54.3 4.5 9.6E-05 22.5 0.1 16 28-43 78-93 (140)
192 KOG2593|consensus 53.8 16 0.00035 24.7 2.5 34 61-98 127-160 (436)
193 TIGR00416 sms DNA repair prote 53.5 6.7 0.00014 26.6 0.8 10 31-40 8-17 (454)
194 KOG0717|consensus 53.5 7.3 0.00016 26.5 1.0 22 2-23 293-314 (508)
195 PF01286 XPA_N: XPA protein N- 53.2 4.7 0.0001 16.7 0.1 14 92-105 4-17 (34)
196 PF08209 Sgf11: Sgf11 (transcr 52.8 14 0.00031 15.1 1.5 20 30-50 4-23 (33)
197 PRK00420 hypothetical protein; 52.3 12 0.00025 20.3 1.5 10 31-40 24-33 (112)
198 cd00924 Cyt_c_Oxidase_Vb Cytoc 52.0 8.8 0.00019 20.1 1.0 15 28-42 77-91 (97)
199 COG5216 Uncharacterized conser 51.4 11 0.00024 17.7 1.1 11 31-42 23-33 (67)
200 PF00301 Rubredoxin: Rubredoxi 50.8 4.5 9.8E-05 18.1 -0.2 13 2-14 2-14 (47)
201 COG4530 Uncharacterized protei 50.7 16 0.00035 19.6 1.8 14 89-102 24-37 (129)
202 CHL00174 accD acetyl-CoA carbo 50.7 8.8 0.00019 24.5 1.0 10 31-40 39-48 (296)
203 PF12760 Zn_Tnp_IS1595: Transp 50.1 6.9 0.00015 17.2 0.4 9 31-39 19-27 (46)
204 PRK11823 DNA repair protein Ra 49.3 8.6 0.00019 26.0 0.8 9 2-10 8-16 (446)
205 COG3091 SprT Zn-dependent meta 48.8 6.7 0.00015 22.4 0.3 35 60-100 115-149 (156)
206 PF14311 DUF4379: Domain of un 48.3 17 0.00037 16.5 1.6 15 30-44 28-42 (55)
207 COG1326 Uncharacterized archae 48.3 17 0.00037 21.7 1.8 14 28-41 28-41 (201)
208 TIGR00515 accD acetyl-CoA carb 47.8 15 0.00033 23.4 1.7 10 31-40 27-36 (285)
209 TIGR01385 TFSII transcription 47.8 4.7 0.0001 25.7 -0.5 41 29-73 257-297 (299)
210 PF01363 FYVE: FYVE zinc finge 47.7 8.9 0.00019 18.3 0.6 11 31-41 10-20 (69)
211 PF11931 DUF3449: Domain of un 46.5 6.6 0.00014 23.5 0.0 22 89-110 99-121 (196)
212 PF10276 zf-CHCC: Zinc-finger 46.4 4.6 9.9E-05 17.4 -0.5 11 91-101 29-39 (40)
213 TIGR00143 hypF [NiFe] hydrogen 46.3 2.7 5.9E-05 30.1 -1.8 58 32-100 92-149 (711)
214 PF13821 DUF4187: Domain of un 46.2 12 0.00026 17.4 0.8 18 93-110 29-46 (55)
215 COG3677 Transposase and inacti 46.0 9.9 0.00021 21.0 0.6 36 63-104 31-66 (129)
216 cd00974 DSRD Desulforedoxin (D 45.6 8 0.00017 15.7 0.2 10 2-11 5-14 (34)
217 PF14787 zf-CCHC_5: GAG-polypr 45.6 14 0.0003 15.5 0.9 15 92-106 3-17 (36)
218 TIGR00319 desulf_FeS4 desulfof 45.4 7.8 0.00017 15.7 0.1 10 2-11 8-17 (34)
219 COG2956 Predicted N-acetylgluc 45.2 20 0.00043 23.6 1.9 14 28-41 352-365 (389)
220 PF10537 WAC_Acf1_DNA_bd: ATP- 45.1 28 0.00061 18.5 2.2 37 2-40 4-40 (102)
221 KOG1280|consensus 45.1 24 0.00052 23.2 2.2 29 89-117 77-105 (381)
222 cd01121 Sms Sms (bacterial rad 44.2 13 0.00027 24.7 1.0 23 2-39 1-23 (372)
223 COG4391 Uncharacterized protei 44.0 15 0.00032 17.5 1.0 14 28-41 46-59 (62)
224 PF11672 DUF3268: Protein of u 44.0 13 0.00027 19.8 0.8 8 31-38 32-39 (102)
225 PRK05654 acetyl-CoA carboxylas 43.9 13 0.00027 23.8 1.0 12 30-41 27-38 (292)
226 PLN02748 tRNA dimethylallyltra 43.4 23 0.00051 24.3 2.1 24 90-113 417-441 (468)
227 TIGR01562 FdhE formate dehydro 43.4 18 0.0004 23.3 1.6 8 63-70 225-232 (305)
228 PF14447 Prok-RING_4: Prokaryo 43.2 13 0.00029 17.3 0.7 16 28-43 37-52 (55)
229 COG4306 Uncharacterized protei 43.1 11 0.00025 20.7 0.6 25 16-40 25-49 (160)
230 PF04810 zf-Sec23_Sec24: Sec23 43.0 4.6 9.9E-05 17.2 -0.8 10 29-38 23-32 (40)
231 KOG2071|consensus 42.9 18 0.00039 25.5 1.6 26 1-26 418-443 (579)
232 PF02891 zf-MIZ: MIZ/SP-RING z 42.2 10 0.00023 17.0 0.3 8 31-38 42-49 (50)
233 KOG2857|consensus 41.5 18 0.00039 20.4 1.2 21 30-50 17-37 (157)
234 PF12773 DZR: Double zinc ribb 41.4 20 0.00044 15.8 1.2 10 32-41 14-23 (50)
235 PF11789 zf-Nse: Zinc-finger o 41.4 12 0.00026 17.4 0.4 16 29-44 23-38 (57)
236 KOG2807|consensus 41.3 32 0.0007 22.5 2.4 19 30-48 290-308 (378)
237 TIGR03829 YokU_near_AblA uncha 41.3 20 0.00044 18.5 1.3 14 3-16 37-50 (89)
238 PRK14892 putative transcriptio 41.0 8 0.00017 20.4 -0.2 8 30-37 21-28 (99)
239 PF02591 DUF164: Putative zinc 40.9 29 0.00062 15.9 1.7 33 31-71 23-55 (56)
240 PF14255 Cys_rich_CPXG: Cystei 40.9 15 0.00033 16.8 0.7 11 32-42 2-12 (52)
241 TIGR00244 transcriptional regu 40.7 14 0.00031 21.0 0.7 16 90-105 27-42 (147)
242 PF14803 Nudix_N_2: Nudix N-te 40.5 8.6 0.00019 15.9 -0.1 8 31-38 23-30 (34)
243 PF14369 zf-RING_3: zinc-finge 40.5 16 0.00035 15.1 0.7 10 32-41 23-32 (35)
244 PRK08222 hydrogenase 4 subunit 40.3 22 0.00049 20.9 1.6 17 2-18 115-131 (181)
245 KOG1842|consensus 40.0 26 0.00057 23.9 1.9 22 29-50 14-35 (505)
246 PF13005 zf-IS66: zinc-finger 39.6 6.1 0.00013 17.2 -0.7 9 4-12 5-13 (47)
247 KOG2272|consensus 38.8 41 0.00089 21.2 2.5 14 91-104 221-234 (332)
248 PF07800 DUF1644: Protein of u 38.2 43 0.00094 19.4 2.4 51 63-116 81-133 (162)
249 PF10071 DUF2310: Zn-ribbon-co 37.6 11 0.00023 23.7 -0.1 30 31-71 221-250 (258)
250 PRK05452 anaerobic nitric oxid 37.5 14 0.00031 25.3 0.5 16 28-43 423-438 (479)
251 smart00132 LIM Zinc-binding do 37.4 20 0.00043 14.3 0.8 10 2-11 28-37 (39)
252 PRK12722 transcriptional activ 37.4 29 0.00063 20.7 1.7 30 29-70 133-162 (187)
253 PTZ00043 cytochrome c oxidase 37.3 20 0.00044 22.0 1.0 16 28-43 179-194 (268)
254 PRK01343 zinc-binding protein; 37.2 25 0.00055 16.5 1.2 12 91-102 9-20 (57)
255 PRK06260 threonine synthase; V 37.2 25 0.00055 23.4 1.6 29 2-43 4-32 (397)
256 KOG4727|consensus 36.6 17 0.00037 21.2 0.7 21 2-22 76-96 (193)
257 KOG2923|consensus 36.5 32 0.00069 16.5 1.4 6 36-41 27-32 (67)
258 PF11023 DUF2614: Protein of u 36.2 13 0.00029 20.0 0.2 15 28-42 67-81 (114)
259 PF14354 Lar_restr_allev: Rest 36.2 26 0.00057 16.2 1.2 11 30-40 3-13 (61)
260 COG1885 Uncharacterized protei 36.1 21 0.00046 19.0 0.9 15 29-43 48-62 (115)
261 COG5112 UFD2 U1-like Zn-finger 35.6 30 0.00064 18.5 1.4 23 62-84 55-77 (126)
262 PRK12387 formate hydrogenlyase 35.0 26 0.00057 20.4 1.3 16 2-17 115-130 (180)
263 PF09332 Mcm10: Mcm10 replicat 34.8 4.5 9.7E-05 26.4 -2.0 12 31-42 253-264 (344)
264 PRK12860 transcriptional activ 34.4 34 0.00074 20.4 1.7 29 29-69 133-161 (189)
265 KOG3214|consensus 34.3 19 0.00041 19.0 0.5 13 63-75 48-60 (109)
266 PF08271 TF_Zn_Ribbon: TFIIB z 34.2 24 0.00053 15.1 0.8 9 92-100 1-9 (43)
267 PF09855 DUF2082: Nucleic-acid 34.1 22 0.00047 17.1 0.7 8 92-99 1-8 (64)
268 TIGR03831 YgiT_finger YgiT-typ 33.8 22 0.00047 15.1 0.7 14 29-42 31-44 (46)
269 cd00065 FYVE FYVE domain; Zinc 33.6 24 0.00051 15.9 0.8 9 33-41 5-13 (57)
270 PRK06450 threonine synthase; V 33.4 30 0.00065 22.6 1.5 27 2-42 4-30 (338)
271 COG5151 SSL1 RNA polymerase II 33.3 1E+02 0.0022 20.3 3.6 24 90-113 387-410 (421)
272 PLN03238 probable histone acet 32.9 43 0.00093 21.5 2.0 24 89-112 46-69 (290)
273 TIGR02159 PA_CoA_Oxy4 phenylac 32.7 12 0.00025 21.3 -0.4 38 30-74 105-142 (146)
274 COG1327 Predicted transcriptio 32.5 22 0.00049 20.3 0.7 16 90-105 27-42 (156)
275 PF14690 zf-ISL3: zinc-finger 32.0 32 0.00069 14.8 1.1 10 91-100 2-11 (47)
276 PF04438 zf-HIT: HIT zinc fing 31.7 18 0.0004 14.4 0.2 13 30-42 13-25 (30)
277 PF03107 C1_2: C1 domain; Int 31.6 39 0.00085 13.2 1.2 9 92-100 1-9 (30)
278 PF08792 A2L_zn_ribbon: A2L zi 31.5 22 0.00048 14.5 0.5 8 93-100 23-30 (33)
279 COG2824 PhnA Uncharacterized Z 31.5 16 0.00036 19.5 0.1 29 3-43 5-33 (112)
280 KOG1940|consensus 30.6 63 0.0014 20.7 2.4 18 31-49 197-214 (276)
281 PRK05580 primosome assembly pr 30.3 23 0.00051 25.5 0.7 12 28-39 419-430 (679)
282 PF01215 COX5B: Cytochrome c o 29.6 15 0.00032 20.6 -0.3 16 28-43 110-125 (136)
283 PF14375 Cys_rich_CWC: Cystein 29.1 37 0.0008 15.2 1.0 6 95-100 2-7 (50)
284 KOG4317|consensus 29.1 21 0.00045 23.2 0.2 20 30-49 19-38 (383)
285 KOG1701|consensus 29.1 10 0.00022 25.6 -1.1 14 30-43 302-315 (468)
286 PF05741 zf-nanos: Nanos RNA b 28.8 21 0.00046 16.6 0.2 11 90-100 32-42 (55)
287 COG0675 Transposase and inacti 28.8 36 0.00078 21.7 1.3 13 62-74 322-334 (364)
288 PF10263 SprT-like: SprT-like 28.7 12 0.00026 21.0 -0.8 32 61-101 122-153 (157)
289 TIGR00595 priA primosomal prot 27.9 27 0.00059 24.2 0.7 10 29-38 252-261 (505)
290 PRK07591 threonine synthase; V 27.6 44 0.00095 22.6 1.5 28 2-43 19-46 (421)
291 smart00064 FYVE Protein presen 27.5 61 0.0013 15.2 1.7 12 31-42 11-22 (68)
292 PF10367 Vps39_2: Vacuolar sor 26.5 41 0.00088 17.4 1.0 12 92-103 79-90 (109)
293 COG3024 Uncharacterized protei 26.4 37 0.00081 16.3 0.8 9 3-11 9-17 (65)
294 PF14599 zinc_ribbon_6: Zinc-r 26.4 14 0.0003 17.6 -0.7 15 31-45 31-45 (61)
295 PF14122 YokU: YokU-like prote 25.2 43 0.00093 17.2 0.9 15 3-17 37-51 (87)
296 PRK14559 putative protein seri 24.9 71 0.0015 23.2 2.2 9 2-10 2-10 (645)
297 KOG4118|consensus 24.9 55 0.0012 15.8 1.2 25 63-87 39-63 (74)
298 PF03833 PolC_DP2: DNA polymer 24.7 25 0.00053 26.2 0.0 9 31-39 656-664 (900)
299 KOG3002|consensus 24.7 1.1E+02 0.0024 19.8 2.8 16 28-43 78-93 (299)
300 KOG3014|consensus 24.6 55 0.0012 20.6 1.4 23 3-25 39-63 (257)
301 PF05129 Elf1: Transcription e 24.4 36 0.00078 17.2 0.6 40 28-75 20-59 (81)
302 KOG0402|consensus 24.2 26 0.00055 17.9 0.0 31 29-73 35-65 (92)
303 PRK03922 hypothetical protein; 24.1 45 0.00098 18.0 0.9 14 30-43 49-62 (113)
304 PF02146 SIR2: Sir2 family; I 23.8 63 0.0014 18.7 1.6 11 31-41 106-116 (178)
305 COG3478 Predicted nucleic-acid 23.6 50 0.0011 16.0 0.9 8 91-98 4-11 (68)
306 PF01844 HNH: HNH endonuclease 23.5 18 0.00039 15.4 -0.6 10 4-13 1-10 (47)
307 PF03966 Trm112p: Trm112p-like 23.4 29 0.00063 16.6 0.1 15 28-42 51-65 (68)
308 PF03145 Sina: Seven in absent 23.1 54 0.0012 19.4 1.2 26 61-87 43-72 (198)
309 PF06676 DUF1178: Protein of u 23.1 1.1E+02 0.0023 17.6 2.3 34 11-49 18-51 (148)
310 KOG0801|consensus 23.1 28 0.0006 20.3 -0.0 12 31-42 139-150 (205)
311 PF13248 zf-ribbon_3: zinc-rib 22.9 33 0.00071 12.9 0.2 8 3-10 4-11 (26)
312 KOG2906|consensus 22.8 11 0.00025 19.7 -1.4 38 31-72 66-103 (105)
313 PF03380 DUF282: Caenorhabditi 22.8 54 0.0012 14.1 0.9 9 4-12 2-10 (39)
314 TIGR00627 tfb4 transcription f 22.7 60 0.0013 20.8 1.4 8 93-100 271-278 (279)
315 PF03884 DUF329: Domain of unk 22.6 33 0.00071 16.1 0.2 12 31-42 3-14 (57)
316 PLN03239 histone acetyltransfe 22.3 58 0.0013 21.6 1.3 24 89-112 104-127 (351)
317 PF06220 zf-U1: U1 zinc finger 22.1 84 0.0018 13.2 1.6 10 92-101 4-13 (38)
318 PF11494 Ta0938: Ta0938; Inte 22.0 51 0.0011 17.4 0.8 12 30-41 14-25 (105)
319 PF02748 PyrI_C: Aspartate car 21.8 30 0.00065 15.8 -0.0 14 89-102 33-46 (52)
320 PF12230 PRP21_like_P: Pre-mRN 21.6 31 0.00067 21.1 0.0 26 89-115 166-191 (229)
321 PTZ00303 phosphatidylinositol 21.6 12 0.00025 27.6 -2.0 13 31-43 461-473 (1374)
322 PF10058 DUF2296: Predicted in 21.4 46 0.00099 15.3 0.5 11 89-99 42-52 (54)
323 PF06170 DUF983: Protein of un 21.3 54 0.0012 16.8 0.8 11 93-103 10-20 (86)
324 COG5152 Uncharacterized conser 21.1 37 0.00081 20.5 0.3 13 1-13 196-208 (259)
325 TIGR03830 CxxCG_CxxCG_HTH puta 21.1 81 0.0018 16.9 1.6 17 2-18 32-48 (127)
326 PF04988 AKAP95: A-kinase anch 20.8 73 0.0016 18.6 1.3 21 31-51 1-21 (165)
327 PF13696 zf-CCHC_2: Zinc knuck 20.7 45 0.00098 13.6 0.4 10 91-100 8-17 (32)
328 PLN00104 MYST -like histone ac 20.7 63 0.0014 22.3 1.2 24 89-112 196-219 (450)
329 COG1066 Sms Predicted ATP-depe 20.7 46 0.001 22.8 0.6 10 31-40 8-17 (456)
330 smart00647 IBR In Between Ring 20.6 74 0.0016 14.5 1.2 11 63-73 41-51 (64)
331 TIGR03655 anti_R_Lar restricti 20.5 52 0.0011 14.9 0.6 8 32-39 3-10 (53)
332 PTZ00064 histone acetyltransfe 20.0 76 0.0016 22.3 1.5 24 89-112 278-301 (552)
No 1
>KOG2462|consensus
Probab=99.98 E-value=6.5e-33 Score=161.79 Aligned_cols=110 Identities=28% Similarity=0.573 Sum_probs=93.4
Q ss_pred ccCCCCCccccchHHHHhhhhhhcCC--CCCccCCCCCcccccchHHHHHhhhhhccCCcccccccCchhhhhhchHHHH
Q psy12028 2 YACDVCGKEYQHKRTLYRHKKDECGQ--EPKFGCPQCPYRSRQKATLNRHLGWEQLQGNAHVMYACDVCGKVYQHKQTLD 79 (118)
Q Consensus 2 ~~C~~C~~~~~~~~~l~~h~~~~~~~--~~~~~C~~c~~~f~~~~~l~~h~~~~~~~~~~~~~~~c~~c~~~~~~~~~l~ 79 (118)
|+|.+||+.|.+..+|.+|+.+|... .+.+.|+.|++.+.+...|..|+++|- .+..|.+||+.|.+++.|+
T Consensus 131 ~~c~eCgk~ysT~snLsrHkQ~H~~~~s~ka~~C~~C~K~YvSmpALkMHirTH~------l~c~C~iCGKaFSRPWLLQ 204 (279)
T KOG2462|consen 131 YKCPECGKSYSTSSNLSRHKQTHRSLDSKKAFSCKYCGKVYVSMPALKMHIRTHT------LPCECGICGKAFSRPWLLQ 204 (279)
T ss_pred eeccccccccccccccchhhcccccccccccccCCCCCceeeehHHHhhHhhccC------CCcccccccccccchHHhh
Confidence 67889999999999999998888753 356889999999999999998876544 4578999999999999999
Q ss_pred HHHhhhcCCCCCccCCCCCCCCCChhHHHHHHhhhcCCC
Q psy12028 80 RHKKDECGQEPKFECPHCPYRSKRKDTLDRHMKIIHFSD 118 (118)
Q Consensus 80 ~h~~~h~~~~~~~~C~~C~~~f~~~~~l~~H~~~~~~~~ 118 (118)
.|+|+||| |+||.|..|+++|+++++|+.||++|.+.|
T Consensus 205 GHiRTHTG-EKPF~C~hC~kAFADRSNLRAHmQTHS~~K 242 (279)
T KOG2462|consen 205 GHIRTHTG-EKPFSCPHCGKAFADRSNLRAHMQTHSDVK 242 (279)
T ss_pred cccccccC-CCCccCCcccchhcchHHHHHHHHhhcCCc
Confidence 99999998 999999999999999999999999887653
No 2
>KOG2462|consensus
Probab=99.96 E-value=1.3e-30 Score=152.19 Aligned_cols=104 Identities=23% Similarity=0.479 Sum_probs=98.1
Q ss_pred ccCCCCCccccchHHHHhhhhhhcCCCCCccCCCCCcccccchHHHHHhhhhhccCCcccccccCchhhhhhchHHHHHH
Q psy12028 2 YACDVCGKEYQHKRTLYRHKKDECGQEPKFGCPQCPYRSRQKATLNRHLGWEQLQGNAHVMYACDVCGKVYQHKQTLDRH 81 (118)
Q Consensus 2 ~~C~~C~~~~~~~~~l~~h~~~~~~~~~~~~C~~c~~~f~~~~~l~~h~~~~~~~~~~~~~~~c~~c~~~~~~~~~l~~h 81 (118)
+.|..|+++|.+..+|.+|+++|+. +..|.+||+.|...+-|+.|+ ..|++||||.|+.|+++|.+.++|+.|
T Consensus 162 ~~C~~C~K~YvSmpALkMHirTH~l---~c~C~iCGKaFSRPWLLQGHi----RTHTGEKPF~C~hC~kAFADRSNLRAH 234 (279)
T KOG2462|consen 162 FSCKYCGKVYVSMPALKMHIRTHTL---PCECGICGKAFSRPWLLQGHI----RTHTGEKPFSCPHCGKAFADRSNLRAH 234 (279)
T ss_pred ccCCCCCceeeehHHHhhHhhccCC---CcccccccccccchHHhhccc----ccccCCCCccCCcccchhcchHHHHHH
Confidence 6899999999999999999999964 799999999999999999995 588899999999999999999999999
Q ss_pred HhhhcCCCCCccCCCCCCCCCChhHHHHHHhh
Q psy12028 82 KKDECGQEPKFECPHCPYRSKRKDTLDRHMKI 113 (118)
Q Consensus 82 ~~~h~~~~~~~~C~~C~~~f~~~~~l~~H~~~ 113 (118)
+++|.+ .++|+|..|+|+|+..+.|.+|...
T Consensus 235 mQTHS~-~K~~qC~~C~KsFsl~SyLnKH~ES 265 (279)
T KOG2462|consen 235 MQTHSD-VKKHQCPRCGKSFALKSYLNKHSES 265 (279)
T ss_pred HHhhcC-CccccCcchhhHHHHHHHHHHhhhh
Confidence 999998 8899999999999999999999753
No 3
>KOG1074|consensus
Probab=99.88 E-value=3.7e-24 Score=140.36 Aligned_cols=53 Identities=26% Similarity=0.495 Sum_probs=50.1
Q ss_pred ccccCchhhhhhchHHHHHHHhhhcCCCCCccCCCCCCCCCChhHHHHHHhhhc
Q psy12028 62 MYACDVCGKVYQHKQTLDRHKKDECGQEPKFECPHCPYRSKRKDTLDRHMKIIH 115 (118)
Q Consensus 62 ~~~c~~c~~~~~~~~~l~~h~~~h~~~~~~~~C~~C~~~f~~~~~l~~H~~~~~ 115 (118)
|.+|.+|.++++=.+.|+.|.++|+| |+||+|.+||++|.++.+|+.|+-+|-
T Consensus 605 PNqCiiC~rVlSC~saLqmHyrtHtG-ERPFkCKiCgRAFtTkGNLkaH~~vHk 657 (958)
T KOG1074|consen 605 PNQCIICLRVLSCPSALQMHYRTHTG-ERPFKCKICGRAFTTKGNLKAHMSVHK 657 (958)
T ss_pred ccceeeeeecccchhhhhhhhhcccC-cCccccccccchhccccchhhcccccc
Confidence 57899999999999999999999999 999999999999999999999997763
No 4
>KOG3576|consensus
Probab=99.84 E-value=1.2e-21 Score=110.66 Aligned_cols=110 Identities=28% Similarity=0.562 Sum_probs=99.3
Q ss_pred ccCCCCCccccchHHHHhhhhhhcCCCCCccCCCCCcccccchHHHHHhhhhhccCCcccccccCchhhhhhchHHHHHH
Q psy12028 2 YACDVCGKEYQHKRTLYRHKKDECGQEPKFGCPQCPYRSRQKATLNRHLGWEQLQGNAHVMYACDVCGKVYQHKQTLDRH 81 (118)
Q Consensus 2 ~~C~~C~~~~~~~~~l~~h~~~~~~~~~~~~C~~c~~~f~~~~~l~~h~~~~~~~~~~~~~~~c~~c~~~~~~~~~l~~h 81 (118)
|.|.+|++.|.-+..|.+|++.|.. .+.+.|..||++|.....|++|++ .|++-+||.|..|+++|...-+|..|
T Consensus 118 ftCrvCgK~F~lQRmlnrh~kch~~-vkr~lct~cgkgfndtfdlkrh~r----thtgvrpykc~~c~kaftqrcslesh 192 (267)
T KOG3576|consen 118 FTCRVCGKKFGLQRMLNRHLKCHSD-VKRHLCTFCGKGFNDTFDLKRHTR----THTGVRPYKCSLCEKAFTQRCSLESH 192 (267)
T ss_pred eeeehhhhhhhHHHHHHHHhhhccH-HHHHHHhhccCcccchhhhhhhhc----cccCccccchhhhhHHHHhhccHHHH
Confidence 7899999999999999999999987 778999999999999999999965 66677999999999999999999999
Q ss_pred HhhhcCC----------CCCccCCCCCCCCCChhHHHHHHhhhcC
Q psy12028 82 KKDECGQ----------EPKFECPHCPYRSKRKDTLDRHMKIIHF 116 (118)
Q Consensus 82 ~~~h~~~----------~~~~~C~~C~~~f~~~~~l~~H~~~~~~ 116 (118)
...-+|. ++.|.|..||++-.....+..|+..+|.
T Consensus 193 l~kvhgv~~~yaykerr~kl~vcedcg~t~~~~e~~~~h~~~~hp 237 (267)
T KOG3576|consen 193 LKKVHGVQHQYAYKERRAKLYVCEDCGYTSERPEVYYLHLKLHHP 237 (267)
T ss_pred HHHHcCchHHHHHHHhhhheeeecccCCCCCChhHHHHHHHhcCC
Confidence 8766652 5679999999999999999999988874
No 5
>KOG1074|consensus
Probab=99.82 E-value=8.1e-21 Score=124.95 Aligned_cols=53 Identities=26% Similarity=0.563 Sum_probs=50.5
Q ss_pred cccCchhhhhhchHHHHHHHhhhcCCCCCccCCCCCCCCCChhHHHHHHhhhcC
Q psy12028 63 YACDVCGKVYQHKQTLDRHKKDECGQEPKFECPHCPYRSKRKDTLDRHMKIIHF 116 (118)
Q Consensus 63 ~~c~~c~~~~~~~~~l~~h~~~h~~~~~~~~C~~C~~~f~~~~~l~~H~~~~~~ 116 (118)
..|.+|++.|..+++|+.|+++|+| ++||.|..|++.|..+.+|+.||.+|+.
T Consensus 880 h~C~vCgk~FsSSsALqiH~rTHtg-~KPF~C~fC~~aFttrgnLKvHMgtH~w 932 (958)
T KOG1074|consen 880 HVCNVCGKQFSSSAALEIHMRTHTG-PKPFFCHFCEEAFTTRGNLKVHMGTHMW 932 (958)
T ss_pred hhhccchhcccchHHHHHhhhcCCC-CCCccchhhhhhhhhhhhhhhhhccccc
Confidence 4799999999999999999999999 9999999999999999999999998864
No 6
>KOG3623|consensus
Probab=99.72 E-value=2e-18 Score=112.83 Aligned_cols=110 Identities=30% Similarity=0.650 Sum_probs=94.6
Q ss_pred ccCCCCCccccchHHHHhhhhh-hcCCCCCccCCCCCcccccchHHHHHhhhhhccC---------CcccccccCchhhh
Q psy12028 2 YACDVCGKEYQHKRTLYRHKKD-ECGQEPKFGCPQCPYRSRQKATLNRHLGWEQLQG---------NAHVMYACDVCGKV 71 (118)
Q Consensus 2 ~~C~~C~~~~~~~~~l~~h~~~-~~~~~~~~~C~~c~~~f~~~~~l~~h~~~~~~~~---------~~~~~~~c~~c~~~ 71 (118)
..|+.|...+.....|..|++- |...+.-|.|..|...|.....|.+||..|-... ..-+.|+|.+|+++
T Consensus 211 ltcpycdrgykrltslkeHikyrhekne~nfsC~lCsytFAyRtQLErhm~~hkpg~dqa~sltqsa~lRKFKCtECgKA 290 (1007)
T KOG3623|consen 211 LTCPYCDRGYKRLTSLKEHIKYRHEKNEPNFSCMLCSYTFAYRTQLERHMQLHKPGGDQAISLTQSALLRKFKCTECGKA 290 (1007)
T ss_pred hcchhHHHHHHHHHHHHHHHHHHHhhCCCCCcchhhhhhhhhHHHHHHHHHhhcCCCcccccccchhhhccccccccchh
Confidence 4699999999999999999874 4433566999999999999999999998553211 12467999999999
Q ss_pred hhchHHHHHHHhhhcCCCCCccCCCCCCCCCChhHHHHHHh
Q psy12028 72 YQHKQTLDRHKKDECGQEPKFECPHCPYRSKRKDTLDRHMK 112 (118)
Q Consensus 72 ~~~~~~l~~h~~~h~~~~~~~~C~~C~~~f~~~~~l~~H~~ 112 (118)
|...--|.-|+|+|.| ++||.|+-|+|+|+....+..||-
T Consensus 291 FKfKHHLKEHlRIHSG-EKPfeCpnCkKRFSHSGSySSHmS 330 (1007)
T KOG3623|consen 291 FKFKHHLKEHLRIHSG-EKPFECPNCKKRFSHSGSYSSHMS 330 (1007)
T ss_pred hhhHHHHHhhheeecC-CCCcCCcccccccccCCccccccc
Confidence 9999999999999999 999999999999999999998874
No 7
>KOG3608|consensus
Probab=99.72 E-value=5.1e-18 Score=103.09 Aligned_cols=108 Identities=19% Similarity=0.465 Sum_probs=54.9
Q ss_pred ccCCCCCccccchHHHHhhhhhhcCCCCCccCCCCCcccccchHHHHHhhhhhccCCcccccccCchhhhhhchHHHHHH
Q psy12028 2 YACDVCGKEYQHKRTLYRHKKDECGQEPKFGCPQCPYRSRQKATLNRHLGWEQLQGNAHVMYACDVCGKVYQHKQTLDRH 81 (118)
Q Consensus 2 ~~C~~C~~~~~~~~~l~~h~~~~~~~~~~~~C~~c~~~f~~~~~l~~h~~~~~~~~~~~~~~~c~~c~~~~~~~~~l~~h 81 (118)
|.|..|.|.|.+...|..|+..|. .-|.||.|..+....++|..||++. |..++||+|..|+..+.+.+.|.+|
T Consensus 238 fqC~~C~KrFaTeklL~~Hv~rHv---n~ykCplCdmtc~~~ssL~~H~r~r---Hs~dkpfKCd~Cd~~c~~esdL~kH 311 (467)
T KOG3608|consen 238 FQCAQCFKRFATEKLLKSHVVRHV---NCYKCPLCDMTCSSASSLTTHIRYR---HSKDKPFKCDECDTRCVRESDLAKH 311 (467)
T ss_pred hHHHHHHHHHhHHHHHHHHHHHhh---hcccccccccCCCChHHHHHHHHhh---hccCCCccccchhhhhccHHHHHHH
Confidence 445555555555555555555442 2455555555555555555555322 2234555555555555555555555
Q ss_pred Hhhhc------------------------------C-CCCCccCCCCCCCCCChhHHHHHHhhhc
Q psy12028 82 KKDEC------------------------------G-QEPKFECPHCPYRSKRKDTLDRHMKIIH 115 (118)
Q Consensus 82 ~~~h~------------------------------~-~~~~~~C~~C~~~f~~~~~l~~H~~~~~ 115 (118)
...|. | ...+|.|..|.+.|.+-.+|.+|+...|
T Consensus 312 ~~~HS~~~y~C~h~~C~~s~r~~~q~~~H~~evhEg~np~~Y~CH~Cdr~ft~G~~L~~HL~kkH 376 (467)
T KOG3608|consen 312 VQVHSKTVYQCEHPDCHYSVRTYTQMRRHFLEVHEGNNPILYACHCCDRFFTSGKSLSAHLMKKH 376 (467)
T ss_pred HHhccccceecCCCCCcHHHHHHHHHHHHHHHhccCCCCCceeeecchhhhccchhHHHHHHHhh
Confidence 44442 1 1334566666666666666666655444
No 8
>KOG3576|consensus
Probab=99.70 E-value=1.9e-18 Score=97.87 Aligned_cols=85 Identities=26% Similarity=0.512 Sum_probs=76.1
Q ss_pred CCCccCCCCCcccccchHHHHHhhhhhccCCcccccccCchhhhhhchHHHHHHHhhhcCCCCCccCCCCCCCCCChhHH
Q psy12028 28 EPKFGCPQCPYRSRQKATLNRHLGWEQLQGNAHVMYACDVCGKVYQHKQTLDRHKKDECGQEPKFECPHCPYRSKRKDTL 107 (118)
Q Consensus 28 ~~~~~C~~c~~~f~~~~~l~~h~~~~~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~h~~~~~~~~C~~C~~~f~~~~~l 107 (118)
...|.|.+|++.|.-..-|.+||+- |..-+.+-|..||+.|.+.-.|.+|+++|+| .+||+|..|+++|.++-.|
T Consensus 115 ~d~ftCrvCgK~F~lQRmlnrh~kc----h~~vkr~lct~cgkgfndtfdlkrh~rthtg-vrpykc~~c~kaftqrcsl 189 (267)
T KOG3576|consen 115 QDSFTCRVCGKKFGLQRMLNRHLKC----HSDVKRHLCTFCGKGFNDTFDLKRHTRTHTG-VRPYKCSLCEKAFTQRCSL 189 (267)
T ss_pred CCeeeeehhhhhhhHHHHHHHHhhh----ccHHHHHHHhhccCcccchhhhhhhhccccC-ccccchhhhhHHHHhhccH
Confidence 3459999999999999989999753 3344678999999999999999999999999 9999999999999999999
Q ss_pred HHHHhhhcCC
Q psy12028 108 DRHMKIIHFS 117 (118)
Q Consensus 108 ~~H~~~~~~~ 117 (118)
..|++..||.
T Consensus 190 eshl~kvhgv 199 (267)
T KOG3576|consen 190 ESHLKKVHGV 199 (267)
T ss_pred HHHHHHHcCc
Confidence 9999888864
No 9
>KOG3608|consensus
Probab=99.69 E-value=3.2e-17 Score=99.67 Aligned_cols=108 Identities=24% Similarity=0.479 Sum_probs=73.4
Q ss_pred CCCCCccccchHHHHhhhhhhcCCCCCccCCCCCcccccchHHHHHhhhhhccCCcccc---------------------
Q psy12028 4 CDVCGKEYQHKRTLYRHKKDECGQEPKFGCPQCPYRSRQKATLNRHLGWEQLQGNAHVM--------------------- 62 (118)
Q Consensus 4 C~~C~~~~~~~~~l~~h~~~~~~~~~~~~C~~c~~~f~~~~~l~~h~~~~~~~~~~~~~--------------------- 62 (118)
+..|-+.+.++..|..|++.|++ ++...||.||..|.+...|.-|++..... ...+
T Consensus 182 W~~Ct~~~~~k~~LreH~r~Hs~-eKvvACp~Cg~~F~~~tkl~DH~rRqt~l--~~n~fqC~~C~KrFaTeklL~~Hv~ 258 (467)
T KOG3608|consen 182 WAMCTKHMGNKYRLREHIRTHSN-EKVVACPHCGELFRTKTKLFDHLRRQTEL--NTNSFQCAQCFKRFATEKLLKSHVV 258 (467)
T ss_pred chhhhhhhccHHHHHHHHHhcCC-CeEEecchHHHHhccccHHHHHHHhhhhh--cCCchHHHHHHHHHhHHHHHHHHHH
Confidence 45688889999999999999987 88889999999999998888887633221 1223
Q ss_pred -----cccCchhhhhhchHHHHHHHhhhcCCCCCccCCCCCCCCCChhHHHHHHhhh
Q psy12028 63 -----YACDVCGKVYQHKQTLDRHKKDECGQEPKFECPHCPYRSKRKDTLDRHMKII 114 (118)
Q Consensus 63 -----~~c~~c~~~~~~~~~l~~h~~~h~~~~~~~~C~~C~~~f~~~~~l~~H~~~~ 114 (118)
|+|+.|+.....+++|..|++..+...+||+|..|.+.|.+.++|.+|..+|
T Consensus 259 rHvn~ykCplCdmtc~~~ssL~~H~r~rHs~dkpfKCd~Cd~~c~~esdL~kH~~~H 315 (467)
T KOG3608|consen 259 RHVNCYKCPLCDMTCSSASSLTTHIRYRHSKDKPFKCDECDTRCVRESDLAKHVQVH 315 (467)
T ss_pred HhhhcccccccccCCCChHHHHHHHHhhhccCCCccccchhhhhccHHHHHHHHHhc
Confidence 4555555555555555555554444456666666666666666666666544
No 10
>KOG3623|consensus
Probab=99.66 E-value=1.8e-17 Score=108.48 Aligned_cols=80 Identities=29% Similarity=0.670 Sum_probs=69.0
Q ss_pred CCCccCCCCCcccccchHHHHHhhhhhccCCcccccccCchhhhhhchHHHHHHHhhhcCCCCCccCCCCCCCCCChhHH
Q psy12028 28 EPKFGCPQCPYRSRQKATLNRHLGWEQLQGNAHVMYACDVCGKVYQHKQTLDRHKKDECGQEPKFECPHCPYRSKRKDTL 107 (118)
Q Consensus 28 ~~~~~C~~c~~~f~~~~~l~~h~~~~~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~h~~~~~~~~C~~C~~~f~~~~~l 107 (118)
+.+|.|..|++.|...+.|.+| -=.|.+.+||.|.+|.++|...--|.-|+|.|.| ++||+|..|+|+|+....+
T Consensus 892 ~gmyaCDqCDK~FqKqSSLaRH----KYEHsGqRPyqC~iCkKAFKHKHHLtEHkRLHSG-EKPfQCdKClKRFSHSGSY 966 (1007)
T KOG3623|consen 892 DGMYACDQCDKAFQKQSSLARH----KYEHSGQRPYQCIICKKAFKHKHHLTEHKRLHSG-EKPFQCDKCLKRFSHSGSY 966 (1007)
T ss_pred cccchHHHHHHHHHhhHHHHHh----hhhhcCCCCcccchhhHhhhhhhhhhhhhhhccC-CCcchhhhhhhhcccccch
Confidence 4568999999999888888888 3467788899999999999998888899999988 9999999999999998888
Q ss_pred HHHHh
Q psy12028 108 DRHMK 112 (118)
Q Consensus 108 ~~H~~ 112 (118)
..||.
T Consensus 967 SQHMN 971 (1007)
T KOG3623|consen 967 SQHMN 971 (1007)
T ss_pred Hhhhc
Confidence 88874
No 11
>PHA00733 hypothetical protein
Probab=99.50 E-value=2.6e-14 Score=77.41 Aligned_cols=85 Identities=18% Similarity=0.203 Sum_probs=70.5
Q ss_pred CCCccCCCCCcccccchHHHHH--hhhhhccCCcccccccCchhhhhhchHHHHHHHhhhcCCCCCccCCCCCCCCCChh
Q psy12028 28 EPKFGCPQCPYRSRQKATLNRH--LGWEQLQGNAHVMYACDVCGKVYQHKQTLDRHKKDECGQEPKFECPHCPYRSKRKD 105 (118)
Q Consensus 28 ~~~~~C~~c~~~f~~~~~l~~h--~~~~~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~h~~~~~~~~C~~C~~~f~~~~ 105 (118)
.+++.|.+|...|.....|..+ +..+. ...+.+||.|+.|++.|.....|..|++.+ +.+|.|..|++.|....
T Consensus 38 ~~~~~~~~~~~~~~~~~~l~~~~~l~~~~-~~~~~kPy~C~~Cgk~Fss~s~L~~H~r~h---~~~~~C~~CgK~F~~~~ 113 (128)
T PHA00733 38 QKRLIRAVVKTLIYNPQLLDESSYLYKLL-TSKAVSPYVCPLCLMPFSSSVSLKQHIRYT---EHSKVCPVCGKEFRNTD 113 (128)
T ss_pred hhhHHHHHHhhhccChhhhcchHHHHhhc-ccCCCCCccCCCCCCcCCCHHHHHHHHhcC---CcCccCCCCCCccCCHH
Confidence 4679999999999888777666 32222 334478999999999999999999999876 34799999999999999
Q ss_pred HHHHHHhhhcC
Q psy12028 106 TLDRHMKIIHF 116 (118)
Q Consensus 106 ~l~~H~~~~~~ 116 (118)
.|..|+...|+
T Consensus 114 sL~~H~~~~h~ 124 (128)
T PHA00733 114 STLDHVCKKHN 124 (128)
T ss_pred HHHHHHHHhcC
Confidence 99999988875
No 12
>PLN03086 PRLI-interacting factor K; Provisional
Probab=99.43 E-value=5.7e-13 Score=86.85 Aligned_cols=102 Identities=22% Similarity=0.460 Sum_probs=81.8
Q ss_pred ccCCCCCccccchHHHHhhhhhhcCCCCCccCCCCCcccccchHHHHHhhhhhccCCcccccccCchhhhhh--------
Q psy12028 2 YACDVCGKEYQHKRTLYRHKKDECGQEPKFGCPQCPYRSRQKATLNRHLGWEQLQGNAHVMYACDVCGKVYQ-------- 73 (118)
Q Consensus 2 ~~C~~C~~~~~~~~~l~~h~~~~~~~~~~~~C~~c~~~f~~~~~l~~h~~~~~~~~~~~~~~~c~~c~~~~~-------- 73 (118)
+.|+.|++.|. ...|..|+..++ .++.|+ |+..+ ....|..|+. .+...+++.|+.|+..+.
T Consensus 454 ~~C~~Cgk~f~-~s~LekH~~~~H---kpv~Cp-Cg~~~-~R~~L~~H~~----thCp~Kpi~C~fC~~~v~~g~~~~d~ 523 (567)
T PLN03086 454 VHCEKCGQAFQ-QGEMEKHMKVFH---EPLQCP-CGVVL-EKEQMVQHQA----STCPLRLITCRFCGDMVQAGGSAMDV 523 (567)
T ss_pred ccCCCCCCccc-hHHHHHHHHhcC---CCccCC-CCCCc-chhHHHhhhh----ccCCCCceeCCCCCCccccCccccch
Confidence 57999999996 678999999875 589999 99755 5678888854 445668999999999885
Q ss_pred --chHHHHHHHhhhcCCCCCccCCCCCCCCCChhHHHHHHhhhcC
Q psy12028 74 --HKQTLDRHKKDECGQEPKFECPHCPYRSKRKDTLDRHMKIIHF 116 (118)
Q Consensus 74 --~~~~l~~h~~~h~~~~~~~~C~~C~~~f~~~~~l~~H~~~~~~ 116 (118)
....|..|.... | .+++.|..||+.+. ...|..|+...|.
T Consensus 524 ~d~~s~Lt~HE~~C-G-~rt~~C~~Cgk~Vr-lrdm~~H~~~~h~ 565 (567)
T PLN03086 524 RDRLRGMSEHESIC-G-SRTAPCDSCGRSVM-LKEMDIHQIAVHQ 565 (567)
T ss_pred hhhhhhHHHHHHhc-C-CcceEccccCCeee-ehhHHHHHHHhhc
Confidence 235788998885 6 89999999998875 5567889887764
No 13
>PHA02768 hypothetical protein; Provisional
Probab=99.29 E-value=1.2e-12 Score=59.79 Aligned_cols=44 Identities=20% Similarity=0.526 Sum_probs=38.4
Q ss_pred ccccCchhhhhhchHHHHHHHhhhcCCCCCccCCCCCCCCCChhHHH
Q psy12028 62 MYACDVCGKVYQHKQTLDRHKKDECGQEPKFECPHCPYRSKRKDTLD 108 (118)
Q Consensus 62 ~~~c~~c~~~~~~~~~l~~h~~~h~~~~~~~~C~~C~~~f~~~~~l~ 108 (118)
.|.|+.||+.|...+.|..|+++|+ ++++|..|++.|.+.+.|.
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 3789999999999999999999986 5889999999998877664
No 14
>PHA00733 hypothetical protein
Probab=99.29 E-value=2.9e-12 Score=69.51 Aligned_cols=80 Identities=16% Similarity=0.270 Sum_probs=62.8
Q ss_pred ccCCCCCccccchHHHHhh--hh--hhcCCCCCccCCCCCcccccchHHHHHhhhhhccCCcccccccCchhhhhhchHH
Q psy12028 2 YACDVCGKEYQHKRTLYRH--KK--DECGQEPKFGCPQCPYRSRQKATLNRHLGWEQLQGNAHVMYACDVCGKVYQHKQT 77 (118)
Q Consensus 2 ~~C~~C~~~~~~~~~l~~h--~~--~~~~~~~~~~C~~c~~~f~~~~~l~~h~~~~~~~~~~~~~~~c~~c~~~~~~~~~ 77 (118)
+.|.+|.+.|.....|..+ .. ..+...++|.|+.|++.|.....|..|++.+ +.++.|+.|++.|.....
T Consensus 41 ~~~~~~~~~~~~~~~l~~~~~l~~~~~~~~~kPy~C~~Cgk~Fss~s~L~~H~r~h------~~~~~C~~CgK~F~~~~s 114 (128)
T PHA00733 41 LIRAVVKTLIYNPQLLDESSYLYKLLTSKAVSPYVCPLCLMPFSSSVSLKQHIRYT------EHSKVCPVCGKEFRNTDS 114 (128)
T ss_pred HHHHHHhhhccChhhhcchHHHHhhcccCCCCCccCCCCCCcCCCHHHHHHHHhcC------CcCccCCCCCCccCCHHH
Confidence 4677888888877766665 11 1222368999999999999999999997532 246899999999999999
Q ss_pred HHHHHhhhcC
Q psy12028 78 LDRHKKDECG 87 (118)
Q Consensus 78 l~~h~~~h~~ 87 (118)
|..|+...++
T Consensus 115 L~~H~~~~h~ 124 (128)
T PHA00733 115 TLDHVCKKHN 124 (128)
T ss_pred HHHHHHHhcC
Confidence 9999887765
No 15
>PHA02768 hypothetical protein; Provisional
Probab=99.24 E-value=4.8e-12 Score=57.81 Aligned_cols=42 Identities=19% Similarity=0.551 Sum_probs=32.7
Q ss_pred ccCCCCCccccchHHHHhhhhhhcCCCCCccCCCCCcccccchHH
Q psy12028 2 YACDVCGKEYQHKRTLYRHKKDECGQEPKFGCPQCPYRSRQKATL 46 (118)
Q Consensus 2 ~~C~~C~~~~~~~~~l~~h~~~~~~~~~~~~C~~c~~~f~~~~~l 46 (118)
|+|+.||+.|.....|..|+++|+ +++.|..|++.|...+.|
T Consensus 6 y~C~~CGK~Fs~~~~L~~H~r~H~---k~~kc~~C~k~f~~~s~l 47 (55)
T PHA02768 6 YECPICGEIYIKRKSMITHLRKHN---TNLKLSNCKRISLRTGEY 47 (55)
T ss_pred cCcchhCCeeccHHHHHHHHHhcC---CcccCCcccceeccccee
Confidence 678888888888888888888876 467888888887765543
No 16
>KOG3993|consensus
Probab=99.20 E-value=4e-12 Score=79.38 Aligned_cols=52 Identities=25% Similarity=0.616 Sum_probs=42.5
Q ss_pred ccCCCCCccccchHHHHhhhhhhcCCCCCccCCCCCcccccchHHHHHhhhhh
Q psy12028 2 YACDVCGKEYQHKRTLYRHKKDECGQEPKFGCPQCPYRSRQKATLNRHLGWEQ 54 (118)
Q Consensus 2 ~~C~~C~~~~~~~~~l~~h~~~~~~~~~~~~C~~c~~~f~~~~~l~~h~~~~~ 54 (118)
|.|..|...|.+.-.|..|+...+- ...|.|++|++.|+...+|..|.+||-
T Consensus 268 yiCqLCK~kYeD~F~LAQHrC~RIV-~vEYrCPEC~KVFsCPANLASHRRWHK 319 (500)
T KOG3993|consen 268 YICQLCKEKYEDAFALAQHRCPRIV-HVEYRCPECDKVFSCPANLASHRRWHK 319 (500)
T ss_pred HHHHHHHHhhhhHHHHhhccCCeeE-EeeecCCcccccccCchhhhhhhcccC
Confidence 6788899999999999998765443 445999999999999999999988663
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=99.11 E-value=2.8e-11 Score=47.70 Aligned_cols=26 Identities=31% Similarity=0.686 Sum_probs=23.3
Q ss_pred HHHHHHhhhcCCCCCccCCCCCCCCCC
Q psy12028 77 TLDRHKKDECGQEPKFECPHCPYRSKR 103 (118)
Q Consensus 77 ~l~~h~~~h~~~~~~~~C~~C~~~f~~ 103 (118)
+|..|+++|+| ++||.|+.|+++|.+
T Consensus 1 ~l~~H~~~H~~-~k~~~C~~C~k~F~~ 26 (26)
T PF13465_consen 1 NLRRHMRTHTG-EKPYKCPYCGKSFSN 26 (26)
T ss_dssp HHHHHHHHHSS-SSSEEESSSSEEESS
T ss_pred CHHHHhhhcCC-CCCCCCCCCcCeeCc
Confidence 47899999999 999999999999864
No 18
>PLN03086 PRLI-interacting factor K; Provisional
Probab=99.06 E-value=5.2e-10 Score=73.40 Aligned_cols=77 Identities=19% Similarity=0.446 Sum_probs=61.8
Q ss_pred CCCccCCCCCcccccchHHHHHhhhhhccCCcccccccCchhhhhhchHHHHHHHhhhcCCCCCccCCCCCCCCC-----
Q psy12028 28 EPKFGCPQCPYRSRQKATLNRHLGWEQLQGNAHVMYACDVCGKVYQHKQTLDRHKKDECGQEPKFECPHCPYRSK----- 102 (118)
Q Consensus 28 ~~~~~C~~c~~~f~~~~~l~~h~~~~~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~h~~~~~~~~C~~C~~~f~----- 102 (118)
++.+.|+.|++.|. ...|..|+..++ +++.|+ |+..+ ....|..|+..|.+ .+++.|..|++.+.
T Consensus 451 ~~H~~C~~Cgk~f~-~s~LekH~~~~H------kpv~Cp-Cg~~~-~R~~L~~H~~thCp-~Kpi~C~fC~~~v~~g~~~ 520 (567)
T PLN03086 451 KNHVHCEKCGQAFQ-QGEMEKHMKVFH------EPLQCP-CGVVL-EKEQMVQHQASTCP-LRLITCRFCGDMVQAGGSA 520 (567)
T ss_pred ccCccCCCCCCccc-hHHHHHHHHhcC------CCccCC-CCCCc-chhHHHhhhhccCC-CCceeCCCCCCccccCccc
Confidence 34578999999996 577899975432 679999 99765 56889999999998 99999999999885
Q ss_pred -----ChhHHHHHHhhh
Q psy12028 103 -----RKDTLDRHMKII 114 (118)
Q Consensus 103 -----~~~~l~~H~~~~ 114 (118)
..+.|..|..+.
T Consensus 521 ~d~~d~~s~Lt~HE~~C 537 (567)
T PLN03086 521 MDVRDRLRGMSEHESIC 537 (567)
T ss_pred cchhhhhhhHHHHHHhc
Confidence 245788898764
No 19
>KOG3993|consensus
Probab=99.06 E-value=2.1e-11 Score=76.20 Aligned_cols=82 Identities=23% Similarity=0.434 Sum_probs=69.3
Q ss_pred ccCCCCCcccccchHHHHHhhhhhccCCcccccccCchhhhhhchHHHHHHHhhhcCC----------------------
Q psy12028 31 FGCPQCPYRSRQKATLNRHLGWEQLQGNAHVMYACDVCGKVYQHKQTLDRHKKDECGQ---------------------- 88 (118)
Q Consensus 31 ~~C~~c~~~f~~~~~l~~h~~~~~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~h~~~---------------------- 88 (118)
|.|..|...|.....|.+|. + .......|.|++|+++|+=+.+|..|.+.|...
T Consensus 268 yiCqLCK~kYeD~F~LAQHr---C-~RIV~vEYrCPEC~KVFsCPANLASHRRWHKPR~eaa~a~~~P~k~~~~~rae~~ 343 (500)
T KOG3993|consen 268 YICQLCKEKYEDAFALAQHR---C-PRIVHVEYRCPECDKVFSCPANLASHRRWHKPRPEAAKAGSPPPKQAVETRAEVQ 343 (500)
T ss_pred HHHHHHHHhhhhHHHHhhcc---C-CeeEEeeecCCcccccccCchhhhhhhcccCCchhhhhcCCCChhhhhhhhhhhh
Confidence 99999999999999999994 2 333445699999999999999999999988531
Q ss_pred ----------CCCccCCCCCCCCCChhHHHHHHhhhcC
Q psy12028 89 ----------EPKFECPHCPYRSKRKDTLDRHMKIIHF 116 (118)
Q Consensus 89 ----------~~~~~C~~C~~~f~~~~~l~~H~~~~~~ 116 (118)
+..|.|..|+|.|.+...|+.|+-+|+.
T Consensus 344 ea~rsg~dss~gi~~C~~C~KkFrRqAYLrKHqlthq~ 381 (500)
T KOG3993|consen 344 EAERSGDDSSSGIFSCHTCGKKFRRQAYLRKHQLTHQR 381 (500)
T ss_pred hccccCCcccCceeecHHhhhhhHHHHHHHHhHHhhhc
Confidence 1248999999999999999999888864
No 20
>PHA00616 hypothetical protein
Probab=98.98 E-value=1.9e-10 Score=50.22 Aligned_cols=33 Identities=24% Similarity=0.502 Sum_probs=23.5
Q ss_pred ccccCchhhhhhchHHHHHHHhhhcCCCCCccCC
Q psy12028 62 MYACDVCGKVYQHKQTLDRHKKDECGQEPKFECP 95 (118)
Q Consensus 62 ~~~c~~c~~~~~~~~~l~~h~~~h~~~~~~~~C~ 95 (118)
||+|+.||..|...+.+..|++.|+| +.++.|+
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~~hg-~~~~~~~ 33 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLSVHK-QNKLTLE 33 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHHhcC-CCcccee
Confidence 46777777777777777777777777 6776664
No 21
>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=98.93 E-value=6.4e-10 Score=43.77 Aligned_cols=26 Identities=31% Similarity=0.645 Sum_probs=22.3
Q ss_pred HHHhhhhhhcCCCCCccCCCCCccccc
Q psy12028 16 TLYRHKKDECGQEPKFGCPQCPYRSRQ 42 (118)
Q Consensus 16 ~l~~h~~~~~~~~~~~~C~~c~~~f~~ 42 (118)
+|..|+++|++ ++||.|+.|++.|.+
T Consensus 1 ~l~~H~~~H~~-~k~~~C~~C~k~F~~ 26 (26)
T PF13465_consen 1 NLRRHMRTHTG-EKPYKCPYCGKSFSN 26 (26)
T ss_dssp HHHHHHHHHSS-SSSEEESSSSEEESS
T ss_pred CHHHHhhhcCC-CCCCCCCCCcCeeCc
Confidence 47889999987 889999999998863
No 22
>PHA00616 hypothetical protein
Probab=98.92 E-value=5.5e-10 Score=48.76 Aligned_cols=34 Identities=24% Similarity=0.446 Sum_probs=29.7
Q ss_pred CccCCCCCccccchHHHHhhhhhhcCCCCCccCCC
Q psy12028 1 MYACDVCGKEYQHKRTLYRHKKDECGQEPKFGCPQ 35 (118)
Q Consensus 1 ~~~C~~C~~~~~~~~~l~~h~~~~~~~~~~~~C~~ 35 (118)
||+|..||+.|....+|..|++.+++ ++++.|+.
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~~hg-~~~~~~~~ 34 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLSVHK-QNKLTLEY 34 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHHhcC-CCccceeE
Confidence 78999999999999999999999998 67777764
No 23
>PHA00732 hypothetical protein
Probab=98.86 E-value=2.8e-09 Score=53.03 Aligned_cols=45 Identities=29% Similarity=0.560 Sum_probs=36.0
Q ss_pred CccCCCCCccccchHHHHhhhhhhcCCCCCccCCCCCcccccchHHHHHhh
Q psy12028 1 MYACDVCGKEYQHKRTLYRHKKDECGQEPKFGCPQCPYRSRQKATLNRHLG 51 (118)
Q Consensus 1 ~~~C~~C~~~~~~~~~l~~h~~~~~~~~~~~~C~~c~~~f~~~~~l~~h~~ 51 (118)
||+|..|++.|.+...|..|++.++. ++.|+.|++.|. .+..|+.
T Consensus 1 py~C~~Cgk~F~s~s~Lk~H~r~~H~---~~~C~~CgKsF~---~l~~H~~ 45 (79)
T PHA00732 1 MFKCPICGFTTVTLFALKQHARRNHT---LTKCPVCNKSYR---RLNQHFY 45 (79)
T ss_pred CccCCCCCCccCCHHHHHHHhhcccC---CCccCCCCCEeC---Chhhhhc
Confidence 78999999999999999999885322 358999999997 3666753
No 24
>PHA00732 hypothetical protein
Probab=98.83 E-value=2.2e-09 Score=53.37 Aligned_cols=48 Identities=27% Similarity=0.621 Sum_probs=27.5
Q ss_pred CccCCCCCcccccchHHHHHhhhhhccCCcccccccCchhhhhhchHHHHHHHhhhc
Q psy12028 30 KFGCPQCPYRSRQKATLNRHLGWEQLQGNAHVMYACDVCGKVYQHKQTLDRHKKDEC 86 (118)
Q Consensus 30 ~~~C~~c~~~f~~~~~l~~h~~~~~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~h~ 86 (118)
||.|+.|++.|.+...|..|++.+ +. ++.|+.|++.|.+ +..|..+..
T Consensus 1 py~C~~Cgk~F~s~s~Lk~H~r~~---H~---~~~C~~CgKsF~~---l~~H~~~~~ 48 (79)
T PHA00732 1 MFKCPICGFTTVTLFALKQHARRN---HT---LTKCPVCNKSYRR---LNQHFYSQY 48 (79)
T ss_pred CccCCCCCCccCCHHHHHHHhhcc---cC---CCccCCCCCEeCC---hhhhhcccC
Confidence 366777777777777777665421 11 2466677766653 455554443
No 25
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=98.76 E-value=1.5e-08 Score=46.94 Aligned_cols=51 Identities=33% Similarity=0.627 Sum_probs=31.5
Q ss_pred cccCchhhhhhchHHHHHHHhhhc-CCCCCccCCCCCCCCCChhHHHHHHhhhcC
Q psy12028 63 YACDVCGKVYQHKQTLDRHKKDEC-GQEPKFECPHCPYRSKRKDTLDRHMKIIHF 116 (118)
Q Consensus 63 ~~c~~c~~~~~~~~~l~~h~~~h~-~~~~~~~C~~C~~~f~~~~~l~~H~~~~~~ 116 (118)
|.||+|++ ..+...|..|....+ .+.+.+.|++|...+. .+|..|+...|+
T Consensus 3 f~CP~C~~-~~~~~~L~~H~~~~H~~~~~~v~CPiC~~~~~--~~l~~Hl~~~H~ 54 (54)
T PF05605_consen 3 FTCPYCGK-GFSESSLVEHCEDEHRSESKNVVCPICSSRVT--DNLIRHLNSQHR 54 (54)
T ss_pred cCCCCCCC-ccCHHHHHHHHHhHCcCCCCCccCCCchhhhh--hHHHHHHHHhcC
Confidence 66777777 445566677755433 3234677777776543 377777776664
No 26
>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=98.60 E-value=1.2e-07 Score=43.93 Aligned_cols=46 Identities=35% Similarity=0.665 Sum_probs=23.5
Q ss_pred ccCCCCCccccchHHHHhhhhhhcC-CCCCccCCCCCcccccchHHHHHh
Q psy12028 2 YACDVCGKEYQHKRTLYRHKKDECG-QEPKFGCPQCPYRSRQKATLNRHL 50 (118)
Q Consensus 2 ~~C~~C~~~~~~~~~l~~h~~~~~~-~~~~~~C~~c~~~f~~~~~l~~h~ 50 (118)
|.|+.|++ ..+...|..|....+. +.+.+.||+|...+. .+|..|+
T Consensus 3 f~CP~C~~-~~~~~~L~~H~~~~H~~~~~~v~CPiC~~~~~--~~l~~Hl 49 (54)
T PF05605_consen 3 FTCPYCGK-GFSESSLVEHCEDEHRSESKNVVCPICSSRVT--DNLIRHL 49 (54)
T ss_pred cCCCCCCC-ccCHHHHHHHHHhHCcCCCCCccCCCchhhhh--hHHHHHH
Confidence 55666666 3445556666444332 224456666655433 2455554
No 27
>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=98.58 E-value=2.5e-08 Score=38.05 Aligned_cols=22 Identities=36% Similarity=0.786 Sum_probs=17.6
Q ss_pred ccCCCCCCCCCChhHHHHHHhh
Q psy12028 92 FECPHCPYRSKRKDTLDRHMKI 113 (118)
Q Consensus 92 ~~C~~C~~~f~~~~~l~~H~~~ 113 (118)
|.|+.|++.|.+.+.|..|++.
T Consensus 1 y~C~~C~~~f~~~~~l~~H~~~ 22 (23)
T PF00096_consen 1 YKCPICGKSFSSKSNLKRHMRR 22 (23)
T ss_dssp EEETTTTEEESSHHHHHHHHHH
T ss_pred CCCCCCCCccCCHHHHHHHHhH
Confidence 5688888888888888888776
No 28
>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=98.53 E-value=6.3e-08 Score=37.13 Aligned_cols=24 Identities=38% Similarity=0.804 Sum_probs=18.8
Q ss_pred ccCCCCCCCCCChhHHHHHHhhhc
Q psy12028 92 FECPHCPYRSKRKDTLDRHMKIIH 115 (118)
Q Consensus 92 ~~C~~C~~~f~~~~~l~~H~~~~~ 115 (118)
|.|++|++.|.+...|..|+.++|
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 678889999999999999988775
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=98.46 E-value=7.3e-08 Score=36.70 Aligned_cols=22 Identities=41% Similarity=0.984 Sum_probs=14.4
Q ss_pred ccCCCCCccccchHHHHhhhhh
Q psy12028 2 YACDVCGKEYQHKRTLYRHKKD 23 (118)
Q Consensus 2 ~~C~~C~~~~~~~~~l~~h~~~ 23 (118)
|+|+.|++.|.+...|..|++.
T Consensus 1 y~C~~C~~~f~~~~~l~~H~~~ 22 (23)
T PF00096_consen 1 YKCPICGKSFSSKSNLKRHMRR 22 (23)
T ss_dssp EEETTTTEEESSHHHHHHHHHH
T ss_pred CCCCCCCCccCCHHHHHHHHhH
Confidence 4566666666666666666654
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=98.40 E-value=1.2e-07 Score=37.50 Aligned_cols=26 Identities=23% Similarity=0.363 Sum_probs=20.5
Q ss_pred CccCCCCCCCCCChhHHHHHHhhhcC
Q psy12028 91 KFECPHCPYRSKRKDTLDRHMKIIHF 116 (118)
Q Consensus 91 ~~~C~~C~~~f~~~~~l~~H~~~~~~ 116 (118)
+|.|..|++.|.+...|..|++.|++
T Consensus 1 ~~~C~~C~~~F~~~~~l~~H~~~h~~ 26 (27)
T PF13912_consen 1 PFECDECGKTFSSLSALREHKRSHCS 26 (27)
T ss_dssp SEEETTTTEEESSHHHHHHHHCTTTT
T ss_pred CCCCCccCCccCChhHHHHHhHHhcC
Confidence 57788888888888888888877654
No 31
>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=98.34 E-value=1.8e-07 Score=37.02 Aligned_cols=25 Identities=36% Similarity=0.913 Sum_probs=18.9
Q ss_pred CccCCCCCccccchHHHHhhhhhhc
Q psy12028 1 MYACDVCGKEYQHKRTLYRHKKDEC 25 (118)
Q Consensus 1 ~~~C~~C~~~~~~~~~l~~h~~~~~ 25 (118)
||+|..|++.|.+...|..|++.|.
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 5777888888888888888776664
No 32
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=98.25 E-value=6.2e-07 Score=46.64 Aligned_cols=73 Identities=18% Similarity=0.271 Sum_probs=21.6
Q ss_pred cCCCCCcccccchHHHHHhhhhhccCCcccccccCchhhhhhchHHHHHHHhhhcCCCCCccCCCCCCCCCChhHHHHHH
Q psy12028 32 GCPQCPYRSRQKATLNRHLGWEQLQGNAHVMYACDVCGKVYQHKQTLDRHKKDECGQEPKFECPHCPYRSKRKDTLDRHM 111 (118)
Q Consensus 32 ~C~~c~~~f~~~~~l~~h~~~~~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~h~~~~~~~~C~~C~~~f~~~~~l~~H~ 111 (118)
+|..|+..|.+...+..||...+..... ....+.....+...+.... ...+.|.+|++.|.....|..|+
T Consensus 1 ~C~~C~~~f~~~~~l~~H~~~~H~~~~~--------~~~~l~~~~~~~~~~~~~~--~~~~~C~~C~~~f~s~~~l~~Hm 70 (100)
T PF12756_consen 1 QCLFCDESFSSVDDLLQHMKKKHGFDIP--------DQKYLVDPNRLLNYLRKKV--KESFRCPYCNKTFRSREALQEHM 70 (100)
T ss_dssp ----------------------------------------------------------SSEEBSSSS-EESSHHHHHHHH
T ss_pred Cccccccccccccccccccccccccccc--------ccccccccccccccccccc--CCCCCCCccCCCCcCHHHHHHHH
Confidence 5899999999999999998533322111 1111123333444443322 33699999999999999999999
Q ss_pred hhh
Q psy12028 112 KII 114 (118)
Q Consensus 112 ~~~ 114 (118)
+.+
T Consensus 71 ~~~ 73 (100)
T PF12756_consen 71 RSK 73 (100)
T ss_dssp HHT
T ss_pred cCc
Confidence 865
No 33
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=98.21 E-value=8.6e-07 Score=33.81 Aligned_cols=23 Identities=30% Similarity=0.883 Sum_probs=12.7
Q ss_pred ccCCCCCccccchHHHHhhhhhh
Q psy12028 2 YACDVCGKEYQHKRTLYRHKKDE 24 (118)
Q Consensus 2 ~~C~~C~~~~~~~~~l~~h~~~~ 24 (118)
|.|+.|++.|.+...|..|+..+
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 45666666666666666666544
No 34
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=98.14 E-value=3.2e-07 Score=56.19 Aligned_cols=70 Identities=20% Similarity=0.335 Sum_probs=40.7
Q ss_pred CCCccCCC--CCcccccchHHHHHhhh-hhccCCcccccccCchhhhhhchHHHHHHHhhhcCCCCCccCCCCCCCCCCh
Q psy12028 28 EPKFGCPQ--CPYRSRQKATLNRHLGW-EQLQGNAHVMYACDVCGKVYQHKQTLDRHKKDECGQEPKFECPHCPYRSKRK 104 (118)
Q Consensus 28 ~~~~~C~~--c~~~f~~~~~l~~h~~~-~~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~h~~~~~~~~C~~C~~~f~~~ 104 (118)
++||.||+ |.+.+++...|+-|+.. |+.....+.| ....+.-.-.. .+||+|++|+|++.+.
T Consensus 347 ~KpykCpV~gC~K~YknqnGLKYH~lhGH~~~~~~~~p--------------~p~~~~~F~~~-~KPYrCevC~KRYKNl 411 (423)
T COG5189 347 GKPYKCPVEGCNKKYKNQNGLKYHMLHGHQNQKLHENP--------------SPEKMNIFSAK-DKPYRCEVCDKRYKNL 411 (423)
T ss_pred CceecCCCCCchhhhccccchhhhhhccccCcccCCCC--------------Ccccccccccc-CCceeccccchhhccC
Confidence 46777765 77777777777766531 1111111111 00111111222 6899999999999999
Q ss_pred hHHHHHHh
Q psy12028 105 DTLDRHMK 112 (118)
Q Consensus 105 ~~l~~H~~ 112 (118)
..|+-|..
T Consensus 412 NGLKYHr~ 419 (423)
T COG5189 412 NGLKYHRK 419 (423)
T ss_pred ccceeccc
Confidence 99988864
No 35
>PF09237 GAGA: GAGA factor; InterPro: IPR015318 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Members of this entry bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognises the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognises the A in the fourth position of the consensus sequence []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1YUI_A 1YUJ_A.
Probab=98.08 E-value=3e-06 Score=37.93 Aligned_cols=29 Identities=34% Similarity=0.676 Sum_probs=14.3
Q ss_pred CCCccCCCCCCCCCChhHHHHHHhhhcCC
Q psy12028 89 EPKFECPHCPYRSKRKDTLDRHMKIIHFS 117 (118)
Q Consensus 89 ~~~~~C~~C~~~f~~~~~l~~H~~~~~~~ 117 (118)
+.|-.|++|+..+....+|++|+.+.|+.
T Consensus 22 ~~PatCP~C~a~~~~srnLrRHle~~H~~ 50 (54)
T PF09237_consen 22 EQPATCPICGAVIRQSRNLRRHLEIRHFK 50 (54)
T ss_dssp S--EE-TTT--EESSHHHHHHHHHHHTTT
T ss_pred CCCCCCCcchhhccchhhHHHHHHHHhcc
Confidence 55556666666666666666666555543
No 36
>smart00355 ZnF_C2H2 zinc finger.
Probab=98.01 E-value=8e-06 Score=31.52 Aligned_cols=23 Identities=35% Similarity=0.730 Sum_probs=17.6
Q ss_pred ccCCCCCCCCCChhHHHHHHhhh
Q psy12028 92 FECPHCPYRSKRKDTLDRHMKII 114 (118)
Q Consensus 92 ~~C~~C~~~f~~~~~l~~H~~~~ 114 (118)
|.|..|++.|...+.|..|++.|
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~~H 23 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMRTH 23 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHHHh
Confidence 46778888888888888887754
No 37
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=97.98 E-value=4.7e-06 Score=31.91 Aligned_cols=24 Identities=46% Similarity=1.048 Sum_probs=18.3
Q ss_pred ccCCCCCCCCCChhHHHHHHhhhcC
Q psy12028 92 FECPHCPYRSKRKDTLDRHMKIIHF 116 (118)
Q Consensus 92 ~~C~~C~~~f~~~~~l~~H~~~~~~ 116 (118)
|+|+.|++... .+.|.+|++.+|+
T Consensus 1 y~C~~C~y~t~-~~~l~~H~~~~H~ 24 (24)
T PF13909_consen 1 YKCPHCSYSTS-KSNLKRHLKRHHP 24 (24)
T ss_dssp EE-SSSS-EES-HHHHHHHHHHHHS
T ss_pred CCCCCCCCcCC-HHHHHHHHHhhCc
Confidence 67888998887 8889999888774
No 38
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=97.97 E-value=4e-06 Score=43.55 Aligned_cols=74 Identities=18% Similarity=0.389 Sum_probs=21.6
Q ss_pred cCCCCCccccchHHHHhhhhhhcCCCCCccCCCCCcccccchHHHHHhhhhhccCCcccccccCchhhhhhchHHHHHHH
Q psy12028 3 ACDVCGKEYQHKRTLYRHKKDECGQEPKFGCPQCPYRSRQKATLNRHLGWEQLQGNAHVMYACDVCGKVYQHKQTLDRHK 82 (118)
Q Consensus 3 ~C~~C~~~~~~~~~l~~h~~~~~~~~~~~~C~~c~~~f~~~~~l~~h~~~~~~~~~~~~~~~c~~c~~~~~~~~~l~~h~ 82 (118)
+|..|+..|.+...|..|+...++...+ . ...+.....+...++ ......+.|..|++.|.+...|..|+
T Consensus 1 ~C~~C~~~f~~~~~l~~H~~~~H~~~~~----~-~~~l~~~~~~~~~~~-----~~~~~~~~C~~C~~~f~s~~~l~~Hm 70 (100)
T PF12756_consen 1 QCLFCDESFSSVDDLLQHMKKKHGFDIP----D-QKYLVDPNRLLNYLR-----KKVKESFRCPYCNKTFRSREALQEHM 70 (100)
T ss_dssp ----------------------------------------------------------SSEEBSSSS-EESSHHHHHHHH
T ss_pred Cccccccccccccccccccccccccccc----c-ccccccccccccccc-----cccCCCCCCCccCCCCcCHHHHHHHH
Confidence 5899999999999999999776652211 1 111112222222321 01112589999999999999999999
Q ss_pred hhhc
Q psy12028 83 KDEC 86 (118)
Q Consensus 83 ~~h~ 86 (118)
+.+.
T Consensus 71 ~~~~ 74 (100)
T PF12756_consen 71 RSKH 74 (100)
T ss_dssp HHTT
T ss_pred cCcc
Confidence 8753
No 39
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=97.95 E-value=2.4e-06 Score=52.52 Aligned_cols=25 Identities=32% Similarity=0.635 Sum_probs=21.8
Q ss_pred CccCCC--CCccccchHHHHhhhhhhc
Q psy12028 1 MYACDV--CGKEYQHKRTLYRHKKDEC 25 (118)
Q Consensus 1 ~~~C~~--C~~~~~~~~~l~~h~~~~~ 25 (118)
||+|++ |+|.|.++..|.-|+..-+
T Consensus 349 pykCpV~gC~K~YknqnGLKYH~lhGH 375 (423)
T COG5189 349 PYKCPVEGCNKKYKNQNGLKYHMLHGH 375 (423)
T ss_pred eecCCCCCchhhhccccchhhhhhccc
Confidence 799998 9999999999999986533
No 40
>smart00355 ZnF_C2H2 zinc finger.
Probab=97.79 E-value=2.4e-05 Score=30.08 Aligned_cols=23 Identities=35% Similarity=0.804 Sum_probs=16.4
Q ss_pred ccCCCCCccccchHHHHhhhhhh
Q psy12028 2 YACDVCGKEYQHKRTLYRHKKDE 24 (118)
Q Consensus 2 ~~C~~C~~~~~~~~~l~~h~~~~ 24 (118)
|.|..|++.|.....|..|++.|
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~~H 23 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMRTH 23 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHHHh
Confidence 46777777777777777777654
No 41
>PF09237 GAGA: GAGA factor; InterPro: IPR015318 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Members of this entry bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognises the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognises the A in the fourth position of the consensus sequence []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1YUI_A 1YUJ_A.
Probab=97.71 E-value=2.8e-05 Score=34.90 Aligned_cols=32 Identities=22% Similarity=0.404 Sum_probs=18.3
Q ss_pred cccccccCchhhhhhchHHHHHHHhhhcCCCCC
Q psy12028 59 AHVMYACDVCGKVYQHKQTLDRHKKDECGQEPK 91 (118)
Q Consensus 59 ~~~~~~c~~c~~~~~~~~~l~~h~~~h~~~~~~ 91 (118)
.+.|-+|++|+..+..+.+|.+|+.+.++ .+|
T Consensus 21 S~~PatCP~C~a~~~~srnLrRHle~~H~-~k~ 52 (54)
T PF09237_consen 21 SEQPATCPICGAVIRQSRNLRRHLEIRHF-KKP 52 (54)
T ss_dssp TS--EE-TTT--EESSHHHHHHHHHHHTT-TS-
T ss_pred cCCCCCCCcchhhccchhhHHHHHHHHhc-ccC
Confidence 34566777777777777777777777666 443
No 42
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=97.64 E-value=2.4e-05 Score=30.14 Aligned_cols=23 Identities=22% Similarity=0.522 Sum_probs=17.2
Q ss_pred ccCCCCCCCCCChhHHHHHHhhh
Q psy12028 92 FECPHCPYRSKRKDTLDRHMKII 114 (118)
Q Consensus 92 ~~C~~C~~~f~~~~~l~~H~~~~ 114 (118)
|.|.+|++.|.+...|..|++.+
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 56778888888888888887653
No 43
>PRK04860 hypothetical protein; Provisional
Probab=97.60 E-value=2.7e-05 Score=44.04 Aligned_cols=40 Identities=30% Similarity=0.621 Sum_probs=34.1
Q ss_pred cccccCchhhhhhchHHHHHHHhhhcCCCCCccCCCCCCCCCChh
Q psy12028 61 VMYACDVCGKVYQHKQTLDRHKKDECGQEPKFECPHCPYRSKRKD 105 (118)
Q Consensus 61 ~~~~c~~c~~~~~~~~~l~~h~~~h~~~~~~~~C~~C~~~f~~~~ 105 (118)
.+|.|. |+. ....+.+|.+++++ +++|.|..|+..|....
T Consensus 118 ~~Y~C~-C~~---~~~~~rrH~ri~~g-~~~YrC~~C~~~l~~~~ 157 (160)
T PRK04860 118 FPYRCK-CQE---HQLTVRRHNRVVRG-EAVYRCRRCGETLVFKG 157 (160)
T ss_pred EEEEcC-CCC---eeCHHHHHHHHhcC-CccEECCCCCceeEEec
Confidence 579998 987 66678899999999 99999999999886543
No 44
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=97.48 E-value=4.7e-05 Score=29.28 Aligned_cols=20 Identities=30% Similarity=0.846 Sum_probs=10.5
Q ss_pred cCCCCCccccchHHHHhhhh
Q psy12028 3 ACDVCGKEYQHKRTLYRHKK 22 (118)
Q Consensus 3 ~C~~C~~~~~~~~~l~~h~~ 22 (118)
.|.+|++.|.+...|..|++
T Consensus 2 ~C~~C~~~f~s~~~~~~H~~ 21 (25)
T PF12874_consen 2 YCDICNKSFSSENSLRQHLR 21 (25)
T ss_dssp EETTTTEEESSHHHHHHHHT
T ss_pred CCCCCCCCcCCHHHHHHHHC
Confidence 45555555555555555543
No 45
>KOG2785|consensus
Probab=97.44 E-value=0.0003 Score=44.56 Aligned_cols=112 Identities=21% Similarity=0.339 Sum_probs=81.9
Q ss_pred ccCCCCCccccchHHHHhhhhhhcC------------------------------------CCCCccCCCCCcccccchH
Q psy12028 2 YACDVCGKEYQHKRTLYRHKKDECG------------------------------------QEPKFGCPQCPYRSRQKAT 45 (118)
Q Consensus 2 ~~C~~C~~~~~~~~~l~~h~~~~~~------------------------------------~~~~~~C~~c~~~f~~~~~ 45 (118)
|.|..|...|.+...-..|.++-.- .+.++.|.+|.+.|.+...
T Consensus 4 ftC~tC~v~F~~ad~Qr~HyKSdWHRYNLKRkVA~lPPItaE~F~~k~~s~~~~~~~~~e~~~~~~~c~~c~k~~~s~~a 83 (390)
T KOG2785|consen 4 FTCNTCNVEFDDADEQRAHYKSDWHRYNLKRKVASLPPITAEEFNEKVLSDDSEKEENLEEAESVVYCEACNKSFASPKA 83 (390)
T ss_pred ceeeceeeeeccHHHHHHHhhhhHHHhhHHhHhhcCCCcCHHHHhHHHhhhhhhhhhhhhhcccceehHHhhccccChhh
Confidence 7899999999998888888776421 1234889999999999888
Q ss_pred HHHHhhhh---------------------hcc-CC----------c----------------------------------
Q psy12028 46 LNRHLGWE---------------------QLQ-GN----------A---------------------------------- 59 (118)
Q Consensus 46 l~~h~~~~---------------------~~~-~~----------~---------------------------------- 59 (118)
...|+.+. +.. -. .
T Consensus 84 ~~~hl~Sk~h~~~~~~~~r~~e~d~a~~~q~~~~~p~~l~~~~e~e~~~~E~~~~~d~~~e~~~dd~~Edi~~d~~~e~e 163 (390)
T KOG2785|consen 84 HENHLKSKKHVENLSNHQRSEEGDSAKISQLPSRRPSNLQNKGESELKWYEVDSDEDSSEEEEEDDEEEDIEEDGDDEDE 163 (390)
T ss_pred HHHHHHHhhcchhhhhhhccccccchhhhhccccCccccccCCCcccchhhcccccccchhhccCcchhhhhhccchhcc
Confidence 88887711 000 00 0
Q ss_pred ccccccCchhhhhhchHHHHHHHhhhcCC----------------------CCCccCCCCC---CCCCChhHHHHHHhh
Q psy12028 60 HVMYACDVCGKVYQHKQTLDRHKKDECGQ----------------------EPKFECPHCP---YRSKRKDTLDRHMKI 113 (118)
Q Consensus 60 ~~~~~c~~c~~~~~~~~~l~~h~~~h~~~----------------------~~~~~C~~C~---~~f~~~~~l~~H~~~ 113 (118)
.-|-.|..|+..+.+......||..++|= ..-+.|..|+ +.|......++||..
T Consensus 164 ~~Pt~CLfC~~~~k~~e~~~~HM~~~HgffIPdreYL~D~~GLl~YLgeKV~~~~~CL~CN~~~~~f~sleavr~HM~~ 242 (390)
T KOG2785|consen 164 LIPTDCLFCDKKSKSLEENLKHMFKEHGFFIPDREYLTDEKGLLKYLGEKVGIGFICLFCNELGRPFSSLEAVRAHMRD 242 (390)
T ss_pred cCCcceeecCCCcccHHHHHHHHhhccCCcCCchHhhhchhHHHHHHHHHhccCceEEEeccccCcccccHHHHHHHhh
Confidence 12456888998888888888898888871 3457888888 888888888888864
No 46
>PRK04860 hypothetical protein; Provisional
Probab=97.40 E-value=0.00011 Score=41.64 Aligned_cols=37 Identities=24% Similarity=0.635 Sum_probs=24.4
Q ss_pred CccCCCCCcccccchHHHHHhhhhhccCCcccccccCchhhhhhc
Q psy12028 30 KFGCPQCPYRSRQKATLNRHLGWEQLQGNAHVMYACDVCGKVYQH 74 (118)
Q Consensus 30 ~~~C~~c~~~f~~~~~l~~h~~~~~~~~~~~~~~~c~~c~~~~~~ 74 (118)
+|.|. |+. ....+..| ...+.++++|.|..|+..|..
T Consensus 119 ~Y~C~-C~~---~~~~~rrH----~ri~~g~~~YrC~~C~~~l~~ 155 (160)
T PRK04860 119 PYRCK-CQE---HQLTVRRH----NRVVRGEAVYRCRRCGETLVF 155 (160)
T ss_pred EEEcC-CCC---eeCHHHHH----HHHhcCCccEECCCCCceeEE
Confidence 57787 776 44456666 345566677888888776654
No 47
>PF12171 zf-C2H2_jaz: Zinc-finger double-stranded RNA-binding; InterPro: IPR022755 This zinc finger is found in archaea and eukaryotes, and is approximately 30 amino acids in length. The mammalian members of this group occur multiple times along the protein, joined by flexible linkers, and are referred to as JAZ - dsRNA-binding ZF protein - zinc-fingers. The JAZ proteins are expressed in all tissues tested and localise in the nucleus, particularly the nucleolus []. JAZ preferentially binds to double-stranded (ds) RNA or RNA/DNA hybrids rather than DNA. In addition to binding double-stranded RNA, these zinc-fingers are required for nucleolar localisation. This entry represents the multiple-adjacent-C2H2 zinc finger, JAZ. ; PDB: 4DGW_A 1ZR9_A.
Probab=97.35 E-value=0.00013 Score=28.65 Aligned_cols=21 Identities=33% Similarity=0.779 Sum_probs=12.6
Q ss_pred ccCCCCCccccchHHHHhhhh
Q psy12028 2 YACDVCGKEYQHKRTLYRHKK 22 (118)
Q Consensus 2 ~~C~~C~~~~~~~~~l~~h~~ 22 (118)
|.|..|++.|.+...+..|++
T Consensus 2 ~~C~~C~k~f~~~~~~~~H~~ 22 (27)
T PF12171_consen 2 FYCDACDKYFSSENQLKQHMK 22 (27)
T ss_dssp CBBTTTTBBBSSHHHHHCCTT
T ss_pred CCcccCCCCcCCHHHHHHHHc
Confidence 456666666666666666654
No 48
>KOG2231|consensus
Probab=97.32 E-value=0.00095 Score=45.60 Aligned_cols=97 Identities=22% Similarity=0.362 Sum_probs=61.4
Q ss_pred ccchHHHHhhhhhhcCCCCCccCCCCCcc---------cccchHHHHHhhhhhccCCccc-ccccCchhhhhhchHHHHH
Q psy12028 11 YQHKRTLYRHKKDECGQEPKFGCPQCPYR---------SRQKATLNRHLGWEQLQGNAHV-MYACDVCGKVYQHKQTLDR 80 (118)
Q Consensus 11 ~~~~~~l~~h~~~~~~~~~~~~C~~c~~~---------f~~~~~l~~h~~~~~~~~~~~~-~~~c~~c~~~~~~~~~l~~ 80 (118)
|.....|..|+...+. .+.|..|-.. .-+...|..|+..-.......+ --.|..|...|.....|.+
T Consensus 124 ~~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 124 FKSVENLKNHMRDQHK---LHLCSLCLQNLKIFINERKLYTRAELNLHLMFGDPDDESCRGHPLCKFCHERFLDDDELYR 200 (669)
T ss_pred hhHHHHHHHHHHHhhh---hhccccccccceeeeeeeehehHHHHHHHHhcCCCccccccCCccchhhhhhhccHHHHHH
Confidence 3477889999876553 3555554422 2334566777653222111111 2478899999999999999
Q ss_pred HHhhhcCCCCCccCCCC------CCCCCChhHHHHHHhhhc
Q psy12028 81 HKKDECGQEPKFECPHC------PYRSKRKDTLDRHMKIIH 115 (118)
Q Consensus 81 h~~~h~~~~~~~~C~~C------~~~f~~~~~l~~H~~~~~ 115 (118)
|++.++- .|..| +.-|...++|..|.+..|
T Consensus 201 H~~~~h~-----~chfC~~~~~~neyy~~~~dLe~HfR~~H 236 (669)
T KOG2231|consen 201 HLRFDHE-----FCHFCDYKTGQNEYYNDYDDLEEHFRKGH 236 (669)
T ss_pred hhcccee-----heeecCcccccchhcccchHHHHHhhhcC
Confidence 9887653 33333 445777889999988776
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=97.29 E-value=8.9e-05 Score=29.13 Aligned_cols=22 Identities=32% Similarity=0.597 Sum_probs=16.2
Q ss_pred ccCCCCCCCCCChhHHHHHHhh
Q psy12028 92 FECPHCPYRSKRKDTLDRHMKI 113 (118)
Q Consensus 92 ~~C~~C~~~f~~~~~l~~H~~~ 113 (118)
|-|..|++.|.+...|..|++.
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 5677777777777777777654
No 50
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=97.24 E-value=0.0002 Score=27.20 Aligned_cols=22 Identities=36% Similarity=0.634 Sum_probs=10.8
Q ss_pred ccCCCCCccccchHHHHhhhhhh
Q psy12028 2 YACDVCGKEYQHKRTLYRHKKDE 24 (118)
Q Consensus 2 ~~C~~C~~~~~~~~~l~~h~~~~ 24 (118)
|+|+.|+.... ...|..|++.+
T Consensus 1 y~C~~C~y~t~-~~~l~~H~~~~ 22 (24)
T PF13909_consen 1 YKCPHCSYSTS-KSNLKRHLKRH 22 (24)
T ss_dssp EE-SSSS-EES-HHHHHHHHHHH
T ss_pred CCCCCCCCcCC-HHHHHHHHHhh
Confidence 45555555554 55555555544
No 51
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=96.98 E-value=0.00087 Score=25.81 Aligned_cols=20 Identities=35% Similarity=0.755 Sum_probs=13.4
Q ss_pred ccCCCCCCCCCChhHHHHHHh
Q psy12028 92 FECPHCPYRSKRKDTLDRHMK 112 (118)
Q Consensus 92 ~~C~~C~~~f~~~~~l~~H~~ 112 (118)
..|+.||+.| ..+.|.+|+.
T Consensus 3 ~~C~~CgR~F-~~~~l~~H~~ 22 (25)
T PF13913_consen 3 VPCPICGRKF-NPDRLEKHEK 22 (25)
T ss_pred CcCCCCCCEE-CHHHHHHHHH
Confidence 3577777777 5666667764
No 52
>KOG4173|consensus
Probab=96.83 E-value=0.00044 Score=40.29 Aligned_cols=80 Identities=20% Similarity=0.399 Sum_probs=61.1
Q ss_pred CCccCCC--CCcccccchHHHHHhhhhhccCCcccccccCchhhhhhchHHHHHHHhhhcC---------CCCCccCCC-
Q psy12028 29 PKFGCPQ--CPYRSRQKATLNRHLGWEQLQGNAHVMYACDVCGKVYQHKQTLDRHKKDECG---------QEPKFECPH- 96 (118)
Q Consensus 29 ~~~~C~~--c~~~f~~~~~l~~h~~~~~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~h~~---------~~~~~~C~~- 96 (118)
+.+.|++ |...|.+...+..|... .|+ ..|.+|.+.|...-.|..|+...+. +.-.|+|.+
T Consensus 78 ~~~~cqvagc~~~~d~lD~~E~hY~~---~h~----~sCs~C~r~~Pt~hLLd~HI~E~HDs~Fqa~veRG~dMy~ClvE 150 (253)
T KOG4173|consen 78 PAFACQVAGCCQVFDALDDYEHHYHT---LHG----NSCSFCKRAFPTGHLLDAHILEWHDSLFQALVERGQDMYQCLVE 150 (253)
T ss_pred ccccccccchHHHHhhhhhHHHhhhh---ccc----chhHHHHHhCCchhhhhHHHHHHHHHHHHHHHHcCccHHHHHHH
Confidence 3478887 66788888878877532 222 3899999999999999999876542 155799954
Q ss_pred -CCCCCCChhHHHHHHhhhc
Q psy12028 97 -CPYRSKRKDTLDRHMKIIH 115 (118)
Q Consensus 97 -C~~~f~~~~~l~~H~~~~~ 115 (118)
|+-.|.+..+...|+...|
T Consensus 151 gCt~KFkT~r~RkdH~I~~H 170 (253)
T KOG4173|consen 151 GCTEKFKTSRDRKDHMIRMH 170 (253)
T ss_pred hhhhhhhhhhhhhhHHHHhc
Confidence 9999999999999987665
No 53
>KOG1146|consensus
Probab=96.72 E-value=0.00044 Score=50.14 Aligned_cols=23 Identities=30% Similarity=0.756 Sum_probs=14.6
Q ss_pred CCccCCCCCCCCCChhHHHHHHh
Q psy12028 90 PKFECPHCPYRSKRKDTLDRHMK 112 (118)
Q Consensus 90 ~~~~C~~C~~~f~~~~~l~~H~~ 112 (118)
..|.|.+|++.-.-..+|+.|+.
T Consensus 588 P~~~C~vc~yetniarnlrihmt 610 (1406)
T KOG1146|consen 588 PSWRCEVCSYETNIARNLRIHMT 610 (1406)
T ss_pred CCcchhhhcchhhhhhccccccc
Confidence 34677777766666666666654
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=96.51 E-value=0.0028 Score=26.25 Aligned_cols=23 Identities=22% Similarity=0.418 Sum_probs=19.2
Q ss_pred CccCCCCCCCCCChhHHHHHHhh
Q psy12028 91 KFECPHCPYRSKRKDTLDRHMKI 113 (118)
Q Consensus 91 ~~~C~~C~~~f~~~~~l~~H~~~ 113 (118)
+|.|.+|++.|.....+..|+..
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~g 25 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLKG 25 (35)
T ss_pred CeEccccCCccCCHHHHHHHHCh
Confidence 57899999999988888888753
No 55
>KOG1146|consensus
Probab=96.40 E-value=0.0018 Score=47.21 Aligned_cols=53 Identities=23% Similarity=0.483 Sum_probs=37.8
Q ss_pred cccccCchhhhhhchHHHHHHHhhhc------------------------CCCCCccCCCCCCCCCChhHHHHHHhh
Q psy12028 61 VMYACDVCGKVYQHKQTLDRHKKDEC------------------------GQEPKFECPHCPYRSKRKDTLDRHMKI 113 (118)
Q Consensus 61 ~~~~c~~c~~~~~~~~~l~~h~~~h~------------------------~~~~~~~C~~C~~~f~~~~~l~~H~~~ 113 (118)
+.+.|+.|+..|.....|..|++.-+ ....+|.|..|.+++....+|.+|+..
T Consensus 464 kt~~cpkc~~~yk~a~~L~vhmRskhp~~~~~~c~~gq~~~~~arg~~~~~~~~p~~C~~C~~stttng~LsihlqS 540 (1406)
T KOG1146|consen 464 KTLKCPKCNWHYKLAQTLGVHMRSKHPESQSAYCKAGQNHPRLARGEVYRCPGKPYPCRACNYSTTTNGNLSIHLQS 540 (1406)
T ss_pred ccccCCccchhhhhHHHhhhcccccccccchhHhHhccccccccccccccCCCCcccceeeeeeeecchHHHHHHHH
Confidence 45566666666666666666665511 125689999999999999999999864
No 56
>smart00451 ZnF_U1 U1-like zinc finger. Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins.
Probab=96.17 E-value=0.004 Score=25.76 Aligned_cols=20 Identities=15% Similarity=0.584 Sum_probs=9.5
Q ss_pred ccCCCCCccccchHHHHhhh
Q psy12028 2 YACDVCGKEYQHKRTLYRHK 21 (118)
Q Consensus 2 ~~C~~C~~~~~~~~~l~~h~ 21 (118)
|.|..|++.|.+...+..|+
T Consensus 4 ~~C~~C~~~~~~~~~~~~H~ 23 (35)
T smart00451 4 FYCKLCNVTFTDEISVEAHL 23 (35)
T ss_pred eEccccCCccCCHHHHHHHH
Confidence 34455555554444444443
No 57
>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=96.11 E-value=0.0038 Score=25.70 Aligned_cols=25 Identities=40% Similarity=0.958 Sum_probs=16.6
Q ss_pred ccCCCCCccccchHHHHhhhhhhcCCCCCccCCCCCcc
Q psy12028 2 YACDVCGKEYQHKRTLYRHKKDECGQEPKFGCPQCPYR 39 (118)
Q Consensus 2 ~~C~~C~~~~~~~~~l~~h~~~~~~~~~~~~C~~c~~~ 39 (118)
|.|.+||.++... ..++.||.|+..
T Consensus 2 ~~C~~CGy~y~~~-------------~~~~~CP~Cg~~ 26 (33)
T cd00350 2 YVCPVCGYIYDGE-------------EAPWVCPVCGAP 26 (33)
T ss_pred EECCCCCCEECCC-------------cCCCcCcCCCCc
Confidence 6788888766432 256788888753
No 58
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=95.83 E-value=0.0094 Score=27.77 Aligned_cols=33 Identities=30% Similarity=0.544 Sum_probs=19.8
Q ss_pred CCccCCCCCcccccchHHHHHhhhhhccCCcccccccCchhh
Q psy12028 29 PKFGCPQCPYRSRQKATLNRHLGWEQLQGNAHVMYACDVCGK 70 (118)
Q Consensus 29 ~~~~C~~c~~~f~~~~~l~~h~~~~~~~~~~~~~~~c~~c~~ 70 (118)
..|.||.||..-......-+- . ..+|.|+.||.
T Consensus 26 v~F~CPnCGe~~I~Rc~~CRk-------~--g~~Y~Cp~CGF 58 (61)
T COG2888 26 VKFPCPNCGEVEIYRCAKCRK-------L--GNPYRCPKCGF 58 (61)
T ss_pred eEeeCCCCCceeeehhhhHHH-------c--CCceECCCcCc
Confidence 348888888665444322221 1 25688888875
No 59
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=95.75 E-value=0.0038 Score=28.60 Aligned_cols=28 Identities=25% Similarity=0.615 Sum_probs=15.3
Q ss_pred ccccccCchhhhhhchHHHHHHHhhhcC
Q psy12028 60 HVMYACDVCGKVYQHKQTLDRHKKDECG 87 (118)
Q Consensus 60 ~~~~~c~~c~~~~~~~~~l~~h~~~h~~ 87 (118)
+.-+.|+-|+..|....++.+|....++
T Consensus 15 E~~lrCPRC~~~FR~~K~Y~RHVNKaH~ 42 (65)
T COG4049 15 EEFLRCPRCGMVFRRRKDYIRHVNKAHG 42 (65)
T ss_pred ceeeeCCchhHHHHHhHHHHHHhhHHhh
Confidence 3445566666666666555555544443
No 60
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=95.69 E-value=0.0028 Score=41.06 Aligned_cols=50 Identities=26% Similarity=0.538 Sum_probs=43.4
Q ss_pred CccCCCCCccccchHHHHhhhh--hhcCCC--CCccCC--CCCcccccchHHHHHhh
Q psy12028 1 MYACDVCGKEYQHKRTLYRHKK--DECGQE--PKFGCP--QCPYRSRQKATLNRHLG 51 (118)
Q Consensus 1 ~~~C~~C~~~~~~~~~l~~h~~--~~~~~~--~~~~C~--~c~~~f~~~~~l~~h~~ 51 (118)
++.|..|...|.....|..|.. .|.+ + +++.|+ .|++.|.....+..|..
T Consensus 289 ~~~~~~~~~~~s~~~~l~~~~~~~~h~~-~~~~~~~~p~~~~~~~~~~~~~~~~~~~ 344 (467)
T COG5048 289 PIKSKQCNISFSRSSPLTRHLRSVNHSG-ESLKPFSCPYSLCGKLFSRNDALKRHIL 344 (467)
T ss_pred CCCCccccCCcccccccccccccccccc-ccCCceeeeccCCCccccccccccCCcc
Confidence 3678889999999999999999 6877 6 899999 79999999988888865
No 61
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=95.29 E-value=0.026 Score=35.94 Aligned_cols=102 Identities=22% Similarity=0.349 Sum_probs=52.6
Q ss_pred ccCCC--CCccccchHHHHhhhhhhcCCCCCccCCCCCc---ccccc------hHHHHHhhhhhccCCcc----cccccC
Q psy12028 2 YACDV--CGKEYQHKRTLYRHKKDECGQEPKFGCPQCPY---RSRQK------ATLNRHLGWEQLQGNAH----VMYACD 66 (118)
Q Consensus 2 ~~C~~--C~~~~~~~~~l~~h~~~~~~~~~~~~C~~c~~---~f~~~------~~l~~h~~~~~~~~~~~----~~~~c~ 66 (118)
|.|+. |..+......|..|.+..++ .+.|.+|-. .|... ..|..| ......+ .--.|.
T Consensus 152 F~CP~skc~~~C~~~k~lk~H~K~~H~---~~~C~~C~~nKk~F~~E~~lF~~~~Lr~H----~~~G~~e~GFKGHP~C~ 224 (493)
T COG5236 152 FKCPKSKCHRRCGSLKELKKHYKAQHG---FVLCSECIGNKKDFWNEIRLFRSSTLRDH----KNGGLEEEGFKGHPLCI 224 (493)
T ss_pred hcCCchhhhhhhhhHHHHHHHHHhhcC---cEEhHhhhcCcccCccceeeeeccccccc----ccCCccccCcCCCchhh
Confidence 44554 44454455667777666544 355555542 23222 223333 2221111 112577
Q ss_pred chhhhhhchHHHHHHHhhhcCCCCCccCCCCCC----CCCChhHHHHHHh
Q psy12028 67 VCGKVYQHKQTLDRHKKDECGQEPKFECPHCPY----RSKRKDTLDRHMK 112 (118)
Q Consensus 67 ~c~~~~~~~~~l~~h~~~h~~~~~~~~C~~C~~----~f~~~~~l~~H~~ 112 (118)
.|...|-+-..|..|++..+ ++-|.|..-+. -|.+-.+|.+|.+
T Consensus 225 FC~~~FYdDDEL~~HcR~~H--E~ChICD~v~p~~~QYFK~Y~~Le~HF~ 272 (493)
T COG5236 225 FCKIYFYDDDELRRHCRLRH--EACHICDMVGPIRYQYFKSYEDLEAHFR 272 (493)
T ss_pred hccceecChHHHHHHHHhhh--hhhhhhhccCccchhhhhCHHHHHHHhh
Confidence 77777777778888877654 44444444332 2455566666654
No 62
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=94.91 E-value=0.0044 Score=40.15 Aligned_cols=55 Identities=27% Similarity=0.550 Sum_probs=43.5
Q ss_pred cccccCchhhhhhchHHHHHHHh--hhcCCC--CCccCC--CCCCCCCChhHHHHHHhhhcC
Q psy12028 61 VMYACDVCGKVYQHKQTLDRHKK--DECGQE--PKFECP--HCPYRSKRKDTLDRHMKIIHF 116 (118)
Q Consensus 61 ~~~~c~~c~~~~~~~~~l~~h~~--~h~~~~--~~~~C~--~C~~~f~~~~~l~~H~~~~~~ 116 (118)
.++.|..|...|.....+..|.+ .|.+ + .++.|+ .|++.|.+...+..|...+.+
T Consensus 288 ~~~~~~~~~~~~s~~~~l~~~~~~~~h~~-~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~ 348 (467)
T COG5048 288 LPIKSKQCNISFSRSSPLTRHLRSVNHSG-ESLKPFSCPYSLCGKLFSRNDALKRHILLHTS 348 (467)
T ss_pred cCCCCccccCCcccccccccccccccccc-ccCCceeeeccCCCccccccccccCCcccccC
Confidence 35778888888888888888888 6777 7 788888 688888888888888776654
No 63
>PF09538 FYDLN_acid: Protein of unknown function (FYDLN_acid); InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=94.52 E-value=0.026 Score=29.96 Aligned_cols=11 Identities=27% Similarity=0.630 Sum_probs=5.5
Q ss_pred ccCCCCCcccc
Q psy12028 31 FGCPQCPYRSR 41 (118)
Q Consensus 31 ~~C~~c~~~f~ 41 (118)
..|+.||..|-
T Consensus 10 R~Cp~CG~kFY 20 (108)
T PF09538_consen 10 RTCPSCGAKFY 20 (108)
T ss_pred ccCCCCcchhc
Confidence 34555555553
No 64
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=94.25 E-value=0.041 Score=25.71 Aligned_cols=33 Identities=27% Similarity=0.481 Sum_probs=19.9
Q ss_pred CCccCCCCCcccccchHHHHHhhhhhccCCcccccccCchhh
Q psy12028 29 PKFGCPQCPYRSRQKATLNRHLGWEQLQGNAHVMYACDVCGK 70 (118)
Q Consensus 29 ~~~~C~~c~~~f~~~~~l~~h~~~~~~~~~~~~~~~c~~c~~ 70 (118)
..|.||.||..-...-.- +... ..+|.|+.||.
T Consensus 24 ~~F~CPnCG~~~I~RC~~-------CRk~--~~~Y~CP~CGF 56 (59)
T PRK14890 24 VKFLCPNCGEVIIYRCEK-------CRKQ--SNPYTCPKCGF 56 (59)
T ss_pred CEeeCCCCCCeeEeechh-------HHhc--CCceECCCCCC
Confidence 458999999873332211 1111 25699999985
No 65
>KOG2482|consensus
Probab=94.13 E-value=0.068 Score=34.02 Aligned_cols=49 Identities=24% Similarity=0.362 Sum_probs=29.2
Q ss_pred cccCchhhhhhchHHHHHHHhhhcC-C-------------------------CCCccCCCCCCCCCChhHHHHHH
Q psy12028 63 YACDVCGKVYQHKQTLDRHKKDECG-Q-------------------------EPKFECPHCPYRSKRKDTLDRHM 111 (118)
Q Consensus 63 ~~c~~c~~~~~~~~~l~~h~~~h~~-~-------------------------~~~~~C~~C~~~f~~~~~l~~H~ 111 (118)
..|..|.....+...|..||..-+. + ...-.|-.|.-.|-....|..|+
T Consensus 280 v~CLfC~~~~en~~~l~eHmk~vHe~Dl~Ki~sd~~Ln~YqrvrviNyiRkq~~~~~c~~cd~~F~~e~~l~~hm 354 (423)
T KOG2482|consen 280 VVCLFCTNFYENPVFLFEHMKIVHEFDLLKIQSDYSLNFYQRVRVINYIRKQKKKSRCAECDLSFWKEPGLLIHM 354 (423)
T ss_pred eEEEeeccchhhHHHHHHHHHHHHHhhHHhhccccccchhhhhhHHHHHHHHhhccccccccccccCcchhhhhc
Confidence 3566677666666666677665432 0 11234566666677777777666
No 66
>KOG2482|consensus
Probab=94.11 E-value=0.14 Score=32.66 Aligned_cols=24 Identities=33% Similarity=0.483 Sum_probs=20.0
Q ss_pred ccCCCCCCCCCChhHHHHHHhhhc
Q psy12028 92 FECPHCPYRSKRKDTLDRHMKIIH 115 (118)
Q Consensus 92 ~~C~~C~~~f~~~~~l~~H~~~~~ 115 (118)
.+|..|.....+...|..||++.|
T Consensus 280 v~CLfC~~~~en~~~l~eHmk~vH 303 (423)
T KOG2482|consen 280 VVCLFCTNFYENPVFLFEHMKIVH 303 (423)
T ss_pred eEEEeeccchhhHHHHHHHHHHHH
Confidence 578888888888888999988776
No 67
>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=94.01 E-value=0.038 Score=22.88 Aligned_cols=25 Identities=32% Similarity=0.717 Sum_probs=15.8
Q ss_pred ccCCCCCccccchHHHHhhhhhhcCCCCCccCCCCCcc
Q psy12028 2 YACDVCGKEYQHKRTLYRHKKDECGQEPKFGCPQCPYR 39 (118)
Q Consensus 2 ~~C~~C~~~~~~~~~l~~h~~~~~~~~~~~~C~~c~~~ 39 (118)
|.|..||..+.. .+.|..||.|+..
T Consensus 3 ~~C~~CG~i~~g-------------~~~p~~CP~Cg~~ 27 (34)
T cd00729 3 WVCPVCGYIHEG-------------EEAPEKCPICGAP 27 (34)
T ss_pred EECCCCCCEeEC-------------CcCCCcCcCCCCc
Confidence 567788876532 1345688888753
No 68
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=93.91 E-value=0.029 Score=23.69 Aligned_cols=32 Identities=25% Similarity=0.554 Sum_probs=14.4
Q ss_pred ccCchhhhhhchHHHHHHHhhhcCCCCCccCCCCCCCC
Q psy12028 64 ACDVCGKVYQHKQTLDRHKKDECGQEPKFECPHCPYRS 101 (118)
Q Consensus 64 ~c~~c~~~~~~~~~l~~h~~~h~~~~~~~~C~~C~~~f 101 (118)
.|+.|+..|.-... +...+ ....+|+.|+..|
T Consensus 4 ~CP~C~~~f~v~~~-----~l~~~-~~~vrC~~C~~~f 35 (37)
T PF13719_consen 4 TCPNCQTRFRVPDD-----KLPAG-GRKVRCPKCGHVF 35 (37)
T ss_pred ECCCCCceEEcCHH-----HcccC-CcEEECCCCCcEe
Confidence 45555555544433 11122 3345566665544
No 69
>KOG4173|consensus
Probab=93.81 E-value=0.022 Score=33.50 Aligned_cols=78 Identities=22% Similarity=0.369 Sum_probs=50.7
Q ss_pred cCCC--CCccccchHHHHhhhhhhcCCCCCccCCCCCcccccchHHHHHhhhh------hccCCcccccccCc--hhhhh
Q psy12028 3 ACDV--CGKEYQHKRTLYRHKKDECGQEPKFGCPQCPYRSRQKATLNRHLGWE------QLQGNAHVMYACDV--CGKVY 72 (118)
Q Consensus 3 ~C~~--C~~~~~~~~~l~~h~~~~~~~~~~~~C~~c~~~f~~~~~l~~h~~~~------~~~~~~~~~~~c~~--c~~~~ 72 (118)
.|++ |..+|........|-.+.++ -.|.+|.+.|.+...|..|+... -.+..+.--|.|-+ |+..|
T Consensus 81 ~cqvagc~~~~d~lD~~E~hY~~~h~----~sCs~C~r~~Pt~hLLd~HI~E~HDs~Fqa~veRG~dMy~ClvEgCt~KF 156 (253)
T KOG4173|consen 81 ACQVAGCCQVFDALDDYEHHYHTLHG----NSCSFCKRAFPTGHLLDAHILEWHDSLFQALVERGQDMYQCLVEGCTEKF 156 (253)
T ss_pred cccccchHHHHhhhhhHHHhhhhccc----chhHHHHHhCCchhhhhHHHHHHHHHHHHHHHHcCccHHHHHHHhhhhhh
Confidence 4554 55666666666666544443 57889999998888888887521 22333333477754 88888
Q ss_pred hchHHHHHHHhh
Q psy12028 73 QHKQTLDRHKKD 84 (118)
Q Consensus 73 ~~~~~l~~h~~~ 84 (118)
.....-..|+-.
T Consensus 157 kT~r~RkdH~I~ 168 (253)
T KOG4173|consen 157 KTSRDRKDHMIR 168 (253)
T ss_pred hhhhhhhhHHHH
Confidence 888777777643
No 70
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=93.39 E-value=0.017 Score=34.51 Aligned_cols=41 Identities=27% Similarity=0.581 Sum_probs=24.1
Q ss_pred ccCCCCCccccchHHHHhhhhhhcC---------CCCC-----ccCCCCCccccc
Q psy12028 2 YACDVCGKEYQHKRTLYRHKKDECG---------QEPK-----FGCPQCPYRSRQ 42 (118)
Q Consensus 2 ~~C~~C~~~~~~~~~l~~h~~~~~~---------~~~~-----~~C~~c~~~f~~ 42 (118)
..|++|++.|.+........+.-.. +..| ..||.||..+..
T Consensus 6 ~~CPvC~~~F~~~~vrs~~~r~~~~d~D~~~~Y~~vnP~~Y~V~vCP~CgyA~~~ 60 (214)
T PF09986_consen 6 ITCPVCGKEFKTKKVRSGKIRVIRRDSDFCPRYKGVNPLFYEVWVCPHCGYAAFE 60 (214)
T ss_pred eECCCCCCeeeeeEEEcCCceEeeecCCCccccCCCCCeeeeEEECCCCCCcccc
Confidence 4688888888777655544433111 1222 668888876543
No 71
>KOG2231|consensus
Probab=93.37 E-value=0.12 Score=35.97 Aligned_cols=82 Identities=20% Similarity=0.245 Sum_probs=47.2
Q ss_pred cCCCCCcccccchHHHHHhhhhhccCCc----ccccccCchhhhhhchHHHHHHHhhhcCCCC----CccCCCCCCCCCC
Q psy12028 32 GCPQCPYRSRQKATLNRHLGWEQLQGNA----HVMYACDVCGKVYQHKQTLDRHKKDECGQEP----KFECPHCPYRSKR 103 (118)
Q Consensus 32 ~C~~c~~~f~~~~~l~~h~~~~~~~~~~----~~~~~c~~c~~~~~~~~~l~~h~~~h~~~~~----~~~C~~C~~~f~~ 103 (118)
.|..| ..|.....|+.||...++.+-- +..-.+..+.+.|.. ..|..|+..--.++. .-.|..|...|-.
T Consensus 117 ~~~~c-~~~~s~~~Lk~H~~~~H~~~~c~lC~~~~kif~~e~k~Yt~-~el~~h~~~gd~d~~s~rGhp~C~~C~~~fld 194 (669)
T KOG2231|consen 117 ECLHC-TEFKSVENLKNHMRDQHKLHLCSLCLQNLKIFINERKLYTR-AELNLHLMFGDPDDESCRGHPLCKFCHERFLD 194 (669)
T ss_pred CCccc-cchhHHHHHHHHHHHhhhhhccccccccceeeeeeeehehH-HHHHHHHhcCCCccccccCCccchhhhhhhcc
Confidence 44555 5555788899998643332110 000012223444444 455566554221122 2468999999999
Q ss_pred hhHHHHHHhhhc
Q psy12028 104 KDTLDRHMKIIH 115 (118)
Q Consensus 104 ~~~l~~H~~~~~ 115 (118)
...|.+|++..|
T Consensus 195 ~~el~rH~~~~h 206 (669)
T KOG2231|consen 195 DDELYRHLRFDH 206 (669)
T ss_pred HHHHHHhhccce
Confidence 999999998766
No 72
>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=93.21 E-value=0.031 Score=23.93 Aligned_cols=12 Identities=33% Similarity=1.162 Sum_probs=7.0
Q ss_pred ccCCCCCccccc
Q psy12028 2 YACDVCGKEYQH 13 (118)
Q Consensus 2 ~~C~~C~~~~~~ 13 (118)
|+|..||..|..
T Consensus 6 y~C~~Cg~~fe~ 17 (41)
T smart00834 6 YRCEDCGHTFEV 17 (41)
T ss_pred EEcCCCCCEEEE
Confidence 556666666543
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=93.08 E-value=0.085 Score=28.01 Aligned_cols=26 Identities=35% Similarity=0.819 Sum_probs=23.9
Q ss_pred CccC----CCCCCCCCChhHHHHHHhhhcC
Q psy12028 91 KFEC----PHCPYRSKRKDTLDRHMKIIHF 116 (118)
Q Consensus 91 ~~~C----~~C~~~f~~~~~l~~H~~~~~~ 116 (118)
-|.| ..|++.+.+...+..|++.+||
T Consensus 80 G~~C~~~~~~C~y~~~~~~~m~~H~~~~Hg 109 (109)
T PF12013_consen 80 GYRCQCDPPHCGYITRSKKTMRKHWRKEHG 109 (109)
T ss_pred CeeeecCCCCCCcEeccHHHHHHHHHHhcC
Confidence 3889 9999999999999999999886
No 74
>KOG2186|consensus
Probab=93.08 E-value=0.052 Score=33.03 Aligned_cols=46 Identities=20% Similarity=0.537 Sum_probs=36.4
Q ss_pred ccCCCCCccccchHHHHhhhhhhcCCCCCccCCCCCcccccchHHHHHhh
Q psy12028 2 YACDVCGKEYQHKRTLYRHKKDECGQEPKFGCPQCPYRSRQKATLNRHLG 51 (118)
Q Consensus 2 ~~C~~C~~~~~~~~~l~~h~~~~~~~~~~~~C~~c~~~f~~~~~l~~h~~ 51 (118)
|.|..||....-.. +..|+..-++ .-|.|..|+..|.. ..+..|..
T Consensus 4 FtCnvCgEsvKKp~-vekH~srCrn--~~fSCIDC~k~F~~-~sYknH~k 49 (276)
T KOG2186|consen 4 FTCNVCGESVKKPQ-VEKHMSRCRN--AYFSCIDCGKTFER-VSYKNHTK 49 (276)
T ss_pred Eehhhhhhhccccc-hHHHHHhccC--CeeEEeeccccccc-chhhhhhh
Confidence 78999998876654 6668887765 45999999999998 66888864
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=92.99 E-value=0.26 Score=26.37 Aligned_cols=84 Identities=13% Similarity=0.120 Sum_probs=45.9
Q ss_pred CCCccCCCCCcccccchHHHHHhhhhhccC-Cccc-------ccccCchhhhhhchHHHHHHHhhhcCCCCCccCCCCCC
Q psy12028 28 EPKFGCPQCPYRSRQKATLNRHLGWEQLQG-NAHV-------MYACDVCGKVYQHKQTLDRHKKDECGQEPKFECPHCPY 99 (118)
Q Consensus 28 ~~~~~C~~c~~~f~~~~~l~~h~~~~~~~~-~~~~-------~~~c~~c~~~~~~~~~l~~h~~~h~~~~~~~~C~~C~~ 99 (118)
+-|..|+.|+........|.+-.......- -.+. ...|-.|...|.......... -.. ...|.|+.|+.
T Consensus 13 ~LP~~CpiCgLtLVss~HLARSyHHLfPl~~f~ev~~~~~~~~~~C~~C~~~f~~~~~~~~~~--~~~-~~~y~C~~C~~ 89 (112)
T TIGR00622 13 ELPVECPICGLTLILSTHLARSYHHLFPLKAFQEIPLEEYNGSRFCFGCQGPFPKPPVSPFDE--LKD-SHRYVCAVCKN 89 (112)
T ss_pred CCCCcCCcCCCEEeccchHHHhhhccCCCcccccccccccCCCCcccCcCCCCCCcccccccc--ccc-ccceeCCCCCC
Confidence 346778888877776666655322000000 0011 123777777776542111000 112 45688999998
Q ss_pred CCCChhHHHHHHhhh
Q psy12028 100 RSKRKDTLDRHMKII 114 (118)
Q Consensus 100 ~f~~~~~l~~H~~~~ 114 (118)
.|-..-+.-.|...|
T Consensus 90 ~FC~dCD~fiHe~Lh 104 (112)
T TIGR00622 90 VFCVDCDVFVHESLH 104 (112)
T ss_pred ccccccchhhhhhcc
Confidence 888777777776655
No 76
>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=92.97 E-value=0.027 Score=24.52 Aligned_cols=12 Identities=42% Similarity=1.292 Sum_probs=6.0
Q ss_pred ccCCCCCccccc
Q psy12028 2 YACDVCGKEYQH 13 (118)
Q Consensus 2 ~~C~~C~~~~~~ 13 (118)
|.|..||..|..
T Consensus 6 y~C~~Cg~~fe~ 17 (42)
T PF09723_consen 6 YRCEECGHEFEV 17 (42)
T ss_pred EEeCCCCCEEEE
Confidence 445555555533
No 77
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=92.95 E-value=0.11 Score=23.91 Aligned_cols=23 Identities=30% Similarity=0.645 Sum_probs=15.4
Q ss_pred CCCccCCCCCcccccchHHHHHh
Q psy12028 28 EPKFGCPQCPYRSRQKATLNRHL 50 (118)
Q Consensus 28 ~~~~~C~~c~~~f~~~~~l~~h~ 50 (118)
+..+.||-|+..|.....+.+|+
T Consensus 15 E~~lrCPRC~~~FR~~K~Y~RHV 37 (65)
T COG4049 15 EEFLRCPRCGMVFRRRKDYIRHV 37 (65)
T ss_pred ceeeeCCchhHHHHHhHHHHHHh
Confidence 45566777777777666666665
No 78
>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=92.84 E-value=0.032 Score=25.35 Aligned_cols=12 Identities=33% Similarity=1.185 Sum_probs=7.1
Q ss_pred ccCCCCCccccc
Q psy12028 2 YACDVCGKEYQH 13 (118)
Q Consensus 2 ~~C~~C~~~~~~ 13 (118)
|+|..|+..|..
T Consensus 6 y~C~~Cg~~fe~ 17 (52)
T TIGR02605 6 YRCTACGHRFEV 17 (52)
T ss_pred EEeCCCCCEeEE
Confidence 556666666653
No 79
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=92.79 E-value=0.056 Score=22.69 Aligned_cols=32 Identities=19% Similarity=0.345 Sum_probs=14.7
Q ss_pred ccCchhhhhhchHHHHHHHhhhcCCCCCccCCCCCCCC
Q psy12028 64 ACDVCGKVYQHKQTLDRHKKDECGQEPKFECPHCPYRS 101 (118)
Q Consensus 64 ~c~~c~~~~~~~~~l~~h~~~h~~~~~~~~C~~C~~~f 101 (118)
.|+.|+..|.-.+.. +... ....+|+.|+..|
T Consensus 4 ~Cp~C~~~y~i~d~~-----ip~~-g~~v~C~~C~~~f 35 (36)
T PF13717_consen 4 TCPNCQAKYEIDDEK-----IPPK-GRKVRCSKCGHVF 35 (36)
T ss_pred ECCCCCCEEeCCHHH-----CCCC-CcEEECCCCCCEe
Confidence 455555555444331 1111 3345566666544
No 80
>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=92.56 E-value=0.057 Score=22.78 Aligned_cols=10 Identities=20% Similarity=0.447 Sum_probs=5.1
Q ss_pred ccCCCCCCCC
Q psy12028 92 FECPHCPYRS 101 (118)
Q Consensus 92 ~~C~~C~~~f 101 (118)
..|+.|+..|
T Consensus 26 v~C~~C~~~~ 35 (38)
T TIGR02098 26 VRCGKCGHVW 35 (38)
T ss_pred EECCCCCCEE
Confidence 4555555443
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=92.41 E-value=0.12 Score=29.43 Aligned_cols=32 Identities=22% Similarity=0.480 Sum_probs=20.0
Q ss_pred CCCccCCCCCcccccchHHHHHhhhhhccCCcccccccCchhhhh
Q psy12028 28 EPKFGCPQCPYRSRQKATLNRHLGWEQLQGNAHVMYACDVCGKVY 72 (118)
Q Consensus 28 ~~~~~C~~c~~~f~~~~~l~~h~~~~~~~~~~~~~~~c~~c~~~~ 72 (118)
...|.||.|+..|.....+.. .|.|+.||...
T Consensus 107 ~~~Y~Cp~c~~r~tf~eA~~~-------------~F~Cp~Cg~~L 138 (158)
T TIGR00373 107 NMFFICPNMCVRFTFNEAMEL-------------NFTCPRCGAML 138 (158)
T ss_pred CCeEECCCCCcEeeHHHHHHc-------------CCcCCCCCCEe
Confidence 345777777777766554431 27777777644
No 82
>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=92.35 E-value=0.25 Score=26.19 Aligned_cols=25 Identities=36% Similarity=0.820 Sum_probs=22.1
Q ss_pred ccc----CchhhhhhchHHHHHHHhhhcC
Q psy12028 63 YAC----DVCGKVYQHKQTLDRHKKDECG 87 (118)
Q Consensus 63 ~~c----~~c~~~~~~~~~l~~h~~~h~~ 87 (118)
|.| ..|+....+...+..|++.++|
T Consensus 81 ~~C~~~~~~C~y~~~~~~~m~~H~~~~Hg 109 (109)
T PF12013_consen 81 YRCQCDPPHCGYITRSKKTMRKHWRKEHG 109 (109)
T ss_pred eeeecCCCCCCcEeccHHHHHHHHHHhcC
Confidence 789 8899999999999999988765
No 83
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=92.19 E-value=0.042 Score=31.11 Aligned_cols=48 Identities=15% Similarity=0.196 Sum_probs=26.6
Q ss_pred ccCCCCCccccchHHHHhhhhhhcCCCCCccCCCCCcccccchHHHHHh
Q psy12028 2 YACDVCGKEYQHKRTLYRHKKDECGQEPKFGCPQCPYRSRQKATLNRHL 50 (118)
Q Consensus 2 ~~C~~C~~~~~~~~~l~~h~~~~~~~~~~~~C~~c~~~f~~~~~l~~h~ 50 (118)
++|+.||........-. -+.--....+.++|+.||..|.....+..-+
T Consensus 1 m~cp~c~~~~~~~~~s~-~~~~~~~~~~~~~c~~c~~~f~~~e~~~~~~ 48 (154)
T PRK00464 1 MRCPFCGHPDTRVIDSR-PAEDGNAIRRRRECLACGKRFTTFERVELVP 48 (154)
T ss_pred CcCCCCCCCCCEeEecc-ccCCCCceeeeeeccccCCcceEeEeccCcc
Confidence 47999997653221111 0000000123499999999998876555443
No 84
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=91.97 E-value=0.096 Score=30.05 Aligned_cols=24 Identities=38% Similarity=0.862 Sum_probs=18.8
Q ss_pred ccccCchhhhhhchHHHHHHHhhhcCCCCCccCCCCCC
Q psy12028 62 MYACDVCGKVYQHKQTLDRHKKDECGQEPKFECPHCPY 99 (118)
Q Consensus 62 ~~~c~~c~~~~~~~~~l~~h~~~h~~~~~~~~C~~C~~ 99 (118)
.|.|++||. ++-| +.|-+||+||-
T Consensus 134 ~~vC~vCGy-------------~~~g-e~P~~CPiCga 157 (166)
T COG1592 134 VWVCPVCGY-------------THEG-EAPEVCPICGA 157 (166)
T ss_pred EEEcCCCCC-------------cccC-CCCCcCCCCCC
Confidence 589999974 3456 88899999984
No 85
>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=91.89 E-value=0.11 Score=29.61 Aligned_cols=30 Identities=17% Similarity=0.492 Sum_probs=24.3
Q ss_pred ccCCCCCccccchHHHHhhhhhhcCCCCCccCCCCCcccc
Q psy12028 2 YACDVCGKEYQHKRTLYRHKKDECGQEPKFGCPQCPYRSR 41 (118)
Q Consensus 2 ~~C~~C~~~~~~~~~l~~h~~~~~~~~~~~~C~~c~~~f~ 41 (118)
|.|+.|+..|+...++. .-|.||.||....
T Consensus 110 Y~Cp~c~~r~tf~eA~~----------~~F~Cp~Cg~~L~ 139 (158)
T TIGR00373 110 FICPNMCVRFTFNEAME----------LNFTCPRCGAMLD 139 (158)
T ss_pred EECCCCCcEeeHHHHHH----------cCCcCCCCCCEee
Confidence 78999999998888774 1499999997643
No 86
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=91.79 E-value=0.055 Score=27.37 Aligned_cols=29 Identities=24% Similarity=0.652 Sum_probs=15.7
Q ss_pred cccCchhhhhhchHHHHHHHhhhcCCCCCccCCCCCCCCC
Q psy12028 63 YACDVCGKVYQHKQTLDRHKKDECGQEPKFECPHCPYRSK 102 (118)
Q Consensus 63 ~~c~~c~~~~~~~~~l~~h~~~h~~~~~~~~C~~C~~~f~ 102 (118)
|.|+.|++. .+.+.-+| -|.|..||..|.
T Consensus 36 ~~Cp~C~~~--------~VkR~a~G---IW~C~kCg~~fA 64 (89)
T COG1997 36 HVCPFCGRT--------TVKRIATG---IWKCRKCGAKFA 64 (89)
T ss_pred CcCCCCCCc--------ceeeeccC---eEEcCCCCCeec
Confidence 566666653 12334333 566766766654
No 87
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=91.78 E-value=0.11 Score=29.18 Aligned_cols=38 Identities=16% Similarity=0.439 Sum_probs=24.8
Q ss_pred CCCccCCCCCcccccchHHHHHhhhhhccCCcccccccCchhhhhh
Q psy12028 28 EPKFGCPQCPYRSRQKATLNRHLGWEQLQGNAHVMYACDVCGKVYQ 73 (118)
Q Consensus 28 ~~~~~C~~c~~~f~~~~~l~~h~~~~~~~~~~~~~~~c~~c~~~~~ 73 (118)
...|.||.|+..|.....+..- .. ...|.|+.|+....
T Consensus 97 ~~~Y~Cp~C~~~y~~~ea~~~~------d~--~~~f~Cp~Cg~~l~ 134 (147)
T smart00531 97 NAYYKCPNCQSKYTFLEANQLL------DM--DGTFTCPRCGEELE 134 (147)
T ss_pred CcEEECcCCCCEeeHHHHHHhc------CC--CCcEECCCCCCEEE
Confidence 4569999999888865433321 11 23389999987653
No 88
>smart00614 ZnF_BED BED zinc finger. DNA-binding domain in chromatin-boundary-element-binding proteins and transposases
Probab=91.71 E-value=0.18 Score=22.74 Aligned_cols=24 Identities=29% Similarity=0.602 Sum_probs=14.9
Q ss_pred ccCCCCCCCCCCh-----hHHHHHHhhhc
Q psy12028 92 FECPHCPYRSKRK-----DTLDRHMKIIH 115 (118)
Q Consensus 92 ~~C~~C~~~f~~~-----~~l~~H~~~~~ 115 (118)
-.|..|++.++.. +.|.+|+...+
T Consensus 19 a~C~~C~~~l~~~~~~gTs~L~rHl~~~h 47 (50)
T smart00614 19 AKCKYCGKKLSRSSKGGTSNLRRHLRRKH 47 (50)
T ss_pred EEecCCCCEeeeCCCCCcHHHHHHHHhHC
Confidence 4577777665443 57777777433
No 89
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=91.67 E-value=0.074 Score=23.55 Aligned_cols=11 Identities=45% Similarity=1.259 Sum_probs=6.6
Q ss_pred ccCCCCCcccc
Q psy12028 2 YACDVCGKEYQ 12 (118)
Q Consensus 2 ~~C~~C~~~~~ 12 (118)
|.|+.||..+.
T Consensus 4 y~C~~CG~~~~ 14 (46)
T PRK00398 4 YKCARCGREVE 14 (46)
T ss_pred EECCCCCCEEE
Confidence 56666666553
No 90
>KOG2186|consensus
Probab=91.34 E-value=0.13 Score=31.34 Aligned_cols=47 Identities=21% Similarity=0.586 Sum_probs=29.3
Q ss_pred CccCCCCCcccccchHHHHHhhhhhccCCcccccccCchhhhhhchHHHHHHHh
Q psy12028 30 KFGCPQCPYRSRQKATLNRHLGWEQLQGNAHVMYACDVCGKVYQHKQTLDRHKK 83 (118)
Q Consensus 30 ~~~C~~c~~~f~~~~~l~~h~~~~~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~ 83 (118)
.|.|..||....-. .+..|+ ..+.+ ..|.|..|+..|.+ ..+..|..
T Consensus 3 ~FtCnvCgEsvKKp-~vekH~----srCrn-~~fSCIDC~k~F~~-~sYknH~k 49 (276)
T KOG2186|consen 3 FFTCNVCGESVKKP-QVEKHM----SRCRN-AYFSCIDCGKTFER-VSYKNHTK 49 (276)
T ss_pred EEehhhhhhhcccc-chHHHH----HhccC-CeeEEeeccccccc-chhhhhhh
Confidence 36788888777654 355564 34444 45778888888776 44455543
No 91
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=91.28 E-value=0.14 Score=29.84 Aligned_cols=33 Identities=24% Similarity=0.621 Sum_probs=23.0
Q ss_pred CCCccCCCCCcccccchHHHHHhhhhhccCCcccccccCchhhhhh
Q psy12028 28 EPKFGCPQCPYRSRQKATLNRHLGWEQLQGNAHVMYACDVCGKVYQ 73 (118)
Q Consensus 28 ~~~~~C~~c~~~f~~~~~l~~h~~~~~~~~~~~~~~~c~~c~~~~~ 73 (118)
...|.||.|+..|.....+.. .|.|+.||....
T Consensus 115 ~~~Y~Cp~C~~rytf~eA~~~-------------~F~Cp~Cg~~L~ 147 (178)
T PRK06266 115 NMFFFCPNCHIRFTFDEAMEY-------------GFRCPQCGEMLE 147 (178)
T ss_pred CCEEECCCCCcEEeHHHHhhc-------------CCcCCCCCCCCe
Confidence 356889888888877665432 178888886543
No 92
>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=91.07 E-value=0.18 Score=27.48 Aligned_cols=13 Identities=8% Similarity=-0.205 Sum_probs=6.0
Q ss_pred CCccCCCCCcccc
Q psy12028 29 PKFGCPQCPYRSR 41 (118)
Q Consensus 29 ~~~~C~~c~~~f~ 41 (118)
.|..||.||..|.
T Consensus 25 ~p~vcP~cg~~~~ 37 (129)
T TIGR02300 25 RPAVSPYTGEQFP 37 (129)
T ss_pred CCccCCCcCCccC
Confidence 3444555554443
No 93
>PF02892 zf-BED: BED zinc finger; InterPro: IPR003656 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents predicted BED-type zinc finger domains. The BED finger which was named after the Drosophila proteins BEAF and DREF, is found in one or more copies in cellular regulatory factors and transposases from plants, animals and fungi. The BED finger is an about 50 to 60 amino acid residues domain that contains a characteristic motif with two highly conserved aromatic positions, as well as a shared pattern of cysteines and histidines that is predicted to form a zinc finger. As diverse BED fingers are able to bind DNA, it has been suggested that DNA-binding is the general function of this domain []. Some proteins known to contain a BED domain include animal, plant and fungi AC1 and Hobo-like transposases; Caenorhabditis elegans Dpy-20 protein, a predicted cuticular gene transcriptional regulator; Drosophila BEAF (boundary element-associated factor), thought to be involved in chromatin insulation; Drosophila DREF, a transcriptional regulator for S-phase genes; and tobacco 3AF1 and tomato E4/E8-BP1, light- and ethylene-regulated DNA binding proteins that contain two BED fingers. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding; PDB: 2DJR_A 2CT5_A.
Probab=91.00 E-value=0.14 Score=22.40 Aligned_cols=27 Identities=33% Similarity=0.506 Sum_probs=14.9
Q ss_pred CCCccCCCCCCCCCC----hhHHHHHHhhhc
Q psy12028 89 EPKFECPHCPYRSKR----KDTLDRHMKIIH 115 (118)
Q Consensus 89 ~~~~~C~~C~~~f~~----~~~l~~H~~~~~ 115 (118)
.....|..|++.+.. .+.|.+|++..|
T Consensus 14 ~~~a~C~~C~~~~~~~~~~ts~l~~HL~~~h 44 (45)
T PF02892_consen 14 KKKAKCKYCGKVIKYSSGGTSNLKRHLKKKH 44 (45)
T ss_dssp SS-EEETTTTEE-----SSTHHHHHHHHHTT
T ss_pred cCeEEeCCCCeEEeeCCCcHHHHHHhhhhhC
Confidence 455677777765544 467777775443
No 94
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=90.95 E-value=0.19 Score=29.31 Aligned_cols=30 Identities=23% Similarity=0.813 Sum_probs=18.9
Q ss_pred cccccCchhhhhhchHHHHHHHhhhcCCCCCccCCCCCCC
Q psy12028 61 VMYACDVCGKVYQHKQTLDRHKKDECGQEPKFECPHCPYR 100 (118)
Q Consensus 61 ~~~~c~~c~~~~~~~~~l~~h~~~h~~~~~~~~C~~C~~~ 100 (118)
.-|.|+.|+..|+.-.++. .+ |.|+.||-.
T Consensus 116 ~~Y~Cp~C~~rytf~eA~~------~~----F~Cp~Cg~~ 145 (178)
T PRK06266 116 MFFFCPNCHIRFTFDEAME------YG----FRCPQCGEM 145 (178)
T ss_pred CEEECCCCCcEEeHHHHhh------cC----CcCCCCCCC
Confidence 3467777777776665542 24 677777754
No 95
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=90.63 E-value=0.19 Score=22.14 Aligned_cols=26 Identities=38% Similarity=0.966 Sum_probs=14.9
Q ss_pred ccCCCCCccccchHHHHhhhhhhcCCCCCccCCCCCcc
Q psy12028 2 YACDVCGKEYQHKRTLYRHKKDECGQEPKFGCPQCPYR 39 (118)
Q Consensus 2 ~~C~~C~~~~~~~~~l~~h~~~~~~~~~~~~C~~c~~~ 39 (118)
|.|..||..|... . ..+..|+.||..
T Consensus 3 Y~C~~Cg~~~~~~-----------~-~~~irC~~CG~r 28 (44)
T smart00659 3 YICGECGRENEIK-----------S-KDVVRCRECGYR 28 (44)
T ss_pred EECCCCCCEeecC-----------C-CCceECCCCCce
Confidence 5677777665432 1 334677777643
No 96
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=90.62 E-value=0.13 Score=28.22 Aligned_cols=28 Identities=29% Similarity=0.710 Sum_probs=19.2
Q ss_pred CccCCCCCccccchHHHHhhhhhhcCCCCCccCCCCCcc
Q psy12028 1 MYACDVCGKEYQHKRTLYRHKKDECGQEPKFGCPQCPYR 39 (118)
Q Consensus 1 ~~~C~~C~~~~~~~~~l~~h~~~~~~~~~~~~C~~c~~~ 39 (118)
|++|..||+.|.+-+. +-.-.||.||-.
T Consensus 1 PH~Ct~Cg~~f~dgs~-----------eil~GCP~CGg~ 28 (131)
T PF09845_consen 1 PHQCTKCGRVFEDGSK-----------EILSGCPECGGN 28 (131)
T ss_pred CcccCcCCCCcCCCcH-----------HHHccCcccCCc
Confidence 7889999999976442 112468888843
No 97
>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=90.56 E-value=0.12 Score=28.48 Aligned_cols=25 Identities=28% Similarity=0.454 Sum_probs=15.2
Q ss_pred CCCccCCCCCCCCCChhHHHHHHhhhcC
Q psy12028 89 EPKFECPHCPYRSKRKDTLDRHMKIIHF 116 (118)
Q Consensus 89 ~~~~~C~~C~~~f~~~~~l~~H~~~~~~ 116 (118)
.....|-+||+.|.. |.+|++.|||
T Consensus 70 ~d~i~clecGk~~k~---LkrHL~~~~g 94 (132)
T PF05443_consen 70 PDYIICLECGKKFKT---LKRHLRTHHG 94 (132)
T ss_dssp SS-EE-TBT--EESB---HHHHHHHTT-
T ss_pred cCeeEEccCCcccch---HHHHHHHccC
Confidence 345779999998864 4899988876
No 98
>smart00734 ZnF_Rad18 Rad18-like CCHC zinc finger. Yeast Rad18p functions with Rad5p in error-free post-replicative DNA repair. This zinc finger is likely to bind nucleic-acids.
Probab=89.48 E-value=0.48 Score=18.26 Aligned_cols=19 Identities=21% Similarity=0.691 Sum_probs=12.4
Q ss_pred cCCCCCCCCCChhHHHHHHh
Q psy12028 93 ECPHCPYRSKRKDTLDRHMK 112 (118)
Q Consensus 93 ~C~~C~~~f~~~~~l~~H~~ 112 (118)
.|++|++.. ....+..|+.
T Consensus 3 ~CPiC~~~v-~~~~in~HLD 21 (26)
T smart00734 3 QCPVCFREV-PENLINSHLD 21 (26)
T ss_pred cCCCCcCcc-cHHHHHHHHH
Confidence 577777776 4556666654
No 99
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=88.94 E-value=0.26 Score=25.21 Aligned_cols=14 Identities=21% Similarity=0.615 Sum_probs=11.1
Q ss_pred CCccCCCCCccccc
Q psy12028 29 PKFGCPQCPYRSRQ 42 (118)
Q Consensus 29 ~~~~C~~c~~~f~~ 42 (118)
.|..|..||..|..
T Consensus 57 ~Pa~CkkCGfef~~ 70 (97)
T COG3357 57 RPARCKKCGFEFRD 70 (97)
T ss_pred cChhhcccCccccc
Confidence 56788888888876
No 100
>KOG4167|consensus
Probab=88.73 E-value=0.069 Score=37.35 Aligned_cols=25 Identities=24% Similarity=0.535 Sum_probs=23.1
Q ss_pred ccCCCCCccccchHHHHhhhhhhcC
Q psy12028 2 YACDVCGKEYQHKRTLYRHKKDECG 26 (118)
Q Consensus 2 ~~C~~C~~~~~~~~~l~~h~~~~~~ 26 (118)
|.|.+|+++|....++..||++|..
T Consensus 793 FpCreC~kvF~KiKSrNAHMK~Hr~ 817 (907)
T KOG4167|consen 793 FPCRECGKVFFKIKSRNAHMKTHRQ 817 (907)
T ss_pred eehHHHHHHHHHHhhhhHHHHHHHH
Confidence 7899999999999999999999864
No 101
>PF14353 CpXC: CpXC protein
Probab=88.67 E-value=0.38 Score=26.29 Aligned_cols=48 Identities=27% Similarity=0.442 Sum_probs=28.0
Q ss_pred ccCCCCCccccchHHHHh--------hhhhhcCCCCCccCCCCCcccccchHHHHH
Q psy12028 2 YACDVCGKEYQHKRTLYR--------HKKDECGQEPKFGCPQCPYRSRQKATLNRH 49 (118)
Q Consensus 2 ~~C~~C~~~~~~~~~l~~--------h~~~~~~~~~~~~C~~c~~~f~~~~~l~~h 49 (118)
..|+.|+..|........ -.+.-.+.-..+.||.||..|.-...+.-|
T Consensus 2 itCP~C~~~~~~~v~~~I~~~~~p~l~e~il~g~l~~~~CP~Cg~~~~~~~p~lY~ 57 (128)
T PF14353_consen 2 ITCPHCGHEFEFEVWTSINADEDPELKEKILDGSLFSFTCPSCGHKFRLEYPLLYH 57 (128)
T ss_pred cCCCCCCCeeEEEEEeEEcCcCCHHHHHHHHcCCcCEEECCCCCCceecCCCEEEE
Confidence 368999888754322111 112223334569999999988765544433
No 102
>KOG2893|consensus
Probab=88.56 E-value=0.09 Score=31.85 Aligned_cols=41 Identities=24% Similarity=0.536 Sum_probs=18.8
Q ss_pred cCchhhhhhchHHHHHHHhhhcCCCCCccCCCCCCCCCChhHHHHH
Q psy12028 65 CDVCGKVYQHKQTLDRHKKDECGQEPKFECPHCPYRSKRKDTLDRH 110 (118)
Q Consensus 65 c~~c~~~~~~~~~l~~h~~~h~~~~~~~~C~~C~~~f~~~~~l~~H 110 (118)
|=+|++.|.+...|..|+. .+-|+|.+|.|..-+--.|..|
T Consensus 13 cwycnrefddekiliqhqk-----akhfkchichkkl~sgpglsih 53 (341)
T KOG2893|consen 13 CWYCNREFDDEKILIQHQK-----AKHFKCHICHKKLFSGPGLSIH 53 (341)
T ss_pred eeecccccchhhhhhhhhh-----hccceeeeehhhhccCCCceee
Confidence 3345555555555544432 2345555555443333333333
No 103
>PF03604 DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa subunit; InterPro: IPR006591 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Each class of RNA polymerase is assembled from 9 to 15 different polypeptides. Rbp10 (RNA polymerase CX) is a domain found in RNA polymerase subunit 10; present in RNA polymerase I, II and III.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_Z 3HKZ_X 2NVX_L 3S1Q_L 2JA6_L 3S17_L 3HOW_L 3HOV_L 3PO2_L 3HOZ_L ....
Probab=88.55 E-value=0.34 Score=19.75 Aligned_cols=26 Identities=38% Similarity=0.907 Sum_probs=14.3
Q ss_pred ccCCCCCccccchHHHHhhhhhhcCCCCCccCCCCCcc
Q psy12028 2 YACDVCGKEYQHKRTLYRHKKDECGQEPKFGCPQCPYR 39 (118)
Q Consensus 2 ~~C~~C~~~~~~~~~l~~h~~~~~~~~~~~~C~~c~~~ 39 (118)
|.|..|+..+... ...+..|+.||..
T Consensus 1 Y~C~~Cg~~~~~~------------~~~~irC~~CG~R 26 (32)
T PF03604_consen 1 YICGECGAEVELK------------PGDPIRCPECGHR 26 (32)
T ss_dssp EBESSSSSSE-BS------------TSSTSSBSSSS-S
T ss_pred CCCCcCCCeeEcC------------CCCcEECCcCCCe
Confidence 5677777766411 1234678888754
No 104
>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=88.46 E-value=0.31 Score=18.83 Aligned_cols=10 Identities=50% Similarity=1.231 Sum_probs=6.5
Q ss_pred cCCCCCCCCC
Q psy12028 93 ECPHCPYRSK 102 (118)
Q Consensus 93 ~C~~C~~~f~ 102 (118)
.|+.||+.|.
T Consensus 16 ~Cp~CG~~F~ 25 (26)
T PF10571_consen 16 FCPHCGYDFE 25 (26)
T ss_pred cCCCCCCCCc
Confidence 5677776664
No 105
>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=87.97 E-value=0.2 Score=30.07 Aligned_cols=29 Identities=28% Similarity=0.450 Sum_probs=22.7
Q ss_pred CCCccCCCCCCCCCChhHHHHHHhhhcCC
Q psy12028 89 EPKFECPHCPYRSKRKDTLDRHMKIIHFS 117 (118)
Q Consensus 89 ~~~~~C~~C~~~f~~~~~l~~H~~~~~~~ 117 (118)
+..|.|..|+|.|.-..-..+|+...|.|
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 55699999999999999999999888865
No 106
>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=87.23 E-value=0.27 Score=30.27 Aligned_cols=26 Identities=19% Similarity=0.526 Sum_probs=18.8
Q ss_pred CCCccCCCCCCCCCChhHHHHHHhhh
Q psy12028 89 EPKFECPHCPYRSKRKDTLDRHMKII 114 (118)
Q Consensus 89 ~~~~~C~~C~~~f~~~~~l~~H~~~~ 114 (118)
.+++.|+.||+.......|..-.++|
T Consensus 207 ~k~~PCPKCg~et~eTkdLSmStR~h 232 (314)
T PF06524_consen 207 GKPIPCPKCGYETQETKDLSMSTRSH 232 (314)
T ss_pred CCCCCCCCCCCcccccccceeeeecc
Confidence 56889999998877776666554443
No 107
>COG5188 PRP9 Splicing factor 3a, subunit 3 [RNA processing and modification]
Probab=86.29 E-value=0.54 Score=30.33 Aligned_cols=23 Identities=39% Similarity=0.834 Sum_probs=18.7
Q ss_pred CCCccCCCCC-CCCCChhHHHHHH
Q psy12028 89 EPKFECPHCP-YRSKRKDTLDRHM 111 (118)
Q Consensus 89 ~~~~~C~~C~-~~f~~~~~l~~H~ 111 (118)
.+.|.|.+|| +.+.-+..+.+|.
T Consensus 372 d~ef~CEICgNyvy~GR~~FdrHF 395 (470)
T COG5188 372 DIEFECEICGNYVYYGRDRFDRHF 395 (470)
T ss_pred CcceeeeecccccccchHHHHhhh
Confidence 6779999998 7777777787775
No 108
>PF08274 PhnA_Zn_Ribbon: PhnA Zinc-Ribbon ; InterPro: IPR013987 The PhnA protein family includes the uncharacterised Escherichia coli protein PhnA and its homologues. The E. coli phnA gene is part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage []. The protein is not related to the characterised phosphonoacetate hydrolase designated PhnA []. This entry represents the N-terminal domain of PhnA, which is predicted to form a zinc-ribbon.; PDB: 2AKL_A.
Probab=86.24 E-value=0.32 Score=19.53 Aligned_cols=26 Identities=31% Similarity=0.738 Sum_probs=10.8
Q ss_pred cCCCCCccccchHHHHhhhhhhcCCCCCccCCCCCccc
Q psy12028 3 ACDVCGKEYQHKRTLYRHKKDECGQEPKFGCPQCPYRS 40 (118)
Q Consensus 3 ~C~~C~~~~~~~~~l~~h~~~~~~~~~~~~C~~c~~~f 40 (118)
+|+.|+..+.- .. ...+.|+.|+..+
T Consensus 4 ~Cp~C~se~~y-----------~D-~~~~vCp~C~~ew 29 (30)
T PF08274_consen 4 KCPLCGSEYTY-----------ED-GELLVCPECGHEW 29 (30)
T ss_dssp --TTT-----E-----------E--SSSEEETTTTEEE
T ss_pred CCCCCCCccee-----------cc-CCEEeCCcccccC
Confidence 46666655543 12 4457777776543
No 109
>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=86.16 E-value=0.33 Score=22.40 Aligned_cols=31 Identities=23% Similarity=0.530 Sum_probs=15.4
Q ss_pred ccCCCCCccccchHHHHhhhhhhcCCCCCccCCCCCcccc
Q psy12028 2 YACDVCGKEYQHKRTLYRHKKDECGQEPKFGCPQCPYRSR 41 (118)
Q Consensus 2 ~~C~~C~~~~~~~~~l~~h~~~~~~~~~~~~C~~c~~~f~ 41 (118)
|+|+.||..+.-.... .+ -...|+.||..+.
T Consensus 3 ~~CP~CG~~iev~~~~-------~G--eiV~Cp~CGaele 33 (54)
T TIGR01206 3 FECPDCGAEIELENPE-------LG--ELVICDECGAELE 33 (54)
T ss_pred cCCCCCCCEEecCCCc-------cC--CEEeCCCCCCEEE
Confidence 5677777655332211 01 2356777765543
No 110
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=86.08 E-value=0.1 Score=22.41 Aligned_cols=11 Identities=27% Similarity=0.627 Sum_probs=6.9
Q ss_pred CccCCCCCccc
Q psy12028 30 KFGCPQCPYRS 40 (118)
Q Consensus 30 ~~~C~~c~~~f 40 (118)
.|.|..|+..|
T Consensus 28 fy~C~~C~~~w 38 (40)
T smart00440 28 FYVCTKCGHRW 38 (40)
T ss_pred EEEeCCCCCEe
Confidence 36676676555
No 111
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=86.00 E-value=0.36 Score=21.77 Aligned_cols=10 Identities=50% Similarity=1.328 Sum_probs=6.0
Q ss_pred ccCCCCCccc
Q psy12028 2 YACDVCGKEY 11 (118)
Q Consensus 2 ~~C~~C~~~~ 11 (118)
|.|..||+.|
T Consensus 7 Y~C~~Cg~~~ 16 (49)
T COG1996 7 YKCARCGREV 16 (49)
T ss_pred EEhhhcCCee
Confidence 5566666655
No 112
>PF13878 zf-C2H2_3: zinc-finger of acetyl-transferase ESCO
Probab=85.46 E-value=1.1 Score=19.36 Aligned_cols=22 Identities=32% Similarity=0.543 Sum_probs=12.7
Q ss_pred cCCCCCcccc--chHHHHhhhhhh
Q psy12028 3 ACDVCGKEYQ--HKRTLYRHKKDE 24 (118)
Q Consensus 3 ~C~~C~~~~~--~~~~l~~h~~~~ 24 (118)
+|+.||.+|. ....-..|.+-|
T Consensus 15 ~C~~CgM~Y~~~~~eD~~~H~~yH 38 (41)
T PF13878_consen 15 TCPTCGMLYSPGSPEDEKLHKKYH 38 (41)
T ss_pred CCCCCCCEECCCCHHHHHHHHHHH
Confidence 5777777764 444455555444
No 113
>PHA00626 hypothetical protein
Probab=85.36 E-value=0.5 Score=21.86 Aligned_cols=15 Identities=20% Similarity=0.740 Sum_probs=12.1
Q ss_pred CCCccCCCCCCCCCC
Q psy12028 89 EPKFECPHCPYRSKR 103 (118)
Q Consensus 89 ~~~~~C~~C~~~f~~ 103 (118)
...|+|+.||+.|+.
T Consensus 21 snrYkCkdCGY~ft~ 35 (59)
T PHA00626 21 SDDYVCCDCGYNDSK 35 (59)
T ss_pred CcceEcCCCCCeech
Confidence 457999999998864
No 114
>COG4957 Predicted transcriptional regulator [Transcription]
Probab=84.90 E-value=0.66 Score=25.64 Aligned_cols=22 Identities=23% Similarity=0.206 Sum_probs=17.6
Q ss_pred ccCCCCCCCCCChhHHHHHHhhhcC
Q psy12028 92 FECPHCPYRSKRKDTLDRHMKIIHF 116 (118)
Q Consensus 92 ~~C~~C~~~f~~~~~l~~H~~~~~~ 116 (118)
+.|..+|+.|. .|++|+.+|++
T Consensus 77 IicLEDGkkfK---SLKRHL~t~~g 98 (148)
T COG4957 77 IICLEDGKKFK---SLKRHLTTHYG 98 (148)
T ss_pred EEEeccCcchH---HHHHHHhcccC
Confidence 67888998874 68899888765
No 115
>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=84.29 E-value=0.51 Score=17.89 Aligned_cols=11 Identities=36% Similarity=1.144 Sum_probs=8.5
Q ss_pred CCCccCCCCCc
Q psy12028 28 EPKFGCPQCPY 38 (118)
Q Consensus 28 ~~~~~C~~c~~ 38 (118)
...|.||.||+
T Consensus 14 ~v~f~CPnCG~ 24 (24)
T PF07754_consen 14 AVPFPCPNCGF 24 (24)
T ss_pred CceEeCCCCCC
Confidence 35699999984
No 116
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=84.24 E-value=1.8 Score=28.08 Aligned_cols=21 Identities=24% Similarity=0.422 Sum_probs=10.8
Q ss_pred CCCCCccccchHHHHhhhhhh
Q psy12028 4 CDVCGKEYQHKRTLYRHKKDE 24 (118)
Q Consensus 4 C~~C~~~~~~~~~l~~h~~~~ 24 (118)
|..|.+-|-+...|..|++..
T Consensus 223 C~FC~~~FYdDDEL~~HcR~~ 243 (493)
T COG5236 223 CIFCKIYFYDDDELRRHCRLR 243 (493)
T ss_pred hhhccceecChHHHHHHHHhh
Confidence 444555555555555555443
No 117
>KOG2893|consensus
Probab=84.17 E-value=0.28 Score=29.85 Aligned_cols=41 Identities=27% Similarity=0.614 Sum_probs=29.8
Q ss_pred CCCCCccccchHHHHhhhhhhcCCCCCccCCCCCcccccchHHHHH
Q psy12028 4 CDVCGKEYQHKRTLYRHKKDECGQEPKFGCPQCPYRSRQKATLNRH 49 (118)
Q Consensus 4 C~~C~~~~~~~~~l~~h~~~~~~~~~~~~C~~c~~~f~~~~~l~~h 49 (118)
|=.|+..|.+...|..|++ .+-|.|.+|-+...+--.|..|
T Consensus 13 cwycnrefddekiliqhqk-----akhfkchichkkl~sgpglsih 53 (341)
T KOG2893|consen 13 CWYCNREFDDEKILIQHQK-----AKHFKCHICHKKLFSGPGLSIH 53 (341)
T ss_pred eeecccccchhhhhhhhhh-----hccceeeeehhhhccCCCceee
Confidence 4568888988888888875 3458888888776555555555
No 118
>PF09963 DUF2197: Uncharacterized protein conserved in bacteria (DUF2197); InterPro: IPR019241 This family represents various hypothetical bacterial proteins with no known function.
Probab=83.98 E-value=0.27 Score=22.85 Aligned_cols=9 Identities=33% Similarity=0.907 Sum_probs=4.5
Q ss_pred CCCCCcccc
Q psy12028 4 CDVCGKEYQ 12 (118)
Q Consensus 4 C~~C~~~~~ 12 (118)
|..|++.+.
T Consensus 5 C~lCdk~~~ 13 (56)
T PF09963_consen 5 CILCDKKEE 13 (56)
T ss_pred EEecCCEEE
Confidence 455555543
No 119
>KOG2785|consensus
Probab=83.68 E-value=1.6 Score=28.57 Aligned_cols=49 Identities=20% Similarity=0.316 Sum_probs=39.1
Q ss_pred cCCCCCccccchHHHHhhhhhhcCC----------------------CCCccCCCCC---cccccchHHHHHhh
Q psy12028 3 ACDVCGKEYQHKRTLYRHKKDECGQ----------------------EPKFGCPQCP---YRSRQKATLNRHLG 51 (118)
Q Consensus 3 ~C~~C~~~~~~~~~l~~h~~~~~~~----------------------~~~~~C~~c~---~~f~~~~~l~~h~~ 51 (118)
.|-.|++.+.+...-..||..+++- ..-+.|-.|. ..|.+....+.||.
T Consensus 168 ~CLfC~~~~k~~e~~~~HM~~~HgffIPdreYL~D~~GLl~YLgeKV~~~~~CL~CN~~~~~f~sleavr~HM~ 241 (390)
T KOG2785|consen 168 DCLFCDKKSKSLEENLKHMFKEHGFFIPDREYLTDEKGLLKYLGEKVGIGFICLFCNELGRPFSSLEAVRAHMR 241 (390)
T ss_pred ceeecCCCcccHHHHHHHHhhccCCcCCchHhhhchhHHHHHHHHHhccCceEEEeccccCcccccHHHHHHHh
Confidence 4778999999999999999988862 1126777777 88888888888987
No 120
>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=83.61 E-value=0.7 Score=24.51 Aligned_cols=30 Identities=27% Similarity=0.727 Sum_probs=21.8
Q ss_pred cCCCCCccccchHHHHhhhhhhcCCCCCccCCCCCcccccch
Q psy12028 3 ACDVCGKEYQHKRTLYRHKKDECGQEPKFGCPQCPYRSRQKA 44 (118)
Q Consensus 3 ~C~~C~~~~~~~~~l~~h~~~~~~~~~~~~C~~c~~~f~~~~ 44 (118)
.|+.|+..|.... ...|.||.|+..|....
T Consensus 4 ~CP~C~seytY~d------------g~~~iCpeC~~EW~~~~ 33 (109)
T TIGR00686 4 PCPKCNSEYTYHD------------GTQLICPSCLYEWNENE 33 (109)
T ss_pred cCCcCCCcceEec------------CCeeECccccccccccc
Confidence 5888887765432 34699999999987653
No 121
>PF15269 zf-C2H2_7: Zinc-finger
Probab=83.42 E-value=0.88 Score=20.00 Aligned_cols=19 Identities=26% Similarity=0.508 Sum_probs=8.6
Q ss_pred cCCCCCccccchHHHHhhh
Q psy12028 3 ACDVCGKEYQHKRTLYRHK 21 (118)
Q Consensus 3 ~C~~C~~~~~~~~~l~~h~ 21 (118)
+|-+|..+...++.|.+||
T Consensus 22 kcfqcpftc~~kshl~nhm 40 (54)
T PF15269_consen 22 KCFQCPFTCNEKSHLFNHM 40 (54)
T ss_pred eeecCCcccchHHHHHHHH
Confidence 3444444444444444444
No 122
>COG3364 Zn-ribbon containing protein [General function prediction only]
Probab=83.10 E-value=0.86 Score=23.90 Aligned_cols=14 Identities=21% Similarity=0.653 Sum_probs=9.4
Q ss_pred CccCCCCCccccch
Q psy12028 1 MYACDVCGKEYQHK 14 (118)
Q Consensus 1 ~~~C~~C~~~~~~~ 14 (118)
|+.|.-||.+|.+-
T Consensus 2 pH~CtrCG~vf~~g 15 (112)
T COG3364 2 PHQCTRCGEVFDDG 15 (112)
T ss_pred Cceecccccccccc
Confidence 56677777777653
No 123
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=82.87 E-value=0.63 Score=19.98 Aligned_cols=21 Identities=19% Similarity=0.200 Sum_probs=13.5
Q ss_pred CCCccCCCCCcccccchHHHH
Q psy12028 28 EPKFGCPQCPYRSRQKATLNR 48 (118)
Q Consensus 28 ~~~~~C~~c~~~f~~~~~l~~ 48 (118)
.....|+.|+-.|.....|..
T Consensus 17 ~~id~C~~C~G~W~d~~el~~ 37 (41)
T PF13453_consen 17 VEIDVCPSCGGIWFDAGELEK 37 (41)
T ss_pred EEEEECCCCCeEEccHHHHHH
Confidence 345677777777766665543
No 124
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=82.32 E-value=0.7 Score=22.72 Aligned_cols=40 Identities=15% Similarity=0.404 Sum_probs=19.2
Q ss_pred ccCCCCCccccchHHHHhhhhhhcCCCCCccCC--CCCcccccch
Q psy12028 2 YACDVCGKEYQHKRTLYRHKKDECGQEPKFGCP--QCPYRSRQKA 44 (118)
Q Consensus 2 ~~C~~C~~~~~~~~~l~~h~~~~~~~~~~~~C~--~c~~~f~~~~ 44 (118)
+.|+.||.......+-..... . .+.-+.|. .||..|....
T Consensus 2 m~CP~Cg~~a~irtSr~~s~~--~-~~~Y~qC~N~eCg~tF~t~e 43 (72)
T PRK09678 2 FHCPLCQHAAHARTSRYITDT--T-KERYHQCQNVNCSATFITYE 43 (72)
T ss_pred ccCCCCCCccEEEEChhcChh--h-heeeeecCCCCCCCEEEEEE
Confidence 467777665532222111111 1 13446676 6777766543
No 125
>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=81.80 E-value=1.4 Score=20.15 Aligned_cols=21 Identities=19% Similarity=0.545 Sum_probs=10.4
Q ss_pred CCccCCCCCcccccchHHHHH
Q psy12028 29 PKFGCPQCPYRSRQKATLNRH 49 (118)
Q Consensus 29 ~~~~C~~c~~~f~~~~~l~~h 49 (118)
..|.|+.|...|-..-.+-.|
T Consensus 20 ~~y~C~~C~~~FC~dCD~fiH 40 (51)
T PF07975_consen 20 SRYRCPKCKNHFCIDCDVFIH 40 (51)
T ss_dssp EEE--TTTT--B-HHHHHTTT
T ss_pred CeEECCCCCCccccCcChhhh
Confidence 458888888887665555545
No 126
>KOG2593|consensus
Probab=81.78 E-value=0.98 Score=29.96 Aligned_cols=18 Identities=22% Similarity=0.624 Sum_probs=10.2
Q ss_pred CccCCCCCcccccchHHH
Q psy12028 30 KFGCPQCPYRSRQKATLN 47 (118)
Q Consensus 30 ~~~C~~c~~~f~~~~~l~ 47 (118)
.|.||.|.+.|.....++
T Consensus 128 ~Y~Cp~C~kkyt~Lea~~ 145 (436)
T KOG2593|consen 128 GYVCPNCQKKYTSLEALQ 145 (436)
T ss_pred cccCCccccchhhhHHHH
Confidence 366666666666554433
No 127
>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=81.20 E-value=0.72 Score=28.51 Aligned_cols=82 Identities=16% Similarity=0.383 Sum_probs=42.5
Q ss_pred ccCCCCCccccchHHHHhhhhh-hcCCCCCccCCCCCcccccchHH-------HHHhhhhhccCCcccccccCchhhhhh
Q psy12028 2 YACDVCGKEYQHKRTLYRHKKD-ECGQEPKFGCPQCPYRSRQKATL-------NRHLGWEQLQGNAHVMYACDVCGKVYQ 73 (118)
Q Consensus 2 ~~C~~C~~~~~~~~~l~~h~~~-~~~~~~~~~C~~c~~~f~~~~~l-------~~h~~~~~~~~~~~~~~~c~~c~~~~~ 73 (118)
|+|..|+..+-....+ .|+.. ...+...|.|.-|++.-... -| ..|++..-......+++.||.|+.-..
T Consensus 143 f~CsfC~~flCEDDQF-EHQAsCQvLe~E~~KC~SCNrlGq~s-CLRCK~cfCddHvrrKg~ky~k~k~~PCPKCg~et~ 220 (314)
T PF06524_consen 143 FKCSFCDNFLCEDDQF-EHQASCQVLESETFKCQSCNRLGQYS-CLRCKICFCDDHVRRKGFKYEKGKPIPCPKCGYETQ 220 (314)
T ss_pred EEeecCCCeeeccchh-hhhhhhhhhhcccccccccccccchh-hhheeeeehhhhhhhcccccccCCCCCCCCCCCccc
Confidence 5666666544333333 34332 22223446666665432111 11 224433222333457889999998777
Q ss_pred chHHHHHHHhhh
Q psy12028 74 HKQTLDRHKKDE 85 (118)
Q Consensus 74 ~~~~l~~h~~~h 85 (118)
....|....++|
T Consensus 221 eTkdLSmStR~h 232 (314)
T PF06524_consen 221 ETKDLSMSTRSH 232 (314)
T ss_pred ccccceeeeecc
Confidence 777766655555
No 128
>KOG2907|consensus
Probab=80.63 E-value=0.95 Score=24.20 Aligned_cols=40 Identities=25% Similarity=0.545 Sum_probs=21.9
Q ss_pred CccCCCCCcccccchHHHHHhhhhhccCCcccccccCchhhhhh
Q psy12028 30 KFGCPQCPYRSRQKATLNRHLGWEQLQGNAHVMYACDVCGKVYQ 73 (118)
Q Consensus 30 ~~~C~~c~~~f~~~~~l~~h~~~~~~~~~~~~~~~c~~c~~~~~ 73 (118)
..+||.||-.=-.-..++.. .-..+...-|+|+.|+..|.
T Consensus 74 ~~kCpkCghe~m~Y~T~QlR----SADEGQTVFYTC~kC~~k~~ 113 (116)
T KOG2907|consen 74 KHKCPKCGHEEMSYHTLQLR----SADEGQTVFYTCPKCKYKFT 113 (116)
T ss_pred hccCcccCCchhhhhhhhcc----cccCCceEEEEcCccceeee
Confidence 36788888543222222221 22333445688888887764
No 129
>PRK10220 hypothetical protein; Provisional
Probab=80.40 E-value=1.3 Score=23.60 Aligned_cols=30 Identities=23% Similarity=0.636 Sum_probs=21.6
Q ss_pred cCCCCCccccchHHHHhhhhhhcCCCCCccCCCCCcccccch
Q psy12028 3 ACDVCGKEYQHKRTLYRHKKDECGQEPKFGCPQCPYRSRQKA 44 (118)
Q Consensus 3 ~C~~C~~~~~~~~~l~~h~~~~~~~~~~~~C~~c~~~f~~~~ 44 (118)
.|+.|+..|.... ...|.||.|+..|....
T Consensus 5 ~CP~C~seytY~d------------~~~~vCpeC~hEW~~~~ 34 (111)
T PRK10220 5 HCPKCNSEYTYED------------NGMYICPECAHEWNDAE 34 (111)
T ss_pred cCCCCCCcceEcC------------CCeEECCcccCcCCccc
Confidence 5888887664422 34599999999887654
No 130
>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=79.84 E-value=1.3 Score=24.99 Aligned_cols=11 Identities=45% Similarity=1.355 Sum_probs=7.1
Q ss_pred ccccCchhhhh
Q psy12028 62 MYACDVCGKVY 72 (118)
Q Consensus 62 ~~~c~~c~~~~ 72 (118)
-+.|+.|++.|
T Consensus 124 f~~C~~C~kiy 134 (147)
T PF01927_consen 124 FWRCPGCGKIY 134 (147)
T ss_pred EEECCCCCCEe
Confidence 45677777655
No 131
>COG4338 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=78.55 E-value=0.86 Score=20.36 Aligned_cols=18 Identities=22% Similarity=0.349 Sum_probs=14.2
Q ss_pred ccCCCCCcccccchHHHH
Q psy12028 31 FGCPQCPYRSRQKATLNR 48 (118)
Q Consensus 31 ~~C~~c~~~f~~~~~l~~ 48 (118)
-+|++|+.+|.....+.+
T Consensus 13 KICpvCqRPFsWRkKW~~ 30 (54)
T COG4338 13 KICPVCQRPFSWRKKWAR 30 (54)
T ss_pred hhhhhhcCchHHHHHHHH
Confidence 579999999987766654
No 132
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=78.51 E-value=2.5 Score=24.35 Aligned_cols=18 Identities=17% Similarity=0.447 Sum_probs=9.5
Q ss_pred CccCCCCCcccccchHHH
Q psy12028 30 KFGCPQCPYRSRQKATLN 47 (118)
Q Consensus 30 ~~~C~~c~~~f~~~~~l~ 47 (118)
.+.|+.||+.|...+.+.
T Consensus 130 f~~C~~CgkiYW~GsHw~ 147 (165)
T COG1656 130 FYRCPKCGKIYWKGSHWR 147 (165)
T ss_pred eeECCCCcccccCchHHH
Confidence 345666665555554443
No 133
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=78.28 E-value=0.91 Score=25.23 Aligned_cols=15 Identities=20% Similarity=0.397 Sum_probs=9.0
Q ss_pred CCccCCCCCcccccc
Q psy12028 29 PKFGCPQCPYRSRQK 43 (118)
Q Consensus 29 ~~~~C~~c~~~f~~~ 43 (118)
..+.|+.||..|...
T Consensus 69 ~~~~C~~CG~~~~~~ 83 (135)
T PRK03824 69 AVLKCRNCGNEWSLK 83 (135)
T ss_pred eEEECCCCCCEEecc
Confidence 346677777666543
No 134
>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=78.14 E-value=0.083 Score=22.58 Aligned_cols=10 Identities=30% Similarity=0.666 Sum_probs=5.5
Q ss_pred ccCCCCCccc
Q psy12028 31 FGCPQCPYRS 40 (118)
Q Consensus 31 ~~C~~c~~~f 40 (118)
|.|..|+..|
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 5566665544
No 135
>PRK04023 DNA polymerase II large subunit; Validated
Probab=77.95 E-value=4.2 Score=30.40 Aligned_cols=10 Identities=30% Similarity=0.863 Sum_probs=5.9
Q ss_pred CccCCCCCcc
Q psy12028 30 KFGCPQCPYR 39 (118)
Q Consensus 30 ~~~C~~c~~~ 39 (118)
...|+.||..
T Consensus 626 ~RfCpsCG~~ 635 (1121)
T PRK04023 626 RRKCPSCGKE 635 (1121)
T ss_pred CccCCCCCCc
Confidence 3556666655
No 136
>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=77.92 E-value=1.1 Score=18.66 Aligned_cols=31 Identities=26% Similarity=0.497 Sum_probs=15.4
Q ss_pred cCchhhhhhchHHHHHHHhhhcCCCCCccCCCCCCCCC
Q psy12028 65 CDVCGKVYQHKQTLDRHKKDECGQEPKFECPHCPYRSK 102 (118)
Q Consensus 65 c~~c~~~~~~~~~l~~h~~~h~~~~~~~~C~~C~~~f~ 102 (118)
|+.|.+-+.++.+ .+.| ..+..|..||..++
T Consensus 2 C~~C~~Ey~~p~~----RR~~---~~~isC~~CGPr~~ 32 (35)
T PF07503_consen 2 CDDCLKEYFDPSN----RRFH---YQFISCTNCGPRYS 32 (35)
T ss_dssp -HHHHHHHCSTTS----TTTT----TT--BTTCC-SCC
T ss_pred CHHHHHHHcCCCC----Cccc---CcCccCCCCCCCEE
Confidence 4556665555443 3444 34677888987764
No 137
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=77.83 E-value=0.75 Score=21.22 Aligned_cols=10 Identities=30% Similarity=0.750 Sum_probs=5.4
Q ss_pred ccCCCCCccc
Q psy12028 31 FGCPQCPYRS 40 (118)
Q Consensus 31 ~~C~~c~~~f 40 (118)
-.|+.|+.++
T Consensus 22 VvCp~Cgapy 31 (54)
T PF14446_consen 22 VVCPECGAPY 31 (54)
T ss_pred EECCCCCCcc
Confidence 4566665544
No 138
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=77.44 E-value=1.2 Score=18.99 Aligned_cols=12 Identities=25% Similarity=0.811 Sum_probs=7.2
Q ss_pred CccCCCCCcccc
Q psy12028 1 MYACDVCGKEYQ 12 (118)
Q Consensus 1 ~~~C~~C~~~~~ 12 (118)
||+|..|++.|-
T Consensus 12 ~f~C~~C~~~FC 23 (39)
T smart00154 12 GFKCRHCGNLFC 23 (39)
T ss_pred CeECCccCCccc
Confidence 456666666664
No 139
>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=76.66 E-value=0.46 Score=33.51 Aligned_cols=58 Identities=19% Similarity=0.494 Sum_probs=34.4
Q ss_pred ccCCCCCcccccchHHHHHhhhhhccCCccccc-ccCchhhhhhchHHHHHHHhhhcCCCCCccCCCCCCC
Q psy12028 31 FGCPQCPYRSRQKATLNRHLGWEQLQGNAHVMY-ACDVCGKVYQHKQTLDRHKKDECGQEPKFECPHCPYR 100 (118)
Q Consensus 31 ~~C~~c~~~f~~~~~l~~h~~~~~~~~~~~~~~-~c~~c~~~~~~~~~l~~h~~~h~~~~~~~~C~~C~~~ 100 (118)
-.|+.||-.|..-..|=-- . ..+.=..| -|+.|.+-+.++.+ +|.| ..|..|+.||..
T Consensus 124 ~~CT~CGPRfTIi~alPYD----R-~nTsM~~F~lC~~C~~EY~dP~n----RRfH---AQp~aCp~CGP~ 182 (750)
T COG0068 124 INCTNCGPRFTIIEALPYD----R-ENTSMADFPLCPFCDKEYKDPLN----RRFH---AQPIACPKCGPH 182 (750)
T ss_pred cccCCCCcceeeeccCCCC----c-ccCccccCcCCHHHHHHhcCccc----cccc---cccccCcccCCC
Confidence 3488899888765432100 0 00111112 58889888888755 3555 457889999863
No 140
>PF12907 zf-met2: Zinc-binding
Probab=76.05 E-value=2 Score=18.53 Aligned_cols=22 Identities=18% Similarity=0.694 Sum_probs=10.5
Q ss_pred cccCchhhhhhc---hHHHHHHHhh
Q psy12028 63 YACDVCGKVYQH---KQTLDRHKKD 84 (118)
Q Consensus 63 ~~c~~c~~~~~~---~~~l~~h~~~ 84 (118)
+.|.+|...|.. ...|..|...
T Consensus 2 i~C~iC~qtF~~t~~~~~L~eH~en 26 (40)
T PF12907_consen 2 IICKICRQTFMQTTNEPQLKEHAEN 26 (40)
T ss_pred cCcHHhhHHHHhcCCHHHHHHHHHc
Confidence 356666644433 2345555443
No 141
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=75.21 E-value=4.4 Score=23.73 Aligned_cols=33 Identities=18% Similarity=0.594 Sum_probs=21.8
Q ss_pred CCCccCCCCCcccccchHHHHHhhhhhccCCcccccccCchhhhhh
Q psy12028 28 EPKFGCPQCPYRSRQKATLNRHLGWEQLQGNAHVMYACDVCGKVYQ 73 (118)
Q Consensus 28 ~~~~~C~~c~~~f~~~~~l~~h~~~~~~~~~~~~~~~c~~c~~~~~ 73 (118)
...|.||.|...+..-..+.. .|.|+.||....
T Consensus 111 ~~~y~C~~~~~r~sfdeA~~~-------------~F~Cp~Cg~~L~ 143 (176)
T COG1675 111 NNYYVCPNCHVKYSFDEAMEL-------------GFTCPKCGEDLE 143 (176)
T ss_pred CCceeCCCCCCcccHHHHHHh-------------CCCCCCCCchhh
Confidence 456899888877765443221 278888887543
No 142
>PF02176 zf-TRAF: TRAF-type zinc finger; PDB: 2EOD_A 2YUC_A 3HCU_A 3HCS_B 3HCT_A.
Probab=75.19 E-value=0.88 Score=21.07 Aligned_cols=41 Identities=22% Similarity=0.383 Sum_probs=18.0
Q ss_pred CCccCCC--CCcccccchHHHHHhhhhhccCCcccccccCc----hhhhhhc
Q psy12028 29 PKFGCPQ--CPYRSRQKATLNRHLGWEQLQGNAHVMYACDV----CGKVYQH 74 (118)
Q Consensus 29 ~~~~C~~--c~~~f~~~~~l~~h~~~~~~~~~~~~~~~c~~----c~~~~~~ 74 (118)
.+..|+. |...+. ...|..|+...+. .++..|+. |+..+..
T Consensus 8 ~~v~C~~~cc~~~i~-r~~l~~H~~~~C~----~~~v~C~~~~~GC~~~~~~ 54 (60)
T PF02176_consen 8 RPVPCPNGCCNEMIP-RKELDDHLENECP----KRPVPCPYSPYGCKERVPR 54 (60)
T ss_dssp SEEE-TT--S-BEEE-CCCHHHHHHTTST----TSEEE-SS----S--EEEH
T ss_pred CEeeCCCCCccccee-HHHHHHHHHccCC----CCcEECCCCCCCCCCccch
Confidence 3456766 333333 3456777542222 24456776 6665544
No 143
>KOG0978|consensus
Probab=74.91 E-value=1.4 Score=31.32 Aligned_cols=20 Identities=25% Similarity=0.491 Sum_probs=15.3
Q ss_pred CccCCCCCCCCCChhHHHHH
Q psy12028 91 KFECPHCPYRSKRKDTLDRH 110 (118)
Q Consensus 91 ~~~C~~C~~~f~~~~~l~~H 110 (118)
.-+||.||.+|+..+-+..|
T Consensus 678 qRKCP~Cn~aFganDv~~I~ 697 (698)
T KOG0978|consen 678 QRKCPKCNAAFGANDVHRIH 697 (698)
T ss_pred cCCCCCCCCCCCcccccccC
Confidence 34799999999887766554
No 144
>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=74.76 E-value=0.76 Score=23.67 Aligned_cols=11 Identities=18% Similarity=0.612 Sum_probs=6.1
Q ss_pred CccCCCCCCCC
Q psy12028 91 KFECPHCPYRS 101 (118)
Q Consensus 91 ~~~C~~C~~~f 101 (118)
.|.|..|++.|
T Consensus 53 IW~C~~C~~~~ 63 (91)
T TIGR00280 53 IWTCRKCGAKF 63 (91)
T ss_pred EEEcCCCCCEE
Confidence 45565555544
No 145
>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=74.15 E-value=2.8 Score=18.26 Aligned_cols=16 Identities=19% Similarity=0.410 Sum_probs=10.9
Q ss_pred cCCCCCCCCCChhHHH
Q psy12028 93 ECPHCPYRSKRKDTLD 108 (118)
Q Consensus 93 ~C~~C~~~f~~~~~l~ 108 (118)
.|.+||..|+....+.
T Consensus 10 ~C~~C~rpf~WRKKW~ 25 (42)
T PF10013_consen 10 ICPVCGRPFTWRKKWA 25 (42)
T ss_pred cCcccCCcchHHHHHH
Confidence 4888888887655443
No 146
>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=74.01 E-value=2.8 Score=28.41 Aligned_cols=25 Identities=24% Similarity=0.505 Sum_probs=15.5
Q ss_pred CccCCCCCCCCCChhHHHHHHhhhc
Q psy12028 91 KFECPHCPYRSKRKDTLDRHMKIIH 115 (118)
Q Consensus 91 ~~~C~~C~~~f~~~~~l~~H~~~~~ 115 (118)
-+.|+.|.+.|.....+..|+...|
T Consensus 57 FWiCp~CskkF~d~~~~~~H~~~eH 81 (466)
T PF04780_consen 57 FWICPRCSKKFSDAESCLSHMEQEH 81 (466)
T ss_pred EeeCCcccceeCCHHHHHHHHHHhh
Confidence 4556666666666666666665444
No 147
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=73.82 E-value=1.6 Score=23.50 Aligned_cols=13 Identities=15% Similarity=0.191 Sum_probs=8.8
Q ss_pred ccCCCCCcccccc
Q psy12028 31 FGCPQCPYRSRQK 43 (118)
Q Consensus 31 ~~C~~c~~~f~~~ 43 (118)
+.|..|+..|...
T Consensus 71 ~~C~~Cg~~~~~~ 83 (113)
T PRK12380 71 AWCWDCSQVVEIH 83 (113)
T ss_pred EEcccCCCEEecC
Confidence 6677777666553
No 148
>KOG4167|consensus
Probab=73.66 E-value=1.7 Score=31.06 Aligned_cols=28 Identities=25% Similarity=0.557 Sum_probs=24.3
Q ss_pred ccccccCchhhhhhchHHHHHHHhhhcC
Q psy12028 60 HVMYACDVCGKVYQHKQTLDRHKKDECG 87 (118)
Q Consensus 60 ~~~~~c~~c~~~~~~~~~l~~h~~~h~~ 87 (118)
...|.|.+|++.|.-..++..||.+|.-
T Consensus 790 ~giFpCreC~kvF~KiKSrNAHMK~Hr~ 817 (907)
T KOG4167|consen 790 TGIFPCRECGKVFFKIKSRNAHMKTHRQ 817 (907)
T ss_pred CceeehHHHHHHHHHHhhhhHHHHHHHH
Confidence 3458999999999999999999999864
No 149
>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=73.54 E-value=2.2 Score=25.81 Aligned_cols=27 Identities=22% Similarity=0.434 Sum_probs=19.9
Q ss_pred CCCccCCCCCcccccchHHHHHhhhhh
Q psy12028 28 EPKFGCPQCPYRSRQKATLNRHLGWEQ 54 (118)
Q Consensus 28 ~~~~~C~~c~~~f~~~~~l~~h~~~~~ 54 (118)
+..|.|+.|++.|+...-+..|+...+
T Consensus 75 ~~K~~C~lc~KlFkg~eFV~KHI~nKH 101 (214)
T PF04959_consen 75 EDKWRCPLCGKLFKGPEFVRKHIFNKH 101 (214)
T ss_dssp SEEEEE-SSS-EESSHHHHHHHHHHH-
T ss_pred CCEECCCCCCcccCChHHHHHHHhhcC
Confidence 344999999999999998999987443
No 150
>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=72.87 E-value=0.74 Score=19.29 Aligned_cols=9 Identities=44% Similarity=1.479 Sum_probs=4.0
Q ss_pred ccCchhhhh
Q psy12028 64 ACDVCGKVY 72 (118)
Q Consensus 64 ~c~~c~~~~ 72 (118)
.|+.|+.+|
T Consensus 3 ~C~~Cg~~Y 11 (36)
T PF05191_consen 3 ICPKCGRIY 11 (36)
T ss_dssp EETTTTEEE
T ss_pred CcCCCCCcc
Confidence 344444444
No 151
>KOG2636|consensus
Probab=72.50 E-value=3.3 Score=27.86 Aligned_cols=28 Identities=29% Similarity=0.573 Sum_probs=21.9
Q ss_pred hhhcCCCCCccCCCCC-CCCCChhHHHHHH
Q psy12028 83 KDECGQEPKFECPHCP-YRSKRKDTLDRHM 111 (118)
Q Consensus 83 ~~h~~~~~~~~C~~C~-~~f~~~~~l~~H~ 111 (118)
+.|.- ...|.|.+|| +++.-+..+.+|.
T Consensus 394 KLHGL-~~ey~CEICGNy~Y~GrkaF~RHF 422 (497)
T KOG2636|consen 394 KLHGL-DIEYNCEICGNYVYKGRKAFDRHF 422 (497)
T ss_pred hhcCC-CcccceeeccCccccCcHHHHHHh
Confidence 44443 7789999998 8888888888886
No 152
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=72.46 E-value=0.87 Score=24.51 Aligned_cols=39 Identities=21% Similarity=0.497 Sum_probs=21.7
Q ss_pred ccCCCCCcccccchHHHHHhhhhhccCCcccccccCchhhhhh
Q psy12028 31 FGCPQCPYRSRQKATLNRHLGWEQLQGNAHVMYACDVCGKVYQ 73 (118)
Q Consensus 31 ~~C~~c~~~f~~~~~l~~h~~~~~~~~~~~~~~~c~~c~~~~~ 73 (118)
..||.|+..=.....++.- ...-....-|.|..||..|.
T Consensus 73 ~~CpkCg~~ea~y~~~QtR----saDEp~T~Fy~C~~Cg~~wr 111 (113)
T COG1594 73 EKCPKCGNKEAYYWQLQTR----SADEPETRFYKCTRCGYRWR 111 (113)
T ss_pred ccCCCCCCceeEEEeeehh----ccCCCceEEEEecccCCEee
Confidence 5688888654433333322 22333345578888887664
No 153
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=71.53 E-value=2.2 Score=15.84 Aligned_cols=6 Identities=50% Similarity=1.542 Sum_probs=3.4
Q ss_pred CCCCCc
Q psy12028 33 CPQCPY 38 (118)
Q Consensus 33 C~~c~~ 38 (118)
|+.||.
T Consensus 16 C~~CG~ 21 (23)
T PF13240_consen 16 CPNCGT 21 (23)
T ss_pred hhhhCC
Confidence 555554
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=71.40 E-value=1.7 Score=23.43 Aligned_cols=13 Identities=15% Similarity=0.506 Sum_probs=8.9
Q ss_pred ccCCCCCcccccc
Q psy12028 31 FGCPQCPYRSRQK 43 (118)
Q Consensus 31 ~~C~~c~~~f~~~ 43 (118)
..|..|+..|...
T Consensus 71 ~~C~~Cg~~~~~~ 83 (115)
T TIGR00100 71 CECEDCSEEVSPE 83 (115)
T ss_pred EEcccCCCEEecC
Confidence 6777777766554
No 155
>KOG1842|consensus
Probab=71.35 E-value=2.3 Score=28.52 Aligned_cols=25 Identities=20% Similarity=0.323 Sum_probs=14.6
Q ss_pred cccCchhhhhhchHHHHHHHhhhcC
Q psy12028 63 YACDVCGKVYQHKQTLDRHKKDECG 87 (118)
Q Consensus 63 ~~c~~c~~~~~~~~~l~~h~~~h~~ 87 (118)
|.||+|...|.+.+.|..|.-..|+
T Consensus 16 flCPiC~~dl~~~~~L~~H~d~eH~ 40 (505)
T KOG1842|consen 16 FLCPICLLDLPNLSALNDHLDVEHF 40 (505)
T ss_pred ccCchHhhhhhhHHHHHHHHhhhcc
Confidence 5566666666666666666554443
No 156
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=71.26 E-value=5.7 Score=18.45 Aligned_cols=15 Identities=27% Similarity=0.747 Sum_probs=11.0
Q ss_pred CCCccCCCCCccccc
Q psy12028 28 EPKFGCPQCPYRSRQ 42 (118)
Q Consensus 28 ~~~~~C~~c~~~f~~ 42 (118)
...|.||.||.++--
T Consensus 12 ~v~~~Cp~cGipthc 26 (55)
T PF13824_consen 12 HVNFECPDCGIPTHC 26 (55)
T ss_pred ccCCcCCCCCCcCcc
Confidence 456899999977544
No 157
>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=71.23 E-value=0.9 Score=17.91 Aligned_cols=9 Identities=22% Similarity=0.626 Sum_probs=4.5
Q ss_pred cCCCCCccc
Q psy12028 32 GCPQCPYRS 40 (118)
Q Consensus 32 ~C~~c~~~f 40 (118)
.|-.|++.|
T Consensus 2 sCiDC~~~F 10 (28)
T PF08790_consen 2 SCIDCSKDF 10 (28)
T ss_dssp EETTTTEEE
T ss_pred eeecCCCCc
Confidence 344555555
No 158
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=71.10 E-value=1 Score=23.17 Aligned_cols=11 Identities=27% Similarity=0.724 Sum_probs=6.1
Q ss_pred CccCCCCCCCC
Q psy12028 91 KFECPHCPYRS 101 (118)
Q Consensus 91 ~~~C~~C~~~f 101 (118)
.|.|..|++.|
T Consensus 54 IW~C~~C~~~~ 64 (90)
T PRK03976 54 IWECRKCGAKF 64 (90)
T ss_pred EEEcCCCCCEE
Confidence 45566665544
No 159
>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=69.82 E-value=3.8 Score=19.60 Aligned_cols=29 Identities=24% Similarity=0.714 Sum_probs=16.4
Q ss_pred ccCCCCCcccccchHHHHHhhhhhccCCcccccccCchhhhhh
Q psy12028 31 FGCPQCPYRSRQKATLNRHLGWEQLQGNAHVMYACDVCGKVYQ 73 (118)
Q Consensus 31 ~~C~~c~~~f~~~~~l~~h~~~~~~~~~~~~~~~c~~c~~~~~ 73 (118)
-.|+.||..-... + ..+.|.|+.||..+.
T Consensus 29 q~C~~CG~~~~~~--~------------~~r~~~C~~Cg~~~~ 57 (69)
T PF07282_consen 29 QTCPRCGHRNKKR--R------------SGRVFTCPNCGFEMD 57 (69)
T ss_pred cCccCcccccccc--c------------ccceEEcCCCCCEEC
Confidence 4577777665540 0 123477777776543
No 160
>KOG1280|consensus
Probab=69.77 E-value=5.3 Score=26.00 Aligned_cols=24 Identities=21% Similarity=0.408 Sum_probs=13.8
Q ss_pred ccCCCCCccccchHHHHhhhhhhc
Q psy12028 2 YACDVCGKEYQHKRTLYRHKKDEC 25 (118)
Q Consensus 2 ~~C~~C~~~~~~~~~l~~h~~~~~ 25 (118)
|.|+.|+..-.+...|..|....+
T Consensus 80 ftCPyC~~~Gfte~~f~~Hv~s~H 103 (381)
T KOG1280|consen 80 FTCPYCGIMGFTERQFGTHVLSQH 103 (381)
T ss_pred ccCCcccccccchhHHHHHhhhcC
Confidence 556666666656666666654433
No 161
>COG1655 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=69.61 E-value=1 Score=27.39 Aligned_cols=20 Identities=15% Similarity=0.527 Sum_probs=9.8
Q ss_pred cCCCCCccccchHHHHhhhh
Q psy12028 3 ACDVCGKEYQHKRTLYRHKK 22 (118)
Q Consensus 3 ~C~~C~~~~~~~~~l~~h~~ 22 (118)
.|++|+..|.....+..-++
T Consensus 21 eCPvC~tkFkkeev~tgsiR 40 (267)
T COG1655 21 ECPVCNTKFKKEEVKTGSIR 40 (267)
T ss_pred ccCcccchhhhhheecccee
Confidence 45555555555444443333
No 162
>COG2331 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=68.94 E-value=1.1 Score=22.23 Aligned_cols=10 Identities=30% Similarity=0.933 Sum_probs=5.5
Q ss_pred ccCCCCCccc
Q psy12028 31 FGCPQCPYRS 40 (118)
Q Consensus 31 ~~C~~c~~~f 40 (118)
|.|..|+..|
T Consensus 13 Y~c~~cg~~~ 22 (82)
T COG2331 13 YECTECGNRF 22 (82)
T ss_pred EeecccchHH
Confidence 5555555544
No 163
>COG4896 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=68.61 E-value=1.8 Score=20.41 Aligned_cols=38 Identities=21% Similarity=0.472 Sum_probs=16.8
Q ss_pred cCCCCCcc-ccchHHHHhhhhhhcCCCCCccCCCCCcccc
Q psy12028 3 ACDVCGKE-YQHKRTLYRHKKDECGQEPKFGCPQCPYRSR 41 (118)
Q Consensus 3 ~C~~C~~~-~~~~~~l~~h~~~~~~~~~~~~C~~c~~~f~ 41 (118)
+|..|+.. +.+...+..-+ ......+.|.|+.|.-...
T Consensus 4 kCiiCd~v~~iD~rt~~tKr-LrN~PIrtymC~eC~~Rva 42 (68)
T COG4896 4 KCIICDRVDEIDNRTFKTKR-LRNKPIRTYMCPECEHRVA 42 (68)
T ss_pred eEEEecceeeecchhHHHHH-hhCCCceeEechhhHhhhc
Confidence 45666543 33333333222 2222234467777654443
No 164
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=67.88 E-value=2.8 Score=18.74 Aligned_cols=13 Identities=31% Similarity=0.871 Sum_probs=9.5
Q ss_pred CccCCCCCccccc
Q psy12028 30 KFGCPQCPYRSRQ 42 (118)
Q Consensus 30 ~~~C~~c~~~f~~ 42 (118)
.+.|+.|+..+..
T Consensus 20 ~~vC~~Cg~~~~~ 32 (52)
T smart00661 20 RFVCRKCGYEEPI 32 (52)
T ss_pred EEECCcCCCeEEC
Confidence 5788888876554
No 165
>KOG3408|consensus
Probab=66.05 E-value=4.7 Score=22.02 Aligned_cols=24 Identities=21% Similarity=0.466 Sum_probs=20.7
Q ss_pred cccccCchhhhhhchHHHHHHHhh
Q psy12028 61 VMYACDVCGKVYQHKQTLDRHKKD 84 (118)
Q Consensus 61 ~~~~c~~c~~~~~~~~~l~~h~~~ 84 (118)
..|.|..|.+.|.+...|..|.++
T Consensus 56 GqfyCi~CaRyFi~~~~l~~H~kt 79 (129)
T KOG3408|consen 56 GQFYCIECARYFIDAKALKTHFKT 79 (129)
T ss_pred ceeehhhhhhhhcchHHHHHHHhc
Confidence 348899999999999999999765
No 166
>PF13451 zf-trcl: Probable zinc-binding domain
Probab=65.60 E-value=3 Score=18.88 Aligned_cols=41 Identities=15% Similarity=0.331 Sum_probs=20.2
Q ss_pred CCCccCCCCCcccccchHHHHHhhhhhccCCcccccccCchhhh
Q psy12028 28 EPKFGCPQCPYRSRQKATLNRHLGWEQLQGNAHVMYACDVCGKV 71 (118)
Q Consensus 28 ~~~~~C~~c~~~f~~~~~l~~h~~~~~~~~~~~~~~~c~~c~~~ 71 (118)
.+.+.|..||..|.....=+.-.. . ..-...|-.|+.|...
T Consensus 2 Dk~l~C~dCg~~FvfTa~EQ~fy~--e-Kgf~n~p~RC~~CR~~ 42 (49)
T PF13451_consen 2 DKTLTCKDCGAEFVFTAGEQKFYA--E-KGFDNEPKRCPSCRQA 42 (49)
T ss_pred CeeEEcccCCCeEEEehhHHHHHH--h-cCCcCCCccCHHHHHH
Confidence 345778888877755432221111 1 1112235567777653
No 167
>PHA02998 RNA polymerase subunit; Provisional
Probab=65.53 E-value=1.5 Score=25.59 Aligned_cols=42 Identities=19% Similarity=0.409 Sum_probs=21.2
Q ss_pred CccCCCCCcccccchHHHHHhhhhhccCCcccccccCchhhhhhch
Q psy12028 30 KFGCPQCPYRSRQKATLNRHLGWEQLQGNAHVMYACDVCGKVYQHK 75 (118)
Q Consensus 30 ~~~C~~c~~~f~~~~~l~~h~~~~~~~~~~~~~~~c~~c~~~~~~~ 75 (118)
...|+.|+..=.....++ ++ ........-|.|..|+..|..+
T Consensus 143 ~v~CPkCg~~~A~f~qlQ--TR--SADEPmT~FYkC~~CG~~wkpp 184 (195)
T PHA02998 143 NTPCPNCKSKNTTPMMIQ--TR--AADEPPLVRHACRDCKKHFKPP 184 (195)
T ss_pred CCCCCCCCCCceEEEEEe--ec--cCCCCceEEEEcCCCCCccCCc
Confidence 367777775433322222 11 1222223456787788776554
No 168
>KOG2071|consensus
Probab=65.24 E-value=5.7 Score=27.71 Aligned_cols=27 Identities=22% Similarity=0.501 Sum_probs=22.8
Q ss_pred CCCccCCCCCCCCCChhHHHHHHhhhc
Q psy12028 89 EPKFECPHCPYRSKRKDTLDRHMKIIH 115 (118)
Q Consensus 89 ~~~~~C~~C~~~f~~~~~l~~H~~~~~ 115 (118)
..|-.|..||.+|.+......||-.|-
T Consensus 416 ~~pnqC~~CG~R~~~~ee~sk~md~H~ 442 (579)
T KOG2071|consen 416 DSPNQCKSCGLRFDDSEERSKHMDIHD 442 (579)
T ss_pred CCcchhcccccccccchhhhhHhhhhh
Confidence 567899999999999998888887664
No 169
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=64.32 E-value=4.6 Score=27.02 Aligned_cols=29 Identities=28% Similarity=0.763 Sum_probs=18.9
Q ss_pred ccCchhhhhhchHHHHHHHhhhcCCCCCccCCCCCCCCCCh
Q psy12028 64 ACDVCGKVYQHKQTLDRHKKDECGQEPKFECPHCPYRSKRK 104 (118)
Q Consensus 64 ~c~~c~~~~~~~~~l~~h~~~h~~~~~~~~C~~C~~~f~~~ 104 (118)
.|+.||....+ .| .+-|+|+.||..+...
T Consensus 352 ~Cp~Cg~~m~S-----------~G-~~g~rC~kCg~~~~~~ 380 (421)
T COG1571 352 VCPRCGGRMKS-----------AG-RNGFRCKKCGTRARET 380 (421)
T ss_pred CCCccCCchhh-----------cC-CCCcccccccccCCcc
Confidence 68888865332 34 3378888888876543
No 170
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=64.27 E-value=3 Score=22.58 Aligned_cols=13 Identities=15% Similarity=0.544 Sum_probs=8.1
Q ss_pred ccCCCCCcccccc
Q psy12028 31 FGCPQCPYRSRQK 43 (118)
Q Consensus 31 ~~C~~c~~~f~~~ 43 (118)
+.|..|+..|...
T Consensus 72 ~~C~~Cg~~~~~~ 84 (117)
T PRK00564 72 LECKDCSHVFKPN 84 (117)
T ss_pred EEhhhCCCccccC
Confidence 6677777666543
No 171
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=64.03 E-value=3.5 Score=22.23 Aligned_cols=12 Identities=17% Similarity=0.312 Sum_probs=7.9
Q ss_pred ccCCCCCccccc
Q psy12028 31 FGCPQCPYRSRQ 42 (118)
Q Consensus 31 ~~C~~c~~~f~~ 42 (118)
+.|..|+..|..
T Consensus 71 ~~C~~Cg~~~~~ 82 (114)
T PRK03681 71 CWCETCQQYVTL 82 (114)
T ss_pred EEcccCCCeeec
Confidence 667777766654
No 172
>PF04423 Rad50_zn_hook: Rad50 zinc hook motif; InterPro: IPR007517 The Mre11 complex (Mre11 Rad50 Nbs1) is central to chromosomal maintenance and functions in homologous recombination, telomere maintenance and sister chromatid association. The Rad50 coiled-coil region contains a dimer interface at the apex of the coiled coils in which pairs of conserved Cys-X-X-Cys motifs form interlocking hooks that bind one Zn ion. This alignment includes the zinc hook motif and a short stretch of coiled-coil on either side.; GO: 0004518 nuclease activity, 0005524 ATP binding, 0008270 zinc ion binding, 0006281 DNA repair; PDB: 1L8D_B.
Probab=63.86 E-value=2.7 Score=19.17 Aligned_cols=12 Identities=25% Similarity=0.645 Sum_probs=6.8
Q ss_pred cCCCCCcccccc
Q psy12028 32 GCPQCPYRSRQK 43 (118)
Q Consensus 32 ~C~~c~~~f~~~ 43 (118)
.||+|+..|...
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 999999998764
No 173
>KOG4124|consensus
Probab=63.03 E-value=1.3 Score=28.66 Aligned_cols=22 Identities=41% Similarity=0.794 Sum_probs=15.2
Q ss_pred CccCCC--CCccccchHHHHhhhh
Q psy12028 1 MYACDV--CGKEYQHKRTLYRHKK 22 (118)
Q Consensus 1 ~~~C~~--C~~~~~~~~~l~~h~~ 22 (118)
||+|++ |.+.+.....|..|..
T Consensus 349 ~~~~~vp~~~~~~~n~ng~~~~~~ 372 (442)
T KOG4124|consen 349 PYKCPVPNCDKAYKNQNGLKYHKL 372 (442)
T ss_pred CCCCCCCcchhhcccCcceeeccc
Confidence 466665 7888877777776644
No 174
>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=61.95 E-value=2.2 Score=18.52 Aligned_cols=12 Identities=33% Similarity=0.750 Sum_probs=7.3
Q ss_pred CCccCCCCCCCC
Q psy12028 90 PKFECPHCPYRS 101 (118)
Q Consensus 90 ~~~~C~~C~~~f 101 (118)
.|+.|..|+..|
T Consensus 12 ~~~~C~~C~~~F 23 (43)
T PF01428_consen 12 LPFKCKHCGKSF 23 (43)
T ss_dssp SHEE-TTTS-EE
T ss_pred CCeECCCCCccc
Confidence 467788888766
No 175
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=60.99 E-value=3.9 Score=21.11 Aligned_cols=33 Identities=21% Similarity=0.520 Sum_probs=19.7
Q ss_pred CCCccCCCCCcccccchHHHHHhhhhhccCCcccccccCchhhhhhc
Q psy12028 28 EPKFGCPQCPYRSRQKATLNRHLGWEQLQGNAHVMYACDVCGKVYQH 74 (118)
Q Consensus 28 ~~~~~C~~c~~~f~~~~~l~~h~~~~~~~~~~~~~~~c~~c~~~~~~ 74 (118)
...|.||+|++.-.... .. ..|.|..|+..|..
T Consensus 34 ~a~y~CpfCgk~~vkR~----------a~----GIW~C~~C~~~~AG 66 (90)
T PTZ00255 34 HAKYFCPFCGKHAVKRQ----------AV----GIWRCKGCKKTVAG 66 (90)
T ss_pred hCCccCCCCCCCceeee----------ee----EEEEcCCCCCEEeC
Confidence 34699999985432211 11 23788888776654
No 176
>PF15135 UPF0515: Uncharacterised protein UPF0515
Probab=60.54 E-value=8.1 Score=23.99 Aligned_cols=14 Identities=21% Similarity=0.565 Sum_probs=10.1
Q ss_pred CCccCCCCCccccc
Q psy12028 29 PKFGCPQCPYRSRQ 42 (118)
Q Consensus 29 ~~~~C~~c~~~f~~ 42 (118)
+.|.|..|...|..
T Consensus 111 rqFaC~~Cd~~WwR 124 (278)
T PF15135_consen 111 RQFACSSCDHMWWR 124 (278)
T ss_pred eeeeccccchHHHh
Confidence 56889999766543
No 177
>PTZ00448 hypothetical protein; Provisional
Probab=59.83 E-value=8.5 Score=25.35 Aligned_cols=23 Identities=13% Similarity=0.446 Sum_probs=20.2
Q ss_pred CccCCCCCCCCCChhHHHHHHhh
Q psy12028 91 KFECPHCPYRSKRKDTLDRHMKI 113 (118)
Q Consensus 91 ~~~C~~C~~~f~~~~~l~~H~~~ 113 (118)
.|.|..|+..|.+....+.|+++
T Consensus 314 ~~tC~~C~v~F~~~~~qR~H~KS 336 (373)
T PTZ00448 314 MLLCRKCNIQLMDHNAFKQHYRS 336 (373)
T ss_pred CccccccccccCCHHHHHHHhhh
Confidence 58899999999988888889875
No 178
>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=59.46 E-value=4.7 Score=18.30 Aligned_cols=12 Identities=42% Similarity=1.193 Sum_probs=9.2
Q ss_pred ccCCCCCccccc
Q psy12028 2 YACDVCGKEYQH 13 (118)
Q Consensus 2 ~~C~~C~~~~~~ 13 (118)
|+|..||.+|.-
T Consensus 2 y~C~~CgyiYd~ 13 (50)
T cd00730 2 YECRICGYIYDP 13 (50)
T ss_pred cCCCCCCeEECC
Confidence 678888888764
No 179
>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=58.90 E-value=3.2 Score=22.30 Aligned_cols=12 Identities=17% Similarity=0.382 Sum_probs=5.5
Q ss_pred ccCCCCCccccc
Q psy12028 31 FGCPQCPYRSRQ 42 (118)
Q Consensus 31 ~~C~~c~~~f~~ 42 (118)
+.|..|+..|..
T Consensus 71 ~~C~~Cg~~~~~ 82 (113)
T PF01155_consen 71 ARCRDCGHEFEP 82 (113)
T ss_dssp EEETTTS-EEEC
T ss_pred EECCCCCCEEec
Confidence 445555555543
No 180
>PTZ00448 hypothetical protein; Provisional
Probab=57.40 E-value=9.2 Score=25.20 Aligned_cols=21 Identities=14% Similarity=0.452 Sum_probs=9.6
Q ss_pred ccCCCCCcccccchHHHHHhh
Q psy12028 31 FGCPQCPYRSRQKATLNRHLG 51 (118)
Q Consensus 31 ~~C~~c~~~f~~~~~l~~h~~ 51 (118)
|.|..|+..|.+....+.|++
T Consensus 315 ~tC~~C~v~F~~~~~qR~H~K 335 (373)
T PTZ00448 315 LLCRKCNIQLMDHNAFKQHYR 335 (373)
T ss_pred ccccccccccCCHHHHHHHhh
Confidence 344445444444444444443
No 181
>COG1773 Rubredoxin [Energy production and conversion]
Probab=57.34 E-value=3.8 Score=19.03 Aligned_cols=12 Identities=42% Similarity=1.126 Sum_probs=8.5
Q ss_pred ccCCCCCccccc
Q psy12028 2 YACDVCGKEYQH 13 (118)
Q Consensus 2 ~~C~~C~~~~~~ 13 (118)
|+|..||.+|.-
T Consensus 4 ~~C~~CG~vYd~ 15 (55)
T COG1773 4 WRCSVCGYVYDP 15 (55)
T ss_pred eEecCCceEecc
Confidence 567888877753
No 182
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=57.29 E-value=5.1 Score=21.95 Aligned_cols=11 Identities=27% Similarity=0.860 Sum_probs=6.9
Q ss_pred ccCCCCCccccc
Q psy12028 31 FGCPQCPYRSRQ 42 (118)
Q Consensus 31 ~~C~~c~~~f~~ 42 (118)
+.| .|+..|..
T Consensus 71 ~~C-~Cg~~~~~ 81 (124)
T PRK00762 71 IEC-ECGYEGVV 81 (124)
T ss_pred EEe-eCcCcccc
Confidence 667 67766554
No 183
>PRK05978 hypothetical protein; Provisional
Probab=57.28 E-value=3.7 Score=23.29 Aligned_cols=9 Identities=33% Similarity=0.700 Sum_probs=6.1
Q ss_pred ccCCCCCcc
Q psy12028 31 FGCPQCPYR 39 (118)
Q Consensus 31 ~~C~~c~~~ 39 (118)
-.||.|++.
T Consensus 34 grCP~CG~G 42 (148)
T PRK05978 34 GRCPACGEG 42 (148)
T ss_pred CcCCCCCCC
Confidence 567777765
No 184
>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=56.78 E-value=3.2 Score=17.46 Aligned_cols=10 Identities=40% Similarity=1.155 Sum_probs=4.5
Q ss_pred ccCCCCCccc
Q psy12028 2 YACDVCGKEY 11 (118)
Q Consensus 2 ~~C~~C~~~~ 11 (118)
|+|..||...
T Consensus 7 YkC~~CGniV 16 (36)
T PF06397_consen 7 YKCEHCGNIV 16 (36)
T ss_dssp EE-TTT--EE
T ss_pred EEccCCCCEE
Confidence 6677777654
No 185
>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=56.62 E-value=2 Score=22.14 Aligned_cols=32 Identities=28% Similarity=0.742 Sum_probs=18.1
Q ss_pred CCccCCCCCcccccchHHHHHhhhhhccCCcccccccCchhhhhhc
Q psy12028 29 PKFGCPQCPYRSRQKATLNRHLGWEQLQGNAHVMYACDVCGKVYQH 74 (118)
Q Consensus 29 ~~~~C~~c~~~f~~~~~l~~h~~~~~~~~~~~~~~~c~~c~~~~~~ 74 (118)
..|.||.|++.-.... .. ..|.|..|+..|..
T Consensus 34 ~ky~Cp~Cgk~~vkR~----------a~----GIW~C~~C~~~~AG 65 (90)
T PF01780_consen 34 AKYTCPFCGKTSVKRV----------AT----GIWKCKKCGKKFAG 65 (90)
T ss_dssp S-BEESSSSSSEEEEE----------ET----TEEEETTTTEEEE-
T ss_pred CCCcCCCCCCceeEEe----------ee----EEeecCCCCCEEeC
Confidence 3588999987653221 11 22777777776543
No 186
>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=56.60 E-value=8.1 Score=26.37 Aligned_cols=23 Identities=17% Similarity=0.440 Sum_probs=20.8
Q ss_pred CCccCCCCCcccccchHHHHHhh
Q psy12028 29 PKFGCPQCPYRSRQKATLNRHLG 51 (118)
Q Consensus 29 ~~~~C~~c~~~f~~~~~l~~h~~ 51 (118)
+.+.|+.|.+.|.....+..|+.
T Consensus 56 rFWiCp~CskkF~d~~~~~~H~~ 78 (466)
T PF04780_consen 56 RFWICPRCSKKFSDAESCLSHME 78 (466)
T ss_pred eEeeCCcccceeCCHHHHHHHHH
Confidence 34889999999999999999986
No 187
>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=56.30 E-value=2.1 Score=22.46 Aligned_cols=40 Identities=23% Similarity=0.561 Sum_probs=22.8
Q ss_pred CccCCCCCcccccchHHHHHhhhhhccCCcccccccCchhhhhh
Q psy12028 30 KFGCPQCPYRSRQKATLNRHLGWEQLQGNAHVMYACDVCGKVYQ 73 (118)
Q Consensus 30 ~~~C~~c~~~f~~~~~l~~h~~~~~~~~~~~~~~~c~~c~~~~~ 73 (118)
...|+.||..-.....++ ++ ........-|.|..|+..+.
T Consensus 62 ~~~Cp~Cg~~~a~f~~~Q--~R--sadE~~T~fy~C~~C~~~w~ 101 (104)
T TIGR01384 62 RVECPKCGHKEAYYWLLQ--TR--RADEPETRFYKCTKCGYVWR 101 (104)
T ss_pred cCCCCCCCCCeeEEEEec--cC--CCCCCcEEEEEeCCCCCeeE
Confidence 478999986544333222 11 12223345688988887654
No 188
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=55.84 E-value=4.9 Score=29.02 Aligned_cols=12 Identities=25% Similarity=0.648 Sum_probs=7.0
Q ss_pred CCCccCCCCCcc
Q psy12028 28 EPKFGCPQCPYR 39 (118)
Q Consensus 28 ~~~~~C~~c~~~ 39 (118)
..|..||.||..
T Consensus 473 ~~p~~Cp~Cgs~ 484 (730)
T COG1198 473 PIPQSCPECGSE 484 (730)
T ss_pred CCCCCCCCCCCC
Confidence 455666666644
No 189
>PLN02294 cytochrome c oxidase subunit Vb
Probab=55.04 E-value=7.2 Score=22.71 Aligned_cols=16 Identities=25% Similarity=0.580 Sum_probs=12.6
Q ss_pred CCCccCCCCCcccccc
Q psy12028 28 EPKFGCPQCPYRSRQK 43 (118)
Q Consensus 28 ~~~~~C~~c~~~f~~~ 43 (118)
.++..|+.||..|.-.
T Consensus 139 Gkp~RCpeCG~~fkL~ 154 (174)
T PLN02294 139 GKSFECPVCTQYFELE 154 (174)
T ss_pred CCceeCCCCCCEEEEE
Confidence 4678999999888643
No 190
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=54.87 E-value=14 Score=28.68 Aligned_cols=32 Identities=25% Similarity=0.585 Sum_probs=19.1
Q ss_pred ccCCCCCcccccchHHHHHhhhhhccCCcc--cccccCchhhh
Q psy12028 31 FGCPQCPYRSRQKATLNRHLGWEQLQGNAH--VMYACDVCGKV 71 (118)
Q Consensus 31 ~~C~~c~~~f~~~~~l~~h~~~~~~~~~~~--~~~~c~~c~~~ 71 (118)
+.||.||..-... . |..|+.. .+|.|+.|+..
T Consensus 668 rkCPkCG~~t~~~------f---CP~CGs~te~vy~CPsCGae 701 (1337)
T PRK14714 668 RRCPSCGTETYEN------R---CPDCGTHTEPVYVCPDCGAE 701 (1337)
T ss_pred EECCCCCCccccc------c---CcccCCcCCCceeCccCCCc
Confidence 7888888753221 1 4444432 35788888874
No 191
>PF05290 Baculo_IE-1: Baculovirus immediate-early protein (IE-0); InterPro: IPR007954 This entry contains the Baculovirus immediate-early protein IE-0.
Probab=54.31 E-value=4.5 Score=22.52 Aligned_cols=16 Identities=19% Similarity=0.465 Sum_probs=12.2
Q ss_pred CCCccCCCCCcccccc
Q psy12028 28 EPKFGCPQCPYRSRQK 43 (118)
Q Consensus 28 ~~~~~C~~c~~~f~~~ 43 (118)
.+.|+|.+|......+
T Consensus 78 ~~lYeCnIC~etS~ee 93 (140)
T PF05290_consen 78 PKLYECNICKETSAEE 93 (140)
T ss_pred CCceeccCcccccchh
Confidence 4679999998877554
No 192
>KOG2593|consensus
Probab=53.84 E-value=16 Score=24.68 Aligned_cols=34 Identities=26% Similarity=0.597 Sum_probs=19.1
Q ss_pred cccccCchhhhhhchHHHHHHHhhhcCCCCCccCCCCC
Q psy12028 61 VMYACDVCGKVYQHKQTLDRHKKDECGQEPKFECPHCP 98 (118)
Q Consensus 61 ~~~~c~~c~~~~~~~~~l~~h~~~h~~~~~~~~C~~C~ 98 (118)
..|.|+.|.+.|+....++ -.-.. .-.|.|..|+
T Consensus 127 ~~Y~Cp~C~kkyt~Lea~~---L~~~~-~~~F~C~~C~ 160 (436)
T KOG2593|consen 127 AGYVCPNCQKKYTSLEALQ---LLDNE-TGEFHCENCG 160 (436)
T ss_pred ccccCCccccchhhhHHHH---hhccc-CceEEEecCC
Confidence 3477777777776654432 22211 2357777776
No 193
>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=53.51 E-value=6.7 Score=26.62 Aligned_cols=10 Identities=40% Similarity=0.860 Sum_probs=5.0
Q ss_pred ccCCCCCccc
Q psy12028 31 FGCPQCPYRS 40 (118)
Q Consensus 31 ~~C~~c~~~f 40 (118)
|.|..||..+
T Consensus 8 y~C~~Cg~~~ 17 (454)
T TIGR00416 8 FVCQHCGADS 17 (454)
T ss_pred EECCcCCCCC
Confidence 5555555443
No 194
>KOG0717|consensus
Probab=53.47 E-value=7.3 Score=26.49 Aligned_cols=22 Identities=27% Similarity=0.699 Sum_probs=18.5
Q ss_pred ccCCCCCccccchHHHHhhhhh
Q psy12028 2 YACDVCGKEYQHKRTLYRHKKD 23 (118)
Q Consensus 2 ~~C~~C~~~~~~~~~l~~h~~~ 23 (118)
+-|.+|++.|.+...+.+|..+
T Consensus 293 lyC~vCnKsFKseKq~kNHEnS 314 (508)
T KOG0717|consen 293 LYCVVCNKSFKSEKQLKNHENS 314 (508)
T ss_pred eEEeeccccccchHHHHhhHHH
Confidence 4589999999999999888654
No 195
>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=53.19 E-value=4.7 Score=16.69 Aligned_cols=14 Identities=14% Similarity=0.199 Sum_probs=6.6
Q ss_pred ccCCCCCCCCCChh
Q psy12028 92 FECPHCPYRSKRKD 105 (118)
Q Consensus 92 ~~C~~C~~~f~~~~ 105 (118)
-.|..|++.|..+.
T Consensus 4 ~~C~eC~~~f~dSy 17 (34)
T PF01286_consen 4 PKCDECGKPFMDSY 17 (34)
T ss_dssp EE-TTT--EES-SS
T ss_pred chHhHhCCHHHHHH
Confidence 35788888876553
No 196
>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=52.79 E-value=14 Score=15.12 Aligned_cols=20 Identities=25% Similarity=0.569 Sum_probs=12.5
Q ss_pred CccCCCCCcccccchHHHHHh
Q psy12028 30 KFGCPQCPYRSRQKATLNRHL 50 (118)
Q Consensus 30 ~~~C~~c~~~f~~~~~l~~h~ 50 (118)
.+.|+.|++.... ..+..|+
T Consensus 4 ~~~C~nC~R~v~a-~RfA~HL 23 (33)
T PF08209_consen 4 YVECPNCGRPVAA-SRFAPHL 23 (33)
T ss_dssp EEE-TTTSSEEEG-GGHHHHH
T ss_pred eEECCCCcCCcch-hhhHHHH
Confidence 4678888887654 3466665
No 197
>PRK00420 hypothetical protein; Validated
Probab=52.30 E-value=12 Score=20.27 Aligned_cols=10 Identities=30% Similarity=0.660 Sum_probs=4.9
Q ss_pred ccCCCCCccc
Q psy12028 31 FGCPQCPYRS 40 (118)
Q Consensus 31 ~~C~~c~~~f 40 (118)
-.||.||..+
T Consensus 24 ~~CP~Cg~pL 33 (112)
T PRK00420 24 KHCPVCGLPL 33 (112)
T ss_pred CCCCCCCCcc
Confidence 3455555443
No 198
>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=51.96 E-value=8.8 Score=20.15 Aligned_cols=15 Identities=20% Similarity=0.412 Sum_probs=11.9
Q ss_pred CCCccCCCCCccccc
Q psy12028 28 EPKFGCPQCPYRSRQ 42 (118)
Q Consensus 28 ~~~~~C~~c~~~f~~ 42 (118)
.++..|+.||..|.-
T Consensus 77 g~~~rC~eCG~~fkL 91 (97)
T cd00924 77 GKPKRCPECGHVFKL 91 (97)
T ss_pred CCceeCCCCCcEEEE
Confidence 368999999988853
No 199
>COG5216 Uncharacterized conserved protein [Function unknown]
Probab=51.39 E-value=11 Score=17.73 Aligned_cols=11 Identities=36% Similarity=0.911 Sum_probs=5.9
Q ss_pred ccCCCCCccccc
Q psy12028 31 FGCPQCPYRSRQ 42 (118)
Q Consensus 31 ~~C~~c~~~f~~ 42 (118)
|.|| ||..|..
T Consensus 23 yPCP-CGDRFeI 33 (67)
T COG5216 23 YPCP-CGDRFEI 33 (67)
T ss_pred ecCC-CCCEeEE
Confidence 4455 6655544
No 200
>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=50.75 E-value=4.5 Score=18.09 Aligned_cols=13 Identities=46% Similarity=1.145 Sum_probs=8.6
Q ss_pred ccCCCCCccccch
Q psy12028 2 YACDVCGKEYQHK 14 (118)
Q Consensus 2 ~~C~~C~~~~~~~ 14 (118)
|+|..|+.+|.-.
T Consensus 2 y~C~~CgyvYd~~ 14 (47)
T PF00301_consen 2 YQCPVCGYVYDPE 14 (47)
T ss_dssp EEETTTSBEEETT
T ss_pred cCCCCCCEEEcCC
Confidence 5677777776543
No 201
>COG4530 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=50.73 E-value=16 Score=19.61 Aligned_cols=14 Identities=7% Similarity=-0.074 Sum_probs=10.1
Q ss_pred CCCccCCCCCCCCC
Q psy12028 89 EPKFECPHCPYRSK 102 (118)
Q Consensus 89 ~~~~~C~~C~~~f~ 102 (118)
..|..|++||++|.
T Consensus 24 rdPiVsPytG~s~P 37 (129)
T COG4530 24 RDPIVSPYTGKSYP 37 (129)
T ss_pred CCccccCcccccch
Confidence 45777888888773
No 202
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=50.71 E-value=8.8 Score=24.54 Aligned_cols=10 Identities=20% Similarity=0.464 Sum_probs=4.5
Q ss_pred ccCCCCCccc
Q psy12028 31 FGCPQCPYRS 40 (118)
Q Consensus 31 ~~C~~c~~~f 40 (118)
.+|+.|+...
T Consensus 39 ~kc~~C~~~~ 48 (296)
T CHL00174 39 VQCENCYGLN 48 (296)
T ss_pred eECCCccchh
Confidence 3445554443
No 203
>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=50.07 E-value=6.9 Score=17.17 Aligned_cols=9 Identities=44% Similarity=1.176 Sum_probs=7.3
Q ss_pred ccCCCCCcc
Q psy12028 31 FGCPQCPYR 39 (118)
Q Consensus 31 ~~C~~c~~~ 39 (118)
+.||.||..
T Consensus 19 ~~CP~Cg~~ 27 (46)
T PF12760_consen 19 FVCPHCGST 27 (46)
T ss_pred CCCCCCCCe
Confidence 779999865
No 204
>PRK11823 DNA repair protein RadA; Provisional
Probab=49.26 E-value=8.6 Score=26.05 Aligned_cols=9 Identities=56% Similarity=1.468 Sum_probs=4.7
Q ss_pred ccCCCCCcc
Q psy12028 2 YACDVCGKE 10 (118)
Q Consensus 2 ~~C~~C~~~ 10 (118)
|.|..||..
T Consensus 8 y~C~~Cg~~ 16 (446)
T PRK11823 8 YVCQECGAE 16 (446)
T ss_pred EECCcCCCC
Confidence 455555543
No 205
>COG3091 SprT Zn-dependent metalloprotease, SprT family [General function prediction only]
Probab=48.79 E-value=6.7 Score=22.37 Aligned_cols=35 Identities=29% Similarity=0.669 Sum_probs=23.2
Q ss_pred ccccccCchhhhhhchHHHHHHHhhhcCCCCCccCCCCCCC
Q psy12028 60 HVMYACDVCGKVYQHKQTLDRHKKDECGQEPKFECPHCPYR 100 (118)
Q Consensus 60 ~~~~~c~~c~~~~~~~~~l~~h~~~h~~~~~~~~C~~C~~~ 100 (118)
..+|.|. |+..+... .+|-..-.| + .|.|..|+-.
T Consensus 115 ~~~Y~C~-C~q~~l~~---RRhn~~~~g-~-~YrC~~C~gk 149 (156)
T COG3091 115 TYPYRCQ-CQQHYLRI---RRHNTVRRG-E-VYRCGKCGGK 149 (156)
T ss_pred ceeEEee-cCCccchh---hhccccccc-c-eEEeccCCce
Confidence 4578888 98876543 334444445 5 7999999753
No 206
>PF14311 DUF4379: Domain of unknown function (DUF4379)
Probab=48.30 E-value=17 Score=16.54 Aligned_cols=15 Identities=20% Similarity=0.603 Sum_probs=11.5
Q ss_pred CccCCCCCcccccch
Q psy12028 30 KFGCPQCPYRSRQKA 44 (118)
Q Consensus 30 ~~~C~~c~~~f~~~~ 44 (118)
-+.|+.|+..|...-
T Consensus 28 ~W~C~~Cgh~w~~~v 42 (55)
T PF14311_consen 28 WWKCPKCGHEWKASV 42 (55)
T ss_pred EEECCCCCCeeEccH
Confidence 488999988887654
No 207
>COG1326 Uncharacterized archaeal Zn-finger protein [General function prediction only]
Probab=48.29 E-value=17 Score=21.73 Aligned_cols=14 Identities=29% Similarity=0.615 Sum_probs=9.9
Q ss_pred CCCccCCCCCcccc
Q psy12028 28 EPKFGCPQCPYRSR 41 (118)
Q Consensus 28 ~~~~~C~~c~~~f~ 41 (118)
+..+.|..||..+.
T Consensus 28 ~~lvrC~eCG~V~~ 41 (201)
T COG1326 28 EPLVRCEECGTVHP 41 (201)
T ss_pred ceEEEccCCCcEee
Confidence 44577888887774
No 208
>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=47.83 E-value=15 Score=23.37 Aligned_cols=10 Identities=30% Similarity=0.713 Sum_probs=4.6
Q ss_pred ccCCCCCccc
Q psy12028 31 FGCPQCPYRS 40 (118)
Q Consensus 31 ~~C~~c~~~f 40 (118)
..|+.|+...
T Consensus 27 ~~c~~c~~~~ 36 (285)
T TIGR00515 27 TKCPKCGQVL 36 (285)
T ss_pred eECCCCcchh
Confidence 3455554443
No 209
>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=47.80 E-value=4.7 Score=25.74 Aligned_cols=41 Identities=17% Similarity=0.452 Sum_probs=22.0
Q ss_pred CCccCCCCCcccccchHHHHHhhhhhccCCcccccccCchhhhhh
Q psy12028 29 PKFGCPQCPYRSRQKATLNRHLGWEQLQGNAHVMYACDVCGKVYQ 73 (118)
Q Consensus 29 ~~~~C~~c~~~f~~~~~l~~h~~~~~~~~~~~~~~~c~~c~~~~~ 73 (118)
..+.|+.|+..=.....++ .+ .........|.|..|+..+.
T Consensus 257 ~~~~C~~C~~~~~~~~q~Q--tr--saDEpmT~f~~C~~Cg~~w~ 297 (299)
T TIGR01385 257 DLFTCGKCKQKKCTYYQLQ--TR--SADEPMTTFVTCEECGNRWK 297 (299)
T ss_pred ccccCCCCCCccceEEEec--cc--CCCCCCeEEEEcCCCCCeee
Confidence 3589999985433322221 11 12222235578988887653
No 210
>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=47.67 E-value=8.9 Score=18.28 Aligned_cols=11 Identities=18% Similarity=0.374 Sum_probs=3.9
Q ss_pred ccCCCCCcccc
Q psy12028 31 FGCPQCPYRSR 41 (118)
Q Consensus 31 ~~C~~c~~~f~ 41 (118)
-.|..|++.|.
T Consensus 10 ~~C~~C~~~F~ 20 (69)
T PF01363_consen 10 SNCMICGKKFS 20 (69)
T ss_dssp SB-TTT--B-B
T ss_pred CcCcCcCCcCC
Confidence 35666666663
No 211
>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=46.47 E-value=6.6 Score=23.46 Aligned_cols=22 Identities=18% Similarity=0.599 Sum_probs=0.0
Q ss_pred CCCccCCCCCC-CCCChhHHHHH
Q psy12028 89 EPKFECPHCPY-RSKRKDTLDRH 110 (118)
Q Consensus 89 ~~~~~C~~C~~-~f~~~~~l~~H 110 (118)
...|.|.+||- +|.-+..+.+|
T Consensus 99 ~~ey~CEICGN~~Y~GrkaFekH 121 (196)
T PF11931_consen 99 GVEYKCEICGNQSYKGRKAFEKH 121 (196)
T ss_dssp -----------------------
T ss_pred CCeeeeEeCCCcceecHHHHHHh
Confidence 34455666552 33334444444
No 212
>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=46.37 E-value=4.6 Score=17.41 Aligned_cols=11 Identities=36% Similarity=0.766 Sum_probs=5.9
Q ss_pred CccCCCCCCCC
Q psy12028 91 KFECPHCPYRS 101 (118)
Q Consensus 91 ~~~C~~C~~~f 101 (118)
+-.|++||..|
T Consensus 29 ~~~CpYCg~~y 39 (40)
T PF10276_consen 29 PVVCPYCGTRY 39 (40)
T ss_dssp EEEETTTTEEE
T ss_pred eEECCCCCCEE
Confidence 34566666544
No 213
>TIGR00143 hypF [NiFe] hydrogenase maturation protein HypF. A previously described regulatory effect of HypF mutatation is attributable to loss of activity of a regulatory hydrogenase. A zinc finger-like region CXXCX(18)CXXCX(24)CXXCX(18)CXXC region further supported the regulatory hypothesis. However, more recent work (PUBMED:11375153) shows the direct effect is on the activity of expressed hydrogenases with nickel/iron centers, rather than on expression.
Probab=46.29 E-value=2.7 Score=30.14 Aligned_cols=58 Identities=21% Similarity=0.403 Sum_probs=30.9
Q ss_pred cCCCCCcccccchHHHHHhhhhhccCCcccccccCchhhhhhchHHHHHHHhhhcCCCCCccCCCCCCC
Q psy12028 32 GCPQCPYRSRQKATLNRHLGWEQLQGNAHVMYACDVCGKVYQHKQTLDRHKKDECGQEPKFECPHCPYR 100 (118)
Q Consensus 32 ~C~~c~~~f~~~~~l~~h~~~~~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~h~~~~~~~~C~~C~~~ 100 (118)
.|+.||-.|.....|---.. .... .+. --|+.|.+-+.++.+ .+.| ..+..|+.||..
T Consensus 92 nCt~CGPr~~i~~~lpydr~--~t~m-~~f-~~C~~C~~ey~~p~~----rr~h---~~~~~C~~Cgp~ 149 (711)
T TIGR00143 92 SCTHCGPRFTIIEALPYDRE--NTSM-ADF-PLCPDCAKEYKDPLD----RRFH---AQPIACPRCGPQ 149 (711)
T ss_pred cccCCCCCeEEeecCCCCCC--CcCC-CCC-cCCHHHHHHhcCCcc----ccCC---CCCccCCCCCcE
Confidence 48888887765443211100 1111 111 257778777766643 3444 346778888854
No 214
>PF13821 DUF4187: Domain of unknown function (DUF4187)
Probab=46.21 E-value=12 Score=17.36 Aligned_cols=18 Identities=22% Similarity=0.551 Sum_probs=12.0
Q ss_pred cCCCCCCCCCChhHHHHH
Q psy12028 93 ECPHCPYRSKRKDTLDRH 110 (118)
Q Consensus 93 ~C~~C~~~f~~~~~l~~H 110 (118)
=|-+||..|.....|..+
T Consensus 29 YC~~Cg~~Y~d~~dL~~~ 46 (55)
T PF13821_consen 29 YCFWCGTKYDDEEDLERN 46 (55)
T ss_pred eeeeeCCccCCHHHHHhC
Confidence 377777777777666543
No 215
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=46.02 E-value=9.9 Score=21.05 Aligned_cols=36 Identities=14% Similarity=0.317 Sum_probs=20.9
Q ss_pred cccCchhhhhhchHHHHHHHhhhcCCCCCccCCCCCCCCCCh
Q psy12028 63 YACDVCGKVYQHKQTLDRHKKDECGQEPKFECPHCPYRSKRK 104 (118)
Q Consensus 63 ~~c~~c~~~~~~~~~l~~h~~~h~~~~~~~~C~~C~~~f~~~ 104 (118)
-.||.|+... . ...-..-.| ...|.|..|++.|...
T Consensus 31 ~~cP~C~s~~-~----~k~g~~~~~-~qRyrC~~C~~tf~~~ 66 (129)
T COG3677 31 VNCPRCKSSN-V----VKIGGIRRG-HQRYKCKSCGSTFTVE 66 (129)
T ss_pred CcCCCCCccc-e----eeECCcccc-ccccccCCcCcceeee
Confidence 4677777543 1 111122223 5569999999988643
No 216
>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=45.63 E-value=8 Score=15.69 Aligned_cols=10 Identities=40% Similarity=1.325 Sum_probs=6.8
Q ss_pred ccCCCCCccc
Q psy12028 2 YACDVCGKEY 11 (118)
Q Consensus 2 ~~C~~C~~~~ 11 (118)
|+|..||...
T Consensus 5 ykC~~CGniv 14 (34)
T cd00974 5 YKCEICGNIV 14 (34)
T ss_pred EEcCCCCcEE
Confidence 6677777665
No 217
>PF14787 zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB: 1CL4_A 1DSV_A.
Probab=45.63 E-value=14 Score=15.53 Aligned_cols=15 Identities=20% Similarity=0.328 Sum_probs=8.5
Q ss_pred ccCCCCCCCCCChhH
Q psy12028 92 FECPHCPYRSKRKDT 106 (118)
Q Consensus 92 ~~C~~C~~~f~~~~~ 106 (118)
-.|+.|++.|-..++
T Consensus 3 ~~CprC~kg~Hwa~~ 17 (36)
T PF14787_consen 3 GLCPRCGKGFHWASE 17 (36)
T ss_dssp -C-TTTSSSCS-TTT
T ss_pred ccCcccCCCcchhhh
Confidence 358888888765443
No 218
>TIGR00319 desulf_FeS4 desulfoferrodoxin FeS4 iron-binding domain. Neelaredoxin, a monomeric blue non-heme iron protein, lacks this domain.
Probab=45.39 E-value=7.8 Score=15.70 Aligned_cols=10 Identities=50% Similarity=1.335 Sum_probs=6.7
Q ss_pred ccCCCCCccc
Q psy12028 2 YACDVCGKEY 11 (118)
Q Consensus 2 ~~C~~C~~~~ 11 (118)
|+|..|+..+
T Consensus 8 ykC~~Cgniv 17 (34)
T TIGR00319 8 YKCEVCGNIV 17 (34)
T ss_pred EEcCCCCcEE
Confidence 5677777665
No 219
>COG2956 Predicted N-acetylglucosaminyl transferase [Carbohydrate transport and metabolism]
Probab=45.18 E-value=20 Score=23.59 Aligned_cols=14 Identities=21% Similarity=1.049 Sum_probs=10.1
Q ss_pred CCCccCCCCCcccc
Q psy12028 28 EPKFGCPQCPYRSR 41 (118)
Q Consensus 28 ~~~~~C~~c~~~f~ 41 (118)
...|.|..||..-.
T Consensus 352 ~~~YRC~~CGF~a~ 365 (389)
T COG2956 352 KPRYRCQNCGFTAH 365 (389)
T ss_pred cCCceecccCCcce
Confidence 45699999986543
No 220
>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=45.11 E-value=28 Score=18.46 Aligned_cols=37 Identities=5% Similarity=0.088 Sum_probs=29.0
Q ss_pred ccCCCCCccccchHHHHhhhhhhcCCCCCccCCCCCccc
Q psy12028 2 YACDVCGKEYQHKRTLYRHKKDECGQEPKFGCPQCPYRS 40 (118)
Q Consensus 2 ~~C~~C~~~~~~~~~l~~h~~~~~~~~~~~~C~~c~~~f 40 (118)
|.|+.-|.+|.+.......+.... .+.+.|...|+.-
T Consensus 4 f~i~~T~EiF~dYe~Y~~R~~~y~--~~vwtC~~TGk~~ 40 (102)
T PF10537_consen 4 FYIPFTGEIFRDYEEYLKRMILYN--QRVWTCEITGKSN 40 (102)
T ss_pred EEeCCCCcccCCHHHHHHHHHHHh--CCeeEEecCCCCC
Confidence 567777888999998888887764 4779998888753
No 221
>KOG1280|consensus
Probab=45.09 E-value=24 Score=23.22 Aligned_cols=29 Identities=21% Similarity=0.399 Sum_probs=18.9
Q ss_pred CCCccCCCCCCCCCChhHHHHHHhhhcCC
Q psy12028 89 EPKFECPHCPYRSKRKDTLDRHMKIIHFS 117 (118)
Q Consensus 89 ~~~~~C~~C~~~f~~~~~l~~H~~~~~~~ 117 (118)
...|.|++|+..--+-..|..|....|.+
T Consensus 77 ~qSftCPyC~~~Gfte~~f~~Hv~s~Hpd 105 (381)
T KOG1280|consen 77 PQSFTCPYCGIMGFTERQFGTHVLSQHPE 105 (381)
T ss_pred cccccCCcccccccchhHHHHHhhhcCcc
Confidence 34677777777655666677777666543
No 222
>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=44.25 E-value=13 Score=24.65 Aligned_cols=23 Identities=30% Similarity=0.641 Sum_probs=15.3
Q ss_pred ccCCCCCccccchHHHHhhhhhhcCCCCCccCCCCCcc
Q psy12028 2 YACDVCGKEYQHKRTLYRHKKDECGQEPKFGCPQCPYR 39 (118)
Q Consensus 2 ~~C~~C~~~~~~~~~l~~h~~~~~~~~~~~~C~~c~~~ 39 (118)
|.|..||.... .-..+||.|+.+
T Consensus 1 ~~c~~cg~~~~---------------~~~g~cp~c~~w 23 (372)
T cd01121 1 YVCSECGYVSP---------------KWLGKCPECGEW 23 (372)
T ss_pred CCCCCCCCCCC---------------CccEECcCCCCc
Confidence 67888887542 223678988754
No 223
>COG4391 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=44.04 E-value=15 Score=17.49 Aligned_cols=14 Identities=43% Similarity=0.831 Sum_probs=9.4
Q ss_pred CCCccCCCCCcccc
Q psy12028 28 EPKFGCPQCPYRSR 41 (118)
Q Consensus 28 ~~~~~C~~c~~~f~ 41 (118)
+..-.||.|+..|.
T Consensus 46 ~gev~CPYC~t~y~ 59 (62)
T COG4391 46 EGEVVCPYCSTRYR 59 (62)
T ss_pred CCcEecCccccEEE
Confidence 44567888877764
No 224
>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=43.99 E-value=13 Score=19.77 Aligned_cols=8 Identities=25% Similarity=0.908 Sum_probs=5.6
Q ss_pred ccCCCCCc
Q psy12028 31 FGCPQCPY 38 (118)
Q Consensus 31 ~~C~~c~~ 38 (118)
|.|+.|+-
T Consensus 32 y~C~~C~A 39 (102)
T PF11672_consen 32 YVCTPCDA 39 (102)
T ss_pred EECCCCCc
Confidence 77877763
No 225
>PRK05654 acetyl-CoA carboxylase subunit beta; Validated
Probab=43.92 E-value=13 Score=23.80 Aligned_cols=12 Identities=25% Similarity=0.412 Sum_probs=6.4
Q ss_pred CccCCCCCcccc
Q psy12028 30 KFGCPQCPYRSR 41 (118)
Q Consensus 30 ~~~C~~c~~~f~ 41 (118)
..+|+.|+....
T Consensus 27 ~~~c~~c~~~~~ 38 (292)
T PRK05654 27 WTKCPSCGQVLY 38 (292)
T ss_pred eeECCCccchhh
Confidence 345666665443
No 226
>PLN02748 tRNA dimethylallyltransferase
Probab=43.44 E-value=23 Score=24.34 Aligned_cols=24 Identities=13% Similarity=0.364 Sum_probs=20.1
Q ss_pred CCccCCCCCC-CCCChhHHHHHHhh
Q psy12028 90 PKFECPHCPY-RSKRKDTLDRHMKI 113 (118)
Q Consensus 90 ~~~~C~~C~~-~f~~~~~l~~H~~~ 113 (118)
+.|.|.+|++ .+.....+..|++.
T Consensus 417 ~~~~Ce~C~~~~~~G~~eW~~Hlks 441 (468)
T PLN02748 417 TQYVCEACGNKVLRGAHEWEQHKQG 441 (468)
T ss_pred ccccccCCCCcccCCHHHHHHHhcc
Confidence 5678999997 79889999999854
No 227
>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=43.38 E-value=18 Score=23.27 Aligned_cols=8 Identities=25% Similarity=0.850 Sum_probs=5.8
Q ss_pred cccCchhh
Q psy12028 63 YACDVCGK 70 (118)
Q Consensus 63 ~~c~~c~~ 70 (118)
..|+.|+.
T Consensus 225 ~~C~~Cg~ 232 (305)
T TIGR01562 225 VKCSHCEE 232 (305)
T ss_pred ccCCCCCC
Confidence 47888875
No 228
>PF14447 Prok-RING_4: Prokaryotic RING finger family 4
Probab=43.18 E-value=13 Score=17.26 Aligned_cols=16 Identities=31% Similarity=0.484 Sum_probs=11.9
Q ss_pred CCCccCCCCCcccccc
Q psy12028 28 EPKFGCPQCPYRSRQK 43 (118)
Q Consensus 28 ~~~~~C~~c~~~f~~~ 43 (118)
++--.||+|+..|...
T Consensus 37 ~rYngCPfC~~~~~~~ 52 (55)
T PF14447_consen 37 ERYNGCPFCGTPFEFD 52 (55)
T ss_pred hhccCCCCCCCcccCC
Confidence 4556799999988653
No 229
>COG4306 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=43.07 E-value=11 Score=20.70 Aligned_cols=25 Identities=24% Similarity=0.513 Sum_probs=11.4
Q ss_pred HHHhhhhhhcCCCCCccCCCCCccc
Q psy12028 16 TLYRHKKDECGQEPKFGCPQCPYRS 40 (118)
Q Consensus 16 ~l~~h~~~~~~~~~~~~C~~c~~~f 40 (118)
.|..-...+.++.....||.|....
T Consensus 25 el~eafcskcgeati~qcp~csasi 49 (160)
T COG4306 25 ELMEAFCSKCGEATITQCPICSASI 49 (160)
T ss_pred HHHHHHHhhhchHHHhcCCccCCcc
Confidence 3333344444433445555555443
No 230
>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=42.98 E-value=4.6 Score=17.21 Aligned_cols=10 Identities=20% Similarity=0.487 Sum_probs=4.1
Q ss_pred CCccCCCCCc
Q psy12028 29 PKFGCPQCPY 38 (118)
Q Consensus 29 ~~~~C~~c~~ 38 (118)
+.+.|++|+.
T Consensus 23 ~~w~C~~C~~ 32 (40)
T PF04810_consen 23 KTWICNFCGT 32 (40)
T ss_dssp TEEEETTT--
T ss_pred CEEECcCCCC
Confidence 3455555543
No 231
>KOG2071|consensus
Probab=42.94 E-value=18 Score=25.47 Aligned_cols=26 Identities=15% Similarity=0.353 Sum_probs=20.7
Q ss_pred CccCCCCCccccchHHHHhhhhhhcC
Q psy12028 1 MYACDVCGKEYQHKRTLYRHKKDECG 26 (118)
Q Consensus 1 ~~~C~~C~~~~~~~~~l~~h~~~~~~ 26 (118)
|-+|..||..|.+......||..|..
T Consensus 418 pnqC~~CG~R~~~~ee~sk~md~H~d 443 (579)
T KOG2071|consen 418 PNQCKSCGLRFDDSEERSKHMDIHDD 443 (579)
T ss_pred cchhcccccccccchhhhhHhhhhhh
Confidence 35799999999988888888777753
No 232
>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=42.20 E-value=10 Score=17.05 Aligned_cols=8 Identities=38% Similarity=1.173 Sum_probs=2.8
Q ss_pred ccCCCCCc
Q psy12028 31 FGCPQCPY 38 (118)
Q Consensus 31 ~~C~~c~~ 38 (118)
+.||.|++
T Consensus 42 W~CPiC~~ 49 (50)
T PF02891_consen 42 WKCPICNK 49 (50)
T ss_dssp -B-TTT--
T ss_pred eECcCCcC
Confidence 66776654
No 233
>KOG2857|consensus
Probab=41.55 E-value=18 Score=20.43 Aligned_cols=21 Identities=24% Similarity=0.569 Sum_probs=19.0
Q ss_pred CccCCCCCcccccchHHHHHh
Q psy12028 30 KFGCPQCPYRSRQKATLNRHL 50 (118)
Q Consensus 30 ~~~C~~c~~~f~~~~~l~~h~ 50 (118)
.|.||.|...+-+..-|+.|.
T Consensus 17 KYKCpkC~vPYCSl~CfKiHk 37 (157)
T KOG2857|consen 17 KYKCPKCSVPYCSLPCFKIHK 37 (157)
T ss_pred hccCCCCCCccccchhhhhcc
Confidence 599999999999999999884
No 234
>PF12773 DZR: Double zinc ribbon
Probab=41.43 E-value=20 Score=15.75 Aligned_cols=10 Identities=30% Similarity=0.640 Sum_probs=4.3
Q ss_pred cCCCCCcccc
Q psy12028 32 GCPQCPYRSR 41 (118)
Q Consensus 32 ~C~~c~~~f~ 41 (118)
-|+.||....
T Consensus 14 fC~~CG~~l~ 23 (50)
T PF12773_consen 14 FCPHCGTPLP 23 (50)
T ss_pred CChhhcCChh
Confidence 3444444433
No 235
>PF11789 zf-Nse: Zinc-finger of the MIZ type in Nse subunit; PDB: 2YU4_A 3HTK_C.
Probab=41.41 E-value=12 Score=17.44 Aligned_cols=16 Identities=13% Similarity=0.187 Sum_probs=8.2
Q ss_pred CCccCCCCCcccccch
Q psy12028 29 PKFGCPQCPYRSRQKA 44 (118)
Q Consensus 29 ~~~~C~~c~~~f~~~~ 44 (118)
.|.....|+-.|....
T Consensus 23 ~PV~s~~C~H~fek~a 38 (57)
T PF11789_consen 23 DPVKSKKCGHTFEKEA 38 (57)
T ss_dssp SEEEESSS--EEEHHH
T ss_pred CCcCcCCCCCeecHHH
Confidence 4555666777776543
No 236
>KOG2807|consensus
Probab=41.28 E-value=32 Score=22.50 Aligned_cols=19 Identities=26% Similarity=0.581 Sum_probs=11.5
Q ss_pred CccCCCCCcccccchHHHH
Q psy12028 30 KFGCPQCPYRSRQKATLNR 48 (118)
Q Consensus 30 ~~~C~~c~~~f~~~~~l~~ 48 (118)
|..||.|+........|.+
T Consensus 290 P~eCpiC~ltLVss~hLAR 308 (378)
T KOG2807|consen 290 PIECPICSLTLVSSPHLAR 308 (378)
T ss_pred CccCCccceeEecchHHHH
Confidence 4666667766665555544
No 237
>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=41.26 E-value=20 Score=18.50 Aligned_cols=14 Identities=50% Similarity=1.073 Sum_probs=7.2
Q ss_pred cCCCCCccccchHH
Q psy12028 3 ACDVCGKEYQHKRT 16 (118)
Q Consensus 3 ~C~~C~~~~~~~~~ 16 (118)
.|+.||..|.+...
T Consensus 37 ~C~~CGe~y~~dev 50 (89)
T TIGR03829 37 SCSHCGMEYQDDTT 50 (89)
T ss_pred cccCCCcEeecHHH
Confidence 45555555554443
No 238
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=41.03 E-value=8 Score=20.38 Aligned_cols=8 Identities=50% Similarity=1.439 Sum_probs=4.3
Q ss_pred CccCCCCC
Q psy12028 30 KFGCPQCP 37 (118)
Q Consensus 30 ~~~C~~c~ 37 (118)
.|.||.|+
T Consensus 21 ~f~CP~Cg 28 (99)
T PRK14892 21 IFECPRCG 28 (99)
T ss_pred EeECCCCC
Confidence 35555555
No 239
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=40.87 E-value=29 Score=15.86 Aligned_cols=33 Identities=15% Similarity=0.402 Sum_probs=17.2
Q ss_pred ccCCCCCcccccchHHHHHhhhhhccCCcccccccCchhhh
Q psy12028 31 FGCPQCPYRSRQKATLNRHLGWEQLQGNAHVMYACDVCGKV 71 (118)
Q Consensus 31 ~~C~~c~~~f~~~~~l~~h~~~~~~~~~~~~~~~c~~c~~~ 71 (118)
-.|.-|........-.... .++....|+.|++.
T Consensus 23 ~~C~gC~~~l~~~~~~~i~--------~~~~i~~Cp~CgRi 55 (56)
T PF02591_consen 23 GTCSGCHMELPPQELNEIR--------KGDEIVFCPNCGRI 55 (56)
T ss_pred CccCCCCEEcCHHHHHHHH--------cCCCeEECcCCCcc
Confidence 4677777666543322211 12344678877764
No 240
>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG
Probab=40.86 E-value=15 Score=16.81 Aligned_cols=11 Identities=27% Similarity=0.588 Sum_probs=7.0
Q ss_pred cCCCCCccccc
Q psy12028 32 GCPQCPYRSRQ 42 (118)
Q Consensus 32 ~C~~c~~~f~~ 42 (118)
.||.||..+..
T Consensus 2 ~CPyCge~~~~ 12 (52)
T PF14255_consen 2 QCPYCGEPIEI 12 (52)
T ss_pred CCCCCCCeeEE
Confidence 57777766543
No 241
>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=40.66 E-value=14 Score=20.98 Aligned_cols=16 Identities=25% Similarity=0.432 Sum_probs=12.0
Q ss_pred CCccCCCCCCCCCChh
Q psy12028 90 PKFECPHCPYRSKRKD 105 (118)
Q Consensus 90 ~~~~C~~C~~~f~~~~ 105 (118)
+.-.|..||+.|++..
T Consensus 27 RRReC~~C~~RFTTyE 42 (147)
T TIGR00244 27 RRRECLECHERFTTFE 42 (147)
T ss_pred ecccCCccCCccceee
Confidence 3457999999997754
No 242
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=40.52 E-value=8.6 Score=15.86 Aligned_cols=8 Identities=38% Similarity=1.356 Sum_probs=4.1
Q ss_pred ccCCCCCc
Q psy12028 31 FGCPQCPY 38 (118)
Q Consensus 31 ~~C~~c~~ 38 (118)
+.|+.|+.
T Consensus 23 ~vC~~Cg~ 30 (34)
T PF14803_consen 23 LVCPACGF 30 (34)
T ss_dssp EEETTTTE
T ss_pred eECCCCCC
Confidence 45555543
No 243
>PF14369 zf-RING_3: zinc-finger
Probab=40.48 E-value=16 Score=15.09 Aligned_cols=10 Identities=30% Similarity=0.723 Sum_probs=8.5
Q ss_pred cCCCCCcccc
Q psy12028 32 GCPQCPYRSR 41 (118)
Q Consensus 32 ~C~~c~~~f~ 41 (118)
.||.|+..|.
T Consensus 23 ~CP~C~~gFv 32 (35)
T PF14369_consen 23 ACPRCHGGFV 32 (35)
T ss_pred CCcCCCCcEe
Confidence 6999998885
No 244
>PRK08222 hydrogenase 4 subunit H; Validated
Probab=40.35 E-value=22 Score=20.86 Aligned_cols=17 Identities=18% Similarity=0.602 Sum_probs=9.2
Q ss_pred ccCCCCCccccchHHHH
Q psy12028 2 YACDVCGKEYQHKRTLY 18 (118)
Q Consensus 2 ~~C~~C~~~~~~~~~l~ 18 (118)
..|..||+.|.....+.
T Consensus 115 ~~C~~Cg~~f~~~k~i~ 131 (181)
T PRK08222 115 QRCSRCERPFAPQKTVA 131 (181)
T ss_pred CcCcccCCccCcHhHHH
Confidence 34666666666544433
No 245
>KOG1842|consensus
Probab=39.97 E-value=26 Score=23.92 Aligned_cols=22 Identities=36% Similarity=0.635 Sum_probs=19.7
Q ss_pred CCccCCCCCcccccchHHHHHh
Q psy12028 29 PKFGCPQCPYRSRQKATLNRHL 50 (118)
Q Consensus 29 ~~~~C~~c~~~f~~~~~l~~h~ 50 (118)
..|.||+|...|.+...|.-|.
T Consensus 14 egflCPiC~~dl~~~~~L~~H~ 35 (505)
T KOG1842|consen 14 EGFLCPICLLDLPNLSALNDHL 35 (505)
T ss_pred hcccCchHhhhhhhHHHHHHHH
Confidence 3499999999999999999996
No 246
>PF13005 zf-IS66: zinc-finger binding domain of transposase IS66 ; InterPro: IPR024474 This entry represents a predicted helix-turn-helix domain from insertion element IS66 transposases [].
Probab=39.64 E-value=6.1 Score=17.24 Aligned_cols=9 Identities=44% Similarity=1.110 Sum_probs=4.5
Q ss_pred CCCCCcccc
Q psy12028 4 CDVCGKEYQ 12 (118)
Q Consensus 4 C~~C~~~~~ 12 (118)
|+.||..+.
T Consensus 5 C~~Cg~~l~ 13 (47)
T PF13005_consen 5 CPDCGGELK 13 (47)
T ss_pred CCCCCceee
Confidence 555555443
No 247
>KOG2272|consensus
Probab=38.78 E-value=41 Score=21.18 Aligned_cols=14 Identities=21% Similarity=0.496 Sum_probs=10.7
Q ss_pred CccCCCCCCCCCCh
Q psy12028 91 KFECPHCPYRSKRK 104 (118)
Q Consensus 91 ~~~C~~C~~~f~~~ 104 (118)
-|.|..|.+.|--.
T Consensus 221 HFvCa~CekPFlGH 234 (332)
T KOG2272|consen 221 HFVCAKCEKPFLGH 234 (332)
T ss_pred heeehhcCCcccch
Confidence 48899999888544
No 248
>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=38.15 E-value=43 Score=19.42 Aligned_cols=51 Identities=18% Similarity=0.375 Sum_probs=26.6
Q ss_pred cccCchhhhhhchHHHHHHHhhhcCCCCCccCCC--CCCCCCChhHHHHHHhhhcC
Q psy12028 63 YACDVCGKVYQHKQTLDRHKKDECGQEPKFECPH--CPYRSKRKDTLDRHMKIIHF 116 (118)
Q Consensus 63 ~~c~~c~~~~~~~~~l~~h~~~h~~~~~~~~C~~--C~~~f~~~~~l~~H~~~~~~ 116 (118)
..|+.|.-.......... .+.+-. .++-.|.. |... .+-..|.+|.+..|.
T Consensus 81 L~CPLCRG~V~GWtvve~-AR~~LN-~K~RsC~~e~C~F~-GtY~eLrKHar~~HP 133 (162)
T PF07800_consen 81 LACPLCRGEVKGWTVVEP-ARRFLN-AKKRSCSQESCSFS-GTYSELRKHARSEHP 133 (162)
T ss_pred ccCccccCceeceEEchH-HHHHhc-cCCccCcccccccc-cCHHHHHHHHHhhCC
Confidence 467777654444433222 233333 44445543 5543 345677788877664
No 249
>PF10071 DUF2310: Zn-ribbon-containing, possibly nucleic-acid-binding protein (DUF2310); InterPro: IPR016908 This group represents uncharacterised conserved proteins.
Probab=37.65 E-value=11 Score=23.66 Aligned_cols=30 Identities=33% Similarity=0.605 Sum_probs=16.6
Q ss_pred ccCCCCCcccccchHHHHHhhhhhccCCcccccccCchhhh
Q psy12028 31 FGCPQCPYRSRQKATLNRHLGWEQLQGNAHVMYACDVCGKV 71 (118)
Q Consensus 31 ~~C~~c~~~f~~~~~l~~h~~~~~~~~~~~~~~~c~~c~~~ 71 (118)
-.||.||..+.-...|.. -..|+|..|.-+
T Consensus 221 r~CP~Cg~~W~L~~plh~-----------iFdFKCD~CRLV 250 (258)
T PF10071_consen 221 RKCPSCGGDWRLKEPLHD-----------IFDFKCDPCRLV 250 (258)
T ss_pred CCCCCCCCccccCCchhh-----------ceeccCCcceee
Confidence 457777776665544411 134666666544
No 250
>PRK05452 anaerobic nitric oxide reductase flavorubredoxin; Provisional
Probab=37.50 E-value=14 Score=25.32 Aligned_cols=16 Identities=19% Similarity=0.640 Sum_probs=11.3
Q ss_pred CCCccCCCCCcccccc
Q psy12028 28 EPKFGCPQCPYRSRQK 43 (118)
Q Consensus 28 ~~~~~C~~c~~~f~~~ 43 (118)
...|.|..|+..+-..
T Consensus 423 ~~~~~c~~c~~~yd~~ 438 (479)
T PRK05452 423 GPRMQCSVCQWIYDPA 438 (479)
T ss_pred CCeEEECCCCeEECCC
Confidence 4568888888776543
No 251
>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=37.44 E-value=20 Score=14.28 Aligned_cols=10 Identities=40% Similarity=1.192 Sum_probs=5.0
Q ss_pred ccCCCCCccc
Q psy12028 2 YACDVCGKEY 11 (118)
Q Consensus 2 ~~C~~C~~~~ 11 (118)
|.|..|++.+
T Consensus 28 f~C~~C~~~L 37 (39)
T smart00132 28 FKCSKCGKPL 37 (39)
T ss_pred CCCcccCCcC
Confidence 4455555543
No 252
>PRK12722 transcriptional activator FlhC; Provisional
Probab=37.36 E-value=29 Score=20.69 Aligned_cols=30 Identities=17% Similarity=0.359 Sum_probs=18.2
Q ss_pred CCccCCCCCcccccchHHHHHhhhhhccCCcccccccCchhh
Q psy12028 29 PKFGCPQCPYRSRQKATLNRHLGWEQLQGNAHVMYACDVCGK 70 (118)
Q Consensus 29 ~~~~C~~c~~~f~~~~~l~~h~~~~~~~~~~~~~~~c~~c~~ 70 (118)
....|..|+-.|..... . ....|.|+.|..
T Consensus 133 ~l~~C~~Cgg~fv~~~~-e-----------~~~~f~CplC~~ 162 (187)
T PRK12722 133 QLSSCNCCGGHFVTHAH-D-----------PVGSFVCGLCQP 162 (187)
T ss_pred eeccCCCCCCCeecccc-c-----------cCCCCcCCCCCC
Confidence 44668888888775432 1 113478888765
No 253
>PTZ00043 cytochrome c oxidase subunit; Provisional
Probab=37.26 E-value=20 Score=22.04 Aligned_cols=16 Identities=13% Similarity=0.166 Sum_probs=13.4
Q ss_pred CCCccCCCCCcccccc
Q psy12028 28 EPKFGCPQCPYRSRQK 43 (118)
Q Consensus 28 ~~~~~C~~c~~~f~~~ 43 (118)
.++.+|+.||..|.-.
T Consensus 179 GkpqRCpECGqVFKLV 194 (268)
T PTZ00043 179 GFLYRCGECDQIFMLV 194 (268)
T ss_pred CCCccCCCCCcEEEEE
Confidence 5689999999999753
No 254
>PRK01343 zinc-binding protein; Provisional
Probab=37.23 E-value=25 Score=16.50 Aligned_cols=12 Identities=33% Similarity=0.697 Sum_probs=8.5
Q ss_pred CccCCCCCCCCC
Q psy12028 91 KFECPHCPYRSK 102 (118)
Q Consensus 91 ~~~C~~C~~~f~ 102 (118)
...|+.|++.+.
T Consensus 9 ~~~CP~C~k~~~ 20 (57)
T PRK01343 9 TRPCPECGKPST 20 (57)
T ss_pred CCcCCCCCCcCc
Confidence 456888888764
No 255
>PRK06260 threonine synthase; Validated
Probab=37.19 E-value=25 Score=23.40 Aligned_cols=29 Identities=34% Similarity=0.700 Sum_probs=19.0
Q ss_pred ccCCCCCccccchHHHHhhhhhhcCCCCCccCCCCCcccccc
Q psy12028 2 YACDVCGKEYQHKRTLYRHKKDECGQEPKFGCPQCPYRSRQK 43 (118)
Q Consensus 2 ~~C~~C~~~~~~~~~l~~h~~~~~~~~~~~~C~~c~~~f~~~ 43 (118)
++|..||..|.. ....+.|+.|+..+...
T Consensus 4 ~~C~~cg~~~~~-------------~~~~~~Cp~cg~~l~~~ 32 (397)
T PRK06260 4 LKCIECGKEYDP-------------DEIIYTCPECGGLLEVI 32 (397)
T ss_pred EEECCCCCCCCC-------------CCccccCCCCCCeEEEE
Confidence 568888887642 13457898887655444
No 256
>KOG4727|consensus
Probab=36.64 E-value=17 Score=21.24 Aligned_cols=21 Identities=29% Similarity=0.596 Sum_probs=16.8
Q ss_pred ccCCCCCccccchHHHHhhhh
Q psy12028 2 YACDVCGKEYQHKRTLYRHKK 22 (118)
Q Consensus 2 ~~C~~C~~~~~~~~~l~~h~~ 22 (118)
|-|.+|+-++.+.-++..|+.
T Consensus 76 yyCdVCdcvvKDSinflDHiN 96 (193)
T KOG4727|consen 76 YYCDVCDCVVKDSINFLDHIN 96 (193)
T ss_pred eeeeecceeehhhHHHHHHhc
Confidence 568888888888888887764
No 257
>KOG2923|consensus
Probab=36.47 E-value=32 Score=16.55 Aligned_cols=6 Identities=33% Similarity=0.584 Sum_probs=2.7
Q ss_pred CCcccc
Q psy12028 36 CPYRSR 41 (118)
Q Consensus 36 c~~~f~ 41 (118)
||-.|.
T Consensus 27 CGDrf~ 32 (67)
T KOG2923|consen 27 CGDRFQ 32 (67)
T ss_pred CCCeee
Confidence 444443
No 258
>PF11023 DUF2614: Protein of unknown function (DUF2614); InterPro: IPR020912 This entry describes proteins of unknown function, which are thought to be membrane proteins.; GO: 0005887 integral to plasma membrane
Probab=36.19 E-value=13 Score=20.03 Aligned_cols=15 Identities=20% Similarity=0.696 Sum_probs=10.3
Q ss_pred CCCccCCCCCccccc
Q psy12028 28 EPKFGCPQCPYRSRQ 42 (118)
Q Consensus 28 ~~~~~C~~c~~~f~~ 42 (118)
.....||.|++..+-
T Consensus 67 av~V~CP~C~K~TKm 81 (114)
T PF11023_consen 67 AVQVECPNCGKQTKM 81 (114)
T ss_pred ceeeECCCCCChHhh
Confidence 455778888876653
No 259
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=36.15 E-value=26 Score=16.17 Aligned_cols=11 Identities=27% Similarity=0.528 Sum_probs=6.5
Q ss_pred CccCCCCCccc
Q psy12028 30 KFGCPQCPYRS 40 (118)
Q Consensus 30 ~~~C~~c~~~f 40 (118)
...||+||...
T Consensus 3 LkPCPFCG~~~ 13 (61)
T PF14354_consen 3 LKPCPFCGSAD 13 (61)
T ss_pred CcCCCCCCCcc
Confidence 34577776544
No 260
>COG1885 Uncharacterized protein conserved in archaea [Function unknown]
Probab=36.11 E-value=21 Score=18.97 Aligned_cols=15 Identities=20% Similarity=0.468 Sum_probs=11.6
Q ss_pred CCccCCCCCcccccc
Q psy12028 29 PKFGCPQCPYRSRQK 43 (118)
Q Consensus 29 ~~~~C~~c~~~f~~~ 43 (118)
....||.||..|...
T Consensus 48 G~t~CP~Cg~~~e~~ 62 (115)
T COG1885 48 GSTSCPKCGEPFESA 62 (115)
T ss_pred ccccCCCCCCcccee
Confidence 347899999987654
No 261
>COG5112 UFD2 U1-like Zn-finger-containing protein [General function prediction only]
Probab=35.62 E-value=30 Score=18.53 Aligned_cols=23 Identities=26% Similarity=0.495 Sum_probs=19.3
Q ss_pred ccccCchhhhhhchHHHHHHHhh
Q psy12028 62 MYACDVCGKVYQHKQTLDRHKKD 84 (118)
Q Consensus 62 ~~~c~~c~~~~~~~~~l~~h~~~ 84 (118)
.+-|..|.+.|.....|..|.+.
T Consensus 55 qhYCieCaryf~t~~aL~~Hkkg 77 (126)
T COG5112 55 QHYCIECARYFITEKALMEHKKG 77 (126)
T ss_pred eeeeehhHHHHHHHHHHHHHhcc
Confidence 36799999999999999888653
No 262
>PRK12387 formate hydrogenlyase complex iron-sulfur subunit; Provisional
Probab=34.98 E-value=26 Score=20.45 Aligned_cols=16 Identities=25% Similarity=0.914 Sum_probs=9.3
Q ss_pred ccCCCCCccccchHHH
Q psy12028 2 YACDVCGKEYQHKRTL 17 (118)
Q Consensus 2 ~~C~~C~~~~~~~~~l 17 (118)
+.|..||+.|.....+
T Consensus 115 ~~C~~CG~~f~~~~~i 130 (180)
T PRK12387 115 CNCRVCGRPFAVQKEI 130 (180)
T ss_pred ccchhhCCccccHHHH
Confidence 4566677766654433
No 263
>PF09332 Mcm10: Mcm10 replication factor; InterPro: IPR015411 Mcm10 is a eukaryotic DNA replication factor that regulates the stability and chromatin association of DNA polymerase alpha []. ; PDB: 2KWQ_A.
Probab=34.79 E-value=4.5 Score=26.38 Aligned_cols=12 Identities=33% Similarity=0.847 Sum_probs=4.5
Q ss_pred ccCCCCCccccc
Q psy12028 31 FGCPQCPYRSRQ 42 (118)
Q Consensus 31 ~~C~~c~~~f~~ 42 (118)
+.|..|.+.+..
T Consensus 253 v~C~~C~yt~~~ 264 (344)
T PF09332_consen 253 VTCKQCKYTAFK 264 (344)
T ss_dssp EEETTT--EESS
T ss_pred EEcCCCCCcccC
Confidence 444555444333
No 264
>PRK12860 transcriptional activator FlhC; Provisional
Probab=34.35 E-value=34 Score=20.44 Aligned_cols=29 Identities=17% Similarity=0.430 Sum_probs=17.6
Q ss_pred CCccCCCCCcccccchHHHHHhhhhhccCCcccccccCchh
Q psy12028 29 PKFGCPQCPYRSRQKATLNRHLGWEQLQGNAHVMYACDVCG 69 (118)
Q Consensus 29 ~~~~C~~c~~~f~~~~~l~~h~~~~~~~~~~~~~~~c~~c~ 69 (118)
....|..|+-.|..... . ....|.|+.|.
T Consensus 133 ~l~~C~~Cgg~fv~~~~-e-----------~~~~f~CplC~ 161 (189)
T PRK12860 133 QLARCCRCGGKFVTHAH-D-----------LRHNFVCGLCQ 161 (189)
T ss_pred eeccCCCCCCCeecccc-c-----------cCCCCcCCCCC
Confidence 45678888888775432 1 11337788776
No 265
>KOG3214|consensus
Probab=34.30 E-value=19 Score=19.03 Aligned_cols=13 Identities=23% Similarity=0.813 Sum_probs=8.8
Q ss_pred cccCchhhhhhch
Q psy12028 63 YACDVCGKVYQHK 75 (118)
Q Consensus 63 ~~c~~c~~~~~~~ 75 (118)
..|.+|+..|...
T Consensus 48 ~sC~iC~esFqt~ 60 (109)
T KOG3214|consen 48 ASCRICEESFQTT 60 (109)
T ss_pred eeeeehhhhhccc
Confidence 4677777777654
No 266
>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=34.16 E-value=24 Score=15.10 Aligned_cols=9 Identities=33% Similarity=1.250 Sum_probs=5.3
Q ss_pred ccCCCCCCC
Q psy12028 92 FECPHCPYR 100 (118)
Q Consensus 92 ~~C~~C~~~ 100 (118)
|.|+.||..
T Consensus 1 m~Cp~Cg~~ 9 (43)
T PF08271_consen 1 MKCPNCGSK 9 (43)
T ss_dssp ESBTTTSSS
T ss_pred CCCcCCcCC
Confidence 456666653
No 267
>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=34.12 E-value=22 Score=17.12 Aligned_cols=8 Identities=38% Similarity=1.435 Sum_probs=4.5
Q ss_pred ccCCCCCC
Q psy12028 92 FECPHCPY 99 (118)
Q Consensus 92 ~~C~~C~~ 99 (118)
|.|+.||-
T Consensus 1 y~C~KCg~ 8 (64)
T PF09855_consen 1 YKCPKCGN 8 (64)
T ss_pred CCCCCCCC
Confidence 45666653
No 268
>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=33.77 E-value=22 Score=15.10 Aligned_cols=14 Identities=36% Similarity=0.764 Sum_probs=10.6
Q ss_pred CCccCCCCCccccc
Q psy12028 29 PKFGCPQCPYRSRQ 42 (118)
Q Consensus 29 ~~~~C~~c~~~f~~ 42 (118)
..+.|+.||..+.+
T Consensus 31 p~~~C~~CGE~~~~ 44 (46)
T TIGR03831 31 PALVCPQCGEEYLD 44 (46)
T ss_pred CccccccCCCEeeC
Confidence 44789999987654
No 269
>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=33.65 E-value=24 Score=15.93 Aligned_cols=9 Identities=22% Similarity=0.445 Sum_probs=4.2
Q ss_pred CCCCCcccc
Q psy12028 33 CPQCPYRSR 41 (118)
Q Consensus 33 C~~c~~~f~ 41 (118)
|..|++.|.
T Consensus 5 C~~C~~~F~ 13 (57)
T cd00065 5 CMGCGKPFT 13 (57)
T ss_pred CcccCcccc
Confidence 444544444
No 270
>PRK06450 threonine synthase; Validated
Probab=33.44 E-value=30 Score=22.59 Aligned_cols=27 Identities=26% Similarity=0.461 Sum_probs=17.3
Q ss_pred ccCCCCCccccchHHHHhhhhhhcCCCCCccCCCCCccccc
Q psy12028 2 YACDVCGKEYQHKRTLYRHKKDECGQEPKFGCPQCPYRSRQ 42 (118)
Q Consensus 2 ~~C~~C~~~~~~~~~l~~h~~~~~~~~~~~~C~~c~~~f~~ 42 (118)
++|..||+.|.. ...+.|+.|+..+..
T Consensus 4 ~~C~~Cg~~~~~--------------~~~~~C~~cg~~l~~ 30 (338)
T PRK06450 4 EVCMKCGKERES--------------IYEIRCKKCGGPFEI 30 (338)
T ss_pred eEECCcCCcCCC--------------cccccCCcCCCEeEE
Confidence 578888887621 223688888755443
No 271
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=33.34 E-value=1e+02 Score=20.26 Aligned_cols=24 Identities=13% Similarity=0.267 Sum_probs=13.3
Q ss_pred CCccCCCCCCCCCChhHHHHHHhh
Q psy12028 90 PKFECPHCPYRSKRKDTLDRHMKI 113 (118)
Q Consensus 90 ~~~~C~~C~~~f~~~~~l~~H~~~ 113 (118)
..|.|+.|...|-..-+...|...
T Consensus 387 ~rY~Ce~CK~~FC~dCdvfiHe~L 410 (421)
T COG5151 387 GRYQCELCKSTFCSDCDVFIHETL 410 (421)
T ss_pred cceechhhhhhhhhhhHHHHHHHH
Confidence 346666666666555555555443
No 272
>PLN03238 probable histone acetyltransferase MYST; Provisional
Probab=32.89 E-value=43 Score=21.51 Aligned_cols=24 Identities=25% Similarity=0.501 Sum_probs=19.7
Q ss_pred CCCccCCCCCCCCCChhHHHHHHh
Q psy12028 89 EPKFECPHCPYRSKRKDTLDRHMK 112 (118)
Q Consensus 89 ~~~~~C~~C~~~f~~~~~l~~H~~ 112 (118)
..-|.|..|-+-|.....|.+|+.
T Consensus 46 ~~lyiCe~Clky~~~~~~l~~H~~ 69 (290)
T PLN03238 46 TKLYICEYCLKYMRKKKSLLRHLA 69 (290)
T ss_pred CeEEEcCCCcchhCCHHHHHHHHH
Confidence 567888888888888888888875
No 273
>TIGR02159 PA_CoA_Oxy4 phenylacetate-CoA oxygenase, PaaJ subunit. Phenylacetate-CoA oxygenase is comprised of a five gene complex responsible for the hydroxylation of phenylacetate-CoA (PA-CoA) as the second catabolic step in phenylacetic acid (PA) degradation. Although the exact function of this enzyme has not been determined, it has been shown to be required for phenylacetic acid degradation and has been proposed to function in a multicomponent oxygenase acting on phenylacetate-CoA.
Probab=32.66 E-value=12 Score=21.29 Aligned_cols=38 Identities=16% Similarity=0.489 Sum_probs=19.3
Q ss_pred CccCCCCCcccccchHHHHHhhhhhccCCcccccccCchhhhhhc
Q psy12028 30 KFGCPQCPYRSRQKATLNRHLGWEQLQGNAHVMYACDVCGKVYQH 74 (118)
Q Consensus 30 ~~~C~~c~~~f~~~~~l~~h~~~~~~~~~~~~~~~c~~c~~~~~~ 74 (118)
.-.||.||-......+.-.- +.+ +-.|.|..|...|..
T Consensus 105 ~~~cp~c~s~~t~~~s~fg~--t~c-----ka~~~c~~c~epf~~ 142 (146)
T TIGR02159 105 SVQCPRCGSADTTITSIFGP--TAC-----KALYRCRACKEPFEY 142 (146)
T ss_pred CCcCCCCCCCCcEeecCCCC--hhh-----HHHhhhhhhCCcHhh
Confidence 36788888654332210000 001 123778888877653
No 274
>COG1327 Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains [Transcription]
Probab=32.47 E-value=22 Score=20.34 Aligned_cols=16 Identities=25% Similarity=0.422 Sum_probs=11.8
Q ss_pred CCccCCCCCCCCCChh
Q psy12028 90 PKFECPHCPYRSKRKD 105 (118)
Q Consensus 90 ~~~~C~~C~~~f~~~~ 105 (118)
+.-.|+.||..|++..
T Consensus 27 RRReC~~C~~RFTTfE 42 (156)
T COG1327 27 RRRECLECGERFTTFE 42 (156)
T ss_pred hhhcccccccccchhh
Confidence 3457999999987753
No 275
>PF14690 zf-ISL3: zinc-finger of transposase IS204/IS1001/IS1096/IS1165
Probab=32.04 E-value=32 Score=14.80 Aligned_cols=10 Identities=40% Similarity=0.939 Sum_probs=7.2
Q ss_pred CccCCCCCCC
Q psy12028 91 KFECPHCPYR 100 (118)
Q Consensus 91 ~~~C~~C~~~ 100 (118)
|..|+.||..
T Consensus 2 ~~~Cp~Cg~~ 11 (47)
T PF14690_consen 2 PPRCPHCGSP 11 (47)
T ss_pred CccCCCcCCC
Confidence 5678888843
No 276
>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=31.73 E-value=18 Score=14.35 Aligned_cols=13 Identities=38% Similarity=0.933 Sum_probs=6.7
Q ss_pred CccCCCCCccccc
Q psy12028 30 KFGCPQCPYRSRQ 42 (118)
Q Consensus 30 ~~~C~~c~~~f~~ 42 (118)
.|.|+.|+..+=+
T Consensus 13 kY~Cp~C~~~~CS 25 (30)
T PF04438_consen 13 KYRCPRCGARYCS 25 (30)
T ss_dssp SEE-TTT--EESS
T ss_pred EEECCCcCCceeC
Confidence 4888888776543
No 277
>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=31.62 E-value=39 Score=13.16 Aligned_cols=9 Identities=33% Similarity=0.852 Sum_probs=4.9
Q ss_pred ccCCCCCCC
Q psy12028 92 FECPHCPYR 100 (118)
Q Consensus 92 ~~C~~C~~~ 100 (118)
|.|.+|++.
T Consensus 1 ~~C~~C~~~ 9 (30)
T PF03107_consen 1 FWCDVCRRK 9 (30)
T ss_pred CCCCCCCCC
Confidence 356666554
No 278
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=31.54 E-value=22 Score=14.48 Aligned_cols=8 Identities=25% Similarity=0.613 Sum_probs=3.4
Q ss_pred cCCCCCCC
Q psy12028 93 ECPHCPYR 100 (118)
Q Consensus 93 ~C~~C~~~ 100 (118)
.|..||..
T Consensus 23 ~C~~Cg~~ 30 (33)
T PF08792_consen 23 VCIFCGSS 30 (33)
T ss_pred EcccCCcE
Confidence 34444443
No 279
>COG2824 PhnA Uncharacterized Zn-ribbon-containing protein involved in phosphonate metabolism [Inorganic ion transport and metabolism]
Probab=31.51 E-value=16 Score=19.49 Aligned_cols=29 Identities=24% Similarity=0.671 Sum_probs=18.7
Q ss_pred cCCCCCccccchHHHHhhhhhhcCCCCCccCCCCCcccccc
Q psy12028 3 ACDVCGKEYQHKRTLYRHKKDECGQEPKFGCPQCPYRSRQK 43 (118)
Q Consensus 3 ~C~~C~~~~~~~~~l~~h~~~~~~~~~~~~C~~c~~~f~~~ 43 (118)
.|+.|+..|.... ...|.||.|...|...
T Consensus 5 ~cp~c~sEytYed------------~~~~~cpec~~ew~~~ 33 (112)
T COG2824 5 PCPKCNSEYTYED------------GGQLICPECAHEWNEN 33 (112)
T ss_pred CCCccCCceEEec------------CceEeCchhccccccc
Confidence 4667765553322 2368999999888743
No 280
>KOG1940|consensus
Probab=30.62 E-value=63 Score=20.65 Aligned_cols=18 Identities=22% Similarity=0.610 Sum_probs=10.9
Q ss_pred ccCCCCCcccccchHHHHH
Q psy12028 31 FGCPQCPYRSRQKATLNRH 49 (118)
Q Consensus 31 ~~C~~c~~~f~~~~~l~~h 49 (118)
|.||.|.+ -.....+-++
T Consensus 197 y~CP~C~~-~~d~~~~~~~ 214 (276)
T KOG1940|consen 197 YTCPICSK-PGDMSHYFRK 214 (276)
T ss_pred CCCCcccc-hHHHHHHHHH
Confidence 88888877 4444444433
No 281
>PRK05580 primosome assembly protein PriA; Validated
Probab=30.26 E-value=23 Score=25.51 Aligned_cols=12 Identities=25% Similarity=0.614 Sum_probs=7.7
Q ss_pred CCCccCCCCCcc
Q psy12028 28 EPKFGCPQCPYR 39 (118)
Q Consensus 28 ~~~~~C~~c~~~ 39 (118)
..+..||.|+..
T Consensus 419 ~~~~~Cp~Cg~~ 430 (679)
T PRK05580 419 PIPKACPECGST 430 (679)
T ss_pred CCCCCCCCCcCC
Confidence 346677877654
No 282
>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=29.59 E-value=15 Score=20.63 Aligned_cols=16 Identities=25% Similarity=0.478 Sum_probs=12.2
Q ss_pred CCCccCCCCCcccccc
Q psy12028 28 EPKFGCPQCPYRSRQK 43 (118)
Q Consensus 28 ~~~~~C~~c~~~f~~~ 43 (118)
.++.+|+.||..|.-.
T Consensus 110 g~~~RCpeCG~~fkL~ 125 (136)
T PF01215_consen 110 GKPQRCPECGQVFKLK 125 (136)
T ss_dssp TSEEEETTTEEEEEEE
T ss_pred CCccCCCCCCeEEEEE
Confidence 3578999999888643
No 283
>PF14375 Cys_rich_CWC: Cysteine-rich CWC
Probab=29.14 E-value=37 Score=15.20 Aligned_cols=6 Identities=33% Similarity=0.833 Sum_probs=2.4
Q ss_pred CCCCCC
Q psy12028 95 PHCPYR 100 (118)
Q Consensus 95 ~~C~~~ 100 (118)
+.||..
T Consensus 2 P~Cg~~ 7 (50)
T PF14375_consen 2 PRCGAP 7 (50)
T ss_pred CCCCCc
Confidence 334433
No 284
>KOG4317|consensus
Probab=29.13 E-value=21 Score=23.15 Aligned_cols=20 Identities=20% Similarity=0.565 Sum_probs=13.5
Q ss_pred CccCCCCCcccccchHHHHH
Q psy12028 30 KFGCPQCPYRSRQKATLNRH 49 (118)
Q Consensus 30 ~~~C~~c~~~f~~~~~l~~h 49 (118)
.|.||-|+..+-+..-++.|
T Consensus 19 ~YtCPRCn~~YCsl~CYr~h 38 (383)
T KOG4317|consen 19 EYTCPRCNLLYCSLKCYRNH 38 (383)
T ss_pred cccCCCCCccceeeeeecCC
Confidence 38888888777665555555
No 285
>KOG1701|consensus
Probab=29.10 E-value=10 Score=25.56 Aligned_cols=14 Identities=21% Similarity=0.520 Sum_probs=7.3
Q ss_pred CccCCCCCcccccc
Q psy12028 30 KFGCPQCPYRSRQK 43 (118)
Q Consensus 30 ~~~C~~c~~~f~~~ 43 (118)
-|.|..|++...-.
T Consensus 302 CFtC~~C~r~L~Gq 315 (468)
T KOG1701|consen 302 CFTCRTCRRQLAGQ 315 (468)
T ss_pred ceehHhhhhhhccc
Confidence 36666665544433
No 286
>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=28.81 E-value=21 Score=16.60 Aligned_cols=11 Identities=36% Similarity=0.905 Sum_probs=3.6
Q ss_pred CCccCCCCCCC
Q psy12028 90 PKFECPHCPYR 100 (118)
Q Consensus 90 ~~~~C~~C~~~ 100 (118)
+.|.|++||-+
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 45788888854
No 287
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=28.80 E-value=36 Score=21.65 Aligned_cols=13 Identities=31% Similarity=0.866 Sum_probs=8.6
Q ss_pred ccccCchhhhhhc
Q psy12028 62 MYACDVCGKVYQH 74 (118)
Q Consensus 62 ~~~c~~c~~~~~~ 74 (118)
.|.|+.||..+..
T Consensus 322 ~~~C~~cg~~~~r 334 (364)
T COG0675 322 LFKCPRCGFVHDR 334 (364)
T ss_pred eEECCCCCCeehh
Confidence 3788888865433
No 288
>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=28.67 E-value=12 Score=21.04 Aligned_cols=32 Identities=28% Similarity=0.860 Sum_probs=19.0
Q ss_pred cccccCchhhhhhchHHHHHHHhhhcCCCCCccCCCCCCCC
Q psy12028 61 VMYACDVCGKVYQHKQTLDRHKKDECGQEPKFECPHCPYRS 101 (118)
Q Consensus 61 ~~~~c~~c~~~~~~~~~l~~h~~~h~~~~~~~~C~~C~~~f 101 (118)
-.|.|..|+..+. ++.+. . ...|.|..|+-.+
T Consensus 122 ~~~~C~~C~~~~~------r~~~~--~-~~~~~C~~C~~~l 153 (157)
T PF10263_consen 122 YVYRCPSCGREYK------RHRRS--K-RKRYRCGRCGGPL 153 (157)
T ss_pred eEEEcCCCCCEee------eeccc--c-hhhEECCCCCCEE
Confidence 3467888886652 23333 1 3348888888654
No 289
>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=27.95 E-value=27 Score=24.19 Aligned_cols=10 Identities=40% Similarity=0.740 Sum_probs=6.4
Q ss_pred CCccCCCCCc
Q psy12028 29 PKFGCPQCPY 38 (118)
Q Consensus 29 ~~~~C~~c~~ 38 (118)
.+..||.|+.
T Consensus 252 ~~~~Cp~C~s 261 (505)
T TIGR00595 252 IPKTCPQCGS 261 (505)
T ss_pred CCCCCCCCCC
Confidence 4566777765
No 290
>PRK07591 threonine synthase; Validated
Probab=27.60 E-value=44 Score=22.60 Aligned_cols=28 Identities=25% Similarity=0.481 Sum_probs=16.7
Q ss_pred ccCCCCCccccchHHHHhhhhhhcCCCCCccCCCCCcccccc
Q psy12028 2 YACDVCGKEYQHKRTLYRHKKDECGQEPKFGCPQCPYRSRQK 43 (118)
Q Consensus 2 ~~C~~C~~~~~~~~~l~~h~~~~~~~~~~~~C~~c~~~f~~~ 43 (118)
++|..||..|.. ... +.|+.|+..+...
T Consensus 19 l~C~~Cg~~~~~-------------~~~-~~C~~cg~~l~~~ 46 (421)
T PRK07591 19 LKCRECGAEYPL-------------GPI-HVCEECFGPLEVA 46 (421)
T ss_pred EEeCCCCCcCCC-------------CCC-ccCCCCCCeEEEE
Confidence 457777776632 122 7788887554443
No 291
>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 PF10367 Vps39_2: Vacuolar sorting protein 39 domain 2; InterPro: IPR019453 This entry represents a domain found in the vacuolar sorting protein Vps39 and transforming growth factor beta receptor-associated protein Trap1. Vps39, a component of the C-Vps complex, is thought to be required for the fusion of endosomes and other types of transport intermediates with the vacuole [, ]. In Saccharomyces cerevisiae (Baker's yeast), Vps39 has been shown to stimulate nucleotide exchange []. Trap1 plays a role in the TGF-beta/activin signaling pathway. It associates with inactive heteromeric TGF-beta and activin receptor complexes, mainly through the type II receptor, and is released upon activation of signaling [, ]. The precise function of this domain has not been characterised In Vps39 this domain is involved in localisation and in mediating the interactions with Vps11 [].
Probab=26.45 E-value=41 Score=17.36 Aligned_cols=12 Identities=17% Similarity=0.360 Sum_probs=9.6
Q ss_pred ccCCCCCCCCCC
Q psy12028 92 FECPHCPYRSKR 103 (118)
Q Consensus 92 ~~C~~C~~~f~~ 103 (118)
-.|.+|++.+.+
T Consensus 79 ~~C~vC~k~l~~ 90 (109)
T PF10367_consen 79 TKCSVCGKPLGN 90 (109)
T ss_pred CCccCcCCcCCC
Confidence 459999998765
No 293
>COG3024 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=26.42 E-value=37 Score=16.34 Aligned_cols=9 Identities=44% Similarity=1.139 Sum_probs=5.3
Q ss_pred cCCCCCccc
Q psy12028 3 ACDVCGKEY 11 (118)
Q Consensus 3 ~C~~C~~~~ 11 (118)
+|+.||+..
T Consensus 9 ~CP~Cgkpv 17 (65)
T COG3024 9 PCPTCGKPV 17 (65)
T ss_pred cCCCCCCcc
Confidence 466666654
No 294
>PF14599 zinc_ribbon_6: Zinc-ribbon; PDB: 2K2D_A.
Probab=26.40 E-value=14 Score=17.61 Aligned_cols=15 Identities=20% Similarity=0.381 Sum_probs=6.7
Q ss_pred ccCCCCCcccccchH
Q psy12028 31 FGCPQCPYRSRQKAT 45 (118)
Q Consensus 31 ~~C~~c~~~f~~~~~ 45 (118)
..|..|+........
T Consensus 31 IlCNDC~~~s~v~fH 45 (61)
T PF14599_consen 31 ILCNDCNAKSEVPFH 45 (61)
T ss_dssp EEESSS--EEEEE--
T ss_pred EECCCCCCccceeee
Confidence 447777776655443
No 295
>PF14122 YokU: YokU-like protein
Probab=25.17 E-value=43 Score=17.20 Aligned_cols=15 Identities=33% Similarity=0.853 Sum_probs=9.4
Q ss_pred cCCCCCccccchHHH
Q psy12028 3 ACDVCGKEYQHKRTL 17 (118)
Q Consensus 3 ~C~~C~~~~~~~~~l 17 (118)
.|..||.+|.....+
T Consensus 37 ~C~~CgmvYq~d~vi 51 (87)
T PF14122_consen 37 ICSNCGMVYQDDEVI 51 (87)
T ss_pred eecCCCcEEehhHHH
Confidence 477777777655443
No 296
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=24.90 E-value=71 Score=23.19 Aligned_cols=9 Identities=33% Similarity=0.715 Sum_probs=5.8
Q ss_pred ccCCCCCcc
Q psy12028 2 YACDVCGKE 10 (118)
Q Consensus 2 ~~C~~C~~~ 10 (118)
..|+.||..
T Consensus 2 ~~Cp~Cg~~ 10 (645)
T PRK14559 2 LICPQCQFE 10 (645)
T ss_pred CcCCCCCCc
Confidence 357777764
No 297
>KOG4118|consensus
Probab=24.85 E-value=55 Score=15.83 Aligned_cols=25 Identities=20% Similarity=0.386 Sum_probs=15.5
Q ss_pred cccCchhhhhhchHHHHHHHhhhcC
Q psy12028 63 YACDVCGKVYQHKQTLDRHKKDECG 87 (118)
Q Consensus 63 ~~c~~c~~~~~~~~~l~~h~~~h~~ 87 (118)
+.|.+|......+..+..|...-+.
T Consensus 39 ~kCtVC~~~mpdpktfkqhfe~kHp 63 (74)
T KOG4118|consen 39 HKCTVCMVQMPDPKTFKQHFENKHP 63 (74)
T ss_pred hhhHhhHhhCCCCchHHHHHhhcCC
Confidence 5666776666666666666554443
No 298
>PF03833 PolC_DP2: DNA polymerase II large subunit DP2; InterPro: IPR016033 DP2 is the large subunit of a two-subunit novel archaebacterial replicative DNA polymerase first characterised for Pyrococcus furiosus. The structure of DP2 appears to be organised as a ~950 residue component separated from a ~300 residue component by a ~150 residue intein. The other subunit, DP1, has sequence similarity to the eukaryotic DNA polymerase delta small subunit. This entry represents the N-terminal ~950 residue component of DP2.; GO: 0003887 DNA-directed DNA polymerase activity; PDB: 3O59_X.
Probab=24.74 E-value=25 Score=26.18 Aligned_cols=9 Identities=33% Similarity=0.910 Sum_probs=0.0
Q ss_pred ccCCCCCcc
Q psy12028 31 FGCPQCPYR 39 (118)
Q Consensus 31 ~~C~~c~~~ 39 (118)
..|+.|+..
T Consensus 656 r~Cp~Cg~~ 664 (900)
T PF03833_consen 656 RRCPKCGKE 664 (900)
T ss_dssp ---------
T ss_pred ccCcccCCc
Confidence 566666654
No 299
>KOG3002|consensus
Probab=24.66 E-value=1.1e+02 Score=19.83 Aligned_cols=16 Identities=19% Similarity=0.416 Sum_probs=9.3
Q ss_pred CCCccCCCCCcccccc
Q psy12028 28 EPKFGCPQCPYRSRQK 43 (118)
Q Consensus 28 ~~~~~C~~c~~~f~~~ 43 (118)
+..-.||.|...+...
T Consensus 78 ~~~~~CP~Cr~~~g~~ 93 (299)
T KOG3002|consen 78 KVSNKCPTCRLPIGNI 93 (299)
T ss_pred hhcccCCccccccccH
Confidence 3445677776666543
No 300
>KOG3014|consensus
Probab=24.61 E-value=55 Score=20.56 Aligned_cols=23 Identities=26% Similarity=0.469 Sum_probs=18.0
Q ss_pred cCCCCCcccc--chHHHHhhhhhhc
Q psy12028 3 ACDVCGKEYQ--HKRTLYRHKKDEC 25 (118)
Q Consensus 3 ~C~~C~~~~~--~~~~l~~h~~~~~ 25 (118)
+|.+|++.|. +..+-..|.+-|+
T Consensus 39 ~C~~Cgm~Yt~~s~EDe~~H~~fH~ 63 (257)
T KOG3014|consen 39 KCKECGMKYTVTSPEDEALHEKFHN 63 (257)
T ss_pred ehhhcCceecCCCHHHHHHHHHHHH
Confidence 5999998875 5666778888886
No 301
>PF05129 Elf1: Transcription elongation factor Elf1 like; InterPro: IPR007808 This family of uncharacterised, mostly short, proteins contain a putative zinc binding domain with four conserved cysteines.; PDB: 1WII_A.
Probab=24.45 E-value=36 Score=17.18 Aligned_cols=40 Identities=25% Similarity=0.640 Sum_probs=14.7
Q ss_pred CCCccCCCCCcccccchHHHHHhhhhhccCCcccccccCchhhhhhch
Q psy12028 28 EPKFGCPQCPYRSRQKATLNRHLGWEQLQGNAHVMYACDVCGKVYQHK 75 (118)
Q Consensus 28 ~~~~~C~~c~~~f~~~~~l~~h~~~~~~~~~~~~~~~c~~c~~~~~~~ 75 (118)
...|.||.|+..-.-.-.+. ...+.....|..|+..|...
T Consensus 20 ~~~F~CPfC~~~~sV~v~id--------kk~~~~~~~C~~Cg~~~~~~ 59 (81)
T PF05129_consen 20 PKVFDCPFCNHEKSVSVKID--------KKEGIGILSCRVCGESFQTK 59 (81)
T ss_dssp SS----TTT--SS-EEEEEE--------TTTTEEEEEESSS--EEEEE
T ss_pred CceEcCCcCCCCCeEEEEEE--------ccCCEEEEEecCCCCeEEEc
Confidence 45699999983322211111 11122335788888777553
No 302
>KOG0402|consensus
Probab=24.25 E-value=26 Score=17.86 Aligned_cols=31 Identities=26% Similarity=0.658 Sum_probs=19.2
Q ss_pred CCccCCCCCcccccchHHHHHhhhhhccCCcccccccCchhhhhh
Q psy12028 29 PKFGCPQCPYRSRQKATLNRHLGWEQLQGNAHVMYACDVCGKVYQ 73 (118)
Q Consensus 29 ~~~~C~~c~~~f~~~~~l~~h~~~~~~~~~~~~~~~c~~c~~~~~ 73 (118)
-.|.|++||+.--.. - .-..|.|..|.+.+.
T Consensus 35 aky~CsfCGK~~vKR-----~---------AvGiW~C~~C~kv~a 65 (92)
T KOG0402|consen 35 AKYTCSFCGKKTVKR-----K---------AVGIWKCGSCKKVVA 65 (92)
T ss_pred hhhhhhhcchhhhhh-----h---------ceeEEecCCccceec
Confidence 359999999754321 1 113477887777654
No 303
>PRK03922 hypothetical protein; Provisional
Probab=24.13 E-value=45 Score=17.99 Aligned_cols=14 Identities=21% Similarity=0.354 Sum_probs=11.0
Q ss_pred CccCCCCCcccccc
Q psy12028 30 KFGCPQCPYRSRQK 43 (118)
Q Consensus 30 ~~~C~~c~~~f~~~ 43 (118)
...||.||..|...
T Consensus 49 ~~~cP~cge~~~~a 62 (113)
T PRK03922 49 LTICPKCGEPFDSA 62 (113)
T ss_pred cccCCCCCCcCCcE
Confidence 36899999988654
No 304
>PF02146 SIR2: Sir2 family; InterPro: IPR003000 These sequences represent the Sirtuin (Sir2-related) family of NAD+-dependent deacetylases. This family of enzymes is broadly conserved from bacteria to humans. In yeast, Sir2 proteins form complexes with other proteins to silence chromatin by accessing histones and deacetylating them. Sir2 proteins have been proposed to play a role in silencing, chromosome stability and ageing []. The bacterial enzyme CobB, an homologue of Sir2, is a phosphoribosyltransferase []. An in vitro ADP ribosyltransferase activity has also been associated with human members of this family []. Sir2-like enzymes employ NAD+ as a cosubstrate in deacetylation reactions [] and catalyse a reaction in which the cleavage of NAD(+)and histone and/or protein deacetylation are coupled to the formation of O-acetyl-ADP-ribose, a novel metabolite. The dependence of the reaction on both NAD(+) and the generation of this potential second messenger offers new clues to understanding the function and regulation of nuclear, cytoplasmic and mitochondrial Sir2-like enzymes []. Silent Information Regulator protein of Saccharomyces cerevisiae (Sir2) is one of several factors critical for silencing at least three loci. Among them, it is unique because it silences the rDNA as well as the mating type loci and telomeres []. Sir2 interacts in a complex with itself and with Sir3 and Sir4, two proteins that are able to interact with nucleosomes. In addition Sir2 also interacts with ubiquitination factors and/or complexes []. Homologues of Sir2 share a core domain including the GAG and NID motifs and a putative C4 Zinc finger. The regions containing these three conserved motifs are individually essential for Sir2 silencing function, as are the four cysteins []. In addition, the conserved residues HG next to the putative Zn finger have been shown to be essential for the ADP ribosyltransferase activity []. ; GO: 0008270 zinc ion binding, 0070403 NAD+ binding, 0006476 protein deacetylation; PDB: 1S5P_A 3PKI_E 3PKJ_F 3K35_A 1ICI_A 1M2K_A 1M2G_A 1M2N_B 1M2H_A 1M2J_A ....
Probab=23.76 E-value=63 Score=18.74 Aligned_cols=11 Identities=18% Similarity=0.618 Sum_probs=5.3
Q ss_pred ccCCCCCcccc
Q psy12028 31 FGCPQCPYRSR 41 (118)
Q Consensus 31 ~~C~~c~~~f~ 41 (118)
..|..|+..+.
T Consensus 106 ~~C~~C~~~~~ 116 (178)
T PF02146_consen 106 LRCSKCGKEYD 116 (178)
T ss_dssp EEETTTSBEEE
T ss_pred eeecCCCcccc
Confidence 44555555443
No 305
>COG3478 Predicted nucleic-acid-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=23.59 E-value=50 Score=15.96 Aligned_cols=8 Identities=50% Similarity=1.555 Sum_probs=4.9
Q ss_pred CccCCCCC
Q psy12028 91 KFECPHCP 98 (118)
Q Consensus 91 ~~~C~~C~ 98 (118)
.++|+.||
T Consensus 4 ~~kCpKCg 11 (68)
T COG3478 4 AFKCPKCG 11 (68)
T ss_pred cccCCCcC
Confidence 35566666
No 306
>PF01844 HNH: HNH endonuclease; InterPro: IPR002711 HNH endonuclease is found in bacteria and viruses [, , ]. This family includes pyocins, colicins and anaredoxins.; GO: 0003676 nucleic acid binding, 0004519 endonuclease activity; PDB: 2QGP_C.
Probab=23.54 E-value=18 Score=15.44 Aligned_cols=10 Identities=40% Similarity=0.956 Sum_probs=2.3
Q ss_pred CCCCCccccc
Q psy12028 4 CDVCGKEYQH 13 (118)
Q Consensus 4 C~~C~~~~~~ 13 (118)
|..|+..+..
T Consensus 1 C~~C~~~~~~ 10 (47)
T PF01844_consen 1 CQYCGKPGSD 10 (47)
T ss_dssp -TTT--B--G
T ss_pred CCCCCCcCcc
Confidence 3445544433
No 307
>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=23.37 E-value=29 Score=16.61 Aligned_cols=15 Identities=27% Similarity=0.563 Sum_probs=12.3
Q ss_pred CCCccCCCCCccccc
Q psy12028 28 EPKFGCPQCPYRSRQ 42 (118)
Q Consensus 28 ~~~~~C~~c~~~f~~ 42 (118)
+....|+.|+..|..
T Consensus 51 eg~L~Cp~c~r~YPI 65 (68)
T PF03966_consen 51 EGELICPECGREYPI 65 (68)
T ss_dssp TTEEEETTTTEEEEE
T ss_pred CCEEEcCCCCCEEeC
Confidence 567899999998864
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=23.08 E-value=54 Score=19.43 Aligned_cols=26 Identities=19% Similarity=0.259 Sum_probs=11.3
Q ss_pred cccccCc----hhhhhhchHHHHHHHhhhcC
Q psy12028 61 VMYACDV----CGKVYQHKQTLDRHKKDECG 87 (118)
Q Consensus 61 ~~~~c~~----c~~~~~~~~~l~~h~~~h~~ 87 (118)
+|+.|+. |+-.- ....|..|....|.
T Consensus 43 ~p~~CP~~~~~C~~~G-~~~~l~~Hl~~~H~ 72 (198)
T PF03145_consen 43 RPCSCPFPGSGCDWQG-SYKELLDHLRDKHS 72 (198)
T ss_dssp SEEE-SSSSTT---EE-ECCCHHHHHHHHTT
T ss_pred cCCcCCCCCCCccccC-CHHHHHHHHHHHCC
Confidence 4566665 43222 22355666665554
No 309
>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=23.06 E-value=1.1e+02 Score=17.63 Aligned_cols=34 Identities=18% Similarity=0.382 Sum_probs=20.7
Q ss_pred ccchHHHHhhhhhhcCCCCCccCCCCCcccccchHHHHH
Q psy12028 11 YQHKRTLYRHKKDECGQEPKFGCPQCPYRSRQKATLNRH 49 (118)
Q Consensus 11 ~~~~~~l~~h~~~~~~~~~~~~C~~c~~~f~~~~~l~~h 49 (118)
|.+...+..... .....||+||-.-..+..+..+
T Consensus 18 F~ss~~fd~Q~~-----~glv~CP~Cgs~~V~K~lmAP~ 51 (148)
T PF06676_consen 18 FRSSAAFDRQQA-----RGLVSCPVCGSTEVSKALMAPA 51 (148)
T ss_pred cCCHHHHHHHHH-----cCCccCCCCCCCeEeeecCCCe
Confidence 445555554432 4578999999776555444333
No 310
>KOG0801|consensus
Probab=23.06 E-value=28 Score=20.26 Aligned_cols=12 Identities=25% Similarity=0.631 Sum_probs=9.1
Q ss_pred ccCCCCCccccc
Q psy12028 31 FGCPQCPYRSRQ 42 (118)
Q Consensus 31 ~~C~~c~~~f~~ 42 (118)
++||+|.+....
T Consensus 139 ~KCPvC~K~V~s 150 (205)
T KOG0801|consen 139 MKCPVCHKVVPS 150 (205)
T ss_pred ccCCccccccCC
Confidence 889999876554
No 311
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=22.89 E-value=33 Score=12.90 Aligned_cols=8 Identities=50% Similarity=1.148 Sum_probs=5.0
Q ss_pred cCCCCCcc
Q psy12028 3 ACDVCGKE 10 (118)
Q Consensus 3 ~C~~C~~~ 10 (118)
.|+.||..
T Consensus 4 ~Cp~Cg~~ 11 (26)
T PF13248_consen 4 FCPNCGAE 11 (26)
T ss_pred CCcccCCc
Confidence 46777763
No 312
>KOG2906|consensus
Probab=22.83 E-value=11 Score=19.73 Aligned_cols=38 Identities=18% Similarity=0.425 Sum_probs=18.6
Q ss_pred ccCCCCCcccccchHHHHHhhhhhccCCcccccccCchhhhh
Q psy12028 31 FGCPQCPYRSRQKATLNRHLGWEQLQGNAHVMYACDVCGKVY 72 (118)
Q Consensus 31 ~~C~~c~~~f~~~~~l~~h~~~~~~~~~~~~~~~c~~c~~~~ 72 (118)
-.||.||-.-.....|+.- .-......-|.|-.|+..+
T Consensus 66 ~~Cp~Cgh~rayF~qlQtR----SADEPmT~FYkC~~C~~~W 103 (105)
T KOG2906|consen 66 ATCPTCGHERAYFMQLQTR----SADEPMTTFYKCCKCKHRW 103 (105)
T ss_pred CcCCCCCCCceEEEEeeec----cCCCcHhHhhhhhcccccc
Confidence 5688887654443333322 1122223346776676543
No 313
>PF03380 DUF282: Caenorhabditis protein of unknown function, DUF282; InterPro: IPR005044 This family consists of proteins of unknown function found in Caenorhabditis species.
Probab=22.80 E-value=54 Score=14.07 Aligned_cols=9 Identities=56% Similarity=1.350 Sum_probs=4.6
Q ss_pred CCCCCcccc
Q psy12028 4 CDVCGKEYQ 12 (118)
Q Consensus 4 C~~C~~~~~ 12 (118)
|..|.+++.
T Consensus 2 Cs~C~~iYd 10 (39)
T PF03380_consen 2 CSVCSKIYD 10 (39)
T ss_pred CcccccccC
Confidence 555555543
No 314
>TIGR00627 tfb4 transcription factor tfb4. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=22.69 E-value=60 Score=20.77 Aligned_cols=8 Identities=25% Similarity=0.679 Sum_probs=3.8
Q ss_pred cCCCCCCC
Q psy12028 93 ECPHCPYR 100 (118)
Q Consensus 93 ~C~~C~~~ 100 (118)
.|+.||-.
T Consensus 271 ~C~~Cgt~ 278 (279)
T TIGR00627 271 ICKTCKTA 278 (279)
T ss_pred CCCCCCCC
Confidence 45555433
No 315
>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=22.58 E-value=33 Score=16.10 Aligned_cols=12 Identities=25% Similarity=0.551 Sum_probs=5.8
Q ss_pred ccCCCCCccccc
Q psy12028 31 FGCPQCPYRSRQ 42 (118)
Q Consensus 31 ~~C~~c~~~f~~ 42 (118)
..||.|++.+..
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 468889887755
No 316
>PLN03239 histone acetyltransferase; Provisional
Probab=22.33 E-value=58 Score=21.58 Aligned_cols=24 Identities=21% Similarity=0.145 Sum_probs=21.0
Q ss_pred CCCccCCCCCCCCCChhHHHHHHh
Q psy12028 89 EPKFECPHCPYRSKRKDTLDRHMK 112 (118)
Q Consensus 89 ~~~~~C~~C~~~f~~~~~l~~H~~ 112 (118)
...|.|..|-+-|.....|.+|+.
T Consensus 104 ~~lYiCE~Clky~~~~~~l~~H~~ 127 (351)
T PLN03239 104 DVLYVCEFSFGFFARKSELLRFQA 127 (351)
T ss_pred ceEEEeccchhhhcCHHHHHHHHH
Confidence 467999999999999999999875
No 317
>PF06220 zf-U1: U1 zinc finger; InterPro: IPR013085 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. C2H2-type (classical) zinc fingers (Znf) were the first class to be characterised. They contain a short beta hairpin and an alpha helix (beta/beta/alpha structure), where a single zinc atom is held in place by Cys(2)His(2) (C2H2) residues in a tetrahedral array. C2H2 Znf's can be divided into three groups based on the number and pattern of fingers: triple-C2H2 (binds single ligand), multiple-adjacent-C2H2 (binds multiple ligands), and separated paired-C2H2 []. C2H2 Znf's are the most common DNA-binding motifs found in eukaryotic transcription factors, and have also been identified in prokaryotes []. Transcription factors usually contain several Znf's (each with a conserved beta/beta/alpha structure) capable of making multiple contacts along the DNA, where the C2H2 Znf motifs recognise DNA sequences by binding to the major groove of DNA via a short alpha-helix in the Znf, the Znf spanning 3-4 bases of the DNA []. C2H2 Znf's can also bind to RNA and protein targets []. This entry represents a C2H2-type zinc finger motif found in several U1 small nuclear ribonucleoprotein C (U1-C) proteins. Some proteins contain multiple copies of this motif. The U1 small nuclear ribonucleoprotein (U1 snRNP) binds to the pre-mRNA 5' splice site at early stages of spliceosome assembly. Recruitment of U1 to a class of weak 5' splice site is promoted by binding of the protein TIA-1 to uridine-rich sequences immediately downstream from the 5' splice site. Binding of TIA-1 in the vicinity of a 5' splice site helps to stabilise U1 snRNP recruitment, at least in part, via a direct interaction with U1-C, thus providing one molecular mechanism for the function of this splicing regulator []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2VRD_A.
Probab=22.11 E-value=84 Score=13.20 Aligned_cols=10 Identities=20% Similarity=0.530 Sum_probs=2.9
Q ss_pred ccCCCCCCCC
Q psy12028 92 FECPHCPYRS 101 (118)
Q Consensus 92 ~~C~~C~~~f 101 (118)
|=|..|+.-+
T Consensus 4 yyCdyC~~~~ 13 (38)
T PF06220_consen 4 YYCDYCKKYL 13 (38)
T ss_dssp -B-TTT--B-
T ss_pred eeccccccee
Confidence 4456666555
No 318
>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=22.01 E-value=51 Score=17.36 Aligned_cols=12 Identities=25% Similarity=0.634 Sum_probs=3.1
Q ss_pred CccCCCCCcccc
Q psy12028 30 KFGCPQCPYRSR 41 (118)
Q Consensus 30 ~~~C~~c~~~f~ 41 (118)
.-.|..|+.++.
T Consensus 14 e~~CalCG~tWg 25 (105)
T PF11494_consen 14 EMGCALCGATWG 25 (105)
T ss_dssp GGS-SS---S--
T ss_pred cccccccCCcHH
Confidence 345555655554
No 319
>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=21.85 E-value=30 Score=15.82 Aligned_cols=14 Identities=21% Similarity=0.377 Sum_probs=8.5
Q ss_pred CCCccCCCCCCCCC
Q psy12028 89 EPKFECPHCPYRSK 102 (118)
Q Consensus 89 ~~~~~C~~C~~~f~ 102 (118)
...|+|.+|++.+.
T Consensus 33 ~~~~rC~YCe~~~~ 46 (52)
T PF02748_consen 33 PIKLRCHYCERIIT 46 (52)
T ss_dssp TCEEEETTT--EEE
T ss_pred CCEEEeeCCCCEec
Confidence 55688888887664
No 320
>PF12230 PRP21_like_P: Pre-mRNA splicing factor PRP21 like protein; InterPro: IPR022030 This domain family is found in eukaryotes, and is typically between 212 and 238 amino acids in length. The family is found in association with PF01805 from PFAM. There are two completely conserved residues (W and H) that may be functionally important. PRP21 is required for assembly of the prespliceosome and it interacts with U2 snRNP and/or pre-mRNA in the prespliceosome. This family also contains proteins similar to PRP21, such as the mammalian SF3a. SF3a also interacts with U2 snRNP from the prespliceosome, converting it to its active form. ; PDB: 4DGW_B.
Probab=21.60 E-value=31 Score=21.06 Aligned_cols=26 Identities=31% Similarity=0.413 Sum_probs=0.0
Q ss_pred CCCccCCCCCCCCCChhHHHHHHhhhc
Q psy12028 89 EPKFECPHCPYRSKRKDTLDRHMKIIH 115 (118)
Q Consensus 89 ~~~~~C~~C~~~f~~~~~l~~H~~~~~ 115 (118)
..-..|++||... -.+.|..||++..
T Consensus 166 ~~~~~cPitGe~I-P~~e~~eHmRi~L 191 (229)
T PF12230_consen 166 EKMIICPITGEMI-PADEMDEHMRIEL 191 (229)
T ss_dssp ---------------------------
T ss_pred ccccccccccccc-ccccccccccccc
Confidence 4557899999764 5677889988753
No 321
>PTZ00303 phosphatidylinositol kinase; Provisional
Probab=21.56 E-value=12 Score=27.64 Aligned_cols=13 Identities=23% Similarity=0.401 Sum_probs=9.3
Q ss_pred ccCCCCCcccccc
Q psy12028 31 FGCPQCPYRSRQK 43 (118)
Q Consensus 31 ~~C~~c~~~f~~~ 43 (118)
-.|..|++.|...
T Consensus 461 dtC~~C~kkFfSl 473 (1374)
T PTZ00303 461 DSCPSCGRAFISL 473 (1374)
T ss_pred CcccCcCCccccc
Confidence 4588888888653
No 322
>PF10058 DUF2296: Predicted integral membrane metal-binding protein (DUF2296); InterPro: IPR019273 This domain, found mainly in the eukaryotic lunapark proteins, has no known function [].
Probab=21.38 E-value=46 Score=15.35 Aligned_cols=11 Identities=36% Similarity=0.987 Sum_probs=6.8
Q ss_pred CCCccCCCCCC
Q psy12028 89 EPKFECPHCPY 99 (118)
Q Consensus 89 ~~~~~C~~C~~ 99 (118)
...|.|+.||.
T Consensus 42 ~i~y~C~~Cg~ 52 (54)
T PF10058_consen 42 EIQYRCPYCGA 52 (54)
T ss_pred ceEEEcCCCCC
Confidence 34577777763
No 323
>PF06170 DUF983: Protein of unknown function (DUF983); InterPro: IPR009325 This family consists of several bacterial proteins of unknown function.
Probab=21.30 E-value=54 Score=16.79 Aligned_cols=11 Identities=36% Similarity=1.026 Sum_probs=7.5
Q ss_pred cCCCCCCCCCC
Q psy12028 93 ECPHCPYRSKR 103 (118)
Q Consensus 93 ~C~~C~~~f~~ 103 (118)
.|+.||-.|..
T Consensus 10 ~C~~CG~d~~~ 20 (86)
T PF06170_consen 10 RCPHCGLDYSH 20 (86)
T ss_pred cccccCCcccc
Confidence 58888866543
No 324
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=21.09 E-value=37 Score=20.48 Aligned_cols=13 Identities=31% Similarity=1.071 Sum_probs=7.0
Q ss_pred CccCCCCCccccc
Q psy12028 1 MYACDVCGKEYQH 13 (118)
Q Consensus 1 ~~~C~~C~~~~~~ 13 (118)
||.|.+|.+.|.+
T Consensus 196 PF~C~iCKkdy~s 208 (259)
T COG5152 196 PFLCGICKKDYES 208 (259)
T ss_pred ceeehhchhhccc
Confidence 4556555555533
No 325
>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=21.08 E-value=81 Score=16.89 Aligned_cols=17 Identities=24% Similarity=0.589 Sum_probs=10.1
Q ss_pred ccCCCCCccccchHHHH
Q psy12028 2 YACDVCGKEYQHKRTLY 18 (118)
Q Consensus 2 ~~C~~C~~~~~~~~~l~ 18 (118)
+.|+.||..+.+.....
T Consensus 32 ~~C~~CGe~~~~~e~~~ 48 (127)
T TIGR03830 32 WYCPACGEELLDPEESK 48 (127)
T ss_pred eECCCCCCEEEcHHHHH
Confidence 35677776666555444
No 326
>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=20.80 E-value=73 Score=18.61 Aligned_cols=21 Identities=29% Similarity=0.828 Sum_probs=17.0
Q ss_pred ccCCCCCcccccchHHHHHhh
Q psy12028 31 FGCPQCPYRSRQKATLNRHLG 51 (118)
Q Consensus 31 ~~C~~c~~~f~~~~~l~~h~~ 51 (118)
|.|.+|.........+..|+.
T Consensus 1 F~Cs~CKfrtf~~~ei~~Hle 21 (165)
T PF04988_consen 1 FTCSFCKFRTFEEKEIEKHLE 21 (165)
T ss_pred CccceeeeecccHHHHHHHHc
Confidence 578889887777788888876
No 327
>PF13696 zf-CCHC_2: Zinc knuckle
Probab=20.73 E-value=45 Score=13.59 Aligned_cols=10 Identities=20% Similarity=0.800 Sum_probs=7.4
Q ss_pred CccCCCCCCC
Q psy12028 91 KFECPHCPYR 100 (118)
Q Consensus 91 ~~~C~~C~~~ 100 (118)
.|.|..|+..
T Consensus 8 ~Y~C~~C~~~ 17 (32)
T PF13696_consen 8 GYVCHRCGQK 17 (32)
T ss_pred CCEeecCCCC
Confidence 4788888764
No 328
>PLN00104 MYST -like histone acetyltransferase; Provisional
Probab=20.66 E-value=63 Score=22.28 Aligned_cols=24 Identities=42% Similarity=0.681 Sum_probs=21.3
Q ss_pred CCCccCCCCCCCCCChhHHHHHHh
Q psy12028 89 EPKFECPHCPYRSKRKDTLDRHMK 112 (118)
Q Consensus 89 ~~~~~C~~C~~~f~~~~~l~~H~~ 112 (118)
...|.|..|-+-|.....|.+|+.
T Consensus 196 ~~lyiCe~Cl~y~~~~~~~~~H~~ 219 (450)
T PLN00104 196 SKLYFCEFCLKFMKRKEQLQRHMK 219 (450)
T ss_pred CeEEEchhhhhhhcCHHHHHHHHh
Confidence 557999999999999999999985
No 329
>COG1066 Sms Predicted ATP-dependent serine protease [Posttranslational modification, protein turnover, chaperones]
Probab=20.66 E-value=46 Score=22.76 Aligned_cols=10 Identities=50% Similarity=1.152 Sum_probs=5.3
Q ss_pred ccCCCCCccc
Q psy12028 31 FGCPQCPYRS 40 (118)
Q Consensus 31 ~~C~~c~~~f 40 (118)
|.|..||..+
T Consensus 8 f~C~~CG~~s 17 (456)
T COG1066 8 FVCQECGYVS 17 (456)
T ss_pred EEcccCCCCC
Confidence 5555555444
No 330
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=20.61 E-value=74 Score=14.45 Aligned_cols=11 Identities=27% Similarity=0.760 Sum_probs=5.8
Q ss_pred cccCchhhhhh
Q psy12028 63 YACDVCGKVYQ 73 (118)
Q Consensus 63 ~~c~~c~~~~~ 73 (118)
..|+.|+..|-
T Consensus 41 v~C~~C~~~fC 51 (64)
T smart00647 41 VTCPKCGFSFC 51 (64)
T ss_pred eECCCCCCeEC
Confidence 45655555543
No 331
>TIGR03655 anti_R_Lar restriction alleviation protein, Lar family. Restriction alleviation proteins provide a countermeasure to host cell restriction enzyme defense against foreign DNA such as phage or plasmids. This family consists of homologs to the phage antirestriction protein Lar, and most members belong to phage genomes or prophage regions of bacterial genomes.
Probab=20.51 E-value=52 Score=14.85 Aligned_cols=8 Identities=38% Similarity=0.841 Sum_probs=4.9
Q ss_pred cCCCCCcc
Q psy12028 32 GCPQCPYR 39 (118)
Q Consensus 32 ~C~~c~~~ 39 (118)
.||+||..
T Consensus 3 PCPfCGg~ 10 (53)
T TIGR03655 3 PCPFCGGA 10 (53)
T ss_pred CCCCCCCc
Confidence 46777653
No 332
>PTZ00064 histone acetyltransferase; Provisional
Probab=20.03 E-value=76 Score=22.33 Aligned_cols=24 Identities=25% Similarity=0.272 Sum_probs=21.5
Q ss_pred CCCccCCCCCCCCCChhHHHHHHh
Q psy12028 89 EPKFECPHCPYRSKRKDTLDRHMK 112 (118)
Q Consensus 89 ~~~~~C~~C~~~f~~~~~l~~H~~ 112 (118)
...|.|..|-+-|.....|.+|+.
T Consensus 278 d~LYICEfCLkY~~s~~~l~rH~~ 301 (552)
T PTZ00064 278 DTLHFCEYCLDFFCFEDELIRHLS 301 (552)
T ss_pred CeEEEccchhhhhCCHHHHHHHHh
Confidence 557999999999999999999975
Done!