Query psy9695
Match_columns 159
No_of_seqs 120 out of 1154
Neff 11.0
Searched_HMMs 46136
Date Fri Aug 16 17:15:33 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy9695.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/9695hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2462|consensus 100.0 4.1E-32 8.8E-37 179.1 2.2 133 13-157 125-260 (279)
2 KOG2462|consensus 99.9 1.3E-23 2.8E-28 139.1 3.5 105 44-157 128-232 (279)
3 KOG1074|consensus 99.8 5.5E-20 1.2E-24 137.1 5.1 77 78-157 606-685 (958)
4 KOG1074|consensus 99.7 3.8E-18 8.3E-23 127.5 1.6 45 106-157 880-924 (958)
5 KOG3576|consensus 99.7 1.2E-18 2.6E-23 110.8 -3.0 104 44-150 115-222 (267)
6 KOG3608|consensus 99.7 3.7E-18 8E-23 116.8 -1.4 146 4-156 193-368 (467)
7 KOG3608|consensus 99.6 1.8E-16 3.9E-21 108.7 2.9 132 17-153 262-399 (467)
8 KOG3623|consensus 99.6 1.9E-16 4.2E-21 117.2 1.9 112 16-127 208-331 (1007)
9 KOG3576|consensus 99.6 1.3E-16 2.9E-21 101.6 0.4 119 9-130 108-237 (267)
10 KOG3623|consensus 99.6 2.6E-16 5.7E-21 116.5 1.0 76 72-154 889-964 (1007)
11 PHA00733 hypothetical protein 99.3 5.6E-13 1.2E-17 81.4 1.4 97 32-130 26-124 (128)
12 PHA02768 hypothetical protein; 99.2 2E-11 4.4E-16 62.3 3.0 46 77-124 5-50 (55)
13 PLN03086 PRLI-interacting fact 99.1 7.3E-11 1.6E-15 87.5 5.2 92 47-154 454-555 (567)
14 PLN03086 PRLI-interacting fact 99.1 1.6E-11 3.5E-16 90.9 0.8 62 78-151 454-515 (567)
15 PHA02768 hypothetical protein; 99.0 2.8E-11 6E-16 61.8 -0.8 43 105-156 5-47 (55)
16 PHA00733 hypothetical protein 99.0 2E-11 4.4E-16 74.6 -2.0 76 73-157 36-116 (128)
17 PF13465 zf-H2C2_2: Zinc-finge 99.0 3.2E-10 7E-15 49.7 1.8 26 92-117 1-26 (26)
18 PHA00616 hypothetical protein 98.5 4.9E-08 1.1E-12 47.6 1.6 34 77-110 1-34 (44)
19 KOG3993|consensus 98.5 9.4E-08 2E-12 67.9 3.6 77 75-158 354-476 (500)
20 PHA00616 hypothetical protein 98.5 6.7E-08 1.4E-12 47.1 1.8 34 18-51 1-34 (44)
21 PHA00732 hypothetical protein 98.5 1.2E-07 2.7E-12 52.9 2.8 47 77-130 1-48 (79)
22 PF13465 zf-H2C2_2: Zinc-finge 98.4 1.8E-07 4E-12 40.8 2.3 25 33-57 1-25 (26)
23 PHA00732 hypothetical protein 98.3 7.5E-08 1.6E-12 53.7 -0.6 39 105-153 1-40 (79)
24 KOG3993|consensus 98.3 5.2E-08 1.1E-12 69.2 -1.9 81 47-131 268-381 (500)
25 COG5189 SFP1 Putative transcri 98.1 1.2E-06 2.5E-11 60.4 1.7 55 103-157 347-415 (423)
26 PF05605 zf-Di19: Drought indu 98.1 2.8E-06 6E-11 44.1 2.3 49 77-128 2-52 (54)
27 PF00096 zf-C2H2: Zinc finger, 97.9 8.8E-06 1.9E-10 34.3 1.5 22 78-99 1-22 (23)
28 COG5189 SFP1 Putative transcri 97.8 1.3E-05 2.8E-10 55.4 2.4 53 75-127 347-420 (423)
29 PF00096 zf-C2H2: Zinc finger, 97.8 1.5E-05 3.4E-10 33.5 1.7 23 19-41 1-23 (23)
30 PF05605 zf-Di19: Drought indu 97.7 5.9E-06 1.3E-10 42.8 -0.1 41 105-151 2-42 (54)
31 PF13912 zf-C2H2_6: C2H2-type 97.7 3.1E-06 6.8E-11 37.3 -1.5 22 78-99 2-23 (27)
32 PF09237 GAGA: GAGA factor; I 97.6 9.5E-05 2E-09 37.0 3.2 42 5-46 11-52 (54)
33 PF13894 zf-C2H2_4: C2H2-type 97.5 9.2E-05 2E-09 31.2 2.0 23 19-41 1-23 (24)
34 PF13912 zf-C2H2_6: C2H2-type 97.5 6.1E-05 1.3E-09 33.0 1.4 26 105-131 1-26 (27)
35 PF13894 zf-C2H2_4: C2H2-type 97.5 0.0001 2.2E-09 31.1 1.9 23 78-100 1-23 (24)
36 PF12756 zf-C2H2_2: C2H2 type 97.4 2.3E-05 5E-10 45.8 -0.8 76 48-131 1-76 (100)
37 PRK04860 hypothetical protein; 97.3 0.00014 3.1E-09 46.2 2.2 39 77-119 119-157 (160)
38 PF12756 zf-C2H2_2: C2H2 type 97.1 0.00041 8.9E-09 40.4 2.5 74 20-101 1-74 (100)
39 PF09237 GAGA: GAGA factor; I 97.0 0.001 2.2E-08 33.3 2.6 34 72-105 19-52 (54)
40 smart00355 ZnF_C2H2 zinc finge 96.9 0.0011 2.4E-08 28.2 2.5 22 79-100 2-23 (26)
41 PRK04860 hypothetical protein; 96.9 0.00016 3.5E-09 46.0 -0.6 40 105-155 119-158 (160)
42 smart00355 ZnF_C2H2 zinc finge 96.9 0.0011 2.4E-08 28.1 2.3 24 19-42 1-24 (26)
43 PF12171 zf-C2H2_jaz: Zinc-fin 96.5 0.00047 1E-08 30.1 -0.5 20 106-125 2-21 (27)
44 PF12874 zf-met: Zinc-finger o 96.2 0.0032 6.9E-08 26.8 1.3 22 19-40 1-22 (25)
45 PF13909 zf-H2C2_5: C2H2-type 96.2 0.0047 1E-07 26.0 1.7 23 19-42 1-23 (24)
46 PF13909 zf-H2C2_5: C2H2-type 95.9 0.0063 1.4E-07 25.6 1.6 22 78-100 1-22 (24)
47 PF12874 zf-met: Zinc-finger o 95.9 0.0043 9.2E-08 26.4 0.9 20 79-98 2-21 (25)
48 COG4049 Uncharacterized protei 95.6 0.008 1.7E-07 30.7 1.4 37 5-41 4-40 (65)
49 cd00350 rubredoxin_like Rubred 95.5 0.0081 1.8E-07 27.6 1.1 10 104-113 16-25 (33)
50 KOG1146|consensus 95.1 0.029 6.2E-07 46.5 3.9 128 15-154 462-632 (1406)
51 KOG2231|consensus 95.1 0.012 2.5E-07 45.6 1.6 45 78-126 183-233 (669)
52 PHA00626 hypothetical protein 94.7 0.012 2.6E-07 30.0 0.5 15 104-118 22-36 (59)
53 TIGR00622 ssl1 transcription f 94.3 0.044 9.4E-07 32.7 2.4 45 79-125 57-101 (112)
54 PF13913 zf-C2HC_2: zinc-finge 94.3 0.052 1.1E-06 23.1 2.0 20 19-39 3-22 (25)
55 KOG2893|consensus 93.9 0.043 9.4E-07 37.0 2.0 48 79-130 12-59 (341)
56 PF09986 DUF2225: Uncharacteri 93.4 0.033 7.1E-07 37.5 0.7 50 104-153 4-61 (214)
57 COG4049 Uncharacterized protei 93.4 0.011 2.3E-07 30.2 -1.2 29 102-130 14-42 (65)
58 smart00451 ZnF_U1 U1-like zinc 92.7 0.11 2.3E-06 23.8 1.8 22 18-39 3-24 (35)
59 PF09986 DUF2225: Uncharacteri 92.6 0.1 2.2E-06 35.2 2.2 10 78-87 49-58 (214)
60 COG5048 FOG: Zn-finger [Genera 92.4 0.062 1.3E-06 39.5 1.2 56 76-132 288-349 (467)
61 cd00729 rubredoxin_SM Rubredox 92.0 0.088 1.9E-06 24.3 1.0 10 78-87 3-12 (34)
62 KOG2186|consensus 92.0 0.069 1.5E-06 36.3 0.9 45 78-125 4-48 (276)
63 PF09723 Zn-ribbon_8: Zinc rib 92.0 0.055 1.2E-06 26.3 0.3 12 78-89 6-17 (42)
64 PRK14890 putative Zn-ribbon RN 91.8 0.054 1.2E-06 28.2 0.2 32 77-113 25-56 (59)
65 COG5048 FOG: Zn-finger [Genera 91.4 0.14 3.1E-06 37.6 2.1 121 17-147 288-453 (467)
66 smart00834 CxxC_CXXC_SSSS Puta 90.9 0.093 2E-06 25.1 0.5 11 78-88 6-16 (41)
67 KOG2893|consensus 90.9 0.054 1.2E-06 36.6 -0.5 42 103-156 9-50 (341)
68 KOG2482|consensus 90.2 0.33 7.3E-06 34.7 2.8 109 18-126 195-355 (423)
69 PF13719 zinc_ribbon_5: zinc-r 90.1 0.23 5.1E-06 23.3 1.5 32 79-115 4-35 (37)
70 TIGR02098 MJ0042_CXXC MJ0042 f 90.1 0.2 4.3E-06 23.6 1.2 13 78-90 3-15 (38)
71 TIGR00622 ssl1 transcription f 89.6 1.3 2.7E-05 26.6 4.5 86 16-112 13-110 (112)
72 PRK00398 rpoP DNA-directed RNA 89.5 0.12 2.5E-06 25.6 0.2 30 77-116 3-32 (46)
73 COG2888 Predicted Zn-ribbon RN 88.9 0.13 2.7E-06 26.8 0.0 32 77-113 27-58 (61)
74 PF13717 zinc_ribbon_4: zinc-r 88.9 0.32 7E-06 22.7 1.4 32 79-115 4-35 (36)
75 TIGR02605 CxxC_CxxC_SSSS putat 88.8 0.17 3.6E-06 25.7 0.4 29 78-113 6-34 (52)
76 COG1592 Rubrerythrin [Energy p 88.6 0.22 4.9E-06 32.0 1.0 24 105-148 134-157 (166)
77 KOG1146|consensus 88.1 0.18 3.9E-06 42.2 0.4 53 76-128 464-541 (1406)
78 smart00440 ZnF_C2C2 C2C2 Zinc 87.7 0.13 2.8E-06 24.7 -0.4 12 139-150 27-38 (40)
79 PF12013 DUF3505: Protein of u 87.6 1 2.2E-05 26.8 3.4 26 15-41 8-33 (109)
80 PF01096 TFIIS_C: Transcriptio 87.1 0.069 1.5E-06 25.5 -1.5 12 139-150 27-38 (39)
81 PF14446 Prok-RING_1: Prokaryo 87.1 0.19 4.2E-06 25.7 0.1 19 141-159 6-24 (54)
82 PF09538 FYDLN_acid: Protein o 86.2 0.5 1.1E-05 28.1 1.5 11 77-87 26-36 (108)
83 KOG4173|consensus 86.2 0.098 2.1E-06 34.5 -1.6 80 45-130 78-171 (253)
84 PRK00464 nrdR transcriptional 85.6 0.13 2.9E-06 32.6 -1.2 16 106-121 29-44 (154)
85 TIGR00373 conserved hypothetic 84.8 0.41 8.9E-06 30.6 0.7 19 103-121 107-125 (158)
86 TIGR00373 conserved hypothetic 84.7 0.76 1.7E-05 29.4 1.9 19 44-62 107-125 (158)
87 KOG4173|consensus 84.6 0.23 4.9E-06 32.9 -0.5 76 76-154 78-160 (253)
88 PF00301 Rubredoxin: Rubredoxi 84.0 0.64 1.4E-05 23.2 1.1 8 140-147 34-41 (47)
89 cd00730 rubredoxin Rubredoxin; 83.6 1.1 2.3E-05 22.7 1.8 11 78-88 2-12 (50)
90 PRK06266 transcription initiat 83.2 0.51 1.1E-05 30.8 0.7 33 104-152 116-148 (178)
91 PF14353 CpXC: CpXC protein 83.1 2.2 4.7E-05 26.2 3.4 22 104-125 37-58 (128)
92 COG1996 RPC10 DNA-directed RNA 82.5 0.66 1.4E-05 23.3 0.7 10 78-87 7-16 (49)
93 PRK06266 transcription initiat 81.0 1.3 2.8E-05 29.0 1.9 31 45-87 116-146 (178)
94 COG1773 Rubredoxin [Energy pro 80.0 1.4 3.1E-05 22.7 1.5 13 77-89 3-15 (55)
95 COG3677 Transposase and inacti 79.8 1 2.3E-05 27.8 1.1 12 105-116 53-64 (129)
96 smart00659 RPOLCX RNA polymera 79.6 1.1 2.3E-05 22.0 0.9 30 19-59 3-32 (44)
97 smart00531 TFIIE Transcription 79.5 1.4 2.9E-05 27.9 1.6 12 46-57 99-110 (147)
98 COG5236 Uncharacterized conser 78.6 2.1 4.5E-05 30.9 2.4 104 19-125 152-271 (493)
99 PF03811 Zn_Tnp_IS1: InsA N-te 78.6 1.6 3.4E-05 20.4 1.3 29 107-146 7-35 (36)
100 PRK09678 DNA-binding transcrip 78.3 0.75 1.6E-05 25.2 0.2 43 19-63 2-46 (72)
101 KOG2907|consensus 78.0 1 2.2E-05 26.8 0.7 14 139-152 101-114 (116)
102 PF01780 Ribosomal_L37ae: Ribo 78.0 0.5 1.1E-05 27.0 -0.6 10 141-150 54-63 (90)
103 TIGR01206 lysW lysine biosynth 77.9 0.95 2.1E-05 23.3 0.5 30 78-115 3-32 (54)
104 PF08274 PhnA_Zn_Ribbon: PhnA 77.6 1.1 2.3E-05 20.0 0.5 11 107-117 4-14 (30)
105 PF07754 DUF1610: Domain of un 77.3 1 2.2E-05 19.0 0.4 8 105-112 16-23 (24)
106 KOG4124|consensus 77.3 2.6 5.7E-05 30.5 2.6 54 103-156 347-414 (442)
107 smart00614 ZnF_BED BED zinc fi 76.4 0.6 1.3E-05 23.5 -0.5 21 78-98 19-44 (50)
108 PF02892 zf-BED: BED zinc fing 76.2 0.34 7.5E-06 23.6 -1.4 22 76-97 15-40 (45)
109 COG0068 HypF Hydrogenase matur 75.5 0.9 2E-05 35.9 0.0 81 19-115 102-183 (750)
110 PHA02998 RNA polymerase subuni 73.1 1.2 2.6E-05 28.8 0.2 40 106-152 144-183 (195)
111 PF13451 zf-trcl: Probable zin 72.7 1.1 2.5E-05 22.5 -0.0 14 77-90 4-17 (49)
112 TIGR02300 FYDLN_acid conserved 72.6 2.7 5.8E-05 25.8 1.5 11 77-87 26-36 (129)
113 PRK03824 hypA hydrogenase nick 72.6 1.2 2.6E-05 27.7 0.1 13 77-89 70-82 (135)
114 KOG2785|consensus 72.5 2.5 5.5E-05 30.9 1.6 52 77-128 166-243 (390)
115 PF05191 ADK_lid: Adenylate ki 72.2 0.92 2E-05 21.2 -0.4 8 107-114 23-30 (36)
116 KOG3214|consensus 72.0 2.3 5E-05 24.7 1.1 13 140-152 47-59 (109)
117 PF05129 Elf1: Transcription e 71.9 1.2 2.6E-05 25.1 -0.1 13 140-152 46-58 (81)
118 KOG2785|consensus 71.7 3.1 6.6E-05 30.5 1.9 82 17-98 2-89 (390)
119 PF06524 NOA36: NOA36 protein; 71.4 4.8 0.0001 28.0 2.6 28 102-130 206-233 (314)
120 PF08790 zf-LYAR: LYAR-type C2 71.4 1.1 2.3E-05 19.7 -0.3 19 106-125 1-19 (28)
121 PF10571 UPF0547: Uncharacteri 71.2 1.9 4.2E-05 18.5 0.5 9 107-115 16-24 (26)
122 PF12907 zf-met2: Zinc-binding 71.2 0.58 1.3E-05 22.4 -1.2 26 106-131 2-30 (40)
123 PF01927 Mut7-C: Mut7-C RNAse 70.7 1.3 2.8E-05 28.0 -0.1 18 139-156 123-140 (147)
124 COG1997 RPL43A Ribosomal prote 69.7 3.1 6.8E-05 23.6 1.3 31 45-88 34-64 (89)
125 PF14803 Nudix_N_2: Nudix N-te 69.0 1.6 3.4E-05 20.1 0.0 9 139-147 21-29 (34)
126 PF04959 ARS2: Arsenite-resist 67.6 0.73 1.6E-05 31.0 -1.8 27 104-130 76-102 (214)
127 PF01286 XPA_N: XPA protein N- 67.3 3.3 7.2E-05 19.1 0.9 16 107-122 5-20 (34)
128 KOG4602|consensus 67.3 1.9 4.1E-05 29.7 0.1 43 107-149 235-277 (318)
129 TIGR03831 YgiT_finger YgiT-typ 66.7 1.4 3.1E-05 21.3 -0.4 13 139-151 31-43 (46)
130 KOG2593|consensus 66.5 3.8 8.2E-05 30.5 1.5 17 46-62 128-144 (436)
131 PRK03564 formate dehydrogenase 66.5 1.8 3.9E-05 30.9 -0.1 37 17-56 186-222 (309)
132 KOG2186|consensus 65.9 3.6 7.7E-05 28.4 1.2 39 18-58 3-41 (276)
133 PRK05978 hypothetical protein; 65.9 2.8 6.2E-05 26.5 0.7 12 107-118 54-65 (148)
134 PF05290 Baculo_IE-1: Baculovi 65.3 3.5 7.7E-05 25.5 1.0 20 43-62 77-96 (140)
135 PF06397 Desulfoferrod_N: Desu 65.1 2.2 4.7E-05 20.0 0.1 12 138-149 4-15 (36)
136 COG5151 SSL1 RNA polymerase II 65.1 12 0.00027 26.8 3.7 25 76-100 387-411 (421)
137 PF03604 DNA_RNApol_7kD: DNA d 65.0 2.8 6.1E-05 19.0 0.4 9 46-54 17-25 (32)
138 PF15269 zf-C2H2_7: Zinc-finge 64.8 13 0.00028 18.2 2.7 22 19-40 21-42 (54)
139 PF01844 HNH: HNH endonuclease 64.5 5 0.00011 19.4 1.4 42 108-149 1-43 (47)
140 PF12013 DUF3505: Protein of u 64.4 6.9 0.00015 23.2 2.1 26 17-42 79-108 (109)
141 PRK04023 DNA polymerase II lar 64.0 7.5 0.00016 32.5 2.8 9 106-114 664-672 (1121)
142 KOG2482|consensus 63.8 2.2 4.8E-05 30.7 -0.1 55 78-132 145-222 (423)
143 PF10276 zf-CHCC: Zinc-finger 63.3 2.1 4.7E-05 20.5 -0.1 11 140-150 29-39 (40)
144 PF04810 zf-Sec23_Sec24: Sec23 62.0 3.2 6.9E-05 19.8 0.3 9 104-112 23-31 (40)
145 PF07975 C1_4: TFIIH C1-like d 61.6 1.4 3E-05 22.4 -1.0 22 104-125 20-41 (51)
146 smart00734 ZnF_Rad18 Rad18-lik 61.1 8.6 0.00019 16.4 1.6 19 20-39 3-21 (26)
147 PF07503 zf-HYPF: HypF finger; 61.0 1.4 3E-05 20.5 -1.0 8 107-114 23-30 (35)
148 COG1594 RPB9 DNA-directed RNA 60.7 2.5 5.5E-05 25.4 -0.2 12 139-150 99-110 (113)
149 COG4338 Uncharacterized protei 60.4 1.2 2.7E-05 22.1 -1.3 14 142-155 14-27 (54)
150 PF09416 UPF1_Zn_bind: RNA hel 59.1 2.7 5.9E-05 26.7 -0.3 7 106-112 61-67 (152)
151 PF04641 Rtf2: Rtf2 RING-finge 58.8 5.4 0.00012 27.8 1.1 50 103-155 111-165 (260)
152 TIGR01384 TFS_arch transcripti 57.4 2.8 6.1E-05 24.6 -0.4 40 106-152 63-102 (104)
153 PF14445 Prok-RING_2: Prokaryo 57.3 1.7 3.7E-05 21.8 -1.1 11 140-150 7-17 (57)
154 KOG2593|consensus 57.0 7.5 0.00016 29.1 1.6 19 104-122 127-145 (436)
155 smart00154 ZnF_AN1 AN1-like Zi 56.9 5.2 0.00011 19.0 0.6 14 105-118 12-25 (39)
156 PF07282 OrfB_Zn_ribbon: Putat 56.1 6.9 0.00015 20.9 1.1 10 105-114 46-55 (69)
157 PF05741 zf-nanos: Nanos RNA b 55.9 2.1 4.6E-05 22.1 -0.9 13 139-151 32-44 (55)
158 cd00924 Cyt_c_Oxidase_Vb Cytoc 55.5 6.4 0.00014 23.0 0.9 18 99-117 74-91 (97)
159 PF13824 zf-Mss51: Zinc-finger 55.3 10 0.00022 19.6 1.5 11 77-87 14-24 (55)
160 PF08394 Arc_trans_TRASH: Arch 55.1 5.2 0.00011 18.8 0.4 14 139-152 22-35 (37)
161 PF13878 zf-C2H2_3: zinc-finge 55.0 16 0.00034 17.5 2.1 24 78-101 14-39 (41)
162 COG1198 PriA Primosomal protei 53.5 11 0.00024 30.5 2.1 8 105-112 475-482 (730)
163 PTZ00255 60S ribosomal protein 53.3 8.5 0.00019 22.1 1.1 31 45-88 35-65 (90)
164 PF05443 ROS_MUCR: ROS/MUCR tr 53.1 9.8 0.00021 23.6 1.5 26 77-105 72-97 (132)
165 PRK12380 hydrogenase nickel in 53.1 6.6 0.00014 23.6 0.7 24 78-113 71-94 (113)
166 COG3357 Predicted transcriptio 53.0 9.1 0.0002 22.0 1.2 14 45-58 57-70 (97)
167 TIGR00100 hypA hydrogenase nic 52.9 5.9 0.00013 23.9 0.5 26 77-114 70-95 (115)
168 KOG1280|consensus 52.6 6.1 0.00013 28.6 0.6 26 105-130 79-104 (381)
169 KOG3408|consensus 52.6 9 0.00019 23.3 1.2 26 74-99 54-79 (129)
170 PF04423 Rad50_zn_hook: Rad50 52.6 5.3 0.00011 20.3 0.2 12 107-118 22-33 (54)
171 PF08271 TF_Zn_Ribbon: TFIIB z 51.9 6 0.00013 19.1 0.3 10 78-87 20-29 (43)
172 PF04780 DUF629: Protein of un 51.7 2.9 6.3E-05 31.7 -1.1 28 105-132 57-84 (466)
173 smart00661 RPOL9 RNA polymeras 51.6 7 0.00015 19.5 0.6 16 105-120 20-35 (52)
174 KOG0696|consensus 51.2 8 0.00017 29.2 1.0 61 73-148 69-129 (683)
175 PRK14714 DNA polymerase II lar 51.2 14 0.0003 31.8 2.4 8 47-54 668-675 (1337)
176 TIGR00280 L37a ribosomal prote 51.1 8.2 0.00018 22.2 0.9 30 45-87 34-63 (91)
177 PRK00432 30S ribosomal protein 50.8 6.2 0.00014 19.9 0.3 12 104-115 36-47 (50)
178 PLN02294 cytochrome c oxidase 50.7 8.5 0.00018 25.0 1.0 17 102-118 138-154 (174)
179 PF10013 DUF2256: Uncharacteri 50.3 3.1 6.7E-05 20.1 -0.8 11 142-152 10-20 (42)
180 PTZ00303 phosphatidylinositol 49.5 17 0.00036 29.8 2.5 69 78-154 461-533 (1374)
181 COG4888 Uncharacterized Zn rib 49.1 8.8 0.00019 22.5 0.8 9 47-55 23-31 (104)
182 PF15135 UPF0515: Uncharacteri 48.5 16 0.00034 25.4 2.0 12 17-28 111-122 (278)
183 PF02176 zf-TRAF: TRAF-type zi 48.3 3.6 7.8E-05 21.2 -0.8 39 77-116 9-53 (60)
184 COG5236 Uncharacterized conser 48.2 29 0.00062 25.4 3.3 72 19-101 221-305 (493)
185 PF01363 FYVE: FYVE zinc finge 47.5 11 0.00024 20.1 1.0 57 78-150 10-67 (69)
186 PF01428 zf-AN1: AN1-like Zinc 47.3 4.4 9.6E-05 19.6 -0.5 16 139-154 12-27 (43)
187 smart00132 LIM Zinc-binding do 47.2 11 0.00024 17.0 0.9 12 139-150 26-37 (39)
188 COG4530 Uncharacterized protei 47.1 11 0.00025 22.4 1.1 14 76-89 25-38 (129)
189 smart00507 HNHc HNH nucleases. 46.6 19 0.00041 17.3 1.8 12 106-117 11-22 (52)
190 PRK03976 rpl37ae 50S ribosomal 46.1 11 0.00024 21.7 0.8 30 45-87 35-64 (90)
191 PRK00762 hypA hydrogenase nick 46.0 9.7 0.00021 23.3 0.7 11 78-89 71-81 (124)
192 PF10621 FpoO: F420H2 dehydrog 45.8 9.2 0.0002 22.8 0.5 65 48-114 3-69 (119)
193 PF10263 SprT-like: SprT-like 45.6 7 0.00015 24.7 0.0 10 106-115 124-133 (157)
194 KOG2807|consensus 45.6 67 0.0015 23.4 4.7 25 105-130 345-369 (378)
195 PF14311 DUF4379: Domain of un 45.3 17 0.00037 18.5 1.5 12 78-89 29-40 (55)
196 PRK00564 hypA hydrogenase nick 45.2 9.3 0.0002 23.1 0.5 13 77-89 71-83 (117)
197 COG3364 Zn-ribbon containing p 45.1 15 0.00032 21.6 1.3 16 18-33 2-17 (112)
198 COG1198 PriA Primosomal protei 44.9 16 0.00036 29.6 1.9 11 139-149 474-484 (730)
199 COG0068 HypF Hydrogenase matur 44.7 5 0.00011 32.0 -0.8 60 78-151 124-184 (750)
200 COG1675 TFA1 Transcription ini 44.2 19 0.00042 23.6 1.9 33 42-86 109-141 (176)
201 smart00401 ZnF_GATA zinc finge 44.1 31 0.00068 17.4 2.3 14 141-154 26-39 (52)
202 COG3091 SprT Zn-dependent meta 43.7 11 0.00023 24.0 0.6 33 77-114 117-149 (156)
203 COG1779 C4-type Zn-finger prot 42.9 5.9 0.00013 26.3 -0.6 12 106-117 44-55 (201)
204 PF09332 Mcm10: Mcm10 replicat 42.8 2.7 5.9E-05 30.5 -2.3 11 139-149 284-294 (344)
205 COG4391 Uncharacterized protei 41.8 6.3 0.00014 20.8 -0.5 11 141-151 49-59 (62)
206 KOG1729|consensus 41.2 21 0.00046 25.4 1.8 58 78-152 169-226 (288)
207 PF10122 Mu-like_Com: Mu-like 39.9 15 0.00033 18.6 0.7 6 107-112 26-31 (51)
208 PF14787 zf-CCHC_5: GAG-polypr 39.5 9.4 0.0002 17.8 -0.1 12 108-119 5-16 (36)
209 PRK14892 putative transcriptio 39.3 12 0.00025 22.1 0.3 35 76-117 20-54 (99)
210 KOG4167|consensus 39.2 6.4 0.00014 31.5 -1.0 25 77-101 792-816 (907)
211 PF02891 zf-MIZ: MIZ/SP-RING z 39.2 11 0.00024 18.9 0.2 9 105-113 41-49 (50)
212 PF09963 DUF2197: Uncharacteri 38.9 8.4 0.00018 20.0 -0.3 8 105-112 31-38 (56)
213 PF01155 HypA: Hydrogenase exp 38.4 10 0.00022 22.8 -0.1 25 78-114 71-95 (113)
214 COG1655 Uncharacterized protei 37.9 14 0.00031 25.3 0.5 16 106-121 20-35 (267)
215 cd00085 HNHc HNH nucleases; HN 37.7 20 0.00044 17.6 1.1 10 106-115 12-21 (57)
216 PRK04351 hypothetical protein; 37.5 16 0.00035 23.2 0.7 13 139-151 131-143 (149)
217 TIGR03830 CxxCG_CxxCG_HTH puta 37.4 35 0.00075 20.5 2.2 20 76-95 30-49 (127)
218 COG1571 Predicted DNA-binding 37.4 18 0.00039 27.2 1.0 14 105-118 367-380 (421)
219 PF14255 Cys_rich_CPXG: Cystei 37.2 16 0.00034 18.7 0.5 11 106-116 1-11 (52)
220 TIGR01562 FdhE formate dehydro 36.4 24 0.00051 25.4 1.5 16 138-153 250-265 (305)
221 cd00065 FYVE FYVE domain; Zinc 36.3 29 0.00063 17.5 1.5 13 105-117 18-30 (57)
222 TIGR01385 TFSII transcription 36.2 11 0.00025 26.9 -0.1 40 105-151 258-297 (299)
223 PF00412 LIM: LIM domain; Int 35.4 24 0.00051 17.8 1.1 12 140-151 26-37 (58)
224 PF02701 zf-Dof: Dof domain, z 35.2 32 0.0007 18.2 1.5 17 106-122 31-47 (63)
225 TIGR00686 phnA alkylphosphonat 34.8 20 0.00043 21.4 0.7 8 78-85 20-27 (109)
226 PF11672 DUF3268: Protein of u 34.5 24 0.00053 20.9 1.1 9 77-85 2-10 (102)
227 PF06220 zf-U1: U1 zinc finger 34.2 22 0.00048 16.7 0.7 15 105-119 3-17 (38)
228 COG1998 RPS31 Ribosomal protei 32.6 18 0.0004 18.2 0.3 10 105-114 37-46 (51)
229 PRK03681 hypA hydrogenase nick 32.4 26 0.00055 21.1 1.0 11 78-88 71-81 (114)
230 KOG0978|consensus 32.4 21 0.00046 28.7 0.8 22 104-125 677-698 (698)
231 smart00064 FYVE Protein presen 32.1 29 0.00062 18.4 1.1 15 104-118 25-39 (68)
232 KOG2071|consensus 31.6 35 0.00075 26.9 1.8 28 15-42 415-442 (579)
233 PF05766 NinG: Bacteriophage L 31.5 31 0.00067 22.9 1.3 31 76-116 5-35 (189)
234 PRK05452 anaerobic nitric oxid 31.4 34 0.00073 26.4 1.7 46 104-151 424-469 (479)
235 KOG4167|consensus 31.3 13 0.00028 30.0 -0.5 24 19-42 793-816 (907)
236 KOG2231|consensus 31.3 49 0.0011 26.7 2.5 21 20-40 184-204 (669)
237 PF12773 DZR: Double zinc ribb 31.2 41 0.0009 16.5 1.5 9 105-113 29-37 (50)
238 PRK10220 hypothetical protein; 31.2 32 0.0007 20.6 1.2 11 47-57 21-31 (111)
239 PF14447 Prok-RING_4: Prokaryo 31.2 16 0.00034 18.9 -0.0 10 107-116 41-50 (55)
240 COG4896 Uncharacterized protei 31.0 32 0.00069 18.2 1.1 8 105-112 31-38 (68)
241 PF04606 Ogr_Delta: Ogr/Delta- 30.9 6 0.00013 19.5 -1.6 15 104-118 24-40 (47)
242 PF10537 WAC_Acf1_DNA_bd: ATP- 30.1 66 0.0014 19.0 2.4 18 46-63 3-20 (102)
243 PF12662 cEGF: Complement Clr- 30.1 20 0.00044 15.0 0.2 6 146-151 6-11 (24)
244 PF07295 DUF1451: Protein of u 30.0 24 0.00053 22.3 0.7 7 106-112 113-119 (146)
245 PF01215 COX5B: Cytochrome c o 29.9 16 0.00035 22.8 -0.1 15 103-117 110-124 (136)
246 PF02748 PyrI_C: Aspartate car 29.8 13 0.00029 18.9 -0.4 15 139-153 34-48 (52)
247 PF04438 zf-HIT: HIT zinc fing 29.3 21 0.00046 15.8 0.2 9 106-114 14-22 (30)
248 PF06467 zf-FCS: MYM-type Zinc 28.2 39 0.00085 15.9 1.1 16 105-120 6-21 (43)
249 cd00974 DSRD Desulforedoxin (D 27.3 22 0.00048 16.0 0.1 12 139-150 3-14 (34)
250 smart00731 SprT SprT homologue 26.9 23 0.0005 22.2 0.2 12 139-150 132-143 (146)
251 PF02591 DUF164: Putative zinc 26.7 56 0.0012 16.6 1.6 11 44-54 44-54 (56)
252 PF10083 DUF2321: Uncharacteri 26.7 77 0.0017 20.4 2.4 43 47-92 40-83 (158)
253 PF14369 zf-RING_3: zinc-finge 26.6 49 0.0011 15.2 1.2 10 48-57 23-32 (35)
254 PTZ00043 cytochrome c oxidase 26.5 36 0.00077 23.3 1.0 27 102-132 178-204 (268)
255 KOG1842|consensus 26.5 13 0.00027 28.1 -1.2 27 106-132 16-42 (505)
256 KOG2906|consensus 26.5 20 0.00044 20.9 -0.1 36 107-149 67-102 (105)
257 PF12760 Zn_Tnp_IS1595: Transp 26.0 92 0.002 15.1 3.3 9 47-55 19-27 (46)
258 PRK01343 zinc-binding protein; 25.9 33 0.00072 17.9 0.6 12 105-116 9-20 (57)
259 TIGR00319 desulf_FeS4 desulfof 25.7 22 0.00048 16.0 -0.1 12 139-150 6-17 (34)
260 PF13453 zf-TFIIB: Transcripti 25.5 69 0.0015 15.1 1.7 23 15-37 16-38 (41)
261 PF04216 FdhE: Protein involve 25.3 15 0.00032 26.1 -1.0 77 18-115 172-248 (290)
262 PF04032 Rpr2: RNAse P Rpr2/Rp 25.1 59 0.0013 18.0 1.6 42 102-147 43-84 (85)
263 KOG3507|consensus 24.9 41 0.00089 17.6 0.8 10 105-114 37-46 (62)
264 COG4957 Predicted transcriptio 24.6 40 0.00086 21.1 0.9 26 77-105 76-101 (148)
265 KOG0402|consensus 24.6 28 0.0006 19.7 0.2 29 46-87 36-64 (92)
266 COG5216 Uncharacterized conser 24.1 23 0.00049 18.5 -0.2 12 139-151 21-32 (67)
267 KOG3352|consensus 24.0 19 0.00042 22.8 -0.6 14 139-152 132-145 (153)
268 COG5112 UFD2 U1-like Zn-finger 24.0 33 0.00071 20.4 0.4 25 75-99 53-77 (126)
269 PF04780 DUF629: Protein of un 24.0 59 0.0013 25.0 1.8 29 74-102 54-83 (466)
270 PRK12860 transcriptional activ 23.9 44 0.00095 22.2 1.0 11 106-116 135-145 (189)
271 KOG2857|consensus 23.8 34 0.00073 21.5 0.5 21 105-125 17-37 (157)
272 PF14279 HNH_5: HNH endonuclea 23.7 71 0.0015 17.4 1.7 10 142-151 32-41 (71)
273 PF08792 A2L_zn_ribbon: A2L zi 23.6 34 0.00074 15.5 0.4 9 78-86 22-30 (33)
274 COG1326 Uncharacterized archae 23.5 74 0.0016 21.3 2.0 38 17-58 5-42 (201)
275 PTZ00448 hypothetical protein; 23.1 63 0.0014 24.0 1.8 23 18-40 314-336 (373)
276 PRK11823 DNA repair protein Ra 23.0 50 0.0011 25.2 1.3 11 46-56 7-17 (446)
277 COG0675 Transposase and inacti 22.9 42 0.00092 23.9 0.9 7 106-112 323-329 (364)
278 PF11023 DUF2614: Protein of u 22.7 36 0.00079 20.5 0.5 33 103-154 67-99 (114)
279 PF05180 zf-DNL: DNL zinc fing 22.3 11 0.00025 20.3 -1.5 34 78-114 5-38 (66)
280 PF03107 C1_2: C1 domain; Int 22.3 32 0.0007 15.0 0.1 10 141-150 1-10 (30)
281 KOG4118|consensus 22.2 69 0.0015 17.2 1.4 25 19-43 39-63 (74)
282 TIGR03829 YokU_near_AblA uncha 21.5 65 0.0014 18.6 1.3 21 16-36 33-53 (89)
283 COG4332 Uncharacterized protei 21.3 30 0.00064 22.8 -0.1 8 106-113 50-57 (203)
284 PF10071 DUF2310: Zn-ribbon-co 21.2 48 0.001 23.3 0.9 30 106-149 221-250 (258)
285 PF14690 zf-ISL3: zinc-finger 21.0 49 0.0011 15.9 0.7 11 105-115 2-12 (47)
286 PRK11295 hypothetical protein; 20.7 45 0.00097 20.2 0.6 47 104-150 23-72 (113)
287 TIGR00627 tfb4 transcription f 20.6 72 0.0016 22.7 1.6 13 104-116 254-266 (279)
288 PF06170 DUF983: Protein of un 20.3 49 0.0011 18.9 0.6 12 107-118 10-21 (86)
No 1
>KOG2462|consensus
Probab=99.97 E-value=4.1e-32 Score=179.09 Aligned_cols=133 Identities=36% Similarity=0.617 Sum_probs=120.5
Q ss_pred cCCCCcccCcccccccCChHHHHHHHHhhc---CCCccccccccccccCccccccccccccccCCCCCccCcccccccCC
Q psy9695 13 VAGMPKHLCHVCHKNFSSSSALQIHMRTHT---GDKPFRCTICQKAFTTKGNLKLIPNAVFNVAGMPKHLCHVCHKNFSS 89 (159)
Q Consensus 13 ~~~~~~~~C~~C~~~f~~~~~~~~h~~~~~---~~~~~~c~~c~~~~~~~~~l~~~~~~~~~~~~~~~~~C~~C~~~~~~ 89 (159)
......|+|+.|++.+.+.++|..|...|. ..+.+.|+.|++.+..-..|.+ +++.|+ .+.+|..||+.|..
T Consensus 125 ~~~~~r~~c~eCgk~ysT~snLsrHkQ~H~~~~s~ka~~C~~C~K~YvSmpALkM---HirTH~--l~c~C~iCGKaFSR 199 (279)
T KOG2462|consen 125 AAKHPRYKCPECGKSYSTSSNLSRHKQTHRSLDSKKAFSCKYCGKVYVSMPALKM---HIRTHT--LPCECGICGKAFSR 199 (279)
T ss_pred cccCCceeccccccccccccccchhhcccccccccccccCCCCCceeeehHHHhh---HhhccC--CCcccccccccccc
Confidence 334556999999999999999999999885 4677999999999999999987 444444 67999999999999
Q ss_pred hHHHHHHHHHccCCCCccCCcccccccccCCceeeehhhccCCCCCcccccccchhhchhhhhccccc
Q psy9695 90 SSALQIHMRTHTGDKPFRCTICQKAFTTKGNLKVREIEINIGSQLPKKAQQHIGAVEGKSFQAKHKTE 157 (159)
Q Consensus 90 ~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~~h~~~~~~~~~~~~~C~~C~~~f~~~~~l~ 157 (159)
+.-|+.|+++|+|||||.|+.|+++|..+++|+.|| ++|.+. +.|+|+.|+|+|...+.|.
T Consensus 200 PWLLQGHiRTHTGEKPF~C~hC~kAFADRSNLRAHm-QTHS~~------K~~qC~~C~KsFsl~SyLn 260 (279)
T KOG2462|consen 200 PWLLQGHIRTHTGEKPFSCPHCGKAFADRSNLRAHM-QTHSDV------KKHQCPRCGKSFALKSYLN 260 (279)
T ss_pred hHHhhcccccccCCCCccCCcccchhcchHHHHHHH-HhhcCC------ccccCcchhhHHHHHHHHH
Confidence 999999999999999999999999999999999999 999999 9999999999999988764
No 2
>KOG2462|consensus
Probab=99.88 E-value=1.3e-23 Score=139.06 Aligned_cols=105 Identities=28% Similarity=0.494 Sum_probs=98.7
Q ss_pred CCccccccccccccCccccccccccccccCCCCCccCcccccccCChHHHHHHHHHccCCCCccCCcccccccccCCcee
Q psy9695 44 DKPFRCTICQKAFTTKGNLKLIPNAVFNVAGMPKHLCHVCHKNFSSSSALQIHMRTHTGDKPFRCTICQKAFTTKGNLKV 123 (159)
Q Consensus 44 ~~~~~c~~c~~~~~~~~~l~~~~~~~~~~~~~~~~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~ 123 (159)
...|.|.+||+.+.+.+.|.+|.+.++.....+.+.|+.|++.|.+...|..|+++|+ -+.+|++|||+|.+.+.|+.
T Consensus 128 ~~r~~c~eCgk~ysT~snLsrHkQ~H~~~~s~ka~~C~~C~K~YvSmpALkMHirTH~--l~c~C~iCGKaFSRPWLLQG 205 (279)
T KOG2462|consen 128 HPRYKCPECGKSYSTSSNLSRHKQTHRSLDSKKAFSCKYCGKVYVSMPALKMHIRTHT--LPCECGICGKAFSRPWLLQG 205 (279)
T ss_pred CCceeccccccccccccccchhhcccccccccccccCCCCCceeeehHHHhhHhhccC--CCcccccccccccchHHhhc
Confidence 4469999999999999999998888777777889999999999999999999999996 58999999999999999999
Q ss_pred eehhhccCCCCCcccccccchhhchhhhhccccc
Q psy9695 124 REIEINIGSQLPKKAQQHIGAVEGKSFQAKHKTE 157 (159)
Q Consensus 124 H~~~~h~~~~~~~~~~~~~C~~C~~~f~~~~~l~ 157 (159)
|+ ++|+|+ +||.|+.|+++|..+++|+
T Consensus 206 Hi-RTHTGE------KPF~C~hC~kAFADRSNLR 232 (279)
T KOG2462|consen 206 HI-RTHTGE------KPFSCPHCGKAFADRSNLR 232 (279)
T ss_pred cc-ccccCC------CCccCCcccchhcchHHHH
Confidence 99 999999 9999999999999999986
No 3
>KOG1074|consensus
Probab=99.80 E-value=5.5e-20 Score=137.13 Aligned_cols=77 Identities=40% Similarity=0.724 Sum_probs=67.9
Q ss_pred ccCcccccccCChHHHHHHHHHccCCCCccCCcccccccccCCceeeehhhccCCCCCcccccccch---hhchhhhhcc
Q psy9695 78 HLCHVCHKNFSSSSALQIHMRTHTGDKPFRCTICQKAFTTKGNLKVREIEINIGSQLPKKAQQHIGA---VEGKSFQAKH 154 (159)
Q Consensus 78 ~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~~h~~~~~~~~~~~~~C~---~C~~~f~~~~ 154 (159)
-.|..|.+++.-.+.|+-|.+.|+|||||+|.+||++|+.+.+|+.|| .+|-.. .+.+ -+|.|+ +|-+.|...-
T Consensus 606 NqCiiC~rVlSC~saLqmHyrtHtGERPFkCKiCgRAFtTkGNLkaH~-~vHka~-p~~R-~q~ScP~~~ic~~kftn~V 682 (958)
T KOG1074|consen 606 NQCIICLRVLSCPSALQMHYRTHTGERPFKCKICGRAFTTKGNLKAHM-SVHKAK-PPAR-VQFSCPSTFICQKKFTNAV 682 (958)
T ss_pred cceeeeeecccchhhhhhhhhcccCcCccccccccchhccccchhhcc-cccccC-cccc-ccccCCchhhhcccccccc
Confidence 559999999999999999999999999999999999999999999999 998765 2222 789999 9999998766
Q ss_pred ccc
Q psy9695 155 KTE 157 (159)
Q Consensus 155 ~l~ 157 (159)
.|.
T Consensus 683 ~lp 685 (958)
T KOG1074|consen 683 TLP 685 (958)
T ss_pred ccc
Confidence 553
No 4
>KOG1074|consensus
Probab=99.70 E-value=3.8e-18 Score=127.47 Aligned_cols=45 Identities=16% Similarity=0.436 Sum_probs=32.6
Q ss_pred ccCCcccccccccCCceeeehhhccCCCCCcccccccchhhchhhhhccccc
Q psy9695 106 FRCTICQKAFTTKGNLKVREIEINIGSQLPKKAQQHIGAVEGKSFQAKHKTE 157 (159)
Q Consensus 106 ~~C~~C~~~f~~~~~l~~H~~~~h~~~~~~~~~~~~~C~~C~~~f~~~~~l~ 157 (159)
..|.+||+.|...+.|..|+ ++|.++ ++|.|..|++.|.++.+|+
T Consensus 880 h~C~vCgk~FsSSsALqiH~-rTHtg~------KPF~C~fC~~aFttrgnLK 924 (958)
T KOG1074|consen 880 HVCNVCGKQFSSSAALEIHM-RTHTGP------KPFFCHFCEEAFTTRGNLK 924 (958)
T ss_pred hhhccchhcccchHHHHHhh-hcCCCC------CCccchhhhhhhhhhhhhh
Confidence 45777777777777777777 777777 6777777777777776653
No 5
>KOG3576|consensus
Probab=99.67 E-value=1.2e-18 Score=110.83 Aligned_cols=104 Identities=28% Similarity=0.560 Sum_probs=83.7
Q ss_pred CCccccccccccccCccccccccccccccCCCCCccCcccccccCChHHHHHHHHHccCCCCccCCcccccccccCCcee
Q psy9695 44 DKPFRCTICQKAFTTKGNLKLIPNAVFNVAGMPKHLCHVCHKNFSSSSALQIHMRTHTGDKPFRCTICQKAFTTKGNLKV 123 (159)
Q Consensus 44 ~~~~~c~~c~~~~~~~~~l~~~~~~~~~~~~~~~~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~ 123 (159)
...|.|.+|++.|.-..-|.+ ++.-|...+.+.|..||+.|....+|.+|.++|+|.+||+|..|+++|+++.+|..
T Consensus 115 ~d~ftCrvCgK~F~lQRmlnr---h~kch~~vkr~lct~cgkgfndtfdlkrh~rthtgvrpykc~~c~kaftqrcsles 191 (267)
T KOG3576|consen 115 QDSFTCRVCGKKFGLQRMLNR---HLKCHSDVKRHLCTFCGKGFNDTFDLKRHTRTHTGVRPYKCSLCEKAFTQRCSLES 191 (267)
T ss_pred CCeeeeehhhhhhhHHHHHHH---HhhhccHHHHHHHhhccCcccchhhhhhhhccccCccccchhhhhHHHHhhccHHH
Confidence 345889999998887777766 45557777789999999999998999999999999999999999999999999999
Q ss_pred eehhhccCCC----CCcccccccchhhchhh
Q psy9695 124 REIEINIGSQ----LPKKAQQHIGAVEGKSF 150 (159)
Q Consensus 124 H~~~~h~~~~----~~~~~~~~~C~~C~~~f 150 (159)
|.+++|.-.. ...+.+.|.|..||..-
T Consensus 192 hl~kvhgv~~~yaykerr~kl~vcedcg~t~ 222 (267)
T KOG3576|consen 192 HLKKVHGVQHQYAYKERRAKLYVCEDCGYTS 222 (267)
T ss_pred HHHHHcCchHHHHHHHhhhheeeecccCCCC
Confidence 9967665321 11344789999998653
No 6
>KOG3608|consensus
Probab=99.67 E-value=3.7e-18 Score=116.81 Aligned_cols=146 Identities=15% Similarity=0.315 Sum_probs=93.1
Q ss_pred ccCCccccccCCCCcccCcccccccCChHHHHHHHHhhc--CCCc--------------------------ccccccccc
Q psy9695 4 KLIPNAVFNVAGMPKHLCHVCHKNFSSSSALQIHMRTHT--GDKP--------------------------FRCTICQKA 55 (159)
Q Consensus 4 ~~~~~~~~~~~~~~~~~C~~C~~~f~~~~~~~~h~~~~~--~~~~--------------------------~~c~~c~~~ 55 (159)
..+.++.+.|++++...|+.||..|++...|-.|++..+ ...+ |+|+.|..+
T Consensus 193 ~~LreH~r~Hs~eKvvACp~Cg~~F~~~tkl~DH~rRqt~l~~n~fqC~~C~KrFaTeklL~~Hv~rHvn~ykCplCdmt 272 (467)
T KOG3608|consen 193 YRLREHIRTHSNEKVVACPHCGELFRTKTKLFDHLRRQTELNTNSFQCAQCFKRFATEKLLKSHVVRHVNCYKCPLCDMT 272 (467)
T ss_pred HHHHHHHHhcCCCeEEecchHHHHhccccHHHHHHHhhhhhcCCchHHHHHHHHHhHHHHHHHHHHHhhhcccccccccC
Confidence 345667788888888888888888888888888875433 2334 444555544
Q ss_pred ccCccccccccccccccCCCCCccCcccccccCChHHHHHHHHHccCCCCccCCc--ccccccccCCceeeehhhccCCC
Q psy9695 56 FTTKGNLKLIPNAVFNVAGMPKHLCHVCHKNFSSSSALQIHMRTHTGDKPFRCTI--CQKAFTTKGNLKVREIEINIGSQ 133 (159)
Q Consensus 56 ~~~~~~l~~~~~~~~~~~~~~~~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~--C~~~f~~~~~l~~H~~~~h~~~~ 133 (159)
....++|..|+ +-.|...+||+|+.|+..+.+.+.|..|...|. +..|+|.. |..+|.+..++.+|++..|.|..
T Consensus 273 c~~~ssL~~H~--r~rHs~dkpfKCd~Cd~~c~~esdL~kH~~~HS-~~~y~C~h~~C~~s~r~~~q~~~H~~evhEg~n 349 (467)
T KOG3608|consen 273 CSSASSLTTHI--RYRHSKDKPFKCDECDTRCVRESDLAKHVQVHS-KTVYQCEHPDCHYSVRTYTQMRRHFLEVHEGNN 349 (467)
T ss_pred CCChHHHHHHH--HhhhccCCCccccchhhhhccHHHHHHHHHhcc-ccceecCCCCCcHHHHHHHHHHHHHHHhccCCC
Confidence 44444444432 123444566777777766666666777766665 55566655 77777777777777755555542
Q ss_pred CCcccccccchhhchhhhhcccc
Q psy9695 134 LPKKAQQHIGAVEGKSFQAKHKT 156 (159)
Q Consensus 134 ~~~~~~~~~C~~C~~~f~~~~~l 156 (159)
. -+|.|-.|++.|.+-..|
T Consensus 350 p----~~Y~CH~Cdr~ft~G~~L 368 (467)
T KOG3608|consen 350 P----ILYACHCCDRFFTSGKSL 368 (467)
T ss_pred C----CceeeecchhhhccchhH
Confidence 2 577788887777765544
No 7
>KOG3608|consensus
Probab=99.62 E-value=1.8e-16 Score=108.67 Aligned_cols=132 Identities=23% Similarity=0.432 Sum_probs=114.5
Q ss_pred CcccCcccccccCChHHHHHHHHh-hcCCCccccccccccccCccccccccccccccCCCCCccCcc--cccccCChHHH
Q psy9695 17 PKHLCHVCHKNFSSSSALQIHMRT-HTGDKPFRCTICQKAFTTKGNLKLIPNAVFNVAGMPKHLCHV--CHKNFSSSSAL 93 (159)
Q Consensus 17 ~~~~C~~C~~~f~~~~~~~~h~~~-~~~~~~~~c~~c~~~~~~~~~l~~~~~~~~~~~~~~~~~C~~--C~~~~~~~~~l 93 (159)
..|+|+.|+++....++|..|++. |..++||+|..|...+...++|..|.. .|. +..|.|.. |..++.+...+
T Consensus 262 n~ykCplCdmtc~~~ssL~~H~r~rHs~dkpfKCd~Cd~~c~~esdL~kH~~---~HS-~~~y~C~h~~C~~s~r~~~q~ 337 (467)
T KOG3608|consen 262 NCYKCPLCDMTCSSASSLTTHIRYRHSKDKPFKCDECDTRCVRESDLAKHVQ---VHS-KTVYQCEHPDCHYSVRTYTQM 337 (467)
T ss_pred hcccccccccCCCChHHHHHHHHhhhccCCCccccchhhhhccHHHHHHHHH---hcc-ccceecCCCCCcHHHHHHHHH
Confidence 458999999999999999999965 778999999999999999999988543 344 56799998 99999999999
Q ss_pred HHHHHHcc-C--CCCccCCcccccccccCCceeeehhhccCCCCCcccccccchhhchhhhhc
Q psy9695 94 QIHMRTHT-G--DKPFRCTICQKAFTTKGNLKVREIEINIGSQLPKKAQQHIGAVEGKSFQAK 153 (159)
Q Consensus 94 ~~H~~~h~-~--~~~~~C~~C~~~f~~~~~l~~H~~~~h~~~~~~~~~~~~~C~~C~~~f~~~ 153 (159)
.+|.+.++ + +.+|.|..|++.|++..+|.+|+ ...++.++|.+...|....|...|...
T Consensus 338 ~~H~~evhEg~np~~Y~CH~Cdr~ft~G~~L~~HL-~kkH~f~~PsGh~RFtYk~~edG~mRL 399 (467)
T KOG3608|consen 338 RRHFLEVHEGNNPILYACHCCDRFFTSGKSLSAHL-MKKHGFRLPSGHKRFTYKVDEDGFMRL 399 (467)
T ss_pred HHHHHHhccCCCCCceeeecchhhhccchhHHHHH-HHhhcccCCCCCCceeeeeccCceeee
Confidence 99999765 4 45699999999999999999999 767777899999999999998888654
No 8
>KOG3623|consensus
Probab=99.61 E-value=1.9e-16 Score=117.17 Aligned_cols=112 Identities=24% Similarity=0.525 Sum_probs=94.5
Q ss_pred CCcccCcccccccCChHHHHHHHHhh--cCCCccccccccccccCccccccccccccccC----------CCCCccCccc
Q psy9695 16 MPKHLCHVCHKNFSSSSALQIHMRTH--TGDKPFRCTICQKAFTTKGNLKLIPNAVFNVA----------GMPKHLCHVC 83 (159)
Q Consensus 16 ~~~~~C~~C~~~f~~~~~~~~h~~~~--~~~~~~~c~~c~~~~~~~~~l~~~~~~~~~~~----------~~~~~~C~~C 83 (159)
....+|+.|++.+.....+..|+... ..+..|.|..|..+|.+..-|.+|+..+.... .-+.|+|.+|
T Consensus 208 sqlltcpycdrgykrltslkeHikyrhekne~nfsC~lCsytFAyRtQLErhm~~hkpg~dqa~sltqsa~lRKFKCtEC 287 (1007)
T KOG3623|consen 208 SQLLTCPYCDRGYKRLTSLKEHIKYRHEKNEPNFSCMLCSYTFAYRTQLERHMQLHKPGGDQAISLTQSALLRKFKCTEC 287 (1007)
T ss_pred hhhhcchhHHHHHHHHHHHHHHHHHHHhhCCCCCcchhhhhhhhhHHHHHHHHHhhcCCCcccccccchhhhcccccccc
Confidence 34489999999999999999998653 35667999999999999998887664332211 1246999999
Q ss_pred ccccCChHHHHHHHHHccCCCCccCCcccccccccCCceeeehh
Q psy9695 84 HKNFSSSSALQIHMRTHTGDKPFRCTICQKAFTTKGNLKVREIE 127 (159)
Q Consensus 84 ~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~ 127 (159)
++.|.....|..|.++|.||+||.|+.|+|.|...+++..||-.
T Consensus 288 gKAFKfKHHLKEHlRIHSGEKPfeCpnCkKRFSHSGSySSHmSS 331 (1007)
T KOG3623|consen 288 GKAFKFKHHLKEHLRIHSGEKPFECPNCKKRFSHSGSYSSHMSS 331 (1007)
T ss_pred chhhhhHHHHHhhheeecCCCCcCCcccccccccCCcccccccc
Confidence 99999999999999999999999999999999999999999933
No 9
>KOG3576|consensus
Probab=99.60 E-value=1.3e-16 Score=101.63 Aligned_cols=119 Identities=23% Similarity=0.408 Sum_probs=102.6
Q ss_pred cccccCCCCcccCcccccccCChHHHHHHHHhhcCCCccccccccccccCccccccccccccccCCCCCccCcccccccC
Q psy9695 9 AVFNVAGMPKHLCHVCHKNFSSSSALQIHMRTHTGDKPFRCTICQKAFTTKGNLKLIPNAVFNVAGMPKHLCHVCHKNFS 88 (159)
Q Consensus 9 ~~~~~~~~~~~~C~~C~~~f~~~~~~~~h~~~~~~~~~~~c~~c~~~~~~~~~l~~~~~~~~~~~~~~~~~C~~C~~~~~ 88 (159)
..-+..+...|.|.+|++.|.-.-.|..|+.-|...+.+.|..||+.|...-+|++ +.+.|+|.+||.|..|+++|.
T Consensus 108 t~gsssd~d~ftCrvCgK~F~lQRmlnrh~kch~~vkr~lct~cgkgfndtfdlkr---h~rthtgvrpykc~~c~kaft 184 (267)
T KOG3576|consen 108 TIGSSSDQDSFTCRVCGKKFGLQRMLNRHLKCHSDVKRHLCTFCGKGFNDTFDLKR---HTRTHTGVRPYKCSLCEKAFT 184 (267)
T ss_pred cccCCCCCCeeeeehhhhhhhHHHHHHHHhhhccHHHHHHHhhccCcccchhhhhh---hhccccCccccchhhhhHHHH
Confidence 33444556779999999999999999999999999999999999999999999988 778899999999999999999
Q ss_pred ChHHHHHHHHHccC-----------CCCccCCcccccccccCCceeeehhhcc
Q psy9695 89 SSSALQIHMRTHTG-----------DKPFRCTICQKAFTTKGNLKVREIEINI 130 (159)
Q Consensus 89 ~~~~l~~H~~~h~~-----------~~~~~C~~C~~~f~~~~~l~~H~~~~h~ 130 (159)
..-.|..|.+.-++ ++.|.|..||..-.....+..|.+..|.
T Consensus 185 qrcsleshl~kvhgv~~~yaykerr~kl~vcedcg~t~~~~e~~~~h~~~~hp 237 (267)
T KOG3576|consen 185 QRCSLESHLKKVHGVQHQYAYKERRAKLYVCEDCGYTSERPEVYYLHLKLHHP 237 (267)
T ss_pred hhccHHHHHHHHcCchHHHHHHHhhhheeeecccCCCCCChhHHHHHHHhcCC
Confidence 99899999775443 4679999999988888888888844443
No 10
>KOG3623|consensus
Probab=99.59 E-value=2.6e-16 Score=116.48 Aligned_cols=76 Identities=28% Similarity=0.498 Sum_probs=67.6
Q ss_pred cCCCCCccCcccccccCChHHHHHHHHHccCCCCccCCcccccccccCCceeeehhhccCCCCCcccccccchhhchhhh
Q psy9695 72 VAGMPKHLCHVCHKNFSSSSALQIHMRTHTGDKPFRCTICQKAFTTKGNLKVREIEINIGSQLPKKAQQHIGAVEGKSFQ 151 (159)
Q Consensus 72 ~~~~~~~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~~h~~~~~~~~~~~~~C~~C~~~f~ 151 (159)
.+....|.|+.|+++|.-.+.|.+|+..|+|.+||+|.+|.|+|...-.|..|+ +.|.|+ +||.|+.|+|+|.
T Consensus 889 kte~gmyaCDqCDK~FqKqSSLaRHKYEHsGqRPyqC~iCkKAFKHKHHLtEHk-RLHSGE------KPfQCdKClKRFS 961 (1007)
T KOG3623|consen 889 KTEDGMYACDQCDKAFQKQSSLARHKYEHSGQRPYQCIICKKAFKHKHHLTEHK-RLHSGE------KPFQCDKCLKRFS 961 (1007)
T ss_pred cCccccchHHHHHHHHHhhHHHHHhhhhhcCCCCcccchhhHhhhhhhhhhhhh-hhccCC------Ccchhhhhhhhcc
Confidence 344557999999999988899999999999999999999999999999999999 999999 8999999999997
Q ss_pred hcc
Q psy9695 152 AKH 154 (159)
Q Consensus 152 ~~~ 154 (159)
...
T Consensus 962 HSG 964 (1007)
T KOG3623|consen 962 HSG 964 (1007)
T ss_pred ccc
Confidence 654
No 11
>PHA00733 hypothetical protein
Probab=99.31 E-value=5.6e-13 Score=81.44 Aligned_cols=97 Identities=16% Similarity=0.239 Sum_probs=73.2
Q ss_pred HHHHHHHHhhcCCCccccccccccccCccccccc--cccccccCCCCCccCcccccccCChHHHHHHHHHccCCCCccCC
Q psy9695 32 SALQIHMRTHTGDKPFRCTICQKAFTTKGNLKLI--PNAVFNVAGMPKHLCHVCHKNFSSSSALQIHMRTHTGDKPFRCT 109 (159)
Q Consensus 32 ~~~~~h~~~~~~~~~~~c~~c~~~~~~~~~l~~~--~~~~~~~~~~~~~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~ 109 (159)
.+|..+-.....++++.|.+|...+.....+..+ ........+..+|.|+.|++.|.+...|..|++.+ +.+|.|+
T Consensus 26 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~l~~~~~~~~~kPy~C~~Cgk~Fss~s~L~~H~r~h--~~~~~C~ 103 (128)
T PHA00733 26 EELKRYHSLTPEQKRLIRAVVKTLIYNPQLLDESSYLYKLLTSKAVSPYVCPLCLMPFSSSVSLKQHIRYT--EHSKVCP 103 (128)
T ss_pred HHhhhhhcCChhhhhHHHHHHhhhccChhhhcchHHHHhhcccCCCCCccCCCCCCcCCCHHHHHHHHhcC--CcCccCC
Confidence 3344333333446779999999988887777653 11122344577899999999999999999999976 4579999
Q ss_pred cccccccccCCceeeehhhcc
Q psy9695 110 ICQKAFTTKGNLKVREIEINI 130 (159)
Q Consensus 110 ~C~~~f~~~~~l~~H~~~~h~ 130 (159)
+|+++|.....|..|+...|.
T Consensus 104 ~CgK~F~~~~sL~~H~~~~h~ 124 (128)
T PHA00733 104 VCGKEFRNTDSTLDHVCKKHN 124 (128)
T ss_pred CCCCccCCHHHHHHHHHHhcC
Confidence 999999999999999955554
No 12
>PHA02768 hypothetical protein; Provisional
Probab=99.18 E-value=2e-11 Score=62.29 Aligned_cols=46 Identities=15% Similarity=0.390 Sum_probs=41.7
Q ss_pred CccCcccccccCChHHHHHHHHHccCCCCccCCcccccccccCCceee
Q psy9695 77 KHLCHVCHKNFSSSSALQIHMRTHTGDKPFRCTICQKAFTTKGNLKVR 124 (159)
Q Consensus 77 ~~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H 124 (159)
.|.|+.||+.|...+.|..|++.|+ ++|+|..|++.|.+.+.|..-
T Consensus 5 ~y~C~~CGK~Fs~~~~L~~H~r~H~--k~~kc~~C~k~f~~~s~l~~~ 50 (55)
T PHA02768 5 GYECPICGEIYIKRKSMITHLRKHN--TNLKLSNCKRISLRTGEYIEI 50 (55)
T ss_pred ccCcchhCCeeccHHHHHHHHHhcC--CcccCCcccceecccceeEEE
Confidence 5899999999999999999999998 799999999999988888643
No 13
>PLN03086 PRLI-interacting factor K; Provisional
Probab=99.14 E-value=7.3e-11 Score=87.50 Aligned_cols=92 Identities=18% Similarity=0.334 Sum_probs=54.3
Q ss_pred cccccccccccCccccccccccccccCCCCCccCcccccccCChHHHHHHHHHccCCCCccCCcccccccc---------
Q psy9695 47 FRCTICQKAFTTKGNLKLIPNAVFNVAGMPKHLCHVCHKNFSSSSALQIHMRTHTGDKPFRCTICQKAFTT--------- 117 (159)
Q Consensus 47 ~~c~~c~~~~~~~~~l~~~~~~~~~~~~~~~~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~--------- 117 (159)
+.|+.|+..|. ...+..|.. .++ .++.|+ |+..+ ....|..|...|..++++.|..|++.|..
T Consensus 454 ~~C~~Cgk~f~-~s~LekH~~---~~H--kpv~Cp-Cg~~~-~R~~L~~H~~thCp~Kpi~C~fC~~~v~~g~~~~d~~d 525 (567)
T PLN03086 454 VHCEKCGQAFQ-QGEMEKHMK---VFH--EPLQCP-CGVVL-EKEQMVQHQASTCPLRLITCRFCGDMVQAGGSAMDVRD 525 (567)
T ss_pred ccCCCCCCccc-hHHHHHHHH---hcC--CCccCC-CCCCc-chhHHHhhhhccCCCCceeCCCCCCccccCccccchhh
Confidence 46777776664 344444322 121 456777 77544 44667777777777777777777776642
Q ss_pred -cCCceeeehhhccCCCCCcccccccchhhchhhhhcc
Q psy9695 118 -KGNLKVREIEINIGSQLPKKAQQHIGAVEGKSFQAKH 154 (159)
Q Consensus 118 -~~~l~~H~~~~h~~~~~~~~~~~~~C~~C~~~f~~~~ 154 (159)
.+.|..|. ... +. +++.|..|++.+..++
T Consensus 526 ~~s~Lt~HE-~~C-G~------rt~~C~~Cgk~Vrlrd 555 (567)
T PLN03086 526 RLRGMSEHE-SIC-GS------RTAPCDSCGRSVMLKE 555 (567)
T ss_pred hhhhHHHHH-Hhc-CC------cceEccccCCeeeehh
Confidence 23566666 443 44 5677777777665543
No 14
>PLN03086 PRLI-interacting factor K; Provisional
Probab=99.11 E-value=1.6e-11 Score=90.88 Aligned_cols=62 Identities=18% Similarity=0.400 Sum_probs=39.0
Q ss_pred ccCcccccccCChHHHHHHHHHccCCCCccCCcccccccccCCceeeehhhccCCCCCcccccccchhhchhhh
Q psy9695 78 HLCHVCHKNFSSSSALQIHMRTHTGDKPFRCTICQKAFTTKGNLKVREIEINIGSQLPKKAQQHIGAVEGKSFQ 151 (159)
Q Consensus 78 ~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~~h~~~~~~~~~~~~~C~~C~~~f~ 151 (159)
+.|+.|++.|. ...|..|+..++ +++.|+ ||+.+ ....|..|+ .+|... +++.|+.|++.|.
T Consensus 454 ~~C~~Cgk~f~-~s~LekH~~~~H--kpv~Cp-Cg~~~-~R~~L~~H~-~thCp~------Kpi~C~fC~~~v~ 515 (567)
T PLN03086 454 VHCEKCGQAFQ-QGEMEKHMKVFH--EPLQCP-CGVVL-EKEQMVQHQ-ASTCPL------RLITCRFCGDMVQ 515 (567)
T ss_pred ccCCCCCCccc-hHHHHHHHHhcC--CCccCC-CCCCc-chhHHHhhh-hccCCC------CceeCCCCCCccc
Confidence 46667766664 455666666653 566676 76543 446666666 666666 6677777766663
No 15
>PHA02768 hypothetical protein; Provisional
Probab=99.02 E-value=2.8e-11 Score=61.79 Aligned_cols=43 Identities=7% Similarity=0.108 Sum_probs=39.0
Q ss_pred CccCCcccccccccCCceeeehhhccCCCCCcccccccchhhchhhhhcccc
Q psy9695 105 PFRCTICQKAFTTKGNLKVREIEINIGSQLPKKAQQHIGAVEGKSFQAKHKT 156 (159)
Q Consensus 105 ~~~C~~C~~~f~~~~~l~~H~~~~h~~~~~~~~~~~~~C~~C~~~f~~~~~l 156 (159)
.|.|+.||+.|+..+.|..|+ ++|. ++|+|..|++.|...+.|
T Consensus 5 ~y~C~~CGK~Fs~~~~L~~H~-r~H~--------k~~kc~~C~k~f~~~s~l 47 (55)
T PHA02768 5 GYECPICGEIYIKRKSMITHL-RKHN--------TNLKLSNCKRISLRTGEY 47 (55)
T ss_pred ccCcchhCCeeccHHHHHHHH-HhcC--------CcccCCcccceeccccee
Confidence 489999999999999999999 8888 368999999999987765
No 16
>PHA00733 hypothetical protein
Probab=99.00 E-value=2e-11 Score=74.59 Aligned_cols=76 Identities=18% Similarity=0.277 Sum_probs=59.9
Q ss_pred CCCCCccCcccccccCChHHHHHHHH-----HccCCCCccCCcccccccccCCceeeehhhccCCCCCcccccccchhhc
Q psy9695 73 AGMPKHLCHVCHKNFSSSSALQIHMR-----THTGDKPFRCTICQKAFTTKGNLKVREIEINIGSQLPKKAQQHIGAVEG 147 (159)
Q Consensus 73 ~~~~~~~C~~C~~~~~~~~~l~~H~~-----~h~~~~~~~C~~C~~~f~~~~~l~~H~~~~h~~~~~~~~~~~~~C~~C~ 147 (159)
..++++.|..|...|..+..|..+.. .+.+++||.|+.||+.|...+.|..|+ +.|. .+|.|+.|+
T Consensus 36 ~~~~~~~~~~~~~~~~~~~~l~~~~~l~~~~~~~~~kPy~C~~Cgk~Fss~s~L~~H~-r~h~--------~~~~C~~Cg 106 (128)
T PHA00733 36 PEQKRLIRAVVKTLIYNPQLLDESSYLYKLLTSKAVSPYVCPLCLMPFSSSVSLKQHI-RYTE--------HSKVCPVCG 106 (128)
T ss_pred hhhhhHHHHHHhhhccChhhhcchHHHHhhcccCCCCCccCCCCCCcCCCHHHHHHHH-hcCC--------cCccCCCCC
Confidence 34567899999988777666555411 234588999999999999999999999 6652 469999999
Q ss_pred hhhhhccccc
Q psy9695 148 KSFQAKHKTE 157 (159)
Q Consensus 148 ~~f~~~~~l~ 157 (159)
++|...+.|.
T Consensus 107 K~F~~~~sL~ 116 (128)
T PHA00733 107 KEFRNTDSTL 116 (128)
T ss_pred CccCCHHHHH
Confidence 9999887764
No 17
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=98.97 E-value=3.2e-10 Score=49.71 Aligned_cols=26 Identities=54% Similarity=1.170 Sum_probs=22.0
Q ss_pred HHHHHHHHccCCCCccCCcccccccc
Q psy9695 92 ALQIHMRTHTGDKPFRCTICQKAFTT 117 (159)
Q Consensus 92 ~l~~H~~~h~~~~~~~C~~C~~~f~~ 117 (159)
+|..|++.|++++||.|++|+++|.+
T Consensus 1 ~l~~H~~~H~~~k~~~C~~C~k~F~~ 26 (26)
T PF13465_consen 1 NLRRHMRTHTGEKPYKCPYCGKSFSN 26 (26)
T ss_dssp HHHHHHHHHSSSSSEEESSSSEEESS
T ss_pred CHHHHhhhcCCCCCCCCCCCcCeeCc
Confidence 47789999999999999999998863
No 18
>PHA00616 hypothetical protein
Probab=98.52 E-value=4.9e-08 Score=47.58 Aligned_cols=34 Identities=12% Similarity=0.180 Sum_probs=23.2
Q ss_pred CccCcccccccCChHHHHHHHHHccCCCCccCCc
Q psy9695 77 KHLCHVCHKNFSSSSALQIHMRTHTGDKPFRCTI 110 (159)
Q Consensus 77 ~~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~ 110 (159)
||.|+.||+.|...+.|..|.+.|++++++.|+.
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~~hg~~~~~~~~ 34 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLSVHKQNKLTLEY 34 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHHhcCCCccceeE
Confidence 4667777777777777777777777776666654
No 19
>KOG3993|consensus
Probab=98.52 E-value=9.4e-08 Score=67.90 Aligned_cols=77 Identities=17% Similarity=0.138 Sum_probs=51.2
Q ss_pred CCCccCcccccccCChHHHHHHHHHccCC----------------------------------------------CCccC
Q psy9695 75 MPKHLCHVCHKNFSSSSALQIHMRTHTGD----------------------------------------------KPFRC 108 (159)
Q Consensus 75 ~~~~~C~~C~~~~~~~~~l~~H~~~h~~~----------------------------------------------~~~~C 108 (159)
...|.|..|++.|.+...|+.|+.+|... ....+
T Consensus 354 ~gi~~C~~C~KkFrRqAYLrKHqlthq~~~~~k~~a~~f~~s~~~~l~~~~~~~a~h~~a~~~~g~~vl~~a~sael~~p 433 (500)
T KOG3993|consen 354 SGIFSCHTCGKKFRRQAYLRKHQLTHQRAPLAKEKAPKFLLSRVIPLMHFNQAVATHSSASDSHGDEVLYVAGSAELELP 433 (500)
T ss_pred CceeecHHhhhhhHHHHHHHHhHHhhhccccchhcccCcchhhcccccccccccccccccccccccceeeeeccccccCC
Confidence 34689999999999999999997765521 01235
Q ss_pred CcccccccccCCceeeehhhccCCCCCcccccccchhhchhhhhcccccC
Q psy9695 109 TICQKAFTTKGNLKVREIEINIGSQLPKKAQQHIGAVEGKSFQAKHKTET 158 (159)
Q Consensus 109 ~~C~~~f~~~~~l~~H~~~~h~~~~~~~~~~~~~C~~C~~~f~~~~~l~~ 158 (159)
++||..+..+..-..+. +.-..+ +.|.|.+|.-.|-+.-+|+|
T Consensus 434 p~~~~ppsss~~sgg~~-rlg~~~------q~f~~ky~~atfyss~~ltr 476 (500)
T KOG3993|consen 434 PYDGSPPSSSGSSGGYG-RLGIAE------QGFTCKYCPATFYSSPGLTR 476 (500)
T ss_pred CCCCCCcccCCCCCccc-cccchh------hccccccchHhhhcCcchHh
Confidence 55665555544444444 333333 67888899888888887764
No 20
>PHA00616 hypothetical protein
Probab=98.50 E-value=6.7e-08 Score=47.09 Aligned_cols=34 Identities=12% Similarity=0.180 Sum_probs=31.7
Q ss_pred cccCcccccccCChHHHHHHHHhhcCCCcccccc
Q psy9695 18 KHLCHVCHKNFSSSSALQIHMRTHTGDKPFRCTI 51 (159)
Q Consensus 18 ~~~C~~C~~~f~~~~~~~~h~~~~~~~~~~~c~~ 51 (159)
||+|+.||+.|....++..|++.+++++++.+..
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~~hg~~~~~~~~ 34 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLSVHKQNKLTLEY 34 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHHhcCCCccceeE
Confidence 6899999999999999999999999999988865
No 21
>PHA00732 hypothetical protein
Probab=98.49 E-value=1.2e-07 Score=52.88 Aligned_cols=47 Identities=26% Similarity=0.462 Sum_probs=37.9
Q ss_pred CccCcccccccCChHHHHHHHHH-ccCCCCccCCcccccccccCCceeeehhhcc
Q psy9695 77 KHLCHVCHKNFSSSSALQIHMRT-HTGDKPFRCTICQKAFTTKGNLKVREIEINI 130 (159)
Q Consensus 77 ~~~C~~C~~~~~~~~~l~~H~~~-h~~~~~~~C~~C~~~f~~~~~l~~H~~~~h~ 130 (159)
||.|..|++.|.+...|..|++. |. ++.|+.|++.|. .|..|. +++.
T Consensus 1 py~C~~Cgk~F~s~s~Lk~H~r~~H~---~~~C~~CgKsF~---~l~~H~-~~~~ 48 (79)
T PHA00732 1 MFKCPICGFTTVTLFALKQHARRNHT---LTKCPVCNKSYR---RLNQHF-YSQY 48 (79)
T ss_pred CccCCCCCCccCCHHHHHHHhhcccC---CCccCCCCCEeC---Chhhhh-cccC
Confidence 57899999999999999999885 54 468999999997 577787 4443
No 22
>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=98.45 E-value=1.8e-07 Score=40.85 Aligned_cols=25 Identities=56% Similarity=1.210 Sum_probs=20.4
Q ss_pred HHHHHHHhhcCCCcccccccccccc
Q psy9695 33 ALQIHMRTHTGDKPFRCTICQKAFT 57 (159)
Q Consensus 33 ~~~~h~~~~~~~~~~~c~~c~~~~~ 57 (159)
+|..|+++|++++||.|++|++.|.
T Consensus 1 ~l~~H~~~H~~~k~~~C~~C~k~F~ 25 (26)
T PF13465_consen 1 NLRRHMRTHTGEKPYKCPYCGKSFS 25 (26)
T ss_dssp HHHHHHHHHSSSSSEEESSSSEEES
T ss_pred CHHHHhhhcCCCCCCCCCCCcCeeC
Confidence 4678888888888888888888875
No 23
>PHA00732 hypothetical protein
Probab=98.32 E-value=7.5e-08 Score=53.75 Aligned_cols=39 Identities=26% Similarity=0.254 Sum_probs=33.3
Q ss_pred CccCCcccccccccCCceeeehh-hccCCCCCcccccccchhhchhhhhc
Q psy9695 105 PFRCTICQKAFTTKGNLKVREIE-INIGSQLPKKAQQHIGAVEGKSFQAK 153 (159)
Q Consensus 105 ~~~C~~C~~~f~~~~~l~~H~~~-~h~~~~~~~~~~~~~C~~C~~~f~~~ 153 (159)
||.|+.|++.|...+.|..|+ + .|.+ +.|+.|+++|...
T Consensus 1 py~C~~Cgk~F~s~s~Lk~H~-r~~H~~---------~~C~~CgKsF~~l 40 (79)
T PHA00732 1 MFKCPICGFTTVTLFALKQHA-RRNHTL---------TKCPVCNKSYRRL 40 (79)
T ss_pred CccCCCCCCccCCHHHHHHHh-hcccCC---------CccCCCCCEeCCh
Confidence 689999999999999999999 5 4542 4799999999853
No 24
>KOG3993|consensus
Probab=98.30 E-value=5.2e-08 Score=69.16 Aligned_cols=81 Identities=22% Similarity=0.395 Sum_probs=55.6
Q ss_pred cccccccccccCccccccccccccccCCCCCccCcccccccCChHHHHHHHHHccC------------------------
Q psy9695 47 FRCTICQKAFTTKGNLKLIPNAVFNVAGMPKHLCHVCHKNFSSSSALQIHMRTHTG------------------------ 102 (159)
Q Consensus 47 ~~c~~c~~~~~~~~~l~~~~~~~~~~~~~~~~~C~~C~~~~~~~~~l~~H~~~h~~------------------------ 102 (159)
|.|.+|...|-..-.|..|.-.. ...--|.|++|+++|.-+.+|-+|.++|.-
T Consensus 268 yiCqLCK~kYeD~F~LAQHrC~R---IV~vEYrCPEC~KVFsCPANLASHRRWHKPR~eaa~a~~~P~k~~~~~rae~~e 344 (500)
T KOG3993|consen 268 YICQLCKEKYEDAFALAQHRCPR---IVHVEYRCPECDKVFSCPANLASHRRWHKPRPEAAKAGSPPPKQAVETRAEVQE 344 (500)
T ss_pred HHHHHHHHhhhhHHHHhhccCCe---eEEeeecCCcccccccCchhhhhhhcccCCchhhhhcCCCChhhhhhhhhhhhh
Confidence 77777777665554444322111 111248888888888888888888887751
Q ss_pred ---------CCCccCCcccccccccCCceeeehhhccC
Q psy9695 103 ---------DKPFRCTICQKAFTTKGNLKVREIEINIG 131 (159)
Q Consensus 103 ---------~~~~~C~~C~~~f~~~~~l~~H~~~~h~~ 131 (159)
+..|.|..|+|.|.+..-|++|+ .+|..
T Consensus 345 a~rsg~dss~gi~~C~~C~KkFrRqAYLrKHq-lthq~ 381 (500)
T KOG3993|consen 345 AERSGDDSSSGIFSCHTCGKKFRRQAYLRKHQ-LTHQR 381 (500)
T ss_pred ccccCCcccCceeecHHhhhhhHHHHHHHHhH-Hhhhc
Confidence 12388999999999999999998 55553
No 25
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=98.13 E-value=1.2e-06 Score=60.37 Aligned_cols=55 Identities=18% Similarity=0.416 Sum_probs=44.7
Q ss_pred CCCccCCc--ccccccccCCceeeehhhccCCC------------CCcccccccchhhchhhhhccccc
Q psy9695 103 DKPFRCTI--CQKAFTTKGNLKVREIEINIGSQ------------LPKKAQQHIGAVEGKSFQAKHKTE 157 (159)
Q Consensus 103 ~~~~~C~~--C~~~f~~~~~l~~H~~~~h~~~~------------~~~~~~~~~C~~C~~~f~~~~~l~ 157 (159)
++||+|++ |+|+|.....|.-|++-=|.... ...+.+||.|.+|+|+++...+|+
T Consensus 347 ~KpykCpV~gC~K~YknqnGLKYH~lhGH~~~~~~~~p~p~~~~~F~~~~KPYrCevC~KRYKNlNGLK 415 (423)
T COG5189 347 GKPYKCPVEGCNKKYKNQNGLKYHMLHGHQNQKLHENPSPEKMNIFSAKDKPYRCEVCDKRYKNLNGLK 415 (423)
T ss_pred CceecCCCCCchhhhccccchhhhhhccccCcccCCCCCccccccccccCCceeccccchhhccCccce
Confidence 59999987 99999999999999966663322 224558999999999999988875
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=98.08 E-value=2.8e-06 Score=44.07 Aligned_cols=49 Identities=31% Similarity=0.448 Sum_probs=35.1
Q ss_pred CccCcccccccCChHHHHHHHHH-ccCC-CCccCCcccccccccCCceeeehhh
Q psy9695 77 KHLCHVCHKNFSSSSALQIHMRT-HTGD-KPFRCTICQKAFTTKGNLKVREIEI 128 (159)
Q Consensus 77 ~~~C~~C~~~~~~~~~l~~H~~~-h~~~-~~~~C~~C~~~f~~~~~l~~H~~~~ 128 (159)
.|.|+.|++. .+...|..|... |..+ +.+.||+|...+. .+|..|+...
T Consensus 2 ~f~CP~C~~~-~~~~~L~~H~~~~H~~~~~~v~CPiC~~~~~--~~l~~Hl~~~ 52 (54)
T PF05605_consen 2 SFTCPYCGKG-FSESSLVEHCEDEHRSESKNVVCPICSSRVT--DNLIRHLNSQ 52 (54)
T ss_pred CcCCCCCCCc-cCHHHHHHHHHhHCcCCCCCccCCCchhhhh--hHHHHHHHHh
Confidence 3789999994 556788888765 4443 4688999998655 4888888433
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=97.87 E-value=8.8e-06 Score=34.32 Aligned_cols=22 Identities=50% Similarity=0.828 Sum_probs=12.5
Q ss_pred ccCcccccccCChHHHHHHHHH
Q psy9695 78 HLCHVCHKNFSSSSALQIHMRT 99 (159)
Q Consensus 78 ~~C~~C~~~~~~~~~l~~H~~~ 99 (159)
|.|+.|++.|.+...|..|++.
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 3455556556555555555554
No 28
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=97.82 E-value=1.3e-05 Score=55.41 Aligned_cols=53 Identities=30% Similarity=0.652 Sum_probs=43.3
Q ss_pred CCCccCcc--cccccCChHHHHHHHHHcc-------------------CCCCccCCcccccccccCCceeeehh
Q psy9695 75 MPKHLCHV--CHKNFSSSSALQIHMRTHT-------------------GDKPFRCTICQKAFTTKGNLKVREIE 127 (159)
Q Consensus 75 ~~~~~C~~--C~~~~~~~~~l~~H~~~h~-------------------~~~~~~C~~C~~~f~~~~~l~~H~~~ 127 (159)
.+||+|+. |++.+.....|.-|+...+ .++||+|++|+|.|.....|.-|..-
T Consensus 347 ~KpykCpV~gC~K~YknqnGLKYH~lhGH~~~~~~~~p~p~~~~~F~~~~KPYrCevC~KRYKNlNGLKYHr~H 420 (423)
T COG5189 347 GKPYKCPVEGCNKKYKNQNGLKYHMLHGHQNQKLHENPSPEKMNIFSAKDKPYRCEVCDKRYKNLNGLKYHRKH 420 (423)
T ss_pred CceecCCCCCchhhhccccchhhhhhccccCcccCCCCCccccccccccCCceeccccchhhccCccceecccc
Confidence 47899987 8888888888888876322 25899999999999999999988743
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=97.80 E-value=1.5e-05 Score=33.53 Aligned_cols=23 Identities=52% Similarity=0.879 Sum_probs=20.4
Q ss_pred ccCcccccccCChHHHHHHHHhh
Q psy9695 19 HLCHVCHKNFSSSSALQIHMRTH 41 (159)
Q Consensus 19 ~~C~~C~~~f~~~~~~~~h~~~~ 41 (159)
|+|+.|++.|.+...|..|+..|
T Consensus 1 y~C~~C~~~f~~~~~l~~H~~~H 23 (23)
T PF00096_consen 1 YKCPICGKSFSSKSNLKRHMRRH 23 (23)
T ss_dssp EEETTTTEEESSHHHHHHHHHHH
T ss_pred CCCCCCCCccCCHHHHHHHHhHC
Confidence 68999999999999999998764
No 30
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=97.75 E-value=5.9e-06 Score=42.84 Aligned_cols=41 Identities=12% Similarity=0.254 Sum_probs=32.3
Q ss_pred CccCCcccccccccCCceeeehhhccCCCCCcccccccchhhchhhh
Q psy9695 105 PFRCTICQKAFTTKGNLKVREIEINIGSQLPKKAQQHIGAVEGKSFQ 151 (159)
Q Consensus 105 ~~~C~~C~~~f~~~~~l~~H~~~~h~~~~~~~~~~~~~C~~C~~~f~ 151 (159)
.|.||+|++. .....|..|....|..+. +.+.||+|...+.
T Consensus 2 ~f~CP~C~~~-~~~~~L~~H~~~~H~~~~-----~~v~CPiC~~~~~ 42 (54)
T PF05605_consen 2 SFTCPYCGKG-FSESSLVEHCEDEHRSES-----KNVVCPICSSRVT 42 (54)
T ss_pred CcCCCCCCCc-cCHHHHHHHHHhHCcCCC-----CCccCCCchhhhh
Confidence 4899999995 455778889977777652 5799999998655
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=97.68 E-value=3.1e-06 Score=37.25 Aligned_cols=22 Identities=50% Similarity=0.733 Sum_probs=10.9
Q ss_pred ccCcccccccCChHHHHHHHHH
Q psy9695 78 HLCHVCHKNFSSSSALQIHMRT 99 (159)
Q Consensus 78 ~~C~~C~~~~~~~~~l~~H~~~ 99 (159)
|.|..|++.|.+...|..|++.
T Consensus 2 ~~C~~C~~~F~~~~~l~~H~~~ 23 (27)
T PF13912_consen 2 FECDECGKTFSSLSALREHKRS 23 (27)
T ss_dssp EEETTTTEEESSHHHHHHHHCT
T ss_pred CCCCccCCccCChhHHHHHhHH
Confidence 4455555555555555555443
No 32
>PF09237 GAGA: GAGA factor; InterPro: IPR015318 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Members of this entry bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognises the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognises the A in the fourth position of the consensus sequence []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1YUI_A 1YUJ_A.
Probab=97.63 E-value=9.5e-05 Score=36.96 Aligned_cols=42 Identities=17% Similarity=0.241 Sum_probs=26.0
Q ss_pred cCCccccccCCCCcccCcccccccCChHHHHHHHHhhcCCCc
Q psy9695 5 LIPNAVFNVAGMPKHLCHVCHKNFSSSSALQIHMRTHTGDKP 46 (159)
Q Consensus 5 ~~~~~~~~~~~~~~~~C~~C~~~f~~~~~~~~h~~~~~~~~~ 46 (159)
+..+.......+.|.+|++|+..++...+|..|+.+.++.+|
T Consensus 11 ~~~~~k~~~~S~~PatCP~C~a~~~~srnLrRHle~~H~~k~ 52 (54)
T PF09237_consen 11 STKKPKSKSQSEQPATCPICGAVIRQSRNLRRHLEIRHFKKP 52 (54)
T ss_dssp -----CCCCTTS--EE-TTT--EESSHHHHHHHHHHHTTTS-
T ss_pred hhhHHHHhhccCCCCCCCcchhhccchhhHHHHHHHHhcccC
Confidence 344455556678889999999999999999999988776654
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=97.50 E-value=9.2e-05 Score=31.20 Aligned_cols=23 Identities=52% Similarity=0.933 Sum_probs=18.8
Q ss_pred ccCcccccccCChHHHHHHHHhh
Q psy9695 19 HLCHVCHKNFSSSSALQIHMRTH 41 (159)
Q Consensus 19 ~~C~~C~~~f~~~~~~~~h~~~~ 41 (159)
|.|+.|+..|.+...+..|+..+
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 67999999999999999999765
No 34
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=97.49 E-value=6.1e-05 Score=33.00 Aligned_cols=26 Identities=27% Similarity=0.664 Sum_probs=22.2
Q ss_pred CccCCcccccccccCCceeeehhhccC
Q psy9695 105 PFRCTICQKAFTTKGNLKVREIEINIG 131 (159)
Q Consensus 105 ~~~C~~C~~~f~~~~~l~~H~~~~h~~ 131 (159)
||.|..|++.|.....|..|+ +.|..
T Consensus 1 ~~~C~~C~~~F~~~~~l~~H~-~~h~~ 26 (27)
T PF13912_consen 1 PFECDECGKTFSSLSALREHK-RSHCS 26 (27)
T ss_dssp SEEETTTTEEESSHHHHHHHH-CTTTT
T ss_pred CCCCCccCCccCChhHHHHHh-HHhcC
Confidence 588999999999999999999 76653
No 35
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=97.47 E-value=0.0001 Score=31.08 Aligned_cols=23 Identities=52% Similarity=0.933 Sum_probs=11.6
Q ss_pred ccCcccccccCChHHHHHHHHHc
Q psy9695 78 HLCHVCHKNFSSSSALQIHMRTH 100 (159)
Q Consensus 78 ~~C~~C~~~~~~~~~l~~H~~~h 100 (159)
|.|+.|+..|.+...|..|+..+
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 34555555555555555555543
No 36
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=97.41 E-value=2.3e-05 Score=45.81 Aligned_cols=76 Identities=18% Similarity=0.355 Sum_probs=22.1
Q ss_pred ccccccccccCccccccccccccccCCCCCccCcccccccCChHHHHHHHHHccCCCCccCCcccccccccCCceeeehh
Q psy9695 48 RCTICQKAFTTKGNLKLIPNAVFNVAGMPKHLCHVCHKNFSSSSALQIHMRTHTGDKPFRCTICQKAFTTKGNLKVREIE 127 (159)
Q Consensus 48 ~c~~c~~~~~~~~~l~~~~~~~~~~~~~~~~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~ 127 (159)
.|..|+..|.+...+..|+...+ + +.-+... .+.....+..+...-. ...+.|.+|++.|.....|..|+..
T Consensus 1 ~C~~C~~~f~~~~~l~~H~~~~H---~---~~~~~~~-~l~~~~~~~~~~~~~~-~~~~~C~~C~~~f~s~~~l~~Hm~~ 72 (100)
T PF12756_consen 1 QCLFCDESFSSVDDLLQHMKKKH---G---FDIPDQK-YLVDPNRLLNYLRKKV-KESFRCPYCNKTFRSREALQEHMRS 72 (100)
T ss_dssp --------------------------------------------------------SSEEBSSSS-EESSHHHHHHHHHH
T ss_pred Ccccccccccccccccccccccc---c---ccccccc-cccccccccccccccc-CCCCCCCccCCCCcCHHHHHHHHcC
Confidence 48889999888888876543211 1 1111111 1112233333333221 2369999999999999999999944
Q ss_pred hccC
Q psy9695 128 INIG 131 (159)
Q Consensus 128 ~h~~ 131 (159)
.++.
T Consensus 73 ~~H~ 76 (100)
T PF12756_consen 73 KHHK 76 (100)
T ss_dssp TTTT
T ss_pred ccCC
Confidence 4443
No 37
>PRK04860 hypothetical protein; Provisional
Probab=97.34 E-value=0.00014 Score=46.22 Aligned_cols=39 Identities=26% Similarity=0.636 Sum_probs=27.1
Q ss_pred CccCcccccccCChHHHHHHHHHccCCCCccCCcccccccccC
Q psy9695 77 KHLCHVCHKNFSSSSALQIHMRTHTGDKPFRCTICQKAFTTKG 119 (159)
Q Consensus 77 ~~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~ 119 (159)
+|.|. |+. ....+..|.+++.++++|.|..|+..|....
T Consensus 119 ~Y~C~-C~~---~~~~~rrH~ri~~g~~~YrC~~C~~~l~~~~ 157 (160)
T PRK04860 119 PYRCK-CQE---HQLTVRRHNRVVRGEAVYRCRRCGETLVFKG 157 (160)
T ss_pred EEEcC-CCC---eeCHHHHHHHHhcCCccEECCCCCceeEEec
Confidence 57776 776 4455677777777777777777777766543
No 38
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=97.12 E-value=0.00041 Score=40.44 Aligned_cols=74 Identities=31% Similarity=0.405 Sum_probs=22.1
Q ss_pred cCcccccccCChHHHHHHHHhhcCCCccccccccccccCccccccccccccccCCCCCccCcccccccCChHHHHHHHHH
Q psy9695 20 LCHVCHKNFSSSSALQIHMRTHTGDKPFRCTICQKAFTTKGNLKLIPNAVFNVAGMPKHLCHVCHKNFSSSSALQIHMRT 99 (159)
Q Consensus 20 ~C~~C~~~f~~~~~~~~h~~~~~~~~~~~c~~c~~~~~~~~~l~~~~~~~~~~~~~~~~~C~~C~~~~~~~~~l~~H~~~ 99 (159)
+|..|+..|.+...+..|+...++...- . .........+.. ..... -...+.|..|++.|.+...|..|++.
T Consensus 1 ~C~~C~~~f~~~~~l~~H~~~~H~~~~~---~-~~~l~~~~~~~~---~~~~~-~~~~~~C~~C~~~f~s~~~l~~Hm~~ 72 (100)
T PF12756_consen 1 QCLFCDESFSSVDDLLQHMKKKHGFDIP---D-QKYLVDPNRLLN---YLRKK-VKESFRCPYCNKTFRSREALQEHMRS 72 (100)
T ss_dssp --------------------------------------------------------SSEEBSSSS-EESSHHHHHHHHHH
T ss_pred Cccccccccccccccccccccccccccc---c-cccccccccccc---ccccc-cCCCCCCCccCCCCcCHHHHHHHHcC
Confidence 5899999999999999999654432111 1 011111111111 11111 11259999999999999999999997
Q ss_pred cc
Q psy9695 100 HT 101 (159)
Q Consensus 100 h~ 101 (159)
+.
T Consensus 73 ~~ 74 (100)
T PF12756_consen 73 KH 74 (100)
T ss_dssp TT
T ss_pred cc
Confidence 53
No 39
>PF09237 GAGA: GAGA factor; InterPro: IPR015318 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Members of this entry bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognises the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognises the A in the fourth position of the consensus sequence []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1YUI_A 1YUJ_A.
Probab=96.97 E-value=0.001 Score=33.32 Aligned_cols=34 Identities=21% Similarity=0.355 Sum_probs=20.7
Q ss_pred cCCCCCccCcccccccCChHHHHHHHHHccCCCC
Q psy9695 72 VAGMPKHLCHVCHKNFSSSSALQIHMRTHTGDKP 105 (159)
Q Consensus 72 ~~~~~~~~C~~C~~~~~~~~~l~~H~~~h~~~~~ 105 (159)
.....|-.|+.|+..+....+|..|+...++.+|
T Consensus 19 ~~S~~PatCP~C~a~~~~srnLrRHle~~H~~k~ 52 (54)
T PF09237_consen 19 SQSEQPATCPICGAVIRQSRNLRRHLEIRHFKKP 52 (54)
T ss_dssp CTTS--EE-TTT--EESSHHHHHHHHHHHTTTS-
T ss_pred hccCCCCCCCcchhhccchhhHHHHHHHHhcccC
Confidence 3455677888888888888888888877666554
No 40
>smart00355 ZnF_C2H2 zinc finger.
Probab=96.94 E-value=0.0011 Score=28.17 Aligned_cols=22 Identities=59% Similarity=0.874 Sum_probs=12.6
Q ss_pred cCcccccccCChHHHHHHHHHc
Q psy9695 79 LCHVCHKNFSSSSALQIHMRTH 100 (159)
Q Consensus 79 ~C~~C~~~~~~~~~l~~H~~~h 100 (159)
.|..|++.|.....|..|++.|
T Consensus 2 ~C~~C~~~f~~~~~l~~H~~~H 23 (26)
T smart00355 2 RCPECGKVFKSKSALKEHMRTH 23 (26)
T ss_pred CCCCCcchhCCHHHHHHHHHHh
Confidence 4555666666655666665543
No 41
>PRK04860 hypothetical protein; Provisional
Probab=96.92 E-value=0.00016 Score=46.04 Aligned_cols=40 Identities=20% Similarity=0.401 Sum_probs=35.3
Q ss_pred CccCCcccccccccCCceeeehhhccCCCCCcccccccchhhchhhhhccc
Q psy9695 105 PFRCTICQKAFTTKGNLKVREIEINIGSQLPKKAQQHIGAVEGKSFQAKHK 155 (159)
Q Consensus 105 ~~~C~~C~~~f~~~~~l~~H~~~~h~~~~~~~~~~~~~C~~C~~~f~~~~~ 155 (159)
+|.|. |+. ....++.|. ++|.++ ++|.|..|+..|.....
T Consensus 119 ~Y~C~-C~~---~~~~~rrH~-ri~~g~------~~YrC~~C~~~l~~~~~ 158 (160)
T PRK04860 119 PYRCK-CQE---HQLTVRRHN-RVVRGE------AVYRCRRCGETLVFKGE 158 (160)
T ss_pred EEEcC-CCC---eeCHHHHHH-HHhcCC------ccEECCCCCceeEEecc
Confidence 69998 997 788889999 999999 89999999999986654
No 42
>smart00355 ZnF_C2H2 zinc finger.
Probab=96.90 E-value=0.0011 Score=28.14 Aligned_cols=24 Identities=54% Similarity=0.721 Sum_probs=20.7
Q ss_pred ccCcccccccCChHHHHHHHHhhc
Q psy9695 19 HLCHVCHKNFSSSSALQIHMRTHT 42 (159)
Q Consensus 19 ~~C~~C~~~f~~~~~~~~h~~~~~ 42 (159)
|.|+.|++.|.....+..|+..|.
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~~H~ 24 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMRTHX 24 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHHHhc
Confidence 579999999999999999988654
No 43
>PF12171 zf-C2H2_jaz: Zinc-finger double-stranded RNA-binding; InterPro: IPR022755 This zinc finger is found in archaea and eukaryotes, and is approximately 30 amino acids in length. The mammalian members of this group occur multiple times along the protein, joined by flexible linkers, and are referred to as JAZ - dsRNA-binding ZF protein - zinc-fingers. The JAZ proteins are expressed in all tissues tested and localise in the nucleus, particularly the nucleolus []. JAZ preferentially binds to double-stranded (ds) RNA or RNA/DNA hybrids rather than DNA. In addition to binding double-stranded RNA, these zinc-fingers are required for nucleolar localisation. This entry represents the multiple-adjacent-C2H2 zinc finger, JAZ. ; PDB: 4DGW_A 1ZR9_A.
Probab=96.50 E-value=0.00047 Score=30.14 Aligned_cols=20 Identities=35% Similarity=0.765 Sum_probs=16.1
Q ss_pred ccCCcccccccccCCceeee
Q psy9695 106 FRCTICQKAFTTKGNLKVRE 125 (159)
Q Consensus 106 ~~C~~C~~~f~~~~~l~~H~ 125 (159)
|.|..|++.|.....|..|+
T Consensus 2 ~~C~~C~k~f~~~~~~~~H~ 21 (27)
T PF12171_consen 2 FYCDACDKYFSSENQLKQHM 21 (27)
T ss_dssp CBBTTTTBBBSSHHHHHCCT
T ss_pred CCcccCCCCcCCHHHHHHHH
Confidence 67888888888888888887
No 44
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=96.20 E-value=0.0032 Score=26.77 Aligned_cols=22 Identities=41% Similarity=0.967 Sum_probs=18.6
Q ss_pred ccCcccccccCChHHHHHHHHh
Q psy9695 19 HLCHVCHKNFSSSSALQIHMRT 40 (159)
Q Consensus 19 ~~C~~C~~~f~~~~~~~~h~~~ 40 (159)
|.|..|+..|.+...+..|++.
T Consensus 1 ~~C~~C~~~f~s~~~~~~H~~s 22 (25)
T PF12874_consen 1 FYCDICNKSFSSENSLRQHLRS 22 (25)
T ss_dssp EEETTTTEEESSHHHHHHHHTT
T ss_pred CCCCCCCCCcCCHHHHHHHHCc
Confidence 5688999999999999988864
No 45
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=96.16 E-value=0.0047 Score=26.01 Aligned_cols=23 Identities=30% Similarity=0.527 Sum_probs=17.3
Q ss_pred ccCcccccccCChHHHHHHHHhhc
Q psy9695 19 HLCHVCHKNFSSSSALQIHMRTHT 42 (159)
Q Consensus 19 ~~C~~C~~~f~~~~~~~~h~~~~~ 42 (159)
|+|+.|+.... ...|..|+..++
T Consensus 1 y~C~~C~y~t~-~~~l~~H~~~~H 23 (24)
T PF13909_consen 1 YKCPHCSYSTS-KSNLKRHLKRHH 23 (24)
T ss_dssp EE-SSSS-EES-HHHHHHHHHHHH
T ss_pred CCCCCCCCcCC-HHHHHHHHHhhC
Confidence 68999998887 888999987754
No 46
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=95.93 E-value=0.0063 Score=25.58 Aligned_cols=22 Identities=32% Similarity=0.555 Sum_probs=11.6
Q ss_pred ccCcccccccCChHHHHHHHHHc
Q psy9695 78 HLCHVCHKNFSSSSALQIHMRTH 100 (159)
Q Consensus 78 ~~C~~C~~~~~~~~~l~~H~~~h 100 (159)
|.|+.|+.... ...|..|++.+
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 45666665555 55666666554
No 47
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=95.86 E-value=0.0043 Score=26.36 Aligned_cols=20 Identities=45% Similarity=1.041 Sum_probs=9.7
Q ss_pred cCcccccccCChHHHHHHHH
Q psy9695 79 LCHVCHKNFSSSSALQIHMR 98 (159)
Q Consensus 79 ~C~~C~~~~~~~~~l~~H~~ 98 (159)
.|..|+..|.+...+..|.+
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 34455555555555544443
No 48
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=95.60 E-value=0.008 Score=30.65 Aligned_cols=37 Identities=19% Similarity=0.180 Sum_probs=30.7
Q ss_pred cCCccccccCCCCcccCcccccccCChHHHHHHHHhh
Q psy9695 5 LIPNAVFNVAGMPKHLCHVCHKNFSSSSALQIHMRTH 41 (159)
Q Consensus 5 ~~~~~~~~~~~~~~~~C~~C~~~f~~~~~~~~h~~~~ 41 (159)
+.+..+.+-+||.-+.|+-|+..|+.......|+...
T Consensus 4 ~KA~Kv~~RDGE~~lrCPRC~~~FR~~K~Y~RHVNKa 40 (65)
T COG4049 4 LKAIKVRDRDGEEFLRCPRCGMVFRRRKDYIRHVNKA 40 (65)
T ss_pred ceeeEeeccCCceeeeCCchhHHHHHhHHHHHHhhHH
Confidence 3445567778999999999999999999999998653
No 49
>cd00350 rubredoxin_like Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center. The family includes rubredoxins, a small electron transfer protein, and a slightly smaller modular rubredoxin domain present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=95.48 E-value=0.0081 Score=27.56 Aligned_cols=10 Identities=30% Similarity=1.119 Sum_probs=5.8
Q ss_pred CCccCCcccc
Q psy9695 104 KPFRCTICQK 113 (159)
Q Consensus 104 ~~~~C~~C~~ 113 (159)
.++.|++||.
T Consensus 16 ~~~~CP~Cg~ 25 (33)
T cd00350 16 APWVCPVCGA 25 (33)
T ss_pred CCCcCcCCCC
Confidence 4566666653
No 50
>KOG1146|consensus
Probab=95.15 E-value=0.029 Score=46.49 Aligned_cols=128 Identities=16% Similarity=0.285 Sum_probs=76.7
Q ss_pred CCCcccCcccccccCChHHHHHHHHhhcCCCccccccccccccCccccccccccccccCCCCCccCcccccccCChHHHH
Q psy9695 15 GMPKHLCHVCHKNFSSSSALQIHMRTHTGDKPFRCTICQKAFTTKGNLKLIPNAVFNVAGMPKHLCHVCHKNFSSSSALQ 94 (159)
Q Consensus 15 ~~~~~~C~~C~~~f~~~~~~~~h~~~~~~~~~~~c~~c~~~~~~~~~l~~~~~~~~~~~~~~~~~C~~C~~~~~~~~~l~ 94 (159)
-.+-++|+.|+..++....|..|++..+.+... ..|- .+.....+.+ -..-..+..+|.|..|...+.....|.
T Consensus 462 ~~kt~~cpkc~~~yk~a~~L~vhmRskhp~~~~--~~c~-~gq~~~~~ar---g~~~~~~~~p~~C~~C~~stttng~Ls 535 (1406)
T KOG1146|consen 462 FFKTLKCPKCNWHYKLAQTLGVHMRSKHPESQS--AYCK-AGQNHPRLAR---GEVYRCPGKPYPCRACNYSTTTNGNLS 535 (1406)
T ss_pred ccccccCCccchhhhhHHHhhhcccccccccch--hHhH-hccccccccc---cccccCCCCcccceeeeeeeecchHHH
Confidence 346689999999999999999998763322111 1111 0101100100 001122345677888887777777777
Q ss_pred HHHHHcc------------------------------------------C-CCCccCCcccccccccCCceeeehhhccC
Q psy9695 95 IHMRTHT------------------------------------------G-DKPFRCTICQKAFTTKGNLKVREIEINIG 131 (159)
Q Consensus 95 ~H~~~h~------------------------------------------~-~~~~~C~~C~~~f~~~~~l~~H~~~~h~~ 131 (159)
.|+.... . .-+|.|.+|+..-.-..+|+.|+...++.
T Consensus 536 ihlqS~~h~~~lee~~~~~g~~v~~~~~~v~s~~P~~ag~~~~ags~~pktkP~~~C~vc~yetniarnlrihmtss~~s 615 (1406)
T KOG1146|consen 536 IHLQSDLHRNELEEAEENAGEQVRLLPASVTSAVPEEAGLGPSAGSSGPKTKPSWRCEVCSYETNIARNLRIHMTASPSS 615 (1406)
T ss_pred HHHHHHhhHHHHHHHHhccccchhhhhhhhcccCcccccCCCCCCCCCCCCCCCcchhhhcchhhhhhccccccccCCCC
Confidence 7766211 0 12489999999888889999999666665
Q ss_pred CCCCcccccccchhhchhhhhcc
Q psy9695 132 SQLPKKAQQHIGAVEGKSFQAKH 154 (159)
Q Consensus 132 ~~~~~~~~~~~C~~C~~~f~~~~ 154 (159)
. .+--+..+...+...+
T Consensus 616 ~------~p~~~Lq~~it~~l~~ 632 (1406)
T KOG1146|consen 616 S------PPSLVLQQNITSSLAS 632 (1406)
T ss_pred C------ChHHHhhhcchhhccc
Confidence 5 4455555555554433
No 51
>KOG2231|consensus
Probab=95.12 E-value=0.012 Score=45.62 Aligned_cols=45 Identities=24% Similarity=0.530 Sum_probs=34.4
Q ss_pred ccCcccccccCChHHHHHHHHHccCCCCccCCcc------cccccccCCceeeeh
Q psy9695 78 HLCHVCHKNFSSSSALQIHMRTHTGDKPFRCTIC------QKAFTTKGNLKVREI 126 (159)
Q Consensus 78 ~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C------~~~f~~~~~l~~H~~ 126 (159)
-.|..|..-|.....|..|++.++ |.|..| +.-|.....|..|..
T Consensus 183 p~C~~C~~~fld~~el~rH~~~~h----~~chfC~~~~~~neyy~~~~dLe~HfR 233 (669)
T KOG2231|consen 183 PLCKFCHERFLDDDELYRHLRFDH----EFCHFCDYKTGQNEYYNDYDDLEEHFR 233 (669)
T ss_pred ccchhhhhhhccHHHHHHhhccce----eheeecCcccccchhcccchHHHHHhh
Confidence 568889999988889999988654 556555 456677788888883
No 52
>PHA00626 hypothetical protein
Probab=94.66 E-value=0.012 Score=30.05 Aligned_cols=15 Identities=13% Similarity=0.352 Sum_probs=8.8
Q ss_pred CCccCCccccccccc
Q psy9695 104 KPFRCTICQKAFTTK 118 (159)
Q Consensus 104 ~~~~C~~C~~~f~~~ 118 (159)
..|.|+.||..|+-.
T Consensus 22 nrYkCkdCGY~ft~~ 36 (59)
T PHA00626 22 DDYVCCDCGYNDSKD 36 (59)
T ss_pred cceEcCCCCCeechh
Confidence 446666666666543
No 53
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=94.33 E-value=0.044 Score=32.67 Aligned_cols=45 Identities=18% Similarity=0.535 Sum_probs=29.6
Q ss_pred cCcccccccCChHHHHHHHHHccCCCCccCCcccccccccCCceeee
Q psy9695 79 LCHVCHKNFSSSSALQIHMRTHTGDKPFRCTICQKAFTTKGNLKVRE 125 (159)
Q Consensus 79 ~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~ 125 (159)
.|-.|...|....... ...-.....|+|+.|...|-..-+.-.|.
T Consensus 57 ~C~~C~~~f~~~~~~~--~~~~~~~~~y~C~~C~~~FC~dCD~fiHe 101 (112)
T TIGR00622 57 FCFGCQGPFPKPPVSP--FDELKDSHRYVCAVCKNVFCVDCDVFVHE 101 (112)
T ss_pred cccCcCCCCCCccccc--ccccccccceeCCCCCCccccccchhhhh
Confidence 4788888776543111 00012244689999999999888888888
No 54
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=94.33 E-value=0.052 Score=23.14 Aligned_cols=20 Identities=25% Similarity=0.688 Sum_probs=14.2
Q ss_pred ccCcccccccCChHHHHHHHH
Q psy9695 19 HLCHVCHKNFSSSSALQIHMR 39 (159)
Q Consensus 19 ~~C~~C~~~f~~~~~~~~h~~ 39 (159)
..|+.|++.| ....+..|+.
T Consensus 3 ~~C~~CgR~F-~~~~l~~H~~ 22 (25)
T PF13913_consen 3 VPCPICGRKF-NPDRLEKHEK 22 (25)
T ss_pred CcCCCCCCEE-CHHHHHHHHH
Confidence 4688888888 5666777754
No 55
>KOG2893|consensus
Probab=93.90 E-value=0.043 Score=36.98 Aligned_cols=48 Identities=25% Similarity=0.652 Sum_probs=40.1
Q ss_pred cCcccccccCChHHHHHHHHHccCCCCccCCcccccccccCCceeeehhhcc
Q psy9695 79 LCHVCHKNFSSSSALQIHMRTHTGDKPFRCTICQKAFTTKGNLKVREIEINI 130 (159)
Q Consensus 79 ~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~~h~ 130 (159)
.|=+|++.|.....|+.|+++ +-|+|.+|.|..-+...|..|--++|.
T Consensus 12 wcwycnrefddekiliqhqka----khfkchichkkl~sgpglsihcmqvhk 59 (341)
T KOG2893|consen 12 WCWYCNREFDDEKILIQHQKA----KHFKCHICHKKLFSGPGLSIHCMQVHK 59 (341)
T ss_pred eeeecccccchhhhhhhhhhh----ccceeeeehhhhccCCCceeehhhhhh
Confidence 477899999999999988874 458999999999888899888756653
No 56
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=93.37 E-value=0.033 Score=37.49 Aligned_cols=50 Identities=20% Similarity=0.175 Sum_probs=23.9
Q ss_pred CCccCCcccccccccCCceeeehhhcc--------CCCCCcccccccchhhchhhhhc
Q psy9695 104 KPFRCTICQKAFTTKGNLKVREIEINI--------GSQLPKKAQQHIGAVEGKSFQAK 153 (159)
Q Consensus 104 ~~~~C~~C~~~f~~~~~l~~H~~~~h~--------~~~~~~~~~~~~C~~C~~~f~~~ 153 (159)
+...||+|++.|....-.....+.... ++..|.-=....||.||.+|...
T Consensus 4 k~~~CPvC~~~F~~~~vrs~~~r~~~~d~D~~~~Y~~vnP~~Y~V~vCP~CgyA~~~~ 61 (214)
T PF09986_consen 4 KKITCPVCGKEFKTKKVRSGKIRVIRRDSDFCPRYKGVNPLFYEVWVCPHCGYAAFEE 61 (214)
T ss_pred CceECCCCCCeeeeeEEEcCCceEeeecCCCccccCCCCCeeeeEEECCCCCCccccc
Confidence 445677777776655444433311111 11111111355677777776544
No 57
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=93.36 E-value=0.011 Score=30.19 Aligned_cols=29 Identities=17% Similarity=0.359 Sum_probs=19.6
Q ss_pred CCCCccCCcccccccccCCceeeehhhcc
Q psy9695 102 GDKPFRCTICQKAFTTKGNLKVREIEINI 130 (159)
Q Consensus 102 ~~~~~~C~~C~~~f~~~~~l~~H~~~~h~ 130 (159)
||..++||-||..|...-+...|..+.|.
T Consensus 14 GE~~lrCPRC~~~FR~~K~Y~RHVNKaH~ 42 (65)
T COG4049 14 GEEFLRCPRCGMVFRRRKDYIRHVNKAHG 42 (65)
T ss_pred CceeeeCCchhHHHHHhHHHHHHhhHHhh
Confidence 45556777777777777777777755553
No 58
>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=92.67 E-value=0.11 Score=23.82 Aligned_cols=22 Identities=18% Similarity=0.711 Sum_probs=18.5
Q ss_pred cccCcccccccCChHHHHHHHH
Q psy9695 18 KHLCHVCHKNFSSSSALQIHMR 39 (159)
Q Consensus 18 ~~~C~~C~~~f~~~~~~~~h~~ 39 (159)
+|.|..|+..|.+...+..|+.
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~ 24 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLK 24 (35)
T ss_pred CeEccccCCccCCHHHHHHHHC
Confidence 5789999999998888888874
No 59
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=92.58 E-value=0.1 Score=35.17 Aligned_cols=10 Identities=20% Similarity=0.494 Sum_probs=6.6
Q ss_pred ccCccccccc
Q psy9695 78 HLCHVCHKNF 87 (159)
Q Consensus 78 ~~C~~C~~~~ 87 (159)
++|+.||.++
T Consensus 49 ~vCP~CgyA~ 58 (214)
T PF09986_consen 49 WVCPHCGYAA 58 (214)
T ss_pred EECCCCCCcc
Confidence 5677777654
No 60
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=92.44 E-value=0.062 Score=39.51 Aligned_cols=56 Identities=34% Similarity=0.627 Sum_probs=49.4
Q ss_pred CCccCcccccccCChHHHHHHHH--HccCC--CCccCC--cccccccccCCceeeehhhccCC
Q psy9695 76 PKHLCHVCHKNFSSSSALQIHMR--THTGD--KPFRCT--ICQKAFTTKGNLKVREIEINIGS 132 (159)
Q Consensus 76 ~~~~C~~C~~~~~~~~~l~~H~~--~h~~~--~~~~C~--~C~~~f~~~~~l~~H~~~~h~~~ 132 (159)
.++.|..|...|.....+..|.. .|.++ +++.|+ .|++.|.+...+..|. ..|.+.
T Consensus 288 ~~~~~~~~~~~~s~~~~l~~~~~~~~h~~~~~~~~~~p~~~~~~~~~~~~~~~~~~-~~~~~~ 349 (467)
T COG5048 288 LPIKSKQCNISFSRSSPLTRHLRSVNHSGESLKPFSCPYSLCGKLFSRNDALKRHI-LLHTSI 349 (467)
T ss_pred cCCCCccccCCccccccccccccccccccccCCceeeeccCCCccccccccccCCc-ccccCC
Confidence 35888999999999999999999 79999 899999 7999999999999999 888766
No 61
>cd00729 rubredoxin_SM Rubredoxin, Small Modular nonheme iron binding domain containing a [Fe(SCys)4] center, present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=92.02 E-value=0.088 Score=24.29 Aligned_cols=10 Identities=30% Similarity=0.664 Sum_probs=5.3
Q ss_pred ccCccccccc
Q psy9695 78 HLCHVCHKNF 87 (159)
Q Consensus 78 ~~C~~C~~~~ 87 (159)
|.|..||..+
T Consensus 3 ~~C~~CG~i~ 12 (34)
T cd00729 3 WVCPVCGYIH 12 (34)
T ss_pred EECCCCCCEe
Confidence 4555555543
No 62
>KOG2186|consensus
Probab=91.99 E-value=0.069 Score=36.32 Aligned_cols=45 Identities=24% Similarity=0.505 Sum_probs=32.0
Q ss_pred ccCcccccccCChHHHHHHHHHccCCCCccCCcccccccccCCceeee
Q psy9695 78 HLCHVCHKNFSSSSALQIHMRTHTGDKPFRCTICQKAFTTKGNLKVRE 125 (159)
Q Consensus 78 ~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~ 125 (159)
|.|..||....-+ .+..|+...++ .-|.|..|++.|.. .+...|.
T Consensus 4 FtCnvCgEsvKKp-~vekH~srCrn-~~fSCIDC~k~F~~-~sYknH~ 48 (276)
T KOG2186|consen 4 FTCNVCGESVKKP-QVEKHMSRCRN-AYFSCIDCGKTFER-VSYKNHT 48 (276)
T ss_pred Eehhhhhhhcccc-chHHHHHhccC-CeeEEeeccccccc-chhhhhh
Confidence 6788888776555 35567777766 55788888888877 6666666
No 63
>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=91.96 E-value=0.055 Score=26.29 Aligned_cols=12 Identities=25% Similarity=0.650 Sum_probs=6.5
Q ss_pred ccCcccccccCC
Q psy9695 78 HLCHVCHKNFSS 89 (159)
Q Consensus 78 ~~C~~C~~~~~~ 89 (159)
|.|..||..|..
T Consensus 6 y~C~~Cg~~fe~ 17 (42)
T PF09723_consen 6 YRCEECGHEFEV 17 (42)
T ss_pred EEeCCCCCEEEE
Confidence 555555555543
No 64
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=91.84 E-value=0.054 Score=28.19 Aligned_cols=32 Identities=25% Similarity=0.580 Sum_probs=16.4
Q ss_pred CccCcccccccCChHHHHHHHHHccCCCCccCCcccc
Q psy9695 77 KHLCHVCHKNFSSSSALQIHMRTHTGDKPFRCTICQK 113 (159)
Q Consensus 77 ~~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~ 113 (159)
.|.|+.||+.....-. .-+ ....+|.|+.||.
T Consensus 25 ~F~CPnCG~~~I~RC~---~CR--k~~~~Y~CP~CGF 56 (59)
T PRK14890 25 KFLCPNCGEVIIYRCE---KCR--KQSNPYTCPKCGF 56 (59)
T ss_pred EeeCCCCCCeeEeech---hHH--hcCCceECCCCCC
Confidence 4777777765322211 011 1235677777774
No 65
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=91.36 E-value=0.14 Score=37.57 Aligned_cols=121 Identities=27% Similarity=0.492 Sum_probs=70.4
Q ss_pred CcccCcccccccCChHHHHHHHH--hhcCC--Cccccc--cccccccCccccccccccccccCCCCCccCcc--------
Q psy9695 17 PKHLCHVCHKNFSSSSALQIHMR--THTGD--KPFRCT--ICQKAFTTKGNLKLIPNAVFNVAGMPKHLCHV-------- 82 (159)
Q Consensus 17 ~~~~C~~C~~~f~~~~~~~~h~~--~~~~~--~~~~c~--~c~~~~~~~~~l~~~~~~~~~~~~~~~~~C~~-------- 82 (159)
.++.|..|...|.....+..|.. .|.++ +++.|+ .|+..|.....+.. +...+.+..++.+..
T Consensus 288 ~~~~~~~~~~~~s~~~~l~~~~~~~~h~~~~~~~~~~p~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~ 364 (467)
T COG5048 288 LPIKSKQCNISFSRSSPLTRHLRSVNHSGESLKPFSCPYSLCGKLFSRNDALKR---HILLHTSISPAKEKLLNSSSKFS 364 (467)
T ss_pred cCCCCccccCCccccccccccccccccccccCCceeeeccCCCccccccccccC---CcccccCCCccccccccCccccc
Confidence 45777778888877777777777 67777 777777 67777777776655 223333333322222
Q ss_pred -----------------------------cccccCChHHHHHHHHHccCCC--CccCCcccccccccCCceeeehhhccC
Q psy9695 83 -----------------------------CHKNFSSSSALQIHMRTHTGDK--PFRCTICQKAFTTKGNLKVREIEINIG 131 (159)
Q Consensus 83 -----------------------------C~~~~~~~~~l~~H~~~h~~~~--~~~C~~C~~~f~~~~~l~~H~~~~h~~ 131 (159)
|...+.....+..|...+.... .+.+..|.+.|.....+..|+ +.|..
T Consensus 365 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~ 443 (467)
T COG5048 365 PLLNNEPPQSLQQYKDLKNDKKSETLSNSCIRNFKRDSNLSLHIITHLSFRPYNCKNPPCSKSFNRHYNLIPHK-KIHTN 443 (467)
T ss_pred cccCCCCccchhhccCccCCccccccccchhhhhccccccccccccccccCCcCCCCCcchhhccCcccccccc-ccccc
Confidence 1112222222222222222222 355677888888888888888 77766
Q ss_pred CCCCcccccccchhhc
Q psy9695 132 SQLPKKAQQHIGAVEG 147 (159)
Q Consensus 132 ~~~~~~~~~~~C~~C~ 147 (159)
. .++.|..++
T Consensus 444 ~------~~~~~~~~~ 453 (467)
T COG5048 444 H------APLLCSILK 453 (467)
T ss_pred C------Cceeecccc
Confidence 5 455554443
No 66
>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=90.94 E-value=0.093 Score=25.09 Aligned_cols=11 Identities=27% Similarity=0.697 Sum_probs=5.9
Q ss_pred ccCcccccccC
Q psy9695 78 HLCHVCHKNFS 88 (159)
Q Consensus 78 ~~C~~C~~~~~ 88 (159)
|.|+.||..|.
T Consensus 6 y~C~~Cg~~fe 16 (41)
T smart00834 6 YRCEDCGHTFE 16 (41)
T ss_pred EEcCCCCCEEE
Confidence 45555555553
No 67
>KOG2893|consensus
Probab=90.92 E-value=0.054 Score=36.55 Aligned_cols=42 Identities=19% Similarity=0.333 Sum_probs=32.5
Q ss_pred CCCccCCcccccccccCCceeeehhhccCCCCCcccccccchhhchhhhhcccc
Q psy9695 103 DKPFRCTICQKAFTTKGNLKVREIEINIGSQLPKKAQQHIGAVEGKSFQAKHKT 156 (159)
Q Consensus 103 ~~~~~C~~C~~~f~~~~~l~~H~~~~h~~~~~~~~~~~~~C~~C~~~f~~~~~l 156 (159)
+++| |.+|++.|-..-.|..|++. +-|+|-+|.+++-+--.|
T Consensus 9 ~kpw-cwycnrefddekiliqhqka-----------khfkchichkkl~sgpgl 50 (341)
T KOG2893|consen 9 DKPW-CWYCNREFDDEKILIQHQKA-----------KHFKCHICHKKLFSGPGL 50 (341)
T ss_pred CCce-eeecccccchhhhhhhhhhh-----------ccceeeeehhhhccCCCc
Confidence 4554 89999999999999888822 458999999987665443
No 68
>KOG2482|consensus
Probab=90.15 E-value=0.33 Score=34.67 Aligned_cols=109 Identities=23% Similarity=0.376 Sum_probs=65.6
Q ss_pred cccCcccccccCChHHHHHHHHh--hcCCCc--------cc--cccccccccCccc-cccccc-ccc-c--------cCC
Q psy9695 18 KHLCHVCHKNFSSSSALQIHMRT--HTGDKP--------FR--CTICQKAFTTKGN-LKLIPN-AVF-N--------VAG 74 (159)
Q Consensus 18 ~~~C~~C~~~f~~~~~~~~h~~~--~~~~~~--------~~--c~~c~~~~~~~~~-l~~~~~-~~~-~--------~~~ 74 (159)
.+.|-.|.+.|+.+..|..||+. |....| |. ...-|++.+.... ..+... ... . ..+
T Consensus 195 r~~CLyCekifrdkntLkeHMrkK~HrrinPknreYDkfyiINY~ev~ks~t~~~~e~dret~~d~~E~D~~wsDw~ed~ 274 (423)
T KOG2482|consen 195 RLRCLYCEKIFRDKNTLKEHMRKKRHRRINPKNREYDKFYIINYLEVGKSWTIVHSEDDRETNEDINETDDTWSDWNEDD 274 (423)
T ss_pred hheeeeeccccCCcHHHHHHHHhccCcccCCCccccceEEEEeHhhcCCccchhhhhhhhhhhccccccccchhhhhcCC
Confidence 47899999999999999999975 322222 11 1112222111100 000000 000 0 001
Q ss_pred CCC--ccCcccccccCChHHHHHHHHHccC-C--------------------------CCccCCcccccccccCCceeee
Q psy9695 75 MPK--HLCHVCHKNFSSSSALQIHMRTHTG-D--------------------------KPFRCTICQKAFTTKGNLKVRE 125 (159)
Q Consensus 75 ~~~--~~C~~C~~~~~~~~~l~~H~~~h~~-~--------------------------~~~~C~~C~~~f~~~~~l~~H~ 125 (159)
..+ .+|..|.....++..|..|++.-+. + ..-.|-.|.-.|.....|..||
T Consensus 275 a~a~~v~CLfC~~~~en~~~l~eHmk~vHe~Dl~Ki~sd~~Ln~YqrvrviNyiRkq~~~~~c~~cd~~F~~e~~l~~hm 354 (423)
T KOG2482|consen 275 AEALSVVCLFCTNFYENPVFLFEHMKIVHEFDLLKIQSDYSLNFYQRVRVINYIRKQKKKSRCAECDLSFWKEPGLLIHM 354 (423)
T ss_pred CCccceEEEeeccchhhHHHHHHHHHHHHHhhHHhhccccccchhhhhhHHHHHHHHhhccccccccccccCcchhhhhc
Confidence 112 5899999999999999999986432 0 1235888999999999999999
Q ss_pred h
Q psy9695 126 I 126 (159)
Q Consensus 126 ~ 126 (159)
.
T Consensus 355 ~ 355 (423)
T KOG2482|consen 355 V 355 (423)
T ss_pred c
Confidence 3
No 69
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=90.09 E-value=0.23 Score=23.31 Aligned_cols=32 Identities=25% Similarity=0.715 Sum_probs=14.6
Q ss_pred cCcccccccCChHHHHHHHHHccCCCCccCCcccccc
Q psy9695 79 LCHVCHKNFSSSSALQIHMRTHTGDKPFRCTICQKAF 115 (159)
Q Consensus 79 ~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~~f 115 (159)
.|+.|+..|.-..+ ++..+.+..+|+.|+..|
T Consensus 4 ~CP~C~~~f~v~~~-----~l~~~~~~vrC~~C~~~f 35 (37)
T PF13719_consen 4 TCPNCQTRFRVPDD-----KLPAGGRKVRCPKCGHVF 35 (37)
T ss_pred ECCCCCceEEcCHH-----HcccCCcEEECCCCCcEe
Confidence 45555555544332 111223345566665544
No 70
>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=90.09 E-value=0.2 Score=23.57 Aligned_cols=13 Identities=23% Similarity=0.572 Sum_probs=6.7
Q ss_pred ccCcccccccCCh
Q psy9695 78 HLCHVCHKNFSSS 90 (159)
Q Consensus 78 ~~C~~C~~~~~~~ 90 (159)
+.|+.|+..|.-.
T Consensus 3 ~~CP~C~~~~~v~ 15 (38)
T TIGR02098 3 IQCPNCKTSFRVV 15 (38)
T ss_pred EECCCCCCEEEeC
Confidence 3455666555443
No 71
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=89.63 E-value=1.3 Score=26.60 Aligned_cols=86 Identities=20% Similarity=0.298 Sum_probs=51.4
Q ss_pred CCcccCcccccccCChHHHHHHHHhhcCCCc------------cccccccccccCccccccccccccccCCCCCccCccc
Q psy9695 16 MPKHLCHVCHKNFSSSSALQIHMRTHTGDKP------------FRCTICQKAFTTKGNLKLIPNAVFNVAGMPKHLCHVC 83 (159)
Q Consensus 16 ~~~~~C~~C~~~f~~~~~~~~h~~~~~~~~~------------~~c~~c~~~~~~~~~l~~~~~~~~~~~~~~~~~C~~C 83 (159)
+-|..|+.|+-+.-....|.+.....-..++ ..|--|+..|........ ........|.|+.|
T Consensus 13 ~LP~~CpiCgLtLVss~HLARSyHHLfPl~~f~ev~~~~~~~~~~C~~C~~~f~~~~~~~~-----~~~~~~~~y~C~~C 87 (112)
T TIGR00622 13 ELPVECPICGLTLILSTHLARSYHHLFPLKAFQEIPLEEYNGSRFCFGCQGPFPKPPVSPF-----DELKDSHRYVCAVC 87 (112)
T ss_pred CCCCcCCcCCCEEeccchHHHhhhccCCCcccccccccccCCCCcccCcCCCCCCcccccc-----cccccccceeCCCC
Confidence 4577899999887776666653221111111 236667777755432110 00123446999999
Q ss_pred ccccCChHHHHHHHHHccCCCCccCCccc
Q psy9695 84 HKNFSSSSALQIHMRTHTGDKPFRCTICQ 112 (159)
Q Consensus 84 ~~~~~~~~~l~~H~~~h~~~~~~~C~~C~ 112 (159)
...|--.=+...|...| .|+-|.
T Consensus 88 ~~~FC~dCD~fiHe~Lh------~CPGC~ 110 (112)
T TIGR00622 88 KNVFCVDCDVFVHESLH------CCPGCI 110 (112)
T ss_pred CCccccccchhhhhhcc------CCcCCC
Confidence 99997776777777666 466664
No 72
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=89.52 E-value=0.12 Score=25.63 Aligned_cols=30 Identities=17% Similarity=0.421 Sum_probs=17.1
Q ss_pred CccCcccccccCChHHHHHHHHHccCCCCccCCccccccc
Q psy9695 77 KHLCHVCHKNFSSSSALQIHMRTHTGDKPFRCTICQKAFT 116 (159)
Q Consensus 77 ~~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~~f~ 116 (159)
.|.|+.||..+..... .....|+.||..+.
T Consensus 3 ~y~C~~CG~~~~~~~~----------~~~~~Cp~CG~~~~ 32 (46)
T PRK00398 3 EYKCARCGREVELDEY----------GTGVRCPYCGYRIL 32 (46)
T ss_pred EEECCCCCCEEEECCC----------CCceECCCCCCeEE
Confidence 4677777766543211 11567888875443
No 73
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=88.92 E-value=0.13 Score=26.82 Aligned_cols=32 Identities=25% Similarity=0.483 Sum_probs=18.3
Q ss_pred CccCcccccccCChHHHHHHHHHccCCCCccCCcccc
Q psy9695 77 KHLCHVCHKNFSSSSALQIHMRTHTGDKPFRCTICQK 113 (159)
Q Consensus 77 ~~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~ 113 (159)
.|.|+.||+.....-. +--....+|+|+.||.
T Consensus 27 ~F~CPnCGe~~I~Rc~-----~CRk~g~~Y~Cp~CGF 58 (61)
T COG2888 27 KFPCPNCGEVEIYRCA-----KCRKLGNPYRCPKCGF 58 (61)
T ss_pred EeeCCCCCceeeehhh-----hHHHcCCceECCCcCc
Confidence 4778888865444321 1111245788888874
No 74
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=88.86 E-value=0.32 Score=22.71 Aligned_cols=32 Identities=19% Similarity=0.582 Sum_probs=14.6
Q ss_pred cCcccccccCChHHHHHHHHHccCCCCccCCcccccc
Q psy9695 79 LCHVCHKNFSSSSALQIHMRTHTGDKPFRCTICQKAF 115 (159)
Q Consensus 79 ~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~~f 115 (159)
.|+.|+..|.-.... +-...+..+|+.|+..|
T Consensus 4 ~Cp~C~~~y~i~d~~-----ip~~g~~v~C~~C~~~f 35 (36)
T PF13717_consen 4 TCPNCQAKYEIDDEK-----IPPKGRKVRCSKCGHVF 35 (36)
T ss_pred ECCCCCCEEeCCHHH-----CCCCCcEEECCCCCCEe
Confidence 455555555444331 11222334566665544
No 75
>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=88.79 E-value=0.17 Score=25.71 Aligned_cols=29 Identities=21% Similarity=0.484 Sum_probs=17.0
Q ss_pred ccCcccccccCChHHHHHHHHHccCCCCccCCcccc
Q psy9695 78 HLCHVCHKNFSSSSALQIHMRTHTGDKPFRCTICQK 113 (159)
Q Consensus 78 ~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~ 113 (159)
|.|..|+..|.....+ .. +.+-.|+.||.
T Consensus 6 y~C~~Cg~~fe~~~~~------~~-~~~~~CP~Cg~ 34 (52)
T TIGR02605 6 YRCTACGHRFEVLQKM------SD-DPLATCPECGG 34 (52)
T ss_pred EEeCCCCCEeEEEEec------CC-CCCCCCCCCCC
Confidence 6788888777543221 11 34456888875
No 76
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=88.64 E-value=0.22 Score=31.98 Aligned_cols=24 Identities=17% Similarity=0.508 Sum_probs=17.9
Q ss_pred CccCCcccccccccCCceeeehhhccCCCCCcccccccchhhch
Q psy9695 105 PFRCTICQKAFTTKGNLKVREIEINIGSQLPKKAQQHIGAVEGK 148 (159)
Q Consensus 105 ~~~C~~C~~~f~~~~~l~~H~~~~h~~~~~~~~~~~~~C~~C~~ 148 (159)
.|.|++||.. +.++ .|-+||+||.
T Consensus 134 ~~vC~vCGy~--------------~~ge------~P~~CPiCga 157 (166)
T COG1592 134 VWVCPVCGYT--------------HEGE------APEVCPICGA 157 (166)
T ss_pred EEEcCCCCCc--------------ccCC------CCCcCCCCCC
Confidence 5999999843 3345 7889999984
No 77
>KOG1146|consensus
Probab=88.15 E-value=0.18 Score=42.17 Aligned_cols=53 Identities=30% Similarity=0.611 Sum_probs=39.6
Q ss_pred CCccCcccccccCChHHHHHHHHH-cc------------------------CCCCccCCcccccccccCCceeeehhh
Q psy9695 76 PKHLCHVCHKNFSSSSALQIHMRT-HT------------------------GDKPFRCTICQKAFTTKGNLKVREIEI 128 (159)
Q Consensus 76 ~~~~C~~C~~~~~~~~~l~~H~~~-h~------------------------~~~~~~C~~C~~~f~~~~~l~~H~~~~ 128 (159)
+.+.|+.|+..|.....|..|++. |. +-++|.|..|..+++...+|..|+...
T Consensus 464 kt~~cpkc~~~yk~a~~L~vhmRskhp~~~~~~c~~gq~~~~~arg~~~~~~~~p~~C~~C~~stttng~LsihlqS~ 541 (1406)
T KOG1146|consen 464 KTLKCPKCNWHYKLAQTLGVHMRSKHPESQSAYCKAGQNHPRLARGEVYRCPGKPYPCRACNYSTTTNGNLSIHLQSD 541 (1406)
T ss_pred ccccCCccchhhhhHHHhhhcccccccccchhHhHhccccccccccccccCCCCcccceeeeeeeecchHHHHHHHHH
Confidence 567788888888888888888776 11 126788888999988888888888443
No 78
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=87.73 E-value=0.13 Score=24.70 Aligned_cols=12 Identities=8% Similarity=0.039 Sum_probs=7.7
Q ss_pred ccccchhhchhh
Q psy9695 139 QQHIGAVEGKSF 150 (159)
Q Consensus 139 ~~~~C~~C~~~f 150 (159)
..|.|..|+..+
T Consensus 27 ~fy~C~~C~~~w 38 (40)
T smart00440 27 VFYVCTKCGHRW 38 (40)
T ss_pred EEEEeCCCCCEe
Confidence 566776666554
No 79
>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=87.58 E-value=1 Score=26.79 Aligned_cols=26 Identities=19% Similarity=0.475 Sum_probs=19.2
Q ss_pred CCCcccCcccccccCChHHHHHHHHhh
Q psy9695 15 GMPKHLCHVCHKNFSSSSALQIHMRTH 41 (159)
Q Consensus 15 ~~~~~~C~~C~~~f~~~~~~~~h~~~~ 41 (159)
.-+-..|..|+.+..- .++..|++..
T Consensus 8 ~~~vlIC~~C~~av~~-~~v~~HL~~~ 33 (109)
T PF12013_consen 8 EYRVLICRQCQYAVQP-SEVESHLRKR 33 (109)
T ss_pred cCCEEEeCCCCcccCc-hHHHHHHHHh
Confidence 3445789999987655 7888898743
No 80
>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=87.12 E-value=0.069 Score=25.49 Aligned_cols=12 Identities=8% Similarity=0.019 Sum_probs=8.4
Q ss_pred ccccchhhchhh
Q psy9695 139 QQHIGAVEGKSF 150 (159)
Q Consensus 139 ~~~~C~~C~~~f 150 (159)
..|.|..|+..|
T Consensus 27 ~fy~C~~C~~~w 38 (39)
T PF01096_consen 27 LFYVCCNCGHRW 38 (39)
T ss_dssp EEEEESSSTEEE
T ss_pred EEEEeCCCCCee
Confidence 577777777654
No 81
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=87.06 E-value=0.19 Score=25.75 Aligned_cols=19 Identities=26% Similarity=0.391 Sum_probs=11.4
Q ss_pred ccchhhchhhhhcccccCC
Q psy9695 141 HIGAVEGKSFQAKHKTETC 159 (159)
Q Consensus 141 ~~C~~C~~~f~~~~~l~~~ 159 (159)
.+|+.||+.|...+.++.|
T Consensus 6 ~~C~~Cg~~~~~~dDiVvC 24 (54)
T PF14446_consen 6 CKCPVCGKKFKDGDDIVVC 24 (54)
T ss_pred ccChhhCCcccCCCCEEEC
Confidence 4566666666666655544
No 82
>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=86.20 E-value=0.5 Score=28.15 Aligned_cols=11 Identities=27% Similarity=0.782 Sum_probs=5.6
Q ss_pred CccCccccccc
Q psy9695 77 KHLCHVCHKNF 87 (159)
Q Consensus 77 ~~~C~~C~~~~ 87 (159)
|.+|+.||..|
T Consensus 26 PivCP~CG~~~ 36 (108)
T PF09538_consen 26 PIVCPKCGTEF 36 (108)
T ss_pred CccCCCCCCcc
Confidence 44555555544
No 83
>KOG4173|consensus
Probab=86.19 E-value=0.098 Score=34.51 Aligned_cols=80 Identities=20% Similarity=0.492 Sum_probs=52.6
Q ss_pred Ccccccc--ccccccCccccccccccccccCCCCCccCcccccccCChHHHHHHHHHcc----------CCCCccCC--c
Q psy9695 45 KPFRCTI--CQKAFTTKGNLKLIPNAVFNVAGMPKHLCHVCHKNFSSSSALQIHMRTHT----------GDKPFRCT--I 110 (159)
Q Consensus 45 ~~~~c~~--c~~~~~~~~~l~~~~~~~~~~~~~~~~~C~~C~~~~~~~~~l~~H~~~h~----------~~~~~~C~--~ 110 (159)
..+.|++ |...+........|. .....-.|..|.+.|.+..-|..|+...+ |.-.|.|- .
T Consensus 78 ~~~~cqvagc~~~~d~lD~~E~hY------~~~h~~sCs~C~r~~Pt~hLLd~HI~E~HDs~Fqa~veRG~dMy~ClvEg 151 (253)
T KOG4173|consen 78 PAFACQVAGCCQVFDALDDYEHHY------HTLHGNSCSFCKRAFPTGHLLDAHILEWHDSLFQALVERGQDMYQCLVEG 151 (253)
T ss_pred ccccccccchHHHHhhhhhHHHhh------hhcccchhHHHHHhCCchhhhhHHHHHHHHHHHHHHHHcCccHHHHHHHh
Confidence 3467776 555555544443221 11223579999999998888888877543 23358884 4
Q ss_pred ccccccccCCceeeehhhcc
Q psy9695 111 CQKAFTTKGNLKVREIEINI 130 (159)
Q Consensus 111 C~~~f~~~~~l~~H~~~~h~ 130 (159)
|+..|.....-..|+...|-
T Consensus 152 Ct~KFkT~r~RkdH~I~~Hk 171 (253)
T KOG4173|consen 152 CTEKFKTSRDRKDHMIRMHK 171 (253)
T ss_pred hhhhhhhhhhhhhHHHHhcc
Confidence 99999988888888866664
No 84
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=85.56 E-value=0.13 Score=32.64 Aligned_cols=16 Identities=38% Similarity=0.619 Sum_probs=10.0
Q ss_pred ccCCcccccccccCCc
Q psy9695 106 FRCTICQKAFTTKGNL 121 (159)
Q Consensus 106 ~~C~~C~~~f~~~~~l 121 (159)
|+|+.||+.|...-.+
T Consensus 29 ~~c~~c~~~f~~~e~~ 44 (154)
T PRK00464 29 RECLACGKRFTTFERV 44 (154)
T ss_pred eeccccCCcceEeEec
Confidence 6677777776655443
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=84.79 E-value=0.41 Score=30.63 Aligned_cols=19 Identities=21% Similarity=0.258 Sum_probs=11.0
Q ss_pred CCCccCCcccccccccCCc
Q psy9695 103 DKPFRCTICQKAFTTKGNL 121 (159)
Q Consensus 103 ~~~~~C~~C~~~f~~~~~l 121 (159)
..-|.|+.|+..|+...-+
T Consensus 107 ~~~Y~Cp~c~~r~tf~eA~ 125 (158)
T TIGR00373 107 NMFFICPNMCVRFTFNEAM 125 (158)
T ss_pred CCeEECCCCCcEeeHHHHH
Confidence 3446677777666555444
No 86
>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=84.69 E-value=0.76 Score=29.41 Aligned_cols=19 Identities=21% Similarity=0.258 Sum_probs=10.1
Q ss_pred CCccccccccccccCcccc
Q psy9695 44 DKPFRCTICQKAFTTKGNL 62 (159)
Q Consensus 44 ~~~~~c~~c~~~~~~~~~l 62 (159)
..-|.|+.|+..|+....+
T Consensus 107 ~~~Y~Cp~c~~r~tf~eA~ 125 (158)
T TIGR00373 107 NMFFICPNMCVRFTFNEAM 125 (158)
T ss_pred CCeEECCCCCcEeeHHHHH
Confidence 3446666666555544433
No 87
>KOG4173|consensus
Probab=84.56 E-value=0.23 Score=32.86 Aligned_cols=76 Identities=22% Similarity=0.394 Sum_probs=53.2
Q ss_pred CCccCcc--cccccCChHHHHHHHHHccCCCCccCCcccccccccCCceeeehhhccCC-C--CCcccccccc--hhhch
Q psy9695 76 PKHLCHV--CHKNFSSSSALQIHMRTHTGDKPFRCTICQKAFTTKGNLKVREIEINIGS-Q--LPKKAQQHIG--AVEGK 148 (159)
Q Consensus 76 ~~~~C~~--C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~~h~~~-~--~~~~~~~~~C--~~C~~ 148 (159)
..+.|+. |.+.|.+......|-.+-++ -.|.+|.+.|.....|..|+.-.|..- + ...+.-.|.| ..|+.
T Consensus 78 ~~~~cqvagc~~~~d~lD~~E~hY~~~h~---~sCs~C~r~~Pt~hLLd~HI~E~HDs~Fqa~veRG~dMy~ClvEgCt~ 154 (253)
T KOG4173|consen 78 PAFACQVAGCCQVFDALDDYEHHYHTLHG---NSCSFCKRAFPTGHLLDAHILEWHDSLFQALVERGQDMYQCLVEGCTE 154 (253)
T ss_pred ccccccccchHHHHhhhhhHHHhhhhccc---chhHHHHHhCCchhhhhHHHHHHHHHHHHHHHHcCccHHHHHHHhhhh
Confidence 3477876 66778777766666655433 389999999999999999986666420 0 1112367999 67999
Q ss_pred hhhhcc
Q psy9695 149 SFQAKH 154 (159)
Q Consensus 149 ~f~~~~ 154 (159)
+|++..
T Consensus 155 KFkT~r 160 (253)
T KOG4173|consen 155 KFKTSR 160 (253)
T ss_pred hhhhhh
Confidence 998754
No 88
>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=84.02 E-value=0.64 Score=23.19 Aligned_cols=8 Identities=25% Similarity=0.356 Sum_probs=2.8
Q ss_pred cccchhhc
Q psy9695 140 QHIGAVEG 147 (159)
Q Consensus 140 ~~~C~~C~ 147 (159)
-|.|++|+
T Consensus 34 ~w~CP~C~ 41 (47)
T PF00301_consen 34 DWVCPVCG 41 (47)
T ss_dssp T-B-TTTS
T ss_pred CCcCcCCC
Confidence 34455544
No 89
>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=83.65 E-value=1.1 Score=22.71 Aligned_cols=11 Identities=18% Similarity=0.637 Sum_probs=5.3
Q ss_pred ccCcccccccC
Q psy9695 78 HLCHVCHKNFS 88 (159)
Q Consensus 78 ~~C~~C~~~~~ 88 (159)
|.|..||..+.
T Consensus 2 y~C~~CgyiYd 12 (50)
T cd00730 2 YECRICGYIYD 12 (50)
T ss_pred cCCCCCCeEEC
Confidence 44555554443
No 90
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=83.22 E-value=0.51 Score=30.84 Aligned_cols=33 Identities=18% Similarity=0.272 Sum_probs=19.2
Q ss_pred CCccCCcccccccccCCceeeehhhccCCCCCcccccccchhhchhhhh
Q psy9695 104 KPFRCTICQKAFTTKGNLKVREIEINIGSQLPKKAQQHIGAVEGKSFQA 152 (159)
Q Consensus 104 ~~~~C~~C~~~f~~~~~l~~H~~~~h~~~~~~~~~~~~~C~~C~~~f~~ 152 (159)
.-|.|+.|+..|+...-+. ..|.|+.||..+..
T Consensus 116 ~~Y~Cp~C~~rytf~eA~~----------------~~F~Cp~Cg~~L~~ 148 (178)
T PRK06266 116 MFFFCPNCHIRFTFDEAME----------------YGFRCPQCGEMLEE 148 (178)
T ss_pred CEEECCCCCcEEeHHHHhh----------------cCCcCCCCCCCCee
Confidence 3467777776666554321 24677777765443
No 91
>PF14353 CpXC: CpXC protein
Probab=83.11 E-value=2.2 Score=26.17 Aligned_cols=22 Identities=23% Similarity=0.460 Sum_probs=16.4
Q ss_pred CCccCCcccccccccCCceeee
Q psy9695 104 KPFRCTICQKAFTTKGNLKVRE 125 (159)
Q Consensus 104 ~~~~C~~C~~~f~~~~~l~~H~ 125 (159)
..|.|+.||..|.-...+.-|-
T Consensus 37 ~~~~CP~Cg~~~~~~~p~lY~D 58 (128)
T PF14353_consen 37 FSFTCPSCGHKFRLEYPLLYHD 58 (128)
T ss_pred CEEECCCCCCceecCCCEEEEc
Confidence 3478888888888777776666
No 92
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=82.45 E-value=0.66 Score=23.31 Aligned_cols=10 Identities=20% Similarity=0.607 Sum_probs=6.1
Q ss_pred ccCccccccc
Q psy9695 78 HLCHVCHKNF 87 (159)
Q Consensus 78 ~~C~~C~~~~ 87 (159)
|.|..|+..|
T Consensus 7 Y~C~~Cg~~~ 16 (49)
T COG1996 7 YKCARCGREV 16 (49)
T ss_pred EEhhhcCCee
Confidence 5666666555
No 93
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=81.03 E-value=1.3 Score=28.99 Aligned_cols=31 Identities=23% Similarity=0.448 Sum_probs=17.1
Q ss_pred CccccccccccccCccccccccccccccCCCCCccCccccccc
Q psy9695 45 KPFRCTICQKAFTTKGNLKLIPNAVFNVAGMPKHLCHVCHKNF 87 (159)
Q Consensus 45 ~~~~c~~c~~~~~~~~~l~~~~~~~~~~~~~~~~~C~~C~~~~ 87 (159)
.-|.|+.|+..|+....+. ..|.|+.||..+
T Consensus 116 ~~Y~Cp~C~~rytf~eA~~------------~~F~Cp~Cg~~L 146 (178)
T PRK06266 116 MFFFCPNCHIRFTFDEAME------------YGFRCPQCGEML 146 (178)
T ss_pred CEEECCCCCcEEeHHHHhh------------cCCcCCCCCCCC
Confidence 4466666666665544331 146666666543
No 94
>COG1773 Rubredoxin [Energy production and conversion]
Probab=80.00 E-value=1.4 Score=22.71 Aligned_cols=13 Identities=23% Similarity=0.672 Sum_probs=7.8
Q ss_pred CccCcccccccCC
Q psy9695 77 KHLCHVCHKNFSS 89 (159)
Q Consensus 77 ~~~C~~C~~~~~~ 89 (159)
.|.|..||..|..
T Consensus 3 ~~~C~~CG~vYd~ 15 (55)
T COG1773 3 RWRCSVCGYVYDP 15 (55)
T ss_pred ceEecCCceEecc
Confidence 3666666666643
No 95
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=79.79 E-value=1 Score=27.75 Aligned_cols=12 Identities=33% Similarity=1.038 Sum_probs=5.8
Q ss_pred CccCCccccccc
Q psy9695 105 PFRCTICQKAFT 116 (159)
Q Consensus 105 ~~~C~~C~~~f~ 116 (159)
.|+|..|++.|.
T Consensus 53 RyrC~~C~~tf~ 64 (129)
T COG3677 53 RYKCKSCGSTFT 64 (129)
T ss_pred ccccCCcCccee
Confidence 345555554444
No 96
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=79.56 E-value=1.1 Score=22.01 Aligned_cols=30 Identities=20% Similarity=0.442 Sum_probs=17.5
Q ss_pred ccCcccccccCChHHHHHHHHhhcCCCccccccccccccCc
Q psy9695 19 HLCHVCHKNFSSSSALQIHMRTHTGDKPFRCTICQKAFTTK 59 (159)
Q Consensus 19 ~~C~~C~~~f~~~~~~~~h~~~~~~~~~~~c~~c~~~~~~~ 59 (159)
|.|..||..|... ...+..|+.||.....+
T Consensus 3 Y~C~~Cg~~~~~~-----------~~~~irC~~CG~rIlyK 32 (44)
T smart00659 3 YICGECGRENEIK-----------SKDVVRCRECGYRILYK 32 (44)
T ss_pred EECCCCCCEeecC-----------CCCceECCCCCceEEEE
Confidence 6677777665432 23456777777655433
No 97
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=79.52 E-value=1.4 Score=27.87 Aligned_cols=12 Identities=33% Similarity=0.971 Sum_probs=5.7
Q ss_pred cccccccccccc
Q psy9695 46 PFRCTICQKAFT 57 (159)
Q Consensus 46 ~~~c~~c~~~~~ 57 (159)
.|.|+.|+..|.
T Consensus 99 ~Y~Cp~C~~~y~ 110 (147)
T smart00531 99 YYKCPNCQSKYT 110 (147)
T ss_pred EEECcCCCCEee
Confidence 344555554444
No 98
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=78.62 E-value=2.1 Score=30.92 Aligned_cols=104 Identities=22% Similarity=0.401 Sum_probs=53.2
Q ss_pred ccCcc--cccccCChHHHHHHHHhhcCCCccccccccc---cccCccc------cccccccccccCC-CCCccCcccccc
Q psy9695 19 HLCHV--CHKNFSSSSALQIHMRTHTGDKPFRCTICQK---AFTTKGN------LKLIPNAVFNVAG-MPKHLCHVCHKN 86 (159)
Q Consensus 19 ~~C~~--C~~~f~~~~~~~~h~~~~~~~~~~~c~~c~~---~~~~~~~------l~~~~~~~~~~~~-~~~~~C~~C~~~ 86 (159)
|.|+. |.........+..|..+.++ .+.|.+|-. .|..... |..|...--...| ...-.|..|...
T Consensus 152 F~CP~skc~~~C~~~k~lk~H~K~~H~--~~~C~~C~~nKk~F~~E~~lF~~~~Lr~H~~~G~~e~GFKGHP~C~FC~~~ 229 (493)
T COG5236 152 FKCPKSKCHRRCGSLKELKKHYKAQHG--FVLCSECIGNKKDFWNEIRLFRSSTLRDHKNGGLEEEGFKGHPLCIFCKIY 229 (493)
T ss_pred hcCCchhhhhhhhhHHHHHHHHHhhcC--cEEhHhhhcCcccCccceeeeecccccccccCCccccCcCCCchhhhccce
Confidence 67764 55555556778888876543 255666532 2322222 2221110000111 112458889988
Q ss_pred cCChHHHHHHHHHccCCCCccCCccc----ccccccCCceeee
Q psy9695 87 FSSSSALQIHMRTHTGDKPFRCTICQ----KAFTTKGNLKVRE 125 (159)
Q Consensus 87 ~~~~~~l~~H~~~h~~~~~~~C~~C~----~~f~~~~~l~~H~ 125 (159)
|-....|..|.+.-+ |+=|.|+.-+ .-|....+|..|.
T Consensus 230 FYdDDEL~~HcR~~H-E~ChICD~v~p~~~QYFK~Y~~Le~HF 271 (493)
T COG5236 230 FYDDDELRRHCRLRH-EACHICDMVGPIRYQYFKSYEDLEAHF 271 (493)
T ss_pred ecChHHHHHHHHhhh-hhhhhhhccCccchhhhhCHHHHHHHh
Confidence 888899999988543 2223332211 2344455555555
No 99
>PF03811 Zn_Tnp_IS1: InsA N-terminal domain; InterPro: IPR003220 Insertion elements are mobile elements in DNA, usually encoding proteins required for transposition, for example transposases. Protein InsA is absolutely required for transposition of insertion element 1. This entry represents a short zinc binding domain found in IS1 InsA family protein. It is found at the N terminus of the protein and may be a DNA-binding domain.; GO: 0006313 transposition, DNA-mediated
Probab=78.61 E-value=1.6 Score=20.41 Aligned_cols=29 Identities=21% Similarity=0.249 Sum_probs=16.9
Q ss_pred cCCcccccccccCCceeeehhhccCCCCCcccccccchhh
Q psy9695 107 RCTICQKAFTTKGNLKVREIEINIGSQLPKKAQQHIGAVE 146 (159)
Q Consensus 107 ~C~~C~~~f~~~~~l~~H~~~~h~~~~~~~~~~~~~C~~C 146 (159)
.|+.|+.. ..+.+|- +...|. +.|.|..|
T Consensus 7 ~CP~C~s~----~~v~k~G-~~~~G~------qryrC~~C 35 (36)
T PF03811_consen 7 HCPRCQST----EGVKKNG-KSPSGH------QRYRCKDC 35 (36)
T ss_pred eCCCCCCC----CcceeCC-CCCCCC------EeEecCcC
Confidence 56666632 2255555 444455 77888776
No 100
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=78.29 E-value=0.75 Score=25.23 Aligned_cols=43 Identities=19% Similarity=0.464 Sum_probs=27.1
Q ss_pred ccCcccccccCChHHHHHHHHhhcCCCccccc--cccccccCccccc
Q psy9695 19 HLCHVCHKNFSSSSALQIHMRTHTGDKPFRCT--ICQKAFTTKGNLK 63 (159)
Q Consensus 19 ~~C~~C~~~f~~~~~~~~h~~~~~~~~~~~c~--~c~~~~~~~~~l~ 63 (159)
+.|+.||.......+-.. .....+..+.|. +||..|....++.
T Consensus 2 m~CP~Cg~~a~irtSr~~--s~~~~~~Y~qC~N~eCg~tF~t~es~s 46 (72)
T PRK09678 2 FHCPLCQHAAHARTSRYI--TDTTKERYHQCQNVNCSATFITYESVQ 46 (72)
T ss_pred ccCCCCCCccEEEEChhc--ChhhheeeeecCCCCCCCEEEEEEEEE
Confidence 468888876533333221 112445668887 8999998877765
No 101
>KOG2907|consensus
Probab=78.03 E-value=1 Score=26.84 Aligned_cols=14 Identities=7% Similarity=-0.220 Sum_probs=8.2
Q ss_pred ccccchhhchhhhh
Q psy9695 139 QQHIGAVEGKSFQA 152 (159)
Q Consensus 139 ~~~~C~~C~~~f~~ 152 (159)
-.|.|+-|+.+|..
T Consensus 101 VFYTC~kC~~k~~e 114 (116)
T KOG2907|consen 101 VFYTCPKCKYKFTE 114 (116)
T ss_pred EEEEcCccceeeec
Confidence 35666666666554
No 102
>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=77.97 E-value=0.5 Score=27.03 Aligned_cols=10 Identities=30% Similarity=0.232 Sum_probs=5.7
Q ss_pred ccchhhchhh
Q psy9695 141 HIGAVEGKSF 150 (159)
Q Consensus 141 ~~C~~C~~~f 150 (159)
+.|..|++.|
T Consensus 54 W~C~~C~~~~ 63 (90)
T PF01780_consen 54 WKCKKCGKKF 63 (90)
T ss_dssp EEETTTTEEE
T ss_pred eecCCCCCEE
Confidence 5555565554
No 103
>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=77.88 E-value=0.95 Score=23.29 Aligned_cols=30 Identities=17% Similarity=0.450 Sum_probs=15.2
Q ss_pred ccCcccccccCChHHHHHHHHHccCCCCccCCcccccc
Q psy9695 78 HLCHVCHKNFSSSSALQIHMRTHTGDKPFRCTICQKAF 115 (159)
Q Consensus 78 ~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~~f 115 (159)
++|+.||..+.-... ..++ ...|+.||..|
T Consensus 3 ~~CP~CG~~iev~~~-------~~Ge-iV~Cp~CGael 32 (54)
T TIGR01206 3 FECPDCGAEIELENP-------ELGE-LVICDECGAEL 32 (54)
T ss_pred cCCCCCCCEEecCCC-------ccCC-EEeCCCCCCEE
Confidence 567777765533221 0122 34677777554
No 104
>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=77.61 E-value=1.1 Score=20.04 Aligned_cols=11 Identities=27% Similarity=1.011 Sum_probs=2.1
Q ss_pred cCCcccccccc
Q psy9695 107 RCTICQKAFTT 117 (159)
Q Consensus 107 ~C~~C~~~f~~ 117 (159)
+|+.|+..++.
T Consensus 4 ~Cp~C~se~~y 14 (30)
T PF08274_consen 4 KCPLCGSEYTY 14 (30)
T ss_dssp --TTT-----E
T ss_pred CCCCCCCccee
Confidence 35555554444
No 105
>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=77.32 E-value=1 Score=18.95 Aligned_cols=8 Identities=50% Similarity=1.373 Sum_probs=3.8
Q ss_pred CccCCccc
Q psy9695 105 PFRCTICQ 112 (159)
Q Consensus 105 ~~~C~~C~ 112 (159)
+|.|+.||
T Consensus 16 ~f~CPnCG 23 (24)
T PF07754_consen 16 PFPCPNCG 23 (24)
T ss_pred eEeCCCCC
Confidence 34455444
No 106
>KOG4124|consensus
Probab=77.32 E-value=2.6 Score=30.47 Aligned_cols=54 Identities=20% Similarity=0.447 Sum_probs=41.4
Q ss_pred CCCccCCc--ccccccccCCceeeehhhccCC-----C-------CCcccccccchhhchhhhhcccc
Q psy9695 103 DKPFRCTI--CQKAFTTKGNLKVREIEINIGS-----Q-------LPKKAQQHIGAVEGKSFQAKHKT 156 (159)
Q Consensus 103 ~~~~~C~~--C~~~f~~~~~l~~H~~~~h~~~-----~-------~~~~~~~~~C~~C~~~f~~~~~l 156 (159)
+++|+|++ |.+.+.....|..|.+..|... + .-...++|.|++|.++++...+|
T Consensus 347 ~~~~~~~vp~~~~~~~n~ng~~~~~~~~h~s~i~~~s~~~~ph~~~~~~nk~~r~~i~~~~~k~~~~l 414 (442)
T KOG4124|consen 347 DKPYKCPVPNCDKAYKNQNGLKYHKLHGHCSPITTPTPAPIPHQGFVVENKPYRCEVCSKRYKNLNGL 414 (442)
T ss_pred cCCCCCCCCcchhhcccCcceeeccccCcCCCCCCCCCCCCCcceeeeccCcccChhhhhhhccCCCC
Confidence 47899965 9999999999998886666531 1 11445899999999999877665
No 107
>smart00614 ZnF_BED BED zinc finger. DNA-binding domain in chromatin-boundary-element-binding proteins and transposases
Probab=76.44 E-value=0.6 Score=23.48 Aligned_cols=21 Identities=43% Similarity=0.744 Sum_probs=11.9
Q ss_pred ccCcccccccCCh-----HHHHHHHH
Q psy9695 78 HLCHVCHKNFSSS-----SALQIHMR 98 (159)
Q Consensus 78 ~~C~~C~~~~~~~-----~~l~~H~~ 98 (159)
-.|..|++.+... +.|..|+.
T Consensus 19 a~C~~C~~~l~~~~~~gTs~L~rHl~ 44 (50)
T smart00614 19 AKCKYCGKKLSRSSKGGTSNLRRHLR 44 (50)
T ss_pred EEecCCCCEeeeCCCCCcHHHHHHHH
Confidence 4566666655332 46666665
No 108
>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=76.24 E-value=0.34 Score=23.62 Aligned_cols=22 Identities=32% Similarity=0.551 Sum_probs=10.7
Q ss_pred CCccCcccccccCC----hHHHHHHH
Q psy9695 76 PKHLCHVCHKNFSS----SSALQIHM 97 (159)
Q Consensus 76 ~~~~C~~C~~~~~~----~~~l~~H~ 97 (159)
....|..|++.+.. .+.|..|.
T Consensus 15 ~~a~C~~C~~~~~~~~~~ts~l~~HL 40 (45)
T PF02892_consen 15 KKAKCKYCGKVIKYSSGGTSNLKRHL 40 (45)
T ss_dssp S-EEETTTTEE-----SSTHHHHHHH
T ss_pred CeEEeCCCCeEEeeCCCcHHHHHHhh
Confidence 34566666665533 35566665
No 109
>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=75.49 E-value=0.9 Score=35.89 Aligned_cols=81 Identities=21% Similarity=0.436 Sum_probs=48.2
Q ss_pred ccCcccccccCChHHHHHHHHhhcCCCccccccccccccCccccccccccccccCCCCC-ccCcccccccCChHHHHHHH
Q psy9695 19 HLCHVCHKNFSSSSALQIHMRTHTGDKPFRCTICQKAFTTKGNLKLIPNAVFNVAGMPK-HLCHVCHKNFSSSSALQIHM 97 (159)
Q Consensus 19 ~~C~~C~~~f~~~~~~~~h~~~~~~~~~~~c~~c~~~~~~~~~l~~~~~~~~~~~~~~~-~~C~~C~~~~~~~~~l~~H~ 97 (159)
=.|+.|-+-+.+..+-.-+ -+-..|..||..|+-...+.- -+..+.... -.|+.|.+.|..+.+-+
T Consensus 102 a~C~~Cl~Ei~dp~~rrY~------YPF~~CT~CGPRfTIi~alPY----DR~nTsM~~F~lC~~C~~EY~dP~nRR--- 168 (750)
T COG0068 102 ATCEDCLEEIFDPNSRRYL------YPFINCTNCGPRFTIIEALPY----DRENTSMADFPLCPFCDKEYKDPLNRR--- 168 (750)
T ss_pred hhhHHHHHHhcCCCCccee------ccccccCCCCcceeeeccCCC----CcccCccccCcCCHHHHHHhcCccccc---
Confidence 3566666554444431111 112568889999987776642 222333333 35999999888776533
Q ss_pred HHccCCCCccCCcccccc
Q psy9695 98 RTHTGDKPFRCTICQKAF 115 (159)
Q Consensus 98 ~~h~~~~~~~C~~C~~~f 115 (159)
-|. .|-.|+.||-..
T Consensus 169 -fHA--Qp~aCp~CGP~~ 183 (750)
T COG0068 169 -FHA--QPIACPKCGPHL 183 (750)
T ss_pred -ccc--ccccCcccCCCe
Confidence 342 367899999644
No 110
>PHA02998 RNA polymerase subunit; Provisional
Probab=73.08 E-value=1.2 Score=28.83 Aligned_cols=40 Identities=20% Similarity=0.179 Sum_probs=22.8
Q ss_pred ccCCcccccccccCCceeeehhhccCCCCCcccccccchhhchhhhh
Q psy9695 106 FRCTICQKAFTTKGNLKVREIEINIGSQLPKKAQQHIGAVEGKSFQA 152 (159)
Q Consensus 106 ~~C~~C~~~f~~~~~l~~H~~~~h~~~~~~~~~~~~~C~~C~~~f~~ 152 (159)
-.|+.|+..=.....++..- ...+.- ..|.|..||..|..
T Consensus 144 v~CPkCg~~~A~f~qlQTRS-ADEPmT------~FYkC~~CG~~wkp 183 (195)
T PHA02998 144 TPCPNCKSKNTTPMMIQTRA-ADEPPL------VRHACRDCKKHFKP 183 (195)
T ss_pred CCCCCCCCCceEEEEEeecc-CCCCce------EEEEcCCCCCccCC
Confidence 47888885533333333222 222222 67889889887754
No 111
>PF13451 zf-trcl: Probable zinc-binding domain
Probab=72.66 E-value=1.1 Score=22.48 Aligned_cols=14 Identities=21% Similarity=0.510 Sum_probs=7.7
Q ss_pred CccCcccccccCCh
Q psy9695 77 KHLCHVCHKNFSSS 90 (159)
Q Consensus 77 ~~~C~~C~~~~~~~ 90 (159)
.+.|..||..|...
T Consensus 4 ~l~C~dCg~~FvfT 17 (49)
T PF13451_consen 4 TLTCKDCGAEFVFT 17 (49)
T ss_pred eEEcccCCCeEEEe
Confidence 45666666655433
No 112
>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=72.65 E-value=2.7 Score=25.75 Aligned_cols=11 Identities=9% Similarity=0.163 Sum_probs=5.7
Q ss_pred CccCccccccc
Q psy9695 77 KHLCHVCHKNF 87 (159)
Q Consensus 77 ~~~C~~C~~~~ 87 (159)
|..|+.||..|
T Consensus 26 p~vcP~cg~~~ 36 (129)
T TIGR02300 26 PAVSPYTGEQF 36 (129)
T ss_pred CccCCCcCCcc
Confidence 44555555544
No 113
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=72.55 E-value=1.2 Score=27.70 Aligned_cols=13 Identities=23% Similarity=0.506 Sum_probs=9.0
Q ss_pred CccCcccccccCC
Q psy9695 77 KHLCHVCHKNFSS 89 (159)
Q Consensus 77 ~~~C~~C~~~~~~ 89 (159)
.+.|..||..|..
T Consensus 70 ~~~C~~CG~~~~~ 82 (135)
T PRK03824 70 VLKCRNCGNEWSL 82 (135)
T ss_pred EEECCCCCCEEec
Confidence 4778888876644
No 114
>KOG2785|consensus
Probab=72.54 E-value=2.5 Score=30.86 Aligned_cols=52 Identities=21% Similarity=0.363 Sum_probs=42.6
Q ss_pred CccCcccccccCChHHHHHHHHHccCC-----------------------CCccCCccc---ccccccCCceeeehhh
Q psy9695 77 KHLCHVCHKNFSSSSALQIHMRTHTGD-----------------------KPFRCTICQ---KAFTTKGNLKVREIEI 128 (159)
Q Consensus 77 ~~~C~~C~~~~~~~~~l~~H~~~h~~~-----------------------~~~~C~~C~---~~f~~~~~l~~H~~~~ 128 (159)
|-.|..|+..+.+...-..|+..+++- ..+.|-+|+ +.|.+....++||..+
T Consensus 166 Pt~CLfC~~~~k~~e~~~~HM~~~HgffIPdreYL~D~~GLl~YLgeKV~~~~~CL~CN~~~~~f~sleavr~HM~~K 243 (390)
T KOG2785|consen 166 PTDCLFCDKKSKSLEENLKHMFKEHGFFIPDREYLTDEKGLLKYLGEKVGIGFICLFCNELGRPFSSLEAVRAHMRDK 243 (390)
T ss_pred CcceeecCCCcccHHHHHHHHhhccCCcCCchHhhhchhHHHHHHHHHhccCceEEEeccccCcccccHHHHHHHhhc
Confidence 477999999999998888999987752 346899999 8888888889999444
No 115
>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=72.22 E-value=0.92 Score=21.18 Aligned_cols=8 Identities=25% Similarity=0.671 Sum_probs=3.8
Q ss_pred cCCccccc
Q psy9695 107 RCTICQKA 114 (159)
Q Consensus 107 ~C~~C~~~ 114 (159)
.|+.||..
T Consensus 23 ~Cd~cg~~ 30 (36)
T PF05191_consen 23 VCDNCGGE 30 (36)
T ss_dssp BCTTTTEB
T ss_pred ccCCCCCe
Confidence 45555543
No 116
>KOG3214|consensus
Probab=71.96 E-value=2.3 Score=24.73 Aligned_cols=13 Identities=23% Similarity=0.240 Sum_probs=7.3
Q ss_pred cccchhhchhhhh
Q psy9695 140 QHIGAVEGKSFQA 152 (159)
Q Consensus 140 ~~~C~~C~~~f~~ 152 (159)
..-|.+|+.+|++
T Consensus 47 ~~sC~iC~esFqt 59 (109)
T KOG3214|consen 47 KASCRICEESFQT 59 (109)
T ss_pred eeeeeehhhhhcc
Confidence 3456666666653
No 117
>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=71.90 E-value=1.2 Score=25.06 Aligned_cols=13 Identities=38% Similarity=0.322 Sum_probs=5.7
Q ss_pred cccchhhchhhhh
Q psy9695 140 QHIGAVEGKSFQA 152 (159)
Q Consensus 140 ~~~C~~C~~~f~~ 152 (159)
...|..|+..|..
T Consensus 46 ~~~C~~Cg~~~~~ 58 (81)
T PF05129_consen 46 ILSCRVCGESFQT 58 (81)
T ss_dssp EEEESSS--EEEE
T ss_pred EEEecCCCCeEEE
Confidence 4555555555543
No 118
>KOG2785|consensus
Probab=71.73 E-value=3.1 Score=30.45 Aligned_cols=82 Identities=18% Similarity=0.304 Sum_probs=43.8
Q ss_pred CcccCcccccccCChHHHHHHHHh--hc----CCCccccccccccccCccccccccccccccCCCCCccCcccccccCCh
Q psy9695 17 PKHLCHVCHKNFSSSSALQIHMRT--HT----GDKPFRCTICQKAFTTKGNLKLIPNAVFNVAGMPKHLCHVCHKNFSSS 90 (159)
Q Consensus 17 ~~~~C~~C~~~f~~~~~~~~h~~~--~~----~~~~~~c~~c~~~~~~~~~l~~~~~~~~~~~~~~~~~C~~C~~~~~~~ 90 (159)
..|+|..|...|.+......|..+ |. +...-.-++.-..|...-.............+..++.|..|.+.|.++
T Consensus 2 t~ftC~tC~v~F~~ad~Qr~HyKSdWHRYNLKRkVA~lPPItaE~F~~k~~s~~~~~~~~~e~~~~~~~c~~c~k~~~s~ 81 (390)
T KOG2785|consen 2 TGFTCNTCNVEFDDADEQRAHYKSDWHRYNLKRKVASLPPITAEEFNEKVLSDDSEKEENLEEAESVVYCEACNKSFASP 81 (390)
T ss_pred CcceeeceeeeeccHHHHHHHhhhhHHHhhHHhHhhcCCCcCHHHHhHHHhhhhhhhhhhhhhcccceehHHhhccccCh
Confidence 358999999999999988888764 32 000011111111222211111000011123345567788888888777
Q ss_pred HHHHHHHH
Q psy9695 91 SALQIHMR 98 (159)
Q Consensus 91 ~~l~~H~~ 98 (159)
.....|..
T Consensus 82 ~a~~~hl~ 89 (390)
T KOG2785|consen 82 KAHENHLK 89 (390)
T ss_pred hhHHHHHH
Confidence 66666655
No 119
>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=71.37 E-value=4.8 Score=27.96 Aligned_cols=28 Identities=18% Similarity=0.356 Sum_probs=22.6
Q ss_pred CCCCccCCcccccccccCCceeeehhhcc
Q psy9695 102 GDKPFRCTICQKAFTTKGNLKVREIEINI 130 (159)
Q Consensus 102 ~~~~~~C~~C~~~f~~~~~l~~H~~~~h~ 130 (159)
..+++.||.||.....-.+|..-. ++|.
T Consensus 206 k~k~~PCPKCg~et~eTkdLSmSt-R~hk 233 (314)
T PF06524_consen 206 KGKPIPCPKCGYETQETKDLSMST-RSHK 233 (314)
T ss_pred cCCCCCCCCCCCcccccccceeee-ecch
Confidence 357899999999888888888777 6665
No 120
>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=71.36 E-value=1.1 Score=19.67 Aligned_cols=19 Identities=32% Similarity=0.669 Sum_probs=11.2
Q ss_pred ccCCcccccccccCCceeee
Q psy9695 106 FRCTICQKAFTTKGNLKVRE 125 (159)
Q Consensus 106 ~~C~~C~~~f~~~~~l~~H~ 125 (159)
|.|..|++.| .......|.
T Consensus 1 ~sCiDC~~~F-~~~~y~~Ht 19 (28)
T PF08790_consen 1 FSCIDCSKDF-DGDSYKSHT 19 (28)
T ss_dssp EEETTTTEEE-EGGGTTT--
T ss_pred CeeecCCCCc-CcCCcCCCC
Confidence 4677888888 445555555
No 121
>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=71.24 E-value=1.9 Score=18.47 Aligned_cols=9 Identities=33% Similarity=0.789 Sum_probs=5.2
Q ss_pred cCCcccccc
Q psy9695 107 RCTICQKAF 115 (159)
Q Consensus 107 ~C~~C~~~f 115 (159)
.|+.||..|
T Consensus 16 ~Cp~CG~~F 24 (26)
T PF10571_consen 16 FCPHCGYDF 24 (26)
T ss_pred cCCCCCCCC
Confidence 455666555
No 122
>PF12907 zf-met2: Zinc-binding
Probab=71.19 E-value=0.58 Score=22.43 Aligned_cols=26 Identities=23% Similarity=0.442 Sum_probs=12.1
Q ss_pred ccCCccccccccc---CCceeeehhhccC
Q psy9695 106 FRCTICQKAFTTK---GNLKVREIEINIG 131 (159)
Q Consensus 106 ~~C~~C~~~f~~~---~~l~~H~~~~h~~ 131 (159)
+.|.+|..+|..- ..|..|....|.+
T Consensus 2 i~C~iC~qtF~~t~~~~~L~eH~enKHpK 30 (40)
T PF12907_consen 2 IICKICRQTFMQTTNEPQLKEHAENKHPK 30 (40)
T ss_pred cCcHHhhHHHHhcCCHHHHHHHHHccCCC
Confidence 3455555444433 2355555444443
No 123
>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=70.74 E-value=1.3 Score=27.97 Aligned_cols=18 Identities=11% Similarity=-0.106 Sum_probs=13.6
Q ss_pred ccccchhhchhhhhcccc
Q psy9695 139 QQHIGAVEGKSFQAKHKT 156 (159)
Q Consensus 139 ~~~~C~~C~~~f~~~~~l 156 (159)
..+.|+.||+.|..-++.
T Consensus 123 ~f~~C~~C~kiyW~GsH~ 140 (147)
T PF01927_consen 123 EFWRCPGCGKIYWEGSHW 140 (147)
T ss_pred eEEECCCCCCEecccccH
Confidence 578888888888766554
No 124
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=69.68 E-value=3.1 Score=23.62 Aligned_cols=31 Identities=16% Similarity=0.489 Sum_probs=18.4
Q ss_pred CccccccccccccCccccccccccccccCCCCCccCcccccccC
Q psy9695 45 KPFRCTICQKAFTTKGNLKLIPNAVFNVAGMPKHLCHVCHKNFS 88 (159)
Q Consensus 45 ~~~~c~~c~~~~~~~~~l~~~~~~~~~~~~~~~~~C~~C~~~~~ 88 (159)
..+.|+.|++.-.-. .+...|.|..|+..|.
T Consensus 34 ~~~~Cp~C~~~~VkR-------------~a~GIW~C~kCg~~fA 64 (89)
T COG1997 34 AKHVCPFCGRTTVKR-------------IATGIWKCRKCGAKFA 64 (89)
T ss_pred cCCcCCCCCCcceee-------------eccCeEEcCCCCCeec
Confidence 457888887552111 1223478888887664
No 125
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=69.04 E-value=1.6 Score=20.12 Aligned_cols=9 Identities=11% Similarity=0.239 Sum_probs=4.2
Q ss_pred ccccchhhc
Q psy9695 139 QQHIGAVEG 147 (159)
Q Consensus 139 ~~~~C~~C~ 147 (159)
..+.|+.||
T Consensus 21 ~R~vC~~Cg 29 (34)
T PF14803_consen 21 ERLVCPACG 29 (34)
T ss_dssp -EEEETTTT
T ss_pred cceECCCCC
Confidence 445555554
No 126
>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=67.60 E-value=0.73 Score=31.04 Aligned_cols=27 Identities=19% Similarity=0.442 Sum_probs=16.9
Q ss_pred CCccCCcccccccccCCceeeehhhcc
Q psy9695 104 KPFRCTICQKAFTTKGNLKVREIEINI 130 (159)
Q Consensus 104 ~~~~C~~C~~~f~~~~~l~~H~~~~h~ 130 (159)
..|.|+.|+|.|.-..-.++|+...|.
T Consensus 76 ~K~~C~lc~KlFkg~eFV~KHI~nKH~ 102 (214)
T PF04959_consen 76 DKWRCPLCGKLFKGPEFVRKHIFNKHP 102 (214)
T ss_dssp EEEEE-SSS-EESSHHHHHHHHHHH-H
T ss_pred CEECCCCCCcccCChHHHHHHHhhcCH
Confidence 347777777777777777777755554
No 127
>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=67.27 E-value=3.3 Score=19.06 Aligned_cols=16 Identities=31% Similarity=0.621 Sum_probs=7.4
Q ss_pred cCCcccccccccCCce
Q psy9695 107 RCTICQKAFTTKGNLK 122 (159)
Q Consensus 107 ~C~~C~~~f~~~~~l~ 122 (159)
.|..|++.|..+..+.
T Consensus 5 ~C~eC~~~f~dSyL~~ 20 (34)
T PF01286_consen 5 KCDECGKPFMDSYLLN 20 (34)
T ss_dssp E-TTT--EES-SSCCC
T ss_pred hHhHhCCHHHHHHHHH
Confidence 5777777776655443
No 128
>KOG4602|consensus
Probab=67.26 E-value=1.9 Score=29.70 Aligned_cols=43 Identities=14% Similarity=0.223 Sum_probs=18.3
Q ss_pred cCCcccccccccCCceeeehhhccCCCCCcccccccchhhchh
Q psy9695 107 RCTICQKAFTTKGNLKVREIEINIGSQLPKKAQQHIGAVEGKS 149 (159)
Q Consensus 107 ~C~~C~~~f~~~~~l~~H~~~~h~~~~~~~~~~~~~C~~C~~~ 149 (159)
.|..|.-.-.....+..|..+...|.++=..-+.|.|++||-+
T Consensus 235 ~CvFC~nN~E~~A~y~tH~lkd~dgRVLCPkLR~YVCPiCGAT 277 (318)
T KOG4602|consen 235 CCVFCFNNAEEFARYHTHPLKDKDGRVLCPKLRSYVCPICGAT 277 (318)
T ss_pred eEEeecCCCchhhheecccccCCCCcEechhHhhhcCcccccc
Confidence 4444443333333344444333333333333345555555543
No 129
>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=66.71 E-value=1.4 Score=21.34 Aligned_cols=13 Identities=8% Similarity=0.159 Sum_probs=7.6
Q ss_pred ccccchhhchhhh
Q psy9695 139 QQHIGAVEGKSFQ 151 (159)
Q Consensus 139 ~~~~C~~C~~~f~ 151 (159)
.-+.|+.||..+-
T Consensus 31 p~~~C~~CGE~~~ 43 (46)
T TIGR03831 31 PALVCPQCGEEYL 43 (46)
T ss_pred CccccccCCCEee
Confidence 3456666666554
No 130
>KOG2593|consensus
Probab=66.54 E-value=3.8 Score=30.54 Aligned_cols=17 Identities=35% Similarity=0.729 Sum_probs=8.5
Q ss_pred ccccccccccccCcccc
Q psy9695 46 PFRCTICQKAFTTKGNL 62 (159)
Q Consensus 46 ~~~c~~c~~~~~~~~~l 62 (159)
.|.|+.|.++|.....+
T Consensus 128 ~Y~Cp~C~kkyt~Lea~ 144 (436)
T KOG2593|consen 128 GYVCPNCQKKYTSLEAL 144 (436)
T ss_pred cccCCccccchhhhHHH
Confidence 35555555555444433
No 131
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=66.51 E-value=1.8 Score=30.94 Aligned_cols=37 Identities=24% Similarity=0.635 Sum_probs=17.0
Q ss_pred CcccCcccccccCChHHHHHHHHhhcCCCccccccccccc
Q psy9695 17 PKHLCHVCHKNFSSSSALQIHMRTHTGDKPFRCTICQKAF 56 (159)
Q Consensus 17 ~~~~C~~C~~~f~~~~~~~~h~~~~~~~~~~~c~~c~~~~ 56 (159)
....|+.||..- ..+.+ +.....|.+...|..|+..+
T Consensus 186 ~~~~CPvCGs~P-~~s~v--~~~~~~G~RyL~CslC~teW 222 (309)
T PRK03564 186 QRQFCPVCGSMP-VSSVV--QIGTTQGLRYLHCNLCESEW 222 (309)
T ss_pred CCCCCCCCCCcc-hhhee--eccCCCCceEEEcCCCCCcc
Confidence 345677777532 11111 11122344556666666554
No 132
>KOG2186|consensus
Probab=65.91 E-value=3.6 Score=28.40 Aligned_cols=39 Identities=26% Similarity=0.565 Sum_probs=27.3
Q ss_pred cccCcccccccCChHHHHHHHHhhcCCCccccccccccccC
Q psy9695 18 KHLCHVCHKNFSSSSALQIHMRTHTGDKPFRCTICQKAFTT 58 (159)
Q Consensus 18 ~~~C~~C~~~f~~~~~~~~h~~~~~~~~~~~c~~c~~~~~~ 58 (159)
-|.|+.||....... +..|+..-++ ..|.|-.|+..|..
T Consensus 3 ~FtCnvCgEsvKKp~-vekH~srCrn-~~fSCIDC~k~F~~ 41 (276)
T KOG2186|consen 3 FFTCNVCGESVKKPQ-VEKHMSRCRN-AYFSCIDCGKTFER 41 (276)
T ss_pred EEehhhhhhhccccc-hHHHHHhccC-CeeEEeeccccccc
Confidence 377888888765544 4557766555 67888888888866
No 133
>PRK05978 hypothetical protein; Provisional
Probab=65.87 E-value=2.8 Score=26.51 Aligned_cols=12 Identities=33% Similarity=0.919 Sum_probs=7.5
Q ss_pred cCCccccccccc
Q psy9695 107 RCTICQKAFTTK 118 (159)
Q Consensus 107 ~C~~C~~~f~~~ 118 (159)
.|+.||..|...
T Consensus 54 ~C~~CG~~~~~~ 65 (148)
T PRK05978 54 HCAACGEDFTHH 65 (148)
T ss_pred CccccCCccccC
Confidence 677777666543
No 134
>PF05290 Baculo_IE-1: Baculovirus immediate-early protein (IE-0); InterPro: IPR007954 This entry contains the Baculovirus immediate-early protein IE-0.
Probab=65.29 E-value=3.5 Score=25.46 Aligned_cols=20 Identities=25% Similarity=0.591 Sum_probs=11.8
Q ss_pred CCCccccccccccccCcccc
Q psy9695 43 GDKPFRCTICQKAFTTKGNL 62 (159)
Q Consensus 43 ~~~~~~c~~c~~~~~~~~~l 62 (159)
+.+.|.|++|...+....-|
T Consensus 77 d~~lYeCnIC~etS~ee~FL 96 (140)
T PF05290_consen 77 DPKLYECNICKETSAEERFL 96 (140)
T ss_pred CCCceeccCcccccchhhcC
Confidence 44567777777666554433
No 135
>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=65.10 E-value=2.2 Score=19.96 Aligned_cols=12 Identities=8% Similarity=-0.166 Sum_probs=6.9
Q ss_pred cccccchhhchh
Q psy9695 138 AQQHIGAVEGKS 149 (159)
Q Consensus 138 ~~~~~C~~C~~~ 149 (159)
.+.|+|.+||--
T Consensus 4 ~~~YkC~~CGni 15 (36)
T PF06397_consen 4 GEFYKCEHCGNI 15 (36)
T ss_dssp TEEEE-TTT--E
T ss_pred ccEEEccCCCCE
Confidence 378999999853
No 136
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=65.09 E-value=12 Score=26.76 Aligned_cols=25 Identities=28% Similarity=0.600 Sum_probs=14.3
Q ss_pred CCccCcccccccCChHHHHHHHHHc
Q psy9695 76 PKHLCHVCHKNFSSSSALQIHMRTH 100 (159)
Q Consensus 76 ~~~~C~~C~~~~~~~~~l~~H~~~h 100 (159)
..|.|+.|...|-..-....|...|
T Consensus 387 ~rY~Ce~CK~~FC~dCdvfiHe~Lh 411 (421)
T COG5151 387 GRYQCELCKSTFCSDCDVFIHETLH 411 (421)
T ss_pred cceechhhhhhhhhhhHHHHHHHHh
Confidence 3466666666665555555555544
No 137
>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=65.04 E-value=2.8 Score=18.98 Aligned_cols=9 Identities=44% Similarity=1.232 Sum_probs=3.8
Q ss_pred ccccccccc
Q psy9695 46 PFRCTICQK 54 (159)
Q Consensus 46 ~~~c~~c~~ 54 (159)
+..|+.||.
T Consensus 17 ~irC~~CG~ 25 (32)
T PF03604_consen 17 PIRCPECGH 25 (32)
T ss_dssp TSSBSSSS-
T ss_pred cEECCcCCC
Confidence 344555543
No 138
>PF15269 zf-C2H2_7: Zinc-finger
Probab=64.81 E-value=13 Score=18.21 Aligned_cols=22 Identities=27% Similarity=0.375 Sum_probs=18.1
Q ss_pred ccCcccccccCChHHHHHHHHh
Q psy9695 19 HLCHVCHKNFSSSSALQIHMRT 40 (159)
Q Consensus 19 ~~C~~C~~~f~~~~~~~~h~~~ 40 (159)
|+|.+|..+...++.|-+|+..
T Consensus 21 ykcfqcpftc~~kshl~nhmky 42 (54)
T PF15269_consen 21 YKCFQCPFTCNEKSHLFNHMKY 42 (54)
T ss_pred ceeecCCcccchHHHHHHHHHH
Confidence 8888998888888888888753
No 139
>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=64.54 E-value=5 Score=19.38 Aligned_cols=42 Identities=17% Similarity=0.196 Sum_probs=19.5
Q ss_pred CCcccccccccCCcee-eehhhccCCCCCcccccccchhhchh
Q psy9695 108 CTICQKAFTTKGNLKV-REIEINIGSQLPKKAQQHIGAVEGKS 149 (159)
Q Consensus 108 C~~C~~~f~~~~~l~~-H~~~~h~~~~~~~~~~~~~C~~C~~~ 149 (159)
|.+|++.|.....+.. |......+.....+.....|+.|...
T Consensus 1 C~~C~~~~~~~~~~~v~Hi~~~~~gg~~~~~Nl~~lC~~Ch~~ 43 (47)
T PF01844_consen 1 CQYCGKPGSDNESLHVHHIIPRSKGGKNDLENLILLCPSCHRK 43 (47)
T ss_dssp -TTT--B--GG-GEEEEESS-TTTT---STTTEEEEEHHHHHH
T ss_pred CCCCCCcCccCcceEeECcCchhcCCCCCHHHHHHHhHHHHHH
Confidence 7788888877644443 44333334545566677778777654
No 140
>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=64.37 E-value=6.9 Score=23.21 Aligned_cols=26 Identities=19% Similarity=0.259 Sum_probs=21.9
Q ss_pred CcccC----cccccccCChHHHHHHHHhhc
Q psy9695 17 PKHLC----HVCHKNFSSSSALQIHMRTHT 42 (159)
Q Consensus 17 ~~~~C----~~C~~~f~~~~~~~~h~~~~~ 42 (159)
..|.| ..|+....+...+.+|...++
T Consensus 79 ~G~~C~~~~~~C~y~~~~~~~m~~H~~~~H 108 (109)
T PF12013_consen 79 DGYRCQCDPPHCGYITRSKKTMRKHWRKEH 108 (109)
T ss_pred CCeeeecCCCCCCcEeccHHHHHHHHHHhc
Confidence 34899 999999999999999987654
No 141
>PRK04023 DNA polymerase II large subunit; Validated
Probab=63.97 E-value=7.5 Score=32.45 Aligned_cols=9 Identities=22% Similarity=0.682 Sum_probs=4.5
Q ss_pred ccCCccccc
Q psy9695 106 FRCTICQKA 114 (159)
Q Consensus 106 ~~C~~C~~~ 114 (159)
|.|+.||..
T Consensus 664 y~CPKCG~E 672 (1121)
T PRK04023 664 DECEKCGRE 672 (1121)
T ss_pred CcCCCCCCC
Confidence 445555543
No 142
>KOG2482|consensus
Probab=63.76 E-value=2.2 Score=30.73 Aligned_cols=55 Identities=24% Similarity=0.422 Sum_probs=39.1
Q ss_pred ccCccccccc-CChHHHHHHHHHccC-C---------------------CCccCCcccccccccCCceeeehhhccCC
Q psy9695 78 HLCHVCHKNF-SSSSALQIHMRTHTG-D---------------------KPFRCTICQKAFTTKGNLKVREIEINIGS 132 (159)
Q Consensus 78 ~~C~~C~~~~-~~~~~l~~H~~~h~~-~---------------------~~~~C~~C~~~f~~~~~l~~H~~~~h~~~ 132 (159)
-.|..|...+ ...+.+..|...-++ . ..++|-+|.+.|..+..|..||.+..+..
T Consensus 145 lqClFCn~e~lgnRs~~l~Hlf~~H~lniGlpDniVyvnelLehLkekL~r~~CLyCekifrdkntLkeHMrkK~Hrr 222 (423)
T KOG2482|consen 145 LQCLFCNNEGLGNRSEILEHLFHVHGLNIGLPDNIVYVNELLEHLKEKLERLRCLYCEKIFRDKNTLKEHMRKKRHRR 222 (423)
T ss_pred eEEEEecchhcccHHHHHHHHHHHhhhccCCCcceeeHHHHHHHHHHHHhhheeeeeccccCCcHHHHHHHHhccCcc
Confidence 5688887654 456777777664221 1 23689999999999999999995555543
No 143
>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=63.28 E-value=2.1 Score=20.49 Aligned_cols=11 Identities=9% Similarity=0.205 Sum_probs=6.9
Q ss_pred cccchhhchhh
Q psy9695 140 QHIGAVEGKSF 150 (159)
Q Consensus 140 ~~~C~~C~~~f 150 (159)
+-.|++|+..|
T Consensus 29 ~~~CpYCg~~y 39 (40)
T PF10276_consen 29 PVVCPYCGTRY 39 (40)
T ss_dssp EEEETTTTEEE
T ss_pred eEECCCCCCEE
Confidence 45666666655
No 144
>PF04810 zf-Sec23_Sec24: Sec23/Sec24 zinc finger; InterPro: IPR006895 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. COPII (coat protein complex II)-coated vesicles carry proteins from the endoplasmic reticulum (ER) to the Golgi complex []. COPII-coated vesicles form on the ER by the stepwise recruitment of three cytosolic components: Sar1-GTP to initiate coat formation, Sec23/24 heterodimer to select SNARE and cargo molecules, and Sec13/31 to induce coat polymerisation and membrane deformation []. Sec23 p and Sec24p are structurally related, folding into five distinct domains: a beta-barrel, a zinc-finger, an alpha/beta trunk domain (IPR006896 from INTERPRO), an all-helical region (IPR006900 from INTERPRO), and a C-terminal gelsolin-like domain (IPR007123 from INTERPRO). This entry describes an approximately 55-residue Sec23/24 zinc-binding domain, which lies against the beta-barrel at the periphery of the complex. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006886 intracellular protein transport, 0006888 ER to Golgi vesicle-mediated transport, 0030127 COPII vesicle coat; PDB: 3EFO_B 3EG9_B 3EGD_A 2YRC_A 2NUP_A 2YRD_A 3EGX_A 2NUT_A 3EH1_A 1PD0_A ....
Probab=61.99 E-value=3.2 Score=19.78 Aligned_cols=9 Identities=33% Similarity=1.036 Sum_probs=3.9
Q ss_pred CCccCCccc
Q psy9695 104 KPFRCTICQ 112 (159)
Q Consensus 104 ~~~~C~~C~ 112 (159)
+.|.|+.|+
T Consensus 23 ~~w~C~~C~ 31 (40)
T PF04810_consen 23 KTWICNFCG 31 (40)
T ss_dssp TEEEETTT-
T ss_pred CEEECcCCC
Confidence 345555554
No 145
>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=61.59 E-value=1.4 Score=22.41 Aligned_cols=22 Identities=23% Similarity=0.665 Sum_probs=10.3
Q ss_pred CCccCCcccccccccCCceeee
Q psy9695 104 KPFRCTICQKAFTTKGNLKVRE 125 (159)
Q Consensus 104 ~~~~C~~C~~~f~~~~~l~~H~ 125 (159)
..|+|+.|+..|--.-++-.|.
T Consensus 20 ~~y~C~~C~~~FC~dCD~fiHE 41 (51)
T PF07975_consen 20 SRYRCPKCKNHFCIDCDVFIHE 41 (51)
T ss_dssp EEE--TTTT--B-HHHHHTTTT
T ss_pred CeEECCCCCCccccCcChhhhc
Confidence 3466666666666666555555
No 146
>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=61.08 E-value=8.6 Score=16.36 Aligned_cols=19 Identities=21% Similarity=0.663 Sum_probs=11.9
Q ss_pred cCcccccccCChHHHHHHHH
Q psy9695 20 LCHVCHKNFSSSSALQIHMR 39 (159)
Q Consensus 20 ~C~~C~~~f~~~~~~~~h~~ 39 (159)
.||.|++.+ ....+..|+.
T Consensus 3 ~CPiC~~~v-~~~~in~HLD 21 (26)
T smart00734 3 QCPVCFREV-PENLINSHLD 21 (26)
T ss_pred cCCCCcCcc-cHHHHHHHHH
Confidence 588888877 4455555543
No 147
>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=60.99 E-value=1.4 Score=20.46 Aligned_cols=8 Identities=38% Similarity=0.845 Sum_probs=3.0
Q ss_pred cCCccccc
Q psy9695 107 RCTICQKA 114 (159)
Q Consensus 107 ~C~~C~~~ 114 (159)
.|..||-.
T Consensus 23 sC~~CGPr 30 (35)
T PF07503_consen 23 SCTNCGPR 30 (35)
T ss_dssp -BTTCC-S
T ss_pred cCCCCCCC
Confidence 45555543
No 148
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=60.66 E-value=2.5 Score=25.42 Aligned_cols=12 Identities=8% Similarity=-0.105 Sum_probs=6.2
Q ss_pred ccccchhhchhh
Q psy9695 139 QQHIGAVEGKSF 150 (159)
Q Consensus 139 ~~~~C~~C~~~f 150 (159)
..|+|..||..|
T Consensus 99 ~Fy~C~~Cg~~w 110 (113)
T COG1594 99 RFYKCTRCGYRW 110 (113)
T ss_pred EEEEecccCCEe
Confidence 445555555444
No 149
>COG4338 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=60.39 E-value=1.2 Score=22.05 Aligned_cols=14 Identities=29% Similarity=0.356 Sum_probs=8.4
Q ss_pred cchhhchhhhhccc
Q psy9695 142 IGAVEGKSFQAKHK 155 (159)
Q Consensus 142 ~C~~C~~~f~~~~~ 155 (159)
.|++|++.|..+-+
T Consensus 14 ICpvCqRPFsWRkK 27 (54)
T COG4338 14 ICPVCQRPFSWRKK 27 (54)
T ss_pred hhhhhcCchHHHHH
Confidence 56666666665443
No 150
>PF09416 UPF1_Zn_bind: RNA helicase (UPF2 interacting domain); InterPro: IPR018999 UPF1 (or regulator of nonsense transcripts 1 homologue) is an essential RNA helicase that detects mRNAs containing premature stop codons and triggers their degradation. This domain contains 3 zinc binding motifs and forms interactions with another protein (UPF2) that is also involved nonsense-mediated mRNA decay (NMD) []. ; GO: 0003677 DNA binding, 0004386 helicase activity, 0005524 ATP binding, 0008270 zinc ion binding, 0000184 nuclear-transcribed mRNA catabolic process, nonsense-mediated decay, 0005737 cytoplasm; PDB: 2IYK_B 2WJY_A 2WJV_A 2XZL_A.
Probab=59.11 E-value=2.7 Score=26.67 Aligned_cols=7 Identities=29% Similarity=0.937 Sum_probs=1.4
Q ss_pred ccCCccc
Q psy9695 106 FRCTICQ 112 (159)
Q Consensus 106 ~~C~~C~ 112 (159)
.+|-.||
T Consensus 61 leCy~Cg 67 (152)
T PF09416_consen 61 LECYNCG 67 (152)
T ss_dssp ---TTT-
T ss_pred EEEEecC
Confidence 3444444
No 151
>PF04641 Rtf2: Rtf2 RING-finger
Probab=58.80 E-value=5.4 Score=27.82 Aligned_cols=50 Identities=22% Similarity=0.351 Sum_probs=26.0
Q ss_pred CCCccCCcccccccccCCceeeehhhccCCCCCcc----c-ccccchhhchhhhhccc
Q psy9695 103 DKPFRCTICQKAFTTKGNLKVREIEINIGSQLPKK----A-QQHIGAVEGKSFQAKHK 155 (159)
Q Consensus 103 ~~~~~C~~C~~~f~~~~~l~~H~~~~h~~~~~~~~----~-~~~~C~~C~~~f~~~~~ 155 (159)
+.+|.||+.++.|.....+..-. -+|.++++. . ..-.|++|+..|...+-
T Consensus 111 ~~~~~CPvt~~~~~~~~~fv~l~---~cG~V~s~~alke~k~~~~Cp~c~~~f~~~Di 165 (260)
T PF04641_consen 111 EGRFICPVTGKEFNGKHKFVYLR---PCGCVFSEKALKELKKSKKCPVCGKPFTEEDI 165 (260)
T ss_pred CceeECCCCCcccCCceeEEEEc---CCCCEeeHHHHHhhcccccccccCCccccCCE
Confidence 44577777777665444443222 222222210 0 13458888888886554
No 152
>TIGR01384 TFS_arch transcription factor S, archaeal. There has been an apparent duplication event in the Halobacteriaceae lineage (Haloarcula, Haloferax, Haloquadratum, Halobacterium and Natromonas). There appears to be a separate duplication in Methanosphaera stadtmanae.
Probab=57.42 E-value=2.8 Score=24.63 Aligned_cols=40 Identities=13% Similarity=0.080 Sum_probs=21.7
Q ss_pred ccCCcccccccccCCceeeehhhccCCCCCcccccccchhhchhhhh
Q psy9695 106 FRCTICQKAFTTKGNLKVREIEINIGSQLPKKAQQHIGAVEGKSFQA 152 (159)
Q Consensus 106 ~~C~~C~~~f~~~~~l~~H~~~~h~~~~~~~~~~~~~C~~C~~~f~~ 152 (159)
..|+.||..-.....++... .....- ..|.|..|+..+..
T Consensus 63 ~~Cp~Cg~~~a~f~~~Q~Rs-adE~~T------~fy~C~~C~~~w~~ 102 (104)
T TIGR01384 63 VECPKCGHKEAYYWLLQTRR-ADEPET------RFYKCTKCGYVWRE 102 (104)
T ss_pred CCCCCCCCCeeEEEEeccCC-CCCCcE------EEEEeCCCCCeeEe
Confidence 57888885544333333111 111222 67888888876543
No 153
>PF14445 Prok-RING_2: Prokaryotic RING finger family 2
Probab=57.34 E-value=1.7 Score=21.82 Aligned_cols=11 Identities=9% Similarity=-0.100 Sum_probs=5.2
Q ss_pred cccchhhchhh
Q psy9695 140 QHIGAVEGKSF 150 (159)
Q Consensus 140 ~~~C~~C~~~f 150 (159)
.|.|+.|..+|
T Consensus 7 ry~CDLCn~~~ 17 (57)
T PF14445_consen 7 RYSCDLCNSSH 17 (57)
T ss_pred hHhHHhhcccC
Confidence 34455554444
No 154
>KOG2593|consensus
Probab=56.96 E-value=7.5 Score=29.06 Aligned_cols=19 Identities=32% Similarity=0.672 Sum_probs=11.7
Q ss_pred CCccCCcccccccccCCce
Q psy9695 104 KPFRCTICQKAFTTKGNLK 122 (159)
Q Consensus 104 ~~~~C~~C~~~f~~~~~l~ 122 (159)
..|.|+.|.+.|+...-++
T Consensus 127 ~~Y~Cp~C~kkyt~Lea~~ 145 (436)
T KOG2593|consen 127 AGYVCPNCQKKYTSLEALQ 145 (436)
T ss_pred ccccCCccccchhhhHHHH
Confidence 4577777777766554443
No 155
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=56.89 E-value=5.2 Score=18.98 Aligned_cols=14 Identities=29% Similarity=0.807 Sum_probs=10.9
Q ss_pred CccCCccccccccc
Q psy9695 105 PFRCTICQKAFTTK 118 (159)
Q Consensus 105 ~~~C~~C~~~f~~~ 118 (159)
|+.|..|++.|-..
T Consensus 12 ~f~C~~C~~~FC~~ 25 (39)
T smart00154 12 GFKCRHCGNLFCGE 25 (39)
T ss_pred CeECCccCCccccc
Confidence 78888888888644
No 156
>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=56.14 E-value=6.9 Score=20.93 Aligned_cols=10 Identities=30% Similarity=0.700 Sum_probs=4.7
Q ss_pred CccCCccccc
Q psy9695 105 PFRCTICQKA 114 (159)
Q Consensus 105 ~~~C~~C~~~ 114 (159)
.|.|+.||..
T Consensus 46 ~~~C~~Cg~~ 55 (69)
T PF07282_consen 46 VFTCPNCGFE 55 (69)
T ss_pred eEEcCCCCCE
Confidence 3455555543
No 157
>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=55.86 E-value=2.1 Score=22.12 Aligned_cols=13 Identities=8% Similarity=0.148 Sum_probs=3.9
Q ss_pred ccccchhhchhhh
Q psy9695 139 QQHIGAVEGKSFQ 151 (159)
Q Consensus 139 ~~~~C~~C~~~f~ 151 (159)
+.|.|++||.+=.
T Consensus 32 r~y~Cp~CgAtGd 44 (55)
T PF05741_consen 32 RKYVCPICGATGD 44 (55)
T ss_dssp GG---TTT---GG
T ss_pred hcCcCCCCcCcCc
Confidence 5566666665433
No 158
>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=55.53 E-value=6.4 Score=23.01 Aligned_cols=18 Identities=39% Similarity=0.813 Sum_probs=13.7
Q ss_pred HccCCCCccCCcccccccc
Q psy9695 99 THTGDKPFRCTICQKAFTT 117 (159)
Q Consensus 99 ~h~~~~~~~C~~C~~~f~~ 117 (159)
.+.+ ++++|+.||..|.-
T Consensus 74 l~~g-~~~rC~eCG~~fkL 91 (97)
T cd00924 74 LEKG-KPKRCPECGHVFKL 91 (97)
T ss_pred EeCC-CceeCCCCCcEEEE
Confidence 3444 79999999988864
No 159
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=55.25 E-value=10 Score=19.58 Aligned_cols=11 Identities=18% Similarity=0.313 Sum_probs=6.8
Q ss_pred CccCccccccc
Q psy9695 77 KHLCHVCHKNF 87 (159)
Q Consensus 77 ~~~C~~C~~~~ 87 (159)
.|.|+.||-.+
T Consensus 14 ~~~Cp~cGipt 24 (55)
T PF13824_consen 14 NFECPDCGIPT 24 (55)
T ss_pred CCcCCCCCCcC
Confidence 46677776543
No 160
>PF08394 Arc_trans_TRASH: Archaeal TRASH domain; InterPro: IPR013603 This region is found in the C terminus of a number of archaeal transcriptional regulators. It is thought to function as a metal-sensing regulatory module [].
Probab=55.07 E-value=5.2 Score=18.81 Aligned_cols=14 Identities=7% Similarity=-0.123 Sum_probs=9.7
Q ss_pred ccccchhhchhhhh
Q psy9695 139 QQHIGAVEGKSFQA 152 (159)
Q Consensus 139 ~~~~C~~C~~~f~~ 152 (159)
..|-|+.|...|..
T Consensus 22 y~fCC~tC~~~fk~ 35 (37)
T PF08394_consen 22 YYFCCPTCLSQFKK 35 (37)
T ss_pred EEEECHHHHHHHHh
Confidence 55666888777764
No 161
>PF13878 zf-C2H2_3: zinc-finger of acetyl-transferase ESCO
Probab=55.01 E-value=16 Score=17.51 Aligned_cols=24 Identities=25% Similarity=0.517 Sum_probs=16.4
Q ss_pred ccCcccccccC--ChHHHHHHHHHcc
Q psy9695 78 HLCHVCHKNFS--SSSALQIHMRTHT 101 (159)
Q Consensus 78 ~~C~~C~~~~~--~~~~l~~H~~~h~ 101 (159)
..|+.||..|. .+..-..|.+-|.
T Consensus 14 ~~C~~CgM~Y~~~~~eD~~~H~~yH~ 39 (41)
T PF13878_consen 14 TTCPTCGMLYSPGSPEDEKLHKKYHD 39 (41)
T ss_pred cCCCCCCCEECCCCHHHHHHHHHHHh
Confidence 58999998764 3456666766553
No 162
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=53.46 E-value=11 Score=30.52 Aligned_cols=8 Identities=38% Similarity=1.007 Sum_probs=4.0
Q ss_pred CccCCccc
Q psy9695 105 PFRCTICQ 112 (159)
Q Consensus 105 ~~~C~~C~ 112 (159)
|..|+.||
T Consensus 475 p~~Cp~Cg 482 (730)
T COG1198 475 PQSCPECG 482 (730)
T ss_pred CCCCCCCC
Confidence 44555555
No 163
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=53.31 E-value=8.5 Score=22.13 Aligned_cols=31 Identities=19% Similarity=0.516 Sum_probs=18.3
Q ss_pred CccccccccccccCccccccccccccccCCCCCccCcccccccC
Q psy9695 45 KPFRCTICQKAFTTKGNLKLIPNAVFNVAGMPKHLCHVCHKNFS 88 (159)
Q Consensus 45 ~~~~c~~c~~~~~~~~~l~~~~~~~~~~~~~~~~~C~~C~~~~~ 88 (159)
..|.|+.|+..-.-. .+...|.|..|++.|.
T Consensus 35 a~y~CpfCgk~~vkR-------------~a~GIW~C~~C~~~~A 65 (90)
T PTZ00255 35 AKYFCPFCGKHAVKR-------------QAVGIWRCKGCKKTVA 65 (90)
T ss_pred CCccCCCCCCCceee-------------eeeEEEEcCCCCCEEe
Confidence 468888887433111 1123588888887653
No 164
>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=53.13 E-value=9.8 Score=23.64 Aligned_cols=26 Identities=42% Similarity=0.820 Sum_probs=16.2
Q ss_pred CccCcccccccCChHHHHHHHHHccCCCC
Q psy9695 77 KHLCHVCHKNFSSSSALQIHMRTHTGDKP 105 (159)
Q Consensus 77 ~~~C~~C~~~~~~~~~l~~H~~~h~~~~~ 105 (159)
...|.+||+.|.. |..|.+.|+|-.|
T Consensus 72 ~i~clecGk~~k~---LkrHL~~~~gltp 97 (132)
T PF05443_consen 72 YIICLECGKKFKT---LKRHLRTHHGLTP 97 (132)
T ss_dssp -EE-TBT--EESB---HHHHHHHTT-S-H
T ss_pred eeEEccCCcccch---HHHHHHHccCCCH
Confidence 4789999999866 5889999976543
No 165
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=53.12 E-value=6.6 Score=23.62 Aligned_cols=24 Identities=17% Similarity=0.494 Sum_probs=13.8
Q ss_pred ccCcccccccCChHHHHHHHHHccCCCCccCCcccc
Q psy9695 78 HLCHVCHKNFSSSSALQIHMRTHTGDKPFRCTICQK 113 (159)
Q Consensus 78 ~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~ 113 (159)
..|..|+..|.... ..+.||.||.
T Consensus 71 ~~C~~Cg~~~~~~~------------~~~~CP~Cgs 94 (113)
T PRK12380 71 AWCWDCSQVVEIHQ------------HDAQCPHCHG 94 (113)
T ss_pred EEcccCCCEEecCC------------cCccCcCCCC
Confidence 66777776553321 2345777773
No 166
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=53.04 E-value=9.1 Score=21.96 Aligned_cols=14 Identities=36% Similarity=0.861 Sum_probs=10.5
Q ss_pred CccccccccccccC
Q psy9695 45 KPFRCTICQKAFTT 58 (159)
Q Consensus 45 ~~~~c~~c~~~~~~ 58 (159)
.|..|..||..|..
T Consensus 57 ~Pa~CkkCGfef~~ 70 (97)
T COG3357 57 RPARCKKCGFEFRD 70 (97)
T ss_pred cChhhcccCccccc
Confidence 46788888887765
No 167
>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=52.88 E-value=5.9 Score=23.88 Aligned_cols=26 Identities=23% Similarity=0.617 Sum_probs=16.2
Q ss_pred CccCcccccccCChHHHHHHHHHccCCCCccCCccccc
Q psy9695 77 KHLCHVCHKNFSSSSALQIHMRTHTGDKPFRCTICQKA 114 (159)
Q Consensus 77 ~~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~~ 114 (159)
...|..|+..|..... .+.||.||..
T Consensus 70 ~~~C~~Cg~~~~~~~~------------~~~CP~Cgs~ 95 (115)
T TIGR00100 70 ECECEDCSEEVSPEID------------LYRCPKCHGI 95 (115)
T ss_pred EEEcccCCCEEecCCc------------CccCcCCcCC
Confidence 3678888866644311 3678888844
No 168
>KOG1280|consensus
Probab=52.65 E-value=6.1 Score=28.62 Aligned_cols=26 Identities=15% Similarity=0.272 Sum_probs=14.7
Q ss_pred CccCCcccccccccCCceeeehhhcc
Q psy9695 105 PFRCTICQKAFTTKGNLKVREIEINI 130 (159)
Q Consensus 105 ~~~C~~C~~~f~~~~~l~~H~~~~h~ 130 (159)
.|.|++|++.-.....|..|....|.
T Consensus 79 SftCPyC~~~Gfte~~f~~Hv~s~Hp 104 (381)
T KOG1280|consen 79 SFTCPYCGIMGFTERQFGTHVLSQHP 104 (381)
T ss_pred cccCCcccccccchhHHHHHhhhcCc
Confidence 56666666655555555556544443
No 169
>KOG3408|consensus
Probab=52.64 E-value=9 Score=23.30 Aligned_cols=26 Identities=31% Similarity=0.632 Sum_probs=22.3
Q ss_pred CCCCccCcccccccCChHHHHHHHHH
Q psy9695 74 GMPKHLCHVCHKNFSSSSALQIHMRT 99 (159)
Q Consensus 74 ~~~~~~C~~C~~~~~~~~~l~~H~~~ 99 (159)
|...|-|..|.+-|.....|..|.+.
T Consensus 54 G~GqfyCi~CaRyFi~~~~l~~H~kt 79 (129)
T KOG3408|consen 54 GGGQFYCIECARYFIDAKALKTHFKT 79 (129)
T ss_pred CCceeehhhhhhhhcchHHHHHHHhc
Confidence 44458999999999999999999874
No 170
>PF04423 Rad50_zn_hook: Rad50 zinc hook motif; InterPro: IPR007517 The Mre11 complex (Mre11 Rad50 Nbs1) is central to chromosomal maintenance and functions in homologous recombination, telomere maintenance and sister chromatid association. The Rad50 coiled-coil region contains a dimer interface at the apex of the coiled coils in which pairs of conserved Cys-X-X-Cys motifs form interlocking hooks that bind one Zn ion. This alignment includes the zinc hook motif and a short stretch of coiled-coil on either side.; GO: 0004518 nuclease activity, 0005524 ATP binding, 0008270 zinc ion binding, 0006281 DNA repair; PDB: 1L8D_B.
Probab=52.58 E-value=5.3 Score=20.34 Aligned_cols=12 Identities=17% Similarity=0.800 Sum_probs=6.0
Q ss_pred cCCccccccccc
Q psy9695 107 RCTICQKAFTTK 118 (159)
Q Consensus 107 ~C~~C~~~f~~~ 118 (159)
.||+|+..|...
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 889998887643
No 171
>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=51.87 E-value=6 Score=19.05 Aligned_cols=10 Identities=20% Similarity=0.531 Sum_probs=5.4
Q ss_pred ccCccccccc
Q psy9695 78 HLCHVCHKNF 87 (159)
Q Consensus 78 ~~C~~C~~~~ 87 (159)
+.|..||...
T Consensus 20 ~vC~~CG~Vl 29 (43)
T PF08271_consen 20 LVCPNCGLVL 29 (43)
T ss_dssp EEETTT-BBE
T ss_pred EECCCCCCEe
Confidence 5677776543
No 172
>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=51.73 E-value=2.9 Score=31.66 Aligned_cols=28 Identities=14% Similarity=0.229 Sum_probs=21.9
Q ss_pred CccCCcccccccccCCceeeehhhccCC
Q psy9695 105 PFRCTICQKAFTTKGNLKVREIEINIGS 132 (159)
Q Consensus 105 ~~~C~~C~~~f~~~~~l~~H~~~~h~~~ 132 (159)
-|.|+.|.+.|.....+..|+...|.+.
T Consensus 57 FWiCp~CskkF~d~~~~~~H~~~eH~~~ 84 (466)
T PF04780_consen 57 FWICPRCSKKFSDAESCLSHMEQEHPAG 84 (466)
T ss_pred EeeCCcccceeCCHHHHHHHHHHhhhhh
Confidence 3678888888888888888886677665
No 173
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=51.55 E-value=7 Score=19.48 Aligned_cols=16 Identities=19% Similarity=0.382 Sum_probs=12.3
Q ss_pred CccCCcccccccccCC
Q psy9695 105 PFRCTICQKAFTTKGN 120 (159)
Q Consensus 105 ~~~C~~C~~~f~~~~~ 120 (159)
.|.|+.||..+.-...
T Consensus 20 ~~vC~~Cg~~~~~~~~ 35 (52)
T smart00661 20 RFVCRKCGYEEPIEQK 35 (52)
T ss_pred EEECCcCCCeEECCCc
Confidence 6889999977766555
No 174
>KOG0696|consensus
Probab=51.22 E-value=8 Score=29.23 Aligned_cols=61 Identities=23% Similarity=0.294 Sum_probs=43.9
Q ss_pred CCCCCccCcccccccCChHHHHHHHHHccCCCCccCCcccccccccCCceeeehhhccCCCCCcccccccchhhch
Q psy9695 73 AGMPKHLCHVCHKNFSSSSALQIHMRTHTGDKPFRCTICQKAFTTKGNLKVREIEINIGSQLPKKAQQHIGAVEGK 148 (159)
Q Consensus 73 ~~~~~~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~~h~~~~~~~~~~~~~C~~C~~ 148 (159)
.|...|.|..|.. ..|++-|. -..|.|+-=++.+.....-.+|..++|+=. -|--|+.||.
T Consensus 69 fgKQGfQCqvC~f--------vvHkrChe-fVtF~CPGadkg~dtDdpr~kHkf~~~tYs------sPTFCDhCGs 129 (683)
T KOG0696|consen 69 FGKQGFQCQVCCF--------VVHKRCHE-FVTFSCPGADKGPDTDDPRSKHKFKIHTYS------SPTFCDHCGS 129 (683)
T ss_pred cccCceeeeEEee--------hhhhhhcc-eEEEECCCCCCCCCCCCcccccceeeeecC------CCchhhhHHH
Confidence 4556788888763 45666553 345788887888888888888887887765 6777888874
No 175
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=51.18 E-value=14 Score=31.81 Aligned_cols=8 Identities=38% Similarity=0.912 Sum_probs=5.1
Q ss_pred cccccccc
Q psy9695 47 FRCTICQK 54 (159)
Q Consensus 47 ~~c~~c~~ 54 (159)
+.|+.||.
T Consensus 668 rkCPkCG~ 675 (1337)
T PRK14714 668 RRCPSCGT 675 (1337)
T ss_pred EECCCCCC
Confidence 56666664
No 176
>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=51.09 E-value=8.2 Score=22.23 Aligned_cols=30 Identities=23% Similarity=0.635 Sum_probs=17.7
Q ss_pred CccccccccccccCccccccccccccccCCCCCccCccccccc
Q psy9695 45 KPFRCTICQKAFTTKGNLKLIPNAVFNVAGMPKHLCHVCHKNF 87 (159)
Q Consensus 45 ~~~~c~~c~~~~~~~~~l~~~~~~~~~~~~~~~~~C~~C~~~~ 87 (159)
..|.|+.|+..-.-.. +...|.|..|++.|
T Consensus 34 a~y~CpfCgk~~vkR~-------------a~GIW~C~~C~~~~ 63 (91)
T TIGR00280 34 AKYVCPFCGKKTVKRG-------------STGIWTCRKCGAKF 63 (91)
T ss_pred cCccCCCCCCCceEEE-------------eeEEEEcCCCCCEE
Confidence 3588888874332111 11248888888765
No 177
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=50.81 E-value=6.2 Score=19.91 Aligned_cols=12 Identities=17% Similarity=0.479 Sum_probs=8.3
Q ss_pred CCccCCcccccc
Q psy9695 104 KPFRCTICQKAF 115 (159)
Q Consensus 104 ~~~~C~~C~~~f 115 (159)
..+.|..||..+
T Consensus 36 ~r~~C~~Cgyt~ 47 (50)
T PRK00432 36 DRWHCGKCGYTE 47 (50)
T ss_pred CcEECCCcCCEE
Confidence 467888888654
No 178
>PLN02294 cytochrome c oxidase subunit Vb
Probab=50.74 E-value=8.5 Score=24.95 Aligned_cols=17 Identities=29% Similarity=0.829 Sum_probs=13.5
Q ss_pred CCCCccCCccccccccc
Q psy9695 102 GDKPFRCTICQKAFTTK 118 (159)
Q Consensus 102 ~~~~~~C~~C~~~f~~~ 118 (159)
..+|++|++||..|.-.
T Consensus 138 kGkp~RCpeCG~~fkL~ 154 (174)
T PLN02294 138 KGKSFECPVCTQYFELE 154 (174)
T ss_pred CCCceeCCCCCCEEEEE
Confidence 35789999999888644
No 179
>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=50.29 E-value=3.1 Score=20.11 Aligned_cols=11 Identities=36% Similarity=0.480 Sum_probs=5.6
Q ss_pred cchhhchhhhh
Q psy9695 142 IGAVEGKSFQA 152 (159)
Q Consensus 142 ~C~~C~~~f~~ 152 (159)
.|++|++.|..
T Consensus 10 ~C~~C~rpf~W 20 (42)
T PF10013_consen 10 ICPVCGRPFTW 20 (42)
T ss_pred cCcccCCcchH
Confidence 45555555543
No 180
>PTZ00303 phosphatidylinositol kinase; Provisional
Probab=49.47 E-value=17 Score=29.80 Aligned_cols=69 Identities=14% Similarity=0.260 Sum_probs=36.3
Q ss_pred ccCcccccccCChHHHHHHHHHccCCCCccCCcccccccccCCc-eeee--hhhccCCCCCcccccc-cchhhchhhhhc
Q psy9695 78 HLCHVCHKNFSSSSALQIHMRTHTGDKPFRCTICQKAFTTKGNL-KVRE--IEINIGSQLPKKAQQH-IGAVEGKSFQAK 153 (159)
Q Consensus 78 ~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l-~~H~--~~~h~~~~~~~~~~~~-~C~~C~~~f~~~ 153 (159)
-.|..|++.|.+.... ...+.+.|..||..|-...+- +.+. .+. .....+.+..++ .|+.|-+.+...
T Consensus 461 dtC~~C~kkFfSlsK~-------L~~RKHHCRkCGrVFC~~CSSnRs~yp~aKL-pKPgsseE~ppRRVCD~CYdq~EnL 532 (1374)
T PTZ00303 461 DSCPSCGRAFISLSRP-------LGTRAHHCRSCGIRLCVFCITKRAHYSFAKL-AKPGSSDEAEERLVCDTCYKEYETV 532 (1374)
T ss_pred CcccCcCCcccccccc-------cccccccccCCccccCccccCCcccCccccc-CCCCCcccccccchhHHHHHHHHhH
Confidence 4588999888654110 123456677788877655332 2221 011 111112222445 899998777554
Q ss_pred c
Q psy9695 154 H 154 (159)
Q Consensus 154 ~ 154 (159)
.
T Consensus 533 l 533 (1374)
T PTZ00303 533 S 533 (1374)
T ss_pred H
Confidence 3
No 181
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=49.06 E-value=8.8 Score=22.49 Aligned_cols=9 Identities=33% Similarity=1.003 Sum_probs=4.1
Q ss_pred ccccccccc
Q psy9695 47 FRCTICQKA 55 (159)
Q Consensus 47 ~~c~~c~~~ 55 (159)
|.|+.|+..
T Consensus 23 FtCp~Cghe 31 (104)
T COG4888 23 FTCPRCGHE 31 (104)
T ss_pred EecCccCCe
Confidence 444444433
No 182
>PF15135 UPF0515: Uncharacterised protein UPF0515
Probab=48.52 E-value=16 Score=25.37 Aligned_cols=12 Identities=17% Similarity=0.653 Sum_probs=6.7
Q ss_pred CcccCccccccc
Q psy9695 17 PKHLCHVCHKNF 28 (159)
Q Consensus 17 ~~~~C~~C~~~f 28 (159)
..|.|..|+..|
T Consensus 111 rqFaC~~Cd~~W 122 (278)
T PF15135_consen 111 RQFACSSCDHMW 122 (278)
T ss_pred eeeeccccchHH
Confidence 346666666543
No 183
>PF02176 zf-TRAF: TRAF-type zinc finger; PDB: 2EOD_A 2YUC_A 3HCU_A 3HCS_B 3HCT_A.
Probab=48.32 E-value=3.6 Score=21.24 Aligned_cols=39 Identities=18% Similarity=0.514 Sum_probs=17.0
Q ss_pred CccCcc--cccccCChHHHHHHHHHccCCCCccCCc----cccccc
Q psy9695 77 KHLCHV--CHKNFSSSSALQIHMRTHTGDKPFRCTI----CQKAFT 116 (159)
Q Consensus 77 ~~~C~~--C~~~~~~~~~l~~H~~~h~~~~~~~C~~----C~~~f~ 116 (159)
+..|+. |...+. ...|..|....-..++-.|++ |+..+.
T Consensus 9 ~v~C~~~cc~~~i~-r~~l~~H~~~~C~~~~v~C~~~~~GC~~~~~ 53 (60)
T PF02176_consen 9 PVPCPNGCCNEMIP-RKELDDHLENECPKRPVPCPYSPYGCKERVP 53 (60)
T ss_dssp EEE-TT--S-BEEE-CCCHHHHHHTTSTTSEEE-SS----S--EEE
T ss_pred EeeCCCCCccccee-HHHHHHHHHccCCCCcEECCCCCCCCCCccc
Confidence 345555 333333 235666666433345556666 665543
No 184
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=48.23 E-value=29 Score=25.42 Aligned_cols=72 Identities=24% Similarity=0.447 Sum_probs=45.5
Q ss_pred ccCcccccccCChHHHHHHHHhhcCCCcccccccccc-------ccCccccccccccccccCCCCCccCcc--cc----c
Q psy9695 19 HLCHVCHKNFSSSSALQIHMRTHTGDKPFRCTICQKA-------FTTKGNLKLIPNAVFNVAGMPKHLCHV--CH----K 85 (159)
Q Consensus 19 ~~C~~C~~~f~~~~~~~~h~~~~~~~~~~~c~~c~~~-------~~~~~~l~~~~~~~~~~~~~~~~~C~~--C~----~ 85 (159)
-+|.+|..-|-+..+|..|++..+ -.|-+|+.- |.+...|.. |.....|.|.. |. .
T Consensus 221 P~C~FC~~~FYdDDEL~~HcR~~H----E~ChICD~v~p~~~QYFK~Y~~Le~-------HF~~~hy~ct~qtc~~~k~~ 289 (493)
T COG5236 221 PLCIFCKIYFYDDDELRRHCRLRH----EACHICDMVGPIRYQYFKSYEDLEA-------HFRNAHYCCTFQTCRVGKCY 289 (493)
T ss_pred chhhhccceecChHHHHHHHHhhh----hhhhhhhccCccchhhhhCHHHHHH-------HhhcCceEEEEEEEecCcEE
Confidence 579999999999999999987544 235555432 444444433 22233466654 32 2
Q ss_pred ccCChHHHHHHHHHcc
Q psy9695 86 NFSSSSALQIHMRTHT 101 (159)
Q Consensus 86 ~~~~~~~l~~H~~~h~ 101 (159)
+|.....|+.|.-.-+
T Consensus 290 vf~~~~el~~h~~~~h 305 (493)
T COG5236 290 VFPYHTELLEHLTRFH 305 (493)
T ss_pred EeccHHHHHHHHHHHh
Confidence 6788888888876543
No 185
>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=47.46 E-value=11 Score=20.11 Aligned_cols=57 Identities=14% Similarity=0.252 Sum_probs=26.0
Q ss_pred ccCcccccccCChHHHHHHHHHccCCCCccCCcccccccccCCceeeehh-hccCCCCCcccccccchhhchhh
Q psy9695 78 HLCHVCHKNFSSSSALQIHMRTHTGDKPFRCTICQKAFTTKGNLKVREIE-INIGSQLPKKAQQHIGAVEGKSF 150 (159)
Q Consensus 78 ~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~-~h~~~~~~~~~~~~~C~~C~~~f 150 (159)
-.|..|++.|.. ..+.+.|..||..|-..-.-..-... ...+ .......|+.|...+
T Consensus 10 ~~C~~C~~~F~~------------~~rrhhCr~CG~~vC~~Cs~~~~~~~~~~~~----~~~~~RvC~~C~~~~ 67 (69)
T PF01363_consen 10 SNCMICGKKFSL------------FRRRHHCRNCGRVVCSSCSSQRIPLPTPSSG----SGEPVRVCDSCYSKL 67 (69)
T ss_dssp SB-TTT--B-BS------------SS-EEE-TTT--EEECCCS-EEEEET--GGT----ESEEEEE-HHHHHHH
T ss_pred CcCcCcCCcCCC------------ceeeEccCCCCCEECCchhCCEEcccccccC----CCCcCEECHHHHHHh
Confidence 468889888843 24567899999998876554322211 0111 122567787776554
No 186
>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=47.33 E-value=4.4 Score=19.58 Aligned_cols=16 Identities=38% Similarity=0.277 Sum_probs=9.0
Q ss_pred ccccchhhchhhhhcc
Q psy9695 139 QQHIGAVEGKSFQAKH 154 (159)
Q Consensus 139 ~~~~C~~C~~~f~~~~ 154 (159)
.++.|+.|+..|=...
T Consensus 12 ~~~~C~~C~~~FC~~H 27 (43)
T PF01428_consen 12 LPFKCKHCGKSFCLKH 27 (43)
T ss_dssp SHEE-TTTS-EE-TTT
T ss_pred CCeECCCCCcccCccc
Confidence 5778888888775443
No 187
>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=47.20 E-value=11 Score=16.98 Aligned_cols=12 Identities=17% Similarity=0.105 Sum_probs=7.4
Q ss_pred ccccchhhchhh
Q psy9695 139 QQHIGAVEGKSF 150 (159)
Q Consensus 139 ~~~~C~~C~~~f 150 (159)
.-|.|..|+..|
T Consensus 26 ~Cf~C~~C~~~L 37 (39)
T smart00132 26 ECFKCSKCGKPL 37 (39)
T ss_pred cCCCCcccCCcC
Confidence 346677666654
No 188
>COG4530 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=47.14 E-value=11 Score=22.39 Aligned_cols=14 Identities=7% Similarity=0.090 Sum_probs=10.1
Q ss_pred CCccCcccccccCC
Q psy9695 76 PKHLCHVCHKNFSS 89 (159)
Q Consensus 76 ~~~~C~~C~~~~~~ 89 (159)
.|.+|+.||++|+.
T Consensus 25 dPiVsPytG~s~P~ 38 (129)
T COG4530 25 DPIVSPYTGKSYPR 38 (129)
T ss_pred CccccCcccccchH
Confidence 36788888888733
No 189
>smart00507 HNHc HNH nucleases.
Probab=46.61 E-value=19 Score=17.27 Aligned_cols=12 Identities=25% Similarity=0.481 Sum_probs=8.1
Q ss_pred ccCCcccccccc
Q psy9695 106 FRCTICQKAFTT 117 (159)
Q Consensus 106 ~~C~~C~~~f~~ 117 (159)
+.|.+|+..+..
T Consensus 11 ~~C~~C~~~~~~ 22 (52)
T smart00507 11 GVCAYCGKPASE 22 (52)
T ss_pred CCCcCCcCCCCC
Confidence 577777766654
No 190
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=46.13 E-value=11 Score=21.70 Aligned_cols=30 Identities=20% Similarity=0.533 Sum_probs=17.7
Q ss_pred CccccccccccccCccccccccccccccCCCCCccCccccccc
Q psy9695 45 KPFRCTICQKAFTTKGNLKLIPNAVFNVAGMPKHLCHVCHKNF 87 (159)
Q Consensus 45 ~~~~c~~c~~~~~~~~~l~~~~~~~~~~~~~~~~~C~~C~~~~ 87 (159)
..|.|+.|+..-.-.. +...|.|..|++.|
T Consensus 35 a~y~CpfCgk~~vkR~-------------a~GIW~C~~C~~~~ 64 (90)
T PRK03976 35 AKHVCPVCGRPKVKRV-------------GTGIWECRKCGAKF 64 (90)
T ss_pred cCccCCCCCCCceEEE-------------EEEEEEcCCCCCEE
Confidence 3588888864432211 11247888888765
No 191
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=46.03 E-value=9.7 Score=23.32 Aligned_cols=11 Identities=18% Similarity=0.193 Sum_probs=6.9
Q ss_pred ccCcccccccCC
Q psy9695 78 HLCHVCHKNFSS 89 (159)
Q Consensus 78 ~~C~~C~~~~~~ 89 (159)
+.| .|+..|..
T Consensus 71 ~~C-~Cg~~~~~ 81 (124)
T PRK00762 71 IEC-ECGYEGVV 81 (124)
T ss_pred EEe-eCcCcccc
Confidence 667 77765543
No 192
>PF10621 FpoO: F420H2 dehydrogenase subunit FpoO ; InterPro: IPR018288 This entry represents the FpoO subunit of membrane-bound multi-subunit F420H2 dehydrogenase, which oxidises the reduced coenzyme F420H2 to coenzyme F420 and feeds the electrons via an FeS cluster into an energy-conserving electron transport chain [, ]. This enzyme plays a role in the methanogenic pathway in methanogenic archaea. Reduced coenzyme F420H2 is the major cytoplasmic electron carrier of methanogens and a reversible hydride donor, much like NADH []. F420H2 + COB-S-S-CoM = F420 + CoM-SH + CoB-SH Where CoB-S-S-CoM (the heterosulphide of 2-mercaptoethanesulphonate and 7-mercaptoheptanoylthreonine phosphate) is the terminal electron acceptor of the methanogenic pathway, and is reduced with the concomitant generation of a transmembrane proton potential and ATP synthesis. The FpoO subunit of F420H2 dehydrogenase probably participates in the reduction of methanophenazine, where it acts as a special mechanism for the reduction of the methanogenic cofactor [].
Probab=45.84 E-value=9.2 Score=22.76 Aligned_cols=65 Identities=20% Similarity=0.432 Sum_probs=31.1
Q ss_pred ccccccccccCccccccccccccc--cCCCCCccCcccccccCChHHHHHHHHHccCCCCccCCccccc
Q psy9695 48 RCTICQKAFTTKGNLKLIPNAVFN--VAGMPKHLCHVCHKNFSSSSALQIHMRTHTGDKPFRCTICQKA 114 (159)
Q Consensus 48 ~c~~c~~~~~~~~~l~~~~~~~~~--~~~~~~~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~~ 114 (159)
.|..||...++...+......... +.|...-.|..|-.+. ......+......-+.=+|..||..
T Consensus 3 DCdLCg~~~Pt~~PvrV~~Pr~~~~yPeGvwKGLC~~CL~sa--~~ty~e~~~~~~s~~~gKC~LCG~k 69 (119)
T PF10621_consen 3 DCDLCGRAIPTVCPVRVFAPRLTLAYPEGVWKGLCETCLDSA--EKTYQEVNENESSCRSGKCDLCGKK 69 (119)
T ss_pred ccchhcCcCCceeEEEeecchhhccCcchHHHhhHHHHHHHH--HHHHHHHhcccccccccceeccCCc
Confidence 366677666555544422111111 2232233466665433 2233334333443455689999955
No 193
>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=45.63 E-value=7 Score=24.69 Aligned_cols=10 Identities=30% Similarity=1.261 Sum_probs=6.4
Q ss_pred ccCCcccccc
Q psy9695 106 FRCTICQKAF 115 (159)
Q Consensus 106 ~~C~~C~~~f 115 (159)
|.|..|+..+
T Consensus 124 ~~C~~C~~~~ 133 (157)
T PF10263_consen 124 YRCPSCGREY 133 (157)
T ss_pred EEcCCCCCEe
Confidence 5676677554
No 194
>KOG2807|consensus
Probab=45.55 E-value=67 Score=23.42 Aligned_cols=25 Identities=20% Similarity=0.607 Sum_probs=17.1
Q ss_pred CccCCcccccccccCCceeeehhhcc
Q psy9695 105 PFRCTICQKAFTTKGNLKVREIEINI 130 (159)
Q Consensus 105 ~~~C~~C~~~f~~~~~l~~H~~~~h~ 130 (159)
.|+|..|...|-...+.-.|- ..|.
T Consensus 345 ~y~C~~Ck~~FCldCDv~iHe-sLh~ 369 (378)
T KOG2807|consen 345 RYRCESCKNVFCLDCDVFIHE-SLHN 369 (378)
T ss_pred cEEchhccceeeccchHHHHh-hhhc
Confidence 477777777777777666666 5553
No 195
>PF14311 DUF4379: Domain of unknown function (DUF4379)
Probab=45.32 E-value=17 Score=18.48 Aligned_cols=12 Identities=17% Similarity=0.617 Sum_probs=6.4
Q ss_pred ccCcccccccCC
Q psy9695 78 HLCHVCHKNFSS 89 (159)
Q Consensus 78 ~~C~~C~~~~~~ 89 (159)
+.|+.|+..+..
T Consensus 29 W~C~~Cgh~w~~ 40 (55)
T PF14311_consen 29 WKCPKCGHEWKA 40 (55)
T ss_pred EECCCCCCeeEc
Confidence 556666554433
No 196
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=45.22 E-value=9.3 Score=23.14 Aligned_cols=13 Identities=23% Similarity=0.588 Sum_probs=8.6
Q ss_pred CccCcccccccCC
Q psy9695 77 KHLCHVCHKNFSS 89 (159)
Q Consensus 77 ~~~C~~C~~~~~~ 89 (159)
.+.|..|+..|..
T Consensus 71 ~~~C~~Cg~~~~~ 83 (117)
T PRK00564 71 ELECKDCSHVFKP 83 (117)
T ss_pred EEEhhhCCCcccc
Confidence 3678888866543
No 197
>COG3364 Zn-ribbon containing protein [General function prediction only]
Probab=45.07 E-value=15 Score=21.61 Aligned_cols=16 Identities=31% Similarity=0.681 Sum_probs=12.2
Q ss_pred cccCcccccccCChHH
Q psy9695 18 KHLCHVCHKNFSSSSA 33 (159)
Q Consensus 18 ~~~C~~C~~~f~~~~~ 33 (159)
|++|.-||..|..-+.
T Consensus 2 pH~CtrCG~vf~~g~~ 17 (112)
T COG3364 2 PHQCTRCGEVFDDGSE 17 (112)
T ss_pred CceecccccccccccH
Confidence 6788888888877543
No 198
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=44.90 E-value=16 Score=29.61 Aligned_cols=11 Identities=9% Similarity=-0.070 Sum_probs=8.6
Q ss_pred ccccchhhchh
Q psy9695 139 QQHIGAVEGKS 149 (159)
Q Consensus 139 ~~~~C~~C~~~ 149 (159)
.+..|+.||..
T Consensus 474 ~p~~Cp~Cgs~ 484 (730)
T COG1198 474 IPQSCPECGSE 484 (730)
T ss_pred CCCCCCCCCCC
Confidence 78888888854
No 199
>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=44.73 E-value=5 Score=32.03 Aligned_cols=60 Identities=23% Similarity=0.347 Sum_probs=36.6
Q ss_pred ccCcccccccCChHHHHHHHHHccCCCCc-cCCcccccccccCCceeeehhhccCCCCCcccccccchhhchhhh
Q psy9695 78 HLCHVCHKNFSSSSALQIHMRTHTGDKPF-RCTICQKAFTTKGNLKVREIEINIGSQLPKKAQQHIGAVEGKSFQ 151 (159)
Q Consensus 78 ~~C~~C~~~~~~~~~l~~H~~~h~~~~~~-~C~~C~~~f~~~~~l~~H~~~~h~~~~~~~~~~~~~C~~C~~~f~ 151 (159)
..|..||..|.-...|-- -+..+.-+.| .|+.|.+.|...-+-+=|. ++.-|+.||=...
T Consensus 124 ~~CT~CGPRfTIi~alPY-DR~nTsM~~F~lC~~C~~EY~dP~nRRfHA-------------Qp~aCp~CGP~~~ 184 (750)
T COG0068 124 INCTNCGPRFTIIEALPY-DRENTSMADFPLCPFCDKEYKDPLNRRFHA-------------QPIACPKCGPHLF 184 (750)
T ss_pred cccCCCCcceeeeccCCC-CcccCccccCcCCHHHHHHhcCcccccccc-------------ccccCcccCCCeE
Confidence 347777765533222111 1122222333 5999999888877777777 8999999996443
No 200
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=44.15 E-value=19 Score=23.57 Aligned_cols=33 Identities=15% Similarity=0.499 Sum_probs=18.4
Q ss_pred cCCCccccccccccccCccccccccccccccCCCCCccCcccccc
Q psy9695 42 TGDKPFRCTICQKAFTTKGNLKLIPNAVFNVAGMPKHLCHVCHKN 86 (159)
Q Consensus 42 ~~~~~~~c~~c~~~~~~~~~l~~~~~~~~~~~~~~~~~C~~C~~~ 86 (159)
....-|.|+.|...+..-..+. ..|.|+.||..
T Consensus 109 ~~~~~y~C~~~~~r~sfdeA~~------------~~F~Cp~Cg~~ 141 (176)
T COG1675 109 TENNYYVCPNCHVKYSFDEAME------------LGFTCPKCGED 141 (176)
T ss_pred ccCCceeCCCCCCcccHHHHHH------------hCCCCCCCCch
Confidence 3445577766665554433221 13777777764
No 201
>smart00401 ZnF_GATA zinc finger binding to DNA consensus sequence [AT]GATA[AG].
Probab=44.12 E-value=31 Score=17.43 Aligned_cols=14 Identities=7% Similarity=0.128 Sum_probs=7.3
Q ss_pred ccchhhchhhhhcc
Q psy9695 141 HIGAVEGKSFQAKH 154 (159)
Q Consensus 141 ~~C~~C~~~f~~~~ 154 (159)
..|..|+..|....
T Consensus 26 ~LCnaCgl~~~k~~ 39 (52)
T smart00401 26 TLCNACGLYYKKHG 39 (52)
T ss_pred cEeecccHHHHHcC
Confidence 55555555554433
No 202
>COG3091 SprT Zn-dependent metalloprotease, SprT family [General function prediction only]
Probab=43.68 E-value=11 Score=24.00 Aligned_cols=33 Identities=21% Similarity=0.625 Sum_probs=17.4
Q ss_pred CccCcccccccCChHHHHHHHHHccCCCCccCCccccc
Q psy9695 77 KHLCHVCHKNFSSSSALQIHMRTHTGDKPFRCTICQKA 114 (159)
Q Consensus 77 ~~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~~ 114 (159)
+|.|. |+..+.+. ..|-..-.|+ .|.|..|+..
T Consensus 117 ~Y~C~-C~q~~l~~---RRhn~~~~g~-~YrC~~C~gk 149 (156)
T COG3091 117 PYRCQ-CQQHYLRI---RRHNTVRRGE-VYRCGKCGGK 149 (156)
T ss_pred eEEee-cCCccchh---hhcccccccc-eEEeccCCce
Confidence 46666 76665443 2233333344 5777766644
No 203
>COG1779 C4-type Zn-finger protein [General function prediction only]
Probab=42.90 E-value=5.9 Score=26.32 Aligned_cols=12 Identities=25% Similarity=0.260 Sum_probs=7.0
Q ss_pred ccCCcccccccc
Q psy9695 106 FRCTICQKAFTT 117 (159)
Q Consensus 106 ~~C~~C~~~f~~ 117 (159)
+.|..||..++.
T Consensus 44 ~~C~~CgYR~~D 55 (201)
T COG1779 44 GVCERCGYRSTD 55 (201)
T ss_pred EEccccCCcccc
Confidence 456667665543
No 204
>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=42.84 E-value=2.7 Score=30.53 Aligned_cols=11 Identities=9% Similarity=-0.130 Sum_probs=3.6
Q ss_pred ccccchhhchh
Q psy9695 139 QQHIGAVEGKS 149 (159)
Q Consensus 139 ~~~~C~~C~~~ 149 (159)
+.|+|..|+.+
T Consensus 284 RFFkC~~C~~R 294 (344)
T PF09332_consen 284 RFFKCKDCGNR 294 (344)
T ss_dssp EEEE-T-TS-E
T ss_pred eeEECCCCCCe
Confidence 44444444443
No 205
>COG4391 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=41.84 E-value=6.3 Score=20.77 Aligned_cols=11 Identities=0% Similarity=0.069 Sum_probs=5.6
Q ss_pred ccchhhchhhh
Q psy9695 141 HIGAVEGKSFQ 151 (159)
Q Consensus 141 ~~C~~C~~~f~ 151 (159)
-.|++|+..|.
T Consensus 49 v~CPYC~t~y~ 59 (62)
T COG4391 49 VVCPYCSTRYR 59 (62)
T ss_pred EecCccccEEE
Confidence 45555555443
No 206
>KOG1729|consensus
Probab=41.20 E-value=21 Score=25.41 Aligned_cols=58 Identities=12% Similarity=0.109 Sum_probs=31.3
Q ss_pred ccCcccccccCChHHHHHHHHHccCCCCccCCcccccccccCCceeeehhhccCCCCCcccccccchhhchhhhh
Q psy9695 78 HLCHVCHKNFSSSSALQIHMRTHTGDKPFRCTICQKAFTTKGNLKVREIEINIGSQLPKKAQQHIGAVEGKSFQA 152 (159)
Q Consensus 78 ~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~~h~~~~~~~~~~~~~C~~C~~~f~~ 152 (159)
-.|..|+.+..+...-+ |+ |..||..|....+-..=+....... ..++|++|-..|..
T Consensus 169 ~~C~~C~~~~Ftl~~RR-----HH------CR~CG~ivC~~Cs~n~~~l~~~~~k------~~rvC~~CF~el~~ 226 (288)
T KOG1729|consen 169 TECMVCGCTEFTLSERR-----HH------CRNCGDIVCAPCSRNRFLLPNLSTK------PIRVCDICFEELEK 226 (288)
T ss_pred eecccCCCccccHHHHH-----HH------HHhcchHhhhhhhcCcccccccCCC------CceecHHHHHHHhc
Confidence 56888888532332222 22 6667777665333322221223333 44599999887753
No 207
>PF10122 Mu-like_Com: Mu-like prophage protein Com; InterPro: IPR019294 Members of this entry belong to the Com family of proteins that act as translational regulators of mom [, ].
Probab=39.95 E-value=15 Score=18.60 Aligned_cols=6 Identities=33% Similarity=1.381 Sum_probs=2.8
Q ss_pred cCCccc
Q psy9695 107 RCTICQ 112 (159)
Q Consensus 107 ~C~~C~ 112 (159)
+|+-|+
T Consensus 26 KCpRC~ 31 (51)
T PF10122_consen 26 KCPRCK 31 (51)
T ss_pred ECCCCC
Confidence 444444
No 208
>PF14787 zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB: 1CL4_A 1DSV_A.
Probab=39.50 E-value=9.4 Score=17.77 Aligned_cols=12 Identities=33% Similarity=0.739 Sum_probs=4.9
Q ss_pred CCcccccccccC
Q psy9695 108 CTICQKAFTTKG 119 (159)
Q Consensus 108 C~~C~~~f~~~~ 119 (159)
|+.|++.|-..+
T Consensus 5 CprC~kg~Hwa~ 16 (36)
T PF14787_consen 5 CPRCGKGFHWAS 16 (36)
T ss_dssp -TTTSSSCS-TT
T ss_pred CcccCCCcchhh
Confidence 555555544433
No 209
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=39.29 E-value=12 Score=22.06 Aligned_cols=35 Identities=17% Similarity=0.154 Sum_probs=18.8
Q ss_pred CCccCcccccccCChHHHHHHHHHccCCCCccCCcccccccc
Q psy9695 76 PKHLCHVCHKNFSSSSALQIHMRTHTGDKPFRCTICQKAFTT 117 (159)
Q Consensus 76 ~~~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~ 117 (159)
..|.|+.|+... -...+.. +.-...|+.||..+..
T Consensus 20 t~f~CP~Cge~~-v~v~~~k------~~~h~~C~~CG~y~~~ 54 (99)
T PRK14892 20 KIFECPRCGKVS-ISVKIKK------NIAIITCGNCGLYTEF 54 (99)
T ss_pred cEeECCCCCCeE-eeeecCC------CcceEECCCCCCccCE
Confidence 358888888422 1111111 2233578888866553
No 210
>KOG4167|consensus
Probab=39.22 E-value=6.4 Score=31.55 Aligned_cols=25 Identities=32% Similarity=0.527 Sum_probs=21.7
Q ss_pred CccCcccccccCChHHHHHHHHHcc
Q psy9695 77 KHLCHVCHKNFSSSSALQIHMRTHT 101 (159)
Q Consensus 77 ~~~C~~C~~~~~~~~~l~~H~~~h~ 101 (159)
.|-|.+|++.|.-...+..|++.|.
T Consensus 792 iFpCreC~kvF~KiKSrNAHMK~Hr 816 (907)
T KOG4167|consen 792 IFPCRECGKVFFKIKSRNAHMKTHR 816 (907)
T ss_pred eeehHHHHHHHHHHhhhhHHHHHHH
Confidence 4899999999988888888888775
No 211
>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=39.18 E-value=11 Score=18.92 Aligned_cols=9 Identities=44% Similarity=1.357 Sum_probs=3.7
Q ss_pred CccCCcccc
Q psy9695 105 PFRCTICQK 113 (159)
Q Consensus 105 ~~~C~~C~~ 113 (159)
.|.|++|++
T Consensus 41 ~W~CPiC~~ 49 (50)
T PF02891_consen 41 KWKCPICNK 49 (50)
T ss_dssp --B-TTT--
T ss_pred CeECcCCcC
Confidence 399999985
No 212
>PF09963 DUF2197: Uncharacterized protein conserved in bacteria (DUF2197); InterPro: IPR019241 This family represents various hypothetical bacterial proteins with no known function.
Probab=38.92 E-value=8.4 Score=19.99 Aligned_cols=8 Identities=25% Similarity=1.053 Sum_probs=4.2
Q ss_pred CccCCccc
Q psy9695 105 PFRCTICQ 112 (159)
Q Consensus 105 ~~~C~~C~ 112 (159)
.|.|+.|.
T Consensus 31 tYmC~eC~ 38 (56)
T PF09963_consen 31 TYMCDECK 38 (56)
T ss_pred ceeChhHH
Confidence 35555554
No 213
>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=38.42 E-value=10 Score=22.79 Aligned_cols=25 Identities=24% Similarity=0.667 Sum_probs=14.4
Q ss_pred ccCcccccccCChHHHHHHHHHccCCCCccCCccccc
Q psy9695 78 HLCHVCHKNFSSSSALQIHMRTHTGDKPFRCTICQKA 114 (159)
Q Consensus 78 ~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~~ 114 (159)
..|..|+..|..... .+.||.||..
T Consensus 71 ~~C~~Cg~~~~~~~~------------~~~CP~Cgs~ 95 (113)
T PF01155_consen 71 ARCRDCGHEFEPDEF------------DFSCPRCGSP 95 (113)
T ss_dssp EEETTTS-EEECHHC------------CHH-SSSSSS
T ss_pred EECCCCCCEEecCCC------------CCCCcCCcCC
Confidence 678888877755322 1448888854
No 214
>COG1655 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=37.86 E-value=14 Score=25.28 Aligned_cols=16 Identities=19% Similarity=0.652 Sum_probs=7.6
Q ss_pred ccCCcccccccccCCc
Q psy9695 106 FRCTICQKAFTTKGNL 121 (159)
Q Consensus 106 ~~C~~C~~~f~~~~~l 121 (159)
..||+|+-.|....-+
T Consensus 20 ieCPvC~tkFkkeev~ 35 (267)
T COG1655 20 IECPVCNTKFKKEEVK 35 (267)
T ss_pred eccCcccchhhhhhee
Confidence 4455555555444333
No 215
>cd00085 HNHc HNH nucleases; HNH endonuclease signature which is found in viral, prokaryotic, and eukaryotic proteins. The alignment includes members of the large group of homing endonucleases, yeast intron 1 protein, MutS, as well as bacterial colicins, pyocins, and anaredoxins.
Probab=37.74 E-value=20 Score=17.59 Aligned_cols=10 Identities=30% Similarity=0.411 Sum_probs=7.4
Q ss_pred ccCCcccccc
Q psy9695 106 FRCTICQKAF 115 (159)
Q Consensus 106 ~~C~~C~~~f 115 (159)
+.|.+|+..+
T Consensus 12 ~~C~~c~~~~ 21 (57)
T cd00085 12 GLCPYCGKPG 21 (57)
T ss_pred CcCccCCCcC
Confidence 6788887766
No 216
>PRK04351 hypothetical protein; Provisional
Probab=37.50 E-value=16 Score=23.22 Aligned_cols=13 Identities=0% Similarity=-0.158 Sum_probs=7.2
Q ss_pred ccccchhhchhhh
Q psy9695 139 QQHIGAVEGKSFQ 151 (159)
Q Consensus 139 ~~~~C~~C~~~f~ 151 (159)
..|.|..|+-.+.
T Consensus 131 ~~yrCg~C~g~L~ 143 (149)
T PRK04351 131 KRYRCGKCRGKLK 143 (149)
T ss_pred CcEEeCCCCcEee
Confidence 3466666665443
No 217
>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=37.37 E-value=35 Score=20.55 Aligned_cols=20 Identities=15% Similarity=0.441 Sum_probs=13.2
Q ss_pred CCccCcccccccCChHHHHH
Q psy9695 76 PKHLCHVCHKNFSSSSALQI 95 (159)
Q Consensus 76 ~~~~C~~C~~~~~~~~~l~~ 95 (159)
..+.|+.||..+.+......
T Consensus 30 ~~~~C~~CGe~~~~~e~~~~ 49 (127)
T TIGR03830 30 PGWYCPACGEELLDPEESKR 49 (127)
T ss_pred eeeECCCCCCEEEcHHHHHH
Confidence 45788888887766544443
No 218
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=37.36 E-value=18 Score=27.20 Aligned_cols=14 Identities=29% Similarity=0.645 Sum_probs=8.2
Q ss_pred CccCCccccccccc
Q psy9695 105 PFRCTICQKAFTTK 118 (159)
Q Consensus 105 ~~~C~~C~~~f~~~ 118 (159)
-|+|+.||..+...
T Consensus 367 g~rC~kCg~~~~~~ 380 (421)
T COG1571 367 GFRCKKCGTRARET 380 (421)
T ss_pred CcccccccccCCcc
Confidence 56666666555443
No 219
>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG
Probab=37.21 E-value=16 Score=18.68 Aligned_cols=11 Identities=18% Similarity=0.797 Sum_probs=7.3
Q ss_pred ccCCccccccc
Q psy9695 106 FRCTICQKAFT 116 (159)
Q Consensus 106 ~~C~~C~~~f~ 116 (159)
+.||+||..+.
T Consensus 1 i~CPyCge~~~ 11 (52)
T PF14255_consen 1 IQCPYCGEPIE 11 (52)
T ss_pred CCCCCCCCeeE
Confidence 36888886654
No 220
>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=36.40 E-value=24 Score=25.44 Aligned_cols=16 Identities=0% Similarity=-0.201 Sum_probs=12.2
Q ss_pred cccccchhhchhhhhc
Q psy9695 138 AQQHIGAVEGKSFQAK 153 (159)
Q Consensus 138 ~~~~~C~~C~~~f~~~ 153 (159)
.+...|..|+..++.-
T Consensus 250 ~r~e~C~~C~~YlK~~ 265 (305)
T TIGR01562 250 LKAETCDSCQGYLKIL 265 (305)
T ss_pred eEEeeccccccchhhh
Confidence 3778999999776654
No 221
>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=36.33 E-value=29 Score=17.50 Aligned_cols=13 Identities=23% Similarity=0.731 Sum_probs=6.6
Q ss_pred CccCCcccccccc
Q psy9695 105 PFRCTICQKAFTT 117 (159)
Q Consensus 105 ~~~C~~C~~~f~~ 117 (159)
.+.|..||..|-.
T Consensus 18 k~~Cr~Cg~~~C~ 30 (57)
T cd00065 18 RHHCRNCGRIFCS 30 (57)
T ss_pred ccccCcCcCCcCh
Confidence 3455555555543
No 222
>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=36.21 E-value=11 Score=26.92 Aligned_cols=40 Identities=18% Similarity=0.196 Sum_probs=23.1
Q ss_pred CccCCcccccccccCCceeeehhhccCCCCCcccccccchhhchhhh
Q psy9695 105 PFRCTICQKAFTTKGNLKVREIEINIGSQLPKKAQQHIGAVEGKSFQ 151 (159)
Q Consensus 105 ~~~C~~C~~~f~~~~~l~~H~~~~h~~~~~~~~~~~~~C~~C~~~f~ 151 (159)
.+.|+.|+..=.....++..- .....- ..|.|..||..+.
T Consensus 258 ~~~C~~C~~~~~~~~q~Qtrs-aDEpmT------~f~~C~~Cg~~w~ 297 (299)
T TIGR01385 258 LFTCGKCKQKKCTYYQLQTRS-ADEPMT------TFVTCEECGNRWK 297 (299)
T ss_pred cccCCCCCCccceEEEecccC-CCCCCe------EEEEcCCCCCeee
Confidence 489999995544333332211 111112 6889999997653
No 223
>PF00412 LIM: LIM domain; InterPro: IPR001781 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 LIM-type zinc finger (Znf) domains. LIM domains coordinate one or more zinc atoms, and are named after the three proteins (LIN-11, Isl1 and MEC-3) in which they were first found. They consist of two zinc-binding motifs that resemble GATA-like Znf's, however the residues holding the zinc atom(s) are variable, involving Cys, His, Asp or Glu residues. LIM domains are involved in proteins with differing functions, including gene expression, and cytoskeleton organisation and development [, ]. Protein containing LIM Znf domains include: Caenorhabditis elegans mec-3; a protein required for the differentiation of the set of six touch receptor neurons in this nematode. C. elegans. lin-11; a protein required for the asymmetric division of vulval blast cells. Vertebrate insulin gene enhancer binding protein isl-1. Isl-1 binds to one of the two cis-acting protein-binding domains of the insulin gene. Vertebrate homeobox proteins lim-1, lim-2 (lim-5) and lim3. Vertebrate lmx-1, which acts as a transcriptional activator by binding to the FLAT element; a beta-cell-specific transcriptional enhancer found in the insulin gene. Mammalian LH-2, a transcriptional regulatory protein involved in the control of cell differentiation in developing lymphoid and neural cell types. Drosophila melanogaster (Fruit fly) protein apterous, required for the normal development of the wing and halter imaginal discs. Vertebrate protein kinases LIMK-1 and LIMK-2. Mammalian rhombotins. Rhombotin 1 (RBTN1 or TTG-1) and rhombotin-2 (RBTN2 or TTG-2) are proteins of about 160 amino acids whose genes are disrupted by chromosomal translocations in T-cell leukemia. Mammalian and avian cysteine-rich protein (CRP), a 192 amino-acid protein of unknown function. Seems to interact with zyxin. Mammalian cysteine-rich intestinal protein (CRIP), a small protein which seems to have a role in zinc absorption and may function as an intracellular zinc transport protein. Vertebrate paxillin, a cytoskeletal focal adhesion protein. Mus musculus (Mouse) testin which should not be confused with rat testin which is a thiol protease homologue (see IPR000169 from INTERPRO). Helianthus annuus (Common sunflower) pollen specific protein SF3. Chicken zyxin. Zyxin is a low-abundance adhesion plaque protein which has been shown to interact with CRP. Yeast protein LRG1 which is involved in sporulation []. Saccharomyces cerevisiae (Baker's yeast) rho-type GTPase activating protein RGA1/DBM1. C. elegans homeobox protein ceh-14. C. elegans homeobox protein unc-97. S. cerevisiae hypothetical protein YKR090w. C. elegans hypothetical proteins C28H8.6. These proteins generally contain two tandem copies of the LIM domain in their N-terminal section. Zyxin and paxillin are exceptions in that they contain respectively three and four LIM domains at their C-terminal extremity. In apterous, isl-1, LH-2, lin-11, lim-1 to lim-3, lmx-1 and ceh-14 and mec-3 there is a homeobox domain some 50 to 95 amino acids after the LIM domains. LIM domains contain seven conserved cysteine residues and a histidine. The arrangement followed by these conserved residues is: C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] LIM domains bind two zinc ions []. LIM does not bind DNA, rather it seems to act as an interface for protein-protein interaction. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CO8_A 2EGQ_A 2CUR_A 3IXE_B 1CTL_A 1B8T_A 1X62_A 2DFY_C 1IML_A 2CUQ_A ....
Probab=35.42 E-value=24 Score=17.79 Aligned_cols=12 Identities=17% Similarity=0.077 Sum_probs=5.4
Q ss_pred cccchhhchhhh
Q psy9695 140 QHIGAVEGKSFQ 151 (159)
Q Consensus 140 ~~~C~~C~~~f~ 151 (159)
-|.|..|++.+.
T Consensus 26 Cf~C~~C~~~l~ 37 (58)
T PF00412_consen 26 CFKCSKCGKPLN 37 (58)
T ss_dssp TSBETTTTCBTT
T ss_pred ccccCCCCCccC
Confidence 344444444443
No 224
>PF02701 zf-Dof: Dof domain, zinc finger; InterPro: IPR003851 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 consists of proteins containing a Dof domain, which is a zinc finger DNA-binding domain that shows resemblance to the Cys2 zinc finger, although it has a longer putative loop where an extra Cys residue is conserved []. AOBP, a DNA-binding protein in pumpkin (Cucurbita maxima), contains a 52 amino acid Dof domain, which is highly conserved in several DNA-binding proteins of higher plants. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding, 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent
Probab=35.22 E-value=32 Score=18.25 Aligned_cols=17 Identities=29% Similarity=0.856 Sum_probs=7.6
Q ss_pred ccCCcccccccccCCce
Q psy9695 106 FRCTICQKAFTTKGNLK 122 (159)
Q Consensus 106 ~~C~~C~~~f~~~~~l~ 122 (159)
|.|..|..-++....|+
T Consensus 31 ~~Ck~C~rywT~GG~lR 47 (63)
T PF02701_consen 31 YFCKSCRRYWTHGGTLR 47 (63)
T ss_pred hhhHHHHHHHHhcceec
Confidence 44444444444444443
No 225
>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=34.79 E-value=20 Score=21.40 Aligned_cols=8 Identities=25% Similarity=0.742 Sum_probs=3.7
Q ss_pred ccCccccc
Q psy9695 78 HLCHVCHK 85 (159)
Q Consensus 78 ~~C~~C~~ 85 (159)
|.|++|+.
T Consensus 20 ~iCpeC~~ 27 (109)
T TIGR00686 20 LICPSCLY 27 (109)
T ss_pred eECccccc
Confidence 44454443
No 226
>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=34.49 E-value=24 Score=20.85 Aligned_cols=9 Identities=22% Similarity=0.678 Sum_probs=6.4
Q ss_pred CccCccccc
Q psy9695 77 KHLCHVCHK 85 (159)
Q Consensus 77 ~~~C~~C~~ 85 (159)
|..|+.||.
T Consensus 2 p~~CpYCg~ 10 (102)
T PF11672_consen 2 PIICPYCGG 10 (102)
T ss_pred CcccCCCCC
Confidence 567888875
No 227
>PF06220 zf-U1: U1 zinc finger; InterPro: IPR013085 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. C2H2-type (classical) zinc fingers (Znf) were the first class to be characterised. They contain a short beta hairpin and an alpha helix (beta/beta/alpha structure), where a single zinc atom is held in place by Cys(2)His(2) (C2H2) residues in a tetrahedral array. C2H2 Znf's can be divided into three groups based on the number and pattern of fingers: triple-C2H2 (binds single ligand), multiple-adjacent-C2H2 (binds multiple ligands), and separated paired-C2H2 []. C2H2 Znf's are the most common DNA-binding motifs found in eukaryotic transcription factors, and have also been identified in prokaryotes []. Transcription factors usually contain several Znf's (each with a conserved beta/beta/alpha structure) capable of making multiple contacts along the DNA, where the C2H2 Znf motifs recognise DNA sequences by binding to the major groove of DNA via a short alpha-helix in the Znf, the Znf spanning 3-4 bases of the DNA []. C2H2 Znf's can also bind to RNA and protein targets []. This entry represents a C2H2-type zinc finger motif found in several U1 small nuclear ribonucleoprotein C (U1-C) proteins. Some proteins contain multiple copies of this motif. The U1 small nuclear ribonucleoprotein (U1 snRNP) binds to the pre-mRNA 5' splice site at early stages of spliceosome assembly. Recruitment of U1 to a class of weak 5' splice site is promoted by binding of the protein TIA-1 to uridine-rich sequences immediately downstream from the 5' splice site. Binding of TIA-1 in the vicinity of a 5' splice site helps to stabilise U1 snRNP recruitment, at least in part, via a direct interaction with U1-C, thus providing one molecular mechanism for the function of this splicing regulator []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2VRD_A.
Probab=34.21 E-value=22 Score=16.71 Aligned_cols=15 Identities=27% Similarity=0.718 Sum_probs=5.7
Q ss_pred CccCCcccccccccC
Q psy9695 105 PFRCTICQKAFTTKG 119 (159)
Q Consensus 105 ~~~C~~C~~~f~~~~ 119 (159)
.|-|++|+..|+..+
T Consensus 3 ryyCdyC~~~~~~d~ 17 (38)
T PF06220_consen 3 RYYCDYCKKYLTHDS 17 (38)
T ss_dssp S-B-TTT--B-S--S
T ss_pred CeecccccceecCCC
Confidence 477888888886554
No 228
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=32.59 E-value=18 Score=18.18 Aligned_cols=10 Identities=20% Similarity=0.647 Sum_probs=6.8
Q ss_pred CccCCccccc
Q psy9695 105 PFRCTICQKA 114 (159)
Q Consensus 105 ~~~C~~C~~~ 114 (159)
.|.|..||..
T Consensus 37 R~~CGkCgyT 46 (51)
T COG1998 37 RWACGKCGYT 46 (51)
T ss_pred eeEeccccce
Confidence 5777777743
No 229
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=32.36 E-value=26 Score=21.13 Aligned_cols=11 Identities=18% Similarity=0.736 Sum_probs=6.1
Q ss_pred ccCcccccccC
Q psy9695 78 HLCHVCHKNFS 88 (159)
Q Consensus 78 ~~C~~C~~~~~ 88 (159)
..|..|+..|.
T Consensus 71 ~~C~~Cg~~~~ 81 (114)
T PRK03681 71 CWCETCQQYVT 81 (114)
T ss_pred EEcccCCCeee
Confidence 55666665543
No 230
>KOG0978|consensus
Probab=32.36 E-value=21 Score=28.73 Aligned_cols=22 Identities=18% Similarity=0.495 Sum_probs=16.7
Q ss_pred CCccCCcccccccccCCceeee
Q psy9695 104 KPFRCTICQKAFTTKGNLKVRE 125 (159)
Q Consensus 104 ~~~~C~~C~~~f~~~~~l~~H~ 125 (159)
+.-+||.|+.+|....-++.|+
T Consensus 677 RqRKCP~Cn~aFganDv~~I~l 698 (698)
T KOG0978|consen 677 RQRKCPKCNAAFGANDVHRIHL 698 (698)
T ss_pred hcCCCCCCCCCCCcccccccCC
Confidence 3458999999998887766653
No 231
>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 KOG2071|consensus
Probab=31.57 E-value=35 Score=26.86 Aligned_cols=28 Identities=25% Similarity=0.434 Sum_probs=23.5
Q ss_pred CCCcccCcccccccCChHHHHHHHHhhc
Q psy9695 15 GMPKHLCHVCHKNFSSSSALQIHMRTHT 42 (159)
Q Consensus 15 ~~~~~~C~~C~~~f~~~~~~~~h~~~~~ 42 (159)
...+.+|..||..|........|+.+|.
T Consensus 415 ~~~pnqC~~CG~R~~~~ee~sk~md~H~ 442 (579)
T KOG2071|consen 415 KDSPNQCKSCGLRFDDSEERSKHMDIHD 442 (579)
T ss_pred cCCcchhcccccccccchhhhhHhhhhh
Confidence 3556899999999999999888887764
No 233
>PF05766 NinG: Bacteriophage Lambda NinG protein; InterPro: IPR008713 The ninR region of phage lambda contains two recombination genes, ninB (also known as orf) and ninG (also known as rap). These genes are involved in the RecF and RecBCD recombination pathways of Escherichia coli that operate on phage lambda [, ]. NinB and NinG participate in Red recombination, the primary pathway operating when wild-type lambda grows lytically in rec+ cells [].
Probab=31.49 E-value=31 Score=22.95 Aligned_cols=31 Identities=19% Similarity=0.484 Sum_probs=19.3
Q ss_pred CCccCcccccccCChHHHHHHHHHccCCCCccCCccccccc
Q psy9695 76 PKHLCHVCHKNFSSSSALQIHMRTHTGDKPFRCTICQKAFT 116 (159)
Q Consensus 76 ~~~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~~f~ 116 (159)
++-.|..|+..|..... ...|-++.|+..+.
T Consensus 5 k~rKCKvCg~~F~P~~s----------~q~vCSpeCa~a~~ 35 (189)
T PF05766_consen 5 KRRKCKVCGEWFVPARS----------NQKVCSPECAIALA 35 (189)
T ss_pred CCCcCcccCCccccCCC----------ceeeeCHHHHhHHH
Confidence 35678888888754322 23466677886554
No 234
>PRK05452 anaerobic nitric oxide reductase flavorubredoxin; Provisional
Probab=31.36 E-value=34 Score=26.37 Aligned_cols=46 Identities=9% Similarity=0.260 Sum_probs=20.9
Q ss_pred CCccCCcccccccccCCceeeehhhccCCCCCcccccccchhhchhhh
Q psy9695 104 KPFRCTICQKAFTTKGNLKVREIEINIGSQLPKKAQQHIGAVEGKSFQ 151 (159)
Q Consensus 104 ~~~~C~~C~~~f~~~~~l~~H~~~~h~~~~~~~~~~~~~C~~C~~~f~ 151 (159)
..|+|..||..|-....-... .+-.|-....=.-.|.||.|+..-.
T Consensus 424 ~~~~c~~c~~~yd~~~g~~~~--~~~~gt~~~~lp~~~~cp~c~~~k~ 469 (479)
T PRK05452 424 PRMQCSVCQWIYDPAKGEPMQ--DVAPGTPWSEVPDNFLCPECSLGKD 469 (479)
T ss_pred CeEEECCCCeEECCCCCCccc--CCCCCCChhhCCCCCcCcCCCCcHH
Confidence 447888888655433221111 1222211100113578888876533
No 235
>KOG4167|consensus
Probab=31.33 E-value=13 Score=29.99 Aligned_cols=24 Identities=33% Similarity=0.578 Sum_probs=22.4
Q ss_pred ccCcccccccCChHHHHHHHHhhc
Q psy9695 19 HLCHVCHKNFSSSSALQIHMRTHT 42 (159)
Q Consensus 19 ~~C~~C~~~f~~~~~~~~h~~~~~ 42 (159)
|.|.+|++.|....++..||..|.
T Consensus 793 FpCreC~kvF~KiKSrNAHMK~Hr 816 (907)
T KOG4167|consen 793 FPCRECGKVFFKIKSRNAHMKTHR 816 (907)
T ss_pred eehHHHHHHHHHHhhhhHHHHHHH
Confidence 999999999999999999999885
No 236
>KOG2231|consensus
Probab=31.27 E-value=49 Score=26.67 Aligned_cols=21 Identities=38% Similarity=0.838 Sum_probs=11.0
Q ss_pred cCcccccccCChHHHHHHHHh
Q psy9695 20 LCHVCHKNFSSSSALQIHMRT 40 (159)
Q Consensus 20 ~C~~C~~~f~~~~~~~~h~~~ 40 (159)
.|..|...|-....+..|+..
T Consensus 184 ~C~~C~~~fld~~el~rH~~~ 204 (669)
T KOG2231|consen 184 LCKFCHERFLDDDELYRHLRF 204 (669)
T ss_pred cchhhhhhhccHHHHHHhhcc
Confidence 455555555555555555443
No 237
>PF12773 DZR: Double zinc ribbon
Probab=31.23 E-value=41 Score=16.47 Aligned_cols=9 Identities=22% Similarity=0.467 Sum_probs=4.7
Q ss_pred CccCCcccc
Q psy9695 105 PFRCTICQK 113 (159)
Q Consensus 105 ~~~C~~C~~ 113 (159)
...|+.||.
T Consensus 29 ~~~C~~Cg~ 37 (50)
T PF12773_consen 29 KKICPNCGA 37 (50)
T ss_pred CCCCcCCcC
Confidence 345555554
No 238
>PRK10220 hypothetical protein; Provisional
Probab=31.18 E-value=32 Score=20.56 Aligned_cols=11 Identities=18% Similarity=0.836 Sum_probs=5.1
Q ss_pred ccccccccccc
Q psy9695 47 FRCTICQKAFT 57 (159)
Q Consensus 47 ~~c~~c~~~~~ 57 (159)
+.|++|+..+.
T Consensus 21 ~vCpeC~hEW~ 31 (111)
T PRK10220 21 YICPECAHEWN 31 (111)
T ss_pred EECCcccCcCC
Confidence 44444444443
No 239
>PF14447 Prok-RING_4: Prokaryotic RING finger family 4
Probab=31.15 E-value=16 Score=18.89 Aligned_cols=10 Identities=30% Similarity=0.979 Sum_probs=5.8
Q ss_pred cCCccccccc
Q psy9695 107 RCTICQKAFT 116 (159)
Q Consensus 107 ~C~~C~~~f~ 116 (159)
-|+.|+..|.
T Consensus 41 gCPfC~~~~~ 50 (55)
T PF14447_consen 41 GCPFCGTPFE 50 (55)
T ss_pred CCCCCCCccc
Confidence 4666666554
No 240
>COG4896 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=31.01 E-value=32 Score=18.17 Aligned_cols=8 Identities=25% Similarity=1.065 Sum_probs=4.1
Q ss_pred CccCCccc
Q psy9695 105 PFRCTICQ 112 (159)
Q Consensus 105 ~~~C~~C~ 112 (159)
.|.|+.|.
T Consensus 31 tymC~eC~ 38 (68)
T COG4896 31 TYMCPECE 38 (68)
T ss_pred eEechhhH
Confidence 35555554
No 241
>PF04606 Ogr_Delta: Ogr/Delta-like zinc finger; InterPro: IPR007684 This entry is represented by Bacteriophage P2, Ogr. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This is a viral family of phage zinc-binding transcriptional activators, which also contains cryptic members in some bacterial genomes []. The P4 phage delta protein contains two such domains attached covalently, while the P2 phage Ogr proteins possess one domain but function as dimers. All the members of this family have the following consensus sequence: C-X(2)-C-X(3)-A-(X)2-R-X(15)-C-X(4)-C-X(3)-F [].; GO: 0006355 regulation of transcription, DNA-dependent
Probab=30.85 E-value=6 Score=19.55 Aligned_cols=15 Identities=27% Similarity=0.596 Sum_probs=7.5
Q ss_pred CCccCCc--cccccccc
Q psy9695 104 KPFRCTI--CQKAFTTK 118 (159)
Q Consensus 104 ~~~~C~~--C~~~f~~~ 118 (159)
.-|+|.. ||..|...
T Consensus 24 ~Y~qC~N~~Cg~tfv~~ 40 (47)
T PF04606_consen 24 LYCQCTNPECGHTFVAN 40 (47)
T ss_pred EEEEECCCcCCCEEEEE
Confidence 3355533 66555443
No 242
>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=30.14 E-value=66 Score=19.01 Aligned_cols=18 Identities=11% Similarity=0.095 Sum_probs=9.1
Q ss_pred ccccccccccccCccccc
Q psy9695 46 PFRCTICQKAFTTKGNLK 63 (159)
Q Consensus 46 ~~~c~~c~~~~~~~~~l~ 63 (159)
.|.|+.-|..|.+.....
T Consensus 3 Vf~i~~T~EiF~dYe~Y~ 20 (102)
T PF10537_consen 3 VFYIPFTGEIFRDYEEYL 20 (102)
T ss_pred eEEeCCCCcccCCHHHHH
Confidence 344555555555555443
No 243
>PF12662 cEGF: Complement Clr-like EGF-like
Probab=30.08 E-value=20 Score=14.98 Aligned_cols=6 Identities=17% Similarity=0.169 Sum_probs=2.4
Q ss_pred hchhhh
Q psy9695 146 EGKSFQ 151 (159)
Q Consensus 146 C~~~f~ 151 (159)
|...|.
T Consensus 6 C~~Gy~ 11 (24)
T PF12662_consen 6 CPPGYQ 11 (24)
T ss_pred CCCCCc
Confidence 444443
No 244
>PF07295 DUF1451: Protein of unknown function (DUF1451); InterPro: IPR009912 This family consists of several hypothetical bacterial proteins of around 160 residues in length. Members of this family contain four highly conserved cysteine resides toward the C-terminal region of the protein. The function of this family is unknown.
Probab=29.98 E-value=24 Score=22.34 Aligned_cols=7 Identities=29% Similarity=0.909 Sum_probs=3.9
Q ss_pred ccCCccc
Q psy9695 106 FRCTICQ 112 (159)
Q Consensus 106 ~~C~~C~ 112 (159)
|.|..||
T Consensus 113 l~C~~Cg 119 (146)
T PF07295_consen 113 LVCENCG 119 (146)
T ss_pred EecccCC
Confidence 5555555
No 245
>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=29.91 E-value=16 Score=22.80 Aligned_cols=15 Identities=40% Similarity=0.884 Sum_probs=12.4
Q ss_pred CCCccCCcccccccc
Q psy9695 103 DKPFRCTICQKAFTT 117 (159)
Q Consensus 103 ~~~~~C~~C~~~f~~ 117 (159)
.++.+|+.||..|.-
T Consensus 110 g~~~RCpeCG~~fkL 124 (136)
T PF01215_consen 110 GKPQRCPECGQVFKL 124 (136)
T ss_dssp TSEEEETTTEEEEEE
T ss_pred CCccCCCCCCeEEEE
Confidence 468999999998864
No 246
>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=29.77 E-value=13 Score=18.91 Aligned_cols=15 Identities=0% Similarity=-0.219 Sum_probs=9.1
Q ss_pred ccccchhhchhhhhc
Q psy9695 139 QQHIGAVEGKSFQAK 153 (159)
Q Consensus 139 ~~~~C~~C~~~f~~~ 153 (159)
..|+|.+|++.|...
T Consensus 34 ~~~rC~YCe~~~~~~ 48 (52)
T PF02748_consen 34 IKLRCHYCERIITED 48 (52)
T ss_dssp CEEEETTT--EEEHH
T ss_pred CEEEeeCCCCEeccc
Confidence 678888888776543
No 247
>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=29.27 E-value=21 Score=15.77 Aligned_cols=9 Identities=33% Similarity=1.054 Sum_probs=3.1
Q ss_pred ccCCccccc
Q psy9695 106 FRCTICQKA 114 (159)
Q Consensus 106 ~~C~~C~~~ 114 (159)
|.|+.|+..
T Consensus 14 Y~Cp~C~~~ 22 (30)
T PF04438_consen 14 YRCPRCGAR 22 (30)
T ss_dssp EE-TTT--E
T ss_pred EECCCcCCc
Confidence 555555544
No 248
>PF06467 zf-FCS: MYM-type Zinc finger with FCS sequence motif; InterPro: IPR010507 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. MYM-type zinc fingers were identified in MYM family proteins []. Human protein Q14202 from SWISSPROT is involved in a chromosomal translocation and may be responsible for X-linked retardation in XQ13.1 []. Q9UBW7 from SWISSPROT is also involved in disease. In myeloproliferative disorders it is fused to FGF receptor 1 []; in atypical myeloproliferative disorders it is rearranged []. Members of the family generally are involved in development. This Zn-finger domain functions as a transcriptional trans-activator of late vaccinia viral genes, and orthologues are also found in all nucleocytoplasmic large DNA viruses, NCLDV. This domain is also found fused to the C termini of recombinases from certain prokaryotic transposons []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2L8E_A 2DAS_A.
Probab=28.16 E-value=39 Score=15.87 Aligned_cols=16 Identities=25% Similarity=0.503 Sum_probs=8.3
Q ss_pred CccCCcccccccccCC
Q psy9695 105 PFRCTICQKAFTTKGN 120 (159)
Q Consensus 105 ~~~C~~C~~~f~~~~~ 120 (159)
...|..|++.+.....
T Consensus 6 ~~~C~~C~~~~~~~~~ 21 (43)
T PF06467_consen 6 MKTCSYCKKYIPNKPT 21 (43)
T ss_dssp CEE-TTT--EEECCC-
T ss_pred CCcCcccCCcccCCCc
Confidence 3568888888866664
No 249
>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=27.32 E-value=22 Score=16.02 Aligned_cols=12 Identities=8% Similarity=-0.006 Sum_probs=8.6
Q ss_pred ccccchhhchhh
Q psy9695 139 QQHIGAVEGKSF 150 (159)
Q Consensus 139 ~~~~C~~C~~~f 150 (159)
+.|+|..||...
T Consensus 3 ~~ykC~~CGniv 14 (34)
T cd00974 3 EVYKCEICGNIV 14 (34)
T ss_pred cEEEcCCCCcEE
Confidence 578888887543
No 250
>smart00731 SprT SprT homologues. Predicted to have roles in transcription elongation. Contains a conserved HExxH motif, indicating a metalloprotease function.
Probab=26.85 E-value=23 Score=22.24 Aligned_cols=12 Identities=8% Similarity=-0.039 Sum_probs=7.1
Q ss_pred ccccchhhchhh
Q psy9695 139 QQHIGAVEGKSF 150 (159)
Q Consensus 139 ~~~~C~~C~~~f 150 (159)
..|.|..|+-.|
T Consensus 132 ~~y~C~~C~g~l 143 (146)
T smart00731 132 SRYRCGKCGGKL 143 (146)
T ss_pred ceEEcCCCCCEE
Confidence 346776676544
No 251
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=26.75 E-value=56 Score=16.62 Aligned_cols=11 Identities=27% Similarity=0.673 Sum_probs=5.6
Q ss_pred CCccccccccc
Q psy9695 44 DKPFRCTICQK 54 (159)
Q Consensus 44 ~~~~~c~~c~~ 54 (159)
+....|+.||+
T Consensus 44 ~~i~~Cp~CgR 54 (56)
T PF02591_consen 44 DEIVFCPNCGR 54 (56)
T ss_pred CCeEECcCCCc
Confidence 44455555553
No 252
>PF10083 DUF2321: Uncharacterized protein conserved in bacteria (DUF2321); InterPro: IPR016891 This entry is represented by Bacteriophage 'Lactobacillus prophage Lj928', Orf-Ljo1454. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=26.67 E-value=77 Score=20.38 Aligned_cols=43 Identities=14% Similarity=0.213 Sum_probs=22.6
Q ss_pred cccccccccccCccccccccccccc-cCCCCCccCcccccccCChHH
Q psy9695 47 FRCTICQKAFTTKGNLKLIPNAVFN-VAGMPKHLCHVCHKNFSSSSA 92 (159)
Q Consensus 47 ~~c~~c~~~~~~~~~l~~~~~~~~~-~~~~~~~~C~~C~~~~~~~~~ 92 (159)
-.|+.|+.......-... .... .....|.-|..||+.|+|-..
T Consensus 40 ~~Cp~C~~~IrG~y~v~g---v~~~g~~~~~PsYC~~CGkpyPWt~~ 83 (158)
T PF10083_consen 40 TSCPNCSTPIRGDYHVEG---VFGLGGHYEAPSYCHNCGKPYPWTEN 83 (158)
T ss_pred HHCcCCCCCCCCceecCC---eeeeCCCCCCChhHHhCCCCCchHHH
Confidence 357777655543322211 1111 222356778888888877543
No 253
>PF14369 zf-RING_3: zinc-finger
Probab=26.61 E-value=49 Score=15.19 Aligned_cols=10 Identities=30% Similarity=0.923 Sum_probs=5.9
Q ss_pred cccccccccc
Q psy9695 48 RCTICQKAFT 57 (159)
Q Consensus 48 ~c~~c~~~~~ 57 (159)
.|+.|+..|.
T Consensus 23 ~CP~C~~gFv 32 (35)
T PF14369_consen 23 ACPRCHGGFV 32 (35)
T ss_pred CCcCCCCcEe
Confidence 4666666553
No 254
>PTZ00043 cytochrome c oxidase subunit; Provisional
Probab=26.51 E-value=36 Score=23.34 Aligned_cols=27 Identities=19% Similarity=0.314 Sum_probs=17.8
Q ss_pred CCCCccCCcccccccccCCceeeehhhccCC
Q psy9695 102 GDKPFRCTICQKAFTTKGNLKVREIEINIGS 132 (159)
Q Consensus 102 ~~~~~~C~~C~~~f~~~~~l~~H~~~~h~~~ 132 (159)
..++.+|+.||..|.. ..+.+....|+
T Consensus 178 EGkpqRCpECGqVFKL----Vr~~~s~~dg~ 204 (268)
T PTZ00043 178 EGFLYRCGECDQIFML----VRVLYSLPDGE 204 (268)
T ss_pred CCCCccCCCCCcEEEE----EEEEeecCCCC
Confidence 3568999999988864 44443444444
No 255
>KOG1842|consensus
Probab=26.47 E-value=13 Score=28.10 Aligned_cols=27 Identities=19% Similarity=0.266 Sum_probs=0.0
Q ss_pred ccCCcccccccccCCceeeehhhccCC
Q psy9695 106 FRCTICQKAFTTKGNLKVREIEINIGS 132 (159)
Q Consensus 106 ~~C~~C~~~f~~~~~l~~H~~~~h~~~ 132 (159)
|.||.|...|.....|..|....|.++
T Consensus 16 flCPiC~~dl~~~~~L~~H~d~eH~~e 42 (505)
T KOG1842|consen 16 FLCPICLLDLPNLSALNDHLDVEHFEE 42 (505)
T ss_pred ccCchHhhhhhhHHHHHHHHhhhcccc
No 256
>KOG2906|consensus
Probab=26.45 E-value=20 Score=20.91 Aligned_cols=36 Identities=11% Similarity=0.006 Sum_probs=20.6
Q ss_pred cCCcccccccccCCceeeehhhccCCCCCcccccccchhhchh
Q psy9695 107 RCTICQKAFTTKGNLKVREIEINIGSQLPKKAQQHIGAVEGKS 149 (159)
Q Consensus 107 ~C~~C~~~f~~~~~l~~H~~~~h~~~~~~~~~~~~~C~~C~~~ 149 (159)
.|+.||..=.+--.|+... ...+.- ..|+|-.|+..
T Consensus 67 ~Cp~Cgh~rayF~qlQtRS-ADEPmT------~FYkC~~C~~~ 102 (105)
T KOG2906|consen 67 TCPTCGHERAYFMQLQTRS-ADEPMT------TFYKCCKCKHR 102 (105)
T ss_pred cCCCCCCCceEEEEeeecc-CCCcHh------Hhhhhhccccc
Confidence 6777775544444444433 333333 67888777654
No 257
>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=26.01 E-value=92 Score=15.07 Aligned_cols=9 Identities=33% Similarity=0.947 Sum_probs=4.9
Q ss_pred ccccccccc
Q psy9695 47 FRCTICQKA 55 (159)
Q Consensus 47 ~~c~~c~~~ 55 (159)
+.|+.||..
T Consensus 19 ~~CP~Cg~~ 27 (46)
T PF12760_consen 19 FVCPHCGST 27 (46)
T ss_pred CCCCCCCCe
Confidence 456666543
No 258
>PRK01343 zinc-binding protein; Provisional
Probab=25.94 E-value=33 Score=17.88 Aligned_cols=12 Identities=33% Similarity=0.517 Sum_probs=8.9
Q ss_pred CccCCccccccc
Q psy9695 105 PFRCTICQKAFT 116 (159)
Q Consensus 105 ~~~C~~C~~~f~ 116 (159)
...|+.|++.+.
T Consensus 9 ~~~CP~C~k~~~ 20 (57)
T PRK01343 9 TRPCPECGKPST 20 (57)
T ss_pred CCcCCCCCCcCc
Confidence 357888988764
No 259
>TIGR00319 desulf_FeS4 desulfoferrodoxin FeS4 iron-binding domain. Neelaredoxin, a monomeric blue non-heme iron protein, lacks this domain.
Probab=25.65 E-value=22 Score=16.01 Aligned_cols=12 Identities=25% Similarity=0.030 Sum_probs=9.1
Q ss_pred ccccchhhchhh
Q psy9695 139 QQHIGAVEGKSF 150 (159)
Q Consensus 139 ~~~~C~~C~~~f 150 (159)
+.|+|..||...
T Consensus 6 ~~ykC~~Cgniv 17 (34)
T TIGR00319 6 QVYKCEVCGNIV 17 (34)
T ss_pred cEEEcCCCCcEE
Confidence 688998888544
No 260
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=25.53 E-value=69 Score=15.07 Aligned_cols=23 Identities=13% Similarity=0.312 Sum_probs=17.8
Q ss_pred CCCcccCcccccccCChHHHHHH
Q psy9695 15 GMPKHLCHVCHKNFSSSSALQIH 37 (159)
Q Consensus 15 ~~~~~~C~~C~~~f~~~~~~~~h 37 (159)
+-.-..|+.|+..|-...++..-
T Consensus 16 ~~~id~C~~C~G~W~d~~el~~~ 38 (41)
T PF13453_consen 16 DVEIDVCPSCGGIWFDAGELEKL 38 (41)
T ss_pred CEEEEECCCCCeEEccHHHHHHH
Confidence 34457899999999888887753
No 261
>PF04216 FdhE: Protein involved in formate dehydrogenase formation; InterPro: IPR006452 This family of sequences describe an accessory protein required for the assembly of formate dehydrogenase of certain proteobacteria although not present in the final complex []. The exact nature of the function of FdhE in the assembly of the complex is unknown, but considering the presence of selenocysteine, molybdopterin, iron-sulphur clusters and cytochrome b556, it is likely to be involved in the insertion of cofactors. ; GO: 0005737 cytoplasm; PDB: 2FIY_B.
Probab=25.31 E-value=15 Score=26.11 Aligned_cols=77 Identities=17% Similarity=0.351 Sum_probs=30.1
Q ss_pred cccCcccccccCChHHHHHHHHhhcCCCccccccccccccCccccccccccccccCCCCCccCcccccccCChHHHHHHH
Q psy9695 18 KHLCHVCHKNFSSSSALQIHMRTHTGDKPFRCTICQKAFTTKGNLKLIPNAVFNVAGMPKHLCHVCHKNFSSSSALQIHM 97 (159)
Q Consensus 18 ~~~C~~C~~~f~~~~~~~~h~~~~~~~~~~~c~~c~~~~~~~~~l~~~~~~~~~~~~~~~~~C~~C~~~~~~~~~l~~H~ 97 (159)
.-.|+.||..- ..+.+..--. .|.+...|..|+..+... ...|+.||..-...-.... .
T Consensus 172 ~g~CPvCGs~P-~~s~l~~~~~--~G~R~L~Cs~C~t~W~~~-----------------R~~Cp~Cg~~~~~~l~~~~-~ 230 (290)
T PF04216_consen 172 RGYCPVCGSPP-VLSVLRGGER--EGKRYLHCSLCGTEWRFV-----------------RIKCPYCGNTDHEKLEYFT-V 230 (290)
T ss_dssp -SS-TTT---E-EEEEEE--------EEEEEETTT--EEE-------------------TTS-TTT---SS-EEE-----
T ss_pred CCcCCCCCCcC-ceEEEecCCC--CccEEEEcCCCCCeeeec-----------------CCCCcCCCCCCCcceeeEe-c
Confidence 35899999642 2222111111 255678899998777332 2569999875433221110 1
Q ss_pred HHccCCCCccCCcccccc
Q psy9695 98 RTHTGDKPFRCTICQKAF 115 (159)
Q Consensus 98 ~~h~~~~~~~C~~C~~~f 115 (159)
....+.+.+.|..|+.-.
T Consensus 231 e~~~~~rve~C~~C~~Yl 248 (290)
T PF04216_consen 231 EGEPAYRVEVCESCGSYL 248 (290)
T ss_dssp ----SEEEEEETTTTEEE
T ss_pred CCCCcEEEEECCcccchH
Confidence 122245567888888443
No 262
>PF04032 Rpr2: RNAse P Rpr2/Rpp21/SNM1 subunit domain; InterPro: IPR007175 This family contains a ribonuclease P subunit of human and yeast. Other members of the family include the probable archaeal homologues. This subunit possibly binds the precursor tRNA [].; PDB: 2K3R_A 2KI7_B 2ZAE_B 1X0T_A.
Probab=25.09 E-value=59 Score=17.99 Aligned_cols=42 Identities=19% Similarity=0.048 Sum_probs=20.1
Q ss_pred CCCCccCCcccccccccCCceeeehhhccCCCCCcccccccchhhc
Q psy9695 102 GDKPFRCTICQKAFTTKGNLKVREIEINIGSQLPKKAQQHIGAVEG 147 (159)
Q Consensus 102 ~~~~~~C~~C~~~f~~~~~l~~H~~~~h~~~~~~~~~~~~~C~~C~ 147 (159)
..+.--|..|+-.+....+......+.. .......+.|..||
T Consensus 43 ~~kr~~Ck~C~~~liPG~~~~vri~~~~----~~~~~l~~~C~~C~ 84 (85)
T PF04032_consen 43 EIKRTICKKCGSLLIPGVNCSVRIRKKK----KKKNFLVYTCLNCG 84 (85)
T ss_dssp TCCCTB-TTT--B--CTTTEEEEEE-------SSS-EEEEEETTTT
T ss_pred HHhcccccCCCCEEeCCCccEEEEEecC----CCCCEEEEEccccC
Confidence 3445568888887777766665552111 11122678888886
No 263
>KOG3507|consensus
Probab=24.93 E-value=41 Score=17.63 Aligned_cols=10 Identities=30% Similarity=0.677 Sum_probs=5.3
Q ss_pred CccCCccccc
Q psy9695 105 PFRCTICQKA 114 (159)
Q Consensus 105 ~~~C~~C~~~ 114 (159)
..+|..||..
T Consensus 37 ~irCReCG~R 46 (62)
T KOG3507|consen 37 VIRCRECGYR 46 (62)
T ss_pred cEehhhcchH
Confidence 3556666543
No 264
>COG4957 Predicted transcriptional regulator [Transcription]
Probab=24.62 E-value=40 Score=21.06 Aligned_cols=26 Identities=38% Similarity=0.558 Sum_probs=20.0
Q ss_pred CccCcccccccCChHHHHHHHHHccCCCC
Q psy9695 77 KHLCHVCHKNFSSSSALQIHMRTHTGDKP 105 (159)
Q Consensus 77 ~~~C~~C~~~~~~~~~l~~H~~~h~~~~~ 105 (159)
...|.++|+.|.+ |.+|..+|.+--|
T Consensus 76 ~IicLEDGkkfKS---LKRHL~t~~gmTP 101 (148)
T COG4957 76 YIICLEDGKKFKS---LKRHLTTHYGLTP 101 (148)
T ss_pred eEEEeccCcchHH---HHHHHhcccCCCH
Confidence 3679999988854 7889998887544
No 265
>KOG0402|consensus
Probab=24.60 E-value=28 Score=19.67 Aligned_cols=29 Identities=21% Similarity=0.553 Sum_probs=16.1
Q ss_pred ccccccccccccCccccccccccccccCCCCCccCccccccc
Q psy9695 46 PFRCTICQKAFTTKGNLKLIPNAVFNVAGMPKHLCHVCHKNF 87 (159)
Q Consensus 46 ~~~c~~c~~~~~~~~~l~~~~~~~~~~~~~~~~~C~~C~~~~ 87 (159)
.|.|+.||+.-.-... ...|.|..|.+.+
T Consensus 36 ky~CsfCGK~~vKR~A-------------vGiW~C~~C~kv~ 64 (92)
T KOG0402|consen 36 KYTCSFCGKKTVKRKA-------------VGIWKCGSCKKVV 64 (92)
T ss_pred hhhhhhcchhhhhhhc-------------eeEEecCCcccee
Confidence 4778887754422211 1236777776654
No 266
>COG5216 Uncharacterized conserved protein [Function unknown]
Probab=24.10 E-value=23 Score=18.52 Aligned_cols=12 Identities=17% Similarity=0.100 Sum_probs=8.0
Q ss_pred ccccchhhchhhh
Q psy9695 139 QQHIGAVEGKSFQ 151 (159)
Q Consensus 139 ~~~~C~~C~~~f~ 151 (159)
-.|.|+ ||.+|.
T Consensus 21 ftyPCP-CGDRFe 32 (67)
T COG5216 21 FTYPCP-CGDRFE 32 (67)
T ss_pred EEecCC-CCCEeE
Confidence 456777 777764
No 267
>KOG3352|consensus
Probab=24.00 E-value=19 Score=22.84 Aligned_cols=14 Identities=14% Similarity=0.157 Sum_probs=10.4
Q ss_pred ccccchhhchhhhh
Q psy9695 139 QQHIGAVEGKSFQA 152 (159)
Q Consensus 139 ~~~~C~~C~~~f~~ 152 (159)
..++|+.||..|+-
T Consensus 132 e~~rc~eCG~~fkL 145 (153)
T KOG3352|consen 132 ETQRCPECGHYFKL 145 (153)
T ss_pred CcccCCcccceEEe
Confidence 46778888888763
No 268
>COG5112 UFD2 U1-like Zn-finger-containing protein [General function prediction only]
Probab=23.99 E-value=33 Score=20.37 Aligned_cols=25 Identities=28% Similarity=0.587 Sum_probs=20.7
Q ss_pred CCCccCcccccccCChHHHHHHHHH
Q psy9695 75 MPKHLCHVCHKNFSSSSALQIHMRT 99 (159)
Q Consensus 75 ~~~~~C~~C~~~~~~~~~l~~H~~~ 99 (159)
...+-|.+|.+.|.+...|..|.+.
T Consensus 53 lGqhYCieCaryf~t~~aL~~Hkkg 77 (126)
T COG5112 53 LGQHYCIECARYFITEKALMEHKKG 77 (126)
T ss_pred CceeeeehhHHHHHHHHHHHHHhcc
Confidence 3347799999999999999998773
No 269
>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=23.97 E-value=59 Score=25.02 Aligned_cols=29 Identities=28% Similarity=0.523 Sum_probs=23.8
Q ss_pred CCCCccCcccccccCChHHHHHHHHH-ccC
Q psy9695 74 GMPKHLCHVCHKNFSSSSALQIHMRT-HTG 102 (159)
Q Consensus 74 ~~~~~~C~~C~~~~~~~~~l~~H~~~-h~~ 102 (159)
..+-|.|+.|.+.|.....+..|+.. |.+
T Consensus 54 sWrFWiCp~CskkF~d~~~~~~H~~~eH~~ 83 (466)
T PF04780_consen 54 SWRFWICPRCSKKFSDAESCLSHMEQEHPA 83 (466)
T ss_pred ceeEeeCCcccceeCCHHHHHHHHHHhhhh
Confidence 34568999999999999999999885 443
No 270
>PRK12860 transcriptional activator FlhC; Provisional
Probab=23.89 E-value=44 Score=22.25 Aligned_cols=11 Identities=36% Similarity=0.818 Sum_probs=6.6
Q ss_pred ccCCccccccc
Q psy9695 106 FRCTICQKAFT 116 (159)
Q Consensus 106 ~~C~~C~~~f~ 116 (159)
..|..||-.|.
T Consensus 135 ~~C~~Cgg~fv 145 (189)
T PRK12860 135 ARCCRCGGKFV 145 (189)
T ss_pred ccCCCCCCCee
Confidence 45666665555
No 271
>KOG2857|consensus
Probab=23.80 E-value=34 Score=21.53 Aligned_cols=21 Identities=14% Similarity=0.599 Sum_probs=17.0
Q ss_pred CccCCcccccccccCCceeee
Q psy9695 105 PFRCTICQKAFTTKGNLKVRE 125 (159)
Q Consensus 105 ~~~C~~C~~~f~~~~~l~~H~ 125 (159)
.|+|+.|...|-+-.-++.|+
T Consensus 17 KYKCpkC~vPYCSl~CfKiHk 37 (157)
T KOG2857|consen 17 KYKCPKCSVPYCSLPCFKIHK 37 (157)
T ss_pred hccCCCCCCccccchhhhhcc
Confidence 488888888888888888787
No 272
>PF14279 HNH_5: HNH endonuclease
Probab=23.72 E-value=71 Score=17.42 Aligned_cols=10 Identities=10% Similarity=0.116 Sum_probs=5.2
Q ss_pred cchhhchhhh
Q psy9695 142 IGAVEGKSFQ 151 (159)
Q Consensus 142 ~C~~C~~~f~ 151 (159)
.|+.|...|-
T Consensus 32 vC~~CN~~~g 41 (71)
T PF14279_consen 32 VCDKCNNKFG 41 (71)
T ss_pred hhHHHhHHHh
Confidence 5555555443
No 273
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=23.58 E-value=34 Score=15.52 Aligned_cols=9 Identities=22% Similarity=0.840 Sum_probs=4.1
Q ss_pred ccCcccccc
Q psy9695 78 HLCHVCHKN 86 (159)
Q Consensus 78 ~~C~~C~~~ 86 (159)
+.|..|+.+
T Consensus 22 ~~C~~Cg~~ 30 (33)
T PF08792_consen 22 EVCIFCGSS 30 (33)
T ss_pred EEcccCCcE
Confidence 444444443
No 274
>COG1326 Uncharacterized archaeal Zn-finger protein [General function prediction only]
Probab=23.54 E-value=74 Score=21.31 Aligned_cols=38 Identities=13% Similarity=0.291 Sum_probs=21.6
Q ss_pred CcccCcccccccCChHHHHHHHHhhcCCCccccccccccccC
Q psy9695 17 PKHLCHVCHKNFSSSSALQIHMRTHTGDKPFRCTICQKAFTT 58 (159)
Q Consensus 17 ~~~~C~~C~~~f~~~~~~~~h~~~~~~~~~~~c~~c~~~~~~ 58 (159)
..+.|+.|+. ...+..=++.-..+....|..||.-++.
T Consensus 5 iy~~Cp~Cg~----eev~hEVik~~g~~~lvrC~eCG~V~~~ 42 (201)
T COG1326 5 IYIECPSCGS----EEVSHEVIKERGREPLVRCEECGTVHPA 42 (201)
T ss_pred EEEECCCCCc----chhhHHHHHhcCCceEEEccCCCcEeec
Confidence 3478999982 1111111233344456899999977744
No 275
>PTZ00448 hypothetical protein; Provisional
Probab=23.09 E-value=63 Score=23.98 Aligned_cols=23 Identities=26% Similarity=0.583 Sum_probs=19.9
Q ss_pred cccCcccccccCChHHHHHHHHh
Q psy9695 18 KHLCHVCHKNFSSSSALQIHMRT 40 (159)
Q Consensus 18 ~~~C~~C~~~f~~~~~~~~h~~~ 40 (159)
.|.|..|+..|.+......|+++
T Consensus 314 ~~tC~~C~v~F~~~~~qR~H~KS 336 (373)
T PTZ00448 314 MLLCRKCNIQLMDHNAFKQHYRS 336 (373)
T ss_pred CccccccccccCCHHHHHHHhhh
Confidence 58899999999888888888864
No 276
>PRK11823 DNA repair protein RadA; Provisional
Probab=22.96 E-value=50 Score=25.18 Aligned_cols=11 Identities=18% Similarity=0.591 Sum_probs=6.6
Q ss_pred ccccccccccc
Q psy9695 46 PFRCTICQKAF 56 (159)
Q Consensus 46 ~~~c~~c~~~~ 56 (159)
.|.|..||..+
T Consensus 7 ~y~C~~Cg~~~ 17 (446)
T PRK11823 7 AYVCQECGAES 17 (446)
T ss_pred eEECCcCCCCC
Confidence 46777776443
No 277
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=22.88 E-value=42 Score=23.95 Aligned_cols=7 Identities=43% Similarity=1.397 Sum_probs=2.8
Q ss_pred ccCCccc
Q psy9695 106 FRCTICQ 112 (159)
Q Consensus 106 ~~C~~C~ 112 (159)
|.|+.||
T Consensus 323 ~~C~~cg 329 (364)
T COG0675 323 FKCPRCG 329 (364)
T ss_pred EECCCCC
Confidence 3344443
No 278
>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=22.75 E-value=36 Score=20.47 Aligned_cols=33 Identities=12% Similarity=0.165 Sum_probs=19.7
Q ss_pred CCCccCCcccccccccCCceeeehhhccCCCCCcccccccchhhchhhhhcc
Q psy9695 103 DKPFRCTICQKAFTTKGNLKVREIEINIGSQLPKKAQQHIGAVEGKSFQAKH 154 (159)
Q Consensus 103 ~~~~~C~~C~~~f~~~~~l~~H~~~~h~~~~~~~~~~~~~C~~C~~~f~~~~ 154 (159)
.....||.|++.. .--| +...|.+|+....-..
T Consensus 67 av~V~CP~C~K~T------------KmLG-------r~D~CM~C~~pLTLd~ 99 (114)
T PF11023_consen 67 AVQVECPNCGKQT------------KMLG-------RVDACMHCKEPLTLDP 99 (114)
T ss_pred ceeeECCCCCChH------------hhhc-------hhhccCcCCCcCccCc
Confidence 3456899998651 1122 3468888876654433
No 279
>PF05180 zf-DNL: DNL zinc finger; InterPro: IPR007853 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The DNL-type zinc finger is found in Tim15, a zinc finger protein essential for protein import into mitochondria. Mitochondrial functions rely on the correct transport of resident proteins synthesized in the cytosol to mitochondria. Protein import into mitochondria is mediated by membrane protein complexes, protein translocators, in the outer and inner mitochondrial membranes, in cooperation with their assistant proteins in the cytosol, intermembrane space and matrix. Proteins destined to the mitochondrial matrix cross the outer membrane with the aid of the outer membrane translocator, the tOM40 complex, and then the inner membrane with the aid of the inner membrane translocator, the TIM23 complex, and mitochondrial motor and chaperone (MMC) proteins including mitochondrial heat- shock protein 70 (mtHsp70), and translocase in the inner mitochondrial membrane (Tim)15. Tim15 is also known as zinc finger motif (Zim)17 or mtHsp70 escort protein (Hep)1. Tim15 contains a zinc-finger motif (CXXC and CXXC) of ~100 residues, which has been named DNL after a short C-terminal motif of D(N/H)L [, , ]. The DNL-type zinc finger is an L-shaped molecule. The two CXXC motifs are located at the end of the L, and are sandwiched by two- stranded antiparallel beta-sheets. Two short alpha-helices constitute another leg of the L. The outer (convex) face of the L has a large acidic groove, which is lined with five acidic residues, whereas the inner (concave) face of the L has two positively charged residues, next to the CXXC motifs []. This entry represents the DNL-type zinc finger.; GO: 0008270 zinc ion binding; PDB: 2E2Z_A.
Probab=22.35 E-value=11 Score=20.26 Aligned_cols=34 Identities=18% Similarity=0.404 Sum_probs=14.8
Q ss_pred ccCcccccccCChHHHHHHHHHccCCCCccCCccccc
Q psy9695 78 HLCHVCHKNFSSSSALQIHMRTHTGDKPFRCTICQKA 114 (159)
Q Consensus 78 ~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~~ 114 (159)
|+|..|+...... +.. ..-+.|..--+|+-|...
T Consensus 5 FTC~~C~~Rs~~~--~sk-~aY~~GvViv~C~gC~~~ 38 (66)
T PF05180_consen 5 FTCNKCGTRSAKM--FSK-QAYHKGVVIVQCPGCKNR 38 (66)
T ss_dssp EEETTTTEEEEEE--EEH-HHHHTSEEEEE-TTS--E
T ss_pred EEcCCCCCcccee--eCH-HHHhCCeEEEECCCCcce
Confidence 6777776432111 111 122445555677777754
No 280
>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=22.29 E-value=32 Score=14.99 Aligned_cols=10 Identities=10% Similarity=-0.031 Sum_probs=5.4
Q ss_pred ccchhhchhh
Q psy9695 141 HIGAVEGKSF 150 (159)
Q Consensus 141 ~~C~~C~~~f 150 (159)
|.|++|++..
T Consensus 1 ~~C~~C~~~~ 10 (30)
T PF03107_consen 1 FWCDVCRRKI 10 (30)
T ss_pred CCCCCCCCCc
Confidence 4566665543
No 281
>KOG4118|consensus
Probab=22.16 E-value=69 Score=17.20 Aligned_cols=25 Identities=20% Similarity=0.535 Sum_probs=17.5
Q ss_pred ccCcccccccCChHHHHHHHHhhcC
Q psy9695 19 HLCHVCHKNFSSSSALQIHMRTHTG 43 (159)
Q Consensus 19 ~~C~~C~~~f~~~~~~~~h~~~~~~ 43 (159)
|+|..|....+....+..|....+.
T Consensus 39 ~kCtVC~~~mpdpktfkqhfe~kHp 63 (74)
T KOG4118|consen 39 HKCTVCMVQMPDPKTFKQHFENKHP 63 (74)
T ss_pred hhhHhhHhhCCCCchHHHHHhhcCC
Confidence 7788887777777777777655443
No 282
>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=21.49 E-value=65 Score=18.58 Aligned_cols=21 Identities=14% Similarity=0.488 Sum_probs=14.9
Q ss_pred CCcccCcccccccCChHHHHH
Q psy9695 16 MPKHLCHVCHKNFSSSSALQI 36 (159)
Q Consensus 16 ~~~~~C~~C~~~f~~~~~~~~ 36 (159)
-+-..|+.||..|-+...+..
T Consensus 33 VPa~~C~~CGe~y~~dev~~e 53 (89)
T TIGR03829 33 TPSISCSHCGMEYQDDTTVKE 53 (89)
T ss_pred CCcccccCCCcEeecHHHHHH
Confidence 344789999988877766554
No 283
>COG4332 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=21.30 E-value=30 Score=22.79 Aligned_cols=8 Identities=38% Similarity=1.244 Sum_probs=4.3
Q ss_pred ccCCcccc
Q psy9695 106 FRCTICQK 113 (159)
Q Consensus 106 ~~C~~C~~ 113 (159)
|+|..|+.
T Consensus 50 YkC~~Cd~ 57 (203)
T COG4332 50 YKCTHCDY 57 (203)
T ss_pred EEeeccCC
Confidence 55555553
No 284
>PF10071 DUF2310: Zn-ribbon-containing, possibly nucleic-acid-binding protein (DUF2310); InterPro: IPR016908 This group represents uncharacterised conserved proteins.
Probab=21.19 E-value=48 Score=23.26 Aligned_cols=30 Identities=13% Similarity=0.038 Sum_probs=19.9
Q ss_pred ccCCcccccccccCCceeeehhhccCCCCCcccccccchhhchh
Q psy9695 106 FRCTICQKAFTTKGNLKVREIEINIGSQLPKKAQQHIGAVEGKS 149 (159)
Q Consensus 106 ~~C~~C~~~f~~~~~l~~H~~~~h~~~~~~~~~~~~~C~~C~~~ 149 (159)
-.||.||+.-.-...|. .- --|+|+.|...
T Consensus 221 r~CP~Cg~~W~L~~plh-------~i-------FdFKCD~CRLV 250 (258)
T PF10071_consen 221 RKCPSCGGDWRLKEPLH-------DI-------FDFKCDPCRLV 250 (258)
T ss_pred CCCCCCCCccccCCchh-------hc-------eeccCCcceee
Confidence 47999997655555552 21 46999999754
No 285
>PF14690 zf-ISL3: zinc-finger of transposase IS204/IS1001/IS1096/IS1165
Probab=20.97 E-value=49 Score=15.87 Aligned_cols=11 Identities=36% Similarity=0.788 Sum_probs=8.1
Q ss_pred CccCCcccccc
Q psy9695 105 PFRCTICQKAF 115 (159)
Q Consensus 105 ~~~C~~C~~~f 115 (159)
|..|+.||..-
T Consensus 2 ~~~Cp~Cg~~~ 12 (47)
T PF14690_consen 2 PPRCPHCGSPS 12 (47)
T ss_pred CccCCCcCCCc
Confidence 56899999443
No 286
>PRK11295 hypothetical protein; Provisional
Probab=20.73 E-value=45 Score=20.16 Aligned_cols=47 Identities=9% Similarity=-0.004 Sum_probs=23.6
Q ss_pred CCccCCcccccccccC---CceeeehhhccCCCCCcccccccchhhchhh
Q psy9695 104 KPFRCTICQKAFTTKG---NLKVREIEINIGSQLPKKAQQHIGAVEGKSF 150 (159)
Q Consensus 104 ~~~~C~~C~~~f~~~~---~l~~H~~~~h~~~~~~~~~~~~~C~~C~~~f 150 (159)
.||.|..|+..|.... ....|+.-.+.+......+-...|..|...-
T Consensus 23 ~p~lC~~Cgr~~~~a~~~a~vVDHIip~~~gd~~D~sNLQ~LC~~CHn~k 72 (113)
T PRK11295 23 YPWVCGRCSREFVYSNLRELTVHHIDHDHDNNPEDGSNWELLCLYCHDHE 72 (113)
T ss_pred CcchhhhhcChhccCCCCCceeeccCCCCCCCCCchhHHHHHhHHHHhHH
Confidence 3567777777643222 2333442223233333455666777776554
No 287
>TIGR00627 tfb4 transcription factor tfb4. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=20.65 E-value=72 Score=22.71 Aligned_cols=13 Identities=23% Similarity=0.743 Sum_probs=8.3
Q ss_pred CCccCCccccccc
Q psy9695 104 KPFRCTICQKAFT 116 (159)
Q Consensus 104 ~~~~C~~C~~~f~ 116 (159)
..|.|++|.-.|.
T Consensus 254 ~GyvCs~Clsi~C 266 (279)
T TIGR00627 254 IGFVCSVCLSVLC 266 (279)
T ss_pred ceEECCCccCCcC
Confidence 3477777776554
No 288
>PF06170 DUF983: Protein of unknown function (DUF983); InterPro: IPR009325 This family consists of several bacterial proteins of unknown function.
Probab=20.30 E-value=49 Score=18.85 Aligned_cols=12 Identities=25% Similarity=0.780 Sum_probs=7.7
Q ss_pred cCCccccccccc
Q psy9695 107 RCTICQKAFTTK 118 (159)
Q Consensus 107 ~C~~C~~~f~~~ 118 (159)
+|+.||..|...
T Consensus 10 ~C~~CG~d~~~~ 21 (86)
T PF06170_consen 10 RCPHCGLDYSHA 21 (86)
T ss_pred cccccCCccccC
Confidence 577777666543
Done!