Query psy691
Match_columns 134
No_of_seqs 204 out of 2345
Neff 10.3
Searched_HMMs 46136
Date Fri Aug 16 21:33:32 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy691.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/691hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2462|consensus 99.9 8.6E-23 1.9E-27 135.8 1.1 74 59-132 187-260 (279)
2 KOG2462|consensus 99.8 1.2E-19 2.6E-24 120.9 2.6 74 57-132 159-232 (279)
3 KOG3576|consensus 99.8 2.4E-19 5.2E-24 114.8 2.6 78 54-131 112-189 (267)
4 KOG3623|consensus 99.7 4.5E-19 9.8E-24 130.9 3.0 82 50-131 885-966 (1007)
5 KOG3623|consensus 99.6 4.8E-16 1.1E-20 115.1 3.0 76 57-132 238-326 (1007)
6 KOG3576|consensus 99.4 7.6E-14 1.7E-18 89.8 0.8 74 55-128 141-225 (267)
7 PHA02768 hypothetical protein; 99.4 4.5E-13 9.8E-18 69.1 2.6 42 60-103 6-47 (55)
8 PHA02768 hypothetical protein; 99.3 1.1E-12 2.4E-17 67.6 2.2 46 87-134 5-50 (55)
9 KOG1074|consensus 99.2 9.8E-12 2.1E-16 93.8 4.1 74 55-128 601-681 (958)
10 KOG3608|consensus 99.2 4.7E-12 1E-16 87.6 1.0 75 56-132 234-309 (467)
11 KOG1074|consensus 99.2 1.1E-11 2.4E-16 93.6 2.9 57 58-114 352-408 (958)
12 PHA00733 hypothetical protein 99.1 5.8E-11 1.3E-15 72.8 1.6 75 55-131 36-115 (128)
13 PF13465 zf-H2C2_2: Zinc-finge 99.1 1.5E-10 3.3E-15 51.4 2.5 25 74-98 1-25 (26)
14 PHA00733 hypothetical protein 99.0 7.1E-10 1.5E-14 68.0 4.5 56 55-112 69-124 (128)
15 PF13465 zf-H2C2_2: Zinc-finge 99.0 3E-10 6.5E-15 50.4 1.8 26 102-127 1-26 (26)
16 KOG3608|consensus 98.9 6E-10 1.3E-14 77.4 2.9 79 53-132 286-369 (467)
17 PHA00616 hypothetical protein 98.9 7.6E-10 1.6E-14 54.5 1.5 32 60-91 2-33 (44)
18 PLN03086 PRLI-interacting fact 98.8 4.4E-09 9.6E-14 78.1 4.8 67 55-126 449-515 (567)
19 PHA00616 hypothetical protein 98.8 2.2E-09 4.9E-14 52.9 1.7 33 87-119 1-33 (44)
20 PHA00732 hypothetical protein 98.7 1.3E-08 2.8E-13 57.2 2.8 48 59-112 1-49 (79)
21 PLN03086 PRLI-interacting fact 98.7 2.2E-08 4.8E-13 74.5 4.3 69 58-129 477-555 (567)
22 PF05605 zf-Di19: Drought indu 98.5 2.7E-07 5.9E-12 48.2 4.2 51 59-112 2-54 (54)
23 COG5189 SFP1 Putative transcri 98.4 4.1E-07 8.9E-12 62.8 3.6 54 56-109 346-420 (423)
24 PF00096 zf-C2H2: Zinc finger, 98.3 4.4E-07 9.5E-12 38.8 2.2 22 60-81 1-22 (23)
25 PF00096 zf-C2H2: Zinc finger, 98.3 5.5E-07 1.2E-11 38.5 2.0 23 88-110 1-23 (23)
26 KOG3993|consensus 98.3 3.9E-07 8.4E-12 65.0 2.0 53 60-112 296-381 (500)
27 PHA00732 hypothetical protein 98.2 7.8E-07 1.7E-11 50.0 2.2 39 87-128 1-40 (79)
28 PF13912 zf-C2H2_6: C2H2-type 98.0 3.3E-06 7.2E-11 37.5 1.8 25 87-111 1-25 (27)
29 PF13894 zf-C2H2_4: C2H2-type 98.0 5.8E-06 1.3E-10 35.4 2.1 22 60-81 1-22 (24)
30 PF13894 zf-C2H2_4: C2H2-type 98.0 8.5E-06 1.8E-10 34.8 2.4 24 88-111 1-24 (24)
31 PF13912 zf-C2H2_6: C2H2-type 97.9 9.4E-06 2E-10 36.0 1.9 25 59-83 1-25 (27)
32 PF09237 GAGA: GAGA factor; I 97.8 4.7E-05 1E-09 38.5 3.7 30 57-86 22-51 (54)
33 PF12756 zf-C2H2_2: C2H2 type 97.8 1.7E-05 3.7E-10 46.2 2.3 50 61-110 1-73 (100)
34 KOG3993|consensus 97.8 2.1E-06 4.5E-11 61.4 -2.3 73 60-132 268-373 (500)
35 PRK04860 hypothetical protein; 97.7 2.1E-05 4.7E-10 50.0 2.1 38 87-128 119-156 (160)
36 PF09237 GAGA: GAGA factor; I 97.7 4.6E-05 9.9E-10 38.5 2.7 39 77-115 13-52 (54)
37 PRK04860 hypothetical protein; 97.5 6.7E-05 1.5E-09 47.8 1.9 40 58-101 118-157 (160)
38 smart00355 ZnF_C2H2 zinc finge 97.5 9.3E-05 2E-09 31.9 1.9 22 61-82 2-23 (26)
39 smart00355 ZnF_C2H2 zinc finge 97.5 0.00013 2.7E-09 31.5 2.3 25 88-112 1-25 (26)
40 PF12874 zf-met: Zinc-finger o 97.4 0.00013 2.8E-09 31.6 1.6 22 60-81 1-22 (25)
41 COG5189 SFP1 Putative transcri 97.3 0.00017 3.7E-09 50.2 2.0 46 84-129 346-412 (423)
42 PF12874 zf-met: Zinc-finger o 97.0 0.00046 1E-08 29.8 1.7 23 88-110 1-23 (25)
43 PF13909 zf-H2C2_5: C2H2-type 97.0 0.00065 1.4E-08 29.0 1.8 21 60-81 1-21 (24)
44 COG5048 FOG: Zn-finger [Genera 96.9 0.0007 1.5E-08 49.0 2.6 62 58-119 288-355 (467)
45 PF13909 zf-H2C2_5: C2H2-type 96.9 0.00085 1.8E-08 28.7 1.8 24 88-112 1-24 (24)
46 PF05605 zf-Di19: Drought indu 96.6 0.0019 4.1E-08 33.5 2.2 39 87-126 2-42 (54)
47 PF12171 zf-C2H2_jaz: Zinc-fin 96.5 0.00049 1.1E-08 30.4 -0.3 21 60-80 2-22 (27)
48 KOG2893|consensus 96.4 0.002 4.3E-08 43.3 1.6 48 54-106 6-53 (341)
49 PF12171 zf-C2H2_jaz: Zinc-fin 96.3 0.00096 2.1E-08 29.4 0.0 22 88-109 2-23 (27)
50 PF13913 zf-C2HC_2: zinc-finge 95.7 0.0085 1.9E-07 25.9 1.5 18 61-79 4-21 (25)
51 smart00451 ZnF_U1 U1-like zinc 95.6 0.013 2.7E-07 27.2 2.1 23 59-81 3-25 (35)
52 smart00451 ZnF_U1 U1-like zinc 95.1 0.017 3.7E-07 26.8 1.7 23 87-109 3-25 (35)
53 PF12756 zf-C2H2_2: C2H2 type 94.2 0.055 1.2E-06 31.1 2.6 24 59-82 50-73 (100)
54 KOG2186|consensus 93.8 0.04 8.7E-07 37.5 1.7 48 59-109 3-50 (276)
55 cd00350 rubredoxin_like Rubred 93.6 0.043 9.2E-07 25.3 1.1 24 60-95 2-25 (33)
56 KOG1146|consensus 93.4 0.052 1.1E-06 44.8 2.0 53 57-109 463-540 (1406)
57 COG4049 Uncharacterized protei 92.9 0.056 1.2E-06 28.0 1.0 31 51-81 9-39 (65)
58 KOG4167|consensus 90.7 0.28 6E-06 38.5 3.0 30 55-84 788-817 (907)
59 PF05443 ROS_MUCR: ROS/MUCR tr 90.5 0.18 3.8E-06 31.2 1.5 25 58-85 71-95 (132)
60 KOG2893|consensus 90.4 0.17 3.7E-06 34.3 1.5 39 89-131 12-50 (341)
61 KOG2785|consensus 89.9 0.52 1.1E-05 34.1 3.6 53 57-109 164-242 (390)
62 PF09538 FYDLN_acid: Protein o 89.7 0.2 4.4E-06 29.8 1.3 30 60-100 10-39 (108)
63 KOG2482|consensus 89.4 0.59 1.3E-05 33.5 3.6 51 59-109 195-301 (423)
64 COG5048 FOG: Zn-finger [Genera 89.0 0.4 8.6E-06 34.7 2.7 62 56-117 30-93 (467)
65 PF05443 ROS_MUCR: ROS/MUCR tr 88.4 0.51 1.1E-05 29.2 2.4 28 85-115 70-97 (132)
66 cd00729 rubredoxin_SM Rubredox 87.9 0.28 6E-06 22.8 0.8 25 59-95 2-26 (34)
67 PF13719 zinc_ribbon_5: zinc-r 87.2 0.57 1.2E-05 22.1 1.7 32 61-97 4-35 (37)
68 TIGR02098 MJ0042_CXXC MJ0042 f 87.2 0.53 1.1E-05 22.2 1.6 34 60-98 3-36 (38)
69 COG4049 Uncharacterized protei 86.8 0.35 7.5E-06 25.1 0.9 32 81-112 11-42 (65)
70 KOG4173|consensus 86.3 0.39 8.4E-06 31.9 1.1 46 59-107 79-126 (253)
71 KOG1146|consensus 86.2 0.62 1.3E-05 39.0 2.4 71 61-131 438-534 (1406)
72 PF02892 zf-BED: BED zinc fing 86.0 0.81 1.8E-05 22.3 2.0 23 57-79 14-40 (45)
73 KOG2186|consensus 85.7 0.47 1E-05 32.5 1.3 41 88-130 4-44 (276)
74 smart00614 ZnF_BED BED zinc fi 85.6 0.88 1.9E-05 22.9 2.1 25 59-83 18-48 (50)
75 KOG4173|consensus 85.5 0.38 8.3E-06 31.9 0.8 49 61-109 108-168 (253)
76 PF04959 ARS2: Arsenite-resist 85.4 0.85 1.9E-05 30.6 2.4 29 55-83 73-101 (214)
77 COG4957 Predicted transcriptio 85.2 2.7 5.8E-05 26.1 4.3 25 60-87 77-101 (148)
78 PF04959 ARS2: Arsenite-resist 85.1 0.39 8.5E-06 32.2 0.8 30 85-114 75-104 (214)
79 PRK09678 DNA-binding transcrip 85.1 0.18 4E-06 27.7 -0.7 18 85-102 25-44 (72)
80 KOG2785|consensus 84.5 1.3 2.7E-05 32.2 3.1 51 59-109 3-90 (390)
81 COG1592 Rubrerythrin [Energy p 84.3 0.64 1.4E-05 29.9 1.4 23 59-94 134-156 (166)
82 smart00659 RPOLCX RNA polymera 84.1 0.79 1.7E-05 22.6 1.4 26 60-96 3-28 (44)
83 PF09986 DUF2225: Uncharacteri 84.1 0.2 4.2E-06 33.7 -1.0 19 58-76 4-22 (214)
84 TIGR00622 ssl1 transcription f 83.6 1.1 2.3E-05 26.9 2.1 65 59-125 15-91 (112)
85 PF13717 zinc_ribbon_4: zinc-r 83.4 1.2 2.6E-05 20.9 1.8 33 60-97 3-35 (36)
86 TIGR02300 FYDLN_acid conserved 82.8 0.86 1.9E-05 27.9 1.5 35 59-104 9-43 (129)
87 PF05290 Baculo_IE-1: Baculovi 81.8 0.89 1.9E-05 28.1 1.3 55 58-130 79-136 (140)
88 TIGR00373 conserved hypothetic 81.6 0.8 1.7E-05 29.2 1.1 33 83-124 105-137 (158)
89 PRK06266 transcription initiat 80.7 0.77 1.7E-05 29.9 0.8 17 87-103 117-133 (178)
90 COG5236 Uncharacterized conser 80.6 0.65 1.4E-05 33.4 0.5 22 60-81 152-175 (493)
91 PRK00398 rpoP DNA-directed RNA 80.6 0.75 1.6E-05 22.8 0.6 30 59-98 3-32 (46)
92 COG2888 Predicted Zn-ribbon RN 79.9 1.8 3.9E-05 22.8 1.9 32 59-95 27-58 (61)
93 smart00531 TFIIE Transcription 79.9 2.4 5.1E-05 26.7 2.8 36 85-124 97-132 (147)
94 PRK00464 nrdR transcriptional 79.4 0.39 8.4E-06 30.6 -0.8 16 87-102 28-43 (154)
95 KOG2593|consensus 79.4 1.8 3.8E-05 32.1 2.3 35 86-123 127-161 (436)
96 PRK14890 putative Zn-ribbon RN 79.2 1.7 3.6E-05 22.9 1.6 31 59-95 25-56 (59)
97 smart00734 ZnF_Rad18 Rad18-lik 78.3 2.2 4.7E-05 18.4 1.6 19 61-80 3-21 (26)
98 COG4957 Predicted transcriptio 77.9 1.3 2.8E-05 27.4 1.1 25 88-115 77-101 (148)
99 PF12013 DUF3505: Protein of u 77.4 8.8 0.00019 22.7 4.6 26 59-84 80-109 (109)
100 KOG4167|consensus 77.3 0.67 1.4E-05 36.5 -0.3 26 87-112 792-817 (907)
101 KOG3408|consensus 75.8 2.1 4.6E-05 26.0 1.6 28 54-81 52-79 (129)
102 TIGR02605 CxxC_CxxC_SSSS putat 75.5 0.59 1.3E-05 23.7 -0.7 11 60-70 6-16 (52)
103 PF12013 DUF3505: Protein of u 75.4 2.5 5.4E-05 25.0 1.9 54 58-112 10-109 (109)
104 TIGR00373 conserved hypothetic 74.3 4.7 0.0001 25.7 3.1 35 56-99 106-140 (158)
105 COG1996 RPC10 DNA-directed RNA 72.9 2.2 4.8E-05 21.6 1.0 28 58-95 5-32 (49)
106 PHA00626 hypothetical protein 72.1 2.6 5.7E-05 21.9 1.2 15 57-71 21-35 (59)
107 KOG2231|consensus 72.1 3.2 6.9E-05 32.6 2.2 21 61-81 184-204 (669)
108 COG1997 RPL43A Ribosomal prote 70.7 1.4 3E-05 25.1 0.0 11 88-98 54-64 (89)
109 PF15269 zf-C2H2_7: Zinc-finge 69.5 3.4 7.4E-05 20.4 1.2 20 89-108 22-41 (54)
110 PRK06266 transcription initiat 67.7 6.9 0.00015 25.6 2.8 34 57-99 115-148 (178)
111 KOG2482|consensus 65.2 5 0.00011 29.0 1.8 51 59-109 144-217 (423)
112 PF03604 DNA_RNApol_7kD: DNA d 64.6 2.8 6E-05 19.2 0.4 11 60-70 1-11 (32)
113 COG4530 Uncharacterized protei 64.1 3.8 8.2E-05 24.5 0.9 32 61-104 11-42 (129)
114 PF13878 zf-C2H2_3: zinc-finge 62.4 9.7 0.00021 18.3 2.1 24 60-83 14-39 (41)
115 COG3091 SprT Zn-dependent meta 62.1 4.1 8.8E-05 25.9 0.9 31 87-122 117-147 (156)
116 PF10571 UPF0547: Uncharacteri 62.0 3.8 8.3E-05 17.7 0.6 11 60-70 15-25 (26)
117 PF08790 zf-LYAR: LYAR-type C2 61.1 2.4 5.2E-05 18.8 -0.2 9 61-69 2-10 (28)
118 PF02176 zf-TRAF: TRAF-type zi 60.7 3.2 6.9E-05 21.5 0.2 40 59-99 9-54 (60)
119 PF13451 zf-trcl: Probable zin 60.6 9 0.0002 19.4 1.8 38 57-94 2-40 (49)
120 KOG2071|consensus 59.2 5.3 0.00012 30.9 1.2 29 85-113 416-444 (579)
121 PF01363 FYVE: FYVE zinc finge 58.3 6.1 0.00013 21.1 1.1 28 60-99 10-37 (69)
122 TIGR01206 lysW lysine biosynth 58.3 3.8 8.3E-05 21.2 0.2 30 60-97 3-32 (54)
123 KOG2593|consensus 58.1 14 0.00031 27.6 3.1 39 55-96 124-162 (436)
124 COG5236 Uncharacterized conser 58.0 11 0.00023 27.5 2.4 22 61-82 222-243 (493)
125 PF04780 DUF629: Protein of un 57.7 9.2 0.0002 28.9 2.2 27 59-85 57-84 (466)
126 COG3357 Predicted transcriptio 57.7 4.8 0.0001 23.2 0.6 14 86-99 57-70 (97)
127 smart00834 CxxC_CXXC_SSSS Puta 57.2 5.3 0.00011 18.8 0.7 29 60-95 6-34 (41)
128 KOG4124|consensus 57.1 1.2 2.6E-05 32.0 -2.2 53 57-109 347-420 (442)
129 PRK03824 hypA hydrogenase nick 57.0 3.5 7.5E-05 25.6 -0.0 15 58-72 69-83 (135)
130 PF05191 ADK_lid: Adenylate ki 55.2 5 0.00011 18.8 0.4 11 60-70 2-12 (36)
131 PF07754 DUF1610: Domain of un 54.1 9.1 0.0002 16.3 1.0 11 57-67 14-24 (24)
132 KOG3408|consensus 53.4 9.5 0.00021 23.2 1.4 26 84-109 54-79 (129)
133 PF09723 Zn-ribbon_8: Zinc rib 51.3 7.6 0.00017 18.7 0.7 29 60-95 6-34 (42)
134 COG4888 Uncharacterized Zn rib 50.2 4.8 0.0001 23.6 -0.2 40 56-99 19-58 (104)
135 PRK12380 hydrogenase nickel in 48.7 8.1 0.00018 23.2 0.6 25 59-95 70-94 (113)
136 PLN03238 probable histone acet 48.7 18 0.00038 25.6 2.3 22 87-108 48-69 (290)
137 PF07282 OrfB_Zn_ribbon: Putat 48.6 13 0.00028 19.8 1.4 14 85-98 44-57 (69)
138 PF06524 NOA36: NOA36 protein; 48.6 23 0.0005 24.7 2.8 75 56-132 139-226 (314)
139 PF14311 DUF4379: Domain of un 48.3 12 0.00027 19.0 1.2 14 59-72 28-41 (55)
140 TIGR00100 hypA hydrogenase nic 48.3 7.7 0.00017 23.4 0.5 25 59-95 70-94 (115)
141 smart00154 ZnF_AN1 AN1-like Zi 47.4 9.7 0.00021 18.1 0.7 14 87-100 12-25 (39)
142 cd00065 FYVE FYVE domain; Zinc 46.6 13 0.00029 18.8 1.2 27 61-99 4-30 (57)
143 COG1773 Rubredoxin [Energy pro 46.5 9.9 0.00021 19.8 0.7 13 59-71 3-15 (55)
144 PF12907 zf-met2: Zinc-binding 46.3 14 0.0003 17.9 1.1 20 61-80 3-25 (40)
145 PF01428 zf-AN1: AN1-like Zinc 46.0 8.2 0.00018 18.7 0.3 15 86-100 12-26 (43)
146 KOG2231|consensus 45.8 15 0.00032 29.2 1.7 23 60-82 100-138 (669)
147 COG4306 Uncharacterized protei 45.6 5.6 0.00012 24.4 -0.4 41 60-100 40-81 (160)
148 PTZ00255 60S ribosomal protein 45.4 7.5 0.00016 22.4 0.1 7 88-94 37-43 (90)
149 PF12760 Zn_Tnp_IS1595: Transp 45.3 20 0.00043 17.5 1.7 8 88-95 19-26 (46)
150 COG2331 Uncharacterized protei 45.0 7.1 0.00015 21.7 -0.0 33 59-98 12-44 (82)
151 KOG2636|consensus 44.8 17 0.00037 27.3 1.8 27 80-106 394-421 (497)
152 PF08209 Sgf11: Sgf11 (transcr 44.5 21 0.00046 16.4 1.5 22 59-81 4-25 (33)
153 PF14445 Prok-RING_2: Prokaryo 44.3 7.1 0.00015 19.8 -0.1 14 59-72 7-20 (57)
154 COG4896 Uncharacterized protei 44.1 13 0.00029 19.7 0.9 40 60-99 3-43 (68)
155 PRK00564 hypA hydrogenase nick 44.1 9.4 0.0002 23.1 0.4 13 59-71 71-83 (117)
156 PF10263 SprT-like: SprT-like 43.8 7 0.00015 24.5 -0.2 31 59-97 123-153 (157)
157 PF01155 HypA: Hydrogenase exp 43.5 9.6 0.00021 22.8 0.4 15 59-73 70-84 (113)
158 smart00064 FYVE Protein presen 43.1 21 0.00045 18.9 1.7 28 60-99 11-38 (68)
159 PF12230 PRP21_like_P: Pre-mRN 42.7 8.2 0.00018 26.1 0.0 30 58-88 167-196 (229)
160 KOG1280|consensus 42.3 29 0.00062 25.3 2.6 37 58-94 78-116 (381)
161 PF09963 DUF2197: Uncharacteri 42.3 14 0.0003 19.3 0.8 37 60-96 3-40 (56)
162 KOG0978|consensus 41.9 8.8 0.00019 30.5 0.1 13 58-70 642-654 (698)
163 KOG4602|consensus 41.7 42 0.0009 23.4 3.2 45 55-99 229-280 (318)
164 TIGR00280 L37a ribosomal prote 41.4 8.3 0.00018 22.3 -0.1 7 88-94 36-42 (91)
165 KOG2636|consensus 40.9 42 0.00091 25.4 3.3 27 54-80 396-423 (497)
166 PF04423 Rad50_zn_hook: Rad50 40.7 11 0.00025 19.1 0.4 12 61-72 22-33 (54)
167 PF08274 PhnA_Zn_Ribbon: PhnA 40.3 12 0.00025 16.8 0.3 8 87-94 19-26 (30)
168 PLN00104 MYST -like histone ac 40.2 21 0.00045 27.0 1.7 25 85-109 196-220 (450)
169 COG5188 PRP9 Splicing factor 3 40.1 46 0.001 24.4 3.3 26 55-80 370-396 (470)
170 PF10276 zf-CHCC: Zinc-finger 39.8 19 0.00042 17.3 1.0 12 58-69 28-39 (40)
171 KOG0717|consensus 38.7 23 0.0005 26.9 1.7 22 60-81 293-314 (508)
172 PF00301 Rubredoxin: Rubredoxi 38.3 15 0.00033 18.3 0.6 12 60-71 2-13 (47)
173 PTZ00064 histone acetyltransfe 38.1 26 0.00056 26.9 2.0 25 85-109 278-302 (552)
174 KOG0717|consensus 37.9 21 0.00045 27.1 1.4 22 88-109 293-314 (508)
175 KOG4727|consensus 37.8 33 0.00072 22.3 2.2 27 54-80 70-96 (193)
176 KOG2923|consensus 37.7 7.8 0.00017 20.7 -0.5 16 116-131 23-38 (67)
177 PTZ00448 hypothetical protein; 37.4 27 0.00059 25.6 1.9 23 59-81 314-336 (373)
178 COG1198 PriA Primosomal protei 37.2 6.1 0.00013 31.6 -1.4 11 60-70 436-446 (730)
179 PLN02748 tRNA dimethylallyltra 37.1 29 0.00063 26.4 2.1 25 57-81 416-441 (468)
180 cd00924 Cyt_c_Oxidase_Vb Cytoc 37.1 18 0.00038 21.2 0.8 24 76-100 69-92 (97)
181 PRK04351 hypothetical protein; 36.5 18 0.00039 22.9 0.8 9 87-95 132-140 (149)
182 PF07975 C1_4: TFIIH C1-like d 36.4 5.2 0.00011 20.4 -1.3 26 57-82 19-44 (51)
183 COG4338 Uncharacterized protei 36.2 12 0.00027 18.8 0.1 12 89-100 14-25 (54)
184 PF10013 DUF2256: Uncharacteri 36.1 24 0.00051 17.2 1.0 15 61-75 10-24 (42)
185 PLN02294 cytochrome c oxidase 35.7 19 0.00041 23.4 0.8 13 58-70 140-152 (174)
186 cd00730 rubredoxin Rubredoxin; 35.1 17 0.00036 18.5 0.4 12 60-71 2-13 (50)
187 PRK03681 hypA hydrogenase nick 35.0 12 0.00027 22.4 -0.0 26 59-95 70-95 (114)
188 PF04780 DUF629: Protein of un 34.9 30 0.00064 26.3 1.9 27 86-112 56-83 (466)
189 KOG2071|consensus 34.4 28 0.00062 27.1 1.7 27 57-83 416-442 (579)
190 KOG2747|consensus 34.3 26 0.00057 26.0 1.5 26 85-110 156-181 (396)
191 PF03811 Zn_Tnp_IS1: InsA N-te 34.1 7 0.00015 18.4 -1.0 7 86-92 28-34 (36)
192 COG1655 Uncharacterized protei 34.1 7.8 0.00017 26.4 -1.1 26 57-82 17-42 (267)
193 PRK03976 rpl37ae 50S ribosomal 34.1 11 0.00024 21.7 -0.3 7 88-94 37-43 (90)
194 PF06220 zf-U1: U1 zinc finger 33.9 32 0.00069 16.2 1.3 11 87-97 3-13 (38)
195 PRK05978 hypothetical protein; 33.4 19 0.0004 22.9 0.5 32 60-100 34-65 (148)
196 PF09845 DUF2072: Zn-ribbon co 33.2 18 0.00038 22.4 0.4 15 87-101 1-15 (131)
197 PF11931 DUF3449: Domain of un 32.9 14 0.00031 24.5 0.0 9 59-67 101-109 (196)
198 KOG2807|consensus 32.3 73 0.0016 23.2 3.3 20 59-78 290-309 (378)
199 COG1327 Predicted transcriptio 31.6 14 0.0003 23.5 -0.2 16 86-101 27-42 (156)
200 PLN03239 histone acetyltransfe 30.8 33 0.00071 25.1 1.5 25 85-109 104-128 (351)
201 COG3677 Transposase and inacti 30.7 27 0.00059 21.5 0.9 16 57-72 51-66 (129)
202 PF07800 DUF1644: Protein of u 30.0 1.6E+02 0.0034 19.1 4.9 56 58-115 79-137 (162)
203 KOG1994|consensus 30.0 37 0.0008 23.2 1.5 22 57-78 237-258 (268)
204 smart00731 SprT SprT homologue 30.0 24 0.00052 22.0 0.6 10 87-96 112-121 (146)
205 COG1571 Predicted DNA-binding 29.9 29 0.00063 26.0 1.1 29 61-100 352-380 (421)
206 KOG1842|consensus 29.6 30 0.00066 26.1 1.1 23 59-81 15-37 (505)
207 COG5112 UFD2 U1-like Zn-finger 29.2 46 0.001 19.8 1.7 26 56-81 52-77 (126)
208 PF04606 Ogr_Delta: Ogr/Delta- 28.7 9 0.0002 19.0 -1.2 16 113-128 23-40 (47)
209 PF04216 FdhE: Protein involve 28.6 13 0.00028 26.1 -0.8 36 87-123 211-246 (290)
210 KOG1280|consensus 28.4 57 0.0012 23.8 2.3 38 86-123 78-117 (381)
211 PRK12387 formate hydrogenlyase 28.2 23 0.00051 23.0 0.4 20 85-104 112-131 (180)
212 KOG1842|consensus 28.0 37 0.0008 25.7 1.4 24 89-112 17-40 (505)
213 KOG3002|consensus 28.0 32 0.00069 24.6 1.0 61 57-121 78-142 (299)
214 PLN03238 probable histone acet 27.9 76 0.0017 22.6 2.8 26 56-81 45-70 (290)
215 PF11672 DUF3268: Protein of u 27.6 26 0.00056 20.7 0.4 10 59-68 2-11 (102)
216 KOG0782|consensus 27.3 18 0.00038 28.3 -0.3 26 74-99 240-265 (1004)
217 PRK00762 hypA hydrogenase nick 26.3 22 0.00048 21.7 -0.0 13 59-72 70-82 (124)
218 PF06397 Desulfoferrod_N: Desu 26.3 31 0.00066 16.2 0.5 12 58-69 5-16 (36)
219 PF05207 zf-CSL: CSL zinc fing 26.2 9.2 0.0002 19.7 -1.4 17 115-131 18-34 (55)
220 PF10537 WAC_Acf1_DNA_bd: ATP- 26.1 1.3E+02 0.0028 17.8 3.2 38 58-96 2-39 (102)
221 PF07503 zf-HYPF: HypF finger; 26.0 5 0.00011 18.7 -2.2 10 88-97 22-31 (35)
222 KOG2461|consensus 25.8 1.2E+02 0.0025 22.8 3.6 56 63-118 335-390 (396)
223 PF11789 zf-Nse: Zinc-finger o 25.4 99 0.0022 16.0 2.4 13 87-99 24-36 (57)
224 PRK03564 formate dehydrogenase 25.2 28 0.00062 24.9 0.4 9 87-95 226-234 (309)
225 COG2879 Uncharacterized small 25.0 95 0.002 16.6 2.2 18 70-87 23-40 (65)
226 COG0675 Transposase and inacti 25.0 40 0.00087 23.7 1.1 15 85-99 320-334 (364)
227 TIGR01562 FdhE formate dehydro 24.6 28 0.00061 24.9 0.3 10 87-96 224-233 (305)
228 PF13824 zf-Mss51: Zinc-finger 24.5 48 0.001 17.2 1.1 12 58-69 13-24 (55)
229 PF08576 DUF1764: Eukaryotic p 24.3 38 0.00083 19.8 0.8 11 111-121 91-101 (102)
230 PF02748 PyrI_C: Aspartate car 24.2 44 0.00096 17.0 0.9 17 55-71 31-47 (52)
231 PF14353 CpXC: CpXC protein 24.1 37 0.0008 20.6 0.7 23 58-80 37-59 (128)
232 COG5151 SSL1 RNA polymerase II 23.8 1E+02 0.0022 22.3 2.8 48 61-110 364-411 (421)
233 PTZ00303 phosphatidylinositol 23.7 45 0.00097 27.4 1.2 33 60-99 461-493 (1374)
234 PTZ00448 hypothetical protein; 23.6 53 0.0011 24.2 1.5 23 87-109 314-336 (373)
235 PF08792 A2L_zn_ribbon: A2L zi 22.9 52 0.0011 15.0 0.9 12 59-70 21-32 (33)
236 PRK04023 DNA polymerase II lar 22.6 68 0.0015 27.1 2.0 10 59-68 626-635 (1121)
237 COG0068 HypF Hydrogenase matur 22.3 13 0.00028 29.7 -1.8 56 61-123 125-181 (750)
238 COG4391 Uncharacterized protei 22.1 53 0.0011 17.5 0.9 14 57-70 46-59 (62)
239 KOG2907|consensus 22.0 36 0.00077 20.5 0.3 11 116-126 103-113 (116)
240 PF01927 Mut7-C: Mut7-C RNAse 21.9 71 0.0015 20.0 1.7 47 60-106 92-143 (147)
241 COG3364 Zn-ribbon containing p 21.7 42 0.00091 19.9 0.6 15 87-101 2-16 (112)
242 TIGR00627 tfb4 transcription f 21.7 61 0.0013 22.9 1.4 12 88-99 256-267 (279)
243 COG5216 Uncharacterized conser 21.6 21 0.00044 18.8 -0.6 16 116-131 23-38 (67)
244 KOG4215|consensus 21.6 39 0.00085 24.9 0.5 18 89-107 38-55 (432)
245 COG5027 SAS2 Histone acetyltra 21.2 59 0.0013 23.9 1.3 25 86-110 157-181 (395)
246 PF06467 zf-FCS: MYM-type Zinc 21.2 16 0.00034 17.4 -1.1 13 60-72 7-19 (43)
247 TIGR00515 accD acetyl-CoA carb 21.1 54 0.0012 23.2 1.1 32 59-99 26-57 (285)
248 PRK12860 transcriptional activ 20.8 49 0.0011 21.9 0.8 30 68-98 116-145 (189)
249 PF13821 DUF4187: Domain of un 20.7 65 0.0014 16.6 1.1 19 59-77 27-45 (55)
250 PF01215 COX5B: Cytochrome c o 20.7 42 0.0009 21.0 0.4 14 58-71 111-124 (136)
251 COG1675 TFA1 Transcription ini 20.6 1.3E+02 0.0028 19.8 2.7 15 85-99 111-125 (176)
252 PRK12722 transcriptional activ 20.6 50 0.0011 21.9 0.8 30 68-98 116-145 (187)
253 PRK11823 DNA repair protein Ra 20.3 82 0.0018 23.8 2.0 25 57-95 5-29 (446)
254 TIGR00416 sms DNA repair prote 20.2 82 0.0018 23.9 2.0 24 58-95 6-29 (454)
No 1
>KOG2462|consensus
Probab=99.85 E-value=8.6e-23 Score=135.80 Aligned_cols=74 Identities=30% Similarity=0.601 Sum_probs=67.9
Q ss_pred ceeccccccccCChHHHHHHHHHcCCCCceecccccccccChhhHHHHHhHhcCCCccccccCCCcccCcccee
Q psy691 59 RFACHLCSKSFSLQRLLNRHMKCHSDVKRYLCTFCGKGFNDTFDLKRHTRTHTGKEEEEEEDGKTNVLTTEYLV 132 (134)
Q Consensus 59 ~~~C~~C~~~f~~~~~l~~H~~~h~~~k~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~c~~~~~~~~~~~~l~ 132 (134)
+++|.+|||.|.+.=.|+.|+|+|+|||||.|..|+|.|..+++|+.||++|.+.|+|.|.-|++.|-...+|.
T Consensus 187 ~c~C~iCGKaFSRPWLLQGHiRTHTGEKPF~C~hC~kAFADRSNLRAHmQTHS~~K~~qC~~C~KsFsl~SyLn 260 (279)
T KOG2462|consen 187 PCECGICGKAFSRPWLLQGHIRTHTGEKPFSCPHCGKAFADRSNLRAHMQTHSDVKKHQCPRCGKSFALKSYLN 260 (279)
T ss_pred CcccccccccccchHHhhcccccccCCCCccCCcccchhcchHHHHHHHHhhcCCccccCcchhhHHHHHHHHH
Confidence 68899999999999999999999999999999999999999999999999999999999998988888777663
No 2
>KOG2462|consensus
Probab=99.77 E-value=1.2e-19 Score=120.90 Aligned_cols=74 Identities=27% Similarity=0.508 Sum_probs=66.4
Q ss_pred CCceeccccccccCChHHHHHHHHHcCCCCceecccccccccChhhHHHHHhHhcCCCccccccCCCcccCcccee
Q psy691 57 NTRFACHLCSKSFSLQRLLNRHMKCHSDVKRYLCTFCGKGFNDTFDLKRHTRTHTGKEEEEEEDGKTNVLTTEYLV 132 (134)
Q Consensus 57 ~~~~~C~~C~~~f~~~~~l~~H~~~h~~~k~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~c~~~~~~~~~~~~l~ 132 (134)
.+.+.|++|+|.|.+-..|+.|+++|+ -+++|.+|||.|.+..-|+-|+|+|||||||.|..|.+.|-.+++|+
T Consensus 159 ~ka~~C~~C~K~YvSmpALkMHirTH~--l~c~C~iCGKaFSRPWLLQGHiRTHTGEKPF~C~hC~kAFADRSNLR 232 (279)
T KOG2462|consen 159 KKAFSCKYCGKVYVSMPALKMHIRTHT--LPCECGICGKAFSRPWLLQGHIRTHTGEKPFSCPHCGKAFADRSNLR 232 (279)
T ss_pred cccccCCCCCceeeehHHHhhHhhccC--CCcccccccccccchHHhhcccccccCCCCccCCcccchhcchHHHH
Confidence 556778888888888888888888886 67999999999999999999999999999999999999999998885
No 3
>KOG3576|consensus
Probab=99.76 E-value=2.4e-19 Score=114.84 Aligned_cols=78 Identities=59% Similarity=0.996 Sum_probs=73.2
Q ss_pred CCCCCceeccccccccCChHHHHHHHHHcCCCCceecccccccccChhhHHHHHhHhcCCCccccccCCCcccCccce
Q psy691 54 RKDNTRFACHLCSKSFSLQRLLNRHMKCHSDVKRYLCTFCGKGFNDTFDLKRHTRTHTGKEEEEEEDGKTNVLTTEYL 131 (134)
Q Consensus 54 ~~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~k~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~c~~~~~~~~~~~~l 131 (134)
......|.|.+|+|.|.....|.+|++-|...+.|.|.+|||.|.....|++|+|+|+|-+||+|..|++.|+.+..|
T Consensus 112 ssd~d~ftCrvCgK~F~lQRmlnrh~kch~~vkr~lct~cgkgfndtfdlkrh~rthtgvrpykc~~c~kaftqrcsl 189 (267)
T KOG3576|consen 112 SSDQDSFTCRVCGKKFGLQRMLNRHLKCHSDVKRHLCTFCGKGFNDTFDLKRHTRTHTGVRPYKCSLCEKAFTQRCSL 189 (267)
T ss_pred CCCCCeeeeehhhhhhhHHHHHHHHhhhccHHHHHHHhhccCcccchhhhhhhhccccCccccchhhhhHHHHhhccH
Confidence 344667999999999999999999999999999999999999999999999999999999999999999999988766
No 4
>KOG3623|consensus
Probab=99.75 E-value=4.5e-19 Score=130.88 Aligned_cols=82 Identities=26% Similarity=0.506 Sum_probs=75.3
Q ss_pred ccCCCCCCCceeccccccccCChHHHHHHHHHcCCCCceecccccccccChhhHHHHHhHhcCCCccccccCCCcccCcc
Q psy691 50 STTGRKDNTRFACHLCSKSFSLQRLLNRHMKCHSDVKRYLCTFCGKGFNDTFDLKRHTRTHTGKEEEEEEDGKTNVLTTE 129 (134)
Q Consensus 50 ~~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~k~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~c~~~~~~~~~~~ 129 (134)
.......+..|.|+.|.|.|.....|.+|..-|+|.+||+|.+|.|.|+.+.+|..|+|.|.|||||.|+.|.++|.++-
T Consensus 885 tk~~kte~gmyaCDqCDK~FqKqSSLaRHKYEHsGqRPyqC~iCkKAFKHKHHLtEHkRLHSGEKPfQCdKClKRFSHSG 964 (1007)
T KOG3623|consen 885 TKHAKTEDGMYACDQCDKAFQKQSSLARHKYEHSGQRPYQCIICKKAFKHKHHLTEHKRLHSGEKPFQCDKCLKRFSHSG 964 (1007)
T ss_pred cccccCccccchHHHHHHHHHhhHHHHHhhhhhcCCCCcccchhhHhhhhhhhhhhhhhhccCCCcchhhhhhhhccccc
Confidence 33456677899999999999999999999999999999999999999999999999999999999999999999998875
Q ss_pred ce
Q psy691 130 YL 131 (134)
Q Consensus 130 ~l 131 (134)
..
T Consensus 965 SY 966 (1007)
T KOG3623|consen 965 SY 966 (1007)
T ss_pred ch
Confidence 43
No 5
>KOG3623|consensus
Probab=99.59 E-value=4.8e-16 Score=115.14 Aligned_cols=76 Identities=33% Similarity=0.630 Sum_probs=68.2
Q ss_pred CCceeccccccccCChHHHHHHHHHcCC-------------CCceecccccccccChhhHHHHHhHhcCCCccccccCCC
Q psy691 57 NTRFACHLCSKSFSLQRLLNRHMKCHSD-------------VKRYLCTFCGKGFNDTFDLKRHTRTHTGKEEEEEEDGKT 123 (134)
Q Consensus 57 ~~~~~C~~C~~~f~~~~~l~~H~~~h~~-------------~k~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~c~~~~~ 123 (134)
..-|.|..|.++|..+..|.+||.+|.. .+.|+|..|+|.|+.+.+|+.|+|+|.|||||.|+-|++
T Consensus 238 e~nfsC~lCsytFAyRtQLErhm~~hkpg~dqa~sltqsa~lRKFKCtECgKAFKfKHHLKEHlRIHSGEKPfeCpnCkK 317 (1007)
T KOG3623|consen 238 EPNFSCMLCSYTFAYRTQLERHMQLHKPGGDQAISLTQSALLRKFKCTECGKAFKFKHHLKEHLRIHSGEKPFECPNCKK 317 (1007)
T ss_pred CCCCcchhhhhhhhhHHHHHHHHHhhcCCCcccccccchhhhccccccccchhhhhHHHHHhhheeecCCCCcCCccccc
Confidence 3458999999999999999999999843 257999999999999999999999999999999999999
Q ss_pred cccCcccee
Q psy691 124 NVLTTEYLV 132 (134)
Q Consensus 124 ~~~~~~~l~ 132 (134)
+|.++-..+
T Consensus 318 RFSHSGSyS 326 (1007)
T KOG3623|consen 318 RFSHSGSYS 326 (1007)
T ss_pred ccccCCccc
Confidence 998876544
No 6
>KOG3576|consensus
Probab=99.39 E-value=7.6e-14 Score=89.78 Aligned_cols=74 Identities=28% Similarity=0.503 Sum_probs=62.8
Q ss_pred CCCCceeccccccccCChHHHHHHHHHcCCCCceecccccccccChhhHHHHHhHhcC-----------CCccccccCCC
Q psy691 55 KDNTRFACHLCSKSFSLQRLLNRHMKCHSDVKRYLCTFCGKGFNDTFDLKRHTRTHTG-----------KEEEEEEDGKT 123 (134)
Q Consensus 55 ~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~k~~~C~~C~~~f~~~~~l~~H~~~h~~-----------~~~~~c~~~~~ 123 (134)
...+.|-|..||+.|.....|++|+|+|+|.+||+|..|+|.|.++-+|..|.+.-+| +|-|.|+.|++
T Consensus 141 ~~vkr~lct~cgkgfndtfdlkrh~rthtgvrpykc~~c~kaftqrcsleshl~kvhgv~~~yaykerr~kl~vcedcg~ 220 (267)
T KOG3576|consen 141 SDVKRHLCTFCGKGFNDTFDLKRHTRTHTGVRPYKCSLCEKAFTQRCSLESHLKKVHGVQHQYAYKERRAKLYVCEDCGY 220 (267)
T ss_pred cHHHHHHHhhccCcccchhhhhhhhccccCccccchhhhhHHHHhhccHHHHHHHHcCchHHHHHHHhhhheeeecccCC
Confidence 4456789999999999999999999999999999999999999999999999775333 35588988887
Q ss_pred cccCc
Q psy691 124 NVLTT 128 (134)
Q Consensus 124 ~~~~~ 128 (134)
.-.+.
T Consensus 221 t~~~~ 225 (267)
T KOG3576|consen 221 TSERP 225 (267)
T ss_pred CCCCh
Confidence 65443
No 7
>PHA02768 hypothetical protein; Provisional
Probab=99.36 E-value=4.5e-13 Score=69.10 Aligned_cols=42 Identities=14% Similarity=0.366 Sum_probs=21.9
Q ss_pred eeccccccccCChHHHHHHHHHcCCCCceecccccccccChhhH
Q psy691 60 FACHLCSKSFSLQRLLNRHMKCHSDVKRYLCTFCGKGFNDTFDL 103 (134)
Q Consensus 60 ~~C~~C~~~f~~~~~l~~H~~~h~~~k~~~C~~C~~~f~~~~~l 103 (134)
|.|++||+.|....+|..|+++|+ ++|+|..|++.|.+.+.|
T Consensus 6 y~C~~CGK~Fs~~~~L~~H~r~H~--k~~kc~~C~k~f~~~s~l 47 (55)
T PHA02768 6 YECPICGEIYIKRKSMITHLRKHN--TNLKLSNCKRISLRTGEY 47 (55)
T ss_pred cCcchhCCeeccHHHHHHHHHhcC--CcccCCcccceeccccee
Confidence 455555555555555555555554 445555555555544443
No 8
>PHA02768 hypothetical protein; Provisional
Probab=99.31 E-value=1.1e-12 Score=67.63 Aligned_cols=46 Identities=22% Similarity=0.369 Sum_probs=42.6
Q ss_pred ceecccccccccChhhHHHHHhHhcCCCccccccCCCcccCccceeeC
Q psy691 87 RYLCTFCGKGFNDTFDLKRHTRTHTGKEEEEEEDGKTNVLTTEYLVVV 134 (134)
Q Consensus 87 ~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~c~~~~~~~~~~~~l~~~ 134 (134)
-|.|+.||+.|.+.++|..|+++|+ ++|+|..|++.|...+.|++|
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 4899999999999999999999998 799999999999999988864
No 9
>KOG1074|consensus
Probab=99.22 E-value=9.8e-12 Score=93.84 Aligned_cols=74 Identities=22% Similarity=0.432 Sum_probs=64.7
Q ss_pred CCCCceeccccccccCChHHHHHHHHHcCCCCceecccccccccChhhHHHHHhHhcCCC----ccccc---cCCCcccC
Q psy691 55 KDNTRFACHLCSKSFSLQRLLNRHMKCHSDVKRYLCTFCGKGFNDTFDLKRHTRTHTGKE----EEEEE---DGKTNVLT 127 (134)
Q Consensus 55 ~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~k~~~C~~C~~~f~~~~~l~~H~~~h~~~~----~~~c~---~~~~~~~~ 127 (134)
+...+..|.+|.+...-+..|+.|.|+|+|+|||+|.+|++.|.++.+|+.|+-+|-..- ++.|+ .|-.-|.+
T Consensus 601 ~~TdPNqCiiC~rVlSC~saLqmHyrtHtGERPFkCKiCgRAFtTkGNLkaH~~vHka~p~~R~q~ScP~~~ic~~kftn 680 (958)
T KOG1074|consen 601 KRTDPNQCIICLRVLSCPSALQMHYRTHTGERPFKCKICGRAFTTKGNLKAHMSVHKAKPPARVQFSCPSTFICQKKFTN 680 (958)
T ss_pred ccCCccceeeeeecccchhhhhhhhhcccCcCccccccccchhccccchhhcccccccCccccccccCCchhhhcccccc
Confidence 344568999999999999999999999999999999999999999999999999997653 47787 77777765
Q ss_pred c
Q psy691 128 T 128 (134)
Q Consensus 128 ~ 128 (134)
.
T Consensus 681 ~ 681 (958)
T KOG1074|consen 681 A 681 (958)
T ss_pred c
Confidence 4
No 10
>KOG3608|consensus
Probab=99.19 E-value=4.7e-12 Score=87.60 Aligned_cols=75 Identities=24% Similarity=0.484 Sum_probs=63.8
Q ss_pred CCCceeccccccccCChHHHHHHHHHcCCCCceecccccccccChhhHHHHHhH-hcCCCccccccCCCcccCcccee
Q psy691 56 DNTRFACHLCSKSFSLQRLLNRHMKCHSDVKRYLCTFCGKGFNDTFDLKRHTRT-HTGKEEEEEEDGKTNVLTTEYLV 132 (134)
Q Consensus 56 ~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~k~~~C~~C~~~f~~~~~l~~H~~~-h~~~~~~~c~~~~~~~~~~~~l~ 132 (134)
..++|.|..|.|.|.....|..|+..|. .-|+|+.|+......+.|.+|++. |..+|||+|++|.+.|++-..|.
T Consensus 234 ~~n~fqC~~C~KrFaTeklL~~Hv~rHv--n~ykCplCdmtc~~~ssL~~H~r~rHs~dkpfKCd~Cd~~c~~esdL~ 309 (467)
T KOG3608|consen 234 NTNSFQCAQCFKRFATEKLLKSHVVRHV--NCYKCPLCDMTCSSASSLTTHIRYRHSKDKPFKCDECDTRCVRESDLA 309 (467)
T ss_pred cCCchHHHHHHHHHhHHHHHHHHHHHhh--hcccccccccCCCChHHHHHHHHhhhccCCCccccchhhhhccHHHHH
Confidence 3457888888888888888888888885 448999999999999999999997 88899999999999998876653
No 11
>KOG1074|consensus
Probab=99.18 E-value=1.1e-11 Score=93.57 Aligned_cols=57 Identities=28% Similarity=0.640 Sum_probs=52.5
Q ss_pred CceeccccccccCChHHHHHHHHHcCCCCceecccccccccChhhHHHHHhHhcCCC
Q psy691 58 TRFACHLCSKSFSLQRLLNRHMKCHSDVKRYLCTFCGKGFNDTFDLKRHTRTHTGKE 114 (134)
Q Consensus 58 ~~~~C~~C~~~f~~~~~l~~H~~~h~~~k~~~C~~C~~~f~~~~~l~~H~~~h~~~~ 114 (134)
-+++|.+|.|.|.....|+.|.|+|+|++||+|.+||.+|.++.+|+.|...|+.+-
T Consensus 352 ~khkCr~CakvfgS~SaLqiHlRSHTGERPfqCnvCG~~FSTkGNLKvH~~rH~e~~ 408 (958)
T KOG1074|consen 352 FKHKCRFCAKVFGSDSALQIHLRSHTGERPFQCNVCGNRFSTKGNLKVHFQRHREKY 408 (958)
T ss_pred ccchhhhhHhhcCchhhhhhhhhccCCCCCeeecccccccccccceeeeeeeccccC
Confidence 357899999999999999999999999999999999999999999999988776543
No 12
>PHA00733 hypothetical protein
Probab=99.06 E-value=5.8e-11 Score=72.81 Aligned_cols=75 Identities=17% Similarity=0.283 Sum_probs=50.3
Q ss_pred CCCCceeccccccccCChHHHHHH--HH---HcCCCCceecccccccccChhhHHHHHhHhcCCCccccccCCCcccCcc
Q psy691 55 KDNTRFACHLCSKSFSLQRLLNRH--MK---CHSDVKRYLCTFCGKGFNDTFDLKRHTRTHTGKEEEEEEDGKTNVLTTE 129 (134)
Q Consensus 55 ~~~~~~~C~~C~~~f~~~~~l~~H--~~---~h~~~k~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~c~~~~~~~~~~~ 129 (134)
..++++.|.+|.+.|.....|..+ +. .+.+.+||.|..|++.|.....|..|++.| +.+|.|..|++.|.+..
T Consensus 36 ~~~~~~~~~~~~~~~~~~~~l~~~~~l~~~~~~~~~kPy~C~~Cgk~Fss~s~L~~H~r~h--~~~~~C~~CgK~F~~~~ 113 (128)
T PHA00733 36 PEQKRLIRAVVKTLIYNPQLLDESSYLYKLLTSKAVSPYVCPLCLMPFSSSVSLKQHIRYT--EHSKVCPVCGKEFRNTD 113 (128)
T ss_pred hhhhhHHHHHHhhhccChhhhcchHHHHhhcccCCCCCccCCCCCCcCCCHHHHHHHHhcC--CcCccCCCCCCccCCHH
Confidence 345567777777777766665554 11 233466788888888888888887777765 34677777777777665
Q ss_pred ce
Q psy691 130 YL 131 (134)
Q Consensus 130 ~l 131 (134)
.|
T Consensus 114 sL 115 (128)
T PHA00733 114 ST 115 (128)
T ss_pred HH
Confidence 54
No 13
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=99.05 E-value=1.5e-10 Score=51.39 Aligned_cols=25 Identities=48% Similarity=1.046 Sum_probs=15.6
Q ss_pred HHHHHHHHcCCCCceeccccccccc
Q psy691 74 LLNRHMKCHSDVKRYLCTFCGKGFN 98 (134)
Q Consensus 74 ~l~~H~~~h~~~k~~~C~~C~~~f~ 98 (134)
+|.+|+++|++++||.|+.|++.|.
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 3556666666666666666666664
No 14
>PHA00733 hypothetical protein
Probab=98.99 E-value=7.1e-10 Score=68.01 Aligned_cols=56 Identities=27% Similarity=0.527 Sum_probs=50.4
Q ss_pred CCCCceeccccccccCChHHHHHHHHHcCCCCceecccccccccChhhHHHHHhHhcC
Q psy691 55 KDNTRFACHLCSKSFSLQRLLNRHMKCHSDVKRYLCTFCGKGFNDTFDLKRHTRTHTG 112 (134)
Q Consensus 55 ~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~k~~~C~~C~~~f~~~~~l~~H~~~h~~ 112 (134)
...++|.|+.|++.|.....|..|++.| ..+|.|..|++.|.....|.+|+...++
T Consensus 69 ~~~kPy~C~~Cgk~Fss~s~L~~H~r~h--~~~~~C~~CgK~F~~~~sL~~H~~~~h~ 124 (128)
T PHA00733 69 KAVSPYVCPLCLMPFSSSVSLKQHIRYT--EHSKVCPVCGKEFRNTDSTLDHVCKKHN 124 (128)
T ss_pred CCCCCccCCCCCCcCCCHHHHHHHHhcC--CcCccCCCCCCccCCHHHHHHHHHHhcC
Confidence 3467899999999999999999999987 4579999999999999999999988765
No 15
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=98.98 E-value=3e-10 Score=50.42 Aligned_cols=26 Identities=31% Similarity=0.409 Sum_probs=23.6
Q ss_pred hHHHHHhHhcCCCccccccCCCcccC
Q psy691 102 DLKRHTRTHTGKEEEEEEDGKTNVLT 127 (134)
Q Consensus 102 ~l~~H~~~h~~~~~~~c~~~~~~~~~ 127 (134)
+|.+|+++|+|++||.|+.|++.|.+
T Consensus 1 ~l~~H~~~H~~~k~~~C~~C~k~F~~ 26 (26)
T PF13465_consen 1 NLRRHMRTHTGEKPYKCPYCGKSFSN 26 (26)
T ss_dssp HHHHHHHHHSSSSSEEESSSSEEESS
T ss_pred CHHHHhhhcCCCCCCCCCCCcCeeCc
Confidence 58899999999999999999998864
No 16
>KOG3608|consensus
Probab=98.93 E-value=6e-10 Score=77.39 Aligned_cols=79 Identities=18% Similarity=0.293 Sum_probs=66.1
Q ss_pred CCCCCCceeccccccccCChHHHHHHHHHcCCCCceeccc--ccccccChhhHHHHHhHhc-CCC--ccccccCCCcccC
Q psy691 53 GRKDNTRFACHLCSKSFSLQRLLNRHMKCHSDVKRYLCTF--CGKGFNDTFDLKRHTRTHT-GKE--EEEEEDGKTNVLT 127 (134)
Q Consensus 53 ~~~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~k~~~C~~--C~~~f~~~~~l~~H~~~h~-~~~--~~~c~~~~~~~~~ 127 (134)
.+..+++|+|+.|.+.+.+...|.+|...|. +..|.|.. |..+|.+...+.+|++-++ |.. +|.|-+|+++|++
T Consensus 286 rHs~dkpfKCd~Cd~~c~~esdL~kH~~~HS-~~~y~C~h~~C~~s~r~~~q~~~H~~evhEg~np~~Y~CH~Cdr~ft~ 364 (467)
T KOG3608|consen 286 RHSKDKPFKCDECDTRCVRESDLAKHVQVHS-KTVYQCEHPDCHYSVRTYTQMRRHFLEVHEGNNPILYACHCCDRFFTS 364 (467)
T ss_pred hhccCCCccccchhhhhccHHHHHHHHHhcc-ccceecCCCCCcHHHHHHHHHHHHHHHhccCCCCCceeeecchhhhcc
Confidence 3445788999999999999999999999887 66799988 9999999999999988744 654 5999999999999
Q ss_pred cccee
Q psy691 128 TEYLV 132 (134)
Q Consensus 128 ~~~l~ 132 (134)
-..|.
T Consensus 365 G~~L~ 369 (467)
T KOG3608|consen 365 GKSLS 369 (467)
T ss_pred chhHH
Confidence 87764
No 17
>PHA00616 hypothetical protein
Probab=98.89 E-value=7.6e-10 Score=54.52 Aligned_cols=32 Identities=13% Similarity=0.324 Sum_probs=15.6
Q ss_pred eeccccccccCChHHHHHHHHHcCCCCceecc
Q psy691 60 FACHLCSKSFSLQRLLNRHMKCHSDVKRYLCT 91 (134)
Q Consensus 60 ~~C~~C~~~f~~~~~l~~H~~~h~~~k~~~C~ 91 (134)
|.|..||+.|..+..|..|++.|++++++.|+
T Consensus 2 YqC~~CG~~F~~~s~l~~H~r~~hg~~~~~~~ 33 (44)
T PHA00616 2 YQCLRCGGIFRKKKEVIEHLLSVHKQNKLTLE 33 (44)
T ss_pred CccchhhHHHhhHHHHHHHHHHhcCCCcccee
Confidence 44444554444444444444444444444444
No 18
>PLN03086 PRLI-interacting factor K; Provisional
Probab=98.84 E-value=4.4e-09 Score=78.08 Aligned_cols=67 Identities=18% Similarity=0.332 Sum_probs=54.8
Q ss_pred CCCCceeccccccccCChHHHHHHHHHcCCCCceecccccccccChhhHHHHHhHhcCCCccccccCCCccc
Q psy691 55 KDNTRFACHLCSKSFSLQRLLNRHMKCHSDVKRYLCTFCGKGFNDTFDLKRHTRTHTGKEEEEEEDGKTNVL 126 (134)
Q Consensus 55 ~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~k~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~c~~~~~~~~ 126 (134)
..++.+.|+.|++.|. ...|..|+..|+ +++.|. |++.+ .+..|..|+.+|..++++.|..|+..|.
T Consensus 449 el~~H~~C~~Cgk~f~-~s~LekH~~~~H--kpv~Cp-Cg~~~-~R~~L~~H~~thCp~Kpi~C~fC~~~v~ 515 (567)
T PLN03086 449 EAKNHVHCEKCGQAFQ-QGEMEKHMKVFH--EPLQCP-CGVVL-EKEQMVQHQASTCPLRLITCRFCGDMVQ 515 (567)
T ss_pred ccccCccCCCCCCccc-hHHHHHHHHhcC--CCccCC-CCCCc-chhHHHhhhhccCCCCceeCCCCCCccc
Confidence 3455678999999986 677899999875 789998 98755 6688999998999999999998888774
No 19
>PHA00616 hypothetical protein
Probab=98.81 E-value=2.2e-09 Score=52.86 Aligned_cols=33 Identities=21% Similarity=0.340 Sum_probs=31.7
Q ss_pred ceecccccccccChhhHHHHHhHhcCCCccccc
Q psy691 87 RYLCTFCGKGFNDTFDLKRHTRTHTGKEEEEEE 119 (134)
Q Consensus 87 ~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~c~ 119 (134)
||+|..||+.|.....|.+|++.|+|++++.|+
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~~hg~~~~~~~ 33 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLSVHKQNKLTLE 33 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHHhcCCCcccee
Confidence 689999999999999999999999999999986
No 20
>PHA00732 hypothetical protein
Probab=98.70 E-value=1.3e-08 Score=57.17 Aligned_cols=48 Identities=23% Similarity=0.505 Sum_probs=40.2
Q ss_pred ceeccccccccCChHHHHHHHHH-cCCCCceecccccccccChhhHHHHHhHhcC
Q psy691 59 RFACHLCSKSFSLQRLLNRHMKC-HSDVKRYLCTFCGKGFNDTFDLKRHTRTHTG 112 (134)
Q Consensus 59 ~~~C~~C~~~f~~~~~l~~H~~~-h~~~k~~~C~~C~~~f~~~~~l~~H~~~h~~ 112 (134)
+|.|..|++.|.....|..|++. |. ++.|..|++.|. .+..|.+++..
T Consensus 1 py~C~~Cgk~F~s~s~Lk~H~r~~H~---~~~C~~CgKsF~---~l~~H~~~~~~ 49 (79)
T PHA00732 1 MFKCPICGFTTVTLFALKQHARRNHT---LTKCPVCNKSYR---RLNQHFYSQYD 49 (79)
T ss_pred CccCCCCCCccCCHHHHHHHhhcccC---CCccCCCCCEeC---ChhhhhcccCC
Confidence 58899999999999999999985 65 358999999998 58888866543
No 21
>PLN03086 PRLI-interacting factor K; Provisional
Probab=98.68 E-value=2.2e-08 Score=74.46 Aligned_cols=69 Identities=16% Similarity=0.366 Sum_probs=59.3
Q ss_pred CceeccccccccCChHHHHHHHHHcCCCCceecccccccccC----------hhhHHHHHhHhcCCCccccccCCCcccC
Q psy691 58 TRFACHLCSKSFSLQRLLNRHMKCHSDVKRYLCTFCGKGFND----------TFDLKRHTRTHTGKEEEEEEDGKTNVLT 127 (134)
Q Consensus 58 ~~~~C~~C~~~f~~~~~l~~H~~~h~~~k~~~C~~C~~~f~~----------~~~l~~H~~~h~~~~~~~c~~~~~~~~~ 127 (134)
.++.|+ |++.+ .+..|..|+..|...+++.|.+|++.|.. ...|..|...+ |.+++.|..|++.|.-
T Consensus 477 kpv~Cp-Cg~~~-~R~~L~~H~~thCp~Kpi~C~fC~~~v~~g~~~~d~~d~~s~Lt~HE~~C-G~rt~~C~~Cgk~Vrl 553 (567)
T PLN03086 477 EPLQCP-CGVVL-EKEQMVQHQASTCPLRLITCRFCGDMVQAGGSAMDVRDRLRGMSEHESIC-GSRTAPCDSCGRSVML 553 (567)
T ss_pred CCccCC-CCCCc-chhHHHhhhhccCCCCceeCCCCCCccccCccccchhhhhhhHHHHHHhc-CCcceEccccCCeeee
Confidence 578999 99766 56899999999999999999999999852 35899999885 9999999988888876
Q ss_pred cc
Q psy691 128 TE 129 (134)
Q Consensus 128 ~~ 129 (134)
++
T Consensus 554 rd 555 (567)
T PLN03086 554 KE 555 (567)
T ss_pred hh
Confidence 65
No 22
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=98.50 E-value=2.7e-07 Score=48.16 Aligned_cols=51 Identities=25% Similarity=0.501 Sum_probs=40.7
Q ss_pred ceeccccccccCChHHHHHHHHH-cCCC-CceecccccccccChhhHHHHHhHhcC
Q psy691 59 RFACHLCSKSFSLQRLLNRHMKC-HSDV-KRYLCTFCGKGFNDTFDLKRHTRTHTG 112 (134)
Q Consensus 59 ~~~C~~C~~~f~~~~~l~~H~~~-h~~~-k~~~C~~C~~~f~~~~~l~~H~~~h~~ 112 (134)
.|.|++|++. .+...|..|... |..+ +.+.|++|...+. .+|..|+..+++
T Consensus 2 ~f~CP~C~~~-~~~~~L~~H~~~~H~~~~~~v~CPiC~~~~~--~~l~~Hl~~~H~ 54 (54)
T PF05605_consen 2 SFTCPYCGKG-FSESSLVEHCEDEHRSESKNVVCPICSSRVT--DNLIRHLNSQHR 54 (54)
T ss_pred CcCCCCCCCc-cCHHHHHHHHHhHCcCCCCCccCCCchhhhh--hHHHHHHHHhcC
Confidence 5899999995 557889999876 6654 5799999998655 489999988654
No 23
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=98.37 E-value=4.1e-07 Score=62.76 Aligned_cols=54 Identities=31% Similarity=0.630 Sum_probs=46.3
Q ss_pred CCCceeccc--cccccCChHHHHHHHHH-cC------------------CCCceecccccccccChhhHHHHHhH
Q psy691 56 DNTRFACHL--CSKSFSLQRLLNRHMKC-HS------------------DVKRYLCTFCGKGFNDTFDLKRHTRT 109 (134)
Q Consensus 56 ~~~~~~C~~--C~~~f~~~~~l~~H~~~-h~------------------~~k~~~C~~C~~~f~~~~~l~~H~~~ 109 (134)
..++|+|++ |.|.++....|+.|+.- |- ..|||.|++|+|+++....|+.|+..
T Consensus 346 d~KpykCpV~gC~K~YknqnGLKYH~lhGH~~~~~~~~p~p~~~~~F~~~~KPYrCevC~KRYKNlNGLKYHr~H 420 (423)
T COG5189 346 DGKPYKCPVEGCNKKYKNQNGLKYHMLHGHQNQKLHENPSPEKMNIFSAKDKPYRCEVCDKRYKNLNGLKYHRKH 420 (423)
T ss_pred cCceecCCCCCchhhhccccchhhhhhccccCcccCCCCCccccccccccCCceeccccchhhccCccceecccc
Confidence 358999998 99999999999999874 41 13899999999999999999998764
No 24
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=98.34 E-value=4.4e-07 Score=38.84 Aligned_cols=22 Identities=45% Similarity=0.922 Sum_probs=12.0
Q ss_pred eeccccccccCChHHHHHHHHH
Q psy691 60 FACHLCSKSFSLQRLLNRHMKC 81 (134)
Q Consensus 60 ~~C~~C~~~f~~~~~l~~H~~~ 81 (134)
|.|++|++.|.....|..|++.
T Consensus 1 y~C~~C~~~f~~~~~l~~H~~~ 22 (23)
T PF00096_consen 1 YKCPICGKSFSSKSNLKRHMRR 22 (23)
T ss_dssp EEETTTTEEESSHHHHHHHHHH
T ss_pred CCCCCCCCccCCHHHHHHHHhH
Confidence 4455555555555555555554
No 25
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=98.29 E-value=5.5e-07 Score=38.52 Aligned_cols=23 Identities=52% Similarity=1.096 Sum_probs=21.6
Q ss_pred eecccccccccChhhHHHHHhHh
Q psy691 88 YLCTFCGKGFNDTFDLKRHTRTH 110 (134)
Q Consensus 88 ~~C~~C~~~f~~~~~l~~H~~~h 110 (134)
|.|..|++.|.....|.+|++.|
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 78999999999999999999875
No 26
>KOG3993|consensus
Probab=98.28 E-value=3.9e-07 Score=64.97 Aligned_cols=53 Identities=32% Similarity=0.600 Sum_probs=46.6
Q ss_pred eeccccccccCChHHHHHHHHHcCC--------C-------------------------CceecccccccccChhhHHHH
Q psy691 60 FACHLCSKSFSLQRLLNRHMKCHSD--------V-------------------------KRYLCTFCGKGFNDTFDLKRH 106 (134)
Q Consensus 60 ~~C~~C~~~f~~~~~l~~H~~~h~~--------~-------------------------k~~~C~~C~~~f~~~~~l~~H 106 (134)
|+|++|+|.|.-..||..|.|.|-- . -.|.|..|+|.|.+...|+.|
T Consensus 296 YrCPEC~KVFsCPANLASHRRWHKPR~eaa~a~~~P~k~~~~~rae~~ea~rsg~dss~gi~~C~~C~KkFrRqAYLrKH 375 (500)
T KOG3993|consen 296 YRCPECDKVFSCPANLASHRRWHKPRPEAAKAGSPPPKQAVETRAEVQEAERSGDDSSSGIFSCHTCGKKFRRQAYLRKH 375 (500)
T ss_pred ecCCcccccccCchhhhhhhcccCCchhhhhcCCCChhhhhhhhhhhhhccccCCcccCceeecHHhhhhhHHHHHHHHh
Confidence 8999999999999999999999821 1 148999999999999999999
Q ss_pred HhHhcC
Q psy691 107 TRTHTG 112 (134)
Q Consensus 107 ~~~h~~ 112 (134)
+-+|+.
T Consensus 376 qlthq~ 381 (500)
T KOG3993|consen 376 QLTHQR 381 (500)
T ss_pred HHhhhc
Confidence 888764
No 27
>PHA00732 hypothetical protein
Probab=98.23 E-value=7.8e-07 Score=49.95 Aligned_cols=39 Identities=26% Similarity=0.362 Sum_probs=33.3
Q ss_pred ceecccccccccChhhHHHHHhH-hcCCCccccccCCCcccCc
Q psy691 87 RYLCTFCGKGFNDTFDLKRHTRT-HTGKEEEEEEDGKTNVLTT 128 (134)
Q Consensus 87 ~~~C~~C~~~f~~~~~l~~H~~~-h~~~~~~~c~~~~~~~~~~ 128 (134)
||.|..|++.|.....|..|++. |++ +.|+.|++.|.+.
T Consensus 1 py~C~~Cgk~F~s~s~Lk~H~r~~H~~---~~C~~CgKsF~~l 40 (79)
T PHA00732 1 MFKCPICGFTTVTLFALKQHARRNHTL---TKCPVCNKSYRRL 40 (79)
T ss_pred CccCCCCCCccCCHHHHHHHhhcccCC---CccCCCCCEeCCh
Confidence 58999999999999999999985 653 5899898888753
No 28
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=98.03 E-value=3.3e-06 Score=37.51 Aligned_cols=25 Identities=36% Similarity=0.775 Sum_probs=14.7
Q ss_pred ceecccccccccChhhHHHHHhHhc
Q psy691 87 RYLCTFCGKGFNDTFDLKRHTRTHT 111 (134)
Q Consensus 87 ~~~C~~C~~~f~~~~~l~~H~~~h~ 111 (134)
+|.|..|++.|.....|..|++.|.
T Consensus 1 ~~~C~~C~~~F~~~~~l~~H~~~h~ 25 (27)
T PF13912_consen 1 PFECDECGKTFSSLSALREHKRSHC 25 (27)
T ss_dssp SEEETTTTEEESSHHHHHHHHCTTT
T ss_pred CCCCCccCCccCChhHHHHHhHHhc
Confidence 3556666666666666666665553
No 29
>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=97.99 E-value=5.8e-06 Score=35.36 Aligned_cols=22 Identities=41% Similarity=0.890 Sum_probs=10.4
Q ss_pred eeccccccccCChHHHHHHHHH
Q psy691 60 FACHLCSKSFSLQRLLNRHMKC 81 (134)
Q Consensus 60 ~~C~~C~~~f~~~~~l~~H~~~ 81 (134)
|.|++|++.|.....|..|++.
T Consensus 1 ~~C~~C~~~~~~~~~l~~H~~~ 22 (24)
T PF13894_consen 1 FQCPICGKSFRSKSELRQHMRT 22 (24)
T ss_dssp EE-SSTS-EESSHHHHHHHHHH
T ss_pred CCCcCCCCcCCcHHHHHHHHHh
Confidence 3455555555555555555544
No 30
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=97.97 E-value=8.5e-06 Score=34.82 Aligned_cols=24 Identities=42% Similarity=1.000 Sum_probs=20.3
Q ss_pred eecccccccccChhhHHHHHhHhc
Q psy691 88 YLCTFCGKGFNDTFDLKRHTRTHT 111 (134)
Q Consensus 88 ~~C~~C~~~f~~~~~l~~H~~~h~ 111 (134)
|.|.+|++.|.....|..|++.|+
T Consensus 1 ~~C~~C~~~~~~~~~l~~H~~~~H 24 (24)
T PF13894_consen 1 FQCPICGKSFRSKSELRQHMRTHH 24 (24)
T ss_dssp EE-SSTS-EESSHHHHHHHHHHHS
T ss_pred CCCcCCCCcCCcHHHHHHHHHhhC
Confidence 689999999999999999999874
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=97.89 E-value=9.4e-06 Score=35.99 Aligned_cols=25 Identities=36% Similarity=0.721 Sum_probs=23.1
Q ss_pred ceeccccccccCChHHHHHHHHHcC
Q psy691 59 RFACHLCSKSFSLQRLLNRHMKCHS 83 (134)
Q Consensus 59 ~~~C~~C~~~f~~~~~l~~H~~~h~ 83 (134)
+|.|..|++.|.....|..|++.|.
T Consensus 1 ~~~C~~C~~~F~~~~~l~~H~~~h~ 25 (27)
T PF13912_consen 1 PFECDECGKTFSSLSALREHKRSHC 25 (27)
T ss_dssp SEEETTTTEEESSHHHHHHHHCTTT
T ss_pred CCCCCccCCccCChhHHHHHhHHhc
Confidence 5899999999999999999998875
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=97.81 E-value=4.7e-05 Score=38.48 Aligned_cols=30 Identities=23% Similarity=0.428 Sum_probs=14.2
Q ss_pred CCceeccccccccCChHHHHHHHHHcCCCC
Q psy691 57 NTRFACHLCSKSFSLQRLLNRHMKCHSDVK 86 (134)
Q Consensus 57 ~~~~~C~~C~~~f~~~~~l~~H~~~h~~~k 86 (134)
+.+..|++|+..+....+|++|+..+++.|
T Consensus 22 ~~PatCP~C~a~~~~srnLrRHle~~H~~k 51 (54)
T PF09237_consen 22 EQPATCPICGAVIRQSRNLRRHLEIRHFKK 51 (54)
T ss_dssp S--EE-TTT--EESSHHHHHHHHHHHTTTS
T ss_pred CCCCCCCcchhhccchhhHHHHHHHHhccc
Confidence 344556666666666666666665544444
No 33
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=97.79 E-value=1.7e-05 Score=46.21 Aligned_cols=50 Identities=32% Similarity=0.654 Sum_probs=21.5
Q ss_pred eccccccccCChHHHHHHHHHcCCC-----------------------CceecccccccccChhhHHHHHhHh
Q psy691 61 ACHLCSKSFSLQRLLNRHMKCHSDV-----------------------KRYLCTFCGKGFNDTFDLKRHTRTH 110 (134)
Q Consensus 61 ~C~~C~~~f~~~~~l~~H~~~h~~~-----------------------k~~~C~~C~~~f~~~~~l~~H~~~h 110 (134)
.|.+|+..|.....|..|+...++. ..+.|.+|++.|.....|..|++.+
T Consensus 1 ~C~~C~~~f~~~~~l~~H~~~~H~~~~~~~~~l~~~~~~~~~~~~~~~~~~~C~~C~~~f~s~~~l~~Hm~~~ 73 (100)
T PF12756_consen 1 QCLFCDESFSSVDDLLQHMKKKHGFDIPDQKYLVDPNRLLNYLRKKVKESFRCPYCNKTFRSREALQEHMRSK 73 (100)
T ss_dssp ------------------------------------------------SSEEBSSSS-EESSHHHHHHHHHHT
T ss_pred CccccccccccccccccccccccccccccccccccccccccccccccCCCCCCCccCCCCcCHHHHHHHHcCc
Confidence 4889999999999999998753221 2489999999999999999999974
No 34
>KOG3993|consensus
Probab=97.75 E-value=2.1e-06 Score=61.36 Aligned_cols=73 Identities=22% Similarity=0.306 Sum_probs=60.3
Q ss_pred eeccccccccCChHHHHHHHHHcCCCCceecccccccccChhhHHHHHhHhcC--------C------------------
Q psy691 60 FACHLCSKSFSLQRLLNRHMKCHSDVKRYLCTFCGKGFNDTFDLKRHTRTHTG--------K------------------ 113 (134)
Q Consensus 60 ~~C~~C~~~f~~~~~l~~H~~~h~~~k~~~C~~C~~~f~~~~~l~~H~~~h~~--------~------------------ 113 (134)
|.|..|-..|.....|.+|.....-..-|+|..|+|.|.-..+|..|+|.|-- .
T Consensus 268 yiCqLCK~kYeD~F~LAQHrC~RIV~vEYrCPEC~KVFsCPANLASHRRWHKPR~eaa~a~~~P~k~~~~~rae~~ea~r 347 (500)
T KOG3993|consen 268 YICQLCKEKYEDAFALAQHRCPRIVHVEYRCPECDKVFSCPANLASHRRWHKPRPEAAKAGSPPPKQAVETRAEVQEAER 347 (500)
T ss_pred HHHHHHHHhhhhHHHHhhccCCeeEEeeecCCcccccccCchhhhhhhcccCCchhhhhcCCCChhhhhhhhhhhhhccc
Confidence 89999999999999999998654444569999999999999999999987741 1
Q ss_pred -------CccccccCCCcccCcccee
Q psy691 114 -------EEEEEEDGKTNVLTTEYLV 132 (134)
Q Consensus 114 -------~~~~c~~~~~~~~~~~~l~ 132 (134)
--|.|..|.+.|.+..+|.
T Consensus 348 sg~dss~gi~~C~~C~KkFrRqAYLr 373 (500)
T KOG3993|consen 348 SGDDSSSGIFSCHTCGKKFRRQAYLR 373 (500)
T ss_pred cCCcccCceeecHHhhhhhHHHHHHH
Confidence 1278988888888887764
No 35
>PRK04860 hypothetical protein; Provisional
Probab=97.72 E-value=2.1e-05 Score=50.02 Aligned_cols=38 Identities=18% Similarity=0.423 Sum_probs=24.3
Q ss_pred ceecccccccccChhhHHHHHhHhcCCCccccccCCCcccCc
Q psy691 87 RYLCTFCGKGFNDTFDLKRHTRTHTGKEEEEEEDGKTNVLTT 128 (134)
Q Consensus 87 ~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~c~~~~~~~~~~ 128 (134)
+|.|. |++ ....+.+|.++|+++++|.|..|+..|...
T Consensus 119 ~Y~C~-C~~---~~~~~rrH~ri~~g~~~YrC~~C~~~l~~~ 156 (160)
T PRK04860 119 PYRCK-CQE---HQLTVRRHNRVVRGEAVYRCRRCGETLVFK 156 (160)
T ss_pred EEEcC-CCC---eeCHHHHHHHHhcCCccEECCCCCceeEEe
Confidence 46666 665 455666777777777777776666665543
No 36
>PF09237 GAGA: GAGA factor; InterPro: IPR015318 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Members of this entry bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognises the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognises the A in the fourth position of the consensus sequence []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1YUI_A 1YUJ_A.
Probab=97.70 E-value=4.6e-05 Score=38.53 Aligned_cols=39 Identities=21% Similarity=0.382 Sum_probs=25.8
Q ss_pred HHHHH-cCCCCceecccccccccChhhHHHHHhHhcCCCc
Q psy691 77 RHMKC-HSDVKRYLCTFCGKGFNDTFDLKRHTRTHTGKEE 115 (134)
Q Consensus 77 ~H~~~-h~~~k~~~C~~C~~~f~~~~~l~~H~~~h~~~~~ 115 (134)
.+.+. +..+.|..|++|+..+.+..+|++|+.++++.||
T Consensus 13 ~~~k~~~~S~~PatCP~C~a~~~~srnLrRHle~~H~~k~ 52 (54)
T PF09237_consen 13 KKPKSKSQSEQPATCPICGAVIRQSRNLRRHLEIRHFKKP 52 (54)
T ss_dssp ---CCCCTTS--EE-TTT--EESSHHHHHHHHHHHTTTS-
T ss_pred hHHHHhhccCCCCCCCcchhhccchhhHHHHHHHHhcccC
Confidence 34433 3457899999999999999999999999888776
No 37
>PRK04860 hypothetical protein; Provisional
Probab=97.48 E-value=6.7e-05 Score=47.77 Aligned_cols=40 Identities=23% Similarity=0.440 Sum_probs=34.7
Q ss_pred CceeccccccccCChHHHHHHHHHcCCCCceecccccccccChh
Q psy691 58 TRFACHLCSKSFSLQRLLNRHMKCHSDVKRYLCTFCGKGFNDTF 101 (134)
Q Consensus 58 ~~~~C~~C~~~f~~~~~l~~H~~~h~~~k~~~C~~C~~~f~~~~ 101 (134)
-+|.|. |++ ....+.+|.++|.++++|.|..|+..|....
T Consensus 118 ~~Y~C~-C~~---~~~~~rrH~ri~~g~~~YrC~~C~~~l~~~~ 157 (160)
T PRK04860 118 FPYRCK-CQE---HQLTVRRHNRVVRGEAVYRCRRCGETLVFKG 157 (160)
T ss_pred EEEEcC-CCC---eeCHHHHHHHHhcCCccEECCCCCceeEEec
Confidence 479998 997 5678899999999999999999999887643
No 38
>smart00355 ZnF_C2H2 zinc finger.
Probab=97.48 E-value=9.3e-05 Score=31.93 Aligned_cols=22 Identities=36% Similarity=0.756 Sum_probs=11.0
Q ss_pred eccccccccCChHHHHHHHHHc
Q psy691 61 ACHLCSKSFSLQRLLNRHMKCH 82 (134)
Q Consensus 61 ~C~~C~~~f~~~~~l~~H~~~h 82 (134)
.|..|++.|.....|..|++.|
T Consensus 2 ~C~~C~~~f~~~~~l~~H~~~H 23 (26)
T smart00355 2 RCPECGKVFKSKSALKEHMRTH 23 (26)
T ss_pred CCCCCcchhCCHHHHHHHHHHh
Confidence 4455555555555555555443
No 39
>smart00355 ZnF_C2H2 zinc finger.
Probab=97.48 E-value=0.00013 Score=31.48 Aligned_cols=25 Identities=48% Similarity=0.778 Sum_probs=22.2
Q ss_pred eecccccccccChhhHHHHHhHhcC
Q psy691 88 YLCTFCGKGFNDTFDLKRHTRTHTG 112 (134)
Q Consensus 88 ~~C~~C~~~f~~~~~l~~H~~~h~~ 112 (134)
|.|..|++.|.....|..|++.|..
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~~H~~ 25 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMRTHXX 25 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHHHhcc
Confidence 5799999999999999999997753
No 40
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=97.36 E-value=0.00013 Score=31.58 Aligned_cols=22 Identities=41% Similarity=0.934 Sum_probs=13.5
Q ss_pred eeccccccccCChHHHHHHHHH
Q psy691 60 FACHLCSKSFSLQRLLNRHMKC 81 (134)
Q Consensus 60 ~~C~~C~~~f~~~~~l~~H~~~ 81 (134)
|.|.+|++.|.+...|..|++.
T Consensus 1 ~~C~~C~~~f~s~~~~~~H~~s 22 (25)
T PF12874_consen 1 FYCDICNKSFSSENSLRQHLRS 22 (25)
T ss_dssp EEETTTTEEESSHHHHHHHHTT
T ss_pred CCCCCCCCCcCCHHHHHHHHCc
Confidence 4566666666666666666553
No 41
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=97.26 E-value=0.00017 Score=50.16 Aligned_cols=46 Identities=24% Similarity=0.333 Sum_probs=37.4
Q ss_pred CCCceeccc--ccccccChhhHHHHHhH-hc------------------CCCccccccCCCcccCcc
Q psy691 84 DVKRYLCTF--CGKGFNDTFDLKRHTRT-HT------------------GKEEEEEEDGKTNVLTTE 129 (134)
Q Consensus 84 ~~k~~~C~~--C~~~f~~~~~l~~H~~~-h~------------------~~~~~~c~~~~~~~~~~~ 129 (134)
++|||+|++ |.|.++....|+.|+.. |. ..|||.|+.|.+....-+
T Consensus 346 d~KpykCpV~gC~K~YknqnGLKYH~lhGH~~~~~~~~p~p~~~~~F~~~~KPYrCevC~KRYKNlN 412 (423)
T COG5189 346 DGKPYKCPVEGCNKKYKNQNGLKYHMLHGHQNQKLHENPSPEKMNIFSAKDKPYRCEVCDKRYKNLN 412 (423)
T ss_pred cCceecCCCCCchhhhccccchhhhhhccccCcccCCCCCccccccccccCCceeccccchhhccCc
Confidence 359999998 99999999999999875 31 238999998988776544
No 42
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=97.05 E-value=0.00046 Score=29.76 Aligned_cols=23 Identities=30% Similarity=0.847 Sum_probs=21.0
Q ss_pred eecccccccccChhhHHHHHhHh
Q psy691 88 YLCTFCGKGFNDTFDLKRHTRTH 110 (134)
Q Consensus 88 ~~C~~C~~~f~~~~~l~~H~~~h 110 (134)
|.|.+|++.|.....|..|++.+
T Consensus 1 ~~C~~C~~~f~s~~~~~~H~~s~ 23 (25)
T PF12874_consen 1 FYCDICNKSFSSENSLRQHLRSK 23 (25)
T ss_dssp EEETTTTEEESSHHHHHHHHTTH
T ss_pred CCCCCCCCCcCCHHHHHHHHCcC
Confidence 67999999999999999998864
No 43
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=96.97 E-value=0.00065 Score=29.03 Aligned_cols=21 Identities=43% Similarity=0.708 Sum_probs=9.9
Q ss_pred eeccccccccCChHHHHHHHHH
Q psy691 60 FACHLCSKSFSLQRLLNRHMKC 81 (134)
Q Consensus 60 ~~C~~C~~~f~~~~~l~~H~~~ 81 (134)
|.|+.|+.... +..|..|++.
T Consensus 1 y~C~~C~y~t~-~~~l~~H~~~ 21 (24)
T PF13909_consen 1 YKCPHCSYSTS-KSNLKRHLKR 21 (24)
T ss_dssp EE-SSSS-EES-HHHHHHHHHH
T ss_pred CCCCCCCCcCC-HHHHHHHHHh
Confidence 34555555554 5555555554
No 44
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=96.91 E-value=0.0007 Score=48.96 Aligned_cols=62 Identities=35% Similarity=0.567 Sum_probs=58.0
Q ss_pred CceeccccccccCChHHHHHHHH--HcCCC--Cceecc--cccccccChhhHHHHHhHhcCCCccccc
Q psy691 58 TRFACHLCSKSFSLQRLLNRHMK--CHSDV--KRYLCT--FCGKGFNDTFDLKRHTRTHTGKEEEEEE 119 (134)
Q Consensus 58 ~~~~C~~C~~~f~~~~~l~~H~~--~h~~~--k~~~C~--~C~~~f~~~~~l~~H~~~h~~~~~~~c~ 119 (134)
.++.|..|...|.....|..|.+ .|.++ +++.|. .|++.|.+...+.+|...|++.+++.+.
T Consensus 288 ~~~~~~~~~~~~s~~~~l~~~~~~~~h~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 355 (467)
T COG5048 288 LPIKSKQCNISFSRSSPLTRHLRSVNHSGESLKPFSCPYSLCGKLFSRNDALKRHILLHTSISPAKEK 355 (467)
T ss_pred cCCCCccccCCccccccccccccccccccccCCceeeeccCCCccccccccccCCcccccCCCccccc
Confidence 46899999999999999999999 79999 999999 7999999999999999999999888874
No 45
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=96.90 E-value=0.00085 Score=28.66 Aligned_cols=24 Identities=33% Similarity=0.678 Sum_probs=19.0
Q ss_pred eecccccccccChhhHHHHHhHhcC
Q psy691 88 YLCTFCGKGFNDTFDLKRHTRTHTG 112 (134)
Q Consensus 88 ~~C~~C~~~f~~~~~l~~H~~~h~~ 112 (134)
|+|..|+.... ...|.+|++.|++
T Consensus 1 y~C~~C~y~t~-~~~l~~H~~~~H~ 24 (24)
T PF13909_consen 1 YKCPHCSYSTS-KSNLKRHLKRHHP 24 (24)
T ss_dssp EE-SSSS-EES-HHHHHHHHHHHHS
T ss_pred CCCCCCCCcCC-HHHHHHHHHhhCc
Confidence 68999998887 8899999998754
No 46
>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=96.61 E-value=0.0019 Score=33.52 Aligned_cols=39 Identities=23% Similarity=0.447 Sum_probs=29.8
Q ss_pred ceecccccccccChhhHHHHHhH-hcCC-CccccccCCCccc
Q psy691 87 RYLCTFCGKGFNDTFDLKRHTRT-HTGK-EEEEEEDGKTNVL 126 (134)
Q Consensus 87 ~~~C~~C~~~f~~~~~l~~H~~~-h~~~-~~~~c~~~~~~~~ 126 (134)
.|.|++|++. .....|..|... |..+ +.+.|+.|...+.
T Consensus 2 ~f~CP~C~~~-~~~~~L~~H~~~~H~~~~~~v~CPiC~~~~~ 42 (54)
T PF05605_consen 2 SFTCPYCGKG-FSESSLVEHCEDEHRSESKNVVCPICSSRVT 42 (54)
T ss_pred CcCCCCCCCc-cCHHHHHHHHHhHCcCCCCCccCCCchhhhh
Confidence 4899999994 556789999777 5554 5699998887544
No 47
>PF12171 zf-C2H2_jaz: Zinc-finger double-stranded RNA-binding; InterPro: IPR022755 This zinc finger is found in archaea and eukaryotes, and is approximately 30 amino acids in length. The mammalian members of this group occur multiple times along the protein, joined by flexible linkers, and are referred to as JAZ - dsRNA-binding ZF protein - zinc-fingers. The JAZ proteins are expressed in all tissues tested and localise in the nucleus, particularly the nucleolus []. JAZ preferentially binds to double-stranded (ds) RNA or RNA/DNA hybrids rather than DNA. In addition to binding double-stranded RNA, these zinc-fingers are required for nucleolar localisation. This entry represents the multiple-adjacent-C2H2 zinc finger, JAZ. ; PDB: 4DGW_A 1ZR9_A.
Probab=96.53 E-value=0.00049 Score=30.37 Aligned_cols=21 Identities=48% Similarity=0.890 Sum_probs=11.2
Q ss_pred eeccccccccCChHHHHHHHH
Q psy691 60 FACHLCSKSFSLQRLLNRHMK 80 (134)
Q Consensus 60 ~~C~~C~~~f~~~~~l~~H~~ 80 (134)
|.|..|++.|.....|..|++
T Consensus 2 ~~C~~C~k~f~~~~~~~~H~~ 22 (27)
T PF12171_consen 2 FYCDACDKYFSSENQLKQHMK 22 (27)
T ss_dssp CBBTTTTBBBSSHHHHHCCTT
T ss_pred CCcccCCCCcCCHHHHHHHHc
Confidence 445555555555555555443
No 48
>KOG2893|consensus
Probab=96.36 E-value=0.002 Score=43.31 Aligned_cols=48 Identities=25% Similarity=0.544 Sum_probs=36.5
Q ss_pred CCCCCceeccccccccCChHHHHHHHHHcCCCCceecccccccccChhhHHHH
Q psy691 54 RKDNTRFACHLCSKSFSLQRLLNRHMKCHSDVKRYLCTFCGKGFNDTFDLKRH 106 (134)
Q Consensus 54 ~~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~k~~~C~~C~~~f~~~~~l~~H 106 (134)
++..++|. =+|++.|....-|..|++ .|.|+|.+|.|....-..|..|
T Consensus 6 kk~~kpwc-wycnrefddekiliqhqk----akhfkchichkkl~sgpglsih 53 (341)
T KOG2893|consen 6 KKVDKPWC-WYCNREFDDEKILIQHQK----AKHFKCHICHKKLFSGPGLSIH 53 (341)
T ss_pred cccCCcee-eecccccchhhhhhhhhh----hccceeeeehhhhccCCCceee
Confidence 34455654 479999999999998887 4569999999776666666666
No 49
>PF12171 zf-C2H2_jaz: Zinc-finger double-stranded RNA-binding; InterPro: IPR022755 This zinc finger is found in archaea and eukaryotes, and is approximately 30 amino acids in length. The mammalian members of this group occur multiple times along the protein, joined by flexible linkers, and are referred to as JAZ - dsRNA-binding ZF protein - zinc-fingers. The JAZ proteins are expressed in all tissues tested and localise in the nucleus, particularly the nucleolus []. JAZ preferentially binds to double-stranded (ds) RNA or RNA/DNA hybrids rather than DNA. In addition to binding double-stranded RNA, these zinc-fingers are required for nucleolar localisation. This entry represents the multiple-adjacent-C2H2 zinc finger, JAZ. ; PDB: 4DGW_A 1ZR9_A.
Probab=96.33 E-value=0.00096 Score=29.42 Aligned_cols=22 Identities=32% Similarity=0.750 Sum_probs=20.2
Q ss_pred eecccccccccChhhHHHHHhH
Q psy691 88 YLCTFCGKGFNDTFDLKRHTRT 109 (134)
Q Consensus 88 ~~C~~C~~~f~~~~~l~~H~~~ 109 (134)
|-|..|++.|.....+..|++.
T Consensus 2 ~~C~~C~k~f~~~~~~~~H~~s 23 (27)
T PF12171_consen 2 FYCDACDKYFSSENQLKQHMKS 23 (27)
T ss_dssp CBBTTTTBBBSSHHHHHCCTTS
T ss_pred CCcccCCCCcCCHHHHHHHHcc
Confidence 7899999999999999999875
No 50
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=95.68 E-value=0.0085 Score=25.90 Aligned_cols=18 Identities=28% Similarity=0.833 Sum_probs=9.1
Q ss_pred eccccccccCChHHHHHHH
Q psy691 61 ACHLCSKSFSLQRLLNRHM 79 (134)
Q Consensus 61 ~C~~C~~~f~~~~~l~~H~ 79 (134)
.|+.|++.|. ...|..|+
T Consensus 4 ~C~~CgR~F~-~~~l~~H~ 21 (25)
T PF13913_consen 4 PCPICGRKFN-PDRLEKHE 21 (25)
T ss_pred cCCCCCCEEC-HHHHHHHH
Confidence 4555555552 44455554
No 51
>smart00451 ZnF_U1 U1-like zinc finger. Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins.
Probab=95.60 E-value=0.013 Score=27.24 Aligned_cols=23 Identities=30% Similarity=0.665 Sum_probs=15.4
Q ss_pred ceeccccccccCChHHHHHHHHH
Q psy691 59 RFACHLCSKSFSLQRLLNRHMKC 81 (134)
Q Consensus 59 ~~~C~~C~~~f~~~~~l~~H~~~ 81 (134)
+|.|.+|++.|.....+..|+..
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~g 25 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLKG 25 (35)
T ss_pred CeEccccCCccCCHHHHHHHHCh
Confidence 46677777777766666666653
No 52
>smart00451 ZnF_U1 U1-like zinc finger. Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins.
Probab=95.12 E-value=0.017 Score=26.77 Aligned_cols=23 Identities=22% Similarity=0.712 Sum_probs=20.7
Q ss_pred ceecccccccccChhhHHHHHhH
Q psy691 87 RYLCTFCGKGFNDTFDLKRHTRT 109 (134)
Q Consensus 87 ~~~C~~C~~~f~~~~~l~~H~~~ 109 (134)
+|.|.+|++.|.....+..|++.
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~g 25 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLKG 25 (35)
T ss_pred CeEccccCCccCCHHHHHHHHCh
Confidence 58899999999999999999775
No 53
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=94.17 E-value=0.055 Score=31.14 Aligned_cols=24 Identities=33% Similarity=0.804 Sum_probs=21.6
Q ss_pred ceeccccccccCChHHHHHHHHHc
Q psy691 59 RFACHLCSKSFSLQRLLNRHMKCH 82 (134)
Q Consensus 59 ~~~C~~C~~~f~~~~~l~~H~~~h 82 (134)
.+.|.+|++.|.+...|..|++.+
T Consensus 50 ~~~C~~C~~~f~s~~~l~~Hm~~~ 73 (100)
T PF12756_consen 50 SFRCPYCNKTFRSREALQEHMRSK 73 (100)
T ss_dssp SEEBSSSS-EESSHHHHHHHHHHT
T ss_pred CCCCCccCCCCcCHHHHHHHHcCc
Confidence 699999999999999999999975
No 54
>KOG2186|consensus
Probab=93.78 E-value=0.04 Score=37.45 Aligned_cols=48 Identities=29% Similarity=0.677 Sum_probs=38.9
Q ss_pred ceeccccccccCChHHHHHHHHHcCCCCceecccccccccChhhHHHHHhH
Q psy691 59 RFACHLCSKSFSLQRLLNRHMKCHSDVKRYLCTFCGKGFNDTFDLKRHTRT 109 (134)
Q Consensus 59 ~~~C~~C~~~f~~~~~l~~H~~~h~~~k~~~C~~C~~~f~~~~~l~~H~~~ 109 (134)
.|.|..||.... +..+.+|+..-++ .-|.|.-|++.|.+ ..+..|..-
T Consensus 3 ~FtCnvCgEsvK-Kp~vekH~srCrn-~~fSCIDC~k~F~~-~sYknH~kC 50 (276)
T KOG2186|consen 3 FFTCNVCGESVK-KPQVEKHMSRCRN-AYFSCIDCGKTFER-VSYKNHTKC 50 (276)
T ss_pred EEehhhhhhhcc-ccchHHHHHhccC-CeeEEeeccccccc-chhhhhhhh
Confidence 488999998877 5567889988776 56999999999998 677778654
No 55
>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=93.58 E-value=0.043 Score=25.35 Aligned_cols=24 Identities=21% Similarity=0.870 Sum_probs=14.8
Q ss_pred eeccccccccCChHHHHHHHHHcCCCCceecccccc
Q psy691 60 FACHLCSKSFSLQRLLNRHMKCHSDVKRYLCTFCGK 95 (134)
Q Consensus 60 ~~C~~C~~~f~~~~~l~~H~~~h~~~k~~~C~~C~~ 95 (134)
|.|.+||..+.... .++.|+.|+.
T Consensus 2 ~~C~~CGy~y~~~~------------~~~~CP~Cg~ 25 (33)
T cd00350 2 YVCPVCGYIYDGEE------------APWVCPVCGA 25 (33)
T ss_pred EECCCCCCEECCCc------------CCCcCcCCCC
Confidence 66777776654322 5567777763
No 56
>KOG1146|consensus
Probab=93.43 E-value=0.052 Score=44.80 Aligned_cols=53 Identities=25% Similarity=0.492 Sum_probs=45.4
Q ss_pred CCceeccccccccCChHHHHHHHHH-cCC------------------------CCceecccccccccChhhHHHHHhH
Q psy691 57 NTRFACHLCSKSFSLQRLLNRHMKC-HSD------------------------VKRYLCTFCGKGFNDTFDLKRHTRT 109 (134)
Q Consensus 57 ~~~~~C~~C~~~f~~~~~l~~H~~~-h~~------------------------~k~~~C~~C~~~f~~~~~l~~H~~~ 109 (134)
.+.+.|+.|+..|+....|..|||. |.. .++|.|..|.-.+..+.+|.+|+..
T Consensus 463 ~kt~~cpkc~~~yk~a~~L~vhmRskhp~~~~~~c~~gq~~~~~arg~~~~~~~~p~~C~~C~~stttng~LsihlqS 540 (1406)
T KOG1146|consen 463 FKTLKCPKCNWHYKLAQTLGVHMRSKHPESQSAYCKAGQNHPRLARGEVYRCPGKPYPCRACNYSTTTNGNLSIHLQS 540 (1406)
T ss_pred cccccCCccchhhhhHHHhhhcccccccccchhHhHhccccccccccccccCCCCcccceeeeeeeecchHHHHHHHH
Confidence 4678999999999999999999998 311 2589999999999999999999875
No 57
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=92.94 E-value=0.056 Score=27.96 Aligned_cols=31 Identities=19% Similarity=0.369 Sum_probs=24.4
Q ss_pred cCCCCCCCceeccccccccCChHHHHHHHHH
Q psy691 51 TTGRKDNTRFACHLCSKSFSLQRLLNRHMKC 81 (134)
Q Consensus 51 ~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~ 81 (134)
...+.++.-+.|+-|+..|.....+.+|...
T Consensus 9 v~~RDGE~~lrCPRC~~~FR~~K~Y~RHVNK 39 (65)
T COG4049 9 VRDRDGEEFLRCPRCGMVFRRRKDYIRHVNK 39 (65)
T ss_pred eeccCCceeeeCCchhHHHHHhHHHHHHhhH
Confidence 3455667778899999999988888888764
No 58
>KOG4167|consensus
Probab=90.74 E-value=0.28 Score=38.45 Aligned_cols=30 Identities=33% Similarity=0.545 Sum_probs=25.4
Q ss_pred CCCCceeccccccccCChHHHHHHHHHcCC
Q psy691 55 KDNTRFACHLCSKSFSLQRLLNRHMKCHSD 84 (134)
Q Consensus 55 ~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~ 84 (134)
....-|.|.+|+|.|.....+..||++|.-
T Consensus 788 ~~~giFpCreC~kvF~KiKSrNAHMK~Hr~ 817 (907)
T KOG4167|consen 788 DPTGIFPCRECGKVFFKIKSRNAHMKTHRQ 817 (907)
T ss_pred CCCceeehHHHHHHHHHHhhhhHHHHHHHH
Confidence 345679999999999998999999999853
No 59
>PF05443 ROS_MUCR: ROS/MUCR transcriptional regulator protein; InterPro: IPR008807 This family consists of several ROS/MUCR transcriptional regulator proteins. The ros chromosomal gene is present in octopine and nopaline strains of Agrobacterium tumefaciens as well as in Rhizobium meliloti (Sinorhizobium meliloti). This gene encodes a 15.5 kDa protein that specifically represses the virC and virD operons in the virulence region of the Ti plasmid [] and is necessary for succinoglycan production []. S. meliloti can produce two types of acidic exopolysaccharides, succinoglycan and galactoglucan, that are interchangeable for infection of Medicago sativa (Alfalfa) nodules. MucR from S. meliloti acts as a transcriptional repressor that blocks the expression of the exp genes responsible for galactoglucan production therefore allowing the exclusive production of succinoglycan [].; GO: 0003677 DNA binding, 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2JSP_A.
Probab=90.52 E-value=0.18 Score=31.22 Aligned_cols=25 Identities=32% Similarity=0.725 Sum_probs=14.6
Q ss_pred CceeccccccccCChHHHHHHHHHcCCC
Q psy691 58 TRFACHLCSKSFSLQRLLNRHMKCHSDV 85 (134)
Q Consensus 58 ~~~~C~~C~~~f~~~~~l~~H~~~h~~~ 85 (134)
..-.|-+||+.|+ .|++|++.|+|-
T Consensus 71 d~i~clecGk~~k---~LkrHL~~~~gl 95 (132)
T PF05443_consen 71 DYIICLECGKKFK---TLKRHLRTHHGL 95 (132)
T ss_dssp S-EE-TBT--EES---BHHHHHHHTT-S
T ss_pred CeeEEccCCcccc---hHHHHHHHccCC
Confidence 3467888888887 358888888665
No 60
>KOG2893|consensus
Probab=90.40 E-value=0.17 Score=34.32 Aligned_cols=39 Identities=18% Similarity=0.354 Sum_probs=30.2
Q ss_pred ecccccccccChhhHHHHHhHhcCCCccccccCCCcccCccce
Q psy691 89 LCTFCGKGFNDTFDLKRHTRTHTGKEEEEEEDGKTNVLTTEYL 131 (134)
Q Consensus 89 ~C~~C~~~f~~~~~l~~H~~~h~~~~~~~c~~~~~~~~~~~~l 131 (134)
.|.+|++.|.....|.+|++. |-|+|..|.+..++---|
T Consensus 12 wcwycnrefddekiliqhqka----khfkchichkkl~sgpgl 50 (341)
T KOG2893|consen 12 WCWYCNREFDDEKILIQHQKA----KHFKCHICHKKLFSGPGL 50 (341)
T ss_pred eeeecccccchhhhhhhhhhh----ccceeeeehhhhccCCCc
Confidence 599999999999999998875 458998776665554433
No 61
>KOG2785|consensus
Probab=89.87 E-value=0.52 Score=34.11 Aligned_cols=53 Identities=21% Similarity=0.405 Sum_probs=44.6
Q ss_pred CCceeccccccccCChHHHHHHHHHcCCC-----------------------Cceeccccc---ccccChhhHHHHHhH
Q psy691 57 NTRFACHLCSKSFSLQRLLNRHMKCHSDV-----------------------KRYLCTFCG---KGFNDTFDLKRHTRT 109 (134)
Q Consensus 57 ~~~~~C~~C~~~f~~~~~l~~H~~~h~~~-----------------------k~~~C~~C~---~~f~~~~~l~~H~~~ 109 (134)
..|-.|-.|++.+..-..-..||..+++- .-|.|.+|+ +.|......+.||..
T Consensus 164 ~~Pt~CLfC~~~~k~~e~~~~HM~~~HgffIPdreYL~D~~GLl~YLgeKV~~~~~CL~CN~~~~~f~sleavr~HM~~ 242 (390)
T KOG2785|consen 164 LIPTDCLFCDKKSKSLEENLKHMFKEHGFFIPDREYLTDEKGLLKYLGEKVGIGFICLFCNELGRPFSSLEAVRAHMRD 242 (390)
T ss_pred cCCcceeecCCCcccHHHHHHHHhhccCCcCCchHhhhchhHHHHHHHHHhccCceEEEeccccCcccccHHHHHHHhh
Confidence 34568999999999988888899987662 358999999 999999999999885
No 62
>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=89.74 E-value=0.2 Score=29.85 Aligned_cols=30 Identities=27% Similarity=0.607 Sum_probs=24.1
Q ss_pred eeccccccccCChHHHHHHHHHcCCCCceecccccccccCh
Q psy691 60 FACHLCSKSFSLQRLLNRHMKCHSDVKRYLCTFCGKGFNDT 100 (134)
Q Consensus 60 ~~C~~C~~~f~~~~~l~~H~~~h~~~k~~~C~~C~~~f~~~ 100 (134)
..|+.||+.|.. | +..|..|+.||..|...
T Consensus 10 R~Cp~CG~kFYD---L--------nk~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 10 RTCPSCGAKFYD---L--------NKDPIVCPKCGTEFPPE 39 (108)
T ss_pred ccCCCCcchhcc---C--------CCCCccCCCCCCccCcc
Confidence 589999999863 3 35788999999988876
No 63
>KOG2482|consensus
Probab=89.41 E-value=0.59 Score=33.45 Aligned_cols=51 Identities=27% Similarity=0.609 Sum_probs=41.1
Q ss_pred ceeccccccccCChHHHHHHHHH--cCCC---------------------------------------------------
Q psy691 59 RFACHLCSKSFSLQRLLNRHMKC--HSDV--------------------------------------------------- 85 (134)
Q Consensus 59 ~~~C~~C~~~f~~~~~l~~H~~~--h~~~--------------------------------------------------- 85 (134)
.+.|-.|.+.|..+..|+.||+. |...
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 48999999999999999999985 4110
Q ss_pred -Cc--eecccccccccChhhHHHHHhH
Q psy691 86 -KR--YLCTFCGKGFNDTFDLKRHTRT 109 (134)
Q Consensus 86 -k~--~~C~~C~~~f~~~~~l~~H~~~ 109 (134)
.+ ..|.+|.........|..||++
T Consensus 275 a~a~~v~CLfC~~~~en~~~l~eHmk~ 301 (423)
T KOG2482|consen 275 AEALSVVCLFCTNFYENPVFLFEHMKI 301 (423)
T ss_pred CCccceEEEeeccchhhHHHHHHHHHH
Confidence 12 4888998888888889899886
No 64
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=89.00 E-value=0.4 Score=34.68 Aligned_cols=62 Identities=32% Similarity=0.641 Sum_probs=53.4
Q ss_pred CCCceeccccccccCChHHHHHHHHHcCCCCceeccc--ccccccChhhHHHHHhHhcCCCccc
Q psy691 56 DNTRFACHLCSKSFSLQRLLNRHMKCHSDVKRYLCTF--CGKGFNDTFDLKRHTRTHTGKEEEE 117 (134)
Q Consensus 56 ~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~k~~~C~~--C~~~f~~~~~l~~H~~~h~~~~~~~ 117 (134)
....+.|+.|...|....+...|.+.|.+++++.|.. |...|.....+.+|.+.++......
T Consensus 30 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 93 (467)
T COG5048 30 APRPDSCPNCTDSFSRLEHLTRHIRSHTGEKPSQCSYSGCDKSFSRPLELSRHLRTHHNNPSDL 93 (467)
T ss_pred CCchhhcccccccccccchhhhhcccccccCCccccccccccccCCcchhhhhccccccccccc
Confidence 3456899999999999999999999999999999987 7788999999999988877655433
No 65
>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=88.38 E-value=0.51 Score=29.22 Aligned_cols=28 Identities=46% Similarity=0.794 Sum_probs=18.3
Q ss_pred CCceecccccccccChhhHHHHHhHhcCCCc
Q psy691 85 VKRYLCTFCGKGFNDTFDLKRHTRTHTGKEE 115 (134)
Q Consensus 85 ~k~~~C~~C~~~f~~~~~l~~H~~~h~~~~~ 115 (134)
..-..|..||+.|.. |.+|.+.|+|-.|
T Consensus 70 ~d~i~clecGk~~k~---LkrHL~~~~gltp 97 (132)
T PF05443_consen 70 PDYIICLECGKKFKT---LKRHLRTHHGLTP 97 (132)
T ss_dssp SS-EE-TBT--EESB---HHHHHHHTT-S-H
T ss_pred cCeeEEccCCcccch---HHHHHHHccCCCH
Confidence 344789999999987 6999999988655
No 66
>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=87.90 E-value=0.28 Score=22.80 Aligned_cols=25 Identities=20% Similarity=0.555 Sum_probs=15.8
Q ss_pred ceeccccccccCChHHHHHHHHHcCCCCceecccccc
Q psy691 59 RFACHLCSKSFSLQRLLNRHMKCHSDVKRYLCTFCGK 95 (134)
Q Consensus 59 ~~~C~~C~~~f~~~~~l~~H~~~h~~~k~~~C~~C~~ 95 (134)
.|.|..||..+... ..|..|+.|+.
T Consensus 2 ~~~C~~CG~i~~g~------------~~p~~CP~Cg~ 26 (34)
T cd00729 2 VWVCPVCGYIHEGE------------EAPEKCPICGA 26 (34)
T ss_pred eEECCCCCCEeECC------------cCCCcCcCCCC
Confidence 37788888665432 14567888764
No 67
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=87.23 E-value=0.57 Score=22.14 Aligned_cols=32 Identities=25% Similarity=0.573 Sum_probs=17.1
Q ss_pred eccccccccCChHHHHHHHHHcCCCCceecccccccc
Q psy691 61 ACHLCSKSFSLQRLLNRHMKCHSDVKRYLCTFCGKGF 97 (134)
Q Consensus 61 ~C~~C~~~f~~~~~l~~H~~~h~~~k~~~C~~C~~~f 97 (134)
.|+.|+..|.-... +.-.+.+..+|..|+..|
T Consensus 4 ~CP~C~~~f~v~~~-----~l~~~~~~vrC~~C~~~f 35 (37)
T PF13719_consen 4 TCPNCQTRFRVPDD-----KLPAGGRKVRCPKCGHVF 35 (37)
T ss_pred ECCCCCceEEcCHH-----HcccCCcEEECCCCCcEe
Confidence 56666666654433 112233456666666555
No 68
>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain. This domain contains a CXXCX(19)CXXC motif suggestive of both zinc fingers and thioredoxin, usually found at the N-terminus of prokaryotic proteins. One partially characterized gene, agmX, is among a large set in Myxococcus whose interruption affects adventurous gliding motility.
Probab=87.18 E-value=0.53 Score=22.18 Aligned_cols=34 Identities=21% Similarity=0.430 Sum_probs=19.4
Q ss_pred eeccccccccCChHHHHHHHHHcCCCCceeccccccccc
Q psy691 60 FACHLCSKSFSLQRLLNRHMKCHSDVKRYLCTFCGKGFN 98 (134)
Q Consensus 60 ~~C~~C~~~f~~~~~l~~H~~~h~~~k~~~C~~C~~~f~ 98 (134)
..|+.|+..|.-..... ........|..|+..|.
T Consensus 3 ~~CP~C~~~~~v~~~~~-----~~~~~~v~C~~C~~~~~ 36 (38)
T TIGR02098 3 IQCPNCKTSFRVVDSQL-----GANGGKVRCGKCGHVWY 36 (38)
T ss_pred EECCCCCCEEEeCHHHc-----CCCCCEEECCCCCCEEE
Confidence 46777777776544321 11222467777776654
No 69
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=86.77 E-value=0.35 Score=25.06 Aligned_cols=32 Identities=25% Similarity=0.380 Sum_probs=26.3
Q ss_pred HcCCCCceecccccccccChhhHHHHHhHhcC
Q psy691 81 CHSDVKRYLCTFCGKGFNDTFDLKRHTRTHTG 112 (134)
Q Consensus 81 ~h~~~k~~~C~~C~~~f~~~~~l~~H~~~h~~ 112 (134)
...|+.-+.|+-|+..|...-.+.+|...-++
T Consensus 11 ~RDGE~~lrCPRC~~~FR~~K~Y~RHVNKaH~ 42 (65)
T COG4049 11 DRDGEEFLRCPRCGMVFRRRKDYIRHVNKAHG 42 (65)
T ss_pred ccCCceeeeCCchhHHHHHhHHHHHHhhHHhh
Confidence 34567778999999999999999999776444
No 70
>KOG4173|consensus
Probab=86.34 E-value=0.39 Score=31.90 Aligned_cols=46 Identities=26% Similarity=0.585 Sum_probs=22.6
Q ss_pred ceeccc--cccccCChHHHHHHHHHcCCCCceecccccccccChhhHHHHH
Q psy691 59 RFACHL--CSKSFSLQRLLNRHMKCHSDVKRYLCTFCGKGFNDTFDLKRHT 107 (134)
Q Consensus 59 ~~~C~~--C~~~f~~~~~l~~H~~~h~~~k~~~C~~C~~~f~~~~~l~~H~ 107 (134)
.|.|++ |...|..-..+..|..+-++. .|.+|.+.|.+...|..|+
T Consensus 79 ~~~cqvagc~~~~d~lD~~E~hY~~~h~~---sCs~C~r~~Pt~hLLd~HI 126 (253)
T KOG4173|consen 79 AFACQVAGCCQVFDALDDYEHHYHTLHGN---SCSFCKRAFPTGHLLDAHI 126 (253)
T ss_pred cccccccchHHHHhhhhhHHHhhhhcccc---hhHHHHHhCCchhhhhHHH
Confidence 355555 445555444444444332222 4555666665555555553
No 71
>KOG1146|consensus
Probab=86.25 E-value=0.62 Score=38.97 Aligned_cols=71 Identities=17% Similarity=0.129 Sum_probs=51.6
Q ss_pred eccccccccCChHHHHHHHHH-cCCCCceecccccccccChhhHHHHHhHhc-------------------------CCC
Q psy691 61 ACHLCSKSFSLQRLLNRHMKC-HSDVKRYLCTFCGKGFNDTFDLKRHTRTHT-------------------------GKE 114 (134)
Q Consensus 61 ~C~~C~~~f~~~~~l~~H~~~-h~~~k~~~C~~C~~~f~~~~~l~~H~~~h~-------------------------~~~ 114 (134)
.|.-|+..+.++..+..|+.. |...+-+.|..|+..|.....|-.|+|.-+ +-+
T Consensus 438 e~~~~e~~~~s~r~~~~~t~~L~S~~kt~~cpkc~~~yk~a~~L~vhmRskhp~~~~~~c~~gq~~~~~arg~~~~~~~~ 517 (1406)
T KOG1146|consen 438 ELTKAEPLLESKRSLEGQTVVLHSFFKTLKCPKCNWHYKLAQTLGVHMRSKHPESQSAYCKAGQNHPRLARGEVYRCPGK 517 (1406)
T ss_pred cccchhhhhhhhcccccceeeeecccccccCCccchhhhhHHHhhhcccccccccchhHhHhccccccccccccccCCCC
Confidence 344566666766666666654 666788999999999999999999999811 115
Q ss_pred ccccccCCCcccCccce
Q psy691 115 EEEEEDGKTNVLTTEYL 131 (134)
Q Consensus 115 ~~~c~~~~~~~~~~~~l 131 (134)
+|.|.-|.+.+.....|
T Consensus 518 p~~C~~C~~stttng~L 534 (1406)
T KOG1146|consen 518 PYPCRACNYSTTTNGNL 534 (1406)
T ss_pred cccceeeeeeeecchHH
Confidence 67777777777665444
No 72
>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=86.04 E-value=0.81 Score=22.33 Aligned_cols=23 Identities=26% Similarity=0.631 Sum_probs=11.2
Q ss_pred CCceeccccccccCCh----HHHHHHH
Q psy691 57 NTRFACHLCSKSFSLQ----RLLNRHM 79 (134)
Q Consensus 57 ~~~~~C~~C~~~f~~~----~~l~~H~ 79 (134)
.....|..|++.+... .+|.+|+
T Consensus 14 ~~~a~C~~C~~~~~~~~~~ts~l~~HL 40 (45)
T PF02892_consen 14 KKKAKCKYCGKVIKYSSGGTSNLKRHL 40 (45)
T ss_dssp SS-EEETTTTEE-----SSTHHHHHHH
T ss_pred cCeEEeCCCCeEEeeCCCcHHHHHHhh
Confidence 3445677777666553 5566665
No 73
>KOG2186|consensus
Probab=85.73 E-value=0.47 Score=32.48 Aligned_cols=41 Identities=15% Similarity=0.318 Sum_probs=33.3
Q ss_pred eecccccccccChhhHHHHHhHhcCCCccccccCCCcccCccc
Q psy691 88 YLCTFCGKGFNDTFDLKRHTRTHTGKEEEEEEDGKTNVLTTEY 130 (134)
Q Consensus 88 ~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~c~~~~~~~~~~~~ 130 (134)
|.|..||....- ..+.+|+...++ ..|.|.-|...|...++
T Consensus 4 FtCnvCgEsvKK-p~vekH~srCrn-~~fSCIDC~k~F~~~sY 44 (276)
T KOG2186|consen 4 FTCNVCGESVKK-PQVEKHMSRCRN-AYFSCIDCGKTFERVSY 44 (276)
T ss_pred Eehhhhhhhccc-cchHHHHHhccC-CeeEEeecccccccchh
Confidence 789999987554 567789988888 88999888888887654
No 74
>smart00614 ZnF_BED BED zinc finger. DNA-binding domain in chromatin-boundary-element-binding proteins and transposases
Probab=85.61 E-value=0.88 Score=22.94 Aligned_cols=25 Identities=36% Similarity=0.699 Sum_probs=18.5
Q ss_pred ceeccccccccCCh-----HHHHHHHH-HcC
Q psy691 59 RFACHLCSKSFSLQ-----RLLNRHMK-CHS 83 (134)
Q Consensus 59 ~~~C~~C~~~f~~~-----~~l~~H~~-~h~ 83 (134)
.-.|..|++.+... ++|.+|+. .|.
T Consensus 18 ~a~C~~C~~~l~~~~~~gTs~L~rHl~~~h~ 48 (50)
T smart00614 18 RAKCKYCGKKLSRSSKGGTSNLRRHLRRKHP 48 (50)
T ss_pred EEEecCCCCEeeeCCCCCcHHHHHHHHhHCc
Confidence 46899999988765 57888877 453
No 75
>KOG4173|consensus
Probab=85.49 E-value=0.38 Score=31.93 Aligned_cols=49 Identities=29% Similarity=0.633 Sum_probs=41.0
Q ss_pred eccccccccCChHHHHHHHHH-c---------CCCCceeccc--ccccccChhhHHHHHhH
Q psy691 61 ACHLCSKSFSLQRLLNRHMKC-H---------SDVKRYLCTF--CGKGFNDTFDLKRHTRT 109 (134)
Q Consensus 61 ~C~~C~~~f~~~~~l~~H~~~-h---------~~~k~~~C~~--C~~~f~~~~~l~~H~~~ 109 (134)
.|.+|.+.|.+...|..|+.. | .|.-.|.|.+ |+..|.+......|+-.
T Consensus 108 sCs~C~r~~Pt~hLLd~HI~E~HDs~Fqa~veRG~dMy~ClvEgCt~KFkT~r~RkdH~I~ 168 (253)
T KOG4173|consen 108 SCSFCKRAFPTGHLLDAHILEWHDSLFQALVERGQDMYQCLVEGCTEKFKTSRDRKDHMIR 168 (253)
T ss_pred hhHHHHHhCCchhhhhHHHHHHHHHHHHHHHHcCccHHHHHHHhhhhhhhhhhhhhhHHHH
Confidence 899999999999999999864 3 3455699976 99999999888888654
No 76
>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=85.38 E-value=0.85 Score=30.64 Aligned_cols=29 Identities=24% Similarity=0.614 Sum_probs=21.5
Q ss_pred CCCCceeccccccccCChHHHHHHHHHcC
Q psy691 55 KDNTRFACHLCSKSFSLQRLLNRHMKCHS 83 (134)
Q Consensus 55 ~~~~~~~C~~C~~~f~~~~~l~~H~~~h~ 83 (134)
..+..|.|.+|+|.|+-...+..|+...+
T Consensus 73 ~~~~K~~C~lc~KlFkg~eFV~KHI~nKH 101 (214)
T PF04959_consen 73 EDEDKWRCPLCGKLFKGPEFVRKHIFNKH 101 (214)
T ss_dssp SSSEEEEE-SSS-EESSHHHHHHHHHHH-
T ss_pred HcCCEECCCCCCcccCChHHHHHHHhhcC
Confidence 44557999999999999999999988733
No 77
>COG4957 Predicted transcriptional regulator [Transcription]
Probab=85.25 E-value=2.7 Score=26.07 Aligned_cols=25 Identities=28% Similarity=0.476 Sum_probs=21.1
Q ss_pred eeccccccccCChHHHHHHHHHcCCCCc
Q psy691 60 FACHLCSKSFSLQRLLNRHMKCHSDVKR 87 (134)
Q Consensus 60 ~~C~~C~~~f~~~~~l~~H~~~h~~~k~ 87 (134)
..|-++|+.|+ .|++|+.+|.+.-|
T Consensus 77 IicLEDGkkfK---SLKRHL~t~~gmTP 101 (148)
T COG4957 77 IICLEDGKKFK---SLKRHLTTHYGLTP 101 (148)
T ss_pred EEEeccCcchH---HHHHHHhcccCCCH
Confidence 57999999997 69999999987543
No 78
>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=85.10 E-value=0.39 Score=32.22 Aligned_cols=30 Identities=20% Similarity=0.493 Sum_probs=23.0
Q ss_pred CCceecccccccccChhhHHHHHhHhcCCC
Q psy691 85 VKRYLCTFCGKGFNDTFDLKRHTRTHTGKE 114 (134)
Q Consensus 85 ~k~~~C~~C~~~f~~~~~l~~H~~~h~~~~ 114 (134)
+..|.|..|+|.|.-......|+..-|.|+
T Consensus 75 ~~K~~C~lc~KlFkg~eFV~KHI~nKH~e~ 104 (214)
T PF04959_consen 75 EDKWRCPLCGKLFKGPEFVRKHIFNKHPEK 104 (214)
T ss_dssp SEEEEE-SSS-EESSHHHHHHHHHHH-HHH
T ss_pred CCEECCCCCCcccCChHHHHHHHhhcCHHH
Confidence 446999999999999999999999865543
No 79
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=85.09 E-value=0.18 Score=27.72 Aligned_cols=18 Identities=17% Similarity=0.241 Sum_probs=9.8
Q ss_pred CCceecc--cccccccChhh
Q psy691 85 VKRYLCT--FCGKGFNDTFD 102 (134)
Q Consensus 85 ~k~~~C~--~C~~~f~~~~~ 102 (134)
++-++|. .||..|.....
T Consensus 25 ~~Y~qC~N~eCg~tF~t~es 44 (72)
T PRK09678 25 ERYHQCQNVNCSATFITYES 44 (72)
T ss_pred eeeeecCCCCCCCEEEEEEE
Confidence 4445665 46666655433
No 80
>KOG2785|consensus
Probab=84.49 E-value=1.3 Score=32.25 Aligned_cols=51 Identities=24% Similarity=0.485 Sum_probs=41.2
Q ss_pred ceeccccccccCChHHHHHHHHH--c-----------------------------------CCCCceecccccccccChh
Q psy691 59 RFACHLCSKSFSLQRLLNRHMKC--H-----------------------------------SDVKRYLCTFCGKGFNDTF 101 (134)
Q Consensus 59 ~~~C~~C~~~f~~~~~l~~H~~~--h-----------------------------------~~~k~~~C~~C~~~f~~~~ 101 (134)
.|.|.-|...|.....-+.|+.+ | ...-++.|..|.+.|....
T Consensus 3 ~ftC~tC~v~F~~ad~Qr~HyKSdWHRYNLKRkVA~lPPItaE~F~~k~~s~~~~~~~~~e~~~~~~~c~~c~k~~~s~~ 82 (390)
T KOG2785|consen 3 GFTCNTCNVEFDDADEQRAHYKSDWHRYNLKRKVASLPPITAEEFNEKVLSDDSEKEENLEEAESVVYCEACNKSFASPK 82 (390)
T ss_pred cceeeceeeeeccHHHHHHHhhhhHHHhhHHhHhhcCCCcCHHHHhHHHhhhhhhhhhhhhhcccceehHHhhccccChh
Confidence 48999999999998888888876 4 1123688999999999988
Q ss_pred hHHHHHhH
Q psy691 102 DLKRHTRT 109 (134)
Q Consensus 102 ~l~~H~~~ 109 (134)
....|+..
T Consensus 83 a~~~hl~S 90 (390)
T KOG2785|consen 83 AHENHLKS 90 (390)
T ss_pred hHHHHHHH
Confidence 88888765
No 81
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=84.34 E-value=0.64 Score=29.94 Aligned_cols=23 Identities=26% Similarity=0.842 Sum_probs=15.0
Q ss_pred ceeccccccccCChHHHHHHHHHcCCCCceeccccc
Q psy691 59 RFACHLCSKSFSLQRLLNRHMKCHSDVKRYLCTFCG 94 (134)
Q Consensus 59 ~~~C~~C~~~f~~~~~l~~H~~~h~~~k~~~C~~C~ 94 (134)
.|.|.+||.. |.++-|-.|++|+
T Consensus 134 ~~vC~vCGy~-------------~~ge~P~~CPiCg 156 (166)
T COG1592 134 VWVCPVCGYT-------------HEGEAPEVCPICG 156 (166)
T ss_pred EEEcCCCCCc-------------ccCCCCCcCCCCC
Confidence 5777777654 3345667777776
No 82
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=84.09 E-value=0.79 Score=22.63 Aligned_cols=26 Identities=19% Similarity=0.567 Sum_probs=16.1
Q ss_pred eeccccccccCChHHHHHHHHHcCCCCceeccccccc
Q psy691 60 FACHLCSKSFSLQRLLNRHMKCHSDVKRYLCTFCGKG 96 (134)
Q Consensus 60 ~~C~~C~~~f~~~~~l~~H~~~h~~~k~~~C~~C~~~ 96 (134)
|.|..||..|... ...+..|+.||..
T Consensus 3 Y~C~~Cg~~~~~~-----------~~~~irC~~CG~r 28 (44)
T smart00659 3 YICGECGRENEIK-----------SKDVVRCRECGYR 28 (44)
T ss_pred EECCCCCCEeecC-----------CCCceECCCCCce
Confidence 6777777776533 2345677777643
No 83
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=84.06 E-value=0.2 Score=33.66 Aligned_cols=19 Identities=21% Similarity=0.744 Sum_probs=11.9
Q ss_pred CceeccccccccCChHHHH
Q psy691 58 TRFACHLCSKSFSLQRLLN 76 (134)
Q Consensus 58 ~~~~C~~C~~~f~~~~~l~ 76 (134)
+...|++|++.|..+....
T Consensus 4 k~~~CPvC~~~F~~~~vrs 22 (214)
T PF09986_consen 4 KKITCPVCGKEFKTKKVRS 22 (214)
T ss_pred CceECCCCCCeeeeeEEEc
Confidence 4567777777777654433
No 84
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=83.58 E-value=1.1 Score=26.91 Aligned_cols=65 Identities=15% Similarity=0.137 Sum_probs=32.7
Q ss_pred ceeccccccccCChHHHHHHHHHcCCCCc------------eecccccccccChhhHHHHHhHhcCCCccccccCCCcc
Q psy691 59 RFACHLCSKSFSLQRLLNRHMKCHSDVKR------------YLCTFCGKGFNDTFDLKRHTRTHTGKEEEEEEDGKTNV 125 (134)
Q Consensus 59 ~~~C~~C~~~f~~~~~l~~H~~~h~~~k~------------~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~c~~~~~~~ 125 (134)
|-.|++|+-......+|.+...--..-++ ..|-.|.+.|........ ..-.....|.|+.|+..|
T Consensus 15 P~~CpiCgLtLVss~HLARSyHHLfPl~~f~ev~~~~~~~~~~C~~C~~~f~~~~~~~~--~~~~~~~~y~C~~C~~~F 91 (112)
T TIGR00622 15 PVECPICGLTLILSTHLARSYHHLFPLKAFQEIPLEEYNGSRFCFGCQGPFPKPPVSPF--DELKDSHRYVCAVCKNVF 91 (112)
T ss_pred CCcCCcCCCEEeccchHHHhhhccCCCcccccccccccCCCCcccCcCCCCCCcccccc--cccccccceeCCCCCCcc
Confidence 45778888777777777653210000111 137777777765431110 001223357776666554
No 85
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=83.39 E-value=1.2 Score=20.93 Aligned_cols=33 Identities=18% Similarity=0.544 Sum_probs=18.3
Q ss_pred eeccccccccCChHHHHHHHHHcCCCCceecccccccc
Q psy691 60 FACHLCSKSFSLQRLLNRHMKCHSDVKRYLCTFCGKGF 97 (134)
Q Consensus 60 ~~C~~C~~~f~~~~~l~~H~~~h~~~k~~~C~~C~~~f 97 (134)
..|+.|+..|.-.... .-......+|..|+..|
T Consensus 3 i~Cp~C~~~y~i~d~~-----ip~~g~~v~C~~C~~~f 35 (36)
T PF13717_consen 3 ITCPNCQAKYEIDDEK-----IPPKGRKVRCSKCGHVF 35 (36)
T ss_pred EECCCCCCEEeCCHHH-----CCCCCcEEECCCCCCEe
Confidence 3566777766655442 12233456777776655
No 86
>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=82.83 E-value=0.86 Score=27.90 Aligned_cols=35 Identities=20% Similarity=0.314 Sum_probs=26.1
Q ss_pred ceeccccccccCChHHHHHHHHHcCCCCceecccccccccChhhHH
Q psy691 59 RFACHLCSKSFSLQRLLNRHMKCHSDVKRYLCTFCGKGFNDTFDLK 104 (134)
Q Consensus 59 ~~~C~~C~~~f~~~~~l~~H~~~h~~~k~~~C~~C~~~f~~~~~l~ 104 (134)
...|+.||+.|.. | +..|..|+.||..|.....+.
T Consensus 9 Kr~Cp~cg~kFYD---L--------nk~p~vcP~cg~~~~~~~~~~ 43 (129)
T TIGR02300 9 KRICPNTGSKFYD---L--------NRRPAVSPYTGEQFPPEEALK 43 (129)
T ss_pred cccCCCcCccccc---c--------CCCCccCCCcCCccCcchhhc
Confidence 3589999999862 2 357899999999887664443
No 87
>PF05290 Baculo_IE-1: Baculovirus immediate-early protein (IE-0); InterPro: IPR007954 This entry contains the Baculovirus immediate-early protein IE-0.
Probab=81.81 E-value=0.89 Score=28.08 Aligned_cols=55 Identities=18% Similarity=0.284 Sum_probs=31.4
Q ss_pred CceeccccccccCChHHHHHHHHHcCCCCceeccc---ccccccChhhHHHHHhHhcCCCccccccCCCcccCccc
Q psy691 58 TRFACHLCSKSFSLQRLLNRHMKCHSDVKRYLCTF---CGKGFNDTFDLKRHTRTHTGKEEEEEEDGKTNVLTTEY 130 (134)
Q Consensus 58 ~~~~C~~C~~~f~~~~~l~~H~~~h~~~k~~~C~~---C~~~f~~~~~l~~H~~~h~~~~~~~c~~~~~~~~~~~~ 130 (134)
+.|+|.+|..+...+..| ||-.|-. |+.- -..|.+|-.+| =.|+.|+++|.+++.
T Consensus 79 ~lYeCnIC~etS~ee~FL----------KPneCCgY~iCn~C---ya~LWK~~~~y-----pvCPvCkTSFKss~~ 136 (140)
T PF05290_consen 79 KLYECNICKETSAEERFL----------KPNECCGYSICNAC---YANLWKFCNLY-----PVCPVCKTSFKSSSS 136 (140)
T ss_pred CceeccCcccccchhhcC----------CcccccchHHHHHH---HHHHHHHcccC-----CCCCccccccccccc
Confidence 457777777665543332 3433321 3322 23455554433 269999999998864
No 88
>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=81.55 E-value=0.8 Score=29.23 Aligned_cols=33 Identities=6% Similarity=-0.032 Sum_probs=20.8
Q ss_pred CCCCceecccccccccChhhHHHHHhHhcCCCccccccCCCc
Q psy691 83 SDVKRYLCTFCGKGFNDTFDLKRHTRTHTGKEEEEEEDGKTN 124 (134)
Q Consensus 83 ~~~k~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~c~~~~~~ 124 (134)
.+..-|.|+.|+..|+....+. ..|.|+.|+..
T Consensus 105 ~~~~~Y~Cp~c~~r~tf~eA~~---------~~F~Cp~Cg~~ 137 (158)
T TIGR00373 105 TNNMFFICPNMCVRFTFNEAME---------LNFTCPRCGAM 137 (158)
T ss_pred cCCCeEECCCCCcEeeHHHHHH---------cCCcCCCCCCE
Confidence 3345577777777777766664 25777666554
No 89
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=80.70 E-value=0.77 Score=29.93 Aligned_cols=17 Identities=18% Similarity=0.413 Sum_probs=9.4
Q ss_pred ceecccccccccChhhH
Q psy691 87 RYLCTFCGKGFNDTFDL 103 (134)
Q Consensus 87 ~~~C~~C~~~f~~~~~l 103 (134)
-|.|+.|+..|+....+
T Consensus 117 ~Y~Cp~C~~rytf~eA~ 133 (178)
T PRK06266 117 FFFCPNCHIRFTFDEAM 133 (178)
T ss_pred EEECCCCCcEEeHHHHh
Confidence 45666666555555444
No 90
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=80.58 E-value=0.65 Score=33.37 Aligned_cols=22 Identities=27% Similarity=0.629 Sum_probs=14.4
Q ss_pred eeccc--cccccCChHHHHHHHHH
Q psy691 60 FACHL--CSKSFSLQRLLNRHMKC 81 (134)
Q Consensus 60 ~~C~~--C~~~f~~~~~l~~H~~~ 81 (134)
|.|+. |.........|+.|.+.
T Consensus 152 F~CP~skc~~~C~~~k~lk~H~K~ 175 (493)
T COG5236 152 FKCPKSKCHRRCGSLKELKKHYKA 175 (493)
T ss_pred hcCCchhhhhhhhhHHHHHHHHHh
Confidence 66765 55555556677777776
No 91
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=80.56 E-value=0.75 Score=22.76 Aligned_cols=30 Identities=20% Similarity=0.625 Sum_probs=17.0
Q ss_pred ceeccccccccCChHHHHHHHHHcCCCCceeccccccccc
Q psy691 59 RFACHLCSKSFSLQRLLNRHMKCHSDVKRYLCTFCGKGFN 98 (134)
Q Consensus 59 ~~~C~~C~~~f~~~~~l~~H~~~h~~~k~~~C~~C~~~f~ 98 (134)
.|.|+.||..|..... .....|+.||..+.
T Consensus 3 ~y~C~~CG~~~~~~~~----------~~~~~Cp~CG~~~~ 32 (46)
T PRK00398 3 EYKCARCGREVELDEY----------GTGVRCPYCGYRIL 32 (46)
T ss_pred EEECCCCCCEEEECCC----------CCceECCCCCCeEE
Confidence 4677777776654221 11467777775443
No 92
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=79.88 E-value=1.8 Score=22.79 Aligned_cols=32 Identities=28% Similarity=0.611 Sum_probs=17.1
Q ss_pred ceeccccccccCChHHHHHHHHHcCCCCceecccccc
Q psy691 59 RFACHLCSKSFSLQRLLNRHMKCHSDVKRYLCTFCGK 95 (134)
Q Consensus 59 ~~~C~~C~~~f~~~~~l~~H~~~h~~~k~~~C~~C~~ 95 (134)
.|.|+.||.....+.. +-..-..+|.|+.||.
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 4778888755433221 1111235677777763
No 93
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=79.88 E-value=2.4 Score=26.70 Aligned_cols=36 Identities=8% Similarity=-0.005 Sum_probs=19.0
Q ss_pred CCceecccccccccChhhHHHHHhHhcCCCccccccCCCc
Q psy691 85 VKRYLCTFCGKGFNDTFDLKRHTRTHTGKEEEEEEDGKTN 124 (134)
Q Consensus 85 ~k~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~c~~~~~~ 124 (134)
..-|.|+.|+..|.....+.- ... +..|.|+.|+..
T Consensus 97 ~~~Y~Cp~C~~~y~~~ea~~~---~d~-~~~f~Cp~Cg~~ 132 (147)
T smart00531 97 NAYYKCPNCQSKYTFLEANQL---LDM-DGTFTCPRCGEE 132 (147)
T ss_pred CcEEECcCCCCEeeHHHHHHh---cCC-CCcEECCCCCCE
Confidence 345777777777765433321 011 233777655554
No 94
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=79.43 E-value=0.39 Score=30.57 Aligned_cols=16 Identities=38% Similarity=0.613 Sum_probs=12.0
Q ss_pred ceecccccccccChhh
Q psy691 87 RYLCTFCGKGFNDTFD 102 (134)
Q Consensus 87 ~~~C~~C~~~f~~~~~ 102 (134)
.++|..||++|..-..
T Consensus 28 ~~~c~~c~~~f~~~e~ 43 (154)
T PRK00464 28 RRECLACGKRFTTFER 43 (154)
T ss_pred eeeccccCCcceEeEe
Confidence 4888899988876443
No 95
>KOG2593|consensus
Probab=79.35 E-value=1.8 Score=32.06 Aligned_cols=35 Identities=20% Similarity=0.287 Sum_probs=17.0
Q ss_pred CceecccccccccChhhHHHHHhHhcCCCccccccCCC
Q psy691 86 KRYLCTFCGKGFNDTFDLKRHTRTHTGKEEEEEEDGKT 123 (134)
Q Consensus 86 k~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~c~~~~~ 123 (134)
.-|.|+.|.+.|.....++ -.--..-.|.|.-|+.
T Consensus 127 ~~Y~Cp~C~kkyt~Lea~~---L~~~~~~~F~C~~C~g 161 (436)
T KOG2593|consen 127 AGYVCPNCQKKYTSLEALQ---LLDNETGEFHCENCGG 161 (436)
T ss_pred ccccCCccccchhhhHHHH---hhcccCceEEEecCCC
Confidence 4466666666665544442 1222233566654443
No 96
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=79.23 E-value=1.7 Score=22.91 Aligned_cols=31 Identities=23% Similarity=0.529 Sum_probs=16.4
Q ss_pred ceeccccccc-cCChHHHHHHHHHcCCCCceecccccc
Q psy691 59 RFACHLCSKS-FSLQRLLNRHMKCHSDVKRYLCTFCGK 95 (134)
Q Consensus 59 ~~~C~~C~~~-f~~~~~l~~H~~~h~~~k~~~C~~C~~ 95 (134)
.|.|+.||.. ..+-..-+ ....+|.|+.||.
T Consensus 25 ~F~CPnCG~~~I~RC~~CR------k~~~~Y~CP~CGF 56 (59)
T PRK14890 25 KFLCPNCGEVIIYRCEKCR------KQSNPYTCPKCGF 56 (59)
T ss_pred EeeCCCCCCeeEeechhHH------hcCCceECCCCCC
Confidence 4777777766 32221111 1135677777763
No 97
>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=78.29 E-value=2.2 Score=18.44 Aligned_cols=19 Identities=26% Similarity=0.756 Sum_probs=11.6
Q ss_pred eccccccccCChHHHHHHHH
Q psy691 61 ACHLCSKSFSLQRLLNRHMK 80 (134)
Q Consensus 61 ~C~~C~~~f~~~~~l~~H~~ 80 (134)
.|++|++.+ ....+..|+.
T Consensus 3 ~CPiC~~~v-~~~~in~HLD 21 (26)
T smart00734 3 QCPVCFREV-PENLINSHLD 21 (26)
T ss_pred cCCCCcCcc-cHHHHHHHHH
Confidence 577777776 3455555654
No 98
>COG4957 Predicted transcriptional regulator [Transcription]
Probab=77.90 E-value=1.3 Score=27.39 Aligned_cols=25 Identities=44% Similarity=0.655 Sum_probs=21.1
Q ss_pred eecccccccccChhhHHHHHhHhcCCCc
Q psy691 88 YLCTFCGKGFNDTFDLKRHTRTHTGKEE 115 (134)
Q Consensus 88 ~~C~~C~~~f~~~~~l~~H~~~h~~~~~ 115 (134)
..|..+|+.|.. |++|..+|.|--|
T Consensus 77 IicLEDGkkfKS---LKRHL~t~~gmTP 101 (148)
T COG4957 77 IICLEDGKKFKS---LKRHLTTHYGLTP 101 (148)
T ss_pred EEEeccCcchHH---HHHHHhcccCCCH
Confidence 578889999875 9999999988655
No 99
>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=77.38 E-value=8.8 Score=22.66 Aligned_cols=26 Identities=12% Similarity=0.378 Sum_probs=22.3
Q ss_pred ceec----cccccccCChHHHHHHHHHcCC
Q psy691 59 RFAC----HLCSKSFSLQRLLNRHMKCHSD 84 (134)
Q Consensus 59 ~~~C----~~C~~~f~~~~~l~~H~~~h~~ 84 (134)
-|.| ..|+....+...+..|++.+++
T Consensus 80 G~~C~~~~~~C~y~~~~~~~m~~H~~~~Hg 109 (109)
T PF12013_consen 80 GYRCQCDPPHCGYITRSKKTMRKHWRKEHG 109 (109)
T ss_pred CeeeecCCCCCCcEeccHHHHHHHHHHhcC
Confidence 3899 8899999999999999987653
No 100
>KOG4167|consensus
Probab=77.32 E-value=0.67 Score=36.48 Aligned_cols=26 Identities=31% Similarity=0.516 Sum_probs=23.7
Q ss_pred ceecccccccccChhhHHHHHhHhcC
Q psy691 87 RYLCTFCGKGFNDTFDLKRHTRTHTG 112 (134)
Q Consensus 87 ~~~C~~C~~~f~~~~~l~~H~~~h~~ 112 (134)
-|.|..|+|.|...-++..||++|.-
T Consensus 792 iFpCreC~kvF~KiKSrNAHMK~Hr~ 817 (907)
T KOG4167|consen 792 IFPCRECGKVFFKIKSRNAHMKTHRQ 817 (907)
T ss_pred eeehHHHHHHHHHHhhhhHHHHHHHH
Confidence 48999999999999999999999864
No 101
>KOG3408|consensus
Probab=75.75 E-value=2.1 Score=25.98 Aligned_cols=28 Identities=25% Similarity=0.479 Sum_probs=24.2
Q ss_pred CCCCCceeccccccccCChHHHHHHHHH
Q psy691 54 RKDNTRFACHLCSKSFSLQRLLNRHMKC 81 (134)
Q Consensus 54 ~~~~~~~~C~~C~~~f~~~~~l~~H~~~ 81 (134)
..+...|.|-+|.+-|.....|..|.++
T Consensus 52 lPG~GqfyCi~CaRyFi~~~~l~~H~kt 79 (129)
T KOG3408|consen 52 LPGGGQFYCIECARYFIDAKALKTHFKT 79 (129)
T ss_pred CCCCceeehhhhhhhhcchHHHHHHHhc
Confidence 3456679999999999999999999875
No 102
>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=75.47 E-value=0.59 Score=23.68 Aligned_cols=11 Identities=27% Similarity=1.029 Sum_probs=7.0
Q ss_pred eeccccccccC
Q psy691 60 FACHLCSKSFS 70 (134)
Q Consensus 60 ~~C~~C~~~f~ 70 (134)
|.|..|+..|.
T Consensus 6 y~C~~Cg~~fe 16 (52)
T TIGR02605 6 YRCTACGHRFE 16 (52)
T ss_pred EEeCCCCCEeE
Confidence 56666666665
No 103
>PF12013 DUF3505: Protein of unknown function (DUF3505); InterPro: IPR022698 This family of proteins is functionally uncharacterised. This protein is found in eukaryotes. Proteins in this family are typically between 247 to 1018 amino acids in length. This region contains two segments that are likely to be C2H2 zinc binding domains.
Probab=75.42 E-value=2.5 Score=25.04 Aligned_cols=54 Identities=20% Similarity=0.469 Sum_probs=40.7
Q ss_pred CceeccccccccCChHHHHHHHHH-cCCC-----------------------------------------Cceec----c
Q psy691 58 TRFACHLCSKSFSLQRLLNRHMKC-HSDV-----------------------------------------KRYLC----T 91 (134)
Q Consensus 58 ~~~~C~~C~~~f~~~~~l~~H~~~-h~~~-----------------------------------------k~~~C----~ 91 (134)
+...|..|+..... ..+..|++. |... .-|.| .
T Consensus 10 ~vlIC~~C~~av~~-~~v~~HL~~~H~~~~~~~~~~i~~~~~~~~~l~~~~~~~~~p~~~~~Pi~gLp~~~G~~C~~~~~ 88 (109)
T PF12013_consen 10 RVLICRQCQYAVQP-SEVESHLRKRHHILKSQERQRIVEAIRQWPDLLPDPDDLQIPPDPSPPIPGLPVYDGYRCQCDPP 88 (109)
T ss_pred CEEEeCCCCcccCc-hHHHHHHHHhcccccHHHHHHHHHHHHhhhhcccCccccCCCCCCCCcCCCCCCCCCeeeecCCC
Confidence 34678888877664 677888874 4211 13899 8
Q ss_pred cccccccChhhHHHHHhHhcC
Q psy691 92 FCGKGFNDTFDLKRHTRTHTG 112 (134)
Q Consensus 92 ~C~~~f~~~~~l~~H~~~h~~ 112 (134)
.|+........+.+|.+.++|
T Consensus 89 ~C~y~~~~~~~m~~H~~~~Hg 109 (109)
T PF12013_consen 89 HCGYITRSKKTMRKHWRKEHG 109 (109)
T ss_pred CCCcEeccHHHHHHHHHHhcC
Confidence 899999999999999998765
No 104
>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=74.31 E-value=4.7 Score=25.73 Aligned_cols=35 Identities=20% Similarity=0.507 Sum_probs=26.4
Q ss_pred CCCceeccccccccCChHHHHHHHHHcCCCCceecccccccccC
Q psy691 56 DNTRFACHLCSKSFSLQRLLNRHMKCHSDVKRYLCTFCGKGFND 99 (134)
Q Consensus 56 ~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~k~~~C~~C~~~f~~ 99 (134)
...-|.|+.|+..|+....+. .-|.|+.||.....
T Consensus 106 ~~~~Y~Cp~c~~r~tf~eA~~---------~~F~Cp~Cg~~L~~ 140 (158)
T TIGR00373 106 NNMFFICPNMCVRFTFNEAME---------LNFTCPRCGAMLDY 140 (158)
T ss_pred CCCeEECCCCCcEeeHHHHHH---------cCCcCCCCCCEeee
Confidence 344589999999998776664 36999999975443
No 105
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=72.92 E-value=2.2 Score=21.59 Aligned_cols=28 Identities=21% Similarity=0.828 Sum_probs=17.3
Q ss_pred CceeccccccccCChHHHHHHHHHcCCCCceecccccc
Q psy691 58 TRFACHLCSKSFSLQRLLNRHMKCHSDVKRYLCTFCGK 95 (134)
Q Consensus 58 ~~~~C~~C~~~f~~~~~l~~H~~~h~~~k~~~C~~C~~ 95 (134)
..|.|..||+.|... .......|+.||.
T Consensus 5 ~~Y~C~~Cg~~~~~~----------~~~~~irCp~Cg~ 32 (49)
T COG1996 5 MEYKCARCGREVELD----------QETRGIRCPYCGS 32 (49)
T ss_pred EEEEhhhcCCeeehh----------hccCceeCCCCCc
Confidence 357888888887211 1234567888874
No 106
>PHA00626 hypothetical protein
Probab=72.14 E-value=2.6 Score=21.91 Aligned_cols=15 Identities=20% Similarity=0.408 Sum_probs=11.8
Q ss_pred CCceeccccccccCC
Q psy691 57 NTRFACHLCSKSFSL 71 (134)
Q Consensus 57 ~~~~~C~~C~~~f~~ 71 (134)
...|.|+.||..|+.
T Consensus 21 snrYkCkdCGY~ft~ 35 (59)
T PHA00626 21 SDDYVCCDCGYNDSK 35 (59)
T ss_pred CcceEcCCCCCeech
Confidence 457899999988874
No 107
>KOG2231|consensus
Probab=72.07 E-value=3.2 Score=32.65 Aligned_cols=21 Identities=29% Similarity=0.665 Sum_probs=13.3
Q ss_pred eccccccccCChHHHHHHHHH
Q psy691 61 ACHLCSKSFSLQRLLNRHMKC 81 (134)
Q Consensus 61 ~C~~C~~~f~~~~~l~~H~~~ 81 (134)
.|..|...|.....|.+|++.
T Consensus 184 ~C~~C~~~fld~~el~rH~~~ 204 (669)
T KOG2231|consen 184 LCKFCHERFLDDDELYRHLRF 204 (669)
T ss_pred cchhhhhhhccHHHHHHhhcc
Confidence 466666666666666666654
No 108
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=70.71 E-value=1.4 Score=25.14 Aligned_cols=11 Identities=36% Similarity=1.008 Sum_probs=5.2
Q ss_pred eeccccccccc
Q psy691 88 YLCTFCGKGFN 98 (134)
Q Consensus 88 ~~C~~C~~~f~ 98 (134)
+.|..|+..|.
T Consensus 54 W~C~kCg~~fA 64 (89)
T COG1997 54 WKCRKCGAKFA 64 (89)
T ss_pred EEcCCCCCeec
Confidence 44555554443
No 109
>PF15269 zf-C2H2_7: Zinc-finger
Probab=69.52 E-value=3.4 Score=20.40 Aligned_cols=20 Identities=25% Similarity=0.378 Sum_probs=8.4
Q ss_pred ecccccccccChhhHHHHHh
Q psy691 89 LCTFCGKGFNDTFDLKRHTR 108 (134)
Q Consensus 89 ~C~~C~~~f~~~~~l~~H~~ 108 (134)
+|-.|......+++|-.||+
T Consensus 22 kcfqcpftc~~kshl~nhmk 41 (54)
T PF15269_consen 22 KCFQCPFTCNEKSHLFNHMK 41 (54)
T ss_pred eeecCCcccchHHHHHHHHH
Confidence 34444333344444444443
No 110
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=67.67 E-value=6.9 Score=25.56 Aligned_cols=34 Identities=24% Similarity=0.643 Sum_probs=25.6
Q ss_pred CCceeccccccccCChHHHHHHHHHcCCCCceecccccccccC
Q psy691 57 NTRFACHLCSKSFSLQRLLNRHMKCHSDVKRYLCTFCGKGFND 99 (134)
Q Consensus 57 ~~~~~C~~C~~~f~~~~~l~~H~~~h~~~k~~~C~~C~~~f~~ 99 (134)
..-|.|+.|+..|+....+. .-|.|+.||.....
T Consensus 115 ~~~Y~Cp~C~~rytf~eA~~---------~~F~Cp~Cg~~L~~ 148 (178)
T PRK06266 115 NMFFFCPNCHIRFTFDEAME---------YGFRCPQCGEMLEE 148 (178)
T ss_pred CCEEECCCCCcEEeHHHHhh---------cCCcCCCCCCCCee
Confidence 34589999999998766542 36999999975544
No 111
>KOG2482|consensus
Probab=65.24 E-value=5 Score=28.99 Aligned_cols=51 Identities=27% Similarity=0.532 Sum_probs=37.3
Q ss_pred ceeccccccccCC-hHHHHHHHHH-cC---CC------------------CceecccccccccChhhHHHHHhH
Q psy691 59 RFACHLCSKSFSL-QRLLNRHMKC-HS---DV------------------KRYLCTFCGKGFNDTFDLKRHTRT 109 (134)
Q Consensus 59 ~~~C~~C~~~f~~-~~~l~~H~~~-h~---~~------------------k~~~C~~C~~~f~~~~~l~~H~~~ 109 (134)
...|-.|...+.- ++.+..|+.. |. |. ..+.|..|.+.|..+..|+.||+.
T Consensus 144 slqClFCn~e~lgnRs~~l~Hlf~~H~lniGlpDniVyvnelLehLkekL~r~~CLyCekifrdkntLkeHMrk 217 (423)
T KOG2482|consen 144 SLQCLFCNNEGLGNRSEILEHLFHVHGLNIGLPDNIVYVNELLEHLKEKLERLRCLYCEKIFRDKNTLKEHMRK 217 (423)
T ss_pred eeEEEEecchhcccHHHHHHHHHHHhhhccCCCcceeeHHHHHHHHHHHHhhheeeeeccccCCcHHHHHHHHh
Confidence 4579899877653 4455556543 42 10 258999999999999999999986
No 112
>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=64.60 E-value=2.8 Score=19.18 Aligned_cols=11 Identities=18% Similarity=0.715 Sum_probs=5.7
Q ss_pred eeccccccccC
Q psy691 60 FACHLCSKSFS 70 (134)
Q Consensus 60 ~~C~~C~~~f~ 70 (134)
|.|..|+..+.
T Consensus 1 Y~C~~Cg~~~~ 11 (32)
T PF03604_consen 1 YICGECGAEVE 11 (32)
T ss_dssp EBESSSSSSE-
T ss_pred CCCCcCCCeeE
Confidence 45666665554
No 113
>COG4530 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=64.06 E-value=3.8 Score=24.46 Aligned_cols=32 Identities=16% Similarity=0.187 Sum_probs=22.4
Q ss_pred eccccccccCChHHHHHHHHHcCCCCceecccccccccChhhHH
Q psy691 61 ACHLCSKSFSLQRLLNRHMKCHSDVKRYLCTFCGKGFNDTFDLK 104 (134)
Q Consensus 61 ~C~~C~~~f~~~~~l~~H~~~h~~~k~~~C~~C~~~f~~~~~l~ 104 (134)
.|+.|++.|.. | +..|..|++||++|.. +.|.
T Consensus 11 idPetg~KFYD---L--------NrdPiVsPytG~s~P~-s~fe 42 (129)
T COG4530 11 IDPETGKKFYD---L--------NRDPIVSPYTGKSYPR-SYFE 42 (129)
T ss_pred cCccccchhhc---c--------CCCccccCcccccchH-HHHH
Confidence 67888888752 2 3578899999998843 4443
No 114
>PF13878 zf-C2H2_3: zinc-finger of acetyl-transferase ESCO
Probab=62.36 E-value=9.7 Score=18.35 Aligned_cols=24 Identities=25% Similarity=0.372 Sum_probs=17.4
Q ss_pred eeccccccccCC--hHHHHHHHHHcC
Q psy691 60 FACHLCSKSFSL--QRLLNRHMKCHS 83 (134)
Q Consensus 60 ~~C~~C~~~f~~--~~~l~~H~~~h~ 83 (134)
-.|+.||..|.. ...-..|.+-|.
T Consensus 14 ~~C~~CgM~Y~~~~~eD~~~H~~yH~ 39 (41)
T PF13878_consen 14 TTCPTCGMLYSPGSPEDEKLHKKYHD 39 (41)
T ss_pred cCCCCCCCEECCCCHHHHHHHHHHHh
Confidence 589999988874 456666776663
No 115
>COG3091 SprT Zn-dependent metalloprotease, SprT family [General function prediction only]
Probab=62.11 E-value=4.1 Score=25.85 Aligned_cols=31 Identities=19% Similarity=0.460 Sum_probs=14.8
Q ss_pred ceecccccccccChhhHHHHHhHhcCCCccccccCC
Q psy691 87 RYLCTFCGKGFNDTFDLKRHTRTHTGKEEEEEEDGK 122 (134)
Q Consensus 87 ~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~c~~~~ 122 (134)
+|.|. |+..|.+ .++|-..-.|+ .|.|..|+
T Consensus 117 ~Y~C~-C~q~~l~---~RRhn~~~~g~-~YrC~~C~ 147 (156)
T COG3091 117 PYRCQ-CQQHYLR---IRRHNTVRRGE-VYRCGKCG 147 (156)
T ss_pred eEEee-cCCccch---hhhcccccccc-eEEeccCC
Confidence 45666 6555433 23333344444 56664443
No 116
>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=62.03 E-value=3.8 Score=17.71 Aligned_cols=11 Identities=27% Similarity=0.618 Sum_probs=8.4
Q ss_pred eeccccccccC
Q psy691 60 FACHLCSKSFS 70 (134)
Q Consensus 60 ~~C~~C~~~f~ 70 (134)
-.|+.||..|.
T Consensus 15 ~~Cp~CG~~F~ 25 (26)
T PF10571_consen 15 KFCPHCGYDFE 25 (26)
T ss_pred CcCCCCCCCCc
Confidence 36888888875
No 117
>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=61.06 E-value=2.4 Score=18.77 Aligned_cols=9 Identities=56% Similarity=1.139 Sum_probs=4.2
Q ss_pred ecccccccc
Q psy691 61 ACHLCSKSF 69 (134)
Q Consensus 61 ~C~~C~~~f 69 (134)
.|-.|++.|
T Consensus 2 sCiDC~~~F 10 (28)
T PF08790_consen 2 SCIDCSKDF 10 (28)
T ss_dssp EETTTTEEE
T ss_pred eeecCCCCc
Confidence 344444444
No 118
>PF02176 zf-TRAF: TRAF-type zinc finger; PDB: 2EOD_A 2YUC_A 3HCU_A 3HCS_B 3HCT_A.
Probab=60.72 E-value=3.2 Score=21.46 Aligned_cols=40 Identities=15% Similarity=0.490 Sum_probs=18.1
Q ss_pred ceeccc--cccccCChHHHHHHHHHcCCCCceeccc----ccccccC
Q psy691 59 RFACHL--CSKSFSLQRLLNRHMKCHSDVKRYLCTF----CGKGFND 99 (134)
Q Consensus 59 ~~~C~~--C~~~f~~~~~l~~H~~~h~~~k~~~C~~----C~~~f~~ 99 (134)
+-.|+. |...+. +..|..|+...=..++..|.+ |...+..
T Consensus 9 ~v~C~~~cc~~~i~-r~~l~~H~~~~C~~~~v~C~~~~~GC~~~~~~ 54 (60)
T PF02176_consen 9 PVPCPNGCCNEMIP-RKELDDHLENECPKRPVPCPYSPYGCKERVPR 54 (60)
T ss_dssp EEE-TT--S-BEEE-CCCHHHHHHTTSTTSEEE-SS----S--EEEH
T ss_pred EeeCCCCCccccee-HHHHHHHHHccCCCCcEECCCCCCCCCCccch
Confidence 345655 434344 345666666443445566666 6655443
No 119
>PF13451 zf-trcl: Probable zinc-binding domain
Probab=60.61 E-value=9 Score=19.39 Aligned_cols=38 Identities=16% Similarity=0.335 Sum_probs=20.1
Q ss_pred CCceeccccccccCChHHHHHHHHH-cCCCCceeccccc
Q psy691 57 NTRFACHLCSKSFSLQRLLNRHMKC-HSDVKRYLCTFCG 94 (134)
Q Consensus 57 ~~~~~C~~C~~~f~~~~~l~~H~~~-h~~~k~~~C~~C~ 94 (134)
++.+.|..||..|.....=+..... -....|-.|..|-
T Consensus 2 Dk~l~C~dCg~~FvfTa~EQ~fy~eKgf~n~p~RC~~CR 40 (49)
T PF13451_consen 2 DKTLTCKDCGAEFVFTAGEQKFYAEKGFDNEPKRCPSCR 40 (49)
T ss_pred CeeEEcccCCCeEEEehhHHHHHHhcCCcCCCccCHHHH
Confidence 3567888888877754333322222 1112455666664
No 120
>KOG2071|consensus
Probab=59.20 E-value=5.3 Score=30.86 Aligned_cols=29 Identities=24% Similarity=0.449 Sum_probs=21.1
Q ss_pred CCceecccccccccChhhHHHHHhHhcCC
Q psy691 85 VKRYLCTFCGKGFNDTFDLKRHTRTHTGK 113 (134)
Q Consensus 85 ~k~~~C~~C~~~f~~~~~l~~H~~~h~~~ 113 (134)
.+|-+|..||.+|........||..|..+
T Consensus 416 ~~pnqC~~CG~R~~~~ee~sk~md~H~dw 444 (579)
T KOG2071|consen 416 DSPNQCKSCGLRFDDSEERSKHMDIHDDW 444 (579)
T ss_pred CCcchhcccccccccchhhhhHhhhhhhh
Confidence 45678888888888877777777666543
No 121
>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=58.32 E-value=6.1 Score=21.09 Aligned_cols=28 Identities=36% Similarity=0.710 Sum_probs=13.4
Q ss_pred eeccccccccCChHHHHHHHHHcCCCCceecccccccccC
Q psy691 60 FACHLCSKSFSLQRLLNRHMKCHSDVKRYLCTFCGKGFND 99 (134)
Q Consensus 60 ~~C~~C~~~f~~~~~l~~H~~~h~~~k~~~C~~C~~~f~~ 99 (134)
-.|..|++.|.. -.+.+.|..||..|-.
T Consensus 10 ~~C~~C~~~F~~------------~~rrhhCr~CG~~vC~ 37 (69)
T PF01363_consen 10 SNCMICGKKFSL------------FRRRHHCRNCGRVVCS 37 (69)
T ss_dssp SB-TTT--B-BS------------SS-EEE-TTT--EEEC
T ss_pred CcCcCcCCcCCC------------ceeeEccCCCCCEECC
Confidence 478889998853 1456778888877664
No 122
>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=58.32 E-value=3.8 Score=21.20 Aligned_cols=30 Identities=23% Similarity=0.548 Sum_probs=16.6
Q ss_pred eeccccccccCChHHHHHHHHHcCCCCceecccccccc
Q psy691 60 FACHLCSKSFSLQRLLNRHMKCHSDVKRYLCTFCGKGF 97 (134)
Q Consensus 60 ~~C~~C~~~f~~~~~l~~H~~~h~~~k~~~C~~C~~~f 97 (134)
|.|+.|+..+.-.... .++ ...|..||..+
T Consensus 3 ~~CP~CG~~iev~~~~-------~Ge-iV~Cp~CGael 32 (54)
T TIGR01206 3 FECPDCGAEIELENPE-------LGE-LVICDECGAEL 32 (54)
T ss_pred cCCCCCCCEEecCCCc-------cCC-EEeCCCCCCEE
Confidence 5777777766433221 122 45777777544
No 123
>KOG2593|consensus
Probab=58.10 E-value=14 Score=27.57 Aligned_cols=39 Identities=18% Similarity=0.512 Sum_probs=26.5
Q ss_pred CCCCceeccccccccCChHHHHHHHHHcCCCCceeccccccc
Q psy691 55 KDNTRFACHLCSKSFSLQRLLNRHMKCHSDVKRYLCTFCGKG 96 (134)
Q Consensus 55 ~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~k~~~C~~C~~~ 96 (134)
....-|.|+.|.+.|+.-..+ +..-...--|.|..|+-.
T Consensus 124 t~~~~Y~Cp~C~kkyt~Lea~---~L~~~~~~~F~C~~C~ge 162 (436)
T KOG2593|consen 124 TNVAGYVCPNCQKKYTSLEAL---QLLDNETGEFHCENCGGE 162 (436)
T ss_pred cccccccCCccccchhhhHHH---HhhcccCceEEEecCCCc
Confidence 344569999999999854443 344433456999999743
No 124
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=57.99 E-value=11 Score=27.48 Aligned_cols=22 Identities=27% Similarity=0.493 Sum_probs=19.8
Q ss_pred eccccccccCChHHHHHHHHHc
Q psy691 61 ACHLCSKSFSLQRLLNRHMKCH 82 (134)
Q Consensus 61 ~C~~C~~~f~~~~~l~~H~~~h 82 (134)
.|.+|...|.....|..|+|..
T Consensus 222 ~C~FC~~~FYdDDEL~~HcR~~ 243 (493)
T COG5236 222 LCIFCKIYFYDDDELRRHCRLR 243 (493)
T ss_pred hhhhccceecChHHHHHHHHhh
Confidence 6999999999999999999863
No 125
>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=57.72 E-value=9.2 Score=28.92 Aligned_cols=27 Identities=33% Similarity=0.437 Sum_probs=23.0
Q ss_pred ceeccccccccCChHHHHHHHHH-cCCC
Q psy691 59 RFACHLCSKSFSLQRLLNRHMKC-HSDV 85 (134)
Q Consensus 59 ~~~C~~C~~~f~~~~~l~~H~~~-h~~~ 85 (134)
-|.|+.|.+.|.....+..|+.. |.+.
T Consensus 57 FWiCp~CskkF~d~~~~~~H~~~eH~~~ 84 (466)
T PF04780_consen 57 FWICPRCSKKFSDAESCLSHMEQEHPAG 84 (466)
T ss_pred EeeCCcccceeCCHHHHHHHHHHhhhhh
Confidence 36899999999999999999985 7653
No 126
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=57.66 E-value=4.8 Score=23.17 Aligned_cols=14 Identities=36% Similarity=0.755 Sum_probs=8.5
Q ss_pred CceecccccccccC
Q psy691 86 KRYLCTFCGKGFND 99 (134)
Q Consensus 86 k~~~C~~C~~~f~~ 99 (134)
+|-.|..||..|..
T Consensus 57 ~Pa~CkkCGfef~~ 70 (97)
T COG3357 57 RPARCKKCGFEFRD 70 (97)
T ss_pred cChhhcccCccccc
Confidence 45566666666554
No 127
>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=57.23 E-value=5.3 Score=18.79 Aligned_cols=29 Identities=21% Similarity=0.596 Sum_probs=17.3
Q ss_pred eeccccccccCChHHHHHHHHHcCCCCceecccccc
Q psy691 60 FACHLCSKSFSLQRLLNRHMKCHSDVKRYLCTFCGK 95 (134)
Q Consensus 60 ~~C~~C~~~f~~~~~l~~H~~~h~~~k~~~C~~C~~ 95 (134)
|.|..||..|...... .. .....|+.|+.
T Consensus 6 y~C~~Cg~~fe~~~~~------~~-~~~~~CP~Cg~ 34 (41)
T smart00834 6 YRCEDCGHTFEVLQKI------SD-DPLATCPECGG 34 (41)
T ss_pred EEcCCCCCEEEEEEec------CC-CCCCCCCCCCC
Confidence 6788888877633221 11 34456777775
No 128
>KOG4124|consensus
Probab=57.13 E-value=1.2 Score=32.04 Aligned_cols=53 Identities=28% Similarity=0.593 Sum_probs=38.3
Q ss_pred CCceeccc--cccccCChHHHHHHHHH-cC------------------CCCceecccccccccChhhHHHHHhH
Q psy691 57 NTRFACHL--CSKSFSLQRLLNRHMKC-HS------------------DVKRYLCTFCGKGFNDTFDLKRHTRT 109 (134)
Q Consensus 57 ~~~~~C~~--C~~~f~~~~~l~~H~~~-h~------------------~~k~~~C~~C~~~f~~~~~l~~H~~~ 109 (134)
.++|.|.+ |.+.++....|..|-.. |- ..|+|+|++|.++++....|..|...
T Consensus 347 ~~~~~~~vp~~~~~~~n~ng~~~~~~~~h~s~i~~~s~~~~ph~~~~~~nk~~r~~i~~~~~k~~~~l~~~~~~ 420 (442)
T KOG4124|consen 347 DKPYKCPVPNCDKAYKNQNGLKYHKLHGHCSPITTPTPAPIPHQGFVVENKPYRCEVCSKRYKNLNGLKYHRTH 420 (442)
T ss_pred cCCCCCCCCcchhhcccCcceeeccccCcCCCCCCCCCCCCCcceeeeccCcccChhhhhhhccCCCCCceeeh
Confidence 55778876 88888877777776543 31 14789999999998888887766544
No 129
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=57.04 E-value=3.5 Score=25.63 Aligned_cols=15 Identities=27% Similarity=0.744 Sum_probs=11.1
Q ss_pred CceeccccccccCCh
Q psy691 58 TRFACHLCSKSFSLQ 72 (134)
Q Consensus 58 ~~~~C~~C~~~f~~~ 72 (134)
..+.|..||..|...
T Consensus 69 ~~~~C~~CG~~~~~~ 83 (135)
T PRK03824 69 AVLKCRNCGNEWSLK 83 (135)
T ss_pred eEEECCCCCCEEecc
Confidence 358898899887653
No 130
>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=55.18 E-value=5 Score=18.81 Aligned_cols=11 Identities=18% Similarity=0.667 Sum_probs=6.2
Q ss_pred eeccccccccC
Q psy691 60 FACHLCSKSFS 70 (134)
Q Consensus 60 ~~C~~C~~~f~ 70 (134)
+.|+.||+.|.
T Consensus 2 r~C~~Cg~~Yh 12 (36)
T PF05191_consen 2 RICPKCGRIYH 12 (36)
T ss_dssp EEETTTTEEEE
T ss_pred cCcCCCCCccc
Confidence 35666666654
No 131
>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=54.06 E-value=9.1 Score=16.25 Aligned_cols=11 Identities=27% Similarity=0.670 Sum_probs=7.5
Q ss_pred CCceecccccc
Q psy691 57 NTRFACHLCSK 67 (134)
Q Consensus 57 ~~~~~C~~C~~ 67 (134)
...|.|+.||+
T Consensus 14 ~v~f~CPnCG~ 24 (24)
T PF07754_consen 14 AVPFPCPNCGF 24 (24)
T ss_pred CceEeCCCCCC
Confidence 34588888874
No 132
>KOG3408|consensus
Probab=53.42 E-value=9.5 Score=23.25 Aligned_cols=26 Identities=31% Similarity=0.538 Sum_probs=22.4
Q ss_pred CCCceecccccccccChhhHHHHHhH
Q psy691 84 DVKRYLCTFCGKGFNDTFDLKRHTRT 109 (134)
Q Consensus 84 ~~k~~~C~~C~~~f~~~~~l~~H~~~ 109 (134)
|.-.|-|..|.+-|.....|..|.++
T Consensus 54 G~GqfyCi~CaRyFi~~~~l~~H~kt 79 (129)
T KOG3408|consen 54 GGGQFYCIECARYFIDAKALKTHFKT 79 (129)
T ss_pred CCceeehhhhhhhhcchHHHHHHHhc
Confidence 34458999999999999999999775
No 133
>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=51.26 E-value=7.6 Score=18.74 Aligned_cols=29 Identities=21% Similarity=0.589 Sum_probs=16.9
Q ss_pred eeccccccccCChHHHHHHHHHcCCCCceecccccc
Q psy691 60 FACHLCSKSFSLQRLLNRHMKCHSDVKRYLCTFCGK 95 (134)
Q Consensus 60 ~~C~~C~~~f~~~~~l~~H~~~h~~~k~~~C~~C~~ 95 (134)
|.|..||..|..... ... .....|+.|+.
T Consensus 6 y~C~~Cg~~fe~~~~------~~~-~~~~~CP~Cg~ 34 (42)
T PF09723_consen 6 YRCEECGHEFEVLQS------ISE-DDPVPCPECGS 34 (42)
T ss_pred EEeCCCCCEEEEEEE------cCC-CCCCcCCCCCC
Confidence 677778777763322 122 34567777765
No 134
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=50.25 E-value=4.8 Score=23.63 Aligned_cols=40 Identities=18% Similarity=0.370 Sum_probs=24.1
Q ss_pred CCCceeccccccccCChHHHHHHHHHcCCCCceecccccccccC
Q psy691 56 DNTRFACHLCSKSFSLQRLLNRHMKCHSDVKRYLCTFCGKGFND 99 (134)
Q Consensus 56 ~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~k~~~C~~C~~~f~~ 99 (134)
-.+.|.|+.|+..-.....++ .-.+.--..|..||.+|.-
T Consensus 19 L~k~FtCp~Cghe~vs~ctvk----k~~~~g~~~Cg~CGls~e~ 58 (104)
T COG4888 19 LPKTFTCPRCGHEKVSSCTVK----KTVNIGTAVCGNCGLSFEC 58 (104)
T ss_pred CCceEecCccCCeeeeEEEEE----ecCceeEEEcccCcceEEE
Confidence 456799999997655433322 1111223578888877753
No 135
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=48.74 E-value=8.1 Score=23.18 Aligned_cols=25 Identities=20% Similarity=0.525 Sum_probs=16.4
Q ss_pred ceeccccccccCChHHHHHHHHHcCCCCceecccccc
Q psy691 59 RFACHLCSKSFSLQRLLNRHMKCHSDVKRYLCTFCGK 95 (134)
Q Consensus 59 ~~~C~~C~~~f~~~~~l~~H~~~h~~~k~~~C~~C~~ 95 (134)
.+.|..|+..|.... ..+.|+.|+.
T Consensus 70 ~~~C~~Cg~~~~~~~------------~~~~CP~Cgs 94 (113)
T PRK12380 70 QAWCWDCSQVVEIHQ------------HDAQCPHCHG 94 (113)
T ss_pred EEEcccCCCEEecCC------------cCccCcCCCC
Confidence 478888887776432 2356888874
No 136
>PLN03238 probable histone acetyltransferase MYST; Provisional
Probab=48.66 E-value=18 Score=25.64 Aligned_cols=22 Identities=32% Similarity=0.631 Sum_probs=11.1
Q ss_pred ceecccccccccChhhHHHHHh
Q psy691 87 RYLCTFCGKGFNDTFDLKRHTR 108 (134)
Q Consensus 87 ~~~C~~C~~~f~~~~~l~~H~~ 108 (134)
-|.|+.|-+-|.....|.+|+.
T Consensus 48 lyiCe~Clky~~~~~~l~~H~~ 69 (290)
T PLN03238 48 LYICEYCLKYMRKKKSLLRHLA 69 (290)
T ss_pred EEEcCCCcchhCCHHHHHHHHH
Confidence 3455555555555555555544
No 137
>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=48.62 E-value=13 Score=19.82 Aligned_cols=14 Identities=21% Similarity=0.655 Sum_probs=8.0
Q ss_pred CCceeccccccccc
Q psy691 85 VKRYLCTFCGKGFN 98 (134)
Q Consensus 85 ~k~~~C~~C~~~f~ 98 (134)
.+-|.|+.||..+.
T Consensus 44 ~r~~~C~~Cg~~~~ 57 (69)
T PF07282_consen 44 GRVFTCPNCGFEMD 57 (69)
T ss_pred cceEEcCCCCCEEC
Confidence 34566666665543
No 138
>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=48.56 E-value=23 Score=24.73 Aligned_cols=75 Identities=15% Similarity=0.211 Sum_probs=41.5
Q ss_pred CCCceeccccccccCChHHHHHHHHH--cCCCCceecccccccccChhhHH-------HHHhH----hcCCCccccccCC
Q psy691 56 DNTRFACHLCSKSFSLQRLLNRHMKC--HSDVKRYLCTFCGKGFNDTFDLK-------RHTRT----HTGKEEEEEEDGK 122 (134)
Q Consensus 56 ~~~~~~C~~C~~~f~~~~~l~~H~~~--h~~~k~~~C~~C~~~f~~~~~l~-------~H~~~----h~~~~~~~c~~~~ 122 (134)
+-+.|.|.+|..-.--.. --.|+.+ -.....|+|..|++. .+-+-|+ .|.+. ....+++.|+.|+
T Consensus 139 GGrif~CsfC~~flCEDD-QFEHQAsCQvLe~E~~KC~SCNrl-Gq~sCLRCK~cfCddHvrrKg~ky~k~k~~PCPKCg 216 (314)
T PF06524_consen 139 GGRIFKCSFCDNFLCEDD-QFEHQASCQVLESETFKCQSCNRL-GQYSCLRCKICFCDDHVRRKGFKYEKGKPIPCPKCG 216 (314)
T ss_pred CCeEEEeecCCCeeeccc-hhhhhhhhhhhhcccccccccccc-cchhhhheeeeehhhhhhhcccccccCCCCCCCCCC
Confidence 456799999886544333 3345543 223345777777652 2222222 34332 3344788898888
Q ss_pred CcccCcccee
Q psy691 123 TNVLTTEYLV 132 (134)
Q Consensus 123 ~~~~~~~~l~ 132 (134)
.-..-...|+
T Consensus 217 ~et~eTkdLS 226 (314)
T PF06524_consen 217 YETQETKDLS 226 (314)
T ss_pred Ccccccccce
Confidence 7666555554
No 139
>PF14311 DUF4379: Domain of unknown function (DUF4379)
Probab=48.30 E-value=12 Score=19.04 Aligned_cols=14 Identities=14% Similarity=0.603 Sum_probs=10.3
Q ss_pred ceeccccccccCCh
Q psy691 59 RFACHLCSKSFSLQ 72 (134)
Q Consensus 59 ~~~C~~C~~~f~~~ 72 (134)
-+.|..|+..|...
T Consensus 28 ~W~C~~Cgh~w~~~ 41 (55)
T PF14311_consen 28 WWKCPKCGHEWKAS 41 (55)
T ss_pred EEECCCCCCeeEcc
Confidence 37888888777654
No 140
>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=48.29 E-value=7.7 Score=23.35 Aligned_cols=25 Identities=28% Similarity=0.515 Sum_probs=16.7
Q ss_pred ceeccccccccCChHHHHHHHHHcCCCCceecccccc
Q psy691 59 RFACHLCSKSFSLQRLLNRHMKCHSDVKRYLCTFCGK 95 (134)
Q Consensus 59 ~~~C~~C~~~f~~~~~l~~H~~~h~~~k~~~C~~C~~ 95 (134)
...|..|+..|..... .+.|+.|+.
T Consensus 70 ~~~C~~Cg~~~~~~~~------------~~~CP~Cgs 94 (115)
T TIGR00100 70 ECECEDCSEEVSPEID------------LYRCPKCHG 94 (115)
T ss_pred EEEcccCCCEEecCCc------------CccCcCCcC
Confidence 4788888877764321 356888874
No 141
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=47.36 E-value=9.7 Score=18.13 Aligned_cols=14 Identities=29% Similarity=0.783 Sum_probs=11.7
Q ss_pred ceecccccccccCh
Q psy691 87 RYLCTFCGKGFNDT 100 (134)
Q Consensus 87 ~~~C~~C~~~f~~~ 100 (134)
||.|..|++.|-..
T Consensus 12 ~f~C~~C~~~FC~~ 25 (39)
T smart00154 12 GFKCRHCGNLFCGE 25 (39)
T ss_pred CeECCccCCccccc
Confidence 78899999888774
No 142
>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=46.56 E-value=13 Score=18.82 Aligned_cols=27 Identities=37% Similarity=0.819 Sum_probs=16.0
Q ss_pred eccccccccCChHHHHHHHHHcCCCCceecccccccccC
Q psy691 61 ACHLCSKSFSLQRLLNRHMKCHSDVKRYLCTFCGKGFND 99 (134)
Q Consensus 61 ~C~~C~~~f~~~~~l~~H~~~h~~~k~~~C~~C~~~f~~ 99 (134)
.|..|++.|.. ..+.+.|..||+.|-.
T Consensus 4 ~C~~C~~~F~~------------~~rk~~Cr~Cg~~~C~ 30 (57)
T cd00065 4 SCMGCGKPFTL------------TRRRHHCRNCGRIFCS 30 (57)
T ss_pred cCcccCccccC------------CccccccCcCcCCcCh
Confidence 46677777763 1234566666666554
No 143
>COG1773 Rubredoxin [Energy production and conversion]
Probab=46.48 E-value=9.9 Score=19.75 Aligned_cols=13 Identities=23% Similarity=0.843 Sum_probs=9.2
Q ss_pred ceeccccccccCC
Q psy691 59 RFACHLCSKSFSL 71 (134)
Q Consensus 59 ~~~C~~C~~~f~~ 71 (134)
.|+|..||..|.-
T Consensus 3 ~~~C~~CG~vYd~ 15 (55)
T COG1773 3 RWRCSVCGYVYDP 15 (55)
T ss_pred ceEecCCceEecc
Confidence 4778888877653
No 144
>PF12907 zf-met2: Zinc-binding
Probab=46.31 E-value=14 Score=17.85 Aligned_cols=20 Identities=25% Similarity=0.747 Sum_probs=8.5
Q ss_pred ecccccccc---CChHHHHHHHH
Q psy691 61 ACHLCSKSF---SLQRLLNRHMK 80 (134)
Q Consensus 61 ~C~~C~~~f---~~~~~l~~H~~ 80 (134)
.|.+|-.+| .+...|..|..
T Consensus 3 ~C~iC~qtF~~t~~~~~L~eH~e 25 (40)
T PF12907_consen 3 ICKICRQTFMQTTNEPQLKEHAE 25 (40)
T ss_pred CcHHhhHHHHhcCCHHHHHHHHH
Confidence 455555332 22344555544
No 145
>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=46.04 E-value=8.2 Score=18.70 Aligned_cols=15 Identities=33% Similarity=0.767 Sum_probs=9.7
Q ss_pred CceecccccccccCh
Q psy691 86 KRYLCTFCGKGFNDT 100 (134)
Q Consensus 86 k~~~C~~C~~~f~~~ 100 (134)
.|+.|..|++.|-..
T Consensus 12 ~~~~C~~C~~~FC~~ 26 (43)
T PF01428_consen 12 LPFKCKHCGKSFCLK 26 (43)
T ss_dssp SHEE-TTTS-EE-TT
T ss_pred CCeECCCCCcccCcc
Confidence 478999999988874
No 146
>KOG2231|consensus
Probab=45.78 E-value=15 Score=29.20 Aligned_cols=23 Identities=35% Similarity=0.834 Sum_probs=16.3
Q ss_pred eecccccccc---------------CChHHHHHHHHH-c
Q psy691 60 FACHLCSKSF---------------SLQRLLNRHMKC-H 82 (134)
Q Consensus 60 ~~C~~C~~~f---------------~~~~~l~~H~~~-h 82 (134)
+.|.+|.+.| .....|+.|+.. |
T Consensus 100 ~~C~~C~~~~~~~~~~~~~~~c~~~~s~~~Lk~H~~~~H 138 (669)
T KOG2231|consen 100 HSCHICDRRFRALYNKKECLHCTEFKSVENLKNHMRDQH 138 (669)
T ss_pred hhcCccccchhhhcccCCCccccchhHHHHHHHHHHHhh
Confidence 5677777666 267888999854 5
No 147
>COG4306 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=45.62 E-value=5.6 Score=24.38 Aligned_cols=41 Identities=22% Similarity=0.354 Sum_probs=21.2
Q ss_pred eeccccccccCChHHHHHHHHH-cCCCCceecccccccccCh
Q psy691 60 FACHLCSKSFSLQRLLNRHMKC-HSDVKRYLCTFCGKGFNDT 100 (134)
Q Consensus 60 ~~C~~C~~~f~~~~~l~~H~~~-h~~~k~~~C~~C~~~f~~~ 100 (134)
..|++|.....-......-+.. |.-+.|--|..||+.|.+.
T Consensus 40 ~qcp~csasirgd~~vegvlglg~dye~psfchncgs~fpwt 81 (160)
T COG4306 40 TQCPICSASIRGDYYVEGVLGLGGDYEPPSFCHNCGSRFPWT 81 (160)
T ss_pred hcCCccCCcccccceeeeeeccCCCCCCcchhhcCCCCCCcH
Confidence 4566666554433222221111 3335566777788777763
No 148
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=45.42 E-value=7.5 Score=22.41 Aligned_cols=7 Identities=71% Similarity=2.209 Sum_probs=3.5
Q ss_pred eeccccc
Q psy691 88 YLCTFCG 94 (134)
Q Consensus 88 ~~C~~C~ 94 (134)
|.|++|+
T Consensus 37 y~CpfCg 43 (90)
T PTZ00255 37 YFCPFCG 43 (90)
T ss_pred ccCCCCC
Confidence 4555554
No 149
>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=45.27 E-value=20 Score=17.55 Aligned_cols=8 Identities=38% Similarity=1.522 Sum_probs=4.5
Q ss_pred eecccccc
Q psy691 88 YLCTFCGK 95 (134)
Q Consensus 88 ~~C~~C~~ 95 (134)
+.|+.|+.
T Consensus 19 ~~CP~Cg~ 26 (46)
T PF12760_consen 19 FVCPHCGS 26 (46)
T ss_pred CCCCCCCC
Confidence 45666653
No 150
>COG2331 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=45.01 E-value=7.1 Score=21.70 Aligned_cols=33 Identities=24% Similarity=0.614 Sum_probs=20.3
Q ss_pred ceeccccccccCChHHHHHHHHHcCCCCceeccccccccc
Q psy691 59 RFACHLCSKSFSLQRLLNRHMKCHSDVKRYLCTFCGKGFN 98 (134)
Q Consensus 59 ~~~C~~C~~~f~~~~~l~~H~~~h~~~k~~~C~~C~~~f~ 98 (134)
.|.|..|+..|. +..||. ...--.|+.|+-.+.
T Consensus 12 ~Y~c~~cg~~~d----vvq~~~---ddplt~ce~c~a~~k 44 (82)
T COG2331 12 SYECTECGNRFD----VVQAMT---DDPLTTCEECGARLK 44 (82)
T ss_pred EEeecccchHHH----HHHhcc---cCccccChhhChHHH
Confidence 489999987753 444443 223347888876543
No 151
>KOG2636|consensus
Probab=44.77 E-value=17 Score=27.35 Aligned_cols=27 Identities=30% Similarity=0.554 Sum_probs=18.1
Q ss_pred HHcCCCCceeccccc-ccccChhhHHHH
Q psy691 80 KCHSDVKRYLCTFCG-KGFNDTFDLKRH 106 (134)
Q Consensus 80 ~~h~~~k~~~C~~C~-~~f~~~~~l~~H 106 (134)
+.|--.+-|.|.+|| ..+..+..+.+|
T Consensus 394 KLHGL~~ey~CEICGNy~Y~GrkaF~RH 421 (497)
T KOG2636|consen 394 KLHGLDIEYNCEICGNYVYKGRKAFDRH 421 (497)
T ss_pred hhcCCCcccceeeccCccccCcHHHHHH
Confidence 345556667777777 666677777777
No 152
>PF08209 Sgf11: Sgf11 (transcriptional regulation protein); InterPro: IPR013246 The Sgf11 family is a SAGA complex subunit in Saccharomyces cerevisiae (Baker's yeast). The SAGA complex is a multisubunit protein complex involved in transcriptional regulation. SAGA combines proteins involved in interactions with DNA-bound activators and TATA-binding protein (TBP), as well as enzymes for histone acetylation and deubiquitylation [].; PDB: 3M99_B 2LO2_A 3MHH_C 3MHS_C.
Probab=44.48 E-value=21 Score=16.39 Aligned_cols=22 Identities=14% Similarity=0.415 Sum_probs=14.3
Q ss_pred ceeccccccccCChHHHHHHHHH
Q psy691 59 RFACHLCSKSFSLQRLLNRHMKC 81 (134)
Q Consensus 59 ~~~C~~C~~~f~~~~~l~~H~~~ 81 (134)
.+.|+.|++.+. ...+..|+..
T Consensus 4 ~~~C~nC~R~v~-a~RfA~HLek 25 (33)
T PF08209_consen 4 YVECPNCGRPVA-ASRFAPHLEK 25 (33)
T ss_dssp EEE-TTTSSEEE-GGGHHHHHHH
T ss_pred eEECCCCcCCcc-hhhhHHHHHH
Confidence 478888888765 4556667654
No 153
>PF14445 Prok-RING_2: Prokaryotic RING finger family 2
Probab=44.32 E-value=7.1 Score=19.83 Aligned_cols=14 Identities=36% Similarity=1.065 Sum_probs=10.4
Q ss_pred ceeccccccccCCh
Q psy691 59 RFACHLCSKSFSLQ 72 (134)
Q Consensus 59 ~~~C~~C~~~f~~~ 72 (134)
.|.|+.|...+..+
T Consensus 7 ry~CDLCn~~~p~~ 20 (57)
T PF14445_consen 7 RYSCDLCNSSHPIS 20 (57)
T ss_pred hHhHHhhcccCcHH
Confidence 47888888887643
No 154
>COG4896 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=44.13 E-value=13 Score=19.68 Aligned_cols=40 Identities=15% Similarity=0.412 Sum_probs=21.9
Q ss_pred eeccccccccC-ChHHHHHHHHHcCCCCceecccccccccC
Q psy691 60 FACHLCSKSFS-LQRLLNRHMKCHSDVKRYLCTFCGKGFND 99 (134)
Q Consensus 60 ~~C~~C~~~f~-~~~~l~~H~~~h~~~k~~~C~~C~~~f~~ 99 (134)
-.|.+|.+.-. ....+..-.......+-|.|+.|..+...
T Consensus 3 vkCiiCd~v~~iD~rt~~tKrLrN~PIrtymC~eC~~Rva~ 43 (68)
T COG4896 3 VKCIICDRVDEIDNRTFKTKRLRNKPIRTYMCPECEHRVAI 43 (68)
T ss_pred ceEEEecceeeecchhHHHHHhhCCCceeEechhhHhhhch
Confidence 36778876533 23334333333334456889988755443
No 155
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=44.08 E-value=9.4 Score=23.07 Aligned_cols=13 Identities=31% Similarity=0.733 Sum_probs=9.7
Q ss_pred ceeccccccccCC
Q psy691 59 RFACHLCSKSFSL 71 (134)
Q Consensus 59 ~~~C~~C~~~f~~ 71 (134)
.+.|..|+..|..
T Consensus 71 ~~~C~~Cg~~~~~ 83 (117)
T PRK00564 71 ELECKDCSHVFKP 83 (117)
T ss_pred EEEhhhCCCcccc
Confidence 4788888877764
No 156
>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=43.83 E-value=7 Score=24.51 Aligned_cols=31 Identities=29% Similarity=0.742 Sum_probs=15.6
Q ss_pred ceeccccccccCChHHHHHHHHHcCCCCceecccccccc
Q psy691 59 RFACHLCSKSFSLQRLLNRHMKCHSDVKRYLCTFCGKGF 97 (134)
Q Consensus 59 ~~~C~~C~~~f~~~~~l~~H~~~h~~~k~~~C~~C~~~f 97 (134)
.|.|..|+..+.+... . ....|.|..|+..+
T Consensus 123 ~~~C~~C~~~~~r~~~------~--~~~~~~C~~C~~~l 153 (157)
T PF10263_consen 123 VYRCPSCGREYKRHRR------S--KRKRYRCGRCGGPL 153 (157)
T ss_pred EEEcCCCCCEeeeecc------c--chhhEECCCCCCEE
Confidence 4667667666533222 1 12236666666444
No 157
>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=43.46 E-value=9.6 Score=22.83 Aligned_cols=15 Identities=27% Similarity=0.640 Sum_probs=9.4
Q ss_pred ceeccccccccCChH
Q psy691 59 RFACHLCSKSFSLQR 73 (134)
Q Consensus 59 ~~~C~~C~~~f~~~~ 73 (134)
.+.|..|+..|....
T Consensus 70 ~~~C~~Cg~~~~~~~ 84 (113)
T PF01155_consen 70 RARCRDCGHEFEPDE 84 (113)
T ss_dssp EEEETTTS-EEECHH
T ss_pred cEECCCCCCEEecCC
Confidence 367878887776543
No 158
>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 PF12230 PRP21_like_P: Pre-mRNA splicing factor PRP21 like protein; InterPro: IPR022030 This domain family is found in eukaryotes, and is typically between 212 and 238 amino acids in length. The family is found in association with PF01805 from PFAM. There are two completely conserved residues (W and H) that may be functionally important. PRP21 is required for assembly of the prespliceosome and it interacts with U2 snRNP and/or pre-mRNA in the prespliceosome. This family also contains proteins similar to PRP21, such as the mammalian SF3a. SF3a also interacts with U2 snRNP from the prespliceosome, converting it to its active form. ; PDB: 4DGW_B.
Probab=42.69 E-value=8.2 Score=26.14 Aligned_cols=30 Identities=13% Similarity=0.296 Sum_probs=0.0
Q ss_pred CceeccccccccCChHHHHHHHHHcCCCCce
Q psy691 58 TRFACHLCSKSFSLQRLLNRHMKCHSDVKRY 88 (134)
Q Consensus 58 ~~~~C~~C~~~f~~~~~l~~H~~~h~~~k~~ 88 (134)
....|++||+... ...|..|||+..-...|
T Consensus 167 ~~~~cPitGe~IP-~~e~~eHmRi~LlDP~w 196 (229)
T PF12230_consen 167 KMIICPITGEMIP-ADEMDEHMRIELLDPRW 196 (229)
T ss_dssp -------------------------------
T ss_pred ccccccccccccc-ccccccccccccccccc
Confidence 3467888887766 45677777776554433
No 160
>KOG1280|consensus
Probab=42.33 E-value=29 Score=25.30 Aligned_cols=37 Identities=22% Similarity=0.594 Sum_probs=25.9
Q ss_pred CceeccccccccCChHHHHHHHHH-cCCCCc-eeccccc
Q psy691 58 TRFACHLCSKSFSLQRLLNRHMKC-HSDVKR-YLCTFCG 94 (134)
Q Consensus 58 ~~~~C~~C~~~f~~~~~l~~H~~~-h~~~k~-~~C~~C~ 94 (134)
..|.|++|++.=.....|..|... |....+ ..|.+|.
T Consensus 78 qSftCPyC~~~Gfte~~f~~Hv~s~Hpda~~~~icp~c~ 116 (381)
T KOG1280|consen 78 QSFTCPYCGIMGFTERQFGTHVLSQHPEASTSVICPLCA 116 (381)
T ss_pred ccccCCcccccccchhHHHHHhhhcCcccCcceeeeccc
Confidence 379999999877778888899876 554331 3455554
No 161
>PF09963 DUF2197: Uncharacterized protein conserved in bacteria (DUF2197); InterPro: IPR019241 This family represents various hypothetical bacterial proteins with no known function.
Probab=42.29 E-value=14 Score=19.30 Aligned_cols=37 Identities=19% Similarity=0.492 Sum_probs=19.8
Q ss_pred eeccccccccCChHHHHHHHHH-cCCCCceeccccccc
Q psy691 60 FACHLCSKSFSLQRLLNRHMKC-HSDVKRYLCTFCGKG 96 (134)
Q Consensus 60 ~~C~~C~~~f~~~~~l~~H~~~-h~~~k~~~C~~C~~~ 96 (134)
-.|.+|++.+.....-..-.+. -.....|.|..|...
T Consensus 3 vkC~lCdk~~~Id~~~~~aKrLrnrPi~tYmC~eC~~R 40 (56)
T PF09963_consen 3 VKCILCDKKEEIDEDTPEAKRLRNRPIHTYMCDECKER 40 (56)
T ss_pred eEEEecCCEEEeccCCHHHHHhhcCCCcceeChhHHHH
Confidence 3677888777643322222222 223445888888643
No 162
>KOG0978|consensus
Probab=41.94 E-value=8.8 Score=30.51 Aligned_cols=13 Identities=15% Similarity=0.728 Sum_probs=9.1
Q ss_pred CceeccccccccC
Q psy691 58 TRFACHLCSKSFS 70 (134)
Q Consensus 58 ~~~~C~~C~~~f~ 70 (134)
....|+.|...++
T Consensus 642 ~~LkCs~Cn~R~K 654 (698)
T KOG0978|consen 642 ELLKCSVCNTRWK 654 (698)
T ss_pred hceeCCCccCchh
Confidence 4578999885554
No 163
>KOG4602|consensus
Probab=41.66 E-value=42 Score=23.44 Aligned_cols=45 Identities=18% Similarity=0.453 Sum_probs=25.7
Q ss_pred CCCCceeccccccccCChHHHHHHHHHcCC-------CCceecccccccccC
Q psy691 55 KDNTRFACHLCSKSFSLQRLLNRHMKCHSD-------VKRYLCTFCGKGFND 99 (134)
Q Consensus 55 ~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~-------~k~~~C~~C~~~f~~ 99 (134)
...++..|.+|...-.....+..|...... -+.|.|++||..-.+
T Consensus 229 ~Q~r~l~CvFC~nN~E~~A~y~tH~lkd~dgRVLCPkLR~YVCPiCGATgDn 280 (318)
T KOG4602|consen 229 NQPRPLCCVFCFNNAEEFARYHTHPLKDKDGRVLCPKLRSYVCPICGATGDN 280 (318)
T ss_pred CCCCceeEEeecCCCchhhheecccccCCCCcEechhHhhhcCccccccCCc
Confidence 344556888886554444444444332221 246999999876544
No 164
>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=41.37 E-value=8.3 Score=22.27 Aligned_cols=7 Identities=71% Similarity=2.199 Sum_probs=3.3
Q ss_pred eeccccc
Q psy691 88 YLCTFCG 94 (134)
Q Consensus 88 ~~C~~C~ 94 (134)
|.|++|+
T Consensus 36 y~CpfCg 42 (91)
T TIGR00280 36 YVCPFCG 42 (91)
T ss_pred ccCCCCC
Confidence 4444444
No 165
>KOG2636|consensus
Probab=40.88 E-value=42 Score=25.40 Aligned_cols=27 Identities=15% Similarity=0.580 Sum_probs=22.1
Q ss_pred CCCCCceeccccc-cccCChHHHHHHHH
Q psy691 54 RKDNTRFACHLCS-KSFSLQRLLNRHMK 80 (134)
Q Consensus 54 ~~~~~~~~C~~C~-~~f~~~~~l~~H~~ 80 (134)
+.-+.-|.|.+|| +++.-...+.+|..
T Consensus 396 HGL~~ey~CEICGNy~Y~GrkaF~RHF~ 423 (497)
T KOG2636|consen 396 HGLDIEYNCEICGNYVYKGRKAFDRHFN 423 (497)
T ss_pred cCCCcccceeeccCccccCcHHHHHHhH
Confidence 3445679999999 88888899999975
No 166
>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=40.70 E-value=11 Score=19.13 Aligned_cols=12 Identities=25% Similarity=0.869 Sum_probs=6.4
Q ss_pred eccccccccCCh
Q psy691 61 ACHLCSKSFSLQ 72 (134)
Q Consensus 61 ~C~~C~~~f~~~ 72 (134)
.|++|++.|...
T Consensus 22 ~CPlC~r~l~~e 33 (54)
T PF04423_consen 22 CCPLCGRPLDEE 33 (54)
T ss_dssp E-TTT--EE-HH
T ss_pred cCCCCCCCCCHH
Confidence 899999998753
No 167
>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=40.35 E-value=12 Score=16.83 Aligned_cols=8 Identities=38% Similarity=1.057 Sum_probs=4.1
Q ss_pred ceeccccc
Q psy691 87 RYLCTFCG 94 (134)
Q Consensus 87 ~~~C~~C~ 94 (134)
.+.|+.|+
T Consensus 19 ~~vCp~C~ 26 (30)
T PF08274_consen 19 LLVCPECG 26 (30)
T ss_dssp SEEETTTT
T ss_pred EEeCCccc
Confidence 35555554
No 168
>PLN00104 MYST -like histone acetyltransferase; Provisional
Probab=40.16 E-value=21 Score=26.97 Aligned_cols=25 Identities=36% Similarity=0.679 Sum_probs=21.6
Q ss_pred CCceecccccccccChhhHHHHHhH
Q psy691 85 VKRYLCTFCGKGFNDTFDLKRHTRT 109 (134)
Q Consensus 85 ~k~~~C~~C~~~f~~~~~l~~H~~~ 109 (134)
..-|.|++|-+-|.....|.+|+..
T Consensus 196 ~~lyiCe~Cl~y~~~~~~~~~H~~~ 220 (450)
T PLN00104 196 SKLYFCEFCLKFMKRKEQLQRHMKK 220 (450)
T ss_pred CeEEEchhhhhhhcCHHHHHHHHhc
Confidence 3468999999999999999999864
No 169
>COG5188 PRP9 Splicing factor 3a, subunit 3 [RNA processing and modification]
Probab=40.14 E-value=46 Score=24.43 Aligned_cols=26 Identities=19% Similarity=0.551 Sum_probs=17.9
Q ss_pred CCCCceeccccc-cccCChHHHHHHHH
Q psy691 55 KDNTRFACHLCS-KSFSLQRLLNRHMK 80 (134)
Q Consensus 55 ~~~~~~~C~~C~-~~f~~~~~l~~H~~ 80 (134)
.-..-|.|.+|| +.+.-...+.+|..
T Consensus 370 gLd~ef~CEICgNyvy~GR~~FdrHF~ 396 (470)
T COG5188 370 GLDIEFECEICGNYVYYGRDRFDRHFE 396 (470)
T ss_pred CCCcceeeeecccccccchHHHHhhhh
Confidence 344568888888 66666677777754
No 170
>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=39.76 E-value=19 Score=17.32 Aligned_cols=12 Identities=17% Similarity=0.708 Sum_probs=9.3
Q ss_pred Cceecccccccc
Q psy691 58 TRFACHLCSKSF 69 (134)
Q Consensus 58 ~~~~C~~C~~~f 69 (134)
+.-.|++|+..|
T Consensus 28 ~~~~CpYCg~~y 39 (40)
T PF10276_consen 28 GPVVCPYCGTRY 39 (40)
T ss_dssp CEEEETTTTEEE
T ss_pred CeEECCCCCCEE
Confidence 357899998876
No 171
>KOG0717|consensus
Probab=38.74 E-value=23 Score=26.87 Aligned_cols=22 Identities=32% Similarity=0.708 Sum_probs=20.1
Q ss_pred eeccccccccCChHHHHHHHHH
Q psy691 60 FACHLCSKSFSLQRLLNRHMKC 81 (134)
Q Consensus 60 ~~C~~C~~~f~~~~~l~~H~~~ 81 (134)
+.|.+|.+.|.+...|..|..+
T Consensus 293 lyC~vCnKsFKseKq~kNHEnS 314 (508)
T KOG0717|consen 293 LYCVVCNKSFKSEKQLKNHENS 314 (508)
T ss_pred eEEeeccccccchHHHHhhHHH
Confidence 8999999999999999999765
No 172
>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=38.26 E-value=15 Score=18.33 Aligned_cols=12 Identities=17% Similarity=0.811 Sum_probs=7.6
Q ss_pred eeccccccccCC
Q psy691 60 FACHLCSKSFSL 71 (134)
Q Consensus 60 ~~C~~C~~~f~~ 71 (134)
|.|..|+..+..
T Consensus 2 y~C~~CgyvYd~ 13 (47)
T PF00301_consen 2 YQCPVCGYVYDP 13 (47)
T ss_dssp EEETTTSBEEET
T ss_pred cCCCCCCEEEcC
Confidence 567777766543
No 173
>PTZ00064 histone acetyltransferase; Provisional
Probab=38.06 E-value=26 Score=26.92 Aligned_cols=25 Identities=24% Similarity=0.313 Sum_probs=21.6
Q ss_pred CCceecccccccccChhhHHHHHhH
Q psy691 85 VKRYLCTFCGKGFNDTFDLKRHTRT 109 (134)
Q Consensus 85 ~k~~~C~~C~~~f~~~~~l~~H~~~ 109 (134)
..-|.|++|-+-|.....|.+|+..
T Consensus 278 d~LYICEfCLkY~~s~~~l~rH~~~ 302 (552)
T PTZ00064 278 DTLHFCEYCLDFFCFEDELIRHLSR 302 (552)
T ss_pred CeEEEccchhhhhCCHHHHHHHHhc
Confidence 3568999999999999999999774
No 174
>KOG0717|consensus
Probab=37.94 E-value=21 Score=27.10 Aligned_cols=22 Identities=32% Similarity=0.729 Sum_probs=19.9
Q ss_pred eecccccccccChhhHHHHHhH
Q psy691 88 YLCTFCGKGFNDTFDLKRHTRT 109 (134)
Q Consensus 88 ~~C~~C~~~f~~~~~l~~H~~~ 109 (134)
+-|.+|.|.|.+...|..|...
T Consensus 293 lyC~vCnKsFKseKq~kNHEnS 314 (508)
T KOG0717|consen 293 LYCVVCNKSFKSEKQLKNHENS 314 (508)
T ss_pred eEEeeccccccchHHHHhhHHH
Confidence 7899999999999999999665
No 175
>KOG4727|consensus
Probab=37.78 E-value=33 Score=22.33 Aligned_cols=27 Identities=15% Similarity=0.349 Sum_probs=21.7
Q ss_pred CCCCCceeccccccccCChHHHHHHHH
Q psy691 54 RKDNTRFACHLCSKSFSLQRLLNRHMK 80 (134)
Q Consensus 54 ~~~~~~~~C~~C~~~f~~~~~l~~H~~ 80 (134)
.....-|-|.+|.-++...-++..|+.
T Consensus 70 ~sq~~GyyCdVCdcvvKDSinflDHiN 96 (193)
T KOG4727|consen 70 RSQKGGYYCDVCDCVVKDSINFLDHIN 96 (193)
T ss_pred ccccCceeeeecceeehhhHHHHHHhc
Confidence 344556999999999999888888875
No 176
>KOG2923|consensus
Probab=37.69 E-value=7.8 Score=20.73 Aligned_cols=16 Identities=25% Similarity=0.027 Sum_probs=12.2
Q ss_pred cccccCCCcccCccce
Q psy691 116 EEEEDGKTNVLTTEYL 131 (134)
Q Consensus 116 ~~c~~~~~~~~~~~~l 131 (134)
|.|+||..+-++.+.|
T Consensus 23 yPCpCGDrf~It~edL 38 (67)
T KOG2923|consen 23 YPCPCGDRFQITLEDL 38 (67)
T ss_pred cCCCCCCeeeecHHHH
Confidence 6788888887777655
No 177
>PTZ00448 hypothetical protein; Provisional
Probab=37.43 E-value=27 Score=25.61 Aligned_cols=23 Identities=13% Similarity=0.427 Sum_probs=20.1
Q ss_pred ceeccccccccCChHHHHHHHHH
Q psy691 59 RFACHLCSKSFSLQRLLNRHMKC 81 (134)
Q Consensus 59 ~~~C~~C~~~f~~~~~l~~H~~~ 81 (134)
.|.|..|+-.|......+.|+++
T Consensus 314 ~~tC~~C~v~F~~~~~qR~H~KS 336 (373)
T PTZ00448 314 MLLCRKCNIQLMDHNAFKQHYRS 336 (373)
T ss_pred CccccccccccCCHHHHHHHhhh
Confidence 58899999999888888888886
No 178
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=37.25 E-value=6.1 Score=31.63 Aligned_cols=11 Identities=18% Similarity=0.449 Sum_probs=7.1
Q ss_pred eeccccccccC
Q psy691 60 FACHLCSKSFS 70 (134)
Q Consensus 60 ~~C~~C~~~f~ 70 (134)
..|..||..+.
T Consensus 436 l~C~~Cg~v~~ 446 (730)
T COG1198 436 LLCRDCGYIAE 446 (730)
T ss_pred eecccCCCccc
Confidence 45777776654
No 179
>PLN02748 tRNA dimethylallyltransferase
Probab=37.13 E-value=29 Score=26.43 Aligned_cols=25 Identities=16% Similarity=0.385 Sum_probs=19.8
Q ss_pred CCceecccccc-ccCChHHHHHHHHH
Q psy691 57 NTRFACHLCSK-SFSLQRLLNRHMKC 81 (134)
Q Consensus 57 ~~~~~C~~C~~-~f~~~~~l~~H~~~ 81 (134)
-+.|.|.+|++ .+.....+..|++.
T Consensus 416 ~~~~~Ce~C~~~~~~G~~eW~~Hlks 441 (468)
T PLN02748 416 WTQYVCEACGNKVLRGAHEWEQHKQG 441 (468)
T ss_pred cccccccCCCCcccCCHHHHHHHhcc
Confidence 45688999997 78888888888764
No 180
>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=37.11 E-value=18 Score=21.20 Aligned_cols=24 Identities=25% Similarity=0.271 Sum_probs=17.8
Q ss_pred HHHHHHcCCCCceecccccccccCh
Q psy691 76 NRHMKCHSDVKRYLCTFCGKGFNDT 100 (134)
Q Consensus 76 ~~H~~~h~~~k~~~C~~C~~~f~~~ 100 (134)
..++..+.+ ++++|..||.-|...
T Consensus 69 v~W~~l~~g-~~~rC~eCG~~fkL~ 92 (97)
T cd00924 69 VIWMWLEKG-KPKRCPECGHVFKLV 92 (97)
T ss_pred EEEEEEeCC-CceeCCCCCcEEEEE
Confidence 344566776 799999999888653
No 181
>PRK04351 hypothetical protein; Provisional
Probab=36.51 E-value=18 Score=22.92 Aligned_cols=9 Identities=44% Similarity=0.992 Sum_probs=4.0
Q ss_pred ceecccccc
Q psy691 87 RYLCTFCGK 95 (134)
Q Consensus 87 ~~~C~~C~~ 95 (134)
.|.|..|+.
T Consensus 132 ~yrCg~C~g 140 (149)
T PRK04351 132 RYRCGKCRG 140 (149)
T ss_pred cEEeCCCCc
Confidence 344444443
No 182
>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=36.36 E-value=5.2 Score=20.43 Aligned_cols=26 Identities=23% Similarity=0.534 Sum_probs=13.2
Q ss_pred CCceeccccccccCChHHHHHHHHHc
Q psy691 57 NTRFACHLCSKSFSLQRLLNRHMKCH 82 (134)
Q Consensus 57 ~~~~~C~~C~~~f~~~~~l~~H~~~h 82 (134)
...|.|+.|...|-..-.+-.|...|
T Consensus 19 ~~~y~C~~C~~~FC~dCD~fiHE~LH 44 (51)
T PF07975_consen 19 SSRYRCPKCKNHFCIDCDVFIHETLH 44 (51)
T ss_dssp -EEE--TTTT--B-HHHHHTTTTTS-
T ss_pred CCeEECCCCCCccccCcChhhhcccc
Confidence 45799999999998766665554333
No 183
>COG4338 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=36.22 E-value=12 Score=18.76 Aligned_cols=12 Identities=25% Similarity=0.794 Sum_probs=6.8
Q ss_pred ecccccccccCh
Q psy691 89 LCTFCGKGFNDT 100 (134)
Q Consensus 89 ~C~~C~~~f~~~ 100 (134)
.|+.|++.|..+
T Consensus 14 ICpvCqRPFsWR 25 (54)
T COG4338 14 ICPVCQRPFSWR 25 (54)
T ss_pred hhhhhcCchHHH
Confidence 456666665554
No 184
>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=36.09 E-value=24 Score=17.24 Aligned_cols=15 Identities=20% Similarity=0.791 Sum_probs=11.5
Q ss_pred eccccccccCChHHH
Q psy691 61 ACHLCSKSFSLQRLL 75 (134)
Q Consensus 61 ~C~~C~~~f~~~~~l 75 (134)
.|..|++.|+...-.
T Consensus 10 ~C~~C~rpf~WRKKW 24 (42)
T PF10013_consen 10 ICPVCGRPFTWRKKW 24 (42)
T ss_pred cCcccCCcchHHHHH
Confidence 688999999865544
No 185
>PLN02294 cytochrome c oxidase subunit Vb
Probab=35.74 E-value=19 Score=23.39 Aligned_cols=13 Identities=31% Similarity=0.996 Sum_probs=8.1
Q ss_pred CceeccccccccC
Q psy691 58 TRFACHLCSKSFS 70 (134)
Q Consensus 58 ~~~~C~~C~~~f~ 70 (134)
++..|++||..|+
T Consensus 140 kp~RCpeCG~~fk 152 (174)
T PLN02294 140 KSFECPVCTQYFE 152 (174)
T ss_pred CceeCCCCCCEEE
Confidence 4566666666665
No 186
>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=35.12 E-value=17 Score=18.46 Aligned_cols=12 Identities=17% Similarity=0.869 Sum_probs=8.8
Q ss_pred eeccccccccCC
Q psy691 60 FACHLCSKSFSL 71 (134)
Q Consensus 60 ~~C~~C~~~f~~ 71 (134)
|.|..||..+..
T Consensus 2 y~C~~CgyiYd~ 13 (50)
T cd00730 2 YECRICGYIYDP 13 (50)
T ss_pred cCCCCCCeEECC
Confidence 678888877764
No 187
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=34.98 E-value=12 Score=22.42 Aligned_cols=26 Identities=19% Similarity=0.447 Sum_probs=16.0
Q ss_pred ceeccccccccCChHHHHHHHHHcCCCCceecccccc
Q psy691 59 RFACHLCSKSFSLQRLLNRHMKCHSDVKRYLCTFCGK 95 (134)
Q Consensus 59 ~~~C~~C~~~f~~~~~l~~H~~~h~~~k~~~C~~C~~ 95 (134)
.+.|..|+..|..... ..+.|+.|+.
T Consensus 70 ~~~C~~Cg~~~~~~~~-----------~~~~CP~Cgs 95 (114)
T PRK03681 70 ECWCETCQQYVTLLTQ-----------RVRRCPQCHG 95 (114)
T ss_pred EEEcccCCCeeecCCc-----------cCCcCcCcCC
Confidence 4788888876653211 1156888874
No 188
>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=34.88 E-value=30 Score=26.35 Aligned_cols=27 Identities=26% Similarity=0.583 Sum_probs=22.8
Q ss_pred CceecccccccccChhhHHHHHhH-hcC
Q psy691 86 KRYLCTFCGKGFNDTFDLKRHTRT-HTG 112 (134)
Q Consensus 86 k~~~C~~C~~~f~~~~~l~~H~~~-h~~ 112 (134)
+=+.|+.|.+.|.....+..|+.. |.+
T Consensus 56 rFWiCp~CskkF~d~~~~~~H~~~eH~~ 83 (466)
T PF04780_consen 56 RFWICPRCSKKFSDAESCLSHMEQEHPA 83 (466)
T ss_pred eEeeCCcccceeCCHHHHHHHHHHhhhh
Confidence 346899999999999999999885 655
No 189
>KOG2071|consensus
Probab=34.38 E-value=28 Score=27.12 Aligned_cols=27 Identities=22% Similarity=0.470 Sum_probs=21.7
Q ss_pred CCceeccccccccCChHHHHHHHHHcC
Q psy691 57 NTRFACHLCSKSFSLQRLLNRHMKCHS 83 (134)
Q Consensus 57 ~~~~~C~~C~~~f~~~~~l~~H~~~h~ 83 (134)
+.+..|..||..|........||..|.
T Consensus 416 ~~pnqC~~CG~R~~~~ee~sk~md~H~ 442 (579)
T KOG2071|consen 416 DSPNQCKSCGLRFDDSEERSKHMDIHD 442 (579)
T ss_pred CCcchhcccccccccchhhhhHhhhhh
Confidence 456789999999998877777777664
No 190
>KOG2747|consensus
Probab=34.29 E-value=26 Score=25.96 Aligned_cols=26 Identities=35% Similarity=0.651 Sum_probs=22.0
Q ss_pred CCceecccccccccChhhHHHHHhHh
Q psy691 85 VKRYLCTFCGKGFNDTFDLKRHTRTH 110 (134)
Q Consensus 85 ~k~~~C~~C~~~f~~~~~l~~H~~~h 110 (134)
..-|.|++|-+-+.....|.+|+...
T Consensus 156 ~~lYiCEfCLkY~~s~~~l~rH~~kC 181 (396)
T KOG2747|consen 156 DKLYICEFCLKYMKSRTSLQRHLKKC 181 (396)
T ss_pred CeEEEehHHHhHhchHHHHHHHHHhc
Confidence 35689999999999999999998764
No 191
>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=34.13 E-value=7 Score=18.36 Aligned_cols=7 Identities=43% Similarity=0.899 Sum_probs=2.8
Q ss_pred Cceeccc
Q psy691 86 KRYLCTF 92 (134)
Q Consensus 86 k~~~C~~ 92 (134)
..|.|..
T Consensus 28 qryrC~~ 34 (36)
T PF03811_consen 28 QRYRCKD 34 (36)
T ss_pred EeEecCc
Confidence 3344433
No 192
>COG1655 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=34.10 E-value=7.8 Score=26.44 Aligned_cols=26 Identities=12% Similarity=0.443 Sum_probs=18.4
Q ss_pred CCceeccccccccCChHHHHHHHHHc
Q psy691 57 NTRFACHLCSKSFSLQRLLNRHMKCH 82 (134)
Q Consensus 57 ~~~~~C~~C~~~f~~~~~l~~H~~~h 82 (134)
++...|++|+-.|.....+..-.|+-
T Consensus 17 kk~ieCPvC~tkFkkeev~tgsiRii 42 (267)
T COG1655 17 KKTIECPVCNTKFKKEEVKTGSIRII 42 (267)
T ss_pred hceeccCcccchhhhhheeccceeEe
Confidence 45689999999998766555444443
No 193
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=34.06 E-value=11 Score=21.70 Aligned_cols=7 Identities=43% Similarity=1.397 Sum_probs=3.5
Q ss_pred eeccccc
Q psy691 88 YLCTFCG 94 (134)
Q Consensus 88 ~~C~~C~ 94 (134)
|.|++|+
T Consensus 37 y~CpfCg 43 (90)
T PRK03976 37 HVCPVCG 43 (90)
T ss_pred ccCCCCC
Confidence 4555554
No 194
>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=33.86 E-value=32 Score=16.25 Aligned_cols=11 Identities=45% Similarity=1.231 Sum_probs=3.6
Q ss_pred ceecccccccc
Q psy691 87 RYLCTFCGKGF 97 (134)
Q Consensus 87 ~~~C~~C~~~f 97 (134)
.|-|+.|...|
T Consensus 3 ryyCdyC~~~~ 13 (38)
T PF06220_consen 3 RYYCDYCKKYL 13 (38)
T ss_dssp S-B-TTT--B-
T ss_pred Ceeccccccee
Confidence 35666666655
No 195
>PRK05978 hypothetical protein; Provisional
Probab=33.38 E-value=19 Score=22.89 Aligned_cols=32 Identities=22% Similarity=0.529 Sum_probs=20.6
Q ss_pred eeccccccccCChHHHHHHHHHcCCCCceecccccccccCh
Q psy691 60 FACHLCSKSFSLQRLLNRHMKCHSDVKRYLCTFCGKGFNDT 100 (134)
Q Consensus 60 ~~C~~C~~~f~~~~~l~~H~~~h~~~k~~~C~~C~~~f~~~ 100 (134)
.+|+.|++.--.+..|+ -.-.|..|+..|...
T Consensus 34 grCP~CG~G~LF~g~Lk---------v~~~C~~CG~~~~~~ 65 (148)
T PRK05978 34 GRCPACGEGKLFRAFLK---------PVDHCAACGEDFTHH 65 (148)
T ss_pred CcCCCCCCCcccccccc---------cCCCccccCCccccC
Confidence 57999987744333332 234799998877653
No 196
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=33.23 E-value=18 Score=22.43 Aligned_cols=15 Identities=40% Similarity=0.716 Sum_probs=11.1
Q ss_pred ceecccccccccChh
Q psy691 87 RYLCTFCGKGFNDTF 101 (134)
Q Consensus 87 ~~~C~~C~~~f~~~~ 101 (134)
|++|..|++.|..-+
T Consensus 1 PH~Ct~Cg~~f~dgs 15 (131)
T PF09845_consen 1 PHQCTKCGRVFEDGS 15 (131)
T ss_pred CcccCcCCCCcCCCc
Confidence 567888888887644
No 197
>PF11931 DUF3449: Domain of unknown function (DUF3449); InterPro: IPR024598 This presumed domain is functionally uncharacterised. It has two conserved sequence motifs: PIP and CEICG and contains a zinc-finger of the C2H2-type.; PDB: 4DGW_A.
Probab=32.88 E-value=14 Score=24.52 Aligned_cols=9 Identities=22% Similarity=1.202 Sum_probs=0.0
Q ss_pred ceecccccc
Q psy691 59 RFACHLCSK 67 (134)
Q Consensus 59 ~~~C~~C~~ 67 (134)
.|.|.+||.
T Consensus 101 ey~CEICGN 109 (196)
T PF11931_consen 101 EYKCEICGN 109 (196)
T ss_dssp ---------
T ss_pred eeeeEeCCC
Confidence 355666653
No 198
>KOG2807|consensus
Probab=32.29 E-value=73 Score=23.19 Aligned_cols=20 Identities=25% Similarity=0.516 Sum_probs=15.2
Q ss_pred ceeccccccccCChHHHHHH
Q psy691 59 RFACHLCSKSFSLQRLLNRH 78 (134)
Q Consensus 59 ~~~C~~C~~~f~~~~~l~~H 78 (134)
|-.|++|+-+.....+|.+-
T Consensus 290 P~eCpiC~ltLVss~hLARS 309 (378)
T KOG2807|consen 290 PIECPICSLTLVSSPHLARS 309 (378)
T ss_pred CccCCccceeEecchHHHHH
Confidence 45788888888888888754
No 199
>COG1327 Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains [Transcription]
Probab=31.57 E-value=14 Score=23.51 Aligned_cols=16 Identities=31% Similarity=0.600 Sum_probs=11.4
Q ss_pred CceecccccccccChh
Q psy691 86 KRYLCTFCGKGFNDTF 101 (134)
Q Consensus 86 k~~~C~~C~~~f~~~~ 101 (134)
+.-.|..|++.|.+..
T Consensus 27 RRReC~~C~~RFTTfE 42 (156)
T COG1327 27 RRRECLECGERFTTFE 42 (156)
T ss_pred hhhcccccccccchhh
Confidence 3457888888887743
No 200
>PLN03239 histone acetyltransferase; Provisional
Probab=30.81 E-value=33 Score=25.07 Aligned_cols=25 Identities=24% Similarity=0.297 Sum_probs=21.5
Q ss_pred CCceecccccccccChhhHHHHHhH
Q psy691 85 VKRYLCTFCGKGFNDTFDLKRHTRT 109 (134)
Q Consensus 85 ~k~~~C~~C~~~f~~~~~l~~H~~~ 109 (134)
..-|.|++|-+-|.....|.+|+..
T Consensus 104 ~~lYiCE~Clky~~~~~~l~~H~~~ 128 (351)
T PLN03239 104 DVLYVCEFSFGFFARKSELLRFQAK 128 (351)
T ss_pred ceEEEeccchhhhcCHHHHHHHHHh
Confidence 4579999999999999999999753
No 201
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=30.73 E-value=27 Score=21.52 Aligned_cols=16 Identities=25% Similarity=0.960 Sum_probs=12.9
Q ss_pred CCceeccccccccCCh
Q psy691 57 NTRFACHLCSKSFSLQ 72 (134)
Q Consensus 57 ~~~~~C~~C~~~f~~~ 72 (134)
...|.|..|++.|...
T Consensus 51 ~qRyrC~~C~~tf~~~ 66 (129)
T COG3677 51 HQRYKCKSCGSTFTVE 66 (129)
T ss_pred ccccccCCcCcceeee
Confidence 5579999999998754
No 202
>PF07800 DUF1644: Protein of unknown function (DUF1644); InterPro: IPR012866 This family consists of sequences found in a number of hypothetical plant proteins of unknown function. The region of interest contains nine highly conserved cysteine residues and is approximately 160 amino acids in length, which probably represent a zinc-binding domain.
Probab=30.05 E-value=1.6e+02 Score=19.07 Aligned_cols=56 Identities=20% Similarity=0.438 Sum_probs=34.2
Q ss_pred CceeccccccccCChHHHHHHHHHcCCCCceeccc--ccccccChhhHHHHHhH-hcCCCc
Q psy691 58 TRFACHLCSKSFSLQRLLNRHMKCHSDVKRYLCTF--CGKGFNDTFDLKRHTRT-HTGKEE 115 (134)
Q Consensus 58 ~~~~C~~C~~~f~~~~~l~~H~~~h~~~k~~~C~~--C~~~f~~~~~l~~H~~~-h~~~~~ 115 (134)
....|+.|.....-.... .--|.+.+.|+-.|.. |... .+-..|++|.+. |-.-+|
T Consensus 79 ~~L~CPLCRG~V~GWtvv-e~AR~~LN~K~RsC~~e~C~F~-GtY~eLrKHar~~HP~~rP 137 (162)
T PF07800_consen 79 PELACPLCRGEVKGWTVV-EPARRFLNAKKRSCSQESCSFS-GTYSELRKHARSEHPSARP 137 (162)
T ss_pred ccccCccccCceeceEEc-hHHHHHhccCCccCcccccccc-cCHHHHHHHHHhhCCCCCC
Confidence 347899987544433222 2355666777766765 6543 345678899876 655555
No 203
>KOG1994|consensus
Probab=29.98 E-value=37 Score=23.24 Aligned_cols=22 Identities=18% Similarity=0.545 Sum_probs=18.9
Q ss_pred CCceeccccccccCChHHHHHH
Q psy691 57 NTRFACHLCSKSFSLQRLLNRH 78 (134)
Q Consensus 57 ~~~~~C~~C~~~f~~~~~l~~H 78 (134)
..-|-|-+||-.|.+...|..|
T Consensus 237 ~eh~YC~fCG~~y~~~edl~eh 258 (268)
T KOG1994|consen 237 SEHYYCFFCGIKYKDEEDLYEH 258 (268)
T ss_pred ccceEEEEeccccCCHHHHHHh
Confidence 3459999999999999998877
No 204
>smart00731 SprT SprT homologues. Predicted to have roles in transcription elongation. Contains a conserved HExxH motif, indicating a metalloprotease function.
Probab=29.97 E-value=24 Score=22.05 Aligned_cols=10 Identities=50% Similarity=1.069 Sum_probs=4.7
Q ss_pred ceeccccccc
Q psy691 87 RYLCTFCGKG 96 (134)
Q Consensus 87 ~~~C~~C~~~ 96 (134)
.|.|..|+..
T Consensus 112 ~y~C~~C~~~ 121 (146)
T smart00731 112 PYRCTGCGQR 121 (146)
T ss_pred EEECCCCCCC
Confidence 3455545443
No 205
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=29.92 E-value=29 Score=25.99 Aligned_cols=29 Identities=21% Similarity=0.550 Sum_probs=18.2
Q ss_pred eccccccccCChHHHHHHHHHcCCCCceecccccccccCh
Q psy691 61 ACHLCSKSFSLQRLLNRHMKCHSDVKRYLCTFCGKGFNDT 100 (134)
Q Consensus 61 ~C~~C~~~f~~~~~l~~H~~~h~~~k~~~C~~C~~~f~~~ 100 (134)
.|+.||....++ |..-|+|..|+..+...
T Consensus 352 ~Cp~Cg~~m~S~-----------G~~g~rC~kCg~~~~~~ 380 (421)
T COG1571 352 VCPRCGGRMKSA-----------GRNGFRCKKCGTRARET 380 (421)
T ss_pred CCCccCCchhhc-----------CCCCcccccccccCCcc
Confidence 677777665433 23367888887766554
No 206
>KOG1842|consensus
Probab=29.56 E-value=30 Score=26.11 Aligned_cols=23 Identities=26% Similarity=0.566 Sum_probs=19.5
Q ss_pred ceeccccccccCChHHHHHHHHH
Q psy691 59 RFACHLCSKSFSLQRLLNRHMKC 81 (134)
Q Consensus 59 ~~~C~~C~~~f~~~~~l~~H~~~ 81 (134)
-|.|++|..-|.....|..|.-.
T Consensus 15 gflCPiC~~dl~~~~~L~~H~d~ 37 (505)
T KOG1842|consen 15 GFLCPICLLDLPNLSALNDHLDV 37 (505)
T ss_pred cccCchHhhhhhhHHHHHHHHhh
Confidence 48899999999888888888775
No 207
>COG5112 UFD2 U1-like Zn-finger-containing protein [General function prediction only]
Probab=29.22 E-value=46 Score=19.83 Aligned_cols=26 Identities=23% Similarity=0.388 Sum_probs=21.2
Q ss_pred CCCceeccccccccCChHHHHHHHHH
Q psy691 56 DNTRFACHLCSKSFSLQRLLNRHMKC 81 (134)
Q Consensus 56 ~~~~~~C~~C~~~f~~~~~l~~H~~~ 81 (134)
+-..|-|-+|.+-|.+...|..|.+.
T Consensus 52 GlGqhYCieCaryf~t~~aL~~Hkkg 77 (126)
T COG5112 52 GLGQHYCIECARYFITEKALMEHKKG 77 (126)
T ss_pred CCceeeeehhHHHHHHHHHHHHHhcc
Confidence 34568899999999999999888764
No 208
>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=28.71 E-value=9 Score=18.98 Aligned_cols=16 Identities=0% Similarity=-0.128 Sum_probs=7.5
Q ss_pred CCcccc--ccCCCcccCc
Q psy691 113 KEEEEE--EDGKTNVLTT 128 (134)
Q Consensus 113 ~~~~~c--~~~~~~~~~~ 128 (134)
+.-+.| ..|+..|+..
T Consensus 23 ~~Y~qC~N~~Cg~tfv~~ 40 (47)
T PF04606_consen 23 ELYCQCTNPECGHTFVAN 40 (47)
T ss_pred EEEEEECCCcCCCEEEEE
Confidence 344555 2355555443
No 209
>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=28.58 E-value=13 Score=26.13 Aligned_cols=36 Identities=17% Similarity=0.325 Sum_probs=13.4
Q ss_pred ceecccccccccChhhHHHHHhHhcCCCccccccCCC
Q psy691 87 RYLCTFCGKGFNDTFDLKRHTRTHTGKEEEEEEDGKT 123 (134)
Q Consensus 87 ~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~c~~~~~ 123 (134)
+..|..||..-...-.+.. ..--.+.+-+.|..|+.
T Consensus 211 R~~Cp~Cg~~~~~~l~~~~-~e~~~~~rve~C~~C~~ 246 (290)
T PF04216_consen 211 RIKCPYCGNTDHEKLEYFT-VEGEPAYRVEVCESCGS 246 (290)
T ss_dssp TTS-TTT---SS-EEE---------SEEEEEETTTTE
T ss_pred CCCCcCCCCCCCcceeeEe-cCCCCcEEEEECCcccc
Confidence 3578888765433322211 11222445577876664
No 210
>KOG1280|consensus
Probab=28.40 E-value=57 Score=23.85 Aligned_cols=38 Identities=11% Similarity=0.197 Sum_probs=29.0
Q ss_pred CceecccccccccChhhHHHHHhHhcCCCcccc--ccCCC
Q psy691 86 KRYLCTFCGKGFNDTFDLKRHTRTHTGKEEEEE--EDGKT 123 (134)
Q Consensus 86 k~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~c--~~~~~ 123 (134)
.-|.|++|++.-.....|..|...-+-+-++.+ +.|..
T Consensus 78 qSftCPyC~~~Gfte~~f~~Hv~s~Hpda~~~~icp~c~~ 117 (381)
T KOG1280|consen 78 QSFTCPYCGIMGFTERQFGTHVLSQHPEASTSVICPLCAA 117 (381)
T ss_pred ccccCCcccccccchhHHHHHhhhcCcccCcceeeecccc
Confidence 469999999988889999999887666666544 44544
No 211
>PRK12387 formate hydrogenlyase complex iron-sulfur subunit; Provisional
Probab=28.18 E-value=23 Score=22.97 Aligned_cols=20 Identities=20% Similarity=0.519 Sum_probs=15.1
Q ss_pred CCceecccccccccChhhHH
Q psy691 85 VKRYLCTFCGKGFNDTFDLK 104 (134)
Q Consensus 85 ~k~~~C~~C~~~f~~~~~l~ 104 (134)
...+.|..||+.|.....+.
T Consensus 112 ~~~~~C~~CG~~f~~~~~i~ 131 (180)
T PRK12387 112 FALCNCRVCGRPFAVQKEID 131 (180)
T ss_pred eCcccchhhCCccccHHHHH
Confidence 35679999999998765544
No 212
>KOG1842|consensus
Probab=28.05 E-value=37 Score=25.69 Aligned_cols=24 Identities=21% Similarity=0.340 Sum_probs=18.6
Q ss_pred ecccccccccChhhHHHHHhHhcC
Q psy691 89 LCTFCGKGFNDTFDLKRHTRTHTG 112 (134)
Q Consensus 89 ~C~~C~~~f~~~~~l~~H~~~h~~ 112 (134)
.|++|...|...+.|..|.-..|+
T Consensus 17 lCPiC~~dl~~~~~L~~H~d~eH~ 40 (505)
T KOG1842|consen 17 LCPICLLDLPNLSALNDHLDVEHF 40 (505)
T ss_pred cCchHhhhhhhHHHHHHHHhhhcc
Confidence 688888888888888888776433
No 213
>KOG3002|consensus
Probab=27.97 E-value=32 Score=24.55 Aligned_cols=61 Identities=16% Similarity=0.176 Sum_probs=36.0
Q ss_pred CCceeccccccccCChHHHHHHHHHcCCCCceeccc----ccccccChhhHHHHHhHhcCCCccccccC
Q psy691 57 NTRFACHLCSKSFSLQRLLNRHMKCHSDVKRYLCTF----CGKGFNDTFDLKRHTRTHTGKEEEEEEDG 121 (134)
Q Consensus 57 ~~~~~C~~C~~~f~~~~~l~~H~~~h~~~k~~~C~~----C~~~f~~~~~l~~H~~~h~~~~~~~c~~~ 121 (134)
+....|+.|...+..... ++|..-.....+.|.. |.+.|..... ..|.+.-.. ++|.|++-
T Consensus 78 ~~~~~CP~Cr~~~g~~R~--~amEkV~e~~~vpC~~~~~GC~~~~~Y~~~-~~HE~~C~f-~~~~CP~p 142 (299)
T KOG3002|consen 78 KVSNKCPTCRLPIGNIRC--RAMEKVAEAVLVPCKNAKLGCTKSFPYGEK-SKHEKVCEF-RPCSCPVP 142 (299)
T ss_pred hhcccCCccccccccHHH--HHHHHHHHhceecccccccCCceeeccccc-ccccccccc-CCcCCCCC
Confidence 345677788777764333 2333323344566664 7778777666 456666555 77887543
No 214
>PLN03238 probable histone acetyltransferase MYST; Provisional
Probab=27.88 E-value=76 Score=22.58 Aligned_cols=26 Identities=23% Similarity=0.447 Sum_probs=23.1
Q ss_pred CCCceeccccccccCChHHHHHHHHH
Q psy691 56 DNTRFACHLCSKSFSLQRLLNRHMKC 81 (134)
Q Consensus 56 ~~~~~~C~~C~~~f~~~~~l~~H~~~ 81 (134)
....|.|..|-+-|.+...|.+|+..
T Consensus 45 ~~~lyiCe~Clky~~~~~~l~~H~~~ 70 (290)
T PLN03238 45 CTKLYICEYCLKYMRKKKSLLRHLAK 70 (290)
T ss_pred CCeEEEcCCCcchhCCHHHHHHHHHh
Confidence 35679999999999999999999873
No 215
>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=27.56 E-value=26 Score=20.74 Aligned_cols=10 Identities=20% Similarity=0.697 Sum_probs=5.7
Q ss_pred ceeccccccc
Q psy691 59 RFACHLCSKS 68 (134)
Q Consensus 59 ~~~C~~C~~~ 68 (134)
+-.|+.||..
T Consensus 2 p~~CpYCg~~ 11 (102)
T PF11672_consen 2 PIICPYCGGP 11 (102)
T ss_pred CcccCCCCCe
Confidence 3456666644
No 216
>KOG0782|consensus
Probab=27.26 E-value=18 Score=28.34 Aligned_cols=26 Identities=35% Similarity=0.602 Sum_probs=10.1
Q ss_pred HHHHHHHHcCCCCceecccccccccC
Q psy691 74 LLNRHMKCHSDVKRYLCTFCGKGFND 99 (134)
Q Consensus 74 ~l~~H~~~h~~~k~~~C~~C~~~f~~ 99 (134)
.|.+|-..|....-=+|..|+|.|.+
T Consensus 240 ~fvrHHWVHrrRqeGkC~~CgKgFQQ 265 (1004)
T KOG0782|consen 240 GFVRHHWVHRRRQEGKCNTCGKGFQQ 265 (1004)
T ss_pred cchHHhHhhHhhhccccchhhhhhhh
Confidence 33444333333222344444444433
No 217
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=26.26 E-value=22 Score=21.71 Aligned_cols=13 Identities=15% Similarity=0.427 Sum_probs=9.1
Q ss_pred ceeccccccccCCh
Q psy691 59 RFACHLCSKSFSLQ 72 (134)
Q Consensus 59 ~~~C~~C~~~f~~~ 72 (134)
.+.| .|+..|...
T Consensus 70 ~~~C-~Cg~~~~~~ 82 (124)
T PRK00762 70 EIEC-ECGYEGVVD 82 (124)
T ss_pred eEEe-eCcCccccc
Confidence 4788 888776643
No 218
>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=26.26 E-value=31 Score=16.22 Aligned_cols=12 Identities=17% Similarity=0.623 Sum_probs=6.4
Q ss_pred Cceecccccccc
Q psy691 58 TRFACHLCSKSF 69 (134)
Q Consensus 58 ~~~~C~~C~~~f 69 (134)
+.|+|..||...
T Consensus 5 ~~YkC~~CGniV 16 (36)
T PF06397_consen 5 EFYKCEHCGNIV 16 (36)
T ss_dssp EEEE-TTT--EE
T ss_pred cEEEccCCCCEE
Confidence 458888888654
No 219
>PF05207 zf-CSL: CSL zinc finger; InterPro: IPR007872 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 probable zinc binding motif that contains four cysteines and may chelate zinc, known as the DPH-type after the diphthamide (DPH) biosynthesis protein in which it was first characterised, including the proteins DPH3 and DPH4. This domain is also found associated with N-terminal domain of heat shock protein DnaJ IPR001623 from INTERPRO domain. Diphthamide is a unique post-translationally modified histidine residue found only in translation elongation factor 2 (eEF-2). It is conserved from archaea to humans and serves as the target for diphteria toxin and Pseudomonas exotoxin A. These two toxins catalyse the transfer of ADP-ribose to diphtamide on eEF-2, thus inactivating eEF-2, halting cellular protein synthesis, and causing cell death []. The biosynthesis of diphtamide is dependent on at least five proteins, DPH1 to -5, and a still unidentified amidating enzyme. DPH3 and DPH4 share a conserved region, which encode a putative zinc finger, the DPH-type or CSL-type (after the conserved motif of the final cysteine) zinc finger [, ]. The function of this motif is unknown. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 2L6L_A 1WGE_A 2JR7_A 1YOP_A 1YWS_A.
Probab=26.17 E-value=9.2 Score=19.75 Aligned_cols=17 Identities=18% Similarity=0.014 Sum_probs=11.4
Q ss_pred ccccccCCCcccCccce
Q psy691 115 EEEEEDGKTNVLTTEYL 131 (134)
Q Consensus 115 ~~~c~~~~~~~~~~~~l 131 (134)
.|.|+||+.+.++.+.|
T Consensus 18 ~y~CRCG~~f~i~e~~l 34 (55)
T PF05207_consen 18 SYPCRCGGEFEISEEDL 34 (55)
T ss_dssp EEEETTSSEEEEEHHHH
T ss_pred EEcCCCCCEEEEcchhc
Confidence 36788888766665544
No 220
>PF10537 WAC_Acf1_DNA_bd: ATP-utilising chromatin assembly and remodelling N-terminal; InterPro: IPR013136 ACF (for ATP-utilising chromatin assembly and remodeling factor) is a chromatin-remodeling complex that catalyzes the ATP-dependent assembly of periodic nucleosome arrays. This reaction utilises the energy of ATP hydrolysis by ISWI, the smaller of the two subunits of ACF. Acf1, the large subunit of ACF, is essential for the full activity of the complex. The WAC (WSTF/Acf1/cbp146) domain is an ~110-residue module present at the N-termini of Acf1-related proteins in a variety of organisms. It is found in association with other domains such as the bromodomain, the PHD-type zinc finger, DDT or WAKS. The DNA-binding region of Acf1 includes the WAC domain, which is necessary for the efficient binding of ACF complex to DNA. It seems probable that the WAC domain will be involved in DNA binding in other related factors [, ]. Some proteins known to contain a WAC domain are the Drosophila melanogaster (Fruit fly) ATP-dependent chromatin assembly factor large subunit Acf1, human WSTF (Williams syndrome transcription factor), mouse cbp146, yeast imitation switch two complex protein 1 (ITC1 or YGL133w), and yeast protein YPL216w.
Probab=26.07 E-value=1.3e+02 Score=17.76 Aligned_cols=38 Identities=16% Similarity=0.226 Sum_probs=27.4
Q ss_pred CceeccccccccCChHHHHHHHHHcCCCCceeccccccc
Q psy691 58 TRFACHLCSKSFSLQRLLNRHMKCHSDVKRYLCTFCGKG 96 (134)
Q Consensus 58 ~~~~C~~C~~~f~~~~~l~~H~~~h~~~k~~~C~~C~~~ 96 (134)
..|.|+.-+..|.....+...+... ..+.|.|...|+.
T Consensus 2 eVf~i~~T~EiF~dYe~Y~~R~~~y-~~~vwtC~~TGk~ 39 (102)
T PF10537_consen 2 EVFYIPFTGEIFRDYEEYLKRMILY-NQRVWTCEITGKS 39 (102)
T ss_pred ceEEeCCCCcccCCHHHHHHHHHHH-hCCeeEEecCCCC
Confidence 3578888888898887776655543 3467899888764
No 221
>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=26.03 E-value=5 Score=18.71 Aligned_cols=10 Identities=40% Similarity=0.989 Sum_probs=3.6
Q ss_pred eecccccccc
Q psy691 88 YLCTFCGKGF 97 (134)
Q Consensus 88 ~~C~~C~~~f 97 (134)
..|..||-.+
T Consensus 22 isC~~CGPr~ 31 (35)
T PF07503_consen 22 ISCTNCGPRY 31 (35)
T ss_dssp --BTTCC-SC
T ss_pred ccCCCCCCCE
Confidence 3455555443
No 222
>KOG2461|consensus
Probab=25.80 E-value=1.2e+02 Score=22.76 Aligned_cols=56 Identities=9% Similarity=-0.164 Sum_probs=24.5
Q ss_pred cccccccCChHHHHHHHHHcCCCCceecccccccccChhhHHHHHhHhcCCCcccc
Q psy691 63 HLCSKSFSLQRLLNRHMKCHSDVKRYLCTFCGKGFNDTFDLKRHTRTHTGKEEEEE 118 (134)
Q Consensus 63 ~~C~~~f~~~~~l~~H~~~h~~~k~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~c 118 (134)
.++.+.+.....+..|...+..+..+.+..+...+.....+..+..+|+..+.+.+
T Consensus 335 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 390 (396)
T KOG2461|consen 335 TIPVRTPAGQLIYTQSHSMEVAEPTDMAPNQIWKIYHTGVLGFLIITTDESECNNM 390 (396)
T ss_pred cccccccccccchhhhhhcccCCCCcccccccccceeccccceeeeeccccccccc
Confidence 33333444444444454445444444444433333333344444444554444444
No 223
>PF11789 zf-Nse: Zinc-finger of the MIZ type in Nse subunit; PDB: 2YU4_A 3HTK_C.
Probab=25.39 E-value=99 Score=15.99 Aligned_cols=13 Identities=23% Similarity=0.483 Sum_probs=4.9
Q ss_pred ceecccccccccC
Q psy691 87 RYLCTFCGKGFND 99 (134)
Q Consensus 87 ~~~C~~C~~~f~~ 99 (134)
|+....|+..|..
T Consensus 24 PV~s~~C~H~fek 36 (57)
T PF11789_consen 24 PVKSKKCGHTFEK 36 (57)
T ss_dssp EEEESSS--EEEH
T ss_pred CcCcCCCCCeecH
Confidence 4444444444444
No 224
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=25.18 E-value=28 Score=24.93 Aligned_cols=9 Identities=33% Similarity=0.874 Sum_probs=6.4
Q ss_pred ceecccccc
Q psy691 87 RYLCTFCGK 95 (134)
Q Consensus 87 ~~~C~~C~~ 95 (134)
+.+|..|+.
T Consensus 226 R~~C~~Cg~ 234 (309)
T PRK03564 226 RVKCSNCEQ 234 (309)
T ss_pred CccCCCCCC
Confidence 457888875
No 225
>COG2879 Uncharacterized small protein [Function unknown]
Probab=25.04 E-value=95 Score=16.64 Aligned_cols=18 Identities=17% Similarity=-0.018 Sum_probs=11.7
Q ss_pred CChHHHHHHHHHcCCCCc
Q psy691 70 SLQRLLNRHMKCHSDVKR 87 (134)
Q Consensus 70 ~~~~~l~~H~~~h~~~k~ 87 (134)
...+++..||+.++..+|
T Consensus 23 pdYdnYVehmr~~hPd~p 40 (65)
T COG2879 23 PDYDNYVEHMRKKHPDKP 40 (65)
T ss_pred CcHHHHHHHHHHhCcCCC
Confidence 456677788887555554
No 226
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=24.96 E-value=40 Score=23.68 Aligned_cols=15 Identities=20% Similarity=0.487 Sum_probs=10.1
Q ss_pred CCceecccccccccC
Q psy691 85 VKRYLCTFCGKGFND 99 (134)
Q Consensus 85 ~k~~~C~~C~~~f~~ 99 (134)
.+-|.|+.||..+.+
T Consensus 320 ~r~~~C~~cg~~~~r 334 (364)
T COG0675 320 GRLFKCPRCGFVHDR 334 (364)
T ss_pred ceeEECCCCCCeehh
Confidence 456788888765544
No 227
>TIGR01562 FdhE formate dehydrogenase accessory protein FdhE. The only sequence scoring between trusted and noise is that from Aquifex aeolicus, which shows certain structural differences from the proteobacterial forms in the alignment. However it is notable that A. aeolicus also has a sequence scoring above trusted to the alpha subunit of formate dehydrogenase (TIGR01553).
Probab=24.58 E-value=28 Score=24.90 Aligned_cols=10 Identities=30% Similarity=0.889 Sum_probs=6.8
Q ss_pred ceeccccccc
Q psy691 87 RYLCTFCGKG 96 (134)
Q Consensus 87 ~~~C~~C~~~ 96 (134)
+.+|..|+..
T Consensus 224 R~~C~~Cg~~ 233 (305)
T TIGR01562 224 RVKCSHCEES 233 (305)
T ss_pred CccCCCCCCC
Confidence 4578888753
No 228
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=24.54 E-value=48 Score=17.22 Aligned_cols=12 Identities=25% Similarity=0.603 Sum_probs=7.1
Q ss_pred Cceecccccccc
Q psy691 58 TRFACHLCSKSF 69 (134)
Q Consensus 58 ~~~~C~~C~~~f 69 (134)
..|.|+.||..+
T Consensus 13 v~~~Cp~cGipt 24 (55)
T PF13824_consen 13 VNFECPDCGIPT 24 (55)
T ss_pred cCCcCCCCCCcC
Confidence 346677776544
No 229
>PF08576 DUF1764: Eukaryotic protein of unknown function (DUF1764); InterPro: IPR013885 This entry consists of eukaryotic proteins of unknown function, including many hypothetical proteins.
Probab=24.34 E-value=38 Score=19.82 Aligned_cols=11 Identities=9% Similarity=-0.342 Sum_probs=7.6
Q ss_pred cCCCccccccC
Q psy691 111 TGKEEEEEEDG 121 (134)
Q Consensus 111 ~~~~~~~c~~~ 121 (134)
|..-||.|.||
T Consensus 91 T~~CPFDC~CC 101 (102)
T PF08576_consen 91 TPLCPFDCDCC 101 (102)
T ss_pred CCCCCCcCCCC
Confidence 34567888877
No 230
>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=24.21 E-value=44 Score=17.03 Aligned_cols=17 Identities=24% Similarity=0.751 Sum_probs=11.1
Q ss_pred CCCCceeccccccccCC
Q psy691 55 KDNTRFACHLCSKSFSL 71 (134)
Q Consensus 55 ~~~~~~~C~~C~~~f~~ 71 (134)
.....+.|.+|++.+..
T Consensus 31 ~~~~~~rC~YCe~~~~~ 47 (52)
T PF02748_consen 31 KEPIKLRCHYCERIITE 47 (52)
T ss_dssp TTTCEEEETTT--EEEH
T ss_pred CCCCEEEeeCCCCEecc
Confidence 44567999999988764
No 231
>PF14353 CpXC: CpXC protein
Probab=24.08 E-value=37 Score=20.59 Aligned_cols=23 Identities=30% Similarity=0.524 Sum_probs=17.0
Q ss_pred CceeccccccccCChHHHHHHHH
Q psy691 58 TRFACHLCSKSFSLQRLLNRHMK 80 (134)
Q Consensus 58 ~~~~C~~C~~~f~~~~~l~~H~~ 80 (134)
..|.|+.||..|.-...+..|..
T Consensus 37 ~~~~CP~Cg~~~~~~~p~lY~D~ 59 (128)
T PF14353_consen 37 FSFTCPSCGHKFRLEYPLLYHDP 59 (128)
T ss_pred CEEECCCCCCceecCCCEEEEcC
Confidence 35899999999987666555543
No 232
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=23.76 E-value=1e+02 Score=22.34 Aligned_cols=48 Identities=23% Similarity=0.488 Sum_probs=27.2
Q ss_pred eccccccccCChHHHHHHHHHcCCCCceecccccccccChhhHHHHHhHh
Q psy691 61 ACHLCSKSFSLQRLLNRHMKCHSDVKRYLCTFCGKGFNDTFDLKRHTRTH 110 (134)
Q Consensus 61 ~C~~C~~~f~~~~~l~~H~~~h~~~k~~~C~~C~~~f~~~~~l~~H~~~h 110 (134)
.|-.|.-.|.....-..- .-+....|+|+.|...|...-..-.|...|
T Consensus 364 ~Cf~CQ~~fp~~~~~~~~--~~~ss~rY~Ce~CK~~FC~dCdvfiHe~Lh 411 (421)
T COG5151 364 HCFVCQGPFPKPPVSPFD--ESTSSGRYQCELCKSTFCSDCDVFIHETLH 411 (421)
T ss_pred cceeccCCCCCCCCCccc--ccccccceechhhhhhhhhhhHHHHHHHHh
Confidence 466666666643321100 112234588888888887776666666555
No 233
>PTZ00303 phosphatidylinositol kinase; Provisional
Probab=23.71 E-value=45 Score=27.44 Aligned_cols=33 Identities=18% Similarity=0.359 Sum_probs=18.5
Q ss_pred eeccccccccCChHHHHHHHHHcCCCCceecccccccccC
Q psy691 60 FACHLCSKSFSLQRLLNRHMKCHSDVKRYLCTFCGKGFND 99 (134)
Q Consensus 60 ~~C~~C~~~f~~~~~l~~H~~~h~~~k~~~C~~C~~~f~~ 99 (134)
-.|..|++.|....- -...+.+-|..||..|..
T Consensus 461 dtC~~C~kkFfSlsK-------~L~~RKHHCRkCGrVFC~ 493 (1374)
T PTZ00303 461 DSCPSCGRAFISLSR-------PLGTRAHHCRSCGIRLCV 493 (1374)
T ss_pred CcccCcCCccccccc-------ccccccccccCCccccCc
Confidence 569999999864311 012234456666665544
No 234
>PTZ00448 hypothetical protein; Provisional
Probab=23.63 E-value=53 Score=24.22 Aligned_cols=23 Identities=30% Similarity=0.535 Sum_probs=20.3
Q ss_pred ceecccccccccChhhHHHHHhH
Q psy691 87 RYLCTFCGKGFNDTFDLKRHTRT 109 (134)
Q Consensus 87 ~~~C~~C~~~f~~~~~l~~H~~~ 109 (134)
.|.|..|+-.|......+.|.++
T Consensus 314 ~~tC~~C~v~F~~~~~qR~H~KS 336 (373)
T PTZ00448 314 MLLCRKCNIQLMDHNAFKQHYRS 336 (373)
T ss_pred CccccccccccCCHHHHHHHhhh
Confidence 58899999999888888888876
No 235
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=22.88 E-value=52 Score=15.01 Aligned_cols=12 Identities=33% Similarity=0.758 Sum_probs=7.1
Q ss_pred ceeccccccccC
Q psy691 59 RFACHLCSKSFS 70 (134)
Q Consensus 59 ~~~C~~C~~~f~ 70 (134)
-+.|..|+..|.
T Consensus 21 ~~~C~~Cg~~~~ 32 (33)
T PF08792_consen 21 YEVCIFCGSSFP 32 (33)
T ss_pred eEEcccCCcEee
Confidence 356666666553
No 236
>PRK04023 DNA polymerase II large subunit; Validated
Probab=22.55 E-value=68 Score=27.12 Aligned_cols=10 Identities=40% Similarity=0.823 Sum_probs=7.2
Q ss_pred ceeccccccc
Q psy691 59 RFACHLCSKS 68 (134)
Q Consensus 59 ~~~C~~C~~~ 68 (134)
...|+.||..
T Consensus 626 ~RfCpsCG~~ 635 (1121)
T PRK04023 626 RRKCPSCGKE 635 (1121)
T ss_pred CccCCCCCCc
Confidence 4578888866
No 237
>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=22.33 E-value=13 Score=29.67 Aligned_cols=56 Identities=20% Similarity=0.519 Sum_probs=35.8
Q ss_pred eccccccccCChHHHHHHHHHcCCCCce-ecccccccccChhhHHHHHhHhcCCCccccccCCC
Q psy691 61 ACHLCSKSFSLQRLLNRHMKCHSDVKRY-LCTFCGKGFNDTFDLKRHTRTHTGKEEEEEEDGKT 123 (134)
Q Consensus 61 ~C~~C~~~f~~~~~l~~H~~~h~~~k~~-~C~~C~~~f~~~~~l~~H~~~h~~~~~~~c~~~~~ 123 (134)
.|..||-.|+.-..|-.. |.++..+.| .|+.|.+.|....+.+ .|. .|..|+.|+-
T Consensus 125 ~CT~CGPRfTIi~alPYD-R~nTsM~~F~lC~~C~~EY~dP~nRR----fHA--Qp~aCp~CGP 181 (750)
T COG0068 125 NCTNCGPRFTIIEALPYD-RENTSMADFPLCPFCDKEYKDPLNRR----FHA--QPIACPKCGP 181 (750)
T ss_pred ccCCCCcceeeeccCCCC-cccCccccCcCCHHHHHHhcCccccc----ccc--ccccCcccCC
Confidence 488899988876665533 334444444 6888988777765543 342 4778875554
No 238
>COG4391 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=22.06 E-value=53 Score=17.48 Aligned_cols=14 Identities=21% Similarity=0.698 Sum_probs=10.6
Q ss_pred CCceeccccccccC
Q psy691 57 NTRFACHLCSKSFS 70 (134)
Q Consensus 57 ~~~~~C~~C~~~f~ 70 (134)
++--.|++|+..|.
T Consensus 46 ~gev~CPYC~t~y~ 59 (62)
T COG4391 46 EGEVVCPYCSTRYR 59 (62)
T ss_pred CCcEecCccccEEE
Confidence 34468999998875
No 239
>KOG2907|consensus
Probab=22.03 E-value=36 Score=20.54 Aligned_cols=11 Identities=9% Similarity=-0.206 Sum_probs=5.7
Q ss_pred cccccCCCccc
Q psy691 116 EEEEDGKTNVL 126 (134)
Q Consensus 116 ~~c~~~~~~~~ 126 (134)
|.|..|++.|.
T Consensus 103 YTC~kC~~k~~ 113 (116)
T KOG2907|consen 103 YTCPKCKYKFT 113 (116)
T ss_pred EEcCccceeee
Confidence 55555555443
No 240
>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=21.86 E-value=71 Score=20.00 Aligned_cols=47 Identities=15% Similarity=0.233 Sum_probs=25.7
Q ss_pred eeccccccccCChHHHHHHHHHc-----CCCCceecccccccccChhhHHHH
Q psy691 60 FACHLCSKSFSLQRLLNRHMKCH-----SDVKRYLCTFCGKGFNDTFDLKRH 106 (134)
Q Consensus 60 ~~C~~C~~~f~~~~~l~~H~~~h-----~~~k~~~C~~C~~~f~~~~~l~~H 106 (134)
-.|..|+.....-..-..--... ....=+.|..|++.|-.-+++.+-
T Consensus 92 sRC~~CN~~L~~v~~~~v~~~vp~~v~~~~~~f~~C~~C~kiyW~GsH~~~~ 143 (147)
T PF01927_consen 92 SRCPKCNGPLRPVSKEEVKDRVPPYVYETYDEFWRCPGCGKIYWEGSHWRRM 143 (147)
T ss_pred CccCCCCcEeeechhhccccccCccccccCCeEEECCCCCCEecccccHHHH
Confidence 47888887654322110000011 112347899999988877766543
No 241
>COG3364 Zn-ribbon containing protein [General function prediction only]
Probab=21.70 E-value=42 Score=19.87 Aligned_cols=15 Identities=40% Similarity=0.713 Sum_probs=12.0
Q ss_pred ceecccccccccChh
Q psy691 87 RYLCTFCGKGFNDTF 101 (134)
Q Consensus 87 ~~~C~~C~~~f~~~~ 101 (134)
|++|..||..|..-+
T Consensus 2 pH~CtrCG~vf~~g~ 16 (112)
T COG3364 2 PHQCTRCGEVFDDGS 16 (112)
T ss_pred Cceeccccccccccc
Confidence 678999999888743
No 242
>TIGR00627 tfb4 transcription factor tfb4. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=21.69 E-value=61 Score=22.93 Aligned_cols=12 Identities=17% Similarity=0.695 Sum_probs=7.4
Q ss_pred eecccccccccC
Q psy691 88 YLCTFCGKGFND 99 (134)
Q Consensus 88 ~~C~~C~~~f~~ 99 (134)
|.|..|.-.|..
T Consensus 256 yvCs~Clsi~C~ 267 (279)
T TIGR00627 256 FVCSVCLSVLCQ 267 (279)
T ss_pred EECCCccCCcCC
Confidence 666666665553
No 243
>COG5216 Uncharacterized conserved protein [Function unknown]
Probab=21.61 E-value=21 Score=18.81 Aligned_cols=16 Identities=19% Similarity=-0.002 Sum_probs=10.5
Q ss_pred cccccCCCcccCccce
Q psy691 116 EEEEDGKTNVLTTEYL 131 (134)
Q Consensus 116 ~~c~~~~~~~~~~~~l 131 (134)
|.|+||.++-++-+.|
T Consensus 23 yPCPCGDRFeIsLeDl 38 (67)
T COG5216 23 YPCPCGDRFEISLEDL 38 (67)
T ss_pred ecCCCCCEeEEEHHHh
Confidence 6788887776655443
No 244
>KOG4215|consensus
Probab=21.60 E-value=39 Score=24.92 Aligned_cols=18 Identities=39% Similarity=0.565 Sum_probs=8.9
Q ss_pred ecccccccccChhhHHHHH
Q psy691 89 LCTFCGKGFNDTFDLKRHT 107 (134)
Q Consensus 89 ~C~~C~~~f~~~~~l~~H~ 107 (134)
.|.-| |.|-+++..++|+
T Consensus 38 SCdGC-KGFFRRSVrk~~~ 55 (432)
T KOG4215|consen 38 SCDGC-KGFFRRSVRKNHQ 55 (432)
T ss_pred ecCcc-hHHHHHHHHhcce
Confidence 45555 3455555555443
No 245
>COG5027 SAS2 Histone acetyltransferase (MYST family) [Chromatin structure and dynamics]
Probab=21.22 E-value=59 Score=23.86 Aligned_cols=25 Identities=32% Similarity=0.664 Sum_probs=21.4
Q ss_pred CceecccccccccChhhHHHHHhHh
Q psy691 86 KRYLCTFCGKGFNDTFDLKRHTRTH 110 (134)
Q Consensus 86 k~~~C~~C~~~f~~~~~l~~H~~~h 110 (134)
.-|.|++|-+-|.....|.+|++..
T Consensus 157 ~vyICefClkY~~s~~~~~rH~~kC 181 (395)
T COG5027 157 IVYICEFCLKYYGSQTSLVRHRKKC 181 (395)
T ss_pred eEEEhhhhHHHhcchhHHHHHHhcC
Confidence 3589999999999999999998753
No 246
>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=21.20 E-value=16 Score=17.36 Aligned_cols=13 Identities=23% Similarity=0.549 Sum_probs=4.7
Q ss_pred eeccccccccCCh
Q psy691 60 FACHLCSKSFSLQ 72 (134)
Q Consensus 60 ~~C~~C~~~f~~~ 72 (134)
..|..|++.+...
T Consensus 7 ~~C~~C~~~~~~~ 19 (43)
T PF06467_consen 7 KTCSYCKKYIPNK 19 (43)
T ss_dssp EE-TTT--EEECC
T ss_pred CcCcccCCcccCC
Confidence 3455555555433
No 247
>TIGR00515 accD acetyl-CoA carboxylase, carboxyl transferase, beta subunit. The enzyme acetyl-CoA carboxylase contains a biotin carboxyl carrier protein or domain, a biotin carboxylase, and a carboxyl transferase. This model represents the beta chain of the carboxyl transferase for cases in which the architecture of the protein is as in E. coli, in which the carboxyltransferase portion consists of two non-identical subnits, alpha and beta.
Probab=21.13 E-value=54 Score=23.23 Aligned_cols=32 Identities=16% Similarity=0.374 Sum_probs=20.1
Q ss_pred ceeccccccccCChHHHHHHHHHcCCCCceecccccccccC
Q psy691 59 RFACHLCSKSFSLQRLLNRHMKCHSDVKRYLCTFCGKGFND 99 (134)
Q Consensus 59 ~~~C~~C~~~f~~~~~l~~H~~~h~~~k~~~C~~C~~~f~~ 99 (134)
..+|+.|+.....+. |. ..-+.|+.|+..|..
T Consensus 26 ~~~c~~c~~~~~~~~-l~--------~~~~vc~~c~~h~rl 57 (285)
T TIGR00515 26 WTKCPKCGQVLYTKE-LE--------RNLEVCPKCDHHMRM 57 (285)
T ss_pred eeECCCCcchhhHHH-HH--------hhCCCCCCCCCcCcC
Confidence 347888887755332 32 123688888877664
No 248
>PRK12860 transcriptional activator FlhC; Provisional
Probab=20.76 E-value=49 Score=21.94 Aligned_cols=30 Identities=20% Similarity=0.318 Sum_probs=13.2
Q ss_pred ccCChHHHHHHHHHcCCCCceeccccccccc
Q psy691 68 SFSLQRLLNRHMKCHSDVKRYLCTFCGKGFN 98 (134)
Q Consensus 68 ~f~~~~~l~~H~~~h~~~k~~~C~~C~~~f~ 98 (134)
.|.+.-.|.+.+... .-....|..|+-.|.
T Consensus 116 s~tRAw~LvRf~~s~-~L~l~~C~~Cgg~fv 145 (189)
T PRK12860 116 DLTRAWTLVRFFDAG-MLQLARCCRCGGKFV 145 (189)
T ss_pred cHHHHHHHHHHhcCC-CeeeccCCCCCCCee
Confidence 344444444444432 122345555555554
No 249
>PF13821 DUF4187: Domain of unknown function (DUF4187)
Probab=20.75 E-value=65 Score=16.63 Aligned_cols=19 Identities=21% Similarity=0.482 Sum_probs=14.6
Q ss_pred ceeccccccccCChHHHHH
Q psy691 59 RFACHLCSKSFSLQRLLNR 77 (134)
Q Consensus 59 ~~~C~~C~~~f~~~~~l~~ 77 (134)
-+-|-+||..|.+...|..
T Consensus 27 ~~YC~~Cg~~Y~d~~dL~~ 45 (55)
T PF13821_consen 27 HNYCFWCGTKYDDEEDLER 45 (55)
T ss_pred CceeeeeCCccCCHHHHHh
Confidence 3578889999888877753
No 250
>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=20.73 E-value=42 Score=21.01 Aligned_cols=14 Identities=29% Similarity=0.646 Sum_probs=11.0
Q ss_pred CceeccccccccCC
Q psy691 58 TRFACHLCSKSFSL 71 (134)
Q Consensus 58 ~~~~C~~C~~~f~~ 71 (134)
++..|..||..|+-
T Consensus 111 ~~~RCpeCG~~fkL 124 (136)
T PF01215_consen 111 KPQRCPECGQVFKL 124 (136)
T ss_dssp SEEEETTTEEEEEE
T ss_pred CccCCCCCCeEEEE
Confidence 46889999988864
No 251
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=20.65 E-value=1.3e+02 Score=19.76 Aligned_cols=15 Identities=20% Similarity=0.527 Sum_probs=7.7
Q ss_pred CCceecccccccccC
Q psy691 85 VKRYLCTFCGKGFND 99 (134)
Q Consensus 85 ~k~~~C~~C~~~f~~ 99 (134)
..-|.|+.|.-.|+.
T Consensus 111 ~~~y~C~~~~~r~sf 125 (176)
T COG1675 111 NNYYVCPNCHVKYSF 125 (176)
T ss_pred CCceeCCCCCCcccH
Confidence 344666555544443
No 252
>PRK12722 transcriptional activator FlhC; Provisional
Probab=20.58 E-value=50 Score=21.89 Aligned_cols=30 Identities=23% Similarity=0.389 Sum_probs=13.4
Q ss_pred ccCChHHHHHHHHHcCCCCceeccccccccc
Q psy691 68 SFSLQRLLNRHMKCHSDVKRYLCTFCGKGFN 98 (134)
Q Consensus 68 ~f~~~~~l~~H~~~h~~~k~~~C~~C~~~f~ 98 (134)
.|.+.-.|.+.+.... -....|..|+-.|.
T Consensus 116 s~tRAw~LvRf~~s~~-L~l~~C~~Cgg~fv 145 (187)
T PRK12722 116 SLTRAWTLVRFVDSGM-LQLSSCNCCGGHFV 145 (187)
T ss_pred cHHHHHHHHHHHhcCc-EeeccCCCCCCCee
Confidence 3444444554444321 12234555555554
No 253
>PRK11823 DNA repair protein RadA; Provisional
Probab=20.25 E-value=82 Score=23.81 Aligned_cols=25 Identities=24% Similarity=0.514 Sum_probs=17.1
Q ss_pred CCceeccccccccCChHHHHHHHHHcCCCCceecccccc
Q psy691 57 NTRFACHLCSKSFSLQRLLNRHMKCHSDVKRYLCTFCGK 95 (134)
Q Consensus 57 ~~~~~C~~C~~~f~~~~~l~~H~~~h~~~k~~~C~~C~~ 95 (134)
+..|.|..||..+.. --.+|+.|+.
T Consensus 5 ~~~y~C~~Cg~~~~~--------------~~g~Cp~C~~ 29 (446)
T PRK11823 5 KTAYVCQECGAESPK--------------WLGRCPECGA 29 (446)
T ss_pred CCeEECCcCCCCCcc--------------cCeeCcCCCC
Confidence 346999999977542 1257888864
No 254
>TIGR00416 sms DNA repair protein RadA. The gene protuct codes for a probable ATP-dependent protease involved in both DNA repair and degradation of proteins, peptides, glycopeptides. Also known as sms. Residues 11-28 of the SEED alignment contain a putative Zn binding domain. Residues 110-117 of the seed contain a putative ATP binding site both documented in Haemophilus and in Listeria monocytogenes. for E.coli see ( J. BACTERIOL. 178:5045-5048(1996)).
Probab=20.24 E-value=82 Score=23.90 Aligned_cols=24 Identities=21% Similarity=0.563 Sum_probs=16.9
Q ss_pred CceeccccccccCChHHHHHHHHHcCCCCceecccccc
Q psy691 58 TRFACHLCSKSFSLQRLLNRHMKCHSDVKRYLCTFCGK 95 (134)
Q Consensus 58 ~~~~C~~C~~~f~~~~~l~~H~~~h~~~k~~~C~~C~~ 95 (134)
..|.|..||..+.. --.+|+.|+.
T Consensus 6 ~~y~C~~Cg~~~~~--------------~~g~Cp~C~~ 29 (454)
T TIGR00416 6 SKFVCQHCGADSPK--------------WQGKCPACHA 29 (454)
T ss_pred CeEECCcCCCCCcc--------------ccEECcCCCC
Confidence 45999999977542 2257888874
Done!