Query psy13123
Match_columns 129
No_of_seqs 106 out of 2416
Neff 11.6
Searched_HMMs 46136
Date Fri Aug 16 20:12:09 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy13123.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/13123hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2462|consensus 100.0 4.8E-32 1E-36 162.7 5.2 107 14-122 159-265 (279)
2 KOG2462|consensus 100.0 7E-31 1.5E-35 157.7 5.2 114 14-129 128-244 (279)
3 KOG3576|consensus 99.8 2.4E-21 5.2E-26 112.4 2.6 118 11-128 112-240 (267)
4 KOG1074|consensus 99.8 9E-21 1.9E-25 128.5 0.7 56 73-128 880-935 (958)
5 KOG1074|consensus 99.8 5.1E-20 1.1E-24 124.9 1.3 56 73-128 606-661 (958)
6 KOG3608|consensus 99.7 3.3E-18 7.1E-23 106.8 4.5 119 4-124 195-316 (467)
7 KOG3623|consensus 99.7 2.8E-17 6E-22 110.8 2.7 79 42-120 892-970 (1007)
8 KOG3623|consensus 99.6 2.5E-16 5.5E-21 106.2 3.5 85 9-93 887-971 (1007)
9 KOG3608|consensus 99.6 9.8E-16 2.1E-20 95.9 5.8 110 18-129 181-293 (467)
10 KOG3576|consensus 99.6 1.1E-16 2.4E-21 93.2 1.4 83 42-124 115-197 (267)
11 PLN03086 PRLI-interacting fact 99.4 1.4E-12 3E-17 87.7 7.5 102 14-122 451-562 (567)
12 PHA00733 hypothetical protein 99.4 5.4E-13 1.2E-17 74.3 3.9 83 41-125 37-124 (128)
13 PHA02768 hypothetical protein; 99.1 2.4E-11 5.1E-16 56.9 1.7 43 72-116 5-47 (55)
14 PLN03086 PRLI-interacting fact 99.0 7E-10 1.5E-14 75.0 6.5 80 43-128 452-541 (567)
15 PHA02768 hypothetical protein; 99.0 1.2E-10 2.6E-15 54.6 1.7 42 17-60 6-47 (55)
16 PF13465 zf-H2C2_2: Zinc-finge 99.0 2.6E-10 5.6E-15 46.0 2.1 25 87-111 1-25 (26)
17 PHA00616 hypothetical protein 99.0 2.9E-10 6.3E-15 50.8 1.9 30 100-129 1-30 (44)
18 PHA00733 hypothetical protein 99.0 1.1E-09 2.5E-14 61.1 4.2 94 2-97 26-124 (128)
19 PHA00616 hypothetical protein 98.8 4.6E-09 1E-13 47.0 1.9 34 16-49 1-34 (44)
20 PF13465 zf-H2C2_2: Zinc-finge 98.7 2E-08 4.3E-13 40.4 2.6 23 60-82 2-24 (26)
21 KOG3993|consensus 98.5 1.9E-08 4.2E-13 65.1 0.4 107 16-122 295-480 (500)
22 PHA00732 hypothetical protein 98.5 1.2E-07 2.6E-12 48.5 2.4 37 44-83 1-38 (79)
23 PF00096 zf-C2H2: Zinc finger, 98.5 1.4E-07 3E-12 36.8 1.8 23 101-123 1-23 (23)
24 KOG3993|consensus 98.4 5.5E-08 1.2E-12 63.1 0.1 108 17-124 268-380 (500)
25 PHA00732 hypothetical protein 98.4 2.2E-07 4.7E-12 47.5 2.1 48 16-69 1-49 (79)
26 PF00096 zf-C2H2: Zinc finger, 98.2 1E-06 2.2E-11 34.2 1.7 23 17-39 1-23 (23)
27 PF13912 zf-C2H2_6: C2H2-type 98.2 1E-06 2.2E-11 35.7 1.3 25 100-124 1-25 (27)
28 PF13894 zf-C2H2_4: C2H2-type 98.1 2.3E-06 5E-11 33.4 2.2 24 101-124 1-24 (24)
29 PF05605 zf-Di19: Drought indu 98.1 1.1E-05 2.4E-10 38.3 4.4 49 73-124 3-53 (54)
30 PF05605 zf-Di19: Drought indu 98.0 2.4E-05 5.1E-10 37.2 4.7 47 17-66 3-51 (54)
31 PF09237 GAGA: GAGA factor; I 97.9 1.5E-05 3.3E-10 36.6 2.6 33 96-128 20-52 (54)
32 PF13912 zf-C2H2_6: C2H2-type 97.9 6E-06 1.3E-10 33.3 1.2 25 16-40 1-25 (27)
33 smart00355 ZnF_C2H2 zinc finge 97.9 1.7E-05 3.6E-10 31.4 2.5 24 101-124 1-24 (26)
34 PF13894 zf-C2H2_4: C2H2-type 97.8 1.6E-05 3.5E-10 30.9 2.0 23 17-39 1-23 (24)
35 PF12756 zf-C2H2_2: C2H2 type 97.8 1.6E-05 3.5E-10 42.4 2.4 73 18-95 1-73 (100)
36 PF09237 GAGA: GAGA factor; I 97.7 0.0001 2.3E-09 33.9 3.3 33 12-44 20-52 (54)
37 PF12756 zf-C2H2_2: C2H2 type 97.6 5.4E-05 1.2E-09 40.4 2.7 73 46-123 1-73 (100)
38 smart00355 ZnF_C2H2 zinc finge 97.4 0.00016 3.5E-09 28.3 2.3 23 17-39 1-23 (26)
39 PF13909 zf-H2C2_5: C2H2-type 97.4 0.00021 4.5E-09 27.9 2.1 23 101-124 1-23 (24)
40 PF12874 zf-met: Zinc-finger o 97.3 0.00015 3.2E-09 28.5 1.2 23 101-123 1-23 (25)
41 COG5189 SFP1 Putative transcri 97.2 7.7E-05 1.7E-09 47.4 0.2 51 70-120 347-418 (423)
42 PRK04860 hypothetical protein; 97.2 0.00027 5.9E-09 41.1 2.4 38 72-113 119-156 (160)
43 COG5189 SFP1 Putative transcri 97.2 0.00015 3.3E-09 46.1 0.9 70 14-93 347-419 (423)
44 PF12874 zf-met: Zinc-finger o 97.0 0.00039 8.4E-09 27.3 1.1 22 17-38 1-22 (25)
45 PRK04860 hypothetical protein; 97.0 0.0004 8.6E-09 40.5 1.4 25 58-82 129-153 (160)
46 PF13909 zf-H2C2_5: C2H2-type 96.9 0.00087 1.9E-08 26.0 1.5 23 17-40 1-23 (24)
47 PF12171 zf-C2H2_jaz: Zinc-fin 96.6 0.00054 1.2E-08 27.5 0.1 22 101-122 2-23 (27)
48 TIGR00622 ssl1 transcription f 96.5 0.0037 8.1E-08 34.1 2.8 80 43-124 14-105 (112)
49 PF13913 zf-C2HC_2: zinc-finge 96.1 0.0076 1.7E-07 23.7 2.1 21 101-122 3-23 (25)
50 smart00451 ZnF_U1 U1-like zinc 95.6 0.012 2.5E-07 24.9 1.7 23 100-122 3-25 (35)
51 KOG1146|consensus 95.4 0.0075 1.6E-07 45.5 1.3 80 11-93 460-539 (1406)
52 KOG2893|consensus 94.6 0.0079 1.7E-07 37.1 -0.4 41 75-119 13-53 (341)
53 cd00350 rubredoxin_like Rubred 94.5 0.028 6E-07 23.7 1.3 10 73-82 2-11 (33)
54 KOG2785|consensus 94.0 0.41 8.8E-06 31.9 6.3 51 72-122 166-242 (390)
55 COG4049 Uncharacterized protei 93.7 0.038 8.2E-07 26.0 1.1 23 98-120 15-37 (65)
56 PF12013 DUF3505: Protein of u 93.5 0.29 6.2E-06 26.7 4.4 25 101-125 81-109 (109)
57 KOG2231|consensus 93.3 0.22 4.8E-06 35.7 4.6 95 24-123 122-235 (669)
58 TIGR00622 ssl1 transcription f 92.9 0.15 3.2E-06 28.0 2.7 85 15-107 14-110 (112)
59 PF13719 zinc_ribbon_5: zinc-r 92.9 0.097 2.1E-06 22.6 1.7 32 74-110 4-35 (37)
60 cd00729 rubredoxin_SM Rubredox 91.7 0.12 2.7E-06 21.9 1.2 25 72-108 2-26 (34)
61 PF13717 zinc_ribbon_4: zinc-r 91.6 0.17 3.7E-06 21.7 1.6 33 73-110 3-35 (36)
62 COG5048 FOG: Zn-finger [Genera 91.6 0.025 5.4E-07 37.9 -1.6 56 72-127 289-350 (467)
63 TIGR02098 MJ0042_CXXC MJ0042 f 91.2 0.16 3.5E-06 21.9 1.4 14 73-86 3-16 (38)
64 KOG2231|consensus 90.7 0.58 1.3E-05 33.7 4.2 79 47-126 118-208 (669)
65 smart00614 ZnF_BED BED zinc fi 90.2 0.24 5.2E-06 22.9 1.5 23 101-123 19-47 (50)
66 PF02892 zf-BED: BED zinc fing 90.0 0.3 6.5E-06 21.9 1.8 25 97-121 13-41 (45)
67 PF09538 FYDLN_acid: Protein o 90.0 0.16 3.6E-06 27.7 1.0 29 18-57 11-39 (108)
68 COG1592 Rubrerythrin [Energy p 89.5 0.22 4.8E-06 29.4 1.3 10 44-53 134-143 (166)
69 KOG2482|consensus 89.5 0.58 1.3E-05 30.9 3.2 103 17-121 196-355 (423)
70 COG2888 Predicted Zn-ribbon RN 88.8 0.21 4.6E-06 23.9 0.7 49 17-80 10-58 (61)
71 TIGR00373 conserved hypothetic 88.6 0.6 1.3E-05 27.4 2.7 33 41-82 106-138 (158)
72 KOG1146|consensus 88.5 0.097 2.1E-06 40.0 -0.7 23 99-122 1328-1350(1406)
73 KOG2186|consensus 88.4 0.29 6.3E-06 30.8 1.4 48 44-94 3-50 (276)
74 COG5048 FOG: Zn-finger [Genera 88.4 0.068 1.5E-06 35.8 -1.5 57 16-72 289-351 (467)
75 smart00531 TFIIE Transcription 87.0 1 2.2E-05 26.1 3.0 38 41-82 96-133 (147)
76 smart00734 ZnF_Rad18 Rad18-lik 86.7 0.83 1.8E-05 18.0 1.8 19 102-121 3-21 (26)
77 KOG2186|consensus 86.7 0.36 7.7E-06 30.4 1.0 49 17-68 4-52 (276)
78 PRK06266 transcription initiat 86.6 0.67 1.5E-05 27.8 2.2 34 41-83 114-147 (178)
79 TIGR02605 CxxC_CxxC_SSSS putat 86.3 0.16 3.5E-06 23.6 -0.5 12 17-28 6-17 (52)
80 PF09986 DUF2225: Uncharacteri 86.3 0.084 1.8E-06 32.5 -1.8 21 14-34 3-23 (214)
81 PRK14890 putative Zn-ribbon RN 86.0 0.84 1.8E-05 22.0 1.9 9 99-107 47-55 (59)
82 TIGR00373 conserved hypothetic 85.6 1.2 2.7E-05 26.1 2.9 35 67-110 104-138 (158)
83 PRK00398 rpoP DNA-directed RNA 85.4 0.33 7.1E-06 22.0 0.3 10 17-26 4-13 (46)
84 PF05443 ROS_MUCR: ROS/MUCR tr 85.1 0.5 1.1E-05 26.9 1.0 24 100-126 72-95 (132)
85 PF13878 zf-C2H2_3: zinc-finge 85.0 1.7 3.7E-05 19.2 2.5 23 17-39 14-38 (41)
86 smart00834 CxxC_CXXC_SSSS Puta 84.9 0.19 4.1E-06 22.0 -0.6 30 16-52 5-34 (41)
87 KOG2593|consensus 84.5 0.33 7.2E-06 32.9 0.2 39 11-52 123-161 (436)
88 PF04959 ARS2: Arsenite-resist 84.3 0.49 1.1E-05 29.2 0.9 23 72-94 77-99 (214)
89 KOG4173|consensus 83.7 1.2 2.6E-05 27.2 2.3 74 45-121 80-167 (253)
90 smart00659 RPOLCX RNA polymera 82.7 0.74 1.6E-05 20.8 0.9 11 17-27 3-13 (44)
91 KOG2482|consensus 82.6 2.5 5.4E-05 28.1 3.5 53 16-68 144-219 (423)
92 COG5236 Uncharacterized conser 82.4 1.5 3.3E-05 29.1 2.5 20 103-122 223-242 (493)
93 PRK00464 nrdR transcriptional 81.2 0.23 4.9E-06 29.0 -1.3 12 73-84 29-40 (154)
94 TIGR02300 FYDLN_acid conserved 80.8 0.95 2.1E-05 25.4 1.1 30 17-57 10-39 (129)
95 COG3357 Predicted transcriptio 79.0 1.2 2.5E-05 23.5 1.0 14 43-56 57-70 (97)
96 PF06524 NOA36: NOA36 protein; 77.2 0.88 1.9E-05 28.9 0.3 26 98-123 207-232 (314)
97 PF15269 zf-C2H2_7: Zinc-finge 76.5 2.2 4.8E-05 19.2 1.4 22 101-122 21-42 (54)
98 KOG4167|consensus 76.2 0.87 1.9E-05 33.2 0.1 28 14-41 790-817 (907)
99 KOG2785|consensus 75.8 5.9 0.00013 26.8 3.7 52 43-94 165-242 (390)
100 PRK03824 hypA hydrogenase nick 75.3 1 2.2E-05 25.7 0.2 14 72-85 70-83 (135)
101 PF08790 zf-LYAR: LYAR-type C2 75.2 0.29 6.2E-06 19.8 -1.5 9 102-110 2-10 (28)
102 PF07754 DUF1610: Domain of un 75.2 1.2 2.5E-05 17.3 0.3 9 16-24 16-24 (24)
103 PF10571 UPF0547: Uncharacteri 75.1 1.6 3.4E-05 17.3 0.6 10 102-111 16-25 (26)
104 PRK03564 formate dehydrogenase 74.9 0.45 9.7E-06 31.1 -1.5 72 15-108 186-260 (309)
105 PF12013 DUF3505: Protein of u 74.5 8.6 0.00019 20.9 3.7 24 17-40 81-108 (109)
106 PHA00626 hypothetical protein 74.0 1.8 3.9E-05 20.6 0.8 15 99-113 22-36 (59)
107 PF09845 DUF2072: Zn-ribbon co 73.8 1.1 2.4E-05 25.4 0.0 28 16-53 1-28 (131)
108 COG1996 RPC10 DNA-directed RNA 73.6 2 4.3E-05 19.9 0.9 10 73-82 7-16 (49)
109 COG1997 RPL43A Ribosomal prote 72.8 1.5 3.2E-05 22.9 0.4 34 43-86 34-67 (89)
110 PRK04023 DNA polymerase II lar 72.5 4.4 9.5E-05 31.1 2.8 9 101-109 664-672 (1121)
111 KOG2807|consensus 72.0 4.5 9.9E-05 26.8 2.5 24 100-123 345-368 (378)
112 PRK09678 DNA-binding transcrip 71.9 1.2 2.5E-05 22.5 -0.1 15 70-84 25-41 (72)
113 KOG4173|consensus 71.9 2.6 5.7E-05 25.9 1.3 48 18-65 108-167 (253)
114 KOG3408|consensus 71.4 4.2 9E-05 22.7 1.9 29 10-38 51-79 (129)
115 PF08274 PhnA_Zn_Ribbon: PhnA 68.8 1.5 3.3E-05 18.0 -0.1 7 73-79 20-26 (30)
116 PF07975 C1_4: TFIIH C1-like d 68.3 0.88 1.9E-05 21.3 -0.9 24 16-39 21-44 (51)
117 PF09723 Zn-ribbon_8: Zinc rib 68.1 2 4.4E-05 19.0 0.3 12 101-112 6-17 (42)
118 PF13453 zf-TFIIB: Transcripti 67.0 2 4.3E-05 18.8 0.1 15 45-59 20-34 (41)
119 PF05191 ADK_lid: Adenylate ki 66.6 1.1 2.3E-05 19.3 -0.8 9 18-26 3-11 (36)
120 KOG4167|consensus 66.5 1.4 3.1E-05 32.2 -0.6 25 100-124 792-816 (907)
121 PF03604 DNA_RNApol_7kD: DNA d 65.7 4 8.6E-05 17.0 0.9 9 100-108 17-25 (32)
122 COG1198 PriA Primosomal protei 64.7 2.3 4.9E-05 31.4 0.1 12 18-29 437-448 (730)
123 PF02176 zf-TRAF: TRAF-type zi 64.6 5.2 0.00011 18.9 1.3 25 86-110 24-52 (60)
124 COG5151 SSL1 RNA polymerase II 64.5 8.9 0.00019 25.3 2.6 78 44-123 322-411 (421)
125 cd00924 Cyt_c_Oxidase_Vb Cytoc 63.6 3 6.4E-05 22.4 0.4 17 11-28 75-91 (97)
126 COG1655 Uncharacterized protei 63.2 1.3 2.7E-05 27.7 -1.1 24 16-39 19-42 (267)
127 PLN02294 cytochrome c oxidase 63.1 3.2 6.9E-05 24.7 0.5 16 14-29 139-154 (174)
128 PF07282 OrfB_Zn_ribbon: Putat 62.2 7.1 0.00015 19.1 1.6 10 100-109 46-55 (69)
129 KOG2893|consensus 62.1 2.1 4.7E-05 26.9 -0.3 47 14-65 9-55 (341)
130 PF14446 Prok-RING_1: Prokaryo 62.0 1.3 2.8E-05 21.0 -1.0 11 18-28 7-17 (54)
131 smart00154 ZnF_AN1 AN1-like Zi 61.9 3.5 7.5E-05 18.0 0.4 14 16-29 12-25 (39)
132 COG5236 Uncharacterized conser 61.6 42 0.00091 22.8 5.3 73 18-95 222-304 (493)
133 TIGR01562 FdhE formate dehydro 61.6 2 4.3E-05 28.2 -0.5 48 17-80 185-232 (305)
134 PF05290 Baculo_IE-1: Baculovi 60.5 11 0.00024 21.6 2.2 15 41-55 77-91 (140)
135 PF04959 ARS2: Arsenite-resist 60.2 4.8 0.0001 25.0 0.9 25 45-69 78-102 (214)
136 TIGR01206 lysW lysine biosynth 60.0 3.7 8E-05 19.5 0.3 10 73-82 3-12 (54)
137 KOG2923|consensus 59.5 5.9 0.00013 19.4 1.0 12 41-52 41-52 (67)
138 KOG2807|consensus 58.9 13 0.00027 24.8 2.6 30 72-107 345-374 (378)
139 KOG2593|consensus 57.3 16 0.00036 25.3 3.0 38 40-80 124-161 (436)
140 COG2331 Uncharacterized protei 56.4 7 0.00015 19.9 1.0 32 15-53 11-42 (82)
141 KOG1280|consensus 56.2 12 0.00026 25.1 2.2 22 16-37 79-100 (381)
142 PF01927 Mut7-C: Mut7-C RNAse 56.2 7.7 0.00017 22.4 1.3 49 73-121 92-145 (147)
143 KOG0978|consensus 56.0 2.2 4.7E-05 31.2 -1.2 15 102-116 680-694 (698)
144 PF12760 Zn_Tnp_IS1595: Transp 55.2 12 0.00026 16.8 1.6 10 99-108 36-45 (46)
145 PTZ00255 60S ribosomal protein 54.5 3.3 7.2E-05 21.9 -0.4 34 43-86 35-68 (90)
146 COG4530 Uncharacterized protei 54.2 6.9 0.00015 21.5 0.8 26 18-54 11-36 (129)
147 smart00661 RPOL9 RNA polymeras 54.0 8 0.00017 17.7 0.9 11 72-82 20-30 (52)
148 COG3364 Zn-ribbon containing p 53.8 8.7 0.00019 20.8 1.1 14 16-29 2-15 (112)
149 PRK14714 DNA polymerase II lar 52.9 18 0.00038 28.9 2.9 10 72-81 692-701 (1337)
150 PF01428 zf-AN1: AN1-like Zinc 52.0 4.7 0.0001 17.9 -0.0 15 15-29 12-26 (43)
151 PF13451 zf-trcl: Probable zin 51.4 6.4 0.00014 18.3 0.4 13 15-27 3-15 (49)
152 PRK12380 hydrogenase nickel in 51.0 7.4 0.00016 21.5 0.6 11 45-55 71-81 (113)
153 smart00440 ZnF_C2C2 C2C2 Zinc 50.6 1 2.2E-05 19.8 -2.3 10 101-110 29-38 (40)
154 PF12773 DZR: Double zinc ribb 49.9 16 0.00034 16.5 1.6 8 73-80 30-37 (50)
155 COG3677 Transposase and inacti 49.9 8.6 0.00019 21.8 0.8 36 73-113 31-66 (129)
156 PF14787 zf-CCHC_5: GAG-polypr 49.6 5.1 0.00011 17.2 -0.1 15 102-116 4-18 (36)
157 COG1656 Uncharacterized conser 49.3 16 0.00035 21.7 1.9 49 73-121 98-151 (165)
158 TIGR00100 hypA hydrogenase nic 49.2 9.1 0.0002 21.2 0.8 12 73-84 71-82 (115)
159 COG1675 TFA1 Transcription ini 49.1 21 0.00046 21.6 2.3 35 39-82 108-142 (176)
160 TIGR00280 L37a ribosomal prote 48.9 3.6 7.7E-05 21.8 -0.7 34 43-86 34-67 (91)
161 PF04216 FdhE: Protein involve 48.8 0.64 1.4E-05 30.1 -4.3 74 17-108 173-246 (290)
162 PF14311 DUF4379: Domain of un 48.1 17 0.00037 17.0 1.6 12 73-84 29-40 (55)
163 COG3091 SprT Zn-dependent meta 47.9 8.7 0.00019 22.5 0.6 35 71-110 116-150 (156)
164 COG0068 HypF Hydrogenase matur 46.8 2.3 5E-05 31.1 -2.1 58 45-109 124-182 (750)
165 PF01780 Ribosomal_L37ae: Ribo 46.6 2.3 4.9E-05 22.5 -1.7 33 43-85 34-66 (90)
166 COG5216 Uncharacterized conser 45.9 9.6 0.00021 18.3 0.5 11 41-51 41-51 (67)
167 TIGR03829 YokU_near_AblA uncha 45.6 15 0.00032 19.5 1.2 17 17-33 36-52 (89)
168 PTZ00043 cytochrome c oxidase 44.9 9.6 0.00021 23.9 0.5 34 13-49 178-211 (268)
169 PRK00432 30S ribosomal protein 44.8 12 0.00026 17.4 0.7 10 100-109 37-46 (50)
170 PF10537 WAC_Acf1_DNA_bd: ATP- 44.6 53 0.0011 17.9 3.8 41 15-56 2-42 (102)
171 PTZ00448 hypothetical protein; 44.2 21 0.00045 24.3 2.0 23 100-122 314-336 (373)
172 COG1571 Predicted DNA-binding 43.5 17 0.00037 25.2 1.5 11 72-82 367-377 (421)
173 KOG2071|consensus 43.3 19 0.0004 26.1 1.7 28 13-40 415-442 (579)
174 PRK00564 hypA hydrogenase nick 42.8 11 0.00023 21.0 0.4 11 45-55 72-82 (117)
175 TIGR00686 phnA alkylphosphonat 42.3 13 0.00029 20.4 0.8 28 18-56 4-31 (109)
176 PF04423 Rad50_zn_hook: Rad50 42.2 9.4 0.0002 17.8 0.2 13 102-114 22-34 (54)
177 PF10013 DUF2256: Uncharacteri 41.8 20 0.00043 16.0 1.1 13 102-114 10-22 (42)
178 COG1773 Rubredoxin [Energy pro 41.7 12 0.00025 17.9 0.4 14 72-85 3-16 (55)
179 PRK03976 rpl37ae 50S ribosomal 41.0 5.1 0.00011 21.2 -0.9 33 43-85 35-67 (90)
180 PHA02998 RNA polymerase subuni 40.8 3.2 6.9E-05 24.9 -1.8 38 73-113 144-184 (195)
181 KOG2907|consensus 40.0 8.6 0.00019 21.2 -0.2 9 45-53 103-111 (116)
182 PF15135 UPF0515: Uncharacteri 39.9 15 0.00031 23.5 0.8 16 10-25 106-121 (278)
183 PF14122 YokU: YokU-like prote 39.2 22 0.00047 18.7 1.2 19 15-33 34-52 (87)
184 COG4957 Predicted transcriptio 38.9 21 0.00046 20.5 1.2 25 17-44 77-101 (148)
185 TIGR00244 transcriptional regu 38.7 4.1 9E-05 23.6 -1.6 17 44-60 28-44 (147)
186 PF10276 zf-CHCC: Zinc-finger 38.6 9.5 0.00021 16.8 -0.1 11 16-26 29-39 (40)
187 PF07295 DUF1451: Protein of u 38.3 11 0.00023 22.0 0.0 8 45-52 113-120 (146)
188 KOG2636|consensus 38.0 26 0.00057 24.5 1.8 29 92-120 393-422 (497)
189 PRK12496 hypothetical protein; 37.9 24 0.00052 21.0 1.5 10 17-26 128-137 (164)
190 TIGR00595 priA primosomal prot 37.9 23 0.0005 25.2 1.6 10 43-52 252-261 (505)
191 PF14353 CpXC: CpXC protein 37.8 13 0.00028 20.8 0.3 17 16-32 38-54 (128)
192 cd00730 rubredoxin Rubredoxin; 37.7 13 0.00028 17.3 0.3 12 17-28 2-13 (50)
193 COG1326 Uncharacterized archae 37.1 39 0.00084 20.8 2.2 11 72-82 30-40 (201)
194 KOG3014|consensus 36.9 27 0.00059 22.4 1.6 31 10-40 28-63 (257)
195 PLN02748 tRNA dimethylallyltra 36.6 30 0.00065 24.5 1.9 24 99-122 417-441 (468)
196 COG1327 Predicted transcriptio 36.3 5.8 0.00012 23.2 -1.2 16 44-59 28-43 (156)
197 PF01155 HypA: Hydrogenase exp 36.2 16 0.00034 20.2 0.5 13 73-85 71-83 (113)
198 PF14369 zf-RING_3: zinc-finge 36.0 20 0.00044 15.2 0.7 31 16-55 2-32 (35)
199 PF10263 SprT-like: SprT-like 35.9 14 0.0003 21.4 0.3 32 72-111 123-154 (157)
200 PF04780 DUF629: Protein of un 35.7 31 0.00067 24.4 1.9 23 17-39 58-80 (466)
201 PF12230 PRP21_like_P: Pre-mRN 35.3 12 0.00027 23.3 0.0 26 99-125 167-192 (229)
202 PF06397 Desulfoferrod_N: Desu 35.3 15 0.00032 15.8 0.2 12 15-26 5-16 (36)
203 PRK10220 hypothetical protein; 35.3 24 0.00051 19.5 1.0 29 18-57 5-33 (111)
204 PF12907 zf-met2: Zinc-binding 34.9 33 0.00072 15.1 1.3 22 17-38 2-26 (40)
205 KOG1842|consensus 34.6 28 0.0006 24.4 1.5 21 101-121 16-36 (505)
206 COG4888 Uncharacterized Zn rib 34.3 4.3 9.2E-05 21.9 -1.8 38 14-55 20-57 (104)
207 PF00301 Rubredoxin: Rubredoxi 34.2 14 0.0003 16.9 0.1 11 17-27 2-12 (47)
208 PF14803 Nudix_N_2: Nudix N-te 34.1 2.7 5.9E-05 17.8 -2.1 8 73-80 23-30 (34)
209 KOG1842|consensus 33.7 32 0.0007 24.1 1.7 24 16-39 15-38 (505)
210 PRK03681 hypA hydrogenase nick 33.7 16 0.00034 20.3 0.2 10 73-82 71-80 (114)
211 PF02891 zf-MIZ: MIZ/SP-RING z 32.2 26 0.00057 16.1 0.8 7 101-107 42-48 (50)
212 TIGR00627 tfb4 transcription f 31.9 38 0.00083 22.2 1.7 11 73-83 256-266 (279)
213 PF09963 DUF2197: Uncharacteri 31.7 30 0.00065 16.6 1.0 36 18-53 4-40 (56)
214 PF02591 DUF164: Putative zinc 31.5 56 0.0012 15.3 1.9 11 70-80 44-54 (56)
215 COG1594 RPB9 DNA-directed RNA 31.4 6 0.00013 21.9 -1.6 10 73-82 101-110 (113)
216 PF01286 XPA_N: XPA protein N- 30.3 21 0.00045 15.2 0.3 12 18-29 5-16 (34)
217 COG1066 Sms Predicted ATP-depe 29.7 30 0.00064 24.2 1.0 9 44-52 7-15 (456)
218 PF10083 DUF2321: Uncharacteri 29.2 22 0.00048 21.0 0.3 20 96-115 64-83 (158)
219 COG2879 Uncharacterized small 29.0 83 0.0018 15.5 2.4 17 112-128 24-40 (65)
220 COG0675 Transposase and inacti 28.7 35 0.00076 22.3 1.3 15 99-113 321-335 (364)
221 TIGR03831 YgiT_finger YgiT-typ 28.5 22 0.00048 15.5 0.2 13 16-28 32-44 (46)
222 smart00731 SprT SprT homologue 27.8 25 0.00053 20.3 0.4 33 72-111 112-144 (146)
223 PF08792 A2L_zn_ribbon: A2L zi 27.7 30 0.00065 14.4 0.5 10 17-26 22-31 (33)
224 COG4338 Uncharacterized protei 27.3 27 0.00059 16.1 0.4 12 103-114 15-26 (54)
225 PF11931 DUF3449: Domain of un 27.3 21 0.00045 22.0 0.0 27 93-119 94-121 (196)
226 PRK04351 hypothetical protein; 27.1 21 0.00045 20.9 -0.0 33 72-112 112-144 (149)
227 cd01121 Sms Sms (bacterial rad 27.0 30 0.00066 23.6 0.7 22 45-80 1-22 (372)
228 PRK11823 DNA repair protein Ra 27.0 34 0.00074 24.0 1.0 24 43-80 6-29 (446)
229 PF01363 FYVE: FYVE zinc finge 26.9 40 0.00086 16.4 1.0 11 45-55 10-20 (69)
230 PRK14873 primosome assembly pr 26.8 42 0.00091 25.0 1.4 34 18-52 385-418 (665)
231 cd00065 FYVE FYVE domain; Zinc 26.7 53 0.0012 15.1 1.4 10 73-82 19-28 (57)
232 PF11023 DUF2614: Protein of u 26.4 37 0.0008 18.9 0.8 10 43-52 68-77 (114)
233 TIGR01384 TFS_arch transcripti 26.0 34 0.00073 18.4 0.7 27 46-84 2-28 (104)
234 smart00064 FYVE Protein presen 26.0 48 0.0011 16.0 1.2 11 45-55 11-21 (68)
235 PRK00420 hypothetical protein; 25.9 41 0.0009 18.7 1.0 12 72-83 40-51 (112)
236 PF15616 TerY-C: TerY-C metal 25.5 7.3 0.00016 22.2 -2.0 13 69-81 102-114 (131)
237 TIGR00416 sms DNA repair prote 25.1 37 0.0008 23.9 0.9 24 43-80 6-29 (454)
238 PF11672 DUF3268: Protein of u 25.0 26 0.00057 19.1 0.1 11 44-54 2-12 (102)
239 PF08209 Sgf11: Sgf11 (transcr 25.0 60 0.0013 13.6 1.2 8 46-53 6-13 (33)
240 PRK00762 hypA hydrogenase nick 24.6 28 0.0006 19.6 0.2 11 73-84 71-81 (124)
241 COG4391 Uncharacterized protei 24.6 35 0.00075 16.7 0.5 11 17-27 49-59 (62)
242 smart00647 IBR In Between Ring 24.1 43 0.00094 15.7 0.8 13 99-111 39-51 (64)
243 TIGR00319 desulf_FeS4 desulfof 23.8 32 0.00069 14.2 0.3 12 15-26 6-17 (34)
244 PF10122 Mu-like_Com: Mu-like 23.6 18 0.00039 16.9 -0.5 7 101-107 25-31 (51)
245 PF13824 zf-Mss51: Zinc-finger 23.6 46 0.001 15.9 0.8 15 96-110 10-24 (55)
246 cd00974 DSRD Desulforedoxin (D 23.5 32 0.0007 14.2 0.3 11 16-26 4-14 (34)
247 COG4896 Uncharacterized protei 23.5 1.1E+02 0.0024 15.0 2.1 11 43-53 30-40 (68)
248 PF06676 DUF1178: Protein of u 23.0 62 0.0013 19.0 1.4 16 72-87 32-47 (148)
249 KOG0717|consensus 22.8 55 0.0012 23.2 1.3 22 101-122 293-314 (508)
250 PF01194 RNA_pol_N: RNA polyme 22.8 56 0.0012 15.9 1.0 16 72-87 4-19 (60)
251 KOG4727|consensus 22.7 57 0.0012 19.7 1.2 22 72-93 75-96 (193)
252 TIGR03830 CxxCG_CxxCG_HTH puta 22.3 73 0.0016 17.5 1.6 21 16-36 31-51 (127)
253 PRK05978 hypothetical protein; 21.7 46 0.001 19.5 0.7 9 102-110 54-62 (148)
254 KOG2857|consensus 21.7 46 0.00099 19.4 0.7 22 100-121 17-38 (157)
255 PF14255 Cys_rich_CPXG: Cystei 21.6 43 0.00092 15.7 0.5 9 102-110 2-10 (52)
256 PRK08222 hydrogenase 4 subunit 21.6 77 0.0017 19.2 1.7 19 99-117 113-131 (181)
257 COG3880 Modulator of heat shoc 21.5 16 0.00034 21.9 -1.2 9 18-26 76-84 (176)
258 PLN03238 probable histone acet 21.3 1.2E+02 0.0025 20.2 2.4 24 71-94 47-70 (290)
259 PF14690 zf-ISL3: zinc-finger 21.2 44 0.00096 14.7 0.5 7 17-23 3-9 (47)
260 COG5188 PRP9 Splicing factor 3 21.0 73 0.0016 21.8 1.6 21 17-37 239-259 (470)
261 PF01215 COX5B: Cytochrome c o 20.9 36 0.00078 19.7 0.2 14 98-111 110-123 (136)
262 PRK05580 primosome assembly pr 20.9 68 0.0015 24.0 1.6 12 42-53 419-430 (679)
263 TIGR00515 accD acetyl-CoA carb 20.5 74 0.0016 21.0 1.5 32 45-85 27-58 (285)
264 PF02748 PyrI_C: Aspartate car 20.3 50 0.0011 15.5 0.6 17 12-28 31-47 (52)
265 PF13821 DUF4187: Domain of un 20.3 63 0.0014 15.3 0.9 15 102-116 29-43 (55)
266 PF08271 TF_Zn_Ribbon: TFIIB z 20.3 42 0.00091 14.7 0.3 11 72-82 19-29 (43)
267 KOG1994|consensus 20.2 69 0.0015 20.4 1.3 23 70-92 237-259 (268)
268 PF01096 TFIIS_C: Transcriptio 20.0 34 0.00073 14.8 -0.0 10 101-110 29-38 (39)
No 1
>KOG2462|consensus
Probab=99.97 E-value=4.8e-32 Score=162.69 Aligned_cols=107 Identities=37% Similarity=0.756 Sum_probs=77.8
Q ss_pred CCccccCcchhccCChhhHHHHHHHhCCCCCccCCcchhhhcchhHHHHHHHHhCCCCCeecccccccccChhHHHHHHH
Q psy13123 14 TSAYQCGECGKQFTRKFSLNAHLHVHYGSSNYKCPLCGKFFIQLCHMKDHIQAHGGLKPYVCTYCGKAFVRASDLKRHID 93 (129)
Q Consensus 14 ~~~~~C~~C~~~~~~~~~l~~h~~~~~~~~~~~c~~c~~~~~~~~~l~~~~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~ 93 (129)
.+.+.|+.|++.|.....|..|+++|+ .+..|.+||+.|...+.|+.|+++|+||+||.|+.|+++|.+.++|..|++
T Consensus 159 ~ka~~C~~C~K~YvSmpALkMHirTH~--l~c~C~iCGKaFSRPWLLQGHiRTHTGEKPF~C~hC~kAFADRSNLRAHmQ 236 (279)
T KOG2462|consen 159 KKAFSCKYCGKVYVSMPALKMHIRTHT--LPCECGICGKAFSRPWLLQGHIRTHTGEKPFSCPHCGKAFADRSNLRAHMQ 236 (279)
T ss_pred cccccCCCCCceeeehHHHhhHhhccC--CCcccccccccccchHHhhcccccccCCCCccCCcccchhcchHHHHHHHH
Confidence 445677777777777777777777775 667777777777777777777777777777777777777777777777777
Q ss_pred HhcCCCcccCCccccccCCHHHHHHHHHH
Q psy13123 94 AHLGVKKFACETCGKLFSSKHGLKYHVRT 122 (129)
Q Consensus 94 ~~~~~~~~~C~~C~~~f~~~~~l~~h~~~ 122 (129)
+|.+.|.|.|..|+|.|...+-|.+|.-.
T Consensus 237 THS~~K~~qC~~C~KsFsl~SyLnKH~ES 265 (279)
T KOG2462|consen 237 THSDVKKHQCPRCGKSFALKSYLNKHSES 265 (279)
T ss_pred hhcCCccccCcchhhHHHHHHHHHHhhhh
Confidence 77777777777777777777777777543
No 2
>KOG2462|consensus
Probab=99.97 E-value=7e-31 Score=157.73 Aligned_cols=114 Identities=37% Similarity=0.777 Sum_probs=106.9
Q ss_pred CCccccCcchhccCChhhHHHHHHHhCC---CCCccCCcchhhhcchhHHHHHHHHhCCCCCeecccccccccChhHHHH
Q psy13123 14 TSAYQCGECGKQFTRKFSLNAHLHVHYG---SSNYKCPLCGKFFIQLCHMKDHIQAHGGLKPYVCTYCGKAFVRASDLKR 90 (129)
Q Consensus 14 ~~~~~C~~C~~~~~~~~~l~~h~~~~~~---~~~~~c~~c~~~~~~~~~l~~~~~~~~~~~~~~c~~c~~~~~~~~~l~~ 90 (129)
..-|.|..||+.+.+.++|.+|.++|-. .+.+.|..|++.|..-..|..|+++|+ .+.+|.+||+.|..++.|+.
T Consensus 128 ~~r~~c~eCgk~ysT~snLsrHkQ~H~~~~s~ka~~C~~C~K~YvSmpALkMHirTH~--l~c~C~iCGKaFSRPWLLQG 205 (279)
T KOG2462|consen 128 HPRYKCPECGKSYSTSSNLSRHKQTHRSLDSKKAFSCKYCGKVYVSMPALKMHIRTHT--LPCECGICGKAFSRPWLLQG 205 (279)
T ss_pred CCceeccccccccccccccchhhcccccccccccccCCCCCceeeehHHHhhHhhccC--CCcccccccccccchHHhhc
Confidence 3448999999999999999999999853 567999999999999999999999998 57899999999999999999
Q ss_pred HHHHhcCCCcccCCccccccCCHHHHHHHHHHhcccCCC
Q psy13123 91 HIDAHLGVKKFACETCGKLFSSKHGLKYHVRTHKGECKR 129 (129)
Q Consensus 91 h~~~~~~~~~~~C~~C~~~f~~~~~l~~h~~~h~~e~p~ 129 (129)
|+++|+|||||.|..|+|+|..+++|+.|++||.+.|+|
T Consensus 206 HiRTHTGEKPF~C~hC~kAFADRSNLRAHmQTHS~~K~~ 244 (279)
T KOG2462|consen 206 HIRTHTGEKPFSCPHCGKAFADRSNLRAHMQTHSDVKKH 244 (279)
T ss_pred ccccccCCCCccCCcccchhcchHHHHHHHHhhcCCccc
Confidence 999999999999999999999999999999999999887
No 3
>KOG3576|consensus
Probab=99.83 E-value=2.4e-21 Score=112.38 Aligned_cols=118 Identities=31% Similarity=0.640 Sum_probs=106.2
Q ss_pred CCCCCccccCcchhccCChhhHHHHHHHhCCCCCccCCcchhhhcchhHHHHHHHHhCCCCCeecccccccccChhHHHH
Q psy13123 11 ATTTSAYQCGECGKQFTRKFSLNAHLHVHYGSSNYKCPLCGKFFIQLCHMKDHIQAHGGLKPYVCTYCGKAFVRASDLKR 90 (129)
Q Consensus 11 ~~~~~~~~C~~C~~~~~~~~~l~~h~~~~~~~~~~~c~~c~~~~~~~~~l~~~~~~~~~~~~~~c~~c~~~~~~~~~l~~ 90 (129)
-++...|.|..|++.|.....|.+|+..|...+.+.|..||+.|...-+|.+|++.|+|-+||.|..|+++|++.-.|..
T Consensus 112 ssd~d~ftCrvCgK~F~lQRmlnrh~kch~~vkr~lct~cgkgfndtfdlkrh~rthtgvrpykc~~c~kaftqrcsles 191 (267)
T KOG3576|consen 112 SSDQDSFTCRVCGKKFGLQRMLNRHLKCHSDVKRHLCTFCGKGFNDTFDLKRHTRTHTGVRPYKCSLCEKAFTQRCSLES 191 (267)
T ss_pred CCCCCeeeeehhhhhhhHHHHHHHHhhhccHHHHHHHhhccCcccchhhhhhhhccccCccccchhhhhHHHHhhccHHH
Confidence 34455699999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHhcC-----------CCcccCCccccccCCHHHHHHHHHHhcccCC
Q psy13123 91 HIDAHLG-----------VKKFACETCGKLFSSKHGLKYHVRTHKGECK 128 (129)
Q Consensus 91 h~~~~~~-----------~~~~~C~~C~~~f~~~~~l~~h~~~h~~e~p 128 (129)
|.+.-++ ++.|.|..||.+-.....+..|+..|+..-|
T Consensus 192 hl~kvhgv~~~yaykerr~kl~vcedcg~t~~~~e~~~~h~~~~hp~Sp 240 (267)
T KOG3576|consen 192 HLKKVHGVQHQYAYKERRAKLYVCEDCGYTSERPEVYYLHLKLHHPFSP 240 (267)
T ss_pred HHHHHcCchHHHHHHHhhhheeeecccCCCCCChhHHHHHHHhcCCCCH
Confidence 9875433 4679999999999999999999998876543
No 4
>KOG1074|consensus
Probab=99.80 E-value=9e-21 Score=128.46 Aligned_cols=56 Identities=36% Similarity=0.669 Sum_probs=53.2
Q ss_pred eecccccccccChhHHHHHHHHhcCCCcccCCccccccCCHHHHHHHHHHhcccCC
Q psy13123 73 YVCTYCGKAFVRASDLKRHIDAHLGVKKFACETCGKLFSSKHGLKYHVRTHKGECK 128 (129)
Q Consensus 73 ~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~f~~~~~l~~h~~~h~~e~p 128 (129)
..|.+|++.|...++|.+|+++|+++|||.|..|+++|....+|..|+.+|.+..|
T Consensus 880 h~C~vCgk~FsSSsALqiH~rTHtg~KPF~C~fC~~aFttrgnLKvHMgtH~w~q~ 935 (958)
T KOG1074|consen 880 HVCNVCGKQFSSSAALEIHMRTHTGPKPFFCHFCEEAFTTRGNLKVHMGTHMWVQP 935 (958)
T ss_pred hhhccchhcccchHHHHHhhhcCCCCCCccchhhhhhhhhhhhhhhhhccccccCC
Confidence 56999999999999999999999999999999999999999999999999988765
No 5
>KOG1074|consensus
Probab=99.77 E-value=5.1e-20 Score=124.88 Aligned_cols=56 Identities=32% Similarity=0.650 Sum_probs=51.4
Q ss_pred eecccccccccChhHHHHHHHHhcCCCcccCCccccccCCHHHHHHHHHHhcccCC
Q psy13123 73 YVCTYCGKAFVRASDLKRHIDAHLGVKKFACETCGKLFSSKHGLKYHVRTHKGECK 128 (129)
Q Consensus 73 ~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~f~~~~~l~~h~~~h~~e~p 128 (129)
-.|..|.++..-...|+.|.+.|+||+||+|.+||++|..+.+|..|+-+|....|
T Consensus 606 NqCiiC~rVlSC~saLqmHyrtHtGERPFkCKiCgRAFtTkGNLkaH~~vHka~p~ 661 (958)
T KOG1074|consen 606 NQCIICLRVLSCPSALQMHYRTHTGERPFKCKICGRAFTTKGNLKAHMSVHKAKPP 661 (958)
T ss_pred cceeeeeecccchhhhhhhhhcccCcCccccccccchhccccchhhcccccccCcc
Confidence 46999999999999999999999999999999999999999999999999875443
No 6
>KOG3608|consensus
Probab=99.73 E-value=3.3e-18 Score=106.82 Aligned_cols=119 Identities=28% Similarity=0.507 Sum_probs=98.9
Q ss_pred CCCCCCCCCCCCccccCcchhccCChhhHHHHHHH--hCCCCCccCCcchhhhcchhHHHHHHHHhCCCCCeeccccccc
Q psy13123 4 IRPRDPLATTTSAYQCGECGKQFTRKFSLNAHLHV--HYGSSNYKCPLCGKFFIQLCHMKDHIQAHGGLKPYVCTYCGKA 81 (129)
Q Consensus 4 l~~~~~~~~~~~~~~C~~C~~~~~~~~~l~~h~~~--~~~~~~~~c~~c~~~~~~~~~l~~~~~~~~~~~~~~c~~c~~~ 81 (129)
|..|.++|++++..-|+.||..|..+..|..|.+- ..+..+|.|..|.+.|.....|..|+..|.. .|.|+.|.-.
T Consensus 195 LreH~r~Hs~eKvvACp~Cg~~F~~~tkl~DH~rRqt~l~~n~fqC~~C~KrFaTeklL~~Hv~rHvn--~ykCplCdmt 272 (467)
T KOG3608|consen 195 LREHIRTHSNEKVVACPHCGELFRTKTKLFDHLRRQTELNTNSFQCAQCFKRFATEKLLKSHVVRHVN--CYKCPLCDMT 272 (467)
T ss_pred HHHHHHhcCCCeEEecchHHHHhccccHHHHHHHhhhhhcCCchHHHHHHHHHhHHHHHHHHHHHhhh--cccccccccC
Confidence 56678888888888888888888888888888653 3355678888888888888888888877664 6889999888
Q ss_pred ccChhHHHHHHH-HhcCCCcccCCccccccCCHHHHHHHHHHhc
Q psy13123 82 FVRASDLKRHID-AHLGVKKFACETCGKLFSSKHGLKYHVRTHK 124 (129)
Q Consensus 82 ~~~~~~l~~h~~-~~~~~~~~~C~~C~~~f~~~~~l~~h~~~h~ 124 (129)
....+.|..|++ .|..++||+|+.|.+.|...++|.+|+.+|.
T Consensus 273 c~~~ssL~~H~r~rHs~dkpfKCd~Cd~~c~~esdL~kH~~~HS 316 (467)
T KOG3608|consen 273 CSSASSLTTHIRYRHSKDKPFKCDECDTRCVRESDLAKHVQVHS 316 (467)
T ss_pred CCChHHHHHHHHhhhccCCCccccchhhhhccHHHHHHHHHhcc
Confidence 888899999988 4778899999999999999999999999886
No 7
>KOG3623|consensus
Probab=99.67 E-value=2.8e-17 Score=110.76 Aligned_cols=79 Identities=34% Similarity=0.668 Sum_probs=50.1
Q ss_pred CCCccCCcchhhhcchhHHHHHHHHhCCCCCeecccccccccChhHHHHHHHHhcCCCcccCCccccccCCHHHHHHHH
Q psy13123 42 SSNYKCPLCGKFFIQLCHMKDHIQAHGGLKPYVCTYCGKAFVRASDLKRHIDAHLGVKKFACETCGKLFSSKHGLKYHV 120 (129)
Q Consensus 42 ~~~~~c~~c~~~~~~~~~l~~~~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~f~~~~~l~~h~ 120 (129)
...|.|+.|.+.|...++|.+|.-.|+|.+||.|..|.++|...-.|..|++.|.|||||.|+.|+|.|..+..+.+|+
T Consensus 892 ~gmyaCDqCDK~FqKqSSLaRHKYEHsGqRPyqC~iCkKAFKHKHHLtEHkRLHSGEKPfQCdKClKRFSHSGSYSQHM 970 (1007)
T KOG3623|consen 892 DGMYACDQCDKAFQKQSSLARHKYEHSGQRPYQCIICKKAFKHKHHLTEHKRLHSGEKPFQCDKCLKRFSHSGSYSQHM 970 (1007)
T ss_pred cccchHHHHHHHHHhhHHHHHhhhhhcCCCCcccchhhHhhhhhhhhhhhhhhccCCCcchhhhhhhhcccccchHhhh
Confidence 3456666666666666666666666666666666666666666666666666666666666666666666666666654
No 8
>KOG3623|consensus
Probab=99.62 E-value=2.5e-16 Score=106.24 Aligned_cols=85 Identities=32% Similarity=0.681 Sum_probs=80.2
Q ss_pred CCCCCCCccccCcchhccCChhhHHHHHHHhCCCCCccCCcchhhhcchhHHHHHHHHhCCCCCeecccccccccChhHH
Q psy13123 9 PLATTTSAYQCGECGKQFTRKFSLNAHLHVHYGSSNYKCPLCGKFFIQLCHMKDHIQAHGGLKPYVCTYCGKAFVRASDL 88 (129)
Q Consensus 9 ~~~~~~~~~~C~~C~~~~~~~~~l~~h~~~~~~~~~~~c~~c~~~~~~~~~l~~~~~~~~~~~~~~c~~c~~~~~~~~~l 88 (129)
...+.+..|.|.+|+++|...+.|.+|.=.|+|.+||.|.+|.+.|+-+..|..|++.|.|++||.|..|++.|..++..
T Consensus 887 ~~kte~gmyaCDqCDK~FqKqSSLaRHKYEHsGqRPyqC~iCkKAFKHKHHLtEHkRLHSGEKPfQCdKClKRFSHSGSY 966 (1007)
T KOG3623|consen 887 HAKTEDGMYACDQCDKAFQKQSSLARHKYEHSGQRPYQCIICKKAFKHKHHLTEHKRLHSGEKPFQCDKCLKRFSHSGSY 966 (1007)
T ss_pred cccCccccchHHHHHHHHHhhHHHHHhhhhhcCCCCcccchhhHhhhhhhhhhhhhhhccCCCcchhhhhhhhcccccch
Confidence 44566778999999999999999999999999999999999999999999999999999999999999999999999998
Q ss_pred HHHHH
Q psy13123 89 KRHID 93 (129)
Q Consensus 89 ~~h~~ 93 (129)
..||.
T Consensus 967 SQHMN 971 (1007)
T KOG3623|consen 967 SQHMN 971 (1007)
T ss_pred Hhhhc
Confidence 88875
No 9
>KOG3608|consensus
Probab=99.62 E-value=9.8e-16 Score=95.93 Aligned_cols=110 Identities=27% Similarity=0.546 Sum_probs=99.9
Q ss_pred ccCcchhccCChhhHHHHHHHhCCCCCccCCcchhhhcchhHHHHHHHHhC--CCCCeecccccccccChhHHHHHHHHh
Q psy13123 18 QCGECGKQFTRKFSLNAHLHVHYGSSNYKCPLCGKFFIQLCHMKDHIQAHG--GLKPYVCTYCGKAFVRASDLKRHIDAH 95 (129)
Q Consensus 18 ~C~~C~~~~~~~~~l~~h~~~~~~~~~~~c~~c~~~~~~~~~l~~~~~~~~--~~~~~~c~~c~~~~~~~~~l~~h~~~~ 95 (129)
.|..|-+.+.++..|.+|++.|++++...|+.||..|.....|..|.+-.+ ..++|.|..|.+.|.....|..|+..|
T Consensus 181 ~W~~Ct~~~~~k~~LreH~r~Hs~eKvvACp~Cg~~F~~~tkl~DH~rRqt~l~~n~fqC~~C~KrFaTeklL~~Hv~rH 260 (467)
T KOG3608|consen 181 NWAMCTKHMGNKYRLREHIRTHSNEKVVACPHCGELFRTKTKLFDHLRRQTELNTNSFQCAQCFKRFATEKLLKSHVVRH 260 (467)
T ss_pred cchhhhhhhccHHHHHHHHHhcCCCeEEecchHHHHhccccHHHHHHHhhhhhcCCchHHHHHHHHHhHHHHHHHHHHHh
Confidence 367799999999999999999999999999999999999999999987644 456899999999999999999999988
Q ss_pred cCCCcccCCccccccCCHHHHHHHHHH-hcccCCC
Q psy13123 96 LGVKKFACETCGKLFSSKHGLKYHVRT-HKGECKR 129 (129)
Q Consensus 96 ~~~~~~~C~~C~~~f~~~~~l~~h~~~-h~~e~p~ 129 (129)
.+-|+|+.|..+.+..+.|++|++. |..++|+
T Consensus 261 --vn~ykCplCdmtc~~~ssL~~H~r~rHs~dkpf 293 (467)
T KOG3608|consen 261 --VNCYKCPLCDMTCSSASSLTTHIRYRHSKDKPF 293 (467)
T ss_pred --hhcccccccccCCCChHHHHHHHHhhhccCCCc
Confidence 4679999999999999999999998 6777774
No 10
>KOG3576|consensus
Probab=99.62 E-value=1.1e-16 Score=93.20 Aligned_cols=83 Identities=34% Similarity=0.764 Sum_probs=78.0
Q ss_pred CCCccCCcchhhhcchhHHHHHHHHhCCCCCeecccccccccChhHHHHHHHHhcCCCcccCCccccccCCHHHHHHHHH
Q psy13123 42 SSNYKCPLCGKFFIQLCHMKDHIQAHGGLKPYVCTYCGKAFVRASDLKRHIDAHLGVKKFACETCGKLFSSKHGLKYHVR 121 (129)
Q Consensus 42 ~~~~~c~~c~~~~~~~~~l~~~~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~f~~~~~l~~h~~ 121 (129)
...+.|..|++.|....-|.+|++.|...+.+.|..||+.|-+.-+|..|.++|+|.+||+|..|+|+|.+.-.|..|++
T Consensus 115 ~d~ftCrvCgK~F~lQRmlnrh~kch~~vkr~lct~cgkgfndtfdlkrh~rthtgvrpykc~~c~kaftqrcsleshl~ 194 (267)
T KOG3576|consen 115 QDSFTCRVCGKKFGLQRMLNRHLKCHSDVKRHLCTFCGKGFNDTFDLKRHTRTHTGVRPYKCSLCEKAFTQRCSLESHLK 194 (267)
T ss_pred CCeeeeehhhhhhhHHHHHHHHhhhccHHHHHHHhhccCcccchhhhhhhhccccCccccchhhhhHHHHhhccHHHHHH
Confidence 45599999999999999999999999999999999999999999999999999999999999999999999999999987
Q ss_pred Hhc
Q psy13123 122 THK 124 (129)
Q Consensus 122 ~h~ 124 (129)
.-+
T Consensus 195 kvh 197 (267)
T KOG3576|consen 195 KVH 197 (267)
T ss_pred HHc
Confidence 543
No 11
>PLN03086 PRLI-interacting factor K; Provisional
Probab=99.40 E-value=1.4e-12 Score=87.68 Aligned_cols=102 Identities=23% Similarity=0.571 Sum_probs=84.1
Q ss_pred CCccccCcchhccCChhhHHHHHHHhCCCCCccCCcchhhhcchhHHHHHHHHhCCCCCeecccccccccC---------
Q psy13123 14 TSAYQCGECGKQFTRKFSLNAHLHVHYGSSNYKCPLCGKFFIQLCHMKDHIQAHGGLKPYVCTYCGKAFVR--------- 84 (129)
Q Consensus 14 ~~~~~C~~C~~~~~~~~~l~~h~~~~~~~~~~~c~~c~~~~~~~~~l~~~~~~~~~~~~~~c~~c~~~~~~--------- 84 (129)
++.+.|+.|++.|. ...|..|+..++ .++.|+ |+..+ ....|..|+..+.+.+++.|..|+..+..
T Consensus 451 ~~H~~C~~Cgk~f~-~s~LekH~~~~H--kpv~Cp-Cg~~~-~R~~L~~H~~thCp~Kpi~C~fC~~~v~~g~~~~d~~d 525 (567)
T PLN03086 451 KNHVHCEKCGQAFQ-QGEMEKHMKVFH--EPLQCP-CGVVL-EKEQMVQHQASTCPLRLITCRFCGDMVQAGGSAMDVRD 525 (567)
T ss_pred ccCccCCCCCCccc-hHHHHHHHHhcC--CCccCC-CCCCc-chhHHHhhhhccCCCCceeCCCCCCccccCccccchhh
Confidence 44578999999996 678999999875 889999 99754 66889999999999999999999988842
Q ss_pred -hhHHHHHHHHhcCCCcccCCccccccCCHHHHHHHHHH
Q psy13123 85 -ASDLKRHIDAHLGVKKFACETCGKLFSSKHGLKYHVRT 122 (129)
Q Consensus 85 -~~~l~~h~~~~~~~~~~~C~~C~~~f~~~~~l~~h~~~ 122 (129)
...|..|.... +.+++.|..||+.+... ++..|+..
T Consensus 526 ~~s~Lt~HE~~C-G~rt~~C~~Cgk~Vrlr-dm~~H~~~ 562 (567)
T PLN03086 526 RLRGMSEHESIC-GSRTAPCDSCGRSVMLK-EMDIHQIA 562 (567)
T ss_pred hhhhHHHHHHhc-CCcceEccccCCeeeeh-hHHHHHHH
Confidence 34788888875 88999999999988554 66677665
No 12
>PHA00733 hypothetical protein
Probab=99.38 E-value=5.4e-13 Score=74.34 Aligned_cols=83 Identities=20% Similarity=0.372 Sum_probs=63.4
Q ss_pred CCCCccCCcchhhhcchhHHHHHH-----HHhCCCCCeecccccccccChhHHHHHHHHhcCCCcccCCccccccCCHHH
Q psy13123 41 GSSNYKCPLCGKFFIQLCHMKDHI-----QAHGGLKPYVCTYCGKAFVRASDLKRHIDAHLGVKKFACETCGKLFSSKHG 115 (129)
Q Consensus 41 ~~~~~~c~~c~~~~~~~~~l~~~~-----~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~f~~~~~ 115 (129)
..+++.|.+|...+.....|..+. ....+.++|.|..|++.|.....|..|+..+ +.++.|..|++.|.....
T Consensus 37 ~~~~~~~~~~~~~~~~~~~l~~~~~l~~~~~~~~~kPy~C~~Cgk~Fss~s~L~~H~r~h--~~~~~C~~CgK~F~~~~s 114 (128)
T PHA00733 37 EQKRLIRAVVKTLIYNPQLLDESSYLYKLLTSKAVSPYVCPLCLMPFSSSVSLKQHIRYT--EHSKVCPVCGKEFRNTDS 114 (128)
T ss_pred hhhhHHHHHHhhhccChhhhcchHHHHhhcccCCCCCccCCCCCCcCCCHHHHHHHHhcC--CcCccCCCCCCccCCHHH
Confidence 356678888877777666555541 1234467899999999999999998888865 457899999999999999
Q ss_pred HHHHHHHhcc
Q psy13123 116 LKYHVRTHKG 125 (129)
Q Consensus 116 l~~h~~~h~~ 125 (129)
|..|+...++
T Consensus 115 L~~H~~~~h~ 124 (128)
T PHA00733 115 TLDHVCKKHN 124 (128)
T ss_pred HHHHHHHhcC
Confidence 9999887654
No 13
>PHA02768 hypothetical protein; Provisional
Probab=99.13 E-value=2.4e-11 Score=56.94 Aligned_cols=43 Identities=16% Similarity=0.517 Sum_probs=34.6
Q ss_pred CeecccccccccChhHHHHHHHHhcCCCcccCCccccccCCHHHH
Q psy13123 72 PYVCTYCGKAFVRASDLKRHIDAHLGVKKFACETCGKLFSSKHGL 116 (129)
Q Consensus 72 ~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~f~~~~~l 116 (129)
.|.|+.||+.|...+.|..|+++|+ ++++|..|++.|.+.+.|
T Consensus 5 ~y~C~~CGK~Fs~~~~L~~H~r~H~--k~~kc~~C~k~f~~~s~l 47 (55)
T PHA02768 5 GYECPICGEIYIKRKSMITHLRKHN--TNLKLSNCKRISLRTGEY 47 (55)
T ss_pred ccCcchhCCeeccHHHHHHHHHhcC--CcccCCcccceeccccee
Confidence 4678888888888888888888887 678888888888776655
No 14
>PLN03086 PRLI-interacting factor K; Provisional
Probab=99.05 E-value=7e-10 Score=74.97 Aligned_cols=80 Identities=21% Similarity=0.565 Sum_probs=65.9
Q ss_pred CCccCCcchhhhcchhHHHHHHHHhCCCCCeecccccccccChhHHHHHHHHhcCCCcccCCccccccCC----------
Q psy13123 43 SNYKCPLCGKFFIQLCHMKDHIQAHGGLKPYVCTYCGKAFVRASDLKRHIDAHLGVKKFACETCGKLFSS---------- 112 (129)
Q Consensus 43 ~~~~c~~c~~~~~~~~~l~~~~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~f~~---------- 112 (129)
..+.|+.|++.|. ...|..|+..++ .++.|+ |+..+ ....|..|+..+..++++.|..|++.|..
T Consensus 452 ~H~~C~~Cgk~f~-~s~LekH~~~~H--kpv~Cp-Cg~~~-~R~~L~~H~~thCp~Kpi~C~fC~~~v~~g~~~~d~~d~ 526 (567)
T PLN03086 452 NHVHCEKCGQAFQ-QGEMEKHMKVFH--EPLQCP-CGVVL-EKEQMVQHQASTCPLRLITCRFCGDMVQAGGSAMDVRDR 526 (567)
T ss_pred cCccCCCCCCccc-hHHHHHHHHhcC--CCccCC-CCCCc-chhHHHhhhhccCCCCceeCCCCCCccccCccccchhhh
Confidence 3478999999886 577999999874 789999 99754 66899999999999999999999999852
Q ss_pred HHHHHHHHHHhcccCC
Q psy13123 113 KHGLKYHVRTHKGECK 128 (129)
Q Consensus 113 ~~~l~~h~~~h~~e~p 128 (129)
.+.|..|..+. |.+|
T Consensus 527 ~s~Lt~HE~~C-G~rt 541 (567)
T PLN03086 527 LRGMSEHESIC-GSRT 541 (567)
T ss_pred hhhHHHHHHhc-CCcc
Confidence 45788998884 6554
No 15
>PHA02768 hypothetical protein; Provisional
Probab=99.03 E-value=1.2e-10 Score=54.59 Aligned_cols=42 Identities=26% Similarity=0.587 Sum_probs=28.4
Q ss_pred cccCcchhccCChhhHHHHHHHhCCCCCccCCcchhhhcchhHH
Q psy13123 17 YQCGECGKQFTRKFSLNAHLHVHYGSSNYKCPLCGKFFIQLCHM 60 (129)
Q Consensus 17 ~~C~~C~~~~~~~~~l~~h~~~~~~~~~~~c~~c~~~~~~~~~l 60 (129)
|.|+.||+.|...+.|..|++.|+ +++.|..|++.|...+.|
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 567777777777777777777776 566677777666655443
No 16
>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=99.01 E-value=2.6e-10 Score=45.98 Aligned_cols=25 Identities=48% Similarity=1.020 Sum_probs=18.9
Q ss_pred HHHHHHHHhcCCCcccCCccccccC
Q psy13123 87 DLKRHIDAHLGVKKFACETCGKLFS 111 (129)
Q Consensus 87 ~l~~h~~~~~~~~~~~C~~C~~~f~ 111 (129)
+|..|++.|++++||.|+.|++.|.
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 3667777788888888888877775
No 17
>PHA00616 hypothetical protein
Probab=98.98 E-value=2.9e-10 Score=50.82 Aligned_cols=30 Identities=23% Similarity=0.492 Sum_probs=19.8
Q ss_pred cccCCccccccCCHHHHHHHHHHhcccCCC
Q psy13123 100 KFACETCGKLFSSKHGLKYHVRTHKGECKR 129 (129)
Q Consensus 100 ~~~C~~C~~~f~~~~~l~~h~~~h~~e~p~ 129 (129)
||.|..||+.|.+.++|..|++.|++++|+
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~~hg~~~~ 30 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLSVHKQNKL 30 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHHhcCCCcc
Confidence 456666666666666666666666666653
No 18
>PHA00733 hypothetical protein
Probab=98.96 E-value=1.1e-09 Score=61.08 Aligned_cols=94 Identities=22% Similarity=0.332 Sum_probs=76.1
Q ss_pred CCCCCCCCCCCCCCccccCcchhccCChhhHHHH--HH---HhCCCCCccCCcchhhhcchhHHHHHHHHhCCCCCeecc
Q psy13123 2 REIRPRDPLATTTSAYQCGECGKQFTRKFSLNAH--LH---VHYGSSNYKCPLCGKFFIQLCHMKDHIQAHGGLKPYVCT 76 (129)
Q Consensus 2 ~~l~~~~~~~~~~~~~~C~~C~~~~~~~~~l~~h--~~---~~~~~~~~~c~~c~~~~~~~~~l~~~~~~~~~~~~~~c~ 76 (129)
++|+++-......+.+.|..|...|.....|..+ +. .+.+.+++.|..|++.|.....|..|+..+ ..++.|.
T Consensus 26 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~l~~~~~~~~~kPy~C~~Cgk~Fss~s~L~~H~r~h--~~~~~C~ 103 (128)
T PHA00733 26 EELKRYHSLTPEQKRLIRAVVKTLIYNPQLLDESSYLYKLLTSKAVSPYVCPLCLMPFSSSVSLKQHIRYT--EHSKVCP 103 (128)
T ss_pred HHhhhhhcCChhhhhHHHHHHhhhccChhhhcchHHHHhhcccCCCCCccCCCCCCcCCCHHHHHHHHhcC--CcCccCC
Confidence 3556655666677889999999999887777655 21 234578999999999999999999998865 3578999
Q ss_pred cccccccChhHHHHHHHHhcC
Q psy13123 77 YCGKAFVRASDLKRHIDAHLG 97 (129)
Q Consensus 77 ~c~~~~~~~~~l~~h~~~~~~ 97 (129)
.|++.|.....|..|+...++
T Consensus 104 ~CgK~F~~~~sL~~H~~~~h~ 124 (128)
T PHA00733 104 VCGKEFRNTDSTLDHVCKKHN 124 (128)
T ss_pred CCCCccCCHHHHHHHHHHhcC
Confidence 999999999999999887654
No 19
>PHA00616 hypothetical protein
Probab=98.77 E-value=4.6e-09 Score=46.98 Aligned_cols=34 Identities=26% Similarity=0.421 Sum_probs=25.6
Q ss_pred ccccCcchhccCChhhHHHHHHHhCCCCCccCCc
Q psy13123 16 AYQCGECGKQFTRKFSLNAHLHVHYGSSNYKCPL 49 (129)
Q Consensus 16 ~~~C~~C~~~~~~~~~l~~h~~~~~~~~~~~c~~ 49 (129)
||.|..||+.|...+.|..|++.+++++++.|+.
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~~hg~~~~~~~~ 34 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLSVHKQNKLTLEY 34 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHHhcCCCccceeE
Confidence 5677778887777777777777777777777653
No 20
>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=98.70 E-value=2e-08 Score=40.41 Aligned_cols=23 Identities=52% Similarity=1.305 Sum_probs=12.1
Q ss_pred HHHHHHHhCCCCCeecccccccc
Q psy13123 60 MKDHIQAHGGLKPYVCTYCGKAF 82 (129)
Q Consensus 60 l~~~~~~~~~~~~~~c~~c~~~~ 82 (129)
|..|++.|++++||.|+.|++.|
T Consensus 2 l~~H~~~H~~~k~~~C~~C~k~F 24 (26)
T PF13465_consen 2 LRRHMRTHTGEKPYKCPYCGKSF 24 (26)
T ss_dssp HHHHHHHHSSSSSEEESSSSEEE
T ss_pred HHHHhhhcCCCCCCCCCCCcCee
Confidence 44455555555555555555544
No 21
>KOG3993|consensus
Probab=98.53 E-value=1.9e-08 Score=65.13 Aligned_cols=107 Identities=26% Similarity=0.459 Sum_probs=65.0
Q ss_pred ccccCcchhccCChhhHHHHHHHhCC---------------------------------CCCccCCcchhhhcchhHHHH
Q psy13123 16 AYQCGECGKQFTRKFSLNAHLHVHYG---------------------------------SSNYKCPLCGKFFIQLCHMKD 62 (129)
Q Consensus 16 ~~~C~~C~~~~~~~~~l~~h~~~~~~---------------------------------~~~~~c~~c~~~~~~~~~l~~ 62 (129)
-|+|++|++.|...-+|..|.+.|-. +..|.|..|++.|.....|..
T Consensus 295 EYrCPEC~KVFsCPANLASHRRWHKPR~eaa~a~~~P~k~~~~~rae~~ea~rsg~dss~gi~~C~~C~KkFrRqAYLrK 374 (500)
T KOG3993|consen 295 EYRCPECDKVFSCPANLASHRRWHKPRPEAAKAGSPPPKQAVETRAEVQEAERSGDDSSSGIFSCHTCGKKFRRQAYLRK 374 (500)
T ss_pred eecCCcccccccCchhhhhhhcccCCchhhhhcCCCChhhhhhhhhhhhhccccCCcccCceeecHHhhhhhHHHHHHHH
Confidence 37888888888888888888877621 112677777777777777777
Q ss_pred HHHHhCCCC------C----------------------------------------eecccccccccChhHHHHHHHHhc
Q psy13123 63 HIQAHGGLK------P----------------------------------------YVCTYCGKAFVRASDLKRHIDAHL 96 (129)
Q Consensus 63 ~~~~~~~~~------~----------------------------------------~~c~~c~~~~~~~~~l~~h~~~~~ 96 (129)
|+.+|.... + ..+..++..+..+..--.+.+...
T Consensus 375 Hqlthq~~~~~k~~a~~f~~s~~~~l~~~~~~~a~h~~a~~~~g~~vl~~a~sael~~pp~~~~ppsss~~sgg~~rlg~ 454 (500)
T KOG3993|consen 375 HQLTHQRAPLAKEKAPKFLLSRVIPLMHFNQAVATHSSASDSHGDEVLYVAGSAELELPPYDGSPPSSSGSSGGYGRLGI 454 (500)
T ss_pred hHHhhhccccchhcccCcchhhcccccccccccccccccccccccceeeeeccccccCCCCCCCCcccCCCCCccccccc
Confidence 765543210 0 112223322222222112222222
Q ss_pred CCCcccCCccccccCCHHHHHHHHHH
Q psy13123 97 GVKKFACETCGKLFSSKHGLKYHVRT 122 (129)
Q Consensus 97 ~~~~~~C~~C~~~f~~~~~l~~h~~~ 122 (129)
.+..|.|.+|.-.|..+.+|.+|...
T Consensus 455 ~~q~f~~ky~~atfyss~~ltrhin~ 480 (500)
T KOG3993|consen 455 AEQGFTCKYCPATFYSSPGLTRHINK 480 (500)
T ss_pred hhhccccccchHhhhcCcchHhHhhh
Confidence 23458899999999999999998765
No 22
>PHA00732 hypothetical protein
Probab=98.48 E-value=1.2e-07 Score=48.48 Aligned_cols=37 Identities=32% Similarity=0.753 Sum_probs=23.2
Q ss_pred CccCCcchhhhcchhHHHHHHHH-hCCCCCeeccccccccc
Q psy13123 44 NYKCPLCGKFFIQLCHMKDHIQA-HGGLKPYVCTYCGKAFV 83 (129)
Q Consensus 44 ~~~c~~c~~~~~~~~~l~~~~~~-~~~~~~~~c~~c~~~~~ 83 (129)
|+.|..|++.|.....|..|++. |.+ +.|..|++.|.
T Consensus 1 py~C~~Cgk~F~s~s~Lk~H~r~~H~~---~~C~~CgKsF~ 38 (79)
T PHA00732 1 MFKCPICGFTTVTLFALKQHARRNHTL---TKCPVCNKSYR 38 (79)
T ss_pred CccCCCCCCccCCHHHHHHHhhcccCC---CccCCCCCEeC
Confidence 35667777777777777777653 432 35666766665
No 23
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=98.45 E-value=1.4e-07 Score=36.78 Aligned_cols=23 Identities=57% Similarity=1.051 Sum_probs=18.8
Q ss_pred ccCCccccccCCHHHHHHHHHHh
Q psy13123 101 FACETCGKLFSSKHGLKYHVRTH 123 (129)
Q Consensus 101 ~~C~~C~~~f~~~~~l~~h~~~h 123 (129)
|.|+.|++.|...+.|..|++.|
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 57888888888888888888764
No 24
>KOG3993|consensus
Probab=98.40 E-value=5.5e-08 Score=63.11 Aligned_cols=108 Identities=24% Similarity=0.438 Sum_probs=61.7
Q ss_pred cccCcchhccCChhhHHHHHHHhCCCCCccCCcchhhhcchhHHHHHHHHhCCCCCee-cccc--cccccChhHHHHHHH
Q psy13123 17 YQCGECGKQFTRKFSLNAHLHVHYGSSNYKCPLCGKFFIQLCHMKDHIQAHGGLKPYV-CTYC--GKAFVRASDLKRHID 93 (129)
Q Consensus 17 ~~C~~C~~~~~~~~~l~~h~~~~~~~~~~~c~~c~~~~~~~~~l~~~~~~~~~~~~~~-c~~c--~~~~~~~~~l~~h~~ 93 (129)
|+|..|-..|.+.-.|.+|.........|.|+.|++.|.-..+|..|.+=|--..-.- -..- .+.....+..+.--+
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 6677777777777777776665555566777777777777777777765443211000 0000 000000010000000
Q ss_pred H--hcCCCcccCCccccccCCHHHHHHHHHHhc
Q psy13123 94 A--HLGVKKFACETCGKLFSSKHGLKYHVRTHK 124 (129)
Q Consensus 94 ~--~~~~~~~~C~~C~~~f~~~~~l~~h~~~h~ 124 (129)
. ...+-.|.|..|+|.|....-|+.|+-+|.
T Consensus 348 sg~dss~gi~~C~~C~KkFrRqAYLrKHqlthq 380 (500)
T KOG3993|consen 348 SGDDSSSGIFSCHTCGKKFRRQAYLRKHQLTHQ 380 (500)
T ss_pred cCCcccCceeecHHhhhhhHHHHHHHHhHHhhh
Confidence 0 012336999999999999999999988875
No 25
>PHA00732 hypothetical protein
Probab=98.39 E-value=2.2e-07 Score=47.51 Aligned_cols=48 Identities=27% Similarity=0.592 Sum_probs=39.1
Q ss_pred ccccCcchhccCChhhHHHHHHH-hCCCCCccCCcchhhhcchhHHHHHHHHhCC
Q psy13123 16 AYQCGECGKQFTRKFSLNAHLHV-HYGSSNYKCPLCGKFFIQLCHMKDHIQAHGG 69 (129)
Q Consensus 16 ~~~C~~C~~~~~~~~~l~~h~~~-~~~~~~~~c~~c~~~~~~~~~l~~~~~~~~~ 69 (129)
||.|..|++.|.....|..|++. |.+ +.|+.|++.|. .+..|+++...
T Consensus 1 py~C~~Cgk~F~s~s~Lk~H~r~~H~~---~~C~~CgKsF~---~l~~H~~~~~~ 49 (79)
T PHA00732 1 MFKCPICGFTTVTLFALKQHARRNHTL---TKCPVCNKSYR---RLNQHFYSQYD 49 (79)
T ss_pred CccCCCCCCccCCHHHHHHHhhcccCC---CccCCCCCEeC---ChhhhhcccCC
Confidence 58899999999999999999984 653 58999999998 47777755443
No 26
>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=98.21 E-value=1e-06 Score=34.25 Aligned_cols=23 Identities=43% Similarity=0.944 Sum_probs=18.1
Q ss_pred cccCcchhccCChhhHHHHHHHh
Q psy13123 17 YQCGECGKQFTRKFSLNAHLHVH 39 (129)
Q Consensus 17 ~~C~~C~~~~~~~~~l~~h~~~~ 39 (129)
|.|+.|++.|.....|..|++.|
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 56888888888888888887753
No 27
>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=98.17 E-value=1e-06 Score=35.69 Aligned_cols=25 Identities=48% Similarity=0.903 Sum_probs=20.6
Q ss_pred cccCCccccccCCHHHHHHHHHHhc
Q psy13123 100 KFACETCGKLFSSKHGLKYHVRTHK 124 (129)
Q Consensus 100 ~~~C~~C~~~f~~~~~l~~h~~~h~ 124 (129)
+|.|..|++.|.....|..|++.|.
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 5788888888888888888888775
No 28
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=98.15 E-value=2.3e-06 Score=33.39 Aligned_cols=24 Identities=54% Similarity=1.027 Sum_probs=17.4
Q ss_pred ccCCccccccCCHHHHHHHHHHhc
Q psy13123 101 FACETCGKLFSSKHGLKYHVRTHK 124 (129)
Q Consensus 101 ~~C~~C~~~f~~~~~l~~h~~~h~ 124 (129)
|.|+.|++.|.....|..|+++|+
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 568888888888888888887763
No 29
>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=98.11 E-value=1.1e-05 Score=38.32 Aligned_cols=49 Identities=29% Similarity=0.638 Sum_probs=26.3
Q ss_pred eecccccccccChhHHHHHHHH-hcCC-CcccCCccccccCCHHHHHHHHHHhc
Q psy13123 73 YVCTYCGKAFVRASDLKRHIDA-HLGV-KKFACETCGKLFSSKHGLKYHVRTHK 124 (129)
Q Consensus 73 ~~c~~c~~~~~~~~~l~~h~~~-~~~~-~~~~C~~C~~~f~~~~~l~~h~~~h~ 124 (129)
|.|+.|++ ..+...|..|... |..+ +.+.|+.|...+. .+|..|+..++
T Consensus 3 f~CP~C~~-~~~~~~L~~H~~~~H~~~~~~v~CPiC~~~~~--~~l~~Hl~~~H 53 (54)
T PF05605_consen 3 FTCPYCGK-GFSESSLVEHCEDEHRSESKNVVCPICSSRVT--DNLIRHLNSQH 53 (54)
T ss_pred cCCCCCCC-ccCHHHHHHHHHhHCcCCCCCccCCCchhhhh--hHHHHHHHHhc
Confidence 55666666 3445556666543 3322 3466666665433 36666666543
No 30
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=98.03 E-value=2.4e-05 Score=37.16 Aligned_cols=47 Identities=28% Similarity=0.536 Sum_probs=23.8
Q ss_pred cccCcchhccCChhhHHHHHHH-hCCC-CCccCCcchhhhcchhHHHHHHHH
Q psy13123 17 YQCGECGKQFTRKFSLNAHLHV-HYGS-SNYKCPLCGKFFIQLCHMKDHIQA 66 (129)
Q Consensus 17 ~~C~~C~~~~~~~~~l~~h~~~-~~~~-~~~~c~~c~~~~~~~~~l~~~~~~ 66 (129)
|.|+.|++ ..+...|..|... |..+ +.+.|+.|...+. .+|..|+..
T Consensus 3 f~CP~C~~-~~~~~~L~~H~~~~H~~~~~~v~CPiC~~~~~--~~l~~Hl~~ 51 (54)
T PF05605_consen 3 FTCPYCGK-GFSESSLVEHCEDEHRSESKNVVCPICSSRVT--DNLIRHLNS 51 (54)
T ss_pred cCCCCCCC-ccCHHHHHHHHHhHCcCCCCCccCCCchhhhh--hHHHHHHHH
Confidence 56666666 3445556666443 3322 3456666655322 245555543
No 31
>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=97.90 E-value=1.5e-05 Score=36.57 Aligned_cols=33 Identities=15% Similarity=0.349 Sum_probs=22.8
Q ss_pred cCCCcccCCccccccCCHHHHHHHHHHhcccCC
Q psy13123 96 LGVKKFACETCGKLFSSKHGLKYHVRTHKGECK 128 (129)
Q Consensus 96 ~~~~~~~C~~C~~~f~~~~~l~~h~~~h~~e~p 128 (129)
..+.|-.|++|+..+.+..+|++|+.+.++-+|
T Consensus 20 ~S~~PatCP~C~a~~~~srnLrRHle~~H~~k~ 52 (54)
T PF09237_consen 20 QSEQPATCPICGAVIRQSRNLRRHLEIRHFKKP 52 (54)
T ss_dssp TTS--EE-TTT--EESSHHHHHHHHHHHTTTS-
T ss_pred ccCCCCCCCcchhhccchhhHHHHHHHHhcccC
Confidence 356788899999999999999999988877766
No 32
>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=97.90 E-value=6e-06 Score=33.33 Aligned_cols=25 Identities=36% Similarity=0.818 Sum_probs=19.7
Q ss_pred ccccCcchhccCChhhHHHHHHHhC
Q psy13123 16 AYQCGECGKQFTRKFSLNAHLHVHY 40 (129)
Q Consensus 16 ~~~C~~C~~~~~~~~~l~~h~~~~~ 40 (129)
||.|..|++.|.+...|..|++.|.
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 5778888888888888888887664
No 33
>smart00355 ZnF_C2H2 zinc finger.
Probab=97.89 E-value=1.7e-05 Score=31.35 Aligned_cols=24 Identities=54% Similarity=1.053 Sum_probs=19.5
Q ss_pred ccCCccccccCCHHHHHHHHHHhc
Q psy13123 101 FACETCGKLFSSKHGLKYHVRTHK 124 (129)
Q Consensus 101 ~~C~~C~~~f~~~~~l~~h~~~h~ 124 (129)
|.|..|++.|...+.|..|++.|.
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~~H~ 24 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMRTHX 24 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHHHhc
Confidence 468888888888888888888764
No 34
>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=97.85 E-value=1.6e-05 Score=30.88 Aligned_cols=23 Identities=43% Similarity=0.915 Sum_probs=15.9
Q ss_pred cccCcchhccCChhhHHHHHHHh
Q psy13123 17 YQCGECGKQFTRKFSLNAHLHVH 39 (129)
Q Consensus 17 ~~C~~C~~~~~~~~~l~~h~~~~ 39 (129)
|.|+.|++.|.+...|..|+..+
T Consensus 1 ~~C~~C~~~~~~~~~l~~H~~~~ 23 (24)
T PF13894_consen 1 FQCPICGKSFRSKSELRQHMRTH 23 (24)
T ss_dssp EE-SSTS-EESSHHHHHHHHHHH
T ss_pred CCCcCCCCcCCcHHHHHHHHHhh
Confidence 56778888888888888877654
No 35
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=97.82 E-value=1.6e-05 Score=42.44 Aligned_cols=73 Identities=21% Similarity=0.436 Sum_probs=17.7
Q ss_pred ccCcchhccCChhhHHHHHHHhCCCCCccCCcchhhhcchhHHHHHHHHhCCCCCeecccccccccChhHHHHHHHHh
Q psy13123 18 QCGECGKQFTRKFSLNAHLHVHYGSSNYKCPLCGKFFIQLCHMKDHIQAHGGLKPYVCTYCGKAFVRASDLKRHIDAH 95 (129)
Q Consensus 18 ~C~~C~~~~~~~~~l~~h~~~~~~~~~~~c~~c~~~~~~~~~l~~~~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~~ 95 (129)
.|..|+..|.....+..|+...++...... ..+.....+........ ...+.|..|+..|.+...|..|++.+
T Consensus 1 ~C~~C~~~f~~~~~l~~H~~~~H~~~~~~~----~~l~~~~~~~~~~~~~~-~~~~~C~~C~~~f~s~~~l~~Hm~~~ 73 (100)
T PF12756_consen 1 QCLFCDESFSSVDDLLQHMKKKHGFDIPDQ----KYLVDPNRLLNYLRKKV-KESFRCPYCNKTFRSREALQEHMRSK 73 (100)
T ss_dssp -----------------------------------------------------SSEEBSSSS-EESSHHHHHHHHHHT
T ss_pred Cccccccccccccccccccccccccccccc----ccccccccccccccccc-CCCCCCCccCCCCcCHHHHHHHHcCc
Confidence 377788888888888888764443322111 11112222222222211 12577888888888888888887753
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=97.66 E-value=0.0001 Score=33.89 Aligned_cols=33 Identities=18% Similarity=0.334 Sum_probs=17.3
Q ss_pred CCCCccccCcchhccCChhhHHHHHHHhCCCCC
Q psy13123 12 TTTSAYQCGECGKQFTRKFSLNAHLHVHYGSSN 44 (129)
Q Consensus 12 ~~~~~~~C~~C~~~~~~~~~l~~h~~~~~~~~~ 44 (129)
..+.|..|++|+..+....+|.+|+...++.+|
T Consensus 20 ~S~~PatCP~C~a~~~~srnLrRHle~~H~~k~ 52 (54)
T PF09237_consen 20 QSEQPATCPICGAVIRQSRNLRRHLEIRHFKKP 52 (54)
T ss_dssp TTS--EE-TTT--EESSHHHHHHHHHHHTTTS-
T ss_pred ccCCCCCCCcchhhccchhhHHHHHHHHhcccC
Confidence 344566677777777777777777766555544
No 37
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=97.64 E-value=5.4e-05 Score=40.39 Aligned_cols=73 Identities=23% Similarity=0.472 Sum_probs=21.6
Q ss_pred cCCcchhhhcchhHHHHHHHHhCCCCCeecccccccccChhHHHHHHHHhcCCCcccCCccccccCCHHHHHHHHHHh
Q psy13123 46 KCPLCGKFFIQLCHMKDHIQAHGGLKPYVCTYCGKAFVRASDLKRHIDAHLGVKKFACETCGKLFSSKHGLKYHVRTH 123 (129)
Q Consensus 46 ~c~~c~~~~~~~~~l~~~~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~f~~~~~l~~h~~~h 123 (129)
+|..|+..|.....|..|+....+... . ....+.....+..+.... ....+.|..|++.|.....|..|++.+
T Consensus 1 ~C~~C~~~f~~~~~l~~H~~~~H~~~~-~---~~~~l~~~~~~~~~~~~~-~~~~~~C~~C~~~f~s~~~l~~Hm~~~ 73 (100)
T PF12756_consen 1 QCLFCDESFSSVDDLLQHMKKKHGFDI-P---DQKYLVDPNRLLNYLRKK-VKESFRCPYCNKTFRSREALQEHMRSK 73 (100)
T ss_dssp -----------------------------------------------------SSEEBSSSS-EESSHHHHHHHHHHT
T ss_pred Ccccccccccccccccccccccccccc-c---cccccccccccccccccc-cCCCCCCCccCCCCcCHHHHHHHHcCc
Confidence 488999999999999999976554321 1 111122333333333321 123689999999999999999999974
No 38
>smart00355 ZnF_C2H2 zinc finger.
Probab=97.45 E-value=0.00016 Score=28.33 Aligned_cols=23 Identities=48% Similarity=1.031 Sum_probs=16.4
Q ss_pred cccCcchhccCChhhHHHHHHHh
Q psy13123 17 YQCGECGKQFTRKFSLNAHLHVH 39 (129)
Q Consensus 17 ~~C~~C~~~~~~~~~l~~h~~~~ 39 (129)
|.|..|++.|.....+..|++.|
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~~H 23 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMRTH 23 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHHHh
Confidence 45777777777777777777654
No 39
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=97.38 E-value=0.00021 Score=27.85 Aligned_cols=23 Identities=35% Similarity=0.707 Sum_probs=15.7
Q ss_pred ccCCccccccCCHHHHHHHHHHhc
Q psy13123 101 FACETCGKLFSSKHGLKYHVRTHK 124 (129)
Q Consensus 101 ~~C~~C~~~f~~~~~l~~h~~~h~ 124 (129)
|+|..|+.... ...|..|++.|+
T Consensus 1 y~C~~C~y~t~-~~~l~~H~~~~H 23 (24)
T PF13909_consen 1 YKCPHCSYSTS-KSNLKRHLKRHH 23 (24)
T ss_dssp EE-SSSS-EES-HHHHHHHHHHHH
T ss_pred CCCCCCCCcCC-HHHHHHHHHhhC
Confidence 56778887776 778888877764
No 40
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=97.29 E-value=0.00015 Score=28.52 Aligned_cols=23 Identities=43% Similarity=0.944 Sum_probs=17.2
Q ss_pred ccCCccccccCCHHHHHHHHHHh
Q psy13123 101 FACETCGKLFSSKHGLKYHVRTH 123 (129)
Q Consensus 101 ~~C~~C~~~f~~~~~l~~h~~~h 123 (129)
|.|..|++.|.....|..|++.+
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 46777888888888888887654
No 41
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=97.24 E-value=7.7e-05 Score=47.40 Aligned_cols=51 Identities=37% Similarity=0.721 Sum_probs=36.1
Q ss_pred CCCeeccc--ccccccChhHHHHHHHHh-------------------cCCCcccCCccccccCCHHHHHHHH
Q psy13123 70 LKPYVCTY--CGKAFVRASDLKRHIDAH-------------------LGVKKFACETCGKLFSSKHGLKYHV 120 (129)
Q Consensus 70 ~~~~~c~~--c~~~~~~~~~l~~h~~~~-------------------~~~~~~~C~~C~~~f~~~~~l~~h~ 120 (129)
++||.|++ |.+.+.....|.-|+.-. ..+|||.|.+|+|.+...-.|.-|.
T Consensus 347 ~KpykCpV~gC~K~YknqnGLKYH~lhGH~~~~~~~~p~p~~~~~F~~~~KPYrCevC~KRYKNlNGLKYHr 418 (423)
T COG5189 347 GKPYKCPVEGCNKKYKNQNGLKYHMLHGHQNQKLHENPSPEKMNIFSAKDKPYRCEVCDKRYKNLNGLKYHR 418 (423)
T ss_pred CceecCCCCCchhhhccccchhhhhhccccCcccCCCCCccccccccccCCceeccccchhhccCccceecc
Confidence 46777766 667777777776665432 2358999999999988777766554
No 42
>PRK04860 hypothetical protein; Provisional
Probab=97.24 E-value=0.00027 Score=41.13 Aligned_cols=38 Identities=29% Similarity=0.712 Sum_probs=31.8
Q ss_pred CeecccccccccChhHHHHHHHHhcCCCcccCCccccccCCH
Q psy13123 72 PYVCTYCGKAFVRASDLKRHIDAHLGVKKFACETCGKLFSSK 113 (129)
Q Consensus 72 ~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~f~~~ 113 (129)
+|.|. |+. ....+..|.++++++++|.|..|+..|...
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 58897 886 566778999999999999999999888654
No 43
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=97.16 E-value=0.00015 Score=46.12 Aligned_cols=70 Identities=23% Similarity=0.392 Sum_probs=43.4
Q ss_pred CCccccCc--chhccCChhhHHHHHHHhC-CCCCccCCcchhhhcchhHHHHHHHHhCCCCCeecccccccccChhHHHH
Q psy13123 14 TSAYQCGE--CGKQFTRKFSLNAHLHVHY-GSSNYKCPLCGKFFIQLCHMKDHIQAHGGLKPYVCTYCGKAFVRASDLKR 90 (129)
Q Consensus 14 ~~~~~C~~--C~~~~~~~~~l~~h~~~~~-~~~~~~c~~c~~~~~~~~~l~~~~~~~~~~~~~~c~~c~~~~~~~~~l~~ 90 (129)
++||+|++ |.+.|+..-.|..|+..-+ ..+..+-+. -..+.......+||+|.+|++.+.....|.-
T Consensus 347 ~KpykCpV~gC~K~YknqnGLKYH~lhGH~~~~~~~~p~----------p~~~~~F~~~~KPYrCevC~KRYKNlNGLKY 416 (423)
T COG5189 347 GKPYKCPVEGCNKKYKNQNGLKYHMLHGHQNQKLHENPS----------PEKMNIFSAKDKPYRCEVCDKRYKNLNGLKY 416 (423)
T ss_pred CceecCCCCCchhhhccccchhhhhhccccCcccCCCCC----------ccccccccccCCceeccccchhhccCcccee
Confidence 48899976 8888888888888876432 222211110 0001112344678899999888888777766
Q ss_pred HHH
Q psy13123 91 HID 93 (129)
Q Consensus 91 h~~ 93 (129)
|+.
T Consensus 417 Hr~ 419 (423)
T COG5189 417 HRK 419 (423)
T ss_pred ccc
Confidence 643
No 44
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=97.00 E-value=0.00039 Score=27.28 Aligned_cols=22 Identities=36% Similarity=0.756 Sum_probs=16.0
Q ss_pred cccCcchhccCChhhHHHHHHH
Q psy13123 17 YQCGECGKQFTRKFSLNAHLHV 38 (129)
Q Consensus 17 ~~C~~C~~~~~~~~~l~~h~~~ 38 (129)
|.|..|++.|.+...+..|++.
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 4677777777777777777654
No 45
>PRK04860 hypothetical protein; Provisional
Probab=96.98 E-value=0.0004 Score=40.47 Aligned_cols=25 Identities=24% Similarity=0.571 Sum_probs=12.1
Q ss_pred hHHHHHHHHhCCCCCeecccccccc
Q psy13123 58 CHMKDHIQAHGGLKPYVCTYCGKAF 82 (129)
Q Consensus 58 ~~l~~~~~~~~~~~~~~c~~c~~~~ 82 (129)
..+..|.++++++++|.|..|+..|
T Consensus 129 ~~~rrH~ri~~g~~~YrC~~C~~~l 153 (160)
T PRK04860 129 LTVRRHNRVVRGEAVYRCRRCGETL 153 (160)
T ss_pred CHHHHHHHHhcCCccEECCCCCcee
Confidence 3344444555555555555554443
No 46
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=96.85 E-value=0.00087 Score=26.01 Aligned_cols=23 Identities=35% Similarity=0.678 Sum_probs=15.8
Q ss_pred cccCcchhccCChhhHHHHHHHhC
Q psy13123 17 YQCGECGKQFTRKFSLNAHLHVHY 40 (129)
Q Consensus 17 ~~C~~C~~~~~~~~~l~~h~~~~~ 40 (129)
|.|+.|+.+.. ...|..|+..+.
T Consensus 1 y~C~~C~y~t~-~~~l~~H~~~~H 23 (24)
T PF13909_consen 1 YKCPHCSYSTS-KSNLKRHLKRHH 23 (24)
T ss_dssp EE-SSSS-EES-HHHHHHHHHHHH
T ss_pred CCCCCCCCcCC-HHHHHHHHHhhC
Confidence 57888888887 778888877653
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=96.61 E-value=0.00054 Score=27.48 Aligned_cols=22 Identities=45% Similarity=0.976 Sum_probs=17.5
Q ss_pred ccCCccccccCCHHHHHHHHHH
Q psy13123 101 FACETCGKLFSSKHGLKYHVRT 122 (129)
Q Consensus 101 ~~C~~C~~~f~~~~~l~~h~~~ 122 (129)
|.|..|++.|.....|..|++.
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 5688888888888888887765
No 48
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=96.48 E-value=0.0037 Score=34.05 Aligned_cols=80 Identities=21% Similarity=0.417 Sum_probs=44.8
Q ss_pred CCccCCcchhhhcchhHHHHHHHHhCCCC------------CeecccccccccChhHHHHHHHHhcCCCcccCCcccccc
Q psy13123 43 SNYKCPLCGKFFIQLCHMKDHIQAHGGLK------------PYVCTYCGKAFVRASDLKRHIDAHLGVKKFACETCGKLF 110 (129)
Q Consensus 43 ~~~~c~~c~~~~~~~~~l~~~~~~~~~~~------------~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~f 110 (129)
.|..|+.|+........|.+.-----..+ ...|..|...|....... ...-.....|.|+.|...|
T Consensus 14 LP~~CpiCgLtLVss~HLARSyHHLfPl~~f~ev~~~~~~~~~~C~~C~~~f~~~~~~~--~~~~~~~~~y~C~~C~~~F 91 (112)
T TIGR00622 14 LPVECPICGLTLILSTHLARSYHHLFPLKAFQEIPLEEYNGSRFCFGCQGPFPKPPVSP--FDELKDSHRYVCAVCKNVF 91 (112)
T ss_pred CCCcCCcCCCEEeccchHHHhhhccCCCcccccccccccCCCCcccCcCCCCCCccccc--ccccccccceeCCCCCCcc
Confidence 45667777776666666665321100001 113777777665432110 0001223468899998888
Q ss_pred CCHHHHHHHHHHhc
Q psy13123 111 SSKHGLKYHVRTHK 124 (129)
Q Consensus 111 ~~~~~l~~h~~~h~ 124 (129)
-.+-+.-.|...|.
T Consensus 92 C~dCD~fiHe~Lh~ 105 (112)
T TIGR00622 92 CVDCDVFVHESLHC 105 (112)
T ss_pred ccccchhhhhhccC
Confidence 88888888876663
No 49
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=96.10 E-value=0.0076 Score=23.69 Aligned_cols=21 Identities=29% Similarity=0.722 Sum_probs=13.0
Q ss_pred ccCCccccccCCHHHHHHHHHH
Q psy13123 101 FACETCGKLFSSKHGLKYHVRT 122 (129)
Q Consensus 101 ~~C~~C~~~f~~~~~l~~h~~~ 122 (129)
..|+.||+.| ..+.|..|+.+
T Consensus 3 ~~C~~CgR~F-~~~~l~~H~~~ 23 (25)
T PF13913_consen 3 VPCPICGRKF-NPDRLEKHEKI 23 (25)
T ss_pred CcCCCCCCEE-CHHHHHHHHHh
Confidence 3577777777 55556666543
No 50
>smart00451 ZnF_U1 U1-like zinc finger. Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins.
Probab=95.57 E-value=0.012 Score=24.94 Aligned_cols=23 Identities=22% Similarity=0.618 Sum_probs=18.8
Q ss_pred cccCCccccccCCHHHHHHHHHH
Q psy13123 100 KFACETCGKLFSSKHGLKYHVRT 122 (129)
Q Consensus 100 ~~~C~~C~~~f~~~~~l~~h~~~ 122 (129)
+|.|..|++.|.....+..|+..
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~g 25 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLKG 25 (35)
T ss_pred CeEccccCCccCCHHHHHHHHCh
Confidence 46789999999988888888764
No 51
>KOG1146|consensus
Probab=95.43 E-value=0.0075 Score=45.52 Aligned_cols=80 Identities=16% Similarity=0.269 Sum_probs=41.3
Q ss_pred CCCCCccccCcchhccCChhhHHHHHHHhCCCCCccCCcchhhhcchhHHHHHHHHhCCCCCeecccccccccChhHHHH
Q psy13123 11 ATTTSAYQCGECGKQFTRKFSLNAHLHVHYGSSNYKCPLCGKFFIQLCHMKDHIQAHGGLKPYVCTYCGKAFVRASDLKR 90 (129)
Q Consensus 11 ~~~~~~~~C~~C~~~~~~~~~l~~h~~~~~~~~~~~c~~c~~~~~~~~~l~~~~~~~~~~~~~~c~~c~~~~~~~~~l~~ 90 (129)
++-.+.++|+.|+..|+....|..||+..+-+... ..|. .+.....+.+....-.+.++|.|..|...+....+|.+
T Consensus 460 ~S~~kt~~cpkc~~~yk~a~~L~vhmRskhp~~~~--~~c~-~gq~~~~~arg~~~~~~~~p~~C~~C~~stttng~Lsi 536 (1406)
T KOG1146|consen 460 HSFFKTLKCPKCNWHYKLAQTLGVHMRSKHPESQS--AYCK-AGQNHPRLARGEVYRCPGKPYPCRACNYSTTTNGNLSI 536 (1406)
T ss_pred ecccccccCCccchhhhhHHHhhhcccccccccch--hHhH-hccccccccccccccCCCCcccceeeeeeeecchHHHH
Confidence 33446677888888888888888888763322111 1111 11111111111112223345666666666666666666
Q ss_pred HHH
Q psy13123 91 HID 93 (129)
Q Consensus 91 h~~ 93 (129)
|+.
T Consensus 537 hlq 539 (1406)
T KOG1146|consen 537 HLQ 539 (1406)
T ss_pred HHH
Confidence 654
No 52
>KOG2893|consensus
Probab=94.57 E-value=0.0079 Score=37.11 Aligned_cols=41 Identities=39% Similarity=0.724 Sum_probs=27.4
Q ss_pred cccccccccChhHHHHHHHHhcCCCcccCCccccccCCHHHHHHH
Q psy13123 75 CTYCGKAFVRASDLKRHIDAHLGVKKFACETCGKLFSSKHGLKYH 119 (129)
Q Consensus 75 c~~c~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~f~~~~~l~~h 119 (129)
|=.|++.|.+.-.|+.|++. +.|+|.+|.|.+-....|..|
T Consensus 13 cwycnrefddekiliqhqka----khfkchichkkl~sgpglsih 53 (341)
T KOG2893|consen 13 CWYCNREFDDEKILIQHQKA----KHFKCHICHKKLFSGPGLSIH 53 (341)
T ss_pred eeecccccchhhhhhhhhhh----ccceeeeehhhhccCCCceee
Confidence 44577777777777766653 457777777766566666666
No 53
>cd00350 rubredoxin_like Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center. The family includes rubredoxins, a small electron transfer protein, and a slightly smaller modular rubredoxin domain present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=94.45 E-value=0.028 Score=23.67 Aligned_cols=10 Identities=50% Similarity=1.398 Sum_probs=5.6
Q ss_pred eecccccccc
Q psy13123 73 YVCTYCGKAF 82 (129)
Q Consensus 73 ~~c~~c~~~~ 82 (129)
|+|..||..+
T Consensus 2 ~~C~~CGy~y 11 (33)
T cd00350 2 YVCPVCGYIY 11 (33)
T ss_pred EECCCCCCEE
Confidence 4566666544
No 54
>KOG2785|consensus
Probab=93.99 E-value=0.41 Score=31.91 Aligned_cols=51 Identities=27% Similarity=0.540 Sum_probs=38.9
Q ss_pred CeecccccccccChhHHHHHHHHhcCC-----------------------CcccCCccc---cccCCHHHHHHHHHH
Q psy13123 72 PYVCTYCGKAFVRASDLKRHIDAHLGV-----------------------KKFACETCG---KLFSSKHGLKYHVRT 122 (129)
Q Consensus 72 ~~~c~~c~~~~~~~~~l~~h~~~~~~~-----------------------~~~~C~~C~---~~f~~~~~l~~h~~~ 122 (129)
|-.|..|+..+.+......||..+++- +-+-|..|+ +.|.+....+.|+..
T Consensus 166 Pt~CLfC~~~~k~~e~~~~HM~~~HgffIPdreYL~D~~GLl~YLgeKV~~~~~CL~CN~~~~~f~sleavr~HM~~ 242 (390)
T KOG2785|consen 166 PTDCLFCDKKSKSLEENLKHMFKEHGFFIPDREYLTDEKGLLKYLGEKVGIGFICLFCNELGRPFSSLEAVRAHMRD 242 (390)
T ss_pred CcceeecCCCcccHHHHHHHHhhccCCcCCchHhhhchhHHHHHHHHHhccCceEEEeccccCcccccHHHHHHHhh
Confidence 456888888888887788888776652 236677888 888888888888775
No 55
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=93.75 E-value=0.038 Score=26.01 Aligned_cols=23 Identities=26% Similarity=0.612 Sum_probs=10.7
Q ss_pred CCcccCCccccccCCHHHHHHHH
Q psy13123 98 VKKFACETCGKLFSSKHGLKYHV 120 (129)
Q Consensus 98 ~~~~~C~~C~~~f~~~~~l~~h~ 120 (129)
|-.+.|+.|+..|.+.-++.+|.
T Consensus 15 E~~lrCPRC~~~FR~~K~Y~RHV 37 (65)
T COG4049 15 EEFLRCPRCGMVFRRRKDYIRHV 37 (65)
T ss_pred ceeeeCCchhHHHHHhHHHHHHh
Confidence 33444444444444444444443
No 56
>PF12013 DUF3505: Protein of unknown function (DUF3505); InterPro: IPR022698 This family of proteins is functionally uncharacterised. This protein is found in eukaryotes. Proteins in this family are typically between 247 to 1018 amino acids in length. This region contains two segments that are likely to be C2H2 zinc binding domains.
Probab=93.49 E-value=0.29 Score=26.71 Aligned_cols=25 Identities=32% Similarity=0.743 Sum_probs=22.7
Q ss_pred ccC----CccccccCCHHHHHHHHHHhcc
Q psy13123 101 FAC----ETCGKLFSSKHGLKYHVRTHKG 125 (129)
Q Consensus 101 ~~C----~~C~~~f~~~~~l~~h~~~h~~ 125 (129)
|.| ..|+..+.....+..|.+.++|
T Consensus 81 ~~C~~~~~~C~y~~~~~~~m~~H~~~~Hg 109 (109)
T PF12013_consen 81 YRCQCDPPHCGYITRSKKTMRKHWRKEHG 109 (109)
T ss_pred eeeecCCCCCCcEeccHHHHHHHHHHhcC
Confidence 889 9999999999999999998764
No 57
>KOG2231|consensus
Probab=93.34 E-value=0.22 Score=35.72 Aligned_cols=95 Identities=19% Similarity=0.373 Sum_probs=50.7
Q ss_pred hccCChhhHHHHHH-HhCCCCCccCCc-------chhhhcchhHHHHHHHH-hCCCC----CeecccccccccChhHHHH
Q psy13123 24 KQFTRKFSLNAHLH-VHYGSSNYKCPL-------CGKFFIQLCHMKDHIQA-HGGLK----PYVCTYCGKAFVRASDLKR 90 (129)
Q Consensus 24 ~~~~~~~~l~~h~~-~~~~~~~~~c~~-------c~~~~~~~~~l~~~~~~-~~~~~----~~~c~~c~~~~~~~~~l~~ 90 (129)
..|.....|..|+. .|..-.-..|.. +.+.| ....|..|++. ..+++ .-.|..|...|.....+..
T Consensus 122 ~~~~s~~~Lk~H~~~~H~~~~c~lC~~~~kif~~e~k~Y-t~~el~~h~~~gd~d~~s~rGhp~C~~C~~~fld~~el~r 200 (669)
T KOG2231|consen 122 TEFKSVENLKNHMRDQHKLHLCSLCLQNLKIFINERKLY-TRAELNLHLMFGDPDDESCRGHPLCKFCHERFLDDDELYR 200 (669)
T ss_pred cchhHHHHHHHHHHHhhhhhccccccccceeeeeeeehe-hHHHHHHHHhcCCCccccccCCccchhhhhhhccHHHHHH
Confidence 33446678888885 443222222221 22223 33445555543 22222 2357778888888888888
Q ss_pred HHHHhcCCCcccCCcc------ccccCCHHHHHHHHHHh
Q psy13123 91 HIDAHLGVKKFACETC------GKLFSSKHGLKYHVRTH 123 (129)
Q Consensus 91 h~~~~~~~~~~~C~~C------~~~f~~~~~l~~h~~~h 123 (129)
|++..+. .|..| +.-|..-.+|..|.|.+
T Consensus 201 H~~~~h~----~chfC~~~~~~neyy~~~~dLe~HfR~~ 235 (669)
T KOG2231|consen 201 HLRFDHE----FCHFCDYKTGQNEYYNDYDDLEEHFRKG 235 (669)
T ss_pred hhcccee----heeecCcccccchhcccchHHHHHhhhc
Confidence 8775543 33333 34455666677776653
No 58
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=92.93 E-value=0.15 Score=28.01 Aligned_cols=85 Identities=21% Similarity=0.327 Sum_probs=53.4
Q ss_pred CccccCcchhccCChhhHHHHHHHhCC-----CC-------CccCCcchhhhcchhHHHHHHHHhCCCCCeecccccccc
Q psy13123 15 SAYQCGECGKQFTRKFSLNAHLHVHYG-----SS-------NYKCPLCGKFFIQLCHMKDHIQAHGGLKPYVCTYCGKAF 82 (129)
Q Consensus 15 ~~~~C~~C~~~~~~~~~l~~h~~~~~~-----~~-------~~~c~~c~~~~~~~~~l~~~~~~~~~~~~~~c~~c~~~~ 82 (129)
-|..|+.||-+......|.+....--. +. ...|-.|...|......... .......|.|..|...|
T Consensus 14 LP~~CpiCgLtLVss~HLARSyHHLfPl~~f~ev~~~~~~~~~~C~~C~~~f~~~~~~~~~--~~~~~~~y~C~~C~~~F 91 (112)
T TIGR00622 14 LPVECPICGLTLILSTHLARSYHHLFPLKAFQEIPLEEYNGSRFCFGCQGPFPKPPVSPFD--ELKDSHRYVCAVCKNVF 91 (112)
T ss_pred CCCcCCcCCCEEeccchHHHhhhccCCCcccccccccccCCCCcccCcCCCCCCccccccc--ccccccceeCCCCCCcc
Confidence 367899999988888877765422111 11 12477788877654311100 02223468999999999
Q ss_pred cChhHHHHHHHHhcCCCcccCCccc
Q psy13123 83 VRASDLKRHIDAHLGVKKFACETCG 107 (129)
Q Consensus 83 ~~~~~l~~h~~~~~~~~~~~C~~C~ 107 (129)
-..-+...|...| .|+.|.
T Consensus 92 C~dCD~fiHe~Lh------~CPGC~ 110 (112)
T TIGR00622 92 CVDCDVFVHESLH------CCPGCI 110 (112)
T ss_pred ccccchhhhhhcc------CCcCCC
Confidence 9888888886655 466653
No 59
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=92.92 E-value=0.097 Score=22.62 Aligned_cols=32 Identities=31% Similarity=0.724 Sum_probs=16.3
Q ss_pred ecccccccccChhHHHHHHHHhcCCCcccCCcccccc
Q psy13123 74 VCTYCGKAFVRASDLKRHIDAHLGVKKFACETCGKLF 110 (129)
Q Consensus 74 ~c~~c~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~f 110 (129)
.|+.|+..|.-..+-. ..+.+..+|..|+..|
T Consensus 4 ~CP~C~~~f~v~~~~l-----~~~~~~vrC~~C~~~f 35 (37)
T PF13719_consen 4 TCPNCQTRFRVPDDKL-----PAGGRKVRCPKCGHVF 35 (37)
T ss_pred ECCCCCceEEcCHHHc-----ccCCcEEECCCCCcEe
Confidence 4666666555544311 1233455666666555
No 60
>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=91.69 E-value=0.12 Score=21.85 Aligned_cols=25 Identities=28% Similarity=0.657 Sum_probs=14.3
Q ss_pred CeecccccccccChhHHHHHHHHhcCCCcccCCcccc
Q psy13123 72 PYVCTYCGKAFVRASDLKRHIDAHLGVKKFACETCGK 108 (129)
Q Consensus 72 ~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~ 108 (129)
.|+|..||..+... +.|..|+.||-
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 36777777655432 13456777764
No 61
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=91.60 E-value=0.17 Score=21.73 Aligned_cols=33 Identities=21% Similarity=0.562 Sum_probs=17.2
Q ss_pred eecccccccccChhHHHHHHHHhcCCCcccCCcccccc
Q psy13123 73 YVCTYCGKAFVRASDLKRHIDAHLGVKKFACETCGKLF 110 (129)
Q Consensus 73 ~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~f 110 (129)
..|+.|+..|.-.+... -...+..+|..|+..|
T Consensus 3 i~Cp~C~~~y~i~d~~i-----p~~g~~v~C~~C~~~f 35 (36)
T PF13717_consen 3 ITCPNCQAKYEIDDEKI-----PPKGRKVRCSKCGHVF 35 (36)
T ss_pred EECCCCCCEEeCCHHHC-----CCCCcEEECCCCCCEe
Confidence 35666666665554422 1223445666666655
No 62
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=91.59 E-value=0.025 Score=37.87 Aligned_cols=56 Identities=41% Similarity=0.743 Sum_probs=36.3
Q ss_pred CeecccccccccChhHHHHHHH--HhcCC--CcccCC--ccccccCCHHHHHHHHHHhcccC
Q psy13123 72 PYVCTYCGKAFVRASDLKRHID--AHLGV--KKFACE--TCGKLFSSKHGLKYHVRTHKGEC 127 (129)
Q Consensus 72 ~~~c~~c~~~~~~~~~l~~h~~--~~~~~--~~~~C~--~C~~~f~~~~~l~~h~~~h~~e~ 127 (129)
++.|..|...|.....+..|.+ .|.++ +++.|. .|++.|.+...+..|..+|++-.
T Consensus 289 ~~~~~~~~~~~s~~~~l~~~~~~~~h~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~ 350 (467)
T COG5048 289 PIKSKQCNISFSRSSPLTRHLRSVNHSGESLKPFSCPYSLCGKLFSRNDALKRHILLHTSIS 350 (467)
T ss_pred CCCCccccCCccccccccccccccccccccCCceeeeccCCCccccccccccCCcccccCCC
Confidence 4556666666666666666666 56666 666666 57777777666666666665433
No 63
>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain. This domain contains a CXXCX(19)CXXC motif suggestive of both zinc fingers and thioredoxin, usually found at the N-terminus of prokaryotic proteins. One partially characterized gene, agmX, is among a large set in Myxococcus whose interruption affects adventurous gliding motility.
Probab=91.23 E-value=0.16 Score=21.90 Aligned_cols=14 Identities=21% Similarity=0.553 Sum_probs=7.1
Q ss_pred eecccccccccChh
Q psy13123 73 YVCTYCGKAFVRAS 86 (129)
Q Consensus 73 ~~c~~c~~~~~~~~ 86 (129)
+.|+.|+..|.-..
T Consensus 3 ~~CP~C~~~~~v~~ 16 (38)
T TIGR02098 3 IQCPNCKTSFRVVD 16 (38)
T ss_pred EECCCCCCEEEeCH
Confidence 34555655554443
No 64
>KOG2231|consensus
Probab=90.68 E-value=0.58 Score=33.75 Aligned_cols=79 Identities=20% Similarity=0.318 Sum_probs=46.4
Q ss_pred CCcchhhhcchhHHHHHHHHhCC-CCCeeccccccccc------ChhHHHHHHHHh-cCCCc----ccCCccccccCCHH
Q psy13123 47 CPLCGKFFIQLCHMKDHIQAHGG-LKPYVCTYCGKAFV------RASDLKRHIDAH-LGVKK----FACETCGKLFSSKH 114 (129)
Q Consensus 47 c~~c~~~~~~~~~l~~~~~~~~~-~~~~~c~~c~~~~~------~~~~l~~h~~~~-~~~~~----~~C~~C~~~f~~~~ 114 (129)
|..| ..|.....|..|+...+. ..-..|....+.|. ....++.|+... .++.. ..|..|...|-...
T Consensus 118 ~~~c-~~~~s~~~Lk~H~~~~H~~~~c~lC~~~~kif~~e~k~Yt~~el~~h~~~gd~d~~s~rGhp~C~~C~~~fld~~ 196 (669)
T KOG2231|consen 118 CLHC-TEFKSVENLKNHMRDQHKLHLCSLCLQNLKIFINERKLYTRAELNLHLMFGDPDDESCRGHPLCKFCHERFLDDD 196 (669)
T ss_pred Cccc-cchhHHHHHHHHHHHhhhhhccccccccceeeeeeeehehHHHHHHHHhcCCCccccccCCccchhhhhhhccHH
Confidence 4444 445577788888865432 11112332222222 235566666542 22332 45888999999999
Q ss_pred HHHHHHHHhccc
Q psy13123 115 GLKYHVRTHKGE 126 (129)
Q Consensus 115 ~l~~h~~~h~~e 126 (129)
.|.+|++.++.+
T Consensus 197 el~rH~~~~h~~ 208 (669)
T KOG2231|consen 197 ELYRHLRFDHEF 208 (669)
T ss_pred HHHHhhccceeh
Confidence 999999976544
No 65
>smart00614 ZnF_BED BED zinc finger. DNA-binding domain in chromatin-boundary-element-binding proteins and transposases
Probab=90.22 E-value=0.24 Score=22.90 Aligned_cols=23 Identities=39% Similarity=0.798 Sum_probs=15.3
Q ss_pred ccCCccccccCCH-----HHHHHHHH-Hh
Q psy13123 101 FACETCGKLFSSK-----HGLKYHVR-TH 123 (129)
Q Consensus 101 ~~C~~C~~~f~~~-----~~l~~h~~-~h 123 (129)
..|..|++.+... ++|.+|++ +|
T Consensus 19 a~C~~C~~~l~~~~~~gTs~L~rHl~~~h 47 (50)
T smart00614 19 AKCKYCGKKLSRSSKGGTSNLRRHLRRKH 47 (50)
T ss_pred EEecCCCCEeeeCCCCCcHHHHHHHHhHC
Confidence 4577777766554 57778877 44
No 66
>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=90.05 E-value=0.3 Score=21.85 Aligned_cols=25 Identities=36% Similarity=0.685 Sum_probs=13.7
Q ss_pred CCCcccCCccccccCCH----HHHHHHHH
Q psy13123 97 GVKKFACETCGKLFSSK----HGLKYHVR 121 (129)
Q Consensus 97 ~~~~~~C~~C~~~f~~~----~~l~~h~~ 121 (129)
+.....|..|++.+... +.|..|++
T Consensus 13 ~~~~a~C~~C~~~~~~~~~~ts~l~~HL~ 41 (45)
T PF02892_consen 13 DKKKAKCKYCGKVIKYSSGGTSNLKRHLK 41 (45)
T ss_dssp CSS-EEETTTTEE-----SSTHHHHHHHH
T ss_pred CcCeEEeCCCCeEEeeCCCcHHHHHHhhh
Confidence 34556777787776654 67777774
No 67
>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=90.03 E-value=0.16 Score=27.71 Aligned_cols=29 Identities=31% Similarity=0.717 Sum_probs=17.2
Q ss_pred ccCcchhccCChhhHHHHHHHhCCCCCccCCcchhhhcch
Q psy13123 18 QCGECGKQFTRKFSLNAHLHVHYGSSNYKCPLCGKFFIQL 57 (129)
Q Consensus 18 ~C~~C~~~~~~~~~l~~h~~~~~~~~~~~c~~c~~~~~~~ 57 (129)
.|+.||..|... +..|..|+.||..|...
T Consensus 11 ~Cp~CG~kFYDL-----------nk~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 11 TCPSCGAKFYDL-----------NKDPIVCPKCGTEFPPE 39 (108)
T ss_pred cCCCCcchhccC-----------CCCCccCCCCCCccCcc
Confidence 566777666432 23566677776666554
No 68
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=89.50 E-value=0.22 Score=29.38 Aligned_cols=10 Identities=40% Similarity=1.162 Sum_probs=5.5
Q ss_pred CccCCcchhh
Q psy13123 44 NYKCPLCGKF 53 (129)
Q Consensus 44 ~~~c~~c~~~ 53 (129)
.|.|+.||.+
T Consensus 134 ~~vC~vCGy~ 143 (166)
T COG1592 134 VWVCPVCGYT 143 (166)
T ss_pred EEEcCCCCCc
Confidence 4556666543
No 69
>KOG2482|consensus
Probab=89.48 E-value=0.58 Score=30.86 Aligned_cols=103 Identities=23% Similarity=0.363 Sum_probs=60.5
Q ss_pred cccCcchhccCChhhHHHHHHH--hCCCCC--------ccCC--cchhhhcch-hHHHHHHHH--hCC------------
Q psy13123 17 YQCGECGKQFTRKFSLNAHLHV--HYGSSN--------YKCP--LCGKFFIQL-CHMKDHIQA--HGG------------ 69 (129)
Q Consensus 17 ~~C~~C~~~~~~~~~l~~h~~~--~~~~~~--------~~c~--~c~~~~~~~-~~l~~~~~~--~~~------------ 69 (129)
+.|-.|.+.|.++..|..||+. |....| |.-. .-++.+... ..+ .+.. ..+
T Consensus 196 ~~CLyCekifrdkntLkeHMrkK~HrrinPknreYDkfyiINY~ev~ks~t~~~~e~--dret~~d~~E~D~~wsDw~ed 273 (423)
T KOG2482|consen 196 LRCLYCEKIFRDKNTLKEHMRKKRHRRINPKNREYDKFYIINYLEVGKSWTIVHSED--DRETNEDINETDDTWSDWNED 273 (423)
T ss_pred heeeeeccccCCcHHHHHHHHhccCcccCCCccccceEEEEeHhhcCCccchhhhhh--hhhhhccccccccchhhhhcC
Confidence 6799999999999999999975 322222 1111 111211111 000 0111 111
Q ss_pred -CCC--eecccccccccChhHHHHHHHHhcC---------------------------CCcccCCccccccCCHHHHHHH
Q psy13123 70 -LKP--YVCTYCGKAFVRASDLKRHIDAHLG---------------------------VKKFACETCGKLFSSKHGLKYH 119 (129)
Q Consensus 70 -~~~--~~c~~c~~~~~~~~~l~~h~~~~~~---------------------------~~~~~C~~C~~~f~~~~~l~~h 119 (129)
..+ .+|..|.....+...+..|++.-+. .+.-.|-.|.-.|.....|..|
T Consensus 274 ~a~a~~v~CLfC~~~~en~~~l~eHmk~vHe~Dl~Ki~sd~~Ln~YqrvrviNyiRkq~~~~~c~~cd~~F~~e~~l~~h 353 (423)
T KOG2482|consen 274 DAEALSVVCLFCTNFYENPVFLFEHMKIVHEFDLLKIQSDYSLNFYQRVRVINYIRKQKKKSRCAECDLSFWKEPGLLIH 353 (423)
T ss_pred CCCccceEEEeeccchhhHHHHHHHHHHHHHhhHHhhccccccchhhhhhHHHHHHHHhhccccccccccccCcchhhhh
Confidence 112 4788888877778888888874221 1124466787889999998888
Q ss_pred HH
Q psy13123 120 VR 121 (129)
Q Consensus 120 ~~ 121 (129)
+-
T Consensus 354 m~ 355 (423)
T KOG2482|consen 354 MV 355 (423)
T ss_pred cc
Confidence 65
No 70
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=88.80 E-value=0.21 Score=23.94 Aligned_cols=49 Identities=29% Similarity=0.701 Sum_probs=29.0
Q ss_pred cccCcchhccCChhhHHHHHHHhCCCCCccCCcchhhhcchhHHHHHHHHhCCCCCeecccccc
Q psy13123 17 YQCGECGKQFTRKFSLNAHLHVHYGSSNYKCPLCGKFFIQLCHMKDHIQAHGGLKPYVCTYCGK 80 (129)
Q Consensus 17 ~~C~~C~~~~~~~~~l~~h~~~~~~~~~~~c~~c~~~~~~~~~l~~~~~~~~~~~~~~c~~c~~ 80 (129)
-.|..||....- ..+...|.|+.||+....... +.-....+|.|+.||.
T Consensus 10 ~~CtSCg~~i~p----------~e~~v~F~CPnCGe~~I~Rc~-----~CRk~g~~Y~Cp~CGF 58 (61)
T COG2888 10 PVCTSCGREIAP----------GETAVKFPCPNCGEVEIYRCA-----KCRKLGNPYRCPKCGF 58 (61)
T ss_pred ceeccCCCEecc----------CCceeEeeCCCCCceeeehhh-----hHHHcCCceECCCcCc
Confidence 467777765422 123456889999866554432 2222345789998873
No 71
>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=88.58 E-value=0.6 Score=27.39 Aligned_cols=33 Identities=21% Similarity=0.420 Sum_probs=17.7
Q ss_pred CCCCccCCcchhhhcchhHHHHHHHHhCCCCCeecccccccc
Q psy13123 41 GSSNYKCPLCGKFFIQLCHMKDHIQAHGGLKPYVCTYCGKAF 82 (129)
Q Consensus 41 ~~~~~~c~~c~~~~~~~~~l~~~~~~~~~~~~~~c~~c~~~~ 82 (129)
+..-|.|+.|+..|.....+. ..|.|+.||...
T Consensus 106 ~~~~Y~Cp~c~~r~tf~eA~~---------~~F~Cp~Cg~~L 138 (158)
T TIGR00373 106 NNMFFICPNMCVRFTFNEAME---------LNFTCPRCGAML 138 (158)
T ss_pred CCCeEECCCCCcEeeHHHHHH---------cCCcCCCCCCEe
Confidence 344466666666555554432 146666666543
No 72
>KOG1146|consensus
Probab=88.46 E-value=0.097 Score=40.05 Aligned_cols=23 Identities=30% Similarity=0.681 Sum_probs=17.8
Q ss_pred CcccCCccccccCCHHHHHHHHHH
Q psy13123 99 KKFACETCGKLFSSKHGLKYHVRT 122 (129)
Q Consensus 99 ~~~~C~~C~~~f~~~~~l~~h~~~ 122 (129)
.+| |..|...|+....|.+|+++
T Consensus 1328 ~~~-c~~c~~~~~~~~alqihm~~ 1350 (1406)
T KOG1146|consen 1328 TYH-CLACEVLLSGREALQIHMRS 1350 (1406)
T ss_pred ccc-chHHHhhcchhHHHHHHHHH
Confidence 345 88888888888888888876
No 73
>KOG2186|consensus
Probab=88.45 E-value=0.29 Score=30.76 Aligned_cols=48 Identities=25% Similarity=0.591 Sum_probs=33.5
Q ss_pred CccCCcchhhhcchhHHHHHHHHhCCCCCeecccccccccChhHHHHHHHH
Q psy13123 44 NYKCPLCGKFFIQLCHMKDHIQAHGGLKPYVCTYCGKAFVRASDLKRHIDA 94 (129)
Q Consensus 44 ~~~c~~c~~~~~~~~~l~~~~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~ 94 (129)
.|.|..||....-.. +..|+..-++ ..|.|..|+..|.. .+...|.+-
T Consensus 3 ~FtCnvCgEsvKKp~-vekH~srCrn-~~fSCIDC~k~F~~-~sYknH~kC 50 (276)
T KOG2186|consen 3 FFTCNVCGESVKKPQ-VEKHMSRCRN-AYFSCIDCGKTFER-VSYKNHTKC 50 (276)
T ss_pred EEehhhhhhhccccc-hHHHHHhccC-CeeEEeeccccccc-chhhhhhhh
Confidence 367888888766444 6668766555 57888889888877 455566553
No 74
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=88.44 E-value=0.068 Score=35.80 Aligned_cols=57 Identities=35% Similarity=0.732 Sum_probs=39.7
Q ss_pred ccccCcchhccCChhhHHHHHH--HhCCC--CCccCC--cchhhhcchhHHHHHHHHhCCCCC
Q psy13123 16 AYQCGECGKQFTRKFSLNAHLH--VHYGS--SNYKCP--LCGKFFIQLCHMKDHIQAHGGLKP 72 (129)
Q Consensus 16 ~~~C~~C~~~~~~~~~l~~h~~--~~~~~--~~~~c~--~c~~~~~~~~~l~~~~~~~~~~~~ 72 (129)
++.|..|...|.....+..|.. .|+++ +++.|+ .|++.|.....+..|...+.+..+
T Consensus 289 ~~~~~~~~~~~s~~~~l~~~~~~~~h~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~ 351 (467)
T COG5048 289 PIKSKQCNISFSRSSPLTRHLRSVNHSGESLKPFSCPYSLCGKLFSRNDALKRHILLHTSISP 351 (467)
T ss_pred CCCCccccCCccccccccccccccccccccCCceeeeccCCCccccccccccCCcccccCCCc
Confidence 5667777777777777777777 67777 677777 677777777766666666665443
No 75
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=87.04 E-value=1 Score=26.06 Aligned_cols=38 Identities=24% Similarity=0.524 Sum_probs=18.5
Q ss_pred CCCCccCCcchhhhcchhHHHHHHHHhCCCCCeecccccccc
Q psy13123 41 GSSNYKCPLCGKFFIQLCHMKDHIQAHGGLKPYVCTYCGKAF 82 (129)
Q Consensus 41 ~~~~~~c~~c~~~~~~~~~l~~~~~~~~~~~~~~c~~c~~~~ 82 (129)
+...|.|+.|+..|.....+.. ... ...|.|+.||...
T Consensus 96 ~~~~Y~Cp~C~~~y~~~ea~~~---~d~-~~~f~Cp~Cg~~l 133 (147)
T smart00531 96 NNAYYKCPNCQSKYTFLEANQL---LDM-DGTFTCPRCGEEL 133 (147)
T ss_pred CCcEEECcCCCCEeeHHHHHHh---cCC-CCcEECCCCCCEE
Confidence 3445667777666654332211 011 2236666666544
No 76
>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=86.71 E-value=0.83 Score=18.00 Aligned_cols=19 Identities=16% Similarity=0.434 Sum_probs=13.0
Q ss_pred cCCccccccCCHHHHHHHHH
Q psy13123 102 ACETCGKLFSSKHGLKYHVR 121 (129)
Q Consensus 102 ~C~~C~~~f~~~~~l~~h~~ 121 (129)
.|+.|++.+ ....+..|+.
T Consensus 3 ~CPiC~~~v-~~~~in~HLD 21 (26)
T smart00734 3 QCPVCFREV-PENLINSHLD 21 (26)
T ss_pred cCCCCcCcc-cHHHHHHHHH
Confidence 577887777 5566667764
No 77
>KOG2186|consensus
Probab=86.67 E-value=0.36 Score=30.37 Aligned_cols=49 Identities=22% Similarity=0.593 Sum_probs=37.2
Q ss_pred cccCcchhccCChhhHHHHHHHhCCCCCccCCcchhhhcchhHHHHHHHHhC
Q psy13123 17 YQCGECGKQFTRKFSLNAHLHVHYGSSNYKCPLCGKFFIQLCHMKDHIQAHG 68 (129)
Q Consensus 17 ~~C~~C~~~~~~~~~l~~h~~~~~~~~~~~c~~c~~~~~~~~~l~~~~~~~~ 68 (129)
|.|..||.+.+.. .+..|+-.-++ .-|.|..|++.|.. .+...|...-+
T Consensus 4 FtCnvCgEsvKKp-~vekH~srCrn-~~fSCIDC~k~F~~-~sYknH~kCIT 52 (276)
T KOG2186|consen 4 FTCNVCGESVKKP-QVEKHMSRCRN-AYFSCIDCGKTFER-VSYKNHTKCIT 52 (276)
T ss_pred Eehhhhhhhcccc-chHHHHHhccC-CeeEEeeccccccc-chhhhhhhhcc
Confidence 7899999988654 45568877766 77899999999987 55666765444
No 78
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=86.60 E-value=0.67 Score=27.78 Aligned_cols=34 Identities=24% Similarity=0.481 Sum_probs=20.8
Q ss_pred CCCCccCCcchhhhcchhHHHHHHHHhCCCCCeeccccccccc
Q psy13123 41 GSSNYKCPLCGKFFIQLCHMKDHIQAHGGLKPYVCTYCGKAFV 83 (129)
Q Consensus 41 ~~~~~~c~~c~~~~~~~~~l~~~~~~~~~~~~~~c~~c~~~~~ 83 (129)
+..-|.|+.|+..|.....+. ..|.|+.||..+.
T Consensus 114 ~~~~Y~Cp~C~~rytf~eA~~---------~~F~Cp~Cg~~L~ 147 (178)
T PRK06266 114 NNMFFFCPNCHIRFTFDEAME---------YGFRCPQCGEMLE 147 (178)
T ss_pred CCCEEECCCCCcEEeHHHHhh---------cCCcCCCCCCCCe
Confidence 345577777777666655432 2577777776443
No 79
>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=86.30 E-value=0.16 Score=23.61 Aligned_cols=12 Identities=42% Similarity=1.243 Sum_probs=7.8
Q ss_pred cccCcchhccCC
Q psy13123 17 YQCGECGKQFTR 28 (129)
Q Consensus 17 ~~C~~C~~~~~~ 28 (129)
|.|..||..|..
T Consensus 6 y~C~~Cg~~fe~ 17 (52)
T TIGR02605 6 YRCTACGHRFEV 17 (52)
T ss_pred EEeCCCCCEeEE
Confidence 667777776643
No 80
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=86.27 E-value=0.084 Score=32.51 Aligned_cols=21 Identities=29% Similarity=0.556 Sum_probs=14.8
Q ss_pred CCccccCcchhccCChhhHHH
Q psy13123 14 TSAYQCGECGKQFTRKFSLNA 34 (129)
Q Consensus 14 ~~~~~C~~C~~~~~~~~~l~~ 34 (129)
++...|+.|+..|..+.....
T Consensus 3 ~k~~~CPvC~~~F~~~~vrs~ 23 (214)
T PF09986_consen 3 DKKITCPVCGKEFKTKKVRSG 23 (214)
T ss_pred CCceECCCCCCeeeeeEEEcC
Confidence 456789999998887655433
No 81
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=85.96 E-value=0.84 Score=21.96 Aligned_cols=9 Identities=33% Similarity=1.298 Sum_probs=4.7
Q ss_pred CcccCCccc
Q psy13123 99 KKFACETCG 107 (129)
Q Consensus 99 ~~~~C~~C~ 107 (129)
.+|.|+.||
T Consensus 47 ~~Y~CP~CG 55 (59)
T PRK14890 47 NPYTCPKCG 55 (59)
T ss_pred CceECCCCC
Confidence 345555554
No 82
>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=85.59 E-value=1.2 Score=26.11 Aligned_cols=35 Identities=17% Similarity=0.493 Sum_probs=26.6
Q ss_pred hCCCCCeecccccccccChhHHHHHHHHhcCCCcccCCcccccc
Q psy13123 67 HGGLKPYVCTYCGKAFVRASDLKRHIDAHLGVKKFACETCGKLF 110 (129)
Q Consensus 67 ~~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~f 110 (129)
.....-|.|+.|+..|+....+. --|.|+.||...
T Consensus 104 e~~~~~Y~Cp~c~~r~tf~eA~~---------~~F~Cp~Cg~~L 138 (158)
T TIGR00373 104 ETNNMFFICPNMCVRFTFNEAME---------LNFTCPRCGAML 138 (158)
T ss_pred ccCCCeEECCCCCcEeeHHHHHH---------cCCcCCCCCCEe
Confidence 44456799999998887776664 259999999764
No 83
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=85.37 E-value=0.33 Score=22.00 Aligned_cols=10 Identities=40% Similarity=1.474 Sum_probs=5.7
Q ss_pred cccCcchhcc
Q psy13123 17 YQCGECGKQF 26 (129)
Q Consensus 17 ~~C~~C~~~~ 26 (129)
|.|+.||..+
T Consensus 4 y~C~~CG~~~ 13 (46)
T PRK00398 4 YKCARCGREV 13 (46)
T ss_pred EECCCCCCEE
Confidence 5566666554
No 84
>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=85.13 E-value=0.5 Score=26.86 Aligned_cols=24 Identities=46% Similarity=0.822 Sum_probs=14.0
Q ss_pred cccCCccccccCCHHHHHHHHHHhccc
Q psy13123 100 KFACETCGKLFSSKHGLKYHVRTHKGE 126 (129)
Q Consensus 100 ~~~C~~C~~~f~~~~~l~~h~~~h~~e 126 (129)
...|-+||+.|... .+|+++|+|-
T Consensus 72 ~i~clecGk~~k~L---krHL~~~~gl 95 (132)
T PF05443_consen 72 YIICLECGKKFKTL---KRHLRTHHGL 95 (132)
T ss_dssp -EE-TBT--EESBH---HHHHHHTT-S
T ss_pred eeEEccCCcccchH---HHHHHHccCC
Confidence 45688888888654 7888888553
No 85
>PF13878 zf-C2H2_3: zinc-finger of acetyl-transferase ESCO
Probab=85.00 E-value=1.7 Score=19.22 Aligned_cols=23 Identities=22% Similarity=0.442 Sum_probs=15.4
Q ss_pred cccCcchhccCCh--hhHHHHHHHh
Q psy13123 17 YQCGECGKQFTRK--FSLNAHLHVH 39 (129)
Q Consensus 17 ~~C~~C~~~~~~~--~~l~~h~~~~ 39 (129)
-.|+.||+.|... .+...|.+.|
T Consensus 14 ~~C~~CgM~Y~~~~~eD~~~H~~yH 38 (41)
T PF13878_consen 14 TTCPTCGMLYSPGSPEDEKLHKKYH 38 (41)
T ss_pred cCCCCCCCEECCCCHHHHHHHHHHH
Confidence 5788899887643 4456666655
No 86
>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=84.87 E-value=0.19 Score=21.97 Aligned_cols=30 Identities=30% Similarity=0.798 Sum_probs=15.5
Q ss_pred ccccCcchhccCChhhHHHHHHHhCCCCCccCCcchh
Q psy13123 16 AYQCGECGKQFTRKFSLNAHLHVHYGSSNYKCPLCGK 52 (129)
Q Consensus 16 ~~~C~~C~~~~~~~~~l~~h~~~~~~~~~~~c~~c~~ 52 (129)
.|.|..||..|...... .......|+.||.
T Consensus 5 ~y~C~~Cg~~fe~~~~~-------~~~~~~~CP~Cg~ 34 (41)
T smart00834 5 EYRCEDCGHTFEVLQKI-------SDDPLATCPECGG 34 (41)
T ss_pred EEEcCCCCCEEEEEEec-------CCCCCCCCCCCCC
Confidence 36677777766433221 1133445666665
No 87
>KOG2593|consensus
Probab=84.46 E-value=0.33 Score=32.86 Aligned_cols=39 Identities=26% Similarity=0.627 Sum_probs=20.0
Q ss_pred CCCCCccccCcchhccCChhhHHHHHHHhCCCCCccCCcchh
Q psy13123 11 ATTTSAYQCGECGKQFTRKFSLNAHLHVHYGSSNYKCPLCGK 52 (129)
Q Consensus 11 ~~~~~~~~C~~C~~~~~~~~~l~~h~~~~~~~~~~~c~~c~~ 52 (129)
-+....|.|+.|.+.|... ...+........|.|..|+.
T Consensus 123 ~t~~~~Y~Cp~C~kkyt~L---ea~~L~~~~~~~F~C~~C~g 161 (436)
T KOG2593|consen 123 DTNVAGYVCPNCQKKYTSL---EALQLLDNETGEFHCENCGG 161 (436)
T ss_pred ccccccccCCccccchhhh---HHHHhhcccCceEEEecCCC
Confidence 3444456677777666333 23333333345566666653
No 88
>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=84.34 E-value=0.49 Score=29.21 Aligned_cols=23 Identities=30% Similarity=0.665 Sum_probs=11.0
Q ss_pred CeecccccccccChhHHHHHHHH
Q psy13123 72 PYVCTYCGKAFVRASDLKRHIDA 94 (129)
Q Consensus 72 ~~~c~~c~~~~~~~~~l~~h~~~ 94 (129)
.|.|..|++.|.....+..|+..
T Consensus 77 K~~C~lc~KlFkg~eFV~KHI~n 99 (214)
T PF04959_consen 77 KWRCPLCGKLFKGPEFVRKHIFN 99 (214)
T ss_dssp EEEE-SSS-EESSHHHHHHHHHH
T ss_pred EECCCCCCcccCChHHHHHHHhh
Confidence 35555555555555555555543
No 89
>KOG4173|consensus
Probab=83.68 E-value=1.2 Score=27.25 Aligned_cols=74 Identities=27% Similarity=0.578 Sum_probs=52.3
Q ss_pred ccCCc--chhhhcchhHHHHHHHHhCCCCCeecccccccccChhHHHHHHHHh----------cCCCcccC--Ccccccc
Q psy13123 45 YKCPL--CGKFFIQLCHMKDHIQAHGGLKPYVCTYCGKAFVRASDLKRHIDAH----------LGVKKFAC--ETCGKLF 110 (129)
Q Consensus 45 ~~c~~--c~~~~~~~~~l~~~~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~~----------~~~~~~~C--~~C~~~f 110 (129)
+.|+. |...|........|...-++. .|.+|.++|...-.|..|+.-. .|.-.|.| ..|+..|
T Consensus 80 ~~cqvagc~~~~d~lD~~E~hY~~~h~~---sCs~C~r~~Pt~hLLd~HI~E~HDs~Fqa~veRG~dMy~ClvEgCt~KF 156 (253)
T KOG4173|consen 80 FACQVAGCCQVFDALDDYEHHYHTLHGN---SCSFCKRAFPTGHLLDAHILEWHDSLFQALVERGQDMYQCLVEGCTEKF 156 (253)
T ss_pred ccccccchHHHHhhhhhHHHhhhhcccc---hhHHHHHhCCchhhhhHHHHHHHHHHHHHHHHcCccHHHHHHHhhhhhh
Confidence 56765 666777777677665543332 7999999998888888887533 33456888 4599999
Q ss_pred CCHHHHHHHHH
Q psy13123 111 SSKHGLKYHVR 121 (129)
Q Consensus 111 ~~~~~l~~h~~ 121 (129)
.....-..|+.
T Consensus 157 kT~r~RkdH~I 167 (253)
T KOG4173|consen 157 KTSRDRKDHMI 167 (253)
T ss_pred hhhhhhhhHHH
Confidence 88888777754
No 90
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=82.74 E-value=0.74 Score=20.75 Aligned_cols=11 Identities=55% Similarity=1.419 Sum_probs=6.2
Q ss_pred cccCcchhccC
Q psy13123 17 YQCGECGKQFT 27 (129)
Q Consensus 17 ~~C~~C~~~~~ 27 (129)
|.|..||..|.
T Consensus 3 Y~C~~Cg~~~~ 13 (44)
T smart00659 3 YICGECGRENE 13 (44)
T ss_pred EECCCCCCEee
Confidence 55666666543
No 91
>KOG2482|consensus
Probab=82.59 E-value=2.5 Score=28.10 Aligned_cols=53 Identities=25% Similarity=0.479 Sum_probs=37.1
Q ss_pred ccccCcchhccC-ChhhHHHHHHH-hC---C------------------CCCccCCcchhhhcchhHHHHHHHHhC
Q psy13123 16 AYQCGECGKQFT-RKFSLNAHLHV-HY---G------------------SSNYKCPLCGKFFIQLCHMKDHIQAHG 68 (129)
Q Consensus 16 ~~~C~~C~~~~~-~~~~l~~h~~~-~~---~------------------~~~~~c~~c~~~~~~~~~l~~~~~~~~ 68 (129)
+..|-.|...+. .++....|+-. |. | -..+.|..|.+.|.....|..||+...
T Consensus 144 slqClFCn~e~lgnRs~~l~Hlf~~H~lniGlpDniVyvnelLehLkekL~r~~CLyCekifrdkntLkeHMrkK~ 219 (423)
T KOG2482|consen 144 SLQCLFCNNEGLGNRSEILEHLFHVHGLNIGLPDNIVYVNELLEHLKEKLERLRCLYCEKIFRDKNTLKEHMRKKR 219 (423)
T ss_pred eeEEEEecchhcccHHHHHHHHHHHhhhccCCCcceeeHHHHHHHHHHHHhhheeeeeccccCCcHHHHHHHHhcc
Confidence 356888886654 45666666642 31 1 123889999999999999999998643
No 92
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=82.37 E-value=1.5 Score=29.08 Aligned_cols=20 Identities=30% Similarity=0.582 Sum_probs=10.4
Q ss_pred CCccccccCCHHHHHHHHHH
Q psy13123 103 CETCGKLFSSKHGLKYHVRT 122 (129)
Q Consensus 103 C~~C~~~f~~~~~l~~h~~~ 122 (129)
|..|...|.....|.+|.|.
T Consensus 223 C~FC~~~FYdDDEL~~HcR~ 242 (493)
T COG5236 223 CIFCKIYFYDDDELRRHCRL 242 (493)
T ss_pred hhhccceecChHHHHHHHHh
Confidence 44555555555555555443
No 93
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=81.15 E-value=0.23 Score=29.02 Aligned_cols=12 Identities=42% Similarity=0.883 Sum_probs=6.5
Q ss_pred eecccccccccC
Q psy13123 73 YVCTYCGKAFVR 84 (129)
Q Consensus 73 ~~c~~c~~~~~~ 84 (129)
+.|+.||..|..
T Consensus 29 ~~c~~c~~~f~~ 40 (154)
T PRK00464 29 RECLACGKRFTT 40 (154)
T ss_pred eeccccCCcceE
Confidence 455556555544
No 94
>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=80.79 E-value=0.95 Score=25.43 Aligned_cols=30 Identities=20% Similarity=0.296 Sum_probs=19.0
Q ss_pred cccCcchhccCChhhHHHHHHHhCCCCCccCCcchhhhcch
Q psy13123 17 YQCGECGKQFTRKFSLNAHLHVHYGSSNYKCPLCGKFFIQL 57 (129)
Q Consensus 17 ~~C~~C~~~~~~~~~l~~h~~~~~~~~~~~c~~c~~~~~~~ 57 (129)
..|+.||..|... +..|..|+.||..|...
T Consensus 10 r~Cp~cg~kFYDL-----------nk~p~vcP~cg~~~~~~ 39 (129)
T TIGR02300 10 RICPNTGSKFYDL-----------NRRPAVSPYTGEQFPPE 39 (129)
T ss_pred ccCCCcCcccccc-----------CCCCccCCCcCCccCcc
Confidence 3577777776432 34667777777766544
No 95
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=78.95 E-value=1.2 Score=23.48 Aligned_cols=14 Identities=29% Similarity=0.586 Sum_probs=8.8
Q ss_pred CCccCCcchhhhcc
Q psy13123 43 SNYKCPLCGKFFIQ 56 (129)
Q Consensus 43 ~~~~c~~c~~~~~~ 56 (129)
.|..|..||..|..
T Consensus 57 ~Pa~CkkCGfef~~ 70 (97)
T COG3357 57 RPARCKKCGFEFRD 70 (97)
T ss_pred cChhhcccCccccc
Confidence 45667777766654
No 96
>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=77.17 E-value=0.88 Score=28.88 Aligned_cols=26 Identities=27% Similarity=0.511 Sum_probs=16.5
Q ss_pred CCcccCCccccccCCHHHHHHHHHHh
Q psy13123 98 VKKFACETCGKLFSSKHGLKYHVRTH 123 (129)
Q Consensus 98 ~~~~~C~~C~~~f~~~~~l~~h~~~h 123 (129)
.+++.|+.||.......+|..-.|+|
T Consensus 207 ~k~~PCPKCg~et~eTkdLSmStR~h 232 (314)
T PF06524_consen 207 GKPIPCPKCGYETQETKDLSMSTRSH 232 (314)
T ss_pred CCCCCCCCCCCcccccccceeeeecc
Confidence 46677888877666665665555544
No 97
>PF15269 zf-C2H2_7: Zinc-finger
Probab=76.49 E-value=2.2 Score=19.19 Aligned_cols=22 Identities=23% Similarity=0.413 Sum_probs=15.3
Q ss_pred ccCCccccccCCHHHHHHHHHH
Q psy13123 101 FACETCGKLFSSKHGLKYHVRT 122 (129)
Q Consensus 101 ~~C~~C~~~f~~~~~l~~h~~~ 122 (129)
|+|-+|..+..-.+.|-.|++.
T Consensus 21 ykcfqcpftc~~kshl~nhmky 42 (54)
T PF15269_consen 21 YKCFQCPFTCNEKSHLFNHMKY 42 (54)
T ss_pred ceeecCCcccchHHHHHHHHHH
Confidence 5577777777777777777653
No 98
>KOG4167|consensus
Probab=76.17 E-value=0.87 Score=33.19 Aligned_cols=28 Identities=43% Similarity=0.736 Sum_probs=22.8
Q ss_pred CCccccCcchhccCChhhHHHHHHHhCC
Q psy13123 14 TSAYQCGECGKQFTRKFSLNAHLHVHYG 41 (129)
Q Consensus 14 ~~~~~C~~C~~~~~~~~~l~~h~~~~~~ 41 (129)
...|.|.+|++.|...-.+..||..|.-
T Consensus 790 ~giFpCreC~kvF~KiKSrNAHMK~Hr~ 817 (907)
T KOG4167|consen 790 TGIFPCRECGKVFFKIKSRNAHMKTHRQ 817 (907)
T ss_pred CceeehHHHHHHHHHHhhhhHHHHHHHH
Confidence 3458899999999888888899988853
No 99
>KOG2785|consensus
Probab=75.77 E-value=5.9 Score=26.79 Aligned_cols=52 Identities=19% Similarity=0.485 Sum_probs=38.3
Q ss_pred CCccCCcchhhhcchhHHHHHHHHhCCC-----------------------CCeeccccc---ccccChhHHHHHHHH
Q psy13123 43 SNYKCPLCGKFFIQLCHMKDHIQAHGGL-----------------------KPYVCTYCG---KAFVRASDLKRHIDA 94 (129)
Q Consensus 43 ~~~~c~~c~~~~~~~~~l~~~~~~~~~~-----------------------~~~~c~~c~---~~~~~~~~l~~h~~~ 94 (129)
.|-.|..|+..+++...-..||..++|- ..+.|..|+ +.|.+......||..
T Consensus 165 ~Pt~CLfC~~~~k~~e~~~~HM~~~HgffIPdreYL~D~~GLl~YLgeKV~~~~~CL~CN~~~~~f~sleavr~HM~~ 242 (390)
T KOG2785|consen 165 IPTDCLFCDKKSKSLEENLKHMFKEHGFFIPDREYLTDEKGLLKYLGEKVGIGFICLFCNELGRPFSSLEAVRAHMRD 242 (390)
T ss_pred CCcceeecCCCcccHHHHHHHHhhccCCcCCchHhhhchhHHHHHHHHHhccCceEEEeccccCcccccHHHHHHHhh
Confidence 3466777777777776667777766652 347888888 888888889999874
No 100
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=75.29 E-value=1 Score=25.72 Aligned_cols=14 Identities=21% Similarity=0.603 Sum_probs=9.5
Q ss_pred CeecccccccccCh
Q psy13123 72 PYVCTYCGKAFVRA 85 (129)
Q Consensus 72 ~~~c~~c~~~~~~~ 85 (129)
.+.|..||..|...
T Consensus 70 ~~~C~~CG~~~~~~ 83 (135)
T PRK03824 70 VLKCRNCGNEWSLK 83 (135)
T ss_pred EEECCCCCCEEecc
Confidence 46788888766543
No 101
>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=75.20 E-value=0.29 Score=19.76 Aligned_cols=9 Identities=44% Similarity=1.036 Sum_probs=4.7
Q ss_pred cCCcccccc
Q psy13123 102 ACETCGKLF 110 (129)
Q Consensus 102 ~C~~C~~~f 110 (129)
.|-.|++.|
T Consensus 2 sCiDC~~~F 10 (28)
T PF08790_consen 2 SCIDCSKDF 10 (28)
T ss_dssp EETTTTEEE
T ss_pred eeecCCCCc
Confidence 344555555
No 102
>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=75.19 E-value=1.2 Score=17.30 Aligned_cols=9 Identities=33% Similarity=1.139 Sum_probs=7.4
Q ss_pred ccccCcchh
Q psy13123 16 AYQCGECGK 24 (129)
Q Consensus 16 ~~~C~~C~~ 24 (129)
.|.|+.||+
T Consensus 16 ~f~CPnCG~ 24 (24)
T PF07754_consen 16 PFPCPNCGF 24 (24)
T ss_pred eEeCCCCCC
Confidence 689999984
No 103
>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=75.13 E-value=1.6 Score=17.27 Aligned_cols=10 Identities=40% Similarity=0.919 Sum_probs=5.9
Q ss_pred cCCccccccC
Q psy13123 102 ACETCGKLFS 111 (129)
Q Consensus 102 ~C~~C~~~f~ 111 (129)
.|+.||..|.
T Consensus 16 ~Cp~CG~~F~ 25 (26)
T PF10571_consen 16 FCPHCGYDFE 25 (26)
T ss_pred cCCCCCCCCc
Confidence 4666666653
No 104
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=74.85 E-value=0.45 Score=31.10 Aligned_cols=72 Identities=21% Similarity=0.444 Sum_probs=36.8
Q ss_pred CccccCcchhccCChhhHHHHHHHhCCCCCccCCcchhhhcchhHHHHHHHHhCCCCCeecccccccccChhHHHHHHHH
Q psy13123 15 SAYQCGECGKQFTRKFSLNAHLHVHYGSSNYKCPLCGKFFIQLCHMKDHIQAHGGLKPYVCTYCGKAFVRASDLKRHIDA 94 (129)
Q Consensus 15 ~~~~C~~C~~~~~~~~~l~~h~~~~~~~~~~~c~~c~~~~~~~~~l~~~~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~ 94 (129)
....|+.||..-.. +.+ +.....|.+-..|..|+-.+... ...|+.|+.. ..+. ....
T Consensus 186 ~~~~CPvCGs~P~~-s~v--~~~~~~G~RyL~CslC~teW~~~--------------R~~C~~Cg~~----~~l~-y~~~ 243 (309)
T PRK03564 186 QRQFCPVCGSMPVS-SVV--QIGTTQGLRYLHCNLCESEWHVV--------------RVKCSNCEQS----GKLH-YWSL 243 (309)
T ss_pred CCCCCCCCCCcchh-hee--eccCCCCceEEEcCCCCCccccc--------------CccCCCCCCC----Ccee-eeee
Confidence 34578888875321 111 12224466777888887544321 2368888852 1111 1111
Q ss_pred h---cCCCcccCCcccc
Q psy13123 95 H---LGVKKFACETCGK 108 (129)
Q Consensus 95 ~---~~~~~~~C~~C~~ 108 (129)
. ...+...|..|+.
T Consensus 244 ~~~~~~~r~e~C~~C~~ 260 (309)
T PRK03564 244 DSEQAAVKAESCGDCGT 260 (309)
T ss_pred cCCCcceEeeecccccc
Confidence 1 2345677888864
No 105
>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=74.52 E-value=8.6 Score=20.91 Aligned_cols=24 Identities=25% Similarity=0.523 Sum_probs=17.5
Q ss_pred ccc----CcchhccCChhhHHHHHHHhC
Q psy13123 17 YQC----GECGKQFTRKFSLNAHLHVHY 40 (129)
Q Consensus 17 ~~C----~~C~~~~~~~~~l~~h~~~~~ 40 (129)
|.| ..|+....+...+..|++.++
T Consensus 81 ~~C~~~~~~C~y~~~~~~~m~~H~~~~H 108 (109)
T PF12013_consen 81 YRCQCDPPHCGYITRSKKTMRKHWRKEH 108 (109)
T ss_pred eeeecCCCCCCcEeccHHHHHHHHHHhc
Confidence 667 777777777777777776554
No 106
>PHA00626 hypothetical protein
Probab=74.00 E-value=1.8 Score=20.56 Aligned_cols=15 Identities=27% Similarity=0.578 Sum_probs=11.1
Q ss_pred CcccCCccccccCCH
Q psy13123 99 KKFACETCGKLFSSK 113 (129)
Q Consensus 99 ~~~~C~~C~~~f~~~ 113 (129)
..|+|+.||..|...
T Consensus 22 nrYkCkdCGY~ft~~ 36 (59)
T PHA00626 22 DDYVCCDCGYNDSKD 36 (59)
T ss_pred cceEcCCCCCeechh
Confidence 568888888877654
No 107
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=73.76 E-value=1.1 Score=25.37 Aligned_cols=28 Identities=32% Similarity=0.680 Sum_probs=18.9
Q ss_pred ccccCcchhccCChhhHHHHHHHhCCCCCccCCcchhh
Q psy13123 16 AYQCGECGKQFTRKFSLNAHLHVHYGSSNYKCPLCGKF 53 (129)
Q Consensus 16 ~~~C~~C~~~~~~~~~l~~h~~~~~~~~~~~c~~c~~~ 53 (129)
|++|-.||..|.+.+. +.-.-|+.||..
T Consensus 1 PH~Ct~Cg~~f~dgs~----------eil~GCP~CGg~ 28 (131)
T PF09845_consen 1 PHQCTKCGRVFEDGSK----------EILSGCPECGGN 28 (131)
T ss_pred CcccCcCCCCcCCCcH----------HHHccCcccCCc
Confidence 6789999999987652 112358888754
No 108
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=73.64 E-value=2 Score=19.90 Aligned_cols=10 Identities=40% Similarity=1.241 Sum_probs=5.6
Q ss_pred eecccccccc
Q psy13123 73 YVCTYCGKAF 82 (129)
Q Consensus 73 ~~c~~c~~~~ 82 (129)
|.|..|++.+
T Consensus 7 Y~C~~Cg~~~ 16 (49)
T COG1996 7 YKCARCGREV 16 (49)
T ss_pred EEhhhcCCee
Confidence 5555555554
No 109
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=72.82 E-value=1.5 Score=22.91 Aligned_cols=34 Identities=24% Similarity=0.643 Sum_probs=22.0
Q ss_pred CCccCCcchhhhcchhHHHHHHHHhCCCCCeecccccccccChh
Q psy13123 43 SNYKCPLCGKFFIQLCHMKDHIQAHGGLKPYVCTYCGKAFVRAS 86 (129)
Q Consensus 43 ~~~~c~~c~~~~~~~~~l~~~~~~~~~~~~~~c~~c~~~~~~~~ 86 (129)
..+.|+.|++.-. .+ .+..-|.|..|+..|...+
T Consensus 34 ~~~~Cp~C~~~~V--------kR--~a~GIW~C~kCg~~fAGga 67 (89)
T COG1997 34 AKHVCPFCGRTTV--------KR--IATGIWKCRKCGAKFAGGA 67 (89)
T ss_pred cCCcCCCCCCcce--------ee--eccCeEEcCCCCCeecccc
Confidence 4678999987511 11 2234789999998776543
No 110
>PRK04023 DNA polymerase II large subunit; Validated
Probab=72.47 E-value=4.4 Score=31.08 Aligned_cols=9 Identities=44% Similarity=1.062 Sum_probs=5.5
Q ss_pred ccCCccccc
Q psy13123 101 FACETCGKL 109 (129)
Q Consensus 101 ~~C~~C~~~ 109 (129)
+.|+.||..
T Consensus 664 y~CPKCG~E 672 (1121)
T PRK04023 664 DECEKCGRE 672 (1121)
T ss_pred CcCCCCCCC
Confidence 557777643
No 111
>KOG2807|consensus
Probab=71.95 E-value=4.5 Score=26.75 Aligned_cols=24 Identities=25% Similarity=0.660 Sum_probs=18.3
Q ss_pred cccCCccccccCCHHHHHHHHHHh
Q psy13123 100 KFACETCGKLFSSKHGLKYHVRTH 123 (129)
Q Consensus 100 ~~~C~~C~~~f~~~~~l~~h~~~h 123 (129)
.|.|..|...|...-+.-.|...|
T Consensus 345 ~y~C~~Ck~~FCldCDv~iHesLh 368 (378)
T KOG2807|consen 345 RYRCESCKNVFCLDCDVFIHESLH 368 (378)
T ss_pred cEEchhccceeeccchHHHHhhhh
Confidence 478888888888887777776655
No 112
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=71.92 E-value=1.2 Score=22.54 Aligned_cols=15 Identities=20% Similarity=0.560 Sum_probs=6.7
Q ss_pred CCCeecc--cccccccC
Q psy13123 70 LKPYVCT--YCGKAFVR 84 (129)
Q Consensus 70 ~~~~~c~--~c~~~~~~ 84 (129)
+..+.|. .||..|..
T Consensus 25 ~~Y~qC~N~eCg~tF~t 41 (72)
T PRK09678 25 ERYHQCQNVNCSATFIT 41 (72)
T ss_pred eeeeecCCCCCCCEEEE
Confidence 3344454 45544433
No 113
>KOG4173|consensus
Probab=71.89 E-value=2.6 Score=25.87 Aligned_cols=48 Identities=31% Similarity=0.578 Sum_probs=23.9
Q ss_pred ccCcchhccCChhhHHHHHH-Hh---------CCCCCccCC--cchhhhcchhHHHHHHH
Q psy13123 18 QCGECGKQFTRKFSLNAHLH-VH---------YGSSNYKCP--LCGKFFIQLCHMKDHIQ 65 (129)
Q Consensus 18 ~C~~C~~~~~~~~~l~~h~~-~~---------~~~~~~~c~--~c~~~~~~~~~l~~~~~ 65 (129)
.|..|.+.|.+...|..|+. .| .|...|.|. .|+..|+....-..|+.
T Consensus 108 sCs~C~r~~Pt~hLLd~HI~E~HDs~Fqa~veRG~dMy~ClvEgCt~KFkT~r~RkdH~I 167 (253)
T KOG4173|consen 108 SCSFCKRAFPTGHLLDAHILEWHDSLFQALVERGQDMYQCLVEGCTEKFKTSRDRKDHMI 167 (253)
T ss_pred hhHHHHHhCCchhhhhHHHHHHHHHHHHHHHHcCccHHHHHHHhhhhhhhhhhhhhhHHH
Confidence 45556666655555555542 11 233445552 35555555555555543
No 114
>KOG3408|consensus
Probab=71.44 E-value=4.2 Score=22.74 Aligned_cols=29 Identities=21% Similarity=0.431 Sum_probs=19.1
Q ss_pred CCCCCCccccCcchhccCChhhHHHHHHH
Q psy13123 10 LATTTSAYQCGECGKQFTRKFSLNAHLHV 38 (129)
Q Consensus 10 ~~~~~~~~~C~~C~~~~~~~~~l~~h~~~ 38 (129)
.-.|...|-|-+|.+-|.+...|..|.+.
T Consensus 51 dlPG~GqfyCi~CaRyFi~~~~l~~H~kt 79 (129)
T KOG3408|consen 51 DLPGGGQFYCIECARYFIDAKALKTHFKT 79 (129)
T ss_pred CCCCCceeehhhhhhhhcchHHHHHHHhc
Confidence 34455567777777777777777777653
No 115
>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=68.79 E-value=1.5 Score=17.98 Aligned_cols=7 Identities=57% Similarity=1.445 Sum_probs=3.2
Q ss_pred eeccccc
Q psy13123 73 YVCTYCG 79 (129)
Q Consensus 73 ~~c~~c~ 79 (129)
++|+.|+
T Consensus 20 ~vCp~C~ 26 (30)
T PF08274_consen 20 LVCPECG 26 (30)
T ss_dssp EEETTTT
T ss_pred EeCCccc
Confidence 4444444
No 116
>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=68.26 E-value=0.88 Score=21.27 Aligned_cols=24 Identities=25% Similarity=0.627 Sum_probs=9.9
Q ss_pred ccccCcchhccCChhhHHHHHHHh
Q psy13123 16 AYQCGECGKQFTRKFSLNAHLHVH 39 (129)
Q Consensus 16 ~~~C~~C~~~~~~~~~l~~h~~~~ 39 (129)
.|.|+.|...|-...++-+|...|
T Consensus 21 ~y~C~~C~~~FC~dCD~fiHE~LH 44 (51)
T PF07975_consen 21 RYRCPKCKNHFCIDCDVFIHETLH 44 (51)
T ss_dssp EE--TTTT--B-HHHHHTTTTTS-
T ss_pred eEECCCCCCccccCcChhhhcccc
Confidence 466666666665555555544444
No 117
>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=68.07 E-value=2 Score=19.01 Aligned_cols=12 Identities=42% Similarity=1.154 Sum_probs=8.3
Q ss_pred ccCCccccccCC
Q psy13123 101 FACETCGKLFSS 112 (129)
Q Consensus 101 ~~C~~C~~~f~~ 112 (129)
|.|..||..|..
T Consensus 6 y~C~~Cg~~fe~ 17 (42)
T PF09723_consen 6 YRCEECGHEFEV 17 (42)
T ss_pred EEeCCCCCEEEE
Confidence 668888876643
No 118
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=67.01 E-value=2 Score=18.84 Aligned_cols=15 Identities=27% Similarity=0.738 Sum_probs=6.3
Q ss_pred ccCCcchhhhcchhH
Q psy13123 45 YKCPLCGKFFIQLCH 59 (129)
Q Consensus 45 ~~c~~c~~~~~~~~~ 59 (129)
..|+.|+..|.....
T Consensus 20 d~C~~C~G~W~d~~e 34 (41)
T PF13453_consen 20 DVCPSCGGIWFDAGE 34 (41)
T ss_pred EECCCCCeEEccHHH
Confidence 334444444444333
No 119
>PF05191 ADK_lid: Adenylate kinase, active site lid; InterPro: IPR007862 Adenylate kinases (ADK; 2.7.4.3 from EC) are phosphotransferases that catalyse the Mg-dependent reversible conversion of ATP and AMP to two molecules of ADP, an essential reaction for many processes in living cells. In large variants of adenylate kinase, the AMP and ATP substrates are buried in a domain that undergoes conformational changes from an open to a closed state when bound to substrate; the ligand is then contained within a highly specific environment required for catalysis. Adenylate kinase is a 3-domain protein consisting of a large central CORE domain flanked by a LID domain on one side and the AMP-binding NMPbind domain on the other []. The LID domain binds ATP and covers the phosphates at the active site. The substrates first bind the CORE domain, followed by closure of the active site by the LID and NMPbind domains. Comparisons of adenylate kinases have revealed a particular divergence in the active site lid. In some organisms, particularly the Gram-positive bacteria, residues in the lid domain have been mutated to cysteines and these cysteine residues (two CX(n)C motifs) are responsible for the binding of a zinc ion. The bound zinc ion in the lid domain is clearly structurally homologous to Zinc-finger domains. However, it is unclear whether the adenylate kinase lid is a novel zinc-finger DNA/RNA binding domain, or that the lid bound zinc serves a purely structural function [].; GO: 0004017 adenylate kinase activity; PDB: 3BE4_A 2OSB_B 2ORI_A 2EU8_A 3DL0_A 1P3J_A 2QAJ_A 2OO7_A 2P3S_A 3DKV_A ....
Probab=66.64 E-value=1.1 Score=19.29 Aligned_cols=9 Identities=33% Similarity=1.228 Sum_probs=4.7
Q ss_pred ccCcchhcc
Q psy13123 18 QCGECGKQF 26 (129)
Q Consensus 18 ~C~~C~~~~ 26 (129)
.|+.||..|
T Consensus 3 ~C~~Cg~~Y 11 (36)
T PF05191_consen 3 ICPKCGRIY 11 (36)
T ss_dssp EETTTTEEE
T ss_pred CcCCCCCcc
Confidence 355555554
No 120
>KOG4167|consensus
Probab=66.54 E-value=1.4 Score=32.20 Aligned_cols=25 Identities=36% Similarity=0.816 Sum_probs=22.6
Q ss_pred cccCCccccccCCHHHHHHHHHHhc
Q psy13123 100 KFACETCGKLFSSKHGLKYHVRTHK 124 (129)
Q Consensus 100 ~~~C~~C~~~f~~~~~l~~h~~~h~ 124 (129)
.|-|..|+|.|--.-.+..|+++|.
T Consensus 792 iFpCreC~kvF~KiKSrNAHMK~Hr 816 (907)
T KOG4167|consen 792 IFPCRECGKVFFKIKSRNAHMKTHR 816 (907)
T ss_pred eeehHHHHHHHHHHhhhhHHHHHHH
Confidence 4889999999999999999999985
No 121
>PF03604 DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa subunit; InterPro: IPR006591 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Each class of RNA polymerase is assembled from 9 to 15 different polypeptides. Rbp10 (RNA polymerase CX) is a domain found in RNA polymerase subunit 10; present in RNA polymerase I, II and III.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_Z 3HKZ_X 2NVX_L 3S1Q_L 2JA6_L 3S17_L 3HOW_L 3HOV_L 3PO2_L 3HOZ_L ....
Probab=65.74 E-value=4 Score=17.02 Aligned_cols=9 Identities=33% Similarity=1.088 Sum_probs=4.7
Q ss_pred cccCCcccc
Q psy13123 100 KFACETCGK 108 (129)
Q Consensus 100 ~~~C~~C~~ 108 (129)
+..|..||.
T Consensus 17 ~irC~~CG~ 25 (32)
T PF03604_consen 17 PIRCPECGH 25 (32)
T ss_dssp TSSBSSSS-
T ss_pred cEECCcCCC
Confidence 346666664
No 122
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=64.65 E-value=2.3 Score=31.42 Aligned_cols=12 Identities=25% Similarity=0.570 Sum_probs=7.1
Q ss_pred ccCcchhccCCh
Q psy13123 18 QCGECGKQFTRK 29 (129)
Q Consensus 18 ~C~~C~~~~~~~ 29 (129)
.|..||..+...
T Consensus 437 ~C~~Cg~v~~Cp 448 (730)
T COG1198 437 LCRDCGYIAECP 448 (730)
T ss_pred ecccCCCcccCC
Confidence 366666665543
No 123
>PF02176 zf-TRAF: TRAF-type zinc finger; PDB: 2EOD_A 2YUC_A 3HCU_A 3HCS_B 3HCT_A.
Probab=64.58 E-value=5.2 Score=18.91 Aligned_cols=25 Identities=16% Similarity=0.466 Sum_probs=10.2
Q ss_pred hHHHHHHHHhcCCCcccCCc----ccccc
Q psy13123 86 SDLKRHIDAHLGVKKFACET----CGKLF 110 (129)
Q Consensus 86 ~~l~~h~~~~~~~~~~~C~~----C~~~f 110 (129)
..|..|....=..++..|.. |+..+
T Consensus 24 ~~l~~H~~~~C~~~~v~C~~~~~GC~~~~ 52 (60)
T PF02176_consen 24 KELDDHLENECPKRPVPCPYSPYGCKERV 52 (60)
T ss_dssp CCHHHHHHTTSTTSEEE-SS----S--EE
T ss_pred HHHHHHHHccCCCCcEECCCCCCCCCCcc
Confidence 34555555322234455555 55444
No 124
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=64.52 E-value=8.9 Score=25.32 Aligned_cols=78 Identities=24% Similarity=0.480 Sum_probs=43.5
Q ss_pred CccCCcchhhhcchhHHHHHHHHhCCCCCe------------ecccccccccChhHHHHHHHHhcCCCcccCCccccccC
Q psy13123 44 NYKCPLCGKFFIQLCHMKDHIQAHGGLKPY------------VCTYCGKAFVRASDLKRHIDAHLGVKKFACETCGKLFS 111 (129)
Q Consensus 44 ~~~c~~c~~~~~~~~~l~~~~~~~~~~~~~------------~c~~c~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~f~ 111 (129)
|-.|+.|.........|.+....--..++| -|..|-..|..+..-.. -..+....|.|..|...|.
T Consensus 322 Pi~CP~Csl~LilsthLarSyhhL~PLk~f~E~p~~~~~ks~~Cf~CQ~~fp~~~~~~~--~~~~ss~rY~Ce~CK~~FC 399 (421)
T COG5151 322 PISCPICSLQLILSTHLARSYHHLYPLKPFVEKPEGTNPKSTHCFVCQGPFPKPPVSPF--DESTSSGRYQCELCKSTFC 399 (421)
T ss_pred CccCcchhHHHHHHHHHHHHHHhhccCcccccccCCCCCCCccceeccCCCCCCCCCcc--cccccccceechhhhhhhh
Confidence 456777776666666666543221111222 25556554443322110 0112234589999999999
Q ss_pred CHHHHHHHHHHh
Q psy13123 112 SKHGLKYHVRTH 123 (129)
Q Consensus 112 ~~~~l~~h~~~h 123 (129)
..-+.-.|...|
T Consensus 400 ~dCdvfiHe~Lh 411 (421)
T COG5151 400 SDCDVFIHETLH 411 (421)
T ss_pred hhhHHHHHHHHh
Confidence 888888887665
No 125
>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=63.57 E-value=3 Score=22.42 Aligned_cols=17 Identities=29% Similarity=0.675 Sum_probs=12.7
Q ss_pred CCCCCccccCcchhccCC
Q psy13123 11 ATTTSAYQCGECGKQFTR 28 (129)
Q Consensus 11 ~~~~~~~~C~~C~~~~~~ 28 (129)
+.+ ++.+|.+||..|+.
T Consensus 75 ~~g-~~~rC~eCG~~fkL 91 (97)
T cd00924 75 EKG-KPKRCPECGHVFKL 91 (97)
T ss_pred eCC-CceeCCCCCcEEEE
Confidence 344 68889999988864
No 126
>COG1655 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=63.20 E-value=1.3 Score=27.70 Aligned_cols=24 Identities=13% Similarity=0.448 Sum_probs=16.1
Q ss_pred ccccCcchhccCChhhHHHHHHHh
Q psy13123 16 AYQCGECGKQFTRKFSLNAHLHVH 39 (129)
Q Consensus 16 ~~~C~~C~~~~~~~~~l~~h~~~~ 39 (129)
-+.|++|+..|..+.......++-
T Consensus 19 ~ieCPvC~tkFkkeev~tgsiRii 42 (267)
T COG1655 19 TIECPVCNTKFKKEEVKTGSIRII 42 (267)
T ss_pred eeccCcccchhhhhheeccceeEe
Confidence 467888888887776655544443
No 127
>PLN02294 cytochrome c oxidase subunit Vb
Probab=63.07 E-value=3.2 Score=24.69 Aligned_cols=16 Identities=19% Similarity=0.646 Sum_probs=12.3
Q ss_pred CCccccCcchhccCCh
Q psy13123 14 TSAYQCGECGKQFTRK 29 (129)
Q Consensus 14 ~~~~~C~~C~~~~~~~ 29 (129)
++|.+|++||..|+.+
T Consensus 139 Gkp~RCpeCG~~fkL~ 154 (174)
T PLN02294 139 GKSFECPVCTQYFELE 154 (174)
T ss_pred CCceeCCCCCCEEEEE
Confidence 4578899999888654
No 128
>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=62.19 E-value=7.1 Score=19.15 Aligned_cols=10 Identities=40% Similarity=0.979 Sum_probs=4.5
Q ss_pred cccCCccccc
Q psy13123 100 KFACETCGKL 109 (129)
Q Consensus 100 ~~~C~~C~~~ 109 (129)
.+.|+.||..
T Consensus 46 ~~~C~~Cg~~ 55 (69)
T PF07282_consen 46 VFTCPNCGFE 55 (69)
T ss_pred eEEcCCCCCE
Confidence 3444444444
No 129
>KOG2893|consensus
Probab=62.11 E-value=2.1 Score=26.86 Aligned_cols=47 Identities=21% Similarity=0.411 Sum_probs=32.0
Q ss_pred CCccccCcchhccCChhhHHHHHHHhCCCCCccCCcchhhhcchhHHHHHHH
Q psy13123 14 TSAYQCGECGKQFTRKFSLNAHLHVHYGSSNYKCPLCGKFFIQLCHMKDHIQ 65 (129)
Q Consensus 14 ~~~~~C~~C~~~~~~~~~l~~h~~~~~~~~~~~c~~c~~~~~~~~~l~~~~~ 65 (129)
.++ .|=.|+..|.+..-|..|+.. +-|.|.+|-+...+...|..|..
T Consensus 9 ~kp-wcwycnrefddekiliqhqka----khfkchichkkl~sgpglsihcm 55 (341)
T KOG2893|consen 9 DKP-WCWYCNREFDDEKILIQHQKA----KHFKCHICHKKLFSGPGLSIHCM 55 (341)
T ss_pred CCc-eeeecccccchhhhhhhhhhh----ccceeeeehhhhccCCCceeehh
Confidence 344 455788888888777776654 34778888876666666665544
No 130
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=61.97 E-value=1.3 Score=20.96 Aligned_cols=11 Identities=45% Similarity=1.183 Sum_probs=6.4
Q ss_pred ccCcchhccCC
Q psy13123 18 QCGECGKQFTR 28 (129)
Q Consensus 18 ~C~~C~~~~~~ 28 (129)
+|..||+.|+.
T Consensus 7 ~C~~Cg~~~~~ 17 (54)
T PF14446_consen 7 KCPVCGKKFKD 17 (54)
T ss_pred cChhhCCcccC
Confidence 46666666543
No 131
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=61.88 E-value=3.5 Score=18.00 Aligned_cols=14 Identities=29% Similarity=0.999 Sum_probs=11.4
Q ss_pred ccccCcchhccCCh
Q psy13123 16 AYQCGECGKQFTRK 29 (129)
Q Consensus 16 ~~~C~~C~~~~~~~ 29 (129)
||.|..|+..|-..
T Consensus 12 ~f~C~~C~~~FC~~ 25 (39)
T smart00154 12 GFKCRHCGNLFCGE 25 (39)
T ss_pred CeECCccCCccccc
Confidence 78899999988654
No 132
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=61.62 E-value=42 Score=22.78 Aligned_cols=73 Identities=22% Similarity=0.481 Sum_probs=43.6
Q ss_pred ccCcchhccCChhhHHHHHHHhCCCCCccCCcch----hhhcchhHHHHHHHHhCCCCCeeccc--cc----ccccChhH
Q psy13123 18 QCGECGKQFTRKFSLNAHLHVHYGSSNYKCPLCG----KFFIQLCHMKDHIQAHGGLKPYVCTY--CG----KAFVRASD 87 (129)
Q Consensus 18 ~C~~C~~~~~~~~~l~~h~~~~~~~~~~~c~~c~----~~~~~~~~l~~~~~~~~~~~~~~c~~--c~----~~~~~~~~ 87 (129)
.|..|..-|.+...|..|++.-+ ++-+.|..-+ ..|+....|..|-... .|.|.+ |. .+|.....
T Consensus 222 ~C~FC~~~FYdDDEL~~HcR~~H-E~ChICD~v~p~~~QYFK~Y~~Le~HF~~~----hy~ct~qtc~~~k~~vf~~~~e 296 (493)
T COG5236 222 LCIFCKIYFYDDDELRRHCRLRH-EACHICDMVGPIRYQYFKSYEDLEAHFRNA----HYCCTFQTCRVGKCYVFPYHTE 296 (493)
T ss_pred hhhhccceecChHHHHHHHHhhh-hhhhhhhccCccchhhhhCHHHHHHHhhcC----ceEEEEEEEecCcEEEeccHHH
Confidence 37788888888888888877543 3444454322 3466666666664432 245433 32 36777777
Q ss_pred HHHHHHHh
Q psy13123 88 LKRHIDAH 95 (129)
Q Consensus 88 l~~h~~~~ 95 (129)
|+.|+..-
T Consensus 297 l~~h~~~~ 304 (493)
T COG5236 297 LLEHLTRF 304 (493)
T ss_pred HHHHHHHH
Confidence 77776543
No 133
>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=61.61 E-value=2 Score=28.17 Aligned_cols=48 Identities=19% Similarity=0.368 Sum_probs=24.9
Q ss_pred cccCcchhccCChhhHHHHHHHhCCCCCccCCcchhhhcchhHHHHHHHHhCCCCCeecccccc
Q psy13123 17 YQCGECGKQFTRKFSLNAHLHVHYGSSNYKCPLCGKFFIQLCHMKDHIQAHGGLKPYVCTYCGK 80 (129)
Q Consensus 17 ~~C~~C~~~~~~~~~l~~h~~~~~~~~~~~c~~c~~~~~~~~~l~~~~~~~~~~~~~~c~~c~~ 80 (129)
-.|+.||..-.. +. ........|.+-..|..|+-.+... -..|+.|+.
T Consensus 185 ~~CPvCGs~P~~-s~-~~~~~~~~G~RyL~CslC~teW~~~--------------R~~C~~Cg~ 232 (305)
T TIGR01562 185 TLCPACGSPPVA-SM-VRQGGKETGLRYLSCSLCATEWHYV--------------RVKCSHCEE 232 (305)
T ss_pred CcCCCCCChhhh-hh-hcccCCCCCceEEEcCCCCCccccc--------------CccCCCCCC
Confidence 468888875211 00 0000013456677788776544321 236888875
No 134
>PF05290 Baculo_IE-1: Baculovirus immediate-early protein (IE-0); InterPro: IPR007954 This entry contains the Baculovirus immediate-early protein IE-0.
Probab=60.48 E-value=11 Score=21.59 Aligned_cols=15 Identities=20% Similarity=0.574 Sum_probs=7.9
Q ss_pred CCCCccCCcchhhhc
Q psy13123 41 GSSNYKCPLCGKFFI 55 (129)
Q Consensus 41 ~~~~~~c~~c~~~~~ 55 (129)
+.+.|+|..|..+..
T Consensus 77 d~~lYeCnIC~etS~ 91 (140)
T PF05290_consen 77 DPKLYECNICKETSA 91 (140)
T ss_pred CCCceeccCcccccc
Confidence 335566666655433
No 135
>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=60.21 E-value=4.8 Score=25.04 Aligned_cols=25 Identities=36% Similarity=0.816 Sum_probs=12.7
Q ss_pred ccCCcchhhhcchhHHHHHHHHhCC
Q psy13123 45 YKCPLCGKFFIQLCHMKDHIQAHGG 69 (129)
Q Consensus 45 ~~c~~c~~~~~~~~~l~~~~~~~~~ 69 (129)
|.|..|++.|.-...+..|+...+.
T Consensus 78 ~~C~lc~KlFkg~eFV~KHI~nKH~ 102 (214)
T PF04959_consen 78 WRCPLCGKLFKGPEFVRKHIFNKHP 102 (214)
T ss_dssp EEE-SSS-EESSHHHHHHHHHHH-H
T ss_pred ECCCCCCcccCChHHHHHHHhhcCH
Confidence 5566666666666555556555443
No 136
>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=60.02 E-value=3.7 Score=19.46 Aligned_cols=10 Identities=30% Similarity=1.022 Sum_probs=4.6
Q ss_pred eecccccccc
Q psy13123 73 YVCTYCGKAF 82 (129)
Q Consensus 73 ~~c~~c~~~~ 82 (129)
+.|+.|+..+
T Consensus 3 ~~CP~CG~~i 12 (54)
T TIGR01206 3 FECPDCGAEI 12 (54)
T ss_pred cCCCCCCCEE
Confidence 3455555433
No 137
>KOG2923|consensus
Probab=59.55 E-value=5.9 Score=19.40 Aligned_cols=12 Identities=33% Similarity=0.899 Sum_probs=6.9
Q ss_pred CCCCccCCcchh
Q psy13123 41 GSSNYKCPLCGK 52 (129)
Q Consensus 41 ~~~~~~c~~c~~ 52 (129)
|+....|+-|+.
T Consensus 41 ge~Va~CpsCSL 52 (67)
T KOG2923|consen 41 GEDVARCPSCSL 52 (67)
T ss_pred CCeeecCCCceE
Confidence 555556666554
No 138
>KOG2807|consensus
Probab=58.91 E-value=13 Score=24.84 Aligned_cols=30 Identities=30% Similarity=0.667 Sum_probs=21.3
Q ss_pred CeecccccccccChhHHHHHHHHhcCCCcccCCccc
Q psy13123 72 PYVCTYCGKAFVRASDLKRHIDAHLGVKKFACETCG 107 (129)
Q Consensus 72 ~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~C~~C~ 107 (129)
.|.|..|...|-.--+...|-..| .|+.|.
T Consensus 345 ~y~C~~Ck~~FCldCDv~iHesLh------~CpgCe 374 (378)
T KOG2807|consen 345 RYRCESCKNVFCLDCDVFIHESLH------NCPGCE 374 (378)
T ss_pred cEEchhccceeeccchHHHHhhhh------cCCCcC
Confidence 477888888887777777776655 566664
No 139
>KOG2593|consensus
Probab=57.31 E-value=16 Score=25.26 Aligned_cols=38 Identities=24% Similarity=0.572 Sum_probs=25.8
Q ss_pred CCCCCccCCcchhhhcchhHHHHHHHHhCCCCCeecccccc
Q psy13123 40 YGSSNYKCPLCGKFFIQLCHMKDHIQAHGGLKPYVCTYCGK 80 (129)
Q Consensus 40 ~~~~~~~c~~c~~~~~~~~~l~~~~~~~~~~~~~~c~~c~~ 80 (129)
+...-|.|+.|++.|.....++ ......-.|.|..|+.
T Consensus 124 t~~~~Y~Cp~C~kkyt~Lea~~---L~~~~~~~F~C~~C~g 161 (436)
T KOG2593|consen 124 TNVAGYVCPNCQKKYTSLEALQ---LLDNETGEFHCENCGG 161 (436)
T ss_pred cccccccCCccccchhhhHHHH---hhcccCceEEEecCCC
Confidence 4556699999999888765443 2333234688998885
No 140
>COG2331 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=56.43 E-value=7 Score=19.91 Aligned_cols=32 Identities=28% Similarity=0.719 Sum_probs=18.8
Q ss_pred CccccCcchhccCChhhHHHHHHHhCCCCCccCCcchhh
Q psy13123 15 SAYQCGECGKQFTRKFSLNAHLHVHYGSSNYKCPLCGKF 53 (129)
Q Consensus 15 ~~~~C~~C~~~~~~~~~l~~h~~~~~~~~~~~c~~c~~~ 53 (129)
..|+|.+|+..| .+..+| +...--.|+.|+..
T Consensus 11 Y~Y~c~~cg~~~----dvvq~~---~ddplt~ce~c~a~ 42 (82)
T COG2331 11 YSYECTECGNRF----DVVQAM---TDDPLTTCEECGAR 42 (82)
T ss_pred eEEeecccchHH----HHHHhc---ccCccccChhhChH
Confidence 458888888865 322222 23344568888764
No 141
>KOG1280|consensus
Probab=56.22 E-value=12 Score=25.12 Aligned_cols=22 Identities=18% Similarity=0.424 Sum_probs=12.5
Q ss_pred ccccCcchhccCChhhHHHHHH
Q psy13123 16 AYQCGECGKQFTRKFSLNAHLH 37 (129)
Q Consensus 16 ~~~C~~C~~~~~~~~~l~~h~~ 37 (129)
.|.|+.|+..-.+...+..|..
T Consensus 79 SftCPyC~~~Gfte~~f~~Hv~ 100 (381)
T KOG1280|consen 79 SFTCPYCGIMGFTERQFGTHVL 100 (381)
T ss_pred cccCCcccccccchhHHHHHhh
Confidence 4666666655555555555544
No 142
>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=56.20 E-value=7.7 Score=22.45 Aligned_cols=49 Identities=14% Similarity=0.271 Sum_probs=28.4
Q ss_pred eecccccccccChhHHHH--HHH---HhcCCCcccCCccccccCCHHHHHHHHH
Q psy13123 73 YVCTYCGKAFVRASDLKR--HID---AHLGVKKFACETCGKLFSSKHGLKYHVR 121 (129)
Q Consensus 73 ~~c~~c~~~~~~~~~l~~--h~~---~~~~~~~~~C~~C~~~f~~~~~l~~h~~ 121 (129)
..|+.|+..+.....-.. -.. ....+..+.|+.||+.|...+++.+-.+
T Consensus 92 sRC~~CN~~L~~v~~~~v~~~vp~~v~~~~~~f~~C~~C~kiyW~GsH~~~~~~ 145 (147)
T PF01927_consen 92 SRCPKCNGPLRPVSKEEVKDRVPPYVYETYDEFWRCPGCGKIYWEGSHWRRMEE 145 (147)
T ss_pred CccCCCCcEeeechhhccccccCccccccCCeEEECCCCCCEecccccHHHHHh
Confidence 468888865533221110 001 1122346789999999988888766543
No 143
>KOG0978|consensus
Probab=55.96 E-value=2.2 Score=31.21 Aligned_cols=15 Identities=20% Similarity=0.567 Sum_probs=9.5
Q ss_pred cCCccccccCCHHHH
Q psy13123 102 ACETCGKLFSSKHGL 116 (129)
Q Consensus 102 ~C~~C~~~f~~~~~l 116 (129)
+||.||.+|....-+
T Consensus 680 KCP~Cn~aFganDv~ 694 (698)
T KOG0978|consen 680 KCPKCNAAFGANDVH 694 (698)
T ss_pred CCCCCCCCCCccccc
Confidence 677777777655443
No 144
>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=55.19 E-value=12 Score=16.83 Aligned_cols=10 Identities=30% Similarity=1.102 Sum_probs=5.3
Q ss_pred CcccCCcccc
Q psy13123 99 KKFACETCGK 108 (129)
Q Consensus 99 ~~~~C~~C~~ 108 (129)
..|+|..|++
T Consensus 36 ~~~~C~~C~~ 45 (46)
T PF12760_consen 36 GRYRCKACRK 45 (46)
T ss_pred CeEECCCCCC
Confidence 4456655543
No 145
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=54.46 E-value=3.3 Score=21.88 Aligned_cols=34 Identities=26% Similarity=0.724 Sum_probs=22.0
Q ss_pred CCccCCcchhhhcchhHHHHHHHHhCCCCCeecccccccccChh
Q psy13123 43 SNYKCPLCGKFFIQLCHMKDHIQAHGGLKPYVCTYCGKAFVRAS 86 (129)
Q Consensus 43 ~~~~c~~c~~~~~~~~~l~~~~~~~~~~~~~~c~~c~~~~~~~~ 86 (129)
..|.|+.|++.-.. -.+...|.|..|++.|...+
T Consensus 35 a~y~CpfCgk~~vk----------R~a~GIW~C~~C~~~~AGGA 68 (90)
T PTZ00255 35 AKYFCPFCGKHAVK----------RQAVGIWRCKGCKKTVAGGA 68 (90)
T ss_pred CCccCCCCCCCcee----------eeeeEEEEcCCCCCEEeCCc
Confidence 47889999753221 12234789999998776543
No 146
>COG4530 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=54.15 E-value=6.9 Score=21.46 Aligned_cols=26 Identities=27% Similarity=0.376 Sum_probs=16.7
Q ss_pred ccCcchhccCChhhHHHHHHHhCCCCCccCCcchhhh
Q psy13123 18 QCGECGKQFTRKFSLNAHLHVHYGSSNYKCPLCGKFF 54 (129)
Q Consensus 18 ~C~~C~~~~~~~~~l~~h~~~~~~~~~~~c~~c~~~~ 54 (129)
+|+.||+.|.. .+..|..|+.||+.|
T Consensus 11 idPetg~KFYD-----------LNrdPiVsPytG~s~ 36 (129)
T COG4530 11 IDPETGKKFYD-----------LNRDPIVSPYTGKSY 36 (129)
T ss_pred cCccccchhhc-----------cCCCccccCcccccc
Confidence 46677776633 145677777777776
No 147
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=54.01 E-value=8 Score=17.66 Aligned_cols=11 Identities=36% Similarity=0.875 Sum_probs=6.1
Q ss_pred Ceecccccccc
Q psy13123 72 PYVCTYCGKAF 82 (129)
Q Consensus 72 ~~~c~~c~~~~ 82 (129)
.+.|+.|+..+
T Consensus 20 ~~vC~~Cg~~~ 30 (52)
T smart00661 20 RFVCRKCGYEE 30 (52)
T ss_pred EEECCcCCCeE
Confidence 45666666543
No 148
>COG3364 Zn-ribbon containing protein [General function prediction only]
Probab=53.80 E-value=8.7 Score=20.81 Aligned_cols=14 Identities=36% Similarity=0.833 Sum_probs=9.1
Q ss_pred ccccCcchhccCCh
Q psy13123 16 AYQCGECGKQFTRK 29 (129)
Q Consensus 16 ~~~C~~C~~~~~~~ 29 (129)
|+.|--||..|.+-
T Consensus 2 pH~CtrCG~vf~~g 15 (112)
T COG3364 2 PHQCTRCGEVFDDG 15 (112)
T ss_pred Cceecccccccccc
Confidence 45677777777654
No 149
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=52.94 E-value=18 Score=28.87 Aligned_cols=10 Identities=50% Similarity=1.195 Sum_probs=6.4
Q ss_pred Ceeccccccc
Q psy13123 72 PYVCTYCGKA 81 (129)
Q Consensus 72 ~~~c~~c~~~ 81 (129)
.+.|+.|+..
T Consensus 692 vy~CPsCGae 701 (1337)
T PRK14714 692 VYVCPDCGAE 701 (1337)
T ss_pred ceeCccCCCc
Confidence 4567777754
No 150
>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=51.96 E-value=4.7 Score=17.89 Aligned_cols=15 Identities=40% Similarity=0.990 Sum_probs=9.4
Q ss_pred CccccCcchhccCCh
Q psy13123 15 SAYQCGECGKQFTRK 29 (129)
Q Consensus 15 ~~~~C~~C~~~~~~~ 29 (129)
-|+.|..|+..|-..
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 478899999988654
No 151
>PF13451 zf-trcl: Probable zinc-binding domain
Probab=51.43 E-value=6.4 Score=18.26 Aligned_cols=13 Identities=31% Similarity=1.030 Sum_probs=6.5
Q ss_pred CccccCcchhccC
Q psy13123 15 SAYQCGECGKQFT 27 (129)
Q Consensus 15 ~~~~C~~C~~~~~ 27 (129)
+.+.|..||..|.
T Consensus 3 k~l~C~dCg~~Fv 15 (49)
T PF13451_consen 3 KTLTCKDCGAEFV 15 (49)
T ss_pred eeEEcccCCCeEE
Confidence 3445555555543
No 152
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=50.98 E-value=7.4 Score=21.50 Aligned_cols=11 Identities=18% Similarity=0.235 Sum_probs=5.6
Q ss_pred ccCCcchhhhc
Q psy13123 45 YKCPLCGKFFI 55 (129)
Q Consensus 45 ~~c~~c~~~~~ 55 (129)
..|..|+..|.
T Consensus 71 ~~C~~Cg~~~~ 81 (113)
T PRK12380 71 AWCWDCSQVVE 81 (113)
T ss_pred EEcccCCCEEe
Confidence 45555554443
No 153
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=50.64 E-value=1 Score=19.80 Aligned_cols=10 Identities=30% Similarity=1.225 Sum_probs=5.4
Q ss_pred ccCCcccccc
Q psy13123 101 FACETCGKLF 110 (129)
Q Consensus 101 ~~C~~C~~~f 110 (129)
|.|..|+..+
T Consensus 29 y~C~~C~~~w 38 (40)
T smart00440 29 YVCTKCGHRW 38 (40)
T ss_pred EEeCCCCCEe
Confidence 5565565543
No 154
>PF12773 DZR: Double zinc ribbon
Probab=49.92 E-value=16 Score=16.55 Aligned_cols=8 Identities=38% Similarity=1.202 Sum_probs=3.6
Q ss_pred eecccccc
Q psy13123 73 YVCTYCGK 80 (129)
Q Consensus 73 ~~c~~c~~ 80 (129)
..|+.|+.
T Consensus 30 ~~C~~Cg~ 37 (50)
T PF12773_consen 30 KICPNCGA 37 (50)
T ss_pred CCCcCCcC
Confidence 34444443
No 155
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=49.85 E-value=8.6 Score=21.84 Aligned_cols=36 Identities=22% Similarity=0.605 Sum_probs=21.0
Q ss_pred eecccccccccChhHHHHHHHHhcCCCcccCCccccccCCH
Q psy13123 73 YVCTYCGKAFVRASDLKRHIDAHLGVKKFACETCGKLFSSK 113 (129)
Q Consensus 73 ~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~f~~~ 113 (129)
-.|+.|+........ ..-.+...|+|..|++.|...
T Consensus 31 ~~cP~C~s~~~~k~g-----~~~~~~qRyrC~~C~~tf~~~ 66 (129)
T COG3677 31 VNCPRCKSSNVVKIG-----GIRRGHQRYKCKSCGSTFTVE 66 (129)
T ss_pred CcCCCCCccceeeEC-----CccccccccccCCcCcceeee
Confidence 468887643311111 112336679999999998543
No 156
>PF14787 zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB: 1CL4_A 1DSV_A.
Probab=49.56 E-value=5.1 Score=17.18 Aligned_cols=15 Identities=33% Similarity=0.602 Sum_probs=8.2
Q ss_pred cCCccccccCCHHHH
Q psy13123 102 ACETCGKLFSSKHGL 116 (129)
Q Consensus 102 ~C~~C~~~f~~~~~l 116 (129)
.|..|++.|...++.
T Consensus 4 ~CprC~kg~Hwa~~C 18 (36)
T PF14787_consen 4 LCPRCGKGFHWASEC 18 (36)
T ss_dssp C-TTTSSSCS-TTT-
T ss_pred cCcccCCCcchhhhh
Confidence 467777777666554
No 157
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=49.29 E-value=16 Score=21.73 Aligned_cols=49 Identities=16% Similarity=0.350 Sum_probs=29.4
Q ss_pred eecccccccccChhHHHHH--HH--H-hcCCCcccCCccccccCCHHHHHHHHH
Q psy13123 73 YVCTYCGKAFVRASDLKRH--ID--A-HLGVKKFACETCGKLFSSKHGLKYHVR 121 (129)
Q Consensus 73 ~~c~~c~~~~~~~~~l~~h--~~--~-~~~~~~~~C~~C~~~f~~~~~l~~h~~ 121 (129)
-.|+.|+......+.-..- .. . -..+.-+.|+.||+.|...+++..-.+
T Consensus 98 ~RCp~CN~~L~~vs~eev~~~Vp~~~~~~~~~f~~C~~CgkiYW~GsHw~~m~~ 151 (165)
T COG1656 98 SRCPECNGELEKVSREEVKEKVPEKVYRNYEEFYRCPKCGKIYWKGSHWRRMVE 151 (165)
T ss_pred ccCcccCCEeccCcHHHHhhccchhhhhcccceeECCCCcccccCchHHHHHHH
Confidence 4689998654433221100 00 0 112345779999999999999877655
No 158
>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=49.15 E-value=9.1 Score=21.21 Aligned_cols=12 Identities=17% Similarity=0.487 Sum_probs=7.1
Q ss_pred eecccccccccC
Q psy13123 73 YVCTYCGKAFVR 84 (129)
Q Consensus 73 ~~c~~c~~~~~~ 84 (129)
..|..|+..|..
T Consensus 71 ~~C~~Cg~~~~~ 82 (115)
T TIGR00100 71 CECEDCSEEVSP 82 (115)
T ss_pred EEcccCCCEEec
Confidence 457777755544
No 159
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=49.11 E-value=21 Score=21.57 Aligned_cols=35 Identities=23% Similarity=0.509 Sum_probs=17.6
Q ss_pred hCCCCCccCCcchhhhcchhHHHHHHHHhCCCCCeecccccccc
Q psy13123 39 HYGSSNYKCPLCGKFFIQLCHMKDHIQAHGGLKPYVCTYCGKAF 82 (129)
Q Consensus 39 ~~~~~~~~c~~c~~~~~~~~~l~~~~~~~~~~~~~~c~~c~~~~ 82 (129)
.++..-|.|+.|...+.....+. . -|.|+.||...
T Consensus 108 ~~~~~~y~C~~~~~r~sfdeA~~------~---~F~Cp~Cg~~L 142 (176)
T COG1675 108 ETENNYYVCPNCHVKYSFDEAME------L---GFTCPKCGEDL 142 (176)
T ss_pred hccCCceeCCCCCCcccHHHHHH------h---CCCCCCCCchh
Confidence 34445566666655544333222 1 16677776543
No 160
>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=48.88 E-value=3.6 Score=21.80 Aligned_cols=34 Identities=32% Similarity=0.886 Sum_probs=21.5
Q ss_pred CCccCCcchhhhcchhHHHHHHHHhCCCCCeecccccccccChh
Q psy13123 43 SNYKCPLCGKFFIQLCHMKDHIQAHGGLKPYVCTYCGKAFVRAS 86 (129)
Q Consensus 43 ~~~~c~~c~~~~~~~~~l~~~~~~~~~~~~~~c~~c~~~~~~~~ 86 (129)
..|.|+.|++.-.. -.+-..|.|..|++.|...+
T Consensus 34 a~y~CpfCgk~~vk----------R~a~GIW~C~~C~~~~AGGA 67 (91)
T TIGR00280 34 AKYVCPFCGKKTVK----------RGSTGIWTCRKCGAKFAGGA 67 (91)
T ss_pred cCccCCCCCCCceE----------EEeeEEEEcCCCCCEEeCCc
Confidence 46889998753221 12234688999988776543
No 161
>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=48.75 E-value=0.64 Score=30.10 Aligned_cols=74 Identities=23% Similarity=0.478 Sum_probs=25.2
Q ss_pred cccCcchhccCChhhHHHHHHHhCCCCCccCCcchhhhcchhHHHHHHHHhCCCCCeecccccccccChhHHHHHHHHhc
Q psy13123 17 YQCGECGKQFTRKFSLNAHLHVHYGSSNYKCPLCGKFFIQLCHMKDHIQAHGGLKPYVCTYCGKAFVRASDLKRHIDAHL 96 (129)
Q Consensus 17 ~~C~~C~~~~~~~~~l~~h~~~~~~~~~~~c~~c~~~~~~~~~l~~~~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~~~ 96 (129)
-.|+.||..-.- +.+..-.. .|.+-..|..|+-.+.... ..|+.||..-....... ......
T Consensus 173 g~CPvCGs~P~~-s~l~~~~~--~G~R~L~Cs~C~t~W~~~R--------------~~Cp~Cg~~~~~~l~~~-~~e~~~ 234 (290)
T PF04216_consen 173 GYCPVCGSPPVL-SVLRGGER--EGKRYLHCSLCGTEWRFVR--------------IKCPYCGNTDHEKLEYF-TVEGEP 234 (290)
T ss_dssp SS-TTT---EEE-EEEE--------EEEEEETTT--EEE--T--------------TS-TTT---SS-EEE---------
T ss_pred CcCCCCCCcCce-EEEecCCC--CccEEEEcCCCCCeeeecC--------------CCCcCCCCCCCcceeeE-ecCCCC
Confidence 367778764221 11111001 2556667777765444321 35777775433332221 112223
Q ss_pred CCCcccCCcccc
Q psy13123 97 GVKKFACETCGK 108 (129)
Q Consensus 97 ~~~~~~C~~C~~ 108 (129)
+.+.+.|..|+.
T Consensus 235 ~~rve~C~~C~~ 246 (290)
T PF04216_consen 235 AYRVEVCESCGS 246 (290)
T ss_dssp SEEEEEETTTTE
T ss_pred cEEEEECCcccc
Confidence 456677888863
No 162
>PF14311 DUF4379: Domain of unknown function (DUF4379)
Probab=48.07 E-value=17 Score=16.97 Aligned_cols=12 Identities=25% Similarity=0.886 Sum_probs=6.8
Q ss_pred eecccccccccC
Q psy13123 73 YVCTYCGKAFVR 84 (129)
Q Consensus 73 ~~c~~c~~~~~~ 84 (129)
|+|..|+..+..
T Consensus 29 W~C~~Cgh~w~~ 40 (55)
T PF14311_consen 29 WKCPKCGHEWKA 40 (55)
T ss_pred EECCCCCCeeEc
Confidence 566666655544
No 163
>COG3091 SprT Zn-dependent metalloprotease, SprT family [General function prediction only]
Probab=47.88 E-value=8.7 Score=22.50 Aligned_cols=35 Identities=31% Similarity=0.848 Sum_probs=21.5
Q ss_pred CCeecccccccccChhHHHHHHHHhcCCCcccCCcccccc
Q psy13123 71 KPYVCTYCGKAFVRASDLKRHIDAHLGVKKFACETCGKLF 110 (129)
Q Consensus 71 ~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~f 110 (129)
-+|.|. |+.-+... ..|-..-.|+ .|.|..|+...
T Consensus 116 ~~Y~C~-C~q~~l~~---RRhn~~~~g~-~YrC~~C~gkL 150 (156)
T COG3091 116 YPYRCQ-CQQHYLRI---RRHNTVRRGE-VYRCGKCGGKL 150 (156)
T ss_pred eeEEee-cCCccchh---hhcccccccc-eEEeccCCceE
Confidence 368888 88765443 2333333455 79999997543
No 164
>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=46.78 E-value=2.3 Score=31.09 Aligned_cols=58 Identities=21% Similarity=0.611 Sum_probs=36.0
Q ss_pred ccCCcchhhhcchhHHHHHHHHhCCCCCe-ecccccccccChhHHHHHHHHhcCCCcccCCccccc
Q psy13123 45 YKCPLCGKFFIQLCHMKDHIQAHGGLKPY-VCTYCGKAFVRASDLKRHIDAHLGVKKFACETCGKL 109 (129)
Q Consensus 45 ~~c~~c~~~~~~~~~l~~~~~~~~~~~~~-~c~~c~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~ 109 (129)
-.|..||..|.....|-=. +.+|.-+.| .|+.|.+.+.++.+-..| -.+..|+.||..
T Consensus 124 ~~CT~CGPRfTIi~alPYD-R~nTsM~~F~lC~~C~~EY~dP~nRRfH------AQp~aCp~CGP~ 182 (750)
T COG0068 124 INCTNCGPRFTIIEALPYD-RENTSMADFPLCPFCDKEYKDPLNRRFH------AQPIACPKCGPH 182 (750)
T ss_pred cccCCCCcceeeeccCCCC-cccCccccCcCCHHHHHHhcCccccccc------cccccCcccCCC
Confidence 4577888888765544211 122222223 488898888888775444 246789999864
No 165
>PF01780 Ribosomal_L37ae: Ribosomal L37ae protein family; InterPro: IPR002674 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This ribosomal protein is found in archaebacteria and eukaryotes []. Ribosomal protein L37 has a single zinc finger-like motif of the C2-C2 type [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 4A1E_Y 4A17_Y 4A1C_Y 4A1A_Y 3O58_g 3IZS_m 3O5H_g 1S1I_9 3IZR_m 1YSH_D ....
Probab=46.62 E-value=2.3 Score=22.48 Aligned_cols=33 Identities=33% Similarity=0.842 Sum_probs=20.2
Q ss_pred CCccCCcchhhhcchhHHHHHHHHhCCCCCeecccccccccCh
Q psy13123 43 SNYKCPLCGKFFIQLCHMKDHIQAHGGLKPYVCTYCGKAFVRA 85 (129)
Q Consensus 43 ~~~~c~~c~~~~~~~~~l~~~~~~~~~~~~~~c~~c~~~~~~~ 85 (129)
..|.|+.|++.-.... .. .-|.|..|+..|...
T Consensus 34 ~ky~Cp~Cgk~~vkR~--------a~--GIW~C~~C~~~~AGG 66 (90)
T PF01780_consen 34 AKYTCPFCGKTSVKRV--------AT--GIWKCKKCGKKFAGG 66 (90)
T ss_dssp S-BEESSSSSSEEEEE--------ET--TEEEETTTTEEEE-B
T ss_pred CCCcCCCCCCceeEEe--------ee--EEeecCCCCCEEeCC
Confidence 4688999987533221 22 368899998876543
No 166
>COG5216 Uncharacterized conserved protein [Function unknown]
Probab=45.92 E-value=9.6 Score=18.33 Aligned_cols=11 Identities=36% Similarity=0.999 Sum_probs=5.3
Q ss_pred CCCCccCCcch
Q psy13123 41 GSSNYKCPLCG 51 (129)
Q Consensus 41 ~~~~~~c~~c~ 51 (129)
|++...|+.|+
T Consensus 41 GE~VArCPSCS 51 (67)
T COG5216 41 GEVVARCPSCS 51 (67)
T ss_pred CceEEEcCCce
Confidence 44444555444
No 167
>TIGR03829 YokU_near_AblA uncharacterized protein, YokU family. Members of this protein family occur in various species of the genus Bacillus, always next to the gene (kamA or ablA) for lysine 2,3-aminomutase. Members have a pair of CXXC motifs, and share homology to the amino-terminal region of a family of putative transcription factors for which the C-terminal is modeled by pfam01381, a helix-turn-helix domain model. This family, however, is shorter and lacks the helix-turn-helix region. The function of this protein family is unknown, but a regulatory role in compatible solute biosynthesis is suggested by local genome context.
Probab=45.57 E-value=15 Score=19.47 Aligned_cols=17 Identities=18% Similarity=0.733 Sum_probs=11.4
Q ss_pred cccCcchhccCChhhHH
Q psy13123 17 YQCGECGKQFTRKFSLN 33 (129)
Q Consensus 17 ~~C~~C~~~~~~~~~l~ 33 (129)
..|++||..|.+...+.
T Consensus 36 ~~C~~CGe~y~~dev~~ 52 (89)
T TIGR03829 36 ISCSHCGMEYQDDTTVK 52 (89)
T ss_pred ccccCCCcEeecHHHHH
Confidence 56778887776665543
No 168
>PTZ00043 cytochrome c oxidase subunit; Provisional
Probab=44.93 E-value=9.6 Score=23.92 Aligned_cols=34 Identities=24% Similarity=0.410 Sum_probs=21.2
Q ss_pred CCCccccCcchhccCChhhHHHHHHHhCCCCCccCCc
Q psy13123 13 TTSAYQCGECGKQFTRKFSLNAHLHVHYGSSNYKCPL 49 (129)
Q Consensus 13 ~~~~~~C~~C~~~~~~~~~l~~h~~~~~~~~~~~c~~ 49 (129)
..++.+|.+||..|+....+. ....|..|+.-..
T Consensus 178 EGkpqRCpECGqVFKLVr~~~---s~~dg~dp~~~dp 211 (268)
T PTZ00043 178 EGFLYRCGECDQIFMLVRVLY---SLPDGEDPFPNDP 211 (268)
T ss_pred CCCCccCCCCCcEEEEEEEEe---ecCCCCCCCCCCC
Confidence 445789999999997644221 1344666665543
No 169
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=44.76 E-value=12 Score=17.38 Aligned_cols=10 Identities=30% Similarity=1.032 Sum_probs=4.8
Q ss_pred cccCCccccc
Q psy13123 100 KFACETCGKL 109 (129)
Q Consensus 100 ~~~C~~C~~~ 109 (129)
.+.|..||..
T Consensus 37 r~~C~~Cgyt 46 (50)
T PRK00432 37 RWHCGKCGYT 46 (50)
T ss_pred cEECCCcCCE
Confidence 3455555543
No 170
>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=44.62 E-value=53 Score=17.89 Aligned_cols=41 Identities=12% Similarity=0.189 Sum_probs=29.4
Q ss_pred CccccCcchhccCChhhHHHHHHHhCCCCCccCCcchhhhcc
Q psy13123 15 SAYQCGECGKQFTRKFSLNAHLHVHYGSSNYKCPLCGKFFIQ 56 (129)
Q Consensus 15 ~~~~C~~C~~~~~~~~~l~~h~~~~~~~~~~~c~~c~~~~~~ 56 (129)
..|.|+..|..|.+.......+... +.+.+.|...|+.-.+
T Consensus 2 eVf~i~~T~EiF~dYe~Y~~R~~~y-~~~vwtC~~TGk~~LT 42 (102)
T PF10537_consen 2 EVFYIPFTGEIFRDYEEYLKRMILY-NQRVWTCEITGKSNLT 42 (102)
T ss_pred ceEEeCCCCcccCCHHHHHHHHHHH-hCCeeEEecCCCCCCC
Confidence 3577888888888887776655554 5678888887775443
No 171
>PTZ00448 hypothetical protein; Provisional
Probab=44.23 E-value=21 Score=24.28 Aligned_cols=23 Identities=22% Similarity=0.545 Sum_probs=19.6
Q ss_pred cccCCccccccCCHHHHHHHHHH
Q psy13123 100 KFACETCGKLFSSKHGLKYHVRT 122 (129)
Q Consensus 100 ~~~C~~C~~~f~~~~~l~~h~~~ 122 (129)
.|.|..|+-.|......+.|.++
T Consensus 314 ~~tC~~C~v~F~~~~~qR~H~KS 336 (373)
T PTZ00448 314 MLLCRKCNIQLMDHNAFKQHYRS 336 (373)
T ss_pred CccccccccccCCHHHHHHHhhh
Confidence 57899999999888888888775
No 172
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=43.52 E-value=17 Score=25.20 Aligned_cols=11 Identities=27% Similarity=0.797 Sum_probs=5.2
Q ss_pred Ceecccccccc
Q psy13123 72 PYVCTYCGKAF 82 (129)
Q Consensus 72 ~~~c~~c~~~~ 82 (129)
.|.|+.|++.+
T Consensus 367 g~rC~kCg~~~ 377 (421)
T COG1571 367 GFRCKKCGTRA 377 (421)
T ss_pred CcccccccccC
Confidence 44555555433
No 173
>KOG2071|consensus
Probab=43.26 E-value=19 Score=26.06 Aligned_cols=28 Identities=29% Similarity=0.583 Sum_probs=21.9
Q ss_pred CCCccccCcchhccCChhhHHHHHHHhC
Q psy13123 13 TTSAYQCGECGKQFTRKFSLNAHLHVHY 40 (129)
Q Consensus 13 ~~~~~~C~~C~~~~~~~~~l~~h~~~~~ 40 (129)
.+.|..|..||..|.+......||..|.
T Consensus 415 ~~~pnqC~~CG~R~~~~ee~sk~md~H~ 442 (579)
T KOG2071|consen 415 KDSPNQCKSCGLRFDDSEERSKHMDIHD 442 (579)
T ss_pred cCCcchhcccccccccchhhhhHhhhhh
Confidence 3456789999999998887777776663
No 174
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=42.81 E-value=11 Score=21.04 Aligned_cols=11 Identities=27% Similarity=0.775 Sum_probs=5.3
Q ss_pred ccCCcchhhhc
Q psy13123 45 YKCPLCGKFFI 55 (129)
Q Consensus 45 ~~c~~c~~~~~ 55 (129)
..|..|+..|.
T Consensus 72 ~~C~~Cg~~~~ 82 (117)
T PRK00564 72 LECKDCSHVFK 82 (117)
T ss_pred EEhhhCCCccc
Confidence 45555554433
No 175
>TIGR00686 phnA alkylphosphonate utilization operon protein PhnA. The protein family includes an uncharacterized member designated phnA in Escherichia coli, part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage. This protein is not related to the characterized phosphonoacetate hydrolase designated PhnA by Kulakova, et al. (2001, 1997).
Probab=42.34 E-value=13 Score=20.35 Aligned_cols=28 Identities=21% Similarity=0.567 Sum_probs=14.6
Q ss_pred ccCcchhccCChhhHHHHHHHhCCCCCccCCcchhhhcc
Q psy13123 18 QCGECGKQFTRKFSLNAHLHVHYGSSNYKCPLCGKFFIQ 56 (129)
Q Consensus 18 ~C~~C~~~~~~~~~l~~h~~~~~~~~~~~c~~c~~~~~~ 56 (129)
.|+.|+..|.+.. ...+.|+.|+..|..
T Consensus 4 ~CP~C~seytY~d-----------g~~~iCpeC~~EW~~ 31 (109)
T TIGR00686 4 PCPKCNSEYTYHD-----------GTQLICPSCLYEWNE 31 (109)
T ss_pred cCCcCCCcceEec-----------CCeeECccccccccc
Confidence 4666666554432 223566666655543
No 176
>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=42.23 E-value=9.4 Score=17.81 Aligned_cols=13 Identities=31% Similarity=0.989 Sum_probs=6.8
Q ss_pred cCCccccccCCHH
Q psy13123 102 ACETCGKLFSSKH 114 (129)
Q Consensus 102 ~C~~C~~~f~~~~ 114 (129)
.|+.|+..|....
T Consensus 22 ~CPlC~r~l~~e~ 34 (54)
T PF04423_consen 22 CCPLCGRPLDEEH 34 (54)
T ss_dssp E-TTT--EE-HHH
T ss_pred cCCCCCCCCCHHH
Confidence 8999998886544
No 177
>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=41.82 E-value=20 Score=16.04 Aligned_cols=13 Identities=31% Similarity=0.953 Sum_probs=7.8
Q ss_pred cCCccccccCCHH
Q psy13123 102 ACETCGKLFSSKH 114 (129)
Q Consensus 102 ~C~~C~~~f~~~~ 114 (129)
.|..||+.|...-
T Consensus 10 ~C~~C~rpf~WRK 22 (42)
T PF10013_consen 10 ICPVCGRPFTWRK 22 (42)
T ss_pred cCcccCCcchHHH
Confidence 3666776665543
No 178
>COG1773 Rubredoxin [Energy production and conversion]
Probab=41.75 E-value=12 Score=17.87 Aligned_cols=14 Identities=21% Similarity=0.726 Sum_probs=11.1
Q ss_pred CeecccccccccCh
Q psy13123 72 PYVCTYCGKAFVRA 85 (129)
Q Consensus 72 ~~~c~~c~~~~~~~ 85 (129)
.|+|..||.+|...
T Consensus 3 ~~~C~~CG~vYd~e 16 (55)
T COG1773 3 RWRCSVCGYVYDPE 16 (55)
T ss_pred ceEecCCceEeccc
Confidence 58899999888654
No 179
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=40.96 E-value=5.1 Score=21.20 Aligned_cols=33 Identities=27% Similarity=0.721 Sum_probs=21.1
Q ss_pred CCccCCcchhhhcchhHHHHHHHHhCCCCCeecccccccccCh
Q psy13123 43 SNYKCPLCGKFFIQLCHMKDHIQAHGGLKPYVCTYCGKAFVRA 85 (129)
Q Consensus 43 ~~~~c~~c~~~~~~~~~l~~~~~~~~~~~~~~c~~c~~~~~~~ 85 (129)
..|.|+.|++.-.. -.+-..|.|..|+..|...
T Consensus 35 a~y~CpfCgk~~vk----------R~a~GIW~C~~C~~~~AGG 67 (90)
T PRK03976 35 AKHVCPVCGRPKVK----------RVGTGIWECRKCGAKFAGG 67 (90)
T ss_pred cCccCCCCCCCceE----------EEEEEEEEcCCCCCEEeCC
Confidence 46889998754221 1122468899998877654
No 180
>PHA02998 RNA polymerase subunit; Provisional
Probab=40.84 E-value=3.2 Score=24.89 Aligned_cols=38 Identities=18% Similarity=0.378 Sum_probs=20.3
Q ss_pred eecccccccccChhHHHHHHHHhcCC---CcccCCccccccCCH
Q psy13123 73 YVCTYCGKAFVRASDLKRHIDAHLGV---KKFACETCGKLFSSK 113 (129)
Q Consensus 73 ~~c~~c~~~~~~~~~l~~h~~~~~~~---~~~~C~~C~~~f~~~ 113 (129)
..|+.|+..-.....++. + .++| ..|.|..||+.|...
T Consensus 144 v~CPkCg~~~A~f~qlQT--R-SADEPmT~FYkC~~CG~~wkpp 184 (195)
T PHA02998 144 TPCPNCKSKNTTPMMIQT--R-AADEPPLVRHACRDCKKHFKPP 184 (195)
T ss_pred CCCCCCCCCceEEEEEee--c-cCCCCceEEEEcCCCCCccCCc
Confidence 468888743322222221 1 1222 348898898887543
No 181
>KOG2907|consensus
Probab=39.96 E-value=8.6 Score=21.24 Aligned_cols=9 Identities=44% Similarity=1.106 Sum_probs=4.2
Q ss_pred ccCCcchhh
Q psy13123 45 YKCPLCGKF 53 (129)
Q Consensus 45 ~~c~~c~~~ 53 (129)
|+|+.|+..
T Consensus 103 YTC~kC~~k 111 (116)
T KOG2907|consen 103 YTCPKCKYK 111 (116)
T ss_pred EEcCcccee
Confidence 455544443
No 182
>PF15135 UPF0515: Uncharacterised protein UPF0515
Probab=39.87 E-value=15 Score=23.54 Aligned_cols=16 Identities=13% Similarity=0.675 Sum_probs=10.2
Q ss_pred CCCCCCccccCcchhc
Q psy13123 10 LATTTSAYQCGECGKQ 25 (129)
Q Consensus 10 ~~~~~~~~~C~~C~~~ 25 (129)
+.+.++.|-|..|...
T Consensus 106 ip~~drqFaC~~Cd~~ 121 (278)
T PF15135_consen 106 IPSVDRQFACSSCDHM 121 (278)
T ss_pred ccccceeeeccccchH
Confidence 3445567778777654
No 183
>PF14122 YokU: YokU-like protein
Probab=39.19 E-value=22 Score=18.67 Aligned_cols=19 Identities=21% Similarity=0.565 Sum_probs=13.2
Q ss_pred CccccCcchhccCChhhHH
Q psy13123 15 SAYQCGECGKQFTRKFSLN 33 (129)
Q Consensus 15 ~~~~C~~C~~~~~~~~~l~ 33 (129)
+...|..||+.+.....+.
T Consensus 34 P~i~C~~CgmvYq~d~vi~ 52 (87)
T PF14122_consen 34 PAIICSNCGMVYQDDEVIK 52 (87)
T ss_pred ceeeecCCCcEEehhHHHH
Confidence 3467888888887665543
No 184
>COG4957 Predicted transcriptional regulator [Transcription]
Probab=38.91 E-value=21 Score=20.50 Aligned_cols=25 Identities=48% Similarity=0.777 Sum_probs=19.4
Q ss_pred cccCcchhccCChhhHHHHHHHhCCCCC
Q psy13123 17 YQCGECGKQFTRKFSLNAHLHVHYGSSN 44 (129)
Q Consensus 17 ~~C~~C~~~~~~~~~l~~h~~~~~~~~~ 44 (129)
..|-++|+.|+ .|.+|+.+|.+-.|
T Consensus 77 IicLEDGkkfK---SLKRHL~t~~gmTP 101 (148)
T COG4957 77 IICLEDGKKFK---SLKRHLTTHYGLTP 101 (148)
T ss_pred EEEeccCcchH---HHHHHHhcccCCCH
Confidence 46899999884 57889988877554
No 185
>TIGR00244 transcriptional regulator NrdR. Members of this almost entirely bacterial family contain an ATP cone domain (PFAM:PF03477). There is never more than one member per genome. Common gene symbols given include nrdR, ybaD, ribX and ytcG. The member from Streptomyces coelicolor is found upstream in the operon of the class II oxygen-independent ribonucleotide reductase gene nrdJ and was shown to repress nrdJ expression. Many members of this family are found near genes for riboflavin biosynthesis in Gram-negative bacteria, suggesting a role in that pathway. However, a phylogenetic profiling study associates members of this family with the presence of a palindromic signal with consensus acaCwAtATaTwGtgt, termed the NrdR-box, an upstream element for most operons for ribonucleotide reductase of all three classes in bacterial genomes.
Probab=38.68 E-value=4.1 Score=23.64 Aligned_cols=17 Identities=18% Similarity=0.383 Sum_probs=10.5
Q ss_pred CccCCcchhhhcchhHH
Q psy13123 44 NYKCPLCGKFFIQLCHM 60 (129)
Q Consensus 44 ~~~c~~c~~~~~~~~~l 60 (129)
.-.|..|++.|.+...+
T Consensus 28 RReC~~C~~RFTTyErv 44 (147)
T TIGR00244 28 RRECLECHERFTTFERA 44 (147)
T ss_pred cccCCccCCccceeeec
Confidence 35677777777665443
No 186
>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=38.59 E-value=9.5 Score=16.82 Aligned_cols=11 Identities=27% Similarity=0.899 Sum_probs=7.3
Q ss_pred ccccCcchhcc
Q psy13123 16 AYQCGECGKQF 26 (129)
Q Consensus 16 ~~~C~~C~~~~ 26 (129)
+-.|+.|+..|
T Consensus 29 ~~~CpYCg~~y 39 (40)
T PF10276_consen 29 PVVCPYCGTRY 39 (40)
T ss_dssp EEEETTTTEEE
T ss_pred eEECCCCCCEE
Confidence 56677777655
No 187
>PF07295 DUF1451: Protein of unknown function (DUF1451); InterPro: IPR009912 This family consists of several hypothetical bacterial proteins of around 160 residues in length. Members of this family contain four highly conserved cysteine resides toward the C-terminal region of the protein. The function of this family is unknown.
Probab=38.31 E-value=11 Score=22.00 Aligned_cols=8 Identities=38% Similarity=1.041 Sum_probs=4.5
Q ss_pred ccCCcchh
Q psy13123 45 YKCPLCGK 52 (129)
Q Consensus 45 ~~c~~c~~ 52 (129)
+.|..||.
T Consensus 113 l~C~~Cg~ 120 (146)
T PF07295_consen 113 LVCENCGH 120 (146)
T ss_pred EecccCCC
Confidence 55555554
No 188
>KOG2636|consensus
Probab=38.02 E-value=26 Score=24.51 Aligned_cols=29 Identities=21% Similarity=0.521 Sum_probs=22.5
Q ss_pred HHHhcCCCcccCCccc-cccCCHHHHHHHH
Q psy13123 92 IDAHLGVKKFACETCG-KLFSSKHGLKYHV 120 (129)
Q Consensus 92 ~~~~~~~~~~~C~~C~-~~f~~~~~l~~h~ 120 (129)
-+.|.-.+-|.|.+|| +++.-...+.+|.
T Consensus 393 yKLHGL~~ey~CEICGNy~Y~GrkaF~RHF 422 (497)
T KOG2636|consen 393 YKLHGLDIEYNCEICGNYVYKGRKAFDRHF 422 (497)
T ss_pred HhhcCCCcccceeeccCccccCcHHHHHHh
Confidence 3667778889999999 6777777777773
No 189
>PRK12496 hypothetical protein; Provisional
Probab=37.92 E-value=24 Score=20.96 Aligned_cols=10 Identities=30% Similarity=0.873 Sum_probs=5.2
Q ss_pred cccCcchhcc
Q psy13123 17 YQCGECGKQF 26 (129)
Q Consensus 17 ~~C~~C~~~~ 26 (129)
+.|.-|++.|
T Consensus 128 ~~C~gC~~~~ 137 (164)
T PRK12496 128 KVCKGCKKKY 137 (164)
T ss_pred EECCCCCccc
Confidence 3455555554
No 190
>TIGR00595 priA primosomal protein N'. All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=37.89 E-value=23 Score=25.20 Aligned_cols=10 Identities=40% Similarity=1.032 Sum_probs=5.9
Q ss_pred CCccCCcchh
Q psy13123 43 SNYKCPLCGK 52 (129)
Q Consensus 43 ~~~~c~~c~~ 52 (129)
.|..|+.|+.
T Consensus 252 ~~~~Cp~C~s 261 (505)
T TIGR00595 252 IPKTCPQCGS 261 (505)
T ss_pred CCCCCCCCCC
Confidence 3556666654
No 191
>PF14353 CpXC: CpXC protein
Probab=37.83 E-value=13 Score=20.85 Aligned_cols=17 Identities=29% Similarity=1.015 Sum_probs=12.3
Q ss_pred ccccCcchhccCChhhH
Q psy13123 16 AYQCGECGKQFTRKFSL 32 (129)
Q Consensus 16 ~~~C~~C~~~~~~~~~l 32 (129)
.+.|+.||..+.-...+
T Consensus 38 ~~~CP~Cg~~~~~~~p~ 54 (128)
T PF14353_consen 38 SFTCPSCGHKFRLEYPL 54 (128)
T ss_pred EEECCCCCCceecCCCE
Confidence 47899999988654443
No 192
>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=37.71 E-value=13 Score=17.28 Aligned_cols=12 Identities=33% Similarity=0.988 Sum_probs=8.1
Q ss_pred cccCcchhccCC
Q psy13123 17 YQCGECGKQFTR 28 (129)
Q Consensus 17 ~~C~~C~~~~~~ 28 (129)
|+|..||..|.-
T Consensus 2 y~C~~CgyiYd~ 13 (50)
T cd00730 2 YECRICGYIYDP 13 (50)
T ss_pred cCCCCCCeEECC
Confidence 567777777653
No 193
>COG1326 Uncharacterized archaeal Zn-finger protein [General function prediction only]
Probab=37.09 E-value=39 Score=20.82 Aligned_cols=11 Identities=27% Similarity=0.652 Sum_probs=6.2
Q ss_pred Ceecccccccc
Q psy13123 72 PYVCTYCGKAF 82 (129)
Q Consensus 72 ~~~c~~c~~~~ 82 (129)
...|..||..+
T Consensus 30 lvrC~eCG~V~ 40 (201)
T COG1326 30 LVRCEECGTVH 40 (201)
T ss_pred EEEccCCCcEe
Confidence 34566666555
No 194
>KOG3014|consensus
Probab=36.95 E-value=27 Score=22.38 Aligned_cols=31 Identities=26% Similarity=0.520 Sum_probs=21.1
Q ss_pred CCCCCCcc---ccCcchhccCCh--hhHHHHHHHhC
Q psy13123 10 LATTTSAY---QCGECGKQFTRK--FSLNAHLHVHY 40 (129)
Q Consensus 10 ~~~~~~~~---~C~~C~~~~~~~--~~l~~h~~~~~ 40 (129)
.-.|++.| .|.+||+.|... .+...|...|.
T Consensus 28 ld~Gqk~fg~~~C~~Cgm~Yt~~s~EDe~~H~~fH~ 63 (257)
T KOG3014|consen 28 LDAGQKDFGAVKCKECGMKYTVTSPEDEALHEKFHN 63 (257)
T ss_pred eecCccccCceehhhcCceecCCCHHHHHHHHHHHH
Confidence 34455444 699999887744 55677888775
No 195
>PLN02748 tRNA dimethylallyltransferase
Probab=36.63 E-value=30 Score=24.48 Aligned_cols=24 Identities=25% Similarity=0.746 Sum_probs=20.3
Q ss_pred CcccCCcccc-ccCCHHHHHHHHHH
Q psy13123 99 KKFACETCGK-LFSSKHGLKYHVRT 122 (129)
Q Consensus 99 ~~~~C~~C~~-~f~~~~~l~~h~~~ 122 (129)
+.|.|..|++ .+.....+..|++.
T Consensus 417 ~~~~Ce~C~~~~~~G~~eW~~Hlks 441 (468)
T PLN02748 417 TQYVCEACGNKVLRGAHEWEQHKQG 441 (468)
T ss_pred ccccccCCCCcccCCHHHHHHHhcc
Confidence 5688999997 79999999999764
No 196
>COG1327 Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains [Transcription]
Probab=36.29 E-value=5.8 Score=23.17 Aligned_cols=16 Identities=25% Similarity=0.588 Sum_probs=9.6
Q ss_pred CccCCcchhhhcchhH
Q psy13123 44 NYKCPLCGKFFIQLCH 59 (129)
Q Consensus 44 ~~~c~~c~~~~~~~~~ 59 (129)
.-.|..|+..|.+...
T Consensus 28 RReC~~C~~RFTTfE~ 43 (156)
T COG1327 28 RRECLECGERFTTFER 43 (156)
T ss_pred hhcccccccccchhhe
Confidence 3567777776665443
No 197
>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=36.15 E-value=16 Score=20.20 Aligned_cols=13 Identities=31% Similarity=0.690 Sum_probs=7.4
Q ss_pred eecccccccccCh
Q psy13123 73 YVCTYCGKAFVRA 85 (129)
Q Consensus 73 ~~c~~c~~~~~~~ 85 (129)
..|..|+..|...
T Consensus 71 ~~C~~Cg~~~~~~ 83 (113)
T PF01155_consen 71 ARCRDCGHEFEPD 83 (113)
T ss_dssp EEETTTS-EEECH
T ss_pred EECCCCCCEEecC
Confidence 4577777666543
No 198
>PF14369 zf-RING_3: zinc-finger
Probab=36.03 E-value=20 Score=15.17 Aligned_cols=31 Identities=29% Similarity=0.607 Sum_probs=16.0
Q ss_pred ccccCcchhccCChhhHHHHHHHhCCCCCccCCcchhhhc
Q psy13123 16 AYQCGECGKQFTRKFSLNAHLHVHYGSSNYKCPLCGKFFI 55 (129)
Q Consensus 16 ~~~C~~C~~~~~~~~~l~~h~~~~~~~~~~~c~~c~~~~~ 55 (129)
.|.|..|...+.-... +...-.|+.|+..|.
T Consensus 2 ~ywCh~C~~~V~~~~~---------~~~~~~CP~C~~gFv 32 (35)
T PF14369_consen 2 RYWCHQCNRFVRIAPS---------PDSDVACPRCHGGFV 32 (35)
T ss_pred CEeCccCCCEeEeCcC---------CCCCcCCcCCCCcEe
Confidence 3667777765432110 111225777777664
No 199
>PF10263 SprT-like: SprT-like family; InterPro: IPR006640 This is a family of uncharacterised bacterial proteins which includes Escherichia coli SprT (P39902 from SWISSPROT). SprT is described as a regulator of bolA gene in stationary phase []. The majority of members contain the metallopeptidase zinc binding signature which has a HExxH motif, however there is no evidence for them being metallopeptidases.
Probab=35.88 E-value=14 Score=21.38 Aligned_cols=32 Identities=28% Similarity=0.757 Sum_probs=18.9
Q ss_pred CeecccccccccChhHHHHHHHHhcCCCcccCCccccccC
Q psy13123 72 PYVCTYCGKAFVRASDLKRHIDAHLGVKKFACETCGKLFS 111 (129)
Q Consensus 72 ~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~f~ 111 (129)
.|.|..|+..+.....+ ....|.|..|+..|.
T Consensus 123 ~~~C~~C~~~~~r~~~~--------~~~~~~C~~C~~~l~ 154 (157)
T PF10263_consen 123 VYRCPSCGREYKRHRRS--------KRKRYRCGRCGGPLV 154 (157)
T ss_pred EEEcCCCCCEeeeeccc--------chhhEECCCCCCEEE
Confidence 46788888665333221 123378888886653
No 200
>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=35.72 E-value=31 Score=24.38 Aligned_cols=23 Identities=26% Similarity=0.579 Sum_probs=20.0
Q ss_pred cccCcchhccCChhhHHHHHHHh
Q psy13123 17 YQCGECGKQFTRKFSLNAHLHVH 39 (129)
Q Consensus 17 ~~C~~C~~~~~~~~~l~~h~~~~ 39 (129)
+.|+.|.+.|.+...+..|+...
T Consensus 58 WiCp~CskkF~d~~~~~~H~~~e 80 (466)
T PF04780_consen 58 WICPRCSKKFSDAESCLSHMEQE 80 (466)
T ss_pred eeCCcccceeCCHHHHHHHHHHh
Confidence 56999999999999999998743
No 201
>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=35.34 E-value=12 Score=23.35 Aligned_cols=26 Identities=19% Similarity=0.377 Sum_probs=0.0
Q ss_pred CcccCCccccccCCHHHHHHHHHHhcc
Q psy13123 99 KKFACETCGKLFSSKHGLKYHVRTHKG 125 (129)
Q Consensus 99 ~~~~C~~C~~~f~~~~~l~~h~~~h~~ 125 (129)
....|+.||... ..+.+..|+|+...
T Consensus 167 ~~~~cPitGe~I-P~~e~~eHmRi~Ll 192 (229)
T PF12230_consen 167 KMIICPITGEMI-PADEMDEHMRIELL 192 (229)
T ss_dssp ---------------------------
T ss_pred cccccccccccc-cccccccccccccc
Confidence 345666666654 34456666666543
No 202
>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=35.27 E-value=15 Score=15.83 Aligned_cols=12 Identities=33% Similarity=0.982 Sum_probs=6.2
Q ss_pred CccccCcchhcc
Q psy13123 15 SAYQCGECGKQF 26 (129)
Q Consensus 15 ~~~~C~~C~~~~ 26 (129)
..|+|..||...
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 357888888764
No 203
>PRK10220 hypothetical protein; Provisional
Probab=35.26 E-value=24 Score=19.47 Aligned_cols=29 Identities=24% Similarity=0.676 Sum_probs=15.8
Q ss_pred ccCcchhccCChhhHHHHHHHhCCCCCccCCcchhhhcch
Q psy13123 18 QCGECGKQFTRKFSLNAHLHVHYGSSNYKCPLCGKFFIQL 57 (129)
Q Consensus 18 ~C~~C~~~~~~~~~l~~h~~~~~~~~~~~c~~c~~~~~~~ 57 (129)
.|++|+..|.+.. ...+.|+.|+.-|...
T Consensus 5 ~CP~C~seytY~d-----------~~~~vCpeC~hEW~~~ 33 (111)
T PRK10220 5 HCPKCNSEYTYED-----------NGMYICPECAHEWNDA 33 (111)
T ss_pred cCCCCCCcceEcC-----------CCeEECCcccCcCCcc
Confidence 4666666654432 2246677766555443
No 204
>PF12907 zf-met2: Zinc-binding
Probab=34.90 E-value=33 Score=15.13 Aligned_cols=22 Identities=23% Similarity=0.443 Sum_probs=10.5
Q ss_pred cccCcchhccC---ChhhHHHHHHH
Q psy13123 17 YQCGECGKQFT---RKFSLNAHLHV 38 (129)
Q Consensus 17 ~~C~~C~~~~~---~~~~l~~h~~~ 38 (129)
+.|..|-.+|. ....|..|...
T Consensus 2 i~C~iC~qtF~~t~~~~~L~eH~en 26 (40)
T PF12907_consen 2 IICKICRQTFMQTTNEPQLKEHAEN 26 (40)
T ss_pred cCcHHhhHHHHhcCCHHHHHHHHHc
Confidence 34666664333 23345555543
No 205
>KOG1842|consensus
Probab=34.64 E-value=28 Score=24.41 Aligned_cols=21 Identities=24% Similarity=0.449 Sum_probs=10.1
Q ss_pred ccCCccccccCCHHHHHHHHH
Q psy13123 101 FACETCGKLFSSKHGLKYHVR 121 (129)
Q Consensus 101 ~~C~~C~~~f~~~~~l~~h~~ 121 (129)
|.|+.|...|.....|..|.-
T Consensus 16 flCPiC~~dl~~~~~L~~H~d 36 (505)
T KOG1842|consen 16 FLCPICLLDLPNLSALNDHLD 36 (505)
T ss_pred ccCchHhhhhhhHHHHHHHHh
Confidence 444455555554444444443
No 206
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=34.29 E-value=4.3 Score=21.89 Aligned_cols=38 Identities=18% Similarity=0.469 Sum_probs=17.6
Q ss_pred CCccccCcchhccCChhhHHHHHHHhCCCCCccCCcchhhhc
Q psy13123 14 TSAYQCGECGKQFTRKFSLNAHLHVHYGSSNYKCPLCGKFFI 55 (129)
Q Consensus 14 ~~~~~C~~C~~~~~~~~~l~~h~~~~~~~~~~~c~~c~~~~~ 55 (129)
++-|.|+.|+..-.....+. .-.+.....|..||..|.
T Consensus 20 ~k~FtCp~Cghe~vs~ctvk----k~~~~g~~~Cg~CGls~e 57 (104)
T COG4888 20 PKTFTCPRCGHEKVSSCTVK----KTVNIGTAVCGNCGLSFE 57 (104)
T ss_pred CceEecCccCCeeeeEEEEE----ecCceeEEEcccCcceEE
Confidence 34577777775432222111 111233455666665544
No 207
>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=34.22 E-value=14 Score=16.92 Aligned_cols=11 Identities=45% Similarity=1.153 Sum_probs=6.9
Q ss_pred cccCcchhccC
Q psy13123 17 YQCGECGKQFT 27 (129)
Q Consensus 17 ~~C~~C~~~~~ 27 (129)
|+|..|+..|.
T Consensus 2 y~C~~CgyvYd 12 (47)
T PF00301_consen 2 YQCPVCGYVYD 12 (47)
T ss_dssp EEETTTSBEEE
T ss_pred cCCCCCCEEEc
Confidence 56667776654
No 208
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=34.06 E-value=2.7 Score=17.79 Aligned_cols=8 Identities=50% Similarity=1.148 Sum_probs=3.7
Q ss_pred eecccccc
Q psy13123 73 YVCTYCGK 80 (129)
Q Consensus 73 ~~c~~c~~ 80 (129)
++|+.|+.
T Consensus 23 ~vC~~Cg~ 30 (34)
T PF14803_consen 23 LVCPACGF 30 (34)
T ss_dssp EEETTTTE
T ss_pred eECCCCCC
Confidence 34555543
No 209
>KOG1842|consensus
Probab=33.74 E-value=32 Score=24.10 Aligned_cols=24 Identities=29% Similarity=0.520 Sum_probs=21.2
Q ss_pred ccccCcchhccCChhhHHHHHHHh
Q psy13123 16 AYQCGECGKQFTRKFSLNAHLHVH 39 (129)
Q Consensus 16 ~~~C~~C~~~~~~~~~l~~h~~~~ 39 (129)
-|.|+.|...|.....|..|....
T Consensus 15 gflCPiC~~dl~~~~~L~~H~d~e 38 (505)
T KOG1842|consen 15 GFLCPICLLDLPNLSALNDHLDVE 38 (505)
T ss_pred cccCchHhhhhhhHHHHHHHHhhh
Confidence 489999999999999999998643
No 210
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=33.67 E-value=16 Score=20.26 Aligned_cols=10 Identities=20% Similarity=0.544 Sum_probs=6.2
Q ss_pred eecccccccc
Q psy13123 73 YVCTYCGKAF 82 (129)
Q Consensus 73 ~~c~~c~~~~ 82 (129)
+.|..|+..|
T Consensus 71 ~~C~~Cg~~~ 80 (114)
T PRK03681 71 CWCETCQQYV 80 (114)
T ss_pred EEcccCCCee
Confidence 5577777544
No 211
>PF02891 zf-MIZ: MIZ/SP-RING zinc finger; InterPro: IPR004181 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents MIZ-type zinc finger domains. Miz1 (Msx-interacting-zinc finger) is a zinc finger-containing protein with homology to the yeast protein, Nfi-1. Miz1 is a sequence specific DNA binding protein that can function as a positive-acting transcription factor. Miz1 binds to the homeobox protein Msx2, enhancing the specific DNA-binding ability of Msx2 []. Other proteins containing this domain include the human pias family (protein inhibitor of activated STAT protein). More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3I2D_A.
Probab=32.24 E-value=26 Score=16.14 Aligned_cols=7 Identities=29% Similarity=1.213 Sum_probs=2.3
Q ss_pred ccCCccc
Q psy13123 101 FACETCG 107 (129)
Q Consensus 101 ~~C~~C~ 107 (129)
+.|+.|+
T Consensus 42 W~CPiC~ 48 (50)
T PF02891_consen 42 WKCPICN 48 (50)
T ss_dssp -B-TTT-
T ss_pred eECcCCc
Confidence 5555554
No 212
>TIGR00627 tfb4 transcription factor tfb4. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=31.88 E-value=38 Score=22.15 Aligned_cols=11 Identities=27% Similarity=0.899 Sum_probs=6.6
Q ss_pred eeccccccccc
Q psy13123 73 YVCTYCGKAFV 83 (129)
Q Consensus 73 ~~c~~c~~~~~ 83 (129)
|+|+.|...|-
T Consensus 256 yvCs~Clsi~C 266 (279)
T TIGR00627 256 FVCSVCLSVLC 266 (279)
T ss_pred EECCCccCCcC
Confidence 66666665553
No 213
>PF09963 DUF2197: Uncharacterized protein conserved in bacteria (DUF2197); InterPro: IPR019241 This family represents various hypothetical bacterial proteins with no known function.
Probab=31.70 E-value=30 Score=16.57 Aligned_cols=36 Identities=19% Similarity=0.258 Sum_probs=16.7
Q ss_pred ccCcchhccCCh-hhHHHHHHHhCCCCCccCCcchhh
Q psy13123 18 QCGECGKQFTRK-FSLNAHLHVHYGSSNYKCPLCGKF 53 (129)
Q Consensus 18 ~C~~C~~~~~~~-~~l~~h~~~~~~~~~~~c~~c~~~ 53 (129)
+|-.|++.+.-. ..+............|.|..|...
T Consensus 4 kC~lCdk~~~Id~~~~~aKrLrnrPi~tYmC~eC~~R 40 (56)
T PF09963_consen 4 KCILCDKKEEIDEDTPEAKRLRNRPIHTYMCDECKER 40 (56)
T ss_pred EEEecCCEEEeccCCHHHHHhhcCCCcceeChhHHHH
Confidence 456666654432 223332222333445666666543
No 214
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=31.49 E-value=56 Score=15.28 Aligned_cols=11 Identities=27% Similarity=0.745 Sum_probs=6.0
Q ss_pred CCCeecccccc
Q psy13123 70 LKPYVCTYCGK 80 (129)
Q Consensus 70 ~~~~~c~~c~~ 80 (129)
+....|+.|++
T Consensus 44 ~~i~~Cp~CgR 54 (56)
T PF02591_consen 44 DEIVFCPNCGR 54 (56)
T ss_pred CCeEECcCCCc
Confidence 34455666654
No 215
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=31.37 E-value=6 Score=21.89 Aligned_cols=10 Identities=50% Similarity=1.241 Sum_probs=4.9
Q ss_pred eecccccccc
Q psy13123 73 YVCTYCGKAF 82 (129)
Q Consensus 73 ~~c~~c~~~~ 82 (129)
|.|..||..|
T Consensus 101 y~C~~Cg~~w 110 (113)
T COG1594 101 YKCTRCGYRW 110 (113)
T ss_pred EEecccCCEe
Confidence 4455555443
No 216
>PF01286 XPA_N: XPA protein N-terminal; InterPro: IPR022652 Xeroderma pigmentosum (XP) [] is a human autosomal recessive disease, characterised by a high incidence of sunlight-induced skin cancer. Skin cells of individual's with this condition are hypersensitive to ultraviolet light, due to defects in the incision step of DNA excision repair. There are a minimum of seven genetic complementation groups involved in this pathway: XP-A to XP-G. XP-A is the most severe form of the disease and is due to defects in a 30 kDa nuclear protein called XPA (or XPAC) []. The sequence of the XPA protein is conserved from higher eukaryotes [] to yeast (gene RAD14) []. XPA is a hydrophilic protein of 247 to 296 amino-acid residues which has a C4-type zinc finger motif in its central section. This entry contains the zinc-finger containing region in the XPA protein. It is found N-terminal to PF05181 from PFAM ; PDB: 1D4U_A 1XPA_A.
Probab=30.26 E-value=21 Score=15.16 Aligned_cols=12 Identities=50% Similarity=1.221 Sum_probs=5.0
Q ss_pred ccCcchhccCCh
Q psy13123 18 QCGECGKQFTRK 29 (129)
Q Consensus 18 ~C~~C~~~~~~~ 29 (129)
.|.+|++.|...
T Consensus 5 ~C~eC~~~f~dS 16 (34)
T PF01286_consen 5 KCDECGKPFMDS 16 (34)
T ss_dssp E-TTT--EES-S
T ss_pred hHhHhCCHHHHH
Confidence 577777776543
No 217
>COG1066 Sms Predicted ATP-dependent serine protease [Posttranslational modification, protein turnover, chaperones]
Probab=29.70 E-value=30 Score=24.20 Aligned_cols=9 Identities=33% Similarity=1.021 Sum_probs=5.4
Q ss_pred CccCCcchh
Q psy13123 44 NYKCPLCGK 52 (129)
Q Consensus 44 ~~~c~~c~~ 52 (129)
.|.|..||.
T Consensus 7 ~f~C~~CG~ 15 (456)
T COG1066 7 AFVCQECGY 15 (456)
T ss_pred EEEcccCCC
Confidence 366666664
No 218
>PF10083 DUF2321: Uncharacterized protein conserved in bacteria (DUF2321); InterPro: IPR016891 This entry is represented by Bacteriophage 'Lactobacillus prophage Lj928', Orf-Ljo1454. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=29.19 E-value=22 Score=20.97 Aligned_cols=20 Identities=20% Similarity=0.346 Sum_probs=15.8
Q ss_pred cCCCcccCCccccccCCHHH
Q psy13123 96 LGVKKFACETCGKLFSSKHG 115 (129)
Q Consensus 96 ~~~~~~~C~~C~~~f~~~~~ 115 (129)
+.+.|.-|..||+.|++-..
T Consensus 64 ~~~~PsYC~~CGkpyPWt~~ 83 (158)
T PF10083_consen 64 HYEAPSYCHNCGKPYPWTEN 83 (158)
T ss_pred CCCCChhHHhCCCCCchHHH
Confidence 44578889999999988653
No 219
>COG2879 Uncharacterized small protein [Function unknown]
Probab=29.03 E-value=83 Score=15.51 Aligned_cols=17 Identities=12% Similarity=0.122 Sum_probs=10.3
Q ss_pred CHHHHHHHHHHhcccCC
Q psy13123 112 SKHGLKYHVRTHKGECK 128 (129)
Q Consensus 112 ~~~~l~~h~~~h~~e~p 128 (129)
.=+++-.|+|.++.++|
T Consensus 24 dYdnYVehmr~~hPd~p 40 (65)
T COG2879 24 DYDNYVEHMRKKHPDKP 40 (65)
T ss_pred cHHHHHHHHHHhCcCCC
Confidence 34456667776666655
No 220
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=28.65 E-value=35 Score=22.34 Aligned_cols=15 Identities=27% Similarity=0.784 Sum_probs=7.7
Q ss_pred CcccCCccccccCCH
Q psy13123 99 KKFACETCGKLFSSK 113 (129)
Q Consensus 99 ~~~~C~~C~~~f~~~ 113 (129)
+.+.|+.||..+..+
T Consensus 321 r~~~C~~cg~~~~rD 335 (364)
T COG0675 321 RLFKCPRCGFVHDRD 335 (364)
T ss_pred eeEECCCCCCeehhh
Confidence 445566666554333
No 221
>TIGR03831 YgiT_finger YgiT-type zinc finger domain. This domain model describes a small domain with two copies of a putative zinc-binding motif CXXC (usually CXXCG). Most member proteins consist largely of this domain or else carry an additional C-terminal helix-turn-helix domain, resembling that of the phage protein Cro and modeled by pfam01381.
Probab=28.49 E-value=22 Score=15.48 Aligned_cols=13 Identities=31% Similarity=0.948 Sum_probs=9.0
Q ss_pred ccccCcchhccCC
Q psy13123 16 AYQCGECGKQFTR 28 (129)
Q Consensus 16 ~~~C~~C~~~~~~ 28 (129)
-+.|+.||..+-+
T Consensus 32 ~~~C~~CGE~~~~ 44 (46)
T TIGR03831 32 ALVCPQCGEEYLD 44 (46)
T ss_pred ccccccCCCEeeC
Confidence 3568888877643
No 222
>smart00731 SprT SprT homologues. Predicted to have roles in transcription elongation. Contains a conserved HExxH motif, indicating a metalloprotease function.
Probab=27.83 E-value=25 Score=20.31 Aligned_cols=33 Identities=33% Similarity=0.839 Sum_probs=18.7
Q ss_pred CeecccccccccChhHHHHHHHHhcCCCcccCCccccccC
Q psy13123 72 PYVCTYCGKAFVRASDLKRHIDAHLGVKKFACETCGKLFS 111 (129)
Q Consensus 72 ~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~f~ 111 (129)
.|.|..|+..+.. +.+ +..-..|.|..|+..+.
T Consensus 112 ~y~C~~C~~~~~~------~rr-~~~~~~y~C~~C~g~l~ 144 (146)
T smart00731 112 PYRCTGCGQRYLR------VRR-SNNVSRYRCGKCGGKLI 144 (146)
T ss_pred EEECCCCCCCCce------Ecc-ccCcceEEcCCCCCEEE
Confidence 5778878765431 111 12225588888876653
No 223
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=27.65 E-value=30 Score=14.44 Aligned_cols=10 Identities=40% Similarity=0.810 Sum_probs=5.8
Q ss_pred cccCcchhcc
Q psy13123 17 YQCGECGKQF 26 (129)
Q Consensus 17 ~~C~~C~~~~ 26 (129)
..|..||.+|
T Consensus 22 ~~C~~Cg~~~ 31 (33)
T PF08792_consen 22 EVCIFCGSSF 31 (33)
T ss_pred EEcccCCcEe
Confidence 4566666554
No 224
>COG4338 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=27.34 E-value=27 Score=16.08 Aligned_cols=12 Identities=33% Similarity=0.863 Sum_probs=7.2
Q ss_pred CCccccccCCHH
Q psy13123 103 CETCGKLFSSKH 114 (129)
Q Consensus 103 C~~C~~~f~~~~ 114 (129)
|+.|++.|....
T Consensus 15 CpvCqRPFsWRk 26 (54)
T COG4338 15 CPVCQRPFSWRK 26 (54)
T ss_pred hhhhcCchHHHH
Confidence 666666665544
No 225
>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=27.27 E-value=21 Score=22.01 Aligned_cols=27 Identities=22% Similarity=0.559 Sum_probs=0.0
Q ss_pred HHhcCCCcccCCcccc-ccCCHHHHHHH
Q psy13123 93 DAHLGVKKFACETCGK-LFSSKHGLKYH 119 (129)
Q Consensus 93 ~~~~~~~~~~C~~C~~-~f~~~~~l~~h 119 (129)
+.|.-.+-|.|.+||. ++.-...+.+|
T Consensus 94 KLhGL~~ey~CEICGN~~Y~GrkaFekH 121 (196)
T PF11931_consen 94 KLHGLGVEYKCEICGNQSYKGRKAFEKH 121 (196)
T ss_dssp ----------------------------
T ss_pred HHhCCCCeeeeEeCCCcceecHHHHHHh
Confidence 4455566788888875 33344445544
No 226
>PRK04351 hypothetical protein; Provisional
Probab=27.06 E-value=21 Score=20.91 Aligned_cols=33 Identities=24% Similarity=0.685 Sum_probs=20.5
Q ss_pred CeecccccccccChhHHHHHHHHhcCCCcccCCccccccCC
Q psy13123 72 PYVCTYCGKAFVRASDLKRHIDAHLGVKKFACETCGKLFSS 112 (129)
Q Consensus 72 ~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~f~~ 112 (129)
.|.|..|+..+... ++ + ....|.|..|+-.+..
T Consensus 112 ~Y~C~~Cg~~~~r~------Rr-~-n~~~yrCg~C~g~L~~ 144 (149)
T PRK04351 112 LYECQSCGQQYLRK------RR-I-NTKRYRCGKCRGKLKL 144 (149)
T ss_pred EEECCCCCCEeeee------ee-c-CCCcEEeCCCCcEeee
Confidence 37788888655332 11 2 2466899999866543
No 227
>cd01121 Sms Sms (bacterial radA) DNA repair protein. This protein is not related to archael radA any more than is to other RecA-like NTPases. Sms has a role in recombination and recombinational repair and is responsible for the stabilization or processing of branched DNA molecules.
Probab=27.05 E-value=30 Score=23.59 Aligned_cols=22 Identities=32% Similarity=0.614 Sum_probs=14.5
Q ss_pred ccCCcchhhhcchhHHHHHHHHhCCCCCeecccccc
Q psy13123 45 YKCPLCGKFFIQLCHMKDHIQAHGGLKPYVCTYCGK 80 (129)
Q Consensus 45 ~~c~~c~~~~~~~~~l~~~~~~~~~~~~~~c~~c~~ 80 (129)
|.|..||.... ...+.|+.|+.
T Consensus 1 ~~c~~cg~~~~--------------~~~g~cp~c~~ 22 (372)
T cd01121 1 YVCSECGYVSP--------------KWLGKCPECGE 22 (372)
T ss_pred CCCCCCCCCCC--------------CccEECcCCCC
Confidence 56888875332 23568999975
No 228
>PRK11823 DNA repair protein RadA; Provisional
Probab=26.97 E-value=34 Score=23.96 Aligned_cols=24 Identities=29% Similarity=0.513 Sum_probs=16.5
Q ss_pred CCccCCcchhhhcchhHHHHHHHHhCCCCCeecccccc
Q psy13123 43 SNYKCPLCGKFFIQLCHMKDHIQAHGGLKPYVCTYCGK 80 (129)
Q Consensus 43 ~~~~c~~c~~~~~~~~~l~~~~~~~~~~~~~~c~~c~~ 80 (129)
..|.|..||.... ...+.|+.|+.
T Consensus 6 ~~y~C~~Cg~~~~--------------~~~g~Cp~C~~ 29 (446)
T PRK11823 6 TAYVCQECGAESP--------------KWLGRCPECGA 29 (446)
T ss_pred CeEECCcCCCCCc--------------ccCeeCcCCCC
Confidence 4588999986433 24578998874
No 229
>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=26.87 E-value=40 Score=16.39 Aligned_cols=11 Identities=45% Similarity=1.029 Sum_probs=3.7
Q ss_pred ccCCcchhhhc
Q psy13123 45 YKCPLCGKFFI 55 (129)
Q Consensus 45 ~~c~~c~~~~~ 55 (129)
..|..|++.|.
T Consensus 10 ~~C~~C~~~F~ 20 (69)
T PF01363_consen 10 SNCMICGKKFS 20 (69)
T ss_dssp SB-TTT--B-B
T ss_pred CcCcCcCCcCC
Confidence 34566666653
No 230
>PRK14873 primosome assembly protein PriA; Provisional
Probab=26.81 E-value=42 Score=24.99 Aligned_cols=34 Identities=18% Similarity=0.530 Sum_probs=16.7
Q ss_pred ccCcchhccCChhhHHHHHHHhCCCCCccCCcchh
Q psy13123 18 QCGECGKQFTRKFSLNAHLHVHYGSSNYKCPLCGK 52 (129)
Q Consensus 18 ~C~~C~~~~~~~~~l~~h~~~~~~~~~~~c~~c~~ 52 (129)
.|..||..+....- ...+..|.......|..||.
T Consensus 385 ~C~~Cg~~~~C~~C-~~~L~~h~~~~~l~Ch~CG~ 418 (665)
T PRK14873 385 ACARCRTPARCRHC-TGPLGLPSAGGTPRCRWCGR 418 (665)
T ss_pred EhhhCcCeeECCCC-CCceeEecCCCeeECCCCcC
Confidence 56666666554421 01122333445566777764
No 231
>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=26.70 E-value=53 Score=15.11 Aligned_cols=10 Identities=40% Similarity=1.089 Sum_probs=5.0
Q ss_pred eecccccccc
Q psy13123 73 YVCTYCGKAF 82 (129)
Q Consensus 73 ~~c~~c~~~~ 82 (129)
..|..||.+|
T Consensus 19 ~~Cr~Cg~~~ 28 (57)
T cd00065 19 HHCRNCGRIF 28 (57)
T ss_pred cccCcCcCCc
Confidence 3455555544
No 232
>PF11023 DUF2614: Protein of unknown function (DUF2614); InterPro: IPR020912 This entry describes proteins of unknown function, which are thought to be membrane proteins.; GO: 0005887 integral to plasma membrane
Probab=26.37 E-value=37 Score=18.88 Aligned_cols=10 Identities=50% Similarity=1.238 Sum_probs=4.9
Q ss_pred CCccCCcchh
Q psy13123 43 SNYKCPLCGK 52 (129)
Q Consensus 43 ~~~~c~~c~~ 52 (129)
....|+.|++
T Consensus 68 v~V~CP~C~K 77 (114)
T PF11023_consen 68 VQVECPNCGK 77 (114)
T ss_pred eeeECCCCCC
Confidence 3344555554
No 233
>TIGR01384 TFS_arch transcription factor S, archaeal. There has been an apparent duplication event in the Halobacteriaceae lineage (Haloarcula, Haloferax, Haloquadratum, Halobacterium and Natromonas). There appears to be a separate duplication in Methanosphaera stadtmanae.
Probab=26.05 E-value=34 Score=18.36 Aligned_cols=27 Identities=33% Similarity=0.754 Sum_probs=16.4
Q ss_pred cCCcchhhhcchhHHHHHHHHhCCCCCeecccccccccC
Q psy13123 46 KCPLCGKFFIQLCHMKDHIQAHGGLKPYVCTYCGKAFVR 84 (129)
Q Consensus 46 ~c~~c~~~~~~~~~l~~~~~~~~~~~~~~c~~c~~~~~~ 84 (129)
.|+.||..+... ...+.|+.|+.....
T Consensus 2 fC~~Cg~~l~~~------------~~~~~C~~C~~~~~~ 28 (104)
T TIGR01384 2 FCPKCGSLMTPK------------NGVYVCPSCGYEKEK 28 (104)
T ss_pred CCcccCcccccC------------CCeEECcCCCCcccc
Confidence 477777655321 125788888865543
No 234
>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 PRK00420 hypothetical protein; Validated
Probab=25.88 E-value=41 Score=18.69 Aligned_cols=12 Identities=33% Similarity=0.808 Sum_probs=6.8
Q ss_pred Ceeccccccccc
Q psy13123 72 PYVCTYCGKAFV 83 (129)
Q Consensus 72 ~~~c~~c~~~~~ 83 (129)
...|+.|+....
T Consensus 40 ~~~Cp~Cg~~~~ 51 (112)
T PRK00420 40 EVVCPVHGKVYI 51 (112)
T ss_pred ceECCCCCCeee
Confidence 356666665443
No 236
>PF15616 TerY-C: TerY-C metal binding domain
Probab=25.45 E-value=7.3 Score=22.22 Aligned_cols=13 Identities=31% Similarity=0.915 Sum_probs=8.4
Q ss_pred CCCCeeccccccc
Q psy13123 69 GLKPYVCTYCGKA 81 (129)
Q Consensus 69 ~~~~~~c~~c~~~ 81 (129)
++....|++|+..
T Consensus 102 g~~~~~CPwCg~~ 114 (131)
T PF15616_consen 102 GEGEVTCPWCGNE 114 (131)
T ss_pred CCCCEECCCCCCe
Confidence 3445678888753
No 237
>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=25.14 E-value=37 Score=23.89 Aligned_cols=24 Identities=25% Similarity=0.434 Sum_probs=17.0
Q ss_pred CCccCCcchhhhcchhHHHHHHHHhCCCCCeecccccc
Q psy13123 43 SNYKCPLCGKFFIQLCHMKDHIQAHGGLKPYVCTYCGK 80 (129)
Q Consensus 43 ~~~~c~~c~~~~~~~~~l~~~~~~~~~~~~~~c~~c~~ 80 (129)
..|.|..||.... ...+.|+.|+.
T Consensus 6 ~~y~C~~Cg~~~~--------------~~~g~Cp~C~~ 29 (454)
T TIGR00416 6 SKFVCQHCGADSP--------------KWQGKCPACHA 29 (454)
T ss_pred CeEECCcCCCCCc--------------cccEECcCCCC
Confidence 3589999986433 24578999975
No 238
>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=25.04 E-value=26 Score=19.09 Aligned_cols=11 Identities=36% Similarity=0.797 Sum_probs=6.6
Q ss_pred CccCCcchhhh
Q psy13123 44 NYKCPLCGKFF 54 (129)
Q Consensus 44 ~~~c~~c~~~~ 54 (129)
|-.|+.||..-
T Consensus 2 p~~CpYCg~~~ 12 (102)
T PF11672_consen 2 PIICPYCGGPA 12 (102)
T ss_pred CcccCCCCCee
Confidence 45677777543
No 239
>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=25.00 E-value=60 Score=13.62 Aligned_cols=8 Identities=50% Similarity=1.427 Sum_probs=3.4
Q ss_pred cCCcchhh
Q psy13123 46 KCPLCGKF 53 (129)
Q Consensus 46 ~c~~c~~~ 53 (129)
.|+.|++.
T Consensus 6 ~C~nC~R~ 13 (33)
T PF08209_consen 6 ECPNCGRP 13 (33)
T ss_dssp E-TTTSSE
T ss_pred ECCCCcCC
Confidence 45555543
No 240
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=24.64 E-value=28 Score=19.62 Aligned_cols=11 Identities=36% Similarity=0.558 Sum_probs=6.6
Q ss_pred eecccccccccC
Q psy13123 73 YVCTYCGKAFVR 84 (129)
Q Consensus 73 ~~c~~c~~~~~~ 84 (129)
+.| .|+..|..
T Consensus 71 ~~C-~Cg~~~~~ 81 (124)
T PRK00762 71 IEC-ECGYEGVV 81 (124)
T ss_pred EEe-eCcCcccc
Confidence 567 77765543
No 241
>COG4391 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=24.63 E-value=35 Score=16.69 Aligned_cols=11 Identities=18% Similarity=0.697 Sum_probs=7.6
Q ss_pred cccCcchhccC
Q psy13123 17 YQCGECGKQFT 27 (129)
Q Consensus 17 ~~C~~C~~~~~ 27 (129)
-.|+.|+..|+
T Consensus 49 v~CPYC~t~y~ 59 (62)
T COG4391 49 VVCPYCSTRYR 59 (62)
T ss_pred EecCccccEEE
Confidence 45777877664
No 242
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=24.11 E-value=43 Score=15.70 Aligned_cols=13 Identities=31% Similarity=0.899 Sum_probs=6.6
Q ss_pred CcccCCccccccC
Q psy13123 99 KKFACETCGKLFS 111 (129)
Q Consensus 99 ~~~~C~~C~~~f~ 111 (129)
....|+.|+..|-
T Consensus 39 ~~v~C~~C~~~fC 51 (64)
T smart00647 39 NRVTCPKCGFSFC 51 (64)
T ss_pred CeeECCCCCCeEC
Confidence 3445555555543
No 243
>TIGR00319 desulf_FeS4 desulfoferrodoxin FeS4 iron-binding domain. Neelaredoxin, a monomeric blue non-heme iron protein, lacks this domain.
Probab=23.76 E-value=32 Score=14.20 Aligned_cols=12 Identities=33% Similarity=0.985 Sum_probs=9.0
Q ss_pred CccccCcchhcc
Q psy13123 15 SAYQCGECGKQF 26 (129)
Q Consensus 15 ~~~~C~~C~~~~ 26 (129)
+-|+|..||...
T Consensus 6 ~~ykC~~Cgniv 17 (34)
T TIGR00319 6 QVYKCEVCGNIV 17 (34)
T ss_pred cEEEcCCCCcEE
Confidence 468888888765
No 244
>PF10122 Mu-like_Com: Mu-like prophage protein Com; InterPro: IPR019294 Members of this entry belong to the Com family of proteins that act as translational regulators of mom [, ].
Probab=23.62 E-value=18 Score=16.92 Aligned_cols=7 Identities=29% Similarity=1.037 Sum_probs=3.0
Q ss_pred ccCCccc
Q psy13123 101 FACETCG 107 (129)
Q Consensus 101 ~~C~~C~ 107 (129)
.+|+.|+
T Consensus 25 IKCpRC~ 31 (51)
T PF10122_consen 25 IKCPRCK 31 (51)
T ss_pred EECCCCC
Confidence 3444443
No 245
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=23.55 E-value=46 Score=15.89 Aligned_cols=15 Identities=27% Similarity=0.552 Sum_probs=11.1
Q ss_pred cCCCcccCCcccccc
Q psy13123 96 LGVKKFACETCGKLF 110 (129)
Q Consensus 96 ~~~~~~~C~~C~~~f 110 (129)
.+...|.|+.||-.+
T Consensus 10 ~~~v~~~Cp~cGipt 24 (55)
T PF13824_consen 10 PAHVNFECPDCGIPT 24 (55)
T ss_pred ccccCCcCCCCCCcC
Confidence 345679999998754
No 246
>cd00974 DSRD Desulforedoxin (DSRD) domain; a small non-heme iron domain present in the desulforedoxin (rubredoxin oxidoreductase) and desulfoferrodoxin proteins of some archeael and bacterial methanogens and sulfate/sulfur reducers. Desulforedoxin is a small, single-domain homodimeric protein; each subunit contains an iron atom bound to four cysteinyl sulfur atoms, Fe(S-Cys)4, in a distorted tetrahedral coordination. Its metal center is similar to that found in rubredoxin type proteins. Desulforedoxin is regarded as a potential redox partner for rubredoxin. Desulfoferrodoxin forms a homodimeric protein, with each protomer comprised of two domains, the N-terminal DSRD domain and C-terminal superoxide reductase-like (SORL) domain. Each domain has a distinct iron center: the DSRD iron center I, Fe(S-Cys)4; and the SORL iron center II, Fe[His4Cys(Glu)].
Probab=23.49 E-value=32 Score=14.19 Aligned_cols=11 Identities=36% Similarity=1.044 Sum_probs=7.7
Q ss_pred ccccCcchhcc
Q psy13123 16 AYQCGECGKQF 26 (129)
Q Consensus 16 ~~~C~~C~~~~ 26 (129)
-|+|..||...
T Consensus 4 ~ykC~~CGniv 14 (34)
T cd00974 4 VYKCEICGNIV 14 (34)
T ss_pred EEEcCCCCcEE
Confidence 47777777664
No 247
>COG4896 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=23.45 E-value=1.1e+02 Score=15.00 Aligned_cols=11 Identities=36% Similarity=0.942 Sum_probs=5.4
Q ss_pred CCccCCcchhh
Q psy13123 43 SNYKCPLCGKF 53 (129)
Q Consensus 43 ~~~~c~~c~~~ 53 (129)
..|.|+.|.-.
T Consensus 30 rtymC~eC~~R 40 (68)
T COG4896 30 RTYMCPECEHR 40 (68)
T ss_pred eeEechhhHhh
Confidence 34555555443
No 248
>PF06676 DUF1178: Protein of unknown function (DUF1178); InterPro: IPR009562 This family consists of several hypothetical bacterial proteins of around 150 residues in length. The function of this family is unknown.
Probab=23.03 E-value=62 Score=19.02 Aligned_cols=16 Identities=25% Similarity=0.436 Sum_probs=9.1
Q ss_pred CeecccccccccChhH
Q psy13123 72 PYVCTYCGKAFVRASD 87 (129)
Q Consensus 72 ~~~c~~c~~~~~~~~~ 87 (129)
-..|++||..-.....
T Consensus 32 lv~CP~Cgs~~V~K~l 47 (148)
T PF06676_consen 32 LVSCPVCGSTEVSKAL 47 (148)
T ss_pred CccCCCCCCCeEeeec
Confidence 4567777754444433
No 249
>KOG0717|consensus
Probab=22.84 E-value=55 Score=23.24 Aligned_cols=22 Identities=36% Similarity=0.670 Sum_probs=18.2
Q ss_pred ccCCccccccCCHHHHHHHHHH
Q psy13123 101 FACETCGKLFSSKHGLKYHVRT 122 (129)
Q Consensus 101 ~~C~~C~~~f~~~~~l~~h~~~ 122 (129)
+-|..|+|.|...-.+..|..+
T Consensus 293 lyC~vCnKsFKseKq~kNHEnS 314 (508)
T KOG0717|consen 293 LYCVVCNKSFKSEKQLKNHENS 314 (508)
T ss_pred eEEeeccccccchHHHHhhHHH
Confidence 6788999999998888888654
No 250
>PF01194 RNA_pol_N: RNA polymerases N / 8 kDa subunit; InterPro: IPR000268 In eukaryotes, there are three different forms of DNA-dependent RNA polymerases (2.7.7.6 from EC) transcribing different sets of genes. Each class of RNA polymerase is an assemblage of ten to twelve different polypeptides. In archaebacteria, there is generally a single form of RNA polymerase which also consists of an oligomeric assemblage of 10 to 13 polypeptides. Archaebacterial subunit N (gene rpoN) [] is a small protein of about 8 kDa, it is evolutionary related [] to a 8.3 kDa component shared by all three forms of eukaryotic RNA polymerases (gene RPB10 in yeast and POLR2J in mammals) as well as to African swine fever virus (ASFV) protein CP80R []. There is a conserved region which is located at the N-terminal extremity of these polymerase subunits; this region contains two cysteines that binds a zinc ion [].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_N 3HKZ_N 1EF4_A 3H0G_V 2Y0S_N 2R92_J 3M4O_J 3S2D_J 1R9S_J 1Y1W_J ....
Probab=22.77 E-value=56 Score=15.92 Aligned_cols=16 Identities=31% Similarity=0.631 Sum_probs=10.9
Q ss_pred CeecccccccccChhH
Q psy13123 72 PYVCTYCGKAFVRASD 87 (129)
Q Consensus 72 ~~~c~~c~~~~~~~~~ 87 (129)
|..|..||+...+...
T Consensus 4 PVRCFTCGkvi~~~~e 19 (60)
T PF01194_consen 4 PVRCFTCGKVIGNKWE 19 (60)
T ss_dssp SSS-STTTSBTCGHHH
T ss_pred ceecCCCCCChhHhHH
Confidence 5678899988766544
No 251
>KOG4727|consensus
Probab=22.75 E-value=57 Score=19.69 Aligned_cols=22 Identities=23% Similarity=0.543 Sum_probs=19.5
Q ss_pred CeecccccccccChhHHHHHHH
Q psy13123 72 PYVCTYCGKAFVRASDLKRHID 93 (129)
Q Consensus 72 ~~~c~~c~~~~~~~~~l~~h~~ 93 (129)
.|-|.+|.-++..+.++..|+.
T Consensus 75 GyyCdVCdcvvKDSinflDHiN 96 (193)
T KOG4727|consen 75 GYYCDVCDCVVKDSINFLDHIN 96 (193)
T ss_pred ceeeeecceeehhhHHHHHHhc
Confidence 4889999999999999999874
No 252
>TIGR03830 CxxCG_CxxCG_HTH putative zinc finger/helix-turn-helix protein, YgiT family. This model describes a family of predicted regulatory proteins with a conserved zinc finger/HTH architecture. The amino-terminal region contains a novel domain, featuring two CXXC motifs and occuring in a number of small bacterial proteins as well as in the present family. The carboxyl-terminal region consists of a helix-turn-helix domain, modeled by pfam01381. The predicted function is DNA binding and transcriptional regulation.
Probab=22.27 E-value=73 Score=17.54 Aligned_cols=21 Identities=14% Similarity=0.431 Sum_probs=15.0
Q ss_pred ccccCcchhccCChhhHHHHH
Q psy13123 16 AYQCGECGKQFTRKFSLNAHL 36 (129)
Q Consensus 16 ~~~C~~C~~~~~~~~~l~~h~ 36 (129)
-+.|+.||..+.+........
T Consensus 31 ~~~C~~CGe~~~~~e~~~~~~ 51 (127)
T TIGR03830 31 GWYCPACGEELLDPEESKRNS 51 (127)
T ss_pred eeECCCCCCEEEcHHHHHHHH
Confidence 367999998887776654443
No 253
>PRK05978 hypothetical protein; Provisional
Probab=21.72 E-value=46 Score=19.54 Aligned_cols=9 Identities=44% Similarity=1.243 Sum_probs=4.7
Q ss_pred cCCcccccc
Q psy13123 102 ACETCGKLF 110 (129)
Q Consensus 102 ~C~~C~~~f 110 (129)
.|..||..|
T Consensus 54 ~C~~CG~~~ 62 (148)
T PRK05978 54 HCAACGEDF 62 (148)
T ss_pred CccccCCcc
Confidence 455555544
No 254
>KOG2857|consensus
Probab=21.70 E-value=46 Score=19.38 Aligned_cols=22 Identities=27% Similarity=0.572 Sum_probs=14.4
Q ss_pred cccCCccccccCCHHHHHHHHH
Q psy13123 100 KFACETCGKLFSSKHGLKYHVR 121 (129)
Q Consensus 100 ~~~C~~C~~~f~~~~~l~~h~~ 121 (129)
.|+|+.|.--+.+-.-+..|.-
T Consensus 17 KYKCpkC~vPYCSl~CfKiHk~ 38 (157)
T KOG2857|consen 17 KYKCPKCSVPYCSLPCFKIHKS 38 (157)
T ss_pred hccCCCCCCccccchhhhhccC
Confidence 4777777666666666666644
No 255
>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG
Probab=21.62 E-value=43 Score=15.75 Aligned_cols=9 Identities=33% Similarity=0.995 Sum_probs=5.3
Q ss_pred cCCcccccc
Q psy13123 102 ACETCGKLF 110 (129)
Q Consensus 102 ~C~~C~~~f 110 (129)
.|+.||..+
T Consensus 2 ~CPyCge~~ 10 (52)
T PF14255_consen 2 QCPYCGEPI 10 (52)
T ss_pred CCCCCCCee
Confidence 466666554
No 256
>PRK08222 hydrogenase 4 subunit H; Validated
Probab=21.61 E-value=77 Score=19.16 Aligned_cols=19 Identities=16% Similarity=0.506 Sum_probs=14.7
Q ss_pred CcccCCccccccCCHHHHH
Q psy13123 99 KKFACETCGKLFSSKHGLK 117 (129)
Q Consensus 99 ~~~~C~~C~~~f~~~~~l~ 117 (129)
....|..||+.|.....+.
T Consensus 113 ~~~~C~~Cg~~f~~~k~i~ 131 (181)
T PRK08222 113 HLQRCSRCERPFAPQKTVA 131 (181)
T ss_pred ccCcCcccCCccCcHhHHH
Confidence 4678999999998665554
No 257
>COG3880 Modulator of heat shock repressor CtsR, McsA [Signal transduction mechanisms]
Probab=21.53 E-value=16 Score=21.87 Aligned_cols=9 Identities=44% Similarity=1.246 Sum_probs=4.1
Q ss_pred ccCcchhcc
Q psy13123 18 QCGECGKQF 26 (129)
Q Consensus 18 ~C~~C~~~~ 26 (129)
.|+.|+++|
T Consensus 76 ~C~~C~~Tf 84 (176)
T COG3880 76 GCHNCGMTF 84 (176)
T ss_pred cCccccccH
Confidence 344444444
No 258
>PLN03238 probable histone acetyltransferase MYST; Provisional
Probab=21.26 E-value=1.2e+02 Score=20.19 Aligned_cols=24 Identities=38% Similarity=0.782 Sum_probs=14.8
Q ss_pred CCeecccccccccChhHHHHHHHH
Q psy13123 71 KPYVCTYCGKAFVRASDLKRHIDA 94 (129)
Q Consensus 71 ~~~~c~~c~~~~~~~~~l~~h~~~ 94 (129)
.-|.|..|-+-|.....+..|+..
T Consensus 47 ~lyiCe~Clky~~~~~~l~~H~~~ 70 (290)
T PLN03238 47 KLYICEYCLKYMRKKKSLLRHLAK 70 (290)
T ss_pred eEEEcCCCcchhCCHHHHHHHHHh
Confidence 346666666666666666666553
No 259
>PF14690 zf-ISL3: zinc-finger of transposase IS204/IS1001/IS1096/IS1165
Probab=21.20 E-value=44 Score=14.70 Aligned_cols=7 Identities=43% Similarity=1.274 Sum_probs=3.3
Q ss_pred cccCcch
Q psy13123 17 YQCGECG 23 (129)
Q Consensus 17 ~~C~~C~ 23 (129)
..|+.||
T Consensus 3 ~~Cp~Cg 9 (47)
T PF14690_consen 3 PRCPHCG 9 (47)
T ss_pred ccCCCcC
Confidence 3445554
No 260
>COG5188 PRP9 Splicing factor 3a, subunit 3 [RNA processing and modification]
Probab=20.99 E-value=73 Score=21.76 Aligned_cols=21 Identities=33% Similarity=0.781 Sum_probs=17.8
Q ss_pred cccCcchhccCChhhHHHHHH
Q psy13123 17 YQCGECGKQFTRKFSLNAHLH 37 (129)
Q Consensus 17 ~~C~~C~~~~~~~~~l~~h~~ 37 (129)
+-|..|++.|.....+..|..
T Consensus 239 ~YC~~C~r~f~~~~VFe~Hl~ 259 (470)
T COG5188 239 VYCVKCGREFSRSKVFEYHLE 259 (470)
T ss_pred eeeHhhhhHhhhhHHHHHHHh
Confidence 569999999999888888874
No 261
>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=20.95 E-value=36 Score=19.66 Aligned_cols=14 Identities=36% Similarity=0.845 Sum_probs=11.3
Q ss_pred CCcccCCccccccC
Q psy13123 98 VKKFACETCGKLFS 111 (129)
Q Consensus 98 ~~~~~C~~C~~~f~ 111 (129)
.++..|..||..|.
T Consensus 110 g~~~RCpeCG~~fk 123 (136)
T PF01215_consen 110 GKPQRCPECGQVFK 123 (136)
T ss_dssp TSEEEETTTEEEEE
T ss_pred CCccCCCCCCeEEE
Confidence 46889999998774
No 262
>PRK05580 primosome assembly protein PriA; Validated
Probab=20.87 E-value=68 Score=23.96 Aligned_cols=12 Identities=33% Similarity=0.764 Sum_probs=6.8
Q ss_pred CCCccCCcchhh
Q psy13123 42 SSNYKCPLCGKF 53 (129)
Q Consensus 42 ~~~~~c~~c~~~ 53 (129)
..+..|+.|+..
T Consensus 419 ~~~~~Cp~Cg~~ 430 (679)
T PRK05580 419 PIPKACPECGST 430 (679)
T ss_pred CCCCCCCCCcCC
Confidence 345667777543
No 263
>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=20.47 E-value=74 Score=20.97 Aligned_cols=32 Identities=25% Similarity=0.580 Sum_probs=18.3
Q ss_pred ccCCcchhhhcchhHHHHHHHHhCCCCCeecccccccccCh
Q psy13123 45 YKCPLCGKFFIQLCHMKDHIQAHGGLKPYVCTYCGKAFVRA 85 (129)
Q Consensus 45 ~~c~~c~~~~~~~~~l~~~~~~~~~~~~~~c~~c~~~~~~~ 85 (129)
..|+.|+.....+. |.. +-++|+.|+.-|.-.
T Consensus 27 ~~c~~c~~~~~~~~-l~~--------~~~vc~~c~~h~rl~ 58 (285)
T TIGR00515 27 TKCPKCGQVLYTKE-LER--------NLEVCPKCDHHMRMD 58 (285)
T ss_pred eECCCCcchhhHHH-HHh--------hCCCCCCCCCcCcCC
Confidence 56777776543332 221 236788888765543
No 264
>PF02748 PyrI_C: Aspartate carbamoyltransferase regulatory chain, metal binding domain; InterPro: IPR020542 Aspartate carbamoyltransferase (aspartate transcarbamylase, ATCase) 2.1.3.2 from EC is an allosteric enzyme that plays a central role in the regulation of the pyrimidine pathway in bacteria. The holoenzyme is a dodecamer composed of six catalytic chains, each with an active site, and six regulatory chains lacking catalytic activity []. The catalytic subunits exist as a dimer of catalytic trimers, (c3)2, while the regulatory subunits exist as a trimer of regulatory dimers, (r2)3, therefore the complete holoenzyme can be represented as (c3)2(r2)3. The association of the catalytic subunits c3 with the regulatory subunits r2 is responsible for the establishment of positive co-operativity between catalytic sites for the binding of aspartate and it dictates the pattern of allosteric response toward nucleotide effectors. ATCase from Escherichia coli is the most extensively studied allosteric enzyme []. The crystal structure of the T-state, the T-state with CTP bound, the R-state with N-phosphonacetyl-L-aspartate (PALA) bound, and the R-state with phosphonoacetamide plus malonate bound have been used in interpreting kinetic and mutational studies. A high-resolution structure of E. coli ATCase in the presence of PALA (a bisubstrate analog) allows a detailed description of the binding at the active site of the enzyme and allows a detailed model of the tetrahedral intermediate to be constructed. The entire regulatory chain has been traced showing that the N-terminal regions of the regulatory chains R1 and R6 are located in close proximity to each other and to the regulatory site. This portion of the molecule may be involved in the observed asymmetry between the regulatory binding sites as well as in the heterotropic response of the enzyme []. The C-terminal domain of the regulatory chains have a rubredoxin-like zinc-bound fold. ATCase from Enterobacter agglomerans (Erwinia herbicola) (Pantoea agglomerans) differs from the other investigated enterobacterial ATCases by its absence of homotropic co-operativity toward the substrate aspartate and its lack of response to ATP which is an allosteric effector (activator) of this family of enzymes. Nevertheless, the E. herbicola ATCase has the same quaternary structure, two trimers of catalytic chains with three dimers of regulatory chains, (c3)2(r2)3, as other enterobacterial ATCases and shows extensive primary structure conservation []. This entry represents the C-terminal domain.; PDB: 2YWW_B 1SKU_D 1Q95_L 8ATC_B 3AT1_D 1RAI_D 4E2F_D 1NBE_B 6AT1_B 2FZC_D ....
Probab=20.33 E-value=50 Score=15.47 Aligned_cols=17 Identities=18% Similarity=0.436 Sum_probs=10.1
Q ss_pred CCCCccccCcchhccCC
Q psy13123 12 TTTSAYQCGECGKQFTR 28 (129)
Q Consensus 12 ~~~~~~~C~~C~~~~~~ 28 (129)
.+...++|..|+..+..
T Consensus 31 ~~~~~~rC~YCe~~~~~ 47 (52)
T PF02748_consen 31 KEPIKLRCHYCERIITE 47 (52)
T ss_dssp TTTCEEEETTT--EEEH
T ss_pred CCCCEEEeeCCCCEecc
Confidence 34456889999987643
No 265
>PF13821 DUF4187: Domain of unknown function (DUF4187)
Probab=20.30 E-value=63 Score=15.33 Aligned_cols=15 Identities=27% Similarity=0.663 Sum_probs=7.4
Q ss_pred cCCccccccCCHHHH
Q psy13123 102 ACETCGKLFSSKHGL 116 (129)
Q Consensus 102 ~C~~C~~~f~~~~~l 116 (129)
-|-+||..|.....|
T Consensus 29 YC~~Cg~~Y~d~~dL 43 (55)
T PF13821_consen 29 YCFWCGTKYDDEEDL 43 (55)
T ss_pred eeeeeCCccCCHHHH
Confidence 455555555554444
No 266
>PF08271 TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013137 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIB (TFIIB). In eukaryotes the initiation of transcription of protein encoding genes by the polymerase II complexe (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least seven different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, and -IIH []. TFIIB and TFIID are responsible for promoter recognition and interaction with pol II; together with Pol II, they form a minimal initiation complex capable of transcription under certain conditions. The TATA box of a Pol II promoter is bound in the initiation complex by the TBP subunit of TFIID, which bends the DNA around the C-terminal domain of TFIIB whereas the N-terminal zinc finger of TFIIB interacts with Pol II [, ]. The TFIIB zinc finger adopts a zinc ribbon fold characterised by two beta-hairpins forming two structurally similar zinc-binding sub-sites []. The zinc finger contacts the rbp1 subunit of Pol II through its dock domain, a conserved region of about 70 amino acids located close to the polymerase active site []. In the Pol II complex this surface is located near the RNA exit groove. Interestingly this sequence is best conserved in the three polymerases that utilise a TFIIB-like general transcription factor (Pol II, Pol III, and archaeal RNA polymerase) but not in Pol I []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1VD4_A 1PFT_A 3K1F_M 3K7A_M 1RO4_A 1RLY_A 1DL6_A.
Probab=20.29 E-value=42 Score=14.70 Aligned_cols=11 Identities=36% Similarity=0.945 Sum_probs=5.3
Q ss_pred Ceecccccccc
Q psy13123 72 PYVCTYCGKAF 82 (129)
Q Consensus 72 ~~~c~~c~~~~ 82 (129)
.+.|..||.+.
T Consensus 19 ~~vC~~CG~Vl 29 (43)
T PF08271_consen 19 ELVCPNCGLVL 29 (43)
T ss_dssp EEEETTT-BBE
T ss_pred eEECCCCCCEe
Confidence 34566666543
No 267
>KOG1994|consensus
Probab=20.22 E-value=69 Score=20.38 Aligned_cols=23 Identities=30% Similarity=0.723 Sum_probs=19.6
Q ss_pred CCCeecccccccccChhHHHHHH
Q psy13123 70 LKPYVCTYCGKAFVRASDLKRHI 92 (129)
Q Consensus 70 ~~~~~c~~c~~~~~~~~~l~~h~ 92 (129)
...|-|.+||--|.+..+|..|-
T Consensus 237 ~eh~YC~fCG~~y~~~edl~ehC 259 (268)
T KOG1994|consen 237 SEHYYCFFCGIKYKDEEDLYEHC 259 (268)
T ss_pred ccceEEEEeccccCCHHHHHHhC
Confidence 34689999999999999998773
No 268
>PF01096 TFIIS_C: Transcription factor S-II (TFIIS); InterPro: IPR001222 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIs (TFIIS). In eukaryotes the initiation of transcription of protein encoding genes by polymerase II (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least eight different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, -IIH and -IIS []. During mRNA elongation, Pol II can encounter DNA sequences that cause reverse movement of the enzyme. Such backtracking involves extrusion of the RNA 3'-end into the pore, and can lead to transcriptional arrest. Escape from arrest requires cleavage of the extruded RNA with the help of TFIIS, which induces mRNA cleavage by enhancing the intrinsic nuclease activity of RNA polymerase (Pol) II, past template-encoded pause sites []. TFIIS extends from the polymerase surface via a pore to the internal active site. Two essential and invariant acidic residues in a TFIIS loop complement the Pol II active site and could position a metal ion and a water molecule for hydrolytic RNA cleavage. TFIIS also induces extensive structural changes in Pol II that would realign nucleic acids in the active centre. TFIIS is a protein of about 300 amino acids. It contains three regions: a variable N-terminal domain not required for TFIIS activity; a conserved central domain required for Pol II binding; and a conserved C-terminal C4-type zinc finger essential for RNA cleavage. The zinc finger folds in a conformation termed a zinc ribbon [] characterised by a three-stranded antiparallel beta-sheet and two beta-hairpins. A backbone model for Pol II-TFIIS complex was obtained from X-ray analysis. It shows that a beta hairpin protrudes from the zinc finger and complements the pol II active site []. Some viral proteins also contain the TFIIS zinc ribbon C-terminal domain. The Vaccinia virus protein, unlike its eukaryotic homologue, is an integral RNA polymerase subunit rather than a readily separable transcription factor []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding, 0006351 transcription, DNA-dependent; PDB: 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I 3I4M_I ....
Probab=20.02 E-value=34 Score=14.78 Aligned_cols=10 Identities=30% Similarity=1.142 Sum_probs=5.5
Q ss_pred ccCCcccccc
Q psy13123 101 FACETCGKLF 110 (129)
Q Consensus 101 ~~C~~C~~~f 110 (129)
|.|..||..|
T Consensus 29 y~C~~C~~~w 38 (39)
T PF01096_consen 29 YVCCNCGHRW 38 (39)
T ss_dssp EEESSSTEEE
T ss_pred EEeCCCCCee
Confidence 5566665543
Done!