Query psy370
Match_columns 111
No_of_seqs 105 out of 1485
Neff 10.3
Searched_HMMs 46136
Date Fri Aug 16 23:20:48 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy370.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/370hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2462|consensus 99.9 5.7E-23 1.2E-27 130.0 4.4 85 20-108 159-243 (279)
2 KOG2462|consensus 99.9 3.2E-22 6.8E-27 126.7 3.3 82 18-101 183-264 (279)
3 KOG3623|consensus 99.7 2.4E-17 5.1E-22 115.9 3.5 85 18-104 890-974 (1007)
4 KOG3576|consensus 99.6 7.1E-17 1.5E-21 98.9 0.2 86 18-105 113-198 (267)
5 KOG3623|consensus 99.5 2.3E-15 5E-20 106.1 0.6 83 18-102 236-331 (1007)
6 KOG3576|consensus 99.4 2.4E-14 5.1E-19 87.9 1.3 95 14-108 137-240 (267)
7 KOG1074|consensus 99.3 5.3E-13 1.2E-17 95.4 2.5 84 19-104 602-692 (958)
8 PHA00733 hypothetical protein 99.2 1.1E-11 2.4E-16 72.3 3.1 81 20-104 38-123 (128)
9 KOG3608|consensus 99.2 7.6E-12 1.6E-16 82.5 2.5 80 22-104 237-316 (467)
10 KOG3608|consensus 99.2 9.4E-12 2E-16 82.1 1.9 92 15-110 200-293 (467)
11 PHA02768 hypothetical protein; 99.1 7.4E-11 1.6E-15 58.3 2.1 41 51-95 6-46 (55)
12 PHA02768 hypothetical protein; 99.0 3.3E-10 7.1E-15 56.1 2.3 44 22-67 5-48 (55)
13 KOG1074|consensus 99.0 3.4E-10 7.3E-15 81.5 2.7 53 22-74 879-931 (958)
14 PLN03086 PRLI-interacting fact 98.9 5.2E-09 1.1E-13 73.7 7.0 84 13-103 444-537 (567)
15 PF13465 zf-H2C2_2: Zinc-finge 98.9 2.5E-09 5.3E-14 45.5 2.5 25 65-91 1-25 (26)
16 PLN03086 PRLI-interacting fact 98.8 9.3E-09 2E-13 72.5 5.5 79 21-105 477-565 (567)
17 PHA00733 hypothetical protein 98.8 1.5E-08 3.2E-13 59.2 5.4 56 17-74 68-123 (128)
18 PF13465 zf-H2C2_2: Zinc-finge 98.7 1.6E-08 3.5E-13 43.0 2.2 25 37-61 1-25 (26)
19 PHA00616 hypothetical protein 98.6 2.5E-08 5.4E-13 47.1 1.9 34 22-55 1-34 (44)
20 PHA00732 hypothetical protein 98.6 4.9E-08 1.1E-12 52.3 3.2 45 22-72 1-46 (79)
21 KOG3993|consensus 98.3 6.1E-08 1.3E-12 65.6 -0.6 89 20-108 265-384 (500)
22 PHA00732 hypothetical protein 98.3 6.9E-07 1.5E-11 47.9 2.9 52 50-109 1-53 (79)
23 PF05605 zf-Di19: Drought indu 98.2 2.3E-06 4.9E-11 42.6 3.4 51 51-104 3-53 (54)
24 PHA00616 hypothetical protein 98.2 7.7E-07 1.7E-11 42.1 1.4 34 50-85 1-34 (44)
25 PF00096 zf-C2H2: Zinc finger, 98.2 1.5E-06 3.2E-11 35.6 1.8 23 23-45 1-23 (23)
26 PF00096 zf-C2H2: Zinc finger, 98.2 5.3E-07 1.1E-11 37.0 0.3 22 81-102 1-22 (23)
27 PF13912 zf-C2H2_6: C2H2-type 98.1 1.7E-06 3.7E-11 36.8 1.6 26 80-105 1-26 (27)
28 PF13894 zf-C2H2_4: C2H2-type 98.0 1.6E-06 3.4E-11 35.6 0.8 24 81-104 1-24 (24)
29 PF05605 zf-Di19: Drought indu 98.0 3E-05 6.6E-10 38.5 4.5 50 22-74 2-53 (54)
30 COG5189 SFP1 Putative transcri 97.9 3.5E-06 7.5E-11 55.6 0.9 71 20-102 347-420 (423)
31 PF12756 zf-C2H2_2: C2H2 type 97.9 6E-06 1.3E-10 45.8 1.4 72 24-103 1-73 (100)
32 PF13912 zf-C2H2_6: C2H2-type 97.8 1.4E-05 3E-10 33.9 1.4 24 22-45 1-24 (27)
33 PF13894 zf-C2H2_4: C2H2-type 97.7 3.2E-05 6.9E-10 31.5 2.0 23 23-45 1-23 (24)
34 KOG3993|consensus 97.4 4.8E-05 1E-09 52.0 0.2 56 50-107 267-322 (500)
35 smart00355 ZnF_C2H2 zinc finge 97.3 0.00028 6.1E-09 29.0 2.5 23 23-45 1-23 (26)
36 smart00355 ZnF_C2H2 zinc finge 97.2 0.00013 2.7E-09 30.1 0.5 23 81-103 1-23 (26)
37 PRK04860 hypothetical protein; 97.1 0.00044 9.6E-09 42.0 2.3 39 50-94 119-157 (160)
38 PF12874 zf-met: Zinc-finger o 97.0 0.00042 9E-09 28.6 1.3 22 23-44 1-22 (25)
39 PF12874 zf-met: Zinc-finger o 96.9 0.00046 1E-08 28.5 0.9 22 81-102 1-22 (25)
40 PF12171 zf-C2H2_jaz: Zinc-fin 96.8 0.00065 1.4E-08 28.7 1.1 22 81-102 2-23 (27)
41 PF09237 GAGA: GAGA factor; I 96.7 0.0024 5.1E-08 31.1 2.7 22 50-71 24-45 (54)
42 PF13909 zf-H2C2_5: C2H2-type 96.7 0.00056 1.2E-08 28.0 0.4 23 81-104 1-23 (24)
43 PRK04860 hypothetical protein; 96.6 0.0013 2.9E-08 39.9 1.8 38 22-63 119-156 (160)
44 PF09237 GAGA: GAGA factor; I 96.3 0.011 2.4E-07 28.8 3.5 33 18-50 20-52 (54)
45 PF12171 zf-C2H2_jaz: Zinc-fin 96.3 0.0011 2.4E-08 28.0 0.0 21 23-43 2-22 (27)
46 PF13913 zf-C2HC_2: zinc-finge 96.1 0.0027 5.8E-08 26.4 0.9 21 81-102 3-23 (25)
47 smart00451 ZnF_U1 U1-like zinc 95.2 0.015 3.2E-07 25.8 1.5 23 80-102 3-25 (35)
48 COG4049 Uncharacterized protei 94.0 0.017 3.7E-07 28.6 0.2 28 77-104 14-41 (65)
49 PF12756 zf-C2H2_2: C2H2 type 93.6 0.1 2.2E-06 28.5 2.9 23 50-72 50-72 (100)
50 COG5048 FOG: Zn-finger [Genera 93.5 0.027 6E-07 38.4 0.6 55 50-106 289-349 (467)
51 KOG2186|consensus 93.3 0.055 1.2E-06 35.1 1.6 47 22-71 3-49 (276)
52 KOG2231|consensus 93.2 0.17 3.8E-06 37.4 4.1 85 23-108 100-210 (669)
53 cd00350 rubredoxin_like Rubred 92.1 0.071 1.5E-06 23.5 0.7 11 23-33 2-12 (33)
54 COG4049 Uncharacterized protei 91.8 0.11 2.4E-06 25.8 1.3 30 15-44 10-39 (65)
55 COG5048 FOG: Zn-finger [Genera 91.8 0.054 1.2E-06 37.0 0.2 62 21-84 288-355 (467)
56 COG5189 SFP1 Putative transcri 91.2 0.069 1.5E-06 36.0 0.3 22 20-41 396-417 (423)
57 PF09538 FYDLN_acid: Protein o 91.2 0.21 4.5E-06 28.4 2.1 29 24-63 11-39 (108)
58 cd00729 rubredoxin_SM Rubredox 90.7 0.16 3.5E-06 22.6 1.1 10 79-88 17-26 (34)
59 PRK06266 transcription initiat 90.0 0.21 4.5E-06 31.0 1.6 31 49-90 116-146 (178)
60 COG1592 Rubrerythrin [Energy p 89.3 0.25 5.4E-06 30.3 1.5 25 49-88 133-157 (166)
61 TIGR00373 conserved hypothetic 88.5 0.35 7.5E-06 29.4 1.8 36 45-91 104-139 (158)
62 KOG1146|consensus 88.2 0.16 3.5E-06 40.1 0.2 25 78-102 516-540 (1406)
63 KOG1146|consensus 87.8 0.49 1.1E-05 37.6 2.5 83 20-102 463-611 (1406)
64 PF09986 DUF2225: Uncharacteri 87.6 0.056 1.2E-06 34.4 -2.1 20 20-39 3-22 (214)
65 KOG2893|consensus 87.4 0.26 5.7E-06 32.0 0.8 32 24-59 12-43 (341)
66 smart00531 TFIIE Transcription 87.1 0.48 1E-05 28.4 1.8 41 46-92 95-135 (147)
67 PRK14890 putative Zn-ribbon RN 86.4 0.86 1.9E-05 23.0 2.1 10 79-88 47-56 (59)
68 KOG2893|consensus 86.1 0.2 4.4E-06 32.5 -0.2 39 53-97 13-51 (341)
69 smart00614 ZnF_BED BED zinc fi 85.3 0.64 1.4E-05 22.4 1.4 22 81-102 19-45 (50)
70 KOG2593|consensus 84.6 0.76 1.6E-05 32.3 2.0 38 18-58 124-161 (436)
71 KOG2186|consensus 84.6 0.73 1.6E-05 30.1 1.8 46 51-101 4-49 (276)
72 PF13719 zinc_ribbon_5: zinc-r 84.1 0.92 2E-05 20.5 1.5 33 52-91 4-36 (37)
73 COG2888 Predicted Zn-ribbon RN 84.0 1.4 3.1E-05 22.2 2.3 11 78-88 48-58 (61)
74 PF05290 Baculo_IE-1: Baculovi 83.4 0.48 1E-05 27.9 0.5 57 20-95 78-136 (140)
75 PF04959 ARS2: Arsenite-resist 83.2 0.37 8.1E-06 30.8 0.1 28 78-105 75-102 (214)
76 TIGR02098 MJ0042_CXXC MJ0042 f 82.8 0.76 1.7E-05 20.6 1.0 11 80-90 25-35 (38)
77 KOG4167|consensus 82.0 0.21 4.5E-06 37.3 -1.6 27 81-107 793-819 (907)
78 PF13717 zinc_ribbon_4: zinc-r 81.9 1 2.3E-05 20.2 1.3 32 52-90 4-35 (36)
79 PF13878 zf-C2H2_3: zinc-finge 81.7 0.65 1.4E-05 21.6 0.5 24 81-104 14-39 (41)
80 TIGR02300 FYDLN_acid conserved 80.1 1.3 2.8E-05 25.9 1.5 29 24-63 11-39 (129)
81 PRK00464 nrdR transcriptional 80.1 0.41 8.9E-06 29.0 -0.6 12 51-62 29-40 (154)
82 PF11931 DUF3449: Domain of un 80.1 0.55 1.2E-05 29.6 0.0 35 9-43 88-123 (196)
83 KOG4167|consensus 79.8 0.94 2E-05 34.1 1.1 27 20-46 790-816 (907)
84 COG1198 PriA Primosomal protei 79.0 0.51 1.1E-05 35.5 -0.4 13 77-89 472-484 (730)
85 PF02892 zf-BED: BED zinc fing 78.8 1.2 2.5E-05 20.8 0.9 25 78-102 14-42 (45)
86 COG5236 Uncharacterized conser 78.4 1 2.2E-05 31.0 0.9 26 82-107 222-247 (493)
87 smart00734 ZnF_Rad18 Rad18-lik 78.0 2.8 6.2E-05 17.3 1.9 18 24-42 3-20 (26)
88 PRK09678 DNA-binding transcrip 78.0 0.75 1.6E-05 24.2 0.1 18 77-94 24-43 (72)
89 COG1996 RPC10 DNA-directed RNA 76.8 1.7 3.7E-05 21.1 1.2 12 49-60 5-16 (49)
90 PF12013 DUF3505: Protein of u 75.3 1.7 3.7E-05 24.5 1.1 25 81-105 81-109 (109)
91 TIGR00622 ssl1 transcription f 74.8 4.6 0.0001 23.2 2.7 79 21-104 14-105 (112)
92 smart00659 RPOLCX RNA polymera 74.2 1.8 4E-05 20.4 0.9 11 80-90 19-29 (44)
93 KOG4173|consensus 73.2 1.8 3.9E-05 27.6 0.9 77 23-102 80-168 (253)
94 PF10571 UPF0547: Uncharacteri 72.0 2.1 4.5E-05 17.8 0.7 9 82-90 16-24 (26)
95 PF07754 DUF1610: Domain of un 70.7 2.5 5.5E-05 17.2 0.8 11 78-88 14-24 (24)
96 KOG2636|consensus 70.4 2.8 6.2E-05 29.8 1.4 35 9-43 388-423 (497)
97 PF08790 zf-LYAR: LYAR-type C2 69.9 2.9 6.4E-05 17.7 0.9 20 81-101 1-20 (28)
98 PF09723 Zn-ribbon_8: Zinc rib 69.2 2.7 5.8E-05 19.5 0.8 17 81-97 6-22 (42)
99 smart00834 CxxC_CXXC_SSSS Puta 68.6 2.9 6.3E-05 18.8 0.9 14 81-94 6-19 (41)
100 smart00154 ZnF_AN1 AN1-like Zi 68.3 3.3 7.1E-05 18.9 1.0 14 80-93 12-25 (39)
101 KOG2231|consensus 68.1 6.4 0.00014 29.6 2.9 47 52-104 184-236 (669)
102 KOG2785|consensus 67.2 6.4 0.00014 27.5 2.6 73 22-101 166-241 (390)
103 PF06524 NOA36: NOA36 protein; 66.5 3.5 7.6E-05 27.3 1.2 86 18-104 138-233 (314)
104 PF02176 zf-TRAF: TRAF-type zi 66.3 4.7 0.0001 19.8 1.5 42 50-93 9-55 (60)
105 PF04959 ARS2: Arsenite-resist 65.7 5 0.00011 25.8 1.8 28 19-46 74-102 (214)
106 PRK03824 hypA hydrogenase nick 65.5 2 4.2E-05 25.5 -0.1 13 50-62 70-82 (135)
107 PHA00626 hypothetical protein 65.4 3.8 8.3E-05 20.4 1.0 16 79-94 22-37 (59)
108 KOG2785|consensus 65.1 15 0.00033 25.7 4.0 24 49-72 216-242 (390)
109 PLN03238 probable histone acet 64.4 5 0.00011 26.9 1.6 23 49-71 47-69 (290)
110 PF15269 zf-C2H2_7: Zinc-finge 62.5 16 0.00035 17.3 3.2 21 23-43 21-41 (54)
111 COG3364 Zn-ribbon containing p 62.0 5.4 0.00012 22.5 1.2 15 22-36 2-16 (112)
112 PF12907 zf-met2: Zinc-binding 62.0 3.3 7.1E-05 19.2 0.3 25 82-106 3-30 (40)
113 TIGR02605 CxxC_CxxC_SSSS putat 60.6 4.8 0.0001 19.3 0.8 13 81-93 6-18 (52)
114 smart00440 ZnF_C2C2 C2C2 Zinc 60.5 1.1 2.4E-05 20.6 -1.4 12 80-91 28-39 (40)
115 PF01428 zf-AN1: AN1-like Zinc 60.1 4.2 9E-05 18.9 0.5 15 79-93 12-26 (43)
116 PRK14873 primosome assembly pr 59.9 1.7 3.7E-05 32.5 -1.2 9 80-88 422-430 (665)
117 PF01363 FYVE: FYVE zinc finge 59.4 7.5 0.00016 19.8 1.5 9 24-32 11-19 (69)
118 PF13451 zf-trcl: Probable zin 57.9 6.2 0.00013 19.1 0.9 17 78-94 2-18 (49)
119 TIGR00595 priA primosomal prot 56.6 2.4 5.3E-05 30.6 -0.9 9 80-88 253-261 (505)
120 PLN03239 histone acetyltransfe 56.3 6.4 0.00014 27.2 1.1 24 78-101 104-127 (351)
121 COG0068 HypF Hydrogenase matur 56.0 1.8 3.9E-05 32.6 -1.6 60 21-89 121-182 (750)
122 PF08271 TF_Zn_Ribbon: TFIIB z 56.0 3.7 8.1E-05 19.0 -0.0 12 81-92 20-31 (43)
123 PF10013 DUF2256: Uncharacteri 55.4 5.1 0.00011 18.7 0.4 13 82-94 10-22 (42)
124 PTZ00064 histone acetyltransfe 55.3 7.4 0.00016 28.3 1.3 33 78-110 278-314 (552)
125 KOG2482|consensus 55.0 5.7 0.00012 27.4 0.7 22 80-101 195-216 (423)
126 PF10537 WAC_Acf1_DNA_bd: ATP- 54.9 20 0.00044 20.2 2.8 39 20-59 1-39 (102)
127 PF08274 PhnA_Zn_Ribbon: PhnA 54.8 7 0.00015 16.8 0.8 11 79-89 18-28 (30)
128 KOG3408|consensus 54.8 6.9 0.00015 22.8 0.9 25 78-102 55-79 (129)
129 PLN02294 cytochrome c oxidase 54.7 7.8 0.00017 24.0 1.2 17 77-93 138-154 (174)
130 COG3091 SprT Zn-dependent meta 54.6 6.2 0.00014 23.9 0.8 35 49-90 116-150 (156)
131 PLN00104 MYST -like histone ac 54.6 7.1 0.00015 28.0 1.1 24 78-101 196-219 (450)
132 KOG0320|consensus 53.9 12 0.00027 23.4 2.0 56 18-95 127-182 (187)
133 KOG1842|consensus 53.4 5.1 0.00011 28.6 0.3 28 80-107 15-42 (505)
134 cd00924 Cyt_c_Oxidase_Vb Cytoc 53.2 8.7 0.00019 21.5 1.2 22 69-93 71-92 (97)
135 COG1571 Predicted DNA-binding 53.1 8.8 0.00019 27.3 1.4 13 50-62 367-379 (421)
136 PF05443 ROS_MUCR: ROS/MUCR tr 53.1 11 0.00023 22.4 1.5 23 22-47 72-94 (132)
137 KOG2747|consensus 52.4 6.3 0.00014 27.7 0.6 33 78-110 156-192 (396)
138 TIGR00100 hypA hydrogenase nic 52.1 8.7 0.00019 22.0 1.1 12 51-62 71-82 (115)
139 PF12760 Zn_Tnp_IS1595: Transp 51.6 26 0.00056 16.4 2.7 10 79-88 36-45 (46)
140 PF10276 zf-CHCC: Zinc-finger 51.4 7.8 0.00017 17.9 0.7 12 79-90 28-39 (40)
141 KOG0978|consensus 51.4 6.1 0.00013 29.8 0.5 19 79-97 677-695 (698)
142 PRK12380 hydrogenase nickel in 51.0 9 0.00019 21.9 1.0 12 51-62 71-82 (113)
143 PRK00398 rpoP DNA-directed RNA 50.1 9.8 0.00021 17.8 0.9 29 50-91 3-32 (46)
144 PF08209 Sgf11: Sgf11 (transcr 50.0 16 0.00035 16.1 1.5 20 80-100 4-23 (33)
145 KOG0717|consensus 49.4 10 0.00023 27.3 1.3 22 23-44 293-314 (508)
146 KOG3214|consensus 49.4 7.1 0.00015 21.9 0.4 43 18-64 19-61 (109)
147 PF01927 Mut7-C: Mut7-C RNAse 48.5 16 0.00034 21.9 1.8 46 23-68 92-142 (147)
148 PF07975 C1_4: TFIIH C1-like d 48.0 9.9 0.00022 18.6 0.8 25 79-103 20-44 (51)
149 PRK00564 hypA hydrogenase nick 47.1 12 0.00025 21.6 1.1 12 51-62 72-83 (117)
150 COG1675 TFA1 Transcription ini 46.9 17 0.00037 22.7 1.9 10 81-90 133-142 (176)
151 KOG2593|consensus 45.7 35 0.00077 24.4 3.4 40 46-90 124-163 (436)
152 PF01155 HypA: Hydrogenase exp 44.5 13 0.00028 21.2 1.0 12 23-34 71-82 (113)
153 PF06397 Desulfoferrod_N: Desu 43.5 9 0.0002 17.3 0.2 12 21-32 5-16 (36)
154 COG3357 Predicted transcriptio 43.3 10 0.00022 20.9 0.4 14 79-92 57-70 (97)
155 COG1773 Rubredoxin [Energy pro 43.1 13 0.00028 18.5 0.8 12 80-91 3-14 (55)
156 cd00065 FYVE FYVE domain; Zinc 43.0 21 0.00044 17.2 1.5 14 49-62 17-30 (57)
157 PF04423 Rad50_zn_hook: Rad50 43.0 9.3 0.0002 18.6 0.2 13 24-36 22-34 (54)
158 COG3677 Transposase and inacti 41.5 14 0.0003 21.8 0.8 18 77-94 50-67 (129)
159 COG4338 Uncharacterized protei 41.5 12 0.00026 18.1 0.5 16 52-67 14-29 (54)
160 PF07282 OrfB_Zn_ribbon: Putat 41.2 46 0.00099 16.8 2.7 17 77-93 43-59 (69)
161 PRK03681 hypA hydrogenase nick 40.6 16 0.00036 20.9 1.0 10 51-60 71-80 (114)
162 PRK05978 hypothetical protein; 40.6 14 0.0003 22.4 0.8 8 23-30 34-41 (148)
163 KOG2907|consensus 40.1 21 0.00045 20.6 1.4 39 51-92 75-114 (116)
164 PRK04023 DNA polymerase II lar 40.0 26 0.00057 28.0 2.2 10 22-31 626-635 (1121)
165 COG1594 RPB9 DNA-directed RNA 39.9 8 0.00017 22.2 -0.3 40 51-92 73-112 (113)
166 smart00064 FYVE Protein presen 39.5 23 0.0005 17.8 1.4 27 24-62 12-38 (68)
167 TIGR00515 accD acetyl-CoA carb 39.3 22 0.00048 24.0 1.6 33 23-64 27-59 (285)
168 COG4391 Uncharacterized protei 39.0 15 0.00031 18.7 0.6 42 43-91 17-59 (62)
169 COG4530 Uncharacterized protei 38.9 15 0.00032 21.1 0.7 16 78-93 24-39 (129)
170 PHA02998 RNA polymerase subuni 38.5 5.8 0.00013 24.7 -1.1 41 51-93 144-184 (195)
171 PF09845 DUF2072: Zn-ribbon co 38.3 17 0.00036 21.6 0.8 15 22-36 1-15 (131)
172 PRK05580 primosome assembly pr 38.2 7.3 0.00016 29.4 -0.8 9 80-88 421-429 (679)
173 COG2331 Uncharacterized protei 38.1 6.3 0.00014 21.0 -0.8 11 22-32 12-22 (82)
174 COG4888 Uncharacterized Zn rib 37.7 34 0.00073 19.3 1.9 39 18-60 18-56 (104)
175 PF14353 CpXC: CpXC protein 37.7 11 0.00023 21.9 -0.0 17 80-96 38-54 (128)
176 COG5216 Uncharacterized conser 37.1 21 0.00046 18.0 1.0 12 77-88 41-52 (67)
177 KOG2482|consensus 36.7 27 0.00058 24.3 1.7 24 22-45 195-218 (423)
178 PF01096 TFIIS_C: Transcriptio 36.1 18 0.00038 16.4 0.6 10 81-90 29-38 (39)
179 COG1997 RPL43A Ribosomal prote 35.6 21 0.00046 19.6 0.9 33 49-93 34-66 (89)
180 COG5112 UFD2 U1-like Zn-finger 35.5 16 0.00034 20.8 0.4 22 80-101 55-76 (126)
181 PRK12496 hypothetical protein; 35.4 29 0.00063 21.3 1.6 11 51-61 128-138 (164)
182 PTZ00043 cytochrome c oxidase 35.1 21 0.00046 23.3 1.0 17 77-93 178-194 (268)
183 COG1326 Uncharacterized archae 34.9 50 0.0011 21.0 2.5 12 79-90 29-40 (201)
184 KOG1280|consensus 34.2 59 0.0013 22.7 3.0 38 20-57 77-116 (381)
185 CHL00174 accD acetyl-CoA carbo 33.9 31 0.00068 23.4 1.7 34 23-65 39-72 (296)
186 COG5236 Uncharacterized conser 33.8 26 0.00057 24.5 1.3 46 25-71 223-272 (493)
187 PF03604 DNA_RNApol_7kD: DNA d 33.5 30 0.00066 15.0 1.1 10 82-91 2-11 (32)
188 PRK05654 acetyl-CoA carboxylas 33.4 29 0.00063 23.5 1.5 33 23-64 28-60 (292)
189 PF01215 COX5B: Cytochrome c o 33.3 18 0.00039 21.6 0.4 16 78-93 110-125 (136)
190 PF02748 PyrI_C: Aspartate car 33.0 25 0.00055 17.2 0.9 17 77-93 32-48 (52)
191 PF04780 DUF629: Protein of un 32.7 37 0.0008 24.7 1.9 25 23-47 58-83 (466)
192 KOG1994|consensus 32.3 42 0.00091 22.0 2.0 21 80-100 239-259 (268)
193 PF04780 DUF629: Protein of un 32.3 22 0.00049 25.7 0.8 25 48-72 55-79 (466)
194 KOG1842|consensus 32.0 34 0.00074 24.7 1.7 29 20-48 13-42 (505)
195 PF13824 zf-Mss51: Zinc-finger 31.8 27 0.00058 17.4 0.8 17 77-93 11-27 (55)
196 TIGR00244 transcriptional regu 31.7 22 0.00048 21.5 0.6 13 81-93 29-41 (147)
197 TIGR01031 rpmF_bact ribosomal 31.5 50 0.0011 16.3 1.8 8 23-30 27-34 (55)
198 PTZ00303 phosphatidylinositol 30.4 34 0.00073 26.9 1.5 32 24-62 462-493 (1374)
199 PRK04351 hypothetical protein; 30.2 32 0.00069 20.8 1.2 14 78-91 130-143 (149)
200 PF00301 Rubredoxin: Rubredoxi 30.2 27 0.00059 16.7 0.7 12 81-92 2-13 (47)
201 PF01286 XPA_N: XPA protein N- 30.2 26 0.00056 15.6 0.6 14 81-94 4-17 (34)
202 PF04606 Ogr_Delta: Ogr/Delta- 29.9 13 0.00028 17.6 -0.5 16 78-93 23-40 (47)
203 PF01780 Ribosomal_L37ae: Ribo 29.8 23 0.00051 19.5 0.5 32 49-92 34-65 (90)
204 PTZ00448 hypothetical protein; 29.5 50 0.0011 23.2 2.1 23 22-44 314-336 (373)
205 KOG4477|consensus 29.3 54 0.0012 20.7 2.0 27 17-57 19-45 (228)
206 PF12230 PRP21_like_P: Pre-mRN 29.3 18 0.00039 23.3 0.0 25 79-104 167-191 (229)
207 PF05191 ADK_lid: Adenylate ki 29.2 19 0.00042 16.1 0.1 10 24-33 3-12 (36)
208 PF11672 DUF3268: Protein of u 29.0 18 0.00038 20.5 -0.1 10 22-31 2-11 (102)
209 COG5188 PRP9 Splicing factor 3 28.9 42 0.0009 23.6 1.6 33 11-43 363-396 (470)
210 COG5027 SAS2 Histone acetyltra 28.5 28 0.00061 24.3 0.8 25 79-103 157-181 (395)
211 TIGR00280 L37a ribosomal prote 28.2 32 0.0007 19.0 0.8 33 49-93 34-66 (91)
212 smart00661 RPOL9 RNA polymeras 28.1 27 0.00059 16.4 0.5 14 80-93 20-33 (52)
213 TIGR03831 YgiT_finger YgiT-typ 28.0 27 0.00059 15.8 0.5 13 22-34 32-44 (46)
214 PRK00420 hypothetical protein; 27.9 26 0.00056 20.2 0.5 8 51-58 41-48 (112)
215 cd00730 rubredoxin Rubredoxin; 27.6 28 0.0006 16.9 0.5 11 23-33 2-12 (50)
216 COG4640 Predicted membrane pro 27.6 40 0.00087 24.0 1.4 26 15-40 8-33 (465)
217 TIGR00686 phnA alkylphosphonat 27.5 40 0.00086 19.3 1.2 11 50-60 19-29 (109)
218 PRK00762 hypA hydrogenase nick 27.4 21 0.00046 20.7 0.1 11 51-62 71-81 (124)
219 PTZ00255 60S ribosomal protein 27.2 35 0.00075 18.9 0.9 33 49-93 35-67 (90)
220 PF14787 zf-CCHC_5: GAG-polypr 26.7 38 0.00082 15.3 0.8 14 82-95 4-17 (36)
221 TIGR01206 lysW lysine biosynth 26.6 31 0.00067 17.0 0.6 13 81-93 3-15 (54)
222 KOG2071|consensus 26.6 35 0.00076 25.4 1.0 27 78-104 416-442 (579)
223 COG1327 Predicted transcriptio 26.5 29 0.00063 21.2 0.5 13 81-93 29-41 (156)
224 PF07295 DUF1451: Protein of u 26.3 19 0.00041 21.7 -0.3 11 49-59 111-121 (146)
225 PF11789 zf-Nse: Zinc-finger o 26.1 36 0.00078 16.9 0.8 12 51-62 25-36 (57)
226 COG4847 Uncharacterized protei 25.9 33 0.00071 19.2 0.6 13 77-89 3-15 (103)
227 PF14446 Prok-RING_1: Prokaryo 25.9 23 0.0005 17.5 0.0 14 81-94 6-19 (54)
228 PRK03976 rpl37ae 50S ribosomal 25.9 38 0.00082 18.7 0.9 33 49-93 35-67 (90)
229 PF13821 DUF4187: Domain of un 25.8 84 0.0018 15.5 2.0 17 81-97 28-44 (55)
230 TIGR00319 desulf_FeS4 desulfof 25.7 42 0.0009 14.5 0.9 12 80-91 7-18 (34)
231 cd00974 DSRD Desulforedoxin (D 25.2 43 0.00093 14.4 0.9 12 80-91 4-15 (34)
232 COG0675 Transposase and inacti 25.0 49 0.0011 22.1 1.5 15 79-93 321-335 (364)
233 PRK14714 DNA polymerase II lar 24.6 74 0.0016 26.3 2.5 9 23-31 668-676 (1337)
234 smart00731 SprT SprT homologue 24.5 44 0.00096 19.8 1.1 9 81-89 134-142 (146)
235 KOG4727|consensus 24.3 46 0.001 20.8 1.1 22 22-43 75-96 (193)
236 PF08792 A2L_zn_ribbon: A2L zi 24.2 44 0.00096 14.6 0.8 11 81-91 22-32 (33)
237 PRK05452 anaerobic nitric oxid 24.2 44 0.00095 24.2 1.2 17 18-34 421-437 (479)
238 PLN02748 tRNA dimethylallyltra 24.1 65 0.0014 23.5 2.0 24 49-72 417-441 (468)
239 PF11023 DUF2614: Protein of u 23.5 33 0.00071 19.8 0.3 12 21-32 68-79 (114)
240 COG3024 Uncharacterized protei 23.1 43 0.00094 17.2 0.7 13 81-93 8-20 (65)
241 TIGR01384 TFS_arch transcripti 23.0 13 0.00027 20.7 -1.4 14 21-34 15-28 (104)
242 KOG1701|consensus 22.9 17 0.00036 26.0 -1.1 41 24-66 276-318 (468)
243 PF10263 SprT-like: SprT-like 22.9 28 0.00061 20.7 -0.0 11 80-90 143-153 (157)
244 TIGR00155 pqiA_fam integral me 22.7 92 0.002 22.2 2.5 10 23-32 14-23 (403)
245 TIGR03829 YokU_near_AblA uncha 22.7 67 0.0015 17.7 1.4 18 22-39 35-52 (89)
246 KOG1940|consensus 22.6 83 0.0018 21.2 2.1 18 23-41 197-214 (276)
247 PF14255 Cys_rich_CPXG: Cystei 22.6 41 0.00088 16.5 0.6 6 53-58 3-8 (52)
248 PF01844 HNH: HNH endonuclease 22.6 22 0.00047 16.2 -0.4 11 83-93 1-11 (47)
249 PF06220 zf-U1: U1 zinc finger 22.5 70 0.0015 14.4 1.3 14 80-93 3-16 (38)
250 COG4306 Uncharacterized protei 22.4 28 0.0006 20.5 -0.1 16 48-63 66-81 (160)
251 PF13453 zf-TFIIB: Transcripti 22.2 67 0.0015 14.5 1.2 18 80-97 19-36 (41)
252 PRK10220 hypothetical protein; 21.9 36 0.00079 19.5 0.3 29 24-63 5-33 (111)
253 PF14354 Lar_restr_allev: Rest 21.7 51 0.0011 16.2 0.8 6 83-88 32-37 (61)
254 PF02891 zf-MIZ: MIZ/SP-RING z 21.5 40 0.00087 16.2 0.4 9 22-30 41-49 (50)
255 PF14311 DUF4379: Domain of un 21.5 58 0.0013 15.7 1.0 16 80-95 28-43 (55)
256 KOG4118|consensus 20.9 37 0.0008 17.6 0.2 24 81-104 39-62 (74)
257 KOG0782|consensus 20.8 9.2 0.0002 28.5 -2.7 51 37-94 240-290 (1004)
258 KOG1088|consensus 20.8 68 0.0015 18.7 1.3 19 77-95 95-113 (124)
259 PRK01343 zinc-binding protein; 20.7 48 0.001 16.6 0.6 12 22-33 9-20 (57)
260 PRK06260 threonine synthase; V 20.7 72 0.0016 22.4 1.6 29 23-63 4-32 (397)
261 KOG3014|consensus 20.5 41 0.00088 22.3 0.4 23 82-104 39-63 (257)
262 COG1655 Uncharacterized protei 20.5 37 0.0008 22.3 0.2 24 48-71 17-40 (267)
263 KOG3352|consensus 20.5 49 0.0011 20.1 0.7 16 78-93 131-146 (153)
264 COG0846 SIR2 NAD-dependent pro 20.4 70 0.0015 21.2 1.5 13 49-61 121-133 (250)
265 PF10083 DUF2321: Uncharacteri 20.4 36 0.00078 20.8 0.1 18 77-94 65-82 (158)
No 1
>KOG2462|consensus
Probab=99.87 E-value=5.7e-23 Score=130.04 Aligned_cols=85 Identities=21% Similarity=0.461 Sum_probs=74.7
Q ss_pred cCcccCCCcccccCCHHHHHHHHHHcCCCCCccccccCcccCCHHHHHHHHHhccCCCCCceecCCCccccccchhHHhh
Q psy370 20 FVASQCPVCKKIYTDQQLFQNHLETHDNEMDYSCEHCDMQFNCKSDMRKHVHSHLSMEERGFVCEICGHVVDEMPVATQS 99 (111)
Q Consensus 20 ~~~~~c~~C~~~f~~~~~l~~h~~~h~~~~~~~c~~c~~~f~~~~~l~~h~~~h~~~~~~~~~C~~C~~~~~~~~~l~~h 99 (111)
.+.+.|++|++.|.....|..|+++|+ .+++|.+||+.|.+++-|+.|+|.|+ |||||.|+.|++.|..++.|+-|
T Consensus 159 ~ka~~C~~C~K~YvSmpALkMHirTH~--l~c~C~iCGKaFSRPWLLQGHiRTHT--GEKPF~C~hC~kAFADRSNLRAH 234 (279)
T KOG2462|consen 159 KKAFSCKYCGKVYVSMPALKMHIRTHT--LPCECGICGKAFSRPWLLQGHIRTHT--GEKPFSCPHCGKAFADRSNLRAH 234 (279)
T ss_pred cccccCCCCCceeeehHHHhhHhhccC--CCcccccccccccchHHhhccccccc--CCCCccCCcccchhcchHHHHHH
Confidence 667889999999999989999999887 68899999999999999999999998 89999999999999999999999
Q ss_pred ccccCcccc
Q psy370 100 SKYPGQQNQ 108 (111)
Q Consensus 100 ~~~~~~~~~ 108 (111)
+.+|-+..+
T Consensus 235 mQTHS~~K~ 243 (279)
T KOG2462|consen 235 MQTHSDVKK 243 (279)
T ss_pred HHhhcCCcc
Confidence 988876654
No 2
>KOG2462|consensus
Probab=99.85 E-value=3.2e-22 Score=126.70 Aligned_cols=82 Identities=28% Similarity=0.619 Sum_probs=77.4
Q ss_pred cccCcccCCCcccccCCHHHHHHHHHHcCCCCCccccccCcccCCHHHHHHHHHhccCCCCCceecCCCccccccchhHH
Q psy370 18 TIFVASQCPVCKKIYTDQQLFQNHLETHDNEMDYSCEHCDMQFNCKSDMRKHVHSHLSMEERGFVCEICGHVVDEMPVAT 97 (111)
Q Consensus 18 ~~~~~~~c~~C~~~f~~~~~l~~h~~~h~~~~~~~c~~c~~~f~~~~~l~~h~~~h~~~~~~~~~C~~C~~~~~~~~~l~ 97 (111)
|..-++.|.+||+.|...=.|+.|+|+|+||+||.|..|+++|...++|.-||+.|. +.|+|.|..|+|+|...+.|.
T Consensus 183 TH~l~c~C~iCGKaFSRPWLLQGHiRTHTGEKPF~C~hC~kAFADRSNLRAHmQTHS--~~K~~qC~~C~KsFsl~SyLn 260 (279)
T KOG2462|consen 183 THTLPCECGICGKAFSRPWLLQGHIRTHTGEKPFSCPHCGKAFADRSNLRAHMQTHS--DVKKHQCPRCGKSFALKSYLN 260 (279)
T ss_pred ccCCCcccccccccccchHHhhcccccccCCCCccCCcccchhcchHHHHHHHHhhc--CCccccCcchhhHHHHHHHHH
Confidence 334589999999999999999999999999999999999999999999999999998 889999999999999999999
Q ss_pred hhcc
Q psy370 98 QSSK 101 (111)
Q Consensus 98 ~h~~ 101 (111)
+|.-
T Consensus 261 KH~E 264 (279)
T KOG2462|consen 261 KHSE 264 (279)
T ss_pred Hhhh
Confidence 9974
No 3
>KOG3623|consensus
Probab=99.68 E-value=2.4e-17 Score=115.92 Aligned_cols=85 Identities=22% Similarity=0.364 Sum_probs=80.1
Q ss_pred cccCcccCCCcccccCCHHHHHHHHHHcCCCCCccccccCcccCCHHHHHHHHHhccCCCCCceecCCCccccccchhHH
Q psy370 18 TIFVASQCPVCKKIYTDQQLFQNHLETHDNEMDYSCEHCDMQFNCKSDMRKHVHSHLSMEERGFVCEICGHVVDEMPVAT 97 (111)
Q Consensus 18 ~~~~~~~c~~C~~~f~~~~~l~~h~~~h~~~~~~~c~~c~~~f~~~~~l~~h~~~h~~~~~~~~~C~~C~~~~~~~~~l~ 97 (111)
+.+..|-|..|+++|-..+.|.+|.--|+|.+||.|.+|.++|..+..|..|+|.|. |||||.|..|+|+|+.+....
T Consensus 890 te~gmyaCDqCDK~FqKqSSLaRHKYEHsGqRPyqC~iCkKAFKHKHHLtEHkRLHS--GEKPfQCdKClKRFSHSGSYS 967 (1007)
T KOG3623|consen 890 TEDGMYACDQCDKAFQKQSSLARHKYEHSGQRPYQCIICKKAFKHKHHLTEHKRLHS--GEKPFQCDKCLKRFSHSGSYS 967 (1007)
T ss_pred CccccchHHHHHHHHHhhHHHHHhhhhhcCCCCcccchhhHhhhhhhhhhhhhhhcc--CCCcchhhhhhhhcccccchH
Confidence 556789999999999999999999999999999999999999999999999999998 999999999999999999999
Q ss_pred hhccccC
Q psy370 98 QSSKYPG 104 (111)
Q Consensus 98 ~h~~~~~ 104 (111)
+||.-+.
T Consensus 968 QHMNHRY 974 (1007)
T KOG3623|consen 968 QHMNHRY 974 (1007)
T ss_pred hhhccch
Confidence 9996443
No 4
>KOG3576|consensus
Probab=99.61 E-value=7.1e-17 Score=98.86 Aligned_cols=86 Identities=22% Similarity=0.419 Sum_probs=79.3
Q ss_pred cccCcccCCCcccccCCHHHHHHHHHHcCCCCCccccccCcccCCHHHHHHHHHhccCCCCCceecCCCccccccchhHH
Q psy370 18 TIFVASQCPVCKKIYTDQQLFQNHLETHDNEMDYSCEHCDMQFNCKSDMRKHVHSHLSMEERGFVCEICGHVVDEMPVAT 97 (111)
Q Consensus 18 ~~~~~~~c~~C~~~f~~~~~l~~h~~~h~~~~~~~c~~c~~~f~~~~~l~~h~~~h~~~~~~~~~C~~C~~~~~~~~~l~ 97 (111)
.+...|.|.+|++.|.-...|..|++.|...+.+.|..||+.|...-.|..|+|.|+ |-+||+|..|++.|+.+-.|.
T Consensus 113 sd~d~ftCrvCgK~F~lQRmlnrh~kch~~vkr~lct~cgkgfndtfdlkrh~rtht--gvrpykc~~c~kaftqrcsle 190 (267)
T KOG3576|consen 113 SDQDSFTCRVCGKKFGLQRMLNRHLKCHSDVKRHLCTFCGKGFNDTFDLKRHTRTHT--GVRPYKCSLCEKAFTQRCSLE 190 (267)
T ss_pred CCCCeeeeehhhhhhhHHHHHHHHhhhccHHHHHHHhhccCcccchhhhhhhhcccc--CccccchhhhhHHHHhhccHH
Confidence 346679999999999999999999999999999999999999999999999999998 899999999999999999999
Q ss_pred hhccccCc
Q psy370 98 QSSKYPGQ 105 (111)
Q Consensus 98 ~h~~~~~~ 105 (111)
.|.+.-|+
T Consensus 191 shl~kvhg 198 (267)
T KOG3576|consen 191 SHLKKVHG 198 (267)
T ss_pred HHHHHHcC
Confidence 99875554
No 5
>KOG3623|consensus
Probab=99.51 E-value=2.3e-15 Score=106.11 Aligned_cols=83 Identities=17% Similarity=0.403 Sum_probs=75.0
Q ss_pred cccCcccCCCcccccCCHHHHHHHHHHcCC-------------CCCccccccCcccCCHHHHHHHHHhccCCCCCceecC
Q psy370 18 TIFVASQCPVCKKIYTDQQLFQNHLETHDN-------------EMDYSCEHCDMQFNCKSDMRKHVHSHLSMEERGFVCE 84 (111)
Q Consensus 18 ~~~~~~~c~~C~~~f~~~~~l~~h~~~h~~-------------~~~~~c~~c~~~f~~~~~l~~h~~~h~~~~~~~~~C~ 84 (111)
-.+..|.|..|..+|.....|.+|+.+|.. .+-|+|..||++|..+..|..|+|+|. |||||+|+
T Consensus 236 kne~nfsC~lCsytFAyRtQLErhm~~hkpg~dqa~sltqsa~lRKFKCtECgKAFKfKHHLKEHlRIHS--GEKPfeCp 313 (1007)
T KOG3623|consen 236 KNEPNFSCMLCSYTFAYRTQLERHMQLHKPGGDQAISLTQSALLRKFKCTECGKAFKFKHHLKEHLRIHS--GEKPFECP 313 (1007)
T ss_pred hCCCCCcchhhhhhhhhHHHHHHHHHhhcCCCcccccccchhhhccccccccchhhhhHHHHHhhheeec--CCCCcCCc
Confidence 446678999999999999999999988752 255999999999999999999999998 99999999
Q ss_pred CCccccccchhHHhhccc
Q psy370 85 ICGHVVDEMPVATQSSKY 102 (111)
Q Consensus 85 ~C~~~~~~~~~l~~h~~~ 102 (111)
.|+|+|+.+..+.+||..
T Consensus 314 nCkKRFSHSGSySSHmSS 331 (1007)
T KOG3623|consen 314 NCKKRFSHSGSYSSHMSS 331 (1007)
T ss_pred ccccccccCCcccccccc
Confidence 999999999999999853
No 6
>KOG3576|consensus
Probab=99.44 E-value=2.4e-14 Score=87.90 Aligned_cols=95 Identities=20% Similarity=0.349 Sum_probs=82.3
Q ss_pred CCCccccCcccCCCcccccCCHHHHHHHHHHcCCCCCccccccCcccCCHHHHHHHHHhccC---------CCCCceecC
Q psy370 14 PGSYTIFVASQCPVCKKIYTDQQLFQNHLETHDNEMDYSCEHCDMQFNCKSDMRKHVHSHLS---------MEERGFVCE 84 (111)
Q Consensus 14 ~~~~~~~~~~~c~~C~~~f~~~~~l~~h~~~h~~~~~~~c~~c~~~f~~~~~l~~h~~~h~~---------~~~~~~~C~ 84 (111)
.+-|+..+.|-|..||+.|.+.-+|..|.++|+|.+||.|..|+++|...-+|..|++.=++ +.++.|.|+
T Consensus 137 ~kch~~vkr~lct~cgkgfndtfdlkrh~rthtgvrpykc~~c~kaftqrcsleshl~kvhgv~~~yaykerr~kl~vce 216 (267)
T KOG3576|consen 137 LKCHSDVKRHLCTFCGKGFNDTFDLKRHTRTHTGVRPYKCSLCEKAFTQRCSLESHLKKVHGVQHQYAYKERRAKLYVCE 216 (267)
T ss_pred hhhccHHHHHHHhhccCcccchhhhhhhhccccCccccchhhhhHHHHhhccHHHHHHHHcCchHHHHHHHhhhheeeec
Confidence 34567788899999999999999999999999999999999999999999999988774322 245779999
Q ss_pred CCccccccchhHHhhccccCcccc
Q psy370 85 ICGHVVDEMPVATQSSKYPGQQNQ 108 (111)
Q Consensus 85 ~C~~~~~~~~~l~~h~~~~~~~~~ 108 (111)
.||.+-.....+..|++.+|...-
T Consensus 217 dcg~t~~~~e~~~~h~~~~hp~Sp 240 (267)
T KOG3576|consen 217 DCGYTSERPEVYYLHLKLHHPFSP 240 (267)
T ss_pred ccCCCCCChhHHHHHHHhcCCCCH
Confidence 999999999999999999986543
No 7
>KOG1074|consensus
Probab=99.33 E-value=5.3e-13 Score=95.43 Aligned_cols=84 Identities=23% Similarity=0.463 Sum_probs=75.6
Q ss_pred ccCcccCCCcccccCCHHHHHHHHHHcCCCCCccccccCcccCCHHHHHHHHHhccCCCC----CceecC---CCccccc
Q psy370 19 IFVASQCPVCKKIYTDQQLFQNHLETHDNEMDYSCEHCDMQFNCKSDMRKHVHSHLSMEE----RGFVCE---ICGHVVD 91 (111)
Q Consensus 19 ~~~~~~c~~C~~~f~~~~~l~~h~~~h~~~~~~~c~~c~~~f~~~~~l~~h~~~h~~~~~----~~~~C~---~C~~~~~ 91 (111)
...+-+|-+|-+.....+.|+.|.++|+|++||+|.+||++|.++.+|..|+..|. -. .++.|+ .|.+.|.
T Consensus 602 ~TdPNqCiiC~rVlSC~saLqmHyrtHtGERPFkCKiCgRAFtTkGNLkaH~~vHk--a~p~~R~q~ScP~~~ic~~kft 679 (958)
T KOG1074|consen 602 RTDPNQCIICLRVLSCPSALQMHYRTHTGERPFKCKICGRAFTTKGNLKAHMSVHK--AKPPARVQFSCPSTFICQKKFT 679 (958)
T ss_pred cCCccceeeeeecccchhhhhhhhhcccCcCccccccccchhccccchhhcccccc--cCccccccccCCchhhhccccc
Confidence 34467899999999999999999999999999999999999999999999999985 22 346799 9999999
Q ss_pred cchhHHhhccccC
Q psy370 92 EMPVATQSSKYPG 104 (111)
Q Consensus 92 ~~~~l~~h~~~~~ 104 (111)
+--.|.+|++.|-
T Consensus 680 n~V~lpQhIriH~ 692 (958)
T KOG1074|consen 680 NAVTLPQHIRIHL 692 (958)
T ss_pred ccccccceEEeec
Confidence 9999999999876
No 8
>PHA00733 hypothetical protein
Probab=99.21 E-value=1.1e-11 Score=72.30 Aligned_cols=81 Identities=21% Similarity=0.347 Sum_probs=67.6
Q ss_pred cCcccCCCcccccCCHHHHHHH--HH---HcCCCCCccccccCcccCCHHHHHHHHHhccCCCCCceecCCCccccccch
Q psy370 20 FVASQCPVCKKIYTDQQLFQNH--LE---THDNEMDYSCEHCDMQFNCKSDMRKHVHSHLSMEERGFVCEICGHVVDEMP 94 (111)
Q Consensus 20 ~~~~~c~~C~~~f~~~~~l~~h--~~---~h~~~~~~~c~~c~~~f~~~~~l~~h~~~h~~~~~~~~~C~~C~~~~~~~~ 94 (111)
.+++.|.+|...|.....|..+ .+ .+.+.++|.|..|++.|.....|..|++.+ +.+|.|..|++.|....
T Consensus 38 ~~~~~~~~~~~~~~~~~~l~~~~~l~~~~~~~~~kPy~C~~Cgk~Fss~s~L~~H~r~h----~~~~~C~~CgK~F~~~~ 113 (128)
T PHA00733 38 QKRLIRAVVKTLIYNPQLLDESSYLYKLLTSKAVSPYVCPLCLMPFSSSVSLKQHIRYT----EHSKVCPVCGKEFRNTD 113 (128)
T ss_pred hhhHHHHHHhhhccChhhhcchHHHHhhcccCCCCCccCCCCCCcCCCHHHHHHHHhcC----CcCccCCCCCCccCCHH
Confidence 5678999999999888777655 21 233478999999999999999999999865 35799999999999999
Q ss_pred hHHhhccccC
Q psy370 95 VATQSSKYPG 104 (111)
Q Consensus 95 ~l~~h~~~~~ 104 (111)
.|..|+...|
T Consensus 114 sL~~H~~~~h 123 (128)
T PHA00733 114 STLDHVCKKH 123 (128)
T ss_pred HHHHHHHHhc
Confidence 9999987665
No 9
>KOG3608|consensus
Probab=99.20 E-value=7.6e-12 Score=82.53 Aligned_cols=80 Identities=23% Similarity=0.484 Sum_probs=50.3
Q ss_pred cccCCCcccccCCHHHHHHHHHHcCCCCCccccccCcccCCHHHHHHHHHhccCCCCCceecCCCccccccchhHHhhcc
Q psy370 22 ASQCPVCKKIYTDQQLFQNHLETHDNEMDYSCEHCDMQFNCKSDMRKHVHSHLSMEERGFVCEICGHVVDEMPVATQSSK 101 (111)
Q Consensus 22 ~~~c~~C~~~f~~~~~l~~h~~~h~~~~~~~c~~c~~~f~~~~~l~~h~~~h~~~~~~~~~C~~C~~~~~~~~~l~~h~~ 101 (111)
+|.|..|.+.|.++..|..|++.|. ..|.|+.|+.+....++|.+|++..++ ..+||+|..|.+.|.+-++|.+|.-
T Consensus 237 ~fqC~~C~KrFaTeklL~~Hv~rHv--n~ykCplCdmtc~~~ssL~~H~r~rHs-~dkpfKCd~Cd~~c~~esdL~kH~~ 313 (467)
T KOG3608|consen 237 SFQCAQCFKRFATEKLLKSHVVRHV--NCYKCPLCDMTCSSASSLTTHIRYRHS-KDKPFKCDECDTRCVRESDLAKHVQ 313 (467)
T ss_pred chHHHHHHHHHhHHHHHHHHHHHhh--hcccccccccCCCChHHHHHHHHhhhc-cCCCccccchhhhhccHHHHHHHHH
Confidence 3444444444444444444444332 346777777777777777777776543 5777888888877777777777776
Q ss_pred ccC
Q psy370 102 YPG 104 (111)
Q Consensus 102 ~~~ 104 (111)
+|.
T Consensus 314 ~HS 316 (467)
T KOG3608|consen 314 VHS 316 (467)
T ss_pred hcc
Confidence 554
No 10
>KOG3608|consensus
Probab=99.18 E-value=9.4e-12 Score=82.10 Aligned_cols=92 Identities=18% Similarity=0.483 Sum_probs=60.6
Q ss_pred CCccccCcccCCCcccccCCHHHHHHHHHHcC--CCCCccccccCcccCCHHHHHHHHHhccCCCCCceecCCCcccccc
Q psy370 15 GSYTIFVASQCPVCKKIYTDQQLFQNHLETHD--NEMDYSCEHCDMQFNCKSDMRKHVHSHLSMEERGFVCEICGHVVDE 92 (111)
Q Consensus 15 ~~~~~~~~~~c~~C~~~f~~~~~l~~h~~~h~--~~~~~~c~~c~~~f~~~~~l~~h~~~h~~~~~~~~~C~~C~~~~~~ 92 (111)
.+|+++|..-|+.||..|.++..|..|.+..+ ...+|.|..|-+.|.+...|..|++.|. .-|+|+.|..+.+.
T Consensus 200 r~Hs~eKvvACp~Cg~~F~~~tkl~DH~rRqt~l~~n~fqC~~C~KrFaTeklL~~Hv~rHv----n~ykCplCdmtc~~ 275 (467)
T KOG3608|consen 200 RTHSNEKVVACPHCGELFRTKTKLFDHLRRQTELNTNSFQCAQCFKRFATEKLLKSHVVRHV----NCYKCPLCDMTCSS 275 (467)
T ss_pred HhcCCCeEEecchHHHHhccccHHHHHHHhhhhhcCCchHHHHHHHHHhHHHHHHHHHHHhh----hcccccccccCCCC
Confidence 34566666666666666666666665555433 2345666666666666666666666553 35788888888888
Q ss_pred chhHHhhccccCcccccc
Q psy370 93 MPVATQSSKYPGQQNQLF 110 (111)
Q Consensus 93 ~~~l~~h~~~~~~~~~~~ 110 (111)
.+.|..|+++.|++.+.|
T Consensus 276 ~ssL~~H~r~rHs~dkpf 293 (467)
T KOG3608|consen 276 ASSLTTHIRYRHSKDKPF 293 (467)
T ss_pred hHHHHHHHHhhhccCCCc
Confidence 888888998888877655
No 11
>PHA02768 hypothetical protein; Provisional
Probab=99.08 E-value=7.4e-11 Score=58.34 Aligned_cols=41 Identities=17% Similarity=0.348 Sum_probs=21.7
Q ss_pred ccccccCcccCCHHHHHHHHHhccCCCCCceecCCCccccccchh
Q psy370 51 YSCEHCDMQFNCKSDMRKHVHSHLSMEERGFVCEICGHVVDEMPV 95 (111)
Q Consensus 51 ~~c~~c~~~f~~~~~l~~h~~~h~~~~~~~~~C~~C~~~~~~~~~ 95 (111)
|.|+.||+.|...++|..|++.|+ ++++|..|++.|...+.
T Consensus 6 y~C~~CGK~Fs~~~~L~~H~r~H~----k~~kc~~C~k~f~~~s~ 46 (55)
T PHA02768 6 YECPICGEIYIKRKSMITHLRKHN----TNLKLSNCKRISLRTGE 46 (55)
T ss_pred cCcchhCCeeccHHHHHHHHHhcC----CcccCCcccceecccce
Confidence 455555555555555555555553 35555555555554443
No 12
>PHA02768 hypothetical protein; Provisional
Probab=98.99 E-value=3.3e-10 Score=56.06 Aligned_cols=44 Identities=20% Similarity=0.517 Sum_probs=39.1
Q ss_pred cccCCCcccccCCHHHHHHHHHHcCCCCCccccccCcccCCHHHHH
Q psy370 22 ASQCPVCKKIYTDQQLFQNHLETHDNEMDYSCEHCDMQFNCKSDMR 67 (111)
Q Consensus 22 ~~~c~~C~~~f~~~~~l~~h~~~h~~~~~~~c~~c~~~f~~~~~l~ 67 (111)
-|.|++||+.|...+.|..|+++|+ +++.|..|++.|...+.|.
T Consensus 5 ~y~C~~CGK~Fs~~~~L~~H~r~H~--k~~kc~~C~k~f~~~s~l~ 48 (55)
T PHA02768 5 GYECPICGEIYIKRKSMITHLRKHN--TNLKLSNCKRISLRTGEYI 48 (55)
T ss_pred ccCcchhCCeeccHHHHHHHHHhcC--CcccCCcccceecccceeE
Confidence 3799999999999999999999998 6899999999998766553
No 13
>KOG1074|consensus
Probab=98.96 E-value=3.4e-10 Score=81.49 Aligned_cols=53 Identities=25% Similarity=0.676 Sum_probs=49.9
Q ss_pred cccCCCcccccCCHHHHHHHHHHcCCCCCccccccCcccCCHHHHHHHHHhcc
Q psy370 22 ASQCPVCKKIYTDQQLFQNHLETHDNEMDYSCEHCDMQFNCKSDMRKHVHSHL 74 (111)
Q Consensus 22 ~~~c~~C~~~f~~~~~l~~h~~~h~~~~~~~c~~c~~~f~~~~~l~~h~~~h~ 74 (111)
...|.+||+.|...++|++|+++|+++++|.|.+|+++|....+|..||..|.
T Consensus 879 ~h~C~vCgk~FsSSsALqiH~rTHtg~KPF~C~fC~~aFttrgnLKvHMgtH~ 931 (958)
T KOG1074|consen 879 AHVCNVCGKQFSSSAALEIHMRTHTGPKPFFCHFCEEAFTTRGNLKVHMGTHM 931 (958)
T ss_pred hhhhccchhcccchHHHHHhhhcCCCCCCccchhhhhhhhhhhhhhhhhcccc
Confidence 47899999999999999999999999999999999999999999999999886
No 14
>PLN03086 PRLI-interacting factor K; Provisional
Probab=98.91 E-value=5.2e-09 Score=73.72 Aligned_cols=84 Identities=18% Similarity=0.366 Sum_probs=62.6
Q ss_pred CCCCccccCcccCCCcccccCCHHHHHHHHHHcCCCCCccccccCcccCCHHHHHHHHHhccCCCCCceecCCCcccccc
Q psy370 13 IPGSYTIFVASQCPVCKKIYTDQQLFQNHLETHDNEMDYSCEHCDMQFNCKSDMRKHVHSHLSMEERGFVCEICGHVVDE 92 (111)
Q Consensus 13 ~~~~~~~~~~~~c~~C~~~f~~~~~l~~h~~~h~~~~~~~c~~c~~~f~~~~~l~~h~~~h~~~~~~~~~C~~C~~~~~~ 92 (111)
.-.....++.+.|+.|++.|. ...+..|+..+. .++.|. |+..+ ....|..|+..|. .++++.|..|++.|..
T Consensus 444 v~~r~el~~H~~C~~Cgk~f~-~s~LekH~~~~H--kpv~Cp-Cg~~~-~R~~L~~H~~thC--p~Kpi~C~fC~~~v~~ 516 (567)
T PLN03086 444 VLRVEEAKNHVHCEKCGQAFQ-QGEMEKHMKVFH--EPLQCP-CGVVL-EKEQMVQHQASTC--PLRLITCRFCGDMVQA 516 (567)
T ss_pred eeeccccccCccCCCCCCccc-hHHHHHHHHhcC--CCccCC-CCCCc-chhHHHhhhhccC--CCCceeCCCCCCcccc
Confidence 334556677788999998885 567888888863 778888 88644 5688888888887 6888889989888842
Q ss_pred ----------chhHHhhcccc
Q psy370 93 ----------MPVATQSSKYP 103 (111)
Q Consensus 93 ----------~~~l~~h~~~~ 103 (111)
...|..|...+
T Consensus 517 g~~~~d~~d~~s~Lt~HE~~C 537 (567)
T PLN03086 517 GGSAMDVRDRLRGMSEHESIC 537 (567)
T ss_pred CccccchhhhhhhHHHHHHhc
Confidence 23577787664
No 15
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=98.86 E-value=2.5e-09 Score=45.50 Aligned_cols=25 Identities=28% Similarity=0.836 Sum_probs=17.9
Q ss_pred HHHHHHHhccCCCCCceecCCCccccc
Q psy370 65 DMRKHVHSHLSMEERGFVCEICGHVVD 91 (111)
Q Consensus 65 ~l~~h~~~h~~~~~~~~~C~~C~~~~~ 91 (111)
+|..|++.|+ |++||.|+.|++.|.
T Consensus 1 ~l~~H~~~H~--~~k~~~C~~C~k~F~ 25 (26)
T PF13465_consen 1 NLRRHMRTHT--GEKPYKCPYCGKSFS 25 (26)
T ss_dssp HHHHHHHHHS--SSSSEEESSSSEEES
T ss_pred CHHHHhhhcC--CCCCCCCCCCcCeeC
Confidence 3567777776 677777777777775
No 16
>PLN03086 PRLI-interacting factor K; Provisional
Probab=98.82 E-value=9.3e-09 Score=72.49 Aligned_cols=79 Identities=19% Similarity=0.288 Sum_probs=66.2
Q ss_pred CcccCCCcccccCCHHHHHHHHHHcCCCCCccccccCcccC----------CHHHHHHHHHhccCCCCCceecCCCcccc
Q psy370 21 VASQCPVCKKIYTDQQLFQNHLETHDNEMDYSCEHCDMQFN----------CKSDMRKHVHSHLSMEERGFVCEICGHVV 90 (111)
Q Consensus 21 ~~~~c~~C~~~f~~~~~l~~h~~~h~~~~~~~c~~c~~~f~----------~~~~l~~h~~~h~~~~~~~~~C~~C~~~~ 90 (111)
+++.|+ ||..+ ....|..|+.+|...+++.|.+|+..+. ..+.+..|.... |.+++.|..||+.+
T Consensus 477 kpv~Cp-Cg~~~-~R~~L~~H~~thCp~Kpi~C~fC~~~v~~g~~~~d~~d~~s~Lt~HE~~C---G~rt~~C~~Cgk~V 551 (567)
T PLN03086 477 EPLQCP-CGVVL-EKEQMVQHQASTCPLRLITCRFCGDMVQAGGSAMDVRDRLRGMSEHESIC---GSRTAPCDSCGRSV 551 (567)
T ss_pred CCccCC-CCCCc-chhHHHhhhhccCCCCceeCCCCCCccccCccccchhhhhhhHHHHHHhc---CCcceEccccCCee
Confidence 678999 99765 6688999999999999999999999884 235788998875 79999999999999
Q ss_pred ccchhHHhhccccCc
Q psy370 91 DEMPVATQSSKYPGQ 105 (111)
Q Consensus 91 ~~~~~l~~h~~~~~~ 105 (111)
..++ +..|+...|.
T Consensus 552 rlrd-m~~H~~~~h~ 565 (567)
T PLN03086 552 MLKE-MDIHQIAVHQ 565 (567)
T ss_pred eehh-HHHHHHHhhc
Confidence 8885 7778766554
No 17
>PHA00733 hypothetical protein
Probab=98.81 E-value=1.5e-08 Score=59.24 Aligned_cols=56 Identities=18% Similarity=0.396 Sum_probs=49.4
Q ss_pred ccccCcccCCCcccccCCHHHHHHHHHHcCCCCCccccccCcccCCHHHHHHHHHhcc
Q psy370 17 YTIFVASQCPVCKKIYTDQQLFQNHLETHDNEMDYSCEHCDMQFNCKSDMRKHVHSHL 74 (111)
Q Consensus 17 ~~~~~~~~c~~C~~~f~~~~~l~~h~~~h~~~~~~~c~~c~~~f~~~~~l~~h~~~h~ 74 (111)
+.++++|.|+.|++.|.....|..|++.+ ..++.|..|++.|.....|..|+...+
T Consensus 68 ~~~~kPy~C~~Cgk~Fss~s~L~~H~r~h--~~~~~C~~CgK~F~~~~sL~~H~~~~h 123 (128)
T PHA00733 68 SKAVSPYVCPLCLMPFSSSVSLKQHIRYT--EHSKVCPVCGKEFRNTDSTLDHVCKKH 123 (128)
T ss_pred cCCCCCccCCCCCCcCCCHHHHHHHHhcC--CcCccCCCCCCccCCHHHHHHHHHHhc
Confidence 34478999999999999999999999976 357999999999999999999988654
No 18
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=98.68 E-value=1.6e-08 Score=42.96 Aligned_cols=25 Identities=32% Similarity=0.739 Sum_probs=22.6
Q ss_pred HHHHHHHHcCCCCCccccccCcccC
Q psy370 37 LFQNHLETHDNEMDYSCEHCDMQFN 61 (111)
Q Consensus 37 ~l~~h~~~h~~~~~~~c~~c~~~f~ 61 (111)
+|..|+++|+++++|.|..|++.|.
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 4789999999999999999999885
No 19
>PHA00616 hypothetical protein
Probab=98.62 E-value=2.5e-08 Score=47.14 Aligned_cols=34 Identities=21% Similarity=0.341 Sum_probs=27.3
Q ss_pred cccCCCcccccCCHHHHHHHHHHcCCCCCccccc
Q psy370 22 ASQCPVCKKIYTDQQLFQNHLETHDNEMDYSCEH 55 (111)
Q Consensus 22 ~~~c~~C~~~f~~~~~l~~h~~~h~~~~~~~c~~ 55 (111)
+|+|..||+.|...+.+..|++.|++++++.|..
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~~hg~~~~~~~~ 34 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLSVHKQNKLTLEY 34 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHHhcCCCccceeE
Confidence 5788888888888888888888888888777653
No 20
>PHA00732 hypothetical protein
Probab=98.61 E-value=4.9e-08 Score=52.33 Aligned_cols=45 Identities=20% Similarity=0.498 Sum_probs=29.3
Q ss_pred cccCCCcccccCCHHHHHHHHHH-cCCCCCccccccCcccCCHHHHHHHHHh
Q psy370 22 ASQCPVCKKIYTDQQLFQNHLET-HDNEMDYSCEHCDMQFNCKSDMRKHVHS 72 (111)
Q Consensus 22 ~~~c~~C~~~f~~~~~l~~h~~~-h~~~~~~~c~~c~~~f~~~~~l~~h~~~ 72 (111)
+|.|..|++.|.....|..|++. |.+ +.|..|++.|. .+..|...
T Consensus 1 py~C~~Cgk~F~s~s~Lk~H~r~~H~~---~~C~~CgKsF~---~l~~H~~~ 46 (79)
T PHA00732 1 MFKCPICGFTTVTLFALKQHARRNHTL---TKCPVCNKSYR---RLNQHFYS 46 (79)
T ss_pred CccCCCCCCccCCHHHHHHHhhcccCC---CccCCCCCEeC---Chhhhhcc
Confidence 46677777777777777777763 442 36777777776 35555543
No 21
>KOG3993|consensus
Probab=98.35 E-value=6.1e-08 Score=65.64 Aligned_cols=89 Identities=20% Similarity=0.419 Sum_probs=66.4
Q ss_pred cCcccCCCcccccCCHHHHHHHHHHcCCCCCccccccCcccCCHHHHHHHHHhccCC------C----------------
Q psy370 20 FVASQCPVCKKIYTDQQLFQNHLETHDNEMDYSCEHCDMQFNCKSDMRKHVHSHLSM------E---------------- 77 (111)
Q Consensus 20 ~~~~~c~~C~~~f~~~~~l~~h~~~h~~~~~~~c~~c~~~f~~~~~l~~h~~~h~~~------~---------------- 77 (111)
...|.|..|...|-+.-.|-+|.=.-.-...|.|..|++.|.-+.+|..|+|=|.-+ +
T Consensus 265 iGdyiCqLCK~kYeD~F~LAQHrC~RIV~vEYrCPEC~KVFsCPANLASHRRWHKPR~eaa~a~~~P~k~~~~~rae~~e 344 (500)
T KOG3993|consen 265 IGDYICQLCKEKYEDAFALAQHRCPRIVHVEYRCPECDKVFSCPANLASHRRWHKPRPEAAKAGSPPPKQAVETRAEVQE 344 (500)
T ss_pred HHHHHHHHHHHhhhhHHHHhhccCCeeEEeeecCCcccccccCchhhhhhhcccCCchhhhhcCCCChhhhhhhhhhhhh
Confidence 335888888888887777777754333445688888888888888888887755210 0
Q ss_pred ---------CCceecCCCccccccchhHHhhccccCcccc
Q psy370 78 ---------ERGFVCEICGHVVDEMPVATQSSKYPGQQNQ 108 (111)
Q Consensus 78 ---------~~~~~C~~C~~~~~~~~~l~~h~~~~~~~~~ 108 (111)
+--|.|..|++.|.+...|.+|+-+|+...+
T Consensus 345 a~rsg~dss~gi~~C~~C~KkFrRqAYLrKHqlthq~~~~ 384 (500)
T KOG3993|consen 345 AERSGDDSSSGIFSCHTCGKKFRRQAYLRKHQLTHQRAPL 384 (500)
T ss_pred ccccCCcccCceeecHHhhhhhHHHHHHHHhHHhhhcccc
Confidence 1138899999999999999999998886654
No 22
>PHA00732 hypothetical protein
Probab=98.31 E-value=6.9e-07 Score=47.92 Aligned_cols=52 Identities=15% Similarity=0.271 Sum_probs=42.9
Q ss_pred CccccccCcccCCHHHHHHHHHh-ccCCCCCceecCCCccccccchhHHhhccccCccccc
Q psy370 50 DYSCEHCDMQFNCKSDMRKHVHS-HLSMEERGFVCEICGHVVDEMPVATQSSKYPGQQNQL 109 (111)
Q Consensus 50 ~~~c~~c~~~f~~~~~l~~h~~~-h~~~~~~~~~C~~C~~~~~~~~~l~~h~~~~~~~~~~ 109 (111)
+|.|..|++.|....++..|++. |. ++.|+.|++.|. .+..|+++..+-..|
T Consensus 1 py~C~~Cgk~F~s~s~Lk~H~r~~H~-----~~~C~~CgKsF~---~l~~H~~~~~~~~~~ 53 (79)
T PHA00732 1 MFKCPICGFTTVTLFALKQHARRNHT-----LTKCPVCNKSYR---RLNQHFYSQYDIEHL 53 (79)
T ss_pred CccCCCCCCccCCHHHHHHHhhcccC-----CCccCCCCCEeC---ChhhhhcccCCccce
Confidence 57899999999999999999985 54 358999999998 477888777665554
No 23
>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=98.21 E-value=2.3e-06 Score=42.65 Aligned_cols=51 Identities=20% Similarity=0.404 Sum_probs=20.5
Q ss_pred ccccccCcccCCHHHHHHHHHhccCCCCCceecCCCccccccchhHHhhccccC
Q psy370 51 YSCEHCDMQFNCKSDMRKHVHSHLSMEERGFVCEICGHVVDEMPVATQSSKYPG 104 (111)
Q Consensus 51 ~~c~~c~~~f~~~~~l~~h~~~h~~~~~~~~~C~~C~~~~~~~~~l~~h~~~~~ 104 (111)
|.|++|++. .....|..|....+....+.+.|+.|...+. ..|..|+..+|
T Consensus 3 f~CP~C~~~-~~~~~L~~H~~~~H~~~~~~v~CPiC~~~~~--~~l~~Hl~~~H 53 (54)
T PF05605_consen 3 FTCPYCGKG-FSESSLVEHCEDEHRSESKNVVCPICSSRVT--DNLIRHLNSQH 53 (54)
T ss_pred cCCCCCCCc-cCHHHHHHHHHhHCcCCCCCccCCCchhhhh--hHHHHHHHHhc
Confidence 344444442 2233444443322111223445555554333 24555554443
No 24
>PHA00616 hypothetical protein
Probab=98.19 E-value=7.7e-07 Score=42.09 Aligned_cols=34 Identities=24% Similarity=0.404 Sum_probs=25.8
Q ss_pred CccccccCcccCCHHHHHHHHHhccCCCCCceecCC
Q psy370 50 DYSCEHCDMQFNCKSDMRKHVHSHLSMEERGFVCEI 85 (111)
Q Consensus 50 ~~~c~~c~~~f~~~~~l~~h~~~h~~~~~~~~~C~~ 85 (111)
+|.|..||..|...+.+..|++.|+ |++++.|+.
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~~h--g~~~~~~~~ 34 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLSVH--KQNKLTLEY 34 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHHhc--CCCccceeE
Confidence 4678888888888888888888777 677776654
No 25
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=98.17 E-value=1.5e-06 Score=35.59 Aligned_cols=23 Identities=26% Similarity=0.843 Sum_probs=16.3
Q ss_pred ccCCCcccccCCHHHHHHHHHHc
Q psy370 23 SQCPVCKKIYTDQQLFQNHLETH 45 (111)
Q Consensus 23 ~~c~~C~~~f~~~~~l~~h~~~h 45 (111)
|.|+.|++.|.+...|..|++.|
T Consensus 1 y~C~~C~~~f~~~~~l~~H~~~H 23 (23)
T PF00096_consen 1 YKCPICGKSFSSKSNLKRHMRRH 23 (23)
T ss_dssp EEETTTTEEESSHHHHHHHHHHH
T ss_pred CCCCCCCCccCCHHHHHHHHhHC
Confidence 56777777777777777777653
No 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=98.15 E-value=5.3e-07 Score=36.97 Aligned_cols=22 Identities=18% Similarity=0.507 Sum_probs=15.5
Q ss_pred eecCCCccccccchhHHhhccc
Q psy370 81 FVCEICGHVVDEMPVATQSSKY 102 (111)
Q Consensus 81 ~~C~~C~~~~~~~~~l~~h~~~ 102 (111)
|.|+.|++.|.+...|..|++.
T Consensus 1 y~C~~C~~~f~~~~~l~~H~~~ 22 (23)
T PF00096_consen 1 YKCPICGKSFSSKSNLKRHMRR 22 (23)
T ss_dssp EEETTTTEEESSHHHHHHHHHH
T ss_pred CCCCCCCCccCCHHHHHHHHhH
Confidence 5677777777777777777664
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=98.12 E-value=1.7e-06 Score=36.83 Aligned_cols=26 Identities=15% Similarity=0.461 Sum_probs=20.5
Q ss_pred ceecCCCccccccchhHHhhccccCc
Q psy370 80 GFVCEICGHVVDEMPVATQSSKYPGQ 105 (111)
Q Consensus 80 ~~~C~~C~~~~~~~~~l~~h~~~~~~ 105 (111)
+|.|..|++.|.+..+|..|++.|++
T Consensus 1 ~~~C~~C~~~F~~~~~l~~H~~~h~~ 26 (27)
T PF13912_consen 1 PFECDECGKTFSSLSALREHKRSHCS 26 (27)
T ss_dssp SEEETTTTEEESSHHHHHHHHCTTTT
T ss_pred CCCCCccCCccCChhHHHHHhHHhcC
Confidence 47788888888888888888877764
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=98.05 E-value=1.6e-06 Score=35.61 Aligned_cols=24 Identities=25% Similarity=0.463 Sum_probs=16.1
Q ss_pred eecCCCccccccchhHHhhccccC
Q psy370 81 FVCEICGHVVDEMPVATQSSKYPG 104 (111)
Q Consensus 81 ~~C~~C~~~~~~~~~l~~h~~~~~ 104 (111)
|.|+.|++.|.+..+|..|++.+|
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 567777777777777777776654
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=97.95 E-value=3e-05 Score=38.54 Aligned_cols=50 Identities=24% Similarity=0.535 Sum_probs=38.7
Q ss_pred cccCCCcccccCCHHHHHHHHHH-cCCC-CCccccccCcccCCHHHHHHHHHhcc
Q psy370 22 ASQCPVCKKIYTDQQLFQNHLET-HDNE-MDYSCEHCDMQFNCKSDMRKHVHSHL 74 (111)
Q Consensus 22 ~~~c~~C~~~f~~~~~l~~h~~~-h~~~-~~~~c~~c~~~f~~~~~l~~h~~~h~ 74 (111)
.|.|+.|++ ..+...|..|... |..+ +.+.|++|...+. .++..|+..++
T Consensus 2 ~f~CP~C~~-~~~~~~L~~H~~~~H~~~~~~v~CPiC~~~~~--~~l~~Hl~~~H 53 (54)
T PF05605_consen 2 SFTCPYCGK-GFSESSLVEHCEDEHRSESKNVVCPICSSRVT--DNLIRHLNSQH 53 (54)
T ss_pred CcCCCCCCC-ccCHHHHHHHHHhHCcCCCCCccCCCchhhhh--hHHHHHHHHhc
Confidence 589999999 6667889999765 6653 5799999997543 48888887653
No 30
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=97.91 E-value=3.5e-06 Score=55.61 Aligned_cols=71 Identities=21% Similarity=0.351 Sum_probs=46.8
Q ss_pred cCcccCCC--cccccCCHHHHHHHHHH-cCCCCCccccccCcccCCHHHHHHHHHhccCCCCCceecCCCccccccchhH
Q psy370 20 FVASQCPV--CKKIYTDQQLFQNHLET-HDNEMDYSCEHCDMQFNCKSDMRKHVHSHLSMEERGFVCEICGHVVDEMPVA 96 (111)
Q Consensus 20 ~~~~~c~~--C~~~f~~~~~l~~h~~~-h~~~~~~~c~~c~~~f~~~~~l~~h~~~h~~~~~~~~~C~~C~~~~~~~~~l 96 (111)
++||+|++ |.+.|++...|+-|+.- |...+...-+--. .+.-+-. ..|||.|+.|+|.+.+...|
T Consensus 347 ~KpykCpV~gC~K~YknqnGLKYH~lhGH~~~~~~~~p~p~----------~~~~F~~--~~KPYrCevC~KRYKNlNGL 414 (423)
T COG5189 347 GKPYKCPVEGCNKKYKNQNGLKYHMLHGHQNQKLHENPSPE----------KMNIFSA--KDKPYRCEVCDKRYKNLNGL 414 (423)
T ss_pred CceecCCCCCchhhhccccchhhhhhccccCcccCCCCCcc----------ccccccc--cCCceeccccchhhccCccc
Confidence 47888876 88888888888877653 3333322221000 0111111 67999999999999999999
Q ss_pred Hhhccc
Q psy370 97 TQSSKY 102 (111)
Q Consensus 97 ~~h~~~ 102 (111)
.-|++-
T Consensus 415 KYHr~H 420 (423)
T COG5189 415 KYHRKH 420 (423)
T ss_pred eecccc
Confidence 988763
No 31
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=97.89 E-value=6e-06 Score=45.78 Aligned_cols=72 Identities=11% Similarity=0.310 Sum_probs=21.2
Q ss_pred cCCCcccccCCHHHHHHHHHH-cCCCCCccccccCcccCCHHHHHHHHHhccCCCCCceecCCCccccccchhHHhhccc
Q psy370 24 QCPVCKKIYTDQQLFQNHLET-HDNEMDYSCEHCDMQFNCKSDMRKHVHSHLSMEERGFVCEICGHVVDEMPVATQSSKY 102 (111)
Q Consensus 24 ~c~~C~~~f~~~~~l~~h~~~-h~~~~~~~c~~c~~~f~~~~~l~~h~~~h~~~~~~~~~C~~C~~~~~~~~~l~~h~~~ 102 (111)
+|..|+..|.+...+..|+.. |.-..+ ....+.....+..+.+... ...+.|..|++.|.+..+|..|++.
T Consensus 1 ~C~~C~~~f~~~~~l~~H~~~~H~~~~~-----~~~~l~~~~~~~~~~~~~~---~~~~~C~~C~~~f~s~~~l~~Hm~~ 72 (100)
T PF12756_consen 1 QCLFCDESFSSVDDLLQHMKKKHGFDIP-----DQKYLVDPNRLLNYLRKKV---KESFRCPYCNKTFRSREALQEHMRS 72 (100)
T ss_dssp --------------------------------------------------------SSEEBSSSS-EESSHHHHHHHHHH
T ss_pred Cccccccccccccccccccccccccccc-----ccccccccccccccccccc---CCCCCCCccCCCCcCHHHHHHHHcC
Confidence 588999999999999999864 432222 1111223333333433322 3368999999999999999999985
Q ss_pred c
Q psy370 103 P 103 (111)
Q Consensus 103 ~ 103 (111)
+
T Consensus 73 ~ 73 (100)
T PF12756_consen 73 K 73 (100)
T ss_dssp T
T ss_pred c
Confidence 4
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=97.78 E-value=1.4e-05 Score=33.92 Aligned_cols=24 Identities=21% Similarity=0.581 Sum_probs=15.5
Q ss_pred cccCCCcccccCCHHHHHHHHHHc
Q psy370 22 ASQCPVCKKIYTDQQLFQNHLETH 45 (111)
Q Consensus 22 ~~~c~~C~~~f~~~~~l~~h~~~h 45 (111)
+|.|..|++.|.+...|..|++.|
T Consensus 1 ~~~C~~C~~~F~~~~~l~~H~~~h 24 (27)
T PF13912_consen 1 PFECDECGKTFSSLSALREHKRSH 24 (27)
T ss_dssp SEEETTTTEEESSHHHHHHHHCTT
T ss_pred CCCCCccCCccCChhHHHHHhHHh
Confidence 356666666666666666666554
No 33
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=97.72 E-value=3.2e-05 Score=31.52 Aligned_cols=23 Identities=35% Similarity=0.871 Sum_probs=13.8
Q ss_pred ccCCCcccccCCHHHHHHHHHHc
Q psy370 23 SQCPVCKKIYTDQQLFQNHLETH 45 (111)
Q Consensus 23 ~~c~~C~~~f~~~~~l~~h~~~h 45 (111)
|.|+.|+..|.+...|..|++++
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 45667777777777777766553
No 34
>KOG3993|consensus
Probab=97.36 E-value=4.8e-05 Score=52.04 Aligned_cols=56 Identities=14% Similarity=0.377 Sum_probs=48.7
Q ss_pred CccccccCcccCCHHHHHHHHHhccCCCCCceecCCCccccccchhHHhhccccCccc
Q psy370 50 DYSCEHCDMQFNCKSDMRKHVHSHLSMEERGFVCEICGHVVDEMPVATQSSKYPGQQN 107 (111)
Q Consensus 50 ~~~c~~c~~~f~~~~~l~~h~~~h~~~~~~~~~C~~C~~~~~~~~~l~~h~~~~~~~~ 107 (111)
.|.|+.|...|...-.|.+|+.... .-.-|+|+.|+|+|.-...|.+|++-|-.+.
T Consensus 267 dyiCqLCK~kYeD~F~LAQHrC~RI--V~vEYrCPEC~KVFsCPANLASHRRWHKPR~ 322 (500)
T KOG3993|consen 267 DYICQLCKEKYEDAFALAQHRCPRI--VHVEYRCPECDKVFSCPANLASHRRWHKPRP 322 (500)
T ss_pred HHHHHHHHHhhhhHHHHhhccCCee--EEeeecCCcccccccCchhhhhhhcccCCch
Confidence 4899999999999999999988665 4456999999999999999999999886543
No 35
>smart00355 ZnF_C2H2 zinc finger.
Probab=97.34 E-value=0.00028 Score=28.97 Aligned_cols=23 Identities=30% Similarity=0.895 Sum_probs=14.1
Q ss_pred ccCCCcccccCCHHHHHHHHHHc
Q psy370 23 SQCPVCKKIYTDQQLFQNHLETH 45 (111)
Q Consensus 23 ~~c~~C~~~f~~~~~l~~h~~~h 45 (111)
|.|..|++.|.....+..|++.|
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~~H 23 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMRTH 23 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHHHh
Confidence 35666666666666666666544
No 36
>smart00355 ZnF_C2H2 zinc finger.
Probab=97.19 E-value=0.00013 Score=30.09 Aligned_cols=23 Identities=17% Similarity=0.466 Sum_probs=16.1
Q ss_pred eecCCCccccccchhHHhhcccc
Q psy370 81 FVCEICGHVVDEMPVATQSSKYP 103 (111)
Q Consensus 81 ~~C~~C~~~~~~~~~l~~h~~~~ 103 (111)
|.|..|++.|.....|..|++.|
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~~H 23 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMRTH 23 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHHHh
Confidence 45777777777777777777643
No 37
>PRK04860 hypothetical protein; Provisional
Probab=97.07 E-value=0.00044 Score=41.98 Aligned_cols=39 Identities=23% Similarity=0.499 Sum_probs=30.6
Q ss_pred CccccccCcccCCHHHHHHHHHhccCCCCCceecCCCccccccch
Q psy370 50 DYSCEHCDMQFNCKSDMRKHVHSHLSMEERGFVCEICGHVVDEMP 94 (111)
Q Consensus 50 ~~~c~~c~~~f~~~~~l~~h~~~h~~~~~~~~~C~~C~~~~~~~~ 94 (111)
+|.|. |+. ...++..|.+.+. ++++|.|..|+..|....
T Consensus 119 ~Y~C~-C~~---~~~~~rrH~ri~~--g~~~YrC~~C~~~l~~~~ 157 (160)
T PRK04860 119 PYRCK-CQE---HQLTVRRHNRVVR--GEAVYRCRRCGETLVFKG 157 (160)
T ss_pred EEEcC-CCC---eeCHHHHHHHHhc--CCccEECCCCCceeEEec
Confidence 57887 876 5667788888887 788899999998887654
No 38
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=97.01 E-value=0.00042 Score=28.63 Aligned_cols=22 Identities=23% Similarity=0.706 Sum_probs=14.2
Q ss_pred ccCCCcccccCCHHHHHHHHHH
Q psy370 23 SQCPVCKKIYTDQQLFQNHLET 44 (111)
Q Consensus 23 ~~c~~C~~~f~~~~~l~~h~~~ 44 (111)
|.|..|+..|.+...+..|++.
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 4566666667666666666553
No 39
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=96.90 E-value=0.00046 Score=28.49 Aligned_cols=22 Identities=23% Similarity=0.490 Sum_probs=14.3
Q ss_pred eecCCCccccccchhHHhhccc
Q psy370 81 FVCEICGHVVDEMPVATQSSKY 102 (111)
Q Consensus 81 ~~C~~C~~~~~~~~~l~~h~~~ 102 (111)
|.|..|++.|.+...|.+|++.
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 4566676777666666666653
No 40
>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=96.83 E-value=0.00065 Score=28.71 Aligned_cols=22 Identities=23% Similarity=0.427 Sum_probs=18.7
Q ss_pred eecCCCccccccchhHHhhccc
Q psy370 81 FVCEICGHVVDEMPVATQSSKY 102 (111)
Q Consensus 81 ~~C~~C~~~~~~~~~l~~h~~~ 102 (111)
|.|..|++.|.+...+.+|++.
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 6788899999998888888875
No 41
>PF09237 GAGA: GAGA factor; InterPro: IPR015318 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Members of this entry bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognises the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognises the A in the fourth position of the consensus sequence []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1YUI_A 1YUJ_A.
Probab=96.71 E-value=0.0024 Score=31.10 Aligned_cols=22 Identities=18% Similarity=0.549 Sum_probs=7.2
Q ss_pred CccccccCcccCCHHHHHHHHH
Q psy370 50 DYSCEHCDMQFNCKSDMRKHVH 71 (111)
Q Consensus 50 ~~~c~~c~~~f~~~~~l~~h~~ 71 (111)
|..|++|+..+....+|..|+.
T Consensus 24 PatCP~C~a~~~~srnLrRHle 45 (54)
T PF09237_consen 24 PATCPICGAVIRQSRNLRRHLE 45 (54)
T ss_dssp -EE-TTT--EESSHHHHHHHHH
T ss_pred CCCCCcchhhccchhhHHHHHH
Confidence 3334444444444444444433
No 42
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=96.68 E-value=0.00056 Score=28.01 Aligned_cols=23 Identities=13% Similarity=0.222 Sum_probs=11.9
Q ss_pred eecCCCccccccchhHHhhccccC
Q psy370 81 FVCEICGHVVDEMPVATQSSKYPG 104 (111)
Q Consensus 81 ~~C~~C~~~~~~~~~l~~h~~~~~ 104 (111)
|.|..|..... ...|..|++.+|
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 45666665555 555666665543
No 43
>PRK04860 hypothetical protein; Provisional
Probab=96.62 E-value=0.0013 Score=39.93 Aligned_cols=38 Identities=24% Similarity=0.531 Sum_probs=32.4
Q ss_pred cccCCCcccccCCHHHHHHHHHHcCCCCCccccccCcccCCH
Q psy370 22 ASQCPVCKKIYTDQQLFQNHLETHDNEMDYSCEHCDMQFNCK 63 (111)
Q Consensus 22 ~~~c~~C~~~f~~~~~l~~h~~~h~~~~~~~c~~c~~~f~~~ 63 (111)
+|.|. |+. ....+..|.++++++++|.|..|+..|...
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 69998 987 556688999999999999999999877543
No 44
>PF09237 GAGA: GAGA factor; InterPro: IPR015318 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Members of this entry bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognises the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognises the A in the fourth position of the consensus sequence []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1YUI_A 1YUJ_A.
Probab=96.30 E-value=0.011 Score=28.80 Aligned_cols=33 Identities=18% Similarity=0.425 Sum_probs=22.1
Q ss_pred cccCcccCCCcccccCCHHHHHHHHHHcCCCCC
Q psy370 18 TIFVASQCPVCKKIYTDQQLFQNHLETHDNEMD 50 (111)
Q Consensus 18 ~~~~~~~c~~C~~~f~~~~~l~~h~~~h~~~~~ 50 (111)
..+.|-.|++|+..+....+|..|+..+.+.++
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 446688999999999999999999976555444
No 45
>PF12171 zf-C2H2_jaz: Zinc-finger double-stranded RNA-binding; InterPro: IPR022755 This zinc finger is found in archaea and eukaryotes, and is approximately 30 amino acids in length. The mammalian members of this group occur multiple times along the protein, joined by flexible linkers, and are referred to as JAZ - dsRNA-binding ZF protein - zinc-fingers. The JAZ proteins are expressed in all tissues tested and localise in the nucleus, particularly the nucleolus []. JAZ preferentially binds to double-stranded (ds) RNA or RNA/DNA hybrids rather than DNA. In addition to binding double-stranded RNA, these zinc-fingers are required for nucleolar localisation. This entry represents the multiple-adjacent-C2H2 zinc finger, JAZ. ; PDB: 4DGW_A 1ZR9_A.
Probab=96.28 E-value=0.0011 Score=28.00 Aligned_cols=21 Identities=19% Similarity=0.683 Sum_probs=14.7
Q ss_pred ccCCCcccccCCHHHHHHHHH
Q psy370 23 SQCPVCKKIYTDQQLFQNHLE 43 (111)
Q Consensus 23 ~~c~~C~~~f~~~~~l~~h~~ 43 (111)
|.|..|++.|.+...+..|++
T Consensus 2 ~~C~~C~k~f~~~~~~~~H~~ 22 (27)
T PF12171_consen 2 FYCDACDKYFSSENQLKQHMK 22 (27)
T ss_dssp CBBTTTTBBBSSHHHHHCCTT
T ss_pred CCcccCCCCcCCHHHHHHHHc
Confidence 567777777777777776654
No 46
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=96.15 E-value=0.0027 Score=26.39 Aligned_cols=21 Identities=24% Similarity=0.460 Sum_probs=14.7
Q ss_pred eecCCCccccccchhHHhhccc
Q psy370 81 FVCEICGHVVDEMPVATQSSKY 102 (111)
Q Consensus 81 ~~C~~C~~~~~~~~~l~~h~~~ 102 (111)
..|+.||+.| ..+.|..|++.
T Consensus 3 ~~C~~CgR~F-~~~~l~~H~~~ 23 (25)
T PF13913_consen 3 VPCPICGRKF-NPDRLEKHEKI 23 (25)
T ss_pred CcCCCCCCEE-CHHHHHHHHHh
Confidence 3678888888 55567777654
No 47
>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=95.17 E-value=0.015 Score=25.79 Aligned_cols=23 Identities=22% Similarity=0.462 Sum_probs=18.4
Q ss_pred ceecCCCccccccchhHHhhccc
Q psy370 80 GFVCEICGHVVDEMPVATQSSKY 102 (111)
Q Consensus 80 ~~~C~~C~~~~~~~~~l~~h~~~ 102 (111)
+|.|..|+..|.+..++..|++.
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~g 25 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLKG 25 (35)
T ss_pred CeEccccCCccCCHHHHHHHHCh
Confidence 47788888888888888888763
No 48
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=93.99 E-value=0.017 Score=28.60 Aligned_cols=28 Identities=18% Similarity=0.203 Sum_probs=21.4
Q ss_pred CCCceecCCCccccccchhHHhhccccC
Q psy370 77 EERGFVCEICGHVVDEMPVATQSSKYPG 104 (111)
Q Consensus 77 ~~~~~~C~~C~~~~~~~~~l~~h~~~~~ 104 (111)
||.-+.|+.||..|..+.+...|+.-.|
T Consensus 14 GE~~lrCPRC~~~FR~~K~Y~RHVNKaH 41 (65)
T COG4049 14 GEEFLRCPRCGMVFRRRKDYIRHVNKAH 41 (65)
T ss_pred CceeeeCCchhHHHHHhHHHHHHhhHHh
Confidence 6677788888888888888888875443
No 49
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=93.63 E-value=0.1 Score=28.51 Aligned_cols=23 Identities=22% Similarity=0.759 Sum_probs=15.3
Q ss_pred CccccccCcccCCHHHHHHHHHh
Q psy370 50 DYSCEHCDMQFNCKSDMRKHVHS 72 (111)
Q Consensus 50 ~~~c~~c~~~f~~~~~l~~h~~~ 72 (111)
.+.|..|+..|.....+..|++.
T Consensus 50 ~~~C~~C~~~f~s~~~l~~Hm~~ 72 (100)
T PF12756_consen 50 SFRCPYCNKTFRSREALQEHMRS 72 (100)
T ss_dssp SEEBSSSS-EESSHHHHHHHHHH
T ss_pred CCCCCccCCCCcCHHHHHHHHcC
Confidence 66777777777777777777664
No 50
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=93.54 E-value=0.027 Score=38.43 Aligned_cols=55 Identities=18% Similarity=0.475 Sum_probs=37.4
Q ss_pred CccccccCcccCCHHHHHHHHH--hccCCCC--CceecC--CCccccccchhHHhhccccCcc
Q psy370 50 DYSCEHCDMQFNCKSDMRKHVH--SHLSMEE--RGFVCE--ICGHVVDEMPVATQSSKYPGQQ 106 (111)
Q Consensus 50 ~~~c~~c~~~f~~~~~l~~h~~--~h~~~~~--~~~~C~--~C~~~~~~~~~l~~h~~~~~~~ 106 (111)
.+.|..|...|.....+..|.+ .|. ++ +++.|. .|++.|.+.+.+..|...+...
T Consensus 289 ~~~~~~~~~~~s~~~~l~~~~~~~~h~--~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~ 349 (467)
T COG5048 289 PIKSKQCNISFSRSSPLTRHLRSVNHS--GESLKPFSCPYSLCGKLFSRNDALKRHILLHTSI 349 (467)
T ss_pred CCCCccccCCccccccccccccccccc--cccCCceeeeccCCCccccccccccCCcccccCC
Confidence 4666667777777777777777 565 56 677777 5777777777777776666543
No 51
>KOG2186|consensus
Probab=93.28 E-value=0.055 Score=35.13 Aligned_cols=47 Identities=21% Similarity=0.485 Sum_probs=36.2
Q ss_pred cccCCCcccccCCHHHHHHHHHHcCCCCCccccccCcccCCHHHHHHHHH
Q psy370 22 ASQCPVCKKIYTDQQLFQNHLETHDNEMDYSCEHCDMQFNCKSDMRKHVH 71 (111)
Q Consensus 22 ~~~c~~C~~~f~~~~~l~~h~~~h~~~~~~~c~~c~~~f~~~~~l~~h~~ 71 (111)
-|.|..||.+..-+ .+..|+....+ ..|.|..|+..|.. .++..|..
T Consensus 3 ~FtCnvCgEsvKKp-~vekH~srCrn-~~fSCIDC~k~F~~-~sYknH~k 49 (276)
T KOG2186|consen 3 FFTCNVCGESVKKP-QVEKHMSRCRN-AYFSCIDCGKTFER-VSYKNHTK 49 (276)
T ss_pred EEehhhhhhhcccc-chHHHHHhccC-CeeEEeeccccccc-chhhhhhh
Confidence 37899999988766 46668776666 67899999999988 66666654
No 52
>KOG2231|consensus
Probab=93.17 E-value=0.17 Score=37.36 Aligned_cols=85 Identities=11% Similarity=0.320 Sum_probs=51.6
Q ss_pred ccCCCcccccC---------------CHHHHHHHHHH-cCCCCCccccc------cCcccCCHHHHHHHHHhccCCCCCc
Q psy370 23 SQCPVCKKIYT---------------DQQLFQNHLET-HDNEMDYSCEH------CDMQFNCKSDMRKHVHSHLSMEERG 80 (111)
Q Consensus 23 ~~c~~C~~~f~---------------~~~~l~~h~~~-h~~~~~~~c~~------c~~~f~~~~~l~~h~~~h~~~~~~~ 80 (111)
+.|.+|.+.+. .-..|+.|+.. |....-..|.. +.....+...++.|+..-.. ++..
T Consensus 100 ~~C~~C~~~~~~~~~~~~~~~c~~~~s~~~Lk~H~~~~H~~~~c~lC~~~~kif~~e~k~Yt~~el~~h~~~gd~-d~~s 178 (669)
T KOG2231|consen 100 HSCHICDRRFRALYNKKECLHCTEFKSVENLKNHMRDQHKLHLCSLCLQNLKIFINERKLYTRAELNLHLMFGDP-DDES 178 (669)
T ss_pred hhcCccccchhhhcccCCCccccchhHHHHHHHHHHHhhhhhccccccccceeeeeeeehehHHHHHHHHhcCCC-cccc
Confidence 56777777662 45667888754 43222112221 11233455677777764321 2222
Q ss_pred ----eecCCCccccccchhHHhhccccCcccc
Q psy370 81 ----FVCEICGHVVDEMPVATQSSKYPGQQNQ 108 (111)
Q Consensus 81 ----~~C~~C~~~~~~~~~l~~h~~~~~~~~~ 108 (111)
-.|..|...|.....|..|++..|..++
T Consensus 179 ~rGhp~C~~C~~~fld~~el~rH~~~~h~~ch 210 (669)
T KOG2231|consen 179 CRGHPLCKFCHERFLDDDELYRHLRFDHEFCH 210 (669)
T ss_pred ccCCccchhhhhhhccHHHHHHhhccceehee
Confidence 3588999999999999999998886544
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=92.13 E-value=0.071 Score=23.53 Aligned_cols=11 Identities=55% Similarity=1.186 Sum_probs=6.2
Q ss_pred ccCCCcccccC
Q psy370 23 SQCPVCKKIYT 33 (111)
Q Consensus 23 ~~c~~C~~~f~ 33 (111)
|.|.+||..+.
T Consensus 2 ~~C~~CGy~y~ 12 (33)
T cd00350 2 YVCPVCGYIYD 12 (33)
T ss_pred EECCCCCCEEC
Confidence 45666665543
No 54
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=91.81 E-value=0.11 Score=25.78 Aligned_cols=30 Identities=13% Similarity=0.330 Sum_probs=24.7
Q ss_pred CCccccCcccCCCcccccCCHHHHHHHHHH
Q psy370 15 GSYTIFVASQCPVCKKIYTDQQLFQNHLET 44 (111)
Q Consensus 15 ~~~~~~~~~~c~~C~~~f~~~~~l~~h~~~ 44 (111)
.+..||..+.|+-||..|....++..|...
T Consensus 10 ~~RDGE~~lrCPRC~~~FR~~K~Y~RHVNK 39 (65)
T COG4049 10 RDRDGEEFLRCPRCGMVFRRRKDYIRHVNK 39 (65)
T ss_pred eccCCceeeeCCchhHHHHHhHHHHHHhhH
Confidence 356788889999999999988888888653
No 55
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=91.78 E-value=0.054 Score=37.01 Aligned_cols=62 Identities=18% Similarity=0.398 Sum_probs=53.6
Q ss_pred CcccCCCcccccCCHHHHHHHHH--HcCCC--CCcccc--ccCcccCCHHHHHHHHHhccCCCCCceecC
Q psy370 21 VASQCPVCKKIYTDQQLFQNHLE--THDNE--MDYSCE--HCDMQFNCKSDMRKHVHSHLSMEERGFVCE 84 (111)
Q Consensus 21 ~~~~c~~C~~~f~~~~~l~~h~~--~h~~~--~~~~c~--~c~~~f~~~~~l~~h~~~h~~~~~~~~~C~ 84 (111)
.++.|..|...|.....+..|.+ .|.++ +++.|. .|+..|.+...+..|...|. +..++.+.
T Consensus 288 ~~~~~~~~~~~~s~~~~l~~~~~~~~h~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~ 355 (467)
T COG5048 288 LPIKSKQCNISFSRSSPLTRHLRSVNHSGESLKPFSCPYSLCGKLFSRNDALKRHILLHT--SISPAKEK 355 (467)
T ss_pred cCCCCccccCCccccccccccccccccccccCCceeeeccCCCccccccccccCCccccc--CCCccccc
Confidence 46889999999999999999999 79999 999999 79999999999999998887 55555543
No 56
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=91.24 E-value=0.069 Score=35.96 Aligned_cols=22 Identities=27% Similarity=0.513 Sum_probs=15.8
Q ss_pred cCcccCCCcccccCCHHHHHHH
Q psy370 20 FVASQCPVCKKIYTDQQLFQNH 41 (111)
Q Consensus 20 ~~~~~c~~C~~~f~~~~~l~~h 41 (111)
.|||.|++|++.|++...|+-|
T Consensus 396 ~KPYrCevC~KRYKNlNGLKYH 417 (423)
T COG5189 396 DKPYRCEVCDKRYKNLNGLKYH 417 (423)
T ss_pred CCceeccccchhhccCccceec
Confidence 3778888888887777666555
No 57
>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=91.18 E-value=0.21 Score=28.44 Aligned_cols=29 Identities=28% Similarity=0.694 Sum_probs=18.7
Q ss_pred cCCCcccccCCHHHHHHHHHHcCCCCCccccccCcccCCH
Q psy370 24 QCPVCKKIYTDQQLFQNHLETHDNEMDYSCEHCDMQFNCK 63 (111)
Q Consensus 24 ~c~~C~~~f~~~~~l~~h~~~h~~~~~~~c~~c~~~f~~~ 63 (111)
.|+.||..|-.. +..|.+|+.||..|...
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 677777777433 22567777777766554
No 58
>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=90.68 E-value=0.16 Score=22.58 Aligned_cols=10 Identities=40% Similarity=0.816 Sum_probs=5.7
Q ss_pred CceecCCCcc
Q psy370 79 RGFVCEICGH 88 (111)
Q Consensus 79 ~~~~C~~C~~ 88 (111)
.|..|+.||.
T Consensus 17 ~p~~CP~Cg~ 26 (34)
T cd00729 17 APEKCPICGA 26 (34)
T ss_pred CCCcCcCCCC
Confidence 3456666664
No 59
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=90.00 E-value=0.21 Score=30.99 Aligned_cols=31 Identities=32% Similarity=0.890 Sum_probs=16.7
Q ss_pred CCccccccCcccCCHHHHHHHHHhccCCCCCceecCCCcccc
Q psy370 49 MDYSCEHCDMQFNCKSDMRKHVHSHLSMEERGFVCEICGHVV 90 (111)
Q Consensus 49 ~~~~c~~c~~~f~~~~~l~~h~~~h~~~~~~~~~C~~C~~~~ 90 (111)
.-|.|+.|+..|.....+. -.|.|+.||...
T Consensus 116 ~~Y~Cp~C~~rytf~eA~~-----------~~F~Cp~Cg~~L 146 (178)
T PRK06266 116 MFFFCPNCHIRFTFDEAME-----------YGFRCPQCGEML 146 (178)
T ss_pred CEEECCCCCcEEeHHHHhh-----------cCCcCCCCCCCC
Confidence 4466666665555444331 136666666544
No 60
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=89.31 E-value=0.25 Score=30.31 Aligned_cols=25 Identities=36% Similarity=0.731 Sum_probs=19.1
Q ss_pred CCccccccCcccCCHHHHHHHHHhccCCCCCceecCCCcc
Q psy370 49 MDYSCEHCDMQFNCKSDMRKHVHSHLSMEERGFVCEICGH 88 (111)
Q Consensus 49 ~~~~c~~c~~~f~~~~~l~~h~~~h~~~~~~~~~C~~C~~ 88 (111)
+.|+|.+||.. +. |+.|.+|+.||.
T Consensus 133 ~~~vC~vCGy~-------------~~--ge~P~~CPiCga 157 (166)
T COG1592 133 KVWVCPVCGYT-------------HE--GEAPEVCPICGA 157 (166)
T ss_pred CEEEcCCCCCc-------------cc--CCCCCcCCCCCC
Confidence 36999999853 22 678899999984
No 61
>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=88.54 E-value=0.35 Score=29.41 Aligned_cols=36 Identities=28% Similarity=0.655 Sum_probs=22.2
Q ss_pred cCCCCCccccccCcccCCHHHHHHHHHhccCCCCCceecCCCccccc
Q psy370 45 HDNEMDYSCEHCDMQFNCKSDMRKHVHSHLSMEERGFVCEICGHVVD 91 (111)
Q Consensus 45 h~~~~~~~c~~c~~~f~~~~~l~~h~~~h~~~~~~~~~C~~C~~~~~ 91 (111)
..+..-|.|+.|+..|.....+. -.|.|+.||....
T Consensus 104 e~~~~~Y~Cp~c~~r~tf~eA~~-----------~~F~Cp~Cg~~L~ 139 (158)
T TIGR00373 104 ETNNMFFICPNMCVRFTFNEAME-----------LNFTCPRCGAMLD 139 (158)
T ss_pred ccCCCeEECCCCCcEeeHHHHHH-----------cCCcCCCCCCEee
Confidence 33445677777776666655553 1378888876553
No 62
>KOG1146|consensus
Probab=88.19 E-value=0.16 Score=40.11 Aligned_cols=25 Identities=8% Similarity=0.175 Sum_probs=21.5
Q ss_pred CCceecCCCccccccchhHHhhccc
Q psy370 78 ERGFVCEICGHVVDEMPVATQSSKY 102 (111)
Q Consensus 78 ~~~~~C~~C~~~~~~~~~l~~h~~~ 102 (111)
-++|.|..|...+...-.|..|+..
T Consensus 516 ~~p~~C~~C~~stttng~LsihlqS 540 (1406)
T KOG1146|consen 516 GKPYPCRACNYSTTTNGNLSIHLQS 540 (1406)
T ss_pred CCcccceeeeeeeecchHHHHHHHH
Confidence 3688999999999999889988853
No 63
>KOG1146|consensus
Probab=87.76 E-value=0.49 Score=37.65 Aligned_cols=83 Identities=20% Similarity=0.438 Sum_probs=62.4
Q ss_pred cCcccCCCcccccCCHHHHHHHHHH-cC------------------------CCCCccccccCcccCCHHHHHHHHHhcc
Q psy370 20 FVASQCPVCKKIYTDQQLFQNHLET-HD------------------------NEMDYSCEHCDMQFNCKSDMRKHVHSHL 74 (111)
Q Consensus 20 ~~~~~c~~C~~~f~~~~~l~~h~~~-h~------------------------~~~~~~c~~c~~~f~~~~~l~~h~~~h~ 74 (111)
.+-+.|+.|+..|+..+.|..|+++ |. +.++|.|..|...+....+|..|+....
T Consensus 463 ~kt~~cpkc~~~yk~a~~L~vhmRskhp~~~~~~c~~gq~~~~~arg~~~~~~~~p~~C~~C~~stttng~LsihlqS~~ 542 (1406)
T KOG1146|consen 463 FKTLKCPKCNWHYKLAQTLGVHMRSKHPESQSAYCKAGQNHPRLARGEVYRCPGKPYPCRACNYSTTTNGNLSIHLQSDL 542 (1406)
T ss_pred cccccCCccchhhhhHHHhhhcccccccccchhHhHhccccccccccccccCCCCcccceeeeeeeecchHHHHHHHHHh
Confidence 4678999999999999999999987 11 1357889999999999999998866321
Q ss_pred CC----------C------------------------------C-CceecCCCccccccchhHHhhccc
Q psy370 75 SM----------E------------------------------E-RGFVCEICGHVVDEMPVATQSSKY 102 (111)
Q Consensus 75 ~~----------~------------------------------~-~~~~C~~C~~~~~~~~~l~~h~~~ 102 (111)
.. | + ..|.|..|+.-..-...|+-|+..
T Consensus 543 h~~~lee~~~~~g~~v~~~~~~v~s~~P~~ag~~~~ags~~pktkP~~~C~vc~yetniarnlrihmts 611 (1406)
T KOG1146|consen 543 HRNELEEAEENAGEQVRLLPASVTSAVPEEAGLGPSAGSSGPKTKPSWRCEVCSYETNIARNLRIHMTA 611 (1406)
T ss_pred hHHHHHHHHhccccchhhhhhhhcccCcccccCCCCCCCCCCCCCCCcchhhhcchhhhhhcccccccc
Confidence 10 0 0 136788898877777778878763
No 64
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=87.64 E-value=0.056 Score=34.45 Aligned_cols=20 Identities=25% Similarity=0.534 Sum_probs=14.9
Q ss_pred cCcccCCCcccccCCHHHHH
Q psy370 20 FVASQCPVCKKIYTDQQLFQ 39 (111)
Q Consensus 20 ~~~~~c~~C~~~f~~~~~l~ 39 (111)
.+.+.|++|++.|..+....
T Consensus 3 ~k~~~CPvC~~~F~~~~vrs 22 (214)
T PF09986_consen 3 DKKITCPVCGKEFKTKKVRS 22 (214)
T ss_pred CCceECCCCCCeeeeeEEEc
Confidence 46678999999998775443
No 65
>KOG2893|consensus
Probab=87.39 E-value=0.26 Score=31.97 Aligned_cols=32 Identities=19% Similarity=0.664 Sum_probs=23.6
Q ss_pred cCCCcccccCCHHHHHHHHHHcCCCCCccccccCcc
Q psy370 24 QCPVCKKIYTDQQLFQNHLETHDNEMDYSCEHCDMQ 59 (111)
Q Consensus 24 ~c~~C~~~f~~~~~l~~h~~~h~~~~~~~c~~c~~~ 59 (111)
.|=.|++-|.....|.+|++. +.|+|.+|-+.
T Consensus 12 wcwycnrefddekiliqhqka----khfkchichkk 43 (341)
T KOG2893|consen 12 WCWYCNREFDDEKILIQHQKA----KHFKCHICHKK 43 (341)
T ss_pred eeeecccccchhhhhhhhhhh----ccceeeeehhh
Confidence 366788888888888887664 67788888654
No 66
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=87.06 E-value=0.48 Score=28.38 Aligned_cols=41 Identities=22% Similarity=0.615 Sum_probs=25.5
Q ss_pred CCCCCccccccCcccCCHHHHHHHHHhccCCCCCceecCCCcccccc
Q psy370 46 DNEMDYSCEHCDMQFNCKSDMRKHVHSHLSMEERGFVCEICGHVVDE 92 (111)
Q Consensus 46 ~~~~~~~c~~c~~~f~~~~~l~~h~~~h~~~~~~~~~C~~C~~~~~~ 92 (111)
.+...|.|+.|+..|........ ... +..|.|+.||.....
T Consensus 95 ~~~~~Y~Cp~C~~~y~~~ea~~~---~d~---~~~f~Cp~Cg~~l~~ 135 (147)
T smart00531 95 TNNAYYKCPNCQSKYTFLEANQL---LDM---DGTFTCPRCGEELEE 135 (147)
T ss_pred cCCcEEECcCCCCEeeHHHHHHh---cCC---CCcEECCCCCCEEEE
Confidence 34567899999987775433321 011 223999999986643
No 67
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=86.38 E-value=0.86 Score=22.96 Aligned_cols=10 Identities=30% Similarity=1.022 Sum_probs=6.8
Q ss_pred CceecCCCcc
Q psy370 79 RGFVCEICGH 88 (111)
Q Consensus 79 ~~~~C~~C~~ 88 (111)
.+|.|+.||.
T Consensus 47 ~~Y~CP~CGF 56 (59)
T PRK14890 47 NPYTCPKCGF 56 (59)
T ss_pred CceECCCCCC
Confidence 4677777774
No 68
>KOG2893|consensus
Probab=86.11 E-value=0.2 Score=32.49 Aligned_cols=39 Identities=23% Similarity=0.517 Sum_probs=29.2
Q ss_pred ccccCcccCCHHHHHHHHHhccCCCCCceecCCCccccccchhHH
Q psy370 53 CEHCDMQFNCKSDMRKHVHSHLSMEERGFVCEICGHVVDEMPVAT 97 (111)
Q Consensus 53 c~~c~~~f~~~~~l~~h~~~h~~~~~~~~~C~~C~~~~~~~~~l~ 97 (111)
|=.|.+.|....-|.+|++. +-|+|..|.+..-+-..|.
T Consensus 13 cwycnrefddekiliqhqka------khfkchichkkl~sgpgls 51 (341)
T KOG2893|consen 13 CWYCNREFDDEKILIQHQKA------KHFKCHICHKKLFSGPGLS 51 (341)
T ss_pred eeecccccchhhhhhhhhhh------ccceeeeehhhhccCCCce
Confidence 56689999999999998874 4499999987554443443
No 69
>smart00614 ZnF_BED BED zinc finger. DNA-binding domain in chromatin-boundary-element-binding proteins and transposases
Probab=85.25 E-value=0.64 Score=22.40 Aligned_cols=22 Identities=14% Similarity=0.353 Sum_probs=15.7
Q ss_pred eecCCCccccccc-----hhHHhhccc
Q psy370 81 FVCEICGHVVDEM-----PVATQSSKY 102 (111)
Q Consensus 81 ~~C~~C~~~~~~~-----~~l~~h~~~ 102 (111)
-.|..|++.+... +.|..|++.
T Consensus 19 a~C~~C~~~l~~~~~~gTs~L~rHl~~ 45 (50)
T smart00614 19 AKCKYCGKKLSRSSKGGTSNLRRHLRR 45 (50)
T ss_pred EEecCCCCEeeeCCCCCcHHHHHHHHh
Confidence 4688888877654 468888873
No 70
>KOG2593|consensus
Probab=84.63 E-value=0.76 Score=32.30 Aligned_cols=38 Identities=29% Similarity=0.616 Sum_probs=21.9
Q ss_pred cccCcccCCCcccccCCHHHHHHHHHHcCCCCCccccccCc
Q psy370 18 TIFVASQCPVCKKIYTDQQLFQNHLETHDNEMDYSCEHCDM 58 (111)
Q Consensus 18 ~~~~~~~c~~C~~~f~~~~~l~~h~~~h~~~~~~~c~~c~~ 58 (111)
+...-|.|+.|++.|.....++ ........|.|..|+.
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 4455577777777766554443 2233345677777764
No 71
>KOG2186|consensus
Probab=84.62 E-value=0.73 Score=30.15 Aligned_cols=46 Identities=20% Similarity=0.432 Sum_probs=33.7
Q ss_pred ccccccCcccCCHHHHHHHHHhccCCCCCceecCCCccccccchhHHhhcc
Q psy370 51 YSCEHCDMQFNCKSDMRKHVHSHLSMEERGFVCEICGHVVDEMPVATQSSK 101 (111)
Q Consensus 51 ~~c~~c~~~f~~~~~l~~h~~~h~~~~~~~~~C~~C~~~~~~~~~l~~h~~ 101 (111)
|.|.+||....-+..- .|+..-+ + ..|-|..|++.|... +..-|.+
T Consensus 4 FtCnvCgEsvKKp~ve-kH~srCr--n-~~fSCIDC~k~F~~~-sYknH~k 49 (276)
T KOG2186|consen 4 FTCNVCGESVKKPQVE-KHMSRCR--N-AYFSCIDCGKTFERV-SYKNHTK 49 (276)
T ss_pred EehhhhhhhccccchH-HHHHhcc--C-CeeEEeecccccccc-hhhhhhh
Confidence 7899999877665444 4776554 3 689999999999884 4666664
No 72
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=84.12 E-value=0.92 Score=20.48 Aligned_cols=33 Identities=30% Similarity=0.705 Sum_probs=16.6
Q ss_pred cccccCcccCCHHHHHHHHHhccCCCCCceecCCCccccc
Q psy370 52 SCEHCDMQFNCKSDMRKHVHSHLSMEERGFVCEICGHVVD 91 (111)
Q Consensus 52 ~c~~c~~~f~~~~~l~~h~~~h~~~~~~~~~C~~C~~~~~ 91 (111)
.|+.|+..|.-..+-.. . +.....|..|+..|.
T Consensus 4 ~CP~C~~~f~v~~~~l~-----~--~~~~vrC~~C~~~f~ 36 (37)
T PF13719_consen 4 TCPNCQTRFRVPDDKLP-----A--GGRKVRCPKCGHVFR 36 (37)
T ss_pred ECCCCCceEEcCHHHcc-----c--CCcEEECCCCCcEee
Confidence 45566655554432211 1 234566777776653
No 73
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=84.03 E-value=1.4 Score=22.22 Aligned_cols=11 Identities=27% Similarity=0.845 Sum_probs=7.0
Q ss_pred CCceecCCCcc
Q psy370 78 ERGFVCEICGH 88 (111)
Q Consensus 78 ~~~~~C~~C~~ 88 (111)
..+|.|+.||.
T Consensus 48 g~~Y~Cp~CGF 58 (61)
T COG2888 48 GNPYRCPKCGF 58 (61)
T ss_pred CCceECCCcCc
Confidence 34677777764
No 74
>PF05290 Baculo_IE-1: Baculovirus immediate-early protein (IE-0); InterPro: IPR007954 This entry contains the Baculovirus immediate-early protein IE-0.
Probab=83.42 E-value=0.48 Score=27.93 Aligned_cols=57 Identities=16% Similarity=0.431 Sum_probs=32.4
Q ss_pred cCcccCCCcccccCCHHHHHHHHHHcCCCCCccccccCcccCCH--HHHHHHHHhccCCCCCceecCCCccccccchh
Q psy370 20 FVASQCPVCKKIYTDQQLFQNHLETHDNEMDYSCEHCDMQFNCK--SDMRKHVHSHLSMEERGFVCEICGHVVDEMPV 95 (111)
Q Consensus 20 ~~~~~c~~C~~~f~~~~~l~~h~~~h~~~~~~~c~~c~~~f~~~--~~l~~h~~~h~~~~~~~~~C~~C~~~~~~~~~ 95 (111)
.+.|+|..|.++......| +|-+| ||...... ..|+.+-..+ -+|+.|.-+|.+++.
T Consensus 78 ~~lYeCnIC~etS~ee~FL----------KPneC--CgY~iCn~Cya~LWK~~~~y-------pvCPvCkTSFKss~~ 136 (140)
T PF05290_consen 78 PKLYECNICKETSAEERFL----------KPNEC--CGYSICNACYANLWKFCNLY-------PVCPVCKTSFKSSSS 136 (140)
T ss_pred CCceeccCcccccchhhcC----------Ccccc--cchHHHHHHHHHHHHHcccC-------CCCCccccccccccc
Confidence 4678888888776555433 23333 34322222 3444443333 379999999977653
No 75
>PF04959 ARS2: Arsenite-resistance protein 2; InterPro: IPR007042 This entry represents Arsenite-resistance protein 2 (also known as Serrate RNA effector molecule homolog) which is thought to play a role in arsenite resistance [], although does not directly confer arsenite resistance but rather modulates arsenic sensitivity []. Arsenite is a carcinogenic compound which can act as a comutagen by inhibiting DNA repair. It is also involved in cell cycle progression at S phase. ; PDB: 3AX1_A.
Probab=83.24 E-value=0.37 Score=30.79 Aligned_cols=28 Identities=14% Similarity=0.330 Sum_probs=19.0
Q ss_pred CCceecCCCccccccchhHHhhccccCc
Q psy370 78 ERGFVCEICGHVVDEMPVATQSSKYPGQ 105 (111)
Q Consensus 78 ~~~~~C~~C~~~~~~~~~l~~h~~~~~~ 105 (111)
+..|.|..|+|.|.-.....+|+...|.
T Consensus 75 ~~K~~C~lc~KlFkg~eFV~KHI~nKH~ 102 (214)
T PF04959_consen 75 EDKWRCPLCGKLFKGPEFVRKHIFNKHP 102 (214)
T ss_dssp SEEEEE-SSS-EESSHHHHHHHHHHH-H
T ss_pred CCEECCCCCCcccCChHHHHHHHhhcCH
Confidence 3457888888888888888888876663
No 76
>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=82.81 E-value=0.76 Score=20.65 Aligned_cols=11 Identities=45% Similarity=0.924 Sum_probs=6.6
Q ss_pred ceecCCCcccc
Q psy370 80 GFVCEICGHVV 90 (111)
Q Consensus 80 ~~~C~~C~~~~ 90 (111)
...|+.|+..|
T Consensus 25 ~v~C~~C~~~~ 35 (38)
T TIGR02098 25 KVRCGKCGHVW 35 (38)
T ss_pred EEECCCCCCEE
Confidence 35666666655
No 77
>KOG4167|consensus
Probab=81.96 E-value=0.21 Score=37.29 Aligned_cols=27 Identities=30% Similarity=0.468 Sum_probs=23.8
Q ss_pred eecCCCccccccchhHHhhccccCccc
Q psy370 81 FVCEICGHVVDEMPVATQSSKYPGQQN 107 (111)
Q Consensus 81 ~~C~~C~~~~~~~~~l~~h~~~~~~~~ 107 (111)
|.|..|+++|-....+.-|||+|...+
T Consensus 793 FpCreC~kvF~KiKSrNAHMK~Hr~q~ 819 (907)
T KOG4167|consen 793 FPCRECGKVFFKIKSRNAHMKTHRQQE 819 (907)
T ss_pred eehHHHHHHHHHHhhhhHHHHHHHHHH
Confidence 899999999999999999999987443
No 78
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=81.92 E-value=1 Score=20.21 Aligned_cols=32 Identities=25% Similarity=0.709 Sum_probs=16.2
Q ss_pred cccccCcccCCHHHHHHHHHhccCCCCCceecCCCcccc
Q psy370 52 SCEHCDMQFNCKSDMRKHVHSHLSMEERGFVCEICGHVV 90 (111)
Q Consensus 52 ~c~~c~~~f~~~~~l~~h~~~h~~~~~~~~~C~~C~~~~ 90 (111)
.|+.|...|.-...... . ......|..|+..|
T Consensus 4 ~Cp~C~~~y~i~d~~ip-----~--~g~~v~C~~C~~~f 35 (36)
T PF13717_consen 4 TCPNCQAKYEIDDEKIP-----P--KGRKVRCSKCGHVF 35 (36)
T ss_pred ECCCCCCEEeCCHHHCC-----C--CCcEEECCCCCCEe
Confidence 45556555554433221 1 23456677777665
No 79
>PF13878 zf-C2H2_3: zinc-finger of acetyl-transferase ESCO
Probab=81.67 E-value=0.65 Score=21.56 Aligned_cols=24 Identities=21% Similarity=0.379 Sum_probs=16.3
Q ss_pred eecCCCccccccc--hhHHhhccccC
Q psy370 81 FVCEICGHVVDEM--PVATQSSKYPG 104 (111)
Q Consensus 81 ~~C~~C~~~~~~~--~~l~~h~~~~~ 104 (111)
-.|..||.++... .+-..|.++|.
T Consensus 14 ~~C~~CgM~Y~~~~~eD~~~H~~yH~ 39 (41)
T PF13878_consen 14 TTCPTCGMLYSPGSPEDEKLHKKYHD 39 (41)
T ss_pred cCCCCCCCEECCCCHHHHHHHHHHHh
Confidence 4788888877444 45667777663
No 80
>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=80.06 E-value=1.3 Score=25.93 Aligned_cols=29 Identities=21% Similarity=0.211 Sum_probs=16.8
Q ss_pred cCCCcccccCCHHHHHHHHHHcCCCCCccccccCcccCCH
Q psy370 24 QCPVCKKIYTDQQLFQNHLETHDNEMDYSCEHCDMQFNCK 63 (111)
Q Consensus 24 ~c~~C~~~f~~~~~l~~h~~~h~~~~~~~c~~c~~~f~~~ 63 (111)
.|+.||+.|-.. +..|..|+.||..|...
T Consensus 11 ~Cp~cg~kFYDL-----------nk~p~vcP~cg~~~~~~ 39 (129)
T TIGR02300 11 ICPNTGSKFYDL-----------NRRPAVSPYTGEQFPPE 39 (129)
T ss_pred cCCCcCcccccc-----------CCCCccCCCcCCccCcc
Confidence 567777666321 23566777777665444
No 81
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=80.05 E-value=0.41 Score=29.03 Aligned_cols=12 Identities=25% Similarity=0.695 Sum_probs=5.9
Q ss_pred ccccccCcccCC
Q psy370 51 YSCEHCDMQFNC 62 (111)
Q Consensus 51 ~~c~~c~~~f~~ 62 (111)
+.|+.||.+|..
T Consensus 29 ~~c~~c~~~f~~ 40 (154)
T PRK00464 29 RECLACGKRFTT 40 (154)
T ss_pred eeccccCCcceE
Confidence 455555554443
No 82
>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=80.05 E-value=0.55 Score=29.60 Aligned_cols=35 Identities=17% Similarity=0.385 Sum_probs=0.0
Q ss_pred CCccCCCCccccCcccCCCccc-ccCCHHHHHHHHH
Q psy370 9 QSEIIPGSYTIFVASQCPVCKK-IYTDQQLFQNHLE 43 (111)
Q Consensus 9 ~~~~~~~~~~~~~~~~c~~C~~-~f~~~~~l~~h~~ 43 (111)
++-|..+-|...+.|.|.+||. +|.-...+..|..
T Consensus 88 IPyWLYKLhGL~~ey~CEICGN~~Y~GrkaFekHF~ 123 (196)
T PF11931_consen 88 IPYWLYKLHGLGVEYKCEICGNQSYKGRKAFEKHFQ 123 (196)
T ss_dssp ------------------------------------
T ss_pred ccHHHHHHhCCCCeeeeEeCCCcceecHHHHHHhcC
Confidence 5678888888888899999987 4545567777754
No 83
>KOG4167|consensus
Probab=79.79 E-value=0.94 Score=34.05 Aligned_cols=27 Identities=22% Similarity=0.401 Sum_probs=23.3
Q ss_pred cCcccCCCcccccCCHHHHHHHHHHcC
Q psy370 20 FVASQCPVCKKIYTDQQLFQNHLETHD 46 (111)
Q Consensus 20 ~~~~~c~~C~~~f~~~~~l~~h~~~h~ 46 (111)
..-|.|.+|++.|-....+..||++|.
T Consensus 790 ~giFpCreC~kvF~KiKSrNAHMK~Hr 816 (907)
T KOG4167|consen 790 TGIFPCRECGKVFFKIKSRNAHMKTHR 816 (907)
T ss_pred CceeehHHHHHHHHHHhhhhHHHHHHH
Confidence 456999999999988888999999886
No 84
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=78.98 E-value=0.51 Score=35.52 Aligned_cols=13 Identities=31% Similarity=0.509 Sum_probs=9.0
Q ss_pred CCCceecCCCccc
Q psy370 77 EERGFVCEICGHV 89 (111)
Q Consensus 77 ~~~~~~C~~C~~~ 89 (111)
...|..|+.||..
T Consensus 472 ~~~p~~Cp~Cgs~ 484 (730)
T COG1198 472 EPIPQSCPECGSE 484 (730)
T ss_pred CCCCCCCCCCCCC
Confidence 3567788888854
No 85
>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=78.83 E-value=1.2 Score=20.76 Aligned_cols=25 Identities=20% Similarity=0.399 Sum_probs=12.8
Q ss_pred CCceecCCCccccccc----hhHHhhccc
Q psy370 78 ERGFVCEICGHVVDEM----PVATQSSKY 102 (111)
Q Consensus 78 ~~~~~C~~C~~~~~~~----~~l~~h~~~ 102 (111)
..-..|..|++.+... ..|..|++.
T Consensus 14 ~~~a~C~~C~~~~~~~~~~ts~l~~HL~~ 42 (45)
T PF02892_consen 14 KKKAKCKYCGKVIKYSSGGTSNLKRHLKK 42 (45)
T ss_dssp SS-EEETTTTEE-----SSTHHHHHHHHH
T ss_pred cCeEEeCCCCeEEeeCCCcHHHHHHhhhh
Confidence 4446777777776553 457777643
No 86
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=78.45 E-value=1 Score=30.96 Aligned_cols=26 Identities=8% Similarity=0.171 Sum_probs=20.4
Q ss_pred ecCCCccccccchhHHhhccccCccc
Q psy370 82 VCEICGHVVDEMPVATQSSKYPGQQN 107 (111)
Q Consensus 82 ~C~~C~~~~~~~~~l~~h~~~~~~~~ 107 (111)
.|..|...|...+.|..|++..|...
T Consensus 222 ~C~FC~~~FYdDDEL~~HcR~~HE~C 247 (493)
T COG5236 222 LCIFCKIYFYDDDELRRHCRLRHEAC 247 (493)
T ss_pred hhhhccceecChHHHHHHHHhhhhhh
Confidence 48888888888888888888777543
No 87
>smart00734 ZnF_Rad18 Rad18-like CCHC zinc finger. Yeast Rad18p functions with Rad5p in error-free post-replicative DNA repair. This zinc finger is likely to bind nucleic-acids.
Probab=78.04 E-value=2.8 Score=17.30 Aligned_cols=18 Identities=44% Similarity=0.936 Sum_probs=10.4
Q ss_pred cCCCcccccCCHHHHHHHH
Q psy370 24 QCPVCKKIYTDQQLFQNHL 42 (111)
Q Consensus 24 ~c~~C~~~f~~~~~l~~h~ 42 (111)
.|++|++.+ ....+..|.
T Consensus 3 ~CPiC~~~v-~~~~in~HL 20 (26)
T smart00734 3 QCPVCFREV-PENLINSHL 20 (26)
T ss_pred cCCCCcCcc-cHHHHHHHH
Confidence 577777776 334455554
No 88
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=78.02 E-value=0.75 Score=24.23 Aligned_cols=18 Identities=22% Similarity=0.388 Sum_probs=11.9
Q ss_pred CCCceecC--CCccccccch
Q psy370 77 EERGFVCE--ICGHVVDEMP 94 (111)
Q Consensus 77 ~~~~~~C~--~C~~~~~~~~ 94 (111)
.+..+.|. .||.+|..--
T Consensus 24 ~~~Y~qC~N~eCg~tF~t~e 43 (72)
T PRK09678 24 KERYHQCQNVNCSATFITYE 43 (72)
T ss_pred heeeeecCCCCCCCEEEEEE
Confidence 34566776 7888776553
No 89
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=76.80 E-value=1.7 Score=21.06 Aligned_cols=12 Identities=33% Similarity=1.074 Sum_probs=7.0
Q ss_pred CCccccccCccc
Q psy370 49 MDYSCEHCDMQF 60 (111)
Q Consensus 49 ~~~~c~~c~~~f 60 (111)
..|.|..||..|
T Consensus 5 ~~Y~C~~Cg~~~ 16 (49)
T COG1996 5 MEYKCARCGREV 16 (49)
T ss_pred EEEEhhhcCCee
Confidence 345666666655
No 90
>PF12013 DUF3505: Protein of unknown function (DUF3505); InterPro: IPR022698 This family of proteins is functionally uncharacterised. This protein is found in eukaryotes. Proteins in this family are typically between 247 to 1018 amino acids in length. This region contains two segments that are likely to be C2H2 zinc binding domains.
Probab=75.28 E-value=1.7 Score=24.53 Aligned_cols=25 Identities=12% Similarity=0.316 Sum_probs=22.5
Q ss_pred eec----CCCccccccchhHHhhccccCc
Q psy370 81 FVC----EICGHVVDEMPVATQSSKYPGQ 105 (111)
Q Consensus 81 ~~C----~~C~~~~~~~~~l~~h~~~~~~ 105 (111)
|.| ..|+..+.+...+..|.+..|+
T Consensus 81 ~~C~~~~~~C~y~~~~~~~m~~H~~~~Hg 109 (109)
T PF12013_consen 81 YRCQCDPPHCGYITRSKKTMRKHWRKEHG 109 (109)
T ss_pred eeeecCCCCCCcEeccHHHHHHHHHHhcC
Confidence 789 9999999999999999988774
No 91
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=74.78 E-value=4.6 Score=23.19 Aligned_cols=79 Identities=15% Similarity=0.243 Sum_probs=45.3
Q ss_pred CcccCCCcccccCCHHHHHHHHHHcC------CCC-------CccccccCcccCCHHHHHHHHHhccCCCCCceecCCCc
Q psy370 21 VASQCPVCKKIYTDQQLFQNHLETHD------NEM-------DYSCEHCDMQFNCKSDMRKHVHSHLSMEERGFVCEICG 87 (111)
Q Consensus 21 ~~~~c~~C~~~f~~~~~l~~h~~~h~------~~~-------~~~c~~c~~~f~~~~~l~~h~~~h~~~~~~~~~C~~C~ 87 (111)
=|..|+.||-+......|.+.-- |. .+. .-.|..|...|........-. . . ....|.|+.|.
T Consensus 14 LP~~CpiCgLtLVss~HLARSyH-HLfPl~~f~ev~~~~~~~~~~C~~C~~~f~~~~~~~~~~-~-~--~~~~y~C~~C~ 88 (112)
T TIGR00622 14 LPVECPICGLTLILSTHLARSYH-HLFPLKAFQEIPLEEYNGSRFCFGCQGPFPKPPVSPFDE-L-K--DSHRYVCAVCK 88 (112)
T ss_pred CCCcCCcCCCEEeccchHHHhhh-ccCCCcccccccccccCCCCcccCcCCCCCCcccccccc-c-c--cccceeCCCCC
Confidence 36778889888777766654211 10 011 123777777776542111000 0 1 23468999999
Q ss_pred cccccchhHHhhccccC
Q psy370 88 HVVDEMPVATQSSKYPG 104 (111)
Q Consensus 88 ~~~~~~~~l~~h~~~~~ 104 (111)
..|=..-++--|..+|.
T Consensus 89 ~~FC~dCD~fiHe~Lh~ 105 (112)
T TIGR00622 89 NVFCVDCDVFVHESLHC 105 (112)
T ss_pred CccccccchhhhhhccC
Confidence 99977776666776653
No 92
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=74.16 E-value=1.8 Score=20.39 Aligned_cols=11 Identities=27% Similarity=0.637 Sum_probs=6.4
Q ss_pred ceecCCCcccc
Q psy370 80 GFVCEICGHVV 90 (111)
Q Consensus 80 ~~~C~~C~~~~ 90 (111)
+..|+.||...
T Consensus 19 ~irC~~CG~rI 29 (44)
T smart00659 19 VVRCRECGYRI 29 (44)
T ss_pred ceECCCCCceE
Confidence 35666666543
No 93
>KOG4173|consensus
Probab=73.17 E-value=1.8 Score=27.60 Aligned_cols=77 Identities=17% Similarity=0.347 Sum_probs=48.5
Q ss_pred ccCCC--cccccCCHHHHHHHHHHcCCCCCccccccCcccCCHHHHHHHHHhccC--------CCCCceec--CCCcccc
Q psy370 23 SQCPV--CKKIYTDQQLFQNHLETHDNEMDYSCEHCDMQFNCKSDMRKHVHSHLS--------MEERGFVC--EICGHVV 90 (111)
Q Consensus 23 ~~c~~--C~~~f~~~~~l~~h~~~h~~~~~~~c~~c~~~f~~~~~l~~h~~~h~~--------~~~~~~~C--~~C~~~~ 90 (111)
+.|++ |-+.|.....+..|-.+-.+ -.|.+|.+.|.+..-|..|+.-.+. +|.--|.| +.|+-.|
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 FACQVAGCCQVFDALDDYEHHYHTLHG---NSCSFCKRAFPTGHLLDAHILEWHDSLFQALVERGQDMYQCLVEGCTEKF 156 (253)
T ss_pred ccccccchHHHHhhhhhHHHhhhhccc---chhHHHHHhCCchhhhhHHHHHHHHHHHHHHHHcCccHHHHHHHhhhhhh
Confidence 44544 66777777777776544222 2788888888888777777653211 24445777 4588888
Q ss_pred ccchhHHhhccc
Q psy370 91 DEMPVATQSSKY 102 (111)
Q Consensus 91 ~~~~~l~~h~~~ 102 (111)
.+..+-..|+-.
T Consensus 157 kT~r~RkdH~I~ 168 (253)
T KOG4173|consen 157 KTSRDRKDHMIR 168 (253)
T ss_pred hhhhhhhhHHHH
Confidence 777666666543
No 94
>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=72.00 E-value=2.1 Score=17.78 Aligned_cols=9 Identities=33% Similarity=0.814 Sum_probs=4.9
Q ss_pred ecCCCcccc
Q psy370 82 VCEICGHVV 90 (111)
Q Consensus 82 ~C~~C~~~~ 90 (111)
.|+.||..|
T Consensus 16 ~Cp~CG~~F 24 (26)
T PF10571_consen 16 FCPHCGYDF 24 (26)
T ss_pred cCCCCCCCC
Confidence 455555555
No 95
>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=70.73 E-value=2.5 Score=17.24 Aligned_cols=11 Identities=36% Similarity=0.842 Sum_probs=7.2
Q ss_pred CCceecCCCcc
Q psy370 78 ERGFVCEICGH 88 (111)
Q Consensus 78 ~~~~~C~~C~~ 88 (111)
...|.|+.||.
T Consensus 14 ~v~f~CPnCG~ 24 (24)
T PF07754_consen 14 AVPFPCPNCGF 24 (24)
T ss_pred CceEeCCCCCC
Confidence 34677777773
No 96
>KOG2636|consensus
Probab=70.40 E-value=2.8 Score=29.78 Aligned_cols=35 Identities=14% Similarity=0.380 Sum_probs=26.5
Q ss_pred CCccCCCCccccCcccCCCcc-cccCCHHHHHHHHH
Q psy370 9 QSEIIPGSYTIFVASQCPVCK-KIYTDQQLFQNHLE 43 (111)
Q Consensus 9 ~~~~~~~~~~~~~~~~c~~C~-~~f~~~~~l~~h~~ 43 (111)
.+-|..+.|.....|.|.+|| .+|.-...+..|..
T Consensus 388 iPyWLyKLHGL~~ey~CEICGNy~Y~GrkaF~RHF~ 423 (497)
T KOG2636|consen 388 IPYWLYKLHGLDIEYNCEICGNYVYKGRKAFDRHFN 423 (497)
T ss_pred CchHHHhhcCCCcccceeeccCccccCcHHHHHHhH
Confidence 456777778888888888888 57777777777765
No 97
>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=69.91 E-value=2.9 Score=17.74 Aligned_cols=20 Identities=20% Similarity=0.330 Sum_probs=9.9
Q ss_pred eecCCCccccccchhHHhhcc
Q psy370 81 FVCEICGHVVDEMPVATQSSK 101 (111)
Q Consensus 81 ~~C~~C~~~~~~~~~l~~h~~ 101 (111)
|-|..|++.|. ......|.+
T Consensus 1 ~sCiDC~~~F~-~~~y~~Ht~ 20 (28)
T PF08790_consen 1 FSCIDCSKDFD-GDSYKSHTS 20 (28)
T ss_dssp EEETTTTEEEE-GGGTTT---
T ss_pred CeeecCCCCcC-cCCcCCCCc
Confidence 35677777773 334555544
No 98
>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=69.23 E-value=2.7 Score=19.48 Aligned_cols=17 Identities=29% Similarity=0.802 Sum_probs=12.6
Q ss_pred eecCCCccccccchhHH
Q psy370 81 FVCEICGHVVDEMPVAT 97 (111)
Q Consensus 81 ~~C~~C~~~~~~~~~l~ 97 (111)
|.|..||..|.....+.
T Consensus 6 y~C~~Cg~~fe~~~~~~ 22 (42)
T PF09723_consen 6 YRCEECGHEFEVLQSIS 22 (42)
T ss_pred EEeCCCCCEEEEEEEcC
Confidence 78999998887664433
No 99
>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=68.65 E-value=2.9 Score=18.85 Aligned_cols=14 Identities=36% Similarity=0.999 Sum_probs=11.0
Q ss_pred eecCCCccccccch
Q psy370 81 FVCEICGHVVDEMP 94 (111)
Q Consensus 81 ~~C~~C~~~~~~~~ 94 (111)
|.|..||..|....
T Consensus 6 y~C~~Cg~~fe~~~ 19 (41)
T smart00834 6 YRCEDCGHTFEVLQ 19 (41)
T ss_pred EEcCCCCCEEEEEE
Confidence 78999999886543
No 100
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=68.29 E-value=3.3 Score=18.94 Aligned_cols=14 Identities=36% Similarity=0.876 Sum_probs=11.5
Q ss_pred ceecCCCccccccc
Q psy370 80 GFVCEICGHVVDEM 93 (111)
Q Consensus 80 ~~~C~~C~~~~~~~ 93 (111)
||.|..|++.|=..
T Consensus 12 ~f~C~~C~~~FC~~ 25 (39)
T smart00154 12 GFKCRHCGNLFCGE 25 (39)
T ss_pred CeECCccCCccccc
Confidence 89999999988544
No 101
>KOG2231|consensus
Probab=68.13 E-value=6.4 Score=29.60 Aligned_cols=47 Identities=13% Similarity=0.350 Sum_probs=25.6
Q ss_pred cccccCcccCCHHHHHHHHHhccCCCCCceecCCCc------cccccchhHHhhccccC
Q psy370 52 SCEHCDMQFNCKSDMRKHVHSHLSMEERGFVCEICG------HVVDEMPVATQSSKYPG 104 (111)
Q Consensus 52 ~c~~c~~~f~~~~~l~~h~~~h~~~~~~~~~C~~C~------~~~~~~~~l~~h~~~~~ 104 (111)
.|..|...|.....+..|++.++ |.|..|. ..|..-++|..|.+..|
T Consensus 184 ~C~~C~~~fld~~el~rH~~~~h------~~chfC~~~~~~neyy~~~~dLe~HfR~~H 236 (669)
T KOG2231|consen 184 LCKFCHERFLDDDELYRHLRFDH------EFCHFCDYKTGQNEYYNDYDDLEEHFRKGH 236 (669)
T ss_pred cchhhhhhhccHHHHHHhhccce------eheeecCcccccchhcccchHHHHHhhhcC
Confidence 45666666666666666666544 4454442 22333345666665554
No 102
>KOG2785|consensus
Probab=67.16 E-value=6.4 Score=27.46 Aligned_cols=73 Identities=12% Similarity=0.283 Sum_probs=40.0
Q ss_pred cccCCCcccccCCHHHHHHHHHHcCCCCCccccccCcccCCHHHHHHHHHhccCCCCCceecCCCc---cccccchhHHh
Q psy370 22 ASQCPVCKKIYTDQQLFQNHLETHDNEMDYSCEHCDMQFNCKSDMRKHVHSHLSMEERGFVCEICG---HVVDEMPVATQ 98 (111)
Q Consensus 22 ~~~c~~C~~~f~~~~~l~~h~~~h~~~~~~~c~~c~~~f~~~~~l~~h~~~h~~~~~~~~~C~~C~---~~~~~~~~l~~ 98 (111)
|-.|-.|++.+.+...-..||..+.+- |... .........|...+..-. ...|.|-.|. +.|.+..+..+
T Consensus 166 Pt~CLfC~~~~k~~e~~~~HM~~~Hgf--fIPd--reYL~D~~GLl~YLgeKV---~~~~~CL~CN~~~~~f~sleavr~ 238 (390)
T KOG2785|consen 166 PTDCLFCDKKSKSLEENLKHMFKEHGF--FIPD--REYLTDEKGLLKYLGEKV---GIGFICLFCNELGRPFSSLEAVRA 238 (390)
T ss_pred CcceeecCCCcccHHHHHHHHhhccCC--cCCc--hHhhhchhHHHHHHHHHh---ccCceEEEeccccCcccccHHHHH
Confidence 345666666666655555555543321 1100 011223333444443332 2457888888 99999999999
Q ss_pred hcc
Q psy370 99 SSK 101 (111)
Q Consensus 99 h~~ 101 (111)
||.
T Consensus 239 HM~ 241 (390)
T KOG2785|consen 239 HMR 241 (390)
T ss_pred HHh
Confidence 994
No 103
>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=66.52 E-value=3.5 Score=27.32 Aligned_cols=86 Identities=15% Similarity=0.268 Sum_probs=49.4
Q ss_pred cccCcccCCCcccccCCHHHHHHHHHHc--CCCCCccccccCcccCCH------HHHHHHHHhcc--CCCCCceecCCCc
Q psy370 18 TIFVASQCPVCKKIYTDQQLFQNHLETH--DNEMDYSCEHCDMQFNCK------SDMRKHVHSHL--SMEERGFVCEICG 87 (111)
Q Consensus 18 ~~~~~~~c~~C~~~f~~~~~l~~h~~~h--~~~~~~~c~~c~~~f~~~------~~l~~h~~~h~--~~~~~~~~C~~C~ 87 (111)
-|-+.|+|..|..-...-..|. |+.+- .....|+|.-|.+.-..+ -....|.+.-. ....+++.|+.||
T Consensus 138 hGGrif~CsfC~~flCEDDQFE-HQAsCQvLe~E~~KC~SCNrlGq~sCLRCK~cfCddHvrrKg~ky~k~k~~PCPKCg 216 (314)
T PF06524_consen 138 HGGRIFKCSFCDNFLCEDDQFE-HQASCQVLESETFKCQSCNRLGQYSCLRCKICFCDDHVRRKGFKYEKGKPIPCPKCG 216 (314)
T ss_pred CCCeEEEeecCCCeeeccchhh-hhhhhhhhhcccccccccccccchhhhheeeeehhhhhhhcccccccCCCCCCCCCC
Confidence 3455789999986655555444 44432 234567776666532211 11224444210 0134788999999
Q ss_pred cccccchhHHhhccccC
Q psy370 88 HVVDEMPVATQSSKYPG 104 (111)
Q Consensus 88 ~~~~~~~~l~~h~~~~~ 104 (111)
.-.....+|....+.|-
T Consensus 217 ~et~eTkdLSmStR~hk 233 (314)
T PF06524_consen 217 YETQETKDLSMSTRSHK 233 (314)
T ss_pred Ccccccccceeeeecch
Confidence 88877777776666553
No 104
>PF02176 zf-TRAF: TRAF-type zinc finger; PDB: 2EOD_A 2YUC_A 3HCU_A 3HCS_B 3HCT_A.
Probab=66.31 E-value=4.7 Score=19.80 Aligned_cols=42 Identities=17% Similarity=0.422 Sum_probs=19.0
Q ss_pred Cccccc-cCcccCCHHHHHHHHHhccCCCCCceecCC----Cccccccc
Q psy370 50 DYSCEH-CDMQFNCKSDMRKHVHSHLSMEERGFVCEI----CGHVVDEM 93 (111)
Q Consensus 50 ~~~c~~-c~~~f~~~~~l~~h~~~h~~~~~~~~~C~~----C~~~~~~~ 93 (111)
+..|+. |+..-.....+..|+...- ..++..|.. |+..+...
T Consensus 9 ~v~C~~~cc~~~i~r~~l~~H~~~~C--~~~~v~C~~~~~GC~~~~~~~ 55 (60)
T PF02176_consen 9 PVPCPNGCCNEMIPRKELDDHLENEC--PKRPVPCPYSPYGCKERVPRE 55 (60)
T ss_dssp EEE-TT--S-BEEECCCHHHHHHTTS--TTSEEE-SS----S--EEEHH
T ss_pred EeeCCCCCcccceeHHHHHHHHHccC--CCCcEECCCCCCCCCCccchh
Confidence 344544 3323233446666766443 345667777 77666554
No 105
>PF04959 ARS2: Arsenite-resistance protein 2; InterPro: IPR007042 This entry represents Arsenite-resistance protein 2 (also known as Serrate RNA effector molecule homolog) which is thought to play a role in arsenite resistance [], although does not directly confer arsenite resistance but rather modulates arsenic sensitivity []. Arsenite is a carcinogenic compound which can act as a comutagen by inhibiting DNA repair. It is also involved in cell cycle progression at S phase. ; PDB: 3AX1_A.
Probab=65.75 E-value=5 Score=25.78 Aligned_cols=28 Identities=21% Similarity=0.553 Sum_probs=20.9
Q ss_pred ccCcccCCCcccccCCHHHHHHHHHH-cC
Q psy370 19 IFVASQCPVCKKIYTDQQLFQNHLET-HD 46 (111)
Q Consensus 19 ~~~~~~c~~C~~~f~~~~~l~~h~~~-h~ 46 (111)
.+..|.|+.|+|-|.-......|+.. |.
T Consensus 74 ~~~K~~C~lc~KlFkg~eFV~KHI~nKH~ 102 (214)
T PF04959_consen 74 DEDKWRCPLCGKLFKGPEFVRKHIFNKHP 102 (214)
T ss_dssp SSEEEEE-SSS-EESSHHHHHHHHHHH-H
T ss_pred cCCEECCCCCCcccCChHHHHHHHhhcCH
Confidence 34469999999999999999999875 44
No 106
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=65.50 E-value=2 Score=25.47 Aligned_cols=13 Identities=15% Similarity=0.626 Sum_probs=8.1
Q ss_pred CccccccCcccCC
Q psy370 50 DYSCEHCDMQFNC 62 (111)
Q Consensus 50 ~~~c~~c~~~f~~ 62 (111)
.+.|..||..|..
T Consensus 70 ~~~C~~CG~~~~~ 82 (135)
T PRK03824 70 VLKCRNCGNEWSL 82 (135)
T ss_pred EEECCCCCCEEec
Confidence 3667777765544
No 107
>PHA00626 hypothetical protein
Probab=65.44 E-value=3.8 Score=20.43 Aligned_cols=16 Identities=25% Similarity=0.476 Sum_probs=12.9
Q ss_pred CceecCCCccccccch
Q psy370 79 RGFVCEICGHVVDEMP 94 (111)
Q Consensus 79 ~~~~C~~C~~~~~~~~ 94 (111)
..|+|..||..|+...
T Consensus 22 nrYkCkdCGY~ft~~~ 37 (59)
T PHA00626 22 DDYVCCDCGYNDSKDA 37 (59)
T ss_pred cceEcCCCCCeechhh
Confidence 3599999999887664
No 108
>KOG2785|consensus
Probab=65.11 E-value=15 Score=25.71 Aligned_cols=24 Identities=21% Similarity=0.649 Sum_probs=18.8
Q ss_pred CCccccccC---cccCCHHHHHHHHHh
Q psy370 49 MDYSCEHCD---MQFNCKSDMRKHVHS 72 (111)
Q Consensus 49 ~~~~c~~c~---~~f~~~~~l~~h~~~ 72 (111)
.-+.|-+|. +.|.+....+.||..
T Consensus 216 ~~~~CL~CN~~~~~f~sleavr~HM~~ 242 (390)
T KOG2785|consen 216 IGFICLFCNELGRPFSSLEAVRAHMRD 242 (390)
T ss_pred cCceEEEeccccCcccccHHHHHHHhh
Confidence 446777777 888888888988874
No 109
>PLN03238 probable histone acetyltransferase MYST; Provisional
Probab=64.40 E-value=5 Score=26.95 Aligned_cols=23 Identities=26% Similarity=0.452 Sum_probs=14.4
Q ss_pred CCccccccCcccCCHHHHHHHHH
Q psy370 49 MDYSCEHCDMQFNCKSDMRKHVH 71 (111)
Q Consensus 49 ~~~~c~~c~~~f~~~~~l~~h~~ 71 (111)
..|.|..|-+.|.....+..|+.
T Consensus 47 ~lyiCe~Clky~~~~~~l~~H~~ 69 (290)
T PLN03238 47 KLYICEYCLKYMRKKKSLLRHLA 69 (290)
T ss_pred eEEEcCCCcchhCCHHHHHHHHH
Confidence 45666666666666666666655
No 110
>PF15269 zf-C2H2_7: Zinc-finger
Probab=62.48 E-value=16 Score=17.33 Aligned_cols=21 Identities=19% Similarity=0.453 Sum_probs=11.0
Q ss_pred ccCCCcccccCCHHHHHHHHH
Q psy370 23 SQCPVCKKIYTDQQLFQNHLE 43 (111)
Q Consensus 23 ~~c~~C~~~f~~~~~l~~h~~ 43 (111)
|+|-+|.-+-..++.|-.||+
T Consensus 21 ykcfqcpftc~~kshl~nhmk 41 (54)
T PF15269_consen 21 YKCFQCPFTCNEKSHLFNHMK 41 (54)
T ss_pred ceeecCCcccchHHHHHHHHH
Confidence 445555544445555555554
No 111
>COG3364 Zn-ribbon containing protein [General function prediction only]
Probab=61.99 E-value=5.4 Score=22.49 Aligned_cols=15 Identities=27% Similarity=0.802 Sum_probs=11.5
Q ss_pred cccCCCcccccCCHH
Q psy370 22 ASQCPVCKKIYTDQQ 36 (111)
Q Consensus 22 ~~~c~~C~~~f~~~~ 36 (111)
|++|..||..|...+
T Consensus 2 pH~CtrCG~vf~~g~ 16 (112)
T COG3364 2 PHQCTRCGEVFDDGS 16 (112)
T ss_pred Cceeccccccccccc
Confidence 678888888887753
No 112
>PF12907 zf-met2: Zinc-binding
Probab=61.98 E-value=3.3 Score=19.17 Aligned_cols=25 Identities=16% Similarity=0.497 Sum_probs=11.8
Q ss_pred ecCCCcccc---ccchhHHhhccccCcc
Q psy370 82 VCEICGHVV---DEMPVATQSSKYPGQQ 106 (111)
Q Consensus 82 ~C~~C~~~~---~~~~~l~~h~~~~~~~ 106 (111)
.|..|..+| .+...|..|....|..
T Consensus 3 ~C~iC~qtF~~t~~~~~L~eH~enKHpK 30 (40)
T PF12907_consen 3 ICKICRQTFMQTTNEPQLKEHAENKHPK 30 (40)
T ss_pred CcHHhhHHHHhcCCHHHHHHHHHccCCC
Confidence 455555333 2334455555544443
No 113
>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=60.57 E-value=4.8 Score=19.29 Aligned_cols=13 Identities=31% Similarity=1.012 Sum_probs=10.5
Q ss_pred eecCCCccccccc
Q psy370 81 FVCEICGHVVDEM 93 (111)
Q Consensus 81 ~~C~~C~~~~~~~ 93 (111)
|.|..||..|...
T Consensus 6 y~C~~Cg~~fe~~ 18 (52)
T TIGR02605 6 YRCTACGHRFEVL 18 (52)
T ss_pred EEeCCCCCEeEEE
Confidence 7899999988655
No 114
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=60.49 E-value=1.1 Score=20.63 Aligned_cols=12 Identities=42% Similarity=0.883 Sum_probs=8.6
Q ss_pred ceecCCCccccc
Q psy370 80 GFVCEICGHVVD 91 (111)
Q Consensus 80 ~~~C~~C~~~~~ 91 (111)
-|.|..|+..|.
T Consensus 28 fy~C~~C~~~w~ 39 (40)
T smart00440 28 FYVCTKCGHRWR 39 (40)
T ss_pred EEEeCCCCCEeC
Confidence 367888887664
No 115
>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=60.08 E-value=4.2 Score=18.89 Aligned_cols=15 Identities=27% Similarity=0.498 Sum_probs=9.4
Q ss_pred CceecCCCccccccc
Q psy370 79 RGFVCEICGHVVDEM 93 (111)
Q Consensus 79 ~~~~C~~C~~~~~~~ 93 (111)
.|+.|..|++.|=..
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 578999999988433
No 116
>PRK14873 primosome assembly protein PriA; Provisional
Probab=59.92 E-value=1.7 Score=32.54 Aligned_cols=9 Identities=33% Similarity=1.043 Sum_probs=5.6
Q ss_pred ceecCCCcc
Q psy370 80 GFVCEICGH 88 (111)
Q Consensus 80 ~~~C~~C~~ 88 (111)
++.|+.||.
T Consensus 422 p~~Cp~Cgs 430 (665)
T PRK14873 422 DWRCPRCGS 430 (665)
T ss_pred CccCCCCcC
Confidence 556666664
No 117
>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=59.36 E-value=7.5 Score=19.77 Aligned_cols=9 Identities=33% Similarity=1.091 Sum_probs=2.6
Q ss_pred cCCCccccc
Q psy370 24 QCPVCKKIY 32 (111)
Q Consensus 24 ~c~~C~~~f 32 (111)
.|..|++.|
T Consensus 11 ~C~~C~~~F 19 (69)
T PF01363_consen 11 NCMICGKKF 19 (69)
T ss_dssp B-TTT--B-
T ss_pred cCcCcCCcC
Confidence 455555555
No 118
>PF13451 zf-trcl: Probable zinc-binding domain
Probab=57.89 E-value=6.2 Score=19.14 Aligned_cols=17 Identities=18% Similarity=0.464 Sum_probs=13.4
Q ss_pred CCceecCCCccccccch
Q psy370 78 ERGFVCEICGHVVDEMP 94 (111)
Q Consensus 78 ~~~~~C~~C~~~~~~~~ 94 (111)
++.+.|..||..|....
T Consensus 2 Dk~l~C~dCg~~FvfTa 18 (49)
T PF13451_consen 2 DKTLTCKDCGAEFVFTA 18 (49)
T ss_pred CeeEEcccCCCeEEEeh
Confidence 46788999999887764
No 119
>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=56.56 E-value=2.4 Score=30.63 Aligned_cols=9 Identities=33% Similarity=0.818 Sum_probs=5.1
Q ss_pred ceecCCCcc
Q psy370 80 GFVCEICGH 88 (111)
Q Consensus 80 ~~~C~~C~~ 88 (111)
|..|+.||.
T Consensus 253 ~~~Cp~C~s 261 (505)
T TIGR00595 253 PKTCPQCGS 261 (505)
T ss_pred CCCCCCCCC
Confidence 455666654
No 120
>PLN03239 histone acetyltransferase; Provisional
Probab=56.30 E-value=6.4 Score=27.22 Aligned_cols=24 Identities=13% Similarity=0.110 Sum_probs=19.0
Q ss_pred CCceecCCCccccccchhHHhhcc
Q psy370 78 ERGFVCEICGHVVDEMPVATQSSK 101 (111)
Q Consensus 78 ~~~~~C~~C~~~~~~~~~l~~h~~ 101 (111)
+.-|.|+.|.+-|.+...|..|+.
T Consensus 104 ~~lYiCE~Clky~~~~~~l~~H~~ 127 (351)
T PLN03239 104 DVLYVCEFSFGFFARKSELLRFQA 127 (351)
T ss_pred ceEEEeccchhhhcCHHHHHHHHH
Confidence 356889999988888888888764
No 121
>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=55.99 E-value=1.8 Score=32.56 Aligned_cols=60 Identities=18% Similarity=0.399 Sum_probs=34.7
Q ss_pred Cccc-CCCcccccCCHHHHHHHHHHcCCCCCc-cccccCcccCCHHHHHHHHHhccCCCCCceecCCCccc
Q psy370 21 VASQ-CPVCKKIYTDQQLFQNHLETHDNEMDY-SCEHCDMQFNCKSDMRKHVHSHLSMEERGFVCEICGHV 89 (111)
Q Consensus 21 ~~~~-c~~C~~~f~~~~~l~~h~~~h~~~~~~-~c~~c~~~f~~~~~l~~h~~~h~~~~~~~~~C~~C~~~ 89 (111)
-||. |..||..|+....|-= -|-++....| .|..|.+.+..+ ..+|.|. .|.-|+.||-.
T Consensus 121 YPF~~CT~CGPRfTIi~alPY-DR~nTsM~~F~lC~~C~~EY~dP----~nRRfHA----Qp~aCp~CGP~ 182 (750)
T COG0068 121 YPFINCTNCGPRFTIIEALPY-DRENTSMADFPLCPFCDKEYKDP----LNRRFHA----QPIACPKCGPH 182 (750)
T ss_pred ccccccCCCCcceeeeccCCC-CcccCccccCcCCHHHHHHhcCc----ccccccc----ccccCcccCCC
Confidence 3555 8889999886655421 1122322222 477777655554 2345564 46789999963
No 122
>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=55.96 E-value=3.7 Score=19.00 Aligned_cols=12 Identities=50% Similarity=1.146 Sum_probs=6.0
Q ss_pred eecCCCcccccc
Q psy370 81 FVCEICGHVVDE 92 (111)
Q Consensus 81 ~~C~~C~~~~~~ 92 (111)
+.|..||.+...
T Consensus 20 ~vC~~CG~Vl~e 31 (43)
T PF08271_consen 20 LVCPNCGLVLEE 31 (43)
T ss_dssp EEETTT-BBEE-
T ss_pred EECCCCCCEeec
Confidence 566667655543
No 123
>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=55.42 E-value=5.1 Score=18.73 Aligned_cols=13 Identities=23% Similarity=0.708 Sum_probs=10.3
Q ss_pred ecCCCccccccch
Q psy370 82 VCEICGHVVDEMP 94 (111)
Q Consensus 82 ~C~~C~~~~~~~~ 94 (111)
.|..||+.|+.+.
T Consensus 10 ~C~~C~rpf~WRK 22 (42)
T PF10013_consen 10 ICPVCGRPFTWRK 22 (42)
T ss_pred cCcccCCcchHHH
Confidence 5888988888764
No 124
>PTZ00064 histone acetyltransferase; Provisional
Probab=55.30 E-value=7.4 Score=28.31 Aligned_cols=33 Identities=12% Similarity=0.140 Sum_probs=24.4
Q ss_pred CCceecCCCccccccchhHHhhcc----ccCcccccc
Q psy370 78 ERGFVCEICGHVVDEMPVATQSSK----YPGQQNQLF 110 (111)
Q Consensus 78 ~~~~~C~~C~~~~~~~~~l~~h~~----~~~~~~~~~ 110 (111)
..-|.|+.|.+-|.....|..|+. .|+.++.+|
T Consensus 278 d~LYICEfCLkY~~s~~~l~rH~~~C~~rhPPG~EIY 314 (552)
T PTZ00064 278 DTLHFCEYCLDFFCFEDELIRHLSRCQLRHPPGNEIY 314 (552)
T ss_pred CeEEEccchhhhhCCHHHHHHHHhcCCCCCCCCCeEE
Confidence 456889999999999888998985 445554443
No 125
>KOG2482|consensus
Probab=54.98 E-value=5.7 Score=27.44 Aligned_cols=22 Identities=9% Similarity=0.354 Sum_probs=20.3
Q ss_pred ceecCCCccccccchhHHhhcc
Q psy370 80 GFVCEICGHVVDEMPVATQSSK 101 (111)
Q Consensus 80 ~~~C~~C~~~~~~~~~l~~h~~ 101 (111)
.+.|-+|.+.|..+..|+.||+
T Consensus 195 r~~CLyCekifrdkntLkeHMr 216 (423)
T KOG2482|consen 195 RLRCLYCEKIFRDKNTLKEHMR 216 (423)
T ss_pred hheeeeeccccCCcHHHHHHHH
Confidence 4689999999999999999996
No 126
>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=54.94 E-value=20 Score=20.18 Aligned_cols=39 Identities=15% Similarity=0.225 Sum_probs=28.7
Q ss_pred cCcccCCCcccccCCHHHHHHHHHHcCCCCCccccccCcc
Q psy370 20 FVASQCPVCKKIYTDQQLFQNHLETHDNEMDYSCEHCDMQ 59 (111)
Q Consensus 20 ~~~~~c~~C~~~f~~~~~l~~h~~~h~~~~~~~c~~c~~~ 59 (111)
++.|.|+.-|+.|.+...+...+... ..+.|.|...|+.
T Consensus 1 eeVf~i~~T~EiF~dYe~Y~~R~~~y-~~~vwtC~~TGk~ 39 (102)
T PF10537_consen 1 EEVFYIPFTGEIFRDYEEYLKRMILY-NQRVWTCEITGKS 39 (102)
T ss_pred CceEEeCCCCcccCCHHHHHHHHHHH-hCCeeEEecCCCC
Confidence 35688899999999998776654433 3477899888864
No 127
>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=54.81 E-value=7 Score=16.82 Aligned_cols=11 Identities=45% Similarity=0.966 Sum_probs=6.4
Q ss_pred CceecCCCccc
Q psy370 79 RGFVCEICGHV 89 (111)
Q Consensus 79 ~~~~C~~C~~~ 89 (111)
..+.|+.|+..
T Consensus 18 ~~~vCp~C~~e 28 (30)
T PF08274_consen 18 ELLVCPECGHE 28 (30)
T ss_dssp SSEEETTTTEE
T ss_pred CEEeCCccccc
Confidence 44666666643
No 128
>KOG3408|consensus
Probab=54.79 E-value=6.9 Score=22.80 Aligned_cols=25 Identities=16% Similarity=0.211 Sum_probs=17.1
Q ss_pred CCceecCCCccccccchhHHhhccc
Q psy370 78 ERGFVCEICGHVVDEMPVATQSSKY 102 (111)
Q Consensus 78 ~~~~~C~~C~~~~~~~~~l~~h~~~ 102 (111)
.-.|.|..|.+-|.+...|..|.+.
T Consensus 55 ~GqfyCi~CaRyFi~~~~l~~H~kt 79 (129)
T KOG3408|consen 55 GGQFYCIECARYFIDAKALKTHFKT 79 (129)
T ss_pred CceeehhhhhhhhcchHHHHHHHhc
Confidence 3346777777777777777777654
No 129
>PLN02294 cytochrome c oxidase subunit Vb
Probab=54.72 E-value=7.8 Score=23.99 Aligned_cols=17 Identities=18% Similarity=0.612 Sum_probs=13.7
Q ss_pred CCCceecCCCccccccc
Q psy370 77 EERGFVCEICGHVVDEM 93 (111)
Q Consensus 77 ~~~~~~C~~C~~~~~~~ 93 (111)
..++..|..||..|.-.
T Consensus 138 kGkp~RCpeCG~~fkL~ 154 (174)
T PLN02294 138 KGKSFECPVCTQYFELE 154 (174)
T ss_pred CCCceeCCCCCCEEEEE
Confidence 35789999999988654
No 130
>COG3091 SprT Zn-dependent metalloprotease, SprT family [General function prediction only]
Probab=54.62 E-value=6.2 Score=23.94 Aligned_cols=35 Identities=20% Similarity=0.518 Sum_probs=19.0
Q ss_pred CCccccccCcccCCHHHHHHHHHhccCCCCCceecCCCcccc
Q psy370 49 MDYSCEHCDMQFNCKSDMRKHVHSHLSMEERGFVCEICGHVV 90 (111)
Q Consensus 49 ~~~~c~~c~~~f~~~~~l~~h~~~h~~~~~~~~~C~~C~~~~ 90 (111)
-+|.|. |+.-+.+..-... ... |+ -|.|..|+-..
T Consensus 116 ~~Y~C~-C~q~~l~~RRhn~---~~~--g~-~YrC~~C~gkL 150 (156)
T COG3091 116 YPYRCQ-CQQHYLRIRRHNT---VRR--GE-VYRCGKCGGKL 150 (156)
T ss_pred eeEEee-cCCccchhhhccc---ccc--cc-eEEeccCCceE
Confidence 457777 7766544322211 111 44 68888887543
No 131
>PLN00104 MYST -like histone acetyltransferase; Provisional
Probab=54.61 E-value=7.1 Score=27.96 Aligned_cols=24 Identities=17% Similarity=0.398 Sum_probs=19.0
Q ss_pred CCceecCCCccccccchhHHhhcc
Q psy370 78 ERGFVCEICGHVVDEMPVATQSSK 101 (111)
Q Consensus 78 ~~~~~C~~C~~~~~~~~~l~~h~~ 101 (111)
..-|.|+.|.+-|.....|..|+.
T Consensus 196 ~~lyiCe~Cl~y~~~~~~~~~H~~ 219 (450)
T PLN00104 196 SKLYFCEFCLKFMKRKEQLQRHMK 219 (450)
T ss_pred CeEEEchhhhhhhcCHHHHHHHHh
Confidence 456788888888888888888875
No 132
>KOG0320|consensus
Probab=53.91 E-value=12 Score=23.35 Aligned_cols=56 Identities=14% Similarity=0.316 Sum_probs=31.3
Q ss_pred cccCcccCCCcccccCCHHHHHHHHHHcCCCCCccccccCcccCCHHHHHHHHHhccCCCCCceecCCCccccccchh
Q psy370 18 TIFVASQCPVCKKIYTDQQLFQNHLETHDNEMDYSCEHCDMQFNCKSDMRKHVHSHLSMEERGFVCEICGHVVDEMPV 95 (111)
Q Consensus 18 ~~~~~~~c~~C~~~f~~~~~l~~h~~~h~~~~~~~c~~c~~~f~~~~~l~~h~~~h~~~~~~~~~C~~C~~~~~~~~~ 95 (111)
..+..|.|++|.-.|..+.. ....||..|... ...-.. ...-+|+.|++....+..
T Consensus 127 ~~~~~~~CPiCl~~~sek~~--------------vsTkCGHvFC~~--Cik~al------k~~~~CP~C~kkIt~k~~ 182 (187)
T KOG0320|consen 127 RKEGTYKCPICLDSVSEKVP--------------VSTKCGHVFCSQ--CIKDAL------KNTNKCPTCRKKITHKQF 182 (187)
T ss_pred ccccccCCCceecchhhccc--------------cccccchhHHHH--HHHHHH------HhCCCCCCcccccchhhh
Confidence 33456999999777655432 334455555442 111111 123589999987666543
No 133
>KOG1842|consensus
Probab=53.42 E-value=5.1 Score=28.57 Aligned_cols=28 Identities=18% Similarity=0.399 Sum_probs=14.9
Q ss_pred ceecCCCccccccchhHHhhccccCccc
Q psy370 80 GFVCEICGHVVDEMPVATQSSKYPGQQN 107 (111)
Q Consensus 80 ~~~C~~C~~~~~~~~~l~~h~~~~~~~~ 107 (111)
.|.|+.|+.-|.+...|..|.-.-|.++
T Consensus 15 gflCPiC~~dl~~~~~L~~H~d~eH~~e 42 (505)
T KOG1842|consen 15 GFLCPICLLDLPNLSALNDHLDVEHFEE 42 (505)
T ss_pred cccCchHhhhhhhHHHHHHHHhhhcccc
Confidence 3555555555555555555555444433
No 134
>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=53.22 E-value=8.7 Score=21.47 Aligned_cols=22 Identities=23% Similarity=0.401 Sum_probs=15.7
Q ss_pred HHHhccCCCCCceecCCCccccccc
Q psy370 69 HVHSHLSMEERGFVCEICGHVVDEM 93 (111)
Q Consensus 69 h~~~h~~~~~~~~~C~~C~~~~~~~ 93 (111)
++..+. .++..|..||..|.-.
T Consensus 71 W~~l~~---g~~~rC~eCG~~fkL~ 92 (97)
T cd00924 71 WMWLEK---GKPKRCPECGHVFKLV 92 (97)
T ss_pred EEEEeC---CCceeCCCCCcEEEEE
Confidence 444553 4799999999988643
No 135
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=53.08 E-value=8.8 Score=27.27 Aligned_cols=13 Identities=15% Similarity=0.662 Sum_probs=6.7
Q ss_pred CccccccCcccCC
Q psy370 50 DYSCEHCDMQFNC 62 (111)
Q Consensus 50 ~~~c~~c~~~f~~ 62 (111)
-|.|..||..+..
T Consensus 367 g~rC~kCg~~~~~ 379 (421)
T COG1571 367 GFRCKKCGTRARE 379 (421)
T ss_pred CcccccccccCCc
Confidence 4555555554443
No 136
>PF05443 ROS_MUCR: ROS/MUCR transcriptional regulator protein; InterPro: IPR008807 This family consists of several ROS/MUCR transcriptional regulator proteins. The ros chromosomal gene is present in octopine and nopaline strains of Agrobacterium tumefaciens as well as in Rhizobium meliloti (Sinorhizobium meliloti). This gene encodes a 15.5 kDa protein that specifically represses the virC and virD operons in the virulence region of the Ti plasmid [] and is necessary for succinoglycan production []. S. meliloti can produce two types of acidic exopolysaccharides, succinoglycan and galactoglucan, that are interchangeable for infection of Medicago sativa (Alfalfa) nodules. MucR from S. meliloti acts as a transcriptional repressor that blocks the expression of the exp genes responsible for galactoglucan production therefore allowing the exclusive production of succinoglycan [].; GO: 0003677 DNA binding, 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2JSP_A.
Probab=53.06 E-value=11 Score=22.40 Aligned_cols=23 Identities=30% Similarity=0.551 Sum_probs=14.3
Q ss_pred cccCCCcccccCCHHHHHHHHHHcCC
Q psy370 22 ASQCPVCKKIYTDQQLFQNHLETHDN 47 (111)
Q Consensus 22 ~~~c~~C~~~f~~~~~l~~h~~~h~~ 47 (111)
...|-+||+.|... ..|.++|-|
T Consensus 72 ~i~clecGk~~k~L---krHL~~~~g 94 (132)
T PF05443_consen 72 YIICLECGKKFKTL---KRHLRTHHG 94 (132)
T ss_dssp -EE-TBT--EESBH---HHHHHHTT-
T ss_pred eeEEccCCcccchH---HHHHHHccC
Confidence 45699999999876 688888744
No 137
>KOG2747|consensus
Probab=52.36 E-value=6.3 Score=27.71 Aligned_cols=33 Identities=15% Similarity=0.410 Sum_probs=24.7
Q ss_pred CCceecCCCccccccchhHHhhcc----ccCcccccc
Q psy370 78 ERGFVCEICGHVVDEMPVATQSSK----YPGQQNQLF 110 (111)
Q Consensus 78 ~~~~~C~~C~~~~~~~~~l~~h~~----~~~~~~~~~ 110 (111)
..-|.|+.|.+-...+..|..|++ .|+.++.+|
T Consensus 156 ~~lYiCEfCLkY~~s~~~l~rH~~kC~~rhPPG~EIY 192 (396)
T KOG2747|consen 156 DKLYICEFCLKYMKSRTSLQRHLKKCKLRHPPGNEIY 192 (396)
T ss_pred CeEEEehHHHhHhchHHHHHHHHHhcCCCCCCcceee
Confidence 345789999999999988999986 455555543
No 138
>TIGR00100 hypA hydrogenase nickel insertion protein HypA. In Hpylori, hypA mutant abolished hydrogenase activity and decrease in urease activity. Nickel supplementation in media restored urease activity and partial hydrogenase activity. HypA probably involved in inserting Ni in enzymes.
Probab=52.11 E-value=8.7 Score=22.04 Aligned_cols=12 Identities=25% Similarity=0.689 Sum_probs=7.6
Q ss_pred ccccccCcccCC
Q psy370 51 YSCEHCDMQFNC 62 (111)
Q Consensus 51 ~~c~~c~~~f~~ 62 (111)
..|..|+..|..
T Consensus 71 ~~C~~Cg~~~~~ 82 (115)
T TIGR00100 71 CECEDCSEEVSP 82 (115)
T ss_pred EEcccCCCEEec
Confidence 667777755544
No 139
>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=51.61 E-value=26 Score=16.36 Aligned_cols=10 Identities=20% Similarity=0.803 Sum_probs=7.2
Q ss_pred CceecCCCcc
Q psy370 79 RGFVCEICGH 88 (111)
Q Consensus 79 ~~~~C~~C~~ 88 (111)
..|.|..|++
T Consensus 36 ~~~~C~~C~~ 45 (46)
T PF12760_consen 36 GRYRCKACRK 45 (46)
T ss_pred CeEECCCCCC
Confidence 4578888775
No 140
>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=51.38 E-value=7.8 Score=17.89 Aligned_cols=12 Identities=33% Similarity=0.719 Sum_probs=9.2
Q ss_pred CceecCCCcccc
Q psy370 79 RGFVCEICGHVV 90 (111)
Q Consensus 79 ~~~~C~~C~~~~ 90 (111)
.+-.|++|+..|
T Consensus 28 ~~~~CpYCg~~y 39 (40)
T PF10276_consen 28 GPVVCPYCGTRY 39 (40)
T ss_dssp CEEEETTTTEEE
T ss_pred CeEECCCCCCEE
Confidence 456889998776
No 141
>KOG0978|consensus
Probab=51.37 E-value=6.1 Score=29.84 Aligned_cols=19 Identities=21% Similarity=0.328 Sum_probs=14.1
Q ss_pred CceecCCCccccccchhHH
Q psy370 79 RGFVCEICGHVVDEMPVAT 97 (111)
Q Consensus 79 ~~~~C~~C~~~~~~~~~l~ 97 (111)
+.-+||.|+..|+--+.+.
T Consensus 677 RqRKCP~Cn~aFganDv~~ 695 (698)
T KOG0978|consen 677 RQRKCPKCNAAFGANDVHR 695 (698)
T ss_pred hcCCCCCCCCCCCcccccc
Confidence 3458999999998776544
No 142
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=51.03 E-value=9 Score=21.92 Aligned_cols=12 Identities=17% Similarity=0.321 Sum_probs=7.3
Q ss_pred ccccccCcccCC
Q psy370 51 YSCEHCDMQFNC 62 (111)
Q Consensus 51 ~~c~~c~~~f~~ 62 (111)
+.|..|+..|..
T Consensus 71 ~~C~~Cg~~~~~ 82 (113)
T PRK12380 71 AWCWDCSQVVEI 82 (113)
T ss_pred EEcccCCCEEec
Confidence 567777755443
No 143
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=50.08 E-value=9.8 Score=17.81 Aligned_cols=29 Identities=28% Similarity=0.663 Sum_probs=17.8
Q ss_pred CccccccCcccCCHHHHHHHHHhccCCCCC-ceecCCCccccc
Q psy370 50 DYSCEHCDMQFNCKSDMRKHVHSHLSMEER-GFVCEICGHVVD 91 (111)
Q Consensus 50 ~~~c~~c~~~f~~~~~l~~h~~~h~~~~~~-~~~C~~C~~~~~ 91 (111)
.|.|..||..|.. . ... .+.|+.||..+.
T Consensus 3 ~y~C~~CG~~~~~-----------~--~~~~~~~Cp~CG~~~~ 32 (46)
T PRK00398 3 EYKCARCGREVEL-----------D--EYGTGVRCPYCGYRIL 32 (46)
T ss_pred EEECCCCCCEEEE-----------C--CCCCceECCCCCCeEE
Confidence 4677777765443 0 234 578888886553
No 144
>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=50.02 E-value=16 Score=16.07 Aligned_cols=20 Identities=20% Similarity=0.267 Sum_probs=11.9
Q ss_pred ceecCCCccccccchhHHhhc
Q psy370 80 GFVCEICGHVVDEMPVATQSS 100 (111)
Q Consensus 80 ~~~C~~C~~~~~~~~~l~~h~ 100 (111)
.+.|+.|++.+.... +..|.
T Consensus 4 ~~~C~nC~R~v~a~R-fA~HL 23 (33)
T PF08209_consen 4 YVECPNCGRPVAASR-FAPHL 23 (33)
T ss_dssp EEE-TTTSSEEEGGG-HHHHH
T ss_pred eEECCCCcCCcchhh-hHHHH
Confidence 467888888776554 44444
No 145
>KOG0717|consensus
Probab=49.42 E-value=10 Score=27.27 Aligned_cols=22 Identities=27% Similarity=0.655 Sum_probs=19.5
Q ss_pred ccCCCcccccCCHHHHHHHHHH
Q psy370 23 SQCPVCKKIYTDQQLFQNHLET 44 (111)
Q Consensus 23 ~~c~~C~~~f~~~~~l~~h~~~ 44 (111)
+.|.+|+++|.+..++..|..+
T Consensus 293 lyC~vCnKsFKseKq~kNHEnS 314 (508)
T KOG0717|consen 293 LYCVVCNKSFKSEKQLKNHENS 314 (508)
T ss_pred eEEeeccccccchHHHHhhHHH
Confidence 7899999999999999988653
No 146
>KOG3214|consensus
Probab=49.41 E-value=7.1 Score=21.93 Aligned_cols=43 Identities=16% Similarity=0.298 Sum_probs=22.6
Q ss_pred cccCcccCCCcccccCCHHHHHHHHHHcCCCCCccccccCcccCCHH
Q psy370 18 TIFVASQCPVCKKIYTDQQLFQNHLETHDNEMDYSCEHCDMQFNCKS 64 (111)
Q Consensus 18 ~~~~~~~c~~C~~~f~~~~~l~~h~~~h~~~~~~~c~~c~~~f~~~~ 64 (111)
..+..|.|+.|+---.-.-.+. ....-....|.+|+..|...-
T Consensus 19 ~ldt~FnClfcnHek~v~~~~D----k~~~iG~~sC~iC~esFqt~i 61 (109)
T KOG3214|consen 19 PLDTQFNCLFCNHEKSVSCTLD----KKHNIGKASCRICEESFQTTI 61 (109)
T ss_pred chheeeccCccccccceeeeeh----hhcCcceeeeeehhhhhccch
Confidence 4455688888853221111111 111224467888888887653
No 147
>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=48.49 E-value=16 Score=21.88 Aligned_cols=46 Identities=17% Similarity=0.302 Sum_probs=24.7
Q ss_pred ccCCCcccccCCHHHHHHHHH----H-cCCCCCccccccCcccCCHHHHHH
Q psy370 23 SQCPVCKKIYTDQQLFQNHLE----T-HDNEMDYSCEHCDMQFNCKSDMRK 68 (111)
Q Consensus 23 ~~c~~C~~~f~~~~~l~~h~~----~-h~~~~~~~c~~c~~~f~~~~~l~~ 68 (111)
..|..|+..+..-+.-..--. + -....-+.|+.|++.|...+.+..
T Consensus 92 sRC~~CN~~L~~v~~~~v~~~vp~~v~~~~~~f~~C~~C~kiyW~GsH~~~ 142 (147)
T PF01927_consen 92 SRCPKCNGPLRPVSKEEVKDRVPPYVYETYDEFWRCPGCGKIYWEGSHWRR 142 (147)
T ss_pred CccCCCCcEeeechhhccccccCccccccCCeEEECCCCCCEecccccHHH
Confidence 468888875543221111000 1 112345788888888877666553
No 148
>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=47.96 E-value=9.9 Score=18.58 Aligned_cols=25 Identities=8% Similarity=0.010 Sum_probs=11.6
Q ss_pred CceecCCCccccccchhHHhhcccc
Q psy370 79 RGFVCEICGHVVDEMPVATQSSKYP 103 (111)
Q Consensus 79 ~~~~C~~C~~~~~~~~~l~~h~~~~ 103 (111)
..|.|+.|+..|=..-++--|..+|
T Consensus 20 ~~y~C~~C~~~FC~dCD~fiHE~LH 44 (51)
T PF07975_consen 20 SRYRCPKCKNHFCIDCDVFIHETLH 44 (51)
T ss_dssp EEE--TTTT--B-HHHHHTTTTTS-
T ss_pred CeEECCCCCCccccCcChhhhcccc
Confidence 3477777777776665555555554
No 149
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=47.12 E-value=12 Score=21.60 Aligned_cols=12 Identities=25% Similarity=0.755 Sum_probs=7.0
Q ss_pred ccccccCcccCC
Q psy370 51 YSCEHCDMQFNC 62 (111)
Q Consensus 51 ~~c~~c~~~f~~ 62 (111)
+.|..|+..|..
T Consensus 72 ~~C~~Cg~~~~~ 83 (117)
T PRK00564 72 LECKDCSHVFKP 83 (117)
T ss_pred EEhhhCCCcccc
Confidence 567777654433
No 150
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=46.92 E-value=17 Score=22.66 Aligned_cols=10 Identities=40% Similarity=1.109 Sum_probs=6.3
Q ss_pred eecCCCcccc
Q psy370 81 FVCEICGHVV 90 (111)
Q Consensus 81 ~~C~~C~~~~ 90 (111)
|.|+.||...
T Consensus 133 F~Cp~Cg~~L 142 (176)
T COG1675 133 FTCPKCGEDL 142 (176)
T ss_pred CCCCCCCchh
Confidence 6777777543
No 151
>KOG2593|consensus
Probab=45.66 E-value=35 Score=24.41 Aligned_cols=40 Identities=25% Similarity=0.579 Sum_probs=27.5
Q ss_pred CCCCCccccccCcccCCHHHHHHHHHhccCCCCCceecCCCcccc
Q psy370 46 DNEMDYSCEHCDMQFNCKSDMRKHVHSHLSMEERGFVCEICGHVV 90 (111)
Q Consensus 46 ~~~~~~~c~~c~~~f~~~~~l~~h~~~h~~~~~~~~~C~~C~~~~ 90 (111)
+....|.|+.|.+.|.....++- ... ..--|.|..|+--.
T Consensus 124 t~~~~Y~Cp~C~kkyt~Lea~~L---~~~--~~~~F~C~~C~gel 163 (436)
T KOG2593|consen 124 TNVAGYVCPNCQKKYTSLEALQL---LDN--ETGEFHCENCGGEL 163 (436)
T ss_pred cccccccCCccccchhhhHHHHh---hcc--cCceEEEecCCCch
Confidence 34567999999998887766553 221 23459999998544
No 152
>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=44.53 E-value=13 Score=21.23 Aligned_cols=12 Identities=17% Similarity=0.636 Sum_probs=5.1
Q ss_pred ccCCCcccccCC
Q psy370 23 SQCPVCKKIYTD 34 (111)
Q Consensus 23 ~~c~~C~~~f~~ 34 (111)
..|..||..|..
T Consensus 71 ~~C~~Cg~~~~~ 82 (113)
T PF01155_consen 71 ARCRDCGHEFEP 82 (113)
T ss_dssp EEETTTS-EEEC
T ss_pred EECCCCCCEEec
Confidence 345555544433
No 153
>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=43.53 E-value=9 Score=17.27 Aligned_cols=12 Identities=25% Similarity=0.514 Sum_probs=6.6
Q ss_pred CcccCCCccccc
Q psy370 21 VASQCPVCKKIY 32 (111)
Q Consensus 21 ~~~~c~~C~~~f 32 (111)
+-|+|..||...
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 458899998765
No 154
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=43.34 E-value=10 Score=20.93 Aligned_cols=14 Identities=29% Similarity=0.667 Sum_probs=11.5
Q ss_pred CceecCCCcccccc
Q psy370 79 RGFVCEICGHVVDE 92 (111)
Q Consensus 79 ~~~~C~~C~~~~~~ 92 (111)
.|-.|..||..|..
T Consensus 57 ~Pa~CkkCGfef~~ 70 (97)
T COG3357 57 RPARCKKCGFEFRD 70 (97)
T ss_pred cChhhcccCccccc
Confidence 46689999998876
No 155
>COG1773 Rubredoxin [Energy production and conversion]
Probab=43.08 E-value=13 Score=18.48 Aligned_cols=12 Identities=42% Similarity=1.063 Sum_probs=7.6
Q ss_pred ceecCCCccccc
Q psy370 80 GFVCEICGHVVD 91 (111)
Q Consensus 80 ~~~C~~C~~~~~ 91 (111)
.|+|..||..|.
T Consensus 3 ~~~C~~CG~vYd 14 (55)
T COG1773 3 RWRCSVCGYVYD 14 (55)
T ss_pred ceEecCCceEec
Confidence 466777776653
No 156
>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=43.04 E-value=21 Score=17.23 Aligned_cols=14 Identities=21% Similarity=0.524 Sum_probs=7.3
Q ss_pred CCccccccCcccCC
Q psy370 49 MDYSCEHCDMQFNC 62 (111)
Q Consensus 49 ~~~~c~~c~~~f~~ 62 (111)
+.+.|..||..|..
T Consensus 17 rk~~Cr~Cg~~~C~ 30 (57)
T cd00065 17 RRHHCRNCGRIFCS 30 (57)
T ss_pred cccccCcCcCCcCh
Confidence 34456666655443
No 157
>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=43.01 E-value=9.3 Score=18.57 Aligned_cols=13 Identities=23% Similarity=0.887 Sum_probs=7.0
Q ss_pred cCCCcccccCCHH
Q psy370 24 QCPVCKKIYTDQQ 36 (111)
Q Consensus 24 ~c~~C~~~f~~~~ 36 (111)
.|++|++.|....
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 7999999987653
No 158
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=41.55 E-value=14 Score=21.75 Aligned_cols=18 Identities=17% Similarity=0.530 Sum_probs=14.1
Q ss_pred CCCceecCCCccccccch
Q psy370 77 EERGFVCEICGHVVDEMP 94 (111)
Q Consensus 77 ~~~~~~C~~C~~~~~~~~ 94 (111)
|...|.|..|+++|....
T Consensus 50 ~~qRyrC~~C~~tf~~~~ 67 (129)
T COG3677 50 GHQRYKCKSCGSTFTVET 67 (129)
T ss_pred cccccccCCcCcceeeec
Confidence 345689999999997663
No 159
>COG4338 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=41.46 E-value=12 Score=18.05 Aligned_cols=16 Identities=19% Similarity=0.549 Sum_probs=11.0
Q ss_pred cccccCcccCCHHHHH
Q psy370 52 SCEHCDMQFNCKSDMR 67 (111)
Q Consensus 52 ~c~~c~~~f~~~~~l~ 67 (111)
.|++|++.|.+...+.
T Consensus 14 ICpvCqRPFsWRkKW~ 29 (54)
T COG4338 14 ICPVCQRPFSWRKKWA 29 (54)
T ss_pred hhhhhcCchHHHHHHH
Confidence 6788888877765444
No 160
>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=41.21 E-value=46 Score=16.78 Aligned_cols=17 Identities=35% Similarity=0.702 Sum_probs=11.7
Q ss_pred CCCceecCCCccccccc
Q psy370 77 EERGFVCEICGHVVDEM 93 (111)
Q Consensus 77 ~~~~~~C~~C~~~~~~~ 93 (111)
..+-|.|+.||..+...
T Consensus 43 ~~r~~~C~~Cg~~~~rD 59 (69)
T PF07282_consen 43 SGRVFTCPNCGFEMDRD 59 (69)
T ss_pred ccceEEcCCCCCEECcH
Confidence 34568888888776544
No 161
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=40.60 E-value=16 Score=20.88 Aligned_cols=10 Identities=30% Similarity=0.693 Sum_probs=6.1
Q ss_pred ccccccCccc
Q psy370 51 YSCEHCDMQF 60 (111)
Q Consensus 51 ~~c~~c~~~f 60 (111)
+.|..|+..|
T Consensus 71 ~~C~~Cg~~~ 80 (114)
T PRK03681 71 CWCETCQQYV 80 (114)
T ss_pred EEcccCCCee
Confidence 5677777533
No 162
>PRK05978 hypothetical protein; Provisional
Probab=40.60 E-value=14 Score=22.37 Aligned_cols=8 Identities=38% Similarity=1.360 Sum_probs=4.0
Q ss_pred ccCCCccc
Q psy370 23 SQCPVCKK 30 (111)
Q Consensus 23 ~~c~~C~~ 30 (111)
-+|+.||+
T Consensus 34 grCP~CG~ 41 (148)
T PRK05978 34 GRCPACGE 41 (148)
T ss_pred CcCCCCCC
Confidence 34555554
No 163
>KOG2907|consensus
Probab=40.13 E-value=21 Score=20.56 Aligned_cols=39 Identities=15% Similarity=0.285 Sum_probs=22.0
Q ss_pred ccccccCcccCCHHHHHHHHHhccCCCC-CceecCCCcccccc
Q psy370 51 YSCEHCDMQFNCKSDMRKHVHSHLSMEE-RGFVCEICGHVVDE 92 (111)
Q Consensus 51 ~~c~~c~~~f~~~~~l~~h~~~h~~~~~-~~~~C~~C~~~~~~ 92 (111)
..|+.||..=..-..++ +|+-. .|. .=|-|..|++.|..
T Consensus 75 ~kCpkCghe~m~Y~T~Q--lRSAD-EGQTVFYTC~kC~~k~~e 114 (116)
T KOG2907|consen 75 HKCPKCGHEEMSYHTLQ--LRSAD-EGQTVFYTCPKCKYKFTE 114 (116)
T ss_pred ccCcccCCchhhhhhhh--ccccc-CCceEEEEcCccceeeec
Confidence 56888885433322222 33332 133 44789999988864
No 164
>PRK04023 DNA polymerase II large subunit; Validated
Probab=40.04 E-value=26 Score=28.00 Aligned_cols=10 Identities=40% Similarity=0.989 Sum_probs=7.6
Q ss_pred cccCCCcccc
Q psy370 22 ASQCPVCKKI 31 (111)
Q Consensus 22 ~~~c~~C~~~ 31 (111)
...|+.||..
T Consensus 626 ~RfCpsCG~~ 635 (1121)
T PRK04023 626 RRKCPSCGKE 635 (1121)
T ss_pred CccCCCCCCc
Confidence 4678888876
No 165
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=39.93 E-value=8 Score=22.20 Aligned_cols=40 Identities=23% Similarity=0.305 Sum_probs=20.7
Q ss_pred ccccccCcccCCHHHHHHHHHhccCCCCCceecCCCcccccc
Q psy370 51 YSCEHCDMQFNCKSDMRKHVHSHLSMEERGFVCEICGHVVDE 92 (111)
Q Consensus 51 ~~c~~c~~~f~~~~~l~~h~~~h~~~~~~~~~C~~C~~~~~~ 92 (111)
..|+.||..=. ..++.+.|.-..+...=|.|..||.+|..
T Consensus 73 ~~CpkCg~~ea--~y~~~QtRsaDEp~T~Fy~C~~Cg~~wre 112 (113)
T COG1594 73 EKCPKCGNKEA--YYWQLQTRSADEPETRFYKCTRCGYRWRE 112 (113)
T ss_pred ccCCCCCCcee--EEEeeehhccCCCceEEEEecccCCEeec
Confidence 45777774222 22223334332112233899999998863
No 166
>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 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=39.27 E-value=22 Score=23.95 Aligned_cols=33 Identities=18% Similarity=0.618 Sum_probs=22.2
Q ss_pred ccCCCcccccCCHHHHHHHHHHcCCCCCccccccCcccCCHH
Q psy370 23 SQCPVCKKIYTDQQLFQNHLETHDNEMDYSCEHCDMQFNCKS 64 (111)
Q Consensus 23 ~~c~~C~~~f~~~~~l~~h~~~h~~~~~~~c~~c~~~f~~~~ 64 (111)
.+|+.|++....+. |.. ..++|+.|+.-|.-..
T Consensus 27 ~~c~~c~~~~~~~~-l~~--------~~~vc~~c~~h~rl~a 59 (285)
T TIGR00515 27 TKCPKCGQVLYTKE-LER--------NLEVCPKCDHHMRMDA 59 (285)
T ss_pred eECCCCcchhhHHH-HHh--------hCCCCCCCCCcCcCCH
Confidence 45999998775553 332 3468999998776543
No 168
>COG4391 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=38.97 E-value=15 Score=18.74 Aligned_cols=42 Identities=10% Similarity=0.212 Sum_probs=22.2
Q ss_pred HHcCCCCCccccccCcccCCHHHHHHHHHhccCCCCC-ceecCCCccccc
Q psy370 43 ETHDNEMDYSCEHCDMQFNCKSDMRKHVHSHLSMEER-GFVCEICGHVVD 91 (111)
Q Consensus 43 ~~h~~~~~~~c~~c~~~f~~~~~l~~h~~~h~~~~~~-~~~C~~C~~~~~ 91 (111)
..+.+..++.|..-+-.+..+..+. .. |+. --.|++|+..|.
T Consensus 17 ~I~~~~~~l~C~g~~~p~~HPrV~L-----~m--g~~gev~CPYC~t~y~ 59 (62)
T COG4391 17 TIEIGDLPLMCPGPEPPNDHPRVFL-----DM--GDEGEVVCPYCSTRYR 59 (62)
T ss_pred EEEeCCeeEEcCCCCCCCCCCEEEE-----Ec--CCCCcEecCccccEEE
Confidence 3445566777765444433322211 11 233 356999998875
No 169
>COG4530 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=38.87 E-value=15 Score=21.08 Aligned_cols=16 Identities=13% Similarity=0.100 Sum_probs=12.3
Q ss_pred CCceecCCCccccccc
Q psy370 78 ERGFVCEICGHVVDEM 93 (111)
Q Consensus 78 ~~~~~C~~C~~~~~~~ 93 (111)
..|..|++||++|+.+
T Consensus 24 rdPiVsPytG~s~P~s 39 (129)
T COG4530 24 RDPIVSPYTGKSYPRS 39 (129)
T ss_pred CCccccCcccccchHH
Confidence 4578899999998544
No 170
>PHA02998 RNA polymerase subunit; Provisional
Probab=38.54 E-value=5.8 Score=24.73 Aligned_cols=41 Identities=10% Similarity=0.151 Sum_probs=21.4
Q ss_pred ccccccCcccCCHHHHHHHHHhccCCCCCceecCCCccccccc
Q psy370 51 YSCEHCDMQFNCKSDMRKHVHSHLSMEERGFVCEICGHVVDEM 93 (111)
Q Consensus 51 ~~c~~c~~~f~~~~~l~~h~~~h~~~~~~~~~C~~C~~~~~~~ 93 (111)
..|+.|+..-.... ..+.|+-..+...=|.|..||+.|.=+
T Consensus 144 v~CPkCg~~~A~f~--qlQTRSADEPmT~FYkC~~CG~~wkpp 184 (195)
T PHA02998 144 TPCPNCKSKNTTPM--MIQTRAADEPPLVRHACRDCKKHFKPP 184 (195)
T ss_pred CCCCCCCCCceEEE--EEeeccCCCCceEEEEcCCCCCccCCc
Confidence 46777874322222 223333221112237899999988654
No 171
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=38.25 E-value=17 Score=21.55 Aligned_cols=15 Identities=27% Similarity=0.840 Sum_probs=12.0
Q ss_pred cccCCCcccccCCHH
Q psy370 22 ASQCPVCKKIYTDQQ 36 (111)
Q Consensus 22 ~~~c~~C~~~f~~~~ 36 (111)
|++|..||+.|...+
T Consensus 1 PH~Ct~Cg~~f~dgs 15 (131)
T PF09845_consen 1 PHQCTKCGRVFEDGS 15 (131)
T ss_pred CcccCcCCCCcCCCc
Confidence 578899999988664
No 172
>PRK05580 primosome assembly protein PriA; Validated
Probab=38.17 E-value=7.3 Score=29.38 Aligned_cols=9 Identities=33% Similarity=0.792 Sum_probs=5.1
Q ss_pred ceecCCCcc
Q psy370 80 GFVCEICGH 88 (111)
Q Consensus 80 ~~~C~~C~~ 88 (111)
+..|+.||.
T Consensus 421 ~~~Cp~Cg~ 429 (679)
T PRK05580 421 PKACPECGS 429 (679)
T ss_pred CCCCCCCcC
Confidence 455666654
No 173
>COG2331 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=38.10 E-value=6.3 Score=20.98 Aligned_cols=11 Identities=18% Similarity=0.742 Sum_probs=7.9
Q ss_pred cccCCCccccc
Q psy370 22 ASQCPVCKKIY 32 (111)
Q Consensus 22 ~~~c~~C~~~f 32 (111)
.|.|..||..|
T Consensus 12 ~Y~c~~cg~~~ 22 (82)
T COG2331 12 SYECTECGNRF 22 (82)
T ss_pred EEeecccchHH
Confidence 47778887665
No 174
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=37.73 E-value=34 Score=19.32 Aligned_cols=39 Identities=18% Similarity=0.364 Sum_probs=19.9
Q ss_pred cccCcccCCCcccccCCHHHHHHHHHHcCCCCCccccccCccc
Q psy370 18 TIFVASQCPVCKKIYTDQQLFQNHLETHDNEMDYSCEHCDMQF 60 (111)
Q Consensus 18 ~~~~~~~c~~C~~~f~~~~~l~~h~~~h~~~~~~~c~~c~~~f 60 (111)
-..+-|.|+.||.--...-.+.. ........|..||..|
T Consensus 18 ~L~k~FtCp~Cghe~vs~ctvkk----~~~~g~~~Cg~CGls~ 56 (104)
T COG4888 18 VLPKTFTCPRCGHEKVSSCTVKK----TVNIGTAVCGNCGLSF 56 (104)
T ss_pred cCCceEecCccCCeeeeEEEEEe----cCceeEEEcccCcceE
Confidence 46777888888764333211111 1122335666777544
No 175
>PF14353 CpXC: CpXC protein
Probab=37.71 E-value=11 Score=21.87 Aligned_cols=17 Identities=29% Similarity=0.548 Sum_probs=11.3
Q ss_pred ceecCCCccccccchhH
Q psy370 80 GFVCEICGHVVDEMPVA 96 (111)
Q Consensus 80 ~~~C~~C~~~~~~~~~l 96 (111)
.+.|+.||..|.-...+
T Consensus 38 ~~~CP~Cg~~~~~~~p~ 54 (128)
T PF14353_consen 38 SFTCPSCGHKFRLEYPL 54 (128)
T ss_pred EEECCCCCCceecCCCE
Confidence 36788888877654433
No 176
>COG5216 Uncharacterized conserved protein [Function unknown]
Probab=37.06 E-value=21 Score=17.99 Aligned_cols=12 Identities=25% Similarity=0.346 Sum_probs=8.9
Q ss_pred CCCceecCCCcc
Q psy370 77 EERGFVCEICGH 88 (111)
Q Consensus 77 ~~~~~~C~~C~~ 88 (111)
|++--.|+.|..
T Consensus 41 GE~VArCPSCSL 52 (67)
T COG5216 41 GEVVARCPSCSL 52 (67)
T ss_pred CceEEEcCCceE
Confidence 677778888864
No 177
>KOG2482|consensus
Probab=36.66 E-value=27 Score=24.33 Aligned_cols=24 Identities=25% Similarity=0.717 Sum_probs=21.4
Q ss_pred cccCCCcccccCCHHHHHHHHHHc
Q psy370 22 ASQCPVCKKIYTDQQLFQNHLETH 45 (111)
Q Consensus 22 ~~~c~~C~~~f~~~~~l~~h~~~h 45 (111)
.+.|-.|.++|..+..|..||+.-
T Consensus 195 r~~CLyCekifrdkntLkeHMrkK 218 (423)
T KOG2482|consen 195 RLRCLYCEKIFRDKNTLKEHMRKK 218 (423)
T ss_pred hheeeeeccccCCcHHHHHHHHhc
Confidence 478999999999999999999863
No 178
>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=36.14 E-value=18 Score=16.40 Aligned_cols=10 Identities=50% Similarity=1.122 Sum_probs=7.8
Q ss_pred eecCCCcccc
Q psy370 81 FVCEICGHVV 90 (111)
Q Consensus 81 ~~C~~C~~~~ 90 (111)
|.|..|+..|
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 6788888776
No 179
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=35.62 E-value=21 Score=19.56 Aligned_cols=33 Identities=15% Similarity=0.302 Sum_probs=21.8
Q ss_pred CCccccccCcccCCHHHHHHHHHhccCCCCCceecCCCccccccc
Q psy370 49 MDYSCEHCDMQFNCKSDMRKHVHSHLSMEERGFVCEICGHVVDEM 93 (111)
Q Consensus 49 ~~~~c~~c~~~f~~~~~l~~h~~~h~~~~~~~~~C~~C~~~~~~~ 93 (111)
..+.|+.|++. ...|. ..-=|.|..||..|.--
T Consensus 34 ~~~~Cp~C~~~--------~VkR~----a~GIW~C~kCg~~fAGg 66 (89)
T COG1997 34 AKHVCPFCGRT--------TVKRI----ATGIWKCRKCGAKFAGG 66 (89)
T ss_pred cCCcCCCCCCc--------ceeee----ccCeEEcCCCCCeeccc
Confidence 46789999864 12222 23358999999988644
No 180
>COG5112 UFD2 U1-like Zn-finger-containing protein [General function prediction only]
Probab=35.49 E-value=16 Score=20.83 Aligned_cols=22 Identities=14% Similarity=0.185 Sum_probs=16.5
Q ss_pred ceecCCCccccccchhHHhhcc
Q psy370 80 GFVCEICGHVVDEMPVATQSSK 101 (111)
Q Consensus 80 ~~~C~~C~~~~~~~~~l~~h~~ 101 (111)
.+-|..|.+-|.+..+|+.|.+
T Consensus 55 qhYCieCaryf~t~~aL~~Hkk 76 (126)
T COG5112 55 QHYCIECARYFITEKALMEHKK 76 (126)
T ss_pred eeeeehhHHHHHHHHHHHHHhc
Confidence 4667778888877777877775
No 181
>PRK12496 hypothetical protein; Provisional
Probab=35.37 E-value=29 Score=21.26 Aligned_cols=11 Identities=18% Similarity=0.742 Sum_probs=7.2
Q ss_pred ccccccCcccC
Q psy370 51 YSCEHCDMQFN 61 (111)
Q Consensus 51 ~~c~~c~~~f~ 61 (111)
+.|.-|++.|.
T Consensus 128 ~~C~gC~~~~~ 138 (164)
T PRK12496 128 KVCKGCKKKYP 138 (164)
T ss_pred EECCCCCcccc
Confidence 56777776553
No 182
>PTZ00043 cytochrome c oxidase subunit; Provisional
Probab=35.15 E-value=21 Score=23.28 Aligned_cols=17 Identities=18% Similarity=0.356 Sum_probs=13.7
Q ss_pred CCCceecCCCccccccc
Q psy370 77 EERGFVCEICGHVVDEM 93 (111)
Q Consensus 77 ~~~~~~C~~C~~~~~~~ 93 (111)
..++..|..||..|.-.
T Consensus 178 EGkpqRCpECGqVFKLV 194 (268)
T PTZ00043 178 EGFLYRCGECDQIFMLV 194 (268)
T ss_pred CCCCccCCCCCcEEEEE
Confidence 45688999999988654
No 183
>COG1326 Uncharacterized archaeal Zn-finger protein [General function prediction only]
Probab=34.87 E-value=50 Score=21.04 Aligned_cols=12 Identities=42% Similarity=0.678 Sum_probs=7.4
Q ss_pred CceecCCCcccc
Q psy370 79 RGFVCEICGHVV 90 (111)
Q Consensus 79 ~~~~C~~C~~~~ 90 (111)
....|..||..+
T Consensus 29 ~lvrC~eCG~V~ 40 (201)
T COG1326 29 PLVRCEECGTVH 40 (201)
T ss_pred eEEEccCCCcEe
Confidence 345677777665
No 184
>KOG1280|consensus
Probab=34.25 E-value=59 Score=22.73 Aligned_cols=38 Identities=21% Similarity=0.472 Sum_probs=24.0
Q ss_pred cCcccCCCcccccCCHHHHHHHHHH-cCCC-CCccccccC
Q psy370 20 FVASQCPVCKKIYTDQQLFQNHLET-HDNE-MDYSCEHCD 57 (111)
Q Consensus 20 ~~~~~c~~C~~~f~~~~~l~~h~~~-h~~~-~~~~c~~c~ 57 (111)
...|.|+.|++.-.+...|..|... |... -.-.|.+|+
T Consensus 77 ~qSftCPyC~~~Gfte~~f~~Hv~s~Hpda~~~~icp~c~ 116 (381)
T KOG1280|consen 77 PQSFTCPYCGIMGFTERQFGTHVLSQHPEASTSVICPLCA 116 (381)
T ss_pred cccccCCcccccccchhHHHHHhhhcCcccCcceeeeccc
Confidence 4468888888877777777777664 4322 223455554
No 185
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=33.89 E-value=31 Score=23.43 Aligned_cols=34 Identities=21% Similarity=0.472 Sum_probs=22.3
Q ss_pred ccCCCcccccCCHHHHHHHHHHcCCCCCccccccCcccCCHHH
Q psy370 23 SQCPVCKKIYTDQQLFQNHLETHDNEMDYSCEHCDMQFNCKSD 65 (111)
Q Consensus 23 ~~c~~C~~~f~~~~~l~~h~~~h~~~~~~~c~~c~~~f~~~~~ 65 (111)
.+|+.|+.....+. |.. ..++|+.|+.-|.....
T Consensus 39 ~kc~~C~~~~~~~~-l~~--------~~~vcp~c~~h~rltAr 72 (296)
T CHL00174 39 VQCENCYGLNYKKF-LKS--------KMNICEQCGYHLKMSSS 72 (296)
T ss_pred eECCCccchhhHHH-HHH--------cCCCCCCCCCCcCCCHH
Confidence 34999988765543 332 35689999987765433
No 186
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=33.82 E-value=26 Score=24.45 Aligned_cols=46 Identities=22% Similarity=0.453 Sum_probs=24.0
Q ss_pred CCCcccccCCHHHHHHHHHHcCCCCCccccccC----cccCCHHHHHHHHH
Q psy370 25 CPVCKKIYTDQQLFQNHLETHDNEMDYSCEHCD----MQFNCKSDMRKHVH 71 (111)
Q Consensus 25 c~~C~~~f~~~~~l~~h~~~h~~~~~~~c~~c~----~~f~~~~~l~~h~~ 71 (111)
|..|...|-+-.-|..|++... ++-+.|..-+ ..|..-..|..|.+
T Consensus 223 C~FC~~~FYdDDEL~~HcR~~H-E~ChICD~v~p~~~QYFK~Y~~Le~HF~ 272 (493)
T COG5236 223 CIFCKIYFYDDDELRRHCRLRH-EACHICDMVGPIRYQYFKSYEDLEAHFR 272 (493)
T ss_pred hhhccceecChHHHHHHHHhhh-hhhhhhhccCccchhhhhCHHHHHHHhh
Confidence 6777766666666766666422 2333443322 23444455555544
No 187
>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=33.52 E-value=30 Score=15.04 Aligned_cols=10 Identities=40% Similarity=1.085 Sum_probs=4.1
Q ss_pred ecCCCccccc
Q psy370 82 VCEICGHVVD 91 (111)
Q Consensus 82 ~C~~C~~~~~ 91 (111)
.|..||..+.
T Consensus 2 ~C~~Cg~~~~ 11 (32)
T PF03604_consen 2 ICGECGAEVE 11 (32)
T ss_dssp BESSSSSSE-
T ss_pred CCCcCCCeeE
Confidence 4444444443
No 188
>PRK05654 acetyl-CoA carboxylase subunit beta; Validated
Probab=33.43 E-value=29 Score=23.48 Aligned_cols=33 Identities=15% Similarity=0.576 Sum_probs=22.1
Q ss_pred ccCCCcccccCCHHHHHHHHHHcCCCCCccccccCcccCCHH
Q psy370 23 SQCPVCKKIYTDQQLFQNHLETHDNEMDYSCEHCDMQFNCKS 64 (111)
Q Consensus 23 ~~c~~C~~~f~~~~~l~~h~~~h~~~~~~~c~~c~~~f~~~~ 64 (111)
.+|+.|+..+..+. |.. ..++|+.|+.-|.-..
T Consensus 28 ~~c~~c~~~~~~~~-l~~--------~~~vc~~c~~h~rl~a 60 (292)
T PRK05654 28 TKCPSCGQVLYRKE-LEA--------NLNVCPKCGHHMRISA 60 (292)
T ss_pred eECCCccchhhHHH-HHh--------cCCCCCCCCCCeeCCH
Confidence 45999998765543 332 2469999998776543
No 189
>PF01215 COX5B: Cytochrome c oxidase subunit Vb This family consists of chains F and S ; InterPro: IPR002124 Cytochrome c oxidase (1.9.3.1 from EC) is an oligomeric enzymatic complex which is a component of the respiratory chain complex and is involved in the transfer of electrons from cytochrome c to oxygen []. In eukaryotes this enzyme complex is located in the mitochondrial inner membrane; in aerobic prokaryotes it is found in the plasma membrane. In eukaryotes, in addition to the three large subunits, I, II and III, that form the catalytic centre of the enzyme complex, there are a variable number of small polypeptidic subunits. One of these subunits, which is known as Vb in mammals, V in Dictyostelium discoideum (Slime mold) and IV in yeast, binds a zinc atom. The sequence of subunit Vb is well conserved and includes three conserved cysteines that coordinate the zinc ion [, ]. Two of these cysteines are clustered in the C-terminal section of the subunit.; GO: 0004129 cytochrome-c oxidase activity, 0005740 mitochondrial envelope; PDB: 2EIL_S 2ZXW_S 3ASN_S 1OCO_S 3AG4_S 3ABK_S 1OCZ_S 1OCC_F 3ASO_S 3ABL_S ....
Probab=33.27 E-value=18 Score=21.57 Aligned_cols=16 Identities=25% Similarity=0.482 Sum_probs=13.0
Q ss_pred CCceecCCCccccccc
Q psy370 78 ERGFVCEICGHVVDEM 93 (111)
Q Consensus 78 ~~~~~C~~C~~~~~~~ 93 (111)
.++..|..||..|.-.
T Consensus 110 g~~~RCpeCG~~fkL~ 125 (136)
T PF01215_consen 110 GKPQRCPECGQVFKLK 125 (136)
T ss_dssp TSEEEETTTEEEEEEE
T ss_pred CCccCCCCCCeEEEEE
Confidence 4689999999988654
No 190
>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=32.96 E-value=25 Score=17.15 Aligned_cols=17 Identities=24% Similarity=0.567 Sum_probs=10.6
Q ss_pred CCCceecCCCccccccc
Q psy370 77 EERGFVCEICGHVVDEM 93 (111)
Q Consensus 77 ~~~~~~C~~C~~~~~~~ 93 (111)
+...++|.+|++.+...
T Consensus 32 ~~~~~rC~YCe~~~~~~ 48 (52)
T PF02748_consen 32 EPIKLRCHYCERIITED 48 (52)
T ss_dssp TTCEEEETTT--EEEHH
T ss_pred CCCEEEeeCCCCEeccc
Confidence 44568899998877654
No 191
>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=32.68 E-value=37 Score=24.67 Aligned_cols=25 Identities=32% Similarity=0.683 Sum_probs=21.2
Q ss_pred ccCCCcccccCCHHHHHHHHHH-cCC
Q psy370 23 SQCPVCKKIYTDQQLFQNHLET-HDN 47 (111)
Q Consensus 23 ~~c~~C~~~f~~~~~l~~h~~~-h~~ 47 (111)
+.|+.|.+.|.....+..|+.. |.+
T Consensus 58 WiCp~CskkF~d~~~~~~H~~~eH~~ 83 (466)
T PF04780_consen 58 WICPRCSKKFSDAESCLSHMEQEHPA 83 (466)
T ss_pred eeCCcccceeCCHHHHHHHHHHhhhh
Confidence 6699999999999999999874 654
No 192
>KOG1994|consensus
Probab=32.31 E-value=42 Score=21.98 Aligned_cols=21 Identities=14% Similarity=0.328 Sum_probs=16.4
Q ss_pred ceecCCCccccccchhHHhhc
Q psy370 80 GFVCEICGHVVDEMPVATQSS 100 (111)
Q Consensus 80 ~~~C~~C~~~~~~~~~l~~h~ 100 (111)
-|-|-.||..|...-+|..|=
T Consensus 239 h~YC~fCG~~y~~~edl~ehC 259 (268)
T KOG1994|consen 239 HYYCFFCGIKYKDEEDLYEHC 259 (268)
T ss_pred ceEEEEeccccCCHHHHHHhC
Confidence 377888888888888887764
No 193
>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=32.27 E-value=22 Score=25.69 Aligned_cols=25 Identities=16% Similarity=0.344 Sum_probs=15.4
Q ss_pred CCCccccccCcccCCHHHHHHHHHh
Q psy370 48 EMDYSCEHCDMQFNCKSDMRKHVHS 72 (111)
Q Consensus 48 ~~~~~c~~c~~~f~~~~~l~~h~~~ 72 (111)
.+-+.|+.|.+.|.....+..|+..
T Consensus 55 WrFWiCp~CskkF~d~~~~~~H~~~ 79 (466)
T PF04780_consen 55 WRFWICPRCSKKFSDAESCLSHMEQ 79 (466)
T ss_pred eeEeeCCcccceeCCHHHHHHHHHH
Confidence 3445666666666666666666653
No 194
>KOG1842|consensus
Probab=32.03 E-value=34 Score=24.69 Aligned_cols=29 Identities=24% Similarity=0.520 Sum_probs=24.0
Q ss_pred cCcccCCCcccccCCHHHHHHHHHH-cCCC
Q psy370 20 FVASQCPVCKKIYTDQQLFQNHLET-HDNE 48 (111)
Q Consensus 20 ~~~~~c~~C~~~f~~~~~l~~h~~~-h~~~ 48 (111)
.+.|-|+.|..-|.+.+.|..|... |.++
T Consensus 13 ~egflCPiC~~dl~~~~~L~~H~d~eH~~e 42 (505)
T KOG1842|consen 13 LEGFLCPICLLDLPNLSALNDHLDVEHFEE 42 (505)
T ss_pred hhcccCchHhhhhhhHHHHHHHHhhhcccc
Confidence 3469999999999999999999875 5543
No 195
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=31.78 E-value=27 Score=17.38 Aligned_cols=17 Identities=24% Similarity=0.417 Sum_probs=12.7
Q ss_pred CCCceecCCCccccccc
Q psy370 77 EERGFVCEICGHVVDEM 93 (111)
Q Consensus 77 ~~~~~~C~~C~~~~~~~ 93 (111)
+...|.|+.||-..-.+
T Consensus 11 ~~v~~~Cp~cGipthcS 27 (55)
T PF13824_consen 11 AHVNFECPDCGIPTHCS 27 (55)
T ss_pred cccCCcCCCCCCcCccC
Confidence 46689999999766444
No 196
>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=31.72 E-value=22 Score=21.51 Aligned_cols=13 Identities=15% Similarity=0.284 Sum_probs=10.4
Q ss_pred eecCCCccccccc
Q psy370 81 FVCEICGHVVDEM 93 (111)
Q Consensus 81 ~~C~~C~~~~~~~ 93 (111)
=+|..||+.|++-
T Consensus 29 ReC~~C~~RFTTy 41 (147)
T TIGR00244 29 RECLECHERFTTF 41 (147)
T ss_pred ccCCccCCcccee
Confidence 4799999999764
No 197
>TIGR01031 rpmF_bact ribosomal protein L32. This protein describes bacterial ribosomal protein L32. The noise cutoff is set low enough to include the equivalent protein from mitochondria and chloroplasts. No related proteins from the Archaea nor from the eukaryotic cytosol are detected by this model. This model is a fragment model; the putative L32 of some species shows similarity only toward the N-terminus.
Probab=31.52 E-value=50 Score=16.30 Aligned_cols=8 Identities=38% Similarity=1.082 Sum_probs=3.9
Q ss_pred ccCCCccc
Q psy370 23 SQCPVCKK 30 (111)
Q Consensus 23 ~~c~~C~~ 30 (111)
..|+.||+
T Consensus 27 ~~C~~cG~ 34 (55)
T TIGR01031 27 VVCPNCGE 34 (55)
T ss_pred eECCCCCC
Confidence 34555554
No 198
>PTZ00303 phosphatidylinositol kinase; Provisional
Probab=30.41 E-value=34 Score=26.86 Aligned_cols=32 Identities=16% Similarity=0.497 Sum_probs=16.3
Q ss_pred cCCCcccccCCHHHHHHHHHHcCCCCCccccccCcccCC
Q psy370 24 QCPVCKKIYTDQQLFQNHLETHDNEMDYSCEHCDMQFNC 62 (111)
Q Consensus 24 ~c~~C~~~f~~~~~l~~h~~~h~~~~~~~c~~c~~~f~~ 62 (111)
.|..|++.|...... ...+.+.|..||..|..
T Consensus 462 tC~~C~kkFfSlsK~-------L~~RKHHCRkCGrVFC~ 493 (1374)
T PTZ00303 462 SCPSCGRAFISLSRP-------LGTRAHHCRSCGIRLCV 493 (1374)
T ss_pred cccCcCCcccccccc-------cccccccccCCccccCc
Confidence 477777777543110 01244566666665543
No 199
>PRK04351 hypothetical protein; Provisional
Probab=30.22 E-value=32 Score=20.80 Aligned_cols=14 Identities=14% Similarity=0.548 Sum_probs=8.2
Q ss_pred CCceecCCCccccc
Q psy370 78 ERGFVCEICGHVVD 91 (111)
Q Consensus 78 ~~~~~C~~C~~~~~ 91 (111)
...|.|..|+..+.
T Consensus 130 ~~~yrCg~C~g~L~ 143 (149)
T PRK04351 130 TKRYRCGKCRGKLK 143 (149)
T ss_pred CCcEEeCCCCcEee
Confidence 45566777765543
No 200
>PF00301 Rubredoxin: Rubredoxin; InterPro: IPR004039 Rubredoxin is a low molecular weight iron-containing bacterial protein involved in electron transfer [, ], sometimes replacing ferredoxin as an electron carrier []. The 3-D structures of a number of rubredoxins have been solved [, ]. The fold belongs to the alpha+beta class, with 2 alpha-helices and 2-3 beta-strands. Its active site contains an iron ion which is co-ordinated by the sulphurs of four conserved cysteine residues forming an almost regular tetrahedron. The conserved cysteines reside on two loops, which are the most conserved regions of the protein. In addition, a ring of acidic residues in the proximity of the [Fe(Cys)4] centre is also well-conserved []. ; GO: 0009055 electron carrier activity, 0046872 metal ion binding; PDB: 2RDV_C 1RDV_A 1S24_A 1T9O_B 1B2J_A 1SMW_A 2PVE_B 1BFY_A 1T9P_C 1C09_C ....
Probab=30.20 E-value=27 Score=16.66 Aligned_cols=12 Identities=42% Similarity=1.112 Sum_probs=8.3
Q ss_pred eecCCCcccccc
Q psy370 81 FVCEICGHVVDE 92 (111)
Q Consensus 81 ~~C~~C~~~~~~ 92 (111)
|+|..||..+.-
T Consensus 2 y~C~~CgyvYd~ 13 (47)
T PF00301_consen 2 YQCPVCGYVYDP 13 (47)
T ss_dssp EEETTTSBEEET
T ss_pred cCCCCCCEEEcC
Confidence 678888876643
No 201
>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=30.18 E-value=26 Score=15.56 Aligned_cols=14 Identities=21% Similarity=0.434 Sum_probs=7.4
Q ss_pred eecCCCccccccch
Q psy370 81 FVCEICGHVVDEMP 94 (111)
Q Consensus 81 ~~C~~C~~~~~~~~ 94 (111)
-.|..|++.|..+-
T Consensus 4 ~~C~eC~~~f~dSy 17 (34)
T PF01286_consen 4 PKCDECGKPFMDSY 17 (34)
T ss_dssp EE-TTT--EES-SS
T ss_pred chHhHhCCHHHHHH
Confidence 36889999887763
No 202
>PF04606 Ogr_Delta: Ogr/Delta-like zinc finger; InterPro: IPR007684 This entry is represented by Bacteriophage P2, Ogr. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This is a viral family of phage zinc-binding transcriptional activators, which also contains cryptic members in some bacterial genomes []. The P4 phage delta protein contains two such domains attached covalently, while the P2 phage Ogr proteins possess one domain but function as dimers. All the members of this family have the following consensus sequence: C-X(2)-C-X(3)-A-(X)2-R-X(15)-C-X(4)-C-X(3)-F [].; GO: 0006355 regulation of transcription, DNA-dependent
Probab=29.89 E-value=13 Score=17.58 Aligned_cols=16 Identities=31% Similarity=0.476 Sum_probs=10.6
Q ss_pred CCceecCC--Cccccccc
Q psy370 78 ERGFVCEI--CGHVVDEM 93 (111)
Q Consensus 78 ~~~~~C~~--C~~~~~~~ 93 (111)
+..+.|.- ||.+|...
T Consensus 23 ~~Y~qC~N~~Cg~tfv~~ 40 (47)
T PF04606_consen 23 ELYCQCTNPECGHTFVAN 40 (47)
T ss_pred EEEEEECCCcCCCEEEEE
Confidence 45567754 88888654
No 203
>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=29.83 E-value=23 Score=19.52 Aligned_cols=32 Identities=19% Similarity=0.450 Sum_probs=19.6
Q ss_pred CCccccccCcccCCHHHHHHHHHhccCCCCCceecCCCcccccc
Q psy370 49 MDYSCEHCDMQFNCKSDMRKHVHSHLSMEERGFVCEICGHVVDE 92 (111)
Q Consensus 49 ~~~~c~~c~~~f~~~~~l~~h~~~h~~~~~~~~~C~~C~~~~~~ 92 (111)
..|.|++|+..-.. +.-. | =|.|..|++.|.-
T Consensus 34 ~ky~Cp~Cgk~~vk--------R~a~--G--IW~C~~C~~~~AG 65 (90)
T PF01780_consen 34 AKYTCPFCGKTSVK--------RVAT--G--IWKCKKCGKKFAG 65 (90)
T ss_dssp S-BEESSSSSSEEE--------EEET--T--EEEETTTTEEEE-
T ss_pred CCCcCCCCCCceeE--------Eeee--E--EeecCCCCCEEeC
Confidence 56899999864211 1111 2 3899999998854
No 204
>PTZ00448 hypothetical protein; Provisional
Probab=29.52 E-value=50 Score=23.21 Aligned_cols=23 Identities=22% Similarity=0.504 Sum_probs=18.4
Q ss_pred cccCCCcccccCCHHHHHHHHHH
Q psy370 22 ASQCPVCKKIYTDQQLFQNHLET 44 (111)
Q Consensus 22 ~~~c~~C~~~f~~~~~l~~h~~~ 44 (111)
.|.|..|+-.|.+......|.++
T Consensus 314 ~~tC~~C~v~F~~~~~qR~H~KS 336 (373)
T PTZ00448 314 MLLCRKCNIQLMDHNAFKQHYRS 336 (373)
T ss_pred CccccccccccCCHHHHHHHhhh
Confidence 57899999999877777778765
No 205
>KOG4477|consensus
Probab=29.27 E-value=54 Score=20.71 Aligned_cols=27 Identities=22% Similarity=0.529 Sum_probs=17.4
Q ss_pred ccccCcccCCCcccccCCHHHHHHHHHHcCCCCCccccccC
Q psy370 17 YTIFVASQCPVCKKIYTDQQLFQNHLETHDNEMDYSCEHCD 57 (111)
Q Consensus 17 ~~~~~~~~c~~C~~~f~~~~~l~~h~~~h~~~~~~~c~~c~ 57 (111)
...++-|-|..| +|.+.. ..|.|.+|+
T Consensus 19 ~~Deg~WdCsvC--TFrNsA------------eAfkC~vCd 45 (228)
T KOG4477|consen 19 NDDEGKWDCSVC--TFRNSA------------EAFKCFVCD 45 (228)
T ss_pred ccccCceeeeee--eecchh------------hhhheeeec
Confidence 355677889988 354442 456777776
No 206
>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=29.26 E-value=18 Score=23.26 Aligned_cols=25 Identities=12% Similarity=0.292 Sum_probs=0.0
Q ss_pred CceecCCCccccccchhHHhhccccC
Q psy370 79 RGFVCEICGHVVDEMPVATQSSKYPG 104 (111)
Q Consensus 79 ~~~~C~~C~~~~~~~~~l~~h~~~~~ 104 (111)
.-..|+.||..++... +..|+++--
T Consensus 167 ~~~~cPitGe~IP~~e-~~eHmRi~L 191 (229)
T PF12230_consen 167 KMIICPITGEMIPADE-MDEHMRIEL 191 (229)
T ss_dssp --------------------------
T ss_pred cccccccccccccccc-ccccccccc
Confidence 4468999999888774 888887643
No 207
>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=29.19 E-value=19 Score=16.08 Aligned_cols=10 Identities=50% Similarity=1.334 Sum_probs=6.0
Q ss_pred cCCCcccccC
Q psy370 24 QCPVCKKIYT 33 (111)
Q Consensus 24 ~c~~C~~~f~ 33 (111)
.|+.||..|.
T Consensus 3 ~C~~Cg~~Yh 12 (36)
T PF05191_consen 3 ICPKCGRIYH 12 (36)
T ss_dssp EETTTTEEEE
T ss_pred CcCCCCCccc
Confidence 4666666664
No 208
>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=29.03 E-value=18 Score=20.48 Aligned_cols=10 Identities=30% Similarity=0.710 Sum_probs=5.1
Q ss_pred cccCCCcccc
Q psy370 22 ASQCPVCKKI 31 (111)
Q Consensus 22 ~~~c~~C~~~ 31 (111)
|-.|+.||..
T Consensus 2 p~~CpYCg~~ 11 (102)
T PF11672_consen 2 PIICPYCGGP 11 (102)
T ss_pred CcccCCCCCe
Confidence 3445555543
No 209
>COG5188 PRP9 Splicing factor 3a, subunit 3 [RNA processing and modification]
Probab=28.88 E-value=42 Score=23.57 Aligned_cols=33 Identities=18% Similarity=0.441 Sum_probs=20.0
Q ss_pred ccCCCCccccCcccCCCcc-cccCCHHHHHHHHH
Q psy370 11 EIIPGSYTIFVASQCPVCK-KIYTDQQLFQNHLE 43 (111)
Q Consensus 11 ~~~~~~~~~~~~~~c~~C~-~~f~~~~~l~~h~~ 43 (111)
-|.-+.|...+.|.|.+|| ..+.-...+..|..
T Consensus 363 ~WL~klhgLd~ef~CEICgNyvy~GR~~FdrHF~ 396 (470)
T COG5188 363 RWLCKLHGLDIEFECEICGNYVYYGRDRFDRHFE 396 (470)
T ss_pred hHHHHhcCCCcceeeeecccccccchHHHHhhhh
Confidence 4455566666777777777 45555555665543
No 210
>COG5027 SAS2 Histone acetyltransferase (MYST family) [Chromatin structure and dynamics]
Probab=28.51 E-value=28 Score=24.28 Aligned_cols=25 Identities=16% Similarity=0.273 Sum_probs=20.5
Q ss_pred CceecCCCccccccchhHHhhcccc
Q psy370 79 RGFVCEICGHVVDEMPVATQSSKYP 103 (111)
Q Consensus 79 ~~~~C~~C~~~~~~~~~l~~h~~~~ 103 (111)
.-|.|..|.+-+.....|..|++-+
T Consensus 157 ~vyICefClkY~~s~~~~~rH~~kC 181 (395)
T COG5027 157 IVYICEFCLKYYGSQTSLVRHRKKC 181 (395)
T ss_pred eEEEhhhhHHHhcchhHHHHHHhcC
Confidence 4578999999999998999998743
No 211
>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=28.23 E-value=32 Score=19.03 Aligned_cols=33 Identities=18% Similarity=0.412 Sum_probs=21.3
Q ss_pred CCccccccCcccCCHHHHHHHHHhccCCCCCceecCCCccccccc
Q psy370 49 MDYSCEHCDMQFNCKSDMRKHVHSHLSMEERGFVCEICGHVVDEM 93 (111)
Q Consensus 49 ~~~~c~~c~~~f~~~~~l~~h~~~h~~~~~~~~~C~~C~~~~~~~ 93 (111)
..|.|++|++.-. + .. ..--|.|..|++.|.--
T Consensus 34 a~y~CpfCgk~~v---------k-R~--a~GIW~C~~C~~~~AGG 66 (91)
T TIGR00280 34 AKYVCPFCGKKTV---------K-RG--STGIWTCRKCGAKFAGG 66 (91)
T ss_pred cCccCCCCCCCce---------E-EE--eeEEEEcCCCCCEEeCC
Confidence 4689999985311 1 11 22358999999988643
No 212
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=28.08 E-value=27 Score=16.44 Aligned_cols=14 Identities=36% Similarity=0.617 Sum_probs=8.9
Q ss_pred ceecCCCccccccc
Q psy370 80 GFVCEICGHVVDEM 93 (111)
Q Consensus 80 ~~~C~~C~~~~~~~ 93 (111)
.+.|+.||..+...
T Consensus 20 ~~vC~~Cg~~~~~~ 33 (52)
T smart00661 20 RFVCRKCGYEEPIE 33 (52)
T ss_pred EEECCcCCCeEECC
Confidence 46777777665443
No 213
>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=27.97 E-value=27 Score=15.82 Aligned_cols=13 Identities=46% Similarity=0.935 Sum_probs=9.6
Q ss_pred cccCCCcccccCC
Q psy370 22 ASQCPVCKKIYTD 34 (111)
Q Consensus 22 ~~~c~~C~~~f~~ 34 (111)
.+.|+.||+.+-+
T Consensus 32 ~~~C~~CGE~~~~ 44 (46)
T TIGR03831 32 ALVCPQCGEEYLD 44 (46)
T ss_pred ccccccCCCEeeC
Confidence 4679999987643
No 214
>PRK00420 hypothetical protein; Validated
Probab=27.89 E-value=26 Score=20.18 Aligned_cols=8 Identities=13% Similarity=0.181 Sum_probs=3.7
Q ss_pred ccccccCc
Q psy370 51 YSCEHCDM 58 (111)
Q Consensus 51 ~~c~~c~~ 58 (111)
..|+.||.
T Consensus 41 ~~Cp~Cg~ 48 (112)
T PRK00420 41 VVCPVHGK 48 (112)
T ss_pred eECCCCCC
Confidence 34444444
No 215
>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=27.64 E-value=28 Score=16.87 Aligned_cols=11 Identities=36% Similarity=1.017 Sum_probs=6.7
Q ss_pred ccCCCcccccC
Q psy370 23 SQCPVCKKIYT 33 (111)
Q Consensus 23 ~~c~~C~~~f~ 33 (111)
|.|..||..|.
T Consensus 2 y~C~~CgyiYd 12 (50)
T cd00730 2 YECRICGYIYD 12 (50)
T ss_pred cCCCCCCeEEC
Confidence 55666666554
No 216
>COG4640 Predicted membrane protein [Function unknown]
Probab=27.59 E-value=40 Score=24.01 Aligned_cols=26 Identities=31% Similarity=0.401 Sum_probs=19.0
Q ss_pred CCccccCcccCCCcccccCCHHHHHH
Q psy370 15 GSYTIFVASQCPVCKKIYTDQQLFQN 40 (111)
Q Consensus 15 ~~~~~~~~~~c~~C~~~f~~~~~l~~ 40 (111)
+++..|..++|+.||..|...+..-.
T Consensus 8 G~qk~Ed~~qC~qCG~~~t~~~sqan 33 (465)
T COG4640 8 GSQKAEDDVQCTQCGHKFTSRQSQAN 33 (465)
T ss_pred ccccccccccccccCCcCCchhhhhh
Confidence 34556677789999999988765443
No 217
>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=27.53 E-value=40 Score=19.30 Aligned_cols=11 Identities=18% Similarity=0.682 Sum_probs=5.4
Q ss_pred CccccccCccc
Q psy370 50 DYSCEHCDMQF 60 (111)
Q Consensus 50 ~~~c~~c~~~f 60 (111)
.|.|+.|+..+
T Consensus 19 ~~iCpeC~~EW 29 (109)
T TIGR00686 19 QLICPSCLYEW 29 (109)
T ss_pred eeECccccccc
Confidence 35555555443
No 218
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=27.37 E-value=21 Score=20.75 Aligned_cols=11 Identities=18% Similarity=0.519 Sum_probs=6.8
Q ss_pred ccccccCcccCC
Q psy370 51 YSCEHCDMQFNC 62 (111)
Q Consensus 51 ~~c~~c~~~f~~ 62 (111)
+.| .|+..|..
T Consensus 71 ~~C-~Cg~~~~~ 81 (124)
T PRK00762 71 IEC-ECGYEGVV 81 (124)
T ss_pred EEe-eCcCcccc
Confidence 567 77765544
No 219
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=27.17 E-value=35 Score=18.86 Aligned_cols=33 Identities=18% Similarity=0.315 Sum_probs=21.5
Q ss_pred CCccccccCcccCCHHHHHHHHHhccCCCCCceecCCCccccccc
Q psy370 49 MDYSCEHCDMQFNCKSDMRKHVHSHLSMEERGFVCEICGHVVDEM 93 (111)
Q Consensus 49 ~~~~c~~c~~~f~~~~~l~~h~~~h~~~~~~~~~C~~C~~~~~~~ 93 (111)
..|.|++|++.-.. .. ..--|.|..|++.|.--
T Consensus 35 a~y~CpfCgk~~vk----------R~--a~GIW~C~~C~~~~AGG 67 (90)
T PTZ00255 35 AKYFCPFCGKHAVK----------RQ--AVGIWRCKGCKKTVAGG 67 (90)
T ss_pred CCccCCCCCCCcee----------ee--eeEEEEcCCCCCEEeCC
Confidence 56899999853111 11 23358999999988653
No 220
>PF14787 zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB: 1CL4_A 1DSV_A.
Probab=26.70 E-value=38 Score=15.26 Aligned_cols=14 Identities=21% Similarity=0.473 Sum_probs=8.3
Q ss_pred ecCCCccccccchh
Q psy370 82 VCEICGHVVDEMPV 95 (111)
Q Consensus 82 ~C~~C~~~~~~~~~ 95 (111)
.|..|++.|-+-++
T Consensus 4 ~CprC~kg~Hwa~~ 17 (36)
T PF14787_consen 4 LCPRCGKGFHWASE 17 (36)
T ss_dssp C-TTTSSSCS-TTT
T ss_pred cCcccCCCcchhhh
Confidence 57788887766554
No 221
>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=26.61 E-value=31 Score=17.05 Aligned_cols=13 Identities=31% Similarity=0.736 Sum_probs=8.4
Q ss_pred eecCCCccccccc
Q psy370 81 FVCEICGHVVDEM 93 (111)
Q Consensus 81 ~~C~~C~~~~~~~ 93 (111)
|.|+.||..+.-.
T Consensus 3 ~~CP~CG~~iev~ 15 (54)
T TIGR01206 3 FECPDCGAEIELE 15 (54)
T ss_pred cCCCCCCCEEecC
Confidence 5777777766443
No 222
>KOG2071|consensus
Probab=26.58 E-value=35 Score=25.43 Aligned_cols=27 Identities=15% Similarity=0.307 Sum_probs=20.6
Q ss_pred CCceecCCCccccccchhHHhhccccC
Q psy370 78 ERGFVCEICGHVVDEMPVATQSSKYPG 104 (111)
Q Consensus 78 ~~~~~C~~C~~~~~~~~~l~~h~~~~~ 104 (111)
..|-.|..||.+|........|+-.|-
T Consensus 416 ~~pnqC~~CG~R~~~~ee~sk~md~H~ 442 (579)
T KOG2071|consen 416 DSPNQCKSCGLRFDDSEERSKHMDIHD 442 (579)
T ss_pred CCcchhcccccccccchhhhhHhhhhh
Confidence 456789999999998877777765553
No 223
>COG1327 Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains [Transcription]
Probab=26.45 E-value=29 Score=21.15 Aligned_cols=13 Identities=23% Similarity=0.488 Sum_probs=10.4
Q ss_pred eecCCCccccccc
Q psy370 81 FVCEICGHVVDEM 93 (111)
Q Consensus 81 ~~C~~C~~~~~~~ 93 (111)
-+|..|+..|++-
T Consensus 29 ReC~~C~~RFTTf 41 (156)
T COG1327 29 RECLECGERFTTF 41 (156)
T ss_pred hcccccccccchh
Confidence 3799999999764
No 224
>PF07295 DUF1451: Protein of unknown function (DUF1451); InterPro: IPR009912 This family consists of several hypothetical bacterial proteins of around 160 residues in length. Members of this family contain four highly conserved cysteine resides toward the C-terminal region of the protein. The function of this family is unknown.
Probab=26.29 E-value=19 Score=21.72 Aligned_cols=11 Identities=27% Similarity=0.721 Sum_probs=7.7
Q ss_pred CCccccccCcc
Q psy370 49 MDYSCEHCDMQ 59 (111)
Q Consensus 49 ~~~~c~~c~~~ 59 (111)
..+.|..||..
T Consensus 111 G~l~C~~Cg~~ 121 (146)
T PF07295_consen 111 GTLVCENCGHE 121 (146)
T ss_pred ceEecccCCCE
Confidence 44788888753
No 225
>PF11789 zf-Nse: Zinc-finger of the MIZ type in Nse subunit; PDB: 2YU4_A 3HTK_C.
Probab=26.10 E-value=36 Score=16.87 Aligned_cols=12 Identities=17% Similarity=0.454 Sum_probs=4.2
Q ss_pred ccccccCcccCC
Q psy370 51 YSCEHCDMQFNC 62 (111)
Q Consensus 51 ~~c~~c~~~f~~ 62 (111)
.....|+..|..
T Consensus 25 V~s~~C~H~fek 36 (57)
T PF11789_consen 25 VKSKKCGHTFEK 36 (57)
T ss_dssp EEESSS--EEEH
T ss_pred cCcCCCCCeecH
Confidence 333444444443
No 226
>COG4847 Uncharacterized protein conserved in archaea [Function unknown]
Probab=25.92 E-value=33 Score=19.15 Aligned_cols=13 Identities=23% Similarity=0.738 Sum_probs=9.7
Q ss_pred CCCceecCCCccc
Q psy370 77 EERGFVCEICGHV 89 (111)
Q Consensus 77 ~~~~~~C~~C~~~ 89 (111)
|-+-|+|..||..
T Consensus 3 ~lkewkC~VCg~~ 15 (103)
T COG4847 3 GLKEWKCYVCGGT 15 (103)
T ss_pred ccceeeEeeeCCE
Confidence 5567889888854
No 227
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=25.90 E-value=23 Score=17.54 Aligned_cols=14 Identities=21% Similarity=0.660 Sum_probs=8.4
Q ss_pred eecCCCccccccch
Q psy370 81 FVCEICGHVVDEMP 94 (111)
Q Consensus 81 ~~C~~C~~~~~~~~ 94 (111)
-.|..||+.|...+
T Consensus 6 ~~C~~Cg~~~~~~d 19 (54)
T PF14446_consen 6 CKCPVCGKKFKDGD 19 (54)
T ss_pred ccChhhCCcccCCC
Confidence 35677777765443
No 228
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=25.86 E-value=38 Score=18.71 Aligned_cols=33 Identities=15% Similarity=0.260 Sum_probs=21.1
Q ss_pred CCccccccCcccCCHHHHHHHHHhccCCCCCceecCCCccccccc
Q psy370 49 MDYSCEHCDMQFNCKSDMRKHVHSHLSMEERGFVCEICGHVVDEM 93 (111)
Q Consensus 49 ~~~~c~~c~~~f~~~~~l~~h~~~h~~~~~~~~~C~~C~~~~~~~ 93 (111)
..|.|++|++.-.. .. ..--|.|..|++.|.--
T Consensus 35 a~y~CpfCgk~~vk----------R~--a~GIW~C~~C~~~~AGG 67 (90)
T PRK03976 35 AKHVCPVCGRPKVK----------RV--GTGIWECRKCGAKFAGG 67 (90)
T ss_pred cCccCCCCCCCceE----------EE--EEEEEEcCCCCCEEeCC
Confidence 46799999753111 11 22358999999988653
No 229
>PF13821 DUF4187: Domain of unknown function (DUF4187)
Probab=25.82 E-value=84 Score=15.50 Aligned_cols=17 Identities=24% Similarity=0.341 Sum_probs=9.8
Q ss_pred eecCCCccccccchhHH
Q psy370 81 FVCEICGHVVDEMPVAT 97 (111)
Q Consensus 81 ~~C~~C~~~~~~~~~l~ 97 (111)
+-|-.||-.+.+..+|.
T Consensus 28 ~YC~~Cg~~Y~d~~dL~ 44 (55)
T PF13821_consen 28 NYCFWCGTKYDDEEDLE 44 (55)
T ss_pred ceeeeeCCccCCHHHHH
Confidence 45666666666555554
No 230
>TIGR00319 desulf_FeS4 desulfoferrodoxin FeS4 iron-binding domain. Neelaredoxin, a monomeric blue non-heme iron protein, lacks this domain.
Probab=25.71 E-value=42 Score=14.46 Aligned_cols=12 Identities=42% Similarity=1.298 Sum_probs=8.9
Q ss_pred ceecCCCccccc
Q psy370 80 GFVCEICGHVVD 91 (111)
Q Consensus 80 ~~~C~~C~~~~~ 91 (111)
=|+|..||..+.
T Consensus 7 ~ykC~~Cgniv~ 18 (34)
T TIGR00319 7 VYKCEVCGNIVE 18 (34)
T ss_pred EEEcCCCCcEEE
Confidence 478888887664
No 231
>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=25.17 E-value=43 Score=14.44 Aligned_cols=12 Identities=50% Similarity=1.323 Sum_probs=8.7
Q ss_pred ceecCCCccccc
Q psy370 80 GFVCEICGHVVD 91 (111)
Q Consensus 80 ~~~C~~C~~~~~ 91 (111)
-|+|..||..+.
T Consensus 4 ~ykC~~CGniv~ 15 (34)
T cd00974 4 VYKCEICGNIVE 15 (34)
T ss_pred EEEcCCCCcEEE
Confidence 478888887664
No 232
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=25.03 E-value=49 Score=22.05 Aligned_cols=15 Identities=47% Similarity=0.793 Sum_probs=8.9
Q ss_pred CceecCCCccccccc
Q psy370 79 RGFVCEICGHVVDEM 93 (111)
Q Consensus 79 ~~~~C~~C~~~~~~~ 93 (111)
+.|.|+.||..+..+
T Consensus 321 r~~~C~~cg~~~~rD 335 (364)
T COG0675 321 RLFKCPRCGFVHDRD 335 (364)
T ss_pred eeEECCCCCCeehhh
Confidence 346677777655444
No 233
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=24.61 E-value=74 Score=26.34 Aligned_cols=9 Identities=33% Similarity=1.006 Sum_probs=5.9
Q ss_pred ccCCCcccc
Q psy370 23 SQCPVCKKI 31 (111)
Q Consensus 23 ~~c~~C~~~ 31 (111)
+.|+.||..
T Consensus 668 rkCPkCG~~ 676 (1337)
T PRK14714 668 RRCPSCGTE 676 (1337)
T ss_pred EECCCCCCc
Confidence 567777753
No 234
>smart00731 SprT SprT homologues. Predicted to have roles in transcription elongation. Contains a conserved HExxH motif, indicating a metalloprotease function.
Probab=24.48 E-value=44 Score=19.84 Aligned_cols=9 Identities=33% Similarity=0.988 Sum_probs=4.3
Q ss_pred eecCCCccc
Q psy370 81 FVCEICGHV 89 (111)
Q Consensus 81 ~~C~~C~~~ 89 (111)
|.|..|+..
T Consensus 134 y~C~~C~g~ 142 (146)
T smart00731 134 YRCGKCGGK 142 (146)
T ss_pred EEcCCCCCE
Confidence 455555443
No 235
>KOG4727|consensus
Probab=24.27 E-value=46 Score=20.76 Aligned_cols=22 Identities=27% Similarity=0.602 Sum_probs=18.9
Q ss_pred cccCCCcccccCCHHHHHHHHH
Q psy370 22 ASQCPVCKKIYTDQQLFQNHLE 43 (111)
Q Consensus 22 ~~~c~~C~~~f~~~~~l~~h~~ 43 (111)
-|.|.+|.-.+...-.+..|+.
T Consensus 75 GyyCdVCdcvvKDSinflDHiN 96 (193)
T KOG4727|consen 75 GYYCDVCDCVVKDSINFLDHIN 96 (193)
T ss_pred ceeeeecceeehhhHHHHHHhc
Confidence 5999999999998888887764
No 236
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=24.24 E-value=44 Score=14.58 Aligned_cols=11 Identities=36% Similarity=0.776 Sum_probs=7.1
Q ss_pred eecCCCccccc
Q psy370 81 FVCEICGHVVD 91 (111)
Q Consensus 81 ~~C~~C~~~~~ 91 (111)
+.|..|+.+|.
T Consensus 22 ~~C~~Cg~~~~ 32 (33)
T PF08792_consen 22 EVCIFCGSSFP 32 (33)
T ss_pred EEcccCCcEee
Confidence 46777776653
No 237
>PRK05452 anaerobic nitric oxide reductase flavorubredoxin; Provisional
Probab=24.22 E-value=44 Score=24.23 Aligned_cols=17 Identities=35% Similarity=0.636 Sum_probs=11.1
Q ss_pred cccCcccCCCcccccCC
Q psy370 18 TIFVASQCPVCKKIYTD 34 (111)
Q Consensus 18 ~~~~~~~c~~C~~~f~~ 34 (111)
.....|.|..||..|..
T Consensus 421 ~~~~~~~c~~c~~~yd~ 437 (479)
T PRK05452 421 DLGPRMQCSVCQWIYDP 437 (479)
T ss_pred CCCCeEEECCCCeEECC
Confidence 34556778888777654
No 238
>PLN02748 tRNA dimethylallyltransferase
Probab=24.13 E-value=65 Score=23.46 Aligned_cols=24 Identities=21% Similarity=0.536 Sum_probs=17.6
Q ss_pred CCccccccCc-ccCCHHHHHHHHHh
Q psy370 49 MDYSCEHCDM-QFNCKSDMRKHVHS 72 (111)
Q Consensus 49 ~~~~c~~c~~-~f~~~~~l~~h~~~ 72 (111)
+.|.|.+|+. .+.....+..|+..
T Consensus 417 ~~~~Ce~C~~~~~~G~~eW~~Hlks 441 (468)
T PLN02748 417 TQYVCEACGNKVLRGAHEWEQHKQG 441 (468)
T ss_pred ccccccCCCCcccCCHHHHHHHhcc
Confidence 4567888886 67777777777664
No 239
>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=23.49 E-value=33 Score=19.78 Aligned_cols=12 Identities=42% Similarity=0.850 Sum_probs=7.6
Q ss_pred CcccCCCccccc
Q psy370 21 VASQCPVCKKIY 32 (111)
Q Consensus 21 ~~~~c~~C~~~f 32 (111)
....|+.|++..
T Consensus 68 v~V~CP~C~K~T 79 (114)
T PF11023_consen 68 VQVECPNCGKQT 79 (114)
T ss_pred eeeECCCCCChH
Confidence 455677777653
No 240
>COG3024 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=23.11 E-value=43 Score=17.21 Aligned_cols=13 Identities=31% Similarity=0.470 Sum_probs=10.5
Q ss_pred eecCCCccccccc
Q psy370 81 FVCEICGHVVDEM 93 (111)
Q Consensus 81 ~~C~~C~~~~~~~ 93 (111)
-+|+.||+.+.+.
T Consensus 8 v~CP~Cgkpv~w~ 20 (65)
T COG3024 8 VPCPTCGKPVVWG 20 (65)
T ss_pred ccCCCCCCccccc
Confidence 4799999988774
No 241
>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=23.04 E-value=13 Score=20.71 Aligned_cols=14 Identities=21% Similarity=0.368 Sum_probs=10.0
Q ss_pred CcccCCCcccccCC
Q psy370 21 VASQCPVCKKIYTD 34 (111)
Q Consensus 21 ~~~~c~~C~~~f~~ 34 (111)
..+.|+.|+..+..
T Consensus 15 ~~~~C~~C~~~~~~ 28 (104)
T TIGR01384 15 GVYVCPSCGYEKEK 28 (104)
T ss_pred CeEECcCCCCcccc
Confidence 36789999876553
No 242
>KOG1701|consensus
Probab=22.92 E-value=17 Score=26.01 Aligned_cols=41 Identities=24% Similarity=0.432 Sum_probs=21.6
Q ss_pred cCCCcccccCCHHHHHHHH--HHcCCCCCccccccCcccCCHHHH
Q psy370 24 QCPVCKKIYTDQQLFQNHL--ETHDNEMDYSCEHCDMQFNCKSDM 66 (111)
Q Consensus 24 ~c~~C~~~f~~~~~l~~h~--~~h~~~~~~~c~~c~~~f~~~~~l 66 (111)
.|..|++...-...-.+=| ..|. .-|.|..|.+.....+.+
T Consensus 276 iC~~C~K~V~g~~~ac~Am~~~fHv--~CFtC~~C~r~L~Gq~FY 318 (468)
T KOG1701|consen 276 ICAFCHKTVSGQGLAVEAMDQLFHV--QCFTCRTCRRQLAGQSFY 318 (468)
T ss_pred hhhhcCCcccCcchHHHHhhhhhcc--cceehHhhhhhhcccccc
Confidence 6888888665443322212 2232 356777776654444333
No 243
>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=22.90 E-value=28 Score=20.68 Aligned_cols=11 Identities=27% Similarity=0.821 Sum_probs=6.6
Q ss_pred ceecCCCcccc
Q psy370 80 GFVCEICGHVV 90 (111)
Q Consensus 80 ~~~C~~C~~~~ 90 (111)
.|.|..|+..+
T Consensus 143 ~~~C~~C~~~l 153 (157)
T PF10263_consen 143 RYRCGRCGGPL 153 (157)
T ss_pred hEECCCCCCEE
Confidence 36677776544
No 244
>TIGR00155 pqiA_fam integral membrane protein, PqiA family. This family consists of uncharacterized predicted integral membrane proteins found, so far, only in the Proteobacteria. Of two members in E. coli, one is induced by paraquat and is designated PqiA, paraquat-inducible protein A.
Probab=22.72 E-value=92 Score=22.16 Aligned_cols=10 Identities=20% Similarity=0.644 Sum_probs=5.9
Q ss_pred ccCCCccccc
Q psy370 23 SQCPVCKKIY 32 (111)
Q Consensus 23 ~~c~~C~~~f 32 (111)
-.|++|+..+
T Consensus 14 ~~C~~Cd~l~ 23 (403)
T TIGR00155 14 ILCSQCDMLV 23 (403)
T ss_pred eeCCCCCCcc
Confidence 3477776543
No 245
>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=22.71 E-value=67 Score=17.70 Aligned_cols=18 Identities=22% Similarity=0.545 Sum_probs=14.3
Q ss_pred cccCCCcccccCCHHHHH
Q psy370 22 ASQCPVCKKIYTDQQLFQ 39 (111)
Q Consensus 22 ~~~c~~C~~~f~~~~~l~ 39 (111)
...|+.||..|-+.+.+.
T Consensus 35 a~~C~~CGe~y~~dev~~ 52 (89)
T TIGR03829 35 SISCSHCGMEYQDDTTVK 52 (89)
T ss_pred cccccCCCcEeecHHHHH
Confidence 366999999998887654
No 246
>KOG1940|consensus
Probab=22.63 E-value=83 Score=21.23 Aligned_cols=18 Identities=28% Similarity=0.672 Sum_probs=10.1
Q ss_pred ccCCCcccccCCHHHHHHH
Q psy370 23 SQCPVCKKIYTDQQLFQNH 41 (111)
Q Consensus 23 ~~c~~C~~~f~~~~~l~~h 41 (111)
|.|+.|.+ ..+...+-.+
T Consensus 197 y~CP~C~~-~~d~~~~~~~ 214 (276)
T KOG1940|consen 197 YTCPICSK-PGDMSHYFRK 214 (276)
T ss_pred CCCCcccc-hHHHHHHHHH
Confidence 67777776 4444444433
No 247
>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG
Probab=22.63 E-value=41 Score=16.47 Aligned_cols=6 Identities=33% Similarity=1.021 Sum_probs=2.7
Q ss_pred ccccCc
Q psy370 53 CEHCDM 58 (111)
Q Consensus 53 c~~c~~ 58 (111)
|+.||.
T Consensus 3 CPyCge 8 (52)
T PF14255_consen 3 CPYCGE 8 (52)
T ss_pred CCCCCC
Confidence 444444
No 248
>PF01844 HNH: HNH endonuclease; InterPro: IPR002711 HNH endonuclease is found in bacteria and viruses [, , ]. This family includes pyocins, colicins and anaredoxins.; GO: 0003676 nucleic acid binding, 0004519 endonuclease activity; PDB: 2QGP_C.
Probab=22.59 E-value=22 Score=16.21 Aligned_cols=11 Identities=27% Similarity=0.821 Sum_probs=3.7
Q ss_pred cCCCccccccc
Q psy370 83 CEICGHVVDEM 93 (111)
Q Consensus 83 C~~C~~~~~~~ 93 (111)
|..|++.+...
T Consensus 1 C~~C~~~~~~~ 11 (47)
T PF01844_consen 1 CQYCGKPGSDN 11 (47)
T ss_dssp -TTT--B--GG
T ss_pred CCCCCCcCccC
Confidence 56677766554
No 249
>PF06220 zf-U1: U1 zinc finger; InterPro: IPR013085 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. C2H2-type (classical) zinc fingers (Znf) were the first class to be characterised. They contain a short beta hairpin and an alpha helix (beta/beta/alpha structure), where a single zinc atom is held in place by Cys(2)His(2) (C2H2) residues in a tetrahedral array. C2H2 Znf's can be divided into three groups based on the number and pattern of fingers: triple-C2H2 (binds single ligand), multiple-adjacent-C2H2 (binds multiple ligands), and separated paired-C2H2 []. C2H2 Znf's are the most common DNA-binding motifs found in eukaryotic transcription factors, and have also been identified in prokaryotes []. Transcription factors usually contain several Znf's (each with a conserved beta/beta/alpha structure) capable of making multiple contacts along the DNA, where the C2H2 Znf motifs recognise DNA sequences by binding to the major groove of DNA via a short alpha-helix in the Znf, the Znf spanning 3-4 bases of the DNA []. C2H2 Znf's can also bind to RNA and protein targets []. This entry represents a C2H2-type zinc finger motif found in several U1 small nuclear ribonucleoprotein C (U1-C) proteins. Some proteins contain multiple copies of this motif. The U1 small nuclear ribonucleoprotein (U1 snRNP) binds to the pre-mRNA 5' splice site at early stages of spliceosome assembly. Recruitment of U1 to a class of weak 5' splice site is promoted by binding of the protein TIA-1 to uridine-rich sequences immediately downstream from the 5' splice site. Binding of TIA-1 in the vicinity of a 5' splice site helps to stabilise U1 snRNP recruitment, at least in part, via a direct interaction with U1-C, thus providing one molecular mechanism for the function of this splicing regulator []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2VRD_A.
Probab=22.51 E-value=70 Score=14.38 Aligned_cols=14 Identities=14% Similarity=0.610 Sum_probs=4.8
Q ss_pred ceecCCCccccccc
Q psy370 80 GFVCEICGHVVDEM 93 (111)
Q Consensus 80 ~~~C~~C~~~~~~~ 93 (111)
.|-|..|..-|...
T Consensus 3 ryyCdyC~~~~~~d 16 (38)
T PF06220_consen 3 RYYCDYCKKYLTHD 16 (38)
T ss_dssp S-B-TTT--B-S--
T ss_pred CeecccccceecCC
Confidence 46688888877433
No 250
>COG4306 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=22.44 E-value=28 Score=20.52 Aligned_cols=16 Identities=25% Similarity=0.538 Sum_probs=8.2
Q ss_pred CCCccccccCcccCCH
Q psy370 48 EMDYSCEHCDMQFNCK 63 (111)
Q Consensus 48 ~~~~~c~~c~~~f~~~ 63 (111)
+.|-.|..||..|.+.
T Consensus 66 e~psfchncgs~fpwt 81 (160)
T COG4306 66 EPPSFCHNCGSRFPWT 81 (160)
T ss_pred CCcchhhcCCCCCCcH
Confidence 3444555555555443
No 251
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=22.24 E-value=67 Score=14.46 Aligned_cols=18 Identities=22% Similarity=0.252 Sum_probs=11.7
Q ss_pred ceecCCCccccccchhHH
Q psy370 80 GFVCEICGHVVDEMPVAT 97 (111)
Q Consensus 80 ~~~C~~C~~~~~~~~~l~ 97 (111)
-..|..|+-.|-....|.
T Consensus 19 id~C~~C~G~W~d~~el~ 36 (41)
T PF13453_consen 19 IDVCPSCGGIWFDAGELE 36 (41)
T ss_pred EEECCCCCeEEccHHHHH
Confidence 356777777776665554
No 252
>PRK10220 hypothetical protein; Provisional
Probab=21.91 E-value=36 Score=19.49 Aligned_cols=29 Identities=31% Similarity=0.754 Sum_probs=16.0
Q ss_pred cCCCcccccCCHHHHHHHHHHcCCCCCccccccCcccCCH
Q psy370 24 QCPVCKKIYTDQQLFQNHLETHDNEMDYSCEHCDMQFNCK 63 (111)
Q Consensus 24 ~c~~C~~~f~~~~~l~~h~~~h~~~~~~~c~~c~~~f~~~ 63 (111)
.|+.|+..|.... ...|.|+.|+..+...
T Consensus 5 ~CP~C~seytY~d-----------~~~~vCpeC~hEW~~~ 33 (111)
T PRK10220 5 HCPKCNSEYTYED-----------NGMYICPECAHEWNDA 33 (111)
T ss_pred cCCCCCCcceEcC-----------CCeEECCcccCcCCcc
Confidence 4666665554332 2346777777655443
No 253
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=21.73 E-value=51 Score=16.16 Aligned_cols=6 Identities=50% Similarity=1.381 Sum_probs=2.9
Q ss_pred cCCCcc
Q psy370 83 CEICGH 88 (111)
Q Consensus 83 C~~C~~ 88 (111)
|..||.
T Consensus 32 C~~Cga 37 (61)
T PF14354_consen 32 CTDCGA 37 (61)
T ss_pred cCCCCC
Confidence 455543
No 254
>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=21.54 E-value=40 Score=16.16 Aligned_cols=9 Identities=44% Similarity=1.313 Sum_probs=3.5
Q ss_pred cccCCCccc
Q psy370 22 ASQCPVCKK 30 (111)
Q Consensus 22 ~~~c~~C~~ 30 (111)
.|.|++|++
T Consensus 41 ~W~CPiC~~ 49 (50)
T PF02891_consen 41 KWKCPICNK 49 (50)
T ss_dssp --B-TTT--
T ss_pred CeECcCCcC
Confidence 488888875
No 255
>PF14311 DUF4379: Domain of unknown function (DUF4379)
Probab=21.52 E-value=58 Score=15.73 Aligned_cols=16 Identities=25% Similarity=0.449 Sum_probs=12.1
Q ss_pred ceecCCCccccccchh
Q psy370 80 GFVCEICGHVVDEMPV 95 (111)
Q Consensus 80 ~~~C~~C~~~~~~~~~ 95 (111)
-++|..||..|..+-.
T Consensus 28 ~W~C~~Cgh~w~~~v~ 43 (55)
T PF14311_consen 28 WWKCPKCGHEWKASVN 43 (55)
T ss_pred EEECCCCCCeeEccHh
Confidence 4789999988876643
No 256
>KOG4118|consensus
Probab=20.90 E-value=37 Score=17.56 Aligned_cols=24 Identities=13% Similarity=0.184 Sum_probs=10.5
Q ss_pred eecCCCccccccchhHHhhccccC
Q psy370 81 FVCEICGHVVDEMPVATQSSKYPG 104 (111)
Q Consensus 81 ~~C~~C~~~~~~~~~l~~h~~~~~ 104 (111)
+.|..|.-.-.....+.+|.-.-|
T Consensus 39 ~kCtVC~~~mpdpktfkqhfe~kH 62 (74)
T KOG4118|consen 39 HKCTVCMVQMPDPKTFKQHFENKH 62 (74)
T ss_pred hhhHhhHhhCCCCchHHHHHhhcC
Confidence 344444444444444444443333
No 257
>KOG0782|consensus
Probab=20.82 E-value=9.2 Score=28.48 Aligned_cols=51 Identities=22% Similarity=0.314 Sum_probs=28.4
Q ss_pred HHHHHHHHcCCCCCccccccCcccCCHHHHHHHHHhccCCCCCceecCCCccccccch
Q psy370 37 LFQNHLETHDNEMDYSCEHCDMQFNCKSDMRKHVHSHLSMEERGFVCEICGHVVDEMP 94 (111)
Q Consensus 37 ~l~~h~~~h~~~~~~~c~~c~~~f~~~~~l~~h~~~h~~~~~~~~~C~~C~~~~~~~~ 94 (111)
.|..|-=+|.....-.|..|++.|..+-.+ |.. ......|..|...|-.+.
T Consensus 240 ~fvrHHWVHrrRqeGkC~~CgKgFQQKf~F------hsK-EivAisCSWCKqayH~Kv 290 (1004)
T KOG0782|consen 240 GFVRHHWVHRRRQEGKCNTCGKGFQQKFFF------HSK-EIVAISCSWCKQAYHLKV 290 (1004)
T ss_pred cchHHhHhhHhhhccccchhhhhhhhheee------ccc-cEEEEEehHHHHHhhcch
Confidence 455555555544455777787777654333 221 223456777777665553
No 258
>KOG1088|consensus
Probab=20.79 E-value=68 Score=18.69 Aligned_cols=19 Identities=26% Similarity=0.251 Sum_probs=14.6
Q ss_pred CCCceecCCCccccccchh
Q psy370 77 EERGFVCEICGHVVDEMPV 95 (111)
Q Consensus 77 ~~~~~~C~~C~~~~~~~~~ 95 (111)
.|-...|+.||+.|.-++.
T Consensus 95 ~EG~l~CpetG~vfpI~~G 113 (124)
T KOG1088|consen 95 IEGELVCPETGRVFPISDG 113 (124)
T ss_pred ccceEecCCCCcEeecccC
Confidence 4456789999999987754
No 259
>PRK01343 zinc-binding protein; Provisional
Probab=20.68 E-value=48 Score=16.62 Aligned_cols=12 Identities=42% Similarity=0.805 Sum_probs=9.5
Q ss_pred cccCCCcccccC
Q psy370 22 ASQCPVCKKIYT 33 (111)
Q Consensus 22 ~~~c~~C~~~f~ 33 (111)
...|++|++.+.
T Consensus 9 ~~~CP~C~k~~~ 20 (57)
T PRK01343 9 TRPCPECGKPST 20 (57)
T ss_pred CCcCCCCCCcCc
Confidence 357999999874
No 260
>PRK06260 threonine synthase; Validated
Probab=20.67 E-value=72 Score=22.42 Aligned_cols=29 Identities=28% Similarity=0.654 Sum_probs=18.0
Q ss_pred ccCCCcccccCCHHHHHHHHHHcCCCCCccccccCcccCCH
Q psy370 23 SQCPVCKKIYTDQQLFQNHLETHDNEMDYSCEHCDMQFNCK 63 (111)
Q Consensus 23 ~~c~~C~~~f~~~~~l~~h~~~h~~~~~~~c~~c~~~f~~~ 63 (111)
+.|..||+.|. .....+.|+.|+..+...
T Consensus 4 ~~C~~cg~~~~------------~~~~~~~Cp~cg~~l~~~ 32 (397)
T PRK06260 4 LKCIECGKEYD------------PDEIIYTCPECGGLLEVI 32 (397)
T ss_pred EEECCCCCCCC------------CCCccccCCCCCCeEEEE
Confidence 56778887652 223457788887654444
No 261
>KOG3014|consensus
Probab=20.53 E-value=41 Score=22.31 Aligned_cols=23 Identities=17% Similarity=0.348 Sum_probs=12.7
Q ss_pred ecCCCccccccch--hHHhhccccC
Q psy370 82 VCEICGHVVDEMP--VATQSSKYPG 104 (111)
Q Consensus 82 ~C~~C~~~~~~~~--~l~~h~~~~~ 104 (111)
.|..||..++..+ +-..|.++|.
T Consensus 39 ~C~~Cgm~Yt~~s~EDe~~H~~fH~ 63 (257)
T KOG3014|consen 39 KCKECGMKYTVTSPEDEALHEKFHN 63 (257)
T ss_pred ehhhcCceecCCCHHHHHHHHHHHH
Confidence 5666666554333 3555666654
No 262
>COG1655 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=20.51 E-value=37 Score=22.32 Aligned_cols=24 Identities=13% Similarity=0.379 Sum_probs=14.6
Q ss_pred CCCccccccCcccCCHHHHHHHHH
Q psy370 48 EMDYSCEHCDMQFNCKSDMRKHVH 71 (111)
Q Consensus 48 ~~~~~c~~c~~~f~~~~~l~~h~~ 71 (111)
.+.+.|++|+..|.....+..-.|
T Consensus 17 kk~ieCPvC~tkFkkeev~tgsiR 40 (267)
T COG1655 17 KKTIECPVCNTKFKKEEVKTGSIR 40 (267)
T ss_pred hceeccCcccchhhhhheecccee
Confidence 355677777777766555444444
No 263
>KOG3352|consensus
Probab=20.48 E-value=49 Score=20.14 Aligned_cols=16 Identities=25% Similarity=0.513 Sum_probs=12.0
Q ss_pred CCceecCCCccccccc
Q psy370 78 ERGFVCEICGHVVDEM 93 (111)
Q Consensus 78 ~~~~~C~~C~~~~~~~ 93 (111)
.+.++|..||..|.-.
T Consensus 131 ge~~rc~eCG~~fkL~ 146 (153)
T KOG3352|consen 131 GETQRCPECGHYFKLV 146 (153)
T ss_pred CCcccCCcccceEEee
Confidence 4567899999988643
No 264
>COG0846 SIR2 NAD-dependent protein deacetylases, SIR2 family [Transcription]
Probab=20.45 E-value=70 Score=21.17 Aligned_cols=13 Identities=23% Similarity=0.644 Sum_probs=6.7
Q ss_pred CCccccccCcccC
Q psy370 49 MDYSCEHCDMQFN 61 (111)
Q Consensus 49 ~~~~c~~c~~~f~ 61 (111)
..+.|..|+..+.
T Consensus 121 ~~~~C~~C~~~~~ 133 (250)
T COG0846 121 KRVRCSKCGNQYY 133 (250)
T ss_pred eeeEeCCCcCccc
Confidence 3455566655444
No 265
>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=20.43 E-value=36 Score=20.82 Aligned_cols=18 Identities=22% Similarity=0.254 Sum_probs=15.0
Q ss_pred CCCceecCCCccccccch
Q psy370 77 EERGFVCEICGHVVDEMP 94 (111)
Q Consensus 77 ~~~~~~C~~C~~~~~~~~ 94 (111)
-+.|.-|..||+.|+|--
T Consensus 65 ~~~PsYC~~CGkpyPWt~ 82 (158)
T PF10083_consen 65 YEAPSYCHNCGKPYPWTE 82 (158)
T ss_pred CCCChhHHhCCCCCchHH
Confidence 457888999999998874
Done!