Query psy9067
Match_columns 189
No_of_seqs 116 out of 1401
Neff 11.0
Searched_HMMs 46136
Date Fri Aug 16 18:02:53 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy9067.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/9067hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2462|consensus 100.0 1.4E-30 3.1E-35 179.5 7.1 136 32-185 127-265 (279)
2 KOG2462|consensus 99.9 2.9E-28 6.3E-33 168.1 6.3 135 5-158 129-266 (279)
3 KOG3623|consensus 99.9 2.6E-23 5.7E-28 159.7 4.3 81 104-184 891-971 (1007)
4 KOG1074|consensus 99.9 3.5E-23 7.5E-28 161.1 1.3 82 107-188 605-693 (958)
5 KOG1074|consensus 99.9 1.5E-22 3.2E-27 157.6 3.9 177 8-188 607-932 (958)
6 KOG3608|consensus 99.9 1.3E-21 2.8E-26 139.4 8.2 174 15-189 187-378 (467)
7 KOG3608|consensus 99.8 2.8E-20 6.1E-25 132.6 6.1 157 14-186 143-315 (467)
8 KOG3576|consensus 99.8 2.9E-19 6.4E-24 118.4 2.2 113 61-189 115-238 (267)
9 KOG3576|consensus 99.7 9E-18 2E-22 111.4 2.7 125 4-134 115-239 (267)
10 KOG3623|consensus 99.6 5.2E-16 1.1E-20 120.2 1.8 108 64-185 211-331 (1007)
11 PLN03086 PRLI-interacting fact 99.4 3.9E-12 8.5E-17 98.6 10.8 146 6-187 407-564 (567)
12 KOG3993|consensus 99.4 5.9E-14 1.3E-18 102.7 0.2 153 35-188 267-483 (500)
13 PHA00733 hypothetical protein 99.4 7.3E-13 1.6E-17 84.5 4.6 86 102-189 35-125 (128)
14 PHA00733 hypothetical protein 99.2 4E-11 8.7E-16 76.6 4.7 64 21-84 26-94 (128)
15 PLN03086 PRLI-interacting fact 99.1 2.7E-10 5.8E-15 88.6 8.2 100 35-157 453-562 (567)
16 PHA02768 hypothetical protein; 99.1 4.1E-11 8.9E-16 63.5 2.2 42 136-179 6-47 (55)
17 PHA02768 hypothetical protein; 98.9 4.3E-10 9.3E-15 59.7 1.7 44 107-152 5-48 (55)
18 PF13465 zf-H2C2_2: Zinc-finge 98.8 2.3E-09 5E-14 48.7 1.9 26 150-175 1-26 (26)
19 KOG3993|consensus 98.7 3E-09 6.6E-14 78.5 -0.4 151 6-157 267-480 (500)
20 PHA00616 hypothetical protein 98.6 2.7E-08 5.7E-13 50.3 1.7 34 135-168 1-34 (44)
21 PHA00732 hypothetical protein 98.6 5.4E-08 1.2E-12 56.6 3.0 46 107-158 1-47 (79)
22 PF13465 zf-H2C2_2: Zinc-finge 98.6 3E-08 6.6E-13 45.0 1.4 24 23-46 2-25 (26)
23 PHA00616 hypothetical protein 98.4 1E-07 2.2E-12 48.2 1.6 34 35-68 1-34 (44)
24 PF05605 zf-Di19: Drought indu 98.4 7.5E-07 1.6E-11 48.1 4.8 51 135-188 2-54 (54)
25 PF00096 zf-C2H2: Zinc finger, 98.4 1.9E-07 4.2E-12 41.1 1.2 23 164-186 1-23 (23)
26 PF13912 zf-C2H2_6: C2H2-type 98.3 3.1E-07 6.8E-12 42.1 1.2 27 163-189 1-27 (27)
27 PHA00732 hypothetical protein 98.2 1.2E-06 2.5E-11 51.0 2.8 46 135-186 1-47 (79)
28 PF13894 zf-C2H2_4: C2H2-type 98.2 8E-07 1.7E-11 39.4 1.7 24 164-187 1-24 (24)
29 PF05605 zf-Di19: Drought indu 98.1 6.1E-06 1.3E-10 44.6 4.0 49 36-87 3-53 (54)
30 PF12756 zf-C2H2_2: C2H2 type 98.0 3.1E-06 6.6E-11 51.9 2.2 73 109-186 1-73 (100)
31 PF00096 zf-C2H2: Zinc finger, 97.9 7.2E-06 1.6E-10 35.9 1.5 22 136-157 1-22 (23)
32 PF13909 zf-H2C2_5: C2H2-type 97.8 1.1E-05 2.4E-10 35.7 1.1 24 164-188 1-24 (24)
33 COG5189 SFP1 Putative transcri 97.7 9.2E-06 2E-10 58.5 0.8 52 133-184 347-419 (423)
34 smart00355 ZnF_C2H2 zinc finge 97.6 4.6E-05 9.9E-10 34.1 2.0 24 164-187 1-24 (26)
35 PF13894 zf-C2H2_4: C2H2-type 97.6 5.4E-05 1.2E-09 33.3 1.9 21 37-57 2-22 (24)
36 PF09237 GAGA: GAGA factor; I 97.6 5.3E-05 1.2E-09 39.2 2.0 29 160-188 21-49 (54)
37 PF12756 zf-C2H2_2: C2H2 type 97.5 4.6E-05 9.9E-10 46.6 1.8 22 108-129 51-72 (100)
38 PF13912 zf-C2H2_6: C2H2-type 97.5 7.4E-05 1.6E-09 34.0 1.6 23 36-58 2-24 (27)
39 COG5189 SFP1 Putative transcri 97.4 6.6E-05 1.4E-09 54.2 1.1 66 60-127 346-418 (423)
40 PF12874 zf-met: Zinc-finger o 97.2 0.00017 3.8E-09 32.1 1.0 23 164-186 1-23 (25)
41 PF09237 GAGA: GAGA factor; I 97.0 0.00061 1.3E-08 35.4 1.9 31 132-162 21-51 (54)
42 smart00355 ZnF_C2H2 zinc finge 97.0 0.00089 1.9E-08 29.7 2.4 24 136-159 1-24 (26)
43 PRK04860 hypothetical protein; 96.8 0.0007 1.5E-08 45.0 2.0 39 134-176 118-156 (160)
44 PF12874 zf-met: Zinc-finger o 96.7 0.001 2.3E-08 29.5 1.2 20 37-56 2-21 (25)
45 PF12171 zf-C2H2_jaz: Zinc-fin 96.6 0.00041 9E-09 31.5 -0.2 22 164-185 2-23 (27)
46 PRK04860 hypothetical protein; 96.1 0.0031 6.8E-08 42.0 1.5 38 35-76 119-156 (160)
47 KOG1146|consensus 96.1 0.0032 6.9E-08 54.0 1.8 85 101-185 459-611 (1406)
48 PF13909 zf-H2C2_5: C2H2-type 96.1 0.0039 8.5E-08 27.3 1.3 22 36-58 1-22 (24)
49 KOG1146|consensus 96.0 0.0011 2.4E-08 56.7 -1.1 145 41-185 442-640 (1406)
50 PF12171 zf-C2H2_jaz: Zinc-fin 95.9 0.0077 1.7E-07 27.2 2.0 22 108-129 2-23 (27)
51 KOG2785|consensus 95.7 0.026 5.7E-07 42.3 5.0 52 134-185 165-242 (390)
52 PF13913 zf-C2HC_2: zinc-finge 95.7 0.0085 1.8E-07 26.6 1.6 20 164-184 3-22 (25)
53 TIGR00622 ssl1 transcription f 95.7 0.033 7.3E-07 34.5 4.7 20 34-53 14-33 (112)
54 KOG2893|consensus 95.6 0.0032 7E-08 43.9 -0.0 50 104-158 8-58 (341)
55 KOG2231|consensus 95.5 0.074 1.6E-06 43.3 7.1 118 46-184 125-260 (669)
56 smart00451 ZnF_U1 U1-like zinc 94.9 0.016 3.5E-07 27.8 1.3 22 163-184 3-24 (35)
57 KOG2893|consensus 94.6 0.0072 1.6E-07 42.3 -0.5 45 7-56 11-55 (341)
58 KOG2482|consensus 94.5 0.17 3.8E-06 37.5 6.2 64 21-85 129-217 (423)
59 cd00350 rubredoxin_like Rubred 94.4 0.025 5.3E-07 27.0 1.2 10 108-117 2-11 (33)
60 COG5048 FOG: Zn-finger [Genera 94.4 0.017 3.7E-07 44.7 1.0 138 34-171 288-454 (467)
61 KOG4173|consensus 94.1 0.029 6.2E-07 38.4 1.5 80 103-185 75-168 (253)
62 smart00451 ZnF_U1 U1-like zinc 93.7 0.057 1.2E-06 25.8 1.8 23 35-57 3-25 (35)
63 COG4049 Uncharacterized protei 93.5 0.033 7.2E-07 29.5 0.8 24 133-156 15-38 (65)
64 KOG2231|consensus 92.9 0.17 3.7E-06 41.3 4.2 111 65-189 117-238 (669)
65 PF10571 UPF0547: Uncharacteri 92.0 0.088 1.9E-06 23.6 0.9 9 165-173 16-24 (26)
66 PF12013 DUF3505: Protein of u 91.5 0.43 9.3E-06 29.7 4.1 26 163-188 80-109 (109)
67 cd00729 rubredoxin_SM Rubredox 91.2 0.14 3E-06 24.6 1.2 10 108-117 3-12 (34)
68 COG4049 Uncharacterized protei 91.1 0.11 2.5E-06 27.5 1.0 28 31-58 13-40 (65)
69 PF09538 FYDLN_acid: Protein o 90.9 0.19 4.1E-06 31.2 1.9 15 106-120 25-39 (108)
70 PF13719 zinc_ribbon_5: zinc-r 90.9 0.19 4.1E-06 24.6 1.6 33 108-145 3-35 (37)
71 KOG2785|consensus 90.7 1.3 2.7E-05 33.7 6.3 51 107-157 166-242 (390)
72 COG5048 FOG: Zn-finger [Genera 90.6 0.053 1.2E-06 42.0 -0.9 54 135-188 289-348 (467)
73 TIGR00622 ssl1 transcription f 90.6 0.66 1.4E-05 28.9 4.1 21 163-183 81-101 (112)
74 PF05443 ROS_MUCR: ROS/MUCR tr 90.4 0.17 3.7E-06 32.6 1.5 25 136-163 73-97 (132)
75 PF13717 zinc_ribbon_4: zinc-r 90.2 0.27 5.8E-06 23.9 1.8 33 108-145 3-35 (36)
76 PF02892 zf-BED: BED zinc fing 89.8 0.19 4.1E-06 25.6 1.1 27 161-187 14-44 (45)
77 smart00531 TFIIE Transcription 89.4 0.82 1.8E-05 30.2 4.1 46 24-73 88-133 (147)
78 COG1592 Rubrerythrin [Energy p 88.7 0.3 6.6E-06 32.7 1.7 10 133-142 147-156 (166)
79 TIGR00373 conserved hypothetic 88.4 0.76 1.6E-05 30.7 3.5 42 23-73 97-138 (158)
80 TIGR02098 MJ0042_CXXC MJ0042 f 88.3 0.36 7.7E-06 23.6 1.4 33 108-145 3-35 (38)
81 KOG2482|consensus 88.2 0.44 9.5E-06 35.5 2.4 26 64-89 280-305 (423)
82 PF09538 FYDLN_acid: Protein o 87.9 0.37 8.1E-06 29.9 1.7 29 109-148 11-39 (108)
83 PF09986 DUF2225: Uncharacteri 87.9 0.13 2.8E-06 36.2 -0.4 43 106-148 4-61 (214)
84 smart00531 TFIIE Transcription 87.6 0.67 1.4E-05 30.6 2.8 41 59-119 95-135 (147)
85 smart00614 ZnF_BED BED zinc fi 87.2 0.5 1.1E-05 24.8 1.7 23 164-186 19-46 (50)
86 PRK06266 transcription initiat 87.2 0.85 1.8E-05 31.2 3.2 43 23-74 105-147 (178)
87 smart00734 ZnF_Rad18 Rad18-lik 86.8 0.53 1.1E-05 21.0 1.4 20 164-184 2-21 (26)
88 TIGR00373 conserved hypothetic 86.2 0.85 1.8E-05 30.5 2.8 34 3-46 106-139 (158)
89 PHA00626 hypothetical protein 85.8 0.29 6.4E-06 26.1 0.3 13 162-174 22-34 (59)
90 PF12013 DUF3505: Protein of u 84.9 2.2 4.7E-05 26.5 4.0 27 134-160 79-109 (109)
91 PF09986 DUF2225: Uncharacteri 84.9 0.17 3.7E-06 35.6 -1.1 13 108-120 49-61 (214)
92 COG5236 Uncharacterized conser 84.0 0.49 1.1E-05 35.4 0.9 78 108-187 152-244 (493)
93 COG1592 Rubrerythrin [Energy p 83.9 1.6 3.4E-05 29.4 3.2 26 33-71 132-157 (166)
94 COG2888 Predicted Zn-ribbon RN 83.6 2 4.4E-05 23.3 2.9 9 62-70 49-57 (61)
95 PRK06266 transcription initiat 83.3 1.3 2.8E-05 30.3 2.7 35 3-47 114-148 (178)
96 PF14369 zf-RING_3: zinc-finge 83.1 0.52 1.1E-05 22.7 0.5 9 37-45 23-31 (35)
97 smart00659 RPOLCX RNA polymera 82.4 0.8 1.7E-05 23.4 1.1 11 108-118 3-13 (44)
98 TIGR02300 FYDLN_acid conserved 82.4 1.2 2.5E-05 28.4 2.0 15 106-120 25-39 (129)
99 COG5151 SSL1 RNA polymerase II 81.3 1.3 2.8E-05 32.7 2.2 23 107-129 388-410 (421)
100 PRK00464 nrdR transcriptional 81.1 0.24 5.3E-06 32.8 -1.4 15 136-150 29-43 (154)
101 PRK00398 rpoP DNA-directed RNA 81.0 1 2.2E-05 23.1 1.2 12 107-118 21-32 (46)
102 PRK14890 putative Zn-ribbon RN 80.8 1.2 2.5E-05 24.2 1.4 10 162-171 47-56 (59)
103 PF03604 DNA_RNApol_7kD: DNA d 80.6 0.96 2.1E-05 21.3 0.9 9 109-117 2-10 (32)
104 smart00834 CxxC_CXXC_SSSS Puta 80.1 0.62 1.3E-05 23.0 0.2 29 108-143 6-34 (41)
105 TIGR02605 CxxC_CxxC_SSSS putat 79.3 0.67 1.5E-05 24.4 0.2 29 108-143 6-34 (52)
106 COG4957 Predicted transcriptio 78.0 1.4 3E-05 28.3 1.3 23 164-189 77-99 (148)
107 COG5236 Uncharacterized conser 77.4 2.3 4.9E-05 32.0 2.5 115 20-157 166-303 (493)
108 PF06524 NOA36: NOA36 protein; 77.2 1.7 3.6E-05 31.3 1.7 11 60-70 139-149 (314)
109 KOG2186|consensus 76.2 1.8 4E-05 31.0 1.6 13 63-75 29-41 (276)
110 COG1198 PriA Primosomal protei 76.1 2.7 5.9E-05 35.3 2.8 10 133-142 473-482 (730)
111 PF13878 zf-C2H2_3: zinc-finge 75.9 2.6 5.7E-05 21.0 1.8 23 164-186 14-38 (41)
112 PRK04023 DNA polymerase II lar 75.0 3.7 8E-05 35.6 3.3 12 163-174 663-674 (1121)
113 TIGR01384 TFS_arch transcripti 74.3 0.57 1.2E-05 28.8 -1.1 9 108-116 63-71 (104)
114 PF05191 ADK_lid: Adenylate ki 74.2 0.78 1.7E-05 22.3 -0.4 8 38-45 4-11 (36)
115 PF07975 C1_4: TFIIH C1-like d 74.2 2.3 5E-05 22.5 1.3 31 105-141 19-49 (51)
116 PF09723 Zn-ribbon_8: Zinc rib 74.1 1.2 2.6E-05 22.4 0.3 30 63-115 5-34 (42)
117 KOG2186|consensus 73.9 1.8 3.9E-05 31.0 1.1 47 107-156 3-49 (276)
118 COG1997 RPL43A Ribosomal prote 73.8 1.9 4.2E-05 25.4 1.1 33 34-76 34-66 (89)
119 COG1996 RPC10 DNA-directed RNA 73.8 1.6 3.4E-05 22.8 0.6 10 108-117 7-16 (49)
120 KOG2593|consensus 73.3 4 8.6E-05 31.7 2.9 39 59-116 124-162 (436)
121 PF02176 zf-TRAF: TRAF-type zi 72.5 2.5 5.5E-05 22.8 1.4 21 20-40 23-43 (60)
122 KOG2593|consensus 72.2 5.4 0.00012 31.0 3.4 38 32-72 125-162 (436)
123 PRK09678 DNA-binding transcrip 71.0 0.95 2.1E-05 25.8 -0.6 14 134-147 26-41 (72)
124 COG5188 PRP9 Splicing factor 3 70.8 6.3 0.00014 29.8 3.3 28 129-156 368-396 (470)
125 COG1326 Uncharacterized archae 70.7 7.1 0.00015 26.9 3.3 42 1-47 1-42 (201)
126 PF14353 CpXC: CpXC protein 70.6 0.42 9.1E-06 30.7 -2.4 14 135-148 38-51 (128)
127 PF13240 zinc_ribbon_2: zinc-r 70.6 1.8 4E-05 18.6 0.4 6 110-115 2-7 (23)
128 PF03811 Zn_Tnp_IS1: InsA N-te 70.4 1.7 3.6E-05 21.1 0.3 34 3-41 2-35 (36)
129 PF04959 ARS2: Arsenite-resist 70.4 1.9 4.1E-05 30.4 0.6 23 164-186 78-100 (214)
130 KOG2807|consensus 69.0 9.1 0.0002 28.7 3.8 35 36-84 277-311 (378)
131 PF15135 UPF0515: Uncharacteri 68.8 14 0.0003 26.7 4.5 16 106-121 154-169 (278)
132 PF12907 zf-met2: Zinc-binding 68.2 4.1 8.9E-05 20.3 1.4 25 164-188 2-29 (40)
133 KOG4173|consensus 67.7 1.5 3.3E-05 30.3 -0.3 73 12-88 87-171 (253)
134 PF14446 Prok-RING_1: Prokaryo 67.1 3.6 7.7E-05 22.0 1.1 25 108-144 6-30 (54)
135 PF08274 PhnA_Zn_Ribbon: PhnA 62.8 3.1 6.8E-05 19.3 0.4 11 109-119 4-14 (30)
136 PF07754 DUF1610: Domain of un 62.3 3.2 6.9E-05 18.1 0.3 8 135-142 16-23 (24)
137 COG4530 Uncharacterized protei 62.1 5.9 0.00013 24.5 1.5 12 134-145 25-36 (129)
138 KOG4124|consensus 61.3 1.4 2.9E-05 33.2 -1.5 49 134-182 348-417 (442)
139 PRK03824 hypA hydrogenase nick 58.9 5 0.00011 26.1 0.9 15 106-120 69-83 (135)
140 PF04216 FdhE: Protein involve 57.6 0.66 1.4E-05 34.4 -3.7 16 104-119 235-250 (290)
141 COG1675 TFA1 Transcription ini 56.7 17 0.00038 24.8 3.2 45 20-73 98-142 (176)
142 COG1655 Uncharacterized protei 56.1 2.6 5.7E-05 29.8 -0.7 26 105-130 17-42 (267)
143 PF10013 DUF2256: Uncharacteri 56.0 5.6 0.00012 20.0 0.6 13 37-49 10-22 (42)
144 PF12760 Zn_Tnp_IS1595: Transp 54.2 8.3 0.00018 19.7 1.1 8 108-115 19-26 (46)
145 PF15269 zf-C2H2_7: Zinc-finge 54.2 7.6 0.00016 19.7 0.9 22 164-185 21-42 (54)
146 COG3357 Predicted transcriptio 53.2 12 0.00026 22.3 1.7 15 61-75 56-70 (97)
147 PTZ00255 60S ribosomal protein 53.1 5 0.00011 24.0 0.2 33 34-76 35-67 (90)
148 COG0068 HypF Hydrogenase matur 52.8 1.3 2.8E-05 36.7 -3.0 57 109-172 125-182 (750)
149 PF05290 Baculo_IE-1: Baculovi 52.7 14 0.0003 23.9 2.1 43 30-77 75-135 (140)
150 COG1198 PriA Primosomal protei 51.9 7.2 0.00015 33.0 1.0 45 109-172 437-484 (730)
151 COG3677 Transposase and inacti 51.6 3.6 7.8E-05 26.5 -0.6 16 133-148 51-66 (129)
152 PF13451 zf-trcl: Probable zin 51.4 13 0.00028 19.5 1.5 37 34-70 3-40 (49)
153 COG0068 HypF Hydrogenase matur 51.0 3.5 7.5E-05 34.3 -0.9 58 65-144 125-182 (750)
154 TIGR01206 lysW lysine biosynth 50.5 9.6 0.00021 20.4 1.0 12 107-118 22-33 (54)
155 KOG4167|consensus 50.1 4.1 8.9E-05 33.9 -0.6 25 163-187 792-816 (907)
156 PF01363 FYVE: FYVE zinc finge 50.1 7.4 0.00016 21.7 0.6 27 108-146 10-36 (69)
157 PF11931 DUF3449: Domain of un 50.1 5.3 0.00012 27.7 0.0 26 5-30 100-125 (196)
158 COG4888 Uncharacterized Zn rib 49.9 2.4 5.2E-05 25.7 -1.5 13 105-117 20-32 (104)
159 KOG2071|consensus 49.8 16 0.00035 29.8 2.6 23 8-31 420-442 (579)
160 smart00661 RPOL9 RNA polymeras 49.7 10 0.00022 19.7 1.1 11 35-45 20-30 (52)
161 PRK12496 hypothetical protein; 49.6 11 0.00025 25.4 1.5 26 136-173 128-153 (164)
162 COG5216 Uncharacterized conser 49.5 25 0.00055 19.0 2.5 36 2-43 17-52 (67)
163 PF08792 A2L_zn_ribbon: A2L zi 49.3 5.3 0.00011 18.9 -0.1 11 163-173 21-31 (33)
164 KOG1280|consensus 49.2 17 0.00038 27.5 2.5 36 35-70 79-116 (381)
165 TIGR00280 L37a ribosomal prote 48.5 5.8 0.00013 23.8 -0.0 33 34-76 34-66 (91)
166 PF04959 ARS2: Arsenite-resist 47.6 5.9 0.00013 28.0 -0.1 30 104-133 74-103 (214)
167 COG3091 SprT Zn-dependent meta 47.6 7 0.00015 25.8 0.3 34 134-172 116-149 (156)
168 PRK03564 formate dehydrogenase 47.4 11 0.00025 28.2 1.3 15 133-147 250-264 (309)
169 KOG1842|consensus 46.8 20 0.00044 28.2 2.6 26 36-61 16-41 (505)
170 PRK12380 hydrogenase nickel in 46.8 9.7 0.00021 23.9 0.8 11 136-146 71-81 (113)
171 KOG3408|consensus 46.2 13 0.00028 23.5 1.2 27 131-157 53-79 (129)
172 PRK00432 30S ribosomal protein 45.8 11 0.00023 19.8 0.7 9 163-171 37-45 (50)
173 TIGR00100 hypA hydrogenase nic 44.5 12 0.00025 23.6 0.9 11 136-146 71-81 (115)
174 TIGR00686 phnA alkylphosphonat 44.3 15 0.00033 22.8 1.3 16 105-120 17-32 (109)
175 cd00065 FYVE FYVE domain; Zinc 44.2 16 0.00035 19.3 1.3 27 109-147 4-30 (57)
176 PF01780 Ribosomal_L37ae: Ribo 43.9 5.2 0.00011 23.9 -0.7 31 34-74 34-64 (90)
177 PRK10220 hypothetical protein; 43.7 18 0.00038 22.5 1.5 17 105-121 18-34 (111)
178 PF13453 zf-TFIIB: Transcripti 43.6 11 0.00024 18.6 0.6 15 36-50 20-34 (41)
179 PF14787 zf-CCHC_5: GAG-polypr 43.3 11 0.00023 18.3 0.4 15 164-178 3-17 (36)
180 PRK00564 hypA hydrogenase nick 43.0 13 0.00028 23.5 1.0 11 136-146 72-82 (117)
181 PRK03976 rpl37ae 50S ribosomal 42.5 7.4 0.00016 23.3 -0.2 33 34-76 35-67 (90)
182 smart00154 ZnF_AN1 AN1-like Zi 41.7 12 0.00025 18.5 0.5 13 163-175 12-24 (39)
183 KOG2272|consensus 41.5 28 0.00061 25.2 2.4 42 9-53 76-117 (332)
184 PF13824 zf-Mss51: Zinc-finger 41.1 35 0.00077 18.3 2.2 14 133-146 12-25 (55)
185 PF13963 Transpos_assoc: Trans 40.9 30 0.00064 19.9 2.2 24 36-59 40-64 (77)
186 KOG1280|consensus 40.6 23 0.0005 26.9 2.0 38 133-170 77-116 (381)
187 PF14311 DUF4379: Domain of un 40.5 25 0.00054 18.6 1.7 15 108-122 29-43 (55)
188 PF08271 TF_Zn_Ribbon: TFIIB z 40.3 11 0.00025 18.8 0.3 9 64-72 20-28 (43)
189 KOG2071|consensus 40.1 19 0.00042 29.4 1.7 27 160-186 415-441 (579)
190 PF05207 zf-CSL: CSL zinc fing 39.9 35 0.00075 18.3 2.2 33 4-43 16-48 (55)
191 PRK14873 primosome assembly pr 39.8 22 0.00048 29.9 2.0 25 132-172 407-431 (665)
192 PF04423 Rad50_zn_hook: Rad50 39.0 11 0.00025 19.9 0.2 11 165-175 22-32 (54)
193 PRK14714 DNA polymerase II lar 38.8 49 0.0011 30.0 3.9 10 107-116 709-718 (1337)
194 PF01428 zf-AN1: AN1-like Zinc 38.6 10 0.00022 19.1 -0.1 14 162-175 12-25 (43)
195 KOG2923|consensus 38.5 49 0.0011 18.3 2.6 36 2-43 17-52 (67)
196 KOG3408|consensus 38.1 21 0.00046 22.6 1.3 26 161-186 55-80 (129)
197 COG1571 Predicted DNA-binding 38.0 22 0.00048 27.9 1.6 14 163-176 367-380 (421)
198 TIGR00595 priA primosomal prot 37.9 28 0.0006 28.2 2.3 10 162-171 252-261 (505)
199 KOG2907|consensus 37.8 13 0.00029 23.1 0.4 13 163-175 102-114 (116)
200 PF01155 HypA: Hydrogenase exp 37.6 7.5 0.00016 24.4 -0.7 12 108-119 71-82 (113)
201 PF08790 zf-LYAR: LYAR-type C2 37.5 4.7 0.0001 18.3 -1.2 10 164-173 1-10 (28)
202 PF13821 DUF4187: Domain of un 37.0 29 0.00063 18.6 1.6 19 36-54 28-46 (55)
203 PF04780 DUF629: Protein of un 36.9 23 0.00049 28.3 1.6 22 135-156 57-78 (466)
204 KOG4167|consensus 36.2 10 0.00022 31.8 -0.4 29 60-88 789-817 (907)
205 PF07282 OrfB_Zn_ribbon: Putat 36.0 30 0.00066 19.2 1.7 29 36-74 29-57 (69)
206 PRK03681 hypA hydrogenase nick 35.7 19 0.0004 22.7 0.8 9 136-144 71-79 (114)
207 KOG2906|consensus 34.9 3.2 6.9E-05 25.1 -2.5 17 63-79 21-37 (105)
208 COG1327 Predicted transcriptio 34.7 9.2 0.0002 25.3 -0.7 13 136-148 29-41 (156)
209 smart00064 FYVE Protein presen 34.6 37 0.0008 18.7 1.9 28 108-147 11-38 (68)
210 PF05495 zf-CHY: CHY zinc fing 34.2 4.8 0.0001 22.9 -1.8 58 108-173 11-71 (71)
211 cd00924 Cyt_c_Oxidase_Vb Cytoc 34.0 17 0.00038 22.1 0.5 15 133-147 77-91 (97)
212 PF10276 zf-CHCC: Zinc-finger 33.8 14 0.00031 18.4 0.1 11 163-173 29-39 (40)
213 TIGR00627 tfb4 transcription f 33.6 28 0.00061 25.8 1.6 24 136-173 256-279 (279)
214 PF08394 Arc_trans_TRASH: Arch 32.3 9 0.0002 18.7 -0.8 17 2-18 18-34 (37)
215 KOG3362|consensus 32.3 15 0.00033 24.0 0.0 22 163-184 129-150 (156)
216 PTZ00448 hypothetical protein; 31.8 30 0.00066 26.6 1.5 23 163-185 314-336 (373)
217 COG1594 RPB9 DNA-directed RNA 31.7 17 0.00036 22.9 0.1 39 36-74 73-111 (113)
218 KOG1994|consensus 31.2 21 0.00046 25.4 0.6 23 34-56 238-260 (268)
219 smart00440 ZnF_C2C2 C2C2 Zinc 31.1 9.5 0.00021 18.9 -0.8 7 164-170 29-35 (40)
220 KOG1842|consensus 30.8 29 0.00062 27.4 1.2 27 7-34 16-42 (505)
221 PF06397 Desulfoferrod_N: Desu 30.4 19 0.00042 17.4 0.2 11 162-172 5-15 (36)
222 KOG0717|consensus 29.6 26 0.00056 27.8 0.9 21 164-184 293-313 (508)
223 COG4896 Uncharacterized protei 29.6 42 0.00092 18.4 1.4 7 64-70 32-38 (68)
224 PF04780 DUF629: Protein of un 29.4 37 0.0008 27.2 1.6 27 64-90 58-84 (466)
225 PLN02294 cytochrome c oxidase 28.6 33 0.00071 23.3 1.1 15 105-119 139-153 (174)
226 PF09963 DUF2197: Uncharacteri 28.1 70 0.0015 17.3 2.1 6 36-41 32-37 (56)
227 KOG2636|consensus 27.6 54 0.0012 26.0 2.2 28 129-156 395-423 (497)
228 KOG4727|consensus 27.6 38 0.00082 23.0 1.2 27 102-128 70-96 (193)
229 PF10537 WAC_Acf1_DNA_bd: ATP- 27.4 56 0.0012 20.1 1.9 40 107-147 3-42 (102)
230 PRK12860 transcriptional activ 27.0 62 0.0014 22.5 2.2 47 15-70 115-161 (189)
231 cd00730 rubredoxin Rubredoxin; 27.0 27 0.00058 18.3 0.4 11 164-174 2-12 (50)
232 PF11672 DUF3268: Protein of u 26.8 44 0.00095 20.6 1.3 38 106-144 1-40 (102)
233 PF06220 zf-U1: U1 zinc finger 26.8 50 0.0011 16.1 1.3 11 35-45 3-13 (38)
234 KOG0717|consensus 26.7 37 0.0008 27.0 1.2 22 136-157 293-314 (508)
235 cd01121 Sms Sms (bacterial rad 26.7 32 0.00069 26.7 0.9 9 108-116 1-9 (372)
236 PF07800 DUF1644: Protein of u 26.7 91 0.002 21.0 2.9 11 178-188 123-133 (162)
237 PF10263 SprT-like: SprT-like 26.5 16 0.00035 24.1 -0.6 31 135-173 123-153 (157)
238 PRK00420 hypothetical protein; 26.4 60 0.0013 20.4 1.9 28 36-74 24-51 (112)
239 PRK11823 DNA repair protein Ra 26.1 37 0.00081 27.0 1.2 31 105-149 5-35 (446)
240 KOG4118|consensus 26.0 49 0.0011 18.4 1.3 25 164-188 39-63 (74)
241 COG1773 Rubredoxin [Energy pro 25.9 31 0.00067 18.6 0.5 14 107-120 3-16 (55)
242 KOG2636|consensus 25.1 57 0.0012 25.9 1.9 23 161-183 399-422 (497)
243 TIGR00416 sms DNA repair prote 25.0 32 0.0007 27.5 0.7 30 106-149 6-35 (454)
244 COG4338 Uncharacterized protei 24.8 21 0.00045 18.5 -0.3 13 165-177 14-26 (54)
245 KOG0978|consensus 24.8 42 0.00092 28.3 1.3 47 36-82 644-697 (698)
246 PF07295 DUF1451: Protein of u 24.6 24 0.00053 23.3 -0.0 35 28-72 101-139 (146)
247 PRK04351 hypothetical protein; 24.4 39 0.00085 22.4 0.9 31 36-74 113-143 (149)
248 TIGR01562 FdhE formate dehydro 23.9 72 0.0016 24.1 2.3 28 31-72 206-233 (305)
249 COG4391 Uncharacterized protei 23.8 44 0.00096 18.4 0.9 15 105-119 46-60 (62)
250 PF12773 DZR: Double zinc ribb 23.7 51 0.0011 16.8 1.1 10 109-118 14-23 (50)
251 PRK05978 hypothetical protein; 23.6 36 0.00079 22.6 0.6 10 109-118 54-63 (148)
252 COG2879 Uncharacterized small 23.3 68 0.0015 17.8 1.5 15 174-188 23-37 (65)
253 TIGR00143 hypF [NiFe] hydrogen 23.2 6.1 0.00013 33.4 -3.7 58 108-172 91-149 (711)
254 PF03145 Sina: Seven in absent 23.1 1.4E+02 0.0031 20.6 3.5 56 2-61 10-73 (198)
255 PF05741 zf-nanos: Nanos RNA b 23.0 29 0.00063 18.7 0.1 10 163-172 33-42 (55)
256 PF12230 PRP21_like_P: Pre-mRN 22.9 28 0.00061 24.8 0.0 24 162-186 167-190 (229)
257 smart00731 SprT SprT homologue 22.7 38 0.00083 22.2 0.6 32 135-173 112-143 (146)
258 PF14255 Cys_rich_CPXG: Cystei 22.6 45 0.00098 17.7 0.8 10 109-118 2-11 (52)
259 PF09845 DUF2072: Zn-ribbon co 22.5 50 0.0011 21.4 1.1 15 63-77 1-15 (131)
260 KOG1940|consensus 22.3 84 0.0018 23.3 2.3 19 36-55 197-215 (276)
261 PF08209 Sgf11: Sgf11 (transcr 21.8 1.1E+02 0.0024 14.5 2.6 20 36-56 5-24 (33)
262 smart00109 C1 Protein kinase C 21.8 68 0.0015 15.8 1.4 7 109-115 13-19 (49)
263 PRK14892 putative transcriptio 21.8 25 0.00055 21.5 -0.3 9 106-114 20-28 (99)
264 PF05180 zf-DNL: DNL zinc fing 21.6 66 0.0014 18.1 1.3 36 5-44 3-38 (66)
265 COG5112 UFD2 U1-like Zn-finger 21.6 36 0.00078 21.0 0.3 25 132-156 52-76 (126)
266 PF01286 XPA_N: XPA protein N- 21.5 41 0.00088 16.1 0.4 14 164-177 4-17 (34)
267 KOG3214|consensus 21.1 39 0.00084 20.6 0.3 16 107-122 47-62 (109)
268 KOG4377|consensus 20.6 1.2E+02 0.0026 23.9 2.9 70 10-85 277-367 (480)
269 PF07535 zf-DBF: DBF zinc fing 20.3 88 0.0019 16.4 1.5 20 34-56 4-23 (49)
270 COG4640 Predicted membrane pro 20.3 87 0.0019 24.5 2.1 20 134-153 14-33 (465)
271 PF11781 RRN7: RNA polymerase 20.2 81 0.0017 15.2 1.3 6 9-14 11-16 (36)
272 PF11023 DUF2614: Protein of u 20.1 48 0.0011 20.8 0.6 8 108-115 70-77 (114)
273 KOG3507|consensus 20.0 38 0.00082 18.4 0.1 10 134-143 36-45 (62)
274 PRK12722 transcriptional activ 20.0 1E+02 0.0022 21.4 2.2 48 15-71 115-162 (187)
No 1
>KOG2462|consensus
Probab=99.97 E-value=1.4e-30 Score=179.49 Aligned_cols=136 Identities=31% Similarity=0.626 Sum_probs=125.6
Q ss_pred CCCcccCCCCCccccchhhHHHHHhhcCC---CCCcccccCcccCCChhHHHhhhhhhcCCCchhhhhhhhhccCCCCCc
Q psy9067 32 EERPHKCSVCERGFKTIASLQNHINTHTG---VKPHKCKYCESRFTTSGELVRHVRYKHTHEKPELVRHVRYKHTHEKPH 108 (189)
Q Consensus 32 ~~~~~~C~~C~~~f~~~~~l~~H~~~~~~---~~~~~C~~C~~~f~~~~~l~~h~~~~h~~~~~~~~~~~~~~~~~~~~~ 108 (189)
....|.|+.||+.+...++|..|...|.. .+.+.|..|++.|.+...|..|+++| .-+.
T Consensus 127 ~~~r~~c~eCgk~ysT~snLsrHkQ~H~~~~s~ka~~C~~C~K~YvSmpALkMHirTH------------------~l~c 188 (279)
T KOG2462|consen 127 KHPRYKCPECGKSYSTSSNLSRHKQTHRSLDSKKAFSCKYCGKVYVSMPALKMHIRTH------------------TLPC 188 (279)
T ss_pred cCCceeccccccccccccccchhhcccccccccccccCCCCCceeeehHHHhhHhhcc------------------CCCc
Confidence 34568999999999999999999998854 45699999999999999999999862 2468
Q ss_pred cCCCCCccccchHHHHhchhhcCCCCCccCccCCccCCChHHHHHHHHHhhCCCcccCccchhccCCchHHHHHHhh
Q psy9067 109 KCSICDYASVELSKMRNHMRSHTGERPYQCAHCTYASPDTFKLKRHLRIHTGEKPYACDICHARFTQSNSLKSHRLI 185 (189)
Q Consensus 109 ~C~~C~~~~~~~~~l~~H~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~ 185 (189)
.|.+|||.|...+.|+-|+++|+|||||.|+.|+++|.-++.|+.|+++|++.+.|+|..|++.|+..+.|.+|...
T Consensus 189 ~C~iCGKaFSRPWLLQGHiRTHTGEKPF~C~hC~kAFADRSNLRAHmQTHS~~K~~qC~~C~KsFsl~SyLnKH~ES 265 (279)
T KOG2462|consen 189 ECGICGKAFSRPWLLQGHIRTHTGEKPFSCPHCGKAFADRSNLRAHMQTHSDVKKHQCPRCGKSFALKSYLNKHSES 265 (279)
T ss_pred ccccccccccchHHhhcccccccCCCCccCCcccchhcchHHHHHHHHhhcCCccccCcchhhHHHHHHHHHHhhhh
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999753
No 2
>KOG2462|consensus
Probab=99.95 E-value=2.9e-28 Score=168.13 Aligned_cols=135 Identities=30% Similarity=0.539 Sum_probs=127.0
Q ss_pred EEeeeCCCcceeeechhHHHHHHhhCCC---CCcccCCCCCccccchhhHHHHHhhcCCCCCcccccCcccCCChhHHHh
Q psy9067 5 IYYWSDTTGYLRYHVMYLLARHLKSHSE---ERPHKCSVCERGFKTIASLQNHINTHTGVKPHKCKYCESRFTTSGELVR 81 (189)
Q Consensus 5 ~~~~c~~c~~~~f~~~~~l~~h~~~~~~---~~~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~C~~C~~~f~~~~~l~~ 81 (189)
..|.|+.|+ ..|.+...|.+|.++|.. ++.+.|+.|++.|-+...|.+|.++|. -+++|.+||+.|...+.|+.
T Consensus 129 ~r~~c~eCg-k~ysT~snLsrHkQ~H~~~~s~ka~~C~~C~K~YvSmpALkMHirTH~--l~c~C~iCGKaFSRPWLLQG 205 (279)
T KOG2462|consen 129 PRYKCPECG-KSYSTSSNLSRHKQTHRSLDSKKAFSCKYCGKVYVSMPALKMHIRTHT--LPCECGICGKAFSRPWLLQG 205 (279)
T ss_pred Cceeccccc-cccccccccchhhcccccccccccccCCCCCceeeehHHHhhHhhccC--CCcccccccccccchHHhhc
Confidence 458999999 799999999999999985 567899999999999999999999986 78999999999999999999
Q ss_pred hhhhhcCCCchhhhhhhhhccCCCCCccCCCCCccccchHHHHhchhhcCCCCCccCccCCccCCChHHHHHHHHHh
Q psy9067 82 HVRYKHTHEKPELVRHVRYKHTHEKPHKCSICDYASVELSKMRNHMRSHTGERPYQCAHCTYASPDTFKLKRHLRIH 158 (189)
Q Consensus 82 h~~~~h~~~~~~~~~~~~~~~~~~~~~~C~~C~~~~~~~~~l~~H~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~h 158 (189)
|+++ +.+++||.|+.|+++|.++++|+.|+++|.+.|+|.|..|++.|..++.|..|....
T Consensus 206 HiRT----------------HTGEKPF~C~hC~kAFADRSNLRAHmQTHS~~K~~qC~~C~KsFsl~SyLnKH~ES~ 266 (279)
T KOG2462|consen 206 HIRT----------------HTGEKPFSCPHCGKAFADRSNLRAHMQTHSDVKKHQCPRCGKSFALKSYLNKHSESA 266 (279)
T ss_pred cccc----------------ccCCCCccCCcccchhcchHHHHHHHHhhcCCccccCcchhhHHHHHHHHHHhhhhc
Confidence 9994 899999999999999999999999999999999999999999999999999998753
No 3
>KOG3623|consensus
Probab=99.88 E-value=2.6e-23 Score=159.73 Aligned_cols=81 Identities=38% Similarity=0.727 Sum_probs=77.0
Q ss_pred CCCCccCCCCCccccchHHHHhchhhcCCCCCccCccCCccCCChHHHHHHHHHhhCCCcccCccchhccCCchHHHHHH
Q psy9067 104 HEKPHKCSICDYASVELSKMRNHMRSHTGERPYQCAHCTYASPDTFKLKRHLRIHTGEKPYACDICHARFTQSNSLKSHR 183 (189)
Q Consensus 104 ~~~~~~C~~C~~~~~~~~~l~~H~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~ 183 (189)
.+..|.|+.|+|+|.-.++|.+|.-.|.|.+||+|.+|.++|..+-.|..|.+.|+||+||+|..|++.|+.+-....||
T Consensus 891 e~gmyaCDqCDK~FqKqSSLaRHKYEHsGqRPyqC~iCkKAFKHKHHLtEHkRLHSGEKPfQCdKClKRFSHSGSYSQHM 970 (1007)
T KOG3623|consen 891 EDGMYACDQCDKAFQKQSSLARHKYEHSGQRPYQCIICKKAFKHKHHLTEHKRLHSGEKPFQCDKCLKRFSHSGSYSQHM 970 (1007)
T ss_pred ccccchHHHHHHHHHhhHHHHHhhhhhcCCCCcccchhhHhhhhhhhhhhhhhhccCCCcchhhhhhhhcccccchHhhh
Confidence 34459999999999999999999999999999999999999999999999999999999999999999999999999998
Q ss_pred h
Q psy9067 184 L 184 (189)
Q Consensus 184 ~ 184 (189)
.
T Consensus 971 N 971 (1007)
T KOG3623|consen 971 N 971 (1007)
T ss_pred c
Confidence 4
No 4
>KOG1074|consensus
Probab=99.86 E-value=3.5e-23 Score=161.10 Aligned_cols=82 Identities=35% Similarity=0.691 Sum_probs=71.3
Q ss_pred CccCCCCCccccchHHHHhchhhcCCCCCccCccCCccCCChHHHHHHHHHhhC----CCcccCc---cchhccCCchHH
Q psy9067 107 PHKCSICDYASVELSKMRNHMRSHTGERPYQCAHCTYASPDTFKLKRHLRIHTG----EKPYACD---ICHARFTQSNSL 179 (189)
Q Consensus 107 ~~~C~~C~~~~~~~~~l~~H~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~----~~~~~C~---~C~~~f~~~~~l 179 (189)
+-+|-+|.+...-.+.|+.|.++|.|++||+|.|||++|.++..|+.|+.+|.. +.++.|+ +|-+.|...-.|
T Consensus 605 PNqCiiC~rVlSC~saLqmHyrtHtGERPFkCKiCgRAFtTkGNLkaH~~vHka~p~~R~q~ScP~~~ic~~kftn~V~l 684 (958)
T KOG1074|consen 605 PNQCIICLRVLSCPSALQMHYRTHTGERPFKCKICGRAFTTKGNLKAHMSVHKAKPPARVQFSCPSTFICQKKFTNAVTL 684 (958)
T ss_pred ccceeeeeecccchhhhhhhhhcccCcCccccccccchhccccchhhcccccccCccccccccCCchhhhcccccccccc
Confidence 357889999999999999999999999999999999999999999999988754 3568899 999999998889
Q ss_pred HHHHhhhCC
Q psy9067 180 KSHRLIHTP 188 (189)
Q Consensus 180 ~~H~~~h~~ 188 (189)
..|+++|.|
T Consensus 685 pQhIriH~~ 693 (958)
T KOG1074|consen 685 PQHIRIHLG 693 (958)
T ss_pred cceEEeecC
Confidence 899888863
No 5
>KOG1074|consensus
Probab=99.86 E-value=1.5e-22 Score=157.61 Aligned_cols=177 Identities=24% Similarity=0.437 Sum_probs=134.7
Q ss_pred eeCCCcceeeechhHHHHHHhhCCCCCcccCCCCCccccchhhHHHHHhhcCCC----CCcccc---cCcccCCChhHHH
Q psy9067 8 WSDTTGYLRYHVMYLLARHLKSHSEERPHKCSVCERGFKTIASLQNHINTHTGV----KPHKCK---YCESRFTTSGELV 80 (189)
Q Consensus 8 ~c~~c~~~~f~~~~~l~~h~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~~~~~----~~~~C~---~C~~~f~~~~~l~ 80 (189)
.|=+|- .+.....+|.+|.++|++++||+|.+||+-|..+.+|..||..|... .+|.|+ +|.+.|...-.|.
T Consensus 607 qCiiC~-rVlSC~saLqmHyrtHtGERPFkCKiCgRAFtTkGNLkaH~~vHka~p~~R~q~ScP~~~ic~~kftn~V~lp 685 (958)
T KOG1074|consen 607 QCIICL-RVLSCPSALQMHYRTHTGERPFKCKICGRAFTTKGNLKAHMSVHKAKPPARVQFSCPSTFICQKKFTNAVTLP 685 (958)
T ss_pred ceeeee-ecccchhhhhhhhhcccCcCccccccccchhccccchhhcccccccCccccccccCCchhhhccccccccccc
Confidence 355666 68899999999999999999999999999999999999999887543 458999 9999999999999
Q ss_pred hhhhhhcCCCchhhhhhhhhccCCCCCccCCCCCccccchHHHHhchhhcCCC---------------------------
Q psy9067 81 RHVRYKHTHEKPELVRHVRYKHTHEKPHKCSICDYASVELSKMRNHMRSHTGE--------------------------- 133 (189)
Q Consensus 81 ~h~~~~h~~~~~~~~~~~~~~~~~~~~~~C~~C~~~~~~~~~l~~H~~~~~~~--------------------------- 133 (189)
.|++.|-....+.-.... ....-.-+|..|.+.|.+...|..++..+.+.
T Consensus 686 QhIriH~~~~~s~g~~a~---e~~~~adq~~~~qk~~~~a~~f~~~~se~~~~~s~~~~~~~~~t~t~~~~~tp~~~e~~ 762 (958)
T KOG1074|consen 686 QHIRIHLGGQISNGGTAA---EGILAADQCSSCQKTFSDARSFSQQISEQPSPESEPDEQMDERTETEELDVTPPPPENS 762 (958)
T ss_pred ceEEeecCCCCCCCcccc---cccchhcccchhhhcccccccchhhhhccCCcccCCcccccccccccccccCCCccccc
Confidence 999986655543110000 00000123444444444443333333222100
Q ss_pred --------------------------------------------------------------------------------
Q psy9067 134 -------------------------------------------------------------------------------- 133 (189)
Q Consensus 134 -------------------------------------------------------------------------------- 133 (189)
T Consensus 763 ~~~~~~~e~~i~~~g~te~asa~~~~vg~~s~~~~~~~~~~T~~k~~~~~~~~~~~~~~~v~~~pvl~~~~~~~l~eg~~ 842 (958)
T KOG1074|consen 763 CGRELEGEMAISVRGSTEEASANLDEVGTVSAAGEAGEEDDTSEKPTQASSFPGEILAPSVNMDPVLWNQETSMLNEGLA 842 (958)
T ss_pred cccccCcccccccccchhhhhcChhhhcCccccchhhhhcccCCCCcccccCCCcCCccccccCchhhcccccccccccc
Confidence
Q ss_pred -----------------------------------CCccCccCCccCCChHHHHHHHHHhhCCCcccCccchhccCCchH
Q psy9067 134 -----------------------------------RPYQCAHCTYASPDTFKLKRHLRIHTGEKPYACDICHARFTQSNS 178 (189)
Q Consensus 134 -----------------------------------~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~ 178 (189)
....|.+||+.|.+...|..|+++|++++||.|.+|++.|.++.+
T Consensus 843 t~~n~~t~~~~~~sv~qs~~~p~l~p~l~~~~pvnn~h~C~vCgk~FsSSsALqiH~rTHtg~KPF~C~fC~~aFttrgn 922 (958)
T KOG1074|consen 843 TKTNEITPEGPADSVIQSGGVPTLEPSLGRPGPVNNAHVCNVCGKQFSSSAALEIHMRTHTGPKPFFCHFCEEAFTTRGN 922 (958)
T ss_pred cccccccCCCcchhhhhhccccccCCCCCCCCcccchhhhccchhcccchHHHHHhhhcCCCCCCccchhhhhhhhhhhh
Confidence 227899999999999999999999999999999999999999999
Q ss_pred HHHHHhhhCC
Q psy9067 179 LKSHRLIHTP 188 (189)
Q Consensus 179 l~~H~~~h~~ 188 (189)
|+.||.+|..
T Consensus 923 LKvHMgtH~w 932 (958)
T KOG1074|consen 923 LKVHMGTHMW 932 (958)
T ss_pred hhhhhccccc
Confidence 9999999853
No 6
>KOG3608|consensus
Probab=99.86 E-value=1.3e-21 Score=139.37 Aligned_cols=174 Identities=31% Similarity=0.602 Sum_probs=142.4
Q ss_pred eeeechhHHHHHHhhCCCCCcccCCCCCccccchhhHHHHHhhcC--CCCCcccccCcccCCChhHHHhhhhhhcCC---
Q psy9067 15 LRYHVMYLLARHLKSHSEERPHKCSVCERGFKTIASLQNHINTHT--GVKPHKCKYCESRFTTSGELVRHVRYKHTH--- 89 (189)
Q Consensus 15 ~~f~~~~~l~~h~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~~~--~~~~~~C~~C~~~f~~~~~l~~h~~~~h~~--- 89 (189)
..|.+...|++|+++|+++|..-|+.||..|+.+..|..|.+..+ ...+|.|..|.+.|..+..|..|+..|-..
T Consensus 187 ~~~~~k~~LreH~r~Hs~eKvvACp~Cg~~F~~~tkl~DH~rRqt~l~~n~fqC~~C~KrFaTeklL~~Hv~rHvn~ykC 266 (467)
T KOG3608|consen 187 KHMGNKYRLREHIRTHSNEKVVACPHCGELFRTKTKLFDHLRRQTELNTNSFQCAQCFKRFATEKLLKSHVVRHVNCYKC 266 (467)
T ss_pred hhhccHHHHHHHHHhcCCCeEEecchHHHHhccccHHHHHHHhhhhhcCCchHHHHHHHHHhHHHHHHHHHHHhhhcccc
Confidence 468899999999999999999999999999999999999988754 345788888888888888888888763321
Q ss_pred --------CchhhhhhhhhccCCCCCccCCCCCccccchHHHHhchhhcCCCCCccCcc--CCccCCChHHHHHHHHHhh
Q psy9067 90 --------EKPELVRHVRYKHTHEKPHKCSICDYASVELSKMRNHMRSHTGERPYQCAH--CTYASPDTFKLKRHLRIHT 159 (189)
Q Consensus 90 --------~~~~~~~~~~~~~~~~~~~~C~~C~~~~~~~~~l~~H~~~~~~~~~~~C~~--C~~~f~~~~~l~~H~~~h~ 159 (189)
..+++..+.+..++.++++.|+.|++.+...+.|.+|...|. +-.|.|.. |..+|++...++.|.+-++
T Consensus 267 plCdmtc~~~ssL~~H~r~rHs~dkpfKCd~Cd~~c~~esdL~kH~~~HS-~~~y~C~h~~C~~s~r~~~q~~~H~~evh 345 (467)
T KOG3608|consen 267 PLCDMTCSSASSLTTHIRYRHSKDKPFKCDECDTRCVRESDLAKHVQVHS-KTVYQCEHPDCHYSVRTYTQMRRHFLEVH 345 (467)
T ss_pred cccccCCCChHHHHHHHHhhhccCCCccccchhhhhccHHHHHHHHHhcc-ccceecCCCCCcHHHHHHHHHHHHHHHhc
Confidence 123556666667888889999999999999999999988775 66788876 8888888888888876543
Q ss_pred -C--CCcccCccchhccCCchHHHHHHhhhCCC
Q psy9067 160 -G--EKPYACDICHARFTQSNSLKSHRLIHTPL 189 (189)
Q Consensus 160 -~--~~~~~C~~C~~~f~~~~~l~~H~~~h~~~ 189 (189)
+ +-+|+|..|.+.|++-.+|.+|++..|++
T Consensus 346 Eg~np~~Y~CH~Cdr~ft~G~~L~~HL~kkH~f 378 (467)
T KOG3608|consen 346 EGNNPILYACHCCDRFFTSGKSLSAHLMKKHGF 378 (467)
T ss_pred cCCCCCceeeecchhhhccchhHHHHHHHhhcc
Confidence 4 44699999999999999999998766654
No 7
>KOG3608|consensus
Probab=99.81 E-value=2.8e-20 Score=132.58 Aligned_cols=157 Identities=25% Similarity=0.538 Sum_probs=113.3
Q ss_pred ceeeechhHHHHHHhhCCC------------CCc-ccCCC--CCccccchhhHHHHHhhcCCCCCcccccCcccCCChhH
Q psy9067 14 YLRYHVMYLLARHLKSHSE------------ERP-HKCSV--CERGFKTIASLQNHINTHTGVKPHKCKYCESRFTTSGE 78 (189)
Q Consensus 14 ~~~f~~~~~l~~h~~~~~~------------~~~-~~C~~--C~~~f~~~~~l~~H~~~~~~~~~~~C~~C~~~f~~~~~ 78 (189)
+..|.+..-+..|...|.- ++| +.|.| |.+.+.++..|.+|.+.|.+++...|+.|+.-|..+..
T Consensus 143 e~~F~s~~ef~dHV~~H~l~ceyd~~~~~~D~~pv~~C~W~~Ct~~~~~k~~LreH~r~Hs~eKvvACp~Cg~~F~~~tk 222 (467)
T KOG3608|consen 143 EREFVSIVEFQDHVVKHALFCEYDIQKTPEDERPVTMCNWAMCTKHMGNKYRLREHIRTHSNEKVVACPHCGELFRTKTK 222 (467)
T ss_pred CCcccCHHHHHHHHHHhhhhhhhhhhhCCCCCCceeeccchhhhhhhccHHHHHHHHHhcCCCeEEecchHHHHhccccH
Confidence 3688888888888776652 112 45654 99999999999999999999999999999999999999
Q ss_pred HHhhhhhhcCCCchhhhhhhhhccCCCCCccCCCCCccccchHHHHhchhhcCCCCCccCccCCccCCChHHHHHHHHH-
Q psy9067 79 LVRHVRYKHTHEKPELVRHVRYKHTHEKPHKCSICDYASVELSKMRNHMRSHTGERPYQCAHCTYASPDTFKLKRHLRI- 157 (189)
Q Consensus 79 l~~h~~~~h~~~~~~~~~~~~~~~~~~~~~~C~~C~~~~~~~~~l~~H~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~- 157 (189)
|-.|.+.. ......+|+|..|.|.|.....|..|+..|. .-|.|+.|+......++|..|++.
T Consensus 223 l~DH~rRq--------------t~l~~n~fqC~~C~KrFaTeklL~~Hv~rHv--n~ykCplCdmtc~~~ssL~~H~r~r 286 (467)
T KOG3608|consen 223 LFDHLRRQ--------------TELNTNSFQCAQCFKRFATEKLLKSHVVRHV--NCYKCPLCDMTCSSASSLTTHIRYR 286 (467)
T ss_pred HHHHHHhh--------------hhhcCCchHHHHHHHHHhHHHHHHHHHHHhh--hcccccccccCCCChHHHHHHHHhh
Confidence 99998742 2233446666666666666666666666552 346666666666666666666663
Q ss_pred hhCCCcccCccchhccCCchHHHHHHhhh
Q psy9067 158 HTGEKPYACDICHARFTQSNSLKSHRLIH 186 (189)
Q Consensus 158 h~~~~~~~C~~C~~~f~~~~~l~~H~~~h 186 (189)
|+..+||+|..|++.|.+.++|.+|..+|
T Consensus 287 Hs~dkpfKCd~Cd~~c~~esdL~kH~~~H 315 (467)
T KOG3608|consen 287 HSKDKPFKCDECDTRCVRESDLAKHVQVH 315 (467)
T ss_pred hccCCCccccchhhhhccHHHHHHHHHhc
Confidence 55566666666666666666666666655
No 8
>KOG3576|consensus
Probab=99.75 E-value=2.9e-19 Score=118.36 Aligned_cols=113 Identities=29% Similarity=0.607 Sum_probs=101.4
Q ss_pred CCCcccccCcccCCChhHHHhhhhhhcCCCchhhhhhhhhccCCCCCccCCCCCccccchHHHHhchhhcCCCCCccCcc
Q psy9067 61 VKPHKCKYCESRFTTSGELVRHVRYKHTHEKPELVRHVRYKHTHEKPHKCSICDYASVELSKMRNHMRSHTGERPYQCAH 140 (189)
Q Consensus 61 ~~~~~C~~C~~~f~~~~~l~~h~~~~h~~~~~~~~~~~~~~~~~~~~~~C~~C~~~~~~~~~l~~H~~~~~~~~~~~C~~ 140 (189)
...|.|.+|++.|....-|.+|++ -+...+.+-|..||+.|.+.-+|.+|.++|.|.+||.|..
T Consensus 115 ~d~ftCrvCgK~F~lQRmlnrh~k----------------ch~~vkr~lct~cgkgfndtfdlkrh~rthtgvrpykc~~ 178 (267)
T KOG3576|consen 115 QDSFTCRVCGKKFGLQRMLNRHLK----------------CHSDVKRHLCTFCGKGFNDTFDLKRHTRTHTGVRPYKCSL 178 (267)
T ss_pred CCeeeeehhhhhhhHHHHHHHHhh----------------hccHHHHHHHhhccCcccchhhhhhhhccccCccccchhh
Confidence 344999999999999999999998 3666778999999999999999999999999999999999
Q ss_pred CCccCCChHHHHHHHHHhhC-----------CCcccCccchhccCCchHHHHHHhhhCCC
Q psy9067 141 CTYASPDTFKLKRHLRIHTG-----------EKPYACDICHARFTQSNSLKSHRLIHTPL 189 (189)
Q Consensus 141 C~~~f~~~~~l~~H~~~h~~-----------~~~~~C~~C~~~f~~~~~l~~H~~~h~~~ 189 (189)
|+++|.+.-.|..|++.-++ .+.|.|..||..-.....+..|+..|||.
T Consensus 179 c~kaftqrcsleshl~kvhgv~~~yaykerr~kl~vcedcg~t~~~~e~~~~h~~~~hp~ 238 (267)
T KOG3576|consen 179 CEKAFTQRCSLESHLKKVHGVQHQYAYKERRAKLYVCEDCGYTSERPEVYYLHLKLHHPF 238 (267)
T ss_pred hhHHHHhhccHHHHHHHHcCchHHHHHHHhhhheeeecccCCCCCChhHHHHHHHhcCCC
Confidence 99999999999999874433 45699999999999999999999999884
No 9
>KOG3576|consensus
Probab=99.69 E-value=9e-18 Score=111.36 Aligned_cols=125 Identities=30% Similarity=0.532 Sum_probs=103.5
Q ss_pred eEEeeeCCCcceeeechhHHHHHHhhCCCCCcccCCCCCccccchhhHHHHHhhcCCCCCcccccCcccCCChhHHHhhh
Q psy9067 4 TIYYWSDTTGYLRYHVMYLLARHLKSHSEERPHKCSVCERGFKTIASLQNHINTHTGVKPHKCKYCESRFTTSGELVRHV 83 (189)
Q Consensus 4 ~~~~~c~~c~~~~f~~~~~l~~h~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~C~~C~~~f~~~~~l~~h~ 83 (189)
...+.|.+|+ ..|.-..+|.+|++-|..-+.+.|..||+.|.+...|.+|+++|++.+||+|..|++.|..+.+|..|.
T Consensus 115 ~d~ftCrvCg-K~F~lQRmlnrh~kch~~vkr~lct~cgkgfndtfdlkrh~rthtgvrpykc~~c~kaftqrcsleshl 193 (267)
T KOG3576|consen 115 QDSFTCRVCG-KKFGLQRMLNRHLKCHSDVKRHLCTFCGKGFNDTFDLKRHTRTHTGVRPYKCSLCEKAFTQRCSLESHL 193 (267)
T ss_pred CCeeeeehhh-hhhhHHHHHHHHhhhccHHHHHHHhhccCcccchhhhhhhhccccCccccchhhhhHHHHhhccHHHHH
Confidence 3568899999 799999999999999999899999999999999999999999999999999999999999999999999
Q ss_pred hhhcCCCchhhhhhhhhccCCCCCccCCCCCccccchHHHHhchhhcCCCC
Q psy9067 84 RYKHTHEKPELVRHVRYKHTHEKPHKCSICDYASVELSKMRNHMRSHTGER 134 (189)
Q Consensus 84 ~~~h~~~~~~~~~~~~~~~~~~~~~~C~~C~~~~~~~~~l~~H~~~~~~~~ 134 (189)
+..|+....-. . -....+-|+|+.||..-.....++.|+..++...
T Consensus 194 ~kvhgv~~~ya---y--kerr~kl~vcedcg~t~~~~e~~~~h~~~~hp~S 239 (267)
T KOG3576|consen 194 KKVHGVQHQYA---Y--KERRAKLYVCEDCGYTSERPEVYYLHLKLHHPFS 239 (267)
T ss_pred HHHcCchHHHH---H--HHhhhheeeecccCCCCCChhHHHHHHHhcCCCC
Confidence 87666542211 1 1234566888888888887888888877765443
No 10
>KOG3623|consensus
Probab=99.58 E-value=5.2e-16 Score=120.17 Aligned_cols=108 Identities=34% Similarity=0.734 Sum_probs=95.1
Q ss_pred cccccCcccCCChhHHHhhhhhhcCCCchhhhhhhhhccCCCCCccCCCCCccccchHHHHhchhhcCC-----------
Q psy9067 64 HKCKYCESRFTTSGELVRHVRYKHTHEKPELVRHVRYKHTHEKPHKCSICDYASVELSKMRNHMRSHTG----------- 132 (189)
Q Consensus 64 ~~C~~C~~~f~~~~~l~~h~~~~h~~~~~~~~~~~~~~~~~~~~~~C~~C~~~~~~~~~l~~H~~~~~~----------- 132 (189)
..|+.|++++.....|+.|++..|. ..+..|.|..|...|.++.-|.+|+..|..
T Consensus 211 ltcpycdrgykrltslkeHikyrhe--------------kne~nfsC~lCsytFAyRtQLErhm~~hkpg~dqa~sltqs 276 (1007)
T KOG3623|consen 211 LTCPYCDRGYKRLTSLKEHIKYRHE--------------KNEPNFSCMLCSYTFAYRTQLERHMQLHKPGGDQAISLTQS 276 (1007)
T ss_pred hcchhHHHHHHHHHHHHHHHHHHHh--------------hCCCCCcchhhhhhhhhHHHHHHHHHhhcCCCcccccccch
Confidence 6899999999999999999986322 334568899999999999999999988742
Q ss_pred --CCCccCccCCccCCChHHHHHHHHHhhCCCcccCccchhccCCchHHHHHHhh
Q psy9067 133 --ERPYQCAHCTYASPDTFKLKRHLRIHTGEKPYACDICHARFTQSNSLKSHRLI 185 (189)
Q Consensus 133 --~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~ 185 (189)
.+-|.|.+||++|..+-.|+.|+++|+||+||.|+.|++.|+.+-.+..||-.
T Consensus 277 a~lRKFKCtECgKAFKfKHHLKEHlRIHSGEKPfeCpnCkKRFSHSGSySSHmSS 331 (1007)
T KOG3623|consen 277 ALLRKFKCTECGKAFKFKHHLKEHLRIHSGEKPFECPNCKKRFSHSGSYSSHMSS 331 (1007)
T ss_pred hhhccccccccchhhhhHHHHHhhheeecCCCCcCCcccccccccCCcccccccc
Confidence 35699999999999999999999999999999999999999998888888743
No 11
>PLN03086 PRLI-interacting factor K; Provisional
Probab=99.39 E-value=3.9e-12 Score=98.58 Aligned_cols=146 Identities=19% Similarity=0.356 Sum_probs=109.9
Q ss_pred EeeeCCCcceeeechhHHHHHHhhCCCCCcccCCC--CCccccchhhHHHHHhhcCCCCCcccccCcccCCChhHHHhhh
Q psy9067 6 YYWSDTTGYLRYHVMYLLARHLKSHSEERPHKCSV--CERGFKTIASLQNHINTHTGVKPHKCKYCESRFTTSGELVRHV 83 (189)
Q Consensus 6 ~~~c~~c~~~~f~~~~~l~~h~~~~~~~~~~~C~~--C~~~f~~~~~l~~H~~~~~~~~~~~C~~C~~~f~~~~~l~~h~ 83 (189)
...|..|. .......|..|... .......|+. |+..|.. ..+ ++.+.|+.|++.|. ...|..|+
T Consensus 407 ~V~C~NC~--~~i~l~~l~lHe~~-C~r~~V~Cp~~~Cg~v~~r-~el---------~~H~~C~~Cgk~f~-~s~LekH~ 472 (567)
T PLN03086 407 TVECRNCK--HYIPSRSIALHEAY-CSRHNVVCPHDGCGIVLRV-EEA---------KNHVHCEKCGQAFQ-QGEMEKHM 472 (567)
T ss_pred eEECCCCC--CccchhHHHHHHhh-CCCcceeCCcccccceeec-ccc---------ccCccCCCCCCccc-hHHHHHHH
Confidence 45688766 34446667777643 4444556874 8888732 222 33358999999996 67799998
Q ss_pred hhhcCCCchhhhhhhhhccCCCCCccCCCCCccccchHHHHhchhhcCCCCCccCccCCccCCC----------hHHHHH
Q psy9067 84 RYKHTHEKPELVRHVRYKHTHEKPHKCSICDYASVELSKMRNHMRSHTGERPYQCAHCTYASPD----------TFKLKR 153 (189)
Q Consensus 84 ~~~h~~~~~~~~~~~~~~~~~~~~~~C~~C~~~~~~~~~l~~H~~~~~~~~~~~C~~C~~~f~~----------~~~l~~ 153 (189)
.. . ..++.|+ ||+.+ ....|..|+..+.+.+++.|+.|+..+.. ...|..
T Consensus 473 ~~----------------~--Hkpv~Cp-Cg~~~-~R~~L~~H~~thCp~Kpi~C~fC~~~v~~g~~~~d~~d~~s~Lt~ 532 (567)
T PLN03086 473 KV----------------F--HEPLQCP-CGVVL-EKEQMVQHQASTCPLRLITCRFCGDMVQAGGSAMDVRDRLRGMSE 532 (567)
T ss_pred Hh----------------c--CCCccCC-CCCCc-chhHHHhhhhccCCCCceeCCCCCCccccCccccchhhhhhhHHH
Confidence 85 2 1578999 99755 67899999999999999999999999852 357889
Q ss_pred HHHHhhCCCcccCccchhccCCchHHHHHHhhhC
Q psy9067 154 HLRIHTGEKPYACDICHARFTQSNSLKSHRLIHT 187 (189)
Q Consensus 154 H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~h~ 187 (189)
|..+ .+.+++.|..||+.+..+- |..|+..-|
T Consensus 533 HE~~-CG~rt~~C~~Cgk~Vrlrd-m~~H~~~~h 564 (567)
T PLN03086 533 HESI-CGSRTAPCDSCGRSVMLKE-MDIHQIAVH 564 (567)
T ss_pred HHHh-cCCcceEccccCCeeeehh-HHHHHHHhh
Confidence 9888 4899999999999988775 888876544
No 12
>KOG3993|consensus
Probab=99.38 E-value=5.9e-14 Score=102.75 Aligned_cols=153 Identities=18% Similarity=0.276 Sum_probs=110.7
Q ss_pred cccCCCCCccccchhhHHHHHhhcCCCCCcccccCcccCCChhHHHhhhhhhcCCCchhh---hhh----------hhhc
Q psy9067 35 PHKCSVCERGFKTIASLQNHINTHTGVKPHKCKYCESRFTTSGELVRHVRYKHTHEKPEL---VRH----------VRYK 101 (189)
Q Consensus 35 ~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~C~~C~~~f~~~~~l~~h~~~~h~~~~~~~---~~~----------~~~~ 101 (189)
.|.|..|...|.+...|.+|.-.-+....|+|+.|+++|+...+|.+|.++ |....... ... .+..
T Consensus 267 dyiCqLCK~kYeD~F~LAQHrC~RIV~vEYrCPEC~KVFsCPANLASHRRW-HKPR~eaa~a~~~P~k~~~~~rae~~ea 345 (500)
T KOG3993|consen 267 DYICQLCKEKYEDAFALAQHRCPRIVHVEYRCPECDKVFSCPANLASHRRW-HKPRPEAAKAGSPPPKQAVETRAEVQEA 345 (500)
T ss_pred HHHHHHHHHhhhhHHHHhhccCCeeEEeeecCCcccccccCchhhhhhhcc-cCCchhhhhcCCCChhhhhhhhhhhhhc
Confidence 489999999999999999999888888889999999999999999999998 43332211 000 0001
Q ss_pred -----cCCCCCccCCCCCccccchHHHHhchhhcCCC-------------------------------------------
Q psy9067 102 -----HTHEKPHKCSICDYASVELSKMRNHMRSHTGE------------------------------------------- 133 (189)
Q Consensus 102 -----~~~~~~~~C~~C~~~~~~~~~l~~H~~~~~~~------------------------------------------- 133 (189)
.+.+..|.|..|++.|.....|+.|+.+|...
T Consensus 346 ~rsg~dss~gi~~C~~C~KkFrRqAYLrKHqlthq~~~~~k~~a~~f~~s~~~~l~~~~~~~a~h~~a~~~~g~~vl~~a 425 (500)
T KOG3993|consen 346 ERSGDDSSSGIFSCHTCGKKFRRQAYLRKHQLTHQRAPLAKEKAPKFLLSRVIPLMHFNQAVATHSSASDSHGDEVLYVA 425 (500)
T ss_pred cccCCcccCceeecHHhhhhhHHHHHHHHhHHhhhccccchhcccCcchhhcccccccccccccccccccccccceeeee
Confidence 13445799999999999999999997765321
Q ss_pred ---CCccCccCCccCCChHHHHHHHHHhhCCCcccCccchhccCCchHHHHHHhhhCC
Q psy9067 134 ---RPYQCAHCTYASPDTFKLKRHLRIHTGEKPYACDICHARFTQSNSLKSHRLIHTP 188 (189)
Q Consensus 134 ---~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~ 188 (189)
.--.++.++-.+.++..--.+.+....++.|.|.+|...|.++.+|.+|+..-||
T Consensus 426 ~sael~~pp~~~~ppsss~~sgg~~rlg~~~q~f~~ky~~atfyss~~ltrhin~~Hp 483 (500)
T KOG3993|consen 426 GSAELELPPYDGSPPSSSGSSGGYGRLGIAEQGFTCKYCPATFYSSPGLTRHINKCHP 483 (500)
T ss_pred ccccccCCCCCCCCcccCCCCCccccccchhhccccccchHhhhcCcchHhHhhhcCh
Confidence 0023444454444443333333333445679999999999999999999876664
No 13
>PHA00733 hypothetical protein
Probab=99.37 E-value=7.3e-13 Score=84.54 Aligned_cols=86 Identities=17% Similarity=0.357 Sum_probs=71.9
Q ss_pred cCCCCCccCCCCCccccchHHHHhc--h---hhcCCCCCccCccCCccCCChHHHHHHHHHhhCCCcccCccchhccCCc
Q psy9067 102 HTHEKPHKCSICDYASVELSKMRNH--M---RSHTGERPYQCAHCTYASPDTFKLKRHLRIHTGEKPYACDICHARFTQS 176 (189)
Q Consensus 102 ~~~~~~~~C~~C~~~~~~~~~l~~H--~---~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~ 176 (189)
.+..+++.|.+|++.|.....|..+ + ....+.+||.|+.|++.|.+...|..|++++ ..+|.|+.|++.|...
T Consensus 35 ~~~~~~~~~~~~~~~~~~~~~l~~~~~l~~~~~~~~~kPy~C~~Cgk~Fss~s~L~~H~r~h--~~~~~C~~CgK~F~~~ 112 (128)
T PHA00733 35 TPEQKRLIRAVVKTLIYNPQLLDESSYLYKLLTSKAVSPYVCPLCLMPFSSSVSLKQHIRYT--EHSKVCPVCGKEFRNT 112 (128)
T ss_pred ChhhhhHHHHHHhhhccChhhhcchHHHHhhcccCCCCCccCCCCCCcCCCHHHHHHHHhcC--CcCccCCCCCCccCCH
Confidence 4567789999999888776665554 1 2234578999999999999999999999976 4579999999999999
Q ss_pred hHHHHHHhhhCCC
Q psy9067 177 NSLKSHRLIHTPL 189 (189)
Q Consensus 177 ~~l~~H~~~h~~~ 189 (189)
..|..|+...|+|
T Consensus 113 ~sL~~H~~~~h~~ 125 (128)
T PHA00733 113 DSTLDHVCKKHNI 125 (128)
T ss_pred HHHHHHHHHhcCc
Confidence 9999999988875
No 14
>PHA00733 hypothetical protein
Probab=99.17 E-value=4e-11 Score=76.56 Aligned_cols=64 Identities=23% Similarity=0.285 Sum_probs=31.6
Q ss_pred hHHHHHHhhCCCCCcccCCCCCccccchhhHHHH--Hh---hcCCCCCcccccCcccCCChhHHHhhhh
Q psy9067 21 YLLARHLKSHSEERPHKCSVCERGFKTIASLQNH--IN---THTGVKPHKCKYCESRFTTSGELVRHVR 84 (189)
Q Consensus 21 ~~l~~h~~~~~~~~~~~C~~C~~~f~~~~~l~~H--~~---~~~~~~~~~C~~C~~~f~~~~~l~~h~~ 84 (189)
..|..+....+.++++.|.+|...|.....|..+ +. ...+..+|.|+.|++.|.....|..|++
T Consensus 26 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~l~~~~~~~~~kPy~C~~Cgk~Fss~s~L~~H~r 94 (128)
T PHA00733 26 EELKRYHSLTPEQKRLIRAVVKTLIYNPQLLDESSYLYKLLTSKAVSPYVCPLCLMPFSSSVSLKQHIR 94 (128)
T ss_pred HHhhhhhcCChhhhhHHHHHHhhhccChhhhcchHHHHhhcccCCCCCccCCCCCCcCCCHHHHHHHHh
Confidence 3344444444455666777776666655554444 11 1122344455555555554444444443
No 15
>PLN03086 PRLI-interacting factor K; Provisional
Probab=99.13 E-value=2.7e-10 Score=88.62 Aligned_cols=100 Identities=19% Similarity=0.425 Sum_probs=82.3
Q ss_pred cccCCCCCccccchhhHHHHHhhcCCCCCcccccCcccCCChhHHHhhhhhhcCCCchhhhhhhhhccCCCCCccCCCCC
Q psy9067 35 PHKCSVCERGFKTIASLQNHINTHTGVKPHKCKYCESRFTTSGELVRHVRYKHTHEKPELVRHVRYKHTHEKPHKCSICD 114 (189)
Q Consensus 35 ~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~C~~C~~~f~~~~~l~~h~~~~h~~~~~~~~~~~~~~~~~~~~~~C~~C~ 114 (189)
.+.|+.|++.|. ...|..|+..++ .++.|+ |+..+ .+..|..|+.. +...+++.|++|+
T Consensus 453 H~~C~~Cgk~f~-~s~LekH~~~~H--kpv~Cp-Cg~~~-~R~~L~~H~~t----------------hCp~Kpi~C~fC~ 511 (567)
T PLN03086 453 HVHCEKCGQAFQ-QGEMEKHMKVFH--EPLQCP-CGVVL-EKEQMVQHQAS----------------TCPLRLITCRFCG 511 (567)
T ss_pred CccCCCCCCccc-hHHHHHHHHhcC--CCccCC-CCCCc-chhHHHhhhhc----------------cCCCCceeCCCCC
Confidence 358999999996 678999999975 889999 99755 67889999873 6778899999999
Q ss_pred ccccc----------hHHHHhchhhcCCCCCccCccCCccCCChHHHHHHHHH
Q psy9067 115 YASVE----------LSKMRNHMRSHTGERPYQCAHCTYASPDTFKLKRHLRI 157 (189)
Q Consensus 115 ~~~~~----------~~~l~~H~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~ 157 (189)
..+.. ...|..|.... +.+++.|..|++.+..+ .+..|+..
T Consensus 512 ~~v~~g~~~~d~~d~~s~Lt~HE~~C-G~rt~~C~~Cgk~Vrlr-dm~~H~~~ 562 (567)
T PLN03086 512 DMVQAGGSAMDVRDRLRGMSEHESIC-GSRTAPCDSCGRSVMLK-EMDIHQIA 562 (567)
T ss_pred CccccCccccchhhhhhhHHHHHHhc-CCcceEccccCCeeeeh-hHHHHHHH
Confidence 99852 35788998886 88999999999999887 55666543
No 16
>PHA02768 hypothetical protein; Provisional
Probab=99.11 E-value=4.1e-11 Score=63.54 Aligned_cols=42 Identities=19% Similarity=0.333 Sum_probs=29.2
Q ss_pred ccCccCCccCCChHHHHHHHHHhhCCCcccCccchhccCCchHH
Q psy9067 136 YQCAHCTYASPDTFKLKRHLRIHTGEKPYACDICHARFTQSNSL 179 (189)
Q Consensus 136 ~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l 179 (189)
|.|+.||+.|...+.|..|+++|+ ++++|..|++.|...+.|
T Consensus 6 y~C~~CGK~Fs~~~~L~~H~r~H~--k~~kc~~C~k~f~~~s~l 47 (55)
T PHA02768 6 YECPICGEIYIKRKSMITHLRKHN--TNLKLSNCKRISLRTGEY 47 (55)
T ss_pred cCcchhCCeeccHHHHHHHHHhcC--CcccCCcccceeccccee
Confidence 567777777777777777777766 567777777777665554
No 17
>PHA02768 hypothetical protein; Provisional
Probab=98.93 E-value=4.3e-10 Score=59.68 Aligned_cols=44 Identities=23% Similarity=0.384 Sum_probs=39.9
Q ss_pred CccCCCCCccccchHHHHhchhhcCCCCCccCccCCccCCChHHHH
Q psy9067 107 PHKCSICDYASVELSKMRNHMRSHTGERPYQCAHCTYASPDTFKLK 152 (189)
Q Consensus 107 ~~~C~~C~~~~~~~~~l~~H~~~~~~~~~~~C~~C~~~f~~~~~l~ 152 (189)
.|.|+.||+.|...+.|..|+++|. +++.|..|++.|...+.|.
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 4899999999999999999999997 7999999999999876653
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=98.82 E-value=2.3e-09 Score=48.73 Aligned_cols=26 Identities=54% Similarity=1.163 Sum_probs=20.7
Q ss_pred HHHHHHHHhhCCCcccCccchhccCC
Q psy9067 150 KLKRHLRIHTGEKPYACDICHARFTQ 175 (189)
Q Consensus 150 ~l~~H~~~h~~~~~~~C~~C~~~f~~ 175 (189)
.|..|+++|++++||.|+.|+++|.+
T Consensus 1 ~l~~H~~~H~~~k~~~C~~C~k~F~~ 26 (26)
T PF13465_consen 1 NLRRHMRTHTGEKPYKCPYCGKSFSN 26 (26)
T ss_dssp HHHHHHHHHSSSSSEEESSSSEEESS
T ss_pred CHHHHhhhcCCCCCCCCCCCcCeeCc
Confidence 36778888888888888888888763
No 19
>KOG3993|consensus
Probab=98.67 E-value=3e-09 Score=78.55 Aligned_cols=151 Identities=17% Similarity=0.233 Sum_probs=108.3
Q ss_pred EeeeCCCcceeeechhHHHHHHhhCCCCCcccCCCCCccccchhhHHHHHhhcC--------------------------
Q psy9067 6 YYWSDTTGYLRYHVMYLLARHLKSHSEERPHKCSVCERGFKTIASLQNHINTHT-------------------------- 59 (189)
Q Consensus 6 ~~~c~~c~~~~f~~~~~l~~h~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~~~-------------------------- 59 (189)
.|-|..|- ..|.+-..|++|.-.-.--..|.|+.|++.|....+|..|.+=|-
T Consensus 267 dyiCqLCK-~kYeD~F~LAQHrC~RIV~vEYrCPEC~KVFsCPANLASHRRWHKPR~eaa~a~~~P~k~~~~~rae~~ea 345 (500)
T KOG3993|consen 267 DYICQLCK-EKYEDAFALAQHRCPRIVHVEYRCPECDKVFSCPANLASHRRWHKPRPEAAKAGSPPPKQAVETRAEVQEA 345 (500)
T ss_pred HHHHHHHH-HhhhhHHHHhhccCCeeEEeeecCCcccccccCchhhhhhhcccCCchhhhhcCCCChhhhhhhhhhhhhc
Confidence 37788898 599999999999776665667999999999999999999976442
Q ss_pred -------CCCCcccccCcccCCChhHHHhhhhhhcCCCchhh--------------------hhhhhh--ccC-------
Q psy9067 60 -------GVKPHKCKYCESRFTTSGELVRHVRYKHTHEKPEL--------------------VRHVRY--KHT------- 103 (189)
Q Consensus 60 -------~~~~~~C~~C~~~f~~~~~l~~h~~~~h~~~~~~~--------------------~~~~~~--~~~------- 103 (189)
.+..|.|..|++.|....-|+.|+..|+....... ..+... .+.
T Consensus 346 ~rsg~dss~gi~~C~~C~KkFrRqAYLrKHqlthq~~~~~k~~a~~f~~s~~~~l~~~~~~~a~h~~a~~~~g~~vl~~a 425 (500)
T KOG3993|consen 346 ERSGDDSSSGIFSCHTCGKKFRRQAYLRKHQLTHQRAPLAKEKAPKFLLSRVIPLMHFNQAVATHSSASDSHGDEVLYVA 425 (500)
T ss_pred cccCCcccCceeecHHhhhhhHHHHHHHHhHHhhhccccchhcccCcchhhcccccccccccccccccccccccceeeee
Confidence 01238999999999999999999887765543310 000000 000
Q ss_pred -CCCCccCCCCCccccchHHHHhchhhcCCCCCccCccCCccCCChHHHHHHHHH
Q psy9067 104 -HEKPHKCSICDYASVELSKMRNHMRSHTGERPYQCAHCTYASPDTFKLKRHLRI 157 (189)
Q Consensus 104 -~~~~~~C~~C~~~~~~~~~l~~H~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~ 157 (189)
...--.++.+|..+.+...--.+.+....+..|.|.+|--.|.+...|.+|+..
T Consensus 426 ~sael~~pp~~~~ppsss~~sgg~~rlg~~~q~f~~ky~~atfyss~~ltrhin~ 480 (500)
T KOG3993|consen 426 GSAELELPPYDGSPPSSSGSSGGYGRLGIAEQGFTCKYCPATFYSSPGLTRHINK 480 (500)
T ss_pred ccccccCCCCCCCCcccCCCCCccccccchhhccccccchHhhhcCcchHhHhhh
Confidence 011124667776666665555555555666789999999999999999999764
No 20
>PHA00616 hypothetical protein
Probab=98.58 E-value=2.7e-08 Score=50.32 Aligned_cols=34 Identities=18% Similarity=0.248 Sum_probs=22.1
Q ss_pred CccCccCCccCCChHHHHHHHHHhhCCCcccCcc
Q psy9067 135 PYQCAHCTYASPDTFKLKRHLRIHTGEKPYACDI 168 (189)
Q Consensus 135 ~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~ 168 (189)
||+|+.||+.|...+.|..|++.|++++++.|+.
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~~hg~~~~~~~~ 34 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLSVHKQNKLTLEY 34 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHHhcCCCccceeE
Confidence 4666666666666666666666666666666543
No 21
>PHA00732 hypothetical protein
Probab=98.57 E-value=5.4e-08 Score=56.59 Aligned_cols=46 Identities=30% Similarity=0.659 Sum_probs=27.2
Q ss_pred CccCCCCCccccchHHHHhchhh-cCCCCCccCccCCccCCChHHHHHHHHHh
Q psy9067 107 PHKCSICDYASVELSKMRNHMRS-HTGERPYQCAHCTYASPDTFKLKRHLRIH 158 (189)
Q Consensus 107 ~~~C~~C~~~~~~~~~l~~H~~~-~~~~~~~~C~~C~~~f~~~~~l~~H~~~h 158 (189)
+|.|+.||+.|.....|..|++. |. ++.|++|++.|.+ +..|.++.
T Consensus 1 py~C~~Cgk~F~s~s~Lk~H~r~~H~---~~~C~~CgKsF~~---l~~H~~~~ 47 (79)
T PHA00732 1 MFKCPICGFTTVTLFALKQHARRNHT---LTKCPVCNKSYRR---LNQHFYSQ 47 (79)
T ss_pred CccCCCCCCccCCHHHHHHHhhcccC---CCccCCCCCEeCC---hhhhhccc
Confidence 35666777777777777766653 32 2466666666663 44455443
No 22
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=98.56 E-value=3e-08 Score=45.00 Aligned_cols=24 Identities=42% Similarity=1.032 Sum_probs=14.8
Q ss_pred HHHHHhhCCCCCcccCCCCCcccc
Q psy9067 23 LARHLKSHSEERPHKCSVCERGFK 46 (189)
Q Consensus 23 l~~h~~~~~~~~~~~C~~C~~~f~ 46 (189)
|..|+++|.+++||.|+.|++.|.
T Consensus 2 l~~H~~~H~~~k~~~C~~C~k~F~ 25 (26)
T PF13465_consen 2 LRRHMRTHTGEKPYKCPYCGKSFS 25 (26)
T ss_dssp HHHHHHHHSSSSSEEESSSSEEES
T ss_pred HHHHhhhcCCCCCCCCCCCcCeeC
Confidence 556666666666666666666553
No 23
>PHA00616 hypothetical protein
Probab=98.45 E-value=1e-07 Score=48.23 Aligned_cols=34 Identities=15% Similarity=0.257 Sum_probs=30.5
Q ss_pred cccCCCCCccccchhhHHHHHhhcCCCCCccccc
Q psy9067 35 PHKCSVCERGFKTIASLQNHINTHTGVKPHKCKY 68 (189)
Q Consensus 35 ~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~C~~ 68 (189)
||+|+.||+.|..++.|..|++.+++++++.|..
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~~hg~~~~~~~~ 34 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLSVHKQNKLTLEY 34 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHHhcCCCccceeE
Confidence 5889999999999999999999999999988764
No 24
>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=98.42 E-value=7.5e-07 Score=48.14 Aligned_cols=51 Identities=25% Similarity=0.442 Sum_probs=33.1
Q ss_pred CccCccCCccCCChHHHHHHHHH-hhC-CCcccCccchhccCCchHHHHHHhhhCC
Q psy9067 135 PYQCAHCTYASPDTFKLKRHLRI-HTG-EKPYACDICHARFTQSNSLKSHRLIHTP 188 (189)
Q Consensus 135 ~~~C~~C~~~f~~~~~l~~H~~~-h~~-~~~~~C~~C~~~f~~~~~l~~H~~~h~~ 188 (189)
.|.||.|++ ......|..|... |.. .+.+.|++|...+. .+|..|+..+|+
T Consensus 2 ~f~CP~C~~-~~~~~~L~~H~~~~H~~~~~~v~CPiC~~~~~--~~l~~Hl~~~H~ 54 (54)
T PF05605_consen 2 SFTCPYCGK-GFSESSLVEHCEDEHRSESKNVVCPICSSRVT--DNLIRHLNSQHR 54 (54)
T ss_pred CcCCCCCCC-ccCHHHHHHHHHhHCcCCCCCccCCCchhhhh--hHHHHHHHHhcC
Confidence 367777777 4455677777554 333 24577888877544 378888877764
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=98.35 E-value=1.9e-07 Score=41.11 Aligned_cols=23 Identities=39% Similarity=0.797 Sum_probs=18.4
Q ss_pred ccCccchhccCCchHHHHHHhhh
Q psy9067 164 YACDICHARFTQSNSLKSHRLIH 186 (189)
Q Consensus 164 ~~C~~C~~~f~~~~~l~~H~~~h 186 (189)
|.|+.|++.|++.++|..|++.|
T Consensus 1 y~C~~C~~~f~~~~~l~~H~~~H 23 (23)
T PF00096_consen 1 YKCPICGKSFSSKSNLKRHMRRH 23 (23)
T ss_dssp EEETTTTEEESSHHHHHHHHHHH
T ss_pred CCCCCCCCccCCHHHHHHHHhHC
Confidence 57888888888888888888764
No 26
>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=98.29 E-value=3.1e-07 Score=42.14 Aligned_cols=27 Identities=33% Similarity=0.812 Sum_probs=22.8
Q ss_pred cccCccchhccCCchHHHHHHhhhCCC
Q psy9067 163 PYACDICHARFTQSNSLKSHRLIHTPL 189 (189)
Q Consensus 163 ~~~C~~C~~~f~~~~~l~~H~~~h~~~ 189 (189)
+|.|..|++.|.+...|..|++.|+++
T Consensus 1 ~~~C~~C~~~F~~~~~l~~H~~~h~~~ 27 (27)
T PF13912_consen 1 PFECDECGKTFSSLSALREHKRSHCSL 27 (27)
T ss_dssp SEEETTTTEEESSHHHHHHHHCTTTT-
T ss_pred CCCCCccCCccCChhHHHHHhHHhcCC
Confidence 578999999999999999999888764
No 27
>PHA00732 hypothetical protein
Probab=98.22 E-value=1.2e-06 Score=51.03 Aligned_cols=46 Identities=28% Similarity=0.670 Sum_probs=39.5
Q ss_pred CccCccCCccCCChHHHHHHHHH-hhCCCcccCccchhccCCchHHHHHHhhh
Q psy9067 135 PYQCAHCTYASPDTFKLKRHLRI-HTGEKPYACDICHARFTQSNSLKSHRLIH 186 (189)
Q Consensus 135 ~~~C~~C~~~f~~~~~l~~H~~~-h~~~~~~~C~~C~~~f~~~~~l~~H~~~h 186 (189)
||.|.+|++.|.+...|..|++. |. ++.|+.||+.|. .|..|.+++
T Consensus 1 py~C~~Cgk~F~s~s~Lk~H~r~~H~---~~~C~~CgKsF~---~l~~H~~~~ 47 (79)
T PHA00732 1 MFKCPICGFTTVTLFALKQHARRNHT---LTKCPVCNKSYR---RLNQHFYSQ 47 (79)
T ss_pred CccCCCCCCccCCHHHHHHHhhcccC---CCccCCCCCEeC---Chhhhhccc
Confidence 68999999999999999999985 54 468999999998 478887665
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=98.22 E-value=8e-07 Score=39.41 Aligned_cols=24 Identities=29% Similarity=0.715 Sum_probs=18.1
Q ss_pred ccCccchhccCCchHHHHHHhhhC
Q psy9067 164 YACDICHARFTQSNSLKSHRLIHT 187 (189)
Q Consensus 164 ~~C~~C~~~f~~~~~l~~H~~~h~ 187 (189)
|.|++|++.|.+...|..|+++||
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 578888888888888888888775
No 29
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=98.10 E-value=6.1e-06 Score=44.55 Aligned_cols=49 Identities=31% Similarity=0.556 Sum_probs=31.4
Q ss_pred ccCCCCCccccchhhHHHHHhhcCCC--CCcccccCcccCCChhHHHhhhhhhc
Q psy9067 36 HKCSVCERGFKTIASLQNHINTHTGV--KPHKCKYCESRFTTSGELVRHVRYKH 87 (189)
Q Consensus 36 ~~C~~C~~~f~~~~~l~~H~~~~~~~--~~~~C~~C~~~f~~~~~l~~h~~~~h 87 (189)
|.||.|++ ..+...|..|....+.. +.+.|++|...+. .+|..|+..+|
T Consensus 3 f~CP~C~~-~~~~~~L~~H~~~~H~~~~~~v~CPiC~~~~~--~~l~~Hl~~~H 53 (54)
T PF05605_consen 3 FTCPYCGK-GFSESSLVEHCEDEHRSESKNVVCPICSSRVT--DNLIRHLNSQH 53 (54)
T ss_pred cCCCCCCC-ccCHHHHHHHHHhHCcCCCCCccCCCchhhhh--hHHHHHHHHhc
Confidence 67777877 44556777776664432 3577888876543 37777776543
No 30
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=98.03 E-value=3.1e-06 Score=51.93 Aligned_cols=73 Identities=21% Similarity=0.362 Sum_probs=20.9
Q ss_pred cCCCCCccccchHHHHhchhhcCCCCCccCccCCccCCChHHHHHHHHHhhCCCcccCccchhccCCchHHHHHHhhh
Q psy9067 109 KCSICDYASVELSKMRNHMRSHTGERPYQCAHCTYASPDTFKLKRHLRIHTGEKPYACDICHARFTQSNSLKSHRLIH 186 (189)
Q Consensus 109 ~C~~C~~~~~~~~~l~~H~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~h 186 (189)
+|..|+..|.+...|..|+...++...- ....+.....+..+.+.- -...+.|.+|++.|.+...|..||+.+
T Consensus 1 ~C~~C~~~f~~~~~l~~H~~~~H~~~~~----~~~~l~~~~~~~~~~~~~-~~~~~~C~~C~~~f~s~~~l~~Hm~~~ 73 (100)
T PF12756_consen 1 QCLFCDESFSSVDDLLQHMKKKHGFDIP----DQKYLVDPNRLLNYLRKK-VKESFRCPYCNKTFRSREALQEHMRSK 73 (100)
T ss_dssp -----------------------------------------------------SSEEBSSSS-EESSHHHHHHHHHHT
T ss_pred Cccccccccccccccccccccccccccc----cccccccccccccccccc-cCCCCCCCccCCCCcCHHHHHHHHcCc
Confidence 5889999999999999998766554221 111111223333333221 123689999999999999999999865
No 31
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=97.89 E-value=7.2e-06 Score=35.93 Aligned_cols=22 Identities=36% Similarity=0.720 Sum_probs=13.0
Q ss_pred ccCccCCccCCChHHHHHHHHH
Q psy9067 136 YQCAHCTYASPDTFKLKRHLRI 157 (189)
Q Consensus 136 ~~C~~C~~~f~~~~~l~~H~~~ 157 (189)
|.|++|++.|.....|..|++.
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 3556666666666666666554
No 32
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=97.77 E-value=1.1e-05 Score=35.72 Aligned_cols=24 Identities=33% Similarity=0.635 Sum_probs=19.1
Q ss_pred ccCccchhccCCchHHHHHHhhhCC
Q psy9067 164 YACDICHARFTQSNSLKSHRLIHTP 188 (189)
Q Consensus 164 ~~C~~C~~~f~~~~~l~~H~~~h~~ 188 (189)
|+|+.|+...+ .++|..|++.+||
T Consensus 1 y~C~~C~y~t~-~~~l~~H~~~~H~ 24 (24)
T PF13909_consen 1 YKCPHCSYSTS-KSNLKRHLKRHHP 24 (24)
T ss_dssp EE-SSSS-EES-HHHHHHHHHHHHS
T ss_pred CCCCCCCCcCC-HHHHHHHHHhhCc
Confidence 68999998888 8899999998876
No 33
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=97.74 E-value=9.2e-06 Score=58.48 Aligned_cols=52 Identities=35% Similarity=0.748 Sum_probs=43.6
Q ss_pred CCCccCcc--CCccCCChHHHHHHHHHhh-------------------CCCcccCccchhccCCchHHHHHHh
Q psy9067 133 ERPYQCAH--CTYASPDTFKLKRHLRIHT-------------------GEKPYACDICHARFTQSNSLKSHRL 184 (189)
Q Consensus 133 ~~~~~C~~--C~~~f~~~~~l~~H~~~h~-------------------~~~~~~C~~C~~~f~~~~~l~~H~~ 184 (189)
++||.|++ |.+.+.....|+-|+.-.+ ..+||+|++|++.+.+..+|+-|+.
T Consensus 347 ~KpykCpV~gC~K~YknqnGLKYH~lhGH~~~~~~~~p~p~~~~~F~~~~KPYrCevC~KRYKNlNGLKYHr~ 419 (423)
T COG5189 347 GKPYKCPVEGCNKKYKNQNGLKYHMLHGHQNQKLHENPSPEKMNIFSAKDKPYRCEVCDKRYKNLNGLKYHRK 419 (423)
T ss_pred CceecCCCCCchhhhccccchhhhhhccccCcccCCCCCccccccccccCCceeccccchhhccCccceeccc
Confidence 48999986 8899999999999875322 2479999999999999999999954
No 34
>smart00355 ZnF_C2H2 zinc finger.
Probab=97.63 E-value=4.6e-05 Score=34.12 Aligned_cols=24 Identities=33% Similarity=0.607 Sum_probs=16.9
Q ss_pred ccCccchhccCCchHHHHHHhhhC
Q psy9067 164 YACDICHARFTQSNSLKSHRLIHT 187 (189)
Q Consensus 164 ~~C~~C~~~f~~~~~l~~H~~~h~ 187 (189)
|.|+.|++.|...+.|..|++.|.
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~~H~ 24 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMRTHX 24 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHHHhc
Confidence 467777777777777777776553
No 35
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=97.59 E-value=5.4e-05 Score=33.26 Aligned_cols=21 Identities=29% Similarity=0.923 Sum_probs=10.0
Q ss_pred cCCCCCccccchhhHHHHHhh
Q psy9067 37 KCSVCERGFKTIASLQNHINT 57 (189)
Q Consensus 37 ~C~~C~~~f~~~~~l~~H~~~ 57 (189)
.|+.|+..|.+...|..|+..
T Consensus 2 ~C~~C~~~~~~~~~l~~H~~~ 22 (24)
T PF13894_consen 2 QCPICGKSFRSKSELRQHMRT 22 (24)
T ss_dssp E-SSTS-EESSHHHHHHHHHH
T ss_pred CCcCCCCcCCcHHHHHHHHHh
Confidence 455555555555555555544
No 36
>PF09237 GAGA: GAGA factor; InterPro: IPR015318 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Members of this entry bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognises the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognises the A in the fourth position of the consensus sequence []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1YUI_A 1YUJ_A.
Probab=97.59 E-value=5.3e-05 Score=39.24 Aligned_cols=29 Identities=38% Similarity=0.595 Sum_probs=14.7
Q ss_pred CCCcccCccchhccCCchHHHHHHhhhCC
Q psy9067 160 GEKPYACDICHARFTQSNSLKSHRLIHTP 188 (189)
Q Consensus 160 ~~~~~~C~~C~~~f~~~~~l~~H~~~h~~ 188 (189)
.+.|-.|++|+..+....+|.+|+.+.|+
T Consensus 21 S~~PatCP~C~a~~~~srnLrRHle~~H~ 49 (54)
T PF09237_consen 21 SEQPATCPICGAVIRQSRNLRRHLEIRHF 49 (54)
T ss_dssp TS--EE-TTT--EESSHHHHHHHHHHHTT
T ss_pred cCCCCCCCcchhhccchhhHHHHHHHHhc
Confidence 34556666666666666666666665554
No 37
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=97.54 E-value=4.6e-05 Score=46.63 Aligned_cols=22 Identities=27% Similarity=0.628 Sum_probs=11.2
Q ss_pred ccCCCCCccccchHHHHhchhh
Q psy9067 108 HKCSICDYASVELSKMRNHMRS 129 (189)
Q Consensus 108 ~~C~~C~~~~~~~~~l~~H~~~ 129 (189)
+.|..|++.|.+...|..|++.
T Consensus 51 ~~C~~C~~~f~s~~~l~~Hm~~ 72 (100)
T PF12756_consen 51 FRCPYCNKTFRSREALQEHMRS 72 (100)
T ss_dssp EEBSSSS-EESSHHHHHHHHHH
T ss_pred CCCCccCCCCcCHHHHHHHHcC
Confidence 4555555555555555555543
No 38
>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=97.48 E-value=7.4e-05 Score=34.02 Aligned_cols=23 Identities=26% Similarity=0.800 Sum_probs=12.0
Q ss_pred ccCCCCCccccchhhHHHHHhhc
Q psy9067 36 HKCSVCERGFKTIASLQNHINTH 58 (189)
Q Consensus 36 ~~C~~C~~~f~~~~~l~~H~~~~ 58 (189)
|.|..|++.|.+...|..|++.+
T Consensus 2 ~~C~~C~~~F~~~~~l~~H~~~h 24 (27)
T PF13912_consen 2 FECDECGKTFSSLSALREHKRSH 24 (27)
T ss_dssp EEETTTTEEESSHHHHHHHHCTT
T ss_pred CCCCccCCccCChhHHHHHhHHh
Confidence 45555555555555555555443
No 39
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=97.37 E-value=6.6e-05 Score=54.21 Aligned_cols=66 Identities=24% Similarity=0.533 Sum_probs=37.9
Q ss_pred CCCCccccc--CcccCCChhHHHhhhhhhcCCCchhhhhh-----hhhccCCCCCccCCCCCccccchHHHHhch
Q psy9067 60 GVKPHKCKY--CESRFTTSGELVRHVRYKHTHEKPELVRH-----VRYKHTHEKPHKCSICDYASVELSKMRNHM 127 (189)
Q Consensus 60 ~~~~~~C~~--C~~~f~~~~~l~~h~~~~h~~~~~~~~~~-----~~~~~~~~~~~~C~~C~~~~~~~~~l~~H~ 127 (189)
+++||+|++ |++.+....-|+-|+.. +.+.+.+... ...-....+||+|++|+|.|++...|.-|+
T Consensus 346 d~KpykCpV~gC~K~YknqnGLKYH~lh--GH~~~~~~~~p~p~~~~~F~~~~KPYrCevC~KRYKNlNGLKYHr 418 (423)
T COG5189 346 DGKPYKCPVEGCNKKYKNQNGLKYHMLH--GHQNQKLHENPSPEKMNIFSAKDKPYRCEVCDKRYKNLNGLKYHR 418 (423)
T ss_pred cCceecCCCCCchhhhccccchhhhhhc--cccCcccCCCCCccccccccccCCceeccccchhhccCccceecc
Confidence 358899986 89999998889999874 3332211100 000123345566666666655555555443
No 40
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=97.18 E-value=0.00017 Score=32.08 Aligned_cols=23 Identities=39% Similarity=0.831 Sum_probs=16.9
Q ss_pred ccCccchhccCCchHHHHHHhhh
Q psy9067 164 YACDICHARFTQSNSLKSHRLIH 186 (189)
Q Consensus 164 ~~C~~C~~~f~~~~~l~~H~~~h 186 (189)
|.|.+|++.|++...|..|++.+
T Consensus 1 ~~C~~C~~~f~s~~~~~~H~~s~ 23 (25)
T PF12874_consen 1 FYCDICNKSFSSENSLRQHLRSK 23 (25)
T ss_dssp EEETTTTEEESSHHHHHHHHTTH
T ss_pred CCCCCCCCCcCCHHHHHHHHCcC
Confidence 46777777777777777777654
No 41
>PF09237 GAGA: GAGA factor; InterPro: IPR015318 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Members of this entry bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognises the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognises the A in the fourth position of the consensus sequence []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1YUI_A 1YUJ_A.
Probab=96.98 E-value=0.00061 Score=35.40 Aligned_cols=31 Identities=32% Similarity=0.553 Sum_probs=14.7
Q ss_pred CCCCccCccCCccCCChHHHHHHHHHhhCCC
Q psy9067 132 GERPYQCAHCTYASPDTFKLKRHLRIHTGEK 162 (189)
Q Consensus 132 ~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~ 162 (189)
.+.|-.|++|+..+.+.-.|..|+++.++.+
T Consensus 21 S~~PatCP~C~a~~~~srnLrRHle~~H~~k 51 (54)
T PF09237_consen 21 SEQPATCPICGAVIRQSRNLRRHLEIRHFKK 51 (54)
T ss_dssp TS--EE-TTT--EESSHHHHHHHHHHHTTTS
T ss_pred cCCCCCCCcchhhccchhhHHHHHHHHhccc
Confidence 3455566666666666666666665555444
No 42
>smart00355 ZnF_C2H2 zinc finger.
Probab=96.97 E-value=0.00089 Score=29.67 Aligned_cols=24 Identities=33% Similarity=0.650 Sum_probs=18.3
Q ss_pred ccCccCCccCCChHHHHHHHHHhh
Q psy9067 136 YQCAHCTYASPDTFKLKRHLRIHT 159 (189)
Q Consensus 136 ~~C~~C~~~f~~~~~l~~H~~~h~ 159 (189)
|.|+.|++.|.....+..|++.|.
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~~H~ 24 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMRTHX 24 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHHHhc
Confidence 467888888888888888877653
No 43
>PRK04860 hypothetical protein; Provisional
Probab=96.85 E-value=0.0007 Score=45.05 Aligned_cols=39 Identities=31% Similarity=0.746 Sum_probs=31.8
Q ss_pred CCccCccCCccCCChHHHHHHHHHhhCCCcccCccchhccCCc
Q psy9067 134 RPYQCAHCTYASPDTFKLKRHLRIHTGEKPYACDICHARFTQS 176 (189)
Q Consensus 134 ~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~ 176 (189)
-+|.|. |+. ....+..|.+++.++++|.|..|+..|...
T Consensus 118 ~~Y~C~-C~~---~~~~~rrH~ri~~g~~~YrC~~C~~~l~~~ 156 (160)
T PRK04860 118 FPYRCK-CQE---HQLTVRRHNRVVRGEAVYRCRRCGETLVFK 156 (160)
T ss_pred EEEEcC-CCC---eeCHHHHHHHHhcCCccEECCCCCceeEEe
Confidence 368897 887 556778899999999999999999887653
No 44
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=96.66 E-value=0.001 Score=29.48 Aligned_cols=20 Identities=30% Similarity=0.860 Sum_probs=9.4
Q ss_pred cCCCCCccccchhhHHHHHh
Q psy9067 37 KCSVCERGFKTIASLQNHIN 56 (189)
Q Consensus 37 ~C~~C~~~f~~~~~l~~H~~ 56 (189)
.|.+|+..|.+...+..|++
T Consensus 2 ~C~~C~~~f~s~~~~~~H~~ 21 (25)
T PF12874_consen 2 YCDICNKSFSSENSLRQHLR 21 (25)
T ss_dssp EETTTTEEESSHHHHHHHHT
T ss_pred CCCCCCCCcCCHHHHHHHHC
Confidence 34444444444444444443
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=96.63 E-value=0.00041 Score=31.52 Aligned_cols=22 Identities=36% Similarity=0.738 Sum_probs=15.4
Q ss_pred ccCccchhccCCchHHHHHHhh
Q psy9067 164 YACDICHARFTQSNSLKSHRLI 185 (189)
Q Consensus 164 ~~C~~C~~~f~~~~~l~~H~~~ 185 (189)
|.|.+|++.|.+...|..|+++
T Consensus 2 ~~C~~C~k~f~~~~~~~~H~~s 23 (27)
T PF12171_consen 2 FYCDACDKYFSSENQLKQHMKS 23 (27)
T ss_dssp CBBTTTTBBBSSHHHHHCCTTS
T ss_pred CCcccCCCCcCCHHHHHHHHcc
Confidence 5677777777777777777654
No 46
>PRK04860 hypothetical protein; Provisional
Probab=96.09 E-value=0.0031 Score=42.00 Aligned_cols=38 Identities=18% Similarity=0.547 Sum_probs=32.9
Q ss_pred cccCCCCCccccchhhHHHHHhhcCCCCCcccccCcccCCCh
Q psy9067 35 PHKCSVCERGFKTIASLQNHINTHTGVKPHKCKYCESRFTTS 76 (189)
Q Consensus 35 ~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~C~~C~~~f~~~ 76 (189)
+|.|. |+. ....+..|.+.+.++++|.|..|+..|...
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 58998 987 668889999999999999999999987654
No 47
>KOG1146|consensus
Probab=96.09 E-value=0.0032 Score=54.02 Aligned_cols=85 Identities=27% Similarity=0.580 Sum_probs=67.2
Q ss_pred ccCCCCCccCCCCCccccchHHHHhchhhcC-------------------------CCCCccCccCCccCCChHHHHHHH
Q psy9067 101 KHTHEKPHKCSICDYASVELSKMRNHMRSHT-------------------------GERPYQCAHCTYASPDTFKLKRHL 155 (189)
Q Consensus 101 ~~~~~~~~~C~~C~~~~~~~~~l~~H~~~~~-------------------------~~~~~~C~~C~~~f~~~~~l~~H~ 155 (189)
.+...+.+.|+.|+..|++...|-.|++.-+ +.++|.|..|..++.....|.+|+
T Consensus 459 L~S~~kt~~cpkc~~~yk~a~~L~vhmRskhp~~~~~~c~~gq~~~~~arg~~~~~~~~p~~C~~C~~stttng~Lsihl 538 (1406)
T KOG1146|consen 459 LHSFFKTLKCPKCNWHYKLAQTLGVHMRSKHPESQSAYCKAGQNHPRLARGEVYRCPGKPYPCRACNYSTTTNGNLSIHL 538 (1406)
T ss_pred eecccccccCCccchhhhhHHHhhhcccccccccchhHhHhccccccccccccccCCCCcccceeeeeeeecchHHHHHH
Confidence 4566688999999999999999999988721 226799999999999999999998
Q ss_pred HH--hh----------C-------------------------------CCcccCccchhccCCchHHHHHHhh
Q psy9067 156 RI--HT----------G-------------------------------EKPYACDICHARFTQSNSLKSHRLI 185 (189)
Q Consensus 156 ~~--h~----------~-------------------------------~~~~~C~~C~~~f~~~~~l~~H~~~ 185 (189)
.. |- + +-++.|.+|++.-+-..+|..||..
T Consensus 539 qS~~h~~~lee~~~~~g~~v~~~~~~v~s~~P~~ag~~~~ags~~pktkP~~~C~vc~yetniarnlrihmts 611 (1406)
T KOG1146|consen 539 QSDLHRNELEEAEENAGEQVRLLPASVTSAVPEEAGLGPSAGSSGPKTKPSWRCEVCSYETNIARNLRIHMTA 611 (1406)
T ss_pred HHHhhHHHHHHHHhccccchhhhhhhhcccCcccccCCCCCCCCCCCCCCCcchhhhcchhhhhhcccccccc
Confidence 63 21 0 1147899999888888888888753
No 48
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=96.07 E-value=0.0039 Score=27.29 Aligned_cols=22 Identities=27% Similarity=0.609 Sum_probs=10.4
Q ss_pred ccCCCCCccccchhhHHHHHhhc
Q psy9067 36 HKCSVCERGFKTIASLQNHINTH 58 (189)
Q Consensus 36 ~~C~~C~~~f~~~~~l~~H~~~~ 58 (189)
|.|+.|+.... ...|..|+..+
T Consensus 1 y~C~~C~y~t~-~~~l~~H~~~~ 22 (24)
T PF13909_consen 1 YKCPHCSYSTS-KSNLKRHLKRH 22 (24)
T ss_dssp EE-SSSS-EES-HHHHHHHHHHH
T ss_pred CCCCCCCCcCC-HHHHHHHHHhh
Confidence 34555555554 55555555543
No 49
>KOG1146|consensus
Probab=96.01 E-value=0.0011 Score=56.65 Aligned_cols=145 Identities=19% Similarity=0.347 Sum_probs=88.1
Q ss_pred CCccccchhhHHHHHhh-cCCCCCcccccCcccCCChhHHHhhhhhhcCCCchhhh---------hhhhhccCCCCCccC
Q psy9067 41 CERGFKTIASLQNHINT-HTGVKPHKCKYCESRFTTSGELVRHVRYKHTHEKPELV---------RHVRYKHTHEKPHKC 110 (189)
Q Consensus 41 C~~~f~~~~~l~~H~~~-~~~~~~~~C~~C~~~f~~~~~l~~h~~~~h~~~~~~~~---------~~~~~~~~~~~~~~C 110 (189)
|+..+.....+..|+.. +...+.+.|+.|+..|.....|-.|++..|........ ..........++|.|
T Consensus 442 ~e~~~~s~r~~~~~t~~L~S~~kt~~cpkc~~~yk~a~~L~vhmRskhp~~~~~~c~~gq~~~~~arg~~~~~~~~p~~C 521 (1406)
T KOG1146|consen 442 AEPLLESKRSLEGQTVVLHSFFKTLKCPKCNWHYKLAQTLGVHMRSKHPESQSAYCKAGQNHPRLARGEVYRCPGKPYPC 521 (1406)
T ss_pred hhhhhhhhcccccceeeeecccccccCCccchhhhhHHHhhhcccccccccchhHhHhccccccccccccccCCCCcccc
Confidence 33333333333333332 23345677777777777777777777764433322111 111112345677999
Q ss_pred CCCCccccchHHHHhchhhcC------------C-------------------------------CCCccCccCCccCCC
Q psy9067 111 SICDYASVELSKMRNHMRSHT------------G-------------------------------ERPYQCAHCTYASPD 147 (189)
Q Consensus 111 ~~C~~~~~~~~~l~~H~~~~~------------~-------------------------------~~~~~C~~C~~~f~~ 147 (189)
..|...+....+|.+|++... + .-.+.|.+|+....-
T Consensus 522 ~~C~~stttng~LsihlqS~~h~~~lee~~~~~g~~v~~~~~~v~s~~P~~ag~~~~ags~~pktkP~~~C~vc~yetni 601 (1406)
T KOG1146|consen 522 RACNYSTTTNGNLSIHLQSDLHRNELEEAEENAGEQVRLLPASVTSAVPEEAGLGPSAGSSGPKTKPSWRCEVCSYETNI 601 (1406)
T ss_pred eeeeeeeecchHHHHHHHHHhhHHHHHHHHhccccchhhhhhhhcccCcccccCCCCCCCCCCCCCCCcchhhhcchhhh
Confidence 999999999999999976421 0 023899999999888
Q ss_pred hHHHHHHHHHhhCCC-cccCccchhccCCchHHHHHHhh
Q psy9067 148 TFKLKRHLRIHTGEK-PYACDICHARFTQSNSLKSHRLI 185 (189)
Q Consensus 148 ~~~l~~H~~~h~~~~-~~~C~~C~~~f~~~~~l~~H~~~ 185 (189)
.-.|..|+..-.... |-.+-.++..+.....+..+.+.
T Consensus 602 arnlrihmtss~~s~~p~~~Lq~~it~~l~~~~~~~~~l 640 (1406)
T KOG1146|consen 602 ARNLRIHMTASPSSSPPSLVLQQNITSSLASLLGGQGRL 640 (1406)
T ss_pred hhccccccccCCCCCChHHHhhhcchhhccccccCcCCC
Confidence 888888987533333 35666666666555555544443
No 50
>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=95.92 E-value=0.0077 Score=27.21 Aligned_cols=22 Identities=27% Similarity=0.581 Sum_probs=15.6
Q ss_pred ccCCCCCccccchHHHHhchhh
Q psy9067 108 HKCSICDYASVELSKMRNHMRS 129 (189)
Q Consensus 108 ~~C~~C~~~~~~~~~l~~H~~~ 129 (189)
|.|..|++.|.+...+..|+.+
T Consensus 2 ~~C~~C~k~f~~~~~~~~H~~s 23 (27)
T PF12171_consen 2 FYCDACDKYFSSENQLKQHMKS 23 (27)
T ss_dssp CBBTTTTBBBSSHHHHHCCTTS
T ss_pred CCcccCCCCcCCHHHHHHHHcc
Confidence 5677777777777777777654
No 51
>KOG2785|consensus
Probab=95.72 E-value=0.026 Score=42.29 Aligned_cols=52 Identities=19% Similarity=0.374 Sum_probs=42.9
Q ss_pred CCccCccCCccCCChHHHHHHHHHhhCC-----------------------CcccCccch---hccCCchHHHHHHhh
Q psy9067 134 RPYQCAHCTYASPDTFKLKRHLRIHTGE-----------------------KPYACDICH---ARFTQSNSLKSHRLI 185 (189)
Q Consensus 134 ~~~~C~~C~~~f~~~~~l~~H~~~h~~~-----------------------~~~~C~~C~---~~f~~~~~l~~H~~~ 185 (189)
.|-.|-.|+..+.+...-..|+..+++- .-+.|-.|+ +.|.+.....+||..
T Consensus 165 ~Pt~CLfC~~~~k~~e~~~~HM~~~HgffIPdreYL~D~~GLl~YLgeKV~~~~~CL~CN~~~~~f~sleavr~HM~~ 242 (390)
T KOG2785|consen 165 IPTDCLFCDKKSKSLEENLKHMFKEHGFFIPDREYLTDEKGLLKYLGEKVGIGFICLFCNELGRPFSSLEAVRAHMRD 242 (390)
T ss_pred CCcceeecCCCcccHHHHHHHHhhccCCcCCchHhhhchhHHHHHHHHHhccCceEEEeccccCcccccHHHHHHHhh
Confidence 4678999999999999999999887662 247888898 888888888999864
No 52
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=95.71 E-value=0.0085 Score=26.60 Aligned_cols=20 Identities=30% Similarity=0.765 Sum_probs=11.2
Q ss_pred ccCccchhccCCchHHHHHHh
Q psy9067 164 YACDICHARFTQSNSLKSHRL 184 (189)
Q Consensus 164 ~~C~~C~~~f~~~~~l~~H~~ 184 (189)
..|+.||+.| ....|.+|+.
T Consensus 3 ~~C~~CgR~F-~~~~l~~H~~ 22 (25)
T PF13913_consen 3 VPCPICGRKF-NPDRLEKHEK 22 (25)
T ss_pred CcCCCCCCEE-CHHHHHHHHH
Confidence 3566666666 3334666654
No 53
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=95.71 E-value=0.033 Score=34.51 Aligned_cols=20 Identities=20% Similarity=0.472 Sum_probs=10.2
Q ss_pred CcccCCCCCccccchhhHHH
Q psy9067 34 RPHKCSVCERGFKTIASLQN 53 (189)
Q Consensus 34 ~~~~C~~C~~~f~~~~~l~~ 53 (189)
-|..|+.|+-+.-...+|.+
T Consensus 14 LP~~CpiCgLtLVss~HLAR 33 (112)
T TIGR00622 14 LPVECPICGLTLILSTHLAR 33 (112)
T ss_pred CCCcCCcCCCEEeccchHHH
Confidence 34456666555544444444
No 54
>KOG2893|consensus
Probab=95.58 E-value=0.0032 Score=43.92 Aligned_cols=50 Identities=20% Similarity=0.450 Sum_probs=39.1
Q ss_pred CCCCccCCCCCccccchHHHHhchhhcCCCCCccCccCCccCCChHHHHHH-HHHh
Q psy9067 104 HEKPHKCSICDYASVELSKMRNHMRSHTGERPYQCAHCTYASPDTFKLKRH-LRIH 158 (189)
Q Consensus 104 ~~~~~~C~~C~~~~~~~~~l~~H~~~~~~~~~~~C~~C~~~f~~~~~l~~H-~~~h 158 (189)
..++| |++|++.|.+..-|+.|+.. +.|.|.+|.+...+-..|..| +.+|
T Consensus 8 ~~kpw-cwycnrefddekiliqhqka----khfkchichkkl~sgpglsihcmqvh 58 (341)
T KOG2893|consen 8 VDKPW-CWYCNREFDDEKILIQHQKA----KHFKCHICHKKLFSGPGLSIHCMQVH 58 (341)
T ss_pred cCCce-eeecccccchhhhhhhhhhh----ccceeeeehhhhccCCCceeehhhhh
Confidence 34554 89999999999999999764 679999998777777677666 4444
No 55
>KOG2231|consensus
Probab=95.48 E-value=0.074 Score=43.28 Aligned_cols=118 Identities=21% Similarity=0.439 Sum_probs=65.6
Q ss_pred cchhhHHHHHhhcCCCCCcccccCc---------ccCCChhHHHhhhhhhcCCCchhhhhhhhhccCCCCCccCCCCCcc
Q psy9067 46 KTIASLQNHINTHTGVKPHKCKYCE---------SRFTTSGELVRHVRYKHTHEKPELVRHVRYKHTHEKPHKCSICDYA 116 (189)
Q Consensus 46 ~~~~~l~~H~~~~~~~~~~~C~~C~---------~~f~~~~~l~~h~~~~h~~~~~~~~~~~~~~~~~~~~~~C~~C~~~ 116 (189)
..-..|..|+...|.. +.|..|- ........|..|+..--. . ......-..|..|...
T Consensus 125 ~s~~~Lk~H~~~~H~~--~~c~lC~~~~kif~~e~k~Yt~~el~~h~~~gd~---------d--~~s~rGhp~C~~C~~~ 191 (669)
T KOG2231|consen 125 KSVENLKNHMRDQHKL--HLCSLCLQNLKIFINERKLYTRAELNLHLMFGDP---------D--DESCRGHPLCKFCHER 191 (669)
T ss_pred hHHHHHHHHHHHhhhh--hccccccccceeeeeeeehehHHHHHHHHhcCCC---------c--cccccCCccchhhhhh
Confidence 3666788888554322 2233332 233455667777653000 0 0111223578899999
Q ss_pred ccchHHHHhchhhcCCCCCccCccC------CccCCChHHHHHHHHHhhCCCcccCc--cch-hccCCchHHHHHHh
Q psy9067 117 SVELSKMRNHMRSHTGERPYQCAHC------TYASPDTFKLKRHLRIHTGEKPYACD--ICH-ARFTQSNSLKSHRL 184 (189)
Q Consensus 117 ~~~~~~l~~H~~~~~~~~~~~C~~C------~~~f~~~~~l~~H~~~h~~~~~~~C~--~C~-~~f~~~~~l~~H~~ 184 (189)
|.....|+.|++.++ |.|..| +..|..-..|..|.+. ..|.|. .|. +.|.....+..+++
T Consensus 192 fld~~el~rH~~~~h----~~chfC~~~~~~neyy~~~~dLe~HfR~----~HflCE~~~C~~~~f~~~~~~ei~lk 260 (669)
T KOG2231|consen 192 FLDDDELYRHLRFDH----EFCHFCDYKTGQNEYYNDYDDLEEHFRK----GHFLCEEEFCRTKKFYVAFELEIELK 260 (669)
T ss_pred hccHHHHHHhhccce----eheeecCcccccchhcccchHHHHHhhh----cCccccccccccceeeehhHHHHHHH
Confidence 999999999887653 445555 3445555666666554 456776 563 44444444555554
No 56
>smart00451 ZnF_U1 U1-like zinc finger. Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins.
Probab=94.94 E-value=0.016 Score=27.84 Aligned_cols=22 Identities=27% Similarity=0.674 Sum_probs=15.0
Q ss_pred cccCccchhccCCchHHHHHHh
Q psy9067 163 PYACDICHARFTQSNSLKSHRL 184 (189)
Q Consensus 163 ~~~C~~C~~~f~~~~~l~~H~~ 184 (189)
+|.|.+|++.|.....+..|++
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~ 24 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLK 24 (35)
T ss_pred CeEccccCCccCCHHHHHHHHC
Confidence 4667777777777666777764
No 57
>KOG2893|consensus
Probab=94.62 E-value=0.0072 Score=42.26 Aligned_cols=45 Identities=20% Similarity=0.363 Sum_probs=31.0
Q ss_pred eeeCCCcceeeechhHHHHHHhhCCCCCcccCCCCCccccchhhHHHHHh
Q psy9067 7 YWSDTTGYLRYHVMYLLARHLKSHSEERPHKCSVCERGFKTIASLQNHIN 56 (189)
Q Consensus 7 ~~c~~c~~~~f~~~~~l~~h~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~ 56 (189)
=||=+|. ..|.....|.+|+++.+ |+|.+|.+...+--.|..|..
T Consensus 11 pwcwycn-refddekiliqhqkakh----fkchichkkl~sgpglsihcm 55 (341)
T KOG2893|consen 11 PWCWYCN-REFDDEKILIQHQKAKH----FKCHICHKKLFSGPGLSIHCM 55 (341)
T ss_pred ceeeecc-cccchhhhhhhhhhhcc----ceeeeehhhhccCCCceeehh
Confidence 5777777 58888888888877643 778888776655444544443
No 58
>KOG2482|consensus
Probab=94.51 E-value=0.17 Score=37.53 Aligned_cols=64 Identities=23% Similarity=0.452 Sum_probs=42.2
Q ss_pred hHHHHHHhhCCCCCc--ccCCCCCcccc-chhhHHHHHhhcCC----------------------CCCcccccCcccCCC
Q psy9067 21 YLLARHLKSHSEERP--HKCSVCERGFK-TIASLQNHINTHTG----------------------VKPHKCKYCESRFTT 75 (189)
Q Consensus 21 ~~l~~h~~~~~~~~~--~~C~~C~~~f~-~~~~l~~H~~~~~~----------------------~~~~~C~~C~~~f~~ 75 (189)
.+|.++|+.. ..+. .+|-.|+..+. .++....|+-..++ ...+.|-.|.+.|.+
T Consensus 129 eaLeqqQ~Er-edt~fslqClFCn~e~lgnRs~~l~Hlf~~H~lniGlpDniVyvnelLehLkekL~r~~CLyCekifrd 207 (423)
T KOG2482|consen 129 EALEQQQKER-EDTIFSLQCLFCNNEGLGNRSEILEHLFHVHGLNIGLPDNIVYVNELLEHLKEKLERLRCLYCEKIFRD 207 (423)
T ss_pred HHHHHHHHHh-cCCeeeeEEEEecchhcccHHHHHHHHHHHhhhccCCCcceeeHHHHHHHHHHHHhhheeeeeccccCC
Confidence 3466666654 3333 46888876654 45555566544332 123789999999999
Q ss_pred hhHHHhhhhh
Q psy9067 76 SGELVRHVRY 85 (189)
Q Consensus 76 ~~~l~~h~~~ 85 (189)
+..|+.||+.
T Consensus 208 kntLkeHMrk 217 (423)
T KOG2482|consen 208 KNTLKEHMRK 217 (423)
T ss_pred cHHHHHHHHh
Confidence 9999999974
No 59
>cd00350 rubredoxin_like Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center. The family includes rubredoxins, a small electron transfer protein, and a slightly smaller modular rubredoxin domain present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=94.44 E-value=0.025 Score=26.97 Aligned_cols=10 Identities=30% Similarity=0.926 Sum_probs=5.1
Q ss_pred ccCCCCCccc
Q psy9067 108 HKCSICDYAS 117 (189)
Q Consensus 108 ~~C~~C~~~~ 117 (189)
|+|..||..+
T Consensus 2 ~~C~~CGy~y 11 (33)
T cd00350 2 YVCPVCGYIY 11 (33)
T ss_pred EECCCCCCEE
Confidence 4555555443
No 60
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=94.38 E-value=0.017 Score=44.72 Aligned_cols=138 Identities=22% Similarity=0.390 Sum_probs=82.9
Q ss_pred CcccCCCCCccccchhhHHHHHh--hcCCC--CCcccc--cCcccCCChhHHHhhhhhhcCCCchhhh------------
Q psy9067 34 RPHKCSVCERGFKTIASLQNHIN--THTGV--KPHKCK--YCESRFTTSGELVRHVRYKHTHEKPELV------------ 95 (189)
Q Consensus 34 ~~~~C~~C~~~f~~~~~l~~H~~--~~~~~--~~~~C~--~C~~~f~~~~~l~~h~~~~h~~~~~~~~------------ 95 (189)
.++.|..|...|.....+..|.. .|..+ +++.|+ .|++.|.....+..|...+.........
T Consensus 288 ~~~~~~~~~~~~s~~~~l~~~~~~~~h~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 367 (467)
T COG5048 288 LPIKSKQCNISFSRSSPLTRHLRSVNHSGESLKPFSCPYSLCGKLFSRNDALKRHILLHTSISPAKEKLLNSSSKFSPLL 367 (467)
T ss_pred cCCCCccccCCccccccccccccccccccccCCceeeeccCCCccccccccccCCcccccCCCccccccccCcccccccc
Confidence 35778888888888888888888 67777 788888 7888888888888888764444322000
Q ss_pred -------hhhhhccCCCCCccCC--CCCccccchHHHHhchhhcCCCC--CccCccCCccCCChHHHHHHHHHhhCCCcc
Q psy9067 96 -------RHVRYKHTHEKPHKCS--ICDYASVELSKMRNHMRSHTGER--PYQCAHCTYASPDTFKLKRHLRIHTGEKPY 164 (189)
Q Consensus 96 -------~~~~~~~~~~~~~~C~--~C~~~~~~~~~l~~H~~~~~~~~--~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~ 164 (189)
..............+. .|...+.....+..|...+.... .+.+..|...+.....+..|++.+....+.
T Consensus 368 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 447 (467)
T COG5048 368 NNEPPQSLQQYKDLKNDKKSETLSNSCIRNFKRDSNLSLHIITHLSFRPYNCKNPPCSKSFNRHYNLIPHKKIHTNHAPL 447 (467)
T ss_pred CCCCccchhhccCccCCccccccccchhhhhccccccccccccccccCCcCCCCCcchhhccCcccccccccccccCCce
Confidence 0000001111112221 13334444444555555554444 355667888888888888887777766666
Q ss_pred cCccchh
Q psy9067 165 ACDICHA 171 (189)
Q Consensus 165 ~C~~C~~ 171 (189)
.|..++.
T Consensus 448 ~~~~~~~ 454 (467)
T COG5048 448 LCSILKS 454 (467)
T ss_pred eeccccc
Confidence 5555443
No 61
>KOG4173|consensus
Probab=94.11 E-value=0.029 Score=38.43 Aligned_cols=80 Identities=25% Similarity=0.538 Sum_probs=61.7
Q ss_pred CCCCCccCCC--CCccccchHHHHhchhhcCCCCCccCccCCccCCChHHHHHHHH-Hh---------hCCCcccCcc--
Q psy9067 103 THEKPHKCSI--CDYASVELSKMRNHMRSHTGERPYQCAHCTYASPDTFKLKRHLR-IH---------TGEKPYACDI-- 168 (189)
Q Consensus 103 ~~~~~~~C~~--C~~~~~~~~~l~~H~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~-~h---------~~~~~~~C~~-- 168 (189)
...+.+.|+. |-..|.+.+.+..|..+.++. .|..|.++|.+.-.|-.|+. .| .|...|.|-+
T Consensus 75 ~~~~~~~cqvagc~~~~d~lD~~E~hY~~~h~~---sCs~C~r~~Pt~hLLd~HI~E~HDs~Fqa~veRG~dMy~ClvEg 151 (253)
T KOG4173|consen 75 PRVPAFACQVAGCCQVFDALDDYEHHYHTLHGN---SCSFCKRAFPTGHLLDAHILEWHDSLFQALVERGQDMYQCLVEG 151 (253)
T ss_pred cccccccccccchHHHHhhhhhHHHhhhhcccc---hhHHHHHhCCchhhhhHHHHHHHHHHHHHHHHcCccHHHHHHHh
Confidence 4445677877 667788888888887665554 89999999999988888864 23 3577899955
Q ss_pred chhccCCchHHHHHHhh
Q psy9067 169 CHARFTQSNSLKSHRLI 185 (189)
Q Consensus 169 C~~~f~~~~~l~~H~~~ 185 (189)
|+..|.+...=..|+-.
T Consensus 152 Ct~KFkT~r~RkdH~I~ 168 (253)
T KOG4173|consen 152 CTEKFKTSRDRKDHMIR 168 (253)
T ss_pred hhhhhhhhhhhhhHHHH
Confidence 99999999888888743
No 62
>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=93.71 E-value=0.057 Score=25.82 Aligned_cols=23 Identities=22% Similarity=0.528 Sum_probs=14.1
Q ss_pred cccCCCCCccccchhhHHHHHhh
Q psy9067 35 PHKCSVCERGFKTIASLQNHINT 57 (189)
Q Consensus 35 ~~~C~~C~~~f~~~~~l~~H~~~ 57 (189)
+|.|..|+..|.+...+..|+..
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~g 25 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLKG 25 (35)
T ss_pred CeEccccCCccCCHHHHHHHHCh
Confidence 35666666666666666666543
No 63
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=93.53 E-value=0.033 Score=29.50 Aligned_cols=24 Identities=21% Similarity=0.391 Sum_probs=11.7
Q ss_pred CCCccCccCCccCCChHHHHHHHH
Q psy9067 133 ERPYQCAHCTYASPDTFKLKRHLR 156 (189)
Q Consensus 133 ~~~~~C~~C~~~f~~~~~l~~H~~ 156 (189)
+.-+.||-|+..|.....+..|..
T Consensus 15 E~~lrCPRC~~~FR~~K~Y~RHVN 38 (65)
T COG4049 15 EEFLRCPRCGMVFRRRKDYIRHVN 38 (65)
T ss_pred ceeeeCCchhHHHHHhHHHHHHhh
Confidence 333455555555555555555543
No 64
>KOG2231|consensus
Probab=92.92 E-value=0.17 Score=41.32 Aligned_cols=111 Identities=21% Similarity=0.294 Sum_probs=67.1
Q ss_pred ccccCcccCCChhHHHhhhhhhcCCCchhhhhhhhhccCCCCCccCCCCCccccchHHHHhchhhc-CCCCC----ccCc
Q psy9067 65 KCKYCESRFTTSGELVRHVRYKHTHEKPELVRHVRYKHTHEKPHKCSICDYASVELSKMRNHMRSH-TGERP----YQCA 139 (189)
Q Consensus 65 ~C~~C~~~f~~~~~l~~h~~~~h~~~~~~~~~~~~~~~~~~~~~~C~~C~~~~~~~~~l~~H~~~~-~~~~~----~~C~ 139 (189)
.|..| ..|.....|+.|+...|....-.+.. ...+ .+..+++.|. ...|..|++.- .+++. -.|.
T Consensus 117 ~~~~c-~~~~s~~~Lk~H~~~~H~~~~c~lC~------~~~k--if~~e~k~Yt-~~el~~h~~~gd~d~~s~rGhp~C~ 186 (669)
T KOG2231|consen 117 ECLHC-TEFKSVENLKNHMRDQHKLHLCSLCL------QNLK--IFINERKLYT-RAELNLHLMFGDPDDESCRGHPLCK 186 (669)
T ss_pred CCccc-cchhHHHHHHHHHHHhhhhhcccccc------ccce--eeeeeeeheh-HHHHHHHHhcCCCccccccCCccch
Confidence 35555 55568888999986544332110000 0001 2223334343 44566665542 22221 4788
Q ss_pred cCCccCCChHHHHHHHHHhhCCCcccCccc------hhccCCchHHHHHHhhhCCC
Q psy9067 140 HCTYASPDTFKLKRHLRIHTGEKPYACDIC------HARFTQSNSLKSHRLIHTPL 189 (189)
Q Consensus 140 ~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C------~~~f~~~~~l~~H~~~h~~~ 189 (189)
.|...|.....|..|++.+ .|.|..| +.-|....+|..|-+..|.|
T Consensus 187 ~C~~~fld~~el~rH~~~~----h~~chfC~~~~~~neyy~~~~dLe~HfR~~Hfl 238 (669)
T KOG2231|consen 187 FCHERFLDDDELYRHLRFD----HEFCHFCDYKTGQNEYYNDYDDLEEHFRKGHFL 238 (669)
T ss_pred hhhhhhccHHHHHHhhccc----eeheeecCcccccchhcccchHHHHHhhhcCcc
Confidence 8999999999999998754 4566666 45577888999999998875
No 65
>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=91.99 E-value=0.088 Score=23.55 Aligned_cols=9 Identities=33% Similarity=0.774 Sum_probs=4.7
Q ss_pred cCccchhcc
Q psy9067 165 ACDICHARF 173 (189)
Q Consensus 165 ~C~~C~~~f 173 (189)
.|+.||..|
T Consensus 16 ~Cp~CG~~F 24 (26)
T PF10571_consen 16 FCPHCGYDF 24 (26)
T ss_pred cCCCCCCCC
Confidence 455555544
No 66
>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=91.54 E-value=0.43 Score=29.68 Aligned_cols=26 Identities=15% Similarity=0.310 Sum_probs=23.9
Q ss_pred cccC----ccchhccCCchHHHHHHhhhCC
Q psy9067 163 PYAC----DICHARFTQSNSLKSHRLIHTP 188 (189)
Q Consensus 163 ~~~C----~~C~~~f~~~~~l~~H~~~h~~ 188 (189)
-|.| ..|+....+...+.+|++.+||
T Consensus 80 G~~C~~~~~~C~y~~~~~~~m~~H~~~~Hg 109 (109)
T PF12013_consen 80 GYRCQCDPPHCGYITRSKKTMRKHWRKEHG 109 (109)
T ss_pred CeeeecCCCCCCcEeccHHHHHHHHHHhcC
Confidence 4899 9999999999999999999886
No 67
>cd00729 rubredoxin_SM Rubredoxin, Small Modular nonheme iron binding domain containing a [Fe(SCys)4] center, present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=91.15 E-value=0.14 Score=24.56 Aligned_cols=10 Identities=30% Similarity=1.029 Sum_probs=5.9
Q ss_pred ccCCCCCccc
Q psy9067 108 HKCSICDYAS 117 (189)
Q Consensus 108 ~~C~~C~~~~ 117 (189)
|+|..||..+
T Consensus 3 ~~C~~CG~i~ 12 (34)
T cd00729 3 WVCPVCGYIH 12 (34)
T ss_pred EECCCCCCEe
Confidence 5666666543
No 68
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=91.13 E-value=0.11 Score=27.52 Aligned_cols=28 Identities=21% Similarity=0.407 Sum_probs=16.7
Q ss_pred CCCCcccCCCCCccccchhhHHHHHhhc
Q psy9067 31 SEERPHKCSVCERGFKTIASLQNHINTH 58 (189)
Q Consensus 31 ~~~~~~~C~~C~~~f~~~~~l~~H~~~~ 58 (189)
.++..+.|+.|+..|+....+..|....
T Consensus 13 DGE~~lrCPRC~~~FR~~K~Y~RHVNKa 40 (65)
T COG4049 13 DGEEFLRCPRCGMVFRRRKDYIRHVNKA 40 (65)
T ss_pred CCceeeeCCchhHHHHHhHHHHHHhhHH
Confidence 3445556666666666666666665543
No 69
>PF09538 FYDLN_acid: Protein of unknown function (FYDLN_acid); InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=90.91 E-value=0.19 Score=31.21 Aligned_cols=15 Identities=20% Similarity=0.352 Sum_probs=11.0
Q ss_pred CCccCCCCCccccch
Q psy9067 106 KPHKCSICDYASVEL 120 (189)
Q Consensus 106 ~~~~C~~C~~~~~~~ 120 (189)
.|.+|+.||..|.-.
T Consensus 25 ~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 25 DPIVCPKCGTEFPPE 39 (108)
T ss_pred CCccCCCCCCccCcc
Confidence 456788888877665
No 70
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=90.86 E-value=0.19 Score=24.56 Aligned_cols=33 Identities=18% Similarity=0.336 Sum_probs=17.4
Q ss_pred ccCCCCCccccchHHHHhchhhcCCCCCccCccCCccC
Q psy9067 108 HKCSICDYASVELSKMRNHMRSHTGERPYQCAHCTYAS 145 (189)
Q Consensus 108 ~~C~~C~~~~~~~~~l~~H~~~~~~~~~~~C~~C~~~f 145 (189)
.+|+.|+..|.-.++- ...+....+|+.|+..|
T Consensus 3 i~CP~C~~~f~v~~~~-----l~~~~~~vrC~~C~~~f 35 (37)
T PF13719_consen 3 ITCPNCQTRFRVPDDK-----LPAGGRKVRCPKCGHVF 35 (37)
T ss_pred EECCCCCceEEcCHHH-----cccCCcEEECCCCCcEe
Confidence 3566666666655541 11223345666666554
No 71
>KOG2785|consensus
Probab=90.65 E-value=1.3 Score=33.73 Aligned_cols=51 Identities=25% Similarity=0.461 Sum_probs=43.6
Q ss_pred CccCCCCCccccchHHHHhchhhcCCC-----------------------CCccCccCC---ccCCChHHHHHHHHH
Q psy9067 107 PHKCSICDYASVELSKMRNHMRSHTGE-----------------------RPYQCAHCT---YASPDTFKLKRHLRI 157 (189)
Q Consensus 107 ~~~C~~C~~~~~~~~~l~~H~~~~~~~-----------------------~~~~C~~C~---~~f~~~~~l~~H~~~ 157 (189)
|-.|.+|++.+++-..-..|+..+++. .-+.|-.|. +.|.+....+.|+..
T Consensus 166 Pt~CLfC~~~~k~~e~~~~HM~~~HgffIPdreYL~D~~GLl~YLgeKV~~~~~CL~CN~~~~~f~sleavr~HM~~ 242 (390)
T KOG2785|consen 166 PTDCLFCDKKSKSLEENLKHMFKEHGFFIPDREYLTDEKGLLKYLGEKVGIGFICLFCNELGRPFSSLEAVRAHMRD 242 (390)
T ss_pred CcceeecCCCcccHHHHHHHHhhccCCcCCchHhhhchhHHHHHHHHHhccCceEEEeccccCcccccHHHHHHHhh
Confidence 468999999999999999999887764 227888887 999999999999975
No 72
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=90.59 E-value=0.053 Score=41.95 Aligned_cols=54 Identities=39% Similarity=0.827 Sum_probs=48.2
Q ss_pred CccCccCCccCCChHHHHHHHH--HhhCC--CcccCc--cchhccCCchHHHHHHhhhCC
Q psy9067 135 PYQCAHCTYASPDTFKLKRHLR--IHTGE--KPYACD--ICHARFTQSNSLKSHRLIHTP 188 (189)
Q Consensus 135 ~~~C~~C~~~f~~~~~l~~H~~--~h~~~--~~~~C~--~C~~~f~~~~~l~~H~~~h~~ 188 (189)
++.|..|...|.....+..|.+ .|.++ +++.|+ .|++.|.+...+..|..+|.+
T Consensus 289 ~~~~~~~~~~~s~~~~l~~~~~~~~h~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~ 348 (467)
T COG5048 289 PIKSKQCNISFSRSSPLTRHLRSVNHSGESLKPFSCPYSLCGKLFSRNDALKRHILLHTS 348 (467)
T ss_pred CCCCccccCCccccccccccccccccccccCCceeeeccCCCccccccccccCCcccccC
Confidence 5788899999999999999999 79999 899999 799999999999998888765
No 73
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=90.57 E-value=0.66 Score=28.90 Aligned_cols=21 Identities=24% Similarity=0.623 Sum_probs=10.0
Q ss_pred cccCccchhccCCchHHHHHH
Q psy9067 163 PYACDICHARFTQSNSLKSHR 183 (189)
Q Consensus 163 ~~~C~~C~~~f~~~~~l~~H~ 183 (189)
.|+|+.|..-|-..=+.-.|-
T Consensus 81 ~y~C~~C~~~FC~dCD~fiHe 101 (112)
T TIGR00622 81 RYVCAVCKNVFCVDCDVFVHE 101 (112)
T ss_pred ceeCCCCCCccccccchhhhh
Confidence 455555555554444444443
No 74
>PF05443 ROS_MUCR: ROS/MUCR transcriptional regulator protein; InterPro: IPR008807 This family consists of several ROS/MUCR transcriptional regulator proteins. The ros chromosomal gene is present in octopine and nopaline strains of Agrobacterium tumefaciens as well as in Rhizobium meliloti (Sinorhizobium meliloti). This gene encodes a 15.5 kDa protein that specifically represses the virC and virD operons in the virulence region of the Ti plasmid [] and is necessary for succinoglycan production []. S. meliloti can produce two types of acidic exopolysaccharides, succinoglycan and galactoglucan, that are interchangeable for infection of Medicago sativa (Alfalfa) nodules. MucR from S. meliloti acts as a transcriptional repressor that blocks the expression of the exp genes responsible for galactoglucan production therefore allowing the exclusive production of succinoglycan [].; GO: 0003677 DNA binding, 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2JSP_A.
Probab=90.41 E-value=0.17 Score=32.59 Aligned_cols=25 Identities=40% Similarity=0.674 Sum_probs=10.7
Q ss_pred ccCccCCccCCChHHHHHHHHHhhCCCc
Q psy9067 136 YQCAHCTYASPDTFKLKRHLRIHTGEKP 163 (189)
Q Consensus 136 ~~C~~C~~~f~~~~~l~~H~~~h~~~~~ 163 (189)
-.|-+||+.|... ..|++.|+|..|
T Consensus 73 i~clecGk~~k~L---krHL~~~~gltp 97 (132)
T PF05443_consen 73 IICLECGKKFKTL---KRHLRTHHGLTP 97 (132)
T ss_dssp EE-TBT--EESBH---HHHHHHTT-S-H
T ss_pred eEEccCCcccchH---HHHHHHccCCCH
Confidence 4555566655532 555555555543
No 75
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=90.23 E-value=0.27 Score=23.90 Aligned_cols=33 Identities=15% Similarity=0.249 Sum_probs=18.3
Q ss_pred ccCCCCCccccchHHHHhchhhcCCCCCccCccCCccC
Q psy9067 108 HKCSICDYASVELSKMRNHMRSHTGERPYQCAHCTYAS 145 (189)
Q Consensus 108 ~~C~~C~~~~~~~~~l~~H~~~~~~~~~~~C~~C~~~f 145 (189)
..|+.|+..|.-.++.. .......+|+.|+..|
T Consensus 3 i~Cp~C~~~y~i~d~~i-----p~~g~~v~C~~C~~~f 35 (36)
T PF13717_consen 3 ITCPNCQAKYEIDDEKI-----PPKGRKVRCSKCGHVF 35 (36)
T ss_pred EECCCCCCEEeCCHHHC-----CCCCcEEECCCCCCEe
Confidence 35777777766665532 1222345666666554
No 76
>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=89.79 E-value=0.19 Score=25.62 Aligned_cols=27 Identities=26% Similarity=0.378 Sum_probs=13.8
Q ss_pred CCcccCccchhccCCc----hHHHHHHhhhC
Q psy9067 161 EKPYACDICHARFTQS----NSLKSHRLIHT 187 (189)
Q Consensus 161 ~~~~~C~~C~~~f~~~----~~l~~H~~~h~ 187 (189)
....+|..|++.+... ++|..|++..|
T Consensus 14 ~~~a~C~~C~~~~~~~~~~ts~l~~HL~~~h 44 (45)
T PF02892_consen 14 KKKAKCKYCGKVIKYSSGGTSNLKRHLKKKH 44 (45)
T ss_dssp SS-EEETTTTEE-----SSTHHHHHHHHHTT
T ss_pred cCeEEeCCCCeEEeeCCCcHHHHHHhhhhhC
Confidence 3445666666665543 66777775544
No 77
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=89.38 E-value=0.82 Score=30.16 Aligned_cols=46 Identities=15% Similarity=0.330 Sum_probs=28.5
Q ss_pred HHHHhhCCCCCcccCCCCCccccchhhHHHHHhhcCCCCCcccccCcccC
Q psy9067 24 ARHLKSHSEERPHKCSVCERGFKTIASLQNHINTHTGVKPHKCKYCESRF 73 (189)
Q Consensus 24 ~~h~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~C~~C~~~f 73 (189)
..-.........|.|+.|+..|.....+.. ......|.|+.||...
T Consensus 88 ~~~l~~e~~~~~Y~Cp~C~~~y~~~ea~~~----~d~~~~f~Cp~Cg~~l 133 (147)
T smart00531 88 EDKLEDETNNAYYKCPNCQSKYTFLEANQL----LDMDGTFTCPRCGEEL 133 (147)
T ss_pred HHHHhcccCCcEEECcCCCCEeeHHHHHHh----cCCCCcEECCCCCCEE
Confidence 333334445567999999999875333221 1123449999999864
No 78
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=88.73 E-value=0.3 Score=32.74 Aligned_cols=10 Identities=40% Similarity=0.880 Sum_probs=5.7
Q ss_pred CCCccCccCC
Q psy9067 133 ERPYQCAHCT 142 (189)
Q Consensus 133 ~~~~~C~~C~ 142 (189)
+-|..||+||
T Consensus 147 e~P~~CPiCg 156 (166)
T COG1592 147 EAPEVCPICG 156 (166)
T ss_pred CCCCcCCCCC
Confidence 4555666665
No 79
>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=88.42 E-value=0.76 Score=30.73 Aligned_cols=42 Identities=14% Similarity=0.252 Sum_probs=29.0
Q ss_pred HHHHHhhCCCCCcccCCCCCccccchhhHHHHHhhcCCCCCcccccCcccC
Q psy9067 23 LARHLKSHSEERPHKCSVCERGFKTIASLQNHINTHTGVKPHKCKYCESRF 73 (189)
Q Consensus 23 l~~h~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~C~~C~~~f 73 (189)
|..-+....+..-|.|+.|+..|+....+. ..|.|+.||...
T Consensus 97 lk~~l~~e~~~~~Y~Cp~c~~r~tf~eA~~---------~~F~Cp~Cg~~L 138 (158)
T TIGR00373 97 LREKLEFETNNMFFICPNMCVRFTFNEAME---------LNFTCPRCGAML 138 (158)
T ss_pred HHHHHhhccCCCeEECCCCCcEeeHHHHHH---------cCCcCCCCCCEe
Confidence 334444445556688999998887666653 369999999763
No 80
>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain. This domain contains a CXXCX(19)CXXC motif suggestive of both zinc fingers and thioredoxin, usually found at the N-terminus of prokaryotic proteins. One partially characterized gene, agmX, is among a large set in Myxococcus whose interruption affects adventurous gliding motility.
Probab=88.26 E-value=0.36 Score=23.60 Aligned_cols=33 Identities=12% Similarity=0.295 Sum_probs=16.3
Q ss_pred ccCCCCCccccchHHHHhchhhcCCCCCccCccCCccC
Q psy9067 108 HKCSICDYASVELSKMRNHMRSHTGERPYQCAHCTYAS 145 (189)
Q Consensus 108 ~~C~~C~~~~~~~~~l~~H~~~~~~~~~~~C~~C~~~f 145 (189)
+.|+.|+..|.-..+... .......|+.|+..|
T Consensus 3 ~~CP~C~~~~~v~~~~~~-----~~~~~v~C~~C~~~~ 35 (38)
T TIGR02098 3 IQCPNCKTSFRVVDSQLG-----ANGGKVRCGKCGHVW 35 (38)
T ss_pred EECCCCCCEEEeCHHHcC-----CCCCEEECCCCCCEE
Confidence 456666666655544211 111134666666554
No 81
>KOG2482|consensus
Probab=88.24 E-value=0.44 Score=35.52 Aligned_cols=26 Identities=19% Similarity=0.473 Sum_probs=21.4
Q ss_pred cccccCcccCCChhHHHhhhhhhcCC
Q psy9067 64 HKCKYCESRFTTSGELVRHVRYKHTH 89 (189)
Q Consensus 64 ~~C~~C~~~f~~~~~l~~h~~~~h~~ 89 (189)
..|-+|.........|..|+++.|.-
T Consensus 280 v~CLfC~~~~en~~~l~eHmk~vHe~ 305 (423)
T KOG2482|consen 280 VVCLFCTNFYENPVFLFEHMKIVHEF 305 (423)
T ss_pred eEEEeeccchhhHHHHHHHHHHHHHh
Confidence 48999998888889999999876643
No 82
>PF09538 FYDLN_acid: Protein of unknown function (FYDLN_acid); InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=87.93 E-value=0.37 Score=29.92 Aligned_cols=29 Identities=24% Similarity=0.617 Sum_probs=17.3
Q ss_pred cCCCCCccccchHHHHhchhhcCCCCCccCccCCccCCCh
Q psy9067 109 KCSICDYASVELSKMRNHMRSHTGERPYQCAHCTYASPDT 148 (189)
Q Consensus 109 ~C~~C~~~~~~~~~l~~H~~~~~~~~~~~C~~C~~~f~~~ 148 (189)
.|+.||+.|-.. +..|-.|+.||..|...
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 677777665332 22566677777666554
No 83
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=87.91 E-value=0.13 Score=36.22 Aligned_cols=43 Identities=26% Similarity=0.590 Sum_probs=24.9
Q ss_pred CCccCCCCCccccchHHHHhchhh---c-------CCCCC-----ccCccCCccCCCh
Q psy9067 106 KPHKCSICDYASVELSKMRNHMRS---H-------TGERP-----YQCAHCTYASPDT 148 (189)
Q Consensus 106 ~~~~C~~C~~~~~~~~~l~~H~~~---~-------~~~~~-----~~C~~C~~~f~~~ 148 (189)
+.+.||+|++.|....-.....+. . .+..| ..||.||.++...
T Consensus 4 k~~~CPvC~~~F~~~~vrs~~~r~~~~d~D~~~~Y~~vnP~~Y~V~vCP~CgyA~~~~ 61 (214)
T PF09986_consen 4 KKITCPVCGKEFKTKKVRSGKIRVIRRDSDFCPRYKGVNPLFYEVWVCPHCGYAAFEE 61 (214)
T ss_pred CceECCCCCCeeeeeEEEcCCceEeeecCCCccccCCCCCeeeeEEECCCCCCccccc
Confidence 457899999888776443333221 1 11222 5777787766644
No 84
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=87.56 E-value=0.67 Score=30.58 Aligned_cols=41 Identities=22% Similarity=0.313 Sum_probs=26.7
Q ss_pred CCCCCcccccCcccCCChhHHHhhhhhhcCCCchhhhhhhhhccCCCCCccCCCCCccccc
Q psy9067 59 TGVKPHKCKYCESRFTTSGELVRHVRYKHTHEKPELVRHVRYKHTHEKPHKCSICDYASVE 119 (189)
Q Consensus 59 ~~~~~~~C~~C~~~f~~~~~l~~h~~~~h~~~~~~~~~~~~~~~~~~~~~~C~~C~~~~~~ 119 (189)
.+...|.|+.|+..|.....+.. .. ....|.||.||.....
T Consensus 95 ~~~~~Y~Cp~C~~~y~~~ea~~~-------------------~d-~~~~f~Cp~Cg~~l~~ 135 (147)
T smart00531 95 TNNAYYKCPNCQSKYTFLEANQL-------------------LD-MDGTFTCPRCGEELEE 135 (147)
T ss_pred cCCcEEECcCCCCEeeHHHHHHh-------------------cC-CCCcEECCCCCCEEEE
Confidence 34556999999999886443321 01 2344999999977543
No 85
>smart00614 ZnF_BED BED zinc finger. DNA-binding domain in chromatin-boundary-element-binding proteins and transposases
Probab=87.21 E-value=0.5 Score=24.78 Aligned_cols=23 Identities=22% Similarity=0.528 Sum_probs=14.9
Q ss_pred ccCccchhccCCc-----hHHHHHHhhh
Q psy9067 164 YACDICHARFTQS-----NSLKSHRLIH 186 (189)
Q Consensus 164 ~~C~~C~~~f~~~-----~~l~~H~~~h 186 (189)
-.|..|++.++.. ++|.+|++..
T Consensus 19 a~C~~C~~~l~~~~~~gTs~L~rHl~~~ 46 (50)
T smart00614 19 AKCKYCGKKLSRSSKGGTSNLRRHLRRK 46 (50)
T ss_pred EEecCCCCEeeeCCCCCcHHHHHHHHhH
Confidence 4566676666544 5788888743
No 86
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=87.15 E-value=0.85 Score=31.16 Aligned_cols=43 Identities=16% Similarity=0.375 Sum_probs=28.8
Q ss_pred HHHHHhhCCCCCcccCCCCCccccchhhHHHHHhhcCCCCCcccccCcccCC
Q psy9067 23 LARHLKSHSEERPHKCSVCERGFKTIASLQNHINTHTGVKPHKCKYCESRFT 74 (189)
Q Consensus 23 l~~h~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~C~~C~~~f~ 74 (189)
|..-+.......-|.|+.|+..|+....+. ..|.|+.||....
T Consensus 105 lk~~l~~e~~~~~Y~Cp~C~~rytf~eA~~---------~~F~Cp~Cg~~L~ 147 (178)
T PRK06266 105 LKEQLEEEENNMFFFCPNCHIRFTFDEAME---------YGFRCPQCGEMLE 147 (178)
T ss_pred HHHHhhhccCCCEEECCCCCcEEeHHHHhh---------cCCcCCCCCCCCe
Confidence 334444444455688999998887655432 3799999997643
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=86.84 E-value=0.53 Score=20.99 Aligned_cols=20 Identities=25% Similarity=0.521 Sum_probs=12.8
Q ss_pred ccCccchhccCCchHHHHHHh
Q psy9067 164 YACDICHARFTQSNSLKSHRL 184 (189)
Q Consensus 164 ~~C~~C~~~f~~~~~l~~H~~ 184 (189)
..||+|++.+ ....+..|+-
T Consensus 2 v~CPiC~~~v-~~~~in~HLD 21 (26)
T smart00734 2 VQCPVCFREV-PENLINSHLD 21 (26)
T ss_pred CcCCCCcCcc-cHHHHHHHHH
Confidence 3577777776 4455667654
No 88
>TIGR00373 conserved hypothetical protein TIGR00373. This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.
Probab=86.19 E-value=0.85 Score=30.52 Aligned_cols=34 Identities=12% Similarity=0.359 Sum_probs=27.5
Q ss_pred ceEEeeeCCCcceeeechhHHHHHHhhCCCCCcccCCCCCcccc
Q psy9067 3 NTIYYWSDTTGYLRYHVMYLLARHLKSHSEERPHKCSVCERGFK 46 (189)
Q Consensus 3 ~~~~~~c~~c~~~~f~~~~~l~~h~~~~~~~~~~~C~~C~~~f~ 46 (189)
|...|.|+.|+ ..|+-..++. .-|.|+.||....
T Consensus 106 ~~~~Y~Cp~c~-~r~tf~eA~~---------~~F~Cp~Cg~~L~ 139 (158)
T TIGR00373 106 NNMFFICPNMC-VRFTFNEAME---------LNFTCPRCGAMLD 139 (158)
T ss_pred CCCeEECCCCC-cEeeHHHHHH---------cCCcCCCCCCEee
Confidence 56789999999 6888888874 2699999998754
No 89
>PHA00626 hypothetical protein
Probab=85.83 E-value=0.29 Score=26.06 Aligned_cols=13 Identities=23% Similarity=0.447 Sum_probs=7.1
Q ss_pred CcccCccchhccC
Q psy9067 162 KPYACDICHARFT 174 (189)
Q Consensus 162 ~~~~C~~C~~~f~ 174 (189)
..|.|+.||..|+
T Consensus 22 nrYkCkdCGY~ft 34 (59)
T PHA00626 22 DDYVCCDCGYNDS 34 (59)
T ss_pred cceEcCCCCCeec
Confidence 3455555555554
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=84.91 E-value=2.2 Score=26.48 Aligned_cols=27 Identities=30% Similarity=0.783 Sum_probs=20.1
Q ss_pred CCccC----ccCCccCCChHHHHHHHHHhhC
Q psy9067 134 RPYQC----AHCTYASPDTFKLKRHLRIHTG 160 (189)
Q Consensus 134 ~~~~C----~~C~~~f~~~~~l~~H~~~h~~ 160 (189)
.-|.| +.|+....+...+..|++.+++
T Consensus 79 ~G~~C~~~~~~C~y~~~~~~~m~~H~~~~Hg 109 (109)
T PF12013_consen 79 DGYRCQCDPPHCGYITRSKKTMRKHWRKEHG 109 (109)
T ss_pred CCeeeecCCCCCCcEeccHHHHHHHHHHhcC
Confidence 34778 7888888888888888776543
No 91
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=84.87 E-value=0.17 Score=35.64 Aligned_cols=13 Identities=38% Similarity=0.795 Sum_probs=10.1
Q ss_pred ccCCCCCccccch
Q psy9067 108 HKCSICDYASVEL 120 (189)
Q Consensus 108 ~~C~~C~~~~~~~ 120 (189)
++||.||.++...
T Consensus 49 ~vCP~CgyA~~~~ 61 (214)
T PF09986_consen 49 WVCPHCGYAAFEE 61 (214)
T ss_pred EECCCCCCccccc
Confidence 5899999886544
No 92
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=83.97 E-value=0.49 Score=35.35 Aligned_cols=78 Identities=21% Similarity=0.404 Sum_probs=41.1
Q ss_pred ccCCC--CCccccchHHHHhchhhcCCCCCccCccC---CccCC------ChHHHHHHHHHhhCCCc----ccCccchhc
Q psy9067 108 HKCSI--CDYASVELSKMRNHMRSHTGERPYQCAHC---TYASP------DTFKLKRHLRIHTGEKP----YACDICHAR 172 (189)
Q Consensus 108 ~~C~~--C~~~~~~~~~l~~H~~~~~~~~~~~C~~C---~~~f~------~~~~l~~H~~~h~~~~~----~~C~~C~~~ 172 (189)
|.||. |.........|..|....++. +-|.+| .+.|. +...|+.|......+.- -.|..|..-
T Consensus 152 F~CP~skc~~~C~~~k~lk~H~K~~H~~--~~C~~C~~nKk~F~~E~~lF~~~~Lr~H~~~G~~e~GFKGHP~C~FC~~~ 229 (493)
T COG5236 152 FKCPKSKCHRRCGSLKELKKHYKAQHGF--VLCSECIGNKKDFWNEIRLFRSSTLRDHKNGGLEEEGFKGHPLCIFCKIY 229 (493)
T ss_pred hcCCchhhhhhhhhHHHHHHHHHhhcCc--EEhHhhhcCcccCccceeeeecccccccccCCccccCcCCCchhhhccce
Confidence 56654 555556667777776654432 233333 12222 33455555544333322 246666666
Q ss_pred cCCchHHHHHHhhhC
Q psy9067 173 FTQSNSLKSHRLIHT 187 (189)
Q Consensus 173 f~~~~~l~~H~~~h~ 187 (189)
|.....|.+|++..|
T Consensus 230 FYdDDEL~~HcR~~H 244 (493)
T COG5236 230 FYDDDELRRHCRLRH 244 (493)
T ss_pred ecChHHHHHHHHhhh
Confidence 666666766666543
No 93
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=83.89 E-value=1.6 Score=29.40 Aligned_cols=26 Identities=27% Similarity=0.681 Sum_probs=19.7
Q ss_pred CCcccCCCCCccccchhhHHHHHhhcCCCCCcccccCcc
Q psy9067 33 ERPHKCSVCERGFKTIASLQNHINTHTGVKPHKCKYCES 71 (189)
Q Consensus 33 ~~~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~C~~C~~ 71 (189)
.+.|.|++||..+ .++-|-.||+|+-
T Consensus 132 ~~~~vC~vCGy~~-------------~ge~P~~CPiCga 157 (166)
T COG1592 132 GKVWVCPVCGYTH-------------EGEAPEVCPICGA 157 (166)
T ss_pred CCEEEcCCCCCcc-------------cCCCCCcCCCCCC
Confidence 3478999998864 3466888999983
No 94
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=83.60 E-value=2 Score=23.30 Aligned_cols=9 Identities=33% Similarity=1.051 Sum_probs=5.3
Q ss_pred CCcccccCc
Q psy9067 62 KPHKCKYCE 70 (189)
Q Consensus 62 ~~~~C~~C~ 70 (189)
.+|.|+.||
T Consensus 49 ~~Y~Cp~CG 57 (61)
T COG2888 49 NPYRCPKCG 57 (61)
T ss_pred CceECCCcC
Confidence 356666665
No 95
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=83.32 E-value=1.3 Score=30.27 Aligned_cols=35 Identities=11% Similarity=0.450 Sum_probs=27.1
Q ss_pred ceEEeeeCCCcceeeechhHHHHHHhhCCCCCcccCCCCCccccc
Q psy9067 3 NTIYYWSDTTGYLRYHVMYLLARHLKSHSEERPHKCSVCERGFKT 47 (189)
Q Consensus 3 ~~~~~~c~~c~~~~f~~~~~l~~h~~~~~~~~~~~C~~C~~~f~~ 47 (189)
+...|.|+.|+ ..|.-..++. .-|.|+.||.....
T Consensus 114 ~~~~Y~Cp~C~-~rytf~eA~~---------~~F~Cp~Cg~~L~~ 148 (178)
T PRK06266 114 NNMFFFCPNCH-IRFTFDEAME---------YGFRCPQCGEMLEE 148 (178)
T ss_pred CCCEEECCCCC-cEEeHHHHhh---------cCCcCCCCCCCCee
Confidence 45689999999 6888777653 36999999987643
No 96
>PF14369 zf-RING_3: zinc-finger
Probab=83.14 E-value=0.52 Score=22.73 Aligned_cols=9 Identities=44% Similarity=1.257 Sum_probs=6.0
Q ss_pred cCCCCCccc
Q psy9067 37 KCSVCERGF 45 (189)
Q Consensus 37 ~C~~C~~~f 45 (189)
.|+.|+..|
T Consensus 23 ~CP~C~~gF 31 (35)
T PF14369_consen 23 ACPRCHGGF 31 (35)
T ss_pred CCcCCCCcE
Confidence 477777665
No 97
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=82.42 E-value=0.8 Score=23.36 Aligned_cols=11 Identities=18% Similarity=0.416 Sum_probs=5.7
Q ss_pred ccCCCCCcccc
Q psy9067 108 HKCSICDYASV 118 (189)
Q Consensus 108 ~~C~~C~~~~~ 118 (189)
|.|..||..+.
T Consensus 3 Y~C~~Cg~~~~ 13 (44)
T smart00659 3 YICGECGRENE 13 (44)
T ss_pred EECCCCCCEee
Confidence 45555555443
No 98
>TIGR02300 FYDLN_acid conserved hypothetical protein TIGR02300. Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=82.40 E-value=1.2 Score=28.37 Aligned_cols=15 Identities=7% Similarity=-0.077 Sum_probs=11.1
Q ss_pred CCccCCCCCccccch
Q psy9067 106 KPHKCSICDYASVEL 120 (189)
Q Consensus 106 ~~~~C~~C~~~~~~~ 120 (189)
.|..|+.||..|.-.
T Consensus 25 ~p~vcP~cg~~~~~~ 39 (129)
T TIGR02300 25 RPAVSPYTGEQFPPE 39 (129)
T ss_pred CCccCCCcCCccCcc
Confidence 467888888887655
No 99
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=81.28 E-value=1.3 Score=32.68 Aligned_cols=23 Identities=13% Similarity=0.218 Sum_probs=11.1
Q ss_pred CccCCCCCccccchHHHHhchhh
Q psy9067 107 PHKCSICDYASVELSKMRNHMRS 129 (189)
Q Consensus 107 ~~~C~~C~~~~~~~~~l~~H~~~ 129 (189)
.|+|+.|...|-..-+...|...
T Consensus 388 rY~Ce~CK~~FC~dCdvfiHe~L 410 (421)
T COG5151 388 RYQCELCKSTFCSDCDVFIHETL 410 (421)
T ss_pred ceechhhhhhhhhhhHHHHHHHH
Confidence 35555555555554444444433
No 100
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=81.12 E-value=0.24 Score=32.84 Aligned_cols=15 Identities=13% Similarity=0.246 Sum_probs=9.7
Q ss_pred ccCccCCccCCChHH
Q psy9067 136 YQCAHCTYASPDTFK 150 (189)
Q Consensus 136 ~~C~~C~~~f~~~~~ 150 (189)
++|+.||..|.....
T Consensus 29 ~~c~~c~~~f~~~e~ 43 (154)
T PRK00464 29 RECLACGKRFTTFER 43 (154)
T ss_pred eeccccCCcceEeEe
Confidence 677777777765443
No 101
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=80.98 E-value=1 Score=23.09 Aligned_cols=12 Identities=25% Similarity=0.808 Sum_probs=8.7
Q ss_pred CccCCCCCcccc
Q psy9067 107 PHKCSICDYASV 118 (189)
Q Consensus 107 ~~~C~~C~~~~~ 118 (189)
...|+.||..+.
T Consensus 21 ~~~Cp~CG~~~~ 32 (46)
T PRK00398 21 GVRCPYCGYRIL 32 (46)
T ss_pred ceECCCCCCeEE
Confidence 578999986543
No 102
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=80.84 E-value=1.2 Score=24.25 Aligned_cols=10 Identities=40% Similarity=1.108 Sum_probs=5.7
Q ss_pred CcccCccchh
Q psy9067 162 KPYACDICHA 171 (189)
Q Consensus 162 ~~~~C~~C~~ 171 (189)
.+|.|+.||.
T Consensus 47 ~~Y~CP~CGF 56 (59)
T PRK14890 47 NPYTCPKCGF 56 (59)
T ss_pred CceECCCCCC
Confidence 3566666654
No 103
>PF03604 DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa subunit; InterPro: IPR006591 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Each class of RNA polymerase is assembled from 9 to 15 different polypeptides. Rbp10 (RNA polymerase CX) is a domain found in RNA polymerase subunit 10; present in RNA polymerase I, II and III.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_Z 3HKZ_X 2NVX_L 3S1Q_L 2JA6_L 3S17_L 3HOW_L 3HOV_L 3PO2_L 3HOZ_L ....
Probab=80.64 E-value=0.96 Score=21.32 Aligned_cols=9 Identities=22% Similarity=0.575 Sum_probs=4.1
Q ss_pred cCCCCCccc
Q psy9067 109 KCSICDYAS 117 (189)
Q Consensus 109 ~C~~C~~~~ 117 (189)
.|..||..+
T Consensus 2 ~C~~Cg~~~ 10 (32)
T PF03604_consen 2 ICGECGAEV 10 (32)
T ss_dssp BESSSSSSE
T ss_pred CCCcCCCee
Confidence 344444443
No 104
>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=80.14 E-value=0.62 Score=23.04 Aligned_cols=29 Identities=21% Similarity=0.432 Sum_probs=15.0
Q ss_pred ccCCCCCccccchHHHHhchhhcCCCCCccCccCCc
Q psy9067 108 HKCSICDYASVELSKMRNHMRSHTGERPYQCAHCTY 143 (189)
Q Consensus 108 ~~C~~C~~~~~~~~~l~~H~~~~~~~~~~~C~~C~~ 143 (189)
|+|+.||..|....... ....-.|+.||.
T Consensus 6 y~C~~Cg~~fe~~~~~~-------~~~~~~CP~Cg~ 34 (41)
T smart00834 6 YRCEDCGHTFEVLQKIS-------DDPLATCPECGG 34 (41)
T ss_pred EEcCCCCCEEEEEEecC-------CCCCCCCCCCCC
Confidence 56777776664433210 123446666664
No 105
>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=79.26 E-value=0.67 Score=24.42 Aligned_cols=29 Identities=24% Similarity=0.488 Sum_probs=16.6
Q ss_pred ccCCCCCccccchHHHHhchhhcCCCCCccCccCCc
Q psy9067 108 HKCSICDYASVELSKMRNHMRSHTGERPYQCAHCTY 143 (189)
Q Consensus 108 ~~C~~C~~~~~~~~~l~~H~~~~~~~~~~~C~~C~~ 143 (189)
|.|..||..|.....+. ...+-.|+.||.
T Consensus 6 y~C~~Cg~~fe~~~~~~-------~~~~~~CP~Cg~ 34 (52)
T TIGR02605 6 YRCTACGHRFEVLQKMS-------DDPLATCPECGG 34 (52)
T ss_pred EEeCCCCCEeEEEEecC-------CCCCCCCCCCCC
Confidence 67778887776442211 123446777774
No 106
>COG4957 Predicted transcriptional regulator [Transcription]
Probab=77.96 E-value=1.4 Score=28.27 Aligned_cols=23 Identities=35% Similarity=0.374 Sum_probs=15.7
Q ss_pred ccCccchhccCCchHHHHHHhhhCCC
Q psy9067 164 YACDICHARFTQSNSLKSHRLIHTPL 189 (189)
Q Consensus 164 ~~C~~C~~~f~~~~~l~~H~~~h~~~ 189 (189)
..|-.+|+.|. .|.+|+.+|+||
T Consensus 77 IicLEDGkkfK---SLKRHL~t~~gm 99 (148)
T COG4957 77 IICLEDGKKFK---SLKRHLTTHYGL 99 (148)
T ss_pred EEEeccCcchH---HHHHHHhcccCC
Confidence 45777777764 477777777765
No 107
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=77.45 E-value=2.3 Score=32.01 Aligned_cols=115 Identities=28% Similarity=0.474 Sum_probs=63.4
Q ss_pred hhHHHHHHhhCCCCCcccCCCCCc---cc------cchhhHHHHHhhcCCCCC----cccccCcccCCChhHHHhhhhhh
Q psy9067 20 MYLLARHLKSHSEERPHKCSVCER---GF------KTIASLQNHINTHTGVKP----HKCKYCESRFTTSGELVRHVRYK 86 (189)
Q Consensus 20 ~~~l~~h~~~~~~~~~~~C~~C~~---~f------~~~~~l~~H~~~~~~~~~----~~C~~C~~~f~~~~~l~~h~~~~ 86 (189)
...|..|.++.++. +.|.+|.. .| ..+..|..|...-..+.. -.|.+|...|.+...|..|.+.
T Consensus 166 ~k~lk~H~K~~H~~--~~C~~C~~nKk~F~~E~~lF~~~~Lr~H~~~G~~e~GFKGHP~C~FC~~~FYdDDEL~~HcR~- 242 (493)
T COG5236 166 LKELKKHYKAQHGF--VLCSECIGNKKDFWNEIRLFRSSTLRDHKNGGLEEEGFKGHPLCIFCKIYFYDDDELRRHCRL- 242 (493)
T ss_pred HHHHHHHHHhhcCc--EEhHhhhcCcccCccceeeeecccccccccCCccccCcCCCchhhhccceecChHHHHHHHHh-
Confidence 44577777776643 35666532 12 233445555443322222 2588888888888888888874
Q ss_pred cCCCchhhhhhhhhccCCCCCccCCCCCc----cccchHHHHhchhhcCCCCCccCcc--CC----ccCCChHHHHHHHH
Q psy9067 87 HTHEKPELVRHVRYKHTHEKPHKCSICDY----ASVELSKMRNHMRSHTGERPYQCAH--CT----YASPDTFKLKRHLR 156 (189)
Q Consensus 87 h~~~~~~~~~~~~~~~~~~~~~~C~~C~~----~~~~~~~l~~H~~~~~~~~~~~C~~--C~----~~f~~~~~l~~H~~ 156 (189)
..++-+.|+.-+. -|++...|..|-+. ..|.|.+ |. .+|....+|..|+.
T Consensus 243 ----------------~HE~ChICD~v~p~~~QYFK~Y~~Le~HF~~----~hy~ct~qtc~~~k~~vf~~~~el~~h~~ 302 (493)
T COG5236 243 ----------------RHEACHICDMVGPIRYQYFKSYEDLEAHFRN----AHYCCTFQTCRVGKCYVFPYHTELLEHLT 302 (493)
T ss_pred ----------------hhhhhhhhhccCccchhhhhCHHHHHHHhhc----CceEEEEEEEecCcEEEeccHHHHHHHHH
Confidence 2223344444332 26666666666442 2344432 21 46777777888865
Q ss_pred H
Q psy9067 157 I 157 (189)
Q Consensus 157 ~ 157 (189)
.
T Consensus 303 ~ 303 (493)
T COG5236 303 R 303 (493)
T ss_pred H
Confidence 4
No 108
>PF06524 NOA36: NOA36 protein; InterPro: IPR010531 This family consists of several NOA36 proteins which contain 29 highly conserved cysteine residues. The function of this protein is unknown.; GO: 0008270 zinc ion binding, 0005634 nucleus
Probab=77.18 E-value=1.7 Score=31.29 Aligned_cols=11 Identities=36% Similarity=1.132 Sum_probs=5.3
Q ss_pred CCCCcccccCc
Q psy9067 60 GVKPHKCKYCE 70 (189)
Q Consensus 60 ~~~~~~C~~C~ 70 (189)
+.+.|.|.+|+
T Consensus 139 GGrif~CsfC~ 149 (314)
T PF06524_consen 139 GGRIFKCSFCD 149 (314)
T ss_pred CCeEEEeecCC
Confidence 44445555553
No 109
>KOG2186|consensus
Probab=76.24 E-value=1.8 Score=30.96 Aligned_cols=13 Identities=23% Similarity=0.534 Sum_probs=6.3
Q ss_pred CcccccCcccCCC
Q psy9067 63 PHKCKYCESRFTT 75 (189)
Q Consensus 63 ~~~C~~C~~~f~~ 75 (189)
-|.|..|+..|..
T Consensus 29 ~fSCIDC~k~F~~ 41 (276)
T KOG2186|consen 29 YFSCIDCGKTFER 41 (276)
T ss_pred eeEEeeccccccc
Confidence 3445555554444
No 110
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=76.08 E-value=2.7 Score=35.31 Aligned_cols=10 Identities=30% Similarity=0.859 Sum_probs=5.5
Q ss_pred CCCccCccCC
Q psy9067 133 ERPYQCAHCT 142 (189)
Q Consensus 133 ~~~~~C~~C~ 142 (189)
..|..|+.||
T Consensus 473 ~~p~~Cp~Cg 482 (730)
T COG1198 473 PIPQSCPECG 482 (730)
T ss_pred CCCCCCCCCC
Confidence 3455566665
No 111
>PF13878 zf-C2H2_3: zinc-finger of acetyl-transferase ESCO
Probab=75.92 E-value=2.6 Score=21.05 Aligned_cols=23 Identities=22% Similarity=0.501 Sum_probs=13.0
Q ss_pred ccCccchhccCC--chHHHHHHhhh
Q psy9067 164 YACDICHARFTQ--SNSLKSHRLIH 186 (189)
Q Consensus 164 ~~C~~C~~~f~~--~~~l~~H~~~h 186 (189)
..|+.||..|.. ..+-..|.+.|
T Consensus 14 ~~C~~CgM~Y~~~~~eD~~~H~~yH 38 (41)
T PF13878_consen 14 TTCPTCGMLYSPGSPEDEKLHKKYH 38 (41)
T ss_pred cCCCCCCCEECCCCHHHHHHHHHHH
Confidence 466666666553 44455665554
No 112
>PRK04023 DNA polymerase II large subunit; Validated
Probab=74.99 E-value=3.7 Score=35.60 Aligned_cols=12 Identities=25% Similarity=0.484 Sum_probs=7.6
Q ss_pred cccCccchhccC
Q psy9067 163 PYACDICHARFT 174 (189)
Q Consensus 163 ~~~C~~C~~~f~ 174 (189)
++.|+.||..-.
T Consensus 663 ~y~CPKCG~El~ 674 (1121)
T PRK04023 663 EDECEKCGREPT 674 (1121)
T ss_pred CCcCCCCCCCCC
Confidence 466888875533
No 113
>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=74.35 E-value=0.57 Score=28.84 Aligned_cols=9 Identities=22% Similarity=0.667 Sum_probs=5.0
Q ss_pred ccCCCCCcc
Q psy9067 108 HKCSICDYA 116 (189)
Q Consensus 108 ~~C~~C~~~ 116 (189)
..|+.||..
T Consensus 63 ~~Cp~Cg~~ 71 (104)
T TIGR01384 63 VECPKCGHK 71 (104)
T ss_pred CCCCCCCCC
Confidence 466666643
No 114
>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=74.22 E-value=0.78 Score=22.28 Aligned_cols=8 Identities=38% Similarity=1.090 Sum_probs=3.6
Q ss_pred CCCCCccc
Q psy9067 38 CSVCERGF 45 (189)
Q Consensus 38 C~~C~~~f 45 (189)
|+.||..|
T Consensus 4 C~~Cg~~Y 11 (36)
T PF05191_consen 4 CPKCGRIY 11 (36)
T ss_dssp ETTTTEEE
T ss_pred cCCCCCcc
Confidence 44444444
No 115
>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=74.16 E-value=2.3 Score=22.46 Aligned_cols=31 Identities=19% Similarity=0.394 Sum_probs=18.4
Q ss_pred CCCccCCCCCccccchHHHHhchhhcCCCCCccCccC
Q psy9067 105 EKPHKCSICDYASVELSKMRNHMRSHTGERPYQCAHC 141 (189)
Q Consensus 105 ~~~~~C~~C~~~~~~~~~l~~H~~~~~~~~~~~C~~C 141 (189)
...|+|+.|+..|-..-+...|...| .||.|
T Consensus 19 ~~~y~C~~C~~~FC~dCD~fiHE~LH------~CPGC 49 (51)
T PF07975_consen 19 SSRYRCPKCKNHFCIDCDVFIHETLH------NCPGC 49 (51)
T ss_dssp -EEE--TTTT--B-HHHHHTTTTTS-------SSSTT
T ss_pred CCeEECCCCCCccccCcChhhhcccc------CCcCC
Confidence 34689999999998888888887665 56655
No 116
>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=74.13 E-value=1.2 Score=22.40 Aligned_cols=30 Identities=20% Similarity=0.606 Sum_probs=20.2
Q ss_pred CcccccCcccCCChhHHHhhhhhhcCCCchhhhhhhhhccCCCCCccCCCCCc
Q psy9067 63 PHKCKYCESRFTTSGELVRHVRYKHTHEKPELVRHVRYKHTHEKPHKCSICDY 115 (189)
Q Consensus 63 ~~~C~~C~~~f~~~~~l~~h~~~~h~~~~~~~~~~~~~~~~~~~~~~C~~C~~ 115 (189)
.|.|..||..|.....+ .. .....|+.||.
T Consensus 5 ey~C~~Cg~~fe~~~~~----------------------~~-~~~~~CP~Cg~ 34 (42)
T PF09723_consen 5 EYRCEECGHEFEVLQSI----------------------SE-DDPVPCPECGS 34 (42)
T ss_pred EEEeCCCCCEEEEEEEc----------------------CC-CCCCcCCCCCC
Confidence 37888998887553321 22 45678999986
No 117
>KOG2186|consensus
Probab=73.93 E-value=1.8 Score=31.01 Aligned_cols=47 Identities=17% Similarity=0.427 Sum_probs=36.2
Q ss_pred CccCCCCCccccchHHHHhchhhcCCCCCccCccCCccCCChHHHHHHHH
Q psy9067 107 PHKCSICDYASVELSKMRNHMRSHTGERPYQCAHCTYASPDTFKLKRHLR 156 (189)
Q Consensus 107 ~~~C~~C~~~~~~~~~l~~H~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~ 156 (189)
.|.|..||...+-. .+-+|+....+ .-|.|-.|++.|.. ..+..|..
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 37899999876654 45568887777 66899999999998 67788864
No 118
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=73.82 E-value=1.9 Score=25.40 Aligned_cols=33 Identities=24% Similarity=0.584 Sum_probs=23.6
Q ss_pred CcccCCCCCccccchhhHHHHHhhcCCCCCcccccCcccCCCh
Q psy9067 34 RPHKCSVCERGFKTIASLQNHINTHTGVKPHKCKYCESRFTTS 76 (189)
Q Consensus 34 ~~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~C~~C~~~f~~~ 76 (189)
.+|.|+.|++.- ..-.....+.|..|+..|.--
T Consensus 34 ~~~~Cp~C~~~~----------VkR~a~GIW~C~kCg~~fAGg 66 (89)
T COG1997 34 AKHVCPFCGRTT----------VKRIATGIWKCRKCGAKFAGG 66 (89)
T ss_pred cCCcCCCCCCcc----------eeeeccCeEEcCCCCCeeccc
Confidence 358899999862 123455679999999988653
No 119
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=73.78 E-value=1.6 Score=22.83 Aligned_cols=10 Identities=30% Similarity=0.667 Sum_probs=5.7
Q ss_pred ccCCCCCccc
Q psy9067 108 HKCSICDYAS 117 (189)
Q Consensus 108 ~~C~~C~~~~ 117 (189)
|.|..||+.+
T Consensus 7 Y~C~~Cg~~~ 16 (49)
T COG1996 7 YKCARCGREV 16 (49)
T ss_pred EEhhhcCCee
Confidence 5555555555
No 120
>KOG2593|consensus
Probab=73.33 E-value=4 Score=31.73 Aligned_cols=39 Identities=21% Similarity=0.402 Sum_probs=24.3
Q ss_pred CCCCCcccccCcccCCChhHHHhhhhhhcCCCchhhhhhhhhccCCCCCccCCCCCcc
Q psy9067 59 TGVKPHKCKYCESRFTTSGELVRHVRYKHTHEKPELVRHVRYKHTHEKPHKCSICDYA 116 (189)
Q Consensus 59 ~~~~~~~C~~C~~~f~~~~~l~~h~~~~h~~~~~~~~~~~~~~~~~~~~~~C~~C~~~ 116 (189)
.....|.|+.|.+.|.....++. .......|.|..|+-.
T Consensus 124 t~~~~Y~Cp~C~kkyt~Lea~~L-------------------~~~~~~~F~C~~C~ge 162 (436)
T KOG2593|consen 124 TNVAGYVCPNCQKKYTSLEALQL-------------------LDNETGEFHCENCGGE 162 (436)
T ss_pred cccccccCCccccchhhhHHHHh-------------------hcccCceEEEecCCCc
Confidence 34456888888888777554432 1233456778887754
No 121
>PF02176 zf-TRAF: TRAF-type zinc finger; PDB: 2EOD_A 2YUC_A 3HCU_A 3HCS_B 3HCT_A.
Probab=72.53 E-value=2.5 Score=22.80 Aligned_cols=21 Identities=29% Similarity=0.487 Sum_probs=9.9
Q ss_pred hhHHHHHHhhCCCCCcccCCC
Q psy9067 20 MYLLARHLKSHSEERPHKCSV 40 (189)
Q Consensus 20 ~~~l~~h~~~~~~~~~~~C~~ 40 (189)
+..|..|....-+..+..|+.
T Consensus 23 r~~l~~H~~~~C~~~~v~C~~ 43 (60)
T PF02176_consen 23 RKELDDHLENECPKRPVPCPY 43 (60)
T ss_dssp CCCHHHHHHTTSTTSEEE-SS
T ss_pred HHHHHHHHHccCCCCcEECCC
Confidence 444555555444444445555
No 122
>KOG2593|consensus
Probab=72.23 E-value=5.4 Score=31.05 Aligned_cols=38 Identities=16% Similarity=0.391 Sum_probs=27.5
Q ss_pred CCCcccCCCCCccccchhhHHHHHhhcCCCCCcccccCccc
Q psy9067 32 EERPHKCSVCERGFKTIASLQNHINTHTGVKPHKCKYCESR 72 (189)
Q Consensus 32 ~~~~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~C~~C~~~ 72 (189)
...-|.|+.|.+.| ..|..-+..-.....|.|..|+-.
T Consensus 125 ~~~~Y~Cp~C~kky---t~Lea~~L~~~~~~~F~C~~C~ge 162 (436)
T KOG2593|consen 125 NVAGYVCPNCQKKY---TSLEALQLLDNETGEFHCENCGGE 162 (436)
T ss_pred ccccccCCccccch---hhhHHHHhhcccCceEEEecCCCc
Confidence 44569999999999 555555444444567999999864
No 123
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=71.01 E-value=0.95 Score=25.84 Aligned_cols=14 Identities=29% Similarity=0.491 Sum_probs=7.0
Q ss_pred CCccCc--cCCccCCC
Q psy9067 134 RPYQCA--HCTYASPD 147 (189)
Q Consensus 134 ~~~~C~--~C~~~f~~ 147 (189)
.-++|. .||..|..
T Consensus 26 ~Y~qC~N~eCg~tF~t 41 (72)
T PRK09678 26 RYHQCQNVNCSATFIT 41 (72)
T ss_pred eeeecCCCCCCCEEEE
Confidence 344554 55555544
No 124
>COG5188 PRP9 Splicing factor 3a, subunit 3 [RNA processing and modification]
Probab=70.79 E-value=6.3 Score=29.84 Aligned_cols=28 Identities=21% Similarity=0.492 Sum_probs=21.1
Q ss_pred hcCCCCCccCccCC-ccCCChHHHHHHHH
Q psy9067 129 SHTGERPYQCAHCT-YASPDTFKLKRHLR 156 (189)
Q Consensus 129 ~~~~~~~~~C~~C~-~~f~~~~~l~~H~~ 156 (189)
.|.-.+.|.|.+|| .++.....+..|..
T Consensus 368 lhgLd~ef~CEICgNyvy~GR~~FdrHF~ 396 (470)
T COG5188 368 LHGLDIEFECEICGNYVYYGRDRFDRHFE 396 (470)
T ss_pred hcCCCcceeeeecccccccchHHHHhhhh
Confidence 34445779999998 77788888888864
No 125
>COG1326 Uncharacterized archaeal Zn-finger protein [General function prediction only]
Probab=70.68 E-value=7.1 Score=26.91 Aligned_cols=42 Identities=19% Similarity=0.282 Sum_probs=25.4
Q ss_pred CcceEEeeeCCCcceeeechhHHHHHHhhCCCCCcccCCCCCccccc
Q psy9067 1 MVNTIYYWSDTTGYLRYHVMYLLARHLKSHSEERPHKCSVCERGFKT 47 (189)
Q Consensus 1 ~~~~~~~~c~~c~~~~f~~~~~l~~h~~~~~~~~~~~C~~C~~~f~~ 47 (189)
|-..+++.|+.|+...+.+ +-++.........|..||..+..
T Consensus 1 m~~~iy~~Cp~Cg~eev~h-----EVik~~g~~~lvrC~eCG~V~~~ 42 (201)
T COG1326 1 MTEEIYIECPSCGSEEVSH-----EVIKERGREPLVRCEECGTVHPA 42 (201)
T ss_pred CcceEEEECCCCCcchhhH-----HHHHhcCCceEEEccCCCcEeec
Confidence 4567889999999433321 22233333345779999988744
No 126
>PF14353 CpXC: CpXC protein
Probab=70.64 E-value=0.42 Score=30.65 Aligned_cols=14 Identities=14% Similarity=0.408 Sum_probs=8.4
Q ss_pred CccCccCCccCCCh
Q psy9067 135 PYQCAHCTYASPDT 148 (189)
Q Consensus 135 ~~~C~~C~~~f~~~ 148 (189)
.+.|+.||..|...
T Consensus 38 ~~~CP~Cg~~~~~~ 51 (128)
T PF14353_consen 38 SFTCPSCGHKFRLE 51 (128)
T ss_pred EEECCCCCCceecC
Confidence 46666666665544
No 127
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=70.58 E-value=1.8 Score=18.58 Aligned_cols=6 Identities=33% Similarity=1.027 Sum_probs=2.6
Q ss_pred CCCCCc
Q psy9067 110 CSICDY 115 (189)
Q Consensus 110 C~~C~~ 115 (189)
|+.||.
T Consensus 2 Cp~CG~ 7 (23)
T PF13240_consen 2 CPNCGA 7 (23)
T ss_pred CcccCC
Confidence 344443
No 128
>PF03811 Zn_Tnp_IS1: InsA N-terminal domain; InterPro: IPR003220 Insertion elements are mobile elements in DNA, usually encoding proteins required for transposition, for example transposases. Protein InsA is absolutely required for transposition of insertion element 1. This entry represents a short zinc binding domain found in IS1 InsA family protein. It is found at the N terminus of the protein and may be a DNA-binding domain.; GO: 0006313 transposition, DNA-mediated
Probab=70.42 E-value=1.7 Score=21.13 Aligned_cols=34 Identities=18% Similarity=0.177 Sum_probs=20.2
Q ss_pred ceEEeeeCCCcceeeechhHHHHHHhhCCCCCcccCCCC
Q psy9067 3 NTIYYWSDTTGYLRYHVMYLLARHLKSHSEERPHKCSVC 41 (189)
Q Consensus 3 ~~~~~~c~~c~~~~f~~~~~l~~h~~~~~~~~~~~C~~C 41 (189)
+++.+.|+.|.... .+.+|-+...+...|.|..|
T Consensus 2 a~i~v~CP~C~s~~-----~v~k~G~~~~G~qryrC~~C 35 (36)
T PF03811_consen 2 AKIDVHCPRCQSTE-----GVKKNGKSPSGHQRYRCKDC 35 (36)
T ss_pred CcEeeeCCCCCCCC-----cceeCCCCCCCCEeEecCcC
Confidence 46777788887522 23345555555555777666
No 129
>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=70.41 E-value=1.9 Score=30.39 Aligned_cols=23 Identities=17% Similarity=0.540 Sum_probs=9.9
Q ss_pred ccCccchhccCCchHHHHHHhhh
Q psy9067 164 YACDICHARFTQSNSLKSHRLIH 186 (189)
Q Consensus 164 ~~C~~C~~~f~~~~~l~~H~~~h 186 (189)
|.|++|+|.|.-..-..+|+.+.
T Consensus 78 ~~C~lc~KlFkg~eFV~KHI~nK 100 (214)
T PF04959_consen 78 WRCPLCGKLFKGPEFVRKHIFNK 100 (214)
T ss_dssp EEE-SSS-EESSHHHHHHHHHHH
T ss_pred ECCCCCCcccCChHHHHHHHhhc
Confidence 44444555544444444444443
No 130
>KOG2807|consensus
Probab=69.02 E-value=9.1 Score=28.73 Aligned_cols=35 Identities=23% Similarity=0.474 Sum_probs=23.3
Q ss_pred ccCCCCCccccchhhHHHHHhhcCCCCCcccccCcccCCChhHHHhhhh
Q psy9067 36 HKCSVCERGFKTIASLQNHINTHTGVKPHKCKYCESRFTTSGELVRHVR 84 (189)
Q Consensus 36 ~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~C~~C~~~f~~~~~l~~h~~ 84 (189)
|.|+.|+-.. =.-|..|+.|+-+......|.+-..
T Consensus 277 y~CP~Ckakv--------------CsLP~eCpiC~ltLVss~hLARSyh 311 (378)
T KOG2807|consen 277 YFCPQCKAKV--------------CSLPIECPICSLTLVSSPHLARSYH 311 (378)
T ss_pred eeCCcccCee--------------ecCCccCCccceeEecchHHHHHHH
Confidence 7787775432 2346788888888777777766544
No 131
>PF15135 UPF0515: Uncharacterised protein UPF0515
Probab=68.82 E-value=14 Score=26.65 Aligned_cols=16 Identities=13% Similarity=0.326 Sum_probs=11.8
Q ss_pred CCccCCCCCccccchH
Q psy9067 106 KPHKCSICDYASVELS 121 (189)
Q Consensus 106 ~~~~C~~C~~~~~~~~ 121 (189)
..|.|+.|+..|....
T Consensus 154 aef~C~~C~h~F~G~~ 169 (278)
T PF15135_consen 154 AEFHCPKCRHNFRGFA 169 (278)
T ss_pred eeeecccccccchhhh
Confidence 3478888888887653
No 132
>PF12907 zf-met2: Zinc-binding
Probab=68.24 E-value=4.1 Score=20.30 Aligned_cols=25 Identities=32% Similarity=0.639 Sum_probs=14.8
Q ss_pred ccCccchhccC---CchHHHHHHhhhCC
Q psy9067 164 YACDICHARFT---QSNSLKSHRLIHTP 188 (189)
Q Consensus 164 ~~C~~C~~~f~---~~~~l~~H~~~h~~ 188 (189)
++|.+|-..|. ....|..|..+.||
T Consensus 2 i~C~iC~qtF~~t~~~~~L~eH~enKHp 29 (40)
T PF12907_consen 2 IICKICRQTFMQTTNEPQLKEHAENKHP 29 (40)
T ss_pred cCcHHhhHHHHhcCCHHHHHHHHHccCC
Confidence 45677764443 44557777665554
No 133
>KOG4173|consensus
Probab=67.74 E-value=1.5 Score=30.33 Aligned_cols=73 Identities=23% Similarity=0.375 Sum_probs=53.1
Q ss_pred CcceeeechhHHHHHHhhCCCCCcccCCCCCccccchhhHHHHHhhcCC----------CCCccccc--CcccCCChhHH
Q psy9067 12 TGYLRYHVMYLLARHLKSHSEERPHKCSVCERGFKTIASLQNHINTHTG----------VKPHKCKY--CESRFTTSGEL 79 (189)
Q Consensus 12 c~~~~f~~~~~l~~h~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~~~~----------~~~~~C~~--C~~~f~~~~~l 79 (189)
|+ ..|........|-.+-++. .|..|.+.|.....|..|....+. .--|.|-+ |+..|.....-
T Consensus 87 c~-~~~d~lD~~E~hY~~~h~~---sCs~C~r~~Pt~hLLd~HI~E~HDs~Fqa~veRG~dMy~ClvEgCt~KFkT~r~R 162 (253)
T KOG4173|consen 87 CC-QVFDALDDYEHHYHTLHGN---SCSFCKRAFPTGHLLDAHILEWHDSLFQALVERGQDMYQCLVEGCTEKFKTSRDR 162 (253)
T ss_pred hH-HHHhhhhhHHHhhhhcccc---hhHHHHHhCCchhhhhHHHHHHHHHHHHHHHHcCccHHHHHHHhhhhhhhhhhhh
Confidence 55 3677666666776665544 599999999999999999887652 22378854 88899988888
Q ss_pred HhhhhhhcC
Q psy9067 80 VRHVRYKHT 88 (189)
Q Consensus 80 ~~h~~~~h~ 88 (189)
..|+...|.
T Consensus 163 kdH~I~~Hk 171 (253)
T KOG4173|consen 163 KDHMIRMHK 171 (253)
T ss_pred hhHHHHhcc
Confidence 888876543
No 134
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=67.07 E-value=3.6 Score=22.01 Aligned_cols=25 Identities=20% Similarity=0.503 Sum_probs=14.7
Q ss_pred ccCCCCCccccchHHHHhchhhcCCCCCccCccCCcc
Q psy9067 108 HKCSICDYASVELSKMRNHMRSHTGERPYQCAHCTYA 144 (189)
Q Consensus 108 ~~C~~C~~~~~~~~~l~~H~~~~~~~~~~~C~~C~~~ 144 (189)
..|+.||+.|... +....|+.|+..
T Consensus 6 ~~C~~Cg~~~~~~------------dDiVvCp~Cgap 30 (54)
T PF14446_consen 6 CKCPVCGKKFKDG------------DDIVVCPECGAP 30 (54)
T ss_pred ccChhhCCcccCC------------CCEEECCCCCCc
Confidence 3677777665432 345577777644
No 135
>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=62.75 E-value=3.1 Score=19.25 Aligned_cols=11 Identities=27% Similarity=0.697 Sum_probs=2.0
Q ss_pred cCCCCCccccc
Q psy9067 109 KCSICDYASVE 119 (189)
Q Consensus 109 ~C~~C~~~~~~ 119 (189)
.|+.|+..+..
T Consensus 4 ~Cp~C~se~~y 14 (30)
T PF08274_consen 4 KCPLCGSEYTY 14 (30)
T ss_dssp --TTT-----E
T ss_pred CCCCCCCccee
Confidence 45555544433
No 136
>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=62.31 E-value=3.2 Score=18.11 Aligned_cols=8 Identities=38% Similarity=1.493 Sum_probs=3.6
Q ss_pred CccCccCC
Q psy9067 135 PYQCAHCT 142 (189)
Q Consensus 135 ~~~C~~C~ 142 (189)
+|.|+.||
T Consensus 16 ~f~CPnCG 23 (24)
T PF07754_consen 16 PFPCPNCG 23 (24)
T ss_pred eEeCCCCC
Confidence 34444444
No 137
>COG4530 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=62.10 E-value=5.9 Score=24.48 Aligned_cols=12 Identities=8% Similarity=-0.031 Sum_probs=6.7
Q ss_pred CCccCccCCccC
Q psy9067 134 RPYQCAHCTYAS 145 (189)
Q Consensus 134 ~~~~C~~C~~~f 145 (189)
.|..|+.||++|
T Consensus 25 dPiVsPytG~s~ 36 (129)
T COG4530 25 DPIVSPYTGKSY 36 (129)
T ss_pred CccccCcccccc
Confidence 455555555555
No 138
>KOG4124|consensus
Probab=61.27 E-value=1.4 Score=33.17 Aligned_cols=49 Identities=37% Similarity=0.750 Sum_probs=36.2
Q ss_pred CCccCcc--CCccCCChHHHHHHHHHhh-------------------CCCcccCccchhccCCchHHHHH
Q psy9067 134 RPYQCAH--CTYASPDTFKLKRHLRIHT-------------------GEKPYACDICHARFTQSNSLKSH 182 (189)
Q Consensus 134 ~~~~C~~--C~~~f~~~~~l~~H~~~h~-------------------~~~~~~C~~C~~~f~~~~~l~~H 182 (189)
++|.|++ |.+.+.....+..|....+ ..++|+|++|.+++....+|.-|
T Consensus 348 ~~~~~~vp~~~~~~~n~ng~~~~~~~~h~s~i~~~s~~~~ph~~~~~~nk~~r~~i~~~~~k~~~~l~~~ 417 (442)
T KOG4124|consen 348 KPYKCPVPNCDKAYKNQNGLKYHKLHGHCSPITTPTPAPIPHQGFVVENKPYRCEVCSKRYKNLNGLKYH 417 (442)
T ss_pred CCCCCCCCcchhhcccCcceeeccccCcCCCCCCCCCCCCCcceeeeccCcccChhhhhhhccCCCCCce
Confidence 6788865 8888888887777754321 15789999999998877766544
No 139
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=58.87 E-value=5 Score=26.07 Aligned_cols=15 Identities=20% Similarity=0.193 Sum_probs=11.0
Q ss_pred CCccCCCCCccccch
Q psy9067 106 KPHKCSICDYASVEL 120 (189)
Q Consensus 106 ~~~~C~~C~~~~~~~ 120 (189)
..+.|..||..|...
T Consensus 69 ~~~~C~~CG~~~~~~ 83 (135)
T PRK03824 69 AVLKCRNCGNEWSLK 83 (135)
T ss_pred eEEECCCCCCEEecc
Confidence 457888888777654
No 140
>PF04216 FdhE: Protein involved in formate dehydrogenase formation; InterPro: IPR006452 This family of sequences describe an accessory protein required for the assembly of formate dehydrogenase of certain proteobacteria although not present in the final complex []. The exact nature of the function of FdhE in the assembly of the complex is unknown, but considering the presence of selenocysteine, molybdopterin, iron-sulphur clusters and cytochrome b556, it is likely to be involved in the insertion of cofactors. ; GO: 0005737 cytoplasm; PDB: 2FIY_B.
Probab=57.63 E-value=0.66 Score=34.36 Aligned_cols=16 Identities=13% Similarity=0.202 Sum_probs=9.3
Q ss_pred CCCCccCCCCCccccc
Q psy9067 104 HEKPHKCSICDYASVE 119 (189)
Q Consensus 104 ~~~~~~C~~C~~~~~~ 119 (189)
..+...|..|+.-++.
T Consensus 235 ~~rve~C~~C~~YlK~ 250 (290)
T PF04216_consen 235 AYRVEVCESCGSYLKT 250 (290)
T ss_dssp SEEEEEETTTTEEEEE
T ss_pred cEEEEECCcccchHHH
Confidence 3444678888754443
No 141
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=56.67 E-value=17 Score=24.80 Aligned_cols=45 Identities=18% Similarity=0.391 Sum_probs=29.2
Q ss_pred hhHHHHHHhhCCCCCcccCCCCCccccchhhHHHHHhhcCCCCCcccccCcccC
Q psy9067 20 MYLLARHLKSHSEERPHKCSVCERGFKTIASLQNHINTHTGVKPHKCKYCESRF 73 (189)
Q Consensus 20 ~~~l~~h~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~C~~C~~~f 73 (189)
...|..-.....+..-|.|+.|...++.... +.. .|.|+.||...
T Consensus 98 le~Lk~~le~~~~~~~y~C~~~~~r~sfdeA----~~~-----~F~Cp~Cg~~L 142 (176)
T COG1675 98 LEKLKRKLEKETENNYYVCPNCHVKYSFDEA----MEL-----GFTCPKCGEDL 142 (176)
T ss_pred HHHHHHHHHhhccCCceeCCCCCCcccHHHH----HHh-----CCCCCCCCchh
Confidence 3445555555666677899999887654333 222 28999999753
No 142
>COG1655 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=56.10 E-value=2.6 Score=29.81 Aligned_cols=26 Identities=15% Similarity=0.311 Sum_probs=17.4
Q ss_pred CCCccCCCCCccccchHHHHhchhhc
Q psy9067 105 EKPHKCSICDYASVELSKMRNHMRSH 130 (189)
Q Consensus 105 ~~~~~C~~C~~~~~~~~~l~~H~~~~ 130 (189)
.+.+.||+|+..|+-..-+..-.+.-
T Consensus 17 kk~ieCPvC~tkFkkeev~tgsiRii 42 (267)
T COG1655 17 KKTIECPVCNTKFKKEEVKTGSIRII 42 (267)
T ss_pred hceeccCcccchhhhhheeccceeEe
Confidence 35578999998887766554444443
No 143
>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=56.04 E-value=5.6 Score=19.98 Aligned_cols=13 Identities=38% Similarity=0.713 Sum_probs=8.3
Q ss_pred cCCCCCccccchh
Q psy9067 37 KCSVCERGFKTIA 49 (189)
Q Consensus 37 ~C~~C~~~f~~~~ 49 (189)
.|+.|++.|.-..
T Consensus 10 ~C~~C~rpf~WRK 22 (42)
T PF10013_consen 10 ICPVCGRPFTWRK 22 (42)
T ss_pred cCcccCCcchHHH
Confidence 4777777775443
No 144
>PF12760 Zn_Tnp_IS1595: Transposase zinc-ribbon domain; InterPro: IPR024442 This zinc binding domain is found in a range of transposase proteins such as ISSPO8, ISSOD11, ISRSSP2 etc. It may be a zinc-binding beta ribbon domain that could bind DNA.
Probab=54.24 E-value=8.3 Score=19.68 Aligned_cols=8 Identities=25% Similarity=0.733 Sum_probs=3.7
Q ss_pred ccCCCCCc
Q psy9067 108 HKCSICDY 115 (189)
Q Consensus 108 ~~C~~C~~ 115 (189)
+.|+.||.
T Consensus 19 ~~CP~Cg~ 26 (46)
T PF12760_consen 19 FVCPHCGS 26 (46)
T ss_pred CCCCCCCC
Confidence 34555543
No 145
>PF15269 zf-C2H2_7: Zinc-finger
Probab=54.20 E-value=7.6 Score=19.71 Aligned_cols=22 Identities=23% Similarity=0.390 Sum_probs=13.9
Q ss_pred ccCccchhccCCchHHHHHHhh
Q psy9067 164 YACDICHARFTQSNSLKSHRLI 185 (189)
Q Consensus 164 ~~C~~C~~~f~~~~~l~~H~~~ 185 (189)
|+|=.|......++.|-.||+.
T Consensus 21 ykcfqcpftc~~kshl~nhmky 42 (54)
T PF15269_consen 21 YKCFQCPFTCNEKSHLFNHMKY 42 (54)
T ss_pred ceeecCCcccchHHHHHHHHHH
Confidence 4566666666666777777653
No 146
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=53.17 E-value=12 Score=22.34 Aligned_cols=15 Identities=40% Similarity=0.961 Sum_probs=12.0
Q ss_pred CCCcccccCcccCCC
Q psy9067 61 VKPHKCKYCESRFTT 75 (189)
Q Consensus 61 ~~~~~C~~C~~~f~~ 75 (189)
.+|-.|..||..|.+
T Consensus 56 v~Pa~CkkCGfef~~ 70 (97)
T COG3357 56 VRPARCKKCGFEFRD 70 (97)
T ss_pred ecChhhcccCccccc
Confidence 357889999988866
No 147
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=53.05 E-value=5 Score=23.98 Aligned_cols=33 Identities=18% Similarity=0.394 Sum_probs=22.5
Q ss_pred CcccCCCCCccccchhhHHHHHhhcCCCCCcccccCcccCCCh
Q psy9067 34 RPHKCSVCERGFKTIASLQNHINTHTGVKPHKCKYCESRFTTS 76 (189)
Q Consensus 34 ~~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~C~~C~~~f~~~ 76 (189)
..|.|+.|++.- ..-.....+.|..|++.|.--
T Consensus 35 a~y~CpfCgk~~----------vkR~a~GIW~C~~C~~~~AGG 67 (90)
T PTZ00255 35 AKYFCPFCGKHA----------VKRQAVGIWRCKGCKKTVAGG 67 (90)
T ss_pred CCccCCCCCCCc----------eeeeeeEEEEcCCCCCEEeCC
Confidence 458899998652 122344568999999987653
No 148
>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=52.84 E-value=1.3 Score=36.66 Aligned_cols=57 Identities=19% Similarity=0.420 Sum_probs=26.7
Q ss_pred cCCCCCccccchHHHHhchhhcCCCCC-ccCccCCccCCChHHHHHHHHHhhCCCcccCccchhc
Q psy9067 109 KCSICDYASVELSKMRNHMRSHTGERP-YQCAHCTYASPDTFKLKRHLRIHTGEKPYACDICHAR 172 (189)
Q Consensus 109 ~C~~C~~~~~~~~~l~~H~~~~~~~~~-~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~ 172 (189)
.|..||..|.-...|---+. .+.-+. -.|+.|.+.+.....-+-| -+|..|+.||-.
T Consensus 125 ~CT~CGPRfTIi~alPYDR~-nTsM~~F~lC~~C~~EY~dP~nRRfH------AQp~aCp~CGP~ 182 (750)
T COG0068 125 NCTNCGPRFTIIEALPYDRE-NTSMADFPLCPFCDKEYKDPLNRRFH------AQPIACPKCGPH 182 (750)
T ss_pred ccCCCCcceeeeccCCCCcc-cCccccCcCCHHHHHHhcCccccccc------cccccCcccCCC
Confidence 56666666654433322211 111111 2566666655554433333 245667777643
No 149
>PF05290 Baculo_IE-1: Baculovirus immediate-early protein (IE-0); InterPro: IPR007954 This entry contains the Baculovirus immediate-early protein IE-0.
Probab=52.67 E-value=14 Score=23.90 Aligned_cols=43 Identities=19% Similarity=0.396 Sum_probs=26.6
Q ss_pred CCCCCcccCCCCCccccchhh------------------HHHHHhhcCCCCCcccccCcccCCChh
Q psy9067 30 HSEERPHKCSVCERGFKTIAS------------------LQNHINTHTGVKPHKCKYCESRFTTSG 77 (189)
Q Consensus 30 ~~~~~~~~C~~C~~~f~~~~~------------------l~~H~~~~~~~~~~~C~~C~~~f~~~~ 77 (189)
....+.|+|++|.+...+... |+.+-..+ -.|+.|.-+|.+.+
T Consensus 75 F~d~~lYeCnIC~etS~ee~FLKPneCCgY~iCn~Cya~LWK~~~~y-----pvCPvCkTSFKss~ 135 (140)
T PF05290_consen 75 FLDPKLYECNICKETSAEERFLKPNECCGYSICNACYANLWKFCNLY-----PVCPVCKTSFKSSS 135 (140)
T ss_pred ecCCCceeccCcccccchhhcCCcccccchHHHHHHHHHHHHHcccC-----CCCCcccccccccc
Confidence 334567888888777654433 34433322 36888988887654
No 150
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=51.95 E-value=7.2 Score=32.96 Aligned_cols=45 Identities=24% Similarity=0.569 Sum_probs=26.4
Q ss_pred cCCCCCccccch---HHHHhchhhcCCCCCccCccCCccCCChHHHHHHHHHhhCCCcccCccchhc
Q psy9067 109 KCSICDYASVEL---SKMRNHMRSHTGERPYQCAHCTYASPDTFKLKRHLRIHTGEKPYACDICHAR 172 (189)
Q Consensus 109 ~C~~C~~~~~~~---~~l~~H~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~ 172 (189)
.|..||..+.-. ..|. .|...+...|..||. ....|..|+.||..
T Consensus 437 ~C~~Cg~v~~Cp~Cd~~lt----~H~~~~~L~CH~Cg~---------------~~~~p~~Cp~Cgs~ 484 (730)
T COG1198 437 LCRDCGYIAECPNCDSPLT----LHKATGQLRCHYCGY---------------QEPIPQSCPECGSE 484 (730)
T ss_pred ecccCCCcccCCCCCcceE----EecCCCeeEeCCCCC---------------CCCCCCCCCCCCCC
Confidence 466666554332 2233 333345677888873 33568999999854
No 151
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=51.55 E-value=3.6 Score=26.51 Aligned_cols=16 Identities=19% Similarity=0.513 Sum_probs=9.2
Q ss_pred CCCccCccCCccCCCh
Q psy9067 133 ERPYQCAHCTYASPDT 148 (189)
Q Consensus 133 ~~~~~C~~C~~~f~~~ 148 (189)
..-|.|+.|++.|...
T Consensus 51 ~qRyrC~~C~~tf~~~ 66 (129)
T COG3677 51 HQRYKCKSCGSTFTVE 66 (129)
T ss_pred ccccccCCcCcceeee
Confidence 3446666666666543
No 152
>PF13451 zf-trcl: Probable zinc-binding domain
Probab=51.44 E-value=13 Score=19.47 Aligned_cols=37 Identities=22% Similarity=0.489 Sum_probs=19.8
Q ss_pred CcccCCCCCccccchhhHHHHHhhcC-CCCCcccccCc
Q psy9067 34 RPHKCSVCERGFKTIASLQNHINTHT-GVKPHKCKYCE 70 (189)
Q Consensus 34 ~~~~C~~C~~~f~~~~~l~~H~~~~~-~~~~~~C~~C~ 70 (189)
+.+.|..||..|.....-+.-..... ...|-.|+.|.
T Consensus 3 k~l~C~dCg~~FvfTa~EQ~fy~eKgf~n~p~RC~~CR 40 (49)
T PF13451_consen 3 KTLTCKDCGAEFVFTAGEQKFYAEKGFDNEPKRCPSCR 40 (49)
T ss_pred eeEEcccCCCeEEEehhHHHHHHhcCCcCCCccCHHHH
Confidence 45677778777755444333333321 23456666664
No 153
>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=51.04 E-value=3.5 Score=34.27 Aligned_cols=58 Identities=24% Similarity=0.468 Sum_probs=39.2
Q ss_pred ccccCcccCCChhHHHhhhhhhcCCCchhhhhhhhhccCCCCCccCCCCCccccchHHHHhchhhcCCCCCccCccCCcc
Q psy9067 65 KCKYCESRFTTSGELVRHVRYKHTHEKPELVRHVRYKHTHEKPHKCSICDYASVELSKMRNHMRSHTGERPYQCAHCTYA 144 (189)
Q Consensus 65 ~C~~C~~~f~~~~~l~~h~~~~h~~~~~~~~~~~~~~~~~~~~~~C~~C~~~~~~~~~l~~H~~~~~~~~~~~C~~C~~~ 144 (189)
.|..||..|.....|.--.. ..+...---|+.|.+.|.+..+-+-|. .|..|+.||-.
T Consensus 125 ~CT~CGPRfTIi~alPYDR~----------------nTsM~~F~lC~~C~~EY~dP~nRRfHA------Qp~aCp~CGP~ 182 (750)
T COG0068 125 NCTNCGPRFTIIEALPYDRE----------------NTSMADFPLCPFCDKEYKDPLNRRFHA------QPIACPKCGPH 182 (750)
T ss_pred ccCCCCcceeeeccCCCCcc----------------cCccccCcCCHHHHHHhcCcccccccc------ccccCcccCCC
Confidence 69999999987666543222 123333357999999998887744443 36699999953
No 154
>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=50.47 E-value=9.6 Score=20.40 Aligned_cols=12 Identities=17% Similarity=0.232 Sum_probs=9.0
Q ss_pred CccCCCCCcccc
Q psy9067 107 PHKCSICDYASV 118 (189)
Q Consensus 107 ~~~C~~C~~~~~ 118 (189)
...|+.||..+.
T Consensus 22 iV~Cp~CGaele 33 (54)
T TIGR01206 22 LVICDECGAELE 33 (54)
T ss_pred EEeCCCCCCEEE
Confidence 468999997653
No 155
>KOG4167|consensus
Probab=50.14 E-value=4.1 Score=33.93 Aligned_cols=25 Identities=24% Similarity=0.449 Sum_probs=22.2
Q ss_pred cccCccchhccCCchHHHHHHhhhC
Q psy9067 163 PYACDICHARFTQSNSLKSHRLIHT 187 (189)
Q Consensus 163 ~~~C~~C~~~f~~~~~l~~H~~~h~ 187 (189)
.|-|..|++.|-.-..++.||++|.
T Consensus 792 iFpCreC~kvF~KiKSrNAHMK~Hr 816 (907)
T KOG4167|consen 792 IFPCRECGKVFFKIKSRNAHMKTHR 816 (907)
T ss_pred eeehHHHHHHHHHHhhhhHHHHHHH
Confidence 4889999999998888999999884
No 156
>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=50.11 E-value=7.4 Score=21.69 Aligned_cols=27 Identities=22% Similarity=0.484 Sum_probs=10.3
Q ss_pred ccCCCCCccccchHHHHhchhhcCCCCCccCccCCccCC
Q psy9067 108 HKCSICDYASVELSKMRNHMRSHTGERPYQCAHCTYASP 146 (189)
Q Consensus 108 ~~C~~C~~~~~~~~~l~~H~~~~~~~~~~~C~~C~~~f~ 146 (189)
-.|..|++.|... .+.+.|..||..|-
T Consensus 10 ~~C~~C~~~F~~~------------~rrhhCr~CG~~vC 36 (69)
T PF01363_consen 10 SNCMICGKKFSLF------------RRRHHCRNCGRVVC 36 (69)
T ss_dssp SB-TTT--B-BSS------------S-EEE-TTT--EEE
T ss_pred CcCcCcCCcCCCc------------eeeEccCCCCCEEC
Confidence 3677777777321 23456666665554
No 157
>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=50.10 E-value=5.3 Score=27.71 Aligned_cols=26 Identities=15% Similarity=0.303 Sum_probs=0.0
Q ss_pred EEeeeCCCcceeeechhHHHHHHhhC
Q psy9067 5 IYYWSDTTGYLRYHVMYLLARHLKSH 30 (189)
Q Consensus 5 ~~~~c~~c~~~~f~~~~~l~~h~~~~ 30 (189)
+.|.|.+||+..|.-+.++.+|-...
T Consensus 100 ~ey~CEICGN~~Y~GrkaFekHF~E~ 125 (196)
T PF11931_consen 100 VEYKCEICGNQSYKGRKAFEKHFQEW 125 (196)
T ss_dssp --------------------------
T ss_pred CeeeeEeCCCcceecHHHHHHhcChh
Confidence 45889999998888888888886553
No 158
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=49.91 E-value=2.4 Score=25.72 Aligned_cols=13 Identities=23% Similarity=0.559 Sum_probs=7.6
Q ss_pred CCCccCCCCCccc
Q psy9067 105 EKPHKCSICDYAS 117 (189)
Q Consensus 105 ~~~~~C~~C~~~~ 117 (189)
++.|.|+.||..-
T Consensus 20 ~k~FtCp~Cghe~ 32 (104)
T COG4888 20 PKTFTCPRCGHEK 32 (104)
T ss_pred CceEecCccCCee
Confidence 4556676666543
No 159
>KOG2071|consensus
Probab=49.80 E-value=16 Score=29.77 Aligned_cols=23 Identities=22% Similarity=0.371 Sum_probs=16.0
Q ss_pred eeCCCcceeeechhHHHHHHhhCC
Q psy9067 8 WSDTTGYLRYHVMYLLARHLKSHS 31 (189)
Q Consensus 8 ~c~~c~~~~f~~~~~l~~h~~~~~ 31 (189)
.|..|| .+|.......+||..|.
T Consensus 420 qC~~CG-~R~~~~ee~sk~md~H~ 442 (579)
T KOG2071|consen 420 QCKSCG-LRFDDSEERSKHMDIHD 442 (579)
T ss_pred hhcccc-cccccchhhhhHhhhhh
Confidence 477777 57777777777766665
No 160
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=49.66 E-value=10 Score=19.68 Aligned_cols=11 Identities=18% Similarity=0.338 Sum_probs=5.5
Q ss_pred cccCCCCCccc
Q psy9067 35 PHKCSVCERGF 45 (189)
Q Consensus 35 ~~~C~~C~~~f 45 (189)
.+.|+.||..+
T Consensus 20 ~~vC~~Cg~~~ 30 (52)
T smart00661 20 RFVCRKCGYEE 30 (52)
T ss_pred EEECCcCCCeE
Confidence 34555555443
No 161
>PRK12496 hypothetical protein; Provisional
Probab=49.63 E-value=11 Score=25.36 Aligned_cols=26 Identities=23% Similarity=0.584 Sum_probs=16.2
Q ss_pred ccCccCCccCCChHHHHHHHHHhhCCCcccCccchhcc
Q psy9067 136 YQCAHCTYASPDTFKLKRHLRIHTGEKPYACDICHARF 173 (189)
Q Consensus 136 ~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f 173 (189)
+.|+.|++.|... ...-.|++||...
T Consensus 128 ~~C~gC~~~~~~~------------~~~~~C~~CG~~~ 153 (164)
T PRK12496 128 KVCKGCKKKYPED------------YPDDVCEICGSPV 153 (164)
T ss_pred EECCCCCccccCC------------CCCCcCCCCCChh
Confidence 6788888777532 1123588888543
No 162
>COG5216 Uncharacterized conserved protein [Function unknown]
Probab=49.52 E-value=25 Score=19.04 Aligned_cols=36 Identities=14% Similarity=0.341 Sum_probs=20.7
Q ss_pred cceEEeeeCCCcceeeechhHHHHHHhhCCCCCcccCCCCCc
Q psy9067 2 VNTIYYWSDTTGYLRYHVMYLLARHLKSHSEERPHKCSVCER 43 (189)
Q Consensus 2 ~~~~~~~c~~c~~~~f~~~~~l~~h~~~~~~~~~~~C~~C~~ 43 (189)
.+++.++-+.||. +|..... -...++..-.|+.|.-
T Consensus 17 e~~~ftyPCPCGD-RFeIsLe-----Dl~~GE~VArCPSCSL 52 (67)
T COG5216 17 EEKTFTYPCPCGD-RFEISLE-----DLRNGEVVARCPSCSL 52 (67)
T ss_pred CCceEEecCCCCC-EeEEEHH-----HhhCCceEEEcCCceE
Confidence 3555566667884 7765533 1123566667777753
No 163
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=49.34 E-value=5.3 Score=18.93 Aligned_cols=11 Identities=27% Similarity=0.637 Sum_probs=6.0
Q ss_pred cccCccchhcc
Q psy9067 163 PYACDICHARF 173 (189)
Q Consensus 163 ~~~C~~C~~~f 173 (189)
-+.|..||..|
T Consensus 21 ~~~C~~Cg~~~ 31 (33)
T PF08792_consen 21 YEVCIFCGSSF 31 (33)
T ss_pred eEEcccCCcEe
Confidence 34566665554
No 164
>KOG1280|consensus
Probab=49.17 E-value=17 Score=27.54 Aligned_cols=36 Identities=17% Similarity=0.295 Sum_probs=26.1
Q ss_pred cccCCCCCccccchhhHHHHHhhcCCCCC--cccccCc
Q psy9067 35 PHKCSVCERGFKTIASLQNHINTHTGVKP--HKCKYCE 70 (189)
Q Consensus 35 ~~~C~~C~~~f~~~~~l~~H~~~~~~~~~--~~C~~C~ 70 (189)
.|.|+.|++.=.....+..|....+.+-+ -.|++|+
T Consensus 79 SftCPyC~~~Gfte~~f~~Hv~s~Hpda~~~~icp~c~ 116 (381)
T KOG1280|consen 79 SFTCPYCGIMGFTERQFGTHVLSQHPEASTSVICPLCA 116 (381)
T ss_pred cccCCcccccccchhHHHHHhhhcCcccCcceeeeccc
Confidence 48888898887777888888887766554 3455554
No 165
>TIGR00280 L37a ribosomal protein L37a. This model finds eukaryotic ribosomal protein L37a and its archaeal orthologs. The nomeclature is tricky because eukaryotes have proteins called both L37 and L37a.
Probab=48.45 E-value=5.8 Score=23.75 Aligned_cols=33 Identities=15% Similarity=0.444 Sum_probs=22.4
Q ss_pred CcccCCCCCccccchhhHHHHHhhcCCCCCcccccCcccCCCh
Q psy9067 34 RPHKCSVCERGFKTIASLQNHINTHTGVKPHKCKYCESRFTTS 76 (189)
Q Consensus 34 ~~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~C~~C~~~f~~~ 76 (189)
..|.|+.|++.- ..-.....+.|..|+..|.--
T Consensus 34 a~y~CpfCgk~~----------vkR~a~GIW~C~~C~~~~AGG 66 (91)
T TIGR00280 34 AKYVCPFCGKKT----------VKRGSTGIWTCRKCGAKFAGG 66 (91)
T ss_pred cCccCCCCCCCc----------eEEEeeEEEEcCCCCCEEeCC
Confidence 358899998652 122344568999999987643
No 166
>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=47.63 E-value=5.9 Score=27.97 Aligned_cols=30 Identities=20% Similarity=0.376 Sum_probs=21.8
Q ss_pred CCCCccCCCCCccccchHHHHhchhhcCCC
Q psy9067 104 HEKPHKCSICDYASVELSKMRNHMRSHTGE 133 (189)
Q Consensus 104 ~~~~~~C~~C~~~~~~~~~l~~H~~~~~~~ 133 (189)
.+.-|.|+.|+|.|....-..+|+..-+.+
T Consensus 74 ~~~K~~C~lc~KlFkg~eFV~KHI~nKH~e 103 (214)
T PF04959_consen 74 DEDKWRCPLCGKLFKGPEFVRKHIFNKHPE 103 (214)
T ss_dssp SSEEEEE-SSS-EESSHHHHHHHHHHH-HH
T ss_pred cCCEECCCCCCcccCChHHHHHHHhhcCHH
Confidence 344599999999999999999998765443
No 167
>COG3091 SprT Zn-dependent metalloprotease, SprT family [General function prediction only]
Probab=47.57 E-value=7 Score=25.82 Aligned_cols=34 Identities=32% Similarity=0.807 Sum_probs=21.3
Q ss_pred CCccCccCCccCCChHHHHHHHHHhhCCCcccCccchhc
Q psy9067 134 RPYQCAHCTYASPDTFKLKRHLRIHTGEKPYACDICHAR 172 (189)
Q Consensus 134 ~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~ 172 (189)
-+|.|. |+..|.+. +.|-.+-.|+ .|.|..|+..
T Consensus 116 ~~Y~C~-C~q~~l~~---RRhn~~~~g~-~YrC~~C~gk 149 (156)
T COG3091 116 YPYRCQ-CQQHYLRI---RRHNTVRRGE-VYRCGKCGGK 149 (156)
T ss_pred eeEEee-cCCccchh---hhcccccccc-eEEeccCCce
Confidence 457787 87765543 4454444555 7888888654
No 168
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=47.37 E-value=11 Score=28.20 Aligned_cols=15 Identities=13% Similarity=0.242 Sum_probs=8.0
Q ss_pred CCCccCccCCccCCC
Q psy9067 133 ERPYQCAHCTYASPD 147 (189)
Q Consensus 133 ~~~~~C~~C~~~f~~ 147 (189)
.+...|..|+...+.
T Consensus 250 ~r~e~C~~C~~YlK~ 264 (309)
T PRK03564 250 VKAESCGDCGTYLKI 264 (309)
T ss_pred eEeeeccccccccee
Confidence 345566666644443
No 169
>KOG1842|consensus
Probab=46.83 E-value=20 Score=28.19 Aligned_cols=26 Identities=15% Similarity=0.478 Sum_probs=16.7
Q ss_pred ccCCCCCccccchhhHHHHHhhcCCC
Q psy9067 36 HKCSVCERGFKTIASLQNHINTHTGV 61 (189)
Q Consensus 36 ~~C~~C~~~f~~~~~l~~H~~~~~~~ 61 (189)
|.||+|...|.+...|..|....|++
T Consensus 16 flCPiC~~dl~~~~~L~~H~d~eH~~ 41 (505)
T KOG1842|consen 16 FLCPICLLDLPNLSALNDHLDVEHFE 41 (505)
T ss_pred ccCchHhhhhhhHHHHHHHHhhhccc
Confidence 56777776666666666666654433
No 170
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=46.79 E-value=9.7 Score=23.88 Aligned_cols=11 Identities=18% Similarity=0.404 Sum_probs=4.9
Q ss_pred ccCccCCccCC
Q psy9067 136 YQCAHCTYASP 146 (189)
Q Consensus 136 ~~C~~C~~~f~ 146 (189)
..|+.|+..|.
T Consensus 71 ~~C~~Cg~~~~ 81 (113)
T PRK12380 71 AWCWDCSQVVE 81 (113)
T ss_pred EEcccCCCEEe
Confidence 44445544333
No 171
>KOG3408|consensus
Probab=46.23 E-value=13 Score=23.55 Aligned_cols=27 Identities=26% Similarity=0.502 Sum_probs=21.8
Q ss_pred CCCCCccCccCCccCCChHHHHHHHHH
Q psy9067 131 TGERPYQCAHCTYASPDTFKLKRHLRI 157 (189)
Q Consensus 131 ~~~~~~~C~~C~~~f~~~~~l~~H~~~ 157 (189)
.|...|.|-.|.+-|.....|..|.++
T Consensus 53 PG~GqfyCi~CaRyFi~~~~l~~H~kt 79 (129)
T KOG3408|consen 53 PGGGQFYCIECARYFIDAKALKTHFKT 79 (129)
T ss_pred CCCceeehhhhhhhhcchHHHHHHHhc
Confidence 345668999999999999999988764
No 172
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=45.80 E-value=11 Score=19.84 Aligned_cols=9 Identities=22% Similarity=0.733 Sum_probs=4.0
Q ss_pred cccCccchh
Q psy9067 163 PYACDICHA 171 (189)
Q Consensus 163 ~~~C~~C~~ 171 (189)
.+.|..||.
T Consensus 37 r~~C~~Cgy 45 (50)
T PRK00432 37 RWHCGKCGY 45 (50)
T ss_pred cEECCCcCC
Confidence 344444443
No 173
>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=44.51 E-value=12 Score=23.62 Aligned_cols=11 Identities=18% Similarity=0.691 Sum_probs=5.1
Q ss_pred ccCccCCccCC
Q psy9067 136 YQCAHCTYASP 146 (189)
Q Consensus 136 ~~C~~C~~~f~ 146 (189)
..|+.|+..|.
T Consensus 71 ~~C~~Cg~~~~ 81 (115)
T TIGR00100 71 CECEDCSEEVS 81 (115)
T ss_pred EEcccCCCEEe
Confidence 44555554443
No 174
>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=44.35 E-value=15 Score=22.75 Aligned_cols=16 Identities=25% Similarity=0.326 Sum_probs=10.8
Q ss_pred CCCccCCCCCccccch
Q psy9067 105 EKPHKCSICDYASVEL 120 (189)
Q Consensus 105 ~~~~~C~~C~~~~~~~ 120 (189)
...|.|+.|+-.+...
T Consensus 17 g~~~iCpeC~~EW~~~ 32 (109)
T TIGR00686 17 GTQLICPSCLYEWNEN 32 (109)
T ss_pred CCeeECcccccccccc
Confidence 3457888888776544
No 175
>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=44.23 E-value=16 Score=19.32 Aligned_cols=27 Identities=19% Similarity=0.328 Sum_probs=16.1
Q ss_pred cCCCCCccccchHHHHhchhhcCCCCCccCccCCccCCC
Q psy9067 109 KCSICDYASVELSKMRNHMRSHTGERPYQCAHCTYASPD 147 (189)
Q Consensus 109 ~C~~C~~~~~~~~~l~~H~~~~~~~~~~~C~~C~~~f~~ 147 (189)
.|..|++.|.. ..+...|..||+.|-.
T Consensus 4 ~C~~C~~~F~~------------~~rk~~Cr~Cg~~~C~ 30 (57)
T cd00065 4 SCMGCGKPFTL------------TRRRHHCRNCGRIFCS 30 (57)
T ss_pred cCcccCccccC------------CccccccCcCcCCcCh
Confidence 46667766654 1234567777776664
No 176
>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=43.95 E-value=5.2 Score=23.91 Aligned_cols=31 Identities=23% Similarity=0.534 Sum_probs=19.7
Q ss_pred CcccCCCCCccccchhhHHHHHhhcCCCCCcccccCcccCC
Q psy9067 34 RPHKCSVCERGFKTIASLQNHINTHTGVKPHKCKYCESRFT 74 (189)
Q Consensus 34 ~~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~C~~C~~~f~ 74 (189)
..|.|+.|++.- ..-.....+.|..|+..|.
T Consensus 34 ~ky~Cp~Cgk~~----------vkR~a~GIW~C~~C~~~~A 64 (90)
T PF01780_consen 34 AKYTCPFCGKTS----------VKRVATGIWKCKKCGKKFA 64 (90)
T ss_dssp S-BEESSSSSSE----------EEEEETTEEEETTTTEEEE
T ss_pred CCCcCCCCCCce----------eEEeeeEEeecCCCCCEEe
Confidence 358899998763 1122334588999988764
No 177
>PRK10220 hypothetical protein; Provisional
Probab=43.66 E-value=18 Score=22.50 Aligned_cols=17 Identities=12% Similarity=0.149 Sum_probs=11.0
Q ss_pred CCCccCCCCCccccchH
Q psy9067 105 EKPHKCSICDYASVELS 121 (189)
Q Consensus 105 ~~~~~C~~C~~~~~~~~ 121 (189)
...|.|+.|+-.+....
T Consensus 18 ~~~~vCpeC~hEW~~~~ 34 (111)
T PRK10220 18 NGMYICPECAHEWNDAE 34 (111)
T ss_pred CCeEECCcccCcCCccc
Confidence 34578888877765543
No 178
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=43.60 E-value=11 Score=18.62 Aligned_cols=15 Identities=13% Similarity=0.335 Sum_probs=6.7
Q ss_pred ccCCCCCccccchhh
Q psy9067 36 HKCSVCERGFKTIAS 50 (189)
Q Consensus 36 ~~C~~C~~~f~~~~~ 50 (189)
..|+.|+-.+.+...
T Consensus 20 d~C~~C~G~W~d~~e 34 (41)
T PF13453_consen 20 DVCPSCGGIWFDAGE 34 (41)
T ss_pred EECCCCCeEEccHHH
Confidence 345555444444333
No 179
>PF14787 zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB: 1CL4_A 1DSV_A.
Probab=43.28 E-value=11 Score=18.28 Aligned_cols=15 Identities=20% Similarity=0.403 Sum_probs=8.9
Q ss_pred ccCccchhccCCchH
Q psy9067 164 YACDICHARFTQSNS 178 (189)
Q Consensus 164 ~~C~~C~~~f~~~~~ 178 (189)
-.|+.|+++|-+.++
T Consensus 3 ~~CprC~kg~Hwa~~ 17 (36)
T PF14787_consen 3 GLCPRCGKGFHWASE 17 (36)
T ss_dssp -C-TTTSSSCS-TTT
T ss_pred ccCcccCCCcchhhh
Confidence 458888888877654
No 180
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=42.96 E-value=13 Score=23.47 Aligned_cols=11 Identities=18% Similarity=0.627 Sum_probs=5.4
Q ss_pred ccCccCCccCC
Q psy9067 136 YQCAHCTYASP 146 (189)
Q Consensus 136 ~~C~~C~~~f~ 146 (189)
..|..|+..|.
T Consensus 72 ~~C~~Cg~~~~ 82 (117)
T PRK00564 72 LECKDCSHVFK 82 (117)
T ss_pred EEhhhCCCccc
Confidence 45555554443
No 181
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=42.52 E-value=7.4 Score=23.27 Aligned_cols=33 Identities=27% Similarity=0.649 Sum_probs=22.0
Q ss_pred CcccCCCCCccccchhhHHHHHhhcCCCCCcccccCcccCCCh
Q psy9067 34 RPHKCSVCERGFKTIASLQNHINTHTGVKPHKCKYCESRFTTS 76 (189)
Q Consensus 34 ~~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~C~~C~~~f~~~ 76 (189)
..|.|+.|++.- ..-.....+.|..|+..|.--
T Consensus 35 a~y~CpfCgk~~----------vkR~a~GIW~C~~C~~~~AGG 67 (90)
T PRK03976 35 AKHVCPVCGRPK----------VKRVGTGIWECRKCGAKFAGG 67 (90)
T ss_pred cCccCCCCCCCc----------eEEEEEEEEEcCCCCCEEeCC
Confidence 358899997652 122344568899999887643
No 182
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=41.67 E-value=12 Score=18.48 Aligned_cols=13 Identities=23% Similarity=0.646 Sum_probs=9.2
Q ss_pred cccCccchhccCC
Q psy9067 163 PYACDICHARFTQ 175 (189)
Q Consensus 163 ~~~C~~C~~~f~~ 175 (189)
|++|..|+..|=.
T Consensus 12 ~f~C~~C~~~FC~ 24 (39)
T smart00154 12 GFKCRHCGNLFCG 24 (39)
T ss_pred CeECCccCCcccc
Confidence 6778888777643
No 183
>KOG2272|consensus
Probab=41.47 E-value=28 Score=25.22 Aligned_cols=42 Identities=12% Similarity=0.298 Sum_probs=23.3
Q ss_pred eCCCcceeeechhHHHHHHhhCCCCCcccCCCCCccccchhhHHH
Q psy9067 9 SDTTGYLRYHVMYLLARHLKSHSEERPHKCSVCERGFKTIASLQN 53 (189)
Q Consensus 9 c~~c~~~~f~~~~~l~~h~~~~~~~~~~~C~~C~~~f~~~~~l~~ 53 (189)
|..|+ .|.....+..--.+.++ .-|.|+.|++...+...+..
T Consensus 76 C~kC~--EFiiGrVikamnnSwHp-~CF~Cd~Cn~~Lad~gf~rn 117 (332)
T KOG2272|consen 76 CGKCG--EFIIGRVIKAMNNSWHP-ACFRCDLCNKHLADQGFYRN 117 (332)
T ss_pred hcccc--cchhhHHHHhhccccCc-ccchhHHHHHHHhhhhhHhh
Confidence 34444 45554444333334433 34788888888776665543
No 184
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=41.12 E-value=35 Score=18.35 Aligned_cols=14 Identities=14% Similarity=0.641 Sum_probs=7.3
Q ss_pred CCCccCccCCccCC
Q psy9067 133 ERPYQCAHCTYASP 146 (189)
Q Consensus 133 ~~~~~C~~C~~~f~ 146 (189)
...|.|+.||..+.
T Consensus 12 ~v~~~Cp~cGipth 25 (55)
T PF13824_consen 12 HVNFECPDCGIPTH 25 (55)
T ss_pred ccCCcCCCCCCcCc
Confidence 34456666664443
No 185
>PF13963 Transpos_assoc: Transposase-associated domain
Probab=40.87 E-value=30 Score=19.95 Aligned_cols=24 Identities=13% Similarity=0.373 Sum_probs=12.0
Q ss_pred ccCCCCC-ccccchhhHHHHHhhcC
Q psy9067 36 HKCSVCE-RGFKTIASLQNHINTHT 59 (189)
Q Consensus 36 ~~C~~C~-~~f~~~~~l~~H~~~~~ 59 (189)
.+|..|. ..+.....+..|+....
T Consensus 40 CPC~~C~N~~~~~~~~V~~HL~~~G 64 (77)
T PF13963_consen 40 CPCRKCKNEKRQSRDDVHEHLVCRG 64 (77)
T ss_pred CCchhhccCccCCHHHHHHHHHHhC
Confidence 3444553 44455555566655543
No 186
>KOG1280|consensus
Probab=40.60 E-value=23 Score=26.94 Aligned_cols=38 Identities=16% Similarity=0.437 Sum_probs=28.7
Q ss_pred CCCccCccCCccCCChHHHHHHHHHhhCCCc--ccCccch
Q psy9067 133 ERPYQCAHCTYASPDTFKLKRHLRIHTGEKP--YACDICH 170 (189)
Q Consensus 133 ~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~--~~C~~C~ 170 (189)
...|.|+.|+.+=.+...|..|....+-+.+ ..|++|+
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 4579999999888888899999876544433 4677775
No 187
>PF14311 DUF4379: Domain of unknown function (DUF4379)
Probab=40.51 E-value=25 Score=18.62 Aligned_cols=15 Identities=20% Similarity=0.319 Sum_probs=9.8
Q ss_pred ccCCCCCccccchHH
Q psy9067 108 HKCSICDYASVELSK 122 (189)
Q Consensus 108 ~~C~~C~~~~~~~~~ 122 (189)
++|+.||-.|...-.
T Consensus 29 W~C~~Cgh~w~~~v~ 43 (55)
T PF14311_consen 29 WKCPKCGHEWKASVN 43 (55)
T ss_pred EECCCCCCeeEccHh
Confidence 677777766665544
No 188
>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=40.32 E-value=11 Score=18.80 Aligned_cols=9 Identities=22% Similarity=0.464 Sum_probs=3.8
Q ss_pred cccccCccc
Q psy9067 64 HKCKYCESR 72 (189)
Q Consensus 64 ~~C~~C~~~ 72 (189)
+.|..||..
T Consensus 20 ~vC~~CG~V 28 (43)
T PF08271_consen 20 LVCPNCGLV 28 (43)
T ss_dssp EEETTT-BB
T ss_pred EECCCCCCE
Confidence 455555443
No 189
>KOG2071|consensus
Probab=40.09 E-value=19 Score=29.38 Aligned_cols=27 Identities=33% Similarity=0.630 Sum_probs=23.0
Q ss_pred CCCcccCccchhccCCchHHHHHHhhh
Q psy9067 160 GEKPYACDICHARFTQSNSLKSHRLIH 186 (189)
Q Consensus 160 ~~~~~~C~~C~~~f~~~~~l~~H~~~h 186 (189)
...+.+|..||..|.......+||..|
T Consensus 415 ~~~pnqC~~CG~R~~~~ee~sk~md~H 441 (579)
T KOG2071|consen 415 KDSPNQCKSCGLRFDDSEERSKHMDIH 441 (579)
T ss_pred cCCcchhcccccccccchhhhhHhhhh
Confidence 356789999999999998888888776
No 190
>PF05207 zf-CSL: CSL zinc finger; InterPro: IPR007872 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a probable zinc binding motif that contains four cysteines and may chelate zinc, known as the DPH-type after the diphthamide (DPH) biosynthesis protein in which it was first characterised, including the proteins DPH3 and DPH4. This domain is also found associated with N-terminal domain of heat shock protein DnaJ IPR001623 from INTERPRO domain. Diphthamide is a unique post-translationally modified histidine residue found only in translation elongation factor 2 (eEF-2). It is conserved from archaea to humans and serves as the target for diphteria toxin and Pseudomonas exotoxin A. These two toxins catalyse the transfer of ADP-ribose to diphtamide on eEF-2, thus inactivating eEF-2, halting cellular protein synthesis, and causing cell death []. The biosynthesis of diphtamide is dependent on at least five proteins, DPH1 to -5, and a still unidentified amidating enzyme. DPH3 and DPH4 share a conserved region, which encode a putative zinc finger, the DPH-type or CSL-type (after the conserved motif of the final cysteine) zinc finger [, ]. The function of this motif is unknown. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 2L6L_A 1WGE_A 2JR7_A 1YOP_A 1YWS_A.
Probab=39.89 E-value=35 Score=18.27 Aligned_cols=33 Identities=18% Similarity=0.039 Sum_probs=17.3
Q ss_pred eEEeeeCCCcceeeechhHHHHHHhhCCCCCcccCCCCCc
Q psy9067 4 TIYYWSDTTGYLRYHVMYLLARHLKSHSEERPHKCSVCER 43 (189)
Q Consensus 4 ~~~~~c~~c~~~~f~~~~~l~~h~~~~~~~~~~~C~~C~~ 43 (189)
...|.| .||....-+...|... .....|+.|.-
T Consensus 16 ~~~y~C-RCG~~f~i~e~~l~~~------~~iv~C~sCSL 48 (55)
T PF05207_consen 16 VYSYPC-RCGGEFEISEEDLEEG------EVIVQCDSCSL 48 (55)
T ss_dssp EEEEEE-TTSSEEEEEHHHHHCT--------EEEETTTTE
T ss_pred EEEEcC-CCCCEEEEcchhccCc------CEEEECCCCcc
Confidence 355667 8886533333444333 44566777754
No 191
>PRK14873 primosome assembly protein PriA; Provisional
Probab=39.78 E-value=22 Score=29.90 Aligned_cols=25 Identities=20% Similarity=0.531 Sum_probs=15.9
Q ss_pred CCCCccCccCCccCCChHHHHHHHHHhhCCCcccCccchhc
Q psy9067 132 GERPYQCAHCTYASPDTFKLKRHLRIHTGEKPYACDICHAR 172 (189)
Q Consensus 132 ~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~ 172 (189)
..+...|..||.. ..+..|+.||..
T Consensus 407 ~~~~l~Ch~CG~~----------------~~p~~Cp~Cgs~ 431 (665)
T PRK14873 407 AGGTPRCRWCGRA----------------APDWRCPRCGSD 431 (665)
T ss_pred CCCeeECCCCcCC----------------CcCccCCCCcCC
Confidence 3456678888732 236788888753
No 192
>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=38.97 E-value=11 Score=19.89 Aligned_cols=11 Identities=18% Similarity=0.800 Sum_probs=5.7
Q ss_pred cCccchhccCC
Q psy9067 165 ACDICHARFTQ 175 (189)
Q Consensus 165 ~C~~C~~~f~~ 175 (189)
.||+|+..|..
T Consensus 22 ~CPlC~r~l~~ 32 (54)
T PF04423_consen 22 CCPLCGRPLDE 32 (54)
T ss_dssp E-TTT--EE-H
T ss_pred cCCCCCCCCCH
Confidence 89999988874
No 193
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=38.81 E-value=49 Score=30.04 Aligned_cols=10 Identities=30% Similarity=0.763 Sum_probs=6.6
Q ss_pred CccCCCCCcc
Q psy9067 107 PHKCSICDYA 116 (189)
Q Consensus 107 ~~~C~~C~~~ 116 (189)
...|+.||..
T Consensus 709 a~~CP~CGtp 718 (1337)
T PRK14714 709 RVECPRCDVE 718 (1337)
T ss_pred cccCCCCCCc
Confidence 3468888844
No 194
>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=38.57 E-value=10 Score=19.07 Aligned_cols=14 Identities=29% Similarity=0.819 Sum_probs=7.6
Q ss_pred CcccCccchhccCC
Q psy9067 162 KPYACDICHARFTQ 175 (189)
Q Consensus 162 ~~~~C~~C~~~f~~ 175 (189)
-++.|..|+..|=.
T Consensus 12 ~~~~C~~C~~~FC~ 25 (43)
T PF01428_consen 12 LPFKCKHCGKSFCL 25 (43)
T ss_dssp SHEE-TTTS-EE-T
T ss_pred CCeECCCCCcccCc
Confidence 36778888877643
No 195
>KOG2923|consensus
Probab=38.51 E-value=49 Score=18.35 Aligned_cols=36 Identities=22% Similarity=0.468 Sum_probs=21.5
Q ss_pred cceEEeeeCCCcceeeechhHHHHHHhhCCCCCcccCCCCCc
Q psy9067 2 VNTIYYWSDTTGYLRYHVMYLLARHLKSHSEERPHKCSVCER 43 (189)
Q Consensus 2 ~~~~~~~c~~c~~~~f~~~~~l~~h~~~~~~~~~~~C~~C~~ 43 (189)
.|.++|.-+.||. .|.....- -..++..-.|+-|.-
T Consensus 17 e~~~y~yPCpCGD-rf~It~ed-----L~~ge~Va~CpsCSL 52 (67)
T KOG2923|consen 17 ENQTYYYPCPCGD-RFQITLED-----LENGEDVARCPSCSL 52 (67)
T ss_pred CCCeEEcCCCCCC-eeeecHHH-----HhCCCeeecCCCceE
Confidence 4667777778885 56654331 123555667777753
No 196
>KOG3408|consensus
Probab=38.12 E-value=21 Score=22.63 Aligned_cols=26 Identities=23% Similarity=0.434 Sum_probs=22.4
Q ss_pred CCcccCccchhccCCchHHHHHHhhh
Q psy9067 161 EKPYACDICHARFTQSNSLKSHRLIH 186 (189)
Q Consensus 161 ~~~~~C~~C~~~f~~~~~l~~H~~~h 186 (189)
--.|-|-.|.+-|.+...|..|.++.
T Consensus 55 ~GqfyCi~CaRyFi~~~~l~~H~ktK 80 (129)
T KOG3408|consen 55 GGQFYCIECARYFIDAKALKTHFKTK 80 (129)
T ss_pred CceeehhhhhhhhcchHHHHHHHhcc
Confidence 34589999999999999999998753
No 197
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=37.97 E-value=22 Score=27.93 Aligned_cols=14 Identities=21% Similarity=0.688 Sum_probs=9.1
Q ss_pred cccCccchhccCCc
Q psy9067 163 PYACDICHARFTQS 176 (189)
Q Consensus 163 ~~~C~~C~~~f~~~ 176 (189)
-|+|+.||..+...
T Consensus 367 g~rC~kCg~~~~~~ 380 (421)
T COG1571 367 GFRCKKCGTRARET 380 (421)
T ss_pred CcccccccccCCcc
Confidence 67777777666543
No 198
>TIGR00595 priA primosomal protein N'. All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=37.85 E-value=28 Score=28.25 Aligned_cols=10 Identities=30% Similarity=0.803 Sum_probs=6.1
Q ss_pred CcccCccchh
Q psy9067 162 KPYACDICHA 171 (189)
Q Consensus 162 ~~~~C~~C~~ 171 (189)
-|..|+.||.
T Consensus 252 ~~~~Cp~C~s 261 (505)
T TIGR00595 252 IPKTCPQCGS 261 (505)
T ss_pred CCCCCCCCCC
Confidence 3566777764
No 199
>KOG2907|consensus
Probab=37.81 E-value=13 Score=23.12 Aligned_cols=13 Identities=38% Similarity=0.950 Sum_probs=9.6
Q ss_pred cccCccchhccCC
Q psy9067 163 PYACDICHARFTQ 175 (189)
Q Consensus 163 ~~~C~~C~~~f~~ 175 (189)
-|.|+.|++.|+.
T Consensus 102 FYTC~kC~~k~~e 114 (116)
T KOG2907|consen 102 FYTCPKCKYKFTE 114 (116)
T ss_pred EEEcCccceeeec
Confidence 3788888887764
No 200
>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=37.59 E-value=7.5 Score=24.36 Aligned_cols=12 Identities=17% Similarity=0.379 Sum_probs=5.2
Q ss_pred ccCCCCCccccc
Q psy9067 108 HKCSICDYASVE 119 (189)
Q Consensus 108 ~~C~~C~~~~~~ 119 (189)
..|..||..|..
T Consensus 71 ~~C~~Cg~~~~~ 82 (113)
T PF01155_consen 71 ARCRDCGHEFEP 82 (113)
T ss_dssp EEETTTS-EEEC
T ss_pred EECCCCCCEEec
Confidence 345555554433
No 201
>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=37.54 E-value=4.7 Score=18.32 Aligned_cols=10 Identities=30% Similarity=0.923 Sum_probs=6.5
Q ss_pred ccCccchhcc
Q psy9067 164 YACDICHARF 173 (189)
Q Consensus 164 ~~C~~C~~~f 173 (189)
|.|-.|++.|
T Consensus 1 ~sCiDC~~~F 10 (28)
T PF08790_consen 1 FSCIDCSKDF 10 (28)
T ss_dssp EEETTTTEEE
T ss_pred CeeecCCCCc
Confidence 3566677777
No 202
>PF13821 DUF4187: Domain of unknown function (DUF4187)
Probab=37.02 E-value=29 Score=18.61 Aligned_cols=19 Identities=16% Similarity=0.443 Sum_probs=13.6
Q ss_pred ccCCCCCccccchhhHHHH
Q psy9067 36 HKCSVCERGFKTIASLQNH 54 (189)
Q Consensus 36 ~~C~~C~~~f~~~~~l~~H 54 (189)
+.|-+||..|.+...|..+
T Consensus 28 ~YC~~Cg~~Y~d~~dL~~~ 46 (55)
T PF13821_consen 28 NYCFWCGTKYDDEEDLERN 46 (55)
T ss_pred ceeeeeCCccCCHHHHHhC
Confidence 5688888888777766544
No 203
>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=36.91 E-value=23 Score=28.31 Aligned_cols=22 Identities=18% Similarity=0.392 Sum_probs=12.5
Q ss_pred CccCccCCccCCChHHHHHHHH
Q psy9067 135 PYQCAHCTYASPDTFKLKRHLR 156 (189)
Q Consensus 135 ~~~C~~C~~~f~~~~~l~~H~~ 156 (189)
-+.|+.|.+.|.....+..|+.
T Consensus 57 FWiCp~CskkF~d~~~~~~H~~ 78 (466)
T PF04780_consen 57 FWICPRCSKKFSDAESCLSHME 78 (466)
T ss_pred EeeCCcccceeCCHHHHHHHHH
Confidence 3455556655666555555554
No 204
>KOG4167|consensus
Probab=36.19 E-value=10 Score=31.83 Aligned_cols=29 Identities=14% Similarity=0.244 Sum_probs=16.4
Q ss_pred CCCCcccccCcccCCChhHHHhhhhhhcC
Q psy9067 60 GVKPHKCKYCESRFTTSGELVRHVRYKHT 88 (189)
Q Consensus 60 ~~~~~~C~~C~~~f~~~~~l~~h~~~~h~ 88 (189)
....|.|..|++.|....++..||+.|..
T Consensus 789 ~~giFpCreC~kvF~KiKSrNAHMK~Hr~ 817 (907)
T KOG4167|consen 789 PTGIFPCRECGKVFFKIKSRNAHMKTHRQ 817 (907)
T ss_pred CCceeehHHHHHHHHHHhhhhHHHHHHHH
Confidence 34445566666666666666666655433
No 205
>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=36.00 E-value=30 Score=19.17 Aligned_cols=29 Identities=17% Similarity=0.455 Sum_probs=17.4
Q ss_pred ccCCCCCccccchhhHHHHHhhcCCCCCcccccCcccCC
Q psy9067 36 HKCSVCERGFKTIASLQNHINTHTGVKPHKCKYCESRFT 74 (189)
Q Consensus 36 ~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~C~~C~~~f~ 74 (189)
-.|+.||..-.. ......|.|+.||..+.
T Consensus 29 q~C~~CG~~~~~----------~~~~r~~~C~~Cg~~~~ 57 (69)
T PF07282_consen 29 QTCPRCGHRNKK----------RRSGRVFTCPNCGFEMD 57 (69)
T ss_pred cCccCccccccc----------ccccceEEcCCCCCEEC
Confidence 357777766433 23445677777776644
No 206
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=35.69 E-value=19 Score=22.67 Aligned_cols=9 Identities=22% Similarity=0.578 Sum_probs=4.1
Q ss_pred ccCccCCcc
Q psy9067 136 YQCAHCTYA 144 (189)
Q Consensus 136 ~~C~~C~~~ 144 (189)
..|..|+..
T Consensus 71 ~~C~~Cg~~ 79 (114)
T PRK03681 71 CWCETCQQY 79 (114)
T ss_pred EEcccCCCe
Confidence 444445433
No 207
>KOG2906|consensus
Probab=34.85 E-value=3.2 Score=25.06 Aligned_cols=17 Identities=29% Similarity=0.639 Sum_probs=11.2
Q ss_pred CcccccCcccCCChhHH
Q psy9067 63 PHKCKYCESRFTTSGEL 79 (189)
Q Consensus 63 ~~~C~~C~~~f~~~~~l 79 (189)
.|.|+.|+..|.....+
T Consensus 21 rf~C~tCpY~~~I~~ei 37 (105)
T KOG2906|consen 21 RFSCRTCPYVFPISREI 37 (105)
T ss_pred eEEcCCCCceeeEeeee
Confidence 47777787777665443
No 208
>COG1327 Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains [Transcription]
Probab=34.68 E-value=9.2 Score=25.25 Aligned_cols=13 Identities=15% Similarity=0.329 Sum_probs=7.0
Q ss_pred ccCccCCccCCCh
Q psy9067 136 YQCAHCTYASPDT 148 (189)
Q Consensus 136 ~~C~~C~~~f~~~ 148 (189)
-.|+.|+.-|++-
T Consensus 29 ReC~~C~~RFTTf 41 (156)
T COG1327 29 RECLECGERFTTF 41 (156)
T ss_pred hcccccccccchh
Confidence 4555555555543
No 209
>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 PF05495 zf-CHY: CHY zinc finger; InterPro: IPR008913 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. Pirh2 is an eukaryotic ubiquitin protein ligase, which has been shown to promote p53 degradation in mammals. Pirh2 physically interacts with p53 and promotes ubiquitination of p53 independently of MDM2. Like MDM2, Pirh2 is thought to participate in an autoregulatory feedback loop that controls p53 function. Pirh2 proteins contain three distinct zinc fingers, the CHY-type, the CTCHY-type which is C-terminal to the CHY-type zinc finger and a RING finger. The CHY-type zinc finger has no currently known function []. As well as Pirh2, the CHY-type zinc finger is also found in the following proteins: Yeast helper of Tim protein 13. Hot13 may have a role in the assembly and recycling of the small Tims, a complex of the mitochondrial intermembrane space that participates in the TIM22 import pathway for assembly of the inner membrane [] Several plant hypothetical proteins that also contain haemerythrin cation binding domains Several protozoan hypothetical proteins that also contain a Myb domain The solution structure of this zinc finger has been solved and binds 3 zinc atoms as shown in the following schematic representation: ++---------+-----+ || | | CXHYxxxxxxxxxCCxxxxxCxxCHxxxxxHxxxxxxxxxxxCxxCxxxxxxxxxCxxC | | | | | | | | +-+-----------------+--+ +--+---------+--+ 'C': conserved cysteine involved in the binding of one zinc atom. 'H': conserved histidine involved in the binding of one zinc atom. More information about these proteins can be found at Protein of the Month: Zinc Fingers []; GO: 0008270 zinc ion binding; PDB: 2DKT_A 2K2C_A.
Probab=34.16 E-value=4.8 Score=22.88 Aligned_cols=58 Identities=19% Similarity=0.329 Sum_probs=24.6
Q ss_pred ccCCCCCccccch---HHHHhchhhcCCCCCccCccCCccCCChHHHHHHHHHhhCCCcccCccchhcc
Q psy9067 108 HKCSICDYASVEL---SKMRNHMRSHTGERPYQCAHCTYASPDTFKLKRHLRIHTGEKPYACDICHARF 173 (189)
Q Consensus 108 ~~C~~C~~~~~~~---~~l~~H~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f 173 (189)
++++-|++.|+-. +.+..|...........|-.|+........ ..+ ..+.|+.|+..|
T Consensus 11 ~~~~cC~~~y~C~~CHde~~~H~~~~~~~~~v~Cg~C~~~~~~~~~-------~c~-~~~~C~~C~~~~ 71 (71)
T PF05495_consen 11 IRFPCCGKYYPCRFCHDELEDHPFDRWPVKRVICGKCRTEQPIDEY-------SCG-ADYFCPICGLYF 71 (71)
T ss_dssp EEETTTTEEESSHHHHHHCSSS---TTT--EEEETTT--EEES-SB-------TT---SEEETTTTEEE
T ss_pred EECCcccCeecHHHHHHHhccCccccccccCeECCCCCCccChhhh-------hcC-CCccCcCcCCCC
Confidence 4455555555433 223344433333445667777655544322 011 457777777543
No 211
>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=34.02 E-value=17 Score=22.11 Aligned_cols=15 Identities=20% Similarity=0.490 Sum_probs=12.6
Q ss_pred CCCccCccCCccCCC
Q psy9067 133 ERPYQCAHCTYASPD 147 (189)
Q Consensus 133 ~~~~~C~~C~~~f~~ 147 (189)
.+|.+|+.||.+|..
T Consensus 77 g~~~rC~eCG~~fkL 91 (97)
T cd00924 77 GKPKRCPECGHVFKL 91 (97)
T ss_pred CCceeCCCCCcEEEE
Confidence 379999999998864
No 212
>PF10276 zf-CHCC: Zinc-finger domain; InterPro: IPR019401 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a short conserved zinc-finger domain. It contains the sequence motif Cx8Hx14Cx2C. ; PDB: 2JVM_A 2JRR_A 2JZ8_A.
Probab=33.79 E-value=14 Score=18.36 Aligned_cols=11 Identities=36% Similarity=1.126 Sum_probs=6.1
Q ss_pred cccCccchhcc
Q psy9067 163 PYACDICHARF 173 (189)
Q Consensus 163 ~~~C~~C~~~f 173 (189)
+..|+.||..|
T Consensus 29 ~~~CpYCg~~y 39 (40)
T PF10276_consen 29 PVVCPYCGTRY 39 (40)
T ss_dssp EEEETTTTEEE
T ss_pred eEECCCCCCEE
Confidence 45566666554
No 213
>TIGR00627 tfb4 transcription factor tfb4. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=33.61 E-value=28 Score=25.80 Aligned_cols=24 Identities=21% Similarity=0.596 Sum_probs=16.5
Q ss_pred ccCccCCccCCChHHHHHHHHHhhCCCcccCccchhcc
Q psy9067 136 YQCAHCTYASPDTFKLKRHLRIHTGEKPYACDICHARF 173 (189)
Q Consensus 136 ~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f 173 (189)
|.|++|.-.|.. -|-.|+.||..|
T Consensus 256 yvCs~Clsi~C~--------------~p~~C~~Cgt~f 279 (279)
T TIGR00627 256 FVCSVCLSVLCQ--------------YTPICKTCKTAF 279 (279)
T ss_pred EECCCccCCcCC--------------CCCCCCCCCCCC
Confidence 788888766663 244888887655
No 214
>PF08394 Arc_trans_TRASH: Archaeal TRASH domain; InterPro: IPR013603 This region is found in the C terminus of a number of archaeal transcriptional regulators. It is thought to function as a metal-sensing regulatory module [].
Probab=32.29 E-value=9 Score=18.71 Aligned_cols=17 Identities=24% Similarity=0.501 Sum_probs=11.4
Q ss_pred cceEEeeeCCCcceeee
Q psy9067 2 VNTIYYWSDTTGYLRYH 18 (189)
Q Consensus 2 ~~~~~~~c~~c~~~~f~ 18 (189)
-|+++|.|+.-|...|.
T Consensus 18 ~~~~y~fCC~tC~~~fk 34 (37)
T PF08394_consen 18 GNKVYYFCCPTCLSQFK 34 (37)
T ss_pred CCeEEEEECHHHHHHHH
Confidence 36788888776654443
No 215
>KOG3362|consensus
Probab=32.29 E-value=15 Score=24.01 Aligned_cols=22 Identities=27% Similarity=0.665 Sum_probs=14.4
Q ss_pred cccCccchhccCCchHHHHHHh
Q psy9067 163 PYACDICHARFTQSNSLKSHRL 184 (189)
Q Consensus 163 ~~~C~~C~~~f~~~~~l~~H~~ 184 (189)
.|.|..||..+-+..-|..|..
T Consensus 129 ~ysC~~CG~kyCsv~C~~~Hne 150 (156)
T KOG3362|consen 129 KYSCVNCGTKYCSVRCLKTHNE 150 (156)
T ss_pred hhHHHhcCCceeechhhhhccc
Confidence 4667777777766666666643
No 216
>PTZ00448 hypothetical protein; Provisional
Probab=31.78 E-value=30 Score=26.61 Aligned_cols=23 Identities=22% Similarity=0.457 Sum_probs=18.0
Q ss_pred cccCccchhccCCchHHHHHHhh
Q psy9067 163 PYACDICHARFTQSNSLKSHRLI 185 (189)
Q Consensus 163 ~~~C~~C~~~f~~~~~l~~H~~~ 185 (189)
.|.|..|+..|.+....+.|+++
T Consensus 314 ~~tC~~C~v~F~~~~~qR~H~KS 336 (373)
T PTZ00448 314 MLLCRKCNIQLMDHNAFKQHYRS 336 (373)
T ss_pred CccccccccccCCHHHHHHHhhh
Confidence 57788888888877777777764
No 217
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=31.71 E-value=17 Score=22.86 Aligned_cols=39 Identities=23% Similarity=0.389 Sum_probs=17.9
Q ss_pred ccCCCCCccccchhhHHHHHhhcCCCCCcccccCcccCC
Q psy9067 36 HKCSVCERGFKTIASLQNHINTHTGVKPHKCKYCESRFT 74 (189)
Q Consensus 36 ~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~C~~C~~~f~ 74 (189)
..|+.||..=.....|+.-........-|.|..||..|.
T Consensus 73 ~~CpkCg~~ea~y~~~QtRsaDEp~T~Fy~C~~Cg~~wr 111 (113)
T COG1594 73 EKCPKCGNKEAYYWQLQTRSADEPETRFYKCTRCGYRWR 111 (113)
T ss_pred ccCCCCCCceeEEEeeehhccCCCceEEEEecccCCEee
Confidence 457777654322222222111111122377877876653
No 218
>KOG1994|consensus
Probab=31.18 E-value=21 Score=25.36 Aligned_cols=23 Identities=22% Similarity=0.353 Sum_probs=19.8
Q ss_pred CcccCCCCCccccchhhHHHHHh
Q psy9067 34 RPHKCSVCERGFKTIASLQNHIN 56 (189)
Q Consensus 34 ~~~~C~~C~~~f~~~~~l~~H~~ 56 (189)
..|.|-+||..|.+...|..|..
T Consensus 238 eh~YC~fCG~~y~~~edl~ehCP 260 (268)
T KOG1994|consen 238 EHYYCFFCGIKYKDEEDLYEHCP 260 (268)
T ss_pred cceEEEEeccccCCHHHHHHhCC
Confidence 45999999999999999988853
No 219
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=31.06 E-value=9.5 Score=18.89 Aligned_cols=7 Identities=43% Similarity=1.303 Sum_probs=2.8
Q ss_pred ccCccch
Q psy9067 164 YACDICH 170 (189)
Q Consensus 164 ~~C~~C~ 170 (189)
|.|..||
T Consensus 29 y~C~~C~ 35 (40)
T smart00440 29 YVCTKCG 35 (40)
T ss_pred EEeCCCC
Confidence 3344443
No 220
>KOG1842|consensus
Probab=30.83 E-value=29 Score=27.44 Aligned_cols=27 Identities=19% Similarity=0.145 Sum_probs=19.4
Q ss_pred eeeCCCcceeeechhHHHHHHhhCCCCC
Q psy9067 7 YWSDTTGYLRYHVMYLLARHLKSHSEER 34 (189)
Q Consensus 7 ~~c~~c~~~~f~~~~~l~~h~~~~~~~~ 34 (189)
+-|++|. ..|.+...|.-|....+.+.
T Consensus 16 flCPiC~-~dl~~~~~L~~H~d~eH~~e 42 (505)
T KOG1842|consen 16 FLCPICL-LDLPNLSALNDHLDVEHFEE 42 (505)
T ss_pred ccCchHh-hhhhhHHHHHHHHhhhcccc
Confidence 5678887 57888888888877765443
No 221
>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=30.36 E-value=19 Score=17.43 Aligned_cols=11 Identities=27% Similarity=0.733 Sum_probs=5.6
Q ss_pred CcccCccchhc
Q psy9067 162 KPYACDICHAR 172 (189)
Q Consensus 162 ~~~~C~~C~~~ 172 (189)
+.|+|.+||-.
T Consensus 5 ~~YkC~~CGni 15 (36)
T PF06397_consen 5 EFYKCEHCGNI 15 (36)
T ss_dssp EEEE-TTT--E
T ss_pred cEEEccCCCCE
Confidence 45888888754
No 222
>KOG0717|consensus
Probab=29.58 E-value=26 Score=27.84 Aligned_cols=21 Identities=29% Similarity=0.660 Sum_probs=16.8
Q ss_pred ccCccchhccCCchHHHHHHh
Q psy9067 164 YACDICHARFTQSNSLKSHRL 184 (189)
Q Consensus 164 ~~C~~C~~~f~~~~~l~~H~~ 184 (189)
+-|.+|+++|.+...|..|-.
T Consensus 293 lyC~vCnKsFKseKq~kNHEn 313 (508)
T KOG0717|consen 293 LYCVVCNKSFKSEKQLKNHEN 313 (508)
T ss_pred eEEeeccccccchHHHHhhHH
Confidence 678888888888888887754
No 223
>COG4896 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=29.56 E-value=42 Score=18.41 Aligned_cols=7 Identities=43% Similarity=0.937 Sum_probs=3.3
Q ss_pred cccccCc
Q psy9067 64 HKCKYCE 70 (189)
Q Consensus 64 ~~C~~C~ 70 (189)
|.|+.|.
T Consensus 32 ymC~eC~ 38 (68)
T COG4896 32 YMCPECE 38 (68)
T ss_pred EechhhH
Confidence 4444443
No 224
>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=29.37 E-value=37 Score=27.20 Aligned_cols=27 Identities=19% Similarity=0.517 Sum_probs=19.9
Q ss_pred cccccCcccCCChhHHHhhhhhhcCCC
Q psy9067 64 HKCKYCESRFTTSGELVRHVRYKHTHE 90 (189)
Q Consensus 64 ~~C~~C~~~f~~~~~l~~h~~~~h~~~ 90 (189)
+.|+.|.+.|.+...+..|+...|...
T Consensus 58 WiCp~CskkF~d~~~~~~H~~~eH~~~ 84 (466)
T PF04780_consen 58 WICPRCSKKFSDAESCLSHMEQEHPAG 84 (466)
T ss_pred eeCCcccceeCCHHHHHHHHHHhhhhh
Confidence 567888888888888888887655554
No 225
>PLN02294 cytochrome c oxidase subunit Vb
Probab=28.61 E-value=33 Score=23.29 Aligned_cols=15 Identities=20% Similarity=0.423 Sum_probs=9.3
Q ss_pred CCCccCCCCCccccc
Q psy9067 105 EKPHKCSICDYASVE 119 (189)
Q Consensus 105 ~~~~~C~~C~~~~~~ 119 (189)
.++.+|++||..|.-
T Consensus 139 Gkp~RCpeCG~~fkL 153 (174)
T PLN02294 139 GKSFECPVCTQYFEL 153 (174)
T ss_pred CCceeCCCCCCEEEE
Confidence 345667777766643
No 226
>PF09963 DUF2197: Uncharacterized protein conserved in bacteria (DUF2197); InterPro: IPR019241 This family represents various hypothetical bacterial proteins with no known function.
Probab=28.07 E-value=70 Score=17.30 Aligned_cols=6 Identities=33% Similarity=0.999 Sum_probs=2.8
Q ss_pred ccCCCC
Q psy9067 36 HKCSVC 41 (189)
Q Consensus 36 ~~C~~C 41 (189)
|-|+.|
T Consensus 32 YmC~eC 37 (56)
T PF09963_consen 32 YMCDEC 37 (56)
T ss_pred eeChhH
Confidence 444444
No 227
>KOG2636|consensus
Probab=27.62 E-value=54 Score=26.03 Aligned_cols=28 Identities=25% Similarity=0.519 Sum_probs=21.3
Q ss_pred hcCCCCCccCccCC-ccCCChHHHHHHHH
Q psy9067 129 SHTGERPYQCAHCT-YASPDTFKLKRHLR 156 (189)
Q Consensus 129 ~~~~~~~~~C~~C~-~~f~~~~~l~~H~~ 156 (189)
.|.-...|.|.||| .++...-+|..|..
T Consensus 395 LHGL~~ey~CEICGNy~Y~GrkaF~RHF~ 423 (497)
T KOG2636|consen 395 LHGLDIEYNCEICGNYVYKGRKAFDRHFN 423 (497)
T ss_pred hcCCCcccceeeccCccccCcHHHHHHhH
Confidence 34445668999998 88888888888854
No 228
>KOG4727|consensus
Probab=27.60 E-value=38 Score=22.98 Aligned_cols=27 Identities=15% Similarity=0.442 Sum_probs=22.0
Q ss_pred cCCCCCccCCCCCccccchHHHHhchh
Q psy9067 102 HTHEKPHKCSICDYASVELSKMRNHMR 128 (189)
Q Consensus 102 ~~~~~~~~C~~C~~~~~~~~~l~~H~~ 128 (189)
.+....|-|++|+-.+.+..++..|+.
T Consensus 70 ~sq~~GyyCdVCdcvvKDSinflDHiN 96 (193)
T KOG4727|consen 70 RSQKGGYYCDVCDCVVKDSINFLDHIN 96 (193)
T ss_pred ccccCceeeeecceeehhhHHHHHHhc
Confidence 344556899999999999999999864
No 229
>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=27.42 E-value=56 Score=20.12 Aligned_cols=40 Identities=8% Similarity=0.025 Sum_probs=30.1
Q ss_pred CccCCCCCccccchHHHHhchhhcCCCCCccCccCCccCCC
Q psy9067 107 PHKCSICDYASVELSKMRNHMRSHTGERPYQCAHCTYASPD 147 (189)
Q Consensus 107 ~~~C~~C~~~~~~~~~l~~H~~~~~~~~~~~C~~C~~~f~~ 147 (189)
.|.|+.=|..|.+...+...+... ..+.|.|.+.|+.-.+
T Consensus 3 Vf~i~~T~EiF~dYe~Y~~R~~~y-~~~vwtC~~TGk~~LT 42 (102)
T PF10537_consen 3 VFYIPFTGEIFRDYEEYLKRMILY-NQRVWTCEITGKSNLT 42 (102)
T ss_pred eEEeCCCCcccCCHHHHHHHHHHH-hCCeeEEecCCCCCCC
Confidence 467888888999998887776544 5578999988875443
No 230
>PRK12860 transcriptional activator FlhC; Provisional
Probab=27.01 E-value=62 Score=22.47 Aligned_cols=47 Identities=21% Similarity=0.400 Sum_probs=30.8
Q ss_pred eeeechhHHHHHHhhCCCCCcccCCCCCccccchhhHHHHHhhcCCCCCcccccCc
Q psy9067 15 LRYHVMYLLARHLKSHSEERPHKCSVCERGFKTIASLQNHINTHTGVKPHKCKYCE 70 (189)
Q Consensus 15 ~~f~~~~~l~~h~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~C~~C~ 70 (189)
..|..-+.|.+...+. .=....|..|+-.|-.. .+.....|.|+.|.
T Consensus 115 Ls~tRAw~LvRf~~s~-~L~l~~C~~Cgg~fv~~--------~~e~~~~f~CplC~ 161 (189)
T PRK12860 115 LDLTRAWTLVRFFDAG-MLQLARCCRCGGKFVTH--------AHDLRHNFVCGLCQ 161 (189)
T ss_pred ecHHHHHHHHHHhcCC-CeeeccCCCCCCCeecc--------ccccCCCCcCCCCC
Confidence 4466667787777654 23346799999888422 12334579999997
No 231
>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=26.96 E-value=27 Score=18.35 Aligned_cols=11 Identities=36% Similarity=1.017 Sum_probs=7.3
Q ss_pred ccCccchhccC
Q psy9067 164 YACDICHARFT 174 (189)
Q Consensus 164 ~~C~~C~~~f~ 174 (189)
|+|..||..+.
T Consensus 2 y~C~~CgyiYd 12 (50)
T cd00730 2 YECRICGYIYD 12 (50)
T ss_pred cCCCCCCeEEC
Confidence 56777776655
No 232
>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=26.81 E-value=44 Score=20.62 Aligned_cols=38 Identities=29% Similarity=0.523 Sum_probs=18.8
Q ss_pred CCccCCCCCcc--ccchHHHHhchhhcCCCCCccCccCCcc
Q psy9067 106 KPHKCSICDYA--SVELSKMRNHMRSHTGERPYQCAHCTYA 144 (189)
Q Consensus 106 ~~~~C~~C~~~--~~~~~~l~~H~~~~~~~~~~~C~~C~~~ 144 (189)
++..|+.||.. +.+.+.++-+.... +.-.|.|..|+-.
T Consensus 1 ~p~~CpYCg~~~~l~~~~~iYg~~~~~-~~~~y~C~~C~Ay 40 (102)
T PF11672_consen 1 KPIICPYCGGPAELVDGSEIYGHRYDD-GPYLYVCTPCDAY 40 (102)
T ss_pred CCcccCCCCCeeEEcccchhcCccCCC-CceeEECCCCCce
Confidence 35678888854 22333333322111 2223788888643
No 233
>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=26.80 E-value=50 Score=16.11 Aligned_cols=11 Identities=18% Similarity=0.579 Sum_probs=3.6
Q ss_pred cccCCCCCccc
Q psy9067 35 PHKCSVCERGF 45 (189)
Q Consensus 35 ~~~C~~C~~~f 45 (189)
.|.|+.|+..+
T Consensus 3 ryyCdyC~~~~ 13 (38)
T PF06220_consen 3 RYYCDYCKKYL 13 (38)
T ss_dssp S-B-TTT--B-
T ss_pred Ceeccccccee
Confidence 35666666666
No 234
>KOG0717|consensus
Probab=26.75 E-value=37 Score=27.04 Aligned_cols=22 Identities=23% Similarity=0.354 Sum_probs=20.0
Q ss_pred ccCccCCccCCChHHHHHHHHH
Q psy9067 136 YQCAHCTYASPDTFKLKRHLRI 157 (189)
Q Consensus 136 ~~C~~C~~~f~~~~~l~~H~~~ 157 (189)
+.|.+|.+.|.+...+..|..+
T Consensus 293 lyC~vCnKsFKseKq~kNHEnS 314 (508)
T KOG0717|consen 293 LYCVVCNKSFKSEKQLKNHENS 314 (508)
T ss_pred eEEeeccccccchHHHHhhHHH
Confidence 8999999999999999999754
No 235
>cd01121 Sms Sms (bacterial radA) DNA repair protein. This protein is not related to archael radA any more than is to other RecA-like NTPases. Sms has a role in recombination and recombinational repair and is responsible for the stabilization or processing of branched DNA molecules.
Probab=26.74 E-value=32 Score=26.69 Aligned_cols=9 Identities=44% Similarity=0.984 Sum_probs=4.6
Q ss_pred ccCCCCCcc
Q psy9067 108 HKCSICDYA 116 (189)
Q Consensus 108 ~~C~~C~~~ 116 (189)
|.|..||..
T Consensus 1 ~~c~~cg~~ 9 (372)
T cd01121 1 YVCSECGYV 9 (372)
T ss_pred CCCCCCCCC
Confidence 455555543
No 236
>PF07800 DUF1644: Protein of unknown function (DUF1644); InterPro: IPR012866 This family consists of sequences found in a number of hypothetical plant proteins of unknown function. The region of interest contains nine highly conserved cysteine residues and is approximately 160 amino acids in length, which probably represent a zinc-binding domain.
Probab=26.74 E-value=91 Score=20.97 Aligned_cols=11 Identities=27% Similarity=0.489 Sum_probs=5.1
Q ss_pred HHHHHHhhhCC
Q psy9067 178 SLKSHRLIHTP 188 (189)
Q Consensus 178 ~l~~H~~~h~~ 188 (189)
.|.+|.+.-||
T Consensus 123 eLrKHar~~HP 133 (162)
T PF07800_consen 123 ELRKHARSEHP 133 (162)
T ss_pred HHHHHHHhhCC
Confidence 35555444443
No 237
>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=26.47 E-value=16 Score=24.07 Aligned_cols=31 Identities=26% Similarity=0.592 Sum_probs=16.8
Q ss_pred CccCccCCccCCChHHHHHHHHHhhCCCcccCccchhcc
Q psy9067 135 PYQCAHCTYASPDTFKLKRHLRIHTGEKPYACDICHARF 173 (189)
Q Consensus 135 ~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f 173 (189)
.|.|..|+..+... .++ ....|.|..|+..+
T Consensus 123 ~~~C~~C~~~~~r~------~~~--~~~~~~C~~C~~~l 153 (157)
T PF10263_consen 123 VYRCPSCGREYKRH------RRS--KRKRYRCGRCGGPL 153 (157)
T ss_pred EEEcCCCCCEeeee------ccc--chhhEECCCCCCEE
Confidence 46777777555332 121 22337777777554
No 238
>PRK00420 hypothetical protein; Validated
Probab=26.39 E-value=60 Score=20.41 Aligned_cols=28 Identities=14% Similarity=0.260 Sum_probs=16.1
Q ss_pred ccCCCCCccccchhhHHHHHhhcCCCCCcccccCcccCC
Q psy9067 36 HKCSVCERGFKTIASLQNHINTHTGVKPHKCKYCESRFT 74 (189)
Q Consensus 36 ~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~C~~C~~~f~ 74 (189)
-.||.||..+.. .......|+.|+....
T Consensus 24 ~~CP~Cg~pLf~-----------lk~g~~~Cp~Cg~~~~ 51 (112)
T PRK00420 24 KHCPVCGLPLFE-----------LKDGEVVCPVHGKVYI 51 (112)
T ss_pred CCCCCCCCccee-----------cCCCceECCCCCCeee
Confidence 358888766521 1233456888877544
No 239
>PRK11823 DNA repair protein RadA; Provisional
Probab=26.09 E-value=37 Score=27.04 Aligned_cols=31 Identities=16% Similarity=0.230 Sum_probs=20.3
Q ss_pred CCCccCCCCCccccchHHHHhchhhcCCCCCccCccCCccCCChH
Q psy9067 105 EKPHKCSICDYASVELSKMRNHMRSHTGERPYQCAHCTYASPDTF 149 (189)
Q Consensus 105 ~~~~~C~~C~~~~~~~~~l~~H~~~~~~~~~~~C~~C~~~f~~~~ 149 (189)
...|.|..||..+.. ...+|+.|+.|=+-..
T Consensus 5 ~~~y~C~~Cg~~~~~--------------~~g~Cp~C~~w~t~~e 35 (446)
T PRK11823 5 KTAYVCQECGAESPK--------------WLGRCPECGAWNTLVE 35 (446)
T ss_pred CCeEECCcCCCCCcc--------------cCeeCcCCCCccceee
Confidence 345999999875433 3457888886655443
No 240
>KOG4118|consensus
Probab=25.96 E-value=49 Score=18.42 Aligned_cols=25 Identities=20% Similarity=0.529 Sum_probs=19.3
Q ss_pred ccCccchhccCCchHHHHHHhhhCC
Q psy9067 164 YACDICHARFTQSNSLKSHRLIHTP 188 (189)
Q Consensus 164 ~~C~~C~~~f~~~~~l~~H~~~h~~ 188 (189)
|+|.+|-..-.....+..|..+.||
T Consensus 39 ~kCtVC~~~mpdpktfkqhfe~kHp 63 (74)
T KOG4118|consen 39 HKCTVCMVQMPDPKTFKQHFENKHP 63 (74)
T ss_pred hhhHhhHhhCCCCchHHHHHhhcCC
Confidence 7888887777777778888777666
No 241
>COG1773 Rubredoxin [Energy production and conversion]
Probab=25.93 E-value=31 Score=18.56 Aligned_cols=14 Identities=29% Similarity=0.695 Sum_probs=9.8
Q ss_pred CccCCCCCccccch
Q psy9067 107 PHKCSICDYASVEL 120 (189)
Q Consensus 107 ~~~C~~C~~~~~~~ 120 (189)
.|+|..||..|.-.
T Consensus 3 ~~~C~~CG~vYd~e 16 (55)
T COG1773 3 RWRCSVCGYVYDPE 16 (55)
T ss_pred ceEecCCceEeccc
Confidence 47888888776443
No 242
>KOG2636|consensus
Probab=25.11 E-value=57 Score=25.90 Aligned_cols=23 Identities=22% Similarity=0.619 Sum_probs=17.4
Q ss_pred CCcccCccch-hccCCchHHHHHH
Q psy9067 161 EKPYACDICH-ARFTQSNSLKSHR 183 (189)
Q Consensus 161 ~~~~~C~~C~-~~f~~~~~l~~H~ 183 (189)
...|.|.+|| +++.=+..+.+|-
T Consensus 399 ~~ey~CEICGNy~Y~GrkaF~RHF 422 (497)
T KOG2636|consen 399 DIEYNCEICGNYVYKGRKAFDRHF 422 (497)
T ss_pred CcccceeeccCccccCcHHHHHHh
Confidence 4568888888 7777777777773
No 243
>TIGR00416 sms DNA repair protein RadA. The gene protuct codes for a probable ATP-dependent protease involved in both DNA repair and degradation of proteins, peptides, glycopeptides. Also known as sms. Residues 11-28 of the SEED alignment contain a putative Zn binding domain. Residues 110-117 of the seed contain a putative ATP binding site both documented in Haemophilus and in Listeria monocytogenes. for E.coli see ( J. BACTERIOL. 178:5045-5048(1996)).
Probab=25.03 E-value=32 Score=27.45 Aligned_cols=30 Identities=20% Similarity=0.288 Sum_probs=20.8
Q ss_pred CCccCCCCCccccchHHHHhchhhcCCCCCccCccCCccCCChH
Q psy9067 106 KPHKCSICDYASVELSKMRNHMRSHTGERPYQCAHCTYASPDTF 149 (189)
Q Consensus 106 ~~~~C~~C~~~~~~~~~l~~H~~~~~~~~~~~C~~C~~~f~~~~ 149 (189)
..|.|..||..+.. ...+||.|+.|=+-..
T Consensus 6 ~~y~C~~Cg~~~~~--------------~~g~Cp~C~~w~t~~~ 35 (454)
T TIGR00416 6 SKFVCQHCGADSPK--------------WQGKCPACHAWNTITE 35 (454)
T ss_pred CeEECCcCCCCCcc--------------ccEECcCCCCccccch
Confidence 35999999875433 3458899987766554
No 244
>COG4338 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=24.76 E-value=21 Score=18.51 Aligned_cols=13 Identities=23% Similarity=0.787 Sum_probs=7.4
Q ss_pred cCccchhccCCch
Q psy9067 165 ACDICHARFTQSN 177 (189)
Q Consensus 165 ~C~~C~~~f~~~~ 177 (189)
.|+.|+.-|+++.
T Consensus 14 ICpvCqRPFsWRk 26 (54)
T COG4338 14 ICPVCQRPFSWRK 26 (54)
T ss_pred hhhhhcCchHHHH
Confidence 4666666665543
No 245
>KOG0978|consensus
Probab=24.76 E-value=42 Score=28.33 Aligned_cols=47 Identities=28% Similarity=0.538 Sum_probs=28.2
Q ss_pred ccCCCCCccccchhhHHH-H------HhhcCCCCCcccccCcccCCChhHHHhh
Q psy9067 36 HKCSVCERGFKTIASLQN-H------INTHTGVKPHKCKYCESRFTTSGELVRH 82 (189)
Q Consensus 36 ~~C~~C~~~f~~~~~l~~-H------~~~~~~~~~~~C~~C~~~f~~~~~l~~h 82 (189)
..|+.|+..+.+..-..- | +......+.=+||.|+..|....-.+.|
T Consensus 644 LkCs~Cn~R~Kd~vI~kC~H~FC~~Cvq~r~etRqRKCP~Cn~aFganDv~~I~ 697 (698)
T KOG0978|consen 644 LKCSVCNTRWKDAVITKCGHVFCEECVQTRYETRQRKCPKCNAAFGANDVHRIH 697 (698)
T ss_pred eeCCCccCchhhHHHHhcchHHHHHHHHHHHHHhcCCCCCCCCCCCcccccccC
Confidence 579999877655433211 2 1122233445799999999876655443
No 246
>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=24.59 E-value=24 Score=23.29 Aligned_cols=35 Identities=20% Similarity=0.340 Sum_probs=20.8
Q ss_pred hhCCCCC----cccCCCCCccccchhhHHHHHhhcCCCCCcccccCccc
Q psy9067 28 KSHSEER----PHKCSVCERGFKTIASLQNHINTHTGVKPHKCKYCESR 72 (189)
Q Consensus 28 ~~~~~~~----~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~C~~C~~~ 72 (189)
..++|+. .|.|..||.... ..+....-.|+.|+..
T Consensus 101 ~Y~sGE~~g~G~l~C~~Cg~~~~----------~~~~~~l~~Cp~C~~~ 139 (146)
T PF07295_consen 101 VYHSGEVVGPGTLVCENCGHEVE----------LTHPERLPPCPKCGHT 139 (146)
T ss_pred CeecCcEecCceEecccCCCEEE----------ecCCCcCCCCCCCCCC
Confidence 4455553 488988887641 1123334568888865
No 247
>PRK04351 hypothetical protein; Provisional
Probab=24.42 E-value=39 Score=22.42 Aligned_cols=31 Identities=16% Similarity=0.534 Sum_probs=20.6
Q ss_pred ccCCCCCccccchhhHHHHHhhcCCCCCcccccCcccCC
Q psy9067 36 HKCSVCERGFKTIASLQNHINTHTGVKPHKCKYCESRFT 74 (189)
Q Consensus 36 ~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~C~~C~~~f~ 74 (189)
|.|..|+..+.... .++...|.|..|+..+.
T Consensus 113 Y~C~~Cg~~~~r~R--------r~n~~~yrCg~C~g~L~ 143 (149)
T PRK04351 113 YECQSCGQQYLRKR--------RINTKRYRCGKCRGKLK 143 (149)
T ss_pred EECCCCCCEeeeee--------ecCCCcEEeCCCCcEee
Confidence 78888887664321 12456788998886654
No 248
>TIGR01562 FdhE formate dehydrogenase accessory protein FdhE. The only sequence scoring between trusted and noise is that from Aquifex aeolicus, which shows certain structural differences from the proteobacterial forms in the alignment. However it is notable that A. aeolicus also has a sequence scoring above trusted to the alpha subunit of formate dehydrogenase (TIGR01553).
Probab=23.86 E-value=72 Score=24.06 Aligned_cols=28 Identities=29% Similarity=0.595 Sum_probs=15.9
Q ss_pred CCCCcccCCCCCccccchhhHHHHHhhcCCCCCcccccCccc
Q psy9067 31 SEERPHKCSVCERGFKTIASLQNHINTHTGVKPHKCKYCESR 72 (189)
Q Consensus 31 ~~~~~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~C~~C~~~ 72 (189)
.+.+-..|..|+..+. -....|+.|+..
T Consensus 206 ~G~RyL~CslC~teW~--------------~~R~~C~~Cg~~ 233 (305)
T TIGR01562 206 TGLRYLSCSLCATEWH--------------YVRVKCSHCEES 233 (305)
T ss_pred CCceEEEcCCCCCccc--------------ccCccCCCCCCC
Confidence 3445556777765541 123568888763
No 249
>COG4391 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=23.82 E-value=44 Score=18.39 Aligned_cols=15 Identities=20% Similarity=0.275 Sum_probs=11.3
Q ss_pred CCCccCCCCCccccc
Q psy9067 105 EKPHKCSICDYASVE 119 (189)
Q Consensus 105 ~~~~~C~~C~~~~~~ 119 (189)
+....|++|+..|..
T Consensus 46 ~gev~CPYC~t~y~l 60 (62)
T COG4391 46 EGEVVCPYCSTRYRL 60 (62)
T ss_pred CCcEecCccccEEEe
Confidence 445689999988753
No 250
>PF12773 DZR: Double zinc ribbon
Probab=23.65 E-value=51 Score=16.81 Aligned_cols=10 Identities=20% Similarity=0.418 Sum_probs=6.2
Q ss_pred cCCCCCcccc
Q psy9067 109 KCSICDYASV 118 (189)
Q Consensus 109 ~C~~C~~~~~ 118 (189)
.|+.||..+.
T Consensus 14 fC~~CG~~l~ 23 (50)
T PF12773_consen 14 FCPHCGTPLP 23 (50)
T ss_pred CChhhcCChh
Confidence 5667766554
No 251
>PRK05978 hypothetical protein; Provisional
Probab=23.64 E-value=36 Score=22.57 Aligned_cols=10 Identities=20% Similarity=0.607 Sum_probs=6.6
Q ss_pred cCCCCCcccc
Q psy9067 109 KCSICDYASV 118 (189)
Q Consensus 109 ~C~~C~~~~~ 118 (189)
.|+.||..|.
T Consensus 54 ~C~~CG~~~~ 63 (148)
T PRK05978 54 HCAACGEDFT 63 (148)
T ss_pred CccccCCccc
Confidence 6777776654
No 252
>COG2879 Uncharacterized small protein [Function unknown]
Probab=23.30 E-value=68 Score=17.76 Aligned_cols=15 Identities=13% Similarity=0.193 Sum_probs=11.4
Q ss_pred CCchHHHHHHhhhCC
Q psy9067 174 TQSNSLKSHRLIHTP 188 (189)
Q Consensus 174 ~~~~~l~~H~~~h~~ 188 (189)
..-.+...||+.+||
T Consensus 23 pdYdnYVehmr~~hP 37 (65)
T COG2879 23 PDYDNYVEHMRKKHP 37 (65)
T ss_pred CcHHHHHHHHHHhCc
Confidence 455678889988887
No 253
>TIGR00143 hypF [NiFe] hydrogenase maturation protein HypF. A previously described regulatory effect of HypF mutatation is attributable to loss of activity of a regulatory hydrogenase. A zinc finger-like region CXXCX(18)CXXCX(24)CXXCX(18)CXXC region further supported the regulatory hypothesis. However, more recent work (PUBMED:11375153) shows the direct effect is on the activity of expressed hydrogenases with nickel/iron centers, rather than on expression.
Probab=23.19 E-value=6.1 Score=33.35 Aligned_cols=58 Identities=19% Similarity=0.390 Sum_probs=24.9
Q ss_pred ccCCCCCccccchHHHHhchhhcCCCC-CccCccCCccCCChHHHHHHHHHhhCCCcccCccchhc
Q psy9067 108 HKCSICDYASVELSKMRNHMRSHTGER-PYQCAHCTYASPDTFKLKRHLRIHTGEKPYACDICHAR 172 (189)
Q Consensus 108 ~~C~~C~~~~~~~~~l~~H~~~~~~~~-~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~ 172 (189)
..|..||-.|.-..+|---.. .+.-. --.|+.|.+.+......+-| -.+..|+.||-.
T Consensus 91 ~nCt~CGPr~~i~~~lpydr~-~t~m~~f~~C~~C~~ey~~p~~rr~h------~~~~~C~~Cgp~ 149 (711)
T TIGR00143 91 ISCTHCGPRFTIIEALPYDRE-NTSMADFPLCPDCAKEYKDPLDRRFH------AQPIACPRCGPQ 149 (711)
T ss_pred ccccCCCCCeEEeecCCCCCC-CcCCCCCcCCHHHHHHhcCCccccCC------CCCccCCCCCcE
Confidence 356666666554433221111 11111 12566665555443222222 234566666644
No 254
>PF03145 Sina: Seven in absentia protein family; InterPro: IPR018121 The seven in absentia (sina) gene was first identified in Drosophila. The Drosophila Sina protein is essential for the determination of the R7 pathway in photoreceptor cell development: the loss of functional Sina results in the transformation of the R7 precursor cell to a non-neuronal cell type. The Sina protein contains an N-terminal RING finger domain C3HC4-type. Through this domain, Sina binds E2 ubiquitin-conjugating enzymes (UbcD1) Sina also interacts with Tramtrack (TTK88) via PHYL. Tramtrack is a transcriptional repressor that blocks photoreceptor determination, while PHYL down-regulates the activity of TTK88. In turn, the activity of PHYL requires the activation of the Sevenless receptor tyrosine kinase, a process essential for R7 determination. It is thought that Sina targets TTK88 for degradation, therefore promoting the R7 pathway. Murine and human homologues of Sina have also been identified. The human homologue Siah-1 [] also binds E2 enzymes (UbcH5) and through a series of physical interactions, targets beta-catenin for ubiquitin degradation. Siah-1 expression is enhanced by p53, itself promoted by DNA damage. Thus this pathway links DNA damage to beta-catenin degradation [, ]. Sina proteins, therefore, physically interact with a variety of proteins. The N-terminal RING finger domain that binds ubiquitin conjugating enzymes is a C3HC4-type, and does not form part of the alignment for this family. The remainder C-terminal part is involved in interactions with other proteins, and is included in this alignment. In addition to the Drosophila protein and mammalian homologues, whose similarity was noted previously, this family also includes putative homologues from Caenorhabditis elegans, Arabidopsis thaliana.; GO: 0006511 ubiquitin-dependent protein catabolic process, 0007275 multicellular organismal development, 0005634 nucleus; PDB: 2A25_A 1K2F_B 2AN6_C.
Probab=23.14 E-value=1.4e+02 Score=20.64 Aligned_cols=56 Identities=14% Similarity=0.230 Sum_probs=24.4
Q ss_pred cceEEeeeCC----CcceeeechhHHHHHHhhCCCCCcccCCC----CCccccchhhHHHHHhhcCCC
Q psy9067 2 VNTIYYWSDT----TGYLRYHVMYLLARHLKSHSEERPHKCSV----CERGFKTIASLQNHINTHTGV 61 (189)
Q Consensus 2 ~~~~~~~c~~----c~~~~f~~~~~l~~h~~~~~~~~~~~C~~----C~~~f~~~~~l~~H~~~~~~~ 61 (189)
.+.+.++|.. |.. . ........|... -.-+|+.|+. |+.. .....|..|....|..
T Consensus 10 ~~~~~~pC~~~~~GC~~-~-~~~~~~~~HE~~-C~~~p~~CP~~~~~C~~~-G~~~~l~~Hl~~~H~~ 73 (198)
T PF03145_consen 10 AESIKFPCKNAKYGCTE-T-FPYSEKREHEEE-CPFRPCSCPFPGSGCDWQ-GSYKELLDHLRDKHSW 73 (198)
T ss_dssp -----EE-CCGGGT----E-E-GGGHHHHHHT--TTSEEE-SSSSTT---E-EECCCHHHHHHHHTTT
T ss_pred HhhceecCCCCCCCCcc-c-ccccChhhHhcc-CCCcCCcCCCCCCCcccc-CCHHHHHHHHHHHCCC
Confidence 3456677776 442 2 334455666544 4556777776 5432 2345677777766554
No 255
>PF05741 zf-nanos: Nanos RNA binding domain; InterPro: IPR024161 Nanos is a highly conserved RNA-binding protein in higher eukaryotes and functions as a key regulatory protein in translational control using a 3' untranslated region during the development and maintenance of germ cells. Nanos comprises a non-conserved amino-terminus and highly conserved carboxy- terminal regions. The C-terminal region has two conserved Cys-Cys-His-Cys (CCHC)-type zinc-finger motifs that are indispensable for nanos function [, , ]. The structure of the nanos-type zinc finger is composed of two independent zinc-finger (ZF) lobes, the N-terminal ZF1 and the C-terminal ZF2, which are connected by a linker helix []. These lobes create a large cleft. Zinc ions in ZF1 and ZF2 are bound to the CCHC motif by tetrahedral coordination.; PDB: 3ALR_B.
Probab=23.01 E-value=29 Score=18.68 Aligned_cols=10 Identities=50% Similarity=1.145 Sum_probs=3.0
Q ss_pred cccCccchhc
Q psy9067 163 PYACDICHAR 172 (189)
Q Consensus 163 ~~~C~~C~~~ 172 (189)
.|.|++||..
T Consensus 33 ~y~Cp~CgAt 42 (55)
T PF05741_consen 33 KYVCPICGAT 42 (55)
T ss_dssp G---TTT---
T ss_pred cCcCCCCcCc
Confidence 4788888865
No 256
>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=22.88 E-value=28 Score=24.83 Aligned_cols=24 Identities=21% Similarity=0.308 Sum_probs=0.0
Q ss_pred CcccCccchhccCCchHHHHHHhhh
Q psy9067 162 KPYACDICHARFTQSNSLKSHRLIH 186 (189)
Q Consensus 162 ~~~~C~~C~~~f~~~~~l~~H~~~h 186 (189)
....|++||....-. .|..|||+-
T Consensus 167 ~~~~cPitGe~IP~~-e~~eHmRi~ 190 (229)
T PF12230_consen 167 KMIICPITGEMIPAD-EMDEHMRIE 190 (229)
T ss_dssp -------------------------
T ss_pred ccccccccccccccc-ccccccccc
Confidence 446788888776554 377787753
No 257
>smart00731 SprT SprT homologues. Predicted to have roles in transcription elongation. Contains a conserved HExxH motif, indicating a metalloprotease function.
Probab=22.65 E-value=38 Score=22.19 Aligned_cols=32 Identities=25% Similarity=0.662 Sum_probs=17.7
Q ss_pred CccCccCCccCCChHHHHHHHHHhhCCCcccCccchhcc
Q psy9067 135 PYQCAHCTYASPDTFKLKRHLRIHTGEKPYACDICHARF 173 (189)
Q Consensus 135 ~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f 173 (189)
.|.|..|+..+... +.+.....|.|..|+..+
T Consensus 112 ~y~C~~C~~~~~~~-------rr~~~~~~y~C~~C~g~l 143 (146)
T smart00731 112 PYRCTGCGQRYLRV-------RRSNNVSRYRCGKCGGKL 143 (146)
T ss_pred EEECCCCCCCCceE-------ccccCcceEEcCCCCCEE
Confidence 57777777665421 111122557787777654
No 258
>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG
Probab=22.64 E-value=45 Score=17.69 Aligned_cols=10 Identities=20% Similarity=0.607 Sum_probs=6.5
Q ss_pred cCCCCCcccc
Q psy9067 109 KCSICDYASV 118 (189)
Q Consensus 109 ~C~~C~~~~~ 118 (189)
.||+||..+.
T Consensus 2 ~CPyCge~~~ 11 (52)
T PF14255_consen 2 QCPYCGEPIE 11 (52)
T ss_pred CCCCCCCeeE
Confidence 5777776543
No 259
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=22.51 E-value=50 Score=21.37 Aligned_cols=15 Identities=33% Similarity=0.906 Sum_probs=11.2
Q ss_pred CcccccCcccCCChh
Q psy9067 63 PHKCKYCESRFTTSG 77 (189)
Q Consensus 63 ~~~C~~C~~~f~~~~ 77 (189)
|++|..|++.|.+-+
T Consensus 1 PH~Ct~Cg~~f~dgs 15 (131)
T PF09845_consen 1 PHQCTKCGRVFEDGS 15 (131)
T ss_pred CcccCcCCCCcCCCc
Confidence 467888888887654
No 260
>KOG1940|consensus
Probab=22.31 E-value=84 Score=23.32 Aligned_cols=19 Identities=11% Similarity=0.473 Sum_probs=8.3
Q ss_pred ccCCCCCccccchhhHHHHH
Q psy9067 36 HKCSVCERGFKTIASLQNHI 55 (189)
Q Consensus 36 ~~C~~C~~~f~~~~~l~~H~ 55 (189)
|.||+|.+ ..+.+.+.+..
T Consensus 197 y~CP~C~~-~~d~~~~~~~~ 215 (276)
T KOG1940|consen 197 YTCPICSK-PGDMSHYFRKL 215 (276)
T ss_pred CCCCcccc-hHHHHHHHHHH
Confidence 44555544 33444433333
No 261
>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=21.85 E-value=1.1e+02 Score=14.47 Aligned_cols=20 Identities=20% Similarity=0.576 Sum_probs=8.6
Q ss_pred ccCCCCCccccchhhHHHHHh
Q psy9067 36 HKCSVCERGFKTIASLQNHIN 56 (189)
Q Consensus 36 ~~C~~C~~~f~~~~~l~~H~~ 56 (189)
+.|+.|++.... +.+..|+.
T Consensus 5 ~~C~nC~R~v~a-~RfA~HLe 24 (33)
T PF08209_consen 5 VECPNCGRPVAA-SRFAPHLE 24 (33)
T ss_dssp EE-TTTSSEEEG-GGHHHHHH
T ss_pred EECCCCcCCcch-hhhHHHHH
Confidence 445666554432 33444443
No 262
>smart00109 C1 Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains). Some bind phorbol esters and diacylglycerol. Some bind RasGTP. Zinc-binding domains.
Probab=21.82 E-value=68 Score=15.85 Aligned_cols=7 Identities=43% Similarity=1.284 Sum_probs=3.2
Q ss_pred cCCCCCc
Q psy9067 109 KCSICDY 115 (189)
Q Consensus 109 ~C~~C~~ 115 (189)
.|..|++
T Consensus 13 ~C~~C~~ 19 (49)
T smart00109 13 KCCVCRK 19 (49)
T ss_pred Ccccccc
Confidence 4444444
No 263
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=21.79 E-value=25 Score=21.51 Aligned_cols=9 Identities=33% Similarity=0.844 Sum_probs=6.1
Q ss_pred CCccCCCCC
Q psy9067 106 KPHKCSICD 114 (189)
Q Consensus 106 ~~~~C~~C~ 114 (189)
..+.|+.||
T Consensus 20 t~f~CP~Cg 28 (99)
T PRK14892 20 KIFECPRCG 28 (99)
T ss_pred cEeECCCCC
Confidence 446777777
No 264
>PF05180 zf-DNL: DNL zinc finger; InterPro: IPR007853 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The DNL-type zinc finger is found in Tim15, a zinc finger protein essential for protein import into mitochondria. Mitochondrial functions rely on the correct transport of resident proteins synthesized in the cytosol to mitochondria. Protein import into mitochondria is mediated by membrane protein complexes, protein translocators, in the outer and inner mitochondrial membranes, in cooperation with their assistant proteins in the cytosol, intermembrane space and matrix. Proteins destined to the mitochondrial matrix cross the outer membrane with the aid of the outer membrane translocator, the tOM40 complex, and then the inner membrane with the aid of the inner membrane translocator, the TIM23 complex, and mitochondrial motor and chaperone (MMC) proteins including mitochondrial heat- shock protein 70 (mtHsp70), and translocase in the inner mitochondrial membrane (Tim)15. Tim15 is also known as zinc finger motif (Zim)17 or mtHsp70 escort protein (Hep)1. Tim15 contains a zinc-finger motif (CXXC and CXXC) of ~100 residues, which has been named DNL after a short C-terminal motif of D(N/H)L [, , ]. The DNL-type zinc finger is an L-shaped molecule. The two CXXC motifs are located at the end of the L, and are sandwiched by two- stranded antiparallel beta-sheets. Two short alpha-helices constitute another leg of the L. The outer (convex) face of the L has a large acidic groove, which is lined with five acidic residues, whereas the inner (concave) face of the L has two positively charged residues, next to the CXXC motifs []. This entry represents the DNL-type zinc finger.; GO: 0008270 zinc ion binding; PDB: 2E2Z_A.
Probab=21.62 E-value=66 Score=18.06 Aligned_cols=36 Identities=11% Similarity=0.206 Sum_probs=19.0
Q ss_pred EEeeeCCCcceeeechhHHHHHHhhCCCCCcccCCCCCcc
Q psy9067 5 IYYWSDTTGYLRYHVMYLLARHLKSHSEERPHKCSVCERG 44 (189)
Q Consensus 5 ~~~~c~~c~~~~f~~~~~l~~h~~~~~~~~~~~C~~C~~~ 44 (189)
+.|+|..|+......... + ..+.+--..+|+-|...
T Consensus 3 l~FTC~~C~~Rs~~~~sk---~-aY~~GvViv~C~gC~~~ 38 (66)
T PF05180_consen 3 LTFTCNKCGTRSAKMFSK---Q-AYHKGVVIVQCPGCKNR 38 (66)
T ss_dssp EEEEETTTTEEEEEEEEH---H-HHHTSEEEEE-TTS--E
T ss_pred EEEEcCCCCCccceeeCH---H-HHhCCeEEEECCCCcce
Confidence 568888888655443332 2 23344455668877654
No 265
>COG5112 UFD2 U1-like Zn-finger-containing protein [General function prediction only]
Probab=21.61 E-value=36 Score=21.00 Aligned_cols=25 Identities=20% Similarity=0.246 Sum_probs=20.1
Q ss_pred CCCCccCccCCccCCChHHHHHHHH
Q psy9067 132 GERPYQCAHCTYASPDTFKLKRHLR 156 (189)
Q Consensus 132 ~~~~~~C~~C~~~f~~~~~l~~H~~ 156 (189)
|-..+.|-.|.+.|-+...|..|.+
T Consensus 52 GlGqhYCieCaryf~t~~aL~~Hkk 76 (126)
T COG5112 52 GLGQHYCIECARYFITEKALMEHKK 76 (126)
T ss_pred CCceeeeehhHHHHHHHHHHHHHhc
Confidence 4455788889989988888888875
No 266
>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=21.45 E-value=41 Score=16.09 Aligned_cols=14 Identities=36% Similarity=0.641 Sum_probs=6.6
Q ss_pred ccCccchhccCCch
Q psy9067 164 YACDICHARFTQSN 177 (189)
Q Consensus 164 ~~C~~C~~~f~~~~ 177 (189)
-.|..|++.|..+.
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 35777887777554
No 267
>KOG3214|consensus
Probab=21.06 E-value=39 Score=20.64 Aligned_cols=16 Identities=19% Similarity=0.401 Sum_probs=10.4
Q ss_pred CccCCCCCccccchHH
Q psy9067 107 PHKCSICDYASVELSK 122 (189)
Q Consensus 107 ~~~C~~C~~~~~~~~~ 122 (189)
...|.+|+..|+....
T Consensus 47 ~~sC~iC~esFqt~it 62 (109)
T KOG3214|consen 47 KASCRICEESFQTTIT 62 (109)
T ss_pred eeeeeehhhhhccchH
Confidence 3567777777766543
No 268
>KOG4377|consensus
Probab=20.63 E-value=1.2e+02 Score=23.92 Aligned_cols=70 Identities=23% Similarity=0.354 Sum_probs=41.0
Q ss_pred CCCcceeeechhHHHHHHhhCCCCC------------cccC--CCCCccccchhhHHHHHhhcCCCC-------Cccccc
Q psy9067 10 DTTGYLRYHVMYLLARHLKSHSEER------------PHKC--SVCERGFKTIASLQNHINTHTGVK-------PHKCKY 68 (189)
Q Consensus 10 ~~c~~~~f~~~~~l~~h~~~~~~~~------------~~~C--~~C~~~f~~~~~l~~H~~~~~~~~-------~~~C~~ 68 (189)
..|.+..+. ...+.+|.+.|.... .|.| ..|.+ +.++...|-..|+... -|.|..
T Consensus 277 e~C~ykr~~-k~DvirH~~~hkkrdnsL~dgf~rfs~syhC~~~~C~k---sTsdV~~h~nFht~~~n~GfrrthfhC~r 352 (480)
T KOG4377|consen 277 EYCFYKRGQ-KNDVIRHVEIHKKRDNSLIDGFHRFSNSYHCTGQICEK---STSDVLLHDNFHTDKRNNGFRRTHFHCQR 352 (480)
T ss_pred ccccccccc-hhhhHHHHHHHhhcccccccchhhcCccchhhhcccCc---ccccccccCccccccccCceecceeEEec
Confidence 567876666 666778877776432 2455 35766 4456666655553221 278888
Q ss_pred CcccCCChhHHHhhhhh
Q psy9067 69 CESRFTTSGELVRHVRY 85 (189)
Q Consensus 69 C~~~f~~~~~l~~h~~~ 85 (189)
++-++..+ +..|...
T Consensus 353 ~gCTdtfK--~~khk~y 367 (480)
T KOG4377|consen 353 IGCTDTFK--DSKHKPY 367 (480)
T ss_pred cCCccccc--ccccccc
Confidence 88544444 4455554
No 269
>PF07535 zf-DBF: DBF zinc finger; InterPro: IPR006572 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. In eukaryotes, initiation of DNA replication requires the assembly of pre-replication complexes (pre-RCs) on chromatin during the G1 phase. In the S phase, pre-RCs are activated by two protein kinases, Cdk2 and Cdc7, which results in the loading of replication factors and the unwinding of replication origins by the MCM helicase complex []. Cdc7 is a serine/threonine kinase that is conserved from yeast to human. It is regulated by its association with a regulatory subunit, the Dbf4 protein. This complex is often referred to as DDK (Dbf4-dependent kinase) []. DBF4 contains an N-terminal BRCT domain and a C-terminal conserved region that could potentially coordinate one zinc atom, the DBF4-type zinc finger. This entry represents the zinc finger, which is important for the interaction with Cdc7 [, ]. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding
Probab=20.34 E-value=88 Score=16.35 Aligned_cols=20 Identities=30% Similarity=0.795 Sum_probs=12.3
Q ss_pred CcccCCCCCccccchhhHHHHHh
Q psy9067 34 RPHKCSVCERGFKTIASLQNHIN 56 (189)
Q Consensus 34 ~~~~C~~C~~~f~~~~~l~~H~~ 56 (189)
++-.|..|...| ..|..|+.
T Consensus 4 k~GYCE~C~~ky---~~l~~Hi~ 23 (49)
T PF07535_consen 4 KPGYCENCRVKY---DDLEEHIQ 23 (49)
T ss_pred CCccCccccchh---hhHHHHhC
Confidence 445677777777 45666654
No 270
>COG4640 Predicted membrane protein [Function unknown]
Probab=20.33 E-value=87 Score=24.54 Aligned_cols=20 Identities=15% Similarity=0.253 Sum_probs=12.2
Q ss_pred CCccCccCCccCCChHHHHH
Q psy9067 134 RPYQCAHCTYASPDTFKLKR 153 (189)
Q Consensus 134 ~~~~C~~C~~~f~~~~~l~~ 153 (189)
..+.|+.||..|...+..-.
T Consensus 14 d~~qC~qCG~~~t~~~sqan 33 (465)
T COG4640 14 DDVQCTQCGHKFTSRQSQAN 33 (465)
T ss_pred ccccccccCCcCCchhhhhh
Confidence 34457777777766655444
No 271
>PF11781 RRN7: RNA polymerase I-specific transcription initiation factor Rrn7; InterPro: IPR021752 Rrn7 is a transcription binding factor that associates strongly with both Rrn6 and Rrn11 to form a complex which itself binds the TATA-binding protein and is required for transcription by the core domain of the RNA PolI promoter [],[].
Probab=20.23 E-value=81 Score=15.18 Aligned_cols=6 Identities=17% Similarity=0.202 Sum_probs=2.8
Q ss_pred eCCCcc
Q psy9067 9 SDTTGY 14 (189)
Q Consensus 9 c~~c~~ 14 (189)
|.+|+.
T Consensus 11 C~~C~~ 16 (36)
T PF11781_consen 11 CPVCGS 16 (36)
T ss_pred CCCCCC
Confidence 444443
No 272
>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=20.10 E-value=48 Score=20.76 Aligned_cols=8 Identities=25% Similarity=0.742 Sum_probs=3.8
Q ss_pred ccCCCCCc
Q psy9067 108 HKCSICDY 115 (189)
Q Consensus 108 ~~C~~C~~ 115 (189)
.+||.|++
T Consensus 70 V~CP~C~K 77 (114)
T PF11023_consen 70 VECPNCGK 77 (114)
T ss_pred eECCCCCC
Confidence 34555544
No 273
>KOG3507|consensus
Probab=20.03 E-value=38 Score=18.42 Aligned_cols=10 Identities=30% Similarity=0.939 Sum_probs=6.4
Q ss_pred CCccCccCCc
Q psy9067 134 RPYQCAHCTY 143 (189)
Q Consensus 134 ~~~~C~~C~~ 143 (189)
.+++|..||.
T Consensus 36 D~irCReCG~ 45 (62)
T KOG3507|consen 36 DVIRCRECGY 45 (62)
T ss_pred CcEehhhcch
Confidence 4567777763
No 274
>PRK12722 transcriptional activator FlhC; Provisional
Probab=20.02 E-value=1e+02 Score=21.38 Aligned_cols=48 Identities=27% Similarity=0.471 Sum_probs=31.0
Q ss_pred eeeechhHHHHHHhhCCCCCcccCCCCCccccchhhHHHHHhhcCCCCCcccccCcc
Q psy9067 15 LRYHVMYLLARHLKSHSEERPHKCSVCERGFKTIASLQNHINTHTGVKPHKCKYCES 71 (189)
Q Consensus 15 ~~f~~~~~l~~h~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~C~~C~~ 71 (189)
..|..-+.|.+...+. .=....|..|+-.|-... +.....|.|+.|..
T Consensus 115 Ls~tRAw~LvRf~~s~-~L~l~~C~~Cgg~fv~~~--------~e~~~~f~CplC~~ 162 (187)
T PRK12722 115 LSLTRAWTLVRFVDSG-MLQLSSCNCCGGHFVTHA--------HDPVGSFVCGLCQP 162 (187)
T ss_pred ecHHHHHHHHHHHhcC-cEeeccCCCCCCCeeccc--------cccCCCCcCCCCCC
Confidence 4566667777777664 223356999998884222 22345799999976
Done!