Query psy12018
Match_columns 148
No_of_seqs 115 out of 1129
Neff 10.8
Searched_HMMs 46136
Date Fri Aug 16 16:33:00 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy12018.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/12018hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2462|consensus 99.9 1.9E-24 4.1E-29 142.2 6.6 105 32-140 159-264 (279)
2 KOG2462|consensus 99.9 1.1E-24 2.3E-29 143.3 5.1 114 31-147 127-243 (279)
3 KOG3576|consensus 99.7 1.4E-17 3.1E-22 105.5 1.7 117 30-147 113-240 (267)
4 KOG1074|consensus 99.7 3.5E-17 7.5E-22 121.5 3.3 56 91-147 606-661 (958)
5 KOG3623|consensus 99.5 4.7E-16 1E-20 114.3 -2.0 106 34-140 210-330 (1007)
6 KOG3623|consensus 99.5 5.8E-15 1.3E-19 108.7 1.7 76 63-139 894-970 (1007)
7 KOG1074|consensus 99.5 5.3E-14 1.1E-18 105.0 5.0 56 91-147 880-935 (958)
8 KOG3576|consensus 99.4 1.4E-14 3E-19 92.1 -0.5 84 61-145 115-199 (267)
9 KOG3608|consensus 99.4 1E-13 2.2E-18 94.8 3.6 104 39-143 184-316 (467)
10 KOG3608|consensus 99.4 5.3E-13 1.1E-17 91.4 3.9 107 32-143 235-345 (467)
11 PLN03086 PRLI-interacting fact 99.3 4.4E-12 9.5E-17 93.1 5.6 109 29-145 448-566 (567)
12 PHA00733 hypothetical protein 99.2 1E-11 2.3E-16 75.4 2.5 80 62-144 39-124 (128)
13 PHA02768 hypothetical protein; 99.0 6.8E-11 1.5E-15 60.2 1.0 43 91-136 6-48 (55)
14 PHA00733 hypothetical protein 99.0 3.6E-10 7.7E-15 68.7 2.5 85 29-115 35-124 (128)
15 PHA02768 hypothetical protein; 98.8 1.3E-09 2.8E-14 55.5 1.6 41 34-77 5-45 (55)
16 KOG3993|consensus 98.8 1.4E-09 3E-14 76.4 1.1 81 33-114 266-380 (500)
17 PF13465 zf-H2C2_2: Zinc-finge 98.8 3.9E-09 8.5E-14 46.1 1.5 26 105-131 1-26 (26)
18 PHA00616 hypothetical protein 98.7 8.8E-09 1.9E-13 50.0 2.4 29 119-147 1-29 (44)
19 PLN03086 PRLI-interacting fact 98.6 2.9E-08 6.3E-13 73.4 4.0 76 62-142 452-537 (567)
20 PF13465 zf-H2C2_2: Zinc-finge 98.5 1.7E-08 3.6E-13 44.1 0.1 25 49-74 1-25 (26)
21 PHA00616 hypothetical protein 98.4 4.5E-08 9.7E-13 47.6 0.3 34 34-68 1-34 (44)
22 PHA00732 hypothetical protein 98.4 1.1E-07 2.4E-12 52.8 1.6 46 90-141 1-46 (79)
23 PF05605 zf-Di19: Drought indu 98.3 1.5E-06 3.3E-11 44.8 4.3 52 90-144 2-54 (54)
24 PHA00732 hypothetical protein 98.2 1.2E-06 2.5E-11 48.7 2.2 40 34-76 1-40 (79)
25 PF00096 zf-C2H2: Zinc finger, 98.2 1.1E-06 2.5E-11 37.0 1.6 22 120-141 1-22 (23)
26 PF13894 zf-C2H2_4: C2H2-type 98.1 2.1E-06 4.6E-11 36.4 2.0 24 120-143 1-24 (24)
27 KOG3993|consensus 98.1 6.6E-07 1.4E-11 63.3 0.3 84 63-146 267-383 (500)
28 PF13912 zf-C2H2_6: C2H2-type 98.0 2.4E-06 5.3E-11 37.5 1.4 26 119-144 1-26 (27)
29 PF00096 zf-C2H2: Zinc finger, 97.9 8.9E-06 1.9E-10 34.2 1.9 23 91-113 1-23 (23)
30 PF09237 GAGA: GAGA factor; I 97.9 9.7E-06 2.1E-10 40.3 1.9 38 110-147 15-52 (54)
31 PF13912 zf-C2H2_6: C2H2-type 97.8 1.1E-05 2.3E-10 35.3 1.0 26 34-59 1-26 (27)
32 PF13894 zf-C2H2_4: C2H2-type 97.6 6.4E-05 1.4E-09 31.6 2.0 24 91-114 1-24 (24)
33 PF12756 zf-C2H2_2: C2H2 type 97.6 5.2E-05 1.1E-09 43.9 2.3 74 65-143 1-74 (100)
34 PF12756 zf-C2H2_2: C2H2 type 97.5 8.2E-05 1.8E-09 43.1 2.2 75 36-115 1-75 (100)
35 smart00355 ZnF_C2H2 zinc finge 97.5 0.00013 2.9E-09 31.1 2.4 23 120-142 1-23 (26)
36 PF05605 zf-Di19: Drought indu 97.4 8.1E-05 1.8E-09 38.3 1.5 37 34-71 2-39 (54)
37 COG5189 SFP1 Putative transcri 97.2 9.2E-05 2E-09 51.0 0.6 53 88-140 347-419 (423)
38 COG5189 SFP1 Putative transcri 97.2 0.0002 4.4E-09 49.4 2.0 72 31-111 346-419 (423)
39 PF09237 GAGA: GAGA factor; I 97.2 0.00023 5E-09 35.5 1.6 37 26-63 16-52 (54)
40 PF13909 zf-H2C2_5: C2H2-type 97.1 0.00046 1E-08 29.1 1.6 24 120-144 1-24 (24)
41 PF12874 zf-met: Zinc-finger o 96.9 0.00055 1.2E-08 29.1 1.3 22 120-141 1-22 (25)
42 smart00355 ZnF_C2H2 zinc finge 96.8 0.00091 2E-08 28.3 1.7 24 91-114 1-24 (26)
43 PRK04860 hypothetical protein; 96.8 0.0012 2.7E-08 41.7 2.5 38 90-132 119-156 (160)
44 PF12171 zf-C2H2_jaz: Zinc-fin 96.5 0.0023 5E-08 27.8 1.9 22 35-56 2-23 (27)
45 PRK04860 hypothetical protein; 96.5 0.001 2.2E-08 42.1 0.8 37 34-75 119-155 (160)
46 PF12874 zf-met: Zinc-finger o 96.4 0.0026 5.6E-08 27.0 1.5 23 91-113 1-23 (25)
47 PF13909 zf-H2C2_5: C2H2-type 96.1 0.006 1.3E-07 25.6 2.0 24 91-115 1-24 (24)
48 PF12171 zf-C2H2_jaz: Zinc-fin 95.6 0.0057 1.2E-07 26.5 0.9 21 91-111 2-22 (27)
49 PF13913 zf-C2HC_2: zinc-finge 95.5 0.011 2.5E-07 25.1 1.6 19 121-140 4-22 (25)
50 KOG2893|consensus 94.8 0.006 1.3E-07 40.7 -0.6 48 93-145 13-60 (341)
51 smart00451 ZnF_U1 U1-like zinc 94.7 0.024 5.3E-07 26.0 1.6 22 119-140 3-24 (35)
52 smart00451 ZnF_U1 U1-like zinc 94.3 0.022 4.7E-07 26.1 0.9 23 34-56 3-25 (35)
53 COG4049 Uncharacterized protei 93.5 0.072 1.6E-06 27.2 1.9 27 117-143 15-41 (65)
54 PF09538 FYDLN_acid: Protein o 93.3 0.077 1.7E-06 31.4 2.1 33 32-76 7-39 (108)
55 COG4049 Uncharacterized protei 92.3 0.041 8.9E-07 28.0 0.1 32 28-59 11-42 (65)
56 KOG1146|consensus 92.2 0.12 2.6E-06 42.8 2.5 75 33-111 464-539 (1406)
57 cd00350 rubredoxin_like Rubred 90.4 0.23 5E-06 22.6 1.5 10 118-127 16-25 (33)
58 COG5048 FOG: Zn-finger [Genera 90.3 0.056 1.2E-06 39.2 -0.9 57 89-146 288-350 (467)
59 COG5048 FOG: Zn-finger [Genera 90.1 0.33 7.2E-06 35.2 3.0 44 33-77 288-337 (467)
60 PF09986 DUF2225: Uncharacteri 89.0 0.21 4.6E-06 33.3 1.2 24 32-55 3-26 (214)
61 TIGR02300 FYDLN_acid conserved 88.6 0.36 7.7E-06 29.3 1.8 33 32-76 7-39 (129)
62 KOG2231|consensus 88.5 0.36 7.9E-06 37.5 2.2 92 45-144 125-237 (669)
63 PRK14890 putative Zn-ribbon RN 88.4 1.4 3E-05 22.9 3.7 11 117-127 46-56 (59)
64 PF04959 ARS2: Arsenite-resist 87.8 0.19 4.1E-06 33.5 0.4 30 86-115 73-102 (214)
65 PF09986 DUF2225: Uncharacteri 87.3 0.16 3.5E-06 33.9 -0.2 16 62-77 4-19 (214)
66 PRK00464 nrdR transcriptional 86.5 0.58 1.3E-05 29.6 2.0 14 64-77 29-42 (154)
67 KOG1146|consensus 86.3 0.12 2.7E-06 42.7 -1.3 108 34-145 1228-1354(1406)
68 COG1592 Rubrerythrin [Energy p 85.7 0.6 1.3E-05 29.9 1.8 24 90-127 134-157 (166)
69 PF02892 zf-BED: BED zinc fing 85.5 0.69 1.5E-05 22.4 1.6 26 118-143 15-44 (45)
70 COG1198 PriA Primosomal protei 85.2 0.87 1.9E-05 36.1 2.7 49 64-128 436-484 (730)
71 cd00729 rubredoxin_SM Rubredox 84.4 0.99 2.1E-05 20.7 1.7 10 118-127 17-26 (34)
72 PF10571 UPF0547: Uncharacteri 84.1 0.86 1.9E-05 19.5 1.4 8 93-100 17-24 (26)
73 TIGR02605 CxxC_CxxC_SSSS putat 84.0 0.43 9.4E-06 24.0 0.5 12 35-46 6-17 (52)
74 PF13719 zinc_ribbon_5: zinc-r 84.0 0.99 2.1E-05 21.0 1.7 10 120-129 26-35 (37)
75 TIGR02098 MJ0042_CXXC MJ0042 f 84.0 0.94 2E-05 21.1 1.6 10 120-129 26-35 (38)
76 PF05443 ROS_MUCR: ROS/MUCR tr 83.1 0.75 1.6E-05 28.3 1.3 24 119-145 72-95 (132)
77 COG2888 Predicted Zn-ribbon RN 83.0 1 2.2E-05 23.4 1.5 33 62-98 26-58 (61)
78 TIGR00373 conserved hypothetic 82.7 0.99 2.1E-05 28.7 1.8 30 62-99 108-137 (158)
79 PRK06266 transcription initiat 82.4 1.1 2.3E-05 29.2 1.9 14 63-76 117-130 (178)
80 smart00659 RPOLCX RNA polymera 82.3 1.5 3.3E-05 21.4 2.0 10 64-73 3-12 (44)
81 PF12013 DUF3505: Protein of u 82.0 1.2 2.6E-05 26.3 1.9 25 120-144 81-109 (109)
82 PF09723 Zn-ribbon_8: Zinc rib 81.7 1.1 2.4E-05 21.5 1.4 11 35-45 6-16 (42)
83 COG1997 RPL43A Ribosomal prote 81.1 0.86 1.9E-05 25.7 1.0 30 63-101 35-64 (89)
84 PRK09678 DNA-binding transcrip 81.1 0.6 1.3E-05 25.5 0.4 42 64-106 2-45 (72)
85 smart00614 ZnF_BED BED zinc fi 81.1 1.4 3.1E-05 22.0 1.7 21 121-141 20-45 (50)
86 PRK00398 rpoP DNA-directed RNA 80.9 1.1 2.4E-05 21.9 1.3 29 63-100 3-31 (46)
87 smart00531 TFIIE Transcription 80.6 1.5 3.1E-05 27.5 2.0 36 62-100 98-133 (147)
88 PF13717 zinc_ribbon_4: zinc-r 80.5 1.6 3.5E-05 20.2 1.7 10 120-129 26-35 (36)
89 smart00834 CxxC_CXXC_SSSS Puta 80.1 0.91 2E-05 21.4 0.8 11 64-74 6-16 (41)
90 PF03604 DNA_RNApol_7kD: DNA d 79.2 1.7 3.7E-05 19.6 1.5 7 120-126 18-24 (32)
91 PF14353 CpXC: CpXC protein 78.9 0.61 1.3E-05 28.4 -0.1 42 35-76 2-51 (128)
92 COG0068 HypF Hydrogenase matur 78.4 1.1 2.4E-05 35.2 1.1 79 35-128 102-182 (750)
93 PRK14873 primosome assembly pr 77.3 2 4.3E-05 33.9 2.2 10 118-127 421-430 (665)
94 PF15135 UPF0515: Uncharacteri 76.8 3.3 7.2E-05 28.3 2.9 21 26-46 104-124 (278)
95 TIGR00622 ssl1 transcription f 76.4 7 0.00015 23.3 3.9 48 92-142 57-104 (112)
96 TIGR00595 priA primosomal prot 76.4 2.5 5.3E-05 32.2 2.5 47 65-127 215-261 (505)
97 KOG4167|consensus 76.3 0.57 1.2E-05 36.7 -0.8 29 31-59 789-817 (907)
98 COG5236 Uncharacterized conser 76.0 4.6 0.0001 29.1 3.5 102 34-140 151-272 (493)
99 PHA00626 hypothetical protein 75.8 3.6 7.9E-05 21.1 2.2 11 90-100 23-33 (59)
100 PF12907 zf-met2: Zinc-binding 75.5 1.2 2.5E-05 21.3 0.4 27 120-146 2-31 (40)
101 PF07975 C1_4: TFIIH C1-like d 73.4 2.8 6.1E-05 21.2 1.5 23 32-54 19-41 (51)
102 smart00734 ZnF_Rad18 Rad18-lik 73.0 3.5 7.6E-05 17.5 1.6 19 121-140 3-21 (26)
103 PF15269 zf-C2H2_7: Zinc-finge 72.9 2.6 5.6E-05 20.5 1.2 22 120-141 21-42 (54)
104 KOG2893|consensus 72.6 1.7 3.6E-05 29.5 0.7 40 31-76 8-47 (341)
105 KOG2186|consensus 72.4 2.6 5.7E-05 28.8 1.6 50 64-115 4-53 (276)
106 COG1996 RPC10 DNA-directed RNA 72.3 2.8 6.1E-05 21.0 1.3 10 64-73 7-16 (49)
107 PTZ00255 60S ribosomal protein 71.4 2.7 5.9E-05 24.0 1.3 32 62-102 35-66 (90)
108 PF01780 Ribosomal_L37ae: Ribo 71.1 1.7 3.6E-05 24.8 0.4 30 63-101 35-64 (90)
109 COG4957 Predicted transcriptio 71.1 2.9 6.3E-05 25.7 1.4 22 120-144 77-98 (148)
110 PF00301 Rubredoxin: Rubredoxi 69.7 5.4 0.00012 19.8 2.0 7 36-42 3-9 (47)
111 cd00730 rubredoxin Rubredoxin; 69.4 6 0.00013 19.9 2.2 8 36-43 3-10 (50)
112 PF04959 ARS2: Arsenite-resist 69.2 4 8.7E-05 27.4 1.9 29 118-146 76-104 (214)
113 KOG4173|consensus 68.9 2.2 4.7E-05 28.3 0.6 80 63-144 79-171 (253)
114 PF06524 NOA36: NOA36 protein; 68.8 1.3 2.7E-05 30.5 -0.5 20 117-136 207-226 (314)
115 KOG4167|consensus 68.3 2.1 4.5E-05 33.8 0.5 25 119-143 792-816 (907)
116 TIGR01206 lysW lysine biosynth 67.4 2.6 5.6E-05 21.6 0.6 10 64-73 3-12 (54)
117 KOG2186|consensus 66.0 2.8 6.1E-05 28.7 0.7 46 34-82 3-48 (276)
118 TIGR00280 L37a ribosomal prote 65.9 2.2 4.8E-05 24.4 0.2 31 63-102 35-65 (91)
119 COG3357 Predicted transcriptio 64.7 3.9 8.5E-05 23.3 1.0 14 62-75 57-70 (97)
120 KOG2785|consensus 64.6 6.5 0.00014 28.6 2.3 53 90-142 166-243 (390)
121 KOG4173|consensus 64.6 2.4 5.3E-05 28.0 0.2 75 35-113 80-169 (253)
122 COG1198 PriA Primosomal protei 63.5 6.7 0.00014 31.4 2.4 45 36-99 437-484 (730)
123 PRK05580 primosome assembly pr 62.9 6.6 0.00014 31.2 2.3 10 118-127 420-429 (679)
124 PF05191 ADK_lid: Adenylate ki 62.3 3.7 8.1E-05 19.0 0.6 11 91-101 2-12 (36)
125 PF04780 DUF629: Protein of un 61.8 6.2 0.00014 29.7 1.9 22 91-112 58-79 (466)
126 COG4391 Uncharacterized protei 60.9 13 0.00029 19.5 2.5 45 53-101 15-59 (62)
127 KOG3408|consensus 60.8 5.2 0.00011 24.1 1.1 27 86-112 53-79 (129)
128 PF07754 DUF1610: Domain of un 60.1 4.7 0.0001 16.9 0.6 8 63-70 16-23 (24)
129 PRK03976 rpl37ae 50S ribosomal 59.9 3.2 6.9E-05 23.7 0.1 30 63-101 36-65 (90)
130 KOG3408|consensus 57.6 7.2 0.00016 23.5 1.3 30 27-56 50-79 (129)
131 COG4530 Uncharacterized protei 57.2 6.8 0.00015 23.2 1.2 27 36-74 11-37 (129)
132 PF13451 zf-trcl: Probable zin 57.1 2.8 6E-05 21.0 -0.4 13 63-75 4-16 (49)
133 KOG2807|consensus 55.4 22 0.00049 25.5 3.6 24 119-142 345-368 (378)
134 PF02176 zf-TRAF: TRAF-type zi 54.7 8.9 0.00019 19.6 1.3 40 90-130 9-53 (60)
135 PF08274 PhnA_Zn_Ribbon: PhnA 54.3 5.6 0.00012 17.7 0.4 9 36-44 4-12 (30)
136 PF12013 DUF3505: Protein of u 52.8 13 0.00027 21.9 1.9 25 91-115 81-109 (109)
137 PF01927 Mut7-C: Mut7-C RNAse 52.5 20 0.00042 22.4 2.8 14 91-104 125-138 (147)
138 COG4888 Uncharacterized Zn rib 51.6 7.9 0.00017 22.5 0.8 43 29-76 17-59 (104)
139 PF07800 DUF1644: Protein of u 51.6 62 0.0014 20.7 5.8 56 89-146 79-135 (162)
140 smart00154 ZnF_AN1 AN1-like Zi 50.9 7.6 0.00016 18.3 0.6 15 34-48 12-26 (39)
141 PRK03824 hypA hydrogenase nick 50.7 8.2 0.00018 23.8 0.9 10 64-73 71-80 (135)
142 PF08271 TF_Zn_Ribbon: TFIIB z 50.2 17 0.00036 17.4 1.8 7 91-97 20-26 (43)
143 KOG4118|consensus 49.0 10 0.00022 20.2 0.9 30 119-148 38-67 (74)
144 PF08790 zf-LYAR: LYAR-type C2 48.6 7.9 0.00017 16.9 0.4 8 93-100 3-10 (28)
145 PF10013 DUF2256: Uncharacteri 48.3 11 0.00023 18.2 0.9 16 92-107 10-25 (42)
146 PF07282 OrfB_Zn_ribbon: Putat 48.2 18 0.00038 19.2 1.9 9 91-99 47-55 (69)
147 smart00440 ZnF_C2C2 C2C2 Zinc 47.8 22 0.00047 16.8 1.9 9 91-99 29-37 (40)
148 PF01096 TFIIS_C: Transcriptio 46.3 15 0.00032 17.3 1.2 9 91-99 29-37 (39)
149 cd00924 Cyt_c_Oxidase_Vb Cytoc 45.3 11 0.00024 21.9 0.8 15 32-46 77-91 (97)
150 PF09845 DUF2072: Zn-ribbon co 45.1 10 0.00022 23.3 0.7 15 34-48 1-15 (131)
151 PRK12380 hydrogenase nickel in 45.0 13 0.00028 22.2 1.1 10 64-73 71-80 (113)
152 PF13453 zf-TFIIB: Transcripti 44.9 24 0.00052 16.6 1.9 15 121-135 21-35 (41)
153 COG3364 Zn-ribbon containing p 44.6 11 0.00023 22.1 0.6 16 33-48 1-16 (112)
154 PRK03564 formate dehydrogenase 44.6 14 0.00031 26.3 1.4 36 32-71 185-220 (309)
155 TIGR00100 hypA hydrogenase nic 44.3 11 0.00024 22.6 0.7 11 64-74 71-81 (115)
156 smart00661 RPOL9 RNA polymeras 44.3 24 0.00052 17.3 1.9 9 91-99 21-29 (52)
157 PF14369 zf-RING_3: zinc-finge 44.0 24 0.00052 16.2 1.7 11 65-75 23-33 (35)
158 PF04216 FdhE: Protein involve 43.8 9.6 0.00021 26.8 0.5 77 34-130 172-249 (290)
159 COG1571 Predicted DNA-binding 43.6 17 0.00038 27.0 1.7 12 90-101 367-378 (421)
160 PF13824 zf-Mss51: Zinc-finger 43.1 25 0.00053 18.1 1.8 9 63-71 14-22 (55)
161 PF08209 Sgf11: Sgf11 (transcr 43.1 36 0.00077 15.5 2.2 23 91-114 5-27 (33)
162 COG5236 Uncharacterized conser 42.9 12 0.00026 27.1 0.8 76 35-115 221-306 (493)
163 PF12760 Zn_Tnp_IS1595: Transp 42.8 25 0.00055 17.0 1.8 10 88-97 35-44 (46)
164 PRK12496 hypothetical protein; 42.5 18 0.00038 23.2 1.5 29 89-130 126-154 (164)
165 COG3677 Transposase and inacti 42.5 21 0.00046 21.9 1.8 14 89-102 52-65 (129)
166 PF01428 zf-AN1: AN1-like Zinc 42.4 8.5 0.00018 18.5 0.0 16 33-48 12-27 (43)
167 PLN02294 cytochrome c oxidase 42.3 13 0.00029 23.9 0.9 15 32-46 139-153 (174)
168 PF13878 zf-C2H2_3: zinc-finge 42.2 26 0.00056 16.7 1.7 10 121-130 15-24 (41)
169 KOG2482|consensus 42.1 13 0.00029 26.8 1.0 52 91-142 145-218 (423)
170 PRK00432 30S ribosomal protein 42.0 26 0.00055 17.6 1.7 9 90-98 37-45 (50)
171 COG1655 Uncharacterized protei 41.9 7.9 0.00017 26.3 -0.1 7 120-126 63-69 (267)
172 PF04423 Rad50_zn_hook: Rad50 41.7 11 0.00025 19.0 0.5 12 92-103 22-33 (54)
173 COG2879 Uncharacterized small 41.2 31 0.00068 18.2 2.0 18 130-147 23-40 (65)
174 smart00132 LIM Zinc-binding do 41.2 28 0.0006 15.4 1.8 6 92-97 29-34 (39)
175 PF01363 FYVE: FYVE zinc finge 40.6 21 0.00046 18.8 1.4 8 37-44 12-19 (69)
176 KOG2593|consensus 40.4 18 0.00039 26.9 1.4 15 33-47 127-141 (436)
177 KOG2785|consensus 40.3 23 0.0005 26.0 1.9 25 117-141 66-90 (390)
178 COG1675 TFA1 Transcription ini 39.2 22 0.00048 23.2 1.5 14 62-75 112-125 (176)
179 TIGR01562 FdhE formate dehydro 39.1 35 0.00076 24.4 2.6 52 32-99 182-233 (305)
180 PRK00564 hypA hydrogenase nick 39.1 18 0.00039 21.7 1.1 10 35-44 72-81 (117)
181 PF07503 zf-HYPF: HypF finger; 38.6 3.6 7.8E-05 19.0 -1.5 11 119-129 21-31 (35)
182 PF05495 zf-CHY: CHY zinc fing 38.1 27 0.00058 18.9 1.6 13 35-47 11-23 (71)
183 PRK04023 DNA polymerase II lar 37.9 82 0.0018 26.7 4.7 10 119-128 663-672 (1121)
184 PF01155 HypA: Hydrogenase exp 37.6 11 0.00024 22.5 0.0 11 35-45 71-81 (113)
185 KOG3214|consensus 37.6 13 0.00028 21.6 0.3 13 120-132 48-60 (109)
186 COG4338 Uncharacterized protei 36.9 13 0.00029 18.4 0.2 16 92-107 14-29 (54)
187 PF14803 Nudix_N_2: Nudix N-te 36.5 30 0.00065 15.8 1.4 7 91-97 23-29 (34)
188 PF11789 zf-Nse: Zinc-finger o 36.1 66 0.0014 16.5 3.1 45 61-124 9-53 (57)
189 KOG2071|consensus 35.8 24 0.00051 27.5 1.5 27 117-143 416-442 (579)
190 COG1594 RPB9 DNA-directed RNA 35.7 36 0.00078 20.3 2.0 18 31-48 19-36 (113)
191 PF11672 DUF3268: Protein of u 35.4 47 0.001 19.5 2.4 7 91-97 32-38 (102)
192 PF01286 XPA_N: XPA protein N- 35.1 13 0.00029 17.0 0.1 12 121-132 5-16 (34)
193 COG2331 Uncharacterized protei 35.0 14 0.00029 20.4 0.1 10 91-100 13-22 (82)
194 COG3091 SprT Zn-dependent meta 34.8 20 0.00043 22.7 0.8 8 90-97 140-147 (156)
195 COG1773 Rubredoxin [Energy pro 34.7 15 0.00032 18.9 0.2 10 120-129 4-13 (55)
196 KOG2482|consensus 34.0 24 0.00051 25.6 1.2 23 90-112 195-217 (423)
197 PF06397 Desulfoferrod_N: Desu 33.5 16 0.00034 17.0 0.2 11 33-43 5-15 (36)
198 cd00065 FYVE FYVE domain; Zinc 33.3 28 0.00061 17.4 1.2 26 65-101 4-29 (57)
199 PRK03681 hypA hydrogenase nick 32.8 24 0.00052 21.1 0.9 10 64-73 71-80 (114)
200 TIGR00143 hypF [NiFe] hydrogen 32.4 25 0.00053 28.3 1.2 80 35-129 69-150 (711)
201 PF09332 Mcm10: Mcm10 replicat 31.5 19 0.00042 26.1 0.4 42 34-75 252-297 (344)
202 KOG1842|consensus 31.4 23 0.0005 26.6 0.8 32 29-60 10-41 (505)
203 COG5152 Uncharacterized conser 31.2 26 0.00057 23.3 0.9 16 61-76 194-209 (259)
204 KOG2907|consensus 30.9 33 0.00072 20.5 1.2 10 91-100 103-112 (116)
205 TIGR00686 phnA alkylphosphonat 30.8 31 0.00068 20.4 1.1 29 65-103 4-32 (109)
206 KOG4124|consensus 30.6 23 0.00049 25.8 0.7 24 31-54 346-371 (442)
207 PRK10220 hypothetical protein; 29.9 35 0.00075 20.3 1.2 29 65-103 5-33 (111)
208 KOG2231|consensus 29.6 31 0.00068 27.4 1.3 43 102-144 161-207 (669)
209 COG5112 UFD2 U1-like Zn-finger 29.4 34 0.00075 20.2 1.1 28 29-56 50-77 (126)
210 PF03811 Zn_Tnp_IS1: InsA N-te 29.0 20 0.00043 16.6 0.1 8 89-96 28-35 (36)
211 COG5151 SSL1 RNA polymerase II 28.3 49 0.0011 23.8 1.9 24 119-142 388-411 (421)
212 TIGR00627 tfb4 transcription f 27.9 40 0.00086 23.8 1.4 9 91-99 256-264 (279)
213 PF10276 zf-CHCC: Zinc-finger 27.3 36 0.00077 16.2 0.8 11 90-100 29-39 (40)
214 PTZ00448 hypothetical protein; 27.2 43 0.00092 24.6 1.5 23 119-141 314-336 (373)
215 smart00064 FYVE Protein presen 27.1 36 0.00079 17.8 1.0 29 63-102 10-38 (68)
216 PF05290 Baculo_IE-1: Baculovi 26.9 40 0.00086 20.9 1.2 15 61-75 78-92 (140)
217 KOG0402|consensus 26.7 25 0.00055 19.7 0.3 29 64-101 37-65 (92)
218 PF05129 Elf1: Transcription e 26.5 39 0.00085 18.9 1.0 10 91-100 47-56 (81)
219 PF01215 COX5B: Cytochrome c o 26.5 29 0.00062 21.6 0.5 16 32-47 110-125 (136)
220 COG4896 Uncharacterized protei 26.2 94 0.002 16.4 2.3 7 91-97 32-38 (68)
221 PF09963 DUF2197: Uncharacteri 26.0 38 0.00082 17.5 0.8 10 119-128 31-40 (56)
222 TIGR00416 sms DNA repair prote 26.0 46 0.001 25.2 1.6 24 62-98 6-29 (454)
223 KOG1842|consensus 25.8 36 0.00078 25.6 1.0 25 91-115 16-40 (505)
224 PTZ00043 cytochrome c oxidase 25.8 36 0.00078 23.2 0.9 17 30-46 177-193 (268)
225 PRK05978 hypothetical protein; 25.8 43 0.00094 21.1 1.2 11 65-75 54-64 (148)
226 PRK14714 DNA polymerase II lar 25.7 58 0.0012 28.2 2.2 35 64-100 668-702 (1337)
227 PF10537 WAC_Acf1_DNA_bd: ATP- 25.5 21 0.00046 20.9 -0.2 35 35-71 4-38 (102)
228 PF04780 DUF629: Protein of un 25.3 56 0.0012 24.9 1.9 14 64-77 58-71 (466)
229 PF04810 zf-Sec23_Sec24: Sec23 25.3 67 0.0014 15.0 1.6 8 90-97 24-31 (40)
230 PF15616 TerY-C: TerY-C metal 25.0 74 0.0016 19.7 2.1 8 65-72 79-86 (131)
231 smart00249 PHD PHD zinc finger 24.6 87 0.0019 14.3 2.9 10 64-73 15-24 (47)
232 PRK11823 DNA repair protein Ra 24.6 52 0.0011 24.9 1.7 24 62-98 6-29 (446)
233 PF10083 DUF2321: Uncharacteri 24.3 59 0.0013 20.7 1.6 18 88-105 66-83 (158)
234 KOG0717|consensus 23.6 47 0.001 25.2 1.2 21 120-140 293-313 (508)
235 smart00731 SprT SprT homologue 23.6 74 0.0016 19.8 2.0 32 90-129 112-143 (146)
236 TIGR00515 accD acetyl-CoA carb 23.6 39 0.00084 23.9 0.8 33 34-76 26-58 (285)
237 PF14787 zf-CCHC_5: GAG-polypr 23.6 39 0.00086 15.7 0.6 14 92-105 4-17 (36)
238 PLN02748 tRNA dimethylallyltra 23.5 54 0.0012 25.0 1.6 24 118-141 417-441 (468)
239 PF04606 Ogr_Delta: Ogr/Delta- 23.5 19 0.00041 17.6 -0.5 7 66-72 2-8 (47)
240 PRK00762 hypA hydrogenase nick 23.3 47 0.001 20.2 1.1 13 33-46 69-81 (124)
241 COG4306 Uncharacterized protei 22.8 55 0.0012 20.0 1.2 16 88-103 66-81 (160)
242 PF10263 SprT-like: SprT-like 22.7 37 0.00081 21.2 0.5 32 90-130 123-154 (157)
243 PLN03238 probable histone acet 22.5 81 0.0018 22.4 2.1 24 117-140 46-69 (290)
244 PF02748 PyrI_C: Aspartate car 22.4 52 0.0011 16.6 0.9 17 86-102 31-47 (52)
245 PF00412 LIM: LIM domain; Int 22.3 59 0.0013 16.1 1.2 12 63-74 26-37 (58)
246 PRK00420 hypothetical protein; 22.0 61 0.0013 19.4 1.3 9 91-99 41-49 (112)
247 COG1327 Predicted transcriptio 22.0 40 0.00088 21.4 0.6 13 64-76 29-41 (156)
248 KOG3507|consensus 21.8 74 0.0016 16.6 1.4 12 119-130 37-48 (62)
249 PRK14892 putative transcriptio 21.8 91 0.002 18.2 2.0 9 33-41 20-28 (99)
250 KOG2272|consensus 21.6 1.1E+02 0.0024 21.3 2.6 13 119-131 221-233 (332)
251 PF03145 Sina: Seven in absent 21.6 94 0.002 20.4 2.3 12 134-145 62-73 (198)
252 PF14446 Prok-RING_1: Prokaryo 21.3 33 0.00071 17.6 0.1 10 65-74 7-16 (54)
253 PRK04351 hypothetical protein; 21.1 51 0.0011 20.8 0.9 32 90-130 112-143 (149)
254 COG4640 Predicted membrane pro 20.7 78 0.0017 23.6 1.8 13 64-76 16-28 (465)
255 CHL00174 accD acetyl-CoA carbo 20.2 49 0.0011 23.6 0.7 32 35-76 39-70 (296)
256 PF07295 DUF1451: Protein of u 20.1 24 0.00053 22.2 -0.7 12 88-99 110-121 (146)
257 KOG4727|consensus 20.0 67 0.0015 20.9 1.2 24 31-54 72-95 (193)
No 1
>KOG2462|consensus
Probab=99.91 E-value=1.9e-24 Score=142.17 Aligned_cols=105 Identities=23% Similarity=0.400 Sum_probs=56.0
Q ss_pred CCccccCccccccCChhHHhcccccccCCCCcccCCCCCCcccccc-cccccccCCCCCceecCccccccccchhHHhhH
Q psy12018 32 YGKFACDVCGKEYQYYRNLYRHKKFECGQEPRYQCPQCPYRTKQKE-LGWESLKPNAYGMYVCDICGKVYQHKRTLYRHK 110 (148)
Q Consensus 32 ~~~~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~~C~~c~~~f~~~~-~~~~~~~~~~~~~~~C~~c~~~f~~~~~l~~H~ 110 (148)
.+.+.|..|++.|.+...|..|+++|. -+++|.+||+.|...= ++-+.+.|+|||||.|+.|++.|..+++|+.|+
T Consensus 159 ~ka~~C~~C~K~YvSmpALkMHirTH~---l~c~C~iCGKaFSRPWLLQGHiRTHTGEKPF~C~hC~kAFADRSNLRAHm 235 (279)
T KOG2462|consen 159 KKAFSCKYCGKVYVSMPALKMHIRTHT---LPCECGICGKAFSRPWLLQGHIRTHTGEKPFSCPHCGKAFADRSNLRAHM 235 (279)
T ss_pred cccccCCCCCceeeehHHHhhHhhccC---CCcccccccccccchHHhhcccccccCCCCccCCcccchhcchHHHHHHH
Confidence 444555555555555555555555553 2455555555555432 334444455555555555555555555555555
Q ss_pred hhhhCCCCceeCCCChhhhhchHHHHHHHH
Q psy12018 111 KDECGQEPRFQCPQCPYRAKQKANLKTHLI 140 (148)
Q Consensus 111 ~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~ 140 (148)
++|.+ .++|+|..|+|.|...+-|.+|..
T Consensus 236 QTHS~-~K~~qC~~C~KsFsl~SyLnKH~E 264 (279)
T KOG2462|consen 236 QTHSD-VKKHQCPRCGKSFALKSYLNKHSE 264 (279)
T ss_pred HhhcC-CccccCcchhhHHHHHHHHHHhhh
Confidence 55555 445555555555555555555543
No 2
>KOG2462|consensus
Probab=99.91 E-value=1.1e-24 Score=143.31 Aligned_cols=114 Identities=26% Similarity=0.479 Sum_probs=99.3
Q ss_pred CCCccccCccccccCChhHHhcccccccCC--CCcccCCCCCCcccccc-cccccccCCCCCceecCccccccccchhHH
Q psy12018 31 LYGKFACDVCGKEYQYYRNLYRHKKFECGQ--EPRYQCPQCPYRTKQKE-LGWESLKPNAYGMYVCDICGKVYQHKRTLY 107 (148)
Q Consensus 31 ~~~~~~C~~C~~~f~~~~~l~~h~~~~~~~--~~~~~C~~c~~~f~~~~-~~~~~~~~~~~~~~~C~~c~~~f~~~~~l~ 107 (148)
....|.|+.|++.+...++|.+|.++|... .+.+.|+.|++.+.+.. +..+.+.| .-+++|..||+.|.+.+.|+
T Consensus 127 ~~~r~~c~eCgk~ysT~snLsrHkQ~H~~~~s~ka~~C~~C~K~YvSmpALkMHirTH--~l~c~C~iCGKaFSRPWLLQ 204 (279)
T KOG2462|consen 127 KHPRYKCPECGKSYSTSSNLSRHKQTHRSLDSKKAFSCKYCGKVYVSMPALKMHIRTH--TLPCECGICGKAFSRPWLLQ 204 (279)
T ss_pred cCCceeccccccccccccccchhhcccccccccccccCCCCCceeeehHHHhhHhhcc--CCCcccccccccccchHHhh
Confidence 455699999999999999999999998753 47899999999999876 33333333 35789999999999999999
Q ss_pred hhHhhhhCCCCceeCCCChhhhhchHHHHHHHHhhcCCcc
Q psy12018 108 RHKKDECGQEPRFQCPQCPYRAKQKANLKTHLIIKHDSVL 147 (148)
Q Consensus 108 ~H~~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~~h~~~~ 147 (148)
.|+|+|+| ||||.|..|+++|..+++|+.||.+|.+-+.
T Consensus 205 GHiRTHTG-EKPF~C~hC~kAFADRSNLRAHmQTHS~~K~ 243 (279)
T KOG2462|consen 205 GHIRTHTG-EKPFSCPHCGKAFADRSNLRAHMQTHSDVKK 243 (279)
T ss_pred cccccccC-CCCccCCcccchhcchHHHHHHHHhhcCCcc
Confidence 99999999 9999999999999999999999999987654
No 3
>KOG3576|consensus
Probab=99.67 E-value=1.4e-17 Score=105.50 Aligned_cols=117 Identities=25% Similarity=0.448 Sum_probs=102.0
Q ss_pred CCCCccccCccccccCChhHHhcccccccCCCCcccCCCCCCcccccc-cccccccCCCCCceecCccccccccchhHHh
Q psy12018 30 KLYGKFACDVCGKEYQYYRNLYRHKKFECGQEPRYQCPQCPYRTKQKE-LGWESLKPNAYGMYVCDICGKVYQHKRTLYR 108 (148)
Q Consensus 30 ~~~~~~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~~C~~c~~~f~~~~-~~~~~~~~~~~~~~~C~~c~~~f~~~~~l~~ 108 (148)
.+...|.|.+|++.|....-|.+|++-|.. .+-+.|..||+.|...- +..+.+.|+|.+||+|..|++.|...-.|..
T Consensus 113 sd~d~ftCrvCgK~F~lQRmlnrh~kch~~-vkr~lct~cgkgfndtfdlkrh~rthtgvrpykc~~c~kaftqrcsles 191 (267)
T KOG3576|consen 113 SDQDSFTCRVCGKKFGLQRMLNRHLKCHSD-VKRHLCTFCGKGFNDTFDLKRHTRTHTGVRPYKCSLCEKAFTQRCSLES 191 (267)
T ss_pred CCCCeeeeehhhhhhhHHHHHHHHhhhccH-HHHHHHhhccCcccchhhhhhhhccccCccccchhhhhHHHHhhccHHH
Confidence 345679999999999999999999999877 78899999999999876 5555567899999999999999999999999
Q ss_pred hHhhhhCC----------CCceeCCCChhhhhchHHHHHHHHhhcCCcc
Q psy12018 109 HKKDECGQ----------EPRFQCPQCPYRAKQKANLKTHLIIKHDSVL 147 (148)
Q Consensus 109 H~~~~~~~----------~~~~~C~~C~~~f~~~~~l~~H~~~~h~~~~ 147 (148)
|.+.-+|. ++-|.|..||..-.....+..|++.+|...+
T Consensus 192 hl~kvhgv~~~yaykerr~kl~vcedcg~t~~~~e~~~~h~~~~hp~Sp 240 (267)
T KOG3576|consen 192 HLKKVHGVQHQYAYKERRAKLYVCEDCGYTSERPEVYYLHLKLHHPFSP 240 (267)
T ss_pred HHHHHcCchHHHHHHHhhhheeeecccCCCCCChhHHHHHHHhcCCCCH
Confidence 98876662 4569999999999999999999999998654
No 4
>KOG1074|consensus
Probab=99.66 E-value=3.5e-17 Score=121.54 Aligned_cols=56 Identities=29% Similarity=0.485 Sum_probs=51.8
Q ss_pred eecCccccccccchhHHhhHhhhhCCCCceeCCCChhhhhchHHHHHHHHhhcCCcc
Q psy12018 91 YVCDICGKVYQHKRTLYRHKKDECGQEPRFQCPQCPYRAKQKANLKTHLIIKHDSVL 147 (148)
Q Consensus 91 ~~C~~c~~~f~~~~~l~~H~~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~~h~~~~ 147 (148)
-.|..|.|.+.=.++|+-|.++|+| |+||+|.+||++|.++.+|+.|+.+|-...+
T Consensus 606 NqCiiC~rVlSC~saLqmHyrtHtG-ERPFkCKiCgRAFtTkGNLkaH~~vHka~p~ 661 (958)
T KOG1074|consen 606 NQCIICLRVLSCPSALQMHYRTHTG-ERPFKCKICGRAFTTKGNLKAHMSVHKAKPP 661 (958)
T ss_pred cceeeeeecccchhhhhhhhhcccC-cCccccccccchhccccchhhcccccccCcc
Confidence 3799999999999999999999999 9999999999999999999999998876543
No 5
>KOG3623|consensus
Probab=99.53 E-value=4.7e-16 Score=114.34 Aligned_cols=106 Identities=25% Similarity=0.579 Sum_probs=89.8
Q ss_pred ccccCccccccCChhHHhccccc-ccCCCCcccCCCCCCcccccccccccccCC--------------CCCceecCcccc
Q psy12018 34 KFACDVCGKEYQYYRNLYRHKKF-ECGQEPRYQCPQCPYRTKQKELGWESLKPN--------------AYGMYVCDICGK 98 (148)
Q Consensus 34 ~~~C~~C~~~f~~~~~l~~h~~~-~~~~~~~~~C~~c~~~f~~~~~~~~~~~~~--------------~~~~~~C~~c~~ 98 (148)
...|+.|.+.+.+...|+.|++- |..++..|.|..|..+|.+...+.+++..+ .-+.|+|.+|++
T Consensus 210 lltcpycdrgykrltslkeHikyrhekne~nfsC~lCsytFAyRtQLErhm~~hkpg~dqa~sltqsa~lRKFKCtECgK 289 (1007)
T KOG3623|consen 210 LLTCPYCDRGYKRLTSLKEHIKYRHEKNEPNFSCMLCSYTFAYRTQLERHMQLHKPGGDQAISLTQSALLRKFKCTECGK 289 (1007)
T ss_pred hhcchhHHHHHHHHHHHHHHHHHHHhhCCCCCcchhhhhhhhhHHHHHHHHHhhcCCCcccccccchhhhccccccccch
Confidence 56799999999999999999754 444467799999999999876555544321 136799999999
Q ss_pred ccccchhHHhhHhhhhCCCCceeCCCChhhhhchHHHHHHHH
Q psy12018 99 VYQHKRTLYRHKKDECGQEPRFQCPQCPYRAKQKANLKTHLI 140 (148)
Q Consensus 99 ~f~~~~~l~~H~~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~ 140 (148)
.|..+..|..|+|+|.| ||||.|.-|+|.|+.+..+..|+.
T Consensus 290 AFKfKHHLKEHlRIHSG-EKPfeCpnCkKRFSHSGSySSHmS 330 (1007)
T KOG3623|consen 290 AFKFKHHLKEHLRIHSG-EKPFECPNCKKRFSHSGSYSSHMS 330 (1007)
T ss_pred hhhhHHHHHhhheeecC-CCCcCCcccccccccCCccccccc
Confidence 99999999999999999 999999999999999988888875
No 6
>KOG3623|consensus
Probab=99.50 E-value=5.8e-15 Score=108.70 Aligned_cols=76 Identities=29% Similarity=0.549 Sum_probs=50.1
Q ss_pred cccCCCCCCcccccccccccc-cCCCCCceecCccccccccchhHHhhHhhhhCCCCceeCCCChhhhhchHHHHHHH
Q psy12018 63 RYQCPQCPYRTKQKELGWESL-KPNAYGMYVCDICGKVYQHKRTLYRHKKDECGQEPRFQCPQCPYRAKQKANLKTHL 139 (148)
Q Consensus 63 ~~~C~~c~~~f~~~~~~~~~~-~~~~~~~~~C~~c~~~f~~~~~l~~H~~~~~~~~~~~~C~~C~~~f~~~~~l~~H~ 139 (148)
.|.|.+|.+.|.-.+.+.+|. .|+|.+||+|.+|.+.|..+..|..|.|.|.| ||||+|..|+|.|+.+..+..||
T Consensus 894 myaCDqCDK~FqKqSSLaRHKYEHsGqRPyqC~iCkKAFKHKHHLtEHkRLHSG-EKPfQCdKClKRFSHSGSYSQHM 970 (1007)
T KOG3623|consen 894 MYACDQCDKAFQKQSSLARHKYEHSGQRPYQCIICKKAFKHKHHLTEHKRLHSG-EKPFQCDKCLKRFSHSGSYSQHM 970 (1007)
T ss_pred cchHHHHHHHHHhhHHHHHhhhhhcCCCCcccchhhHhhhhhhhhhhhhhhccC-CCcchhhhhhhhcccccchHhhh
Confidence 344444444443333222222 24555566677777777777788888888888 88888888888888888887776
No 7
>KOG1074|consensus
Probab=99.47 E-value=5.3e-14 Score=104.98 Aligned_cols=56 Identities=27% Similarity=0.469 Sum_probs=52.2
Q ss_pred eecCccccccccchhHHhhHhhhhCCCCceeCCCChhhhhchHHHHHHHHhhcCCcc
Q psy12018 91 YVCDICGKVYQHKRTLYRHKKDECGQEPRFQCPQCPYRAKQKANLKTHLIIKHDSVL 147 (148)
Q Consensus 91 ~~C~~c~~~f~~~~~l~~H~~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~~h~~~~ 147 (148)
..|..|++.|...++|..|+++|++ ++||.|..|++.|.+...|..||..|+...+
T Consensus 880 h~C~vCgk~FsSSsALqiH~rTHtg-~KPF~C~fC~~aFttrgnLKvHMgtH~w~q~ 935 (958)
T KOG1074|consen 880 HVCNVCGKQFSSSAALEIHMRTHTG-PKPFFCHFCEEAFTTRGNLKVHMGTHMWVQP 935 (958)
T ss_pred hhhccchhcccchHHHHHhhhcCCC-CCCccchhhhhhhhhhhhhhhhhccccccCC
Confidence 4699999999999999999999999 8999999999999999999999999876543
No 8
>KOG3576|consensus
Probab=99.43 E-value=1.4e-14 Score=92.08 Aligned_cols=84 Identities=23% Similarity=0.467 Sum_probs=74.6
Q ss_pred CCcccCCCCCCccccccccccccc-CCCCCceecCccccccccchhHHhhHhhhhCCCCceeCCCChhhhhchHHHHHHH
Q psy12018 61 EPRYQCPQCPYRTKQKELGWESLK-PNAYGMYVCDICGKVYQHKRTLYRHKKDECGQEPRFQCPQCPYRAKQKANLKTHL 139 (148)
Q Consensus 61 ~~~~~C~~c~~~f~~~~~~~~~~~-~~~~~~~~C~~c~~~f~~~~~l~~H~~~~~~~~~~~~C~~C~~~f~~~~~l~~H~ 139 (148)
...|.|..|++.|.....+.+++. |...+.|.|..||+.|...-+|.+|.++|+| -+||+|+.|+|+|.++..|..|+
T Consensus 115 ~d~ftCrvCgK~F~lQRmlnrh~kch~~vkr~lct~cgkgfndtfdlkrh~rthtg-vrpykc~~c~kaftqrcsleshl 193 (267)
T KOG3576|consen 115 QDSFTCRVCGKKFGLQRMLNRHLKCHSDVKRHLCTFCGKGFNDTFDLKRHTRTHTG-VRPYKCSLCEKAFTQRCSLESHL 193 (267)
T ss_pred CCeeeeehhhhhhhHHHHHHHHhhhccHHHHHHHhhccCcccchhhhhhhhccccC-ccccchhhhhHHHHhhccHHHHH
Confidence 356999999999998776666654 5556889999999999999999999999999 89999999999999999999999
Q ss_pred HhhcCC
Q psy12018 140 IIKHDS 145 (148)
Q Consensus 140 ~~~h~~ 145 (148)
+..||-
T Consensus 194 ~kvhgv 199 (267)
T KOG3576|consen 194 KKVHGV 199 (267)
T ss_pred HHHcCc
Confidence 988763
No 9
>KOG3608|consensus
Probab=99.43 E-value=1e-13 Score=94.77 Aligned_cols=104 Identities=20% Similarity=0.407 Sum_probs=78.1
Q ss_pred ccccccCChhHHhcccccccCCCCcccCCCCCCcccccc-cccccccC----------------------------CCCC
Q psy12018 39 VCGKEYQYYRNLYRHKKFECGQEPRYQCPQCPYRTKQKE-LGWESLKP----------------------------NAYG 89 (148)
Q Consensus 39 ~C~~~f~~~~~l~~h~~~~~~~~~~~~C~~c~~~f~~~~-~~~~~~~~----------------------------~~~~ 89 (148)
.|-+.|..++.|+.|++.|.+ ||...|+.||.-|.+.. ++.+.+.. ....
T Consensus 184 ~Ct~~~~~k~~LreH~r~Hs~-eKvvACp~Cg~~F~~~tkl~DH~rRqt~l~~n~fqC~~C~KrFaTeklL~~Hv~rHvn 262 (467)
T KOG3608|consen 184 MCTKHMGNKYRLREHIRTHSN-EKVVACPHCGELFRTKTKLFDHLRRQTELNTNSFQCAQCFKRFATEKLLKSHVVRHVN 262 (467)
T ss_pred hhhhhhccHHHHHHHHHhcCC-CeEEecchHHHHhccccHHHHHHHhhhhhcCCchHHHHHHHHHhHHHHHHHHHHHhhh
Confidence 377788888888888888877 67777777777777653 22221111 1124
Q ss_pred ceecCccccccccchhHHhhHhhhhCCCCceeCCCChhhhhchHHHHHHHHhhc
Q psy12018 90 MYVCDICGKVYQHKRTLYRHKKDECGQEPRFQCPQCPYRAKQKANLKTHLIIKH 143 (148)
Q Consensus 90 ~~~C~~c~~~f~~~~~l~~H~~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~~h 143 (148)
.|+|+.|+.+....+.|..|++.-+...+||+|..|.+.|.+-+.|.+|..+|.
T Consensus 263 ~ykCplCdmtc~~~ssL~~H~r~rHs~dkpfKCd~Cd~~c~~esdL~kH~~~HS 316 (467)
T KOG3608|consen 263 CYKCPLCDMTCSSASSLTTHIRYRHSKDKPFKCDECDTRCVRESDLAKHVQVHS 316 (467)
T ss_pred cccccccccCCCChHHHHHHHHhhhccCCCccccchhhhhccHHHHHHHHHhcc
Confidence 588999999999999999998876666899999999999999999999988665
No 10
>KOG3608|consensus
Probab=99.36 E-value=5.3e-13 Score=91.35 Aligned_cols=107 Identities=20% Similarity=0.436 Sum_probs=79.9
Q ss_pred CCccccCccccccCChhHHhcccccccCCCCcccCCCCCCcccccccccccc--cCCCCCceecCccccccccchhHHhh
Q psy12018 32 YGKFACDVCGKEYQYYRNLYRHKKFECGQEPRYQCPQCPYRTKQKELGWESL--KPNAYGMYVCDICGKVYQHKRTLYRH 109 (148)
Q Consensus 32 ~~~~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~~C~~c~~~f~~~~~~~~~~--~~~~~~~~~C~~c~~~f~~~~~l~~H 109 (148)
..+|.|..|.+.|.....|..|++.|. ..|+|+.|..+....+.+..++ .|..+++|+|..|+..|...+.|.+|
T Consensus 235 ~n~fqC~~C~KrFaTeklL~~Hv~rHv---n~ykCplCdmtc~~~ssL~~H~r~rHs~dkpfKCd~Cd~~c~~esdL~kH 311 (467)
T KOG3608|consen 235 TNSFQCAQCFKRFATEKLLKSHVVRHV---NCYKCPLCDMTCSSASSLTTHIRYRHSKDKPFKCDECDTRCVRESDLAKH 311 (467)
T ss_pred CCchHHHHHHHHHhHHHHHHHHHHHhh---hcccccccccCCCChHHHHHHHHhhhccCCCccccchhhhhccHHHHHHH
Confidence 458888888888888888888887773 4688888888777766443333 24557888888888888888888888
Q ss_pred HhhhhCCCCceeCCC--ChhhhhchHHHHHHHHhhc
Q psy12018 110 KKDECGQEPRFQCPQ--CPYRAKQKANLKTHLIIKH 143 (148)
Q Consensus 110 ~~~~~~~~~~~~C~~--C~~~f~~~~~l~~H~~~~h 143 (148)
...|. +..|+|.. |..+|.+..++.+|++-+|
T Consensus 312 ~~~HS--~~~y~C~h~~C~~s~r~~~q~~~H~~evh 345 (467)
T KOG3608|consen 312 VQVHS--KTVYQCEHPDCHYSVRTYTQMRRHFLEVH 345 (467)
T ss_pred HHhcc--ccceecCCCCCcHHHHHHHHHHHHHHHhc
Confidence 88775 35677766 7777777777777777666
No 11
>PLN03086 PRLI-interacting factor K; Provisional
Probab=99.30 E-value=4.4e-12 Score=93.08 Aligned_cols=109 Identities=21% Similarity=0.442 Sum_probs=86.1
Q ss_pred CCCCCccccCccccccCChhHHhcccccccCCCCcccCCCCCCcccccccccccccCCCCCceecCcccccccc------
Q psy12018 29 PKLYGKFACDVCGKEYQYYRNLYRHKKFECGQEPRYQCPQCPYRTKQKELGWESLKPNAYGMYVCDICGKVYQH------ 102 (148)
Q Consensus 29 ~~~~~~~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~~C~~c~~~f~~~~~~~~~~~~~~~~~~~C~~c~~~f~~------ 102 (148)
...++.+.|+.|++.|. ...|..|+++++ +++.|+ |+..+....+..+...+...+++.|..|+..|..
T Consensus 448 ~el~~H~~C~~Cgk~f~-~s~LekH~~~~H---kpv~Cp-Cg~~~~R~~L~~H~~thCp~Kpi~C~fC~~~v~~g~~~~d 522 (567)
T PLN03086 448 EEAKNHVHCEKCGQAFQ-QGEMEKHMKVFH---EPLQCP-CGVVLEKEQMVQHQASTCPLRLITCRFCGDMVQAGGSAMD 522 (567)
T ss_pred cccccCccCCCCCCccc-hHHHHHHHHhcC---CCccCC-CCCCcchhHHHhhhhccCCCCceeCCCCCCccccCccccc
Confidence 34567789999999996 578999999874 589999 9976644334444455778899999999998852
Q ss_pred ----chhHHhhHhhhhCCCCceeCCCChhhhhchHHHHHHHHhhcCC
Q psy12018 103 ----KRTLYRHKKDECGQEPRFQCPQCPYRAKQKANLKTHLIIKHDS 145 (148)
Q Consensus 103 ----~~~l~~H~~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~~h~~ 145 (148)
...|..|.... | .+++.|..||+.+..+ .+..|+...|..
T Consensus 523 ~~d~~s~Lt~HE~~C-G-~rt~~C~~Cgk~Vrlr-dm~~H~~~~h~~ 566 (567)
T PLN03086 523 VRDRLRGMSEHESIC-G-SRTAPCDSCGRSVMLK-EMDIHQIAVHQK 566 (567)
T ss_pred hhhhhhhHHHHHHhc-C-CcceEccccCCeeeeh-hHHHHHHHhhcC
Confidence 35799999886 5 7899999999999887 567898877754
No 12
>PHA00733 hypothetical protein
Probab=99.19 E-value=1e-11 Score=75.39 Aligned_cols=80 Identities=21% Similarity=0.291 Sum_probs=60.3
Q ss_pred CcccCCCCCCccccccccc------ccccCCCCCceecCccccccccchhHHhhHhhhhCCCCceeCCCChhhhhchHHH
Q psy12018 62 PRYQCPQCPYRTKQKELGW------ESLKPNAYGMYVCDICGKVYQHKRTLYRHKKDECGQEPRFQCPQCPYRAKQKANL 135 (148)
Q Consensus 62 ~~~~C~~c~~~f~~~~~~~------~~~~~~~~~~~~C~~c~~~f~~~~~l~~H~~~~~~~~~~~~C~~C~~~f~~~~~l 135 (148)
+++.|.+|...|....++. ++....+.++|.|..|++.|.....|..|++.+ +.++.|..|++.|.....|
T Consensus 39 ~~~~~~~~~~~~~~~~~l~~~~~l~~~~~~~~~kPy~C~~Cgk~Fss~s~L~~H~r~h---~~~~~C~~CgK~F~~~~sL 115 (128)
T PHA00733 39 KRLIRAVVKTLIYNPQLLDESSYLYKLLTSKAVSPYVCPLCLMPFSSSVSLKQHIRYT---EHSKVCPVCGKEFRNTDST 115 (128)
T ss_pred hhHHHHHHhhhccChhhhcchHHHHhhcccCCCCCccCCCCCCcCCCHHHHHHHHhcC---CcCccCCCCCCccCCHHHH
Confidence 4555655555555443221 223344577899999999999999999999876 3469999999999999999
Q ss_pred HHHHHhhcC
Q psy12018 136 KTHLIIKHD 144 (148)
Q Consensus 136 ~~H~~~~h~ 144 (148)
..|+...|+
T Consensus 116 ~~H~~~~h~ 124 (128)
T PHA00733 116 LDHVCKKHN 124 (128)
T ss_pred HHHHHHhcC
Confidence 999998886
No 13
>PHA02768 hypothetical protein; Provisional
Probab=99.03 E-value=6.8e-11 Score=60.18 Aligned_cols=43 Identities=19% Similarity=0.576 Sum_probs=39.2
Q ss_pred eecCccccccccchhHHhhHhhhhCCCCceeCCCChhhhhchHHHH
Q psy12018 91 YVCDICGKVYQHKRTLYRHKKDECGQEPRFQCPQCPYRAKQKANLK 136 (148)
Q Consensus 91 ~~C~~c~~~f~~~~~l~~H~~~~~~~~~~~~C~~C~~~f~~~~~l~ 136 (148)
|.|+.||+.|...+.|..|+++|+ +++.|..|++.|.+.+.|.
T Consensus 6 y~C~~CGK~Fs~~~~L~~H~r~H~---k~~kc~~C~k~f~~~s~l~ 48 (55)
T PHA02768 6 YECPICGEIYIKRKSMITHLRKHN---TNLKLSNCKRISLRTGEYI 48 (55)
T ss_pred cCcchhCCeeccHHHHHHHHHhcC---CcccCCcccceecccceeE
Confidence 789999999999999999999996 5799999999999887763
No 14
>PHA00733 hypothetical protein
Probab=98.97 E-value=3.6e-10 Score=68.72 Aligned_cols=85 Identities=14% Similarity=0.153 Sum_probs=65.8
Q ss_pred CCCCCccccCccccccCChhHHhcc--c---ccccCCCCcccCCCCCCcccccccccccccCCCCCceecCccccccccc
Q psy12018 29 PKLYGKFACDVCGKEYQYYRNLYRH--K---KFECGQEPRYQCPQCPYRTKQKELGWESLKPNAYGMYVCDICGKVYQHK 103 (148)
Q Consensus 29 ~~~~~~~~C~~C~~~f~~~~~l~~h--~---~~~~~~~~~~~C~~c~~~f~~~~~~~~~~~~~~~~~~~C~~c~~~f~~~ 103 (148)
+...+++.|..|.+.|.....|..+ + ..+.+ ++||.|+.|++.|.+...+..+...+ ..+|.|..|++.|...
T Consensus 35 ~~~~~~~~~~~~~~~~~~~~~l~~~~~l~~~~~~~~-~kPy~C~~Cgk~Fss~s~L~~H~r~h-~~~~~C~~CgK~F~~~ 112 (128)
T PHA00733 35 TPEQKRLIRAVVKTLIYNPQLLDESSYLYKLLTSKA-VSPYVCPLCLMPFSSSVSLKQHIRYT-EHSKVCPVCGKEFRNT 112 (128)
T ss_pred ChhhhhHHHHHHhhhccChhhhcchHHHHhhcccCC-CCCccCCCCCCcCCCHHHHHHHHhcC-CcCccCCCCCCccCCH
Confidence 5567889999999998887777665 1 12223 67999999999999987544444322 4579999999999999
Q ss_pred hhHHhhHhhhhC
Q psy12018 104 RTLYRHKKDECG 115 (148)
Q Consensus 104 ~~l~~H~~~~~~ 115 (148)
..|..|+...++
T Consensus 113 ~sL~~H~~~~h~ 124 (128)
T PHA00733 113 DSTLDHVCKKHN 124 (128)
T ss_pred HHHHHHHHHhcC
Confidence 999999987765
No 15
>PHA02768 hypothetical protein; Provisional
Probab=98.84 E-value=1.3e-09 Score=55.50 Aligned_cols=41 Identities=15% Similarity=0.426 Sum_probs=37.0
Q ss_pred ccccCccccccCChhHHhcccccccCCCCcccCCCCCCcccccc
Q psy12018 34 KFACDVCGKEYQYYRNLYRHKKFECGQEPRYQCPQCPYRTKQKE 77 (148)
Q Consensus 34 ~~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~~C~~c~~~f~~~~ 77 (148)
.|.|+.||+.|....+|..|+++|. +++.|..|++.|...+
T Consensus 5 ~y~C~~CGK~Fs~~~~L~~H~r~H~---k~~kc~~C~k~f~~~s 45 (55)
T PHA02768 5 GYECPICGEIYIKRKSMITHLRKHN---TNLKLSNCKRISLRTG 45 (55)
T ss_pred ccCcchhCCeeccHHHHHHHHHhcC---CcccCCcccceecccc
Confidence 4899999999999999999999986 5899999999988765
No 16
>KOG3993|consensus
Probab=98.80 E-value=1.4e-09 Score=76.39 Aligned_cols=81 Identities=21% Similarity=0.474 Sum_probs=53.5
Q ss_pred CccccCccccccCChhHHhcccccccCCCCcccCCCCCCcccccccccccccCC--------------------------
Q psy12018 33 GKFACDVCGKEYQYYRNLYRHKKFECGQEPRYQCPQCPYRTKQKELGWESLKPN-------------------------- 86 (148)
Q Consensus 33 ~~~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~~C~~c~~~f~~~~~~~~~~~~~-------------------------- 86 (148)
+.|+|+.|...|.....|.+|.-..+. ...|.|++|++.|.....+..|+..+
T Consensus 266 GdyiCqLCK~kYeD~F~LAQHrC~RIV-~vEYrCPEC~KVFsCPANLASHRRWHKPR~eaa~a~~~P~k~~~~~rae~~e 344 (500)
T KOG3993|consen 266 GDYICQLCKEKYEDAFALAQHRCPRIV-HVEYRCPECDKVFSCPANLASHRRWHKPRPEAAKAGSPPPKQAVETRAEVQE 344 (500)
T ss_pred HHHHHHHHHHhhhhHHHHhhccCCeeE-EeeecCCcccccccCchhhhhhhcccCCchhhhhcCCCChhhhhhhhhhhhh
Confidence 358899999999999999998654444 34589999999888764322222211
Q ss_pred --------CCCceecCccccccccchhHHhhHhhhh
Q psy12018 87 --------AYGMYVCDICGKVYQHKRTLYRHKKDEC 114 (148)
Q Consensus 87 --------~~~~~~C~~c~~~f~~~~~l~~H~~~~~ 114 (148)
.+..|.|..|++.|.....|+.|+.+|.
T Consensus 345 a~rsg~dss~gi~~C~~C~KkFrRqAYLrKHqlthq 380 (500)
T KOG3993|consen 345 AERSGDDSSSGIFSCHTCGKKFRRQAYLRKHQLTHQ 380 (500)
T ss_pred ccccCCcccCceeecHHhhhhhHHHHHHHHhHHhhh
Confidence 1234666777777766666666655443
No 17
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=98.76 E-value=3.9e-09 Score=46.09 Aligned_cols=26 Identities=31% Similarity=0.685 Sum_probs=23.3
Q ss_pred hHHhhHhhhhCCCCceeCCCChhhhhc
Q psy12018 105 TLYRHKKDECGQEPRFQCPQCPYRAKQ 131 (148)
Q Consensus 105 ~l~~H~~~~~~~~~~~~C~~C~~~f~~ 131 (148)
+|..|+++|++ ++||.|+.|++.|.+
T Consensus 1 ~l~~H~~~H~~-~k~~~C~~C~k~F~~ 26 (26)
T PF13465_consen 1 NLRRHMRTHTG-EKPYKCPYCGKSFSN 26 (26)
T ss_dssp HHHHHHHHHSS-SSSEEESSSSEEESS
T ss_pred CHHHHhhhcCC-CCCCCCCCCcCeeCc
Confidence 47899999999 899999999999864
No 18
>PHA00616 hypothetical protein
Probab=98.74 E-value=8.8e-09 Score=50.01 Aligned_cols=29 Identities=24% Similarity=0.429 Sum_probs=15.3
Q ss_pred ceeCCCChhhhhchHHHHHHHHhhcCCcc
Q psy12018 119 RFQCPQCPYRAKQKANLKTHLIIKHDSVL 147 (148)
Q Consensus 119 ~~~C~~C~~~f~~~~~l~~H~~~~h~~~~ 147 (148)
||+|..||+.|...+.|.+|++.+|++++
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~~hg~~~ 29 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLSVHKQNK 29 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHHhcCCCc
Confidence 34555555555555555555555555543
No 19
>PLN03086 PRLI-interacting factor K; Provisional
Probab=98.65 E-value=2.9e-08 Score=73.40 Aligned_cols=76 Identities=20% Similarity=0.333 Sum_probs=56.9
Q ss_pred CcccCCCCCCcccccccccccccCCCCCceecCccccccccchhHHhhHhhhhCCCCceeCCCChhhhhc----------
Q psy12018 62 PRYQCPQCPYRTKQKELGWESLKPNAYGMYVCDICGKVYQHKRTLYRHKKDECGQEPRFQCPQCPYRAKQ---------- 131 (148)
Q Consensus 62 ~~~~C~~c~~~f~~~~~~~~~~~~~~~~~~~C~~c~~~f~~~~~l~~H~~~~~~~~~~~~C~~C~~~f~~---------- 131 (148)
+++.|+.|++.|....+..+...+ .+++.|+ |++.+ ....|..|+..+.. ++++.|..|++.|..
T Consensus 452 ~H~~C~~Cgk~f~~s~LekH~~~~--Hkpv~Cp-Cg~~~-~R~~L~~H~~thCp-~Kpi~C~fC~~~v~~g~~~~d~~d~ 526 (567)
T PLN03086 452 NHVHCEKCGQAFQQGEMEKHMKVF--HEPLQCP-CGVVL-EKEQMVQHQASTCP-LRLITCRFCGDMVQAGGSAMDVRDR 526 (567)
T ss_pred cCccCCCCCCccchHHHHHHHHhc--CCCccCC-CCCCc-chhHHHhhhhccCC-CCceeCCCCCCccccCccccchhhh
Confidence 456788998888644333333333 3789999 99765 56899999999988 899999999999852
Q ss_pred hHHHHHHHHhh
Q psy12018 132 KANLKTHLIIK 142 (148)
Q Consensus 132 ~~~l~~H~~~~ 142 (148)
.+.|..|..+.
T Consensus 527 ~s~Lt~HE~~C 537 (567)
T PLN03086 527 LRGMSEHESIC 537 (567)
T ss_pred hhhHHHHHHhc
Confidence 35788898774
No 20
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=98.53 E-value=1.7e-08 Score=44.08 Aligned_cols=25 Identities=40% Similarity=0.754 Sum_probs=21.2
Q ss_pred HHhcccccccCCCCcccCCCCCCccc
Q psy12018 49 NLYRHKKFECGQEPRYQCPQCPYRTK 74 (148)
Q Consensus 49 ~l~~h~~~~~~~~~~~~C~~c~~~f~ 74 (148)
+|..|+++|.+ ++||.|+.|++.|.
T Consensus 1 ~l~~H~~~H~~-~k~~~C~~C~k~F~ 25 (26)
T PF13465_consen 1 NLRRHMRTHTG-EKPYKCPYCGKSFS 25 (26)
T ss_dssp HHHHHHHHHSS-SSSEEESSSSEEES
T ss_pred CHHHHhhhcCC-CCCCCCCCCcCeeC
Confidence 47889998888 78999999998875
No 21
>PHA00616 hypothetical protein
Probab=98.44 E-value=4.5e-08 Score=47.56 Aligned_cols=34 Identities=12% Similarity=0.250 Sum_probs=30.7
Q ss_pred ccccCccccccCChhHHhcccccccCCCCcccCCC
Q psy12018 34 KFACDVCGKEYQYYRNLYRHKKFECGQEPRYQCPQ 68 (148)
Q Consensus 34 ~~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~~C~~ 68 (148)
||.|..||+.|...+.|..|++.+++ ++++.|..
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~~hg-~~~~~~~~ 34 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLSVHK-QNKLTLEY 34 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHHhcC-CCccceeE
Confidence 68999999999999999999999999 67888754
No 22
>PHA00732 hypothetical protein
Probab=98.43 E-value=1.1e-07 Score=52.82 Aligned_cols=46 Identities=26% Similarity=0.538 Sum_probs=29.1
Q ss_pred ceecCccccccccchhHHhhHhhhhCCCCceeCCCChhhhhchHHHHHHHHh
Q psy12018 90 MYVCDICGKVYQHKRTLYRHKKDECGQEPRFQCPQCPYRAKQKANLKTHLII 141 (148)
Q Consensus 90 ~~~C~~c~~~f~~~~~l~~H~~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~ 141 (148)
+|.|..|++.|.....|..|++.++. ++.|+.|++.|.+ |..|.+.
T Consensus 1 py~C~~Cgk~F~s~s~Lk~H~r~~H~---~~~C~~CgKsF~~---l~~H~~~ 46 (79)
T PHA00732 1 MFKCPICGFTTVTLFALKQHARRNHT---LTKCPVCNKSYRR---LNQHFYS 46 (79)
T ss_pred CccCCCCCCccCCHHHHHHHhhcccC---CCccCCCCCEeCC---hhhhhcc
Confidence 36677777777777777777764222 2467777777763 4555543
No 23
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=98.31 E-value=1.5e-06 Score=44.82 Aligned_cols=52 Identities=33% Similarity=0.602 Sum_probs=40.5
Q ss_pred ceecCccccccccchhHHhhHhhhhCC-CCceeCCCChhhhhchHHHHHHHHhhcC
Q psy12018 90 MYVCDICGKVYQHKRTLYRHKKDECGQ-EPRFQCPQCPYRAKQKANLKTHLIIKHD 144 (148)
Q Consensus 90 ~~~C~~c~~~f~~~~~l~~H~~~~~~~-~~~~~C~~C~~~f~~~~~l~~H~~~~h~ 144 (148)
.|.|++|++. .+...|..|....+.. .+.+.|++|...+. ..|..|+..+|+
T Consensus 2 ~f~CP~C~~~-~~~~~L~~H~~~~H~~~~~~v~CPiC~~~~~--~~l~~Hl~~~H~ 54 (54)
T PF05605_consen 2 SFTCPYCGKG-FSESSLVEHCEDEHRSESKNVVCPICSSRVT--DNLIRHLNSQHR 54 (54)
T ss_pred CcCCCCCCCc-cCHHHHHHHHHhHCcCCCCCccCCCchhhhh--hHHHHHHHHhcC
Confidence 4889999995 4567899997765543 45789999998655 489999998885
No 24
>PHA00732 hypothetical protein
Probab=98.18 E-value=1.2e-06 Score=48.73 Aligned_cols=40 Identities=23% Similarity=0.463 Sum_probs=32.1
Q ss_pred ccccCccccccCChhHHhcccccccCCCCcccCCCCCCccccc
Q psy12018 34 KFACDVCGKEYQYYRNLYRHKKFECGQEPRYQCPQCPYRTKQK 76 (148)
Q Consensus 34 ~~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~~C~~c~~~f~~~ 76 (148)
||.|..|++.|.....|..|++.++. ++.|+.|++.|.+.
T Consensus 1 py~C~~Cgk~F~s~s~Lk~H~r~~H~---~~~C~~CgKsF~~l 40 (79)
T PHA00732 1 MFKCPICGFTTVTLFALKQHARRNHT---LTKCPVCNKSYRRL 40 (79)
T ss_pred CccCCCCCCccCCHHHHHHHhhcccC---CCccCCCCCEeCCh
Confidence 58899999999999999999875322 35788898888753
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=98.18 E-value=1.1e-06 Score=36.99 Aligned_cols=22 Identities=36% Similarity=0.735 Sum_probs=15.7
Q ss_pred eeCCCChhhhhchHHHHHHHHh
Q psy12018 120 FQCPQCPYRAKQKANLKTHLII 141 (148)
Q Consensus 120 ~~C~~C~~~f~~~~~l~~H~~~ 141 (148)
|.|..|++.|.+.+.|..|++.
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 5677777777777777777765
No 26
>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=98.13 E-value=2.1e-06 Score=36.35 Aligned_cols=24 Identities=38% Similarity=0.825 Sum_probs=17.4
Q ss_pred eeCCCChhhhhchHHHHHHHHhhc
Q psy12018 120 FQCPQCPYRAKQKANLKTHLIIKH 143 (148)
Q Consensus 120 ~~C~~C~~~f~~~~~l~~H~~~~h 143 (148)
|.|+.|++.|.+...|..|++.+|
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 578888888888888888887765
No 27
>KOG3993|consensus
Probab=98.11 E-value=6.6e-07 Score=63.31 Aligned_cols=84 Identities=20% Similarity=0.372 Sum_probs=64.7
Q ss_pred cccCCCCCCcccccccccccccCC-CCCceecCccccccccchhHHhhHhhhhCC-------------------------
Q psy12018 63 RYQCPQCPYRTKQKELGWESLKPN-AYGMYVCDICGKVYQHKRTLYRHKKDECGQ------------------------- 116 (148)
Q Consensus 63 ~~~C~~c~~~f~~~~~~~~~~~~~-~~~~~~C~~c~~~f~~~~~l~~H~~~~~~~------------------------- 116 (148)
.|.|..|...|...-.+.+|+-.. ..-.|+|++|++.|.=..+|..|++.|-..
T Consensus 267 dyiCqLCK~kYeD~F~LAQHrC~RIV~vEYrCPEC~KVFsCPANLASHRRWHKPR~eaa~a~~~P~k~~~~~rae~~ea~ 346 (500)
T KOG3993|consen 267 DYICQLCKEKYEDAFALAQHRCPRIVHVEYRCPECDKVFSCPANLASHRRWHKPRPEAAKAGSPPPKQAVETRAEVQEAE 346 (500)
T ss_pred HHHHHHHHHhhhhHHHHhhccCCeeEEeeecCCcccccccCchhhhhhhcccCCchhhhhcCCCChhhhhhhhhhhhhcc
Confidence 388988988777765455554332 223599999999999999999999866321
Q ss_pred -------CCceeCCCChhhhhchHHHHHHHHhhcCCc
Q psy12018 117 -------EPRFQCPQCPYRAKQKANLKTHLIIKHDSV 146 (148)
Q Consensus 117 -------~~~~~C~~C~~~f~~~~~l~~H~~~~h~~~ 146 (148)
+-.|.|..|+|.|....=|++|+..||...
T Consensus 347 rsg~dss~gi~~C~~C~KkFrRqAYLrKHqlthq~~~ 383 (500)
T KOG3993|consen 347 RSGDDSSSGIFSCHTCGKKFRRQAYLRKHQLTHQRAP 383 (500)
T ss_pred ccCCcccCceeecHHhhhhhHHHHHHHHhHHhhhccc
Confidence 113899999999999999999999888653
No 28
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=98.05 E-value=2.4e-06 Score=37.46 Aligned_cols=26 Identities=19% Similarity=0.395 Sum_probs=19.5
Q ss_pred ceeCCCChhhhhchHHHHHHHHhhcC
Q psy12018 119 RFQCPQCPYRAKQKANLKTHLIIKHD 144 (148)
Q Consensus 119 ~~~C~~C~~~f~~~~~l~~H~~~~h~ 144 (148)
||.|..|++.|.+...|..|++.|++
T Consensus 1 ~~~C~~C~~~F~~~~~l~~H~~~h~~ 26 (27)
T PF13912_consen 1 PFECDECGKTFSSLSALREHKRSHCS 26 (27)
T ss_dssp SEEETTTTEEESSHHHHHHHHCTTTT
T ss_pred CCCCCccCCccCChhHHHHHhHHhcC
Confidence 46777788888887778778777654
No 29
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=97.91 E-value=8.9e-06 Score=34.17 Aligned_cols=23 Identities=43% Similarity=0.924 Sum_probs=21.0
Q ss_pred eecCccccccccchhHHhhHhhh
Q psy12018 91 YVCDICGKVYQHKRTLYRHKKDE 113 (148)
Q Consensus 91 ~~C~~c~~~f~~~~~l~~H~~~~ 113 (148)
|+|+.|++.|.....|..|++.|
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 68999999999999999999864
No 30
>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=97.88 E-value=9.7e-06 Score=40.33 Aligned_cols=38 Identities=32% Similarity=0.463 Sum_probs=22.6
Q ss_pred HhhhhCCCCceeCCCChhhhhchHHHHHHHHhhcCCcc
Q psy12018 110 KKDECGQEPRFQCPQCPYRAKQKANLKTHLIIKHDSVL 147 (148)
Q Consensus 110 ~~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~~h~~~~ 147 (148)
.+.+...+.|..|++|+..+++..+|++|+.+.|+.++
T Consensus 15 ~k~~~~S~~PatCP~C~a~~~~srnLrRHle~~H~~k~ 52 (54)
T PF09237_consen 15 PKSKSQSEQPATCPICGAVIRQSRNLRRHLEIRHFKKP 52 (54)
T ss_dssp -CCCCTTS--EE-TTT--EESSHHHHHHHHHHHTTTS-
T ss_pred HHHhhccCCCCCCCcchhhccchhhHHHHHHHHhcccC
Confidence 33333446778888888888888888888888887653
No 31
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=97.77 E-value=1.1e-05 Score=35.35 Aligned_cols=26 Identities=38% Similarity=0.881 Sum_probs=23.3
Q ss_pred ccccCccccccCChhHHhcccccccC
Q psy12018 34 KFACDVCGKEYQYYRNLYRHKKFECG 59 (148)
Q Consensus 34 ~~~C~~C~~~f~~~~~l~~h~~~~~~ 59 (148)
+|.|..|++.|.....|..|++.|..
T Consensus 1 ~~~C~~C~~~F~~~~~l~~H~~~h~~ 26 (27)
T PF13912_consen 1 PFECDECGKTFSSLSALREHKRSHCS 26 (27)
T ss_dssp SEEETTTTEEESSHHHHHHHHCTTTT
T ss_pred CCCCCccCCccCChhHHHHHhHHhcC
Confidence 68999999999999999999987753
No 32
>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=97.58 E-value=6.4e-05 Score=31.58 Aligned_cols=24 Identities=33% Similarity=0.807 Sum_probs=19.7
Q ss_pred eecCccccccccchhHHhhHhhhh
Q psy12018 91 YVCDICGKVYQHKRTLYRHKKDEC 114 (148)
Q Consensus 91 ~~C~~c~~~f~~~~~l~~H~~~~~ 114 (148)
|.|+.|++.|.....|..|+..++
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 689999999999999999998764
No 33
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=97.58 E-value=5.2e-05 Score=43.94 Aligned_cols=74 Identities=19% Similarity=0.253 Sum_probs=22.0
Q ss_pred cCCCCCCcccccccccccccCCCCCceecCccccccccchhHHhhHhhhhCCCCceeCCCChhhhhchHHHHHHHHhhc
Q psy12018 65 QCPQCPYRTKQKELGWESLKPNAYGMYVCDICGKVYQHKRTLYRHKKDECGQEPRFQCPQCPYRAKQKANLKTHLIIKH 143 (148)
Q Consensus 65 ~C~~c~~~f~~~~~~~~~~~~~~~~~~~C~~c~~~f~~~~~l~~H~~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~~h 143 (148)
+|..|+..|.+...+..|+.....-.. + ....+.....+..+.+.... ..+.|..|++.|.+...|..|++.++
T Consensus 1 ~C~~C~~~f~~~~~l~~H~~~~H~~~~--~-~~~~l~~~~~~~~~~~~~~~--~~~~C~~C~~~f~s~~~l~~Hm~~~~ 74 (100)
T PF12756_consen 1 QCLFCDESFSSVDDLLQHMKKKHGFDI--P-DQKYLVDPNRLLNYLRKKVK--ESFRCPYCNKTFRSREALQEHMRSKH 74 (100)
T ss_dssp -----------------------------------------------------SSEEBSSSS-EESSHHHHHHHHHHTT
T ss_pred Ccccccccccccccccccccccccccc--c-cccccccccccccccccccC--CCCCCCccCCCCcCHHHHHHHHcCcc
Confidence 478888888887644445432222111 1 11112233334444443322 36999999999999999999998653
No 34
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=97.48 E-value=8.2e-05 Score=43.09 Aligned_cols=75 Identities=16% Similarity=0.332 Sum_probs=22.7
Q ss_pred ccCccccccCChhHHhcccccccCCCCcccCCCCCCcccccccccccccCCCCCceecCccccccccchhHHhhHhhhhC
Q psy12018 36 ACDVCGKEYQYYRNLYRHKKFECGQEPRYQCPQCPYRTKQKELGWESLKPNAYGMYVCDICGKVYQHKRTLYRHKKDECG 115 (148)
Q Consensus 36 ~C~~C~~~f~~~~~l~~h~~~~~~~~~~~~C~~c~~~f~~~~~~~~~~~~~~~~~~~C~~c~~~f~~~~~l~~H~~~~~~ 115 (148)
.|..|+..|.....|..|+...++...+ . ...+.............-...+.|..|++.|.+...|..|++.+..
T Consensus 1 ~C~~C~~~f~~~~~l~~H~~~~H~~~~~----~-~~~l~~~~~~~~~~~~~~~~~~~C~~C~~~f~s~~~l~~Hm~~~~H 75 (100)
T PF12756_consen 1 QCLFCDESFSSVDDLLQHMKKKHGFDIP----D-QKYLVDPNRLLNYLRKKVKESFRCPYCNKTFRSREALQEHMRSKHH 75 (100)
T ss_dssp -----------------------------------------------------SSEEBSSSS-EESSHHHHHHHHHHTTT
T ss_pred Cccccccccccccccccccccccccccc----c-ccccccccccccccccccCCCCCCCccCCCCcCHHHHHHHHcCccC
Confidence 4889999999999999999665552221 1 1111111111111111222369999999999999999999997643
No 35
>smart00355 ZnF_C2H2 zinc finger.
Probab=97.48 E-value=0.00013 Score=31.07 Aligned_cols=23 Identities=35% Similarity=0.751 Sum_probs=16.8
Q ss_pred eeCCCChhhhhchHHHHHHHHhh
Q psy12018 120 FQCPQCPYRAKQKANLKTHLIIK 142 (148)
Q Consensus 120 ~~C~~C~~~f~~~~~l~~H~~~~ 142 (148)
|.|..|++.|.+...|..|++.|
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~~H 23 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMRTH 23 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHHHh
Confidence 46777777777777777777744
No 36
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=97.42 E-value=8.1e-05 Score=38.33 Aligned_cols=37 Identities=30% Similarity=0.560 Sum_probs=21.4
Q ss_pred ccccCccccccCChhHHhcccccccC-CCCcccCCCCCC
Q psy12018 34 KFACDVCGKEYQYYRNLYRHKKFECG-QEPRYQCPQCPY 71 (148)
Q Consensus 34 ~~~C~~C~~~f~~~~~l~~h~~~~~~-~~~~~~C~~c~~ 71 (148)
.|.|+.|++. .+...|..|....+. +.+.+.||+|..
T Consensus 2 ~f~CP~C~~~-~~~~~L~~H~~~~H~~~~~~v~CPiC~~ 39 (54)
T PF05605_consen 2 SFTCPYCGKG-FSESSLVEHCEDEHRSESKNVVCPICSS 39 (54)
T ss_pred CcCCCCCCCc-cCHHHHHHHHHhHCcCCCCCccCCCchh
Confidence 4677888774 445677777544333 224455655553
No 37
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=97.25 E-value=9.2e-05 Score=51.02 Aligned_cols=53 Identities=26% Similarity=0.488 Sum_probs=38.5
Q ss_pred CCceecCc--cccccccchhHHhhHhhhh------------------CCCCceeCCCChhhhhchHHHHHHHH
Q psy12018 88 YGMYVCDI--CGKVYQHKRTLYRHKKDEC------------------GQEPRFQCPQCPYRAKQKANLKTHLI 140 (148)
Q Consensus 88 ~~~~~C~~--c~~~f~~~~~l~~H~~~~~------------------~~~~~~~C~~C~~~f~~~~~l~~H~~ 140 (148)
+++|+|+. |++.+...-.|.-|+..-+ ...|||+|++|+|.+....-|.-|..
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 47788866 7788877777776654222 12589999999999998877765554
No 38
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=97.22 E-value=0.0002 Score=49.39 Aligned_cols=72 Identities=22% Similarity=0.361 Sum_probs=44.8
Q ss_pred CCCccccCc--cccccCChhHHhcccccccCCCCcccCCCCCCcccccccccccccCCCCCceecCccccccccchhHHh
Q psy12018 31 LYGKFACDV--CGKEYQYYRNLYRHKKFECGQEPRYQCPQCPYRTKQKELGWESLKPNAYGMYVCDICGKVYQHKRTLYR 108 (148)
Q Consensus 31 ~~~~~~C~~--C~~~f~~~~~l~~h~~~~~~~~~~~~C~~c~~~f~~~~~~~~~~~~~~~~~~~C~~c~~~f~~~~~l~~ 108 (148)
.++||.|++ |.+.|.....|+-|+..-+-..+..+-+ +--....-....|||.|+.|++.+...-.|.-
T Consensus 346 d~KpykCpV~gC~K~YknqnGLKYH~lhGH~~~~~~~~p---------~p~~~~~F~~~~KPYrCevC~KRYKNlNGLKY 416 (423)
T COG5189 346 DGKPYKCPVEGCNKKYKNQNGLKYHMLHGHQNQKLHENP---------SPEKMNIFSAKDKPYRCEVCDKRYKNLNGLKY 416 (423)
T ss_pred cCceecCCCCCchhhhccccchhhhhhccccCcccCCCC---------CccccccccccCCceeccccchhhccCcccee
Confidence 458999988 8899999888888864322111111111 00000111234689999999999988888877
Q ss_pred hHh
Q psy12018 109 HKK 111 (148)
Q Consensus 109 H~~ 111 (148)
|+.
T Consensus 417 Hr~ 419 (423)
T COG5189 417 HRK 419 (423)
T ss_pred ccc
Confidence 654
No 39
>PF09237 GAGA: GAGA factor; InterPro: IPR015318 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Members of this entry bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognises the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognises the A in the fourth position of the consensus sequence []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1YUI_A 1YUJ_A.
Probab=97.20 E-value=0.00023 Score=35.50 Aligned_cols=37 Identities=24% Similarity=0.322 Sum_probs=25.3
Q ss_pred CCCCCCCCccccCccccccCChhHHhcccccccCCCCc
Q psy12018 26 PFKPKLYGKFACDVCGKEYQYYRNLYRHKKFECGQEPR 63 (148)
Q Consensus 26 ~~~~~~~~~~~C~~C~~~f~~~~~l~~h~~~~~~~~~~ 63 (148)
......+.|..|+.|+..+....+|.+|+.+.++ .+|
T Consensus 16 k~~~~S~~PatCP~C~a~~~~srnLrRHle~~H~-~k~ 52 (54)
T PF09237_consen 16 KSKSQSEQPATCPICGAVIRQSRNLRRHLEIRHF-KKP 52 (54)
T ss_dssp CCCCTTS--EE-TTT--EESSHHHHHHHHHHHTT-TS-
T ss_pred HHhhccCCCCCCCcchhhccchhhHHHHHHHHhc-ccC
Confidence 3445678899999999999999999999988776 443
No 40
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=97.05 E-value=0.00046 Score=29.11 Aligned_cols=24 Identities=46% Similarity=1.021 Sum_probs=14.4
Q ss_pred eeCCCChhhhhchHHHHHHHHhhcC
Q psy12018 120 FQCPQCPYRAKQKANLKTHLIIKHD 144 (148)
Q Consensus 120 ~~C~~C~~~f~~~~~l~~H~~~~h~ 144 (148)
|+|+.|+.... ...|.+|++.+|+
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 46677766665 6677777776654
No 41
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=96.91 E-value=0.00055 Score=29.13 Aligned_cols=22 Identities=27% Similarity=0.528 Sum_probs=14.8
Q ss_pred eeCCCChhhhhchHHHHHHHHh
Q psy12018 120 FQCPQCPYRAKQKANLKTHLII 141 (148)
Q Consensus 120 ~~C~~C~~~f~~~~~l~~H~~~ 141 (148)
|.|..|++.|.+...|..|++.
T Consensus 1 ~~C~~C~~~f~s~~~~~~H~~s 22 (25)
T PF12874_consen 1 FYCDICNKSFSSENSLRQHLRS 22 (25)
T ss_dssp EEETTTTEEESSHHHHHHHHTT
T ss_pred CCCCCCCCCcCCHHHHHHHHCc
Confidence 4566777777777777776654
No 42
>smart00355 ZnF_C2H2 zinc finger.
Probab=96.84 E-value=0.00091 Score=28.32 Aligned_cols=24 Identities=38% Similarity=0.811 Sum_probs=20.9
Q ss_pred eecCccccccccchhHHhhHhhhh
Q psy12018 91 YVCDICGKVYQHKRTLYRHKKDEC 114 (148)
Q Consensus 91 ~~C~~c~~~f~~~~~l~~H~~~~~ 114 (148)
|.|..|++.|.....|..|++.|.
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~~H~ 24 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMRTHX 24 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHHHhc
Confidence 579999999999999999998654
No 43
>PRK04860 hypothetical protein; Provisional
Probab=96.76 E-value=0.0012 Score=41.75 Aligned_cols=38 Identities=32% Similarity=0.649 Sum_probs=32.9
Q ss_pred ceecCccccccccchhHHhhHhhhhCCCCceeCCCChhhhhch
Q psy12018 90 MYVCDICGKVYQHKRTLYRHKKDECGQEPRFQCPQCPYRAKQK 132 (148)
Q Consensus 90 ~~~C~~c~~~f~~~~~l~~H~~~~~~~~~~~~C~~C~~~f~~~ 132 (148)
+|.|. |+. ....+..|.+++.+ +++|.|..|+..|...
T Consensus 119 ~Y~C~-C~~---~~~~~rrH~ri~~g-~~~YrC~~C~~~l~~~ 156 (160)
T PRK04860 119 PYRCK-CQE---HQLTVRRHNRVVRG-EAVYRCRRCGETLVFK 156 (160)
T ss_pred EEEcC-CCC---eeCHHHHHHHHhcC-CccEECCCCCceeEEe
Confidence 58998 987 67778999999999 8899999999988754
No 44
>PF12171 zf-C2H2_jaz: Zinc-finger double-stranded RNA-binding; InterPro: IPR022755 This zinc finger is found in archaea and eukaryotes, and is approximately 30 amino acids in length. The mammalian members of this group occur multiple times along the protein, joined by flexible linkers, and are referred to as JAZ - dsRNA-binding ZF protein - zinc-fingers. The JAZ proteins are expressed in all tissues tested and localise in the nucleus, particularly the nucleolus []. JAZ preferentially binds to double-stranded (ds) RNA or RNA/DNA hybrids rather than DNA. In addition to binding double-stranded RNA, these zinc-fingers are required for nucleolar localisation. This entry represents the multiple-adjacent-C2H2 zinc finger, JAZ. ; PDB: 4DGW_A 1ZR9_A.
Probab=96.53 E-value=0.0023 Score=27.77 Aligned_cols=22 Identities=36% Similarity=0.656 Sum_probs=19.9
Q ss_pred cccCccccccCChhHHhccccc
Q psy12018 35 FACDVCGKEYQYYRNLYRHKKF 56 (148)
Q Consensus 35 ~~C~~C~~~f~~~~~l~~h~~~ 56 (148)
|.|..|++.|.....+..|++.
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 6899999999999999999864
No 45
>PRK04860 hypothetical protein; Provisional
Probab=96.51 E-value=0.001 Score=42.14 Aligned_cols=37 Identities=24% Similarity=0.573 Sum_probs=22.9
Q ss_pred ccccCccccccCChhHHhcccccccCCCCcccCCCCCCcccc
Q psy12018 34 KFACDVCGKEYQYYRNLYRHKKFECGQEPRYQCPQCPYRTKQ 75 (148)
Q Consensus 34 ~~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~~C~~c~~~f~~ 75 (148)
+|.|. |+. ....+..|.+++.+ +++|.|..|+..|..
T Consensus 119 ~Y~C~-C~~---~~~~~rrH~ri~~g-~~~YrC~~C~~~l~~ 155 (160)
T PRK04860 119 PYRCK-CQE---HQLTVRRHNRVVRG-EAVYRCRRCGETLVF 155 (160)
T ss_pred EEEcC-CCC---eeCHHHHHHHHhcC-CccEECCCCCceeEE
Confidence 56665 665 44556666666666 556777666665543
No 46
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=96.38 E-value=0.0026 Score=26.96 Aligned_cols=23 Identities=30% Similarity=0.846 Sum_probs=20.4
Q ss_pred eecCccccccccchhHHhhHhhh
Q psy12018 91 YVCDICGKVYQHKRTLYRHKKDE 113 (148)
Q Consensus 91 ~~C~~c~~~f~~~~~l~~H~~~~ 113 (148)
|.|..|++.|.+...+..|++.+
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 67999999999999999998754
No 47
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=96.14 E-value=0.006 Score=25.56 Aligned_cols=24 Identities=33% Similarity=0.504 Sum_probs=18.4
Q ss_pred eecCccccccccchhHHhhHhhhhC
Q psy12018 91 YVCDICGKVYQHKRTLYRHKKDECG 115 (148)
Q Consensus 91 ~~C~~c~~~f~~~~~l~~H~~~~~~ 115 (148)
|+|+.|+.... ...|..|++.+++
T Consensus 1 y~C~~C~y~t~-~~~l~~H~~~~H~ 24 (24)
T PF13909_consen 1 YKCPHCSYSTS-KSNLKRHLKRHHP 24 (24)
T ss_dssp EE-SSSS-EES-HHHHHHHHHHHHS
T ss_pred CCCCCCCCcCC-HHHHHHHHHhhCc
Confidence 68999998887 8899999988753
No 48
>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=95.65 E-value=0.0057 Score=26.49 Aligned_cols=21 Identities=33% Similarity=0.808 Sum_probs=13.4
Q ss_pred eecCccccccccchhHHhhHh
Q psy12018 91 YVCDICGKVYQHKRTLYRHKK 111 (148)
Q Consensus 91 ~~C~~c~~~f~~~~~l~~H~~ 111 (148)
|-|..|++.|.+...|..|++
T Consensus 2 ~~C~~C~k~f~~~~~~~~H~~ 22 (27)
T PF12171_consen 2 FYCDACDKYFSSENQLKQHMK 22 (27)
T ss_dssp CBBTTTTBBBSSHHHHHCCTT
T ss_pred CCcccCCCCcCCHHHHHHHHc
Confidence 456666666666666666654
No 49
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=95.52 E-value=0.011 Score=25.14 Aligned_cols=19 Identities=26% Similarity=0.562 Sum_probs=8.7
Q ss_pred eCCCChhhhhchHHHHHHHH
Q psy12018 121 QCPQCPYRAKQKANLKTHLI 140 (148)
Q Consensus 121 ~C~~C~~~f~~~~~l~~H~~ 140 (148)
.|..||+.| ..+.|.+|+.
T Consensus 4 ~C~~CgR~F-~~~~l~~H~~ 22 (25)
T PF13913_consen 4 PCPICGRKF-NPDRLEKHEK 22 (25)
T ss_pred cCCCCCCEE-CHHHHHHHHH
Confidence 344555555 3334444443
No 50
>KOG2893|consensus
Probab=94.75 E-value=0.006 Score=40.70 Aligned_cols=48 Identities=23% Similarity=0.559 Sum_probs=35.5
Q ss_pred cCccccccccchhHHhhHhhhhCCCCceeCCCChhhhhchHHHHHHHHhhcCC
Q psy12018 93 CDICGKVYQHKRTLYRHKKDECGQEPRFQCPQCPYRAKQKANLKTHLIIKHDS 145 (148)
Q Consensus 93 C~~c~~~f~~~~~l~~H~~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~~h~~ 145 (148)
|=+|.+.|.....|.+|++ .+.|+|..|.|...+..-|..|-...|.+
T Consensus 13 cwycnrefddekiliqhqk-----akhfkchichkkl~sgpglsihcmqvhke 60 (341)
T KOG2893|consen 13 CWYCNREFDDEKILIQHQK-----AKHFKCHICHKKLFSGPGLSIHCMQVHKE 60 (341)
T ss_pred eeecccccchhhhhhhhhh-----hccceeeeehhhhccCCCceeehhhhhhh
Confidence 6678888888888888875 45688888887776666666666655544
No 51
>smart00451 ZnF_U1 U1-like zinc finger. Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins.
Probab=94.73 E-value=0.024 Score=25.96 Aligned_cols=22 Identities=23% Similarity=0.522 Sum_probs=17.4
Q ss_pred ceeCCCChhhhhchHHHHHHHH
Q psy12018 119 RFQCPQCPYRAKQKANLKTHLI 140 (148)
Q Consensus 119 ~~~C~~C~~~f~~~~~l~~H~~ 140 (148)
+|.|..|++.|.+...+..|+.
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~ 24 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLK 24 (35)
T ss_pred CeEccccCCccCCHHHHHHHHC
Confidence 4778888888888888877775
No 52
>smart00451 ZnF_U1 U1-like zinc finger. Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins.
Probab=94.31 E-value=0.022 Score=26.13 Aligned_cols=23 Identities=22% Similarity=0.379 Sum_probs=19.5
Q ss_pred ccccCccccccCChhHHhccccc
Q psy12018 34 KFACDVCGKEYQYYRNLYRHKKF 56 (148)
Q Consensus 34 ~~~C~~C~~~f~~~~~l~~h~~~ 56 (148)
+|.|..|++.|.....+..|+..
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~g 25 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLKG 25 (35)
T ss_pred CeEccccCCccCCHHHHHHHHCh
Confidence 58899999999988888888653
No 53
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=93.54 E-value=0.072 Score=27.17 Aligned_cols=27 Identities=22% Similarity=0.547 Sum_probs=15.7
Q ss_pred CCceeCCCChhhhhchHHHHHHHHhhc
Q psy12018 117 EPRFQCPQCPYRAKQKANLKTHLIIKH 143 (148)
Q Consensus 117 ~~~~~C~~C~~~f~~~~~l~~H~~~~h 143 (148)
|.-+.|+-||+.|.....+.+|.-..|
T Consensus 15 E~~lrCPRC~~~FR~~K~Y~RHVNKaH 41 (65)
T COG4049 15 EEFLRCPRCGMVFRRRKDYIRHVNKAH 41 (65)
T ss_pred ceeeeCCchhHHHHHhHHHHHHhhHHh
Confidence 444566666666666666666654433
No 54
>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=93.29 E-value=0.077 Score=31.38 Aligned_cols=33 Identities=21% Similarity=0.503 Sum_probs=22.4
Q ss_pred CCccccCccccccCChhHHhcccccccCCCCcccCCCCCCccccc
Q psy12018 32 YGKFACDVCGKEYQYYRNLYRHKKFECGQEPRYQCPQCPYRTKQK 76 (148)
Q Consensus 32 ~~~~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~~C~~c~~~f~~~ 76 (148)
.....|+.||+.|.... ..|..||.||..|.-.
T Consensus 7 GtKR~Cp~CG~kFYDLn------------k~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 7 GTKRTCPSCGAKFYDLN------------KDPIVCPKCGTEFPPE 39 (108)
T ss_pred CCcccCCCCcchhccCC------------CCCccCCCCCCccCcc
Confidence 44557888888875532 3577788888777654
No 55
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=92.27 E-value=0.041 Score=28.03 Aligned_cols=32 Identities=19% Similarity=0.344 Sum_probs=25.9
Q ss_pred CCCCCCccccCccccccCChhHHhcccccccC
Q psy12018 28 KPKLYGKFACDVCGKEYQYYRNLYRHKKFECG 59 (148)
Q Consensus 28 ~~~~~~~~~C~~C~~~f~~~~~l~~h~~~~~~ 59 (148)
...++..++|+-|+..|....+..+|....++
T Consensus 11 ~RDGE~~lrCPRC~~~FR~~K~Y~RHVNKaH~ 42 (65)
T COG4049 11 DRDGEEFLRCPRCGMVFRRRKDYIRHVNKAHG 42 (65)
T ss_pred ccCCceeeeCCchhHHHHHhHHHHHHhhHHhh
Confidence 34567789999999999999999999765544
No 56
>KOG1146|consensus
Probab=92.22 E-value=0.12 Score=42.76 Aligned_cols=75 Identities=16% Similarity=0.263 Sum_probs=40.1
Q ss_pred CccccCccccccCChhHHhcccccccCCCCcccCCCCCCcccccc-cccccccCCCCCceecCccccccccchhHHhhHh
Q psy12018 33 GKFACDVCGKEYQYYRNLYRHKKFECGQEPRYQCPQCPYRTKQKE-LGWESLKPNAYGMYVCDICGKVYQHKRTLYRHKK 111 (148)
Q Consensus 33 ~~~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~~C~~c~~~f~~~~-~~~~~~~~~~~~~~~C~~c~~~f~~~~~l~~H~~ 111 (148)
+.|.|++|...|.....|..|+|.-+.+-.. ..|.. +.... ...-....-+.++|.|..|...+.....|..|+.
T Consensus 464 kt~~cpkc~~~yk~a~~L~vhmRskhp~~~~---~~c~~-gq~~~~~arg~~~~~~~~p~~C~~C~~stttng~Lsihlq 539 (1406)
T KOG1146|consen 464 KTLKCPKCNWHYKLAQTLGVHMRSKHPESQS---AYCKA-GQNHPRLARGEVYRCPGKPYPCRACNYSTTTNGNLSIHLQ 539 (1406)
T ss_pred ccccCCccchhhhhHHHhhhcccccccccch---hHhHh-ccccccccccccccCCCCcccceeeeeeeecchHHHHHHH
Confidence 5677777777777777777777763331111 11110 00000 0000001122466788888888877777777765
No 57
>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=90.39 E-value=0.23 Score=22.56 Aligned_cols=10 Identities=30% Similarity=0.893 Sum_probs=5.9
Q ss_pred CceeCCCChh
Q psy12018 118 PRFQCPQCPY 127 (148)
Q Consensus 118 ~~~~C~~C~~ 127 (148)
.++.|+.||.
T Consensus 16 ~~~~CP~Cg~ 25 (33)
T cd00350 16 APWVCPVCGA 25 (33)
T ss_pred CCCcCcCCCC
Confidence 3566666654
No 58
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=90.29 E-value=0.056 Score=39.22 Aligned_cols=57 Identities=23% Similarity=0.458 Sum_probs=47.7
Q ss_pred CceecCccccccccchhHHhhHh--hhhCCC--CceeCC--CChhhhhchHHHHHHHHhhcCCc
Q psy12018 89 GMYVCDICGKVYQHKRTLYRHKK--DECGQE--PRFQCP--QCPYRAKQKANLKTHLIIKHDSV 146 (148)
Q Consensus 89 ~~~~C~~c~~~f~~~~~l~~H~~--~~~~~~--~~~~C~--~C~~~f~~~~~l~~H~~~~h~~~ 146 (148)
.++.|..|...|.....|..|.+ .|.+ + +++.|. .|++.|.....+..|...+.+..
T Consensus 288 ~~~~~~~~~~~~s~~~~l~~~~~~~~h~~-~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~ 350 (467)
T COG5048 288 LPIKSKQCNISFSRSSPLTRHLRSVNHSG-ESLKPFSCPYSLCGKLFSRNDALKRHILLHTSIS 350 (467)
T ss_pred cCCCCccccCCcccccccccccccccccc-ccCCceeeeccCCCccccccccccCCcccccCCC
Confidence 35788889999999999999999 7887 6 889998 79999999888888888777654
No 59
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=90.15 E-value=0.33 Score=35.23 Aligned_cols=44 Identities=20% Similarity=0.425 Sum_probs=34.2
Q ss_pred CccccCccccccCChhHHhcccc--cccCCC--CcccCC--CCCCcccccc
Q psy12018 33 GKFACDVCGKEYQYYRNLYRHKK--FECGQE--PRYQCP--QCPYRTKQKE 77 (148)
Q Consensus 33 ~~~~C~~C~~~f~~~~~l~~h~~--~~~~~~--~~~~C~--~c~~~f~~~~ 77 (148)
.++.|..|...|.....|..|.+ .|.+ + +++.|+ .|++.|....
T Consensus 288 ~~~~~~~~~~~~s~~~~l~~~~~~~~h~~-~~~~~~~~p~~~~~~~~~~~~ 337 (467)
T COG5048 288 LPIKSKQCNISFSRSSPLTRHLRSVNHSG-ESLKPFSCPYSLCGKLFSRND 337 (467)
T ss_pred cCCCCccccCCcccccccccccccccccc-ccCCceeeeccCCCccccccc
Confidence 46788888888888888888888 6766 5 788888 6888777764
No 60
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=88.98 E-value=0.21 Score=33.34 Aligned_cols=24 Identities=29% Similarity=0.545 Sum_probs=15.4
Q ss_pred CCccccCccccccCChhHHhcccc
Q psy12018 32 YGKFACDVCGKEYQYYRNLYRHKK 55 (148)
Q Consensus 32 ~~~~~C~~C~~~f~~~~~l~~h~~ 55 (148)
++...|++|++.|....-.....+
T Consensus 3 ~k~~~CPvC~~~F~~~~vrs~~~r 26 (214)
T PF09986_consen 3 DKKITCPVCGKEFKTKKVRSGKIR 26 (214)
T ss_pred CCceECCCCCCeeeeeEEEcCCce
Confidence 355778888888877654444443
No 61
>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=88.63 E-value=0.36 Score=29.26 Aligned_cols=33 Identities=12% Similarity=0.071 Sum_probs=21.8
Q ss_pred CCccccCccccccCChhHHhcccccccCCCCcccCCCCCCccccc
Q psy12018 32 YGKFACDVCGKEYQYYRNLYRHKKFECGQEPRYQCPQCPYRTKQK 76 (148)
Q Consensus 32 ~~~~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~~C~~c~~~f~~~ 76 (148)
.....|+.||+.|.... ..|..|+.||..|.-.
T Consensus 7 GtKr~Cp~cg~kFYDLn------------k~p~vcP~cg~~~~~~ 39 (129)
T TIGR02300 7 GTKRICPNTGSKFYDLN------------RRPAVSPYTGEQFPPE 39 (129)
T ss_pred CccccCCCcCccccccC------------CCCccCCCcCCccCcc
Confidence 44557888888875532 4577788888776544
No 62
>KOG2231|consensus
Probab=88.52 E-value=0.36 Score=37.47 Aligned_cols=92 Identities=21% Similarity=0.303 Sum_probs=55.5
Q ss_pred CChhHHhcccccccCCCCcccCCCCC---Cccccc-------ccccccccC-CC----CCceecCccccccccchhHHhh
Q psy12018 45 QYYRNLYRHKKFECGQEPRYQCPQCP---YRTKQK-------ELGWESLKP-NA----YGMYVCDICGKVYQHKRTLYRH 109 (148)
Q Consensus 45 ~~~~~l~~h~~~~~~~~~~~~C~~c~---~~f~~~-------~~~~~~~~~-~~----~~~~~C~~c~~~f~~~~~l~~H 109 (148)
.....|+.|++..+. .+.|..|- +.|... .+..+.+.. .+ .+.-.|..|...|.....|..|
T Consensus 125 ~s~~~Lk~H~~~~H~---~~~c~lC~~~~kif~~e~k~Yt~~el~~h~~~gd~d~~s~rGhp~C~~C~~~fld~~el~rH 201 (669)
T KOG2231|consen 125 KSVENLKNHMRDQHK---LHLCSLCLQNLKIFINERKLYTRAELNLHLMFGDPDDESCRGHPLCKFCHERFLDDDELYRH 201 (669)
T ss_pred hHHHHHHHHHHHhhh---hhccccccccceeeeeeeehehHHHHHHHHhcCCCccccccCCccchhhhhhhccHHHHHHh
Confidence 367888999855443 35555543 233332 122222211 11 1234788999999999999998
Q ss_pred HhhhhCCCCceeCCCC------hhhhhchHHHHHHHHhhcC
Q psy12018 110 KKDECGQEPRFQCPQC------PYRAKQKANLKTHLIIKHD 144 (148)
Q Consensus 110 ~~~~~~~~~~~~C~~C------~~~f~~~~~l~~H~~~~h~ 144 (148)
++.++. -|..| +.-|.....|..|-+..|-
T Consensus 202 ~~~~h~-----~chfC~~~~~~neyy~~~~dLe~HfR~~Hf 237 (669)
T KOG2231|consen 202 LRFDHE-----FCHFCDYKTGQNEYYNDYDDLEEHFRKGHF 237 (669)
T ss_pred hcccee-----heeecCcccccchhcccchHHHHHhhhcCc
Confidence 876554 34434 4566777888888887764
No 63
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=88.41 E-value=1.4 Score=22.92 Aligned_cols=11 Identities=27% Similarity=1.183 Sum_probs=6.8
Q ss_pred CCceeCCCChh
Q psy12018 117 EPRFQCPQCPY 127 (148)
Q Consensus 117 ~~~~~C~~C~~ 127 (148)
..+|.|+.||.
T Consensus 46 ~~~Y~CP~CGF 56 (59)
T PRK14890 46 SNPYTCPKCGF 56 (59)
T ss_pred CCceECCCCCC
Confidence 34677777763
No 64
>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=87.82 E-value=0.19 Score=33.49 Aligned_cols=30 Identities=17% Similarity=0.468 Sum_probs=17.4
Q ss_pred CCCCceecCccccccccchhHHhhHhhhhC
Q psy12018 86 NAYGMYVCDICGKVYQHKRTLYRHKKDECG 115 (148)
Q Consensus 86 ~~~~~~~C~~c~~~f~~~~~l~~H~~~~~~ 115 (148)
..+..|.|..|++.|........|+..-|.
T Consensus 73 ~~~~K~~C~lc~KlFkg~eFV~KHI~nKH~ 102 (214)
T PF04959_consen 73 EDEDKWRCPLCGKLFKGPEFVRKHIFNKHP 102 (214)
T ss_dssp SSSEEEEE-SSS-EESSHHHHHHHHHHH-H
T ss_pred HcCCEECCCCCCcccCChHHHHHHHhhcCH
Confidence 344557777777777777777777665554
No 65
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=87.29 E-value=0.16 Score=33.93 Aligned_cols=16 Identities=31% Similarity=0.679 Sum_probs=11.4
Q ss_pred CcccCCCCCCcccccc
Q psy12018 62 PRYQCPQCPYRTKQKE 77 (148)
Q Consensus 62 ~~~~C~~c~~~f~~~~ 77 (148)
+...||.|+..|..+.
T Consensus 4 k~~~CPvC~~~F~~~~ 19 (214)
T PF09986_consen 4 KKITCPVCGKEFKTKK 19 (214)
T ss_pred CceECCCCCCeeeeeE
Confidence 4567888888777764
No 66
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=86.49 E-value=0.58 Score=29.58 Aligned_cols=14 Identities=29% Similarity=0.467 Sum_probs=9.4
Q ss_pred ccCCCCCCcccccc
Q psy12018 64 YQCPQCPYRTKQKE 77 (148)
Q Consensus 64 ~~C~~c~~~f~~~~ 77 (148)
+.|+.||.+|....
T Consensus 29 ~~c~~c~~~f~~~e 42 (154)
T PRK00464 29 RECLACGKRFTTFE 42 (154)
T ss_pred eeccccCCcceEeE
Confidence 66777777776643
No 67
>KOG1146|consensus
Probab=86.30 E-value=0.12 Score=42.66 Aligned_cols=108 Identities=11% Similarity=0.122 Sum_probs=67.7
Q ss_pred ccccCccccccCChhHHhcccccccC---CCCcccCCCCCCcccccccccccccCCCCCceecCccccccccchhHHhhH
Q psy12018 34 KFACDVCGKEYQYYRNLYRHKKFECG---QEPRYQCPQCPYRTKQKELGWESLKPNAYGMYVCDICGKVYQHKRTLYRHK 110 (148)
Q Consensus 34 ~~~C~~C~~~f~~~~~l~~h~~~~~~---~~~~~~C~~c~~~f~~~~~~~~~~~~~~~~~~~C~~c~~~f~~~~~l~~H~ 110 (148)
...|..|...|........+-+-.-. ....+.|..|.+.+...-... +.. -..+|.|..|...|.....|..|+
T Consensus 1228 gl~~~~~e~~f~~~~~~~~~a~~~~~~~~~sGe~~c~~~~~~~~~~~~~~-~l~--~~~~~~~~~~~~~~~~~~~l~~~~ 1304 (1406)
T KOG1146|consen 1228 GLLPNALEQPFPQEPEPTATAPPKPPELPASGEGECGAVDELLTPSFGIS-TLD--VTHRYLCRQCKMAFDGEAPLTAHQ 1304 (1406)
T ss_pred cccHHhhhcCccCcccccccCCCCCCcCcCCCcchhhhccccccCcccee-ecc--cchhHHHHHHHhhhcchhHHHHHH
Confidence 34567777777777666555322111 013466777776655432111 111 123578888888888888888887
Q ss_pred hhhhC----------------CCCceeCCCChhhhhchHHHHHHHHhhcCC
Q psy12018 111 KDECG----------------QEPRFQCPQCPYRAKQKANLKTHLIIKHDS 145 (148)
Q Consensus 111 ~~~~~----------------~~~~~~C~~C~~~f~~~~~l~~H~~~~h~~ 145 (148)
+...- +..+| |..|...|+....|+.|+++.++.
T Consensus 1305 ~k~~~~~~~~~~~~~~~l~~~d~~~~-c~~c~~~~~~~~alqihm~~~~~~ 1354 (1406)
T KOG1146|consen 1305 RKFCFAGRGSGGSMPPPLRVPDCTYH-CLACEVLLSGREALQIHMRSSAHR 1354 (1406)
T ss_pred HHHHhccCccccCCCCcccCcccccc-chHHHhhcchhHHHHHHHHHhhhc
Confidence 53211 13456 999999999999999999876653
No 68
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=85.73 E-value=0.6 Score=29.86 Aligned_cols=24 Identities=38% Similarity=0.873 Sum_probs=17.9
Q ss_pred ceecCccccccccchhHHhhHhhhhCCCCceeCCCChh
Q psy12018 90 MYVCDICGKVYQHKRTLYRHKKDECGQEPRFQCPQCPY 127 (148)
Q Consensus 90 ~~~C~~c~~~f~~~~~l~~H~~~~~~~~~~~~C~~C~~ 127 (148)
-|.|+.||.++ .+ +.|.+|+.||.
T Consensus 134 ~~vC~vCGy~~-------------~g-e~P~~CPiCga 157 (166)
T COG1592 134 VWVCPVCGYTH-------------EG-EAPEVCPICGA 157 (166)
T ss_pred EEEcCCCCCcc-------------cC-CCCCcCCCCCC
Confidence 58899998553 34 67888999873
No 69
>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=85.47 E-value=0.69 Score=22.37 Aligned_cols=26 Identities=38% Similarity=0.565 Sum_probs=12.6
Q ss_pred CceeCCCChhhhhch----HHHHHHHHhhc
Q psy12018 118 PRFQCPQCPYRAKQK----ANLKTHLIIKH 143 (148)
Q Consensus 118 ~~~~C~~C~~~f~~~----~~l~~H~~~~h 143 (148)
....|..|++.+... +.|.+|++..|
T Consensus 15 ~~a~C~~C~~~~~~~~~~ts~l~~HL~~~h 44 (45)
T PF02892_consen 15 KKAKCKYCGKVIKYSSGGTSNLKRHLKKKH 44 (45)
T ss_dssp S-EEETTTTEE-----SSTHHHHHHHHHTT
T ss_pred CeEEeCCCCeEEeeCCCcHHHHHHhhhhhC
Confidence 345666666666543 56667765443
No 70
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=85.25 E-value=0.87 Score=36.09 Aligned_cols=49 Identities=22% Similarity=0.448 Sum_probs=25.3
Q ss_pred ccCCCCCCcccccccccccccCCCCCceecCccccccccchhHHhhHhhhhCCCCceeCCCChhh
Q psy12018 64 YQCPQCPYRTKQKELGWESLKPNAYGMYVCDICGKVYQHKRTLYRHKKDECGQEPRFQCPQCPYR 128 (148)
Q Consensus 64 ~~C~~c~~~f~~~~~~~~~~~~~~~~~~~C~~c~~~f~~~~~l~~H~~~~~~~~~~~~C~~C~~~ 128 (148)
..|..||..+....--.....|...+...|.+||.. . ..|..|+.||..
T Consensus 436 l~C~~Cg~v~~Cp~Cd~~lt~H~~~~~L~CH~Cg~~---------------~-~~p~~Cp~Cgs~ 484 (730)
T COG1198 436 LLCRDCGYIAECPNCDSPLTLHKATGQLRCHYCGYQ---------------E-PIPQSCPECGSE 484 (730)
T ss_pred eecccCCCcccCCCCCcceEEecCCCeeEeCCCCCC---------------C-CCCCCCCCCCCC
Confidence 446666665554431111112223345677777632 2 567788888753
No 71
>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=84.44 E-value=0.99 Score=20.65 Aligned_cols=10 Identities=30% Similarity=0.730 Sum_probs=6.1
Q ss_pred CceeCCCChh
Q psy12018 118 PRFQCPQCPY 127 (148)
Q Consensus 118 ~~~~C~~C~~ 127 (148)
.|..|+.||.
T Consensus 17 ~p~~CP~Cg~ 26 (34)
T cd00729 17 APEKCPICGA 26 (34)
T ss_pred CCCcCcCCCC
Confidence 4556777764
No 72
>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=84.09 E-value=0.86 Score=19.51 Aligned_cols=8 Identities=38% Similarity=1.115 Sum_probs=3.4
Q ss_pred cCcccccc
Q psy12018 93 CDICGKVY 100 (148)
Q Consensus 93 C~~c~~~f 100 (148)
|+.||..|
T Consensus 17 Cp~CG~~F 24 (26)
T PF10571_consen 17 CPHCGYDF 24 (26)
T ss_pred CCCCCCCC
Confidence 44444443
No 73
>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=84.05 E-value=0.43 Score=23.99 Aligned_cols=12 Identities=25% Similarity=1.135 Sum_probs=8.1
Q ss_pred cccCccccccCC
Q psy12018 35 FACDVCGKEYQY 46 (148)
Q Consensus 35 ~~C~~C~~~f~~ 46 (148)
|.|..|+..|..
T Consensus 6 y~C~~Cg~~fe~ 17 (52)
T TIGR02605 6 YRCTACGHRFEV 17 (52)
T ss_pred EEeCCCCCEeEE
Confidence 677777776653
No 74
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=84.02 E-value=0.99 Score=21.05 Aligned_cols=10 Identities=30% Similarity=0.853 Sum_probs=4.6
Q ss_pred eeCCCChhhh
Q psy12018 120 FQCPQCPYRA 129 (148)
Q Consensus 120 ~~C~~C~~~f 129 (148)
.+|..|+..|
T Consensus 26 vrC~~C~~~f 35 (37)
T PF13719_consen 26 VRCPKCGHVF 35 (37)
T ss_pred EECCCCCcEe
Confidence 4444444443
No 75
>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=84.02 E-value=0.94 Score=21.06 Aligned_cols=10 Identities=20% Similarity=0.504 Sum_probs=5.4
Q ss_pred eeCCCChhhh
Q psy12018 120 FQCPQCPYRA 129 (148)
Q Consensus 120 ~~C~~C~~~f 129 (148)
..|+.|+..|
T Consensus 26 v~C~~C~~~~ 35 (38)
T TIGR02098 26 VRCGKCGHVW 35 (38)
T ss_pred EECCCCCCEE
Confidence 4555555544
No 76
>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=83.06 E-value=0.75 Score=28.28 Aligned_cols=24 Identities=29% Similarity=0.447 Sum_probs=13.3
Q ss_pred ceeCCCChhhhhchHHHHHHHHhhcCC
Q psy12018 119 RFQCPQCPYRAKQKANLKTHLIIKHDS 145 (148)
Q Consensus 119 ~~~C~~C~~~f~~~~~l~~H~~~~h~~ 145 (148)
...|-+||+.|..- .+|++.|||-
T Consensus 72 ~i~clecGk~~k~L---krHL~~~~gl 95 (132)
T PF05443_consen 72 YIICLECGKKFKTL---KRHLRTHHGL 95 (132)
T ss_dssp -EE-TBT--EESBH---HHHHHHTT-S
T ss_pred eeEEccCCcccchH---HHHHHHccCC
Confidence 35777788877754 6777777764
No 77
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=82.96 E-value=1 Score=23.44 Aligned_cols=33 Identities=21% Similarity=0.430 Sum_probs=17.5
Q ss_pred CcccCCCCCCcccccccccccccCCCCCceecCcccc
Q psy12018 62 PRYQCPQCPYRTKQKELGWESLKPNAYGMYVCDICGK 98 (148)
Q Consensus 62 ~~~~C~~c~~~f~~~~~~~~~~~~~~~~~~~C~~c~~ 98 (148)
..|.|+.||+.....-. +--....+|.|+.||.
T Consensus 26 v~F~CPnCGe~~I~Rc~----~CRk~g~~Y~Cp~CGF 58 (61)
T COG2888 26 VKFPCPNCGEVEIYRCA----KCRKLGNPYRCPKCGF 58 (61)
T ss_pred eEeeCCCCCceeeehhh----hHHHcCCceECCCcCc
Confidence 34778888764333221 1112234678888774
No 78
>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=82.73 E-value=0.99 Score=28.68 Aligned_cols=30 Identities=23% Similarity=0.378 Sum_probs=15.9
Q ss_pred CcccCCCCCCcccccccccccccCCCCCceecCccccc
Q psy12018 62 PRYQCPQCPYRTKQKELGWESLKPNAYGMYVCDICGKV 99 (148)
Q Consensus 62 ~~~~C~~c~~~f~~~~~~~~~~~~~~~~~~~C~~c~~~ 99 (148)
.-|.|+.|+..|....... .-|.|+.||..
T Consensus 108 ~~Y~Cp~c~~r~tf~eA~~--------~~F~Cp~Cg~~ 137 (158)
T TIGR00373 108 MFFICPNMCVRFTFNEAME--------LNFTCPRCGAM 137 (158)
T ss_pred CeEECCCCCcEeeHHHHHH--------cCCcCCCCCCE
Confidence 3466666666555543221 13666666644
No 79
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=82.41 E-value=1.1 Score=29.17 Aligned_cols=14 Identities=29% Similarity=0.698 Sum_probs=7.7
Q ss_pred cccCCCCCCccccc
Q psy12018 63 RYQCPQCPYRTKQK 76 (148)
Q Consensus 63 ~~~C~~c~~~f~~~ 76 (148)
-|.|+.|+..|...
T Consensus 117 ~Y~Cp~C~~rytf~ 130 (178)
T PRK06266 117 FFFCPNCHIRFTFD 130 (178)
T ss_pred EEECCCCCcEEeHH
Confidence 45666666555543
No 80
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=82.31 E-value=1.5 Score=21.36 Aligned_cols=10 Identities=30% Similarity=0.883 Sum_probs=4.8
Q ss_pred ccCCCCCCcc
Q psy12018 64 YQCPQCPYRT 73 (148)
Q Consensus 64 ~~C~~c~~~f 73 (148)
|.|..||..|
T Consensus 3 Y~C~~Cg~~~ 12 (44)
T smart00659 3 YICGECGREN 12 (44)
T ss_pred EECCCCCCEe
Confidence 4455555443
No 81
>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=82.04 E-value=1.2 Score=26.25 Aligned_cols=25 Identities=28% Similarity=0.836 Sum_probs=22.3
Q ss_pred eeC----CCChhhhhchHHHHHHHHhhcC
Q psy12018 120 FQC----PQCPYRAKQKANLKTHLIIKHD 144 (148)
Q Consensus 120 ~~C----~~C~~~f~~~~~l~~H~~~~h~ 144 (148)
|.| ..|+....+...+++|.+.+||
T Consensus 81 ~~C~~~~~~C~y~~~~~~~m~~H~~~~Hg 109 (109)
T PF12013_consen 81 YRCQCDPPHCGYITRSKKTMRKHWRKEHG 109 (109)
T ss_pred eeeecCCCCCCcEeccHHHHHHHHHHhcC
Confidence 788 8899999999999999998886
No 82
>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=81.69 E-value=1.1 Score=21.53 Aligned_cols=11 Identities=36% Similarity=1.389 Sum_probs=5.9
Q ss_pred cccCccccccC
Q psy12018 35 FACDVCGKEYQ 45 (148)
Q Consensus 35 ~~C~~C~~~f~ 45 (148)
|.|..||..|.
T Consensus 6 y~C~~Cg~~fe 16 (42)
T PF09723_consen 6 YRCEECGHEFE 16 (42)
T ss_pred EEeCCCCCEEE
Confidence 45555555553
No 83
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=81.14 E-value=0.86 Score=25.68 Aligned_cols=30 Identities=30% Similarity=0.711 Sum_probs=15.4
Q ss_pred cccCCCCCCcccccccccccccCCCCCceecCccccccc
Q psy12018 63 RYQCPQCPYRTKQKELGWESLKPNAYGMYVCDICGKVYQ 101 (148)
Q Consensus 63 ~~~C~~c~~~f~~~~~~~~~~~~~~~~~~~C~~c~~~f~ 101 (148)
.|.|+.|++.-.. -...+.|.|..|+..|.
T Consensus 35 ~~~Cp~C~~~~Vk---------R~a~GIW~C~kCg~~fA 64 (89)
T COG1997 35 KHVCPFCGRTTVK---------RIATGIWKCRKCGAKFA 64 (89)
T ss_pred CCcCCCCCCccee---------eeccCeEEcCCCCCeec
Confidence 4666666654111 11233466666666654
No 84
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=81.09 E-value=0.6 Score=25.45 Aligned_cols=42 Identities=12% Similarity=0.433 Sum_probs=22.1
Q ss_pred ccCCCCCCcccccccccccccCCCCCceecC--ccccccccchhH
Q psy12018 64 YQCPQCPYRTKQKELGWESLKPNAYGMYVCD--ICGKVYQHKRTL 106 (148)
Q Consensus 64 ~~C~~c~~~f~~~~~~~~~~~~~~~~~~~C~--~c~~~f~~~~~l 106 (148)
+.|+.||............ ....+..+.|. .||.+|.....+
T Consensus 2 m~CP~Cg~~a~irtSr~~s-~~~~~~Y~qC~N~eCg~tF~t~es~ 45 (72)
T PRK09678 2 FHCPLCQHAAHARTSRYIT-DTTKERYHQCQNVNCSATFITYESV 45 (72)
T ss_pred ccCCCCCCccEEEEChhcC-hhhheeeeecCCCCCCCEEEEEEEE
Confidence 4578887654322111111 11345567776 788877665443
No 85
>smart00614 ZnF_BED BED zinc finger. DNA-binding domain in chromatin-boundary-element-binding proteins and transposases
Probab=81.06 E-value=1.4 Score=21.96 Aligned_cols=21 Identities=29% Similarity=0.608 Sum_probs=10.8
Q ss_pred eCCCChhhhhch-----HHHHHHHHh
Q psy12018 121 QCPQCPYRAKQK-----ANLKTHLII 141 (148)
Q Consensus 121 ~C~~C~~~f~~~-----~~l~~H~~~ 141 (148)
.|..|++.+... +.|.+|+..
T Consensus 20 ~C~~C~~~l~~~~~~gTs~L~rHl~~ 45 (50)
T smart00614 20 KCKYCGKKLSRSSKGGTSNLRRHLRR 45 (50)
T ss_pred EecCCCCEeeeCCCCCcHHHHHHHHh
Confidence 455555544332 466666663
No 86
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=80.91 E-value=1.1 Score=21.93 Aligned_cols=29 Identities=24% Similarity=0.540 Sum_probs=16.4
Q ss_pred cccCCCCCCcccccccccccccCCCCCceecCcccccc
Q psy12018 63 RYQCPQCPYRTKQKELGWESLKPNAYGMYVCDICGKVY 100 (148)
Q Consensus 63 ~~~C~~c~~~f~~~~~~~~~~~~~~~~~~~C~~c~~~f 100 (148)
.|.|+.||..|..... .....|+.||..+
T Consensus 3 ~y~C~~CG~~~~~~~~---------~~~~~Cp~CG~~~ 31 (46)
T PRK00398 3 EYKCARCGREVELDEY---------GTGVRCPYCGYRI 31 (46)
T ss_pred EEECCCCCCEEEECCC---------CCceECCCCCCeE
Confidence 4677777766554321 0146777777544
No 87
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=80.61 E-value=1.5 Score=27.52 Aligned_cols=36 Identities=25% Similarity=0.562 Sum_probs=20.3
Q ss_pred CcccCCCCCCcccccccccccccCCCCCceecCcccccc
Q psy12018 62 PRYQCPQCPYRTKQKELGWESLKPNAYGMYVCDICGKVY 100 (148)
Q Consensus 62 ~~~~C~~c~~~f~~~~~~~~~~~~~~~~~~~C~~c~~~f 100 (148)
.-|.|+.|+..|......... .. .+.|.|+.||...
T Consensus 98 ~~Y~Cp~C~~~y~~~ea~~~~-d~--~~~f~Cp~Cg~~l 133 (147)
T smart00531 98 AYYKCPNCQSKYTFLEANQLL-DM--DGTFTCPRCGEEL 133 (147)
T ss_pred cEEECcCCCCEeeHHHHHHhc-CC--CCcEECCCCCCEE
Confidence 457788887776654321111 11 3347888887654
No 88
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=80.53 E-value=1.6 Score=20.21 Aligned_cols=10 Identities=20% Similarity=0.614 Sum_probs=4.3
Q ss_pred eeCCCChhhh
Q psy12018 120 FQCPQCPYRA 129 (148)
Q Consensus 120 ~~C~~C~~~f 129 (148)
.+|..|+..|
T Consensus 26 v~C~~C~~~f 35 (36)
T PF13717_consen 26 VRCSKCGHVF 35 (36)
T ss_pred EECCCCCCEe
Confidence 3444444433
No 89
>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=80.15 E-value=0.91 Score=21.38 Aligned_cols=11 Identities=27% Similarity=0.839 Sum_probs=5.0
Q ss_pred ccCCCCCCccc
Q psy12018 64 YQCPQCPYRTK 74 (148)
Q Consensus 64 ~~C~~c~~~f~ 74 (148)
|.|+.||..|.
T Consensus 6 y~C~~Cg~~fe 16 (41)
T smart00834 6 YRCEDCGHTFE 16 (41)
T ss_pred EEcCCCCCEEE
Confidence 44444444443
No 90
>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=79.21 E-value=1.7 Score=19.63 Aligned_cols=7 Identities=43% Similarity=1.578 Sum_probs=3.3
Q ss_pred eeCCCCh
Q psy12018 120 FQCPQCP 126 (148)
Q Consensus 120 ~~C~~C~ 126 (148)
.+|..||
T Consensus 18 irC~~CG 24 (32)
T PF03604_consen 18 IRCPECG 24 (32)
T ss_dssp SSBSSSS
T ss_pred EECCcCC
Confidence 3444444
No 91
>PF14353 CpXC: CpXC protein
Probab=78.90 E-value=0.61 Score=28.38 Aligned_cols=42 Identities=21% Similarity=0.513 Sum_probs=22.6
Q ss_pred cccCccccccCChhHHhccc--------ccccCCCCcccCCCCCCccccc
Q psy12018 35 FACDVCGKEYQYYRNLYRHK--------KFECGQEPRYQCPQCPYRTKQK 76 (148)
Q Consensus 35 ~~C~~C~~~f~~~~~l~~h~--------~~~~~~~~~~~C~~c~~~f~~~ 76 (148)
.+|+.|+..|.......... ++..+.-..+.||.||..|.-.
T Consensus 2 itCP~C~~~~~~~v~~~I~~~~~p~l~e~il~g~l~~~~CP~Cg~~~~~~ 51 (128)
T PF14353_consen 2 ITCPHCGHEFEFEVWTSINADEDPELKEKILDGSLFSFTCPSCGHKFRLE 51 (128)
T ss_pred cCCCCCCCeeEEEEEeEEcCcCCHHHHHHHHcCCcCEEECCCCCCceecC
Confidence 36888887765543322111 1112222457788888776543
No 92
>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=78.39 E-value=1.1 Score=35.16 Aligned_cols=79 Identities=19% Similarity=0.270 Sum_probs=47.4
Q ss_pred cccCccccccCChhHHhcccccccCCCCc-ccCCCCCCcccccccccccccCCCCCc-eecCccccccccchhHHhhHhh
Q psy12018 35 FACDVCGKEYQYYRNLYRHKKFECGQEPR-YQCPQCPYRTKQKELGWESLKPNAYGM-YVCDICGKVYQHKRTLYRHKKD 112 (148)
Q Consensus 35 ~~C~~C~~~f~~~~~l~~h~~~~~~~~~~-~~C~~c~~~f~~~~~~~~~~~~~~~~~-~~C~~c~~~f~~~~~l~~H~~~ 112 (148)
-.|+.|-+.....++-+- .-| ..|..||-+|.-...+.--+.++.=+. -.|+.|.+.+....+.+-|
T Consensus 102 a~C~~Cl~Ei~dp~~rrY--------~YPF~~CT~CGPRfTIi~alPYDR~nTsM~~F~lC~~C~~EY~dP~nRRfH--- 170 (750)
T COG0068 102 ATCEDCLEEIFDPNSRRY--------LYPFINCTNCGPRFTIIEALPYDRENTSMADFPLCPFCDKEYKDPLNRRFH--- 170 (750)
T ss_pred hhhHHHHHHhcCCCCcce--------eccccccCCCCcceeeeccCCCCcccCccccCcCCHHHHHHhcCccccccc---
Confidence 357777665544433111 112 348899999887653333333333222 3699999988877665433
Q ss_pred hhCCCCceeCCCChhh
Q psy12018 113 ECGQEPRFQCPQCPYR 128 (148)
Q Consensus 113 ~~~~~~~~~C~~C~~~ 128 (148)
-.|..|+.||-.
T Consensus 171 ----AQp~aCp~CGP~ 182 (750)
T COG0068 171 ----AQPIACPKCGPH 182 (750)
T ss_pred ----cccccCcccCCC
Confidence 347899999863
No 93
>PRK14873 primosome assembly protein PriA; Provisional
Probab=77.33 E-value=2 Score=33.90 Aligned_cols=10 Identities=40% Similarity=1.364 Sum_probs=6.5
Q ss_pred CceeCCCChh
Q psy12018 118 PRFQCPQCPY 127 (148)
Q Consensus 118 ~~~~C~~C~~ 127 (148)
.|+.|+.||.
T Consensus 421 ~p~~Cp~Cgs 430 (665)
T PRK14873 421 PDWRCPRCGS 430 (665)
T ss_pred cCccCCCCcC
Confidence 3567777764
No 94
>PF15135 UPF0515: Uncharacterised protein UPF0515
Probab=76.84 E-value=3.3 Score=28.26 Aligned_cols=21 Identities=24% Similarity=0.578 Sum_probs=14.8
Q ss_pred CCCCCCCCccccCccccccCC
Q psy12018 26 PFKPKLYGKFACDVCGKEYQY 46 (148)
Q Consensus 26 ~~~~~~~~~~~C~~C~~~f~~ 46 (148)
...+..++-|.|..|+.....
T Consensus 104 ~~ip~~drqFaC~~Cd~~WwR 124 (278)
T PF15135_consen 104 NLIPSVDRQFACSSCDHMWWR 124 (278)
T ss_pred ccccccceeeeccccchHHHh
Confidence 345677788999999765433
No 95
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=76.43 E-value=7 Score=23.34 Aligned_cols=48 Identities=13% Similarity=0.189 Sum_probs=24.4
Q ss_pred ecCccccccccchhHHhhHhhhhCCCCceeCCCChhhhhchHHHHHHHHhh
Q psy12018 92 VCDICGKVYQHKRTLYRHKKDECGQEPRFQCPQCPYRAKQKANLKTHLIIK 142 (148)
Q Consensus 92 ~C~~c~~~f~~~~~l~~H~~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~~ 142 (148)
.|-.|...|........-. -.. ...|+|..|...|--.-+.-.|..+|
T Consensus 57 ~C~~C~~~f~~~~~~~~~~--~~~-~~~y~C~~C~~~FC~dCD~fiHe~Lh 104 (112)
T TIGR00622 57 FCFGCQGPFPKPPVSPFDE--LKD-SHRYVCAVCKNVFCVDCDVFVHESLH 104 (112)
T ss_pred cccCcCCCCCCcccccccc--ccc-ccceeCCCCCCccccccchhhhhhcc
Confidence 3666766665432111000 111 23577777777776655555565544
No 96
>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=76.39 E-value=2.5 Score=32.21 Aligned_cols=47 Identities=23% Similarity=0.386 Sum_probs=22.6
Q ss_pred cCCCCCCcccccccccccccCCCCCceecCccccccccchhHHhhHhhhhCCCCceeCCCChh
Q psy12018 65 QCPQCPYRTKQKELGWESLKPNAYGMYVCDICGKVYQHKRTLYRHKKDECGQEPRFQCPQCPY 127 (148)
Q Consensus 65 ~C~~c~~~f~~~~~~~~~~~~~~~~~~~C~~c~~~f~~~~~l~~H~~~~~~~~~~~~C~~C~~ 127 (148)
.|..||.......--.....|.......|.+||... ..|..|+.|+.
T Consensus 215 ~C~~Cg~~~~C~~C~~~l~~h~~~~~l~Ch~Cg~~~----------------~~~~~Cp~C~s 261 (505)
T TIGR00595 215 LCRSCGYILCCPNCDVSLTYHKKEGKLRCHYCGYQE----------------PIPKTCPQCGS 261 (505)
T ss_pred EhhhCcCccCCCCCCCceEEecCCCeEEcCCCcCcC----------------CCCCCCCCCCC
Confidence 466666554443211111112233456677776332 44667777764
No 97
>KOG4167|consensus
Probab=76.27 E-value=0.57 Score=36.68 Aligned_cols=29 Identities=28% Similarity=0.440 Sum_probs=25.7
Q ss_pred CCCccccCccccccCChhHHhcccccccC
Q psy12018 31 LYGKFACDVCGKEYQYYRNLYRHKKFECG 59 (148)
Q Consensus 31 ~~~~~~C~~C~~~f~~~~~l~~h~~~~~~ 59 (148)
.+.-|.|..|++.|.....+.+||+.|.-
T Consensus 789 ~~giFpCreC~kvF~KiKSrNAHMK~Hr~ 817 (907)
T KOG4167|consen 789 PTGIFPCRECGKVFFKIKSRNAHMKTHRQ 817 (907)
T ss_pred CCceeehHHHHHHHHHHhhhhHHHHHHHH
Confidence 36679999999999999999999998864
No 98
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=75.98 E-value=4.6 Score=29.06 Aligned_cols=102 Identities=20% Similarity=0.275 Sum_probs=54.6
Q ss_pred ccccCc--cccccCChhHHhcccccccCCCCcccCCCCC---Ccccccc-------cccccccCC-C---CCceecCccc
Q psy12018 34 KFACDV--CGKEYQYYRNLYRHKKFECGQEPRYQCPQCP---YRTKQKE-------LGWESLKPN-A---YGMYVCDICG 97 (148)
Q Consensus 34 ~~~C~~--C~~~f~~~~~l~~h~~~~~~~~~~~~C~~c~---~~f~~~~-------~~~~~~~~~-~---~~~~~C~~c~ 97 (148)
.|.|+. |...-..-..|..|.++.++ -+.|.+|- +.|...- +..+...-. + .+--.|..|.
T Consensus 151 ~F~CP~skc~~~C~~~k~lk~H~K~~H~---~~~C~~C~~nKk~F~~E~~lF~~~~Lr~H~~~G~~e~GFKGHP~C~FC~ 227 (493)
T COG5236 151 SFKCPKSKCHRRCGSLKELKKHYKAQHG---FVLCSECIGNKKDFWNEIRLFRSSTLRDHKNGGLEEEGFKGHPLCIFCK 227 (493)
T ss_pred HhcCCchhhhhhhhhHHHHHHHHHhhcC---cEEhHhhhcCcccCccceeeeecccccccccCCccccCcCCCchhhhcc
Confidence 356665 55444445677777766554 25566653 2343332 111111111 1 1234689999
Q ss_pred cccccchhHHhhHhhhhCCCCceeCCCC----hhhhhchHHHHHHHH
Q psy12018 98 KVYQHKRTLYRHKKDECGQEPRFQCPQC----PYRAKQKANLKTHLI 140 (148)
Q Consensus 98 ~~f~~~~~l~~H~~~~~~~~~~~~C~~C----~~~f~~~~~l~~H~~ 140 (148)
..|-.-..|..|.+..+. +=+.|..- .+-|.+...|..|.+
T Consensus 228 ~~FYdDDEL~~HcR~~HE--~ChICD~v~p~~~QYFK~Y~~Le~HF~ 272 (493)
T COG5236 228 IYFYDDDELRRHCRLRHE--ACHICDMVGPIRYQYFKSYEDLEAHFR 272 (493)
T ss_pred ceecChHHHHHHHHhhhh--hhhhhhccCccchhhhhCHHHHHHHhh
Confidence 889888889888886553 22333221 134555556666654
No 99
>PHA00626 hypothetical protein
Probab=75.80 E-value=3.6 Score=21.13 Aligned_cols=11 Identities=45% Similarity=0.718 Sum_probs=5.7
Q ss_pred ceecCcccccc
Q psy12018 90 MYVCDICGKVY 100 (148)
Q Consensus 90 ~~~C~~c~~~f 100 (148)
.|+|+.|+..|
T Consensus 23 rYkCkdCGY~f 33 (59)
T PHA00626 23 DYVCCDCGYND 33 (59)
T ss_pred ceEcCCCCCee
Confidence 35555555544
No 100
>PF12907 zf-met2: Zinc-binding
Probab=75.45 E-value=1.2 Score=21.32 Aligned_cols=27 Identities=30% Similarity=0.381 Sum_probs=17.7
Q ss_pred eeCCCChhhhhc---hHHHHHHHHhhcCCc
Q psy12018 120 FQCPQCPYRAKQ---KANLKTHLIIKHDSV 146 (148)
Q Consensus 120 ~~C~~C~~~f~~---~~~l~~H~~~~h~~~ 146 (148)
+.|.+|-..|.. ...|..|....|...
T Consensus 2 i~C~iC~qtF~~t~~~~~L~eH~enKHpK~ 31 (40)
T PF12907_consen 2 IICKICRQTFMQTTNEPQLKEHAENKHPKN 31 (40)
T ss_pred cCcHHhhHHHHhcCCHHHHHHHHHccCCCC
Confidence 467777766653 356777777777654
No 101
>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=73.37 E-value=2.8 Score=21.18 Aligned_cols=23 Identities=13% Similarity=0.541 Sum_probs=13.3
Q ss_pred CCccccCccccccCChhHHhccc
Q psy12018 32 YGKFACDVCGKEYQYYRNLYRHK 54 (148)
Q Consensus 32 ~~~~~C~~C~~~f~~~~~l~~h~ 54 (148)
...|.|+.|...|-..-++-.|.
T Consensus 19 ~~~y~C~~C~~~FC~dCD~fiHE 41 (51)
T PF07975_consen 19 SSRYRCPKCKNHFCIDCDVFIHE 41 (51)
T ss_dssp -EEE--TTTT--B-HHHHHTTTT
T ss_pred CCeEECCCCCCccccCcChhhhc
Confidence 45688999999888888877774
No 102
>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=73.01 E-value=3.5 Score=17.53 Aligned_cols=19 Identities=32% Similarity=0.627 Sum_probs=12.0
Q ss_pred eCCCChhhhhchHHHHHHHH
Q psy12018 121 QCPQCPYRAKQKANLKTHLI 140 (148)
Q Consensus 121 ~C~~C~~~f~~~~~l~~H~~ 140 (148)
.|+.|++.+ ....+..|+.
T Consensus 3 ~CPiC~~~v-~~~~in~HLD 21 (26)
T smart00734 3 QCPVCFREV-PENLINSHLD 21 (26)
T ss_pred cCCCCcCcc-cHHHHHHHHH
Confidence 577777776 4456666654
No 103
>PF15269 zf-C2H2_7: Zinc-finger
Probab=72.92 E-value=2.6 Score=20.53 Aligned_cols=22 Identities=32% Similarity=0.859 Sum_probs=16.1
Q ss_pred eeCCCChhhhhchHHHHHHHHh
Q psy12018 120 FQCPQCPYRAKQKANLKTHLII 141 (148)
Q Consensus 120 ~~C~~C~~~f~~~~~l~~H~~~ 141 (148)
|+|-+|.-.....++|..|++-
T Consensus 21 ykcfqcpftc~~kshl~nhmky 42 (54)
T PF15269_consen 21 YKCFQCPFTCNEKSHLFNHMKY 42 (54)
T ss_pred ceeecCCcccchHHHHHHHHHH
Confidence 5677777777777888777763
No 104
>KOG2893|consensus
Probab=72.56 E-value=1.7 Score=29.48 Aligned_cols=40 Identities=20% Similarity=0.448 Sum_probs=30.1
Q ss_pred CCCccccCccccccCChhHHhcccccccCCCCcccCCCCCCccccc
Q psy12018 31 LYGKFACDVCGKEYQYYRNLYRHKKFECGQEPRYQCPQCPYRTKQK 76 (148)
Q Consensus 31 ~~~~~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~~C~~c~~~f~~~ 76 (148)
..++ .|=.|.+.|....-|.+|++ .+.|+|.+|-+.+-+.
T Consensus 8 ~~kp-wcwycnrefddekiliqhqk-----akhfkchichkkl~sg 47 (341)
T KOG2893|consen 8 VDKP-WCWYCNREFDDEKILIQHQK-----AKHFKCHICHKKLFSG 47 (341)
T ss_pred cCCc-eeeecccccchhhhhhhhhh-----hccceeeeehhhhccC
Confidence 3444 56679999999999999985 3578999997765443
No 105
>KOG2186|consensus
Probab=72.41 E-value=2.6 Score=28.80 Aligned_cols=50 Identities=18% Similarity=0.405 Sum_probs=30.0
Q ss_pred ccCCCCCCcccccccccccccCCCCCceecCccccccccchhHHhhHhhhhC
Q psy12018 64 YQCPQCPYRTKQKELGWESLKPNAYGMYVCDICGKVYQHKRTLYRHKKDECG 115 (148)
Q Consensus 64 ~~C~~c~~~f~~~~~~~~~~~~~~~~~~~C~~c~~~f~~~~~l~~H~~~~~~ 115 (148)
|.|..||....-..+ ..|+..-....|.|..|+..|.. .....|..--+.
T Consensus 4 FtCnvCgEsvKKp~v-ekH~srCrn~~fSCIDC~k~F~~-~sYknH~kCITE 53 (276)
T KOG2186|consen 4 FTCNVCGESVKKPQV-EKHMSRCRNAYFSCIDCGKTFER-VSYKNHTKCITE 53 (276)
T ss_pred Eehhhhhhhccccch-HHHHHhccCCeeEEeeccccccc-chhhhhhhhcch
Confidence 677778776665432 22443333466788888888766 455556554444
No 106
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=72.29 E-value=2.8 Score=20.97 Aligned_cols=10 Identities=30% Similarity=1.035 Sum_probs=5.3
Q ss_pred ccCCCCCCcc
Q psy12018 64 YQCPQCPYRT 73 (148)
Q Consensus 64 ~~C~~c~~~f 73 (148)
|.|..||+.|
T Consensus 7 Y~C~~Cg~~~ 16 (49)
T COG1996 7 YKCARCGREV 16 (49)
T ss_pred EEhhhcCCee
Confidence 5555555544
No 107
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=71.36 E-value=2.7 Score=23.98 Aligned_cols=32 Identities=28% Similarity=0.669 Sum_probs=17.8
Q ss_pred CcccCCCCCCcccccccccccccCCCCCceecCcccccccc
Q psy12018 62 PRYQCPQCPYRTKQKELGWESLKPNAYGMYVCDICGKVYQH 102 (148)
Q Consensus 62 ~~~~C~~c~~~f~~~~~~~~~~~~~~~~~~~C~~c~~~f~~ 102 (148)
..|.|+.|++.-.. -...+.|.|..|++.|.-
T Consensus 35 a~y~CpfCgk~~vk---------R~a~GIW~C~~C~~~~AG 66 (90)
T PTZ00255 35 AKYFCPFCGKHAVK---------RQAVGIWRCKGCKKTVAG 66 (90)
T ss_pred CCccCCCCCCCcee---------eeeeEEEEcCCCCCEEeC
Confidence 35777777753111 122345777777776643
No 108
>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=71.08 E-value=1.7 Score=24.84 Aligned_cols=30 Identities=33% Similarity=0.879 Sum_probs=15.9
Q ss_pred cccCCCCCCcccccccccccccCCCCCceecCccccccc
Q psy12018 63 RYQCPQCPYRTKQKELGWESLKPNAYGMYVCDICGKVYQ 101 (148)
Q Consensus 63 ~~~C~~c~~~f~~~~~~~~~~~~~~~~~~~C~~c~~~f~ 101 (148)
.|.|+.|++.-.- -.....|.|..|++.|.
T Consensus 35 ky~Cp~Cgk~~vk---------R~a~GIW~C~~C~~~~A 64 (90)
T PF01780_consen 35 KYTCPFCGKTSVK---------RVATGIWKCKKCGKKFA 64 (90)
T ss_dssp -BEESSSSSSEEE---------EEETTEEEETTTTEEEE
T ss_pred CCcCCCCCCceeE---------EeeeEEeecCCCCCEEe
Confidence 4777777764211 11233566777776654
No 109
>COG4957 Predicted transcriptional regulator [Transcription]
Probab=71.07 E-value=2.9 Score=25.70 Aligned_cols=22 Identities=27% Similarity=0.333 Sum_probs=12.1
Q ss_pred eeCCCChhhhhchHHHHHHHHhhcC
Q psy12018 120 FQCPQCPYRAKQKANLKTHLIIKHD 144 (148)
Q Consensus 120 ~~C~~C~~~f~~~~~l~~H~~~~h~ 144 (148)
..|-++|+.|. .|.+|+.+|++
T Consensus 77 IicLEDGkkfK---SLKRHL~t~~g 98 (148)
T COG4957 77 IICLEDGKKFK---SLKRHLTTHYG 98 (148)
T ss_pred EEEeccCcchH---HHHHHHhcccC
Confidence 45556666555 34556655554
No 110
>PF00301 Rubredoxin: Rubredoxin; InterPro: IPR004039 Rubredoxin is a low molecular weight iron-containing bacterial protein involved in electron transfer [, ], sometimes replacing ferredoxin as an electron carrier []. The 3-D structures of a number of rubredoxins have been solved [, ]. The fold belongs to the alpha+beta class, with 2 alpha-helices and 2-3 beta-strands. Its active site contains an iron ion which is co-ordinated by the sulphurs of four conserved cysteine residues forming an almost regular tetrahedron. The conserved cysteines reside on two loops, which are the most conserved regions of the protein. In addition, a ring of acidic residues in the proximity of the [Fe(Cys)4] centre is also well-conserved []. ; GO: 0009055 electron carrier activity, 0046872 metal ion binding; PDB: 2RDV_C 1RDV_A 1S24_A 1T9O_B 1B2J_A 1SMW_A 2PVE_B 1BFY_A 1T9P_C 1C09_C ....
Probab=69.65 E-value=5.4 Score=19.78 Aligned_cols=7 Identities=57% Similarity=1.426 Sum_probs=2.8
Q ss_pred ccCcccc
Q psy12018 36 ACDVCGK 42 (148)
Q Consensus 36 ~C~~C~~ 42 (148)
.|..|+-
T Consensus 3 ~C~~Cgy 9 (47)
T PF00301_consen 3 QCPVCGY 9 (47)
T ss_dssp EETTTSB
T ss_pred CCCCCCE
Confidence 3444443
No 111
>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=69.41 E-value=6 Score=19.88 Aligned_cols=8 Identities=38% Similarity=1.149 Sum_probs=3.3
Q ss_pred ccCccccc
Q psy12018 36 ACDVCGKE 43 (148)
Q Consensus 36 ~C~~C~~~ 43 (148)
.|..||-.
T Consensus 3 ~C~~Cgyi 10 (50)
T cd00730 3 ECRICGYI 10 (50)
T ss_pred CCCCCCeE
Confidence 34444433
No 112
>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=69.16 E-value=4 Score=27.36 Aligned_cols=29 Identities=24% Similarity=0.518 Sum_probs=18.7
Q ss_pred CceeCCCChhhhhchHHHHHHHHhhcCCc
Q psy12018 118 PRFQCPQCPYRAKQKANLKTHLIIKHDSV 146 (148)
Q Consensus 118 ~~~~C~~C~~~f~~~~~l~~H~~~~h~~~ 146 (148)
..|.|..|+|.|.-..=+.+|+...|.+.
T Consensus 76 ~K~~C~lc~KlFkg~eFV~KHI~nKH~e~ 104 (214)
T PF04959_consen 76 DKWRCPLCGKLFKGPEFVRKHIFNKHPEK 104 (214)
T ss_dssp EEEEE-SSS-EESSHHHHHHHHHHH-HHH
T ss_pred CEECCCCCCcccCChHHHHHHHhhcCHHH
Confidence 34777777777777777777777777654
No 113
>KOG4173|consensus
Probab=68.89 E-value=2.2 Score=28.29 Aligned_cols=80 Identities=19% Similarity=0.328 Sum_probs=52.8
Q ss_pred cccCCC--CCCcccccccccccccCCCCCceecCccccccccchhHHhhHhhhhCC---------CCceeCC--CChhhh
Q psy12018 63 RYQCPQ--CPYRTKQKELGWESLKPNAYGMYVCDICGKVYQHKRTLYRHKKDECGQ---------EPRFQCP--QCPYRA 129 (148)
Q Consensus 63 ~~~C~~--c~~~f~~~~~~~~~~~~~~~~~~~C~~c~~~f~~~~~l~~H~~~~~~~---------~~~~~C~--~C~~~f 129 (148)
.+.|+. |.+.|.+..-+.++ .++... -.|..|.+.|.....|..|+.-.+.- ..-|+|- .|+-.|
T Consensus 79 ~~~cqvagc~~~~d~lD~~E~h-Y~~~h~-~sCs~C~r~~Pt~hLLd~HI~E~HDs~Fqa~veRG~dMy~ClvEgCt~KF 156 (253)
T KOG4173|consen 79 AFACQVAGCCQVFDALDDYEHH-YHTLHG-NSCSFCKRAFPTGHLLDAHILEWHDSLFQALVERGQDMYQCLVEGCTEKF 156 (253)
T ss_pred cccccccchHHHHhhhhhHHHh-hhhccc-chhHHHHHhCCchhhhhHHHHHHHHHHHHHHHHcCccHHHHHHHhhhhhh
Confidence 366765 44555554322222 111111 26999999999999999998755431 2237784 599999
Q ss_pred hchHHHHHHHHhhcC
Q psy12018 130 KQKANLKTHLIIKHD 144 (148)
Q Consensus 130 ~~~~~l~~H~~~~h~ 144 (148)
.+...-..|+-..|.
T Consensus 157 kT~r~RkdH~I~~Hk 171 (253)
T KOG4173|consen 157 KTSRDRKDHMIRMHK 171 (253)
T ss_pred hhhhhhhhHHHHhcc
Confidence 999999999988775
No 114
>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=68.82 E-value=1.3 Score=30.45 Aligned_cols=20 Identities=25% Similarity=0.783 Sum_probs=12.9
Q ss_pred CCceeCCCChhhhhchHHHH
Q psy12018 117 EPRFQCPQCPYRAKQKANLK 136 (148)
Q Consensus 117 ~~~~~C~~C~~~f~~~~~l~ 136 (148)
.++++|+.||........|.
T Consensus 207 ~k~~PCPKCg~et~eTkdLS 226 (314)
T PF06524_consen 207 GKPIPCPKCGYETQETKDLS 226 (314)
T ss_pred CCCCCCCCCCCcccccccce
Confidence 46778888876665554443
No 115
>KOG4167|consensus
Probab=68.29 E-value=2.1 Score=33.79 Aligned_cols=25 Identities=16% Similarity=0.312 Sum_probs=21.0
Q ss_pred ceeCCCChhhhhchHHHHHHHHhhc
Q psy12018 119 RFQCPQCPYRAKQKANLKTHLIIKH 143 (148)
Q Consensus 119 ~~~C~~C~~~f~~~~~l~~H~~~~h 143 (148)
-|.|.+|+|.|-.-..+..||+.|-
T Consensus 792 iFpCreC~kvF~KiKSrNAHMK~Hr 816 (907)
T KOG4167|consen 792 IFPCRECGKVFFKIKSRNAHMKTHR 816 (907)
T ss_pred eeehHHHHHHHHHHhhhhHHHHHHH
Confidence 4889999999988888888888774
No 116
>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=67.36 E-value=2.6 Score=21.60 Aligned_cols=10 Identities=30% Similarity=1.142 Sum_probs=5.6
Q ss_pred ccCCCCCCcc
Q psy12018 64 YQCPQCPYRT 73 (148)
Q Consensus 64 ~~C~~c~~~f 73 (148)
+.|+.|+..+
T Consensus 3 ~~CP~CG~~i 12 (54)
T TIGR01206 3 FECPDCGAEI 12 (54)
T ss_pred cCCCCCCCEE
Confidence 4566666544
No 117
>KOG2186|consensus
Probab=66.05 E-value=2.8 Score=28.68 Aligned_cols=46 Identities=17% Similarity=0.399 Sum_probs=34.5
Q ss_pred ccccCccccccCChhHHhcccccccCCCCcccCCCCCCccccccccccc
Q psy12018 34 KFACDVCGKEYQYYRNLYRHKKFECGQEPRYQCPQCPYRTKQKELGWES 82 (148)
Q Consensus 34 ~~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~~C~~c~~~f~~~~~~~~~ 82 (148)
-|.|..||..... ..+-.|+....+ .-|.|-.|++.|-..+...+.
T Consensus 3 ~FtCnvCgEsvKK-p~vekH~srCrn--~~fSCIDC~k~F~~~sYknH~ 48 (276)
T KOG2186|consen 3 FFTCNVCGESVKK-PQVEKHMSRCRN--AYFSCIDCGKTFERVSYKNHT 48 (276)
T ss_pred EEehhhhhhhccc-cchHHHHHhccC--CeeEEeecccccccchhhhhh
Confidence 3789999998765 466679877766 469999999999886543333
No 118
>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=65.93 E-value=2.2 Score=24.38 Aligned_cols=31 Identities=29% Similarity=0.847 Sum_probs=17.2
Q ss_pred cccCCCCCCcccccccccccccCCCCCceecCcccccccc
Q psy12018 63 RYQCPQCPYRTKQKELGWESLKPNAYGMYVCDICGKVYQH 102 (148)
Q Consensus 63 ~~~C~~c~~~f~~~~~~~~~~~~~~~~~~~C~~c~~~f~~ 102 (148)
.|.|+.|++.-.. -..-+.|.|..|++.|.-
T Consensus 35 ~y~CpfCgk~~vk---------R~a~GIW~C~~C~~~~AG 65 (91)
T TIGR00280 35 KYVCPFCGKKTVK---------RGSTGIWTCRKCGAKFAG 65 (91)
T ss_pred CccCCCCCCCceE---------EEeeEEEEcCCCCCEEeC
Confidence 4777777753111 122345677777776643
No 119
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=64.70 E-value=3.9 Score=23.28 Aligned_cols=14 Identities=14% Similarity=0.636 Sum_probs=7.7
Q ss_pred CcccCCCCCCcccc
Q psy12018 62 PRYQCPQCPYRTKQ 75 (148)
Q Consensus 62 ~~~~C~~c~~~f~~ 75 (148)
.|..|..||..|..
T Consensus 57 ~Pa~CkkCGfef~~ 70 (97)
T COG3357 57 RPARCKKCGFEFRD 70 (97)
T ss_pred cChhhcccCccccc
Confidence 45556666655544
No 120
>KOG2785|consensus
Probab=64.61 E-value=6.5 Score=28.64 Aligned_cols=53 Identities=21% Similarity=0.263 Sum_probs=43.3
Q ss_pred ceecCccccccccchhHHhhHhhhhCC----------------------CCceeCCCCh---hhhhchHHHHHHHHhh
Q psy12018 90 MYVCDICGKVYQHKRTLYRHKKDECGQ----------------------EPRFQCPQCP---YRAKQKANLKTHLIIK 142 (148)
Q Consensus 90 ~~~C~~c~~~f~~~~~l~~H~~~~~~~----------------------~~~~~C~~C~---~~f~~~~~l~~H~~~~ 142 (148)
|-.|.+|+..+........|+..++|- .+.+.|-.|+ +.|++-...+.||...
T Consensus 166 Pt~CLfC~~~~k~~e~~~~HM~~~HgffIPdreYL~D~~GLl~YLgeKV~~~~~CL~CN~~~~~f~sleavr~HM~~K 243 (390)
T KOG2785|consen 166 PTDCLFCDKKSKSLEENLKHMFKEHGFFIPDREYLTDEKGLLKYLGEKVGIGFICLFCNELGRPFSSLEAVRAHMRDK 243 (390)
T ss_pred CcceeecCCCcccHHHHHHHHhhccCCcCCchHhhhchhHHHHHHHHHhccCceEEEeccccCcccccHHHHHHHhhc
Confidence 356999999999998899999988873 2247788887 9999999999999754
No 121
>KOG4173|consensus
Probab=64.61 E-value=2.4 Score=28.05 Aligned_cols=75 Identities=21% Similarity=0.355 Sum_probs=37.1
Q ss_pred cccCc--cccccCChhHHhcccccccCCCCcccCCCCCCccccccccccccc-----------CCCCCceecC--ccccc
Q psy12018 35 FACDV--CGKEYQYYRNLYRHKKFECGQEPRYQCPQCPYRTKQKELGWESLK-----------PNAYGMYVCD--ICGKV 99 (148)
Q Consensus 35 ~~C~~--C~~~f~~~~~l~~h~~~~~~~~~~~~C~~c~~~f~~~~~~~~~~~-----------~~~~~~~~C~--~c~~~ 99 (148)
+.|+. |-..|........|--+.++ ..|..|.+.|.+.-++..|.. ..|..-|.|. .|+-.
T Consensus 80 ~~cqvagc~~~~d~lD~~E~hY~~~h~----~sCs~C~r~~Pt~hLLd~HI~E~HDs~Fqa~veRG~dMy~ClvEgCt~K 155 (253)
T KOG4173|consen 80 FACQVAGCCQVFDALDDYEHHYHTLHG----NSCSFCKRAFPTGHLLDAHILEWHDSLFQALVERGQDMYQCLVEGCTEK 155 (253)
T ss_pred ccccccchHHHHhhhhhHHHhhhhccc----chhHHHHHhCCchhhhhHHHHHHHHHHHHHHHHcCccHHHHHHHhhhhh
Confidence 55655 44555554444444322222 356667776666533222221 1223346663 36666
Q ss_pred cccchhHHhhHhhh
Q psy12018 100 YQHKRTLYRHKKDE 113 (148)
Q Consensus 100 f~~~~~l~~H~~~~ 113 (148)
|........|+-.-
T Consensus 156 FkT~r~RkdH~I~~ 169 (253)
T KOG4173|consen 156 FKTSRDRKDHMIRM 169 (253)
T ss_pred hhhhhhhhhHHHHh
Confidence 66666666665443
No 122
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=63.46 E-value=6.7 Score=31.40 Aligned_cols=45 Identities=27% Similarity=0.481 Sum_probs=25.6
Q ss_pred ccCccccccCCh---hHHhcccccccCCCCcccCCCCCCcccccccccccccCCCCCceecCccccc
Q psy12018 36 ACDVCGKEYQYY---RNLYRHKKFECGQEPRYQCPQCPYRTKQKELGWESLKPNAYGMYVCDICGKV 99 (148)
Q Consensus 36 ~C~~C~~~f~~~---~~l~~h~~~~~~~~~~~~C~~c~~~f~~~~~~~~~~~~~~~~~~~C~~c~~~ 99 (148)
.|..||..+... ..|.-|+. .....|..||.. ...|..|+.||..
T Consensus 437 ~C~~Cg~v~~Cp~Cd~~lt~H~~-----~~~L~CH~Cg~~--------------~~~p~~Cp~Cgs~ 484 (730)
T COG1198 437 LCRDCGYIAECPNCDSPLTLHKA-----TGQLRCHYCGYQ--------------EPIPQSCPECGSE 484 (730)
T ss_pred ecccCCCcccCCCCCcceEEecC-----CCeeEeCCCCCC--------------CCCCCCCCCCCCC
Confidence 377777776554 23333332 345667777742 2335678888754
No 123
>PRK05580 primosome assembly protein PriA; Validated
Probab=62.88 E-value=6.6 Score=31.17 Aligned_cols=10 Identities=30% Similarity=0.727 Sum_probs=5.7
Q ss_pred CceeCCCChh
Q psy12018 118 PRFQCPQCPY 127 (148)
Q Consensus 118 ~~~~C~~C~~ 127 (148)
.|..|+.||.
T Consensus 420 ~~~~Cp~Cg~ 429 (679)
T PRK05580 420 IPKACPECGS 429 (679)
T ss_pred CCCCCCCCcC
Confidence 4556666654
No 124
>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=62.33 E-value=3.7 Score=19.03 Aligned_cols=11 Identities=36% Similarity=1.298 Sum_probs=6.5
Q ss_pred eecCccccccc
Q psy12018 91 YVCDICGKVYQ 101 (148)
Q Consensus 91 ~~C~~c~~~f~ 101 (148)
+.|+.|++.|.
T Consensus 2 r~C~~Cg~~Yh 12 (36)
T PF05191_consen 2 RICPKCGRIYH 12 (36)
T ss_dssp EEETTTTEEEE
T ss_pred cCcCCCCCccc
Confidence 35666666654
No 125
>PF04780 DUF629: Protein of unknown function (DUF629); InterPro: IPR006865 This domain represents a region of several plant proteins of unknown function. A C2H2 zinc finger is predicted in this region in some family members, but the spacing between the cysteine residues is not conserved throughout the family.
Probab=61.83 E-value=6.2 Score=29.71 Aligned_cols=22 Identities=18% Similarity=0.625 Sum_probs=11.2
Q ss_pred eecCccccccccchhHHhhHhh
Q psy12018 91 YVCDICGKVYQHKRTLYRHKKD 112 (148)
Q Consensus 91 ~~C~~c~~~f~~~~~l~~H~~~ 112 (148)
+.|+.|.+.|.....+..|+..
T Consensus 58 WiCp~CskkF~d~~~~~~H~~~ 79 (466)
T PF04780_consen 58 WICPRCSKKFSDAESCLSHMEQ 79 (466)
T ss_pred eeCCcccceeCCHHHHHHHHHH
Confidence 3455555555555555555443
No 126
>COG4391 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=60.93 E-value=13 Score=19.50 Aligned_cols=45 Identities=22% Similarity=0.426 Sum_probs=18.8
Q ss_pred ccccccCCCCcccCCCCCCcccccccccccccCCCCCceecCccccccc
Q psy12018 53 HKKFECGQEPRYQCPQCPYRTKQKELGWESLKPNAYGMYVCDICGKVYQ 101 (148)
Q Consensus 53 h~~~~~~~~~~~~C~~c~~~f~~~~~~~~~~~~~~~~~~~C~~c~~~f~ 101 (148)
|..+..+ ..++.|+--+-.+.....+... .. ++.-.|++|+..|.
T Consensus 15 ~~~I~~~-~~~l~C~g~~~p~~HPrV~L~m-g~--~gev~CPYC~t~y~ 59 (62)
T COG4391 15 HETIEIG-DLPLMCPGPEPPNDHPRVFLDM-GD--EGEVVCPYCSTRYR 59 (62)
T ss_pred ceEEEeC-CeeEEcCCCCCCCCCCEEEEEc-CC--CCcEecCccccEEE
Confidence 3334434 4556665443333332222222 11 22345666665553
No 127
>KOG3408|consensus
Probab=60.81 E-value=5.2 Score=24.13 Aligned_cols=27 Identities=22% Similarity=0.469 Sum_probs=22.9
Q ss_pred CCCCceecCccccccccchhHHhhHhh
Q psy12018 86 NAYGMYVCDICGKVYQHKRTLYRHKKD 112 (148)
Q Consensus 86 ~~~~~~~C~~c~~~f~~~~~l~~H~~~ 112 (148)
.|.+.|-|..|.+.|.....|..|.++
T Consensus 53 PG~GqfyCi~CaRyFi~~~~l~~H~kt 79 (129)
T KOG3408|consen 53 PGGGQFYCIECARYFIDAKALKTHFKT 79 (129)
T ss_pred CCCceeehhhhhhhhcchHHHHHHHhc
Confidence 355668999999999999999999774
No 128
>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=60.09 E-value=4.7 Score=16.90 Aligned_cols=8 Identities=38% Similarity=1.402 Sum_probs=4.6
Q ss_pred cccCCCCC
Q psy12018 63 RYQCPQCP 70 (148)
Q Consensus 63 ~~~C~~c~ 70 (148)
+|.|+.||
T Consensus 16 ~f~CPnCG 23 (24)
T PF07754_consen 16 PFPCPNCG 23 (24)
T ss_pred eEeCCCCC
Confidence 45566555
No 129
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=59.90 E-value=3.2 Score=23.70 Aligned_cols=30 Identities=23% Similarity=0.672 Sum_probs=16.5
Q ss_pred cccCCCCCCcccccccccccccCCCCCceecCccccccc
Q psy12018 63 RYQCPQCPYRTKQKELGWESLKPNAYGMYVCDICGKVYQ 101 (148)
Q Consensus 63 ~~~C~~c~~~f~~~~~~~~~~~~~~~~~~~C~~c~~~f~ 101 (148)
.|.|+.|++.-.. -..-+.|.|..|++.|.
T Consensus 36 ~y~CpfCgk~~vk---------R~a~GIW~C~~C~~~~A 65 (90)
T PRK03976 36 KHVCPVCGRPKVK---------RVGTGIWECRKCGAKFA 65 (90)
T ss_pred CccCCCCCCCceE---------EEEEEEEEcCCCCCEEe
Confidence 4777777653111 11234567777776664
No 130
>KOG3408|consensus
Probab=57.62 E-value=7.2 Score=23.54 Aligned_cols=30 Identities=23% Similarity=0.247 Sum_probs=24.1
Q ss_pred CCCCCCCccccCccccccCChhHHhccccc
Q psy12018 27 FKPKLYGKFACDVCGKEYQYYRNLYRHKKF 56 (148)
Q Consensus 27 ~~~~~~~~~~C~~C~~~f~~~~~l~~h~~~ 56 (148)
.+-.+-.-|.|-.|.+-|.....|..|.++
T Consensus 50 ~dlPG~GqfyCi~CaRyFi~~~~l~~H~kt 79 (129)
T KOG3408|consen 50 PDLPGGGQFYCIECARYFIDAKALKTHFKT 79 (129)
T ss_pred CCCCCCceeehhhhhhhhcchHHHHHHHhc
Confidence 344456678999999999999999999754
No 131
>COG4530 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=57.23 E-value=6.8 Score=23.20 Aligned_cols=27 Identities=11% Similarity=0.009 Sum_probs=14.8
Q ss_pred ccCccccccCChhHHhcccccccCCCCcccCCCCCCccc
Q psy12018 36 ACDVCGKEYQYYRNLYRHKKFECGQEPRYQCPQCPYRTK 74 (148)
Q Consensus 36 ~C~~C~~~f~~~~~l~~h~~~~~~~~~~~~C~~c~~~f~ 74 (148)
+|+.|++.|.... ..|..|+.||+.|.
T Consensus 11 idPetg~KFYDLN------------rdPiVsPytG~s~P 37 (129)
T COG4530 11 IDPETGKKFYDLN------------RDPIVSPYTGKSYP 37 (129)
T ss_pred cCccccchhhccC------------CCccccCcccccch
Confidence 5666666654321 34566666666653
No 132
>PF13451 zf-trcl: Probable zinc-binding domain
Probab=57.12 E-value=2.8 Score=21.01 Aligned_cols=13 Identities=15% Similarity=0.340 Sum_probs=6.2
Q ss_pred cccCCCCCCcccc
Q psy12018 63 RYQCPQCPYRTKQ 75 (148)
Q Consensus 63 ~~~C~~c~~~f~~ 75 (148)
.+.|..||..|..
T Consensus 4 ~l~C~dCg~~Fvf 16 (49)
T PF13451_consen 4 TLTCKDCGAEFVF 16 (49)
T ss_pred eEEcccCCCeEEE
Confidence 3445555554443
No 133
>KOG2807|consensus
Probab=55.36 E-value=22 Score=25.52 Aligned_cols=24 Identities=17% Similarity=0.407 Sum_probs=16.1
Q ss_pred ceeCCCChhhhhchHHHHHHHHhh
Q psy12018 119 RFQCPQCPYRAKQKANLKTHLIIK 142 (148)
Q Consensus 119 ~~~C~~C~~~f~~~~~l~~H~~~~ 142 (148)
.|.|..|...|-.-.+.-.|...|
T Consensus 345 ~y~C~~Ck~~FCldCDv~iHesLh 368 (378)
T KOG2807|consen 345 RYRCESCKNVFCLDCDVFIHESLH 368 (378)
T ss_pred cEEchhccceeeccchHHHHhhhh
Confidence 478888888887665555565543
No 134
>PF02176 zf-TRAF: TRAF-type zinc finger; PDB: 2EOD_A 2YUC_A 3HCU_A 3HCS_B 3HCT_A.
Probab=54.73 E-value=8.9 Score=19.56 Aligned_cols=40 Identities=25% Similarity=0.534 Sum_probs=20.0
Q ss_pred ceecCc-cccccccchhHHhhHhhhhCCCCceeCCC----Chhhhh
Q psy12018 90 MYVCDI-CGKVYQHKRTLYRHKKDECGQEPRFQCPQ----CPYRAK 130 (148)
Q Consensus 90 ~~~C~~-c~~~f~~~~~l~~H~~~~~~~~~~~~C~~----C~~~f~ 130 (148)
+..|+. |+..-.....|..|+...-. .++..|.. |+..+.
T Consensus 9 ~v~C~~~cc~~~i~r~~l~~H~~~~C~-~~~v~C~~~~~GC~~~~~ 53 (60)
T PF02176_consen 9 PVPCPNGCCNEMIPRKELDDHLENECP-KRPVPCPYSPYGCKERVP 53 (60)
T ss_dssp EEE-TT--S-BEEECCCHHHHHHTTST-TSEEE-SS----S--EEE
T ss_pred EeeCCCCCcccceeHHHHHHHHHccCC-CCcEECCCCCCCCCCccc
Confidence 356766 33332345667778774444 45677877 766554
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=54.29 E-value=5.6 Score=17.66 Aligned_cols=9 Identities=56% Similarity=1.545 Sum_probs=1.5
Q ss_pred ccCcccccc
Q psy12018 36 ACDVCGKEY 44 (148)
Q Consensus 36 ~C~~C~~~f 44 (148)
.|+.|+..+
T Consensus 4 ~Cp~C~se~ 12 (30)
T PF08274_consen 4 KCPLCGSEY 12 (30)
T ss_dssp --TTT----
T ss_pred CCCCCCCcc
Confidence 344554443
No 136
>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=52.83 E-value=13 Score=21.89 Aligned_cols=25 Identities=36% Similarity=0.795 Sum_probs=22.3
Q ss_pred eec----CccccccccchhHHhhHhhhhC
Q psy12018 91 YVC----DICGKVYQHKRTLYRHKKDECG 115 (148)
Q Consensus 91 ~~C----~~c~~~f~~~~~l~~H~~~~~~ 115 (148)
|.| ..|+..+.+...+..|.+..+|
T Consensus 81 ~~C~~~~~~C~y~~~~~~~m~~H~~~~Hg 109 (109)
T PF12013_consen 81 YRCQCDPPHCGYITRSKKTMRKHWRKEHG 109 (109)
T ss_pred eeeecCCCCCCcEeccHHHHHHHHHHhcC
Confidence 889 9999999999999999987764
No 137
>PF01927 Mut7-C: Mut7-C RNAse domain; InterPro: IPR002782 This prokaryotic family of proteins have no known function. The proteins contain four conserved cysteines that may be involved in metal binding or disulphide bridges.
Probab=52.45 E-value=20 Score=22.45 Aligned_cols=14 Identities=36% Similarity=0.880 Sum_probs=6.6
Q ss_pred eecCccccccccch
Q psy12018 91 YVCDICGKVYQHKR 104 (148)
Q Consensus 91 ~~C~~c~~~f~~~~ 104 (148)
+.|+.|++.|-..+
T Consensus 125 ~~C~~C~kiyW~Gs 138 (147)
T PF01927_consen 125 WRCPGCGKIYWEGS 138 (147)
T ss_pred EECCCCCCEecccc
Confidence 44555555544333
No 138
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=51.65 E-value=7.9 Score=22.54 Aligned_cols=43 Identities=19% Similarity=0.298 Sum_probs=23.6
Q ss_pred CCCCCccccCccccccCChhHHhcccccccCCCCcccCCCCCCccccc
Q psy12018 29 PKLYGKFACDVCGKEYQYYRNLYRHKKFECGQEPRYQCPQCPYRTKQK 76 (148)
Q Consensus 29 ~~~~~~~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~~C~~c~~~f~~~ 76 (148)
...++.|.|+.|+..-.....+..-. . .....|..||..|...
T Consensus 17 ~~L~k~FtCp~Cghe~vs~ctvkk~~----~-~g~~~Cg~CGls~e~e 59 (104)
T COG4888 17 QVLPKTFTCPRCGHEKVSSCTVKKTV----N-IGTAVCGNCGLSFECE 59 (104)
T ss_pred ccCCceEecCccCCeeeeEEEEEecC----c-eeEEEcccCcceEEEe
Confidence 34677788888887543332222111 1 2345677777766543
No 139
>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=51.55 E-value=62 Score=20.72 Aligned_cols=56 Identities=14% Similarity=0.212 Sum_probs=34.1
Q ss_pred CceecCccccccccchhHHhhHhhhhCCCCceeCCCChhhhh-chHHHHHHHHhhcCCc
Q psy12018 89 GMYVCDICGKVYQHKRTLYRHKKDECGQEPRFQCPQCPYRAK-QKANLKTHLIIKHDSV 146 (148)
Q Consensus 89 ~~~~C~~c~~~f~~~~~l~~H~~~~~~~~~~~~C~~C~~~f~-~~~~l~~H~~~~h~~~ 146 (148)
....|+.|.-........ ...+.+.. .|+-.|..=+-.|. +...|++|.+..|+..
T Consensus 79 ~~L~CPLCRG~V~GWtvv-e~AR~~LN-~K~RsC~~e~C~F~GtY~eLrKHar~~HP~~ 135 (162)
T PF07800_consen 79 PELACPLCRGEVKGWTVV-EPARRFLN-AKKRSCSQESCSFSGTYSELRKHARSEHPSA 135 (162)
T ss_pred ccccCccccCceeceEEc-hHHHHHhc-cCCccCcccccccccCHHHHHHHHHhhCCCC
Confidence 346799987443322222 22444444 56667766444554 5678999999988754
No 140
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=50.87 E-value=7.6 Score=18.31 Aligned_cols=15 Identities=27% Similarity=0.609 Sum_probs=12.5
Q ss_pred ccccCccccccCChh
Q psy12018 34 KFACDVCGKEYQYYR 48 (148)
Q Consensus 34 ~~~C~~C~~~f~~~~ 48 (148)
|+.|..|++.|...-
T Consensus 12 ~f~C~~C~~~FC~~H 26 (39)
T smart00154 12 GFKCRHCGNLFCGEH 26 (39)
T ss_pred CeECCccCCcccccc
Confidence 789999999998753
No 141
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=50.74 E-value=8.2 Score=23.84 Aligned_cols=10 Identities=20% Similarity=0.607 Sum_probs=4.7
Q ss_pred ccCCCCCCcc
Q psy12018 64 YQCPQCPYRT 73 (148)
Q Consensus 64 ~~C~~c~~~f 73 (148)
+.|..||..|
T Consensus 71 ~~C~~CG~~~ 80 (135)
T PRK03824 71 LKCRNCGNEW 80 (135)
T ss_pred EECCCCCCEE
Confidence 4455555443
No 142
>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=50.24 E-value=17 Score=17.36 Aligned_cols=7 Identities=57% Similarity=1.402 Sum_probs=2.6
Q ss_pred eecCccc
Q psy12018 91 YVCDICG 97 (148)
Q Consensus 91 ~~C~~c~ 97 (148)
+.|..||
T Consensus 20 ~vC~~CG 26 (43)
T PF08271_consen 20 LVCPNCG 26 (43)
T ss_dssp EEETTT-
T ss_pred EECCCCC
Confidence 3444444
No 143
>KOG4118|consensus
Probab=48.97 E-value=10 Score=20.17 Aligned_cols=30 Identities=23% Similarity=0.410 Sum_probs=20.9
Q ss_pred ceeCCCChhhhhchHHHHHHHHhhcCCccC
Q psy12018 119 RFQCPQCPYRAKQKANLKTHLIIKHDSVLL 148 (148)
Q Consensus 119 ~~~C~~C~~~f~~~~~l~~H~~~~h~~~~~ 148 (148)
.|.|.+|...-...-.+..|....|+..+|
T Consensus 38 ~~kCtVC~~~mpdpktfkqhfe~kHpk~~~ 67 (74)
T KOG4118|consen 38 HHKCTVCMVQMPDPKTFKQHFENKHPKEPL 67 (74)
T ss_pred HhhhHhhHhhCCCCchHHHHHhhcCCCCCC
Confidence 367777777666777777777777776554
No 144
>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=48.64 E-value=7.9 Score=16.89 Aligned_cols=8 Identities=38% Similarity=0.883 Sum_probs=3.5
Q ss_pred cCcccccc
Q psy12018 93 CDICGKVY 100 (148)
Q Consensus 93 C~~c~~~f 100 (148)
|..|++.|
T Consensus 3 CiDC~~~F 10 (28)
T PF08790_consen 3 CIDCSKDF 10 (28)
T ss_dssp ETTTTEEE
T ss_pred eecCCCCc
Confidence 44444444
No 145
>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=48.25 E-value=11 Score=18.21 Aligned_cols=16 Identities=19% Similarity=0.893 Sum_probs=12.0
Q ss_pred ecCccccccccchhHH
Q psy12018 92 VCDICGKVYQHKRTLY 107 (148)
Q Consensus 92 ~C~~c~~~f~~~~~l~ 107 (148)
.|..|++.|.+...+.
T Consensus 10 ~C~~C~rpf~WRKKW~ 25 (42)
T PF10013_consen 10 ICPVCGRPFTWRKKWA 25 (42)
T ss_pred cCcccCCcchHHHHHH
Confidence 5888998888766554
No 146
>PF07282 OrfB_Zn_ribbon: Putative transposase DNA-binding domain; InterPro: IPR010095 This entry represents a region of a sequence similarity between a family of putative transposases of Thermoanaerobacter tengcongensis, smaller related proteins from Bacillus anthracis, putative transposes described by IPR001959 from INTERPRO, and other proteins. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=48.22 E-value=18 Score=19.17 Aligned_cols=9 Identities=33% Similarity=0.962 Sum_probs=4.0
Q ss_pred eecCccccc
Q psy12018 91 YVCDICGKV 99 (148)
Q Consensus 91 ~~C~~c~~~ 99 (148)
|.|+.||..
T Consensus 47 ~~C~~Cg~~ 55 (69)
T PF07282_consen 47 FTCPNCGFE 55 (69)
T ss_pred EEcCCCCCE
Confidence 444444433
No 147
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=47.76 E-value=22 Score=16.81 Aligned_cols=9 Identities=56% Similarity=1.379 Sum_probs=4.3
Q ss_pred eecCccccc
Q psy12018 91 YVCDICGKV 99 (148)
Q Consensus 91 ~~C~~c~~~ 99 (148)
|.|..|+..
T Consensus 29 y~C~~C~~~ 37 (40)
T smart00440 29 YVCTKCGHR 37 (40)
T ss_pred EEeCCCCCE
Confidence 455555533
No 148
>PF01096 TFIIS_C: Transcription factor S-II (TFIIS); InterPro: IPR001222 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIs (TFIIS). In eukaryotes the initiation of transcription of protein encoding genes by polymerase II (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least eight different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, -IIH and -IIS []. During mRNA elongation, Pol II can encounter DNA sequences that cause reverse movement of the enzyme. Such backtracking involves extrusion of the RNA 3'-end into the pore, and can lead to transcriptional arrest. Escape from arrest requires cleavage of the extruded RNA with the help of TFIIS, which induces mRNA cleavage by enhancing the intrinsic nuclease activity of RNA polymerase (Pol) II, past template-encoded pause sites []. TFIIS extends from the polymerase surface via a pore to the internal active site. Two essential and invariant acidic residues in a TFIIS loop complement the Pol II active site and could position a metal ion and a water molecule for hydrolytic RNA cleavage. TFIIS also induces extensive structural changes in Pol II that would realign nucleic acids in the active centre. TFIIS is a protein of about 300 amino acids. It contains three regions: a variable N-terminal domain not required for TFIIS activity; a conserved central domain required for Pol II binding; and a conserved C-terminal C4-type zinc finger essential for RNA cleavage. The zinc finger folds in a conformation termed a zinc ribbon [] characterised by a three-stranded antiparallel beta-sheet and two beta-hairpins. A backbone model for Pol II-TFIIS complex was obtained from X-ray analysis. It shows that a beta hairpin protrudes from the zinc finger and complements the pol II active site []. Some viral proteins also contain the TFIIS zinc ribbon C-terminal domain. The Vaccinia virus protein, unlike its eukaryotic homologue, is an integral RNA polymerase subunit rather than a readily separable transcription factor []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding, 0006351 transcription, DNA-dependent; PDB: 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I 3I4M_I ....
Probab=46.31 E-value=15 Score=17.26 Aligned_cols=9 Identities=56% Similarity=1.235 Sum_probs=4.8
Q ss_pred eecCccccc
Q psy12018 91 YVCDICGKV 99 (148)
Q Consensus 91 ~~C~~c~~~ 99 (148)
|.|..|+..
T Consensus 29 y~C~~C~~~ 37 (39)
T PF01096_consen 29 YVCCNCGHR 37 (39)
T ss_dssp EEESSSTEE
T ss_pred EEeCCCCCe
Confidence 555555543
No 149
>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=45.29 E-value=11 Score=21.92 Aligned_cols=15 Identities=20% Similarity=0.505 Sum_probs=11.0
Q ss_pred CCccccCccccccCC
Q psy12018 32 YGKFACDVCGKEYQY 46 (148)
Q Consensus 32 ~~~~~C~~C~~~f~~ 46 (148)
.++++|..||..|.-
T Consensus 77 g~~~rC~eCG~~fkL 91 (97)
T cd00924 77 GKPKRCPECGHVFKL 91 (97)
T ss_pred CCceeCCCCCcEEEE
Confidence 367888888887743
No 150
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=45.12 E-value=10 Score=23.27 Aligned_cols=15 Identities=20% Similarity=0.614 Sum_probs=12.3
Q ss_pred ccccCccccccCChh
Q psy12018 34 KFACDVCGKEYQYYR 48 (148)
Q Consensus 34 ~~~C~~C~~~f~~~~ 48 (148)
|++|..||+.|..-+
T Consensus 1 PH~Ct~Cg~~f~dgs 15 (131)
T PF09845_consen 1 PHQCTKCGRVFEDGS 15 (131)
T ss_pred CcccCcCCCCcCCCc
Confidence 678999999998654
No 151
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=45.03 E-value=13 Score=22.18 Aligned_cols=10 Identities=20% Similarity=0.358 Sum_probs=4.7
Q ss_pred ccCCCCCCcc
Q psy12018 64 YQCPQCPYRT 73 (148)
Q Consensus 64 ~~C~~c~~~f 73 (148)
..|..|+..|
T Consensus 71 ~~C~~Cg~~~ 80 (113)
T PRK12380 71 AWCWDCSQVV 80 (113)
T ss_pred EEcccCCCEE
Confidence 4455555433
No 152
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=44.93 E-value=24 Score=16.61 Aligned_cols=15 Identities=27% Similarity=0.452 Sum_probs=6.2
Q ss_pred eCCCChhhhhchHHH
Q psy12018 121 QCPQCPYRAKQKANL 135 (148)
Q Consensus 121 ~C~~C~~~f~~~~~l 135 (148)
.|..|+-.+-....|
T Consensus 21 ~C~~C~G~W~d~~el 35 (41)
T PF13453_consen 21 VCPSCGGIWFDAGEL 35 (41)
T ss_pred ECCCCCeEEccHHHH
Confidence 344444444433333
No 153
>COG3364 Zn-ribbon containing protein [General function prediction only]
Probab=44.64 E-value=11 Score=22.10 Aligned_cols=16 Identities=19% Similarity=0.449 Sum_probs=12.7
Q ss_pred CccccCccccccCChh
Q psy12018 33 GKFACDVCGKEYQYYR 48 (148)
Q Consensus 33 ~~~~C~~C~~~f~~~~ 48 (148)
+|++|..||..|..-+
T Consensus 1 MpH~CtrCG~vf~~g~ 16 (112)
T COG3364 1 MPHQCTRCGEVFDDGS 16 (112)
T ss_pred CCceeccccccccccc
Confidence 4788999999988743
No 154
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=44.62 E-value=14 Score=26.33 Aligned_cols=36 Identities=19% Similarity=0.295 Sum_probs=18.9
Q ss_pred CCccccCccccccCChhHHhcccccccCCCCcccCCCCCC
Q psy12018 32 YGKFACDVCGKEYQYYRNLYRHKKFECGQEPRYQCPQCPY 71 (148)
Q Consensus 32 ~~~~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~~C~~c~~ 71 (148)
+..-.|++||..= ..+ + .+.....| .+-..|+.|+-
T Consensus 185 ~~~~~CPvCGs~P-~~s-~-v~~~~~~G-~RyL~CslC~t 220 (309)
T PRK03564 185 EQRQFCPVCGSMP-VSS-V-VQIGTTQG-LRYLHCNLCES 220 (309)
T ss_pred cCCCCCCCCCCcc-hhh-e-eeccCCCC-ceEEEcCCCCC
Confidence 3456799999751 111 1 12222223 45667777764
No 155
>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=44.34 E-value=11 Score=22.58 Aligned_cols=11 Identities=18% Similarity=0.691 Sum_probs=5.4
Q ss_pred ccCCCCCCccc
Q psy12018 64 YQCPQCPYRTK 74 (148)
Q Consensus 64 ~~C~~c~~~f~ 74 (148)
..|+.|+..|.
T Consensus 71 ~~C~~Cg~~~~ 81 (115)
T TIGR00100 71 CECEDCSEEVS 81 (115)
T ss_pred EEcccCCCEEe
Confidence 44555554443
No 156
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=44.26 E-value=24 Score=17.34 Aligned_cols=9 Identities=44% Similarity=1.172 Sum_probs=4.3
Q ss_pred eecCccccc
Q psy12018 91 YVCDICGKV 99 (148)
Q Consensus 91 ~~C~~c~~~ 99 (148)
+.|+.|+..
T Consensus 21 ~vC~~Cg~~ 29 (52)
T smart00661 21 FVCRKCGYE 29 (52)
T ss_pred EECCcCCCe
Confidence 445555533
No 157
>PF14369 zf-RING_3: zinc-finger
Probab=43.98 E-value=24 Score=16.15 Aligned_cols=11 Identities=27% Similarity=0.715 Sum_probs=7.6
Q ss_pred cCCCCCCcccc
Q psy12018 65 QCPQCPYRTKQ 75 (148)
Q Consensus 65 ~C~~c~~~f~~ 75 (148)
.|+.|+..|..
T Consensus 23 ~CP~C~~gFvE 33 (35)
T PF14369_consen 23 ACPRCHGGFVE 33 (35)
T ss_pred CCcCCCCcEeE
Confidence 58888777753
No 158
>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=43.77 E-value=9.6 Score=26.78 Aligned_cols=77 Identities=21% Similarity=0.340 Sum_probs=27.0
Q ss_pred ccccCccccccCChhHHhcccccccCCCCcccCCCCCCcccccccccccccCCCCCceecCccccccccc-hhHHhhHhh
Q psy12018 34 KFACDVCGKEYQYYRNLYRHKKFECGQEPRYQCPQCPYRTKQKELGWESLKPNAYGMYVCDICGKVYQHK-RTLYRHKKD 112 (148)
Q Consensus 34 ~~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~~C~~c~~~f~~~~~~~~~~~~~~~~~~~C~~c~~~f~~~-~~l~~H~~~ 112 (148)
.-.|++||.. ...+.|..-.. .| .+-..|+.|+-..... +..|+.||..-... ..+.. ..
T Consensus 172 ~g~CPvCGs~-P~~s~l~~~~~--~G-~R~L~Cs~C~t~W~~~-------------R~~Cp~Cg~~~~~~l~~~~~--e~ 232 (290)
T PF04216_consen 172 RGYCPVCGSP-PVLSVLRGGER--EG-KRYLHCSLCGTEWRFV-------------RIKCPYCGNTDHEKLEYFTV--EG 232 (290)
T ss_dssp -SS-TTT----EEEEEEE---------EEEEEETTT--EEE---------------TTS-TTT---SS-EEE--------
T ss_pred CCcCCCCCCc-CceEEEecCCC--Cc-cEEEEcCCCCCeeeec-------------CCCCcCCCCCCCcceeeEec--CC
Confidence 3578888874 11111111110 13 4567788887543321 24699998553222 11111 11
Q ss_pred hhCCCCceeCCCChhhhh
Q psy12018 113 ECGQEPRFQCPQCPYRAK 130 (148)
Q Consensus 113 ~~~~~~~~~C~~C~~~f~ 130 (148)
..+ .+...|..|+.-++
T Consensus 233 ~~~-~rve~C~~C~~YlK 249 (290)
T PF04216_consen 233 EPA-YRVEVCESCGSYLK 249 (290)
T ss_dssp --S-EEEEEETTTTEEEE
T ss_pred CCc-EEEEECCcccchHH
Confidence 112 45578998975443
No 159
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=43.57 E-value=17 Score=27.04 Aligned_cols=12 Identities=25% Similarity=0.695 Sum_probs=6.0
Q ss_pred ceecCccccccc
Q psy12018 90 MYVCDICGKVYQ 101 (148)
Q Consensus 90 ~~~C~~c~~~f~ 101 (148)
-|+|+.|+..+.
T Consensus 367 g~rC~kCg~~~~ 378 (421)
T COG1571 367 GFRCKKCGTRAR 378 (421)
T ss_pred CcccccccccCC
Confidence 355555554443
No 160
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=43.10 E-value=25 Score=18.13 Aligned_cols=9 Identities=33% Similarity=1.342 Sum_probs=4.6
Q ss_pred cccCCCCCC
Q psy12018 63 RYQCPQCPY 71 (148)
Q Consensus 63 ~~~C~~c~~ 71 (148)
.|.|+.||-
T Consensus 14 ~~~Cp~cGi 22 (55)
T PF13824_consen 14 NFECPDCGI 22 (55)
T ss_pred CCcCCCCCC
Confidence 455555554
No 161
>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=43.05 E-value=36 Score=15.46 Aligned_cols=23 Identities=17% Similarity=0.327 Sum_probs=14.0
Q ss_pred eecCccccccccchhHHhhHhhhh
Q psy12018 91 YVCDICGKVYQHKRTLYRHKKDEC 114 (148)
Q Consensus 91 ~~C~~c~~~f~~~~~l~~H~~~~~ 114 (148)
+.|+.|++.+. .+.+..|+..-.
T Consensus 5 ~~C~nC~R~v~-a~RfA~HLekCm 27 (33)
T PF08209_consen 5 VECPNCGRPVA-ASRFAPHLEKCM 27 (33)
T ss_dssp EE-TTTSSEEE-GGGHHHHHHHHT
T ss_pred EECCCCcCCcc-hhhhHHHHHHHH
Confidence 67888887754 455666765443
No 162
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=42.94 E-value=12 Score=27.10 Aligned_cols=76 Identities=20% Similarity=0.185 Sum_probs=43.2
Q ss_pred cccCccccccCChhHHhcccccccCCCCcccCCCCCCc----ccccccccccccCCCCCceecCc--cc----cccccch
Q psy12018 35 FACDVCGKEYQYYRNLYRHKKFECGQEPRYQCPQCPYR----TKQKELGWESLKPNAYGMYVCDI--CG----KVYQHKR 104 (148)
Q Consensus 35 ~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~~C~~c~~~----f~~~~~~~~~~~~~~~~~~~C~~--c~----~~f~~~~ 104 (148)
..|..|..-|.....|..|.+..+ |+-+.|.+-+.. |++...+..| .....|.|-. |. ..|....
T Consensus 221 P~C~FC~~~FYdDDEL~~HcR~~H--E~ChICD~v~p~~~QYFK~Y~~Le~H---F~~~hy~ct~qtc~~~k~~vf~~~~ 295 (493)
T COG5236 221 PLCIFCKIYFYDDDELRRHCRLRH--EACHICDMVGPIRYQYFKSYEDLEAH---FRNAHYCCTFQTCRVGKCYVFPYHT 295 (493)
T ss_pred chhhhccceecChHHHHHHHHhhh--hhhhhhhccCccchhhhhCHHHHHHH---hhcCceEEEEEEEecCcEEEeccHH
Confidence 468888888888888888887644 344555443311 2221122222 2223355533 43 3577777
Q ss_pred hHHhhHhhhhC
Q psy12018 105 TLYRHKKDECG 115 (148)
Q Consensus 105 ~l~~H~~~~~~ 115 (148)
.|..|+...++
T Consensus 296 el~~h~~~~h~ 306 (493)
T COG5236 296 ELLEHLTRFHK 306 (493)
T ss_pred HHHHHHHHHhh
Confidence 78888776655
No 163
>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=42.85 E-value=25 Score=17.02 Aligned_cols=10 Identities=40% Similarity=1.019 Sum_probs=5.4
Q ss_pred CCceecCccc
Q psy12018 88 YGMYVCDICG 97 (148)
Q Consensus 88 ~~~~~C~~c~ 97 (148)
...|.|..|+
T Consensus 35 ~~~~~C~~C~ 44 (46)
T PF12760_consen 35 RGRYRCKACR 44 (46)
T ss_pred CCeEECCCCC
Confidence 3446666654
No 164
>PRK12496 hypothetical protein; Provisional
Probab=42.54 E-value=18 Score=23.24 Aligned_cols=29 Identities=31% Similarity=0.489 Sum_probs=18.8
Q ss_pred CceecCccccccccchhHHhhHhhhhCCCCceeCCCChhhhh
Q psy12018 89 GMYVCDICGKVYQHKRTLYRHKKDECGQEPRFQCPQCPYRAK 130 (148)
Q Consensus 89 ~~~~C~~c~~~f~~~~~l~~H~~~~~~~~~~~~C~~C~~~f~ 130 (148)
+.|.|..|++.|.... ..-.|+.||....
T Consensus 126 w~~~C~gC~~~~~~~~-------------~~~~C~~CG~~~~ 154 (164)
T PRK12496 126 WRKVCKGCKKKYPEDY-------------PDDVCEICGSPVK 154 (164)
T ss_pred eeEECCCCCccccCCC-------------CCCcCCCCCChhh
Confidence 4588999998885311 1135999986543
No 165
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=42.52 E-value=21 Score=21.90 Aligned_cols=14 Identities=29% Similarity=0.831 Sum_probs=8.3
Q ss_pred CceecCcccccccc
Q psy12018 89 GMYVCDICGKVYQH 102 (148)
Q Consensus 89 ~~~~C~~c~~~f~~ 102 (148)
..|+|..|++.|..
T Consensus 52 qRyrC~~C~~tf~~ 65 (129)
T COG3677 52 QRYKCKSCGSTFTV 65 (129)
T ss_pred cccccCCcCcceee
Confidence 34666666666643
No 166
>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=42.44 E-value=8.5 Score=18.46 Aligned_cols=16 Identities=31% Similarity=0.715 Sum_probs=10.6
Q ss_pred CccccCccccccCChh
Q psy12018 33 GKFACDVCGKEYQYYR 48 (148)
Q Consensus 33 ~~~~C~~C~~~f~~~~ 48 (148)
.|+.|..|++.|-..-
T Consensus 12 ~~~~C~~C~~~FC~~H 27 (43)
T PF01428_consen 12 LPFKCKHCGKSFCLKH 27 (43)
T ss_dssp SHEE-TTTS-EE-TTT
T ss_pred CCeECCCCCcccCccc
Confidence 6889999999998763
No 167
>PLN02294 cytochrome c oxidase subunit Vb
Probab=42.27 E-value=13 Score=23.93 Aligned_cols=15 Identities=27% Similarity=0.716 Sum_probs=8.8
Q ss_pred CCccccCccccccCC
Q psy12018 32 YGKFACDVCGKEYQY 46 (148)
Q Consensus 32 ~~~~~C~~C~~~f~~ 46 (148)
.++++|..||..|.-
T Consensus 139 Gkp~RCpeCG~~fkL 153 (174)
T PLN02294 139 GKSFECPVCTQYFEL 153 (174)
T ss_pred CCceeCCCCCCEEEE
Confidence 346666666666543
No 168
>PF13878 zf-C2H2_3: zinc-finger of acetyl-transferase ESCO
Probab=42.17 E-value=26 Score=16.66 Aligned_cols=10 Identities=30% Similarity=0.816 Sum_probs=4.8
Q ss_pred eCCCChhhhh
Q psy12018 121 QCPQCPYRAK 130 (148)
Q Consensus 121 ~C~~C~~~f~ 130 (148)
.|..||..|.
T Consensus 15 ~C~~CgM~Y~ 24 (41)
T PF13878_consen 15 TCPTCGMLYS 24 (41)
T ss_pred CCCCCCCEEC
Confidence 4555554443
No 169
>KOG2482|consensus
Probab=42.13 E-value=13 Score=26.79 Aligned_cols=52 Identities=23% Similarity=0.413 Sum_probs=36.4
Q ss_pred eecCcccccc-ccchhHHhhHhhhhCCC---------------------CceeCCCChhhhhchHHHHHHHHhh
Q psy12018 91 YVCDICGKVY-QHKRTLYRHKKDECGQE---------------------PRFQCPQCPYRAKQKANLKTHLIIK 142 (148)
Q Consensus 91 ~~C~~c~~~f-~~~~~l~~H~~~~~~~~---------------------~~~~C~~C~~~f~~~~~l~~H~~~~ 142 (148)
-+|-.|...+ ..++.+..|...-++-. -.++|-.|.+.|+.+..|..||+..
T Consensus 145 lqClFCn~e~lgnRs~~l~Hlf~~H~lniGlpDniVyvnelLehLkekL~r~~CLyCekifrdkntLkeHMrkK 218 (423)
T KOG2482|consen 145 LQCLFCNNEGLGNRSEILEHLFHVHGLNIGLPDNIVYVNELLEHLKEKLERLRCLYCEKIFRDKNTLKEHMRKK 218 (423)
T ss_pred eEEEEecchhcccHHHHHHHHHHHhhhccCCCcceeeHHHHHHHHHHHHhhheeeeeccccCCcHHHHHHHHhc
Confidence 4788888554 34455556655433310 1378999999999999999999854
No 170
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=42.02 E-value=26 Score=17.58 Aligned_cols=9 Identities=33% Similarity=0.958 Sum_probs=4.4
Q ss_pred ceecCcccc
Q psy12018 90 MYVCDICGK 98 (148)
Q Consensus 90 ~~~C~~c~~ 98 (148)
.+.|..|+.
T Consensus 37 r~~C~~Cgy 45 (50)
T PRK00432 37 RWHCGKCGY 45 (50)
T ss_pred cEECCCcCC
Confidence 345555553
No 171
>COG1655 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=41.93 E-value=7.9 Score=26.26 Aligned_cols=7 Identities=43% Similarity=1.151 Sum_probs=4.8
Q ss_pred eeCCCCh
Q psy12018 120 FQCPQCP 126 (148)
Q Consensus 120 ~~C~~C~ 126 (148)
+.|+.|+
T Consensus 63 vvCP~C~ 69 (267)
T COG1655 63 VVCPICY 69 (267)
T ss_pred EEcchhh
Confidence 5677775
No 172
>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=41.69 E-value=11 Score=18.97 Aligned_cols=12 Identities=25% Similarity=0.974 Sum_probs=6.1
Q ss_pred ecCccccccccc
Q psy12018 92 VCDICGKVYQHK 103 (148)
Q Consensus 92 ~C~~c~~~f~~~ 103 (148)
.|+.|++.|...
T Consensus 22 ~CPlC~r~l~~e 33 (54)
T PF04423_consen 22 CCPLCGRPLDEE 33 (54)
T ss_dssp E-TTT--EE-HH
T ss_pred cCCCCCCCCCHH
Confidence 788898888654
No 173
>COG2879 Uncharacterized small protein [Function unknown]
Probab=41.22 E-value=31 Score=18.24 Aligned_cols=18 Identities=22% Similarity=0.172 Sum_probs=14.5
Q ss_pred hchHHHHHHHHhhcCCcc
Q psy12018 130 KQKANLKTHLIIKHDSVL 147 (148)
Q Consensus 130 ~~~~~l~~H~~~~h~~~~ 147 (148)
++.+.+..|++.+|++.+
T Consensus 23 pdYdnYVehmr~~hPd~p 40 (65)
T COG2879 23 PDYDNYVEHMRKKHPDKP 40 (65)
T ss_pred CcHHHHHHHHHHhCcCCC
Confidence 466788899999998765
No 174
>smart00132 LIM Zinc-binding domain present in Lin-11, Isl-1, Mec-3. Zinc-binding domain family. Some LIM domains bind protein partners via tyrosine-containing motifs. LIM domains are found in many key regulators of developmental pathways.
Probab=41.19 E-value=28 Score=15.41 Aligned_cols=6 Identities=50% Similarity=1.459 Sum_probs=2.3
Q ss_pred ecCccc
Q psy12018 92 VCDICG 97 (148)
Q Consensus 92 ~C~~c~ 97 (148)
.|..|+
T Consensus 29 ~C~~C~ 34 (39)
T smart00132 29 KCSKCG 34 (39)
T ss_pred CCcccC
Confidence 333333
No 175
>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=40.58 E-value=21 Score=18.82 Aligned_cols=8 Identities=50% Similarity=1.630 Sum_probs=1.8
Q ss_pred cCcccccc
Q psy12018 37 CDVCGKEY 44 (148)
Q Consensus 37 C~~C~~~f 44 (148)
|..|++.|
T Consensus 12 C~~C~~~F 19 (69)
T PF01363_consen 12 CMICGKKF 19 (69)
T ss_dssp -TTT--B-
T ss_pred CcCcCCcC
Confidence 44444444
No 176
>KOG2593|consensus
Probab=40.39 E-value=18 Score=26.94 Aligned_cols=15 Identities=27% Similarity=0.755 Sum_probs=7.4
Q ss_pred CccccCccccccCCh
Q psy12018 33 GKFACDVCGKEYQYY 47 (148)
Q Consensus 33 ~~~~C~~C~~~f~~~ 47 (148)
..|.|+.|.+.|...
T Consensus 127 ~~Y~Cp~C~kkyt~L 141 (436)
T KOG2593|consen 127 AGYVCPNCQKKYTSL 141 (436)
T ss_pred ccccCCccccchhhh
Confidence 345555555555443
No 177
>KOG2785|consensus
Probab=40.29 E-value=23 Score=25.96 Aligned_cols=25 Identities=20% Similarity=0.289 Sum_probs=20.7
Q ss_pred CCceeCCCChhhhhchHHHHHHHHh
Q psy12018 117 EPRFQCPQCPYRAKQKANLKTHLII 141 (148)
Q Consensus 117 ~~~~~C~~C~~~f~~~~~l~~H~~~ 141 (148)
+-++.|..|.+.|.+......|+..
T Consensus 66 ~~~~~c~~c~k~~~s~~a~~~hl~S 90 (390)
T KOG2785|consen 66 ESVVYCEACNKSFASPKAHENHLKS 90 (390)
T ss_pred ccceehHHhhccccChhhHHHHHHH
Confidence 4578899999999998888888764
No 178
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=39.23 E-value=22 Score=23.16 Aligned_cols=14 Identities=29% Similarity=0.738 Sum_probs=7.6
Q ss_pred CcccCCCCCCcccc
Q psy12018 62 PRYQCPQCPYRTKQ 75 (148)
Q Consensus 62 ~~~~C~~c~~~f~~ 75 (148)
.-|.|+.|...+..
T Consensus 112 ~~y~C~~~~~r~sf 125 (176)
T COG1675 112 NYYVCPNCHVKYSF 125 (176)
T ss_pred CceeCCCCCCcccH
Confidence 34666666554443
No 179
>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=39.11 E-value=35 Score=24.39 Aligned_cols=52 Identities=19% Similarity=0.337 Sum_probs=27.1
Q ss_pred CCccccCccccccCChhHHhcccccccCCCCcccCCCCCCcccccccccccccCCCCCceecCccccc
Q psy12018 32 YGKFACDVCGKEYQYYRNLYRHKKFECGQEPRYQCPQCPYRTKQKELGWESLKPNAYGMYVCDICGKV 99 (148)
Q Consensus 32 ~~~~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~~C~~c~~~f~~~~~~~~~~~~~~~~~~~C~~c~~~ 99 (148)
...-.|++||..= ..+-+ .......| .+-..|+.|+-.... .+-+|+.||..
T Consensus 182 ~~~~~CPvCGs~P-~~s~~-~~~~~~~G-~RyL~CslC~teW~~-------------~R~~C~~Cg~~ 233 (305)
T TIGR01562 182 ESRTLCPACGSPP-VASMV-RQGGKETG-LRYLSCSLCATEWHY-------------VRVKCSHCEES 233 (305)
T ss_pred CCCCcCCCCCChh-hhhhh-cccCCCCC-ceEEEcCCCCCcccc-------------cCccCCCCCCC
Confidence 3345799998751 11111 11111223 556778888753222 13579999964
No 180
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=39.06 E-value=18 Score=21.74 Aligned_cols=10 Identities=20% Similarity=0.893 Sum_probs=4.7
Q ss_pred cccCcccccc
Q psy12018 35 FACDVCGKEY 44 (148)
Q Consensus 35 ~~C~~C~~~f 44 (148)
..|..|+..|
T Consensus 72 ~~C~~Cg~~~ 81 (117)
T PRK00564 72 LECKDCSHVF 81 (117)
T ss_pred EEhhhCCCcc
Confidence 4455555443
No 181
>PF07503 zf-HYPF: HypF finger; InterPro: IPR011125 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Proteins of the HypF family are involved in the maturation and regulation of hydrogenase []. In the N terminus they appear to have two zinc finger domains that are similar to those found in the DnaJ chaperone []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3TTD_A 3TSQ_A 3TTC_A 3TSP_A 3TTF_A 3TSU_A.
Probab=38.63 E-value=3.6 Score=18.99 Aligned_cols=11 Identities=27% Similarity=0.594 Sum_probs=5.0
Q ss_pred ceeCCCChhhh
Q psy12018 119 RFQCPQCPYRA 129 (148)
Q Consensus 119 ~~~C~~C~~~f 129 (148)
+..|..||-.+
T Consensus 21 ~isC~~CGPr~ 31 (35)
T PF07503_consen 21 FISCTNCGPRY 31 (35)
T ss_dssp T--BTTCC-SC
T ss_pred CccCCCCCCCE
Confidence 45677776554
No 182
>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=38.09 E-value=27 Score=18.89 Aligned_cols=13 Identities=31% Similarity=0.585 Sum_probs=6.8
Q ss_pred cccCccccccCCh
Q psy12018 35 FACDVCGKEYQYY 47 (148)
Q Consensus 35 ~~C~~C~~~f~~~ 47 (148)
++++-|++.|.-.
T Consensus 11 ~~~~cC~~~y~C~ 23 (71)
T PF05495_consen 11 IRFPCCGKYYPCR 23 (71)
T ss_dssp EEETTTTEEESSH
T ss_pred EECCcccCeecHH
Confidence 4455556655544
No 183
>PRK04023 DNA polymerase II large subunit; Validated
Probab=37.95 E-value=82 Score=26.68 Aligned_cols=10 Identities=20% Similarity=0.620 Sum_probs=6.3
Q ss_pred ceeCCCChhh
Q psy12018 119 RFQCPQCPYR 128 (148)
Q Consensus 119 ~~~C~~C~~~ 128 (148)
++.|+.||..
T Consensus 663 ~y~CPKCG~E 672 (1121)
T PRK04023 663 EDECEKCGRE 672 (1121)
T ss_pred CCcCCCCCCC
Confidence 3567777653
No 184
>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=37.65 E-value=11 Score=22.46 Aligned_cols=11 Identities=36% Similarity=1.044 Sum_probs=4.8
Q ss_pred cccCccccccC
Q psy12018 35 FACDVCGKEYQ 45 (148)
Q Consensus 35 ~~C~~C~~~f~ 45 (148)
..|..|+..|.
T Consensus 71 ~~C~~Cg~~~~ 81 (113)
T PF01155_consen 71 ARCRDCGHEFE 81 (113)
T ss_dssp EEETTTS-EEE
T ss_pred EECCCCCCEEe
Confidence 44555555443
No 185
>KOG3214|consensus
Probab=37.60 E-value=13 Score=21.65 Aligned_cols=13 Identities=15% Similarity=0.360 Sum_probs=7.4
Q ss_pred eeCCCChhhhhch
Q psy12018 120 FQCPQCPYRAKQK 132 (148)
Q Consensus 120 ~~C~~C~~~f~~~ 132 (148)
..|.+|+.+|.+.
T Consensus 48 ~sC~iC~esFqt~ 60 (109)
T KOG3214|consen 48 ASCRICEESFQTT 60 (109)
T ss_pred eeeeehhhhhccc
Confidence 4566666666543
No 186
>COG4338 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=36.90 E-value=13 Score=18.42 Aligned_cols=16 Identities=13% Similarity=0.740 Sum_probs=11.8
Q ss_pred ecCccccccccchhHH
Q psy12018 92 VCDICGKVYQHKRTLY 107 (148)
Q Consensus 92 ~C~~c~~~f~~~~~l~ 107 (148)
.|+.|++.|.+...+.
T Consensus 14 ICpvCqRPFsWRkKW~ 29 (54)
T COG4338 14 ICPVCQRPFSWRKKWA 29 (54)
T ss_pred hhhhhcCchHHHHHHH
Confidence 5889999988765543
No 187
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=36.52 E-value=30 Score=15.78 Aligned_cols=7 Identities=57% Similarity=1.497 Sum_probs=3.2
Q ss_pred eecCccc
Q psy12018 91 YVCDICG 97 (148)
Q Consensus 91 ~~C~~c~ 97 (148)
+.|+.|+
T Consensus 23 ~vC~~Cg 29 (34)
T PF14803_consen 23 LVCPACG 29 (34)
T ss_dssp EEETTTT
T ss_pred eECCCCC
Confidence 4444444
No 188
>PF11789 zf-Nse: Zinc-finger of the MIZ type in Nse subunit; PDB: 2YU4_A 3HTK_C.
Probab=36.06 E-value=66 Score=16.54 Aligned_cols=45 Identities=16% Similarity=0.344 Sum_probs=21.5
Q ss_pred CCcccCCCCCCcccccccccccccCCCCCceecCccccccccchhHHhhHhhhhCCCCceeCCC
Q psy12018 61 EPRYQCPQCPYRTKQKELGWESLKPNAYGMYVCDICGKVYQHKRTLYRHKKDECGQEPRFQCPQ 124 (148)
Q Consensus 61 ~~~~~C~~c~~~f~~~~~~~~~~~~~~~~~~~C~~c~~~f~~~~~l~~H~~~~~~~~~~~~C~~ 124 (148)
...+.|++..+.|.. |.....|+-.|...+.+ .++ +......|++
T Consensus 9 ~~~~~CPiT~~~~~~--------------PV~s~~C~H~fek~aI~-~~i----~~~~~~~CPv 53 (57)
T PF11789_consen 9 TISLKCPITLQPFED--------------PVKSKKCGHTFEKEAIL-QYI----QRNGSKRCPV 53 (57)
T ss_dssp B--SB-TTTSSB-SS--------------EEEESSS--EEEHHHHH-HHC----TTTS-EE-SC
T ss_pred EeccCCCCcCChhhC--------------CcCcCCCCCeecHHHHH-HHH----HhcCCCCCCC
Confidence 456778776665554 45566788787655443 343 2244577876
No 189
>KOG2071|consensus
Probab=35.79 E-value=24 Score=27.47 Aligned_cols=27 Identities=22% Similarity=0.441 Sum_probs=22.3
Q ss_pred CCceeCCCChhhhhchHHHHHHHHhhc
Q psy12018 117 EPRFQCPQCPYRAKQKANLKTHLIIKH 143 (148)
Q Consensus 117 ~~~~~C~~C~~~f~~~~~l~~H~~~~h 143 (148)
..|..|..||..|........||-+|-
T Consensus 416 ~~pnqC~~CG~R~~~~ee~sk~md~H~ 442 (579)
T KOG2071|consen 416 DSPNQCKSCGLRFDDSEERSKHMDIHD 442 (579)
T ss_pred CCcchhcccccccccchhhhhHhhhhh
Confidence 457899999999999888888877664
No 190
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=35.66 E-value=36 Score=20.35 Aligned_cols=18 Identities=33% Similarity=0.545 Sum_probs=12.7
Q ss_pred CCCccccCccccccCChh
Q psy12018 31 LYGKFACDVCGKEYQYYR 48 (148)
Q Consensus 31 ~~~~~~C~~C~~~f~~~~ 48 (148)
+..-+.|..||-.+....
T Consensus 19 ~~~~l~C~kCgye~~~~~ 36 (113)
T COG1594 19 EGGKLVCRKCGYEEEASN 36 (113)
T ss_pred CCcEEECCCCCcchhccc
Confidence 344788999998766553
No 191
>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=35.37 E-value=47 Score=19.53 Aligned_cols=7 Identities=57% Similarity=1.507 Sum_probs=3.4
Q ss_pred eecCccc
Q psy12018 91 YVCDICG 97 (148)
Q Consensus 91 ~~C~~c~ 97 (148)
|.|..|+
T Consensus 32 y~C~~C~ 38 (102)
T PF11672_consen 32 YVCTPCD 38 (102)
T ss_pred EECCCCC
Confidence 4454444
No 192
>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=35.15 E-value=13 Score=16.99 Aligned_cols=12 Identities=17% Similarity=0.506 Sum_probs=5.5
Q ss_pred eCCCChhhhhch
Q psy12018 121 QCPQCPYRAKQK 132 (148)
Q Consensus 121 ~C~~C~~~f~~~ 132 (148)
.|.+|++.|..+
T Consensus 5 ~C~eC~~~f~dS 16 (34)
T PF01286_consen 5 KCDECGKPFMDS 16 (34)
T ss_dssp E-TTT--EES-S
T ss_pred hHhHhCCHHHHH
Confidence 577777777654
No 193
>COG2331 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=35.02 E-value=14 Score=20.40 Aligned_cols=10 Identities=40% Similarity=1.222 Sum_probs=5.4
Q ss_pred eecCcccccc
Q psy12018 91 YVCDICGKVY 100 (148)
Q Consensus 91 ~~C~~c~~~f 100 (148)
|+|..|+..|
T Consensus 13 Y~c~~cg~~~ 22 (82)
T COG2331 13 YECTECGNRF 22 (82)
T ss_pred EeecccchHH
Confidence 5556665443
No 194
>COG3091 SprT Zn-dependent metalloprotease, SprT family [General function prediction only]
Probab=34.85 E-value=20 Score=22.70 Aligned_cols=8 Identities=50% Similarity=1.456 Sum_probs=4.2
Q ss_pred ceecCccc
Q psy12018 90 MYVCDICG 97 (148)
Q Consensus 90 ~~~C~~c~ 97 (148)
.|.|..|+
T Consensus 140 ~YrC~~C~ 147 (156)
T COG3091 140 VYRCGKCG 147 (156)
T ss_pred eEEeccCC
Confidence 45555554
No 195
>COG1773 Rubredoxin [Energy production and conversion]
Probab=34.67 E-value=15 Score=18.92 Aligned_cols=10 Identities=30% Similarity=0.966 Sum_probs=6.0
Q ss_pred eeCCCChhhh
Q psy12018 120 FQCPQCPYRA 129 (148)
Q Consensus 120 ~~C~~C~~~f 129 (148)
|+|..||..|
T Consensus 4 ~~C~~CG~vY 13 (55)
T COG1773 4 WRCSVCGYVY 13 (55)
T ss_pred eEecCCceEe
Confidence 5666666554
No 196
>KOG2482|consensus
Probab=33.95 E-value=24 Score=25.60 Aligned_cols=23 Identities=30% Similarity=0.626 Sum_probs=20.7
Q ss_pred ceecCccccccccchhHHhhHhh
Q psy12018 90 MYVCDICGKVYQHKRTLYRHKKD 112 (148)
Q Consensus 90 ~~~C~~c~~~f~~~~~l~~H~~~ 112 (148)
.+.|..|++.|..+..|..|++.
T Consensus 195 r~~CLyCekifrdkntLkeHMrk 217 (423)
T KOG2482|consen 195 RLRCLYCEKIFRDKNTLKEHMRK 217 (423)
T ss_pred hheeeeeccccCCcHHHHHHHHh
Confidence 36899999999999999999883
No 197
>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=33.52 E-value=16 Score=17.03 Aligned_cols=11 Identities=27% Similarity=0.878 Sum_probs=4.7
Q ss_pred CccccCccccc
Q psy12018 33 GKFACDVCGKE 43 (148)
Q Consensus 33 ~~~~C~~C~~~ 43 (148)
+-|+|..||..
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 34666666655
No 198
>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=33.30 E-value=28 Score=17.42 Aligned_cols=26 Identities=19% Similarity=0.487 Sum_probs=14.6
Q ss_pred cCCCCCCcccccccccccccCCCCCceecCccccccc
Q psy12018 65 QCPQCPYRTKQKELGWESLKPNAYGMYVCDICGKVYQ 101 (148)
Q Consensus 65 ~C~~c~~~f~~~~~~~~~~~~~~~~~~~C~~c~~~f~ 101 (148)
.|..|++.|... .+.+.|..||+.|-
T Consensus 4 ~C~~C~~~F~~~-----------~rk~~Cr~Cg~~~C 29 (57)
T cd00065 4 SCMGCGKPFTLT-----------RRRHHCRNCGRIFC 29 (57)
T ss_pred cCcccCccccCC-----------ccccccCcCcCCcC
Confidence 466677666641 22345666666654
No 199
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=32.75 E-value=24 Score=21.09 Aligned_cols=10 Identities=20% Similarity=0.521 Sum_probs=4.6
Q ss_pred ccCCCCCCcc
Q psy12018 64 YQCPQCPYRT 73 (148)
Q Consensus 64 ~~C~~c~~~f 73 (148)
..|..|+..|
T Consensus 71 ~~C~~Cg~~~ 80 (114)
T PRK03681 71 CWCETCQQYV 80 (114)
T ss_pred EEcccCCCee
Confidence 4455555433
No 200
>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=32.42 E-value=25 Score=28.32 Aligned_cols=80 Identities=19% Similarity=0.250 Sum_probs=44.6
Q ss_pred cccCccccccCChhHHhcccccccCCCCc-ccCCCCCCcccccccccccccCC-CCCceecCccccccccchhHHhhHhh
Q psy12018 35 FACDVCGKEYQYYRNLYRHKKFECGQEPR-YQCPQCPYRTKQKELGWESLKPN-AYGMYVCDICGKVYQHKRTLYRHKKD 112 (148)
Q Consensus 35 ~~C~~C~~~f~~~~~l~~h~~~~~~~~~~-~~C~~c~~~f~~~~~~~~~~~~~-~~~~~~C~~c~~~f~~~~~l~~H~~~ 112 (148)
-.|+.|-+.+....+-+ + .-| ..|..||-.|.-...+..-..++ ...--.|+.|.+.+....+.+-|
T Consensus 69 a~C~~Cl~E~~dp~~Rr-----y---~YpF~nCt~CGPr~~i~~~lpydr~~t~m~~f~~C~~C~~ey~~p~~rr~h--- 137 (711)
T TIGR00143 69 ATCSDCLEEMLDKNDRR-----Y---LYPFISCTHCGPRFTIIEALPYDRENTSMADFPLCPDCAKEYKDPLDRRFH--- 137 (711)
T ss_pred hhHHHHHHHhcCCCccc-----c---cCCcccccCCCCCeEEeecCCCCCCCcCCCCCcCCHHHHHHhcCCccccCC---
Confidence 46777876655543211 1 123 34889998887654222122222 22223688888887766543322
Q ss_pred hhCCCCceeCCCChhhh
Q psy12018 113 ECGQEPRFQCPQCPYRA 129 (148)
Q Consensus 113 ~~~~~~~~~C~~C~~~f 129 (148)
-.+..|..||-..
T Consensus 138 ----~~~~~C~~Cgp~l 150 (711)
T TIGR00143 138 ----AQPIACPRCGPQL 150 (711)
T ss_pred ----CCCccCCCCCcEE
Confidence 3467899998544
No 201
>PF09332 Mcm10: Mcm10 replication factor; InterPro: IPR015411 Mcm10 is a eukaryotic DNA replication factor that regulates the stability and chromatin association of DNA polymerase alpha []. ; PDB: 2KWQ_A.
Probab=31.45 E-value=19 Score=26.11 Aligned_cols=42 Identities=19% Similarity=0.347 Sum_probs=16.2
Q ss_pred ccccCccccccCChhHHh---cc-cccccCCCCcccCCCCCCcccc
Q psy12018 34 KFACDVCGKEYQYYRNLY---RH-KKFECGQEPRYQCPQCPYRTKQ 75 (148)
Q Consensus 34 ~~~C~~C~~~f~~~~~l~---~h-~~~~~~~~~~~~C~~c~~~f~~ 75 (148)
-+.|..|..++....... .| +..+.+...-|.|..|++...+
T Consensus 252 av~C~~C~yt~~~~~~~C~~~~H~l~~~~a~KRFFkC~~C~~Rt~s 297 (344)
T PF09332_consen 252 AVTCKQCKYTAFKPSDRCKEEGHPLKWHDAVKRFFKCKDCGNRTIS 297 (344)
T ss_dssp EEEETTT--EESS--HHHHHTT--EEEEEEE-EEEE-T-TS-EEEE
T ss_pred EEEcCCCCCcccCcchhHHhcCCceEEeeeeeeeEECCCCCCeeee
Confidence 456777766555544442 22 1222232345677777765443
No 202
>KOG1842|consensus
Probab=31.36 E-value=23 Score=26.61 Aligned_cols=32 Identities=19% Similarity=0.328 Sum_probs=26.1
Q ss_pred CCCCCccccCccccccCChhHHhcccccccCC
Q psy12018 29 PKLYGKFACDVCGKEYQYYRNLYRHKKFECGQ 60 (148)
Q Consensus 29 ~~~~~~~~C~~C~~~f~~~~~l~~h~~~~~~~ 60 (148)
..+-..|.|+.|...|.....|..|....+++
T Consensus 10 ~~i~egflCPiC~~dl~~~~~L~~H~d~eH~~ 41 (505)
T KOG1842|consen 10 GEILEGFLCPICLLDLPNLSALNDHLDVEHFE 41 (505)
T ss_pred chhhhcccCchHhhhhhhHHHHHHHHhhhccc
Confidence 34456799999999999999999998765543
No 203
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=31.15 E-value=26 Score=23.27 Aligned_cols=16 Identities=13% Similarity=0.347 Sum_probs=10.9
Q ss_pred CCcccCCCCCCccccc
Q psy12018 61 EPRYQCPQCPYRTKQK 76 (148)
Q Consensus 61 ~~~~~C~~c~~~f~~~ 76 (148)
.-||.|.+|.+.|.+.
T Consensus 194 ~IPF~C~iCKkdy~sp 209 (259)
T COG5152 194 KIPFLCGICKKDYESP 209 (259)
T ss_pred CCceeehhchhhccch
Confidence 3577777777776654
No 204
>KOG2907|consensus
Probab=30.92 E-value=33 Score=20.51 Aligned_cols=10 Identities=30% Similarity=0.939 Sum_probs=5.0
Q ss_pred eecCcccccc
Q psy12018 91 YVCDICGKVY 100 (148)
Q Consensus 91 ~~C~~c~~~f 100 (148)
|.|+.|+..|
T Consensus 103 YTC~kC~~k~ 112 (116)
T KOG2907|consen 103 YTCPKCKYKF 112 (116)
T ss_pred EEcCccceee
Confidence 4555555443
No 205
>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=30.85 E-value=31 Score=20.45 Aligned_cols=29 Identities=17% Similarity=0.511 Sum_probs=16.6
Q ss_pred cCCCCCCcccccccccccccCCCCCceecCccccccccc
Q psy12018 65 QCPQCPYRTKQKELGWESLKPNAYGMYVCDICGKVYQHK 103 (148)
Q Consensus 65 ~C~~c~~~f~~~~~~~~~~~~~~~~~~~C~~c~~~f~~~ 103 (148)
.||.|+..+.... ...|.|++|+..+...
T Consensus 4 ~CP~C~seytY~d----------g~~~iCpeC~~EW~~~ 32 (109)
T TIGR00686 4 PCPKCNSEYTYHD----------GTQLICPSCLYEWNEN 32 (109)
T ss_pred cCCcCCCcceEec----------CCeeECcccccccccc
Confidence 4777766555431 2237788887665433
No 206
>KOG4124|consensus
Probab=30.63 E-value=23 Score=25.76 Aligned_cols=24 Identities=33% Similarity=0.656 Sum_probs=18.0
Q ss_pred CCCccccCc--cccccCChhHHhccc
Q psy12018 31 LYGKFACDV--CGKEYQYYRNLYRHK 54 (148)
Q Consensus 31 ~~~~~~C~~--C~~~f~~~~~l~~h~ 54 (148)
.+++|.|.+ |.+.+.....|..|.
T Consensus 346 ~~~~~~~~vp~~~~~~~n~ng~~~~~ 371 (442)
T KOG4124|consen 346 VDKPYKCPVPNCDKAYKNQNGLKYHK 371 (442)
T ss_pred ecCCCCCCCCcchhhcccCcceeecc
Confidence 467888877 888888877776664
No 207
>PRK10220 hypothetical protein; Provisional
Probab=29.93 E-value=35 Score=20.31 Aligned_cols=29 Identities=28% Similarity=0.865 Sum_probs=17.3
Q ss_pred cCCCCCCcccccccccccccCCCCCceecCccccccccc
Q psy12018 65 QCPQCPYRTKQKELGWESLKPNAYGMYVCDICGKVYQHK 103 (148)
Q Consensus 65 ~C~~c~~~f~~~~~~~~~~~~~~~~~~~C~~c~~~f~~~ 103 (148)
.||+|+..+.... ...|.|++|+..+...
T Consensus 5 ~CP~C~seytY~d----------~~~~vCpeC~hEW~~~ 33 (111)
T PRK10220 5 HCPKCNSEYTYED----------NGMYICPECAHEWNDA 33 (111)
T ss_pred cCCCCCCcceEcC----------CCeEECCcccCcCCcc
Confidence 5777776555431 2247788887666543
No 208
>KOG2231|consensus
Probab=29.58 E-value=31 Score=27.45 Aligned_cols=43 Identities=21% Similarity=0.239 Sum_probs=27.8
Q ss_pred cchhHHhhHhhhhCCCC----ceeCCCChhhhhchHHHHHHHHhhcC
Q psy12018 102 HKRTLYRHKKDECGQEP----RFQCPQCPYRAKQKANLKTHLIIKHD 144 (148)
Q Consensus 102 ~~~~l~~H~~~~~~~~~----~~~C~~C~~~f~~~~~l~~H~~~~h~ 144 (148)
....|..|+..-..+++ .-.|..|...|-....|.+|++..|-
T Consensus 161 t~~el~~h~~~gd~d~~s~rGhp~C~~C~~~fld~~el~rH~~~~h~ 207 (669)
T KOG2231|consen 161 TRAELNLHLMFGDPDDESCRGHPLCKFCHERFLDDDELYRHLRFDHE 207 (669)
T ss_pred hHHHHHHHHhcCCCccccccCCccchhhhhhhccHHHHHHhhcccee
Confidence 34556666553222121 13577888999999999999987664
No 209
>COG5112 UFD2 U1-like Zn-finger-containing protein [General function prediction only]
Probab=29.37 E-value=34 Score=20.18 Aligned_cols=28 Identities=25% Similarity=0.343 Sum_probs=21.9
Q ss_pred CCCCCccccCccccccCChhHHhccccc
Q psy12018 29 PKLYGKFACDVCGKEYQYYRNLYRHKKF 56 (148)
Q Consensus 29 ~~~~~~~~C~~C~~~f~~~~~l~~h~~~ 56 (148)
-.+-+-+-|-+|.+-|.....|..|.+.
T Consensus 50 lPGlGqhYCieCaryf~t~~aL~~Hkkg 77 (126)
T COG5112 50 LPGLGQHYCIECARYFITEKALMEHKKG 77 (126)
T ss_pred CCCCceeeeehhHHHHHHHHHHHHHhcc
Confidence 3345568899999999999999888643
No 210
>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=29.03 E-value=20 Score=16.62 Aligned_cols=8 Identities=38% Similarity=0.949 Sum_probs=4.0
Q ss_pred CceecCcc
Q psy12018 89 GMYVCDIC 96 (148)
Q Consensus 89 ~~~~C~~c 96 (148)
-.|.|..|
T Consensus 28 qryrC~~C 35 (36)
T PF03811_consen 28 QRYRCKDC 35 (36)
T ss_pred EeEecCcC
Confidence 34555544
No 211
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=28.27 E-value=49 Score=23.75 Aligned_cols=24 Identities=21% Similarity=0.458 Sum_probs=16.4
Q ss_pred ceeCCCChhhhhchHHHHHHHHhh
Q psy12018 119 RFQCPQCPYRAKQKANLKTHLIIK 142 (148)
Q Consensus 119 ~~~C~~C~~~f~~~~~l~~H~~~~ 142 (148)
.|+|..|...|-.....-.|...|
T Consensus 388 rY~Ce~CK~~FC~dCdvfiHe~Lh 411 (421)
T COG5151 388 RYQCELCKSTFCSDCDVFIHETLH 411 (421)
T ss_pred ceechhhhhhhhhhhHHHHHHHHh
Confidence 488888888887666655665443
No 212
>TIGR00627 tfb4 transcription factor tfb4. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=27.88 E-value=40 Score=23.78 Aligned_cols=9 Identities=44% Similarity=1.265 Sum_probs=4.1
Q ss_pred eecCccccc
Q psy12018 91 YVCDICGKV 99 (148)
Q Consensus 91 ~~C~~c~~~ 99 (148)
|.|+.|...
T Consensus 256 yvCs~Clsi 264 (279)
T TIGR00627 256 FVCSVCLSV 264 (279)
T ss_pred EECCCccCC
Confidence 444444433
No 213
>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=27.32 E-value=36 Score=16.22 Aligned_cols=11 Identities=45% Similarity=1.029 Sum_probs=6.2
Q ss_pred ceecCcccccc
Q psy12018 90 MYVCDICGKVY 100 (148)
Q Consensus 90 ~~~C~~c~~~f 100 (148)
.-.|++|+..|
T Consensus 29 ~~~CpYCg~~y 39 (40)
T PF10276_consen 29 PVVCPYCGTRY 39 (40)
T ss_dssp EEEETTTTEEE
T ss_pred eEECCCCCCEE
Confidence 35566666554
No 214
>PTZ00448 hypothetical protein; Provisional
Probab=27.16 E-value=43 Score=24.61 Aligned_cols=23 Identities=17% Similarity=0.400 Sum_probs=18.9
Q ss_pred ceeCCCChhhhhchHHHHHHHHh
Q psy12018 119 RFQCPQCPYRAKQKANLKTHLII 141 (148)
Q Consensus 119 ~~~C~~C~~~f~~~~~l~~H~~~ 141 (148)
.|.|..|+-.|.+....+.|.+.
T Consensus 314 ~~tC~~C~v~F~~~~~qR~H~KS 336 (373)
T PTZ00448 314 MLLCRKCNIQLMDHNAFKQHYRS 336 (373)
T ss_pred CccccccccccCCHHHHHHHhhh
Confidence 57899999999888888888763
No 215
>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 PF05290 Baculo_IE-1: Baculovirus immediate-early protein (IE-0); InterPro: IPR007954 This entry contains the Baculovirus immediate-early protein IE-0.
Probab=26.93 E-value=40 Score=20.91 Aligned_cols=15 Identities=20% Similarity=0.572 Sum_probs=9.6
Q ss_pred CCcccCCCCCCcccc
Q psy12018 61 EPRYQCPQCPYRTKQ 75 (148)
Q Consensus 61 ~~~~~C~~c~~~f~~ 75 (148)
.+.|+|.+|......
T Consensus 78 ~~lYeCnIC~etS~e 92 (140)
T PF05290_consen 78 PKLYECNICKETSAE 92 (140)
T ss_pred CCceeccCcccccch
Confidence 366777777765443
No 217
>KOG0402|consensus
Probab=26.71 E-value=25 Score=19.72 Aligned_cols=29 Identities=34% Similarity=0.824 Sum_probs=15.1
Q ss_pred ccCCCCCCcccccccccccccCCCCCceecCccccccc
Q psy12018 64 YQCPQCPYRTKQKELGWESLKPNAYGMYVCDICGKVYQ 101 (148)
Q Consensus 64 ~~C~~c~~~f~~~~~~~~~~~~~~~~~~~C~~c~~~f~ 101 (148)
|.|+.||+.-.-. .....|.|..|.+.+.
T Consensus 37 y~CsfCGK~~vKR---------~AvGiW~C~~C~kv~a 65 (92)
T KOG0402|consen 37 YTCSFCGKKTVKR---------KAVGIWKCGSCKKVVA 65 (92)
T ss_pred hhhhhcchhhhhh---------hceeEEecCCccceec
Confidence 6777777632211 1223466666666553
No 218
>PF05129 Elf1: Transcription elongation factor Elf1 like; InterPro: IPR007808 This family of uncharacterised, mostly short, proteins contain a putative zinc binding domain with four conserved cysteines.; PDB: 1WII_A.
Probab=26.49 E-value=39 Score=18.86 Aligned_cols=10 Identities=30% Similarity=1.222 Sum_probs=3.6
Q ss_pred eecCcccccc
Q psy12018 91 YVCDICGKVY 100 (148)
Q Consensus 91 ~~C~~c~~~f 100 (148)
..|..|+..|
T Consensus 47 ~~C~~Cg~~~ 56 (81)
T PF05129_consen 47 LSCRVCGESF 56 (81)
T ss_dssp EEESSS--EE
T ss_pred EEecCCCCeE
Confidence 3444444443
No 219
>PF01215 COX5B: Cytochrome c oxidase subunit Vb This family consists of chains F and S ; InterPro: IPR002124 Cytochrome c oxidase (1.9.3.1 from EC) is an oligomeric enzymatic complex which is a component of the respiratory chain complex and is involved in the transfer of electrons from cytochrome c to oxygen []. In eukaryotes this enzyme complex is located in the mitochondrial inner membrane; in aerobic prokaryotes it is found in the plasma membrane. In eukaryotes, in addition to the three large subunits, I, II and III, that form the catalytic centre of the enzyme complex, there are a variable number of small polypeptidic subunits. One of these subunits, which is known as Vb in mammals, V in Dictyostelium discoideum (Slime mold) and IV in yeast, binds a zinc atom. The sequence of subunit Vb is well conserved and includes three conserved cysteines that coordinate the zinc ion [, ]. Two of these cysteines are clustered in the C-terminal section of the subunit.; GO: 0004129 cytochrome-c oxidase activity, 0005740 mitochondrial envelope; PDB: 2EIL_S 2ZXW_S 3ASN_S 1OCO_S 3AG4_S 3ABK_S 1OCZ_S 1OCC_F 3ASO_S 3ABL_S ....
Probab=26.48 E-value=29 Score=21.59 Aligned_cols=16 Identities=19% Similarity=0.463 Sum_probs=11.9
Q ss_pred CCccccCccccccCCh
Q psy12018 32 YGKFACDVCGKEYQYY 47 (148)
Q Consensus 32 ~~~~~C~~C~~~f~~~ 47 (148)
.++.+|..||..|.-.
T Consensus 110 g~~~RCpeCG~~fkL~ 125 (136)
T PF01215_consen 110 GKPQRCPECGQVFKLK 125 (136)
T ss_dssp TSEEEETTTEEEEEEE
T ss_pred CCccCCCCCCeEEEEE
Confidence 4578899999887543
No 220
>COG4896 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=26.19 E-value=94 Score=16.39 Aligned_cols=7 Identities=43% Similarity=1.341 Sum_probs=3.5
Q ss_pred eecCccc
Q psy12018 91 YVCDICG 97 (148)
Q Consensus 91 ~~C~~c~ 97 (148)
|-|++|.
T Consensus 32 ymC~eC~ 38 (68)
T COG4896 32 YMCPECE 38 (68)
T ss_pred EechhhH
Confidence 4455554
No 221
>PF09963 DUF2197: Uncharacterized protein conserved in bacteria (DUF2197); InterPro: IPR019241 This family represents various hypothetical bacterial proteins with no known function.
Probab=25.99 E-value=38 Score=17.51 Aligned_cols=10 Identities=30% Similarity=0.976 Sum_probs=6.0
Q ss_pred ceeCCCChhh
Q psy12018 119 RFQCPQCPYR 128 (148)
Q Consensus 119 ~~~C~~C~~~ 128 (148)
.|.|..|...
T Consensus 31 tYmC~eC~~R 40 (56)
T PF09963_consen 31 TYMCDECKER 40 (56)
T ss_pred ceeChhHHHH
Confidence 4667776543
No 222
>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=25.96 E-value=46 Score=25.19 Aligned_cols=24 Identities=17% Similarity=0.483 Sum_probs=16.6
Q ss_pred CcccCCCCCCcccccccccccccCCCCCceecCcccc
Q psy12018 62 PRYQCPQCPYRTKQKELGWESLKPNAYGMYVCDICGK 98 (148)
Q Consensus 62 ~~~~C~~c~~~f~~~~~~~~~~~~~~~~~~~C~~c~~ 98 (148)
..|.|..||.. ...+-++|+.|+.
T Consensus 6 ~~y~C~~Cg~~-------------~~~~~g~Cp~C~~ 29 (454)
T TIGR00416 6 SKFVCQHCGAD-------------SPKWQGKCPACHA 29 (454)
T ss_pred CeEECCcCCCC-------------CccccEECcCCCC
Confidence 45999999963 1234478999973
No 223
>KOG1842|consensus
Probab=25.83 E-value=36 Score=25.64 Aligned_cols=25 Identities=24% Similarity=0.321 Sum_probs=15.6
Q ss_pred eecCccccccccchhHHhhHhhhhC
Q psy12018 91 YVCDICGKVYQHKRTLYRHKKDECG 115 (148)
Q Consensus 91 ~~C~~c~~~f~~~~~l~~H~~~~~~ 115 (148)
|.|+.|...|.....|..|....+.
T Consensus 16 flCPiC~~dl~~~~~L~~H~d~eH~ 40 (505)
T KOG1842|consen 16 FLCPICLLDLPNLSALNDHLDVEHF 40 (505)
T ss_pred ccCchHhhhhhhHHHHHHHHhhhcc
Confidence 5666666666666666666655444
No 224
>PTZ00043 cytochrome c oxidase subunit; Provisional
Probab=25.80 E-value=36 Score=23.16 Aligned_cols=17 Identities=12% Similarity=0.340 Sum_probs=12.3
Q ss_pred CCCCccccCccccccCC
Q psy12018 30 KLYGKFACDVCGKEYQY 46 (148)
Q Consensus 30 ~~~~~~~C~~C~~~f~~ 46 (148)
...++.+|..||..|.-
T Consensus 177 rEGkpqRCpECGqVFKL 193 (268)
T PTZ00043 177 REGFLYRCGECDQIFML 193 (268)
T ss_pred cCCCCccCCCCCcEEEE
Confidence 34567888888888754
No 225
>PRK05978 hypothetical protein; Provisional
Probab=25.80 E-value=43 Score=21.15 Aligned_cols=11 Identities=18% Similarity=0.570 Sum_probs=6.1
Q ss_pred cCCCCCCcccc
Q psy12018 65 QCPQCPYRTKQ 75 (148)
Q Consensus 65 ~C~~c~~~f~~ 75 (148)
.|+.||..|..
T Consensus 54 ~C~~CG~~~~~ 64 (148)
T PRK05978 54 HCAACGEDFTH 64 (148)
T ss_pred CccccCCcccc
Confidence 46666655443
No 226
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=25.72 E-value=58 Score=28.19 Aligned_cols=35 Identities=26% Similarity=0.469 Sum_probs=16.5
Q ss_pred ccCCCCCCcccccccccccccCCCCCceecCcccccc
Q psy12018 64 YQCPQCPYRTKQKELGWESLKPNAYGMYVCDICGKVY 100 (148)
Q Consensus 64 ~~C~~c~~~f~~~~~~~~~~~~~~~~~~~C~~c~~~f 100 (148)
+.|+.||...... .-.....++ ...|.|+.|+...
T Consensus 668 rkCPkCG~~t~~~-fCP~CGs~t-e~vy~CPsCGaev 702 (1337)
T PRK14714 668 RRCPSCGTETYEN-RCPDCGTHT-EPVYVCPDCGAEV 702 (1337)
T ss_pred EECCCCCCccccc-cCcccCCcC-CCceeCccCCCcc
Confidence 6677777632111 111111111 2246788888653
No 227
>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=25.52 E-value=21 Score=20.92 Aligned_cols=35 Identities=11% Similarity=0.246 Sum_probs=14.7
Q ss_pred cccCccccccCChhHHhcccccccCCCCcccCCCCCC
Q psy12018 35 FACDVCGKEYQYYRNLYRHKKFECGQEPRYQCPQCPY 71 (148)
Q Consensus 35 ~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~~C~~c~~ 71 (148)
|.|+.-+..|.+.......+.... .+.+.|...|+
T Consensus 4 f~i~~T~EiF~dYe~Y~~R~~~y~--~~vwtC~~TGk 38 (102)
T PF10537_consen 4 FYIPFTGEIFRDYEEYLKRMILYN--QRVWTCEITGK 38 (102)
T ss_pred EEeCCCCcccCCHHHHHHHHHHHh--CCeeEEecCCC
Confidence 334444445555444443333322 23344544443
No 228
>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=25.33 E-value=56 Score=24.93 Aligned_cols=14 Identities=29% Similarity=0.888 Sum_probs=7.9
Q ss_pred ccCCCCCCcccccc
Q psy12018 64 YQCPQCPYRTKQKE 77 (148)
Q Consensus 64 ~~C~~c~~~f~~~~ 77 (148)
..|+.|.+.|.+..
T Consensus 58 WiCp~CskkF~d~~ 71 (466)
T PF04780_consen 58 WICPRCSKKFSDAE 71 (466)
T ss_pred eeCCcccceeCCHH
Confidence 45666666555543
No 229
>PF04810 zf-Sec23_Sec24: Sec23/Sec24 zinc finger; InterPro: IPR006895 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. COPII (coat protein complex II)-coated vesicles carry proteins from the endoplasmic reticulum (ER) to the Golgi complex []. COPII-coated vesicles form on the ER by the stepwise recruitment of three cytosolic components: Sar1-GTP to initiate coat formation, Sec23/24 heterodimer to select SNARE and cargo molecules, and Sec13/31 to induce coat polymerisation and membrane deformation []. Sec23 p and Sec24p are structurally related, folding into five distinct domains: a beta-barrel, a zinc-finger, an alpha/beta trunk domain (IPR006896 from INTERPRO), an all-helical region (IPR006900 from INTERPRO), and a C-terminal gelsolin-like domain (IPR007123 from INTERPRO). This entry describes an approximately 55-residue Sec23/24 zinc-binding domain, which lies against the beta-barrel at the periphery of the complex. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006886 intracellular protein transport, 0006888 ER to Golgi vesicle-mediated transport, 0030127 COPII vesicle coat; PDB: 3EFO_B 3EG9_B 3EGD_A 2YRC_A 2NUP_A 2YRD_A 3EGX_A 2NUT_A 3EH1_A 1PD0_A ....
Probab=25.28 E-value=67 Score=15.04 Aligned_cols=8 Identities=38% Similarity=1.638 Sum_probs=3.2
Q ss_pred ceecCccc
Q psy12018 90 MYVCDICG 97 (148)
Q Consensus 90 ~~~C~~c~ 97 (148)
.|.|..|+
T Consensus 24 ~w~C~~C~ 31 (40)
T PF04810_consen 24 TWICNFCG 31 (40)
T ss_dssp EEEETTT-
T ss_pred EEECcCCC
Confidence 34444444
No 230
>PF15616 TerY-C: TerY-C metal binding domain
Probab=24.99 E-value=74 Score=19.69 Aligned_cols=8 Identities=38% Similarity=1.219 Sum_probs=4.7
Q ss_pred cCCCCCCc
Q psy12018 65 QCPQCPYR 72 (148)
Q Consensus 65 ~C~~c~~~ 72 (148)
.||.||..
T Consensus 79 gCP~CGn~ 86 (131)
T PF15616_consen 79 GCPHCGNQ 86 (131)
T ss_pred CCCCCcCh
Confidence 46666654
No 231
>smart00249 PHD PHD zinc finger. The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the PRK11823 DNA repair protein RadA; Provisional
Probab=24.65 E-value=52 Score=24.86 Aligned_cols=24 Identities=25% Similarity=0.620 Sum_probs=16.6
Q ss_pred CcccCCCCCCcccccccccccccCCCCCceecCcccc
Q psy12018 62 PRYQCPQCPYRTKQKELGWESLKPNAYGMYVCDICGK 98 (148)
Q Consensus 62 ~~~~C~~c~~~f~~~~~~~~~~~~~~~~~~~C~~c~~ 98 (148)
..|.|..||.. ...+-++|+.|+.
T Consensus 6 ~~y~C~~Cg~~-------------~~~~~g~Cp~C~~ 29 (446)
T PRK11823 6 TAYVCQECGAE-------------SPKWLGRCPECGA 29 (446)
T ss_pred CeEECCcCCCC-------------CcccCeeCcCCCC
Confidence 46999999963 2234468999974
No 233
>PF10083 DUF2321: Uncharacterized protein conserved in bacteria (DUF2321); InterPro: IPR016891 This entry is represented by Bacteriophage 'Lactobacillus prophage Lj928', Orf-Ljo1454. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=24.33 E-value=59 Score=20.75 Aligned_cols=18 Identities=28% Similarity=0.534 Sum_probs=12.1
Q ss_pred CCceecCccccccccchh
Q psy12018 88 YGMYVCDICGKVYQHKRT 105 (148)
Q Consensus 88 ~~~~~C~~c~~~f~~~~~ 105 (148)
+.|.=|..||+.|+|-..
T Consensus 66 ~~PsYC~~CGkpyPWt~~ 83 (158)
T PF10083_consen 66 EAPSYCHNCGKPYPWTEN 83 (158)
T ss_pred CCChhHHhCCCCCchHHH
Confidence 456667778888777543
No 234
>KOG0717|consensus
Probab=23.65 E-value=47 Score=25.25 Aligned_cols=21 Identities=29% Similarity=0.437 Sum_probs=18.6
Q ss_pred eeCCCChhhhhchHHHHHHHH
Q psy12018 120 FQCPQCPYRAKQKANLKTHLI 140 (148)
Q Consensus 120 ~~C~~C~~~f~~~~~l~~H~~ 140 (148)
+-|.+|.+.|.+--.|..|..
T Consensus 293 lyC~vCnKsFKseKq~kNHEn 313 (508)
T KOG0717|consen 293 LYCVVCNKSFKSEKQLKNHEN 313 (508)
T ss_pred eEEeeccccccchHHHHhhHH
Confidence 789999999999999988875
No 235
>smart00731 SprT SprT homologues. Predicted to have roles in transcription elongation. Contains a conserved HExxH motif, indicating a metalloprotease function.
Probab=23.64 E-value=74 Score=19.77 Aligned_cols=32 Identities=25% Similarity=0.692 Sum_probs=17.1
Q ss_pred ceecCccccccccchhHHhhHhhhhCCCCceeCCCChhhh
Q psy12018 90 MYVCDICGKVYQHKRTLYRHKKDECGQEPRFQCPQCPYRA 129 (148)
Q Consensus 90 ~~~C~~c~~~f~~~~~l~~H~~~~~~~~~~~~C~~C~~~f 129 (148)
.|.|..|+..+.. +.+... -..|.|..|+..+
T Consensus 112 ~y~C~~C~~~~~~------~rr~~~--~~~y~C~~C~g~l 143 (146)
T smart00731 112 PYRCTGCGQRYLR------VRRSNN--VSRYRCGKCGGKL 143 (146)
T ss_pred EEECCCCCCCCce------EccccC--cceEEcCCCCCEE
Confidence 5777777765532 222111 1347787777554
No 236
>TIGR00515 accD acetyl-CoA carboxylase, carboxyl transferase, beta subunit. The enzyme acetyl-CoA carboxylase contains a biotin carboxyl carrier protein or domain, a biotin carboxylase, and a carboxyl transferase. This model represents the beta chain of the carboxyl transferase for cases in which the architecture of the protein is as in E. coli, in which the carboxyltransferase portion consists of two non-identical subnits, alpha and beta.
Probab=23.59 E-value=39 Score=23.90 Aligned_cols=33 Identities=21% Similarity=0.417 Sum_probs=20.3
Q ss_pred ccccCccccccCChhHHhcccccccCCCCcccCCCCCCccccc
Q psy12018 34 KFACDVCGKEYQYYRNLYRHKKFECGQEPRYQCPQCPYRTKQK 76 (148)
Q Consensus 34 ~~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~~C~~c~~~f~~~ 76 (148)
-.+|+.|+.....+. |. +..+.|+.|+..|.-.
T Consensus 26 ~~~c~~c~~~~~~~~-l~---------~~~~vc~~c~~h~rl~ 58 (285)
T TIGR00515 26 WTKCPKCGQVLYTKE-LE---------RNLEVCPKCDHHMRMD 58 (285)
T ss_pred eeECCCCcchhhHHH-HH---------hhCCCCCCCCCcCcCC
Confidence 356888888755432 22 2236788888776643
No 237
>PF14787 zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB: 1CL4_A 1DSV_A.
Probab=23.56 E-value=39 Score=15.67 Aligned_cols=14 Identities=29% Similarity=0.786 Sum_probs=6.9
Q ss_pred ecCccccccccchh
Q psy12018 92 VCDICGKVYQHKRT 105 (148)
Q Consensus 92 ~C~~c~~~f~~~~~ 105 (148)
.|+.|++.|.+.+.
T Consensus 4 ~CprC~kg~Hwa~~ 17 (36)
T PF14787_consen 4 LCPRCGKGFHWASE 17 (36)
T ss_dssp C-TTTSSSCS-TTT
T ss_pred cCcccCCCcchhhh
Confidence 36666666655443
No 238
>PLN02748 tRNA dimethylallyltransferase
Probab=23.54 E-value=54 Score=25.01 Aligned_cols=24 Identities=13% Similarity=0.289 Sum_probs=19.7
Q ss_pred CceeCCCChh-hhhchHHHHHHHHh
Q psy12018 118 PRFQCPQCPY-RAKQKANLKTHLII 141 (148)
Q Consensus 118 ~~~~C~~C~~-~f~~~~~l~~H~~~ 141 (148)
+.|.|..|++ .+.....|..|++.
T Consensus 417 ~~~~Ce~C~~~~~~G~~eW~~Hlks 441 (468)
T PLN02748 417 TQYVCEACGNKVLRGAHEWEQHKQG 441 (468)
T ss_pred ccccccCCCCcccCCHHHHHHHhcc
Confidence 4578999997 79888899888853
No 239
>PF04606 Ogr_Delta: Ogr/Delta-like zinc finger; InterPro: IPR007684 This entry is represented by Bacteriophage P2, Ogr. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This is a viral family of phage zinc-binding transcriptional activators, which also contains cryptic members in some bacterial genomes []. The P4 phage delta protein contains two such domains attached covalently, while the P2 phage Ogr proteins possess one domain but function as dimers. All the members of this family have the following consensus sequence: C-X(2)-C-X(3)-A-(X)2-R-X(15)-C-X(4)-C-X(3)-F [].; GO: 0006355 regulation of transcription, DNA-dependent
Probab=23.54 E-value=19 Score=17.64 Aligned_cols=7 Identities=43% Similarity=1.473 Sum_probs=3.7
Q ss_pred CCCCCCc
Q psy12018 66 CPQCPYR 72 (148)
Q Consensus 66 C~~c~~~ 72 (148)
||.||..
T Consensus 2 CP~Cg~~ 8 (47)
T PF04606_consen 2 CPHCGSK 8 (47)
T ss_pred cCCCCCe
Confidence 5555543
No 240
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=23.34 E-value=47 Score=20.16 Aligned_cols=13 Identities=31% Similarity=0.552 Sum_probs=6.9
Q ss_pred CccccCccccccCC
Q psy12018 33 GKFACDVCGKEYQY 46 (148)
Q Consensus 33 ~~~~C~~C~~~f~~ 46 (148)
....| .|+..|..
T Consensus 69 ~~~~C-~Cg~~~~~ 81 (124)
T PRK00762 69 VEIEC-ECGYEGVV 81 (124)
T ss_pred eeEEe-eCcCcccc
Confidence 34556 66655443
No 241
>COG4306 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=22.84 E-value=55 Score=20.01 Aligned_cols=16 Identities=19% Similarity=0.438 Sum_probs=10.9
Q ss_pred CCceecCccccccccc
Q psy12018 88 YGMYVCDICGKVYQHK 103 (148)
Q Consensus 88 ~~~~~C~~c~~~f~~~ 103 (148)
+-|--|..||+.|.|-
T Consensus 66 e~psfchncgs~fpwt 81 (160)
T COG4306 66 EPPSFCHNCGSRFPWT 81 (160)
T ss_pred CCcchhhcCCCCCCcH
Confidence 3445577888888774
No 242
>PF10263 SprT-like: SprT-like family; InterPro: IPR006640 This is a family of uncharacterised bacterial proteins which includes Escherichia coli SprT (P39902 from SWISSPROT). SprT is described as a regulator of bolA gene in stationary phase []. The majority of members contain the metallopeptidase zinc binding signature which has a HExxH motif, however there is no evidence for them being metallopeptidases.
Probab=22.67 E-value=37 Score=21.15 Aligned_cols=32 Identities=25% Similarity=0.783 Sum_probs=18.3
Q ss_pred ceecCccccccccchhHHhhHhhhhCCCCceeCCCChhhhh
Q psy12018 90 MYVCDICGKVYQHKRTLYRHKKDECGQEPRFQCPQCPYRAK 130 (148)
Q Consensus 90 ~~~C~~c~~~f~~~~~l~~H~~~~~~~~~~~~C~~C~~~f~ 130 (148)
.|.|..|+..+... .+. . ...|.|..|+..|.
T Consensus 123 ~~~C~~C~~~~~r~------~~~--~-~~~~~C~~C~~~l~ 154 (157)
T PF10263_consen 123 VYRCPSCGREYKRH------RRS--K-RKRYRCGRCGGPLV 154 (157)
T ss_pred EEEcCCCCCEeeee------ccc--c-hhhEECCCCCCEEE
Confidence 46788888665332 222 1 23477888875543
No 243
>PLN03238 probable histone acetyltransferase MYST; Provisional
Probab=22.51 E-value=81 Score=22.40 Aligned_cols=24 Identities=25% Similarity=0.459 Sum_probs=16.1
Q ss_pred CCceeCCCChhhhhchHHHHHHHH
Q psy12018 117 EPRFQCPQCPYRAKQKANLKTHLI 140 (148)
Q Consensus 117 ~~~~~C~~C~~~f~~~~~l~~H~~ 140 (148)
..-|.|..|-+-|.+...|.+|+.
T Consensus 46 ~~lyiCe~Clky~~~~~~l~~H~~ 69 (290)
T PLN03238 46 TKLYICEYCLKYMRKKKSLLRHLA 69 (290)
T ss_pred CeEEEcCCCcchhCCHHHHHHHHH
Confidence 345677777777777777777765
No 244
>PF02748 PyrI_C: Aspartate carbamoyltransferase regulatory chain, metal binding domain; InterPro: IPR020542 Aspartate carbamoyltransferase (aspartate transcarbamylase, ATCase) 2.1.3.2 from EC is an allosteric enzyme that plays a central role in the regulation of the pyrimidine pathway in bacteria. The holoenzyme is a dodecamer composed of six catalytic chains, each with an active site, and six regulatory chains lacking catalytic activity []. The catalytic subunits exist as a dimer of catalytic trimers, (c3)2, while the regulatory subunits exist as a trimer of regulatory dimers, (r2)3, therefore the complete holoenzyme can be represented as (c3)2(r2)3. The association of the catalytic subunits c3 with the regulatory subunits r2 is responsible for the establishment of positive co-operativity between catalytic sites for the binding of aspartate and it dictates the pattern of allosteric response toward nucleotide effectors. ATCase from Escherichia coli is the most extensively studied allosteric enzyme []. The crystal structure of the T-state, the T-state with CTP bound, the R-state with N-phosphonacetyl-L-aspartate (PALA) bound, and the R-state with phosphonoacetamide plus malonate bound have been used in interpreting kinetic and mutational studies. A high-resolution structure of E. coli ATCase in the presence of PALA (a bisubstrate analog) allows a detailed description of the binding at the active site of the enzyme and allows a detailed model of the tetrahedral intermediate to be constructed. The entire regulatory chain has been traced showing that the N-terminal regions of the regulatory chains R1 and R6 are located in close proximity to each other and to the regulatory site. This portion of the molecule may be involved in the observed asymmetry between the regulatory binding sites as well as in the heterotropic response of the enzyme []. The C-terminal domain of the regulatory chains have a rubredoxin-like zinc-bound fold. ATCase from Enterobacter agglomerans (Erwinia herbicola) (Pantoea agglomerans) differs from the other investigated enterobacterial ATCases by its absence of homotropic co-operativity toward the substrate aspartate and its lack of response to ATP which is an allosteric effector (activator) of this family of enzymes. Nevertheless, the E. herbicola ATCase has the same quaternary structure, two trimers of catalytic chains with three dimers of regulatory chains, (c3)2(r2)3, as other enterobacterial ATCases and shows extensive primary structure conservation []. This entry represents the C-terminal domain.; PDB: 2YWW_B 1SKU_D 1Q95_L 8ATC_B 3AT1_D 1RAI_D 4E2F_D 1NBE_B 6AT1_B 2FZC_D ....
Probab=22.37 E-value=52 Score=16.63 Aligned_cols=17 Identities=12% Similarity=0.338 Sum_probs=10.5
Q ss_pred CCCCceecCcccccccc
Q psy12018 86 NAYGMYVCDICGKVYQH 102 (148)
Q Consensus 86 ~~~~~~~C~~c~~~f~~ 102 (148)
.....|+|.+|++.+..
T Consensus 31 ~~~~~~rC~YCe~~~~~ 47 (52)
T PF02748_consen 31 KEPIKLRCHYCERIITE 47 (52)
T ss_dssp TTTCEEEETTT--EEEH
T ss_pred CCCCEEEeeCCCCEecc
Confidence 34556889999887754
No 245
>PF00412 LIM: LIM domain; InterPro: IPR001781 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents LIM-type zinc finger (Znf) domains. LIM domains coordinate one or more zinc atoms, and are named after the three proteins (LIN-11, Isl1 and MEC-3) in which they were first found. They consist of two zinc-binding motifs that resemble GATA-like Znf's, however the residues holding the zinc atom(s) are variable, involving Cys, His, Asp or Glu residues. LIM domains are involved in proteins with differing functions, including gene expression, and cytoskeleton organisation and development [, ]. Protein containing LIM Znf domains include: Caenorhabditis elegans mec-3; a protein required for the differentiation of the set of six touch receptor neurons in this nematode. C. elegans. lin-11; a protein required for the asymmetric division of vulval blast cells. Vertebrate insulin gene enhancer binding protein isl-1. Isl-1 binds to one of the two cis-acting protein-binding domains of the insulin gene. Vertebrate homeobox proteins lim-1, lim-2 (lim-5) and lim3. Vertebrate lmx-1, which acts as a transcriptional activator by binding to the FLAT element; a beta-cell-specific transcriptional enhancer found in the insulin gene. Mammalian LH-2, a transcriptional regulatory protein involved in the control of cell differentiation in developing lymphoid and neural cell types. Drosophila melanogaster (Fruit fly) protein apterous, required for the normal development of the wing and halter imaginal discs. Vertebrate protein kinases LIMK-1 and LIMK-2. Mammalian rhombotins. Rhombotin 1 (RBTN1 or TTG-1) and rhombotin-2 (RBTN2 or TTG-2) are proteins of about 160 amino acids whose genes are disrupted by chromosomal translocations in T-cell leukemia. Mammalian and avian cysteine-rich protein (CRP), a 192 amino-acid protein of unknown function. Seems to interact with zyxin. Mammalian cysteine-rich intestinal protein (CRIP), a small protein which seems to have a role in zinc absorption and may function as an intracellular zinc transport protein. Vertebrate paxillin, a cytoskeletal focal adhesion protein. Mus musculus (Mouse) testin which should not be confused with rat testin which is a thiol protease homologue (see IPR000169 from INTERPRO). Helianthus annuus (Common sunflower) pollen specific protein SF3. Chicken zyxin. Zyxin is a low-abundance adhesion plaque protein which has been shown to interact with CRP. Yeast protein LRG1 which is involved in sporulation []. Saccharomyces cerevisiae (Baker's yeast) rho-type GTPase activating protein RGA1/DBM1. C. elegans homeobox protein ceh-14. C. elegans homeobox protein unc-97. S. cerevisiae hypothetical protein YKR090w. C. elegans hypothetical proteins C28H8.6. These proteins generally contain two tandem copies of the LIM domain in their N-terminal section. Zyxin and paxillin are exceptions in that they contain respectively three and four LIM domains at their C-terminal extremity. In apterous, isl-1, LH-2, lin-11, lim-1 to lim-3, lmx-1 and ceh-14 and mec-3 there is a homeobox domain some 50 to 95 amino acids after the LIM domains. LIM domains contain seven conserved cysteine residues and a histidine. The arrangement followed by these conserved residues is: C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] LIM domains bind two zinc ions []. LIM does not bind DNA, rather it seems to act as an interface for protein-protein interaction. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CO8_A 2EGQ_A 2CUR_A 3IXE_B 1CTL_A 1B8T_A 1X62_A 2DFY_C 1IML_A 2CUQ_A ....
Probab=22.25 E-value=59 Score=16.12 Aligned_cols=12 Identities=17% Similarity=0.672 Sum_probs=5.6
Q ss_pred cccCCCCCCccc
Q psy12018 63 RYQCPQCPYRTK 74 (148)
Q Consensus 63 ~~~C~~c~~~f~ 74 (148)
-|.|..|++.+.
T Consensus 26 Cf~C~~C~~~l~ 37 (58)
T PF00412_consen 26 CFKCSKCGKPLN 37 (58)
T ss_dssp TSBETTTTCBTT
T ss_pred ccccCCCCCccC
Confidence 344555554443
No 246
>PRK00420 hypothetical protein; Validated
Probab=22.01 E-value=61 Score=19.42 Aligned_cols=9 Identities=56% Similarity=1.040 Sum_probs=4.7
Q ss_pred eecCccccc
Q psy12018 91 YVCDICGKV 99 (148)
Q Consensus 91 ~~C~~c~~~ 99 (148)
..|+.|+..
T Consensus 41 ~~Cp~Cg~~ 49 (112)
T PRK00420 41 VVCPVHGKV 49 (112)
T ss_pred eECCCCCCe
Confidence 445555543
No 247
>COG1327 Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains [Transcription]
Probab=21.96 E-value=40 Score=21.36 Aligned_cols=13 Identities=23% Similarity=0.444 Sum_probs=8.1
Q ss_pred ccCCCCCCccccc
Q psy12018 64 YQCPQCPYRTKQK 76 (148)
Q Consensus 64 ~~C~~c~~~f~~~ 76 (148)
=.|+.|+..|.+-
T Consensus 29 ReC~~C~~RFTTf 41 (156)
T COG1327 29 RECLECGERFTTF 41 (156)
T ss_pred hcccccccccchh
Confidence 3466677666664
No 248
>KOG3507|consensus
Probab=21.81 E-value=74 Score=16.62 Aligned_cols=12 Identities=33% Similarity=0.897 Sum_probs=7.7
Q ss_pred ceeCCCChhhhh
Q psy12018 119 RFQCPQCPYRAK 130 (148)
Q Consensus 119 ~~~C~~C~~~f~ 130 (148)
+++|.+||....
T Consensus 37 ~irCReCG~RIl 48 (62)
T KOG3507|consen 37 VIRCRECGYRIL 48 (62)
T ss_pred cEehhhcchHHH
Confidence 567777776543
No 249
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=21.77 E-value=91 Score=18.23 Aligned_cols=9 Identities=44% Similarity=1.136 Sum_probs=4.3
Q ss_pred CccccCccc
Q psy12018 33 GKFACDVCG 41 (148)
Q Consensus 33 ~~~~C~~C~ 41 (148)
..|.|+.|+
T Consensus 20 t~f~CP~Cg 28 (99)
T PRK14892 20 KIFECPRCG 28 (99)
T ss_pred cEeECCCCC
Confidence 344455554
No 250
>KOG2272|consensus
Probab=21.64 E-value=1.1e+02 Score=21.30 Aligned_cols=13 Identities=23% Similarity=0.565 Sum_probs=8.0
Q ss_pred ceeCCCChhhhhc
Q psy12018 119 RFQCPQCPYRAKQ 131 (148)
Q Consensus 119 ~~~C~~C~~~f~~ 131 (148)
.|.|..|.+-|--
T Consensus 221 HFvCa~CekPFlG 233 (332)
T KOG2272|consen 221 HFVCAKCEKPFLG 233 (332)
T ss_pred heeehhcCCcccc
Confidence 4667666666643
No 251
>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=21.59 E-value=94 Score=20.40 Aligned_cols=12 Identities=42% Similarity=0.362 Sum_probs=5.7
Q ss_pred HHHHHHHhhcCC
Q psy12018 134 NLKTHLIIKHDS 145 (148)
Q Consensus 134 ~l~~H~~~~h~~ 145 (148)
.|..|....|..
T Consensus 62 ~l~~Hl~~~H~~ 73 (198)
T PF03145_consen 62 ELLDHLRDKHSW 73 (198)
T ss_dssp CHHHHHHHHTTT
T ss_pred HHHHHHHHHCCC
Confidence 444555544443
No 252
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=21.26 E-value=33 Score=17.60 Aligned_cols=10 Identities=40% Similarity=1.019 Sum_probs=4.4
Q ss_pred cCCCCCCccc
Q psy12018 65 QCPQCPYRTK 74 (148)
Q Consensus 65 ~C~~c~~~f~ 74 (148)
.|+.|++.|.
T Consensus 7 ~C~~Cg~~~~ 16 (54)
T PF14446_consen 7 KCPVCGKKFK 16 (54)
T ss_pred cChhhCCccc
Confidence 3444444443
No 253
>PRK04351 hypothetical protein; Provisional
Probab=21.12 E-value=51 Score=20.81 Aligned_cols=32 Identities=31% Similarity=0.818 Sum_probs=18.8
Q ss_pred ceecCccccccccchhHHhhHhhhhCCCCceeCCCChhhhh
Q psy12018 90 MYVCDICGKVYQHKRTLYRHKKDECGQEPRFQCPQCPYRAK 130 (148)
Q Consensus 90 ~~~C~~c~~~f~~~~~l~~H~~~~~~~~~~~~C~~C~~~f~ 130 (148)
.|.|..|+..+... +.+. ...|.|..|+..+.
T Consensus 112 ~Y~C~~Cg~~~~r~-------Rr~n--~~~yrCg~C~g~L~ 143 (149)
T PRK04351 112 LYECQSCGQQYLRK-------RRIN--TKRYRCGKCRGKLK 143 (149)
T ss_pred EEECCCCCCEeeee-------eecC--CCcEEeCCCCcEee
Confidence 37888888655432 1121 34588888876554
No 254
>COG4640 Predicted membrane protein [Function unknown]
Probab=20.68 E-value=78 Score=23.61 Aligned_cols=13 Identities=31% Similarity=0.695 Sum_probs=7.2
Q ss_pred ccCCCCCCccccc
Q psy12018 64 YQCPQCPYRTKQK 76 (148)
Q Consensus 64 ~~C~~c~~~f~~~ 76 (148)
..|++||..|...
T Consensus 16 ~qC~qCG~~~t~~ 28 (465)
T COG4640 16 VQCTQCGHKFTSR 28 (465)
T ss_pred ccccccCCcCCch
Confidence 3466666655554
No 255
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=20.20 E-value=49 Score=23.56 Aligned_cols=32 Identities=25% Similarity=0.361 Sum_probs=19.8
Q ss_pred cccCccccccCChhHHhcccccccCCCCcccCCCCCCccccc
Q psy12018 35 FACDVCGKEYQYYRNLYRHKKFECGQEPRYQCPQCPYRTKQK 76 (148)
Q Consensus 35 ~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~~C~~c~~~f~~~ 76 (148)
.+|+.|+.....+. |. +..+.|+.|+..|.-.
T Consensus 39 ~kc~~C~~~~~~~~-l~---------~~~~vcp~c~~h~rlt 70 (296)
T CHL00174 39 VQCENCYGLNYKKF-LK---------SKMNICEQCGYHLKMS 70 (296)
T ss_pred eECCCccchhhHHH-HH---------HcCCCCCCCCCCcCCC
Confidence 46888887654432 21 2346788888766643
No 256
>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=20.10 E-value=24 Score=22.18 Aligned_cols=12 Identities=42% Similarity=0.957 Sum_probs=7.3
Q ss_pred CCceecCccccc
Q psy12018 88 YGMYVCDICGKV 99 (148)
Q Consensus 88 ~~~~~C~~c~~~ 99 (148)
.+.|.|..||..
T Consensus 110 ~G~l~C~~Cg~~ 121 (146)
T PF07295_consen 110 PGTLVCENCGHE 121 (146)
T ss_pred CceEecccCCCE
Confidence 345677777644
No 257
>KOG4727|consensus
Probab=20.02 E-value=67 Score=20.85 Aligned_cols=24 Identities=29% Similarity=0.472 Sum_probs=19.9
Q ss_pred CCCccccCccccccCChhHHhccc
Q psy12018 31 LYGKFACDVCGKEYQYYRNLYRHK 54 (148)
Q Consensus 31 ~~~~~~C~~C~~~f~~~~~l~~h~ 54 (148)
....|-|++|.-+|....++..|+
T Consensus 72 q~~GyyCdVCdcvvKDSinflDHi 95 (193)
T KOG4727|consen 72 QKGGYYCDVCDCVVKDSINFLDHI 95 (193)
T ss_pred ccCceeeeecceeehhhHHHHHHh
Confidence 345689999999999888888886
Done!