Query psy4084
Match_columns 86
No_of_seqs 122 out of 1828
Neff 11.9
Searched_HMMs 46136
Date Sat Aug 17 00:53:37 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy4084.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/4084hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2462|consensus 99.9 5.7E-28 1.2E-32 126.6 4.7 84 1-86 164-250 (279)
2 KOG2462|consensus 99.9 1.2E-25 2.7E-30 117.9 2.4 74 1-74 190-266 (279)
3 KOG3623|consensus 99.7 4.1E-17 8.9E-22 95.6 3.4 86 1-86 213-316 (1007)
4 KOG3576|consensus 99.6 4.2E-16 9.1E-21 79.8 2.3 77 1-77 148-238 (267)
5 KOG3623|consensus 99.6 2.6E-16 5.7E-21 92.3 1.4 72 1-72 897-971 (1007)
6 KOG3576|consensus 99.6 2.1E-16 4.5E-21 80.9 0.3 86 1-86 120-219 (267)
7 KOG1074|consensus 99.6 1.5E-15 3.2E-20 90.1 3.0 46 1-46 356-401 (958)
8 KOG3608|consensus 99.6 3.4E-15 7.5E-20 81.8 3.4 84 3-86 184-299 (467)
9 KOG1074|consensus 99.5 7.1E-16 1.5E-20 91.3 -0.3 75 1-75 608-692 (958)
10 PHA00733 hypothetical protein 99.4 8.4E-13 1.8E-17 64.3 4.6 76 1-76 43-124 (128)
11 KOG3608|consensus 99.4 6.8E-13 1.5E-17 73.0 4.7 80 2-84 241-324 (467)
12 PLN03086 PRLI-interacting fact 99.4 2.9E-12 6.3E-17 74.6 5.8 80 1-86 456-548 (567)
13 PHA02768 hypothetical protein; 99.3 3.2E-12 6.9E-17 53.1 1.6 40 1-42 8-47 (55)
14 PHA02768 hypothetical protein; 99.2 1.8E-11 3.9E-16 50.9 2.7 38 27-64 6-44 (55)
15 PHA00616 hypothetical protein 99.2 1.5E-11 3.2E-16 48.9 1.4 34 51-84 1-34 (44)
16 PF13465 zf-H2C2_2: Zinc-finge 99.1 4.9E-11 1.1E-15 42.8 2.4 25 13-37 1-25 (26)
17 PHA00733 hypothetical protein 99.0 4.7E-10 1E-14 54.8 3.1 74 11-86 25-106 (128)
18 PLN03086 PRLI-interacting fact 98.9 2.2E-09 4.7E-14 63.0 3.3 60 24-86 451-511 (567)
19 PHA00616 hypothetical protein 98.8 2.8E-09 6.2E-14 42.4 2.0 32 1-32 4-35 (44)
20 PF13465 zf-H2C2_2: Zinc-finge 98.8 2E-09 4.3E-14 38.6 1.2 21 66-86 1-21 (26)
21 PHA00732 hypothetical protein 98.8 4.6E-09 9.9E-14 47.2 2.5 42 1-48 4-46 (79)
22 PF00096 zf-C2H2: Zinc finger, 98.7 2.1E-08 4.5E-13 34.8 1.8 23 52-74 1-23 (23)
23 PF12756 zf-C2H2_2: C2H2 type 98.5 9.9E-08 2.2E-12 44.5 2.9 70 1-74 2-73 (100)
24 PF13912 zf-C2H2_6: C2H2-type 98.5 1.1E-07 2.4E-12 34.2 2.2 26 51-76 1-26 (27)
25 PF05605 zf-Di19: Drought indu 98.5 2.4E-07 5.3E-12 38.8 3.3 47 26-75 2-53 (54)
26 PF13894 zf-C2H2_4: C2H2-type 98.5 1.5E-07 3.3E-12 32.7 2.0 24 52-75 1-24 (24)
27 PHA00732 hypothetical protein 98.5 2.3E-07 4.9E-12 41.8 3.0 47 26-75 1-48 (79)
28 KOG3993|consensus 98.4 9.5E-08 2.1E-12 54.3 1.0 76 1-76 270-381 (500)
29 PF00096 zf-C2H2: Zinc finger, 98.4 2.9E-07 6.4E-12 31.8 1.5 21 1-21 3-23 (23)
30 PF09237 GAGA: GAGA factor; I 98.3 4.1E-07 8.9E-12 37.1 1.8 35 45-79 18-52 (54)
31 PF13894 zf-C2H2_4: C2H2-type 98.1 2.6E-06 5.6E-11 29.4 1.9 22 1-22 3-24 (24)
32 smart00355 ZnF_C2H2 zinc finge 98.0 1E-05 2.2E-10 28.3 2.2 24 52-75 1-24 (26)
33 PF05605 zf-Di19: Drought indu 97.9 2.2E-05 4.7E-10 32.9 3.0 35 51-86 2-38 (54)
34 PF09237 GAGA: GAGA factor; I 97.8 2.3E-05 5.1E-10 32.1 2.4 26 1-26 27-52 (54)
35 COG5189 SFP1 Putative transcri 97.8 5E-06 1.1E-10 46.1 0.3 48 24-71 347-418 (423)
36 PF13912 zf-C2H2_6: C2H2-type 97.8 8.6E-06 1.9E-10 29.1 0.6 22 1-22 4-25 (27)
37 PF12874 zf-met: Zinc-finger o 97.8 2E-05 4.3E-10 27.6 1.5 23 52-74 1-23 (25)
38 smart00355 ZnF_C2H2 zinc finge 97.7 4.9E-05 1.1E-09 26.4 2.1 22 1-22 3-24 (26)
39 PF13909 zf-H2C2_5: C2H2-type 97.7 3.4E-05 7.4E-10 26.8 1.3 23 52-75 1-23 (24)
40 PRK04860 hypothetical protein; 97.4 0.00012 2.5E-09 37.4 2.1 32 51-86 119-150 (160)
41 PF12874 zf-met: Zinc-finger o 97.4 8.8E-05 1.9E-09 25.9 0.9 21 1-21 3-23 (25)
42 PF13913 zf-C2HC_2: zinc-finge 97.2 0.0004 8.6E-09 24.4 1.9 20 52-72 3-22 (25)
43 PF12171 zf-C2H2_jaz: Zinc-fin 97.2 8.3E-05 1.8E-09 26.6 0.1 22 52-73 2-23 (27)
44 COG5189 SFP1 Putative transcri 97.2 0.00024 5.1E-09 39.8 1.5 38 49-86 347-405 (423)
45 PRK04860 hypothetical protein; 97.0 0.00035 7.7E-09 35.6 1.2 35 26-64 119-156 (160)
46 KOG3993|consensus 97.0 0.00022 4.7E-09 41.3 0.2 49 26-74 267-318 (500)
47 smart00451 ZnF_U1 U1-like zinc 96.5 0.0034 7.3E-08 23.5 2.1 23 51-73 3-25 (35)
48 cd00350 rubredoxin_like Rubred 96.2 0.0041 8.9E-08 23.3 1.4 24 27-59 2-25 (33)
49 PF12756 zf-C2H2_2: C2H2 type 95.2 0.016 3.4E-07 26.8 1.6 21 1-21 53-73 (100)
50 KOG1146|consensus 95.0 0.014 3.1E-07 38.6 1.4 25 49-73 516-540 (1406)
51 COG1592 Rubrerythrin [Energy p 94.8 0.03 6.6E-07 28.9 2.1 11 76-86 146-156 (166)
52 PF13717 zinc_ribbon_4: zinc-r 94.4 0.058 1.3E-06 20.6 2.0 33 27-61 3-35 (36)
53 PF09538 FYDLN_acid: Protein o 94.3 0.026 5.7E-07 27.1 1.1 30 27-64 10-39 (108)
54 COG2888 Predicted Zn-ribbon RN 94.0 0.078 1.7E-06 22.6 2.1 10 49-58 48-57 (61)
55 KOG2893|consensus 93.8 0.01 2.2E-07 32.4 -0.8 41 29-70 13-53 (341)
56 PF13719 zinc_ribbon_5: zinc-r 93.8 0.084 1.8E-06 20.2 1.9 34 27-62 3-36 (37)
57 TIGR02098 MJ0042_CXXC MJ0042 f 93.7 0.049 1.1E-06 20.8 1.2 34 27-62 3-36 (38)
58 COG4049 Uncharacterized protei 93.6 0.033 7.1E-07 23.4 0.7 23 51-73 17-39 (65)
59 PF09986 DUF2225: Uncharacteri 93.6 0.025 5.3E-07 30.4 0.3 40 25-64 4-61 (214)
60 PF10571 UPF0547: Uncharacteri 93.5 0.045 9.8E-07 19.3 0.9 10 53-62 16-25 (26)
61 PRK14890 putative Zn-ribbon RN 93.2 0.1 2.3E-06 22.2 1.9 9 50-58 47-55 (59)
62 smart00531 TFIIE Transcription 93.2 0.18 3.9E-06 25.5 3.0 38 23-61 96-133 (147)
63 smart00734 ZnF_Rad18 Rad18-lik 92.9 0.14 3E-06 18.1 1.7 20 52-72 2-21 (26)
64 TIGR00373 conserved hypothetic 92.5 0.11 2.4E-06 26.7 1.7 16 52-67 110-125 (158)
65 cd00729 rubredoxin_SM Rubredox 92.5 0.12 2.6E-06 19.4 1.4 25 26-59 2-26 (34)
66 smart00614 ZnF_BED BED zinc fi 92.4 0.19 4.2E-06 20.5 2.1 23 52-74 19-47 (50)
67 PHA00626 hypothetical protein 92.3 0.064 1.4E-06 22.6 0.6 14 50-63 22-35 (59)
68 PF12013 DUF3505: Protein of u 92.1 0.2 4.3E-06 24.0 2.2 27 50-76 79-109 (109)
69 KOG4167|consensus 92.1 0.028 6.2E-07 35.3 -0.8 25 51-75 792-816 (907)
70 KOG2785|consensus 92.0 0.39 8.3E-06 28.2 3.6 69 1-73 169-242 (390)
71 PRK06266 transcription initiat 91.9 0.14 3E-06 26.9 1.7 17 51-67 117-133 (178)
72 PF02892 zf-BED: BED zinc fing 91.7 0.33 7.2E-06 19.1 2.4 24 50-73 15-42 (45)
73 PRK00398 rpoP DNA-directed RNA 91.4 0.13 2.9E-06 20.6 1.1 29 26-61 3-31 (46)
74 smart00834 CxxC_CXXC_SSSS Puta 90.4 0.072 1.6E-06 20.6 -0.1 29 27-59 6-34 (41)
75 KOG2893|consensus 90.4 0.17 3.6E-06 27.9 1.1 33 49-86 9-41 (341)
76 TIGR02300 FYDLN_acid conserved 90.2 0.19 4.1E-06 24.9 1.2 30 27-64 10-39 (129)
77 PRK09678 DNA-binding transcrip 90.1 0.12 2.5E-06 23.1 0.4 14 49-62 25-40 (72)
78 COG5048 FOG: Zn-finger [Genera 90.0 0.093 2E-06 30.3 0.1 55 26-80 289-352 (467)
79 KOG2231|consensus 89.9 0.81 1.8E-05 29.0 3.8 64 9-74 125-205 (669)
80 PF12760 Zn_Tnp_IS1595: Transp 89.8 0.72 1.6E-05 18.5 2.6 39 15-59 7-45 (46)
81 PF09723 Zn-ribbon_8: Zinc rib 89.7 0.075 1.6E-06 21.0 -0.4 29 27-59 6-34 (42)
82 smart00659 RPOLCX RNA polymera 89.5 0.3 6.5E-06 19.6 1.3 26 27-60 3-28 (44)
83 PF05443 ROS_MUCR: ROS/MUCR tr 89.5 0.33 7.2E-06 24.3 1.7 28 49-79 70-97 (132)
84 TIGR02605 CxxC_CxxC_SSSS putat 89.4 0.1 2.2E-06 21.4 -0.1 29 27-59 6-34 (52)
85 TIGR00622 ssl1 transcription f 89.4 0.61 1.3E-05 22.7 2.5 46 29-74 58-104 (112)
86 COG5048 FOG: Zn-finger [Genera 88.4 0.088 1.9E-06 30.4 -0.8 48 1-48 292-345 (467)
87 COG1996 RPC10 DNA-directed RNA 87.7 0.45 9.6E-06 19.6 1.3 29 25-60 5-33 (49)
88 PRK00464 nrdR transcriptional 86.9 0.22 4.9E-06 25.5 0.2 12 27-38 29-40 (154)
89 KOG2186|consensus 86.8 0.52 1.1E-05 26.2 1.6 13 26-38 29-41 (276)
90 KOG2785|consensus 86.4 1.3 2.9E-05 26.1 3.1 73 1-73 6-90 (390)
91 PF07754 DUF1610: Domain of un 86.0 0.48 1E-05 16.4 0.8 9 50-58 15-23 (24)
92 PF04959 ARS2: Arsenite-resist 85.8 0.72 1.6E-05 25.1 1.8 27 49-75 75-101 (214)
93 KOG2231|consensus 85.7 1.9 4.1E-05 27.5 3.6 46 28-74 184-235 (669)
94 KOG4173|consensus 84.5 0.5 1.1E-05 25.5 0.8 67 4-73 87-168 (253)
95 PF03604 DNA_RNApol_7kD: DNA d 84.2 0.68 1.5E-05 17.2 0.9 9 51-59 17-25 (32)
96 KOG1146|consensus 84.1 0.54 1.2E-05 32.0 1.0 49 24-73 1282-1350(1406)
97 KOG2593|consensus 83.5 0.72 1.6E-05 27.6 1.2 34 50-86 127-160 (436)
98 COG1997 RPL43A Ribosomal prote 83.0 0.85 1.8E-05 21.1 1.1 33 25-64 34-66 (89)
99 KOG2593|consensus 82.5 2.3 4.9E-05 25.7 2.9 40 21-60 123-162 (436)
100 PF15269 zf-C2H2_7: Zinc-finge 82.0 1.7 3.6E-05 17.5 1.7 22 52-73 21-42 (54)
101 PRK04023 DNA polymerase II lar 81.9 2.1 4.5E-05 28.8 2.8 7 28-34 628-634 (1121)
102 PF04606 Ogr_Delta: Ogr/Delta- 81.6 0.44 9.6E-06 19.2 -0.0 34 29-62 2-38 (47)
103 COG1198 PriA Primosomal protei 81.1 1.3 2.9E-05 28.5 1.8 30 28-58 437-469 (730)
104 COG5236 Uncharacterized conser 80.9 4.8 0.0001 23.8 3.8 71 1-73 223-303 (493)
105 KOG2482|consensus 80.3 1.4 2.9E-05 25.9 1.5 23 51-73 195-217 (423)
106 KOG3408|consensus 80.2 1.3 2.8E-05 21.9 1.2 23 26-48 57-79 (129)
107 PF10537 WAC_Acf1_DNA_bd: ATP- 80.1 3.1 6.8E-05 19.9 2.5 29 5-34 10-38 (102)
108 PF13878 zf-C2H2_3: zinc-finge 78.8 3.2 6.8E-05 16.3 2.0 22 1-22 16-39 (41)
109 PF14311 DUF4379: Domain of un 78.8 2.6 5.6E-05 17.5 1.8 17 50-66 27-43 (55)
110 COG3357 Predicted transcriptio 78.3 1.1 2.4E-05 20.9 0.7 13 26-38 58-70 (97)
111 PF02176 zf-TRAF: TRAF-type zi 78.1 1.5 3.2E-05 18.3 1.1 40 24-63 7-54 (60)
112 COG4530 Uncharacterized protei 78.1 1.1 2.5E-05 21.7 0.7 28 28-63 11-38 (129)
113 PF08274 PhnA_Zn_Ribbon: PhnA 77.6 1.3 2.7E-05 16.2 0.6 11 50-60 18-28 (30)
114 COG0068 HypF Hydrogenase matur 77.1 0.28 6.1E-06 31.1 -1.8 57 1-61 126-183 (750)
115 PRK03824 hypA hydrogenase nick 76.4 1.1 2.4E-05 22.5 0.5 10 52-61 71-80 (135)
116 smart00154 ZnF_AN1 AN1-like Zi 75.4 1.8 4E-05 16.7 0.9 14 51-64 12-25 (39)
117 COG3364 Zn-ribbon containing p 75.4 2.2 4.7E-05 20.5 1.2 16 26-41 2-17 (112)
118 PF12907 zf-met2: Zinc-binding 75.0 2.5 5.3E-05 16.6 1.2 25 52-76 2-30 (40)
119 TIGR01206 lysW lysine biosynth 74.3 1.7 3.6E-05 18.3 0.7 30 27-61 3-32 (54)
120 KOG4167|consensus 74.2 1.2 2.6E-05 28.7 0.3 24 1-24 795-818 (907)
121 COG5236 Uncharacterized conser 74.0 5.1 0.00011 23.7 2.6 19 29-47 223-241 (493)
122 PRK14873 primosome assembly pr 74.0 1.4 3E-05 28.1 0.5 9 51-59 422-430 (665)
123 COG5151 SSL1 RNA polymerase II 72.3 6.4 0.00014 23.0 2.7 26 49-74 386-411 (421)
124 PF04423 Rad50_zn_hook: Rad50 72.1 1.3 2.8E-05 18.3 0.1 11 1-11 23-33 (54)
125 COG3677 Transposase and inacti 72.0 1.3 2.9E-05 22.1 0.1 35 27-63 31-65 (129)
126 PF04780 DUF629: Protein of un 71.9 4.4 9.6E-05 24.9 2.2 23 51-73 57-79 (466)
127 PF01428 zf-AN1: AN1-like Zinc 71.7 1.9 4.1E-05 17.0 0.5 15 50-64 12-26 (43)
128 PF13451 zf-trcl: Probable zin 71.6 2.3 5.1E-05 17.5 0.8 18 49-66 2-19 (49)
129 TIGR00595 priA primosomal prot 70.9 0.9 1.9E-05 27.8 -0.7 9 51-59 253-261 (505)
130 PF11672 DUF3268: Protein of u 70.1 1.5 3.2E-05 21.1 0.0 10 25-34 1-10 (102)
131 PF10071 DUF2310: Zn-ribbon-co 69.5 1.9 4.1E-05 24.2 0.4 30 49-85 218-247 (258)
132 COG4957 Predicted transcriptio 69.3 5.4 0.00012 20.2 1.8 25 52-79 77-101 (148)
133 PRK12380 hydrogenase nickel in 68.3 3.3 7.2E-05 20.1 1.0 10 52-61 71-80 (113)
134 TIGR00100 hypA hydrogenase nic 68.1 2.8 6.1E-05 20.4 0.8 11 52-62 71-81 (115)
135 PF07282 OrfB_Zn_ribbon: Putat 68.1 9.2 0.0002 16.5 2.9 33 27-66 29-61 (69)
136 COG1773 Rubredoxin [Energy pro 67.5 2.9 6.2E-05 17.7 0.6 12 51-62 3-14 (55)
137 PF01927 Mut7-C: Mut7-C RNAse 67.5 4.9 0.00011 20.4 1.6 43 27-69 92-142 (147)
138 COG1675 TFA1 Transcription ini 67.4 7.6 0.00016 20.6 2.3 43 13-61 100-142 (176)
139 PF10013 DUF2256: Uncharacteri 67.4 4.7 0.0001 16.0 1.2 15 53-67 10-24 (42)
140 TIGR00686 phnA alkylphosphonat 67.3 3.5 7.6E-05 20.0 1.0 14 51-64 19-32 (109)
141 PF07503 zf-HYPF: HypF finger; 66.7 0.91 2E-05 17.2 -0.9 10 52-61 22-31 (35)
142 PF04810 zf-Sec23_Sec24: Sec23 66.4 2.3 4.9E-05 16.5 0.2 12 49-60 22-33 (40)
143 PTZ00255 60S ribosomal protein 64.6 3.4 7.5E-05 19.3 0.6 32 25-63 35-66 (90)
144 PF02891 zf-MIZ: MIZ/SP-RING z 63.0 3.5 7.6E-05 16.9 0.5 7 27-33 42-48 (50)
145 KOG0978|consensus 63.0 4.5 9.8E-05 26.1 1.1 21 50-70 677-697 (698)
146 PF13824 zf-Mss51: Zinc-finger 62.0 6.2 0.00013 16.7 1.1 12 24-35 12-23 (55)
147 PF08209 Sgf11: Sgf11 (transcr 62.0 8.8 0.00019 14.4 1.4 21 51-72 4-24 (33)
148 COG4338 Uncharacterized protei 60.6 3.7 8E-05 16.8 0.3 15 53-67 14-28 (54)
149 PF12230 PRP21_like_P: Pre-mRN 60.5 2.9 6.2E-05 22.9 0.0 31 50-81 167-197 (229)
150 PF10276 zf-CHCC: Zinc-finger 60.5 4.4 9.4E-05 15.9 0.5 12 50-61 28-39 (40)
151 KOG1842|consensus 60.4 6.5 0.00014 24.1 1.4 25 51-75 15-39 (505)
152 PF14803 Nudix_N_2: Nudix N-te 60.0 2.3 4.9E-05 16.0 -0.3 8 52-59 23-30 (34)
153 KOG1994|consensus 59.6 7.7 0.00017 21.6 1.5 25 50-74 238-262 (268)
154 PF14446 Prok-RING_1: Prokaryo 59.3 3.2 6.9E-05 17.5 0.0 10 28-37 7-16 (54)
155 PF11789 zf-Nse: Zinc-finger o 58.9 6.2 0.00013 16.7 0.9 32 49-84 22-53 (57)
156 PF08790 zf-LYAR: LYAR-type C2 58.8 1.5 3.4E-05 15.8 -0.8 8 29-36 3-10 (28)
157 PF00301 Rubredoxin: Rubredoxi 58.8 5.4 0.00012 16.2 0.7 12 52-63 2-13 (47)
158 KOG0717|consensus 57.3 9.4 0.0002 23.6 1.7 22 52-73 293-314 (508)
159 PF01155 HypA: Hydrogenase exp 56.8 5.1 0.00011 19.4 0.5 11 52-62 71-81 (113)
160 PRK00564 hypA hydrogenase nick 56.0 6.5 0.00014 19.3 0.8 9 52-60 72-80 (117)
161 COG1571 Predicted DNA-binding 55.1 7.5 0.00016 23.6 1.1 13 51-63 367-379 (421)
162 PRK10220 hypothetical protein; 54.7 10 0.00022 18.5 1.3 13 51-63 20-32 (111)
163 COG4888 Uncharacterized Zn rib 54.6 3 6.5E-05 19.9 -0.4 38 24-62 20-57 (104)
164 PF12773 DZR: Double zinc ribb 54.3 7.5 0.00016 15.5 0.8 25 28-60 14-38 (50)
165 COG3091 SprT Zn-dependent meta 54.0 9.8 0.00021 19.8 1.3 32 50-86 116-147 (156)
166 PRK03681 hypA hydrogenase nick 53.7 7.5 0.00016 18.9 0.8 10 27-36 71-80 (114)
167 smart00440 ZnF_C2C2 C2C2 Zinc 53.4 3.2 6.9E-05 16.1 -0.4 10 52-61 29-38 (40)
168 cd00730 rubredoxin Rubredoxin; 52.9 5.9 0.00013 16.3 0.3 12 52-63 2-13 (50)
169 PF07975 C1_4: TFIIH C1-like d 52.7 2.4 5.1E-05 17.6 -0.9 17 51-67 21-37 (51)
170 PF15135 UPF0515: Uncharacteri 52.4 12 0.00027 21.1 1.6 14 51-64 155-168 (278)
171 PLN02294 cytochrome c oxidase 52.2 8.1 0.00018 20.4 0.8 14 25-38 140-153 (174)
172 PF02591 DUF164: Putative zinc 52.1 18 0.00039 15.0 1.8 32 28-60 24-55 (56)
173 COG2879 Uncharacterized small 52.0 22 0.00047 15.6 2.1 18 9-26 23-40 (65)
174 PF01363 FYVE: FYVE zinc finge 52.0 13 0.00028 16.0 1.4 10 28-37 11-20 (69)
175 PF07295 DUF1451: Protein of u 51.7 3.1 6.8E-05 21.3 -0.7 30 25-61 111-140 (146)
176 PRK00432 30S ribosomal protein 51.3 13 0.00027 15.3 1.2 12 50-61 36-47 (50)
177 PF09845 DUF2072: Zn-ribbon co 50.6 6.8 0.00015 19.8 0.4 13 52-64 2-14 (131)
178 PF14353 CpXC: CpXC protein 50.2 9.4 0.0002 18.8 0.9 15 50-64 37-51 (128)
179 COG5112 UFD2 U1-like Zn-finger 48.5 8.5 0.00019 18.7 0.5 24 25-48 54-77 (126)
180 COG1326 Uncharacterized archae 48.2 26 0.00056 19.1 2.3 37 26-63 6-42 (201)
181 KOG2071|consensus 47.8 12 0.00026 23.8 1.2 23 1-23 421-443 (579)
182 PTZ00448 hypothetical protein; 47.3 19 0.00041 21.6 1.8 24 51-74 314-337 (373)
183 COG5188 PRP9 Splicing factor 3 46.8 11 0.00024 22.5 0.9 20 1-20 241-260 (470)
184 TIGR03829 YokU_near_AblA uncha 46.6 13 0.00028 17.5 1.0 15 1-15 38-52 (89)
185 PF05191 ADK_lid: Adenylate ki 46.4 10 0.00022 14.4 0.5 11 52-62 2-12 (36)
186 KOG2636|consensus 45.5 45 0.00098 20.8 3.2 24 49-72 399-423 (497)
187 cd00924 Cyt_c_Oxidase_Vb Cytoc 45.5 12 0.00026 17.8 0.8 14 25-38 78-91 (97)
188 COG0675 Transposase and inacti 45.5 32 0.00069 19.6 2.6 22 49-70 320-341 (364)
189 PF03811 Zn_Tnp_IS1: InsA N-te 45.2 1.8 3.8E-05 16.6 -1.7 8 50-57 28-35 (36)
190 PF13453 zf-TFIIB: Transcripti 44.1 23 0.0005 13.6 1.4 16 1-16 22-37 (41)
191 COG4391 Uncharacterized protei 44.1 4.5 9.8E-05 17.5 -0.7 45 17-62 15-59 (62)
192 PF01286 XPA_N: XPA protein N- 44.1 7.6 0.00016 14.7 0.0 6 3-8 8-13 (34)
193 PLN03238 probable histone acet 43.8 33 0.00072 19.9 2.4 25 49-73 46-70 (290)
194 KOG2907|consensus 43.6 16 0.00035 18.0 1.0 11 52-62 103-113 (116)
195 TIGR00143 hypF [NiFe] hydrogen 43.5 1.7 3.6E-05 28.0 -2.8 11 51-61 140-150 (711)
196 KOG3507|consensus 43.2 19 0.0004 15.5 1.1 28 26-61 20-47 (62)
197 PRK05580 primosome assembly pr 43.1 27 0.00058 22.8 2.2 9 51-59 421-429 (679)
198 PF14369 zf-RING_3: zinc-finge 43.1 9.6 0.00021 14.4 0.2 8 1-8 24-31 (35)
199 cd00065 FYVE FYVE domain; Zinc 43.0 19 0.00041 14.7 1.2 9 53-61 20-28 (57)
200 KOG0782|consensus 42.1 4.3 9.4E-05 25.8 -1.2 51 13-65 240-290 (1004)
201 PF14255 Cys_rich_CPXG: Cystei 41.7 11 0.00025 15.7 0.3 9 53-61 2-10 (52)
202 TIGR00515 accD acetyl-CoA carb 41.0 21 0.00046 20.6 1.4 10 52-61 46-55 (285)
203 PLN02748 tRNA dimethylallyltra 40.8 28 0.0006 21.7 1.9 24 50-73 417-441 (468)
204 TIGR01562 FdhE formate dehydro 40.7 20 0.00044 20.9 1.3 9 27-35 185-193 (305)
205 PF03966 Trm112p: Trm112p-like 40.5 12 0.00026 16.2 0.4 14 49-62 51-64 (68)
206 PF06397 Desulfoferrod_N: Desu 40.2 16 0.00034 14.0 0.6 10 51-60 6-15 (36)
207 TIGR02159 PA_CoA_Oxy4 phenylac 40.2 4.4 9.6E-05 20.7 -1.2 11 51-61 130-140 (146)
208 PRK05452 anaerobic nitric oxid 40.0 14 0.00031 22.8 0.7 13 25-37 424-436 (479)
209 KOG2807|consensus 40.0 40 0.00087 20.1 2.4 24 51-74 345-368 (378)
210 COG1656 Uncharacterized conser 39.5 28 0.0006 18.4 1.6 46 27-72 98-151 (165)
211 PRK14714 DNA polymerase II lar 39.4 24 0.00051 25.0 1.6 6 53-58 711-716 (1337)
212 COG1998 RPS31 Ribosomal protei 39.4 28 0.00062 14.4 1.3 10 51-60 37-46 (51)
213 TIGR03831 YgiT_finger YgiT-typ 38.6 15 0.00032 14.1 0.5 11 52-62 33-43 (46)
214 PF13821 DUF4187: Domain of un 38.5 22 0.00048 14.9 1.0 22 49-70 25-46 (55)
215 COG4306 Uncharacterized protei 38.5 13 0.00028 18.7 0.3 17 49-65 66-82 (160)
216 PF14205 Cys_rich_KTR: Cystein 38.4 9.8 0.00021 16.1 -0.1 11 50-60 27-37 (55)
217 PF08792 A2L_zn_ribbon: A2L zi 37.9 19 0.00041 13.4 0.7 12 51-62 21-32 (33)
218 PRK00420 hypothetical protein; 37.3 27 0.0006 17.2 1.3 28 27-62 24-51 (112)
219 PF00130 C1_1: Phorbol esters/ 37.1 32 0.00069 13.8 1.4 28 25-60 10-37 (53)
220 PF06524 NOA36: NOA36 protein; 36.5 7 0.00015 22.2 -0.8 24 49-72 207-230 (314)
221 PF05129 Elf1: Transcription e 35.9 18 0.00039 16.5 0.6 9 50-58 21-29 (81)
222 PHA02998 RNA polymerase subuni 35.7 13 0.00029 19.9 0.1 11 52-62 172-182 (195)
223 KOG1280|consensus 35.5 50 0.0011 19.9 2.3 27 50-76 78-104 (381)
224 PRK05978 hypothetical protein; 35.5 22 0.00049 18.4 0.9 30 27-62 34-63 (148)
225 PRK14559 putative protein seri 35.5 15 0.00033 23.7 0.4 12 53-64 43-54 (645)
226 TIGR01384 TFS_arch transcripti 35.3 14 0.00031 17.4 0.2 25 1-37 3-27 (104)
227 PRK04351 hypothetical protein; 35.1 24 0.00051 18.3 0.9 28 51-86 112-139 (149)
228 CHL00174 accD acetyl-CoA carbo 35.1 30 0.00065 20.2 1.4 11 27-37 58-68 (296)
229 PF14690 zf-ISL3: zinc-finger 35.1 20 0.00043 14.0 0.6 10 51-60 2-11 (47)
230 PRK03564 formate dehydrogenase 34.8 39 0.00085 19.8 1.9 11 25-35 186-196 (309)
231 PF10263 SprT-like: SprT-like 34.8 12 0.00025 19.0 -0.1 11 51-61 123-133 (157)
232 PF08271 TF_Zn_Ribbon: TFIIB z 34.7 22 0.00047 13.8 0.7 9 52-60 1-9 (43)
233 PF02701 zf-Dof: Dof domain, z 34.6 1.9 4E-05 18.7 -2.5 43 24-66 3-45 (63)
234 PRK01343 zinc-binding protein; 34.5 26 0.00055 15.0 0.9 10 52-61 10-19 (57)
235 smart00109 C1 Protein kinase C 34.4 29 0.00064 13.3 1.1 9 51-59 27-35 (49)
236 smart00064 FYVE Protein presen 34.2 27 0.00059 14.9 1.0 26 28-62 12-37 (68)
237 PF09963 DUF2197: Uncharacteri 34.0 23 0.00051 15.1 0.7 34 27-60 3-40 (56)
238 PRK00762 hypA hydrogenase nick 33.9 31 0.00067 17.1 1.2 9 52-61 71-79 (124)
239 COG1579 Zn-ribbon protein, pos 33.8 30 0.00066 19.5 1.3 34 28-62 199-232 (239)
240 PRK12860 transcriptional activ 33.7 42 0.0009 18.3 1.7 28 51-86 134-161 (189)
241 KOG2817|consensus 33.5 44 0.00096 20.4 1.9 35 49-86 347-381 (394)
242 PF01780 Ribosomal_L37ae: Ribo 33.4 18 0.0004 17.0 0.4 31 25-62 34-64 (90)
243 PRK12722 transcriptional activ 33.2 42 0.00092 18.2 1.7 27 52-86 135-161 (187)
244 PF03884 DUF329: Domain of unk 33.2 22 0.00047 15.2 0.5 12 52-63 3-14 (57)
245 PF10083 DUF2321: Uncharacteri 33.2 15 0.00033 19.2 0.1 19 49-67 66-84 (158)
246 KOG2747|consensus 32.9 31 0.00067 21.0 1.3 25 49-73 156-180 (396)
247 COG2331 Uncharacterized protei 32.8 29 0.00063 15.8 0.9 30 27-60 13-42 (82)
248 PLN00104 MYST -like histone ac 32.8 44 0.00095 20.8 1.9 25 49-73 196-220 (450)
249 PRK05654 acetyl-CoA carboxylas 32.2 44 0.00095 19.4 1.8 10 52-61 47-56 (292)
250 PLN03239 histone acetyltransfe 32.1 49 0.0011 19.9 1.9 25 49-73 104-128 (351)
251 PF02146 SIR2: Sir2 family; I 31.8 78 0.0017 16.6 2.6 13 52-64 106-118 (178)
252 PF14787 zf-CCHC_5: GAG-polypr 31.4 21 0.00046 13.7 0.3 14 53-66 4-17 (36)
253 PF09416 UPF1_Zn_bind: RNA hel 31.4 43 0.00093 17.5 1.5 34 1-34 17-68 (152)
254 PF01215 COX5B: Cytochrome c o 31.4 23 0.0005 18.1 0.5 14 49-62 110-123 (136)
255 COG5216 Uncharacterized conser 30.5 40 0.00087 14.5 1.1 11 49-59 42-52 (67)
256 COG5109 Uncharacterized conser 30.4 53 0.0011 19.6 1.9 10 76-85 373-382 (396)
257 PRK08222 hydrogenase 4 subunit 30.2 41 0.0009 17.9 1.4 19 50-68 113-131 (181)
258 PF05741 zf-nanos: Nanos RNA b 29.9 16 0.00034 15.5 -0.1 10 50-59 32-41 (55)
259 PTZ00064 histone acetyltransfe 29.4 60 0.0013 20.7 2.1 25 49-73 278-302 (552)
260 PF04641 Rtf2: Rtf2 RING-finge 29.4 21 0.00046 20.1 0.3 15 24-38 111-125 (260)
261 PHA02942 putative transposase; 29.1 1.2E+02 0.0025 18.5 3.2 30 28-65 327-356 (383)
262 KOG2857|consensus 29.1 31 0.00068 17.8 0.8 23 50-72 16-38 (157)
263 PF13248 zf-ribbon_3: zinc-rib 29.0 21 0.00047 12.2 0.2 7 28-34 4-10 (26)
264 TIGR03830 CxxCG_CxxCG_HTH puta 29.0 78 0.0017 15.3 2.2 21 50-70 30-50 (127)
265 KOG4727|consensus 28.8 46 0.001 17.8 1.4 22 51-72 75-96 (193)
266 PF06220 zf-U1: U1 zinc finger 28.7 48 0.001 12.7 1.4 10 52-61 4-13 (38)
267 cd00974 DSRD Desulforedoxin (D 28.7 34 0.00075 12.5 0.7 11 51-61 4-14 (34)
268 TIGR00627 tfb4 transcription f 28.7 50 0.0011 19.1 1.6 14 49-62 253-266 (279)
269 COG1327 Predicted transcriptio 28.6 22 0.00048 18.5 0.3 13 1-13 31-43 (156)
270 TIGR00280 L37a ribosomal prote 28.5 31 0.00067 16.3 0.7 32 25-63 34-65 (91)
271 PTZ00043 cytochrome c oxidase 28.4 29 0.00063 19.5 0.6 17 24-40 179-195 (268)
272 TIGR00319 desulf_FeS4 desulfof 28.3 36 0.00078 12.4 0.7 11 51-61 7-17 (34)
273 PF01096 TFIIS_C: Transcriptio 28.3 30 0.00064 13.3 0.5 11 51-61 28-38 (39)
274 PF05495 zf-CHY: CHY zinc fing 27.7 10 0.00023 16.7 -0.9 12 51-62 41-52 (71)
275 PF02748 PyrI_C: Aspartate car 27.6 28 0.00061 14.5 0.4 16 49-64 33-48 (52)
276 PRK11827 hypothetical protein; 27.3 54 0.0012 14.2 1.3 16 51-66 26-41 (60)
277 smart00661 RPOL9 RNA polymeras 27.2 35 0.00077 13.6 0.7 13 51-63 20-32 (52)
278 KOG1088|consensus 26.8 38 0.00083 16.9 0.8 19 21-39 93-111 (124)
279 COG4640 Predicted membrane pro 26.8 47 0.001 20.5 1.3 20 25-44 14-33 (465)
280 PF10122 Mu-like_Com: Mu-like 26.7 21 0.00046 14.9 0.0 10 51-60 24-33 (51)
281 cd00122 MBD MeCP2, MBD1, MBD2, 26.7 60 0.0013 13.8 1.4 18 4-21 33-50 (62)
282 PF00641 zf-RanBP: Zn-finger i 26.1 27 0.0006 12.2 0.2 6 80-85 5-10 (30)
283 COG3024 Uncharacterized protei 26.1 37 0.00081 14.9 0.7 12 52-63 8-19 (65)
284 PTZ00409 Sir2 (Silent Informat 26.1 94 0.002 17.9 2.4 15 51-65 137-151 (271)
285 PF09889 DUF2116: Uncharacteri 26.0 34 0.00075 14.7 0.6 7 1-7 6-12 (59)
286 TIGR01053 LSD1 zinc finger dom 25.6 39 0.00084 12.4 0.6 6 80-85 20-25 (31)
287 cd01413 SIR2_Af2 SIR2_Af2: Arc 25.5 94 0.002 17.1 2.3 14 51-64 113-126 (222)
288 PRK12387 formate hydrogenlyase 25.4 58 0.0013 17.2 1.4 19 50-68 113-131 (180)
289 PF06170 DUF983: Protein of un 25.4 30 0.00064 16.1 0.3 8 1-8 11-18 (86)
290 PRK03976 rpl37ae 50S ribosomal 25.3 39 0.00084 16.0 0.7 32 25-63 35-66 (90)
291 TIGR00244 transcriptional regu 25.1 27 0.00059 18.1 0.2 14 1-14 31-44 (147)
292 smart00391 MBD Methyl-CpG bind 24.9 59 0.0013 14.7 1.2 19 4-22 36-54 (77)
293 COG1594 RPB9 DNA-directed RNA 24.8 8.4 0.00018 18.8 -1.6 12 51-62 100-111 (113)
294 PF04988 AKAP95: A-kinase anch 24.2 65 0.0014 17.1 1.4 22 52-73 1-22 (165)
295 PF01844 HNH: HNH endonuclease 23.6 31 0.00067 13.2 0.2 9 1-9 1-9 (47)
296 cd04476 RPA1_DBD_C RPA1_DBD_C: 23.6 21 0.00046 18.4 -0.4 12 50-61 50-61 (166)
297 KOG4118|consensus 23.5 49 0.0011 14.6 0.8 29 51-79 38-66 (74)
298 KOG0801|consensus 23.4 18 0.00038 19.1 -0.6 17 67-86 129-145 (205)
299 PF09082 DUF1922: Domain of un 22.8 29 0.00062 15.5 0.0 7 53-60 22-28 (68)
300 COG5027 SAS2 Histone acetyltra 22.7 54 0.0012 19.8 1.1 25 49-73 156-180 (395)
301 KOG1940|consensus 22.6 1.3E+02 0.0027 17.6 2.4 8 27-34 197-204 (276)
302 cd01410 SIRT7 SIRT7: Eukaryoti 22.3 1.3E+02 0.0027 16.5 2.3 6 29-34 98-103 (206)
303 PF14447 Prok-RING_4: Prokaryo 22.2 52 0.0011 14.0 0.7 15 49-63 37-51 (55)
304 KOG2923|consensus 22.0 93 0.002 13.7 1.7 10 49-58 42-51 (67)
305 COG1779 C4-type Zn-finger prot 22.0 24 0.00052 19.3 -0.3 14 50-63 42-55 (201)
306 KOG0402|consensus 22.0 51 0.0011 15.4 0.7 23 38-60 18-45 (92)
307 PF14149 YhfH: YhfH-like prote 21.5 29 0.00062 13.4 -0.1 7 1-7 16-22 (37)
308 PF11931 DUF3449: Domain of un 21.3 32 0.00068 18.8 0.0 14 73-86 95-108 (196)
309 PRK14138 NAD-dependent deacety 21.3 1.3E+02 0.0028 16.9 2.3 16 51-66 119-134 (244)
310 smart00132 LIM Zinc-binding do 21.1 46 0.001 11.8 0.5 10 52-61 28-37 (39)
311 PF14354 Lar_restr_allev: Rest 21.1 53 0.0011 13.7 0.7 8 53-60 5-12 (61)
312 PF10367 Vps39_2: Vacuolar sor 20.9 39 0.00085 15.7 0.3 6 2-7 82-87 (109)
313 PRK11032 hypothetical protein; 20.8 47 0.001 17.5 0.6 30 25-61 123-152 (160)
314 PRK00418 DNA gyrase inhibitor; 20.8 59 0.0013 14.2 0.8 11 51-61 6-16 (62)
315 COG0846 SIR2 NAD-dependent pro 20.6 93 0.002 17.7 1.7 11 52-62 123-133 (250)
316 PF11023 DUF2614: Protein of u 20.4 56 0.0012 16.2 0.7 13 49-61 67-79 (114)
317 KOG3352|consensus 20.2 43 0.00094 17.5 0.3 14 25-38 132-145 (153)
318 PF07649 C1_3: C1-like domain; 20.1 58 0.0012 11.4 0.6 11 50-60 14-24 (30)
319 KOG4602|consensus 20.0 48 0.001 19.1 0.5 11 50-60 267-277 (318)
No 1
>KOG2462|consensus
Probab=99.95 E-value=5.7e-28 Score=126.62 Aligned_cols=84 Identities=25% Similarity=0.478 Sum_probs=79.4
Q ss_pred CcchhhhccChHHHHhhHHHHhCCCceecccccccCCChHHHhhhhhC---CcceecccccccccCHHHHHHHHHhCCCC
Q psy4084 1 MSECMGKFTEYQVIRKHIRTFHSDRQFACHMCIKVFPSQDKLRMHMLS---DRQFACHMCIKVFPSQDKLRMHMLSGLQT 77 (86)
Q Consensus 1 c~~C~~~~~~~~~l~~h~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~---~~~~~C~~C~~~~~~~~~l~~h~~~~~~~ 77 (86)
|++||+.|.+...|.+|+++|+ -+++|.+||+.|....-|+.|+++ +|||.|+.|+++|++.++|+.||++|.+.
T Consensus 164 C~~C~K~YvSmpALkMHirTH~--l~c~C~iCGKaFSRPWLLQGHiRTHTGEKPF~C~hC~kAFADRSNLRAHmQTHS~~ 241 (279)
T KOG2462|consen 164 CKYCGKVYVSMPALKMHIRTHT--LPCECGICGKAFSRPWLLQGHIRTHTGEKPFSCPHCGKAFADRSNLRAHMQTHSDV 241 (279)
T ss_pred CCCCCceeeehHHHhhHhhccC--CCcccccccccccchHHhhcccccccCCCCccCCcccchhcchHHHHHHHHhhcCC
Confidence 7899999999999999999997 479999999999999999999997 99999999999999999999999999999
Q ss_pred ccCCCCcCC
Q psy4084 78 FDLKSKLCT 86 (86)
Q Consensus 78 ~~~~c~~C~ 86 (86)
+.|+|..|+
T Consensus 242 K~~qC~~C~ 250 (279)
T KOG2462|consen 242 KKHQCPRCG 250 (279)
T ss_pred ccccCcchh
Confidence 999999885
No 2
>KOG2462|consensus
Probab=99.91 E-value=1.2e-25 Score=117.93 Aligned_cols=74 Identities=30% Similarity=0.548 Sum_probs=71.1
Q ss_pred CcchhhhccChHHHHhhHHHHhCCCceecccccccCCChHHHhhhhhC---CcceecccccccccCHHHHHHHHHhC
Q psy4084 1 MSECMGKFTEYQVIRKHIRTFHSDRQFACHMCIKVFPSQDKLRMHMLS---DRQFACHMCIKVFPSQDKLRMHMLSG 74 (86)
Q Consensus 1 c~~C~~~~~~~~~l~~h~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~---~~~~~C~~C~~~~~~~~~l~~h~~~~ 74 (86)
|.+||++|....-|+.|+|+|+||+||.|+.|++.|...++|+.||.+ .++|+|..|++.|+..+.|+.|....
T Consensus 190 C~iCGKaFSRPWLLQGHiRTHTGEKPF~C~hC~kAFADRSNLRAHmQTHS~~K~~qC~~C~KsFsl~SyLnKH~ES~ 266 (279)
T KOG2462|consen 190 CGICGKAFSRPWLLQGHIRTHTGEKPFSCPHCGKAFADRSNLRAHMQTHSDVKKHQCPRCGKSFALKSYLNKHSESA 266 (279)
T ss_pred cccccccccchHHhhcccccccCCCCccCCcccchhcchHHHHHHHHhhcCCccccCcchhhHHHHHHHHHHhhhhc
Confidence 789999999999999999999999999999999999999999999998 68999999999999999999998764
No 3
>KOG3623|consensus
Probab=99.67 E-value=4.1e-17 Score=95.59 Aligned_cols=86 Identities=23% Similarity=0.481 Sum_probs=77.0
Q ss_pred CcchhhhccChHHHHhhHHHHhC--CCceecccccccCCChHHHhhhhhC----------------Ccceeccccccccc
Q psy4084 1 MSECMGKFTEYQVIRKHIRTFHS--DRQFACHMCIKVFPSQDKLRMHMLS----------------DRQFACHMCIKVFP 62 (86)
Q Consensus 1 c~~C~~~~~~~~~l~~h~~~~~~--~~~~~c~~c~~~~~~~~~l~~h~~~----------------~~~~~C~~C~~~~~ 62 (86)
|++|.+.+.+...|+.|+...+. +..|.|..|...|.....|.+|+.. .+.|+|.+||++|.
T Consensus 213 cpycdrgykrltslkeHikyrhekne~nfsC~lCsytFAyRtQLErhm~~hkpg~dqa~sltqsa~lRKFKCtECgKAFK 292 (1007)
T KOG3623|consen 213 CPYCDRGYKRLTSLKEHIKYRHEKNEPNFSCMLCSYTFAYRTQLERHMQLHKPGGDQAISLTQSALLRKFKCTECGKAFK 292 (1007)
T ss_pred chhHHHHHHHHHHHHHHHHHHHhhCCCCCcchhhhhhhhhHHHHHHHHHhhcCCCcccccccchhhhccccccccchhhh
Confidence 78899999999999999885443 4568999999999999999999853 37799999999999
Q ss_pred CHHHHHHHHHhCCCCccCCCCcCC
Q psy4084 63 SQDKLRMHMLSGLQTFDLKSKLCT 86 (86)
Q Consensus 63 ~~~~l~~h~~~~~~~~~~~c~~C~ 86 (86)
++..|..|+++|.+++||.|.+|.
T Consensus 293 fKHHLKEHlRIHSGEKPfeCpnCk 316 (1007)
T KOG3623|consen 293 FKHHLKEHLRIHSGEKPFECPNCK 316 (1007)
T ss_pred hHHHHHhhheeecCCCCcCCcccc
Confidence 999999999999999999999984
No 4
>KOG3576|consensus
Probab=99.60 E-value=4.2e-16 Score=79.76 Aligned_cols=77 Identities=19% Similarity=0.395 Sum_probs=54.5
Q ss_pred CcchhhhccChHHHHhhHHHHhCCCceecccccccCCChHHHhhhhhC--------------CcceecccccccccCHHH
Q psy4084 1 MSECMGKFTEYQVIRKHIRTFHSDRQFACHMCIKVFPSQDKLRMHMLS--------------DRQFACHMCIKVFPSQDK 66 (86)
Q Consensus 1 c~~C~~~~~~~~~l~~h~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~--------------~~~~~C~~C~~~~~~~~~ 66 (86)
|..||+.|....+|++|+|+|+|.+||.|..|++.|...-+|..|... .+.|.|+.||.+......
T Consensus 148 ct~cgkgfndtfdlkrh~rthtgvrpykc~~c~kaftqrcsleshl~kvhgv~~~yaykerr~kl~vcedcg~t~~~~e~ 227 (267)
T KOG3576|consen 148 CTFCGKGFNDTFDLKRHTRTHTGVRPYKCSLCEKAFTQRCSLESHLKKVHGVQHQYAYKERRAKLYVCEDCGYTSERPEV 227 (267)
T ss_pred HhhccCcccchhhhhhhhccccCccccchhhhhHHHHhhccHHHHHHHHcCchHHHHHHHhhhheeeecccCCCCCChhH
Confidence 445777777777777777777777777777777777777777666542 355777777777777777
Q ss_pred HHHHHHhCCCC
Q psy4084 67 LRMHMLSGLQT 77 (86)
Q Consensus 67 l~~h~~~~~~~ 77 (86)
+..|+..|+-.
T Consensus 228 ~~~h~~~~hp~ 238 (267)
T KOG3576|consen 228 YYLHLKLHHPF 238 (267)
T ss_pred HHHHHHhcCCC
Confidence 77777766543
No 5
>KOG3623|consensus
Probab=99.60 E-value=2.6e-16 Score=92.31 Aligned_cols=72 Identities=24% Similarity=0.548 Sum_probs=63.4
Q ss_pred CcchhhhccChHHHHhhHHHHhCCCceecccccccCCChHHHhhhhhC---CcceecccccccccCHHHHHHHHH
Q psy4084 1 MSECMGKFTEYQVIRKHIRTFHSDRQFACHMCIKVFPSQDKLRMHMLS---DRQFACHMCIKVFPSQDKLRMHML 72 (86)
Q Consensus 1 c~~C~~~~~~~~~l~~h~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~---~~~~~C~~C~~~~~~~~~l~~h~~ 72 (86)
|+.|+++|...+.|-+|.-.|+|.+||+|.+|.+.|..+-.|..|++. ++||+|..|++.|...+...+||.
T Consensus 897 CDqCDK~FqKqSSLaRHKYEHsGqRPyqC~iCkKAFKHKHHLtEHkRLHSGEKPfQCdKClKRFSHSGSYSQHMN 971 (1007)
T KOG3623|consen 897 CDQCDKAFQKQSSLARHKYEHSGQRPYQCIICKKAFKHKHHLTEHKRLHSGEKPFQCDKCLKRFSHSGSYSQHMN 971 (1007)
T ss_pred HHHHHHHHHhhHHHHHhhhhhcCCCCcccchhhHhhhhhhhhhhhhhhccCCCcchhhhhhhhcccccchHhhhc
Confidence 678899998888899998899999999999999999998888888875 889999999999998888888885
No 6
>KOG3576|consensus
Probab=99.59 E-value=2.1e-16 Score=80.86 Aligned_cols=86 Identities=21% Similarity=0.405 Sum_probs=69.5
Q ss_pred CcchhhhccChHHHHhhHHHHhCCCceecccccccCCChHHHhhhhhC---CcceecccccccccCHHHHHHHHHhCC--
Q psy4084 1 MSECMGKFTEYQVIRKHIRTFHSDRQFACHMCIKVFPSQDKLRMHMLS---DRQFACHMCIKVFPSQDKLRMHMLSGL-- 75 (86)
Q Consensus 1 c~~C~~~~~~~~~l~~h~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~---~~~~~C~~C~~~~~~~~~l~~h~~~~~-- 75 (86)
|.+||+.|....-|.+|+.-|...+.+-|..||++|...-.|.+|+++ .+||+|..|+++|...-.|..|++.-+
T Consensus 120 CrvCgK~F~lQRmlnrh~kch~~vkr~lct~cgkgfndtfdlkrh~rthtgvrpykc~~c~kaftqrcsleshl~kvhgv 199 (267)
T KOG3576|consen 120 CRVCGKKFGLQRMLNRHLKCHSDVKRHLCTFCGKGFNDTFDLKRHTRTHTGVRPYKCSLCEKAFTQRCSLESHLKKVHGV 199 (267)
T ss_pred eehhhhhhhHHHHHHHHhhhccHHHHHHHhhccCcccchhhhhhhhccccCccccchhhhhHHHHhhccHHHHHHHHcCc
Confidence 677888888888888888888888888888899988888888888886 688899999999888888888887532
Q ss_pred ---------CCccCCCCcCC
Q psy4084 76 ---------QTFDLKSKLCT 86 (86)
Q Consensus 76 ---------~~~~~~c~~C~ 86 (86)
+++-|.|+.|+
T Consensus 200 ~~~yaykerr~kl~vcedcg 219 (267)
T KOG3576|consen 200 QHQYAYKERRAKLYVCEDCG 219 (267)
T ss_pred hHHHHHHHhhhheeeecccC
Confidence 34446676664
No 7
>KOG1074|consensus
Probab=99.57 E-value=1.5e-15 Score=90.05 Aligned_cols=46 Identities=24% Similarity=0.617 Sum_probs=35.5
Q ss_pred CcchhhhccChHHHHhhHHHHhCCCceecccccccCCChHHHhhhh
Q psy4084 1 MSECMGKFTEYQVIRKHIRTFHSDRQFACHMCIKVFPSQDKLRMHM 46 (86)
Q Consensus 1 c~~C~~~~~~~~~l~~h~~~~~~~~~~~c~~c~~~~~~~~~l~~h~ 46 (86)
|..|++.|.+.+.|+.|+|+|+|++||+|++||..|.++.+|..|.
T Consensus 356 Cr~CakvfgS~SaLqiHlRSHTGERPfqCnvCG~~FSTkGNLKvH~ 401 (958)
T KOG1074|consen 356 CRFCAKVFGSDSALQIHLRSHTGERPFQCNVCGNRFSTKGNLKVHF 401 (958)
T ss_pred hhhhHhhcCchhhhhhhhhccCCCCCeeecccccccccccceeeee
Confidence 5677788888888888888888888888888888887777776654
No 8
>KOG3608|consensus
Probab=99.56 E-value=3.4e-15 Score=81.76 Aligned_cols=84 Identities=24% Similarity=0.437 Sum_probs=63.4
Q ss_pred chhhhccChHHHHhhHHHHhCCCceecccccccCCChHHHhhhhhC-------------------------------Ccc
Q psy4084 3 ECMGKFTEYQVIRKHIRTFHSDRQFACHMCIKVFPSQDKLRMHMLS-------------------------------DRQ 51 (86)
Q Consensus 3 ~C~~~~~~~~~l~~h~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~-------------------------------~~~ 51 (86)
.|-+.+.++..|..|+++|++++...|+.||..|.....|..|.+. ..-
T Consensus 184 ~Ct~~~~~k~~LreH~r~Hs~eKvvACp~Cg~~F~~~tkl~DH~rRqt~l~~n~fqC~~C~KrFaTeklL~~Hv~rHvn~ 263 (467)
T KOG3608|consen 184 MCTKHMGNKYRLREHIRTHSNEKVVACPHCGELFRTKTKLFDHLRRQTELNTNSFQCAQCFKRFATEKLLKSHVVRHVNC 263 (467)
T ss_pred hhhhhhccHHHHHHHHHhcCCCeEEecchHHHHhccccHHHHHHHhhhhhcCCchHHHHHHHHHhHHHHHHHHHHHhhhc
Confidence 3667778888888888888888888888888888888777777642 234
Q ss_pred eecccccccccCHHHHHHHHHh-CCCCccCCCCcCC
Q psy4084 52 FACHMCIKVFPSQDKLRMHMLS-GLQTFDLKSKLCT 86 (86)
Q Consensus 52 ~~C~~C~~~~~~~~~l~~h~~~-~~~~~~~~c~~C~ 86 (86)
|.|+.|.-+....+.|..|++. |.+++||+|+.|+
T Consensus 264 ykCplCdmtc~~~ssL~~H~r~rHs~dkpfKCd~Cd 299 (467)
T KOG3608|consen 264 YKCPLCDMTCSSASSLTTHIRYRHSKDKPFKCDECD 299 (467)
T ss_pred ccccccccCCCChHHHHHHHHhhhccCCCccccchh
Confidence 5666677777777777777775 7788999998875
No 9
>KOG1074|consensus
Probab=99.54 E-value=7.1e-16 Score=91.32 Aligned_cols=75 Identities=28% Similarity=0.571 Sum_probs=69.7
Q ss_pred CcchhhhccChHHHHhhHHHHhCCCceecccccccCCChHHHhhhhhC-------Ccceecc---cccccccCHHHHHHH
Q psy4084 1 MSECMGKFTEYQVIRKHIRTFHSDRQFACHMCIKVFPSQDKLRMHMLS-------DRQFACH---MCIKVFPSQDKLRMH 70 (86)
Q Consensus 1 c~~C~~~~~~~~~l~~h~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~-------~~~~~C~---~C~~~~~~~~~l~~h 70 (86)
|..|-+...-++.|+.|.|+|+|++||+|.+|++.|.++.+|+.|+.. ..++.|+ +|-+.|.....|..|
T Consensus 608 CiiC~rVlSC~saLqmHyrtHtGERPFkCKiCgRAFtTkGNLkaH~~vHka~p~~R~q~ScP~~~ic~~kftn~V~lpQh 687 (958)
T KOG1074|consen 608 CIICLRVLSCPSALQMHYRTHTGERPFKCKICGRAFTTKGNLKAHMSVHKAKPPARVQFSCPSTFICQKKFTNAVTLPQH 687 (958)
T ss_pred eeeeeecccchhhhhhhhhcccCcCccccccccchhccccchhhcccccccCccccccccCCchhhhcccccccccccce
Confidence 778999999999999999999999999999999999999999999975 3468899 899999999999999
Q ss_pred HHhCC
Q psy4084 71 MLSGL 75 (86)
Q Consensus 71 ~~~~~ 75 (86)
++.|.
T Consensus 688 IriH~ 692 (958)
T KOG1074|consen 688 IRIHL 692 (958)
T ss_pred EEeec
Confidence 99987
No 10
>PHA00733 hypothetical protein
Probab=99.40 E-value=8.4e-13 Score=64.28 Aligned_cols=76 Identities=18% Similarity=0.323 Sum_probs=59.3
Q ss_pred CcchhhhccChHHHHhh--HH---HHhCCCceecccccccCCChHHHhhhhhC-CcceecccccccccCHHHHHHHHHhC
Q psy4084 1 MSECMGKFTEYQVIRKH--IR---TFHSDRQFACHMCIKVFPSQDKLRMHMLS-DRQFACHMCIKVFPSQDKLRMHMLSG 74 (86)
Q Consensus 1 c~~C~~~~~~~~~l~~h--~~---~~~~~~~~~c~~c~~~~~~~~~l~~h~~~-~~~~~C~~C~~~~~~~~~l~~h~~~~ 74 (86)
|.+|++.|.....|..+ ++ .+.+.+||.|..|++.|.....|..|+.. ..++.|..|++.|.....|..|+...
T Consensus 43 ~~~~~~~~~~~~~l~~~~~l~~~~~~~~~kPy~C~~Cgk~Fss~s~L~~H~r~h~~~~~C~~CgK~F~~~~sL~~H~~~~ 122 (128)
T PHA00733 43 RAVVKTLIYNPQLLDESSYLYKLLTSKAVSPYVCPLCLMPFSSSVSLKQHIRYTEHSKVCPVCGKEFRNTDSTLDHVCKK 122 (128)
T ss_pred HHHHhhhccChhhhcchHHHHhhcccCCCCCccCCCCCCcCCCHHHHHHHHhcCCcCccCCCCCCccCCHHHHHHHHHHh
Confidence 34566666666555544 22 23347899999999999999999999885 56799999999999999999999875
Q ss_pred CC
Q psy4084 75 LQ 76 (86)
Q Consensus 75 ~~ 76 (86)
++
T Consensus 123 h~ 124 (128)
T PHA00733 123 HN 124 (128)
T ss_pred cC
Confidence 53
No 11
>KOG3608|consensus
Probab=99.39 E-value=6.8e-13 Score=73.00 Aligned_cols=80 Identities=18% Similarity=0.404 Sum_probs=58.6
Q ss_pred cchhhhccChHHHHhhHHHHhCCCceecccccccCCChHHHhhhhhC----CcceecccccccccCHHHHHHHHHhCCCC
Q psy4084 2 SECMGKFTEYQVIRKHIRTFHSDRQFACHMCIKVFPSQDKLRMHMLS----DRQFACHMCIKVFPSQDKLRMHMLSGLQT 77 (86)
Q Consensus 2 ~~C~~~~~~~~~l~~h~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~----~~~~~C~~C~~~~~~~~~l~~h~~~~~~~ 77 (86)
..|.+.|.....|+.|++.|. +-|.|+.|..+....++|..|++. ++||+|..|.+.+.+.+.|+.|...|. +
T Consensus 241 ~~C~KrFaTeklL~~Hv~rHv--n~ykCplCdmtc~~~ssL~~H~r~rHs~dkpfKCd~Cd~~c~~esdL~kH~~~HS-~ 317 (467)
T KOG3608|consen 241 AQCFKRFATEKLLKSHVVRHV--NCYKCPLCDMTCSSASSLTTHIRYRHSKDKPFKCDECDTRCVRESDLAKHVQVHS-K 317 (467)
T ss_pred HHHHHHHhHHHHHHHHHHHhh--hcccccccccCCCChHHHHHHHHhhhccCCCccccchhhhhccHHHHHHHHHhcc-c
Confidence 344455555555555555543 347888888888888888888875 788899888888888888888888775 6
Q ss_pred ccCCCCc
Q psy4084 78 FDLKSKL 84 (86)
Q Consensus 78 ~~~~c~~ 84 (86)
..|.|+.
T Consensus 318 ~~y~C~h 324 (467)
T KOG3608|consen 318 TVYQCEH 324 (467)
T ss_pred cceecCC
Confidence 7788775
No 12
>PLN03086 PRLI-interacting factor K; Provisional
Probab=99.35 E-value=2.9e-12 Score=74.61 Aligned_cols=80 Identities=20% Similarity=0.416 Sum_probs=67.1
Q ss_pred CcchhhhccChHHHHhhHHHHhCCCceecccccccCCChHHHhhhhhC---CcceecccccccccC----------HHHH
Q psy4084 1 MSECMGKFTEYQVIRKHIRTFHSDRQFACHMCIKVFPSQDKLRMHMLS---DRQFACHMCIKVFPS----------QDKL 67 (86)
Q Consensus 1 c~~C~~~~~~~~~l~~h~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~---~~~~~C~~C~~~~~~----------~~~l 67 (86)
|+.|++.|. ...|..|+..++ .++.|+ |+..+ ....|..|+.. .+++.|+.|+..+.. ...|
T Consensus 456 C~~Cgk~f~-~s~LekH~~~~H--kpv~Cp-Cg~~~-~R~~L~~H~~thCp~Kpi~C~fC~~~v~~g~~~~d~~d~~s~L 530 (567)
T PLN03086 456 CEKCGQAFQ-QGEMEKHMKVFH--EPLQCP-CGVVL-EKEQMVQHQASTCPLRLITCRFCGDMVQAGGSAMDVRDRLRGM 530 (567)
T ss_pred CCCCCCccc-hHHHHHHHHhcC--CCccCC-CCCCc-chhHHHhhhhccCCCCceeCCCCCCccccCccccchhhhhhhH
Confidence 788999996 677999999975 789999 99654 66888899875 789999999999852 4589
Q ss_pred HHHHHhCCCCccCCCCcCC
Q psy4084 68 RMHMLSGLQTFDLKSKLCT 86 (86)
Q Consensus 68 ~~h~~~~~~~~~~~c~~C~ 86 (86)
..|... .+.+++.|..|+
T Consensus 531 t~HE~~-CG~rt~~C~~Cg 548 (567)
T PLN03086 531 SEHESI-CGSRTAPCDSCG 548 (567)
T ss_pred HHHHHh-cCCcceEccccC
Confidence 999988 499999999996
No 13
>PHA02768 hypothetical protein; Provisional
Probab=99.25 E-value=3.2e-12 Score=53.08 Aligned_cols=40 Identities=10% Similarity=0.257 Sum_probs=27.2
Q ss_pred CcchhhhccChHHHHhhHHHHhCCCceecccccccCCChHHH
Q psy4084 1 MSECMGKFTEYQVIRKHIRTFHSDRQFACHMCIKVFPSQDKL 42 (86)
Q Consensus 1 c~~C~~~~~~~~~l~~h~~~~~~~~~~~c~~c~~~~~~~~~l 42 (86)
|+.||+.|...++|..|+++|+ +++.|..|++.|...+.|
T Consensus 8 C~~CGK~Fs~~~~L~~H~r~H~--k~~kc~~C~k~f~~~s~l 47 (55)
T PHA02768 8 CPICGEIYIKRKSMITHLRKHN--TNLKLSNCKRISLRTGEY 47 (55)
T ss_pred cchhCCeeccHHHHHHHHHhcC--CcccCCcccceeccccee
Confidence 6677777777777777777776 466777777766654443
No 14
>PHA02768 hypothetical protein; Provisional
Probab=99.20 E-value=1.8e-11 Score=50.87 Aligned_cols=38 Identities=11% Similarity=0.447 Sum_probs=18.3
Q ss_pred eecccccccCCChHHHhhhhhC-CcceecccccccccCH
Q psy4084 27 FACHMCIKVFPSQDKLRMHMLS-DRQFACHMCIKVFPSQ 64 (86)
Q Consensus 27 ~~c~~c~~~~~~~~~l~~h~~~-~~~~~C~~C~~~~~~~ 64 (86)
|+|+.||+.|...+.|..|++. .++++|..|++.|...
T Consensus 6 y~C~~CGK~Fs~~~~L~~H~r~H~k~~kc~~C~k~f~~~ 44 (55)
T PHA02768 6 YECPICGEIYIKRKSMITHLRKHNTNLKLSNCKRISLRT 44 (55)
T ss_pred cCcchhCCeeccHHHHHHHHHhcCCcccCCcccceeccc
Confidence 4455555555555555555544 2344555555544433
No 15
>PHA00616 hypothetical protein
Probab=99.16 E-value=1.5e-11 Score=48.87 Aligned_cols=34 Identities=21% Similarity=0.388 Sum_probs=31.5
Q ss_pred ceecccccccccCHHHHHHHHHhCCCCccCCCCc
Q psy4084 51 QFACHMCIKVFPSQDKLRMHMLSGLQTFDLKSKL 84 (86)
Q Consensus 51 ~~~C~~C~~~~~~~~~l~~h~~~~~~~~~~~c~~ 84 (86)
||+|+.||+.|.....|..|+++|+++.++.|+.
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~~hg~~~~~~~~ 34 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLSVHKQNKLTLEY 34 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHHhcCCCccceeE
Confidence 6899999999999999999999999999998763
No 16
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=99.14 E-value=4.9e-11 Score=42.85 Aligned_cols=25 Identities=32% Similarity=0.805 Sum_probs=22.8
Q ss_pred HHHhhHHHHhCCCceecccccccCC
Q psy4084 13 VIRKHIRTFHSDRQFACHMCIKVFP 37 (86)
Q Consensus 13 ~l~~h~~~~~~~~~~~c~~c~~~~~ 37 (86)
+|..|+++|++++||.|+.|++.|.
T Consensus 1 ~l~~H~~~H~~~k~~~C~~C~k~F~ 25 (26)
T PF13465_consen 1 NLRRHMRTHTGEKPYKCPYCGKSFS 25 (26)
T ss_dssp HHHHHHHHHSSSSSEEESSSSEEES
T ss_pred CHHHHhhhcCCCCCCCCCCCcCeeC
Confidence 4889999999999999999998875
No 17
>PHA00733 hypothetical protein
Probab=99.00 E-value=4.7e-10 Score=54.75 Aligned_cols=74 Identities=12% Similarity=0.257 Sum_probs=54.8
Q ss_pred hHHHHhhHHHHhCCCceecccccccCCChHHHhhh------hhC--CcceecccccccccCHHHHHHHHHhCCCCccCCC
Q psy4084 11 YQVIRKHIRTFHSDRQFACHMCIKVFPSQDKLRMH------MLS--DRQFACHMCIKVFPSQDKLRMHMLSGLQTFDLKS 82 (86)
Q Consensus 11 ~~~l~~h~~~~~~~~~~~c~~c~~~~~~~~~l~~h------~~~--~~~~~C~~C~~~~~~~~~l~~h~~~~~~~~~~~c 82 (86)
.+.|.++-......+++.|.+|...+.....|..+ +.. .+||.|+.|++.|.....|..|++.+ +.++.|
T Consensus 25 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~l~~~~~~~~~kPy~C~~Cgk~Fss~s~L~~H~r~h--~~~~~C 102 (128)
T PHA00733 25 LEELKRYHSLTPEQKRLIRAVVKTLIYNPQLLDESSYLYKLLTSKAVSPYVCPLCLMPFSSSVSLKQHIRYT--EHSKVC 102 (128)
T ss_pred HHHhhhhhcCChhhhhHHHHHHhhhccChhhhcchHHHHhhcccCCCCCccCCCCCCcCCCHHHHHHHHhcC--CcCccC
Confidence 34444443434456788999998877776655544 222 67999999999999999999999976 356899
Q ss_pred CcCC
Q psy4084 83 KLCT 86 (86)
Q Consensus 83 ~~C~ 86 (86)
..|+
T Consensus 103 ~~Cg 106 (128)
T PHA00733 103 PVCG 106 (128)
T ss_pred CCCC
Confidence 9885
No 18
>PLN03086 PRLI-interacting factor K; Provisional
Probab=98.87 E-value=2.2e-09 Score=63.01 Aligned_cols=60 Identities=20% Similarity=0.458 Sum_probs=51.0
Q ss_pred CCceecccccccCCChHHHhhhhhC-CcceecccccccccCHHHHHHHHHhCCCCccCCCCcCC
Q psy4084 24 DRQFACHMCIKVFPSQDKLRMHMLS-DRQFACHMCIKVFPSQDKLRMHMLSGLQTFDLKSKLCT 86 (86)
Q Consensus 24 ~~~~~c~~c~~~~~~~~~l~~h~~~-~~~~~C~~C~~~~~~~~~l~~h~~~~~~~~~~~c~~C~ 86 (86)
++.+.|+.|++.|. ...+..|+.. .+++.|+ ||..+ ....|..|+.+|...+++.|.+|+
T Consensus 451 ~~H~~C~~Cgk~f~-~s~LekH~~~~Hkpv~Cp-Cg~~~-~R~~L~~H~~thCp~Kpi~C~fC~ 511 (567)
T PLN03086 451 KNHVHCEKCGQAFQ-QGEMEKHMKVFHEPLQCP-CGVVL-EKEQMVQHQASTCPLRLITCRFCG 511 (567)
T ss_pred ccCccCCCCCCccc-hHHHHHHHHhcCCCccCC-CCCCc-chhHHHhhhhccCCCCceeCCCCC
Confidence 34568999999986 5778899886 6889999 99755 668999999999999999999995
No 19
>PHA00616 hypothetical protein
Probab=98.83 E-value=2.8e-09 Score=42.39 Aligned_cols=32 Identities=16% Similarity=0.364 Sum_probs=29.0
Q ss_pred CcchhhhccChHHHHhhHHHHhCCCceecccc
Q psy4084 1 MSECMGKFTEYQVIRKHIRTFHSDRQFACHMC 32 (86)
Q Consensus 1 c~~C~~~~~~~~~l~~h~~~~~~~~~~~c~~c 32 (86)
|+.||+.|..++.|..|++.|++++++.+..-
T Consensus 4 C~~CG~~F~~~s~l~~H~r~~hg~~~~~~~~~ 35 (44)
T PHA00616 4 CLRCGGIFRKKKEVIEHLLSVHKQNKLTLEYF 35 (44)
T ss_pred cchhhHHHhhHHHHHHHHHHhcCCCccceeEE
Confidence 78999999999999999999999999887653
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=98.82 E-value=2e-09 Score=38.60 Aligned_cols=21 Identities=29% Similarity=0.362 Sum_probs=19.4
Q ss_pred HHHHHHHhCCCCccCCCCcCC
Q psy4084 66 KLRMHMLSGLQTFDLKSKLCT 86 (86)
Q Consensus 66 ~l~~h~~~~~~~~~~~c~~C~ 86 (86)
+|..|+++|+++++|.|+.|+
T Consensus 1 ~l~~H~~~H~~~k~~~C~~C~ 21 (26)
T PF13465_consen 1 NLRRHMRTHTGEKPYKCPYCG 21 (26)
T ss_dssp HHHHHHHHHSSSSSEEESSSS
T ss_pred CHHHHhhhcCCCCCCCCCCCc
Confidence 588999999999999999996
No 21
>PHA00732 hypothetical protein
Probab=98.81 E-value=4.6e-09 Score=47.22 Aligned_cols=42 Identities=21% Similarity=0.393 Sum_probs=24.8
Q ss_pred CcchhhhccChHHHHhhHHH-HhCCCceecccccccCCChHHHhhhhhC
Q psy4084 1 MSECMGKFTEYQVIRKHIRT-FHSDRQFACHMCIKVFPSQDKLRMHMLS 48 (86)
Q Consensus 1 c~~C~~~~~~~~~l~~h~~~-~~~~~~~~c~~c~~~~~~~~~l~~h~~~ 48 (86)
|..||+.|.+...|..|++. |.+ +.|+.|++.|. .+..|+.+
T Consensus 4 C~~Cgk~F~s~s~Lk~H~r~~H~~---~~C~~CgKsF~---~l~~H~~~ 46 (79)
T PHA00732 4 CPICGFTTVTLFALKQHARRNHTL---TKCPVCNKSYR---RLNQHFYS 46 (79)
T ss_pred CCCCCCccCCHHHHHHHhhcccCC---CccCCCCCEeC---Chhhhhcc
Confidence 56667777777777777663 432 35666666665 24455543
No 22
>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=98.65 E-value=2.1e-08 Score=34.80 Aligned_cols=23 Identities=35% Similarity=0.735 Sum_probs=19.8
Q ss_pred eecccccccccCHHHHHHHHHhC
Q psy4084 52 FACHMCIKVFPSQDKLRMHMLSG 74 (86)
Q Consensus 52 ~~C~~C~~~~~~~~~l~~h~~~~ 74 (86)
|.|+.|++.|.....|..|++.|
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 67899999999999999998763
No 23
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=98.54 E-value=9.9e-08 Score=44.49 Aligned_cols=70 Identities=23% Similarity=0.334 Sum_probs=21.9
Q ss_pred CcchhhhccChHHHHhhHHHHhCCCceecccccccCCChHHHhhhhhC--CcceecccccccccCHHHHHHHHHhC
Q psy4084 1 MSECMGKFTEYQVIRKHIRTFHSDRQFACHMCIKVFPSQDKLRMHMLS--DRQFACHMCIKVFPSQDKLRMHMLSG 74 (86)
Q Consensus 1 c~~C~~~~~~~~~l~~h~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~--~~~~~C~~C~~~~~~~~~l~~h~~~~ 74 (86)
|..|+..|.+...|..|+...++-..-.. ..+.....+...... ...+.|..|+..|.+...|..||+.+
T Consensus 2 C~~C~~~f~~~~~l~~H~~~~H~~~~~~~----~~l~~~~~~~~~~~~~~~~~~~C~~C~~~f~s~~~l~~Hm~~~ 73 (100)
T PF12756_consen 2 CLFCDESFSSVDDLLQHMKKKHGFDIPDQ----KYLVDPNRLLNYLRKKVKESFRCPYCNKTFRSREALQEHMRSK 73 (100)
T ss_dssp ---------------------------------------------------SSEEBSSSS-EESSHHHHHHHHHHT
T ss_pred ccccccccccccccccccccccccccccc----cccccccccccccccccCCCCCCCccCCCCcCHHHHHHHHcCc
Confidence 78899999999999999987665432111 111122222223222 34689999999999999999999974
No 24
>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=98.52 E-value=1.1e-07 Score=34.20 Aligned_cols=26 Identities=38% Similarity=0.560 Sum_probs=22.9
Q ss_pred ceecccccccccCHHHHHHHHHhCCC
Q psy4084 51 QFACHMCIKVFPSQDKLRMHMLSGLQ 76 (86)
Q Consensus 51 ~~~C~~C~~~~~~~~~l~~h~~~~~~ 76 (86)
||.|..|++.|.+...|..|++.|.+
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 57899999999999999999988754
No 25
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=98.50 E-value=2.4e-07 Score=38.80 Aligned_cols=47 Identities=28% Similarity=0.441 Sum_probs=30.6
Q ss_pred ceecccccccCCChHHHhhhhhC-----CcceecccccccccCHHHHHHHHHhCC
Q psy4084 26 QFACHMCIKVFPSQDKLRMHMLS-----DRQFACHMCIKVFPSQDKLRMHMLSGL 75 (86)
Q Consensus 26 ~~~c~~c~~~~~~~~~l~~h~~~-----~~~~~C~~C~~~~~~~~~l~~h~~~~~ 75 (86)
.|.|+.|++ ......|..|... .+.+.|+.|...+. .+|..|+..++
T Consensus 2 ~f~CP~C~~-~~~~~~L~~H~~~~H~~~~~~v~CPiC~~~~~--~~l~~Hl~~~H 53 (54)
T PF05605_consen 2 SFTCPYCGK-GFSESSLVEHCEDEHRSESKNVVCPICSSRVT--DNLIRHLNSQH 53 (54)
T ss_pred CcCCCCCCC-ccCHHHHHHHHHhHCcCCCCCccCCCchhhhh--hHHHHHHHHhc
Confidence 367777777 4445667777654 34577888876533 47788887654
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=98.47 E-value=1.5e-07 Score=32.66 Aligned_cols=24 Identities=42% Similarity=0.755 Sum_probs=19.0
Q ss_pred eecccccccccCHHHHHHHHHhCC
Q psy4084 52 FACHMCIKVFPSQDKLRMHMLSGL 75 (86)
Q Consensus 52 ~~C~~C~~~~~~~~~l~~h~~~~~ 75 (86)
|.|+.|++.|.+...|..|+.+++
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 679999999999999999998753
No 27
>PHA00732 hypothetical protein
Probab=98.47 E-value=2.3e-07 Score=41.77 Aligned_cols=47 Identities=23% Similarity=0.424 Sum_probs=39.7
Q ss_pred ceecccccccCCChHHHhhhhhC-CcceecccccccccCHHHHHHHHHhCC
Q psy4084 26 QFACHMCIKVFPSQDKLRMHMLS-DRQFACHMCIKVFPSQDKLRMHMLSGL 75 (86)
Q Consensus 26 ~~~c~~c~~~~~~~~~l~~h~~~-~~~~~C~~C~~~~~~~~~l~~h~~~~~ 75 (86)
||.|..|++.|.....|..|+.. ..++.|+.|++.|. .+..|++++.
T Consensus 1 py~C~~Cgk~F~s~s~Lk~H~r~~H~~~~C~~CgKsF~---~l~~H~~~~~ 48 (79)
T PHA00732 1 MFKCPICGFTTVTLFALKQHARRNHTLTKCPVCNKSYR---RLNQHFYSQY 48 (79)
T ss_pred CccCCCCCCccCCHHHHHHHhhcccCCCccCCCCCEeC---ChhhhhcccC
Confidence 57899999999999999999974 56779999999998 4778886653
No 28
>KOG3993|consensus
Probab=98.40 E-value=9.5e-08 Score=54.29 Aligned_cols=76 Identities=28% Similarity=0.441 Sum_probs=54.8
Q ss_pred CcchhhhccChHHHHhhHHHHhCCCceecccccccCCChHHHhhhhhC--------------------------------
Q psy4084 1 MSECMGKFTEYQVIRKHIRTFHSDRQFACHMCIKVFPSQDKLRMHMLS-------------------------------- 48 (86)
Q Consensus 1 c~~C~~~~~~~~~l~~h~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~-------------------------------- 48 (86)
|..|...|.....|-.|.-.-.-..-|.|+.|+++|.-..+|..|.+=
T Consensus 270 CqLCK~kYeD~F~LAQHrC~RIV~vEYrCPEC~KVFsCPANLASHRRWHKPR~eaa~a~~~P~k~~~~~rae~~ea~rsg 349 (500)
T KOG3993|consen 270 CQLCKEKYEDAFALAQHRCPRIVHVEYRCPECDKVFSCPANLASHRRWHKPRPEAAKAGSPPPKQAVETRAEVQEAERSG 349 (500)
T ss_pred HHHHHHhhhhHHHHhhccCCeeEEeeecCCcccccccCchhhhhhhcccCCchhhhhcCCCChhhhhhhhhhhhhccccC
Confidence 345666666666666664433333448888888888888888777630
Q ss_pred ----CcceecccccccccCHHHHHHHHHhCCC
Q psy4084 49 ----DRQFACHMCIKVFPSQDKLRMHMLSGLQ 76 (86)
Q Consensus 49 ----~~~~~C~~C~~~~~~~~~l~~h~~~~~~ 76 (86)
+-.|.|..|++.|.+...|+.|..+|+.
T Consensus 350 ~dss~gi~~C~~C~KkFrRqAYLrKHqlthq~ 381 (500)
T KOG3993|consen 350 DDSSSGIFSCHTCGKKFRRQAYLRKHQLTHQR 381 (500)
T ss_pred CcccCceeecHHhhhhhHHHHHHHHhHHhhhc
Confidence 1238899999999999999999888753
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=98.36 E-value=2.9e-07 Score=31.80 Aligned_cols=21 Identities=19% Similarity=0.469 Sum_probs=18.2
Q ss_pred CcchhhhccChHHHHhhHHHH
Q psy4084 1 MSECMGKFTEYQVIRKHIRTF 21 (86)
Q Consensus 1 c~~C~~~~~~~~~l~~h~~~~ 21 (86)
|+.|++.|.....|..|++.|
T Consensus 3 C~~C~~~f~~~~~l~~H~~~H 23 (23)
T PF00096_consen 3 CPICGKSFSSKSNLKRHMRRH 23 (23)
T ss_dssp ETTTTEEESSHHHHHHHHHHH
T ss_pred CCCCCCccCCHHHHHHHHhHC
Confidence 688999999999999998864
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=98.33 E-value=4.1e-07 Score=37.10 Aligned_cols=35 Identities=20% Similarity=0.266 Sum_probs=24.2
Q ss_pred hhhCCcceecccccccccCHHHHHHHHHhCCCCcc
Q psy4084 45 HMLSDRQFACHMCIKVFPSQDKLRMHMLSGLQTFD 79 (86)
Q Consensus 45 h~~~~~~~~C~~C~~~~~~~~~l~~h~~~~~~~~~ 79 (86)
++.++.|..|++|+..+....+|++|+...+..++
T Consensus 18 ~~~S~~PatCP~C~a~~~~srnLrRHle~~H~~k~ 52 (54)
T PF09237_consen 18 KSQSEQPATCPICGAVIRQSRNLRRHLEIRHFKKP 52 (54)
T ss_dssp CCTTS--EE-TTT--EESSHHHHHHHHHHHTTTS-
T ss_pred hhccCCCCCCCcchhhccchhhHHHHHHHHhcccC
Confidence 34447899999999999999999999988776654
No 31
>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=2.6e-06 Score=29.39 Aligned_cols=22 Identities=32% Similarity=0.570 Sum_probs=17.5
Q ss_pred CcchhhhccChHHHHhhHHHHh
Q psy4084 1 MSECMGKFTEYQVIRKHIRTFH 22 (86)
Q Consensus 1 c~~C~~~~~~~~~l~~h~~~~~ 22 (86)
|+.|+..|.+...|..|+.+++
T Consensus 3 C~~C~~~~~~~~~l~~H~~~~H 24 (24)
T PF13894_consen 3 CPICGKSFRSKSELRQHMRTHH 24 (24)
T ss_dssp -SSTS-EESSHHHHHHHHHHHS
T ss_pred CcCCCCcCCcHHHHHHHHHhhC
Confidence 7889999999999999988763
No 32
>smart00355 ZnF_C2H2 zinc finger.
Probab=97.97 E-value=1e-05 Score=28.27 Aligned_cols=24 Identities=38% Similarity=0.683 Sum_probs=20.2
Q ss_pred eecccccccccCHHHHHHHHHhCC
Q psy4084 52 FACHMCIKVFPSQDKLRMHMLSGL 75 (86)
Q Consensus 52 ~~C~~C~~~~~~~~~l~~h~~~~~ 75 (86)
+.|..|++.|.....|..|++.|.
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~~H~ 24 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMRTHX 24 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHHHhc
Confidence 468889999999999999988654
No 33
>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=97.92 E-value=2.2e-05 Score=32.88 Aligned_cols=35 Identities=23% Similarity=0.380 Sum_probs=27.4
Q ss_pred ceecccccccccCHHHHHHHHHhCC-C-CccCCCCcCC
Q psy4084 51 QFACHMCIKVFPSQDKLRMHMLSGL-Q-TFDLKSKLCT 86 (86)
Q Consensus 51 ~~~C~~C~~~~~~~~~l~~h~~~~~-~-~~~~~c~~C~ 86 (86)
.|.|++|++ ..+...|..|....+ . .+.+.|++|.
T Consensus 2 ~f~CP~C~~-~~~~~~L~~H~~~~H~~~~~~v~CPiC~ 38 (54)
T PF05605_consen 2 SFTCPYCGK-GFSESSLVEHCEDEHRSESKNVVCPICS 38 (54)
T ss_pred CcCCCCCCC-ccCHHHHHHHHHhHCcCCCCCccCCCch
Confidence 478999999 566788999988744 3 3568999984
No 34
>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=97.85 E-value=2.3e-05 Score=32.06 Aligned_cols=26 Identities=15% Similarity=0.326 Sum_probs=20.2
Q ss_pred CcchhhhccChHHHHhhHHHHhCCCc
Q psy4084 1 MSECMGKFTEYQVIRKHIRTFHSDRQ 26 (86)
Q Consensus 1 c~~C~~~~~~~~~l~~h~~~~~~~~~ 26 (86)
|++|+..+.+..+|++|+...++.+|
T Consensus 27 CP~C~a~~~~srnLrRHle~~H~~k~ 52 (54)
T PF09237_consen 27 CPICGAVIRQSRNLRRHLEIRHFKKP 52 (54)
T ss_dssp -TTT--EESSHHHHHHHHHHHTTTS-
T ss_pred CCcchhhccchhhHHHHHHHHhcccC
Confidence 88999999999999999998888765
No 35
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=97.81 E-value=5e-06 Score=46.14 Aligned_cols=48 Identities=29% Similarity=0.758 Sum_probs=36.4
Q ss_pred CCceeccc--ccccCCChHHHhhhhhC----------------------CcceecccccccccCHHHHHHHH
Q psy4084 24 DRQFACHM--CIKVFPSQDKLRMHMLS----------------------DRQFACHMCIKVFPSQDKLRMHM 71 (86)
Q Consensus 24 ~~~~~c~~--c~~~~~~~~~l~~h~~~----------------------~~~~~C~~C~~~~~~~~~l~~h~ 71 (86)
++||.|++ |.+.+.....|.-|+.. .+||.|++|++.+.....|.-|+
T Consensus 347 ~KpykCpV~gC~K~YknqnGLKYH~lhGH~~~~~~~~p~p~~~~~F~~~~KPYrCevC~KRYKNlNGLKYHr 418 (423)
T COG5189 347 GKPYKCPVEGCNKKYKNQNGLKYHMLHGHQNQKLHENPSPEKMNIFSAKDKPYRCEVCDKRYKNLNGLKYHR 418 (423)
T ss_pred CceecCCCCCchhhhccccchhhhhhccccCcccCCCCCccccccccccCCceeccccchhhccCccceecc
Confidence 47888886 88888888888777642 47888888888887777776554
No 36
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=97.78 E-value=8.6e-06 Score=29.11 Aligned_cols=22 Identities=27% Similarity=0.555 Sum_probs=18.4
Q ss_pred CcchhhhccChHHHHhhHHHHh
Q psy4084 1 MSECMGKFTEYQVIRKHIRTFH 22 (86)
Q Consensus 1 c~~C~~~~~~~~~l~~h~~~~~ 22 (86)
|..|++.|.+...|..|++.|.
T Consensus 4 C~~C~~~F~~~~~l~~H~~~h~ 25 (27)
T PF13912_consen 4 CDECGKTFSSLSALREHKRSHC 25 (27)
T ss_dssp ETTTTEEESSHHHHHHHHCTTT
T ss_pred CCccCCccCChhHHHHHhHHhc
Confidence 6788999999999999887764
No 37
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=97.77 E-value=2e-05 Score=27.60 Aligned_cols=23 Identities=43% Similarity=0.856 Sum_probs=18.6
Q ss_pred eecccccccccCHHHHHHHHHhC
Q psy4084 52 FACHMCIKVFPSQDKLRMHMLSG 74 (86)
Q Consensus 52 ~~C~~C~~~~~~~~~l~~h~~~~ 74 (86)
|.|..|+..|.+...+..|++.+
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 56888888888888888888753
No 38
>smart00355 ZnF_C2H2 zinc finger.
Probab=97.69 E-value=4.9e-05 Score=26.40 Aligned_cols=22 Identities=27% Similarity=0.535 Sum_probs=18.8
Q ss_pred CcchhhhccChHHHHhhHHHHh
Q psy4084 1 MSECMGKFTEYQVIRKHIRTFH 22 (86)
Q Consensus 1 c~~C~~~~~~~~~l~~h~~~~~ 22 (86)
|+.|++.|.....|..|++.|.
T Consensus 3 C~~C~~~f~~~~~l~~H~~~H~ 24 (26)
T smart00355 3 CPECGKVFKSKSALKEHMRTHX 24 (26)
T ss_pred CCCCcchhCCHHHHHHHHHHhc
Confidence 7789999999999999988654
No 39
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=97.65 E-value=3.4e-05 Score=26.77 Aligned_cols=23 Identities=17% Similarity=0.430 Sum_probs=17.6
Q ss_pred eecccccccccCHHHHHHHHHhCC
Q psy4084 52 FACHMCIKVFPSQDKLRMHMLSGL 75 (86)
Q Consensus 52 ~~C~~C~~~~~~~~~l~~h~~~~~ 75 (86)
|+|+.|+.... ...|..|++.++
T Consensus 1 y~C~~C~y~t~-~~~l~~H~~~~H 23 (24)
T PF13909_consen 1 YKCPHCSYSTS-KSNLKRHLKRHH 23 (24)
T ss_dssp EE-SSSS-EES-HHHHHHHHHHHH
T ss_pred CCCCCCCCcCC-HHHHHHHHHhhC
Confidence 67999999887 889999998753
No 40
>PRK04860 hypothetical protein; Provisional
Probab=97.44 E-value=0.00012 Score=37.36 Aligned_cols=32 Identities=19% Similarity=0.346 Sum_probs=28.2
Q ss_pred ceecccccccccCHHHHHHHHHhCCCCccCCCCcCC
Q psy4084 51 QFACHMCIKVFPSQDKLRMHMLSGLQTFDLKSKLCT 86 (86)
Q Consensus 51 ~~~C~~C~~~~~~~~~l~~h~~~~~~~~~~~c~~C~ 86 (86)
+|.|. |+. ....+.+|.++|.++++|.|..|+
T Consensus 119 ~Y~C~-C~~---~~~~~rrH~ri~~g~~~YrC~~C~ 150 (160)
T PRK04860 119 PYRCK-CQE---HQLTVRRHNRVVRGEAVYRCRRCG 150 (160)
T ss_pred EEEcC-CCC---eeCHHHHHHHHhcCCccEECCCCC
Confidence 68998 987 677789999999999999999985
No 41
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=97.37 E-value=8.8e-05 Score=25.87 Aligned_cols=21 Identities=24% Similarity=0.502 Sum_probs=16.7
Q ss_pred CcchhhhccChHHHHhhHHHH
Q psy4084 1 MSECMGKFTEYQVIRKHIRTF 21 (86)
Q Consensus 1 c~~C~~~~~~~~~l~~h~~~~ 21 (86)
|..|+..|.+...+..|++.+
T Consensus 3 C~~C~~~f~s~~~~~~H~~s~ 23 (25)
T PF12874_consen 3 CDICNKSFSSENSLRQHLRSK 23 (25)
T ss_dssp ETTTTEEESSHHHHHHHHTTH
T ss_pred CCCCCCCcCCHHHHHHHHCcC
Confidence 677888888888888887754
No 42
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=97.23 E-value=0.0004 Score=24.42 Aligned_cols=20 Identities=30% Similarity=0.688 Sum_probs=14.6
Q ss_pred eecccccccccCHHHHHHHHH
Q psy4084 52 FACHMCIKVFPSQDKLRMHML 72 (86)
Q Consensus 52 ~~C~~C~~~~~~~~~l~~h~~ 72 (86)
.+|+.||+.| ..+.|..|++
T Consensus 3 ~~C~~CgR~F-~~~~l~~H~~ 22 (25)
T PF13913_consen 3 VPCPICGRKF-NPDRLEKHEK 22 (25)
T ss_pred CcCCCCCCEE-CHHHHHHHHH
Confidence 4688888888 5666777765
No 43
>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=97.22 E-value=8.3e-05 Score=26.56 Aligned_cols=22 Identities=45% Similarity=0.862 Sum_probs=15.2
Q ss_pred eecccccccccCHHHHHHHHHh
Q psy4084 52 FACHMCIKVFPSQDKLRMHMLS 73 (86)
Q Consensus 52 ~~C~~C~~~~~~~~~l~~h~~~ 73 (86)
|.|..|++.|.+...+..|+++
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 4577777777777777666654
No 44
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=97.17 E-value=0.00024 Score=39.83 Aligned_cols=38 Identities=26% Similarity=0.697 Sum_probs=31.9
Q ss_pred Ccceeccc--ccccccCHHHHHHHHHhC-------------------CCCccCCCCcCC
Q psy4084 49 DRQFACHM--CIKVFPSQDKLRMHMLSG-------------------LQTFDLKSKLCT 86 (86)
Q Consensus 49 ~~~~~C~~--C~~~~~~~~~l~~h~~~~-------------------~~~~~~~c~~C~ 86 (86)
++||+|++ |.+.+..+..|.-|+.-. .+++||.|+.|+
T Consensus 347 ~KpykCpV~gC~K~YknqnGLKYH~lhGH~~~~~~~~p~p~~~~~F~~~~KPYrCevC~ 405 (423)
T COG5189 347 GKPYKCPVEGCNKKYKNQNGLKYHMLHGHQNQKLHENPSPEKMNIFSAKDKPYRCEVCD 405 (423)
T ss_pred CceecCCCCCchhhhccccchhhhhhccccCcccCCCCCccccccccccCCceeccccc
Confidence 59999987 999999999999998632 256899999985
No 45
>PRK04860 hypothetical protein; Provisional
Probab=97.01 E-value=0.00035 Score=35.64 Aligned_cols=35 Identities=20% Similarity=0.513 Sum_probs=23.3
Q ss_pred ceecccccccCCChHHHhhhhhC---CcceecccccccccCH
Q psy4084 26 QFACHMCIKVFPSQDKLRMHMLS---DRQFACHMCIKVFPSQ 64 (86)
Q Consensus 26 ~~~c~~c~~~~~~~~~l~~h~~~---~~~~~C~~C~~~~~~~ 64 (86)
+|.|. |+. ...++.+|.+. +++|.|..|+..+...
T Consensus 119 ~Y~C~-C~~---~~~~~rrH~ri~~g~~~YrC~~C~~~l~~~ 156 (160)
T PRK04860 119 PYRCK-CQE---HQLTVRRHNRVVRGEAVYRCRRCGETLVFK 156 (160)
T ss_pred EEEcC-CCC---eeCHHHHHHHHhcCCccEECCCCCceeEEe
Confidence 57887 776 44455566543 5778888888876543
No 46
>KOG3993|consensus
Probab=96.96 E-value=0.00022 Score=41.30 Aligned_cols=49 Identities=22% Similarity=0.475 Sum_probs=41.9
Q ss_pred ceecccccccCCChHHHhhhhhC---CcceecccccccccCHHHHHHHHHhC
Q psy4084 26 QFACHMCIKVFPSQDKLRMHMLS---DRQFACHMCIKVFPSQDKLRMHMLSG 74 (86)
Q Consensus 26 ~~~c~~c~~~~~~~~~l~~h~~~---~~~~~C~~C~~~~~~~~~l~~h~~~~ 74 (86)
.|.|..|...|...=.|..|.-. ...|.|++|++.|.-..+|..|.+=|
T Consensus 267 dyiCqLCK~kYeD~F~LAQHrC~RIV~vEYrCPEC~KVFsCPANLASHRRWH 318 (500)
T KOG3993|consen 267 DYICQLCKEKYEDAFALAQHRCPRIVHVEYRCPECDKVFSCPANLASHRRWH 318 (500)
T ss_pred HHHHHHHHHhhhhHHHHhhccCCeeEEeeecCCcccccccCchhhhhhhccc
Confidence 48899998888888888888654 45799999999999999999999865
No 47
>smart00451 ZnF_U1 U1-like zinc finger. Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins.
Probab=96.52 E-value=0.0034 Score=23.52 Aligned_cols=23 Identities=22% Similarity=0.579 Sum_probs=18.1
Q ss_pred ceecccccccccCHHHHHHHHHh
Q psy4084 51 QFACHMCIKVFPSQDKLRMHMLS 73 (86)
Q Consensus 51 ~~~C~~C~~~~~~~~~l~~h~~~ 73 (86)
+|.|..|+..|.....+..|+..
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~g 25 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLKG 25 (35)
T ss_pred CeEccccCCccCCHHHHHHHHCh
Confidence 46788888888888888888764
No 48
>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=96.18 E-value=0.0041 Score=23.27 Aligned_cols=24 Identities=17% Similarity=0.776 Sum_probs=14.2
Q ss_pred eecccccccCCChHHHhhhhhCCcceecccccc
Q psy4084 27 FACHMCIKVFPSQDKLRMHMLSDRQFACHMCIK 59 (86)
Q Consensus 27 ~~c~~c~~~~~~~~~l~~h~~~~~~~~C~~C~~ 59 (86)
|+|..||..+... ..++.|+.||.
T Consensus 2 ~~C~~CGy~y~~~---------~~~~~CP~Cg~ 25 (33)
T cd00350 2 YVCPVCGYIYDGE---------EAPWVCPVCGA 25 (33)
T ss_pred EECCCCCCEECCC---------cCCCcCcCCCC
Confidence 5677777554332 24667777764
No 49
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=95.20 E-value=0.016 Score=26.81 Aligned_cols=21 Identities=19% Similarity=0.461 Sum_probs=17.3
Q ss_pred CcchhhhccChHHHHhhHHHH
Q psy4084 1 MSECMGKFTEYQVIRKHIRTF 21 (86)
Q Consensus 1 c~~C~~~~~~~~~l~~h~~~~ 21 (86)
|..|++.|.+...|..|++.+
T Consensus 53 C~~C~~~f~s~~~l~~Hm~~~ 73 (100)
T PF12756_consen 53 CPYCNKTFRSREALQEHMRSK 73 (100)
T ss_dssp BSSSS-EESSHHHHHHHHHHT
T ss_pred CCccCCCCcCHHHHHHHHcCc
Confidence 778999999999999999864
No 50
>KOG1146|consensus
Probab=94.97 E-value=0.014 Score=38.64 Aligned_cols=25 Identities=20% Similarity=0.557 Sum_probs=21.7
Q ss_pred CcceecccccccccCHHHHHHHHHh
Q psy4084 49 DRQFACHMCIKVFPSQDKLRMHMLS 73 (86)
Q Consensus 49 ~~~~~C~~C~~~~~~~~~l~~h~~~ 73 (86)
.++|.|..|...+....+|.+|+..
T Consensus 516 ~~p~~C~~C~~stttng~LsihlqS 540 (1406)
T KOG1146|consen 516 GKPYPCRACNYSTTTNGNLSIHLQS 540 (1406)
T ss_pred CCcccceeeeeeeecchHHHHHHHH
Confidence 3688999999999999999999875
No 51
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=94.82 E-value=0.03 Score=28.93 Aligned_cols=11 Identities=9% Similarity=0.126 Sum_probs=5.5
Q ss_pred CCccCCCCcCC
Q psy4084 76 QTFDLKSKLCT 86 (86)
Q Consensus 76 ~~~~~~c~~C~ 86 (86)
++.|..|++|+
T Consensus 146 ge~P~~CPiCg 156 (166)
T COG1592 146 GEAPEVCPICG 156 (166)
T ss_pred CCCCCcCCCCC
Confidence 34555555553
No 52
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=94.38 E-value=0.058 Score=20.58 Aligned_cols=33 Identities=24% Similarity=0.533 Sum_probs=21.4
Q ss_pred eecccccccCCChHHHhhhhhCCcceecccccccc
Q psy4084 27 FACHMCIKVFPSQDKLRMHMLSDRQFACHMCIKVF 61 (86)
Q Consensus 27 ~~c~~c~~~~~~~~~l~~h~~~~~~~~C~~C~~~~ 61 (86)
..|+.|...|........- .....+|+.|+..|
T Consensus 3 i~Cp~C~~~y~i~d~~ip~--~g~~v~C~~C~~~f 35 (36)
T PF13717_consen 3 ITCPNCQAKYEIDDEKIPP--KGRKVRCSKCGHVF 35 (36)
T ss_pred EECCCCCCEEeCCHHHCCC--CCcEEECCCCCCEe
Confidence 4688888777766654321 13457888888766
No 53
>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=94.28 E-value=0.026 Score=27.09 Aligned_cols=30 Identities=23% Similarity=0.537 Sum_probs=18.5
Q ss_pred eecccccccCCChHHHhhhhhCCcceecccccccccCH
Q psy4084 27 FACHMCIKVFPSQDKLRMHMLSDRQFACHMCIKVFPSQ 64 (86)
Q Consensus 27 ~~c~~c~~~~~~~~~l~~h~~~~~~~~C~~C~~~~~~~ 64 (86)
..|+.||..|.-.. ..|..|+.||..|.-.
T Consensus 10 R~Cp~CG~kFYDLn--------k~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 10 RTCPSCGAKFYDLN--------KDPIVCPKCGTEFPPE 39 (108)
T ss_pred ccCCCCcchhccCC--------CCCccCCCCCCccCcc
Confidence 36777776665432 3466777777776544
No 54
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=93.97 E-value=0.078 Score=22.60 Aligned_cols=10 Identities=20% Similarity=0.690 Sum_probs=5.0
Q ss_pred Ccceeccccc
Q psy4084 49 DRQFACHMCI 58 (86)
Q Consensus 49 ~~~~~C~~C~ 58 (86)
..+|.|+.||
T Consensus 48 g~~Y~Cp~CG 57 (61)
T COG2888 48 GNPYRCPKCG 57 (61)
T ss_pred CCceECCCcC
Confidence 3455555554
No 55
>KOG2893|consensus
Probab=93.85 E-value=0.01 Score=32.37 Aligned_cols=41 Identities=32% Similarity=0.661 Sum_probs=31.7
Q ss_pred cccccccCCChHHHhhhhhCCcceecccccccccCHHHHHHH
Q psy4084 29 CHMCIKVFPSQDKLRMHMLSDRQFACHMCIKVFPSQDKLRMH 70 (86)
Q Consensus 29 c~~c~~~~~~~~~l~~h~~~~~~~~C~~C~~~~~~~~~l~~h 70 (86)
|..|++.|..-..|..|++ .+.|+|-+|-+...+...|..|
T Consensus 13 cwycnrefddekiliqhqk-akhfkchichkkl~sgpglsih 53 (341)
T KOG2893|consen 13 CWYCNREFDDEKILIQHQK-AKHFKCHICHKKLFSGPGLSIH 53 (341)
T ss_pred eeecccccchhhhhhhhhh-hccceeeeehhhhccCCCceee
Confidence 6778888888888888877 4678888887776666666665
No 56
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=93.75 E-value=0.084 Score=20.23 Aligned_cols=34 Identities=26% Similarity=0.511 Sum_probs=21.2
Q ss_pred eecccccccCCChHHHhhhhhCCcceeccccccccc
Q psy4084 27 FACHMCIKVFPSQDKLRMHMLSDRQFACHMCIKVFP 62 (86)
Q Consensus 27 ~~c~~c~~~~~~~~~l~~h~~~~~~~~C~~C~~~~~ 62 (86)
..|+.|+..|.....-.. .......|+.|+..|.
T Consensus 3 i~CP~C~~~f~v~~~~l~--~~~~~vrC~~C~~~f~ 36 (37)
T PF13719_consen 3 ITCPNCQTRFRVPDDKLP--AGGRKVRCPKCGHVFR 36 (37)
T ss_pred EECCCCCceEEcCHHHcc--cCCcEEECCCCCcEee
Confidence 467888877776654221 1144678888887663
No 57
>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=93.69 E-value=0.049 Score=20.82 Aligned_cols=34 Identities=21% Similarity=0.353 Sum_probs=19.6
Q ss_pred eecccccccCCChHHHhhhhhCCcceeccccccccc
Q psy4084 27 FACHMCIKVFPSQDKLRMHMLSDRQFACHMCIKVFP 62 (86)
Q Consensus 27 ~~c~~c~~~~~~~~~l~~h~~~~~~~~C~~C~~~~~ 62 (86)
+.|+.|+..|.......... ...+.|+.|+..|.
T Consensus 3 ~~CP~C~~~~~v~~~~~~~~--~~~v~C~~C~~~~~ 36 (38)
T TIGR02098 3 IQCPNCKTSFRVVDSQLGAN--GGKVRCGKCGHVWY 36 (38)
T ss_pred EECCCCCCEEEeCHHHcCCC--CCEEECCCCCCEEE
Confidence 56777877766554432211 22467888877653
No 58
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=93.65 E-value=0.033 Score=23.39 Aligned_cols=23 Identities=22% Similarity=0.371 Sum_probs=12.9
Q ss_pred ceecccccccccCHHHHHHHHHh
Q psy4084 51 QFACHMCIKVFPSQDKLRMHMLS 73 (86)
Q Consensus 51 ~~~C~~C~~~~~~~~~l~~h~~~ 73 (86)
-+.|+.|+..|.......+|...
T Consensus 17 ~lrCPRC~~~FR~~K~Y~RHVNK 39 (65)
T COG4049 17 FLRCPRCGMVFRRRKDYIRHVNK 39 (65)
T ss_pred eeeCCchhHHHHHhHHHHHHhhH
Confidence 34566666666655555555543
No 59
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=93.60 E-value=0.025 Score=30.42 Aligned_cols=40 Identities=15% Similarity=0.317 Sum_probs=25.6
Q ss_pred CceecccccccCCChHHHhhhhhC-------------C-----cceecccccccccCH
Q psy4084 25 RQFACHMCIKVFPSQDKLRMHMLS-------------D-----RQFACHMCIKVFPSQ 64 (86)
Q Consensus 25 ~~~~c~~c~~~~~~~~~l~~h~~~-------------~-----~~~~C~~C~~~~~~~ 64 (86)
+...|+.|++.|..........+. . ..+.|+.||.++...
T Consensus 4 k~~~CPvC~~~F~~~~vrs~~~r~~~~d~D~~~~Y~~vnP~~Y~V~vCP~CgyA~~~~ 61 (214)
T PF09986_consen 4 KKITCPVCGKEFKTKKVRSGKIRVIRRDSDFCPRYKGVNPLFYEVWVCPHCGYAAFEE 61 (214)
T ss_pred CceECCCCCCeeeeeEEEcCCceEeeecCCCccccCCCCCeeeeEEECCCCCCccccc
Confidence 456788888888766544433321 1 235799999987643
No 60
>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=93.55 E-value=0.045 Score=19.35 Aligned_cols=10 Identities=30% Similarity=0.510 Sum_probs=7.0
Q ss_pred eccccccccc
Q psy4084 53 ACHMCIKVFP 62 (86)
Q Consensus 53 ~C~~C~~~~~ 62 (86)
.|+.||..|.
T Consensus 16 ~Cp~CG~~F~ 25 (26)
T PF10571_consen 16 FCPHCGYDFE 25 (26)
T ss_pred cCCCCCCCCc
Confidence 5777777764
No 61
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=93.23 E-value=0.1 Score=22.23 Aligned_cols=9 Identities=22% Similarity=0.807 Sum_probs=4.2
Q ss_pred cceeccccc
Q psy4084 50 RQFACHMCI 58 (86)
Q Consensus 50 ~~~~C~~C~ 58 (86)
.+|.|+.||
T Consensus 47 ~~Y~CP~CG 55 (59)
T PRK14890 47 NPYTCPKCG 55 (59)
T ss_pred CceECCCCC
Confidence 344444444
No 62
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=93.20 E-value=0.18 Score=25.54 Aligned_cols=38 Identities=16% Similarity=0.414 Sum_probs=23.5
Q ss_pred CCCceecccccccCCChHHHhhhhhCCcceecccccccc
Q psy4084 23 SDRQFACHMCIKVFPSQDKLRMHMLSDRQFACHMCIKVF 61 (86)
Q Consensus 23 ~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~C~~C~~~~ 61 (86)
....|.|+.|+..|.....+..- .....|.|+.||...
T Consensus 96 ~~~~Y~Cp~C~~~y~~~ea~~~~-d~~~~f~Cp~Cg~~l 133 (147)
T smart00531 96 NNAYYKCPNCQSKYTFLEANQLL-DMDGTFTCPRCGEEL 133 (147)
T ss_pred CCcEEECcCCCCEeeHHHHHHhc-CCCCcEECCCCCCEE
Confidence 34568888888877765543321 112338888888765
No 63
>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=92.88 E-value=0.14 Score=18.06 Aligned_cols=20 Identities=15% Similarity=0.567 Sum_probs=14.4
Q ss_pred eecccccccccCHHHHHHHHH
Q psy4084 52 FACHMCIKVFPSQDKLRMHML 72 (86)
Q Consensus 52 ~~C~~C~~~~~~~~~l~~h~~ 72 (86)
..|+.|++.+ ....++.|+.
T Consensus 2 v~CPiC~~~v-~~~~in~HLD 21 (26)
T smart00734 2 VQCPVCFREV-PENLINSHLD 21 (26)
T ss_pred CcCCCCcCcc-cHHHHHHHHH
Confidence 3588888887 5567777765
No 64
>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=92.48 E-value=0.11 Score=26.65 Aligned_cols=16 Identities=19% Similarity=0.393 Sum_probs=8.2
Q ss_pred eecccccccccCHHHH
Q psy4084 52 FACHMCIKVFPSQDKL 67 (86)
Q Consensus 52 ~~C~~C~~~~~~~~~l 67 (86)
|.|+.|+..|.....+
T Consensus 110 Y~Cp~c~~r~tf~eA~ 125 (158)
T TIGR00373 110 FICPNMCVRFTFNEAM 125 (158)
T ss_pred EECCCCCcEeeHHHHH
Confidence 4555555555544444
No 65
>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=92.45 E-value=0.12 Score=19.42 Aligned_cols=25 Identities=16% Similarity=0.545 Sum_probs=15.0
Q ss_pred ceecccccccCCChHHHhhhhhCCcceecccccc
Q psy4084 26 QFACHMCIKVFPSQDKLRMHMLSDRQFACHMCIK 59 (86)
Q Consensus 26 ~~~c~~c~~~~~~~~~l~~h~~~~~~~~C~~C~~ 59 (86)
.|.|..||..+... +.|..|+.||.
T Consensus 2 ~~~C~~CG~i~~g~---------~~p~~CP~Cg~ 26 (34)
T cd00729 2 VWVCPVCGYIHEGE---------EAPEKCPICGA 26 (34)
T ss_pred eEECCCCCCEeECC---------cCCCcCcCCCC
Confidence 36777777554321 24567887775
No 66
>smart00614 ZnF_BED BED zinc finger. DNA-binding domain in chromatin-boundary-element-binding proteins and transposases
Probab=92.43 E-value=0.19 Score=20.50 Aligned_cols=23 Identities=26% Similarity=0.489 Sum_probs=16.8
Q ss_pred eecccccccccCH-----HHHHHHHH-hC
Q psy4084 52 FACHMCIKVFPSQ-----DKLRMHML-SG 74 (86)
Q Consensus 52 ~~C~~C~~~~~~~-----~~l~~h~~-~~ 74 (86)
..|..|++.+... ++|.+|+. .|
T Consensus 19 a~C~~C~~~l~~~~~~gTs~L~rHl~~~h 47 (50)
T smart00614 19 AKCKYCGKKLSRSSKGGTSNLRRHLRRKH 47 (50)
T ss_pred EEecCCCCEeeeCCCCCcHHHHHHHHhHC
Confidence 5688888877554 68888888 44
No 67
>PHA00626 hypothetical protein
Probab=92.32 E-value=0.064 Score=22.57 Aligned_cols=14 Identities=14% Similarity=0.280 Sum_probs=8.8
Q ss_pred cceecccccccccC
Q psy4084 50 RQFACHMCIKVFPS 63 (86)
Q Consensus 50 ~~~~C~~C~~~~~~ 63 (86)
..|.|+.||+.|..
T Consensus 22 nrYkCkdCGY~ft~ 35 (59)
T PHA00626 22 DDYVCCDCGYNDSK 35 (59)
T ss_pred cceEcCCCCCeech
Confidence 45677777766543
No 68
>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=92.08 E-value=0.2 Score=23.97 Aligned_cols=27 Identities=19% Similarity=0.332 Sum_probs=23.8
Q ss_pred cceec----ccccccccCHHHHHHHHHhCCC
Q psy4084 50 RQFAC----HMCIKVFPSQDKLRMHMLSGLQ 76 (86)
Q Consensus 50 ~~~~C----~~C~~~~~~~~~l~~h~~~~~~ 76 (86)
.-|.| ..|++...+...+..|++.+++
T Consensus 79 ~G~~C~~~~~~C~y~~~~~~~m~~H~~~~Hg 109 (109)
T PF12013_consen 79 DGYRCQCDPPHCGYITRSKKTMRKHWRKEHG 109 (109)
T ss_pred CCeeeecCCCCCCcEeccHHHHHHHHHHhcC
Confidence 45899 9999999999999999998764
No 69
>KOG4167|consensus
Probab=92.06 E-value=0.028 Score=35.29 Aligned_cols=25 Identities=32% Similarity=0.462 Sum_probs=23.0
Q ss_pred ceecccccccccCHHHHHHHHHhCC
Q psy4084 51 QFACHMCIKVFPSQDKLRMHMLSGL 75 (86)
Q Consensus 51 ~~~C~~C~~~~~~~~~l~~h~~~~~ 75 (86)
-|.|..|++.|.-...++.||++|.
T Consensus 792 iFpCreC~kvF~KiKSrNAHMK~Hr 816 (907)
T KOG4167|consen 792 IFPCRECGKVFFKIKSRNAHMKTHR 816 (907)
T ss_pred eeehHHHHHHHHHHhhhhHHHHHHH
Confidence 4899999999999999999999985
No 70
>KOG2785|consensus
Probab=92.03 E-value=0.39 Score=28.20 Aligned_cols=69 Identities=20% Similarity=0.205 Sum_probs=39.2
Q ss_pred CcchhhhccChHHHHhhHHHHhCCCceecccccccCCChHHHhhhhhC--Ccceeccccc---ccccCHHHHHHHHHh
Q psy4084 1 MSECMGKFTEYQVIRKHIRTFHSDRQFACHMCIKVFPSQDKLRMHMLS--DRQFACHMCI---KVFPSQDKLRMHMLS 73 (86)
Q Consensus 1 c~~C~~~~~~~~~l~~h~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~--~~~~~C~~C~---~~~~~~~~l~~h~~~ 73 (86)
|-.|++.+.+-.....||..++|--. ... ........|...+.- ..-+.|..|+ +.|.+....+.||..
T Consensus 169 CLfC~~~~k~~e~~~~HM~~~HgffI--Pdr--eYL~D~~GLl~YLgeKV~~~~~CL~CN~~~~~f~sleavr~HM~~ 242 (390)
T KOG2785|consen 169 CLFCDKKSKSLEENLKHMFKEHGFFI--PDR--EYLTDEKGLLKYLGEKVGIGFICLFCNELGRPFSSLEAVRAHMRD 242 (390)
T ss_pred eeecCCCcccHHHHHHHHhhccCCcC--Cch--HhhhchhHHHHHHHHHhccCceEEEeccccCcccccHHHHHHHhh
Confidence 44566666666666666666555211 000 112222233333221 4567888887 889999999999874
No 71
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=91.87 E-value=0.14 Score=26.87 Aligned_cols=17 Identities=24% Similarity=0.507 Sum_probs=9.2
Q ss_pred ceecccccccccCHHHH
Q psy4084 51 QFACHMCIKVFPSQDKL 67 (86)
Q Consensus 51 ~~~C~~C~~~~~~~~~l 67 (86)
-|.|+.|+..|.....+
T Consensus 117 ~Y~Cp~C~~rytf~eA~ 133 (178)
T PRK06266 117 FFFCPNCHIRFTFDEAM 133 (178)
T ss_pred EEECCCCCcEEeHHHHh
Confidence 35566666555555443
No 72
>PF02892 zf-BED: BED zinc finger; InterPro: IPR003656 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents predicted BED-type zinc finger domains. The BED finger which was named after the Drosophila proteins BEAF and DREF, is found in one or more copies in cellular regulatory factors and transposases from plants, animals and fungi. The BED finger is an about 50 to 60 amino acid residues domain that contains a characteristic motif with two highly conserved aromatic positions, as well as a shared pattern of cysteines and histidines that is predicted to form a zinc finger. As diverse BED fingers are able to bind DNA, it has been suggested that DNA-binding is the general function of this domain []. Some proteins known to contain a BED domain include animal, plant and fungi AC1 and Hobo-like transposases; Caenorhabditis elegans Dpy-20 protein, a predicted cuticular gene transcriptional regulator; Drosophila BEAF (boundary element-associated factor), thought to be involved in chromatin insulation; Drosophila DREF, a transcriptional regulator for S-phase genes; and tobacco 3AF1 and tomato E4/E8-BP1, light- and ethylene-regulated DNA binding proteins that contain two BED fingers. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding; PDB: 2DJR_A 2CT5_A.
Probab=91.66 E-value=0.33 Score=19.13 Aligned_cols=24 Identities=25% Similarity=0.537 Sum_probs=14.3
Q ss_pred cceecccccccccC----HHHHHHHHHh
Q psy4084 50 RQFACHMCIKVFPS----QDKLRMHMLS 73 (86)
Q Consensus 50 ~~~~C~~C~~~~~~----~~~l~~h~~~ 73 (86)
....|..|++.+.. .++|..|++.
T Consensus 15 ~~a~C~~C~~~~~~~~~~ts~l~~HL~~ 42 (45)
T PF02892_consen 15 KKAKCKYCGKVIKYSSGGTSNLKRHLKK 42 (45)
T ss_dssp S-EEETTTTEE-----SSTHHHHHHHHH
T ss_pred CeEEeCCCCeEEeeCCCcHHHHHHhhhh
Confidence 44678888777665 3778888743
No 73
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=91.43 E-value=0.13 Score=20.60 Aligned_cols=29 Identities=14% Similarity=0.400 Sum_probs=17.7
Q ss_pred ceecccccccCCChHHHhhhhhCCcceecccccccc
Q psy4084 26 QFACHMCIKVFPSQDKLRMHMLSDRQFACHMCIKVF 61 (86)
Q Consensus 26 ~~~c~~c~~~~~~~~~l~~h~~~~~~~~C~~C~~~~ 61 (86)
.|.|+.||..+..... ...+.|+.||..+
T Consensus 3 ~y~C~~CG~~~~~~~~-------~~~~~Cp~CG~~~ 31 (46)
T PRK00398 3 EYKCARCGREVELDEY-------GTGVRCPYCGYRI 31 (46)
T ss_pred EEECCCCCCEEEECCC-------CCceECCCCCCeE
Confidence 4778888766544321 1256788887654
No 74
>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=90.40 E-value=0.072 Score=20.58 Aligned_cols=29 Identities=24% Similarity=0.500 Sum_probs=16.4
Q ss_pred eecccccccCCChHHHhhhhhCCcceecccccc
Q psy4084 27 FACHMCIKVFPSQDKLRMHMLSDRQFACHMCIK 59 (86)
Q Consensus 27 ~~c~~c~~~~~~~~~l~~h~~~~~~~~C~~C~~ 59 (86)
|.|..|+..|........ .....|+.||.
T Consensus 6 y~C~~Cg~~fe~~~~~~~----~~~~~CP~Cg~ 34 (41)
T smart00834 6 YRCEDCGHTFEVLQKISD----DPLATCPECGG 34 (41)
T ss_pred EEcCCCCCEEEEEEecCC----CCCCCCCCCCC
Confidence 677777776654332211 23446777775
No 75
>KOG2893|consensus
Probab=90.39 E-value=0.17 Score=27.89 Aligned_cols=33 Identities=24% Similarity=0.599 Sum_probs=25.9
Q ss_pred CcceecccccccccCHHHHHHHHHhCCCCccCCCCcCC
Q psy4084 49 DRQFACHMCIKVFPSQDKLRMHMLSGLQTFDLKSKLCT 86 (86)
Q Consensus 49 ~~~~~C~~C~~~~~~~~~l~~h~~~~~~~~~~~c~~C~ 86 (86)
.++| |=+|++.|.....|.+|.+. +.|+|.+|.
T Consensus 9 ~kpw-cwycnrefddekiliqhqka----khfkchich 41 (341)
T KOG2893|consen 9 DKPW-CWYCNREFDDEKILIQHQKA----KHFKCHICH 41 (341)
T ss_pred CCce-eeecccccchhhhhhhhhhh----ccceeeeeh
Confidence 4565 67899999999999888764 448998883
No 76
>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=90.24 E-value=0.19 Score=24.90 Aligned_cols=30 Identities=17% Similarity=0.166 Sum_probs=19.0
Q ss_pred eecccccccCCChHHHhhhhhCCcceecccccccccCH
Q psy4084 27 FACHMCIKVFPSQDKLRMHMLSDRQFACHMCIKVFPSQ 64 (86)
Q Consensus 27 ~~c~~c~~~~~~~~~l~~h~~~~~~~~C~~C~~~~~~~ 64 (86)
..|+.|+..|.-.. ..|..|+.||..|.-.
T Consensus 10 r~Cp~cg~kFYDLn--------k~p~vcP~cg~~~~~~ 39 (129)
T TIGR02300 10 RICPNTGSKFYDLN--------RRPAVSPYTGEQFPPE 39 (129)
T ss_pred ccCCCcCccccccC--------CCCccCCCcCCccCcc
Confidence 36777777665432 3567777787776544
No 77
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=90.11 E-value=0.12 Score=23.06 Aligned_cols=14 Identities=29% Similarity=0.705 Sum_probs=7.1
Q ss_pred Ccceecc--ccccccc
Q psy4084 49 DRQFACH--MCIKVFP 62 (86)
Q Consensus 49 ~~~~~C~--~C~~~~~ 62 (86)
++.++|. .||..|.
T Consensus 25 ~~Y~qC~N~eCg~tF~ 40 (72)
T PRK09678 25 ERYHQCQNVNCSATFI 40 (72)
T ss_pred eeeeecCCCCCCCEEE
Confidence 3445555 5555554
No 78
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=90.04 E-value=0.093 Score=30.31 Aligned_cols=55 Identities=24% Similarity=0.491 Sum_probs=30.0
Q ss_pred ceecccccccCCChHHHhhhhh--C---C--cceecc--cccccccCHHHHHHHHHhCCCCccC
Q psy4084 26 QFACHMCIKVFPSQDKLRMHML--S---D--RQFACH--MCIKVFPSQDKLRMHMLSGLQTFDL 80 (86)
Q Consensus 26 ~~~c~~c~~~~~~~~~l~~h~~--~---~--~~~~C~--~C~~~~~~~~~l~~h~~~~~~~~~~ 80 (86)
++.+..|...+.....+..|.. . + +++.|+ .|++.|.+...+..|...|....+.
T Consensus 289 ~~~~~~~~~~~s~~~~l~~~~~~~~h~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~ 352 (467)
T COG5048 289 PIKSKQCNISFSRSSPLTRHLRSVNHSGESLKPFSCPYSLCGKLFSRNDALKRHILLHTSISPA 352 (467)
T ss_pred CCCCccccCCccccccccccccccccccccCCceeeeccCCCccccccccccCCcccccCCCcc
Confidence 3445555555555555555544 2 3 556666 4666666666666666655554443
No 79
>KOG2231|consensus
Probab=89.85 E-value=0.81 Score=29.02 Aligned_cols=64 Identities=22% Similarity=0.526 Sum_probs=33.9
Q ss_pred cChHHHHhhHHHHhCCCceeccccc---------ccCCChHHHhhhhhC-------Cc-ceecccccccccCHHHHHHHH
Q psy4084 9 TEYQVIRKHIRTFHSDRQFACHMCI---------KVFPSQDKLRMHMLS-------DR-QFACHMCIKVFPSQDKLRMHM 71 (86)
Q Consensus 9 ~~~~~l~~h~~~~~~~~~~~c~~c~---------~~~~~~~~l~~h~~~-------~~-~~~C~~C~~~~~~~~~l~~h~ 71 (86)
.....|+.|++..++. +-|..|. ........|..|+.. .+ ...|..|...|.....|..|+
T Consensus 125 ~s~~~Lk~H~~~~H~~--~~c~lC~~~~kif~~e~k~Yt~~el~~h~~~gd~d~~s~rGhp~C~~C~~~fld~~el~rH~ 202 (669)
T KOG2231|consen 125 KSVENLKNHMRDQHKL--HLCSLCLQNLKIFINERKLYTRAELNLHLMFGDPDDESCRGHPLCKFCHERFLDDDELYRHL 202 (669)
T ss_pred hHHHHHHHHHHHhhhh--hccccccccceeeeeeeehehHHHHHHHHhcCCCccccccCCccchhhhhhhccHHHHHHhh
Confidence 3667788888643331 1222211 122344555556543 11 135677777777777777777
Q ss_pred HhC
Q psy4084 72 LSG 74 (86)
Q Consensus 72 ~~~ 74 (86)
+.+
T Consensus 203 ~~~ 205 (669)
T KOG2231|consen 203 RFD 205 (669)
T ss_pred ccc
Confidence 654
No 80
>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=89.79 E-value=0.72 Score=18.46 Aligned_cols=39 Identities=21% Similarity=0.549 Sum_probs=19.8
Q ss_pred HhhHHHHhCCCceecccccccCCChHHHhhhhhCCcceecccccc
Q psy4084 15 RKHIRTFHSDRQFACHMCIKVFPSQDKLRMHMLSDRQFACHMCIK 59 (86)
Q Consensus 15 ~~h~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~C~~C~~ 59 (86)
..++....-...+.|+.|+.. ....+. ....|.|..|++
T Consensus 7 ~~~l~~~RW~~g~~CP~Cg~~--~~~~~~----~~~~~~C~~C~~ 45 (46)
T PF12760_consen 7 REYLEEIRWPDGFVCPHCGST--KHYRLK----TRGRYRCKACRK 45 (46)
T ss_pred HHHHHHhcCCCCCCCCCCCCe--eeEEeC----CCCeEECCCCCC
Confidence 344443333334678888754 111111 135677877765
No 81
>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=89.68 E-value=0.075 Score=20.97 Aligned_cols=29 Identities=21% Similarity=0.526 Sum_probs=17.4
Q ss_pred eecccccccCCChHHHhhhhhCCcceecccccc
Q psy4084 27 FACHMCIKVFPSQDKLRMHMLSDRQFACHMCIK 59 (86)
Q Consensus 27 ~~c~~c~~~~~~~~~l~~h~~~~~~~~C~~C~~ 59 (86)
|.|..||..|.....+.. ..+..|+.||.
T Consensus 6 y~C~~Cg~~fe~~~~~~~----~~~~~CP~Cg~ 34 (42)
T PF09723_consen 6 YRCEECGHEFEVLQSISE----DDPVPCPECGS 34 (42)
T ss_pred EEeCCCCCEEEEEEEcCC----CCCCcCCCCCC
Confidence 677778776655443222 24456777776
No 82
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=89.52 E-value=0.3 Score=19.56 Aligned_cols=26 Identities=19% Similarity=0.382 Sum_probs=17.0
Q ss_pred eecccccccCCChHHHhhhhhCCcceeccccccc
Q psy4084 27 FACHMCIKVFPSQDKLRMHMLSDRQFACHMCIKV 60 (86)
Q Consensus 27 ~~c~~c~~~~~~~~~l~~h~~~~~~~~C~~C~~~ 60 (86)
|.|..||..+... ..-+..|+.||..
T Consensus 3 Y~C~~Cg~~~~~~--------~~~~irC~~CG~r 28 (44)
T smart00659 3 YICGECGRENEIK--------SKDVVRCRECGYR 28 (44)
T ss_pred EECCCCCCEeecC--------CCCceECCCCCce
Confidence 6778887766543 1345788888754
No 83
>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=89.50 E-value=0.33 Score=24.28 Aligned_cols=28 Identities=18% Similarity=0.246 Sum_probs=17.0
Q ss_pred CcceecccccccccCHHHHHHHHHhCCCCcc
Q psy4084 49 DRQFACHMCIKVFPSQDKLRMHMLSGLQTFD 79 (86)
Q Consensus 49 ~~~~~C~~C~~~~~~~~~l~~h~~~~~~~~~ 79 (86)
.....|-+||+.|... .+|+..|++-.+
T Consensus 70 ~d~i~clecGk~~k~L---krHL~~~~gltp 97 (132)
T PF05443_consen 70 PDYIICLECGKKFKTL---KRHLRTHHGLTP 97 (132)
T ss_dssp SS-EE-TBT--EESBH---HHHHHHTT-S-H
T ss_pred cCeeEEccCCcccchH---HHHHHHccCCCH
Confidence 3457899999998765 889999876443
No 84
>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=89.39 E-value=0.1 Score=21.41 Aligned_cols=29 Identities=24% Similarity=0.495 Sum_probs=16.4
Q ss_pred eecccccccCCChHHHhhhhhCCcceecccccc
Q psy4084 27 FACHMCIKVFPSQDKLRMHMLSDRQFACHMCIK 59 (86)
Q Consensus 27 ~~c~~c~~~~~~~~~l~~h~~~~~~~~C~~C~~ 59 (86)
|.|..|+..|.....+.. ..+..|+.||.
T Consensus 6 y~C~~Cg~~fe~~~~~~~----~~~~~CP~Cg~ 34 (52)
T TIGR02605 6 YRCTACGHRFEVLQKMSD----DPLATCPECGG 34 (52)
T ss_pred EEeCCCCCEeEEEEecCC----CCCCCCCCCCC
Confidence 667777776654432211 23446777775
No 85
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=89.36 E-value=0.61 Score=22.68 Aligned_cols=46 Identities=20% Similarity=0.438 Sum_probs=26.4
Q ss_pred cccccccCCChHHHhhh-hhCCcceecccccccccCHHHHHHHHHhC
Q psy4084 29 CHMCIKVFPSQDKLRMH-MLSDRQFACHMCIKVFPSQDKLRMHMLSG 74 (86)
Q Consensus 29 c~~c~~~~~~~~~l~~h-~~~~~~~~C~~C~~~~~~~~~l~~h~~~~ 74 (86)
|-.|...|........- +.....|.|+.|...|-..-.+-.|...|
T Consensus 58 C~~C~~~f~~~~~~~~~~~~~~~~y~C~~C~~~FC~dCD~fiHe~Lh 104 (112)
T TIGR00622 58 CFGCQGPFPKPPVSPFDELKDSHRYVCAVCKNVFCVDCDVFVHESLH 104 (112)
T ss_pred ccCcCCCCCCcccccccccccccceeCCCCCCccccccchhhhhhcc
Confidence 66666666543211100 11134578888888887776666676665
No 86
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=88.40 E-value=0.088 Score=30.40 Aligned_cols=48 Identities=27% Similarity=0.668 Sum_probs=40.4
Q ss_pred CcchhhhccChHHHHhhHH--HHhCC--Cceecc--cccccCCChHHHhhhhhC
Q psy4084 1 MSECMGKFTEYQVIRKHIR--TFHSD--RQFACH--MCIKVFPSQDKLRMHMLS 48 (86)
Q Consensus 1 c~~C~~~~~~~~~l~~h~~--~~~~~--~~~~c~--~c~~~~~~~~~l~~h~~~ 48 (86)
|..|...|.....+..|.+ .|.++ +++.|+ .|++.|.....+..|...
T Consensus 292 ~~~~~~~~s~~~~l~~~~~~~~h~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~ 345 (467)
T COG5048 292 SKQCNISFSRSSPLTRHLRSVNHSGESLKPFSCPYSLCGKLFSRNDALKRHILL 345 (467)
T ss_pred CccccCCccccccccccccccccccccCCceeeeccCCCccccccccccCCccc
Confidence 3567788888999999999 79999 899999 799999988888777653
No 87
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=87.71 E-value=0.45 Score=19.58 Aligned_cols=29 Identities=17% Similarity=0.465 Sum_probs=17.2
Q ss_pred CceecccccccCCChHHHhhhhhCCcceeccccccc
Q psy4084 25 RQFACHMCIKVFPSQDKLRMHMLSDRQFACHMCIKV 60 (86)
Q Consensus 25 ~~~~c~~c~~~~~~~~~l~~h~~~~~~~~C~~C~~~ 60 (86)
..|.|..|++.+.... ......|+.||..
T Consensus 5 ~~Y~C~~Cg~~~~~~~-------~~~~irCp~Cg~r 33 (49)
T COG1996 5 MEYKCARCGREVELDQ-------ETRGIRCPYCGSR 33 (49)
T ss_pred EEEEhhhcCCeeehhh-------ccCceeCCCCCcE
Confidence 3477888887762211 1345678888754
No 88
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=86.89 E-value=0.22 Score=25.53 Aligned_cols=12 Identities=33% Similarity=0.625 Sum_probs=5.5
Q ss_pred eecccccccCCC
Q psy4084 27 FACHMCIKVFPS 38 (86)
Q Consensus 27 ~~c~~c~~~~~~ 38 (86)
++|+.||..|..
T Consensus 29 ~~c~~c~~~f~~ 40 (154)
T PRK00464 29 RECLACGKRFTT 40 (154)
T ss_pred eeccccCCcceE
Confidence 444444444443
No 89
>KOG2186|consensus
Probab=86.83 E-value=0.52 Score=26.22 Aligned_cols=13 Identities=38% Similarity=0.748 Sum_probs=6.5
Q ss_pred ceecccccccCCC
Q psy4084 26 QFACHMCIKVFPS 38 (86)
Q Consensus 26 ~~~c~~c~~~~~~ 38 (86)
-|.|..|+..|..
T Consensus 29 ~fSCIDC~k~F~~ 41 (276)
T KOG2186|consen 29 YFSCIDCGKTFER 41 (276)
T ss_pred eeEEeeccccccc
Confidence 3455555555544
No 90
>KOG2785|consensus
Probab=86.44 E-value=1.3 Score=26.13 Aligned_cols=73 Identities=16% Similarity=0.200 Sum_probs=43.0
Q ss_pred CcchhhhccChHHHHhhHHHHhCC-----Cce-ecccccccCCChHHHhhhhh------CCcceecccccccccCHHHHH
Q psy4084 1 MSECMGKFTEYQVIRKHIRTFHSD-----RQF-ACHMCIKVFPSQDKLRMHML------SDRQFACHMCIKVFPSQDKLR 68 (86)
Q Consensus 1 c~~C~~~~~~~~~l~~h~~~~~~~-----~~~-~c~~c~~~~~~~~~l~~h~~------~~~~~~C~~C~~~~~~~~~l~ 68 (86)
|..|...|.....-+.|+.+-+-. +.. ..++....|........-.. ..-++.|..|.+.|.....-.
T Consensus 6 C~tC~v~F~~ad~Qr~HyKSdWHRYNLKRkVA~lPPItaE~F~~k~~s~~~~~~~~~e~~~~~~~c~~c~k~~~s~~a~~ 85 (390)
T KOG2785|consen 6 CNTCNVEFDDADEQRAHYKSDWHRYNLKRKVASLPPITAEEFNEKVLSDDSEKEENLEEAESVVYCEACNKSFASPKAHE 85 (390)
T ss_pred eeceeeeeccHHHHHHHhhhhHHHhhHHhHhhcCCCcCHHHHhHHHhhhhhhhhhhhhhcccceehHHhhccccChhhHH
Confidence 677888888887777787764321 111 11233333332211111111 145688999999999998888
Q ss_pred HHHHh
Q psy4084 69 MHMLS 73 (86)
Q Consensus 69 ~h~~~ 73 (86)
.|+..
T Consensus 86 ~hl~S 90 (390)
T KOG2785|consen 86 NHLKS 90 (390)
T ss_pred HHHHH
Confidence 88864
No 91
>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=86.02 E-value=0.48 Score=16.43 Aligned_cols=9 Identities=33% Similarity=0.752 Sum_probs=5.5
Q ss_pred cceeccccc
Q psy4084 50 RQFACHMCI 58 (86)
Q Consensus 50 ~~~~C~~C~ 58 (86)
.+|.|+.||
T Consensus 15 v~f~CPnCG 23 (24)
T PF07754_consen 15 VPFPCPNCG 23 (24)
T ss_pred ceEeCCCCC
Confidence 456666665
No 92
>PF04959 ARS2: Arsenite-resistance protein 2; InterPro: IPR007042 This entry represents Arsenite-resistance protein 2 (also known as Serrate RNA effector molecule homolog) which is thought to play a role in arsenite resistance [], although does not directly confer arsenite resistance but rather modulates arsenic sensitivity []. Arsenite is a carcinogenic compound which can act as a comutagen by inhibiting DNA repair. It is also involved in cell cycle progression at S phase. ; PDB: 3AX1_A.
Probab=85.81 E-value=0.72 Score=25.08 Aligned_cols=27 Identities=22% Similarity=0.637 Sum_probs=20.6
Q ss_pred CcceecccccccccCHHHHHHHHHhCC
Q psy4084 49 DRQFACHMCIKVFPSQDKLRMHMLSGL 75 (86)
Q Consensus 49 ~~~~~C~~C~~~~~~~~~l~~h~~~~~ 75 (86)
+..|.|+.|++.|....-+..|+.+.|
T Consensus 75 ~~K~~C~lc~KlFkg~eFV~KHI~nKH 101 (214)
T PF04959_consen 75 EDKWRCPLCGKLFKGPEFVRKHIFNKH 101 (214)
T ss_dssp SEEEEE-SSS-EESSHHHHHHHHHHH-
T ss_pred CCEECCCCCCcccCChHHHHHHHhhcC
Confidence 346899999999999999999998644
No 93
>KOG2231|consensus
Probab=85.72 E-value=1.9 Score=27.52 Aligned_cols=46 Identities=30% Similarity=0.635 Sum_probs=22.8
Q ss_pred ecccccccCCChHHHhhhhhCCcceecccc------cccccCHHHHHHHHHhC
Q psy4084 28 ACHMCIKVFPSQDKLRMHMLSDRQFACHMC------IKVFPSQDKLRMHMLSG 74 (86)
Q Consensus 28 ~c~~c~~~~~~~~~l~~h~~~~~~~~C~~C------~~~~~~~~~l~~h~~~~ 74 (86)
.|..|...|-....+.+|+..+ -+.|..| +.-|.....|..|.+.+
T Consensus 184 ~C~~C~~~fld~~el~rH~~~~-h~~chfC~~~~~~neyy~~~~dLe~HfR~~ 235 (669)
T KOG2231|consen 184 LCKFCHERFLDDDELYRHLRFD-HEFCHFCDYKTGQNEYYNDYDDLEEHFRKG 235 (669)
T ss_pred cchhhhhhhccHHHHHHhhccc-eeheeecCcccccchhcccchHHHHHhhhc
Confidence 4555666666666666665531 2233333 22344555555555543
No 94
>KOG4173|consensus
Probab=84.45 E-value=0.5 Score=25.53 Aligned_cols=67 Identities=27% Similarity=0.641 Sum_probs=47.7
Q ss_pred hhhhccChHHHHhhHHHHhCCCceecccccccCCChHHHhhhhhC----------Cc---ceecc--cccccccCHHHHH
Q psy4084 4 CMGKFTEYQVIRKHIRTFHSDRQFACHMCIKVFPSQDKLRMHMLS----------DR---QFACH--MCIKVFPSQDKLR 68 (86)
Q Consensus 4 C~~~~~~~~~l~~h~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~----------~~---~~~C~--~C~~~~~~~~~l~ 68 (86)
|-+.|.....+..|..+.++ -.|..|.+.|.+.--|..|+.. ++ -|+|. .|+..|.+.....
T Consensus 87 c~~~~d~lD~~E~hY~~~h~---~sCs~C~r~~Pt~hLLd~HI~E~HDs~Fqa~veRG~dMy~ClvEgCt~KFkT~r~Rk 163 (253)
T KOG4173|consen 87 CCQVFDALDDYEHHYHTLHG---NSCSFCKRAFPTGHLLDAHILEWHDSLFQALVERGQDMYQCLVEGCTEKFKTSRDRK 163 (253)
T ss_pred hHHHHhhhhhHHHhhhhccc---chhHHHHHhCCchhhhhHHHHHHHHHHHHHHHHcCccHHHHHHHhhhhhhhhhhhhh
Confidence 45666666667777655444 3788999999988888888752 22 26674 4888898888888
Q ss_pred HHHHh
Q psy4084 69 MHMLS 73 (86)
Q Consensus 69 ~h~~~ 73 (86)
.|+-.
T Consensus 164 dH~I~ 168 (253)
T KOG4173|consen 164 DHMIR 168 (253)
T ss_pred hHHHH
Confidence 88754
No 95
>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=84.17 E-value=0.68 Score=17.21 Aligned_cols=9 Identities=22% Similarity=0.601 Sum_probs=4.8
Q ss_pred ceecccccc
Q psy4084 51 QFACHMCIK 59 (86)
Q Consensus 51 ~~~C~~C~~ 59 (86)
+..|+.||.
T Consensus 17 ~irC~~CG~ 25 (32)
T PF03604_consen 17 PIRCPECGH 25 (32)
T ss_dssp TSSBSSSS-
T ss_pred cEECCcCCC
Confidence 456666664
No 96
>KOG1146|consensus
Probab=84.09 E-value=0.54 Score=31.98 Aligned_cols=49 Identities=22% Similarity=0.519 Sum_probs=34.6
Q ss_pred CCceecccccccCCChHHHhhhhhC--------------------CcceecccccccccCHHHHHHHHHh
Q psy4084 24 DRQFACHMCIKVFPSQDKLRMHMLS--------------------DRQFACHMCIKVFPSQDKLRMHMLS 73 (86)
Q Consensus 24 ~~~~~c~~c~~~~~~~~~l~~h~~~--------------------~~~~~C~~C~~~~~~~~~l~~h~~~ 73 (86)
+.+|.|..|...|.....+..|... -.++ |..|...|.....|..||+.
T Consensus 1282 ~~~~~~~~~~~~~~~~~~l~~~~~k~~~~~~~~~~~~~~~l~~~d~~~~-c~~c~~~~~~~~alqihm~~ 1350 (1406)
T KOG1146|consen 1282 THRYLCRQCKMAFDGEAPLTAHQRKFCFAGRGSGGSMPPPLRVPDCTYH-CLACEVLLSGREALQIHMRS 1350 (1406)
T ss_pred chhHHHHHHHhhhcchhHHHHHHHHHHhccCccccCCCCcccCcccccc-chHHHhhcchhHHHHHHHHH
Confidence 3456666666666666666555421 2345 99999999999999999986
No 97
>KOG2593|consensus
Probab=83.50 E-value=0.72 Score=27.61 Aligned_cols=34 Identities=24% Similarity=0.476 Sum_probs=22.5
Q ss_pred cceecccccccccCHHHHHHHHHhCCCCccCCCCcCC
Q psy4084 50 RQFACHMCIKVFPSQDKLRMHMLSGLQTFDLKSKLCT 86 (86)
Q Consensus 50 ~~~~C~~C~~~~~~~~~l~~h~~~~~~~~~~~c~~C~ 86 (86)
..|.|+.|.+.|.....++ ......-.|.|..|+
T Consensus 127 ~~Y~Cp~C~kkyt~Lea~~---L~~~~~~~F~C~~C~ 160 (436)
T KOG2593|consen 127 AGYVCPNCQKKYTSLEALQ---LLDNETGEFHCENCG 160 (436)
T ss_pred ccccCCccccchhhhHHHH---hhcccCceEEEecCC
Confidence 5688888888887776654 223334457777775
No 98
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=83.03 E-value=0.85 Score=21.13 Aligned_cols=33 Identities=15% Similarity=0.470 Sum_probs=20.8
Q ss_pred CceecccccccCCChHHHhhhhhCCcceecccccccccCH
Q psy4084 25 RQFACHMCIKVFPSQDKLRMHMLSDRQFACHMCIKVFPSQ 64 (86)
Q Consensus 25 ~~~~c~~c~~~~~~~~~l~~h~~~~~~~~C~~C~~~~~~~ 64 (86)
..+.|+.|++.--.. . ..--|.|..||..|+-.
T Consensus 34 ~~~~Cp~C~~~~VkR------~-a~GIW~C~kCg~~fAGg 66 (89)
T COG1997 34 AKHVCPFCGRTTVKR------I-ATGIWKCRKCGAKFAGG 66 (89)
T ss_pred cCCcCCCCCCcceee------e-ccCeEEcCCCCCeeccc
Confidence 468899998651110 0 13468899999888643
No 99
>KOG2593|consensus
Probab=82.53 E-value=2.3 Score=25.66 Aligned_cols=40 Identities=20% Similarity=0.380 Sum_probs=26.9
Q ss_pred HhCCCceecccccccCCChHHHhhhhhCCcceeccccccc
Q psy4084 21 FHSDRQFACHMCIKVFPSQDKLRMHMLSDRQFACHMCIKV 60 (86)
Q Consensus 21 ~~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~C~~C~~~ 60 (86)
.+...-|.|+.|.+.|.....+..=....-.|.|..|+-.
T Consensus 123 ~t~~~~Y~Cp~C~kkyt~Lea~~L~~~~~~~F~C~~C~ge 162 (436)
T KOG2593|consen 123 DTNVAGYVCPNCQKKYTSLEALQLLDNETGEFHCENCGGE 162 (436)
T ss_pred ccccccccCCccccchhhhHHHHhhcccCceEEEecCCCc
Confidence 3345679999999999887765432111346889888654
No 100
>PF15269 zf-C2H2_7: Zinc-finger
Probab=81.97 E-value=1.7 Score=17.50 Aligned_cols=22 Identities=23% Similarity=0.406 Sum_probs=17.6
Q ss_pred eecccccccccCHHHHHHHHHh
Q psy4084 52 FACHMCIKVFPSQDKLRMHMLS 73 (86)
Q Consensus 52 ~~C~~C~~~~~~~~~l~~h~~~ 73 (86)
|+|-+|..+....+.|-.||+-
T Consensus 21 ykcfqcpftc~~kshl~nhmky 42 (54)
T PF15269_consen 21 YKCFQCPFTCNEKSHLFNHMKY 42 (54)
T ss_pred ceeecCCcccchHHHHHHHHHH
Confidence 5788888888888888888864
No 101
>PRK04023 DNA polymerase II large subunit; Validated
Probab=81.85 E-value=2.1 Score=28.80 Aligned_cols=7 Identities=43% Similarity=0.895 Sum_probs=3.2
Q ss_pred ecccccc
Q psy4084 28 ACHMCIK 34 (86)
Q Consensus 28 ~c~~c~~ 34 (86)
.|+.||.
T Consensus 628 fCpsCG~ 634 (1121)
T PRK04023 628 KCPSCGK 634 (1121)
T ss_pred cCCCCCC
Confidence 4444443
No 102
>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=81.62 E-value=0.44 Score=19.22 Aligned_cols=34 Identities=18% Similarity=0.351 Sum_probs=16.2
Q ss_pred cccccccCCChHHHhhhhhC-Ccceeccc--cccccc
Q psy4084 29 CHMCIKVFPSQDKLRMHMLS-DRQFACHM--CIKVFP 62 (86)
Q Consensus 29 c~~c~~~~~~~~~l~~h~~~-~~~~~C~~--C~~~~~ 62 (86)
|+.||.......+...+... +..++|.. ||..|.
T Consensus 2 CP~Cg~~a~ir~S~~~s~~~~~~Y~qC~N~~Cg~tfv 38 (47)
T PF04606_consen 2 CPHCGSKARIRTSRQLSPLTRELYCQCTNPECGHTFV 38 (47)
T ss_pred cCCCCCeeEEEEchhhCcceEEEEEEECCCcCCCEEE
Confidence 56666544333332222222 44566654 776664
No 103
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=81.06 E-value=1.3 Score=28.51 Aligned_cols=30 Identities=27% Similarity=0.588 Sum_probs=12.6
Q ss_pred ecccccccCCC---hHHHhhhhhCCcceeccccc
Q psy4084 28 ACHMCIKVFPS---QDKLRMHMLSDRQFACHMCI 58 (86)
Q Consensus 28 ~c~~c~~~~~~---~~~l~~h~~~~~~~~C~~C~ 58 (86)
.|..||..+.- ...|.-|+.. ....|.+||
T Consensus 437 ~C~~Cg~v~~Cp~Cd~~lt~H~~~-~~L~CH~Cg 469 (730)
T COG1198 437 LCRDCGYIAECPNCDSPLTLHKAT-GQLRCHYCG 469 (730)
T ss_pred ecccCCCcccCCCCCcceEEecCC-CeeEeCCCC
Confidence 35555544322 1334444432 334455554
No 104
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=80.88 E-value=4.8 Score=23.82 Aligned_cols=71 Identities=27% Similarity=0.496 Sum_probs=38.5
Q ss_pred CcchhhhccChHHHHhhHHHHhCCCceeccc----ccccCCChHHHhhhhhCCcceeccc--c----cccccCHHHHHHH
Q psy4084 1 MSECMGKFTEYQVIRKHIRTFHSDRQFACHM----CIKVFPSQDKLRMHMLSDRQFACHM--C----IKVFPSQDKLRMH 70 (86)
Q Consensus 1 c~~C~~~~~~~~~l~~h~~~~~~~~~~~c~~----c~~~~~~~~~l~~h~~~~~~~~C~~--C----~~~~~~~~~l~~h 70 (86)
|..|...|.....|..|+|..+.. -+.|.. ..+.|..-..|..|... ..|.|.. | -..|.....|..|
T Consensus 223 C~FC~~~FYdDDEL~~HcR~~HE~-ChICD~v~p~~~QYFK~Y~~Le~HF~~-~hy~ct~qtc~~~k~~vf~~~~el~~h 300 (493)
T COG5236 223 CIFCKIYFYDDDELRRHCRLRHEA-CHICDMVGPIRYQYFKSYEDLEAHFRN-AHYCCTFQTCRVGKCYVFPYHTELLEH 300 (493)
T ss_pred hhhccceecChHHHHHHHHhhhhh-hhhhhccCccchhhhhCHHHHHHHhhc-CceEEEEEEEecCcEEEeccHHHHHHH
Confidence 556777777777788887764432 122222 12345555666666553 2233321 2 1346777777777
Q ss_pred HHh
Q psy4084 71 MLS 73 (86)
Q Consensus 71 ~~~ 73 (86)
+..
T Consensus 301 ~~~ 303 (493)
T COG5236 301 LTR 303 (493)
T ss_pred HHH
Confidence 654
No 105
>KOG2482|consensus
Probab=80.29 E-value=1.4 Score=25.86 Aligned_cols=23 Identities=30% Similarity=0.735 Sum_probs=21.3
Q ss_pred ceecccccccccCHHHHHHHHHh
Q psy4084 51 QFACHMCIKVFPSQDKLRMHMLS 73 (86)
Q Consensus 51 ~~~C~~C~~~~~~~~~l~~h~~~ 73 (86)
.+.|..|.+.|.....|..||+.
T Consensus 195 r~~CLyCekifrdkntLkeHMrk 217 (423)
T KOG2482|consen 195 RLRCLYCEKIFRDKNTLKEHMRK 217 (423)
T ss_pred hheeeeeccccCCcHHHHHHHHh
Confidence 47899999999999999999986
No 106
>KOG3408|consensus
Probab=80.18 E-value=1.3 Score=21.90 Aligned_cols=23 Identities=30% Similarity=0.652 Sum_probs=12.0
Q ss_pred ceecccccccCCChHHHhhhhhC
Q psy4084 26 QFACHMCIKVFPSQDKLRMHMLS 48 (86)
Q Consensus 26 ~~~c~~c~~~~~~~~~l~~h~~~ 48 (86)
.|.|..|.+.|.....+..|.++
T Consensus 57 qfyCi~CaRyFi~~~~l~~H~kt 79 (129)
T KOG3408|consen 57 QFYCIECARYFIDAKALKTHFKT 79 (129)
T ss_pred eeehhhhhhhhcchHHHHHHHhc
Confidence 35555555555555555555443
No 107
>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=80.06 E-value=3.1 Score=19.92 Aligned_cols=29 Identities=21% Similarity=0.346 Sum_probs=12.2
Q ss_pred hhhccChHHHHhhHHHHhCCCceecccccc
Q psy4084 5 MGKFTEYQVIRKHIRTFHSDRQFACHMCIK 34 (86)
Q Consensus 5 ~~~~~~~~~l~~h~~~~~~~~~~~c~~c~~ 34 (86)
|..|.+...+...+.. -..+.|.|...|+
T Consensus 10 ~EiF~dYe~Y~~R~~~-y~~~vwtC~~TGk 38 (102)
T PF10537_consen 10 GEIFRDYEEYLKRMIL-YNQRVWTCEITGK 38 (102)
T ss_pred CcccCCHHHHHHHHHH-HhCCeeEEecCCC
Confidence 3444444443333222 2234455555554
No 108
>PF13878 zf-C2H2_3: zinc-finger of acetyl-transferase ESCO
Probab=78.85 E-value=3.2 Score=16.26 Aligned_cols=22 Identities=9% Similarity=0.111 Sum_probs=13.5
Q ss_pred Ccchhhhcc--ChHHHHhhHHHHh
Q psy4084 1 MSECMGKFT--EYQVIRKHIRTFH 22 (86)
Q Consensus 1 c~~C~~~~~--~~~~l~~h~~~~~ 22 (86)
|+.||-.|. ...+-..|.+.|.
T Consensus 16 C~~CgM~Y~~~~~eD~~~H~~yH~ 39 (41)
T PF13878_consen 16 CPTCGMLYSPGSPEDEKLHKKYHD 39 (41)
T ss_pred CCCCCCEECCCCHHHHHHHHHHHh
Confidence 667776664 4455666766553
No 109
>PF14311 DUF4379: Domain of unknown function (DUF4379)
Probab=78.80 E-value=2.6 Score=17.49 Aligned_cols=17 Identities=12% Similarity=0.303 Sum_probs=11.7
Q ss_pred cceecccccccccCHHH
Q psy4084 50 RQFACHMCIKVFPSQDK 66 (86)
Q Consensus 50 ~~~~C~~C~~~~~~~~~ 66 (86)
.-+.|+.||..+.....
T Consensus 27 v~W~C~~Cgh~w~~~v~ 43 (55)
T PF14311_consen 27 VWWKCPKCGHEWKASVN 43 (55)
T ss_pred EEEECCCCCCeeEccHh
Confidence 34788888877765544
No 110
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=78.33 E-value=1.1 Score=20.92 Aligned_cols=13 Identities=23% Similarity=0.411 Sum_probs=6.7
Q ss_pred ceecccccccCCC
Q psy4084 26 QFACHMCIKVFPS 38 (86)
Q Consensus 26 ~~~c~~c~~~~~~ 38 (86)
|-.|..||..|..
T Consensus 58 Pa~CkkCGfef~~ 70 (97)
T COG3357 58 PARCKKCGFEFRD 70 (97)
T ss_pred ChhhcccCccccc
Confidence 4455555555443
No 111
>PF02176 zf-TRAF: TRAF-type zinc finger; PDB: 2EOD_A 2YUC_A 3HCU_A 3HCS_B 3HCT_A.
Probab=78.15 E-value=1.5 Score=18.30 Aligned_cols=40 Identities=23% Similarity=0.499 Sum_probs=19.3
Q ss_pred CCceeccc-ccccCCChHHHhhhhhC---Ccceeccc----ccccccC
Q psy4084 24 DRQFACHM-CIKVFPSQDKLRMHMLS---DRQFACHM----CIKVFPS 63 (86)
Q Consensus 24 ~~~~~c~~-c~~~~~~~~~l~~h~~~---~~~~~C~~----C~~~~~~ 63 (86)
..+..|+. |+........|..|... .++..|+. |+..+..
T Consensus 7 ~~~v~C~~~cc~~~i~r~~l~~H~~~~C~~~~v~C~~~~~GC~~~~~~ 54 (60)
T PF02176_consen 7 FRPVPCPNGCCNEMIPRKELDDHLENECPKRPVPCPYSPYGCKERVPR 54 (60)
T ss_dssp TSEEE-TT--S-BEEECCCHHHHHHTTSTTSEEE-SS----S--EEEH
T ss_pred CCEeeCCCCCcccceeHHHHHHHHHccCCCCcEECCCCCCCCCCccch
Confidence 34556766 33332334566777773 55677777 7766543
No 112
>COG4530 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=78.13 E-value=1.1 Score=21.67 Aligned_cols=28 Identities=14% Similarity=0.040 Sum_probs=16.2
Q ss_pred ecccccccCCChHHHhhhhhCCcceecccccccccC
Q psy4084 28 ACHMCIKVFPSQDKLRMHMLSDRQFACHMCIKVFPS 63 (86)
Q Consensus 28 ~c~~c~~~~~~~~~l~~h~~~~~~~~C~~C~~~~~~ 63 (86)
.|+.|++.|.... ..|..|++||++|+.
T Consensus 11 idPetg~KFYDLN--------rdPiVsPytG~s~P~ 38 (129)
T COG4530 11 IDPETGKKFYDLN--------RDPIVSPYTGKSYPR 38 (129)
T ss_pred cCccccchhhccC--------CCccccCcccccchH
Confidence 4555655553322 356777778877743
No 113
>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=77.61 E-value=1.3 Score=16.25 Aligned_cols=11 Identities=18% Similarity=0.456 Sum_probs=6.2
Q ss_pred cceeccccccc
Q psy4084 50 RQFACHMCIKV 60 (86)
Q Consensus 50 ~~~~C~~C~~~ 60 (86)
..+.|+.|+..
T Consensus 18 ~~~vCp~C~~e 28 (30)
T PF08274_consen 18 ELLVCPECGHE 28 (30)
T ss_dssp SSEEETTTTEE
T ss_pred CEEeCCccccc
Confidence 34566666643
No 114
>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=77.07 E-value=0.28 Score=31.10 Aligned_cols=57 Identities=25% Similarity=0.455 Sum_probs=28.8
Q ss_pred CcchhhhccChHHHHhhHHHHhCCCce-ecccccccCCChHHHhhhhhCCcceecccccccc
Q psy4084 1 MSECMGKFTEYQVIRKHIRTFHSDRQF-ACHMCIKVFPSQDKLRMHMLSDRQFACHMCIKVF 61 (86)
Q Consensus 1 c~~C~~~~~~~~~l~~h~~~~~~~~~~-~c~~c~~~~~~~~~l~~h~~~~~~~~C~~C~~~~ 61 (86)
|-.||-+|+--..|-.- |.++..+.| -|+.|.+.|.....-+-| -+|..|+.||...
T Consensus 126 CT~CGPRfTIi~alPYD-R~nTsM~~F~lC~~C~~EY~dP~nRRfH---AQp~aCp~CGP~~ 183 (750)
T COG0068 126 CTNCGPRFTIIEALPYD-RENTSMADFPLCPFCDKEYKDPLNRRFH---AQPIACPKCGPHL 183 (750)
T ss_pred cCCCCcceeeeccCCCC-cccCccccCcCCHHHHHHhcCccccccc---cccccCcccCCCe
Confidence 44455555444433221 223333333 366666666555544444 4566777777643
No 115
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=76.41 E-value=1.1 Score=22.45 Aligned_cols=10 Identities=20% Similarity=0.700 Sum_probs=4.6
Q ss_pred eecccccccc
Q psy4084 52 FACHMCIKVF 61 (86)
Q Consensus 52 ~~C~~C~~~~ 61 (86)
+.|..||..|
T Consensus 71 ~~C~~CG~~~ 80 (135)
T PRK03824 71 LKCRNCGNEW 80 (135)
T ss_pred EECCCCCCEE
Confidence 4444444444
No 116
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=75.43 E-value=1.8 Score=16.74 Aligned_cols=14 Identities=29% Similarity=0.762 Sum_probs=11.1
Q ss_pred ceecccccccccCH
Q psy4084 51 QFACHMCIKVFPSQ 64 (86)
Q Consensus 51 ~~~C~~C~~~~~~~ 64 (86)
|+.|..|+..|-..
T Consensus 12 ~f~C~~C~~~FC~~ 25 (39)
T smart00154 12 GFKCRHCGNLFCGE 25 (39)
T ss_pred CeECCccCCccccc
Confidence 78899999887544
No 117
>COG3364 Zn-ribbon containing protein [General function prediction only]
Probab=75.39 E-value=2.2 Score=20.47 Aligned_cols=16 Identities=25% Similarity=0.586 Sum_probs=10.4
Q ss_pred ceecccccccCCChHH
Q psy4084 26 QFACHMCIKVFPSQDK 41 (86)
Q Consensus 26 ~~~c~~c~~~~~~~~~ 41 (86)
|.+|..||..|...+.
T Consensus 2 pH~CtrCG~vf~~g~~ 17 (112)
T COG3364 2 PHQCTRCGEVFDDGSE 17 (112)
T ss_pred CceecccccccccccH
Confidence 4567777777776543
No 118
>PF12907 zf-met2: Zinc-binding
Probab=75.04 E-value=2.5 Score=16.63 Aligned_cols=25 Identities=20% Similarity=0.558 Sum_probs=15.6
Q ss_pred eecccccccc---cCHHHHHHHHHh-CCC
Q psy4084 52 FACHMCIKVF---PSQDKLRMHMLS-GLQ 76 (86)
Q Consensus 52 ~~C~~C~~~~---~~~~~l~~h~~~-~~~ 76 (86)
+.|.+|..+| .....|..|... |.+
T Consensus 2 i~C~iC~qtF~~t~~~~~L~eH~enKHpK 30 (40)
T PF12907_consen 2 IICKICRQTFMQTTNEPQLKEHAENKHPK 30 (40)
T ss_pred cCcHHhhHHHHhcCCHHHHHHHHHccCCC
Confidence 4577776443 455678888775 444
No 119
>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=74.27 E-value=1.7 Score=18.29 Aligned_cols=30 Identities=17% Similarity=0.341 Sum_probs=15.2
Q ss_pred eecccccccCCChHHHhhhhhCCcceecccccccc
Q psy4084 27 FACHMCIKVFPSQDKLRMHMLSDRQFACHMCIKVF 61 (86)
Q Consensus 27 ~~c~~c~~~~~~~~~l~~h~~~~~~~~C~~C~~~~ 61 (86)
+.|+.|+..+....... .-...|+.||..+
T Consensus 3 ~~CP~CG~~iev~~~~~-----GeiV~Cp~CGael 32 (54)
T TIGR01206 3 FECPDCGAEIELENPEL-----GELVICDECGAEL 32 (54)
T ss_pred cCCCCCCCEEecCCCcc-----CCEEeCCCCCCEE
Confidence 46777776554333211 1234666666543
No 120
>KOG4167|consensus
Probab=74.15 E-value=1.2 Score=28.71 Aligned_cols=24 Identities=21% Similarity=0.366 Sum_probs=20.3
Q ss_pred CcchhhhccChHHHHhhHHHHhCC
Q psy4084 1 MSECMGKFTEYQVIRKHIRTFHSD 24 (86)
Q Consensus 1 c~~C~~~~~~~~~l~~h~~~~~~~ 24 (86)
|.+|++.|..--++..||.+|.-.
T Consensus 795 CreC~kvF~KiKSrNAHMK~Hr~q 818 (907)
T KOG4167|consen 795 CRECGKVFFKIKSRNAHMKTHRQQ 818 (907)
T ss_pred hHHHHHHHHHHhhhhHHHHHHHHH
Confidence 678999999888888999988753
No 121
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=73.98 E-value=5.1 Score=23.74 Aligned_cols=19 Identities=37% Similarity=0.670 Sum_probs=10.0
Q ss_pred cccccccCCChHHHhhhhh
Q psy4084 29 CHMCIKVFPSQDKLRMHML 47 (86)
Q Consensus 29 c~~c~~~~~~~~~l~~h~~ 47 (86)
|..|...|...+.|..|++
T Consensus 223 C~FC~~~FYdDDEL~~HcR 241 (493)
T COG5236 223 CIFCKIYFYDDDELRRHCR 241 (493)
T ss_pred hhhccceecChHHHHHHHH
Confidence 4445555555555555554
No 122
>PRK14873 primosome assembly protein PriA; Provisional
Probab=73.97 E-value=1.4 Score=28.10 Aligned_cols=9 Identities=22% Similarity=0.730 Sum_probs=4.5
Q ss_pred ceecccccc
Q psy4084 51 QFACHMCIK 59 (86)
Q Consensus 51 ~~~C~~C~~ 59 (86)
|+.|+.||.
T Consensus 422 p~~Cp~Cgs 430 (665)
T PRK14873 422 DWRCPRCGS 430 (665)
T ss_pred CccCCCCcC
Confidence 445555544
No 123
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=72.25 E-value=6.4 Score=22.99 Aligned_cols=26 Identities=19% Similarity=0.446 Sum_probs=21.2
Q ss_pred CcceecccccccccCHHHHHHHHHhC
Q psy4084 49 DRQFACHMCIKVFPSQDKLRMHMLSG 74 (86)
Q Consensus 49 ~~~~~C~~C~~~~~~~~~l~~h~~~~ 74 (86)
.-.|+|+.|...|-..-+.-.|...|
T Consensus 386 s~rY~Ce~CK~~FC~dCdvfiHe~Lh 411 (421)
T COG5151 386 SGRYQCELCKSTFCSDCDVFIHETLH 411 (421)
T ss_pred ccceechhhhhhhhhhhHHHHHHHHh
Confidence 45689999999998888887787776
No 124
>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=72.06 E-value=1.3 Score=18.32 Aligned_cols=11 Identities=18% Similarity=0.184 Sum_probs=5.0
Q ss_pred CcchhhhccCh
Q psy4084 1 MSECMGKFTEY 11 (86)
Q Consensus 1 c~~C~~~~~~~ 11 (86)
||.|++.|...
T Consensus 23 CPlC~r~l~~e 33 (54)
T PF04423_consen 23 CPLCGRPLDEE 33 (54)
T ss_dssp -TTT--EE-HH
T ss_pred CCCCCCCCCHH
Confidence 77888887654
No 125
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=72.00 E-value=1.3 Score=22.05 Aligned_cols=35 Identities=17% Similarity=0.357 Sum_probs=18.8
Q ss_pred eecccccccCCChHHHhhhhhCCcceecccccccccC
Q psy4084 27 FACHMCIKVFPSQDKLRMHMLSDRQFACHMCIKVFPS 63 (86)
Q Consensus 27 ~~c~~c~~~~~~~~~l~~h~~~~~~~~C~~C~~~~~~ 63 (86)
..|+.|+... .............|.|..|++.|..
T Consensus 31 ~~cP~C~s~~--~~k~g~~~~~~qRyrC~~C~~tf~~ 65 (129)
T COG3677 31 VNCPRCKSSN--VVKIGGIRRGHQRYKCKSCGSTFTV 65 (129)
T ss_pred CcCCCCCccc--eeeECCccccccccccCCcCcceee
Confidence 4577776443 1111111112456889999888753
No 126
>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=71.91 E-value=4.4 Score=24.86 Aligned_cols=23 Identities=26% Similarity=0.482 Sum_probs=19.9
Q ss_pred ceecccccccccCHHHHHHHHHh
Q psy4084 51 QFACHMCIKVFPSQDKLRMHMLS 73 (86)
Q Consensus 51 ~~~C~~C~~~~~~~~~l~~h~~~ 73 (86)
=+.|+.|.+.|.....+..|+..
T Consensus 57 FWiCp~CskkF~d~~~~~~H~~~ 79 (466)
T PF04780_consen 57 FWICPRCSKKFSDAESCLSHMEQ 79 (466)
T ss_pred EeeCCcccceeCCHHHHHHHHHH
Confidence 36899999999999999999875
No 127
>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=71.75 E-value=1.9 Score=16.99 Aligned_cols=15 Identities=33% Similarity=0.611 Sum_probs=9.2
Q ss_pred cceecccccccccCH
Q psy4084 50 RQFACHMCIKVFPSQ 64 (86)
Q Consensus 50 ~~~~C~~C~~~~~~~ 64 (86)
.|+.|+.|+..|-..
T Consensus 12 ~~~~C~~C~~~FC~~ 26 (43)
T PF01428_consen 12 LPFKCKHCGKSFCLK 26 (43)
T ss_dssp SHEE-TTTS-EE-TT
T ss_pred CCeECCCCCcccCcc
Confidence 478899999888544
No 128
>PF13451 zf-trcl: Probable zinc-binding domain
Probab=71.58 E-value=2.3 Score=17.50 Aligned_cols=18 Identities=22% Similarity=0.460 Sum_probs=13.5
Q ss_pred CcceecccccccccCHHH
Q psy4084 49 DRQFACHMCIKVFPSQDK 66 (86)
Q Consensus 49 ~~~~~C~~C~~~~~~~~~ 66 (86)
++++.|..||..|.....
T Consensus 2 Dk~l~C~dCg~~FvfTa~ 19 (49)
T PF13451_consen 2 DKTLTCKDCGAEFVFTAG 19 (49)
T ss_pred CeeEEcccCCCeEEEehh
Confidence 467889999998865543
No 129
>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=70.90 E-value=0.9 Score=27.83 Aligned_cols=9 Identities=22% Similarity=0.504 Sum_probs=5.3
Q ss_pred ceecccccc
Q psy4084 51 QFACHMCIK 59 (86)
Q Consensus 51 ~~~C~~C~~ 59 (86)
|..|+.|+.
T Consensus 253 ~~~Cp~C~s 261 (505)
T TIGR00595 253 PKTCPQCGS 261 (505)
T ss_pred CCCCCCCCC
Confidence 455666654
No 130
>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=70.06 E-value=1.5 Score=21.06 Aligned_cols=10 Identities=20% Similarity=0.627 Sum_probs=6.1
Q ss_pred Cceecccccc
Q psy4084 25 RQFACHMCIK 34 (86)
Q Consensus 25 ~~~~c~~c~~ 34 (86)
+|..|+.|+.
T Consensus 1 ~p~~CpYCg~ 10 (102)
T PF11672_consen 1 KPIICPYCGG 10 (102)
T ss_pred CCcccCCCCC
Confidence 3556777764
No 131
>PF10071 DUF2310: Zn-ribbon-containing, possibly nucleic-acid-binding protein (DUF2310); InterPro: IPR016908 This group represents uncharacterised conserved proteins.
Probab=69.52 E-value=1.9 Score=24.21 Aligned_cols=30 Identities=23% Similarity=0.509 Sum_probs=21.1
Q ss_pred CcceecccccccccCHHHHHHHHHhCCCCccCCCCcC
Q psy4084 49 DRQFACHMCIKVFPSQDKLRMHMLSGLQTFDLKSKLC 85 (86)
Q Consensus 49 ~~~~~C~~C~~~~~~~~~l~~h~~~~~~~~~~~c~~C 85 (86)
+..-.||.||....-...| ++-..|+|+.|
T Consensus 218 e~~r~CP~Cg~~W~L~~pl-------h~iFdFKCD~C 247 (258)
T PF10071_consen 218 EQARKCPSCGGDWRLKEPL-------HDIFDFKCDPC 247 (258)
T ss_pred hhCCCCCCCCCccccCCch-------hhceeccCCcc
Confidence 3445799999877666554 45566899887
No 132
>COG4957 Predicted transcriptional regulator [Transcription]
Probab=69.32 E-value=5.4 Score=20.24 Aligned_cols=25 Identities=20% Similarity=0.208 Sum_probs=19.1
Q ss_pred eecccccccccCHHHHHHHHHhCCCCcc
Q psy4084 52 FACHMCIKVFPSQDKLRMHMLSGLQTFD 79 (86)
Q Consensus 52 ~~C~~C~~~~~~~~~l~~h~~~~~~~~~ 79 (86)
..|.++|+.|. .|.+|+.+|.+-.|
T Consensus 77 IicLEDGkkfK---SLKRHL~t~~gmTP 101 (148)
T COG4957 77 IICLEDGKKFK---SLKRHLTTHYGLTP 101 (148)
T ss_pred EEEeccCcchH---HHHHHHhcccCCCH
Confidence 56888898874 57899999876544
No 133
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=68.29 E-value=3.3 Score=20.12 Aligned_cols=10 Identities=30% Similarity=0.551 Sum_probs=4.9
Q ss_pred eecccccccc
Q psy4084 52 FACHMCIKVF 61 (86)
Q Consensus 52 ~~C~~C~~~~ 61 (86)
+.|..|+..|
T Consensus 71 ~~C~~Cg~~~ 80 (113)
T PRK12380 71 AWCWDCSQVV 80 (113)
T ss_pred EEcccCCCEE
Confidence 4455555443
No 134
>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=68.12 E-value=2.8 Score=20.44 Aligned_cols=11 Identities=18% Similarity=0.534 Sum_probs=5.8
Q ss_pred eeccccccccc
Q psy4084 52 FACHMCIKVFP 62 (86)
Q Consensus 52 ~~C~~C~~~~~ 62 (86)
+.|..|+..|.
T Consensus 71 ~~C~~Cg~~~~ 81 (115)
T TIGR00100 71 CECEDCSEEVS 81 (115)
T ss_pred EEcccCCCEEe
Confidence 45555655443
No 135
>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=68.05 E-value=9.2 Score=16.48 Aligned_cols=33 Identities=21% Similarity=0.278 Sum_probs=20.4
Q ss_pred eecccccccCCChHHHhhhhhCCcceecccccccccCHHH
Q psy4084 27 FACHMCIKVFPSQDKLRMHMLSDRQFACHMCIKVFPSQDK 66 (86)
Q Consensus 27 ~~c~~c~~~~~~~~~l~~h~~~~~~~~C~~C~~~~~~~~~ 66 (86)
-.|+.||..... ....+.+.|+.||.......+
T Consensus 29 q~C~~CG~~~~~-------~~~~r~~~C~~Cg~~~~rD~n 61 (69)
T PF07282_consen 29 QTCPRCGHRNKK-------RRSGRVFTCPNCGFEMDRDVN 61 (69)
T ss_pred cCccCccccccc-------ccccceEEcCCCCCEECcHHH
Confidence 346677655433 112567899999988665543
No 136
>COG1773 Rubredoxin [Energy production and conversion]
Probab=67.54 E-value=2.9 Score=17.70 Aligned_cols=12 Identities=25% Similarity=0.836 Sum_probs=8.9
Q ss_pred ceeccccccccc
Q psy4084 51 QFACHMCIKVFP 62 (86)
Q Consensus 51 ~~~C~~C~~~~~ 62 (86)
.|+|..||..|.
T Consensus 3 ~~~C~~CG~vYd 14 (55)
T COG1773 3 RWRCSVCGYVYD 14 (55)
T ss_pred ceEecCCceEec
Confidence 577888887764
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=67.47 E-value=4.9 Score=20.42 Aligned_cols=43 Identities=19% Similarity=0.299 Sum_probs=26.3
Q ss_pred eecccccccCCChHHHh--hhhhC------CcceecccccccccCHHHHHH
Q psy4084 27 FACHMCIKVFPSQDKLR--MHMLS------DRQFACHMCIKVFPSQDKLRM 69 (86)
Q Consensus 27 ~~c~~c~~~~~~~~~l~--~h~~~------~~~~~C~~C~~~~~~~~~l~~ 69 (86)
-.|..|+..+.....-. .-+.. +.=+.|+.||+.|...+.+..
T Consensus 92 sRC~~CN~~L~~v~~~~v~~~vp~~v~~~~~~f~~C~~C~kiyW~GsH~~~ 142 (147)
T PF01927_consen 92 SRCPKCNGPLRPVSKEEVKDRVPPYVYETYDEFWRCPGCGKIYWEGSHWRR 142 (147)
T ss_pred CccCCCCcEeeechhhccccccCccccccCCeEEECCCCCCEecccccHHH
Confidence 57899987654432211 11111 345789999999988766553
No 138
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=67.45 E-value=7.6 Score=20.65 Aligned_cols=43 Identities=12% Similarity=0.455 Sum_probs=26.6
Q ss_pred HHHhhHHHHhCCCceecccccccCCChHHHhhhhhCCcceecccccccc
Q psy4084 13 VIRKHIRTFHSDRQFACHMCIKVFPSQDKLRMHMLSDRQFACHMCIKVF 61 (86)
Q Consensus 13 ~l~~h~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~C~~C~~~~ 61 (86)
.|+.-+..-....-|.|+.|...++..... +..|.|+.||...
T Consensus 100 ~Lk~~le~~~~~~~y~C~~~~~r~sfdeA~------~~~F~Cp~Cg~~L 142 (176)
T COG1675 100 KLKRKLEKETENNYYVCPNCHVKYSFDEAM------ELGFTCPKCGEDL 142 (176)
T ss_pred HHHHHHHhhccCCceeCCCCCCcccHHHHH------HhCCCCCCCCchh
Confidence 344444445556678898777665554433 2348899998764
No 139
>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=67.35 E-value=4.7 Score=16.04 Aligned_cols=15 Identities=27% Similarity=0.609 Sum_probs=9.8
Q ss_pred ecccccccccCHHHH
Q psy4084 53 ACHMCIKVFPSQDKL 67 (86)
Q Consensus 53 ~C~~C~~~~~~~~~l 67 (86)
.|..|++.|...-..
T Consensus 10 ~C~~C~rpf~WRKKW 24 (42)
T PF10013_consen 10 ICPVCGRPFTWRKKW 24 (42)
T ss_pred cCcccCCcchHHHHH
Confidence 577788777655443
No 140
>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=67.29 E-value=3.5 Score=19.99 Aligned_cols=14 Identities=21% Similarity=0.638 Sum_probs=8.8
Q ss_pred ceecccccccccCH
Q psy4084 51 QFACHMCIKVFPSQ 64 (86)
Q Consensus 51 ~~~C~~C~~~~~~~ 64 (86)
.|.|+.|+..++..
T Consensus 19 ~~iCpeC~~EW~~~ 32 (109)
T TIGR00686 19 QLICPSCLYEWNEN 32 (109)
T ss_pred eeECcccccccccc
Confidence 46777777766533
No 141
>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=66.69 E-value=0.91 Score=17.24 Aligned_cols=10 Identities=20% Similarity=0.687 Sum_probs=3.5
Q ss_pred eecccccccc
Q psy4084 52 FACHMCIKVF 61 (86)
Q Consensus 52 ~~C~~C~~~~ 61 (86)
..|..||..+
T Consensus 22 isC~~CGPr~ 31 (35)
T PF07503_consen 22 ISCTNCGPRY 31 (35)
T ss_dssp --BTTCC-SC
T ss_pred ccCCCCCCCE
Confidence 3455555443
No 142
>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=66.44 E-value=2.3 Score=16.50 Aligned_cols=12 Identities=17% Similarity=0.703 Sum_probs=6.4
Q ss_pred Ccceeccccccc
Q psy4084 49 DRQFACHMCIKV 60 (86)
Q Consensus 49 ~~~~~C~~C~~~ 60 (86)
.+.|.|..|+..
T Consensus 22 ~~~w~C~~C~~~ 33 (40)
T PF04810_consen 22 GKTWICNFCGTK 33 (40)
T ss_dssp TTEEEETTT--E
T ss_pred CCEEECcCCCCc
Confidence 356777777654
No 143
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=64.59 E-value=3.4 Score=19.35 Aligned_cols=32 Identities=19% Similarity=0.445 Sum_probs=19.5
Q ss_pred CceecccccccCCChHHHhhhhhCCcceecccccccccC
Q psy4084 25 RQFACHMCIKVFPSQDKLRMHMLSDRQFACHMCIKVFPS 63 (86)
Q Consensus 25 ~~~~c~~c~~~~~~~~~l~~h~~~~~~~~C~~C~~~~~~ 63 (86)
..|.|+.|++.--... ..-.|.|..|++.|+-
T Consensus 35 a~y~CpfCgk~~vkR~-------a~GIW~C~~C~~~~AG 66 (90)
T PTZ00255 35 AKYFCPFCGKHAVKRQ-------AVGIWRCKGCKKTVAG 66 (90)
T ss_pred CCccCCCCCCCceeee-------eeEEEEcCCCCCEEeC
Confidence 4588999974311100 0235889999888753
No 144
>PF02891 zf-MIZ: MIZ/SP-RING zinc finger; InterPro: IPR004181 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents MIZ-type zinc finger domains. Miz1 (Msx-interacting-zinc finger) is a zinc finger-containing protein with homology to the yeast protein, Nfi-1. Miz1 is a sequence specific DNA binding protein that can function as a positive-acting transcription factor. Miz1 binds to the homeobox protein Msx2, enhancing the specific DNA-binding ability of Msx2 []. Other proteins containing this domain include the human pias family (protein inhibitor of activated STAT protein). More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3I2D_A.
Probab=63.04 E-value=3.5 Score=16.87 Aligned_cols=7 Identities=29% Similarity=1.179 Sum_probs=2.1
Q ss_pred eeccccc
Q psy4084 27 FACHMCI 33 (86)
Q Consensus 27 ~~c~~c~ 33 (86)
|.|+.|+
T Consensus 42 W~CPiC~ 48 (50)
T PF02891_consen 42 WKCPICN 48 (50)
T ss_dssp -B-TTT-
T ss_pred eECcCCc
Confidence 5555554
No 145
>KOG0978|consensus
Probab=62.97 E-value=4.5 Score=26.13 Aligned_cols=21 Identities=38% Similarity=0.678 Sum_probs=15.1
Q ss_pred cceecccccccccCHHHHHHH
Q psy4084 50 RQFACHMCIKVFPSQDKLRMH 70 (86)
Q Consensus 50 ~~~~C~~C~~~~~~~~~l~~h 70 (86)
+.-.||.|+.+|...+-+..|
T Consensus 677 RqRKCP~Cn~aFganDv~~I~ 697 (698)
T KOG0978|consen 677 RQRKCPKCNAAFGANDVHRIH 697 (698)
T ss_pred hcCCCCCCCCCCCcccccccC
Confidence 445899999999877655443
No 146
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=62.04 E-value=6.2 Score=16.70 Aligned_cols=12 Identities=25% Similarity=0.462 Sum_probs=6.4
Q ss_pred CCceeccccccc
Q psy4084 24 DRQFACHMCIKV 35 (86)
Q Consensus 24 ~~~~~c~~c~~~ 35 (86)
...|+|+.||-.
T Consensus 12 ~v~~~Cp~cGip 23 (55)
T PF13824_consen 12 HVNFECPDCGIP 23 (55)
T ss_pred ccCCcCCCCCCc
Confidence 344566666543
No 147
>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=62.00 E-value=8.8 Score=14.36 Aligned_cols=21 Identities=14% Similarity=0.380 Sum_probs=11.1
Q ss_pred ceecccccccccCHHHHHHHHH
Q psy4084 51 QFACHMCIKVFPSQDKLRMHML 72 (86)
Q Consensus 51 ~~~C~~C~~~~~~~~~l~~h~~ 72 (86)
.+.|+.|++..... -+..|+.
T Consensus 4 ~~~C~nC~R~v~a~-RfA~HLe 24 (33)
T PF08209_consen 4 YVECPNCGRPVAAS-RFAPHLE 24 (33)
T ss_dssp EEE-TTTSSEEEGG-GHHHHHH
T ss_pred eEECCCCcCCcchh-hhHHHHH
Confidence 35677777765433 3455554
No 148
>COG4338 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=60.63 E-value=3.7 Score=16.82 Aligned_cols=15 Identities=27% Similarity=0.673 Sum_probs=10.3
Q ss_pred ecccccccccCHHHH
Q psy4084 53 ACHMCIKVFPSQDKL 67 (86)
Q Consensus 53 ~C~~C~~~~~~~~~l 67 (86)
.|+.|++.|.+....
T Consensus 14 ICpvCqRPFsWRkKW 28 (54)
T COG4338 14 ICPVCQRPFSWRKKW 28 (54)
T ss_pred hhhhhcCchHHHHHH
Confidence 578888888765443
No 149
>PF12230 PRP21_like_P: Pre-mRNA splicing factor PRP21 like protein; InterPro: IPR022030 This domain family is found in eukaryotes, and is typically between 212 and 238 amino acids in length. The family is found in association with PF01805 from PFAM. There are two completely conserved residues (W and H) that may be functionally important. PRP21 is required for assembly of the prespliceosome and it interacts with U2 snRNP and/or pre-mRNA in the prespliceosome. This family also contains proteins similar to PRP21, such as the mammalian SF3a. SF3a also interacts with U2 snRNP from the prespliceosome, converting it to its active form. ; PDB: 4DGW_B.
Probab=60.46 E-value=2.9 Score=22.88 Aligned_cols=31 Identities=19% Similarity=0.337 Sum_probs=0.0
Q ss_pred cceecccccccccCHHHHHHHHHhCCCCccCC
Q psy4084 50 RQFACHMCIKVFPSQDKLRMHMLSGLQTFDLK 81 (86)
Q Consensus 50 ~~~~C~~C~~~~~~~~~l~~h~~~~~~~~~~~ 81 (86)
....|+.||...+.. .+..||++...+..|+
T Consensus 167 ~~~~cPitGe~IP~~-e~~eHmRi~LlDP~wk 197 (229)
T PF12230_consen 167 KMIICPITGEMIPAD-EMDEHMRIELLDPRWK 197 (229)
T ss_dssp --------------------------------
T ss_pred ccccccccccccccc-cccccccccccccccc
Confidence 346899999886644 6889999887776664
No 150
>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=60.46 E-value=4.4 Score=15.91 Aligned_cols=12 Identities=17% Similarity=0.540 Sum_probs=9.0
Q ss_pred cceecccccccc
Q psy4084 50 RQFACHMCIKVF 61 (86)
Q Consensus 50 ~~~~C~~C~~~~ 61 (86)
.+..|++|+..|
T Consensus 28 ~~~~CpYCg~~y 39 (40)
T PF10276_consen 28 GPVVCPYCGTRY 39 (40)
T ss_dssp CEEEETTTTEEE
T ss_pred CeEECCCCCCEE
Confidence 457888888765
No 151
>KOG1842|consensus
Probab=60.43 E-value=6.5 Score=24.09 Aligned_cols=25 Identities=24% Similarity=0.513 Sum_probs=16.5
Q ss_pred ceecccccccccCHHHHHHHHHhCC
Q psy4084 51 QFACHMCIKVFPSQDKLRMHMLSGL 75 (86)
Q Consensus 51 ~~~C~~C~~~~~~~~~l~~h~~~~~ 75 (86)
.|.|+.|...|.....|..|....|
T Consensus 15 gflCPiC~~dl~~~~~L~~H~d~eH 39 (505)
T KOG1842|consen 15 GFLCPICLLDLPNLSALNDHLDVEH 39 (505)
T ss_pred cccCchHhhhhhhHHHHHHHHhhhc
Confidence 4667777777777777777766543
No 152
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=59.98 E-value=2.3 Score=16.04 Aligned_cols=8 Identities=25% Similarity=0.646 Sum_probs=4.1
Q ss_pred eecccccc
Q psy4084 52 FACHMCIK 59 (86)
Q Consensus 52 ~~C~~C~~ 59 (86)
+.|+.||.
T Consensus 23 ~vC~~Cg~ 30 (34)
T PF14803_consen 23 LVCPACGF 30 (34)
T ss_dssp EEETTTTE
T ss_pred eECCCCCC
Confidence 44555554
No 153
>KOG1994|consensus
Probab=59.58 E-value=7.7 Score=21.57 Aligned_cols=25 Identities=16% Similarity=0.410 Sum_probs=21.2
Q ss_pred cceecccccccccCHHHHHHHHHhC
Q psy4084 50 RQFACHMCIKVFPSQDKLRMHMLSG 74 (86)
Q Consensus 50 ~~~~C~~C~~~~~~~~~l~~h~~~~ 74 (86)
-.|.|-+||..|.+...|..|-...
T Consensus 238 eh~YC~fCG~~y~~~edl~ehCPGv 262 (268)
T KOG1994|consen 238 EHYYCFFCGIKYKDEEDLYEHCPGV 262 (268)
T ss_pred cceEEEEeccccCCHHHHHHhCCCC
Confidence 4588999999999999999887643
No 154
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=59.27 E-value=3.2 Score=17.50 Aligned_cols=10 Identities=40% Similarity=0.883 Sum_probs=5.8
Q ss_pred ecccccccCC
Q psy4084 28 ACHMCIKVFP 37 (86)
Q Consensus 28 ~c~~c~~~~~ 37 (86)
.|..|++.|.
T Consensus 7 ~C~~Cg~~~~ 16 (54)
T PF14446_consen 7 KCPVCGKKFK 16 (54)
T ss_pred cChhhCCccc
Confidence 4666666554
No 155
>PF11789 zf-Nse: Zinc-finger of the MIZ type in Nse subunit; PDB: 2YU4_A 3HTK_C.
Probab=58.91 E-value=6.2 Score=16.68 Aligned_cols=32 Identities=9% Similarity=0.164 Sum_probs=16.4
Q ss_pred CcceecccccccccCHHHHHHHHHhCCCCccCCCCc
Q psy4084 49 DRQFACHMCIKVFPSQDKLRMHMLSGLQTFDLKSKL 84 (86)
Q Consensus 49 ~~~~~C~~C~~~~~~~~~l~~h~~~~~~~~~~~c~~ 84 (86)
+.|+....|+..|.....+ .++ ......+|+.
T Consensus 22 ~~PV~s~~C~H~fek~aI~-~~i---~~~~~~~CPv 53 (57)
T PF11789_consen 22 EDPVKSKKCGHTFEKEAIL-QYI---QRNGSKRCPV 53 (57)
T ss_dssp SSEEEESSS--EEEHHHHH-HHC---TTTS-EE-SC
T ss_pred hCCcCcCCCCCeecHHHHH-HHH---HhcCCCCCCC
Confidence 4577777888887655443 344 2344566665
No 156
>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=58.82 E-value=1.5 Score=15.77 Aligned_cols=8 Identities=50% Similarity=0.970 Sum_probs=3.7
Q ss_pred cccccccC
Q psy4084 29 CHMCIKVF 36 (86)
Q Consensus 29 c~~c~~~~ 36 (86)
|..|++.|
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 157
>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=58.76 E-value=5.4 Score=16.23 Aligned_cols=12 Identities=25% Similarity=0.833 Sum_probs=8.9
Q ss_pred eecccccccccC
Q psy4084 52 FACHMCIKVFPS 63 (86)
Q Consensus 52 ~~C~~C~~~~~~ 63 (86)
|+|..|+..+.-
T Consensus 2 y~C~~CgyvYd~ 13 (47)
T PF00301_consen 2 YQCPVCGYVYDP 13 (47)
T ss_dssp EEETTTSBEEET
T ss_pred cCCCCCCEEEcC
Confidence 678888877643
No 158
>KOG0717|consensus
Probab=57.31 E-value=9.4 Score=23.60 Aligned_cols=22 Identities=36% Similarity=0.634 Sum_probs=19.0
Q ss_pred eecccccccccCHHHHHHHHHh
Q psy4084 52 FACHMCIKVFPSQDKLRMHMLS 73 (86)
Q Consensus 52 ~~C~~C~~~~~~~~~l~~h~~~ 73 (86)
+.|..|.+.|.+.-.+..|..+
T Consensus 293 lyC~vCnKsFKseKq~kNHEnS 314 (508)
T KOG0717|consen 293 LYCVVCNKSFKSEKQLKNHENS 314 (508)
T ss_pred eEEeeccccccchHHHHhhHHH
Confidence 7799999999999999888764
No 159
>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=56.79 E-value=5.1 Score=19.44 Aligned_cols=11 Identities=27% Similarity=0.558 Sum_probs=5.1
Q ss_pred eeccccccccc
Q psy4084 52 FACHMCIKVFP 62 (86)
Q Consensus 52 ~~C~~C~~~~~ 62 (86)
+.|..||..|.
T Consensus 71 ~~C~~Cg~~~~ 81 (113)
T PF01155_consen 71 ARCRDCGHEFE 81 (113)
T ss_dssp EEETTTS-EEE
T ss_pred EECCCCCCEEe
Confidence 44555555544
No 160
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=56.04 E-value=6.5 Score=19.26 Aligned_cols=9 Identities=33% Similarity=0.918 Sum_probs=4.0
Q ss_pred eeccccccc
Q psy4084 52 FACHMCIKV 60 (86)
Q Consensus 52 ~~C~~C~~~ 60 (86)
+.|..||..
T Consensus 72 ~~C~~Cg~~ 80 (117)
T PRK00564 72 LECKDCSHV 80 (117)
T ss_pred EEhhhCCCc
Confidence 344444433
No 161
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=55.12 E-value=7.5 Score=23.63 Aligned_cols=13 Identities=23% Similarity=0.467 Sum_probs=7.2
Q ss_pred ceecccccccccC
Q psy4084 51 QFACHMCIKVFPS 63 (86)
Q Consensus 51 ~~~C~~C~~~~~~ 63 (86)
-|.|+.||..+..
T Consensus 367 g~rC~kCg~~~~~ 379 (421)
T COG1571 367 GFRCKKCGTRARE 379 (421)
T ss_pred CcccccccccCCc
Confidence 5566666655443
No 162
>PRK10220 hypothetical protein; Provisional
Probab=54.68 E-value=10 Score=18.51 Aligned_cols=13 Identities=15% Similarity=0.623 Sum_probs=7.6
Q ss_pred ceecccccccccC
Q psy4084 51 QFACHMCIKVFPS 63 (86)
Q Consensus 51 ~~~C~~C~~~~~~ 63 (86)
.|.|+.|+.-+..
T Consensus 20 ~~vCpeC~hEW~~ 32 (111)
T PRK10220 20 MYICPECAHEWND 32 (111)
T ss_pred eEECCcccCcCCc
Confidence 4566666665543
No 163
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=54.56 E-value=3 Score=19.93 Aligned_cols=38 Identities=18% Similarity=0.273 Sum_probs=20.1
Q ss_pred CCceecccccccCCChHHHhhhhhCCcceeccccccccc
Q psy4084 24 DRQFACHMCIKVFPSQDKLRMHMLSDRQFACHMCIKVFP 62 (86)
Q Consensus 24 ~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~C~~C~~~~~ 62 (86)
.+.|.|+.|+..-...-.+..-.. .-...|..||..|.
T Consensus 20 ~k~FtCp~Cghe~vs~ctvkk~~~-~g~~~Cg~CGls~e 57 (104)
T COG4888 20 PKTFTCPRCGHEKVSSCTVKKTVN-IGTAVCGNCGLSFE 57 (104)
T ss_pred CceEecCccCCeeeeEEEEEecCc-eeEEEcccCcceEE
Confidence 456899999865433222211100 12356777776653
No 164
>PF12773 DZR: Double zinc ribbon
Probab=54.32 E-value=7.5 Score=15.55 Aligned_cols=25 Identities=20% Similarity=0.381 Sum_probs=13.1
Q ss_pred ecccccccCCChHHHhhhhhCCcceeccccccc
Q psy4084 28 ACHMCIKVFPSQDKLRMHMLSDRQFACHMCIKV 60 (86)
Q Consensus 28 ~c~~c~~~~~~~~~l~~h~~~~~~~~C~~C~~~ 60 (86)
.|+.||..+. ........|+.|+..
T Consensus 14 fC~~CG~~l~--------~~~~~~~~C~~Cg~~ 38 (50)
T PF12773_consen 14 FCPHCGTPLP--------PPDQSKKICPNCGAE 38 (50)
T ss_pred CChhhcCChh--------hccCCCCCCcCCcCC
Confidence 4666665544 111334567777764
No 165
>COG3091 SprT Zn-dependent metalloprotease, SprT family [General function prediction only]
Probab=53.98 E-value=9.8 Score=19.76 Aligned_cols=32 Identities=16% Similarity=0.338 Sum_probs=18.2
Q ss_pred cceecccccccccCHHHHHHHHHhCCCCccCCCCcCC
Q psy4084 50 RQFACHMCIKVFPSQDKLRMHMLSGLQTFDLKSKLCT 86 (86)
Q Consensus 50 ~~~~C~~C~~~~~~~~~l~~h~~~~~~~~~~~c~~C~ 86 (86)
-+|.|. |+..+.+. ++|-..-.++ .|.|-.|+
T Consensus 116 ~~Y~C~-C~q~~l~~---RRhn~~~~g~-~YrC~~C~ 147 (156)
T COG3091 116 YPYRCQ-CQQHYLRI---RRHNTVRRGE-VYRCGKCG 147 (156)
T ss_pred eeEEee-cCCccchh---hhcccccccc-eEEeccCC
Confidence 367788 87765544 2233333344 67777774
No 166
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=53.75 E-value=7.5 Score=18.95 Aligned_cols=10 Identities=20% Similarity=0.567 Sum_probs=5.5
Q ss_pred eecccccccC
Q psy4084 27 FACHMCIKVF 36 (86)
Q Consensus 27 ~~c~~c~~~~ 36 (86)
..|..|+..|
T Consensus 71 ~~C~~Cg~~~ 80 (114)
T PRK03681 71 CWCETCQQYV 80 (114)
T ss_pred EEcccCCCee
Confidence 4566666443
No 167
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=53.42 E-value=3.2 Score=16.13 Aligned_cols=10 Identities=20% Similarity=0.806 Sum_probs=6.5
Q ss_pred eecccccccc
Q psy4084 52 FACHMCIKVF 61 (86)
Q Consensus 52 ~~C~~C~~~~ 61 (86)
|.|..|+..+
T Consensus 29 y~C~~C~~~w 38 (40)
T smart00440 29 YVCTKCGHRW 38 (40)
T ss_pred EEeCCCCCEe
Confidence 6677777654
No 168
>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=52.90 E-value=5.9 Score=16.35 Aligned_cols=12 Identities=17% Similarity=0.902 Sum_probs=9.4
Q ss_pred eecccccccccC
Q psy4084 52 FACHMCIKVFPS 63 (86)
Q Consensus 52 ~~C~~C~~~~~~ 63 (86)
|+|..||..+.-
T Consensus 2 y~C~~CgyiYd~ 13 (50)
T cd00730 2 YECRICGYIYDP 13 (50)
T ss_pred cCCCCCCeEECC
Confidence 678899988763
No 169
>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=52.66 E-value=2.4 Score=17.64 Aligned_cols=17 Identities=18% Similarity=0.497 Sum_probs=5.7
Q ss_pred ceecccccccccCHHHH
Q psy4084 51 QFACHMCIKVFPSQDKL 67 (86)
Q Consensus 51 ~~~C~~C~~~~~~~~~l 67 (86)
.|.|+.|+..|-..-.+
T Consensus 21 ~y~C~~C~~~FC~dCD~ 37 (51)
T PF07975_consen 21 RYRCPKCKNHFCIDCDV 37 (51)
T ss_dssp EE--TTTT--B-HHHHH
T ss_pred eEECCCCCCccccCcCh
Confidence 45555555555444333
No 170
>PF15135 UPF0515: Uncharacterised protein UPF0515
Probab=52.44 E-value=12 Score=21.12 Aligned_cols=14 Identities=29% Similarity=0.674 Sum_probs=9.4
Q ss_pred ceecccccccccCH
Q psy4084 51 QFACHMCIKVFPSQ 64 (86)
Q Consensus 51 ~~~C~~C~~~~~~~ 64 (86)
.|.|+.|+..|...
T Consensus 155 ef~C~~C~h~F~G~ 168 (278)
T PF15135_consen 155 EFHCPKCRHNFRGF 168 (278)
T ss_pred eeecccccccchhh
Confidence 46777777777543
No 171
>PLN02294 cytochrome c oxidase subunit Vb
Probab=52.15 E-value=8.1 Score=20.45 Aligned_cols=14 Identities=29% Similarity=0.895 Sum_probs=10.1
Q ss_pred CceecccccccCCC
Q psy4084 25 RQFACHMCIKVFPS 38 (86)
Q Consensus 25 ~~~~c~~c~~~~~~ 38 (86)
++.+|+.||..|..
T Consensus 140 kp~RCpeCG~~fkL 153 (174)
T PLN02294 140 KSFECPVCTQYFEL 153 (174)
T ss_pred CceeCCCCCCEEEE
Confidence 57778888877654
No 172
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=52.11 E-value=18 Score=15.00 Aligned_cols=32 Identities=22% Similarity=0.482 Sum_probs=15.4
Q ss_pred ecccccccCCChHHHhhhhhCCcceeccccccc
Q psy4084 28 ACHMCIKVFPSQDKLRMHMLSDRQFACHMCIKV 60 (86)
Q Consensus 28 ~c~~c~~~~~~~~~l~~h~~~~~~~~C~~C~~~ 60 (86)
.|..|.-..+....... ...+....|+.||+.
T Consensus 24 ~C~gC~~~l~~~~~~~i-~~~~~i~~Cp~CgRi 55 (56)
T PF02591_consen 24 TCSGCHMELPPQELNEI-RKGDEIVFCPNCGRI 55 (56)
T ss_pred ccCCCCEEcCHHHHHHH-HcCCCeEECcCCCcc
Confidence 46666544433322221 111345678887763
No 173
>COG2879 Uncharacterized small protein [Function unknown]
Probab=51.99 E-value=22 Score=15.56 Aligned_cols=18 Identities=28% Similarity=0.582 Sum_probs=14.1
Q ss_pred cChHHHHhhHHHHhCCCc
Q psy4084 9 TEYQVIRKHIRTFHSDRQ 26 (86)
Q Consensus 9 ~~~~~l~~h~~~~~~~~~ 26 (86)
+..+++..|++.++..+|
T Consensus 23 pdYdnYVehmr~~hPd~p 40 (65)
T COG2879 23 PDYDNYVEHMRKKHPDKP 40 (65)
T ss_pred CcHHHHHHHHHHhCcCCC
Confidence 566788889998887766
No 174
>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=51.96 E-value=13 Score=15.98 Aligned_cols=10 Identities=40% Similarity=0.942 Sum_probs=3.3
Q ss_pred ecccccccCC
Q psy4084 28 ACHMCIKVFP 37 (86)
Q Consensus 28 ~c~~c~~~~~ 37 (86)
.|..|++.|.
T Consensus 11 ~C~~C~~~F~ 20 (69)
T PF01363_consen 11 NCMICGKKFS 20 (69)
T ss_dssp B-TTT--B-B
T ss_pred cCcCcCCcCC
Confidence 4556666653
No 175
>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=51.65 E-value=3.1 Score=21.30 Aligned_cols=30 Identities=17% Similarity=0.332 Sum_probs=18.0
Q ss_pred CceecccccccCCChHHHhhhhhCCcceecccccccc
Q psy4084 25 RQFACHMCIKVFPSQDKLRMHMLSDRQFACHMCIKVF 61 (86)
Q Consensus 25 ~~~~c~~c~~~~~~~~~l~~h~~~~~~~~C~~C~~~~ 61 (86)
..+.|..||....... +..--.|+.|+...
T Consensus 111 G~l~C~~Cg~~~~~~~-------~~~l~~Cp~C~~~~ 140 (146)
T PF07295_consen 111 GTLVCENCGHEVELTH-------PERLPPCPKCGHTE 140 (146)
T ss_pred ceEecccCCCEEEecC-------CCcCCCCCCCCCCe
Confidence 4588999986533211 12334788887653
No 176
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=51.34 E-value=13 Score=15.32 Aligned_cols=12 Identities=17% Similarity=0.382 Sum_probs=7.1
Q ss_pred cceecccccccc
Q psy4084 50 RQFACHMCIKVF 61 (86)
Q Consensus 50 ~~~~C~~C~~~~ 61 (86)
..+.|..||..+
T Consensus 36 ~r~~C~~Cgyt~ 47 (50)
T PRK00432 36 DRWHCGKCGYTE 47 (50)
T ss_pred CcEECCCcCCEE
Confidence 345676666553
No 177
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=50.64 E-value=6.8 Score=19.75 Aligned_cols=13 Identities=31% Similarity=0.733 Sum_probs=7.0
Q ss_pred eecccccccccCH
Q psy4084 52 FACHMCIKVFPSQ 64 (86)
Q Consensus 52 ~~C~~C~~~~~~~ 64 (86)
.+|..||+.|...
T Consensus 2 H~Ct~Cg~~f~dg 14 (131)
T PF09845_consen 2 HQCTKCGRVFEDG 14 (131)
T ss_pred cccCcCCCCcCCC
Confidence 3555566665543
No 178
>PF14353 CpXC: CpXC protein
Probab=50.19 E-value=9.4 Score=18.79 Aligned_cols=15 Identities=27% Similarity=0.561 Sum_probs=11.2
Q ss_pred cceecccccccccCH
Q psy4084 50 RQFACHMCIKVFPSQ 64 (86)
Q Consensus 50 ~~~~C~~C~~~~~~~ 64 (86)
..+.|+.||..+.-.
T Consensus 37 ~~~~CP~Cg~~~~~~ 51 (128)
T PF14353_consen 37 FSFTCPSCGHKFRLE 51 (128)
T ss_pred CEEECCCCCCceecC
Confidence 358899999887543
No 179
>COG5112 UFD2 U1-like Zn-finger-containing protein [General function prediction only]
Probab=48.47 E-value=8.5 Score=18.66 Aligned_cols=24 Identities=25% Similarity=0.416 Sum_probs=18.4
Q ss_pred CceecccccccCCChHHHhhhhhC
Q psy4084 25 RQFACHMCIKVFPSQDKLRMHMLS 48 (86)
Q Consensus 25 ~~~~c~~c~~~~~~~~~l~~h~~~ 48 (86)
..+.|..|.+.|.+...|..|.++
T Consensus 54 GqhYCieCaryf~t~~aL~~Hkkg 77 (126)
T COG5112 54 GQHYCIECARYFITEKALMEHKKG 77 (126)
T ss_pred ceeeeehhHHHHHHHHHHHHHhcc
Confidence 347788888888888888887754
No 180
>COG1326 Uncharacterized archaeal Zn-finger protein [General function prediction only]
Probab=48.23 E-value=26 Score=19.11 Aligned_cols=37 Identities=16% Similarity=0.313 Sum_probs=20.1
Q ss_pred ceecccccccCCChHHHhhhhhCCcceecccccccccC
Q psy4084 26 QFACHMCIKVFPSQDKLRMHMLSDRQFACHMCIKVFPS 63 (86)
Q Consensus 26 ~~~c~~c~~~~~~~~~l~~h~~~~~~~~C~~C~~~~~~ 63 (86)
-++|+.|+.. ...-.+..-...+..+.|..||..++.
T Consensus 6 y~~Cp~Cg~e-ev~hEVik~~g~~~lvrC~eCG~V~~~ 42 (201)
T COG1326 6 YIECPSCGSE-EVSHEVIKERGREPLVRCEECGTVHPA 42 (201)
T ss_pred EEECCCCCcc-hhhHHHHHhcCCceEEEccCCCcEeec
Confidence 4689999821 111122211111445789999988744
No 181
>KOG2071|consensus
Probab=47.82 E-value=12 Score=23.79 Aligned_cols=23 Identities=17% Similarity=0.324 Sum_probs=17.8
Q ss_pred CcchhhhccChHHHHhhHHHHhC
Q psy4084 1 MSECMGKFTEYQVIRKHIRTFHS 23 (86)
Q Consensus 1 c~~C~~~~~~~~~l~~h~~~~~~ 23 (86)
|..||.+|........|+..|..
T Consensus 421 C~~CG~R~~~~ee~sk~md~H~d 443 (579)
T KOG2071|consen 421 CKSCGLRFDDSEERSKHMDIHDD 443 (579)
T ss_pred hcccccccccchhhhhHhhhhhh
Confidence 77899999988777777666554
No 182
>PTZ00448 hypothetical protein; Provisional
Probab=47.34 E-value=19 Score=21.64 Aligned_cols=24 Identities=17% Similarity=0.382 Sum_probs=20.7
Q ss_pred ceecccccccccCHHHHHHHHHhC
Q psy4084 51 QFACHMCIKVFPSQDKLRMHMLSG 74 (86)
Q Consensus 51 ~~~C~~C~~~~~~~~~l~~h~~~~ 74 (86)
.+.|..|+-.|.+....+.|+++.
T Consensus 314 ~~tC~~C~v~F~~~~~qR~H~KSD 337 (373)
T PTZ00448 314 MLLCRKCNIQLMDHNAFKQHYRSE 337 (373)
T ss_pred CccccccccccCCHHHHHHHhhhh
Confidence 577999999999888889998873
No 183
>COG5188 PRP9 Splicing factor 3a, subunit 3 [RNA processing and modification]
Probab=46.77 E-value=11 Score=22.47 Aligned_cols=20 Identities=20% Similarity=0.448 Sum_probs=16.4
Q ss_pred CcchhhhccChHHHHhhHHH
Q psy4084 1 MSECMGKFTEYQVIRKHIRT 20 (86)
Q Consensus 1 c~~C~~~~~~~~~l~~h~~~ 20 (86)
|+.|++.|.....+..|...
T Consensus 241 C~~C~r~f~~~~VFe~Hl~g 260 (470)
T COG5188 241 CVKCGREFSRSKVFEYHLEG 260 (470)
T ss_pred eHhhhhHhhhhHHHHHHHhh
Confidence 78899999988888888653
No 184
>TIGR03829 YokU_near_AblA uncharacterized protein, YokU family. Members of this protein family occur in various species of the genus Bacillus, always next to the gene (kamA or ablA) for lysine 2,3-aminomutase. Members have a pair of CXXC motifs, and share homology to the amino-terminal region of a family of putative transcription factors for which the C-terminal is modeled by pfam01381, a helix-turn-helix domain model. This family, however, is shorter and lacks the helix-turn-helix region. The function of this protein family is unknown, but a regulatory role in compatible solute biosynthesis is suggested by local genome context.
Probab=46.63 E-value=13 Score=17.46 Aligned_cols=15 Identities=13% Similarity=0.405 Sum_probs=9.0
Q ss_pred CcchhhhccChHHHH
Q psy4084 1 MSECMGKFTEYQVIR 15 (86)
Q Consensus 1 c~~C~~~~~~~~~l~ 15 (86)
|+.||..|.+.+-+.
T Consensus 38 C~~CGe~y~~dev~~ 52 (89)
T TIGR03829 38 CSHCGMEYQDDTTVK 52 (89)
T ss_pred ccCCCcEeecHHHHH
Confidence 566776666555443
No 185
>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=46.43 E-value=10 Score=14.43 Aligned_cols=11 Identities=18% Similarity=0.661 Sum_probs=8.0
Q ss_pred eeccccccccc
Q psy4084 52 FACHMCIKVFP 62 (86)
Q Consensus 52 ~~C~~C~~~~~ 62 (86)
+.|+.||..|.
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 46788888875
No 186
>KOG2636|consensus
Probab=45.54 E-value=45 Score=20.81 Aligned_cols=24 Identities=21% Similarity=0.592 Sum_probs=16.5
Q ss_pred Ccceeccccc-ccccCHHHHHHHHH
Q psy4084 49 DRQFACHMCI-KVFPSQDKLRMHML 72 (86)
Q Consensus 49 ~~~~~C~~C~-~~~~~~~~l~~h~~ 72 (86)
...|.|.+|| +++.-...+.+|..
T Consensus 399 ~~ey~CEICGNy~Y~GrkaF~RHF~ 423 (497)
T KOG2636|consen 399 DIEYNCEICGNYVYKGRKAFDRHFN 423 (497)
T ss_pred CcccceeeccCccccCcHHHHHHhH
Confidence 5667777776 66666667776654
No 187
>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=45.52 E-value=12 Score=17.84 Aligned_cols=14 Identities=29% Similarity=0.532 Sum_probs=10.0
Q ss_pred CceecccccccCCC
Q psy4084 25 RQFACHMCIKVFPS 38 (86)
Q Consensus 25 ~~~~c~~c~~~~~~ 38 (86)
++..|..||..|..
T Consensus 78 ~~~rC~eCG~~fkL 91 (97)
T cd00924 78 KPKRCPECGHVFKL 91 (97)
T ss_pred CceeCCCCCcEEEE
Confidence 57788888877654
No 188
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=45.47 E-value=32 Score=19.64 Aligned_cols=22 Identities=23% Similarity=0.389 Sum_probs=15.1
Q ss_pred CcceecccccccccCHHHHHHH
Q psy4084 49 DRQFACHMCIKVFPSQDKLRMH 70 (86)
Q Consensus 49 ~~~~~C~~C~~~~~~~~~l~~h 70 (86)
.+.+.|+.||..+....+-...
T Consensus 320 ~r~~~C~~cg~~~~rD~naa~N 341 (364)
T COG0675 320 GRLFKCPRCGFVHDRDVNAALN 341 (364)
T ss_pred ceeEECCCCCCeehhhHHHHHH
Confidence 5678999999886655444333
No 189
>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=45.20 E-value=1.8 Score=16.56 Aligned_cols=8 Identities=25% Similarity=1.169 Sum_probs=4.5
Q ss_pred cceecccc
Q psy4084 50 RQFACHMC 57 (86)
Q Consensus 50 ~~~~C~~C 57 (86)
..|.|..|
T Consensus 28 qryrC~~C 35 (36)
T PF03811_consen 28 QRYRCKDC 35 (36)
T ss_pred EeEecCcC
Confidence 44666655
No 190
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=44.12 E-value=23 Score=13.60 Aligned_cols=16 Identities=19% Similarity=0.368 Sum_probs=8.7
Q ss_pred CcchhhhccChHHHHh
Q psy4084 1 MSECMGKFTEYQVIRK 16 (86)
Q Consensus 1 c~~C~~~~~~~~~l~~ 16 (86)
|+.|+..+.....|.+
T Consensus 22 C~~C~G~W~d~~el~~ 37 (41)
T PF13453_consen 22 CPSCGGIWFDAGELEK 37 (41)
T ss_pred CCCCCeEEccHHHHHH
Confidence 4556655555555543
No 191
>COG4391 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=44.10 E-value=4.5 Score=17.50 Aligned_cols=45 Identities=13% Similarity=0.145 Sum_probs=25.6
Q ss_pred hHHHHhCCCceecccccccCCChHHHhhhhhCCcceeccccccccc
Q psy4084 17 HIRTFHSDRQFACHMCIKVFPSQDKLRMHMLSDRQFACHMCIKVFP 62 (86)
Q Consensus 17 h~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~C~~C~~~~~ 62 (86)
|...+.+..++.|+.-+..+.....+. .+..+.-..|++|+..|.
T Consensus 15 ~~~I~~~~~~l~C~g~~~p~~HPrV~L-~mg~~gev~CPYC~t~y~ 59 (62)
T COG4391 15 HETIEIGDLPLMCPGPEPPNDHPRVFL-DMGDEGEVVCPYCSTRYR 59 (62)
T ss_pred ceEEEeCCeeEEcCCCCCCCCCCEEEE-EcCCCCcEecCccccEEE
Confidence 444555667788876655543333221 112244568999988774
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=44.09 E-value=7.6 Score=14.68 Aligned_cols=6 Identities=50% Similarity=0.938 Sum_probs=1.6
Q ss_pred chhhhc
Q psy4084 3 ECMGKF 8 (86)
Q Consensus 3 ~C~~~~ 8 (86)
+|++.|
T Consensus 8 eC~~~f 13 (34)
T PF01286_consen 8 ECGKPF 13 (34)
T ss_dssp TT--EE
T ss_pred HhCCHH
Confidence 344433
No 193
>PLN03238 probable histone acetyltransferase MYST; Provisional
Probab=43.77 E-value=33 Score=19.94 Aligned_cols=25 Identities=20% Similarity=0.590 Sum_probs=22.3
Q ss_pred CcceecccccccccCHHHHHHHHHh
Q psy4084 49 DRQFACHMCIKVFPSQDKLRMHMLS 73 (86)
Q Consensus 49 ~~~~~C~~C~~~~~~~~~l~~h~~~ 73 (86)
..-|.|+.|-+-|.+...+.+|+..
T Consensus 46 ~~lyiCe~Clky~~~~~~l~~H~~~ 70 (290)
T PLN03238 46 TKLYICEYCLKYMRKKKSLLRHLAK 70 (290)
T ss_pred CeEEEcCCCcchhCCHHHHHHHHHh
Confidence 5679999999999999999999874
No 194
>KOG2907|consensus
Probab=43.58 E-value=16 Score=17.98 Aligned_cols=11 Identities=27% Similarity=0.830 Sum_probs=6.3
Q ss_pred eeccccccccc
Q psy4084 52 FACHMCIKVFP 62 (86)
Q Consensus 52 ~~C~~C~~~~~ 62 (86)
|.|+.|++.|.
T Consensus 103 YTC~kC~~k~~ 113 (116)
T KOG2907|consen 103 YTCPKCKYKFT 113 (116)
T ss_pred EEcCccceeee
Confidence 55666665543
No 195
>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=43.49 E-value=1.7 Score=28.01 Aligned_cols=11 Identities=27% Similarity=0.570 Sum_probs=6.2
Q ss_pred ceecccccccc
Q psy4084 51 QFACHMCIKVF 61 (86)
Q Consensus 51 ~~~C~~C~~~~ 61 (86)
+..|..||...
T Consensus 140 ~~~C~~Cgp~l 150 (711)
T TIGR00143 140 PIACPRCGPQL 150 (711)
T ss_pred CccCCCCCcEE
Confidence 44566666543
No 196
>KOG3507|consensus
Probab=43.17 E-value=19 Score=15.53 Aligned_cols=28 Identities=14% Similarity=0.256 Sum_probs=16.3
Q ss_pred ceecccccccCCChHHHhhhhhCCcceecccccccc
Q psy4084 26 QFACHMCIKVFPSQDKLRMHMLSDRQFACHMCIKVF 61 (86)
Q Consensus 26 ~~~c~~c~~~~~~~~~l~~h~~~~~~~~C~~C~~~~ 61 (86)
.|.|-.|+..-.. ...-.+.|.+||...
T Consensus 20 iYiCgdC~~en~l--------k~~D~irCReCG~RI 47 (62)
T KOG3507|consen 20 IYICGDCGQENTL--------KRGDVIRCRECGYRI 47 (62)
T ss_pred EEEeccccccccc--------cCCCcEehhhcchHH
Confidence 3677777643211 113467888888653
No 197
>PRK05580 primosome assembly protein PriA; Validated
Probab=43.13 E-value=27 Score=22.76 Aligned_cols=9 Identities=33% Similarity=0.534 Sum_probs=4.6
Q ss_pred ceecccccc
Q psy4084 51 QFACHMCIK 59 (86)
Q Consensus 51 ~~~C~~C~~ 59 (86)
|..|+.||.
T Consensus 421 ~~~Cp~Cg~ 429 (679)
T PRK05580 421 PKACPECGS 429 (679)
T ss_pred CCCCCCCcC
Confidence 445555544
No 198
>PF14369 zf-RING_3: zinc-finger
Probab=43.07 E-value=9.6 Score=14.36 Aligned_cols=8 Identities=38% Similarity=0.941 Sum_probs=3.8
Q ss_pred Ccchhhhc
Q psy4084 1 MSECMGKF 8 (86)
Q Consensus 1 c~~C~~~~ 8 (86)
|+.|+..|
T Consensus 24 CP~C~~gF 31 (35)
T PF14369_consen 24 CPRCHGGF 31 (35)
T ss_pred CcCCCCcE
Confidence 44455444
No 199
>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=42.96 E-value=19 Score=14.67 Aligned_cols=9 Identities=33% Similarity=1.069 Sum_probs=3.9
Q ss_pred ecccccccc
Q psy4084 53 ACHMCIKVF 61 (86)
Q Consensus 53 ~C~~C~~~~ 61 (86)
.|..||..|
T Consensus 20 ~Cr~Cg~~~ 28 (57)
T cd00065 20 HCRNCGRIF 28 (57)
T ss_pred ccCcCcCCc
Confidence 344444443
No 200
>KOG0782|consensus
Probab=42.06 E-value=4.3 Score=25.79 Aligned_cols=51 Identities=14% Similarity=0.231 Sum_probs=31.0
Q ss_pred HHHhhHHHHhCCCceecccccccCCChHHHhhhhhCCcceecccccccccCHH
Q psy4084 13 VIRKHIRTFHSDRQFACHMCIKVFPSQDKLRMHMLSDRQFACHMCIKVFPSQD 65 (86)
Q Consensus 13 ~l~~h~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~C~~C~~~~~~~~ 65 (86)
.+.+|-=.|.....=.|..|+++|..+-.+. .+.-....|.+|..+|-.+.
T Consensus 240 ~fvrHHWVHrrRqeGkC~~CgKgFQQKf~Fh--sKEivAisCSWCKqayH~Kv 290 (1004)
T KOG0782|consen 240 GFVRHHWVHRRRQEGKCNTCGKGFQQKFFFH--SKEIVAISCSWCKQAYHLKV 290 (1004)
T ss_pred cchHHhHhhHhhhccccchhhhhhhhheeec--cccEEEEEehHHHHHhhcch
Confidence 4555544454444557999999987765432 22224567888887775543
No 201
>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG
Probab=41.67 E-value=11 Score=15.68 Aligned_cols=9 Identities=22% Similarity=0.645 Sum_probs=6.0
Q ss_pred ecccccccc
Q psy4084 53 ACHMCIKVF 61 (86)
Q Consensus 53 ~C~~C~~~~ 61 (86)
.|++||..+
T Consensus 2 ~CPyCge~~ 10 (52)
T PF14255_consen 2 QCPYCGEPI 10 (52)
T ss_pred CCCCCCCee
Confidence 577777654
No 202
>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=41.04 E-value=21 Score=20.57 Aligned_cols=10 Identities=20% Similarity=0.438 Sum_probs=5.0
Q ss_pred eecccccccc
Q psy4084 52 FACHMCIKVF 61 (86)
Q Consensus 52 ~~C~~C~~~~ 61 (86)
+.|+.|++-|
T Consensus 46 ~vc~~c~~h~ 55 (285)
T TIGR00515 46 EVCPKCDHHM 55 (285)
T ss_pred CCCCCCCCcC
Confidence 3455555544
No 203
>PLN02748 tRNA dimethylallyltransferase
Probab=40.78 E-value=28 Score=21.71 Aligned_cols=24 Identities=21% Similarity=0.488 Sum_probs=20.0
Q ss_pred cceecccccc-cccCHHHHHHHHHh
Q psy4084 50 RQFACHMCIK-VFPSQDKLRMHMLS 73 (86)
Q Consensus 50 ~~~~C~~C~~-~~~~~~~l~~h~~~ 73 (86)
+.|.|..|+. .+.....+..|++.
T Consensus 417 ~~~~Ce~C~~~~~~G~~eW~~Hlks 441 (468)
T PLN02748 417 TQYVCEACGNKVLRGAHEWEQHKQG 441 (468)
T ss_pred ccccccCCCCcccCCHHHHHHHhcc
Confidence 4578999997 78888889999875
No 204
>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=40.74 E-value=20 Score=20.90 Aligned_cols=9 Identities=22% Similarity=0.431 Sum_probs=5.9
Q ss_pred eeccccccc
Q psy4084 27 FACHMCIKV 35 (86)
Q Consensus 27 ~~c~~c~~~ 35 (86)
-.|++||..
T Consensus 185 ~~CPvCGs~ 193 (305)
T TIGR01562 185 TLCPACGSP 193 (305)
T ss_pred CcCCCCCCh
Confidence 367777754
No 205
>PF03966 Trm112p: Trm112p-like protein; InterPro: IPR005651 This family of short proteins have no known function. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. The function of this family is uncertain. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. The entry contains 2 families: Trm112, which is required for tRNA methylation in Saccharomyces cerevisiae (Baker's yeast) and is found in complexes with 2 tRNA methylases (TRM9 and TRM11) also with putative methyltransferase YDR140W []. The zinc-finger protein Ynr046w is plurifunctional and a component of the eRF1 methyltransferase in yeast []. The crystal structure of Ynr046w has been determined to 1.7 A resolution. It comprises a zinc-binding domain built from both the N- and C-terminal sequences and an inserted domain, absent from bacterial and archaeal orthologs of the protein, composed of three alpha-helices []. UPF0434, which are proteins that are functionally uncharacterised. ; PDB: 3Q87_A 2KPI_A 2K5R_A 2HF1_A 2JS4_A 2J6A_A 2JR6_A 2PK7_A 2JNY_A.
Probab=40.50 E-value=12 Score=16.24 Aligned_cols=14 Identities=21% Similarity=0.797 Sum_probs=10.2
Q ss_pred Ccceeccccccccc
Q psy4084 49 DRQFACHMCIKVFP 62 (86)
Q Consensus 49 ~~~~~C~~C~~~~~ 62 (86)
+-...|+.|++.|+
T Consensus 51 eg~L~Cp~c~r~YP 64 (68)
T PF03966_consen 51 EGELICPECGREYP 64 (68)
T ss_dssp TTEEEETTTTEEEE
T ss_pred CCEEEcCCCCCEEe
Confidence 44578888888775
No 206
>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=40.21 E-value=16 Score=14.02 Aligned_cols=10 Identities=20% Similarity=0.786 Sum_probs=4.7
Q ss_pred ceeccccccc
Q psy4084 51 QFACHMCIKV 60 (86)
Q Consensus 51 ~~~C~~C~~~ 60 (86)
-|.|..||-.
T Consensus 6 ~YkC~~CGni 15 (36)
T PF06397_consen 6 FYKCEHCGNI 15 (36)
T ss_dssp EEE-TTT--E
T ss_pred EEEccCCCCE
Confidence 4778777754
No 207
>TIGR02159 PA_CoA_Oxy4 phenylacetate-CoA oxygenase, PaaJ subunit. Phenylacetate-CoA oxygenase is comprised of a five gene complex responsible for the hydroxylation of phenylacetate-CoA (PA-CoA) as the second catabolic step in phenylacetic acid (PA) degradation. Although the exact function of this enzyme has not been determined, it has been shown to be required for phenylacetic acid degradation and has been proposed to function in a multicomponent oxygenase acting on phenylacetate-CoA.
Probab=40.15 E-value=4.4 Score=20.74 Aligned_cols=11 Identities=27% Similarity=0.911 Sum_probs=6.2
Q ss_pred ceecccccccc
Q psy4084 51 QFACHMCIKVF 61 (86)
Q Consensus 51 ~~~C~~C~~~~ 61 (86)
.|.|..|...|
T Consensus 130 ~~~c~~c~epf 140 (146)
T TIGR02159 130 LYRCRACKEPF 140 (146)
T ss_pred HhhhhhhCCcH
Confidence 45566665554
No 208
>PRK05452 anaerobic nitric oxide reductase flavorubredoxin; Provisional
Probab=40.04 E-value=14 Score=22.77 Aligned_cols=13 Identities=15% Similarity=0.731 Sum_probs=7.7
Q ss_pred CceecccccccCC
Q psy4084 25 RQFACHMCIKVFP 37 (86)
Q Consensus 25 ~~~~c~~c~~~~~ 37 (86)
..|+|..|+..+.
T Consensus 424 ~~~~c~~c~~~yd 436 (479)
T PRK05452 424 PRMQCSVCQWIYD 436 (479)
T ss_pred CeEEECCCCeEEC
Confidence 3466666665554
No 209
>KOG2807|consensus
Probab=39.97 E-value=40 Score=20.10 Aligned_cols=24 Identities=21% Similarity=0.412 Sum_probs=16.8
Q ss_pred ceecccccccccCHHHHHHHHHhC
Q psy4084 51 QFACHMCIKVFPSQDKLRMHMLSG 74 (86)
Q Consensus 51 ~~~C~~C~~~~~~~~~l~~h~~~~ 74 (86)
.|.|+.|.-.|-..-+.-.|...|
T Consensus 345 ~y~C~~Ck~~FCldCDv~iHesLh 368 (378)
T KOG2807|consen 345 RYRCESCKNVFCLDCDVFIHESLH 368 (378)
T ss_pred cEEchhccceeeccchHHHHhhhh
Confidence 467777777777766666676665
No 210
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=39.49 E-value=28 Score=18.43 Aligned_cols=46 Identities=13% Similarity=0.294 Sum_probs=26.8
Q ss_pred eecccccccCCChH--HHhhhhh------CCcceecccccccccCHHHHHHHHH
Q psy4084 27 FACHMCIKVFPSQD--KLRMHML------SDRQFACHMCIKVFPSQDKLRMHML 72 (86)
Q Consensus 27 ~~c~~c~~~~~~~~--~l~~h~~------~~~~~~C~~C~~~~~~~~~l~~h~~ 72 (86)
-.|+.|+......+ ....... ...-+.|+.||+.|.-.+.+..-.+
T Consensus 98 ~RCp~CN~~L~~vs~eev~~~Vp~~~~~~~~~f~~C~~CgkiYW~GsHw~~m~~ 151 (165)
T COG1656 98 SRCPECNGELEKVSREEVKEKVPEKVYRNYEEFYRCPKCGKIYWKGSHWRRMVE 151 (165)
T ss_pred ccCcccCCEeccCcHHHHhhccchhhhhcccceeECCCCcccccCchHHHHHHH
Confidence 46888886543322 2111111 1334679999999988877654433
No 211
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=39.43 E-value=24 Score=25.00 Aligned_cols=6 Identities=33% Similarity=0.911 Sum_probs=3.1
Q ss_pred eccccc
Q psy4084 53 ACHMCI 58 (86)
Q Consensus 53 ~C~~C~ 58 (86)
.|+.|+
T Consensus 711 ~CP~CG 716 (1337)
T PRK14714 711 ECPRCD 716 (1337)
T ss_pred cCCCCC
Confidence 355554
No 212
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=39.40 E-value=28 Score=14.44 Aligned_cols=10 Identities=30% Similarity=0.703 Sum_probs=6.0
Q ss_pred ceeccccccc
Q psy4084 51 QFACHMCIKV 60 (86)
Q Consensus 51 ~~~C~~C~~~ 60 (86)
.+.|..||.+
T Consensus 37 R~~CGkCgyT 46 (51)
T COG1998 37 RWACGKCGYT 46 (51)
T ss_pred eeEeccccce
Confidence 4566666654
No 213
>TIGR03831 YgiT_finger YgiT-type zinc finger domain. This domain model describes a small domain with two copies of a putative zinc-binding motif CXXC (usually CXXCG). Most member proteins consist largely of this domain or else carry an additional C-terminal helix-turn-helix domain, resembling that of the phage protein Cro and modeled by pfam01381.
Probab=38.57 E-value=15 Score=14.12 Aligned_cols=11 Identities=18% Similarity=0.624 Sum_probs=7.9
Q ss_pred eeccccccccc
Q psy4084 52 FACHMCIKVFP 62 (86)
Q Consensus 52 ~~C~~C~~~~~ 62 (86)
+.|+.||..+.
T Consensus 33 ~~C~~CGE~~~ 43 (46)
T TIGR03831 33 LVCPQCGEEYL 43 (46)
T ss_pred cccccCCCEee
Confidence 56888887654
No 214
>PF13821 DUF4187: Domain of unknown function (DUF4187)
Probab=38.49 E-value=22 Score=14.94 Aligned_cols=22 Identities=14% Similarity=0.433 Sum_probs=15.5
Q ss_pred CcceecccccccccCHHHHHHH
Q psy4084 49 DRQFACHMCIKVFPSQDKLRMH 70 (86)
Q Consensus 49 ~~~~~C~~C~~~~~~~~~l~~h 70 (86)
.+-+-|-+||..|.+...|..+
T Consensus 25 ~~~~YC~~Cg~~Y~d~~dL~~~ 46 (55)
T PF13821_consen 25 EEHNYCFWCGTKYDDEEDLERN 46 (55)
T ss_pred hhCceeeeeCCccCCHHHHHhC
Confidence 3455688888888888777544
No 215
>COG4306 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=38.47 E-value=13 Score=18.67 Aligned_cols=17 Identities=29% Similarity=0.606 Sum_probs=12.0
Q ss_pred CcceecccccccccCHH
Q psy4084 49 DRQFACHMCIKVFPSQD 65 (86)
Q Consensus 49 ~~~~~C~~C~~~~~~~~ 65 (86)
+.|--|..||..|++..
T Consensus 66 e~psfchncgs~fpwte 82 (160)
T COG4306 66 EPPSFCHNCGSRFPWTE 82 (160)
T ss_pred CCcchhhcCCCCCCcHH
Confidence 45666888888887653
No 216
>PF14205 Cys_rich_KTR: Cysteine-rich KTR
Probab=38.38 E-value=9.8 Score=16.08 Aligned_cols=11 Identities=18% Similarity=0.437 Sum_probs=6.2
Q ss_pred cceeccccccc
Q psy4084 50 RQFACHMCIKV 60 (86)
Q Consensus 50 ~~~~C~~C~~~ 60 (86)
-|+-|+.|...
T Consensus 27 fPlyCpKCK~E 37 (55)
T PF14205_consen 27 FPLYCPKCKQE 37 (55)
T ss_pred ccccCCCCCce
Confidence 35566666543
No 217
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=37.95 E-value=19 Score=13.39 Aligned_cols=12 Identities=33% Similarity=0.725 Sum_probs=7.9
Q ss_pred ceeccccccccc
Q psy4084 51 QFACHMCIKVFP 62 (86)
Q Consensus 51 ~~~C~~C~~~~~ 62 (86)
-+.|..|+..|.
T Consensus 21 ~~~C~~Cg~~~~ 32 (33)
T PF08792_consen 21 YEVCIFCGSSFP 32 (33)
T ss_pred eEEcccCCcEee
Confidence 456777877653
No 218
>PRK00420 hypothetical protein; Validated
Probab=37.32 E-value=27 Score=17.16 Aligned_cols=28 Identities=21% Similarity=0.349 Sum_probs=15.8
Q ss_pred eecccccccCCChHHHhhhhhCCcceeccccccccc
Q psy4084 27 FACHMCIKVFPSQDKLRMHMLSDRQFACHMCIKVFP 62 (86)
Q Consensus 27 ~~c~~c~~~~~~~~~l~~h~~~~~~~~C~~C~~~~~ 62 (86)
-.|+.||..+.... .-...|+.||....
T Consensus 24 ~~CP~Cg~pLf~lk--------~g~~~Cp~Cg~~~~ 51 (112)
T PRK00420 24 KHCPVCGLPLFELK--------DGEVVCPVHGKVYI 51 (112)
T ss_pred CCCCCCCCcceecC--------CCceECCCCCCeee
Confidence 46888875432211 23456888877543
No 219
>PF00130 C1_1: Phorbol esters/diacylglycerol binding domain (C1 domain); InterPro: IPR002219 Diacylglycerol (DAG) is an important second messenger. Phorbol esters (PE) are analogues of DAG and potent tumour promoters that cause a variety of physiological changes when administered to both cells and tissues. DAG activates a family of serine/threonine protein kinases, collectively known as protein kinase C (PKC) []. Phorbol esters can directly stimulate PKC. The N-terminal region of PKC, known as C1, has been shown [] to bind PE and DAG in a phospholipid and zinc-dependent fashion. The C1 region contains one or two copies (depending on the isozyme of PKC) of a cysteine-rich domain, which is about 50 amino-acid residues long, and which is essential for DAG/PE-binding. The DAG/PE-binding domain binds two zinc ions; the ligands of these metal ions are probably the six cysteines and two histidines that are conserved in this domain.; GO: 0035556 intracellular signal transduction; PDB: 1RFH_A 2FNF_X 3PFQ_A 1PTQ_A 1PTR_A 2VRW_B 1XA6_A 2ENN_A 1TBN_A 1TBO_A ....
Probab=37.13 E-value=32 Score=13.78 Aligned_cols=28 Identities=25% Similarity=0.558 Sum_probs=14.1
Q ss_pred CceecccccccCCChHHHhhhhhCCcceeccccccc
Q psy4084 25 RQFACHMCIKVFPSQDKLRMHMLSDRQFACHMCIKV 60 (86)
Q Consensus 25 ~~~~c~~c~~~~~~~~~l~~h~~~~~~~~C~~C~~~ 60 (86)
+|-.|..|++.... .....+.|..|+..
T Consensus 10 ~~~~C~~C~~~i~g--------~~~~g~~C~~C~~~ 37 (53)
T PF00130_consen 10 KPTYCDVCGKFIWG--------LGKQGYRCSWCGLV 37 (53)
T ss_dssp STEB-TTSSSBECS--------SSSCEEEETTTT-E
T ss_pred CCCCCcccCcccCC--------CCCCeEEECCCCCh
Confidence 45567777655411 11345777777654
No 220
>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=36.46 E-value=7 Score=22.22 Aligned_cols=24 Identities=17% Similarity=0.277 Sum_probs=13.0
Q ss_pred CcceecccccccccCHHHHHHHHH
Q psy4084 49 DRQFACHMCIKVFPSQDKLRMHML 72 (86)
Q Consensus 49 ~~~~~C~~C~~~~~~~~~l~~h~~ 72 (86)
.++++|+.||........|....+
T Consensus 207 ~k~~PCPKCg~et~eTkdLSmStR 230 (314)
T PF06524_consen 207 GKPIPCPKCGYETQETKDLSMSTR 230 (314)
T ss_pred CCCCCCCCCCCcccccccceeeee
Confidence 356666666666555444443333
No 221
>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=35.85 E-value=18 Score=16.55 Aligned_cols=9 Identities=33% Similarity=1.058 Sum_probs=2.1
Q ss_pred cceeccccc
Q psy4084 50 RQFACHMCI 58 (86)
Q Consensus 50 ~~~~C~~C~ 58 (86)
+.|.|+.|+
T Consensus 21 ~~F~CPfC~ 29 (81)
T PF05129_consen 21 KVFDCPFCN 29 (81)
T ss_dssp S----TTT-
T ss_pred ceEcCCcCC
Confidence 445555553
No 222
>PHA02998 RNA polymerase subunit; Provisional
Probab=35.70 E-value=13 Score=19.86 Aligned_cols=11 Identities=45% Similarity=0.860 Sum_probs=7.9
Q ss_pred eeccccccccc
Q psy4084 52 FACHMCIKVFP 62 (86)
Q Consensus 52 ~~C~~C~~~~~ 62 (86)
|.|..||..|.
T Consensus 172 YkC~~CG~~wk 182 (195)
T PHA02998 172 HACRDCKKHFK 182 (195)
T ss_pred EEcCCCCCccC
Confidence 67888877654
No 223
>KOG1280|consensus
Probab=35.54 E-value=50 Score=19.87 Aligned_cols=27 Identities=22% Similarity=0.402 Sum_probs=19.1
Q ss_pred cceecccccccccCHHHHHHHHHhCCC
Q psy4084 50 RQFACHMCIKVFPSQDKLRMHMLSGLQ 76 (86)
Q Consensus 50 ~~~~C~~C~~~~~~~~~l~~h~~~~~~ 76 (86)
.-|.|++|+..=.+...|..|....+-
T Consensus 78 qSftCPyC~~~Gfte~~f~~Hv~s~Hp 104 (381)
T KOG1280|consen 78 QSFTCPYCGIMGFTERQFGTHVLSQHP 104 (381)
T ss_pred ccccCCcccccccchhHHHHHhhhcCc
Confidence 457788887777777777777766443
No 224
>PRK05978 hypothetical protein; Provisional
Probab=35.48 E-value=22 Score=18.38 Aligned_cols=30 Identities=20% Similarity=0.221 Sum_probs=16.3
Q ss_pred eecccccccCCChHHHhhhhhCCcceeccccccccc
Q psy4084 27 FACHMCIKVFPSQDKLRMHMLSDRQFACHMCIKVFP 62 (86)
Q Consensus 27 ~~c~~c~~~~~~~~~l~~h~~~~~~~~C~~C~~~~~ 62 (86)
-.|+.|++.--....|. ..-.|+.||..|.
T Consensus 34 grCP~CG~G~LF~g~Lk------v~~~C~~CG~~~~ 63 (148)
T PRK05978 34 GRCPACGEGKLFRAFLK------PVDHCAACGEDFT 63 (148)
T ss_pred CcCCCCCCCcccccccc------cCCCccccCCccc
Confidence 36788876533333322 2235777776654
No 225
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=35.47 E-value=15 Score=23.75 Aligned_cols=12 Identities=17% Similarity=0.221 Sum_probs=7.2
Q ss_pred ecccccccccCH
Q psy4084 53 ACHMCIKVFPSQ 64 (86)
Q Consensus 53 ~C~~C~~~~~~~ 64 (86)
-|+.||......
T Consensus 43 fC~~CG~~~~~~ 54 (645)
T PRK14559 43 HCPNCGAETGTI 54 (645)
T ss_pred cccccCCcccch
Confidence 477777665443
No 226
>TIGR01384 TFS_arch transcription factor S, archaeal. There has been an apparent duplication event in the Halobacteriaceae lineage (Haloarcula, Haloferax, Haloquadratum, Halobacterium and Natromonas). There appears to be a separate duplication in Methanosphaera stadtmanae.
Probab=35.33 E-value=14 Score=17.42 Aligned_cols=25 Identities=16% Similarity=0.290 Sum_probs=15.4
Q ss_pred CcchhhhccChHHHHhhHHHHhCCCceecccccccCC
Q psy4084 1 MSECMGKFTEYQVIRKHIRTFHSDRQFACHMCIKVFP 37 (86)
Q Consensus 1 c~~C~~~~~~~~~l~~h~~~~~~~~~~~c~~c~~~~~ 37 (86)
|+.||..+... ...+.|+.|+....
T Consensus 3 C~~Cg~~l~~~------------~~~~~C~~C~~~~~ 27 (104)
T TIGR01384 3 CPKCGSLMTPK------------NGVYVCPSCGYEKE 27 (104)
T ss_pred CcccCcccccC------------CCeEECcCCCCccc
Confidence 67777665321 23578888886544
No 227
>PRK04351 hypothetical protein; Provisional
Probab=35.08 E-value=24 Score=18.25 Aligned_cols=28 Identities=14% Similarity=0.352 Sum_probs=15.2
Q ss_pred ceecccccccccCHHHHHHHHHhCCCCccCCCCcCC
Q psy4084 51 QFACHMCIKVFPSQDKLRMHMLSGLQTFDLKSKLCT 86 (86)
Q Consensus 51 ~~~C~~C~~~~~~~~~l~~h~~~~~~~~~~~c~~C~ 86 (86)
.|.|..|+..+.+. +.+ ....|.|..|.
T Consensus 112 ~Y~C~~Cg~~~~r~-------Rr~-n~~~yrCg~C~ 139 (149)
T PRK04351 112 LYECQSCGQQYLRK-------RRI-NTKRYRCGKCR 139 (149)
T ss_pred EEECCCCCCEeeee-------eec-CCCcEEeCCCC
Confidence 46777777655332 111 33557776663
No 228
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=35.08 E-value=30 Score=20.19 Aligned_cols=11 Identities=18% Similarity=0.344 Sum_probs=4.8
Q ss_pred eecccccccCC
Q psy4084 27 FACHMCIKVFP 37 (86)
Q Consensus 27 ~~c~~c~~~~~ 37 (86)
+.|+.|+..|.
T Consensus 58 ~vcp~c~~h~r 68 (296)
T CHL00174 58 NICEQCGYHLK 68 (296)
T ss_pred CCCCCCCCCcC
Confidence 34444444443
No 229
>PF14690 zf-ISL3: zinc-finger of transposase IS204/IS1001/IS1096/IS1165
Probab=35.06 E-value=20 Score=13.98 Aligned_cols=10 Identities=20% Similarity=0.328 Sum_probs=6.5
Q ss_pred ceeccccccc
Q psy4084 51 QFACHMCIKV 60 (86)
Q Consensus 51 ~~~C~~C~~~ 60 (86)
|..|+.||..
T Consensus 2 ~~~Cp~Cg~~ 11 (47)
T PF14690_consen 2 PPRCPHCGSP 11 (47)
T ss_pred CccCCCcCCC
Confidence 4567888743
No 230
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=34.85 E-value=39 Score=19.85 Aligned_cols=11 Identities=18% Similarity=0.570 Sum_probs=7.6
Q ss_pred Cceeccccccc
Q psy4084 25 RQFACHMCIKV 35 (86)
Q Consensus 25 ~~~~c~~c~~~ 35 (86)
..-.|++||..
T Consensus 186 ~~~~CPvCGs~ 196 (309)
T PRK03564 186 QRQFCPVCGSM 196 (309)
T ss_pred CCCCCCCCCCc
Confidence 34578888865
No 231
>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=34.83 E-value=12 Score=18.98 Aligned_cols=11 Identities=18% Similarity=0.754 Sum_probs=6.9
Q ss_pred ceecccccccc
Q psy4084 51 QFACHMCIKVF 61 (86)
Q Consensus 51 ~~~C~~C~~~~ 61 (86)
.|.|..|+..+
T Consensus 123 ~~~C~~C~~~~ 133 (157)
T PF10263_consen 123 VYRCPSCGREY 133 (157)
T ss_pred EEEcCCCCCEe
Confidence 35677777654
No 232
>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=34.75 E-value=22 Score=13.82 Aligned_cols=9 Identities=22% Similarity=0.549 Sum_probs=5.1
Q ss_pred eeccccccc
Q psy4084 52 FACHMCIKV 60 (86)
Q Consensus 52 ~~C~~C~~~ 60 (86)
+.|+.|+..
T Consensus 1 m~Cp~Cg~~ 9 (43)
T PF08271_consen 1 MKCPNCGSK 9 (43)
T ss_dssp ESBTTTSSS
T ss_pred CCCcCCcCC
Confidence 346666654
No 233
>PF02701 zf-Dof: Dof domain, zinc finger; InterPro: IPR003851 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 consists of proteins containing a Dof domain, which is a zinc finger DNA-binding domain that shows resemblance to the Cys2 zinc finger, although it has a longer putative loop where an extra Cys residue is conserved []. AOBP, a DNA-binding protein in pumpkin (Cucurbita maxima), contains a 52 amino acid Dof domain, which is highly conserved in several DNA-binding proteins of higher plants. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding, 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent
Probab=34.64 E-value=1.9 Score=18.68 Aligned_cols=43 Identities=14% Similarity=0.314 Sum_probs=19.9
Q ss_pred CCceecccccccCCChHHHhhhhhCCcceecccccccccCHHH
Q psy4084 24 DRQFACHMCIKVFPSQDKLRMHMLSDRQFACHMCIKVFPSQDK 66 (86)
Q Consensus 24 ~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~C~~C~~~~~~~~~ 66 (86)
+.+..|+.|+..-..--.+......+..+.|..|.+-+...+.
T Consensus 3 ~~~~~CPRC~S~nTKFcYyNNy~~~QPR~~Ck~C~rywT~GG~ 45 (63)
T PF02701_consen 3 EQPLPCPRCDSTNTKFCYYNNYNLSQPRYFCKSCRRYWTHGGT 45 (63)
T ss_pred ccCCCCCCcCCCCCEEEeecCCCCCCcchhhHHHHHHHHhcce
Confidence 3456777776432221222222222334566666655544433
No 234
>PRK01343 zinc-binding protein; Provisional
Probab=34.49 E-value=26 Score=15.02 Aligned_cols=10 Identities=30% Similarity=0.371 Sum_probs=6.0
Q ss_pred eecccccccc
Q psy4084 52 FACHMCIKVF 61 (86)
Q Consensus 52 ~~C~~C~~~~ 61 (86)
..|+.|++.+
T Consensus 10 ~~CP~C~k~~ 19 (57)
T PRK01343 10 RPCPECGKPS 19 (57)
T ss_pred CcCCCCCCcC
Confidence 4566666654
No 235
>smart00109 C1 Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains). Some bind phorbol esters and diacylglycerol. Some bind RasGTP. Zinc-binding domains.
Probab=34.40 E-value=29 Score=13.28 Aligned_cols=9 Identities=22% Similarity=0.682 Sum_probs=5.3
Q ss_pred ceecccccc
Q psy4084 51 QFACHMCIK 59 (86)
Q Consensus 51 ~~~C~~C~~ 59 (86)
.+.|..|+.
T Consensus 27 ~~~C~~C~~ 35 (49)
T smart00109 27 GLRCSWCKV 35 (49)
T ss_pred CcCCCCCCc
Confidence 456666654
No 236
>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 PF09963 DUF2197: Uncharacterized protein conserved in bacteria (DUF2197); InterPro: IPR019241 This family represents various hypothetical bacterial proteins with no known function.
Probab=33.95 E-value=23 Score=15.07 Aligned_cols=34 Identities=15% Similarity=0.365 Sum_probs=17.3
Q ss_pred eecccccccCCChHHHh--hhhhC--Ccceeccccccc
Q psy4084 27 FACHMCIKVFPSQDKLR--MHMLS--DRQFACHMCIKV 60 (86)
Q Consensus 27 ~~c~~c~~~~~~~~~l~--~h~~~--~~~~~C~~C~~~ 60 (86)
..|..|++.+.-..... ..++. -..|.|..|...
T Consensus 3 vkC~lCdk~~~Id~~~~~aKrLrnrPi~tYmC~eC~~R 40 (56)
T PF09963_consen 3 VKCILCDKKEEIDEDTPEAKRLRNRPIHTYMCDECKER 40 (56)
T ss_pred eEEEecCCEEEeccCCHHHHHhhcCCCcceeChhHHHH
Confidence 35777776654332211 11111 345888888643
No 238
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=33.89 E-value=31 Score=17.14 Aligned_cols=9 Identities=22% Similarity=0.309 Sum_probs=4.1
Q ss_pred eecccccccc
Q psy4084 52 FACHMCIKVF 61 (86)
Q Consensus 52 ~~C~~C~~~~ 61 (86)
+.| .||..|
T Consensus 71 ~~C-~Cg~~~ 79 (124)
T PRK00762 71 IEC-ECGYEG 79 (124)
T ss_pred EEe-eCcCcc
Confidence 345 455443
No 239
>COG1579 Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only]
Probab=33.85 E-value=30 Score=19.48 Aligned_cols=34 Identities=24% Similarity=0.488 Sum_probs=17.2
Q ss_pred ecccccccCCChHHHhhhhhCCcceeccccccccc
Q psy4084 28 ACHMCIKVFPSQDKLRMHMLSDRQFACHMCIKVFP 62 (86)
Q Consensus 28 ~c~~c~~~~~~~~~l~~h~~~~~~~~C~~C~~~~~ 62 (86)
.|..|....+......... ......||+||+...
T Consensus 199 ~C~GC~m~l~~~~~~~V~~-~d~iv~CP~CgRILy 232 (239)
T COG1579 199 VCGGCHMKLPSQTLSKVRK-KDEIVFCPYCGRILY 232 (239)
T ss_pred cccCCeeeecHHHHHHHhc-CCCCccCCccchHHH
Confidence 4666654443332211111 244567899987643
No 240
>PRK12860 transcriptional activator FlhC; Provisional
Probab=33.74 E-value=42 Score=18.25 Aligned_cols=28 Identities=18% Similarity=0.305 Sum_probs=15.7
Q ss_pred ceecccccccccCHHHHHHHHHhCCCCccCCCCcCC
Q psy4084 51 QFACHMCIKVFPSQDKLRMHMLSGLQTFDLKSKLCT 86 (86)
Q Consensus 51 ~~~C~~C~~~~~~~~~l~~h~~~~~~~~~~~c~~C~ 86 (86)
...|..||-.|.... +.-...|.|..|+
T Consensus 134 l~~C~~Cgg~fv~~~--------~e~~~~f~CplC~ 161 (189)
T PRK12860 134 LARCCRCGGKFVTHA--------HDLRHNFVCGLCQ 161 (189)
T ss_pred eccCCCCCCCeeccc--------cccCCCCcCCCCC
Confidence 346777776665321 2233457777774
No 241
>KOG2817|consensus
Probab=33.53 E-value=44 Score=20.37 Aligned_cols=35 Identities=20% Similarity=0.295 Sum_probs=17.7
Q ss_pred CcceecccccccccCHHHHHHHHHhCCCCccCCCCcCC
Q psy4084 49 DRQFACHMCIKVFPSQDKLRMHMLSGLQTFDLKSKLCT 86 (86)
Q Consensus 49 ~~~~~C~~C~~~~~~~~~l~~h~~~~~~~~~~~c~~C~ 86 (86)
+.|-.-..||..- +...+++-.+. +...|+|+.|+
T Consensus 347 eNPPm~L~CGHVI-SkdAlnrLS~n--g~~sfKCPYCP 381 (394)
T KOG2817|consen 347 ENPPMMLICGHVI-SKDALNRLSKN--GSQSFKCPYCP 381 (394)
T ss_pred CCCCeeeecccee-cHHHHHHHhhC--CCeeeeCCCCC
Confidence 4443334566653 34444433333 33368888774
No 242
>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=33.39 E-value=18 Score=17.02 Aligned_cols=31 Identities=23% Similarity=0.561 Sum_probs=19.0
Q ss_pred CceecccccccCCChHHHhhhhhCCcceeccccccccc
Q psy4084 25 RQFACHMCIKVFPSQDKLRMHMLSDRQFACHMCIKVFP 62 (86)
Q Consensus 25 ~~~~c~~c~~~~~~~~~l~~h~~~~~~~~C~~C~~~~~ 62 (86)
..|.|+.|++.--. + . ..--|.|..|++.|+
T Consensus 34 ~ky~Cp~Cgk~~vk-----R-~-a~GIW~C~~C~~~~A 64 (90)
T PF01780_consen 34 AKYTCPFCGKTSVK-----R-V-ATGIWKCKKCGKKFA 64 (90)
T ss_dssp S-BEESSSSSSEEE-----E-E-ETTEEEETTTTEEEE
T ss_pred CCCcCCCCCCceeE-----E-e-eeEEeecCCCCCEEe
Confidence 45899999864211 0 0 022489999998874
No 243
>PRK12722 transcriptional activator FlhC; Provisional
Probab=33.23 E-value=42 Score=18.19 Aligned_cols=27 Identities=19% Similarity=0.324 Sum_probs=14.0
Q ss_pred eecccccccccCHHHHHHHHHhCCCCccCCCCcCC
Q psy4084 52 FACHMCIKVFPSQDKLRMHMLSGLQTFDLKSKLCT 86 (86)
Q Consensus 52 ~~C~~C~~~~~~~~~l~~h~~~~~~~~~~~c~~C~ 86 (86)
..|..||-.|.... +.-...|.|..|+
T Consensus 135 ~~C~~Cgg~fv~~~--------~e~~~~f~CplC~ 161 (187)
T PRK12722 135 SSCNCCGGHFVTHA--------HDPVGSFVCGLCQ 161 (187)
T ss_pred ccCCCCCCCeeccc--------cccCCCCcCCCCC
Confidence 45666766654321 1223457777764
No 244
>PF03884 DUF329: Domain of unknown function (DUF329); InterPro: IPR005584 The biological function of these short proteins is unknown, but they contain four conserved cysteines, suggesting that they all bind zinc. YacG (Q5X8H6 from SWISSPROT) from Escherichia coli has been shown to bind zinc and contains the structural motifs typical of zinc-binding proteins []. The conserved four cysteine motif in these proteins (-C-X(2)-C-X(15)-C-X(3)-C-) is not found in other zinc-binding proteins with known structures.; GO: 0008270 zinc ion binding; PDB: 1LV3_A.
Probab=33.18 E-value=22 Score=15.21 Aligned_cols=12 Identities=25% Similarity=0.481 Sum_probs=5.4
Q ss_pred eecccccccccC
Q psy4084 52 FACHMCIKVFPS 63 (86)
Q Consensus 52 ~~C~~C~~~~~~ 63 (86)
..|+.|++.+..
T Consensus 3 v~CP~C~k~~~~ 14 (57)
T PF03884_consen 3 VKCPICGKPVEW 14 (57)
T ss_dssp EE-TTT--EEE-
T ss_pred ccCCCCCCeecc
Confidence 468888777544
No 245
>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=33.17 E-value=15 Score=19.16 Aligned_cols=19 Identities=26% Similarity=0.567 Sum_probs=15.2
Q ss_pred CcceecccccccccCHHHH
Q psy4084 49 DRQFACHMCIKVFPSQDKL 67 (86)
Q Consensus 49 ~~~~~C~~C~~~~~~~~~l 67 (86)
+.|.-|..||+.|++....
T Consensus 66 ~~PsYC~~CGkpyPWt~~~ 84 (158)
T PF10083_consen 66 EAPSYCHNCGKPYPWTENA 84 (158)
T ss_pred CCChhHHhCCCCCchHHHH
Confidence 5788899999999876543
No 246
>KOG2747|consensus
Probab=32.86 E-value=31 Score=21.03 Aligned_cols=25 Identities=28% Similarity=0.739 Sum_probs=22.1
Q ss_pred CcceecccccccccCHHHHHHHHHh
Q psy4084 49 DRQFACHMCIKVFPSQDKLRMHMLS 73 (86)
Q Consensus 49 ~~~~~C~~C~~~~~~~~~l~~h~~~ 73 (86)
..-|.|+.|-+-+.+...|.+|+..
T Consensus 156 ~~lYiCEfCLkY~~s~~~l~rH~~k 180 (396)
T KOG2747|consen 156 DKLYICEFCLKYMKSRTSLQRHLKK 180 (396)
T ss_pred CeEEEehHHHhHhchHHHHHHHHHh
Confidence 4568999999999999999999985
No 247
>COG2331 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=32.78 E-value=29 Score=15.85 Aligned_cols=30 Identities=23% Similarity=0.479 Sum_probs=15.1
Q ss_pred eecccccccCCChHHHhhhhhCCcceeccccccc
Q psy4084 27 FACHMCIKVFPSQDKLRMHMLSDRQFACHMCIKV 60 (86)
Q Consensus 27 ~~c~~c~~~~~~~~~l~~h~~~~~~~~C~~C~~~ 60 (86)
|+|..|+..|. +..++.....-.|+.|+-.
T Consensus 13 Y~c~~cg~~~d----vvq~~~ddplt~ce~c~a~ 42 (82)
T COG2331 13 YECTECGNRFD----VVQAMTDDPLTTCEECGAR 42 (82)
T ss_pred EeecccchHHH----HHHhcccCccccChhhChH
Confidence 67777776543 2233332222356666643
No 248
>PLN00104 MYST -like histone acetyltransferase; Provisional
Probab=32.76 E-value=44 Score=20.83 Aligned_cols=25 Identities=24% Similarity=0.721 Sum_probs=22.2
Q ss_pred CcceecccccccccCHHHHHHHHHh
Q psy4084 49 DRQFACHMCIKVFPSQDKLRMHMLS 73 (86)
Q Consensus 49 ~~~~~C~~C~~~~~~~~~l~~h~~~ 73 (86)
..-|.|+.|-+-|.....|.+|+..
T Consensus 196 ~~lyiCe~Cl~y~~~~~~~~~H~~~ 220 (450)
T PLN00104 196 SKLYFCEFCLKFMKRKEQLQRHMKK 220 (450)
T ss_pred CeEEEchhhhhhhcCHHHHHHHHhc
Confidence 4578999999999999999999874
No 249
>PRK05654 acetyl-CoA carboxylase subunit beta; Validated
Probab=32.19 E-value=44 Score=19.43 Aligned_cols=10 Identities=20% Similarity=0.441 Sum_probs=5.1
Q ss_pred eecccccccc
Q psy4084 52 FACHMCIKVF 61 (86)
Q Consensus 52 ~~C~~C~~~~ 61 (86)
+.|+.|++-|
T Consensus 47 ~vc~~c~~h~ 56 (292)
T PRK05654 47 NVCPKCGHHM 56 (292)
T ss_pred CCCCCCCCCe
Confidence 3455555544
No 250
>PLN03239 histone acetyltransferase; Provisional
Probab=32.11 E-value=49 Score=19.90 Aligned_cols=25 Identities=16% Similarity=0.376 Sum_probs=21.7
Q ss_pred CcceecccccccccCHHHHHHHHHh
Q psy4084 49 DRQFACHMCIKVFPSQDKLRMHMLS 73 (86)
Q Consensus 49 ~~~~~C~~C~~~~~~~~~l~~h~~~ 73 (86)
..-|.|+.|-+-|.+...|.+|+..
T Consensus 104 ~~lYiCE~Clky~~~~~~l~~H~~~ 128 (351)
T PLN03239 104 DVLYVCEFSFGFFARKSELLRFQAK 128 (351)
T ss_pred ceEEEeccchhhhcCHHHHHHHHHh
Confidence 4578999999999999999999864
No 251
>PF02146 SIR2: Sir2 family; InterPro: IPR003000 These sequences represent the Sirtuin (Sir2-related) family of NAD+-dependent deacetylases. This family of enzymes is broadly conserved from bacteria to humans. In yeast, Sir2 proteins form complexes with other proteins to silence chromatin by accessing histones and deacetylating them. Sir2 proteins have been proposed to play a role in silencing, chromosome stability and ageing []. The bacterial enzyme CobB, an homologue of Sir2, is a phosphoribosyltransferase []. An in vitro ADP ribosyltransferase activity has also been associated with human members of this family []. Sir2-like enzymes employ NAD+ as a cosubstrate in deacetylation reactions [] and catalyse a reaction in which the cleavage of NAD(+)and histone and/or protein deacetylation are coupled to the formation of O-acetyl-ADP-ribose, a novel metabolite. The dependence of the reaction on both NAD(+) and the generation of this potential second messenger offers new clues to understanding the function and regulation of nuclear, cytoplasmic and mitochondrial Sir2-like enzymes []. Silent Information Regulator protein of Saccharomyces cerevisiae (Sir2) is one of several factors critical for silencing at least three loci. Among them, it is unique because it silences the rDNA as well as the mating type loci and telomeres []. Sir2 interacts in a complex with itself and with Sir3 and Sir4, two proteins that are able to interact with nucleosomes. In addition Sir2 also interacts with ubiquitination factors and/or complexes []. Homologues of Sir2 share a core domain including the GAG and NID motifs and a putative C4 Zinc finger. The regions containing these three conserved motifs are individually essential for Sir2 silencing function, as are the four cysteins []. In addition, the conserved residues HG next to the putative Zn finger have been shown to be essential for the ADP ribosyltransferase activity []. ; GO: 0008270 zinc ion binding, 0070403 NAD+ binding, 0006476 protein deacetylation; PDB: 1S5P_A 3PKI_E 3PKJ_F 3K35_A 1ICI_A 1M2K_A 1M2G_A 1M2N_B 1M2H_A 1M2J_A ....
Probab=31.76 E-value=78 Score=16.57 Aligned_cols=13 Identities=23% Similarity=0.654 Sum_probs=7.9
Q ss_pred eecccccccccCH
Q psy4084 52 FACHMCIKVFPSQ 64 (86)
Q Consensus 52 ~~C~~C~~~~~~~ 64 (86)
..|..|++.+...
T Consensus 106 ~~C~~C~~~~~~~ 118 (178)
T PF02146_consen 106 LRCSKCGKEYDRE 118 (178)
T ss_dssp EEETTTSBEEEGH
T ss_pred eeecCCCccccch
Confidence 4666676666544
No 252
>PF14787 zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB: 1CL4_A 1DSV_A.
Probab=31.44 E-value=21 Score=13.69 Aligned_cols=14 Identities=29% Similarity=0.441 Sum_probs=7.8
Q ss_pred ecccccccccCHHH
Q psy4084 53 ACHMCIKVFPSQDK 66 (86)
Q Consensus 53 ~C~~C~~~~~~~~~ 66 (86)
.|+.|++.|-+.+.
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 47778777755543
No 253
>PF09416 UPF1_Zn_bind: RNA helicase (UPF2 interacting domain); InterPro: IPR018999 UPF1 (or regulator of nonsense transcripts 1 homologue) is an essential RNA helicase that detects mRNAs containing premature stop codons and triggers their degradation. This domain contains 3 zinc binding motifs and forms interactions with another protein (UPF2) that is also involved nonsense-mediated mRNA decay (NMD) []. ; GO: 0003677 DNA binding, 0004386 helicase activity, 0005524 ATP binding, 0008270 zinc ion binding, 0000184 nuclear-transcribed mRNA catabolic process, nonsense-mediated decay, 0005737 cytoplasm; PDB: 2IYK_B 2WJY_A 2WJV_A 2XZL_A.
Probab=31.43 E-value=43 Score=17.51 Aligned_cols=34 Identities=21% Similarity=0.318 Sum_probs=14.0
Q ss_pred Ccchhhhcc------ChHHHHhhHHHHh------------CCCceecccccc
Q psy4084 1 MSECMGKFT------EYQVIRKHIRTFH------------SDRQFACHMCIK 34 (86)
Q Consensus 1 c~~C~~~~~------~~~~l~~h~~~~~------------~~~~~~c~~c~~ 34 (86)
|..|++.|- ..+.+..|+.... ++..++|-.||.
T Consensus 17 C~~c~kWFCNg~~~~s~SHIv~HLv~srh~ev~LH~~s~lgdt~leCy~Cg~ 68 (152)
T PF09416_consen 17 CNTCNKWFCNGRGNTSGSHIVNHLVRSRHKEVSLHPDSPLGDTVLECYNCGS 68 (152)
T ss_dssp ETTTTEEEES--TTSSS-HHHHHHHHHT---EEE-TTSTT-S-B---TTT--
T ss_pred cCCCCcEeecCCCCCcccHHHHHHHHccCCceeeCCCCCCCCcEEEEEecCC
Confidence 445666663 4455666655311 234577877764
No 254
>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=31.36 E-value=23 Score=18.09 Aligned_cols=14 Identities=29% Similarity=0.622 Sum_probs=11.6
Q ss_pred Ccceeccccccccc
Q psy4084 49 DRQFACHMCIKVFP 62 (86)
Q Consensus 49 ~~~~~C~~C~~~~~ 62 (86)
.++..|+.||..|.
T Consensus 110 g~~~RCpeCG~~fk 123 (136)
T PF01215_consen 110 GKPQRCPECGQVFK 123 (136)
T ss_dssp TSEEEETTTEEEEE
T ss_pred CCccCCCCCCeEEE
Confidence 56889999998774
No 255
>COG5216 Uncharacterized conserved protein [Function unknown]
Probab=30.51 E-value=40 Score=14.53 Aligned_cols=11 Identities=18% Similarity=0.392 Sum_probs=6.4
Q ss_pred Ccceecccccc
Q psy4084 49 DRQFACHMCIK 59 (86)
Q Consensus 49 ~~~~~C~~C~~ 59 (86)
++...|+.|.-
T Consensus 42 E~VArCPSCSL 52 (67)
T COG5216 42 EVVARCPSCSL 52 (67)
T ss_pred ceEEEcCCceE
Confidence 55556766643
No 256
>COG5109 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=30.38 E-value=53 Score=19.58 Aligned_cols=10 Identities=20% Similarity=0.590 Sum_probs=5.5
Q ss_pred CCccCCCCcC
Q psy4084 76 QTFDLKSKLC 85 (86)
Q Consensus 76 ~~~~~~c~~C 85 (86)
|.-.|+|+.|
T Consensus 373 G~~~FKCPYC 382 (396)
T COG5109 373 GVLSFKCPYC 382 (396)
T ss_pred CcEEeeCCCC
Confidence 3345666665
No 257
>PRK08222 hydrogenase 4 subunit H; Validated
Probab=30.15 E-value=41 Score=17.87 Aligned_cols=19 Identities=21% Similarity=0.480 Sum_probs=14.7
Q ss_pred cceecccccccccCHHHHH
Q psy4084 50 RQFACHMCIKVFPSQDKLR 68 (86)
Q Consensus 50 ~~~~C~~C~~~~~~~~~l~ 68 (86)
....|..||+.|.....+.
T Consensus 113 ~~~~C~~Cg~~f~~~k~i~ 131 (181)
T PRK08222 113 HLQRCSRCERPFAPQKTVA 131 (181)
T ss_pred ccCcCcccCCccCcHhHHH
Confidence 4678999999998765554
No 258
>PF05741 zf-nanos: Nanos RNA binding domain; InterPro: IPR024161 Nanos is a highly conserved RNA-binding protein in higher eukaryotes and functions as a key regulatory protein in translational control using a 3' untranslated region during the development and maintenance of germ cells. Nanos comprises a non-conserved amino-terminus and highly conserved carboxy- terminal regions. The C-terminal region has two conserved Cys-Cys-His-Cys (CCHC)-type zinc-finger motifs that are indispensable for nanos function [, , ]. The structure of the nanos-type zinc finger is composed of two independent zinc-finger (ZF) lobes, the N-terminal ZF1 and the C-terminal ZF2, which are connected by a linker helix []. These lobes create a large cleft. Zinc ions in ZF1 and ZF2 are bound to the CCHC motif by tetrahedral coordination.; PDB: 3ALR_B.
Probab=29.95 E-value=16 Score=15.51 Aligned_cols=10 Identities=30% Similarity=1.029 Sum_probs=2.9
Q ss_pred cceecccccc
Q psy4084 50 RQFACHMCIK 59 (86)
Q Consensus 50 ~~~~C~~C~~ 59 (86)
+.|.|+.||.
T Consensus 32 r~y~Cp~CgA 41 (55)
T PF05741_consen 32 RKYVCPICGA 41 (55)
T ss_dssp GG---TTT--
T ss_pred hcCcCCCCcC
Confidence 3456666664
No 259
>PTZ00064 histone acetyltransferase; Provisional
Probab=29.45 E-value=60 Score=20.72 Aligned_cols=25 Identities=28% Similarity=0.563 Sum_probs=22.3
Q ss_pred CcceecccccccccCHHHHHHHHHh
Q psy4084 49 DRQFACHMCIKVFPSQDKLRMHMLS 73 (86)
Q Consensus 49 ~~~~~C~~C~~~~~~~~~l~~h~~~ 73 (86)
..-|.|+.|-+-|.....|.+|+..
T Consensus 278 d~LYICEfCLkY~~s~~~l~rH~~~ 302 (552)
T PTZ00064 278 DTLHFCEYCLDFFCFEDELIRHLSR 302 (552)
T ss_pred CeEEEccchhhhhCCHHHHHHHHhc
Confidence 4578999999999999999999874
No 260
>PF04641 Rtf2: Rtf2 RING-finger
Probab=29.39 E-value=21 Score=20.11 Aligned_cols=15 Identities=27% Similarity=0.538 Sum_probs=10.2
Q ss_pred CCceecccccccCCC
Q psy4084 24 DRQFACHMCIKVFPS 38 (86)
Q Consensus 24 ~~~~~c~~c~~~~~~ 38 (86)
..+|.|++++..|..
T Consensus 111 ~~~~~CPvt~~~~~~ 125 (260)
T PF04641_consen 111 EGRFICPVTGKEFNG 125 (260)
T ss_pred CceeECCCCCcccCC
Confidence 456888887776643
No 261
>PHA02942 putative transposase; Provisional
Probab=29.06 E-value=1.2e+02 Score=18.53 Aligned_cols=30 Identities=20% Similarity=0.396 Sum_probs=18.8
Q ss_pred ecccccccCCChHHHhhhhhCCcceecccccccccCHH
Q psy4084 28 ACHMCIKVFPSQDKLRMHMLSDRQFACHMCIKVFPSQD 65 (86)
Q Consensus 28 ~c~~c~~~~~~~~~l~~h~~~~~~~~C~~C~~~~~~~~ 65 (86)
.|+.||..... ...+.|.|+.||.......
T Consensus 327 ~Cs~CG~~~~~--------l~~r~f~C~~CG~~~drD~ 356 (383)
T PHA02942 327 SCPKCGHKMVE--------IAHRYFHCPSCGYENDRDV 356 (383)
T ss_pred cCCCCCCccCc--------CCCCEEECCCCCCEeCcHH
Confidence 47777754321 1246789999998765553
No 262
>KOG2857|consensus
Probab=29.05 E-value=31 Score=17.80 Aligned_cols=23 Identities=17% Similarity=0.404 Sum_probs=18.8
Q ss_pred cceecccccccccCHHHHHHHHH
Q psy4084 50 RQFACHMCIKVFPSQDKLRMHML 72 (86)
Q Consensus 50 ~~~~C~~C~~~~~~~~~l~~h~~ 72 (86)
..|+|+.|...+-+...++.|..
T Consensus 16 ~KYKCpkC~vPYCSl~CfKiHk~ 38 (157)
T KOG2857|consen 16 IKYKCPKCSVPYCSLPCFKIHKS 38 (157)
T ss_pred hhccCCCCCCccccchhhhhccC
Confidence 35889999988888888888765
No 263
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=29.02 E-value=21 Score=12.19 Aligned_cols=7 Identities=29% Similarity=0.596 Sum_probs=3.8
Q ss_pred ecccccc
Q psy4084 28 ACHMCIK 34 (86)
Q Consensus 28 ~c~~c~~ 34 (86)
.|+.|+.
T Consensus 4 ~Cp~Cg~ 10 (26)
T PF13248_consen 4 FCPNCGA 10 (26)
T ss_pred CCcccCC
Confidence 4555654
No 264
>TIGR03830 CxxCG_CxxCG_HTH putative zinc finger/helix-turn-helix protein, YgiT family. This model describes a family of predicted regulatory proteins with a conserved zinc finger/HTH architecture. The amino-terminal region contains a novel domain, featuring two CXXC motifs and occuring in a number of small bacterial proteins as well as in the present family. The carboxyl-terminal region consists of a helix-turn-helix domain, modeled by pfam01381. The predicted function is DNA binding and transcriptional regulation.
Probab=28.97 E-value=78 Score=15.29 Aligned_cols=21 Identities=10% Similarity=0.311 Sum_probs=13.9
Q ss_pred cceecccccccccCHHHHHHH
Q psy4084 50 RQFACHMCIKVFPSQDKLRMH 70 (86)
Q Consensus 50 ~~~~C~~C~~~~~~~~~l~~h 70 (86)
..+.|+.||..+.........
T Consensus 30 ~~~~C~~CGe~~~~~e~~~~~ 50 (127)
T TIGR03830 30 PGWYCPACGEELLDPEESKRN 50 (127)
T ss_pred eeeECCCCCCEEEcHHHHHHH
Confidence 346788888887776655443
No 265
>KOG4727|consensus
Probab=28.85 E-value=46 Score=17.84 Aligned_cols=22 Identities=18% Similarity=0.353 Sum_probs=19.0
Q ss_pred ceecccccccccCHHHHHHHHH
Q psy4084 51 QFACHMCIKVFPSQDKLRMHML 72 (86)
Q Consensus 51 ~~~C~~C~~~~~~~~~l~~h~~ 72 (86)
.|.|.+|.-++....++..|+.
T Consensus 75 GyyCdVCdcvvKDSinflDHiN 96 (193)
T KOG4727|consen 75 GYYCDVCDCVVKDSINFLDHIN 96 (193)
T ss_pred ceeeeecceeehhhHHHHHHhc
Confidence 4889999999999888888875
No 266
>PF06220 zf-U1: U1 zinc finger; InterPro: IPR013085 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. C2H2-type (classical) zinc fingers (Znf) were the first class to be characterised. They contain a short beta hairpin and an alpha helix (beta/beta/alpha structure), where a single zinc atom is held in place by Cys(2)His(2) (C2H2) residues in a tetrahedral array. C2H2 Znf's can be divided into three groups based on the number and pattern of fingers: triple-C2H2 (binds single ligand), multiple-adjacent-C2H2 (binds multiple ligands), and separated paired-C2H2 []. C2H2 Znf's are the most common DNA-binding motifs found in eukaryotic transcription factors, and have also been identified in prokaryotes []. Transcription factors usually contain several Znf's (each with a conserved beta/beta/alpha structure) capable of making multiple contacts along the DNA, where the C2H2 Znf motifs recognise DNA sequences by binding to the major groove of DNA via a short alpha-helix in the Znf, the Znf spanning 3-4 bases of the DNA []. C2H2 Znf's can also bind to RNA and protein targets []. This entry represents a C2H2-type zinc finger motif found in several U1 small nuclear ribonucleoprotein C (U1-C) proteins. Some proteins contain multiple copies of this motif. The U1 small nuclear ribonucleoprotein (U1 snRNP) binds to the pre-mRNA 5' splice site at early stages of spliceosome assembly. Recruitment of U1 to a class of weak 5' splice site is promoted by binding of the protein TIA-1 to uridine-rich sequences immediately downstream from the 5' splice site. Binding of TIA-1 in the vicinity of a 5' splice site helps to stabilise U1 snRNP recruitment, at least in part, via a direct interaction with U1-C, thus providing one molecular mechanism for the function of this splicing regulator []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2VRD_A.
Probab=28.74 E-value=48 Score=12.69 Aligned_cols=10 Identities=30% Similarity=0.936 Sum_probs=3.1
Q ss_pred eecccccccc
Q psy4084 52 FACHMCIKVF 61 (86)
Q Consensus 52 ~~C~~C~~~~ 61 (86)
|-|..|..-+
T Consensus 4 yyCdyC~~~~ 13 (38)
T PF06220_consen 4 YYCDYCKKYL 13 (38)
T ss_dssp -B-TTT--B-
T ss_pred eeccccccee
Confidence 4566666655
No 267
>cd00974 DSRD Desulforedoxin (DSRD) domain; a small non-heme iron domain present in the desulforedoxin (rubredoxin oxidoreductase) and desulfoferrodoxin proteins of some archeael and bacterial methanogens and sulfate/sulfur reducers. Desulforedoxin is a small, single-domain homodimeric protein; each subunit contains an iron atom bound to four cysteinyl sulfur atoms, Fe(S-Cys)4, in a distorted tetrahedral coordination. Its metal center is similar to that found in rubredoxin type proteins. Desulforedoxin is regarded as a potential redox partner for rubredoxin. Desulfoferrodoxin forms a homodimeric protein, with each protomer comprised of two domains, the N-terminal DSRD domain and C-terminal superoxide reductase-like (SORL) domain. Each domain has a distinct iron center: the DSRD iron center I, Fe(S-Cys)4; and the SORL iron center II, Fe[His4Cys(Glu)].
Probab=28.70 E-value=34 Score=12.48 Aligned_cols=11 Identities=18% Similarity=0.866 Sum_probs=7.0
Q ss_pred ceecccccccc
Q psy4084 51 QFACHMCIKVF 61 (86)
Q Consensus 51 ~~~C~~C~~~~ 61 (86)
-|+|..||-..
T Consensus 4 ~ykC~~CGniv 14 (34)
T cd00974 4 VYKCEICGNIV 14 (34)
T ss_pred EEEcCCCCcEE
Confidence 46777776543
No 268
>TIGR00627 tfb4 transcription factor tfb4. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=28.66 E-value=50 Score=19.10 Aligned_cols=14 Identities=29% Similarity=0.804 Sum_probs=9.4
Q ss_pred Ccceeccccccccc
Q psy4084 49 DRQFACHMCIKVFP 62 (86)
Q Consensus 49 ~~~~~C~~C~~~~~ 62 (86)
...|.|+.|.-.|.
T Consensus 253 ~~GyvCs~Clsi~C 266 (279)
T TIGR00627 253 SIGFVCSVCLSVLC 266 (279)
T ss_pred cceEECCCccCCcC
Confidence 44578888776654
No 269
>COG1327 Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains [Transcription]
Probab=28.62 E-value=22 Score=18.52 Aligned_cols=13 Identities=31% Similarity=0.634 Sum_probs=8.8
Q ss_pred CcchhhhccChHH
Q psy4084 1 MSECMGKFTEYQV 13 (86)
Q Consensus 1 c~~C~~~~~~~~~ 13 (86)
|+.||..|+....
T Consensus 31 C~~C~~RFTTfE~ 43 (156)
T COG1327 31 CLECGERFTTFER 43 (156)
T ss_pred ccccccccchhhe
Confidence 6778877765543
No 270
>TIGR00280 L37a ribosomal protein L37a. This model finds eukaryotic ribosomal protein L37a and its archaeal orthologs. The nomeclature is tricky because eukaryotes have proteins called both L37 and L37a.
Probab=28.55 E-value=31 Score=16.32 Aligned_cols=32 Identities=22% Similarity=0.453 Sum_probs=20.1
Q ss_pred CceecccccccCCChHHHhhhhhCCcceecccccccccC
Q psy4084 25 RQFACHMCIKVFPSQDKLRMHMLSDRQFACHMCIKVFPS 63 (86)
Q Consensus 25 ~~~~c~~c~~~~~~~~~l~~h~~~~~~~~C~~C~~~~~~ 63 (86)
..|.|+.|++.--. + ...-.|.|..|++.|+-
T Consensus 34 a~y~CpfCgk~~vk-----R--~a~GIW~C~~C~~~~AG 65 (91)
T TIGR00280 34 AKYVCPFCGKKTVK-----R--GSTGIWTCRKCGAKFAG 65 (91)
T ss_pred cCccCCCCCCCceE-----E--EeeEEEEcCCCCCEEeC
Confidence 45899999743110 0 01235899999998753
No 271
>PTZ00043 cytochrome c oxidase subunit; Provisional
Probab=28.42 E-value=29 Score=19.49 Aligned_cols=17 Identities=18% Similarity=0.411 Sum_probs=13.2
Q ss_pred CCceecccccccCCChH
Q psy4084 24 DRQFACHMCIKVFPSQD 40 (86)
Q Consensus 24 ~~~~~c~~c~~~~~~~~ 40 (86)
.++.+|+.||..|....
T Consensus 179 GkpqRCpECGqVFKLVr 195 (268)
T PTZ00043 179 GFLYRCGECDQIFMLVR 195 (268)
T ss_pred CCCccCCCCCcEEEEEE
Confidence 45789999999887643
No 272
>TIGR00319 desulf_FeS4 desulfoferrodoxin FeS4 iron-binding domain. Neelaredoxin, a monomeric blue non-heme iron protein, lacks this domain.
Probab=28.29 E-value=36 Score=12.40 Aligned_cols=11 Identities=18% Similarity=0.839 Sum_probs=7.3
Q ss_pred ceecccccccc
Q psy4084 51 QFACHMCIKVF 61 (86)
Q Consensus 51 ~~~C~~C~~~~ 61 (86)
-|+|..||-..
T Consensus 7 ~ykC~~Cgniv 17 (34)
T TIGR00319 7 VYKCEVCGNIV 17 (34)
T ss_pred EEEcCCCCcEE
Confidence 47787777553
No 273
>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=28.27 E-value=30 Score=13.26 Aligned_cols=11 Identities=18% Similarity=0.601 Sum_probs=7.6
Q ss_pred ceecccccccc
Q psy4084 51 QFACHMCIKVF 61 (86)
Q Consensus 51 ~~~C~~C~~~~ 61 (86)
-|.|..|+..|
T Consensus 28 fy~C~~C~~~w 38 (39)
T PF01096_consen 28 FYVCCNCGHRW 38 (39)
T ss_dssp EEEESSSTEEE
T ss_pred EEEeCCCCCee
Confidence 36788887654
No 274
>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=27.71 E-value=10 Score=16.72 Aligned_cols=12 Identities=25% Similarity=0.606 Sum_probs=4.9
Q ss_pred ceeccccccccc
Q psy4084 51 QFACHMCIKVFP 62 (86)
Q Consensus 51 ~~~C~~C~~~~~ 62 (86)
...|..|+....
T Consensus 41 ~v~Cg~C~~~~~ 52 (71)
T PF05495_consen 41 RVICGKCRTEQP 52 (71)
T ss_dssp EEEETTT--EEE
T ss_pred CeECCCCCCccC
Confidence 445555554443
No 275
>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=27.62 E-value=28 Score=14.47 Aligned_cols=16 Identities=19% Similarity=0.706 Sum_probs=9.7
Q ss_pred CcceecccccccccCH
Q psy4084 49 DRQFACHMCIKVFPSQ 64 (86)
Q Consensus 49 ~~~~~C~~C~~~~~~~ 64 (86)
...+.|.+|++.+...
T Consensus 33 ~~~~rC~YCe~~~~~~ 48 (52)
T PF02748_consen 33 PIKLRCHYCERIITED 48 (52)
T ss_dssp TCEEEETTT--EEEHH
T ss_pred CCEEEeeCCCCEeccc
Confidence 3468899998876544
No 276
>PRK11827 hypothetical protein; Provisional
Probab=27.35 E-value=54 Score=14.18 Aligned_cols=16 Identities=25% Similarity=0.571 Sum_probs=9.9
Q ss_pred ceecccccccccCHHH
Q psy4084 51 QFACHMCIKVFPSQDK 66 (86)
Q Consensus 51 ~~~C~~C~~~~~~~~~ 66 (86)
.+.|..|+..|+=...
T Consensus 26 ~Lic~~~~laYPI~dg 41 (60)
T PRK11827 26 ELICKLDNLAFPLRDG 41 (60)
T ss_pred eEECCccCeeccccCC
Confidence 4667777777764433
No 277
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=27.19 E-value=35 Score=13.56 Aligned_cols=13 Identities=31% Similarity=0.621 Sum_probs=9.2
Q ss_pred ceecccccccccC
Q psy4084 51 QFACHMCIKVFPS 63 (86)
Q Consensus 51 ~~~C~~C~~~~~~ 63 (86)
.+.|+.||..+.-
T Consensus 20 ~~vC~~Cg~~~~~ 32 (52)
T smart00661 20 RFVCRKCGYEEPI 32 (52)
T ss_pred EEECCcCCCeEEC
Confidence 5778888876543
No 278
>KOG1088|consensus
Probab=26.85 E-value=38 Score=16.88 Aligned_cols=19 Identities=21% Similarity=0.347 Sum_probs=12.4
Q ss_pred HhCCCceecccccccCCCh
Q psy4084 21 FHSDRQFACHMCIKVFPSQ 39 (86)
Q Consensus 21 ~~~~~~~~c~~c~~~~~~~ 39 (86)
+..+...+|+.||..|.-.
T Consensus 93 ~v~EG~l~CpetG~vfpI~ 111 (124)
T KOG1088|consen 93 DVIEGELVCPETGRVFPIS 111 (124)
T ss_pred hhccceEecCCCCcEeecc
Confidence 3346667788887776544
No 279
>COG4640 Predicted membrane protein [Function unknown]
Probab=26.76 E-value=47 Score=20.45 Aligned_cols=20 Identities=20% Similarity=0.401 Sum_probs=11.8
Q ss_pred CceecccccccCCChHHHhh
Q psy4084 25 RQFACHMCIKVFPSQDKLRM 44 (86)
Q Consensus 25 ~~~~c~~c~~~~~~~~~l~~ 44 (86)
....|..||..+....+...
T Consensus 14 d~~qC~qCG~~~t~~~sqan 33 (465)
T COG4640 14 DDVQCTQCGHKFTSRQSQAN 33 (465)
T ss_pred ccccccccCCcCCchhhhhh
Confidence 33447777777666555443
No 280
>PF10122 Mu-like_Com: Mu-like prophage protein Com; InterPro: IPR019294 Members of this entry belong to the Com family of proteins that act as translational regulators of mom [, ].
Probab=26.74 E-value=21 Score=14.86 Aligned_cols=10 Identities=20% Similarity=0.786 Sum_probs=6.1
Q ss_pred ceeccccccc
Q psy4084 51 QFACHMCIKV 60 (86)
Q Consensus 51 ~~~C~~C~~~ 60 (86)
..+|+.|+..
T Consensus 24 eIKCpRC~ti 33 (51)
T PF10122_consen 24 EIKCPRCKTI 33 (51)
T ss_pred EEECCCCCcc
Confidence 4567777654
No 281
>cd00122 MBD MeCP2, MBD1, MBD2, MBD3, MBD4, CLLD8-like, and BAZ2A-like proteins constitute a family of proteins that share the methyl-CpG-binding domain (MBD). The MBD consists of about 70 residues and is defined as the minimal region required for binding to methylated DNA by a methyl-CpG-binding protein which binds specifically to methylated DNA. The MBD can recognize a single symmetrically methylated CpG either as naked DNA or within chromatin. MeCP2, MBD1 and MBD2 (and likely MBD3) form complexes with histone deacetylase and are involved in histone deacetylase-dependent repression of transcription. MBD4 is an endonuclease that forms a complex with the DNA mismatch-repair protein MLH1. The MBDs present in putative chromatin remodelling subunit, BAZ2A, and putative histone methyltransferase, CLLD8, represent two phylogenetically distinct groups within the MBD protein family.
Probab=26.72 E-value=60 Score=13.78 Aligned_cols=18 Identities=11% Similarity=0.224 Sum_probs=13.5
Q ss_pred hhhhccChHHHHhhHHHH
Q psy4084 4 CMGKFTEYQVIRKHIRTF 21 (86)
Q Consensus 4 C~~~~~~~~~l~~h~~~~ 21 (86)
||+.|.+...+.+++..+
T Consensus 33 ~Gk~~Rs~~ev~~yL~~~ 50 (62)
T cd00122 33 CGKKLRSKPEVARYLEKT 50 (62)
T ss_pred CCceecCHHHHHHHHHhC
Confidence 677888888887776654
No 282
>PF00641 zf-RanBP: Zn-finger in Ran binding protein and others; InterPro: IPR001876 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 zinc finger domain found in RanBP2 proteins. Ran is an evolutionary conserved member of the Ras superfamily that regulates all receptor-mediated transport between the nucleus and the cytoplasm. Ran binding protein 2 (RanBP2) is a 358kDa nucleoporin located on the cytoplasmic side of the nuclear pore complex which plays a role in nuclear protein import []. RanBP2 contains multiple zinc fingers which mediate binding to RanGDP []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9G_A 2EBR_A 2WX0_C 2WX1_C 2WWZ_C 3GJ6_B 2LK0_A 2LK1_A 3GJ5_B 3GJ8_B ....
Probab=26.11 E-value=27 Score=12.24 Aligned_cols=6 Identities=33% Similarity=0.634 Sum_probs=2.4
Q ss_pred CCCCcC
Q psy4084 80 LKSKLC 85 (86)
Q Consensus 80 ~~c~~C 85 (86)
|.|..|
T Consensus 5 W~C~~C 10 (30)
T PF00641_consen 5 WKCPSC 10 (30)
T ss_dssp EEETTT
T ss_pred ccCCCC
Confidence 444433
No 283
>COG3024 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=26.10 E-value=37 Score=14.92 Aligned_cols=12 Identities=25% Similarity=0.379 Sum_probs=8.9
Q ss_pred eecccccccccC
Q psy4084 52 FACHMCIKVFPS 63 (86)
Q Consensus 52 ~~C~~C~~~~~~ 63 (86)
.+|+.||+...+
T Consensus 8 v~CP~Cgkpv~w 19 (65)
T COG3024 8 VPCPTCGKPVVW 19 (65)
T ss_pred ccCCCCCCcccc
Confidence 578888887655
No 284
>PTZ00409 Sir2 (Silent Information Regulator) protein; Provisional
Probab=26.06 E-value=94 Score=17.88 Aligned_cols=15 Identities=20% Similarity=0.459 Sum_probs=9.3
Q ss_pred ceecccccccccCHH
Q psy4084 51 QFACHMCIKVFPSQD 65 (86)
Q Consensus 51 ~~~C~~C~~~~~~~~ 65 (86)
...|..|+..+....
T Consensus 137 ~~~C~~C~~~~~~~~ 151 (271)
T PTZ00409 137 EARCCTCRKTIQLNK 151 (271)
T ss_pred cceeCCCCCCcccCH
Confidence 356777877665443
No 285
>PF09889 DUF2116: Uncharacterized protein containing a Zn-ribbon (DUF2116); InterPro: IPR019216 This entry contains various hypothetical prokaryotic proteins whose functions are unknown. They contain a conserved zinc ribbon motif in the N-terminal part and a predicted transmembrane segment in the C-terminal part.
Probab=26.03 E-value=34 Score=14.71 Aligned_cols=7 Identities=14% Similarity=0.187 Sum_probs=2.9
Q ss_pred Ccchhhh
Q psy4084 1 MSECMGK 7 (86)
Q Consensus 1 c~~C~~~ 7 (86)
|+.||+.
T Consensus 6 C~~CG~~ 12 (59)
T PF09889_consen 6 CPVCGKP 12 (59)
T ss_pred CCcCCCc
Confidence 3444433
No 286
>TIGR01053 LSD1 zinc finger domain, LSD1 subclass. This model describes a putative zinc finger domain found in three closely spaced copies in Arabidopsis protein LSD1 and in two copies in other proteins from the same species. The motif resembles CxxCRxxLMYxxGASxVxCxxC
Probab=25.60 E-value=39 Score=12.38 Aligned_cols=6 Identities=33% Similarity=1.093 Sum_probs=2.5
Q ss_pred CCCCcC
Q psy4084 80 LKSKLC 85 (86)
Q Consensus 80 ~~c~~C 85 (86)
++|..|
T Consensus 20 vrCs~C 25 (31)
T TIGR01053 20 VRCALC 25 (31)
T ss_pred EECCCC
Confidence 444443
No 287
>cd01413 SIR2_Af2 SIR2_Af2: Archaeal and prokaryotic group which includes Archaeoglobus fulgidus Sir2-Af2, Sulfolobus solfataricus ssSir2, and several bacterial homologs; and are members of the SIR2 family of proteins, silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation. Sir2 proteins have been shown to regulate gene silencing, DNA repair, metabolic enzymes, and life span. The Sir2 homolog from the archaea Sulfolobus solftaricus deacetylates the non-specific DNA protein Alba to mediate transcription repression.
Probab=25.51 E-value=94 Score=17.11 Aligned_cols=14 Identities=14% Similarity=0.292 Sum_probs=8.7
Q ss_pred ceecccccccccCH
Q psy4084 51 QFACHMCIKVFPSQ 64 (86)
Q Consensus 51 ~~~C~~C~~~~~~~ 64 (86)
...|..|+..+...
T Consensus 113 ~~~C~~C~~~~~~~ 126 (222)
T cd01413 113 TAYCVNCGSKYDLE 126 (222)
T ss_pred cceECCCCCCcchh
Confidence 35677777766544
No 288
>PRK12387 formate hydrogenlyase complex iron-sulfur subunit; Provisional
Probab=25.45 E-value=58 Score=17.20 Aligned_cols=19 Identities=21% Similarity=0.553 Sum_probs=14.3
Q ss_pred cceecccccccccCHHHHH
Q psy4084 50 RQFACHMCIKVFPSQDKLR 68 (86)
Q Consensus 50 ~~~~C~~C~~~~~~~~~l~ 68 (86)
.++.|..||+.|.....+.
T Consensus 113 ~~~~C~~CG~~f~~~~~i~ 131 (180)
T PRK12387 113 ALCNCRVCGRPFAVQKEID 131 (180)
T ss_pred CcccchhhCCccccHHHHH
Confidence 4578999999998665443
No 289
>PF06170 DUF983: Protein of unknown function (DUF983); InterPro: IPR009325 This family consists of several bacterial proteins of unknown function.
Probab=25.44 E-value=30 Score=16.09 Aligned_cols=8 Identities=13% Similarity=0.380 Sum_probs=3.8
Q ss_pred Ccchhhhc
Q psy4084 1 MSECMGKF 8 (86)
Q Consensus 1 c~~C~~~~ 8 (86)
|+.||..|
T Consensus 11 C~~CG~d~ 18 (86)
T PF06170_consen 11 CPHCGLDY 18 (86)
T ss_pred ccccCCcc
Confidence 44555444
No 290
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=25.31 E-value=39 Score=15.98 Aligned_cols=32 Identities=16% Similarity=0.405 Sum_probs=19.8
Q ss_pred CceecccccccCCChHHHhhhhhCCcceecccccccccC
Q psy4084 25 RQFACHMCIKVFPSQDKLRMHMLSDRQFACHMCIKVFPS 63 (86)
Q Consensus 25 ~~~~c~~c~~~~~~~~~l~~h~~~~~~~~C~~C~~~~~~ 63 (86)
..|.|+.|++.--... ..-.|.|..|++.|+-
T Consensus 35 a~y~CpfCgk~~vkR~-------a~GIW~C~~C~~~~AG 66 (90)
T PRK03976 35 AKHVCPVCGRPKVKRV-------GTGIWECRKCGAKFAG 66 (90)
T ss_pred cCccCCCCCCCceEEE-------EEEEEEcCCCCCEEeC
Confidence 3588999964311100 1235899999988754
No 291
>TIGR00244 transcriptional regulator NrdR. Members of this almost entirely bacterial family contain an ATP cone domain (PFAM:PF03477). There is never more than one member per genome. Common gene symbols given include nrdR, ybaD, ribX and ytcG. The member from Streptomyces coelicolor is found upstream in the operon of the class II oxygen-independent ribonucleotide reductase gene nrdJ and was shown to repress nrdJ expression. Many members of this family are found near genes for riboflavin biosynthesis in Gram-negative bacteria, suggesting a role in that pathway. However, a phylogenetic profiling study associates members of this family with the presence of a palindromic signal with consensus acaCwAtATaTwGtgt, termed the NrdR-box, an upstream element for most operons for ribonucleotide reductase of all three classes in bacterial genomes.
Probab=25.06 E-value=27 Score=18.09 Aligned_cols=14 Identities=29% Similarity=0.622 Sum_probs=9.5
Q ss_pred CcchhhhccChHHH
Q psy4084 1 MSECMGKFTEYQVI 14 (86)
Q Consensus 1 c~~C~~~~~~~~~l 14 (86)
|..||+.|+....+
T Consensus 31 C~~C~~RFTTyErv 44 (147)
T TIGR00244 31 CLECHERFTTFERA 44 (147)
T ss_pred CCccCCccceeeec
Confidence 66788888766543
No 292
>smart00391 MBD Methyl-CpG binding domain. Methyl-CpG binding domain, also known as the TAM (TTF-IIP5, ARBP, MeCP1) domain
Probab=24.87 E-value=59 Score=14.69 Aligned_cols=19 Identities=11% Similarity=0.177 Sum_probs=14.4
Q ss_pred hhhhccChHHHHhhHHHHh
Q psy4084 4 CMGKFTEYQVIRKHIRTFH 22 (86)
Q Consensus 4 C~~~~~~~~~l~~h~~~~~ 22 (86)
||+.+.+...+..++..+.
T Consensus 36 ~GkklRs~~ev~~YL~~~~ 54 (77)
T smart00391 36 CGKKLRSKSELARYLHKNG 54 (77)
T ss_pred CCCeeeCHHHHHHHHHhCC
Confidence 7888888888888876543
No 293
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=24.78 E-value=8.4 Score=18.83 Aligned_cols=12 Identities=17% Similarity=0.479 Sum_probs=9.6
Q ss_pred ceeccccccccc
Q psy4084 51 QFACHMCIKVFP 62 (86)
Q Consensus 51 ~~~C~~C~~~~~ 62 (86)
=|.|..||..|.
T Consensus 100 Fy~C~~Cg~~wr 111 (113)
T COG1594 100 FYKCTRCGYRWR 111 (113)
T ss_pred EEEecccCCEee
Confidence 378999998764
No 294
>PF04988 AKAP95: A-kinase anchoring protein 95 (AKAP95); InterPro: IPR007071 A-kinase (or PKA)-anchoring protein AKAP95 is implicated in mitotic chromosome condensation by acting as a targeting molecule for the condensin complex. The protein contains two zinc fingers which are thought to mediate the binding of AKAP95 to DNA [].; GO: 0003677 DNA binding, 0005634 nucleus
Probab=24.20 E-value=65 Score=17.12 Aligned_cols=22 Identities=23% Similarity=0.489 Sum_probs=16.5
Q ss_pred eecccccccccCHHHHHHHHHh
Q psy4084 52 FACHMCIKVFPSQDKLRMHMLS 73 (86)
Q Consensus 52 ~~C~~C~~~~~~~~~l~~h~~~ 73 (86)
|.|..|.........+..|+.+
T Consensus 1 F~Cs~CKfrtf~~~ei~~HleS 22 (165)
T PF04988_consen 1 FTCSFCKFRTFEEKEIEKHLES 22 (165)
T ss_pred CccceeeeecccHHHHHHHHcc
Confidence 4577888777777788888764
No 295
>PF01844 HNH: HNH endonuclease; InterPro: IPR002711 HNH endonuclease is found in bacteria and viruses [, , ]. This family includes pyocins, colicins and anaredoxins.; GO: 0003676 nucleic acid binding, 0004519 endonuclease activity; PDB: 2QGP_C.
Probab=23.60 E-value=31 Score=13.23 Aligned_cols=9 Identities=11% Similarity=-0.027 Sum_probs=1.9
Q ss_pred Ccchhhhcc
Q psy4084 1 MSECMGKFT 9 (86)
Q Consensus 1 c~~C~~~~~ 9 (86)
|..|++.+.
T Consensus 1 C~~C~~~~~ 9 (47)
T PF01844_consen 1 CQYCGKPGS 9 (47)
T ss_dssp -TTT--B--
T ss_pred CCCCCCcCc
Confidence 344444443
No 296
>cd04476 RPA1_DBD_C RPA1_DBD_C: A subfamily of OB folds corresponding to the C-terminal OB fold, the ssDNA-binding domain (DBD)-C, of human RPA1 (also called RPA70). RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). In addition to DBD-C, RPA1 contains three other OB folds: DBD-A, DBD-B, and RPA1N. The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B. RPA1 DBD-C is involved in DNA binding and trimerization. It contains two structural insertions not found to date in other OB-folds: a zinc ribbon and a three-helix bundle. RPA1 DBD-C also contains a Cys4-type zinc-binding motif, which plays a role in the ssDNA binding fun
Probab=23.58 E-value=21 Score=18.39 Aligned_cols=12 Identities=25% Similarity=0.694 Sum_probs=7.3
Q ss_pred cceecccccccc
Q psy4084 50 RQFACHMCIKVF 61 (86)
Q Consensus 50 ~~~~C~~C~~~~ 61 (86)
..|.|+.|+...
T Consensus 50 ~~~~C~~C~~~~ 61 (166)
T cd04476 50 GTYRCEKCNKSV 61 (166)
T ss_pred CcEECCCCCCcC
Confidence 346677776653
No 297
>KOG4118|consensus
Probab=23.49 E-value=49 Score=14.62 Aligned_cols=29 Identities=14% Similarity=0.416 Sum_probs=20.1
Q ss_pred ceecccccccccCHHHHHHHHHhCCCCcc
Q psy4084 51 QFACHMCIKVFPSQDKLRMHMLSGLQTFD 79 (86)
Q Consensus 51 ~~~C~~C~~~~~~~~~l~~h~~~~~~~~~ 79 (86)
.+.|.+|--..+....+..|...-+...+
T Consensus 38 ~~kCtVC~~~mpdpktfkqhfe~kHpk~~ 66 (74)
T KOG4118|consen 38 HHKCTVCMVQMPDPKTFKQHFENKHPKEP 66 (74)
T ss_pred HhhhHhhHhhCCCCchHHHHHhhcCCCCC
Confidence 36788887777777778888776544333
No 298
>KOG0801|consensus
Probab=23.39 E-value=18 Score=19.13 Aligned_cols=17 Identities=24% Similarity=0.620 Sum_probs=9.4
Q ss_pred HHHHHHhCCCCccCCCCcCC
Q psy4084 67 LRMHMLSGLQTFDLKSKLCT 86 (86)
Q Consensus 67 l~~h~~~~~~~~~~~c~~C~ 86 (86)
|..|+-.|. .++|+.|+
T Consensus 129 lP~hi~~~~---g~KCPvC~ 145 (205)
T KOG0801|consen 129 LPVHIMDHS---GMKCPVCH 145 (205)
T ss_pred cceeeeccC---CccCCccc
Confidence 344444443 37888774
No 299
>PF09082 DUF1922: Domain of unknown function (DUF1922); InterPro: IPR015166 Members of this family consist of a beta-sheet region followed by an alpha-helix and an unstructured C terminus. The beta-sheet region contains a CXCX...XCXC sequence with Cys residues located in two proximal loops and pointing towards each other. This precise function of this set of bacterial proteins is, as yet, unknown []. ; PDB: 1GH9_A.
Probab=22.80 E-value=29 Score=15.47 Aligned_cols=7 Identities=43% Similarity=1.089 Sum_probs=3.0
Q ss_pred eccccccc
Q psy4084 53 ACHMCIKV 60 (86)
Q Consensus 53 ~C~~C~~~ 60 (86)
.| .||+.
T Consensus 22 kC-~CG~~ 28 (68)
T PF09082_consen 22 KC-VCGKT 28 (68)
T ss_dssp EE-TTTEE
T ss_pred Ee-cCCCe
Confidence 44 44443
No 300
>COG5027 SAS2 Histone acetyltransferase (MYST family) [Chromatin structure and dynamics]
Probab=22.68 E-value=54 Score=19.82 Aligned_cols=25 Identities=32% Similarity=0.615 Sum_probs=21.8
Q ss_pred CcceecccccccccCHHHHHHHHHh
Q psy4084 49 DRQFACHMCIKVFPSQDKLRMHMLS 73 (86)
Q Consensus 49 ~~~~~C~~C~~~~~~~~~l~~h~~~ 73 (86)
...|.|..|-+-+.+...|.+|...
T Consensus 156 d~vyICefClkY~~s~~~~~rH~~k 180 (395)
T COG5027 156 DIVYICEFCLKYYGSQTSLVRHRKK 180 (395)
T ss_pred ceEEEhhhhHHHhcchhHHHHHHhc
Confidence 4568999999999999999999875
No 301
>KOG1940|consensus
Probab=22.60 E-value=1.3e+02 Score=17.62 Aligned_cols=8 Identities=38% Similarity=1.310 Sum_probs=6.3
Q ss_pred eecccccc
Q psy4084 27 FACHMCIK 34 (86)
Q Consensus 27 ~~c~~c~~ 34 (86)
|.|++|.+
T Consensus 197 y~CP~C~~ 204 (276)
T KOG1940|consen 197 YTCPICSK 204 (276)
T ss_pred CCCCcccc
Confidence 78888776
No 302
>cd01410 SIRT7 SIRT7: Eukaryotic and prokaryotic group (class4) which includes human sirtuin SIRT6, SIRT7, and several bacterial homologs; and are members of the SIR2 family of proteins, silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation. Sir2 proteins have been shown to regulate gene silencing, DNA repair, metabolic enzymes, and life span.
Probab=22.29 E-value=1.3e+02 Score=16.47 Aligned_cols=6 Identities=33% Similarity=0.949 Sum_probs=2.5
Q ss_pred cccccc
Q psy4084 29 CHMCIK 34 (86)
Q Consensus 29 c~~c~~ 34 (86)
|..|+.
T Consensus 98 C~~C~~ 103 (206)
T cd01410 98 CKSCGP 103 (206)
T ss_pred CCCCCC
Confidence 444443
No 303
>PF14447 Prok-RING_4: Prokaryotic RING finger family 4
Probab=22.24 E-value=52 Score=14.00 Aligned_cols=15 Identities=27% Similarity=0.536 Sum_probs=9.9
Q ss_pred CcceecccccccccC
Q psy4084 49 DRQFACHMCIKVFPS 63 (86)
Q Consensus 49 ~~~~~C~~C~~~~~~ 63 (86)
++--.|+.|+..|..
T Consensus 37 ~rYngCPfC~~~~~~ 51 (55)
T PF14447_consen 37 ERYNGCPFCGTPFEF 51 (55)
T ss_pred hhccCCCCCCCcccC
Confidence 344468888887754
No 304
>KOG2923|consensus
Probab=22.05 E-value=93 Score=13.73 Aligned_cols=10 Identities=20% Similarity=0.557 Sum_probs=5.3
Q ss_pred Ccceeccccc
Q psy4084 49 DRQFACHMCI 58 (86)
Q Consensus 49 ~~~~~C~~C~ 58 (86)
+....|+.|.
T Consensus 42 e~Va~CpsCS 51 (67)
T KOG2923|consen 42 EDVARCPSCS 51 (67)
T ss_pred CeeecCCCce
Confidence 3445566654
No 305
>COG1779 C4-type Zn-finger protein [General function prediction only]
Probab=22.01 E-value=24 Score=19.29 Aligned_cols=14 Identities=14% Similarity=0.135 Sum_probs=9.1
Q ss_pred cceecccccccccC
Q psy4084 50 RQFACHMCIKVFPS 63 (86)
Q Consensus 50 ~~~~C~~C~~~~~~ 63 (86)
..+.|..||+.+..
T Consensus 42 ~t~~C~~CgYR~~D 55 (201)
T COG1779 42 STGVCERCGYRSTD 55 (201)
T ss_pred EEEEccccCCcccc
Confidence 44677788876544
No 306
>KOG0402|consensus
Probab=21.96 E-value=51 Score=15.35 Aligned_cols=23 Identities=22% Similarity=0.449 Sum_probs=13.8
Q ss_pred ChHHHhhhhhC-----Ccceeccccccc
Q psy4084 38 SQDKLRMHMLS-----DRQFACHMCIKV 60 (86)
Q Consensus 38 ~~~~l~~h~~~-----~~~~~C~~C~~~ 60 (86)
..++|+.-+.. ...|.|+.||+.
T Consensus 18 YGaSLrk~vKkiei~Qhaky~CsfCGK~ 45 (92)
T KOG0402|consen 18 YGASLRKMVKKIEIQQHAKYTCSFCGKK 45 (92)
T ss_pred hhHHHHHHHHHHHHHHhhhhhhhhcchh
Confidence 34555544432 345888888875
No 307
>PF14149 YhfH: YhfH-like protein
Probab=21.49 E-value=29 Score=13.43 Aligned_cols=7 Identities=29% Similarity=0.586 Sum_probs=3.3
Q ss_pred Ccchhhh
Q psy4084 1 MSECMGK 7 (86)
Q Consensus 1 c~~C~~~ 7 (86)
|+.||+.
T Consensus 16 C~~CG~~ 22 (37)
T PF14149_consen 16 CTECGKE 22 (37)
T ss_pred cHHHHHH
Confidence 4455543
No 308
>PF11931 DUF3449: Domain of unknown function (DUF3449); InterPro: IPR024598 This presumed domain is functionally uncharacterised. It has two conserved sequence motifs: PIP and CEICG and contains a zinc-finger of the C2H2-type.; PDB: 4DGW_A.
Probab=21.29 E-value=32 Score=18.79 Aligned_cols=14 Identities=14% Similarity=0.237 Sum_probs=0.0
Q ss_pred hCCCCccCCCCcCC
Q psy4084 73 SGLQTFDLKSKLCT 86 (86)
Q Consensus 73 ~~~~~~~~~c~~C~ 86 (86)
.|--...|+|.+|+
T Consensus 95 LhGL~~ey~CEICG 108 (196)
T PF11931_consen 95 LHGLGVEYKCEICG 108 (196)
T ss_dssp --------------
T ss_pred HhCCCCeeeeEeCC
Confidence 34445567777775
No 309
>PRK14138 NAD-dependent deacetylase; Provisional
Probab=21.27 E-value=1.3e+02 Score=16.93 Aligned_cols=16 Identities=25% Similarity=0.615 Sum_probs=9.8
Q ss_pred ceecccccccccCHHH
Q psy4084 51 QFACHMCIKVFPSQDK 66 (86)
Q Consensus 51 ~~~C~~C~~~~~~~~~ 66 (86)
...|..|++.+.....
T Consensus 119 ~~~C~~C~~~~~~~~~ 134 (244)
T PRK14138 119 EYYCVRCGKRYTVEDV 134 (244)
T ss_pred eeEECCCCCcccHHHH
Confidence 3567777777655433
No 310
>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=21.09 E-value=46 Score=11.79 Aligned_cols=10 Identities=40% Similarity=0.896 Sum_probs=5.4
Q ss_pred eecccccccc
Q psy4084 52 FACHMCIKVF 61 (86)
Q Consensus 52 ~~C~~C~~~~ 61 (86)
|.|..|+..+
T Consensus 28 f~C~~C~~~L 37 (39)
T smart00132 28 FKCSKCGKPL 37 (39)
T ss_pred CCCcccCCcC
Confidence 4555565543
No 311
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=21.05 E-value=53 Score=13.66 Aligned_cols=8 Identities=25% Similarity=0.812 Sum_probs=4.8
Q ss_pred eccccccc
Q psy4084 53 ACHMCIKV 60 (86)
Q Consensus 53 ~C~~C~~~ 60 (86)
.|+.||..
T Consensus 5 PCPFCG~~ 12 (61)
T PF14354_consen 5 PCPFCGSA 12 (61)
T ss_pred CCCCCCCc
Confidence 56667644
No 312
>PF10367 Vps39_2: Vacuolar sorting protein 39 domain 2; InterPro: IPR019453 This entry represents a domain found in the vacuolar sorting protein Vps39 and transforming growth factor beta receptor-associated protein Trap1. Vps39, a component of the C-Vps complex, is thought to be required for the fusion of endosomes and other types of transport intermediates with the vacuole [, ]. In Saccharomyces cerevisiae (Baker's yeast), Vps39 has been shown to stimulate nucleotide exchange []. Trap1 plays a role in the TGF-beta/activin signaling pathway. It associates with inactive heteromeric TGF-beta and activin receptor complexes, mainly through the type II receptor, and is released upon activation of signaling [, ]. The precise function of this domain has not been characterised In Vps39 this domain is involved in localisation and in mediating the interactions with Vps11 [].
Probab=20.95 E-value=39 Score=15.70 Aligned_cols=6 Identities=33% Similarity=0.368 Sum_probs=2.3
Q ss_pred cchhhh
Q psy4084 2 SECMGK 7 (86)
Q Consensus 2 ~~C~~~ 7 (86)
+.|++.
T Consensus 82 ~vC~k~ 87 (109)
T PF10367_consen 82 SVCGKP 87 (109)
T ss_pred cCcCCc
Confidence 334433
No 313
>PRK11032 hypothetical protein; Provisional
Probab=20.84 E-value=47 Score=17.52 Aligned_cols=30 Identities=13% Similarity=0.264 Sum_probs=17.6
Q ss_pred CceecccccccCCChHHHhhhhhCCcceecccccccc
Q psy4084 25 RQFACHMCIKVFPSQDKLRMHMLSDRQFACHMCIKVF 61 (86)
Q Consensus 25 ~~~~c~~c~~~~~~~~~l~~h~~~~~~~~C~~C~~~~ 61 (86)
..+.|..|+....... +..--.|+.|+...
T Consensus 123 G~LvC~~Cg~~~~~~~-------p~~i~pCp~C~~~~ 152 (160)
T PRK11032 123 GNLVCEKCHHHLAFYT-------PEVLPLCPKCGHDQ 152 (160)
T ss_pred ceEEecCCCCEEEecC-------CCcCCCCCCCCCCe
Confidence 4588998985532111 13334788888663
No 314
>PRK00418 DNA gyrase inhibitor; Reviewed
Probab=20.75 E-value=59 Score=14.21 Aligned_cols=11 Identities=27% Similarity=0.549 Sum_probs=7.7
Q ss_pred ceecccccccc
Q psy4084 51 QFACHMCIKVF 61 (86)
Q Consensus 51 ~~~C~~C~~~~ 61 (86)
...|+.|++..
T Consensus 6 ~v~CP~C~k~~ 16 (62)
T PRK00418 6 TVNCPTCGKPV 16 (62)
T ss_pred cccCCCCCCcc
Confidence 35688888764
No 315
>COG0846 SIR2 NAD-dependent protein deacetylases, SIR2 family [Transcription]
Probab=20.65 E-value=93 Score=17.74 Aligned_cols=11 Identities=18% Similarity=0.537 Sum_probs=5.2
Q ss_pred eeccccccccc
Q psy4084 52 FACHMCIKVFP 62 (86)
Q Consensus 52 ~~C~~C~~~~~ 62 (86)
+.|..|+..+.
T Consensus 123 ~~C~~C~~~~~ 133 (250)
T COG0846 123 VRCSKCGNQYY 133 (250)
T ss_pred eEeCCCcCccc
Confidence 44555544443
No 316
>PF11023 DUF2614: Protein of unknown function (DUF2614); InterPro: IPR020912 This entry describes proteins of unknown function, which are thought to be membrane proteins.; GO: 0005887 integral to plasma membrane
Probab=20.39 E-value=56 Score=16.17 Aligned_cols=13 Identities=31% Similarity=0.391 Sum_probs=9.8
Q ss_pred Ccceecccccccc
Q psy4084 49 DRQFACHMCIKVF 61 (86)
Q Consensus 49 ~~~~~C~~C~~~~ 61 (86)
.....|+.|++..
T Consensus 67 av~V~CP~C~K~T 79 (114)
T PF11023_consen 67 AVQVECPNCGKQT 79 (114)
T ss_pred ceeeECCCCCChH
Confidence 3567899998875
No 317
>KOG3352|consensus
Probab=20.22 E-value=43 Score=17.49 Aligned_cols=14 Identities=21% Similarity=0.392 Sum_probs=8.7
Q ss_pred CceecccccccCCC
Q psy4084 25 RQFACHMCIKVFPS 38 (86)
Q Consensus 25 ~~~~c~~c~~~~~~ 38 (86)
+.++|+.||..|..
T Consensus 132 e~~rc~eCG~~fkL 145 (153)
T KOG3352|consen 132 ETQRCPECGHYFKL 145 (153)
T ss_pred CcccCCcccceEEe
Confidence 34567777766643
No 318
>PF07649 C1_3: C1-like domain; InterPro: IPR011424 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in IPR002219 from INTERPRO. C1 domains are protein kinase C-like zinc finger structures. Diacylglycerol (DAG) kinases (DGKs) have a two or three commonly conserved cysteine-rich C1 domains []. DGKs modulate the balance between the two signaling lipids, DAG and phosphatidic acid (PA), by phosphorylating DAG to yield PA []. The PKD (protein kinase D) family are novel DAG receptors. They have twin C1 domains, designated C1a and C1b, which bind DAG or phorbol esters. Individual C1 domains differ in ligand-binding activity and selectivity []. ; GO: 0047134 protein-disulfide reductase activity, 0055114 oxidation-reduction process; PDB: 1V5N_A.
Probab=20.11 E-value=58 Score=11.40 Aligned_cols=11 Identities=18% Similarity=0.338 Sum_probs=4.4
Q ss_pred cceeccccccc
Q psy4084 50 RQFACHMCIKV 60 (86)
Q Consensus 50 ~~~~C~~C~~~ 60 (86)
..|.|..|+..
T Consensus 14 ~~Y~C~~Cdf~ 24 (30)
T PF07649_consen 14 WFYRCSECDFD 24 (30)
T ss_dssp -EEE-TTT---
T ss_pred ceEECccCCCc
Confidence 45777777654
No 319
>KOG4602|consensus
Probab=20.04 E-value=48 Score=19.07 Aligned_cols=11 Identities=27% Similarity=0.896 Sum_probs=7.2
Q ss_pred cceeccccccc
Q psy4084 50 RQFACHMCIKV 60 (86)
Q Consensus 50 ~~~~C~~C~~~ 60 (86)
+.|.|++||-+
T Consensus 267 R~YVCPiCGAT 277 (318)
T KOG4602|consen 267 RSYVCPICGAT 277 (318)
T ss_pred hhhcCcccccc
Confidence 45777777754
Done!