Query psy3948
Match_columns 143
No_of_seqs 105 out of 2275
Neff 10.7
Searched_HMMs 46136
Date Fri Aug 16 21:27:18 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy3948.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/3948hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2462|consensus 99.9 5E-27 1.1E-31 154.6 5.5 119 4-122 127-265 (279)
2 KOG2462|consensus 99.9 8.2E-26 1.8E-30 148.9 5.5 105 29-135 132-250 (279)
3 KOG3608|consensus 99.6 2.1E-15 4.6E-20 103.1 4.0 139 2-141 202-365 (467)
4 KOG3576|consensus 99.5 1.1E-15 2.3E-20 97.4 1.1 82 44-125 117-198 (267)
5 KOG3576|consensus 99.5 6.2E-15 1.3E-19 93.9 2.7 116 5-129 115-241 (267)
6 KOG3623|consensus 99.5 3.7E-15 8E-20 109.9 0.8 80 42-121 892-971 (1007)
7 KOG3623|consensus 99.5 4.1E-15 8.8E-20 109.7 0.9 109 6-122 209-331 (1007)
8 KOG1074|consensus 99.5 1.1E-14 2.3E-19 108.8 2.4 59 72-130 605-663 (958)
9 KOG3608|consensus 99.3 2.8E-12 6E-17 88.1 5.6 124 4-128 234-380 (467)
10 KOG1074|consensus 99.2 7.1E-12 1.5E-16 94.1 4.0 60 73-132 880-939 (958)
11 PLN03086 PRLI-interacting fact 99.2 8.9E-11 1.9E-15 86.4 7.8 126 8-139 408-553 (567)
12 PHA00733 hypothetical protein 99.2 3E-11 6.4E-16 73.6 3.7 82 42-125 38-124 (128)
13 PHA02768 hypothetical protein; 99.0 1.5E-10 3.3E-15 59.1 1.8 44 72-117 5-48 (55)
14 PLN03086 PRLI-interacting fact 99.0 2.2E-09 4.8E-14 79.3 7.1 110 9-124 435-564 (567)
15 PF13465 zf-H2C2_2: Zinc-finge 98.9 8.1E-10 1.7E-14 48.5 2.5 26 87-112 1-26 (26)
16 PHA00616 hypothetical protein 98.9 1.3E-09 2.8E-14 53.1 2.0 33 100-132 1-33 (44)
17 PHA02768 hypothetical protein; 98.6 1.5E-08 3.4E-13 51.8 1.4 42 45-88 6-47 (55)
18 PHA00733 hypothetical protein 98.6 8.6E-08 1.9E-12 58.5 4.8 84 5-96 38-123 (128)
19 PF00096 zf-C2H2: Zinc finger, 98.3 8.8E-07 1.9E-11 37.5 2.4 23 101-123 1-23 (23)
20 PHA00616 hypothetical protein 98.2 6.2E-07 1.3E-11 43.8 1.5 33 72-104 1-33 (44)
21 PF13465 zf-H2C2_2: Zinc-finge 98.2 4.8E-07 1E-11 39.5 1.0 25 59-83 1-25 (26)
22 PHA00732 hypothetical protein 98.2 1.4E-06 3.1E-11 48.5 2.2 42 73-120 2-44 (79)
23 KOG3993|consensus 98.2 5.7E-07 1.2E-11 63.7 0.8 120 7-126 295-484 (500)
24 KOG3993|consensus 98.1 8E-07 1.7E-11 63.0 0.8 85 44-128 295-384 (500)
25 PF05605 zf-Di19: Drought indu 98.0 1.8E-05 3.8E-10 40.9 4.6 50 73-125 3-54 (54)
26 PF13894 zf-C2H2_4: C2H2-type 98.0 6.4E-06 1.4E-10 34.9 2.4 24 101-124 1-24 (24)
27 PF13912 zf-C2H2_6: C2H2-type 98.0 3E-06 6.4E-11 37.3 1.1 26 100-125 1-26 (27)
28 PF09237 GAGA: GAGA factor; I 97.7 5.8E-05 1.3E-09 37.7 2.9 33 96-128 20-52 (54)
29 PHA00732 hypothetical protein 97.6 4.5E-05 9.8E-10 42.5 2.4 46 44-95 1-47 (79)
30 PF13909 zf-H2C2_5: C2H2-type 97.5 0.00016 3.5E-09 30.7 2.6 24 101-125 1-24 (24)
31 smart00355 ZnF_C2H2 zinc finge 97.4 0.00013 2.7E-09 31.2 2.0 24 101-124 1-24 (26)
32 PF00096 zf-C2H2: Zinc finger, 97.4 8.9E-05 1.9E-09 31.1 1.1 20 46-65 2-21 (23)
33 PF12756 zf-C2H2_2: C2H2 type 97.3 0.00019 4.1E-09 41.6 2.6 78 46-128 1-79 (100)
34 PF05605 zf-Di19: Drought indu 97.1 0.00099 2.2E-08 34.3 3.5 48 45-95 3-52 (54)
35 PF13912 zf-C2H2_6: C2H2-type 96.9 0.00049 1.1E-08 30.0 1.3 23 45-67 2-24 (27)
36 PF12874 zf-met: Zinc-finger o 96.9 0.0006 1.3E-08 29.1 1.4 23 101-123 1-23 (25)
37 COG5189 SFP1 Putative transcri 96.9 0.00027 5.8E-09 48.9 0.4 52 70-121 347-419 (423)
38 PRK04860 hypothetical protein; 96.9 0.00076 1.7E-08 42.7 2.1 37 72-112 119-155 (160)
39 PF13894 zf-C2H2_4: C2H2-type 96.7 0.0017 3.6E-08 27.1 2.0 21 74-94 2-22 (24)
40 COG5189 SFP1 Putative transcri 96.5 0.0015 3.2E-08 45.4 1.9 19 4-22 346-366 (423)
41 PF12171 zf-C2H2_jaz: Zinc-fin 96.3 0.00066 1.4E-08 29.7 -0.7 22 101-122 2-23 (27)
42 smart00355 ZnF_C2H2 zinc finge 96.2 0.0075 1.6E-07 25.3 2.7 22 74-95 2-23 (26)
43 PF13913 zf-C2HC_2: zinc-finge 95.9 0.0078 1.7E-07 25.8 1.9 21 101-122 3-23 (25)
44 COG4049 Uncharacterized protei 95.6 0.01 2.2E-07 30.3 1.7 32 95-126 12-43 (65)
45 PF09237 GAGA: GAGA factor; I 95.4 0.019 4.2E-07 28.9 2.4 33 68-100 20-52 (54)
46 PRK04860 hypothetical protein; 95.4 0.017 3.7E-07 36.7 2.7 36 100-139 119-155 (160)
47 smart00451 ZnF_U1 U1-like zinc 95.1 0.018 3.9E-07 26.5 1.7 22 100-121 3-24 (35)
48 PF12756 zf-C2H2_2: C2H2 type 94.4 0.04 8.8E-07 31.6 2.4 24 72-95 50-73 (100)
49 COG5048 FOG: Zn-finger [Genera 92.6 0.021 4.6E-07 41.4 -1.1 62 71-132 288-355 (467)
50 COG2888 Predicted Zn-ribbon RN 91.6 0.22 4.7E-06 25.9 2.3 9 99-107 49-57 (61)
51 PF07754 DUF1610: Domain of un 91.4 0.24 5.1E-06 20.9 1.9 10 42-51 14-23 (24)
52 PF13717 zinc_ribbon_4: zinc-r 90.6 0.2 4.4E-06 23.3 1.5 11 44-54 25-35 (36)
53 TIGR00622 ssl1 transcription f 90.6 0.6 1.3E-05 27.8 3.7 87 6-95 14-104 (112)
54 PF02892 zf-BED: BED zinc fing 89.9 0.44 9.6E-06 23.1 2.5 28 97-124 13-44 (45)
55 PF13719 zinc_ribbon_5: zinc-r 88.8 0.3 6.4E-06 22.9 1.3 10 45-54 26-35 (37)
56 COG1198 PriA Primosomal protei 88.7 0.46 1E-05 37.5 2.9 10 71-80 474-483 (730)
57 PF15135 UPF0515: Uncharacteri 88.5 0.3 6.5E-06 33.1 1.6 55 4-58 109-169 (278)
58 PF09538 FYDLN_acid: Protein o 88.1 0.39 8.6E-06 28.5 1.8 28 30-57 12-39 (108)
59 smart00614 ZnF_BED BED zinc fi 87.7 0.69 1.5E-05 23.2 2.3 23 101-123 19-46 (50)
60 PRK14890 putative Zn-ribbon RN 86.2 0.84 1.8E-05 23.8 2.1 11 43-53 24-34 (59)
61 cd00350 rubredoxin_like Rubred 86.1 0.42 9E-06 21.8 0.9 9 45-53 2-10 (33)
62 KOG1146|consensus 86.1 0.31 6.8E-06 40.5 0.8 23 99-121 517-539 (1406)
63 PF10571 UPF0547: Uncharacteri 85.7 0.75 1.6E-05 19.8 1.6 8 47-54 17-24 (26)
64 smart00834 CxxC_CXXC_SSSS Puta 85.0 0.16 3.5E-06 24.2 -0.8 15 7-21 5-19 (41)
65 TIGR02098 MJ0042_CXXC MJ0042 f 85.0 0.59 1.3E-05 21.8 1.2 10 8-17 3-12 (38)
66 PF09723 Zn-ribbon_8: Zinc rib 84.9 0.13 2.9E-06 24.9 -1.1 15 8-22 6-20 (42)
67 COG5048 FOG: Zn-finger [Genera 84.5 0.32 7E-06 35.2 0.2 62 43-104 288-355 (467)
68 PF09845 DUF2072: Zn-ribbon co 83.8 0.62 1.3E-05 28.5 1.1 27 7-35 1-27 (131)
69 KOG2186|consensus 83.3 0.72 1.6E-05 31.5 1.4 38 45-84 4-41 (276)
70 KOG1146|consensus 83.1 0.86 1.9E-05 38.1 2.0 65 1-66 459-540 (1406)
71 TIGR02605 CxxC_CxxC_SSSS putat 83.0 0.21 4.6E-06 25.2 -0.9 15 7-21 5-19 (52)
72 PF12013 DUF3505: Protein of u 83.0 1.3 2.7E-05 26.2 2.3 25 101-125 81-109 (109)
73 PRK00398 rpoP DNA-directed RNA 82.6 0.87 1.9E-05 22.4 1.2 11 7-17 3-13 (46)
74 KOG2893|consensus 81.8 0.46 1E-05 32.1 0.1 21 43-63 33-53 (341)
75 KOG2231|consensus 81.8 2 4.3E-05 33.7 3.3 93 29-125 101-207 (669)
76 smart00659 RPOLCX RNA polymera 81.6 0.91 2E-05 22.2 1.1 13 44-56 19-31 (44)
77 PRK06266 transcription initiat 81.5 0.64 1.4E-05 30.2 0.6 10 45-54 137-146 (178)
78 TIGR02300 FYDLN_acid conserved 81.0 1.3 2.9E-05 26.9 1.8 28 30-57 12-39 (129)
79 PF15269 zf-C2H2_7: Zinc-finge 80.5 1.5 3.2E-05 21.5 1.5 28 101-128 21-48 (54)
80 PF04959 ARS2: Arsenite-resist 80.0 1.2 2.5E-05 29.9 1.5 30 98-127 75-104 (214)
81 COG1592 Rubrerythrin [Energy p 79.6 1 2.3E-05 28.8 1.1 24 72-108 134-157 (166)
82 smart00531 TFIIE Transcription 79.5 1.4 3.1E-05 27.6 1.7 35 44-82 99-133 (147)
83 smart00734 ZnF_Rad18 Rad18-lik 79.4 2.1 4.6E-05 18.3 1.7 19 102-121 3-21 (26)
84 PF06524 NOA36: NOA36 protein; 79.3 0.74 1.6E-05 31.5 0.4 94 29-124 127-233 (314)
85 PF08274 PhnA_Zn_Ribbon: PhnA 78.9 0.71 1.5E-05 20.6 0.2 23 30-52 5-27 (30)
86 KOG2186|consensus 78.5 1.1 2.4E-05 30.6 1.0 54 73-129 4-57 (276)
87 PF05443 ROS_MUCR: ROS/MUCR tr 78.1 1.8 3.9E-05 26.7 1.8 27 99-128 71-97 (132)
88 PF15616 TerY-C: TerY-C metal 78.0 1.3 2.9E-05 27.2 1.2 15 39-53 100-114 (131)
89 PF09986 DUF2225: Uncharacteri 77.6 1.3 2.9E-05 29.6 1.2 14 45-58 6-19 (214)
90 TIGR00686 phnA alkylphosphonat 77.5 1.5 3.3E-05 25.8 1.3 29 29-57 4-32 (109)
91 PF03604 DNA_RNApol_7kD: DNA d 77.2 1.2 2.5E-05 20.2 0.6 10 45-54 18-27 (32)
92 PRK10220 hypothetical protein; 76.9 2.2 4.8E-05 25.2 1.8 30 29-58 5-34 (111)
93 PRK09678 DNA-binding transcrip 76.2 0.9 1.9E-05 24.8 0.1 17 97-113 24-42 (72)
94 PF08790 zf-LYAR: LYAR-type C2 75.7 0.67 1.5E-05 20.3 -0.4 20 101-121 1-20 (28)
95 COG1198 PriA Primosomal protei 74.7 2.5 5.3E-05 33.7 2.2 29 66-109 456-484 (730)
96 PRK00464 nrdR transcriptional 72.1 0.82 1.8E-05 29.0 -0.8 13 73-85 29-41 (154)
97 PHA00626 hypothetical protein 71.7 2.4 5.3E-05 21.8 1.0 16 98-113 21-36 (59)
98 PF10083 DUF2321: Uncharacteri 71.6 3.1 6.6E-05 26.3 1.7 17 71-87 67-83 (158)
99 PF14353 CpXC: CpXC protein 70.5 3.3 7.2E-05 25.1 1.7 11 9-19 3-13 (128)
100 TIGR00595 priA primosomal prot 69.1 5.1 0.00011 30.5 2.7 6 74-79 255-260 (505)
101 PRK04023 DNA polymerase II lar 68.4 6 0.00013 32.7 3.0 9 45-53 639-647 (1121)
102 PF02176 zf-TRAF: TRAF-type zi 68.0 4 8.7E-05 21.0 1.5 25 87-111 25-53 (60)
103 COG3364 Zn-ribbon containing p 67.4 2.9 6.3E-05 24.4 0.9 27 7-35 2-28 (112)
104 TIGR00373 conserved hypothetic 67.3 5.9 0.00013 25.2 2.4 32 70-110 107-138 (158)
105 COG5151 SSL1 RNA polymerase II 66.9 6.7 0.00015 27.8 2.7 25 71-95 387-411 (421)
106 PF07975 C1_4: TFIIH C1-like d 65.6 1.7 3.7E-05 22.0 -0.3 24 43-66 20-43 (51)
107 PF05290 Baculo_IE-1: Baculovi 64.5 3 6.6E-05 25.6 0.6 56 43-115 79-136 (140)
108 smart00154 ZnF_AN1 AN1-like Zi 64.4 2.4 5.3E-05 20.1 0.2 14 7-20 12-25 (39)
109 PF08209 Sgf11: Sgf11 (transcr 63.5 8.2 0.00018 17.6 1.8 23 100-123 4-26 (33)
110 COG5236 Uncharacterized conser 63.4 2.6 5.6E-05 30.3 0.2 23 102-124 222-244 (493)
111 PRK03681 hypA hydrogenase nick 62.7 4.8 0.0001 24.1 1.3 6 46-51 89-94 (114)
112 PRK14873 primosome assembly pr 62.5 6.9 0.00015 31.0 2.3 10 72-81 422-431 (665)
113 PRK00420 hypothetical protein; 62.0 7.4 0.00016 23.3 1.9 27 29-55 25-51 (112)
114 KOG2593|consensus 61.3 6.9 0.00015 29.0 2.0 19 4-22 125-143 (436)
115 KOG3408|consensus 60.9 6.8 0.00015 23.7 1.6 22 100-121 57-78 (129)
116 cd00729 rubredoxin_SM Rubredox 60.0 5.4 0.00012 18.2 0.9 9 45-53 3-11 (34)
117 PF08271 TF_Zn_Ribbon: TFIIB z 59.9 1.1 2.5E-05 21.6 -1.5 10 45-54 20-29 (43)
118 PF12907 zf-met2: Zinc-binding 59.8 5.5 0.00012 19.1 0.9 27 101-127 2-31 (40)
119 PRK00432 30S ribosomal protein 59.3 8.8 0.00019 19.3 1.7 7 73-79 38-44 (50)
120 PF12773 DZR: Double zinc ribb 58.8 7.7 0.00017 19.1 1.4 6 47-52 15-20 (50)
121 PF04780 DUF629: Protein of un 58.8 9.2 0.0002 28.9 2.3 26 100-125 57-82 (466)
122 PRK00564 hypA hydrogenase nick 58.1 6.7 0.00015 23.6 1.3 10 45-54 72-81 (117)
123 COG5236 Uncharacterized conser 58.0 19 0.00042 26.1 3.7 75 46-125 222-306 (493)
124 COG4530 Uncharacterized protei 57.7 6.9 0.00015 23.2 1.3 26 30-55 12-37 (129)
125 PRK05580 primosome assembly pr 57.6 11 0.00023 30.0 2.7 6 74-79 423-428 (679)
126 KOG0978|consensus 57.5 1.6 3.4E-05 34.4 -1.8 12 74-85 680-691 (698)
127 KOG2785|consensus 56.6 13 0.00028 27.2 2.7 27 97-123 65-91 (390)
128 TIGR01206 lysW lysine biosynth 56.6 1.9 4.1E-05 22.2 -1.0 10 8-17 3-12 (54)
129 smart00440 ZnF_C2C2 C2C2 Zinc 55.6 1.2 2.7E-05 21.2 -1.7 11 100-110 28-38 (40)
130 PRK11823 DNA repair protein Ra 55.6 6.7 0.00015 29.4 1.2 32 1-38 1-32 (446)
131 KOG2907|consensus 55.4 6.5 0.00014 23.4 0.9 39 72-112 74-114 (116)
132 PF13240 zinc_ribbon_2: zinc-r 55.4 11 0.00024 15.5 1.4 6 47-52 16-21 (23)
133 PF10276 zf-CHCC: Zinc-finger 52.1 4.6 9.9E-05 19.3 -0.1 11 7-17 29-39 (40)
134 PTZ00255 60S ribosomal protein 51.6 8.1 0.00018 22.1 0.9 32 72-113 36-67 (90)
135 PRK12496 hypothetical protein; 51.1 12 0.00025 24.1 1.6 8 30-37 130-137 (164)
136 COG1773 Rubredoxin [Energy pro 50.8 8.2 0.00018 19.9 0.7 12 100-111 3-14 (55)
137 PRK03824 hypA hydrogenase nick 49.8 8.9 0.00019 23.7 0.9 15 43-57 69-83 (135)
138 PF01363 FYVE: FYVE zinc finge 49.5 8.9 0.00019 20.3 0.8 27 30-57 12-38 (69)
139 PF13248 zf-ribbon_3: zinc-rib 49.3 14 0.00031 15.5 1.3 6 47-52 19-24 (26)
140 KOG4167|consensus 49.1 6.8 0.00015 31.2 0.4 28 100-127 792-819 (907)
141 cd00924 Cyt_c_Oxidase_Vb Cytoc 49.0 11 0.00023 22.0 1.1 18 94-112 74-91 (97)
142 PLN03238 probable histone acet 49.0 19 0.00041 25.4 2.5 28 98-125 46-73 (290)
143 COG0068 HypF Hydrogenase matur 48.6 3 6.5E-05 32.9 -1.5 76 29-111 103-184 (750)
144 COG4957 Predicted transcriptio 47.8 11 0.00024 23.3 1.1 25 101-128 77-101 (148)
145 PLN02294 cytochrome c oxidase 47.3 11 0.00024 24.3 1.1 16 98-113 139-154 (174)
146 PF01428 zf-AN1: AN1-like Zinc 47.3 8.8 0.00019 18.5 0.5 15 99-113 12-26 (43)
147 PF04216 FdhE: Protein involve 47.0 4.1 8.9E-05 28.6 -0.9 69 29-112 174-250 (290)
148 KOG2785|consensus 46.9 41 0.00089 24.7 3.9 59 71-129 165-250 (390)
149 PRK03564 formate dehydrogenase 46.4 14 0.0003 26.4 1.6 14 99-112 251-264 (309)
150 PF07282 OrfB_Zn_ribbon: Putat 45.9 17 0.00037 19.2 1.6 7 73-79 47-53 (69)
151 PRK12380 hydrogenase nickel in 45.9 12 0.00025 22.4 1.0 8 45-52 71-78 (113)
152 KOG2893|consensus 45.5 6.6 0.00014 26.8 -0.1 41 47-91 13-53 (341)
153 TIGR00416 sms DNA repair prote 44.8 12 0.00026 28.2 1.1 30 3-38 3-32 (454)
154 PF13878 zf-C2H2_3: zinc-finge 44.7 31 0.00068 16.4 2.2 10 102-111 15-24 (41)
155 COG5112 UFD2 U1-like Zn-finger 44.1 16 0.00034 21.6 1.3 22 100-121 55-76 (126)
156 PF06397 Desulfoferrod_N: Desu 43.2 8.5 0.00018 18.0 0.1 12 6-17 5-16 (36)
157 PF12760 Zn_Tnp_IS1595: Transp 43.1 17 0.00038 17.6 1.2 11 98-108 35-45 (46)
158 TIGR00100 hypA hydrogenase nic 42.9 15 0.00032 22.0 1.1 11 45-55 71-81 (115)
159 cd00065 FYVE FYVE domain; Zinc 42.6 21 0.00046 17.9 1.6 11 45-55 19-29 (57)
160 PF01155 HypA: Hydrogenase exp 42.4 3.9 8.4E-05 24.4 -1.4 11 45-55 71-81 (113)
161 KOG1842|consensus 42.1 16 0.00035 27.4 1.4 24 101-124 16-39 (505)
162 KOG1280|consensus 41.9 22 0.00047 25.8 1.9 32 98-129 77-108 (381)
163 PF14369 zf-RING_3: zinc-finge 41.8 9.4 0.0002 17.6 0.1 10 9-18 23-32 (35)
164 COG4888 Uncharacterized Zn rib 41.5 4.5 9.9E-05 23.6 -1.1 13 5-17 20-32 (104)
165 PF13451 zf-trcl: Probable zin 41.4 12 0.00026 18.8 0.5 18 5-22 2-19 (49)
166 PF00301 Rubredoxin: Rubredoxi 41.4 14 0.00031 18.3 0.7 12 101-112 2-13 (47)
167 PF14446 Prok-RING_1: Prokaryo 41.4 26 0.00056 18.0 1.7 6 46-51 23-28 (54)
168 PF01286 XPA_N: XPA protein N- 41.4 12 0.00026 17.2 0.4 12 102-113 5-16 (34)
169 KOG2482|consensus 41.2 18 0.00039 26.2 1.5 23 100-122 195-217 (423)
170 KOG2231|consensus 40.9 75 0.0016 25.5 4.8 22 46-67 184-205 (669)
171 KOG2272|consensus 40.9 21 0.00047 24.6 1.7 15 8-22 164-178 (332)
172 COG1997 RPL43A Ribosomal prote 40.8 23 0.0005 20.2 1.6 28 29-56 37-65 (89)
173 smart00661 RPOL9 RNA polymeras 40.8 32 0.00069 16.9 2.1 12 44-55 20-31 (52)
174 PF10013 DUF2256: Uncharacteri 40.3 12 0.00026 18.1 0.4 16 102-117 10-25 (42)
175 COG1996 RPC10 DNA-directed RNA 40.1 16 0.00034 18.4 0.8 11 7-17 6-16 (49)
176 COG3677 Transposase and inacti 39.9 14 0.00029 22.7 0.7 17 97-113 50-66 (129)
177 COG2331 Uncharacterized protei 39.8 4.4 9.4E-05 22.3 -1.3 31 7-37 12-43 (82)
178 cd00730 rubredoxin Rubredoxin; 38.0 14 0.0003 18.6 0.4 12 101-112 2-13 (50)
179 smart00064 FYVE Protein presen 37.8 26 0.00056 18.4 1.5 11 45-55 27-37 (68)
180 PF05191 ADK_lid: Adenylate ki 36.0 18 0.00039 16.8 0.6 12 101-112 2-13 (36)
181 PF14255 Cys_rich_CPXG: Cystei 35.7 5.6 0.00012 20.3 -1.2 14 9-22 2-15 (52)
182 PF08792 A2L_zn_ribbon: A2L zi 34.6 30 0.00066 15.7 1.2 10 45-54 22-31 (33)
183 COG1066 Sms Predicted ATP-depe 34.5 23 0.00049 26.6 1.2 31 2-38 2-32 (456)
184 PLN00104 MYST -like histone ac 34.1 29 0.00063 26.2 1.7 27 98-124 196-222 (450)
185 PF14803 Nudix_N_2: Nudix N-te 33.6 25 0.00053 16.1 0.8 7 45-51 23-29 (34)
186 PTZ00064 histone acetyltransfe 33.6 34 0.00075 26.2 2.0 27 99-125 279-305 (552)
187 COG3024 Uncharacterized protei 33.5 24 0.00051 18.8 0.8 10 7-16 7-16 (65)
188 PF02748 PyrI_C: Aspartate car 33.4 15 0.00032 18.7 0.1 15 4-18 32-46 (52)
189 PRK00762 hypA hydrogenase nick 33.0 27 0.00059 21.2 1.2 10 45-55 71-80 (124)
190 COG3091 SprT Zn-dependent meta 32.4 25 0.00054 22.3 1.0 10 100-110 117-126 (156)
191 PF02591 DUF164: Putative zinc 32.2 34 0.00073 17.4 1.3 7 73-79 47-53 (56)
192 PF13453 zf-TFIIB: Transcripti 32.0 45 0.00098 15.7 1.7 20 99-118 18-37 (41)
193 KOG2807|consensus 31.8 65 0.0014 23.3 3.0 27 99-125 344-370 (378)
194 PLN03239 histone acetyltransfe 31.5 38 0.00082 24.7 1.8 25 98-122 104-128 (351)
195 COG1327 Predicted transcriptio 31.5 15 0.00033 23.2 -0.1 9 9-17 2-10 (156)
196 cd00974 DSRD Desulforedoxin (D 31.0 20 0.00044 16.1 0.3 10 7-16 4-13 (34)
197 TIGR00319 desulf_FeS4 desulfof 29.9 29 0.00063 15.5 0.8 9 45-53 8-16 (34)
198 KOG2636|consensus 29.8 40 0.00087 25.4 1.8 29 93-121 394-423 (497)
199 COG4306 Uncharacterized protei 29.5 44 0.00096 20.4 1.7 10 46-55 70-79 (160)
200 COG4391 Uncharacterized protei 29.3 24 0.00052 18.6 0.5 9 9-17 50-58 (62)
201 PF14787 zf-CCHC_5: GAG-polypr 29.2 18 0.00039 16.9 -0.0 15 8-22 3-17 (36)
202 KOG1994|consensus 29.0 33 0.00072 23.3 1.2 21 99-119 238-258 (268)
203 PF14354 Lar_restr_allev: Rest 28.8 28 0.0006 17.9 0.7 9 7-15 3-11 (61)
204 PF09788 Tmemb_55A: Transmembr 28.7 16 0.00036 25.1 -0.3 29 8-36 158-186 (256)
205 PF01215 COX5B: Cytochrome c o 28.1 30 0.00066 21.5 0.8 19 94-113 107-125 (136)
206 PF11672 DUF3268: Protein of u 27.6 28 0.00061 20.5 0.6 10 44-53 2-11 (102)
207 COG1571 Predicted DNA-binding 27.6 45 0.00097 25.0 1.7 28 30-57 353-380 (421)
208 KOG4684|consensus 27.6 28 0.00062 23.4 0.7 29 8-37 171-199 (275)
209 TIGR01562 FdhE formate dehydro 26.6 58 0.0013 23.3 2.1 14 99-112 251-264 (305)
210 COG1326 Uncharacterized archae 26.4 81 0.0018 21.0 2.5 12 99-110 29-40 (201)
211 PHA02998 RNA polymerase subuni 26.4 12 0.00025 24.4 -1.2 12 100-111 171-182 (195)
212 KOG0717|consensus 26.2 48 0.001 25.2 1.7 21 101-121 293-313 (508)
213 PF06677 Auto_anti-p27: Sjogre 25.8 49 0.0011 15.9 1.2 22 29-50 19-40 (41)
214 PF04423 Rad50_zn_hook: Rad50 25.6 72 0.0016 16.0 1.9 12 102-113 22-33 (54)
215 KOG2071|consensus 25.2 53 0.0011 25.7 1.8 28 97-124 415-442 (579)
216 KOG4118|consensus 25.0 35 0.00076 18.2 0.6 30 100-129 38-67 (74)
217 PF02318 FYVE_2: FYVE-type zin 25.0 18 0.0004 21.7 -0.5 12 97-108 91-102 (118)
218 KOG4167|consensus 24.9 14 0.0003 29.6 -1.2 25 44-68 792-816 (907)
219 PF05129 Elf1: Transcription e 24.4 33 0.00073 19.2 0.5 10 5-14 20-29 (81)
220 PF09332 Mcm10: Mcm10 replicat 24.1 13 0.00027 27.0 -1.5 17 6-22 251-267 (344)
221 KOG4173|consensus 23.6 40 0.00086 22.7 0.8 77 45-124 80-170 (253)
222 cd01121 Sms Sms (bacterial rad 23.6 36 0.00077 25.0 0.6 25 8-38 1-25 (372)
223 COG1439 Predicted nucleic acid 23.3 45 0.00098 21.8 1.0 22 29-53 141-162 (177)
224 KOG1701|consensus 23.3 15 0.00032 27.4 -1.3 12 100-111 427-438 (468)
225 COG1594 RPB9 DNA-directed RNA 23.2 21 0.00046 21.3 -0.5 12 100-111 100-111 (113)
226 COG5188 PRP9 Splicing factor 3 23.0 63 0.0014 23.7 1.7 28 93-120 367-395 (470)
227 COG1645 Uncharacterized Zn-fin 22.7 63 0.0014 20.0 1.5 25 29-54 30-54 (131)
228 PTZ00043 cytochrome c oxidase 22.3 46 0.001 22.7 0.9 16 98-113 179-194 (268)
229 COG2824 PhnA Uncharacterized Z 22.3 51 0.0011 19.6 1.0 26 30-55 6-31 (112)
230 PRK14559 putative protein seri 21.8 67 0.0014 25.7 1.8 11 47-57 44-54 (645)
231 PF06827 zf-FPG_IleRS: Zinc fi 21.8 11 0.00024 16.4 -1.4 9 9-17 3-11 (30)
232 PF03833 PolC_DP2: DNA polymer 20.7 33 0.00071 28.1 0.0 9 8-16 656-664 (900)
233 PTZ00303 phosphatidylinositol 20.7 49 0.0011 27.1 0.9 29 8-37 461-491 (1374)
234 PHA02942 putative transposase; 20.5 92 0.002 23.1 2.2 10 72-81 342-351 (383)
235 PRK12722 transcriptional activ 20.4 73 0.0016 21.0 1.5 10 29-38 136-145 (187)
236 PF01096 TFIIS_C: Transcriptio 20.3 53 0.0012 15.4 0.7 10 101-110 29-38 (39)
237 COG1675 TFA1 Transcription ini 20.0 1.2E+02 0.0025 19.9 2.4 32 69-109 110-141 (176)
No 1
>KOG2462|consensus
Probab=99.94 E-value=5e-27 Score=154.61 Aligned_cols=119 Identities=25% Similarity=0.462 Sum_probs=69.9
Q ss_pred CCccccCCcchhhhccchh---hHHHhh--------hcccCCCCCC---------CCCCcceeccCCCCccCCcchHHHh
Q psy3948 4 DHTILKCTFCNIIFNKLQD---EELIMT--------HCKSCKKPKR---------PDKSYNYACFICTYHTRKHGDMIGH 63 (143)
Q Consensus 4 ~~~~~~C~~C~~~f~~~~~---~~~~~~--------~c~~c~~~~~---------~~~~~~~~c~~c~~~~~~~~~l~~h 63 (143)
....|+|+.||+.+.+..+ |+..|- .|+.|++.|. .+..-+++|.+||+.|.....|+.|
T Consensus 127 ~~~r~~c~eCgk~ysT~snLsrHkQ~H~~~~s~ka~~C~~C~K~YvSmpALkMHirTH~l~c~C~iCGKaFSRPWLLQGH 206 (279)
T KOG2462|consen 127 KHPRYKCPECGKSYSTSSNLSRHKQTHRSLDSKKAFSCKYCGKVYVSMPALKMHIRTHTLPCECGICGKAFSRPWLLQGH 206 (279)
T ss_pred cCCceeccccccccccccccchhhcccccccccccccCCCCCceeeehHHHhhHhhccCCCcccccccccccchHHhhcc
Confidence 4567899999999866665 443332 3555555554 1223345555555555555555555
Q ss_pred hhhcCCCCCccCCCCCCCCCChHHHHHHHHHhcCCCceecccccccccchHHHHHHHHH
Q psy3948 64 MRKHTGVKPLKCSSCNYSCSTKSALSVHQKRHTGLKAHKCANVIIIAIMYHILEIMLED 122 (143)
Q Consensus 64 ~~~~~~~~~~~c~~c~~~f~~~~~l~~h~~~h~~e~~~~C~~C~~~f~~~s~l~~h~~~ 122 (143)
+++|+|++||.|+.|+++|...++|..|+++|.+.++|+|..|++.|+..|.|.+|.+.
T Consensus 207 iRTHTGEKPF~C~hC~kAFADRSNLRAHmQTHS~~K~~qC~~C~KsFsl~SyLnKH~ES 265 (279)
T KOG2462|consen 207 IRTHTGEKPFSCPHCGKAFADRSNLRAHMQTHSDVKKHQCPRCGKSFALKSYLNKHSES 265 (279)
T ss_pred cccccCCCCccCCcccchhcchHHHHHHHHhhcCCccccCcchhhHHHHHHHHHHhhhh
Confidence 55555555555555555555555555555555555555555555555555555555543
No 2
>KOG2462|consensus
Probab=99.92 E-value=8.2e-26 Score=148.91 Aligned_cols=105 Identities=20% Similarity=0.285 Sum_probs=97.4
Q ss_pred hcccCCCCCCCCC--------------CcceeccCCCCccCCcchHHHhhhhcCCCCCccCCCCCCCCCChHHHHHHHHH
Q psy3948 29 HCKSCKKPKRPDK--------------SYNYACFICTYHTRKHGDMIGHMRKHTGVKPLKCSSCNYSCSTKSALSVHQKR 94 (143)
Q Consensus 29 ~c~~c~~~~~~~~--------------~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~c~~c~~~f~~~~~l~~h~~~ 94 (143)
.|..|++.+.... .+.+.|++||+.+.....|..|+++|+ .+++|..||+.|.+.+.|+.|+|+
T Consensus 132 ~c~eCgk~ysT~snLsrHkQ~H~~~~s~ka~~C~~C~K~YvSmpALkMHirTH~--l~c~C~iCGKaFSRPWLLQGHiRT 209 (279)
T KOG2462|consen 132 KCPECGKSYSTSSNLSRHKQTHRSLDSKKAFSCKYCGKVYVSMPALKMHIRTHT--LPCECGICGKAFSRPWLLQGHIRT 209 (279)
T ss_pred eccccccccccccccchhhcccccccccccccCCCCCceeeehHHHhhHhhccC--CCcccccccccccchHHhhccccc
Confidence 6999999997433 567999999999999999999999998 588999999999999999999999
Q ss_pred hcCCCceecccccccccchHHHHHHHHHHhcCCCcccceee
Q psy3948 95 HTGLKAHKCANVIIIAIMYHILEIMLEDIQGRDHINVNIAL 135 (143)
Q Consensus 95 h~~e~~~~C~~C~~~f~~~s~l~~h~~~~~~~~~~~~~~~~ 135 (143)
|||||||.|+.|++.|.++|+|+-|+++|...+.|.|....
T Consensus 210 HTGEKPF~C~hC~kAFADRSNLRAHmQTHS~~K~~qC~~C~ 250 (279)
T KOG2462|consen 210 HTGEKPFSCPHCGKAFADRSNLRAHMQTHSDVKKHQCPRCG 250 (279)
T ss_pred ccCCCCccCCcccchhcchHHHHHHHHhhcCCccccCcchh
Confidence 99999999999999999999999999999999999999443
No 3
>KOG3608|consensus
Probab=99.57 E-value=2.1e-15 Score=103.10 Aligned_cols=139 Identities=19% Similarity=0.415 Sum_probs=104.5
Q ss_pred CCCCccccCCcchhhhccchh---hHHHhh-------hcccCCCCCCC---------CCCcceeccCCCCccCCcchHHH
Q psy3948 2 FVDHTILKCTFCNIIFNKLQD---EELIMT-------HCKSCKKPKRP---------DKSYNYACFICTYHTRKHGDMIG 62 (143)
Q Consensus 2 ~~~~~~~~C~~C~~~f~~~~~---~~~~~~-------~c~~c~~~~~~---------~~~~~~~c~~c~~~~~~~~~l~~ 62 (143)
|+++|...|+.||..|..... |.+..+ .|..|.+.|.. ..-..|+|+.|+......++|..
T Consensus 202 Hs~eKvvACp~Cg~~F~~~tkl~DH~rRqt~l~~n~fqC~~C~KrFaTeklL~~Hv~rHvn~ykCplCdmtc~~~ssL~~ 281 (467)
T KOG3608|consen 202 HSNEKVVACPHCGELFRTKTKLFDHLRRQTELNTNSFQCAQCFKRFATEKLLKSHVVRHVNCYKCPLCDMTCSSASSLTT 281 (467)
T ss_pred cCCCeEEecchHHHHhccccHHHHHHHhhhhhcCCchHHHHHHHHHhHHHHHHHHHHHhhhcccccccccCCCChHHHHH
Confidence 678899999999999966554 443322 47777777762 11234788888888888888888
Q ss_pred hhh-hcCCCCCccCCCCCCCCCChHHHHHHHHHhcCCCceeccc--ccccccchHHHHHHHHHHh-cC--CCcccceeee
Q psy3948 63 HMR-KHTGVKPLKCSSCNYSCSTKSALSVHQKRHTGLKAHKCAN--VIIIAIMYHILEIMLEDIQ-GR--DHINVNIALT 136 (143)
Q Consensus 63 h~~-~~~~~~~~~c~~c~~~f~~~~~l~~h~~~h~~e~~~~C~~--C~~~f~~~s~l~~h~~~~~-~~--~~~~~~~~~~ 136 (143)
|++ .|...+||.|..|...+.....|++|...|. +..|.|.. |...|.+.-.+.+|.+.++ +. .+|.|....+
T Consensus 282 H~r~rHs~dkpfKCd~Cd~~c~~esdL~kH~~~HS-~~~y~C~h~~C~~s~r~~~q~~~H~~evhEg~np~~Y~CH~Cdr 360 (467)
T KOG3608|consen 282 HIRYRHSKDKPFKCDECDTRCVRESDLAKHVQVHS-KTVYQCEHPDCHYSVRTYTQMRRHFLEVHEGNNPILYACHCCDR 360 (467)
T ss_pred HHHhhhccCCCccccchhhhhccHHHHHHHHHhcc-ccceecCCCCCcHHHHHHHHHHHHHHHhccCCCCCceeeecchh
Confidence 865 4666788889888888888888998888776 67788876 8888888888888877555 44 4478887666
Q ss_pred eeeee
Q psy3948 137 LQFSA 141 (143)
Q Consensus 137 ~~~~~ 141 (143)
+.+++
T Consensus 361 ~ft~G 365 (467)
T KOG3608|consen 361 FFTSG 365 (467)
T ss_pred hhccc
Confidence 66654
No 4
>KOG3576|consensus
Probab=99.55 E-value=1.1e-15 Score=97.37 Aligned_cols=82 Identities=23% Similarity=0.412 Sum_probs=52.6
Q ss_pred ceeccCCCCccCCcchHHHhhhhcCCCCCccCCCCCCCCCChHHHHHHHHHhcCCCceecccccccccchHHHHHHHHHH
Q psy3948 44 NYACFICTYHTRKHGDMIGHMRKHTGVKPLKCSSCNYSCSTKSALSVHQKRHTGLKAHKCANVIIIAIMYHILEIMLEDI 123 (143)
Q Consensus 44 ~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~c~~c~~~f~~~~~l~~h~~~h~~e~~~~C~~C~~~f~~~s~l~~h~~~~ 123 (143)
.|.|.+|++.|....-|..|+..|...+.+.|..||+.|...-.|..|.++|+|-+||+|..|++.|+.+-.|..|+++.
T Consensus 117 ~ftCrvCgK~F~lQRmlnrh~kch~~vkr~lct~cgkgfndtfdlkrh~rthtgvrpykc~~c~kaftqrcsleshl~kv 196 (267)
T KOG3576|consen 117 SFTCRVCGKKFGLQRMLNRHLKCHSDVKRHLCTFCGKGFNDTFDLKRHTRTHTGVRPYKCSLCEKAFTQRCSLESHLKKV 196 (267)
T ss_pred eeeeehhhhhhhHHHHHHHHhhhccHHHHHHHhhccCcccchhhhhhhhccccCccccchhhhhHHHHhhccHHHHHHHH
Confidence 46666666666666666666666666666666666666666666666666666666666666666666666666666655
Q ss_pred hc
Q psy3948 124 QG 125 (143)
Q Consensus 124 ~~ 125 (143)
|+
T Consensus 197 hg 198 (267)
T KOG3576|consen 197 HG 198 (267)
T ss_pred cC
Confidence 54
No 5
>KOG3576|consensus
Probab=99.52 E-value=6.2e-15 Score=93.91 Aligned_cols=116 Identities=22% Similarity=0.342 Sum_probs=91.9
Q ss_pred CccccCCcchhhhccchhhHHHhhhcccCCCCCCCCCCcceeccCCCCccCCcchHHHhhhhcCCCCCccCCCCCCCCCC
Q psy3948 5 HTILKCTFCNIIFNKLQDEELIMTHCKSCKKPKRPDKSYNYACFICTYHTRKHGDMIGHMRKHTGVKPLKCSSCNYSCST 84 (143)
Q Consensus 5 ~~~~~C~~C~~~f~~~~~~~~~~~~c~~c~~~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~c~~c~~~f~~ 84 (143)
...|.|..|++.|....-..++. .|. ..-+.+.|..||+.|.+.-.|..|.++|+|.+||.|..|+++|..
T Consensus 115 ~d~ftCrvCgK~F~lQRmlnrh~-kch--------~~vkr~lct~cgkgfndtfdlkrh~rthtgvrpykc~~c~kaftq 185 (267)
T KOG3576|consen 115 QDSFTCRVCGKKFGLQRMLNRHL-KCH--------SDVKRHLCTFCGKGFNDTFDLKRHTRTHTGVRPYKCSLCEKAFTQ 185 (267)
T ss_pred CCeeeeehhhhhhhHHHHHHHHh-hhc--------cHHHHHHHhhccCcccchhhhhhhhccccCccccchhhhhHHHHh
Confidence 45678888998885443322221 121 122446799999999999999999999999999999999999999
Q ss_pred hHHHHHHHH-Hhc----------CCCceecccccccccchHHHHHHHHHHhcCCCc
Q psy3948 85 KSALSVHQK-RHT----------GLKAHKCANVIIIAIMYHILEIMLEDIQGRDHI 129 (143)
Q Consensus 85 ~~~l~~h~~-~h~----------~e~~~~C~~C~~~f~~~s~l~~h~~~~~~~~~~ 129 (143)
.-+|..|.+ .|. .++-|.|..||.+-.....+..|++.|+..-++
T Consensus 186 rcsleshl~kvhgv~~~yaykerr~kl~vcedcg~t~~~~e~~~~h~~~~hp~Spa 241 (267)
T KOG3576|consen 186 RCSLESHLKKVHGVQHQYAYKERRAKLYVCEDCGYTSERPEVYYLHLKLHHPFSPA 241 (267)
T ss_pred hccHHHHHHHHcCchHHHHHHHhhhheeeecccCCCCCChhHHHHHHHhcCCCCHH
Confidence 999999986 342 246799999999999999999999999876553
No 6
>KOG3623|consensus
Probab=99.50 E-value=3.7e-15 Score=109.90 Aligned_cols=80 Identities=23% Similarity=0.421 Sum_probs=76.5
Q ss_pred CcceeccCCCCccCCcchHHHhhhhcCCCCCccCCCCCCCCCChHHHHHHHHHhcCCCceecccccccccchHHHHHHHH
Q psy3948 42 SYNYACFICTYHTRKHGDMIGHMRKHTGVKPLKCSSCNYSCSTKSALSVHQKRHTGLKAHKCANVIIIAIMYHILEIMLE 121 (143)
Q Consensus 42 ~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~c~~c~~~f~~~~~l~~h~~~h~~e~~~~C~~C~~~f~~~s~l~~h~~ 121 (143)
+-.|.|..|+++|...++|.+|...|+|.+||.|..|.++|..+-.|..|.|.|.|||||+|+.|++.|+.+..+..|+.
T Consensus 892 ~gmyaCDqCDK~FqKqSSLaRHKYEHsGqRPyqC~iCkKAFKHKHHLtEHkRLHSGEKPfQCdKClKRFSHSGSYSQHMN 971 (1007)
T KOG3623|consen 892 DGMYACDQCDKAFQKQSSLARHKYEHSGQRPYQCIICKKAFKHKHHLTEHKRLHSGEKPFQCDKCLKRFSHSGSYSQHMN 971 (1007)
T ss_pred cccchHHHHHHHHHhhHHHHHhhhhhcCCCCcccchhhHhhhhhhhhhhhhhhccCCCcchhhhhhhhcccccchHhhhc
Confidence 34699999999999999999999999999999999999999999999999999999999999999999999999999964
No 7
>KOG3623|consensus
Probab=99.50 E-value=4.1e-15 Score=109.69 Aligned_cols=109 Identities=22% Similarity=0.471 Sum_probs=88.2
Q ss_pred ccccCCcchhhhccchhhHHHhhhcccCCCCCCCCC-CcceeccCCCCccCCcchHHHhhhhcCC-------------CC
Q psy3948 6 TILKCTFCNIIFNKLQDEELIMTHCKSCKKPKRPDK-SYNYACFICTYHTRKHGDMIGHMRKHTG-------------VK 71 (143)
Q Consensus 6 ~~~~C~~C~~~f~~~~~~~~~~~~c~~c~~~~~~~~-~~~~~c~~c~~~~~~~~~l~~h~~~~~~-------------~~ 71 (143)
....|++|++++.++...+.+.. +++.+ +..|.|..|..+|.+...|..|+..|.. .+
T Consensus 209 qlltcpycdrgykrltslkeHik--------yrhekne~nfsC~lCsytFAyRtQLErhm~~hkpg~dqa~sltqsa~lR 280 (1007)
T KOG3623|consen 209 QLLTCPYCDRGYKRLTSLKEHIK--------YRHEKNEPNFSCMLCSYTFAYRTQLERHMQLHKPGGDQAISLTQSALLR 280 (1007)
T ss_pred hhhcchhHHHHHHHHHHHHHHHH--------HHHhhCCCCCcchhhhhhhhhHHHHHHHHHhhcCCCcccccccchhhhc
Confidence 35689999999876665332211 11112 2347899999999999999999887653 34
Q ss_pred CccCCCCCCCCCChHHHHHHHHHhcCCCceecccccccccchHHHHHHHHH
Q psy3948 72 PLKCSSCNYSCSTKSALSVHQKRHTGLKAHKCANVIIIAIMYHILEIMLED 122 (143)
Q Consensus 72 ~~~c~~c~~~f~~~~~l~~h~~~h~~e~~~~C~~C~~~f~~~s~l~~h~~~ 122 (143)
.|.|..|+++|..+-.|..|+|+|.|||||.|+.|++.|+.+..+..|+..
T Consensus 281 KFKCtECgKAFKfKHHLKEHlRIHSGEKPfeCpnCkKRFSHSGSySSHmSS 331 (1007)
T KOG3623|consen 281 KFKCTECGKAFKFKHHLKEHLRIHSGEKPFECPNCKKRFSHSGSYSSHMSS 331 (1007)
T ss_pred cccccccchhhhhHHHHHhhheeecCCCCcCCcccccccccCCcccccccc
Confidence 599999999999999999999999999999999999999999999999764
No 8
>KOG1074|consensus
Probab=99.49 E-value=1.1e-14 Score=108.77 Aligned_cols=59 Identities=24% Similarity=0.279 Sum_probs=51.4
Q ss_pred CccCCCCCCCCCChHHHHHHHHHhcCCCceecccccccccchHHHHHHHHHHhcCCCcc
Q psy3948 72 PLKCSSCNYSCSTKSALSVHQKRHTGLKAHKCANVIIIAIMYHILEIMLEDIQGRDHIN 130 (143)
Q Consensus 72 ~~~c~~c~~~f~~~~~l~~h~~~h~~e~~~~C~~C~~~f~~~s~l~~h~~~~~~~~~~~ 130 (143)
|-.|..|.+.+.=...|+-|.++|+|||||+|..||+.|+++.+|+.|+-+|....+++
T Consensus 605 PNqCiiC~rVlSC~saLqmHyrtHtGERPFkCKiCgRAFtTkGNLkaH~~vHka~p~~R 663 (958)
T KOG1074|consen 605 PNQCIICLRVLSCPSALQMHYRTHTGERPFKCKICGRAFTTKGNLKAHMSVHKAKPPAR 663 (958)
T ss_pred ccceeeeeecccchhhhhhhhhcccCcCccccccccchhccccchhhcccccccCcccc
Confidence 45677888888888999999999999999999999999999999999999888776654
No 9
>KOG3608|consensus
Probab=99.33 E-value=2.8e-12 Score=88.09 Aligned_cols=124 Identities=19% Similarity=0.315 Sum_probs=101.5
Q ss_pred CCccccCCcchhhhccchh---hHH-Hhh--hcccCCCCCC------------CCCCcceeccCCCCccCCcchHHHhhh
Q psy3948 4 DHTILKCTFCNIIFNKLQD---EEL-IMT--HCKSCKKPKR------------PDKSYNYACFICTYHTRKHGDMIGHMR 65 (143)
Q Consensus 4 ~~~~~~C~~C~~~f~~~~~---~~~-~~~--~c~~c~~~~~------------~~~~~~~~c~~c~~~~~~~~~l~~h~~ 65 (143)
...+|.|..|-+.|.++.- |++ +.. .|+.|..+-+ +.+.++|+|..|+..+...+.|..|..
T Consensus 234 ~~n~fqC~~C~KrFaTeklL~~Hv~rHvn~ykCplCdmtc~~~ssL~~H~r~rHs~dkpfKCd~Cd~~c~~esdL~kH~~ 313 (467)
T KOG3608|consen 234 NTNSFQCAQCFKRFATEKLLKSHVVRHVNCYKCPLCDMTCSSASSLTTHIRYRHSKDKPFKCDECDTRCVRESDLAKHVQ 313 (467)
T ss_pred cCCchHHHHHHHHHhHHHHHHHHHHHhhhcccccccccCCCChHHHHHHHHhhhccCCCccccchhhhhccHHHHHHHHH
Confidence 4568999999999977655 333 332 6888887654 677899999999999999999999999
Q ss_pred hcCCCCCccCCC--CCCCCCChHHHHHHHHH-hcC--CCceecccccccccchHHHHHHHHHHhcCCC
Q psy3948 66 KHTGVKPLKCSS--CNYSCSTKSALSVHQKR-HTG--LKAHKCANVIIIAIMYHILEIMLEDIQGRDH 128 (143)
Q Consensus 66 ~~~~~~~~~c~~--c~~~f~~~~~l~~h~~~-h~~--e~~~~C~~C~~~f~~~s~l~~h~~~~~~~~~ 128 (143)
+|. ...|.|.. |..++.+...+..|.+. |.| +.+|.|..|++.|++-.+|..|+...|+=+.
T Consensus 314 ~HS-~~~y~C~h~~C~~s~r~~~q~~~H~~evhEg~np~~Y~CH~Cdr~ft~G~~L~~HL~kkH~f~~ 380 (467)
T KOG3608|consen 314 VHS-KTVYQCEHPDCHYSVRTYTQMRRHFLEVHEGNNPILYACHCCDRFFTSGKSLSAHLMKKHGFRL 380 (467)
T ss_pred hcc-ccceecCCCCCcHHHHHHHHHHHHHHHhccCCCCCceeeecchhhhccchhHHHHHHHhhcccC
Confidence 888 55688887 98899999999999874 445 4569999999999999999999887775443
No 10
>KOG1074|consensus
Probab=99.23 E-value=7.1e-12 Score=94.05 Aligned_cols=60 Identities=20% Similarity=0.224 Sum_probs=55.7
Q ss_pred ccCCCCCCCCCChHHHHHHHHHhcCCCceecccccccccchHHHHHHHHHHhcCCCcccc
Q psy3948 73 LKCSSCNYSCSTKSALSVHQKRHTGLKAHKCANVIIIAIMYHILEIMLEDIQGRDHINVN 132 (143)
Q Consensus 73 ~~c~~c~~~f~~~~~l~~h~~~h~~e~~~~C~~C~~~f~~~s~l~~h~~~~~~~~~~~~~ 132 (143)
..|.+|++.|.....|+.|+++|+++|||.|..|++.|+.+.+|+.|+.+|....+....
T Consensus 880 h~C~vCgk~FsSSsALqiH~rTHtg~KPF~C~fC~~aFttrgnLKvHMgtH~w~q~~srr 939 (958)
T KOG1074|consen 880 HVCNVCGKQFSSSAALEIHMRTHTGPKPFFCHFCEEAFTTRGNLKVHMGTHMWVQPPSRR 939 (958)
T ss_pred hhhccchhcccchHHHHHhhhcCCCCCCccchhhhhhhhhhhhhhhhhccccccCCCccC
Confidence 678999999999999999999999999999999999999999999999999977766544
No 11
>PLN03086 PRLI-interacting factor K; Provisional
Probab=99.19 E-value=8.9e-11 Score=86.43 Aligned_cols=126 Identities=17% Similarity=0.293 Sum_probs=93.9
Q ss_pred ccCCcchhhhccchh--hHHHhh----hcc--cCCCCCC-CCCCcceeccCCCCccCCcchHHHhhhhcCCCCCccCCCC
Q psy3948 8 LKCTFCNIIFNKLQD--EELIMT----HCK--SCKKPKR-PDKSYNYACFICTYHTRKHGDMIGHMRKHTGVKPLKCSSC 78 (143)
Q Consensus 8 ~~C~~C~~~f~~~~~--~~~~~~----~c~--~c~~~~~-~~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~c~~c 78 (143)
-.|+.|++......- |...-. .|+ .|+..|. ...+..+.|+.|+..|. ...+..|...++ .++.|+ |
T Consensus 408 V~C~NC~~~i~l~~l~lHe~~C~r~~V~Cp~~~Cg~v~~r~el~~H~~C~~Cgk~f~-~s~LekH~~~~H--kpv~Cp-C 483 (567)
T PLN03086 408 VECRNCKHYIPSRSIALHEAYCSRHNVVCPHDGCGIVLRVEEAKNHVHCEKCGQAFQ-QGEMEKHMKVFH--EPLQCP-C 483 (567)
T ss_pred EECCCCCCccchhHHHHHHhhCCCcceeCCcccccceeeccccccCccCCCCCCccc-hHHHHHHHHhcC--CCccCC-C
Confidence 469999886433222 322211 476 4888875 34456688999999996 567899988874 789999 9
Q ss_pred CCCCCChHHHHHHHHHhcCCCceeccccccccc----------chHHHHHHHHHHhcCCCcccc-eeeeeee
Q psy3948 79 NYSCSTKSALSVHQKRHTGLKAHKCANVIIIAI----------MYHILEIMLEDIQGRDHINVN-IALTLQF 139 (143)
Q Consensus 79 ~~~f~~~~~l~~h~~~h~~e~~~~C~~C~~~f~----------~~s~l~~h~~~~~~~~~~~~~-~~~~~~~ 139 (143)
+..+ ....|..|+.+|..++++.|..|++.|. ..+.|..|... .+.+++.|. +...+..
T Consensus 484 g~~~-~R~~L~~H~~thCp~Kpi~C~fC~~~v~~g~~~~d~~d~~s~Lt~HE~~-CG~rt~~C~~Cgk~Vrl 553 (567)
T PLN03086 484 GVVL-EKEQMVQHQASTCPLRLITCRFCGDMVQAGGSAMDVRDRLRGMSEHESI-CGSRTAPCDSCGRSVML 553 (567)
T ss_pred CCCc-chhHHHhhhhccCCCCceeCCCCCCccccCccccchhhhhhhHHHHHHh-cCCcceEccccCCeeee
Confidence 9654 6689999999999999999999999985 24689999887 489999998 4444443
No 12
>PHA00733 hypothetical protein
Probab=99.17 E-value=3e-11 Score=73.57 Aligned_cols=82 Identities=10% Similarity=0.001 Sum_probs=65.1
Q ss_pred CcceeccCCCCccCCcchHHHh--h---hhcCCCCCccCCCCCCCCCChHHHHHHHHHhcCCCceecccccccccchHHH
Q psy3948 42 SYNYACFICTYHTRKHGDMIGH--M---RKHTGVKPLKCSSCNYSCSTKSALSVHQKRHTGLKAHKCANVIIIAIMYHIL 116 (143)
Q Consensus 42 ~~~~~c~~c~~~~~~~~~l~~h--~---~~~~~~~~~~c~~c~~~f~~~~~l~~h~~~h~~e~~~~C~~C~~~f~~~s~l 116 (143)
.+.+.|.+|...+.+...|..+ + ..+.+.+||.|..|++.|.....|..|++.+ +.+|.|..|++.|...+.|
T Consensus 38 ~~~~~~~~~~~~~~~~~~l~~~~~l~~~~~~~~~kPy~C~~Cgk~Fss~s~L~~H~r~h--~~~~~C~~CgK~F~~~~sL 115 (128)
T PHA00733 38 QKRLIRAVVKTLIYNPQLLDESSYLYKLLTSKAVSPYVCPLCLMPFSSSVSLKQHIRYT--EHSKVCPVCGKEFRNTDST 115 (128)
T ss_pred hhhHHHHHHhhhccChhhhcchHHHHhhcccCCCCCccCCCCCCcCCCHHHHHHHHhcC--CcCccCCCCCCccCCHHHH
Confidence 3556778887777666555433 1 1234478999999999999999999999876 4579999999999999999
Q ss_pred HHHHHHHhc
Q psy3948 117 EIMLEDIQG 125 (143)
Q Consensus 117 ~~h~~~~~~ 125 (143)
..|+...|+
T Consensus 116 ~~H~~~~h~ 124 (128)
T PHA00733 116 LDHVCKKHN 124 (128)
T ss_pred HHHHHHhcC
Confidence 999988774
No 13
>PHA02768 hypothetical protein; Provisional
Probab=99.01 E-value=1.5e-10 Score=59.15 Aligned_cols=44 Identities=16% Similarity=0.256 Sum_probs=38.5
Q ss_pred CccCCCCCCCCCChHHHHHHHHHhcCCCceecccccccccchHHHH
Q psy3948 72 PLKCSSCNYSCSTKSALSVHQKRHTGLKAHKCANVIIIAIMYHILE 117 (143)
Q Consensus 72 ~~~c~~c~~~f~~~~~l~~h~~~h~~e~~~~C~~C~~~f~~~s~l~ 117 (143)
.|.|+.|++.|...++|..|+++|+ ++|+|..|++.|...+.|.
T Consensus 5 ~y~C~~CGK~Fs~~~~L~~H~r~H~--k~~kc~~C~k~f~~~s~l~ 48 (55)
T PHA02768 5 GYECPICGEIYIKRKSMITHLRKHN--TNLKLSNCKRISLRTGEYI 48 (55)
T ss_pred ccCcchhCCeeccHHHHHHHHHhcC--CcccCCcccceecccceeE
Confidence 4789999999999999999999988 6899999999998877765
No 14
>PLN03086 PRLI-interacting factor K; Provisional
Probab=98.97 E-value=2.2e-09 Score=79.27 Aligned_cols=110 Identities=15% Similarity=0.336 Sum_probs=78.7
Q ss_pred cCCc--chhhhccchhhHHHhhhcccCCCCCCC--------CCCcceeccCCCCccCCcchHHHhhhhcCCCCCccCCCC
Q psy3948 9 KCTF--CNIIFNKLQDEELIMTHCKSCKKPKRP--------DKSYNYACFICTYHTRKHGDMIGHMRKHTGVKPLKCSSC 78 (143)
Q Consensus 9 ~C~~--C~~~f~~~~~~~~~~~~c~~c~~~~~~--------~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~c~~c 78 (143)
.|+. |+.+|....- ..|..|+.|++.|.. .-..++.|+ ||..+ ....|..|+..|...+++.|..|
T Consensus 435 ~Cp~~~Cg~v~~r~el--~~H~~C~~Cgk~f~~s~LekH~~~~Hkpv~Cp-Cg~~~-~R~~L~~H~~thCp~Kpi~C~fC 510 (567)
T PLN03086 435 VCPHDGCGIVLRVEEA--KNHVHCEKCGQAFQQGEMEKHMKVFHEPLQCP-CGVVL-EKEQMVQHQASTCPLRLITCRFC 510 (567)
T ss_pred eCCcccccceeecccc--ccCccCCCCCCccchHHHHHHHHhcCCCccCC-CCCCc-chhHHHhhhhccCCCCceeCCCC
Confidence 4653 7776632221 111257777776651 012668899 99765 55789999999999999999999
Q ss_pred CCCCCC----------hHHHHHHHHHhcCCCceecccccccccchHHHHHHHHHHh
Q psy3948 79 NYSCST----------KSALSVHQKRHTGLKAHKCANVIIIAIMYHILEIMLEDIQ 124 (143)
Q Consensus 79 ~~~f~~----------~~~l~~h~~~h~~e~~~~C~~C~~~f~~~s~l~~h~~~~~ 124 (143)
+..+.. ...|..|.... |.+++.|..||+.+..+ +|..|+...|
T Consensus 511 ~~~v~~g~~~~d~~d~~s~Lt~HE~~C-G~rt~~C~~Cgk~Vrlr-dm~~H~~~~h 564 (567)
T PLN03086 511 GDMVQAGGSAMDVRDRLRGMSEHESIC-GSRTAPCDSCGRSVMLK-EMDIHQIAVH 564 (567)
T ss_pred CCccccCccccchhhhhhhHHHHHHhc-CCcceEccccCCeeeeh-hHHHHHHHhh
Confidence 987742 34788888775 89999999999988855 6888876554
No 15
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=98.94 E-value=8.1e-10 Score=48.50 Aligned_cols=26 Identities=31% Similarity=0.277 Sum_probs=23.4
Q ss_pred HHHHHHHHhcCCCceecccccccccc
Q psy3948 87 ALSVHQKRHTGLKAHKCANVIIIAIM 112 (143)
Q Consensus 87 ~l~~h~~~h~~e~~~~C~~C~~~f~~ 112 (143)
+|..|+++|++++||.|+.|++.|.+
T Consensus 1 ~l~~H~~~H~~~k~~~C~~C~k~F~~ 26 (26)
T PF13465_consen 1 NLRRHMRTHTGEKPYKCPYCGKSFSN 26 (26)
T ss_dssp HHHHHHHHHSSSSSEEESSSSEEESS
T ss_pred CHHHHhhhcCCCCCCCCCCCcCeeCc
Confidence 47889999999999999999999863
No 16
>PHA00616 hypothetical protein
Probab=98.87 E-value=1.3e-09 Score=53.11 Aligned_cols=33 Identities=9% Similarity=0.045 Sum_probs=30.9
Q ss_pred ceecccccccccchHHHHHHHHHHhcCCCcccc
Q psy3948 100 AHKCANVIIIAIMYHILEIMLEDIQGRDHINVN 132 (143)
Q Consensus 100 ~~~C~~C~~~f~~~s~l~~h~~~~~~~~~~~~~ 132 (143)
||+|+.||++|...++|.+|+++||+++++.+.
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~~hg~~~~~~~ 33 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLSVHKQNKLTLE 33 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHHhcCCCcccee
Confidence 689999999999999999999999999998776
No 17
>PHA02768 hypothetical protein; Provisional
Probab=98.62 E-value=1.5e-08 Score=51.79 Aligned_cols=42 Identities=36% Similarity=0.551 Sum_probs=36.7
Q ss_pred eeccCCCCccCCcchHHHhhhhcCCCCCccCCCCCCCCCChHHH
Q psy3948 45 YACFICTYHTRKHGDMIGHMRKHTGVKPLKCSSCNYSCSTKSAL 88 (143)
Q Consensus 45 ~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~c~~c~~~f~~~~~l 88 (143)
|+|+.||+.|...+.|..|++.|+ +++.|..|++.|...+.|
T Consensus 6 y~C~~CGK~Fs~~~~L~~H~r~H~--k~~kc~~C~k~f~~~s~l 47 (55)
T PHA02768 6 YECPICGEIYIKRKSMITHLRKHN--TNLKLSNCKRISLRTGEY 47 (55)
T ss_pred cCcchhCCeeccHHHHHHHHHhcC--CcccCCcccceeccccee
Confidence 689999999999999999999998 688999999988866544
No 18
>PHA00733 hypothetical protein
Probab=98.61 E-value=8.6e-08 Score=58.46 Aligned_cols=84 Identities=13% Similarity=0.156 Sum_probs=59.4
Q ss_pred CccccCCcchhhhccchhhHHH--hhhcccCCCCCCCCCCcceeccCCCCccCCcchHHHhhhhcCCCCCccCCCCCCCC
Q psy3948 5 HTILKCTFCNIIFNKLQDEELI--MTHCKSCKKPKRPDKSYNYACFICTYHTRKHGDMIGHMRKHTGVKPLKCSSCNYSC 82 (143)
Q Consensus 5 ~~~~~C~~C~~~f~~~~~~~~~--~~~c~~c~~~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~c~~c~~~f 82 (143)
.+.++|..|+..|......... .. +--...+..+|.|+.||+.|.....|..|++.+ ..++.|..|++.|
T Consensus 38 ~~~~~~~~~~~~~~~~~~l~~~~~l~------~~~~~~~~kPy~C~~Cgk~Fss~s~L~~H~r~h--~~~~~C~~CgK~F 109 (128)
T PHA00733 38 QKRLIRAVVKTLIYNPQLLDESSYLY------KLLTSKAVSPYVCPLCLMPFSSSVSLKQHIRYT--EHSKVCPVCGKEF 109 (128)
T ss_pred hhhHHHHHHhhhccChhhhcchHHHH------hhcccCCCCCccCCCCCCcCCCHHHHHHHHhcC--CcCccCCCCCCcc
Confidence 4567777777766443321000 00 000134467899999999999999999998866 3578999999999
Q ss_pred CChHHHHHHHHHhc
Q psy3948 83 STKSALSVHQKRHT 96 (143)
Q Consensus 83 ~~~~~l~~h~~~h~ 96 (143)
.....|..|+....
T Consensus 110 ~~~~sL~~H~~~~h 123 (128)
T PHA00733 110 RNTDSTLDHVCKKH 123 (128)
T ss_pred CCHHHHHHHHHHhc
Confidence 99999999987543
No 19
>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=98.28 E-value=8.8e-07 Score=37.49 Aligned_cols=23 Identities=13% Similarity=-0.096 Sum_probs=20.9
Q ss_pred eecccccccccchHHHHHHHHHH
Q psy3948 101 HKCANVIIIAIMYHILEIMLEDI 123 (143)
Q Consensus 101 ~~C~~C~~~f~~~s~l~~h~~~~ 123 (143)
|.|+.|++.|.+.+.|..|++.|
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 68999999999999999999874
No 20
>PHA00616 hypothetical protein
Probab=98.23 E-value=6.2e-07 Score=43.77 Aligned_cols=33 Identities=12% Similarity=0.094 Sum_probs=22.8
Q ss_pred CccCCCCCCCCCChHHHHHHHHHhcCCCceecc
Q psy3948 72 PLKCSSCNYSCSTKSALSVHQKRHTGLKAHKCA 104 (143)
Q Consensus 72 ~~~c~~c~~~f~~~~~l~~h~~~h~~e~~~~C~ 104 (143)
||.|+.||+.|.....+..|++.|+|++++.|+
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~~hg~~~~~~~ 33 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLSVHKQNKLTLE 33 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHHhcCCCcccee
Confidence 456777777777777777777777777766654
No 21
>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=98.22 E-value=4.8e-07 Score=39.54 Aligned_cols=25 Identities=52% Similarity=0.897 Sum_probs=22.2
Q ss_pred hHHHhhhhcCCCCCccCCCCCCCCC
Q psy3948 59 DMIGHMRKHTGVKPLKCSSCNYSCS 83 (143)
Q Consensus 59 ~l~~h~~~~~~~~~~~c~~c~~~f~ 83 (143)
+|..|++.|++++||.|+.|++.|.
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 3778999999999999999998875
No 22
>PHA00732 hypothetical protein
Probab=98.16 E-value=1.4e-06 Score=48.53 Aligned_cols=42 Identities=29% Similarity=0.426 Sum_probs=22.2
Q ss_pred ccCCCCCCCCCChHHHHHHHH-HhcCCCceecccccccccchHHHHHHH
Q psy3948 73 LKCSSCNYSCSTKSALSVHQK-RHTGLKAHKCANVIIIAIMYHILEIML 120 (143)
Q Consensus 73 ~~c~~c~~~f~~~~~l~~h~~-~h~~e~~~~C~~C~~~f~~~s~l~~h~ 120 (143)
|.|..|++.|.+...|..|++ .|. ++.|+.|++.|. .|..|.
T Consensus 2 y~C~~Cgk~F~s~s~Lk~H~r~~H~---~~~C~~CgKsF~---~l~~H~ 44 (79)
T PHA00732 2 FKCPICGFTTVTLFALKQHARRNHT---LTKCPVCNKSYR---RLNQHF 44 (79)
T ss_pred ccCCCCCCccCCHHHHHHHhhcccC---CCccCCCCCEeC---Chhhhh
Confidence 455555555555555555554 233 235666666555 244444
No 23
>KOG3993|consensus
Probab=98.16 E-value=5.7e-07 Score=63.72 Aligned_cols=120 Identities=11% Similarity=0.074 Sum_probs=71.8
Q ss_pred cccCCcchhhhccchh---hHHHhhhcccCC-------C--------------CCCCCCCcceeccCCCCccCCcchHHH
Q psy3948 7 ILKCTFCNIIFNKLQD---EELIMTHCKSCK-------K--------------PKRPDKSYNYACFICTYHTRKHGDMIG 62 (143)
Q Consensus 7 ~~~C~~C~~~f~~~~~---~~~~~~~c~~c~-------~--------------~~~~~~~~~~~c~~c~~~~~~~~~l~~ 62 (143)
-|.|++|+|+|.--.+ |.|+|-.=..-. + +-....+..|.|.+|++.|.....|..
T Consensus 295 EYrCPEC~KVFsCPANLASHRRWHKPR~eaa~a~~~P~k~~~~~rae~~ea~rsg~dss~gi~~C~~C~KkFrRqAYLrK 374 (500)
T KOG3993|consen 295 EYRCPECDKVFSCPANLASHRRWHKPRPEAAKAGSPPPKQAVETRAEVQEAERSGDDSSSGIFSCHTCGKKFRRQAYLRK 374 (500)
T ss_pred eecCCcccccccCchhhhhhhcccCCchhhhhcCCCChhhhhhhhhhhhhccccCCcccCceeecHHhhhhhHHHHHHHH
Confidence 4789999999966555 766654000000 0 000122347999999999999999999
Q ss_pred hhhhcCCCCC----------------------------------------------ccCCCCCCCCCChHHHHHHHHHhc
Q psy3948 63 HMRKHTGVKP----------------------------------------------LKCSSCNYSCSTKSALSVHQKRHT 96 (143)
Q Consensus 63 h~~~~~~~~~----------------------------------------------~~c~~c~~~f~~~~~l~~h~~~h~ 96 (143)
|+.+|..... ..++.++..+.++..-..+.+...
T Consensus 375 Hqlthq~~~~~k~~a~~f~~s~~~~l~~~~~~~a~h~~a~~~~g~~vl~~a~sael~~pp~~~~ppsss~~sgg~~rlg~ 454 (500)
T KOG3993|consen 375 HQLTHQRAPLAKEKAPKFLLSRVIPLMHFNQAVATHSSASDSHGDEVLYVAGSAELELPPYDGSPPSSSGSSGGYGRLGI 454 (500)
T ss_pred hHHhhhccccchhcccCcchhhcccccccccccccccccccccccceeeeeccccccCCCCCCCCcccCCCCCccccccc
Confidence 9765543100 011112222222222222222222
Q ss_pred CCCceecccccccccchHHHHHHHHHHhcC
Q psy3948 97 GLKAHKCANVIIIAIMYHILEIMLEDIQGR 126 (143)
Q Consensus 97 ~e~~~~C~~C~~~f~~~s~l~~h~~~~~~~ 126 (143)
.+..|.|..|...|.++.+|.+|+...|-.
T Consensus 455 ~~q~f~~ky~~atfyss~~ltrhin~~Hps 484 (500)
T KOG3993|consen 455 AEQGFTCKYCPATFYSSPGLTRHINKCHPS 484 (500)
T ss_pred hhhccccccchHhhhcCcchHhHhhhcChH
Confidence 234588999999999999999999887754
No 24
>KOG3993|consensus
Probab=98.11 E-value=8e-07 Score=63.02 Aligned_cols=85 Identities=12% Similarity=0.005 Sum_probs=52.4
Q ss_pred ceeccCCCCccCCcchHHHhhhhcCCCCCccCCC--CCCCCCChHHHHHH-HHHh--cCCCceecccccccccchHHHHH
Q psy3948 44 NYACFICTYHTRKHGDMIGHMRKHTGVKPLKCSS--CNYSCSTKSALSVH-QKRH--TGLKAHKCANVIIIAIMYHILEI 118 (143)
Q Consensus 44 ~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~c~~--c~~~f~~~~~l~~h-~~~h--~~e~~~~C~~C~~~f~~~s~l~~ 118 (143)
-|+|++|++.|.-..+|..|+++|.-...-.-.. -.+.-...-.+.+. .+.. ..+-.|.|..|++.|.+...|++
T Consensus 295 EYrCPEC~KVFsCPANLASHRRWHKPR~eaa~a~~~P~k~~~~~rae~~ea~rsg~dss~gi~~C~~C~KkFrRqAYLrK 374 (500)
T KOG3993|consen 295 EYRCPECDKVFSCPANLASHRRWHKPRPEAAKAGSPPPKQAVETRAEVQEAERSGDDSSSGIFSCHTCGKKFRRQAYLRK 374 (500)
T ss_pred eecCCcccccccCchhhhhhhcccCCchhhhhcCCCChhhhhhhhhhhhhccccCCcccCceeecHHhhhhhHHHHHHHH
Confidence 3889999999999999999988886532211000 00000000000000 0100 12347999999999999999999
Q ss_pred HHHHHhcCCC
Q psy3948 119 MLEDIQGRDH 128 (143)
Q Consensus 119 h~~~~~~~~~ 128 (143)
|+..|+...-
T Consensus 375 Hqlthq~~~~ 384 (500)
T KOG3993|consen 375 HQLTHQRAPL 384 (500)
T ss_pred hHHhhhcccc
Confidence 9999885543
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=98.02 E-value=1.8e-05 Score=40.94 Aligned_cols=50 Identities=20% Similarity=0.224 Sum_probs=37.2
Q ss_pred ccCCCCCCCCCChHHHHHHHH-HhcCC-CceecccccccccchHHHHHHHHHHhc
Q psy3948 73 LKCSSCNYSCSTKSALSVHQK-RHTGL-KAHKCANVIIIAIMYHILEIMLEDIQG 125 (143)
Q Consensus 73 ~~c~~c~~~f~~~~~l~~h~~-~h~~e-~~~~C~~C~~~f~~~s~l~~h~~~~~~ 125 (143)
|.|+.|++ ..+...|..|.. .|..+ +.+.|+.|...+. .+|..|+...|+
T Consensus 3 f~CP~C~~-~~~~~~L~~H~~~~H~~~~~~v~CPiC~~~~~--~~l~~Hl~~~H~ 54 (54)
T PF05605_consen 3 FTCPYCGK-GFSESSLVEHCEDEHRSESKNVVCPICSSRVT--DNLIRHLNSQHR 54 (54)
T ss_pred cCCCCCCC-ccCHHHHHHHHHhHCcCCCCCccCCCchhhhh--hHHHHHHHHhcC
Confidence 67888888 566778888865 45443 4688999998654 489999887763
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=98.01 E-value=6.4e-06 Score=34.92 Aligned_cols=24 Identities=8% Similarity=-0.076 Sum_probs=19.5
Q ss_pred eecccccccccchHHHHHHHHHHh
Q psy3948 101 HKCANVIIIAIMYHILEIMLEDIQ 124 (143)
Q Consensus 101 ~~C~~C~~~f~~~s~l~~h~~~~~ 124 (143)
|.|+.|++.|.+...|..|++.++
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 689999999999999999998775
No 27
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=97.98 E-value=3e-06 Score=37.31 Aligned_cols=26 Identities=8% Similarity=-0.064 Sum_probs=22.6
Q ss_pred ceecccccccccchHHHHHHHHHHhc
Q psy3948 100 AHKCANVIIIAIMYHILEIMLEDIQG 125 (143)
Q Consensus 100 ~~~C~~C~~~f~~~s~l~~h~~~~~~ 125 (143)
||.|..|++.|.+.+.|..|++.|++
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 68999999999999999999877653
No 28
>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=97.69 E-value=5.8e-05 Score=37.74 Aligned_cols=33 Identities=12% Similarity=-0.024 Sum_probs=23.8
Q ss_pred cCCCceecccccccccchHHHHHHHHHHhcCCC
Q psy3948 96 TGLKAHKCANVIIIAIMYHILEIMLEDIQGRDH 128 (143)
Q Consensus 96 ~~e~~~~C~~C~~~f~~~s~l~~h~~~~~~~~~ 128 (143)
..+.|-.|+.|+..+.++-+|++|++..|..++
T Consensus 20 ~S~~PatCP~C~a~~~~srnLrRHle~~H~~k~ 52 (54)
T PF09237_consen 20 QSEQPATCPICGAVIRQSRNLRRHLEIRHFKKP 52 (54)
T ss_dssp TTS--EE-TTT--EESSHHHHHHHHHHHTTTS-
T ss_pred ccCCCCCCCcchhhccchhhHHHHHHHHhcccC
Confidence 346788999999999999999999999887765
No 29
>PHA00732 hypothetical protein
Probab=97.64 E-value=4.5e-05 Score=42.51 Aligned_cols=46 Identities=33% Similarity=0.538 Sum_probs=34.4
Q ss_pred ceeccCCCCccCCcchHHHhhhh-cCCCCCccCCCCCCCCCChHHHHHHHHHh
Q psy3948 44 NYACFICTYHTRKHGDMIGHMRK-HTGVKPLKCSSCNYSCSTKSALSVHQKRH 95 (143)
Q Consensus 44 ~~~c~~c~~~~~~~~~l~~h~~~-~~~~~~~~c~~c~~~f~~~~~l~~h~~~h 95 (143)
+|.|..|++.|.....|..|++. |. ++.|+.|++.|.+ +..|..+.
T Consensus 1 py~C~~Cgk~F~s~s~Lk~H~r~~H~---~~~C~~CgKsF~~---l~~H~~~~ 47 (79)
T PHA00732 1 MFKCPICGFTTVTLFALKQHARRNHT---LTKCPVCNKSYRR---LNQHFYSQ 47 (79)
T ss_pred CccCCCCCCccCCHHHHHHHhhcccC---CCccCCCCCEeCC---hhhhhccc
Confidence 36788999999988889888873 54 3579999988874 66666543
No 30
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=97.48 E-value=0.00016 Score=30.68 Aligned_cols=24 Identities=17% Similarity=0.102 Sum_probs=19.5
Q ss_pred eecccccccccchHHHHHHHHHHhc
Q psy3948 101 HKCANVIIIAIMYHILEIMLEDIQG 125 (143)
Q Consensus 101 ~~C~~C~~~f~~~s~l~~h~~~~~~ 125 (143)
|.|..|+.... .+.|.+|++.+++
T Consensus 1 y~C~~C~y~t~-~~~l~~H~~~~H~ 24 (24)
T PF13909_consen 1 YKCPHCSYSTS-KSNLKRHLKRHHP 24 (24)
T ss_dssp EE-SSSS-EES-HHHHHHHHHHHHS
T ss_pred CCCCCCCCcCC-HHHHHHHHHhhCc
Confidence 78999999998 9999999998874
No 31
>smart00355 ZnF_C2H2 zinc finger.
Probab=97.43 E-value=0.00013 Score=31.23 Aligned_cols=24 Identities=8% Similarity=0.044 Sum_probs=20.5
Q ss_pred eecccccccccchHHHHHHHHHHh
Q psy3948 101 HKCANVIIIAIMYHILEIMLEDIQ 124 (143)
Q Consensus 101 ~~C~~C~~~f~~~s~l~~h~~~~~ 124 (143)
|.|..|++.|...+.|..|++.|.
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~~H~ 24 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMRTHX 24 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHHHhc
Confidence 578899999999999999988554
No 32
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=97.37 E-value=8.9e-05 Score=31.11 Aligned_cols=20 Identities=30% Similarity=0.584 Sum_probs=10.2
Q ss_pred eccCCCCccCCcchHHHhhh
Q psy3948 46 ACFICTYHTRKHGDMIGHMR 65 (143)
Q Consensus 46 ~c~~c~~~~~~~~~l~~h~~ 65 (143)
.|+.|++.|.....|..|++
T Consensus 2 ~C~~C~~~f~~~~~l~~H~~ 21 (23)
T PF00096_consen 2 KCPICGKSFSSKSNLKRHMR 21 (23)
T ss_dssp EETTTTEEESSHHHHHHHHH
T ss_pred CCCCCCCccCCHHHHHHHHh
Confidence 45555555555555555543
No 33
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=97.34 E-value=0.00019 Score=41.56 Aligned_cols=78 Identities=13% Similarity=0.205 Sum_probs=23.2
Q ss_pred eccCCCCccCCcchHHHhhhhcCCCCCccCCCCCCCCCChHHHHHHHHHhcCCCceecccccccccchHHHHHHHHHH-h
Q psy3948 46 ACFICTYHTRKHGDMIGHMRKHTGVKPLKCSSCNYSCSTKSALSVHQKRHTGLKAHKCANVIIIAIMYHILEIMLEDI-Q 124 (143)
Q Consensus 46 ~c~~c~~~~~~~~~l~~h~~~~~~~~~~~c~~c~~~f~~~~~l~~h~~~h~~e~~~~C~~C~~~f~~~s~l~~h~~~~-~ 124 (143)
+|..|+..|.+...+..|+....+... . ....+.....+..+.+.-. ...+.|..|++.|.+...|..|++.+ |
T Consensus 1 ~C~~C~~~f~~~~~l~~H~~~~H~~~~-~---~~~~l~~~~~~~~~~~~~~-~~~~~C~~C~~~f~s~~~l~~Hm~~~~H 75 (100)
T PF12756_consen 1 QCLFCDESFSSVDDLLQHMKKKHGFDI-P---DQKYLVDPNRLLNYLRKKV-KESFRCPYCNKTFRSREALQEHMRSKHH 75 (100)
T ss_dssp -----------------------------------------------------SSEEBSSSS-EESSHHHHHHHHHHTTT
T ss_pred Ccccccccccccccccccccccccccc-c---ccccccccccccccccccc-CCCCCCCccCCCCcCHHHHHHHHcCccC
Confidence 377888888888888888754443211 1 0011112222222222211 22689999999999999999999965 4
Q ss_pred cCCC
Q psy3948 125 GRDH 128 (143)
Q Consensus 125 ~~~~ 128 (143)
....
T Consensus 76 ~~~~ 79 (100)
T PF12756_consen 76 KKRN 79 (100)
T ss_dssp TC-S
T ss_pred CCcc
Confidence 4433
No 34
>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=97.11 E-value=0.00099 Score=34.32 Aligned_cols=48 Identities=19% Similarity=0.453 Sum_probs=31.1
Q ss_pred eeccCCCCccCCcchHHHhhh-hcCCC-CCccCCCCCCCCCChHHHHHHHHHh
Q psy3948 45 YACFICTYHTRKHGDMIGHMR-KHTGV-KPLKCSSCNYSCSTKSALSVHQKRH 95 (143)
Q Consensus 45 ~~c~~c~~~~~~~~~l~~h~~-~~~~~-~~~~c~~c~~~f~~~~~l~~h~~~h 95 (143)
|.|+.|++ -.+...|..|.. .|..+ +.+.|++|...+. .+|..|+..+
T Consensus 3 f~CP~C~~-~~~~~~L~~H~~~~H~~~~~~v~CPiC~~~~~--~~l~~Hl~~~ 52 (54)
T PF05605_consen 3 FTCPYCGK-GFSESSLVEHCEDEHRSESKNVVCPICSSRVT--DNLIRHLNSQ 52 (54)
T ss_pred cCCCCCCC-ccCHHHHHHHHHhHCcCCCCCccCCCchhhhh--hHHHHHHHHh
Confidence 67888888 455667777744 34443 4578888886433 4777777654
No 35
>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=96.95 E-value=0.00049 Score=29.99 Aligned_cols=23 Identities=22% Similarity=0.411 Sum_probs=12.0
Q ss_pred eeccCCCCccCCcchHHHhhhhc
Q psy3948 45 YACFICTYHTRKHGDMIGHMRKH 67 (143)
Q Consensus 45 ~~c~~c~~~~~~~~~l~~h~~~~ 67 (143)
|.|..|++.|.+...|..|++.|
T Consensus 2 ~~C~~C~~~F~~~~~l~~H~~~h 24 (27)
T PF13912_consen 2 FECDECGKTFSSLSALREHKRSH 24 (27)
T ss_dssp EEETTTTEEESSHHHHHHHHCTT
T ss_pred CCCCccCCccCChhHHHHHhHHh
Confidence 45555555555555555554443
No 36
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=96.92 E-value=0.0006 Score=29.11 Aligned_cols=23 Identities=13% Similarity=-0.074 Sum_probs=19.6
Q ss_pred eecccccccccchHHHHHHHHHH
Q psy3948 101 HKCANVIIIAIMYHILEIMLEDI 123 (143)
Q Consensus 101 ~~C~~C~~~f~~~s~l~~h~~~~ 123 (143)
|.|..|++.|.+...|..|++.+
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 67899999999999999998643
No 37
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=96.91 E-value=0.00027 Score=48.91 Aligned_cols=52 Identities=21% Similarity=0.226 Sum_probs=38.5
Q ss_pred CCCccCCC--CCCCCCChHHHHHHHHHhc-------------------CCCceecccccccccchHHHHHHHH
Q psy3948 70 VKPLKCSS--CNYSCSTKSALSVHQKRHT-------------------GLKAHKCANVIIIAIMYHILEIMLE 121 (143)
Q Consensus 70 ~~~~~c~~--c~~~f~~~~~l~~h~~~h~-------------------~e~~~~C~~C~~~f~~~s~l~~h~~ 121 (143)
++||.|++ |.+.|.....|..|+.... ..|||.|+.|++.+.....|+=|+.
T Consensus 347 ~KpykCpV~gC~K~YknqnGLKYH~lhGH~~~~~~~~p~p~~~~~F~~~~KPYrCevC~KRYKNlNGLKYHr~ 419 (423)
T COG5189 347 GKPYKCPVEGCNKKYKNQNGLKYHMLHGHQNQKLHENPSPEKMNIFSAKDKPYRCEVCDKRYKNLNGLKYHRK 419 (423)
T ss_pred CceecCCCCCchhhhccccchhhhhhccccCcccCCCCCccccccccccCCceeccccchhhccCccceeccc
Confidence 47777776 6677777777777764211 2489999999999999888887743
No 38
>PRK04860 hypothetical protein; Provisional
Probab=96.85 E-value=0.00076 Score=42.75 Aligned_cols=37 Identities=16% Similarity=0.423 Sum_probs=20.3
Q ss_pred CccCCCCCCCCCChHHHHHHHHHhcCCCceecccccccccc
Q psy3948 72 PLKCSSCNYSCSTKSALSVHQKRHTGLKAHKCANVIIIAIM 112 (143)
Q Consensus 72 ~~~c~~c~~~f~~~~~l~~h~~~h~~e~~~~C~~C~~~f~~ 112 (143)
+|.|. |+. ....+..|.++++++++|.|..|+..|..
T Consensus 119 ~Y~C~-C~~---~~~~~rrH~ri~~g~~~YrC~~C~~~l~~ 155 (160)
T PRK04860 119 PYRCK-CQE---HQLTVRRHNRVVRGEAVYRCRRCGETLVF 155 (160)
T ss_pred EEEcC-CCC---eeCHHHHHHHHhcCCccEECCCCCceeEE
Confidence 35554 543 44445555566666666666666655543
No 39
>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=96.70 E-value=0.0017 Score=27.08 Aligned_cols=21 Identities=33% Similarity=0.624 Sum_probs=9.5
Q ss_pred cCCCCCCCCCChHHHHHHHHH
Q psy3948 74 KCSSCNYSCSTKSALSVHQKR 94 (143)
Q Consensus 74 ~c~~c~~~f~~~~~l~~h~~~ 94 (143)
.|+.|+..|.+...|..|+..
T Consensus 2 ~C~~C~~~~~~~~~l~~H~~~ 22 (24)
T PF13894_consen 2 QCPICGKSFRSKSELRQHMRT 22 (24)
T ss_dssp E-SSTS-EESSHHHHHHHHHH
T ss_pred CCcCCCCcCCcHHHHHHHHHh
Confidence 444555555555555555443
No 40
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=96.55 E-value=0.0015 Score=45.37 Aligned_cols=19 Identities=26% Similarity=0.574 Sum_probs=14.4
Q ss_pred CCccccCCc--chhhhccchh
Q psy3948 4 DHTILKCTF--CNIIFNKLQD 22 (143)
Q Consensus 4 ~~~~~~C~~--C~~~f~~~~~ 22 (143)
+.|||+|+. |+|.+....-
T Consensus 346 d~KpykCpV~gC~K~YknqnG 366 (423)
T COG5189 346 DGKPYKCPVEGCNKKYKNQNG 366 (423)
T ss_pred cCceecCCCCCchhhhccccc
Confidence 349999998 9998865443
No 41
>PF12171 zf-C2H2_jaz: Zinc-finger double-stranded RNA-binding; InterPro: IPR022755 This zinc finger is found in archaea and eukaryotes, and is approximately 30 amino acids in length. The mammalian members of this group occur multiple times along the protein, joined by flexible linkers, and are referred to as JAZ - dsRNA-binding ZF protein - zinc-fingers. The JAZ proteins are expressed in all tissues tested and localise in the nucleus, particularly the nucleolus []. JAZ preferentially binds to double-stranded (ds) RNA or RNA/DNA hybrids rather than DNA. In addition to binding double-stranded RNA, these zinc-fingers are required for nucleolar localisation. This entry represents the multiple-adjacent-C2H2 zinc finger, JAZ. ; PDB: 4DGW_A 1ZR9_A.
Probab=96.27 E-value=0.00066 Score=29.67 Aligned_cols=22 Identities=9% Similarity=-0.002 Sum_probs=18.8
Q ss_pred eecccccccccchHHHHHHHHH
Q psy3948 101 HKCANVIIIAIMYHILEIMLED 122 (143)
Q Consensus 101 ~~C~~C~~~f~~~s~l~~h~~~ 122 (143)
|.|..|++.|.+...|..|++.
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 6799999999999999988763
No 42
>smart00355 ZnF_C2H2 zinc finger.
Probab=96.23 E-value=0.0075 Score=25.34 Aligned_cols=22 Identities=36% Similarity=0.726 Sum_probs=13.4
Q ss_pred cCCCCCCCCCChHHHHHHHHHh
Q psy3948 74 KCSSCNYSCSTKSALSVHQKRH 95 (143)
Q Consensus 74 ~c~~c~~~f~~~~~l~~h~~~h 95 (143)
.|..|+..|.....+..|++.|
T Consensus 2 ~C~~C~~~f~~~~~l~~H~~~H 23 (26)
T smart00355 2 RCPECGKVFKSKSALKEHMRTH 23 (26)
T ss_pred CCCCCcchhCCHHHHHHHHHHh
Confidence 4566666666666666666544
No 43
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=95.94 E-value=0.0078 Score=25.75 Aligned_cols=21 Identities=14% Similarity=-0.210 Sum_probs=15.8
Q ss_pred eecccccccccchHHHHHHHHH
Q psy3948 101 HKCANVIIIAIMYHILEIMLED 122 (143)
Q Consensus 101 ~~C~~C~~~f~~~s~l~~h~~~ 122 (143)
..|+.||+.| ..+.|.+|++.
T Consensus 3 ~~C~~CgR~F-~~~~l~~H~~~ 23 (25)
T PF13913_consen 3 VPCPICGRKF-NPDRLEKHEKI 23 (25)
T ss_pred CcCCCCCCEE-CHHHHHHHHHh
Confidence 3688888888 57778888664
No 44
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=95.57 E-value=0.01 Score=30.31 Aligned_cols=32 Identities=9% Similarity=0.087 Sum_probs=27.1
Q ss_pred hcCCCceecccccccccchHHHHHHHHHHhcC
Q psy3948 95 HTGLKAHKCANVIIIAIMYHILEIMLEDIQGR 126 (143)
Q Consensus 95 h~~e~~~~C~~C~~~f~~~s~l~~h~~~~~~~ 126 (143)
-.||--+.|+-||..|..+.+..+|+...|+-
T Consensus 12 RDGE~~lrCPRC~~~FR~~K~Y~RHVNKaH~~ 43 (65)
T COG4049 12 RDGEEFLRCPRCGMVFRRRKDYIRHVNKAHGW 43 (65)
T ss_pred cCCceeeeCCchhHHHHHhHHHHHHhhHHhhh
Confidence 34677789999999999999999999877753
No 45
>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=95.42 E-value=0.019 Score=28.86 Aligned_cols=33 Identities=18% Similarity=0.255 Sum_probs=17.4
Q ss_pred CCCCCccCCCCCCCCCChHHHHHHHHHhcCCCc
Q psy3948 68 TGVKPLKCSSCNYSCSTKSALSVHQKRHTGLKA 100 (143)
Q Consensus 68 ~~~~~~~c~~c~~~f~~~~~l~~h~~~h~~e~~ 100 (143)
....|..|+.|+..+.+.-+|..|+....+.+|
T Consensus 20 ~S~~PatCP~C~a~~~~srnLrRHle~~H~~k~ 52 (54)
T PF09237_consen 20 QSEQPATCPICGAVIRQSRNLRRHLEIRHFKKP 52 (54)
T ss_dssp TTS--EE-TTT--EESSHHHHHHHHHHHTTTS-
T ss_pred ccCCCCCCCcchhhccchhhHHHHHHHHhcccC
Confidence 344566777777777777777777765555444
No 46
>PRK04860 hypothetical protein; Provisional
Probab=95.39 E-value=0.017 Score=36.71 Aligned_cols=36 Identities=14% Similarity=0.119 Sum_probs=30.4
Q ss_pred ceecccccccccchHHHHHHHHHHhcCCCcccc-eeeeeee
Q psy3948 100 AHKCANVIIIAIMYHILEIMLEDIQGRDHINVN-IALTLQF 139 (143)
Q Consensus 100 ~~~C~~C~~~f~~~s~l~~h~~~~~~~~~~~~~-~~~~~~~ 139 (143)
+|.|. |+. ....+.+|.+++.++.+|.|+ +...+.+
T Consensus 119 ~Y~C~-C~~---~~~~~rrH~ri~~g~~~YrC~~C~~~l~~ 155 (160)
T PRK04860 119 PYRCK-CQE---HQLTVRRHNRVVRGEAVYRCRRCGETLVF 155 (160)
T ss_pred EEEcC-CCC---eeCHHHHHHHHhcCCccEECCCCCceeEE
Confidence 69998 997 678899999999999999997 6555544
No 47
>smart00451 ZnF_U1 U1-like zinc finger. Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins.
Probab=95.07 E-value=0.018 Score=26.47 Aligned_cols=22 Identities=14% Similarity=0.033 Sum_probs=19.5
Q ss_pred ceecccccccccchHHHHHHHH
Q psy3948 100 AHKCANVIIIAIMYHILEIMLE 121 (143)
Q Consensus 100 ~~~C~~C~~~f~~~s~l~~h~~ 121 (143)
+|.|..|+..|.+...+..|++
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~ 24 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLK 24 (35)
T ss_pred CeEccccCCccCCHHHHHHHHC
Confidence 5789999999999999999976
No 48
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=94.42 E-value=0.04 Score=31.61 Aligned_cols=24 Identities=25% Similarity=0.639 Sum_probs=17.4
Q ss_pred CccCCCCCCCCCChHHHHHHHHHh
Q psy3948 72 PLKCSSCNYSCSTKSALSVHQKRH 95 (143)
Q Consensus 72 ~~~c~~c~~~f~~~~~l~~h~~~h 95 (143)
.+.|..|+..|.+...|..|++.+
T Consensus 50 ~~~C~~C~~~f~s~~~l~~Hm~~~ 73 (100)
T PF12756_consen 50 SFRCPYCNKTFRSREALQEHMRSK 73 (100)
T ss_dssp SEEBSSSS-EESSHHHHHHHHHHT
T ss_pred CCCCCccCCCCcCHHHHHHHHcCc
Confidence 567888888888888888887754
No 49
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=92.59 E-value=0.021 Score=41.36 Aligned_cols=62 Identities=23% Similarity=0.255 Sum_probs=53.5
Q ss_pred CCccCCCCCCCCCChHHHHHHHH--HhcCC--Cceecc--cccccccchHHHHHHHHHHhcCCCcccc
Q psy3948 71 KPLKCSSCNYSCSTKSALSVHQK--RHTGL--KAHKCA--NVIIIAIMYHILEIMLEDIQGRDHINVN 132 (143)
Q Consensus 71 ~~~~c~~c~~~f~~~~~l~~h~~--~h~~e--~~~~C~--~C~~~f~~~s~l~~h~~~~~~~~~~~~~ 132 (143)
.++.+..|...|.....+..|.+ .|.++ +++.|+ .|++.|.+...+..|...|.+..++.+.
T Consensus 288 ~~~~~~~~~~~~s~~~~l~~~~~~~~h~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 355 (467)
T COG5048 288 LPIKSKQCNISFSRSSPLTRHLRSVNHSGESLKPFSCPYSLCGKLFSRNDALKRHILLHTSISPAKEK 355 (467)
T ss_pred cCCCCccccCCccccccccccccccccccccCCceeeeccCCCccccccccccCCcccccCCCccccc
Confidence 35778888889999999999998 79999 999999 7999999999999999999888765544
No 50
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=91.64 E-value=0.22 Score=25.93 Aligned_cols=9 Identities=11% Similarity=0.360 Sum_probs=5.0
Q ss_pred Cceeccccc
Q psy3948 99 KAHKCANVI 107 (143)
Q Consensus 99 ~~~~C~~C~ 107 (143)
.+|.|+.||
T Consensus 49 ~~Y~Cp~CG 57 (61)
T COG2888 49 NPYRCPKCG 57 (61)
T ss_pred CceECCCcC
Confidence 455555555
No 51
>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=91.43 E-value=0.24 Score=20.91 Aligned_cols=10 Identities=20% Similarity=0.660 Sum_probs=6.5
Q ss_pred CcceeccCCC
Q psy3948 42 SYNYACFICT 51 (143)
Q Consensus 42 ~~~~~c~~c~ 51 (143)
...|.|+.||
T Consensus 14 ~v~f~CPnCG 23 (24)
T PF07754_consen 14 AVPFPCPNCG 23 (24)
T ss_pred CceEeCCCCC
Confidence 3457777776
No 52
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=90.57 E-value=0.2 Score=23.35 Aligned_cols=11 Identities=18% Similarity=0.295 Sum_probs=5.8
Q ss_pred ceeccCCCCcc
Q psy3948 44 NYACFICTYHT 54 (143)
Q Consensus 44 ~~~c~~c~~~~ 54 (143)
..+|+.|+..|
T Consensus 25 ~v~C~~C~~~f 35 (36)
T PF13717_consen 25 KVRCSKCGHVF 35 (36)
T ss_pred EEECCCCCCEe
Confidence 34555555544
No 53
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=90.56 E-value=0.6 Score=27.82 Aligned_cols=87 Identities=14% Similarity=0.139 Sum_probs=44.6
Q ss_pred ccccCCcchhhhccchhhHHHhhhcccCCCCCC----CCCCcceeccCCCCccCCcchHHHhhhhcCCCCCccCCCCCCC
Q psy3948 6 TILKCTFCNIIFNKLQDEELIMTHCKSCKKPKR----PDKSYNYACFICTYHTRKHGDMIGHMRKHTGVKPLKCSSCNYS 81 (143)
Q Consensus 6 ~~~~C~~C~~~f~~~~~~~~~~~~c~~c~~~~~----~~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~c~~c~~~ 81 (143)
-|-.|+.||.+..+.-+..|... --..-+.|. ......-.|-.|...|+.......- .......|.|+.|...
T Consensus 14 LP~~CpiCgLtLVss~HLARSyH-HLfPl~~f~ev~~~~~~~~~~C~~C~~~f~~~~~~~~~--~~~~~~~y~C~~C~~~ 90 (112)
T TIGR00622 14 LPVECPICGLTLILSTHLARSYH-HLFPLKAFQEIPLEEYNGSRFCFGCQGPFPKPPVSPFD--ELKDSHRYVCAVCKNV 90 (112)
T ss_pred CCCcCCcCCCEEeccchHHHhhh-ccCCCcccccccccccCCCCcccCcCCCCCCccccccc--ccccccceeCCCCCCc
Confidence 35678888887655555333211 000011111 0011112366777776654211100 0122346889889888
Q ss_pred CCChHHHHHHHHHh
Q psy3948 82 CSTKSALSVHQKRH 95 (143)
Q Consensus 82 f~~~~~l~~h~~~h 95 (143)
|.-.-+...|...|
T Consensus 91 FC~dCD~fiHe~Lh 104 (112)
T TIGR00622 91 FCVDCDVFVHESLH 104 (112)
T ss_pred cccccchhhhhhcc
Confidence 88888888887665
No 54
>PF02892 zf-BED: BED zinc finger; InterPro: IPR003656 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents predicted BED-type zinc finger domains. The BED finger which was named after the Drosophila proteins BEAF and DREF, is found in one or more copies in cellular regulatory factors and transposases from plants, animals and fungi. The BED finger is an about 50 to 60 amino acid residues domain that contains a characteristic motif with two highly conserved aromatic positions, as well as a shared pattern of cysteines and histidines that is predicted to form a zinc finger. As diverse BED fingers are able to bind DNA, it has been suggested that DNA-binding is the general function of this domain []. Some proteins known to contain a BED domain include animal, plant and fungi AC1 and Hobo-like transposases; Caenorhabditis elegans Dpy-20 protein, a predicted cuticular gene transcriptional regulator; Drosophila BEAF (boundary element-associated factor), thought to be involved in chromatin insulation; Drosophila DREF, a transcriptional regulator for S-phase genes; and tobacco 3AF1 and tomato E4/E8-BP1, light- and ethylene-regulated DNA binding proteins that contain two BED fingers. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding; PDB: 2DJR_A 2CT5_A.
Probab=89.86 E-value=0.44 Score=23.14 Aligned_cols=28 Identities=18% Similarity=0.094 Sum_probs=17.6
Q ss_pred CCCceecccccccccch----HHHHHHHHHHh
Q psy3948 97 GLKAHKCANVIIIAIMY----HILEIMLEDIQ 124 (143)
Q Consensus 97 ~e~~~~C~~C~~~f~~~----s~l~~h~~~~~ 124 (143)
+.....|..|++.+... +.|.+|++..+
T Consensus 13 ~~~~a~C~~C~~~~~~~~~~ts~l~~HL~~~h 44 (45)
T PF02892_consen 13 DKKKAKCKYCGKVIKYSSGGTSNLKRHLKKKH 44 (45)
T ss_dssp CSS-EEETTTTEE-----SSTHHHHHHHHHTT
T ss_pred CcCeEEeCCCCeEEeeCCCcHHHHHHhhhhhC
Confidence 44557899999988774 88999986543
No 55
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=88.84 E-value=0.3 Score=22.92 Aligned_cols=10 Identities=20% Similarity=0.265 Sum_probs=4.9
Q ss_pred eeccCCCCcc
Q psy3948 45 YACFICTYHT 54 (143)
Q Consensus 45 ~~c~~c~~~~ 54 (143)
..|+.|+..|
T Consensus 26 vrC~~C~~~f 35 (37)
T PF13719_consen 26 VRCPKCGHVF 35 (37)
T ss_pred EECCCCCcEe
Confidence 4455555444
No 56
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=88.66 E-value=0.46 Score=37.53 Aligned_cols=10 Identities=30% Similarity=0.869 Sum_probs=6.1
Q ss_pred CCccCCCCCC
Q psy3948 71 KPLKCSSCNY 80 (143)
Q Consensus 71 ~~~~c~~c~~ 80 (143)
.|..|+.|+.
T Consensus 474 ~p~~Cp~Cgs 483 (730)
T COG1198 474 IPQSCPECGS 483 (730)
T ss_pred CCCCCCCCCC
Confidence 4566666664
No 57
>PF15135 UPF0515: Uncharacterised protein UPF0515
Probab=88.54 E-value=0.3 Score=33.12 Aligned_cols=55 Identities=16% Similarity=0.437 Sum_probs=38.1
Q ss_pred CCccccCCcchhhhccchhhHHHhhhcccCCCCCCCCC------CcceeccCCCCccCCcc
Q psy3948 4 DHTILKCTFCNIIFNKLQDEELIMTHCKSCKKPKRPDK------SYNYACFICTYHTRKHG 58 (143)
Q Consensus 4 ~~~~~~C~~C~~~f~~~~~~~~~~~~c~~c~~~~~~~~------~~~~~c~~c~~~~~~~~ 58 (143)
.+..|.|..|+..++...-.......|..|.+.|.+.. ---|.|+.|+..|....
T Consensus 109 ~drqFaC~~Cd~~WwRrvp~rKeVSRCr~C~~rYDPVP~dkmwG~aef~C~~C~h~F~G~~ 169 (278)
T PF15135_consen 109 VDRQFACSSCDHMWWRRVPQRKEVSRCRKCRKRYDPVPCDKMWGIAEFHCPKCRHNFRGFA 169 (278)
T ss_pred cceeeeccccchHHHhccCcccccccccccccccCCCccccccceeeeecccccccchhhh
Confidence 35689999998887654433333447999998886311 12388999999998654
No 58
>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=88.10 E-value=0.39 Score=28.46 Aligned_cols=28 Identities=18% Similarity=0.246 Sum_probs=12.6
Q ss_pred cccCCCCCCCCCCcceeccCCCCccCCc
Q psy3948 30 CKSCKKPKRPDKSYNYACFICTYHTRKH 57 (143)
Q Consensus 30 c~~c~~~~~~~~~~~~~c~~c~~~~~~~ 57 (143)
|+.||+.|=--.+.|..|+.||..|.-.
T Consensus 12 Cp~CG~kFYDLnk~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 12 CPSCGAKFYDLNKDPIVCPKCGTEFPPE 39 (108)
T ss_pred CCCCcchhccCCCCCccCCCCCCccCcc
Confidence 4444444432222344556666555543
No 59
>smart00614 ZnF_BED BED zinc finger. DNA-binding domain in chromatin-boundary-element-binding proteins and transposases
Probab=87.70 E-value=0.69 Score=23.18 Aligned_cols=23 Identities=17% Similarity=-0.048 Sum_probs=17.1
Q ss_pred eecccccccccch-----HHHHHHHHHH
Q psy3948 101 HKCANVIIIAIMY-----HILEIMLEDI 123 (143)
Q Consensus 101 ~~C~~C~~~f~~~-----s~l~~h~~~~ 123 (143)
-.|..|++.++.. +.|.+|++..
T Consensus 19 a~C~~C~~~l~~~~~~gTs~L~rHl~~~ 46 (50)
T smart00614 19 AKCKYCGKKLSRSSKGGTSNLRRHLRRK 46 (50)
T ss_pred EEecCCCCEeeeCCCCCcHHHHHHHHhH
Confidence 4688888887665 6899998843
No 60
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=86.19 E-value=0.84 Score=23.79 Aligned_cols=11 Identities=18% Similarity=0.431 Sum_probs=6.3
Q ss_pred cceeccCCCCc
Q psy3948 43 YNYACFICTYH 53 (143)
Q Consensus 43 ~~~~c~~c~~~ 53 (143)
..|.|+.||..
T Consensus 24 ~~F~CPnCG~~ 34 (59)
T PRK14890 24 VKFLCPNCGEV 34 (59)
T ss_pred CEeeCCCCCCe
Confidence 44666666644
No 61
>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=86.14 E-value=0.42 Score=21.76 Aligned_cols=9 Identities=44% Similarity=1.283 Sum_probs=4.4
Q ss_pred eeccCCCCc
Q psy3948 45 YACFICTYH 53 (143)
Q Consensus 45 ~~c~~c~~~ 53 (143)
+.|..||..
T Consensus 2 ~~C~~CGy~ 10 (33)
T cd00350 2 YVCPVCGYI 10 (33)
T ss_pred EECCCCCCE
Confidence 345555544
No 62
>KOG1146|consensus
Probab=86.06 E-value=0.31 Score=40.47 Aligned_cols=23 Identities=22% Similarity=0.181 Sum_probs=21.2
Q ss_pred CceecccccccccchHHHHHHHH
Q psy3948 99 KAHKCANVIIIAIMYHILEIMLE 121 (143)
Q Consensus 99 ~~~~C~~C~~~f~~~s~l~~h~~ 121 (143)
++|.|..|.+.++...+|.+|+.
T Consensus 517 ~p~~C~~C~~stttng~Lsihlq 539 (1406)
T KOG1146|consen 517 KPYPCRACNYSTTTNGNLSIHLQ 539 (1406)
T ss_pred CcccceeeeeeeecchHHHHHHH
Confidence 57999999999999999999976
No 63
>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=85.73 E-value=0.75 Score=19.76 Aligned_cols=8 Identities=38% Similarity=0.912 Sum_probs=4.2
Q ss_pred ccCCCCcc
Q psy3948 47 CFICTYHT 54 (143)
Q Consensus 47 c~~c~~~~ 54 (143)
|+.||..|
T Consensus 17 Cp~CG~~F 24 (26)
T PF10571_consen 17 CPHCGYDF 24 (26)
T ss_pred CCCCCCCC
Confidence 55555544
No 64
>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=85.03 E-value=0.16 Score=24.15 Aligned_cols=15 Identities=33% Similarity=0.642 Sum_probs=10.5
Q ss_pred cccCCcchhhhccch
Q psy3948 7 ILKCTFCNIIFNKLQ 21 (143)
Q Consensus 7 ~~~C~~C~~~f~~~~ 21 (143)
-|.|+.||..|....
T Consensus 5 ~y~C~~Cg~~fe~~~ 19 (41)
T smart00834 5 EYRCEDCGHTFEVLQ 19 (41)
T ss_pred EEEcCCCCCEEEEEE
Confidence 467888888875443
No 65
>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain. This domain contains a CXXCX(19)CXXC motif suggestive of both zinc fingers and thioredoxin, usually found at the N-terminus of prokaryotic proteins. One partially characterized gene, agmX, is among a large set in Myxococcus whose interruption affects adventurous gliding motility.
Probab=84.98 E-value=0.59 Score=21.83 Aligned_cols=10 Identities=30% Similarity=0.989 Sum_probs=5.3
Q ss_pred ccCCcchhhh
Q psy3948 8 LKCTFCNIIF 17 (143)
Q Consensus 8 ~~C~~C~~~f 17 (143)
..|+.|+..|
T Consensus 3 ~~CP~C~~~~ 12 (38)
T TIGR02098 3 IQCPNCKTSF 12 (38)
T ss_pred EECCCCCCEE
Confidence 3455555554
No 66
>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=84.88 E-value=0.13 Score=24.85 Aligned_cols=15 Identities=33% Similarity=0.680 Sum_probs=10.9
Q ss_pred ccCCcchhhhccchh
Q psy3948 8 LKCTFCNIIFNKLQD 22 (143)
Q Consensus 8 ~~C~~C~~~f~~~~~ 22 (143)
|.|+.||..|.....
T Consensus 6 y~C~~Cg~~fe~~~~ 20 (42)
T PF09723_consen 6 YRCEECGHEFEVLQS 20 (42)
T ss_pred EEeCCCCCEEEEEEE
Confidence 678888888855544
No 67
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=84.52 E-value=0.32 Score=35.21 Aligned_cols=62 Identities=26% Similarity=0.430 Sum_probs=52.5
Q ss_pred cceeccCCCCccCCcchHHHhhh--hcCCC--CCccCC--CCCCCCCChHHHHHHHHHhcCCCceecc
Q psy3948 43 YNYACFICTYHTRKHGDMIGHMR--KHTGV--KPLKCS--SCNYSCSTKSALSVHQKRHTGLKAHKCA 104 (143)
Q Consensus 43 ~~~~c~~c~~~~~~~~~l~~h~~--~~~~~--~~~~c~--~c~~~f~~~~~l~~h~~~h~~e~~~~C~ 104 (143)
.++.|..|...+.....+..|.+ .|.++ +++.|+ .|++.|.+...+..|...|++.+++.+.
T Consensus 288 ~~~~~~~~~~~~s~~~~l~~~~~~~~h~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 355 (467)
T COG5048 288 LPIKSKQCNISFSRSSPLTRHLRSVNHSGESLKPFSCPYSLCGKLFSRNDALKRHILLHTSISPAKEK 355 (467)
T ss_pred cCCCCccccCCccccccccccccccccccccCCceeeeccCCCccccccccccCCcccccCCCccccc
Confidence 35778889999999999999988 79998 899999 7999999999999998888877665553
No 68
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=83.75 E-value=0.62 Score=28.48 Aligned_cols=27 Identities=30% Similarity=0.582 Sum_probs=18.6
Q ss_pred cccCCcchhhhccchhhHHHhhhcccCCC
Q psy3948 7 ILKCTFCNIIFNKLQDEELIMTHCKSCKK 35 (143)
Q Consensus 7 ~~~C~~C~~~f~~~~~~~~~~~~c~~c~~ 35 (143)
||+|..||++|..-+..+.. =|+.||.
T Consensus 1 PH~Ct~Cg~~f~dgs~eil~--GCP~CGg 27 (131)
T PF09845_consen 1 PHQCTKCGRVFEDGSKEILS--GCPECGG 27 (131)
T ss_pred CcccCcCCCCcCCCcHHHHc--cCcccCC
Confidence 68999999999765543222 3777764
No 69
>KOG2186|consensus
Probab=83.33 E-value=0.72 Score=31.45 Aligned_cols=38 Identities=18% Similarity=0.520 Sum_probs=15.8
Q ss_pred eeccCCCCccCCcchHHHhhhhcCCCCCccCCCCCCCCCC
Q psy3948 45 YACFICTYHTRKHGDMIGHMRKHTGVKPLKCSSCNYSCST 84 (143)
Q Consensus 45 ~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~c~~c~~~f~~ 84 (143)
|.|.+||.+..-+ .+..|+..-++ ..|.|..|+..|..
T Consensus 4 FtCnvCgEsvKKp-~vekH~srCrn-~~fSCIDC~k~F~~ 41 (276)
T KOG2186|consen 4 FTCNVCGESVKKP-QVEKHMSRCRN-AYFSCIDCGKTFER 41 (276)
T ss_pred Eehhhhhhhcccc-chHHHHHhccC-CeeEEeeccccccc
Confidence 3444444444422 33334333333 23444445444444
No 70
>KOG1146|consensus
Probab=83.12 E-value=0.86 Score=38.10 Aligned_cols=65 Identities=22% Similarity=0.379 Sum_probs=42.9
Q ss_pred CCCCCccccCCcchhhhccchh---hHHHhhhc---ccC----------C-CCCCCCCCcceeccCCCCccCCcchHHHh
Q psy3948 1 MFVDHTILKCTFCNIIFNKLQD---EELIMTHC---KSC----------K-KPKRPDKSYNYACFICTYHTRKHGDMIGH 63 (143)
Q Consensus 1 ~~~~~~~~~C~~C~~~f~~~~~---~~~~~~~c---~~c----------~-~~~~~~~~~~~~c~~c~~~~~~~~~l~~h 63 (143)
|+.-.+.++|+.|+..|..... |++..... ..| . ..+ ....+++.|..|..++.....|.+|
T Consensus 459 L~S~~kt~~cpkc~~~yk~a~~L~vhmRskhp~~~~~~c~~gq~~~~~arg~~~-~~~~~p~~C~~C~~stttng~Lsih 537 (1406)
T KOG1146|consen 459 LHSFFKTLKCPKCNWHYKLAQTLGVHMRSKHPESQSAYCKAGQNHPRLARGEVY-RCPGKPYPCRACNYSTTTNGNLSIH 537 (1406)
T ss_pred eecccccccCCccchhhhhHHHhhhcccccccccchhHhHhccccccccccccc-cCCCCcccceeeeeeeecchHHHHH
Confidence 3455689999999999977776 55542200 111 0 111 2334678899999999888888888
Q ss_pred hhh
Q psy3948 64 MRK 66 (143)
Q Consensus 64 ~~~ 66 (143)
+..
T Consensus 538 lqS 540 (1406)
T KOG1146|consen 538 LQS 540 (1406)
T ss_pred HHH
Confidence 764
No 71
>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=83.02 E-value=0.21 Score=25.19 Aligned_cols=15 Identities=40% Similarity=0.709 Sum_probs=11.0
Q ss_pred cccCCcchhhhccch
Q psy3948 7 ILKCTFCNIIFNKLQ 21 (143)
Q Consensus 7 ~~~C~~C~~~f~~~~ 21 (143)
-|.|+.||..|..+.
T Consensus 5 ey~C~~Cg~~fe~~~ 19 (52)
T TIGR02605 5 EYRCTACGHRFEVLQ 19 (52)
T ss_pred EEEeCCCCCEeEEEE
Confidence 367999998885543
No 72
>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=83.01 E-value=1.3 Score=26.20 Aligned_cols=25 Identities=12% Similarity=0.163 Sum_probs=23.1
Q ss_pred eec----ccccccccchHHHHHHHHHHhc
Q psy3948 101 HKC----ANVIIIAIMYHILEIMLEDIQG 125 (143)
Q Consensus 101 ~~C----~~C~~~f~~~s~l~~h~~~~~~ 125 (143)
|.| ..|++...+...+.+|.+.+|+
T Consensus 81 ~~C~~~~~~C~y~~~~~~~m~~H~~~~Hg 109 (109)
T PF12013_consen 81 YRCQCDPPHCGYITRSKKTMRKHWRKEHG 109 (109)
T ss_pred eeeecCCCCCCcEeccHHHHHHHHHHhcC
Confidence 899 9999999999999999998875
No 73
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=82.64 E-value=0.87 Score=22.37 Aligned_cols=11 Identities=27% Similarity=0.495 Sum_probs=6.0
Q ss_pred cccCCcchhhh
Q psy3948 7 ILKCTFCNIIF 17 (143)
Q Consensus 7 ~~~C~~C~~~f 17 (143)
.|.|+.||..|
T Consensus 3 ~y~C~~CG~~~ 13 (46)
T PRK00398 3 EYKCARCGREV 13 (46)
T ss_pred EEECCCCCCEE
Confidence 35555555554
No 74
>KOG2893|consensus
Probab=81.80 E-value=0.46 Score=32.10 Aligned_cols=21 Identities=19% Similarity=0.384 Sum_probs=13.9
Q ss_pred cceeccCCCCccCCcchHHHh
Q psy3948 43 YNYACFICTYHTRKHGDMIGH 63 (143)
Q Consensus 43 ~~~~c~~c~~~~~~~~~l~~h 63 (143)
+.|+|.+|.+.+.+-..|..|
T Consensus 33 khfkchichkkl~sgpglsih 53 (341)
T KOG2893|consen 33 KHFKCHICHKKLFSGPGLSIH 53 (341)
T ss_pred ccceeeeehhhhccCCCceee
Confidence 457777777776666666555
No 75
>KOG2231|consensus
Probab=81.76 E-value=2 Score=33.67 Aligned_cols=93 Identities=18% Similarity=0.201 Sum_probs=47.4
Q ss_pred hcccCCCCCCCCCCcceeccCCCCccCCcchHHHhhhhcCCCCCccCCCCC---------CCCCChHHHHHHHHHhcC-C
Q psy3948 29 HCKSCKKPKRPDKSYNYACFICTYHTRKHGDMIGHMRKHTGVKPLKCSSCN---------YSCSTKSALSVHQKRHTG-L 98 (143)
Q Consensus 29 ~c~~c~~~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~c~~c~---------~~f~~~~~l~~h~~~h~~-e 98 (143)
.|..|++.+.- ......|..| ..|.....|..|+..... -+.|..|. ...-+...|+.|.....- +
T Consensus 101 ~C~~C~~~~~~-~~~~~~~~~c-~~~~s~~~Lk~H~~~~H~--~~~c~lC~~~~kif~~e~k~Yt~~el~~h~~~gd~d~ 176 (669)
T KOG2231|consen 101 SCHICDRRFRA-LYNKKECLHC-TEFKSVENLKNHMRDQHK--LHLCSLCLQNLKIFINERKLYTRAELNLHLMFGDPDD 176 (669)
T ss_pred hcCccccchhh-hcccCCCccc-cchhHHHHHHHHHHHhhh--hhccccccccceeeeeeeehehHHHHHHHHhcCCCcc
Confidence 57777766631 0111235556 455555666777632221 12333322 123344556666553221 2
Q ss_pred C----ceecccccccccchHHHHHHHHHHhc
Q psy3948 99 K----AHKCANVIIIAIMYHILEIMLEDIQG 125 (143)
Q Consensus 99 ~----~~~C~~C~~~f~~~s~l~~h~~~~~~ 125 (143)
+ .-.|..|...|.....|.+|++.+|.
T Consensus 177 ~s~rGhp~C~~C~~~fld~~el~rH~~~~h~ 207 (669)
T KOG2231|consen 177 ESCRGHPLCKFCHERFLDDDELYRHLRFDHE 207 (669)
T ss_pred ccccCCccchhhhhhhccHHHHHHhhcccee
Confidence 1 12577777777777777777776653
No 76
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=81.55 E-value=0.91 Score=22.23 Aligned_cols=13 Identities=23% Similarity=0.401 Sum_probs=7.0
Q ss_pred ceeccCCCCccCC
Q psy3948 44 NYACFICTYHTRK 56 (143)
Q Consensus 44 ~~~c~~c~~~~~~ 56 (143)
...|+.||.....
T Consensus 19 ~irC~~CG~rIly 31 (44)
T smart00659 19 VVRCRECGYRILY 31 (44)
T ss_pred ceECCCCCceEEE
Confidence 3456666655443
No 77
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=81.47 E-value=0.64 Score=30.19 Aligned_cols=10 Identities=20% Similarity=0.514 Sum_probs=4.9
Q ss_pred eeccCCCCcc
Q psy3948 45 YACFICTYHT 54 (143)
Q Consensus 45 ~~c~~c~~~~ 54 (143)
|.|+.||...
T Consensus 137 F~Cp~Cg~~L 146 (178)
T PRK06266 137 FRCPQCGEML 146 (178)
T ss_pred CcCCCCCCCC
Confidence 4455555443
No 78
>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=81.03 E-value=1.3 Score=26.93 Aligned_cols=28 Identities=4% Similarity=-0.177 Sum_probs=15.0
Q ss_pred cccCCCCCCCCCCcceeccCCCCccCCc
Q psy3948 30 CKSCKKPKRPDKSYNYACFICTYHTRKH 57 (143)
Q Consensus 30 c~~c~~~~~~~~~~~~~c~~c~~~~~~~ 57 (143)
|+.|++.|---.+.|..|+.||..+.-.
T Consensus 12 Cp~cg~kFYDLnk~p~vcP~cg~~~~~~ 39 (129)
T TIGR02300 12 CPNTGSKFYDLNRRPAVSPYTGEQFPPE 39 (129)
T ss_pred CCCcCccccccCCCCccCCCcCCccCcc
Confidence 5555555543333455666676665544
No 79
>PF15269 zf-C2H2_7: Zinc-finger
Probab=80.54 E-value=1.5 Score=21.46 Aligned_cols=28 Identities=11% Similarity=-0.040 Sum_probs=22.3
Q ss_pred eecccccccccchHHHHHHHHHHhcCCC
Q psy3948 101 HKCANVIIIAIMYHILEIMLEDIQGRDH 128 (143)
Q Consensus 101 ~~C~~C~~~f~~~s~l~~h~~~~~~~~~ 128 (143)
|+|-.|..+..-.|.|..|++-.-+++.
T Consensus 21 ykcfqcpftc~~kshl~nhmky~lckns 48 (54)
T PF15269_consen 21 YKCFQCPFTCNEKSHLFNHMKYSLCKNS 48 (54)
T ss_pred ceeecCCcccchHHHHHHHHHHHhhhhh
Confidence 6888898888899999999886554443
No 80
>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=80.00 E-value=1.2 Score=29.89 Aligned_cols=30 Identities=3% Similarity=-0.076 Sum_probs=21.5
Q ss_pred CCceecccccccccchHHHHHHHHHHhcCC
Q psy3948 98 LKAHKCANVIIIAIMYHILEIMLEDIQGRD 127 (143)
Q Consensus 98 e~~~~C~~C~~~f~~~s~l~~h~~~~~~~~ 127 (143)
+..|.|+.|++.|.-..-..+|+...|.+.
T Consensus 75 ~~K~~C~lc~KlFkg~eFV~KHI~nKH~e~ 104 (214)
T PF04959_consen 75 EDKWRCPLCGKLFKGPEFVRKHIFNKHPEK 104 (214)
T ss_dssp SEEEEE-SSS-EESSHHHHHHHHHHH-HHH
T ss_pred CCEECCCCCCcccCChHHHHHHHhhcCHHH
Confidence 446889999999999888999988777553
No 81
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=79.62 E-value=1 Score=28.82 Aligned_cols=24 Identities=25% Similarity=0.531 Sum_probs=16.3
Q ss_pred CccCCCCCCCCCChHHHHHHHHHhcCCCceecccccc
Q psy3948 72 PLKCSSCNYSCSTKSALSVHQKRHTGLKAHKCANVII 108 (143)
Q Consensus 72 ~~~c~~c~~~f~~~~~l~~h~~~h~~e~~~~C~~C~~ 108 (143)
.|.|++||. ++.|+.|.+||.||-
T Consensus 134 ~~vC~vCGy-------------~~~ge~P~~CPiCga 157 (166)
T COG1592 134 VWVCPVCGY-------------THEGEAPEVCPICGA 157 (166)
T ss_pred EEEcCCCCC-------------cccCCCCCcCCCCCC
Confidence 577888863 334577778888873
No 82
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=79.51 E-value=1.4 Score=27.57 Aligned_cols=35 Identities=14% Similarity=0.159 Sum_probs=18.3
Q ss_pred ceeccCCCCccCCcchHHHhhhhcCCCCCccCCCCCCCC
Q psy3948 44 NYACFICTYHTRKHGDMIGHMRKHTGVKPLKCSSCNYSC 82 (143)
Q Consensus 44 ~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~c~~c~~~f 82 (143)
.|.|+.|+..|.....+.... . ...|.|+.|+...
T Consensus 99 ~Y~Cp~C~~~y~~~ea~~~~d---~-~~~f~Cp~Cg~~l 133 (147)
T smart00531 99 YYKCPNCQSKYTFLEANQLLD---M-DGTFTCPRCGEEL 133 (147)
T ss_pred EEECcCCCCEeeHHHHHHhcC---C-CCcEECCCCCCEE
Confidence 466777776666544333211 1 2236777776543
No 83
>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=79.39 E-value=2.1 Score=18.29 Aligned_cols=19 Identities=11% Similarity=0.235 Sum_probs=14.1
Q ss_pred ecccccccccchHHHHHHHH
Q psy3948 102 KCANVIIIAIMYHILEIMLE 121 (143)
Q Consensus 102 ~C~~C~~~f~~~s~l~~h~~ 121 (143)
.|+.|++.+ ....+..|+.
T Consensus 3 ~CPiC~~~v-~~~~in~HLD 21 (26)
T smart00734 3 QCPVCFREV-PENLINSHLD 21 (26)
T ss_pred cCCCCcCcc-cHHHHHHHHH
Confidence 578888877 5677777776
No 84
>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=79.29 E-value=0.74 Score=31.55 Aligned_cols=94 Identities=17% Similarity=0.268 Sum_probs=54.3
Q ss_pred hcccCCCCCCCCCCcceeccCCCCccCCcchHHHhhhh-c-CCCCCccCCCCCCCCCChHHH-------HHHHH----Hh
Q psy3948 29 HCKSCKKPKRPDKSYNYACFICTYHTRKHGDMIGHMRK-H-TGVKPLKCSSCNYSCSTKSAL-------SVHQK----RH 95 (143)
Q Consensus 29 ~c~~c~~~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~-~-~~~~~~~c~~c~~~f~~~~~l-------~~h~~----~h 95 (143)
.|..|.+..+..+.+.|.|..|..-+---..+. |+.. . .....|.|..|.+. ...+-| ..|.+ ..
T Consensus 127 ~C~EC~R~vw~hGGrif~CsfC~~flCEDDQFE-HQAsCQvLe~E~~KC~SCNrl-Gq~sCLRCK~cfCddHvrrKg~ky 204 (314)
T PF06524_consen 127 VCIECERGVWDHGGRIFKCSFCDNFLCEDDQFE-HQASCQVLESETFKCQSCNRL-GQYSCLRCKICFCDDHVRRKGFKY 204 (314)
T ss_pred EeeeeecccccCCCeEEEeecCCCeeeccchhh-hhhhhhhhhcccccccccccc-cchhhhheeeeehhhhhhhccccc
Confidence 355666666678888999999986554444443 3221 1 11123566655431 111111 12333 23
Q ss_pred cCCCceecccccccccchHHHHHHHHHHh
Q psy3948 96 TGLKAHKCANVIIIAIMYHILEIMLEDIQ 124 (143)
Q Consensus 96 ~~e~~~~C~~C~~~f~~~s~l~~h~~~~~ 124 (143)
...+++.|+.|+.-.....+|....+.|.
T Consensus 205 ~k~k~~PCPKCg~et~eTkdLSmStR~hk 233 (314)
T PF06524_consen 205 EKGKPIPCPKCGYETQETKDLSMSTRSHK 233 (314)
T ss_pred ccCCCCCCCCCCCcccccccceeeeecch
Confidence 34578999999998888878877666654
No 85
>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=78.86 E-value=0.71 Score=20.61 Aligned_cols=23 Identities=17% Similarity=0.358 Sum_probs=8.4
Q ss_pred cccCCCCCCCCCCcceeccCCCC
Q psy3948 30 CKSCKKPKRPDKSYNYACFICTY 52 (143)
Q Consensus 30 c~~c~~~~~~~~~~~~~c~~c~~ 52 (143)
|+.|+..+.......+.|+.|+.
T Consensus 5 Cp~C~se~~y~D~~~~vCp~C~~ 27 (30)
T PF08274_consen 5 CPLCGSEYTYEDGELLVCPECGH 27 (30)
T ss_dssp -TTT-----EE-SSSEEETTTTE
T ss_pred CCCCCCcceeccCCEEeCCcccc
Confidence 44444444333344566666654
No 86
>KOG2186|consensus
Probab=78.50 E-value=1.1 Score=30.60 Aligned_cols=54 Identities=15% Similarity=0.170 Sum_probs=39.5
Q ss_pred ccCCCCCCCCCChHHHHHHHHHhcCCCceecccccccccchHHHHHHHHHHhcCCCc
Q psy3948 73 LKCSSCNYSCSTKSALSVHQKRHTGLKAHKCANVIIIAIMYHILEIMLEDIQGRDHI 129 (143)
Q Consensus 73 ~~c~~c~~~f~~~~~l~~h~~~h~~e~~~~C~~C~~~f~~~s~l~~h~~~~~~~~~~ 129 (143)
|.|..|+... -...+..|+....+ ..|.|..|++.|-. .++..|.+=.+....|
T Consensus 4 FtCnvCgEsv-KKp~vekH~srCrn-~~fSCIDC~k~F~~-~sYknH~kCITEaQKY 57 (276)
T KOG2186|consen 4 FTCNVCGESV-KKPQVEKHMSRCRN-AYFSCIDCGKTFER-VSYKNHTKCITEAQKY 57 (276)
T ss_pred Eehhhhhhhc-cccchHHHHHhccC-CeeEEeeccccccc-chhhhhhhhcchHHHh
Confidence 5788888653 44566778776655 56999999999997 7788887766655444
No 87
>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=78.09 E-value=1.8 Score=26.68 Aligned_cols=27 Identities=15% Similarity=-0.001 Sum_probs=17.5
Q ss_pred CceecccccccccchHHHHHHHHHHhcCCC
Q psy3948 99 KAHKCANVIIIAIMYHILEIMLEDIQGRDH 128 (143)
Q Consensus 99 ~~~~C~~C~~~f~~~s~l~~h~~~~~~~~~ 128 (143)
.-..|-+||+.|.. |.+|+..|++-.+
T Consensus 71 d~i~clecGk~~k~---LkrHL~~~~gltp 97 (132)
T PF05443_consen 71 DYIICLECGKKFKT---LKRHLRTHHGLTP 97 (132)
T ss_dssp S-EE-TBT--EESB---HHHHHHHTT-S-H
T ss_pred CeeEEccCCcccch---HHHHHHHccCCCH
Confidence 34689999999886 4999999987765
No 88
>PF15616 TerY-C: TerY-C metal binding domain
Probab=78.04 E-value=1.3 Score=27.18 Aligned_cols=15 Identities=20% Similarity=0.288 Sum_probs=8.2
Q ss_pred CCCCcceeccCCCCc
Q psy3948 39 PDKSYNYACFICTYH 53 (143)
Q Consensus 39 ~~~~~~~~c~~c~~~ 53 (143)
..++....|+.|++.
T Consensus 100 i~g~~~~~CPwCg~~ 114 (131)
T PF15616_consen 100 IDGEGEVTCPWCGNE 114 (131)
T ss_pred eCCCCCEECCCCCCe
Confidence 344445566666654
No 89
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=77.63 E-value=1.3 Score=29.62 Aligned_cols=14 Identities=14% Similarity=0.465 Sum_probs=7.3
Q ss_pred eeccCCCCccCCcc
Q psy3948 45 YACFICTYHTRKHG 58 (143)
Q Consensus 45 ~~c~~c~~~~~~~~ 58 (143)
..||+|+..|..+.
T Consensus 6 ~~CPvC~~~F~~~~ 19 (214)
T PF09986_consen 6 ITCPVCGKEFKTKK 19 (214)
T ss_pred eECCCCCCeeeeeE
Confidence 44555555555443
No 90
>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=77.54 E-value=1.5 Score=25.81 Aligned_cols=29 Identities=17% Similarity=0.452 Sum_probs=20.7
Q ss_pred hcccCCCCCCCCCCcceeccCCCCccCCc
Q psy3948 29 HCKSCKKPKRPDKSYNYACFICTYHTRKH 57 (143)
Q Consensus 29 ~c~~c~~~~~~~~~~~~~c~~c~~~~~~~ 57 (143)
.|+.|...|.......+.|++|+..|...
T Consensus 4 ~CP~C~seytY~dg~~~iCpeC~~EW~~~ 32 (109)
T TIGR00686 4 PCPKCNSEYTYHDGTQLICPSCLYEWNEN 32 (109)
T ss_pred cCCcCCCcceEecCCeeECcccccccccc
Confidence 46667666665566668899998887654
No 91
>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=77.17 E-value=1.2 Score=20.24 Aligned_cols=10 Identities=20% Similarity=0.398 Sum_probs=4.8
Q ss_pred eeccCCCCcc
Q psy3948 45 YACFICTYHT 54 (143)
Q Consensus 45 ~~c~~c~~~~ 54 (143)
..|+.||...
T Consensus 18 irC~~CG~RI 27 (32)
T PF03604_consen 18 IRCPECGHRI 27 (32)
T ss_dssp SSBSSSS-SE
T ss_pred EECCcCCCeE
Confidence 3566665443
No 92
>PRK10220 hypothetical protein; Provisional
Probab=76.91 E-value=2.2 Score=25.22 Aligned_cols=30 Identities=20% Similarity=0.439 Sum_probs=21.5
Q ss_pred hcccCCCCCCCCCCcceeccCCCCccCCcc
Q psy3948 29 HCKSCKKPKRPDKSYNYACFICTYHTRKHG 58 (143)
Q Consensus 29 ~c~~c~~~~~~~~~~~~~c~~c~~~~~~~~ 58 (143)
.|+.|...|.......+.|+.|+..|....
T Consensus 5 ~CP~C~seytY~d~~~~vCpeC~hEW~~~~ 34 (111)
T PRK10220 5 HCPKCNSEYTYEDNGMYICPECAHEWNDAE 34 (111)
T ss_pred cCCCCCCcceEcCCCeEECCcccCcCCccc
Confidence 467777767666666788999888876553
No 93
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=76.25 E-value=0.9 Score=24.84 Aligned_cols=17 Identities=29% Similarity=0.489 Sum_probs=10.2
Q ss_pred CCCceecc--cccccccch
Q psy3948 97 GLKAHKCA--NVIIIAIMY 113 (143)
Q Consensus 97 ~e~~~~C~--~C~~~f~~~ 113 (143)
.++.++|. +||..|+..
T Consensus 24 ~~~Y~qC~N~eCg~tF~t~ 42 (72)
T PRK09678 24 KERYHQCQNVNCSATFITY 42 (72)
T ss_pred heeeeecCCCCCCCEEEEE
Confidence 34556665 677776653
No 94
>PF08790 zf-LYAR: LYAR-type C2HC zinc finger ; InterPro: IPR014898 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This C2HC zinc finger domain is found in LYAR proteins such as Q08288 from SWISSPROT, which are involved in cell growth regulation. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1WJV_A.
Probab=75.73 E-value=0.67 Score=20.31 Aligned_cols=20 Identities=5% Similarity=-0.139 Sum_probs=11.5
Q ss_pred eecccccccccchHHHHHHHH
Q psy3948 101 HKCANVIIIAIMYHILEIMLE 121 (143)
Q Consensus 101 ~~C~~C~~~f~~~s~l~~h~~ 121 (143)
|.|..|++.| .......|.+
T Consensus 1 ~sCiDC~~~F-~~~~y~~Ht~ 20 (28)
T PF08790_consen 1 FSCIDCSKDF-DGDSYKSHTS 20 (28)
T ss_dssp EEETTTTEEE-EGGGTTT---
T ss_pred CeeecCCCCc-CcCCcCCCCc
Confidence 4677888888 4455555544
No 95
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=74.75 E-value=2.5 Score=33.67 Aligned_cols=29 Identities=21% Similarity=0.453 Sum_probs=18.8
Q ss_pred hcCCCCCccCCCCCCCCCChHHHHHHHHHhcCCCceeccccccc
Q psy3948 66 KHTGVKPLKCSSCNYSCSTKSALSVHQKRHTGLKAHKCANVIII 109 (143)
Q Consensus 66 ~~~~~~~~~c~~c~~~f~~~~~l~~h~~~h~~e~~~~C~~C~~~ 109 (143)
.|.......|..|+.. ...|..|+.||..
T Consensus 456 ~H~~~~~L~CH~Cg~~---------------~~~p~~Cp~Cgs~ 484 (730)
T COG1198 456 LHKATGQLRCHYCGYQ---------------EPIPQSCPECGSE 484 (730)
T ss_pred EecCCCeeEeCCCCCC---------------CCCCCCCCCCCCC
Confidence 3444456688888742 2357889988865
No 96
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=72.08 E-value=0.82 Score=28.96 Aligned_cols=13 Identities=23% Similarity=0.488 Sum_probs=7.8
Q ss_pred ccCCCCCCCCCCh
Q psy3948 73 LKCSSCNYSCSTK 85 (143)
Q Consensus 73 ~~c~~c~~~f~~~ 85 (143)
+.|+.|+..|...
T Consensus 29 ~~c~~c~~~f~~~ 41 (154)
T PRK00464 29 RECLACGKRFTTF 41 (154)
T ss_pred eeccccCCcceEe
Confidence 5666666665543
No 97
>PHA00626 hypothetical protein
Probab=71.68 E-value=2.4 Score=21.82 Aligned_cols=16 Identities=6% Similarity=-0.120 Sum_probs=12.8
Q ss_pred CCceecccccccccch
Q psy3948 98 LKAHKCANVIIIAIMY 113 (143)
Q Consensus 98 e~~~~C~~C~~~f~~~ 113 (143)
...|.|+.||+.|+..
T Consensus 21 snrYkCkdCGY~ft~~ 36 (59)
T PHA00626 21 SDDYVCCDCGYNDSKD 36 (59)
T ss_pred CcceEcCCCCCeechh
Confidence 3579999999998854
No 98
>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=71.62 E-value=3.1 Score=26.32 Aligned_cols=17 Identities=18% Similarity=0.429 Sum_probs=11.2
Q ss_pred CCccCCCCCCCCCChHH
Q psy3948 71 KPLKCSSCNYSCSTKSA 87 (143)
Q Consensus 71 ~~~~c~~c~~~f~~~~~ 87 (143)
.|.-|..||+.|.+...
T Consensus 67 ~PsYC~~CGkpyPWt~~ 83 (158)
T PF10083_consen 67 APSYCHNCGKPYPWTEN 83 (158)
T ss_pred CChhHHhCCCCCchHHH
Confidence 56667777777766543
No 99
>PF14353 CpXC: CpXC protein
Probab=70.52 E-value=3.3 Score=25.15 Aligned_cols=11 Identities=27% Similarity=0.703 Sum_probs=8.1
Q ss_pred cCCcchhhhcc
Q psy3948 9 KCTFCNIIFNK 19 (143)
Q Consensus 9 ~C~~C~~~f~~ 19 (143)
.||.|+..|..
T Consensus 3 tCP~C~~~~~~ 13 (128)
T PF14353_consen 3 TCPHCGHEFEF 13 (128)
T ss_pred CCCCCCCeeEE
Confidence 58888888744
No 100
>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=69.15 E-value=5.1 Score=30.55 Aligned_cols=6 Identities=33% Similarity=1.337 Sum_probs=2.5
Q ss_pred cCCCCC
Q psy3948 74 KCSSCN 79 (143)
Q Consensus 74 ~c~~c~ 79 (143)
.|+.|+
T Consensus 255 ~Cp~C~ 260 (505)
T TIGR00595 255 TCPQCG 260 (505)
T ss_pred CCCCCC
Confidence 344443
No 101
>PRK04023 DNA polymerase II large subunit; Validated
Probab=68.39 E-value=6 Score=32.67 Aligned_cols=9 Identities=33% Similarity=0.770 Sum_probs=4.4
Q ss_pred eeccCCCCc
Q psy3948 45 YACFICTYH 53 (143)
Q Consensus 45 ~~c~~c~~~ 53 (143)
+.|+.||..
T Consensus 639 frCP~CG~~ 647 (1121)
T PRK04023 639 RRCPFCGTH 647 (1121)
T ss_pred ccCCCCCCC
Confidence 445555543
No 102
>PF02176 zf-TRAF: TRAF-type zinc finger; PDB: 2EOD_A 2YUC_A 3HCU_A 3HCS_B 3HCT_A.
Probab=68.00 E-value=4 Score=20.95 Aligned_cols=25 Identities=12% Similarity=0.066 Sum_probs=10.8
Q ss_pred HHHHHHHHhcCCCceeccc----cccccc
Q psy3948 87 ALSVHQKRHTGLKAHKCAN----VIIIAI 111 (143)
Q Consensus 87 ~l~~h~~~h~~e~~~~C~~----C~~~f~ 111 (143)
.|..|....-..++..|+. |+..+.
T Consensus 25 ~l~~H~~~~C~~~~v~C~~~~~GC~~~~~ 53 (60)
T PF02176_consen 25 ELDDHLENECPKRPVPCPYSPYGCKERVP 53 (60)
T ss_dssp CHHHHHHTTSTTSEEE-SS----S--EEE
T ss_pred HHHHHHHccCCCCcEECCCCCCCCCCccc
Confidence 4455554333344555655 555544
No 103
>COG3364 Zn-ribbon containing protein [General function prediction only]
Probab=67.45 E-value=2.9 Score=24.39 Aligned_cols=27 Identities=26% Similarity=0.626 Sum_probs=17.6
Q ss_pred cccCCcchhhhccchhhHHHhhhcccCCC
Q psy3948 7 ILKCTFCNIIFNKLQDEELIMTHCKSCKK 35 (143)
Q Consensus 7 ~~~C~~C~~~f~~~~~~~~~~~~c~~c~~ 35 (143)
++.|..||.+|..-+..+ ..-|+.|+.
T Consensus 2 pH~CtrCG~vf~~g~~~i--l~GCp~CG~ 28 (112)
T COG3364 2 PHQCTRCGEVFDDGSEEI--LSGCPKCGC 28 (112)
T ss_pred CceecccccccccccHHH--HccCccccc
Confidence 789999999996643322 223777763
No 104
>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=67.26 E-value=5.9 Score=25.19 Aligned_cols=32 Identities=9% Similarity=0.126 Sum_probs=20.7
Q ss_pred CCCccCCCCCCCCCChHHHHHHHHHhcCCCceecccccccc
Q psy3948 70 VKPLKCSSCNYSCSTKSALSVHQKRHTGLKAHKCANVIIIA 110 (143)
Q Consensus 70 ~~~~~c~~c~~~f~~~~~l~~h~~~h~~e~~~~C~~C~~~f 110 (143)
..-|.|+.|+..|+...++. .-|.|+.||...
T Consensus 107 ~~~Y~Cp~c~~r~tf~eA~~---------~~F~Cp~Cg~~L 138 (158)
T TIGR00373 107 NMFFICPNMCVRFTFNEAME---------LNFTCPRCGAML 138 (158)
T ss_pred CCeEECCCCCcEeeHHHHHH---------cCCcCCCCCCEe
Confidence 34467777777776666553 247788887663
No 105
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=66.95 E-value=6.7 Score=27.85 Aligned_cols=25 Identities=16% Similarity=0.478 Sum_probs=19.5
Q ss_pred CCccCCCCCCCCCChHHHHHHHHHh
Q psy3948 71 KPLKCSSCNYSCSTKSALSVHQKRH 95 (143)
Q Consensus 71 ~~~~c~~c~~~f~~~~~l~~h~~~h 95 (143)
..|.|+.|...|...-....|...|
T Consensus 387 ~rY~Ce~CK~~FC~dCdvfiHe~Lh 411 (421)
T COG5151 387 GRYQCELCKSTFCSDCDVFIHETLH 411 (421)
T ss_pred cceechhhhhhhhhhhHHHHHHHHh
Confidence 4578888888888888777777665
No 106
>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=65.59 E-value=1.7 Score=22.05 Aligned_cols=24 Identities=25% Similarity=0.332 Sum_probs=10.5
Q ss_pred cceeccCCCCccCCcchHHHhhhh
Q psy3948 43 YNYACFICTYHTRKHGDMIGHMRK 66 (143)
Q Consensus 43 ~~~~c~~c~~~~~~~~~l~~h~~~ 66 (143)
..|.|+.|...|-..-.+..|...
T Consensus 20 ~~y~C~~C~~~FC~dCD~fiHE~L 43 (51)
T PF07975_consen 20 SRYRCPKCKNHFCIDCDVFIHETL 43 (51)
T ss_dssp EEE--TTTT--B-HHHHHTTTTTS
T ss_pred CeEECCCCCCccccCcChhhhccc
Confidence 346677776666655555555433
No 107
>PF05290 Baculo_IE-1: Baculovirus immediate-early protein (IE-0); InterPro: IPR007954 This entry contains the Baculovirus immediate-early protein IE-0.
Probab=64.53 E-value=3 Score=25.65 Aligned_cols=56 Identities=21% Similarity=0.314 Sum_probs=32.6
Q ss_pred cceeccCCCCccCCcchHHHhhhhcCCCCCccCCCCCCCCCCh--HHHHHHHHHhcCCCceecccccccccchHH
Q psy3948 43 YNYACFICTYHTRKHGDMIGHMRKHTGVKPLKCSSCNYSCSTK--SALSVHQKRHTGLKAHKCANVIIIAIMYHI 115 (143)
Q Consensus 43 ~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~c~~c~~~f~~~--~~l~~h~~~h~~e~~~~C~~C~~~f~~~s~ 115 (143)
+.|+|.+|..++..+..| +|=+| ||...... ..|+.|-.+|. .|+.|.-+|.+++.
T Consensus 79 ~lYeCnIC~etS~ee~FL----------KPneC--CgY~iCn~Cya~LWK~~~~yp-----vCPvCkTSFKss~~ 136 (140)
T PF05290_consen 79 KLYECNICKETSAEERFL----------KPNEC--CGYSICNACYANLWKFCNLYP-----VCPVCKTSFKSSSS 136 (140)
T ss_pred CceeccCcccccchhhcC----------Ccccc--cchHHHHHHHHHHHHHcccCC-----CCCccccccccccc
Confidence 779999998776654322 23233 33221111 34555554443 69999999887653
No 108
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=64.37 E-value=2.4 Score=20.07 Aligned_cols=14 Identities=29% Similarity=0.598 Sum_probs=10.0
Q ss_pred cccCCcchhhhccc
Q psy3948 7 ILKCTFCNIIFNKL 20 (143)
Q Consensus 7 ~~~C~~C~~~f~~~ 20 (143)
+++|.+|+++|-..
T Consensus 12 ~f~C~~C~~~FC~~ 25 (39)
T smart00154 12 GFKCRHCGNLFCGE 25 (39)
T ss_pred CeECCccCCccccc
Confidence 67788888887433
No 109
>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=63.52 E-value=8.2 Score=17.61 Aligned_cols=23 Identities=17% Similarity=0.041 Sum_probs=15.9
Q ss_pred ceecccccccccchHHHHHHHHHH
Q psy3948 100 AHKCANVIIIAIMYHILEIMLEDI 123 (143)
Q Consensus 100 ~~~C~~C~~~f~~~s~l~~h~~~~ 123 (143)
.+.|+.|++... .+-+..|+..-
T Consensus 4 ~~~C~nC~R~v~-a~RfA~HLekC 26 (33)
T PF08209_consen 4 YVECPNCGRPVA-ASRFAPHLEKC 26 (33)
T ss_dssp EEE-TTTSSEEE-GGGHHHHHHHH
T ss_pred eEECCCCcCCcc-hhhhHHHHHHH
Confidence 468999998655 56688887754
No 110
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=63.45 E-value=2.6 Score=30.31 Aligned_cols=23 Identities=13% Similarity=-0.142 Sum_probs=13.2
Q ss_pred ecccccccccchHHHHHHHHHHh
Q psy3948 102 KCANVIIIAIMYHILEIMLEDIQ 124 (143)
Q Consensus 102 ~C~~C~~~f~~~s~l~~h~~~~~ 124 (143)
.|..|...|-+...|.+|.+..|
T Consensus 222 ~C~FC~~~FYdDDEL~~HcR~~H 244 (493)
T COG5236 222 LCIFCKIYFYDDDELRRHCRLRH 244 (493)
T ss_pred hhhhccceecChHHHHHHHHhhh
Confidence 35556666666666666655443
No 111
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=62.65 E-value=4.8 Score=24.08 Aligned_cols=6 Identities=33% Similarity=0.910 Sum_probs=2.7
Q ss_pred eccCCC
Q psy3948 46 ACFICT 51 (143)
Q Consensus 46 ~c~~c~ 51 (143)
.||.||
T Consensus 89 ~CP~Cg 94 (114)
T PRK03681 89 RCPQCH 94 (114)
T ss_pred cCcCcC
Confidence 344444
No 112
>PRK14873 primosome assembly protein PriA; Provisional
Probab=62.54 E-value=6.9 Score=31.00 Aligned_cols=10 Identities=20% Similarity=0.783 Sum_probs=6.1
Q ss_pred CccCCCCCCC
Q psy3948 72 PLKCSSCNYS 81 (143)
Q Consensus 72 ~~~c~~c~~~ 81 (143)
|..|+.|+..
T Consensus 422 p~~Cp~Cgs~ 431 (665)
T PRK14873 422 DWRCPRCGSD 431 (665)
T ss_pred CccCCCCcCC
Confidence 4567777643
No 113
>PRK00420 hypothetical protein; Validated
Probab=62.05 E-value=7.4 Score=23.28 Aligned_cols=27 Identities=22% Similarity=0.268 Sum_probs=17.2
Q ss_pred hcccCCCCCCCCCCcceeccCCCCccC
Q psy3948 29 HCKSCKKPKRPDKSYNYACFICTYHTR 55 (143)
Q Consensus 29 ~c~~c~~~~~~~~~~~~~c~~c~~~~~ 55 (143)
.|+.|+.++..-.+....|+.||....
T Consensus 25 ~CP~Cg~pLf~lk~g~~~Cp~Cg~~~~ 51 (112)
T PRK00420 25 HCPVCGLPLFELKDGEVVCPVHGKVYI 51 (112)
T ss_pred CCCCCCCcceecCCCceECCCCCCeee
Confidence 688888666432444556888887544
No 114
>KOG2593|consensus
Probab=61.27 E-value=6.9 Score=29.03 Aligned_cols=19 Identities=16% Similarity=0.391 Sum_probs=13.0
Q ss_pred CCccccCCcchhhhccchh
Q psy3948 4 DHTILKCTFCNIIFNKLQD 22 (143)
Q Consensus 4 ~~~~~~C~~C~~~f~~~~~ 22 (143)
...-|.|+.|++.|..+.-
T Consensus 125 ~~~~Y~Cp~C~kkyt~Lea 143 (436)
T KOG2593|consen 125 NVAGYVCPNCQKKYTSLEA 143 (436)
T ss_pred ccccccCCccccchhhhHH
Confidence 4456778888877766655
No 115
>KOG3408|consensus
Probab=60.88 E-value=6.8 Score=23.69 Aligned_cols=22 Identities=14% Similarity=0.125 Sum_probs=19.6
Q ss_pred ceecccccccccchHHHHHHHH
Q psy3948 100 AHKCANVIIIAIMYHILEIMLE 121 (143)
Q Consensus 100 ~~~C~~C~~~f~~~s~l~~h~~ 121 (143)
.|-|..|.+.|.+...|..|.+
T Consensus 57 qfyCi~CaRyFi~~~~l~~H~k 78 (129)
T KOG3408|consen 57 QFYCIECARYFIDAKALKTHFK 78 (129)
T ss_pred eeehhhhhhhhcchHHHHHHHh
Confidence 4789999999999999999966
No 116
>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=60.00 E-value=5.4 Score=18.21 Aligned_cols=9 Identities=33% Similarity=1.147 Sum_probs=4.3
Q ss_pred eeccCCCCc
Q psy3948 45 YACFICTYH 53 (143)
Q Consensus 45 ~~c~~c~~~ 53 (143)
+.|..||..
T Consensus 3 ~~C~~CG~i 11 (34)
T cd00729 3 WVCPVCGYI 11 (34)
T ss_pred EECCCCCCE
Confidence 445555543
No 117
>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=59.86 E-value=1.1 Score=21.58 Aligned_cols=10 Identities=20% Similarity=0.404 Sum_probs=5.4
Q ss_pred eeccCCCCcc
Q psy3948 45 YACFICTYHT 54 (143)
Q Consensus 45 ~~c~~c~~~~ 54 (143)
+.|..||...
T Consensus 20 ~vC~~CG~Vl 29 (43)
T PF08271_consen 20 LVCPNCGLVL 29 (43)
T ss_dssp EEETTT-BBE
T ss_pred EECCCCCCEe
Confidence 4677776543
No 118
>PF12907 zf-met2: Zinc-binding
Probab=59.79 E-value=5.5 Score=19.06 Aligned_cols=27 Identities=11% Similarity=0.012 Sum_probs=18.6
Q ss_pred eecccccccccc---hHHHHHHHHHHhcCC
Q psy3948 101 HKCANVIIIAIM---YHILEIMLEDIQGRD 127 (143)
Q Consensus 101 ~~C~~C~~~f~~---~s~l~~h~~~~~~~~ 127 (143)
+.|..|...|.. ...|..|....|.+.
T Consensus 2 i~C~iC~qtF~~t~~~~~L~eH~enKHpK~ 31 (40)
T PF12907_consen 2 IICKICRQTFMQTTNEPQLKEHAENKHPKN 31 (40)
T ss_pred cCcHHhhHHHHhcCCHHHHHHHHHccCCCC
Confidence 568888865544 567888888666554
No 119
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=59.32 E-value=8.8 Score=19.31 Aligned_cols=7 Identities=29% Similarity=1.132 Sum_probs=3.6
Q ss_pred ccCCCCC
Q psy3948 73 LKCSSCN 79 (143)
Q Consensus 73 ~~c~~c~ 79 (143)
+.|..|+
T Consensus 38 ~~C~~Cg 44 (50)
T PRK00432 38 WHCGKCG 44 (50)
T ss_pred EECCCcC
Confidence 4555554
No 120
>PF12773 DZR: Double zinc ribbon
Probab=58.85 E-value=7.7 Score=19.13 Aligned_cols=6 Identities=33% Similarity=0.778 Sum_probs=2.3
Q ss_pred ccCCCC
Q psy3948 47 CFICTY 52 (143)
Q Consensus 47 c~~c~~ 52 (143)
|+.||.
T Consensus 15 C~~CG~ 20 (50)
T PF12773_consen 15 CPHCGT 20 (50)
T ss_pred ChhhcC
Confidence 334443
No 121
>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=58.81 E-value=9.2 Score=28.87 Aligned_cols=26 Identities=8% Similarity=-0.164 Sum_probs=22.7
Q ss_pred ceecccccccccchHHHHHHHHHHhc
Q psy3948 100 AHKCANVIIIAIMYHILEIMLEDIQG 125 (143)
Q Consensus 100 ~~~C~~C~~~f~~~s~l~~h~~~~~~ 125 (143)
-|.|+.|.+.|.+...+..|+...|-
T Consensus 57 FWiCp~CskkF~d~~~~~~H~~~eH~ 82 (466)
T PF04780_consen 57 FWICPRCSKKFSDAESCLSHMEQEHP 82 (466)
T ss_pred EeeCCcccceeCCHHHHHHHHHHhhh
Confidence 46899999999999999999986663
No 122
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=58.13 E-value=6.7 Score=23.60 Aligned_cols=10 Identities=20% Similarity=0.368 Sum_probs=4.6
Q ss_pred eeccCCCCcc
Q psy3948 45 YACFICTYHT 54 (143)
Q Consensus 45 ~~c~~c~~~~ 54 (143)
+.|..||..|
T Consensus 72 ~~C~~Cg~~~ 81 (117)
T PRK00564 72 LECKDCSHVF 81 (117)
T ss_pred EEhhhCCCcc
Confidence 4455555333
No 123
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=58.05 E-value=19 Score=26.11 Aligned_cols=75 Identities=13% Similarity=0.123 Sum_probs=43.7
Q ss_pred eccCCCCccCCcchHHHhhhhcCCCCCccCCCCCC----CCCChHHHHHHHHHhcCCCceeccc--cc----ccccchHH
Q psy3948 46 ACFICTYHTRKHGDMIGHMRKHTGVKPLKCSSCNY----SCSTKSALSVHQKRHTGLKAHKCAN--VI----IIAIMYHI 115 (143)
Q Consensus 46 ~c~~c~~~~~~~~~l~~h~~~~~~~~~~~c~~c~~----~f~~~~~l~~h~~~h~~e~~~~C~~--C~----~~f~~~s~ 115 (143)
.|..|...|-.-..|..|.+.. .++-+.|.+-+. -|..-..|..|-+. -.|.|.. |. +.|.+...
T Consensus 222 ~C~FC~~~FYdDDEL~~HcR~~-HE~ChICD~v~p~~~QYFK~Y~~Le~HF~~----~hy~ct~qtc~~~k~~vf~~~~e 296 (493)
T COG5236 222 LCIFCKIYFYDDDELRRHCRLR-HEACHICDMVGPIRYQYFKSYEDLEAHFRN----AHYCCTFQTCRVGKCYVFPYHTE 296 (493)
T ss_pred hhhhccceecChHHHHHHHHhh-hhhhhhhhccCccchhhhhCHHHHHHHhhc----CceEEEEEEEecCcEEEeccHHH
Confidence 4777777777777777776642 233344444332 24555566666542 1355543 22 35778888
Q ss_pred HHHHHHHHhc
Q psy3948 116 LEIMLEDIQG 125 (143)
Q Consensus 116 l~~h~~~~~~ 125 (143)
|..|+..-|+
T Consensus 297 l~~h~~~~h~ 306 (493)
T COG5236 297 LLEHLTRFHK 306 (493)
T ss_pred HHHHHHHHhh
Confidence 8888776664
No 124
>COG4530 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=57.72 E-value=6.9 Score=23.22 Aligned_cols=26 Identities=4% Similarity=-0.345 Sum_probs=12.8
Q ss_pred cccCCCCCCCCCCcceeccCCCCccC
Q psy3948 30 CKSCKKPKRPDKSYNYACFICTYHTR 55 (143)
Q Consensus 30 c~~c~~~~~~~~~~~~~c~~c~~~~~ 55 (143)
|+.|++.|---...|..|+.||++|+
T Consensus 12 dPetg~KFYDLNrdPiVsPytG~s~P 37 (129)
T COG4530 12 DPETGKKFYDLNRDPIVSPYTGKSYP 37 (129)
T ss_pred CccccchhhccCCCccccCcccccch
Confidence 44444444322234455666666664
No 125
>PRK05580 primosome assembly protein PriA; Validated
Probab=57.64 E-value=11 Score=30.02 Aligned_cols=6 Identities=33% Similarity=1.309 Sum_probs=2.4
Q ss_pred cCCCCC
Q psy3948 74 KCSSCN 79 (143)
Q Consensus 74 ~c~~c~ 79 (143)
.|+.|+
T Consensus 423 ~Cp~Cg 428 (679)
T PRK05580 423 ACPECG 428 (679)
T ss_pred CCCCCc
Confidence 344443
No 126
>KOG0978|consensus
Probab=57.48 E-value=1.6 Score=34.37 Aligned_cols=12 Identities=33% Similarity=0.844 Sum_probs=6.5
Q ss_pred cCCCCCCCCCCh
Q psy3948 74 KCSSCNYSCSTK 85 (143)
Q Consensus 74 ~c~~c~~~f~~~ 85 (143)
.||.|+.+|..-
T Consensus 680 KCP~Cn~aFgan 691 (698)
T KOG0978|consen 680 KCPKCNAAFGAN 691 (698)
T ss_pred CCCCCCCCCCcc
Confidence 455665555443
No 127
>KOG2785|consensus
Probab=56.63 E-value=13 Score=27.22 Aligned_cols=27 Identities=11% Similarity=-0.100 Sum_probs=22.0
Q ss_pred CCCceecccccccccchHHHHHHHHHH
Q psy3948 97 GLKAHKCANVIIIAIMYHILEIMLEDI 123 (143)
Q Consensus 97 ~e~~~~C~~C~~~f~~~s~l~~h~~~~ 123 (143)
++-++.|..|.+.|.+......|++..
T Consensus 65 ~~~~~~c~~c~k~~~s~~a~~~hl~Sk 91 (390)
T KOG2785|consen 65 AESVVYCEACNKSFASPKAHENHLKSK 91 (390)
T ss_pred cccceehHHhhccccChhhHHHHHHHh
Confidence 445788999999999999888887743
No 128
>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=56.56 E-value=1.9 Score=22.16 Aligned_cols=10 Identities=20% Similarity=0.657 Sum_probs=6.5
Q ss_pred ccCCcchhhh
Q psy3948 8 LKCTFCNIIF 17 (143)
Q Consensus 8 ~~C~~C~~~f 17 (143)
++|+.||..+
T Consensus 3 ~~CP~CG~~i 12 (54)
T TIGR01206 3 FECPDCGAEI 12 (54)
T ss_pred cCCCCCCCEE
Confidence 4677777754
No 129
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=55.62 E-value=1.2 Score=21.20 Aligned_cols=11 Identities=9% Similarity=-0.179 Sum_probs=6.7
Q ss_pred ceecccccccc
Q psy3948 100 AHKCANVIIIA 110 (143)
Q Consensus 100 ~~~C~~C~~~f 110 (143)
-|.|..|+..+
T Consensus 28 fy~C~~C~~~w 38 (40)
T smart00440 28 FYVCTKCGHRW 38 (40)
T ss_pred EEEeCCCCCEe
Confidence 36666666554
No 130
>PRK11823 DNA repair protein RadA; Provisional
Probab=55.61 E-value=6.7 Score=29.41 Aligned_cols=32 Identities=22% Similarity=0.335 Sum_probs=23.2
Q ss_pred CCCCCccccCCcchhhhccchhhHHHhhhcccCCCCCC
Q psy3948 1 MFVDHTILKCTFCNIIFNKLQDEELIMTHCKSCKKPKR 38 (143)
Q Consensus 1 ~~~~~~~~~C~~C~~~f~~~~~~~~~~~~c~~c~~~~~ 38 (143)
|-..+..|.|..||-.+.+... .|+.|+.+-.
T Consensus 1 m~~~~~~y~C~~Cg~~~~~~~g------~Cp~C~~w~t 32 (446)
T PRK11823 1 MAKKKTAYVCQECGAESPKWLG------RCPECGAWNT 32 (446)
T ss_pred CCCCCCeEECCcCCCCCcccCe------eCcCCCCccc
Confidence 4445678999999998755544 4999987654
No 131
>KOG2907|consensus
Probab=55.43 E-value=6.5 Score=23.45 Aligned_cols=39 Identities=15% Similarity=0.245 Sum_probs=21.9
Q ss_pred CccCCCCCCCCCChHHHHHHHHH-hcCC-Cceecccccccccc
Q psy3948 72 PLKCSSCNYSCSTKSALSVHQKR-HTGL-KAHKCANVIIIAIM 112 (143)
Q Consensus 72 ~~~c~~c~~~f~~~~~l~~h~~~-h~~e-~~~~C~~C~~~f~~ 112 (143)
...|+.|+..=..-..++. |+ -.|+ .-|.|+.|++.|+.
T Consensus 74 ~~kCpkCghe~m~Y~T~Ql--RSADEGQTVFYTC~kC~~k~~e 114 (116)
T KOG2907|consen 74 KHKCPKCGHEEMSYHTLQL--RSADEGQTVFYTCPKCKYKFTE 114 (116)
T ss_pred hccCcccCCchhhhhhhhc--ccccCCceEEEEcCccceeeec
Confidence 3578888854222222221 22 1222 35899999998874
No 132
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=55.37 E-value=11 Score=15.50 Aligned_cols=6 Identities=33% Similarity=0.744 Sum_probs=2.8
Q ss_pred ccCCCC
Q psy3948 47 CFICTY 52 (143)
Q Consensus 47 c~~c~~ 52 (143)
|+.||.
T Consensus 16 C~~CG~ 21 (23)
T PF13240_consen 16 CPNCGT 21 (23)
T ss_pred hhhhCC
Confidence 444443
No 133
>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=52.11 E-value=4.6 Score=19.34 Aligned_cols=11 Identities=18% Similarity=0.854 Sum_probs=6.6
Q ss_pred cccCCcchhhh
Q psy3948 7 ILKCTFCNIIF 17 (143)
Q Consensus 7 ~~~C~~C~~~f 17 (143)
+-.|++|+..|
T Consensus 29 ~~~CpYCg~~y 39 (40)
T PF10276_consen 29 PVVCPYCGTRY 39 (40)
T ss_dssp EEEETTTTEEE
T ss_pred eEECCCCCCEE
Confidence 45666666654
No 134
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=51.62 E-value=8.1 Score=22.13 Aligned_cols=32 Identities=9% Similarity=0.190 Sum_probs=19.0
Q ss_pred CccCCCCCCCCCChHHHHHHHHHhcCCCceecccccccccch
Q psy3948 72 PLKCSSCNYSCSTKSALSVHQKRHTGLKAHKCANVIIIAIMY 113 (143)
Q Consensus 72 ~~~c~~c~~~f~~~~~l~~h~~~h~~e~~~~C~~C~~~f~~~ 113 (143)
.|.|+.|++.-.. +.. .-.|.|..|++.|..-
T Consensus 36 ~y~CpfCgk~~vk--------R~a--~GIW~C~~C~~~~AGG 67 (90)
T PTZ00255 36 KYFCPFCGKHAVK--------RQA--VGIWRCKGCKKTVAGG 67 (90)
T ss_pred CccCCCCCCCcee--------eee--eEEEEcCCCCCEEeCC
Confidence 5778888643111 122 2368888888887653
No 135
>PRK12496 hypothetical protein; Provisional
Probab=51.09 E-value=12 Score=24.07 Aligned_cols=8 Identities=63% Similarity=1.261 Sum_probs=3.9
Q ss_pred cccCCCCC
Q psy3948 30 CKSCKKPK 37 (143)
Q Consensus 30 c~~c~~~~ 37 (143)
|+.|++.|
T Consensus 130 C~gC~~~~ 137 (164)
T PRK12496 130 CKGCKKKY 137 (164)
T ss_pred CCCCCccc
Confidence 44454444
No 136
>COG1773 Rubredoxin [Energy production and conversion]
Probab=50.77 E-value=8.2 Score=19.89 Aligned_cols=12 Identities=8% Similarity=0.102 Sum_probs=8.7
Q ss_pred ceeccccccccc
Q psy3948 100 AHKCANVIIIAI 111 (143)
Q Consensus 100 ~~~C~~C~~~f~ 111 (143)
.|+|..||.+|-
T Consensus 3 ~~~C~~CG~vYd 14 (55)
T COG1773 3 RWRCSVCGYVYD 14 (55)
T ss_pred ceEecCCceEec
Confidence 577888887764
No 137
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=49.83 E-value=8.9 Score=23.72 Aligned_cols=15 Identities=13% Similarity=0.111 Sum_probs=10.1
Q ss_pred cceeccCCCCccCCc
Q psy3948 43 YNYACFICTYHTRKH 57 (143)
Q Consensus 43 ~~~~c~~c~~~~~~~ 57 (143)
..+.|..||..|...
T Consensus 69 ~~~~C~~CG~~~~~~ 83 (135)
T PRK03824 69 AVLKCRNCGNEWSLK 83 (135)
T ss_pred eEEECCCCCCEEecc
Confidence 447788888776543
No 138
>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=49.49 E-value=8.9 Score=20.34 Aligned_cols=27 Identities=19% Similarity=0.194 Sum_probs=8.9
Q ss_pred cccCCCCCCCCCCcceeccCCCCccCCc
Q psy3948 30 CKSCKKPKRPDKSYNYACFICTYHTRKH 57 (143)
Q Consensus 30 c~~c~~~~~~~~~~~~~c~~c~~~~~~~ 57 (143)
|..|++.|. ...+.+.|..||..+-..
T Consensus 12 C~~C~~~F~-~~~rrhhCr~CG~~vC~~ 38 (69)
T PF01363_consen 12 CMICGKKFS-LFRRRHHCRNCGRVVCSS 38 (69)
T ss_dssp -TTT--B-B-SSS-EEE-TTT--EEECC
T ss_pred CcCcCCcCC-CceeeEccCCCCCEECCc
Confidence 455555552 223345566666655433
No 139
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=49.27 E-value=14 Score=15.52 Aligned_cols=6 Identities=33% Similarity=0.728 Sum_probs=2.7
Q ss_pred ccCCCC
Q psy3948 47 CFICTY 52 (143)
Q Consensus 47 c~~c~~ 52 (143)
|+.||.
T Consensus 19 C~~CG~ 24 (26)
T PF13248_consen 19 CPNCGA 24 (26)
T ss_pred ChhhCC
Confidence 444443
No 140
>KOG4167|consensus
Probab=49.11 E-value=6.8 Score=31.16 Aligned_cols=28 Identities=4% Similarity=0.065 Sum_probs=24.6
Q ss_pred ceecccccccccchHHHHHHHHHHhcCC
Q psy3948 100 AHKCANVIIIAIMYHILEIMLEDIQGRD 127 (143)
Q Consensus 100 ~~~C~~C~~~f~~~s~l~~h~~~~~~~~ 127 (143)
.|.|.+|++.|-.-..+.-|++.|.-+.
T Consensus 792 iFpCreC~kvF~KiKSrNAHMK~Hr~q~ 819 (907)
T KOG4167|consen 792 IFPCRECGKVFFKIKSRNAHMKTHRQQE 819 (907)
T ss_pred eeehHHHHHHHHHHhhhhHHHHHHHHHH
Confidence 5899999999999889999999888554
No 141
>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=49.00 E-value=11 Score=22.01 Aligned_cols=18 Identities=17% Similarity=0.357 Sum_probs=14.0
Q ss_pred HhcCCCceecccccccccc
Q psy3948 94 RHTGLKAHKCANVIIIAIM 112 (143)
Q Consensus 94 ~h~~e~~~~C~~C~~~f~~ 112 (143)
.+.+ +|+.|.+||..|..
T Consensus 74 l~~g-~~~rC~eCG~~fkL 91 (97)
T cd00924 74 LEKG-KPKRCPECGHVFKL 91 (97)
T ss_pred EeCC-CceeCCCCCcEEEE
Confidence 4445 68999999999875
No 142
>PLN03238 probable histone acetyltransferase MYST; Provisional
Probab=48.96 E-value=19 Score=25.40 Aligned_cols=28 Identities=14% Similarity=-0.045 Sum_probs=23.7
Q ss_pred CCceecccccccccchHHHHHHHHHHhc
Q psy3948 98 LKAHKCANVIIIAIMYHILEIMLEDIQG 125 (143)
Q Consensus 98 e~~~~C~~C~~~f~~~s~l~~h~~~~~~ 125 (143)
..-|.|..|-+-|.+...|.+|+....-
T Consensus 46 ~~lyiCe~Clky~~~~~~l~~H~~~C~~ 73 (290)
T PLN03238 46 TKLYICEYCLKYMRKKKSLLRHLAKCDI 73 (290)
T ss_pred CeEEEcCCCcchhCCHHHHHHHHHhCCC
Confidence 4579999999999999999999886553
No 143
>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=48.61 E-value=3 Score=32.89 Aligned_cols=76 Identities=16% Similarity=0.315 Sum_probs=42.7
Q ss_pred hcccCCCCCCCCCC----ccee-ccCCCCccCCcchHHHhhhhcCCCCCc-cCCCCCCCCCChHHHHHHHHHhcCCCcee
Q psy3948 29 HCKSCKKPKRPDKS----YNYA-CFICTYHTRKHGDMIGHMRKHTGVKPL-KCSSCNYSCSTKSALSVHQKRHTGLKAHK 102 (143)
Q Consensus 29 ~c~~c~~~~~~~~~----~~~~-c~~c~~~~~~~~~l~~h~~~~~~~~~~-~c~~c~~~f~~~~~l~~h~~~h~~e~~~~ 102 (143)
.|+.|.+......+ +||. |..||.+|.....+--. |.++.-.+| .|+.|.+.|....+ +|.|. .|..
T Consensus 103 ~C~~Cl~Ei~dp~~rrY~YPF~~CT~CGPRfTIi~alPYD-R~nTsM~~F~lC~~C~~EY~dP~n----RRfHA--Qp~a 175 (750)
T COG0068 103 TCEDCLEEIFDPNSRRYLYPFINCTNCGPRFTIIEALPYD-RENTSMADFPLCPFCDKEYKDPLN----RRFHA--QPIA 175 (750)
T ss_pred hhHHHHHHhcCCCCcceeccccccCCCCcceeeeccCCCC-cccCccccCcCCHHHHHHhcCccc----ccccc--cccc
Confidence 46666543322221 2333 88888888766555332 334444555 47777766655543 23343 3678
Q ss_pred ccccccccc
Q psy3948 103 CANVIIIAI 111 (143)
Q Consensus 103 C~~C~~~f~ 111 (143)
|+.||-...
T Consensus 176 Cp~CGP~~~ 184 (750)
T COG0068 176 CPKCGPHLF 184 (750)
T ss_pred CcccCCCeE
Confidence 888887433
No 144
>COG4957 Predicted transcriptional regulator [Transcription]
Probab=47.85 E-value=11 Score=23.31 Aligned_cols=25 Identities=16% Similarity=-0.079 Sum_probs=20.5
Q ss_pred eecccccccccchHHHHHHHHHHhcCCC
Q psy3948 101 HKCANVIIIAIMYHILEIMLEDIQGRDH 128 (143)
Q Consensus 101 ~~C~~C~~~f~~~s~l~~h~~~~~~~~~ 128 (143)
..|-++|+.|. .|++|+.+|.+-.|
T Consensus 77 IicLEDGkkfK---SLKRHL~t~~gmTP 101 (148)
T COG4957 77 IICLEDGKKFK---SLKRHLTTHYGLTP 101 (148)
T ss_pred EEEeccCcchH---HHHHHHhcccCCCH
Confidence 57999999987 48999999887655
No 145
>PLN02294 cytochrome c oxidase subunit Vb
Probab=47.29 E-value=11 Score=24.27 Aligned_cols=16 Identities=13% Similarity=0.054 Sum_probs=13.2
Q ss_pred CCceecccccccccch
Q psy3948 98 LKAHKCANVIIIAIMY 113 (143)
Q Consensus 98 e~~~~C~~C~~~f~~~ 113 (143)
.+|+.|++||..|...
T Consensus 139 Gkp~RCpeCG~~fkL~ 154 (174)
T PLN02294 139 GKSFECPVCTQYFELE 154 (174)
T ss_pred CCceeCCCCCCEEEEE
Confidence 3688999999999754
No 146
>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=47.26 E-value=8.8 Score=18.46 Aligned_cols=15 Identities=13% Similarity=0.058 Sum_probs=9.5
Q ss_pred Cceecccccccccch
Q psy3948 99 KAHKCANVIIIAIMY 113 (143)
Q Consensus 99 ~~~~C~~C~~~f~~~ 113 (143)
.|+.|..|+..|=..
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 478999999988754
No 147
>PF04216 FdhE: Protein involved in formate dehydrogenase formation; InterPro: IPR006452 This family of sequences describe an accessory protein required for the assembly of formate dehydrogenase of certain proteobacteria although not present in the final complex []. The exact nature of the function of FdhE in the assembly of the complex is unknown, but considering the presence of selenocysteine, molybdopterin, iron-sulphur clusters and cytochrome b556, it is likely to be involved in the insertion of cofactors. ; GO: 0005737 cytoplasm; PDB: 2FIY_B.
Probab=47.05 E-value=4.1 Score=28.58 Aligned_cols=69 Identities=16% Similarity=0.292 Sum_probs=25.7
Q ss_pred hcccCCCCCC------CC--CCcceeccCCCCccCCcchHHHhhhhcCCCCCccCCCCCCCCCChHHHHHHHHHhcCCCc
Q psy3948 29 HCKSCKKPKR------PD--KSYNYACFICTYHTRKHGDMIGHMRKHTGVKPLKCSSCNYSCSTKSALSVHQKRHTGLKA 100 (143)
Q Consensus 29 ~c~~c~~~~~------~~--~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~c~~c~~~f~~~~~l~~h~~~h~~e~~ 100 (143)
.|+.||.... .. +.+-..|..|+..+... ...|+.|+..-...-.... ..--.+.+.
T Consensus 174 ~CPvCGs~P~~s~l~~~~~~G~R~L~Cs~C~t~W~~~--------------R~~Cp~Cg~~~~~~l~~~~-~e~~~~~rv 238 (290)
T PF04216_consen 174 YCPVCGSPPVLSVLRGGEREGKRYLHCSLCGTEWRFV--------------RIKCPYCGNTDHEKLEYFT-VEGEPAYRV 238 (290)
T ss_dssp S-TTT---EEEEEEE------EEEEEETTT--EEE----------------TTS-TTT---SS-EEE---------SEEE
T ss_pred cCCCCCCcCceEEEecCCCCccEEEEcCCCCCeeeec--------------CCCCcCCCCCCCcceeeEe-cCCCCcEEE
Confidence 4666665443 11 23445577776554432 2468888754222211100 011123456
Q ss_pred eecccccccccc
Q psy3948 101 HKCANVIIIAIM 112 (143)
Q Consensus 101 ~~C~~C~~~f~~ 112 (143)
+.|..|+...+.
T Consensus 239 e~C~~C~~YlK~ 250 (290)
T PF04216_consen 239 EVCESCGSYLKT 250 (290)
T ss_dssp EEETTTTEEEEE
T ss_pred EECCcccchHHH
Confidence 788888866544
No 148
>KOG2785|consensus
Probab=46.91 E-value=41 Score=24.74 Aligned_cols=59 Identities=10% Similarity=0.082 Sum_probs=45.1
Q ss_pred CCccCCCCCCCCCChHHHHHHHHHhcCC-----------------------Cceeccccc---ccccchHHHHHHHH-HH
Q psy3948 71 KPLKCSSCNYSCSTKSALSVHQKRHTGL-----------------------KAHKCANVI---IIAIMYHILEIMLE-DI 123 (143)
Q Consensus 71 ~~~~c~~c~~~f~~~~~l~~h~~~h~~e-----------------------~~~~C~~C~---~~f~~~s~l~~h~~-~~ 123 (143)
.|-.|..|++.+.....-..|+..++|= +-+.|-.|. +.|.+....+.|+. +.
T Consensus 165 ~Pt~CLfC~~~~k~~e~~~~HM~~~HgffIPdreYL~D~~GLl~YLgeKV~~~~~CL~CN~~~~~f~sleavr~HM~~K~ 244 (390)
T KOG2785|consen 165 IPTDCLFCDKKSKSLEENLKHMFKEHGFFIPDREYLTDEKGLLKYLGEKVGIGFICLFCNELGRPFSSLEAVRAHMRDKG 244 (390)
T ss_pred CCcceeecCCCcccHHHHHHHHhhccCCcCCchHhhhchhHHHHHHHHHhccCceEEEeccccCcccccHHHHHHHhhcc
Confidence 3567888888888887778887655441 236788888 89999999999977 77
Q ss_pred hcCCCc
Q psy3948 124 QGRDHI 129 (143)
Q Consensus 124 ~~~~~~ 129 (143)
|++.+|
T Consensus 245 HCkl~y 250 (390)
T KOG2785|consen 245 HCKLPY 250 (390)
T ss_pred CcccCC
Confidence 788887
No 149
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=46.41 E-value=14 Score=26.41 Aligned_cols=14 Identities=21% Similarity=0.328 Sum_probs=8.5
Q ss_pred Cceecccccccccc
Q psy3948 99 KAHKCANVIIIAIM 112 (143)
Q Consensus 99 ~~~~C~~C~~~f~~ 112 (143)
+...|..|+...+.
T Consensus 251 r~e~C~~C~~YlK~ 264 (309)
T PRK03564 251 KAESCGDCGTYLKI 264 (309)
T ss_pred Eeeeccccccccee
Confidence 45677777755443
No 150
>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=45.94 E-value=17 Score=19.22 Aligned_cols=7 Identities=29% Similarity=1.274 Sum_probs=3.3
Q ss_pred ccCCCCC
Q psy3948 73 LKCSSCN 79 (143)
Q Consensus 73 ~~c~~c~ 79 (143)
+.|+.|+
T Consensus 47 ~~C~~Cg 53 (69)
T PF07282_consen 47 FTCPNCG 53 (69)
T ss_pred EEcCCCC
Confidence 4444444
No 151
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=45.92 E-value=12 Score=22.39 Aligned_cols=8 Identities=25% Similarity=0.700 Sum_probs=3.5
Q ss_pred eeccCCCC
Q psy3948 45 YACFICTY 52 (143)
Q Consensus 45 ~~c~~c~~ 52 (143)
..|..||.
T Consensus 71 ~~C~~Cg~ 78 (113)
T PRK12380 71 AWCWDCSQ 78 (113)
T ss_pred EEcccCCC
Confidence 34444443
No 152
>KOG2893|consensus
Probab=45.46 E-value=6.6 Score=26.78 Aligned_cols=41 Identities=27% Similarity=0.585 Sum_probs=21.9
Q ss_pred ccCCCCccCCcchHHHhhhhcCCCCCccCCCCCCCCCChHHHHHH
Q psy3948 47 CFICTYHTRKHGDMIGHMRKHTGVKPLKCSSCNYSCSTKSALSVH 91 (143)
Q Consensus 47 c~~c~~~~~~~~~l~~h~~~~~~~~~~~c~~c~~~f~~~~~l~~h 91 (143)
|=+|++.|-.+..|..|++ .+-|.|..|.+.+.+...|..|
T Consensus 13 cwycnrefddekiliqhqk----akhfkchichkkl~sgpglsih 53 (341)
T KOG2893|consen 13 CWYCNREFDDEKILIQHQK----AKHFKCHICHKKLFSGPGLSIH 53 (341)
T ss_pred eeecccccchhhhhhhhhh----hccceeeeehhhhccCCCceee
Confidence 4456666666655555433 2445666665554444444444
No 153
>TIGR00416 sms DNA repair protein RadA. The gene protuct codes for a probable ATP-dependent protease involved in both DNA repair and degradation of proteins, peptides, glycopeptides. Also known as sms. Residues 11-28 of the SEED alignment contain a putative Zn binding domain. Residues 110-117 of the seed contain a putative ATP binding site both documented in Haemophilus and in Listeria monocytogenes. for E.coli see ( J. BACTERIOL. 178:5045-5048(1996)).
Probab=44.81 E-value=12 Score=28.20 Aligned_cols=30 Identities=20% Similarity=0.429 Sum_probs=21.5
Q ss_pred CCCccccCCcchhhhccchhhHHHhhhcccCCCCCC
Q psy3948 3 VDHTILKCTFCNIIFNKLQDEELIMTHCKSCKKPKR 38 (143)
Q Consensus 3 ~~~~~~~C~~C~~~f~~~~~~~~~~~~c~~c~~~~~ 38 (143)
..+..|.|..||-.+.++.. .|+.|+.+-.
T Consensus 3 ~~~~~y~C~~Cg~~~~~~~g------~Cp~C~~w~t 32 (454)
T TIGR00416 3 KAKSKFVCQHCGADSPKWQG------KCPACHAWNT 32 (454)
T ss_pred CCCCeEECCcCCCCCccccE------ECcCCCCccc
Confidence 34567999999998755443 4888886543
No 154
>PF13878 zf-C2H2_3: zinc-finger of acetyl-transferase ESCO
Probab=44.71 E-value=31 Score=16.40 Aligned_cols=10 Identities=10% Similarity=0.308 Sum_probs=4.6
Q ss_pred eccccccccc
Q psy3948 102 KCANVIIIAI 111 (143)
Q Consensus 102 ~C~~C~~~f~ 111 (143)
.|+.||-.|.
T Consensus 15 ~C~~CgM~Y~ 24 (41)
T PF13878_consen 15 TCPTCGMLYS 24 (41)
T ss_pred CCCCCCCEEC
Confidence 4445544433
No 155
>COG5112 UFD2 U1-like Zn-finger-containing protein [General function prediction only]
Probab=44.07 E-value=16 Score=21.61 Aligned_cols=22 Identities=18% Similarity=0.104 Sum_probs=19.4
Q ss_pred ceecccccccccchHHHHHHHH
Q psy3948 100 AHKCANVIIIAIMYHILEIMLE 121 (143)
Q Consensus 100 ~~~C~~C~~~f~~~s~l~~h~~ 121 (143)
.+-|.+|.+.|.+...|..|++
T Consensus 55 qhYCieCaryf~t~~aL~~Hkk 76 (126)
T COG5112 55 QHYCIECARYFITEKALMEHKK 76 (126)
T ss_pred eeeeehhHHHHHHHHHHHHHhc
Confidence 3679999999999999999976
No 156
>PF06397 Desulfoferrod_N: Desulfoferrodoxin, N-terminal domain; InterPro: IPR004462 This domain is found as essentially the full length of desulforedoxin, a 37-residue homodimeric non-haem iron protein. It is also found as the N-terminal domain of desulfoferrodoxin (rbo), a homodimeric non-haem iron protein with 2 Fe atoms per monomer in different oxidation states. This domain binds the ferric rather than the ferrous Fe of desulfoferrodoxin. Neelaredoxin, a monomeric blue non-haem iron protein, lacks this domain.; GO: 0005506 iron ion binding; PDB: 1DFX_A 1VZI_B 2JI2_D 1VZH_B 2JI3_C 2JI1_C 1VZG_A 1CFW_A 2LK5_B 1DHG_B ....
Probab=43.18 E-value=8.5 Score=17.95 Aligned_cols=12 Identities=33% Similarity=0.794 Sum_probs=5.1
Q ss_pred ccccCCcchhhh
Q psy3948 6 TILKCTFCNIIF 17 (143)
Q Consensus 6 ~~~~C~~C~~~f 17 (143)
+.|+|+.||-..
T Consensus 5 ~~YkC~~CGniV 16 (36)
T PF06397_consen 5 EFYKCEHCGNIV 16 (36)
T ss_dssp EEEE-TTT--EE
T ss_pred cEEEccCCCCEE
Confidence 456666666543
No 157
>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=43.11 E-value=17 Score=17.64 Aligned_cols=11 Identities=9% Similarity=0.090 Sum_probs=7.4
Q ss_pred CCceecccccc
Q psy3948 98 LKAHKCANVII 108 (143)
Q Consensus 98 e~~~~C~~C~~ 108 (143)
...|.|..|++
T Consensus 35 ~~~~~C~~C~~ 45 (46)
T PF12760_consen 35 RGRYRCKACRK 45 (46)
T ss_pred CCeEECCCCCC
Confidence 45677777764
No 158
>TIGR00100 hypA hydrogenase nickel insertion protein HypA. In Hpylori, hypA mutant abolished hydrogenase activity and decrease in urease activity. Nickel supplementation in media restored urease activity and partial hydrogenase activity. HypA probably involved in inserting Ni in enzymes.
Probab=42.87 E-value=15 Score=22.04 Aligned_cols=11 Identities=18% Similarity=0.419 Sum_probs=5.0
Q ss_pred eeccCCCCccC
Q psy3948 45 YACFICTYHTR 55 (143)
Q Consensus 45 ~~c~~c~~~~~ 55 (143)
..|..||..|.
T Consensus 71 ~~C~~Cg~~~~ 81 (115)
T TIGR00100 71 CECEDCSEEVS 81 (115)
T ss_pred EEcccCCCEEe
Confidence 44555554433
No 159
>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=42.60 E-value=21 Score=17.94 Aligned_cols=11 Identities=18% Similarity=0.138 Sum_probs=5.5
Q ss_pred eeccCCCCccC
Q psy3948 45 YACFICTYHTR 55 (143)
Q Consensus 45 ~~c~~c~~~~~ 55 (143)
+.|..||+.+-
T Consensus 19 ~~Cr~Cg~~~C 29 (57)
T cd00065 19 HHCRNCGRIFC 29 (57)
T ss_pred cccCcCcCCcC
Confidence 34555555544
No 160
>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=42.36 E-value=3.9 Score=24.42 Aligned_cols=11 Identities=18% Similarity=0.259 Sum_probs=4.3
Q ss_pred eeccCCCCccC
Q psy3948 45 YACFICTYHTR 55 (143)
Q Consensus 45 ~~c~~c~~~~~ 55 (143)
..|..||..|.
T Consensus 71 ~~C~~Cg~~~~ 81 (113)
T PF01155_consen 71 ARCRDCGHEFE 81 (113)
T ss_dssp EEETTTS-EEE
T ss_pred EECCCCCCEEe
Confidence 34444444443
No 161
>KOG1842|consensus
Probab=42.10 E-value=16 Score=27.35 Aligned_cols=24 Identities=13% Similarity=0.054 Sum_probs=13.2
Q ss_pred eecccccccccchHHHHHHHHHHh
Q psy3948 101 HKCANVIIIAIMYHILEIMLEDIQ 124 (143)
Q Consensus 101 ~~C~~C~~~f~~~s~l~~h~~~~~ 124 (143)
|.|+.|+..|..-+.|..|+...|
T Consensus 16 flCPiC~~dl~~~~~L~~H~d~eH 39 (505)
T KOG1842|consen 16 FLCPICLLDLPNLSALNDHLDVEH 39 (505)
T ss_pred ccCchHhhhhhhHHHHHHHHhhhc
Confidence 455555555555555555555444
No 162
>KOG1280|consensus
Probab=41.91 E-value=22 Score=25.80 Aligned_cols=32 Identities=6% Similarity=0.058 Sum_probs=22.3
Q ss_pred CCceecccccccccchHHHHHHHHHHhcCCCc
Q psy3948 98 LKAHKCANVIIIAIMYHILEIMLEDIQGRDHI 129 (143)
Q Consensus 98 e~~~~C~~C~~~f~~~s~l~~h~~~~~~~~~~ 129 (143)
+.-|.|+.|+.+-.+...|..|+...|.+-.+
T Consensus 77 ~qSftCPyC~~~Gfte~~f~~Hv~s~Hpda~~ 108 (381)
T KOG1280|consen 77 PQSFTCPYCGIMGFTERQFGTHVLSQHPEAST 108 (381)
T ss_pred cccccCCcccccccchhHHHHHhhhcCcccCc
Confidence 34577777777777777777777777655543
No 163
>PF14369 zf-RING_3: zinc-finger
Probab=41.78 E-value=9.4 Score=17.59 Aligned_cols=10 Identities=30% Similarity=0.550 Sum_probs=8.2
Q ss_pred cCCcchhhhc
Q psy3948 9 KCTFCNIIFN 18 (143)
Q Consensus 9 ~C~~C~~~f~ 18 (143)
.|+.|+.+|.
T Consensus 23 ~CP~C~~gFv 32 (35)
T PF14369_consen 23 ACPRCHGGFV 32 (35)
T ss_pred CCcCCCCcEe
Confidence 5999998884
No 164
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=41.53 E-value=4.5 Score=23.55 Aligned_cols=13 Identities=15% Similarity=0.324 Sum_probs=9.4
Q ss_pred CccccCCcchhhh
Q psy3948 5 HTILKCTFCNIIF 17 (143)
Q Consensus 5 ~~~~~C~~C~~~f 17 (143)
++.|.|+.||..-
T Consensus 20 ~k~FtCp~Cghe~ 32 (104)
T COG4888 20 PKTFTCPRCGHEK 32 (104)
T ss_pred CceEecCccCCee
Confidence 4567888888764
No 165
>PF13451 zf-trcl: Probable zinc-binding domain
Probab=41.43 E-value=12 Score=18.78 Aligned_cols=18 Identities=22% Similarity=0.364 Sum_probs=11.4
Q ss_pred CccccCCcchhhhccchh
Q psy3948 5 HTILKCTFCNIIFNKLQD 22 (143)
Q Consensus 5 ~~~~~C~~C~~~f~~~~~ 22 (143)
++.+.|-.||..|.....
T Consensus 2 Dk~l~C~dCg~~FvfTa~ 19 (49)
T PF13451_consen 2 DKTLTCKDCGAEFVFTAG 19 (49)
T ss_pred CeeEEcccCCCeEEEehh
Confidence 456677777777655444
No 166
>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=41.39 E-value=14 Score=18.32 Aligned_cols=12 Identities=8% Similarity=-0.042 Sum_probs=8.9
Q ss_pred eecccccccccc
Q psy3948 101 HKCANVIIIAIM 112 (143)
Q Consensus 101 ~~C~~C~~~f~~ 112 (143)
|+|..|+.++--
T Consensus 2 y~C~~CgyvYd~ 13 (47)
T PF00301_consen 2 YQCPVCGYVYDP 13 (47)
T ss_dssp EEETTTSBEEET
T ss_pred cCCCCCCEEEcC
Confidence 788888877643
No 167
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=41.38 E-value=26 Score=18.01 Aligned_cols=6 Identities=33% Similarity=0.861 Sum_probs=2.8
Q ss_pred eccCCC
Q psy3948 46 ACFICT 51 (143)
Q Consensus 46 ~c~~c~ 51 (143)
.|+.|+
T Consensus 23 vCp~Cg 28 (54)
T PF14446_consen 23 VCPECG 28 (54)
T ss_pred ECCCCC
Confidence 344444
No 168
>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=41.37 E-value=12 Score=17.23 Aligned_cols=12 Identities=17% Similarity=0.041 Sum_probs=6.3
Q ss_pred ecccccccccch
Q psy3948 102 KCANVIIIAIMY 113 (143)
Q Consensus 102 ~C~~C~~~f~~~ 113 (143)
.|.+|++.|..+
T Consensus 5 ~C~eC~~~f~dS 16 (34)
T PF01286_consen 5 KCDECGKPFMDS 16 (34)
T ss_dssp E-TTT--EES-S
T ss_pred hHhHhCCHHHHH
Confidence 688899888765
No 169
>KOG2482|consensus
Probab=41.20 E-value=18 Score=26.17 Aligned_cols=23 Identities=13% Similarity=0.060 Sum_probs=20.7
Q ss_pred ceecccccccccchHHHHHHHHH
Q psy3948 100 AHKCANVIIIAIMYHILEIMLED 122 (143)
Q Consensus 100 ~~~C~~C~~~f~~~s~l~~h~~~ 122 (143)
.+.|-.|.++|..+..|+.|+++
T Consensus 195 r~~CLyCekifrdkntLkeHMrk 217 (423)
T KOG2482|consen 195 RLRCLYCEKIFRDKNTLKEHMRK 217 (423)
T ss_pred hheeeeeccccCCcHHHHHHHHh
Confidence 47899999999999999999873
No 170
>KOG2231|consensus
Probab=40.89 E-value=75 Score=25.46 Aligned_cols=22 Identities=18% Similarity=0.427 Sum_probs=13.2
Q ss_pred eccCCCCccCCcchHHHhhhhc
Q psy3948 46 ACFICTYHTRKHGDMIGHMRKH 67 (143)
Q Consensus 46 ~c~~c~~~~~~~~~l~~h~~~~ 67 (143)
.|..|...|.....+..|++.+
T Consensus 184 ~C~~C~~~fld~~el~rH~~~~ 205 (669)
T KOG2231|consen 184 LCKFCHERFLDDDELYRHLRFD 205 (669)
T ss_pred cchhhhhhhccHHHHHHhhccc
Confidence 3666666666666666665543
No 171
>KOG2272|consensus
Probab=40.88 E-value=21 Score=24.64 Aligned_cols=15 Identities=27% Similarity=0.494 Sum_probs=9.1
Q ss_pred ccCCcchhhhccchh
Q psy3948 8 LKCTFCNIIFNKLQD 22 (143)
Q Consensus 8 ~~C~~C~~~f~~~~~ 22 (143)
|+|..|++...+...
T Consensus 164 FkCt~C~keL~sdaR 178 (332)
T KOG2272|consen 164 FKCTTCGKELTSDAR 178 (332)
T ss_pred eecccccccccchhh
Confidence 457777776655444
No 172
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=40.81 E-value=23 Score=20.16 Aligned_cols=28 Identities=14% Similarity=0.261 Sum_probs=14.9
Q ss_pred hcccCCCCCC-CCCCcceeccCCCCccCC
Q psy3948 29 HCKSCKKPKR-PDKSYNYACFICTYHTRK 56 (143)
Q Consensus 29 ~c~~c~~~~~-~~~~~~~~c~~c~~~~~~ 56 (143)
.|+.|++.-. ..+..++.|.-||..|..
T Consensus 37 ~Cp~C~~~~VkR~a~GIW~C~kCg~~fAG 65 (89)
T COG1997 37 VCPFCGRTTVKRIATGIWKCRKCGAKFAG 65 (89)
T ss_pred cCCCCCCcceeeeccCeEEcCCCCCeecc
Confidence 4666655421 233345667767666553
No 173
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=40.77 E-value=32 Score=16.89 Aligned_cols=12 Identities=25% Similarity=0.813 Sum_probs=6.4
Q ss_pred ceeccCCCCccC
Q psy3948 44 NYACFICTYHTR 55 (143)
Q Consensus 44 ~~~c~~c~~~~~ 55 (143)
.+.|+.||..+.
T Consensus 20 ~~vC~~Cg~~~~ 31 (52)
T smart00661 20 RFVCRKCGYEEP 31 (52)
T ss_pred EEECCcCCCeEE
Confidence 355666664433
No 174
>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=40.33 E-value=12 Score=18.10 Aligned_cols=16 Identities=6% Similarity=-0.203 Sum_probs=11.9
Q ss_pred ecccccccccchHHHH
Q psy3948 102 KCANVIIIAIMYHILE 117 (143)
Q Consensus 102 ~C~~C~~~f~~~s~l~ 117 (143)
.|..|++.|+.+....
T Consensus 10 ~C~~C~rpf~WRKKW~ 25 (42)
T PF10013_consen 10 ICPVCGRPFTWRKKWA 25 (42)
T ss_pred cCcccCCcchHHHHHH
Confidence 6888999888875443
No 175
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=40.12 E-value=16 Score=18.39 Aligned_cols=11 Identities=27% Similarity=0.495 Sum_probs=5.7
Q ss_pred cccCCcchhhh
Q psy3948 7 ILKCTFCNIIF 17 (143)
Q Consensus 7 ~~~C~~C~~~f 17 (143)
.|.|..||+.|
T Consensus 6 ~Y~C~~Cg~~~ 16 (49)
T COG1996 6 EYKCARCGREV 16 (49)
T ss_pred EEEhhhcCCee
Confidence 34555555554
No 176
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=39.94 E-value=14 Score=22.74 Aligned_cols=17 Identities=18% Similarity=0.153 Sum_probs=13.2
Q ss_pred CCCceecccccccccch
Q psy3948 97 GLKAHKCANVIIIAIMY 113 (143)
Q Consensus 97 ~e~~~~C~~C~~~f~~~ 113 (143)
|...|.|..|++.|...
T Consensus 50 ~~qRyrC~~C~~tf~~~ 66 (129)
T COG3677 50 GHQRYKCKSCGSTFTVE 66 (129)
T ss_pred cccccccCCcCcceeee
Confidence 35568999999998764
No 177
>COG2331 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=39.82 E-value=4.4 Score=22.33 Aligned_cols=31 Identities=26% Similarity=0.462 Sum_probs=17.4
Q ss_pred cccCCcchhhhccchhhHHH-hhhcccCCCCC
Q psy3948 7 ILKCTFCNIIFNKLQDEELI-MTHCKSCKKPK 37 (143)
Q Consensus 7 ~~~C~~C~~~f~~~~~~~~~-~~~c~~c~~~~ 37 (143)
.|+|..|+-.|.-.+...+. ..+|+.|+..+
T Consensus 12 ~Y~c~~cg~~~dvvq~~~ddplt~ce~c~a~~ 43 (82)
T COG2331 12 SYECTECGNRFDVVQAMTDDPLTTCEECGARL 43 (82)
T ss_pred EEeecccchHHHHHHhcccCccccChhhChHH
Confidence 57899999877444332111 11566665544
No 178
>cd00730 rubredoxin Rubredoxin; nonheme iron binding domains containing a [Fe(SCys)4] center. Rubredoxins are small nonheme iron proteins. The iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc. They are believed to be involved in electron transfer.
Probab=37.98 E-value=14 Score=18.61 Aligned_cols=12 Identities=17% Similarity=-0.067 Sum_probs=9.2
Q ss_pred eecccccccccc
Q psy3948 101 HKCANVIIIAIM 112 (143)
Q Consensus 101 ~~C~~C~~~f~~ 112 (143)
|+|..||+++--
T Consensus 2 y~C~~CgyiYd~ 13 (50)
T cd00730 2 YECRICGYIYDP 13 (50)
T ss_pred cCCCCCCeEECC
Confidence 778888888763
No 179
>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 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=35.97 E-value=18 Score=16.75 Aligned_cols=12 Identities=17% Similarity=0.177 Sum_probs=8.7
Q ss_pred eecccccccccc
Q psy3948 101 HKCANVIIIAIM 112 (143)
Q Consensus 101 ~~C~~C~~~f~~ 112 (143)
+.|+.||.+|..
T Consensus 2 r~C~~Cg~~Yh~ 13 (36)
T PF05191_consen 2 RICPKCGRIYHI 13 (36)
T ss_dssp EEETTTTEEEET
T ss_pred cCcCCCCCcccc
Confidence 468888888764
No 181
>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG
Probab=35.68 E-value=5.6 Score=20.26 Aligned_cols=14 Identities=29% Similarity=0.748 Sum_probs=9.1
Q ss_pred cCCcchhhhccchh
Q psy3948 9 KCTFCNIIFNKLQD 22 (143)
Q Consensus 9 ~C~~C~~~f~~~~~ 22 (143)
.||+||..+...-+
T Consensus 2 ~CPyCge~~~~~iD 15 (52)
T PF14255_consen 2 QCPYCGEPIEILID 15 (52)
T ss_pred CCCCCCCeeEEEEe
Confidence 58888887644333
No 182
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=34.64 E-value=30 Score=15.65 Aligned_cols=10 Identities=20% Similarity=0.567 Sum_probs=4.7
Q ss_pred eeccCCCCcc
Q psy3948 45 YACFICTYHT 54 (143)
Q Consensus 45 ~~c~~c~~~~ 54 (143)
..|..||..+
T Consensus 22 ~~C~~Cg~~~ 31 (33)
T PF08792_consen 22 EVCIFCGSSF 31 (33)
T ss_pred EEcccCCcEe
Confidence 3455555443
No 183
>COG1066 Sms Predicted ATP-dependent serine protease [Posttranslational modification, protein turnover, chaperones]
Probab=34.47 E-value=23 Score=26.58 Aligned_cols=31 Identities=19% Similarity=0.394 Sum_probs=21.2
Q ss_pred CCCCccccCCcchhhhccchhhHHHhhhcccCCCCCC
Q psy3948 2 FVDHTILKCTFCNIIFNKLQDEELIMTHCKSCKKPKR 38 (143)
Q Consensus 2 ~~~~~~~~C~~C~~~f~~~~~~~~~~~~c~~c~~~~~ 38 (143)
-.....|.|..||-.+.++.- .|+.|+.+-.
T Consensus 2 aK~~t~f~C~~CG~~s~KW~G------kCp~Cg~Wns 32 (456)
T COG1066 2 AKKKTAFVCQECGYVSPKWLG------KCPACGAWNT 32 (456)
T ss_pred CCcccEEEcccCCCCCccccc------cCCCCCCccc
Confidence 334477999999998754433 5888886543
No 184
>PLN00104 MYST -like histone acetyltransferase; Provisional
Probab=34.12 E-value=29 Score=26.21 Aligned_cols=27 Identities=11% Similarity=0.036 Sum_probs=23.4
Q ss_pred CCceecccccccccchHHHHHHHHHHh
Q psy3948 98 LKAHKCANVIIIAIMYHILEIMLEDIQ 124 (143)
Q Consensus 98 e~~~~C~~C~~~f~~~s~l~~h~~~~~ 124 (143)
..-|.|..|.+-|.+...|.+|+....
T Consensus 196 ~~lyiCe~Cl~y~~~~~~~~~H~~~C~ 222 (450)
T PLN00104 196 SKLYFCEFCLKFMKRKEQLQRHMKKCD 222 (450)
T ss_pred CeEEEchhhhhhhcCHHHHHHHHhcCC
Confidence 346999999999999999999987554
No 185
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=33.63 E-value=25 Score=16.11 Aligned_cols=7 Identities=29% Similarity=0.828 Sum_probs=3.4
Q ss_pred eeccCCC
Q psy3948 45 YACFICT 51 (143)
Q Consensus 45 ~~c~~c~ 51 (143)
+.|+.||
T Consensus 23 ~vC~~Cg 29 (34)
T PF14803_consen 23 LVCPACG 29 (34)
T ss_dssp EEETTTT
T ss_pred eECCCCC
Confidence 4455554
No 186
>PTZ00064 histone acetyltransferase; Provisional
Probab=33.56 E-value=34 Score=26.24 Aligned_cols=27 Identities=19% Similarity=0.047 Sum_probs=23.3
Q ss_pred CceecccccccccchHHHHHHHHHHhc
Q psy3948 99 KAHKCANVIIIAIMYHILEIMLEDIQG 125 (143)
Q Consensus 99 ~~~~C~~C~~~f~~~s~l~~h~~~~~~ 125 (143)
.-|.|..|-+-|.+...|.+|+....-
T Consensus 279 ~LYICEfCLkY~~s~~~l~rH~~~C~~ 305 (552)
T PTZ00064 279 TLHFCEYCLDFFCFEDELIRHLSRCQL 305 (552)
T ss_pred eEEEccchhhhhCCHHHHHHHHhcCCC
Confidence 458999999999999999999886553
No 187
>COG3024 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=33.49 E-value=24 Score=18.80 Aligned_cols=10 Identities=20% Similarity=0.574 Sum_probs=4.4
Q ss_pred cccCCcchhh
Q psy3948 7 ILKCTFCNII 16 (143)
Q Consensus 7 ~~~C~~C~~~ 16 (143)
.-+|+.||+.
T Consensus 7 ~v~CP~Cgkp 16 (65)
T COG3024 7 TVPCPTCGKP 16 (65)
T ss_pred cccCCCCCCc
Confidence 3344444443
No 188
>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=33.38 E-value=15 Score=18.66 Aligned_cols=15 Identities=27% Similarity=0.831 Sum_probs=8.5
Q ss_pred CCccccCCcchhhhc
Q psy3948 4 DHTILKCTFCNIIFN 18 (143)
Q Consensus 4 ~~~~~~C~~C~~~f~ 18 (143)
+...+.|.||++.+.
T Consensus 32 ~~~~~rC~YCe~~~~ 46 (52)
T PF02748_consen 32 EPIKLRCHYCERIIT 46 (52)
T ss_dssp TTCEEEETTT--EEE
T ss_pred CCCEEEeeCCCCEec
Confidence 445677888887653
No 189
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=33.01 E-value=27 Score=21.21 Aligned_cols=10 Identities=30% Similarity=0.786 Sum_probs=5.5
Q ss_pred eeccCCCCccC
Q psy3948 45 YACFICTYHTR 55 (143)
Q Consensus 45 ~~c~~c~~~~~ 55 (143)
+.| .||..|.
T Consensus 71 ~~C-~Cg~~~~ 80 (124)
T PRK00762 71 IEC-ECGYEGV 80 (124)
T ss_pred EEe-eCcCccc
Confidence 456 6665544
No 190
>COG3091 SprT Zn-dependent metalloprotease, SprT family [General function prediction only]
Probab=32.41 E-value=25 Score=22.31 Aligned_cols=10 Identities=10% Similarity=0.132 Sum_probs=4.9
Q ss_pred ceecccccccc
Q psy3948 100 AHKCANVIIIA 110 (143)
Q Consensus 100 ~~~C~~C~~~f 110 (143)
+|.|. |+..|
T Consensus 117 ~Y~C~-C~q~~ 126 (156)
T COG3091 117 PYRCQ-CQQHY 126 (156)
T ss_pred eEEee-cCCcc
Confidence 35555 55443
No 191
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=32.22 E-value=34 Score=17.37 Aligned_cols=7 Identities=29% Similarity=1.103 Sum_probs=3.3
Q ss_pred ccCCCCC
Q psy3948 73 LKCSSCN 79 (143)
Q Consensus 73 ~~c~~c~ 79 (143)
..|+.|+
T Consensus 47 ~~Cp~Cg 53 (56)
T PF02591_consen 47 VFCPNCG 53 (56)
T ss_pred EECcCCC
Confidence 3455554
No 192
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=32.04 E-value=45 Score=15.65 Aligned_cols=20 Identities=20% Similarity=0.009 Sum_probs=14.4
Q ss_pred CceecccccccccchHHHHH
Q psy3948 99 KAHKCANVIIIAIMYHILEI 118 (143)
Q Consensus 99 ~~~~C~~C~~~f~~~s~l~~ 118 (143)
..+.|+.|+-++.+...|.+
T Consensus 18 ~id~C~~C~G~W~d~~el~~ 37 (41)
T PF13453_consen 18 EIDVCPSCGGIWFDAGELEK 37 (41)
T ss_pred EEEECCCCCeEEccHHHHHH
Confidence 34678888888777777765
No 193
>KOG2807|consensus
Probab=31.78 E-value=65 Score=23.33 Aligned_cols=27 Identities=7% Similarity=-0.103 Sum_probs=21.4
Q ss_pred CceecccccccccchHHHHHHHHHHhc
Q psy3948 99 KAHKCANVIIIAIMYHILEIMLEDIQG 125 (143)
Q Consensus 99 ~~~~C~~C~~~f~~~s~l~~h~~~~~~ 125 (143)
-.|.|..|...|-..=+...|-..|-+
T Consensus 344 ~~y~C~~Ck~~FCldCDv~iHesLh~C 370 (378)
T KOG2807|consen 344 GRYRCESCKNVFCLDCDVFIHESLHNC 370 (378)
T ss_pred CcEEchhccceeeccchHHHHhhhhcC
Confidence 458999999999888888888766653
No 194
>PLN03239 histone acetyltransferase; Provisional
Probab=31.53 E-value=38 Score=24.70 Aligned_cols=25 Identities=8% Similarity=-0.215 Sum_probs=22.2
Q ss_pred CCceecccccccccchHHHHHHHHH
Q psy3948 98 LKAHKCANVIIIAIMYHILEIMLED 122 (143)
Q Consensus 98 e~~~~C~~C~~~f~~~s~l~~h~~~ 122 (143)
..-|.|..|.+-|.+...|.+|+..
T Consensus 104 ~~lYiCE~Clky~~~~~~l~~H~~~ 128 (351)
T PLN03239 104 DVLYVCEFSFGFFARKSELLRFQAK 128 (351)
T ss_pred ceEEEeccchhhhcCHHHHHHHHHh
Confidence 4579999999999999999999765
No 195
>COG1327 Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains [Transcription]
Probab=31.52 E-value=15 Score=23.21 Aligned_cols=9 Identities=44% Similarity=0.899 Sum_probs=6.2
Q ss_pred cCCcchhhh
Q psy3948 9 KCTFCNIIF 17 (143)
Q Consensus 9 ~C~~C~~~f 17 (143)
.||+|+-.-
T Consensus 2 ~CPfC~~~~ 10 (156)
T COG1327 2 KCPFCGHED 10 (156)
T ss_pred CCCCCCCCC
Confidence 478887654
No 196
>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=31.03 E-value=20 Score=16.11 Aligned_cols=10 Identities=40% Similarity=1.059 Sum_probs=5.1
Q ss_pred cccCCcchhh
Q psy3948 7 ILKCTFCNII 16 (143)
Q Consensus 7 ~~~C~~C~~~ 16 (143)
.|+|+.||-.
T Consensus 4 ~ykC~~CGni 13 (34)
T cd00974 4 VYKCEICGNI 13 (34)
T ss_pred EEEcCCCCcE
Confidence 4555555544
No 197
>TIGR00319 desulf_FeS4 desulfoferrodoxin FeS4 iron-binding domain. Neelaredoxin, a monomeric blue non-heme iron protein, lacks this domain.
Probab=29.86 E-value=29 Score=15.55 Aligned_cols=9 Identities=33% Similarity=0.921 Sum_probs=4.2
Q ss_pred eeccCCCCc
Q psy3948 45 YACFICTYH 53 (143)
Q Consensus 45 ~~c~~c~~~ 53 (143)
|+|..||..
T Consensus 8 ykC~~Cgni 16 (34)
T TIGR00319 8 YKCEVCGNI 16 (34)
T ss_pred EEcCCCCcE
Confidence 444444444
No 198
>KOG2636|consensus
Probab=29.81 E-value=40 Score=25.43 Aligned_cols=29 Identities=10% Similarity=-0.058 Sum_probs=24.1
Q ss_pred HHhcCCCceeccccc-ccccchHHHHHHHH
Q psy3948 93 KRHTGLKAHKCANVI-IIAIMYHILEIMLE 121 (143)
Q Consensus 93 ~~h~~e~~~~C~~C~-~~f~~~s~l~~h~~ 121 (143)
+.|.-..-|.|..|| +++..+..+.+|-.
T Consensus 394 KLHGL~~ey~CEICGNy~Y~GrkaF~RHF~ 423 (497)
T KOG2636|consen 394 KLHGLDIEYNCEICGNYVYKGRKAFDRHFN 423 (497)
T ss_pred hhcCCCcccceeeccCccccCcHHHHHHhH
Confidence 566667789999999 88888999999944
No 199
>COG4306 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=29.48 E-value=44 Score=20.44 Aligned_cols=10 Identities=20% Similarity=0.411 Sum_probs=4.7
Q ss_pred eccCCCCccC
Q psy3948 46 ACFICTYHTR 55 (143)
Q Consensus 46 ~c~~c~~~~~ 55 (143)
-|..||..|+
T Consensus 70 fchncgs~fp 79 (160)
T COG4306 70 FCHNCGSRFP 79 (160)
T ss_pred hhhcCCCCCC
Confidence 3444554444
No 200
>COG4391 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=29.34 E-value=24 Score=18.61 Aligned_cols=9 Identities=22% Similarity=1.091 Sum_probs=5.3
Q ss_pred cCCcchhhh
Q psy3948 9 KCTFCNIIF 17 (143)
Q Consensus 9 ~C~~C~~~f 17 (143)
.|++|+..|
T Consensus 50 ~CPYC~t~y 58 (62)
T COG4391 50 VCPYCSTRY 58 (62)
T ss_pred ecCccccEE
Confidence 466666554
No 201
>PF14787 zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB: 1CL4_A 1DSV_A.
Probab=29.20 E-value=18 Score=16.85 Aligned_cols=15 Identities=20% Similarity=0.304 Sum_probs=8.3
Q ss_pred ccCCcchhhhccchh
Q psy3948 8 LKCTFCNIIFNKLQD 22 (143)
Q Consensus 8 ~~C~~C~~~f~~~~~ 22 (143)
-.|+.|+++|-+.++
T Consensus 3 ~~CprC~kg~Hwa~~ 17 (36)
T PF14787_consen 3 GLCPRCGKGFHWASE 17 (36)
T ss_dssp -C-TTTSSSCS-TTT
T ss_pred ccCcccCCCcchhhh
Confidence 358888888755544
No 202
>KOG1994|consensus
Probab=29.01 E-value=33 Score=23.34 Aligned_cols=21 Identities=14% Similarity=-0.259 Sum_probs=19.1
Q ss_pred CceecccccccccchHHHHHH
Q psy3948 99 KAHKCANVIIIAIMYHILEIM 119 (143)
Q Consensus 99 ~~~~C~~C~~~f~~~s~l~~h 119 (143)
-.|-|-.||..|.+.-+|..|
T Consensus 238 eh~YC~fCG~~y~~~edl~eh 258 (268)
T KOG1994|consen 238 EHYYCFFCGIKYKDEEDLYEH 258 (268)
T ss_pred cceEEEEeccccCCHHHHHHh
Confidence 458899999999999999988
No 203
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=28.77 E-value=28 Score=17.88 Aligned_cols=9 Identities=33% Similarity=1.065 Sum_probs=4.6
Q ss_pred cccCCcchh
Q psy3948 7 ILKCTFCNI 15 (143)
Q Consensus 7 ~~~C~~C~~ 15 (143)
+.+||.||.
T Consensus 3 LkPCPFCG~ 11 (61)
T PF14354_consen 3 LKPCPFCGS 11 (61)
T ss_pred CcCCCCCCC
Confidence 345555544
No 204
>PF09788 Tmemb_55A: Transmembrane protein 55A; InterPro: IPR019178 Members of this family catalyse the hydrolysis of the 4-position phosphate of phosphatidylinositol 4,5-bisphosphate, in the reaction: 1-phosphatidyl-myo-inositol 4,5-bisphosphate + H(2)O = 1-phosphatidyl-1D-myo-inositol 5-phosphate + phosphate.
Probab=28.74 E-value=16 Score=25.15 Aligned_cols=29 Identities=21% Similarity=0.455 Sum_probs=13.8
Q ss_pred ccCCcchhhhccchhhHHHhhhcccCCCC
Q psy3948 8 LKCTFCNIIFNKLQDEELIMTHCKSCKKP 36 (143)
Q Consensus 8 ~~C~~C~~~f~~~~~~~~~~~~c~~c~~~ 36 (143)
+.|.+|+.+|.+..-..+....|+.|.+.
T Consensus 158 v~CghC~~~Fl~~~~~~~tlARCPHCrKv 186 (256)
T PF09788_consen 158 VICGHCSNTFLFNTLTSNTLARCPHCRKV 186 (256)
T ss_pred EECCCCCCcEeccCCCCCccccCCCCcee
Confidence 45666666664443222222345555443
No 205
>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=28.13 E-value=30 Score=21.51 Aligned_cols=19 Identities=21% Similarity=0.415 Sum_probs=14.2
Q ss_pred HhcCCCceecccccccccch
Q psy3948 94 RHTGLKAHKCANVIIIAIMY 113 (143)
Q Consensus 94 ~h~~e~~~~C~~C~~~f~~~ 113 (143)
.+.+ +|..|++||..|...
T Consensus 107 l~~g-~~~RCpeCG~~fkL~ 125 (136)
T PF01215_consen 107 LHKG-KPQRCPECGQVFKLK 125 (136)
T ss_dssp EETT-SEEEETTTEEEEEEE
T ss_pred EeCC-CccCCCCCCeEEEEE
Confidence 3444 588999999998753
No 206
>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=27.62 E-value=28 Score=20.48 Aligned_cols=10 Identities=20% Similarity=0.331 Sum_probs=6.0
Q ss_pred ceeccCCCCc
Q psy3948 44 NYACFICTYH 53 (143)
Q Consensus 44 ~~~c~~c~~~ 53 (143)
+-.|+.||..
T Consensus 2 p~~CpYCg~~ 11 (102)
T PF11672_consen 2 PIICPYCGGP 11 (102)
T ss_pred CcccCCCCCe
Confidence 3457777754
No 207
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=27.60 E-value=45 Score=25.01 Aligned_cols=28 Identities=18% Similarity=0.526 Sum_probs=13.6
Q ss_pred cccCCCCCCCCCCcceeccCCCCccCCc
Q psy3948 30 CKSCKKPKRPDKSYNYACFICTYHTRKH 57 (143)
Q Consensus 30 c~~c~~~~~~~~~~~~~c~~c~~~~~~~ 57 (143)
|+.|+.+-...+..-|.|+-||..++..
T Consensus 353 Cp~Cg~~m~S~G~~g~rC~kCg~~~~~~ 380 (421)
T COG1571 353 CPRCGGRMKSAGRNGFRCKKCGTRARET 380 (421)
T ss_pred CCccCCchhhcCCCCcccccccccCCcc
Confidence 4444443332222246666666665544
No 208
>KOG4684|consensus
Probab=27.56 E-value=28 Score=23.44 Aligned_cols=29 Identities=28% Similarity=0.591 Sum_probs=19.5
Q ss_pred ccCCcchhhhccchhhHHHhhhcccCCCCC
Q psy3948 8 LKCTFCNIIFNKLQDEELIMTHCKSCKKPK 37 (143)
Q Consensus 8 ~~C~~C~~~f~~~~~~~~~~~~c~~c~~~~ 37 (143)
.+|.+|+.+|.+...+. ....|+-|.+..
T Consensus 171 V~CgHC~~tFLfnt~tn-aLArCPHCrKvS 199 (275)
T KOG4684|consen 171 VKCGHCNETFLFNTLTN-ALARCPHCRKVS 199 (275)
T ss_pred EEecCccceeehhhHHH-HHhcCCcccchh
Confidence 47999999997665543 333577776654
No 209
>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=26.61 E-value=58 Score=23.31 Aligned_cols=14 Identities=21% Similarity=0.247 Sum_probs=9.0
Q ss_pred Cceecccccccccc
Q psy3948 99 KAHKCANVIIIAIM 112 (143)
Q Consensus 99 ~~~~C~~C~~~f~~ 112 (143)
+...|..|+...+.
T Consensus 251 r~e~C~~C~~YlK~ 264 (305)
T TIGR01562 251 KAETCDSCQGYLKI 264 (305)
T ss_pred EEeeccccccchhh
Confidence 45678888755443
No 210
>COG1326 Uncharacterized archaeal Zn-finger protein [General function prediction only]
Probab=26.45 E-value=81 Score=20.98 Aligned_cols=12 Identities=8% Similarity=0.238 Sum_probs=7.8
Q ss_pred Cceecccccccc
Q psy3948 99 KAHKCANVIIIA 110 (143)
Q Consensus 99 ~~~~C~~C~~~f 110 (143)
.-+.|..||..+
T Consensus 29 ~lvrC~eCG~V~ 40 (201)
T COG1326 29 PLVRCEECGTVH 40 (201)
T ss_pred eEEEccCCCcEe
Confidence 346777777665
No 211
>PHA02998 RNA polymerase subunit; Provisional
Probab=26.41 E-value=12 Score=24.42 Aligned_cols=12 Identities=17% Similarity=0.204 Sum_probs=8.8
Q ss_pred ceeccccccccc
Q psy3948 100 AHKCANVIIIAI 111 (143)
Q Consensus 100 ~~~C~~C~~~f~ 111 (143)
-|.|..||..|.
T Consensus 171 FYkC~~CG~~wk 182 (195)
T PHA02998 171 RHACRDCKKHFK 182 (195)
T ss_pred EEEcCCCCCccC
Confidence 378888887765
No 212
>KOG0717|consensus
Probab=26.25 E-value=48 Score=25.22 Aligned_cols=21 Identities=10% Similarity=-0.186 Sum_probs=18.9
Q ss_pred eecccccccccchHHHHHHHH
Q psy3948 101 HKCANVIIIAIMYHILEIMLE 121 (143)
Q Consensus 101 ~~C~~C~~~f~~~s~l~~h~~ 121 (143)
+-|..|.+.|.+...|..|..
T Consensus 293 lyC~vCnKsFKseKq~kNHEn 313 (508)
T KOG0717|consen 293 LYCVVCNKSFKSEKQLKNHEN 313 (508)
T ss_pred eEEeeccccccchHHHHhhHH
Confidence 679999999999999999954
No 213
>PF06677 Auto_anti-p27: Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27); InterPro: IPR009563 The proteins in this entry are functionally uncharacterised and include several proteins that characterise Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27). It is thought that the potential association of anti-p27 with anti-centromere antibodies suggests that autoantigen p27 might play a role in mitosis [].
Probab=25.84 E-value=49 Score=15.87 Aligned_cols=22 Identities=36% Similarity=0.824 Sum_probs=10.4
Q ss_pred hcccCCCCCCCCCCcceeccCC
Q psy3948 29 HCKSCKKPKRPDKSYNYACFIC 50 (143)
Q Consensus 29 ~c~~c~~~~~~~~~~~~~c~~c 50 (143)
.|+.|+.+.-..++....|..|
T Consensus 19 ~Cp~C~~PL~~~k~g~~~Cv~C 40 (41)
T PF06677_consen 19 HCPDCGTPLMRDKDGKIYCVSC 40 (41)
T ss_pred ccCCCCCeeEEecCCCEECCCC
Confidence 5666654443223333445554
No 214
>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=25.57 E-value=72 Score=15.98 Aligned_cols=12 Identities=8% Similarity=-0.363 Sum_probs=5.8
Q ss_pred ecccccccccch
Q psy3948 102 KCANVIIIAIMY 113 (143)
Q Consensus 102 ~C~~C~~~f~~~ 113 (143)
.|+.|++.|...
T Consensus 22 ~CPlC~r~l~~e 33 (54)
T PF04423_consen 22 CCPLCGRPLDEE 33 (54)
T ss_dssp E-TTT--EE-HH
T ss_pred cCCCCCCCCCHH
Confidence 788888887753
No 215
>KOG2071|consensus
Probab=25.24 E-value=53 Score=25.70 Aligned_cols=28 Identities=4% Similarity=-0.145 Sum_probs=23.9
Q ss_pred CCCceecccccccccchHHHHHHHHHHh
Q psy3948 97 GLKAHKCANVIIIAIMYHILEIMLEDIQ 124 (143)
Q Consensus 97 ~e~~~~C~~C~~~f~~~s~l~~h~~~~~ 124 (143)
...|..|..||..|-......+|+..|-
T Consensus 415 ~~~pnqC~~CG~R~~~~ee~sk~md~H~ 442 (579)
T KOG2071|consen 415 KDSPNQCKSCGLRFDDSEERSKHMDIHD 442 (579)
T ss_pred cCCcchhcccccccccchhhhhHhhhhh
Confidence 4567899999999999999998887776
No 216
>KOG4118|consensus
Probab=25.01 E-value=35 Score=18.24 Aligned_cols=30 Identities=13% Similarity=0.279 Sum_probs=24.4
Q ss_pred ceecccccccccchHHHHHHHHHHhcCCCc
Q psy3948 100 AHKCANVIIIAIMYHILEIMLEDIQGRDHI 129 (143)
Q Consensus 100 ~~~C~~C~~~f~~~s~l~~h~~~~~~~~~~ 129 (143)
.|.|..|...-...-.+..|...-|...++
T Consensus 38 ~~kCtVC~~~mpdpktfkqhfe~kHpk~~~ 67 (74)
T KOG4118|consen 38 HHKCTVCMVQMPDPKTFKQHFENKHPKEPL 67 (74)
T ss_pred HhhhHhhHhhCCCCchHHHHHhhcCCCCCC
Confidence 478999998888888899998877766654
No 217
>PF02318 FYVE_2: FYVE-type zinc finger; InterPro: IPR003315 This entry represents the zinc-binding domain found in rabphilin Rab3A. The small G protein Rab3A plays an important role in the regulation of neurotransmitter release. The crystal structure of the small G protein Rab3A complexed with the effector domain of rabphilin-3A shows that the effector domain of rabphilin-3A contacts Rab3A in two distinct areas. The first interface involves the Rab3A switch I and switch II regions, which are sensitive to the nucleotide-binding state of Rab3A. The second interface consists of a deep pocket in Rab3A that interacts with a SGAWFF structural element of rabphilin-3A. Sequence and structure analysis, and biochemical data suggest that this pocket, or Rab complementarity-determining region (RabCDR), establishes a specific interaction between each Rab protein and its effectors. It has been suggested that RabCDRs could be major determinants of effector specificity during vesicle trafficking and fusion [].; GO: 0008270 zinc ion binding, 0017137 Rab GTPase binding, 0006886 intracellular protein transport; PDB: 2CSZ_A 2ZET_C 1ZBD_B 3BC1_B 2CJS_C 2A20_A.
Probab=24.95 E-value=18 Score=21.66 Aligned_cols=12 Identities=8% Similarity=-0.089 Sum_probs=6.5
Q ss_pred CCCceecccccc
Q psy3948 97 GLKAHKCANVII 108 (143)
Q Consensus 97 ~e~~~~C~~C~~ 108 (143)
++..|.|..|-+
T Consensus 91 ~~~~WlC~vC~k 102 (118)
T PF02318_consen 91 KEPIWLCKVCQK 102 (118)
T ss_dssp SSCCEEEHHHHH
T ss_pred CCCCEEChhhHH
Confidence 344566666543
No 218
>KOG4167|consensus
Probab=24.90 E-value=14 Score=29.56 Aligned_cols=25 Identities=24% Similarity=0.327 Sum_probs=15.2
Q ss_pred ceeccCCCCccCCcchHHHhhhhcC
Q psy3948 44 NYACFICTYHTRKHGDMIGHMRKHT 68 (143)
Q Consensus 44 ~~~c~~c~~~~~~~~~l~~h~~~~~ 68 (143)
.|.|.+|++.|....++..|+++|.
T Consensus 792 iFpCreC~kvF~KiKSrNAHMK~Hr 816 (907)
T KOG4167|consen 792 IFPCRECGKVFFKIKSRNAHMKTHR 816 (907)
T ss_pred eeehHHHHHHHHHHhhhhHHHHHHH
Confidence 4666666666665555666665554
No 219
>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=24.42 E-value=33 Score=19.16 Aligned_cols=10 Identities=40% Similarity=1.281 Sum_probs=3.4
Q ss_pred CccccCCcch
Q psy3948 5 HTILKCTFCN 14 (143)
Q Consensus 5 ~~~~~C~~C~ 14 (143)
.+.|.|+.||
T Consensus 20 ~~~F~CPfC~ 29 (81)
T PF05129_consen 20 PKVFDCPFCN 29 (81)
T ss_dssp SS----TTT-
T ss_pred CceEcCCcCC
Confidence 3567788888
No 220
>PF09332 Mcm10: Mcm10 replication factor; InterPro: IPR015411 Mcm10 is a eukaryotic DNA replication factor that regulates the stability and chromatin association of DNA polymerase alpha []. ; PDB: 2KWQ_A.
Probab=24.14 E-value=13 Score=27.01 Aligned_cols=17 Identities=24% Similarity=0.425 Sum_probs=9.0
Q ss_pred ccccCCcchhhhccchh
Q psy3948 6 TILKCTFCNIIFNKLQD 22 (143)
Q Consensus 6 ~~~~C~~C~~~f~~~~~ 22 (143)
+.+.|..|+.++.....
T Consensus 251 kav~C~~C~yt~~~~~~ 267 (344)
T PF09332_consen 251 KAVTCKQCKYTAFKPSD 267 (344)
T ss_dssp EEEEETTT--EESS--H
T ss_pred EEEEcCCCCCcccCcch
Confidence 45678888877655554
No 221
>KOG4173|consensus
Probab=23.59 E-value=40 Score=22.65 Aligned_cols=77 Identities=19% Similarity=0.279 Sum_probs=46.0
Q ss_pred eeccC--CCCccCCcchHHHhhhhcCCCCCccCCCCCCCCCChHHHHHHHHH-h---------cCCCceec--ccccccc
Q psy3948 45 YACFI--CTYHTRKHGDMIGHMRKHTGVKPLKCSSCNYSCSTKSALSVHQKR-H---------TGLKAHKC--ANVIIIA 110 (143)
Q Consensus 45 ~~c~~--c~~~~~~~~~l~~h~~~~~~~~~~~c~~c~~~f~~~~~l~~h~~~-h---------~~e~~~~C--~~C~~~f 110 (143)
+.|++ |-..+.....+..|-....+. .|..|.+.|.+.--|..|..- | -|..-|+| ..|+..|
T Consensus 80 ~~cqvagc~~~~d~lD~~E~hY~~~h~~---sCs~C~r~~Pt~hLLd~HI~E~HDs~Fqa~veRG~dMy~ClvEgCt~KF 156 (253)
T KOG4173|consen 80 FACQVAGCCQVFDALDDYEHHYHTLHGN---SCSFCKRAFPTGHLLDAHILEWHDSLFQALVERGQDMYQCLVEGCTEKF 156 (253)
T ss_pred ccccccchHHHHhhhhhHHHhhhhcccc---hhHHHHHhCCchhhhhHHHHHHHHHHHHHHHHcCccHHHHHHHhhhhhh
Confidence 34444 445555555555553332221 677787877777777776541 2 13334777 4588888
Q ss_pred cchHHHHHHHHHHh
Q psy3948 111 IMYHILEIMLEDIQ 124 (143)
Q Consensus 111 ~~~s~l~~h~~~~~ 124 (143)
.+.-+-..|+-..|
T Consensus 157 kT~r~RkdH~I~~H 170 (253)
T KOG4173|consen 157 KTSRDRKDHMIRMH 170 (253)
T ss_pred hhhhhhhhHHHHhc
Confidence 88888888865444
No 222
>cd01121 Sms Sms (bacterial radA) DNA repair protein. This protein is not related to archael radA any more than is to other RecA-like NTPases. Sms has a role in recombination and recombinational repair and is responsible for the stabilization or processing of branched DNA molecules.
Probab=23.59 E-value=36 Score=25.03 Aligned_cols=25 Identities=20% Similarity=0.506 Sum_probs=16.0
Q ss_pred ccCCcchhhhccchhhHHHhhhcccCCCCCC
Q psy3948 8 LKCTFCNIIFNKLQDEELIMTHCKSCKKPKR 38 (143)
Q Consensus 8 ~~C~~C~~~f~~~~~~~~~~~~c~~c~~~~~ 38 (143)
|.|..||-.+.+... .|+.|+.+-.
T Consensus 1 ~~c~~cg~~~~~~~g------~cp~c~~w~~ 25 (372)
T cd01121 1 YVCSECGYVSPKWLG------KCPECGEWNT 25 (372)
T ss_pred CCCCCCCCCCCCccE------ECcCCCCcee
Confidence 678888887644433 4777776543
No 223
>COG1439 Predicted nucleic acid-binding protein, consists of a PIN domain and a Zn-ribbon module [General function prediction only]
Probab=23.31 E-value=45 Score=21.77 Aligned_cols=22 Identities=27% Similarity=0.540 Sum_probs=11.0
Q ss_pred hcccCCCCCCCCCCcceeccCCCCc
Q psy3948 29 HCKSCKKPKRPDKSYNYACFICTYH 53 (143)
Q Consensus 29 ~c~~c~~~~~~~~~~~~~c~~c~~~ 53 (143)
.|..|.+.|. ...-.|+.||..
T Consensus 141 rC~GC~~~f~---~~~~~Cp~CG~~ 162 (177)
T COG1439 141 RCHGCKRIFP---EPKDFCPICGSP 162 (177)
T ss_pred EEecCceecC---CCCCcCCCCCCc
Confidence 4666666554 122335666544
No 224
>KOG1701|consensus
Probab=23.26 E-value=15 Score=27.38 Aligned_cols=12 Identities=17% Similarity=0.371 Sum_probs=9.5
Q ss_pred ceeccccccccc
Q psy3948 100 AHKCANVIIIAI 111 (143)
Q Consensus 100 ~~~C~~C~~~f~ 111 (143)
-|.|..||...+
T Consensus 427 CY~CEDCg~~LS 438 (468)
T KOG1701|consen 427 CYKCEDCGLLLS 438 (468)
T ss_pred ceehhhcCcccc
Confidence 488999997765
No 225
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=23.15 E-value=21 Score=21.35 Aligned_cols=12 Identities=17% Similarity=-0.067 Sum_probs=9.8
Q ss_pred ceeccccccccc
Q psy3948 100 AHKCANVIIIAI 111 (143)
Q Consensus 100 ~~~C~~C~~~f~ 111 (143)
-|.|..||..+.
T Consensus 100 Fy~C~~Cg~~wr 111 (113)
T COG1594 100 FYKCTRCGYRWR 111 (113)
T ss_pred EEEecccCCEee
Confidence 489999998765
No 226
>COG5188 PRP9 Splicing factor 3a, subunit 3 [RNA processing and modification]
Probab=22.97 E-value=63 Score=23.67 Aligned_cols=28 Identities=11% Similarity=-0.046 Sum_probs=23.4
Q ss_pred HHhcCCCceeccccc-ccccchHHHHHHH
Q psy3948 93 KRHTGLKAHKCANVI-IIAIMYHILEIML 120 (143)
Q Consensus 93 ~~h~~e~~~~C~~C~-~~f~~~s~l~~h~ 120 (143)
+.|.-.+.|.|..|| +.+..+..+.+|-
T Consensus 367 klhgLd~ef~CEICgNyvy~GR~~FdrHF 395 (470)
T COG5188 367 KLHGLDIEFECEICGNYVYYGRDRFDRHF 395 (470)
T ss_pred HhcCCCcceeeeecccccccchHHHHhhh
Confidence 567677889999999 8888899998883
No 227
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=22.71 E-value=63 Score=19.99 Aligned_cols=25 Identities=32% Similarity=0.741 Sum_probs=16.8
Q ss_pred hcccCCCCCCCCCCcceeccCCCCcc
Q psy3948 29 HCKSCKKPKRPDKSYNYACFICTYHT 54 (143)
Q Consensus 29 ~c~~c~~~~~~~~~~~~~c~~c~~~~ 54 (143)
+|+.|+.+.-- +.-.-.|++|+...
T Consensus 30 hCp~Cg~PLF~-KdG~v~CPvC~~~~ 54 (131)
T COG1645 30 HCPKCGTPLFR-KDGEVFCPVCGYRE 54 (131)
T ss_pred hCcccCCccee-eCCeEECCCCCceE
Confidence 79999976543 33334599999544
No 228
>PTZ00043 cytochrome c oxidase subunit; Provisional
Probab=22.27 E-value=46 Score=22.68 Aligned_cols=16 Identities=13% Similarity=0.100 Sum_probs=13.2
Q ss_pred CCceecccccccccch
Q psy3948 98 LKAHKCANVIIIAIMY 113 (143)
Q Consensus 98 e~~~~C~~C~~~f~~~ 113 (143)
.++..|++||..|...
T Consensus 179 GkpqRCpECGqVFKLV 194 (268)
T PTZ00043 179 GFLYRCGECDQIFMLV 194 (268)
T ss_pred CCCccCCCCCcEEEEE
Confidence 3578999999999864
No 229
>COG2824 PhnA Uncharacterized Zn-ribbon-containing protein involved in phosphonate metabolism [Inorganic ion transport and metabolism]
Probab=22.27 E-value=51 Score=19.57 Aligned_cols=26 Identities=15% Similarity=0.374 Sum_probs=13.6
Q ss_pred cccCCCCCCCCCCcceeccCCCCccC
Q psy3948 30 CKSCKKPKRPDKSYNYACFICTYHTR 55 (143)
Q Consensus 30 c~~c~~~~~~~~~~~~~c~~c~~~~~ 55 (143)
|+.|...|.....-.+.|+.|+..+.
T Consensus 6 cp~c~sEytYed~~~~~cpec~~ew~ 31 (112)
T COG2824 6 CPKCNSEYTYEDGGQLICPECAHEWN 31 (112)
T ss_pred CCccCCceEEecCceEeCchhccccc
Confidence 44444444433333566777766655
No 230
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=21.83 E-value=67 Score=25.67 Aligned_cols=11 Identities=27% Similarity=0.392 Sum_probs=6.1
Q ss_pred ccCCCCccCCc
Q psy3948 47 CFICTYHTRKH 57 (143)
Q Consensus 47 c~~c~~~~~~~ 57 (143)
|+.||......
T Consensus 44 C~~CG~~~~~~ 54 (645)
T PRK14559 44 CPNCGAETGTI 54 (645)
T ss_pred ccccCCcccch
Confidence 66666554443
No 231
>PF06827 zf-FPG_IleRS: Zinc finger found in FPG and IleRS; InterPro: IPR010663 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 domain found at the C-terminal in both DNA glycosylase/AP lyase enzymes and in isoleucyl tRNA synthetase. In these two types of enzymes, the C-terminal domain forms a zinc finger. Some related proteins may not bind zinc. DNA glycosylase/AP lyase enzymes are involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. These enzymes have both DNA glycosylase activity (3.2.2 from EC) and AP lyase activity (4.2.99.18 from EC) []. Examples include formamidopyrimidine-DNA glycosylases (Fpg; MutM) and endonuclease VIII (Nei). Formamidopyrimidine-DNA glycosylases (Fpg, MutM) is a trifunctional DNA base excision repair enzyme that removes a wide range of oxidation-damaged bases (N-glycosylase activity; 3.2.2.23 from EC) and cleaves both the 3'- and 5'-phosphodiester bonds of the resulting apurinic/apyrimidinic site (AP lyase activity; 4.2.99.18 from EC). Fpg has a preference for oxidised purines, excising oxidized purine bases such as 7,8-dihydro-8-oxoguanine (8-oxoG). ITs AP (apurinic/apyrimidinic) lyase activity introduces nicks in the DNA strand, cleaving the DNA backbone by beta-delta elimination to generate a single-strand break at the site of the removed base with both 3'- and 5'-phosphates. Fpg is a monomer composed of 2 domains connected by a flexible hinge []. The two DNA-binding motifs (a zinc finger and the helix-two-turns-helix motifs) suggest that the oxidized base is flipped out from double-stranded DNA in the binding mode and excised by a catalytic mechanism similar to that of bifunctional base excision repair enzymes []. Fpg binds one ion of zinc at the C terminus, which contains four conserved and essential cysteines []. Endonuclease VIII (Nei) has the same enzyme activities as Fpg above, but with a preference for oxidized pyrimidines, such as thymine glycol, 5,6-dihydrouracil and 5,6-dihydrothymine [, ]. An Fpg-type zinc finger is also found at the C terminus of isoleucyl tRNA synthetase (6.1.1.5 from EC) [, ]. This enzyme catalyses the attachment of isoleucine to tRNA(Ile). As IleRS can inadvertently accommodate and process structurally similar amino acids such as valine, to avoid such errors it has two additional distinct tRNA(Ile)-dependent editing activities. One activity is designated as 'pre-transfer' editing and involves the hydrolysis of activated Val-AMP. The other activity is designated 'post-transfer' editing and involves deacylation of mischarged Val-tRNA(Ile) []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003824 catalytic activity; PDB: 1K82_C 1Q39_A 2OQ4_B 2OPF_A 1K3X_A 1K3W_A 1Q3B_A 2EA0_A 1Q3C_A 2XZF_A ....
Probab=21.75 E-value=11 Score=16.37 Aligned_cols=9 Identities=33% Similarity=0.630 Sum_probs=3.0
Q ss_pred cCCcchhhh
Q psy3948 9 KCTFCNIIF 17 (143)
Q Consensus 9 ~C~~C~~~f 17 (143)
+|+.|+...
T Consensus 3 ~C~rC~~~~ 11 (30)
T PF06827_consen 3 KCPRCWNYI 11 (30)
T ss_dssp B-TTT--BB
T ss_pred cCccCCCcc
Confidence 455555543
No 232
>PF03833 PolC_DP2: DNA polymerase II large subunit DP2; InterPro: IPR016033 DP2 is the large subunit of a two-subunit novel archaebacterial replicative DNA polymerase first characterised for Pyrococcus furiosus. The structure of DP2 appears to be organised as a ~950 residue component separated from a ~300 residue component by a ~150 residue intein. The other subunit, DP1, has sequence similarity to the eukaryotic DNA polymerase delta small subunit. This entry represents the N-terminal ~950 residue component of DP2.; GO: 0003887 DNA-directed DNA polymerase activity; PDB: 3O59_X.
Probab=20.74 E-value=33 Score=28.13 Aligned_cols=9 Identities=22% Similarity=0.589 Sum_probs=0.0
Q ss_pred ccCCcchhh
Q psy3948 8 LKCTFCNII 16 (143)
Q Consensus 8 ~~C~~C~~~ 16 (143)
..|+.||..
T Consensus 656 r~Cp~Cg~~ 664 (900)
T PF03833_consen 656 RRCPKCGKE 664 (900)
T ss_dssp ---------
T ss_pred ccCcccCCc
Confidence 356666654
No 233
>PTZ00303 phosphatidylinositol kinase; Provisional
Probab=20.66 E-value=49 Score=27.14 Aligned_cols=29 Identities=28% Similarity=0.510 Sum_probs=15.1
Q ss_pred ccCCcchhhhccchh--hHHHhhhcccCCCCC
Q psy3948 8 LKCTFCNIIFNKLQD--EELIMTHCKSCKKPK 37 (143)
Q Consensus 8 ~~C~~C~~~f~~~~~--~~~~~~~c~~c~~~~ 37 (143)
-.|..|++.|.+... ..|.| .|..||..|
T Consensus 461 dtC~~C~kkFfSlsK~L~~RKH-HCRkCGrVF 491 (1374)
T PTZ00303 461 DSCPSCGRAFISLSRPLGTRAH-HCRSCGIRL 491 (1374)
T ss_pred CcccCcCCcccccccccccccc-cccCCcccc
Confidence 457777777754321 11111 366666665
No 234
>PHA02942 putative transposase; Provisional
Probab=20.53 E-value=92 Score=23.07 Aligned_cols=10 Identities=40% Similarity=1.115 Sum_probs=6.3
Q ss_pred CccCCCCCCC
Q psy3948 72 PLKCSSCNYS 81 (143)
Q Consensus 72 ~~~c~~c~~~ 81 (143)
.|.|+.||..
T Consensus 342 ~f~C~~CG~~ 351 (383)
T PHA02942 342 YFHCPSCGYE 351 (383)
T ss_pred EEECCCCCCE
Confidence 4677777643
No 235
>PRK12722 transcriptional activator FlhC; Provisional
Probab=20.37 E-value=73 Score=21.04 Aligned_cols=10 Identities=20% Similarity=0.504 Sum_probs=4.7
Q ss_pred hcccCCCCCC
Q psy3948 29 HCKSCKKPKR 38 (143)
Q Consensus 29 ~c~~c~~~~~ 38 (143)
.|..|+..|.
T Consensus 136 ~C~~Cgg~fv 145 (187)
T PRK12722 136 SCNCCGGHFV 145 (187)
T ss_pred cCCCCCCCee
Confidence 3555554443
No 236
>PF01096 TFIIS_C: Transcription factor S-II (TFIIS); InterPro: IPR001222 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIs (TFIIS). In eukaryotes the initiation of transcription of protein encoding genes by polymerase II (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least eight different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, -IIH and -IIS []. During mRNA elongation, Pol II can encounter DNA sequences that cause reverse movement of the enzyme. Such backtracking involves extrusion of the RNA 3'-end into the pore, and can lead to transcriptional arrest. Escape from arrest requires cleavage of the extruded RNA with the help of TFIIS, which induces mRNA cleavage by enhancing the intrinsic nuclease activity of RNA polymerase (Pol) II, past template-encoded pause sites []. TFIIS extends from the polymerase surface via a pore to the internal active site. Two essential and invariant acidic residues in a TFIIS loop complement the Pol II active site and could position a metal ion and a water molecule for hydrolytic RNA cleavage. TFIIS also induces extensive structural changes in Pol II that would realign nucleic acids in the active centre. TFIIS is a protein of about 300 amino acids. It contains three regions: a variable N-terminal domain not required for TFIIS activity; a conserved central domain required for Pol II binding; and a conserved C-terminal C4-type zinc finger essential for RNA cleavage. The zinc finger folds in a conformation termed a zinc ribbon [] characterised by a three-stranded antiparallel beta-sheet and two beta-hairpins. A backbone model for Pol II-TFIIS complex was obtained from X-ray analysis. It shows that a beta hairpin protrudes from the zinc finger and complements the pol II active site []. Some viral proteins also contain the TFIIS zinc ribbon C-terminal domain. The Vaccinia virus protein, unlike its eukaryotic homologue, is an integral RNA polymerase subunit rather than a readily separable transcription factor []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding, 0006351 transcription, DNA-dependent; PDB: 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I 3I4M_I ....
Probab=20.28 E-value=53 Score=15.36 Aligned_cols=10 Identities=20% Similarity=-0.024 Sum_probs=5.5
Q ss_pred eecccccccc
Q psy3948 101 HKCANVIIIA 110 (143)
Q Consensus 101 ~~C~~C~~~f 110 (143)
|.|..|+..+
T Consensus 29 y~C~~C~~~w 38 (39)
T PF01096_consen 29 YVCCNCGHRW 38 (39)
T ss_dssp EEESSSTEEE
T ss_pred EEeCCCCCee
Confidence 5566665543
No 237
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=20.02 E-value=1.2e+02 Score=19.90 Aligned_cols=32 Identities=16% Similarity=0.253 Sum_probs=17.7
Q ss_pred CCCCccCCCCCCCCCChHHHHHHHHHhcCCCceeccccccc
Q psy3948 69 GVKPLKCSSCNYSCSTKSALSVHQKRHTGLKAHKCANVIII 109 (143)
Q Consensus 69 ~~~~~~c~~c~~~f~~~~~l~~h~~~h~~e~~~~C~~C~~~ 109 (143)
...-|.|+.|...++...+. .. -|.|+.||..
T Consensus 110 ~~~~y~C~~~~~r~sfdeA~------~~---~F~Cp~Cg~~ 141 (176)
T COG1675 110 ENNYYVCPNCHVKYSFDEAM------EL---GFTCPKCGED 141 (176)
T ss_pred cCCceeCCCCCCcccHHHHH------Hh---CCCCCCCCch
Confidence 34457777666555443221 11 1778888765
Done!