Query psy3949
Match_columns 103
No_of_seqs 103 out of 1932
Neff 11.1
Searched_HMMs 46136
Date Fri Aug 16 21:28:28 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy3949.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/3949hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2462|consensus 99.9 2.6E-28 5.6E-33 143.4 3.0 90 2-103 163-253 (279)
2 KOG2462|consensus 99.9 1E-23 2.2E-28 124.2 4.1 94 1-103 131-225 (279)
3 KOG3576|consensus 99.7 2.3E-19 5E-24 102.2 -1.2 92 1-102 118-221 (267)
4 KOG3623|consensus 99.7 4.4E-18 9.6E-23 111.4 0.5 67 37-103 894-960 (1007)
5 KOG3623|consensus 99.6 8.4E-17 1.8E-21 105.6 0.2 75 1-85 895-970 (1007)
6 KOG1074|consensus 99.6 2E-16 4.4E-21 104.8 0.7 47 2-58 355-402 (958)
7 KOG3576|consensus 99.6 4E-16 8.8E-21 89.1 -0.0 67 37-103 117-183 (267)
8 KOG3608|consensus 99.4 1.3E-13 2.7E-18 84.7 1.0 92 2-103 209-302 (467)
9 KOG3608|consensus 99.2 1.9E-12 4.2E-17 79.5 1.2 66 37-103 292-362 (467)
10 PHA02768 hypothetical protein; 99.2 5.5E-12 1.2E-16 58.2 1.7 44 37-82 5-48 (55)
11 PF13465 zf-H2C2_2: Zinc-finge 99.2 1.7E-12 3.7E-17 51.8 -0.0 24 80-103 1-24 (26)
12 PLN03086 PRLI-interacting fact 99.2 3.7E-11 8E-16 78.6 4.7 86 2-103 455-551 (567)
13 PHA00733 hypothetical protein 99.1 2.5E-11 5.4E-16 66.1 1.2 65 37-103 40-109 (128)
14 PHA02768 hypothetical protein; 99.1 1E-10 2.2E-15 54.0 2.3 37 65-103 5-41 (55)
15 KOG1074|consensus 99.1 7.8E-11 1.7E-15 79.0 2.6 67 37-103 605-678 (958)
16 PHA00733 hypothetical protein 99.0 1.6E-10 3.4E-15 63.0 2.9 80 2-90 42-124 (128)
17 PLN03086 PRLI-interacting fact 98.9 3E-09 6.6E-14 69.9 4.4 64 35-103 451-514 (567)
18 PHA00616 hypothetical protein 98.8 8.1E-10 1.8E-14 48.7 0.5 33 65-97 1-33 (44)
19 PF13465 zf-H2C2_2: Zinc-finge 98.8 6.4E-09 1.4E-13 41.3 2.2 25 52-76 1-25 (26)
20 PHA00732 hypothetical protein 98.5 6E-08 1.3E-12 48.6 1.9 46 37-88 1-47 (79)
21 PHA00616 hypothetical protein 98.5 7.1E-08 1.5E-12 42.6 1.2 34 37-70 1-34 (44)
22 PHA00732 hypothetical protein 98.3 8E-07 1.7E-11 44.5 2.9 43 1-59 2-46 (79)
23 KOG3993|consensus 98.2 1.3E-07 2.9E-12 59.8 -2.1 24 66-89 357-380 (500)
24 PF00096 zf-C2H2: Zinc finger, 97.9 3.2E-06 7E-11 32.3 0.5 22 38-59 1-22 (23)
25 KOG3993|consensus 97.9 7.6E-07 1.6E-11 56.6 -2.2 51 38-88 268-318 (500)
26 PF00096 zf-C2H2: Zinc finger, 97.9 1.1E-05 2.3E-10 30.8 1.8 22 66-87 1-22 (23)
27 PF05605 zf-Di19: Drought indu 97.9 2.5E-05 5.5E-10 36.3 3.3 50 37-89 2-53 (54)
28 PRK04860 hypothetical protein; 97.9 7E-06 1.5E-10 46.4 1.3 35 65-103 119-153 (160)
29 PF13912 zf-C2H2_6: C2H2-type 97.7 1.4E-05 3.1E-10 31.7 0.8 24 65-88 1-24 (27)
30 PF05605 zf-Di19: Drought indu 97.7 5.8E-05 1.3E-09 35.1 2.7 48 1-60 3-52 (54)
31 PF13894 zf-C2H2_4: C2H2-type 97.6 2.8E-05 6.1E-10 29.6 0.9 22 38-59 1-22 (24)
32 PF13894 zf-C2H2_4: C2H2-type 97.5 0.00013 2.7E-09 27.7 2.2 23 66-88 1-23 (24)
33 PF09237 GAGA: GAGA factor; I 97.5 5.9E-05 1.3E-09 34.2 1.2 32 62-93 21-52 (54)
34 PF13912 zf-C2H2_6: C2H2-type 97.4 8.2E-05 1.8E-09 29.4 1.1 25 37-61 1-25 (27)
35 PF12756 zf-C2H2_2: C2H2 type 97.1 0.00031 6.7E-09 36.3 1.6 71 2-88 1-73 (100)
36 smart00355 ZnF_C2H2 zinc finge 97.1 0.00034 7.4E-09 26.8 1.2 21 39-59 2-22 (26)
37 PRK04860 hypothetical protein; 97.0 0.00096 2.1E-08 37.9 2.9 40 36-79 118-157 (160)
38 smart00355 ZnF_C2H2 zinc finge 96.9 0.0011 2.3E-08 25.4 2.0 22 67-88 2-23 (26)
39 PF09237 GAGA: GAGA factor; I 96.6 0.0028 6.1E-08 28.9 2.4 29 37-65 24-52 (54)
40 PF12874 zf-met: Zinc-finger o 96.5 0.0017 3.7E-08 25.0 1.3 21 38-58 1-21 (25)
41 PF12756 zf-C2H2_2: C2H2 type 96.5 0.0039 8.4E-08 32.1 2.7 25 37-61 50-74 (100)
42 COG5189 SFP1 Putative transcri 96.4 0.0015 3.2E-08 40.8 0.9 18 1-18 350-369 (423)
43 PF13909 zf-H2C2_5: C2H2-type 96.2 0.0019 4.1E-08 24.6 0.6 20 67-87 2-21 (24)
44 COG5189 SFP1 Putative transcri 96.0 0.0037 8E-08 39.1 1.4 24 36-59 348-373 (423)
45 PF12171 zf-C2H2_jaz: Zinc-fin 95.9 0.0044 9.4E-08 24.4 0.9 22 66-87 2-23 (27)
46 cd00350 rubredoxin_like Rubred 95.8 0.0081 1.8E-07 24.9 1.7 9 92-100 16-24 (33)
47 PF13913 zf-C2HC_2: zinc-finge 95.2 0.012 2.7E-07 22.8 1.1 18 67-85 4-21 (25)
48 PF09986 DUF2225: Uncharacteri 94.2 0.019 4.1E-07 34.3 0.7 17 37-53 5-21 (214)
49 COG5048 FOG: Zn-finger [Genera 93.8 0.024 5.2E-07 36.4 0.6 61 37-97 289-355 (467)
50 COG1592 Rubrerythrin [Energy p 93.7 0.13 2.8E-06 29.5 3.3 23 65-100 134-156 (166)
51 smart00451 ZnF_U1 U1-like zinc 93.4 0.11 2.4E-06 21.4 2.2 22 37-58 3-24 (35)
52 COG2888 Predicted Zn-ribbon RN 93.3 0.059 1.3E-06 25.4 1.3 34 64-102 26-59 (61)
53 KOG2893|consensus 93.0 0.032 7E-07 33.8 0.3 45 36-85 10-54 (341)
54 TIGR00373 conserved hypothetic 92.7 0.12 2.5E-06 29.5 2.2 30 64-102 108-137 (158)
55 cd00729 rubredoxin_SM Rubredox 92.2 0.15 3.2E-06 21.3 1.7 10 37-46 2-11 (34)
56 PRK06266 transcription initiat 92.0 0.17 3.7E-06 29.4 2.3 29 65-102 117-145 (178)
57 KOG2893|consensus 91.7 0.11 2.3E-06 31.6 1.3 42 3-57 13-54 (341)
58 PRK00464 nrdR transcriptional 91.5 0.086 1.9E-06 29.9 0.8 13 66-78 29-41 (154)
59 PF13719 zinc_ribbon_5: zinc-r 91.4 0.12 2.7E-06 21.9 1.1 33 38-75 3-35 (37)
60 smart00531 TFIIE Transcription 91.3 0.14 3.1E-06 28.7 1.5 35 64-102 98-132 (147)
61 PRK14890 putative Zn-ribbon RN 91.3 0.15 3.3E-06 24.0 1.4 34 64-102 24-57 (59)
62 PF09538 FYDLN_acid: Protein o 91.1 0.19 4.2E-06 26.8 1.8 30 38-78 10-39 (108)
63 TIGR00622 ssl1 transcription f 91.0 0.4 8.6E-06 25.8 2.9 18 37-54 15-32 (112)
64 PF13717 zinc_ribbon_4: zinc-r 90.8 0.28 6E-06 20.7 1.8 12 39-50 4-15 (36)
65 COG1997 RPL43A Ribosomal prote 90.7 0.11 2.5E-06 26.4 0.7 13 64-76 52-64 (89)
66 TIGR02098 MJ0042_CXXC MJ0042 f 90.6 0.13 2.9E-06 21.7 0.8 33 38-75 3-35 (38)
67 PF07754 DUF1610: Domain of un 90.2 0.12 2.6E-06 19.8 0.4 10 92-101 15-24 (24)
68 KOG2186|consensus 89.9 0.19 4.1E-06 30.8 1.2 46 38-86 4-49 (276)
69 COG5048 FOG: Zn-finger [Genera 89.7 0.21 4.5E-06 32.1 1.5 40 64-103 288-333 (467)
70 PF10571 UPF0547: Uncharacteri 89.5 0.2 4.3E-06 19.6 0.8 9 95-103 16-24 (26)
71 KOG2186|consensus 89.3 0.14 3.1E-06 31.2 0.5 37 65-103 3-39 (276)
72 PHA00626 hypothetical protein 89.2 0.15 3.2E-06 23.8 0.4 12 92-103 22-33 (59)
73 TIGR02605 CxxC_CxxC_SSSS putat 88.4 0.31 6.7E-06 22.1 1.2 31 36-73 4-34 (52)
74 smart00834 CxxC_CXXC_SSSS Puta 88.3 0.33 7.1E-06 20.7 1.2 31 36-73 4-34 (41)
75 PF09723 Zn-ribbon_8: Zinc rib 88.1 0.34 7.4E-06 21.1 1.1 31 36-73 4-34 (42)
76 PRK00398 rpoP DNA-directed RNA 87.0 0.37 8E-06 21.4 1.0 29 37-75 3-31 (46)
77 PF15135 UPF0515: Uncharacteri 86.2 1.3 2.8E-05 27.3 3.1 59 32-103 107-165 (278)
78 COG4049 Uncharacterized protei 85.7 0.25 5.4E-06 23.0 0.1 22 37-58 17-38 (65)
79 KOG1146|consensus 85.5 0.3 6.4E-06 36.5 0.3 51 37-87 465-540 (1406)
80 TIGR00373 conserved hypothetic 85.3 1.5 3.3E-05 25.0 3.1 30 37-75 109-138 (158)
81 TIGR02300 FYDLN_acid conserved 85.2 0.84 1.8E-05 25.1 1.9 33 38-81 10-42 (129)
82 COG3357 Predicted transcriptio 84.7 0.84 1.8E-05 23.5 1.6 27 64-100 57-83 (97)
83 COG0068 HypF Hydrogenase matur 83.6 0.26 5.6E-06 34.5 -0.6 55 39-100 125-180 (750)
84 COG1996 RPC10 DNA-directed RNA 83.4 0.62 1.3E-05 21.2 0.8 28 37-74 6-33 (49)
85 smart00659 RPOLCX RNA polymera 82.7 1.6 3.4E-05 19.3 1.9 27 37-74 2-28 (44)
86 PRK09678 DNA-binding transcrip 81.1 0.74 1.6E-05 22.7 0.6 42 39-82 3-46 (72)
87 PF00301 Rubredoxin: Rubredoxi 81.1 1.7 3.7E-05 19.5 1.8 7 94-100 35-41 (47)
88 PF08790 zf-LYAR: LYAR-type C2 80.7 0.85 1.8E-05 18.1 0.6 19 67-86 2-20 (28)
89 cd00730 rubredoxin Rubredoxin; 80.5 1.6 3.4E-05 19.9 1.6 8 93-100 34-41 (50)
90 PF10013 DUF2256: Uncharacteri 80.3 1.1 2.3E-05 19.7 0.9 9 95-103 10-18 (42)
91 TIGR00280 L37a ribosomal prote 80.2 0.59 1.3E-05 24.1 0.1 11 65-75 53-63 (91)
92 PTZ00255 60S ribosomal protein 79.2 0.81 1.8E-05 23.6 0.5 11 65-75 54-64 (90)
93 TIGR01562 FdhE formate dehydro 79.0 4.2 9E-05 26.0 3.6 9 92-100 251-259 (305)
94 smart00154 ZnF_AN1 AN1-like Zi 78.8 0.85 1.8E-05 19.6 0.4 11 93-103 12-22 (39)
95 cd00924 Cyt_c_Oxidase_Vb Cytoc 78.6 0.85 1.8E-05 23.9 0.4 17 86-103 73-89 (97)
96 PF01780 Ribosomal_L37ae: Ribo 78.4 0.38 8.3E-06 24.8 -0.9 12 65-76 53-64 (90)
97 PF03604 DNA_RNApol_7kD: DNA d 78.3 2.2 4.9E-05 17.5 1.6 9 65-73 17-25 (32)
98 PLN02294 cytochrome c oxidase 78.0 0.95 2.1E-05 26.2 0.5 13 91-103 139-151 (174)
99 PRK03976 rpl37ae 50S ribosomal 77.2 0.81 1.8E-05 23.6 0.1 11 65-75 54-64 (90)
100 PF13451 zf-trcl: Probable zin 77.0 1.2 2.6E-05 20.2 0.6 18 37-54 4-21 (49)
101 COG5151 SSL1 RNA polymerase II 76.9 1.7 3.7E-05 27.7 1.4 11 93-103 388-398 (421)
102 smart00440 ZnF_C2C2 C2C2 Zinc 76.3 0.7 1.5E-05 19.9 -0.2 11 37-47 28-38 (40)
103 PF12760 Zn_Tnp_IS1595: Transp 75.9 5.8 0.00012 17.5 2.8 27 66-101 19-45 (46)
104 PF05443 ROS_MUCR: ROS/MUCR tr 75.1 1.4 3E-05 24.5 0.7 24 66-92 73-96 (132)
105 PF13240 zinc_ribbon_2: zinc-r 74.7 2 4.4E-05 16.1 0.9 6 96-101 16-21 (23)
106 PRK03824 hypA hydrogenase nick 74.6 2.3 5E-05 23.6 1.5 10 38-47 71-80 (135)
107 smart00614 ZnF_BED BED zinc fi 74.0 2.4 5.2E-05 19.1 1.2 21 66-86 19-44 (50)
108 COG3677 Transposase and inacti 73.5 1.9 4.1E-05 23.8 0.9 14 90-103 50-63 (129)
109 PF01927 Mut7-C: Mut7-C RNAse 71.3 2.8 6.1E-05 23.6 1.3 46 38-83 92-142 (147)
110 PRK03564 formate dehydrogenase 71.3 3.5 7.5E-05 26.4 1.8 9 92-100 251-259 (309)
111 PF12013 DUF3505: Protein of u 71.1 2.4 5.2E-05 22.5 1.0 25 66-90 81-109 (109)
112 PRK14873 primosome assembly pr 69.7 3.1 6.7E-05 29.4 1.5 11 92-102 421-431 (665)
113 PF02892 zf-BED: BED zinc fing 69.4 3.3 7.1E-05 17.9 1.1 21 65-85 16-40 (45)
114 PF08274 PhnA_Zn_Ribbon: PhnA 69.1 1.4 3E-05 17.8 -0.1 8 65-72 19-26 (30)
115 PF04959 ARS2: Arsenite-resist 69.0 1.2 2.7E-05 26.7 -0.4 26 65-90 77-102 (214)
116 PF01096 TFIIS_C: Transcriptio 68.8 0.26 5.7E-06 21.2 -2.5 11 37-47 28-38 (39)
117 KOG1146|consensus 68.2 3.8 8.2E-05 31.2 1.7 59 1-59 466-540 (1406)
118 PRK00432 30S ribosomal protein 67.8 2.5 5.3E-05 19.3 0.5 10 93-102 37-46 (50)
119 PTZ00043 cytochrome c oxidase 67.8 2.5 5.5E-05 25.7 0.7 14 90-103 178-191 (268)
120 PRK03681 hypA hydrogenase nick 67.7 3.3 7.1E-05 22.3 1.1 7 94-100 88-94 (114)
121 PF01428 zf-AN1: AN1-like Zinc 67.5 0.96 2.1E-05 19.8 -0.8 11 93-103 13-23 (43)
122 KOG4173|consensus 67.2 1.4 2.9E-05 26.4 -0.5 50 38-87 107-168 (253)
123 cd00065 FYVE FYVE domain; Zinc 67.0 5.3 0.00012 18.2 1.6 26 39-76 4-29 (57)
124 COG1571 Predicted DNA-binding 66.9 4.3 9.4E-05 27.0 1.6 12 65-76 367-378 (421)
125 TIGR00100 hypA hydrogenase nic 66.6 4.2 9E-05 21.9 1.3 9 67-75 72-80 (115)
126 smart00064 FYVE Protein presen 66.4 5 0.00011 19.1 1.5 27 38-76 11-37 (68)
127 PF01286 XPA_N: XPA protein N- 66.2 3.6 7.9E-05 17.2 0.8 13 67-79 5-17 (34)
128 TIGR00595 priA primosomal prot 66.1 3.3 7.3E-05 28.2 1.1 10 92-101 252-261 (505)
129 PRK12380 hydrogenase nickel in 65.5 4.5 9.8E-05 21.7 1.3 9 67-75 72-80 (113)
130 PF01363 FYVE: FYVE zinc finge 65.3 2.3 4.9E-05 20.4 0.1 27 38-76 10-36 (69)
131 PF04810 zf-Sec23_Sec24: Sec23 64.0 2.4 5.1E-05 18.2 0.1 11 90-100 21-31 (40)
132 PF07282 OrfB_Zn_ribbon: Putat 63.9 3.3 7.3E-05 19.8 0.6 14 63-76 44-57 (69)
133 KOG2785|consensus 61.9 8.9 0.00019 25.3 2.3 51 37-87 166-242 (390)
134 PRK00564 hypA hydrogenase nick 60.1 5.8 0.00013 21.5 1.1 9 38-46 72-80 (117)
135 PF02891 zf-MIZ: MIZ/SP-RING z 59.0 3.5 7.6E-05 18.7 0.2 9 93-101 41-49 (50)
136 PF02176 zf-TRAF: TRAF-type zi 58.9 3.9 8.4E-05 18.9 0.3 34 37-70 9-43 (60)
137 PF14353 CpXC: CpXC protein 58.5 3.4 7.5E-05 22.5 0.1 11 93-103 38-48 (128)
138 PF11672 DUF3268: Protein of u 58.4 7.3 0.00016 20.7 1.3 10 37-46 2-11 (102)
139 COG1675 TFA1 Transcription ini 58.0 16 0.00034 21.5 2.7 29 64-101 112-140 (176)
140 PF10537 WAC_Acf1_DNA_bd: ATP- 58.0 10 0.00022 20.1 1.8 37 1-48 4-41 (102)
141 smart00132 LIM Zinc-binding do 57.8 7 0.00015 15.8 1.0 9 94-102 28-36 (39)
142 KOG2593|consensus 57.2 11 0.00023 25.4 2.1 34 37-73 128-161 (436)
143 KOG4167|consensus 55.4 3.3 7.2E-05 29.6 -0.3 25 37-61 792-816 (907)
144 PF04423 Rad50_zn_hook: Rad50 54.9 3.7 7.9E-05 18.8 -0.1 8 95-102 22-29 (54)
145 smart00734 ZnF_Rad18 Rad18-lik 54.4 14 0.00031 14.2 1.6 8 40-47 4-11 (26)
146 PF07649 C1_3: C1-like domain; 53.4 3.7 8E-05 16.2 -0.2 11 92-102 14-24 (30)
147 PF06524 NOA36: NOA36 protein; 53.4 14 0.0003 23.2 2.1 10 92-101 208-217 (314)
148 COG1327 Predicted transcriptio 53.4 4.8 0.0001 22.9 0.1 17 37-53 28-44 (156)
149 KOG4167|consensus 53.4 2 4.4E-05 30.5 -1.5 26 64-89 791-816 (907)
150 PF10058 DUF2296: Predicted in 53.3 7.4 0.00016 18.0 0.7 9 93-101 44-52 (54)
151 COG4957 Predicted transcriptio 52.5 7.4 0.00016 21.8 0.8 10 81-90 89-98 (148)
152 PF14311 DUF4379: Domain of un 52.4 14 0.00031 16.8 1.7 11 66-76 29-39 (55)
153 PF14446 Prok-RING_1: Prokaryo 52.3 6.8 0.00015 18.2 0.5 14 2-15 7-20 (54)
154 PF01155 HypA: Hydrogenase exp 52.3 6.5 0.00014 21.1 0.5 10 38-47 71-80 (113)
155 COG3091 SprT Zn-dependent meta 52.0 5.8 0.00013 22.6 0.3 31 65-100 117-147 (156)
156 TIGR00244 transcriptional regu 51.7 4.5 9.8E-05 22.9 -0.1 17 37-53 28-44 (147)
157 COG1198 PriA Primosomal protei 51.5 11 0.00023 27.3 1.6 13 90-102 472-484 (730)
158 KOG2231|consensus 51.4 14 0.0003 26.4 2.0 41 49-89 161-206 (669)
159 PF01215 COX5B: Cytochrome c o 50.7 3 6.5E-05 23.3 -0.9 16 87-103 107-122 (136)
160 COG1326 Uncharacterized archae 50.6 11 0.00023 22.5 1.2 35 37-77 6-42 (201)
161 PF06397 Desulfoferrod_N: Desu 50.5 4.4 9.5E-05 17.1 -0.2 11 92-102 5-15 (36)
162 PF07975 C1_4: TFIIH C1-like d 50.5 3.8 8.2E-05 18.8 -0.5 24 37-60 21-44 (51)
163 KOG2807|consensus 50.2 23 0.00051 23.0 2.7 16 66-81 346-361 (378)
164 smart00661 RPOL9 RNA polymeras 49.8 5.5 0.00012 17.8 0.0 10 93-102 20-29 (52)
165 PF03107 C1_2: C1 domain; Int 49.3 11 0.00024 14.9 0.9 8 94-101 1-8 (30)
166 COG1655 Uncharacterized protei 48.6 2.7 5.9E-05 25.7 -1.3 23 37-59 19-41 (267)
167 KOG0801|consensus 48.4 7.6 0.00016 22.5 0.4 20 80-102 128-147 (205)
168 COG2331 Uncharacterized protei 48.3 6 0.00013 19.8 0.0 31 36-73 11-41 (82)
169 PF08792 A2L_zn_ribbon: A2L zi 47.1 6.3 0.00014 16.2 -0.0 10 94-103 22-31 (33)
170 COG1594 RPB9 DNA-directed RNA 46.4 8.4 0.00018 20.8 0.4 37 38-76 73-111 (113)
171 PRK00762 hypA hydrogenase nick 46.2 12 0.00027 20.4 1.1 6 95-100 94-99 (124)
172 PF10263 SprT-like: SprT-like 46.0 6.9 0.00015 21.9 0.0 29 66-102 124-152 (157)
173 PF15269 zf-C2H2_7: Zinc-finge 45.9 30 0.00065 15.4 2.2 24 36-59 19-42 (54)
174 PRK04023 DNA polymerase II lar 45.8 23 0.0005 26.7 2.5 9 93-101 663-671 (1121)
175 cd00974 DSRD Desulforedoxin (D 45.8 6.1 0.00013 16.1 -0.2 9 93-101 4-12 (34)
176 COG1779 C4-type Zn-finger prot 45.5 5.1 0.00011 23.9 -0.5 40 2-49 16-55 (201)
177 TIGR03831 YgiT_finger YgiT-typ 44.9 9.4 0.0002 16.3 0.4 10 93-102 32-41 (46)
178 KOG3408|consensus 44.2 17 0.00036 20.0 1.3 23 37-59 57-79 (129)
179 PF10276 zf-CHCC: Zinc-finger 43.8 5.5 0.00012 17.3 -0.4 11 93-103 29-39 (40)
180 PF05741 zf-nanos: Nanos RNA b 43.7 10 0.00022 17.7 0.4 11 92-102 32-42 (55)
181 PF09845 DUF2072: Zn-ribbon co 42.9 15 0.00032 20.5 1.0 10 67-76 3-12 (131)
182 TIGR00319 desulf_FeS4 desulfof 42.6 6.6 0.00014 16.0 -0.3 9 93-101 7-15 (34)
183 KOG0402|consensus 41.8 7.1 0.00015 19.9 -0.3 9 37-45 36-44 (92)
184 PRK05452 anaerobic nitric oxid 41.6 20 0.00042 24.5 1.6 14 64-77 424-437 (479)
185 PHA02998 RNA polymerase subuni 40.5 9.8 0.00021 22.4 0.1 39 38-78 144-184 (195)
186 PF02591 DUF164: Putative zinc 40.2 18 0.0004 16.6 1.0 10 64-73 45-54 (56)
187 COG3364 Zn-ribbon containing p 39.6 23 0.0005 18.8 1.4 13 37-49 2-14 (112)
188 COG0675 Transposase and inacti 39.4 14 0.0003 23.3 0.7 9 65-73 322-330 (364)
189 PF02748 PyrI_C: Aspartate car 39.3 5.5 0.00012 18.3 -0.8 14 90-103 32-45 (52)
190 TIGR01206 lysW lysine biosynth 39.3 19 0.00041 16.7 0.9 31 1-48 3-33 (54)
191 PF10164 DUF2367: Uncharacteri 39.3 17 0.00038 19.1 0.9 13 91-103 86-98 (98)
192 PF12907 zf-met2: Zinc-binding 39.2 10 0.00023 16.4 0.1 14 2-15 3-16 (40)
193 KOG2071|consensus 39.1 26 0.00056 24.6 1.9 27 35-61 416-442 (579)
194 PF09963 DUF2197: Uncharacteri 38.9 19 0.00041 16.9 0.9 14 2-15 4-17 (56)
195 COG4391 Uncharacterized protei 38.9 11 0.00024 18.0 0.1 43 56-103 15-58 (62)
196 KOG3507|consensus 38.3 14 0.00031 17.4 0.5 29 36-75 19-47 (62)
197 PF04780 DUF629: Protein of un 37.6 35 0.00075 23.4 2.2 27 37-63 57-84 (466)
198 COG1773 Rubredoxin [Energy pro 37.2 13 0.00027 17.4 0.2 13 1-13 4-16 (55)
199 KOG1280|consensus 36.5 27 0.00058 22.9 1.5 22 37-58 79-100 (381)
200 TIGR01385 TFSII transcription 36.3 12 0.00027 23.8 0.1 38 37-76 258-297 (299)
201 KOG2482|consensus 36.3 50 0.0011 21.8 2.7 57 31-87 138-217 (423)
202 PTZ00303 phosphatidylinositol 36.3 27 0.00059 25.8 1.7 12 39-50 462-473 (1374)
203 PF11789 zf-Nse: Zinc-finger o 35.5 11 0.00023 17.6 -0.2 31 64-98 23-53 (57)
204 PRK01343 zinc-binding protein; 35.4 22 0.00047 16.8 0.8 10 93-102 9-18 (57)
205 PF13824 zf-Mss51: Zinc-finger 35.3 25 0.00054 16.4 1.0 12 90-101 11-22 (55)
206 KOG3352|consensus 35.3 19 0.00041 20.6 0.7 12 92-103 132-143 (153)
207 PF14255 Cys_rich_CPXG: Cystei 35.0 23 0.00049 16.3 0.8 11 2-12 2-12 (52)
208 COG4888 Uncharacterized Zn rib 34.4 12 0.00026 19.8 -0.2 37 36-76 21-57 (104)
209 KOG3002|consensus 33.1 84 0.0018 20.3 3.3 58 37-98 80-141 (299)
210 CHL00174 accD acetyl-CoA carbo 32.9 20 0.00043 22.9 0.6 12 65-76 57-68 (296)
211 PF00412 LIM: LIM domain; Int 32.8 22 0.00048 16.0 0.6 13 66-78 27-39 (58)
212 PRK04351 hypothetical protein; 32.6 22 0.00047 20.3 0.7 10 92-101 131-140 (149)
213 TIGR01384 TFS_arch transcripti 32.6 14 0.00031 19.3 -0.0 38 37-76 62-101 (104)
214 PF02150 RNA_POL_M_15KD: RNA p 32.6 7.7 0.00017 16.1 -0.9 8 67-74 22-29 (35)
215 smart00109 C1 Protein kinase C 32.5 49 0.0011 14.0 1.8 6 40-45 14-19 (49)
216 PF13878 zf-C2H2_3: zinc-finge 32.5 51 0.0011 14.2 1.9 23 38-60 14-38 (41)
217 PF14369 zf-RING_3: zinc-finge 32.5 24 0.00052 14.6 0.6 9 3-11 24-32 (35)
218 TIGR00143 hypF [NiFe] hydrogen 32.4 7.9 0.00017 27.7 -1.3 55 39-100 92-147 (711)
219 COG1656 Uncharacterized conser 31.9 19 0.00041 20.9 0.4 12 92-103 129-140 (165)
220 PF14787 zf-CCHC_5: GAG-polypr 31.9 26 0.00056 14.8 0.7 8 95-102 4-11 (36)
221 PF08271 TF_Zn_Ribbon: TFIIB z 31.1 22 0.00048 15.3 0.4 11 37-47 19-29 (43)
222 smart00731 SprT SprT homologue 30.7 24 0.00051 19.8 0.6 11 92-102 132-142 (146)
223 COG4896 Uncharacterized protei 30.1 19 0.00041 17.2 0.1 12 65-76 31-42 (68)
224 KOG1088|consensus 30.0 21 0.00046 19.5 0.3 16 88-103 93-108 (124)
225 COG4306 Uncharacterized protei 29.9 27 0.00059 19.3 0.7 14 37-50 68-81 (160)
226 PF05191 ADK_lid: Adenylate ki 29.3 25 0.00053 14.7 0.4 12 2-13 3-14 (36)
227 PRK08222 hydrogenase 4 subunit 29.2 33 0.00072 20.1 1.1 17 2-18 116-132 (181)
228 PHA02942 putative transposase; 28.2 34 0.00075 22.7 1.1 11 92-102 341-351 (383)
229 TIGR00515 accD acetyl-CoA carb 28.1 35 0.00075 21.7 1.1 29 39-76 28-56 (285)
230 PRK05580 primosome assembly pr 28.0 33 0.00071 24.6 1.0 12 90-101 418-429 (679)
231 PF12230 PRP21_like_P: Pre-mRN 27.8 20 0.00043 21.7 0.0 29 65-94 168-196 (229)
232 COG1379 PHP family phosphoeste 27.3 23 0.00051 23.1 0.2 10 93-102 265-274 (403)
233 PRK14559 putative protein seri 27.3 38 0.00082 24.3 1.2 8 2-9 3-10 (645)
234 PRK14714 DNA polymerase II lar 27.2 81 0.0018 24.8 2.8 8 38-45 668-675 (1337)
235 KOG2907|consensus 27.1 34 0.00074 18.6 0.8 37 38-76 75-113 (116)
236 KOG0978|consensus 26.8 16 0.00035 26.2 -0.6 18 64-81 677-694 (698)
237 PF04606 Ogr_Delta: Ogr/Delta- 26.7 16 0.00034 16.2 -0.4 10 40-49 2-11 (47)
238 PF14952 zf-tcix: Putative tre 26.6 32 0.00068 15.3 0.5 7 94-100 12-18 (44)
239 TIGR02986 restrict_Alw26I type 26.6 23 0.0005 23.6 0.1 13 89-103 80-92 (424)
240 COG4338 Uncharacterized protei 26.5 21 0.00046 16.2 -0.0 14 3-16 15-28 (54)
241 PF09332 Mcm10: Mcm10 replicat 26.4 21 0.00046 23.3 -0.1 40 37-76 252-296 (344)
242 PRK07591 threonine synthase; V 26.3 47 0.001 22.3 1.5 26 37-75 18-43 (421)
243 PRK05978 hypothetical protein; 26.2 55 0.0012 18.7 1.5 30 38-76 34-63 (148)
244 PF06676 DUF1178: Protein of u 26.0 44 0.00095 19.1 1.1 7 94-100 33-39 (148)
245 PF13453 zf-TFIIB: Transcripti 25.9 26 0.00057 14.9 0.2 11 3-13 22-32 (41)
246 TIGR00627 tfb4 transcription f 25.2 80 0.0017 20.1 2.2 25 65-103 255-279 (279)
247 TIGR00240 ATCase_reg aspartate 25.1 16 0.00034 20.9 -0.7 11 93-103 132-142 (150)
248 PF14375 Cys_rich_CWC: Cystein 25.0 38 0.00083 15.2 0.7 8 3-10 1-8 (50)
249 COG1545 Predicted nucleic-acid 24.9 25 0.00054 19.7 0.0 8 95-102 31-38 (140)
250 COG1885 Uncharacterized protei 24.8 42 0.00091 18.0 0.9 9 94-102 50-58 (115)
251 PF07295 DUF1451: Protein of u 24.6 30 0.00065 19.7 0.3 11 91-101 128-138 (146)
252 PF02148 zf-UBP: Zn-finger in 24.2 21 0.00046 16.8 -0.3 14 37-50 11-24 (63)
253 PF13696 zf-CCHC_2: Zinc knuck 24.1 28 0.00061 14.3 0.1 8 94-101 9-16 (32)
254 PRK12722 transcriptional activ 24.1 75 0.0016 19.0 1.9 27 66-100 135-161 (187)
255 PF14149 YhfH: YhfH-like prote 24.0 13 0.00027 15.9 -0.9 8 94-101 14-21 (37)
256 PF03811 Zn_Tnp_IS1: InsA N-te 23.6 34 0.00074 14.4 0.3 14 86-99 22-35 (36)
257 PF00628 PHD: PHD-finger; Int 23.5 28 0.00061 15.3 0.1 8 93-100 42-49 (51)
258 PF09082 DUF1922: Domain of un 23.5 10 0.00023 18.5 -1.4 8 94-102 21-28 (68)
259 COG5236 Uncharacterized conser 23.4 54 0.0012 21.7 1.3 21 39-59 222-242 (493)
260 PF10071 DUF2310: Zn-ribbon-co 23.3 58 0.0013 20.5 1.4 28 66-100 221-248 (258)
261 PF08996 zf-DNA_Pol: DNA Polym 23.2 42 0.0009 19.8 0.8 44 2-57 20-64 (188)
262 PF03884 DUF329: Domain of unk 23.2 30 0.00066 16.3 0.2 11 2-12 4-14 (57)
263 PRK05654 acetyl-CoA carboxylas 22.8 47 0.001 21.2 0.9 29 39-76 29-57 (292)
264 KOG1842|consensus 22.5 32 0.0007 23.4 0.2 23 37-59 15-37 (505)
265 KOG2817|consensus 22.5 46 0.00099 22.3 0.9 36 63-101 347-382 (394)
266 PF11931 DUF3449: Domain of un 22.4 29 0.00063 20.8 0.0 16 86-101 94-109 (196)
267 PF09665 RE_Alw26IDE: Type II 22.3 31 0.00067 23.7 0.1 13 89-103 80-92 (511)
268 PRK12860 transcriptional activ 22.2 82 0.0018 18.9 1.8 27 66-100 135-161 (189)
269 COG5319 Uncharacterized protei 21.8 59 0.0013 18.1 1.1 12 64-75 31-42 (142)
270 KOG4602|consensus 21.8 39 0.00084 21.3 0.4 11 92-102 267-277 (318)
271 COG3024 Uncharacterized protei 21.7 47 0.001 16.1 0.6 11 2-12 9-19 (65)
272 COG1781 PyrI Aspartate carbamo 21.6 20 0.00043 20.5 -0.8 11 93-103 135-145 (153)
273 PF05180 zf-DNL: DNL zinc fing 21.4 8 0.00017 18.8 -2.0 35 37-74 4-38 (66)
274 COG4530 Uncharacterized protei 21.2 57 0.0012 17.7 0.9 11 64-74 25-35 (129)
275 PRK00893 aspartate carbamoyltr 20.9 25 0.00054 20.2 -0.4 14 90-103 131-144 (152)
276 PF12773 DZR: Double zinc ribb 20.7 93 0.002 13.5 1.5 11 64-74 28-38 (50)
277 PF05876 Terminase_GpA: Phage 20.7 51 0.0011 23.1 0.9 13 37-49 229-241 (557)
278 PLN03238 probable histone acet 20.6 1.4E+02 0.0031 19.2 2.7 22 37-58 48-69 (290)
279 smart00547 ZnF_RBZ Zinc finger 20.4 59 0.0013 11.9 0.7 7 94-100 3-9 (26)
280 PF05129 Elf1: Transcription e 20.4 48 0.001 16.7 0.6 11 90-100 19-29 (81)
281 KOG4727|consensus 20.3 69 0.0015 18.9 1.2 21 38-58 76-96 (193)
282 cd07153 Fur_like Ferric uptake 20.1 30 0.00066 18.2 -0.2 10 94-103 74-83 (116)
No 1
>KOG2462|consensus
Probab=99.94 E-value=2.6e-28 Score=143.40 Aligned_cols=90 Identities=22% Similarity=0.480 Sum_probs=77.8
Q ss_pred cccCCCcccccccCHHH-HHhhhCCCccccCCCCCcceecCCCCCCccchhHHHHHHHHhhCCCCccCCcCcccccCcch
Q psy3949 2 RCQYCKHSLSVSNGFEI-VLSHTKSCTYISRPDHNYRFVCYTCPYHTTYSQSMKSHLRKHSGEKPYKCLFCDYHCTQSGP 80 (103)
Q Consensus 2 ~C~~C~~~f~~~~~l~~-~~~h~~~~~~~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~c~~c~~~f~~~~~ 80 (103)
.|+.|||.+.+.-.|.. +++|. .+..|.+||+.|...+.|+.|+++|+|+|||.|..|+++|...++
T Consensus 163 ~C~~C~K~YvSmpALkMHirTH~------------l~c~C~iCGKaFSRPWLLQGHiRTHTGEKPF~C~hC~kAFADRSN 230 (279)
T KOG2462|consen 163 SCKYCGKVYVSMPALKMHIRTHT------------LPCECGICGKAFSRPWLLQGHIRTHTGEKPFSCPHCGKAFADRSN 230 (279)
T ss_pred cCCCCCceeeehHHHhhHhhccC------------CCcccccccccccchHHhhcccccccCCCCccCCcccchhcchHH
Confidence 45555555555555555 55443 368999999999999999999999999999999999999999999
Q ss_pred hhhhhhhcccCccCCCCCccccC
Q psy3949 81 LRRHMKIKHLMESSNSHDITFVM 103 (103)
Q Consensus 81 l~~h~~~~~~e~~~~C~~C~~~~ 103 (103)
|..|+++|.+.|+|+|..|+|+|
T Consensus 231 LRAHmQTHS~~K~~qC~~C~KsF 253 (279)
T KOG2462|consen 231 LRAHMQTHSDVKKHQCPRCGKSF 253 (279)
T ss_pred HHHHHHhhcCCccccCcchhhHH
Confidence 99999999999999999999998
No 2
>KOG2462|consensus
Probab=99.89 E-value=1e-23 Score=124.15 Aligned_cols=94 Identities=19% Similarity=0.320 Sum_probs=84.9
Q ss_pred CcccCCCcccccccCHHH-HHhhhCCCccccCCCCCcceecCCCCCCccchhHHHHHHHHhhCCCCccCCcCcccccCcc
Q psy3949 1 VRCQYCKHSLSVSNGFEI-VLSHTKSCTYISRPDHNYRFVCYTCPYHTTYSQSMKSHLRKHSGEKPYKCLFCDYHCTQSG 79 (103)
Q Consensus 1 ~~C~~C~~~f~~~~~l~~-~~~h~~~~~~~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~c~~c~~~f~~~~ 79 (103)
|.|+.||+.+.+.++|.. ...|.... .++.+.|..|++.+.+-..|..|+++|+ .+..|.+||+.|..+=
T Consensus 131 ~~c~eCgk~ysT~snLsrHkQ~H~~~~-------s~ka~~C~~C~K~YvSmpALkMHirTH~--l~c~C~iCGKaFSRPW 201 (279)
T KOG2462|consen 131 YKCPECGKSYSTSSNLSRHKQTHRSLD-------SKKAFSCKYCGKVYVSMPALKMHIRTHT--LPCECGICGKAFSRPW 201 (279)
T ss_pred eeccccccccccccccchhhccccccc-------ccccccCCCCCceeeehHHHhhHhhccC--CCcccccccccccchH
Confidence 579999999999999999 77885431 2337899999999999999999999985 6899999999999999
Q ss_pred hhhhhhhhcccCccCCCCCccccC
Q psy3949 80 PLRRHMKIKHLMESSNSHDITFVM 103 (103)
Q Consensus 80 ~l~~h~~~~~~e~~~~C~~C~~~~ 103 (103)
.|+.|+|+|+|||||.|+.|++.|
T Consensus 202 LLQGHiRTHTGEKPF~C~hC~kAF 225 (279)
T KOG2462|consen 202 LLQGHIRTHTGEKPFSCPHCGKAF 225 (279)
T ss_pred HhhcccccccCCCCccCCcccchh
Confidence 999999999999999999999988
No 3
>KOG3576|consensus
Probab=99.73 E-value=2.3e-19 Score=102.17 Aligned_cols=92 Identities=24% Similarity=0.496 Sum_probs=82.9
Q ss_pred CcccCCCcccccccCHHH-HHhhhCCCccccCCCCCcceecCCCCCCccchhHHHHHHHHhhCCCCccCCcCcccccCcc
Q psy3949 1 VRCQYCKHSLSVSNGFEI-VLSHTKSCTYISRPDHNYRFVCYTCPYHTTYSQSMKSHLRKHSGEKPYKCLFCDYHCTQSG 79 (103)
Q Consensus 1 ~~C~~C~~~f~~~~~l~~-~~~h~~~~~~~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~c~~c~~~f~~~~ 79 (103)
|.|.+|+|.|.....|.. +..|... + .+-|..||+.|-..-.|..|++.|+|.+||+|..|+++|.+.-
T Consensus 118 ftCrvCgK~F~lQRmlnrh~kch~~v-----k-----r~lct~cgkgfndtfdlkrh~rthtgvrpykc~~c~kaftqrc 187 (267)
T KOG3576|consen 118 FTCRVCGKKFGLQRMLNRHLKCHSDV-----K-----RHLCTFCGKGFNDTFDLKRHTRTHTGVRPYKCSLCEKAFTQRC 187 (267)
T ss_pred eeeehhhhhhhHHHHHHHHhhhccHH-----H-----HHHHhhccCcccchhhhhhhhccccCccccchhhhhHHHHhhc
Confidence 469999999999988999 9999988 8 8999999999999999999999999999999999999999999
Q ss_pred hhhhhhhh-cc----------cCccCCCCCcccc
Q psy3949 80 PLRRHMKI-KH----------LMESSNSHDITFV 102 (103)
Q Consensus 80 ~l~~h~~~-~~----------~e~~~~C~~C~~~ 102 (103)
+|..|.+. |. .+|.|.|.+||+|
T Consensus 188 sleshl~kvhgv~~~yaykerr~kl~vcedcg~t 221 (267)
T KOG3576|consen 188 SLESHLKKVHGVQHQYAYKERRAKLYVCEDCGYT 221 (267)
T ss_pred cHHHHHHHHcCchHHHHHHHhhhheeeecccCCC
Confidence 99999775 32 3467999999986
No 4
>KOG3623|consensus
Probab=99.68 E-value=4.4e-18 Score=111.41 Aligned_cols=67 Identities=19% Similarity=0.425 Sum_probs=63.5
Q ss_pred ceecCCCCCCccchhHHHHHHHHhhCCCCccCCcCcccccCcchhhhhhhhcccCccCCCCCccccC
Q psy3949 37 RFVCYTCPYHTTYSQSMKSHLRKHSGEKPYKCLFCDYHCTQSGPLRRHMKIKHLMESSNSHDITFVM 103 (103)
Q Consensus 37 ~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~c~~c~~~f~~~~~l~~h~~~~~~e~~~~C~~C~~~~ 103 (103)
.|.|+.|++.|...+.|..|.-.|+|.+||+|.+|.++|.....|..|.|+|.|||||.|+.|+|-|
T Consensus 894 myaCDqCDK~FqKqSSLaRHKYEHsGqRPyqC~iCkKAFKHKHHLtEHkRLHSGEKPfQCdKClKRF 960 (1007)
T KOG3623|consen 894 MYACDQCDKAFQKQSSLARHKYEHSGQRPYQCIICKKAFKHKHHLTEHKRLHSGEKPFQCDKCLKRF 960 (1007)
T ss_pred cchHHHHHHHHHhhHHHHHhhhhhcCCCCcccchhhHhhhhhhhhhhhhhhccCCCcchhhhhhhhc
Confidence 5899999999999999999999999999999999999999999999999999999999999999876
No 5
>KOG3623|consensus
Probab=99.61 E-value=8.4e-17 Score=105.56 Aligned_cols=75 Identities=27% Similarity=0.579 Sum_probs=72.0
Q ss_pred CcccCCCcccccccCHHH-HHhhhCCCccccCCCCCcceecCCCCCCccchhHHHHHHHHhhCCCCccCCcCcccccCcc
Q psy3949 1 VRCQYCKHSLSVSNGFEI-VLSHTKSCTYISRPDHNYRFVCYTCPYHTTYSQSMKSHLRKHSGEKPYKCLFCDYHCTQSG 79 (103)
Q Consensus 1 ~~C~~C~~~f~~~~~l~~-~~~h~~~~~~~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~c~~c~~~f~~~~ 79 (103)
|.|+.|+|+|.-.++|.. .-.|+|. + ||.|.+|.+.|..+-+|..|.+.|.|++||+|.+|++.|+.+.
T Consensus 895 yaCDqCDK~FqKqSSLaRHKYEHsGq-----R-----PyqC~iCkKAFKHKHHLtEHkRLHSGEKPfQCdKClKRFSHSG 964 (1007)
T KOG3623|consen 895 YACDQCDKAFQKQSSLARHKYEHSGQ-----R-----PYQCIICKKAFKHKHHLTEHKRLHSGEKPFQCDKCLKRFSHSG 964 (1007)
T ss_pred chHHHHHHHHHhhHHHHHhhhhhcCC-----C-----CcccchhhHhhhhhhhhhhhhhhccCCCcchhhhhhhhccccc
Confidence 679999999999999999 8889999 9 9999999999999999999999999999999999999999999
Q ss_pred hhhhhh
Q psy3949 80 PLRRHM 85 (103)
Q Consensus 80 ~l~~h~ 85 (103)
++.+|+
T Consensus 965 SYSQHM 970 (1007)
T KOG3623|consen 965 SYSQHM 970 (1007)
T ss_pred chHhhh
Confidence 999887
No 6
>KOG1074|consensus
Probab=99.59 E-value=2e-16 Score=104.80 Aligned_cols=47 Identities=26% Similarity=0.655 Sum_probs=32.0
Q ss_pred cccCCCcccccccCHHH-HHhhhCCCccccCCCCCcceecCCCCCCccchhHHHHHHH
Q psy3949 2 RCQYCKHSLSVSNGFEI-VLSHTKSCTYISRPDHNYRFVCYTCPYHTTYSQSMKSHLR 58 (103)
Q Consensus 2 ~C~~C~~~f~~~~~l~~-~~~h~~~~~~~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~ 58 (103)
+|..|.+.|.+.+.|+. .++|+|+ + ||.|.+||..|..+.+|..|..
T Consensus 355 kCr~CakvfgS~SaLqiHlRSHTGE-----R-----PfqCnvCG~~FSTkGNLKvH~~ 402 (958)
T KOG1074|consen 355 KCRFCAKVFGSDSALQIHLRSHTGE-----R-----PFQCNVCGNRFSTKGNLKVHFQ 402 (958)
T ss_pred hhhhhHhhcCchhhhhhhhhccCCC-----C-----Ceeecccccccccccceeeeee
Confidence 46667777777777776 6677777 6 6777777777777666666643
No 7
>KOG3576|consensus
Probab=99.56 E-value=4e-16 Score=89.10 Aligned_cols=67 Identities=21% Similarity=0.351 Sum_probs=64.7
Q ss_pred ceecCCCCCCccchhHHHHHHHHhhCCCCccCCcCcccccCcchhhhhhhhcccCccCCCCCccccC
Q psy3949 37 RFVCYTCPYHTTYSQSMKSHLRKHSGEKPYKCLFCDYHCTQSGPLRRHMKIKHLMESSNSHDITFVM 103 (103)
Q Consensus 37 ~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~c~~c~~~f~~~~~l~~h~~~~~~e~~~~C~~C~~~~ 103 (103)
.+.|.+|++.|.....|..|+.-|...+.+.|..||+.|.....|.+|.++|+|-+||+|..|++.|
T Consensus 117 ~ftCrvCgK~F~lQRmlnrh~kch~~vkr~lct~cgkgfndtfdlkrh~rthtgvrpykc~~c~kaf 183 (267)
T KOG3576|consen 117 SFTCRVCGKKFGLQRMLNRHLKCHSDVKRHLCTFCGKGFNDTFDLKRHTRTHTGVRPYKCSLCEKAF 183 (267)
T ss_pred eeeeehhhhhhhHHHHHHHHhhhccHHHHHHHhhccCcccchhhhhhhhccccCccccchhhhhHHH
Confidence 5899999999999999999999999999999999999999999999999999999999999999987
No 8
>KOG3608|consensus
Probab=99.37 E-value=1.3e-13 Score=84.65 Aligned_cols=92 Identities=20% Similarity=0.397 Sum_probs=65.3
Q ss_pred cccCCCcccccccCHHH-HHhhhCCCccccCCCCCcceecCCCCCCccchhHHHHHHHHhhCCCCccCCcCcccccCcch
Q psy3949 2 RCQYCKHSLSVSNGFEI-VLSHTKSCTYISRPDHNYRFVCYTCPYHTTYSQSMKSHLRKHSGEKPYKCLFCDYHCTQSGP 80 (103)
Q Consensus 2 ~C~~C~~~f~~~~~l~~-~~~h~~~~~~~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~c~~c~~~f~~~~~ 80 (103)
.|+.||..|+....|-+ .+..+.. ++. +|.|..|.+.|.....|..|++.|. +-|+|+.|....+..++
T Consensus 209 ACp~Cg~~F~~~tkl~DH~rRqt~l---~~n-----~fqC~~C~KrFaTeklL~~Hv~rHv--n~ykCplCdmtc~~~ss 278 (467)
T KOG3608|consen 209 ACPHCGELFRTKTKLFDHLRRQTEL---NTN-----SFQCAQCFKRFATEKLLKSHVVRHV--NCYKCPLCDMTCSSASS 278 (467)
T ss_pred ecchHHHHhccccHHHHHHHhhhhh---cCC-----chHHHHHHHHHhHHHHHHHHHHHhh--hcccccccccCCCChHH
Confidence 37778888877777766 4433221 113 6778888888888777777777773 35778888888888888
Q ss_pred hhhhhhh-cccCccCCCCCccccC
Q psy3949 81 LRRHMKI-KHLMESSNSHDITFVM 103 (103)
Q Consensus 81 l~~h~~~-~~~e~~~~C~~C~~~~ 103 (103)
|.+|++. |...|||+|+.|.+.|
T Consensus 279 L~~H~r~rHs~dkpfKCd~Cd~~c 302 (467)
T KOG3608|consen 279 LTTHIRYRHSKDKPFKCDECDTRC 302 (467)
T ss_pred HHHHHHhhhccCCCccccchhhhh
Confidence 8888876 7777888888887643
No 9
>KOG3608|consensus
Probab=99.24 E-value=1.9e-12 Score=79.55 Aligned_cols=66 Identities=23% Similarity=0.400 Sum_probs=36.6
Q ss_pred ceecCCCCCCccchhHHHHHHHHhhCCCCccCCc--CcccccCcchhhhhhhhcc-cC--ccCCCCCccccC
Q psy3949 37 RFVCYTCPYHTTYSQSMKSHLRKHSGEKPYKCLF--CDYHCTQSGPLRRHMKIKH-LM--ESSNSHDITFVM 103 (103)
Q Consensus 37 ~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~c~~--c~~~f~~~~~l~~h~~~~~-~e--~~~~C~~C~~~~ 103 (103)
|+.|+.|++.+.....|+.|...|. +..|+|.. |...+.+...+.+|.+.++ |. .+|.|..|+++|
T Consensus 292 pfKCd~Cd~~c~~esdL~kH~~~HS-~~~y~C~h~~C~~s~r~~~q~~~H~~evhEg~np~~Y~CH~Cdr~f 362 (467)
T KOG3608|consen 292 PFKCDECDTRCVRESDLAKHVQVHS-KTVYQCEHPDCHYSVRTYTQMRRHFLEVHEGNNPILYACHCCDRFF 362 (467)
T ss_pred CccccchhhhhccHHHHHHHHHhcc-ccceecCCCCCcHHHHHHHHHHHHHHHhccCCCCCceeeecchhhh
Confidence 5566666666665666666655554 34455544 5555555555555555432 32 346666666654
No 10
>PHA02768 hypothetical protein; Provisional
Probab=99.22 E-value=5.5e-12 Score=58.18 Aligned_cols=44 Identities=27% Similarity=0.392 Sum_probs=35.3
Q ss_pred ceecCCCCCCccchhHHHHHHHHhhCCCCccCCcCcccccCcchhh
Q psy3949 37 RFVCYTCPYHTTYSQSMKSHLRKHSGEKPYKCLFCDYHCTQSGPLR 82 (103)
Q Consensus 37 ~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~c~~c~~~f~~~~~l~ 82 (103)
-|.|+.||+.|....+|..|++.|. ++++|..|++.|...+.|.
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 4788888888888888888888887 5788888888888766654
No 11
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=99.22 E-value=1.7e-12 Score=51.77 Aligned_cols=24 Identities=21% Similarity=0.149 Sum_probs=20.6
Q ss_pred hhhhhhhhcccCccCCCCCccccC
Q psy3949 80 PLRRHMKIKHLMESSNSHDITFVM 103 (103)
Q Consensus 80 ~l~~h~~~~~~e~~~~C~~C~~~~ 103 (103)
+|.+|+++|+|++||.|++|++.|
T Consensus 1 ~l~~H~~~H~~~k~~~C~~C~k~F 24 (26)
T PF13465_consen 1 NLRRHMRTHTGEKPYKCPYCGKSF 24 (26)
T ss_dssp HHHHHHHHHSSSSSEEESSSSEEE
T ss_pred CHHHHhhhcCCCCCCCCCCCcCee
Confidence 477899999999999999999876
No 12
>PLN03086 PRLI-interacting factor K; Provisional
Probab=99.18 E-value=3.7e-11 Score=78.58 Aligned_cols=86 Identities=14% Similarity=0.244 Sum_probs=67.9
Q ss_pred cccCCCcccccccCHHH-HHhhhCCCccccCCCCCcceecCCCCCCccchhHHHHHHHHhhCCCCccCCcCcccccC---
Q psy3949 2 RCQYCKHSLSVSNGFEI-VLSHTKSCTYISRPDHNYRFVCYTCPYHTTYSQSMKSHLRKHSGEKPYKCLFCDYHCTQ--- 77 (103)
Q Consensus 2 ~C~~C~~~f~~~~~l~~-~~~h~~~~~~~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~c~~c~~~f~~--- 77 (103)
.|+.|++.|. ...+.. +..+. . ++.|+ |+..+ ....|..|+..|-..+++.|..|+..+..
T Consensus 455 ~C~~Cgk~f~-~s~LekH~~~~H-------k-----pv~Cp-Cg~~~-~R~~L~~H~~thCp~Kpi~C~fC~~~v~~g~~ 519 (567)
T PLN03086 455 HCEKCGQAFQ-QGEMEKHMKVFH-------E-----PLQCP-CGVVL-EKEQMVQHQASTCPLRLITCRFCGDMVQAGGS 519 (567)
T ss_pred cCCCCCCccc-hHHHHHHHHhcC-------C-----CccCC-CCCCc-chhHHHhhhhccCCCCceeCCCCCCccccCcc
Confidence 5889999885 455666 55542 4 78899 99755 56889999988999999999999998852
Q ss_pred -------cchhhhhhhhcccCccCCCCCccccC
Q psy3949 78 -------SGPLRRHMKIKHLMESSNSHDITFVM 103 (103)
Q Consensus 78 -------~~~l~~h~~~~~~e~~~~C~~C~~~~ 103 (103)
.+.|..|.... |.+++.|..||+.|
T Consensus 520 ~~d~~d~~s~Lt~HE~~C-G~rt~~C~~Cgk~V 551 (567)
T PLN03086 520 AMDVRDRLRGMSEHESIC-GSRTAPCDSCGRSV 551 (567)
T ss_pred ccchhhhhhhHHHHHHhc-CCcceEccccCCee
Confidence 34788898885 88999999999864
No 13
>PHA00733 hypothetical protein
Probab=99.10 E-value=2.5e-11 Score=66.11 Aligned_cols=65 Identities=17% Similarity=0.213 Sum_probs=37.6
Q ss_pred ceecCCCCCCccchhHHHHH--HH---HhhCCCCccCCcCcccccCcchhhhhhhhcccCccCCCCCccccC
Q psy3949 37 RFVCYTCPYHTTYSQSMKSH--LR---KHSGEKPYKCLFCDYHCTQSGPLRRHMKIKHLMESSNSHDITFVM 103 (103)
Q Consensus 37 ~~~c~~c~~~~~~~~~l~~h--~~---~~~~~~~~~c~~c~~~f~~~~~l~~h~~~~~~e~~~~C~~C~~~~ 103 (103)
++.|.+|...+.....|..+ +. .+.+.+||.|..|++.|.....|..|++.+ +.+|.|++|++.|
T Consensus 40 ~~~~~~~~~~~~~~~~l~~~~~l~~~~~~~~~kPy~C~~Cgk~Fss~s~L~~H~r~h--~~~~~C~~CgK~F 109 (128)
T PHA00733 40 RLIRAVVKTLIYNPQLLDESSYLYKLLTSKAVSPYVCPLCLMPFSSSVSLKQHIRYT--EHSKVCPVCGKEF 109 (128)
T ss_pred hHHHHHHhhhccChhhhcchHHHHhhcccCCCCCccCCCCCCcCCCHHHHHHHHhcC--CcCccCCCCCCcc
Confidence 55666666655555444443 11 223355666666666666666666666654 3456666666655
No 14
>PHA02768 hypothetical protein; Provisional
Probab=99.07 E-value=1e-10 Score=54.04 Aligned_cols=37 Identities=11% Similarity=0.291 Sum_probs=33.4
Q ss_pred CccCCcCcccccCcchhhhhhhhcccCccCCCCCccccC
Q psy3949 65 PYKCLFCDYHCTQSGPLRRHMKIKHLMESSNSHDITFVM 103 (103)
Q Consensus 65 ~~~c~~c~~~f~~~~~l~~h~~~~~~e~~~~C~~C~~~~ 103 (103)
-|.|+.||+.|...++|..|+++|+ ++|+|..|++.|
T Consensus 5 ~y~C~~CGK~Fs~~~~L~~H~r~H~--k~~kc~~C~k~f 41 (55)
T PHA02768 5 GYECPICGEIYIKRKSMITHLRKHN--TNLKLSNCKRIS 41 (55)
T ss_pred ccCcchhCCeeccHHHHHHHHHhcC--CcccCCccccee
Confidence 4789999999999999999999998 789999999876
No 15
>KOG1074|consensus
Probab=99.07 E-value=7.8e-11 Score=79.03 Aligned_cols=67 Identities=24% Similarity=0.475 Sum_probs=58.0
Q ss_pred ceecCCCCCCccchhHHHHHHHHhhCCCCccCCcCcccccCcchhhhhhhhcccCcc----CCCC---CccccC
Q psy3949 37 RFVCYTCPYHTTYSQSMKSHLRKHSGEKPYKCLFCDYHCTQSGPLRRHMKIKHLMES----SNSH---DITFVM 103 (103)
Q Consensus 37 ~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~c~~c~~~f~~~~~l~~h~~~~~~e~~----~~C~---~C~~~~ 103 (103)
+..|.+|.++..-.+.|+.|.+.|+|++||+|.+|+++|....+|..|+.+|....+ ++|+ +|.+-|
T Consensus 605 PNqCiiC~rVlSC~saLqmHyrtHtGERPFkCKiCgRAFtTkGNLkaH~~vHka~p~~R~q~ScP~~~ic~~kf 678 (958)
T KOG1074|consen 605 PNQCIICLRVLSCPSALQMHYRTHTGERPFKCKICGRAFTTKGNLKAHMSVHKAKPPARVQFSCPSTFICQKKF 678 (958)
T ss_pred ccceeeeeecccchhhhhhhhhcccCcCccccccccchhccccchhhcccccccCccccccccCCchhhhcccc
Confidence 678999999999999999999999999999999999999999999999998876543 6788 776544
No 16
>PHA00733 hypothetical protein
Probab=99.05 E-value=1.6e-10 Score=62.97 Aligned_cols=80 Identities=19% Similarity=0.227 Sum_probs=58.4
Q ss_pred cccCCCcccccccCHHH---HHhhhCCCccccCCCCCcceecCCCCCCccchhHHHHHHHHhhCCCCccCCcCcccccCc
Q psy3949 2 RCQYCKHSLSVSNGFEI---VLSHTKSCTYISRPDHNYRFVCYTCPYHTTYSQSMKSHLRKHSGEKPYKCLFCDYHCTQS 78 (103)
Q Consensus 2 ~C~~C~~~f~~~~~l~~---~~~h~~~~~~~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~c~~c~~~f~~~ 78 (103)
.|..|++.|.....+.. +..|.. .....+|.|+.|++.|.....|..|++.+ ..++.|..|++.|...
T Consensus 42 ~~~~~~~~~~~~~~l~~~~~l~~~~~-------~~~~kPy~C~~Cgk~Fss~s~L~~H~r~h--~~~~~C~~CgK~F~~~ 112 (128)
T PHA00733 42 IRAVVKTLIYNPQLLDESSYLYKLLT-------SKAVSPYVCPLCLMPFSSSVSLKQHIRYT--EHSKVCPVCGKEFRNT 112 (128)
T ss_pred HHHHHhhhccChhhhcchHHHHhhcc-------cCCCCCccCCCCCCcCCCHHHHHHHHhcC--CcCccCCCCCCccCCH
Confidence 35667766666544433 111111 11123899999999999999999999876 4579999999999999
Q ss_pred chhhhhhhhccc
Q psy3949 79 GPLRRHMKIKHL 90 (103)
Q Consensus 79 ~~l~~h~~~~~~ 90 (103)
..|..|+...++
T Consensus 113 ~sL~~H~~~~h~ 124 (128)
T PHA00733 113 DSTLDHVCKKHN 124 (128)
T ss_pred HHHHHHHHHhcC
Confidence 999999887553
No 17
>PLN03086 PRLI-interacting factor K; Provisional
Probab=98.88 E-value=3e-09 Score=69.87 Aligned_cols=64 Identities=13% Similarity=0.252 Sum_probs=54.8
Q ss_pred CcceecCCCCCCccchhHHHHHHHHhhCCCCccCCcCcccccCcchhhhhhhhcccCccCCCCCccccC
Q psy3949 35 NYRFVCYTCPYHTTYSQSMKSHLRKHSGEKPYKCLFCDYHCTQSGPLRRHMKIKHLMESSNSHDITFVM 103 (103)
Q Consensus 35 ~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~c~~c~~~f~~~~~l~~h~~~~~~e~~~~C~~C~~~~ 103 (103)
...|.|+.|+..|. ...|..|+..+. .++.|. |+..+ ....|..|+.+|.+++++.|+.|++.|
T Consensus 451 ~~H~~C~~Cgk~f~-~s~LekH~~~~H--kpv~Cp-Cg~~~-~R~~L~~H~~thCp~Kpi~C~fC~~~v 514 (567)
T PLN03086 451 KNHVHCEKCGQAFQ-QGEMEKHMKVFH--EPLQCP-CGVVL-EKEQMVQHQASTCPLRLITCRFCGDMV 514 (567)
T ss_pred ccCccCCCCCCccc-hHHHHHHHHhcC--CCccCC-CCCCc-chhHHHhhhhccCCCCceeCCCCCCcc
Confidence 33789999999986 577899999873 789999 99754 668999999999999999999999864
No 18
>PHA00616 hypothetical protein
Probab=98.83 E-value=8.1e-10 Score=48.74 Aligned_cols=33 Identities=18% Similarity=0.276 Sum_probs=20.9
Q ss_pred CccCCcCcccccCcchhhhhhhhcccCccCCCC
Q psy3949 65 PYKCLFCDYHCTQSGPLRRHMKIKHLMESSNSH 97 (103)
Q Consensus 65 ~~~c~~c~~~f~~~~~l~~h~~~~~~e~~~~C~ 97 (103)
|++|..||+.|...+.+..|++.|+|++++.|+
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~~hg~~~~~~~ 33 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLSVHKQNKLTLE 33 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHHhcCCCcccee
Confidence 456666666666666666666666666666554
No 19
>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=98.78 E-value=6.4e-09 Score=41.30 Aligned_cols=25 Identities=44% Similarity=1.113 Sum_probs=22.1
Q ss_pred HHHHHHHHhhCCCCccCCcCccccc
Q psy3949 52 SMKSHLRKHSGEKPYKCLFCDYHCT 76 (103)
Q Consensus 52 ~l~~h~~~~~~~~~~~c~~c~~~f~ 76 (103)
+|..|++.|.+++||.|..|++.|.
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 4788999999999999999999885
No 20
>PHA00732 hypothetical protein
Probab=98.52 E-value=6e-08 Score=48.56 Aligned_cols=46 Identities=28% Similarity=0.566 Sum_probs=37.0
Q ss_pred ceecCCCCCCccchhHHHHHHHH-hhCCCCccCCcCcccccCcchhhhhhhhc
Q psy3949 37 RFVCYTCPYHTTYSQSMKSHLRK-HSGEKPYKCLFCDYHCTQSGPLRRHMKIK 88 (103)
Q Consensus 37 ~~~c~~c~~~~~~~~~l~~h~~~-~~~~~~~~c~~c~~~f~~~~~l~~h~~~~ 88 (103)
||.|..|++.|.....|..|++. |. ++.|..|++.|. .+..|.+++
T Consensus 1 py~C~~Cgk~F~s~s~Lk~H~r~~H~---~~~C~~CgKsF~---~l~~H~~~~ 47 (79)
T PHA00732 1 MFKCPICGFTTVTLFALKQHARRNHT---LTKCPVCNKSYR---RLNQHFYSQ 47 (79)
T ss_pred CccCCCCCCccCCHHHHHHHhhcccC---CCccCCCCCEeC---Chhhhhccc
Confidence 47899999999999999999874 54 358999999987 466777554
No 21
>PHA00616 hypothetical protein
Probab=98.46 E-value=7.1e-08 Score=42.59 Aligned_cols=34 Identities=12% Similarity=0.211 Sum_probs=30.1
Q ss_pred ceecCCCCCCccchhHHHHHHHHhhCCCCccCCc
Q psy3949 37 RFVCYTCPYHTTYSQSMKSHLRKHSGEKPYKCLF 70 (103)
Q Consensus 37 ~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~c~~ 70 (103)
||.|..||+.|...+.|..|++.|++++++.++.
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~~hg~~~~~~~~ 34 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLSVHKQNKLTLEY 34 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHHhcCCCccceeE
Confidence 4789999999999999999999999999887653
No 22
>PHA00732 hypothetical protein
Probab=98.30 E-value=8e-07 Score=44.52 Aligned_cols=43 Identities=16% Similarity=0.343 Sum_probs=32.1
Q ss_pred CcccCCCcccccccCHHH-HHh-hhCCCccccCCCCCcceecCCCCCCccchhHHHHHHHH
Q psy3949 1 VRCQYCKHSLSVSNGFEI-VLS-HTKSCTYISRPDHNYRFVCYTCPYHTTYSQSMKSHLRK 59 (103)
Q Consensus 1 ~~C~~C~~~f~~~~~l~~-~~~-h~~~~~~~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~ 59 (103)
|.|..||+.|.+..+|.. +.. |. ++.|+.|++.|. .+..|...
T Consensus 2 y~C~~Cgk~F~s~s~Lk~H~r~~H~-------------~~~C~~CgKsF~---~l~~H~~~ 46 (79)
T PHA00732 2 FKCPICGFTTVTLFALKQHARRNHT-------------LTKCPVCNKSYR---RLNQHFYS 46 (79)
T ss_pred ccCCCCCCccCCHHHHHHHhhcccC-------------CCccCCCCCEeC---Chhhhhcc
Confidence 679999999999888888 653 42 347999999886 35666643
No 23
>KOG3993|consensus
Probab=98.16 E-value=1.3e-07 Score=59.84 Aligned_cols=24 Identities=21% Similarity=0.505 Sum_probs=15.3
Q ss_pred ccCCcCcccccCcchhhhhhhhcc
Q psy3949 66 YKCLFCDYHCTQSGPLRRHMKIKH 89 (103)
Q Consensus 66 ~~c~~c~~~f~~~~~l~~h~~~~~ 89 (103)
|.|..|++.|....-|..|+.+|+
T Consensus 357 ~~C~~C~KkFrRqAYLrKHqlthq 380 (500)
T KOG3993|consen 357 FSCHTCGKKFRRQAYLRKHQLTHQ 380 (500)
T ss_pred eecHHhhhhhHHHHHHHHhHHhhh
Confidence 556666666666666666665544
No 24
>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=97.92 E-value=3.2e-06 Score=32.29 Aligned_cols=22 Identities=23% Similarity=0.597 Sum_probs=11.3
Q ss_pred eecCCCCCCccchhHHHHHHHH
Q psy3949 38 FVCYTCPYHTTYSQSMKSHLRK 59 (103)
Q Consensus 38 ~~c~~c~~~~~~~~~l~~h~~~ 59 (103)
|.|+.|++.|.....|..|++.
T Consensus 1 y~C~~C~~~f~~~~~l~~H~~~ 22 (23)
T PF00096_consen 1 YKCPICGKSFSSKSNLKRHMRR 22 (23)
T ss_dssp EEETTTTEEESSHHHHHHHHHH
T ss_pred CCCCCCCCccCCHHHHHHHHhH
Confidence 3455555555555555555443
No 25
>KOG3993|consensus
Probab=97.90 E-value=7.6e-07 Score=56.57 Aligned_cols=51 Identities=18% Similarity=0.346 Sum_probs=28.2
Q ss_pred eecCCCCCCccchhHHHHHHHHhhCCCCccCCcCcccccCcchhhhhhhhc
Q psy3949 38 FVCYTCPYHTTYSQSMKSHLRKHSGEKPYKCLFCDYHCTQSGPLRRHMKIK 88 (103)
Q Consensus 38 ~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~c~~c~~~f~~~~~l~~h~~~~ 88 (103)
|.|..|...|...-.|.+|.-...-..-|+|..|+++|+-..+|..|.|=|
T Consensus 268 yiCqLCK~kYeD~F~LAQHrC~RIV~vEYrCPEC~KVFsCPANLASHRRWH 318 (500)
T KOG3993|consen 268 YICQLCKEKYEDAFALAQHRCPRIVHVEYRCPECDKVFSCPANLASHRRWH 318 (500)
T ss_pred HHHHHHHHhhhhHHHHhhccCCeeEEeeecCCcccccccCchhhhhhhccc
Confidence 556666655555555555543333333456666666666666666665544
No 26
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=97.90 E-value=1.1e-05 Score=30.79 Aligned_cols=22 Identities=36% Similarity=0.803 Sum_probs=15.1
Q ss_pred ccCCcCcccccCcchhhhhhhh
Q psy3949 66 YKCLFCDYHCTQSGPLRRHMKI 87 (103)
Q Consensus 66 ~~c~~c~~~f~~~~~l~~h~~~ 87 (103)
|.|..|++.|.....|..|++.
T Consensus 1 y~C~~C~~~f~~~~~l~~H~~~ 22 (23)
T PF00096_consen 1 YKCPICGKSFSSKSNLKRHMRR 22 (23)
T ss_dssp EEETTTTEEESSHHHHHHHHHH
T ss_pred CCCCCCCCccCCHHHHHHHHhH
Confidence 4566777777777777777665
No 27
>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=97.88 E-value=2.5e-05 Score=36.30 Aligned_cols=50 Identities=30% Similarity=0.525 Sum_probs=33.5
Q ss_pred ceecCCCCCCccchhHHHHHHHH-hhCC-CCccCCcCcccccCcchhhhhhhhcc
Q psy3949 37 RFVCYTCPYHTTYSQSMKSHLRK-HSGE-KPYKCLFCDYHCTQSGPLRRHMKIKH 89 (103)
Q Consensus 37 ~~~c~~c~~~~~~~~~l~~h~~~-~~~~-~~~~c~~c~~~f~~~~~l~~h~~~~~ 89 (103)
.|.|+.|++ ..+...|..|... |..+ +.+.|+.|...+. .+|.+|+..++
T Consensus 2 ~f~CP~C~~-~~~~~~L~~H~~~~H~~~~~~v~CPiC~~~~~--~~l~~Hl~~~H 53 (54)
T PF05605_consen 2 SFTCPYCGK-GFSESSLVEHCEDEHRSESKNVVCPICSSRVT--DNLIRHLNSQH 53 (54)
T ss_pred CcCCCCCCC-ccCHHHHHHHHHhHCcCCCCCccCCCchhhhh--hHHHHHHHHhc
Confidence 467888888 4556778888664 5443 4578888876533 37777877654
No 28
>PRK04860 hypothetical protein; Provisional
Probab=97.85 E-value=7e-06 Score=46.45 Aligned_cols=35 Identities=20% Similarity=0.402 Sum_probs=27.2
Q ss_pred CccCCcCcccccCcchhhhhhhhcccCccCCCCCccccC
Q psy3949 65 PYKCLFCDYHCTQSGPLRRHMKIKHLMESSNSHDITFVM 103 (103)
Q Consensus 65 ~~~c~~c~~~f~~~~~l~~h~~~~~~e~~~~C~~C~~~~ 103 (103)
+|.|. |+. ....+.+|.++++++++|.|..|+..|
T Consensus 119 ~Y~C~-C~~---~~~~~rrH~ri~~g~~~YrC~~C~~~l 153 (160)
T PRK04860 119 PYRCK-CQE---HQLTVRRHNRVVRGEAVYRCRRCGETL 153 (160)
T ss_pred EEEcC-CCC---eeCHHHHHHHHhcCCccEECCCCCcee
Confidence 47776 776 666678888888888888888888764
No 29
>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=97.70 E-value=1.4e-05 Score=31.65 Aligned_cols=24 Identities=25% Similarity=0.575 Sum_probs=13.5
Q ss_pred CccCCcCcccccCcchhhhhhhhc
Q psy3949 65 PYKCLFCDYHCTQSGPLRRHMKIK 88 (103)
Q Consensus 65 ~~~c~~c~~~f~~~~~l~~h~~~~ 88 (103)
|+.|..|++.|....+|..|++.|
T Consensus 1 ~~~C~~C~~~F~~~~~l~~H~~~h 24 (27)
T PF13912_consen 1 PFECDECGKTFSSLSALREHKRSH 24 (27)
T ss_dssp SEEETTTTEEESSHHHHHHHHCTT
T ss_pred CCCCCccCCccCChhHHHHHhHHh
Confidence 345555555565555555555544
No 30
>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=97.67 E-value=5.8e-05 Score=35.09 Aligned_cols=48 Identities=23% Similarity=0.533 Sum_probs=33.1
Q ss_pred CcccCCCcccccccCHHH--HHhhhCCCccccCCCCCcceecCCCCCCccchhHHHHHHHHh
Q psy3949 1 VRCQYCKHSLSVSNGFEI--VLSHTKSCTYISRPDHNYRFVCYTCPYHTTYSQSMKSHLRKH 60 (103)
Q Consensus 1 ~~C~~C~~~f~~~~~l~~--~~~h~~~~~~~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~~ 60 (103)
|.|+.|++.|. ...|.. ...|... + + .+.|+.|...+. ..|..|+..+
T Consensus 3 f~CP~C~~~~~-~~~L~~H~~~~H~~~-~---~-----~v~CPiC~~~~~--~~l~~Hl~~~ 52 (54)
T PF05605_consen 3 FTCPYCGKGFS-ESSLVEHCEDEHRSE-S---K-----NVVCPICSSRVT--DNLIRHLNSQ 52 (54)
T ss_pred cCCCCCCCccC-HHHHHHHHHhHCcCC-C---C-----CccCCCchhhhh--hHHHHHHHHh
Confidence 78999999554 445666 5556554 1 2 689999997543 5788887754
No 31
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=97.60 E-value=2.8e-05 Score=29.62 Aligned_cols=22 Identities=23% Similarity=0.552 Sum_probs=10.8
Q ss_pred eecCCCCCCccchhHHHHHHHH
Q psy3949 38 FVCYTCPYHTTYSQSMKSHLRK 59 (103)
Q Consensus 38 ~~c~~c~~~~~~~~~l~~h~~~ 59 (103)
|.|+.|+..|.....|..|+..
T Consensus 1 ~~C~~C~~~~~~~~~l~~H~~~ 22 (24)
T PF13894_consen 1 FQCPICGKSFRSKSELRQHMRT 22 (24)
T ss_dssp EE-SSTS-EESSHHHHHHHHHH
T ss_pred CCCcCCCCcCCcHHHHHHHHHh
Confidence 3455555555555555555543
No 32
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=97.50 E-value=0.00013 Score=27.70 Aligned_cols=23 Identities=26% Similarity=0.703 Sum_probs=15.6
Q ss_pred ccCCcCcccccCcchhhhhhhhc
Q psy3949 66 YKCLFCDYHCTQSGPLRRHMKIK 88 (103)
Q Consensus 66 ~~c~~c~~~f~~~~~l~~h~~~~ 88 (103)
|.|..|+..|.....|..|+..+
T Consensus 1 ~~C~~C~~~~~~~~~l~~H~~~~ 23 (24)
T PF13894_consen 1 FQCPICGKSFRSKSELRQHMRTH 23 (24)
T ss_dssp EE-SSTS-EESSHHHHHHHHHHH
T ss_pred CCCcCCCCcCCcHHHHHHHHHhh
Confidence 46777888888888888777664
No 33
>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=97.49 E-value=5.9e-05 Score=34.21 Aligned_cols=32 Identities=38% Similarity=0.715 Sum_probs=17.4
Q ss_pred CCCCccCCcCcccccCcchhhhhhhhcccCcc
Q psy3949 62 GEKPYKCLFCDYHCTQSGPLRRHMKIKHLMES 93 (103)
Q Consensus 62 ~~~~~~c~~c~~~f~~~~~l~~h~~~~~~e~~ 93 (103)
.+.|..|+.|+..+.++.+|.+|+.+.++.||
T Consensus 21 S~~PatCP~C~a~~~~srnLrRHle~~H~~k~ 52 (54)
T PF09237_consen 21 SEQPATCPICGAVIRQSRNLRRHLEIRHFKKP 52 (54)
T ss_dssp TS--EE-TTT--EESSHHHHHHHHHHHTTTS-
T ss_pred cCCCCCCCcchhhccchhhHHHHHHHHhcccC
Confidence 34566677777777777777777766666554
No 34
>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=97.41 E-value=8.2e-05 Score=29.40 Aligned_cols=25 Identities=24% Similarity=0.499 Sum_probs=20.6
Q ss_pred ceecCCCCCCccchhHHHHHHHHhh
Q psy3949 37 RFVCYTCPYHTTYSQSMKSHLRKHS 61 (103)
Q Consensus 37 ~~~c~~c~~~~~~~~~l~~h~~~~~ 61 (103)
++.|..|++.|.+...|..|++.|.
T Consensus 1 ~~~C~~C~~~F~~~~~l~~H~~~h~ 25 (27)
T PF13912_consen 1 PFECDECGKTFSSLSALREHKRSHC 25 (27)
T ss_dssp SEEETTTTEEESSHHHHHHHHCTTT
T ss_pred CCCCCccCCccCChhHHHHHhHHhc
Confidence 4789999999999999988887653
No 35
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=97.10 E-value=0.00031 Score=36.32 Aligned_cols=71 Identities=20% Similarity=0.421 Sum_probs=18.7
Q ss_pred cccCCCcccccccCHHH-HHh-hhCCCccccCCCCCcceecCCCCCCccchhHHHHHHHHhhCCCCccCCcCcccccCcc
Q psy3949 2 RCQYCKHSLSVSNGFEI-VLS-HTKSCTYISRPDHNYRFVCYTCPYHTTYSQSMKSHLRKHSGEKPYKCLFCDYHCTQSG 79 (103)
Q Consensus 2 ~C~~C~~~f~~~~~l~~-~~~-h~~~~~~~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~c~~c~~~f~~~~ 79 (103)
+|..|+..|.+...+.. +.. |.-. - + . ...+.....+........ ...+.|..|+..|....
T Consensus 1 ~C~~C~~~f~~~~~l~~H~~~~H~~~-----~-----~----~-~~~l~~~~~~~~~~~~~~-~~~~~C~~C~~~f~s~~ 64 (100)
T PF12756_consen 1 QCLFCDESFSSVDDLLQHMKKKHGFD-----I-----P----D-QKYLVDPNRLLNYLRKKV-KESFRCPYCNKTFRSRE 64 (100)
T ss_dssp ----------------------------------------------------------------SSEEBSSSS-EESSHH
T ss_pred Cccccccccccccccccccccccccc-----c-----c----c-cccccccccccccccccc-CCCCCCCccCCCCcCHH
Confidence 58899999999888777 543 4222 1 1 0 011112222222222111 12578888888888888
Q ss_pred hhhhhhhhc
Q psy3949 80 PLRRHMKIK 88 (103)
Q Consensus 80 ~l~~h~~~~ 88 (103)
.|..|++.+
T Consensus 65 ~l~~Hm~~~ 73 (100)
T PF12756_consen 65 ALQEHMRSK 73 (100)
T ss_dssp HHHHHHHHT
T ss_pred HHHHHHcCc
Confidence 888888763
No 36
>smart00355 ZnF_C2H2 zinc finger.
Probab=97.06 E-value=0.00034 Score=26.82 Aligned_cols=21 Identities=24% Similarity=0.466 Sum_probs=10.6
Q ss_pred ecCCCCCCccchhHHHHHHHH
Q psy3949 39 VCYTCPYHTTYSQSMKSHLRK 59 (103)
Q Consensus 39 ~c~~c~~~~~~~~~l~~h~~~ 59 (103)
.|..|++.|.....+..|+..
T Consensus 2 ~C~~C~~~f~~~~~l~~H~~~ 22 (26)
T smart00355 2 RCPECGKVFKSKSALKEHMRT 22 (26)
T ss_pred CCCCCcchhCCHHHHHHHHHH
Confidence 345555555555555555443
No 37
>PRK04860 hypothetical protein; Provisional
Probab=96.98 E-value=0.00096 Score=37.92 Aligned_cols=40 Identities=25% Similarity=0.558 Sum_probs=33.8
Q ss_pred cceecCCCCCCccchhHHHHHHHHhhCCCCccCCcCcccccCcc
Q psy3949 36 YRFVCYTCPYHTTYSQSMKSHLRKHSGEKPYKCLFCDYHCTQSG 79 (103)
Q Consensus 36 ~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~c~~c~~~f~~~~ 79 (103)
.+|.|. |+. ....+..|.+++.++++|.|..|+..+....
T Consensus 118 ~~Y~C~-C~~---~~~~~rrH~ri~~g~~~YrC~~C~~~l~~~~ 157 (160)
T PRK04860 118 FPYRCK-CQE---HQLTVRRHNRVVRGEAVYRCRRCGETLVFKG 157 (160)
T ss_pred EEEEcC-CCC---eeCHHHHHHHHhcCCccEECCCCCceeEEec
Confidence 569998 987 5677889999999999999999999876543
No 38
>smart00355 ZnF_C2H2 zinc finger.
Probab=96.91 E-value=0.0011 Score=25.36 Aligned_cols=22 Identities=23% Similarity=0.545 Sum_probs=13.6
Q ss_pred cCCcCcccccCcchhhhhhhhc
Q psy3949 67 KCLFCDYHCTQSGPLRRHMKIK 88 (103)
Q Consensus 67 ~c~~c~~~f~~~~~l~~h~~~~ 88 (103)
.|..|++.|.....+..|++.|
T Consensus 2 ~C~~C~~~f~~~~~l~~H~~~H 23 (26)
T smart00355 2 RCPECGKVFKSKSALKEHMRTH 23 (26)
T ss_pred CCCCCcchhCCHHHHHHHHHHh
Confidence 4566666666666666666544
No 39
>PF09237 GAGA: GAGA factor; InterPro: IPR015318 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Members of this entry bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognises the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognises the A in the fourth position of the consensus sequence []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1YUI_A 1YUJ_A.
Probab=96.63 E-value=0.0028 Score=28.85 Aligned_cols=29 Identities=24% Similarity=0.383 Sum_probs=22.0
Q ss_pred ceecCCCCCCccchhHHHHHHHHhhCCCC
Q psy3949 37 RFVCYTCPYHTTYSQSMKSHLRKHSGEKP 65 (103)
Q Consensus 37 ~~~c~~c~~~~~~~~~l~~h~~~~~~~~~ 65 (103)
|-.|++|+..+....+|..|+..+.+.+|
T Consensus 24 PatCP~C~a~~~~srnLrRHle~~H~~k~ 52 (54)
T PF09237_consen 24 PATCPICGAVIRQSRNLRRHLEIRHFKKP 52 (54)
T ss_dssp -EE-TTT--EESSHHHHHHHHHHHTTTS-
T ss_pred CCCCCcchhhccchhhHHHHHHHHhcccC
Confidence 78999999999999999999988877665
No 40
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=96.54 E-value=0.0017 Score=24.95 Aligned_cols=21 Identities=33% Similarity=0.686 Sum_probs=11.0
Q ss_pred eecCCCCCCccchhHHHHHHH
Q psy3949 38 FVCYTCPYHTTYSQSMKSHLR 58 (103)
Q Consensus 38 ~~c~~c~~~~~~~~~l~~h~~ 58 (103)
|.|+.|+..|.+...+..|++
T Consensus 1 ~~C~~C~~~f~s~~~~~~H~~ 21 (25)
T PF12874_consen 1 FYCDICNKSFSSENSLRQHLR 21 (25)
T ss_dssp EEETTTTEEESSHHHHHHHHT
T ss_pred CCCCCCCCCcCCHHHHHHHHC
Confidence 345555555555555555544
No 41
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=96.45 E-value=0.0039 Score=32.13 Aligned_cols=25 Identities=20% Similarity=0.485 Sum_probs=21.6
Q ss_pred ceecCCCCCCccchhHHHHHHHHhh
Q psy3949 37 RFVCYTCPYHTTYSQSMKSHLRKHS 61 (103)
Q Consensus 37 ~~~c~~c~~~~~~~~~l~~h~~~~~ 61 (103)
.+.|..|+..|.+...|..|+..+.
T Consensus 50 ~~~C~~C~~~f~s~~~l~~Hm~~~~ 74 (100)
T PF12756_consen 50 SFRCPYCNKTFRSREALQEHMRSKH 74 (100)
T ss_dssp SEEBSSSS-EESSHHHHHHHHHHTT
T ss_pred CCCCCccCCCCcCHHHHHHHHcCcc
Confidence 5899999999999999999998653
No 42
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=96.36 E-value=0.0015 Score=40.82 Aligned_cols=18 Identities=22% Similarity=0.663 Sum_probs=14.5
Q ss_pred CcccC--CCcccccccCHHH
Q psy3949 1 VRCQY--CKHSLSVSNGFEI 18 (103)
Q Consensus 1 ~~C~~--C~~~f~~~~~l~~ 18 (103)
|+|++ |.|++.....|+-
T Consensus 350 ykCpV~gC~K~YknqnGLKY 369 (423)
T COG5189 350 YKCPVEGCNKKYKNQNGLKY 369 (423)
T ss_pred ecCCCCCchhhhccccchhh
Confidence 56776 8899988888877
No 43
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=96.24 E-value=0.0019 Score=24.62 Aligned_cols=20 Identities=40% Similarity=0.891 Sum_probs=7.9
Q ss_pred cCCcCcccccCcchhhhhhhh
Q psy3949 67 KCLFCDYHCTQSGPLRRHMKI 87 (103)
Q Consensus 67 ~c~~c~~~f~~~~~l~~h~~~ 87 (103)
+|..|+.... ...|.+|++.
T Consensus 2 ~C~~C~y~t~-~~~l~~H~~~ 21 (24)
T PF13909_consen 2 KCPHCSYSTS-KSNLKRHLKR 21 (24)
T ss_dssp E-SSSS-EES-HHHHHHHHHH
T ss_pred CCCCCCCcCC-HHHHHHHHHh
Confidence 3444444443 4444444444
No 44
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=96.01 E-value=0.0037 Score=39.14 Aligned_cols=24 Identities=17% Similarity=0.380 Sum_probs=20.7
Q ss_pred cceecCC--CCCCccchhHHHHHHHH
Q psy3949 36 YRFVCYT--CPYHTTYSQSMKSHLRK 59 (103)
Q Consensus 36 ~~~~c~~--c~~~~~~~~~l~~h~~~ 59 (103)
+||.|++ |.+.+.....|.-|+..
T Consensus 348 KpykCpV~gC~K~YknqnGLKYH~lh 373 (423)
T COG5189 348 KPYKCPVEGCNKKYKNQNGLKYHMLH 373 (423)
T ss_pred ceecCCCCCchhhhccccchhhhhhc
Confidence 6999998 99999999999888763
No 45
>PF12171 zf-C2H2_jaz: Zinc-finger double-stranded RNA-binding; InterPro: IPR022755 This zinc finger is found in archaea and eukaryotes, and is approximately 30 amino acids in length. The mammalian members of this group occur multiple times along the protein, joined by flexible linkers, and are referred to as JAZ - dsRNA-binding ZF protein - zinc-fingers. The JAZ proteins are expressed in all tissues tested and localise in the nucleus, particularly the nucleolus []. JAZ preferentially binds to double-stranded (ds) RNA or RNA/DNA hybrids rather than DNA. In addition to binding double-stranded RNA, these zinc-fingers are required for nucleolar localisation. This entry represents the multiple-adjacent-C2H2 zinc finger, JAZ. ; PDB: 4DGW_A 1ZR9_A.
Probab=95.87 E-value=0.0044 Score=24.37 Aligned_cols=22 Identities=32% Similarity=0.626 Sum_probs=15.3
Q ss_pred ccCCcCcccccCcchhhhhhhh
Q psy3949 66 YKCLFCDYHCTQSGPLRRHMKI 87 (103)
Q Consensus 66 ~~c~~c~~~f~~~~~l~~h~~~ 87 (103)
|-|..|++.|.....+..|+++
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 4567777777777777777654
No 46
>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=95.84 E-value=0.0081 Score=24.90 Aligned_cols=9 Identities=0% Similarity=-0.411 Sum_probs=4.2
Q ss_pred ccCCCCCcc
Q psy3949 92 ESSNSHDIT 100 (103)
Q Consensus 92 ~~~~C~~C~ 100 (103)
.++.|++||
T Consensus 16 ~~~~CP~Cg 24 (33)
T cd00350 16 APWVCPVCG 24 (33)
T ss_pred CCCcCcCCC
Confidence 344455444
No 47
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=95.20 E-value=0.012 Score=22.75 Aligned_cols=18 Identities=22% Similarity=0.567 Sum_probs=7.8
Q ss_pred cCCcCcccccCcchhhhhh
Q psy3949 67 KCLFCDYHCTQSGPLRRHM 85 (103)
Q Consensus 67 ~c~~c~~~f~~~~~l~~h~ 85 (103)
.|..|++.| ....|.+|+
T Consensus 4 ~C~~CgR~F-~~~~l~~H~ 21 (25)
T PF13913_consen 4 PCPICGRKF-NPDRLEKHE 21 (25)
T ss_pred cCCCCCCEE-CHHHHHHHH
Confidence 344455444 333344443
No 48
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=94.23 E-value=0.019 Score=34.26 Aligned_cols=17 Identities=12% Similarity=0.299 Sum_probs=10.7
Q ss_pred ceecCCCCCCccchhHH
Q psy3949 37 RFVCYTCPYHTTYSQSM 53 (103)
Q Consensus 37 ~~~c~~c~~~~~~~~~l 53 (103)
...|+.|+..|......
T Consensus 5 ~~~CPvC~~~F~~~~vr 21 (214)
T PF09986_consen 5 KITCPVCGKEFKTKKVR 21 (214)
T ss_pred ceECCCCCCeeeeeEEE
Confidence 45677777777665443
No 49
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=93.77 E-value=0.024 Score=36.38 Aligned_cols=61 Identities=26% Similarity=0.579 Sum_probs=49.5
Q ss_pred ceecCCCCCCccchhHHHHHHH--HhhCC--CCccCC--cCcccccCcchhhhhhhhcccCccCCCC
Q psy3949 37 RFVCYTCPYHTTYSQSMKSHLR--KHSGE--KPYKCL--FCDYHCTQSGPLRRHMKIKHLMESSNSH 97 (103)
Q Consensus 37 ~~~c~~c~~~~~~~~~l~~h~~--~~~~~--~~~~c~--~c~~~f~~~~~l~~h~~~~~~e~~~~C~ 97 (103)
++.+..|...+.....+..|.. .|.++ +++.|. .|++.|.....+..|..+|++-.+..+.
T Consensus 289 ~~~~~~~~~~~s~~~~l~~~~~~~~h~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 355 (467)
T COG5048 289 PIKSKQCNISFSRSSPLTRHLRSVNHSGESLKPFSCPYSLCGKLFSRNDALKRHILLHTSISPAKEK 355 (467)
T ss_pred CCCCccccCCccccccccccccccccccccCCceeeeccCCCccccccccccCCcccccCCCccccc
Confidence 5678888888888888888888 78888 888888 6888888888888888888877665544
No 50
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=93.69 E-value=0.13 Score=29.55 Aligned_cols=23 Identities=13% Similarity=0.219 Sum_probs=17.3
Q ss_pred CccCCcCcccccCcchhhhhhhhcccCccCCCCCcc
Q psy3949 65 PYKCLFCDYHCTQSGPLRRHMKIKHLMESSNSHDIT 100 (103)
Q Consensus 65 ~~~c~~c~~~f~~~~~l~~h~~~~~~e~~~~C~~C~ 100 (103)
.|.|.+||.. +.|+.|.+||.||
T Consensus 134 ~~vC~vCGy~-------------~~ge~P~~CPiCg 156 (166)
T COG1592 134 VWVCPVCGYT-------------HEGEAPEVCPICG 156 (166)
T ss_pred EEEcCCCCCc-------------ccCCCCCcCCCCC
Confidence 5888888753 4567788888887
No 51
>smart00451 ZnF_U1 U1-like zinc finger. Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins.
Probab=93.36 E-value=0.11 Score=21.35 Aligned_cols=22 Identities=32% Similarity=0.558 Sum_probs=17.2
Q ss_pred ceecCCCCCCccchhHHHHHHH
Q psy3949 37 RFVCYTCPYHTTYSQSMKSHLR 58 (103)
Q Consensus 37 ~~~c~~c~~~~~~~~~l~~h~~ 58 (103)
+|.|+.|+..|.....+..|+.
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~ 24 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLK 24 (35)
T ss_pred CeEccccCCccCCHHHHHHHHC
Confidence 5778888888887777777765
No 52
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=93.28 E-value=0.059 Score=25.38 Aligned_cols=34 Identities=15% Similarity=0.159 Sum_probs=19.8
Q ss_pred CCccCCcCcccccCcchhhhhhhhcccCccCCCCCcccc
Q psy3949 64 KPYKCLFCDYHCTQSGPLRRHMKIKHLMESSNSHDITFV 102 (103)
Q Consensus 64 ~~~~c~~c~~~f~~~~~l~~h~~~~~~e~~~~C~~C~~~ 102 (103)
..|.|+.||..-..... +--....+|.|+.||+.
T Consensus 26 v~F~CPnCGe~~I~Rc~-----~CRk~g~~Y~Cp~CGF~ 59 (61)
T COG2888 26 VKFPCPNCGEVEIYRCA-----KCRKLGNPYRCPKCGFE 59 (61)
T ss_pred eEeeCCCCCceeeehhh-----hHHHcCCceECCCcCcc
Confidence 45778878754433322 11122367999999874
No 53
>KOG2893|consensus
Probab=93.02 E-value=0.032 Score=33.76 Aligned_cols=45 Identities=20% Similarity=0.431 Sum_probs=34.5
Q ss_pred cceecCCCCCCccchhHHHHHHHHhhCCCCccCCcCcccccCcchhhhhh
Q psy3949 36 YRFVCYTCPYHTTYSQSMKSHLRKHSGEKPYKCLFCDYHCTQSGPLRRHM 85 (103)
Q Consensus 36 ~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~c~~c~~~f~~~~~l~~h~ 85 (103)
++| |=.|++.|.....|.+|+. .+-|+|.+|-+...+.-.|..|.
T Consensus 10 kpw-cwycnrefddekiliqhqk----akhfkchichkkl~sgpglsihc 54 (341)
T KOG2893|consen 10 KPW-CWYCNREFDDEKILIQHQK----AKHFKCHICHKKLFSGPGLSIHC 54 (341)
T ss_pred Cce-eeecccccchhhhhhhhhh----hccceeeeehhhhccCCCceeeh
Confidence 366 6678999998888888776 56789999987766666777663
No 54
>TIGR00373 conserved hypothetical protein TIGR00373. This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.
Probab=92.69 E-value=0.12 Score=29.50 Aligned_cols=30 Identities=7% Similarity=-0.068 Sum_probs=19.2
Q ss_pred CCccCCcCcccccCcchhhhhhhhcccCccCCCCCcccc
Q psy3949 64 KPYKCLFCDYHCTQSGPLRRHMKIKHLMESSNSHDITFV 102 (103)
Q Consensus 64 ~~~~c~~c~~~f~~~~~l~~h~~~~~~e~~~~C~~C~~~ 102 (103)
.-|.|+.|+..|+...++. .-|.|+.||.+
T Consensus 108 ~~Y~Cp~c~~r~tf~eA~~---------~~F~Cp~Cg~~ 137 (158)
T TIGR00373 108 MFFICPNMCVRFTFNEAME---------LNFTCPRCGAM 137 (158)
T ss_pred CeEECCCCCcEeeHHHHHH---------cCCcCCCCCCE
Confidence 3467777777776666653 24777777754
No 55
>cd00729 rubredoxin_SM Rubredoxin, Small Modular nonheme iron binding domain containing a [Fe(SCys)4] center, present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=92.21 E-value=0.15 Score=21.26 Aligned_cols=10 Identities=40% Similarity=0.962 Sum_probs=5.8
Q ss_pred ceecCCCCCC
Q psy3949 37 RFVCYTCPYH 46 (103)
Q Consensus 37 ~~~c~~c~~~ 46 (103)
.|.|..||..
T Consensus 2 ~~~C~~CG~i 11 (34)
T cd00729 2 VWVCPVCGYI 11 (34)
T ss_pred eEECCCCCCE
Confidence 3566666654
No 56
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=91.96 E-value=0.17 Score=29.43 Aligned_cols=29 Identities=10% Similarity=0.103 Sum_probs=18.1
Q ss_pred CccCCcCcccccCcchhhhhhhhcccCccCCCCCcccc
Q psy3949 65 PYKCLFCDYHCTQSGPLRRHMKIKHLMESSNSHDITFV 102 (103)
Q Consensus 65 ~~~c~~c~~~f~~~~~l~~h~~~~~~e~~~~C~~C~~~ 102 (103)
-|.|+.|+..|+...++. .-|.|+.||-.
T Consensus 117 ~Y~Cp~C~~rytf~eA~~---------~~F~Cp~Cg~~ 145 (178)
T PRK06266 117 FFFCPNCHIRFTFDEAME---------YGFRCPQCGEM 145 (178)
T ss_pred EEECCCCCcEEeHHHHhh---------cCCcCCCCCCC
Confidence 466777777666665542 24777777754
No 57
>KOG2893|consensus
Probab=91.67 E-value=0.11 Score=31.59 Aligned_cols=42 Identities=21% Similarity=0.540 Sum_probs=25.4
Q ss_pred ccCCCcccccccCHHHHHhhhCCCccccCCCCCcceecCCCCCCccchhHHHHHH
Q psy3949 3 CQYCKHSLSVSNGFEIVLSHTKSCTYISRPDHNYRFVCYTCPYHTTYSQSMKSHL 57 (103)
Q Consensus 3 C~~C~~~f~~~~~l~~~~~h~~~~~~~~~~~~~~~~~c~~c~~~~~~~~~l~~h~ 57 (103)
|=.|+..|....- +..|... + .|.|-+|-+.+.+.-.|.+|.
T Consensus 13 cwycnrefddeki---liqhqka-----k-----hfkchichkkl~sgpglsihc 54 (341)
T KOG2893|consen 13 CWYCNREFDDEKI---LIQHQKA-----K-----HFKCHICHKKLFSGPGLSIHC 54 (341)
T ss_pred eeecccccchhhh---hhhhhhh-----c-----cceeeeehhhhccCCCceeeh
Confidence 4456666654311 3445556 6 778888777666666666664
No 58
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=91.49 E-value=0.086 Score=29.93 Aligned_cols=13 Identities=31% Similarity=0.554 Sum_probs=7.4
Q ss_pred ccCCcCcccccCc
Q psy3949 66 YKCLFCDYHCTQS 78 (103)
Q Consensus 66 ~~c~~c~~~f~~~ 78 (103)
++|..||.+|...
T Consensus 29 ~~c~~c~~~f~~~ 41 (154)
T PRK00464 29 RECLACGKRFTTF 41 (154)
T ss_pred eeccccCCcceEe
Confidence 5566666665543
No 59
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=91.39 E-value=0.12 Score=21.89 Aligned_cols=33 Identities=15% Similarity=0.372 Sum_probs=18.8
Q ss_pred eecCCCCCCccchhHHHHHHHHhhCCCCccCCcCcccc
Q psy3949 38 FVCYTCPYHTTYSQSMKSHLRKHSGEKPYKCLFCDYHC 75 (103)
Q Consensus 38 ~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~c~~c~~~f 75 (103)
..|+.|+..|.....- ...+.....|..|+..|
T Consensus 3 i~CP~C~~~f~v~~~~-----l~~~~~~vrC~~C~~~f 35 (37)
T PF13719_consen 3 ITCPNCQTRFRVPDDK-----LPAGGRKVRCPKCGHVF 35 (37)
T ss_pred EECCCCCceEEcCHHH-----cccCCcEEECCCCCcEe
Confidence 4677777766654431 22333456777776655
No 60
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=91.31 E-value=0.14 Score=28.74 Aligned_cols=35 Identities=14% Similarity=0.053 Sum_probs=19.2
Q ss_pred CCccCCcCcccccCcchhhhhhhhcccCccCCCCCcccc
Q psy3949 64 KPYKCLFCDYHCTQSGPLRRHMKIKHLMESSNSHDITFV 102 (103)
Q Consensus 64 ~~~~c~~c~~~f~~~~~l~~h~~~~~~e~~~~C~~C~~~ 102 (103)
.-|.|+.|+..|....++... . .+..|.|+.||..
T Consensus 98 ~~Y~Cp~C~~~y~~~ea~~~~---d-~~~~f~Cp~Cg~~ 132 (147)
T smart00531 98 AYYKCPNCQSKYTFLEANQLL---D-MDGTFTCPRCGEE 132 (147)
T ss_pred cEEECcCCCCEeeHHHHHHhc---C-CCCcEECCCCCCE
Confidence 346777777777654443210 1 1223777777754
No 61
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=91.30 E-value=0.15 Score=23.99 Aligned_cols=34 Identities=12% Similarity=0.123 Sum_probs=18.9
Q ss_pred CCccCCcCcccccCcchhhhhhhhcccCccCCCCCcccc
Q psy3949 64 KPYKCLFCDYHCTQSGPLRRHMKIKHLMESSNSHDITFV 102 (103)
Q Consensus 64 ~~~~c~~c~~~f~~~~~l~~h~~~~~~e~~~~C~~C~~~ 102 (103)
..|.|+.||..-...-. +--....+|.|+.||+.
T Consensus 24 ~~F~CPnCG~~~I~RC~-----~CRk~~~~Y~CP~CGF~ 57 (59)
T PRK14890 24 VKFLCPNCGEVIIYRCE-----KCRKQSNPYTCPKCGFE 57 (59)
T ss_pred CEeeCCCCCCeeEeech-----hHHhcCCceECCCCCCc
Confidence 35777777765222211 11112257999999974
No 62
>PF09538 FYDLN_acid: Protein of unknown function (FYDLN_acid); InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=91.07 E-value=0.19 Score=26.80 Aligned_cols=30 Identities=17% Similarity=0.319 Sum_probs=23.5
Q ss_pred eecCCCCCCccchhHHHHHHHHhhCCCCccCCcCcccccCc
Q psy3949 38 FVCYTCPYHTTYSQSMKSHLRKHSGEKPYKCLFCDYHCTQS 78 (103)
Q Consensus 38 ~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~c~~c~~~f~~~ 78 (103)
..|+.||..|.-. +..|..|++||..|...
T Consensus 10 R~Cp~CG~kFYDL-----------nk~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 10 RTCPSCGAKFYDL-----------NKDPIVCPKCGTEFPPE 39 (108)
T ss_pred ccCCCCcchhccC-----------CCCCccCCCCCCccCcc
Confidence 4899999988642 24688899999988766
No 63
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=91.01 E-value=0.4 Score=25.77 Aligned_cols=18 Identities=17% Similarity=0.320 Sum_probs=9.0
Q ss_pred ceecCCCCCCccchhHHH
Q psy3949 37 RFVCYTCPYHTTYSQSMK 54 (103)
Q Consensus 37 ~~~c~~c~~~~~~~~~l~ 54 (103)
|-.|+.||....++.+|.
T Consensus 15 P~~CpiCgLtLVss~HLA 32 (112)
T TIGR00622 15 PVECPICGLTLILSTHLA 32 (112)
T ss_pred CCcCCcCCCEEeccchHH
Confidence 344555555555544443
No 64
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=90.79 E-value=0.28 Score=20.69 Aligned_cols=12 Identities=17% Similarity=0.456 Sum_probs=5.9
Q ss_pred ecCCCCCCccch
Q psy3949 39 VCYTCPYHTTYS 50 (103)
Q Consensus 39 ~c~~c~~~~~~~ 50 (103)
.|+.|+..|...
T Consensus 4 ~Cp~C~~~y~i~ 15 (36)
T PF13717_consen 4 TCPNCQAKYEID 15 (36)
T ss_pred ECCCCCCEEeCC
Confidence 455555544433
No 65
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=90.72 E-value=0.11 Score=26.41 Aligned_cols=13 Identities=23% Similarity=0.498 Sum_probs=7.1
Q ss_pred CCccCCcCccccc
Q psy3949 64 KPYKCLFCDYHCT 76 (103)
Q Consensus 64 ~~~~c~~c~~~f~ 76 (103)
..|.|..|+..|.
T Consensus 52 GIW~C~kCg~~fA 64 (89)
T COG1997 52 GIWKCRKCGAKFA 64 (89)
T ss_pred CeEEcCCCCCeec
Confidence 3456666665553
No 66
>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=90.59 E-value=0.13 Score=21.74 Aligned_cols=33 Identities=15% Similarity=0.225 Sum_probs=16.4
Q ss_pred eecCCCCCCccchhHHHHHHHHhhCCCCccCCcCcccc
Q psy3949 38 FVCYTCPYHTTYSQSMKSHLRKHSGEKPYKCLFCDYHC 75 (103)
Q Consensus 38 ~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~c~~c~~~f 75 (103)
..|+.|+..|....... ........|..|+..|
T Consensus 3 ~~CP~C~~~~~v~~~~~-----~~~~~~v~C~~C~~~~ 35 (38)
T TIGR02098 3 IQCPNCKTSFRVVDSQL-----GANGGKVRCGKCGHVW 35 (38)
T ss_pred EECCCCCCEEEeCHHHc-----CCCCCEEECCCCCCEE
Confidence 46777776665443321 1111235666666554
No 67
>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=90.21 E-value=0.12 Score=19.83 Aligned_cols=10 Identities=10% Similarity=0.029 Sum_probs=7.0
Q ss_pred ccCCCCCccc
Q psy3949 92 ESSNSHDITF 101 (103)
Q Consensus 92 ~~~~C~~C~~ 101 (103)
-+|.|+.||+
T Consensus 15 v~f~CPnCG~ 24 (24)
T PF07754_consen 15 VPFPCPNCGF 24 (24)
T ss_pred ceEeCCCCCC
Confidence 3577888875
No 68
>KOG2186|consensus
Probab=89.88 E-value=0.19 Score=30.76 Aligned_cols=46 Identities=20% Similarity=0.496 Sum_probs=21.5
Q ss_pred eecCCCCCCccchhHHHHHHHHhhCCCCccCCcCcccccCcchhhhhhh
Q psy3949 38 FVCYTCPYHTTYSQSMKSHLRKHSGEKPYKCLFCDYHCTQSGPLRRHMK 86 (103)
Q Consensus 38 ~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~c~~c~~~f~~~~~l~~h~~ 86 (103)
|.|..||....... +..|+..-.+ .-|.|..|+..|.. ..+..|.+
T Consensus 4 FtCnvCgEsvKKp~-vekH~srCrn-~~fSCIDC~k~F~~-~sYknH~k 49 (276)
T KOG2186|consen 4 FTCNVCGESVKKPQ-VEKHMSRCRN-AYFSCIDCGKTFER-VSYKNHTK 49 (276)
T ss_pred Eehhhhhhhccccc-hHHHHHhccC-CeeEEeeccccccc-chhhhhhh
Confidence 45555555444332 2334443333 34555555555554 34444443
No 69
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=89.68 E-value=0.21 Score=32.12 Aligned_cols=40 Identities=20% Similarity=0.272 Sum_probs=35.5
Q ss_pred CCccCCcCcccccCcchhhhhhh--hcccC--ccCCCC--CccccC
Q psy3949 64 KPYKCLFCDYHCTQSGPLRRHMK--IKHLM--ESSNSH--DITFVM 103 (103)
Q Consensus 64 ~~~~c~~c~~~f~~~~~l~~h~~--~~~~e--~~~~C~--~C~~~~ 103 (103)
.++.|..|...|.....+..|.+ .|.++ +++.|+ .|++.|
T Consensus 288 ~~~~~~~~~~~~s~~~~l~~~~~~~~h~~~~~~~~~~p~~~~~~~~ 333 (467)
T COG5048 288 LPIKSKQCNISFSRSSPLTRHLRSVNHSGESLKPFSCPYSLCGKLF 333 (467)
T ss_pred cCCCCccccCCccccccccccccccccccccCCceeeeccCCCccc
Confidence 36778889999999999999999 89999 999999 788765
No 70
>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=89.48 E-value=0.2 Score=19.58 Aligned_cols=9 Identities=0% Similarity=-0.075 Sum_probs=5.7
Q ss_pred CCCCccccC
Q psy3949 95 NSHDITFVM 103 (103)
Q Consensus 95 ~C~~C~~~~ 103 (103)
.|+.||+.|
T Consensus 16 ~Cp~CG~~F 24 (26)
T PF10571_consen 16 FCPHCGYDF 24 (26)
T ss_pred cCCCCCCCC
Confidence 466666665
No 71
>KOG2186|consensus
Probab=89.35 E-value=0.14 Score=31.25 Aligned_cols=37 Identities=14% Similarity=0.210 Sum_probs=29.6
Q ss_pred CccCCcCcccccCcchhhhhhhhcccCccCCCCCccccC
Q psy3949 65 PYKCLFCDYHCTQSGPLRRHMKIKHLMESSNSHDITFVM 103 (103)
Q Consensus 65 ~~~c~~c~~~f~~~~~l~~h~~~~~~e~~~~C~~C~~~~ 103 (103)
.|.|..||-...-+ .+.+|+...++ .-|.|-.|+++|
T Consensus 3 ~FtCnvCgEsvKKp-~vekH~srCrn-~~fSCIDC~k~F 39 (276)
T KOG2186|consen 3 FFTCNVCGESVKKP-QVEKHMSRCRN-AYFSCIDCGKTF 39 (276)
T ss_pred EEehhhhhhhcccc-chHHHHHhccC-CeeEEeeccccc
Confidence 47788898765554 56779988777 779999999998
No 72
>PHA00626 hypothetical protein
Probab=89.19 E-value=0.15 Score=23.76 Aligned_cols=12 Identities=8% Similarity=0.011 Sum_probs=9.6
Q ss_pred ccCCCCCccccC
Q psy3949 92 ESSNSHDITFVM 103 (103)
Q Consensus 92 ~~~~C~~C~~~~ 103 (103)
..|+|+.||+.|
T Consensus 22 nrYkCkdCGY~f 33 (59)
T PHA00626 22 DDYVCCDCGYND 33 (59)
T ss_pred cceEcCCCCCee
Confidence 468899998876
No 73
>TIGR02605 CxxC_CxxC_SSSS putative regulatory protein, FmdB family. This model represents a region of about 50 amino acids found in a number of small proteins in a wide range of bacteria. The region begins usually with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One member of this family is has been noted as a putative regulatory protein, designated FmdB (PubMed:8841393). Most members of this family have a C-terminal region containing highly degenerate sequence, such as SSTSESTKSSGSSGSSGSSESKASGSTEKSTSSTTAAAAV in Mycobacterium tuberculosis and VAVGGSAPAPSPAPRAGGGGGGCCGGGCCG in Streptomyces avermitilis. These low complexity regions, which are not included in the model, resemble low-complexity C-terminal regions of some heterocycle-containing bacteriocin precursors.
Probab=88.40 E-value=0.31 Score=22.13 Aligned_cols=31 Identities=23% Similarity=0.456 Sum_probs=20.6
Q ss_pred cceecCCCCCCccchhHHHHHHHHhhCCCCccCCcCcc
Q psy3949 36 YRFVCYTCPYHTTYSQSMKSHLRKHSGEKPYKCLFCDY 73 (103)
Q Consensus 36 ~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~c~~c~~ 73 (103)
+.|.|..||..|...... .. ..+..|+.|+.
T Consensus 4 Yey~C~~Cg~~fe~~~~~------~~-~~~~~CP~Cg~ 34 (52)
T TIGR02605 4 YEYRCTACGHRFEVLQKM------SD-DPLATCPECGG 34 (52)
T ss_pred EEEEeCCCCCEeEEEEec------CC-CCCCCCCCCCC
Confidence 468999999888754322 11 34567888885
No 74
>smart00834 CxxC_CXXC_SSSS Putative regulatory protein. CxxC_CXXC_SSSS represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=88.31 E-value=0.33 Score=20.71 Aligned_cols=31 Identities=19% Similarity=0.412 Sum_probs=17.6
Q ss_pred cceecCCCCCCccchhHHHHHHHHhhCCCCccCCcCcc
Q psy3949 36 YRFVCYTCPYHTTYSQSMKSHLRKHSGEKPYKCLFCDY 73 (103)
Q Consensus 36 ~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~c~~c~~ 73 (103)
+.|.|..||..|...... .. .....|+.|+.
T Consensus 4 Y~y~C~~Cg~~fe~~~~~------~~-~~~~~CP~Cg~ 34 (41)
T smart00834 4 YEYRCEDCGHTFEVLQKI------SD-DPLATCPECGG 34 (41)
T ss_pred EEEEcCCCCCEEEEEEec------CC-CCCCCCCCCCC
Confidence 357788888776543322 11 23456777765
No 75
>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=88.06 E-value=0.34 Score=21.13 Aligned_cols=31 Identities=26% Similarity=0.582 Sum_probs=18.0
Q ss_pred cceecCCCCCCccchhHHHHHHHHhhCCCCccCCcCcc
Q psy3949 36 YRFVCYTCPYHTTYSQSMKSHLRKHSGEKPYKCLFCDY 73 (103)
Q Consensus 36 ~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~c~~c~~ 73 (103)
+.|.|..||..|...... .. ..+..|+.|+.
T Consensus 4 Yey~C~~Cg~~fe~~~~~------~~-~~~~~CP~Cg~ 34 (42)
T PF09723_consen 4 YEYRCEECGHEFEVLQSI------SE-DDPVPCPECGS 34 (42)
T ss_pred EEEEeCCCCCEEEEEEEc------CC-CCCCcCCCCCC
Confidence 457788887776643321 11 34556777765
No 76
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=87.02 E-value=0.37 Score=21.38 Aligned_cols=29 Identities=17% Similarity=0.622 Sum_probs=18.5
Q ss_pred ceecCCCCCCccchhHHHHHHHHhhCCCCccCCcCcccc
Q psy3949 37 RFVCYTCPYHTTYSQSMKSHLRKHSGEKPYKCLFCDYHC 75 (103)
Q Consensus 37 ~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~c~~c~~~f 75 (103)
.|.|+.||..+..... ...+.|+.||..+
T Consensus 3 ~y~C~~CG~~~~~~~~----------~~~~~Cp~CG~~~ 31 (46)
T PRK00398 3 EYKCARCGREVELDEY----------GTGVRCPYCGYRI 31 (46)
T ss_pred EEECCCCCCEEEECCC----------CCceECCCCCCeE
Confidence 6788888876654221 1257788887644
No 77
>PF15135 UPF0515: Uncharacterised protein UPF0515
Probab=86.16 E-value=1.3 Score=27.26 Aligned_cols=59 Identities=12% Similarity=0.152 Sum_probs=32.0
Q ss_pred CCCCcceecCCCCCCccchhHHHHHHHHhhCCCCccCCcCcccccCcchhhhhhhhcccCccCCCCCccccC
Q psy3949 32 PDHNYRFVCYTCPYHTTYSQSMKSHLRKHSGEKPYKCLFCDYHCTQSGPLRRHMKIKHLMESSNSHDITFVM 103 (103)
Q Consensus 32 ~~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~c~~c~~~f~~~~~l~~h~~~~~~e~~~~C~~C~~~~ 103 (103)
|+..+.|.|..|+..+- .+.......-.|..|.+.|..... ....|---|.|+.|+.+|
T Consensus 107 p~~drqFaC~~Cd~~Ww--------Rrvp~rKeVSRCr~C~~rYDPVP~-----dkmwG~aef~C~~C~h~F 165 (278)
T PF15135_consen 107 PSVDRQFACSSCDHMWW--------RRVPQRKEVSRCRKCRKRYDPVPC-----DKMWGIAEFHCPKCRHNF 165 (278)
T ss_pred cccceeeeccccchHHH--------hccCcccccccccccccccCCCcc-----ccccceeeeecccccccc
Confidence 44555889998864321 122222223457777766543321 112344457888888776
No 78
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=85.74 E-value=0.25 Score=22.98 Aligned_cols=22 Identities=14% Similarity=0.242 Sum_probs=12.5
Q ss_pred ceecCCCCCCccchhHHHHHHH
Q psy3949 37 RFVCYTCPYHTTYSQSMKSHLR 58 (103)
Q Consensus 37 ~~~c~~c~~~~~~~~~l~~h~~ 58 (103)
-+.|+.|+..|........|.-
T Consensus 17 ~lrCPRC~~~FR~~K~Y~RHVN 38 (65)
T COG4049 17 FLRCPRCGMVFRRRKDYIRHVN 38 (65)
T ss_pred eeeCCchhHHHHHhHHHHHHhh
Confidence 4566666666665555555543
No 79
>KOG1146|consensus
Probab=85.50 E-value=0.3 Score=36.50 Aligned_cols=51 Identities=33% Similarity=0.757 Sum_probs=37.3
Q ss_pred ceecCCCCCCccchhHHHHHHHH-hh------------------------CCCCccCCcCcccccCcchhhhhhhh
Q psy3949 37 RFVCYTCPYHTTYSQSMKSHLRK-HS------------------------GEKPYKCLFCDYHCTQSGPLRRHMKI 87 (103)
Q Consensus 37 ~~~c~~c~~~~~~~~~l~~h~~~-~~------------------------~~~~~~c~~c~~~f~~~~~l~~h~~~ 87 (103)
.+.|+.|+..+.....|..|++. |. +.+++.|..|...+....+|.+|+..
T Consensus 465 t~~cpkc~~~yk~a~~L~vhmRskhp~~~~~~c~~gq~~~~~arg~~~~~~~~p~~C~~C~~stttng~LsihlqS 540 (1406)
T KOG1146|consen 465 TLKCPKCNWHYKLAQTLGVHMRSKHPESQSAYCKAGQNHPRLARGEVYRCPGKPYPCRACNYSTTTNGNLSIHLQS 540 (1406)
T ss_pred cccCCccchhhhhHHHhhhcccccccccchhHhHhccccccccccccccCCCCcccceeeeeeeecchHHHHHHHH
Confidence 68888899888888888888875 21 13466777777777777777777653
No 80
>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=85.30 E-value=1.5 Score=25.03 Aligned_cols=30 Identities=20% Similarity=0.453 Sum_probs=24.7
Q ss_pred ceecCCCCCCccchhHHHHHHHHhhCCCCccCCcCcccc
Q psy3949 37 RFVCYTCPYHTTYSQSMKSHLRKHSGEKPYKCLFCDYHC 75 (103)
Q Consensus 37 ~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~c~~c~~~f 75 (103)
-|.|+.|+..|....++. .-|.|+.||...
T Consensus 109 ~Y~Cp~c~~r~tf~eA~~---------~~F~Cp~Cg~~L 138 (158)
T TIGR00373 109 FFICPNMCVRFTFNEAME---------LNFTCPRCGAML 138 (158)
T ss_pred eEECCCCCcEeeHHHHHH---------cCCcCCCCCCEe
Confidence 799999999988877763 369999999754
No 81
>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=85.18 E-value=0.84 Score=25.08 Aligned_cols=33 Identities=9% Similarity=0.077 Sum_probs=24.5
Q ss_pred eecCCCCCCccchhHHHHHHHHhhCCCCccCCcCcccccCcchh
Q psy3949 38 FVCYTCPYHTTYSQSMKSHLRKHSGEKPYKCLFCDYHCTQSGPL 81 (103)
Q Consensus 38 ~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~c~~c~~~f~~~~~l 81 (103)
..|+.||..|.- .+..|..|++||..+.....+
T Consensus 10 r~Cp~cg~kFYD-----------Lnk~p~vcP~cg~~~~~~~~~ 42 (129)
T TIGR02300 10 RICPNTGSKFYD-----------LNRRPAVSPYTGEQFPPEEAL 42 (129)
T ss_pred ccCCCcCccccc-----------cCCCCccCCCcCCccCcchhh
Confidence 589999998864 234689999999987655333
No 82
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=84.66 E-value=0.84 Score=23.52 Aligned_cols=27 Identities=15% Similarity=0.461 Sum_probs=17.1
Q ss_pred CCccCCcCcccccCcchhhhhhhhcccCccCCCCCcc
Q psy3949 64 KPYKCLFCDYHCTQSGPLRRHMKIKHLMESSNSHDIT 100 (103)
Q Consensus 64 ~~~~c~~c~~~f~~~~~l~~h~~~~~~e~~~~C~~C~ 100 (103)
+|..|..||..|.... -.+|..|+.|-
T Consensus 57 ~Pa~CkkCGfef~~~~----------ik~pSRCP~CK 83 (97)
T COG3357 57 RPARCKKCGFEFRDDK----------IKKPSRCPKCK 83 (97)
T ss_pred cChhhcccCccccccc----------cCCcccCCcch
Confidence 4667888887776521 23567777763
No 83
>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=83.63 E-value=0.26 Score=34.53 Aligned_cols=55 Identities=18% Similarity=0.304 Sum_probs=32.1
Q ss_pred ecCCCCCCccchhHHHHHHHHhhCCCCc-cCCcCcccccCcchhhhhhhhcccCccCCCCCcc
Q psy3949 39 VCYTCPYHTTYSQSMKSHLRKHSGEKPY-KCLFCDYHCTQSGPLRRHMKIKHLMESSNSHDIT 100 (103)
Q Consensus 39 ~c~~c~~~~~~~~~l~~h~~~~~~~~~~-~c~~c~~~f~~~~~l~~h~~~~~~e~~~~C~~C~ 100 (103)
.|-.||-+|.....| ...+.++..+.| .|+.|.+-+..+.+..-| . .|-.|+.||
T Consensus 125 ~CT~CGPRfTIi~al-PYDR~nTsM~~F~lC~~C~~EY~dP~nRRfH----A--Qp~aCp~CG 180 (750)
T COG0068 125 NCTNCGPRFTIIEAL-PYDRENTSMADFPLCPFCDKEYKDPLNRRFH----A--QPIACPKCG 180 (750)
T ss_pred ccCCCCcceeeeccC-CCCcccCccccCcCCHHHHHHhcCccccccc----c--ccccCcccC
Confidence 566788777766554 222334444443 577777766666553322 2 467788887
No 84
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=83.36 E-value=0.62 Score=21.17 Aligned_cols=28 Identities=14% Similarity=0.580 Sum_probs=17.1
Q ss_pred ceecCCCCCCccchhHHHHHHHHhhCCCCccCCcCccc
Q psy3949 37 RFVCYTCPYHTTYSQSMKSHLRKHSGEKPYKCLFCDYH 74 (103)
Q Consensus 37 ~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~c~~c~~~ 74 (103)
.|.|..||+.+.. ........|+.||..
T Consensus 6 ~Y~C~~Cg~~~~~----------~~~~~~irCp~Cg~r 33 (49)
T COG1996 6 EYKCARCGREVEL----------DQETRGIRCPYCGSR 33 (49)
T ss_pred EEEhhhcCCeeeh----------hhccCceeCCCCCcE
Confidence 6888888877621 112345677778753
No 85
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=82.69 E-value=1.6 Score=19.31 Aligned_cols=27 Identities=19% Similarity=0.603 Sum_probs=15.9
Q ss_pred ceecCCCCCCccchhHHHHHHHHhhCCCCccCCcCccc
Q psy3949 37 RFVCYTCPYHTTYSQSMKSHLRKHSGEKPYKCLFCDYH 74 (103)
Q Consensus 37 ~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~c~~c~~~ 74 (103)
.|.|..||..+... ...+..|..||..
T Consensus 2 ~Y~C~~Cg~~~~~~-----------~~~~irC~~CG~r 28 (44)
T smart00659 2 IYICGECGRENEIK-----------SKDVVRCRECGYR 28 (44)
T ss_pred EEECCCCCCEeecC-----------CCCceECCCCCce
Confidence 46777777655432 2235677777753
No 86
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=81.15 E-value=0.74 Score=22.73 Aligned_cols=42 Identities=14% Similarity=0.177 Sum_probs=23.2
Q ss_pred ecCCCCCCccchhHHHHHHHHhhCCCCccCC--cCcccccCcchhh
Q psy3949 39 VCYTCPYHTTYSQSMKSHLRKHSGEKPYKCL--FCDYHCTQSGPLR 82 (103)
Q Consensus 39 ~c~~c~~~~~~~~~l~~h~~~~~~~~~~~c~--~c~~~f~~~~~l~ 82 (103)
.|+.||.......+-.... ...+.-+.|. .||..|.....+.
T Consensus 3 ~CP~Cg~~a~irtSr~~s~--~~~~~Y~qC~N~eCg~tF~t~es~s 46 (72)
T PRK09678 3 HCPLCQHAAHARTSRYITD--TTKERYHQCQNVNCSATFITYESVQ 46 (72)
T ss_pred cCCCCCCccEEEEChhcCh--hhheeeeecCCCCCCCEEEEEEEEE
Confidence 5888886553333222111 1334456776 7888887655544
No 87
>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=81.14 E-value=1.7 Score=19.53 Aligned_cols=7 Identities=0% Similarity=-0.548 Sum_probs=3.4
Q ss_pred CCCCCcc
Q psy3949 94 SNSHDIT 100 (103)
Q Consensus 94 ~~C~~C~ 100 (103)
|.|++|+
T Consensus 35 w~CP~C~ 41 (47)
T PF00301_consen 35 WVCPVCG 41 (47)
T ss_dssp -B-TTTS
T ss_pred CcCcCCC
Confidence 6677775
No 88
>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=80.70 E-value=0.85 Score=18.15 Aligned_cols=19 Identities=16% Similarity=0.513 Sum_probs=8.1
Q ss_pred cCCcCcccccCcchhhhhhh
Q psy3949 67 KCLFCDYHCTQSGPLRRHMK 86 (103)
Q Consensus 67 ~c~~c~~~f~~~~~l~~h~~ 86 (103)
.|..|++.| .......|.+
T Consensus 2 sCiDC~~~F-~~~~y~~Ht~ 20 (28)
T PF08790_consen 2 SCIDCSKDF-DGDSYKSHTS 20 (28)
T ss_dssp EETTTTEEE-EGGGTTT---
T ss_pred eeecCCCCc-CcCCcCCCCc
Confidence 455566666 3334444443
No 89
>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=80.55 E-value=1.6 Score=19.91 Aligned_cols=8 Identities=0% Similarity=-0.459 Sum_probs=4.9
Q ss_pred cCCCCCcc
Q psy3949 93 SSNSHDIT 100 (103)
Q Consensus 93 ~~~C~~C~ 100 (103)
.|.|++|+
T Consensus 34 ~w~CP~C~ 41 (50)
T cd00730 34 DWVCPVCG 41 (50)
T ss_pred CCCCCCCC
Confidence 36666665
No 90
>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=80.33 E-value=1.1 Score=19.67 Aligned_cols=9 Identities=0% Similarity=-0.451 Sum_probs=6.1
Q ss_pred CCCCccccC
Q psy3949 95 NSHDITFVM 103 (103)
Q Consensus 95 ~C~~C~~~~ 103 (103)
.|.+||..|
T Consensus 10 ~C~~C~rpf 18 (42)
T PF10013_consen 10 ICPVCGRPF 18 (42)
T ss_pred cCcccCCcc
Confidence 377777765
No 91
>TIGR00280 L37a ribosomal protein L37a. This model finds eukaryotic ribosomal protein L37a and its archaeal orthologs. The nomeclature is tricky because eukaryotes have proteins called both L37 and L37a.
Probab=80.19 E-value=0.59 Score=24.13 Aligned_cols=11 Identities=18% Similarity=0.510 Sum_probs=5.6
Q ss_pred CccCCcCcccc
Q psy3949 65 PYKCLFCDYHC 75 (103)
Q Consensus 65 ~~~c~~c~~~f 75 (103)
.|.|..|++.|
T Consensus 53 IW~C~~C~~~~ 63 (91)
T TIGR00280 53 IWTCRKCGAKF 63 (91)
T ss_pred EEEcCCCCCEE
Confidence 45555555544
No 92
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=79.24 E-value=0.81 Score=23.60 Aligned_cols=11 Identities=18% Similarity=0.546 Sum_probs=5.4
Q ss_pred CccCCcCcccc
Q psy3949 65 PYKCLFCDYHC 75 (103)
Q Consensus 65 ~~~c~~c~~~f 75 (103)
.|.|..|++.|
T Consensus 54 IW~C~~C~~~~ 64 (90)
T PTZ00255 54 IWRCKGCKKTV 64 (90)
T ss_pred EEEcCCCCCEE
Confidence 44555555444
No 93
>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=79.04 E-value=4.2 Score=25.96 Aligned_cols=9 Identities=0% Similarity=0.110 Sum_probs=6.0
Q ss_pred ccCCCCCcc
Q psy3949 92 ESSNSHDIT 100 (103)
Q Consensus 92 ~~~~C~~C~ 100 (103)
+...|..|+
T Consensus 251 r~e~C~~C~ 259 (305)
T TIGR01562 251 KAETCDSCQ 259 (305)
T ss_pred EEeeccccc
Confidence 445677776
No 94
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=78.78 E-value=0.85 Score=19.58 Aligned_cols=11 Identities=0% Similarity=-0.070 Sum_probs=7.3
Q ss_pred cCCCCCccccC
Q psy3949 93 SSNSHDITFVM 103 (103)
Q Consensus 93 ~~~C~~C~~~~ 103 (103)
|+.|..|+.+|
T Consensus 12 ~f~C~~C~~~F 22 (39)
T smart00154 12 GFKCRHCGNLF 22 (39)
T ss_pred CeECCccCCcc
Confidence 56677777665
No 95
>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=78.63 E-value=0.85 Score=23.89 Aligned_cols=17 Identities=6% Similarity=0.063 Sum_probs=13.1
Q ss_pred hhcccCccCCCCCccccC
Q psy3949 86 KIKHLMESSNSHDITFVM 103 (103)
Q Consensus 86 ~~~~~e~~~~C~~C~~~~ 103 (103)
..+.| +++.|++||..|
T Consensus 73 ~l~~g-~~~rC~eCG~~f 89 (97)
T cd00924 73 WLEKG-KPKRCPECGHVF 89 (97)
T ss_pred EEeCC-CceeCCCCCcEE
Confidence 34556 799999999876
No 96
>PF01780 Ribosomal_L37ae: Ribosomal L37ae protein family; InterPro: IPR002674 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This ribosomal protein is found in archaebacteria and eukaryotes []. Ribosomal protein L37 has a single zinc finger-like motif of the C2-C2 type [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 4A1E_Y 4A17_Y 4A1C_Y 4A1A_Y 3O58_g 3IZS_m 3O5H_g 1S1I_9 3IZR_m 1YSH_D ....
Probab=78.42 E-value=0.38 Score=24.77 Aligned_cols=12 Identities=25% Similarity=0.575 Sum_probs=6.7
Q ss_pred CccCCcCccccc
Q psy3949 65 PYKCLFCDYHCT 76 (103)
Q Consensus 65 ~~~c~~c~~~f~ 76 (103)
.|.|..|++.|.
T Consensus 53 IW~C~~C~~~~A 64 (90)
T PF01780_consen 53 IWKCKKCGKKFA 64 (90)
T ss_dssp EEEETTTTEEEE
T ss_pred EeecCCCCCEEe
Confidence 456666665543
No 97
>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=78.31 E-value=2.2 Score=17.48 Aligned_cols=9 Identities=33% Similarity=0.899 Sum_probs=4.2
Q ss_pred CccCCcCcc
Q psy3949 65 PYKCLFCDY 73 (103)
Q Consensus 65 ~~~c~~c~~ 73 (103)
+..|..||.
T Consensus 17 ~irC~~CG~ 25 (32)
T PF03604_consen 17 PIRCPECGH 25 (32)
T ss_dssp TSSBSSSS-
T ss_pred cEECCcCCC
Confidence 345555554
No 98
>PLN02294 cytochrome c oxidase subunit Vb
Probab=78.01 E-value=0.95 Score=26.16 Aligned_cols=13 Identities=15% Similarity=-0.166 Sum_probs=10.9
Q ss_pred CccCCCCCccccC
Q psy3949 91 MESSNSHDITFVM 103 (103)
Q Consensus 91 e~~~~C~~C~~~~ 103 (103)
.+|+.|++||..|
T Consensus 139 Gkp~RCpeCG~~f 151 (174)
T PLN02294 139 GKSFECPVCTQYF 151 (174)
T ss_pred CCceeCCCCCCEE
Confidence 3789999999876
No 99
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=77.21 E-value=0.81 Score=23.60 Aligned_cols=11 Identities=18% Similarity=0.543 Sum_probs=5.2
Q ss_pred CccCCcCcccc
Q psy3949 65 PYKCLFCDYHC 75 (103)
Q Consensus 65 ~~~c~~c~~~f 75 (103)
.|.|..|++.|
T Consensus 54 IW~C~~C~~~~ 64 (90)
T PRK03976 54 IWECRKCGAKF 64 (90)
T ss_pred EEEcCCCCCEE
Confidence 34455555443
No 100
>PF13451 zf-trcl: Probable zinc-binding domain
Probab=77.01 E-value=1.2 Score=20.23 Aligned_cols=18 Identities=11% Similarity=0.434 Sum_probs=12.6
Q ss_pred ceecCCCCCCccchhHHH
Q psy3949 37 RFVCYTCPYHTTYSQSMK 54 (103)
Q Consensus 37 ~~~c~~c~~~~~~~~~l~ 54 (103)
.+.|..||..|.....-+
T Consensus 4 ~l~C~dCg~~FvfTa~EQ 21 (49)
T PF13451_consen 4 TLTCKDCGAEFVFTAGEQ 21 (49)
T ss_pred eEEcccCCCeEEEehhHH
Confidence 677888887777765544
No 101
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=76.87 E-value=1.7 Score=27.71 Aligned_cols=11 Identities=0% Similarity=-0.212 Sum_probs=6.3
Q ss_pred cCCCCCccccC
Q psy3949 93 SSNSHDITFVM 103 (103)
Q Consensus 93 ~~~C~~C~~~~ 103 (103)
.|.|+.|-.+|
T Consensus 388 rY~Ce~CK~~F 398 (421)
T COG5151 388 RYQCELCKSTF 398 (421)
T ss_pred ceechhhhhhh
Confidence 46666665544
No 102
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=76.30 E-value=0.7 Score=19.93 Aligned_cols=11 Identities=27% Similarity=0.600 Sum_probs=8.0
Q ss_pred ceecCCCCCCc
Q psy3949 37 RFVCYTCPYHT 47 (103)
Q Consensus 37 ~~~c~~c~~~~ 47 (103)
-|.|..|+..|
T Consensus 28 fy~C~~C~~~w 38 (40)
T smart00440 28 FYVCTKCGHRW 38 (40)
T ss_pred EEEeCCCCCEe
Confidence 57888887655
No 103
>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=75.91 E-value=5.8 Score=17.49 Aligned_cols=27 Identities=11% Similarity=0.189 Sum_probs=15.5
Q ss_pred ccCCcCcccccCcchhhhhhhhcccCccCCCCCccc
Q psy3949 66 YKCLFCDYHCTQSGPLRRHMKIKHLMESSNSHDITF 101 (103)
Q Consensus 66 ~~c~~c~~~f~~~~~l~~h~~~~~~e~~~~C~~C~~ 101 (103)
+.|+.|+.. ....+. ....|+|..|++
T Consensus 19 ~~CP~Cg~~--~~~~~~-------~~~~~~C~~C~~ 45 (46)
T PF12760_consen 19 FVCPHCGST--KHYRLK-------TRGRYRCKACRK 45 (46)
T ss_pred CCCCCCCCe--eeEEeC-------CCCeEECCCCCC
Confidence 568888754 111111 146688888875
No 104
>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=75.14 E-value=1.4 Score=24.47 Aligned_cols=24 Identities=29% Similarity=0.631 Sum_probs=12.1
Q ss_pred ccCCcCcccccCcchhhhhhhhcccCc
Q psy3949 66 YKCLFCDYHCTQSGPLRRHMKIKHLME 92 (103)
Q Consensus 66 ~~c~~c~~~f~~~~~l~~h~~~~~~e~ 92 (103)
..|.+||+.|.. |.+|++.|+|-.
T Consensus 73 i~clecGk~~k~---LkrHL~~~~glt 96 (132)
T PF05443_consen 73 IICLECGKKFKT---LKRHLRTHHGLT 96 (132)
T ss_dssp EE-TBT--EESB---HHHHHHHTT-S-
T ss_pred eEEccCCcccch---HHHHHHHccCCC
Confidence 457777776554 367777776643
No 105
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=74.69 E-value=2 Score=16.08 Aligned_cols=6 Identities=0% Similarity=-0.175 Sum_probs=3.2
Q ss_pred CCCccc
Q psy3949 96 SHDITF 101 (103)
Q Consensus 96 C~~C~~ 101 (103)
|+.||.
T Consensus 16 C~~CG~ 21 (23)
T PF13240_consen 16 CPNCGT 21 (23)
T ss_pred hhhhCC
Confidence 555554
No 106
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=74.59 E-value=2.3 Score=23.62 Aligned_cols=10 Identities=20% Similarity=0.531 Sum_probs=4.8
Q ss_pred eecCCCCCCc
Q psy3949 38 FVCYTCPYHT 47 (103)
Q Consensus 38 ~~c~~c~~~~ 47 (103)
+.|..||..|
T Consensus 71 ~~C~~CG~~~ 80 (135)
T PRK03824 71 LKCRNCGNEW 80 (135)
T ss_pred EECCCCCCEE
Confidence 4455555443
No 107
>smart00614 ZnF_BED BED zinc finger. DNA-binding domain in chromatin-boundary-element-binding proteins and transposases
Probab=74.02 E-value=2.4 Score=19.05 Aligned_cols=21 Identities=38% Similarity=0.852 Sum_probs=10.5
Q ss_pred ccCCcCcccccCc-----chhhhhhh
Q psy3949 66 YKCLFCDYHCTQS-----GPLRRHMK 86 (103)
Q Consensus 66 ~~c~~c~~~f~~~-----~~l~~h~~ 86 (103)
..|..|++.+... ++|.+|+.
T Consensus 19 a~C~~C~~~l~~~~~~gTs~L~rHl~ 44 (50)
T smart00614 19 AKCKYCGKKLSRSSKGGTSNLRRHLR 44 (50)
T ss_pred EEecCCCCEeeeCCCCCcHHHHHHHH
Confidence 3455555544332 45555555
No 108
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=73.54 E-value=1.9 Score=23.82 Aligned_cols=14 Identities=0% Similarity=-0.176 Sum_probs=11.3
Q ss_pred cCccCCCCCccccC
Q psy3949 90 LMESSNSHDITFVM 103 (103)
Q Consensus 90 ~e~~~~C~~C~~~~ 103 (103)
|...|+|+.|+++|
T Consensus 50 ~~qRyrC~~C~~tf 63 (129)
T COG3677 50 GHQRYKCKSCGSTF 63 (129)
T ss_pred cccccccCCcCcce
Confidence 35569999999987
No 109
>PF01927 Mut7-C: Mut7-C RNAse domain; InterPro: IPR002782 This prokaryotic family of proteins have no known function. The proteins contain four conserved cysteines that may be involved in metal binding or disulphide bridges.
Probab=71.33 E-value=2.8 Score=23.56 Aligned_cols=46 Identities=15% Similarity=0.175 Sum_probs=27.9
Q ss_pred eecCCCCCCccchhHHHHHHHH-----hhCCCCccCCcCcccccCcchhhh
Q psy3949 38 FVCYTCPYHTTYSQSMKSHLRK-----HSGEKPYKCLFCDYHCTQSGPLRR 83 (103)
Q Consensus 38 ~~c~~c~~~~~~~~~l~~h~~~-----~~~~~~~~c~~c~~~f~~~~~l~~ 83 (103)
..|..|+..+.....-...... ...+.-+.|..|++.|...+.+.+
T Consensus 92 sRC~~CN~~L~~v~~~~v~~~vp~~v~~~~~~f~~C~~C~kiyW~GsH~~~ 142 (147)
T PF01927_consen 92 SRCPKCNGPLRPVSKEEVKDRVPPYVYETYDEFWRCPGCGKIYWEGSHWRR 142 (147)
T ss_pred CccCCCCcEeeechhhccccccCccccccCCeEEECCCCCCEecccccHHH
Confidence 4799999766554332211111 122335789999999988776543
No 110
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=71.32 E-value=3.5 Score=26.36 Aligned_cols=9 Identities=11% Similarity=0.172 Sum_probs=6.0
Q ss_pred ccCCCCCcc
Q psy3949 92 ESSNSHDIT 100 (103)
Q Consensus 92 ~~~~C~~C~ 100 (103)
+...|..|+
T Consensus 251 r~e~C~~C~ 259 (309)
T PRK03564 251 KAESCGDCG 259 (309)
T ss_pred Eeeeccccc
Confidence 456777776
No 111
>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=71.13 E-value=2.4 Score=22.46 Aligned_cols=25 Identities=28% Similarity=0.720 Sum_probs=20.4
Q ss_pred ccC----CcCcccccCcchhhhhhhhccc
Q psy3949 66 YKC----LFCDYHCTQSGPLRRHMKIKHL 90 (103)
Q Consensus 66 ~~c----~~c~~~f~~~~~l~~h~~~~~~ 90 (103)
|.| ..|+....+...+.+|.+.++|
T Consensus 81 ~~C~~~~~~C~y~~~~~~~m~~H~~~~Hg 109 (109)
T PF12013_consen 81 YRCQCDPPHCGYITRSKKTMRKHWRKEHG 109 (109)
T ss_pred eeeecCCCCCCcEeccHHHHHHHHHHhcC
Confidence 578 8888888888889988887654
No 112
>PRK14873 primosome assembly protein PriA; Provisional
Probab=69.70 E-value=3.1 Score=29.43 Aligned_cols=11 Identities=0% Similarity=-0.366 Sum_probs=8.0
Q ss_pred ccCCCCCcccc
Q psy3949 92 ESSNSHDITFV 102 (103)
Q Consensus 92 ~~~~C~~C~~~ 102 (103)
.|+.|+.||-.
T Consensus 421 ~p~~Cp~Cgs~ 431 (665)
T PRK14873 421 PDWRCPRCGSD 431 (665)
T ss_pred cCccCCCCcCC
Confidence 36788888853
No 113
>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=69.36 E-value=3.3 Score=17.94 Aligned_cols=21 Identities=29% Similarity=0.649 Sum_probs=8.9
Q ss_pred CccCCcCcccccC----cchhhhhh
Q psy3949 65 PYKCLFCDYHCTQ----SGPLRRHM 85 (103)
Q Consensus 65 ~~~c~~c~~~f~~----~~~l~~h~ 85 (103)
...|..|++.+.. .+.|.+|+
T Consensus 16 ~a~C~~C~~~~~~~~~~ts~l~~HL 40 (45)
T PF02892_consen 16 KAKCKYCGKVIKYSSGGTSNLKRHL 40 (45)
T ss_dssp -EEETTTTEE-----SSTHHHHHHH
T ss_pred eEEeCCCCeEEeeCCCcHHHHHHhh
Confidence 3455555554443 24555555
No 114
>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=69.13 E-value=1.4 Score=17.83 Aligned_cols=8 Identities=25% Similarity=0.538 Sum_probs=3.6
Q ss_pred CccCCcCc
Q psy3949 65 PYKCLFCD 72 (103)
Q Consensus 65 ~~~c~~c~ 72 (103)
.+.|..|+
T Consensus 19 ~~vCp~C~ 26 (30)
T PF08274_consen 19 LLVCPECG 26 (30)
T ss_dssp SEEETTTT
T ss_pred EEeCCccc
Confidence 34444444
No 115
>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=68.99 E-value=1.2 Score=26.75 Aligned_cols=26 Identities=23% Similarity=0.483 Sum_probs=15.1
Q ss_pred CccCCcCcccccCcchhhhhhhhccc
Q psy3949 65 PYKCLFCDYHCTQSGPLRRHMKIKHL 90 (103)
Q Consensus 65 ~~~c~~c~~~f~~~~~l~~h~~~~~~ 90 (103)
.|.|..|++.|.......+|+...+.
T Consensus 77 K~~C~lc~KlFkg~eFV~KHI~nKH~ 102 (214)
T PF04959_consen 77 KWRCPLCGKLFKGPEFVRKHIFNKHP 102 (214)
T ss_dssp EEEE-SSS-EESSHHHHHHHHHHH-H
T ss_pred EECCCCCCcccCChHHHHHHHhhcCH
Confidence 36677777777777777777665433
No 116
>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=68.81 E-value=0.26 Score=21.15 Aligned_cols=11 Identities=27% Similarity=0.655 Sum_probs=8.1
Q ss_pred ceecCCCCCCc
Q psy3949 37 RFVCYTCPYHT 47 (103)
Q Consensus 37 ~~~c~~c~~~~ 47 (103)
-|.|..|+..|
T Consensus 28 fy~C~~C~~~w 38 (39)
T PF01096_consen 28 FYVCCNCGHRW 38 (39)
T ss_dssp EEEESSSTEEE
T ss_pred EEEeCCCCCee
Confidence 57888887654
No 117
>KOG1146|consensus
Probab=68.25 E-value=3.8 Score=31.22 Aligned_cols=59 Identities=20% Similarity=0.425 Sum_probs=40.5
Q ss_pred CcccCCCcccccccCHHH-HHh-hhCCCcc--------------ccCCCCCcceecCCCCCCccchhHHHHHHHH
Q psy3949 1 VRCQYCKHSLSVSNGFEI-VLS-HTKSCTY--------------ISRPDHNYRFVCYTCPYHTTYSQSMKSHLRK 59 (103)
Q Consensus 1 ~~C~~C~~~f~~~~~l~~-~~~-h~~~~~~--------------~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~ 59 (103)
+.|+.|+..++....|.. |+. |...... .+..-..++|.|..|...+.....|.+|+..
T Consensus 466 ~~cpkc~~~yk~a~~L~vhmRskhp~~~~~~c~~gq~~~~~arg~~~~~~~~p~~C~~C~~stttng~LsihlqS 540 (1406)
T KOG1146|consen 466 LKCPKCNWHYKLAQTLGVHMRSKHPESQSAYCKAGQNHPRLARGEVYRCPGKPYPCRACNYSTTTNGNLSIHLQS 540 (1406)
T ss_pred ccCCccchhhhhHHHhhhcccccccccchhHhHhccccccccccccccCCCCcccceeeeeeeecchHHHHHHHH
Confidence 579999999988877777 665 2221000 0011224479999999999999999999864
No 118
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=67.82 E-value=2.5 Score=19.26 Aligned_cols=10 Identities=0% Similarity=-0.004 Sum_probs=5.1
Q ss_pred cCCCCCcccc
Q psy3949 93 SSNSHDITFV 102 (103)
Q Consensus 93 ~~~C~~C~~~ 102 (103)
.+.|..||++
T Consensus 37 r~~C~~Cgyt 46 (50)
T PRK00432 37 RWHCGKCGYT 46 (50)
T ss_pred cEECCCcCCE
Confidence 3455555544
No 119
>PTZ00043 cytochrome c oxidase subunit; Provisional
Probab=67.81 E-value=2.5 Score=25.68 Aligned_cols=14 Identities=0% Similarity=-0.270 Sum_probs=11.4
Q ss_pred cCccCCCCCccccC
Q psy3949 90 LMESSNSHDITFVM 103 (103)
Q Consensus 90 ~e~~~~C~~C~~~~ 103 (103)
..++.+|++||..|
T Consensus 178 EGkpqRCpECGqVF 191 (268)
T PTZ00043 178 EGFLYRCGECDQIF 191 (268)
T ss_pred CCCCccCCCCCcEE
Confidence 34689999999876
No 120
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=67.73 E-value=3.3 Score=22.32 Aligned_cols=7 Identities=0% Similarity=-0.064 Sum_probs=3.6
Q ss_pred CCCCCcc
Q psy3949 94 SNSHDIT 100 (103)
Q Consensus 94 ~~C~~C~ 100 (103)
+.||.||
T Consensus 88 ~~CP~Cg 94 (114)
T PRK03681 88 RRCPQCH 94 (114)
T ss_pred CcCcCcC
Confidence 3455555
No 121
>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=67.50 E-value=0.96 Score=19.76 Aligned_cols=11 Identities=0% Similarity=-0.160 Sum_probs=5.3
Q ss_pred cCCCCCccccC
Q psy3949 93 SSNSHDITFVM 103 (103)
Q Consensus 93 ~~~C~~C~~~~ 103 (103)
|+.|+.|++.|
T Consensus 13 ~~~C~~C~~~F 23 (43)
T PF01428_consen 13 PFKCKHCGKSF 23 (43)
T ss_dssp HEE-TTTS-EE
T ss_pred CeECCCCCccc
Confidence 56666666554
No 122
>KOG4173|consensus
Probab=67.17 E-value=1.4 Score=26.43 Aligned_cols=50 Identities=22% Similarity=0.398 Sum_probs=34.5
Q ss_pred eecCCCCCCccchhHHHHHHHH-h---------hCCCCccC--CcCcccccCcchhhhhhhh
Q psy3949 38 FVCYTCPYHTTYSQSMKSHLRK-H---------SGEKPYKC--LFCDYHCTQSGPLRRHMKI 87 (103)
Q Consensus 38 ~~c~~c~~~~~~~~~l~~h~~~-~---------~~~~~~~c--~~c~~~f~~~~~l~~h~~~ 87 (103)
..|..|.+.|.+.-.|..|+.. | .|.-.|+| +.|+-.|........|+-.
T Consensus 107 ~sCs~C~r~~Pt~hLLd~HI~E~HDs~Fqa~veRG~dMy~ClvEgCt~KFkT~r~RkdH~I~ 168 (253)
T KOG4173|consen 107 NSCSFCKRAFPTGHLLDAHILEWHDSLFQALVERGQDMYQCLVEGCTEKFKTSRDRKDHMIR 168 (253)
T ss_pred chhHHHHHhCCchhhhhHHHHHHHHHHHHHHHHcCccHHHHHHHhhhhhhhhhhhhhhHHHH
Confidence 3688888888888888888652 2 23334777 4488888877777777543
No 123
>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=67.04 E-value=5.3 Score=18.18 Aligned_cols=26 Identities=19% Similarity=0.363 Sum_probs=15.6
Q ss_pred ecCCCCCCccchhHHHHHHHHhhCCCCccCCcCccccc
Q psy3949 39 VCYTCPYHTTYSQSMKSHLRKHSGEKPYKCLFCDYHCT 76 (103)
Q Consensus 39 ~c~~c~~~~~~~~~l~~h~~~~~~~~~~~c~~c~~~f~ 76 (103)
.|..|++.|.. ..+.+.|..||..|-
T Consensus 4 ~C~~C~~~F~~------------~~rk~~Cr~Cg~~~C 29 (57)
T cd00065 4 SCMGCGKPFTL------------TRRRHHCRNCGRIFC 29 (57)
T ss_pred cCcccCccccC------------CccccccCcCcCCcC
Confidence 57778776653 123455666776654
No 124
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=66.91 E-value=4.3 Score=27.05 Aligned_cols=12 Identities=17% Similarity=0.636 Sum_probs=6.8
Q ss_pred CccCCcCccccc
Q psy3949 65 PYKCLFCDYHCT 76 (103)
Q Consensus 65 ~~~c~~c~~~f~ 76 (103)
-|.|..|+..+.
T Consensus 367 g~rC~kCg~~~~ 378 (421)
T COG1571 367 GFRCKKCGTRAR 378 (421)
T ss_pred CcccccccccCC
Confidence 566666665443
No 125
>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=66.58 E-value=4.2 Score=21.94 Aligned_cols=9 Identities=22% Similarity=0.560 Sum_probs=4.2
Q ss_pred cCCcCcccc
Q psy3949 67 KCLFCDYHC 75 (103)
Q Consensus 67 ~c~~c~~~f 75 (103)
.|..|+..|
T Consensus 72 ~C~~Cg~~~ 80 (115)
T TIGR00100 72 ECEDCSEEV 80 (115)
T ss_pred EcccCCCEE
Confidence 455555443
No 126
>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 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=66.24 E-value=3.6 Score=17.15 Aligned_cols=13 Identities=31% Similarity=0.332 Sum_probs=5.0
Q ss_pred cCCcCcccccCcc
Q psy3949 67 KCLFCDYHCTQSG 79 (103)
Q Consensus 67 ~c~~c~~~f~~~~ 79 (103)
.|..|++.|..+.
T Consensus 5 ~C~eC~~~f~dSy 17 (34)
T PF01286_consen 5 KCDECGKPFMDSY 17 (34)
T ss_dssp E-TTT--EES-SS
T ss_pred hHhHhCCHHHHHH
Confidence 4556666665553
No 128
>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=66.07 E-value=3.3 Score=28.19 Aligned_cols=10 Identities=0% Similarity=-0.223 Sum_probs=6.5
Q ss_pred ccCCCCCccc
Q psy3949 92 ESSNSHDITF 101 (103)
Q Consensus 92 ~~~~C~~C~~ 101 (103)
.|..|+.||-
T Consensus 252 ~~~~Cp~C~s 261 (505)
T TIGR00595 252 IPKTCPQCGS 261 (505)
T ss_pred CCCCCCCCCC
Confidence 4567777764
No 129
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=65.54 E-value=4.5 Score=21.73 Aligned_cols=9 Identities=22% Similarity=0.412 Sum_probs=4.4
Q ss_pred cCCcCcccc
Q psy3949 67 KCLFCDYHC 75 (103)
Q Consensus 67 ~c~~c~~~f 75 (103)
.|..|+..|
T Consensus 72 ~C~~Cg~~~ 80 (113)
T PRK12380 72 WCWDCSQVV 80 (113)
T ss_pred EcccCCCEE
Confidence 455555443
No 130
>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=65.26 E-value=2.3 Score=20.39 Aligned_cols=27 Identities=15% Similarity=0.277 Sum_probs=10.8
Q ss_pred eecCCCCCCccchhHHHHHHHHhhCCCCccCCcCccccc
Q psy3949 38 FVCYTCPYHTTYSQSMKSHLRKHSGEKPYKCLFCDYHCT 76 (103)
Q Consensus 38 ~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~c~~c~~~f~ 76 (103)
-.|..|++.|.. -.+.+-|..||..|-
T Consensus 10 ~~C~~C~~~F~~------------~~rrhhCr~CG~~vC 36 (69)
T PF01363_consen 10 SNCMICGKKFSL------------FRRRHHCRNCGRVVC 36 (69)
T ss_dssp SB-TTT--B-BS------------SS-EEE-TTT--EEE
T ss_pred CcCcCcCCcCCC------------ceeeEccCCCCCEEC
Confidence 368888887742 134456666776554
No 131
>PF04810 zf-Sec23_Sec24: Sec23/Sec24 zinc finger; InterPro: IPR006895 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. COPII (coat protein complex II)-coated vesicles carry proteins from the endoplasmic reticulum (ER) to the Golgi complex []. COPII-coated vesicles form on the ER by the stepwise recruitment of three cytosolic components: Sar1-GTP to initiate coat formation, Sec23/24 heterodimer to select SNARE and cargo molecules, and Sec13/31 to induce coat polymerisation and membrane deformation []. Sec23 p and Sec24p are structurally related, folding into five distinct domains: a beta-barrel, a zinc-finger, an alpha/beta trunk domain (IPR006896 from INTERPRO), an all-helical region (IPR006900 from INTERPRO), and a C-terminal gelsolin-like domain (IPR007123 from INTERPRO). This entry describes an approximately 55-residue Sec23/24 zinc-binding domain, which lies against the beta-barrel at the periphery of the complex. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006886 intracellular protein transport, 0006888 ER to Golgi vesicle-mediated transport, 0030127 COPII vesicle coat; PDB: 3EFO_B 3EG9_B 3EGD_A 2YRC_A 2NUP_A 2YRD_A 3EGX_A 2NUT_A 3EH1_A 1PD0_A ....
Probab=63.99 E-value=2.4 Score=18.21 Aligned_cols=11 Identities=0% Similarity=-0.502 Sum_probs=4.9
Q ss_pred cCccCCCCCcc
Q psy3949 90 LMESSNSHDIT 100 (103)
Q Consensus 90 ~e~~~~C~~C~ 100 (103)
+.+.|.|..|+
T Consensus 21 ~~~~w~C~~C~ 31 (40)
T PF04810_consen 21 GGKTWICNFCG 31 (40)
T ss_dssp TTTEEEETTT-
T ss_pred CCCEEECcCCC
Confidence 33445555554
No 132
>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=63.88 E-value=3.3 Score=19.82 Aligned_cols=14 Identities=14% Similarity=0.657 Sum_probs=8.1
Q ss_pred CCCccCCcCccccc
Q psy3949 63 EKPYKCLFCDYHCT 76 (103)
Q Consensus 63 ~~~~~c~~c~~~f~ 76 (103)
.+.+.|..||....
T Consensus 44 ~r~~~C~~Cg~~~~ 57 (69)
T PF07282_consen 44 GRVFTCPNCGFEMD 57 (69)
T ss_pred cceEEcCCCCCEEC
Confidence 34566766765443
No 133
>KOG2785|consensus
Probab=61.93 E-value=8.9 Score=25.27 Aligned_cols=51 Identities=24% Similarity=0.450 Sum_probs=38.0
Q ss_pred ceecCCCCCCccchhHHHHHHHHhhC-----------------------CCCccCCcCc---ccccCcchhhhhhhh
Q psy3949 37 RFVCYTCPYHTTYSQSMKSHLRKHSG-----------------------EKPYKCLFCD---YHCTQSGPLRRHMKI 87 (103)
Q Consensus 37 ~~~c~~c~~~~~~~~~l~~h~~~~~~-----------------------~~~~~c~~c~---~~f~~~~~l~~h~~~ 87 (103)
|-.|-.|+..+........||..+.| .+-+.|..|. +.|.+..+.+.|+..
T Consensus 166 Pt~CLfC~~~~k~~e~~~~HM~~~HgffIPdreYL~D~~GLl~YLgeKV~~~~~CL~CN~~~~~f~sleavr~HM~~ 242 (390)
T KOG2785|consen 166 PTDCLFCDKKSKSLEENLKHMFKEHGFFIPDREYLTDEKGLLKYLGEKVGIGFICLFCNELGRPFSSLEAVRAHMRD 242 (390)
T ss_pred CcceeecCCCcccHHHHHHHHhhccCCcCCchHhhhchhHHHHHHHHHhccCceEEEeccccCcccccHHHHHHHhh
Confidence 34677888888888877888876554 2335677777 888899899988764
No 134
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=60.05 E-value=5.8 Score=21.48 Aligned_cols=9 Identities=22% Similarity=0.637 Sum_probs=4.1
Q ss_pred eecCCCCCC
Q psy3949 38 FVCYTCPYH 46 (103)
Q Consensus 38 ~~c~~c~~~ 46 (103)
..|..||..
T Consensus 72 ~~C~~Cg~~ 80 (117)
T PRK00564 72 LECKDCSHV 80 (117)
T ss_pred EEhhhCCCc
Confidence 344444433
No 135
>PF02891 zf-MIZ: MIZ/SP-RING zinc finger; InterPro: IPR004181 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents MIZ-type zinc finger domains. Miz1 (Msx-interacting-zinc finger) is a zinc finger-containing protein with homology to the yeast protein, Nfi-1. Miz1 is a sequence specific DNA binding protein that can function as a positive-acting transcription factor. Miz1 binds to the homeobox protein Msx2, enhancing the specific DNA-binding ability of Msx2 []. Other proteins containing this domain include the human pias family (protein inhibitor of activated STAT protein). More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3I2D_A.
Probab=59.04 E-value=3.5 Score=18.66 Aligned_cols=9 Identities=0% Similarity=-0.407 Sum_probs=2.9
Q ss_pred cCCCCCccc
Q psy3949 93 SSNSHDITF 101 (103)
Q Consensus 93 ~~~C~~C~~ 101 (103)
.|+|+.|++
T Consensus 41 ~W~CPiC~~ 49 (50)
T PF02891_consen 41 KWKCPICNK 49 (50)
T ss_dssp --B-TTT--
T ss_pred CeECcCCcC
Confidence 377777764
No 136
>PF02176 zf-TRAF: TRAF-type zinc finger; PDB: 2EOD_A 2YUC_A 3HCU_A 3HCS_B 3HCT_A.
Probab=58.88 E-value=3.9 Score=18.86 Aligned_cols=34 Identities=18% Similarity=0.480 Sum_probs=14.0
Q ss_pred ceecCC-CCCCccchhHHHHHHHHhhCCCCccCCc
Q psy3949 37 RFVCYT-CPYHTTYSQSMKSHLRKHSGEKPYKCLF 70 (103)
Q Consensus 37 ~~~c~~-c~~~~~~~~~l~~h~~~~~~~~~~~c~~ 70 (103)
+..|+. |+..-.....|..|+...=..++..|..
T Consensus 9 ~v~C~~~cc~~~i~r~~l~~H~~~~C~~~~v~C~~ 43 (60)
T PF02176_consen 9 PVPCPNGCCNEMIPRKELDDHLENECPKRPVPCPY 43 (60)
T ss_dssp EEE-TT--S-BEEECCCHHHHHHTTSTTSEEE-SS
T ss_pred EeeCCCCCcccceeHHHHHHHHHccCCCCcEECCC
Confidence 445665 3322223455566655333334455555
No 137
>PF14353 CpXC: CpXC protein
Probab=58.49 E-value=3.4 Score=22.49 Aligned_cols=11 Identities=9% Similarity=-0.088 Sum_probs=7.0
Q ss_pred cCCCCCccccC
Q psy3949 93 SSNSHDITFVM 103 (103)
Q Consensus 93 ~~~C~~C~~~~ 103 (103)
.|.|+.||..|
T Consensus 38 ~~~CP~Cg~~~ 48 (128)
T PF14353_consen 38 SFTCPSCGHKF 48 (128)
T ss_pred EEECCCCCCce
Confidence 36677777654
No 138
>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=58.38 E-value=7.3 Score=20.66 Aligned_cols=10 Identities=20% Similarity=0.484 Sum_probs=6.1
Q ss_pred ceecCCCCCC
Q psy3949 37 RFVCYTCPYH 46 (103)
Q Consensus 37 ~~~c~~c~~~ 46 (103)
|-.|+.||..
T Consensus 2 p~~CpYCg~~ 11 (102)
T PF11672_consen 2 PIICPYCGGP 11 (102)
T ss_pred CcccCCCCCe
Confidence 4467777753
No 139
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=58.03 E-value=16 Score=21.48 Aligned_cols=29 Identities=10% Similarity=0.135 Sum_probs=14.2
Q ss_pred CCccCCcCcccccCcchhhhhhhhcccCccCCCCCccc
Q psy3949 64 KPYKCLFCDYHCTQSGPLRRHMKIKHLMESSNSHDITF 101 (103)
Q Consensus 64 ~~~~c~~c~~~f~~~~~l~~h~~~~~~e~~~~C~~C~~ 101 (103)
.-|.|+.|.-.++...+.. .-|.|+.||-
T Consensus 112 ~~y~C~~~~~r~sfdeA~~---------~~F~Cp~Cg~ 140 (176)
T COG1675 112 NYYVCPNCHVKYSFDEAME---------LGFTCPKCGE 140 (176)
T ss_pred CceeCCCCCCcccHHHHHH---------hCCCCCCCCc
Confidence 3456655554444443322 1266666664
No 140
>PF10537 WAC_Acf1_DNA_bd: ATP-utilising chromatin assembly and remodelling N-terminal; InterPro: IPR013136 ACF (for ATP-utilising chromatin assembly and remodeling factor) is a chromatin-remodeling complex that catalyzes the ATP-dependent assembly of periodic nucleosome arrays. This reaction utilises the energy of ATP hydrolysis by ISWI, the smaller of the two subunits of ACF. Acf1, the large subunit of ACF, is essential for the full activity of the complex. The WAC (WSTF/Acf1/cbp146) domain is an ~110-residue module present at the N-termini of Acf1-related proteins in a variety of organisms. It is found in association with other domains such as the bromodomain, the PHD-type zinc finger, DDT or WAKS. The DNA-binding region of Acf1 includes the WAC domain, which is necessary for the efficient binding of ACF complex to DNA. It seems probable that the WAC domain will be involved in DNA binding in other related factors [, ]. Some proteins known to contain a WAC domain are the Drosophila melanogaster (Fruit fly) ATP-dependent chromatin assembly factor large subunit Acf1, human WSTF (Williams syndrome transcription factor), mouse cbp146, yeast imitation switch two complex protein 1 (ITC1 or YGL133w), and yeast protein YPL216w.
Probab=58.00 E-value=10 Score=20.10 Aligned_cols=37 Identities=5% Similarity=0.064 Sum_probs=25.7
Q ss_pred CcccCCCcccccccCHHH-HHhhhCCCccccCCCCCcceecCCCCCCcc
Q psy3949 1 VRCQYCKHSLSVSNGFEI-VLSHTKSCTYISRPDHNYRFVCYTCPYHTT 48 (103)
Q Consensus 1 ~~C~~C~~~f~~~~~l~~-~~~h~~~~~~~~~~~~~~~~~c~~c~~~~~ 48 (103)
|.|+.-|+.|.+..++.. +... .. + .|.|...|+.-.
T Consensus 4 f~i~~T~EiF~dYe~Y~~R~~~y-~~-----~-----vwtC~~TGk~~L 41 (102)
T PF10537_consen 4 FYIPFTGEIFRDYEEYLKRMILY-NQ-----R-----VWTCEITGKSNL 41 (102)
T ss_pred EEeCCCCcccCCHHHHHHHHHHH-hC-----C-----eeEEecCCCCCC
Confidence 457778889988888776 5443 23 4 799998886443
No 141
>smart00132 LIM Zinc-binding domain present in Lin-11, Isl-1, Mec-3. Zinc-binding domain family. Some LIM domains bind protein partners via tyrosine-containing motifs. LIM domains are found in many key regulators of developmental pathways.
Probab=57.83 E-value=7 Score=15.79 Aligned_cols=9 Identities=0% Similarity=-0.326 Sum_probs=5.4
Q ss_pred CCCCCcccc
Q psy3949 94 SNSHDITFV 102 (103)
Q Consensus 94 ~~C~~C~~~ 102 (103)
|+|..|+..
T Consensus 28 f~C~~C~~~ 36 (39)
T smart00132 28 FKCSKCGKP 36 (39)
T ss_pred CCCcccCCc
Confidence 556666654
No 142
>KOG2593|consensus
Probab=57.20 E-value=11 Score=25.36 Aligned_cols=34 Identities=18% Similarity=0.426 Sum_probs=20.4
Q ss_pred ceecCCCCCCccchhHHHHHHHHhhCCCCccCCcCcc
Q psy3949 37 RFVCYTCPYHTTYSQSMKSHLRKHSGEKPYKCLFCDY 73 (103)
Q Consensus 37 ~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~c~~c~~ 73 (103)
.|.|+.|.+.|.....++ ......--|.|..|+.
T Consensus 128 ~Y~Cp~C~kkyt~Lea~~---L~~~~~~~F~C~~C~g 161 (436)
T KOG2593|consen 128 GYVCPNCQKKYTSLEALQ---LLDNETGEFHCENCGG 161 (436)
T ss_pred cccCCccccchhhhHHHH---hhcccCceEEEecCCC
Confidence 678888887776555442 3333233577777764
No 143
>KOG4167|consensus
Probab=55.44 E-value=3.3 Score=29.59 Aligned_cols=25 Identities=24% Similarity=0.417 Sum_probs=20.2
Q ss_pred ceecCCCCCCccchhHHHHHHHHhh
Q psy3949 37 RFVCYTCPYHTTYSQSMKSHLRKHS 61 (103)
Q Consensus 37 ~~~c~~c~~~~~~~~~l~~h~~~~~ 61 (103)
.|.|..|++.|....++..||..|.
T Consensus 792 iFpCreC~kvF~KiKSrNAHMK~Hr 816 (907)
T KOG4167|consen 792 IFPCRECGKVFFKIKSRNAHMKTHR 816 (907)
T ss_pred eeehHHHHHHHHHHhhhhHHHHHHH
Confidence 4788888888888888888887764
No 144
>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=54.88 E-value=3.7 Score=18.79 Aligned_cols=8 Identities=0% Similarity=-0.579 Sum_probs=3.1
Q ss_pred CCCCcccc
Q psy3949 95 NSHDITFV 102 (103)
Q Consensus 95 ~C~~C~~~ 102 (103)
.||+|+..
T Consensus 22 ~CPlC~r~ 29 (54)
T PF04423_consen 22 CCPLCGRP 29 (54)
T ss_dssp E-TTT--E
T ss_pred cCCCCCCC
Confidence 67776654
No 145
>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=54.37 E-value=14 Score=14.16 Aligned_cols=8 Identities=25% Similarity=0.613 Sum_probs=4.2
Q ss_pred cCCCCCCc
Q psy3949 40 CYTCPYHT 47 (103)
Q Consensus 40 c~~c~~~~ 47 (103)
|+.|++.+
T Consensus 4 CPiC~~~v 11 (26)
T smart00734 4 CPVCFREV 11 (26)
T ss_pred CCCCcCcc
Confidence 55555544
No 146
>PF07649 C1_3: C1-like domain; InterPro: IPR011424 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in IPR002219 from INTERPRO. C1 domains are protein kinase C-like zinc finger structures. Diacylglycerol (DAG) kinases (DGKs) have a two or three commonly conserved cysteine-rich C1 domains []. DGKs modulate the balance between the two signaling lipids, DAG and phosphatidic acid (PA), by phosphorylating DAG to yield PA []. The PKD (protein kinase D) family are novel DAG receptors. They have twin C1 domains, designated C1a and C1b, which bind DAG or phorbol esters. Individual C1 domains differ in ligand-binding activity and selectivity []. ; GO: 0047134 protein-disulfide reductase activity, 0055114 oxidation-reduction process; PDB: 1V5N_A.
Probab=53.45 E-value=3.7 Score=16.24 Aligned_cols=11 Identities=9% Similarity=-0.091 Sum_probs=4.1
Q ss_pred ccCCCCCcccc
Q psy3949 92 ESSNSHDITFV 102 (103)
Q Consensus 92 ~~~~C~~C~~~ 102 (103)
..|.|.+|++.
T Consensus 14 ~~Y~C~~Cdf~ 24 (30)
T PF07649_consen 14 WFYRCSECDFD 24 (30)
T ss_dssp -EEE-TTT---
T ss_pred ceEECccCCCc
Confidence 34667777664
No 147
>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=53.44 E-value=14 Score=23.19 Aligned_cols=10 Identities=0% Similarity=0.046 Sum_probs=5.9
Q ss_pred ccCCCCCccc
Q psy3949 92 ESSNSHDITF 101 (103)
Q Consensus 92 ~~~~C~~C~~ 101 (103)
+++.||.||+
T Consensus 208 k~~PCPKCg~ 217 (314)
T PF06524_consen 208 KPIPCPKCGY 217 (314)
T ss_pred CCCCCCCCCC
Confidence 5556666654
No 148
>COG1327 Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains [Transcription]
Probab=53.43 E-value=4.8 Score=22.95 Aligned_cols=17 Identities=24% Similarity=0.299 Sum_probs=12.6
Q ss_pred ceecCCCCCCccchhHH
Q psy3949 37 RFVCYTCPYHTTYSQSM 53 (103)
Q Consensus 37 ~~~c~~c~~~~~~~~~l 53 (103)
.-.|..|+..|......
T Consensus 28 RReC~~C~~RFTTfE~~ 44 (156)
T COG1327 28 RRECLECGERFTTFERA 44 (156)
T ss_pred hhcccccccccchhhee
Confidence 45799999998876543
No 149
>KOG4167|consensus
Probab=53.40 E-value=2 Score=30.55 Aligned_cols=26 Identities=19% Similarity=0.275 Sum_probs=22.8
Q ss_pred CCccCCcCcccccCcchhhhhhhhcc
Q psy3949 64 KPYKCLFCDYHCTQSGPLRRHMKIKH 89 (103)
Q Consensus 64 ~~~~c~~c~~~f~~~~~l~~h~~~~~ 89 (103)
..|.|..|++.|....++..|+++|.
T Consensus 791 giFpCreC~kvF~KiKSrNAHMK~Hr 816 (907)
T KOG4167|consen 791 GIFPCRECGKVFFKIKSRNAHMKTHR 816 (907)
T ss_pred ceeehHHHHHHHHHHhhhhHHHHHHH
Confidence 35789999999999999999999874
No 150
>PF10058 DUF2296: Predicted integral membrane metal-binding protein (DUF2296); InterPro: IPR019273 This domain, found mainly in the eukaryotic lunapark proteins, has no known function [].
Probab=53.32 E-value=7.4 Score=18.02 Aligned_cols=9 Identities=0% Similarity=-0.356 Sum_probs=4.9
Q ss_pred cCCCCCccc
Q psy3949 93 SSNSHDITF 101 (103)
Q Consensus 93 ~~~C~~C~~ 101 (103)
.|.|+.||.
T Consensus 44 ~y~C~~Cg~ 52 (54)
T PF10058_consen 44 QYRCPYCGA 52 (54)
T ss_pred EEEcCCCCC
Confidence 355665554
No 151
>COG4957 Predicted transcriptional regulator [Transcription]
Probab=52.54 E-value=7.4 Score=21.77 Aligned_cols=10 Identities=30% Similarity=0.458 Sum_probs=4.7
Q ss_pred hhhhhhhccc
Q psy3949 81 LRRHMKIKHL 90 (103)
Q Consensus 81 l~~h~~~~~~ 90 (103)
|.+|+.+|.|
T Consensus 89 LKRHL~t~~g 98 (148)
T COG4957 89 LKRHLTTHYG 98 (148)
T ss_pred HHHHHhcccC
Confidence 4445555444
No 152
>PF14311 DUF4379: Domain of unknown function (DUF4379)
Probab=52.43 E-value=14 Score=16.83 Aligned_cols=11 Identities=27% Similarity=0.670 Sum_probs=5.5
Q ss_pred ccCCcCccccc
Q psy3949 66 YKCLFCDYHCT 76 (103)
Q Consensus 66 ~~c~~c~~~f~ 76 (103)
+.|..|+..+.
T Consensus 29 W~C~~Cgh~w~ 39 (55)
T PF14311_consen 29 WKCPKCGHEWK 39 (55)
T ss_pred EECCCCCCeeE
Confidence 45555554443
No 153
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=52.34 E-value=6.8 Score=18.23 Aligned_cols=14 Identities=14% Similarity=0.617 Sum_probs=9.5
Q ss_pred cccCCCcccccccC
Q psy3949 2 RCQYCKHSLSVSNG 15 (103)
Q Consensus 2 ~C~~C~~~f~~~~~ 15 (103)
.|+.||+.|....+
T Consensus 7 ~C~~Cg~~~~~~dD 20 (54)
T PF14446_consen 7 KCPVCGKKFKDGDD 20 (54)
T ss_pred cChhhCCcccCCCC
Confidence 47788888865443
No 154
>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=52.25 E-value=6.5 Score=21.08 Aligned_cols=10 Identities=20% Similarity=0.378 Sum_probs=4.2
Q ss_pred eecCCCCCCc
Q psy3949 38 FVCYTCPYHT 47 (103)
Q Consensus 38 ~~c~~c~~~~ 47 (103)
..|..||..|
T Consensus 71 ~~C~~Cg~~~ 80 (113)
T PF01155_consen 71 ARCRDCGHEF 80 (113)
T ss_dssp EEETTTS-EE
T ss_pred EECCCCCCEE
Confidence 3455554444
No 155
>COG3091 SprT Zn-dependent metalloprotease, SprT family [General function prediction only]
Probab=51.96 E-value=5.8 Score=22.63 Aligned_cols=31 Identities=26% Similarity=0.542 Sum_probs=14.8
Q ss_pred CccCCcCcccccCcchhhhhhhhcccCccCCCCCcc
Q psy3949 65 PYKCLFCDYHCTQSGPLRRHMKIKHLMESSNSHDIT 100 (103)
Q Consensus 65 ~~~c~~c~~~f~~~~~l~~h~~~~~~e~~~~C~~C~ 100 (103)
+|.|. |+..+... .+|-..-.|| .|.|..|+
T Consensus 117 ~Y~C~-C~q~~l~~---RRhn~~~~g~-~YrC~~C~ 147 (156)
T COG3091 117 PYRCQ-CQQHYLRI---RRHNTVRRGE-VYRCGKCG 147 (156)
T ss_pred eEEee-cCCccchh---hhcccccccc-eEEeccCC
Confidence 35555 55443322 2333333444 56666665
No 156
>TIGR00244 transcriptional regulator NrdR. Members of this almost entirely bacterial family contain an ATP cone domain (PFAM:PF03477). There is never more than one member per genome. Common gene symbols given include nrdR, ybaD, ribX and ytcG. The member from Streptomyces coelicolor is found upstream in the operon of the class II oxygen-independent ribonucleotide reductase gene nrdJ and was shown to repress nrdJ expression. Many members of this family are found near genes for riboflavin biosynthesis in Gram-negative bacteria, suggesting a role in that pathway. However, a phylogenetic profiling study associates members of this family with the presence of a palindromic signal with consensus acaCwAtATaTwGtgt, termed the NrdR-box, an upstream element for most operons for ribonucleotide reductase of all three classes in bacterial genomes.
Probab=51.65 E-value=4.5 Score=22.92 Aligned_cols=17 Identities=24% Similarity=0.309 Sum_probs=12.6
Q ss_pred ceecCCCCCCccchhHH
Q psy3949 37 RFVCYTCPYHTTYSQSM 53 (103)
Q Consensus 37 ~~~c~~c~~~~~~~~~l 53 (103)
.-.|..|++.|......
T Consensus 28 RReC~~C~~RFTTyErv 44 (147)
T TIGR00244 28 RRECLECHERFTTFERA 44 (147)
T ss_pred cccCCccCCccceeeec
Confidence 34799999998876544
No 157
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=51.51 E-value=11 Score=27.26 Aligned_cols=13 Identities=0% Similarity=-0.294 Sum_probs=9.4
Q ss_pred cCccCCCCCcccc
Q psy3949 90 LMESSNSHDITFV 102 (103)
Q Consensus 90 ~e~~~~C~~C~~~ 102 (103)
...|..|+.||-.
T Consensus 472 ~~~p~~Cp~Cgs~ 484 (730)
T COG1198 472 EPIPQSCPECGSE 484 (730)
T ss_pred CCCCCCCCCCCCC
Confidence 4567889988853
No 158
>KOG2231|consensus
Probab=51.39 E-value=14 Score=26.39 Aligned_cols=41 Identities=22% Similarity=0.425 Sum_probs=24.4
Q ss_pred chhHHHHHHHHh-hCCC----CccCCcCcccccCcchhhhhhhhcc
Q psy3949 49 YSQSMKSHLRKH-SGEK----PYKCLFCDYHCTQSGPLRRHMKIKH 89 (103)
Q Consensus 49 ~~~~l~~h~~~~-~~~~----~~~c~~c~~~f~~~~~l~~h~~~~~ 89 (103)
....|+.|+... .++. -..|..|...|.....+.+|++.++
T Consensus 161 t~~el~~h~~~gd~d~~s~rGhp~C~~C~~~fld~~el~rH~~~~h 206 (669)
T KOG2231|consen 161 TRAELNLHLMFGDPDDESCRGHPLCKFCHERFLDDDELYRHLRFDH 206 (669)
T ss_pred hHHHHHHHHhcCCCccccccCCccchhhhhhhccHHHHHHhhccce
Confidence 345556665531 1121 1357778888888888887777644
No 159
>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=50.73 E-value=3 Score=23.30 Aligned_cols=16 Identities=6% Similarity=0.077 Sum_probs=12.0
Q ss_pred hcccCccCCCCCccccC
Q psy3949 87 IKHLMESSNSHDITFVM 103 (103)
Q Consensus 87 ~~~~e~~~~C~~C~~~~ 103 (103)
.+.| ++.+|++||..|
T Consensus 107 l~~g-~~~RCpeCG~~f 122 (136)
T PF01215_consen 107 LHKG-KPQRCPECGQVF 122 (136)
T ss_dssp EETT-SEEEETTTEEEE
T ss_pred EeCC-CccCCCCCCeEE
Confidence 3445 588999999865
No 160
>COG1326 Uncharacterized archaeal Zn-finger protein [General function prediction only]
Probab=50.55 E-value=11 Score=22.53 Aligned_cols=35 Identities=20% Similarity=0.283 Sum_probs=20.6
Q ss_pred ceecCCCCCCccchhHHHHHHHHhh--CCCCccCCcCcccccC
Q psy3949 37 RFVCYTCPYHTTYSQSMKSHLRKHS--GEKPYKCLFCDYHCTQ 77 (103)
Q Consensus 37 ~~~c~~c~~~~~~~~~l~~h~~~~~--~~~~~~c~~c~~~f~~ 77 (103)
.+.|+.|+. . . ..|...-. .+..+.|..||..++.
T Consensus 6 y~~Cp~Cg~--e--e--v~hEVik~~g~~~lvrC~eCG~V~~~ 42 (201)
T COG1326 6 YIECPSCGS--E--E--VSHEVIKERGREPLVRCEECGTVHPA 42 (201)
T ss_pred EEECCCCCc--c--h--hhHHHHHhcCCceEEEccCCCcEeec
Confidence 468999982 1 1 12332222 2335789999987744
No 161
>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=50.52 E-value=4.4 Score=17.14 Aligned_cols=11 Identities=9% Similarity=-0.046 Sum_probs=5.5
Q ss_pred ccCCCCCcccc
Q psy3949 92 ESSNSHDITFV 102 (103)
Q Consensus 92 ~~~~C~~C~~~ 102 (103)
+-|+|..||-+
T Consensus 5 ~~YkC~~CGni 15 (36)
T PF06397_consen 5 EFYKCEHCGNI 15 (36)
T ss_dssp EEEE-TTT--E
T ss_pred cEEEccCCCCE
Confidence 35888888754
No 162
>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=50.50 E-value=3.8 Score=18.80 Aligned_cols=24 Identities=25% Similarity=0.423 Sum_probs=13.0
Q ss_pred ceecCCCCCCccchhHHHHHHHHh
Q psy3949 37 RFVCYTCPYHTTYSQSMKSHLRKH 60 (103)
Q Consensus 37 ~~~c~~c~~~~~~~~~l~~h~~~~ 60 (103)
.|.|+.|...|-..-.+-.|...|
T Consensus 21 ~y~C~~C~~~FC~dCD~fiHE~LH 44 (51)
T PF07975_consen 21 RYRCPKCKNHFCIDCDVFIHETLH 44 (51)
T ss_dssp EE--TTTT--B-HHHHHTTTTTS-
T ss_pred eEECCCCCCccccCcChhhhcccc
Confidence 799999999998776666664433
No 163
>KOG2807|consensus
Probab=50.23 E-value=23 Score=23.03 Aligned_cols=16 Identities=19% Similarity=0.453 Sum_probs=7.6
Q ss_pred ccCCcCcccccCcchh
Q psy3949 66 YKCLFCDYHCTQSGPL 81 (103)
Q Consensus 66 ~~c~~c~~~f~~~~~l 81 (103)
|.|..|...|--.-..
T Consensus 346 y~C~~Ck~~FCldCDv 361 (378)
T KOG2807|consen 346 YRCESCKNVFCLDCDV 361 (378)
T ss_pred EEchhccceeeccchH
Confidence 4555555555444333
No 164
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=49.80 E-value=5.5 Score=17.78 Aligned_cols=10 Identities=0% Similarity=-0.097 Sum_probs=6.4
Q ss_pred cCCCCCcccc
Q psy3949 93 SSNSHDITFV 102 (103)
Q Consensus 93 ~~~C~~C~~~ 102 (103)
.|.|+.||+.
T Consensus 20 ~~vC~~Cg~~ 29 (52)
T smart00661 20 RFVCRKCGYE 29 (52)
T ss_pred EEECCcCCCe
Confidence 4667777654
No 165
>PF03107 C1_2: C1 domain; InterPro: IPR004146 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in DAG_PE-bind (IPR002219 from INTERPRO), therefore we have termed this domain DC1 for divergent C1 domain. This domain probably also binds to two zinc ions. The function of proteins with this domain is uncertain, however this domain may bind to molecules such as diacylglycerol. This family are found in plant proteins.
Probab=49.34 E-value=11 Score=14.90 Aligned_cols=8 Identities=0% Similarity=-0.550 Sum_probs=3.8
Q ss_pred CCCCCccc
Q psy3949 94 SNSHDITF 101 (103)
Q Consensus 94 ~~C~~C~~ 101 (103)
|.|..|++
T Consensus 1 ~~C~~C~~ 8 (30)
T PF03107_consen 1 FWCDVCRR 8 (30)
T ss_pred CCCCCCCC
Confidence 34555544
No 166
>COG1655 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=48.62 E-value=2.7 Score=25.66 Aligned_cols=23 Identities=13% Similarity=0.257 Sum_probs=14.6
Q ss_pred ceecCCCCCCccchhHHHHHHHH
Q psy3949 37 RFVCYTCPYHTTYSQSMKSHLRK 59 (103)
Q Consensus 37 ~~~c~~c~~~~~~~~~l~~h~~~ 59 (103)
...|++|+..|.....+....++
T Consensus 19 ~ieCPvC~tkFkkeev~tgsiRi 41 (267)
T COG1655 19 TIECPVCNTKFKKEEVKTGSIRI 41 (267)
T ss_pred eeccCcccchhhhhheeccceeE
Confidence 56788888777665555444443
No 167
>KOG0801|consensus
Probab=48.36 E-value=7.6 Score=22.47 Aligned_cols=20 Identities=15% Similarity=-0.081 Sum_probs=12.4
Q ss_pred hhhhhhhhcccCccCCCCCcccc
Q psy3949 80 PLRRHMKIKHLMESSNSHDITFV 102 (103)
Q Consensus 80 ~l~~h~~~~~~e~~~~C~~C~~~ 102 (103)
+|..|+-.|.| ++|++|.|.
T Consensus 128 slP~hi~~~~g---~KCPvC~K~ 147 (205)
T KOG0801|consen 128 SLPVHIMDHSG---MKCPVCHKV 147 (205)
T ss_pred ccceeeeccCC---ccCCccccc
Confidence 34444444444 789999875
No 168
>COG2331 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=48.34 E-value=6 Score=19.77 Aligned_cols=31 Identities=16% Similarity=0.446 Sum_probs=17.5
Q ss_pred cceecCCCCCCccchhHHHHHHHHhhCCCCccCCcCcc
Q psy3949 36 YRFVCYTCPYHTTYSQSMKSHLRKHSGEKPYKCLFCDY 73 (103)
Q Consensus 36 ~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~c~~c~~ 73 (103)
+.|.|..|+..|. +.+++. .+..-.|+.|+.
T Consensus 11 Y~Y~c~~cg~~~d----vvq~~~---ddplt~ce~c~a 41 (82)
T COG2331 11 YSYECTECGNRFD----VVQAMT---DDPLTTCEECGA 41 (82)
T ss_pred eEEeecccchHHH----HHHhcc---cCccccChhhCh
Confidence 3589999987654 223322 222346777764
No 169
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=47.07 E-value=6.3 Score=16.22 Aligned_cols=10 Identities=0% Similarity=-0.429 Sum_probs=5.3
Q ss_pred CCCCCccccC
Q psy3949 94 SNSHDITFVM 103 (103)
Q Consensus 94 ~~C~~C~~~~ 103 (103)
+.|..||.+|
T Consensus 22 ~~C~~Cg~~~ 31 (33)
T PF08792_consen 22 EVCIFCGSSF 31 (33)
T ss_pred EEcccCCcEe
Confidence 4466665543
No 170
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=46.40 E-value=8.4 Score=20.77 Aligned_cols=37 Identities=27% Similarity=0.556 Sum_probs=19.9
Q ss_pred eecCCCCCCccchhHHHHHHHH-hhCC-CCccCCcCccccc
Q psy3949 38 FVCYTCPYHTTYSQSMKSHLRK-HSGE-KPYKCLFCDYHCT 76 (103)
Q Consensus 38 ~~c~~c~~~~~~~~~l~~h~~~-~~~~-~~~~c~~c~~~f~ 76 (103)
..|+.||..=.....+ +++. .... .-|.|..||..|.
T Consensus 73 ~~CpkCg~~ea~y~~~--QtRsaDEp~T~Fy~C~~Cg~~wr 111 (113)
T COG1594 73 EKCPKCGNKEAYYWQL--QTRSADEPETRFYKCTRCGYRWR 111 (113)
T ss_pred ccCCCCCCceeEEEee--ehhccCCCceEEEEecccCCEee
Confidence 3577777544433333 3333 3333 3477888877654
No 171
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=46.25 E-value=12 Score=20.43 Aligned_cols=6 Identities=0% Similarity=-0.285 Sum_probs=2.8
Q ss_pred CCCCcc
Q psy3949 95 NSHDIT 100 (103)
Q Consensus 95 ~C~~C~ 100 (103)
.||.||
T Consensus 94 ~CP~Cg 99 (124)
T PRK00762 94 ECPVCG 99 (124)
T ss_pred cCcCCC
Confidence 344444
No 172
>PF10263 SprT-like: SprT-like family; InterPro: IPR006640 This is a family of uncharacterised bacterial proteins which includes Escherichia coli SprT (P39902 from SWISSPROT). SprT is described as a regulator of bolA gene in stationary phase []. The majority of members contain the metallopeptidase zinc binding signature which has a HExxH motif, however there is no evidence for them being metallopeptidases.
Probab=45.97 E-value=6.9 Score=21.95 Aligned_cols=29 Identities=14% Similarity=0.211 Sum_probs=14.7
Q ss_pred ccCCcCcccccCcchhhhhhhhcccCccCCCCCcccc
Q psy3949 66 YKCLFCDYHCTQSGPLRRHMKIKHLMESSNSHDITFV 102 (103)
Q Consensus 66 ~~c~~c~~~f~~~~~l~~h~~~~~~e~~~~C~~C~~~ 102 (103)
|.|..|+..+.. |.++ ....|.|..|+-.
T Consensus 124 ~~C~~C~~~~~r------~~~~--~~~~~~C~~C~~~ 152 (157)
T PF10263_consen 124 YRCPSCGREYKR------HRRS--KRKRYRCGRCGGP 152 (157)
T ss_pred EEcCCCCCEeee------eccc--chhhEECCCCCCE
Confidence 566666654422 2222 2233777777643
No 173
>PF15269 zf-C2H2_7: Zinc-finger
Probab=45.86 E-value=30 Score=15.41 Aligned_cols=24 Identities=17% Similarity=0.818 Sum_probs=17.2
Q ss_pred cceecCCCCCCccchhHHHHHHHH
Q psy3949 36 YRFVCYTCPYHTTYSQSMKSHLRK 59 (103)
Q Consensus 36 ~~~~c~~c~~~~~~~~~l~~h~~~ 59 (103)
..|.|-+|.-..-.+++|..|+..
T Consensus 19 ~~ykcfqcpftc~~kshl~nhmky 42 (54)
T PF15269_consen 19 FKYKCFQCPFTCNEKSHLFNHMKY 42 (54)
T ss_pred ccceeecCCcccchHHHHHHHHHH
Confidence 346777777777777888888764
No 174
>PRK04023 DNA polymerase II large subunit; Validated
Probab=45.82 E-value=23 Score=26.74 Aligned_cols=9 Identities=0% Similarity=-0.101 Sum_probs=6.2
Q ss_pred cCCCCCccc
Q psy3949 93 SSNSHDITF 101 (103)
Q Consensus 93 ~~~C~~C~~ 101 (103)
++.|+.||.
T Consensus 663 ~y~CPKCG~ 671 (1121)
T PRK04023 663 EDECEKCGR 671 (1121)
T ss_pred CCcCCCCCC
Confidence 466777775
No 175
>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=45.75 E-value=6.1 Score=16.14 Aligned_cols=9 Identities=0% Similarity=-0.392 Sum_probs=5.4
Q ss_pred cCCCCCccc
Q psy3949 93 SSNSHDITF 101 (103)
Q Consensus 93 ~~~C~~C~~ 101 (103)
-|+|..||.
T Consensus 4 ~ykC~~CGn 12 (34)
T cd00974 4 VYKCEICGN 12 (34)
T ss_pred EEEcCCCCc
Confidence 366666664
No 176
>COG1779 C4-type Zn-finger protein [General function prediction only]
Probab=45.54 E-value=5.1 Score=23.87 Aligned_cols=40 Identities=20% Similarity=0.297 Sum_probs=21.8
Q ss_pred cccCCCcccccccCHHHHHhhhCCCccccCCCCCcceecCCCCCCccc
Q psy3949 2 RCQYCKHSLSVSNGFEIVLSHTKSCTYISRPDHNYRFVCYTCPYHTTY 49 (103)
Q Consensus 2 ~C~~C~~~f~~~~~l~~~~~h~~~~~~~~~~~~~~~~~c~~c~~~~~~ 49 (103)
.|+.||..+.....+.. .-|.|.... . .+.|..||.++..
T Consensus 16 ~CPvCg~~l~~~~~~~~-IPyFG~V~i--~-----t~~C~~CgYR~~D 55 (201)
T COG1779 16 DCPVCGGTLKAHMYLYD-IPYFGEVLI--S-----TGVCERCGYRSTD 55 (201)
T ss_pred cCCcccceeeEEEeeec-CCccceEEE--E-----EEEccccCCcccc
Confidence 48999985544333222 223333111 2 5789999976543
No 177
>TIGR03831 YgiT_finger YgiT-type zinc finger domain. This domain model describes a small domain with two copies of a putative zinc-binding motif CXXC (usually CXXCG). Most member proteins consist largely of this domain or else carry an additional C-terminal helix-turn-helix domain, resembling that of the phage protein Cro and modeled by pfam01381.
Probab=44.93 E-value=9.4 Score=16.35 Aligned_cols=10 Identities=0% Similarity=-0.373 Sum_probs=6.8
Q ss_pred cCCCCCcccc
Q psy3949 93 SSNSHDITFV 102 (103)
Q Consensus 93 ~~~C~~C~~~ 102 (103)
.+.|+.||..
T Consensus 32 ~~~C~~CGE~ 41 (46)
T TIGR03831 32 ALVCPQCGEE 41 (46)
T ss_pred ccccccCCCE
Confidence 4678888754
No 178
>KOG3408|consensus
Probab=44.17 E-value=17 Score=20.01 Aligned_cols=23 Identities=22% Similarity=0.613 Sum_probs=19.6
Q ss_pred ceecCCCCCCccchhHHHHHHHH
Q psy3949 37 RFVCYTCPYHTTYSQSMKSHLRK 59 (103)
Q Consensus 37 ~~~c~~c~~~~~~~~~l~~h~~~ 59 (103)
.|.|-.|.+.|.....|..|.+.
T Consensus 57 qfyCi~CaRyFi~~~~l~~H~kt 79 (129)
T KOG3408|consen 57 QFYCIECARYFIDAKALKTHFKT 79 (129)
T ss_pred eeehhhhhhhhcchHHHHHHHhc
Confidence 47899999999999999988763
No 179
>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=43.83 E-value=5.5 Score=17.25 Aligned_cols=11 Identities=0% Similarity=-0.396 Sum_probs=7.1
Q ss_pred cCCCCCccccC
Q psy3949 93 SSNSHDITFVM 103 (103)
Q Consensus 93 ~~~C~~C~~~~ 103 (103)
+-.|++||..|
T Consensus 29 ~~~CpYCg~~y 39 (40)
T PF10276_consen 29 PVVCPYCGTRY 39 (40)
T ss_dssp EEEETTTTEEE
T ss_pred eEECCCCCCEE
Confidence 45677777654
No 180
>PF05741 zf-nanos: Nanos RNA binding domain; InterPro: IPR024161 Nanos is a highly conserved RNA-binding protein in higher eukaryotes and functions as a key regulatory protein in translational control using a 3' untranslated region during the development and maintenance of germ cells. Nanos comprises a non-conserved amino-terminus and highly conserved carboxy- terminal regions. The C-terminal region has two conserved Cys-Cys-His-Cys (CCHC)-type zinc-finger motifs that are indispensable for nanos function [, , ]. The structure of the nanos-type zinc finger is composed of two independent zinc-finger (ZF) lobes, the N-terminal ZF1 and the C-terminal ZF2, which are connected by a linker helix []. These lobes create a large cleft. Zinc ions in ZF1 and ZF2 are bound to the CCHC motif by tetrahedral coordination.; PDB: 3ALR_B.
Probab=43.73 E-value=10 Score=17.72 Aligned_cols=11 Identities=0% Similarity=-0.387 Sum_probs=3.4
Q ss_pred ccCCCCCcccc
Q psy3949 92 ESSNSHDITFV 102 (103)
Q Consensus 92 ~~~~C~~C~~~ 102 (103)
+.|.|+.||-+
T Consensus 32 r~y~Cp~CgAt 42 (55)
T PF05741_consen 32 RKYVCPICGAT 42 (55)
T ss_dssp GG---TTT---
T ss_pred hcCcCCCCcCc
Confidence 35778888753
No 181
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=42.88 E-value=15 Score=20.49 Aligned_cols=10 Identities=20% Similarity=0.511 Sum_probs=4.2
Q ss_pred cCCcCccccc
Q psy3949 67 KCLFCDYHCT 76 (103)
Q Consensus 67 ~c~~c~~~f~ 76 (103)
+|..|++.|.
T Consensus 3 ~Ct~Cg~~f~ 12 (131)
T PF09845_consen 3 QCTKCGRVFE 12 (131)
T ss_pred ccCcCCCCcC
Confidence 3444444443
No 182
>TIGR00319 desulf_FeS4 desulfoferrodoxin FeS4 iron-binding domain. Neelaredoxin, a monomeric blue non-heme iron protein, lacks this domain.
Probab=42.61 E-value=6.6 Score=16.01 Aligned_cols=9 Identities=0% Similarity=-0.359 Sum_probs=5.3
Q ss_pred cCCCCCccc
Q psy3949 93 SSNSHDITF 101 (103)
Q Consensus 93 ~~~C~~C~~ 101 (103)
-|+|..||.
T Consensus 7 ~ykC~~Cgn 15 (34)
T TIGR00319 7 VYKCEVCGN 15 (34)
T ss_pred EEEcCCCCc
Confidence 466666654
No 183
>KOG0402|consensus
Probab=41.75 E-value=7.1 Score=19.87 Aligned_cols=9 Identities=22% Similarity=0.851 Sum_probs=5.3
Q ss_pred ceecCCCCC
Q psy3949 37 RFVCYTCPY 45 (103)
Q Consensus 37 ~~~c~~c~~ 45 (103)
.|.|+.||+
T Consensus 36 ky~CsfCGK 44 (92)
T KOG0402|consen 36 KYTCSFCGK 44 (92)
T ss_pred hhhhhhcch
Confidence 356666664
No 184
>PRK05452 anaerobic nitric oxide reductase flavorubredoxin; Provisional
Probab=41.61 E-value=20 Score=24.49 Aligned_cols=14 Identities=14% Similarity=0.546 Sum_probs=8.7
Q ss_pred CCccCCcCcccccC
Q psy3949 64 KPYKCLFCDYHCTQ 77 (103)
Q Consensus 64 ~~~~c~~c~~~f~~ 77 (103)
..|.|..|+..+..
T Consensus 424 ~~~~c~~c~~~yd~ 437 (479)
T PRK05452 424 PRMQCSVCQWIYDP 437 (479)
T ss_pred CeEEECCCCeEECC
Confidence 34667777766553
No 185
>PHA02998 RNA polymerase subunit; Provisional
Probab=40.47 E-value=9.8 Score=22.38 Aligned_cols=39 Identities=18% Similarity=0.234 Sum_probs=21.4
Q ss_pred eecCCCCCCccchhHHHHHHHH-hhC-CCCccCCcCcccccCc
Q psy3949 38 FVCYTCPYHTTYSQSMKSHLRK-HSG-EKPYKCLFCDYHCTQS 78 (103)
Q Consensus 38 ~~c~~c~~~~~~~~~l~~h~~~-~~~-~~~~~c~~c~~~f~~~ 78 (103)
-.|+.|+..-.... +.++++ .+. ..-|.|..|+..|..+
T Consensus 144 v~CPkCg~~~A~f~--qlQTRSADEPmT~FYkC~~CG~~wkpp 184 (195)
T PHA02998 144 TPCPNCKSKNTTPM--MIQTRAADEPPLVRHACRDCKKHFKPP 184 (195)
T ss_pred CCCCCCCCCceEEE--EEeeccCCCCceEEEEcCCCCCccCCc
Confidence 46777775443333 333443 222 2346787788777655
No 186
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=40.24 E-value=18 Score=16.56 Aligned_cols=10 Identities=20% Similarity=0.338 Sum_probs=4.6
Q ss_pred CCccCCcCcc
Q psy3949 64 KPYKCLFCDY 73 (103)
Q Consensus 64 ~~~~c~~c~~ 73 (103)
....|+.|++
T Consensus 45 ~i~~Cp~CgR 54 (56)
T PF02591_consen 45 EIVFCPNCGR 54 (56)
T ss_pred CeEECcCCCc
Confidence 3444555543
No 187
>COG3364 Zn-ribbon containing protein [General function prediction only]
Probab=39.58 E-value=23 Score=18.84 Aligned_cols=13 Identities=15% Similarity=0.184 Sum_probs=7.7
Q ss_pred ceecCCCCCCccc
Q psy3949 37 RFVCYTCPYHTTY 49 (103)
Q Consensus 37 ~~~c~~c~~~~~~ 49 (103)
|+.|-.||..|..
T Consensus 2 pH~CtrCG~vf~~ 14 (112)
T COG3364 2 PHQCTRCGEVFDD 14 (112)
T ss_pred Cceeccccccccc
Confidence 4556666666654
No 188
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=39.36 E-value=14 Score=23.26 Aligned_cols=9 Identities=33% Similarity=1.062 Sum_probs=4.1
Q ss_pred CccCCcCcc
Q psy3949 65 PYKCLFCDY 73 (103)
Q Consensus 65 ~~~c~~c~~ 73 (103)
.+.|+.||.
T Consensus 322 ~~~C~~cg~ 330 (364)
T COG0675 322 LFKCPRCGF 330 (364)
T ss_pred eEECCCCCC
Confidence 344444444
No 189
>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=39.33 E-value=5.5 Score=18.30 Aligned_cols=14 Identities=7% Similarity=-0.119 Sum_probs=8.0
Q ss_pred cCccCCCCCccccC
Q psy3949 90 LMESSNSHDITFVM 103 (103)
Q Consensus 90 ~e~~~~C~~C~~~~ 103 (103)
+...|+|.+|++.|
T Consensus 32 ~~~~~rC~YCe~~~ 45 (52)
T PF02748_consen 32 EPIKLRCHYCERII 45 (52)
T ss_dssp TTCEEEETTT--EE
T ss_pred CCCEEEeeCCCCEe
Confidence 44568888888753
No 190
>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=39.33 E-value=19 Score=16.73 Aligned_cols=31 Identities=16% Similarity=0.412 Sum_probs=18.7
Q ss_pred CcccCCCcccccccCHHHHHhhhCCCccccCCCCCcceecCCCCCCcc
Q psy3949 1 VRCQYCKHSLSVSNGFEIVLSHTKSCTYISRPDHNYRFVCYTCPYHTT 48 (103)
Q Consensus 1 ~~C~~C~~~f~~~~~l~~~~~h~~~~~~~~~~~~~~~~~c~~c~~~~~ 48 (103)
|.|+.||..+..... . .+. ...|+.||..+.
T Consensus 3 ~~CP~CG~~iev~~~---~---~Ge-----------iV~Cp~CGaele 33 (54)
T TIGR01206 3 FECPDCGAEIELENP---E---LGE-----------LVICDECGAELE 33 (54)
T ss_pred cCCCCCCCEEecCCC---c---cCC-----------EEeCCCCCCEEE
Confidence 578888876643221 1 133 467888887654
No 191
>PF10164 DUF2367: Uncharacterized conserved protein (DUF2367); InterPro: IPR019317 This is a highly conserved set of proteins which contains three pairs of cysteine residues within a length of 42 amino acids and is rich in proline residues towards the N terminus. It includes a membrane protein that has been found to be highly expressed in the mouse brain and consequently, several members have been assigned as brain protein i3 (Bri3). Their function is unknown.
Probab=39.28 E-value=17 Score=19.09 Aligned_cols=13 Identities=8% Similarity=0.110 Sum_probs=9.9
Q ss_pred CccCCCCCccccC
Q psy3949 91 MESSNSHDITFVM 103 (103)
Q Consensus 91 e~~~~C~~C~~~~ 103 (103)
.+..+|..||.+|
T Consensus 86 ~r~~rC~nCG~~f 98 (98)
T PF10164_consen 86 MRERRCSNCGATF 98 (98)
T ss_pred cCccccCCCCccC
Confidence 4667788888876
No 192
>PF12907 zf-met2: Zinc-binding
Probab=39.17 E-value=10 Score=16.41 Aligned_cols=14 Identities=14% Similarity=0.674 Sum_probs=7.6
Q ss_pred cccCCCcccccccC
Q psy3949 2 RCQYCKHSLSVSNG 15 (103)
Q Consensus 2 ~C~~C~~~f~~~~~ 15 (103)
.|.+|-..|....+
T Consensus 3 ~C~iC~qtF~~t~~ 16 (40)
T PF12907_consen 3 ICKICRQTFMQTTN 16 (40)
T ss_pred CcHHhhHHHHhcCC
Confidence 45556655555444
No 193
>KOG2071|consensus
Probab=39.06 E-value=26 Score=24.61 Aligned_cols=27 Identities=19% Similarity=0.331 Sum_probs=21.3
Q ss_pred CcceecCCCCCCccchhHHHHHHHHhh
Q psy3949 35 NYRFVCYTCPYHTTYSQSMKSHLRKHS 61 (103)
Q Consensus 35 ~~~~~c~~c~~~~~~~~~l~~h~~~~~ 61 (103)
+++..|..||.+|........||-.|.
T Consensus 416 ~~pnqC~~CG~R~~~~ee~sk~md~H~ 442 (579)
T KOG2071|consen 416 DSPNQCKSCGLRFDDSEERSKHMDIHD 442 (579)
T ss_pred CCcchhcccccccccchhhhhHhhhhh
Confidence 337899999999999987777766553
No 194
>PF09963 DUF2197: Uncharacterized protein conserved in bacteria (DUF2197); InterPro: IPR019241 This family represents various hypothetical bacterial proteins with no known function.
Probab=38.92 E-value=19 Score=16.90 Aligned_cols=14 Identities=14% Similarity=0.643 Sum_probs=8.2
Q ss_pred cccCCCcccccccC
Q psy3949 2 RCQYCKHSLSVSNG 15 (103)
Q Consensus 2 ~C~~C~~~f~~~~~ 15 (103)
+|..|++.+....+
T Consensus 4 kC~lCdk~~~Id~~ 17 (56)
T PF09963_consen 4 KCILCDKKEEIDED 17 (56)
T ss_pred EEEecCCEEEeccC
Confidence 46677776644433
No 195
>COG4391 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=38.88 E-value=11 Score=17.98 Aligned_cols=43 Identities=9% Similarity=-0.042 Sum_probs=21.6
Q ss_pred HHHHhhCCCCccCCcCcccccCcchhhhhhhhcccC-ccCCCCCccccC
Q psy3949 56 HLRKHSGEKPYKCLFCDYHCTQSGPLRRHMKIKHLM-ESSNSHDITFVM 103 (103)
Q Consensus 56 h~~~~~~~~~~~c~~c~~~f~~~~~l~~h~~~~~~e-~~~~C~~C~~~~ 103 (103)
|..++.+..++.|.--+..+..+..+ +-.|+ .--.|++|+..|
T Consensus 15 ~~~I~~~~~~l~C~g~~~p~~HPrV~-----L~mg~~gev~CPYC~t~y 58 (62)
T COG4391 15 HETIEIGDLPLMCPGPEPPNDHPRVF-----LDMGDEGEVVCPYCSTRY 58 (62)
T ss_pred ceEEEeCCeeEEcCCCCCCCCCCEEE-----EEcCCCCcEecCccccEE
Confidence 44456667777776433333222111 11132 234699998764
No 196
>KOG3507|consensus
Probab=38.35 E-value=14 Score=17.44 Aligned_cols=29 Identities=21% Similarity=0.552 Sum_probs=17.1
Q ss_pred cceecCCCCCCccchhHHHHHHHHhhCCCCccCCcCcccc
Q psy3949 36 YRFVCYTCPYHTTYSQSMKSHLRKHSGEKPYKCLFCDYHC 75 (103)
Q Consensus 36 ~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~c~~c~~~f 75 (103)
+-|.|..|+..-.. ...-++.|..||...
T Consensus 19 miYiCgdC~~en~l-----------k~~D~irCReCG~RI 47 (62)
T KOG3507|consen 19 MIYICGDCGQENTL-----------KRGDVIRCRECGYRI 47 (62)
T ss_pred EEEEeccccccccc-----------cCCCcEehhhcchHH
Confidence 35888888753211 112357888888654
No 197
>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=37.65 E-value=35 Score=23.42 Aligned_cols=27 Identities=22% Similarity=0.486 Sum_probs=23.2
Q ss_pred ceecCCCCCCccchhHHHHHHH-HhhCC
Q psy3949 37 RFVCYTCPYHTTYSQSMKSHLR-KHSGE 63 (103)
Q Consensus 37 ~~~c~~c~~~~~~~~~l~~h~~-~~~~~ 63 (103)
-|.|+.|.+.|.....+..|+. .|.+.
T Consensus 57 FWiCp~CskkF~d~~~~~~H~~~eH~~~ 84 (466)
T PF04780_consen 57 FWICPRCSKKFSDAESCLSHMEQEHPAG 84 (466)
T ss_pred EeeCCcccceeCCHHHHHHHHHHhhhhh
Confidence 5899999999999999999997 46554
No 198
>COG1773 Rubredoxin [Energy production and conversion]
Probab=37.23 E-value=13 Score=17.42 Aligned_cols=13 Identities=23% Similarity=0.483 Sum_probs=8.5
Q ss_pred CcccCCCcccccc
Q psy3949 1 VRCQYCKHSLSVS 13 (103)
Q Consensus 1 ~~C~~C~~~f~~~ 13 (103)
|+|..||..|.-.
T Consensus 4 ~~C~~CG~vYd~e 16 (55)
T COG1773 4 WRCSVCGYVYDPE 16 (55)
T ss_pred eEecCCceEeccc
Confidence 4677777776543
No 199
>KOG1280|consensus
Probab=36.49 E-value=27 Score=22.94 Aligned_cols=22 Identities=18% Similarity=0.387 Sum_probs=11.3
Q ss_pred ceecCCCCCCccchhHHHHHHH
Q psy3949 37 RFVCYTCPYHTTYSQSMKSHLR 58 (103)
Q Consensus 37 ~~~c~~c~~~~~~~~~l~~h~~ 58 (103)
.|+|+.|+..-.....++.|..
T Consensus 79 SftCPyC~~~Gfte~~f~~Hv~ 100 (381)
T KOG1280|consen 79 SFTCPYCGIMGFTERQFGTHVL 100 (381)
T ss_pred cccCCcccccccchhHHHHHhh
Confidence 3555555554444455555544
No 200
>TIGR01385 TFSII transcription elongation factor S-II. This model represents eukaryotic transcription elongation factor S-II. This protein allows stalled RNA transcription complexes to perform a cleavage of the nascent RNA and restart at the newly generated 3-prime end.
Probab=36.33 E-value=12 Score=23.84 Aligned_cols=38 Identities=16% Similarity=0.247 Sum_probs=21.5
Q ss_pred ceecCCCCCCccchhHHHHHHHH-hhC-CCCccCCcCccccc
Q psy3949 37 RFVCYTCPYHTTYSQSMKSHLRK-HSG-EKPYKCLFCDYHCT 76 (103)
Q Consensus 37 ~~~c~~c~~~~~~~~~l~~h~~~-~~~-~~~~~c~~c~~~f~ 76 (103)
.+.|+.|+..-..... .+++. ..+ ..-|.|..|+..|.
T Consensus 258 ~~~C~~C~~~~~~~~q--~QtrsaDEpmT~f~~C~~Cg~~w~ 297 (299)
T TIGR01385 258 LFTCGKCKQKKCTYYQ--LQTRSADEPMTTFVTCEECGNRWK 297 (299)
T ss_pred cccCCCCCCccceEEE--ecccCCCCCCeEEEEcCCCCCeee
Confidence 4678888755443333 33443 233 23467888887654
No 201
>KOG2482|consensus
Probab=36.27 E-value=50 Score=21.81 Aligned_cols=57 Identities=25% Similarity=0.557 Sum_probs=37.0
Q ss_pred CCCCCcceecCCCCCCccch-hHHHHHHHH-hh---C------------------CCCccCCcCcccccCcchhhhhhhh
Q psy3949 31 RPDHNYRFVCYTCPYHTTYS-QSMKSHLRK-HS---G------------------EKPYKCLFCDYHCTQSGPLRRHMKI 87 (103)
Q Consensus 31 ~~~~~~~~~c~~c~~~~~~~-~~l~~h~~~-~~---~------------------~~~~~c~~c~~~f~~~~~l~~h~~~ 87 (103)
+.+......|..|...+... +....|+.. |. | -..+.|..|-+.|.....|..||+.
T Consensus 138 redt~fslqClFCn~e~lgnRs~~l~Hlf~~H~lniGlpDniVyvnelLehLkekL~r~~CLyCekifrdkntLkeHMrk 217 (423)
T KOG2482|consen 138 REDTIFSLQCLFCNNEGLGNRSEILEHLFHVHGLNIGLPDNIVYVNELLEHLKEKLERLRCLYCEKIFRDKNTLKEHMRK 217 (423)
T ss_pred hcCCeeeeEEEEecchhcccHHHHHHHHHHHhhhccCCCcceeeHHHHHHHHHHHHhhheeeeeccccCCcHHHHHHHHh
Confidence 34444467888888655443 444445431 21 1 1134688999999999999999986
No 202
>PTZ00303 phosphatidylinositol kinase; Provisional
Probab=36.26 E-value=27 Score=25.85 Aligned_cols=12 Identities=17% Similarity=0.262 Sum_probs=7.6
Q ss_pred ecCCCCCCccch
Q psy3949 39 VCYTCPYHTTYS 50 (103)
Q Consensus 39 ~c~~c~~~~~~~ 50 (103)
.|..|++.|.+.
T Consensus 462 tC~~C~kkFfSl 473 (1374)
T PTZ00303 462 SCPSCGRAFISL 473 (1374)
T ss_pred cccCcCCccccc
Confidence 477777766543
No 203
>PF11789 zf-Nse: Zinc-finger of the MIZ type in Nse subunit; PDB: 2YU4_A 3HTK_C.
Probab=35.45 E-value=11 Score=17.62 Aligned_cols=31 Identities=16% Similarity=0.144 Sum_probs=12.9
Q ss_pred CCccCCcCcccccCcchhhhhhhhcccCccCCCCC
Q psy3949 64 KPYKCLFCDYHCTQSGPLRRHMKIKHLMESSNSHD 98 (103)
Q Consensus 64 ~~~~c~~c~~~f~~~~~l~~h~~~~~~e~~~~C~~ 98 (103)
.|.....|+..|...+-+ .++ ......+|++
T Consensus 23 ~PV~s~~C~H~fek~aI~-~~i---~~~~~~~CPv 53 (57)
T PF11789_consen 23 DPVKSKKCGHTFEKEAIL-QYI---QRNGSKRCPV 53 (57)
T ss_dssp SEEEESSS--EEEHHHHH-HHC---TTTS-EE-SC
T ss_pred CCcCcCCCCCeecHHHHH-HHH---HhcCCCCCCC
Confidence 455555676666554332 222 2234455665
No 204
>PRK01343 zinc-binding protein; Provisional
Probab=35.36 E-value=22 Score=16.78 Aligned_cols=10 Identities=0% Similarity=-0.170 Sum_probs=5.7
Q ss_pred cCCCCCcccc
Q psy3949 93 SSNSHDITFV 102 (103)
Q Consensus 93 ~~~C~~C~~~ 102 (103)
...|+.|++.
T Consensus 9 ~~~CP~C~k~ 18 (57)
T PRK01343 9 TRPCPECGKP 18 (57)
T ss_pred CCcCCCCCCc
Confidence 3456666654
No 205
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=35.34 E-value=25 Score=16.43 Aligned_cols=12 Identities=8% Similarity=-0.078 Sum_probs=8.3
Q ss_pred cCccCCCCCccc
Q psy3949 90 LMESSNSHDITF 101 (103)
Q Consensus 90 ~e~~~~C~~C~~ 101 (103)
+.-.|.|+.||-
T Consensus 11 ~~v~~~Cp~cGi 22 (55)
T PF13824_consen 11 AHVNFECPDCGI 22 (55)
T ss_pred cccCCcCCCCCC
Confidence 344688888875
No 206
>KOG3352|consensus
Probab=35.29 E-value=19 Score=20.57 Aligned_cols=12 Identities=8% Similarity=0.155 Sum_probs=9.3
Q ss_pred ccCCCCCccccC
Q psy3949 92 ESSNSHDITFVM 103 (103)
Q Consensus 92 ~~~~C~~C~~~~ 103 (103)
+..+|++||..|
T Consensus 132 e~~rc~eCG~~f 143 (153)
T KOG3352|consen 132 ETQRCPECGHYF 143 (153)
T ss_pred CcccCCcccceE
Confidence 567799999765
No 207
>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG
Probab=35.01 E-value=23 Score=16.32 Aligned_cols=11 Identities=27% Similarity=1.147 Sum_probs=6.8
Q ss_pred cccCCCccccc
Q psy3949 2 RCQYCKHSLSV 12 (103)
Q Consensus 2 ~C~~C~~~f~~ 12 (103)
.|+.||..+..
T Consensus 2 ~CPyCge~~~~ 12 (52)
T PF14255_consen 2 QCPYCGEPIEI 12 (52)
T ss_pred CCCCCCCeeEE
Confidence 57777766544
No 208
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=34.40 E-value=12 Score=19.82 Aligned_cols=37 Identities=22% Similarity=0.312 Sum_probs=19.5
Q ss_pred cceecCCCCCCccchhHHHHHHHHhhCCCCccCCcCccccc
Q psy3949 36 YRFVCYTCPYHTTYSQSMKSHLRKHSGEKPYKCLFCDYHCT 76 (103)
Q Consensus 36 ~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~c~~c~~~f~ 76 (103)
+.|.|+.|+..-.+.-.+. .-.+.-...|..||..|-
T Consensus 21 k~FtCp~Cghe~vs~ctvk----k~~~~g~~~Cg~CGls~e 57 (104)
T COG4888 21 KTFTCPRCGHEKVSSCTVK----KTVNIGTAVCGNCGLSFE 57 (104)
T ss_pred ceEecCccCCeeeeEEEEE----ecCceeEEEcccCcceEE
Confidence 3689999986443322211 111112356778887663
No 209
>KOG3002|consensus
Probab=33.08 E-value=84 Score=20.25 Aligned_cols=58 Identities=12% Similarity=0.116 Sum_probs=33.8
Q ss_pred ceecCCCCCCccchhHHHHHHHHhhCCCCccCC----cCcccccCcchhhhhhhhcccCccCCCCC
Q psy3949 37 RFVCYTCPYHTTYSQSMKSHLRKHSGEKPYKCL----FCDYHCTQSGPLRRHMKIKHLMESSNSHD 98 (103)
Q Consensus 37 ~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~c~----~c~~~f~~~~~l~~h~~~~~~e~~~~C~~ 98 (103)
...|+.|..-+.....+..-.. .....+.|. -|.+.|..... ..|.+.... .||.|+.
T Consensus 80 ~~~CP~Cr~~~g~~R~~amEkV--~e~~~vpC~~~~~GC~~~~~Y~~~-~~HE~~C~f-~~~~CP~ 141 (299)
T KOG3002|consen 80 SNKCPTCRLPIGNIRCRAMEKV--AEAVLVPCKNAKLGCTKSFPYGEK-SKHEKVCEF-RPCSCPV 141 (299)
T ss_pred cccCCccccccccHHHHHHHHH--HHhceecccccccCCceeeccccc-ccccccccc-CCcCCCC
Confidence 5678888776665443322222 222345554 37777776665 567766555 7888875
No 210
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=32.91 E-value=20 Score=22.95 Aligned_cols=12 Identities=33% Similarity=0.672 Sum_probs=6.7
Q ss_pred CccCCcCccccc
Q psy3949 65 PYKCLFCDYHCT 76 (103)
Q Consensus 65 ~~~c~~c~~~f~ 76 (103)
.+.|+.|+.-|.
T Consensus 57 ~~vcp~c~~h~r 68 (296)
T CHL00174 57 MNICEQCGYHLK 68 (296)
T ss_pred CCCCCCCCCCcC
Confidence 456666665443
No 211
>PF00412 LIM: LIM domain; InterPro: IPR001781 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents LIM-type zinc finger (Znf) domains. LIM domains coordinate one or more zinc atoms, and are named after the three proteins (LIN-11, Isl1 and MEC-3) in which they were first found. They consist of two zinc-binding motifs that resemble GATA-like Znf's, however the residues holding the zinc atom(s) are variable, involving Cys, His, Asp or Glu residues. LIM domains are involved in proteins with differing functions, including gene expression, and cytoskeleton organisation and development [, ]. Protein containing LIM Znf domains include: Caenorhabditis elegans mec-3; a protein required for the differentiation of the set of six touch receptor neurons in this nematode. C. elegans. lin-11; a protein required for the asymmetric division of vulval blast cells. Vertebrate insulin gene enhancer binding protein isl-1. Isl-1 binds to one of the two cis-acting protein-binding domains of the insulin gene. Vertebrate homeobox proteins lim-1, lim-2 (lim-5) and lim3. Vertebrate lmx-1, which acts as a transcriptional activator by binding to the FLAT element; a beta-cell-specific transcriptional enhancer found in the insulin gene. Mammalian LH-2, a transcriptional regulatory protein involved in the control of cell differentiation in developing lymphoid and neural cell types. Drosophila melanogaster (Fruit fly) protein apterous, required for the normal development of the wing and halter imaginal discs. Vertebrate protein kinases LIMK-1 and LIMK-2. Mammalian rhombotins. Rhombotin 1 (RBTN1 or TTG-1) and rhombotin-2 (RBTN2 or TTG-2) are proteins of about 160 amino acids whose genes are disrupted by chromosomal translocations in T-cell leukemia. Mammalian and avian cysteine-rich protein (CRP), a 192 amino-acid protein of unknown function. Seems to interact with zyxin. Mammalian cysteine-rich intestinal protein (CRIP), a small protein which seems to have a role in zinc absorption and may function as an intracellular zinc transport protein. Vertebrate paxillin, a cytoskeletal focal adhesion protein. Mus musculus (Mouse) testin which should not be confused with rat testin which is a thiol protease homologue (see IPR000169 from INTERPRO). Helianthus annuus (Common sunflower) pollen specific protein SF3. Chicken zyxin. Zyxin is a low-abundance adhesion plaque protein which has been shown to interact with CRP. Yeast protein LRG1 which is involved in sporulation []. Saccharomyces cerevisiae (Baker's yeast) rho-type GTPase activating protein RGA1/DBM1. C. elegans homeobox protein ceh-14. C. elegans homeobox protein unc-97. S. cerevisiae hypothetical protein YKR090w. C. elegans hypothetical proteins C28H8.6. These proteins generally contain two tandem copies of the LIM domain in their N-terminal section. Zyxin and paxillin are exceptions in that they contain respectively three and four LIM domains at their C-terminal extremity. In apterous, isl-1, LH-2, lin-11, lim-1 to lim-3, lmx-1 and ceh-14 and mec-3 there is a homeobox domain some 50 to 95 amino acids after the LIM domains. LIM domains contain seven conserved cysteine residues and a histidine. The arrangement followed by these conserved residues is: C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] LIM domains bind two zinc ions []. LIM does not bind DNA, rather it seems to act as an interface for protein-protein interaction. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CO8_A 2EGQ_A 2CUR_A 3IXE_B 1CTL_A 1B8T_A 1X62_A 2DFY_C 1IML_A 2CUQ_A ....
Probab=32.77 E-value=22 Score=15.96 Aligned_cols=13 Identities=23% Similarity=0.593 Sum_probs=7.5
Q ss_pred ccCCcCcccccCc
Q psy3949 66 YKCLFCDYHCTQS 78 (103)
Q Consensus 66 ~~c~~c~~~f~~~ 78 (103)
|.|..|+..+...
T Consensus 27 f~C~~C~~~l~~~ 39 (58)
T PF00412_consen 27 FKCSKCGKPLNDG 39 (58)
T ss_dssp SBETTTTCBTTTS
T ss_pred cccCCCCCccCCC
Confidence 5666676655443
No 212
>PRK04351 hypothetical protein; Provisional
Probab=32.65 E-value=22 Score=20.25 Aligned_cols=10 Identities=0% Similarity=-0.260 Sum_probs=5.7
Q ss_pred ccCCCCCccc
Q psy3949 92 ESSNSHDITF 101 (103)
Q Consensus 92 ~~~~C~~C~~ 101 (103)
..|.|..|+-
T Consensus 131 ~~yrCg~C~g 140 (149)
T PRK04351 131 KRYRCGKCRG 140 (149)
T ss_pred CcEEeCCCCc
Confidence 4566666653
No 213
>TIGR01384 TFS_arch transcription factor S, archaeal. There has been an apparent duplication event in the Halobacteriaceae lineage (Haloarcula, Haloferax, Haloquadratum, Halobacterium and Natromonas). There appears to be a separate duplication in Methanosphaera stadtmanae.
Probab=32.59 E-value=14 Score=19.25 Aligned_cols=38 Identities=29% Similarity=0.588 Sum_probs=22.7
Q ss_pred ceecCCCCCCccchhHHHHHHHH-hhCC-CCccCCcCccccc
Q psy3949 37 RFVCYTCPYHTTYSQSMKSHLRK-HSGE-KPYKCLFCDYHCT 76 (103)
Q Consensus 37 ~~~c~~c~~~~~~~~~l~~h~~~-~~~~-~~~~c~~c~~~f~ 76 (103)
...|+.||..-.....+ +++. ..+. .-|.|..|+..+.
T Consensus 62 ~~~Cp~Cg~~~a~f~~~--Q~RsadE~~T~fy~C~~C~~~w~ 101 (104)
T TIGR01384 62 RVECPKCGHKEAYYWLL--QTRRADEPETRFYKCTKCGYVWR 101 (104)
T ss_pred cCCCCCCCCCeeEEEEe--ccCCCCCCcEEEEEeCCCCCeeE
Confidence 45799998665444333 3443 3333 4578888887654
No 214
>PF02150 RNA_POL_M_15KD: RNA polymerases M/15 Kd subunit; InterPro: IPR001529 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. In archaebacteria, there is generally a single form of RNA polymerase which also consist of an oligomeric assemblage of 10 to 13 polypeptides. It has recently been shown [], [] that small subunits of about 15 kDa, found in polymerase types I and II, are highly conserved. These proteins contain a probable zinc finger in their N-terminal region and a C-terminal zinc ribbon domain (see IPR001222 from INTERPRO).; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3H0G_I 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I ....
Probab=32.58 E-value=7.7 Score=16.12 Aligned_cols=8 Identities=38% Similarity=1.103 Sum_probs=3.1
Q ss_pred cCCcCccc
Q psy3949 67 KCLFCDYH 74 (103)
Q Consensus 67 ~c~~c~~~ 74 (103)
.|..|+..
T Consensus 22 ~C~~C~Y~ 29 (35)
T PF02150_consen 22 ACRTCGYE 29 (35)
T ss_dssp EESSSS-E
T ss_pred CCCCCCCc
Confidence 34444443
No 215
>smart00109 C1 Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains). Some bind phorbol esters and diacylglycerol. Some bind RasGTP. Zinc-binding domains.
Probab=32.53 E-value=49 Score=14.00 Aligned_cols=6 Identities=33% Similarity=1.082 Sum_probs=2.6
Q ss_pred cCCCCC
Q psy3949 40 CYTCPY 45 (103)
Q Consensus 40 c~~c~~ 45 (103)
|..|++
T Consensus 14 C~~C~~ 19 (49)
T smart00109 14 CCVCRK 19 (49)
T ss_pred cccccc
Confidence 444443
No 216
>PF13878 zf-C2H2_3: zinc-finger of acetyl-transferase ESCO
Probab=32.50 E-value=51 Score=14.15 Aligned_cols=23 Identities=26% Similarity=0.366 Sum_probs=13.3
Q ss_pred eecCCCCCCccch--hHHHHHHHHh
Q psy3949 38 FVCYTCPYHTTYS--QSMKSHLRKH 60 (103)
Q Consensus 38 ~~c~~c~~~~~~~--~~l~~h~~~~ 60 (103)
-.|+.||..+... ..-..|.+.|
T Consensus 14 ~~C~~CgM~Y~~~~~eD~~~H~~yH 38 (41)
T PF13878_consen 14 TTCPTCGMLYSPGSPEDEKLHKKYH 38 (41)
T ss_pred cCCCCCCCEECCCCHHHHHHHHHHH
Confidence 3788888665443 4444454444
No 217
>PF14369 zf-RING_3: zinc-finger
Probab=32.48 E-value=24 Score=14.65 Aligned_cols=9 Identities=22% Similarity=0.800 Sum_probs=5.8
Q ss_pred ccCCCcccc
Q psy3949 3 CQYCKHSLS 11 (103)
Q Consensus 3 C~~C~~~f~ 11 (103)
|+.|+..|-
T Consensus 24 CP~C~~gFv 32 (35)
T PF14369_consen 24 CPRCHGGFV 32 (35)
T ss_pred CcCCCCcEe
Confidence 666776663
No 218
>TIGR00143 hypF [NiFe] hydrogenase maturation protein HypF. A previously described regulatory effect of HypF mutatation is attributable to loss of activity of a regulatory hydrogenase. A zinc finger-like region CXXCX(18)CXXCX(24)CXXCX(18)CXXC region further supported the regulatory hypothesis. However, more recent work (PUBMED:11375153) shows the direct effect is on the activity of expressed hydrogenases with nickel/iron centers, rather than on expression.
Probab=32.40 E-value=7.9 Score=27.74 Aligned_cols=55 Identities=13% Similarity=0.192 Sum_probs=24.3
Q ss_pred ecCCCCCCccchhHHHHHHHHhhCCCCc-cCCcCcccccCcchhhhhhhhcccCccCCCCCcc
Q psy3949 39 VCYTCPYHTTYSQSMKSHLRKHSGEKPY-KCLFCDYHCTQSGPLRRHMKIKHLMESSNSHDIT 100 (103)
Q Consensus 39 ~c~~c~~~~~~~~~l~~h~~~~~~~~~~-~c~~c~~~f~~~~~l~~h~~~~~~e~~~~C~~C~ 100 (103)
.|-.||-.|.....|-- .+.++.-..| .|..|.+-+..+.+.. .|. .+-.|+.||
T Consensus 92 nCt~CGPr~~i~~~lpy-dr~~t~m~~f~~C~~C~~ey~~p~~rr----~h~--~~~~C~~Cg 147 (711)
T TIGR00143 92 SCTHCGPRFTIIEALPY-DRENTSMADFPLCPDCAKEYKDPLDRR----FHA--QPIACPRCG 147 (711)
T ss_pred cccCCCCCeEEeecCCC-CCCCcCCCCCcCCHHHHHHhcCCcccc----CCC--CCccCCCCC
Confidence 56667766655444321 1112222222 4555655554443321 111 244566665
No 219
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=31.92 E-value=19 Score=20.90 Aligned_cols=12 Identities=8% Similarity=-0.105 Sum_probs=8.9
Q ss_pred ccCCCCCccccC
Q psy3949 92 ESSNSHDITFVM 103 (103)
Q Consensus 92 ~~~~C~~C~~~~ 103 (103)
.-|.|+.||+.+
T Consensus 129 ~f~~C~~CgkiY 140 (165)
T COG1656 129 EFYRCPKCGKIY 140 (165)
T ss_pred ceeECCCCcccc
Confidence 346799999864
No 220
>PF14787 zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB: 1CL4_A 1DSV_A.
Probab=31.89 E-value=26 Score=14.81 Aligned_cols=8 Identities=0% Similarity=-0.541 Sum_probs=3.6
Q ss_pred CCCCcccc
Q psy3949 95 NSHDITFV 102 (103)
Q Consensus 95 ~C~~C~~~ 102 (103)
.|+.|++.
T Consensus 4 ~CprC~kg 11 (36)
T PF14787_consen 4 LCPRCGKG 11 (36)
T ss_dssp C-TTTSSS
T ss_pred cCcccCCC
Confidence 35555554
No 221
>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=31.07 E-value=22 Score=15.28 Aligned_cols=11 Identities=27% Similarity=0.646 Sum_probs=6.2
Q ss_pred ceecCCCCCCc
Q psy3949 37 RFVCYTCPYHT 47 (103)
Q Consensus 37 ~~~c~~c~~~~ 47 (103)
.+.|..||...
T Consensus 19 ~~vC~~CG~Vl 29 (43)
T PF08271_consen 19 ELVCPNCGLVL 29 (43)
T ss_dssp EEEETTT-BBE
T ss_pred eEECCCCCCEe
Confidence 46777777543
No 222
>smart00731 SprT SprT homologues. Predicted to have roles in transcription elongation. Contains a conserved HExxH motif, indicating a metalloprotease function.
Probab=30.70 E-value=24 Score=19.77 Aligned_cols=11 Identities=0% Similarity=-0.345 Sum_probs=6.7
Q ss_pred ccCCCCCcccc
Q psy3949 92 ESSNSHDITFV 102 (103)
Q Consensus 92 ~~~~C~~C~~~ 102 (103)
..|.|..|+-.
T Consensus 132 ~~y~C~~C~g~ 142 (146)
T smart00731 132 SRYRCGKCGGK 142 (146)
T ss_pred ceEEcCCCCCE
Confidence 44677777643
No 223
>COG4896 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=30.12 E-value=19 Score=17.24 Aligned_cols=12 Identities=25% Similarity=0.694 Sum_probs=7.9
Q ss_pred CccCCcCccccc
Q psy3949 65 PYKCLFCDYHCT 76 (103)
Q Consensus 65 ~~~c~~c~~~f~ 76 (103)
.|.|+.|.....
T Consensus 31 tymC~eC~~Rva 42 (68)
T COG4896 31 TYMCPECEHRVA 42 (68)
T ss_pred eEechhhHhhhc
Confidence 478888865443
No 224
>KOG1088|consensus
Probab=30.00 E-value=21 Score=19.49 Aligned_cols=16 Identities=6% Similarity=-0.076 Sum_probs=10.9
Q ss_pred cccCccCCCCCccccC
Q psy3949 88 KHLMESSNSHDITFVM 103 (103)
Q Consensus 88 ~~~e~~~~C~~C~~~~ 103 (103)
+..|-.-+|++||.+|
T Consensus 93 ~v~EG~l~CpetG~vf 108 (124)
T KOG1088|consen 93 DVIEGELVCPETGRVF 108 (124)
T ss_pred hhccceEecCCCCcEe
Confidence 4445567788888776
No 225
>COG4306 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=29.89 E-value=27 Score=19.34 Aligned_cols=14 Identities=14% Similarity=0.437 Sum_probs=9.2
Q ss_pred ceecCCCCCCccch
Q psy3949 37 RFVCYTCPYHTTYS 50 (103)
Q Consensus 37 ~~~c~~c~~~~~~~ 50 (103)
|.-|..||+.|.+.
T Consensus 68 psfchncgs~fpwt 81 (160)
T COG4306 68 PSFCHNCGSRFPWT 81 (160)
T ss_pred cchhhcCCCCCCcH
Confidence 45577777777665
No 226
>PF05191 ADK_lid: Adenylate kinase, active site lid; InterPro: IPR007862 Adenylate kinases (ADK; 2.7.4.3 from EC) are phosphotransferases that catalyse the Mg-dependent reversible conversion of ATP and AMP to two molecules of ADP, an essential reaction for many processes in living cells. In large variants of adenylate kinase, the AMP and ATP substrates are buried in a domain that undergoes conformational changes from an open to a closed state when bound to substrate; the ligand is then contained within a highly specific environment required for catalysis. Adenylate kinase is a 3-domain protein consisting of a large central CORE domain flanked by a LID domain on one side and the AMP-binding NMPbind domain on the other []. The LID domain binds ATP and covers the phosphates at the active site. The substrates first bind the CORE domain, followed by closure of the active site by the LID and NMPbind domains. Comparisons of adenylate kinases have revealed a particular divergence in the active site lid. In some organisms, particularly the Gram-positive bacteria, residues in the lid domain have been mutated to cysteines and these cysteine residues (two CX(n)C motifs) are responsible for the binding of a zinc ion. The bound zinc ion in the lid domain is clearly structurally homologous to Zinc-finger domains. However, it is unclear whether the adenylate kinase lid is a novel zinc-finger DNA/RNA binding domain, or that the lid bound zinc serves a purely structural function [].; GO: 0004017 adenylate kinase activity; PDB: 3BE4_A 2OSB_B 2ORI_A 2EU8_A 3DL0_A 1P3J_A 2QAJ_A 2OO7_A 2P3S_A 3DKV_A ....
Probab=29.30 E-value=25 Score=14.74 Aligned_cols=12 Identities=17% Similarity=0.531 Sum_probs=7.8
Q ss_pred cccCCCcccccc
Q psy3949 2 RCQYCKHSLSVS 13 (103)
Q Consensus 2 ~C~~C~~~f~~~ 13 (103)
.|+.||..|...
T Consensus 3 ~C~~Cg~~Yh~~ 14 (36)
T PF05191_consen 3 ICPKCGRIYHIE 14 (36)
T ss_dssp EETTTTEEEETT
T ss_pred CcCCCCCccccc
Confidence 367777777543
No 227
>PRK08222 hydrogenase 4 subunit H; Validated
Probab=29.19 E-value=33 Score=20.07 Aligned_cols=17 Identities=18% Similarity=0.636 Sum_probs=12.2
Q ss_pred cccCCCcccccccCHHH
Q psy3949 2 RCQYCKHSLSVSNGFEI 18 (103)
Q Consensus 2 ~C~~C~~~f~~~~~l~~ 18 (103)
.|..||+.|.....+..
T Consensus 116 ~C~~Cg~~f~~~k~i~~ 132 (181)
T PRK08222 116 RCSRCERPFAPQKTVAL 132 (181)
T ss_pred cCcccCCccCcHhHHHH
Confidence 58888888886655554
No 228
>PHA02942 putative transposase; Provisional
Probab=28.24 E-value=34 Score=22.67 Aligned_cols=11 Identities=0% Similarity=-0.076 Sum_probs=7.9
Q ss_pred ccCCCCCcccc
Q psy3949 92 ESSNSHDITFV 102 (103)
Q Consensus 92 ~~~~C~~C~~~ 102 (103)
+.|.|+.||..
T Consensus 341 r~f~C~~CG~~ 351 (383)
T PHA02942 341 RYFHCPSCGYE 351 (383)
T ss_pred CEEECCCCCCE
Confidence 46788888764
No 229
>TIGR00515 accD acetyl-CoA carboxylase, carboxyl transferase, beta subunit. The enzyme acetyl-CoA carboxylase contains a biotin carboxyl carrier protein or domain, a biotin carboxylase, and a carboxyl transferase. This model represents the beta chain of the carboxyl transferase for cases in which the architecture of the protein is as in E. coli, in which the carboxyltransferase portion consists of two non-identical subnits, alpha and beta.
Probab=28.12 E-value=35 Score=21.72 Aligned_cols=29 Identities=21% Similarity=0.357 Sum_probs=15.2
Q ss_pred ecCCCCCCccchhHHHHHHHHhhCCCCccCCcCccccc
Q psy3949 39 VCYTCPYHTTYSQSMKSHLRKHSGEKPYKCLFCDYHCT 76 (103)
Q Consensus 39 ~c~~c~~~~~~~~~l~~h~~~~~~~~~~~c~~c~~~f~ 76 (103)
.|+.|+.....+. | ..+.+.|+.|+.-|.
T Consensus 28 ~c~~c~~~~~~~~-l--------~~~~~vc~~c~~h~r 56 (285)
T TIGR00515 28 KCPKCGQVLYTKE-L--------ERNLEVCPKCDHHMR 56 (285)
T ss_pred ECCCCcchhhHHH-H--------HhhCCCCCCCCCcCc
Confidence 6777776433211 1 123356777776544
No 230
>PRK05580 primosome assembly protein PriA; Validated
Probab=27.98 E-value=33 Score=24.61 Aligned_cols=12 Identities=0% Similarity=-0.302 Sum_probs=8.5
Q ss_pred cCccCCCCCccc
Q psy3949 90 LMESSNSHDITF 101 (103)
Q Consensus 90 ~e~~~~C~~C~~ 101 (103)
...|..|+.||.
T Consensus 418 ~~~~~~Cp~Cg~ 429 (679)
T PRK05580 418 EPIPKACPECGS 429 (679)
T ss_pred CCCCCCCCCCcC
Confidence 445778888875
No 231
>PF12230 PRP21_like_P: Pre-mRNA splicing factor PRP21 like protein; InterPro: IPR022030 This domain family is found in eukaryotes, and is typically between 212 and 238 amino acids in length. The family is found in association with PF01805 from PFAM. There are two completely conserved residues (W and H) that may be functionally important. PRP21 is required for assembly of the prespliceosome and it interacts with U2 snRNP and/or pre-mRNA in the prespliceosome. This family also contains proteins similar to PRP21, such as the mammalian SF3a. SF3a also interacts with U2 snRNP from the prespliceosome, converting it to its active form. ; PDB: 4DGW_B.
Probab=27.76 E-value=20 Score=21.73 Aligned_cols=29 Identities=17% Similarity=0.191 Sum_probs=0.0
Q ss_pred CccCCcCcccccCcchhhhhhhhcccCccC
Q psy3949 65 PYKCLFCDYHCTQSGPLRRHMKIKHLMESS 94 (103)
Q Consensus 65 ~~~c~~c~~~f~~~~~l~~h~~~~~~e~~~ 94 (103)
...|+.||...+ .+.+..|+|+......|
T Consensus 168 ~~~cPitGe~IP-~~e~~eHmRi~LlDP~w 196 (229)
T PF12230_consen 168 MIICPITGEMIP-ADEMDEHMRIELLDPRW 196 (229)
T ss_dssp ------------------------------
T ss_pred cccccccccccc-ccccccccccccccccc
Confidence 356677766533 33566677766554444
No 232
>COG1379 PHP family phosphoesterase with a Zn ribbon [General function prediction only]
Probab=27.28 E-value=23 Score=23.13 Aligned_cols=10 Identities=0% Similarity=-0.423 Sum_probs=6.4
Q ss_pred cCCCCCcccc
Q psy3949 93 SSNSHDITFV 102 (103)
Q Consensus 93 ~~~C~~C~~~ 102 (103)
.|+|+.||.+
T Consensus 265 ~wrCpkCGg~ 274 (403)
T COG1379 265 RWRCPKCGGK 274 (403)
T ss_pred cccCcccccc
Confidence 3677777754
No 233
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=27.27 E-value=38 Score=24.28 Aligned_cols=8 Identities=25% Similarity=0.845 Sum_probs=4.3
Q ss_pred cccCCCcc
Q psy3949 2 RCQYCKHS 9 (103)
Q Consensus 2 ~C~~C~~~ 9 (103)
.|+.||..
T Consensus 3 ~Cp~Cg~~ 10 (645)
T PRK14559 3 ICPQCQFE 10 (645)
T ss_pred cCCCCCCc
Confidence 35666644
No 234
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=27.18 E-value=81 Score=24.79 Aligned_cols=8 Identities=25% Similarity=0.530 Sum_probs=5.3
Q ss_pred eecCCCCC
Q psy3949 38 FVCYTCPY 45 (103)
Q Consensus 38 ~~c~~c~~ 45 (103)
..|+.||.
T Consensus 668 rkCPkCG~ 675 (1337)
T PRK14714 668 RRCPSCGT 675 (1337)
T ss_pred EECCCCCC
Confidence 56777765
No 235
>KOG2907|consensus
Probab=27.15 E-value=34 Score=18.57 Aligned_cols=37 Identities=27% Similarity=0.577 Sum_probs=22.7
Q ss_pred eecCCCCCCccchhHHHHHHHH-hhCCCC-ccCCcCccccc
Q psy3949 38 FVCYTCPYHTTYSQSMKSHLRK-HSGEKP-YKCLFCDYHCT 76 (103)
Q Consensus 38 ~~c~~c~~~~~~~~~l~~h~~~-~~~~~~-~~c~~c~~~f~ 76 (103)
..|+.||..--.... .++++ ..|+-. |.|..|+..|.
T Consensus 75 ~kCpkCghe~m~Y~T--~QlRSADEGQTVFYTC~kC~~k~~ 113 (116)
T KOG2907|consen 75 HKCPKCGHEEMSYHT--LQLRSADEGQTVFYTCPKCKYKFT 113 (116)
T ss_pred ccCcccCCchhhhhh--hhcccccCCceEEEEcCccceeee
Confidence 478888854333333 34554 566644 78888887664
No 236
>KOG0978|consensus
Probab=26.85 E-value=16 Score=26.24 Aligned_cols=18 Identities=17% Similarity=0.292 Sum_probs=10.4
Q ss_pred CCccCCcCcccccCcchh
Q psy3949 64 KPYKCLFCDYHCTQSGPL 81 (103)
Q Consensus 64 ~~~~c~~c~~~f~~~~~l 81 (103)
+--+|+.|+..|.....+
T Consensus 677 RqRKCP~Cn~aFganDv~ 694 (698)
T KOG0978|consen 677 RQRKCPKCNAAFGANDVH 694 (698)
T ss_pred hcCCCCCCCCCCCccccc
Confidence 344567777766655443
No 237
>PF04606 Ogr_Delta: Ogr/Delta-like zinc finger; InterPro: IPR007684 This entry is represented by Bacteriophage P2, Ogr. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This is a viral family of phage zinc-binding transcriptional activators, which also contains cryptic members in some bacterial genomes []. The P4 phage delta protein contains two such domains attached covalently, while the P2 phage Ogr proteins possess one domain but function as dimers. All the members of this family have the following consensus sequence: C-X(2)-C-X(3)-A-(X)2-R-X(15)-C-X(4)-C-X(3)-F [].; GO: 0006355 regulation of transcription, DNA-dependent
Probab=26.70 E-value=16 Score=16.20 Aligned_cols=10 Identities=20% Similarity=0.547 Sum_probs=5.0
Q ss_pred cCCCCCCccc
Q psy3949 40 CYTCPYHTTY 49 (103)
Q Consensus 40 c~~c~~~~~~ 49 (103)
|+.||.....
T Consensus 2 CP~Cg~~a~i 11 (47)
T PF04606_consen 2 CPHCGSKARI 11 (47)
T ss_pred cCCCCCeeEE
Confidence 5556554433
No 238
>PF14952 zf-tcix: Putative treble-clef, zinc-finger, Zn-binding
Probab=26.60 E-value=32 Score=15.26 Aligned_cols=7 Identities=0% Similarity=-0.097 Sum_probs=4.4
Q ss_pred CCCCCcc
Q psy3949 94 SNSHDIT 100 (103)
Q Consensus 94 ~~C~~C~ 100 (103)
-+|+.||
T Consensus 12 rkCp~CG 18 (44)
T PF14952_consen 12 RKCPKCG 18 (44)
T ss_pred ccCCcCc
Confidence 3577776
No 239
>TIGR02986 restrict_Alw26I type II restriction endonuclease, Alw26I/Eco31I/Esp3I family. Members of this family are type II restriction endonucleases of the Alw26I/Eco31I/Esp3I family. Characterized specificities of three members are GGTCTC, CGTCTC, and the shared subsequence GTCTC.
Probab=26.59 E-value=23 Score=23.64 Aligned_cols=13 Identities=8% Similarity=-0.033 Sum_probs=9.9
Q ss_pred ccCccCCCCCccccC
Q psy3949 89 HLMESSNSHDITFVM 103 (103)
Q Consensus 89 ~~e~~~~C~~C~~~~ 103 (103)
++.+| |..||++|
T Consensus 80 T~~kp--C~~CG~~m 92 (424)
T TIGR02986 80 TGVKP--CQTCGKTM 92 (424)
T ss_pred CCCcc--hHhcCCee
Confidence 56666 99999875
No 240
>COG4338 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=26.51 E-value=21 Score=16.16 Aligned_cols=14 Identities=21% Similarity=0.688 Sum_probs=8.6
Q ss_pred ccCCCcccccccCH
Q psy3949 3 CQYCKHSLSVSNGF 16 (103)
Q Consensus 3 C~~C~~~f~~~~~l 16 (103)
|++|+..|......
T Consensus 15 CpvCqRPFsWRkKW 28 (54)
T COG4338 15 CPVCQRPFSWRKKW 28 (54)
T ss_pred hhhhcCchHHHHHH
Confidence 66777777655443
No 241
>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=26.40 E-value=21 Score=23.34 Aligned_cols=40 Identities=20% Similarity=0.380 Sum_probs=16.6
Q ss_pred ceecCCCCCCccchhHHH---HHHH-HhhCC-CCccCCcCccccc
Q psy3949 37 RFVCYTCPYHTTYSQSMK---SHLR-KHSGE-KPYKCLFCDYHCT 76 (103)
Q Consensus 37 ~~~c~~c~~~~~~~~~l~---~h~~-~~~~~-~~~~c~~c~~~f~ 76 (103)
.+.|..|.+........- .|.. .+.+. +-|.|..|++...
T Consensus 252 av~C~~C~yt~~~~~~~C~~~~H~l~~~~a~KRFFkC~~C~~Rt~ 296 (344)
T PF09332_consen 252 AVTCKQCKYTAFKPSDRCKEEGHPLKWHDAVKRFFKCKDCGNRTI 296 (344)
T ss_dssp EEEETTT--EESS--HHHHHTT--EEEEEEE-EEEE-T-TS-EEE
T ss_pred EEEcCCCCCcccCcchhHHhcCCceEEeeeeeeeEECCCCCCeee
Confidence 478888876655544332 1211 12222 3478888887644
No 242
>PRK07591 threonine synthase; Validated
Probab=26.26 E-value=47 Score=22.26 Aligned_cols=26 Identities=19% Similarity=0.269 Sum_probs=16.8
Q ss_pred ceecCCCCCCccchhHHHHHHHHhhCCCCccCCcCcccc
Q psy3949 37 RFVCYTCPYHTTYSQSMKSHLRKHSGEKPYKCLFCDYHC 75 (103)
Q Consensus 37 ~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~c~~c~~~f 75 (103)
.+.|..||+.+.. ... +.|+.|+..+
T Consensus 18 ~l~C~~Cg~~~~~------------~~~-~~C~~cg~~l 43 (421)
T PRK07591 18 ALKCRECGAEYPL------------GPI-HVCEECFGPL 43 (421)
T ss_pred EEEeCCCCCcCCC------------CCC-ccCCCCCCeE
Confidence 4788889876541 123 7788887543
No 243
>PRK05978 hypothetical protein; Provisional
Probab=26.22 E-value=55 Score=18.72 Aligned_cols=30 Identities=17% Similarity=0.298 Sum_probs=14.8
Q ss_pred eecCCCCCCccchhHHHHHHHHhhCCCCccCCcCccccc
Q psy3949 38 FVCYTCPYHTTYSQSMKSHLRKHSGEKPYKCLFCDYHCT 76 (103)
Q Consensus 38 ~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~c~~c~~~f~ 76 (103)
-.|+.||+.-....-| ...-.|..|+..|.
T Consensus 34 grCP~CG~G~LF~g~L---------kv~~~C~~CG~~~~ 63 (148)
T PRK05978 34 GRCPACGEGKLFRAFL---------KPVDHCAACGEDFT 63 (148)
T ss_pred CcCCCCCCCccccccc---------ccCCCccccCCccc
Confidence 4677777643332211 12345666766554
No 244
>PF06676 DUF1178: Protein of unknown function (DUF1178); InterPro: IPR009562 This family consists of several hypothetical bacterial proteins of around 150 residues in length. The function of this family is unknown.
Probab=26.01 E-value=44 Score=19.11 Aligned_cols=7 Identities=0% Similarity=-0.292 Sum_probs=3.5
Q ss_pred CCCCCcc
Q psy3949 94 SNSHDIT 100 (103)
Q Consensus 94 ~~C~~C~ 100 (103)
-.|++||
T Consensus 33 v~CP~Cg 39 (148)
T PF06676_consen 33 VSCPVCG 39 (148)
T ss_pred ccCCCCC
Confidence 4455554
No 245
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=25.92 E-value=26 Score=14.87 Aligned_cols=11 Identities=18% Similarity=0.344 Sum_probs=4.7
Q ss_pred ccCCCcccccc
Q psy3949 3 CQYCKHSLSVS 13 (103)
Q Consensus 3 C~~C~~~f~~~ 13 (103)
|+.|+..|-..
T Consensus 22 C~~C~G~W~d~ 32 (41)
T PF13453_consen 22 CPSCGGIWFDA 32 (41)
T ss_pred CCCCCeEEccH
Confidence 44444444333
No 246
>TIGR00627 tfb4 transcription factor tfb4. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=25.16 E-value=80 Score=20.13 Aligned_cols=25 Identities=12% Similarity=0.162 Sum_probs=18.0
Q ss_pred CccCCcCcccccCcchhhhhhhhcccCccCCCCCccccC
Q psy3949 65 PYKCLFCDYHCTQSGPLRRHMKIKHLMESSNSHDITFVM 103 (103)
Q Consensus 65 ~~~c~~c~~~f~~~~~l~~h~~~~~~e~~~~C~~C~~~~ 103 (103)
-|.|..|.-.|... |=.|+.||-.|
T Consensus 255 GyvCs~Clsi~C~~--------------p~~C~~Cgt~f 279 (279)
T TIGR00627 255 GFVCSVCLSVLCQY--------------TPICKTCKTAF 279 (279)
T ss_pred eEECCCccCCcCCC--------------CCCCCCCCCCC
Confidence 48899888766543 23799998766
No 247
>TIGR00240 ATCase_reg aspartate carbamoyltransferase, regulatory subunit. The presence of this regulatory subunit allows feedback inhibition by CTP on aspartate carbamoyltransferase, the first step in the synthesis of CTP from aspartate. In many species, this regulatory subunit is not present. In Thermotoga maritima, the catalytic and regulatory subunits are encoded by a fused gene and the regulatory region has enough sequence differences to score below the trusted cutoff.
Probab=25.13 E-value=16 Score=20.89 Aligned_cols=11 Identities=0% Similarity=-0.284 Sum_probs=9.2
Q ss_pred cCCCCCccccC
Q psy3949 93 SSNSHDITFVM 103 (103)
Q Consensus 93 ~~~C~~C~~~~ 103 (103)
.|+|.+|++.|
T Consensus 132 ~lrC~YCe~~~ 142 (150)
T TIGR00240 132 ALRCYYCEKEI 142 (150)
T ss_pred EEEEECCCCEE
Confidence 59999999865
No 248
>PF14375 Cys_rich_CWC: Cysteine-rich CWC
Probab=24.99 E-value=38 Score=15.18 Aligned_cols=8 Identities=25% Similarity=0.895 Sum_probs=3.3
Q ss_pred ccCCCccc
Q psy3949 3 CQYCKHSL 10 (103)
Q Consensus 3 C~~C~~~f 10 (103)
|+.||..|
T Consensus 1 CP~Cg~~f 8 (50)
T PF14375_consen 1 CPRCGAPF 8 (50)
T ss_pred CCCCCCcC
Confidence 33444444
No 249
>COG1545 Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]
Probab=24.89 E-value=25 Score=19.72 Aligned_cols=8 Identities=13% Similarity=0.003 Sum_probs=3.8
Q ss_pred CCCCcccc
Q psy3949 95 NSHDITFV 102 (103)
Q Consensus 95 ~C~~C~~~ 102 (103)
+|+.||.+
T Consensus 31 kC~~CG~v 38 (140)
T COG1545 31 KCKKCGRV 38 (140)
T ss_pred EcCCCCeE
Confidence 35555543
No 250
>COG1885 Uncharacterized protein conserved in archaea [Function unknown]
Probab=24.82 E-value=42 Score=17.96 Aligned_cols=9 Identities=0% Similarity=-0.219 Sum_probs=5.9
Q ss_pred CCCCCcccc
Q psy3949 94 SNSHDITFV 102 (103)
Q Consensus 94 ~~C~~C~~~ 102 (103)
..||.||.-
T Consensus 50 t~CP~Cg~~ 58 (115)
T COG1885 50 TSCPKCGEP 58 (115)
T ss_pred ccCCCCCCc
Confidence 567777754
No 251
>PF07295 DUF1451: Protein of unknown function (DUF1451); InterPro: IPR009912 This family consists of several hypothetical bacterial proteins of around 160 residues in length. Members of this family contain four highly conserved cysteine resides toward the C-terminal region of the protein. The function of this family is unknown.
Probab=24.59 E-value=30 Score=19.66 Aligned_cols=11 Identities=0% Similarity=-0.209 Sum_probs=6.5
Q ss_pred CccCCCCCccc
Q psy3949 91 MESSNSHDITF 101 (103)
Q Consensus 91 e~~~~C~~C~~ 101 (103)
+..=.|+.||.
T Consensus 128 ~~l~~Cp~C~~ 138 (146)
T PF07295_consen 128 ERLPPCPKCGH 138 (146)
T ss_pred CcCCCCCCCCC
Confidence 34456777764
No 252
>PF02148 zf-UBP: Zn-finger in ubiquitin-hydrolases and other protein; InterPro: IPR001607 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 UBP-type zinc finger domains, which display some similarity with the Zn-binding domain of the insulinase family. The UBP-type zinc finger domain is found only in a small subfamily of ubiquitin C-terminal hydrolases (deubiquitinases or UBP) [, ], All members of this subfamily are isopeptidase-T, which are known to cleave isopeptide bonds between ubiquitin moieties. Some of the proteins containing an UBP zinc finger include: Homo sapiens (Human) deubiquitinating enzyme 13 (UBPD) Human deubiquitinating enzyme 5 (UBP5) Dictyostelium discoideum (Slime mold) deubiquitinating enzyme A (UBPA) Saccharomyces cerevisiae (Baker's yeast) deubiquitinating enzyme 8 (UBP8) Yeast deubiquitinating enzyme 14 (UBP14) More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3GV4_A 3PHD_B 3C5K_A 2UZG_A 3IHP_B 2G43_B 2G45_D 2I50_A 3MHH_A 3MHS_A ....
Probab=24.17 E-value=21 Score=16.80 Aligned_cols=14 Identities=29% Similarity=0.645 Sum_probs=8.8
Q ss_pred ceecCCCCCCccch
Q psy3949 37 RFVCYTCPYHTTYS 50 (103)
Q Consensus 37 ~~~c~~c~~~~~~~ 50 (103)
.|.|-.|+..+-..
T Consensus 11 lw~CL~Cg~~~C~~ 24 (63)
T PF02148_consen 11 LWLCLTCGYVGCGR 24 (63)
T ss_dssp EEEETTTS-EEETT
T ss_pred eEEeCCCCcccccC
Confidence 67777777766654
No 253
>PF13696 zf-CCHC_2: Zinc knuckle
Probab=24.11 E-value=28 Score=14.28 Aligned_cols=8 Identities=13% Similarity=-0.126 Sum_probs=5.0
Q ss_pred CCCCCccc
Q psy3949 94 SNSHDITF 101 (103)
Q Consensus 94 ~~C~~C~~ 101 (103)
|.|..|++
T Consensus 9 Y~C~~C~~ 16 (32)
T PF13696_consen 9 YVCHRCGQ 16 (32)
T ss_pred CEeecCCC
Confidence 66666654
No 254
>PRK12722 transcriptional activator FlhC; Provisional
Probab=24.06 E-value=75 Score=18.97 Aligned_cols=27 Identities=15% Similarity=0.096 Sum_probs=13.7
Q ss_pred ccCCcCcccccCcchhhhhhhhcccCccCCCCCcc
Q psy3949 66 YKCLFCDYHCTQSGPLRRHMKIKHLMESSNSHDIT 100 (103)
Q Consensus 66 ~~c~~c~~~f~~~~~l~~h~~~~~~e~~~~C~~C~ 100 (103)
..|..|+..|..... .....|.|+.|.
T Consensus 135 ~~C~~Cgg~fv~~~~--------e~~~~f~CplC~ 161 (187)
T PRK12722 135 SSCNCCGGHFVTHAH--------DPVGSFVCGLCQ 161 (187)
T ss_pred ccCCCCCCCeecccc--------ccCCCCcCCCCC
Confidence 346666665553321 122356677664
No 255
>PF14149 YhfH: YhfH-like protein
Probab=24.00 E-value=13 Score=15.87 Aligned_cols=8 Identities=0% Similarity=-0.085 Sum_probs=4.8
Q ss_pred CCCCCccc
Q psy3949 94 SNSHDITF 101 (103)
Q Consensus 94 ~~C~~C~~ 101 (103)
-+|.+||+
T Consensus 14 K~C~~CG~ 21 (37)
T PF14149_consen 14 KKCTECGK 21 (37)
T ss_pred cccHHHHH
Confidence 34666665
No 256
>PF03811 Zn_Tnp_IS1: InsA N-terminal domain; InterPro: IPR003220 Insertion elements are mobile elements in DNA, usually encoding proteins required for transposition, for example transposases. Protein InsA is absolutely required for transposition of insertion element 1. This entry represents a short zinc binding domain found in IS1 InsA family protein. It is found at the N terminus of the protein and may be a DNA-binding domain.; GO: 0006313 transposition, DNA-mediated
Probab=23.59 E-value=34 Score=14.36 Aligned_cols=14 Identities=14% Similarity=-0.019 Sum_probs=8.1
Q ss_pred hhcccCccCCCCCc
Q psy3949 86 KIKHLMESSNSHDI 99 (103)
Q Consensus 86 ~~~~~e~~~~C~~C 99 (103)
+...|...|.|..|
T Consensus 22 ~~~~G~qryrC~~C 35 (36)
T PF03811_consen 22 KSPSGHQRYRCKDC 35 (36)
T ss_pred CCCCCCEeEecCcC
Confidence 33445556777666
No 257
>PF00628 PHD: PHD-finger; InterPro: IPR019787 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 PHD (homeodomain) zinc finger domain [,], which is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in chromatin-mediated transcriptional regulation. The PHD finger motif is reminiscent of, but distinct from the C3HC4 type RING finger. The function of this domain is not yet known but in analogy with the LIM domain it could be involved in protein-protein interaction and be important for the assembly or activity of multicomponent complexes involved in transcriptional activation or repression. Alternatively, the interactions could be intra-molecular and be important in maintaining the structural integrity of the protein. In similarity to the RING finger and the LIM domain, the PHD finger is thought to bind two zinc ions. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0005515 protein binding; PDB: 3ZVY_A 2LGG_A 3SOW_A 3SOU_B 3ASL_A 3ASK_A 3ZVZ_B 3T6R_A 2LGK_A 3SOX_B ....
Probab=23.54 E-value=28 Score=15.26 Aligned_cols=8 Identities=0% Similarity=-0.176 Sum_probs=4.7
Q ss_pred cCCCCCcc
Q psy3949 93 SSNSHDIT 100 (103)
Q Consensus 93 ~~~C~~C~ 100 (103)
.|.|+.|.
T Consensus 42 ~w~C~~C~ 49 (51)
T PF00628_consen 42 DWYCPNCR 49 (51)
T ss_dssp SBSSHHHH
T ss_pred cEECcCCc
Confidence 56666553
No 258
>PF09082 DUF1922: Domain of unknown function (DUF1922); InterPro: IPR015166 Members of this family consist of a beta-sheet region followed by an alpha-helix and an unstructured C terminus. The beta-sheet region contains a CXCX...XCXC sequence with Cys residues located in two proximal loops and pointing towards each other. This precise function of this set of bacterial proteins is, as yet, unknown []. ; PDB: 1GH9_A.
Probab=23.48 E-value=10 Score=18.50 Aligned_cols=8 Identities=0% Similarity=-0.305 Sum_probs=3.7
Q ss_pred CCCCCcccc
Q psy3949 94 SNSHDITFV 102 (103)
Q Consensus 94 ~~C~~C~~~ 102 (103)
-+| +||++
T Consensus 21 kkC-~CG~~ 28 (68)
T PF09082_consen 21 KKC-VCGKT 28 (68)
T ss_dssp EEE-TTTEE
T ss_pred eEe-cCCCe
Confidence 345 55543
No 259
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=23.42 E-value=54 Score=21.72 Aligned_cols=21 Identities=19% Similarity=0.406 Sum_probs=15.9
Q ss_pred ecCCCCCCccchhHHHHHHHH
Q psy3949 39 VCYTCPYHTTYSQSMKSHLRK 59 (103)
Q Consensus 39 ~c~~c~~~~~~~~~l~~h~~~ 59 (103)
.|..|...|.....|..|++.
T Consensus 222 ~C~FC~~~FYdDDEL~~HcR~ 242 (493)
T COG5236 222 LCIFCKIYFYDDDELRRHCRL 242 (493)
T ss_pred hhhhccceecChHHHHHHHHh
Confidence 577788888877888877773
No 260
>PF10071 DUF2310: Zn-ribbon-containing, possibly nucleic-acid-binding protein (DUF2310); InterPro: IPR016908 This group represents uncharacterised conserved proteins.
Probab=23.32 E-value=58 Score=20.50 Aligned_cols=28 Identities=21% Similarity=0.258 Sum_probs=16.8
Q ss_pred ccCCcCcccccCcchhhhhhhhcccCccCCCCCcc
Q psy3949 66 YKCLFCDYHCTQSGPLRRHMKIKHLMESSNSHDIT 100 (103)
Q Consensus 66 ~~c~~c~~~f~~~~~l~~h~~~~~~e~~~~C~~C~ 100 (103)
-.|+.||+.+.-...+ ++--.|+|+.|.
T Consensus 221 r~CP~Cg~~W~L~~pl-------h~iFdFKCD~CR 248 (258)
T PF10071_consen 221 RKCPSCGGDWRLKEPL-------HDIFDFKCDPCR 248 (258)
T ss_pred CCCCCCCCccccCCch-------hhceeccCCcce
Confidence 3577777765544443 233457888775
No 261
>PF08996 zf-DNA_Pol: DNA Polymerase alpha zinc finger; InterPro: IPR015088 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 DNA Polymerase alpha zinc finger domain adopts an alpha-helix-like structure, followed by three turns, all of which involve proline. The resulting motif is a helix-turn-helix motif, in contrast to other zinc finger domains, which show anti-parallel sheet and helix conformation. Zinc binding occurs due to the presence of four cysteine residues positioned to bind the metal centre in a tetrahedral coordination geometry. The function of this domain is uncertain: it has been proposed that the zinc finger motif may be an essential part of the DNA binding domain []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0001882 nucleoside binding, 0003887 DNA-directed DNA polymerase activity, 0006260 DNA replication; PDB: 3FLO_D 1N5G_A 1K0P_A 1K18_A.
Probab=23.23 E-value=42 Score=19.79 Aligned_cols=44 Identities=18% Similarity=0.326 Sum_probs=17.3
Q ss_pred cccCCCcccccccCHHH-HHhhhCCCccccCCCCCcceecCCCCCCccchhHHHHHH
Q psy3949 2 RCQYCKHSLSVSNGFEI-VLSHTKSCTYISRPDHNYRFVCYTCPYHTTYSQSMKSHL 57 (103)
Q Consensus 2 ~C~~C~~~f~~~~~l~~-~~~h~~~~~~~~~~~~~~~~~c~~c~~~~~~~~~l~~h~ 57 (103)
.|+.|+..|....-+.. ...... . -..|+.|+..+ ....+..++
T Consensus 20 ~C~~C~~~~~f~g~~~~~~~~~~~------~-----~~~C~~C~~~~-~~~~l~Nql 64 (188)
T PF08996_consen 20 TCPSCGTEFEFPGVFEEDGDDVSP------S-----GLQCPNCSTPL-SPASLVNQL 64 (188)
T ss_dssp E-TTT--EEEE-SSS--SSEEEET------T-----EEEETTT--B---HHHHHHHH
T ss_pred ECCCCCCCccccccccCCcccccc------C-----cCcCCCCCCcC-CHHHHHHHH
Confidence 57788887765543332 111111 2 46888888743 334444443
No 262
>PF03884 DUF329: Domain of unknown function (DUF329); InterPro: IPR005584 The biological function of these short proteins is unknown, but they contain four conserved cysteines, suggesting that they all bind zinc. YacG (Q5X8H6 from SWISSPROT) from Escherichia coli has been shown to bind zinc and contains the structural motifs typical of zinc-binding proteins []. The conserved four cysteine motif in these proteins (-C-X(2)-C-X(15)-C-X(3)-C-) is not found in other zinc-binding proteins with known structures.; GO: 0008270 zinc ion binding; PDB: 1LV3_A.
Probab=23.19 E-value=30 Score=16.26 Aligned_cols=11 Identities=18% Similarity=0.730 Sum_probs=3.8
Q ss_pred cccCCCccccc
Q psy3949 2 RCQYCKHSLSV 12 (103)
Q Consensus 2 ~C~~C~~~f~~ 12 (103)
.|+.|++.+..
T Consensus 4 ~CP~C~k~~~~ 14 (57)
T PF03884_consen 4 KCPICGKPVEW 14 (57)
T ss_dssp E-TTT--EEE-
T ss_pred cCCCCCCeecc
Confidence 36666665433
No 263
>PRK05654 acetyl-CoA carboxylase subunit beta; Validated
Probab=22.78 E-value=47 Score=21.24 Aligned_cols=29 Identities=17% Similarity=0.332 Sum_probs=15.8
Q ss_pred ecCCCCCCccchhHHHHHHHHhhCCCCccCCcCccccc
Q psy3949 39 VCYTCPYHTTYSQSMKSHLRKHSGEKPYKCLFCDYHCT 76 (103)
Q Consensus 39 ~c~~c~~~~~~~~~l~~h~~~~~~~~~~~c~~c~~~f~ 76 (103)
.|+.|+.....+. | ..+.+.|+.|+.-|.
T Consensus 29 ~c~~c~~~~~~~~-l--------~~~~~vc~~c~~h~r 57 (292)
T PRK05654 29 KCPSCGQVLYRKE-L--------EANLNVCPKCGHHMR 57 (292)
T ss_pred ECCCccchhhHHH-H--------HhcCCCCCCCCCCee
Confidence 7888876432211 1 123457888887554
No 264
>KOG1842|consensus
Probab=22.55 E-value=32 Score=23.44 Aligned_cols=23 Identities=22% Similarity=0.492 Sum_probs=17.5
Q ss_pred ceecCCCCCCccchhHHHHHHHH
Q psy3949 37 RFVCYTCPYHTTYSQSMKSHLRK 59 (103)
Q Consensus 37 ~~~c~~c~~~~~~~~~l~~h~~~ 59 (103)
-+.|+.|...|.+...|..|...
T Consensus 15 gflCPiC~~dl~~~~~L~~H~d~ 37 (505)
T KOG1842|consen 15 GFLCPICLLDLPNLSALNDHLDV 37 (505)
T ss_pred cccCchHhhhhhhHHHHHHHHhh
Confidence 57788888888888888777653
No 265
>KOG2817|consensus
Probab=22.52 E-value=46 Score=22.27 Aligned_cols=36 Identities=22% Similarity=0.211 Sum_probs=19.2
Q ss_pred CCCccCCcCcccccCcchhhhhhhhcccCccCCCCCccc
Q psy3949 63 EKPYKCLFCDYHCTQSGPLRRHMKIKHLMESSNSHDITF 101 (103)
Q Consensus 63 ~~~~~c~~c~~~f~~~~~l~~h~~~~~~e~~~~C~~C~~ 101 (103)
++|-.=..||...+.. ++.+ -+-.|...|+||+|+.
T Consensus 347 eNPPm~L~CGHVISkd-Alnr--LS~ng~~sfKCPYCP~ 382 (394)
T KOG2817|consen 347 ENPPMMLICGHVISKD-ALNR--LSKNGSQSFKCPYCPV 382 (394)
T ss_pred CCCCeeeeccceecHH-HHHH--HhhCCCeeeeCCCCCc
Confidence 3443334577664333 3332 2344555899999974
No 266
>PF11931 DUF3449: Domain of unknown function (DUF3449); InterPro: IPR024598 This presumed domain is functionally uncharacterised. It has two conserved sequence motifs: PIP and CEICG and contains a zinc-finger of the C2H2-type.; PDB: 4DGW_A.
Probab=22.42 E-value=29 Score=20.81 Aligned_cols=16 Identities=13% Similarity=-0.116 Sum_probs=0.0
Q ss_pred hhcccCccCCCCCccc
Q psy3949 86 KIKHLMESSNSHDITF 101 (103)
Q Consensus 86 ~~~~~e~~~~C~~C~~ 101 (103)
+.|.-.+.|.|..||-
T Consensus 94 KLhGL~~ey~CEICGN 109 (196)
T PF11931_consen 94 KLHGLGVEYKCEICGN 109 (196)
T ss_dssp ----------------
T ss_pred HHhCCCCeeeeEeCCC
Confidence 3455567799999984
No 267
>PF09665 RE_Alw26IDE: Type II restriction endonuclease (RE_Alw26IDE); InterPro: IPR014328 There are four classes of restriction endonucleases: types I, II,III and IV. All types of enzymes recognise specific short DNA sequences and carry out the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. They differ in their recognition sequence, subunit composition, cleavage position, and cofactor requirements [, ], as summarised below: Type I enzymes (3.1.21.3 from EC) cleave at sites remote from recognition site; require both ATP and S-adenosyl-L-methionine to function; multifunctional protein with both restriction and methylase (2.1.1.72 from EC) activities. Type II enzymes (3.1.21.4 from EC) cleave within or at short specific distances from recognition site; most require magnesium; single function (restriction) enzymes independent of methylase. Type III enzymes (3.1.21.5 from EC) cleave at sites a short distance from recognition site; require ATP (but doesn't hydrolyse it); S-adenosyl-L-methionine stimulates reaction but is not required; exists as part of a complex with a modification methylase methylase (2.1.1.72 from EC). Type IV enzymes target methylated DNA. Type II restriction endonucleases (3.1.21.4 from EC) are components of prokaryotic DNA restriction-modification mechanisms that protect the organism against invading foreign DNA. These site-specific deoxyribonucleases catalyse the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. Of the 3000 restriction endonucleases that have been characterised, most are homodimeric or tetrameric enzymes that cleave target DNA at sequence-specific sites close to the recognition site. For homodimeric enzymes, the recognition site is usually a palindromic sequence 4-8 bp in length. Most enzymes require magnesium ions as a cofactor for catalysis. Although they can vary in their mode of recognition, many restriction endonucleases share a similar structural core comprising four beta-strands and one alpha-helix, as well as a similar mechanism of cleavage, suggesting a common ancestral origin []. However, there is still considerable diversity amongst restriction endonucleases [, ]. The target site recognition process triggers large conformational changes of the enzyme and the target DNA, leading to the activation of the catalytic centres. Like other DNA binding proteins, restriction enzymes are capable of non-specific DNA binding as well, which is the prerequisite for efficient target site location by facilitated diffusion. Non-specific binding usually does not involve interactions with the bases but only with the DNA backbone []. This entry represents type II restriction endonucleases of the Alw26I/Eco31I/Esp3I family [], whose recognition sequences are 5'-GTCTC-3' (Alw26I), 5'-GGTCTC-3' (Eco31I) and 5'-CGTCTC-3' (Esp3I).
Probab=22.26 E-value=31 Score=23.66 Aligned_cols=13 Identities=8% Similarity=0.023 Sum_probs=9.8
Q ss_pred ccCccCCCCCccccC
Q psy3949 89 HLMESSNSHDITFVM 103 (103)
Q Consensus 89 ~~e~~~~C~~C~~~~ 103 (103)
++.+| |..||++|
T Consensus 80 T~~kp--Ck~CG~~m 92 (511)
T PF09665_consen 80 TKQKP--CKTCGKIM 92 (511)
T ss_pred CCCcc--hHhcCCee
Confidence 45555 99999875
No 268
>PRK12860 transcriptional activator FlhC; Provisional
Probab=22.20 E-value=82 Score=18.85 Aligned_cols=27 Identities=11% Similarity=0.082 Sum_probs=14.0
Q ss_pred ccCCcCcccccCcchhhhhhhhcccCccCCCCCcc
Q psy3949 66 YKCLFCDYHCTQSGPLRRHMKIKHLMESSNSHDIT 100 (103)
Q Consensus 66 ~~c~~c~~~f~~~~~l~~h~~~~~~e~~~~C~~C~ 100 (103)
..|..|+..|..... .....|.|+.|.
T Consensus 135 ~~C~~Cgg~fv~~~~--------e~~~~f~CplC~ 161 (189)
T PRK12860 135 ARCCRCGGKFVTHAH--------DLRHNFVCGLCQ 161 (189)
T ss_pred ccCCCCCCCeecccc--------ccCCCCcCCCCC
Confidence 456667666553311 222356777663
No 269
>COG5319 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=21.82 E-value=59 Score=18.14 Aligned_cols=12 Identities=17% Similarity=0.315 Sum_probs=6.8
Q ss_pred CCccCCcCcccc
Q psy3949 64 KPYKCLFCDYHC 75 (103)
Q Consensus 64 ~~~~c~~c~~~f 75 (103)
....|+.|+.+-
T Consensus 31 gLv~CPvCgs~~ 42 (142)
T COG5319 31 GLVTCPVCGSTE 42 (142)
T ss_pred CceeCCCCCcHH
Confidence 345666666543
No 270
>KOG4602|consensus
Probab=21.81 E-value=39 Score=21.28 Aligned_cols=11 Identities=9% Similarity=-0.324 Sum_probs=8.8
Q ss_pred ccCCCCCcccc
Q psy3949 92 ESSNSHDITFV 102 (103)
Q Consensus 92 ~~~~C~~C~~~ 102 (103)
+.|.|+.||-+
T Consensus 267 R~YVCPiCGAT 277 (318)
T KOG4602|consen 267 RSYVCPICGAT 277 (318)
T ss_pred hhhcCcccccc
Confidence 56999999854
No 271
>COG3024 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=21.65 E-value=47 Score=16.07 Aligned_cols=11 Identities=18% Similarity=0.549 Sum_probs=7.0
Q ss_pred cccCCCccccc
Q psy3949 2 RCQYCKHSLSV 12 (103)
Q Consensus 2 ~C~~C~~~f~~ 12 (103)
+|+.||+....
T Consensus 9 ~CP~Cgkpv~w 19 (65)
T COG3024 9 PCPTCGKPVVW 19 (65)
T ss_pred cCCCCCCcccc
Confidence 47777776543
No 272
>COG1781 PyrI Aspartate carbamoyltransferase, regulatory subunit [Nucleotide transport and metabolism]
Probab=21.56 E-value=20 Score=20.53 Aligned_cols=11 Identities=0% Similarity=-0.170 Sum_probs=9.1
Q ss_pred cCCCCCccccC
Q psy3949 93 SSNSHDITFVM 103 (103)
Q Consensus 93 ~~~C~~C~~~~ 103 (103)
.++|.+|+++|
T Consensus 135 ~lrC~YCe~~~ 145 (153)
T COG1781 135 ALRCKYCEKTF 145 (153)
T ss_pred EEEEEecCcEe
Confidence 48999999875
No 273
>PF05180 zf-DNL: DNL zinc finger; InterPro: IPR007853 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The DNL-type zinc finger is found in Tim15, a zinc finger protein essential for protein import into mitochondria. Mitochondrial functions rely on the correct transport of resident proteins synthesized in the cytosol to mitochondria. Protein import into mitochondria is mediated by membrane protein complexes, protein translocators, in the outer and inner mitochondrial membranes, in cooperation with their assistant proteins in the cytosol, intermembrane space and matrix. Proteins destined to the mitochondrial matrix cross the outer membrane with the aid of the outer membrane translocator, the tOM40 complex, and then the inner membrane with the aid of the inner membrane translocator, the TIM23 complex, and mitochondrial motor and chaperone (MMC) proteins including mitochondrial heat- shock protein 70 (mtHsp70), and translocase in the inner mitochondrial membrane (Tim)15. Tim15 is also known as zinc finger motif (Zim)17 or mtHsp70 escort protein (Hep)1. Tim15 contains a zinc-finger motif (CXXC and CXXC) of ~100 residues, which has been named DNL after a short C-terminal motif of D(N/H)L [, , ]. The DNL-type zinc finger is an L-shaped molecule. The two CXXC motifs are located at the end of the L, and are sandwiched by two- stranded antiparallel beta-sheets. Two short alpha-helices constitute another leg of the L. The outer (convex) face of the L has a large acidic groove, which is lined with five acidic residues, whereas the inner (concave) face of the L has two positively charged residues, next to the CXXC motifs []. This entry represents the DNL-type zinc finger.; GO: 0008270 zinc ion binding; PDB: 2E2Z_A.
Probab=21.42 E-value=8 Score=18.79 Aligned_cols=35 Identities=26% Similarity=0.471 Sum_probs=18.3
Q ss_pred ceecCCCCCCccchhHHHHHHHHhhCCCCccCCcCccc
Q psy3949 37 RFVCYTCPYHTTYSQSMKSHLRKHSGEKPYKCLFCDYH 74 (103)
Q Consensus 37 ~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~c~~c~~~ 74 (103)
.|+|..|+.+-. .....+..+.|....+|+.|...
T Consensus 4 ~FTC~~C~~Rs~---~~~sk~aY~~GvViv~C~gC~~~ 38 (66)
T PF05180_consen 4 TFTCNKCGTRSA---KMFSKQAYHKGVVIVQCPGCKNR 38 (66)
T ss_dssp EEEETTTTEEEE---EEEEHHHHHTSEEEEE-TTS--E
T ss_pred EEEcCCCCCccc---eeeCHHHHhCCeEEEECCCCcce
Confidence 577888874322 12233445667666778777653
No 274
>COG4530 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=21.20 E-value=57 Score=17.69 Aligned_cols=11 Identities=9% Similarity=0.181 Sum_probs=5.6
Q ss_pred CCccCCcCccc
Q psy3949 64 KPYKCLFCDYH 74 (103)
Q Consensus 64 ~~~~c~~c~~~ 74 (103)
.|..|+.||++
T Consensus 25 dPiVsPytG~s 35 (129)
T COG4530 25 DPIVSPYTGKS 35 (129)
T ss_pred CccccCccccc
Confidence 45555555543
No 275
>PRK00893 aspartate carbamoyltransferase regulatory subunit; Reviewed
Probab=20.93 E-value=25 Score=20.16 Aligned_cols=14 Identities=0% Similarity=-0.389 Sum_probs=10.4
Q ss_pred cCccCCCCCccccC
Q psy3949 90 LMESSNSHDITFVM 103 (103)
Q Consensus 90 ~e~~~~C~~C~~~~ 103 (103)
....|+|.+|++.|
T Consensus 131 ~~~~~rC~YCe~~~ 144 (152)
T PRK00893 131 EPIKLRCKYCEKEF 144 (152)
T ss_pred CCCEEEeeCCCCEe
Confidence 34468999999864
No 276
>PF12773 DZR: Double zinc ribbon
Probab=20.72 E-value=93 Score=13.55 Aligned_cols=11 Identities=18% Similarity=0.341 Sum_probs=6.6
Q ss_pred CCccCCcCccc
Q psy3949 64 KPYKCLFCDYH 74 (103)
Q Consensus 64 ~~~~c~~c~~~ 74 (103)
....|..|+..
T Consensus 28 ~~~~C~~Cg~~ 38 (50)
T PF12773_consen 28 SKKICPNCGAE 38 (50)
T ss_pred CCCCCcCCcCC
Confidence 34567777654
No 277
>PF05876 Terminase_GpA: Phage terminase large subunit (GpA); InterPro: IPR008866 This entry is represented by Bacteriophage lambda, GpA. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry consists of several phage terminase large subunit proteins as well as related sequences from several bacterial species. The DNA packaging enzyme of bacteriophage lambda, terminase, is a heteromultimer composed of a small subunit, gpNu1, and a large subunit, gpA, products of the Nu1 and A genes, respectively. Terminase is involved in the site-specific binding and cutting of the DNA in the initial stages of packaging. It is now known that gpA is actively involved in late stages of packaging, including DNA translocation, and that this enzyme contains separate functional domains for its early and late packaging activities [].
Probab=20.70 E-value=51 Score=23.12 Aligned_cols=13 Identities=31% Similarity=0.710 Sum_probs=9.6
Q ss_pred ceecCCCCCCccc
Q psy3949 37 RFVCYTCPYHTTY 49 (103)
Q Consensus 37 ~~~c~~c~~~~~~ 49 (103)
.|.|+.||..+..
T Consensus 229 ~y~C~~Cg~~i~e 241 (557)
T PF05876_consen 229 RYVCPHCGCEIEE 241 (557)
T ss_pred EEECCCCcCCCCH
Confidence 5888888876653
No 278
>PLN03238 probable histone acetyltransferase MYST; Provisional
Probab=20.58 E-value=1.4e+02 Score=19.21 Aligned_cols=22 Identities=23% Similarity=0.434 Sum_probs=17.0
Q ss_pred ceecCCCCCCccchhHHHHHHH
Q psy3949 37 RFVCYTCPYHTTYSQSMKSHLR 58 (103)
Q Consensus 37 ~~~c~~c~~~~~~~~~l~~h~~ 58 (103)
-|.|+.|-+-+.+...+..|+.
T Consensus 48 lyiCe~Clky~~~~~~l~~H~~ 69 (290)
T PLN03238 48 LYICEYCLKYMRKKKSLLRHLA 69 (290)
T ss_pred EEEcCCCcchhCCHHHHHHHHH
Confidence 4778888888888888777765
No 279
>smart00547 ZnF_RBZ Zinc finger domain. Zinc finger domain in Ran-binding proteins (RanBPs), and other proteins. In RanBPs, this domain binds RanGDP.
Probab=20.44 E-value=59 Score=11.93 Aligned_cols=7 Identities=14% Similarity=-0.107 Sum_probs=3.7
Q ss_pred CCCCCcc
Q psy3949 94 SNSHDIT 100 (103)
Q Consensus 94 ~~C~~C~ 100 (103)
|.|+.|+
T Consensus 3 W~C~~C~ 9 (26)
T smart00547 3 WECPACT 9 (26)
T ss_pred ccCCCCC
Confidence 4555554
No 280
>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=20.40 E-value=48 Score=16.72 Aligned_cols=11 Identities=9% Similarity=-0.146 Sum_probs=3.6
Q ss_pred cCccCCCCCcc
Q psy3949 90 LMESSNSHDIT 100 (103)
Q Consensus 90 ~e~~~~C~~C~ 100 (103)
-.+.|.|+.|+
T Consensus 19 l~~~F~CPfC~ 29 (81)
T PF05129_consen 19 LPKVFDCPFCN 29 (81)
T ss_dssp -SS----TTT-
T ss_pred CCceEcCCcCC
Confidence 34668888887
No 281
>KOG4727|consensus
Probab=20.33 E-value=69 Score=18.89 Aligned_cols=21 Identities=19% Similarity=0.455 Sum_probs=18.2
Q ss_pred eecCCCCCCccchhHHHHHHH
Q psy3949 38 FVCYTCPYHTTYSQSMKSHLR 58 (103)
Q Consensus 38 ~~c~~c~~~~~~~~~l~~h~~ 58 (103)
|-|++|+-.+..+-.+..|+-
T Consensus 76 yyCdVCdcvvKDSinflDHiN 96 (193)
T KOG4727|consen 76 YYCDVCDCVVKDSINFLDHIN 96 (193)
T ss_pred eeeeecceeehhhHHHHHHhc
Confidence 789999999999888888863
No 282
>cd07153 Fur_like Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators. Ferric uptake regulator (Fur) and related metalloregulatory proteins are iron-dependent, DNA-binding repressors and activators mainly involved in iron metabolism. A general model for Fur repression under iron-rich conditions is that activated Fur (a dimer having one Fe2+ coordinated per monomer) binds to specific DNA sequences (Fur boxes) in the promoter region of iron-responsive genes, hindering access of RNA polymerase, and repressing transcription. Positive regulation by Fur can be direct or indirect, as in the Fur repression of an anti-sense regulatory small RNA. Some members sense metal ions other than Fe2+. For example, the zinc uptake regulator (Zur) responds to Zn2+, the manganese uptake regulator (Mur) responds to Mn2+, and the nickel uptake regulator (Nur) responds to Ni2+. Other members sense signals other than metal ions.
Probab=20.10 E-value=30 Score=18.18 Aligned_cols=10 Identities=10% Similarity=-0.137 Sum_probs=8.1
Q ss_pred CCCCCccccC
Q psy3949 94 SNSHDITFVM 103 (103)
Q Consensus 94 ~~C~~C~~~~ 103 (103)
+.|..||+++
T Consensus 74 ~~C~~Cg~i~ 83 (116)
T cd07153 74 LICTKCGKVI 83 (116)
T ss_pred eEeCCCCCEE
Confidence 7899999864
Done!