Query 031430
Match_columns 159
No_of_seqs 176 out of 1968
Neff 10.2
Searched_HMMs 46136
Date Fri Mar 29 13:59:35 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/031430.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/031430hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2462 C2H2-type Zn-finger pr 99.9 1.3E-24 2.8E-29 150.9 2.6 109 10-120 137-251 (279)
2 KOG2462 C2H2-type Zn-finger pr 99.8 5.3E-22 1.1E-26 138.0 1.2 96 11-108 169-267 (279)
3 KOG3623 Homeobox transcription 99.5 8.7E-16 1.9E-20 119.0 0.2 78 28-105 891-971 (1007)
4 KOG1074 Transcriptional repres 99.5 5.5E-15 1.2E-19 116.0 2.9 51 7-57 357-407 (958)
5 KOG3576 Ovo and related transc 99.5 2.3E-15 5E-20 100.8 -0.5 104 9-112 123-240 (267)
6 KOG3576 Ovo and related transc 99.3 5.2E-13 1.1E-17 89.6 1.0 79 28-106 114-195 (267)
7 KOG3608 Zn finger proteins [Ge 99.3 8.8E-14 1.9E-18 100.2 -4.2 138 10-148 186-369 (467)
8 KOG3623 Homeobox transcription 99.3 1.9E-12 4.2E-17 100.8 1.9 68 8-75 899-966 (1007)
9 KOG1074 Transcriptional repres 99.0 1.1E-10 2.5E-15 92.3 3.0 80 31-110 605-694 (958)
10 PHA00733 hypothetical protein 99.0 9.1E-11 2E-15 75.2 2.0 90 20-109 29-124 (128)
11 PHA02768 hypothetical protein; 99.0 5E-10 1.1E-14 60.1 2.8 44 31-76 5-48 (55)
12 KOG3608 Zn finger proteins [Ge 98.9 5.1E-10 1.1E-14 81.1 1.1 89 17-106 277-374 (467)
13 PHA02768 hypothetical protein; 98.8 3.5E-09 7.6E-14 56.9 2.8 44 84-148 5-48 (55)
14 PF13465 zf-H2C2_2: Zinc-finge 98.8 1.8E-09 3.8E-14 49.7 0.9 24 19-42 2-25 (26)
15 PLN03086 PRLI-interacting fact 98.6 7.7E-08 1.7E-12 75.0 6.3 85 28-118 450-547 (567)
16 PHA00616 hypothetical protein 98.6 3.4E-08 7.5E-13 50.5 1.6 32 84-115 1-32 (44)
17 PF13465 zf-H2C2_2: Zinc-finge 98.6 2.8E-08 6.1E-13 45.7 1.2 25 46-70 1-25 (26)
18 PHA00733 hypothetical protein 98.5 3.4E-08 7.3E-13 63.3 0.9 54 19-75 62-115 (128)
19 PLN03086 PRLI-interacting fact 98.5 1.4E-07 3E-12 73.6 3.8 85 16-105 465-561 (567)
20 KOG3993 Transcription factor ( 98.4 2E-07 4.3E-12 69.3 3.4 93 18-110 282-382 (500)
21 PHA00616 hypothetical protein 98.4 1E-07 2.2E-12 48.8 1.2 34 31-64 1-34 (44)
22 PF00096 zf-C2H2: Zinc finger, 98.2 7.2E-07 1.6E-11 39.6 1.7 23 85-107 1-23 (23)
23 PHA00732 hypothetical protein 98.0 5.6E-06 1.2E-10 48.5 2.8 38 31-71 1-39 (79)
24 COG5189 SFP1 Putative transcri 97.9 4.2E-06 9.2E-11 60.4 1.9 70 29-105 347-419 (423)
25 PF00096 zf-C2H2: Zinc finger, 97.9 7E-06 1.5E-10 36.3 1.6 23 32-54 1-23 (23)
26 PF13912 zf-C2H2_6: C2H2-type 97.9 7.4E-06 1.6E-10 37.8 1.4 26 84-109 1-26 (27)
27 PF13894 zf-C2H2_4: C2H2-type 97.8 1.3E-05 2.8E-10 35.6 2.0 24 85-108 1-24 (24)
28 PHA00732 hypothetical protein 97.8 2.5E-05 5.5E-10 45.7 3.2 23 84-106 1-23 (79)
29 PF13912 zf-C2H2_6: C2H2-type 97.6 3.9E-05 8.4E-10 35.3 1.5 25 31-55 1-25 (27)
30 smart00355 ZnF_C2H2 zinc finge 97.5 0.00011 2.4E-09 33.0 2.3 25 85-109 1-25 (26)
31 PF13894 zf-C2H2_4: C2H2-type 97.4 0.00015 3.3E-09 32.0 2.0 23 32-54 1-23 (24)
32 PF09237 GAGA: GAGA factor; I 97.4 0.00026 5.6E-09 37.2 3.1 35 78-112 18-52 (54)
33 PF05605 zf-Di19: Drought indu 97.4 0.00051 1.1E-08 37.2 4.3 51 31-108 2-53 (54)
34 PF12756 zf-C2H2_2: C2H2 type 97.4 0.00014 3.1E-09 44.2 2.3 72 33-108 1-74 (100)
35 smart00355 ZnF_C2H2 zinc finge 97.0 0.00081 1.8E-08 30.0 2.2 24 32-55 1-24 (26)
36 PF09237 GAGA: GAGA factor; I 97.0 0.001 2.2E-08 35.0 2.7 35 25-59 18-52 (54)
37 PF12874 zf-met: Zinc-finger o 96.9 0.0005 1.1E-08 30.8 1.2 23 85-107 1-23 (25)
38 KOG3993 Transcription factor ( 96.8 0.00014 3E-09 54.6 -1.7 85 60-145 268-370 (500)
39 PRK04860 hypothetical protein; 96.8 0.0011 2.4E-08 44.2 2.6 36 31-70 119-154 (160)
40 PF13909 zf-H2C2_5: C2H2-type 96.5 0.0021 4.6E-08 28.5 1.7 23 85-108 1-23 (24)
41 PF12874 zf-met: Zinc-finger o 96.2 0.0026 5.6E-08 28.4 1.2 23 32-54 1-23 (25)
42 PF13913 zf-C2HC_2: zinc-finge 96.1 0.0059 1.3E-07 27.4 2.0 21 85-106 3-23 (25)
43 PF12171 zf-C2H2_jaz: Zinc-fin 95.9 0.0022 4.8E-08 29.3 0.1 22 85-106 2-23 (27)
44 PF12171 zf-C2H2_jaz: Zinc-fin 95.3 0.0063 1.4E-07 27.8 0.5 22 32-53 2-23 (27)
45 KOG1146 Homeobox protein [Gene 95.3 0.018 4E-07 49.4 3.5 81 25-106 459-540 (1406)
46 PF13909 zf-H2C2_5: C2H2-type 95.0 0.017 3.7E-07 25.4 1.4 23 32-55 1-23 (24)
47 PRK04860 hypothetical protein; 94.8 0.034 7.3E-07 37.1 3.0 35 82-120 117-151 (160)
48 smart00451 ZnF_U1 U1-like zinc 94.7 0.025 5.3E-07 27.3 1.7 23 84-106 3-25 (35)
49 PF05605 zf-Di19: Drought indu 93.6 0.09 2E-06 28.3 2.6 35 84-119 2-38 (54)
50 smart00451 ZnF_U1 U1-like zinc 93.1 0.098 2.1E-06 25.1 2.1 23 31-53 3-25 (35)
51 KOG2893 Zn finger protein [Gen 92.7 0.015 3.2E-07 40.9 -1.6 45 62-107 13-58 (341)
52 COG5189 SFP1 Putative transcri 92.4 0.14 3E-06 37.7 2.9 62 81-143 346-410 (423)
53 PRK00464 nrdR transcriptional 89.7 0.24 5.2E-06 32.9 1.8 12 85-96 29-40 (154)
54 PF09538 FYDLN_acid: Protein o 89.7 0.3 6.4E-06 30.4 2.1 31 59-97 9-39 (108)
55 cd00350 rubredoxin_like Rubred 89.7 0.24 5.2E-06 23.7 1.4 10 83-92 16-25 (33)
56 PF12756 zf-C2H2_2: C2H2 type 88.4 0.45 9.8E-06 28.5 2.3 24 31-54 50-73 (100)
57 PF09986 DUF2225: Uncharacteri 88.4 0.48 1E-05 33.3 2.7 17 29-45 3-19 (214)
58 TIGR00622 ssl1 transcription f 88.3 1.4 3.1E-05 27.5 4.4 77 30-108 14-105 (112)
59 COG4049 Uncharacterized protei 87.8 0.29 6.2E-06 26.3 1.0 30 24-53 10-39 (65)
60 PF10571 UPF0547: Uncharacteri 87.7 0.5 1.1E-05 21.3 1.6 10 86-95 16-25 (26)
61 COG5048 FOG: Zn-finger [Genera 86.6 0.38 8.2E-06 36.6 1.4 51 11-61 297-353 (467)
62 COG4049 Uncharacterized protei 85.6 0.38 8.2E-06 25.9 0.7 28 79-106 12-39 (65)
63 TIGR00373 conserved hypothetic 85.1 1.6 3.5E-05 29.1 3.7 42 19-69 97-138 (158)
64 PF09986 DUF2225: Uncharacteri 85.0 0.2 4.4E-06 35.1 -0.6 41 57-97 3-61 (214)
65 PRK06266 transcription initiat 84.9 1.6 3.5E-05 29.7 3.7 42 19-69 105-146 (178)
66 PF13719 zinc_ribbon_5: zinc-r 84.2 0.85 1.8E-05 22.4 1.6 12 33-44 4-15 (37)
67 smart00614 ZnF_BED BED zinc fi 83.9 0.97 2.1E-05 23.7 1.8 24 85-108 19-48 (50)
68 PF13717 zinc_ribbon_4: zinc-r 83.8 1.3 2.8E-05 21.6 2.1 13 33-45 4-16 (36)
69 TIGR02098 MJ0042_CXXC MJ0042 f 83.5 0.83 1.8E-05 22.4 1.4 13 32-44 3-15 (38)
70 TIGR00622 ssl1 transcription f 83.4 4 8.7E-05 25.6 4.6 18 129-146 79-96 (112)
71 PF09723 Zn-ribbon_8: Zinc rib 83.1 0.43 9.3E-06 24.2 0.2 10 32-41 6-15 (42)
72 TIGR02300 FYDLN_acid conserved 82.5 1.3 2.9E-05 28.2 2.3 34 59-100 9-42 (129)
73 smart00531 TFIIE Transcription 82.5 2.4 5.1E-05 27.9 3.6 39 27-69 95-133 (147)
74 COG1592 Rubrerythrin [Energy p 82.1 1 2.2E-05 30.3 1.8 24 58-91 133-156 (166)
75 smart00834 CxxC_CXXC_SSSS Puta 81.7 0.62 1.3E-05 23.1 0.5 10 32-41 6-15 (41)
76 PRK00398 rpoP DNA-directed RNA 81.7 0.96 2.1E-05 23.3 1.3 10 32-41 4-13 (46)
77 KOG2186 Cell growth-regulating 81.1 0.48 1E-05 33.8 -0.0 25 84-109 29-53 (276)
78 TIGR02605 CxxC_CxxC_SSSS putat 81.1 0.7 1.5E-05 24.4 0.6 11 32-42 6-16 (52)
79 COG5048 FOG: Zn-finger [Genera 81.1 1.1 2.4E-05 34.1 1.9 46 30-75 288-339 (467)
80 cd00729 rubredoxin_SM Rubredox 81.0 1.1 2.4E-05 21.6 1.2 10 83-92 17-26 (34)
81 smart00531 TFIIE Transcription 80.8 0.96 2.1E-05 29.7 1.3 38 56-94 96-133 (147)
82 PF02892 zf-BED: BED zinc fing 79.9 1.6 3.5E-05 22.1 1.8 25 81-105 13-41 (45)
83 PF08790 zf-LYAR: LYAR-type C2 78.9 0.39 8.5E-06 22.1 -0.7 21 85-106 1-21 (28)
84 smart00659 RPOLCX RNA polymera 78.0 1.9 4.1E-05 22.1 1.6 11 32-42 3-13 (44)
85 PF07754 DUF1610: Domain of un 77.0 2.7 5.9E-05 18.5 1.7 10 83-92 15-24 (24)
86 COG1997 RPL43A Ribosomal prote 76.1 1.9 4.1E-05 25.6 1.4 33 58-97 34-66 (89)
87 PF05443 ROS_MUCR: ROS/MUCR tr 75.0 1.6 3.5E-05 28.2 1.1 28 82-112 70-97 (132)
88 PF15135 UPF0515: Uncharacteri 74.0 4.3 9.4E-05 29.1 3.0 59 27-95 108-166 (278)
89 COG1996 RPC10 DNA-directed RNA 73.6 1.8 3.9E-05 22.8 0.8 11 31-41 6-16 (49)
90 COG2888 Predicted Zn-ribbon RN 73.6 2.3 5E-05 23.3 1.3 33 58-92 26-58 (61)
91 COG1198 PriA Primosomal protei 73.0 1.6 3.5E-05 36.3 0.9 48 33-93 437-484 (730)
92 PHA00626 hypothetical protein 73.0 2.9 6.3E-05 22.6 1.5 14 83-96 22-35 (59)
93 PF03604 DNA_RNApol_7kD: DNA d 72.4 2.9 6.2E-05 19.9 1.3 9 84-92 17-25 (32)
94 smart00734 ZnF_Rad18 Rad18-lik 71.8 4 8.7E-05 18.3 1.7 20 85-105 2-21 (26)
95 KOG2807 RNA polymerase II tran 71.0 8.4 0.00018 28.8 4.0 66 82-147 288-361 (378)
96 PF14353 CpXC: CpXC protein 69.7 1.6 3.4E-05 27.9 0.1 12 33-44 3-14 (128)
97 COG3357 Predicted transcriptio 69.6 3.9 8.4E-05 24.5 1.7 28 58-92 57-84 (97)
98 KOG4167 Predicted DNA-binding 68.6 1.1 2.3E-05 36.9 -0.9 27 83-109 791-817 (907)
99 KOG1146 Homeobox protein [Gene 67.1 5.3 0.00012 35.4 2.7 71 29-108 1282-1352(1406)
100 KOG2186 Cell growth-regulating 66.7 3.3 7.2E-05 29.7 1.2 38 32-71 4-41 (276)
101 KOG2593 Transcription initiati 65.4 3.5 7.5E-05 31.9 1.2 34 58-91 127-160 (436)
102 COG3091 SprT Zn-dependent meta 64.0 3.8 8.1E-05 27.1 1.0 31 59-91 117-147 (156)
103 PRK09678 DNA-binding transcrip 62.9 4.1 8.8E-05 23.4 0.9 18 81-98 24-43 (72)
104 TIGR00595 priA primosomal prot 62.1 3.6 7.8E-05 32.8 0.8 48 33-93 215-262 (505)
105 PF12013 DUF3505: Protein of u 62.0 7 0.00015 24.1 2.0 27 83-109 79-109 (109)
106 COG3677 Transposase and inacti 61.4 6.3 0.00014 25.4 1.7 14 82-95 51-64 (129)
107 KOG2893 Zn finger protein [Gen 61.3 5.4 0.00012 28.4 1.5 35 33-71 12-46 (341)
108 PF04959 ARS2: Arsenite-resist 60.9 4 8.6E-05 28.7 0.8 29 28-56 74-102 (214)
109 PF07975 C1_4: TFIIH C1-like d 60.1 0.37 8.1E-06 25.6 -3.4 26 29-54 19-44 (51)
110 PRK14873 primosome assembly pr 59.9 6.3 0.00014 32.7 1.8 47 33-93 385-431 (665)
111 KOG2593 Transcription initiati 58.8 15 0.00032 28.6 3.5 44 24-70 121-164 (436)
112 PF15269 zf-C2H2_7: Zinc-finge 58.2 25 0.00053 18.1 3.6 24 83-106 19-42 (54)
113 PF09845 DUF2072: Zn-ribbon co 57.5 5.1 0.00011 25.8 0.8 10 60-69 2-11 (131)
114 COG4957 Predicted transcriptio 57.2 6.8 0.00015 25.3 1.3 26 84-112 76-101 (148)
115 PF13240 zinc_ribbon_2: zinc-r 57.0 10 0.00022 16.4 1.5 6 87-92 16-21 (23)
116 COG4888 Uncharacterized Zn rib 56.5 3.2 7E-05 25.3 -0.2 12 29-40 20-31 (104)
117 PF06524 NOA36: NOA36 protein; 56.3 7.6 0.00017 28.1 1.5 82 27-109 138-234 (314)
118 COG4530 Uncharacterized protei 55.1 7.5 0.00016 24.2 1.2 32 61-101 11-42 (129)
119 PRK14890 putative Zn-ribbon RN 53.2 5 0.00011 22.0 0.2 33 58-92 24-56 (59)
120 PF01286 XPA_N: XPA protein N- 52.0 9 0.0002 18.5 1.0 11 61-71 5-15 (34)
121 PF13451 zf-trcl: Probable zin 51.7 6.2 0.00013 20.8 0.4 18 82-99 2-19 (49)
122 TIGR01206 lysW lysine biosynth 51.5 11 0.00025 20.2 1.4 10 85-94 23-32 (54)
123 KOG4167 Predicted DNA-binding 51.3 3 6.6E-05 34.5 -1.2 25 31-55 792-816 (907)
124 cd00924 Cyt_c_Oxidase_Vb Cytoc 50.4 8.1 0.00018 23.6 0.8 16 79-95 75-90 (97)
125 COG1198 PriA Primosomal protei 49.4 4.2 9.2E-05 34.0 -0.7 40 10-68 445-484 (730)
126 PRK03824 hypA hydrogenase nick 48.9 7.2 0.00016 25.3 0.5 14 30-43 69-82 (135)
127 PF04959 ARS2: Arsenite-resist 48.6 9.9 0.00022 26.8 1.1 26 81-106 74-99 (214)
128 PF08274 PhnA_Zn_Ribbon: PhnA 48.6 7.4 0.00016 18.2 0.4 8 59-66 19-26 (30)
129 PTZ00255 60S ribosomal protein 48.0 9.4 0.0002 22.9 0.8 32 58-96 35-66 (90)
130 KOG2231 Predicted E3 ubiquitin 47.7 12 0.00025 31.0 1.5 23 86-108 184-206 (669)
131 smart00440 ZnF_C2C2 C2C2 Zinc 47.3 10 0.00022 18.9 0.8 11 84-94 28-38 (40)
132 COG0068 HypF Hydrogenase matur 47.1 4.5 9.7E-05 33.5 -0.8 56 33-92 125-181 (750)
133 PF04810 zf-Sec23_Sec24: Sec23 46.4 3.3 7.2E-05 20.6 -1.1 24 15-38 8-31 (40)
134 TIGR00244 transcriptional regu 46.1 19 0.0004 23.8 2.0 11 61-71 30-40 (147)
135 PRK12380 hydrogenase nickel in 45.9 12 0.00025 23.5 1.0 11 60-70 71-81 (113)
136 PF12013 DUF3505: Protein of u 45.8 20 0.00043 22.1 2.1 25 32-56 81-109 (109)
137 PF07295 DUF1451: Protein of u 45.7 19 0.00041 23.7 2.1 8 60-67 113-120 (146)
138 KOG2636 Splicing factor 3a, su 45.5 13 0.00027 29.2 1.4 29 77-105 394-423 (497)
139 smart00154 ZnF_AN1 AN1-like Zi 45.3 28 0.0006 17.2 2.2 13 59-71 12-24 (39)
140 PF14446 Prok-RING_1: Prokaryo 45.3 16 0.00034 19.7 1.3 8 34-41 8-15 (54)
141 PRK05580 primosome assembly pr 43.6 19 0.00041 30.1 2.2 46 32-93 382-430 (679)
142 PRK04023 DNA polymerase II lar 43.3 32 0.00069 30.1 3.4 10 31-40 626-635 (1121)
143 PF07282 OrfB_Zn_ribbon: Putat 43.3 19 0.00041 20.0 1.6 29 61-96 30-58 (69)
144 PLN02294 cytochrome c oxidase 43.2 12 0.00026 25.3 0.8 15 82-96 139-153 (174)
145 TIGR00100 hypA hydrogenase nic 43.1 14 0.00031 23.2 1.1 11 60-70 71-81 (115)
146 smart00661 RPOL9 RNA polymeras 42.8 27 0.00059 18.0 2.1 11 84-94 20-30 (52)
147 TIGR00280 L37a ribosomal prote 42.7 9.7 0.00021 22.9 0.3 32 58-96 34-65 (91)
148 KOG2482 Predicted C2H2-type Zn 42.2 17 0.00037 27.5 1.5 30 83-112 194-225 (423)
149 COG1327 Predicted transcriptio 42.1 21 0.00046 23.6 1.8 12 60-71 29-40 (156)
150 PF01428 zf-AN1: AN1-like Zinc 41.7 8.7 0.00019 19.4 0.0 15 83-97 12-26 (43)
151 COG1655 Uncharacterized protei 41.4 6.3 0.00014 28.0 -0.7 29 29-57 17-45 (267)
152 KOG4173 Alpha-SNAP protein [In 41.3 4.4 9.5E-05 28.2 -1.4 74 31-108 79-171 (253)
153 COG3364 Zn-ribbon containing p 40.8 15 0.00032 22.6 0.9 18 141-158 70-87 (112)
154 PF13248 zf-ribbon_3: zinc-rib 39.4 26 0.00057 15.4 1.4 7 61-67 4-10 (26)
155 PF11931 DUF3449: Domain of un 38.9 10 0.00022 26.3 0.0 28 77-104 94-122 (196)
156 PF08394 Arc_trans_TRASH: Arch 38.9 2.6 5.7E-05 20.7 -2.1 33 62-94 1-33 (37)
157 PF13878 zf-C2H2_3: zinc-finge 38.6 39 0.00084 16.9 2.1 24 85-108 14-39 (41)
158 KOG3408 U1-like Zn-finger-cont 37.8 21 0.00045 22.7 1.2 35 81-115 54-96 (129)
159 PRK03976 rpl37ae 50S ribosomal 37.2 13 0.00027 22.4 0.2 32 58-96 35-66 (90)
160 COG1656 Uncharacterized conser 37.1 32 0.0007 23.1 2.1 24 82-105 128-151 (165)
161 PRK11823 DNA repair protein Ra 37.1 23 0.00051 27.9 1.7 8 60-67 8-15 (446)
162 COG5151 SSL1 RNA polymerase II 37.0 49 0.0011 24.8 3.2 47 62-108 365-412 (421)
163 TIGR00416 sms DNA repair prote 37.0 23 0.0005 28.0 1.7 10 59-68 7-16 (454)
164 KOG0978 E3 ubiquitin ligase in 36.8 4.7 0.0001 33.3 -2.1 18 82-99 676-693 (698)
165 smart00731 SprT SprT homologue 36.7 27 0.00058 22.8 1.7 32 59-94 112-143 (146)
166 PF13453 zf-TFIIB: Transcripti 36.7 8.1 0.00018 19.2 -0.6 20 29-48 17-36 (41)
167 PRK03681 hypA hydrogenase nick 36.5 21 0.00046 22.3 1.2 11 60-70 71-81 (114)
168 PRK00564 hypA hydrogenase nick 36.0 24 0.00052 22.2 1.3 10 60-69 72-81 (117)
169 PHA02998 RNA polymerase subuni 35.9 18 0.00039 24.6 0.8 12 85-96 172-183 (195)
170 COG5236 Uncharacterized conser 35.8 61 0.0013 24.8 3.5 73 32-106 152-242 (493)
171 PRK12496 hypothetical protein; 35.7 32 0.00069 23.1 2.0 11 60-70 128-138 (164)
172 COG4306 Uncharacterized protei 35.2 38 0.00082 21.7 2.1 39 60-98 40-82 (160)
173 COG1773 Rubredoxin [Energy pro 34.9 16 0.00035 19.7 0.4 14 83-96 2-15 (55)
174 KOG4124 Putative transcription 34.7 11 0.00023 28.6 -0.4 23 81-103 395-417 (442)
175 cd00065 FYVE FYVE domain; Zinc 34.5 33 0.00072 18.0 1.6 12 85-96 19-30 (57)
176 cd01121 Sms Sms (bacterial rad 33.8 30 0.00065 26.6 1.8 10 84-93 14-23 (372)
177 COG1571 Predicted DNA-binding 33.8 31 0.00067 27.0 1.8 29 61-97 352-380 (421)
178 PRK00432 30S ribosomal protein 33.6 33 0.00071 18.1 1.4 11 84-94 37-47 (50)
179 PF04780 DUF629: Protein of un 33.4 31 0.00067 27.4 1.8 32 79-110 52-84 (466)
180 KOG0717 Molecular chaperone (D 33.3 26 0.00056 27.7 1.4 21 85-105 293-313 (508)
181 KOG2785 C2H2-type Zn-finger pr 33.2 56 0.0012 25.2 3.0 66 31-106 166-242 (390)
182 PTZ00303 phosphatidylinositol 33.1 40 0.00087 28.8 2.4 34 31-71 460-493 (1374)
183 PF01780 Ribosomal_L37ae: Ribo 32.6 8.9 0.00019 23.0 -0.9 31 58-95 34-64 (90)
184 KOG3507 DNA-directed RNA polym 32.3 31 0.00068 18.9 1.2 12 83-94 36-47 (62)
185 KOG2071 mRNA cleavage and poly 32.3 30 0.00065 28.2 1.6 28 28-55 415-442 (579)
186 COG1675 TFA1 Transcription ini 31.8 66 0.0014 22.0 3.0 40 20-68 102-141 (176)
187 KOG2071 mRNA cleavage and poly 31.7 34 0.00074 27.8 1.8 28 81-108 415-442 (579)
188 PF01363 FYVE: FYVE zinc finge 31.6 24 0.00051 19.6 0.7 13 83-95 24-36 (69)
189 PF11789 zf-Nse: Zinc-finger o 31.1 37 0.0008 18.4 1.4 32 29-64 22-53 (57)
190 smart00064 FYVE Protein presen 30.7 39 0.00084 18.6 1.6 12 85-96 27-38 (68)
191 COG5188 PRP9 Splicing factor 3 30.7 24 0.00052 26.9 0.8 28 78-105 368-396 (470)
192 COG4391 Uncharacterized protei 30.7 21 0.00045 19.7 0.4 13 83-95 47-59 (62)
193 PF04423 Rad50_zn_hook: Rad50 30.3 18 0.00039 19.1 0.1 14 33-46 22-35 (54)
194 COG2331 Uncharacterized protei 30.3 32 0.00069 19.9 1.1 11 31-41 12-22 (82)
195 PF10083 DUF2321: Uncharacteri 29.9 44 0.00095 22.3 1.8 20 81-100 65-84 (158)
196 PF14787 zf-CCHC_5: GAG-polypr 29.8 28 0.00061 17.0 0.7 14 86-99 4-17 (36)
197 PRK04351 hypothetical protein; 29.3 32 0.0007 22.7 1.2 9 85-93 113-121 (149)
198 PF01155 HypA: Hydrogenase exp 29.3 19 0.00041 22.5 0.1 12 32-43 71-82 (113)
199 PTZ00448 hypothetical protein; 29.0 43 0.00092 25.7 1.9 23 84-106 314-336 (373)
200 COG1326 Uncharacterized archae 27.7 64 0.0014 22.4 2.4 15 57-71 28-42 (201)
201 cd00730 rubredoxin Rubredoxin; 27.2 26 0.00057 18.5 0.4 12 85-96 2-13 (50)
202 PF10013 DUF2256: Uncharacteri 27.2 41 0.00088 17.1 1.0 14 86-99 10-23 (42)
203 KOG1842 FYVE finger-containing 27.1 37 0.0008 26.7 1.3 30 82-111 13-43 (505)
204 PF01215 COX5B: Cytochrome c o 27.0 22 0.00049 23.1 0.1 15 82-96 110-124 (136)
205 PF10263 SprT-like: SprT-like 26.9 29 0.00064 22.6 0.7 30 60-94 124-153 (157)
206 PF08882 Acetone_carb_G: Aceto 26.9 21 0.00045 22.3 -0.0 29 130-158 73-103 (112)
207 PF01927 Mut7-C: Mut7-C RNAse 26.6 45 0.00097 21.8 1.5 46 60-105 92-145 (147)
208 KOG3214 Uncharacterized Zn rib 26.5 31 0.00068 21.1 0.7 13 85-97 48-60 (109)
209 PF12760 Zn_Tnp_IS1595: Transp 26.4 1E+02 0.0022 15.6 3.3 11 82-92 35-45 (46)
210 PTZ00043 cytochrome c oxidase 26.3 35 0.00075 24.3 0.9 17 81-97 178-194 (268)
211 PF05290 Baculo_IE-1: Baculovi 26.3 71 0.0015 20.8 2.3 20 56-75 77-96 (140)
212 PF12773 DZR: Double zinc ribb 25.8 89 0.0019 15.9 2.3 7 61-67 31-37 (50)
213 PF10276 zf-CHCC: Zinc-finger 25.4 38 0.00082 16.9 0.8 12 30-41 28-39 (40)
214 PRK10220 hypothetical protein; 24.5 60 0.0013 20.3 1.6 12 85-96 21-32 (111)
215 PRK14892 putative transcriptio 24.5 53 0.0012 20.1 1.4 9 30-38 20-28 (99)
216 PF14369 zf-RING_3: zinc-finge 24.4 82 0.0018 15.1 1.8 12 133-144 23-34 (35)
217 COG5216 Uncharacterized conser 24.3 44 0.00094 18.3 0.9 29 32-66 23-51 (67)
218 PF13824 zf-Mss51: Zinc-finger 24.2 68 0.0015 17.3 1.6 8 84-91 14-21 (55)
219 PF12907 zf-met2: Zinc-binding 24.1 15 0.00033 18.4 -0.8 26 85-110 2-31 (40)
220 KOG2482 Predicted C2H2-type Zn 23.9 53 0.0011 25.0 1.6 76 31-106 195-301 (423)
221 TIGR00686 phnA alkylphosphonat 23.7 51 0.0011 20.5 1.2 12 85-96 20-31 (109)
222 PF00301 Rubredoxin: Rubredoxi 23.5 31 0.00068 17.9 0.3 12 85-96 2-13 (47)
223 KOG0717 Molecular chaperone (D 23.4 56 0.0012 26.0 1.6 21 32-52 293-313 (508)
224 PF06397 Desulfoferrod_N: Desu 23.3 42 0.0009 16.4 0.7 11 30-40 5-15 (36)
225 COG4640 Predicted membrane pro 23.3 70 0.0015 24.9 2.1 17 86-102 17-33 (465)
226 COG1998 RPS31 Ribosomal protei 22.9 58 0.0013 17.2 1.2 10 84-93 37-46 (51)
227 TIGR01562 FdhE formate dehydro 22.8 80 0.0017 23.7 2.3 50 31-93 184-233 (305)
228 PF05129 Elf1: Transcription e 22.5 12 0.00026 21.9 -1.6 11 85-95 47-57 (81)
229 PRK00762 hypA hydrogenase nick 21.8 42 0.00092 21.3 0.7 6 86-91 94-99 (124)
230 PRK06260 threonine synthase; V 21.3 70 0.0015 24.7 1.9 10 32-41 4-13 (397)
231 PF08209 Sgf11: Sgf11 (transcr 21.3 73 0.0016 15.2 1.3 25 84-109 4-28 (33)
232 PLN02748 tRNA dimethylallyltra 21.3 74 0.0016 25.4 2.0 25 82-106 416-441 (468)
233 COG1594 RPB9 DNA-directed RNA 20.9 48 0.001 20.8 0.7 16 29-44 20-35 (113)
234 cd01410 SIRT7 SIRT7: Eukaryoti 20.8 1.6E+02 0.0035 20.5 3.4 18 25-42 89-106 (206)
235 PRK05978 hypothetical protein; 20.6 89 0.0019 20.7 2.0 11 86-96 54-64 (148)
236 PF03811 Zn_Tnp_IS1: InsA N-te 20.2 1.2E+02 0.0025 14.7 1.9 10 81-90 26-35 (36)
237 KOG2231 Predicted E3 ubiquitin 20.2 66 0.0014 26.9 1.6 21 33-53 184-204 (669)
238 COG1779 C4-type Zn-finger prot 20.1 28 0.0006 24.2 -0.5 9 32-40 15-23 (201)
No 1
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=99.90 E-value=1.3e-24 Score=150.86 Aligned_cols=109 Identities=25% Similarity=0.357 Sum_probs=93.9
Q ss_pred cchHHHHHHHHhhccccC---CCceeecccccccCCChHHHHHhHHhcCCCCccccCCCCCCCCCCCCCC---CCCCCCC
Q 031430 10 IDTANCLMLLSKVGETDQ---GKRVFACKTCNKEFPSFQALGGHRASHKKPKLMTMASSGEDFDQTQMPP---ASPRKPK 83 (159)
Q Consensus 10 ~~~~~~~~~l~~h~~~h~---~~k~~~C~~C~~~f~~~~~l~~h~~~h~~~~~~~c~~c~~~f~~~~~l~---~~~~~~k 83 (159)
.+.....+.|.+|+.+|- ..+.+.|+.|+|.|.....|+.|+++|+ -+++|..||+.|.....|+ +.|+|||
T Consensus 137 gk~ysT~snLsrHkQ~H~~~~s~ka~~C~~C~K~YvSmpALkMHirTH~--l~c~C~iCGKaFSRPWLLQGHiRTHTGEK 214 (279)
T KOG2462|consen 137 GKSYSTSSNLSRHKQTHRSLDSKKAFSCKYCGKVYVSMPALKMHIRTHT--LPCECGICGKAFSRPWLLQGHIRTHTGEK 214 (279)
T ss_pred ccccccccccchhhcccccccccccccCCCCCceeeehHHHhhHhhccC--CCcccccccccccchHHhhcccccccCCC
Confidence 334445667899999994 5778999999999999999999999998 7899999999999855443 8899999
Q ss_pred cccccccccccCChhHHHHHHHHcccccCCCccccCC
Q 031430 84 THECSICGLEFAIGQALGGHMRRHRAAAAMGAVADGL 120 (159)
Q Consensus 84 ~~~C~~Cgk~f~~~~~l~~H~~~h~~~~~~~~~~~~~ 120 (159)
||.|..|+|+|.+.++|+.||++|.+.++|.|..|+.
T Consensus 215 PF~C~hC~kAFADRSNLRAHmQTHS~~K~~qC~~C~K 251 (279)
T KOG2462|consen 215 PFSCPHCGKAFADRSNLRAHMQTHSDVKKHQCPRCGK 251 (279)
T ss_pred CccCCcccchhcchHHHHHHHHhhcCCccccCcchhh
Confidence 9999999999999999999999999999995543333
No 2
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=99.83 E-value=5.3e-22 Score=137.98 Aligned_cols=96 Identities=23% Similarity=0.334 Sum_probs=87.2
Q ss_pred chHHHHHHHHhhccccCCCceeecccccccCCChHHHHHhHHhcCCCCccccCCCCCCCCCCCCCC---CCCCCCCcccc
Q 031430 11 DTANCLMLLSKVGETDQGKRVFACKTCNKEFPSFQALGGHRASHKKPKLMTMASSGEDFDQTQMPP---ASPRKPKTHEC 87 (159)
Q Consensus 11 ~~~~~~~~l~~h~~~h~~~k~~~C~~C~~~f~~~~~l~~h~~~h~~~~~~~c~~c~~~f~~~~~l~---~~~~~~k~~~C 87 (159)
+.+.-+..|+.|+++|+ .+++|.+|||.|.+..-|..|+|+|+||+||.|..|++.|.+.++|. +.|.+.|+|.|
T Consensus 169 K~YvSmpALkMHirTH~--l~c~C~iCGKaFSRPWLLQGHiRTHTGEKPF~C~hC~kAFADRSNLRAHmQTHS~~K~~qC 246 (279)
T KOG2462|consen 169 KVYVSMPALKMHIRTHT--LPCECGICGKAFSRPWLLQGHIRTHTGEKPFSCPHCGKAFADRSNLRAHMQTHSDVKKHQC 246 (279)
T ss_pred ceeeehHHHhhHhhccC--CCcccccccccccchHHhhcccccccCCCCccCCcccchhcchHHHHHHHHhhcCCccccC
Confidence 44445667999999999 68999999999999999999999999999999999999999998886 66889999999
Q ss_pred cccccccCChhHHHHHHHHcc
Q 031430 88 SICGLEFAIGQALGGHMRRHR 108 (159)
Q Consensus 88 ~~Cgk~f~~~~~l~~H~~~h~ 108 (159)
..|+|+|...+.|..|...-.
T Consensus 247 ~~C~KsFsl~SyLnKH~ES~C 267 (279)
T KOG2462|consen 247 PRCGKSFALKSYLNKHSESAC 267 (279)
T ss_pred cchhhHHHHHHHHHHhhhhcc
Confidence 999999999999999987544
No 3
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=99.54 E-value=8.7e-16 Score=119.02 Aligned_cols=78 Identities=19% Similarity=0.392 Sum_probs=73.3
Q ss_pred CCceeecccccccCCChHHHHHhHHhcCCCCccccCCCCCCCCCCCCCC---CCCCCCCcccccccccccCChhHHHHHH
Q 031430 28 GKRVFACKTCNKEFPSFQALGGHRASHKKPKLMTMASSGEDFDQTQMPP---ASPRKPKTHECSICGLEFAIGQALGGHM 104 (159)
Q Consensus 28 ~~k~~~C~~C~~~f~~~~~l~~h~~~h~~~~~~~c~~c~~~f~~~~~l~---~~~~~~k~~~C~~Cgk~f~~~~~l~~H~ 104 (159)
.+-.|.|+.|+|.|...+.|.+|.--|+|.+||+|.+|.+.|+.+.||. +.|.|+|||.|+.|+|.|+..+++.+||
T Consensus 891 e~gmyaCDqCDK~FqKqSSLaRHKYEHsGqRPyqC~iCkKAFKHKHHLtEHkRLHSGEKPfQCdKClKRFSHSGSYSQHM 970 (1007)
T KOG3623|consen 891 EDGMYACDQCDKAFQKQSSLARHKYEHSGQRPYQCIICKKAFKHKHHLTEHKRLHSGEKPFQCDKCLKRFSHSGSYSQHM 970 (1007)
T ss_pred ccccchHHHHHHHHHhhHHHHHhhhhhcCCCCcccchhhHhhhhhhhhhhhhhhccCCCcchhhhhhhhcccccchHhhh
Confidence 3458999999999999999999999999999999999999999999986 6688999999999999999999999999
Q ss_pred H
Q 031430 105 R 105 (159)
Q Consensus 105 ~ 105 (159)
-
T Consensus 971 N 971 (1007)
T KOG3623|consen 971 N 971 (1007)
T ss_pred c
Confidence 5
No 4
>KOG1074 consensus Transcriptional repressor SALM [Transcription]
Probab=99.51 E-value=5.5e-15 Score=116.02 Aligned_cols=51 Identities=20% Similarity=0.291 Sum_probs=45.4
Q ss_pred ccccchHHHHHHHHhhccccCCCceeecccccccCCChHHHHHhHHhcCCC
Q 031430 7 MAAIDTANCLMLLSKVGETDQGKRVFACKTCNKEFPSFQALGGHRASHKKP 57 (159)
Q Consensus 7 ~~~~~~~~~~~~l~~h~~~h~~~k~~~C~~C~~~f~~~~~l~~h~~~h~~~ 57 (159)
+..-+.|++.+.|+.|.++|+|++||+|++||..|.++.+|++|...|+..
T Consensus 357 r~CakvfgS~SaLqiHlRSHTGERPfqCnvCG~~FSTkGNLKvH~~rH~e~ 407 (958)
T KOG1074|consen 357 RFCAKVFGSDSALQIHLRSHTGERPFQCNVCGNRFSTKGNLKVHFQRHREK 407 (958)
T ss_pred hhhHhhcCchhhhhhhhhccCCCCCeeecccccccccccceeeeeeecccc
Confidence 355678999999999999999999999999999999999999998766543
No 5
>KOG3576 consensus Ovo and related transcription factors [Transcription]
Probab=99.50 E-value=2.3e-15 Score=100.76 Aligned_cols=104 Identities=15% Similarity=0.183 Sum_probs=70.1
Q ss_pred ccchHHHHHHHHhhccccCCCceeecccccccCCChHHHHHhHHhcCCCCccccCCCCCCCCCCCCC----CCCCC----
Q 031430 9 AIDTANCLMLLSKVGETDQGKRVFACKTCNKEFPSFQALGGHRASHKKPKLMTMASSGEDFDQTQMP----PASPR---- 80 (159)
Q Consensus 9 ~~~~~~~~~~l~~h~~~h~~~k~~~C~~C~~~f~~~~~l~~h~~~h~~~~~~~c~~c~~~f~~~~~l----~~~~~---- 80 (159)
..+.|..+-.|.+|+.-|...+.|-|..||+.|.....|++|.++|+|.+||+|..|++.|.+.-.| .+.|.
T Consensus 123 CgK~F~lQRmlnrh~kch~~vkr~lct~cgkgfndtfdlkrh~rthtgvrpykc~~c~kaftqrcsleshl~kvhgv~~~ 202 (267)
T KOG3576|consen 123 CGKKFGLQRMLNRHLKCHSDVKRHLCTFCGKGFNDTFDLKRHTRTHTGVRPYKCSLCEKAFTQRCSLESHLKKVHGVQHQ 202 (267)
T ss_pred hhhhhhHHHHHHHHhhhccHHHHHHHhhccCcccchhhhhhhhccccCccccchhhhhHHHHhhccHHHHHHHHcCchHH
Confidence 4456777777777777777777777777777777777777777777777777777777777663332 22222
Q ss_pred ------CCCcccccccccccCChhHHHHHHHHcccccC
Q 031430 81 ------KPKTHECSICGLEFAIGQALGGHMRRHRAAAA 112 (159)
Q Consensus 81 ------~~k~~~C~~Cgk~f~~~~~l~~H~~~h~~~~~ 112 (159)
..+-|.|.+||.+-.....+-.|.+.|+...+
T Consensus 203 yaykerr~kl~vcedcg~t~~~~e~~~~h~~~~hp~Sp 240 (267)
T KOG3576|consen 203 YAYKERRAKLYVCEDCGYTSERPEVYYLHLKLHHPFSP 240 (267)
T ss_pred HHHHHhhhheeeecccCCCCCChhHHHHHHHhcCCCCH
Confidence 34567777777777777777777776665433
No 6
>KOG3576 consensus Ovo and related transcription factors [Transcription]
Probab=99.30 E-value=5.2e-13 Score=89.62 Aligned_cols=79 Identities=23% Similarity=0.439 Sum_probs=71.0
Q ss_pred CCceeecccccccCCChHHHHHhHHhcCCCCccccCCCCCCCCCCCCCC---CCCCCCCcccccccccccCChhHHHHHH
Q 031430 28 GKRVFACKTCNKEFPSFQALGGHRASHKKPKLMTMASSGEDFDQTQMPP---ASPRKPKTHECSICGLEFAIGQALGGHM 104 (159)
Q Consensus 28 ~~k~~~C~~C~~~f~~~~~l~~h~~~h~~~~~~~c~~c~~~f~~~~~l~---~~~~~~k~~~C~~Cgk~f~~~~~l~~H~ 104 (159)
+...|.|.+|+|.|...--|.+|+.-|...+.+.|..||+.|.+.-.|. +.|+|.+||+|..|+++|.+..+|..|.
T Consensus 114 d~d~ftCrvCgK~F~lQRmlnrh~kch~~vkr~lct~cgkgfndtfdlkrh~rthtgvrpykc~~c~kaftqrcsleshl 193 (267)
T KOG3576|consen 114 DQDSFTCRVCGKKFGLQRMLNRHLKCHSDVKRHLCTFCGKGFNDTFDLKRHTRTHTGVRPYKCSLCEKAFTQRCSLESHL 193 (267)
T ss_pred CCCeeeeehhhhhhhHHHHHHHHhhhccHHHHHHHhhccCcccchhhhhhhhccccCccccchhhhhHHHHhhccHHHHH
Confidence 4557999999999999999999999999999999999999998844443 7799999999999999999999999998
Q ss_pred HH
Q 031430 105 RR 106 (159)
Q Consensus 105 ~~ 106 (159)
+.
T Consensus 194 ~k 195 (267)
T KOG3576|consen 194 KK 195 (267)
T ss_pred HH
Confidence 64
No 7
>KOG3608 consensus Zn finger proteins [General function prediction only]
Probab=99.27 E-value=8.8e-14 Score=100.21 Aligned_cols=138 Identities=16% Similarity=0.185 Sum_probs=101.9
Q ss_pred cchHHHHHHHHhhccccCCCceeecccccccCCChHHHHHhHHhcC--CCCcc--------------------------c
Q 031430 10 IDTANCLMLLSKVGETDQGKRVFACKTCNKEFPSFQALGGHRASHK--KPKLM--------------------------T 61 (159)
Q Consensus 10 ~~~~~~~~~l~~h~~~h~~~k~~~C~~C~~~f~~~~~l~~h~~~h~--~~~~~--------------------------~ 61 (159)
.+.+.....|..|+++|+++|...|+.||.-|..+..|-.|.+-.+ ...+| +
T Consensus 186 t~~~~~k~~LreH~r~Hs~eKvvACp~Cg~~F~~~tkl~DH~rRqt~l~~n~fqC~~C~KrFaTeklL~~Hv~rHvn~yk 265 (467)
T KOG3608|consen 186 TKHMGNKYRLREHIRTHSNEKVVACPHCGELFRTKTKLFDHLRRQTELNTNSFQCAQCFKRFATEKLLKSHVVRHVNCYK 265 (467)
T ss_pred hhhhccHHHHHHHHHhcCCCeEEecchHHHHhccccHHHHHHHhhhhhcCCchHHHHHHHHHhHHHHHHHHHHHhhhccc
Confidence 4567778899999999999999999999999999999988876443 23344 5
Q ss_pred cCCCCCCCCCCCCCC----CCCCCCCcccccccccccCChhHHHHHHHHcccccCCCccc--cCCcc------------C
Q 031430 62 MASSGEDFDQTQMPP----ASPRKPKTHECSICGLEFAIGQALGGHMRRHRAAAAMGAVA--DGLVT------------R 123 (159)
Q Consensus 62 c~~c~~~f~~~~~l~----~~~~~~k~~~C~~Cgk~f~~~~~l~~H~~~h~~~~~~~~~~--~~~~~------------~ 123 (159)
|+.|+.+....+.|. -.|...|||+|+.|++.|.+.+.|..|..+|+ +..|.|.- +.-.+ .
T Consensus 266 CplCdmtc~~~ssL~~H~r~rHs~dkpfKCd~Cd~~c~~esdL~kH~~~HS-~~~y~C~h~~C~~s~r~~~q~~~H~~ev 344 (467)
T KOG3608|consen 266 CPLCDMTCSSASSLTTHIRYRHSKDKPFKCDECDTRCVRESDLAKHVQVHS-KTVYQCEHPDCHYSVRTYTQMRRHFLEV 344 (467)
T ss_pred ccccccCCCChHHHHHHHHhhhccCCCccccchhhhhccHHHHHHHHHhcc-ccceecCCCCCcHHHHHHHHHHHHHHHh
Confidence 555655555433332 23567999999999999999999999999998 66777654 22221 1
Q ss_pred CCCCCcchhccCCCCceeeeccCCC
Q 031430 124 PLLPLPVLKKSNSCKRVFCLDLNLM 148 (159)
Q Consensus 124 ~~~~~~~~~~~~~~~~~~~~~~~l~ 148 (159)
.....+..++|.-|.+.|..-.+|.
T Consensus 345 hEg~np~~Y~CH~Cdr~ft~G~~L~ 369 (467)
T KOG3608|consen 345 HEGNNPILYACHCCDRFFTSGKSLS 369 (467)
T ss_pred ccCCCCCceeeecchhhhccchhHH
Confidence 2344567788999998887766654
No 8
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=99.25 E-value=1.9e-12 Score=100.82 Aligned_cols=68 Identities=18% Similarity=0.244 Sum_probs=63.2
Q ss_pred cccchHHHHHHHHhhccccCCCceeecccccccCCChHHHHHhHHhcCCCCccccCCCCCCCCCCCCC
Q 031430 8 AAIDTANCLMLLSKVGETDQGKRVFACKTCNKEFPSFQALGGHRASHKKPKLMTMASSGEDFDQTQMP 75 (159)
Q Consensus 8 ~~~~~~~~~~~l~~h~~~h~~~k~~~C~~C~~~f~~~~~l~~h~~~h~~~~~~~c~~c~~~f~~~~~l 75 (159)
...++|.-.+.|.+|.=.|+|.+||.|.+|.|+|+.+.+|..|.|.|.|++||.|+.|++.|......
T Consensus 899 qCDK~FqKqSSLaRHKYEHsGqRPyqC~iCkKAFKHKHHLtEHkRLHSGEKPfQCdKClKRFSHSGSY 966 (1007)
T KOG3623|consen 899 QCDKAFQKQSSLARHKYEHSGQRPYQCIICKKAFKHKHHLTEHKRLHSGEKPFQCDKCLKRFSHSGSY 966 (1007)
T ss_pred HHHHHHHhhHHHHHhhhhhcCCCCcccchhhHhhhhhhhhhhhhhhccCCCcchhhhhhhhcccccch
Confidence 45678888999999999999999999999999999999999999999999999999999999875554
No 9
>KOG1074 consensus Transcriptional repressor SALM [Transcription]
Probab=99.04 E-value=1.1e-10 Score=92.32 Aligned_cols=80 Identities=21% Similarity=0.304 Sum_probs=61.0
Q ss_pred eeecccccccCCChHHHHHhHHhcCCCCccccCCCCCCCCCCCCCCCCCCC-------CCccccc---ccccccCChhHH
Q 031430 31 VFACKTCNKEFPSFQALGGHRASHKKPKLMTMASSGEDFDQTQMPPASPRK-------PKTHECS---ICGLEFAIGQAL 100 (159)
Q Consensus 31 ~~~C~~C~~~f~~~~~l~~h~~~h~~~~~~~c~~c~~~f~~~~~l~~~~~~-------~k~~~C~---~Cgk~f~~~~~l 100 (159)
|-.|-.|-+.....+.|+.|.++|+|++||+|.+||+.|..+.+|+.|..+ .-.|.|+ +|-+.|.+.-.|
T Consensus 605 PNqCiiC~rVlSC~saLqmHyrtHtGERPFkCKiCgRAFtTkGNLkaH~~vHka~p~~R~q~ScP~~~ic~~kftn~V~l 684 (958)
T KOG1074|consen 605 PNQCIICLRVLSCPSALQMHYRTHTGERPFKCKICGRAFTTKGNLKAHMSVHKAKPPARVQFSCPSTFICQKKFTNAVTL 684 (958)
T ss_pred ccceeeeeecccchhhhhhhhhcccCcCccccccccchhccccchhhcccccccCccccccccCCchhhhcccccccccc
Confidence 456777777777777777777777777777777777777777777433221 2458899 999999999999
Q ss_pred HHHHHHcccc
Q 031430 101 GGHMRRHRAA 110 (159)
Q Consensus 101 ~~H~~~h~~~ 110 (159)
..|+++|.+.
T Consensus 685 pQhIriH~~~ 694 (958)
T KOG1074|consen 685 PQHIRIHLGG 694 (958)
T ss_pred cceEEeecCC
Confidence 9999999954
No 10
>PHA00733 hypothetical protein
Probab=99.04 E-value=9.1e-11 Score=75.15 Aligned_cols=90 Identities=12% Similarity=0.115 Sum_probs=66.8
Q ss_pred HhhccccCCCceeecccccccCCChHHHHHh--HH---hcCCCCccccCCCCCCCCCCCCCCCCCC-CCCcccccccccc
Q 031430 20 SKVGETDQGKRVFACKTCNKEFPSFQALGGH--RA---SHKKPKLMTMASSGEDFDQTQMPPASPR-KPKTHECSICGLE 93 (159)
Q Consensus 20 ~~h~~~h~~~k~~~C~~C~~~f~~~~~l~~h--~~---~h~~~~~~~c~~c~~~f~~~~~l~~~~~-~~k~~~C~~Cgk~ 93 (159)
..+...-...+++.|.+|.+.|.....|..+ +. .+.++++|.|..||+.|.....|..+.. ...+|.|..|++.
T Consensus 29 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~l~~~~~~~~~kPy~C~~Cgk~Fss~s~L~~H~r~h~~~~~C~~CgK~ 108 (128)
T PHA00733 29 KRYHSLTPEQKRLIRAVVKTLIYNPQLLDESSYLYKLLTSKAVSPYVCPLCLMPFSSSVSLKQHIRYTEHSKVCPVCGKE 108 (128)
T ss_pred hhhhcCChhhhhHHHHHHhhhccChhhhcchHHHHhhcccCCCCCccCCCCCCcCCCHHHHHHHHhcCCcCccCCCCCCc
Confidence 3333334457789999999988887777665 21 2345789999999999998766643222 1567999999999
Q ss_pred cCChhHHHHHHHHccc
Q 031430 94 FAIGQALGGHMRRHRA 109 (159)
Q Consensus 94 f~~~~~l~~H~~~h~~ 109 (159)
|.+...|..|+...++
T Consensus 109 F~~~~sL~~H~~~~h~ 124 (128)
T PHA00733 109 FRNTDSTLDHVCKKHN 124 (128)
T ss_pred cCCHHHHHHHHHHhcC
Confidence 9999999999976654
No 11
>PHA02768 hypothetical protein; Provisional
Probab=98.97 E-value=5e-10 Score=60.11 Aligned_cols=44 Identities=11% Similarity=0.159 Sum_probs=39.4
Q ss_pred eeecccccccCCChHHHHHhHHhcCCCCccccCCCCCCCCCCCCCC
Q 031430 31 VFACKTCNKEFPSFQALGGHRASHKKPKLMTMASSGEDFDQTQMPP 76 (159)
Q Consensus 31 ~~~C~~C~~~f~~~~~l~~h~~~h~~~~~~~c~~c~~~f~~~~~l~ 76 (159)
-|.|+.||+.|...++|..|++.|+ ++++|..|++.|...+.+.
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 4799999999999999999999999 6899999999988766664
No 12
>KOG3608 consensus Zn finger proteins [General function prediction only]
Probab=98.88 E-value=5.1e-10 Score=81.13 Aligned_cols=89 Identities=16% Similarity=0.256 Sum_probs=51.4
Q ss_pred HHHHhhcc-ccCCCceeecccccccCCChHHHHHhHHhcCCCCccccCC--CCCCCCCC----CCCCCCCCC--CCcccc
Q 031430 17 MLLSKVGE-TDQGKRVFACKTCNKEFPSFQALGGHRASHKKPKLMTMAS--SGEDFDQT----QMPPASPRK--PKTHEC 87 (159)
Q Consensus 17 ~~l~~h~~-~h~~~k~~~C~~C~~~f~~~~~l~~h~~~h~~~~~~~c~~--c~~~f~~~----~~l~~~~~~--~k~~~C 87 (159)
+.|..|++ .|...+||+|+.|++.|...+.|..|...|+ +..|.|.. |...+... .+...+|.| +.+|.|
T Consensus 277 ssL~~H~r~rHs~dkpfKCd~Cd~~c~~esdL~kH~~~HS-~~~y~C~h~~C~~s~r~~~q~~~H~~evhEg~np~~Y~C 355 (467)
T KOG3608|consen 277 SSLTTHIRYRHSKDKPFKCDECDTRCVRESDLAKHVQVHS-KTVYQCEHPDCHYSVRTYTQMRRHFLEVHEGNNPILYAC 355 (467)
T ss_pred HHHHHHHHhhhccCCCccccchhhhhccHHHHHHHHHhcc-ccceecCCCCCcHHHHHHHHHHHHHHHhccCCCCCceee
Confidence 34444444 3445555555555555555555555555554 44455544 44433331 111133433 567899
Q ss_pred cccccccCChhHHHHHHHH
Q 031430 88 SICGLEFAIGQALGGHMRR 106 (159)
Q Consensus 88 ~~Cgk~f~~~~~l~~H~~~ 106 (159)
..|++.|.+..+|..|+..
T Consensus 356 H~Cdr~ft~G~~L~~HL~k 374 (467)
T KOG3608|consen 356 HCCDRFFTSGKSLSAHLMK 374 (467)
T ss_pred ecchhhhccchhHHHHHHH
Confidence 9999999999999999754
No 13
>PHA02768 hypothetical protein; Provisional
Probab=98.82 E-value=3.5e-09 Score=56.87 Aligned_cols=44 Identities=27% Similarity=0.556 Sum_probs=35.3
Q ss_pred cccccccccccCChhHHHHHHHHcccccCCCccccCCccCCCCCCcchhccCCCCceeeeccCCC
Q 031430 84 THECSICGLEFAIGQALGGHMRRHRAAAAMGAVADGLVTRPLLPLPVLKKSNSCKRVFCLDLNLM 148 (159)
Q Consensus 84 ~~~C~~Cgk~f~~~~~l~~H~~~h~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~ 148 (159)
-|.|++||+.|...++|..|+++|+ +++ +|..|++.|....+|.
T Consensus 5 ~y~C~~CGK~Fs~~~~L~~H~r~H~--k~~-------------------kc~~C~k~f~~~s~l~ 48 (55)
T PHA02768 5 GYECPICGEIYIKRKSMITHLRKHN--TNL-------------------KLSNCKRISLRTGEYI 48 (55)
T ss_pred ccCcchhCCeeccHHHHHHHHHhcC--Ccc-------------------cCCcccceecccceeE
Confidence 4799999999999999999999999 455 4566667776666554
No 14
>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=98.79 E-value=1.8e-09 Score=49.73 Aligned_cols=24 Identities=29% Similarity=0.686 Sum_probs=18.1
Q ss_pred HHhhccccCCCceeecccccccCC
Q 031430 19 LSKVGETDQGKRVFACKTCNKEFP 42 (159)
Q Consensus 19 l~~h~~~h~~~k~~~C~~C~~~f~ 42 (159)
|..|+++|++++||.|+.|++.|.
T Consensus 2 l~~H~~~H~~~k~~~C~~C~k~F~ 25 (26)
T PF13465_consen 2 LRRHMRTHTGEKPYKCPYCGKSFS 25 (26)
T ss_dssp HHHHHHHHSSSSSEEESSSSEEES
T ss_pred HHHHhhhcCCCCCCCCCCCcCeeC
Confidence 667777777777777777777774
No 15
>PLN03086 PRLI-interacting factor K; Provisional
Probab=98.64 E-value=7.7e-08 Score=75.03 Aligned_cols=85 Identities=14% Similarity=0.223 Sum_probs=61.8
Q ss_pred CCceeecccccccCCChHHHHHhHHhcCCCCccccCCCCCCCCCCCCCC---CCCCCCCcccccccccccCC--------
Q 031430 28 GKRVFACKTCNKEFPSFQALGGHRASHKKPKLMTMASSGEDFDQTQMPP---ASPRKPKTHECSICGLEFAI-------- 96 (159)
Q Consensus 28 ~~k~~~C~~C~~~f~~~~~l~~h~~~h~~~~~~~c~~c~~~f~~~~~l~---~~~~~~k~~~C~~Cgk~f~~-------- 96 (159)
-++.+.|+.|++.|. ...|..|+..++ .++.|+ ||..+. ...|. ..|...+++.|..|++.|..
T Consensus 450 l~~H~~C~~Cgk~f~-~s~LekH~~~~H--kpv~Cp-Cg~~~~-R~~L~~H~~thCp~Kpi~C~fC~~~v~~g~~~~d~~ 524 (567)
T PLN03086 450 AKNHVHCEKCGQAFQ-QGEMEKHMKVFH--EPLQCP-CGVVLE-KEQMVQHQASTCPLRLITCRFCGDMVQAGGSAMDVR 524 (567)
T ss_pred cccCccCCCCCCccc-hHHHHHHHHhcC--CCccCC-CCCCcc-hhHHHhhhhccCCCCceeCCCCCCccccCccccchh
Confidence 355678999999985 677899998875 789998 997553 33332 33557899999999999852
Q ss_pred --hhHHHHHHHHcccccCCCcccc
Q 031430 97 --GQALGGHMRRHRAAAAMGAVAD 118 (159)
Q Consensus 97 --~~~l~~H~~~h~~~~~~~~~~~ 118 (159)
.+.|..|...+ +.+++.|..|
T Consensus 525 d~~s~Lt~HE~~C-G~rt~~C~~C 547 (567)
T PLN03086 525 DRLRGMSEHESIC-GSRTAPCDSC 547 (567)
T ss_pred hhhhhHHHHHHhc-CCcceEcccc
Confidence 34788888875 7777654333
No 16
>PHA00616 hypothetical protein
Probab=98.55 E-value=3.4e-08 Score=50.53 Aligned_cols=32 Identities=16% Similarity=0.234 Sum_probs=30.1
Q ss_pred cccccccccccCChhHHHHHHHHcccccCCCc
Q 031430 84 THECSICGLEFAIGQALGGHMRRHRAAAAMGA 115 (159)
Q Consensus 84 ~~~C~~Cgk~f~~~~~l~~H~~~h~~~~~~~~ 115 (159)
||+|..||+.|.+.+.|..|++.|++++++.+
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~~hg~~~~~~ 32 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLSVHKQNKLTL 32 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHHhcCCCccce
Confidence 68999999999999999999999999988865
No 17
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=98.55 E-value=2.8e-08 Score=45.67 Aligned_cols=25 Identities=24% Similarity=0.343 Sum_probs=22.3
Q ss_pred HHHHhHHhcCCCCccccCCCCCCCC
Q 031430 46 ALGGHRASHKKPKLMTMASSGEDFD 70 (159)
Q Consensus 46 ~l~~h~~~h~~~~~~~c~~c~~~f~ 70 (159)
+|..|++.|+++++|.|+.|++.|.
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 4789999999999999999998875
No 18
>PHA00733 hypothetical protein
Probab=98.50 E-value=3.4e-08 Score=63.35 Aligned_cols=54 Identities=20% Similarity=0.292 Sum_probs=44.9
Q ss_pred HHhhccccCCCceeecccccccCCChHHHHHhHHhcCCCCccccCCCCCCCCCCCCC
Q 031430 19 LSKVGETDQGKRVFACKTCNKEFPSFQALGGHRASHKKPKLMTMASSGEDFDQTQMP 75 (159)
Q Consensus 19 l~~h~~~h~~~k~~~C~~C~~~f~~~~~l~~h~~~h~~~~~~~c~~c~~~f~~~~~l 75 (159)
|.+|+.++ +.+||.|+.|++.|.....|..|++.+ ..++.|..|++.|.....|
T Consensus 62 l~~~~~~~-~~kPy~C~~Cgk~Fss~s~L~~H~r~h--~~~~~C~~CgK~F~~~~sL 115 (128)
T PHA00733 62 LYKLLTSK-AVSPYVCPLCLMPFSSSVSLKQHIRYT--EHSKVCPVCGKEFRNTDST 115 (128)
T ss_pred HHhhcccC-CCCCccCCCCCCcCCCHHHHHHHHhcC--CcCccCCCCCCccCCHHHH
Confidence 45554444 488999999999999999999999976 3579999999999886665
No 19
>PLN03086 PRLI-interacting factor K; Provisional
Probab=98.47 E-value=1.4e-07 Score=73.61 Aligned_cols=85 Identities=16% Similarity=0.218 Sum_probs=66.0
Q ss_pred HHHHHhhccccCCCceeecccccccCCChHHHHHhHHhcCCCCccccCCCCCCCCCC----------CCCCCCC--CCCC
Q 031430 16 LMLLSKVGETDQGKRVFACKTCNKEFPSFQALGGHRASHKKPKLMTMASSGEDFDQT----------QMPPASP--RKPK 83 (159)
Q Consensus 16 ~~~l~~h~~~h~~~k~~~C~~C~~~f~~~~~l~~h~~~h~~~~~~~c~~c~~~f~~~----------~~l~~~~--~~~k 83 (159)
...|..|..+|. +++.|+ |++.+ ....|..|+..|.+.+++.|..|+..+... ..|..|. -+.+
T Consensus 465 ~s~LekH~~~~H--kpv~Cp-Cg~~~-~R~~L~~H~~thCp~Kpi~C~fC~~~v~~g~~~~d~~d~~s~Lt~HE~~CG~r 540 (567)
T PLN03086 465 QGEMEKHMKVFH--EPLQCP-CGVVL-EKEQMVQHQASTCPLRLITCRFCGDMVQAGGSAMDVRDRLRGMSEHESICGSR 540 (567)
T ss_pred hHHHHHHHHhcC--CCccCC-CCCCc-chhHHHhhhhccCCCCceeCCCCCCccccCccccchhhhhhhHHHHHHhcCCc
Confidence 456899999984 899999 99765 678999999999999999999999988521 1232221 2899
Q ss_pred cccccccccccCChhHHHHHHH
Q 031430 84 THECSICGLEFAIGQALGGHMR 105 (159)
Q Consensus 84 ~~~C~~Cgk~f~~~~~l~~H~~ 105 (159)
++.|..||+.|.... +..|+.
T Consensus 541 t~~C~~Cgk~Vrlrd-m~~H~~ 561 (567)
T PLN03086 541 TAPCDSCGRSVMLKE-MDIHQI 561 (567)
T ss_pred ceEccccCCeeeehh-HHHHHH
Confidence 999999999987764 455653
No 20
>KOG3993 consensus Transcription factor (contains Zn finger) [Transcription]
Probab=98.42 E-value=2e-07 Score=69.29 Aligned_cols=93 Identities=19% Similarity=0.281 Sum_probs=60.6
Q ss_pred HHHhhccccCCCceeecccccccCCChHHHHHhHHhcCCCCccc--cCCCCC-CCCCCCCC-----CCCCCCCCcccccc
Q 031430 18 LLSKVGETDQGKRVFACKTCNKEFPSFQALGGHRASHKKPKLMT--MASSGE-DFDQTQMP-----PASPRKPKTHECSI 89 (159)
Q Consensus 18 ~l~~h~~~h~~~k~~~C~~C~~~f~~~~~l~~h~~~h~~~~~~~--c~~c~~-~f~~~~~l-----~~~~~~~k~~~C~~ 89 (159)
.|.+|.-...-.-.|+|++|+|.|....+|..|+|+|.-..... -..-.+ ........ ......+-.|.|..
T Consensus 282 ~LAQHrC~RIV~vEYrCPEC~KVFsCPANLASHRRWHKPR~eaa~a~~~P~k~~~~~rae~~ea~rsg~dss~gi~~C~~ 361 (500)
T KOG3993|consen 282 ALAQHRCPRIVHVEYRCPECDKVFSCPANLASHRRWHKPRPEAAKAGSPPPKQAVETRAEVQEAERSGDDSSSGIFSCHT 361 (500)
T ss_pred HHhhccCCeeEEeeecCCcccccccCchhhhhhhcccCCchhhhhcCCCChhhhhhhhhhhhhccccCCcccCceeecHH
Confidence 56777765555557999999999999999999999996322110 000000 00000000 00012244799999
Q ss_pred cccccCChhHHHHHHHHcccc
Q 031430 90 CGLEFAIGQALGGHMRRHRAA 110 (159)
Q Consensus 90 Cgk~f~~~~~l~~H~~~h~~~ 110 (159)
|+|.|.+...|+.|+-+|...
T Consensus 362 C~KkFrRqAYLrKHqlthq~~ 382 (500)
T KOG3993|consen 362 CGKKFRRQAYLRKHQLTHQRA 382 (500)
T ss_pred hhhhhHHHHHHHHhHHhhhcc
Confidence 999999999999999888754
No 21
>PHA00616 hypothetical protein
Probab=98.41 E-value=1e-07 Score=48.83 Aligned_cols=34 Identities=21% Similarity=0.354 Sum_probs=31.4
Q ss_pred eeecccccccCCChHHHHHhHHhcCCCCccccCC
Q 031430 31 VFACKTCNKEFPSFQALGGHRASHKKPKLMTMAS 64 (159)
Q Consensus 31 ~~~C~~C~~~f~~~~~l~~h~~~h~~~~~~~c~~ 64 (159)
||.|..||+.|..++.|..|++.|+|++++.|+.
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~~hg~~~~~~~~ 34 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLSVHKQNKLTLEY 34 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHHhcCCCccceeE
Confidence 6899999999999999999999999999988753
No 22
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=98.23 E-value=7.2e-07 Score=39.63 Aligned_cols=23 Identities=48% Similarity=0.924 Sum_probs=21.5
Q ss_pred ccccccccccCChhHHHHHHHHc
Q 031430 85 HECSICGLEFAIGQALGGHMRRH 107 (159)
Q Consensus 85 ~~C~~Cgk~f~~~~~l~~H~~~h 107 (159)
|.|+.||+.|.+...|..|++.|
T Consensus 1 y~C~~C~~~f~~~~~l~~H~~~H 23 (23)
T PF00096_consen 1 YKCPICGKSFSSKSNLKRHMRRH 23 (23)
T ss_dssp EEETTTTEEESSHHHHHHHHHHH
T ss_pred CCCCCCCCccCCHHHHHHHHhHC
Confidence 68999999999999999999875
No 23
>PHA00732 hypothetical protein
Probab=98.00 E-value=5.6e-06 Score=48.48 Aligned_cols=38 Identities=18% Similarity=0.380 Sum_probs=31.3
Q ss_pred eeecccccccCCChHHHHHhHHh-cCCCCccccCCCCCCCCC
Q 031430 31 VFACKTCNKEFPSFQALGGHRAS-HKKPKLMTMASSGEDFDQ 71 (159)
Q Consensus 31 ~~~C~~C~~~f~~~~~l~~h~~~-h~~~~~~~c~~c~~~f~~ 71 (159)
||.|..|++.|.....|..|++. |.+ +.|+.||+.|..
T Consensus 1 py~C~~Cgk~F~s~s~Lk~H~r~~H~~---~~C~~CgKsF~~ 39 (79)
T PHA00732 1 MFKCPICGFTTVTLFALKQHARRNHTL---TKCPVCNKSYRR 39 (79)
T ss_pred CccCCCCCCccCCHHHHHHHhhcccCC---CccCCCCCEeCC
Confidence 58899999999999999999984 543 468888887764
No 24
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=97.95 E-value=4.2e-06 Score=60.36 Aligned_cols=70 Identities=23% Similarity=0.390 Sum_probs=48.8
Q ss_pred Cceeeccc--ccccCCChHHHHHhHHh-cCCCCccccCCCCCCCCCCCCCCCCCCCCCcccccccccccCChhHHHHHHH
Q 031430 29 KRVFACKT--CNKEFPSFQALGGHRAS-HKKPKLMTMASSGEDFDQTQMPPASPRKPKTHECSICGLEFAIGQALGGHMR 105 (159)
Q Consensus 29 ~k~~~C~~--C~~~f~~~~~l~~h~~~-h~~~~~~~c~~c~~~f~~~~~l~~~~~~~k~~~C~~Cgk~f~~~~~l~~H~~ 105 (159)
+|||+|++ |+|.|.....|+.|+.- |...+...-+. .......-...|||+|+.|+|.|.+...|+.|..
T Consensus 347 ~KpykCpV~gC~K~YknqnGLKYH~lhGH~~~~~~~~p~-------p~~~~~F~~~~KPYrCevC~KRYKNlNGLKYHr~ 419 (423)
T COG5189 347 GKPYKCPVEGCNKKYKNQNGLKYHMLHGHQNQKLHENPS-------PEKMNIFSAKDKPYRCEVCDKRYKNLNGLKYHRK 419 (423)
T ss_pred CceecCCCCCchhhhccccchhhhhhccccCcccCCCCC-------ccccccccccCCceeccccchhhccCccceeccc
Confidence 59999998 99999999999998653 33332222110 0011111235799999999999999999988864
No 25
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=97.90 E-value=7e-06 Score=36.34 Aligned_cols=23 Identities=35% Similarity=0.694 Sum_probs=21.3
Q ss_pred eecccccccCCChHHHHHhHHhc
Q 031430 32 FACKTCNKEFPSFQALGGHRASH 54 (159)
Q Consensus 32 ~~C~~C~~~f~~~~~l~~h~~~h 54 (159)
|.|+.|++.|.....|..|++.|
T Consensus 1 y~C~~C~~~f~~~~~l~~H~~~H 23 (23)
T PF00096_consen 1 YKCPICGKSFSSKSNLKRHMRRH 23 (23)
T ss_dssp EEETTTTEEESSHHHHHHHHHHH
T ss_pred CCCCCCCCccCCHHHHHHHHhHC
Confidence 78999999999999999999864
No 26
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=97.87 E-value=7.4e-06 Score=37.79 Aligned_cols=26 Identities=38% Similarity=0.635 Sum_probs=23.8
Q ss_pred cccccccccccCChhHHHHHHHHccc
Q 031430 84 THECSICGLEFAIGQALGGHMRRHRA 109 (159)
Q Consensus 84 ~~~C~~Cgk~f~~~~~l~~H~~~h~~ 109 (159)
+|.|..|++.|.....|..|++.|..
T Consensus 1 ~~~C~~C~~~F~~~~~l~~H~~~h~~ 26 (27)
T PF13912_consen 1 PFECDECGKTFSSLSALREHKRSHCS 26 (27)
T ss_dssp SEEETTTTEEESSHHHHHHHHCTTTT
T ss_pred CCCCCccCCccCChhHHHHHhHHhcC
Confidence 68999999999999999999998764
No 27
>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=97.85 E-value=1.3e-05 Score=35.61 Aligned_cols=24 Identities=42% Similarity=0.844 Sum_probs=20.0
Q ss_pred ccccccccccCChhHHHHHHHHcc
Q 031430 85 HECSICGLEFAIGQALGGHMRRHR 108 (159)
Q Consensus 85 ~~C~~Cgk~f~~~~~l~~H~~~h~ 108 (159)
|.|++|++.|.+...|..|++.|.
T Consensus 1 ~~C~~C~~~~~~~~~l~~H~~~~H 24 (24)
T PF13894_consen 1 FQCPICGKSFRSKSELRQHMRTHH 24 (24)
T ss_dssp EE-SSTS-EESSHHHHHHHHHHHS
T ss_pred CCCcCCCCcCCcHHHHHHHHHhhC
Confidence 689999999999999999998763
No 28
>PHA00732 hypothetical protein
Probab=97.80 E-value=2.5e-05 Score=45.72 Aligned_cols=23 Identities=39% Similarity=0.663 Sum_probs=15.2
Q ss_pred cccccccccccCChhHHHHHHHH
Q 031430 84 THECSICGLEFAIGQALGGHMRR 106 (159)
Q Consensus 84 ~~~C~~Cgk~f~~~~~l~~H~~~ 106 (159)
||.|..||+.|.+...|..|++.
T Consensus 1 py~C~~Cgk~F~s~s~Lk~H~r~ 23 (79)
T PHA00732 1 MFKCPICGFTTVTLFALKQHARR 23 (79)
T ss_pred CccCCCCCCccCCHHHHHHHhhc
Confidence 45666677777776667766663
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=97.59 E-value=3.9e-05 Score=35.30 Aligned_cols=25 Identities=44% Similarity=0.826 Sum_probs=23.1
Q ss_pred eeecccccccCCChHHHHHhHHhcC
Q 031430 31 VFACKTCNKEFPSFQALGGHRASHK 55 (159)
Q Consensus 31 ~~~C~~C~~~f~~~~~l~~h~~~h~ 55 (159)
||.|..|++.|.....|..|++.|.
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 6899999999999999999998875
No 30
>smart00355 ZnF_C2H2 zinc finger.
Probab=97.49 E-value=0.00011 Score=33.00 Aligned_cols=25 Identities=40% Similarity=0.664 Sum_probs=22.3
Q ss_pred ccccccccccCChhHHHHHHHHccc
Q 031430 85 HECSICGLEFAIGQALGGHMRRHRA 109 (159)
Q Consensus 85 ~~C~~Cgk~f~~~~~l~~H~~~h~~ 109 (159)
|.|..|++.|.....|..|++.|..
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~~H~~ 25 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMRTHXX 25 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHHHhcc
Confidence 5799999999999999999997753
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=97.39 E-value=0.00015 Score=31.99 Aligned_cols=23 Identities=39% Similarity=0.736 Sum_probs=19.4
Q ss_pred eecccccccCCChHHHHHhHHhc
Q 031430 32 FACKTCNKEFPSFQALGGHRASH 54 (159)
Q Consensus 32 ~~C~~C~~~f~~~~~l~~h~~~h 54 (159)
|.|+.|++.|.....|..|+..|
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 68999999999999999999875
No 32
>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=97.39 E-value=0.00026 Score=37.21 Aligned_cols=35 Identities=17% Similarity=0.387 Sum_probs=25.5
Q ss_pred CCCCCCcccccccccccCChhHHHHHHHHcccccC
Q 031430 78 SPRKPKTHECSICGLEFAIGQALGGHMRRHRAAAA 112 (159)
Q Consensus 78 ~~~~~k~~~C~~Cgk~f~~~~~l~~H~~~h~~~~~ 112 (159)
.+..+.|-.|++|+..+.+..+|.+|+.++++.+|
T Consensus 18 ~~~S~~PatCP~C~a~~~~srnLrRHle~~H~~k~ 52 (54)
T PF09237_consen 18 KSQSEQPATCPICGAVIRQSRNLRRHLEIRHFKKP 52 (54)
T ss_dssp CCTTS--EE-TTT--EESSHHHHHHHHHHHTTTS-
T ss_pred hhccCCCCCCCcchhhccchhhHHHHHHHHhcccC
Confidence 34468899999999999999999999999888766
No 33
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=97.36 E-value=0.00051 Score=37.17 Aligned_cols=51 Identities=27% Similarity=0.491 Sum_probs=32.0
Q ss_pred eeecccccccCCChHHHHHhHHh-cCCCCccccCCCCCCCCCCCCCCCCCCCCCcccccccccccCChhHHHHHHHHcc
Q 031430 31 VFACKTCNKEFPSFQALGGHRAS-HKKPKLMTMASSGEDFDQTQMPPASPRKPKTHECSICGLEFAIGQALGGHMRRHR 108 (159)
Q Consensus 31 ~~~C~~C~~~f~~~~~l~~h~~~-h~~~~~~~c~~c~~~f~~~~~l~~~~~~~k~~~C~~Cgk~f~~~~~l~~H~~~h~ 108 (159)
.|.|+.|++. .....|..|... |..+ .+.+.|++|...+. ..|..|+..++
T Consensus 2 ~f~CP~C~~~-~~~~~L~~H~~~~H~~~------------------------~~~v~CPiC~~~~~--~~l~~Hl~~~H 53 (54)
T PF05605_consen 2 SFTCPYCGKG-FSESSLVEHCEDEHRSE------------------------SKNVVCPICSSRVT--DNLIRHLNSQH 53 (54)
T ss_pred CcCCCCCCCc-cCHHHHHHHHHhHCcCC------------------------CCCccCCCchhhhh--hHHHHHHHHhc
Confidence 4789999994 556788888665 3322 12345666665433 37777876654
No 34
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=97.36 E-value=0.00014 Score=44.23 Aligned_cols=72 Identities=19% Similarity=0.329 Sum_probs=22.5
Q ss_pred ecccccccCCChHHHHHhHHhcCCCCccccCCCCCCCCCCCCCCCC--CCCCCcccccccccccCChhHHHHHHHHcc
Q 031430 33 ACKTCNKEFPSFQALGGHRASHKKPKLMTMASSGEDFDQTQMPPAS--PRKPKTHECSICGLEFAIGQALGGHMRRHR 108 (159)
Q Consensus 33 ~C~~C~~~f~~~~~l~~h~~~h~~~~~~~c~~c~~~f~~~~~l~~~--~~~~k~~~C~~Cgk~f~~~~~l~~H~~~h~ 108 (159)
.|..|+..|.....|..|+....+-..-.... +.....+... ......+.|..|++.|.+...|..|++.+.
T Consensus 1 ~C~~C~~~f~~~~~l~~H~~~~H~~~~~~~~~----l~~~~~~~~~~~~~~~~~~~C~~C~~~f~s~~~l~~Hm~~~~ 74 (100)
T PF12756_consen 1 QCLFCDESFSSVDDLLQHMKKKHGFDIPDQKY----LVDPNRLLNYLRKKVKESFRCPYCNKTFRSREALQEHMRSKH 74 (100)
T ss_dssp ----------------------------------------------------SSEEBSSSS-EESSHHHHHHHHHHTT
T ss_pred Cccccccccccccccccccccccccccccccc----cccccccccccccccCCCCCCCccCCCCcCHHHHHHHHcCcc
Confidence 48899999999999999986544321111100 1111111111 112336999999999999999999999754
No 35
>smart00355 ZnF_C2H2 zinc finger.
Probab=96.97 E-value=0.00081 Score=29.99 Aligned_cols=24 Identities=38% Similarity=0.681 Sum_probs=21.5
Q ss_pred eecccccccCCChHHHHHhHHhcC
Q 031430 32 FACKTCNKEFPSFQALGGHRASHK 55 (159)
Q Consensus 32 ~~C~~C~~~f~~~~~l~~h~~~h~ 55 (159)
|.|..|++.|.....|..|++.|.
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~~H~ 24 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMRTHX 24 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHHHhc
Confidence 579999999999999999998764
No 36
>PF09237 GAGA: GAGA factor; InterPro: IPR015318 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Members of this entry bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognises the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognises the A in the fourth position of the consensus sequence []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1YUI_A 1YUJ_A.
Probab=96.96 E-value=0.001 Score=35.02 Aligned_cols=35 Identities=17% Similarity=0.227 Sum_probs=24.6
Q ss_pred ccCCCceeecccccccCCChHHHHHhHHhcCCCCc
Q 031430 25 TDQGKRVFACKTCNKEFPSFQALGGHRASHKKPKL 59 (159)
Q Consensus 25 ~h~~~k~~~C~~C~~~f~~~~~l~~h~~~h~~~~~ 59 (159)
.+..+.|..|++|+..+.+..+|.+|+..+.+.+|
T Consensus 18 ~~~S~~PatCP~C~a~~~~srnLrRHle~~H~~k~ 52 (54)
T PF09237_consen 18 KSQSEQPATCPICGAVIRQSRNLRRHLEIRHFKKP 52 (54)
T ss_dssp CCTTS--EE-TTT--EESSHHHHHHHHHHHTTTS-
T ss_pred hhccCCCCCCCcchhhccchhhHHHHHHHHhcccC
Confidence 34567899999999999999999999988776654
No 37
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=96.90 E-value=0.0005 Score=30.84 Aligned_cols=23 Identities=30% Similarity=0.673 Sum_probs=20.8
Q ss_pred ccccccccccCChhHHHHHHHHc
Q 031430 85 HECSICGLEFAIGQALGGHMRRH 107 (159)
Q Consensus 85 ~~C~~Cgk~f~~~~~l~~H~~~h 107 (159)
|.|..|++.|.+...|..|++.+
T Consensus 1 ~~C~~C~~~f~s~~~~~~H~~s~ 23 (25)
T PF12874_consen 1 FYCDICNKSFSSENSLRQHLRSK 23 (25)
T ss_dssp EEETTTTEEESSHHHHHHHHTTH
T ss_pred CCCCCCCCCcCCHHHHHHHHCcC
Confidence 67999999999999999999754
No 38
>KOG3993 consensus Transcription factor (contains Zn finger) [Transcription]
Probab=96.82 E-value=0.00014 Score=54.61 Aligned_cols=85 Identities=13% Similarity=0.157 Sum_probs=50.0
Q ss_pred cccCCCCCCCCCCCCCCCCCC----CCCcccccccccccCChhHHHHHHHHcccccCCCccccCC--------------c
Q 031430 60 MTMASSGEDFDQTQMPPASPR----KPKTHECSICGLEFAIGQALGGHMRRHRAAAAMGAVADGL--------------V 121 (159)
Q Consensus 60 ~~c~~c~~~f~~~~~l~~~~~----~~k~~~C~~Cgk~f~~~~~l~~H~~~h~~~~~~~~~~~~~--------------~ 121 (159)
|.|..|...|.+.=.|. .|+ ....|+|++|+|.|+-..+|..|.|=|........+.... .
T Consensus 268 yiCqLCK~kYeD~F~LA-QHrC~RIV~vEYrCPEC~KVFsCPANLASHRRWHKPR~eaa~a~~~P~k~~~~~rae~~ea~ 346 (500)
T KOG3993|consen 268 YICQLCKEKYEDAFALA-QHRCPRIVHVEYRCPECDKVFSCPANLASHRRWHKPRPEAAKAGSPPPKQAVETRAEVQEAE 346 (500)
T ss_pred HHHHHHHHhhhhHHHHh-hccCCeeEEeeecCCcccccccCchhhhhhhcccCCchhhhhcCCCChhhhhhhhhhhhhcc
Confidence 56666666555432331 122 3456899999999999999999999886543222111000 0
Q ss_pred cCCCCCCcchhccCCCCceeeecc
Q 031430 122 TRPLLPLPVLKKSNSCKRVFCLDL 145 (159)
Q Consensus 122 ~~~~~~~~~~~~~~~~~~~~~~~~ 145 (159)
-.-.........|..|+|.|.-..
T Consensus 347 rsg~dss~gi~~C~~C~KkFrRqA 370 (500)
T KOG3993|consen 347 RSGDDSSSGIFSCHTCGKKFRRQA 370 (500)
T ss_pred ccCCcccCceeecHHhhhhhHHHH
Confidence 011223445788999999886543
No 39
>PRK04860 hypothetical protein; Provisional
Probab=96.80 E-value=0.0011 Score=44.18 Aligned_cols=36 Identities=17% Similarity=0.365 Sum_probs=27.3
Q ss_pred eeecccccccCCChHHHHHhHHhcCCCCccccCCCCCCCC
Q 031430 31 VFACKTCNKEFPSFQALGGHRASHKKPKLMTMASSGEDFD 70 (159)
Q Consensus 31 ~~~C~~C~~~f~~~~~l~~h~~~h~~~~~~~c~~c~~~f~ 70 (159)
+|.|. |+. ....+.+|.++|+++++|.|..|+..|.
T Consensus 119 ~Y~C~-C~~---~~~~~rrH~ri~~g~~~YrC~~C~~~l~ 154 (160)
T PRK04860 119 PYRCK-CQE---HQLTVRRHNRVVRGEAVYRCRRCGETLV 154 (160)
T ss_pred EEEcC-CCC---eeCHHHHHHHHhcCCccEECCCCCceeE
Confidence 67886 876 5566778888888888888888877664
No 40
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=96.49 E-value=0.0021 Score=28.46 Aligned_cols=23 Identities=26% Similarity=0.626 Sum_probs=18.5
Q ss_pred ccccccccccCChhHHHHHHHHcc
Q 031430 85 HECSICGLEFAIGQALGGHMRRHR 108 (159)
Q Consensus 85 ~~C~~Cgk~f~~~~~l~~H~~~h~ 108 (159)
|.|..|+.... ...|..|++.|.
T Consensus 1 y~C~~C~y~t~-~~~l~~H~~~~H 23 (24)
T PF13909_consen 1 YKCPHCSYSTS-KSNLKRHLKRHH 23 (24)
T ss_dssp EE-SSSS-EES-HHHHHHHHHHHH
T ss_pred CCCCCCCCcCC-HHHHHHHHHhhC
Confidence 68999999888 899999999865
No 41
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=96.24 E-value=0.0026 Score=28.41 Aligned_cols=23 Identities=43% Similarity=0.730 Sum_probs=20.6
Q ss_pred eecccccccCCChHHHHHhHHhc
Q 031430 32 FACKTCNKEFPSFQALGGHRASH 54 (159)
Q Consensus 32 ~~C~~C~~~f~~~~~l~~h~~~h 54 (159)
|.|.+|++.|.....|..|++.+
T Consensus 1 ~~C~~C~~~f~s~~~~~~H~~s~ 23 (25)
T PF12874_consen 1 FYCDICNKSFSSENSLRQHLRSK 23 (25)
T ss_dssp EEETTTTEEESSHHHHHHHHTTH
T ss_pred CCCCCCCCCcCCHHHHHHHHCcC
Confidence 67999999999999999998754
No 42
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=96.09 E-value=0.0059 Score=27.43 Aligned_cols=21 Identities=33% Similarity=0.632 Sum_probs=17.7
Q ss_pred ccccccccccCChhHHHHHHHH
Q 031430 85 HECSICGLEFAIGQALGGHMRR 106 (159)
Q Consensus 85 ~~C~~Cgk~f~~~~~l~~H~~~ 106 (159)
..|+.||+.| ....|..|+.+
T Consensus 3 ~~C~~CgR~F-~~~~l~~H~~~ 23 (25)
T PF13913_consen 3 VPCPICGRKF-NPDRLEKHEKI 23 (25)
T ss_pred CcCCCCCCEE-CHHHHHHHHHh
Confidence 4699999999 77889999865
No 43
>PF12171 zf-C2H2_jaz: Zinc-finger double-stranded RNA-binding; InterPro: IPR022755 This zinc finger is found in archaea and eukaryotes, and is approximately 30 amino acids in length. The mammalian members of this group occur multiple times along the protein, joined by flexible linkers, and are referred to as JAZ - dsRNA-binding ZF protein - zinc-fingers. The JAZ proteins are expressed in all tissues tested and localise in the nucleus, particularly the nucleolus []. JAZ preferentially binds to double-stranded (ds) RNA or RNA/DNA hybrids rather than DNA. In addition to binding double-stranded RNA, these zinc-fingers are required for nucleolar localisation. This entry represents the multiple-adjacent-C2H2 zinc finger, JAZ. ; PDB: 4DGW_A 1ZR9_A.
Probab=95.89 E-value=0.0022 Score=29.34 Aligned_cols=22 Identities=27% Similarity=0.545 Sum_probs=19.7
Q ss_pred ccccccccccCChhHHHHHHHH
Q 031430 85 HECSICGLEFAIGQALGGHMRR 106 (159)
Q Consensus 85 ~~C~~Cgk~f~~~~~l~~H~~~ 106 (159)
|-|..|++.|.+...+..|++.
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 6799999999999999998764
No 44
>PF12171 zf-C2H2_jaz: Zinc-finger double-stranded RNA-binding; InterPro: IPR022755 This zinc finger is found in archaea and eukaryotes, and is approximately 30 amino acids in length. The mammalian members of this group occur multiple times along the protein, joined by flexible linkers, and are referred to as JAZ - dsRNA-binding ZF protein - zinc-fingers. The JAZ proteins are expressed in all tissues tested and localise in the nucleus, particularly the nucleolus []. JAZ preferentially binds to double-stranded (ds) RNA or RNA/DNA hybrids rather than DNA. In addition to binding double-stranded RNA, these zinc-fingers are required for nucleolar localisation. This entry represents the multiple-adjacent-C2H2 zinc finger, JAZ. ; PDB: 4DGW_A 1ZR9_A.
Probab=95.34 E-value=0.0063 Score=27.77 Aligned_cols=22 Identities=41% Similarity=0.694 Sum_probs=19.5
Q ss_pred eecccccccCCChHHHHHhHHh
Q 031430 32 FACKTCNKEFPSFQALGGHRAS 53 (159)
Q Consensus 32 ~~C~~C~~~f~~~~~l~~h~~~ 53 (159)
|.|..|++.|.....+..|++.
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 6799999999999999988754
No 45
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=95.32 E-value=0.018 Score=49.38 Aligned_cols=81 Identities=17% Similarity=0.251 Sum_probs=54.2
Q ss_pred ccCCCceeecccccccCCChHHHHHhHHhcCCC-CccccCCCCCCCCCCCCCCCCCCCCCcccccccccccCChhHHHHH
Q 031430 25 TDQGKRVFACKTCNKEFPSFQALGGHRASHKKP-KLMTMASSGEDFDQTQMPPASPRKPKTHECSICGLEFAIGQALGGH 103 (159)
Q Consensus 25 ~h~~~k~~~C~~C~~~f~~~~~l~~h~~~h~~~-~~~~c~~c~~~f~~~~~l~~~~~~~k~~~C~~Cgk~f~~~~~l~~H 103 (159)
.|+-.+.|.|+.|+..|.....|..|+|..+-+ ..-.|.. ++.-.........-.+.++|.|..|..++..+..|.+|
T Consensus 459 L~S~~kt~~cpkc~~~yk~a~~L~vhmRskhp~~~~~~c~~-gq~~~~~arg~~~~~~~~p~~C~~C~~stttng~Lsih 537 (1406)
T KOG1146|consen 459 LHSFFKTLKCPKCNWHYKLAQTLGVHMRSKHPESQSAYCKA-GQNHPRLARGEVYRCPGKPYPCRACNYSTTTNGNLSIH 537 (1406)
T ss_pred eecccccccCCccchhhhhHHHhhhcccccccccchhHhHh-ccccccccccccccCCCCcccceeeeeeeecchHHHHH
Confidence 455568899999999999999999999873321 1111211 11111111111112257899999999999999999999
Q ss_pred HHH
Q 031430 104 MRR 106 (159)
Q Consensus 104 ~~~ 106 (159)
+..
T Consensus 538 lqS 540 (1406)
T KOG1146|consen 538 LQS 540 (1406)
T ss_pred HHH
Confidence 874
No 46
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=95.00 E-value=0.017 Score=25.40 Aligned_cols=23 Identities=22% Similarity=0.469 Sum_probs=17.7
Q ss_pred eecccccccCCChHHHHHhHHhcC
Q 031430 32 FACKTCNKEFPSFQALGGHRASHK 55 (159)
Q Consensus 32 ~~C~~C~~~f~~~~~l~~h~~~h~ 55 (159)
|.|+.|+.... ...|..|++.+.
T Consensus 1 y~C~~C~y~t~-~~~l~~H~~~~H 23 (24)
T PF13909_consen 1 YKCPHCSYSTS-KSNLKRHLKRHH 23 (24)
T ss_dssp EE-SSSS-EES-HHHHHHHHHHHH
T ss_pred CCCCCCCCcCC-HHHHHHHHHhhC
Confidence 78999998887 889999988753
No 47
>PRK04860 hypothetical protein; Provisional
Probab=94.81 E-value=0.034 Score=37.14 Aligned_cols=35 Identities=20% Similarity=0.188 Sum_probs=27.9
Q ss_pred CCcccccccccccCChhHHHHHHHHcccccCCCccccCC
Q 031430 82 PKTHECSICGLEFAIGQALGGHMRRHRAAAAMGAVADGL 120 (159)
Q Consensus 82 ~k~~~C~~Cgk~f~~~~~l~~H~~~h~~~~~~~~~~~~~ 120 (159)
.-+|.|. |+. ....+.+|.++|.++++|.|..|..
T Consensus 117 ~~~Y~C~-C~~---~~~~~rrH~ri~~g~~~YrC~~C~~ 151 (160)
T PRK04860 117 TFPYRCK-CQE---HQLTVRRHNRVVRGEAVYRCRRCGE 151 (160)
T ss_pred EEEEEcC-CCC---eeCHHHHHHHHhcCCccEECCCCCc
Confidence 3579998 998 6778899999999999996644433
No 48
>smart00451 ZnF_U1 U1-like zinc finger. Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins.
Probab=94.72 E-value=0.025 Score=27.31 Aligned_cols=23 Identities=17% Similarity=0.556 Sum_probs=20.3
Q ss_pred cccccccccccCChhHHHHHHHH
Q 031430 84 THECSICGLEFAIGQALGGHMRR 106 (159)
Q Consensus 84 ~~~C~~Cgk~f~~~~~l~~H~~~ 106 (159)
+|.|..|++.|.....+..|+..
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~g 25 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLKG 25 (35)
T ss_pred CeEccccCCccCCHHHHHHHHCh
Confidence 57899999999999999999864
No 49
>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=93.62 E-value=0.09 Score=28.26 Aligned_cols=35 Identities=20% Similarity=0.322 Sum_probs=23.6
Q ss_pred cccccccccccCChhHHHHHHHH-cccc-cCCCccccC
Q 031430 84 THECSICGLEFAIGQALGGHMRR-HRAA-AAMGAVADG 119 (159)
Q Consensus 84 ~~~C~~Cgk~f~~~~~l~~H~~~-h~~~-~~~~~~~~~ 119 (159)
.|.|+.||+. .+...|..|... |..+ +.+.|..+.
T Consensus 2 ~f~CP~C~~~-~~~~~L~~H~~~~H~~~~~~v~CPiC~ 38 (54)
T PF05605_consen 2 SFTCPYCGKG-FSESSLVEHCEDEHRSESKNVVCPICS 38 (54)
T ss_pred CcCCCCCCCc-cCHHHHHHHHHhHCcCCCCCccCCCch
Confidence 4899999995 556789999765 5543 344454443
No 50
>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=93.08 E-value=0.098 Score=25.11 Aligned_cols=23 Identities=30% Similarity=0.531 Sum_probs=19.8
Q ss_pred eeecccccccCCChHHHHHhHHh
Q 031430 31 VFACKTCNKEFPSFQALGGHRAS 53 (159)
Q Consensus 31 ~~~C~~C~~~f~~~~~l~~h~~~ 53 (159)
+|.|++|+..|.....+..|+..
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~g 25 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLKG 25 (35)
T ss_pred CeEccccCCccCCHHHHHHHHCh
Confidence 58899999999999988888754
No 51
>KOG2893 consensus Zn finger protein [General function prediction only]
Probab=92.72 E-value=0.015 Score=40.87 Aligned_cols=45 Identities=27% Similarity=0.459 Sum_probs=20.8
Q ss_pred cCCCCCCCCCCCCCCCCCCCCCcccccccccccCChhHHHHH-HHHc
Q 031430 62 MASSGEDFDQTQMPPASPRKPKTHECSICGLEFAIGQALGGH-MRRH 107 (159)
Q Consensus 62 c~~c~~~f~~~~~l~~~~~~~k~~~C~~Cgk~f~~~~~l~~H-~~~h 107 (159)
|..|++.|.+..-|+ .|..-|.|+|.+|-|...+...|..| +++|
T Consensus 13 cwycnrefddekili-qhqkakhfkchichkkl~sgpglsihcmqvh 58 (341)
T KOG2893|consen 13 CWYCNREFDDEKILI-QHQKAKHFKCHICHKKLFSGPGLSIHCMQVH 58 (341)
T ss_pred eeecccccchhhhhh-hhhhhccceeeeehhhhccCCCceeehhhhh
Confidence 444555554443332 23334455555555544444444444 3444
No 52
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=92.45 E-value=0.14 Score=37.68 Aligned_cols=62 Identities=13% Similarity=0.213 Sum_probs=39.0
Q ss_pred CCCcccccc--cccccCChhHHHHHHH-HcccccCCCccccCCccCCCCCCcchhccCCCCceeee
Q 031430 81 KPKTHECSI--CGLEFAIGQALGGHMR-RHRAAAAMGAVADGLVTRPLLPLPVLKKSNSCKRVFCL 143 (159)
Q Consensus 81 ~~k~~~C~~--Cgk~f~~~~~l~~H~~-~h~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 143 (159)
++|||.|++ |+|.|.+...|+.|+. -|...+.....+..+- ..+......+.|.-|+|.+..
T Consensus 346 d~KpykCpV~gC~K~YknqnGLKYH~lhGH~~~~~~~~p~p~~~-~~F~~~~KPYrCevC~KRYKN 410 (423)
T COG5189 346 DGKPYKCPVEGCNKKYKNQNGLKYHMLHGHQNQKLHENPSPEKM-NIFSAKDKPYRCEVCDKRYKN 410 (423)
T ss_pred cCceecCCCCCchhhhccccchhhhhhccccCcccCCCCCcccc-ccccccCCceeccccchhhcc
Confidence 359999998 9999999999999985 3433332222111111 112223355688888888763
No 53
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=89.74 E-value=0.24 Score=32.86 Aligned_cols=12 Identities=42% Similarity=1.005 Sum_probs=5.8
Q ss_pred ccccccccccCC
Q 031430 85 HECSICGLEFAI 96 (159)
Q Consensus 85 ~~C~~Cgk~f~~ 96 (159)
+.|+.||++|..
T Consensus 29 ~~c~~c~~~f~~ 40 (154)
T PRK00464 29 RECLACGKRFTT 40 (154)
T ss_pred eeccccCCcceE
Confidence 445555554443
No 54
>PF09538 FYDLN_acid: Protein of unknown function (FYDLN_acid); InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=89.71 E-value=0.3 Score=30.40 Aligned_cols=31 Identities=29% Similarity=0.443 Sum_probs=22.2
Q ss_pred ccccCCCCCCCCCCCCCCCCCCCCCcccccccccccCCh
Q 031430 59 LMTMASSGEDFDQTQMPPASPRKPKTHECSICGLEFAIG 97 (159)
Q Consensus 59 ~~~c~~c~~~f~~~~~l~~~~~~~k~~~C~~Cgk~f~~~ 97 (159)
...|+.||..|.. | +..|..|+.||..|.-.
T Consensus 9 KR~Cp~CG~kFYD---L-----nk~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 9 KRTCPSCGAKFYD---L-----NKDPIVCPKCGTEFPPE 39 (108)
T ss_pred cccCCCCcchhcc---C-----CCCCccCCCCCCccCcc
Confidence 3568888888763 2 12577899999888765
No 55
>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=89.68 E-value=0.24 Score=23.69 Aligned_cols=10 Identities=30% Similarity=0.963 Sum_probs=5.8
Q ss_pred Cccccccccc
Q 031430 83 KTHECSICGL 92 (159)
Q Consensus 83 k~~~C~~Cgk 92 (159)
.++.|++||.
T Consensus 16 ~~~~CP~Cg~ 25 (33)
T cd00350 16 APWVCPVCGA 25 (33)
T ss_pred CCCcCcCCCC
Confidence 4556666653
No 56
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=88.41 E-value=0.45 Score=28.47 Aligned_cols=24 Identities=46% Similarity=0.704 Sum_probs=21.4
Q ss_pred eeecccccccCCChHHHHHhHHhc
Q 031430 31 VFACKTCNKEFPSFQALGGHRASH 54 (159)
Q Consensus 31 ~~~C~~C~~~f~~~~~l~~h~~~h 54 (159)
.+.|..|++.|.....|..|++.+
T Consensus 50 ~~~C~~C~~~f~s~~~l~~Hm~~~ 73 (100)
T PF12756_consen 50 SFRCPYCNKTFRSREALQEHMRSK 73 (100)
T ss_dssp SEEBSSSS-EESSHHHHHHHHHHT
T ss_pred CCCCCccCCCCcCHHHHHHHHcCc
Confidence 689999999999999999999875
No 57
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=88.40 E-value=0.48 Score=33.25 Aligned_cols=17 Identities=29% Similarity=0.761 Sum_probs=11.7
Q ss_pred CceeecccccccCCChH
Q 031430 29 KRVFACKTCNKEFPSFQ 45 (159)
Q Consensus 29 ~k~~~C~~C~~~f~~~~ 45 (159)
++...|++|++.|....
T Consensus 3 ~k~~~CPvC~~~F~~~~ 19 (214)
T PF09986_consen 3 DKKITCPVCGKEFKTKK 19 (214)
T ss_pred CCceECCCCCCeeeeeE
Confidence 35567888888876553
No 58
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=88.30 E-value=1.4 Score=27.48 Aligned_cols=77 Identities=14% Similarity=0.210 Sum_probs=49.4
Q ss_pred ceeecccccccCCChHHHHHhHHhcC-------CCC-------ccccCCCCCCCCCCCCCC-CCCCCCCccccccccccc
Q 031430 30 RVFACKTCNKEFPSFQALGGHRASHK-------KPK-------LMTMASSGEDFDQTQMPP-ASPRKPKTHECSICGLEF 94 (159)
Q Consensus 30 k~~~C~~C~~~f~~~~~l~~h~~~h~-------~~~-------~~~c~~c~~~f~~~~~l~-~~~~~~k~~~C~~Cgk~f 94 (159)
-|..|+.|+-..-...+|.+. .|. .+. ...|..|...|....... ..-.....|+|+.|...|
T Consensus 14 LP~~CpiCgLtLVss~HLARS--yHHLfPl~~f~ev~~~~~~~~~~C~~C~~~f~~~~~~~~~~~~~~~~y~C~~C~~~F 91 (112)
T TIGR00622 14 LPVECPICGLTLILSTHLARS--YHHLFPLKAFQEIPLEEYNGSRFCFGCQGPFPKPPVSPFDELKDSHRYVCAVCKNVF 91 (112)
T ss_pred CCCcCCcCCCEEeccchHHHh--hhccCCCcccccccccccCCCCcccCcCCCCCCcccccccccccccceeCCCCCCcc
Confidence 467899999888877777753 111 011 123777888776532211 001234568999999999
Q ss_pred CChhHHHHHHHHcc
Q 031430 95 AIGQALGGHMRRHR 108 (159)
Q Consensus 95 ~~~~~l~~H~~~h~ 108 (159)
-..-..-.|...|.
T Consensus 92 C~dCD~fiHe~Lh~ 105 (112)
T TIGR00622 92 CVDCDVFVHESLHC 105 (112)
T ss_pred ccccchhhhhhccC
Confidence 98887777877665
No 59
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=87.83 E-value=0.29 Score=26.33 Aligned_cols=30 Identities=17% Similarity=0.359 Sum_probs=25.9
Q ss_pred cccCCCceeecccccccCCChHHHHHhHHh
Q 031430 24 ETDQGKRVFACKTCNKEFPSFQALGGHRAS 53 (159)
Q Consensus 24 ~~h~~~k~~~C~~C~~~f~~~~~l~~h~~~ 53 (159)
++..||..+.|+-|+..|.....+.+|+..
T Consensus 10 ~~RDGE~~lrCPRC~~~FR~~K~Y~RHVNK 39 (65)
T COG4049 10 RDRDGEEFLRCPRCGMVFRRRKDYIRHVNK 39 (65)
T ss_pred eccCCceeeeCCchhHHHHHhHHHHHHhhH
Confidence 456788899999999999999999999764
No 60
>PF10571 UPF0547: Uncharacterised protein family UPF0547; InterPro: IPR018886 This domain may well be a type of zinc-finger as it carries two pairs of highly conserved cysteine residues though with no accompanying histidines. Several members are annotated as putative helicases.
Probab=87.71 E-value=0.5 Score=21.32 Aligned_cols=10 Identities=40% Similarity=1.119 Sum_probs=6.1
Q ss_pred cccccccccC
Q 031430 86 ECSICGLEFA 95 (159)
Q Consensus 86 ~C~~Cgk~f~ 95 (159)
.|+.||..|.
T Consensus 16 ~Cp~CG~~F~ 25 (26)
T PF10571_consen 16 FCPHCGYDFE 25 (26)
T ss_pred cCCCCCCCCc
Confidence 4666766663
No 61
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=86.59 E-value=0.38 Score=36.59 Aligned_cols=51 Identities=22% Similarity=0.268 Sum_probs=28.7
Q ss_pred chHHHHHHHHhhcc--ccCCC--ceeecc--cccccCCChHHHHHhHHhcCCCCccc
Q 031430 11 DTANCLMLLSKVGE--TDQGK--RVFACK--TCNKEFPSFQALGGHRASHKKPKLMT 61 (159)
Q Consensus 11 ~~~~~~~~l~~h~~--~h~~~--k~~~C~--~C~~~f~~~~~l~~h~~~h~~~~~~~ 61 (159)
..|.....|..|.+ .|.++ +++.|+ .|++.|.....+..|...|.+..+..
T Consensus 297 ~~~s~~~~l~~~~~~~~h~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 (467)
T COG5048 297 ISFSRSSPLTRHLRSVNHSGESLKPFSCPYSLCGKLFSRNDALKRHILLHTSISPAK 353 (467)
T ss_pred CCccccccccccccccccccccCCceeeeccCCCccccccccccCCcccccCCCccc
Confidence 34444445555555 56666 666666 46666666666666665555544443
No 62
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=85.62 E-value=0.38 Score=25.88 Aligned_cols=28 Identities=18% Similarity=0.388 Sum_probs=23.5
Q ss_pred CCCCCcccccccccccCChhHHHHHHHH
Q 031430 79 PRKPKTHECSICGLEFAIGQALGGHMRR 106 (159)
Q Consensus 79 ~~~~k~~~C~~Cgk~f~~~~~l~~H~~~ 106 (159)
..|+.-+.|+-||..|.....+.+|.-.
T Consensus 12 RDGE~~lrCPRC~~~FR~~K~Y~RHVNK 39 (65)
T COG4049 12 RDGEEFLRCPRCGMVFRRRKDYIRHVNK 39 (65)
T ss_pred cCCceeeeCCchhHHHHHhHHHHHHhhH
Confidence 3467888999999999999999999753
No 63
>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=85.11 E-value=1.6 Score=29.12 Aligned_cols=42 Identities=19% Similarity=0.219 Sum_probs=26.2
Q ss_pred HHhhccccCCCceeecccccccCCChHHHHHhHHhcCCCCccccCCCCCCC
Q 031430 19 LSKVGETDQGKRVFACKTCNKEFPSFQALGGHRASHKKPKLMTMASSGEDF 69 (159)
Q Consensus 19 l~~h~~~h~~~k~~~C~~C~~~f~~~~~l~~h~~~h~~~~~~~c~~c~~~f 69 (159)
|+.-..-..+..-|.|+.|+..|.....+. ..|.|+.||...
T Consensus 97 lk~~l~~e~~~~~Y~Cp~c~~r~tf~eA~~---------~~F~Cp~Cg~~L 138 (158)
T TIGR00373 97 LREKLEFETNNMFFICPNMCVRFTFNEAME---------LNFTCPRCGAML 138 (158)
T ss_pred HHHHHhhccCCCeEECCCCCcEeeHHHHHH---------cCCcCCCCCCEe
Confidence 333444445556678888887777666653 257777777643
No 64
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=84.97 E-value=0.2 Score=35.10 Aligned_cols=41 Identities=17% Similarity=0.272 Sum_probs=26.3
Q ss_pred CCccccCCCCCCCCCCC----CCC---------CCCCCCCc-----ccccccccccCCh
Q 031430 57 PKLMTMASSGEDFDQTQ----MPP---------ASPRKPKT-----HECSICGLEFAIG 97 (159)
Q Consensus 57 ~~~~~c~~c~~~f~~~~----~l~---------~~~~~~k~-----~~C~~Cgk~f~~~ 97 (159)
++...|+.|++.|.... .+. ....+..| ..|+.||.+|...
T Consensus 3 ~k~~~CPvC~~~F~~~~vrs~~~r~~~~d~D~~~~Y~~vnP~~Y~V~vCP~CgyA~~~~ 61 (214)
T PF09986_consen 3 DKKITCPVCGKEFKTKKVRSGKIRVIRRDSDFCPRYKGVNPLFYEVWVCPHCGYAAFEE 61 (214)
T ss_pred CCceECCCCCCeeeeeEEEcCCceEeeecCCCccccCCCCCeeeeEEECCCCCCccccc
Confidence 46678999999998721 111 11223334 5899999887654
No 65
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=84.89 E-value=1.6 Score=29.74 Aligned_cols=42 Identities=21% Similarity=0.348 Sum_probs=25.2
Q ss_pred HHhhccccCCCceeecccccccCCChHHHHHhHHhcCCCCccccCCCCCCC
Q 031430 19 LSKVGETDQGKRVFACKTCNKEFPSFQALGGHRASHKKPKLMTMASSGEDF 69 (159)
Q Consensus 19 l~~h~~~h~~~k~~~C~~C~~~f~~~~~l~~h~~~h~~~~~~~c~~c~~~f 69 (159)
|+.-..--....-|.|+.|+..|.....+. ..|.|+.||...
T Consensus 105 lk~~l~~e~~~~~Y~Cp~C~~rytf~eA~~---------~~F~Cp~Cg~~L 146 (178)
T PRK06266 105 LKEQLEEEENNMFFFCPNCHIRFTFDEAME---------YGFRCPQCGEML 146 (178)
T ss_pred HHHHhhhccCCCEEECCCCCcEEeHHHHhh---------cCCcCCCCCCCC
Confidence 333333334455678888887776665542 357777777654
No 66
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=84.22 E-value=0.85 Score=22.40 Aligned_cols=12 Identities=25% Similarity=0.722 Sum_probs=6.3
Q ss_pred ecccccccCCCh
Q 031430 33 ACKTCNKEFPSF 44 (159)
Q Consensus 33 ~C~~C~~~f~~~ 44 (159)
.|+.|+..|.-.
T Consensus 4 ~CP~C~~~f~v~ 15 (37)
T PF13719_consen 4 TCPNCQTRFRVP 15 (37)
T ss_pred ECCCCCceEEcC
Confidence 455555555433
No 67
>smart00614 ZnF_BED BED zinc finger. DNA-binding domain in chromatin-boundary-element-binding proteins and transposases
Probab=83.91 E-value=0.97 Score=23.75 Aligned_cols=24 Identities=29% Similarity=0.733 Sum_probs=17.2
Q ss_pred ccccccccccCCh-----hHHHHHHH-Hcc
Q 031430 85 HECSICGLEFAIG-----QALGGHMR-RHR 108 (159)
Q Consensus 85 ~~C~~Cgk~f~~~-----~~l~~H~~-~h~ 108 (159)
-.|..|++.+... ++|.+|++ .|.
T Consensus 19 a~C~~C~~~l~~~~~~gTs~L~rHl~~~h~ 48 (50)
T smart00614 19 AKCKYCGKKLSRSSKGGTSNLRRHLRRKHP 48 (50)
T ss_pred EEecCCCCEeeeCCCCCcHHHHHHHHhHCc
Confidence 4577777777554 68999998 554
No 68
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=83.80 E-value=1.3 Score=21.62 Aligned_cols=13 Identities=15% Similarity=0.621 Sum_probs=6.6
Q ss_pred ecccccccCCChH
Q 031430 33 ACKTCNKEFPSFQ 45 (159)
Q Consensus 33 ~C~~C~~~f~~~~ 45 (159)
.|+.|+..|.-..
T Consensus 4 ~Cp~C~~~y~i~d 16 (36)
T PF13717_consen 4 TCPNCQAKYEIDD 16 (36)
T ss_pred ECCCCCCEEeCCH
Confidence 4555555554433
No 69
>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=83.49 E-value=0.83 Score=22.37 Aligned_cols=13 Identities=23% Similarity=0.769 Sum_probs=6.8
Q ss_pred eecccccccCCCh
Q 031430 32 FACKTCNKEFPSF 44 (159)
Q Consensus 32 ~~C~~C~~~f~~~ 44 (159)
+.|+.|+..|.-.
T Consensus 3 ~~CP~C~~~~~v~ 15 (38)
T TIGR02098 3 IQCPNCKTSFRVV 15 (38)
T ss_pred EECCCCCCEEEeC
Confidence 4555565555443
No 70
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=83.38 E-value=4 Score=25.55 Aligned_cols=18 Identities=33% Similarity=0.654 Sum_probs=12.2
Q ss_pred cchhccCCCCceeeeccC
Q 031430 129 PVLKKSNSCKRVFCLDLN 146 (159)
Q Consensus 129 ~~~~~~~~~~~~~~~~~~ 146 (159)
...+.|..|...|-.|-.
T Consensus 79 ~~~y~C~~C~~~FC~dCD 96 (112)
T TIGR00622 79 SHRYVCAVCKNVFCVDCD 96 (112)
T ss_pred ccceeCCCCCCccccccc
Confidence 345678888888876654
No 71
>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=83.08 E-value=0.43 Score=24.19 Aligned_cols=10 Identities=40% Similarity=1.338 Sum_probs=4.9
Q ss_pred eecccccccC
Q 031430 32 FACKTCNKEF 41 (159)
Q Consensus 32 ~~C~~C~~~f 41 (159)
|.|..||..|
T Consensus 6 y~C~~Cg~~f 15 (42)
T PF09723_consen 6 YRCEECGHEF 15 (42)
T ss_pred EEeCCCCCEE
Confidence 4455555444
No 72
>TIGR02300 FYDLN_acid conserved hypothetical protein TIGR02300. Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=82.47 E-value=1.3 Score=28.21 Aligned_cols=34 Identities=18% Similarity=0.240 Sum_probs=22.3
Q ss_pred ccccCCCCCCCCCCCCCCCCCCCCCcccccccccccCChhHH
Q 031430 59 LMTMASSGEDFDQTQMPPASPRKPKTHECSICGLEFAIGQAL 100 (159)
Q Consensus 59 ~~~c~~c~~~f~~~~~l~~~~~~~k~~~C~~Cgk~f~~~~~l 100 (159)
...|+.||+.|.. | +..|..|+.||..|.-...+
T Consensus 9 Kr~Cp~cg~kFYD---L-----nk~p~vcP~cg~~~~~~~~~ 42 (129)
T TIGR02300 9 KRICPNTGSKFYD---L-----NRRPAVSPYTGEQFPPEEAL 42 (129)
T ss_pred cccCCCcCccccc---c-----CCCCccCCCcCCccCcchhh
Confidence 3568888887753 2 23577888888887655333
No 73
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=82.46 E-value=2.4 Score=27.89 Aligned_cols=39 Identities=15% Similarity=0.354 Sum_probs=21.9
Q ss_pred CCCceeecccccccCCChHHHHHhHHhcCCCCccccCCCCCCC
Q 031430 27 QGKRVFACKTCNKEFPSFQALGGHRASHKKPKLMTMASSGEDF 69 (159)
Q Consensus 27 ~~~k~~~C~~C~~~f~~~~~l~~h~~~h~~~~~~~c~~c~~~f 69 (159)
.+..-|.|+.|+..|.....+.. .. ....|.|+.||...
T Consensus 95 ~~~~~Y~Cp~C~~~y~~~ea~~~---~d-~~~~f~Cp~Cg~~l 133 (147)
T smart00531 95 TNNAYYKCPNCQSKYTFLEANQL---LD-MDGTFTCPRCGEEL 133 (147)
T ss_pred cCCcEEECcCCCCEeeHHHHHHh---cC-CCCcEECCCCCCEE
Confidence 44556788888877765443321 01 12337777777643
No 74
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=82.08 E-value=1 Score=30.26 Aligned_cols=24 Identities=25% Similarity=0.519 Sum_probs=17.1
Q ss_pred CccccCCCCCCCCCCCCCCCCCCCCCcccccccc
Q 031430 58 KLMTMASSGEDFDQTQMPPASPRKPKTHECSICG 91 (159)
Q Consensus 58 ~~~~c~~c~~~f~~~~~l~~~~~~~k~~~C~~Cg 91 (159)
+.|.|..||.++ .++-|..|++||
T Consensus 133 ~~~vC~vCGy~~----------~ge~P~~CPiCg 156 (166)
T COG1592 133 KVWVCPVCGYTH----------EGEAPEVCPICG 156 (166)
T ss_pred CEEEcCCCCCcc----------cCCCCCcCCCCC
Confidence 368888887653 346777888888
No 75
>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=81.73 E-value=0.62 Score=23.14 Aligned_cols=10 Identities=30% Similarity=1.218 Sum_probs=4.7
Q ss_pred eecccccccC
Q 031430 32 FACKTCNKEF 41 (159)
Q Consensus 32 ~~C~~C~~~f 41 (159)
|.|..||..|
T Consensus 6 y~C~~Cg~~f 15 (41)
T smart00834 6 YRCEDCGHTF 15 (41)
T ss_pred EEcCCCCCEE
Confidence 4444454444
No 76
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=81.73 E-value=0.96 Score=23.30 Aligned_cols=10 Identities=30% Similarity=1.129 Sum_probs=4.5
Q ss_pred eecccccccC
Q 031430 32 FACKTCNKEF 41 (159)
Q Consensus 32 ~~C~~C~~~f 41 (159)
|.|+.||..|
T Consensus 4 y~C~~CG~~~ 13 (46)
T PRK00398 4 YKCARCGREV 13 (46)
T ss_pred EECCCCCCEE
Confidence 4444444443
No 77
>KOG2186 consensus Cell growth-regulating nucleolar protein [Cell cycle control, cell division, chromosome partitioning]
Probab=81.15 E-value=0.48 Score=33.79 Aligned_cols=25 Identities=20% Similarity=0.361 Sum_probs=12.3
Q ss_pred cccccccccccCChhHHHHHHHHccc
Q 031430 84 THECSICGLEFAIGQALGGHMRRHRA 109 (159)
Q Consensus 84 ~~~C~~Cgk~f~~~~~l~~H~~~h~~ 109 (159)
-|.|-.||+.|-. ..+..|...-++
T Consensus 29 ~fSCIDC~k~F~~-~sYknH~kCITE 53 (276)
T KOG2186|consen 29 YFSCIDCGKTFER-VSYKNHTKCITE 53 (276)
T ss_pred eeEEeeccccccc-chhhhhhhhcch
Confidence 3555555555554 344555544433
No 78
>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=81.11 E-value=0.7 Score=24.41 Aligned_cols=11 Identities=27% Similarity=1.093 Sum_probs=6.1
Q ss_pred eecccccccCC
Q 031430 32 FACKTCNKEFP 42 (159)
Q Consensus 32 ~~C~~C~~~f~ 42 (159)
|.|..||..|.
T Consensus 6 y~C~~Cg~~fe 16 (52)
T TIGR02605 6 YRCTACGHRFE 16 (52)
T ss_pred EEeCCCCCEeE
Confidence 55555655554
No 79
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=81.08 E-value=1.1 Score=34.06 Aligned_cols=46 Identities=22% Similarity=0.301 Sum_probs=32.2
Q ss_pred ceeecccccccCCChHHHHHhHH--hcCCC--CccccC--CCCCCCCCCCCC
Q 031430 30 RVFACKTCNKEFPSFQALGGHRA--SHKKP--KLMTMA--SSGEDFDQTQMP 75 (159)
Q Consensus 30 k~~~C~~C~~~f~~~~~l~~h~~--~h~~~--~~~~c~--~c~~~f~~~~~l 75 (159)
.++.|..|...|.....|..|.+ .|.++ +++.|. .|++.|.....+
T Consensus 288 ~~~~~~~~~~~~s~~~~l~~~~~~~~h~~~~~~~~~~p~~~~~~~~~~~~~~ 339 (467)
T COG5048 288 LPIKSKQCNISFSRSSPLTRHLRSVNHSGESLKPFSCPYSLCGKLFSRNDAL 339 (467)
T ss_pred cCCCCccccCCccccccccccccccccccccCCceeeeccCCCccccccccc
Confidence 35677777777777777777777 67777 777777 577776664443
No 80
>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=80.98 E-value=1.1 Score=21.59 Aligned_cols=10 Identities=40% Similarity=1.135 Sum_probs=5.5
Q ss_pred Cccccccccc
Q 031430 83 KTHECSICGL 92 (159)
Q Consensus 83 k~~~C~~Cgk 92 (159)
.|..|+.||.
T Consensus 17 ~p~~CP~Cg~ 26 (34)
T cd00729 17 APEKCPICGA 26 (34)
T ss_pred CCCcCcCCCC
Confidence 3446666663
No 81
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=80.85 E-value=0.96 Score=29.73 Aligned_cols=38 Identities=13% Similarity=0.228 Sum_probs=24.2
Q ss_pred CCCccccCCCCCCCCCCCCCCCCCCCCCccccccccccc
Q 031430 56 KPKLMTMASSGEDFDQTQMPPASPRKPKTHECSICGLEF 94 (159)
Q Consensus 56 ~~~~~~c~~c~~~f~~~~~l~~~~~~~k~~~C~~Cgk~f 94 (159)
+...|.|+.|+..|.....+..... ...|.|+.||...
T Consensus 96 ~~~~Y~Cp~C~~~y~~~ea~~~~d~-~~~f~Cp~Cg~~l 133 (147)
T smart00531 96 NNAYYKCPNCQSKYTFLEANQLLDM-DGTFTCPRCGEEL 133 (147)
T ss_pred CCcEEECcCCCCEeeHHHHHHhcCC-CCcEECCCCCCEE
Confidence 4457899999988875322211111 3449999999765
No 82
>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=79.92 E-value=1.6 Score=22.13 Aligned_cols=25 Identities=24% Similarity=0.543 Sum_probs=15.9
Q ss_pred CCCcccccccccccCC----hhHHHHHHH
Q 031430 81 KPKTHECSICGLEFAI----GQALGGHMR 105 (159)
Q Consensus 81 ~~k~~~C~~Cgk~f~~----~~~l~~H~~ 105 (159)
+.....|..|++.+.. .+.|.+|++
T Consensus 13 ~~~~a~C~~C~~~~~~~~~~ts~l~~HL~ 41 (45)
T PF02892_consen 13 DKKKAKCKYCGKVIKYSSGGTSNLKRHLK 41 (45)
T ss_dssp CSS-EEETTTTEE-----SSTHHHHHHHH
T ss_pred CcCeEEeCCCCeEEeeCCCcHHHHHHhhh
Confidence 3455688889988766 478999984
No 83
>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=78.86 E-value=0.39 Score=22.07 Aligned_cols=21 Identities=24% Similarity=0.518 Sum_probs=11.7
Q ss_pred ccccccccccCChhHHHHHHHH
Q 031430 85 HECSICGLEFAIGQALGGHMRR 106 (159)
Q Consensus 85 ~~C~~Cgk~f~~~~~l~~H~~~ 106 (159)
|.|-.|++.| .....+.|..-
T Consensus 1 ~sCiDC~~~F-~~~~y~~Ht~C 21 (28)
T PF08790_consen 1 FSCIDCSKDF-DGDSYKSHTSC 21 (28)
T ss_dssp EEETTTTEEE-EGGGTTT----
T ss_pred CeeecCCCCc-CcCCcCCCCcc
Confidence 5688888888 44455555543
No 84
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=78.04 E-value=1.9 Score=22.14 Aligned_cols=11 Identities=27% Similarity=0.884 Sum_probs=5.6
Q ss_pred eecccccccCC
Q 031430 32 FACKTCNKEFP 42 (159)
Q Consensus 32 ~~C~~C~~~f~ 42 (159)
|.|..||..|.
T Consensus 3 Y~C~~Cg~~~~ 13 (44)
T smart00659 3 YICGECGRENE 13 (44)
T ss_pred EECCCCCCEee
Confidence 45555555443
No 85
>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=76.95 E-value=2.7 Score=18.55 Aligned_cols=10 Identities=30% Similarity=0.899 Sum_probs=6.2
Q ss_pred Cccccccccc
Q 031430 83 KTHECSICGL 92 (159)
Q Consensus 83 k~~~C~~Cgk 92 (159)
..|.|+.||+
T Consensus 15 v~f~CPnCG~ 24 (24)
T PF07754_consen 15 VPFPCPNCGF 24 (24)
T ss_pred ceEeCCCCCC
Confidence 4567777763
No 86
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=76.08 E-value=1.9 Score=25.57 Aligned_cols=33 Identities=21% Similarity=0.299 Sum_probs=19.9
Q ss_pred CccccCCCCCCCCCCCCCCCCCCCCCcccccccccccCCh
Q 031430 58 KLMTMASSGEDFDQTQMPPASPRKPKTHECSICGLEFAIG 97 (159)
Q Consensus 58 ~~~~c~~c~~~f~~~~~l~~~~~~~k~~~C~~Cgk~f~~~ 97 (159)
..|.|+.|++.- +.+ .+..-|.|..||..|.-.
T Consensus 34 ~~~~Cp~C~~~~-----VkR--~a~GIW~C~kCg~~fAGg 66 (89)
T COG1997 34 AKHVCPFCGRTT-----VKR--IATGIWKCRKCGAKFAGG 66 (89)
T ss_pred cCCcCCCCCCcc-----eee--eccCeEEcCCCCCeeccc
Confidence 467788887641 111 123457788888887543
No 87
>PF05443 ROS_MUCR: ROS/MUCR transcriptional regulator protein; InterPro: IPR008807 This family consists of several ROS/MUCR transcriptional regulator proteins. The ros chromosomal gene is present in octopine and nopaline strains of Agrobacterium tumefaciens as well as in Rhizobium meliloti (Sinorhizobium meliloti). This gene encodes a 15.5 kDa protein that specifically represses the virC and virD operons in the virulence region of the Ti plasmid [] and is necessary for succinoglycan production []. S. meliloti can produce two types of acidic exopolysaccharides, succinoglycan and galactoglucan, that are interchangeable for infection of Medicago sativa (Alfalfa) nodules. MucR from S. meliloti acts as a transcriptional repressor that blocks the expression of the exp genes responsible for galactoglucan production therefore allowing the exclusive production of succinoglycan [].; GO: 0003677 DNA binding, 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2JSP_A.
Probab=75.02 E-value=1.6 Score=28.16 Aligned_cols=28 Identities=32% Similarity=0.634 Sum_probs=17.4
Q ss_pred CCcccccccccccCChhHHHHHHHHcccccC
Q 031430 82 PKTHECSICGLEFAIGQALGGHMRRHRAAAA 112 (159)
Q Consensus 82 ~k~~~C~~Cgk~f~~~~~l~~H~~~h~~~~~ 112 (159)
.....|-+||+.|.. |++|++.|+|-.+
T Consensus 70 ~d~i~clecGk~~k~---LkrHL~~~~gltp 97 (132)
T PF05443_consen 70 PDYIICLECGKKFKT---LKRHLRTHHGLTP 97 (132)
T ss_dssp SS-EE-TBT--EESB---HHHHHHHTT-S-H
T ss_pred cCeeEEccCCcccch---HHHHHHHccCCCH
Confidence 455789999999976 4899999976533
No 88
>PF15135 UPF0515: Uncharacterised protein UPF0515
Probab=74.04 E-value=4.3 Score=29.07 Aligned_cols=59 Identities=15% Similarity=0.332 Sum_probs=32.5
Q ss_pred CCCceeecccccccCCChHHHHHhHHhcCCCCccccCCCCCCCCCCCCCCCCCCCCCcccccccccccC
Q 031430 27 QGKRVFACKTCNKEFPSFQALGGHRASHKKPKLMTMASSGEDFDQTQMPPASPRKPKTHECSICGLEFA 95 (159)
Q Consensus 27 ~~~k~~~C~~C~~~f~~~~~l~~h~~~h~~~~~~~c~~c~~~f~~~~~l~~~~~~~k~~~C~~Cgk~f~ 95 (159)
.-.+.|.|..|+..+.. +.-.....-.|..|.+.|.-.. .....|.-.|.|..|+..|.
T Consensus 108 ~~drqFaC~~Cd~~WwR--------rvp~rKeVSRCr~C~~rYDPVP--~dkmwG~aef~C~~C~h~F~ 166 (278)
T PF15135_consen 108 SVDRQFACSSCDHMWWR--------RVPQRKEVSRCRKCRKRYDPVP--CDKMWGIAEFHCPKCRHNFR 166 (278)
T ss_pred ccceeeeccccchHHHh--------ccCcccccccccccccccCCCc--cccccceeeeecccccccch
Confidence 34578999999754322 1212223345666766654321 12233555677777777775
No 89
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=73.62 E-value=1.8 Score=22.79 Aligned_cols=11 Identities=27% Similarity=0.969 Sum_probs=5.8
Q ss_pred eeecccccccC
Q 031430 31 VFACKTCNKEF 41 (159)
Q Consensus 31 ~~~C~~C~~~f 41 (159)
.|.|..||+.|
T Consensus 6 ~Y~C~~Cg~~~ 16 (49)
T COG1996 6 EYKCARCGREV 16 (49)
T ss_pred EEEhhhcCCee
Confidence 45555555554
No 90
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=73.58 E-value=2.3 Score=23.27 Aligned_cols=33 Identities=15% Similarity=0.199 Sum_probs=17.2
Q ss_pred CccccCCCCCCCCCCCCCCCCCCCCCccccccccc
Q 031430 58 KLMTMASSGEDFDQTQMPPASPRKPKTHECSICGL 92 (159)
Q Consensus 58 ~~~~c~~c~~~f~~~~~l~~~~~~~k~~~C~~Cgk 92 (159)
..|.|+.||+.......- -..-..+|.|+.||.
T Consensus 26 v~F~CPnCGe~~I~Rc~~--CRk~g~~Y~Cp~CGF 58 (61)
T COG2888 26 VKFPCPNCGEVEIYRCAK--CRKLGNPYRCPKCGF 58 (61)
T ss_pred eEeeCCCCCceeeehhhh--HHHcCCceECCCcCc
Confidence 456777777543221111 011246788888874
No 91
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=73.04 E-value=1.6 Score=36.28 Aligned_cols=48 Identities=21% Similarity=0.401 Sum_probs=26.6
Q ss_pred ecccccccCCChHHHHHhHHhcCCCCccccCCCCCCCCCCCCCCCCCCCCCcccccccccc
Q 031430 33 ACKTCNKEFPSFQALGGHRASHKKPKLMTMASSGEDFDQTQMPPASPRKPKTHECSICGLE 93 (159)
Q Consensus 33 ~C~~C~~~f~~~~~l~~h~~~h~~~~~~~c~~c~~~f~~~~~l~~~~~~~k~~~C~~Cgk~ 93 (159)
.|..||..+....- ..-+..|.......|..||.. ...|..|+.||..
T Consensus 437 ~C~~Cg~v~~Cp~C-d~~lt~H~~~~~L~CH~Cg~~------------~~~p~~Cp~Cgs~ 484 (730)
T COG1198 437 LCRDCGYIAECPNC-DSPLTLHKATGQLRCHYCGYQ------------EPIPQSCPECGSE 484 (730)
T ss_pred ecccCCCcccCCCC-CcceEEecCCCeeEeCCCCCC------------CCCCCCCCCCCCC
Confidence 57777766544321 001223334455667777642 3467888888855
No 92
>PHA00626 hypothetical protein
Probab=73.01 E-value=2.9 Score=22.57 Aligned_cols=14 Identities=21% Similarity=0.422 Sum_probs=9.0
Q ss_pred CcccccccccccCC
Q 031430 83 KTHECSICGLEFAI 96 (159)
Q Consensus 83 k~~~C~~Cgk~f~~ 96 (159)
..|.|..||..|..
T Consensus 22 nrYkCkdCGY~ft~ 35 (59)
T PHA00626 22 DDYVCCDCGYNDSK 35 (59)
T ss_pred cceEcCCCCCeech
Confidence 45777777766644
No 93
>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=72.43 E-value=2.9 Score=19.87 Aligned_cols=9 Identities=33% Similarity=0.877 Sum_probs=5.0
Q ss_pred ccccccccc
Q 031430 84 THECSICGL 92 (159)
Q Consensus 84 ~~~C~~Cgk 92 (159)
+..|..||.
T Consensus 17 ~irC~~CG~ 25 (32)
T PF03604_consen 17 PIRCPECGH 25 (32)
T ss_dssp TSSBSSSS-
T ss_pred cEECCcCCC
Confidence 456666663
No 94
>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=71.77 E-value=4 Score=18.27 Aligned_cols=20 Identities=20% Similarity=0.512 Sum_probs=14.6
Q ss_pred ccccccccccCChhHHHHHHH
Q 031430 85 HECSICGLEFAIGQALGGHMR 105 (159)
Q Consensus 85 ~~C~~Cgk~f~~~~~l~~H~~ 105 (159)
..|++|++.+ ....+..|..
T Consensus 2 v~CPiC~~~v-~~~~in~HLD 21 (26)
T smart00734 2 VQCPVCFREV-PENLINSHLD 21 (26)
T ss_pred CcCCCCcCcc-cHHHHHHHHH
Confidence 3688999888 5567777764
No 95
>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]
Probab=71.02 E-value=8.4 Score=28.82 Aligned_cols=66 Identities=23% Similarity=0.369 Sum_probs=41.8
Q ss_pred CCcccccccccccCChhHHHHHHHHcccccCCCccccCCcc--------CCCCCCcchhccCCCCceeeeccCC
Q 031430 82 PKTHECSICGLEFAIGQALGGHMRRHRAAAAMGAVADGLVT--------RPLLPLPVLKKSNSCKRVFCLDLNL 147 (159)
Q Consensus 82 ~k~~~C~~Cgk~f~~~~~l~~H~~~h~~~~~~~~~~~~~~~--------~~~~~~~~~~~~~~~~~~~~~~~~l 147 (159)
.-|.+|+.|+-......+|.+-.+.--.-+++......... .........+.|..|+.+|..|.+.
T Consensus 288 sLP~eCpiC~ltLVss~hLARSyhhL~PL~~F~Eip~~~~~~~~~Cf~C~~~~~~~~~y~C~~Ck~~FCldCDv 361 (378)
T KOG2807|consen 288 SLPIECPICSLTLVSSPHLARSYHHLFPLKPFVEIPETEYNGSRFCFACQGELLSSGRYRCESCKNVFCLDCDV 361 (378)
T ss_pred cCCccCCccceeEecchHHHHHHHhhcCCcchhhccccccCCCcceeeeccccCCCCcEEchhccceeeccchH
Confidence 35789999999998888888766644444444432221110 0112344567899999999988653
No 96
>PF14353 CpXC: CpXC protein
Probab=69.71 E-value=1.6 Score=27.90 Aligned_cols=12 Identities=33% Similarity=0.753 Sum_probs=7.6
Q ss_pred ecccccccCCCh
Q 031430 33 ACKTCNKEFPSF 44 (159)
Q Consensus 33 ~C~~C~~~f~~~ 44 (159)
.|+.|+..|...
T Consensus 3 tCP~C~~~~~~~ 14 (128)
T PF14353_consen 3 TCPHCGHEFEFE 14 (128)
T ss_pred CCCCCCCeeEEE
Confidence 577777766544
No 97
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=69.58 E-value=3.9 Score=24.47 Aligned_cols=28 Identities=18% Similarity=0.356 Sum_probs=19.0
Q ss_pred CccccCCCCCCCCCCCCCCCCCCCCCccccccccc
Q 031430 58 KLMTMASSGEDFDQTQMPPASPRKPKTHECSICGL 92 (159)
Q Consensus 58 ~~~~c~~c~~~f~~~~~l~~~~~~~k~~~C~~Cgk 92 (159)
.|..|..||..|.. .. ..+|..|+.|-.
T Consensus 57 ~Pa~CkkCGfef~~-~~------ik~pSRCP~CKS 84 (97)
T COG3357 57 RPARCKKCGFEFRD-DK------IKKPSRCPKCKS 84 (97)
T ss_pred cChhhcccCccccc-cc------cCCcccCCcchh
Confidence 46688889988864 11 235778888763
No 98
>KOG4167 consensus Predicted DNA-binding protein, contains SANT and ELM2 domains [Transcription]
Probab=68.57 E-value=1.1 Score=36.90 Aligned_cols=27 Identities=30% Similarity=0.533 Sum_probs=24.1
Q ss_pred CcccccccccccCChhHHHHHHHHccc
Q 031430 83 KTHECSICGLEFAIGQALGGHMRRHRA 109 (159)
Q Consensus 83 k~~~C~~Cgk~f~~~~~l~~H~~~h~~ 109 (159)
--|.|.+|||.|..--++..||++|.-
T Consensus 791 giFpCreC~kvF~KiKSrNAHMK~Hr~ 817 (907)
T KOG4167|consen 791 GIFPCRECGKVFFKIKSRNAHMKTHRQ 817 (907)
T ss_pred ceeehHHHHHHHHHHhhhhHHHHHHHH
Confidence 458999999999999999999999863
No 99
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=67.09 E-value=5.3 Score=35.36 Aligned_cols=71 Identities=21% Similarity=0.301 Sum_probs=40.6
Q ss_pred CceeecccccccCCChHHHHHhHHhcCCCCccccCCCCCCCCCCCCCCCCCCCCCcccccccccccCChhHHHHHHHHcc
Q 031430 29 KRVFACKTCNKEFPSFQALGGHRASHKKPKLMTMASSGEDFDQTQMPPASPRKPKTHECSICGLEFAIGQALGGHMRRHR 108 (159)
Q Consensus 29 ~k~~~C~~C~~~f~~~~~l~~h~~~h~~~~~~~c~~c~~~f~~~~~l~~~~~~~k~~~C~~Cgk~f~~~~~l~~H~~~h~ 108 (159)
..+|.|..|...|.....|..|.+.-. +.+ ..-+.. ....| .+-....| |..|...|.....|..|++.-.
T Consensus 1282 ~~~~~~~~~~~~~~~~~~l~~~~~k~~--~~~--~~~~~~--~~~~l--~~~d~~~~-c~~c~~~~~~~~alqihm~~~~ 1352 (1406)
T KOG1146|consen 1282 THRYLCRQCKMAFDGEAPLTAHQRKFC--FAG--RGSGGS--MPPPL--RVPDCTYH-CLACEVLLSGREALQIHMRSSA 1352 (1406)
T ss_pred chhHHHHHHHhhhcchhHHHHHHHHHH--hcc--CccccC--CCCcc--cCcccccc-chHHHhhcchhHHHHHHHHHhh
Confidence 345667777777777666666652110 000 000000 01111 12234566 9999999999999999998643
No 100
>KOG2186 consensus Cell growth-regulating nucleolar protein [Cell cycle control, cell division, chromosome partitioning]
Probab=66.70 E-value=3.3 Score=29.70 Aligned_cols=38 Identities=16% Similarity=0.530 Sum_probs=24.9
Q ss_pred eecccccccCCChHHHHHhHHhcCCCCccccCCCCCCCCC
Q 031430 32 FACKTCNKEFPSFQALGGHRASHKKPKLMTMASSGEDFDQ 71 (159)
Q Consensus 32 ~~C~~C~~~f~~~~~l~~h~~~h~~~~~~~c~~c~~~f~~ 71 (159)
|.|..||..-.- -.+..|+-..++ .-|.|.-|++.|..
T Consensus 4 FtCnvCgEsvKK-p~vekH~srCrn-~~fSCIDC~k~F~~ 41 (276)
T KOG2186|consen 4 FTCNVCGESVKK-PQVEKHMSRCRN-AYFSCIDCGKTFER 41 (276)
T ss_pred Eehhhhhhhccc-cchHHHHHhccC-CeeEEeeccccccc
Confidence 677777766543 345557666555 56777778877765
No 101
>KOG2593 consensus Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=65.42 E-value=3.5 Score=31.92 Aligned_cols=34 Identities=9% Similarity=0.220 Sum_probs=15.5
Q ss_pred CccccCCCCCCCCCCCCCCCCCCCCCcccccccc
Q 031430 58 KLMTMASSGEDFDQTQMPPASPRKPKTHECSICG 91 (159)
Q Consensus 58 ~~~~c~~c~~~f~~~~~l~~~~~~~k~~~C~~Cg 91 (159)
..|.|+.|.+.|.....+.-.-...-.|.|..|+
T Consensus 127 ~~Y~Cp~C~kkyt~Lea~~L~~~~~~~F~C~~C~ 160 (436)
T KOG2593|consen 127 AGYVCPNCQKKYTSLEALQLLDNETGEFHCENCG 160 (436)
T ss_pred ccccCCccccchhhhHHHHhhcccCceEEEecCC
Confidence 4456666666555433222111122345565555
No 102
>COG3091 SprT Zn-dependent metalloprotease, SprT family [General function prediction only]
Probab=64.01 E-value=3.8 Score=27.07 Aligned_cols=31 Identities=13% Similarity=0.271 Sum_probs=14.0
Q ss_pred ccccCCCCCCCCCCCCCCCCCCCCCcccccccc
Q 031430 59 LMTMASSGEDFDQTQMPPASPRKPKTHECSICG 91 (159)
Q Consensus 59 ~~~c~~c~~~f~~~~~l~~~~~~~k~~~C~~Cg 91 (159)
+|.|. |+..|...........|+ .|.|..|+
T Consensus 117 ~Y~C~-C~q~~l~~RRhn~~~~g~-~YrC~~C~ 147 (156)
T COG3091 117 PYRCQ-CQQHYLRIRRHNTVRRGE-VYRCGKCG 147 (156)
T ss_pred eEEee-cCCccchhhhcccccccc-eEEeccCC
Confidence 45555 555544332222222334 55555555
No 103
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=62.86 E-value=4.1 Score=23.38 Aligned_cols=18 Identities=28% Similarity=0.630 Sum_probs=11.7
Q ss_pred CCCccccc--ccccccCChh
Q 031430 81 KPKTHECS--ICGLEFAIGQ 98 (159)
Q Consensus 81 ~~k~~~C~--~Cgk~f~~~~ 98 (159)
.+.-+.|. +||..|....
T Consensus 24 ~~~Y~qC~N~eCg~tF~t~e 43 (72)
T PRK09678 24 KERYHQCQNVNCSATFITYE 43 (72)
T ss_pred heeeeecCCCCCCCEEEEEE
Confidence 45556777 6777776543
No 104
>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=62.13 E-value=3.6 Score=32.85 Aligned_cols=48 Identities=23% Similarity=0.387 Sum_probs=25.7
Q ss_pred ecccccccCCChHHHHHhHHhcCCCCccccCCCCCCCCCCCCCCCCCCCCCcccccccccc
Q 031430 33 ACKTCNKEFPSFQALGGHRASHKKPKLMTMASSGEDFDQTQMPPASPRKPKTHECSICGLE 93 (159)
Q Consensus 33 ~C~~C~~~f~~~~~l~~h~~~h~~~~~~~c~~c~~~f~~~~~l~~~~~~~k~~~C~~Cgk~ 93 (159)
.|..||.......- ...+..|.......|..||... ..|..|+.||..
T Consensus 215 ~C~~Cg~~~~C~~C-~~~l~~h~~~~~l~Ch~Cg~~~------------~~~~~Cp~C~s~ 262 (505)
T TIGR00595 215 LCRSCGYILCCPNC-DVSLTYHKKEGKLRCHYCGYQE------------PIPKTCPQCGSE 262 (505)
T ss_pred EhhhCcCccCCCCC-CCceEEecCCCeEEcCCCcCcC------------CCCCCCCCCCCC
Confidence 56666655443311 1123334445566777777432 245678888853
No 105
>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=61.97 E-value=7 Score=24.11 Aligned_cols=27 Identities=19% Similarity=0.417 Sum_probs=23.2
Q ss_pred Ccccc----cccccccCChhHHHHHHHHccc
Q 031430 83 KTHEC----SICGLEFAIGQALGGHMRRHRA 109 (159)
Q Consensus 83 k~~~C----~~Cgk~f~~~~~l~~H~~~h~~ 109 (159)
.-|.| ..|+....+...+..|.+.+++
T Consensus 79 ~G~~C~~~~~~C~y~~~~~~~m~~H~~~~Hg 109 (109)
T PF12013_consen 79 DGYRCQCDPPHCGYITRSKKTMRKHWRKEHG 109 (109)
T ss_pred CCeeeecCCCCCCcEeccHHHHHHHHHHhcC
Confidence 34889 9999999999999999987654
No 106
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=61.42 E-value=6.3 Score=25.38 Aligned_cols=14 Identities=29% Similarity=0.774 Sum_probs=7.0
Q ss_pred CCcccccccccccC
Q 031430 82 PKTHECSICGLEFA 95 (159)
Q Consensus 82 ~k~~~C~~Cgk~f~ 95 (159)
...|.|..|++.|.
T Consensus 51 ~qRyrC~~C~~tf~ 64 (129)
T COG3677 51 HQRYKCKSCGSTFT 64 (129)
T ss_pred ccccccCCcCccee
Confidence 34455555555553
No 107
>KOG2893 consensus Zn finger protein [General function prediction only]
Probab=61.28 E-value=5.4 Score=28.44 Aligned_cols=35 Identities=23% Similarity=0.306 Sum_probs=26.0
Q ss_pred ecccccccCCChHHHHHhHHhcCCCCccccCCCCCCCCC
Q 031430 33 ACKTCNKEFPSFQALGGHRASHKKPKLMTMASSGEDFDQ 71 (159)
Q Consensus 33 ~C~~C~~~f~~~~~l~~h~~~h~~~~~~~c~~c~~~f~~ 71 (159)
.|=.|++.|....-|..|++. +-|+|.+|.+.+..
T Consensus 12 wcwycnrefddekiliqhqka----khfkchichkkl~s 46 (341)
T KOG2893|consen 12 WCWYCNREFDDEKILIQHQKA----KHFKCHICHKKLFS 46 (341)
T ss_pred eeeecccccchhhhhhhhhhh----ccceeeeehhhhcc
Confidence 466889999888888777654 56888888765544
No 108
>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=60.89 E-value=4 Score=28.72 Aligned_cols=29 Identities=17% Similarity=0.336 Sum_probs=22.2
Q ss_pred CCceeecccccccCCChHHHHHhHHhcCC
Q 031430 28 GKRVFACKTCNKEFPSFQALGGHRASHKK 56 (159)
Q Consensus 28 ~~k~~~C~~C~~~f~~~~~l~~h~~~h~~ 56 (159)
.+..|.|.+|+|.|.-......|+...+.
T Consensus 74 ~~~K~~C~lc~KlFkg~eFV~KHI~nKH~ 102 (214)
T PF04959_consen 74 DEDKWRCPLCGKLFKGPEFVRKHIFNKHP 102 (214)
T ss_dssp SSEEEEE-SSS-EESSHHHHHHHHHHH-H
T ss_pred cCCEECCCCCCcccCChHHHHHHHhhcCH
Confidence 46679999999999999999999876443
No 109
>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=60.13 E-value=0.37 Score=25.60 Aligned_cols=26 Identities=19% Similarity=0.319 Sum_probs=12.5
Q ss_pred CceeecccccccCCChHHHHHhHHhc
Q 031430 29 KRVFACKTCNKEFPSFQALGGHRASH 54 (159)
Q Consensus 29 ~k~~~C~~C~~~f~~~~~l~~h~~~h 54 (159)
...|.|+.|...|-..-.+-.|...|
T Consensus 19 ~~~y~C~~C~~~FC~dCD~fiHE~LH 44 (51)
T PF07975_consen 19 SSRYRCPKCKNHFCIDCDVFIHETLH 44 (51)
T ss_dssp -EEE--TTTT--B-HHHHHTTTTTS-
T ss_pred CCeEECCCCCCccccCcChhhhcccc
Confidence 35688888888887666655554443
No 110
>PRK14873 primosome assembly protein PriA; Provisional
Probab=59.88 E-value=6.3 Score=32.69 Aligned_cols=47 Identities=17% Similarity=0.301 Sum_probs=27.3
Q ss_pred ecccccccCCChHHHHHhHHhcCCCCccccCCCCCCCCCCCCCCCCCCCCCcccccccccc
Q 031430 33 ACKTCNKEFPSFQALGGHRASHKKPKLMTMASSGEDFDQTQMPPASPRKPKTHECSICGLE 93 (159)
Q Consensus 33 ~C~~C~~~f~~~~~l~~h~~~h~~~~~~~c~~c~~~f~~~~~l~~~~~~~k~~~C~~Cgk~ 93 (159)
.|..||..+....- ...+..|.......|..||.. ..++.|+.||..
T Consensus 385 ~C~~Cg~~~~C~~C-~~~L~~h~~~~~l~Ch~CG~~-------------~~p~~Cp~Cgs~ 431 (665)
T PRK14873 385 ACARCRTPARCRHC-TGPLGLPSAGGTPRCRWCGRA-------------APDWRCPRCGSD 431 (665)
T ss_pred EhhhCcCeeECCCC-CCceeEecCCCeeECCCCcCC-------------CcCccCCCCcCC
Confidence 67777766544321 011223444556778888742 136789999854
No 111
>KOG2593 consensus Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=58.75 E-value=15 Score=28.63 Aligned_cols=44 Identities=18% Similarity=0.409 Sum_probs=30.1
Q ss_pred cccCCCceeecccccccCCChHHHHHhHHhcCCCCccccCCCCCCCC
Q 031430 24 ETDQGKRVFACKTCNKEFPSFQALGGHRASHKKPKLMTMASSGEDFD 70 (159)
Q Consensus 24 ~~h~~~k~~~C~~C~~~f~~~~~l~~h~~~h~~~~~~~c~~c~~~f~ 70 (159)
+--+...-|.|+.|.+.|.....+. ..-...-.|.|..|+....
T Consensus 121 ~d~t~~~~Y~Cp~C~kkyt~Lea~~---L~~~~~~~F~C~~C~gelv 164 (436)
T KOG2593|consen 121 RDDTNVAGYVCPNCQKKYTSLEALQ---LLDNETGEFHCENCGGELV 164 (436)
T ss_pred hhccccccccCCccccchhhhHHHH---hhcccCceEEEecCCCchh
Confidence 3345667799999999997655543 3333345799999986543
No 112
>PF15269 zf-C2H2_7: Zinc-finger
Probab=58.20 E-value=25 Score=18.08 Aligned_cols=24 Identities=21% Similarity=0.270 Sum_probs=19.9
Q ss_pred CcccccccccccCChhHHHHHHHH
Q 031430 83 KTHECSICGLEFAIGQALGGHMRR 106 (159)
Q Consensus 83 k~~~C~~Cgk~f~~~~~l~~H~~~ 106 (159)
-.|.|-+|..+...+++|-.||+-
T Consensus 19 ~~ykcfqcpftc~~kshl~nhmky 42 (54)
T PF15269_consen 19 FKYKCFQCPFTCNEKSHLFNHMKY 42 (54)
T ss_pred ccceeecCCcccchHHHHHHHHHH
Confidence 346788899888999999999874
No 113
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=57.49 E-value=5.1 Score=25.76 Aligned_cols=10 Identities=20% Similarity=0.324 Sum_probs=4.7
Q ss_pred cccCCCCCCC
Q 031430 60 MTMASSGEDF 69 (159)
Q Consensus 60 ~~c~~c~~~f 69 (159)
++|..||+.|
T Consensus 2 H~Ct~Cg~~f 11 (131)
T PF09845_consen 2 HQCTKCGRVF 11 (131)
T ss_pred cccCcCCCCc
Confidence 4444454444
No 114
>COG4957 Predicted transcriptional regulator [Transcription]
Probab=57.18 E-value=6.8 Score=25.33 Aligned_cols=26 Identities=23% Similarity=0.319 Sum_probs=20.8
Q ss_pred cccccccccccCChhHHHHHHHHcccccC
Q 031430 84 THECSICGLEFAIGQALGGHMRRHRAAAA 112 (159)
Q Consensus 84 ~~~C~~Cgk~f~~~~~l~~H~~~h~~~~~ 112 (159)
-..|-++|+.|. +|++|+.+|.+--|
T Consensus 76 ~IicLEDGkkfK---SLKRHL~t~~gmTP 101 (148)
T COG4957 76 YIICLEDGKKFK---SLKRHLTTHYGLTP 101 (148)
T ss_pred eEEEeccCcchH---HHHHHHhcccCCCH
Confidence 367999999986 58999999886544
No 115
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=57.01 E-value=10 Score=16.40 Aligned_cols=6 Identities=50% Similarity=1.436 Sum_probs=3.2
Q ss_pred cccccc
Q 031430 87 CSICGL 92 (159)
Q Consensus 87 C~~Cgk 92 (159)
|+.||.
T Consensus 16 C~~CG~ 21 (23)
T PF13240_consen 16 CPNCGT 21 (23)
T ss_pred hhhhCC
Confidence 555554
No 116
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=56.48 E-value=3.2 Score=25.29 Aligned_cols=12 Identities=33% Similarity=1.013 Sum_probs=6.6
Q ss_pred Cceeeccccccc
Q 031430 29 KRVFACKTCNKE 40 (159)
Q Consensus 29 ~k~~~C~~C~~~ 40 (159)
++.|.|+.|+..
T Consensus 20 ~k~FtCp~Cghe 31 (104)
T COG4888 20 PKTFTCPRCGHE 31 (104)
T ss_pred CceEecCccCCe
Confidence 445666666543
No 117
>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=56.29 E-value=7.6 Score=28.09 Aligned_cols=82 Identities=22% Similarity=0.306 Sum_probs=48.9
Q ss_pred CCCceeecccccccCCChHHHHHhHHhc--CCCCccccCCCCCCCCC----------CCCCCC---CCCCCCcccccccc
Q 031430 27 QGKRVFACKTCNKEFPSFQALGGHRASH--KKPKLMTMASSGEDFDQ----------TQMPPA---SPRKPKTHECSICG 91 (159)
Q Consensus 27 ~~~k~~~C~~C~~~f~~~~~l~~h~~~h--~~~~~~~c~~c~~~f~~----------~~~l~~---~~~~~k~~~C~~Cg 91 (159)
.|-+.|.|..|.........+ .|+..- .....|+|..|++.=.. -.|..+ .....+++.|+.||
T Consensus 138 hGGrif~CsfC~~flCEDDQF-EHQAsCQvLe~E~~KC~SCNrlGq~sCLRCK~cfCddHvrrKg~ky~k~k~~PCPKCg 216 (314)
T PF06524_consen 138 HGGRIFKCSFCDNFLCEDDQF-EHQASCQVLESETFKCQSCNRLGQYSCLRCKICFCDDHVRRKGFKYEKGKPIPCPKCG 216 (314)
T ss_pred CCCeEEEeecCCCeeeccchh-hhhhhhhhhhcccccccccccccchhhhheeeeehhhhhhhcccccccCCCCCCCCCC
Confidence 466889999987654443333 454432 23456788777653211 111110 01135889999999
Q ss_pred cccCChhHHHHHHHHccc
Q 031430 92 LEFAIGQALGGHMRRHRA 109 (159)
Q Consensus 92 k~f~~~~~l~~H~~~h~~ 109 (159)
........|..-.|+|.-
T Consensus 217 ~et~eTkdLSmStR~hky 234 (314)
T PF06524_consen 217 YETQETKDLSMSTRSHKY 234 (314)
T ss_pred Ccccccccceeeeecchh
Confidence 887777777777777653
No 118
>COG4530 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=55.08 E-value=7.5 Score=24.16 Aligned_cols=32 Identities=9% Similarity=0.143 Sum_probs=21.1
Q ss_pred ccCCCCCCCCCCCCCCCCCCCCCcccccccccccCChhHHH
Q 031430 61 TMASSGEDFDQTQMPPASPRKPKTHECSICGLEFAIGQALG 101 (159)
Q Consensus 61 ~c~~c~~~f~~~~~l~~~~~~~k~~~C~~Cgk~f~~~~~l~ 101 (159)
.|+.||+.|.. | ...|..|+.||++|. .+.|.
T Consensus 11 idPetg~KFYD---L-----NrdPiVsPytG~s~P-~s~fe 42 (129)
T COG4530 11 IDPETGKKFYD---L-----NRDPIVSPYTGKSYP-RSYFE 42 (129)
T ss_pred cCccccchhhc---c-----CCCccccCcccccch-HHHHH
Confidence 57777777753 2 236788899999983 34444
No 119
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=53.15 E-value=5 Score=21.97 Aligned_cols=33 Identities=15% Similarity=0.274 Sum_probs=18.4
Q ss_pred CccccCCCCCCCCCCCCCCCCCCCCCccccccccc
Q 031430 58 KLMTMASSGEDFDQTQMPPASPRKPKTHECSICGL 92 (159)
Q Consensus 58 ~~~~c~~c~~~f~~~~~l~~~~~~~k~~~C~~Cgk 92 (159)
..|.|+.||......-. +-..-..+|.|+.||.
T Consensus 24 ~~F~CPnCG~~~I~RC~--~CRk~~~~Y~CP~CGF 56 (59)
T PRK14890 24 VKFLCPNCGEVIIYRCE--KCRKQSNPYTCPKCGF 56 (59)
T ss_pred CEeeCCCCCCeeEeech--hHHhcCCceECCCCCC
Confidence 46788888875221111 0011236788988884
No 120
>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=51.97 E-value=9 Score=18.46 Aligned_cols=11 Identities=18% Similarity=0.341 Sum_probs=4.4
Q ss_pred ccCCCCCCCCC
Q 031430 61 TMASSGEDFDQ 71 (159)
Q Consensus 61 ~c~~c~~~f~~ 71 (159)
.|..|++.|..
T Consensus 5 ~C~eC~~~f~d 15 (34)
T PF01286_consen 5 KCDECGKPFMD 15 (34)
T ss_dssp E-TTT--EES-
T ss_pred hHhHhCCHHHH
Confidence 46666666654
No 121
>PF13451 zf-trcl: Probable zinc-binding domain
Probab=51.73 E-value=6.2 Score=20.78 Aligned_cols=18 Identities=39% Similarity=0.715 Sum_probs=14.2
Q ss_pred CCcccccccccccCChhH
Q 031430 82 PKTHECSICGLEFAIGQA 99 (159)
Q Consensus 82 ~k~~~C~~Cgk~f~~~~~ 99 (159)
++.+.|..||..|.....
T Consensus 2 Dk~l~C~dCg~~FvfTa~ 19 (49)
T PF13451_consen 2 DKTLTCKDCGAEFVFTAG 19 (49)
T ss_pred CeeEEcccCCCeEEEehh
Confidence 467899999999876543
No 122
>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=51.52 E-value=11 Score=20.20 Aligned_cols=10 Identities=40% Similarity=0.903 Sum_probs=4.8
Q ss_pred cccccccccc
Q 031430 85 HECSICGLEF 94 (159)
Q Consensus 85 ~~C~~Cgk~f 94 (159)
..|+.||..|
T Consensus 23 V~Cp~CGael 32 (54)
T TIGR01206 23 VICDECGAEL 32 (54)
T ss_pred EeCCCCCCEE
Confidence 3555555443
No 123
>KOG4167 consensus Predicted DNA-binding protein, contains SANT and ELM2 domains [Transcription]
Probab=51.29 E-value=3 Score=34.48 Aligned_cols=25 Identities=28% Similarity=0.765 Sum_probs=22.3
Q ss_pred eeecccccccCCChHHHHHhHHhcC
Q 031430 31 VFACKTCNKEFPSFQALGGHRASHK 55 (159)
Q Consensus 31 ~~~C~~C~~~f~~~~~l~~h~~~h~ 55 (159)
.|.|.+|++.|..-.++..|++.|.
T Consensus 792 iFpCreC~kvF~KiKSrNAHMK~Hr 816 (907)
T KOG4167|consen 792 IFPCRECGKVFFKIKSRNAHMKTHR 816 (907)
T ss_pred eeehHHHHHHHHHHhhhhHHHHHHH
Confidence 5899999999998888888988885
No 124
>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=50.40 E-value=8.1 Score=23.55 Aligned_cols=16 Identities=31% Similarity=0.740 Sum_probs=12.9
Q ss_pred CCCCCcccccccccccC
Q 031430 79 PRKPKTHECSICGLEFA 95 (159)
Q Consensus 79 ~~~~k~~~C~~Cgk~f~ 95 (159)
+.+ ++++|.+||..|.
T Consensus 75 ~~g-~~~rC~eCG~~fk 90 (97)
T cd00924 75 EKG-KPKRCPECGHVFK 90 (97)
T ss_pred eCC-CceeCCCCCcEEE
Confidence 334 7999999999885
No 125
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=49.41 E-value=4.2 Score=33.96 Aligned_cols=40 Identities=20% Similarity=0.389 Sum_probs=24.5
Q ss_pred cchHHHHHHHHhhccccCCCceeecccccccCCChHHHHHhHHhcCCCCccccCCCCCC
Q 031430 10 IDTANCLMLLSKVGETDQGKRVFACKTCNKEFPSFQALGGHRASHKKPKLMTMASSGED 68 (159)
Q Consensus 10 ~~~~~~~~~l~~h~~~h~~~k~~~C~~C~~~f~~~~~l~~h~~~h~~~~~~~c~~c~~~ 68 (159)
.+|.+|...|.-|+.. +...|..|| +....|..|+.||..
T Consensus 445 ~~Cp~Cd~~lt~H~~~----~~L~CH~Cg---------------~~~~~p~~Cp~Cgs~ 484 (730)
T COG1198 445 AECPNCDSPLTLHKAT----GQLRCHYCG---------------YQEPIPQSCPECGSE 484 (730)
T ss_pred ccCCCCCcceEEecCC----CeeEeCCCC---------------CCCCCCCCCCCCCCC
Confidence 3555555555555443 445666665 234578899999865
No 126
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=48.94 E-value=7.2 Score=25.27 Aligned_cols=14 Identities=29% Similarity=0.888 Sum_probs=9.6
Q ss_pred ceeecccccccCCC
Q 031430 30 RVFACKTCNKEFPS 43 (159)
Q Consensus 30 k~~~C~~C~~~f~~ 43 (159)
..+.|..||..|..
T Consensus 69 ~~~~C~~CG~~~~~ 82 (135)
T PRK03824 69 AVLKCRNCGNEWSL 82 (135)
T ss_pred eEEECCCCCCEEec
Confidence 45778888876654
No 127
>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=48.59 E-value=9.9 Score=26.77 Aligned_cols=26 Identities=19% Similarity=0.428 Sum_probs=20.1
Q ss_pred CCCcccccccccccCChhHHHHHHHH
Q 031430 81 KPKTHECSICGLEFAIGQALGGHMRR 106 (159)
Q Consensus 81 ~~k~~~C~~Cgk~f~~~~~l~~H~~~ 106 (159)
.+..|.|..|+|.|.-..-...|+..
T Consensus 74 ~~~K~~C~lc~KlFkg~eFV~KHI~n 99 (214)
T PF04959_consen 74 DEDKWRCPLCGKLFKGPEFVRKHIFN 99 (214)
T ss_dssp SSEEEEE-SSS-EESSHHHHHHHHHH
T ss_pred cCCEECCCCCCcccCChHHHHHHHhh
Confidence 44569999999999999999999864
No 128
>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=48.58 E-value=7.4 Score=18.16 Aligned_cols=8 Identities=25% Similarity=0.546 Sum_probs=3.6
Q ss_pred ccccCCCC
Q 031430 59 LMTMASSG 66 (159)
Q Consensus 59 ~~~c~~c~ 66 (159)
.+.|+.|+
T Consensus 19 ~~vCp~C~ 26 (30)
T PF08274_consen 19 LLVCPECG 26 (30)
T ss_dssp SEEETTTT
T ss_pred EEeCCccc
Confidence 34444443
No 129
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=48.04 E-value=9.4 Score=22.91 Aligned_cols=32 Identities=13% Similarity=0.056 Sum_probs=19.2
Q ss_pred CccccCCCCCCCCCCCCCCCCCCCCCcccccccccccCC
Q 031430 58 KLMTMASSGEDFDQTQMPPASPRKPKTHECSICGLEFAI 96 (159)
Q Consensus 58 ~~~~c~~c~~~f~~~~~l~~~~~~~k~~~C~~Cgk~f~~ 96 (159)
..|.|+.||+.- +.+ .+.-.|.|..|++.|.-
T Consensus 35 a~y~CpfCgk~~-----vkR--~a~GIW~C~~C~~~~AG 66 (90)
T PTZ00255 35 AKYFCPFCGKHA-----VKR--QAVGIWRCKGCKKTVAG 66 (90)
T ss_pred CCccCCCCCCCc-----eee--eeeEEEEcCCCCCEEeC
Confidence 467888887531 111 12345778888887754
No 130
>KOG2231 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=47.69 E-value=12 Score=31.04 Aligned_cols=23 Identities=26% Similarity=0.447 Sum_probs=14.0
Q ss_pred cccccccccCChhHHHHHHHHcc
Q 031430 86 ECSICGLEFAIGQALGGHMRRHR 108 (159)
Q Consensus 86 ~C~~Cgk~f~~~~~l~~H~~~h~ 108 (159)
.|..|...|.....|..|++.++
T Consensus 184 ~C~~C~~~fld~~el~rH~~~~h 206 (669)
T KOG2231|consen 184 LCKFCHERFLDDDELYRHLRFDH 206 (669)
T ss_pred cchhhhhhhccHHHHHHhhccce
Confidence 45666666666666666666444
No 131
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=47.26 E-value=10 Score=18.88 Aligned_cols=11 Identities=27% Similarity=0.751 Sum_probs=6.6
Q ss_pred ccccccccccc
Q 031430 84 THECSICGLEF 94 (159)
Q Consensus 84 ~~~C~~Cgk~f 94 (159)
-|.|..||..+
T Consensus 28 fy~C~~C~~~w 38 (40)
T smart00440 28 FYVCTKCGHRW 38 (40)
T ss_pred EEEeCCCCCEe
Confidence 36666666554
No 132
>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=47.14 E-value=4.5 Score=33.47 Aligned_cols=56 Identities=16% Similarity=0.329 Sum_probs=29.8
Q ss_pred ecccccccCCChHHHHHhHHhcCCCCcc-ccCCCCCCCCCCCCCCCCCCCCCccccccccc
Q 031430 33 ACKTCNKEFPSFQALGGHRASHKKPKLM-TMASSGEDFDQTQMPPASPRKPKTHECSICGL 92 (159)
Q Consensus 33 ~C~~C~~~f~~~~~l~~h~~~h~~~~~~-~c~~c~~~f~~~~~l~~~~~~~k~~~C~~Cgk 92 (159)
.|..||-.|.--..|---+ -.+.-..| .|+.|.+.|.+..+- +.|. .|..|+.||-
T Consensus 125 ~CT~CGPRfTIi~alPYDR-~nTsM~~F~lC~~C~~EY~dP~nR-RfHA--Qp~aCp~CGP 181 (750)
T COG0068 125 NCTNCGPRFTIIEALPYDR-ENTSMADFPLCPFCDKEYKDPLNR-RFHA--QPIACPKCGP 181 (750)
T ss_pred ccCCCCcceeeeccCCCCc-ccCccccCcCCHHHHHHhcCcccc-cccc--ccccCcccCC
Confidence 4666777766554443222 22222222 477777666654443 3443 4667888884
No 133
>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=46.37 E-value=3.3 Score=20.63 Aligned_cols=24 Identities=25% Similarity=0.682 Sum_probs=8.7
Q ss_pred HHHHHHhhccccCCCceeeccccc
Q 031430 15 CLMLLSKVGETDQGKRVFACKTCN 38 (159)
Q Consensus 15 ~~~~l~~h~~~h~~~k~~~C~~C~ 38 (159)
|...|.....+..+.+.+.|..|+
T Consensus 8 C~aylNp~~~~~~~~~~w~C~~C~ 31 (40)
T PF04810_consen 8 CRAYLNPFCQFDDGGKTWICNFCG 31 (40)
T ss_dssp T--BS-TTSEEETTTTEEEETTT-
T ss_pred CCCEECCcceEcCCCCEEECcCCC
Confidence 333333444444444444444444
No 134
>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=46.07 E-value=19 Score=23.78 Aligned_cols=11 Identities=18% Similarity=0.214 Sum_probs=6.2
Q ss_pred ccCCCCCCCCC
Q 031430 61 TMASSGEDFDQ 71 (159)
Q Consensus 61 ~c~~c~~~f~~ 71 (159)
.|..||+.|..
T Consensus 30 eC~~C~~RFTT 40 (147)
T TIGR00244 30 ECLECHERFTT 40 (147)
T ss_pred cCCccCCccce
Confidence 45556655554
No 135
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=45.85 E-value=12 Score=23.50 Aligned_cols=11 Identities=0% Similarity=-0.182 Sum_probs=5.8
Q ss_pred cccCCCCCCCC
Q 031430 60 MTMASSGEDFD 70 (159)
Q Consensus 60 ~~c~~c~~~f~ 70 (159)
..|..||..|.
T Consensus 71 ~~C~~Cg~~~~ 81 (113)
T PRK12380 71 AWCWDCSQVVE 81 (113)
T ss_pred EEcccCCCEEe
Confidence 35666665443
No 136
>PF12013 DUF3505: Protein of unknown function (DUF3505); InterPro: IPR022698 This family of proteins is functionally uncharacterised. This protein is found in eukaryotes. Proteins in this family are typically between 247 to 1018 amino acids in length. This region contains two segments that are likely to be C2H2 zinc binding domains.
Probab=45.84 E-value=20 Score=22.07 Aligned_cols=25 Identities=16% Similarity=0.329 Sum_probs=21.8
Q ss_pred eec----ccccccCCChHHHHHhHHhcCC
Q 031430 32 FAC----KTCNKEFPSFQALGGHRASHKK 56 (159)
Q Consensus 32 ~~C----~~C~~~f~~~~~l~~h~~~h~~ 56 (159)
|.| ..|+........+..|.+.+.|
T Consensus 81 ~~C~~~~~~C~y~~~~~~~m~~H~~~~Hg 109 (109)
T PF12013_consen 81 YRCQCDPPHCGYITRSKKTMRKHWRKEHG 109 (109)
T ss_pred eeeecCCCCCCcEeccHHHHHHHHHHhcC
Confidence 789 9999999999999999887653
No 137
>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=45.66 E-value=19 Score=23.74 Aligned_cols=8 Identities=13% Similarity=0.413 Sum_probs=4.8
Q ss_pred cccCCCCC
Q 031430 60 MTMASSGE 67 (159)
Q Consensus 60 ~~c~~c~~ 67 (159)
|.|..||.
T Consensus 113 l~C~~Cg~ 120 (146)
T PF07295_consen 113 LVCENCGH 120 (146)
T ss_pred EecccCCC
Confidence 56666664
No 138
>KOG2636 consensus Splicing factor 3a, subunit 3 [RNA processing and modification]
Probab=45.52 E-value=13 Score=29.16 Aligned_cols=29 Identities=21% Similarity=0.382 Sum_probs=23.5
Q ss_pred CCCCCCCcccccccc-cccCChhHHHHHHH
Q 031430 77 ASPRKPKTHECSICG-LEFAIGQALGGHMR 105 (159)
Q Consensus 77 ~~~~~~k~~~C~~Cg-k~f~~~~~l~~H~~ 105 (159)
+.|.-.+.|.|.+|| +++.-..++.+|-.
T Consensus 394 KLHGL~~ey~CEICGNy~Y~GrkaF~RHF~ 423 (497)
T KOG2636|consen 394 KLHGLDIEYNCEICGNYVYKGRKAFDRHFN 423 (497)
T ss_pred hhcCCCcccceeeccCccccCcHHHHHHhH
Confidence 345557789999999 88888999999964
No 139
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=45.32 E-value=28 Score=17.20 Aligned_cols=13 Identities=15% Similarity=0.053 Sum_probs=6.3
Q ss_pred ccccCCCCCCCCC
Q 031430 59 LMTMASSGEDFDQ 71 (159)
Q Consensus 59 ~~~c~~c~~~f~~ 71 (159)
++.|..|++.|-.
T Consensus 12 ~f~C~~C~~~FC~ 24 (39)
T smart00154 12 GFKCRHCGNLFCG 24 (39)
T ss_pred CeECCccCCcccc
Confidence 4445555554443
No 140
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=45.27 E-value=16 Score=19.67 Aligned_cols=8 Identities=50% Similarity=1.423 Sum_probs=3.5
Q ss_pred cccccccC
Q 031430 34 CKTCNKEF 41 (159)
Q Consensus 34 C~~C~~~f 41 (159)
|..|++.|
T Consensus 8 C~~Cg~~~ 15 (54)
T PF14446_consen 8 CPVCGKKF 15 (54)
T ss_pred ChhhCCcc
Confidence 44444443
No 141
>PRK05580 primosome assembly protein PriA; Validated
Probab=43.60 E-value=19 Score=30.05 Aligned_cols=46 Identities=20% Similarity=0.415 Sum_probs=25.5
Q ss_pred eecccccccCCCh---HHHHHhHHhcCCCCccccCCCCCCCCCCCCCCCCCCCCCcccccccccc
Q 031430 32 FACKTCNKEFPSF---QALGGHRASHKKPKLMTMASSGEDFDQTQMPPASPRKPKTHECSICGLE 93 (159)
Q Consensus 32 ~~C~~C~~~f~~~---~~l~~h~~~h~~~~~~~c~~c~~~f~~~~~l~~~~~~~k~~~C~~Cgk~ 93 (159)
..|..||...... ..| ..|.......|..||... ..+..|+.||..
T Consensus 382 ~~C~~Cg~~~~C~~C~~~l----~~h~~~~~l~Ch~Cg~~~------------~~~~~Cp~Cg~~ 430 (679)
T PRK05580 382 LLCRDCGWVAECPHCDASL----TLHRFQRRLRCHHCGYQE------------PIPKACPECGST 430 (679)
T ss_pred eEhhhCcCccCCCCCCCce----eEECCCCeEECCCCcCCC------------CCCCCCCCCcCC
Confidence 3577776554322 222 233444566777777532 345678888754
No 142
>PRK04023 DNA polymerase II large subunit; Validated
Probab=43.33 E-value=32 Score=30.09 Aligned_cols=10 Identities=40% Similarity=0.850 Sum_probs=7.0
Q ss_pred eeeccccccc
Q 031430 31 VFACKTCNKE 40 (159)
Q Consensus 31 ~~~C~~C~~~ 40 (159)
...|+.||..
T Consensus 626 ~RfCpsCG~~ 635 (1121)
T PRK04023 626 RRKCPSCGKE 635 (1121)
T ss_pred CccCCCCCCc
Confidence 4568888865
No 143
>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=43.33 E-value=19 Score=20.02 Aligned_cols=29 Identities=24% Similarity=0.505 Sum_probs=17.1
Q ss_pred ccCCCCCCCCCCCCCCCCCCCCCcccccccccccCC
Q 031430 61 TMASSGEDFDQTQMPPASPRKPKTHECSICGLEFAI 96 (159)
Q Consensus 61 ~c~~c~~~f~~~~~l~~~~~~~k~~~C~~Cgk~f~~ 96 (159)
.|+.||..... ....+.|.|+.||..+..
T Consensus 30 ~C~~CG~~~~~-------~~~~r~~~C~~Cg~~~~r 58 (69)
T PF07282_consen 30 TCPRCGHRNKK-------RRSGRVFTCPNCGFEMDR 58 (69)
T ss_pred CccCccccccc-------ccccceEEcCCCCCEECc
Confidence 46666654332 224567888888876544
No 144
>PLN02294 cytochrome c oxidase subunit Vb
Probab=43.18 E-value=12 Score=25.27 Aligned_cols=15 Identities=33% Similarity=0.833 Sum_probs=12.6
Q ss_pred CCcccccccccccCC
Q 031430 82 PKTHECSICGLEFAI 96 (159)
Q Consensus 82 ~k~~~C~~Cgk~f~~ 96 (159)
.++++|++||..|.-
T Consensus 139 Gkp~RCpeCG~~fkL 153 (174)
T PLN02294 139 GKSFECPVCTQYFEL 153 (174)
T ss_pred CCceeCCCCCCEEEE
Confidence 478999999998854
No 145
>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=43.14 E-value=14 Score=23.16 Aligned_cols=11 Identities=9% Similarity=0.184 Sum_probs=5.6
Q ss_pred cccCCCCCCCC
Q 031430 60 MTMASSGEDFD 70 (159)
Q Consensus 60 ~~c~~c~~~f~ 70 (159)
..|..||..|.
T Consensus 71 ~~C~~Cg~~~~ 81 (115)
T TIGR00100 71 CECEDCSEEVS 81 (115)
T ss_pred EEcccCCCEEe
Confidence 34555655443
No 146
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=42.79 E-value=27 Score=18.01 Aligned_cols=11 Identities=36% Similarity=0.751 Sum_probs=6.5
Q ss_pred ccccccccccc
Q 031430 84 THECSICGLEF 94 (159)
Q Consensus 84 ~~~C~~Cgk~f 94 (159)
.+.|+.||..+
T Consensus 20 ~~vC~~Cg~~~ 30 (52)
T smart00661 20 RFVCRKCGYEE 30 (52)
T ss_pred EEECCcCCCeE
Confidence 45666666544
No 147
>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=42.68 E-value=9.7 Score=22.89 Aligned_cols=32 Identities=19% Similarity=0.271 Sum_probs=18.4
Q ss_pred CccccCCCCCCCCCCCCCCCCCCCCCcccccccccccCC
Q 031430 58 KLMTMASSGEDFDQTQMPPASPRKPKTHECSICGLEFAI 96 (159)
Q Consensus 58 ~~~~c~~c~~~f~~~~~l~~~~~~~k~~~C~~Cgk~f~~ 96 (159)
..|.|+.||+.- +.+ .+.-.|.|..|++.|.-
T Consensus 34 a~y~CpfCgk~~-----vkR--~a~GIW~C~~C~~~~AG 65 (91)
T TIGR00280 34 AKYVCPFCGKKT-----VKR--GSTGIWTCRKCGAKFAG 65 (91)
T ss_pred cCccCCCCCCCc-----eEE--EeeEEEEcCCCCCEEeC
Confidence 467788887531 111 12334678888877754
No 148
>KOG2482 consensus Predicted C2H2-type Zn-finger protein [Transcription]
Probab=42.23 E-value=17 Score=27.51 Aligned_cols=30 Identities=30% Similarity=0.512 Sum_probs=24.3
Q ss_pred CcccccccccccCChhHHHHHHHH--cccccC
Q 031430 83 KTHECSICGLEFAIGQALGGHMRR--HRAAAA 112 (159)
Q Consensus 83 k~~~C~~Cgk~f~~~~~l~~H~~~--h~~~~~ 112 (159)
..++|-.|.+.|..+..|..||+. |...+|
T Consensus 194 ~r~~CLyCekifrdkntLkeHMrkK~HrrinP 225 (423)
T KOG2482|consen 194 ERLRCLYCEKIFRDKNTLKEHMRKKRHRRINP 225 (423)
T ss_pred hhheeeeeccccCCcHHHHHHHHhccCcccCC
Confidence 347999999999999999999974 544444
No 149
>COG1327 Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains [Transcription]
Probab=42.09 E-value=21 Score=23.63 Aligned_cols=12 Identities=25% Similarity=0.371 Sum_probs=7.8
Q ss_pred cccCCCCCCCCC
Q 031430 60 MTMASSGEDFDQ 71 (159)
Q Consensus 60 ~~c~~c~~~f~~ 71 (159)
-.|..||..|..
T Consensus 29 ReC~~C~~RFTT 40 (156)
T COG1327 29 RECLECGERFTT 40 (156)
T ss_pred hcccccccccch
Confidence 357777776665
No 150
>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=41.72 E-value=8.7 Score=19.39 Aligned_cols=15 Identities=27% Similarity=0.753 Sum_probs=10.0
Q ss_pred CcccccccccccCCh
Q 031430 83 KTHECSICGLEFAIG 97 (159)
Q Consensus 83 k~~~C~~Cgk~f~~~ 97 (159)
-|+.|..|++.|-..
T Consensus 12 ~~~~C~~C~~~FC~~ 26 (43)
T PF01428_consen 12 LPFKCKHCGKSFCLK 26 (43)
T ss_dssp SHEE-TTTS-EE-TT
T ss_pred CCeECCCCCcccCcc
Confidence 589999999999764
No 151
>COG1655 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=41.43 E-value=6.3 Score=28.00 Aligned_cols=29 Identities=21% Similarity=0.378 Sum_probs=18.6
Q ss_pred CceeecccccccCCChHHHHHhHHhcCCC
Q 031430 29 KRVFACKTCNKEFPSFQALGGHRASHKKP 57 (159)
Q Consensus 29 ~k~~~C~~C~~~f~~~~~l~~h~~~h~~~ 57 (159)
++.+.|++|+..|....-+..-.++-.|+
T Consensus 17 kk~ieCPvC~tkFkkeev~tgsiRiiagD 45 (267)
T COG1655 17 KKTIECPVCNTKFKKEEVKTGSIRIIAGD 45 (267)
T ss_pred hceeccCcccchhhhhheeccceeEeccc
Confidence 45678999998887665544444444443
No 152
>KOG4173 consensus Alpha-SNAP protein [Intracellular trafficking, secretion, and vesicular transport]
Probab=41.30 E-value=4.4 Score=28.21 Aligned_cols=74 Identities=19% Similarity=0.382 Sum_probs=41.3
Q ss_pred eeeccc--ccccCCChHHHHHhHHhcCCCCccccCCCCCCCCCCCCCCCCC--------------CCCCcccccc--ccc
Q 031430 31 VFACKT--CNKEFPSFQALGGHRASHKKPKLMTMASSGEDFDQTQMPPASP--------------RKPKTHECSI--CGL 92 (159)
Q Consensus 31 ~~~C~~--C~~~f~~~~~l~~h~~~h~~~~~~~c~~c~~~f~~~~~l~~~~--------------~~~k~~~C~~--Cgk 92 (159)
.|.|.+ |-..|.....+..|-..-. ...|..|.+.|.....| ..| +|.-.|+|-. |+-
T Consensus 79 ~~~cqvagc~~~~d~lD~~E~hY~~~h---~~sCs~C~r~~Pt~hLL-d~HI~E~HDs~Fqa~veRG~dMy~ClvEgCt~ 154 (253)
T KOG4173|consen 79 AFACQVAGCCQVFDALDDYEHHYHTLH---GNSCSFCKRAFPTGHLL-DAHILEWHDSLFQALVERGQDMYQCLVEGCTE 154 (253)
T ss_pred cccccccchHHHHhhhhhHHHhhhhcc---cchhHHHHHhCCchhhh-hHHHHHHHHHHHHHHHHcCccHHHHHHHhhhh
Confidence 355655 4455554444444422211 12466666666643222 222 2455688875 899
Q ss_pred ccCChhHHHHHHH-Hcc
Q 031430 93 EFAIGQALGGHMR-RHR 108 (159)
Q Consensus 93 ~f~~~~~l~~H~~-~h~ 108 (159)
.|.+....+.|+- .|.
T Consensus 155 KFkT~r~RkdH~I~~Hk 171 (253)
T KOG4173|consen 155 KFKTSRDRKDHMIRMHK 171 (253)
T ss_pred hhhhhhhhhhHHHHhcc
Confidence 9998888888874 453
No 153
>COG3364 Zn-ribbon containing protein [General function prediction only]
Probab=40.84 E-value=15 Score=22.55 Aligned_cols=18 Identities=22% Similarity=0.113 Sum_probs=10.2
Q ss_pred eeeccCCCCCcccccccc
Q 031430 141 FCLDLNLMPTGDDLKLWV 158 (159)
Q Consensus 141 ~~~~~~l~~~~~~~~~~~ 158 (159)
-.+.+||+...++-.+.|
T Consensus 70 G~YeiNl~~Lld~~~iVv 87 (112)
T COG3364 70 GVYEINLESLLDRDEIVV 87 (112)
T ss_pred ceEEEehhhhccCCceEE
Confidence 356667776655544433
No 154
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=39.38 E-value=26 Score=15.43 Aligned_cols=7 Identities=14% Similarity=0.230 Sum_probs=3.4
Q ss_pred ccCCCCC
Q 031430 61 TMASSGE 67 (159)
Q Consensus 61 ~c~~c~~ 67 (159)
.|+.||.
T Consensus 4 ~Cp~Cg~ 10 (26)
T PF13248_consen 4 FCPNCGA 10 (26)
T ss_pred CCcccCC
Confidence 3555554
No 155
>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=38.89 E-value=10 Score=26.31 Aligned_cols=28 Identities=21% Similarity=0.383 Sum_probs=0.0
Q ss_pred CCCCCCCcccccccc-cccCChhHHHHHH
Q 031430 77 ASPRKPKTHECSICG-LEFAIGQALGGHM 104 (159)
Q Consensus 77 ~~~~~~k~~~C~~Cg-k~f~~~~~l~~H~ 104 (159)
+.|.-.+.|.|.+|| .+|.-..++.+|-
T Consensus 94 KLhGL~~ey~CEICGN~~Y~GrkaFekHF 122 (196)
T PF11931_consen 94 KLHGLGVEYKCEICGNQSYKGRKAFEKHF 122 (196)
T ss_dssp -----------------------------
T ss_pred HHhCCCCeeeeEeCCCcceecHHHHHHhc
Confidence 334446778999998 4454566666664
No 156
>PF08394 Arc_trans_TRASH: Archaeal TRASH domain; InterPro: IPR013603 This region is found in the C terminus of a number of archaeal transcriptional regulators. It is thought to function as a metal-sensing regulatory module [].
Probab=38.85 E-value=2.6 Score=20.75 Aligned_cols=33 Identities=15% Similarity=0.203 Sum_probs=16.7
Q ss_pred cCCCCCCCCCCCCCCCCCCCCCccccccccccc
Q 031430 62 MASSGEDFDQTQMPPASPRKPKTHECSICGLEF 94 (159)
Q Consensus 62 c~~c~~~f~~~~~l~~~~~~~k~~~C~~Cgk~f 94 (159)
|+.||..........+......-|-|+.|-..|
T Consensus 1 Cd~CG~~I~~eP~~~k~~~~~y~fCC~tC~~~f 33 (37)
T PF08394_consen 1 CDYCGGEITGEPIVVKIGNKVYYFCCPTCLSQF 33 (37)
T ss_pred CCccCCcccCCEEEEEECCeEEEEECHHHHHHH
Confidence 567777665544333333333334456565554
No 157
>PF13878 zf-C2H2_3: zinc-finger of acetyl-transferase ESCO
Probab=38.63 E-value=39 Score=16.86 Aligned_cols=24 Identities=21% Similarity=0.491 Sum_probs=15.0
Q ss_pred ccccccccccCC--hhHHHHHHHHcc
Q 031430 85 HECSICGLEFAI--GQALGGHMRRHR 108 (159)
Q Consensus 85 ~~C~~Cgk~f~~--~~~l~~H~~~h~ 108 (159)
-.|..||-.|.. ...-..|.+-|.
T Consensus 14 ~~C~~CgM~Y~~~~~eD~~~H~~yH~ 39 (41)
T PF13878_consen 14 TTCPTCGMLYSPGSPEDEKLHKKYHD 39 (41)
T ss_pred cCCCCCCCEECCCCHHHHHHHHHHHh
Confidence 478888877754 344555666553
No 158
>KOG3408 consensus U1-like Zn-finger-containing protein, probabl erole in RNA processing/splicing [RNA processing and modification]
Probab=37.82 E-value=21 Score=22.70 Aligned_cols=35 Identities=20% Similarity=0.332 Sum_probs=27.1
Q ss_pred CCCcccccccccccCChhHHHHHHHH--cc------cccCCCc
Q 031430 81 KPKTHECSICGLEFAIGQALGGHMRR--HR------AAAAMGA 115 (159)
Q Consensus 81 ~~k~~~C~~Cgk~f~~~~~l~~H~~~--h~------~~~~~~~ 115 (159)
|.-.|-|-.|.+-|.+...|..|.++ |. .+.||.+
T Consensus 54 G~GqfyCi~CaRyFi~~~~l~~H~ktK~HKrRvK~l~~~PySQ 96 (129)
T KOG3408|consen 54 GGGQFYCIECARYFIDAKALKTHFKTKVHKRRVKELREVPYSQ 96 (129)
T ss_pred CCceeehhhhhhhhcchHHHHHHHhccHHHHHHHhcccCCccH
Confidence 44568899999999999999999874 42 4566664
No 159
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=37.16 E-value=13 Score=22.37 Aligned_cols=32 Identities=22% Similarity=0.251 Sum_probs=18.4
Q ss_pred CccccCCCCCCCCCCCCCCCCCCCCCcccccccccccCC
Q 031430 58 KLMTMASSGEDFDQTQMPPASPRKPKTHECSICGLEFAI 96 (159)
Q Consensus 58 ~~~~c~~c~~~f~~~~~l~~~~~~~k~~~C~~Cgk~f~~ 96 (159)
..|.|+.|++.-. .+ .+.-.|.|..|++.|.-
T Consensus 35 a~y~CpfCgk~~v-----kR--~a~GIW~C~~C~~~~AG 66 (90)
T PRK03976 35 AKHVCPVCGRPKV-----KR--VGTGIWECRKCGAKFAG 66 (90)
T ss_pred cCccCCCCCCCce-----EE--EEEEEEEcCCCCCEEeC
Confidence 4677888865311 11 12334678888877754
No 160
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=37.09 E-value=32 Score=23.15 Aligned_cols=24 Identities=17% Similarity=0.324 Sum_probs=18.4
Q ss_pred CCcccccccccccCChhHHHHHHH
Q 031430 82 PKTHECSICGLEFAIGQALGGHMR 105 (159)
Q Consensus 82 ~k~~~C~~Cgk~f~~~~~l~~H~~ 105 (159)
..-+.|+.||+.|=-.+++..-.+
T Consensus 128 ~~f~~C~~CgkiYW~GsHw~~m~~ 151 (165)
T COG1656 128 EEFYRCPKCGKIYWKGSHWRRMVE 151 (165)
T ss_pred cceeECCCCcccccCchHHHHHHH
Confidence 345779999999988877766555
No 161
>PRK11823 DNA repair protein RadA; Provisional
Probab=37.06 E-value=23 Score=27.86 Aligned_cols=8 Identities=13% Similarity=0.235 Sum_probs=3.8
Q ss_pred cccCCCCC
Q 031430 60 MTMASSGE 67 (159)
Q Consensus 60 ~~c~~c~~ 67 (159)
|.|..||.
T Consensus 8 y~C~~Cg~ 15 (446)
T PRK11823 8 YVCQECGA 15 (446)
T ss_pred EECCcCCC
Confidence 44444443
No 162
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=37.03 E-value=49 Score=24.81 Aligned_cols=47 Identities=15% Similarity=0.227 Sum_probs=30.2
Q ss_pred cCCCCCCCCCCCCCC-CCCCCCCcccccccccccCChhHHHHHHHHcc
Q 031430 62 MASSGEDFDQTQMPP-ASPRKPKTHECSICGLEFAIGQALGGHMRRHR 108 (159)
Q Consensus 62 c~~c~~~f~~~~~l~-~~~~~~k~~~C~~Cgk~f~~~~~l~~H~~~h~ 108 (159)
|..|-..|....... .--+..-.|.|+.|...|......-.|...|.
T Consensus 365 Cf~CQ~~fp~~~~~~~~~~~ss~rY~Ce~CK~~FC~dCdvfiHe~Lh~ 412 (421)
T COG5151 365 CFVCQGPFPKPPVSPFDESTSSGRYQCELCKSTFCSDCDVFIHETLHF 412 (421)
T ss_pred ceeccCCCCCCCCCcccccccccceechhhhhhhhhhhHHHHHHHHhh
Confidence 666655555422211 11223456999999999999888888877663
No 163
>TIGR00416 sms DNA repair protein RadA. The gene protuct codes for a probable ATP-dependent protease involved in both DNA repair and degradation of proteins, peptides, glycopeptides. Also known as sms. Residues 11-28 of the SEED alignment contain a putative Zn binding domain. Residues 110-117 of the seed contain a putative ATP binding site both documented in Haemophilus and in Listeria monocytogenes. for E.coli see ( J. BACTERIOL. 178:5045-5048(1996)).
Probab=36.99 E-value=23 Score=27.98 Aligned_cols=10 Identities=20% Similarity=0.321 Sum_probs=5.4
Q ss_pred ccccCCCCCC
Q 031430 59 LMTMASSGED 68 (159)
Q Consensus 59 ~~~c~~c~~~ 68 (159)
.|.|..||..
T Consensus 7 ~y~C~~Cg~~ 16 (454)
T TIGR00416 7 KFVCQHCGAD 16 (454)
T ss_pred eEECCcCCCC
Confidence 3556666543
No 164
>KOG0978 consensus E3 ubiquitin ligase involved in syntaxin degradation [Posttranslational modification, protein turnover, chaperones]
Probab=36.84 E-value=4.7 Score=33.34 Aligned_cols=18 Identities=17% Similarity=0.615 Sum_probs=11.3
Q ss_pred CCcccccccccccCChhH
Q 031430 82 PKTHECSICGLEFAIGQA 99 (159)
Q Consensus 82 ~k~~~C~~Cgk~f~~~~~ 99 (159)
.+.-.||.||.+|....-
T Consensus 676 tRqRKCP~Cn~aFganDv 693 (698)
T KOG0978|consen 676 TRQRKCPKCNAAFGANDV 693 (698)
T ss_pred HhcCCCCCCCCCCCcccc
Confidence 344567777777765543
No 165
>smart00731 SprT SprT homologues. Predicted to have roles in transcription elongation. Contains a conserved HExxH motif, indicating a metalloprotease function.
Probab=36.73 E-value=27 Score=22.81 Aligned_cols=32 Identities=13% Similarity=0.354 Sum_probs=15.0
Q ss_pred ccccCCCCCCCCCCCCCCCCCCCCCccccccccccc
Q 031430 59 LMTMASSGEDFDQTQMPPASPRKPKTHECSICGLEF 94 (159)
Q Consensus 59 ~~~c~~c~~~f~~~~~l~~~~~~~k~~~C~~Cgk~f 94 (159)
.|.|..|+..+.... -+.....|.|..|+..+
T Consensus 112 ~y~C~~C~~~~~~~r----r~~~~~~y~C~~C~g~l 143 (146)
T smart00731 112 PYRCTGCGQRYLRVR----RSNNVSRYRCGKCGGKL 143 (146)
T ss_pred EEECCCCCCCCceEc----cccCcceEEcCCCCCEE
Confidence 456666665543211 11112446666666544
No 166
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=36.73 E-value=8.1 Score=19.21 Aligned_cols=20 Identities=15% Similarity=0.303 Sum_probs=11.2
Q ss_pred CceeecccccccCCChHHHH
Q 031430 29 KRVFACKTCNKEFPSFQALG 48 (159)
Q Consensus 29 ~k~~~C~~C~~~f~~~~~l~ 48 (159)
-..+.|+.|+..|.....|.
T Consensus 17 ~~id~C~~C~G~W~d~~el~ 36 (41)
T PF13453_consen 17 VEIDVCPSCGGIWFDAGELE 36 (41)
T ss_pred EEEEECCCCCeEEccHHHHH
Confidence 34456666666665555443
No 167
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=36.45 E-value=21 Score=22.34 Aligned_cols=11 Identities=0% Similarity=-0.170 Sum_probs=6.1
Q ss_pred cccCCCCCCCC
Q 031430 60 MTMASSGEDFD 70 (159)
Q Consensus 60 ~~c~~c~~~f~ 70 (159)
..|..||..|.
T Consensus 71 ~~C~~Cg~~~~ 81 (114)
T PRK03681 71 CWCETCQQYVT 81 (114)
T ss_pred EEcccCCCeee
Confidence 45666665443
No 168
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=36.00 E-value=24 Score=22.24 Aligned_cols=10 Identities=10% Similarity=0.232 Sum_probs=5.4
Q ss_pred cccCCCCCCC
Q 031430 60 MTMASSGEDF 69 (159)
Q Consensus 60 ~~c~~c~~~f 69 (159)
+.|..||..|
T Consensus 72 ~~C~~Cg~~~ 81 (117)
T PRK00564 72 LECKDCSHVF 81 (117)
T ss_pred EEhhhCCCcc
Confidence 3566666544
No 169
>PHA02998 RNA polymerase subunit; Provisional
Probab=35.89 E-value=18 Score=24.64 Aligned_cols=12 Identities=33% Similarity=0.728 Sum_probs=8.2
Q ss_pred ccccccccccCC
Q 031430 85 HECSICGLEFAI 96 (159)
Q Consensus 85 ~~C~~Cgk~f~~ 96 (159)
|.|..||..|.-
T Consensus 172 YkC~~CG~~wkp 183 (195)
T PHA02998 172 HACRDCKKHFKP 183 (195)
T ss_pred EEcCCCCCccCC
Confidence 677777776643
No 170
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=35.78 E-value=61 Score=24.76 Aligned_cols=73 Identities=21% Similarity=0.343 Sum_probs=38.3
Q ss_pred eeccc--ccccCCChHHHHHhHHhcCCCCccccCCCC---CCCCC------CCCCCCCCC------CCC-cccccccccc
Q 031430 32 FACKT--CNKEFPSFQALGGHRASHKKPKLMTMASSG---EDFDQ------TQMPPASPR------KPK-THECSICGLE 93 (159)
Q Consensus 32 ~~C~~--C~~~f~~~~~l~~h~~~h~~~~~~~c~~c~---~~f~~------~~~l~~~~~------~~k-~~~C~~Cgk~ 93 (159)
|.|+. |.........|..|.....+ .+.|..|- +.|.. ...|..+.. |-+ .-.|..|..-
T Consensus 152 F~CP~skc~~~C~~~k~lk~H~K~~H~--~~~C~~C~~nKk~F~~E~~lF~~~~Lr~H~~~G~~e~GFKGHP~C~FC~~~ 229 (493)
T COG5236 152 FKCPKSKCHRRCGSLKELKKHYKAQHG--FVLCSECIGNKKDFWNEIRLFRSSTLRDHKNGGLEEEGFKGHPLCIFCKIY 229 (493)
T ss_pred hcCCchhhhhhhhhHHHHHHHHHhhcC--cEEhHhhhcCcccCccceeeeecccccccccCCccccCcCCCchhhhccce
Confidence 56654 55554455666667665432 34455543 22322 222322222 111 1257778888
Q ss_pred cCChhHHHHHHHH
Q 031430 94 FAIGQALGGHMRR 106 (159)
Q Consensus 94 f~~~~~l~~H~~~ 106 (159)
|.....|-.|+|.
T Consensus 230 FYdDDEL~~HcR~ 242 (493)
T COG5236 230 FYDDDELRRHCRL 242 (493)
T ss_pred ecChHHHHHHHHh
Confidence 8888777777764
No 171
>PRK12496 hypothetical protein; Provisional
Probab=35.74 E-value=32 Score=23.11 Aligned_cols=11 Identities=0% Similarity=0.087 Sum_probs=7.5
Q ss_pred cccCCCCCCCC
Q 031430 60 MTMASSGEDFD 70 (159)
Q Consensus 60 ~~c~~c~~~f~ 70 (159)
+.|.-|++.|.
T Consensus 128 ~~C~gC~~~~~ 138 (164)
T PRK12496 128 KVCKGCKKKYP 138 (164)
T ss_pred EECCCCCcccc
Confidence 56777777664
No 172
>COG4306 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=35.25 E-value=38 Score=21.70 Aligned_cols=39 Identities=10% Similarity=0.127 Sum_probs=23.9
Q ss_pred cccCCCCCCCCCCCCCC----CCCCCCCcccccccccccCChh
Q 031430 60 MTMASSGEDFDQTQMPP----ASPRKPKTHECSICGLEFAIGQ 98 (159)
Q Consensus 60 ~~c~~c~~~f~~~~~l~----~~~~~~k~~~C~~Cgk~f~~~~ 98 (159)
..|+.|.....-..+.. --+.-+.|--|..||+.|.|..
T Consensus 40 ~qcp~csasirgd~~vegvlglg~dye~psfchncgs~fpwte 82 (160)
T COG4306 40 TQCPICSASIRGDYYVEGVLGLGGDYEPPSFCHNCGSRFPWTE 82 (160)
T ss_pred hcCCccCCcccccceeeeeeccCCCCCCcchhhcCCCCCCcHH
Confidence 46777766554322221 1223356777999999999864
No 173
>COG1773 Rubredoxin [Energy production and conversion]
Probab=34.89 E-value=16 Score=19.72 Aligned_cols=14 Identities=36% Similarity=0.899 Sum_probs=10.9
Q ss_pred CcccccccccccCC
Q 031430 83 KTHECSICGLEFAI 96 (159)
Q Consensus 83 k~~~C~~Cgk~f~~ 96 (159)
+.|+|..||..|.-
T Consensus 2 ~~~~C~~CG~vYd~ 15 (55)
T COG1773 2 KRWRCSVCGYVYDP 15 (55)
T ss_pred CceEecCCceEecc
Confidence 35889999988754
No 174
>KOG4124 consensus Putative transcriptional repressor regulating G2/M transition [Transcription; Cell cycle control, cell division, chromosome partitioning]
Probab=34.66 E-value=11 Score=28.61 Aligned_cols=23 Identities=22% Similarity=0.442 Sum_probs=17.9
Q ss_pred CCCcccccccccccCChhHHHHH
Q 031430 81 KPKTHECSICGLEFAIGQALGGH 103 (159)
Q Consensus 81 ~~k~~~C~~Cgk~f~~~~~l~~H 103 (159)
..|+|+|++|.+.+.....|..|
T Consensus 395 ~nk~~r~~i~~~~~k~~~~l~~~ 417 (442)
T KOG4124|consen 395 ENKPYRCEVCSKRYKNLNGLKYH 417 (442)
T ss_pred ccCcccChhhhhhhccCCCCCce
Confidence 46899999999988877665544
No 175
>cd00065 FYVE FYVE domain; Zinc-binding domain; targets proteins to membrane lipids via interaction with phosphatidylinositol-3-phosphate, PI3P; present in Fab1, YOTB, Vac1, and EEA1;
Probab=34.46 E-value=33 Score=18.03 Aligned_cols=12 Identities=42% Similarity=0.938 Sum_probs=5.8
Q ss_pred ccccccccccCC
Q 031430 85 HECSICGLEFAI 96 (159)
Q Consensus 85 ~~C~~Cgk~f~~ 96 (159)
+.|..||+.|-.
T Consensus 19 ~~Cr~Cg~~~C~ 30 (57)
T cd00065 19 HHCRNCGRIFCS 30 (57)
T ss_pred cccCcCcCCcCh
Confidence 345555555443
No 176
>cd01121 Sms Sms (bacterial radA) DNA repair protein. This protein is not related to archael radA any more than is to other RecA-like NTPases. Sms has a role in recombination and recombinational repair and is responsible for the stabilization or processing of branched DNA molecules.
Probab=33.80 E-value=30 Score=26.59 Aligned_cols=10 Identities=30% Similarity=0.624 Sum_probs=5.7
Q ss_pred cccccccccc
Q 031430 84 THECSICGLE 93 (159)
Q Consensus 84 ~~~C~~Cgk~ 93 (159)
..+|+.|+.+
T Consensus 14 ~g~cp~c~~w 23 (372)
T cd01121 14 LGKCPECGEW 23 (372)
T ss_pred cEECcCCCCc
Confidence 3466666644
No 177
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=33.76 E-value=31 Score=26.98 Aligned_cols=29 Identities=14% Similarity=0.283 Sum_probs=16.3
Q ss_pred ccCCCCCCCCCCCCCCCCCCCCCcccccccccccCCh
Q 031430 61 TMASSGEDFDQTQMPPASPRKPKTHECSICGLEFAIG 97 (159)
Q Consensus 61 ~c~~c~~~f~~~~~l~~~~~~~k~~~C~~Cgk~f~~~ 97 (159)
.|+.||....+ .|..-|+|..||..+...
T Consensus 352 ~Cp~Cg~~m~S--------~G~~g~rC~kCg~~~~~~ 380 (421)
T COG1571 352 VCPRCGGRMKS--------AGRNGFRCKKCGTRARET 380 (421)
T ss_pred CCCccCCchhh--------cCCCCcccccccccCCcc
Confidence 46666655332 122357777777666554
No 178
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=33.61 E-value=33 Score=18.05 Aligned_cols=11 Identities=27% Similarity=0.706 Sum_probs=6.2
Q ss_pred ccccccccccc
Q 031430 84 THECSICGLEF 94 (159)
Q Consensus 84 ~~~C~~Cgk~f 94 (159)
.+.|..||..+
T Consensus 37 r~~C~~Cgyt~ 47 (50)
T PRK00432 37 RWHCGKCGYTE 47 (50)
T ss_pred cEECCCcCCEE
Confidence 45666666543
No 179
>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=33.45 E-value=31 Score=27.41 Aligned_cols=32 Identities=22% Similarity=0.372 Sum_probs=26.3
Q ss_pred CCCCCcccccccccccCChhHHHHHHH-Hcccc
Q 031430 79 PRKPKTHECSICGLEFAIGQALGGHMR-RHRAA 110 (159)
Q Consensus 79 ~~~~k~~~C~~Cgk~f~~~~~l~~H~~-~h~~~ 110 (159)
+...+-+.|+.|.+.|.....+..|+. .|.+.
T Consensus 52 n~sWrFWiCp~CskkF~d~~~~~~H~~~eH~~~ 84 (466)
T PF04780_consen 52 NKSWRFWICPRCSKKFSDAESCLSHMEQEHPAG 84 (466)
T ss_pred cCceeEeeCCcccceeCCHHHHHHHHHHhhhhh
Confidence 344667899999999999999999986 56654
No 180
>KOG0717 consensus Molecular chaperone (DnaJ superfamily) [Posttranslational modification, protein turnover, chaperones]
Probab=33.29 E-value=26 Score=27.73 Aligned_cols=21 Identities=24% Similarity=0.507 Sum_probs=18.9
Q ss_pred ccccccccccCChhHHHHHHH
Q 031430 85 HECSICGLEFAIGQALGGHMR 105 (159)
Q Consensus 85 ~~C~~Cgk~f~~~~~l~~H~~ 105 (159)
+-|.+|+++|.+.-.+..|..
T Consensus 293 lyC~vCnKsFKseKq~kNHEn 313 (508)
T KOG0717|consen 293 LYCVVCNKSFKSEKQLKNHEN 313 (508)
T ss_pred eEEeeccccccchHHHHhhHH
Confidence 679999999999999999964
No 181
>KOG2785 consensus C2H2-type Zn-finger protein [General function prediction only]
Probab=33.20 E-value=56 Score=25.19 Aligned_cols=66 Identities=18% Similarity=0.244 Sum_probs=42.2
Q ss_pred eeecccccccCCChHHHHHhHHhcCCCCccccCCCCCCCCCCCCCCCC--------CCCCCcccccccc---cccCChhH
Q 031430 31 VFACKTCNKEFPSFQALGGHRASHKKPKLMTMASSGEDFDQTQMPPAS--------PRKPKTHECSICG---LEFAIGQA 99 (159)
Q Consensus 31 ~~~C~~C~~~f~~~~~l~~h~~~h~~~~~~~c~~c~~~f~~~~~l~~~--------~~~~k~~~C~~Cg---k~f~~~~~ 99 (159)
|-.|-.|++.+..-..-..|+..++|- |. .....|... -....-|.|-.|+ +.|..-.+
T Consensus 166 Pt~CLfC~~~~k~~e~~~~HM~~~Hgf--fI--------PdreYL~D~~GLl~YLgeKV~~~~~CL~CN~~~~~f~slea 235 (390)
T KOG2785|consen 166 PTDCLFCDKKSKSLEENLKHMFKEHGF--FI--------PDREYLTDEKGLLKYLGEKVGIGFICLFCNELGRPFSSLEA 235 (390)
T ss_pred CcceeecCCCcccHHHHHHHHhhccCC--cC--------CchHhhhchhHHHHHHHHHhccCceEEEeccccCcccccHH
Confidence 456888888888887777887776642 11 001111100 0023457788888 99999999
Q ss_pred HHHHHHH
Q 031430 100 LGGHMRR 106 (159)
Q Consensus 100 l~~H~~~ 106 (159)
...||..
T Consensus 236 vr~HM~~ 242 (390)
T KOG2785|consen 236 VRAHMRD 242 (390)
T ss_pred HHHHHhh
Confidence 9999964
No 182
>PTZ00303 phosphatidylinositol kinase; Provisional
Probab=33.10 E-value=40 Score=28.81 Aligned_cols=34 Identities=18% Similarity=0.244 Sum_probs=19.3
Q ss_pred eeecccccccCCChHHHHHhHHhcCCCCccccCCCCCCCCC
Q 031430 31 VFACKTCNKEFPSFQALGGHRASHKKPKLMTMASSGEDFDQ 71 (159)
Q Consensus 31 ~~~C~~C~~~f~~~~~l~~h~~~h~~~~~~~c~~c~~~f~~ 71 (159)
.-.|..|++.|.....+. +.+.+-|..||..|..
T Consensus 460 SdtC~~C~kkFfSlsK~L-------~~RKHHCRkCGrVFC~ 493 (1374)
T PTZ00303 460 SDSCPSCGRAFISLSRPL-------GTRAHHCRSCGIRLCV 493 (1374)
T ss_pred CCcccCcCCccccccccc-------ccccccccCCccccCc
Confidence 356999999996542111 1133446666665544
No 183
>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=32.61 E-value=8.9 Score=23.01 Aligned_cols=31 Identities=23% Similarity=0.353 Sum_probs=17.3
Q ss_pred CccccCCCCCCCCCCCCCCCCCCCCCcccccccccccC
Q 031430 58 KLMTMASSGEDFDQTQMPPASPRKPKTHECSICGLEFA 95 (159)
Q Consensus 58 ~~~~c~~c~~~f~~~~~l~~~~~~~k~~~C~~Cgk~f~ 95 (159)
..|.|+.||+.- +.+.- .--|.|..|++.|.
T Consensus 34 ~ky~Cp~Cgk~~-----vkR~a--~GIW~C~~C~~~~A 64 (90)
T PF01780_consen 34 AKYTCPFCGKTS-----VKRVA--TGIWKCKKCGKKFA 64 (90)
T ss_dssp S-BEESSSSSSE-----EEEEE--TTEEEETTTTEEEE
T ss_pred CCCcCCCCCCce-----eEEee--eEEeecCCCCCEEe
Confidence 467788887642 11111 22377888887774
No 184
>KOG3507 consensus DNA-directed RNA polymerase, subunit RPB7.0 [Transcription]
Probab=32.35 E-value=31 Score=18.85 Aligned_cols=12 Identities=25% Similarity=0.744 Sum_probs=7.7
Q ss_pred Cccccccccccc
Q 031430 83 KTHECSICGLEF 94 (159)
Q Consensus 83 k~~~C~~Cgk~f 94 (159)
-.+.|.+||...
T Consensus 36 D~irCReCG~RI 47 (62)
T KOG3507|consen 36 DVIRCRECGYRI 47 (62)
T ss_pred CcEehhhcchHH
Confidence 356788887543
No 185
>KOG2071 consensus mRNA cleavage and polyadenylation factor I/II complex, subunit Pcf11 [RNA processing and modification]
Probab=32.31 E-value=30 Score=28.16 Aligned_cols=28 Identities=21% Similarity=0.382 Sum_probs=22.4
Q ss_pred CCceeecccccccCCChHHHHHhHHhcC
Q 031430 28 GKRVFACKTCNKEFPSFQALGGHRASHK 55 (159)
Q Consensus 28 ~~k~~~C~~C~~~f~~~~~l~~h~~~h~ 55 (159)
..++..|..||..|........|+..|.
T Consensus 415 ~~~pnqC~~CG~R~~~~ee~sk~md~H~ 442 (579)
T KOG2071|consen 415 KDSPNQCKSCGLRFDDSEERSKHMDIHD 442 (579)
T ss_pred cCCcchhcccccccccchhhhhHhhhhh
Confidence 3556899999999999988877776653
No 186
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=31.76 E-value=66 Score=22.00 Aligned_cols=40 Identities=20% Similarity=0.407 Sum_probs=20.8
Q ss_pred HhhccccCCCceeecccccccCCChHHHHHhHHhcCCCCccccCCCCCC
Q 031430 20 SKVGETDQGKRVFACKTCNKEFPSFQALGGHRASHKKPKLMTMASSGED 68 (159)
Q Consensus 20 ~~h~~~h~~~k~~~C~~C~~~f~~~~~l~~h~~~h~~~~~~~c~~c~~~ 68 (159)
+.-...-++..-|.|+.|.-.|...... .. .|.|+.||..
T Consensus 102 k~~le~~~~~~~y~C~~~~~r~sfdeA~------~~---~F~Cp~Cg~~ 141 (176)
T COG1675 102 KRKLEKETENNYYVCPNCHVKYSFDEAM------EL---GFTCPKCGED 141 (176)
T ss_pred HHHHHhhccCCceeCCCCCCcccHHHHH------Hh---CCCCCCCCch
Confidence 3333344555567776666555443332 11 2677777654
No 187
>KOG2071 consensus mRNA cleavage and polyadenylation factor I/II complex, subunit Pcf11 [RNA processing and modification]
Probab=31.71 E-value=34 Score=27.85 Aligned_cols=28 Identities=32% Similarity=0.635 Sum_probs=23.5
Q ss_pred CCCcccccccccccCChhHHHHHHHHcc
Q 031430 81 KPKTHECSICGLEFAIGQALGGHMRRHR 108 (159)
Q Consensus 81 ~~k~~~C~~Cgk~f~~~~~l~~H~~~h~ 108 (159)
...|-.|..||..|.+......||..|.
T Consensus 415 ~~~pnqC~~CG~R~~~~ee~sk~md~H~ 442 (579)
T KOG2071|consen 415 KDSPNQCKSCGLRFDDSEERSKHMDIHD 442 (579)
T ss_pred cCCcchhcccccccccchhhhhHhhhhh
Confidence 3567899999999999988888887774
No 188
>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=31.59 E-value=24 Score=19.57 Aligned_cols=13 Identities=31% Similarity=0.820 Sum_probs=4.8
Q ss_pred CcccccccccccC
Q 031430 83 KTHECSICGLEFA 95 (159)
Q Consensus 83 k~~~C~~Cgk~f~ 95 (159)
+.+.|..||..|-
T Consensus 24 rrhhCr~CG~~vC 36 (69)
T PF01363_consen 24 RRHHCRNCGRVVC 36 (69)
T ss_dssp -EEE-TTT--EEE
T ss_pred eeEccCCCCCEEC
Confidence 3445666665554
No 189
>PF11789 zf-Nse: Zinc-finger of the MIZ type in Nse subunit; PDB: 2YU4_A 3HTK_C.
Probab=31.13 E-value=37 Score=18.37 Aligned_cols=32 Identities=13% Similarity=0.123 Sum_probs=15.6
Q ss_pred CceeecccccccCCChHHHHHhHHhcCCCCccccCC
Q 031430 29 KRVFACKTCNKEFPSFQALGGHRASHKKPKLMTMAS 64 (159)
Q Consensus 29 ~k~~~C~~C~~~f~~~~~l~~h~~~h~~~~~~~c~~ 64 (159)
+.|.....|+..|...+-+ ..+ .......|+.
T Consensus 22 ~~PV~s~~C~H~fek~aI~-~~i---~~~~~~~CPv 53 (57)
T PF11789_consen 22 EDPVKSKKCGHTFEKEAIL-QYI---QRNGSKRCPV 53 (57)
T ss_dssp SSEEEESSS--EEEHHHHH-HHC---TTTS-EE-SC
T ss_pred hCCcCcCCCCCeecHHHHH-HHH---HhcCCCCCCC
Confidence 4567777788888755433 222 2334566665
No 190
>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 COG5188 PRP9 Splicing factor 3a, subunit 3 [RNA processing and modification]
Probab=30.67 E-value=24 Score=26.88 Aligned_cols=28 Identities=21% Similarity=0.394 Sum_probs=22.0
Q ss_pred CCCCCCcccccccc-cccCChhHHHHHHH
Q 031430 78 SPRKPKTHECSICG-LEFAIGQALGGHMR 105 (159)
Q Consensus 78 ~~~~~k~~~C~~Cg-k~f~~~~~l~~H~~ 105 (159)
.|.-.+.|.|.+|| +.+.-...+.+|-.
T Consensus 368 lhgLd~ef~CEICgNyvy~GR~~FdrHF~ 396 (470)
T COG5188 368 LHGLDIEFECEICGNYVYYGRDRFDRHFE 396 (470)
T ss_pred hcCCCcceeeeecccccccchHHHHhhhh
Confidence 34457889999999 88888888888853
No 192
>COG4391 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=30.66 E-value=21 Score=19.74 Aligned_cols=13 Identities=15% Similarity=0.554 Sum_probs=6.9
Q ss_pred CcccccccccccC
Q 031430 83 KTHECSICGLEFA 95 (159)
Q Consensus 83 k~~~C~~Cgk~f~ 95 (159)
..-.|+.|+..|.
T Consensus 47 gev~CPYC~t~y~ 59 (62)
T COG4391 47 GEVVCPYCSTRYR 59 (62)
T ss_pred CcEecCccccEEE
Confidence 3345666665553
No 193
>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=30.31 E-value=18 Score=19.15 Aligned_cols=14 Identities=14% Similarity=0.534 Sum_probs=7.7
Q ss_pred ecccccccCCChHH
Q 031430 33 ACKTCNKEFPSFQA 46 (159)
Q Consensus 33 ~C~~C~~~f~~~~~ 46 (159)
.|++|++.|.....
T Consensus 22 ~CPlC~r~l~~e~~ 35 (54)
T PF04423_consen 22 CCPLCGRPLDEEHR 35 (54)
T ss_dssp E-TTT--EE-HHHH
T ss_pred cCCCCCCCCCHHHH
Confidence 89999999976544
No 194
>COG2331 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=30.25 E-value=32 Score=19.94 Aligned_cols=11 Identities=27% Similarity=1.081 Sum_probs=7.7
Q ss_pred eeecccccccC
Q 031430 31 VFACKTCNKEF 41 (159)
Q Consensus 31 ~~~C~~C~~~f 41 (159)
.|+|..|+..|
T Consensus 12 ~Y~c~~cg~~~ 22 (82)
T COG2331 12 SYECTECGNRF 22 (82)
T ss_pred EEeecccchHH
Confidence 47788887655
No 195
>PF10083 DUF2321: Uncharacterized protein conserved in bacteria (DUF2321); InterPro: IPR016891 This entry is represented by Bacteriophage 'Lactobacillus prophage Lj928', Orf-Ljo1454. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=29.90 E-value=44 Score=22.29 Aligned_cols=20 Identities=15% Similarity=0.350 Sum_probs=15.9
Q ss_pred CCCcccccccccccCChhHH
Q 031430 81 KPKTHECSICGLEFAIGQAL 100 (159)
Q Consensus 81 ~~k~~~C~~Cgk~f~~~~~l 100 (159)
-+.|.=|..||+.|.|...-
T Consensus 65 ~~~PsYC~~CGkpyPWt~~~ 84 (158)
T PF10083_consen 65 YEAPSYCHNCGKPYPWTENA 84 (158)
T ss_pred CCCChhHHhCCCCCchHHHH
Confidence 35788899999999996543
No 196
>PF14787 zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB: 1CL4_A 1DSV_A.
Probab=29.84 E-value=28 Score=16.97 Aligned_cols=14 Identities=29% Similarity=0.643 Sum_probs=8.7
Q ss_pred cccccccccCChhH
Q 031430 86 ECSICGLEFAIGQA 99 (159)
Q Consensus 86 ~C~~Cgk~f~~~~~ 99 (159)
.|..|++.|-+.+.
T Consensus 4 ~CprC~kg~Hwa~~ 17 (36)
T PF14787_consen 4 LCPRCGKGFHWASE 17 (36)
T ss_dssp C-TTTSSSCS-TTT
T ss_pred cCcccCCCcchhhh
Confidence 57888888877653
No 197
>PRK04351 hypothetical protein; Provisional
Probab=29.35 E-value=32 Score=22.73 Aligned_cols=9 Identities=44% Similarity=1.091 Sum_probs=4.1
Q ss_pred ccccccccc
Q 031430 85 HECSICGLE 93 (159)
Q Consensus 85 ~~C~~Cgk~ 93 (159)
|.|..||..
T Consensus 113 Y~C~~Cg~~ 121 (149)
T PRK04351 113 YECQSCGQQ 121 (149)
T ss_pred EECCCCCCE
Confidence 444444433
No 198
>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=29.30 E-value=19 Score=22.48 Aligned_cols=12 Identities=33% Similarity=0.952 Sum_probs=6.3
Q ss_pred eecccccccCCC
Q 031430 32 FACKTCNKEFPS 43 (159)
Q Consensus 32 ~~C~~C~~~f~~ 43 (159)
+.|..||..|..
T Consensus 71 ~~C~~Cg~~~~~ 82 (113)
T PF01155_consen 71 ARCRDCGHEFEP 82 (113)
T ss_dssp EEETTTS-EEEC
T ss_pred EECCCCCCEEec
Confidence 556666665543
No 199
>PTZ00448 hypothetical protein; Provisional
Probab=29.05 E-value=43 Score=25.72 Aligned_cols=23 Identities=22% Similarity=0.431 Sum_probs=20.6
Q ss_pred cccccccccccCChhHHHHHHHH
Q 031430 84 THECSICGLEFAIGQALGGHMRR 106 (159)
Q Consensus 84 ~~~C~~Cgk~f~~~~~l~~H~~~ 106 (159)
.|.|..|+-.|.+....+.|.++
T Consensus 314 ~~tC~~C~v~F~~~~~qR~H~KS 336 (373)
T PTZ00448 314 MLLCRKCNIQLMDHNAFKQHYRS 336 (373)
T ss_pred CccccccccccCCHHHHHHHhhh
Confidence 58899999999998999999885
No 200
>COG1326 Uncharacterized archaeal Zn-finger protein [General function prediction only]
Probab=27.66 E-value=64 Score=22.42 Aligned_cols=15 Identities=13% Similarity=0.142 Sum_probs=10.1
Q ss_pred CCccccCCCCCCCCC
Q 031430 57 PKLMTMASSGEDFDQ 71 (159)
Q Consensus 57 ~~~~~c~~c~~~f~~ 71 (159)
+....|..||..+..
T Consensus 28 ~~lvrC~eCG~V~~~ 42 (201)
T COG1326 28 EPLVRCEECGTVHPA 42 (201)
T ss_pred ceEEEccCCCcEeec
Confidence 345678888877643
No 201
>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=27.23 E-value=26 Score=18.45 Aligned_cols=12 Identities=42% Similarity=0.952 Sum_probs=9.5
Q ss_pred ccccccccccCC
Q 031430 85 HECSICGLEFAI 96 (159)
Q Consensus 85 ~~C~~Cgk~f~~ 96 (159)
|.|..||..|.-
T Consensus 2 y~C~~CgyiYd~ 13 (50)
T cd00730 2 YECRICGYIYDP 13 (50)
T ss_pred cCCCCCCeEECC
Confidence 789999988754
No 202
>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=27.19 E-value=41 Score=17.06 Aligned_cols=14 Identities=29% Similarity=0.800 Sum_probs=10.3
Q ss_pred cccccccccCChhH
Q 031430 86 ECSICGLEFAIGQA 99 (159)
Q Consensus 86 ~C~~Cgk~f~~~~~ 99 (159)
.|..||+.|.+.-.
T Consensus 10 ~C~~C~rpf~WRKK 23 (42)
T PF10013_consen 10 ICPVCGRPFTWRKK 23 (42)
T ss_pred cCcccCCcchHHHH
Confidence 58888888876543
No 203
>KOG1842 consensus FYVE finger-containing protein [General function prediction only]
Probab=27.05 E-value=37 Score=26.73 Aligned_cols=30 Identities=27% Similarity=0.399 Sum_probs=24.4
Q ss_pred CCcccccccccccCChhHHHHHHHH-ccccc
Q 031430 82 PKTHECSICGLEFAIGQALGGHMRR-HRAAA 111 (159)
Q Consensus 82 ~k~~~C~~Cgk~f~~~~~l~~H~~~-h~~~~ 111 (159)
..-|.|++|..-|.+-..|..|... |.++.
T Consensus 13 ~egflCPiC~~dl~~~~~L~~H~d~eH~~ed 43 (505)
T KOG1842|consen 13 LEGFLCPICLLDLPNLSALNDHLDVEHFEED 43 (505)
T ss_pred hhcccCchHhhhhhhHHHHHHHHhhhccccc
Confidence 3568999999999999999999865 44443
No 204
>PF01215 COX5B: Cytochrome c oxidase subunit Vb This family consists of chains F and S ; InterPro: IPR002124 Cytochrome c oxidase (1.9.3.1 from EC) is an oligomeric enzymatic complex which is a component of the respiratory chain complex and is involved in the transfer of electrons from cytochrome c to oxygen []. In eukaryotes this enzyme complex is located in the mitochondrial inner membrane; in aerobic prokaryotes it is found in the plasma membrane. In eukaryotes, in addition to the three large subunits, I, II and III, that form the catalytic centre of the enzyme complex, there are a variable number of small polypeptidic subunits. One of these subunits, which is known as Vb in mammals, V in Dictyostelium discoideum (Slime mold) and IV in yeast, binds a zinc atom. The sequence of subunit Vb is well conserved and includes three conserved cysteines that coordinate the zinc ion [, ]. Two of these cysteines are clustered in the C-terminal section of the subunit.; GO: 0004129 cytochrome-c oxidase activity, 0005740 mitochondrial envelope; PDB: 2EIL_S 2ZXW_S 3ASN_S 1OCO_S 3AG4_S 3ABK_S 1OCZ_S 1OCC_F 3ASO_S 3ABL_S ....
Probab=26.96 E-value=22 Score=23.11 Aligned_cols=15 Identities=33% Similarity=0.811 Sum_probs=12.3
Q ss_pred CCcccccccccccCC
Q 031430 82 PKTHECSICGLEFAI 96 (159)
Q Consensus 82 ~k~~~C~~Cgk~f~~ 96 (159)
.++.+|.+||..|.-
T Consensus 110 g~~~RCpeCG~~fkL 124 (136)
T PF01215_consen 110 GKPQRCPECGQVFKL 124 (136)
T ss_dssp TSEEEETTTEEEEEE
T ss_pred CCccCCCCCCeEEEE
Confidence 468999999998853
No 205
>PF10263 SprT-like: SprT-like family; InterPro: IPR006640 This is a family of uncharacterised bacterial proteins which includes Escherichia coli SprT (P39902 from SWISSPROT). SprT is described as a regulator of bolA gene in stationary phase []. The majority of members contain the metallopeptidase zinc binding signature which has a HExxH motif, however there is no evidence for them being metallopeptidases.
Probab=26.94 E-value=29 Score=22.65 Aligned_cols=30 Identities=23% Similarity=0.514 Sum_probs=14.0
Q ss_pred cccCCCCCCCCCCCCCCCCCCCCCccccccccccc
Q 031430 60 MTMASSGEDFDQTQMPPASPRKPKTHECSICGLEF 94 (159)
Q Consensus 60 ~~c~~c~~~f~~~~~l~~~~~~~k~~~C~~Cgk~f 94 (159)
|.|..|+..+...... ....|.|..|+..|
T Consensus 124 ~~C~~C~~~~~r~~~~-----~~~~~~C~~C~~~l 153 (157)
T PF10263_consen 124 YRCPSCGREYKRHRRS-----KRKRYRCGRCGGPL 153 (157)
T ss_pred EEcCCCCCEeeeeccc-----chhhEECCCCCCEE
Confidence 4566666544321111 22336666666444
No 206
>PF08882 Acetone_carb_G: Acetone carboxylase gamma subunit; InterPro: IPR014979 Acetone carboxylase is the key enzyme of bacterial acetone metabolism, catalysing the condensation of acetone and CO2 to form acetoacetate [] according to the following reaction: CH3COCH3 + CO2 + ATP = CH3COCH2COO- + AMP + 2P(i) + H+ It has the subunit composition: (alpha(2)beta(2)gamma(2) multimers of 85kDa, 78kDa, and 20kDa subunits). It is expressed to high levels (17 to 25% of soluble protein) in cells grown with acetone as the carbon source but are not present at detectable levels in cells grown with other carbon sources []. Acetone carboxylase may enable Helicobacter pylori to survive off acetone in the stomach of humans and other mammals where it is the etiological agent of peptic ulcer disease []. This entry represents the family of gamma subunit-related acetone carboxylase proteins.
Probab=26.94 E-value=21 Score=22.31 Aligned_cols=29 Identities=10% Similarity=0.038 Sum_probs=20.3
Q ss_pred chhccCCCCceeeeccCCC--CCcccccccc
Q 031430 130 VLKKSNSCKRVFCLDLNLM--PTGDDLKLWV 158 (159)
Q Consensus 130 ~~~~~~~~~~~~~~~~~l~--~~~~~~~~~~ 158 (159)
..+=|+.||...-.+.--+ |+..|+++.|
T Consensus 73 rEyyCP~Cgt~levE~~~Pg~P~~hD~epDi 103 (112)
T PF08882_consen 73 REYYCPGCGTQLEVEAPPPGYPPIHDFEPDI 103 (112)
T ss_pred EEEECCCCcceeEEccCCCCCCceEecccCH
Confidence 4567899997766655555 7777777665
No 207
>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=26.64 E-value=45 Score=21.84 Aligned_cols=46 Identities=9% Similarity=0.070 Sum_probs=27.8
Q ss_pred cccCCCCCCCCCCCCCC--------CCCCCCCcccccccccccCChhHHHHHHH
Q 031430 60 MTMASSGEDFDQTQMPP--------ASPRKPKTHECSICGLEFAIGQALGGHMR 105 (159)
Q Consensus 60 ~~c~~c~~~f~~~~~l~--------~~~~~~k~~~C~~Cgk~f~~~~~l~~H~~ 105 (159)
-.|..|+..+.....-. .......-+.|+.||+.|=..+++.+..+
T Consensus 92 sRC~~CN~~L~~v~~~~v~~~vp~~v~~~~~~f~~C~~C~kiyW~GsH~~~~~~ 145 (147)
T PF01927_consen 92 SRCPKCNGPLRPVSKEEVKDRVPPYVYETYDEFWRCPGCGKIYWEGSHWRRMEE 145 (147)
T ss_pred CccCCCCcEeeechhhccccccCccccccCCeEEECCCCCCEecccccHHHHHh
Confidence 47888886554311110 01112456899999999977777765543
No 208
>KOG3214 consensus Uncharacterized Zn ribbon-containing protein [Function unknown]
Probab=26.55 E-value=31 Score=21.09 Aligned_cols=13 Identities=31% Similarity=0.715 Sum_probs=9.0
Q ss_pred ccccccccccCCh
Q 031430 85 HECSICGLEFAIG 97 (159)
Q Consensus 85 ~~C~~Cgk~f~~~ 97 (159)
..|.+|+.+|...
T Consensus 48 ~sC~iC~esFqt~ 60 (109)
T KOG3214|consen 48 ASCRICEESFQTT 60 (109)
T ss_pred eeeeehhhhhccc
Confidence 4677777777654
No 209
>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=26.37 E-value=1e+02 Score=15.60 Aligned_cols=11 Identities=18% Similarity=0.462 Sum_probs=7.0
Q ss_pred CCccccccccc
Q 031430 82 PKTHECSICGL 92 (159)
Q Consensus 82 ~k~~~C~~Cgk 92 (159)
...|.|..|++
T Consensus 35 ~~~~~C~~C~~ 45 (46)
T PF12760_consen 35 RGRYRCKACRK 45 (46)
T ss_pred CCeEECCCCCC
Confidence 45677777764
No 210
>PTZ00043 cytochrome c oxidase subunit; Provisional
Probab=26.30 E-value=35 Score=24.32 Aligned_cols=17 Identities=18% Similarity=0.305 Sum_probs=13.7
Q ss_pred CCCcccccccccccCCh
Q 031430 81 KPKTHECSICGLEFAIG 97 (159)
Q Consensus 81 ~~k~~~C~~Cgk~f~~~ 97 (159)
..++.+|.+||..|.-.
T Consensus 178 EGkpqRCpECGqVFKLV 194 (268)
T PTZ00043 178 EGFLYRCGECDQIFMLV 194 (268)
T ss_pred CCCCccCCCCCcEEEEE
Confidence 45689999999998653
No 211
>PF05290 Baculo_IE-1: Baculovirus immediate-early protein (IE-0); InterPro: IPR007954 This entry contains the Baculovirus immediate-early protein IE-0.
Probab=26.30 E-value=71 Score=20.77 Aligned_cols=20 Identities=20% Similarity=0.233 Sum_probs=11.2
Q ss_pred CCCccccCCCCCCCCCCCCC
Q 031430 56 KPKLMTMASSGEDFDQTQMP 75 (159)
Q Consensus 56 ~~~~~~c~~c~~~f~~~~~l 75 (159)
..+.|+|..|..+......|
T Consensus 77 d~~lYeCnIC~etS~ee~FL 96 (140)
T PF05290_consen 77 DPKLYECNICKETSAEERFL 96 (140)
T ss_pred CCCceeccCcccccchhhcC
Confidence 33556666666655544444
No 212
>PF12773 DZR: Double zinc ribbon
Probab=25.83 E-value=89 Score=15.88 Aligned_cols=7 Identities=14% Similarity=0.306 Sum_probs=2.9
Q ss_pred ccCCCCC
Q 031430 61 TMASSGE 67 (159)
Q Consensus 61 ~c~~c~~ 67 (159)
.|..||.
T Consensus 31 ~C~~Cg~ 37 (50)
T PF12773_consen 31 ICPNCGA 37 (50)
T ss_pred CCcCCcC
Confidence 3444443
No 213
>PF10276 zf-CHCC: Zinc-finger domain; InterPro: IPR019401 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a short conserved zinc-finger domain. It contains the sequence motif Cx8Hx14Cx2C. ; PDB: 2JVM_A 2JRR_A 2JZ8_A.
Probab=25.36 E-value=38 Score=16.95 Aligned_cols=12 Identities=17% Similarity=0.664 Sum_probs=8.0
Q ss_pred ceeecccccccC
Q 031430 30 RVFACKTCNKEF 41 (159)
Q Consensus 30 k~~~C~~C~~~f 41 (159)
.+-.|+.|+..|
T Consensus 28 ~~~~CpYCg~~y 39 (40)
T PF10276_consen 28 GPVVCPYCGTRY 39 (40)
T ss_dssp CEEEETTTTEEE
T ss_pred CeEECCCCCCEE
Confidence 356777777665
No 214
>PRK10220 hypothetical protein; Provisional
Probab=24.55 E-value=60 Score=20.26 Aligned_cols=12 Identities=25% Similarity=0.487 Sum_probs=6.9
Q ss_pred ccccccccccCC
Q 031430 85 HECSICGLEFAI 96 (159)
Q Consensus 85 ~~C~~Cgk~f~~ 96 (159)
|.|++|+..+..
T Consensus 21 ~vCpeC~hEW~~ 32 (111)
T PRK10220 21 YICPECAHEWND 32 (111)
T ss_pred EECCcccCcCCc
Confidence 566666655543
No 215
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=24.52 E-value=53 Score=20.10 Aligned_cols=9 Identities=33% Similarity=1.309 Sum_probs=5.3
Q ss_pred ceeeccccc
Q 031430 30 RVFACKTCN 38 (159)
Q Consensus 30 k~~~C~~C~ 38 (159)
..|.|+.|+
T Consensus 20 t~f~CP~Cg 28 (99)
T PRK14892 20 KIFECPRCG 28 (99)
T ss_pred cEeECCCCC
Confidence 346666666
No 216
>PF14369 zf-RING_3: zinc-finger
Probab=24.39 E-value=82 Score=15.09 Aligned_cols=12 Identities=17% Similarity=0.371 Sum_probs=9.2
Q ss_pred ccCCCCceeeec
Q 031430 133 KSNSCKRVFCLD 144 (159)
Q Consensus 133 ~~~~~~~~~~~~ 144 (159)
.|+.|+..|..+
T Consensus 23 ~CP~C~~gFvEe 34 (35)
T PF14369_consen 23 ACPRCHGGFVEE 34 (35)
T ss_pred CCcCCCCcEeEe
Confidence 688888888754
No 217
>COG5216 Uncharacterized conserved protein [Function unknown]
Probab=24.26 E-value=44 Score=18.29 Aligned_cols=29 Identities=14% Similarity=0.324 Sum_probs=16.8
Q ss_pred eecccccccCCChHHHHHhHHhcCCCCccccCCCC
Q 031430 32 FACKTCNKEFPSFQALGGHRASHKKPKLMTMASSG 66 (159)
Q Consensus 32 ~~C~~C~~~f~~~~~l~~h~~~h~~~~~~~c~~c~ 66 (159)
|.|+ ||-.|...-. ....|+....|+.|.
T Consensus 23 yPCP-CGDRFeIsLe-----Dl~~GE~VArCPSCS 51 (67)
T COG5216 23 YPCP-CGDRFEISLE-----DLRNGEVVARCPSCS 51 (67)
T ss_pred ecCC-CCCEeEEEHH-----HhhCCceEEEcCCce
Confidence 4564 7777653321 234567777777775
No 218
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=24.16 E-value=68 Score=17.35 Aligned_cols=8 Identities=50% Similarity=1.257 Sum_probs=3.8
Q ss_pred cccccccc
Q 031430 84 THECSICG 91 (159)
Q Consensus 84 ~~~C~~Cg 91 (159)
.|.|+.||
T Consensus 14 ~~~Cp~cG 21 (55)
T PF13824_consen 14 NFECPDCG 21 (55)
T ss_pred CCcCCCCC
Confidence 34444444
No 219
>PF12907 zf-met2: Zinc-binding
Probab=24.14 E-value=15 Score=18.41 Aligned_cols=26 Identities=27% Similarity=0.483 Sum_probs=17.8
Q ss_pred ccccccccccCC---hhHHHHHHH-Hcccc
Q 031430 85 HECSICGLEFAI---GQALGGHMR-RHRAA 110 (159)
Q Consensus 85 ~~C~~Cgk~f~~---~~~l~~H~~-~h~~~ 110 (159)
+.|.+|-.+|.. ...|..|.. .|...
T Consensus 2 i~C~iC~qtF~~t~~~~~L~eH~enKHpK~ 31 (40)
T PF12907_consen 2 IICKICRQTFMQTTNEPQLKEHAENKHPKN 31 (40)
T ss_pred cCcHHhhHHHHhcCCHHHHHHHHHccCCCC
Confidence 578889977754 456888876 45443
No 220
>KOG2482 consensus Predicted C2H2-type Zn-finger protein [Transcription]
Probab=23.90 E-value=53 Score=25.02 Aligned_cols=76 Identities=16% Similarity=0.239 Sum_probs=45.4
Q ss_pred eeecccccccCCChHHHHHhHHhc--CCCCc--------cc--cCCCCCCCCC-CCCC--------CCCC--------CC
Q 031430 31 VFACKTCNKEFPSFQALGGHRASH--KKPKL--------MT--MASSGEDFDQ-TQMP--------PASP--------RK 81 (159)
Q Consensus 31 ~~~C~~C~~~f~~~~~l~~h~~~h--~~~~~--------~~--c~~c~~~f~~-~~~l--------~~~~--------~~ 81 (159)
.+.|-.|.+.|..+..|+.|++.. ..-.| |. ....|+.... .+.. ...- .+
T Consensus 195 r~~CLyCekifrdkntLkeHMrkK~HrrinPknreYDkfyiINY~ev~ks~t~~~~e~dret~~d~~E~D~~wsDw~ed~ 274 (423)
T KOG2482|consen 195 RLRCLYCEKIFRDKNTLKEHMRKKRHRRINPKNREYDKFYIINYLEVGKSWTIVHSEDDRETNEDINETDDTWSDWNEDD 274 (423)
T ss_pred hheeeeeccccCCcHHHHHHHHhccCcccCCCccccceEEEEeHhhcCCccchhhhhhhhhhhccccccccchhhhhcCC
Confidence 478999999999999999999863 22111 11 1122332211 0000 0000 01
Q ss_pred CCc--ccccccccccCChhHHHHHHHH
Q 031430 82 PKT--HECSICGLEFAIGQALGGHMRR 106 (159)
Q Consensus 82 ~k~--~~C~~Cgk~f~~~~~l~~H~~~ 106 (159)
..+ ..|-.|....-+...|..||++
T Consensus 275 a~a~~v~CLfC~~~~en~~~l~eHmk~ 301 (423)
T KOG2482|consen 275 AEALSVVCLFCTNFYENPVFLFEHMKI 301 (423)
T ss_pred CCccceEEEeeccchhhHHHHHHHHHH
Confidence 122 5888999999889999999975
No 221
>TIGR00686 phnA alkylphosphonate utilization operon protein PhnA. The protein family includes an uncharacterized member designated phnA in Escherichia coli, part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage. This protein is not related to the characterized phosphonoacetate hydrolase designated PhnA by Kulakova, et al. (2001, 1997).
Probab=23.68 E-value=51 Score=20.51 Aligned_cols=12 Identities=25% Similarity=0.468 Sum_probs=6.9
Q ss_pred ccccccccccCC
Q 031430 85 HECSICGLEFAI 96 (159)
Q Consensus 85 ~~C~~Cgk~f~~ 96 (159)
|.|++|+..+..
T Consensus 20 ~iCpeC~~EW~~ 31 (109)
T TIGR00686 20 LICPSCLYEWNE 31 (109)
T ss_pred eECccccccccc
Confidence 566666655443
No 222
>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=23.53 E-value=31 Score=17.91 Aligned_cols=12 Identities=25% Similarity=0.913 Sum_probs=9.2
Q ss_pred ccccccccccCC
Q 031430 85 HECSICGLEFAI 96 (159)
Q Consensus 85 ~~C~~Cgk~f~~ 96 (159)
|.|..||..|.-
T Consensus 2 y~C~~CgyvYd~ 13 (47)
T PF00301_consen 2 YQCPVCGYVYDP 13 (47)
T ss_dssp EEETTTSBEEET
T ss_pred cCCCCCCEEEcC
Confidence 678899977644
No 223
>KOG0717 consensus Molecular chaperone (DnaJ superfamily) [Posttranslational modification, protein turnover, chaperones]
Probab=23.37 E-value=56 Score=25.98 Aligned_cols=21 Identities=38% Similarity=0.694 Sum_probs=18.9
Q ss_pred eecccccccCCChHHHHHhHH
Q 031430 32 FACKTCNKEFPSFQALGGHRA 52 (159)
Q Consensus 32 ~~C~~C~~~f~~~~~l~~h~~ 52 (159)
+-|.+|++.|.+.-.|..|..
T Consensus 293 lyC~vCnKsFKseKq~kNHEn 313 (508)
T KOG0717|consen 293 LYCVVCNKSFKSEKQLKNHEN 313 (508)
T ss_pred eEEeeccccccchHHHHhhHH
Confidence 789999999999999998864
No 224
>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=23.28 E-value=42 Score=16.39 Aligned_cols=11 Identities=18% Similarity=0.836 Sum_probs=4.7
Q ss_pred ceeeccccccc
Q 031430 30 RVFACKTCNKE 40 (159)
Q Consensus 30 k~~~C~~C~~~ 40 (159)
+.|+|..||..
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 34667776643
No 225
>COG4640 Predicted membrane protein [Function unknown]
Probab=23.27 E-value=70 Score=24.92 Aligned_cols=17 Identities=29% Similarity=0.747 Sum_probs=10.2
Q ss_pred cccccccccCChhHHHH
Q 031430 86 ECSICGLEFAIGQALGG 102 (159)
Q Consensus 86 ~C~~Cgk~f~~~~~l~~ 102 (159)
.|.+||..|....++.+
T Consensus 17 qC~qCG~~~t~~~sqan 33 (465)
T COG4640 17 QCTQCGHKFTSRQSQAN 33 (465)
T ss_pred cccccCCcCCchhhhhh
Confidence 37777776666555443
No 226
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=22.86 E-value=58 Score=17.19 Aligned_cols=10 Identities=30% Similarity=0.893 Sum_probs=5.7
Q ss_pred cccccccccc
Q 031430 84 THECSICGLE 93 (159)
Q Consensus 84 ~~~C~~Cgk~ 93 (159)
.+.|..||.+
T Consensus 37 R~~CGkCgyT 46 (51)
T COG1998 37 RWACGKCGYT 46 (51)
T ss_pred eeEeccccce
Confidence 3566666643
No 227
>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=22.78 E-value=80 Score=23.66 Aligned_cols=50 Identities=10% Similarity=0.238 Sum_probs=24.4
Q ss_pred eeecccccccCCChHHHHHhHHhcCCCCccccCCCCCCCCCCCCCCCCCCCCCcccccccccc
Q 031430 31 VFACKTCNKEFPSFQALGGHRASHKKPKLMTMASSGEDFDQTQMPPASPRKPKTHECSICGLE 93 (159)
Q Consensus 31 ~~~C~~C~~~f~~~~~l~~h~~~h~~~~~~~c~~c~~~f~~~~~l~~~~~~~k~~~C~~Cgk~ 93 (159)
.-.|++||..=. ..+........|.+-..|..|+.... -....|..||..
T Consensus 184 ~~~CPvCGs~P~--~s~~~~~~~~~G~RyL~CslC~teW~-----------~~R~~C~~Cg~~ 233 (305)
T TIGR01562 184 RTLCPACGSPPV--ASMVRQGGKETGLRYLSCSLCATEWH-----------YVRVKCSHCEES 233 (305)
T ss_pred CCcCCCCCChhh--hhhhcccCCCCCceEEEcCCCCCccc-----------ccCccCCCCCCC
Confidence 347999985421 11111001134555567777765332 122467777753
No 228
>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=22.47 E-value=12 Score=21.92 Aligned_cols=11 Identities=36% Similarity=1.059 Sum_probs=5.0
Q ss_pred ccccccccccC
Q 031430 85 HECSICGLEFA 95 (159)
Q Consensus 85 ~~C~~Cgk~f~ 95 (159)
..|..||..|.
T Consensus 47 ~~C~~Cg~~~~ 57 (81)
T PF05129_consen 47 LSCRVCGESFQ 57 (81)
T ss_dssp EEESSS--EEE
T ss_pred EEecCCCCeEE
Confidence 45666665553
No 229
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=21.76 E-value=42 Score=21.35 Aligned_cols=6 Identities=67% Similarity=2.034 Sum_probs=2.9
Q ss_pred cccccc
Q 031430 86 ECSICG 91 (159)
Q Consensus 86 ~C~~Cg 91 (159)
.|+.||
T Consensus 94 ~CP~Cg 99 (124)
T PRK00762 94 ECPVCG 99 (124)
T ss_pred cCcCCC
Confidence 455554
No 230
>PRK06260 threonine synthase; Validated
Probab=21.33 E-value=70 Score=24.73 Aligned_cols=10 Identities=40% Similarity=1.155 Sum_probs=4.4
Q ss_pred eecccccccC
Q 031430 32 FACKTCNKEF 41 (159)
Q Consensus 32 ~~C~~C~~~f 41 (159)
+.|..||+.|
T Consensus 4 ~~C~~cg~~~ 13 (397)
T PRK06260 4 LKCIECGKEY 13 (397)
T ss_pred EEECCCCCCC
Confidence 3444444443
No 231
>PF08209 Sgf11: Sgf11 (transcriptional regulation protein); InterPro: IPR013246 The Sgf11 family is a SAGA complex subunit in Saccharomyces cerevisiae (Baker's yeast). The SAGA complex is a multisubunit protein complex involved in transcriptional regulation. SAGA combines proteins involved in interactions with DNA-bound activators and TATA-binding protein (TBP), as well as enzymes for histone acetylation and deubiquitylation [].; PDB: 3M99_B 2LO2_A 3MHH_C 3MHS_C.
Probab=21.26 E-value=73 Score=15.17 Aligned_cols=25 Identities=24% Similarity=0.495 Sum_probs=16.1
Q ss_pred cccccccccccCChhHHHHHHHHccc
Q 031430 84 THECSICGLEFAIGQALGGHMRRHRA 109 (159)
Q Consensus 84 ~~~C~~Cgk~f~~~~~l~~H~~~h~~ 109 (159)
.+.|+.|++.+. .+.+..|+..-.+
T Consensus 4 ~~~C~nC~R~v~-a~RfA~HLekCmg 28 (33)
T PF08209_consen 4 YVECPNCGRPVA-ASRFAPHLEKCMG 28 (33)
T ss_dssp EEE-TTTSSEEE-GGGHHHHHHHHTC
T ss_pred eEECCCCcCCcc-hhhhHHHHHHHHc
Confidence 467889998753 4567778765443
No 232
>PLN02748 tRNA dimethylallyltransferase
Probab=21.25 E-value=74 Score=25.42 Aligned_cols=25 Identities=16% Similarity=0.219 Sum_probs=20.8
Q ss_pred CCccccccccc-ccCChhHHHHHHHH
Q 031430 82 PKTHECSICGL-EFAIGQALGGHMRR 106 (159)
Q Consensus 82 ~k~~~C~~Cgk-~f~~~~~l~~H~~~ 106 (159)
.+.|.|..|++ .+........|++.
T Consensus 416 ~~~~~Ce~C~~~~~~G~~eW~~Hlks 441 (468)
T PLN02748 416 WTQYVCEACGNKVLRGAHEWEQHKQG 441 (468)
T ss_pred cccccccCCCCcccCCHHHHHHHhcc
Confidence 57889999997 89888888888753
No 233
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=20.94 E-value=48 Score=20.80 Aligned_cols=16 Identities=19% Similarity=0.416 Sum_probs=11.8
Q ss_pred CceeecccccccCCCh
Q 031430 29 KRVFACKTCNKEFPSF 44 (159)
Q Consensus 29 ~k~~~C~~C~~~f~~~ 44 (159)
...+.|..||..+...
T Consensus 20 ~~~l~C~kCgye~~~~ 35 (113)
T COG1594 20 GGKLVCRKCGYEEEAS 35 (113)
T ss_pred CcEEECCCCCcchhcc
Confidence 3478999998776655
No 234
>cd01410 SIRT7 SIRT7: Eukaryotic and prokaryotic group (class4) which includes human sirtuin SIRT6, SIRT7, and several bacterial homologs; and are members of the SIR2 family of proteins, silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation. Sir2 proteins have been shown to regulate gene silencing, DNA repair, metabolic enzymes, and life span.
Probab=20.80 E-value=1.6e+02 Score=20.50 Aligned_cols=18 Identities=22% Similarity=0.512 Sum_probs=9.2
Q ss_pred ccCCCceeecccccccCC
Q 031430 25 TDQGKRVFACKTCNKEFP 42 (159)
Q Consensus 25 ~h~~~k~~~C~~C~~~f~ 42 (159)
.|..-....|..|+..+.
T Consensus 89 lHG~~~~~~C~~C~~~~~ 106 (206)
T cd01410 89 LHGNMFIEVCKSCGPEYV 106 (206)
T ss_pred ecCCcCcccCCCCCCccc
Confidence 444444455666665543
No 235
>PRK05978 hypothetical protein; Provisional
Probab=20.60 E-value=89 Score=20.71 Aligned_cols=11 Identities=36% Similarity=1.078 Sum_probs=7.2
Q ss_pred cccccccccCC
Q 031430 86 ECSICGLEFAI 96 (159)
Q Consensus 86 ~C~~Cgk~f~~ 96 (159)
.|+.||..|..
T Consensus 54 ~C~~CG~~~~~ 64 (148)
T PRK05978 54 HCAACGEDFTH 64 (148)
T ss_pred CccccCCcccc
Confidence 57777766643
No 236
>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=20.25 E-value=1.2e+02 Score=14.74 Aligned_cols=10 Identities=20% Similarity=0.554 Sum_probs=5.2
Q ss_pred CCCccccccc
Q 031430 81 KPKTHECSIC 90 (159)
Q Consensus 81 ~~k~~~C~~C 90 (159)
|...|.|..|
T Consensus 26 G~qryrC~~C 35 (36)
T PF03811_consen 26 GHQRYRCKDC 35 (36)
T ss_pred CCEeEecCcC
Confidence 4445666555
No 237
>KOG2231 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=20.24 E-value=66 Score=26.90 Aligned_cols=21 Identities=29% Similarity=0.423 Sum_probs=11.9
Q ss_pred ecccccccCCChHHHHHhHHh
Q 031430 33 ACKTCNKEFPSFQALGGHRAS 53 (159)
Q Consensus 33 ~C~~C~~~f~~~~~l~~h~~~ 53 (159)
.|..|...|.....|..|++.
T Consensus 184 ~C~~C~~~fld~~el~rH~~~ 204 (669)
T KOG2231|consen 184 LCKFCHERFLDDDELYRHLRF 204 (669)
T ss_pred cchhhhhhhccHHHHHHhhcc
Confidence 355566666666665555543
No 238
>COG1779 C4-type Zn-finger protein [General function prediction only]
Probab=20.10 E-value=28 Score=24.22 Aligned_cols=9 Identities=22% Similarity=0.826 Sum_probs=6.0
Q ss_pred eeccccccc
Q 031430 32 FACKTCNKE 40 (159)
Q Consensus 32 ~~C~~C~~~ 40 (159)
..|++||..
T Consensus 15 ~~CPvCg~~ 23 (201)
T COG1779 15 IDCPVCGGT 23 (201)
T ss_pred ecCCcccce
Confidence 467777754
Done!