Query psy7353
Match_columns 139
No_of_seqs 121 out of 2185
Neff 10.6
Searched_HMMs 46136
Date Sat Aug 17 00:35:03 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy7353.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/7353hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2462|consensus 99.9 5.5E-29 1.2E-33 163.5 3.5 121 2-133 142-265 (279)
2 KOG2462|consensus 99.9 9E-26 2E-30 148.4 4.7 114 15-136 127-240 (279)
3 KOG3576|consensus 99.8 9.1E-20 2E-24 115.5 1.5 115 14-136 113-237 (267)
4 KOG3623|consensus 99.7 2.2E-17 4.8E-22 121.0 3.7 110 18-134 210-332 (1007)
5 KOG3608|consensus 99.7 8.6E-18 1.9E-22 114.4 -0.2 125 2-134 191-315 (467)
6 KOG1074|consensus 99.6 3.4E-16 7.3E-21 116.3 2.5 84 55-139 606-696 (958)
7 KOG3623|consensus 99.6 2.8E-16 6E-21 115.4 1.3 83 52-135 892-974 (1007)
8 KOG1074|consensus 99.6 4.5E-16 9.7E-21 115.6 1.8 52 82-134 605-656 (958)
9 KOG3576|consensus 99.5 4E-16 8.6E-21 99.1 -0.7 85 52-137 115-199 (267)
10 KOG3608|consensus 99.5 5.7E-15 1.2E-19 100.8 3.2 110 18-135 263-376 (467)
11 PHA00733 hypothetical protein 99.2 3.8E-12 8.3E-17 77.3 2.4 82 52-136 38-124 (128)
12 PHA00733 hypothetical protein 99.2 7.5E-12 1.6E-16 76.0 3.2 97 2-107 24-124 (128)
13 PLN03086 PRLI-interacting fact 99.2 4.8E-11 1E-15 87.6 6.9 110 12-137 447-566 (567)
14 PHA02768 hypothetical protein; 99.1 9.1E-11 2E-15 59.9 2.6 44 82-128 5-48 (55)
15 PHA02768 hypothetical protein; 98.9 9.4E-10 2E-14 56.2 1.8 44 54-99 5-48 (55)
16 PF13465 zf-H2C2_2: Zinc-finge 98.8 2.1E-09 4.5E-14 47.1 0.6 24 98-122 2-25 (26)
17 PHA00732 hypothetical protein 98.7 2E-08 4.3E-13 55.9 3.2 37 83-122 2-38 (79)
18 PLN03086 PRLI-interacting fact 98.7 9.1E-08 2E-12 70.7 7.0 103 19-133 408-536 (567)
19 PF13465 zf-H2C2_2: Zinc-finge 98.6 3.1E-08 6.6E-13 43.4 2.2 25 69-93 1-25 (26)
20 KOG3993|consensus 98.6 2.8E-09 6.1E-14 74.9 -2.8 85 54-138 267-383 (500)
21 PHA00616 hypothetical protein 98.4 1.1E-07 2.3E-12 46.4 1.0 35 82-117 1-35 (44)
22 PF05605 zf-Di19: Drought indu 98.4 2.8E-07 6.1E-12 47.6 2.6 51 82-135 2-53 (54)
23 PHA00616 hypothetical protein 98.1 1.5E-06 3.2E-11 42.4 1.3 31 55-85 2-32 (44)
24 PHA00732 hypothetical protein 98.1 3.5E-06 7.6E-11 46.9 2.9 37 19-65 2-38 (79)
25 PF05605 zf-Di19: Drought indu 98.1 1.4E-05 3.1E-10 41.2 4.6 48 19-75 3-50 (54)
26 COG5189 SFP1 Putative transcri 98.0 4E-06 8.7E-11 57.5 2.1 56 80-135 347-422 (423)
27 KOG3993|consensus 98.0 4.1E-06 8.9E-11 59.4 1.8 27 111-137 458-484 (500)
28 PF13912 zf-C2H2_6: C2H2-type 97.8 1.9E-06 4E-11 37.9 -1.3 22 83-104 2-23 (27)
29 PF00096 zf-C2H2: Zinc finger, 97.8 1.3E-05 2.8E-10 33.7 1.1 22 83-104 1-22 (23)
30 PF13894 zf-C2H2_4: C2H2-type 97.8 2E-06 4.4E-11 36.5 -1.5 23 83-105 1-23 (24)
31 PF13894 zf-C2H2_4: C2H2-type 97.7 2.5E-05 5.4E-10 33.0 1.6 22 113-134 2-23 (24)
32 PF13912 zf-C2H2_6: C2H2-type 97.6 2.9E-05 6.2E-10 34.0 1.3 25 111-135 1-25 (27)
33 PF00096 zf-C2H2: Zinc finger, 97.5 8.5E-05 1.8E-09 31.1 2.1 22 19-45 1-22 (23)
34 PF12756 zf-C2H2_2: C2H2 type 97.5 1.3E-05 2.7E-10 46.5 -0.8 73 56-134 1-73 (100)
35 PF12756 zf-C2H2_2: C2H2 type 97.3 0.00017 3.6E-09 41.7 2.4 74 20-106 1-74 (100)
36 PF12171 zf-C2H2_jaz: Zinc-fin 97.2 0.00011 2.4E-09 32.2 0.3 22 112-133 2-23 (27)
37 COG5189 SFP1 Putative transcri 97.1 0.00013 2.9E-09 50.2 0.4 71 16-103 347-419 (423)
38 PRK04860 hypothetical protein; 97.1 0.00028 6.1E-09 44.6 1.4 40 82-126 119-158 (160)
39 smart00355 ZnF_C2H2 zinc finge 97.0 0.00017 3.7E-09 30.7 -0.1 21 112-132 1-21 (26)
40 PF12874 zf-met: Zinc-finger o 96.8 8.1E-05 1.7E-09 31.9 -1.8 20 84-103 2-21 (25)
41 PF13909 zf-H2C2_5: C2H2-type 96.8 0.00083 1.8E-08 28.4 1.2 23 83-106 1-23 (24)
42 smart00355 ZnF_C2H2 zinc finge 96.7 0.0017 3.8E-08 27.4 2.0 22 83-104 1-22 (26)
43 PF09237 GAGA: GAGA factor; I 96.7 0.0032 6.9E-08 31.6 3.0 30 52-81 22-51 (54)
44 PF09237 GAGA: GAGA factor; I 96.7 0.00016 3.4E-09 36.2 -1.6 25 80-104 22-46 (54)
45 PF12171 zf-C2H2_jaz: Zinc-fin 96.5 0.0022 4.8E-08 27.9 1.7 22 83-104 2-23 (27)
46 PF13909 zf-H2C2_5: C2H2-type 96.5 0.00022 4.7E-09 30.2 -1.7 24 112-136 1-24 (24)
47 PRK04860 hypothetical protein; 96.2 0.0054 1.2E-07 38.9 2.9 39 53-95 118-156 (160)
48 PF12874 zf-met: Zinc-finger o 96.0 0.0036 7.8E-08 26.6 1.1 22 112-133 1-22 (25)
49 cd00350 rubredoxin_like Rubred 95.2 0.016 3.5E-07 26.5 1.6 10 110-119 16-25 (33)
50 KOG2231|consensus 95.1 0.043 9.4E-07 42.2 4.5 97 32-135 123-236 (669)
51 smart00451 ZnF_U1 U1-like zinc 95.0 0.0056 1.2E-07 28.2 -0.2 23 111-133 3-25 (35)
52 KOG2893|consensus 94.6 0.013 2.7E-07 39.2 0.6 35 52-91 9-43 (341)
53 PF13913 zf-C2HC_2: zinc-finge 94.4 0.036 7.8E-07 23.6 1.6 19 84-103 4-22 (25)
54 COG5048 FOG: Zn-finger [Genera 93.8 0.043 9.4E-07 39.6 2.0 55 82-136 289-348 (467)
55 KOG1146|consensus 93.8 0.013 2.9E-07 47.7 -0.7 25 109-133 516-540 (1406)
56 PF09986 DUF2225: Uncharacteri 93.1 0.035 7.7E-07 36.9 0.6 13 112-124 49-61 (214)
57 COG5236 Uncharacterized conser 92.7 0.047 1E-06 38.6 0.8 16 120-135 290-305 (493)
58 COG1592 Rubrerythrin [Energy p 92.7 0.092 2E-06 33.4 2.0 25 81-119 133-157 (166)
59 KOG2893|consensus 92.7 0.048 1.1E-06 36.5 0.8 43 17-72 10-52 (341)
60 PF06524 NOA36: NOA36 protein; 92.4 0.089 1.9E-06 35.7 1.7 82 15-104 139-231 (314)
61 COG2888 Predicted Zn-ribbon RN 91.8 0.13 2.8E-06 26.7 1.6 8 111-118 50-57 (61)
62 KOG1146|consensus 91.1 0.076 1.6E-06 43.7 0.4 56 80-135 516-613 (1406)
63 cd00729 rubredoxin_SM Rubredox 90.8 0.25 5.4E-06 22.7 1.8 25 82-119 2-26 (34)
64 COG5048 FOG: Zn-finger [Genera 89.3 0.18 3.9E-06 36.4 1.0 60 54-114 289-354 (467)
65 COG4049 Uncharacterized protei 89.2 0.051 1.1E-06 27.8 -1.3 29 78-106 13-41 (65)
66 PHA00626 hypothetical protein 88.8 0.15 3.3E-06 26.1 0.3 14 110-123 22-35 (59)
67 COG4049 Uncharacterized protei 88.5 0.38 8.2E-06 24.7 1.6 31 12-47 11-41 (65)
68 PRK14890 putative Zn-ribbon RN 87.5 0.38 8.2E-06 25.0 1.3 10 110-119 47-56 (59)
69 KOG2482|consensus 87.1 0.73 1.6E-05 32.8 2.9 51 83-133 280-356 (423)
70 PRK00464 nrdR transcriptional 86.8 0.21 4.6E-06 31.5 0.1 15 112-126 29-43 (154)
71 TIGR00373 conserved hypothetic 85.7 1.3 2.7E-05 28.1 3.2 17 81-97 108-124 (158)
72 TIGR00622 ssl1 transcription f 84.2 1.9 4.2E-05 25.6 3.3 47 85-134 58-104 (112)
73 PF09538 FYDLN_acid: Protein o 84.0 1 2.2E-05 26.7 2.1 15 81-95 25-39 (108)
74 KOG2186|consensus 83.3 0.89 1.9E-05 31.0 1.8 49 18-77 3-51 (276)
75 PRK06266 transcription initiat 82.0 2.1 4.5E-05 27.8 3.1 14 82-95 117-130 (178)
76 smart00834 CxxC_CXXC_SSSS Puta 80.6 0.88 1.9E-05 21.4 0.8 11 83-93 6-16 (41)
77 PF09723 Zn-ribbon_8: Zinc rib 80.4 0.72 1.6E-05 22.2 0.5 13 83-95 6-18 (42)
78 PF13717 zinc_ribbon_4: zinc-r 79.7 1.6 3.5E-05 20.2 1.5 10 112-121 26-35 (36)
79 KOG2186|consensus 78.8 1.7 3.6E-05 29.7 1.9 47 54-103 3-49 (276)
80 KOG4173|consensus 77.5 1.1 2.5E-05 29.5 0.9 70 32-107 90-171 (253)
81 PF02892 zf-BED: BED zinc fing 77.3 1.4 3E-05 21.3 0.9 20 83-102 17-40 (45)
82 COG0068 HypF Hydrogenase matur 77.0 0.31 6.7E-06 37.9 -2.1 56 57-120 126-182 (750)
83 PF13451 zf-trcl: Probable zin 76.8 1.2 2.6E-05 22.3 0.6 17 81-97 3-19 (49)
84 PF12013 DUF3505: Protein of u 75.8 0.69 1.5E-05 27.3 -0.5 25 112-136 81-109 (109)
85 KOG2482|consensus 75.7 6.5 0.00014 28.2 4.1 53 52-104 142-217 (423)
86 TIGR02605 CxxC_CxxC_SSSS putat 75.4 1.1 2.3E-05 22.5 0.2 11 55-65 6-16 (52)
87 smart00531 TFIIE Transcription 74.2 5.2 0.00011 25.0 3.2 36 80-120 97-132 (147)
88 smart00734 ZnF_Rad18 Rad18-lik 74.0 1.2 2.6E-05 19.1 0.2 19 113-132 3-21 (26)
89 PRK00398 rpoP DNA-directed RNA 72.4 1.7 3.7E-05 21.3 0.6 11 82-92 3-13 (46)
90 PF10571 UPF0547: Uncharacteri 72.4 2.5 5.3E-05 18.1 1.0 10 113-122 16-25 (26)
91 KOG4173|consensus 71.5 0.54 1.2E-05 31.0 -1.7 76 53-131 78-166 (253)
92 PF14353 CpXC: CpXC protein 71.3 4.5 9.7E-05 24.5 2.4 12 112-123 39-50 (128)
93 smart00614 ZnF_BED BED zinc fi 69.9 3.8 8.2E-05 20.4 1.5 20 84-103 20-44 (50)
94 PRK09678 DNA-binding transcrip 69.5 0.91 2E-05 24.8 -0.9 14 111-124 27-42 (72)
95 TIGR02300 FYDLN_acid conserved 69.5 5 0.00011 24.5 2.2 15 81-95 25-39 (129)
96 COG1997 RPL43A Ribosomal prote 68.5 2.7 5.8E-05 23.8 0.8 31 54-94 35-65 (89)
97 PF04959 ARS2: Arsenite-resist 68.5 2.9 6.3E-05 28.0 1.2 27 81-107 76-102 (214)
98 KOG2231|consensus 67.4 6.5 0.00014 30.9 2.9 78 37-119 163-246 (669)
99 PF08274 PhnA_Zn_Ribbon: PhnA 66.2 1.6 3.5E-05 19.5 -0.3 8 82-89 19-26 (30)
100 COG1198 PriA Primosomal protei 65.7 4.1 8.8E-05 32.4 1.6 12 109-120 473-484 (730)
101 PF12907 zf-met2: Zinc-binding 64.9 2.9 6.4E-05 20.0 0.5 26 84-109 3-31 (40)
102 KOG1280|consensus 64.4 9.8 0.00021 27.4 3.1 40 16-61 77-116 (381)
103 KOG2785|consensus 63.9 14 0.00029 27.0 3.8 58 55-112 167-250 (390)
104 PF04959 ARS2: Arsenite-resist 63.2 11 0.00024 25.3 3.1 29 15-48 74-102 (214)
105 PF13240 zinc_ribbon_2: zinc-r 62.8 4.2 9.2E-05 16.8 0.7 6 114-119 16-21 (23)
106 KOG4124|consensus 62.4 3.6 7.8E-05 29.5 0.8 52 81-132 348-419 (442)
107 PF03604 DNA_RNApol_7kD: DNA d 61.8 12 0.00026 16.9 2.2 10 111-120 17-26 (32)
108 PF07754 DUF1610: Domain of un 61.0 5.3 0.00012 16.8 0.9 11 16-26 14-24 (24)
109 COG5236 Uncharacterized conser 60.6 3.1 6.8E-05 29.8 0.2 13 91-103 290-302 (493)
110 PF12013 DUF3505: Protein of u 60.4 6.8 0.00015 23.0 1.6 24 83-106 81-108 (109)
111 PF04780 DUF629: Protein of un 59.7 2.4 5.3E-05 31.7 -0.5 30 79-108 54-83 (466)
112 smart00661 RPOL9 RNA polymeras 59.6 8.1 0.00018 19.1 1.6 16 111-126 20-35 (52)
113 PRK04023 DNA polymerase II lar 57.7 18 0.00039 30.1 3.8 10 111-120 663-672 (1121)
114 PF05191 ADK_lid: Adenylate ki 57.6 3.8 8.2E-05 19.0 0.1 11 111-121 21-31 (36)
115 PF07800 DUF1644: Protein of u 56.6 19 0.00041 23.0 3.1 57 54-112 80-138 (162)
116 PRK03824 hypA hydrogenase nick 56.4 4.9 0.00011 24.8 0.5 11 54-64 70-80 (135)
117 PF12760 Zn_Tnp_IS1595: Transp 56.2 16 0.00035 17.7 2.3 10 110-119 36-45 (46)
118 COG1655 Uncharacterized protei 55.7 2.9 6.3E-05 28.2 -0.5 16 53-68 18-33 (267)
119 COG4888 Uncharacterized Zn rib 55.2 1.5 3.3E-05 25.4 -1.6 11 52-62 20-30 (104)
120 TIGR00595 priA primosomal prot 54.4 8 0.00017 29.4 1.5 10 110-119 252-261 (505)
121 KOG2785|consensus 54.4 22 0.00047 26.0 3.5 56 16-76 164-242 (390)
122 PRK14714 DNA polymerase II lar 53.9 25 0.00054 30.1 4.1 10 82-91 692-701 (1337)
123 PF08790 zf-LYAR: LYAR-type C2 52.2 2.1 4.5E-05 18.7 -1.1 20 112-132 1-20 (28)
124 smart00440 ZnF_C2C2 C2C2 Zinc 51.9 2 4.4E-05 20.4 -1.3 10 112-121 29-38 (40)
125 COG1779 C4-type Zn-finger prot 51.5 1.8 3.9E-05 28.4 -2.0 16 112-127 44-59 (201)
126 COG1996 RPC10 DNA-directed RNA 51.4 11 0.00025 18.9 1.3 6 20-25 8-13 (49)
127 PRK10220 hypothetical protein; 51.3 12 0.00026 22.2 1.5 10 83-92 21-30 (111)
128 PF07503 zf-HYPF: HypF finger; 50.3 1.3 2.8E-05 20.5 -2.1 11 112-122 22-32 (35)
129 KOG3002|consensus 50.1 18 0.0004 25.6 2.6 82 52-139 78-167 (299)
130 PTZ00255 60S ribosomal protein 50.0 5.4 0.00012 22.8 -0.0 32 53-94 35-66 (90)
131 KOG3408|consensus 49.1 4 8.7E-05 24.6 -0.6 23 82-104 57-79 (129)
132 TIGR00686 phnA alkylphosphonat 48.3 12 0.00025 22.2 1.2 10 112-121 20-29 (109)
133 PF05290 Baculo_IE-1: Baculovi 48.0 31 0.00067 21.3 3.0 57 52-126 78-136 (140)
134 KOG2907|consensus 47.3 12 0.00025 22.4 1.1 40 83-124 75-115 (116)
135 PRK14873 primosome assembly pr 46.6 14 0.00029 29.3 1.7 11 110-120 421-431 (665)
136 KOG2593|consensus 45.8 21 0.00045 26.6 2.4 38 78-119 124-161 (436)
137 PF07975 C1_4: TFIIH C1-like d 45.7 14 0.0003 18.7 1.1 24 81-104 20-43 (51)
138 COG1675 TFA1 Transcription ini 45.5 41 0.00088 21.9 3.5 8 112-119 133-140 (176)
139 PF07282 OrfB_Zn_ribbon: Putat 44.9 16 0.00035 19.3 1.4 11 81-91 45-55 (69)
140 PF05443 ROS_MUCR: ROS/MUCR tr 44.8 4.1 8.8E-05 25.1 -1.1 20 83-105 73-92 (132)
141 PRK12380 hydrogenase nickel in 43.4 16 0.00035 21.7 1.4 10 83-92 71-80 (113)
142 COG1571 Predicted DNA-binding 43.1 22 0.00048 26.4 2.2 11 82-92 367-377 (421)
143 PRK00432 30S ribosomal protein 42.7 11 0.00023 19.0 0.4 10 111-120 37-46 (50)
144 KOG2593|consensus 41.4 21 0.00046 26.5 1.9 38 14-62 124-161 (436)
145 PF13453 zf-TFIIB: Transcripti 40.8 13 0.00028 17.6 0.5 13 56-68 21-33 (41)
146 PF14311 DUF4379: Domain of un 40.7 26 0.00057 17.6 1.7 13 83-95 29-41 (55)
147 PF01286 XPA_N: XPA protein N- 40.4 9.6 0.00021 17.5 0.0 15 113-127 5-19 (34)
148 PF04780 DUF629: Protein of un 39.8 29 0.00062 26.3 2.4 29 17-50 56-84 (466)
149 KOG0717|consensus 39.2 7.6 0.00016 29.1 -0.6 23 112-134 293-315 (508)
150 PRK05978 hypothetical protein; 38.8 21 0.00044 22.5 1.3 11 113-123 54-64 (148)
151 COG1998 RPS31 Ribosomal protei 38.3 19 0.0004 18.1 0.9 10 111-120 37-46 (51)
152 PF15269 zf-C2H2_7: Zinc-finge 38.1 23 0.00049 17.4 1.1 22 83-104 21-42 (54)
153 PF01927 Mut7-C: Mut7-C RNAse 38.0 11 0.00024 23.5 0.1 10 112-121 125-134 (147)
154 PF10013 DUF2256: Uncharacteri 37.7 23 0.0005 17.1 1.1 16 84-99 10-25 (42)
155 PF13824 zf-Mss51: Zinc-finger 37.7 41 0.00089 17.3 2.1 11 80-90 12-22 (55)
156 TIGR00143 hypF [NiFe] hydrogen 37.6 2.6 5.6E-05 33.4 -3.4 58 56-121 92-150 (711)
157 PF02176 zf-TRAF: TRAF-type zi 37.5 15 0.00032 18.7 0.5 18 70-87 26-43 (60)
158 PRK05580 primosome assembly pr 36.2 30 0.00065 27.5 2.1 10 110-119 420-429 (679)
159 COG1326 Uncharacterized archae 35.4 28 0.00061 23.0 1.6 12 81-92 29-40 (201)
160 KOG4118|consensus 34.9 11 0.00023 20.1 -0.3 24 112-135 39-62 (74)
161 COG3357 Predicted transcriptio 34.8 20 0.00044 20.5 0.8 14 110-123 57-70 (97)
162 KOG2636|consensus 34.6 19 0.00042 26.9 0.8 27 106-132 396-423 (497)
163 PF01096 TFIIS_C: Transcriptio 34.4 0.93 2E-05 21.5 -4.0 10 112-121 29-38 (39)
164 COG2331 Uncharacterized protei 34.3 8.9 0.00019 21.1 -0.7 9 54-62 12-20 (82)
165 PF11672 DUF3268: Protein of u 33.9 24 0.00052 20.7 1.0 7 112-118 32-38 (102)
166 TIGR00100 hypA hydrogenase nic 33.8 24 0.00051 21.1 1.0 10 55-64 71-80 (115)
167 COG3364 Zn-ribbon containing p 33.8 31 0.00068 20.2 1.4 9 18-26 2-10 (112)
168 smart00154 ZnF_AN1 AN1-like Zi 33.4 21 0.00046 16.8 0.6 13 111-123 12-24 (39)
169 PF11494 Ta0938: Ta0938; Inte 33.2 40 0.00086 19.6 1.8 38 52-95 12-50 (105)
170 PF10083 DUF2321: Uncharacteri 33.2 18 0.0004 22.9 0.5 19 79-97 65-83 (158)
171 TIGR00244 transcriptional regu 33.1 21 0.00045 22.5 0.7 19 110-128 27-45 (147)
172 TIGR03831 YgiT_finger YgiT-typ 33.0 22 0.00048 16.8 0.7 12 112-123 33-44 (46)
173 COG4957 Predicted transcriptio 32.9 15 0.00033 22.7 0.1 18 84-104 78-95 (148)
174 PRK00564 hypA hydrogenase nick 32.9 32 0.0007 20.6 1.5 10 83-92 72-81 (117)
175 KOG4167|consensus 31.9 6.9 0.00015 31.0 -1.8 25 81-105 791-815 (907)
176 COG4896 Uncharacterized protei 31.8 22 0.00048 18.7 0.6 9 53-61 30-38 (68)
177 PF12773 DZR: Double zinc ribb 31.7 53 0.0011 16.0 2.0 10 111-120 29-38 (50)
178 COG1773 Rubredoxin [Energy pro 31.6 14 0.00031 19.0 -0.1 10 112-121 4-13 (55)
179 KOG1842|consensus 31.5 26 0.00056 26.3 1.1 29 17-50 14-42 (505)
180 cd00730 rubredoxin Rubredoxin; 31.4 20 0.00044 18.0 0.4 11 112-122 2-12 (50)
181 KOG2071|consensus 31.0 25 0.00055 27.2 1.0 28 108-135 415-442 (579)
182 KOG0978|consensus 30.6 40 0.00088 26.9 2.0 19 110-128 677-695 (698)
183 PHA02998 RNA polymerase subuni 30.6 12 0.00026 24.3 -0.7 36 83-122 144-182 (195)
184 KOG4167|consensus 30.6 13 0.00027 29.7 -0.6 25 16-45 790-814 (907)
185 COG1327 Predicted transcriptio 30.5 24 0.00051 22.3 0.6 17 111-127 28-44 (156)
186 PRK05452 anaerobic nitric oxid 30.5 24 0.00052 26.7 0.8 39 80-120 423-467 (479)
187 COG4306 Uncharacterized protei 30.5 31 0.00068 21.0 1.1 16 80-95 66-81 (160)
188 TIGR00627 tfb4 transcription f 30.4 64 0.0014 22.7 2.8 25 82-121 255-279 (279)
189 COG3091 SprT Zn-dependent meta 29.2 34 0.00074 21.7 1.2 34 81-120 116-149 (156)
190 PF07535 zf-DBF: DBF zinc fing 28.8 34 0.00075 17.1 1.0 20 111-133 5-24 (49)
191 PF07295 DUF1451: Protein of u 28.7 16 0.00034 23.0 -0.3 9 54-62 112-120 (146)
192 PF14787 zf-CCHC_5: GAG-polypr 28.3 46 0.00099 15.5 1.2 15 113-127 4-18 (36)
193 PF06397 Desulfoferrod_N: Desu 27.9 31 0.00067 16.1 0.6 10 17-26 5-14 (36)
194 PF13821 DUF4187: Domain of un 27.4 34 0.00073 17.5 0.8 18 82-99 27-44 (55)
195 PTZ00448 hypothetical protein; 27.1 25 0.00054 25.7 0.4 23 111-133 314-336 (373)
196 PRK12496 hypothetical protein; 26.5 63 0.0014 20.7 2.1 11 83-93 128-138 (164)
197 smart00586 ZnF_DBF Zinc finger 26.4 22 0.00048 17.8 0.0 21 110-133 4-24 (49)
198 PF04423 Rad50_zn_hook: Rad50 26.0 20 0.00044 18.0 -0.2 10 113-122 22-31 (54)
199 PRK06260 threonine synthase; V 25.7 54 0.0012 24.1 1.9 12 80-91 17-28 (397)
200 PF14803 Nudix_N_2: Nudix N-te 25.6 19 0.00041 16.5 -0.3 11 52-62 20-30 (34)
201 KOG4727|consensus 25.6 34 0.00073 22.1 0.7 22 82-103 75-96 (193)
202 PF15135 UPF0515: Uncharacteri 25.5 80 0.0017 21.9 2.5 10 52-61 110-119 (278)
203 PF14369 zf-RING_3: zinc-finge 25.5 37 0.00079 15.6 0.7 10 113-122 23-32 (35)
204 PRK14811 formamidopyrimidine-D 25.2 45 0.00098 23.2 1.4 32 84-124 237-268 (269)
205 PF14446 Prok-RING_1: Prokaryo 24.8 40 0.00086 17.3 0.8 14 113-126 7-20 (54)
206 smart00731 SprT SprT homologue 24.8 35 0.00076 21.2 0.7 32 82-121 112-143 (146)
207 PF10537 WAC_Acf1_DNA_bd: ATP- 24.6 1.6E+02 0.0034 17.3 4.9 42 17-67 2-43 (102)
208 smart00064 FYVE Protein presen 24.4 62 0.0013 16.9 1.6 27 56-94 12-38 (68)
209 PRK03681 hypA hydrogenase nick 23.7 53 0.0012 19.6 1.3 9 83-91 71-79 (114)
210 KOG1842|consensus 23.6 41 0.00089 25.3 0.9 31 49-79 10-40 (505)
211 PF09845 DUF2072: Zn-ribbon co 23.6 45 0.00098 20.6 1.0 15 82-96 1-15 (131)
212 COG4391 Uncharacterized protei 23.5 28 0.0006 18.4 0.1 46 73-123 15-60 (62)
213 COG3677 Transposase and inacti 23.4 46 0.00099 20.4 1.0 16 109-124 51-66 (129)
214 PF00301 Rubredoxin: Rubredoxi 23.4 43 0.00092 16.6 0.7 10 111-120 34-43 (47)
215 PLN02294 cytochrome c oxidase 23.1 45 0.00098 21.6 0.9 11 16-26 139-149 (174)
216 PF09963 DUF2197: Uncharacteri 23.0 19 0.00041 18.6 -0.6 36 56-91 4-40 (56)
217 PLN02748 tRNA dimethylallyltra 23.0 36 0.00077 25.8 0.6 25 110-134 417-442 (468)
218 KOG1994|consensus 22.7 40 0.00086 22.9 0.7 24 80-103 237-260 (268)
219 CHL00174 accD acetyl-CoA carbo 22.6 32 0.00069 24.4 0.2 32 55-95 39-70 (296)
220 cd00924 Cyt_c_Oxidase_Vb Cytoc 21.6 50 0.0011 19.2 0.9 10 17-26 78-87 (97)
221 PF03145 Sina: Seven in absent 21.5 24 0.00052 23.1 -0.5 37 69-107 32-72 (198)
222 PF13878 zf-C2H2_3: zinc-finge 21.4 43 0.00094 15.9 0.5 13 112-124 14-26 (41)
223 PRK14892 putative transcriptio 21.3 32 0.00069 20.1 0.0 9 53-61 20-28 (99)
224 COG5188 PRP9 Splicing factor 3 21.2 40 0.00087 24.6 0.5 27 106-132 369-396 (470)
225 PRK12860 transcriptional activ 21.1 84 0.0018 20.8 1.9 46 63-118 116-161 (189)
226 COG4338 Uncharacterized protei 20.9 36 0.00078 17.0 0.1 16 84-99 14-29 (54)
227 COG1594 RPB9 DNA-directed RNA 20.7 20 0.00042 21.4 -1.0 11 112-122 101-111 (113)
228 COG5151 SSL1 RNA polymerase II 20.7 41 0.00088 24.1 0.4 23 110-132 387-409 (421)
229 cd00065 FYVE FYVE domain; Zinc 20.4 1E+02 0.0023 15.2 1.9 12 83-94 19-30 (57)
230 TIGR00515 accD acetyl-CoA carb 20.2 38 0.00083 23.9 0.2 32 55-95 27-58 (285)
231 PF08271 TF_Zn_Ribbon: TFIIB z 20.0 56 0.0012 15.5 0.7 9 112-120 1-9 (43)
No 1
>KOG2462|consensus
Probab=99.95 E-value=5.5e-29 Score=163.50 Aligned_cols=121 Identities=26% Similarity=0.529 Sum_probs=108.5
Q ss_pred CcccCceeeeccCC---CcceecCCCCCcchhcccCCHHHHHHHHHHhccCCCCceeecCCCCCcCCChHHHHHHHHHhc
Q psy7353 2 SVRGLNLFRYASVT---EGIYKCMECAKVDVIKTFKNKYSFQRHAFLYHEGCQRKVFPCPVCGKEFSRPDKMKNHMKTGC 78 (139)
Q Consensus 2 s~~~l~~~~~~~~~---~~~~~C~~c~~~~~~~~f~~~~~l~~h~~~~~~~~~~~~~~c~~C~~~~~~~~~l~~h~~~~~ 78 (139)
+..+|.+|++.|-. .+-+.|+.|++ .|.+...|+-|+++ |. -+..|.+||+.|...|.|+.|+++|+
T Consensus 142 T~snLsrHkQ~H~~~~s~ka~~C~~C~K-----~YvSmpALkMHirT-H~----l~c~C~iCGKaFSRPWLLQGHiRTHT 211 (279)
T KOG2462|consen 142 TSSNLSRHKQTHRSLDSKKAFSCKYCGK-----VYVSMPALKMHIRT-HT----LPCECGICGKAFSRPWLLQGHIRTHT 211 (279)
T ss_pred cccccchhhcccccccccccccCCCCCc-----eeeehHHHhhHhhc-cC----CCcccccccccccchHHhhccccccc
Confidence 34567777776554 56688999999 89999999999887 63 47899999999999999999999999
Q ss_pred CCCcccCCCCCccCCChhHHHhhhhhhcCCCCCCCCCCCCCCCCCCcchhccccc
Q psy7353 79 QRKVFPCPVCGKEFSRPDKMKNHMKTVHDCFMPATTPQGQRGQRASPVIDFHKDS 133 (139)
Q Consensus 79 ~~~~~~C~~C~~~f~~~~~l~~H~~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~ 133 (139)
||+||.|+.|+++|.++++|+.|++| |.+.++|+|..|++.|.....|.+|..+
T Consensus 212 GEKPF~C~hC~kAFADRSNLRAHmQT-HS~~K~~qC~~C~KsFsl~SyLnKH~ES 265 (279)
T KOG2462|consen 212 GEKPFSCPHCGKAFADRSNLRAHMQT-HSDVKKHQCPRCGKSFALKSYLNKHSES 265 (279)
T ss_pred CCCCccCCcccchhcchHHHHHHHHh-hcCCccccCcchhhHHHHHHHHHHhhhh
Confidence 99999999999999999999999999 8999999999999999999999999754
No 2
>KOG2462|consensus
Probab=99.92 E-value=9e-26 Score=148.43 Aligned_cols=114 Identities=27% Similarity=0.512 Sum_probs=104.8
Q ss_pred CCcceecCCCCCcchhcccCCHHHHHHHHHHhccCCCCceeecCCCCCcCCChHHHHHHHHHhcCCCcccCCCCCccCCC
Q psy7353 15 TEGIYKCMECAKVDVIKTFKNKYSFQRHAFLYHEGCQRKVFPCPVCGKEFSRPDKMKNHMKTGCQRKVFPCPVCGKEFSR 94 (139)
Q Consensus 15 ~~~~~~C~~c~~~~~~~~f~~~~~l~~h~~~~~~~~~~~~~~c~~C~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~f~~ 94 (139)
....|.|++||+ .+.+.++|.+|.+.+-..++.+.+.|+.|++.|....+|..|+++|+ .+.+|..||+.|+.
T Consensus 127 ~~~r~~c~eCgk-----~ysT~snLsrHkQ~H~~~~s~ka~~C~~C~K~YvSmpALkMHirTH~--l~c~C~iCGKaFSR 199 (279)
T KOG2462|consen 127 KHPRYKCPECGK-----SYSTSSNLSRHKQTHRSLDSKKAFSCKYCGKVYVSMPALKMHIRTHT--LPCECGICGKAFSR 199 (279)
T ss_pred cCCceecccccc-----ccccccccchhhcccccccccccccCCCCCceeeehHHHhhHhhccC--CCcccccccccccc
Confidence 345699999999 99999999999887555556788999999999999999999999997 67899999999999
Q ss_pred hhHHHhhhhhhcCCCCCCCCCCCCCCCCCCcchhcccccccC
Q psy7353 95 PDKMKNHMKTVHDCFMPATTPQGQRGQRASPVIDFHKDSVFN 136 (139)
Q Consensus 95 ~~~l~~H~~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~~~~ 136 (139)
++-|+-|+++ |+|||||.|+.|++.|-++.+|+.|+++|-+
T Consensus 200 PWLLQGHiRT-HTGEKPF~C~hC~kAFADRSNLRAHmQTHS~ 240 (279)
T KOG2462|consen 200 PWLLQGHIRT-HTGEKPFSCPHCGKAFADRSNLRAHMQTHSD 240 (279)
T ss_pred hHHhhccccc-ccCCCCccCCcccchhcchHHHHHHHHhhcC
Confidence 9999999999 9999999999999999999999999999864
No 3
>KOG3576|consensus
Probab=99.77 E-value=9.1e-20 Score=115.51 Aligned_cols=115 Identities=23% Similarity=0.405 Sum_probs=103.4
Q ss_pred CCCcceecCCCCCcchhcccCCHHHHHHHHHHhccCCCCceeecCCCCCcCCChHHHHHHHHHhcCCCcccCCCCCccCC
Q psy7353 14 VTEGIYKCMECAKVDVIKTFKNKYSFQRHAFLYHEGCQRKVFPCPVCGKEFSRPDKMKNHMKTGCQRKVFPCPVCGKEFS 93 (139)
Q Consensus 14 ~~~~~~~C~~c~~~~~~~~f~~~~~l~~h~~~~~~~~~~~~~~c~~C~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~f~ 93 (139)
.+...|.|..|+| .|.-.-.|.+|+.. |.. .+.+.|..||++|.+.-+|++|+++|+|.+||.|..|+++|.
T Consensus 113 sd~d~ftCrvCgK-----~F~lQRmlnrh~kc-h~~--vkr~lct~cgkgfndtfdlkrh~rthtgvrpykc~~c~kaft 184 (267)
T KOG3576|consen 113 SDQDSFTCRVCGK-----KFGLQRMLNRHLKC-HSD--VKRHLCTFCGKGFNDTFDLKRHTRTHTGVRPYKCSLCEKAFT 184 (267)
T ss_pred CCCCeeeeehhhh-----hhhHHHHHHHHhhh-ccH--HHHHHHhhccCcccchhhhhhhhccccCccccchhhhhHHHH
Confidence 3456699999999 89999899999876 655 788999999999999999999999999999999999999999
Q ss_pred ChhHHHhhhhhhcCC----------CCCCCCCCCCCCCCCCcchhcccccccC
Q psy7353 94 RPDKMKNHMKTVHDC----------FMPATTPQGQRGQRASPVIDFHKDSVFN 136 (139)
Q Consensus 94 ~~~~l~~H~~~~h~~----------~~~~~C~~C~~~f~~~~~l~~H~~~~~~ 136 (139)
+..+|..|.+.+|.. ++.|.|++||+.-.....+..|++.+|.
T Consensus 185 qrcsleshl~kvhgv~~~yaykerr~kl~vcedcg~t~~~~e~~~~h~~~~hp 237 (267)
T KOG3576|consen 185 QRCSLESHLKKVHGVQHQYAYKERRAKLYVCEDCGYTSERPEVYYLHLKLHHP 237 (267)
T ss_pred hhccHHHHHHHHcCchHHHHHHHhhhheeeecccCCCCCChhHHHHHHHhcCC
Confidence 999999999877763 4558999999999999999999998874
No 4
>KOG3623|consensus
Probab=99.68 E-value=2.2e-17 Score=121.05 Aligned_cols=110 Identities=25% Similarity=0.468 Sum_probs=98.9
Q ss_pred ceecCCCCCcchhcccCCHHHHHHHHHHhccCCCCceeecCCCCCcCCChHHHHHHHHHhcCC-------------Cccc
Q psy7353 18 IYKCMECAKVDVIKTFKNKYSFQRHAFLYHEGCQRKVFPCPVCGKEFSRPDKMKNHMKTGCQR-------------KVFP 84 (139)
Q Consensus 18 ~~~C~~c~~~~~~~~f~~~~~l~~h~~~~~~~~~~~~~~c~~C~~~~~~~~~l~~h~~~~~~~-------------~~~~ 84 (139)
...|++|.. ++.....|+.|+...|... +..|.|..|...|.....|.+|+..|... +-|+
T Consensus 210 lltcpycdr-----gykrltslkeHikyrhekn-e~nfsC~lCsytFAyRtQLErhm~~hkpg~dqa~sltqsa~lRKFK 283 (1007)
T KOG3623|consen 210 LLTCPYCDR-----GYKRLTSLKEHIKYRHEKN-EPNFSCMLCSYTFAYRTQLERHMQLHKPGGDQAISLTQSALLRKFK 283 (1007)
T ss_pred hhcchhHHH-----HHHHHHHHHHHHHHHHhhC-CCCCcchhhhhhhhhHHHHHHHHHhhcCCCcccccccchhhhcccc
Confidence 367999998 9999999999998877653 45789999999999999999999987532 5699
Q ss_pred CCCCCccCCChhHHHhhhhhhcCCCCCCCCCCCCCCCCCCcchhcccccc
Q psy7353 85 CPVCGKEFSRPDKMKNHMKTVHDCFMPATTPQGQRGQRASPVIDFHKDSV 134 (139)
Q Consensus 85 C~~C~~~f~~~~~l~~H~~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~~ 134 (139)
|.+||++|+.+-.|..|+++ |.|++||.|+.|+++|+..+.+..|+.++
T Consensus 284 CtECgKAFKfKHHLKEHlRI-HSGEKPfeCpnCkKRFSHSGSySSHmSSK 332 (1007)
T KOG3623|consen 284 CTECGKAFKFKHHLKEHLRI-HSGEKPFECPNCKKRFSHSGSYSSHMSSK 332 (1007)
T ss_pred ccccchhhhhHHHHHhhhee-ecCCCCcCCcccccccccCCccccccccc
Confidence 99999999999999999999 99999999999999999999999998765
No 5
>KOG3608|consensus
Probab=99.66 E-value=8.6e-18 Score=114.41 Aligned_cols=125 Identities=18% Similarity=0.309 Sum_probs=97.1
Q ss_pred CcccCceeeeccCCCcceecCCCCCcchhcccCCHHHHHHHHHHhccCCCCceeecCCCCCcCCChHHHHHHHHHhcCCC
Q psy7353 2 SVRGLNLFRYASVTEGIYKCMECAKVDVIKTFKNKYSFQRHAFLYHEGCQRKVFPCPVCGKEFSRPDKMKNHMKTGCQRK 81 (139)
Q Consensus 2 s~~~l~~~~~~~~~~~~~~C~~c~~~~~~~~f~~~~~l~~h~~~~~~~~~~~~~~c~~C~~~~~~~~~l~~h~~~~~~~~ 81 (139)
++..|..|+++|.+++...|+.||. .|.....|-.|.+..... ...+|.|..|.+.|..+..|..|+..|- .
T Consensus 191 ~k~~LreH~r~Hs~eKvvACp~Cg~-----~F~~~tkl~DH~rRqt~l-~~n~fqC~~C~KrFaTeklL~~Hv~rHv--n 262 (467)
T KOG3608|consen 191 NKYRLREHIRTHSNEKVVACPHCGE-----LFRTKTKLFDHLRRQTEL-NTNSFQCAQCFKRFATEKLLKSHVVRHV--N 262 (467)
T ss_pred cHHHHHHHHHhcCCCeEEecchHHH-----HhccccHHHHHHHhhhhh-cCCchHHHHHHHHHhHHHHHHHHHHHhh--h
Confidence 3456788899999999999999998 888888888887642222 2457778888888888888888877764 3
Q ss_pred cccCCCCCccCCChhHHHhhhhhhcCCCCCCCCCCCCCCCCCCcchhcccccc
Q psy7353 82 VFPCPVCGKEFSRPDKMKNHMKTVHDCFMPATTPQGQRGQRASPVIDFHKDSV 134 (139)
Q Consensus 82 ~~~C~~C~~~f~~~~~l~~H~~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~~ 134 (139)
-|.|+.|+-....++.|..|++.-|..++||+|+.|++.|....+|.+|.+.|
T Consensus 263 ~ykCplCdmtc~~~ssL~~H~r~rHs~dkpfKCd~Cd~~c~~esdL~kH~~~H 315 (467)
T KOG3608|consen 263 CYKCPLCDMTCSSASSLTTHIRYRHSKDKPFKCDECDTRCVRESDLAKHVQVH 315 (467)
T ss_pred cccccccccCCCChHHHHHHHHhhhccCCCccccchhhhhccHHHHHHHHHhc
Confidence 57788888888888888888887777788888888888888888888887744
No 6
>KOG1074|consensus
Probab=99.60 E-value=3.4e-16 Score=116.28 Aligned_cols=84 Identities=23% Similarity=0.466 Sum_probs=71.1
Q ss_pred eecCCCCCcCCChHHHHHHHHHhcCCCcccCCCCCccCCChhHHHhhhhhhcCCC----CCCCCC---CCCCCCCCCcch
Q psy7353 55 FPCPVCGKEFSRPDKMKNHMKTGCQRKVFPCPVCGKEFSRPDKMKNHMKTVHDCF----MPATTP---QGQRGQRASPVI 127 (139)
Q Consensus 55 ~~c~~C~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~~h~~~----~~~~C~---~C~~~f~~~~~l 127 (139)
-.|-+|.+.+.-.++|+.|++.|+|++||+|.+||++|..+.+|+.|+.. |... -++.|+ +|...|+..-.|
T Consensus 606 NqCiiC~rVlSC~saLqmHyrtHtGERPFkCKiCgRAFtTkGNLkaH~~v-Hka~p~~R~q~ScP~~~ic~~kftn~V~l 684 (958)
T KOG1074|consen 606 NQCIICLRVLSCPSALQMHYRTHTGERPFKCKICGRAFTTKGNLKAHMSV-HKAKPPARVQFSCPSTFICQKKFTNAVTL 684 (958)
T ss_pred cceeeeeecccchhhhhhhhhcccCcCccccccccchhccccchhhcccc-cccCccccccccCCchhhhcccccccccc
Confidence 44888999999999999999999999999999999999999999999887 4322 348899 899999999999
Q ss_pred hcccccccCcCC
Q psy7353 128 DFHKDSVFNKDI 139 (139)
Q Consensus 128 ~~H~~~~~~~~~ 139 (139)
.-|++.|...+|
T Consensus 685 pQhIriH~~~~~ 696 (958)
T KOG1074|consen 685 PQHIRIHLGGQI 696 (958)
T ss_pred cceEEeecCCCC
Confidence 999998886554
No 7
>KOG3623|consensus
Probab=99.59 E-value=2.8e-16 Score=115.43 Aligned_cols=83 Identities=17% Similarity=0.400 Sum_probs=74.5
Q ss_pred CceeecCCCCCcCCChHHHHHHHHHhcCCCcccCCCCCccCCChhHHHhhhhhhcCCCCCCCCCCCCCCCCCCcchhccc
Q psy7353 52 RKVFPCPVCGKEFSRPDKMKNHMKTGCQRKVFPCPVCGKEFSRPDKMKNHMKTVHDCFMPATTPQGQRGQRASPVIDFHK 131 (139)
Q Consensus 52 ~~~~~c~~C~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~~h~~~~~~~C~~C~~~f~~~~~l~~H~ 131 (139)
...|.|+.|++.|.-.+.|.+|.--|+|.+||+|.+|.++|+.+-.|+.|++. |.|++||+|+.|+++|+..+.+..|+
T Consensus 892 ~gmyaCDqCDK~FqKqSSLaRHKYEHsGqRPyqC~iCkKAFKHKHHLtEHkRL-HSGEKPfQCdKClKRFSHSGSYSQHM 970 (1007)
T KOG3623|consen 892 DGMYACDQCDKAFQKQSSLARHKYEHSGQRPYQCIICKKAFKHKHHLTEHKRL-HSGEKPFQCDKCLKRFSHSGSYSQHM 970 (1007)
T ss_pred cccchHHHHHHHHHhhHHHHHhhhhhcCCCCcccchhhHhhhhhhhhhhhhhh-ccCCCcchhhhhhhhcccccchHhhh
Confidence 56788999999999999999999999999999999999999999999999998 89999999999999999999998887
Q ss_pred cccc
Q psy7353 132 DSVF 135 (139)
Q Consensus 132 ~~~~ 135 (139)
.-.+
T Consensus 971 NHRY 974 (1007)
T KOG3623|consen 971 NHRY 974 (1007)
T ss_pred ccch
Confidence 6443
No 8
>KOG1074|consensus
Probab=99.58 E-value=4.5e-16 Score=115.62 Aligned_cols=52 Identities=19% Similarity=0.244 Sum_probs=48.4
Q ss_pred cccCCCCCccCCChhHHHhhhhhhcCCCCCCCCCCCCCCCCCCcchhcccccc
Q psy7353 82 VFPCPVCGKEFSRPDKMKNHMKTVHDCFMPATTPQGQRGQRASPVIDFHKDSV 134 (139)
Q Consensus 82 ~~~C~~C~~~f~~~~~l~~H~~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~~ 134 (139)
|-+|..|.+..+.++.|+.|.++ |+||+||+|.+|++.|+++.+|+.|+--|
T Consensus 605 PNqCiiC~rVlSC~saLqmHyrt-HtGERPFkCKiCgRAFtTkGNLkaH~~vH 656 (958)
T KOG1074|consen 605 PNQCIICLRVLSCPSALQMHYRT-HTGERPFKCKICGRAFTTKGNLKAHMSVH 656 (958)
T ss_pred ccceeeeeecccchhhhhhhhhc-ccCcCccccccccchhccccchhhccccc
Confidence 35699999999999999999999 99999999999999999999999997655
No 9
>KOG3576|consensus
Probab=99.55 E-value=4e-16 Score=99.14 Aligned_cols=85 Identities=26% Similarity=0.485 Sum_probs=79.6
Q ss_pred CceeecCCCCCcCCChHHHHHHHHHhcCCCcccCCCCCccCCChhHHHhhhhhhcCCCCCCCCCCCCCCCCCCcchhccc
Q psy7353 52 RKVFPCPVCGKEFSRPDKMKNHMKTGCQRKVFPCPVCGKEFSRPDKMKNHMKTVHDCFMPATTPQGQRGQRASPVIDFHK 131 (139)
Q Consensus 52 ~~~~~c~~C~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~~h~~~~~~~C~~C~~~f~~~~~l~~H~ 131 (139)
.-.|.|.+|++.|.-..-|.+|++-|...+.+-|..||+.|.+.-+|.+|+++ |+|.+||.|..|++.|+.+..|+.|.
T Consensus 115 ~d~ftCrvCgK~F~lQRmlnrh~kch~~vkr~lct~cgkgfndtfdlkrh~rt-htgvrpykc~~c~kaftqrcsleshl 193 (267)
T KOG3576|consen 115 QDSFTCRVCGKKFGLQRMLNRHLKCHSDVKRHLCTFCGKGFNDTFDLKRHTRT-HTGVRPYKCSLCEKAFTQRCSLESHL 193 (267)
T ss_pred CCeeeeehhhhhhhHHHHHHHHhhhccHHHHHHHhhccCcccchhhhhhhhcc-ccCccccchhhhhHHHHhhccHHHHH
Confidence 34688999999999999999999999999999999999999999999999999 99999999999999999999999999
Q ss_pred ccccCc
Q psy7353 132 DSVFNK 137 (139)
Q Consensus 132 ~~~~~~ 137 (139)
+..|+.
T Consensus 194 ~kvhgv 199 (267)
T KOG3576|consen 194 KKVHGV 199 (267)
T ss_pred HHHcCc
Confidence 888753
No 10
>KOG3608|consensus
Probab=99.52 E-value=5.7e-15 Score=100.83 Aligned_cols=110 Identities=21% Similarity=0.336 Sum_probs=70.3
Q ss_pred ceecCCCCCcchhcccCCHHHHHHHHHHhccCCCCceeecCCCCCcCCChHHHHHHHHHhcCCCcccCCC--CCccCCCh
Q psy7353 18 IYKCMECAKVDVIKTFKNKYSFQRHAFLYHEGCQRKVFPCPVCGKEFSRPDKMKNHMKTGCQRKVFPCPV--CGKEFSRP 95 (139)
Q Consensus 18 ~~~C~~c~~~~~~~~f~~~~~l~~h~~~~~~~~~~~~~~c~~C~~~~~~~~~l~~h~~~~~~~~~~~C~~--C~~~f~~~ 95 (139)
-|.|+.|.. +....+.|..|++..|.. .+||+|..|+..+...+.|..|...|. +..|.|.. |.+++.+.
T Consensus 263 ~ykCplCdm-----tc~~~ssL~~H~r~rHs~--dkpfKCd~Cd~~c~~esdL~kH~~~HS-~~~y~C~h~~C~~s~r~~ 334 (467)
T KOG3608|consen 263 CYKCPLCDM-----TCSSASSLTTHIRYRHSK--DKPFKCDECDTRCVRESDLAKHVQVHS-KTVYQCEHPDCHYSVRTY 334 (467)
T ss_pred ccccccccc-----CCCChHHHHHHHHhhhcc--CCCccccchhhhhccHHHHHHHHHhcc-ccceecCCCCCcHHHHHH
Confidence 456666665 566666666666665655 666666666666666666666666555 45566655 66666666
Q ss_pred hHHHhhhhhhcCCCC--CCCCCCCCCCCCCCcchhccccccc
Q psy7353 96 DKMKNHMKTVHDCFM--PATTPQGQRGQRASPVIDFHKDSVF 135 (139)
Q Consensus 96 ~~l~~H~~~~h~~~~--~~~C~~C~~~f~~~~~l~~H~~~~~ 135 (139)
.++.+|.+.+|.|.+ +|.|-.|++.|++-.+|..|....|
T Consensus 335 ~q~~~H~~evhEg~np~~Y~CH~Cdr~ft~G~~L~~HL~kkH 376 (467)
T KOG3608|consen 335 TQMRRHFLEVHEGNNPILYACHCCDRFFTSGKSLSAHLMKKH 376 (467)
T ss_pred HHHHHHHHHhccCCCCCceeeecchhhhccchhHHHHHHHhh
Confidence 666666666565543 3677777777777777766655554
No 11
>PHA00733 hypothetical protein
Probab=99.24 E-value=3.8e-12 Score=77.30 Aligned_cols=82 Identities=18% Similarity=0.218 Sum_probs=66.4
Q ss_pred CceeecCCCCCcCCChHHHHHH--H---HHhcCCCcccCCCCCccCCChhHHHhhhhhhcCCCCCCCCCCCCCCCCCCcc
Q psy7353 52 RKVFPCPVCGKEFSRPDKMKNH--M---KTGCQRKVFPCPVCGKEFSRPDKMKNHMKTVHDCFMPATTPQGQRGQRASPV 126 (139)
Q Consensus 52 ~~~~~c~~C~~~~~~~~~l~~h--~---~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~~h~~~~~~~C~~C~~~f~~~~~ 126 (139)
.+++.|.+|...+.....|..+ + ....+.++|.|..|++.|...+.|..|++. + +.+|.|+.|++.|.....
T Consensus 38 ~~~~~~~~~~~~~~~~~~l~~~~~l~~~~~~~~~kPy~C~~Cgk~Fss~s~L~~H~r~-h--~~~~~C~~CgK~F~~~~s 114 (128)
T PHA00733 38 QKRLIRAVVKTLIYNPQLLDESSYLYKLLTSKAVSPYVCPLCLMPFSSSVSLKQHIRY-T--EHSKVCPVCGKEFRNTDS 114 (128)
T ss_pred hhhHHHHHHhhhccChhhhcchHHHHhhcccCCCCCccCCCCCCcCCCHHHHHHHHhc-C--CcCccCCCCCCccCCHHH
Confidence 5678888888777766655554 1 133457899999999999999999999987 4 357999999999999999
Q ss_pred hhcccccccC
Q psy7353 127 IDFHKDSVFN 136 (139)
Q Consensus 127 l~~H~~~~~~ 136 (139)
|..|+...||
T Consensus 115 L~~H~~~~h~ 124 (128)
T PHA00733 115 TLDHVCKKHN 124 (128)
T ss_pred HHHHHHHhcC
Confidence 9999999886
No 12
>PHA00733 hypothetical protein
Probab=99.23 E-value=7.5e-12 Score=76.00 Aligned_cols=97 Identities=22% Similarity=0.417 Sum_probs=75.4
Q ss_pred CcccCceeeeccCCCcceecCCCCCcchhcccCCHHHHHHHHH----HhccCCCCceeecCCCCCcCCChHHHHHHHHHh
Q psy7353 2 SVRGLNLFRYASVTEGIYKCMECAKVDVIKTFKNKYSFQRHAF----LYHEGCQRKVFPCPVCGKEFSRPDKMKNHMKTG 77 (139)
Q Consensus 2 s~~~l~~~~~~~~~~~~~~C~~c~~~~~~~~f~~~~~l~~h~~----~~~~~~~~~~~~c~~C~~~~~~~~~l~~h~~~~ 77 (139)
|+.+|..........+++.|..|.+ .|.....|..+.. ..+.+ .++|.|+.|++.|.....|..|++.+
T Consensus 24 ~~~~~~~~~~~~~~~~~~~~~~~~~-----~~~~~~~l~~~~~l~~~~~~~~--~kPy~C~~Cgk~Fss~s~L~~H~r~h 96 (128)
T PHA00733 24 TLEELKRYHSLTPEQKRLIRAVVKT-----LIYNPQLLDESSYLYKLLTSKA--VSPYVCPLCLMPFSSSVSLKQHIRYT 96 (128)
T ss_pred CHHHhhhhhcCChhhhhHHHHHHhh-----hccChhhhcchHHHHhhcccCC--CCCccCCCCCCcCCCHHHHHHHHhcC
Confidence 4455666655556678899999998 6777666555411 11223 67999999999999999999999875
Q ss_pred cCCCcccCCCCCccCCChhHHHhhhhhhcC
Q psy7353 78 CQRKVFPCPVCGKEFSRPDKMKNHMKTVHD 107 (139)
Q Consensus 78 ~~~~~~~C~~C~~~f~~~~~l~~H~~~~h~ 107 (139)
..++.|..|++.|.....|..|+...|+
T Consensus 97 --~~~~~C~~CgK~F~~~~sL~~H~~~~h~ 124 (128)
T PHA00733 97 --EHSKVCPVCGKEFRNTDSTLDHVCKKHN 124 (128)
T ss_pred --CcCccCCCCCCccCCHHHHHHHHHHhcC
Confidence 4579999999999999999999987665
No 13
>PLN03086 PRLI-interacting factor K; Provisional
Probab=99.20 E-value=4.8e-11 Score=87.56 Aligned_cols=110 Identities=21% Similarity=0.467 Sum_probs=88.9
Q ss_pred ccCCCcceecCCCCCcchhcccCCHHHHHHHHHHhccCCCCceeecCCCCCcCCChHHHHHHHHHhcCCCcccCCCCCcc
Q psy7353 12 ASVTEGIYKCMECAKVDVIKTFKNKYSFQRHAFLYHEGCQRKVFPCPVCGKEFSRPDKMKNHMKTGCQRKVFPCPVCGKE 91 (139)
Q Consensus 12 ~~~~~~~~~C~~c~~~~~~~~f~~~~~l~~h~~~~~~~~~~~~~~c~~C~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~ 91 (139)
....++.+.|+.|++ .|. ...|..|...+| +++.|+ |+..+ ....|..|+..+...+++.|..|+..
T Consensus 447 r~el~~H~~C~~Cgk-----~f~-~s~LekH~~~~H-----kpv~Cp-Cg~~~-~R~~L~~H~~thCp~Kpi~C~fC~~~ 513 (567)
T PLN03086 447 VEEAKNHVHCEKCGQ-----AFQ-QGEMEKHMKVFH-----EPLQCP-CGVVL-EKEQMVQHQASTCPLRLITCRFCGDM 513 (567)
T ss_pred ccccccCccCCCCCC-----ccc-hHHHHHHHHhcC-----CCccCC-CCCCc-chhHHHhhhhccCCCCceeCCCCCCc
Confidence 334566789999998 785 577999988744 468899 99754 66899999999999999999999998
Q ss_pred CCC----------hhHHHhhhhhhcCCCCCCCCCCCCCCCCCCcchhcccccccCc
Q psy7353 92 FSR----------PDKMKNHMKTVHDCFMPATTPQGQRGQRASPVIDFHKDSVFNK 137 (139)
Q Consensus 92 f~~----------~~~l~~H~~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~~~~~ 137 (139)
+.. ...|..|... .|.+++.|..|++.+..+ +|..|....|.+
T Consensus 514 v~~g~~~~d~~d~~s~Lt~HE~~--CG~rt~~C~~Cgk~Vrlr-dm~~H~~~~h~~ 566 (567)
T PLN03086 514 VQAGGSAMDVRDRLRGMSEHESI--CGSRTAPCDSCGRSVMLK-EMDIHQIAVHQK 566 (567)
T ss_pred cccCccccchhhhhhhHHHHHHh--cCCcceEccccCCeeeeh-hHHHHHHHhhcC
Confidence 852 3589999987 378999999999998887 466888777643
No 14
>PHA02768 hypothetical protein; Provisional
Probab=99.08 E-value=9.1e-11 Score=59.88 Aligned_cols=44 Identities=18% Similarity=0.426 Sum_probs=35.0
Q ss_pred cccCCCCCccCCChhHHHhhhhhhcCCCCCCCCCCCCCCCCCCcchh
Q psy7353 82 VFPCPVCGKEFSRPDKMKNHMKTVHDCFMPATTPQGQRGQRASPVID 128 (139)
Q Consensus 82 ~~~C~~C~~~f~~~~~l~~H~~~~h~~~~~~~C~~C~~~f~~~~~l~ 128 (139)
-|.|+.||+.|...++|..|+++ |. ++|.|..|++.|...+.|-
T Consensus 5 ~y~C~~CGK~Fs~~~~L~~H~r~-H~--k~~kc~~C~k~f~~~s~l~ 48 (55)
T PHA02768 5 GYECPICGEIYIKRKSMITHLRK-HN--TNLKLSNCKRISLRTGEYI 48 (55)
T ss_pred ccCcchhCCeeccHHHHHHHHHh-cC--CcccCCcccceecccceeE
Confidence 36788888888888888888888 44 5788888888888777764
No 15
>PHA02768 hypothetical protein; Provisional
Probab=98.88 E-value=9.4e-10 Score=56.19 Aligned_cols=44 Identities=18% Similarity=0.472 Sum_probs=36.0
Q ss_pred eeecCCCCCcCCChHHHHHHHHHhcCCCcccCCCCCccCCChhHHH
Q psy7353 54 VFPCPVCGKEFSRPDKMKNHMKTGCQRKVFPCPVCGKEFSRPDKMK 99 (139)
Q Consensus 54 ~~~c~~C~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~f~~~~~l~ 99 (139)
.|.|+.||+.|...++|..|++.|+ +++.|..|++.|...+.|.
T Consensus 5 ~y~C~~CGK~Fs~~~~L~~H~r~H~--k~~kc~~C~k~f~~~s~l~ 48 (55)
T PHA02768 5 GYECPICGEIYIKRKSMITHLRKHN--TNLKLSNCKRISLRTGEYI 48 (55)
T ss_pred ccCcchhCCeeccHHHHHHHHHhcC--CcccCCcccceecccceeE
Confidence 4788888888888888888888887 6788888888888776654
No 16
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=98.76 E-value=2.1e-09 Score=47.14 Aligned_cols=24 Identities=25% Similarity=0.393 Sum_probs=14.2
Q ss_pred HHhhhhhhcCCCCCCCCCCCCCCCC
Q psy7353 98 MKNHMKTVHDCFMPATTPQGQRGQR 122 (139)
Q Consensus 98 l~~H~~~~h~~~~~~~C~~C~~~f~ 122 (139)
|.+|+++ |.+++||.|+.|++.|.
T Consensus 2 l~~H~~~-H~~~k~~~C~~C~k~F~ 25 (26)
T PF13465_consen 2 LRRHMRT-HTGEKPYKCPYCGKSFS 25 (26)
T ss_dssp HHHHHHH-HSSSSSEEESSSSEEES
T ss_pred HHHHhhh-cCCCCCCCCCCCcCeeC
Confidence 5556665 55666666666666554
No 17
>PHA00732 hypothetical protein
Probab=98.69 E-value=2e-08 Score=55.86 Aligned_cols=37 Identities=27% Similarity=0.539 Sum_probs=17.6
Q ss_pred ccCCCCCccCCChhHHHhhhhhhcCCCCCCCCCCCCCCCC
Q psy7353 83 FPCPVCGKEFSRPDKMKNHMKTVHDCFMPATTPQGQRGQR 122 (139)
Q Consensus 83 ~~C~~C~~~f~~~~~l~~H~~~~h~~~~~~~C~~C~~~f~ 122 (139)
|.|..|++.|.....|..|++.+|. ++.|+.|++.|.
T Consensus 2 y~C~~Cgk~F~s~s~Lk~H~r~~H~---~~~C~~CgKsF~ 38 (79)
T PHA00732 2 FKCPICGFTTVTLFALKQHARRNHT---LTKCPVCNKSYR 38 (79)
T ss_pred ccCCCCCCccCCHHHHHHHhhcccC---CCccCCCCCEeC
Confidence 4455555555555555555542232 234555555554
No 18
>PLN03086 PRLI-interacting factor K; Provisional
Probab=98.67 E-value=9.1e-08 Score=70.73 Aligned_cols=103 Identities=20% Similarity=0.348 Sum_probs=76.1
Q ss_pred eecCCCCCcchhcccCCHHHHHHHHHHhccC----------------CCCceeecCCCCCcCCChHHHHHHHHHhcCCCc
Q psy7353 19 YKCMECAKVDVIKTFKNKYSFQRHAFLYHEG----------------CQRKVFPCPVCGKEFSRPDKMKNHMKTGCQRKV 82 (139)
Q Consensus 19 ~~C~~c~~~~~~~~f~~~~~l~~h~~~~~~~----------------~~~~~~~c~~C~~~~~~~~~l~~h~~~~~~~~~ 82 (139)
-.|+-|.+ ......|..|...+.-. .....+.|+.|++.|. ...|..|+..++ .+
T Consensus 408 V~C~NC~~------~i~l~~l~lHe~~C~r~~V~Cp~~~Cg~v~~r~el~~H~~C~~Cgk~f~-~s~LekH~~~~H--kp 478 (567)
T PLN03086 408 VECRNCKH------YIPSRSIALHEAYCSRHNVVCPHDGCGIVLRVEEAKNHVHCEKCGQAFQ-QGEMEKHMKVFH--EP 478 (567)
T ss_pred EECCCCCC------ccchhHHHHHHhhCCCcceeCCcccccceeeccccccCccCCCCCCccc-hHHHHHHHHhcC--CC
Confidence 46888886 44445666776432111 0135678999999885 677999999875 78
Q ss_pred ccCCCCCccCCChhHHHhhhhhhcCCCCCCCCCCCCCCCCC----------Ccchhccccc
Q psy7353 83 FPCPVCGKEFSRPDKMKNHMKTVHDCFMPATTPQGQRGQRA----------SPVIDFHKDS 133 (139)
Q Consensus 83 ~~C~~C~~~f~~~~~l~~H~~~~h~~~~~~~C~~C~~~f~~----------~~~l~~H~~~ 133 (139)
+.|+ |+..+ ....|..|+.+ |...+++.|+.|+..|.. ...|..|...
T Consensus 479 v~Cp-Cg~~~-~R~~L~~H~~t-hCp~Kpi~C~fC~~~v~~g~~~~d~~d~~s~Lt~HE~~ 536 (567)
T PLN03086 479 LQCP-CGVVL-EKEQMVQHQAS-TCPLRLITCRFCGDMVQAGGSAMDVRDRLRGMSEHESI 536 (567)
T ss_pred ccCC-CCCCc-chhHHHhhhhc-cCCCCceeCCCCCCccccCccccchhhhhhhHHHHHHh
Confidence 9999 99755 67899999987 788899999999999852 2367777654
No 19
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=98.62 E-value=3.1e-08 Score=43.37 Aligned_cols=25 Identities=44% Similarity=0.988 Sum_probs=20.9
Q ss_pred HHHHHHHHhcCCCcccCCCCCccCC
Q psy7353 69 KMKNHMKTGCQRKVFPCPVCGKEFS 93 (139)
Q Consensus 69 ~l~~h~~~~~~~~~~~C~~C~~~f~ 93 (139)
+|..|++.|++++||.|+.|++.|.
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 4678888888899999999988875
No 20
>KOG3993|consensus
Probab=98.57 E-value=2.8e-09 Score=74.85 Aligned_cols=85 Identities=15% Similarity=0.249 Sum_probs=64.0
Q ss_pred eeecCCCCCcCCChHHHHHHHHHhcCCCcccCCCCCccCCChhHHHhhhhhhcC-------CC-----------------
Q psy7353 54 VFPCPVCGKEFSRPDKMKNHMKTGCQRKVFPCPVCGKEFSRPDKMKNHMKTVHD-------CF----------------- 109 (139)
Q Consensus 54 ~~~c~~C~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~~h~-------~~----------------- 109 (139)
.|.|..|...|.+.-.|..|...-..-.-|.|++|+++|..+.+|..|.+=|-+ +.
T Consensus 267 dyiCqLCK~kYeD~F~LAQHrC~RIV~vEYrCPEC~KVFsCPANLASHRRWHKPR~eaa~a~~~P~k~~~~~rae~~ea~ 346 (500)
T KOG3993|consen 267 DYICQLCKEKYEDAFALAQHRCPRIVHVEYRCPECDKVFSCPANLASHRRWHKPRPEAAKAGSPPPKQAVETRAEVQEAE 346 (500)
T ss_pred HHHHHHHHHhhhhHHHHhhccCCeeEEeeecCCcccccccCchhhhhhhcccCCchhhhhcCCCChhhhhhhhhhhhhcc
Confidence 467888887888888887777655555567888888888888888888764211 11
Q ss_pred --------CCCCCCCCCCCCCCCcchhcccccccCcC
Q psy7353 110 --------MPATTPQGQRGQRASPVIDFHKDSVFNKD 138 (139)
Q Consensus 110 --------~~~~C~~C~~~f~~~~~l~~H~~~~~~~~ 138 (139)
-.|.|..|++.|.....|++|..+|+..+
T Consensus 347 rsg~dss~gi~~C~~C~KkFrRqAYLrKHqlthq~~~ 383 (500)
T KOG3993|consen 347 RSGDDSSSGIFSCHTCGKKFRRQAYLRKHQLTHQRAP 383 (500)
T ss_pred ccCCcccCceeecHHhhhhhHHHHHHHHhHHhhhccc
Confidence 13889999999999999999999888654
No 21
>PHA00616 hypothetical protein
Probab=98.40 E-value=1.1e-07 Score=46.38 Aligned_cols=35 Identities=17% Similarity=0.287 Sum_probs=24.7
Q ss_pred cccCCCCCccCCChhHHHhhhhhhcCCCCCCCCCCC
Q psy7353 82 VFPCPVCGKEFSRPDKMKNHMKTVHDCFMPATTPQG 117 (139)
Q Consensus 82 ~~~C~~C~~~f~~~~~l~~H~~~~h~~~~~~~C~~C 117 (139)
||+|+.||..|...++|..|++. |.+++++.|+.-
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~-~hg~~~~~~~~~ 35 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLS-VHKQNKLTLEYF 35 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHH-hcCCCccceeEE
Confidence 56777777777777777777776 556677766543
No 22
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=98.39 E-value=2.8e-07 Score=47.64 Aligned_cols=51 Identities=22% Similarity=0.286 Sum_probs=34.5
Q ss_pred cccCCCCCccCCChhHHHhhhhhhcCCC-CCCCCCCCCCCCCCCcchhccccccc
Q psy7353 82 VFPCPVCGKEFSRPDKMKNHMKTVHDCF-MPATTPQGQRGQRASPVIDFHKDSVF 135 (139)
Q Consensus 82 ~~~C~~C~~~f~~~~~l~~H~~~~h~~~-~~~~C~~C~~~f~~~~~l~~H~~~~~ 135 (139)
.|.|+.|++ ..+...|..|....|..+ +.+.||.|...++ .+|..|+...|
T Consensus 2 ~f~CP~C~~-~~~~~~L~~H~~~~H~~~~~~v~CPiC~~~~~--~~l~~Hl~~~H 53 (54)
T PF05605_consen 2 SFTCPYCGK-GFSESSLVEHCEDEHRSESKNVVCPICSSRVT--DNLIRHLNSQH 53 (54)
T ss_pred CcCCCCCCC-ccCHHHHHHHHHhHCcCCCCCccCCCchhhhh--hHHHHHHHHhc
Confidence 367777877 344567778877666654 5677888887644 36777777665
No 23
>PHA00616 hypothetical protein
Probab=98.10 E-value=1.5e-06 Score=42.41 Aligned_cols=31 Identities=16% Similarity=0.471 Sum_probs=16.8
Q ss_pred eecCCCCCcCCChHHHHHHHHHhcCCCcccC
Q psy7353 55 FPCPVCGKEFSRPDKMKNHMKTGCQRKVFPC 85 (139)
Q Consensus 55 ~~c~~C~~~~~~~~~l~~h~~~~~~~~~~~C 85 (139)
|.|+.||..|...+.|..|++.++++.++.|
T Consensus 2 YqC~~CG~~F~~~s~l~~H~r~~hg~~~~~~ 32 (44)
T PHA00616 2 YQCLRCGGIFRKKKEVIEHLLSVHKQNKLTL 32 (44)
T ss_pred CccchhhHHHhhHHHHHHHHHHhcCCCccce
Confidence 4555555555555555555555555555444
No 24
>PHA00732 hypothetical protein
Probab=98.09 E-value=3.5e-06 Score=46.86 Aligned_cols=37 Identities=32% Similarity=0.672 Sum_probs=17.9
Q ss_pred eecCCCCCcchhcccCCHHHHHHHHHHhccCCCCceeecCCCCCcCC
Q psy7353 19 YKCMECAKVDVIKTFKNKYSFQRHAFLYHEGCQRKVFPCPVCGKEFS 65 (139)
Q Consensus 19 ~~C~~c~~~~~~~~f~~~~~l~~h~~~~~~~~~~~~~~c~~C~~~~~ 65 (139)
|.|..|++ .|.+...|+.|++..|.+ +.|+.|++.|.
T Consensus 2 y~C~~Cgk-----~F~s~s~Lk~H~r~~H~~-----~~C~~CgKsF~ 38 (79)
T PHA00732 2 FKCPICGF-----TTVTLFALKQHARRNHTL-----TKCPVCNKSYR 38 (79)
T ss_pred ccCCCCCC-----ccCCHHHHHHHhhcccCC-----CccCCCCCEeC
Confidence 45555555 555555555554322321 24555555544
No 25
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=98.05 E-value=1.4e-05 Score=41.20 Aligned_cols=48 Identities=25% Similarity=0.534 Sum_probs=22.4
Q ss_pred eecCCCCCcchhcccCCHHHHHHHHHHhccCCCCceeecCCCCCcCCChHHHHHHHH
Q psy7353 19 YKCMECAKVDVIKTFKNKYSFQRHAFLYHEGCQRKVFPCPVCGKEFSRPDKMKNHMK 75 (139)
Q Consensus 19 ~~C~~c~~~~~~~~f~~~~~l~~h~~~~~~~~~~~~~~c~~C~~~~~~~~~l~~h~~ 75 (139)
|.||.|++ . .+...|..|....|... .+.+.||+|...+. ..|..|+.
T Consensus 3 f~CP~C~~-----~-~~~~~L~~H~~~~H~~~-~~~v~CPiC~~~~~--~~l~~Hl~ 50 (54)
T PF05605_consen 3 FTCPYCGK-----G-FSESSLVEHCEDEHRSE-SKNVVCPICSSRVT--DNLIRHLN 50 (54)
T ss_pred cCCCCCCC-----c-cCHHHHHHHHHhHCcCC-CCCccCCCchhhhh--hHHHHHHH
Confidence 45566665 3 22345555555544442 23455555554322 24444444
No 26
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=97.97 E-value=4e-06 Score=57.48 Aligned_cols=56 Identities=21% Similarity=0.420 Sum_probs=38.8
Q ss_pred CCcccCCC--CCccCCChhHHHhhhhhhc------------------CCCCCCCCCCCCCCCCCCcchhccccccc
Q psy7353 80 RKVFPCPV--CGKEFSRPDKMKNHMKTVH------------------DCFMPATTPQGQRGQRASPVIDFHKDSVF 135 (139)
Q Consensus 80 ~~~~~C~~--C~~~f~~~~~l~~H~~~~h------------------~~~~~~~C~~C~~~f~~~~~l~~H~~~~~ 135 (139)
++||.|++ |.+.|+..--|.-|+.-.| ..++||.|+.|++++...+-|+-|+.-.|
T Consensus 347 ~KpykCpV~gC~K~YknqnGLKYH~lhGH~~~~~~~~p~p~~~~~F~~~~KPYrCevC~KRYKNlNGLKYHr~Hsh 422 (423)
T COG5189 347 GKPYKCPVEGCNKKYKNQNGLKYHMLHGHQNQKLHENPSPEKMNIFSAKDKPYRCEVCDKRYKNLNGLKYHRKHSH 422 (423)
T ss_pred CceecCCCCCchhhhccccchhhhhhccccCcccCCCCCccccccccccCCceeccccchhhccCccceecccccC
Confidence 35555544 5555555555555544222 24589999999999999999999987654
No 27
>KOG3993|consensus
Probab=97.95 E-value=4.1e-06 Score=59.39 Aligned_cols=27 Identities=15% Similarity=0.003 Sum_probs=22.2
Q ss_pred CCCCCCCCCCCCCCcchhcccccccCc
Q psy7353 111 PATTPQGQRGQRASPVIDFHKDSVFNK 137 (139)
Q Consensus 111 ~~~C~~C~~~f~~~~~l~~H~~~~~~~ 137 (139)
-|.|..|...|.+...|.+|+..-|..
T Consensus 458 ~f~~ky~~atfyss~~ltrhin~~Hps 484 (500)
T KOG3993|consen 458 GFTCKYCPATFYSSPGLTRHINKCHPS 484 (500)
T ss_pred ccccccchHhhhcCcchHhHhhhcChH
Confidence 367888999999999999998877743
No 28
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=97.79 E-value=1.9e-06 Score=37.94 Aligned_cols=22 Identities=36% Similarity=0.887 Sum_probs=12.2
Q ss_pred ccCCCCCccCCChhHHHhhhhh
Q psy7353 83 FPCPVCGKEFSRPDKMKNHMKT 104 (139)
Q Consensus 83 ~~C~~C~~~f~~~~~l~~H~~~ 104 (139)
|.|..|+..|.....|..|++.
T Consensus 2 ~~C~~C~~~F~~~~~l~~H~~~ 23 (27)
T PF13912_consen 2 FECDECGKTFSSLSALREHKRS 23 (27)
T ss_dssp EEETTTTEEESSHHHHHHHHCT
T ss_pred CCCCccCCccCChhHHHHHhHH
Confidence 4555555555555555555554
No 29
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=97.76 E-value=1.3e-05 Score=33.73 Aligned_cols=22 Identities=45% Similarity=1.165 Sum_probs=11.7
Q ss_pred ccCCCCCccCCChhHHHhhhhh
Q psy7353 83 FPCPVCGKEFSRPDKMKNHMKT 104 (139)
Q Consensus 83 ~~C~~C~~~f~~~~~l~~H~~~ 104 (139)
|.|+.|++.|.....|..|++.
T Consensus 1 y~C~~C~~~f~~~~~l~~H~~~ 22 (23)
T PF00096_consen 1 YKCPICGKSFSSKSNLKRHMRR 22 (23)
T ss_dssp EEETTTTEEESSHHHHHHHHHH
T ss_pred CCCCCCCCccCCHHHHHHHHhH
Confidence 3455555555555555555543
No 30
>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=97.76 E-value=2e-06 Score=36.49 Aligned_cols=23 Identities=43% Similarity=1.128 Sum_probs=12.7
Q ss_pred ccCCCCCccCCChhHHHhhhhhh
Q psy7353 83 FPCPVCGKEFSRPDKMKNHMKTV 105 (139)
Q Consensus 83 ~~C~~C~~~f~~~~~l~~H~~~~ 105 (139)
|.|+.|+..|.....|..|+.++
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 45666666666666666666553
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=97.70 E-value=2.5e-05 Score=32.97 Aligned_cols=22 Identities=14% Similarity=0.166 Sum_probs=10.7
Q ss_pred CCCCCCCCCCCCcchhcccccc
Q psy7353 113 TTPQGQRGQRASPVIDFHKDSV 134 (139)
Q Consensus 113 ~C~~C~~~f~~~~~l~~H~~~~ 134 (139)
.|+.|++.|.+...|..|+..+
T Consensus 2 ~C~~C~~~~~~~~~l~~H~~~~ 23 (24)
T PF13894_consen 2 QCPICGKSFRSKSELRQHMRTH 23 (24)
T ss_dssp E-SSTS-EESSHHHHHHHHHHH
T ss_pred CCcCCCCcCCcHHHHHHHHHhh
Confidence 4555555555555555555444
No 32
>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=97.64 E-value=2.9e-05 Score=34.03 Aligned_cols=25 Identities=16% Similarity=0.108 Sum_probs=15.6
Q ss_pred CCCCCCCCCCCCCCcchhccccccc
Q psy7353 111 PATTPQGQRGQRASPVIDFHKDSVF 135 (139)
Q Consensus 111 ~~~C~~C~~~f~~~~~l~~H~~~~~ 135 (139)
||.|+.|+..|.+...|..|++.|+
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 3566666666666666666666554
No 33
>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=97.54 E-value=8.5e-05 Score=31.13 Aligned_cols=22 Identities=41% Similarity=0.794 Sum_probs=14.1
Q ss_pred eecCCCCCcchhcccCCHHHHHHHHHH
Q psy7353 19 YKCMECAKVDVIKTFKNKYSFQRHAFL 45 (139)
Q Consensus 19 ~~C~~c~~~~~~~~f~~~~~l~~h~~~ 45 (139)
|.|+.|++ .|.+...|+.|++.
T Consensus 1 y~C~~C~~-----~f~~~~~l~~H~~~ 22 (23)
T PF00096_consen 1 YKCPICGK-----SFSSKSNLKRHMRR 22 (23)
T ss_dssp EEETTTTE-----EESSHHHHHHHHHH
T ss_pred CCCCCCCC-----ccCCHHHHHHHHhH
Confidence 45666666 66666666666643
No 34
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=97.53 E-value=1.3e-05 Score=46.47 Aligned_cols=73 Identities=21% Similarity=0.303 Sum_probs=18.2
Q ss_pred ecCCCCCcCCChHHHHHHHHHhcCCCcccCCCCCccCCChhHHHhhhhhhcCCCCCCCCCCCCCCCCCCcchhcccccc
Q psy7353 56 PCPVCGKEFSRPDKMKNHMKTGCQRKVFPCPVCGKEFSRPDKMKNHMKTVHDCFMPATTPQGQRGQRASPVIDFHKDSV 134 (139)
Q Consensus 56 ~c~~C~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~~ 134 (139)
.|..|+..|.....+..|+...++-..- ....+.....+..+++. .....+.|..|+..|.+...|..|++++
T Consensus 1 ~C~~C~~~f~~~~~l~~H~~~~H~~~~~----~~~~l~~~~~~~~~~~~--~~~~~~~C~~C~~~f~s~~~l~~Hm~~~ 73 (100)
T PF12756_consen 1 QCLFCDESFSSVDDLLQHMKKKHGFDIP----DQKYLVDPNRLLNYLRK--KVKESFRCPYCNKTFRSREALQEHMRSK 73 (100)
T ss_dssp ------------------------------------------------------SSEEBSSSS-EESSHHHHHHHHHHT
T ss_pred Cccccccccccccccccccccccccccc----ccccccccccccccccc--ccCCCCCCCccCCCCcCHHHHHHHHcCc
Confidence 3888999999999999998755542211 01112233333333332 1122577888888888888888887764
No 35
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=97.34 E-value=0.00017 Score=41.70 Aligned_cols=74 Identities=23% Similarity=0.515 Sum_probs=22.0
Q ss_pred ecCCCCCcchhcccCCHHHHHHHHHHhccCCCCceeecCCCCCcCCChHHHHHHHHHhcCCCcccCCCCCccCCChhHHH
Q psy7353 20 KCMECAKVDVIKTFKNKYSFQRHAFLYHEGCQRKVFPCPVCGKEFSRPDKMKNHMKTGCQRKVFPCPVCGKEFSRPDKMK 99 (139)
Q Consensus 20 ~C~~c~~~~~~~~f~~~~~l~~h~~~~~~~~~~~~~~c~~C~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~f~~~~~l~ 99 (139)
.|..|+. .|.+...+..|+...|.- ..+ ....+.....+....... ....+.|..|+..|.....|.
T Consensus 1 ~C~~C~~-----~f~~~~~l~~H~~~~H~~--~~~-----~~~~l~~~~~~~~~~~~~-~~~~~~C~~C~~~f~s~~~l~ 67 (100)
T PF12756_consen 1 QCLFCDE-----SFSSVDDLLQHMKKKHGF--DIP-----DQKYLVDPNRLLNYLRKK-VKESFRCPYCNKTFRSREALQ 67 (100)
T ss_dssp -------------------------------------------------------------SSEEBSSSS-EESSHHHHH
T ss_pred Ccccccc-----cccccccccccccccccc--ccc-----cccccccccccccccccc-cCCCCCCCccCCCCcCHHHHH
Confidence 4888998 899999999999776653 111 111122333333333322 223689999999999999999
Q ss_pred hhhhhhc
Q psy7353 100 NHMKTVH 106 (139)
Q Consensus 100 ~H~~~~h 106 (139)
.|++.++
T Consensus 68 ~Hm~~~~ 74 (100)
T PF12756_consen 68 EHMRSKH 74 (100)
T ss_dssp HHHHHTT
T ss_pred HHHcCcc
Confidence 9999743
No 36
>PF12171 zf-C2H2_jaz: Zinc-finger double-stranded RNA-binding; InterPro: IPR022755 This zinc finger is found in archaea and eukaryotes, and is approximately 30 amino acids in length. The mammalian members of this group occur multiple times along the protein, joined by flexible linkers, and are referred to as JAZ - dsRNA-binding ZF protein - zinc-fingers. The JAZ proteins are expressed in all tissues tested and localise in the nucleus, particularly the nucleolus []. JAZ preferentially binds to double-stranded (ds) RNA or RNA/DNA hybrids rather than DNA. In addition to binding double-stranded RNA, these zinc-fingers are required for nucleolar localisation. This entry represents the multiple-adjacent-C2H2 zinc finger, JAZ. ; PDB: 4DGW_A 1ZR9_A.
Probab=97.18 E-value=0.00011 Score=32.18 Aligned_cols=22 Identities=9% Similarity=-0.056 Sum_probs=14.2
Q ss_pred CCCCCCCCCCCCCcchhccccc
Q psy7353 112 ATTPQGQRGQRASPVIDFHKDS 133 (139)
Q Consensus 112 ~~C~~C~~~f~~~~~l~~H~~~ 133 (139)
|.|..|++.|.+...|..|+++
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 4566666666666666666654
No 37
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=97.12 E-value=0.00013 Score=50.22 Aligned_cols=71 Identities=27% Similarity=0.514 Sum_probs=44.3
Q ss_pred CcceecCC--CCCcchhcccCCHHHHHHHHHHhccCCCCceeecCCCCCcCCChHHHHHHHHHhcCCCcccCCCCCccCC
Q psy7353 16 EGIYKCME--CAKVDVIKTFKNKYSFQRHAFLYHEGCQRKVFPCPVCGKEFSRPDKMKNHMKTGCQRKVFPCPVCGKEFS 93 (139)
Q Consensus 16 ~~~~~C~~--c~~~~~~~~f~~~~~l~~h~~~~~~~~~~~~~~c~~C~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~f~ 93 (139)
++||.|+. |.| .|+....|+-|+..-|.. .+...-+ +-..+.......+||.|++|++.|+
T Consensus 347 ~KpykCpV~gC~K-----~YknqnGLKYH~lhGH~~--~~~~~~p----------~p~~~~~F~~~~KPYrCevC~KRYK 409 (423)
T COG5189 347 GKPYKCPVEGCNK-----KYKNQNGLKYHMLHGHQN--QKLHENP----------SPEKMNIFSAKDKPYRCEVCDKRYK 409 (423)
T ss_pred CceecCCCCCchh-----hhccccchhhhhhccccC--cccCCCC----------CccccccccccCCceeccccchhhc
Confidence 58899876 666 888888898886432322 1111111 0011122244568999999999888
Q ss_pred ChhHHHhhhh
Q psy7353 94 RPDKMKNHMK 103 (139)
Q Consensus 94 ~~~~l~~H~~ 103 (139)
..--|.-|+.
T Consensus 410 NlNGLKYHr~ 419 (423)
T COG5189 410 NLNGLKYHRK 419 (423)
T ss_pred cCccceeccc
Confidence 8888877765
No 38
>PRK04860 hypothetical protein; Provisional
Probab=97.06 E-value=0.00028 Score=44.58 Aligned_cols=40 Identities=8% Similarity=0.057 Sum_probs=33.5
Q ss_pred cccCCCCCccCCChhHHHhhhhhhcCCCCCCCCCCCCCCCCCCcc
Q psy7353 82 VFPCPVCGKEFSRPDKMKNHMKTVHDCFMPATTPQGQRGQRASPV 126 (139)
Q Consensus 82 ~~~C~~C~~~f~~~~~l~~H~~~~h~~~~~~~C~~C~~~f~~~~~ 126 (139)
+|.|. |+. ....+.+|.++ +.++++|.|..|+..|....+
T Consensus 119 ~Y~C~-C~~---~~~~~rrH~ri-~~g~~~YrC~~C~~~l~~~~~ 158 (160)
T PRK04860 119 PYRCK-CQE---HQLTVRRHNRV-VRGEAVYRCRRCGETLVFKGE 158 (160)
T ss_pred EEEcC-CCC---eeCHHHHHHHH-hcCCccEECCCCCceeEEecc
Confidence 68897 986 67788899998 899999999999998876543
No 39
>smart00355 ZnF_C2H2 zinc finger.
Probab=96.97 E-value=0.00017 Score=30.75 Aligned_cols=21 Identities=10% Similarity=0.134 Sum_probs=12.3
Q ss_pred CCCCCCCCCCCCCcchhcccc
Q psy7353 112 ATTPQGQRGQRASPVIDFHKD 132 (139)
Q Consensus 112 ~~C~~C~~~f~~~~~l~~H~~ 132 (139)
|.|+.|++.|.....|..|++
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~ 21 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMR 21 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHH
Confidence 345566666666666666655
No 40
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=96.83 E-value=8.1e-05 Score=31.90 Aligned_cols=20 Identities=30% Similarity=0.909 Sum_probs=9.9
Q ss_pred cCCCCCccCCChhHHHhhhh
Q psy7353 84 PCPVCGKEFSRPDKMKNHMK 103 (139)
Q Consensus 84 ~C~~C~~~f~~~~~l~~H~~ 103 (139)
.|..|+..|.....|..|++
T Consensus 2 ~C~~C~~~f~s~~~~~~H~~ 21 (25)
T PF12874_consen 2 YCDICNKSFSSENSLRQHLR 21 (25)
T ss_dssp EETTTTEEESSHHHHHHHHT
T ss_pred CCCCCCCCcCCHHHHHHHHC
Confidence 34455555555555555443
No 41
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=96.77 E-value=0.00083 Score=28.38 Aligned_cols=23 Identities=35% Similarity=0.788 Sum_probs=11.7
Q ss_pred ccCCCCCccCCChhHHHhhhhhhc
Q psy7353 83 FPCPVCGKEFSRPDKMKNHMKTVH 106 (139)
Q Consensus 83 ~~C~~C~~~f~~~~~l~~H~~~~h 106 (139)
|.|+.|++... ...|.+|++.+|
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 34556665555 556666665543
No 42
>smart00355 ZnF_C2H2 zinc finger.
Probab=96.68 E-value=0.0017 Score=27.41 Aligned_cols=22 Identities=45% Similarity=1.053 Sum_probs=15.1
Q ss_pred ccCCCCCccCCChhHHHhhhhh
Q psy7353 83 FPCPVCGKEFSRPDKMKNHMKT 104 (139)
Q Consensus 83 ~~C~~C~~~f~~~~~l~~H~~~ 104 (139)
|.|..|++.|.....|..|++.
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~~ 22 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMRT 22 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHHH
Confidence 3566777777777777777664
No 43
>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=96.67 E-value=0.0032 Score=31.58 Aligned_cols=30 Identities=20% Similarity=0.615 Sum_probs=14.6
Q ss_pred CceeecCCCCCcCCChHHHHHHHHHhcCCC
Q psy7353 52 RKVFPCPVCGKEFSRPDKMKNHMKTGCQRK 81 (139)
Q Consensus 52 ~~~~~c~~C~~~~~~~~~l~~h~~~~~~~~ 81 (139)
+.|..|++|+..+.+..+|.+|+...++.+
T Consensus 22 ~~PatCP~C~a~~~~srnLrRHle~~H~~k 51 (54)
T PF09237_consen 22 EQPATCPICGAVIRQSRNLRRHLEIRHFKK 51 (54)
T ss_dssp S--EE-TTT--EESSHHHHHHHHHHHTTTS
T ss_pred CCCCCCCcchhhccchhhHHHHHHHHhccc
Confidence 445566666666666666666665555444
No 44
>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=96.65 E-value=0.00016 Score=36.19 Aligned_cols=25 Identities=20% Similarity=0.724 Sum_probs=11.1
Q ss_pred CCcccCCCCCccCCChhHHHhhhhh
Q psy7353 80 RKVFPCPVCGKEFSRPDKMKNHMKT 104 (139)
Q Consensus 80 ~~~~~C~~C~~~f~~~~~l~~H~~~ 104 (139)
+.|-.|++|+..+.+..+|.+|+.+
T Consensus 22 ~~PatCP~C~a~~~~srnLrRHle~ 46 (54)
T PF09237_consen 22 EQPATCPICGAVIRQSRNLRRHLEI 46 (54)
T ss_dssp S--EE-TTT--EESSHHHHHHHHHH
T ss_pred CCCCCCCcchhhccchhhHHHHHHH
Confidence 3455555555555555555555544
No 45
>PF12171 zf-C2H2_jaz: Zinc-finger double-stranded RNA-binding; InterPro: IPR022755 This zinc finger is found in archaea and eukaryotes, and is approximately 30 amino acids in length. The mammalian members of this group occur multiple times along the protein, joined by flexible linkers, and are referred to as JAZ - dsRNA-binding ZF protein - zinc-fingers. The JAZ proteins are expressed in all tissues tested and localise in the nucleus, particularly the nucleolus []. JAZ preferentially binds to double-stranded (ds) RNA or RNA/DNA hybrids rather than DNA. In addition to binding double-stranded RNA, these zinc-fingers are required for nucleolar localisation. This entry represents the multiple-adjacent-C2H2 zinc finger, JAZ. ; PDB: 4DGW_A 1ZR9_A.
Probab=96.50 E-value=0.0022 Score=27.92 Aligned_cols=22 Identities=45% Similarity=0.920 Sum_probs=18.9
Q ss_pred ccCCCCCccCCChhHHHhhhhh
Q psy7353 83 FPCPVCGKEFSRPDKMKNHMKT 104 (139)
Q Consensus 83 ~~C~~C~~~f~~~~~l~~H~~~ 104 (139)
|.|..|++.|.+...|..|+++
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 6788999999999999988875
No 46
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=96.45 E-value=0.00022 Score=30.24 Aligned_cols=24 Identities=8% Similarity=0.036 Sum_probs=19.3
Q ss_pred CCCCCCCCCCCCCcchhcccccccC
Q psy7353 112 ATTPQGQRGQRASPVIDFHKDSVFN 136 (139)
Q Consensus 112 ~~C~~C~~~f~~~~~l~~H~~~~~~ 136 (139)
|.|+.|++... ...|.+|.+.+|+
T Consensus 1 y~C~~C~y~t~-~~~l~~H~~~~H~ 24 (24)
T PF13909_consen 1 YKCPHCSYSTS-KSNLKRHLKRHHP 24 (24)
T ss_dssp EE-SSSS-EES-HHHHHHHHHHHHS
T ss_pred CCCCCCCCcCC-HHHHHHHHHhhCc
Confidence 68999999998 8899999998874
No 47
>PRK04860 hypothetical protein; Provisional
Probab=96.20 E-value=0.0054 Score=38.85 Aligned_cols=39 Identities=18% Similarity=0.474 Sum_probs=33.1
Q ss_pred ceeecCCCCCcCCChHHHHHHHHHhcCCCcccCCCCCccCCCh
Q psy7353 53 KVFPCPVCGKEFSRPDKMKNHMKTGCQRKVFPCPVCGKEFSRP 95 (139)
Q Consensus 53 ~~~~c~~C~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~f~~~ 95 (139)
-+|.|. |+. ....+..|.++++++++|.|..|+..|...
T Consensus 118 ~~Y~C~-C~~---~~~~~rrH~ri~~g~~~YrC~~C~~~l~~~ 156 (160)
T PRK04860 118 FPYRCK-CQE---HQLTVRRHNRVVRGEAVYRCRRCGETLVFK 156 (160)
T ss_pred EEEEcC-CCC---eeCHHHHHHHHhcCCccEECCCCCceeEEe
Confidence 468998 986 667788999999999999999999887654
No 48
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=96.03 E-value=0.0036 Score=26.56 Aligned_cols=22 Identities=9% Similarity=-0.046 Sum_probs=13.2
Q ss_pred CCCCCCCCCCCCCcchhccccc
Q psy7353 112 ATTPQGQRGQRASPVIDFHKDS 133 (139)
Q Consensus 112 ~~C~~C~~~f~~~~~l~~H~~~ 133 (139)
|.|+.|++.|.+...|..|.++
T Consensus 1 ~~C~~C~~~f~s~~~~~~H~~s 22 (25)
T PF12874_consen 1 FYCDICNKSFSSENSLRQHLRS 22 (25)
T ss_dssp EEETTTTEEESSHHHHHHHHTT
T ss_pred CCCCCCCCCcCCHHHHHHHHCc
Confidence 3466666666666666666554
No 49
>cd00350 rubredoxin_like Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center. The family includes rubredoxins, a small electron transfer protein, and a slightly smaller modular rubredoxin domain present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=95.19 E-value=0.016 Score=26.49 Aligned_cols=10 Identities=20% Similarity=0.179 Sum_probs=6.8
Q ss_pred CCCCCCCCCC
Q psy7353 110 MPATTPQGQR 119 (139)
Q Consensus 110 ~~~~C~~C~~ 119 (139)
.++.|+.|+.
T Consensus 16 ~~~~CP~Cg~ 25 (33)
T cd00350 16 APWVCPVCGA 25 (33)
T ss_pred CCCcCcCCCC
Confidence 4677777765
No 50
>KOG2231|consensus
Probab=95.10 E-value=0.043 Score=42.15 Aligned_cols=97 Identities=15% Similarity=0.223 Sum_probs=62.5
Q ss_pred ccCCHHHHHHHHHHhccCCCCceeecCCCC---------CcCCChHHHHHHHHHhcC-CC----cccCCCCCccCCChhH
Q psy7353 32 TFKNKYSFQRHAFLYHEGCQRKVFPCPVCG---------KEFSRPDKMKNHMKTGCQ-RK----VFPCPVCGKEFSRPDK 97 (139)
Q Consensus 32 ~f~~~~~l~~h~~~~~~~~~~~~~~c~~C~---------~~~~~~~~l~~h~~~~~~-~~----~~~C~~C~~~f~~~~~ 97 (139)
.|.+...|+.|+...|.. +.|..|. ........|..|+..... +. .-.|..|...|.....
T Consensus 123 ~~~s~~~Lk~H~~~~H~~-----~~c~lC~~~~kif~~e~k~Yt~~el~~h~~~gd~d~~s~rGhp~C~~C~~~fld~~e 197 (669)
T KOG2231|consen 123 EFKSVENLKNHMRDQHKL-----HLCSLCLQNLKIFINERKLYTRAELNLHLMFGDPDDESCRGHPLCKFCHERFLDDDE 197 (669)
T ss_pred chhHHHHHHHHHHHhhhh-----hccccccccceeeeeeeehehHHHHHHHHhcCCCccccccCCccchhhhhhhccHHH
Confidence 455778899998766653 3344432 223445566777664332 21 2468889889999999
Q ss_pred HHhhhhhhcCCCCCCCC---CCCCCCCCCCcchhccccccc
Q psy7353 98 MKNHMKTVHDCFMPATT---PQGQRGQRASPVIDFHKDSVF 135 (139)
Q Consensus 98 l~~H~~~~h~~~~~~~C---~~C~~~f~~~~~l~~H~~~~~ 135 (139)
|.+|++..|.. -..| +.+..-|....+|..|.+..|
T Consensus 198 l~rH~~~~h~~--chfC~~~~~~neyy~~~~dLe~HfR~~H 236 (669)
T KOG2231|consen 198 LYRHLRFDHEF--CHFCDYKTGQNEYYNDYDDLEEHFRKGH 236 (669)
T ss_pred HHHhhccceeh--eeecCcccccchhcccchHHHHHhhhcC
Confidence 99999875542 1234 234567788888888877766
No 51
>smart00451 ZnF_U1 U1-like zinc finger. Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins.
Probab=94.99 E-value=0.0056 Score=28.21 Aligned_cols=23 Identities=4% Similarity=-0.158 Sum_probs=13.5
Q ss_pred CCCCCCCCCCCCCCcchhccccc
Q psy7353 111 PATTPQGQRGQRASPVIDFHKDS 133 (139)
Q Consensus 111 ~~~C~~C~~~f~~~~~l~~H~~~ 133 (139)
+|.|+.|+..|.+...+..|+++
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~g 25 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLKG 25 (35)
T ss_pred CeEccccCCccCCHHHHHHHHCh
Confidence 35566666666666666666543
No 52
>KOG2893|consensus
Probab=94.60 E-value=0.013 Score=39.24 Aligned_cols=35 Identities=34% Similarity=0.743 Sum_probs=20.6
Q ss_pred CceeecCCCCCcCCChHHHHHHHHHhcCCCcccCCCCCcc
Q psy7353 52 RKVFPCPVCGKEFSRPDKMKNHMKTGCQRKVFPCPVCGKE 91 (139)
Q Consensus 52 ~~~~~c~~C~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~ 91 (139)
.++| |..|++.|.++.-|+.|++ .+.|+|-.|.+.
T Consensus 9 ~kpw-cwycnrefddekiliqhqk----akhfkchichkk 43 (341)
T KOG2893|consen 9 DKPW-CWYCNREFDDEKILIQHQK----AKHFKCHICHKK 43 (341)
T ss_pred CCce-eeecccccchhhhhhhhhh----hccceeeeehhh
Confidence 3454 5566666666666666654 345666666543
No 53
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=94.37 E-value=0.036 Score=23.63 Aligned_cols=19 Identities=53% Similarity=1.508 Sum_probs=10.1
Q ss_pred cCCCCCccCCChhHHHhhhh
Q psy7353 84 PCPVCGKEFSRPDKMKNHMK 103 (139)
Q Consensus 84 ~C~~C~~~f~~~~~l~~H~~ 103 (139)
+|+.||+.| ....|.+|++
T Consensus 4 ~C~~CgR~F-~~~~l~~H~~ 22 (25)
T PF13913_consen 4 PCPICGRKF-NPDRLEKHEK 22 (25)
T ss_pred cCCCCCCEE-CHHHHHHHHH
Confidence 455566555 4444555544
No 54
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=93.80 E-value=0.043 Score=39.56 Aligned_cols=55 Identities=16% Similarity=0.202 Sum_probs=44.0
Q ss_pred cccCCCCCccCCChhHHHhhhhh-hcCCC--CCCCCC--CCCCCCCCCcchhcccccccC
Q psy7353 82 VFPCPVCGKEFSRPDKMKNHMKT-VHDCF--MPATTP--QGQRGQRASPVIDFHKDSVFN 136 (139)
Q Consensus 82 ~~~C~~C~~~f~~~~~l~~H~~~-~h~~~--~~~~C~--~C~~~f~~~~~l~~H~~~~~~ 136 (139)
++.|..|...|.....|..|.+. .|.++ +++.|+ .|++.|.....+..|...+.+
T Consensus 289 ~~~~~~~~~~~s~~~~l~~~~~~~~h~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~ 348 (467)
T COG5048 289 PIKSKQCNISFSRSSPLTRHLRSVNHSGESLKPFSCPYSLCGKLFSRNDALKRHILLHTS 348 (467)
T ss_pred CCCCccccCCccccccccccccccccccccCCceeeeccCCCccccccccccCCcccccC
Confidence 57778888888888888888883 37777 888888 688888888888888777664
No 55
>KOG1146|consensus
Probab=93.79 E-value=0.013 Score=47.74 Aligned_cols=25 Identities=12% Similarity=0.048 Sum_probs=21.7
Q ss_pred CCCCCCCCCCCCCCCCcchhccccc
Q psy7353 109 FMPATTPQGQRGQRASPVIDFHKDS 133 (139)
Q Consensus 109 ~~~~~C~~C~~~f~~~~~l~~H~~~ 133 (139)
-.+|.|..|.+.++...+|..|.++
T Consensus 516 ~~p~~C~~C~~stttng~LsihlqS 540 (1406)
T KOG1146|consen 516 GKPYPCRACNYSTTTNGNLSIHLQS 540 (1406)
T ss_pred CCcccceeeeeeeecchHHHHHHHH
Confidence 3578999999999999999999765
No 56
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=93.07 E-value=0.035 Score=36.93 Aligned_cols=13 Identities=8% Similarity=-0.069 Sum_probs=10.0
Q ss_pred CCCCCCCCCCCCC
Q psy7353 112 ATTPQGQRGQRAS 124 (139)
Q Consensus 112 ~~C~~C~~~f~~~ 124 (139)
+.||.||+.|...
T Consensus 49 ~vCP~CgyA~~~~ 61 (214)
T PF09986_consen 49 WVCPHCGYAAFEE 61 (214)
T ss_pred EECCCCCCccccc
Confidence 5799999877654
No 57
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=92.73 E-value=0.047 Score=38.60 Aligned_cols=16 Identities=6% Similarity=-0.255 Sum_probs=8.3
Q ss_pred CCCCCcchhccccccc
Q psy7353 120 GQRASPVIDFHKDSVF 135 (139)
Q Consensus 120 ~f~~~~~l~~H~~~~~ 135 (139)
.|.+...|..|+...|
T Consensus 290 vf~~~~el~~h~~~~h 305 (493)
T COG5236 290 VFPYHTELLEHLTRFH 305 (493)
T ss_pred EeccHHHHHHHHHHHh
Confidence 4555555555554444
No 58
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=92.71 E-value=0.092 Score=33.45 Aligned_cols=25 Identities=40% Similarity=0.775 Sum_probs=19.7
Q ss_pred CcccCCCCCccCCChhHHHhhhhhhcCCCCCCCCCCCCC
Q psy7353 81 KVFPCPVCGKEFSRPDKMKNHMKTVHDCFMPATTPQGQR 119 (139)
Q Consensus 81 ~~~~C~~C~~~f~~~~~l~~H~~~~h~~~~~~~C~~C~~ 119 (139)
+.|.|++||.. +.|+.|..||.|+.
T Consensus 133 ~~~vC~vCGy~--------------~~ge~P~~CPiCga 157 (166)
T COG1592 133 KVWVCPVCGYT--------------HEGEAPEVCPICGA 157 (166)
T ss_pred CEEEcCCCCCc--------------ccCCCCCcCCCCCC
Confidence 46999999864 45578899999984
No 59
>KOG2893|consensus
Probab=92.68 E-value=0.048 Score=36.55 Aligned_cols=43 Identities=21% Similarity=0.491 Sum_probs=25.2
Q ss_pred cceecCCCCCcchhcccCCHHHHHHHHHHhccCCCCceeecCCCCCcCCChHHHHH
Q psy7353 17 GIYKCMECAKVDVIKTFKNKYSFQRHAFLYHEGCQRKVFPCPVCGKEFSRPDKMKN 72 (139)
Q Consensus 17 ~~~~C~~c~~~~~~~~f~~~~~l~~h~~~~~~~~~~~~~~c~~C~~~~~~~~~l~~ 72 (139)
++| |.+|+. .|-+..-|.+|+.. +.|+|-+|.+.+.....|..
T Consensus 10 kpw-cwycnr-----efddekiliqhqka-------khfkchichkkl~sgpglsi 52 (341)
T KOG2893|consen 10 KPW-CWYCNR-----EFDDEKILIQHQKA-------KHFKCHICHKKLFSGPGLSI 52 (341)
T ss_pred Cce-eeeccc-----ccchhhhhhhhhhh-------ccceeeeehhhhccCCCcee
Confidence 444 666776 77777766666532 44677777665444444433
No 60
>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=92.37 E-value=0.089 Score=35.73 Aligned_cols=82 Identities=21% Similarity=0.408 Sum_probs=49.1
Q ss_pred CCcceecCCCCCcchhcccCCHHHHHHHHHHhccCCCCceeecCCCCCcCCChHHHH-------HHHH----HhcCCCcc
Q psy7353 15 TEGIYKCMECAKVDVIKTFKNKYSFQRHAFLYHEGCQRKVFPCPVCGKEFSRPDKMK-------NHMK----TGCQRKVF 83 (139)
Q Consensus 15 ~~~~~~C~~c~~~~~~~~f~~~~~l~~h~~~~~~~~~~~~~~c~~C~~~~~~~~~l~-------~h~~----~~~~~~~~ 83 (139)
+.+.|.|..|.. |...-.--.|+.+....+ ...|+|.-|++.-.. +-|. .|.+ .....+++
T Consensus 139 GGrif~CsfC~~------flCEDDQFEHQAsCQvLe-~E~~KC~SCNrlGq~-sCLRCK~cfCddHvrrKg~ky~k~k~~ 210 (314)
T PF06524_consen 139 GGRIFKCSFCDN------FLCEDDQFEHQASCQVLE-SETFKCQSCNRLGQY-SCLRCKICFCDDHVRRKGFKYEKGKPI 210 (314)
T ss_pred CCeEEEeecCCC------eeeccchhhhhhhhhhhh-cccccccccccccch-hhhheeeeehhhhhhhcccccccCCCC
Confidence 677899999996 665544444544433322 345777777653221 1111 2222 12234688
Q ss_pred cCCCCCccCCChhHHHhhhhh
Q psy7353 84 PCPVCGKEFSRPDKMKNHMKT 104 (139)
Q Consensus 84 ~C~~C~~~f~~~~~l~~H~~~ 104 (139)
+|+.|+........|..-.++
T Consensus 211 PCPKCg~et~eTkdLSmStR~ 231 (314)
T PF06524_consen 211 PCPKCGYETQETKDLSMSTRS 231 (314)
T ss_pred CCCCCCCcccccccceeeeec
Confidence 999999888887777777666
No 61
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=91.80 E-value=0.13 Score=26.70 Aligned_cols=8 Identities=25% Similarity=0.451 Sum_probs=4.3
Q ss_pred CCCCCCCC
Q psy7353 111 PATTPQGQ 118 (139)
Q Consensus 111 ~~~C~~C~ 118 (139)
+|.|+.||
T Consensus 50 ~Y~Cp~CG 57 (61)
T COG2888 50 PYRCPKCG 57 (61)
T ss_pred ceECCCcC
Confidence 45555554
No 62
>KOG1146|consensus
Probab=91.06 E-value=0.076 Score=43.66 Aligned_cols=56 Identities=11% Similarity=0.153 Sum_probs=42.9
Q ss_pred CCcccCCCCCccCCChhHHHhhhhhhcC------------------------------------C-----C-CCCCCCCC
Q psy7353 80 RKVFPCPVCGKEFSRPDKMKNHMKTVHD------------------------------------C-----F-MPATTPQG 117 (139)
Q Consensus 80 ~~~~~C~~C~~~f~~~~~l~~H~~~~h~------------------------------------~-----~-~~~~C~~C 117 (139)
.++|.|..|...++...+|..|++.... + . -.|.|..|
T Consensus 516 ~~p~~C~~C~~stttng~LsihlqS~~h~~~lee~~~~~g~~v~~~~~~v~s~~P~~ag~~~~ags~~pktkP~~~C~vc 595 (1406)
T KOG1146|consen 516 GKPYPCRACNYSTTTNGNLSIHLQSDLHRNELEEAEENAGEQVRLLPASVTSAVPEEAGLGPSAGSSGPKTKPSWRCEVC 595 (1406)
T ss_pred CCcccceeeeeeeecchHHHHHHHHHhhHHHHHHHHhccccchhhhhhhhcccCcccccCCCCCCCCCCCCCCCcchhhh
Confidence 4689999999999999999999764210 1 1 13899999
Q ss_pred CCCCCCCcchhccccccc
Q psy7353 118 QRGQRASPVIDFHKDSVF 135 (139)
Q Consensus 118 ~~~f~~~~~l~~H~~~~~ 135 (139)
++.-+-..+|.-|+.+-+
T Consensus 596 ~yetniarnlrihmtss~ 613 (1406)
T KOG1146|consen 596 SYETNIARNLRIHMTASP 613 (1406)
T ss_pred cchhhhhhccccccccCC
Confidence 999888888988876543
No 63
>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=90.76 E-value=0.25 Score=22.70 Aligned_cols=25 Identities=32% Similarity=0.591 Sum_probs=14.4
Q ss_pred cccCCCCCccCCChhHHHhhhhhhcCCCCCCCCCCCCC
Q psy7353 82 VFPCPVCGKEFSRPDKMKNHMKTVHDCFMPATTPQGQR 119 (139)
Q Consensus 82 ~~~C~~C~~~f~~~~~l~~H~~~~h~~~~~~~C~~C~~ 119 (139)
.|.|..||..+... +.|..|+.|+.
T Consensus 2 ~~~C~~CG~i~~g~-------------~~p~~CP~Cg~ 26 (34)
T cd00729 2 VWVCPVCGYIHEGE-------------EAPEKCPICGA 26 (34)
T ss_pred eEECCCCCCEeECC-------------cCCCcCcCCCC
Confidence 36677777543211 23567777775
No 64
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=89.27 E-value=0.18 Score=36.38 Aligned_cols=60 Identities=35% Similarity=0.704 Sum_probs=44.4
Q ss_pred eeecCCCCCcCCChHHHHHHHH--HhcCC--CcccCC--CCCccCCChhHHHhhhhhhcCCCCCCCC
Q psy7353 54 VFPCPVCGKEFSRPDKMKNHMK--TGCQR--KVFPCP--VCGKEFSRPDKMKNHMKTVHDCFMPATT 114 (139)
Q Consensus 54 ~~~c~~C~~~~~~~~~l~~h~~--~~~~~--~~~~C~--~C~~~f~~~~~l~~H~~~~h~~~~~~~C 114 (139)
++.|..|...+.....+..|.. .|.++ +++.|+ .|++.|.+...+..|..+ |.+..+..+
T Consensus 289 ~~~~~~~~~~~s~~~~l~~~~~~~~h~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~ 354 (467)
T COG5048 289 PIKSKQCNISFSRSSPLTRHLRSVNHSGESLKPFSCPYSLCGKLFSRNDALKRHILL-HTSISPAKE 354 (467)
T ss_pred CCCCccccCCccccccccccccccccccccCCceeeeccCCCccccccccccCCccc-ccCCCcccc
Confidence 5667777777888888888877 67777 788887 688888888888888776 555555444
No 65
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=89.17 E-value=0.051 Score=27.79 Aligned_cols=29 Identities=28% Similarity=0.629 Sum_probs=19.2
Q ss_pred cCCCcccCCCCCccCCChhHHHhhhhhhc
Q psy7353 78 CQRKVFPCPVCGKEFSRPDKMKNHMKTVH 106 (139)
Q Consensus 78 ~~~~~~~C~~C~~~f~~~~~l~~H~~~~h 106 (139)
.|+..+.|+.|+..|.+.-+..+|...-|
T Consensus 13 DGE~~lrCPRC~~~FR~~K~Y~RHVNKaH 41 (65)
T COG4049 13 DGEEFLRCPRCGMVFRRRKDYIRHVNKAH 41 (65)
T ss_pred CCceeeeCCchhHHHHHhHHHHHHhhHHh
Confidence 45556677777777777777777766534
No 66
>PHA00626 hypothetical protein
Probab=88.75 E-value=0.15 Score=26.09 Aligned_cols=14 Identities=0% Similarity=-0.299 Sum_probs=7.9
Q ss_pred CCCCCCCCCCCCCC
Q psy7353 110 MPATTPQGQRGQRA 123 (139)
Q Consensus 110 ~~~~C~~C~~~f~~ 123 (139)
..|.|+.|++.|+.
T Consensus 22 nrYkCkdCGY~ft~ 35 (59)
T PHA00626 22 DDYVCCDCGYNDSK 35 (59)
T ss_pred cceEcCCCCCeech
Confidence 34666666665554
No 67
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=88.55 E-value=0.38 Score=24.65 Aligned_cols=31 Identities=23% Similarity=0.493 Sum_probs=22.5
Q ss_pred ccCCCcceecCCCCCcchhcccCCHHHHHHHHHHhc
Q psy7353 12 ASVTEGIYKCMECAKVDVIKTFKNKYSFQRHAFLYH 47 (139)
Q Consensus 12 ~~~~~~~~~C~~c~~~~~~~~f~~~~~l~~h~~~~~ 47 (139)
.-+++..+.|+-|+. .|.....+.+|....|
T Consensus 11 ~RDGE~~lrCPRC~~-----~FR~~K~Y~RHVNKaH 41 (65)
T COG4049 11 DRDGEEFLRCPRCGM-----VFRRRKDYIRHVNKAH 41 (65)
T ss_pred ccCCceeeeCCchhH-----HHHHhHHHHHHhhHHh
Confidence 456677788888888 7888777777765434
No 68
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=87.54 E-value=0.38 Score=25.03 Aligned_cols=10 Identities=30% Similarity=0.272 Sum_probs=5.5
Q ss_pred CCCCCCCCCC
Q psy7353 110 MPATTPQGQR 119 (139)
Q Consensus 110 ~~~~C~~C~~ 119 (139)
.+|.|+.||.
T Consensus 47 ~~Y~CP~CGF 56 (59)
T PRK14890 47 NPYTCPKCGF 56 (59)
T ss_pred CceECCCCCC
Confidence 3556666653
No 69
>KOG2482|consensus
Probab=87.13 E-value=0.73 Score=32.78 Aligned_cols=51 Identities=20% Similarity=0.265 Sum_probs=40.0
Q ss_pred ccCCCCCccCCChhHHHhhhhhhcCCC----------C----------------CCCCCCCCCCCCCCcchhccccc
Q psy7353 83 FPCPVCGKEFSRPDKMKNHMKTVHDCF----------M----------------PATTPQGQRGQRASPVIDFHKDS 133 (139)
Q Consensus 83 ~~C~~C~~~f~~~~~l~~H~~~~h~~~----------~----------------~~~C~~C~~~f~~~~~l~~H~~~ 133 (139)
..|..|......+..|..|+++.|.-+ + .-.|..|+..|-....|..|+..
T Consensus 280 v~CLfC~~~~en~~~l~eHmk~vHe~Dl~Ki~sd~~Ln~YqrvrviNyiRkq~~~~~c~~cd~~F~~e~~l~~hm~e 356 (423)
T KOG2482|consen 280 VVCLFCTNFYENPVFLFEHMKIVHEFDLLKIQSDYSLNFYQRVRVINYIRKQKKKSRCAECDLSFWKEPGLLIHMVE 356 (423)
T ss_pred eEEEeeccchhhHHHHHHHHHHHHHhhHHhhccccccchhhhhhHHHHHHHHhhccccccccccccCcchhhhhccc
Confidence 478889888888999999998876511 0 12588999999999999999654
No 70
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=86.77 E-value=0.21 Score=31.48 Aligned_cols=15 Identities=0% Similarity=-0.274 Sum_probs=8.9
Q ss_pred CCCCCCCCCCCCCcc
Q psy7353 112 ATTPQGQRGQRASPV 126 (139)
Q Consensus 112 ~~C~~C~~~f~~~~~ 126 (139)
++|+.|+.+|.+.-.
T Consensus 29 ~~c~~c~~~f~~~e~ 43 (154)
T PRK00464 29 RECLACGKRFTTFER 43 (154)
T ss_pred eeccccCCcceEeEe
Confidence 566666666665443
No 71
>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=85.66 E-value=1.3 Score=28.15 Aligned_cols=17 Identities=24% Similarity=0.442 Sum_probs=7.9
Q ss_pred CcccCCCCCccCCChhH
Q psy7353 81 KVFPCPVCGKEFSRPDK 97 (139)
Q Consensus 81 ~~~~C~~C~~~f~~~~~ 97 (139)
.-|.|+.|+..|+....
T Consensus 108 ~~Y~Cp~c~~r~tf~eA 124 (158)
T TIGR00373 108 MFFICPNMCVRFTFNEA 124 (158)
T ss_pred CeEECCCCCcEeeHHHH
Confidence 34455555544444433
No 72
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=84.22 E-value=1.9 Score=25.65 Aligned_cols=47 Identities=11% Similarity=-0.005 Sum_probs=26.4
Q ss_pred CCCCCccCCChhHHHhhhhhhcCCCCCCCCCCCCCCCCCCcchhcccccc
Q psy7353 85 CPVCGKEFSRPDKMKNHMKTVHDCFMPATTPQGQRGQRASPVIDFHKDSV 134 (139)
Q Consensus 85 C~~C~~~f~~~~~l~~H~~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~~ 134 (139)
|..|...|........ .. -.....|.|+.|...|=..-++.-|..-|
T Consensus 58 C~~C~~~f~~~~~~~~--~~-~~~~~~y~C~~C~~~FC~dCD~fiHe~Lh 104 (112)
T TIGR00622 58 CFGCQGPFPKPPVSPF--DE-LKDSHRYVCAVCKNVFCVDCDVFVHESLH 104 (112)
T ss_pred ccCcCCCCCCcccccc--cc-cccccceeCCCCCCccccccchhhhhhcc
Confidence 6677776655431110 00 11233577888888877777766665444
No 73
>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=83.99 E-value=1 Score=26.70 Aligned_cols=15 Identities=40% Similarity=0.957 Sum_probs=8.0
Q ss_pred CcccCCCCCccCCCh
Q psy7353 81 KVFPCPVCGKEFSRP 95 (139)
Q Consensus 81 ~~~~C~~C~~~f~~~ 95 (139)
.|..|+.||..|.-.
T Consensus 25 ~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 25 DPIVCPKCGTEFPPE 39 (108)
T ss_pred CCccCCCCCCccCcc
Confidence 455566666555444
No 74
>KOG2186|consensus
Probab=83.27 E-value=0.89 Score=30.95 Aligned_cols=49 Identities=31% Similarity=0.553 Sum_probs=35.7
Q ss_pred ceecCCCCCcchhcccCCHHHHHHHHHHhccCCCCceeecCCCCCcCCChHHHHHHHHHh
Q psy7353 18 IYKCMECAKVDVIKTFKNKYSFQRHAFLYHEGCQRKVFPCPVCGKEFSRPDKMKNHMKTG 77 (139)
Q Consensus 18 ~~~C~~c~~~~~~~~f~~~~~l~~h~~~~~~~~~~~~~~c~~C~~~~~~~~~l~~h~~~~ 77 (139)
.|.|..||. -.-+-.+.+|+..++ ...|.|-.|+..|.. ..+..|..--
T Consensus 3 ~FtCnvCgE------svKKp~vekH~srCr----n~~fSCIDC~k~F~~-~sYknH~kCI 51 (276)
T KOG2186|consen 3 FFTCNVCGE------SVKKPQVEKHMSRCR----NAYFSCIDCGKTFER-VSYKNHTKCI 51 (276)
T ss_pred EEehhhhhh------hccccchHHHHHhcc----CCeeEEeeccccccc-chhhhhhhhc
Confidence 478999996 333446777876656 357899999999988 6678886633
No 75
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=82.05 E-value=2.1 Score=27.79 Aligned_cols=14 Identities=36% Similarity=0.790 Sum_probs=6.5
Q ss_pred cccCCCCCccCCCh
Q psy7353 82 VFPCPVCGKEFSRP 95 (139)
Q Consensus 82 ~~~C~~C~~~f~~~ 95 (139)
.|.|+.|+..|+..
T Consensus 117 ~Y~Cp~C~~rytf~ 130 (178)
T PRK06266 117 FFFCPNCHIRFTFD 130 (178)
T ss_pred EEECCCCCcEEeHH
Confidence 34555555444433
No 76
>smart00834 CxxC_CXXC_SSSS Putative regulatory protein. CxxC_CXXC_SSSS represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=80.65 E-value=0.88 Score=21.43 Aligned_cols=11 Identities=36% Similarity=1.153 Sum_probs=6.1
Q ss_pred ccCCCCCccCC
Q psy7353 83 FPCPVCGKEFS 93 (139)
Q Consensus 83 ~~C~~C~~~f~ 93 (139)
|.|..||..|.
T Consensus 6 y~C~~Cg~~fe 16 (41)
T smart00834 6 YRCEDCGHTFE 16 (41)
T ss_pred EEcCCCCCEEE
Confidence 45666665553
No 77
>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=80.40 E-value=0.72 Score=22.21 Aligned_cols=13 Identities=38% Similarity=0.986 Sum_probs=7.2
Q ss_pred ccCCCCCccCCCh
Q psy7353 83 FPCPVCGKEFSRP 95 (139)
Q Consensus 83 ~~C~~C~~~f~~~ 95 (139)
|.|..||..|...
T Consensus 6 y~C~~Cg~~fe~~ 18 (42)
T PF09723_consen 6 YRCEECGHEFEVL 18 (42)
T ss_pred EEeCCCCCEEEEE
Confidence 5566666555433
No 78
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=79.69 E-value=1.6 Score=20.23 Aligned_cols=10 Identities=0% Similarity=-0.230 Sum_probs=4.7
Q ss_pred CCCCCCCCCC
Q psy7353 112 ATTPQGQRGQ 121 (139)
Q Consensus 112 ~~C~~C~~~f 121 (139)
.+|+.|+..|
T Consensus 26 v~C~~C~~~f 35 (36)
T PF13717_consen 26 VRCSKCGHVF 35 (36)
T ss_pred EECCCCCCEe
Confidence 3455555443
No 79
>KOG2186|consensus
Probab=78.82 E-value=1.7 Score=29.71 Aligned_cols=47 Identities=40% Similarity=0.851 Sum_probs=33.6
Q ss_pred eeecCCCCCcCCChHHHHHHHHHhcCCCcccCCCCCccCCChhHHHhhhh
Q psy7353 54 VFPCPVCGKEFSRPDKMKNHMKTGCQRKVFPCPVCGKEFSRPDKMKNHMK 103 (139)
Q Consensus 54 ~~~c~~C~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~ 103 (139)
-|.|..||....-.. +..|+....+ ..|.|.-|+..|.. .+...|.+
T Consensus 3 ~FtCnvCgEsvKKp~-vekH~srCrn-~~fSCIDC~k~F~~-~sYknH~k 49 (276)
T KOG2186|consen 3 FFTCNVCGESVKKPQ-VEKHMSRCRN-AYFSCIDCGKTFER-VSYKNHTK 49 (276)
T ss_pred EEehhhhhhhccccc-hHHHHHhccC-CeeEEeeccccccc-chhhhhhh
Confidence 367888887665544 4557777766 56888889888877 56667765
No 80
>KOG4173|consensus
Probab=77.50 E-value=1.1 Score=29.51 Aligned_cols=70 Identities=20% Similarity=0.510 Sum_probs=48.6
Q ss_pred ccCCHHHHHHHHHHhccCCCCceeecCCCCCcCCChHHHHHHHHHhc----------CCCcccC--CCCCccCCChhHHH
Q psy7353 32 TFKNKYSFQRHAFLYHEGCQRKVFPCPVCGKEFSRPDKMKNHMKTGC----------QRKVFPC--PVCGKEFSRPDKMK 99 (139)
Q Consensus 32 ~f~~~~~l~~h~~~~~~~~~~~~~~c~~C~~~~~~~~~l~~h~~~~~----------~~~~~~C--~~C~~~f~~~~~l~ 99 (139)
.|.....+..|-.+.|.+ .|.+|.+.|+....|-.|+...+ |.-.|+| ..|+..|.......
T Consensus 90 ~~d~lD~~E~hY~~~h~~------sCs~C~r~~Pt~hLLd~HI~E~HDs~Fqa~veRG~dMy~ClvEgCt~KFkT~r~Rk 163 (253)
T KOG4173|consen 90 VFDALDDYEHHYHTLHGN------SCSFCKRAFPTGHLLDAHILEWHDSLFQALVERGQDMYQCLVEGCTEKFKTSRDRK 163 (253)
T ss_pred HHhhhhhHHHhhhhcccc------hhHHHHHhCCchhhhhHHHHHHHHHHHHHHHHcCccHHHHHHHhhhhhhhhhhhhh
Confidence 566655566665444432 69999999999888888875332 3346788 44888898888888
Q ss_pred hhhhhhcC
Q psy7353 100 NHMKTVHD 107 (139)
Q Consensus 100 ~H~~~~h~ 107 (139)
.|+...|.
T Consensus 164 dH~I~~Hk 171 (253)
T KOG4173|consen 164 DHMIRMHK 171 (253)
T ss_pred hHHHHhcc
Confidence 88765454
No 81
>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=77.29 E-value=1.4 Score=21.30 Aligned_cols=20 Identities=30% Similarity=0.702 Sum_probs=8.4
Q ss_pred ccCCCCCccCCC----hhHHHhhh
Q psy7353 83 FPCPVCGKEFSR----PDKMKNHM 102 (139)
Q Consensus 83 ~~C~~C~~~f~~----~~~l~~H~ 102 (139)
..|..|+..+.. .+.|.+|+
T Consensus 17 a~C~~C~~~~~~~~~~ts~l~~HL 40 (45)
T PF02892_consen 17 AKCKYCGKVIKYSSGGTSNLKRHL 40 (45)
T ss_dssp EEETTTTEE-----SSTHHHHHHH
T ss_pred EEeCCCCeEEeeCCCcHHHHHHhh
Confidence 345555544433 24555555
No 82
>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=77.04 E-value=0.31 Score=37.90 Aligned_cols=56 Identities=23% Similarity=0.507 Sum_probs=40.0
Q ss_pred cCCCCCcCCChHHHHHHHHHhcCCCc-ccCCCCCccCCChhHHHhhhhhhcCCCCCCCCCCCCCC
Q psy7353 57 CPVCGKEFSRPDKMKNHMKTGCQRKV-FPCPVCGKEFSRPDKMKNHMKTVHDCFMPATTPQGQRG 120 (139)
Q Consensus 57 c~~C~~~~~~~~~l~~h~~~~~~~~~-~~C~~C~~~f~~~~~l~~H~~~~h~~~~~~~C~~C~~~ 120 (139)
|..||..|....+|..-+. ++..+. -.|+.|.+.|.++-+..-|.+ |-.|+.||..
T Consensus 126 CT~CGPRfTIi~alPYDR~-nTsM~~F~lC~~C~~EY~dP~nRRfHAQ-------p~aCp~CGP~ 182 (750)
T COG0068 126 CTNCGPRFTIIEALPYDRE-NTSMADFPLCPFCDKEYKDPLNRRFHAQ-------PIACPKCGPH 182 (750)
T ss_pred cCCCCcceeeeccCCCCcc-cCccccCcCCHHHHHHhcCccccccccc-------cccCcccCCC
Confidence 8889999888877655433 333333 369999999999988655544 4589999974
No 83
>PF13451 zf-trcl: Probable zinc-binding domain
Probab=76.79 E-value=1.2 Score=22.33 Aligned_cols=17 Identities=35% Similarity=0.708 Sum_probs=7.9
Q ss_pred CcccCCCCCccCCChhH
Q psy7353 81 KVFPCPVCGKEFSRPDK 97 (139)
Q Consensus 81 ~~~~C~~C~~~f~~~~~ 97 (139)
+.+.|..||..|...+.
T Consensus 3 k~l~C~dCg~~FvfTa~ 19 (49)
T PF13451_consen 3 KTLTCKDCGAEFVFTAG 19 (49)
T ss_pred eeEEcccCCCeEEEehh
Confidence 34445555554444433
No 84
>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=75.80 E-value=0.69 Score=27.27 Aligned_cols=25 Identities=12% Similarity=0.023 Sum_probs=22.2
Q ss_pred CCC----CCCCCCCCCCcchhcccccccC
Q psy7353 112 ATT----PQGQRGQRASPVIDFHKDSVFN 136 (139)
Q Consensus 112 ~~C----~~C~~~f~~~~~l~~H~~~~~~ 136 (139)
|.| +.|++.+.+...+.+|.+.+|+
T Consensus 81 ~~C~~~~~~C~y~~~~~~~m~~H~~~~Hg 109 (109)
T PF12013_consen 81 YRCQCDPPHCGYITRSKKTMRKHWRKEHG 109 (109)
T ss_pred eeeecCCCCCCcEeccHHHHHHHHHHhcC
Confidence 789 8899999999999999988875
No 85
>KOG2482|consensus
Probab=75.69 E-value=6.5 Score=28.25 Aligned_cols=53 Identities=19% Similarity=0.418 Sum_probs=31.1
Q ss_pred CceeecCCCCC-cCCChHHHHHHHHHhcCC----------------------CcccCCCCCccCCChhHHHhhhhh
Q psy7353 52 RKVFPCPVCGK-EFSRPDKMKNHMKTGCQR----------------------KVFPCPVCGKEFSRPDKMKNHMKT 104 (139)
Q Consensus 52 ~~~~~c~~C~~-~~~~~~~l~~h~~~~~~~----------------------~~~~C~~C~~~f~~~~~l~~H~~~ 104 (139)
.....|-.|+. ..-..+.+..|+..-++- ..+.|..|.+.|.++..|..||+.
T Consensus 142 ~fslqClFCn~e~lgnRs~~l~Hlf~~H~lniGlpDniVyvnelLehLkekL~r~~CLyCekifrdkntLkeHMrk 217 (423)
T KOG2482|consen 142 IFSLQCLFCNNEGLGNRSEILEHLFHVHGLNIGLPDNIVYVNELLEHLKEKLERLRCLYCEKIFRDKNTLKEHMRK 217 (423)
T ss_pred eeeeEEEEecchhcccHHHHHHHHHHHhhhccCCCcceeeHHHHHHHHHHHHhhheeeeeccccCCcHHHHHHHHh
Confidence 44556777774 334456666776532211 124567777777777777777654
No 86
>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=75.42 E-value=1.1 Score=22.54 Aligned_cols=11 Identities=36% Similarity=1.277 Sum_probs=5.1
Q ss_pred eecCCCCCcCC
Q psy7353 55 FPCPVCGKEFS 65 (139)
Q Consensus 55 ~~c~~C~~~~~ 65 (139)
|.|..|+..|.
T Consensus 6 y~C~~Cg~~fe 16 (52)
T TIGR02605 6 YRCTACGHRFE 16 (52)
T ss_pred EEeCCCCCEeE
Confidence 44555554443
No 87
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=74.22 E-value=5.2 Score=25.00 Aligned_cols=36 Identities=14% Similarity=0.236 Sum_probs=17.9
Q ss_pred CCcccCCCCCccCCChhHHHhhhhhhcCCCCCCCCCCCCCC
Q psy7353 80 RKVFPCPVCGKEFSRPDKMKNHMKTVHDCFMPATTPQGQRG 120 (139)
Q Consensus 80 ~~~~~C~~C~~~f~~~~~l~~H~~~~h~~~~~~~C~~C~~~ 120 (139)
...|.|+.|+..|.....+.. . .. +..|.|+.|+..
T Consensus 97 ~~~Y~Cp~C~~~y~~~ea~~~---~-d~-~~~f~Cp~Cg~~ 132 (147)
T smart00531 97 NAYYKCPNCQSKYTFLEANQL---L-DM-DGTFTCPRCGEE 132 (147)
T ss_pred CcEEECcCCCCEeeHHHHHHh---c-CC-CCcEECCCCCCE
Confidence 345667777766654332211 0 01 223677777754
No 88
>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=74.04 E-value=1.2 Score=19.07 Aligned_cols=19 Identities=26% Similarity=0.296 Sum_probs=10.1
Q ss_pred CCCCCCCCCCCCcchhcccc
Q psy7353 113 TTPQGQRGQRASPVIDFHKD 132 (139)
Q Consensus 113 ~C~~C~~~f~~~~~l~~H~~ 132 (139)
.||.|+..+ ....+..|.+
T Consensus 3 ~CPiC~~~v-~~~~in~HLD 21 (26)
T smart00734 3 QCPVCFREV-PENLINSHLD 21 (26)
T ss_pred cCCCCcCcc-cHHHHHHHHH
Confidence 466666665 3345555544
No 89
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=72.42 E-value=1.7 Score=21.26 Aligned_cols=11 Identities=36% Similarity=1.117 Sum_probs=5.8
Q ss_pred cccCCCCCccC
Q psy7353 82 VFPCPVCGKEF 92 (139)
Q Consensus 82 ~~~C~~C~~~f 92 (139)
.|.|+.||..|
T Consensus 3 ~y~C~~CG~~~ 13 (46)
T PRK00398 3 EYKCARCGREV 13 (46)
T ss_pred EEECCCCCCEE
Confidence 35555565544
No 90
>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=72.42 E-value=2.5 Score=18.13 Aligned_cols=10 Identities=10% Similarity=-0.024 Sum_probs=5.9
Q ss_pred CCCCCCCCCC
Q psy7353 113 TTPQGQRGQR 122 (139)
Q Consensus 113 ~C~~C~~~f~ 122 (139)
.|+.||+.|.
T Consensus 16 ~Cp~CG~~F~ 25 (26)
T PF10571_consen 16 FCPHCGYDFE 25 (26)
T ss_pred cCCCCCCCCc
Confidence 5666666653
No 91
>KOG4173|consensus
Probab=71.50 E-value=0.54 Score=30.97 Aligned_cols=76 Identities=21% Similarity=0.304 Sum_probs=52.0
Q ss_pred ceeecCC--CCCcCCChHHHHHHHHHhcCCCcccCCCCCccCCChhHHHhhhhhhcC---------CCCCCCC--CCCCC
Q psy7353 53 KVFPCPV--CGKEFSRPDKMKNHMKTGCQRKVFPCPVCGKEFSRPDKMKNHMKTVHD---------CFMPATT--PQGQR 119 (139)
Q Consensus 53 ~~~~c~~--C~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~~h~---------~~~~~~C--~~C~~ 119 (139)
..+.|++ |...+.....+..|.-.-++ -.|..|.+.|....-|..|+..-|. |.--|.| +.|+.
T Consensus 78 ~~~~cqvagc~~~~d~lD~~E~hY~~~h~---~sCs~C~r~~Pt~hLLd~HI~E~HDs~Fqa~veRG~dMy~ClvEgCt~ 154 (253)
T KOG4173|consen 78 PAFACQVAGCCQVFDALDDYEHHYHTLHG---NSCSFCKRAFPTGHLLDAHILEWHDSLFQALVERGQDMYQCLVEGCTE 154 (253)
T ss_pred ccccccccchHHHHhhhhhHHHhhhhccc---chhHHHHHhCCchhhhhHHHHHHHHHHHHHHHHcCccHHHHHHHhhhh
Confidence 4566777 55566666656555433222 2799999999999999988865443 3233888 56999
Q ss_pred CCCCCcchhccc
Q psy7353 120 GQRASPVIDFHK 131 (139)
Q Consensus 120 ~f~~~~~l~~H~ 131 (139)
.|.+.-.-..|.
T Consensus 155 KFkT~r~RkdH~ 166 (253)
T KOG4173|consen 155 KFKTSRDRKDHM 166 (253)
T ss_pred hhhhhhhhhhHH
Confidence 999887766663
No 92
>PF14353 CpXC: CpXC protein
Probab=71.31 E-value=4.5 Score=24.51 Aligned_cols=12 Identities=25% Similarity=0.138 Sum_probs=5.7
Q ss_pred CCCCCCCCCCCC
Q psy7353 112 ATTPQGQRGQRA 123 (139)
Q Consensus 112 ~~C~~C~~~f~~ 123 (139)
|.|+.||..|..
T Consensus 39 ~~CP~Cg~~~~~ 50 (128)
T PF14353_consen 39 FTCPSCGHKFRL 50 (128)
T ss_pred EECCCCCCceec
Confidence 445555544433
No 93
>smart00614 ZnF_BED BED zinc finger. DNA-binding domain in chromatin-boundary-element-binding proteins and transposases
Probab=69.92 E-value=3.8 Score=20.39 Aligned_cols=20 Identities=35% Similarity=0.992 Sum_probs=10.4
Q ss_pred cCCCCCccCCCh-----hHHHhhhh
Q psy7353 84 PCPVCGKEFSRP-----DKMKNHMK 103 (139)
Q Consensus 84 ~C~~C~~~f~~~-----~~l~~H~~ 103 (139)
.|..|+..++.. ++|.+|++
T Consensus 20 ~C~~C~~~l~~~~~~gTs~L~rHl~ 44 (50)
T smart00614 20 KCKYCGKKLSRSSKGGTSNLRRHLR 44 (50)
T ss_pred EecCCCCEeeeCCCCCcHHHHHHHH
Confidence 455555444332 46666665
No 94
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=69.52 E-value=0.91 Score=24.78 Aligned_cols=14 Identities=0% Similarity=-0.323 Sum_probs=6.7
Q ss_pred CCCCC--CCCCCCCCC
Q psy7353 111 PATTP--QGQRGQRAS 124 (139)
Q Consensus 111 ~~~C~--~C~~~f~~~ 124 (139)
.++|. +|+.+|+..
T Consensus 27 Y~qC~N~eCg~tF~t~ 42 (72)
T PRK09678 27 YHQCQNVNCSATFITY 42 (72)
T ss_pred eeecCCCCCCCEEEEE
Confidence 34454 455555444
No 95
>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=69.52 E-value=5 Score=24.46 Aligned_cols=15 Identities=20% Similarity=0.410 Sum_probs=7.5
Q ss_pred CcccCCCCCccCCCh
Q psy7353 81 KVFPCPVCGKEFSRP 95 (139)
Q Consensus 81 ~~~~C~~C~~~f~~~ 95 (139)
.|..|+.||..|...
T Consensus 25 ~p~vcP~cg~~~~~~ 39 (129)
T TIGR02300 25 RPAVSPYTGEQFPPE 39 (129)
T ss_pred CCccCCCcCCccCcc
Confidence 345555555554333
No 96
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=68.53 E-value=2.7 Score=23.79 Aligned_cols=31 Identities=26% Similarity=0.801 Sum_probs=17.9
Q ss_pred eeecCCCCCcCCChHHHHHHHHHhcCCCcccCCCCCccCCC
Q psy7353 54 VFPCPVCGKEFSRPDKMKNHMKTGCQRKVFPCPVCGKEFSR 94 (139)
Q Consensus 54 ~~~c~~C~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~f~~ 94 (139)
.+.|+.|++. ...+ .....|.|..|+..|.-
T Consensus 35 ~~~Cp~C~~~--------~VkR--~a~GIW~C~kCg~~fAG 65 (89)
T COG1997 35 KHVCPFCGRT--------TVKR--IATGIWKCRKCGAKFAG 65 (89)
T ss_pred CCcCCCCCCc--------ceee--eccCeEEcCCCCCeecc
Confidence 4678887753 1111 22346778888776644
No 97
>PF04959 ARS2: Arsenite-resistance protein 2; InterPro: IPR007042 This entry represents Arsenite-resistance protein 2 (also known as Serrate RNA effector molecule homolog) which is thought to play a role in arsenite resistance [], although does not directly confer arsenite resistance but rather modulates arsenic sensitivity []. Arsenite is a carcinogenic compound which can act as a comutagen by inhibiting DNA repair. It is also involved in cell cycle progression at S phase. ; PDB: 3AX1_A.
Probab=68.46 E-value=2.9 Score=27.96 Aligned_cols=27 Identities=33% Similarity=0.844 Sum_probs=18.0
Q ss_pred CcccCCCCCccCCChhHHHhhhhhhcC
Q psy7353 81 KVFPCPVCGKEFSRPDKMKNHMKTVHD 107 (139)
Q Consensus 81 ~~~~C~~C~~~f~~~~~l~~H~~~~h~ 107 (139)
.-|.|..|++.|.-......|+...|+
T Consensus 76 ~K~~C~lc~KlFkg~eFV~KHI~nKH~ 102 (214)
T PF04959_consen 76 DKWRCPLCGKLFKGPEFVRKHIFNKHP 102 (214)
T ss_dssp EEEEE-SSS-EESSHHHHHHHHHHH-H
T ss_pred CEECCCCCCcccCChHHHHHHHhhcCH
Confidence 347788888888888888888776565
No 98
>KOG2231|consensus
Probab=67.40 E-value=6.5 Score=30.89 Aligned_cols=78 Identities=13% Similarity=0.173 Sum_probs=49.8
Q ss_pred HHHHHHHHHhcc-CCCCc-eeecCCCCCcCCChHHHHHHHHHhcCCCccc--CCCCCccCCChhHHHhhhhhhcCCCCCC
Q psy7353 37 YSFQRHAFLYHE-GCQRK-VFPCPVCGKEFSRPDKMKNHMKTGCQRKVFP--CPVCGKEFSRPDKMKNHMKTVHDCFMPA 112 (139)
Q Consensus 37 ~~l~~h~~~~~~-~~~~~-~~~c~~C~~~~~~~~~l~~h~~~~~~~~~~~--C~~C~~~f~~~~~l~~H~~~~h~~~~~~ 112 (139)
..|+.|++..-. .+..+ .-.|..|...|.+...+..|++.++....|. -..++.-|.....|..|-+..| |
T Consensus 163 ~el~~h~~~gd~d~~s~rGhp~C~~C~~~fld~~el~rH~~~~h~~chfC~~~~~~neyy~~~~dLe~HfR~~H-----f 237 (669)
T KOG2231|consen 163 AELNLHLMFGDPDDESCRGHPLCKFCHERFLDDDELYRHLRFDHEFCHFCDYKTGQNEYYNDYDDLEEHFRKGH-----F 237 (669)
T ss_pred HHHHHHHhcCCCccccccCCccchhhhhhhccHHHHHHhhccceeheeecCcccccchhcccchHHHHHhhhcC-----c
Confidence 456667654222 11111 2468899999999999999998765443321 1223456788899999988766 4
Q ss_pred CCC--CCCC
Q psy7353 113 TTP--QGQR 119 (139)
Q Consensus 113 ~C~--~C~~ 119 (139)
.|+ .|..
T Consensus 238 lCE~~~C~~ 246 (669)
T KOG2231|consen 238 LCEEEFCRT 246 (669)
T ss_pred ccccccccc
Confidence 666 4553
No 99
>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=66.22 E-value=1.6 Score=19.45 Aligned_cols=8 Identities=50% Similarity=1.551 Sum_probs=3.4
Q ss_pred cccCCCCC
Q psy7353 82 VFPCPVCG 89 (139)
Q Consensus 82 ~~~C~~C~ 89 (139)
.+.|+.|+
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 100
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=65.72 E-value=4.1 Score=32.41 Aligned_cols=12 Identities=17% Similarity=0.346 Sum_probs=8.7
Q ss_pred CCCCCCCCCCCC
Q psy7353 109 FMPATTPQGQRG 120 (139)
Q Consensus 109 ~~~~~C~~C~~~ 120 (139)
..|..|+.|+-.
T Consensus 473 ~~p~~Cp~Cgs~ 484 (730)
T COG1198 473 PIPQSCPECGSE 484 (730)
T ss_pred CCCCCCCCCCCC
Confidence 457788888854
No 101
>PF12907 zf-met2: Zinc-binding
Probab=64.93 E-value=2.9 Score=19.98 Aligned_cols=26 Identities=19% Similarity=0.447 Sum_probs=13.1
Q ss_pred cCCCCCcc---CCChhHHHhhhhhhcCCC
Q psy7353 84 PCPVCGKE---FSRPDKMKNHMKTVHDCF 109 (139)
Q Consensus 84 ~C~~C~~~---f~~~~~l~~H~~~~h~~~ 109 (139)
.|.+|... ......|..|....|++.
T Consensus 3 ~C~iC~qtF~~t~~~~~L~eH~enKHpK~ 31 (40)
T PF12907_consen 3 ICKICRQTFMQTTNEPQLKEHAENKHPKN 31 (40)
T ss_pred CcHHhhHHHHhcCCHHHHHHHHHccCCCC
Confidence 45555532 233455666655545543
No 102
>KOG1280|consensus
Probab=64.40 E-value=9.8 Score=27.37 Aligned_cols=40 Identities=20% Similarity=0.452 Sum_probs=24.7
Q ss_pred CcceecCCCCCcchhcccCCHHHHHHHHHHhccCCCCceeecCCCC
Q psy7353 16 EGIYKCMECAKVDVIKTFKNKYSFQRHAFLYHEGCQRKVFPCPVCG 61 (139)
Q Consensus 16 ~~~~~C~~c~~~~~~~~f~~~~~l~~h~~~~~~~~~~~~~~c~~C~ 61 (139)
+..|.|++|+. +=.+...|+.|....|.... ....|++|.
T Consensus 77 ~qSftCPyC~~-----~Gfte~~f~~Hv~s~Hpda~-~~~icp~c~ 116 (381)
T KOG1280|consen 77 PQSFTCPYCGI-----MGFTERQFGTHVLSQHPEAS-TSVICPLCA 116 (381)
T ss_pred cccccCCcccc-----cccchhHHHHHhhhcCcccC-cceeeeccc
Confidence 44688888887 44455567777766666432 334566664
No 103
>KOG2785|consensus
Probab=63.92 E-value=14 Score=27.02 Aligned_cols=58 Identities=24% Similarity=0.464 Sum_probs=37.7
Q ss_pred eecCCCCCcCCChHHHHHHHHHhcCC-----------------------CcccCCCCC---ccCCChhHHHhhhhhhcCC
Q psy7353 55 FPCPVCGKEFSRPDKMKNHMKTGCQR-----------------------KVFPCPVCG---KEFSRPDKMKNHMKTVHDC 108 (139)
Q Consensus 55 ~~c~~C~~~~~~~~~l~~h~~~~~~~-----------------------~~~~C~~C~---~~f~~~~~l~~H~~~~h~~ 108 (139)
-.|..|+..+.+......||..+++- .-+.|..|. +.|......+.||...-..
T Consensus 167 t~CLfC~~~~k~~e~~~~HM~~~HgffIPdreYL~D~~GLl~YLgeKV~~~~~CL~CN~~~~~f~sleavr~HM~~K~HC 246 (390)
T KOG2785|consen 167 TDCLFCDKKSKSLEENLKHMFKEHGFFIPDREYLTDEKGLLKYLGEKVGIGFICLFCNELGRPFSSLEAVRAHMRDKGHC 246 (390)
T ss_pred cceeecCCCcccHHHHHHHHhhccCCcCCchHhhhchhHHHHHHHHHhccCceEEEeccccCcccccHHHHHHHhhccCc
Confidence 44666766666666666666655542 335677777 7888888888888754444
Q ss_pred CCCC
Q psy7353 109 FMPA 112 (139)
Q Consensus 109 ~~~~ 112 (139)
..+|
T Consensus 247 kl~y 250 (390)
T KOG2785|consen 247 KLPY 250 (390)
T ss_pred ccCC
Confidence 4555
No 104
>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=63.18 E-value=11 Score=25.27 Aligned_cols=29 Identities=31% Similarity=0.575 Sum_probs=20.0
Q ss_pred CCcceecCCCCCcchhcccCCHHHHHHHHHHhcc
Q psy7353 15 TEGIYKCMECAKVDVIKTFKNKYSFQRHAFLYHE 48 (139)
Q Consensus 15 ~~~~~~C~~c~~~~~~~~f~~~~~l~~h~~~~~~ 48 (139)
.+..|.|+.|+| .|.-.....+|+..-|.
T Consensus 74 ~~~K~~C~lc~K-----lFkg~eFV~KHI~nKH~ 102 (214)
T PF04959_consen 74 DEDKWRCPLCGK-----LFKGPEFVRKHIFNKHP 102 (214)
T ss_dssp SSEEEEE-SSS------EESSHHHHHHHHHHH-H
T ss_pred cCCEECCCCCCc-----ccCChHHHHHHHhhcCH
Confidence 455688888888 88888888888866554
No 105
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=62.76 E-value=4.2 Score=16.76 Aligned_cols=6 Identities=17% Similarity=0.257 Sum_probs=2.9
Q ss_pred CCCCCC
Q psy7353 114 TPQGQR 119 (139)
Q Consensus 114 C~~C~~ 119 (139)
|+.||.
T Consensus 16 C~~CG~ 21 (23)
T PF13240_consen 16 CPNCGT 21 (23)
T ss_pred hhhhCC
Confidence 455543
No 106
>KOG4124|consensus
Probab=62.39 E-value=3.6 Score=29.54 Aligned_cols=52 Identities=21% Similarity=0.402 Sum_probs=36.5
Q ss_pred CcccCCC--CCccCCChhHHHhhhhhhcC------------------CCCCCCCCCCCCCCCCCcchhcccc
Q psy7353 81 KVFPCPV--CGKEFSRPDKMKNHMKTVHD------------------CFMPATTPQGQRGQRASPVIDFHKD 132 (139)
Q Consensus 81 ~~~~C~~--C~~~f~~~~~l~~H~~~~h~------------------~~~~~~C~~C~~~f~~~~~l~~H~~ 132 (139)
++|.|.+ |++.++..-.|..|..+.|. ..++|.|++|.+++...+.|.-|+.
T Consensus 348 ~~~~~~vp~~~~~~~n~ng~~~~~~~~h~s~i~~~s~~~~ph~~~~~~nk~~r~~i~~~~~k~~~~l~~~~~ 419 (442)
T KOG4124|consen 348 KPYKCPVPNCDKAYKNQNGLKYHKLHGHCSPITTPTPAPIPHQGFVVENKPYRCEVCSKRYKNLNGLKYHRT 419 (442)
T ss_pred CCCCCCCCcchhhcccCcceeeccccCcCCCCCCCCCCCCCcceeeeccCcccChhhhhhhccCCCCCceee
Confidence 6777854 88888776666655443222 2467999999999988888876643
No 107
>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=61.81 E-value=12 Score=16.90 Aligned_cols=10 Identities=20% Similarity=0.401 Sum_probs=5.3
Q ss_pred CCCCCCCCCC
Q psy7353 111 PATTPQGQRG 120 (139)
Q Consensus 111 ~~~C~~C~~~ 120 (139)
+-.|+.||.+
T Consensus 17 ~irC~~CG~R 26 (32)
T PF03604_consen 17 PIRCPECGHR 26 (32)
T ss_dssp TSSBSSSS-S
T ss_pred cEECCcCCCe
Confidence 3466666654
No 108
>PF07754 DUF1610: Domain of unknown function (DUF1610); InterPro: IPR011668 This domain is found in archaeal species. It is likely to bind zinc via its four well-conserved cysteine residues.
Probab=60.97 E-value=5.3 Score=16.77 Aligned_cols=11 Identities=18% Similarity=0.525 Sum_probs=8.5
Q ss_pred CcceecCCCCC
Q psy7353 16 EGIYKCMECAK 26 (139)
Q Consensus 16 ~~~~~C~~c~~ 26 (139)
...|.|+.||+
T Consensus 14 ~v~f~CPnCG~ 24 (24)
T PF07754_consen 14 AVPFPCPNCGF 24 (24)
T ss_pred CceEeCCCCCC
Confidence 45789999984
No 109
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=60.62 E-value=3.1 Score=29.84 Aligned_cols=13 Identities=15% Similarity=0.368 Sum_probs=7.4
Q ss_pred cCCChhHHHhhhh
Q psy7353 91 EFSRPDKMKNHMK 103 (139)
Q Consensus 91 ~f~~~~~l~~H~~ 103 (139)
.|.+...|+.|+-
T Consensus 290 vf~~~~el~~h~~ 302 (493)
T COG5236 290 VFPYHTELLEHLT 302 (493)
T ss_pred EeccHHHHHHHHH
Confidence 4555566666653
No 110
>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=60.36 E-value=6.8 Score=22.98 Aligned_cols=24 Identities=29% Similarity=0.718 Sum_probs=21.6
Q ss_pred ccC----CCCCccCCChhHHHhhhhhhc
Q psy7353 83 FPC----PVCGKEFSRPDKMKNHMKTVH 106 (139)
Q Consensus 83 ~~C----~~C~~~f~~~~~l~~H~~~~h 106 (139)
|.| ..|++.......+..|.+.+|
T Consensus 81 ~~C~~~~~~C~y~~~~~~~m~~H~~~~H 108 (109)
T PF12013_consen 81 YRCQCDPPHCGYITRSKKTMRKHWRKEH 108 (109)
T ss_pred eeeecCCCCCCcEeccHHHHHHHHHHhc
Confidence 789 999999999999999998765
No 111
>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=59.65 E-value=2.4 Score=31.68 Aligned_cols=30 Identities=30% Similarity=0.679 Sum_probs=23.4
Q ss_pred CCCcccCCCCCccCCChhHHHhhhhhhcCC
Q psy7353 79 QRKVFPCPVCGKEFSRPDKMKNHMKTVHDC 108 (139)
Q Consensus 79 ~~~~~~C~~C~~~f~~~~~l~~H~~~~h~~ 108 (139)
.-+-|.|+.|.+.|.....+..|+-..|.+
T Consensus 54 sWrFWiCp~CskkF~d~~~~~~H~~~eH~~ 83 (466)
T PF04780_consen 54 SWRFWICPRCSKKFSDAESCLSHMEQEHPA 83 (466)
T ss_pred ceeEeeCCcccceeCCHHHHHHHHHHhhhh
Confidence 345678888888888888888888766764
No 112
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=59.59 E-value=8.1 Score=19.10 Aligned_cols=16 Identities=0% Similarity=-0.213 Sum_probs=9.5
Q ss_pred CCCCCCCCCCCCCCcc
Q psy7353 111 PATTPQGQRGQRASPV 126 (139)
Q Consensus 111 ~~~C~~C~~~f~~~~~ 126 (139)
.|.|+.|++.+.-.+.
T Consensus 20 ~~vC~~Cg~~~~~~~~ 35 (52)
T smart00661 20 RFVCRKCGYEEPIEQK 35 (52)
T ss_pred EEECCcCCCeEECCCc
Confidence 4667777766555443
No 113
>PRK04023 DNA polymerase II large subunit; Validated
Probab=57.66 E-value=18 Score=30.07 Aligned_cols=10 Identities=10% Similarity=0.019 Sum_probs=6.1
Q ss_pred CCCCCCCCCC
Q psy7353 111 PATTPQGQRG 120 (139)
Q Consensus 111 ~~~C~~C~~~ 120 (139)
++.|+.|+..
T Consensus 663 ~y~CPKCG~E 672 (1121)
T PRK04023 663 EDECEKCGRE 672 (1121)
T ss_pred CCcCCCCCCC
Confidence 3567777654
No 114
>PF05191 ADK_lid: Adenylate kinase, active site lid; InterPro: IPR007862 Adenylate kinases (ADK; 2.7.4.3 from EC) are phosphotransferases that catalyse the Mg-dependent reversible conversion of ATP and AMP to two molecules of ADP, an essential reaction for many processes in living cells. In large variants of adenylate kinase, the AMP and ATP substrates are buried in a domain that undergoes conformational changes from an open to a closed state when bound to substrate; the ligand is then contained within a highly specific environment required for catalysis. Adenylate kinase is a 3-domain protein consisting of a large central CORE domain flanked by a LID domain on one side and the AMP-binding NMPbind domain on the other []. The LID domain binds ATP and covers the phosphates at the active site. The substrates first bind the CORE domain, followed by closure of the active site by the LID and NMPbind domains. Comparisons of adenylate kinases have revealed a particular divergence in the active site lid. In some organisms, particularly the Gram-positive bacteria, residues in the lid domain have been mutated to cysteines and these cysteine residues (two CX(n)C motifs) are responsible for the binding of a zinc ion. The bound zinc ion in the lid domain is clearly structurally homologous to Zinc-finger domains. However, it is unclear whether the adenylate kinase lid is a novel zinc-finger DNA/RNA binding domain, or that the lid bound zinc serves a purely structural function [].; GO: 0004017 adenylate kinase activity; PDB: 3BE4_A 2OSB_B 2ORI_A 2EU8_A 3DL0_A 1P3J_A 2QAJ_A 2OO7_A 2P3S_A 3DKV_A ....
Probab=57.59 E-value=3.8 Score=19.05 Aligned_cols=11 Identities=0% Similarity=-0.206 Sum_probs=6.1
Q ss_pred CCCCCCCCCCC
Q psy7353 111 PATTPQGQRGQ 121 (139)
Q Consensus 111 ~~~C~~C~~~f 121 (139)
+-.|+.|+-.+
T Consensus 21 ~~~Cd~cg~~L 31 (36)
T PF05191_consen 21 EGVCDNCGGEL 31 (36)
T ss_dssp TTBCTTTTEBE
T ss_pred CCccCCCCCee
Confidence 34666666543
No 115
>PF07800 DUF1644: Protein of unknown function (DUF1644); InterPro: IPR012866 This family consists of sequences found in a number of hypothetical plant proteins of unknown function. The region of interest contains nine highly conserved cysteine residues and is approximately 160 amino acids in length, which probably represent a zinc-binding domain.
Probab=56.65 E-value=19 Score=22.97 Aligned_cols=57 Identities=18% Similarity=0.376 Sum_probs=30.7
Q ss_pred eeecCCCCCcCCChHHHHHHHHHhcCCCcccCCC--CCccCCChhHHHhhhhhhcCCCCCC
Q psy7353 54 VFPCPVCGKEFSRPDKMKNHMKTGCQRKVFPCPV--CGKEFSRPDKMKNHMKTVHDCFMPA 112 (139)
Q Consensus 54 ~~~c~~C~~~~~~~~~l~~h~~~~~~~~~~~C~~--C~~~f~~~~~l~~H~~~~h~~~~~~ 112 (139)
...|+.|.-.... +.....-+.+...|+-.|.. |.+. -....|.+|.+..|+..+|-
T Consensus 80 ~L~CPLCRG~V~G-Wtvve~AR~~LN~K~RsC~~e~C~F~-GtY~eLrKHar~~HP~~rP~ 138 (162)
T PF07800_consen 80 ELACPLCRGEVKG-WTVVEPARRFLNAKKRSCSQESCSFS-GTYSELRKHARSEHPSARPS 138 (162)
T ss_pred cccCccccCceec-eEEchHHHHHhccCCccCcccccccc-cCHHHHHHHHHhhCCCCCCc
Confidence 3457777632221 11222234445556666644 5432 33467888888878876663
No 116
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=56.42 E-value=4.9 Score=24.79 Aligned_cols=11 Identities=45% Similarity=1.189 Sum_probs=5.6
Q ss_pred eeecCCCCCcC
Q psy7353 54 VFPCPVCGKEF 64 (139)
Q Consensus 54 ~~~c~~C~~~~ 64 (139)
.+.|..|+..|
T Consensus 70 ~~~C~~CG~~~ 80 (135)
T PRK03824 70 VLKCRNCGNEW 80 (135)
T ss_pred EEECCCCCCEE
Confidence 35555555443
No 117
>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=56.21 E-value=16 Score=17.74 Aligned_cols=10 Identities=0% Similarity=-0.193 Sum_probs=6.0
Q ss_pred CCCCCCCCCC
Q psy7353 110 MPATTPQGQR 119 (139)
Q Consensus 110 ~~~~C~~C~~ 119 (139)
..|.|..|++
T Consensus 36 ~~~~C~~C~~ 45 (46)
T PF12760_consen 36 GRYRCKACRK 45 (46)
T ss_pred CeEECCCCCC
Confidence 4566666654
No 118
>COG1655 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=55.72 E-value=2.9 Score=28.22 Aligned_cols=16 Identities=38% Similarity=1.070 Sum_probs=9.3
Q ss_pred ceeecCCCCCcCCChH
Q psy7353 53 KVFPCPVCGKEFSRPD 68 (139)
Q Consensus 53 ~~~~c~~C~~~~~~~~ 68 (139)
+.+.||+|+..|....
T Consensus 18 k~ieCPvC~tkFkkee 33 (267)
T COG1655 18 KTIECPVCNTKFKKEE 33 (267)
T ss_pred ceeccCcccchhhhhh
Confidence 3456666666655544
No 119
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=55.22 E-value=1.5 Score=25.39 Aligned_cols=11 Identities=55% Similarity=1.367 Sum_probs=6.9
Q ss_pred CceeecCCCCC
Q psy7353 52 RKVFPCPVCGK 62 (139)
Q Consensus 52 ~~~~~c~~C~~ 62 (139)
.+.|.|+.|+.
T Consensus 20 ~k~FtCp~Cgh 30 (104)
T COG4888 20 PKTFTCPRCGH 30 (104)
T ss_pred CceEecCccCC
Confidence 45566777764
No 120
>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=54.41 E-value=8 Score=29.43 Aligned_cols=10 Identities=40% Similarity=0.627 Sum_probs=6.8
Q ss_pred CCCCCCCCCC
Q psy7353 110 MPATTPQGQR 119 (139)
Q Consensus 110 ~~~~C~~C~~ 119 (139)
.|..|+.|+-
T Consensus 252 ~~~~Cp~C~s 261 (505)
T TIGR00595 252 IPKTCPQCGS 261 (505)
T ss_pred CCCCCCCCCC
Confidence 3667777765
No 121
>KOG2785|consensus
Probab=54.35 E-value=22 Score=26.03 Aligned_cols=56 Identities=25% Similarity=0.364 Sum_probs=42.9
Q ss_pred CcceecCCCCCcchhcccCCHHHHHHHHHHhccCC--------------------CCceeecCCCC---CcCCChHHHHH
Q psy7353 16 EGIYKCMECAKVDVIKTFKNKYSFQRHAFLYHEGC--------------------QRKVFPCPVCG---KEFSRPDKMKN 72 (139)
Q Consensus 16 ~~~~~C~~c~~~~~~~~f~~~~~l~~h~~~~~~~~--------------------~~~~~~c~~C~---~~~~~~~~l~~ 72 (139)
..|-.|-.|++ .+.+...-..||...|.-. +...+.|..|+ ..|....+...
T Consensus 164 ~~Pt~CLfC~~-----~~k~~e~~~~HM~~~HgffIPdreYL~D~~GLl~YLgeKV~~~~~CL~CN~~~~~f~sleavr~ 238 (390)
T KOG2785|consen 164 LIPTDCLFCDK-----KSKSLEENLKHMFKEHGFFIPDREYLTDEKGLLKYLGEKVGIGFICLFCNELGRPFSSLEAVRA 238 (390)
T ss_pred cCCcceeecCC-----CcccHHHHHHHHhhccCCcCCchHhhhchhHHHHHHHHHhccCceEEEeccccCcccccHHHHH
Confidence 34567889999 8999888888987655421 23567888888 88999999999
Q ss_pred HHHH
Q psy7353 73 HMKT 76 (139)
Q Consensus 73 h~~~ 76 (139)
||..
T Consensus 239 HM~~ 242 (390)
T KOG2785|consen 239 HMRD 242 (390)
T ss_pred HHhh
Confidence 9873
No 122
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=53.92 E-value=25 Score=30.05 Aligned_cols=10 Identities=60% Similarity=1.471 Sum_probs=6.0
Q ss_pred cccCCCCCcc
Q psy7353 82 VFPCPVCGKE 91 (139)
Q Consensus 82 ~~~C~~C~~~ 91 (139)
+|.|+.||..
T Consensus 692 vy~CPsCGae 701 (1337)
T PRK14714 692 VYVCPDCGAE 701 (1337)
T ss_pred ceeCccCCCc
Confidence 4566666654
No 123
>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=52.23 E-value=2.1 Score=18.74 Aligned_cols=20 Identities=5% Similarity=-0.040 Sum_probs=10.6
Q ss_pred CCCCCCCCCCCCCcchhcccc
Q psy7353 112 ATTPQGQRGQRASPVIDFHKD 132 (139)
Q Consensus 112 ~~C~~C~~~f~~~~~l~~H~~ 132 (139)
|.|-.|++.| ....++.|..
T Consensus 1 ~sCiDC~~~F-~~~~y~~Ht~ 20 (28)
T PF08790_consen 1 FSCIDCSKDF-DGDSYKSHTS 20 (28)
T ss_dssp EEETTTTEEE-EGGGTTT---
T ss_pred CeeecCCCCc-CcCCcCCCCc
Confidence 3566677777 5555656643
No 124
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=51.89 E-value=2 Score=20.44 Aligned_cols=10 Identities=0% Similarity=-0.237 Sum_probs=6.3
Q ss_pred CCCCCCCCCC
Q psy7353 112 ATTPQGQRGQ 121 (139)
Q Consensus 112 ~~C~~C~~~f 121 (139)
|.|..|+..+
T Consensus 29 y~C~~C~~~w 38 (40)
T smart00440 29 YVCTKCGHRW 38 (40)
T ss_pred EEeCCCCCEe
Confidence 6666666554
No 125
>COG1779 C4-type Zn-finger protein [General function prediction only]
Probab=51.54 E-value=1.8 Score=28.44 Aligned_cols=16 Identities=0% Similarity=-0.078 Sum_probs=9.6
Q ss_pred CCCCCCCCCCCCCcch
Q psy7353 112 ATTPQGQRGQRASPVI 127 (139)
Q Consensus 112 ~~C~~C~~~f~~~~~l 127 (139)
+.|..|+++++..-.|
T Consensus 44 ~~C~~CgYR~~DV~~~ 59 (201)
T COG1779 44 GVCERCGYRSTDVKTL 59 (201)
T ss_pred EEccccCCcccceeec
Confidence 5677777766654433
No 126
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=51.38 E-value=11 Score=18.85 Aligned_cols=6 Identities=50% Similarity=1.464 Sum_probs=2.2
Q ss_pred ecCCCC
Q psy7353 20 KCMECA 25 (139)
Q Consensus 20 ~C~~c~ 25 (139)
.|..||
T Consensus 8 ~C~~Cg 13 (49)
T COG1996 8 KCARCG 13 (49)
T ss_pred EhhhcC
Confidence 333333
No 127
>PRK10220 hypothetical protein; Provisional
Probab=51.29 E-value=12 Score=22.20 Aligned_cols=10 Identities=40% Similarity=1.315 Sum_probs=4.6
Q ss_pred ccCCCCCccC
Q psy7353 83 FPCPVCGKEF 92 (139)
Q Consensus 83 ~~C~~C~~~f 92 (139)
|.|++|+..+
T Consensus 21 ~vCpeC~hEW 30 (111)
T PRK10220 21 YICPECAHEW 30 (111)
T ss_pred EECCcccCcC
Confidence 4445444433
No 128
>PF07503 zf-HYPF: HypF finger; InterPro: IPR011125 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Proteins of the HypF family are involved in the maturation and regulation of hydrogenase []. In the N terminus they appear to have two zinc finger domains that are similar to those found in the DnaJ chaperone []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3TTD_A 3TSQ_A 3TTC_A 3TSP_A 3TTF_A 3TSU_A.
Probab=50.27 E-value=1.3 Score=20.52 Aligned_cols=11 Identities=0% Similarity=-0.173 Sum_probs=5.2
Q ss_pred CCCCCCCCCCC
Q psy7353 112 ATTPQGQRGQR 122 (139)
Q Consensus 112 ~~C~~C~~~f~ 122 (139)
-.|..||..++
T Consensus 22 isC~~CGPr~~ 32 (35)
T PF07503_consen 22 ISCTNCGPRYS 32 (35)
T ss_dssp --BTTCC-SCC
T ss_pred ccCCCCCCCEE
Confidence 36677776654
No 129
>KOG3002|consensus
Probab=50.12 E-value=18 Score=25.59 Aligned_cols=82 Identities=20% Similarity=0.336 Sum_probs=47.3
Q ss_pred CceeecCCCCCcCCChHHHHHHHHHhcCCCcccCC----CCCccCCChhHHHhhhhhhcCCCCCCCCCC----CCCCCCC
Q psy7353 52 RKVFPCPVCGKEFSRPDKMKNHMKTGCQRKVFPCP----VCGKEFSRPDKMKNHMKTVHDCFMPATTPQ----GQRGQRA 123 (139)
Q Consensus 52 ~~~~~c~~C~~~~~~~~~l~~h~~~~~~~~~~~C~----~C~~~f~~~~~l~~H~~~~h~~~~~~~C~~----C~~~f~~ 123 (139)
.....|+.|...+.....+.. ..-.....++|+ .|.+.|.+... ..|.+.. .. .||.|+. |.+.- .
T Consensus 78 ~~~~~CP~Cr~~~g~~R~~am--EkV~e~~~vpC~~~~~GC~~~~~Y~~~-~~HE~~C-~f-~~~~CP~p~~~C~~~G-~ 151 (299)
T KOG3002|consen 78 KVSNKCPTCRLPIGNIRCRAM--EKVAEAVLVPCKNAKLGCTKSFPYGEK-SKHEKVC-EF-RPCSCPVPGAECKYTG-S 151 (299)
T ss_pred hhcccCCccccccccHHHHHH--HHHHHhceecccccccCCceeeccccc-ccccccc-cc-CCcCCCCCcccCCccC-c
Confidence 345679999877665544432 222333445554 48888877766 5666642 22 6888864 55432 3
Q ss_pred CcchhcccccccCcCC
Q psy7353 124 SPVIDFHKDSVFNKDI 139 (139)
Q Consensus 124 ~~~l~~H~~~~~~~~~ 139 (139)
..+|..|...-|..||
T Consensus 152 ~~~l~~H~~~~hk~~~ 167 (299)
T KOG3002|consen 152 YKDLYAHLNDTHKSDI 167 (299)
T ss_pred HHHHHHHHHhhChhhh
Confidence 3456667655565543
No 130
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=50.01 E-value=5.4 Score=22.80 Aligned_cols=32 Identities=25% Similarity=0.624 Sum_probs=18.3
Q ss_pred ceeecCCCCCcCCChHHHHHHHHHhcCCCcccCCCCCccCCC
Q psy7353 53 KVFPCPVCGKEFSRPDKMKNHMKTGCQRKVFPCPVCGKEFSR 94 (139)
Q Consensus 53 ~~~~c~~C~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~f~~ 94 (139)
..|.|+.|++.-.. -...-+|.|..|++.|.-
T Consensus 35 a~y~CpfCgk~~vk----------R~a~GIW~C~~C~~~~AG 66 (90)
T PTZ00255 35 AKYFCPFCGKHAVK----------RQAVGIWRCKGCKKTVAG 66 (90)
T ss_pred CCccCCCCCCCcee----------eeeeEEEEcCCCCCEEeC
Confidence 35778888753111 112246788888776643
No 131
>KOG3408|consensus
Probab=49.07 E-value=4 Score=24.61 Aligned_cols=23 Identities=35% Similarity=0.674 Sum_probs=14.0
Q ss_pred cccCCCCCccCCChhHHHhhhhh
Q psy7353 82 VFPCPVCGKEFSRPDKMKNHMKT 104 (139)
Q Consensus 82 ~~~C~~C~~~f~~~~~l~~H~~~ 104 (139)
.|.|..|.+-|.+...|..|.++
T Consensus 57 qfyCi~CaRyFi~~~~l~~H~kt 79 (129)
T KOG3408|consen 57 QFYCIECARYFIDAKALKTHFKT 79 (129)
T ss_pred eeehhhhhhhhcchHHHHHHHhc
Confidence 35566666666666666666554
No 132
>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=48.33 E-value=12 Score=22.19 Aligned_cols=10 Identities=10% Similarity=-0.110 Sum_probs=4.6
Q ss_pred CCCCCCCCCC
Q psy7353 112 ATTPQGQRGQ 121 (139)
Q Consensus 112 ~~C~~C~~~f 121 (139)
|.|++|+...
T Consensus 20 ~iCpeC~~EW 29 (109)
T TIGR00686 20 LICPSCLYEW 29 (109)
T ss_pred eECccccccc
Confidence 4444444443
No 133
>PF05290 Baculo_IE-1: Baculovirus immediate-early protein (IE-0); InterPro: IPR007954 This entry contains the Baculovirus immediate-early protein IE-0.
Probab=48.02 E-value=31 Score=21.34 Aligned_cols=57 Identities=16% Similarity=0.334 Sum_probs=30.9
Q ss_pred CceeecCCCCCcCCChHHHHHHHHHhcCCCcccCCCCCccCC--ChhHHHhhhhhhcCCCCCCCCCCCCCCCCCCcc
Q psy7353 52 RKVFPCPVCGKEFSRPDKMKNHMKTGCQRKVFPCPVCGKEFS--RPDKMKNHMKTVHDCFMPATTPQGQRGQRASPV 126 (139)
Q Consensus 52 ~~~~~c~~C~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~f~--~~~~l~~H~~~~h~~~~~~~C~~C~~~f~~~~~ 126 (139)
.+-|.|.+|.....++..| +|-+| ||+..- --.+|=.|-.+ |+ .||.|.-.|.+...
T Consensus 78 ~~lYeCnIC~etS~ee~FL----------KPneC--CgY~iCn~Cya~LWK~~~~-yp-----vCPvCkTSFKss~~ 136 (140)
T PF05290_consen 78 PKLYECNICKETSAEERFL----------KPNEC--CGYSICNACYANLWKFCNL-YP-----VCPVCKTSFKSSSS 136 (140)
T ss_pred CCceeccCcccccchhhcC----------Ccccc--cchHHHHHHHHHHHHHccc-CC-----CCCccccccccccc
Confidence 4567777776554443322 23333 333211 12344444444 55 89999999987654
No 134
>KOG2907|consensus
Probab=47.34 E-value=12 Score=22.36 Aligned_cols=40 Identities=18% Similarity=0.304 Sum_probs=20.8
Q ss_pred ccCCCCCccCCChhHHHhhhhh-hcCCCCCCCCCCCCCCCCCC
Q psy7353 83 FPCPVCGKEFSRPDKMKNHMKT-VHDCFMPATTPQGQRGQRAS 124 (139)
Q Consensus 83 ~~C~~C~~~f~~~~~l~~H~~~-~h~~~~~~~C~~C~~~f~~~ 124 (139)
..|+.||..=.....| .+|. .-+-.--|.|+.|++.|+..
T Consensus 75 ~kCpkCghe~m~Y~T~--QlRSADEGQTVFYTC~kC~~k~~e~ 115 (116)
T KOG2907|consen 75 HKCPKCGHEEMSYHTL--QLRSADEGQTVFYTCPKCKYKFTEN 115 (116)
T ss_pred ccCcccCCchhhhhhh--hcccccCCceEEEEcCccceeeecc
Confidence 4688888532222221 1222 01111248999999988753
No 135
>PRK14873 primosome assembly protein PriA; Provisional
Probab=46.62 E-value=14 Score=29.32 Aligned_cols=11 Identities=9% Similarity=-0.040 Sum_probs=7.7
Q ss_pred CCCCCCCCCCC
Q psy7353 110 MPATTPQGQRG 120 (139)
Q Consensus 110 ~~~~C~~C~~~ 120 (139)
.|+.|+.|+-.
T Consensus 421 ~p~~Cp~Cgs~ 431 (665)
T PRK14873 421 PDWRCPRCGSD 431 (665)
T ss_pred cCccCCCCcCC
Confidence 36788888754
No 136
>KOG2593|consensus
Probab=45.81 E-value=21 Score=26.58 Aligned_cols=38 Identities=11% Similarity=0.164 Sum_probs=22.0
Q ss_pred cCCCcccCCCCCccCCChhHHHhhhhhhcCCCCCCCCCCCCC
Q psy7353 78 CQRKVFPCPVCGKEFSRPDKMKNHMKTVHDCFMPATTPQGQR 119 (139)
Q Consensus 78 ~~~~~~~C~~C~~~f~~~~~l~~H~~~~h~~~~~~~C~~C~~ 119 (139)
+...-|.|+.|.+.|+.-..++--. ...-.|.|..|+-
T Consensus 124 t~~~~Y~Cp~C~kkyt~Lea~~L~~----~~~~~F~C~~C~g 161 (436)
T KOG2593|consen 124 TNVAGYVCPNCQKKYTSLEALQLLD----NETGEFHCENCGG 161 (436)
T ss_pred cccccccCCccccchhhhHHHHhhc----ccCceEEEecCCC
Confidence 3445678888887776655542221 2223577777764
No 137
>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=45.71 E-value=14 Score=18.69 Aligned_cols=24 Identities=21% Similarity=0.430 Sum_probs=10.1
Q ss_pred CcccCCCCCccCCChhHHHhhhhh
Q psy7353 81 KVFPCPVCGKEFSRPDKMKNHMKT 104 (139)
Q Consensus 81 ~~~~C~~C~~~f~~~~~l~~H~~~ 104 (139)
..|.|+.|...|-..-+.-.|...
T Consensus 20 ~~y~C~~C~~~FC~dCD~fiHE~L 43 (51)
T PF07975_consen 20 SRYRCPKCKNHFCIDCDVFIHETL 43 (51)
T ss_dssp EEE--TTTT--B-HHHHHTTTTTS
T ss_pred CeEECCCCCCccccCcChhhhccc
Confidence 345666666666555555445443
No 138
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=45.52 E-value=41 Score=21.90 Aligned_cols=8 Identities=25% Similarity=0.260 Sum_probs=5.0
Q ss_pred CCCCCCCC
Q psy7353 112 ATTPQGQR 119 (139)
Q Consensus 112 ~~C~~C~~ 119 (139)
|.||.||.
T Consensus 133 F~Cp~Cg~ 140 (176)
T COG1675 133 FTCPKCGE 140 (176)
T ss_pred CCCCCCCc
Confidence 56666664
No 139
>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=44.85 E-value=16 Score=19.29 Aligned_cols=11 Identities=64% Similarity=1.467 Sum_probs=5.2
Q ss_pred CcccCCCCCcc
Q psy7353 81 KVFPCPVCGKE 91 (139)
Q Consensus 81 ~~~~C~~C~~~ 91 (139)
+.|.|+.||..
T Consensus 45 r~~~C~~Cg~~ 55 (69)
T PF07282_consen 45 RVFTCPNCGFE 55 (69)
T ss_pred ceEEcCCCCCE
Confidence 34455555543
No 140
>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=44.76 E-value=4.1 Score=25.09 Aligned_cols=20 Identities=40% Similarity=0.889 Sum_probs=8.8
Q ss_pred ccCCCCCccCCChhHHHhhhhhh
Q psy7353 83 FPCPVCGKEFSRPDKMKNHMKTV 105 (139)
Q Consensus 83 ~~C~~C~~~f~~~~~l~~H~~~~ 105 (139)
..|.+||+.|.. |.+|++++
T Consensus 73 i~clecGk~~k~---LkrHL~~~ 92 (132)
T PF05443_consen 73 IICLECGKKFKT---LKRHLRTH 92 (132)
T ss_dssp EE-TBT--EESB---HHHHHHHT
T ss_pred eEEccCCcccch---HHHHHHHc
Confidence 456666665543 35666653
No 141
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=43.44 E-value=16 Score=21.74 Aligned_cols=10 Identities=20% Similarity=0.265 Sum_probs=6.6
Q ss_pred ccCCCCCccC
Q psy7353 83 FPCPVCGKEF 92 (139)
Q Consensus 83 ~~C~~C~~~f 92 (139)
+.|..|+..|
T Consensus 71 ~~C~~Cg~~~ 80 (113)
T PRK12380 71 AWCWDCSQVV 80 (113)
T ss_pred EEcccCCCEE
Confidence 5677777554
No 142
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=43.15 E-value=22 Score=26.44 Aligned_cols=11 Identities=36% Similarity=0.857 Sum_probs=5.5
Q ss_pred cccCCCCCccC
Q psy7353 82 VFPCPVCGKEF 92 (139)
Q Consensus 82 ~~~C~~C~~~f 92 (139)
-|.|+.||..+
T Consensus 367 g~rC~kCg~~~ 377 (421)
T COG1571 367 GFRCKKCGTRA 377 (421)
T ss_pred CcccccccccC
Confidence 45555555443
No 143
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=42.73 E-value=11 Score=18.98 Aligned_cols=10 Identities=0% Similarity=-0.373 Sum_probs=4.9
Q ss_pred CCCCCCCCCC
Q psy7353 111 PATTPQGQRG 120 (139)
Q Consensus 111 ~~~C~~C~~~ 120 (139)
.+.|+.|++.
T Consensus 37 r~~C~~Cgyt 46 (50)
T PRK00432 37 RWHCGKCGYT 46 (50)
T ss_pred cEECCCcCCE
Confidence 3455555543
No 144
>KOG2593|consensus
Probab=41.44 E-value=21 Score=26.54 Aligned_cols=38 Identities=24% Similarity=0.473 Sum_probs=25.3
Q ss_pred CCCcceecCCCCCcchhcccCCHHHHHHHHHHhccCCCCceeecCCCCC
Q psy7353 14 VTEGIYKCMECAKVDVIKTFKNKYSFQRHAFLYHEGCQRKVFPCPVCGK 62 (139)
Q Consensus 14 ~~~~~~~C~~c~~~~~~~~f~~~~~l~~h~~~~~~~~~~~~~~c~~C~~ 62 (139)
+...-|.|+.|.+ .|.+...++.-.. - .-.|.|..|+.
T Consensus 124 t~~~~Y~Cp~C~k-----kyt~Lea~~L~~~--~----~~~F~C~~C~g 161 (436)
T KOG2593|consen 124 TNVAGYVCPNCQK-----KYTSLEALQLLDN--E----TGEFHCENCGG 161 (436)
T ss_pred cccccccCCcccc-----chhhhHHHHhhcc--c----CceEEEecCCC
Confidence 3445688999998 7887766653321 1 34688888874
No 145
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=40.81 E-value=13 Score=17.58 Aligned_cols=13 Identities=31% Similarity=0.807 Sum_probs=5.3
Q ss_pred ecCCCCCcCCChH
Q psy7353 56 PCPVCGKEFSRPD 68 (139)
Q Consensus 56 ~c~~C~~~~~~~~ 68 (139)
.|+.|+-.+.+..
T Consensus 21 ~C~~C~G~W~d~~ 33 (41)
T PF13453_consen 21 VCPSCGGIWFDAG 33 (41)
T ss_pred ECCCCCeEEccHH
Confidence 3444444444333
No 146
>PF14311 DUF4379: Domain of unknown function (DUF4379)
Probab=40.74 E-value=26 Score=17.64 Aligned_cols=13 Identities=38% Similarity=1.183 Sum_probs=6.5
Q ss_pred ccCCCCCccCCCh
Q psy7353 83 FPCPVCGKEFSRP 95 (139)
Q Consensus 83 ~~C~~C~~~f~~~ 95 (139)
+.|..||..|...
T Consensus 29 W~C~~Cgh~w~~~ 41 (55)
T PF14311_consen 29 WKCPKCGHEWKAS 41 (55)
T ss_pred EECCCCCCeeEcc
Confidence 4555555544433
No 147
>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=40.36 E-value=9.6 Score=17.50 Aligned_cols=15 Identities=7% Similarity=-0.046 Sum_probs=7.6
Q ss_pred CCCCCCCCCCCCcch
Q psy7353 113 TTPQGQRGQRASPVI 127 (139)
Q Consensus 113 ~C~~C~~~f~~~~~l 127 (139)
.|.+|++.|.....+
T Consensus 5 ~C~eC~~~f~dSyL~ 19 (34)
T PF01286_consen 5 KCDECGKPFMDSYLL 19 (34)
T ss_dssp E-TTT--EES-SSCC
T ss_pred hHhHhCCHHHHHHHH
Confidence 577788877776555
No 148
>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=39.77 E-value=29 Score=26.28 Aligned_cols=29 Identities=24% Similarity=0.395 Sum_probs=24.6
Q ss_pred cceecCCCCCcchhcccCCHHHHHHHHHHhccCC
Q psy7353 17 GIYKCMECAKVDVIKTFKNKYSFQRHAFLYHEGC 50 (139)
Q Consensus 17 ~~~~C~~c~~~~~~~~f~~~~~l~~h~~~~~~~~ 50 (139)
+.|.|+.|.+ .|.+...+..|+...|.+.
T Consensus 56 rFWiCp~Csk-----kF~d~~~~~~H~~~eH~~~ 84 (466)
T PF04780_consen 56 RFWICPRCSK-----KFSDAESCLSHMEQEHPAG 84 (466)
T ss_pred eEeeCCcccc-----eeCCHHHHHHHHHHhhhhh
Confidence 4588999998 8999999999998777763
No 149
>KOG0717|consensus
Probab=39.19 E-value=7.6 Score=29.09 Aligned_cols=23 Identities=9% Similarity=0.065 Sum_probs=19.3
Q ss_pred CCCCCCCCCCCCCcchhcccccc
Q psy7353 112 ATTPQGQRGQRASPVIDFHKDSV 134 (139)
Q Consensus 112 ~~C~~C~~~f~~~~~l~~H~~~~ 134 (139)
+.|..|.+.|.+...|..|..++
T Consensus 293 lyC~vCnKsFKseKq~kNHEnSK 315 (508)
T KOG0717|consen 293 LYCVVCNKSFKSEKQLKNHENSK 315 (508)
T ss_pred eEEeeccccccchHHHHhhHHHH
Confidence 67889999999999998887664
No 150
>PRK05978 hypothetical protein; Provisional
Probab=38.78 E-value=21 Score=22.54 Aligned_cols=11 Identities=0% Similarity=-0.203 Sum_probs=6.2
Q ss_pred CCCCCCCCCCC
Q psy7353 113 TTPQGQRGQRA 123 (139)
Q Consensus 113 ~C~~C~~~f~~ 123 (139)
.|+.|+..|..
T Consensus 54 ~C~~CG~~~~~ 64 (148)
T PRK05978 54 HCAACGEDFTH 64 (148)
T ss_pred CccccCCcccc
Confidence 56666655543
No 151
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=38.35 E-value=19 Score=18.12 Aligned_cols=10 Identities=0% Similarity=-0.343 Sum_probs=6.0
Q ss_pred CCCCCCCCCC
Q psy7353 111 PATTPQGQRG 120 (139)
Q Consensus 111 ~~~C~~C~~~ 120 (139)
.|.|..|++.
T Consensus 37 R~~CGkCgyT 46 (51)
T COG1998 37 RWACGKCGYT 46 (51)
T ss_pred eeEeccccce
Confidence 4566666653
No 152
>PF15269 zf-C2H2_7: Zinc-finger
Probab=38.14 E-value=23 Score=17.37 Aligned_cols=22 Identities=27% Similarity=0.502 Sum_probs=13.5
Q ss_pred ccCCCCCccCCChhHHHhhhhh
Q psy7353 83 FPCPVCGKEFSRPDKMKNHMKT 104 (139)
Q Consensus 83 ~~C~~C~~~f~~~~~l~~H~~~ 104 (139)
|.|-.|.....-.+.|-.|++.
T Consensus 21 ykcfqcpftc~~kshl~nhmky 42 (54)
T PF15269_consen 21 YKCFQCPFTCNEKSHLFNHMKY 42 (54)
T ss_pred ceeecCCcccchHHHHHHHHHH
Confidence 4566666655666666666653
No 153
>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=38.00 E-value=11 Score=23.47 Aligned_cols=10 Identities=10% Similarity=-0.137 Sum_probs=5.7
Q ss_pred CCCCCCCCCC
Q psy7353 112 ATTPQGQRGQ 121 (139)
Q Consensus 112 ~~C~~C~~~f 121 (139)
|.|+.|++.|
T Consensus 125 ~~C~~C~kiy 134 (147)
T PF01927_consen 125 WRCPGCGKIY 134 (147)
T ss_pred EECCCCCCEe
Confidence 5566666554
No 154
>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=37.73 E-value=23 Score=17.11 Aligned_cols=16 Identities=44% Similarity=1.010 Sum_probs=10.8
Q ss_pred cCCCCCccCCChhHHH
Q psy7353 84 PCPVCGKEFSRPDKMK 99 (139)
Q Consensus 84 ~C~~C~~~f~~~~~l~ 99 (139)
.|..|+..|++.-.+.
T Consensus 10 ~C~~C~rpf~WRKKW~ 25 (42)
T PF10013_consen 10 ICPVCGRPFTWRKKWA 25 (42)
T ss_pred cCcccCCcchHHHHHH
Confidence 4777777777765543
No 155
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=37.68 E-value=41 Score=17.33 Aligned_cols=11 Identities=45% Similarity=1.071 Sum_probs=6.5
Q ss_pred CCcccCCCCCc
Q psy7353 80 RKVFPCPVCGK 90 (139)
Q Consensus 80 ~~~~~C~~C~~ 90 (139)
...|.|+.||-
T Consensus 12 ~v~~~Cp~cGi 22 (55)
T PF13824_consen 12 HVNFECPDCGI 22 (55)
T ss_pred ccCCcCCCCCC
Confidence 44566666664
No 156
>TIGR00143 hypF [NiFe] hydrogenase maturation protein HypF. A previously described regulatory effect of HypF mutatation is attributable to loss of activity of a regulatory hydrogenase. A zinc finger-like region CXXCX(18)CXXCX(24)CXXCX(18)CXXC region further supported the regulatory hypothesis. However, more recent work (PUBMED:11375153) shows the direct effect is on the activity of expressed hydrogenases with nickel/iron centers, rather than on expression.
Probab=37.57 E-value=2.6 Score=33.43 Aligned_cols=58 Identities=22% Similarity=0.480 Sum_probs=36.1
Q ss_pred ecCCCCCcCCChHHHHHHHHHhcCCC-cccCCCCCccCCChhHHHhhhhhhcCCCCCCCCCCCCCCC
Q psy7353 56 PCPVCGKEFSRPDKMKNHMKTGCQRK-VFPCPVCGKEFSRPDKMKNHMKTVHDCFMPATTPQGQRGQ 121 (139)
Q Consensus 56 ~c~~C~~~~~~~~~l~~h~~~~~~~~-~~~C~~C~~~f~~~~~l~~H~~~~h~~~~~~~C~~C~~~f 121 (139)
.|..||..|.....|..-. ..+... .-.|+.|.+.+.++.+...|-. +-.|+.||.+.
T Consensus 92 nCt~CGPr~~i~~~lpydr-~~t~m~~f~~C~~C~~ey~~p~~rr~h~~-------~~~C~~Cgp~l 150 (711)
T TIGR00143 92 SCTHCGPRFTIIEALPYDR-ENTSMADFPLCPDCAKEYKDPLDRRFHAQ-------PIACPRCGPQL 150 (711)
T ss_pred cccCCCCCeEEeecCCCCC-CCcCCCCCcCCHHHHHHhcCCccccCCCC-------CccCCCCCcEE
Confidence 3888998877766544322 222223 2368889888887766433322 44899999754
No 157
>PF02176 zf-TRAF: TRAF-type zinc finger; PDB: 2EOD_A 2YUC_A 3HCU_A 3HCS_B 3HCT_A.
Probab=37.51 E-value=15 Score=18.69 Aligned_cols=18 Identities=28% Similarity=1.032 Sum_probs=6.5
Q ss_pred HHHHHHHhcCCCcccCCC
Q psy7353 70 MKNHMKTGCQRKVFPCPV 87 (139)
Q Consensus 70 l~~h~~~~~~~~~~~C~~ 87 (139)
|..|....-..++..|+.
T Consensus 26 l~~H~~~~C~~~~v~C~~ 43 (60)
T PF02176_consen 26 LDDHLENECPKRPVPCPY 43 (60)
T ss_dssp HHHHHHTTSTTSEEE-SS
T ss_pred HHHHHHccCCCCcEECCC
Confidence 444444333333334433
No 158
>PRK05580 primosome assembly protein PriA; Validated
Probab=36.20 E-value=30 Score=27.53 Aligned_cols=10 Identities=20% Similarity=0.531 Sum_probs=6.3
Q ss_pred CCCCCCCCCC
Q psy7353 110 MPATTPQGQR 119 (139)
Q Consensus 110 ~~~~C~~C~~ 119 (139)
.|+.|+.|+.
T Consensus 420 ~~~~Cp~Cg~ 429 (679)
T PRK05580 420 IPKACPECGS 429 (679)
T ss_pred CCCCCCCCcC
Confidence 3567777754
No 159
>COG1326 Uncharacterized archaeal Zn-finger protein [General function prediction only]
Probab=35.37 E-value=28 Score=22.99 Aligned_cols=12 Identities=25% Similarity=0.714 Sum_probs=7.3
Q ss_pred CcccCCCCCccC
Q psy7353 81 KVFPCPVCGKEF 92 (139)
Q Consensus 81 ~~~~C~~C~~~f 92 (139)
..+.|..||..+
T Consensus 29 ~lvrC~eCG~V~ 40 (201)
T COG1326 29 PLVRCEECGTVH 40 (201)
T ss_pred eEEEccCCCcEe
Confidence 356677776554
No 160
>KOG4118|consensus
Probab=34.92 E-value=11 Score=20.11 Aligned_cols=24 Identities=4% Similarity=-0.103 Sum_probs=11.7
Q ss_pred CCCCCCCCCCCCCcchhccccccc
Q psy7353 112 ATTPQGQRGQRASPVIDFHKDSVF 135 (139)
Q Consensus 112 ~~C~~C~~~f~~~~~l~~H~~~~~ 135 (139)
|.|..|.....+.-.++-|+...|
T Consensus 39 ~kCtVC~~~mpdpktfkqhfe~kH 62 (74)
T KOG4118|consen 39 HKCTVCMVQMPDPKTFKQHFENKH 62 (74)
T ss_pred hhhHhhHhhCCCCchHHHHHhhcC
Confidence 445555554444444444444444
No 161
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=34.82 E-value=20 Score=20.50 Aligned_cols=14 Identities=21% Similarity=0.081 Sum_probs=9.4
Q ss_pred CCCCCCCCCCCCCC
Q psy7353 110 MPATTPQGQRGQRA 123 (139)
Q Consensus 110 ~~~~C~~C~~~f~~ 123 (139)
.|-.|..||+.|.+
T Consensus 57 ~Pa~CkkCGfef~~ 70 (97)
T COG3357 57 RPARCKKCGFEFRD 70 (97)
T ss_pred cChhhcccCccccc
Confidence 35677777777766
No 162
>KOG2636|consensus
Probab=34.59 E-value=19 Score=26.92 Aligned_cols=27 Identities=11% Similarity=-0.027 Sum_probs=22.0
Q ss_pred cCCCCCCCCCCCC-CCCCCCcchhcccc
Q psy7353 106 HDCFMPATTPQGQ-RGQRASPVIDFHKD 132 (139)
Q Consensus 106 h~~~~~~~C~~C~-~~f~~~~~l~~H~~ 132 (139)
|+-...|.|.+|| +.+.=+-.+++|..
T Consensus 396 HGL~~ey~CEICGNy~Y~GrkaF~RHF~ 423 (497)
T KOG2636|consen 396 HGLDIEYNCEICGNYVYKGRKAFDRHFN 423 (497)
T ss_pred cCCCcccceeeccCccccCcHHHHHHhH
Confidence 5666779999999 88888888888854
No 163
>PF01096 TFIIS_C: Transcription factor S-II (TFIIS); InterPro: IPR001222 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIs (TFIIS). In eukaryotes the initiation of transcription of protein encoding genes by polymerase II (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least eight different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, -IIH and -IIS []. During mRNA elongation, Pol II can encounter DNA sequences that cause reverse movement of the enzyme. Such backtracking involves extrusion of the RNA 3'-end into the pore, and can lead to transcriptional arrest. Escape from arrest requires cleavage of the extruded RNA with the help of TFIIS, which induces mRNA cleavage by enhancing the intrinsic nuclease activity of RNA polymerase (Pol) II, past template-encoded pause sites []. TFIIS extends from the polymerase surface via a pore to the internal active site. Two essential and invariant acidic residues in a TFIIS loop complement the Pol II active site and could position a metal ion and a water molecule for hydrolytic RNA cleavage. TFIIS also induces extensive structural changes in Pol II that would realign nucleic acids in the active centre. TFIIS is a protein of about 300 amino acids. It contains three regions: a variable N-terminal domain not required for TFIIS activity; a conserved central domain required for Pol II binding; and a conserved C-terminal C4-type zinc finger essential for RNA cleavage. The zinc finger folds in a conformation termed a zinc ribbon [] characterised by a three-stranded antiparallel beta-sheet and two beta-hairpins. A backbone model for Pol II-TFIIS complex was obtained from X-ray analysis. It shows that a beta hairpin protrudes from the zinc finger and complements the pol II active site []. Some viral proteins also contain the TFIIS zinc ribbon C-terminal domain. The Vaccinia virus protein, unlike its eukaryotic homologue, is an integral RNA polymerase subunit rather than a readily separable transcription factor []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding, 0006351 transcription, DNA-dependent; PDB: 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I 3I4M_I ....
Probab=34.36 E-value=0.93 Score=21.47 Aligned_cols=10 Identities=0% Similarity=-0.369 Sum_probs=6.3
Q ss_pred CCCCCCCCCC
Q psy7353 112 ATTPQGQRGQ 121 (139)
Q Consensus 112 ~~C~~C~~~f 121 (139)
|.|..|+..|
T Consensus 29 y~C~~C~~~w 38 (39)
T PF01096_consen 29 YVCCNCGHRW 38 (39)
T ss_dssp EEESSSTEEE
T ss_pred EEeCCCCCee
Confidence 6676676554
No 164
>COG2331 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=34.30 E-value=8.9 Score=21.12 Aligned_cols=9 Identities=33% Similarity=1.191 Sum_probs=4.7
Q ss_pred eeecCCCCC
Q psy7353 54 VFPCPVCGK 62 (139)
Q Consensus 54 ~~~c~~C~~ 62 (139)
.|.|..|+.
T Consensus 12 ~Y~c~~cg~ 20 (82)
T COG2331 12 SYECTECGN 20 (82)
T ss_pred EEeecccch
Confidence 355555554
No 165
>PF11672 DUF3268: Protein of unknown function (DUF3268); InterPro: IPR021686 This entry is represented by Listeria phage P100, Gp150. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=33.86 E-value=24 Score=20.71 Aligned_cols=7 Identities=0% Similarity=-0.182 Sum_probs=3.3
Q ss_pred CCCCCCC
Q psy7353 112 ATTPQGQ 118 (139)
Q Consensus 112 ~~C~~C~ 118 (139)
|.|+.|+
T Consensus 32 y~C~~C~ 38 (102)
T PF11672_consen 32 YVCTPCD 38 (102)
T ss_pred EECCCCC
Confidence 4454444
No 166
>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=33.84 E-value=24 Score=21.09 Aligned_cols=10 Identities=30% Similarity=0.786 Sum_probs=4.9
Q ss_pred eecCCCCCcC
Q psy7353 55 FPCPVCGKEF 64 (139)
Q Consensus 55 ~~c~~C~~~~ 64 (139)
..|..|+..|
T Consensus 71 ~~C~~Cg~~~ 80 (115)
T TIGR00100 71 CECEDCSEEV 80 (115)
T ss_pred EEcccCCCEE
Confidence 4455555433
No 167
>COG3364 Zn-ribbon containing protein [General function prediction only]
Probab=33.79 E-value=31 Score=20.22 Aligned_cols=9 Identities=22% Similarity=0.785 Sum_probs=4.9
Q ss_pred ceecCCCCC
Q psy7353 18 IYKCMECAK 26 (139)
Q Consensus 18 ~~~C~~c~~ 26 (139)
|+.|..||.
T Consensus 2 pH~CtrCG~ 10 (112)
T COG3364 2 PHQCTRCGE 10 (112)
T ss_pred Cceeccccc
Confidence 445555555
No 168
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=33.37 E-value=21 Score=16.77 Aligned_cols=13 Identities=0% Similarity=-0.391 Sum_probs=9.5
Q ss_pred CCCCCCCCCCCCC
Q psy7353 111 PATTPQGQRGQRA 123 (139)
Q Consensus 111 ~~~C~~C~~~f~~ 123 (139)
|+.|..|+..|=.
T Consensus 12 ~f~C~~C~~~FC~ 24 (39)
T smart00154 12 GFKCRHCGNLFCG 24 (39)
T ss_pred CeECCccCCcccc
Confidence 7788888877643
No 169
>PF11494 Ta0938: Ta0938; InterPro: IPR021585 Ta0938 is a protein of unknown function however the structure has been determined. The protein has a novel fold and a putative Zn-binding motif. The structure has two different parts, one region contains a beta sheet flanked by two alpha helices and the other contains a bundle of loops which contain all cysteines in the protein. ; PDB: 2FQH_A.
Probab=33.23 E-value=40 Score=19.56 Aligned_cols=38 Identities=26% Similarity=0.549 Sum_probs=12.3
Q ss_pred CceeecCCCCCcCCChHHHHHHHHHhcCCC-cccCCCCCccCCCh
Q psy7353 52 RKVFPCPVCGKEFSRPDKMKNHMKTGCQRK-VFPCPVCGKEFSRP 95 (139)
Q Consensus 52 ~~~~~c~~C~~~~~~~~~l~~h~~~~~~~~-~~~C~~C~~~f~~~ 95 (139)
.+.-.|..|+.++-... .--.+++ .|.|..|-+.|...
T Consensus 12 ~ke~~CalCG~tWg~~y------~Ev~G~rLfFCCd~ca~EF~nm 50 (105)
T PF11494_consen 12 TKEMGCALCGATWGDYY------EEVDGERLFFCCDDCAKEFKNM 50 (105)
T ss_dssp SGGGS-SS---S---SS-------B-TT--BSSS--SSSS-TTS-
T ss_pred cccccccccCCcHHHHH------HhhcCCEEEEEcHHHHHHHHHH
Confidence 34446778876654321 1123334 45567777777654
No 170
>PF10083 DUF2321: Uncharacterized protein conserved in bacteria (DUF2321); InterPro: IPR016891 This entry is represented by Bacteriophage 'Lactobacillus prophage Lj928', Orf-Ljo1454. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=33.18 E-value=18 Score=22.89 Aligned_cols=19 Identities=21% Similarity=0.476 Sum_probs=11.5
Q ss_pred CCCcccCCCCCccCCChhH
Q psy7353 79 QRKVFPCPVCGKEFSRPDK 97 (139)
Q Consensus 79 ~~~~~~C~~C~~~f~~~~~ 97 (139)
.+.|..|..||+.|.|...
T Consensus 65 ~~~PsYC~~CGkpyPWt~~ 83 (158)
T PF10083_consen 65 YEAPSYCHNCGKPYPWTEN 83 (158)
T ss_pred CCCChhHHhCCCCCchHHH
Confidence 3456666667776666543
No 171
>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=33.11 E-value=21 Score=22.46 Aligned_cols=19 Identities=0% Similarity=-0.197 Sum_probs=14.5
Q ss_pred CCCCCCCCCCCCCCCcchh
Q psy7353 110 MPATTPQGQRGQRASPVID 128 (139)
Q Consensus 110 ~~~~C~~C~~~f~~~~~l~ 128 (139)
+--.|..|+++|++..-++
T Consensus 27 RRReC~~C~~RFTTyErve 45 (147)
T TIGR00244 27 RRRECLECHERFTTFERAE 45 (147)
T ss_pred ecccCCccCCccceeeecc
Confidence 3468999999999875543
No 172
>TIGR03831 YgiT_finger YgiT-type zinc finger domain. This domain model describes a small domain with two copies of a putative zinc-binding motif CXXC (usually CXXCG). Most member proteins consist largely of this domain or else carry an additional C-terminal helix-turn-helix domain, resembling that of the phage protein Cro and modeled by pfam01381.
Probab=32.97 E-value=22 Score=16.78 Aligned_cols=12 Identities=17% Similarity=0.030 Sum_probs=7.3
Q ss_pred CCCCCCCCCCCC
Q psy7353 112 ATTPQGQRGQRA 123 (139)
Q Consensus 112 ~~C~~C~~~f~~ 123 (139)
+.|+.|+..+.+
T Consensus 33 ~~C~~CGE~~~~ 44 (46)
T TIGR03831 33 LVCPQCGEEYLD 44 (46)
T ss_pred cccccCCCEeeC
Confidence 567777765543
No 173
>COG4957 Predicted transcriptional regulator [Transcription]
Probab=32.94 E-value=15 Score=22.65 Aligned_cols=18 Identities=39% Similarity=0.700 Sum_probs=8.7
Q ss_pred cCCCCCccCCChhHHHhhhhh
Q psy7353 84 PCPVCGKEFSRPDKMKNHMKT 104 (139)
Q Consensus 84 ~C~~C~~~f~~~~~l~~H~~~ 104 (139)
.|.++|+.| -+|.+|+.+
T Consensus 78 icLEDGkkf---KSLKRHL~t 95 (148)
T COG4957 78 ICLEDGKKF---KSLKRHLTT 95 (148)
T ss_pred EEeccCcch---HHHHHHHhc
Confidence 345555444 234555555
No 174
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=32.91 E-value=32 Score=20.61 Aligned_cols=10 Identities=30% Similarity=0.903 Sum_probs=6.7
Q ss_pred ccCCCCCccC
Q psy7353 83 FPCPVCGKEF 92 (139)
Q Consensus 83 ~~C~~C~~~f 92 (139)
+.|..|+..|
T Consensus 72 ~~C~~Cg~~~ 81 (117)
T PRK00564 72 LECKDCSHVF 81 (117)
T ss_pred EEhhhCCCcc
Confidence 5677777554
No 175
>KOG4167|consensus
Probab=31.89 E-value=6.9 Score=31.05 Aligned_cols=25 Identities=44% Similarity=0.832 Sum_probs=21.4
Q ss_pred CcccCCCCCccCCChhHHHhhhhhh
Q psy7353 81 KVFPCPVCGKEFSRPDKMKNHMKTV 105 (139)
Q Consensus 81 ~~~~C~~C~~~f~~~~~l~~H~~~~ 105 (139)
-.|.|.+|++.|.-.-++..||++|
T Consensus 791 giFpCreC~kvF~KiKSrNAHMK~H 815 (907)
T KOG4167|consen 791 GIFPCRECGKVFFKIKSRNAHMKTH 815 (907)
T ss_pred ceeehHHHHHHHHHHhhhhHHHHHH
Confidence 4689999999998888888888883
No 176
>COG4896 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=31.79 E-value=22 Score=18.70 Aligned_cols=9 Identities=33% Similarity=1.231 Sum_probs=4.1
Q ss_pred ceeecCCCC
Q psy7353 53 KVFPCPVCG 61 (139)
Q Consensus 53 ~~~~c~~C~ 61 (139)
+.|-|+.|.
T Consensus 30 rtymC~eC~ 38 (68)
T COG4896 30 RTYMCPECE 38 (68)
T ss_pred eeEechhhH
Confidence 334454443
No 177
>PF12773 DZR: Double zinc ribbon
Probab=31.74 E-value=53 Score=15.95 Aligned_cols=10 Identities=10% Similarity=0.062 Sum_probs=6.8
Q ss_pred CCCCCCCCCC
Q psy7353 111 PATTPQGQRG 120 (139)
Q Consensus 111 ~~~C~~C~~~ 120 (139)
...|+.|+..
T Consensus 29 ~~~C~~Cg~~ 38 (50)
T PF12773_consen 29 KKICPNCGAE 38 (50)
T ss_pred CCCCcCCcCC
Confidence 4577777765
No 178
>COG1773 Rubredoxin [Energy production and conversion]
Probab=31.61 E-value=14 Score=19.00 Aligned_cols=10 Identities=0% Similarity=-0.502 Sum_probs=5.8
Q ss_pred CCCCCCCCCC
Q psy7353 112 ATTPQGQRGQ 121 (139)
Q Consensus 112 ~~C~~C~~~f 121 (139)
|+|..|++.|
T Consensus 4 ~~C~~CG~vY 13 (55)
T COG1773 4 WRCSVCGYVY 13 (55)
T ss_pred eEecCCceEe
Confidence 5666666544
No 179
>KOG1842|consensus
Probab=31.51 E-value=26 Score=26.28 Aligned_cols=29 Identities=17% Similarity=0.171 Sum_probs=23.7
Q ss_pred cceecCCCCCcchhcccCCHHHHHHHHHHhccCC
Q psy7353 17 GIYKCMECAKVDVIKTFKNKYSFQRHAFLYHEGC 50 (139)
Q Consensus 17 ~~~~C~~c~~~~~~~~f~~~~~l~~h~~~~~~~~ 50 (139)
.-|.||.|.. .|.+...|..|....|.++
T Consensus 14 egflCPiC~~-----dl~~~~~L~~H~d~eH~~e 42 (505)
T KOG1842|consen 14 EGFLCPICLL-----DLPNLSALNDHLDVEHFEE 42 (505)
T ss_pred hcccCchHhh-----hhhhHHHHHHHHhhhcccc
Confidence 3478999998 8999999999987777663
No 180
>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=31.38 E-value=20 Score=17.99 Aligned_cols=11 Identities=0% Similarity=-0.508 Sum_probs=7.4
Q ss_pred CCCCCCCCCCC
Q psy7353 112 ATTPQGQRGQR 122 (139)
Q Consensus 112 ~~C~~C~~~f~ 122 (139)
|.|..|++.+.
T Consensus 2 y~C~~CgyiYd 12 (50)
T cd00730 2 YECRICGYIYD 12 (50)
T ss_pred cCCCCCCeEEC
Confidence 66777776654
No 181
>KOG2071|consensus
Probab=31.01 E-value=25 Score=27.24 Aligned_cols=28 Identities=14% Similarity=-0.188 Sum_probs=23.6
Q ss_pred CCCCCCCCCCCCCCCCCcchhccccccc
Q psy7353 108 CFMPATTPQGQRGQRASPVIDFHKDSVF 135 (139)
Q Consensus 108 ~~~~~~C~~C~~~f~~~~~l~~H~~~~~ 135 (139)
..+|-.|.-||.+|.......+|++.|-
T Consensus 415 ~~~pnqC~~CG~R~~~~ee~sk~md~H~ 442 (579)
T KOG2071|consen 415 KDSPNQCKSCGLRFDDSEERSKHMDIHD 442 (579)
T ss_pred cCCcchhcccccccccchhhhhHhhhhh
Confidence 4677899999999999998888877664
No 182
>KOG0978|consensus
Probab=30.62 E-value=40 Score=26.91 Aligned_cols=19 Identities=16% Similarity=0.085 Sum_probs=12.6
Q ss_pred CCCCCCCCCCCCCCCcchh
Q psy7353 110 MPATTPQGQRGQRASPVID 128 (139)
Q Consensus 110 ~~~~C~~C~~~f~~~~~l~ 128 (139)
+.-.||.|+..|...+-+.
T Consensus 677 RqRKCP~Cn~aFganDv~~ 695 (698)
T KOG0978|consen 677 RQRKCPKCNAAFGANDVHR 695 (698)
T ss_pred hcCCCCCCCCCCCcccccc
Confidence 3457888888887665443
No 183
>PHA02998 RNA polymerase subunit; Provisional
Probab=30.61 E-value=12 Score=24.33 Aligned_cols=36 Identities=14% Similarity=0.242 Sum_probs=18.9
Q ss_pred ccCCCCCccCCChhHHHhhhhhhcCCCC---CCCCCCCCCCCC
Q psy7353 83 FPCPVCGKEFSRPDKMKNHMKTVHDCFM---PATTPQGQRGQR 122 (139)
Q Consensus 83 ~~C~~C~~~f~~~~~l~~H~~~~h~~~~---~~~C~~C~~~f~ 122 (139)
..|+.|+..=.... +..++. ++|. -|.|..|+..|.
T Consensus 144 v~CPkCg~~~A~f~--qlQTRS--ADEPmT~FYkC~~CG~~wk 182 (195)
T PHA02998 144 TPCPNCKSKNTTPM--MIQTRA--ADEPPLVRHACRDCKKHFK 182 (195)
T ss_pred CCCCCCCCCceEEE--EEeecc--CCCCceEEEEcCCCCCccC
Confidence 46888875322222 222222 2222 278988987664
No 184
>KOG4167|consensus
Probab=30.57 E-value=13 Score=29.72 Aligned_cols=25 Identities=36% Similarity=0.583 Sum_probs=19.0
Q ss_pred CcceecCCCCCcchhcccCCHHHHHHHHHH
Q psy7353 16 EGIYKCMECAKVDVIKTFKNKYSFQRHAFL 45 (139)
Q Consensus 16 ~~~~~C~~c~~~~~~~~f~~~~~l~~h~~~ 45 (139)
.+.|.|.+|++ .|.....+..||..
T Consensus 790 ~giFpCreC~k-----vF~KiKSrNAHMK~ 814 (907)
T KOG4167|consen 790 TGIFPCRECGK-----VFFKIKSRNAHMKT 814 (907)
T ss_pred CceeehHHHHH-----HHHHHhhhhHHHHH
Confidence 56788888888 67777777777765
No 185
>COG1327 Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains [Transcription]
Probab=30.54 E-value=24 Score=22.34 Aligned_cols=17 Identities=0% Similarity=-0.283 Sum_probs=13.1
Q ss_pred CCCCCCCCCCCCCCcch
Q psy7353 111 PATTPQGQRGQRASPVI 127 (139)
Q Consensus 111 ~~~C~~C~~~f~~~~~l 127 (139)
--.|+.|+.+|++..-.
T Consensus 28 RReC~~C~~RFTTfE~~ 44 (156)
T COG1327 28 RRECLECGERFTTFERA 44 (156)
T ss_pred hhcccccccccchhhee
Confidence 46899999999986443
No 186
>PRK05452 anaerobic nitric oxide reductase flavorubredoxin; Provisional
Probab=30.51 E-value=24 Score=26.71 Aligned_cols=39 Identities=13% Similarity=0.171 Sum_probs=22.6
Q ss_pred CCcccCCCCCccCCChhHHHhhhhhhcCC----CC--CCCCCCCCCC
Q psy7353 80 RKVFPCPVCGKEFSRPDKMKNHMKTVHDC----FM--PATTPQGQRG 120 (139)
Q Consensus 80 ~~~~~C~~C~~~f~~~~~l~~H~~~~h~~----~~--~~~C~~C~~~ 120 (139)
...|.|..|+..|....--... .+ -+| +. .|.||.|+..
T Consensus 423 ~~~~~c~~c~~~yd~~~g~~~~-~~-~~gt~~~~lp~~~~cp~c~~~ 467 (479)
T PRK05452 423 GPRMQCSVCQWIYDPAKGEPMQ-DV-APGTPWSEVPDNFLCPECSLG 467 (479)
T ss_pred CCeEEECCCCeEECCCCCCccc-CC-CCCCChhhCCCCCcCcCCCCc
Confidence 4568999999887654211111 11 121 22 3899999975
No 187
>COG4306 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=30.47 E-value=31 Score=21.04 Aligned_cols=16 Identities=25% Similarity=0.503 Sum_probs=9.9
Q ss_pred CCcccCCCCCccCCCh
Q psy7353 80 RKVFPCPVCGKEFSRP 95 (139)
Q Consensus 80 ~~~~~C~~C~~~f~~~ 95 (139)
+.|--|.-||+.|.+.
T Consensus 66 e~psfchncgs~fpwt 81 (160)
T COG4306 66 EPPSFCHNCGSRFPWT 81 (160)
T ss_pred CCcchhhcCCCCCCcH
Confidence 3455566677777665
No 188
>TIGR00627 tfb4 transcription factor tfb4. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=30.44 E-value=64 Score=22.71 Aligned_cols=25 Identities=16% Similarity=0.254 Sum_probs=16.8
Q ss_pred cccCCCCCccCCChhHHHhhhhhhcCCCCCCCCCCCCCCC
Q psy7353 82 VFPCPVCGKEFSRPDKMKNHMKTVHDCFMPATTPQGQRGQ 121 (139)
Q Consensus 82 ~~~C~~C~~~f~~~~~l~~H~~~~h~~~~~~~C~~C~~~f 121 (139)
-|.|+.|...|... |-.|+.|+-.|
T Consensus 255 GyvCs~Clsi~C~~---------------p~~C~~Cgt~f 279 (279)
T TIGR00627 255 GFVCSVCLSVLCQY---------------TPICKTCKTAF 279 (279)
T ss_pred eEECCCccCCcCCC---------------CCCCCCCCCCC
Confidence 38888887766432 12788888765
No 189
>COG3091 SprT Zn-dependent metalloprotease, SprT family [General function prediction only]
Probab=29.17 E-value=34 Score=21.67 Aligned_cols=34 Identities=12% Similarity=0.203 Sum_probs=20.6
Q ss_pred CcccCCCCCccCCChhHHHhhhhhhcCCCCCCCCCCCCCC
Q psy7353 81 KVFPCPVCGKEFSRPDKMKNHMKTVHDCFMPATTPQGQRG 120 (139)
Q Consensus 81 ~~~~C~~C~~~f~~~~~l~~H~~~~h~~~~~~~C~~C~~~ 120 (139)
-+|.|. |+..|... .+|-.. -.|+ .|.|..|+..
T Consensus 116 ~~Y~C~-C~q~~l~~---RRhn~~-~~g~-~YrC~~C~gk 149 (156)
T COG3091 116 YPYRCQ-CQQHYLRI---RRHNTV-RRGE-VYRCGKCGGK 149 (156)
T ss_pred eeEEee-cCCccchh---hhcccc-cccc-eEEeccCCce
Confidence 468888 88665433 233332 3445 7888888754
No 190
>PF07535 zf-DBF: DBF zinc finger; InterPro: IPR006572 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. In eukaryotes, initiation of DNA replication requires the assembly of pre-replication complexes (pre-RCs) on chromatin during the G1 phase. In the S phase, pre-RCs are activated by two protein kinases, Cdk2 and Cdc7, which results in the loading of replication factors and the unwinding of replication origins by the MCM helicase complex []. Cdc7 is a serine/threonine kinase that is conserved from yeast to human. It is regulated by its association with a regulatory subunit, the Dbf4 protein. This complex is often referred to as DDK (Dbf4-dependent kinase) []. DBF4 contains an N-terminal BRCT domain and a C-terminal conserved region that could potentially coordinate one zinc atom, the DBF4-type zinc finger. This entry represents the zinc finger, which is important for the interaction with Cdc7 [, ]. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding
Probab=28.78 E-value=34 Score=17.10 Aligned_cols=20 Identities=15% Similarity=0.102 Sum_probs=12.3
Q ss_pred CCCCCCCCCCCCCCcchhccccc
Q psy7353 111 PATTPQGQRGQRASPVIDFHKDS 133 (139)
Q Consensus 111 ~~~C~~C~~~f~~~~~l~~H~~~ 133 (139)
+=.|+.|...|. +|..|+.+
T Consensus 5 ~GYCE~C~~ky~---~l~~Hi~s 24 (49)
T PF07535_consen 5 PGYCENCRVKYD---DLEEHIQS 24 (49)
T ss_pred CccCccccchhh---hHHHHhCC
Confidence 345777777665 36666654
No 191
>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=28.66 E-value=16 Score=22.96 Aligned_cols=9 Identities=33% Similarity=1.025 Sum_probs=5.4
Q ss_pred eeecCCCCC
Q psy7353 54 VFPCPVCGK 62 (139)
Q Consensus 54 ~~~c~~C~~ 62 (139)
.+.|..|+.
T Consensus 112 ~l~C~~Cg~ 120 (146)
T PF07295_consen 112 TLVCENCGH 120 (146)
T ss_pred eEecccCCC
Confidence 456666664
No 192
>PF14787 zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB: 1CL4_A 1DSV_A.
Probab=28.32 E-value=46 Score=15.49 Aligned_cols=15 Identities=13% Similarity=0.147 Sum_probs=7.6
Q ss_pred CCCCCCCCCCCCcch
Q psy7353 113 TTPQGQRGQRASPVI 127 (139)
Q Consensus 113 ~C~~C~~~f~~~~~l 127 (139)
.|+.|+++|-...+-
T Consensus 4 ~CprC~kg~Hwa~~C 18 (36)
T PF14787_consen 4 LCPRCGKGFHWASEC 18 (36)
T ss_dssp C-TTTSSSCS-TTT-
T ss_pred cCcccCCCcchhhhh
Confidence 466777776655443
No 193
>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=27.87 E-value=31 Score=16.06 Aligned_cols=10 Identities=40% Similarity=1.129 Sum_probs=5.4
Q ss_pred cceecCCCCC
Q psy7353 17 GIYKCMECAK 26 (139)
Q Consensus 17 ~~~~C~~c~~ 26 (139)
..|+|..||+
T Consensus 5 ~~YkC~~CGn 14 (36)
T PF06397_consen 5 EFYKCEHCGN 14 (36)
T ss_dssp EEEE-TTT--
T ss_pred cEEEccCCCC
Confidence 4688888887
No 194
>PF13821 DUF4187: Domain of unknown function (DUF4187)
Probab=27.43 E-value=34 Score=17.55 Aligned_cols=18 Identities=17% Similarity=0.525 Sum_probs=9.5
Q ss_pred cccCCCCCccCCChhHHH
Q psy7353 82 VFPCPVCGKEFSRPDKMK 99 (139)
Q Consensus 82 ~~~C~~C~~~f~~~~~l~ 99 (139)
.+-|--||..|.+...|.
T Consensus 27 ~~YC~~Cg~~Y~d~~dL~ 44 (55)
T PF13821_consen 27 HNYCFWCGTKYDDEEDLE 44 (55)
T ss_pred CceeeeeCCccCCHHHHH
Confidence 344555555555555543
No 195
>PTZ00448 hypothetical protein; Provisional
Probab=27.06 E-value=25 Score=25.69 Aligned_cols=23 Identities=9% Similarity=-0.133 Sum_probs=19.4
Q ss_pred CCCCCCCCCCCCCCcchhccccc
Q psy7353 111 PATTPQGQRGQRASPVIDFHKDS 133 (139)
Q Consensus 111 ~~~C~~C~~~f~~~~~l~~H~~~ 133 (139)
.|.|..|+..|.+....+.|.++
T Consensus 314 ~~tC~~C~v~F~~~~~qR~H~KS 336 (373)
T PTZ00448 314 MLLCRKCNIQLMDHNAFKQHYRS 336 (373)
T ss_pred CccccccccccCCHHHHHHHhhh
Confidence 68899999999888888888665
No 196
>PRK12496 hypothetical protein; Provisional
Probab=26.53 E-value=63 Score=20.67 Aligned_cols=11 Identities=27% Similarity=0.691 Sum_probs=8.0
Q ss_pred ccCCCCCccCC
Q psy7353 83 FPCPVCGKEFS 93 (139)
Q Consensus 83 ~~C~~C~~~f~ 93 (139)
|.|..|++.|.
T Consensus 128 ~~C~gC~~~~~ 138 (164)
T PRK12496 128 KVCKGCKKKYP 138 (164)
T ss_pred EECCCCCcccc
Confidence 67888887663
No 197
>smart00586 ZnF_DBF Zinc finger in DBF-like proteins.
Probab=26.40 E-value=22 Score=17.81 Aligned_cols=21 Identities=14% Similarity=0.063 Sum_probs=12.0
Q ss_pred CCCCCCCCCCCCCCCcchhccccc
Q psy7353 110 MPATTPQGQRGQRASPVIDFHKDS 133 (139)
Q Consensus 110 ~~~~C~~C~~~f~~~~~l~~H~~~ 133 (139)
+|=.|+.|...|. .|..|+.+
T Consensus 4 k~GYCE~Cr~kfd---~l~~Hi~s 24 (49)
T smart00586 4 KPGYCENCREKYD---DLETHLLS 24 (49)
T ss_pred CCcccccHhHHHh---hHHHHhcc
Confidence 4446777776654 35555543
No 198
>PF04423 Rad50_zn_hook: Rad50 zinc hook motif; InterPro: IPR007517 The Mre11 complex (Mre11 Rad50 Nbs1) is central to chromosomal maintenance and functions in homologous recombination, telomere maintenance and sister chromatid association. The Rad50 coiled-coil region contains a dimer interface at the apex of the coiled coils in which pairs of conserved Cys-X-X-Cys motifs form interlocking hooks that bind one Zn ion. This alignment includes the zinc hook motif and a short stretch of coiled-coil on either side.; GO: 0004518 nuclease activity, 0005524 ATP binding, 0008270 zinc ion binding, 0006281 DNA repair; PDB: 1L8D_B.
Probab=25.96 E-value=20 Score=18.02 Aligned_cols=10 Identities=20% Similarity=0.109 Sum_probs=3.6
Q ss_pred CCCCCCCCCC
Q psy7353 113 TTPQGQRGQR 122 (139)
Q Consensus 113 ~C~~C~~~f~ 122 (139)
.||.|+..|.
T Consensus 22 ~CPlC~r~l~ 31 (54)
T PF04423_consen 22 CCPLCGRPLD 31 (54)
T ss_dssp E-TTT--EE-
T ss_pred cCCCCCCCCC
Confidence 5666666553
No 199
>PRK06260 threonine synthase; Validated
Probab=25.69 E-value=54 Score=24.12 Aligned_cols=12 Identities=33% Similarity=1.054 Sum_probs=7.6
Q ss_pred CCcccCCCCCcc
Q psy7353 80 RKVFPCPVCGKE 91 (139)
Q Consensus 80 ~~~~~C~~C~~~ 91 (139)
+..+.|+.|+..
T Consensus 17 ~~~~~Cp~cg~~ 28 (397)
T PRK06260 17 EIIYTCPECGGL 28 (397)
T ss_pred CccccCCCCCCe
Confidence 345678778654
No 200
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=25.60 E-value=19 Score=16.46 Aligned_cols=11 Identities=45% Similarity=1.153 Sum_probs=6.4
Q ss_pred CceeecCCCCC
Q psy7353 52 RKVFPCPVCGK 62 (139)
Q Consensus 52 ~~~~~c~~C~~ 62 (139)
...+.|+.|+.
T Consensus 20 r~R~vC~~Cg~ 30 (34)
T PF14803_consen 20 RERLVCPACGF 30 (34)
T ss_dssp S-EEEETTTTE
T ss_pred ccceECCCCCC
Confidence 44566777764
No 201
>KOG4727|consensus
Probab=25.59 E-value=34 Score=22.15 Aligned_cols=22 Identities=18% Similarity=0.427 Sum_probs=19.4
Q ss_pred cccCCCCCccCCChhHHHhhhh
Q psy7353 82 VFPCPVCGKEFSRPDKMKNHMK 103 (139)
Q Consensus 82 ~~~C~~C~~~f~~~~~l~~H~~ 103 (139)
-|.|.+|+-.+.+..++..|+.
T Consensus 75 GyyCdVCdcvvKDSinflDHiN 96 (193)
T KOG4727|consen 75 GYYCDVCDCVVKDSINFLDHIN 96 (193)
T ss_pred ceeeeecceeehhhHHHHHHhc
Confidence 4889999999999999998875
No 202
>PF15135 UPF0515: Uncharacterised protein UPF0515
Probab=25.50 E-value=80 Score=21.88 Aligned_cols=10 Identities=30% Similarity=1.022 Sum_probs=6.5
Q ss_pred CceeecCCCC
Q psy7353 52 RKVFPCPVCG 61 (139)
Q Consensus 52 ~~~~~c~~C~ 61 (139)
.+.|.|..|.
T Consensus 110 drqFaC~~Cd 119 (278)
T PF15135_consen 110 DRQFACSSCD 119 (278)
T ss_pred ceeeeccccc
Confidence 3567777775
No 203
>PF14369 zf-RING_3: zinc-finger
Probab=25.47 E-value=37 Score=15.56 Aligned_cols=10 Identities=20% Similarity=0.315 Sum_probs=6.9
Q ss_pred CCCCCCCCCC
Q psy7353 113 TTPQGQRGQR 122 (139)
Q Consensus 113 ~C~~C~~~f~ 122 (139)
.|+.|+-+|.
T Consensus 23 ~CP~C~~gFv 32 (35)
T PF14369_consen 23 ACPRCHGGFV 32 (35)
T ss_pred CCcCCCCcEe
Confidence 5777777764
No 204
>PRK14811 formamidopyrimidine-DNA glycosylase; Provisional
Probab=25.23 E-value=45 Score=23.17 Aligned_cols=32 Identities=28% Similarity=0.418 Sum_probs=19.7
Q ss_pred cCCCCCccCCChhHHHhhhhhhcCCCCCCCCCCCCCCCCCC
Q psy7353 84 PCPVCGKEFSRPDKMKNHMKTVHDCFMPATTPQGQRGQRAS 124 (139)
Q Consensus 84 ~C~~C~~~f~~~~~l~~H~~~~h~~~~~~~C~~C~~~f~~~ 124 (139)
.|+.||..... ....+-..|.|+.|+..+..+
T Consensus 237 pC~~Cg~~I~~---------~~~~gR~ty~Cp~CQ~~~~~~ 268 (269)
T PRK14811 237 PCPRCGTPIEK---------IVVGGRGTHFCPQCQPLRPLR 268 (269)
T ss_pred CCCcCCCeeEE---------EEECCCCcEECCCCcCCCCCC
Confidence 57778744211 113445568999999876543
No 205
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=24.82 E-value=40 Score=17.31 Aligned_cols=14 Identities=7% Similarity=0.024 Sum_probs=8.3
Q ss_pred CCCCCCCCCCCCcc
Q psy7353 113 TTPQGQRGQRASPV 126 (139)
Q Consensus 113 ~C~~C~~~f~~~~~ 126 (139)
.|+.|+..|....+
T Consensus 7 ~C~~Cg~~~~~~dD 20 (54)
T PF14446_consen 7 KCPVCGKKFKDGDD 20 (54)
T ss_pred cChhhCCcccCCCC
Confidence 56667766654433
No 206
>smart00731 SprT SprT homologues. Predicted to have roles in transcription elongation. Contains a conserved HExxH motif, indicating a metalloprotease function.
Probab=24.76 E-value=35 Score=21.18 Aligned_cols=32 Identities=9% Similarity=0.224 Sum_probs=17.4
Q ss_pred cccCCCCCccCCChhHHHhhhhhhcCCCCCCCCCCCCCCC
Q psy7353 82 VFPCPVCGKEFSRPDKMKNHMKTVHDCFMPATTPQGQRGQ 121 (139)
Q Consensus 82 ~~~C~~C~~~f~~~~~l~~H~~~~h~~~~~~~C~~C~~~f 121 (139)
.|.|..|+..+. ++.+ +.....|.|..|+-.+
T Consensus 112 ~y~C~~C~~~~~------~~rr--~~~~~~y~C~~C~g~l 143 (146)
T smart00731 112 PYRCTGCGQRYL------RVRR--SNNVSRYRCGKCGGKL 143 (146)
T ss_pred EEECCCCCCCCc------eEcc--ccCcceEEcCCCCCEE
Confidence 567777776543 2222 1222457777777654
No 207
>PF10537 WAC_Acf1_DNA_bd: ATP-utilising chromatin assembly and remodelling N-terminal; InterPro: IPR013136 ACF (for ATP-utilising chromatin assembly and remodeling factor) is a chromatin-remodeling complex that catalyzes the ATP-dependent assembly of periodic nucleosome arrays. This reaction utilises the energy of ATP hydrolysis by ISWI, the smaller of the two subunits of ACF. Acf1, the large subunit of ACF, is essential for the full activity of the complex. The WAC (WSTF/Acf1/cbp146) domain is an ~110-residue module present at the N-termini of Acf1-related proteins in a variety of organisms. It is found in association with other domains such as the bromodomain, the PHD-type zinc finger, DDT or WAKS. The DNA-binding region of Acf1 includes the WAC domain, which is necessary for the efficient binding of ACF complex to DNA. It seems probable that the WAC domain will be involved in DNA binding in other related factors [, ]. Some proteins known to contain a WAC domain are the Drosophila melanogaster (Fruit fly) ATP-dependent chromatin assembly factor large subunit Acf1, human WSTF (Williams syndrome transcription factor), mouse cbp146, yeast imitation switch two complex protein 1 (ITC1 or YGL133w), and yeast protein YPL216w.
Probab=24.64 E-value=1.6e+02 Score=17.28 Aligned_cols=42 Identities=17% Similarity=0.416 Sum_probs=29.4
Q ss_pred cceecCCCCCcchhcccCCHHHHHHHHHHhccCCCCceeecCCCCCcCCCh
Q psy7353 17 GIYKCMECAKVDVIKTFKNKYSFQRHAFLYHEGCQRKVFPCPVCGKEFSRP 67 (139)
Q Consensus 17 ~~~~C~~c~~~~~~~~f~~~~~l~~h~~~~~~~~~~~~~~c~~C~~~~~~~ 67 (139)
..|.|+.-|. .|.+...+-..+.... .+-|.|...|+.-...
T Consensus 2 eVf~i~~T~E-----iF~dYe~Y~~R~~~y~----~~vwtC~~TGk~~LTy 43 (102)
T PF10537_consen 2 EVFYIPFTGE-----IFRDYEEYLKRMILYN----QRVWTCEITGKSNLTY 43 (102)
T ss_pred ceEEeCCCCc-----ccCCHHHHHHHHHHHh----CCeeEEecCCCCCCCH
Confidence 3577888887 8998887766655433 5678999888754444
No 208
>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 PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=23.68 E-value=53 Score=19.56 Aligned_cols=9 Identities=22% Similarity=0.538 Sum_probs=5.6
Q ss_pred ccCCCCCcc
Q psy7353 83 FPCPVCGKE 91 (139)
Q Consensus 83 ~~C~~C~~~ 91 (139)
+.|..|+..
T Consensus 71 ~~C~~Cg~~ 79 (114)
T PRK03681 71 CWCETCQQY 79 (114)
T ss_pred EEcccCCCe
Confidence 567777653
No 210
>KOG1842|consensus
Probab=23.61 E-value=41 Score=25.32 Aligned_cols=31 Identities=19% Similarity=0.462 Sum_probs=24.5
Q ss_pred CCCCceeecCCCCCcCCChHHHHHHHHHhcC
Q psy7353 49 GCQRKVFPCPVCGKEFSRPDKMKNHMKTGCQ 79 (139)
Q Consensus 49 ~~~~~~~~c~~C~~~~~~~~~l~~h~~~~~~ 79 (139)
+.....|.||+|...|.....|..|....+.
T Consensus 10 ~~i~egflCPiC~~dl~~~~~L~~H~d~eH~ 40 (505)
T KOG1842|consen 10 GEILEGFLCPICLLDLPNLSALNDHLDVEHF 40 (505)
T ss_pred chhhhcccCchHhhhhhhHHHHHHHHhhhcc
Confidence 3335678999999999999999999876554
No 211
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=23.55 E-value=45 Score=20.55 Aligned_cols=15 Identities=27% Similarity=0.722 Sum_probs=11.1
Q ss_pred cccCCCCCccCCChh
Q psy7353 82 VFPCPVCGKEFSRPD 96 (139)
Q Consensus 82 ~~~C~~C~~~f~~~~ 96 (139)
|..|..||..|.+.+
T Consensus 1 PH~Ct~Cg~~f~dgs 15 (131)
T PF09845_consen 1 PHQCTKCGRVFEDGS 15 (131)
T ss_pred CcccCcCCCCcCCCc
Confidence 457888888887665
No 212
>COG4391 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=23.52 E-value=28 Score=18.36 Aligned_cols=46 Identities=13% Similarity=0.055 Sum_probs=24.0
Q ss_pred HHHHhcCCCcccCCCCCccCCChhHHHhhhhhhcCCCCCCCCCCCCCCCCC
Q psy7353 73 HMKTGCQRKVFPCPVCGKEFSRPDKMKNHMKTVHDCFMPATTPQGQRGQRA 123 (139)
Q Consensus 73 h~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~~h~~~~~~~C~~C~~~f~~ 123 (139)
+...+.++.++.|+.=+..|..+.-+ +- -..+..-.|+.|+.+|+.
T Consensus 15 ~~~I~~~~~~l~C~g~~~p~~HPrV~---L~--mg~~gev~CPYC~t~y~l 60 (62)
T COG4391 15 HETIEIGDLPLMCPGPEPPNDHPRVF---LD--MGDEGEVVCPYCSTRYRL 60 (62)
T ss_pred ceEEEeCCeeEEcCCCCCCCCCCEEE---EE--cCCCCcEecCccccEEEe
Confidence 34455566777776544333322111 11 122334588889888764
No 213
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=23.40 E-value=46 Score=20.39 Aligned_cols=16 Identities=0% Similarity=-0.242 Sum_probs=11.0
Q ss_pred CCCCCCCCCCCCCCCC
Q psy7353 109 FMPATTPQGQRGQRAS 124 (139)
Q Consensus 109 ~~~~~C~~C~~~f~~~ 124 (139)
...|.|..|++.|+..
T Consensus 51 ~qRyrC~~C~~tf~~~ 66 (129)
T COG3677 51 HQRYKCKSCGSTFTVE 66 (129)
T ss_pred ccccccCCcCcceeee
Confidence 4457788888777654
No 214
>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=23.38 E-value=43 Score=16.57 Aligned_cols=10 Identities=10% Similarity=-0.127 Sum_probs=5.7
Q ss_pred CCCCCCCCCC
Q psy7353 111 PATTPQGQRG 120 (139)
Q Consensus 111 ~~~C~~C~~~ 120 (139)
-|.|+.|+..
T Consensus 34 ~w~CP~C~a~ 43 (47)
T PF00301_consen 34 DWVCPVCGAP 43 (47)
T ss_dssp T-B-TTTSSB
T ss_pred CCcCcCCCCc
Confidence 3888888764
No 215
>PLN02294 cytochrome c oxidase subunit Vb
Probab=23.06 E-value=45 Score=21.57 Aligned_cols=11 Identities=18% Similarity=0.709 Sum_probs=9.1
Q ss_pred CcceecCCCCC
Q psy7353 16 EGIYKCMECAK 26 (139)
Q Consensus 16 ~~~~~C~~c~~ 26 (139)
.++.+|++||.
T Consensus 139 Gkp~RCpeCG~ 149 (174)
T PLN02294 139 GKSFECPVCTQ 149 (174)
T ss_pred CCceeCCCCCC
Confidence 46888999997
No 216
>PF09963 DUF2197: Uncharacterized protein conserved in bacteria (DUF2197); InterPro: IPR019241 This family represents various hypothetical bacterial proteins with no known function.
Probab=23.04 E-value=19 Score=18.63 Aligned_cols=36 Identities=14% Similarity=0.393 Sum_probs=16.1
Q ss_pred ecCCCCCcCCChHHHHHHHH-HhcCCCcccCCCCCcc
Q psy7353 56 PCPVCGKEFSRPDKMKNHMK-TGCQRKVFPCPVCGKE 91 (139)
Q Consensus 56 ~c~~C~~~~~~~~~l~~h~~-~~~~~~~~~C~~C~~~ 91 (139)
.|..|++.+........-.+ .......|.|..|...
T Consensus 4 kC~lCdk~~~Id~~~~~aKrLrnrPi~tYmC~eC~~R 40 (56)
T PF09963_consen 4 KCILCDKKEEIDEDTPEAKRLRNRPIHTYMCDECKER 40 (56)
T ss_pred EEEecCCEEEeccCCHHHHHhhcCCCcceeChhHHHH
Confidence 56667654433322111111 2223345777777543
No 217
>PLN02748 tRNA dimethylallyltransferase
Probab=23.00 E-value=36 Score=25.85 Aligned_cols=25 Identities=12% Similarity=-0.020 Sum_probs=20.9
Q ss_pred CCCCCCCCCC-CCCCCcchhcccccc
Q psy7353 110 MPATTPQGQR-GQRASPVIDFHKDSV 134 (139)
Q Consensus 110 ~~~~C~~C~~-~f~~~~~l~~H~~~~ 134 (139)
+.|.|+.|+. .+.-...+..|++++
T Consensus 417 ~~~~Ce~C~~~~~~G~~eW~~Hlksr 442 (468)
T PLN02748 417 TQYVCEACGNKVLRGAHEWEQHKQGR 442 (468)
T ss_pred ccccccCCCCcccCCHHHHHHHhcch
Confidence 5688999997 788888899998764
No 218
>KOG1994|consensus
Probab=22.72 E-value=40 Score=22.93 Aligned_cols=24 Identities=17% Similarity=0.552 Sum_probs=20.1
Q ss_pred CCcccCCCCCccCCChhHHHhhhh
Q psy7353 80 RKVFPCPVCGKEFSRPDKMKNHMK 103 (139)
Q Consensus 80 ~~~~~C~~C~~~f~~~~~l~~H~~ 103 (139)
.-.|.|..||..|.+..+|..|-.
T Consensus 237 ~eh~YC~fCG~~y~~~edl~ehCP 260 (268)
T KOG1994|consen 237 SEHYYCFFCGIKYKDEEDLYEHCP 260 (268)
T ss_pred ccceEEEEeccccCCHHHHHHhCC
Confidence 456889999999999999988843
No 219
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=22.63 E-value=32 Score=24.39 Aligned_cols=32 Identities=19% Similarity=0.364 Sum_probs=18.4
Q ss_pred eecCCCCCcCCChHHHHHHHHHhcCCCcccCCCCCccCCCh
Q psy7353 55 FPCPVCGKEFSRPDKMKNHMKTGCQRKVFPCPVCGKEFSRP 95 (139)
Q Consensus 55 ~~c~~C~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~f~~~ 95 (139)
.+|+.|+..+.... | .+..+.|+.|+.-|.-.
T Consensus 39 ~kc~~C~~~~~~~~-l--------~~~~~vcp~c~~h~rlt 70 (296)
T CHL00174 39 VQCENCYGLNYKKF-L--------KSKMNICEQCGYHLKMS 70 (296)
T ss_pred eECCCccchhhHHH-H--------HHcCCCCCCCCCCcCCC
Confidence 35887875433221 1 12346888888766544
No 220
>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=21.63 E-value=50 Score=19.19 Aligned_cols=10 Identities=30% Similarity=0.740 Sum_probs=8.8
Q ss_pred cceecCCCCC
Q psy7353 17 GIYKCMECAK 26 (139)
Q Consensus 17 ~~~~C~~c~~ 26 (139)
.+.+|++||.
T Consensus 78 ~~~rC~eCG~ 87 (97)
T cd00924 78 KPKRCPECGH 87 (97)
T ss_pred CceeCCCCCc
Confidence 6889999997
No 221
>PF03145 Sina: Seven in absentia protein family; InterPro: IPR018121 The seven in absentia (sina) gene was first identified in Drosophila. The Drosophila Sina protein is essential for the determination of the R7 pathway in photoreceptor cell development: the loss of functional Sina results in the transformation of the R7 precursor cell to a non-neuronal cell type. The Sina protein contains an N-terminal RING finger domain C3HC4-type. Through this domain, Sina binds E2 ubiquitin-conjugating enzymes (UbcD1) Sina also interacts with Tramtrack (TTK88) via PHYL. Tramtrack is a transcriptional repressor that blocks photoreceptor determination, while PHYL down-regulates the activity of TTK88. In turn, the activity of PHYL requires the activation of the Sevenless receptor tyrosine kinase, a process essential for R7 determination. It is thought that Sina targets TTK88 for degradation, therefore promoting the R7 pathway. Murine and human homologues of Sina have also been identified. The human homologue Siah-1 [] also binds E2 enzymes (UbcH5) and through a series of physical interactions, targets beta-catenin for ubiquitin degradation. Siah-1 expression is enhanced by p53, itself promoted by DNA damage. Thus this pathway links DNA damage to beta-catenin degradation [, ]. Sina proteins, therefore, physically interact with a variety of proteins. The N-terminal RING finger domain that binds ubiquitin conjugating enzymes is a C3HC4-type, and does not form part of the alignment for this family. The remainder C-terminal part is involved in interactions with other proteins, and is included in this alignment. In addition to the Drosophila protein and mammalian homologues, whose similarity was noted previously, this family also includes putative homologues from Caenorhabditis elegans, Arabidopsis thaliana.; GO: 0006511 ubiquitin-dependent protein catabolic process, 0007275 multicellular organismal development, 0005634 nucleus; PDB: 2A25_A 1K2F_B 2AN6_C.
Probab=21.47 E-value=24 Score=23.08 Aligned_cols=37 Identities=16% Similarity=0.457 Sum_probs=16.2
Q ss_pred HHHHHHHHhcCCCcccCCC----CCccCCChhHHHhhhhhhcC
Q psy7353 69 KMKNHMKTGCQRKVFPCPV----CGKEFSRPDKMKNHMKTVHD 107 (139)
Q Consensus 69 ~l~~h~~~~~~~~~~~C~~----C~~~f~~~~~l~~H~~~~h~ 107 (139)
....|.... .-+|+.|+. |+.. -....|..|....|.
T Consensus 32 ~~~~HE~~C-~~~p~~CP~~~~~C~~~-G~~~~l~~Hl~~~H~ 72 (198)
T PF03145_consen 32 EKREHEEEC-PFRPCSCPFPGSGCDWQ-GSYKELLDHLRDKHS 72 (198)
T ss_dssp GHHHHHHT--TTSEEE-SSSSTT---E-EECCCHHHHHHHHTT
T ss_pred ChhhHhccC-CCcCCcCCCCCCCcccc-CCHHHHHHHHHHHCC
Confidence 444555432 235666655 4321 123356677766564
No 222
>PF13878 zf-C2H2_3: zinc-finger of acetyl-transferase ESCO
Probab=21.42 E-value=43 Score=15.89 Aligned_cols=13 Identities=15% Similarity=0.000 Sum_probs=9.4
Q ss_pred CCCCCCCCCCCCC
Q psy7353 112 ATTPQGQRGQRAS 124 (139)
Q Consensus 112 ~~C~~C~~~f~~~ 124 (139)
-.|+.|+..|...
T Consensus 14 ~~C~~CgM~Y~~~ 26 (41)
T PF13878_consen 14 TTCPTCGMLYSPG 26 (41)
T ss_pred cCCCCCCCEECCC
Confidence 5889999766543
No 223
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=21.30 E-value=32 Score=20.09 Aligned_cols=9 Identities=67% Similarity=1.774 Sum_probs=5.1
Q ss_pred ceeecCCCC
Q psy7353 53 KVFPCPVCG 61 (139)
Q Consensus 53 ~~~~c~~C~ 61 (139)
..|.|+.|+
T Consensus 20 t~f~CP~Cg 28 (99)
T PRK14892 20 KIFECPRCG 28 (99)
T ss_pred cEeECCCCC
Confidence 345666665
No 224
>COG5188 PRP9 Splicing factor 3a, subunit 3 [RNA processing and modification]
Probab=21.19 E-value=40 Score=24.55 Aligned_cols=27 Identities=11% Similarity=-0.112 Sum_probs=22.1
Q ss_pred cCCCCCCCCCCCC-CCCCCCcchhcccc
Q psy7353 106 HDCFMPATTPQGQ-RGQRASPVIDFHKD 132 (139)
Q Consensus 106 h~~~~~~~C~~C~-~~f~~~~~l~~H~~ 132 (139)
|+-++.|.|.+|+ +.+.-+..+++|..
T Consensus 369 hgLd~ef~CEICgNyvy~GR~~FdrHF~ 396 (470)
T COG5188 369 HGLDIEFECEICGNYVYYGRDRFDRHFE 396 (470)
T ss_pred cCCCcceeeeecccccccchHHHHhhhh
Confidence 6667779999999 88888888888853
No 225
>PRK12860 transcriptional activator FlhC; Provisional
Probab=21.10 E-value=84 Score=20.75 Aligned_cols=46 Identities=20% Similarity=0.299 Sum_probs=26.3
Q ss_pred cCCChHHHHHHHHHhcCCCcccCCCCCccCCChhHHHhhhhhhcCCCCCCCCCCCC
Q psy7353 63 EFSRPDKMKNHMKTGCQRKVFPCPVCGKEFSRPDKMKNHMKTVHDCFMPATTPQGQ 118 (139)
Q Consensus 63 ~~~~~~~l~~h~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~~h~~~~~~~C~~C~ 118 (139)
.+...+.|....... .-....|..||-.|.... +.....|.|+.|.
T Consensus 116 s~tRAw~LvRf~~s~-~L~l~~C~~Cgg~fv~~~---------~e~~~~f~CplC~ 161 (189)
T PRK12860 116 DLTRAWTLVRFFDAG-MLQLARCCRCGGKFVTHA---------HDLRHNFVCGLCQ 161 (189)
T ss_pred cHHHHHHHHHHhcCC-CeeeccCCCCCCCeeccc---------cccCCCCcCCCCC
Confidence 344555555544422 123467888988776332 1222368999987
No 226
>COG4338 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=20.92 E-value=36 Score=16.97 Aligned_cols=16 Identities=44% Similarity=0.866 Sum_probs=9.6
Q ss_pred cCCCCCccCCChhHHH
Q psy7353 84 PCPVCGKEFSRPDKMK 99 (139)
Q Consensus 84 ~C~~C~~~f~~~~~l~ 99 (139)
.|++|+.-|++...+.
T Consensus 14 ICpvCqRPFsWRkKW~ 29 (54)
T COG4338 14 ICPVCQRPFSWRKKWA 29 (54)
T ss_pred hhhhhcCchHHHHHHH
Confidence 4667777776654443
No 227
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=20.73 E-value=20 Score=21.45 Aligned_cols=11 Identities=9% Similarity=-0.142 Sum_probs=8.7
Q ss_pred CCCCCCCCCCC
Q psy7353 112 ATTPQGQRGQR 122 (139)
Q Consensus 112 ~~C~~C~~~f~ 122 (139)
|.|..|+..++
T Consensus 101 y~C~~Cg~~wr 111 (113)
T COG1594 101 YKCTRCGYRWR 111 (113)
T ss_pred EEecccCCEee
Confidence 88888888765
No 228
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=20.71 E-value=41 Score=24.08 Aligned_cols=23 Identities=4% Similarity=-0.191 Sum_probs=15.7
Q ss_pred CCCCCCCCCCCCCCCcchhcccc
Q psy7353 110 MPATTPQGQRGQRASPVIDFHKD 132 (139)
Q Consensus 110 ~~~~C~~C~~~f~~~~~l~~H~~ 132 (139)
..|+|+.|...|-...+.--|..
T Consensus 387 ~rY~Ce~CK~~FC~dCdvfiHe~ 409 (421)
T COG5151 387 GRYQCELCKSTFCSDCDVFIHET 409 (421)
T ss_pred cceechhhhhhhhhhhHHHHHHH
Confidence 45888888887776666555544
No 229
>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=20.35 E-value=1e+02 Score=15.21 Aligned_cols=12 Identities=33% Similarity=0.894 Sum_probs=6.2
Q ss_pred ccCCCCCccCCC
Q psy7353 83 FPCPVCGKEFSR 94 (139)
Q Consensus 83 ~~C~~C~~~f~~ 94 (139)
..|..||..|-.
T Consensus 19 ~~Cr~Cg~~~C~ 30 (57)
T cd00065 19 HHCRNCGRIFCS 30 (57)
T ss_pred cccCcCcCCcCh
Confidence 445555555443
No 230
>TIGR00515 accD acetyl-CoA carboxylase, carboxyl transferase, beta subunit. The enzyme acetyl-CoA carboxylase contains a biotin carboxyl carrier protein or domain, a biotin carboxylase, and a carboxyl transferase. This model represents the beta chain of the carboxyl transferase for cases in which the architecture of the protein is as in E. coli, in which the carboxyltransferase portion consists of two non-identical subnits, alpha and beta.
Probab=20.16 E-value=38 Score=23.85 Aligned_cols=32 Identities=25% Similarity=0.718 Sum_probs=19.1
Q ss_pred eecCCCCCcCCChHHHHHHHHHhcCCCcccCCCCCccCCCh
Q psy7353 55 FPCPVCGKEFSRPDKMKNHMKTGCQRKVFPCPVCGKEFSRP 95 (139)
Q Consensus 55 ~~c~~C~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~f~~~ 95 (139)
..|+.|+..+.... |. ...+.|+.|+.-|.-.
T Consensus 27 ~~c~~c~~~~~~~~-l~--------~~~~vc~~c~~h~rl~ 58 (285)
T TIGR00515 27 TKCPKCGQVLYTKE-LE--------RNLEVCPKCDHHMRMD 58 (285)
T ss_pred eECCCCcchhhHHH-HH--------hhCCCCCCCCCcCcCC
Confidence 46888876533322 11 2346899999876544
No 231
>PF08271 TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013137 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIB (TFIIB). In eukaryotes the initiation of transcription of protein encoding genes by the polymerase II complexe (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least seven different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, and -IIH []. TFIIB and TFIID are responsible for promoter recognition and interaction with pol II; together with Pol II, they form a minimal initiation complex capable of transcription under certain conditions. The TATA box of a Pol II promoter is bound in the initiation complex by the TBP subunit of TFIID, which bends the DNA around the C-terminal domain of TFIIB whereas the N-terminal zinc finger of TFIIB interacts with Pol II [, ]. The TFIIB zinc finger adopts a zinc ribbon fold characterised by two beta-hairpins forming two structurally similar zinc-binding sub-sites []. The zinc finger contacts the rbp1 subunit of Pol II through its dock domain, a conserved region of about 70 amino acids located close to the polymerase active site []. In the Pol II complex this surface is located near the RNA exit groove. Interestingly this sequence is best conserved in the three polymerases that utilise a TFIIB-like general transcription factor (Pol II, Pol III, and archaeal RNA polymerase) but not in Pol I []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1VD4_A 1PFT_A 3K1F_M 3K7A_M 1RO4_A 1RLY_A 1DL6_A.
Probab=20.01 E-value=56 Score=15.47 Aligned_cols=9 Identities=11% Similarity=0.110 Sum_probs=5.4
Q ss_pred CCCCCCCCC
Q psy7353 112 ATTPQGQRG 120 (139)
Q Consensus 112 ~~C~~C~~~ 120 (139)
|.|+.|+..
T Consensus 1 m~Cp~Cg~~ 9 (43)
T PF08271_consen 1 MKCPNCGSK 9 (43)
T ss_dssp ESBTTTSSS
T ss_pred CCCcCCcCC
Confidence 456666654
Done!