Query psy12196
Match_columns 150
No_of_seqs 128 out of 1347
Neff 11.7
Searched_HMMs 46136
Date Fri Aug 16 21:17:26 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy12196.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/12196hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2462|consensus 100.0 4.5E-36 9.7E-41 185.5 5.6 138 1-141 131-269 (279)
2 KOG2462|consensus 100.0 2.8E-29 6.2E-34 155.5 5.7 116 29-148 129-248 (279)
3 KOG3608|consensus 99.8 8.9E-21 1.9E-25 121.7 7.1 105 3-108 210-315 (467)
4 KOG3608|consensus 99.8 5.5E-20 1.2E-24 118.1 8.1 139 1-144 238-381 (467)
5 KOG1074|consensus 99.8 9.2E-22 2E-26 137.6 -0.0 53 1-55 354-406 (958)
6 KOG3576|consensus 99.8 5E-20 1.1E-24 110.0 3.8 116 28-144 115-241 (267)
7 KOG1074|consensus 99.8 5.9E-20 1.3E-24 128.8 2.3 77 2-81 607-692 (958)
8 KOG3623|consensus 99.7 2.1E-18 4.5E-23 119.8 3.0 105 2-106 212-330 (1007)
9 KOG3623|consensus 99.7 3.1E-17 6.6E-22 114.2 2.2 79 55-135 892-970 (1007)
10 KOG3576|consensus 99.7 2.2E-17 4.9E-22 98.8 1.1 85 56-142 116-200 (267)
11 PLN03086 PRLI-interacting fact 99.4 9.4E-13 2E-17 91.5 6.2 104 30-141 453-566 (567)
12 PHA00733 hypothetical protein 99.4 7.9E-13 1.7E-17 75.9 3.6 84 53-140 36-124 (128)
13 PHA00733 hypothetical protein 99.2 4.4E-11 9.5E-16 68.8 3.9 82 27-110 37-124 (128)
14 PLN03086 PRLI-interacting fact 99.1 1.1E-10 2.3E-15 81.5 5.5 124 3-147 410-545 (567)
15 PHA02768 hypothetical protein; 99.1 2.5E-11 5.3E-16 58.3 1.3 42 86-131 6-47 (55)
16 PHA02768 hypothetical protein; 99.1 3.8E-11 8.2E-16 57.7 1.8 44 57-102 5-48 (55)
17 PHA00616 hypothetical protein 99.0 1.4E-10 3.1E-15 53.0 2.2 32 115-146 1-32 (44)
18 KOG3993|consensus 98.9 3.1E-10 6.6E-15 75.5 -0.1 78 1-81 268-380 (500)
19 PF13465 zf-H2C2_2: Zinc-finge 98.8 2E-09 4.2E-14 44.4 1.7 24 73-96 2-25 (26)
20 PF05605 zf-Di19: Drought indu 98.8 2.5E-08 5.4E-13 48.8 4.4 53 85-140 2-54 (54)
21 PF13465 zf-H2C2_2: Zinc-finge 98.7 4.6E-09 1E-13 43.3 1.0 26 100-127 1-26 (26)
22 KOG3993|consensus 98.7 1.2E-08 2.5E-13 68.2 2.5 107 31-139 268-380 (500)
23 PF05605 zf-Di19: Drought indu 98.6 7.7E-08 1.7E-12 47.0 4.3 48 1-51 3-50 (54)
24 PHA00616 hypothetical protein 98.6 1.7E-08 3.7E-13 46.3 1.7 32 57-88 1-32 (44)
25 PHA00732 hypothetical protein 98.6 2.8E-08 6.1E-13 52.2 1.8 46 57-108 1-47 (79)
26 PHA00732 hypothetical protein 98.5 1.6E-07 3.4E-12 49.4 2.7 37 31-68 2-38 (79)
27 PF00096 zf-C2H2: Zinc finger, 98.4 9.1E-08 2E-12 38.2 0.9 23 116-138 1-23 (23)
28 PF13894 zf-C2H2_4: C2H2-type 98.3 3.6E-07 7.7E-12 36.8 1.4 24 116-139 1-24 (24)
29 PF00096 zf-C2H2: Zinc finger, 98.2 7.4E-07 1.6E-11 35.5 1.5 22 1-22 1-22 (23)
30 PF12756 zf-C2H2_2: C2H2 type 98.2 1.2E-06 2.6E-11 48.4 2.3 73 2-80 1-73 (100)
31 PF13894 zf-C2H2_4: C2H2-type 98.1 2E-06 4.3E-11 34.5 1.7 24 1-24 1-24 (24)
32 PF13912 zf-C2H2_6: C2H2-type 98.1 6.7E-07 1.4E-11 37.1 -0.0 25 115-139 1-25 (27)
33 PF09237 GAGA: GAGA factor; I 98.0 3.5E-06 7.6E-11 39.5 2.0 31 114-144 23-53 (54)
34 PF12756 zf-C2H2_2: C2H2 type 98.0 2.8E-06 6E-11 47.0 1.3 73 59-138 1-73 (100)
35 smart00355 ZnF_C2H2 zinc finge 97.8 2.6E-05 5.6E-10 31.6 2.2 23 116-138 1-23 (26)
36 COG5189 SFP1 Putative transcri 97.7 1.1E-05 2.3E-10 52.7 0.7 69 55-135 347-418 (423)
37 PF13909 zf-H2C2_5: C2H2-type 97.7 2.1E-05 4.5E-10 31.5 1.2 24 116-140 1-24 (24)
38 PF13912 zf-C2H2_6: C2H2-type 97.7 3.2E-05 6.8E-10 31.9 1.5 19 59-77 3-21 (27)
39 COG5189 SFP1 Putative transcri 97.6 2.6E-05 5.6E-10 50.9 0.9 25 115-139 349-375 (423)
40 smart00355 ZnF_C2H2 zinc finge 97.6 0.00012 2.5E-09 29.6 2.6 22 1-22 1-22 (26)
41 KOG2231|consensus 97.4 0.00063 1.4E-08 49.3 6.3 134 2-144 101-272 (669)
42 PF12874 zf-met: Zinc-finger o 97.4 3.8E-05 8.3E-10 31.1 0.1 23 116-138 1-23 (25)
43 PF13909 zf-H2C2_5: C2H2-type 97.4 0.00017 3.6E-09 28.8 1.7 23 1-24 1-23 (24)
44 PF09237 GAGA: GAGA factor; I 97.3 0.00029 6.3E-09 33.2 2.5 30 56-85 23-52 (54)
45 PF12171 zf-C2H2_jaz: Zinc-fin 96.9 8.8E-05 1.9E-09 30.6 -1.1 22 116-137 2-23 (27)
46 PRK04860 hypothetical protein; 96.9 0.00047 1E-08 41.4 1.5 38 85-128 119-156 (160)
47 PRK04860 hypothetical protein; 96.9 0.00036 7.8E-09 41.9 1.0 28 115-146 119-146 (160)
48 PF12874 zf-met: Zinc-finger o 96.8 0.0011 2.3E-08 26.6 1.6 19 60-78 3-21 (25)
49 PF12171 zf-C2H2_jaz: Zinc-fin 96.6 0.00082 1.8E-08 27.6 0.6 21 1-21 2-22 (27)
50 PF13913 zf-C2HC_2: zinc-finge 96.2 0.0069 1.5E-07 24.4 2.3 19 2-21 4-22 (25)
51 KOG1146|consensus 96.1 0.0015 3.2E-08 50.6 0.1 51 56-106 464-539 (1406)
52 smart00451 ZnF_U1 U1-like zinc 95.7 0.0052 1.1E-07 26.8 1.0 24 115-138 3-26 (35)
53 COG5236 Uncharacterized conser 95.6 0.022 4.8E-07 38.3 3.9 125 1-140 152-306 (493)
54 TIGR00622 ssl1 transcription f 95.5 0.02 4.3E-07 32.2 2.7 25 115-139 81-105 (112)
55 cd00350 rubredoxin_like Rubred 94.9 0.012 2.7E-07 25.4 0.7 9 115-123 17-25 (33)
56 KOG2482|consensus 94.8 0.11 2.3E-06 35.1 5.1 51 87-137 281-356 (423)
57 KOG1146|consensus 94.6 0.016 3.6E-07 45.3 1.2 58 81-138 461-541 (1406)
58 COG4049 Uncharacterized protei 94.5 0.029 6.4E-07 27.0 1.6 25 115-139 17-41 (65)
59 KOG2231|consensus 93.5 0.15 3.3E-06 37.7 4.2 98 38-139 122-236 (669)
60 KOG2893|consensus 93.1 0.03 6.4E-07 35.7 0.2 40 60-103 13-52 (341)
61 KOG4173|consensus 92.5 0.061 1.3E-06 33.5 1.0 79 58-139 80-170 (253)
62 KOG2482|consensus 92.1 0.3 6.5E-06 33.1 3.8 50 58-107 280-356 (423)
63 KOG2186|consensus 91.5 0.13 2.8E-06 33.2 1.6 45 1-50 4-48 (276)
64 KOG4173|consensus 91.2 0.13 2.9E-06 32.1 1.4 77 31-109 80-170 (253)
65 PF10571 UPF0547: Uncharacteri 91.1 0.13 2.8E-06 20.9 0.9 9 59-67 16-24 (26)
66 COG4049 Uncharacterized protei 91.0 0.16 3.4E-06 24.6 1.3 21 2-22 19-39 (65)
67 COG5048 FOG: Zn-finger [Genera 90.8 0.045 9.7E-07 38.1 -1.0 58 85-144 289-352 (467)
68 PF12907 zf-met2: Zinc-binding 90.2 0.24 5.2E-06 22.4 1.4 33 116-148 2-38 (40)
69 KOG2893|consensus 90.0 0.075 1.6E-06 33.9 -0.4 49 87-141 12-60 (341)
70 PF05443 ROS_MUCR: ROS/MUCR tr 89.9 0.21 4.6E-06 29.2 1.4 26 115-143 72-97 (132)
71 PF09538 FYDLN_acid: Protein o 89.7 0.26 5.7E-06 27.7 1.7 29 32-70 11-39 (108)
72 COG1592 Rubrerythrin [Energy p 89.6 0.2 4.4E-06 30.4 1.3 24 84-122 133-156 (166)
73 cd00729 rubredoxin_SM Rubredox 89.6 0.18 4E-06 21.9 0.8 10 86-95 3-12 (34)
74 PF15269 zf-C2H2_7: Zinc-finge 89.5 0.28 6E-06 22.6 1.4 29 110-138 15-43 (54)
75 TIGR02098 MJ0042_CXXC MJ0042 f 89.4 0.15 3.4E-06 22.6 0.5 32 32-67 4-35 (38)
76 COG2888 Predicted Zn-ribbon RN 89.4 0.18 4E-06 24.7 0.8 9 56-64 26-34 (61)
77 PF12013 DUF3505: Protein of u 89.2 1.1 2.3E-05 25.2 3.9 26 115-140 80-109 (109)
78 smart00734 ZnF_Rad18 Rad18-lik 88.7 0.36 7.9E-06 19.5 1.3 20 117-137 3-22 (26)
79 PF12013 DUF3505: Protein of u 88.7 0.3 6.6E-06 27.4 1.5 26 85-110 80-109 (109)
80 COG5236 Uncharacterized conser 88.7 1.4 3E-05 30.1 4.7 22 3-24 223-244 (493)
81 PHA00626 hypothetical protein 88.6 0.081 1.8E-06 25.6 -0.7 11 86-96 24-34 (59)
82 smart00614 ZnF_BED BED zinc fi 88.6 0.37 8.1E-06 22.9 1.6 24 116-139 19-47 (50)
83 PF09986 DUF2225: Uncharacteri 88.5 0.063 1.4E-06 34.2 -1.5 13 116-128 49-61 (214)
84 TIGR02605 CxxC_CxxC_SSSS putat 88.3 0.13 2.9E-06 24.6 -0.1 29 86-123 6-34 (52)
85 smart00659 RPOLCX RNA polymera 87.7 0.26 5.7E-06 22.8 0.7 11 86-96 3-13 (44)
86 TIGR00373 conserved hypothetic 87.2 0.76 1.6E-05 27.8 2.7 34 82-126 106-139 (158)
87 smart00834 CxxC_CXXC_SSSS Puta 86.9 0.18 3.9E-06 22.7 -0.1 29 86-123 6-34 (41)
88 COG5048 FOG: Zn-finger [Genera 86.3 0.16 3.5E-06 35.4 -0.6 56 57-112 289-350 (467)
89 PF13717 zinc_ribbon_4: zinc-r 86.1 0.75 1.6E-05 20.2 1.7 9 33-41 5-13 (36)
90 KOG2186|consensus 85.9 0.31 6.7E-06 31.5 0.5 49 31-81 4-52 (276)
91 PF04959 ARS2: Arsenite-resist 85.8 0.19 4E-06 32.0 -0.5 29 114-142 76-104 (214)
92 PF02892 zf-BED: BED zinc fing 85.8 0.34 7.3E-06 22.3 0.5 24 115-138 16-43 (45)
93 PRK06266 transcription initiat 83.9 1.1 2.4E-05 27.7 2.3 33 83-126 115-147 (178)
94 PF09723 Zn-ribbon_8: Zinc rib 83.9 0.39 8.4E-06 21.9 0.2 31 29-65 4-34 (42)
95 PRK14890 putative Zn-ribbon RN 83.1 0.51 1.1E-05 23.3 0.5 8 115-122 48-55 (59)
96 smart00531 TFIIE Transcription 82.1 1.3 2.9E-05 26.4 2.1 39 82-126 96-134 (147)
97 PF04780 DUF629: Protein of un 81.7 0.96 2.1E-05 32.3 1.6 29 115-143 57-85 (466)
98 PRK00398 rpoP DNA-directed RNA 81.1 1.2 2.5E-05 20.7 1.3 10 31-40 4-13 (46)
99 PF14353 CpXC: CpXC protein 81.1 2.4 5.2E-05 24.6 2.9 21 29-49 37-57 (128)
100 TIGR02300 FYDLN_acid conserved 80.6 1.3 2.9E-05 25.6 1.6 30 31-70 10-39 (129)
101 KOG2785|consensus 80.6 3.4 7.4E-05 28.7 3.7 24 115-138 68-91 (390)
102 KOG1842|consensus 79.7 1.3 2.9E-05 31.3 1.7 29 115-143 15-43 (505)
103 KOG4118|consensus 79.2 1.7 3.7E-05 21.8 1.6 31 115-145 38-68 (74)
104 KOG4167|consensus 79.1 0.66 1.4E-05 34.8 0.2 26 115-140 792-817 (907)
105 PRK00464 nrdR transcriptional 76.3 0.35 7.7E-06 29.1 -1.5 15 58-72 29-43 (154)
106 KOG3408|consensus 76.3 1.9 4.1E-05 24.7 1.4 24 115-138 57-80 (129)
107 PF09845 DUF2072: Zn-ribbon co 75.5 1.5 3.3E-05 25.5 0.9 11 32-42 3-13 (131)
108 COG2879 Uncharacterized small 75.2 3.5 7.7E-05 20.6 2.0 19 126-144 23-41 (65)
109 PF08274 PhnA_Zn_Ribbon: PhnA 74.9 1.1 2.3E-05 18.9 0.1 6 116-121 20-25 (30)
110 KOG1280|consensus 74.6 3.4 7.4E-05 28.3 2.4 37 1-37 80-116 (381)
111 PF00301 Rubredoxin: Rubredoxi 74.3 0.59 1.3E-05 22.0 -0.8 13 86-98 2-14 (47)
112 COG4957 Predicted transcriptio 74.3 1.1 2.4E-05 26.1 0.1 23 116-141 77-99 (148)
113 PF07754 DUF1610: Domain of un 74.2 1 2.3E-05 17.9 0.0 9 115-123 16-24 (24)
114 PF13451 zf-trcl: Probable zin 73.3 3.6 7.8E-05 19.6 1.7 17 84-100 3-19 (49)
115 KOG2807|consensus 72.5 5.8 0.00013 27.1 3.1 24 115-138 345-368 (378)
116 PF03604 DNA_RNApol_7kD: DNA d 72.0 3.9 8.5E-05 17.5 1.5 6 59-64 19-24 (32)
117 PRK09678 DNA-binding transcrip 71.6 1.2 2.5E-05 23.1 -0.1 41 1-45 2-44 (72)
118 COG3364 Zn-ribbon containing p 71.4 2.4 5.3E-05 23.4 1.0 11 32-42 4-14 (112)
119 PF04959 ARS2: Arsenite-resist 70.0 3.2 7E-05 26.6 1.5 25 1-25 78-102 (214)
120 KOG4167|consensus 69.7 1.2 2.7E-05 33.5 -0.4 24 1-24 793-816 (907)
121 COG5151 SSL1 RNA polymerase II 68.6 3.7 8.1E-05 27.7 1.6 24 115-138 388-411 (421)
122 KOG2785|consensus 67.7 10 0.00022 26.5 3.5 23 3-25 169-191 (390)
123 PF06524 NOA36: NOA36 protein; 67.7 1.9 4.1E-05 28.3 0.1 77 27-104 139-228 (314)
124 KOG2593|consensus 67.4 4.3 9.4E-05 28.7 1.8 36 82-122 125-160 (436)
125 COG1996 RPC10 DNA-directed RNA 67.2 3 6.4E-05 19.8 0.7 10 86-95 7-16 (49)
126 PRK03824 hypA hydrogenase nick 66.0 2.3 5.1E-05 25.0 0.3 13 85-97 70-82 (135)
127 COG1997 RPL43A Ribosomal prote 66.0 3.7 8.1E-05 22.1 1.0 11 86-96 54-64 (89)
128 PTZ00255 60S ribosomal protein 63.9 7.8 0.00017 21.1 2.0 14 55-68 52-65 (90)
129 COG0068 HypF Hydrogenase matur 63.1 0.66 1.4E-05 34.7 -2.7 57 58-123 124-181 (750)
130 PF13453 zf-TFIIB: Transcripti 62.8 6.9 0.00015 17.6 1.5 18 31-48 20-37 (41)
131 PF05290 Baculo_IE-1: Baculovi 61.4 5.6 0.00012 23.3 1.2 13 117-129 123-135 (140)
132 TIGR00280 L37a ribosomal prote 60.9 8.1 0.00018 21.1 1.7 29 31-68 36-64 (91)
133 PRK04023 DNA polymerase II lar 60.4 11 0.00024 30.1 2.9 10 115-124 663-672 (1121)
134 PF04780 DUF629: Protein of un 60.0 9 0.00019 27.7 2.3 24 2-25 59-82 (466)
135 PF07503 zf-HYPF: HypF finger; 59.3 3.1 6.6E-05 18.2 -0.0 12 56-67 20-31 (35)
136 COG0068 HypF Hydrogenase matur 59.2 1.7 3.6E-05 32.8 -1.3 28 33-65 154-181 (750)
137 PF01780 Ribosomal_L37ae: Ribo 58.7 4.4 9.6E-05 22.0 0.5 28 31-67 36-63 (90)
138 PRK03976 rpl37ae 50S ribosomal 57.4 9.8 0.00021 20.7 1.7 29 31-68 37-65 (90)
139 smart00440 ZnF_C2C2 C2C2 Zinc 56.8 0.89 1.9E-05 20.5 -2.0 12 115-126 28-39 (40)
140 KOG2593|consensus 56.6 8.7 0.00019 27.3 1.8 38 28-67 126-163 (436)
141 COG1198 PriA Primosomal protei 55.0 5.1 0.00011 30.7 0.5 10 115-124 475-484 (730)
142 PF13878 zf-C2H2_3: zinc-finge 54.8 20 0.00044 16.2 2.3 23 58-80 14-38 (41)
143 PF15135 UPF0515: Uncharacteri 54.5 7.3 0.00016 25.5 1.1 13 115-127 155-167 (278)
144 PF12760 Zn_Tnp_IS1595: Transp 52.9 13 0.00029 17.1 1.6 8 115-122 37-44 (46)
145 KOG2636|consensus 51.0 13 0.00028 26.7 1.9 21 115-135 401-422 (497)
146 TIGR00595 priA primosomal prot 49.8 7.8 0.00017 28.4 0.8 9 115-123 253-261 (505)
147 COG4530 Uncharacterized protei 49.7 6.4 0.00014 22.2 0.2 11 85-95 26-36 (129)
148 COG1675 TFA1 Transcription ini 49.6 28 0.0006 21.7 3.0 33 81-124 109-141 (176)
149 PRK00432 30S ribosomal protein 48.6 13 0.00027 17.8 1.1 9 86-94 38-46 (50)
150 KOG2272|consensus 48.3 11 0.00024 24.8 1.2 19 1-19 100-118 (332)
151 PLN03238 probable histone acet 48.2 15 0.00033 24.7 1.8 25 115-139 48-72 (290)
152 COG1655 Uncharacterized protei 44.9 4.8 0.0001 26.0 -0.7 6 87-92 64-69 (267)
153 KOG2907|consensus 44.3 9.6 0.00021 21.6 0.4 40 86-127 75-114 (116)
154 PF08790 zf-LYAR: LYAR-type C2 44.2 6.5 0.00014 16.2 -0.2 8 88-95 3-10 (28)
155 TIGR00100 hypA hydrogenase nic 44.1 8.7 0.00019 21.9 0.3 10 58-67 71-80 (115)
156 COG5112 UFD2 U1-like Zn-finger 43.5 12 0.00027 20.9 0.8 24 115-138 55-78 (126)
157 PLN02294 cytochrome c oxidase 42.6 12 0.00025 23.1 0.6 15 114-128 140-154 (174)
158 smart00154 ZnF_AN1 AN1-like Zi 42.6 9 0.00019 17.1 0.1 14 115-128 12-25 (39)
159 KOG1280|consensus 42.3 22 0.00047 24.7 1.9 38 85-122 79-116 (381)
160 cd00924 Cyt_c_Oxidase_Vb Cytoc 42.2 11 0.00024 20.9 0.5 13 115-127 79-91 (97)
161 PF08209 Sgf11: Sgf11 (transcr 42.2 21 0.00046 15.4 1.2 22 116-138 5-26 (33)
162 PF04423 Rad50_zn_hook: Rad50 41.9 8.2 0.00018 18.5 -0.1 21 117-137 22-44 (54)
163 KOG1842|consensus 41.4 20 0.00043 25.8 1.6 28 1-28 16-43 (505)
164 PF06397 Desulfoferrod_N: Desu 41.2 6.9 0.00015 17.3 -0.3 6 2-7 8-13 (36)
165 PRK05978 hypothetical protein; 41.2 7.6 0.00017 23.3 -0.3 10 59-68 54-63 (148)
166 PF10013 DUF2256: Uncharacteri 41.1 16 0.00034 16.8 0.8 16 87-102 10-25 (42)
167 COG1594 RPB9 DNA-directed RNA 41.0 4.1 8.9E-05 23.2 -1.4 40 86-127 73-112 (113)
168 PF02891 zf-MIZ: MIZ/SP-RING z 40.9 9.6 0.00021 18.1 0.1 9 115-123 41-49 (50)
169 PRK11823 DNA repair protein Ra 40.8 12 0.00026 27.0 0.6 8 86-93 8-15 (446)
170 PRK12380 hydrogenase nickel in 40.4 22 0.00049 20.2 1.5 10 58-67 71-80 (113)
171 TIGR00416 sms DNA repair prote 40.1 11 0.00025 27.2 0.4 9 86-94 8-16 (454)
172 PF07800 DUF1644: Protein of u 39.0 93 0.002 19.1 4.6 53 86-141 81-134 (162)
173 PRK14714 DNA polymerase II lar 37.7 42 0.00091 27.9 3.0 10 85-94 692-701 (1337)
174 COG3677 Transposase and inacti 37.3 13 0.00029 21.7 0.3 14 115-128 53-66 (129)
175 COG3357 Predicted transcriptio 37.2 13 0.00028 20.2 0.3 14 114-127 57-70 (97)
176 PRK14873 primosome assembly pr 36.7 16 0.00034 28.0 0.7 10 115-124 422-431 (665)
177 COG5152 Uncharacterized conser 35.7 33 0.00071 21.8 1.8 15 56-70 195-209 (259)
178 COG5188 PRP9 Splicing factor 3 35.7 22 0.00049 24.7 1.2 24 115-138 238-261 (470)
179 PF14255 Cys_rich_CPXG: Cystei 35.6 20 0.00043 17.3 0.7 8 2-9 2-9 (52)
180 TIGR01562 FdhE formate dehydro 35.5 28 0.00062 23.8 1.7 8 86-93 225-232 (305)
181 PF14311 DUF4379: Domain of un 35.2 36 0.00077 16.3 1.6 6 87-92 30-35 (55)
182 PF07975 C1_4: TFIIH C1-like d 35.0 16 0.00034 17.6 0.3 23 84-106 20-42 (51)
183 PLN00104 MYST -like histone ac 34.7 26 0.00057 25.4 1.5 25 115-139 198-222 (450)
184 PTZ00064 histone acetyltransfe 34.7 29 0.00063 25.5 1.7 25 115-139 280-304 (552)
185 PF11931 DUF3449: Domain of un 34.5 13 0.00028 23.5 0.0 21 115-135 101-122 (196)
186 PF04606 Ogr_Delta: Ogr/Delta- 34.3 6.2 0.00013 18.4 -1.1 12 3-14 2-13 (47)
187 COG1773 Rubredoxin [Energy pro 33.9 13 0.00027 18.2 -0.1 13 115-127 3-15 (55)
188 PF04328 DUF466: Protein of un 33.8 38 0.00083 17.2 1.6 16 129-144 26-41 (65)
189 PF07282 OrfB_Zn_ribbon: Putat 33.7 69 0.0015 16.0 2.8 31 32-71 30-60 (69)
190 PF01428 zf-AN1: AN1-like Zinc 33.5 19 0.00042 16.3 0.5 14 29-42 12-25 (43)
191 KOG0717|consensus 33.4 27 0.00058 25.4 1.3 21 2-22 294-314 (508)
192 PTZ00448 hypothetical protein; 32.8 38 0.00082 23.8 1.9 22 1-22 315-336 (373)
193 KOG2071|consensus 32.8 30 0.00065 25.9 1.5 26 114-139 417-442 (579)
194 TIGR00686 phnA alkylphosphonat 32.5 14 0.00031 20.8 -0.1 11 86-96 20-30 (109)
195 PTZ00448 hypothetical protein; 32.4 32 0.0007 24.2 1.5 23 115-137 314-336 (373)
196 PF11672 DUF3268: Protein of u 32.2 17 0.00037 20.3 0.2 9 57-65 2-10 (102)
197 PRK03681 hypA hydrogenase nick 31.9 36 0.00079 19.4 1.5 10 58-67 71-80 (114)
198 PF13824 zf-Mss51: Zinc-finger 31.3 45 0.00098 16.3 1.5 10 57-66 14-23 (55)
199 PF05495 zf-CHY: CHY zinc fing 31.3 3.4 7.5E-05 21.3 -2.5 13 85-97 41-53 (71)
200 PRK10220 hypothetical protein; 30.3 19 0.00041 20.4 0.2 10 86-95 21-30 (111)
201 KOG3002|consensus 30.0 1.5E+02 0.0032 20.5 4.2 73 2-79 82-161 (299)
202 PHA02998 RNA polymerase subuni 29.8 8.6 0.00019 23.8 -1.3 40 85-128 143-184 (195)
203 PF01363 FYVE: FYVE zinc finge 29.1 32 0.00069 17.3 0.9 8 33-40 12-19 (69)
204 PRK05580 primosome assembly pr 29.0 25 0.00055 27.0 0.7 8 115-122 421-428 (679)
205 COG4888 Uncharacterized Zn rib 29.0 3.1 6.6E-05 23.0 -2.9 8 31-38 23-30 (104)
206 PF10122 Mu-like_Com: Mu-like 28.7 11 0.00024 18.1 -0.8 31 85-125 4-34 (51)
207 cd00974 DSRD Desulforedoxin (D 28.5 20 0.00042 15.3 0.0 6 2-7 6-11 (34)
208 PF14369 zf-RING_3: zinc-finge 28.5 29 0.00063 15.1 0.6 8 3-10 24-31 (35)
209 PF07295 DUF1451: Protein of u 28.3 21 0.00046 21.5 0.2 31 83-125 110-140 (146)
210 cd00730 rubredoxin Rubredoxin; 28.2 29 0.00063 16.5 0.6 9 2-10 3-11 (50)
211 KOG2071|consensus 28.1 44 0.00096 25.1 1.7 26 56-81 417-442 (579)
212 PRK05452 anaerobic nitric oxid 28.0 16 0.00035 26.6 -0.4 39 84-123 424-466 (479)
213 PF01155 HypA: Hydrogenase exp 27.9 32 0.00069 19.6 0.8 11 31-41 71-81 (113)
214 PLN02748 tRNA dimethylallyltra 27.7 38 0.00083 24.8 1.4 25 114-138 417-442 (468)
215 PF01286 XPA_N: XPA protein N- 26.9 25 0.00054 15.3 0.2 12 117-128 5-16 (34)
216 PRK03564 formate dehydrogenase 26.5 29 0.00063 23.8 0.6 8 115-122 252-259 (309)
217 PF08271 TF_Zn_Ribbon: TFIIB z 26.5 25 0.00053 15.9 0.2 9 31-39 20-28 (43)
218 PRK00564 hypA hydrogenase nick 26.3 45 0.00098 19.1 1.3 13 57-69 71-83 (117)
219 TIGR00143 hypF [NiFe] hydrogen 26.3 4.1 8.8E-05 31.2 -3.7 61 32-98 70-131 (711)
220 PRK00762 hypA hydrogenase nick 25.9 22 0.00048 20.6 -0.0 6 117-122 94-99 (124)
221 COG4338 Uncharacterized protei 25.9 24 0.00051 16.7 0.1 16 87-102 14-29 (54)
222 COG1326 Uncharacterized archae 25.8 64 0.0014 20.5 1.9 10 58-67 31-40 (201)
223 PRK14892 putative transcriptio 25.7 19 0.00042 20.0 -0.3 10 86-95 43-52 (99)
224 COG4896 Uncharacterized protei 25.6 30 0.00064 17.3 0.4 6 86-91 32-37 (68)
225 PLN03239 histone acetyltransfe 25.3 56 0.0012 22.9 1.7 23 115-137 106-128 (351)
226 COG1571 Predicted DNA-binding 25.3 47 0.001 23.9 1.4 30 59-99 352-381 (421)
227 KOG4124|consensus 24.6 18 0.0004 25.1 -0.6 53 83-135 347-418 (442)
228 KOG0782|consensus 24.5 21 0.00045 26.7 -0.4 52 71-129 239-290 (1004)
229 PF10276 zf-CHCC: Zinc-finger 24.4 31 0.00068 15.6 0.3 11 30-40 29-39 (40)
230 cd00065 FYVE FYVE domain; Zinc 24.2 60 0.0013 15.4 1.3 6 60-65 21-26 (57)
231 PF14803 Nudix_N_2: Nudix N-te 23.8 23 0.0005 15.3 -0.2 9 115-123 22-30 (34)
232 KOG2747|consensus 23.8 55 0.0012 23.3 1.5 28 114-141 157-184 (396)
233 COG1656 Uncharacterized conser 23.4 71 0.0015 19.7 1.7 11 58-68 131-141 (165)
234 PF14787 zf-CCHC_5: GAG-polypr 23.3 28 0.00061 15.3 0.0 14 117-130 4-17 (36)
235 TIGR01206 lysW lysine biosynth 23.1 41 0.0009 16.4 0.6 8 2-9 4-11 (54)
236 KOG2923|consensus 22.9 73 0.0016 16.1 1.4 12 53-64 40-51 (67)
237 KOG1940|consensus 22.7 1.7E+02 0.0036 20.0 3.4 18 31-49 197-214 (276)
238 COG4391 Uncharacterized protei 22.4 38 0.00083 17.0 0.4 13 115-127 48-60 (62)
239 PF13821 DUF4187: Domain of un 22.4 48 0.001 16.2 0.8 17 3-19 30-46 (55)
240 PF03470 zf-XS: XS zinc finger 22.3 83 0.0018 14.6 1.5 8 13-20 14-21 (43)
241 PF13240 zinc_ribbon_2: zinc-r 22.1 29 0.00062 13.4 -0.0 6 3-8 2-7 (23)
242 PF12773 DZR: Double zinc ribb 21.8 46 0.00099 15.4 0.6 6 87-92 31-36 (50)
243 KOG1813|consensus 21.8 75 0.0016 21.7 1.7 15 56-70 240-254 (313)
244 PF12230 PRP21_like_P: Pre-mRN 21.8 30 0.00066 22.4 0.0 29 115-144 168-196 (229)
245 PRK01343 zinc-binding protein; 21.3 42 0.00091 16.6 0.4 12 115-126 9-20 (57)
246 TIGR03831 YgiT_finger YgiT-typ 21.3 42 0.00091 15.0 0.4 11 58-68 33-43 (46)
247 KOG3352|consensus 21.0 43 0.00093 20.3 0.5 13 115-127 133-145 (153)
248 PF09963 DUF2197: Uncharacteri 20.8 27 0.0006 17.2 -0.3 8 115-122 31-38 (56)
249 smart00064 FYVE Protein presen 20.3 69 0.0015 15.9 1.2 9 33-41 13-21 (68)
250 PF06220 zf-U1: U1 zinc finger 20.2 78 0.0017 14.0 1.2 9 2-10 5-13 (38)
251 PF02591 DUF164: Putative zinc 20.2 1.3E+02 0.0027 14.5 2.4 10 56-65 45-54 (56)
252 KOG4577|consensus 20.1 31 0.00068 23.3 -0.2 33 2-37 35-67 (383)
No 1
>KOG2462|consensus
Probab=100.00 E-value=4.5e-36 Score=185.49 Aligned_cols=138 Identities=25% Similarity=0.485 Sum_probs=128.9
Q ss_pred CCCCcccccccCHHHHHHHHHHHhh-CCCcceecccccccccChHHHHHHHhccCCcccccCCCCcccCChHHHHHHHHh
Q psy12196 1 MSCVPCDVLFHNKATLYKHLYLEHK-ATSLSIQCNMCSLVLDSKESLVTHISQTHTLMFTCRRCPSTFLNSATLSKHVKM 79 (150)
Q Consensus 1 ~~C~~C~~~f~~~~~l~~h~~~~~~-~~~~~~~c~~c~~~f~~~~~l~~h~~~~~~~~~~c~~c~~~f~~~~~l~~h~~~ 79 (150)
|+|+.||+.+.+.++|.+|...|-. ...+.+.|+.|++.+.....|..|+ ++|..+++|.+||++|...+.|+-|+++
T Consensus 131 ~~c~eCgk~ysT~snLsrHkQ~H~~~~s~ka~~C~~C~K~YvSmpALkMHi-rTH~l~c~C~iCGKaFSRPWLLQGHiRT 209 (279)
T KOG2462|consen 131 YKCPECGKSYSTSSNLSRHKQTHRSLDSKKAFSCKYCGKVYVSMPALKMHI-RTHTLPCECGICGKAFSRPWLLQGHIRT 209 (279)
T ss_pred eeccccccccccccccchhhcccccccccccccCCCCCceeeehHHHhhHh-hccCCCcccccccccccchHHhhccccc
Confidence 6899999999999999999988543 3467789999999999999999999 9999999999999999999999999999
Q ss_pred hcCCCcccCCCChhhhcchhHHhhHHhhhcCCCCCCcCCcchhhhccCchHHHHHHHHhcCC
Q psy12196 80 EHNSKSYQCNECPESFERLNKLKRHKFQAHNDSVHQIQCPYCITDFSEDKNLIQHIVSVHLG 141 (150)
Q Consensus 80 ~~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~~~~~ 141 (150)
|+|||||.|..|++.|..+++|+.|+++|.+.+ +|+|..|+|.|...+.|.+|.++--..
T Consensus 210 HTGEKPF~C~hC~kAFADRSNLRAHmQTHS~~K--~~qC~~C~KsFsl~SyLnKH~ES~C~~ 269 (279)
T KOG2462|consen 210 HTGEKPFSCPHCGKAFADRSNLRAHMQTHSDVK--KHQCPRCGKSFALKSYLNKHSESACLK 269 (279)
T ss_pred ccCCCCccCCcccchhcchHHHHHHHHhhcCCc--cccCcchhhHHHHHHHHHHhhhhcccc
Confidence 999999999999999999999999999999988 999999999999999999999876433
No 2
>KOG2462|consensus
Probab=99.96 E-value=2.8e-29 Score=155.51 Aligned_cols=116 Identities=21% Similarity=0.454 Sum_probs=107.7
Q ss_pred cceecccccccccChHHHHHHHhccC----CcccccCCCCcccCChHHHHHHHHhhcCCCcccCCCChhhhcchhHHhhH
Q psy12196 29 LSIQCNMCSLVLDSKESLVTHISQTH----TLMFTCRRCPSTFLNSATLSKHVKMEHNSKSYQCNECPESFERLNKLKRH 104 (150)
Q Consensus 29 ~~~~c~~c~~~f~~~~~l~~h~~~~~----~~~~~c~~c~~~f~~~~~l~~h~~~~~~~~~~~c~~c~~~~~~~~~l~~h 104 (150)
..|+|+.|++.+.+.++|..|.+.+. .+.+.|..|++.|.+...|..|+++|+ -+.+|.+||+.|...|-|+.|
T Consensus 129 ~r~~c~eCgk~ysT~snLsrHkQ~H~~~~s~ka~~C~~C~K~YvSmpALkMHirTH~--l~c~C~iCGKaFSRPWLLQGH 206 (279)
T KOG2462|consen 129 PRYKCPECGKSYSTSSNLSRHKQTHRSLDSKKAFSCKYCGKVYVSMPALKMHIRTHT--LPCECGICGKAFSRPWLLQGH 206 (279)
T ss_pred CceeccccccccccccccchhhcccccccccccccCCCCCceeeehHHHhhHhhccC--CCcccccccccccchHHhhcc
Confidence 44899999999999999999974433 278999999999999999999999998 568999999999999999999
Q ss_pred HhhhcCCCCCCcCCcchhhhccCchHHHHHHHHhcCCCCCCCCC
Q psy12196 105 KFQAHNDSVHQIQCPYCITDFSEDKNLIQHIVSVHLGKEGTAPA 148 (150)
Q Consensus 105 ~~~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~~~~ 148 (150)
+++|+||+ ||.|+.|+|+|.++++|+.||++|.+.|.|+|+.
T Consensus 207 iRTHTGEK--PF~C~hC~kAFADRSNLRAHmQTHS~~K~~qC~~ 248 (279)
T KOG2462|consen 207 IRTHTGEK--PFSCPHCGKAFADRSNLRAHMQTHSDVKKHQCPR 248 (279)
T ss_pred cccccCCC--CccCCcccchhcchHHHHHHHHhhcCCccccCcc
Confidence 99999999 9999999999999999999999999999999974
No 3
>KOG3608|consensus
Probab=99.84 E-value=8.9e-21 Score=121.68 Aligned_cols=105 Identities=26% Similarity=0.566 Sum_probs=50.8
Q ss_pred CCcccccccCHHHHHHHHHHHhhCCCcceecccccccccChHHHHHHHhccCCcccccCCCCcccCChHHHHHHHHh-hc
Q psy12196 3 CVPCDVLFHNKATLYKHLYLEHKATSLSIQCNMCSLVLDSKESLVTHISQTHTLMFTCRRCPSTFLNSATLSKHVKM-EH 81 (150)
Q Consensus 3 C~~C~~~f~~~~~l~~h~~~~~~~~~~~~~c~~c~~~f~~~~~l~~h~~~~~~~~~~c~~c~~~f~~~~~l~~h~~~-~~ 81 (150)
|+.||..|.+...|..|++..+.....+|+|..|.+.|..+..|..|+ ..|...|+|+.|+......++|..|++. |.
T Consensus 210 Cp~Cg~~F~~~tkl~DH~rRqt~l~~n~fqC~~C~KrFaTeklL~~Hv-~rHvn~ykCplCdmtc~~~ssL~~H~r~rHs 288 (467)
T KOG3608|consen 210 CPHCGELFRTKTKLFDHLRRQTELNTNSFQCAQCFKRFATEKLLKSHV-VRHVNCYKCPLCDMTCSSASSLTTHIRYRHS 288 (467)
T ss_pred cchHHHHhccccHHHHHHHhhhhhcCCchHHHHHHHHHhHHHHHHHHH-HHhhhcccccccccCCCChHHHHHHHHhhhc
Confidence 444444444444444444443333333444444444444444444444 3334445555555555555555555543 44
Q ss_pred CCCcccCCCChhhhcchhHHhhHHhhh
Q psy12196 82 NSKSYQCNECPESFERLNKLKRHKFQA 108 (150)
Q Consensus 82 ~~~~~~c~~c~~~~~~~~~l~~h~~~~ 108 (150)
..+||+|..|++.+...++|.+|...|
T Consensus 289 ~dkpfKCd~Cd~~c~~esdL~kH~~~H 315 (467)
T KOG3608|consen 289 KDKPFKCDECDTRCVRESDLAKHVQVH 315 (467)
T ss_pred cCCCccccchhhhhccHHHHHHHHHhc
Confidence 455555555555555555555555443
No 4
>KOG3608|consensus
Probab=99.82 E-value=5.5e-20 Score=118.11 Aligned_cols=139 Identities=27% Similarity=0.525 Sum_probs=123.8
Q ss_pred CCCCcccccccCHHHHHHHHHHHhhCCCcceecccccccccChHHHHHHHhccC--CcccccCCCCcccCChHHHHHHHH
Q psy12196 1 MSCVPCDVLFHNKATLYKHLYLEHKATSLSIQCNMCSLVLDSKESLVTHISQTH--TLMFTCRRCPSTFLNSATLSKHVK 78 (150)
Q Consensus 1 ~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~~~c~~c~~~f~~~~~l~~h~~~~~--~~~~~c~~c~~~f~~~~~l~~h~~ 78 (150)
|+|..|.+.|.+...|..|+.. |. ..|+|+.|+.+.+..++|..|+.-.| .+||+|..|++.+.+...|..|..
T Consensus 238 fqC~~C~KrFaTeklL~~Hv~r-Hv---n~ykCplCdmtc~~~ssL~~H~r~rHs~dkpfKCd~Cd~~c~~esdL~kH~~ 313 (467)
T KOG3608|consen 238 FQCAQCFKRFATEKLLKSHVVR-HV---NCYKCPLCDMTCSSASSLTTHIRYRHSKDKPFKCDECDTRCVRESDLAKHVQ 313 (467)
T ss_pred hHHHHHHHHHhHHHHHHHHHHH-hh---hcccccccccCCCChHHHHHHHHhhhccCCCccccchhhhhccHHHHHHHHH
Confidence 6899999999999999999887 43 34899999999999999999985433 499999999999999999999999
Q ss_pred hhcCCCcccCCC--ChhhhcchhHHhhHHhhhc-CCCCCCcCCcchhhhccCchHHHHHHHHhcCCCCC
Q psy12196 79 MEHNSKSYQCNE--CPESFERLNKLKRHKFQAH-NDSVHQIQCPYCITDFSEDKNLIQHIVSVHLGKEG 144 (150)
Q Consensus 79 ~~~~~~~~~c~~--c~~~~~~~~~l~~h~~~~~-~~~~~~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~ 144 (150)
.|. +..|.|.. |..++.+...+++|++.++ +..+-+|.|-.|++.|++--+|.+|+...|+-+..
T Consensus 314 ~HS-~~~y~C~h~~C~~s~r~~~q~~~H~~evhEg~np~~Y~CH~Cdr~ft~G~~L~~HL~kkH~f~~P 381 (467)
T KOG3608|consen 314 VHS-KTVYQCEHPDCHYSVRTYTQMRRHFLEVHEGNNPILYACHCCDRFFTSGKSLSAHLMKKHGFRLP 381 (467)
T ss_pred hcc-ccceecCCCCCcHHHHHHHHHHHHHHHhccCCCCCceeeecchhhhccchhHHHHHHHhhcccCC
Confidence 887 67799988 9999999999999998876 66667899999999999999999999988876654
No 5
>KOG1074|consensus
Probab=99.82 E-value=9.2e-22 Score=137.65 Aligned_cols=53 Identities=25% Similarity=0.468 Sum_probs=45.5
Q ss_pred CCCCcccccccCHHHHHHHHHHHhhCCCcceecccccccccChHHHHHHHhccCC
Q psy12196 1 MSCVPCDVLFHNKATLYKHLYLEHKATSLSIQCNMCSLVLDSKESLVTHISQTHT 55 (150)
Q Consensus 1 ~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~~~c~~c~~~f~~~~~l~~h~~~~~~ 55 (150)
.+|.+|.+.|...+.|+.|.+.|+ ++.+|+|..|+..|+.+.+|..|.+++++
T Consensus 354 hkCr~CakvfgS~SaLqiHlRSHT--GERPfqCnvCG~~FSTkGNLKvH~~rH~e 406 (958)
T KOG1074|consen 354 HKCRFCAKVFGSDSALQIHLRSHT--GERPFQCNVCGNRFSTKGNLKVHFQRHRE 406 (958)
T ss_pred chhhhhHhhcCchhhhhhhhhccC--CCCCeeecccccccccccceeeeeeeccc
Confidence 369999999999999999999844 67789999999999999999998755443
No 6
>KOG3576|consensus
Probab=99.80 E-value=5e-20 Score=110.03 Aligned_cols=116 Identities=19% Similarity=0.368 Sum_probs=102.0
Q ss_pred CcceecccccccccChHHHHHHHhccCC--cccccCCCCcccCChHHHHHHHHhhcCCCcccCCCChhhhcchhHHhhHH
Q psy12196 28 SLSIQCNMCSLVLDSKESLVTHISQTHT--LMFTCRRCPSTFLNSATLSKHVKMEHNSKSYQCNECPESFERLNKLKRHK 105 (150)
Q Consensus 28 ~~~~~c~~c~~~f~~~~~l~~h~~~~~~--~~~~c~~c~~~f~~~~~l~~h~~~~~~~~~~~c~~c~~~~~~~~~l~~h~ 105 (150)
...+.|..|++.|..-.-|.+|+ ..|. +.+.|..||+.|.+.-+|.+|+++|+|.+||+|..|++.|.+...|..|.
T Consensus 115 ~d~ftCrvCgK~F~lQRmlnrh~-kch~~vkr~lct~cgkgfndtfdlkrh~rthtgvrpykc~~c~kaftqrcsleshl 193 (267)
T KOG3576|consen 115 QDSFTCRVCGKKFGLQRMLNRHL-KCHSDVKRHLCTFCGKGFNDTFDLKRHTRTHTGVRPYKCSLCEKAFTQRCSLESHL 193 (267)
T ss_pred CCeeeeehhhhhhhHHHHHHHHh-hhccHHHHHHHhhccCcccchhhhhhhhccccCccccchhhhhHHHHhhccHHHHH
Confidence 34589999999999888888898 4443 78899999999999999999999999999999999999999999999998
Q ss_pred hhhcCC---------CCCCcCCcchhhhccCchHHHHHHHHhcCCCCC
Q psy12196 106 FQAHND---------SVHQIQCPYCITDFSEDKNLIQHIVSVHLGKEG 144 (150)
Q Consensus 106 ~~~~~~---------~~~~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~ 144 (150)
...++. +.+.|.|..||..-.....+..|++.+|+..|+
T Consensus 194 ~kvhgv~~~yaykerr~kl~vcedcg~t~~~~e~~~~h~~~~hp~Spa 241 (267)
T KOG3576|consen 194 KKVHGVQHQYAYKERRAKLYVCEDCGYTSERPEVYYLHLKLHHPFSPA 241 (267)
T ss_pred HHHcCchHHHHHHHhhhheeeecccCCCCCChhHHHHHHHhcCCCCHH
Confidence 876653 345799999999999999999999999976653
No 7
>KOG1074|consensus
Probab=99.78 E-value=5.9e-20 Score=128.77 Aligned_cols=77 Identities=25% Similarity=0.608 Sum_probs=66.2
Q ss_pred CCCcccccccCHHHHHHHHHHHhhCCCcceecccccccccChHHHHHHHhccCC------cccccC---CCCcccCChHH
Q psy12196 2 SCVPCDVLFHNKATLYKHLYLEHKATSLSIQCNMCSLVLDSKESLVTHISQTHT------LMFTCR---RCPSTFLNSAT 72 (150)
Q Consensus 2 ~C~~C~~~f~~~~~l~~h~~~~~~~~~~~~~c~~c~~~f~~~~~l~~h~~~~~~------~~~~c~---~c~~~f~~~~~ 72 (150)
+|-.|-+.++..+.|+.|.+. |. ++.+|+|..|++.|..+.+|..|+ ..|. ..+.|+ +|-+.|.+...
T Consensus 607 qCiiC~rVlSC~saLqmHyrt-Ht-GERPFkCKiCgRAFtTkGNLkaH~-~vHka~p~~R~q~ScP~~~ic~~kftn~V~ 683 (958)
T KOG1074|consen 607 QCIICLRVLSCPSALQMHYRT-HT-GERPFKCKICGRAFTTKGNLKAHM-SVHKAKPPARVQFSCPSTFICQKKFTNAVT 683 (958)
T ss_pred ceeeeeecccchhhhhhhhhc-cc-CcCccccccccchhccccchhhcc-cccccCccccccccCCchhhhccccccccc
Confidence 577899999999999999888 44 677899999999999999999998 4443 568899 89999999999
Q ss_pred HHHHHHhhc
Q psy12196 73 LSKHVKMEH 81 (150)
Q Consensus 73 l~~h~~~~~ 81 (150)
|..|++.|.
T Consensus 684 lpQhIriH~ 692 (958)
T KOG1074|consen 684 LPQHIRIHL 692 (958)
T ss_pred ccceEEeec
Confidence 999988886
No 8
>KOG3623|consensus
Probab=99.72 E-value=2.1e-18 Score=119.82 Aligned_cols=105 Identities=21% Similarity=0.530 Sum_probs=85.6
Q ss_pred CCCcccccccCHHHHHHHHHHHhhCCCcceecccccccccChHHHHHHHhccCC--------------cccccCCCCccc
Q psy12196 2 SCVPCDVLFHNKATLYKHLYLEHKATSLSIQCNMCSLVLDSKESLVTHISQTHT--------------LMFTCRRCPSTF 67 (150)
Q Consensus 2 ~C~~C~~~f~~~~~l~~h~~~~~~~~~~~~~c~~c~~~f~~~~~l~~h~~~~~~--------------~~~~c~~c~~~f 67 (150)
.|++|+..+.....|+.|++..|...+..|.|..|..+|.....|.+|++.+.. +.|+|.+|+++|
T Consensus 212 tcpycdrgykrltslkeHikyrhekne~nfsC~lCsytFAyRtQLErhm~~hkpg~dqa~sltqsa~lRKFKCtECgKAF 291 (1007)
T KOG3623|consen 212 TCPYCDRGYKRLTSLKEHIKYRHEKNEPNFSCMLCSYTFAYRTQLERHMQLHKPGGDQAISLTQSALLRKFKCTECGKAF 291 (1007)
T ss_pred cchhHHHHHHHHHHHHHHHHHHHhhCCCCCcchhhhhhhhhHHHHHHHHHhhcCCCcccccccchhhhccccccccchhh
Confidence 688999999999999999988777666678899999999999999888732211 568888888888
Q ss_pred CChHHHHHHHHhhcCCCcccCCCChhhhcchhHHhhHHh
Q psy12196 68 LNSATLSKHVKMEHNSKSYQCNECPESFERLNKLKRHKF 106 (150)
Q Consensus 68 ~~~~~l~~h~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~ 106 (150)
..+.-|.-|+++|.|+|||.|..|++.|.....+..|+.
T Consensus 292 KfKHHLKEHlRIHSGEKPfeCpnCkKRFSHSGSySSHmS 330 (1007)
T KOG3623|consen 292 KFKHHLKEHLRIHSGEKPFECPNCKKRFSHSGSYSSHMS 330 (1007)
T ss_pred hhHHHHHhhheeecCCCCcCCcccccccccCCccccccc
Confidence 888888888888888888888888888888888777754
No 9
>KOG3623|consensus
Probab=99.66 E-value=3.1e-17 Score=114.17 Aligned_cols=79 Identities=27% Similarity=0.615 Sum_probs=76.5
Q ss_pred CcccccCCCCcccCChHHHHHHHHhhcCCCcccCCCChhhhcchhHHhhHHhhhcCCCCCCcCCcchhhhccCchHHHHH
Q psy12196 55 TLMFTCRRCPSTFLNSATLSKHVKMEHNSKSYQCNECPESFERLNKLKRHKFQAHNDSVHQIQCPYCITDFSEDKNLIQH 134 (150)
Q Consensus 55 ~~~~~c~~c~~~f~~~~~l~~h~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~~C~~C~~~f~~~~~l~~H 134 (150)
...|.|..|+++|.-..+|.+|...|+|.+||.|.+|.+.|...-.|.-|++.|.|++ ||+|..|+|.|...+++..|
T Consensus 892 ~gmyaCDqCDK~FqKqSSLaRHKYEHsGqRPyqC~iCkKAFKHKHHLtEHkRLHSGEK--PfQCdKClKRFSHSGSYSQH 969 (1007)
T KOG3623|consen 892 DGMYACDQCDKAFQKQSSLARHKYEHSGQRPYQCIICKKAFKHKHHLTEHKRLHSGEK--PFQCDKCLKRFSHSGSYSQH 969 (1007)
T ss_pred cccchHHHHHHHHHhhHHHHHhhhhhcCCCCcccchhhHhhhhhhhhhhhhhhccCCC--cchhhhhhhhcccccchHhh
Confidence 3689999999999999999999999999999999999999999999999999999998 99999999999999999999
Q ss_pred H
Q psy12196 135 I 135 (150)
Q Consensus 135 ~ 135 (150)
|
T Consensus 970 M 970 (1007)
T KOG3623|consen 970 M 970 (1007)
T ss_pred h
Confidence 8
No 10
>KOG3576|consensus
Probab=99.65 E-value=2.2e-17 Score=98.80 Aligned_cols=85 Identities=28% Similarity=0.474 Sum_probs=80.5
Q ss_pred cccccCCCCcccCChHHHHHHHHhhcCCCcccCCCChhhhcchhHHhhHHhhhcCCCCCCcCCcchhhhccCchHHHHHH
Q psy12196 56 LMFTCRRCPSTFLNSATLSKHVKMEHNSKSYQCNECPESFERLNKLKRHKFQAHNDSVHQIQCPYCITDFSEDKNLIQHI 135 (150)
Q Consensus 56 ~~~~c~~c~~~f~~~~~l~~h~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~~C~~C~~~f~~~~~l~~H~ 135 (150)
..|.|.+|++.|..-..|.+|++.|...+.+.|..||+.|...-+|.+|.++|++.+ ||+|..|+|+|+...+|..|+
T Consensus 116 d~ftCrvCgK~F~lQRmlnrh~kch~~vkr~lct~cgkgfndtfdlkrh~rthtgvr--pykc~~c~kaftqrcsleshl 193 (267)
T KOG3576|consen 116 DSFTCRVCGKKFGLQRMLNRHLKCHSDVKRHLCTFCGKGFNDTFDLKRHTRTHTGVR--PYKCSLCEKAFTQRCSLESHL 193 (267)
T ss_pred CeeeeehhhhhhhHHHHHHHHhhhccHHHHHHHhhccCcccchhhhhhhhccccCcc--ccchhhhhHHHHhhccHHHHH
Confidence 568999999999999999999999999999999999999999999999999999988 999999999999999999999
Q ss_pred HHhcCCC
Q psy12196 136 VSVHLGK 142 (150)
Q Consensus 136 ~~~~~~~ 142 (150)
+..||..
T Consensus 194 ~kvhgv~ 200 (267)
T KOG3576|consen 194 KKVHGVQ 200 (267)
T ss_pred HHHcCch
Confidence 9888643
No 11
>PLN03086 PRLI-interacting factor K; Provisional
Probab=99.39 E-value=9.4e-13 Score=91.48 Aligned_cols=104 Identities=15% Similarity=0.373 Sum_probs=83.1
Q ss_pred ceecccccccccChHHHHHHHhccCCcccccCCCCcccCChHHHHHHHHhhcCCCcccCCCChhhhc----------chh
Q psy12196 30 SIQCNMCSLVLDSKESLVTHISQTHTLMFTCRRCPSTFLNSATLSKHVKMEHNSKSYQCNECPESFE----------RLN 99 (150)
Q Consensus 30 ~~~c~~c~~~f~~~~~l~~h~~~~~~~~~~c~~c~~~f~~~~~l~~h~~~~~~~~~~~c~~c~~~~~----------~~~ 99 (150)
.+.|+.|++.|. ...+..|+... ..++.|+ |+..+ ....|..|+..|.+.+++.|..|+..+. ..+
T Consensus 453 H~~C~~Cgk~f~-~s~LekH~~~~-Hkpv~Cp-Cg~~~-~R~~L~~H~~thCp~Kpi~C~fC~~~v~~g~~~~d~~d~~s 528 (567)
T PLN03086 453 HVHCEKCGQAFQ-QGEMEKHMKVF-HEPLQCP-CGVVL-EKEQMVQHQASTCPLRLITCRFCGDMVQAGGSAMDVRDRLR 528 (567)
T ss_pred CccCCCCCCccc-hHHHHHHHHhc-CCCccCC-CCCCc-chhHHHhhhhccCCCCceeCCCCCCccccCccccchhhhhh
Confidence 357999999986 57788997444 4889999 99655 6688999999999999999999998884 235
Q ss_pred HHhhHHhhhcCCCCCCcCCcchhhhccCchHHHHHHHHhcCC
Q psy12196 100 KLKRHKFQAHNDSVHQIQCPYCITDFSEDKNLIQHIVSVHLG 141 (150)
Q Consensus 100 ~l~~h~~~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~~~~~ 141 (150)
.|..|.... +.+ ++.|..|++.+..+ ++..|+...|..
T Consensus 529 ~Lt~HE~~C-G~r--t~~C~~Cgk~Vrlr-dm~~H~~~~h~~ 566 (567)
T PLN03086 529 GMSEHESIC-GSR--TAPCDSCGRSVMLK-EMDIHQIAVHQK 566 (567)
T ss_pred hHHHHHHhc-CCc--ceEccccCCeeeeh-hHHHHHHHhhcC
Confidence 788888763 555 88999999998885 688898877753
No 12
>PHA00733 hypothetical protein
Probab=99.35 E-value=7.9e-13 Score=75.95 Aligned_cols=84 Identities=18% Similarity=0.330 Sum_probs=67.0
Q ss_pred cCCcccccCCCCcccCChHHHHHH--H---HhhcCCCcccCCCChhhhcchhHHhhHHhhhcCCCCCCcCCcchhhhccC
Q psy12196 53 THTLMFTCRRCPSTFLNSATLSKH--V---KMEHNSKSYQCNECPESFERLNKLKRHKFQAHNDSVHQIQCPYCITDFSE 127 (150)
Q Consensus 53 ~~~~~~~c~~c~~~f~~~~~l~~h--~---~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~~C~~C~~~f~~ 127 (150)
...+++.|.+|...|..+..|..+ + ..+.+.++|.|..||+.|...+.|..|++.+ +. +|.|+.|+++|..
T Consensus 36 ~~~~~~~~~~~~~~~~~~~~l~~~~~l~~~~~~~~~kPy~C~~Cgk~Fss~s~L~~H~r~h--~~--~~~C~~CgK~F~~ 111 (128)
T PHA00733 36 PEQKRLIRAVVKTLIYNPQLLDESSYLYKLLTSKAVSPYVCPLCLMPFSSSVSLKQHIRYT--EH--SKVCPVCGKEFRN 111 (128)
T ss_pred hhhhhHHHHHHhhhccChhhhcchHHHHhhcccCCCCCccCCCCCCcCCCHHHHHHHHhcC--Cc--CccCCCCCCccCC
Confidence 334778888888887777666554 1 1334578999999999999999999998754 33 7899999999999
Q ss_pred chHHHHHHHHhcC
Q psy12196 128 DKNLIQHIVSVHL 140 (150)
Q Consensus 128 ~~~l~~H~~~~~~ 140 (150)
...|..|+...|+
T Consensus 112 ~~sL~~H~~~~h~ 124 (128)
T PHA00733 112 TDSTLDHVCKKHN 124 (128)
T ss_pred HHHHHHHHHHhcC
Confidence 9999999988875
No 13
>PHA00733 hypothetical protein
Probab=99.16 E-value=4.4e-11 Score=68.79 Aligned_cols=82 Identities=17% Similarity=0.348 Sum_probs=66.9
Q ss_pred CCcceecccccccccChHHHHHH------HhccCCcccccCCCCcccCChHHHHHHHHhhcCCCcccCCCChhhhcchhH
Q psy12196 27 TSLSIQCNMCSLVLDSKESLVTH------ISQTHTLMFTCRRCPSTFLNSATLSKHVKMEHNSKSYQCNECPESFERLNK 100 (150)
Q Consensus 27 ~~~~~~c~~c~~~f~~~~~l~~h------~~~~~~~~~~c~~c~~~f~~~~~l~~h~~~~~~~~~~~c~~c~~~~~~~~~ 100 (150)
+++.+.|..|.+.|.....+..+ +......+|.|+.|++.|.+...|..|+..+ ..++.|.+|++.|.....
T Consensus 37 ~~~~~~~~~~~~~~~~~~~l~~~~~l~~~~~~~~~kPy~C~~Cgk~Fss~s~L~~H~r~h--~~~~~C~~CgK~F~~~~s 114 (128)
T PHA00733 37 EQKRLIRAVVKTLIYNPQLLDESSYLYKLLTSKAVSPYVCPLCLMPFSSSVSLKQHIRYT--EHSKVCPVCGKEFRNTDS 114 (128)
T ss_pred hhhhHHHHHHhhhccChhhhcchHHHHhhcccCCCCCccCCCCCCcCCCHHHHHHHHhcC--CcCccCCCCCCccCCHHH
Confidence 46678899999888776665554 2222348999999999999999999999876 356999999999999999
Q ss_pred HhhHHhhhcC
Q psy12196 101 LKRHKFQAHN 110 (150)
Q Consensus 101 l~~h~~~~~~ 110 (150)
|..|+...++
T Consensus 115 L~~H~~~~h~ 124 (128)
T PHA00733 115 TLDHVCKKHN 124 (128)
T ss_pred HHHHHHHhcC
Confidence 9999887665
No 14
>PLN03086 PRLI-interacting factor K; Provisional
Probab=99.13 E-value=1.1e-10 Score=81.53 Aligned_cols=124 Identities=19% Similarity=0.393 Sum_probs=87.2
Q ss_pred CCcccccccCHHHHHHHHHHHhhCCCcceeccc--ccccccChHHHHHHHhccCCcccccCCCCcccCChHHHHHHHHhh
Q psy12196 3 CVPCDVLFHNKATLYKHLYLEHKATSLSIQCNM--CSLVLDSKESLVTHISQTHTLMFTCRRCPSTFLNSATLSKHVKME 80 (150)
Q Consensus 3 C~~C~~~f~~~~~l~~h~~~~~~~~~~~~~c~~--c~~~f~~~~~l~~h~~~~~~~~~~c~~c~~~f~~~~~l~~h~~~~ 80 (150)
|+.|...... ..|..|.... . . ..-.|+. |+..|. ...+. ..+.|+.|++.|. ...+..|+..+
T Consensus 410 C~NC~~~i~l-~~l~lHe~~C-~-r-~~V~Cp~~~Cg~v~~-r~el~--------~H~~C~~Cgk~f~-~s~LekH~~~~ 475 (567)
T PLN03086 410 CRNCKHYIPS-RSIALHEAYC-S-R-HNVVCPHDGCGIVLR-VEEAK--------NHVHCEKCGQAFQ-QGEMEKHMKVF 475 (567)
T ss_pred CCCCCCccch-hHHHHHHhhC-C-C-cceeCCcccccceee-ccccc--------cCccCCCCCCccc-hHHHHHHHHhc
Confidence 5555544433 3344665432 1 1 1235774 888773 22222 3458999999996 57799999998
Q ss_pred cCCCcccCCCChhhhcchhHHhhHHhhhcCCCCCCcCCcchhhhccC----------chHHHHHHHHhcCCCCCCCC
Q psy12196 81 HNSKSYQCNECPESFERLNKLKRHKFQAHNDSVHQIQCPYCITDFSE----------DKNLIQHIVSVHLGKEGTAP 147 (150)
Q Consensus 81 ~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~~C~~C~~~f~~----------~~~l~~H~~~~~~~~~~~~~ 147 (150)
+ +++.|. ||..+ ....|..|+..+...+ ++.|+.|++.|.. .+.|..|..+. |.+++.|.
T Consensus 476 H--kpv~Cp-Cg~~~-~R~~L~~H~~thCp~K--pi~C~fC~~~v~~g~~~~d~~d~~s~Lt~HE~~C-G~rt~~C~ 545 (567)
T PLN03086 476 H--EPLQCP-CGVVL-EKEQMVQHQASTCPLR--LITCRFCGDMVQAGGSAMDVRDRLRGMSEHESIC-GSRTAPCD 545 (567)
T ss_pred C--CCccCC-CCCCc-chhHHHhhhhccCCCC--ceeCCCCCCccccCccccchhhhhhhHHHHHHhc-CCcceEcc
Confidence 6 789999 99755 5689999988777777 9999999999952 35788998774 88888874
No 15
>PHA02768 hypothetical protein; Provisional
Probab=99.11 E-value=2.5e-11 Score=58.30 Aligned_cols=42 Identities=14% Similarity=0.324 Sum_probs=21.3
Q ss_pred ccCCCChhhhcchhHHhhHHhhhcCCCCCCcCCcchhhhccCchHH
Q psy12196 86 YQCNECPESFERLNKLKRHKFQAHNDSVHQIQCPYCITDFSEDKNL 131 (150)
Q Consensus 86 ~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~~C~~C~~~f~~~~~l 131 (150)
|.|++||+.|...+.|..|+++|+ + +++|..|++.|...+.|
T Consensus 6 y~C~~CGK~Fs~~~~L~~H~r~H~--k--~~kc~~C~k~f~~~s~l 47 (55)
T PHA02768 6 YECPICGEIYIKRKSMITHLRKHN--T--NLKLSNCKRISLRTGEY 47 (55)
T ss_pred cCcchhCCeeccHHHHHHHHHhcC--C--cccCCcccceeccccee
Confidence 455555555555555555555544 2 44555555555544433
No 16
>PHA02768 hypothetical protein; Provisional
Probab=99.11 E-value=3.8e-11 Score=57.66 Aligned_cols=44 Identities=11% Similarity=0.381 Sum_probs=34.5
Q ss_pred ccccCCCCcccCChHHHHHHHHhhcCCCcccCCCChhhhcchhHHh
Q psy12196 57 MFTCRRCPSTFLNSATLSKHVKMEHNSKSYQCNECPESFERLNKLK 102 (150)
Q Consensus 57 ~~~c~~c~~~f~~~~~l~~h~~~~~~~~~~~c~~c~~~~~~~~~l~ 102 (150)
-|.|++||+.|.....|..|++.|+ +++.|..|++.|...+.|.
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 3678888888888888888888888 6788888888887766553
No 17
>PHA00616 hypothetical protein
Probab=99.04 E-value=1.4e-10 Score=53.04 Aligned_cols=32 Identities=34% Similarity=0.507 Sum_probs=27.7
Q ss_pred CcCCcchhhhccCchHHHHHHHHhcCCCCCCC
Q psy12196 115 QIQCPYCITDFSEDKNLIQHIVSVHLGKEGTA 146 (150)
Q Consensus 115 ~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~~ 146 (150)
||+|+.||+.|..+++|.+|++.+|+++++.+
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~~hg~~~~~~ 32 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLSVHKQNKLTL 32 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHHhcCCCccce
Confidence 57899999999999999999999999888754
No 18
>KOG3993|consensus
Probab=98.88 E-value=3.1e-10 Score=75.46 Aligned_cols=78 Identities=23% Similarity=0.481 Sum_probs=50.4
Q ss_pred CCCCcccccccCHHHHHHHHHHHhhCCCcceecccccccccChHHHHHHHhccC--------------------------
Q psy12196 1 MSCVPCDVLFHNKATLYKHLYLEHKATSLSIQCNMCSLVLDSKESLVTHISQTH-------------------------- 54 (150)
Q Consensus 1 ~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~~~c~~c~~~f~~~~~l~~h~~~~~-------------------------- 54 (150)
|.|..|-..|.+...|.+|.-. ......|+|+.|++.|+...+|..|. +=|
T Consensus 268 yiCqLCK~kYeD~F~LAQHrC~--RIV~vEYrCPEC~KVFsCPANLASHR-RWHKPR~eaa~a~~~P~k~~~~~rae~~e 344 (500)
T KOG3993|consen 268 YICQLCKEKYEDAFALAQHRCP--RIVHVEYRCPECDKVFSCPANLASHR-RWHKPRPEAAKAGSPPPKQAVETRAEVQE 344 (500)
T ss_pred HHHHHHHHhhhhHHHHhhccCC--eeEEeeecCCcccccccCchhhhhhh-cccCCchhhhhcCCCChhhhhhhhhhhhh
Confidence 4566677777777777766422 11234467777777777777776664 111
Q ss_pred ---------CcccccCCCCcccCChHHHHHHHHhhc
Q psy12196 55 ---------TLMFTCRRCPSTFLNSATLSKHVKMEH 81 (150)
Q Consensus 55 ---------~~~~~c~~c~~~f~~~~~l~~h~~~~~ 81 (150)
...|.|..|++.|.....|..|+.+|+
T Consensus 345 a~rsg~dss~gi~~C~~C~KkFrRqAYLrKHqlthq 380 (500)
T KOG3993|consen 345 AERSGDDSSSGIFSCHTCGKKFRRQAYLRKHQLTHQ 380 (500)
T ss_pred ccccCCcccCceeecHHhhhhhHHHHHHHHhHHhhh
Confidence 124778888888888888888877775
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=98.83 E-value=2e-09 Score=44.42 Aligned_cols=24 Identities=33% Similarity=0.808 Sum_probs=14.8
Q ss_pred HHHHHHhhcCCCcccCCCChhhhc
Q psy12196 73 LSKHVKMEHNSKSYQCNECPESFE 96 (150)
Q Consensus 73 l~~h~~~~~~~~~~~c~~c~~~~~ 96 (150)
|..|++.|++++||.|++|++.|.
T Consensus 2 l~~H~~~H~~~k~~~C~~C~k~F~ 25 (26)
T PF13465_consen 2 LRRHMRTHTGEKPYKCPYCGKSFS 25 (26)
T ss_dssp HHHHHHHHSSSSSEEESSSSEEES
T ss_pred HHHHhhhcCCCCCCCCCCCcCeeC
Confidence 556666666666666666666553
No 20
>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=98.75 E-value=2.5e-08 Score=48.76 Aligned_cols=53 Identities=28% Similarity=0.521 Sum_probs=38.7
Q ss_pred cccCCCChhhhcchhHHhhHHhhhcCCCCCCcCCcchhhhccCchHHHHHHHHhcC
Q psy12196 85 SYQCNECPESFERLNKLKRHKFQAHNDSVHQIQCPYCITDFSEDKNLIQHIVSVHL 140 (150)
Q Consensus 85 ~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~~~~ 140 (150)
.|.|+.|++ ......|..|....+....+.+.||+|...+. .+|..|+..+|+
T Consensus 2 ~f~CP~C~~-~~~~~~L~~H~~~~H~~~~~~v~CPiC~~~~~--~~l~~Hl~~~H~ 54 (54)
T PF05605_consen 2 SFTCPYCGK-GFSESSLVEHCEDEHRSESKNVVCPICSSRVT--DNLIRHLNSQHR 54 (54)
T ss_pred CcCCCCCCC-ccCHHHHHHHHHhHCcCCCCCccCCCchhhhh--hHHHHHHHHhcC
Confidence 377888888 44556788887776655555788999987655 488889888774
No 21
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=98.72 E-value=4.6e-09 Score=43.28 Aligned_cols=26 Identities=35% Similarity=0.781 Sum_probs=22.9
Q ss_pred HHhhHHhhhcCCCCCCcCCcchhhhccC
Q psy12196 100 KLKRHKFQAHNDSVHQIQCPYCITDFSE 127 (150)
Q Consensus 100 ~l~~h~~~~~~~~~~~~~C~~C~~~f~~ 127 (150)
+|..|+++|++++ ||.|+.|++.|.+
T Consensus 1 ~l~~H~~~H~~~k--~~~C~~C~k~F~~ 26 (26)
T PF13465_consen 1 NLRRHMRTHTGEK--PYKCPYCGKSFSN 26 (26)
T ss_dssp HHHHHHHHHSSSS--SEEESSSSEEESS
T ss_pred CHHHHhhhcCCCC--CCCCCCCcCeeCc
Confidence 4788999999988 9999999999863
No 22
>KOG3993|consensus
Probab=98.68 E-value=1.2e-08 Score=68.17 Aligned_cols=107 Identities=15% Similarity=0.318 Sum_probs=72.3
Q ss_pred eecccccccccChHHHHHHH-hccCCcccccCCCCcccCChHHHHHHHHhhcCCCccc---CCCChhhhcchhHHhhHHh
Q psy12196 31 IQCNMCSLVLDSKESLVTHI-SQTHTLMFTCRRCPSTFLNSATLSKHVKMEHNSKSYQ---CNECPESFERLNKLKRHKF 106 (150)
Q Consensus 31 ~~c~~c~~~f~~~~~l~~h~-~~~~~~~~~c~~c~~~f~~~~~l~~h~~~~~~~~~~~---c~~c~~~~~~~~~l~~h~~ 106 (150)
|.|..|...|.+...|.+|. .++....|.|++|++.|.-..+|..|.+=|....... -+-=..........+.-.+
T Consensus 268 yiCqLCK~kYeD~F~LAQHrC~RIV~vEYrCPEC~KVFsCPANLASHRRWHKPR~eaa~a~~~P~k~~~~~rae~~ea~r 347 (500)
T KOG3993|consen 268 YICQLCKEKYEDAFALAQHRCPRIVHVEYRCPECDKVFSCPANLASHRRWHKPRPEAAKAGSPPPKQAVETRAEVQEAER 347 (500)
T ss_pred HHHHHHHHhhhhHHHHhhccCCeeEEeeecCCcccccccCchhhhhhhcccCCchhhhhcCCCChhhhhhhhhhhhhccc
Confidence 88999999999999999994 2233378999999999999999999988775432111 0000000001100000000
Q ss_pred --hhcCCCCCCcCCcchhhhccCchHHHHHHHHhc
Q psy12196 107 --QAHNDSVHQIQCPYCITDFSEDKNLIQHIVSVH 139 (150)
Q Consensus 107 --~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~~~ 139 (150)
....++ .|.|..|+|.|.....|..|+.+|+
T Consensus 348 sg~dss~g--i~~C~~C~KkFrRqAYLrKHqlthq 380 (500)
T KOG3993|consen 348 SGDDSSSG--IFSCHTCGKKFRRQAYLRKHQLTHQ 380 (500)
T ss_pred cCCcccCc--eeecHHhhhhhHHHHHHHHhHHhhh
Confidence 012233 7999999999999999999999997
No 23
>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=98.65 E-value=7.7e-08 Score=47.02 Aligned_cols=48 Identities=25% Similarity=0.566 Sum_probs=27.6
Q ss_pred CCCCcccccccCHHHHHHHHHHHhhCCCcceecccccccccChHHHHHHHh
Q psy12196 1 MSCVPCDVLFHNKATLYKHLYLEHKATSLSIQCNMCSLVLDSKESLVTHIS 51 (150)
Q Consensus 1 ~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~~~c~~c~~~f~~~~~l~~h~~ 51 (150)
|.|++|++ --+...|..|....|....+.+.||.|...+. ..|..|+.
T Consensus 3 f~CP~C~~-~~~~~~L~~H~~~~H~~~~~~v~CPiC~~~~~--~~l~~Hl~ 50 (54)
T PF05605_consen 3 FTCPYCGK-GFSESSLVEHCEDEHRSESKNVVCPICSSRVT--DNLIRHLN 50 (54)
T ss_pred cCCCCCCC-ccCHHHHHHHHHhHCcCCCCCccCCCchhhhh--hHHHHHHH
Confidence 55666666 34456666666666654445566666665433 25555553
No 24
>PHA00616 hypothetical protein
Probab=98.64 E-value=1.7e-08 Score=46.25 Aligned_cols=32 Identities=22% Similarity=0.504 Sum_probs=17.7
Q ss_pred ccccCCCCcccCChHHHHHHHHhhcCCCcccC
Q psy12196 57 MFTCRRCPSTFLNSATLSKHVKMEHNSKSYQC 88 (150)
Q Consensus 57 ~~~c~~c~~~f~~~~~l~~h~~~~~~~~~~~c 88 (150)
||+|+.||+.|.....+..|++.|+|++++.|
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~~hg~~~~~~ 32 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLSVHKQNKLTL 32 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHHhcCCCccce
Confidence 34555555555555555555555555555544
No 25
>PHA00732 hypothetical protein
Probab=98.58 E-value=2.8e-08 Score=52.19 Aligned_cols=46 Identities=28% Similarity=0.594 Sum_probs=34.4
Q ss_pred ccccCCCCcccCChHHHHHHHHh-hcCCCcccCCCChhhhcchhHHhhHHhhh
Q psy12196 57 MFTCRRCPSTFLNSATLSKHVKM-EHNSKSYQCNECPESFERLNKLKRHKFQA 108 (150)
Q Consensus 57 ~~~c~~c~~~f~~~~~l~~h~~~-~~~~~~~~c~~c~~~~~~~~~l~~h~~~~ 108 (150)
||.|..|++.|.+...|..|++. |.+ +.|++|++.|.. +..|.++.
T Consensus 1 py~C~~Cgk~F~s~s~Lk~H~r~~H~~---~~C~~CgKsF~~---l~~H~~~~ 47 (79)
T PHA00732 1 MFKCPICGFTTVTLFALKQHARRNHTL---TKCPVCNKSYRR---LNQHFYSQ 47 (79)
T ss_pred CccCCCCCCccCCHHHHHHHhhcccCC---CccCCCCCEeCC---hhhhhccc
Confidence 57788888888888888888874 543 578888888873 56676443
No 26
>PHA00732 hypothetical protein
Probab=98.46 E-value=1.6e-07 Score=49.37 Aligned_cols=37 Identities=22% Similarity=0.578 Sum_probs=19.4
Q ss_pred eecccccccccChHHHHHHHhccCCcccccCCCCcccC
Q psy12196 31 IQCNMCSLVLDSKESLVTHISQTHTLMFTCRRCPSTFL 68 (150)
Q Consensus 31 ~~c~~c~~~f~~~~~l~~h~~~~~~~~~~c~~c~~~f~ 68 (150)
|.|..|++.|.+...|..|+...+. ++.|+.|++.|.
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 4555666666665556655422222 335556665554
No 27
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=98.42 E-value=9.1e-08 Score=38.23 Aligned_cols=23 Identities=35% Similarity=0.700 Sum_probs=18.3
Q ss_pred cCCcchhhhccCchHHHHHHHHh
Q psy12196 116 IQCPYCITDFSEDKNLIQHIVSV 138 (150)
Q Consensus 116 ~~C~~C~~~f~~~~~l~~H~~~~ 138 (150)
|.|+.|++.|.....|..|++.|
T Consensus 1 y~C~~C~~~f~~~~~l~~H~~~H 23 (23)
T PF00096_consen 1 YKCPICGKSFSSKSNLKRHMRRH 23 (23)
T ss_dssp EEETTTTEEESSHHHHHHHHHHH
T ss_pred CCCCCCCCccCCHHHHHHHHhHC
Confidence 56888888888888888888763
No 28
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=98.30 E-value=3.6e-07 Score=36.76 Aligned_cols=24 Identities=38% Similarity=0.757 Sum_probs=18.2
Q ss_pred cCCcchhhhccCchHHHHHHHHhc
Q psy12196 116 IQCPYCITDFSEDKNLIQHIVSVH 139 (150)
Q Consensus 116 ~~C~~C~~~f~~~~~l~~H~~~~~ 139 (150)
|.|+.|++.|.+...|..|+.++|
T Consensus 1 ~~C~~C~~~~~~~~~l~~H~~~~H 24 (24)
T PF13894_consen 1 FQCPICGKSFRSKSELRQHMRTHH 24 (24)
T ss_dssp EE-SSTS-EESSHHHHHHHHHHHS
T ss_pred CCCcCCCCcCCcHHHHHHHHHhhC
Confidence 568888888888888888888775
No 29
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=98.23 E-value=7.4e-07 Score=35.51 Aligned_cols=22 Identities=27% Similarity=0.557 Sum_probs=17.5
Q ss_pred CCCCcccccccCHHHHHHHHHH
Q psy12196 1 MSCVPCDVLFHNKATLYKHLYL 22 (150)
Q Consensus 1 ~~C~~C~~~f~~~~~l~~h~~~ 22 (150)
|.|+.|++.|.+...|..|++.
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 5688888888888888888765
No 30
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=98.19 E-value=1.2e-06 Score=48.42 Aligned_cols=73 Identities=22% Similarity=0.398 Sum_probs=19.5
Q ss_pred CCCcccccccCHHHHHHHHHHHhhCCCcceecccccccccChHHHHHHHhccCCcccccCCCCcccCChHHHHHHHHhh
Q psy12196 2 SCVPCDVLFHNKATLYKHLYLEHKATSLSIQCNMCSLVLDSKESLVTHISQTHTLMFTCRRCPSTFLNSATLSKHVKME 80 (150)
Q Consensus 2 ~C~~C~~~f~~~~~l~~h~~~~~~~~~~~~~c~~c~~~f~~~~~l~~h~~~~~~~~~~c~~c~~~f~~~~~l~~h~~~~ 80 (150)
+|..|+..|.+...|..|+...|.... + ....+.....+...+...-...+.|..|+..|.+...|..|+..+
T Consensus 1 ~C~~C~~~f~~~~~l~~H~~~~H~~~~-----~-~~~~l~~~~~~~~~~~~~~~~~~~C~~C~~~f~s~~~l~~Hm~~~ 73 (100)
T PF12756_consen 1 QCLFCDESFSSVDDLLQHMKKKHGFDI-----P-DQKYLVDPNRLLNYLRKKVKESFRCPYCNKTFRSREALQEHMRSK 73 (100)
T ss_dssp ------------------------------------------------------SSEEBSSSS-EESSHHHHHHHHHHT
T ss_pred Ccccccccccccccccccccccccccc-----c-cccccccccccccccccccCCCCCCCccCCCCcCHHHHHHHHcCc
Confidence 588899999999999999877665211 1 111112233333333222224678888888888888888888864
No 31
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=98.11 E-value=2e-06 Score=34.46 Aligned_cols=24 Identities=29% Similarity=0.628 Sum_probs=17.1
Q ss_pred CCCCcccccccCHHHHHHHHHHHh
Q psy12196 1 MSCVPCDVLFHNKATLYKHLYLEH 24 (150)
Q Consensus 1 ~~C~~C~~~f~~~~~l~~h~~~~~ 24 (150)
|+|+.|+..|.+...|..|+..+|
T Consensus 1 ~~C~~C~~~~~~~~~l~~H~~~~H 24 (24)
T PF13894_consen 1 FQCPICGKSFRSKSELRQHMRTHH 24 (24)
T ss_dssp EE-SSTS-EESSHHHHHHHHHHHS
T ss_pred CCCcCCCCcCCcHHHHHHHHHhhC
Confidence 568888888888888888877643
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=98.08 E-value=6.7e-07 Score=37.15 Aligned_cols=25 Identities=28% Similarity=0.361 Sum_probs=18.3
Q ss_pred CcCCcchhhhccCchHHHHHHHHhc
Q psy12196 115 QIQCPYCITDFSEDKNLIQHIVSVH 139 (150)
Q Consensus 115 ~~~C~~C~~~f~~~~~l~~H~~~~~ 139 (150)
+|.|..|++.|.+..+|..|++.|+
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 4667777777777777777776664
No 33
>PF09237 GAGA: GAGA factor; InterPro: IPR015318 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Members of this entry bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognises the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognises the A in the fourth position of the consensus sequence []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1YUI_A 1YUJ_A.
Probab=98.05 E-value=3.5e-06 Score=39.53 Aligned_cols=31 Identities=29% Similarity=0.594 Sum_probs=22.7
Q ss_pred CCcCCcchhhhccCchHHHHHHHHhcCCCCC
Q psy12196 114 HQIQCPYCITDFSEDKNLIQHIVSVHLGKEG 144 (150)
Q Consensus 114 ~~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~ 144 (150)
.|-.|++|+..+....+|.+|++..|+.+|.
T Consensus 23 ~PatCP~C~a~~~~srnLrRHle~~H~~k~~ 53 (54)
T PF09237_consen 23 QPATCPICGAVIRQSRNLRRHLEIRHFKKPG 53 (54)
T ss_dssp --EE-TTT--EESSHHHHHHHHHHHTTTS--
T ss_pred CCCCCCcchhhccchhhHHHHHHHHhcccCC
Confidence 3788999999999999999999999988874
No 34
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=97.99 E-value=2.8e-06 Score=46.96 Aligned_cols=73 Identities=23% Similarity=0.408 Sum_probs=17.8
Q ss_pred ccCCCCcccCChHHHHHHHHhhcCCCcccCCCChhhhcchhHHhhHHhhhcCCCCCCcCCcchhhhccCchHHHHHHHHh
Q psy12196 59 TCRRCPSTFLNSATLSKHVKMEHNSKSYQCNECPESFERLNKLKRHKFQAHNDSVHQIQCPYCITDFSEDKNLIQHIVSV 138 (150)
Q Consensus 59 ~c~~c~~~f~~~~~l~~h~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~~ 138 (150)
+|..|+..|.+...+..|+...++-..-.. ..+.....+..+.... -.. .+.|..|++.|.+...|..|+..+
T Consensus 1 ~C~~C~~~f~~~~~l~~H~~~~H~~~~~~~----~~l~~~~~~~~~~~~~-~~~--~~~C~~C~~~f~s~~~l~~Hm~~~ 73 (100)
T PF12756_consen 1 QCLFCDESFSSVDDLLQHMKKKHGFDIPDQ----KYLVDPNRLLNYLRKK-VKE--SFRCPYCNKTFRSREALQEHMRSK 73 (100)
T ss_dssp -----------------------------------------------------S--SEEBSSSS-EESSHHHHHHHHHHT
T ss_pred Cccccccccccccccccccccccccccccc----cccccccccccccccc-cCC--CCCCCccCCCCcCHHHHHHHHcCc
Confidence 366677777777777777765544321100 1111222222222111 111 467888888888888888888765
No 35
>smart00355 ZnF_C2H2 zinc finger.
Probab=97.78 E-value=2.6e-05 Score=31.63 Aligned_cols=23 Identities=26% Similarity=0.560 Sum_probs=17.6
Q ss_pred cCCcchhhhccCchHHHHHHHHh
Q psy12196 116 IQCPYCITDFSEDKNLIQHIVSV 138 (150)
Q Consensus 116 ~~C~~C~~~f~~~~~l~~H~~~~ 138 (150)
|.|+.|++.|.....|..|+..|
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~~H 23 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMRTH 23 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHHHh
Confidence 46778888888888888887754
No 36
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=97.71 E-value=1.1e-05 Score=52.67 Aligned_cols=69 Identities=17% Similarity=0.296 Sum_probs=42.4
Q ss_pred CcccccCC--CCcccCChHHHHHHHHhhc-CCCcccCCCChhhhcchhHHhhHHhhhcCCCCCCcCCcchhhhccCchHH
Q psy12196 55 TLMFTCRR--CPSTFLNSATLSKHVKMEH-NSKSYQCNECPESFERLNKLKRHKFQAHNDSVHQIQCPYCITDFSEDKNL 131 (150)
Q Consensus 55 ~~~~~c~~--c~~~f~~~~~l~~h~~~~~-~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~~C~~C~~~f~~~~~l 131 (150)
++||+|++ |+++|.+...|.-|+...+ ..+...-+ .-..+... ..+.+||+|+.|+|.+...-.|
T Consensus 347 ~KpykCpV~gC~K~YknqnGLKYH~lhGH~~~~~~~~p----------~p~~~~~F--~~~~KPYrCevC~KRYKNlNGL 414 (423)
T COG5189 347 GKPYKCPVEGCNKKYKNQNGLKYHMLHGHQNQKLHENP----------SPEKMNIF--SAKDKPYRCEVCDKRYKNLNGL 414 (423)
T ss_pred CceecCCCCCchhhhccccchhhhhhccccCcccCCCC----------Cccccccc--cccCCceeccccchhhccCccc
Confidence 38999988 9999999999999877533 22211100 00011111 2233478888888887777777
Q ss_pred HHHH
Q psy12196 132 IQHI 135 (150)
Q Consensus 132 ~~H~ 135 (150)
..|.
T Consensus 415 KYHr 418 (423)
T COG5189 415 KYHR 418 (423)
T ss_pred eecc
Confidence 6665
No 37
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=97.69 E-value=2.1e-05 Score=31.54 Aligned_cols=24 Identities=33% Similarity=0.589 Sum_probs=17.7
Q ss_pred cCCcchhhhccCchHHHHHHHHhcC
Q psy12196 116 IQCPYCITDFSEDKNLIQHIVSVHL 140 (150)
Q Consensus 116 ~~C~~C~~~f~~~~~l~~H~~~~~~ 140 (150)
|+|+.|+.... ...|.+|++.+|+
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 57888888887 8888888888774
No 38
>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=97.65 E-value=3.2e-05 Score=31.95 Aligned_cols=19 Identities=32% Similarity=0.679 Sum_probs=7.3
Q ss_pred ccCCCCcccCChHHHHHHH
Q psy12196 59 TCRRCPSTFLNSATLSKHV 77 (150)
Q Consensus 59 ~c~~c~~~f~~~~~l~~h~ 77 (150)
.|..|+..|.+...|..|+
T Consensus 3 ~C~~C~~~F~~~~~l~~H~ 21 (27)
T PF13912_consen 3 ECDECGKTFSSLSALREHK 21 (27)
T ss_dssp EETTTTEEESSHHHHHHHH
T ss_pred CCCccCCccCChhHHHHHh
Confidence 3333333333333333333
No 39
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=97.57 E-value=2.6e-05 Score=50.93 Aligned_cols=25 Identities=24% Similarity=0.655 Sum_probs=16.7
Q ss_pred CcCCcc--hhhhccCchHHHHHHHHhc
Q psy12196 115 QIQCPY--CITDFSEDKNLIQHIVSVH 139 (150)
Q Consensus 115 ~~~C~~--C~~~f~~~~~l~~H~~~~~ 139 (150)
||+|++ |+|.+...-.|..|+.-.|
T Consensus 349 pykCpV~gC~K~YknqnGLKYH~lhGH 375 (423)
T COG5189 349 PYKCPVEGCNKKYKNQNGLKYHMLHGH 375 (423)
T ss_pred eecCCCCCchhhhccccchhhhhhccc
Confidence 777754 7777777777777765444
No 40
>smart00355 ZnF_C2H2 zinc finger.
Probab=97.56 E-value=0.00012 Score=29.58 Aligned_cols=22 Identities=27% Similarity=0.647 Sum_probs=18.7
Q ss_pred CCCCcccccccCHHHHHHHHHH
Q psy12196 1 MSCVPCDVLFHNKATLYKHLYL 22 (150)
Q Consensus 1 ~~C~~C~~~f~~~~~l~~h~~~ 22 (150)
|.|+.|++.|.....|..|++.
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~~ 22 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMRT 22 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHHH
Confidence 5788899999999998888875
No 41
>KOG2231|consensus
Probab=97.43 E-value=0.00063 Score=49.35 Aligned_cols=134 Identities=23% Similarity=0.364 Sum_probs=82.3
Q ss_pred CCCcccccc---------------cCHHHHHHHHHHHhhCCCcceecccccc---------cccChHHHHHHHhccCC--
Q psy12196 2 SCVPCDVLF---------------HNKATLYKHLYLEHKATSLSIQCNMCSL---------VLDSKESLVTHISQTHT-- 55 (150)
Q Consensus 2 ~C~~C~~~f---------------~~~~~l~~h~~~~~~~~~~~~~c~~c~~---------~f~~~~~l~~h~~~~~~-- 55 (150)
.|..|+..| .....|+.|+...|. .+-|..|.. .......|..|+ +.+.
T Consensus 101 ~C~~C~~~~~~~~~~~~~~~c~~~~s~~~Lk~H~~~~H~----~~~c~lC~~~~kif~~e~k~Yt~~el~~h~-~~gd~d 175 (669)
T KOG2231|consen 101 SCHICDRRFRALYNKKECLHCTEFKSVENLKNHMRDQHK----LHLCSLCLQNLKIFINERKLYTRAELNLHL-MFGDPD 175 (669)
T ss_pred hcCccccchhhhcccCCCccccchhHHHHHHHHHHHhhh----hhccccccccceeeeeeeehehHHHHHHHH-hcCCCc
Confidence 577777666 367889999877664 234555532 233456777776 2221
Q ss_pred -----cccccCCCCcccCChHHHHHHHHhhcCCCcccCCCCh------hhhcchhHHhhHHhhhcCCCC-CCcCCcchhh
Q psy12196 56 -----LMFTCRRCPSTFLNSATLSKHVKMEHNSKSYQCNECP------ESFERLNKLKRHKFQAHNDSV-HQIQCPYCIT 123 (150)
Q Consensus 56 -----~~~~c~~c~~~f~~~~~l~~h~~~~~~~~~~~c~~c~------~~~~~~~~l~~h~~~~~~~~~-~~~~C~~C~~ 123 (150)
.--.|..|...|.....|..|++.++ |.|..|+ ..|....+|..|-+..|-.-+ -...+..+..
T Consensus 176 ~~s~rGhp~C~~C~~~fld~~el~rH~~~~h----~~chfC~~~~~~neyy~~~~dLe~HfR~~HflCE~~~C~~~~f~~ 251 (669)
T KOG2231|consen 176 DESCRGHPLCKFCHERFLDDDELYRHLRFDH----EFCHFCDYKTGQNEYYNDYDDLEEHFRKGHFLCEEEFCRTKKFYV 251 (669)
T ss_pred cccccCCccchhhhhhhccHHHHHHhhccce----eheeecCcccccchhcccchHHHHHhhhcCccccccccccceeee
Confidence 22468889999999999999999876 5666663 445667788888776543221 0222334444
Q ss_pred hccCchHHHHHHHHhcCCCCC
Q psy12196 124 DFSEDKNLIQHIVSVHLGKEG 144 (150)
Q Consensus 124 ~f~~~~~l~~H~~~~~~~~~~ 144 (150)
+|.....|.+|-+.+..|+.|
T Consensus 252 ~~~~ei~lk~~~~~~~~e~~~ 272 (669)
T KOG2231|consen 252 AFELEIELKAHNRFIQHEKCY 272 (669)
T ss_pred hhHHHHHHHhhccccchheec
Confidence 555566666555444444444
No 42
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=97.40 E-value=3.8e-05 Score=31.06 Aligned_cols=23 Identities=35% Similarity=0.639 Sum_probs=17.6
Q ss_pred cCCcchhhhccCchHHHHHHHHh
Q psy12196 116 IQCPYCITDFSEDKNLIQHIVSV 138 (150)
Q Consensus 116 ~~C~~C~~~f~~~~~l~~H~~~~ 138 (150)
|.|..|++.|.+...|..|++++
T Consensus 1 ~~C~~C~~~f~s~~~~~~H~~s~ 23 (25)
T PF12874_consen 1 FYCDICNKSFSSENSLRQHLRSK 23 (25)
T ss_dssp EEETTTTEEESSHHHHHHHHTTH
T ss_pred CCCCCCCCCcCCHHHHHHHHCcC
Confidence 45778888888888888887654
No 43
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=97.35 E-value=0.00017 Score=28.84 Aligned_cols=23 Identities=30% Similarity=0.528 Sum_probs=17.4
Q ss_pred CCCCcccccccCHHHHHHHHHHHh
Q psy12196 1 MSCVPCDVLFHNKATLYKHLYLEH 24 (150)
Q Consensus 1 ~~C~~C~~~f~~~~~l~~h~~~~~ 24 (150)
|+|+.|+.... ...|..|+..+|
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 67999998887 888999988765
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=97.32 E-value=0.00029 Score=33.22 Aligned_cols=30 Identities=27% Similarity=0.468 Sum_probs=16.6
Q ss_pred cccccCCCCcccCChHHHHHHHHhhcCCCc
Q psy12196 56 LMFTCRRCPSTFLNSATLSKHVKMEHNSKS 85 (150)
Q Consensus 56 ~~~~c~~c~~~f~~~~~l~~h~~~~~~~~~ 85 (150)
.|..||+|+..+..+.+|..|+...++.+|
T Consensus 23 ~PatCP~C~a~~~~srnLrRHle~~H~~k~ 52 (54)
T PF09237_consen 23 QPATCPICGAVIRQSRNLRRHLEIRHFKKP 52 (54)
T ss_dssp --EE-TTT--EESSHHHHHHHHHHHTTTS-
T ss_pred CCCCCCcchhhccchhhHHHHHHHHhcccC
Confidence 566677777777777777777766666554
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=96.94 E-value=8.8e-05 Score=30.62 Aligned_cols=22 Identities=36% Similarity=0.608 Sum_probs=14.2
Q ss_pred cCCcchhhhccCchHHHHHHHH
Q psy12196 116 IQCPYCITDFSEDKNLIQHIVS 137 (150)
Q Consensus 116 ~~C~~C~~~f~~~~~l~~H~~~ 137 (150)
|.|..|++.|.+...|..|+.+
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 4566677777776666666644
No 46
>PRK04860 hypothetical protein; Provisional
Probab=96.94 E-value=0.00047 Score=41.41 Aligned_cols=38 Identities=21% Similarity=0.543 Sum_probs=26.0
Q ss_pred cccCCCChhhhcchhHHhhHHhhhcCCCCCCcCCcchhhhccCc
Q psy12196 85 SYQCNECPESFERLNKLKRHKFQAHNDSVHQIQCPYCITDFSED 128 (150)
Q Consensus 85 ~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~~C~~C~~~f~~~ 128 (150)
+|.|. |+. ....+.+|.+++.+++ +|.|..|+..|...
T Consensus 119 ~Y~C~-C~~---~~~~~rrH~ri~~g~~--~YrC~~C~~~l~~~ 156 (160)
T PRK04860 119 PYRCK-CQE---HQLTVRRHNRVVRGEA--VYRCRRCGETLVFK 156 (160)
T ss_pred EEEcC-CCC---eeCHHHHHHHHhcCCc--cEECCCCCceeEEe
Confidence 47776 765 4556677777777766 77777777776654
No 47
>PRK04860 hypothetical protein; Provisional
Probab=96.93 E-value=0.00036 Score=41.90 Aligned_cols=28 Identities=14% Similarity=0.176 Sum_probs=13.3
Q ss_pred CcCCcchhhhccCchHHHHHHHHhcCCCCCCC
Q psy12196 115 QIQCPYCITDFSEDKNLIQHIVSVHLGKEGTA 146 (150)
Q Consensus 115 ~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~~ 146 (150)
+|.|. |++ ....+.+|.+++.++++|.|
T Consensus 119 ~Y~C~-C~~---~~~~~rrH~ri~~g~~~YrC 146 (160)
T PRK04860 119 PYRCK-CQE---HQLTVRRHNRVVRGEAVYRC 146 (160)
T ss_pred EEEcC-CCC---eeCHHHHHHHHhcCCccEEC
Confidence 44454 443 33444455555555555444
No 48
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=96.77 E-value=0.0011 Score=26.64 Aligned_cols=19 Identities=26% Similarity=0.772 Sum_probs=8.5
Q ss_pred cCCCCcccCChHHHHHHHH
Q psy12196 60 CRRCPSTFLNSATLSKHVK 78 (150)
Q Consensus 60 c~~c~~~f~~~~~l~~h~~ 78 (150)
|.+|+..|.+...+..|++
T Consensus 3 C~~C~~~f~s~~~~~~H~~ 21 (25)
T PF12874_consen 3 CDICNKSFSSENSLRQHLR 21 (25)
T ss_dssp ETTTTEEESSHHHHHHHHT
T ss_pred CCCCCCCcCCHHHHHHHHC
Confidence 4444444444444444443
No 49
>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=96.60 E-value=0.00082 Score=27.63 Aligned_cols=21 Identities=29% Similarity=0.664 Sum_probs=15.7
Q ss_pred CCCCcccccccCHHHHHHHHH
Q psy12196 1 MSCVPCDVLFHNKATLYKHLY 21 (150)
Q Consensus 1 ~~C~~C~~~f~~~~~l~~h~~ 21 (150)
|-|..|++.|.+...+..|+.
T Consensus 2 ~~C~~C~k~f~~~~~~~~H~~ 22 (27)
T PF12171_consen 2 FYCDACDKYFSSENQLKQHMK 22 (27)
T ss_dssp CBBTTTTBBBSSHHHHHCCTT
T ss_pred CCcccCCCCcCCHHHHHHHHc
Confidence 567788888888888777754
No 50
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=96.23 E-value=0.0069 Score=24.39 Aligned_cols=19 Identities=37% Similarity=0.532 Sum_probs=11.0
Q ss_pred CCCcccccccCHHHHHHHHH
Q psy12196 2 SCVPCDVLFHNKATLYKHLY 21 (150)
Q Consensus 2 ~C~~C~~~f~~~~~l~~h~~ 21 (150)
.|+.||+.| ....|..|+.
T Consensus 4 ~C~~CgR~F-~~~~l~~H~~ 22 (25)
T PF13913_consen 4 PCPICGRKF-NPDRLEKHEK 22 (25)
T ss_pred cCCCCCCEE-CHHHHHHHHH
Confidence 466666666 5555555543
No 51
>KOG1146|consensus
Probab=96.12 E-value=0.0015 Score=50.64 Aligned_cols=51 Identities=25% Similarity=0.479 Sum_probs=31.7
Q ss_pred cccccCCCCcccCChHHHHHHHHhhc-------------------------CCCcccCCCChhhhcchhHHhhHHh
Q psy12196 56 LMFTCRRCPSTFLNSATLSKHVKMEH-------------------------NSKSYQCNECPESFERLNKLKRHKF 106 (150)
Q Consensus 56 ~~~~c~~c~~~f~~~~~l~~h~~~~~-------------------------~~~~~~c~~c~~~~~~~~~l~~h~~ 106 (150)
+.+.|+.|+..|.....|..|+++.+ +.++|.|..|...+....+|.+|++
T Consensus 464 kt~~cpkc~~~yk~a~~L~vhmRskhp~~~~~~c~~gq~~~~~arg~~~~~~~~p~~C~~C~~stttng~Lsihlq 539 (1406)
T KOG1146|consen 464 KTLKCPKCNWHYKLAQTLGVHMRSKHPESQSAYCKAGQNHPRLARGEVYRCPGKPYPCRACNYSTTTNGNLSIHLQ 539 (1406)
T ss_pred ccccCCccchhhhhHHHhhhcccccccccchhHhHhccccccccccccccCCCCcccceeeeeeeecchHHHHHHH
Confidence 55666666666666666666666522 2355666666666666666666654
No 52
>smart00451 ZnF_U1 U1-like zinc finger. Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins.
Probab=95.74 E-value=0.0052 Score=26.78 Aligned_cols=24 Identities=17% Similarity=0.491 Sum_probs=19.4
Q ss_pred CcCCcchhhhccCchHHHHHHHHh
Q psy12196 115 QIQCPYCITDFSEDKNLIQHIVSV 138 (150)
Q Consensus 115 ~~~C~~C~~~f~~~~~l~~H~~~~ 138 (150)
+|.|..|++.|.+...+..|+.+.
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~gk 26 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLKGK 26 (35)
T ss_pred CeEccccCCccCCHHHHHHHHChH
Confidence 577888999998888888887654
No 53
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=95.62 E-value=0.022 Score=38.25 Aligned_cols=125 Identities=22% Similarity=0.423 Sum_probs=80.4
Q ss_pred CCCCc--ccccccCHHHHHHHHHHHhhCCCcceecccccc---ccc------ChHHHHHHHhccCC------cccccCCC
Q psy12196 1 MSCVP--CDVLFHNKATLYKHLYLEHKATSLSIQCNMCSL---VLD------SKESLVTHISQTHT------LMFTCRRC 63 (150)
Q Consensus 1 ~~C~~--C~~~f~~~~~l~~h~~~~~~~~~~~~~c~~c~~---~f~------~~~~l~~h~~~~~~------~~~~c~~c 63 (150)
|.|+. |+........|..|.+..|. -+.|..|.. .|. ....|..|. ..+. .--.|..|
T Consensus 152 F~CP~skc~~~C~~~k~lk~H~K~~H~----~~~C~~C~~nKk~F~~E~~lF~~~~Lr~H~-~~G~~e~GFKGHP~C~FC 226 (493)
T COG5236 152 FKCPKSKCHRRCGSLKELKKHYKAQHG----FVLCSECIGNKKDFWNEIRLFRSSTLRDHK-NGGLEEEGFKGHPLCIFC 226 (493)
T ss_pred hcCCchhhhhhhhhHHHHHHHHHhhcC----cEEhHhhhcCcccCccceeeeecccccccc-cCCccccCcCCCchhhhc
Confidence 44554 67777778899999888664 245666632 232 334555564 2221 23469999
Q ss_pred CcccCChHHHHHHHHhhcCCCcccCCCChh-------hhcchhHHhhHHhhhcCCCCCCcCCcc--hh----hhccCchH
Q psy12196 64 PSTFLNSATLSKHVKMEHNSKSYQCNECPE-------SFERLNKLKRHKFQAHNDSVHQIQCPY--CI----TDFSEDKN 130 (150)
Q Consensus 64 ~~~f~~~~~l~~h~~~~~~~~~~~c~~c~~-------~~~~~~~l~~h~~~~~~~~~~~~~C~~--C~----~~f~~~~~ 130 (150)
...|.+...|..|++..+. .|-+|+. .|.....|..|.... -|.|.. |. ..|...-.
T Consensus 227 ~~~FYdDDEL~~HcR~~HE----~ChICD~v~p~~~QYFK~Y~~Le~HF~~~------hy~ct~qtc~~~k~~vf~~~~e 296 (493)
T COG5236 227 KIYFYDDDELRRHCRLRHE----ACHICDMVGPIRYQYFKSYEDLEAHFRNA------HYCCTFQTCRVGKCYVFPYHTE 296 (493)
T ss_pred cceecChHHHHHHHHhhhh----hhhhhhccCccchhhhhCHHHHHHHhhcC------ceEEEEEEEecCcEEEeccHHH
Confidence 9999999999999997663 4555543 355666777775422 334422 21 36888999
Q ss_pred HHHHHHHhcC
Q psy12196 131 LIQHIVSVHL 140 (150)
Q Consensus 131 l~~H~~~~~~ 140 (150)
|+.|+...|+
T Consensus 297 l~~h~~~~h~ 306 (493)
T COG5236 297 LLEHLTRFHK 306 (493)
T ss_pred HHHHHHHHhh
Confidence 9999988774
No 54
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=95.45 E-value=0.02 Score=32.20 Aligned_cols=25 Identities=20% Similarity=0.328 Sum_probs=18.3
Q ss_pred CcCCcchhhhccCchHHHHHHHHhc
Q psy12196 115 QIQCPYCITDFSEDKNLIQHIVSVH 139 (150)
Q Consensus 115 ~~~C~~C~~~f~~~~~l~~H~~~~~ 139 (150)
.|+|+.|...|...-++-.|-..|.
T Consensus 81 ~y~C~~C~~~FC~dCD~fiHe~Lh~ 105 (112)
T TIGR00622 81 RYVCAVCKNVFCVDCDVFVHESLHC 105 (112)
T ss_pred ceeCCCCCCccccccchhhhhhccC
Confidence 6778888888887777777765553
No 55
>cd00350 rubredoxin_like Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center. The family includes rubredoxins, a small electron transfer protein, and a slightly smaller modular rubredoxin domain present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=94.90 E-value=0.012 Score=25.39 Aligned_cols=9 Identities=33% Similarity=0.818 Sum_probs=5.9
Q ss_pred CcCCcchhh
Q psy12196 115 QIQCPYCIT 123 (150)
Q Consensus 115 ~~~C~~C~~ 123 (150)
++.||.|+.
T Consensus 17 ~~~CP~Cg~ 25 (33)
T cd00350 17 PWVCPVCGA 25 (33)
T ss_pred CCcCcCCCC
Confidence 667777763
No 56
>KOG2482|consensus
Probab=94.77 E-value=0.11 Score=35.07 Aligned_cols=51 Identities=25% Similarity=0.438 Sum_probs=29.3
Q ss_pred cCCCChhhhcchhHHhhHHhhhcC--------C-----------------CCCCcCCcchhhhccCchHHHHHHHH
Q psy12196 87 QCNECPESFERLNKLKRHKFQAHN--------D-----------------SVHQIQCPYCITDFSEDKNLIQHIVS 137 (150)
Q Consensus 87 ~c~~c~~~~~~~~~l~~h~~~~~~--------~-----------------~~~~~~C~~C~~~f~~~~~l~~H~~~ 137 (150)
+|-.|.....+...|..|+.+.+. + ..+...|-.|.-.|-....|..||.-
T Consensus 281 ~CLfC~~~~en~~~l~eHmk~vHe~Dl~Ki~sd~~Ln~YqrvrviNyiRkq~~~~~c~~cd~~F~~e~~l~~hm~e 356 (423)
T KOG2482|consen 281 VCLFCTNFYENPVFLFEHMKIVHEFDLLKIQSDYSLNFYQRVRVINYIRKQKKKSRCAECDLSFWKEPGLLIHMVE 356 (423)
T ss_pred EEEeeccchhhHHHHHHHHHHHHHhhHHhhccccccchhhhhhHHHHHHHHhhccccccccccccCcchhhhhccc
Confidence 566666666666666666654331 0 01223466677677777777777643
No 57
>KOG1146|consensus
Probab=94.60 E-value=0.016 Score=45.31 Aligned_cols=58 Identities=21% Similarity=0.317 Sum_probs=47.6
Q ss_pred cCCCcccCCCChhhhcchhHHhhHHhhhcCC-----------------------CCCCcCCcchhhhccCchHHHHHHHH
Q psy12196 81 HNSKSYQCNECPESFERLNKLKRHKFQAHND-----------------------SVHQIQCPYCITDFSEDKNLIQHIVS 137 (150)
Q Consensus 81 ~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~-----------------------~~~~~~C~~C~~~f~~~~~l~~H~~~ 137 (150)
.-.+.+.|.+|+..|.....|..|++..+.+ ..++|.|..|...++...+|..|+.+
T Consensus 461 S~~kt~~cpkc~~~yk~a~~L~vhmRskhp~~~~~~c~~gq~~~~~arg~~~~~~~~p~~C~~C~~stttng~LsihlqS 540 (1406)
T KOG1146|consen 461 SFFKTLKCPKCNWHYKLAQTLGVHMRSKHPESQSAYCKAGQNHPRLARGEVYRCPGKPYPCRACNYSTTTNGNLSIHLQS 540 (1406)
T ss_pred cccccccCCccchhhhhHHHhhhcccccccccchhHhHhccccccccccccccCCCCcccceeeeeeeecchHHHHHHHH
Confidence 3457899999999999999999999874311 12578999999999999999999865
Q ss_pred h
Q psy12196 138 V 138 (150)
Q Consensus 138 ~ 138 (150)
-
T Consensus 541 ~ 541 (1406)
T KOG1146|consen 541 D 541 (1406)
T ss_pred H
Confidence 3
No 58
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=94.54 E-value=0.029 Score=27.00 Aligned_cols=25 Identities=32% Similarity=0.712 Sum_probs=21.2
Q ss_pred CcCCcchhhhccCchHHHHHHHHhc
Q psy12196 115 QIQCPYCITDFSEDKNLIQHIVSVH 139 (150)
Q Consensus 115 ~~~C~~C~~~f~~~~~l~~H~~~~~ 139 (150)
-+.||.|+..|....++.+|...-|
T Consensus 17 ~lrCPRC~~~FR~~K~Y~RHVNKaH 41 (65)
T COG4049 17 FLRCPRCGMVFRRRKDYIRHVNKAH 41 (65)
T ss_pred eeeCCchhHHHHHhHHHHHHhhHHh
Confidence 7889999999999999999975555
No 59
>KOG2231|consensus
Probab=93.53 E-value=0.15 Score=37.69 Aligned_cols=98 Identities=23% Similarity=0.367 Sum_probs=61.1
Q ss_pred ccccChHHHHHHHhccCCcccccCCC---C------cccCChHHHHHHHHhhcC-CC----cccCCCChhhhcchhHHhh
Q psy12196 38 LVLDSKESLVTHISQTHTLMFTCRRC---P------STFLNSATLSKHVKMEHN-SK----SYQCNECPESFERLNKLKR 103 (150)
Q Consensus 38 ~~f~~~~~l~~h~~~~~~~~~~c~~c---~------~~f~~~~~l~~h~~~~~~-~~----~~~c~~c~~~~~~~~~l~~ 103 (150)
..|.....|..|+...|+. +.|.+| . ........|..|+...-. ++ ...|..|...|.....|.+
T Consensus 122 ~~~~s~~~Lk~H~~~~H~~-~~c~lC~~~~kif~~e~k~Yt~~el~~h~~~gd~d~~s~rGhp~C~~C~~~fld~~el~r 200 (669)
T KOG2231|consen 122 TEFKSVENLKNHMRDQHKL-HLCSLCLQNLKIFINERKLYTRAELNLHLMFGDPDDESCRGHPLCKFCHERFLDDDELYR 200 (669)
T ss_pred cchhHHHHHHHHHHHhhhh-hccccccccceeeeeeeehehHHHHHHHHhcCCCccccccCCccchhhhhhhccHHHHHH
Confidence 3344678888887555542 233333 1 222345566666654322 21 2468889999999999999
Q ss_pred HHhhhcCCCCCCcCC---cchhhhccCchHHHHHHHHhc
Q psy12196 104 HKFQAHNDSVHQIQC---PYCITDFSEDKNLIQHIVSVH 139 (150)
Q Consensus 104 h~~~~~~~~~~~~~C---~~C~~~f~~~~~l~~H~~~~~ 139 (150)
|++..+..- -| | +.++.-|....+|..|.+..|
T Consensus 201 H~~~~h~~c--hf-C~~~~~~neyy~~~~dLe~HfR~~H 236 (669)
T KOG2231|consen 201 HLRFDHEFC--HF-CDYKTGQNEYYNDYDDLEEHFRKGH 236 (669)
T ss_pred hhccceehe--ee-cCcccccchhcccchHHHHHhhhcC
Confidence 987654432 22 3 345566888899999998887
No 60
>KOG2893|consensus
Probab=93.07 E-value=0.03 Score=35.68 Aligned_cols=40 Identities=25% Similarity=0.519 Sum_probs=19.9
Q ss_pred cCCCCcccCChHHHHHHHHhhcCCCcccCCCChhhhcchhHHhh
Q psy12196 60 CRRCPSTFLNSATLSKHVKMEHNSKSYQCNECPESFERLNKLKR 103 (150)
Q Consensus 60 c~~c~~~f~~~~~l~~h~~~~~~~~~~~c~~c~~~~~~~~~l~~ 103 (150)
|..|++.|.....|.+|++..+ |+|.+|-+..-+-..|..
T Consensus 13 cwycnrefddekiliqhqkakh----fkchichkkl~sgpglsi 52 (341)
T KOG2893|consen 13 CWYCNREFDDEKILIQHQKAKH----FKCHICHKKLFSGPGLSI 52 (341)
T ss_pred eeecccccchhhhhhhhhhhcc----ceeeeehhhhccCCCcee
Confidence 4455555555555555544332 555555544433333333
No 61
>KOG4173|consensus
Probab=92.48 E-value=0.061 Score=33.49 Aligned_cols=79 Identities=23% Similarity=0.516 Sum_probs=41.8
Q ss_pred cccCC--CCcccCChHHHHHHHHhhcCCCcccCCCChhhhcchhHHhhHHhhhcC--------CCCCCcCC--cchhhhc
Q psy12196 58 FTCRR--CPSTFLNSATLSKHVKMEHNSKSYQCNECPESFERLNKLKRHKFQAHN--------DSVHQIQC--PYCITDF 125 (150)
Q Consensus 58 ~~c~~--c~~~f~~~~~l~~h~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~--------~~~~~~~C--~~C~~~f 125 (150)
+.|++ |...|.+-.....|+..-++. .|.+|.+.|.+.--|..|+..-+. .+.-.|+| ..|+-.|
T Consensus 80 ~~cqvagc~~~~d~lD~~E~hY~~~h~~---sCs~C~r~~Pt~hLLd~HI~E~HDs~Fqa~veRG~dMy~ClvEgCt~KF 156 (253)
T KOG4173|consen 80 FACQVAGCCQVFDALDDYEHHYHTLHGN---SCSFCKRAFPTGHLLDAHILEWHDSLFQALVERGQDMYQCLVEGCTEKF 156 (253)
T ss_pred ccccccchHHHHhhhhhHHHhhhhcccc---hhHHHHHhCCchhhhhHHHHHHHHHHHHHHHHcCccHHHHHHHhhhhhh
Confidence 44554 445555555555555443332 566666666665555555433221 11114555 3477777
Q ss_pred cCchHHHHHHHHhc
Q psy12196 126 SEDKNLIQHIVSVH 139 (150)
Q Consensus 126 ~~~~~l~~H~~~~~ 139 (150)
.+..+-..|+-..|
T Consensus 157 kT~r~RkdH~I~~H 170 (253)
T KOG4173|consen 157 KTSRDRKDHMIRMH 170 (253)
T ss_pred hhhhhhhhHHHHhc
Confidence 77777767765554
No 62
>KOG2482|consensus
Probab=92.08 E-value=0.3 Score=33.08 Aligned_cols=50 Identities=30% Similarity=0.508 Sum_probs=36.9
Q ss_pred cccCCCCcccCChHHHHHHHHhhcC---------------------------CCcccCCCChhhhcchhHHhhHHhh
Q psy12196 58 FTCRRCPSTFLNSATLSKHVKMEHN---------------------------SKSYQCNECPESFERLNKLKRHKFQ 107 (150)
Q Consensus 58 ~~c~~c~~~f~~~~~l~~h~~~~~~---------------------------~~~~~c~~c~~~~~~~~~l~~h~~~ 107 (150)
..|-.|...+.+...|..||...+. ...-.|.+|.-.|-....|..|+..
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 4677788777778888888876441 1224688888889999999998754
No 63
>KOG2186|consensus
Probab=91.54 E-value=0.13 Score=33.21 Aligned_cols=45 Identities=18% Similarity=0.335 Sum_probs=26.0
Q ss_pred CCCCcccccccCHHHHHHHHHHHhhCCCcceecccccccccChHHHHHHH
Q psy12196 1 MSCVPCDVLFHNKATLYKHLYLEHKATSLSIQCNMCSLVLDSKESLVTHI 50 (150)
Q Consensus 1 ~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~~~c~~c~~~f~~~~~l~~h~ 50 (150)
|.|+.||........ ..|+.+.+. .-|.|-.|+++|.. ..+..|.
T Consensus 4 FtCnvCgEsvKKp~v-ekH~srCrn---~~fSCIDC~k~F~~-~sYknH~ 48 (276)
T KOG2186|consen 4 FTCNVCGESVKKPQV-EKHMSRCRN---AYFSCIDCGKTFER-VSYKNHT 48 (276)
T ss_pred Eehhhhhhhccccch-HHHHHhccC---CeeEEeeccccccc-chhhhhh
Confidence 456667666654433 336655433 23667777777766 5566665
No 64
>KOG4173|consensus
Probab=91.18 E-value=0.13 Score=32.08 Aligned_cols=77 Identities=27% Similarity=0.553 Sum_probs=50.0
Q ss_pred eeccc--ccccccChHHHHHHHhccCCcccccCCCCcccCChHHHHHHHHhhc----------CCCcccCCC--Chhhhc
Q psy12196 31 IQCNM--CSLVLDSKESLVTHISQTHTLMFTCRRCPSTFLNSATLSKHVKMEH----------NSKSYQCNE--CPESFE 96 (150)
Q Consensus 31 ~~c~~--c~~~f~~~~~l~~h~~~~~~~~~~c~~c~~~f~~~~~l~~h~~~~~----------~~~~~~c~~--c~~~~~ 96 (150)
+.|+. |...|..-.....|-...|.. .|..|.+.|.+...|..|+...+ |.-.|.|-+ |+..|.
T Consensus 80 ~~cqvagc~~~~d~lD~~E~hY~~~h~~--sCs~C~r~~Pt~hLLd~HI~E~HDs~Fqa~veRG~dMy~ClvEgCt~KFk 157 (253)
T KOG4173|consen 80 FACQVAGCCQVFDALDDYEHHYHTLHGN--SCSFCKRAFPTGHLLDAHILEWHDSLFQALVERGQDMYQCLVEGCTEKFK 157 (253)
T ss_pred ccccccchHHHHhhhhhHHHhhhhcccc--hhHHHHHhCCchhhhhHHHHHHHHHHHHHHHHcCccHHHHHHHhhhhhhh
Confidence 45654 556666555555553233332 58888888888888888877644 455688844 888888
Q ss_pred chhHHhhHHhhhc
Q psy12196 97 RLNKLKRHKFQAH 109 (150)
Q Consensus 97 ~~~~l~~h~~~~~ 109 (150)
+...-..|+-..+
T Consensus 158 T~r~RkdH~I~~H 170 (253)
T KOG4173|consen 158 TSRDRKDHMIRMH 170 (253)
T ss_pred hhhhhhhHHHHhc
Confidence 7777677765433
No 65
>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=91.10 E-value=0.13 Score=20.87 Aligned_cols=9 Identities=33% Similarity=0.888 Sum_probs=5.1
Q ss_pred ccCCCCccc
Q psy12196 59 TCRRCPSTF 67 (150)
Q Consensus 59 ~c~~c~~~f 67 (150)
.|+.||..|
T Consensus 16 ~Cp~CG~~F 24 (26)
T PF10571_consen 16 FCPHCGYDF 24 (26)
T ss_pred cCCCCCCCC
Confidence 456666555
No 66
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=91.05 E-value=0.16 Score=24.55 Aligned_cols=21 Identities=19% Similarity=0.637 Sum_probs=12.7
Q ss_pred CCCcccccccCHHHHHHHHHH
Q psy12196 2 SCVPCDVLFHNKATLYKHLYL 22 (150)
Q Consensus 2 ~C~~C~~~f~~~~~l~~h~~~ 22 (150)
.|+-||..|....+..+|...
T Consensus 19 rCPRC~~~FR~~K~Y~RHVNK 39 (65)
T COG4049 19 RCPRCGMVFRRRKDYIRHVNK 39 (65)
T ss_pred eCCchhHHHHHhHHHHHHhhH
Confidence 466666666666666666544
No 67
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=90.77 E-value=0.045 Score=38.13 Aligned_cols=58 Identities=26% Similarity=0.437 Sum_probs=37.1
Q ss_pred cccCCCChhhhcchhHHhhHHh--hhcCC--CCCCcCCc--chhhhccCchHHHHHHHHhcCCCCC
Q psy12196 85 SYQCNECPESFERLNKLKRHKF--QAHND--SVHQIQCP--YCITDFSEDKNLIQHIVSVHLGKEG 144 (150)
Q Consensus 85 ~~~c~~c~~~~~~~~~l~~h~~--~~~~~--~~~~~~C~--~C~~~f~~~~~l~~H~~~~~~~~~~ 144 (150)
++.|..|...|.....|..|.. .|.++ . ++.|+ .|++.|.....+..|...+.+-.+.
T Consensus 289 ~~~~~~~~~~~s~~~~l~~~~~~~~h~~~~~~--~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~ 352 (467)
T COG5048 289 PIKSKQCNISFSRSSPLTRHLRSVNHSGESLK--PFSCPYSLCGKLFSRNDALKRHILLHTSISPA 352 (467)
T ss_pred CCCCccccCCccccccccccccccccccccCC--ceeeeccCCCccccccccccCCcccccCCCcc
Confidence 4566666666666666666666 45555 4 66666 5777777777676666666655544
No 68
>PF12907 zf-met2: Zinc-binding
Probab=90.16 E-value=0.24 Score=22.42 Aligned_cols=33 Identities=21% Similarity=0.367 Sum_probs=23.1
Q ss_pred cCCcchhhhcc---CchHHHHHHHHhcCCCC-CCCCC
Q psy12196 116 IQCPYCITDFS---EDKNLIQHIVSVHLGKE-GTAPA 148 (150)
Q Consensus 116 ~~C~~C~~~f~---~~~~l~~H~~~~~~~~~-~~~~~ 148 (150)
++|.+|-..|. ....|..|....|.... .+|.+
T Consensus 2 i~C~iC~qtF~~t~~~~~L~eH~enKHpK~~~~~CFP 38 (40)
T PF12907_consen 2 IICKICRQTFMQTTNEPQLKEHAENKHPKNTFEECFP 38 (40)
T ss_pred cCcHHhhHHHHhcCCHHHHHHHHHccCCCCCHHHcCC
Confidence 57888886655 44679999988887763 35543
No 69
>KOG2893|consensus
Probab=89.99 E-value=0.075 Score=33.94 Aligned_cols=49 Identities=22% Similarity=0.430 Sum_probs=36.8
Q ss_pred cCCCChhhhcchhHHhhHHhhhcCCCCCCcCCcchhhhccCchHHHHHHHHhcCC
Q psy12196 87 QCNECPESFERLNKLKRHKFQAHNDSVHQIQCPYCITDFSEDKNLIQHIVSVHLG 141 (150)
Q Consensus 87 ~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~~~~~ 141 (150)
=|..|.+.|.....|..|+.. +-|+|-+|-|...+--.|..|-...|.|
T Consensus 12 wcwycnrefddekiliqhqka------khfkchichkkl~sgpglsihcmqvhke 60 (341)
T KOG2893|consen 12 WCWYCNREFDDEKILIQHQKA------KHFKCHICHKKLFSGPGLSIHCMQVHKE 60 (341)
T ss_pred eeeecccccchhhhhhhhhhh------ccceeeeehhhhccCCCceeehhhhhhh
Confidence 388899999999999888653 3789999998877666666664444433
No 70
>PF05443 ROS_MUCR: ROS/MUCR transcriptional regulator protein; InterPro: IPR008807 This family consists of several ROS/MUCR transcriptional regulator proteins. The ros chromosomal gene is present in octopine and nopaline strains of Agrobacterium tumefaciens as well as in Rhizobium meliloti (Sinorhizobium meliloti). This gene encodes a 15.5 kDa protein that specifically represses the virC and virD operons in the virulence region of the Ti plasmid [] and is necessary for succinoglycan production []. S. meliloti can produce two types of acidic exopolysaccharides, succinoglycan and galactoglucan, that are interchangeable for infection of Medicago sativa (Alfalfa) nodules. MucR from S. meliloti acts as a transcriptional repressor that blocks the expression of the exp genes responsible for galactoglucan production therefore allowing the exclusive production of succinoglycan [].; GO: 0003677 DNA binding, 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2JSP_A.
Probab=89.88 E-value=0.21 Score=29.15 Aligned_cols=26 Identities=27% Similarity=0.360 Sum_probs=16.4
Q ss_pred CcCCcchhhhccCchHHHHHHHHhcCCCC
Q psy12196 115 QIQCPYCITDFSEDKNLIQHIVSVHLGKE 143 (150)
Q Consensus 115 ~~~C~~C~~~f~~~~~l~~H~~~~~~~~~ 143 (150)
...|-+||+.|.. |.+|+..|||-.|
T Consensus 72 ~i~clecGk~~k~---LkrHL~~~~gltp 97 (132)
T PF05443_consen 72 YIICLECGKKFKT---LKRHLRTHHGLTP 97 (132)
T ss_dssp -EE-TBT--EESB---HHHHHHHTT-S-H
T ss_pred eeEEccCCcccch---HHHHHHHccCCCH
Confidence 4579999999887 6899999986543
No 71
>PF09538 FYDLN_acid: Protein of unknown function (FYDLN_acid); InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=89.70 E-value=0.26 Score=27.72 Aligned_cols=29 Identities=17% Similarity=0.464 Sum_probs=15.2
Q ss_pred ecccccccccChHHHHHHHhccCCcccccCCCCcccCCh
Q psy12196 32 QCNMCSLVLDSKESLVTHISQTHTLMFTCRRCPSTFLNS 70 (150)
Q Consensus 32 ~c~~c~~~f~~~~~l~~h~~~~~~~~~~c~~c~~~f~~~ 70 (150)
.|+.||+.|..- ...|..||.||..|...
T Consensus 11 ~Cp~CG~kFYDL----------nk~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 11 TCPSCGAKFYDL----------NKDPIVCPKCGTEFPPE 39 (108)
T ss_pred cCCCCcchhccC----------CCCCccCCCCCCccCcc
Confidence 566666666421 11344566666665544
No 72
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=89.64 E-value=0.2 Score=30.41 Aligned_cols=24 Identities=25% Similarity=0.653 Sum_probs=17.3
Q ss_pred CcccCCCChhhhcchhHHhhHHhhhcCCCCCCcCCcchh
Q psy12196 84 KSYQCNECPESFERLNKLKRHKFQAHNDSVHQIQCPYCI 122 (150)
Q Consensus 84 ~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~~C~~C~ 122 (150)
+.|.|.+||.. +.++. |.+||+|+
T Consensus 133 ~~~vC~vCGy~-------------~~ge~--P~~CPiCg 156 (166)
T COG1592 133 KVWVCPVCGYT-------------HEGEA--PEVCPICG 156 (166)
T ss_pred CEEEcCCCCCc-------------ccCCC--CCcCCCCC
Confidence 36999999863 23333 78899998
No 73
>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=89.59 E-value=0.18 Score=21.88 Aligned_cols=10 Identities=20% Similarity=0.554 Sum_probs=6.1
Q ss_pred ccCCCChhhh
Q psy12196 86 YQCNECPESF 95 (150)
Q Consensus 86 ~~c~~c~~~~ 95 (150)
|.|.+||..+
T Consensus 3 ~~C~~CG~i~ 12 (34)
T cd00729 3 WVCPVCGYIH 12 (34)
T ss_pred EECCCCCCEe
Confidence 5666676543
No 74
>PF15269 zf-C2H2_7: Zinc-finger
Probab=89.55 E-value=0.28 Score=22.56 Aligned_cols=29 Identities=17% Similarity=0.317 Sum_probs=22.6
Q ss_pred CCCCCCcCCcchhhhccCchHHHHHHHHh
Q psy12196 110 NDSVHQIQCPYCITDFSEDKNLIQHIVSV 138 (150)
Q Consensus 110 ~~~~~~~~C~~C~~~f~~~~~l~~H~~~~ 138 (150)
..++..|+|-+|......++.|..||+-.
T Consensus 15 ~gkp~~ykcfqcpftc~~kshl~nhmky~ 43 (54)
T PF15269_consen 15 PGKPFKYKCFQCPFTCNEKSHLFNHMKYS 43 (54)
T ss_pred CCCCccceeecCCcccchHHHHHHHHHHH
Confidence 34455678999999999999999998643
No 75
>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain. This domain contains a CXXCX(19)CXXC motif suggestive of both zinc fingers and thioredoxin, usually found at the N-terminus of prokaryotic proteins. One partially characterized gene, agmX, is among a large set in Myxococcus whose interruption affects adventurous gliding motility.
Probab=89.39 E-value=0.15 Score=22.56 Aligned_cols=32 Identities=19% Similarity=0.467 Sum_probs=14.5
Q ss_pred ecccccccccChHHHHHHHhccCCcccccCCCCccc
Q psy12196 32 QCNMCSLVLDSKESLVTHISQTHTLMFTCRRCPSTF 67 (150)
Q Consensus 32 ~c~~c~~~f~~~~~l~~h~~~~~~~~~~c~~c~~~f 67 (150)
.|+.|+..|.-...... .......|+.|+..|
T Consensus 4 ~CP~C~~~~~v~~~~~~----~~~~~v~C~~C~~~~ 35 (38)
T TIGR02098 4 QCPNCKTSFRVVDSQLG----ANGGKVRCGKCGHVW 35 (38)
T ss_pred ECCCCCCEEEeCHHHcC----CCCCEEECCCCCCEE
Confidence 46666665554333111 111234566666544
No 76
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=89.36 E-value=0.18 Score=24.75 Aligned_cols=9 Identities=33% Similarity=1.047 Sum_probs=4.5
Q ss_pred cccccCCCC
Q psy12196 56 LMFTCRRCP 64 (150)
Q Consensus 56 ~~~~c~~c~ 64 (150)
..|.||.||
T Consensus 26 v~F~CPnCG 34 (61)
T COG2888 26 VKFPCPNCG 34 (61)
T ss_pred eEeeCCCCC
Confidence 344555555
No 77
>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=89.16 E-value=1.1 Score=25.22 Aligned_cols=26 Identities=23% Similarity=0.308 Sum_probs=23.4
Q ss_pred CcCC----cchhhhccCchHHHHHHHHhcC
Q psy12196 115 QIQC----PYCITDFSEDKNLIQHIVSVHL 140 (150)
Q Consensus 115 ~~~C----~~C~~~f~~~~~l~~H~~~~~~ 140 (150)
-|.| +.|+..+.+...+..|+..+||
T Consensus 80 G~~C~~~~~~C~y~~~~~~~m~~H~~~~Hg 109 (109)
T PF12013_consen 80 GYRCQCDPPHCGYITRSKKTMRKHWRKEHG 109 (109)
T ss_pred CeeeecCCCCCCcEeccHHHHHHHHHHhcC
Confidence 3789 9999999999999999999885
No 78
>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=88.72 E-value=0.36 Score=19.52 Aligned_cols=20 Identities=30% Similarity=0.735 Sum_probs=15.0
Q ss_pred CCcchhhhccCchHHHHHHHH
Q psy12196 117 QCPYCITDFSEDKNLIQHIVS 137 (150)
Q Consensus 117 ~C~~C~~~f~~~~~l~~H~~~ 137 (150)
.||+|++.+ ....+.+|+..
T Consensus 3 ~CPiC~~~v-~~~~in~HLD~ 22 (26)
T smart00734 3 QCPVCFREV-PENLINSHLDS 22 (26)
T ss_pred cCCCCcCcc-cHHHHHHHHHH
Confidence 588998888 55677788753
No 79
>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=88.72 E-value=0.3 Score=27.45 Aligned_cols=26 Identities=19% Similarity=0.492 Sum_probs=22.4
Q ss_pred cccC----CCChhhhcchhHHhhHHhhhcC
Q psy12196 85 SYQC----NECPESFERLNKLKRHKFQAHN 110 (150)
Q Consensus 85 ~~~c----~~c~~~~~~~~~l~~h~~~~~~ 110 (150)
.|.| ..|++.......+..|.+..++
T Consensus 80 G~~C~~~~~~C~y~~~~~~~m~~H~~~~Hg 109 (109)
T PF12013_consen 80 GYRCQCDPPHCGYITRSKKTMRKHWRKEHG 109 (109)
T ss_pred CeeeecCCCCCCcEeccHHHHHHHHHHhcC
Confidence 3899 9999999999999999887653
No 80
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=88.71 E-value=1.4 Score=30.12 Aligned_cols=22 Identities=32% Similarity=0.772 Sum_probs=11.2
Q ss_pred CCcccccccCHHHHHHHHHHHh
Q psy12196 3 CVPCDVLFHNKATLYKHLYLEH 24 (150)
Q Consensus 3 C~~C~~~f~~~~~l~~h~~~~~ 24 (150)
|..|...|-+-..|..|++..|
T Consensus 223 C~FC~~~FYdDDEL~~HcR~~H 244 (493)
T COG5236 223 CIFCKIYFYDDDELRRHCRLRH 244 (493)
T ss_pred hhhccceecChHHHHHHHHhhh
Confidence 4445555555555555554433
No 81
>PHA00626 hypothetical protein
Probab=88.62 E-value=0.081 Score=25.58 Aligned_cols=11 Identities=27% Similarity=0.682 Sum_probs=5.3
Q ss_pred ccCCCChhhhc
Q psy12196 86 YQCNECPESFE 96 (150)
Q Consensus 86 ~~c~~c~~~~~ 96 (150)
|.|..||..|+
T Consensus 24 YkCkdCGY~ft 34 (59)
T PHA00626 24 YVCCDCGYNDS 34 (59)
T ss_pred eEcCCCCCeec
Confidence 45555544443
No 82
>smart00614 ZnF_BED BED zinc finger. DNA-binding domain in chromatin-boundary-element-binding proteins and transposases
Probab=88.60 E-value=0.37 Score=22.88 Aligned_cols=24 Identities=33% Similarity=0.695 Sum_probs=16.3
Q ss_pred cCCcchhhhccCc-----hHHHHHHHHhc
Q psy12196 116 IQCPYCITDFSED-----KNLIQHIVSVH 139 (150)
Q Consensus 116 ~~C~~C~~~f~~~-----~~l~~H~~~~~ 139 (150)
-.|..|++.+... +.|.+|+...+
T Consensus 19 a~C~~C~~~l~~~~~~gTs~L~rHl~~~h 47 (50)
T smart00614 19 AKCKYCGKKLSRSSKGGTSNLRRHLRRKH 47 (50)
T ss_pred EEecCCCCEeeeCCCCCcHHHHHHHHhHC
Confidence 4577777776554 68888887543
No 83
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=88.54 E-value=0.063 Score=34.16 Aligned_cols=13 Identities=31% Similarity=0.503 Sum_probs=10.2
Q ss_pred cCCcchhhhccCc
Q psy12196 116 IQCPYCITDFSED 128 (150)
Q Consensus 116 ~~C~~C~~~f~~~ 128 (150)
..||.||.++...
T Consensus 49 ~vCP~CgyA~~~~ 61 (214)
T PF09986_consen 49 WVCPHCGYAAFEE 61 (214)
T ss_pred EECCCCCCccccc
Confidence 4699999887754
No 84
>TIGR02605 CxxC_CxxC_SSSS putative regulatory protein, FmdB family. This model represents a region of about 50 amino acids found in a number of small proteins in a wide range of bacteria. The region begins usually with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One member of this family is has been noted as a putative regulatory protein, designated FmdB (PubMed:8841393). Most members of this family have a C-terminal region containing highly degenerate sequence, such as SSTSESTKSSGSSGSSGSSESKASGSTEKSTSSTTAAAAV in Mycobacterium tuberculosis and VAVGGSAPAPSPAPRAGGGGGGCCGGGCCG in Streptomyces avermitilis. These low complexity regions, which are not included in the model, resemble low-complexity C-terminal regions of some heterocycle-containing bacteriocin precursors.
Probab=88.31 E-value=0.13 Score=24.59 Aligned_cols=29 Identities=38% Similarity=0.893 Sum_probs=16.3
Q ss_pred ccCCCChhhhcchhHHhhHHhhhcCCCCCCcCCcchhh
Q psy12196 86 YQCNECPESFERLNKLKRHKFQAHNDSVHQIQCPYCIT 123 (150)
Q Consensus 86 ~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~~C~~C~~ 123 (150)
|.|..||..|.....+ ..+. ...|+.|+.
T Consensus 6 y~C~~Cg~~fe~~~~~-------~~~~--~~~CP~Cg~ 34 (52)
T TIGR02605 6 YRCTACGHRFEVLQKM-------SDDP--LATCPECGG 34 (52)
T ss_pred EEeCCCCCEeEEEEec-------CCCC--CCCCCCCCC
Confidence 6777787777653211 1122 446777774
No 85
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=87.71 E-value=0.26 Score=22.82 Aligned_cols=11 Identities=45% Similarity=0.981 Sum_probs=6.2
Q ss_pred ccCCCChhhhc
Q psy12196 86 YQCNECPESFE 96 (150)
Q Consensus 86 ~~c~~c~~~~~ 96 (150)
|.|..||..+.
T Consensus 3 Y~C~~Cg~~~~ 13 (44)
T smart00659 3 YICGECGRENE 13 (44)
T ss_pred EECCCCCCEee
Confidence 55666665444
No 86
>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=87.25 E-value=0.76 Score=27.84 Aligned_cols=34 Identities=18% Similarity=0.377 Sum_probs=23.1
Q ss_pred CCCcccCCCChhhhcchhHHhhHHhhhcCCCCCCcCCcchhhhcc
Q psy12196 82 NSKSYQCNECPESFERLNKLKRHKFQAHNDSVHQIQCPYCITDFS 126 (150)
Q Consensus 82 ~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~~C~~C~~~f~ 126 (150)
+..-|.|+.|+..|+....+. . .|.||.||....
T Consensus 106 ~~~~Y~Cp~c~~r~tf~eA~~---------~--~F~Cp~Cg~~L~ 139 (158)
T TIGR00373 106 NNMFFICPNMCVRFTFNEAME---------L--NFTCPRCGAMLD 139 (158)
T ss_pred CCCeEECCCCCcEeeHHHHHH---------c--CCcCCCCCCEee
Confidence 445678888887777766553 1 678888886643
No 87
>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=86.92 E-value=0.18 Score=22.66 Aligned_cols=29 Identities=38% Similarity=0.948 Sum_probs=16.7
Q ss_pred ccCCCChhhhcchhHHhhHHhhhcCCCCCCcCCcchhh
Q psy12196 86 YQCNECPESFERLNKLKRHKFQAHNDSVHQIQCPYCIT 123 (150)
Q Consensus 86 ~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~~C~~C~~ 123 (150)
|.|..||..|...... .... ...|+.||.
T Consensus 6 y~C~~Cg~~fe~~~~~-------~~~~--~~~CP~Cg~ 34 (41)
T smart00834 6 YRCEDCGHTFEVLQKI-------SDDP--LATCPECGG 34 (41)
T ss_pred EEcCCCCCEEEEEEec-------CCCC--CCCCCCCCC
Confidence 6777788776654322 1122 446888775
No 88
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=86.31 E-value=0.16 Score=35.36 Aligned_cols=56 Identities=27% Similarity=0.536 Sum_probs=41.3
Q ss_pred ccccCCCCcccCChHHHHHHHH--hhcCC--CcccCC--CChhhhcchhHHhhHHhhhcCCC
Q psy12196 57 MFTCRRCPSTFLNSATLSKHVK--MEHNS--KSYQCN--ECPESFERLNKLKRHKFQAHNDS 112 (150)
Q Consensus 57 ~~~c~~c~~~f~~~~~l~~h~~--~~~~~--~~~~c~--~c~~~~~~~~~l~~h~~~~~~~~ 112 (150)
++.|..|...|.....+..|.. .|.++ +++.|. .|++.|.....+..|...+.+..
T Consensus 289 ~~~~~~~~~~~s~~~~l~~~~~~~~h~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~ 350 (467)
T COG5048 289 PIKSKQCNISFSRSSPLTRHLRSVNHSGESLKPFSCPYSLCGKLFSRNDALKRHILLHTSIS 350 (467)
T ss_pred CCCCccccCCccccccccccccccccccccCCceeeeccCCCccccccccccCCcccccCCC
Confidence 5667777777777777777777 67777 777777 67777777777777766666544
No 89
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=86.12 E-value=0.75 Score=20.22 Aligned_cols=9 Identities=22% Similarity=0.737 Sum_probs=4.1
Q ss_pred ccccccccc
Q psy12196 33 CNMCSLVLD 41 (150)
Q Consensus 33 c~~c~~~f~ 41 (150)
|+.|...|.
T Consensus 5 Cp~C~~~y~ 13 (36)
T PF13717_consen 5 CPNCQAKYE 13 (36)
T ss_pred CCCCCCEEe
Confidence 444444443
No 90
>KOG2186|consensus
Probab=85.87 E-value=0.31 Score=31.54 Aligned_cols=49 Identities=24% Similarity=0.555 Sum_probs=36.0
Q ss_pred eecccccccccChHHHHHHHhccCCcccccCCCCcccCChHHHHHHHHhhc
Q psy12196 31 IQCNMCSLVLDSKESLVTHISQTHTLMFTCRRCPSTFLNSATLSKHVKMEH 81 (150)
Q Consensus 31 ~~c~~c~~~f~~~~~l~~h~~~~~~~~~~c~~c~~~f~~~~~l~~h~~~~~ 81 (150)
|.|..|+....-+ .+..|+.+.+...|.|..|+..|.. .+...|...-+
T Consensus 4 FtCnvCgEsvKKp-~vekH~srCrn~~fSCIDC~k~F~~-~sYknH~kCIT 52 (276)
T KOG2186|consen 4 FTCNVCGESVKKP-QVEKHMSRCRNAYFSCIDCGKTFER-VSYKNHTKCIT 52 (276)
T ss_pred Eehhhhhhhcccc-chHHHHHhccCCeeEEeeccccccc-chhhhhhhhcc
Confidence 6788888877643 5566887777788889889999887 56666655444
No 91
>PF04959 ARS2: Arsenite-resistance protein 2; InterPro: IPR007042 This entry represents Arsenite-resistance protein 2 (also known as Serrate RNA effector molecule homolog) which is thought to play a role in arsenite resistance [], although does not directly confer arsenite resistance but rather modulates arsenic sensitivity []. Arsenite is a carcinogenic compound which can act as a comutagen by inhibiting DNA repair. It is also involved in cell cycle progression at S phase. ; PDB: 3AX1_A.
Probab=85.80 E-value=0.19 Score=31.97 Aligned_cols=29 Identities=28% Similarity=0.504 Sum_probs=21.0
Q ss_pred CCcCCcchhhhccCchHHHHHHHHhcCCC
Q psy12196 114 HQIQCPYCITDFSEDKNLIQHIVSVHLGK 142 (150)
Q Consensus 114 ~~~~C~~C~~~f~~~~~l~~H~~~~~~~~ 142 (150)
..|.|+.|+|.|.-..-+..|+...|+++
T Consensus 76 ~K~~C~lc~KlFkg~eFV~KHI~nKH~e~ 104 (214)
T PF04959_consen 76 DKWRCPLCGKLFKGPEFVRKHIFNKHPEK 104 (214)
T ss_dssp EEEEE-SSS-EESSHHHHHHHHHHH-HHH
T ss_pred CEECCCCCCcccCChHHHHHHHhhcCHHH
Confidence 36888889998888888888888888653
No 92
>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=85.79 E-value=0.34 Score=22.30 Aligned_cols=24 Identities=25% Similarity=0.505 Sum_probs=12.9
Q ss_pred CcCCcchhhhccC----chHHHHHHHHh
Q psy12196 115 QIQCPYCITDFSE----DKNLIQHIVSV 138 (150)
Q Consensus 115 ~~~C~~C~~~f~~----~~~l~~H~~~~ 138 (150)
...|..|++.+.. .+.|.+|++..
T Consensus 16 ~a~C~~C~~~~~~~~~~ts~l~~HL~~~ 43 (45)
T PF02892_consen 16 KAKCKYCGKVIKYSSGGTSNLKRHLKKK 43 (45)
T ss_dssp -EEETTTTEE-----SSTHHHHHHHHHT
T ss_pred eEEeCCCCeEEeeCCCcHHHHHHhhhhh
Confidence 4567777766654 36777777543
No 93
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=83.90 E-value=1.1 Score=27.73 Aligned_cols=33 Identities=18% Similarity=0.460 Sum_probs=21.2
Q ss_pred CCcccCCCChhhhcchhHHhhHHhhhcCCCCCCcCCcchhhhcc
Q psy12196 83 SKSYQCNECPESFERLNKLKRHKFQAHNDSVHQIQCPYCITDFS 126 (150)
Q Consensus 83 ~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~~C~~C~~~f~ 126 (150)
..-|.|+.|+..|+....+. . .|.|+.||....
T Consensus 115 ~~~Y~Cp~C~~rytf~eA~~---------~--~F~Cp~Cg~~L~ 147 (178)
T PRK06266 115 NMFFFCPNCHIRFTFDEAME---------Y--GFRCPQCGEMLE 147 (178)
T ss_pred CCEEECCCCCcEEeHHHHhh---------c--CCcCCCCCCCCe
Confidence 34577877877777665431 1 677888876543
No 94
>PF09723 Zn-ribbon_8: Zinc ribbon domain; InterPro: IPR013429 This entry represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB []. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=83.86 E-value=0.39 Score=21.93 Aligned_cols=31 Identities=19% Similarity=0.475 Sum_probs=17.3
Q ss_pred cceecccccccccChHHHHHHHhccCCcccccCCCCc
Q psy12196 29 LSIQCNMCSLVLDSKESLVTHISQTHTLMFTCRRCPS 65 (150)
Q Consensus 29 ~~~~c~~c~~~f~~~~~l~~h~~~~~~~~~~c~~c~~ 65 (150)
+.|.|..|+..|.....+. ......|+.|+.
T Consensus 4 Yey~C~~Cg~~fe~~~~~~------~~~~~~CP~Cg~ 34 (42)
T PF09723_consen 4 YEYRCEECGHEFEVLQSIS------EDDPVPCPECGS 34 (42)
T ss_pred EEEEeCCCCCEEEEEEEcC------CCCCCcCCCCCC
Confidence 3477777777765332211 134556777775
No 95
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=83.11 E-value=0.51 Score=23.26 Aligned_cols=8 Identities=38% Similarity=0.962 Sum_probs=4.4
Q ss_pred CcCCcchh
Q psy12196 115 QIQCPYCI 122 (150)
Q Consensus 115 ~~~C~~C~ 122 (150)
+|.|+.||
T Consensus 48 ~Y~CP~CG 55 (59)
T PRK14890 48 PYTCPKCG 55 (59)
T ss_pred ceECCCCC
Confidence 55555554
No 96
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=82.08 E-value=1.3 Score=26.42 Aligned_cols=39 Identities=23% Similarity=0.595 Sum_probs=22.0
Q ss_pred CCCcccCCCChhhhcchhHHhhHHhhhcCCCCCCcCCcchhhhcc
Q psy12196 82 NSKSYQCNECPESFERLNKLKRHKFQAHNDSVHQIQCPYCITDFS 126 (150)
Q Consensus 82 ~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~~C~~C~~~f~ 126 (150)
+..-|.|+.|+..|.....+.. ...++ .|.||.||....
T Consensus 96 ~~~~Y~Cp~C~~~y~~~ea~~~----~d~~~--~f~Cp~Cg~~l~ 134 (147)
T smart00531 96 NNAYYKCPNCQSKYTFLEANQL----LDMDG--TFTCPRCGEELE 134 (147)
T ss_pred CCcEEECcCCCCEeeHHHHHHh----cCCCC--cEECCCCCCEEE
Confidence 3445778888777765433221 01133 578888876643
No 97
>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=81.70 E-value=0.96 Score=32.33 Aligned_cols=29 Identities=24% Similarity=0.480 Sum_probs=24.8
Q ss_pred CcCCcchhhhccCchHHHHHHHHhcCCCC
Q psy12196 115 QIQCPYCITDFSEDKNLIQHIVSVHLGKE 143 (150)
Q Consensus 115 ~~~C~~C~~~f~~~~~l~~H~~~~~~~~~ 143 (150)
-|.|+.|.+.|.+...+..|+...|.++-
T Consensus 57 FWiCp~CskkF~d~~~~~~H~~~eH~~~l 85 (466)
T PF04780_consen 57 FWICPRCSKKFSDAESCLSHMEQEHPAGL 85 (466)
T ss_pred EeeCCcccceeCCHHHHHHHHHHhhhhhc
Confidence 46899999999999999999998885543
No 98
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=81.12 E-value=1.2 Score=20.71 Aligned_cols=10 Identities=20% Similarity=0.663 Sum_probs=5.6
Q ss_pred eecccccccc
Q psy12196 31 IQCNMCSLVL 40 (150)
Q Consensus 31 ~~c~~c~~~f 40 (150)
|.|+.|+..|
T Consensus 4 y~C~~CG~~~ 13 (46)
T PRK00398 4 YKCARCGREV 13 (46)
T ss_pred EECCCCCCEE
Confidence 5555555554
No 99
>PF14353 CpXC: CpXC protein
Probab=81.06 E-value=2.4 Score=24.59 Aligned_cols=21 Identities=24% Similarity=0.494 Sum_probs=12.0
Q ss_pred cceecccccccccChHHHHHH
Q psy12196 29 LSIQCNMCSLVLDSKESLVTH 49 (150)
Q Consensus 29 ~~~~c~~c~~~f~~~~~l~~h 49 (150)
..+.|+.||..|.-...+..|
T Consensus 37 ~~~~CP~Cg~~~~~~~p~lY~ 57 (128)
T PF14353_consen 37 FSFTCPSCGHKFRLEYPLLYH 57 (128)
T ss_pred CEEECCCCCCceecCCCEEEE
Confidence 346677777766554444444
No 100
>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=80.61 E-value=1.3 Score=25.60 Aligned_cols=30 Identities=7% Similarity=-0.084 Sum_probs=16.0
Q ss_pred eecccccccccChHHHHHHHhccCCcccccCCCCcccCCh
Q psy12196 31 IQCNMCSLVLDSKESLVTHISQTHTLMFTCRRCPSTFLNS 70 (150)
Q Consensus 31 ~~c~~c~~~f~~~~~l~~h~~~~~~~~~~c~~c~~~f~~~ 70 (150)
..|+.|++.|.. ....|..||.||..|...
T Consensus 10 r~Cp~cg~kFYD----------Lnk~p~vcP~cg~~~~~~ 39 (129)
T TIGR02300 10 RICPNTGSKFYD----------LNRRPAVSPYTGEQFPPE 39 (129)
T ss_pred ccCCCcCccccc----------cCCCCccCCCcCCccCcc
Confidence 356666666642 112445566666665444
No 101
>KOG2785|consensus
Probab=80.60 E-value=3.4 Score=28.69 Aligned_cols=24 Identities=25% Similarity=0.448 Sum_probs=15.7
Q ss_pred CcCCcchhhhccCchHHHHHHHHh
Q psy12196 115 QIQCPYCITDFSEDKNLIQHIVSV 138 (150)
Q Consensus 115 ~~~C~~C~~~f~~~~~l~~H~~~~ 138 (150)
++.|..|.+.|....+...|+.+.
T Consensus 68 ~~~c~~c~k~~~s~~a~~~hl~Sk 91 (390)
T KOG2785|consen 68 VVYCEACNKSFASPKAHENHLKSK 91 (390)
T ss_pred ceehHHhhccccChhhHHHHHHHh
Confidence 556777777777666666666554
No 102
>KOG1842|consensus
Probab=79.75 E-value=1.3 Score=31.27 Aligned_cols=29 Identities=24% Similarity=0.573 Sum_probs=21.2
Q ss_pred CcCCcchhhhccCchHHHHHHHHhcCCCC
Q psy12196 115 QIQCPYCITDFSEDKNLIQHIVSVHLGKE 143 (150)
Q Consensus 115 ~~~C~~C~~~f~~~~~l~~H~~~~~~~~~ 143 (150)
-|.||+|...|.+...|..|+..-|++..
T Consensus 15 gflCPiC~~dl~~~~~L~~H~d~eH~~ed 43 (505)
T KOG1842|consen 15 GFLCPICLLDLPNLSALNDHLDVEHFEED 43 (505)
T ss_pred cccCchHhhhhhhHHHHHHHHhhhccccc
Confidence 56777777777777777777777776554
No 103
>KOG4118|consensus
Probab=79.23 E-value=1.7 Score=21.81 Aligned_cols=31 Identities=19% Similarity=0.426 Sum_probs=26.5
Q ss_pred CcCCcchhhhccCchHHHHHHHHhcCCCCCC
Q psy12196 115 QIQCPYCITDFSEDKNLIQHIVSVHLGKEGT 145 (150)
Q Consensus 115 ~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~ 145 (150)
-|+|..|.-.....-.+..|+...|+..|.+
T Consensus 38 ~~kCtVC~~~mpdpktfkqhfe~kHpk~~~P 68 (74)
T KOG4118|consen 38 HHKCTVCMVQMPDPKTFKQHFENKHPKEPLP 68 (74)
T ss_pred HhhhHhhHhhCCCCchHHHHHhhcCCCCCCC
Confidence 4679999988888889999999999888765
No 104
>KOG4167|consensus
Probab=79.14 E-value=0.66 Score=34.81 Aligned_cols=26 Identities=19% Similarity=0.217 Sum_probs=23.7
Q ss_pred CcCCcchhhhccCchHHHHHHHHhcC
Q psy12196 115 QIQCPYCITDFSEDKNLIQHIVSVHL 140 (150)
Q Consensus 115 ~~~C~~C~~~f~~~~~l~~H~~~~~~ 140 (150)
.|-|..|+|.|.-..++..||++|-.
T Consensus 792 iFpCreC~kvF~KiKSrNAHMK~Hr~ 817 (907)
T KOG4167|consen 792 IFPCRECGKVFFKIKSRNAHMKTHRQ 817 (907)
T ss_pred eeehHHHHHHHHHHhhhhHHHHHHHH
Confidence 58899999999999999999999963
No 105
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=76.35 E-value=0.35 Score=29.09 Aligned_cols=15 Identities=20% Similarity=0.410 Sum_probs=9.8
Q ss_pred cccCCCCcccCChHH
Q psy12196 58 FTCRRCPSTFLNSAT 72 (150)
Q Consensus 58 ~~c~~c~~~f~~~~~ 72 (150)
++|+.||..|.....
T Consensus 29 ~~c~~c~~~f~~~e~ 43 (154)
T PRK00464 29 RECLACGKRFTTFER 43 (154)
T ss_pred eeccccCCcceEeEe
Confidence 667777777765433
No 106
>KOG3408|consensus
Probab=76.31 E-value=1.9 Score=24.69 Aligned_cols=24 Identities=29% Similarity=0.465 Sum_probs=19.5
Q ss_pred CcCCcchhhhccCchHHHHHHHHh
Q psy12196 115 QIQCPYCITDFSEDKNLIQHIVSV 138 (150)
Q Consensus 115 ~~~C~~C~~~f~~~~~l~~H~~~~ 138 (150)
.|-|-.|.+-|.+...|..|+++.
T Consensus 57 qfyCi~CaRyFi~~~~l~~H~ktK 80 (129)
T KOG3408|consen 57 QFYCIECARYFIDAKALKTHFKTK 80 (129)
T ss_pred eeehhhhhhhhcchHHHHHHHhcc
Confidence 677888888888888888887665
No 107
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=75.48 E-value=1.5 Score=25.52 Aligned_cols=11 Identities=36% Similarity=0.957 Sum_probs=4.9
Q ss_pred ecccccccccC
Q psy12196 32 QCNMCSLVLDS 42 (150)
Q Consensus 32 ~c~~c~~~f~~ 42 (150)
+|..|++.|..
T Consensus 3 ~Ct~Cg~~f~d 13 (131)
T PF09845_consen 3 QCTKCGRVFED 13 (131)
T ss_pred ccCcCCCCcCC
Confidence 34444444443
No 108
>COG2879 Uncharacterized small protein [Function unknown]
Probab=75.20 E-value=3.5 Score=20.61 Aligned_cols=19 Identities=21% Similarity=0.338 Sum_probs=15.4
Q ss_pred cCchHHHHHHHHhcCCCCC
Q psy12196 126 SEDKNLIQHIVSVHLGKEG 144 (150)
Q Consensus 126 ~~~~~l~~H~~~~~~~~~~ 144 (150)
++..+...||+.+|+++|+
T Consensus 23 pdYdnYVehmr~~hPd~p~ 41 (65)
T COG2879 23 PDYDNYVEHMRKKHPDKPP 41 (65)
T ss_pred CcHHHHHHHHHHhCcCCCc
Confidence 4557888999999988875
No 109
>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=74.92 E-value=1.1 Score=18.92 Aligned_cols=6 Identities=50% Similarity=1.619 Sum_probs=2.3
Q ss_pred cCCcch
Q psy12196 116 IQCPYC 121 (150)
Q Consensus 116 ~~C~~C 121 (150)
+.|+.|
T Consensus 20 ~vCp~C 25 (30)
T PF08274_consen 20 LVCPEC 25 (30)
T ss_dssp EEETTT
T ss_pred EeCCcc
Confidence 334433
No 110
>KOG1280|consensus
Probab=74.62 E-value=3.4 Score=28.32 Aligned_cols=37 Identities=22% Similarity=0.584 Sum_probs=19.2
Q ss_pred CCCCcccccccCHHHHHHHHHHHhhCCCcceeccccc
Q psy12196 1 MSCVPCDVLFHNKATLYKHLYLEHKATSLSIQCNMCS 37 (150)
Q Consensus 1 ~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~~~c~~c~ 37 (150)
|.|++|+..=-+...|.-|+...|.+......|+.|.
T Consensus 80 ftCPyC~~~Gfte~~f~~Hv~s~Hpda~~~~icp~c~ 116 (381)
T KOG1280|consen 80 FTCPYCGIMGFTERQFGTHVLSQHPEASTSVICPLCA 116 (381)
T ss_pred ccCCcccccccchhHHHHHhhhcCcccCcceeeeccc
Confidence 4556665554455555555555554444444455553
No 111
>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=74.29 E-value=0.59 Score=22.01 Aligned_cols=13 Identities=31% Similarity=0.756 Sum_probs=7.9
Q ss_pred ccCCCChhhhcch
Q psy12196 86 YQCNECPESFERL 98 (150)
Q Consensus 86 ~~c~~c~~~~~~~ 98 (150)
|+|.+|+..+...
T Consensus 2 y~C~~CgyvYd~~ 14 (47)
T PF00301_consen 2 YQCPVCGYVYDPE 14 (47)
T ss_dssp EEETTTSBEEETT
T ss_pred cCCCCCCEEEcCC
Confidence 5677777665543
No 112
>COG4957 Predicted transcriptional regulator [Transcription]
Probab=74.28 E-value=1.1 Score=26.14 Aligned_cols=23 Identities=22% Similarity=0.140 Sum_probs=18.2
Q ss_pred cCCcchhhhccCchHHHHHHHHhcCC
Q psy12196 116 IQCPYCITDFSEDKNLIQHIVSVHLG 141 (150)
Q Consensus 116 ~~C~~C~~~f~~~~~l~~H~~~~~~~ 141 (150)
..|-++|+.|.+ |.+|+.+|++=
T Consensus 77 IicLEDGkkfKS---LKRHL~t~~gm 99 (148)
T COG4957 77 IICLEDGKKFKS---LKRHLTTHYGL 99 (148)
T ss_pred EEEeccCcchHH---HHHHHhcccCC
Confidence 468889988865 88999888753
No 113
>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=74.16 E-value=1 Score=17.85 Aligned_cols=9 Identities=33% Similarity=0.855 Sum_probs=6.0
Q ss_pred CcCCcchhh
Q psy12196 115 QIQCPYCIT 123 (150)
Q Consensus 115 ~~~C~~C~~ 123 (150)
.|.||.||+
T Consensus 16 ~f~CPnCG~ 24 (24)
T PF07754_consen 16 PFPCPNCGF 24 (24)
T ss_pred eEeCCCCCC
Confidence 677777763
No 114
>PF13451 zf-trcl: Probable zinc-binding domain
Probab=73.27 E-value=3.6 Score=19.56 Aligned_cols=17 Identities=24% Similarity=0.569 Sum_probs=9.7
Q ss_pred CcccCCCChhhhcchhH
Q psy12196 84 KSYQCNECPESFERLNK 100 (150)
Q Consensus 84 ~~~~c~~c~~~~~~~~~ 100 (150)
+.+.|..||..|.....
T Consensus 3 k~l~C~dCg~~FvfTa~ 19 (49)
T PF13451_consen 3 KTLTCKDCGAEFVFTAG 19 (49)
T ss_pred eeEEcccCCCeEEEehh
Confidence 34566666666655443
No 115
>KOG2807|consensus
Probab=72.46 E-value=5.8 Score=27.08 Aligned_cols=24 Identities=21% Similarity=0.361 Sum_probs=19.7
Q ss_pred CcCCcchhhhccCchHHHHHHHHh
Q psy12196 115 QIQCPYCITDFSEDKNLIQHIVSV 138 (150)
Q Consensus 115 ~~~C~~C~~~f~~~~~l~~H~~~~ 138 (150)
-|+|..|...|....+...|-..|
T Consensus 345 ~y~C~~Ck~~FCldCDv~iHesLh 368 (378)
T KOG2807|consen 345 RYRCESCKNVFCLDCDVFIHESLH 368 (378)
T ss_pred cEEchhccceeeccchHHHHhhhh
Confidence 688999999999888888776655
No 116
>PF03604 DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa subunit; InterPro: IPR006591 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Each class of RNA polymerase is assembled from 9 to 15 different polypeptides. Rbp10 (RNA polymerase CX) is a domain found in RNA polymerase subunit 10; present in RNA polymerase I, II and III.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_Z 3HKZ_X 2NVX_L 3S1Q_L 2JA6_L 3S17_L 3HOW_L 3HOV_L 3PO2_L 3HOZ_L ....
Probab=72.02 E-value=3.9 Score=17.47 Aligned_cols=6 Identities=33% Similarity=1.149 Sum_probs=2.4
Q ss_pred ccCCCC
Q psy12196 59 TCRRCP 64 (150)
Q Consensus 59 ~c~~c~ 64 (150)
.|+.||
T Consensus 19 rC~~CG 24 (32)
T PF03604_consen 19 RCPECG 24 (32)
T ss_dssp SBSSSS
T ss_pred ECCcCC
Confidence 344443
No 117
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=71.60 E-value=1.2 Score=23.15 Aligned_cols=41 Identities=24% Similarity=0.365 Sum_probs=19.8
Q ss_pred CCCCcccccccCHHHHHHHHHHHhhCCCcceecc--cccccccChHH
Q psy12196 1 MSCVPCDVLFHNKATLYKHLYLEHKATSLSIQCN--MCSLVLDSKES 45 (150)
Q Consensus 1 ~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~~~c~--~c~~~f~~~~~ 45 (150)
+.|+.||.......+-...... ...-++|. .|+.+|.....
T Consensus 2 m~CP~Cg~~a~irtSr~~s~~~----~~~Y~qC~N~eCg~tF~t~es 44 (72)
T PRK09678 2 FHCPLCQHAAHARTSRYITDTT----KERYHQCQNVNCSATFITYES 44 (72)
T ss_pred ccCCCCCCccEEEEChhcChhh----heeeeecCCCCCCCEEEEEEE
Confidence 4577777655333332222111 22235666 67777765433
No 118
>COG3364 Zn-ribbon containing protein [General function prediction only]
Probab=71.41 E-value=2.4 Score=23.44 Aligned_cols=11 Identities=45% Similarity=0.990 Sum_probs=5.7
Q ss_pred ecccccccccC
Q psy12196 32 QCNMCSLVLDS 42 (150)
Q Consensus 32 ~c~~c~~~f~~ 42 (150)
+|..||..|..
T Consensus 4 ~CtrCG~vf~~ 14 (112)
T COG3364 4 QCTRCGEVFDD 14 (112)
T ss_pred eeccccccccc
Confidence 45555555554
No 119
>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=70.01 E-value=3.2 Score=26.56 Aligned_cols=25 Identities=28% Similarity=0.614 Sum_probs=18.7
Q ss_pred CCCCcccccccCHHHHHHHHHHHhh
Q psy12196 1 MSCVPCDVLFHNKATLYKHLYLEHK 25 (150)
Q Consensus 1 ~~C~~C~~~f~~~~~l~~h~~~~~~ 25 (150)
|.|..|++.|.....+..|+...|.
T Consensus 78 ~~C~lc~KlFkg~eFV~KHI~nKH~ 102 (214)
T PF04959_consen 78 WRCPLCGKLFKGPEFVRKHIFNKHP 102 (214)
T ss_dssp EEE-SSS-EESSHHHHHHHHHHH-H
T ss_pred ECCCCCCcccCChHHHHHHHhhcCH
Confidence 4588899999999999999888776
No 120
>KOG4167|consensus
Probab=69.71 E-value=1.2 Score=33.49 Aligned_cols=24 Identities=17% Similarity=0.443 Sum_probs=21.2
Q ss_pred CCCCcccccccCHHHHHHHHHHHh
Q psy12196 1 MSCVPCDVLFHNKATLYKHLYLEH 24 (150)
Q Consensus 1 ~~C~~C~~~f~~~~~l~~h~~~~~ 24 (150)
|.|..|++.|-...++..||+.|.
T Consensus 793 FpCreC~kvF~KiKSrNAHMK~Hr 816 (907)
T KOG4167|consen 793 FPCRECGKVFFKIKSRNAHMKTHR 816 (907)
T ss_pred eehHHHHHHHHHHhhhhHHHHHHH
Confidence 679999999999999999998853
No 121
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=68.64 E-value=3.7 Score=27.74 Aligned_cols=24 Identities=25% Similarity=0.513 Sum_probs=20.8
Q ss_pred CcCCcchhhhccCchHHHHHHHHh
Q psy12196 115 QIQCPYCITDFSEDKNLIQHIVSV 138 (150)
Q Consensus 115 ~~~C~~C~~~f~~~~~l~~H~~~~ 138 (150)
.|+|+.|...|....+.-.|-..|
T Consensus 388 rY~Ce~CK~~FC~dCdvfiHe~Lh 411 (421)
T COG5151 388 RYQCELCKSTFCSDCDVFIHETLH 411 (421)
T ss_pred ceechhhhhhhhhhhHHHHHHHHh
Confidence 799999999999999888887665
No 122
>KOG2785|consensus
Probab=67.75 E-value=10 Score=26.52 Aligned_cols=23 Identities=30% Similarity=0.564 Sum_probs=13.8
Q ss_pred CCcccccccCHHHHHHHHHHHhh
Q psy12196 3 CVPCDVLFHNKATLYKHLYLEHK 25 (150)
Q Consensus 3 C~~C~~~f~~~~~l~~h~~~~~~ 25 (150)
|-.|+..+.+...-..||..+|+
T Consensus 169 CLfC~~~~k~~e~~~~HM~~~Hg 191 (390)
T KOG2785|consen 169 CLFCDKKSKSLEENLKHMFKEHG 191 (390)
T ss_pred eeecCCCcccHHHHHHHHhhccC
Confidence 55566666666666666655443
No 123
>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=67.65 E-value=1.9 Score=28.28 Aligned_cols=77 Identities=18% Similarity=0.349 Sum_probs=35.3
Q ss_pred CCcceecccccccccChHHHHHHHh---ccCCcccccCCCCcccCChHH------HHHHHHh----hcCCCcccCCCChh
Q psy12196 27 TSLSIQCNMCSLVLDSKESLVTHIS---QTHTLMFTCRRCPSTFLNSAT------LSKHVKM----EHNSKSYQCNECPE 93 (150)
Q Consensus 27 ~~~~~~c~~c~~~f~~~~~l~~h~~---~~~~~~~~c~~c~~~f~~~~~------l~~h~~~----~~~~~~~~c~~c~~ 93 (150)
+...|.|.+|..-.- .-.-..|+. ......|+|..|++.-..+-. -..|.+. ....+++.|+.||.
T Consensus 139 GGrif~CsfC~~flC-EDDQFEHQAsCQvLe~E~~KC~SCNrlGq~sCLRCK~cfCddHvrrKg~ky~k~k~~PCPKCg~ 217 (314)
T PF06524_consen 139 GGRIFKCSFCDNFLC-EDDQFEHQASCQVLESETFKCQSCNRLGQYSCLRCKICFCDDHVRRKGFKYEKGKPIPCPKCGY 217 (314)
T ss_pred CCeEEEeecCCCeee-ccchhhhhhhhhhhhcccccccccccccchhhhheeeeehhhhhhhcccccccCCCCCCCCCCC
Confidence 455688888876432 222223331 222255666666533221110 0122221 12235666777776
Q ss_pred hhcchhHHhhH
Q psy12196 94 SFERLNKLKRH 104 (150)
Q Consensus 94 ~~~~~~~l~~h 104 (150)
.......|...
T Consensus 218 et~eTkdLSmS 228 (314)
T PF06524_consen 218 ETQETKDLSMS 228 (314)
T ss_pred cccccccceee
Confidence 66655555443
No 124
>KOG2593|consensus
Probab=67.43 E-value=4.3 Score=28.73 Aligned_cols=36 Identities=22% Similarity=0.620 Sum_probs=17.6
Q ss_pred CCCcccCCCChhhhcchhHHhhHHhhhcCCCCCCcCCcchh
Q psy12196 82 NSKSYQCNECPESFERLNKLKRHKFQAHNDSVHQIQCPYCI 122 (150)
Q Consensus 82 ~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~~C~~C~ 122 (150)
....|.|+.|.+.|+....++- .-..++ .|.|..|+
T Consensus 125 ~~~~Y~Cp~C~kkyt~Lea~~L---~~~~~~--~F~C~~C~ 160 (436)
T KOG2593|consen 125 NVAGYVCPNCQKKYTSLEALQL---LDNETG--EFHCENCG 160 (436)
T ss_pred ccccccCCccccchhhhHHHHh---hcccCc--eEEEecCC
Confidence 3444666666666555444321 222233 55665555
No 125
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=67.21 E-value=3 Score=19.84 Aligned_cols=10 Identities=30% Similarity=1.049 Sum_probs=4.1
Q ss_pred ccCCCChhhh
Q psy12196 86 YQCNECPESF 95 (150)
Q Consensus 86 ~~c~~c~~~~ 95 (150)
|.|..||+.+
T Consensus 7 Y~C~~Cg~~~ 16 (49)
T COG1996 7 YKCARCGREV 16 (49)
T ss_pred EEhhhcCCee
Confidence 3444444433
No 126
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=66.01 E-value=2.3 Score=25.02 Aligned_cols=13 Identities=15% Similarity=0.662 Sum_probs=8.0
Q ss_pred cccCCCChhhhcc
Q psy12196 85 SYQCNECPESFER 97 (150)
Q Consensus 85 ~~~c~~c~~~~~~ 97 (150)
.+.|..||..|..
T Consensus 70 ~~~C~~CG~~~~~ 82 (135)
T PRK03824 70 VLKCRNCGNEWSL 82 (135)
T ss_pred EEECCCCCCEEec
Confidence 3667777765554
No 127
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=65.98 E-value=3.7 Score=22.07 Aligned_cols=11 Identities=27% Similarity=1.078 Sum_probs=5.2
Q ss_pred ccCCCChhhhc
Q psy12196 86 YQCNECPESFE 96 (150)
Q Consensus 86 ~~c~~c~~~~~ 96 (150)
|.|..||..|.
T Consensus 54 W~C~kCg~~fA 64 (89)
T COG1997 54 WKCRKCGAKFA 64 (89)
T ss_pred EEcCCCCCeec
Confidence 44444544443
No 128
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=63.92 E-value=7.8 Score=21.10 Aligned_cols=14 Identities=21% Similarity=0.645 Sum_probs=7.6
Q ss_pred CcccccCCCCcccC
Q psy12196 55 TLMFTCRRCPSTFL 68 (150)
Q Consensus 55 ~~~~~c~~c~~~f~ 68 (150)
...+.|..|++.|.
T Consensus 52 ~GIW~C~~C~~~~A 65 (90)
T PTZ00255 52 VGIWRCKGCKKTVA 65 (90)
T ss_pred eEEEEcCCCCCEEe
Confidence 34555666655553
No 129
>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=63.08 E-value=0.66 Score=34.73 Aligned_cols=57 Identities=18% Similarity=0.385 Sum_probs=27.6
Q ss_pred cccCCCCcccCChHHHHHHHHhhcCCCc-ccCCCChhhhcchhHHhhHHhhhcCCCCCCcCCcchhh
Q psy12196 58 FTCRRCPSTFLNSATLSKHVKMEHNSKS-YQCNECPESFERLNKLKRHKFQAHNDSVHQIQCPYCIT 123 (150)
Q Consensus 58 ~~c~~c~~~f~~~~~l~~h~~~~~~~~~-~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~~C~~C~~ 123 (150)
..|..||-+|.-...|.- -+..+.=.. --|..|.+.+....+-+ .|.. +..|+.||=
T Consensus 124 ~~CT~CGPRfTIi~alPY-DR~nTsM~~F~lC~~C~~EY~dP~nRR----fHAQ----p~aCp~CGP 181 (750)
T COG0068 124 INCTNCGPRFTIIEALPY-DRENTSMADFPLCPFCDKEYKDPLNRR----FHAQ----PIACPKCGP 181 (750)
T ss_pred cccCCCCcceeeeccCCC-CcccCccccCcCCHHHHHHhcCccccc----cccc----cccCcccCC
Confidence 357777777654433221 122222111 24777777666554322 2222 556777774
No 130
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=62.76 E-value=6.9 Score=17.57 Aligned_cols=18 Identities=17% Similarity=0.206 Sum_probs=9.6
Q ss_pred eecccccccccChHHHHH
Q psy12196 31 IQCNMCSLVLDSKESLVT 48 (150)
Q Consensus 31 ~~c~~c~~~f~~~~~l~~ 48 (150)
..|+.|+-.|.....+..
T Consensus 20 d~C~~C~G~W~d~~el~~ 37 (41)
T PF13453_consen 20 DVCPSCGGIWFDAGELEK 37 (41)
T ss_pred EECCCCCeEEccHHHHHH
Confidence 446666655555554443
No 131
>PF05290 Baculo_IE-1: Baculovirus immediate-early protein (IE-0); InterPro: IPR007954 This entry contains the Baculovirus immediate-early protein IE-0.
Probab=61.41 E-value=5.6 Score=23.35 Aligned_cols=13 Identities=38% Similarity=0.943 Sum_probs=8.9
Q ss_pred CCcchhhhccCch
Q psy12196 117 QCPYCITDFSEDK 129 (150)
Q Consensus 117 ~C~~C~~~f~~~~ 129 (150)
+||.|.-+|.+.+
T Consensus 123 vCPvCkTSFKss~ 135 (140)
T PF05290_consen 123 VCPVCKTSFKSSS 135 (140)
T ss_pred CCCcccccccccc
Confidence 5777777776654
No 132
>TIGR00280 L37a ribosomal protein L37a. This model finds eukaryotic ribosomal protein L37a and its archaeal orthologs. The nomeclature is tricky because eukaryotes have proteins called both L37 and L37a.
Probab=60.88 E-value=8.1 Score=21.08 Aligned_cols=29 Identities=28% Similarity=0.721 Sum_probs=15.6
Q ss_pred eecccccccccChHHHHHHHhccCCcccccCCCCcccC
Q psy12196 31 IQCNMCSLVLDSKESLVTHISQTHTLMFTCRRCPSTFL 68 (150)
Q Consensus 31 ~~c~~c~~~f~~~~~l~~h~~~~~~~~~~c~~c~~~f~ 68 (150)
|.|+.|++.- +.+.....+.|..|++.|.
T Consensus 36 y~CpfCgk~~---------vkR~a~GIW~C~~C~~~~A 64 (91)
T TIGR00280 36 YVCPFCGKKT---------VKRGSTGIWTCRKCGAKFA 64 (91)
T ss_pred ccCCCCCCCc---------eEEEeeEEEEcCCCCCEEe
Confidence 5666666531 1233445566666666553
No 133
>PRK04023 DNA polymerase II large subunit; Validated
Probab=60.43 E-value=11 Score=30.08 Aligned_cols=10 Identities=20% Similarity=0.601 Sum_probs=5.7
Q ss_pred CcCCcchhhh
Q psy12196 115 QIQCPYCITD 124 (150)
Q Consensus 115 ~~~C~~C~~~ 124 (150)
++.|+.|+..
T Consensus 663 ~y~CPKCG~E 672 (1121)
T PRK04023 663 EDECEKCGRE 672 (1121)
T ss_pred CCcCCCCCCC
Confidence 4556666643
No 134
>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=60.05 E-value=9 Score=27.73 Aligned_cols=24 Identities=25% Similarity=0.520 Sum_probs=19.0
Q ss_pred CCCcccccccCHHHHHHHHHHHhh
Q psy12196 2 SCVPCDVLFHNKATLYKHLYLEHK 25 (150)
Q Consensus 2 ~C~~C~~~f~~~~~l~~h~~~~~~ 25 (150)
.|+.|++.|.+...++.|+...|.
T Consensus 59 iCp~CskkF~d~~~~~~H~~~eH~ 82 (466)
T PF04780_consen 59 ICPRCSKKFSDAESCLSHMEQEHP 82 (466)
T ss_pred eCCcccceeCCHHHHHHHHHHhhh
Confidence 578888888888888888877665
No 135
>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=59.29 E-value=3.1 Score=18.22 Aligned_cols=12 Identities=17% Similarity=0.814 Sum_probs=4.8
Q ss_pred cccccCCCCccc
Q psy12196 56 LMFTCRRCPSTF 67 (150)
Q Consensus 56 ~~~~c~~c~~~f 67 (150)
.+..|+.||-.+
T Consensus 20 ~~isC~~CGPr~ 31 (35)
T PF07503_consen 20 QFISCTNCGPRY 31 (35)
T ss_dssp TT--BTTCC-SC
T ss_pred cCccCCCCCCCE
Confidence 444566665443
No 136
>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=59.22 E-value=1.7 Score=32.80 Aligned_cols=28 Identities=18% Similarity=0.543 Sum_probs=12.7
Q ss_pred cccccccccChHHHHHHHhccCCcccccCCCCc
Q psy12196 33 CNMCSLVLDSKESLVTHISQTHTLMFTCRRCPS 65 (150)
Q Consensus 33 c~~c~~~f~~~~~l~~h~~~~~~~~~~c~~c~~ 65 (150)
|+.|.+.+.++.. ++-|..|..|+.||-
T Consensus 154 C~~C~~EY~dP~n-----RRfHAQp~aCp~CGP 181 (750)
T COG0068 154 CPFCDKEYKDPLN-----RRFHAQPIACPKCGP 181 (750)
T ss_pred CHHHHHHhcCccc-----cccccccccCcccCC
Confidence 5555554444433 223334445555553
No 137
>PF01780 Ribosomal_L37ae: Ribosomal L37ae protein family; InterPro: IPR002674 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This ribosomal protein is found in archaebacteria and eukaryotes []. Ribosomal protein L37 has a single zinc finger-like motif of the C2-C2 type [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 4A1E_Y 4A17_Y 4A1C_Y 4A1A_Y 3O58_g 3IZS_m 3O5H_g 1S1I_9 3IZR_m 1YSH_D ....
Probab=58.68 E-value=4.4 Score=22.03 Aligned_cols=28 Identities=21% Similarity=0.660 Sum_probs=14.7
Q ss_pred eecccccccccChHHHHHHHhccCCcccccCCCCccc
Q psy12196 31 IQCNMCSLVLDSKESLVTHISQTHTLMFTCRRCPSTF 67 (150)
Q Consensus 31 ~~c~~c~~~f~~~~~l~~h~~~~~~~~~~c~~c~~~f 67 (150)
|.|+.|++.-- .+....-|.|..|++.|
T Consensus 36 y~Cp~Cgk~~v---------kR~a~GIW~C~~C~~~~ 63 (90)
T PF01780_consen 36 YTCPFCGKTSV---------KRVATGIWKCKKCGKKF 63 (90)
T ss_dssp BEESSSSSSEE---------EEEETTEEEETTTTEEE
T ss_pred CcCCCCCCcee---------EEeeeEEeecCCCCCEE
Confidence 56666666421 13333446666666555
No 138
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=57.39 E-value=9.8 Score=20.72 Aligned_cols=29 Identities=24% Similarity=0.661 Sum_probs=15.2
Q ss_pred eecccccccccChHHHHHHHhccCCcccccCCCCcccC
Q psy12196 31 IQCNMCSLVLDSKESLVTHISQTHTLMFTCRRCPSTFL 68 (150)
Q Consensus 31 ~~c~~c~~~f~~~~~l~~h~~~~~~~~~~c~~c~~~f~ 68 (150)
|.|+.|++.- +.+.....+.|..|++.|.
T Consensus 37 y~CpfCgk~~---------vkR~a~GIW~C~~C~~~~A 65 (90)
T PRK03976 37 HVCPVCGRPK---------VKRVGTGIWECRKCGAKFA 65 (90)
T ss_pred ccCCCCCCCc---------eEEEEEEEEEcCCCCCEEe
Confidence 5666665431 1233345566666665553
No 139
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=56.76 E-value=0.89 Score=20.52 Aligned_cols=12 Identities=17% Similarity=0.404 Sum_probs=8.1
Q ss_pred CcCCcchhhhcc
Q psy12196 115 QIQCPYCITDFS 126 (150)
Q Consensus 115 ~~~C~~C~~~f~ 126 (150)
-|.|..|+..+.
T Consensus 28 fy~C~~C~~~w~ 39 (40)
T smart00440 28 FYVCTKCGHRWR 39 (40)
T ss_pred EEEeCCCCCEeC
Confidence 477877876654
No 140
>KOG2593|consensus
Probab=56.62 E-value=8.7 Score=27.33 Aligned_cols=38 Identities=24% Similarity=0.399 Sum_probs=23.5
Q ss_pred CcceecccccccccChHHHHHHHhccCCcccccCCCCccc
Q psy12196 28 SLSIQCNMCSLVLDSKESLVTHISQTHTLMFTCRRCPSTF 67 (150)
Q Consensus 28 ~~~~~c~~c~~~f~~~~~l~~h~~~~~~~~~~c~~c~~~f 67 (150)
...|.|+.|.+.|..-..+..- ......|.|..|+...
T Consensus 126 ~~~Y~Cp~C~kkyt~Lea~~L~--~~~~~~F~C~~C~gel 163 (436)
T KOG2593|consen 126 VAGYVCPNCQKKYTSLEALQLL--DNETGEFHCENCGGEL 163 (436)
T ss_pred cccccCCccccchhhhHHHHhh--cccCceEEEecCCCch
Confidence 4568899999888754333321 2234577888886544
No 141
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=55.02 E-value=5.1 Score=30.73 Aligned_cols=10 Identities=30% Similarity=0.856 Sum_probs=6.9
Q ss_pred CcCCcchhhh
Q psy12196 115 QIQCPYCITD 124 (150)
Q Consensus 115 ~~~C~~C~~~ 124 (150)
|..|+.||..
T Consensus 475 p~~Cp~Cgs~ 484 (730)
T COG1198 475 PQSCPECGSE 484 (730)
T ss_pred CCCCCCCCCC
Confidence 6677777744
No 142
>PF13878 zf-C2H2_3: zinc-finger of acetyl-transferase ESCO
Probab=54.80 E-value=20 Score=16.16 Aligned_cols=23 Identities=22% Similarity=0.365 Sum_probs=11.6
Q ss_pred cccCCCCcccC--ChHHHHHHHHhh
Q psy12196 58 FTCRRCPSTFL--NSATLSKHVKME 80 (150)
Q Consensus 58 ~~c~~c~~~f~--~~~~l~~h~~~~ 80 (150)
..|+.||..|. ...+...|.+-|
T Consensus 14 ~~C~~CgM~Y~~~~~eD~~~H~~yH 38 (41)
T PF13878_consen 14 TTCPTCGMLYSPGSPEDEKLHKKYH 38 (41)
T ss_pred cCCCCCCCEECCCCHHHHHHHHHHH
Confidence 35666665554 234444554444
No 143
>PF15135 UPF0515: Uncharacterised protein UPF0515
Probab=54.53 E-value=7.3 Score=25.52 Aligned_cols=13 Identities=31% Similarity=0.971 Sum_probs=6.8
Q ss_pred CcCCcchhhhccC
Q psy12196 115 QIQCPYCITDFSE 127 (150)
Q Consensus 115 ~~~C~~C~~~f~~ 127 (150)
.|.|+.|+..|+.
T Consensus 155 ef~C~~C~h~F~G 167 (278)
T PF15135_consen 155 EFHCPKCRHNFRG 167 (278)
T ss_pred eeecccccccchh
Confidence 4555555555543
No 144
>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=52.93 E-value=13 Score=17.13 Aligned_cols=8 Identities=25% Similarity=0.837 Sum_probs=3.9
Q ss_pred CcCCcchh
Q psy12196 115 QIQCPYCI 122 (150)
Q Consensus 115 ~~~C~~C~ 122 (150)
.|+|..|.
T Consensus 37 ~~~C~~C~ 44 (46)
T PF12760_consen 37 RYRCKACR 44 (46)
T ss_pred eEECCCCC
Confidence 44555543
No 145
>KOG2636|consensus
Probab=50.98 E-value=13 Score=26.69 Aligned_cols=21 Identities=19% Similarity=0.444 Sum_probs=19.1
Q ss_pred CcCCcchh-hhccCchHHHHHH
Q psy12196 115 QIQCPYCI-TDFSEDKNLIQHI 135 (150)
Q Consensus 115 ~~~C~~C~-~~f~~~~~l~~H~ 135 (150)
.|.|.+|| +++.-..+|.+|+
T Consensus 401 ey~CEICGNy~Y~GrkaF~RHF 422 (497)
T KOG2636|consen 401 EYNCEICGNYVYKGRKAFDRHF 422 (497)
T ss_pred ccceeeccCccccCcHHHHHHh
Confidence 78999999 8888999999997
No 146
>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=49.84 E-value=7.8 Score=28.40 Aligned_cols=9 Identities=33% Similarity=0.873 Sum_probs=4.9
Q ss_pred CcCCcchhh
Q psy12196 115 QIQCPYCIT 123 (150)
Q Consensus 115 ~~~C~~C~~ 123 (150)
+..|+.|+.
T Consensus 253 ~~~Cp~C~s 261 (505)
T TIGR00595 253 PKTCPQCGS 261 (505)
T ss_pred CCCCCCCCC
Confidence 445666653
No 147
>COG4530 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=49.67 E-value=6.4 Score=22.18 Aligned_cols=11 Identities=9% Similarity=0.036 Sum_probs=4.9
Q ss_pred cccCCCChhhh
Q psy12196 85 SYQCNECPESF 95 (150)
Q Consensus 85 ~~~c~~c~~~~ 95 (150)
|..|+.||++|
T Consensus 26 PiVsPytG~s~ 36 (129)
T COG4530 26 PIVSPYTGKSY 36 (129)
T ss_pred ccccCcccccc
Confidence 34444444444
No 148
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=49.57 E-value=28 Score=21.72 Aligned_cols=33 Identities=21% Similarity=0.564 Sum_probs=18.1
Q ss_pred cCCCcccCCCChhhhcchhHHhhHHhhhcCCCCCCcCCcchhhh
Q psy12196 81 HNSKSYQCNECPESFERLNKLKRHKFQAHNDSVHQIQCPYCITD 124 (150)
Q Consensus 81 ~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~~C~~C~~~ 124 (150)
.+..-|.|+.|...++...+... .|.||.||-.
T Consensus 109 ~~~~~y~C~~~~~r~sfdeA~~~-----------~F~Cp~Cg~~ 141 (176)
T COG1675 109 TENNYYVCPNCHVKYSFDEAMEL-----------GFTCPKCGED 141 (176)
T ss_pred ccCCceeCCCCCCcccHHHHHHh-----------CCCCCCCCch
Confidence 34556777666655544332210 3677777754
No 149
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=48.62 E-value=13 Score=17.77 Aligned_cols=9 Identities=22% Similarity=1.003 Sum_probs=4.9
Q ss_pred ccCCCChhh
Q psy12196 86 YQCNECPES 94 (150)
Q Consensus 86 ~~c~~c~~~ 94 (150)
+.|..||..
T Consensus 38 ~~C~~Cgyt 46 (50)
T PRK00432 38 WHCGKCGYT 46 (50)
T ss_pred EECCCcCCE
Confidence 556666543
No 150
>KOG2272|consensus
Probab=48.35 E-value=11 Score=24.79 Aligned_cols=19 Identities=11% Similarity=0.373 Sum_probs=10.6
Q ss_pred CCCCcccccccCHHHHHHH
Q psy12196 1 MSCVPCDVLFHNKATLYKH 19 (150)
Q Consensus 1 ~~C~~C~~~f~~~~~l~~h 19 (150)
|.|+.|.+.+.+...++..
T Consensus 100 F~Cd~Cn~~Lad~gf~rnq 118 (332)
T KOG2272|consen 100 FRCDLCNKHLADQGFYRNQ 118 (332)
T ss_pred chhHHHHHHHhhhhhHhhc
Confidence 3456666666665555543
No 151
>PLN03238 probable histone acetyltransferase MYST; Provisional
Probab=48.15 E-value=15 Score=24.73 Aligned_cols=25 Identities=24% Similarity=0.681 Sum_probs=18.5
Q ss_pred CcCCcchhhhccCchHHHHHHHHhc
Q psy12196 115 QIQCPYCITDFSEDKNLIQHIVSVH 139 (150)
Q Consensus 115 ~~~C~~C~~~f~~~~~l~~H~~~~~ 139 (150)
-|.|..|-+-|.+...|.+|+....
T Consensus 48 lyiCe~Clky~~~~~~l~~H~~~C~ 72 (290)
T PLN03238 48 LYICEYCLKYMRKKKSLLRHLAKCD 72 (290)
T ss_pred EEEcCCCcchhCCHHHHHHHHHhCC
Confidence 6777778877778778888876543
No 152
>COG1655 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=44.86 E-value=4.8 Score=26.01 Aligned_cols=6 Identities=33% Similarity=0.822 Sum_probs=3.3
Q ss_pred cCCCCh
Q psy12196 87 QCNECP 92 (150)
Q Consensus 87 ~c~~c~ 92 (150)
.|+.|.
T Consensus 64 vCP~C~ 69 (267)
T COG1655 64 VCPICY 69 (267)
T ss_pred Ecchhh
Confidence 455554
No 153
>KOG2907|consensus
Probab=44.32 E-value=9.6 Score=21.64 Aligned_cols=40 Identities=23% Similarity=0.443 Sum_probs=21.9
Q ss_pred ccCCCChhhhcchhHHhhHHhhhcCCCCCCcCCcchhhhccC
Q psy12196 86 YQCNECPESFERLNKLKRHKFQAHNDSVHQIQCPYCITDFSE 127 (150)
Q Consensus 86 ~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~~C~~C~~~f~~ 127 (150)
.+|+.||-.-.....|+ ++........-|.|+.|++.|..
T Consensus 75 ~kCpkCghe~m~Y~T~Q--lRSADEGQTVFYTC~kC~~k~~e 114 (116)
T KOG2907|consen 75 HKCPKCGHEEMSYHTLQ--LRSADEGQTVFYTCPKCKYKFTE 114 (116)
T ss_pred ccCcccCCchhhhhhhh--cccccCCceEEEEcCccceeeec
Confidence 46888875433333332 12222222335889999888765
No 154
>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=44.22 E-value=6.5 Score=16.25 Aligned_cols=8 Identities=38% Similarity=1.331 Sum_probs=3.3
Q ss_pred CCCChhhh
Q psy12196 88 CNECPESF 95 (150)
Q Consensus 88 c~~c~~~~ 95 (150)
|-.|++.|
T Consensus 3 CiDC~~~F 10 (28)
T PF08790_consen 3 CIDCSKDF 10 (28)
T ss_dssp ETTTTEEE
T ss_pred eecCCCCc
Confidence 33344444
No 155
>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=44.07 E-value=8.7 Score=21.93 Aligned_cols=10 Identities=20% Similarity=0.760 Sum_probs=4.4
Q ss_pred cccCCCCccc
Q psy12196 58 FTCRRCPSTF 67 (150)
Q Consensus 58 ~~c~~c~~~f 67 (150)
..|..|+..|
T Consensus 71 ~~C~~Cg~~~ 80 (115)
T TIGR00100 71 CECEDCSEEV 80 (115)
T ss_pred EEcccCCCEE
Confidence 3444444443
No 156
>COG5112 UFD2 U1-like Zn-finger-containing protein [General function prediction only]
Probab=43.50 E-value=12 Score=20.90 Aligned_cols=24 Identities=29% Similarity=0.452 Sum_probs=17.6
Q ss_pred CcCCcchhhhccCchHHHHHHHHh
Q psy12196 115 QIQCPYCITDFSEDKNLIQHIVSV 138 (150)
Q Consensus 115 ~~~C~~C~~~f~~~~~l~~H~~~~ 138 (150)
.+-|-.|.+-|-+...|..|.+..
T Consensus 55 qhYCieCaryf~t~~aL~~Hkkgk 78 (126)
T COG5112 55 QHYCIECARYFITEKALMEHKKGK 78 (126)
T ss_pred eeeeehhHHHHHHHHHHHHHhccc
Confidence 556777888888888888877543
No 157
>PLN02294 cytochrome c oxidase subunit Vb
Probab=42.65 E-value=12 Score=23.11 Aligned_cols=15 Identities=27% Similarity=0.815 Sum_probs=12.5
Q ss_pred CCcCCcchhhhccCc
Q psy12196 114 HQIQCPYCITDFSED 128 (150)
Q Consensus 114 ~~~~C~~C~~~f~~~ 128 (150)
++..|++||..|..+
T Consensus 140 kp~RCpeCG~~fkL~ 154 (174)
T PLN02294 140 KSFECPVCTQYFELE 154 (174)
T ss_pred CceeCCCCCCEEEEE
Confidence 388999999998754
No 158
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=42.60 E-value=9 Score=17.13 Aligned_cols=14 Identities=21% Similarity=0.534 Sum_probs=11.6
Q ss_pred CcCCcchhhhccCc
Q psy12196 115 QIQCPYCITDFSED 128 (150)
Q Consensus 115 ~~~C~~C~~~f~~~ 128 (150)
++.|..|++.|-..
T Consensus 12 ~f~C~~C~~~FC~~ 25 (39)
T smart00154 12 GFKCRHCGNLFCGE 25 (39)
T ss_pred CeECCccCCccccc
Confidence 77899999888765
No 159
>KOG1280|consensus
Probab=42.35 E-value=22 Score=24.71 Aligned_cols=38 Identities=21% Similarity=0.496 Sum_probs=25.0
Q ss_pred cccCCCChhhhcchhHHhhHHhhhcCCCCCCcCCcchh
Q psy12196 85 SYQCNECPESFERLNKLKRHKFQAHNDSVHQIQCPYCI 122 (150)
Q Consensus 85 ~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~~C~~C~ 122 (150)
-|.|..|+..-.+...|..|....+.+......|+.|+
T Consensus 79 SftCPyC~~~Gfte~~f~~Hv~s~Hpda~~~~icp~c~ 116 (381)
T KOG1280|consen 79 SFTCPYCGIMGFTERQFGTHVLSQHPEASTSVICPLCA 116 (381)
T ss_pred cccCCcccccccchhHHHHHhhhcCcccCcceeeeccc
Confidence 47777777666666677777766665554445666665
No 160
>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=42.23 E-value=11 Score=20.86 Aligned_cols=13 Identities=31% Similarity=0.608 Sum_probs=11.1
Q ss_pred CcCCcchhhhccC
Q psy12196 115 QIQCPYCITDFSE 127 (150)
Q Consensus 115 ~~~C~~C~~~f~~ 127 (150)
+.+|+.||..|..
T Consensus 79 ~~rC~eCG~~fkL 91 (97)
T cd00924 79 PKRCPECGHVFKL 91 (97)
T ss_pred ceeCCCCCcEEEE
Confidence 8899999988864
No 161
>PF08209 Sgf11: Sgf11 (transcriptional regulation protein); InterPro: IPR013246 The Sgf11 family is a SAGA complex subunit in Saccharomyces cerevisiae (Baker's yeast). The SAGA complex is a multisubunit protein complex involved in transcriptional regulation. SAGA combines proteins involved in interactions with DNA-bound activators and TATA-binding protein (TBP), as well as enzymes for histone acetylation and deubiquitylation [].; PDB: 3M99_B 2LO2_A 3MHH_C 3MHS_C.
Probab=42.16 E-value=21 Score=15.36 Aligned_cols=22 Identities=18% Similarity=0.585 Sum_probs=10.8
Q ss_pred cCCcchhhhccCchHHHHHHHHh
Q psy12196 116 IQCPYCITDFSEDKNLIQHIVSV 138 (150)
Q Consensus 116 ~~C~~C~~~f~~~~~l~~H~~~~ 138 (150)
+.|+.|++.+... -+..|+...
T Consensus 5 ~~C~nC~R~v~a~-RfA~HLekC 26 (33)
T PF08209_consen 5 VECPNCGRPVAAS-RFAPHLEKC 26 (33)
T ss_dssp EE-TTTSSEEEGG-GHHHHHHHH
T ss_pred EECCCCcCCcchh-hhHHHHHHH
Confidence 4566666554442 355555443
No 162
>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=41.86 E-value=8.2 Score=18.54 Aligned_cols=21 Identities=33% Similarity=0.649 Sum_probs=10.8
Q ss_pred CCcchhhhccC--chHHHHHHHH
Q psy12196 117 QCPYCITDFSE--DKNLIQHIVS 137 (150)
Q Consensus 117 ~C~~C~~~f~~--~~~l~~H~~~ 137 (150)
.||.|++.|.. ...|..++..
T Consensus 22 ~CPlC~r~l~~e~~~~li~~~~~ 44 (54)
T PF04423_consen 22 CCPLCGRPLDEEHRQELIKKYKS 44 (54)
T ss_dssp E-TTT--EE-HHHHHHHHHHHHH
T ss_pred cCCCCCCCCCHHHHHHHHHHHHH
Confidence 79999999885 3455555443
No 163
>KOG1842|consensus
Probab=41.38 E-value=20 Score=25.84 Aligned_cols=28 Identities=29% Similarity=0.418 Sum_probs=24.3
Q ss_pred CCCCcccccccCHHHHHHHHHHHhhCCC
Q psy12196 1 MSCVPCDVLFHNKATLYKHLYLEHKATS 28 (150)
Q Consensus 1 ~~C~~C~~~f~~~~~l~~h~~~~~~~~~ 28 (150)
|.|+.|...|.+...|..|.-..|.++.
T Consensus 16 flCPiC~~dl~~~~~L~~H~d~eH~~ed 43 (505)
T KOG1842|consen 16 FLCPICLLDLPNLSALNDHLDVEHFEED 43 (505)
T ss_pred ccCchHhhhhhhHHHHHHHHhhhccccc
Confidence 5799999999999999999988876443
No 164
>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=41.23 E-value=6.9 Score=17.26 Aligned_cols=6 Identities=33% Similarity=1.121 Sum_probs=1.6
Q ss_pred CCCccc
Q psy12196 2 SCVPCD 7 (150)
Q Consensus 2 ~C~~C~ 7 (150)
+|..||
T Consensus 8 kC~~CG 13 (36)
T PF06397_consen 8 KCEHCG 13 (36)
T ss_dssp E-TTT-
T ss_pred EccCCC
Confidence 344443
No 165
>PRK05978 hypothetical protein; Provisional
Probab=41.16 E-value=7.6 Score=23.34 Aligned_cols=10 Identities=30% Similarity=0.859 Sum_probs=5.6
Q ss_pred ccCCCCcccC
Q psy12196 59 TCRRCPSTFL 68 (150)
Q Consensus 59 ~c~~c~~~f~ 68 (150)
.|+.||..|.
T Consensus 54 ~C~~CG~~~~ 63 (148)
T PRK05978 54 HCAACGEDFT 63 (148)
T ss_pred CccccCCccc
Confidence 4666665553
No 166
>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=41.10 E-value=16 Score=16.77 Aligned_cols=16 Identities=25% Similarity=0.491 Sum_probs=11.8
Q ss_pred cCCCChhhhcchhHHh
Q psy12196 87 QCNECPESFERLNKLK 102 (150)
Q Consensus 87 ~c~~c~~~~~~~~~l~ 102 (150)
.|.+|++.|+....+.
T Consensus 10 ~C~~C~rpf~WRKKW~ 25 (42)
T PF10013_consen 10 ICPVCGRPFTWRKKWA 25 (42)
T ss_pred cCcccCCcchHHHHHH
Confidence 6888888888765544
No 167
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=40.99 E-value=4.1 Score=23.22 Aligned_cols=40 Identities=18% Similarity=0.331 Sum_probs=22.0
Q ss_pred ccCCCChhhhcchhHHhhHHhhhcCCCCCCcCCcchhhhccC
Q psy12196 86 YQCNECPESFERLNKLKRHKFQAHNDSVHQIQCPYCITDFSE 127 (150)
Q Consensus 86 ~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~~C~~C~~~f~~ 127 (150)
..|+.||..-.....|+. +........-|.|..||..|+.
T Consensus 73 ~~CpkCg~~ea~y~~~Qt--RsaDEp~T~Fy~C~~Cg~~wre 112 (113)
T COG1594 73 EKCPKCGNKEAYYWQLQT--RSADEPETRFYKCTRCGYRWRE 112 (113)
T ss_pred ccCCCCCCceeEEEeeeh--hccCCCceEEEEecccCCEeec
Confidence 568888765444333322 2222222234889999987764
No 168
>PF02891 zf-MIZ: MIZ/SP-RING zinc finger; InterPro: IPR004181 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents MIZ-type zinc finger domains. Miz1 (Msx-interacting-zinc finger) is a zinc finger-containing protein with homology to the yeast protein, Nfi-1. Miz1 is a sequence specific DNA binding protein that can function as a positive-acting transcription factor. Miz1 binds to the homeobox protein Msx2, enhancing the specific DNA-binding ability of Msx2 []. Other proteins containing this domain include the human pias family (protein inhibitor of activated STAT protein). More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3I2D_A.
Probab=40.92 E-value=9.6 Score=18.10 Aligned_cols=9 Identities=33% Similarity=1.051 Sum_probs=3.1
Q ss_pred CcCCcchhh
Q psy12196 115 QIQCPYCIT 123 (150)
Q Consensus 115 ~~~C~~C~~ 123 (150)
.|+|++|++
T Consensus 41 ~W~CPiC~~ 49 (50)
T PF02891_consen 41 KWKCPICNK 49 (50)
T ss_dssp --B-TTT--
T ss_pred CeECcCCcC
Confidence 467777764
No 169
>PRK11823 DNA repair protein RadA; Provisional
Probab=40.80 E-value=12 Score=26.99 Aligned_cols=8 Identities=50% Similarity=1.331 Sum_probs=4.3
Q ss_pred ccCCCChh
Q psy12196 86 YQCNECPE 93 (150)
Q Consensus 86 ~~c~~c~~ 93 (150)
|.|..||.
T Consensus 8 y~C~~Cg~ 15 (446)
T PRK11823 8 YVCQECGA 15 (446)
T ss_pred EECCcCCC
Confidence 55555554
No 170
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=40.42 E-value=22 Score=20.22 Aligned_cols=10 Identities=20% Similarity=0.534 Sum_probs=4.9
Q ss_pred cccCCCCccc
Q psy12196 58 FTCRRCPSTF 67 (150)
Q Consensus 58 ~~c~~c~~~f 67 (150)
..|..|+..|
T Consensus 71 ~~C~~Cg~~~ 80 (113)
T PRK12380 71 AWCWDCSQVV 80 (113)
T ss_pred EEcccCCCEE
Confidence 4455555444
No 171
>TIGR00416 sms DNA repair protein RadA. The gene protuct codes for a probable ATP-dependent protease involved in both DNA repair and degradation of proteins, peptides, glycopeptides. Also known as sms. Residues 11-28 of the SEED alignment contain a putative Zn binding domain. Residues 110-117 of the seed contain a putative ATP binding site both documented in Haemophilus and in Listeria monocytogenes. for E.coli see ( J. BACTERIOL. 178:5045-5048(1996)).
Probab=40.13 E-value=11 Score=27.17 Aligned_cols=9 Identities=22% Similarity=0.984 Sum_probs=4.9
Q ss_pred ccCCCChhh
Q psy12196 86 YQCNECPES 94 (150)
Q Consensus 86 ~~c~~c~~~ 94 (150)
|.|..||..
T Consensus 8 y~C~~Cg~~ 16 (454)
T TIGR00416 8 FVCQHCGAD 16 (454)
T ss_pred EECCcCCCC
Confidence 555555543
No 172
>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=39.05 E-value=93 Score=19.13 Aligned_cols=53 Identities=19% Similarity=0.225 Sum_probs=28.0
Q ss_pred ccCCCChhhhcchhHHhhHHhhhcCCCCCCcCCcchhhhcc-CchHHHHHHHHhcCC
Q psy12196 86 YQCNECPESFERLNKLKRHKFQAHNDSVHQIQCPYCITDFS-EDKNLIQHIVSVHLG 141 (150)
Q Consensus 86 ~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~~C~~C~~~f~-~~~~l~~H~~~~~~~ 141 (150)
..|+.|.-...... .....+...+.+.+......|. |. +...|.+|.+..|+.
T Consensus 81 L~CPLCRG~V~GWt-vve~AR~~LN~K~RsC~~e~C~--F~GtY~eLrKHar~~HP~ 134 (162)
T PF07800_consen 81 LACPLCRGEVKGWT-VVEPARRFLNAKKRSCSQESCS--FSGTYSELRKHARSEHPS 134 (162)
T ss_pred ccCccccCceeceE-EchHHHHHhccCCccCcccccc--cccCHHHHHHHHHhhCCC
Confidence 56777754332221 1122333445553333334454 43 578899999888843
No 173
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=37.70 E-value=42 Score=27.90 Aligned_cols=10 Identities=30% Similarity=0.956 Sum_probs=5.6
Q ss_pred cccCCCChhh
Q psy12196 85 SYQCNECPES 94 (150)
Q Consensus 85 ~~~c~~c~~~ 94 (150)
.|.|+.||..
T Consensus 692 vy~CPsCGae 701 (1337)
T PRK14714 692 VYVCPDCGAE 701 (1337)
T ss_pred ceeCccCCCc
Confidence 3566666653
No 174
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=37.25 E-value=13 Score=21.72 Aligned_cols=14 Identities=21% Similarity=0.693 Sum_probs=11.0
Q ss_pred CcCCcchhhhccCc
Q psy12196 115 QIQCPYCITDFSED 128 (150)
Q Consensus 115 ~~~C~~C~~~f~~~ 128 (150)
.|+|+.|++.|...
T Consensus 53 RyrC~~C~~tf~~~ 66 (129)
T COG3677 53 RYKCKSCGSTFTVE 66 (129)
T ss_pred ccccCCcCcceeee
Confidence 67888888888753
No 175
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=37.21 E-value=13 Score=20.22 Aligned_cols=14 Identities=21% Similarity=0.641 Sum_probs=11.3
Q ss_pred CCcCCcchhhhccC
Q psy12196 114 HQIQCPYCITDFSE 127 (150)
Q Consensus 114 ~~~~C~~C~~~f~~ 127 (150)
.|-+|..||..|..
T Consensus 57 ~Pa~CkkCGfef~~ 70 (97)
T COG3357 57 RPARCKKCGFEFRD 70 (97)
T ss_pred cChhhcccCccccc
Confidence 36789999988877
No 176
>PRK14873 primosome assembly protein PriA; Provisional
Probab=36.67 E-value=16 Score=27.99 Aligned_cols=10 Identities=40% Similarity=1.036 Sum_probs=6.2
Q ss_pred CcCCcchhhh
Q psy12196 115 QIQCPYCITD 124 (150)
Q Consensus 115 ~~~C~~C~~~ 124 (150)
++.|+.|+..
T Consensus 422 p~~Cp~Cgs~ 431 (665)
T PRK14873 422 DWRCPRCGSD 431 (665)
T ss_pred CccCCCCcCC
Confidence 5567777643
No 177
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=35.72 E-value=33 Score=21.81 Aligned_cols=15 Identities=20% Similarity=0.640 Sum_probs=10.6
Q ss_pred cccccCCCCcccCCh
Q psy12196 56 LMFTCRRCPSTFLNS 70 (150)
Q Consensus 56 ~~~~c~~c~~~f~~~ 70 (150)
.||.|.+|-+.|.++
T Consensus 195 IPF~C~iCKkdy~sp 209 (259)
T COG5152 195 IPFLCGICKKDYESP 209 (259)
T ss_pred Cceeehhchhhccch
Confidence 577777777777654
No 178
>COG5188 PRP9 Splicing factor 3a, subunit 3 [RNA processing and modification]
Probab=35.69 E-value=22 Score=24.73 Aligned_cols=24 Identities=25% Similarity=0.477 Sum_probs=20.7
Q ss_pred CcCCcchhhhccCchHHHHHHHHh
Q psy12196 115 QIQCPYCITDFSEDKNLIQHIVSV 138 (150)
Q Consensus 115 ~~~C~~C~~~f~~~~~l~~H~~~~ 138 (150)
.+-|+.|++.|....-+..|+...
T Consensus 238 ~~YC~~C~r~f~~~~VFe~Hl~gK 261 (470)
T COG5188 238 KVYCVKCGREFSRSKVFEYHLEGK 261 (470)
T ss_pred ceeeHhhhhHhhhhHHHHHHHhhh
Confidence 455999999999999999998665
No 179
>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG
Probab=35.63 E-value=20 Score=17.32 Aligned_cols=8 Identities=25% Similarity=0.592 Sum_probs=3.7
Q ss_pred CCCccccc
Q psy12196 2 SCVPCDVL 9 (150)
Q Consensus 2 ~C~~C~~~ 9 (150)
.|++||..
T Consensus 2 ~CPyCge~ 9 (52)
T PF14255_consen 2 QCPYCGEP 9 (52)
T ss_pred CCCCCCCe
Confidence 34555443
No 180
>TIGR01562 FdhE formate dehydrogenase accessory protein FdhE. The only sequence scoring between trusted and noise is that from Aquifex aeolicus, which shows certain structural differences from the proteobacterial forms in the alignment. However it is notable that A. aeolicus also has a sequence scoring above trusted to the alpha subunit of formate dehydrogenase (TIGR01553).
Probab=35.53 E-value=28 Score=23.81 Aligned_cols=8 Identities=38% Similarity=1.157 Sum_probs=4.8
Q ss_pred ccCCCChh
Q psy12196 86 YQCNECPE 93 (150)
Q Consensus 86 ~~c~~c~~ 93 (150)
..|..||.
T Consensus 225 ~~C~~Cg~ 232 (305)
T TIGR01562 225 VKCSHCEE 232 (305)
T ss_pred ccCCCCCC
Confidence 35666664
No 181
>PF14311 DUF4379: Domain of unknown function (DUF4379)
Probab=35.16 E-value=36 Score=16.33 Aligned_cols=6 Identities=33% Similarity=1.287 Sum_probs=2.3
Q ss_pred cCCCCh
Q psy12196 87 QCNECP 92 (150)
Q Consensus 87 ~c~~c~ 92 (150)
+|..||
T Consensus 30 ~C~~Cg 35 (55)
T PF14311_consen 30 KCPKCG 35 (55)
T ss_pred ECCCCC
Confidence 344443
No 182
>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=34.99 E-value=16 Score=17.60 Aligned_cols=23 Identities=22% Similarity=0.436 Sum_probs=12.2
Q ss_pred CcccCCCChhhhcchhHHhhHHh
Q psy12196 84 KSYQCNECPESFERLNKLKRHKF 106 (150)
Q Consensus 84 ~~~~c~~c~~~~~~~~~l~~h~~ 106 (150)
..|.|+.|...|=..-++..|..
T Consensus 20 ~~y~C~~C~~~FC~dCD~fiHE~ 42 (51)
T PF07975_consen 20 SRYRCPKCKNHFCIDCDVFIHET 42 (51)
T ss_dssp EEE--TTTT--B-HHHHHTTTTT
T ss_pred CeEECCCCCCccccCcChhhhcc
Confidence 45778888777777777666643
No 183
>PLN00104 MYST -like histone acetyltransferase; Provisional
Probab=34.75 E-value=26 Score=25.36 Aligned_cols=25 Identities=16% Similarity=0.488 Sum_probs=22.1
Q ss_pred CcCCcchhhhccCchHHHHHHHHhc
Q psy12196 115 QIQCPYCITDFSEDKNLIQHIVSVH 139 (150)
Q Consensus 115 ~~~C~~C~~~f~~~~~l~~H~~~~~ 139 (150)
-|.|..|-+-|.+...|.+|+....
T Consensus 198 lyiCe~Cl~y~~~~~~~~~H~~~C~ 222 (450)
T PLN00104 198 LYFCEFCLKFMKRKEQLQRHMKKCD 222 (450)
T ss_pred EEEchhhhhhhcCHHHHHHHHhcCC
Confidence 6889999999999999999997554
No 184
>PTZ00064 histone acetyltransferase; Provisional
Probab=34.67 E-value=29 Score=25.54 Aligned_cols=25 Identities=28% Similarity=0.638 Sum_probs=22.1
Q ss_pred CcCCcchhhhccCchHHHHHHHHhc
Q psy12196 115 QIQCPYCITDFSEDKNLIQHIVSVH 139 (150)
Q Consensus 115 ~~~C~~C~~~f~~~~~l~~H~~~~~ 139 (150)
-|.|..|-+-|.....|.+|+....
T Consensus 280 LYICEfCLkY~~s~~~l~rH~~~C~ 304 (552)
T PTZ00064 280 LHFCEYCLDFFCFEDELIRHLSRCQ 304 (552)
T ss_pred EEEccchhhhhCCHHHHHHHHhcCC
Confidence 5789999999999999999998654
No 185
>PF11931 DUF3449: Domain of unknown function (DUF3449); InterPro: IPR024598 This presumed domain is functionally uncharacterised. It has two conserved sequence motifs: PIP and CEICG and contains a zinc-finger of the C2H2-type.; PDB: 4DGW_A.
Probab=34.55 E-value=13 Score=23.53 Aligned_cols=21 Identities=19% Similarity=0.572 Sum_probs=0.0
Q ss_pred CcCCcchhhh-ccCchHHHHHH
Q psy12196 115 QIQCPYCITD-FSEDKNLIQHI 135 (150)
Q Consensus 115 ~~~C~~C~~~-f~~~~~l~~H~ 135 (150)
.|.|.+||-. +.-+.+|.+|+
T Consensus 101 ey~CEICGN~~Y~GrkaFekHF 122 (196)
T PF11931_consen 101 EYKCEICGNQSYKGRKAFEKHF 122 (196)
T ss_dssp ----------------------
T ss_pred eeeeEeCCCcceecHHHHHHhc
Confidence 7889999844 44677788886
No 186
>PF04606 Ogr_Delta: Ogr/Delta-like zinc finger; InterPro: IPR007684 This entry is represented by Bacteriophage P2, Ogr. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This is a viral family of phage zinc-binding transcriptional activators, which also contains cryptic members in some bacterial genomes []. The P4 phage delta protein contains two such domains attached covalently, while the P2 phage Ogr proteins possess one domain but function as dimers. All the members of this family have the following consensus sequence: C-X(2)-C-X(3)-A-(X)2-R-X(15)-C-X(4)-C-X(3)-F [].; GO: 0006355 regulation of transcription, DNA-dependent
Probab=34.32 E-value=6.2 Score=18.42 Aligned_cols=12 Identities=17% Similarity=0.443 Sum_probs=6.0
Q ss_pred CCcccccccCHH
Q psy12196 3 CVPCDVLFHNKA 14 (150)
Q Consensus 3 C~~C~~~f~~~~ 14 (150)
|+.||.......
T Consensus 2 CP~Cg~~a~ir~ 13 (47)
T PF04606_consen 2 CPHCGSKARIRT 13 (47)
T ss_pred cCCCCCeeEEEE
Confidence 566665444333
No 187
>COG1773 Rubredoxin [Energy production and conversion]
Probab=33.85 E-value=13 Score=18.24 Aligned_cols=13 Identities=15% Similarity=0.496 Sum_probs=8.1
Q ss_pred CcCCcchhhhccC
Q psy12196 115 QIQCPYCITDFSE 127 (150)
Q Consensus 115 ~~~C~~C~~~f~~ 127 (150)
.|+|..||..|.-
T Consensus 3 ~~~C~~CG~vYd~ 15 (55)
T COG1773 3 RWRCSVCGYVYDP 15 (55)
T ss_pred ceEecCCceEecc
Confidence 4667777766543
No 188
>PF04328 DUF466: Protein of unknown function (DUF466); InterPro: IPR007423 This is a small bacterial protein of unknown function.
Probab=33.81 E-value=38 Score=17.18 Aligned_cols=16 Identities=13% Similarity=0.283 Sum_probs=11.6
Q ss_pred hHHHHHHHHhcCCCCC
Q psy12196 129 KNLIQHIVSVHLGKEG 144 (150)
Q Consensus 129 ~~l~~H~~~~~~~~~~ 144 (150)
..+..|++.+|++.|.
T Consensus 26 e~Yv~H~~~~HP~~p~ 41 (65)
T PF04328_consen 26 ERYVEHMRRHHPDEPP 41 (65)
T ss_pred HHHHHHHHHHCcCCCC
Confidence 4566788888877764
No 189
>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=33.75 E-value=69 Score=16.04 Aligned_cols=31 Identities=19% Similarity=0.429 Sum_probs=20.1
Q ss_pred ecccccccccChHHHHHHHhccCCcccccCCCCcccCChH
Q psy12196 32 QCNMCSLVLDSKESLVTHISQTHTLMFTCRRCPSTFLNSA 71 (150)
Q Consensus 32 ~c~~c~~~f~~~~~l~~h~~~~~~~~~~c~~c~~~f~~~~ 71 (150)
.|+.|+..... ......+.|+.||.......
T Consensus 30 ~C~~CG~~~~~---------~~~~r~~~C~~Cg~~~~rD~ 60 (69)
T PF07282_consen 30 TCPRCGHRNKK---------RRSGRVFTCPNCGFEMDRDV 60 (69)
T ss_pred CccCccccccc---------ccccceEEcCCCCCEECcHH
Confidence 47888876543 23335678999987765443
No 190
>PF01428 zf-AN1: AN1-like Zinc finger; InterPro: IPR000058 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the AN1-type zinc finger domain, which has a dimetal (zinc)-bound alpha/beta fold. This domain was first identified as a zinc finger at the C terminus of AN1 Q91889 from SWISSPROT, a ubiquitin-like protein in Xenopus laevis []. The AN1-type zinc finger contains six conserved cysteines and two histidines that could potentially coordinate 2 zinc atoms. Certain stress-associated proteins (SAP) contain AN1 domain, often in combination with A20 zinc finger domains (SAP8) or C2H2 domains (SAP16) []. For example, the human protein Znf216 has an A20 zinc-finger at the N terminus and an AN1 zinc-finger at the C terminus, acting to negatively regulate the NFkappaB activation pathway and to interact with components of the immune response like RIP, IKKgamma and TRAF6. The interact of Znf216 with IKK-gamma and RIP is mediated by the A20 zinc-finger domain, while its interaction with TRAF6 is mediated by the AN1 zinc-finger domain; therefore, both zinc-finger domains are involved in regulating the immune response []. The AN1 zinc finger domain is also found in proteins containing a ubiquitin-like domain, which are involved in the ubiquitination pathway []. Proteins containing an AN1-type zinc finger include: Ascidian posterior end mark 6 (pem-6) protein []. Human AWP1 protein (associated with PRK1), which is expressed during early embryogenesis []. Human immunoglobulin mu binding protein 2 (SMUBP-2), mutations in which cause muscular atrophy with respiratory distress type 1 []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 1WFP_A 1WYS_A 1WG2_A 1WFH_A 1X4W_A 1WFE_A 1WFL_A 1X4V_A.
Probab=33.52 E-value=19 Score=16.33 Aligned_cols=14 Identities=21% Similarity=0.558 Sum_probs=7.9
Q ss_pred cceecccccccccC
Q psy12196 29 LSIQCNMCSLVLDS 42 (150)
Q Consensus 29 ~~~~c~~c~~~f~~ 42 (150)
.++.|..|++.|=.
T Consensus 12 ~~~~C~~C~~~FC~ 25 (43)
T PF01428_consen 12 LPFKCKHCGKSFCL 25 (43)
T ss_dssp SHEE-TTTS-EE-T
T ss_pred CCeECCCCCcccCc
Confidence 56778888887753
No 191
>KOG0717|consensus
Probab=33.44 E-value=27 Score=25.38 Aligned_cols=21 Identities=29% Similarity=0.521 Sum_probs=18.5
Q ss_pred CCCcccccccCHHHHHHHHHH
Q psy12196 2 SCVPCDVLFHNKATLYKHLYL 22 (150)
Q Consensus 2 ~C~~C~~~f~~~~~l~~h~~~ 22 (150)
-|..|++.|.+...|..|...
T Consensus 294 yC~vCnKsFKseKq~kNHEnS 314 (508)
T KOG0717|consen 294 YCVVCNKSFKSEKQLKNHENS 314 (508)
T ss_pred EEeeccccccchHHHHhhHHH
Confidence 489999999999999999765
No 192
>PTZ00448 hypothetical protein; Provisional
Probab=32.84 E-value=38 Score=23.84 Aligned_cols=22 Identities=14% Similarity=0.487 Sum_probs=17.6
Q ss_pred CCCCcccccccCHHHHHHHHHH
Q psy12196 1 MSCVPCDVLFHNKATLYKHLYL 22 (150)
Q Consensus 1 ~~C~~C~~~f~~~~~l~~h~~~ 22 (150)
|.|..|+..|.+....+.|.+.
T Consensus 315 ~tC~~C~v~F~~~~~qR~H~KS 336 (373)
T PTZ00448 315 LLCRKCNIQLMDHNAFKQHYRS 336 (373)
T ss_pred ccccccccccCCHHHHHHHhhh
Confidence 4588888888888888888775
No 193
>KOG2071|consensus
Probab=32.84 E-value=30 Score=25.90 Aligned_cols=26 Identities=19% Similarity=0.340 Sum_probs=22.4
Q ss_pred CCcCCcchhhhccCchHHHHHHHHhc
Q psy12196 114 HQIQCPYCITDFSEDKNLIQHIVSVH 139 (150)
Q Consensus 114 ~~~~C~~C~~~f~~~~~l~~H~~~~~ 139 (150)
.+-+|..||..|........||..|-
T Consensus 417 ~pnqC~~CG~R~~~~ee~sk~md~H~ 442 (579)
T KOG2071|consen 417 SPNQCKSCGLRFDDSEERSKHMDIHD 442 (579)
T ss_pred CcchhcccccccccchhhhhHhhhhh
Confidence 46789999999999999888887774
No 194
>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=32.47 E-value=14 Score=20.84 Aligned_cols=11 Identities=18% Similarity=0.610 Sum_probs=5.3
Q ss_pred ccCCCChhhhc
Q psy12196 86 YQCNECPESFE 96 (150)
Q Consensus 86 ~~c~~c~~~~~ 96 (150)
|.|++|+..+.
T Consensus 20 ~iCpeC~~EW~ 30 (109)
T TIGR00686 20 LICPSCLYEWN 30 (109)
T ss_pred eECcccccccc
Confidence 45555554443
No 195
>PTZ00448 hypothetical protein; Provisional
Probab=32.40 E-value=32 Score=24.17 Aligned_cols=23 Identities=22% Similarity=0.436 Sum_probs=20.0
Q ss_pred CcCCcchhhhccCchHHHHHHHH
Q psy12196 115 QIQCPYCITDFSEDKNLIQHIVS 137 (150)
Q Consensus 115 ~~~C~~C~~~f~~~~~l~~H~~~ 137 (150)
.|.|..|+-.|.+......|+++
T Consensus 314 ~~tC~~C~v~F~~~~~qR~H~KS 336 (373)
T PTZ00448 314 MLLCRKCNIQLMDHNAFKQHYRS 336 (373)
T ss_pred CccccccccccCCHHHHHHHhhh
Confidence 57899999999988888888865
No 196
>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=32.16 E-value=17 Score=20.34 Aligned_cols=9 Identities=22% Similarity=0.633 Sum_probs=4.6
Q ss_pred ccccCCCCc
Q psy12196 57 MFTCRRCPS 65 (150)
Q Consensus 57 ~~~c~~c~~ 65 (150)
|..|+-|+.
T Consensus 2 p~~CpYCg~ 10 (102)
T PF11672_consen 2 PIICPYCGG 10 (102)
T ss_pred CcccCCCCC
Confidence 345555554
No 197
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=31.88 E-value=36 Score=19.41 Aligned_cols=10 Identities=20% Similarity=0.571 Sum_probs=4.6
Q ss_pred cccCCCCccc
Q psy12196 58 FTCRRCPSTF 67 (150)
Q Consensus 58 ~~c~~c~~~f 67 (150)
+.|..|+..|
T Consensus 71 ~~C~~Cg~~~ 80 (114)
T PRK03681 71 CWCETCQQYV 80 (114)
T ss_pred EEcccCCCee
Confidence 4455555433
No 198
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=31.29 E-value=45 Score=16.34 Aligned_cols=10 Identities=30% Similarity=0.773 Sum_probs=4.5
Q ss_pred ccccCCCCcc
Q psy12196 57 MFTCRRCPST 66 (150)
Q Consensus 57 ~~~c~~c~~~ 66 (150)
.|.|+.||.-
T Consensus 14 ~~~Cp~cGip 23 (55)
T PF13824_consen 14 NFECPDCGIP 23 (55)
T ss_pred CCcCCCCCCc
Confidence 3444444433
No 199
>PF05495 zf-CHY: CHY zinc finger; InterPro: IPR008913 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Pirh2 is an eukaryotic ubiquitin protein ligase, which has been shown to promote p53 degradation in mammals. Pirh2 physically interacts with p53 and promotes ubiquitination of p53 independently of MDM2. Like MDM2, Pirh2 is thought to participate in an autoregulatory feedback loop that controls p53 function. Pirh2 proteins contain three distinct zinc fingers, the CHY-type, the CTCHY-type which is C-terminal to the CHY-type zinc finger and a RING finger. The CHY-type zinc finger has no currently known function []. As well as Pirh2, the CHY-type zinc finger is also found in the following proteins: Yeast helper of Tim protein 13. Hot13 may have a role in the assembly and recycling of the small Tims, a complex of the mitochondrial intermembrane space that participates in the TIM22 import pathway for assembly of the inner membrane [] Several plant hypothetical proteins that also contain haemerythrin cation binding domains Several protozoan hypothetical proteins that also contain a Myb domain The solution structure of this zinc finger has been solved and binds 3 zinc atoms as shown in the following schematic representation: ++---------+-----+ || | | CXHYxxxxxxxxxCCxxxxxCxxCHxxxxxHxxxxxxxxxxxCxxCxxxxxxxxxCxxC | | | | | | | | +-+-----------------+--+ +--+---------+--+ 'C': conserved cysteine involved in the binding of one zinc atom. 'H': conserved histidine involved in the binding of one zinc atom. More information about these proteins can be found at Protein of the Month: Zinc Fingers []; GO: 0008270 zinc ion binding; PDB: 2DKT_A 2K2C_A.
Probab=31.27 E-value=3.4 Score=21.29 Aligned_cols=13 Identities=15% Similarity=0.388 Sum_probs=6.4
Q ss_pred cccCCCChhhhcc
Q psy12196 85 SYQCNECPESFER 97 (150)
Q Consensus 85 ~~~c~~c~~~~~~ 97 (150)
...|..|+..++.
T Consensus 41 ~v~Cg~C~~~~~~ 53 (71)
T PF05495_consen 41 RVICGKCRTEQPI 53 (71)
T ss_dssp EEEETTT--EEES
T ss_pred CeECCCCCCccCh
Confidence 4566666655544
No 200
>PRK10220 hypothetical protein; Provisional
Probab=30.29 E-value=19 Score=20.39 Aligned_cols=10 Identities=40% Similarity=1.202 Sum_probs=4.7
Q ss_pred ccCCCChhhh
Q psy12196 86 YQCNECPESF 95 (150)
Q Consensus 86 ~~c~~c~~~~ 95 (150)
|.|++|+..+
T Consensus 21 ~vCpeC~hEW 30 (111)
T PRK10220 21 YICPECAHEW 30 (111)
T ss_pred EECCcccCcC
Confidence 4455554443
No 201
>KOG3002|consensus
Probab=30.00 E-value=1.5e+02 Score=20.47 Aligned_cols=73 Identities=14% Similarity=0.202 Sum_probs=38.1
Q ss_pred CCCcccccccCHHHHHHHHHHHhhCCCcceecc----cccccccChHHHHHHHhccCCcccccCCCC--cccC-ChHHHH
Q psy12196 2 SCVPCDVLFHNKATLYKHLYLEHKATSLSIQCN----MCSLVLDSKESLVTHISQTHTLMFTCRRCP--STFL-NSATLS 74 (150)
Q Consensus 2 ~C~~C~~~f~~~~~l~~h~~~~~~~~~~~~~c~----~c~~~f~~~~~l~~h~~~~~~~~~~c~~c~--~~f~-~~~~l~ 74 (150)
.|+.|...+.+...+.....+ +.....|+ -|.++|..... ..|.....-.++.||.-+ -.+. ....+.
T Consensus 82 ~CP~Cr~~~g~~R~~amEkV~----e~~~vpC~~~~~GC~~~~~Y~~~-~~HE~~C~f~~~~CP~p~~~C~~~G~~~~l~ 156 (299)
T KOG3002|consen 82 KCPTCRLPIGNIRCRAMEKVA----EAVLVPCKNAKLGCTKSFPYGEK-SKHEKVCEFRPCSCPVPGAECKYTGSYKDLY 156 (299)
T ss_pred cCCccccccccHHHHHHHHHH----HhceecccccccCCceeeccccc-cccccccccCCcCCCCCcccCCccCcHHHHH
Confidence 477787777777666655444 22334555 37777765544 334322223666666542 1122 234455
Q ss_pred HHHHh
Q psy12196 75 KHVKM 79 (150)
Q Consensus 75 ~h~~~ 79 (150)
.|...
T Consensus 157 ~H~~~ 161 (299)
T KOG3002|consen 157 AHLND 161 (299)
T ss_pred HHHHh
Confidence 66553
No 202
>PHA02998 RNA polymerase subunit; Provisional
Probab=29.84 E-value=8.6 Score=23.82 Aligned_cols=40 Identities=15% Similarity=0.353 Sum_probs=23.1
Q ss_pred cccCCCChhhhcchhHHhhHHhhhcCCC--CCCcCCcchhhhccCc
Q psy12196 85 SYQCNECPESFERLNKLKRHKFQAHNDS--VHQIQCPYCITDFSED 128 (150)
Q Consensus 85 ~~~c~~c~~~~~~~~~l~~h~~~~~~~~--~~~~~C~~C~~~f~~~ 128 (150)
...|+.|+..-.....++ +...+. ..-|.|..|++.|.-.
T Consensus 143 ~v~CPkCg~~~A~f~qlQ----TRSADEPmT~FYkC~~CG~~wkpp 184 (195)
T PHA02998 143 NTPCPNCKSKNTTPMMIQ----TRAADEPPLVRHACRDCKKHFKPP 184 (195)
T ss_pred CCCCCCCCCCceEEEEEe----eccCCCCceEEEEcCCCCCccCCc
Confidence 357888886544333222 333333 2347899999887643
No 203
>PF01363 FYVE: FYVE zinc finger; InterPro: IPR000306 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The FYVE zinc finger is named after four proteins that it has been found in: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two zinc ions []. The FYVE finger has eight potential zinc coordinating cysteine positions. Many members of this family also include two histidines in a motif R+HHC+XCG, where + represents a charged residue and X any residue. FYVE-type domains are divided into two known classes: FYVE domains that specifically bind to phosphatidylinositol 3-phosphate in lipid bilayers and FYVE-related domains of undetermined function []. Those that bind to phosphatidylinositol 3-phosphate are often found in proteins targeted to lipid membranes that are involved in regulating membrane traffic [, , ]. Most FYVE domains target proteins to endosomes by binding specifically to phosphatidylinositol-3-phosphate at the membrane surface. By contrast, the CARP2 FYVE-like domain is not optimized to bind to phosphoinositides or insert into lipid bilayers. FYVE domains are distinguished from other zinc fingers by three signature sequences: an N-terminal WxxD motif, a basic R(R/K)HHCR patch, and a C-terminal RVC motif. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0046872 metal ion binding; PDB: 1HYI_A 1JOC_B 1HYJ_A 1DVP_A 3ZYQ_A 4AVX_A 1VFY_A 3T7L_A 1X4U_A 1WFK_A ....
Probab=29.07 E-value=32 Score=17.28 Aligned_cols=8 Identities=25% Similarity=0.912 Sum_probs=1.6
Q ss_pred cccccccc
Q psy12196 33 CNMCSLVL 40 (150)
Q Consensus 33 c~~c~~~f 40 (150)
|..|++.|
T Consensus 12 C~~C~~~F 19 (69)
T PF01363_consen 12 CMICGKKF 19 (69)
T ss_dssp -TTT--B-
T ss_pred CcCcCCcC
Confidence 34444444
No 204
>PRK05580 primosome assembly protein PriA; Validated
Probab=29.04 E-value=25 Score=26.98 Aligned_cols=8 Identities=38% Similarity=0.870 Sum_probs=3.7
Q ss_pred CcCCcchh
Q psy12196 115 QIQCPYCI 122 (150)
Q Consensus 115 ~~~C~~C~ 122 (150)
+..|+.|+
T Consensus 421 ~~~Cp~Cg 428 (679)
T PRK05580 421 PKACPECG 428 (679)
T ss_pred CCCCCCCc
Confidence 33455554
No 205
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=28.98 E-value=3.1 Score=23.02 Aligned_cols=8 Identities=25% Similarity=0.829 Sum_probs=3.7
Q ss_pred eecccccc
Q psy12196 31 IQCNMCSL 38 (150)
Q Consensus 31 ~~c~~c~~ 38 (150)
|.|+.|+.
T Consensus 23 FtCp~Cgh 30 (104)
T COG4888 23 FTCPRCGH 30 (104)
T ss_pred EecCccCC
Confidence 44444444
No 206
>PF10122 Mu-like_Com: Mu-like prophage protein Com; InterPro: IPR019294 Members of this entry belong to the Com family of proteins that act as translational regulators of mom [, ].
Probab=28.70 E-value=11 Score=18.08 Aligned_cols=31 Identities=23% Similarity=0.623 Sum_probs=16.4
Q ss_pred cccCCCChhhhcchhHHhhHHhhhcCCCCCCcCCcchhhhc
Q psy12196 85 SYQCNECPESFERLNKLKRHKFQAHNDSVHQIQCPYCITDF 125 (150)
Q Consensus 85 ~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~~C~~C~~~f 125 (150)
.++|..|++.......+. +. ..+|+.|+...
T Consensus 4 eiRC~~CnklLa~~g~~~--------~l--eIKCpRC~tiN 34 (51)
T PF10122_consen 4 EIRCGHCNKLLAKAGEVI--------EL--EIKCPRCKTIN 34 (51)
T ss_pred ceeccchhHHHhhhcCcc--------EE--EEECCCCCccc
Confidence 356777776544321111 11 55788887543
No 207
>cd00974 DSRD Desulforedoxin (DSRD) domain; a small non-heme iron domain present in the desulforedoxin (rubredoxin oxidoreductase) and desulfoferrodoxin proteins of some archeael and bacterial methanogens and sulfate/sulfur reducers. Desulforedoxin is a small, single-domain homodimeric protein; each subunit contains an iron atom bound to four cysteinyl sulfur atoms, Fe(S-Cys)4, in a distorted tetrahedral coordination. Its metal center is similar to that found in rubredoxin type proteins. Desulforedoxin is regarded as a potential redox partner for rubredoxin. Desulfoferrodoxin forms a homodimeric protein, with each protomer comprised of two domains, the N-terminal DSRD domain and C-terminal superoxide reductase-like (SORL) domain. Each domain has a distinct iron center: the DSRD iron center I, Fe(S-Cys)4; and the SORL iron center II, Fe[His4Cys(Glu)].
Probab=28.53 E-value=20 Score=15.29 Aligned_cols=6 Identities=33% Similarity=1.038 Sum_probs=2.4
Q ss_pred CCCccc
Q psy12196 2 SCVPCD 7 (150)
Q Consensus 2 ~C~~C~ 7 (150)
+|..||
T Consensus 6 kC~~CG 11 (34)
T cd00974 6 KCEICG 11 (34)
T ss_pred EcCCCC
Confidence 334443
No 208
>PF14369 zf-RING_3: zinc-finger
Probab=28.52 E-value=29 Score=15.07 Aligned_cols=8 Identities=38% Similarity=0.833 Sum_probs=4.3
Q ss_pred CCcccccc
Q psy12196 3 CVPCDVLF 10 (150)
Q Consensus 3 C~~C~~~f 10 (150)
|+.|+..|
T Consensus 24 CP~C~~gF 31 (35)
T PF14369_consen 24 CPRCHGGF 31 (35)
T ss_pred CcCCCCcE
Confidence 55555544
No 209
>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=28.25 E-value=21 Score=21.45 Aligned_cols=31 Identities=19% Similarity=0.403 Sum_probs=17.3
Q ss_pred CCcccCCCChhhhcchhHHhhHHhhhcCCCCCCcCCcchhhhc
Q psy12196 83 SKSYQCNECPESFERLNKLKRHKFQAHNDSVHQIQCPYCITDF 125 (150)
Q Consensus 83 ~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~~C~~C~~~f 125 (150)
...+.|..||...... +.+. --.|+.|+..-
T Consensus 110 ~G~l~C~~Cg~~~~~~---------~~~~---l~~Cp~C~~~~ 140 (146)
T PF07295_consen 110 PGTLVCENCGHEVELT---------HPER---LPPCPKCGHTE 140 (146)
T ss_pred CceEecccCCCEEEec---------CCCc---CCCCCCCCCCe
Confidence 3458888888643321 1222 22588888653
No 210
>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=28.19 E-value=29 Score=16.55 Aligned_cols=9 Identities=22% Similarity=0.944 Sum_probs=3.8
Q ss_pred CCCcccccc
Q psy12196 2 SCVPCDVLF 10 (150)
Q Consensus 2 ~C~~C~~~f 10 (150)
+|..||..+
T Consensus 3 ~C~~CgyiY 11 (50)
T cd00730 3 ECRICGYIY 11 (50)
T ss_pred CCCCCCeEE
Confidence 344444433
No 211
>KOG2071|consensus
Probab=28.09 E-value=44 Score=25.08 Aligned_cols=26 Identities=27% Similarity=0.461 Sum_probs=22.3
Q ss_pred cccccCCCCcccCChHHHHHHHHhhc
Q psy12196 56 LMFTCRRCPSTFLNSATLSKHVKMEH 81 (150)
Q Consensus 56 ~~~~c~~c~~~f~~~~~l~~h~~~~~ 81 (150)
.+-+|..||.+|........||..|-
T Consensus 417 ~pnqC~~CG~R~~~~ee~sk~md~H~ 442 (579)
T KOG2071|consen 417 SPNQCKSCGLRFDDSEERSKHMDIHD 442 (579)
T ss_pred CcchhcccccccccchhhhhHhhhhh
Confidence 67889999999999988888887774
No 212
>PRK05452 anaerobic nitric oxide reductase flavorubredoxin; Provisional
Probab=28.03 E-value=16 Score=26.62 Aligned_cols=39 Identities=18% Similarity=0.342 Sum_probs=21.5
Q ss_pred CcccCCCChhhhcchhHHhhHHhhhcC----CCCCCcCCcchhh
Q psy12196 84 KSYQCNECPESFERLNKLKRHKFQAHN----DSVHQIQCPYCIT 123 (150)
Q Consensus 84 ~~~~c~~c~~~~~~~~~l~~h~~~~~~----~~~~~~~C~~C~~ 123 (150)
..|+|..||..+.....-... .+..+ +-+-.|.||.|+-
T Consensus 424 ~~~~c~~c~~~yd~~~g~~~~-~~~~gt~~~~lp~~~~cp~c~~ 466 (479)
T PRK05452 424 PRMQCSVCQWIYDPAKGEPMQ-DVAPGTPWSEVPDNFLCPECSL 466 (479)
T ss_pred CeEEECCCCeEECCCCCCccc-CCCCCCChhhCCCCCcCcCCCC
Confidence 458999999877643221110 01111 2223589999984
No 213
>PF01155 HypA: Hydrogenase expression/synthesis hypA family; InterPro: IPR000688 Bacterial membrane-bound nickel-dependent hydrogenases requires a number of accessory proteins which are involved in their maturation. The exact role of these proteins is not yet clear, but some seem to be required for the incorporation of the nickel ions []. One of these proteins is generally known as hypA. It is a protein of about 12 to 14 kDa that contains, in its C-terminal region, four conserved cysteines that form a zinc-finger like motif. Escherichia coli has two proteins that belong to this family, hypA and hybF. A homologue, MJ0214, has also been found in a number of archaeal species, including the genome of Methanocaldococcus jannaschii (Methanococcus jannaschii).; GO: 0016151 nickel ion binding, 0006464 protein modification process; PDB: 2KDX_A 3A44_D 3A43_B.
Probab=27.89 E-value=32 Score=19.57 Aligned_cols=11 Identities=18% Similarity=0.676 Sum_probs=5.1
Q ss_pred eeccccccccc
Q psy12196 31 IQCNMCSLVLD 41 (150)
Q Consensus 31 ~~c~~c~~~f~ 41 (150)
..|..|+..|.
T Consensus 71 ~~C~~Cg~~~~ 81 (113)
T PF01155_consen 71 ARCRDCGHEFE 81 (113)
T ss_dssp EEETTTS-EEE
T ss_pred EECCCCCCEEe
Confidence 34555555554
No 214
>PLN02748 tRNA dimethylallyltransferase
Probab=27.67 E-value=38 Score=24.78 Aligned_cols=25 Identities=20% Similarity=0.214 Sum_probs=20.9
Q ss_pred CCcCCcchhh-hccCchHHHHHHHHh
Q psy12196 114 HQIQCPYCIT-DFSEDKNLIQHIVSV 138 (150)
Q Consensus 114 ~~~~C~~C~~-~f~~~~~l~~H~~~~ 138 (150)
+.|.|..|++ .+.....+..|+++.
T Consensus 417 ~~~~Ce~C~~~~~~G~~eW~~Hlksr 442 (468)
T PLN02748 417 TQYVCEACGNKVLRGAHEWEQHKQGR 442 (468)
T ss_pred ccccccCCCCcccCCHHHHHHHhcch
Confidence 4678999997 799888999998654
No 215
>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=26.88 E-value=25 Score=15.29 Aligned_cols=12 Identities=25% Similarity=0.689 Sum_probs=5.5
Q ss_pred CCcchhhhccCc
Q psy12196 117 QCPYCITDFSED 128 (150)
Q Consensus 117 ~C~~C~~~f~~~ 128 (150)
.|..|++.|..+
T Consensus 5 ~C~eC~~~f~dS 16 (34)
T PF01286_consen 5 KCDECGKPFMDS 16 (34)
T ss_dssp E-TTT--EES-S
T ss_pred hHhHhCCHHHHH
Confidence 577788777654
No 216
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=26.52 E-value=29 Score=23.81 Aligned_cols=8 Identities=25% Similarity=0.476 Sum_probs=5.1
Q ss_pred CcCCcchh
Q psy12196 115 QIQCPYCI 122 (150)
Q Consensus 115 ~~~C~~C~ 122 (150)
-..|..|+
T Consensus 252 ~e~C~~C~ 259 (309)
T PRK03564 252 AESCGDCG 259 (309)
T ss_pred eeeccccc
Confidence 45677776
No 217
>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=26.46 E-value=25 Score=15.91 Aligned_cols=9 Identities=44% Similarity=1.073 Sum_probs=4.1
Q ss_pred eeccccccc
Q psy12196 31 IQCNMCSLV 39 (150)
Q Consensus 31 ~~c~~c~~~ 39 (150)
+.|+.||..
T Consensus 20 ~vC~~CG~V 28 (43)
T PF08271_consen 20 LVCPNCGLV 28 (43)
T ss_dssp EEETTT-BB
T ss_pred EECCCCCCE
Confidence 455555543
No 218
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=26.32 E-value=45 Score=19.13 Aligned_cols=13 Identities=23% Similarity=0.756 Sum_probs=7.0
Q ss_pred ccccCCCCcccCC
Q psy12196 57 MFTCRRCPSTFLN 69 (150)
Q Consensus 57 ~~~c~~c~~~f~~ 69 (150)
.+.|..|+..|..
T Consensus 71 ~~~C~~Cg~~~~~ 83 (117)
T PRK00564 71 ELECKDCSHVFKP 83 (117)
T ss_pred EEEhhhCCCcccc
Confidence 3556666655543
No 219
>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=26.27 E-value=4.1 Score=31.17 Aligned_cols=61 Identities=15% Similarity=0.338 Sum_probs=26.4
Q ss_pred ecccccccccChHHHHHHHhccCCcccccCCCCcccCChHHHHHHHHhhcCCC-cccCCCChhhhcch
Q psy12196 32 QCNMCSLVLDSKESLVTHISQTHTLMFTCRRCPSTFLNSATLSKHVKMEHNSK-SYQCNECPESFERL 98 (150)
Q Consensus 32 ~c~~c~~~f~~~~~l~~h~~~~~~~~~~c~~c~~~f~~~~~l~~h~~~~~~~~-~~~c~~c~~~~~~~ 98 (150)
.|..|-+.+.++.. .+.+.....|..||-.|.-...|.- -+..+.-. ---|..|-+.+...
T Consensus 70 ~C~~Cl~E~~dp~~-----Rry~YpF~nCt~CGPr~~i~~~lpy-dr~~t~m~~f~~C~~C~~ey~~p 131 (711)
T TIGR00143 70 TCSDCLEEMLDKND-----RRYLYPFISCTHCGPRFTIIEALPY-DRENTSMADFPLCPDCAKEYKDP 131 (711)
T ss_pred hHHHHHHHhcCCCc-----ccccCCcccccCCCCCeEEeecCCC-CCCCcCCCCCcCCHHHHHHhcCC
Confidence 35555554443332 1222233457777766654333221 11111111 12466666665544
No 220
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=25.94 E-value=22 Score=20.63 Aligned_cols=6 Identities=50% Similarity=1.481 Sum_probs=2.9
Q ss_pred CCcchh
Q psy12196 117 QCPYCI 122 (150)
Q Consensus 117 ~C~~C~ 122 (150)
.||.|+
T Consensus 94 ~CP~Cg 99 (124)
T PRK00762 94 ECPVCG 99 (124)
T ss_pred cCcCCC
Confidence 355554
No 221
>COG4338 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=25.87 E-value=24 Score=16.67 Aligned_cols=16 Identities=25% Similarity=0.526 Sum_probs=11.4
Q ss_pred cCCCChhhhcchhHHh
Q psy12196 87 QCNECPESFERLNKLK 102 (150)
Q Consensus 87 ~c~~c~~~~~~~~~l~ 102 (150)
.|++|++.|+....+.
T Consensus 14 ICpvCqRPFsWRkKW~ 29 (54)
T COG4338 14 ICPVCQRPFSWRKKWA 29 (54)
T ss_pred hhhhhcCchHHHHHHH
Confidence 6888888887765443
No 222
>COG1326 Uncharacterized archaeal Zn-finger protein [General function prediction only]
Probab=25.84 E-value=64 Score=20.53 Aligned_cols=10 Identities=20% Similarity=0.783 Sum_probs=4.6
Q ss_pred cccCCCCccc
Q psy12196 58 FTCRRCPSTF 67 (150)
Q Consensus 58 ~~c~~c~~~f 67 (150)
..|..||..+
T Consensus 31 vrC~eCG~V~ 40 (201)
T COG1326 31 VRCEECGTVH 40 (201)
T ss_pred EEccCCCcEe
Confidence 3455555443
No 223
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=25.73 E-value=19 Score=20.04 Aligned_cols=10 Identities=20% Similarity=0.504 Sum_probs=5.0
Q ss_pred ccCCCChhhh
Q psy12196 86 YQCNECPESF 95 (150)
Q Consensus 86 ~~c~~c~~~~ 95 (150)
..|..||..+
T Consensus 43 ~~C~~CG~y~ 52 (99)
T PRK14892 43 ITCGNCGLYT 52 (99)
T ss_pred EECCCCCCcc
Confidence 4555555443
No 224
>COG4896 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=25.59 E-value=30 Score=17.31 Aligned_cols=6 Identities=67% Similarity=1.802 Sum_probs=2.4
Q ss_pred ccCCCC
Q psy12196 86 YQCNEC 91 (150)
Q Consensus 86 ~~c~~c 91 (150)
|-|++|
T Consensus 32 ymC~eC 37 (68)
T COG4896 32 YMCPEC 37 (68)
T ss_pred Eechhh
Confidence 334333
No 225
>PLN03239 histone acetyltransferase; Provisional
Probab=25.31 E-value=56 Score=22.90 Aligned_cols=23 Identities=13% Similarity=0.353 Sum_probs=19.7
Q ss_pred CcCCcchhhhccCchHHHHHHHH
Q psy12196 115 QIQCPYCITDFSEDKNLIQHIVS 137 (150)
Q Consensus 115 ~~~C~~C~~~f~~~~~l~~H~~~ 137 (150)
-|.|..|-+-|.+...|.+|+..
T Consensus 106 lYiCE~Clky~~~~~~l~~H~~~ 128 (351)
T PLN03239 106 LYVCEFSFGFFARKSELLRFQAK 128 (351)
T ss_pred EEEeccchhhhcCHHHHHHHHHh
Confidence 78899999988889999998764
No 226
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=25.30 E-value=47 Score=23.94 Aligned_cols=30 Identities=17% Similarity=0.560 Sum_probs=18.7
Q ss_pred ccCCCCcccCChHHHHHHHHhhcCCCcccCCCChhhhcchh
Q psy12196 59 TCRRCPSTFLNSATLSKHVKMEHNSKSYQCNECPESFERLN 99 (150)
Q Consensus 59 ~c~~c~~~f~~~~~l~~h~~~~~~~~~~~c~~c~~~~~~~~ 99 (150)
.|+.||..-.+ .|...|+|..||..+....
T Consensus 352 ~Cp~Cg~~m~S-----------~G~~g~rC~kCg~~~~~~~ 381 (421)
T COG1571 352 VCPRCGGRMKS-----------AGRNGFRCKKCGTRARETL 381 (421)
T ss_pred CCCccCCchhh-----------cCCCCcccccccccCCccc
Confidence 67778754322 2333688888887776653
No 227
>KOG4124|consensus
Probab=24.57 E-value=18 Score=25.08 Aligned_cols=53 Identities=26% Similarity=0.555 Sum_probs=33.2
Q ss_pred CCcccCCC--ChhhhcchhHHhhHHhhhcC-----------------CCCCCcCCcchhhhccCchHHHHHH
Q psy12196 83 SKSYQCNE--CPESFERLNKLKRHKFQAHN-----------------DSVHQIQCPYCITDFSEDKNLIQHI 135 (150)
Q Consensus 83 ~~~~~c~~--c~~~~~~~~~l~~h~~~~~~-----------------~~~~~~~C~~C~~~f~~~~~l~~H~ 135 (150)
.++|.|.+ |++.+.....|..|...-+. ...++|+|++|.+.....-.|.-|.
T Consensus 347 ~~~~~~~vp~~~~~~~n~ng~~~~~~~~h~s~i~~~s~~~~ph~~~~~~nk~~r~~i~~~~~k~~~~l~~~~ 418 (442)
T KOG4124|consen 347 DKPYKCPVPNCDKAYKNQNGLKYHKLHGHCSPITTPTPAPIPHQGFVVENKPYRCEVCSKRYKNLNGLKYHR 418 (442)
T ss_pred cCCCCCCCCcchhhcccCcceeeccccCcCCCCCCCCCCCCCcceeeeccCcccChhhhhhhccCCCCCcee
Confidence 35677766 77777766666655332111 1125899999999888765555543
No 228
>KOG0782|consensus
Probab=24.46 E-value=21 Score=26.75 Aligned_cols=52 Identities=15% Similarity=0.450 Sum_probs=32.2
Q ss_pred HHHHHHHHhhcCCCcccCCCChhhhcchhHHhhHHhhhcCCCCCCcCCcchhhhccCch
Q psy12196 71 ATLSKHVKMEHNSKSYQCNECPESFERLNKLKRHKFQAHNDSVHQIQCPYCITDFSEDK 129 (150)
Q Consensus 71 ~~l~~h~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~~C~~C~~~f~~~~ 129 (150)
..+..|-=+|.....-+|..||+.|.+.-.+ |..+ .....|.+|..+|-.+-
T Consensus 239 ~~fvrHHWVHrrRqeGkC~~CgKgFQQKf~F------hsKE-ivAisCSWCKqayH~Kv 290 (1004)
T KOG0782|consen 239 SGFVRHHWVHRRRQEGKCNTCGKGFQQKFFF------HSKE-IVAISCSWCKQAYHLKV 290 (1004)
T ss_pred ccchHHhHhhHhhhccccchhhhhhhhheee------cccc-EEEEEehHHHHHhhcch
Confidence 3555555555544445788899888765332 2222 22557888988887664
No 229
>PF10276 zf-CHCC: Zinc-finger domain; InterPro: IPR019401 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a short conserved zinc-finger domain. It contains the sequence motif Cx8Hx14Cx2C. ; PDB: 2JVM_A 2JRR_A 2JZ8_A.
Probab=24.43 E-value=31 Score=15.59 Aligned_cols=11 Identities=18% Similarity=0.637 Sum_probs=8.8
Q ss_pred ceecccccccc
Q psy12196 30 SIQCNMCSLVL 40 (150)
Q Consensus 30 ~~~c~~c~~~f 40 (150)
...|+.|+..|
T Consensus 29 ~~~CpYCg~~y 39 (40)
T PF10276_consen 29 PVVCPYCGTRY 39 (40)
T ss_dssp EEEETTTTEEE
T ss_pred eEECCCCCCEE
Confidence 46899998876
No 230
>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=24.25 E-value=60 Score=15.40 Aligned_cols=6 Identities=50% Similarity=1.453 Sum_probs=2.2
Q ss_pred cCCCCc
Q psy12196 60 CRRCPS 65 (150)
Q Consensus 60 c~~c~~ 65 (150)
|..||.
T Consensus 21 Cr~Cg~ 26 (57)
T cd00065 21 CRNCGR 26 (57)
T ss_pred cCcCcC
Confidence 333333
No 231
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=23.80 E-value=23 Score=15.33 Aligned_cols=9 Identities=33% Similarity=0.907 Sum_probs=5.0
Q ss_pred CcCCcchhh
Q psy12196 115 QIQCPYCIT 123 (150)
Q Consensus 115 ~~~C~~C~~ 123 (150)
.+.|+.|+.
T Consensus 22 R~vC~~Cg~ 30 (34)
T PF14803_consen 22 RLVCPACGF 30 (34)
T ss_dssp EEEETTTTE
T ss_pred ceECCCCCC
Confidence 345666654
No 232
>KOG2747|consensus
Probab=23.75 E-value=55 Score=23.35 Aligned_cols=28 Identities=18% Similarity=0.490 Sum_probs=24.0
Q ss_pred CCcCCcchhhhccCchHHHHHHHHhcCC
Q psy12196 114 HQIQCPYCITDFSEDKNLIQHIVSVHLG 141 (150)
Q Consensus 114 ~~~~C~~C~~~f~~~~~l~~H~~~~~~~ 141 (150)
.-|.|..|-+-+.+...|++|+......
T Consensus 157 ~lYiCEfCLkY~~s~~~l~rH~~kC~~r 184 (396)
T KOG2747|consen 157 KLYICEFCLKYMKSRTSLQRHLKKCKLR 184 (396)
T ss_pred eEEEehHHHhHhchHHHHHHHHHhcCCC
Confidence 3688999999999999999999877644
No 233
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=23.37 E-value=71 Score=19.73 Aligned_cols=11 Identities=18% Similarity=0.969 Sum_probs=5.3
Q ss_pred cccCCCCcccC
Q psy12196 58 FTCRRCPSTFL 68 (150)
Q Consensus 58 ~~c~~c~~~f~ 68 (150)
+.|+.|++.|+
T Consensus 131 ~~C~~CgkiYW 141 (165)
T COG1656 131 YRCPKCGKIYW 141 (165)
T ss_pred eECCCCccccc
Confidence 34555554444
No 234
>PF14787 zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB: 1CL4_A 1DSV_A.
Probab=23.26 E-value=28 Score=15.33 Aligned_cols=14 Identities=29% Similarity=0.622 Sum_probs=7.9
Q ss_pred CCcchhhhccCchH
Q psy12196 117 QCPYCITDFSEDKN 130 (150)
Q Consensus 117 ~C~~C~~~f~~~~~ 130 (150)
.|+.|++.|-+.++
T Consensus 4 ~CprC~kg~Hwa~~ 17 (36)
T PF14787_consen 4 LCPRCGKGFHWASE 17 (36)
T ss_dssp C-TTTSSSCS-TTT
T ss_pred cCcccCCCcchhhh
Confidence 47778777765543
No 235
>TIGR01206 lysW lysine biosynthesis protein LysW. This very small, poorly characterized protein has been shown essential in Thermus thermophilus for an unusual pathway of Lys biosynthesis from aspartate by way of alpha-aminoadipate (AAA) rather than diaminopimelate. It is found also in Deinococcus radiodurans and Pyrococcus horikoshii, which appear to share the AAA pathway.
Probab=23.09 E-value=41 Score=16.37 Aligned_cols=8 Identities=25% Similarity=0.754 Sum_probs=3.6
Q ss_pred CCCccccc
Q psy12196 2 SCVPCDVL 9 (150)
Q Consensus 2 ~C~~C~~~ 9 (150)
.|+.||..
T Consensus 4 ~CP~CG~~ 11 (54)
T TIGR01206 4 ECPDCGAE 11 (54)
T ss_pred CCCCCCCE
Confidence 34444443
No 236
>KOG2923|consensus
Probab=22.94 E-value=73 Score=16.14 Aligned_cols=12 Identities=17% Similarity=0.456 Sum_probs=6.0
Q ss_pred cCCcccccCCCC
Q psy12196 53 THTLMFTCRRCP 64 (150)
Q Consensus 53 ~~~~~~~c~~c~ 64 (150)
.++.-..|+.|.
T Consensus 40 ~ge~Va~CpsCS 51 (67)
T KOG2923|consen 40 NGEDVARCPSCS 51 (67)
T ss_pred CCCeeecCCCce
Confidence 344444566664
No 237
>KOG1940|consensus
Probab=22.67 E-value=1.7e+02 Score=19.98 Aligned_cols=18 Identities=17% Similarity=0.397 Sum_probs=12.4
Q ss_pred eecccccccccChHHHHHH
Q psy12196 31 IQCNMCSLVLDSKESLVTH 49 (150)
Q Consensus 31 ~~c~~c~~~f~~~~~l~~h 49 (150)
|.||.|.+ ..+...+...
T Consensus 197 y~CP~C~~-~~d~~~~~~~ 214 (276)
T KOG1940|consen 197 YTCPICSK-PGDMSHYFRK 214 (276)
T ss_pred CCCCcccc-hHHHHHHHHH
Confidence 88999988 5555555444
No 238
>COG4391 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=22.43 E-value=38 Score=16.98 Aligned_cols=13 Identities=38% Similarity=1.132 Sum_probs=9.1
Q ss_pred CcCCcchhhhccC
Q psy12196 115 QIQCPYCITDFSE 127 (150)
Q Consensus 115 ~~~C~~C~~~f~~ 127 (150)
.-.|+.|+..|..
T Consensus 48 ev~CPYC~t~y~l 60 (62)
T COG4391 48 EVVCPYCSTRYRL 60 (62)
T ss_pred cEecCccccEEEe
Confidence 4578888877753
No 239
>PF13821 DUF4187: Domain of unknown function (DUF4187)
Probab=22.38 E-value=48 Score=16.16 Aligned_cols=17 Identities=18% Similarity=0.593 Sum_probs=11.8
Q ss_pred CCcccccccCHHHHHHH
Q psy12196 3 CVPCDVLFHNKATLYKH 19 (150)
Q Consensus 3 C~~C~~~f~~~~~l~~h 19 (150)
|-.||..|.+...|..+
T Consensus 30 C~~Cg~~Y~d~~dL~~~ 46 (55)
T PF13821_consen 30 CFWCGTKYDDEEDLERN 46 (55)
T ss_pred eeeeCCccCCHHHHHhC
Confidence 66777777777776544
No 240
>PF03470 zf-XS: XS zinc finger domain; InterPro: IPR005381 This domain is a putative nucleic acid binding zinc finger and is found at the N terminus of proteins that also contain an adjacent XS domain IPR005380 from INTERPRO and in some proteins a C-terminal XH domain IPR005379 from INTERPRO.
Probab=22.30 E-value=83 Score=14.55 Aligned_cols=8 Identities=25% Similarity=0.314 Sum_probs=4.1
Q ss_pred HHHHHHHH
Q psy12196 13 KATLYKHL 20 (150)
Q Consensus 13 ~~~l~~h~ 20 (150)
...|..|-
T Consensus 14 ~~~LlqHA 21 (43)
T PF03470_consen 14 YRELLQHA 21 (43)
T ss_pred hhHHHHHH
Confidence 45555554
No 241
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=22.12 E-value=29 Score=13.41 Aligned_cols=6 Identities=33% Similarity=1.137 Sum_probs=2.5
Q ss_pred CCcccc
Q psy12196 3 CVPCDV 8 (150)
Q Consensus 3 C~~C~~ 8 (150)
|+.||.
T Consensus 2 Cp~CG~ 7 (23)
T PF13240_consen 2 CPNCGA 7 (23)
T ss_pred CcccCC
Confidence 344443
No 242
>PF12773 DZR: Double zinc ribbon
Probab=21.80 E-value=46 Score=15.40 Aligned_cols=6 Identities=33% Similarity=1.082 Sum_probs=2.5
Q ss_pred cCCCCh
Q psy12196 87 QCNECP 92 (150)
Q Consensus 87 ~c~~c~ 92 (150)
.|..|+
T Consensus 31 ~C~~Cg 36 (50)
T PF12773_consen 31 ICPNCG 36 (50)
T ss_pred CCcCCc
Confidence 344443
No 243
>KOG1813|consensus
Probab=21.80 E-value=75 Score=21.73 Aligned_cols=15 Identities=33% Similarity=0.691 Sum_probs=11.7
Q ss_pred cccccCCCCcccCCh
Q psy12196 56 LMFTCRRCPSTFLNS 70 (150)
Q Consensus 56 ~~~~c~~c~~~f~~~ 70 (150)
.||.|.+|.+.|.++
T Consensus 240 ~Pf~c~icr~~f~~p 254 (313)
T KOG1813|consen 240 LPFKCFICRKYFYRP 254 (313)
T ss_pred CCccccccccccccc
Confidence 578888888887665
No 244
>PF12230 PRP21_like_P: Pre-mRNA splicing factor PRP21 like protein; InterPro: IPR022030 This domain family is found in eukaryotes, and is typically between 212 and 238 amino acids in length. The family is found in association with PF01805 from PFAM. There are two completely conserved residues (W and H) that may be functionally important. PRP21 is required for assembly of the prespliceosome and it interacts with U2 snRNP and/or pre-mRNA in the prespliceosome. This family also contains proteins similar to PRP21, such as the mammalian SF3a. SF3a also interacts with U2 snRNP from the prespliceosome, converting it to its active form. ; PDB: 4DGW_B.
Probab=21.77 E-value=30 Score=22.39 Aligned_cols=29 Identities=17% Similarity=0.182 Sum_probs=0.0
Q ss_pred CcCCcchhhhccCchHHHHHHHHhcCCCCC
Q psy12196 115 QIQCPYCITDFSEDKNLIQHIVSVHLGKEG 144 (150)
Q Consensus 115 ~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~ 144 (150)
...||+||..... +.|..||++.-....|
T Consensus 168 ~~~cPitGe~IP~-~e~~eHmRi~LlDP~w 196 (229)
T PF12230_consen 168 MIICPITGEMIPA-DEMDEHMRIELLDPRW 196 (229)
T ss_dssp ------------------------------
T ss_pred ccccccccccccc-cccccccccccccccc
Confidence 4689999988887 4688898887655444
No 245
>PRK01343 zinc-binding protein; Provisional
Probab=21.30 E-value=42 Score=16.59 Aligned_cols=12 Identities=25% Similarity=0.526 Sum_probs=8.7
Q ss_pred CcCCcchhhhcc
Q psy12196 115 QIQCPYCITDFS 126 (150)
Q Consensus 115 ~~~C~~C~~~f~ 126 (150)
...|++|++.+.
T Consensus 9 ~~~CP~C~k~~~ 20 (57)
T PRK01343 9 TRPCPECGKPST 20 (57)
T ss_pred CCcCCCCCCcCc
Confidence 346889988765
No 246
>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=21.30 E-value=42 Score=14.99 Aligned_cols=11 Identities=27% Similarity=1.005 Sum_probs=6.7
Q ss_pred cccCCCCcccC
Q psy12196 58 FTCRRCPSTFL 68 (150)
Q Consensus 58 ~~c~~c~~~f~ 68 (150)
+.|+.||..+.
T Consensus 33 ~~C~~CGE~~~ 43 (46)
T TIGR03831 33 LVCPQCGEEYL 43 (46)
T ss_pred cccccCCCEee
Confidence 45777766554
No 247
>KOG3352|consensus
Probab=21.00 E-value=43 Score=20.27 Aligned_cols=13 Identities=31% Similarity=0.621 Sum_probs=10.8
Q ss_pred CcCCcchhhhccC
Q psy12196 115 QIQCPYCITDFSE 127 (150)
Q Consensus 115 ~~~C~~C~~~f~~ 127 (150)
..+|++||..|..
T Consensus 133 ~~rc~eCG~~fkL 145 (153)
T KOG3352|consen 133 TQRCPECGHYFKL 145 (153)
T ss_pred cccCCcccceEEe
Confidence 6689999988864
No 248
>PF09963 DUF2197: Uncharacterized protein conserved in bacteria (DUF2197); InterPro: IPR019241 This family represents various hypothetical bacterial proteins with no known function.
Probab=20.81 E-value=27 Score=17.15 Aligned_cols=8 Identities=25% Similarity=0.658 Sum_probs=3.7
Q ss_pred CcCCcchh
Q psy12196 115 QIQCPYCI 122 (150)
Q Consensus 115 ~~~C~~C~ 122 (150)
.|.|..|.
T Consensus 31 tYmC~eC~ 38 (56)
T PF09963_consen 31 TYMCDECK 38 (56)
T ss_pred ceeChhHH
Confidence 44444443
No 249
>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 PF06220 zf-U1: U1 zinc finger; InterPro: IPR013085 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. C2H2-type (classical) zinc fingers (Znf) were the first class to be characterised. They contain a short beta hairpin and an alpha helix (beta/beta/alpha structure), where a single zinc atom is held in place by Cys(2)His(2) (C2H2) residues in a tetrahedral array. C2H2 Znf's can be divided into three groups based on the number and pattern of fingers: triple-C2H2 (binds single ligand), multiple-adjacent-C2H2 (binds multiple ligands), and separated paired-C2H2 []. C2H2 Znf's are the most common DNA-binding motifs found in eukaryotic transcription factors, and have also been identified in prokaryotes []. Transcription factors usually contain several Znf's (each with a conserved beta/beta/alpha structure) capable of making multiple contacts along the DNA, where the C2H2 Znf motifs recognise DNA sequences by binding to the major groove of DNA via a short alpha-helix in the Znf, the Znf spanning 3-4 bases of the DNA []. C2H2 Znf's can also bind to RNA and protein targets []. This entry represents a C2H2-type zinc finger motif found in several U1 small nuclear ribonucleoprotein C (U1-C) proteins. Some proteins contain multiple copies of this motif. The U1 small nuclear ribonucleoprotein (U1 snRNP) binds to the pre-mRNA 5' splice site at early stages of spliceosome assembly. Recruitment of U1 to a class of weak 5' splice site is promoted by binding of the protein TIA-1 to uridine-rich sequences immediately downstream from the 5' splice site. Binding of TIA-1 in the vicinity of a 5' splice site helps to stabilise U1 snRNP recruitment, at least in part, via a direct interaction with U1-C, thus providing one molecular mechanism for the function of this splicing regulator []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2VRD_A.
Probab=20.17 E-value=78 Score=14.00 Aligned_cols=9 Identities=22% Similarity=0.589 Sum_probs=3.5
Q ss_pred CCCcccccc
Q psy12196 2 SCVPCDVLF 10 (150)
Q Consensus 2 ~C~~C~~~f 10 (150)
=|+.|+.-|
T Consensus 5 yCdyC~~~~ 13 (38)
T PF06220_consen 5 YCDYCKKYL 13 (38)
T ss_dssp B-TTT--B-
T ss_pred eccccccee
Confidence 377888777
No 251
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=20.16 E-value=1.3e+02 Score=14.47 Aligned_cols=10 Identities=20% Similarity=0.607 Sum_probs=4.9
Q ss_pred cccccCCCCc
Q psy12196 56 LMFTCRRCPS 65 (150)
Q Consensus 56 ~~~~c~~c~~ 65 (150)
....|+.|++
T Consensus 45 ~i~~Cp~CgR 54 (56)
T PF02591_consen 45 EIVFCPNCGR 54 (56)
T ss_pred CeEECcCCCc
Confidence 3345555553
No 252
>KOG4577|consensus
Probab=20.06 E-value=31 Score=23.31 Aligned_cols=33 Identities=21% Similarity=0.380 Sum_probs=18.3
Q ss_pred CCCcccccccCHHHHHHHHHHHhhCCCcceeccccc
Q psy12196 2 SCVPCDVLFHNKATLYKHLYLEHKATSLSIQCNMCS 37 (150)
Q Consensus 2 ~C~~C~~~f~~~~~l~~h~~~~~~~~~~~~~c~~c~ 37 (150)
+|.-|+..+.++..|+.--+.+|. +-.+|..|.
T Consensus 35 ~CagC~q~IlDrFilKvl~R~wHs---~CLkCs~C~ 67 (383)
T KOG4577|consen 35 ICAGCDQHILDRFILKVLDRHWHS---SCLKCSDCH 67 (383)
T ss_pred cccchHHHHHHHHHHHHHhhhhhh---hhcchhhhh
Confidence 356667766676666655444444 223555553
Done!