Query psy16646
Match_columns 159
No_of_seqs 149 out of 2111
Neff 10.5
Searched_HMMs 46136
Date Fri Aug 16 18:23:22 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy16646.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/16646hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2462|consensus 99.9 2.9E-28 6.3E-33 166.0 4.4 119 29-150 127-247 (279)
2 KOG2462|consensus 99.9 1.6E-26 3.4E-31 157.5 4.7 131 5-140 127-265 (279)
3 KOG3576|consensus 99.8 1.1E-19 2.5E-24 119.0 2.6 122 23-146 108-240 (267)
4 KOG3608|consensus 99.7 1.6E-18 3.4E-23 122.1 0.7 133 14-149 189-322 (467)
5 KOG1074|consensus 99.7 5.8E-18 1.3E-22 130.2 1.9 64 90-154 606-669 (958)
6 KOG3623|consensus 99.7 1E-17 2.2E-22 127.3 1.9 108 32-140 210-331 (1007)
7 KOG1074|consensus 99.6 3.4E-17 7.4E-22 126.0 1.1 57 90-147 880-936 (958)
8 KOG3608|consensus 99.6 3E-16 6.5E-21 110.8 1.5 139 5-149 204-355 (467)
9 KOG3576|consensus 99.6 1.7E-16 3.7E-21 104.2 -1.1 81 61-142 116-198 (267)
10 KOG3623|consensus 99.6 6.1E-16 1.3E-20 117.9 1.3 77 61-138 893-970 (1007)
11 PLN03086 PRLI-interacting fact 99.4 1.8E-12 4E-17 98.6 6.6 119 8-142 433-565 (567)
12 PHA00733 hypothetical protein 99.2 1.2E-11 2.6E-16 77.8 3.0 79 61-142 39-123 (128)
13 PHA02768 hypothetical protein; 99.1 2.7E-11 5.9E-16 63.8 0.6 43 90-135 6-48 (55)
14 PHA00733 hypothetical protein 99.0 1.2E-10 2.6E-15 73.4 2.6 83 30-114 38-124 (128)
15 PLN03086 PRLI-interacting fact 99.0 2.6E-10 5.6E-15 87.1 4.1 83 61-149 452-544 (567)
16 PHA02768 hypothetical protein; 98.9 7.2E-10 1.6E-14 58.4 2.4 44 62-106 5-48 (55)
17 PF13465 zf-H2C2_2: Zinc-finge 98.7 4.6E-09 9.9E-14 47.5 0.6 24 105-129 2-25 (26)
18 PF13465 zf-H2C2_2: Zinc-finge 98.6 3.7E-08 8.1E-13 44.4 1.9 23 78-100 2-25 (26)
19 PHA00616 hypothetical protein 98.5 1.3E-08 2.8E-13 51.1 -0.0 28 90-117 2-29 (44)
20 PHA00616 hypothetical protein 98.5 2.8E-08 6E-13 50.0 1.0 32 119-150 2-33 (44)
21 PHA00732 hypothetical protein 98.5 7.7E-08 1.7E-12 55.3 1.5 44 63-111 2-46 (79)
22 KOG3993|consensus 98.3 2.7E-07 5.7E-12 67.5 2.2 130 11-142 270-482 (500)
23 KOG3993|consensus 98.2 1.7E-07 3.7E-12 68.5 -0.7 83 63-145 268-383 (500)
24 PHA00732 hypothetical protein 98.1 2.1E-06 4.7E-11 49.4 2.4 47 32-85 1-47 (79)
25 PF00096 zf-C2H2: Zinc finger, 98.1 1.1E-06 2.3E-11 38.4 0.7 22 119-140 1-22 (23)
26 PF13912 zf-C2H2_6: C2H2-type 97.9 9.2E-06 2E-10 36.8 1.8 25 119-143 2-26 (27)
27 PF05605 zf-Di19: Drought indu 97.8 3.3E-05 7E-10 41.2 2.9 8 119-126 32-39 (54)
28 PF00096 zf-C2H2: Zinc finger, 97.7 6.8E-06 1.5E-10 35.7 0.2 22 90-111 1-22 (23)
29 PF05605 zf-Di19: Drought indu 97.7 8.8E-05 1.9E-09 39.5 4.4 48 63-113 3-53 (54)
30 PF13894 zf-C2H2_4: C2H2-type 97.7 1.4E-05 3E-10 34.9 0.8 23 119-141 1-23 (24)
31 PF13894 zf-C2H2_4: C2H2-type 97.4 3.7E-05 8.1E-10 33.5 0.3 23 90-112 1-23 (24)
32 PF12756 zf-C2H2_2: C2H2 type 97.4 7.9E-05 1.7E-09 44.7 1.7 74 64-143 1-75 (100)
33 PF13912 zf-C2H2_6: C2H2-type 97.4 3.9E-05 8.5E-10 34.7 0.2 25 89-113 1-25 (27)
34 smart00355 ZnF_C2H2 zinc finge 97.4 0.00012 2.6E-09 32.3 1.5 24 119-142 1-24 (26)
35 PF12756 zf-C2H2_2: C2H2 type 97.3 8.4E-05 1.8E-09 44.6 0.7 73 34-112 1-73 (100)
36 PF09237 GAGA: GAGA factor; I 97.2 0.00014 3.1E-09 37.4 1.1 28 119-146 25-52 (54)
37 PF12874 zf-met: Zinc-finger o 97.0 0.00039 8.5E-09 30.6 1.0 23 119-141 1-23 (25)
38 COG5189 SFP1 Putative transcri 96.9 0.00035 7.6E-09 49.9 1.0 52 86-138 346-418 (423)
39 PRK04860 hypothetical protein; 96.8 0.00044 9.6E-09 45.3 0.7 39 89-132 119-157 (160)
40 smart00355 ZnF_C2H2 zinc finge 96.7 0.0006 1.3E-08 29.9 0.6 23 90-112 1-23 (26)
41 PF13909 zf-H2C2_5: C2H2-type 96.6 0.00058 1.3E-08 29.8 0.2 22 119-141 1-22 (24)
42 PF09237 GAGA: GAGA factor; I 96.6 0.00068 1.5E-08 35.0 0.3 32 86-117 21-52 (54)
43 PF12171 zf-C2H2_jaz: Zinc-fin 96.5 0.0014 3E-08 29.5 1.2 22 119-140 2-23 (27)
44 COG5189 SFP1 Putative transcri 96.2 0.0026 5.6E-08 45.7 1.6 71 28-109 345-418 (423)
45 PF13909 zf-H2C2_5: C2H2-type 96.1 0.0016 3.5E-08 28.3 0.2 23 90-113 1-23 (24)
46 PRK04860 hypothetical protein; 96.0 0.004 8.7E-08 40.8 1.7 37 62-102 119-156 (160)
47 PF12874 zf-met: Zinc-finger o 95.5 0.0075 1.6E-07 26.3 1.1 17 35-51 3-19 (25)
48 KOG2231|consensus 95.2 0.039 8.5E-07 43.9 4.7 97 35-141 118-235 (669)
49 PF13913 zf-C2HC_2: zinc-finge 95.0 0.017 3.7E-07 25.4 1.4 20 119-139 3-22 (25)
50 PF12171 zf-C2H2_jaz: Zinc-fin 94.9 0.0091 2E-07 26.7 0.3 22 90-111 2-23 (27)
51 KOG2893|consensus 94.9 0.0052 1.1E-07 42.4 -0.7 47 61-111 10-56 (341)
52 COG5048 FOG: Zn-finger [Genera 94.4 0.019 4.2E-07 43.1 1.2 63 89-152 289-357 (467)
53 smart00451 ZnF_U1 U1-like zinc 93.8 0.042 9.2E-07 26.0 1.4 23 119-141 4-26 (35)
54 PF09986 DUF2225: Uncharacteri 92.9 0.035 7.5E-07 38.3 0.4 44 88-131 4-61 (214)
55 cd00350 rubredoxin_like Rubred 92.9 0.067 1.4E-06 25.2 1.3 8 119-126 18-25 (33)
56 KOG2893|consensus 92.8 0.047 1E-06 37.8 0.9 46 34-85 12-58 (341)
57 smart00451 ZnF_U1 U1-like zinc 92.6 0.12 2.5E-06 24.4 1.9 23 32-54 3-25 (35)
58 PF12013 DUF3505: Protein of u 92.2 0.11 2.4E-06 31.8 1.9 25 119-143 81-109 (109)
59 TIGR00622 ssl1 transcription f 91.4 0.36 7.7E-06 29.7 3.4 49 91-142 57-105 (112)
60 PF13719 zinc_ribbon_5: zinc-r 91.3 0.077 1.7E-06 25.7 0.4 34 9-43 3-36 (37)
61 COG4049 Uncharacterized protei 91.1 0.068 1.5E-06 28.2 0.1 20 119-138 18-37 (65)
62 COG5048 FOG: Zn-finger [Genera 90.5 0.11 2.3E-06 39.1 0.8 59 62-121 289-354 (467)
63 PF12907 zf-met2: Zinc-binding 90.4 0.097 2.1E-06 25.9 0.3 35 119-153 2-40 (40)
64 COG4049 Uncharacterized protei 90.4 0.084 1.8E-06 27.8 0.1 29 86-114 14-42 (65)
65 PF13717 zinc_ribbon_4: zinc-r 90.3 0.12 2.7E-06 24.9 0.6 33 9-42 3-35 (36)
66 TIGR02098 MJ0042_CXXC MJ0042 f 89.6 0.099 2.1E-06 25.4 -0.1 33 9-42 3-35 (38)
67 PF03811 Zn_Tnp_IS1: InsA N-te 89.0 0.37 8E-06 23.2 1.7 35 4-38 1-35 (36)
68 PRK00464 nrdR transcriptional 88.7 0.16 3.4E-06 33.2 0.4 12 90-101 29-40 (154)
69 KOG1146|consensus 87.7 0.21 4.6E-06 42.7 0.6 90 33-140 1261-1350(1406)
70 KOG2186|consensus 86.4 0.32 7E-06 34.1 0.9 52 63-116 4-55 (276)
71 cd00729 rubredoxin_SM Rubredox 86.1 0.33 7E-06 23.0 0.6 8 119-126 19-26 (34)
72 smart00659 RPOLCX RNA polymera 84.9 0.5 1.1E-05 23.9 0.9 11 90-100 3-13 (44)
73 KOG4173|consensus 84.5 0.4 8.6E-06 32.6 0.6 77 63-142 80-171 (253)
74 smart00834 CxxC_CXXC_SSSS Puta 84.2 0.36 7.8E-06 23.6 0.2 30 8-40 5-34 (41)
75 PRK09678 DNA-binding transcrip 84.1 0.45 9.8E-06 26.8 0.6 42 90-134 2-45 (72)
76 PF14353 CpXC: CpXC protein 83.7 0.43 9.2E-06 30.1 0.5 21 9-29 2-22 (128)
77 PF01096 TFIIS_C: Transcriptio 83.7 0.22 4.8E-06 24.4 -0.7 33 10-42 2-38 (39)
78 smart00531 TFIIE Transcription 83.6 0.33 7.3E-06 31.4 -0.1 14 31-44 98-111 (147)
79 COG5236 Uncharacterized conser 83.5 0.97 2.1E-05 33.4 2.2 12 127-138 290-301 (493)
80 smart00440 ZnF_C2C2 C2C2 Zinc 82.3 0.64 1.4E-05 22.9 0.7 33 10-42 2-38 (40)
81 PRK00398 rpoP DNA-directed RNA 82.2 0.71 1.5E-05 23.4 0.9 29 8-42 3-31 (46)
82 KOG1146|consensus 82.1 0.37 8E-06 41.4 -0.3 25 87-111 516-540 (1406)
83 COG2888 Predicted Zn-ribbon RN 81.9 0.85 1.8E-05 24.5 1.1 10 87-96 48-57 (61)
84 TIGR02605 CxxC_CxxC_SSSS putat 80.9 0.59 1.3E-05 24.3 0.3 29 9-40 6-34 (52)
85 COG1996 RPC10 DNA-directed RNA 80.9 0.67 1.5E-05 24.0 0.5 11 89-99 6-16 (49)
86 PF09538 FYDLN_acid: Protein o 80.7 1.2 2.5E-05 27.3 1.6 29 64-102 11-39 (108)
87 COG1592 Rubrerythrin [Energy p 79.9 1 2.3E-05 29.8 1.2 8 89-96 134-141 (166)
88 KOG3408|consensus 79.8 0.48 1E-05 29.4 -0.3 36 119-154 58-93 (129)
89 PHA02998 RNA polymerase subuni 79.2 1.1 2.3E-05 29.9 1.1 37 7-43 142-182 (195)
90 TIGR00373 conserved hypothetic 78.8 0.65 1.4E-05 30.5 0.0 31 88-128 108-138 (158)
91 PRK06266 transcription initiat 78.5 0.66 1.4E-05 31.1 0.0 32 89-130 117-148 (178)
92 COG1997 RPL43A Ribosomal prote 78.3 0.98 2.1E-05 26.3 0.7 12 89-100 53-64 (89)
93 PF09723 Zn-ribbon_8: Zinc rib 78.1 0.65 1.4E-05 23.1 -0.1 12 9-20 6-17 (42)
94 PRK14890 putative Zn-ribbon RN 74.7 1.6 3.4E-05 23.5 0.8 8 119-126 49-56 (59)
95 KOG2186|consensus 74.3 2.3 5E-05 30.0 1.7 46 33-83 4-49 (276)
96 COG1594 RPB9 DNA-directed RNA 73.7 1.6 3.6E-05 26.9 0.8 11 63-73 101-111 (113)
97 smart00614 ZnF_BED BED zinc fi 73.7 2.5 5.3E-05 21.8 1.4 21 119-139 19-44 (50)
98 COG3677 Transposase and inacti 73.6 2.5 5.4E-05 26.8 1.7 39 5-44 27-65 (129)
99 smart00734 ZnF_Rad18 Rad18-lik 73.5 2.7 5.8E-05 18.5 1.3 19 120-139 3-21 (26)
100 PHA00626 hypothetical protein 71.9 1.7 3.6E-05 23.1 0.5 14 118-131 23-36 (59)
101 PF10571 UPF0547: Uncharacteri 71.5 1.9 4.2E-05 19.0 0.6 10 120-129 16-25 (26)
102 COG1198 PriA Primosomal protei 71.5 3.4 7.4E-05 34.0 2.3 25 9-39 445-469 (730)
103 PF02176 zf-TRAF: TRAF-type zi 71.0 2.4 5.1E-05 22.6 1.0 42 89-131 9-55 (60)
104 PF02892 zf-BED: BED zinc fing 70.1 3 6.5E-05 20.7 1.2 20 119-138 17-40 (45)
105 PF05443 ROS_MUCR: ROS/MUCR tr 69.9 1.9 4.1E-05 27.4 0.5 28 87-117 70-97 (132)
106 PF03604 DNA_RNApol_7kD: DNA d 69.0 3 6.4E-05 19.5 0.9 10 119-128 18-27 (32)
107 PF12013 DUF3505: Protein of u 68.8 2 4.2E-05 26.2 0.4 25 90-114 81-109 (109)
108 PF09845 DUF2072: Zn-ribbon co 68.7 3.1 6.7E-05 26.3 1.2 15 62-76 1-15 (131)
109 PF08790 zf-LYAR: LYAR-type C2 68.3 1.8 3.9E-05 19.5 0.1 17 120-137 2-18 (28)
110 PF04959 ARS2: Arsenite-resist 68.2 1.8 3.9E-05 29.9 0.2 30 87-116 75-104 (214)
111 TIGR02300 FYDLN_acid conserved 67.5 4 8.6E-05 25.7 1.5 30 63-102 10-39 (129)
112 cd00730 rubredoxin Rubredoxin; 66.1 4.1 8.9E-05 21.2 1.2 8 119-126 35-42 (50)
113 PF07754 DUF1610: Domain of un 65.5 3.5 7.5E-05 17.9 0.7 10 7-16 15-24 (24)
114 PF14205 Cys_rich_KTR: Cystein 65.4 4.2 9.1E-05 21.5 1.2 32 9-40 5-36 (55)
115 PF07975 C1_4: TFIIH C1-like d 65.0 2.9 6.4E-05 21.8 0.5 25 118-142 21-45 (51)
116 PF00301 Rubredoxin: Rubredoxi 63.3 8 0.00017 19.8 1.9 8 119-126 35-42 (47)
117 PF06524 NOA36: NOA36 protein; 62.1 7.3 0.00016 27.8 2.2 19 88-106 208-226 (314)
118 KOG2482|consensus 61.3 9.2 0.0002 28.4 2.6 22 33-54 196-217 (423)
119 PF13451 zf-trcl: Probable zin 60.0 3.2 7E-05 21.5 0.2 13 89-101 4-16 (49)
120 PF08274 PhnA_Zn_Ribbon: PhnA 59.9 2.9 6.3E-05 19.2 -0.0 8 119-126 20-27 (30)
121 KOG2482|consensus 58.8 18 0.00038 27.1 3.7 50 62-111 144-217 (423)
122 TIGR00595 priA primosomal prot 57.8 9.4 0.0002 30.1 2.4 26 9-40 223-248 (505)
123 COG5112 UFD2 U1-like Zn-finger 57.8 1.9 4E-05 26.1 -1.1 33 119-151 56-88 (126)
124 PRK03824 hypA hydrogenase nick 57.4 5.3 0.00012 25.5 0.8 14 89-102 70-83 (135)
125 PF11672 DUF3268: Protein of u 56.9 5.6 0.00012 24.1 0.8 8 63-70 3-10 (102)
126 smart00778 Prim_Zn_Ribbon Zinc 56.8 16 0.00034 17.7 2.2 31 8-40 3-33 (37)
127 PF13453 zf-TFIIB: Transcripti 56.4 11 0.00023 18.5 1.7 37 10-50 1-37 (41)
128 PF11494 Ta0938: Ta0938; Inte 56.4 7.5 0.00016 23.2 1.3 39 87-131 12-50 (105)
129 PF12760 Zn_Tnp_IS1595: Transp 55.5 6 0.00013 19.9 0.7 8 119-126 38-45 (46)
130 PF01780 Ribosomal_L37ae: Ribo 55.3 3.3 7.1E-05 24.4 -0.3 11 90-100 54-64 (90)
131 COG1655 Uncharacterized protei 54.8 3.3 7.1E-05 28.9 -0.4 41 87-127 17-71 (267)
132 PF13878 zf-C2H2_3: zinc-finge 54.5 7.3 0.00016 19.2 0.9 12 119-130 14-25 (41)
133 COG3357 Predicted transcriptio 54.1 7.3 0.00016 23.0 1.0 13 89-101 58-70 (97)
134 COG3091 SprT Zn-dependent meta 53.3 5.1 0.00011 26.1 0.3 34 89-128 117-150 (156)
135 COG4306 Uncharacterized protei 53.2 6.1 0.00013 24.8 0.6 14 89-102 68-81 (160)
136 PF05129 Elf1: Transcription e 52.8 2.7 5.8E-05 24.3 -1.0 10 30-39 20-29 (81)
137 PRK12380 hydrogenase nickel in 52.6 7.6 0.00016 24.0 1.0 25 89-126 70-94 (113)
138 PF04606 Ogr_Delta: Ogr/Delta- 52.5 4.9 0.00011 20.5 0.1 38 92-132 2-41 (47)
139 KOG4173|consensus 51.9 8.2 0.00018 26.5 1.1 75 32-111 79-168 (253)
140 COG5151 SSL1 RNA polymerase II 51.8 12 0.00025 27.5 1.9 48 92-142 365-412 (421)
141 PF09332 Mcm10: Mcm10 replicat 51.3 3.1 6.7E-05 31.0 -1.0 45 90-134 253-301 (344)
142 TIGR00100 hypA hydrogenase nic 51.2 8.4 0.00018 23.8 1.0 26 89-127 70-95 (115)
143 COG1326 Uncharacterized archae 49.6 5.8 0.00013 26.9 0.1 38 4-43 2-41 (201)
144 PF14803 Nudix_N_2: Nudix N-te 49.0 6 0.00013 18.7 0.1 10 118-127 22-31 (34)
145 PF04810 zf-Sec23_Sec24: Sec23 48.8 8.9 0.00019 18.7 0.7 9 119-127 25-33 (40)
146 PF11023 DUF2614: Protein of u 48.0 7.9 0.00017 23.8 0.5 31 6-44 67-97 (114)
147 KOG3408|consensus 48.0 12 0.00027 23.3 1.3 26 29-54 54-79 (129)
148 COG1327 Predicted transcriptio 47.9 9.8 0.00021 24.8 0.9 13 90-102 29-41 (156)
149 PRK14892 putative transcriptio 47.4 13 0.00029 22.4 1.4 9 31-39 20-28 (99)
150 KOG3214|consensus 47.2 13 0.00027 22.4 1.2 42 28-75 19-60 (109)
151 TIGR00240 ATCase_reg aspartate 46.8 15 0.00032 24.0 1.6 35 9-43 104-143 (150)
152 KOG2593|consensus 46.3 7.5 0.00016 29.8 0.3 34 7-40 127-161 (436)
153 PRK00564 hypA hydrogenase nick 46.2 11 0.00024 23.4 1.0 14 89-102 71-84 (117)
154 smart00661 RPOL9 RNA polymeras 46.1 20 0.00044 18.2 1.9 11 32-42 20-30 (52)
155 PF15135 UPF0515: Uncharacteri 45.5 15 0.00033 26.0 1.6 38 6-44 130-167 (278)
156 PF14446 Prok-RING_1: Prokaryo 45.3 17 0.00037 19.3 1.4 29 6-42 3-31 (54)
157 PF04216 FdhE: Protein involve 45.2 1.9 4.1E-05 31.3 -2.9 8 33-40 173-180 (290)
158 KOG4167|consensus 45.0 4.3 9.3E-05 33.2 -1.2 27 89-115 792-818 (907)
159 PF02748 PyrI_C: Aspartate car 44.9 15 0.00032 19.3 1.2 33 12-44 12-47 (52)
160 COG2331 Uncharacterized protei 44.2 7.3 0.00016 22.1 -0.0 10 63-72 13-22 (82)
161 TIGR01206 lysW lysine biosynth 44.0 16 0.00035 19.3 1.3 30 9-42 3-32 (54)
162 PRK00432 30S ribosomal protein 43.9 16 0.00036 18.9 1.3 8 63-70 38-45 (50)
163 PF13824 zf-Mss51: Zinc-finger 43.0 23 0.00049 18.8 1.7 13 29-41 11-23 (55)
164 TIGR01384 TFS_arch transcripti 42.3 13 0.00029 22.3 0.9 40 32-73 62-101 (104)
165 KOG1280|consensus 42.1 29 0.00063 26.0 2.6 39 31-69 78-116 (381)
166 PTZ00255 60S ribosomal protein 42.0 11 0.00025 22.2 0.5 13 89-101 54-66 (90)
167 PRK05580 primosome assembly pr 41.5 23 0.00051 29.1 2.4 27 8-40 390-416 (679)
168 PF01927 Mut7-C: Mut7-C RNAse 41.4 15 0.00033 23.7 1.1 46 63-108 92-143 (147)
169 PRK03681 hypA hydrogenase nick 41.4 14 0.0003 22.8 0.9 13 89-101 70-82 (114)
170 PF05191 ADK_lid: Adenylate ki 41.3 15 0.00032 17.6 0.8 11 119-129 22-32 (36)
171 PRK14873 primosome assembly pr 40.8 21 0.00046 29.3 2.0 17 23-39 401-417 (665)
172 KOG2907|consensus 40.7 11 0.00023 23.2 0.3 13 118-130 102-114 (116)
173 KOG4377|consensus 39.9 33 0.00072 26.3 2.7 111 29-143 268-428 (480)
174 COG1779 C4-type Zn-finger prot 39.8 8.6 0.00019 26.2 -0.2 11 119-129 44-54 (201)
175 COG1998 RPS31 Ribosomal protei 39.8 18 0.0004 18.7 1.0 10 7-16 18-27 (51)
176 smart00154 ZnF_AN1 AN1-like Zi 39.0 16 0.00034 17.8 0.7 11 119-129 13-23 (39)
177 KOG4727|consensus 37.6 18 0.00039 24.1 1.0 27 113-139 70-96 (193)
178 PF01363 FYVE: FYVE zinc finge 37.2 16 0.00034 20.0 0.6 10 64-73 11-20 (69)
179 PF01155 HypA: Hydrogenase exp 36.9 12 0.00026 23.0 0.1 13 90-102 71-83 (113)
180 PF10276 zf-CHCC: Zinc-finger 36.7 14 0.00031 18.2 0.3 22 21-42 18-39 (40)
181 PF15269 zf-C2H2_7: Zinc-finge 36.2 23 0.00051 17.8 1.0 22 119-140 21-42 (54)
182 cd00924 Cyt_c_Oxidase_Vb Cytoc 36.1 16 0.00035 21.9 0.5 18 25-43 73-90 (97)
183 PF10537 WAC_Acf1_DNA_bd: ATP- 36.1 34 0.00074 20.7 2.0 37 32-71 3-39 (102)
184 PF14311 DUF4379: Domain of un 35.9 19 0.00041 18.8 0.8 12 90-101 29-40 (55)
185 smart00132 LIM Zinc-binding do 35.1 20 0.00044 16.5 0.8 10 119-128 28-37 (39)
186 KOG4317|consensus 35.1 12 0.00026 27.5 -0.1 19 119-137 20-38 (383)
187 KOG4167|consensus 35.1 9.9 0.00021 31.3 -0.6 25 61-85 791-815 (907)
188 PRK05978 hypothetical protein; 35.0 22 0.00047 23.2 1.0 8 92-99 55-62 (148)
189 COG4391 Uncharacterized protei 34.7 11 0.00025 20.4 -0.2 44 82-130 16-60 (62)
190 PF08209 Sgf11: Sgf11 (transcr 34.7 30 0.00065 16.2 1.2 21 118-139 4-24 (33)
191 PF07282 OrfB_Zn_ribbon: Putat 34.7 39 0.00085 18.4 2.0 12 61-72 45-56 (69)
192 PF01428 zf-AN1: AN1-like Zinc 34.4 24 0.00052 17.4 1.0 11 119-129 14-24 (43)
193 COG0068 HypF Hydrogenase matur 34.3 16 0.00035 30.0 0.5 9 89-97 173-181 (750)
194 TIGR00280 L37a ribosomal prote 34.2 16 0.00035 21.6 0.3 14 89-102 53-66 (91)
195 COG4888 Uncharacterized Zn rib 33.8 14 0.0003 22.2 0.1 40 28-73 18-57 (104)
196 COG1571 Predicted DNA-binding 33.2 23 0.00049 27.3 1.0 30 91-132 352-381 (421)
197 COG4957 Predicted transcriptio 33.1 1E+02 0.0022 19.8 3.7 35 17-54 61-95 (148)
198 PLN02294 cytochrome c oxidase 33.1 21 0.00045 23.8 0.7 20 83-102 135-154 (174)
199 PF07295 DUF1451: Protein of u 32.9 16 0.00036 23.7 0.2 30 89-129 112-141 (146)
200 smart00064 FYVE Protein presen 32.8 28 0.0006 18.9 1.1 10 64-73 12-21 (68)
201 PRK04023 DNA polymerase II lar 32.7 63 0.0014 28.1 3.5 8 33-40 627-634 (1121)
202 KOG2785|consensus 32.6 37 0.00079 25.8 2.0 25 61-85 165-189 (390)
203 KOG2231|consensus 32.0 45 0.00097 27.5 2.5 98 44-150 161-275 (669)
204 KOG2785|consensus 31.1 29 0.00063 26.3 1.3 52 89-140 166-242 (390)
205 PF10083 DUF2321: Uncharacteri 30.9 17 0.00038 23.8 0.1 13 119-131 69-81 (158)
206 PF04780 DUF629: Protein of un 30.4 27 0.00059 27.3 1.1 21 90-110 58-78 (466)
207 PF00412 LIM: LIM domain; Int 30.1 24 0.00053 18.2 0.6 12 119-130 27-38 (58)
208 PRK03976 rpl37ae 50S ribosomal 29.8 21 0.00045 21.1 0.3 13 89-101 54-66 (90)
209 TIGR03831 YgiT_finger YgiT-typ 29.8 25 0.00054 17.2 0.6 14 117-130 31-44 (46)
210 PF10263 SprT-like: SprT-like 29.6 22 0.00047 22.9 0.4 32 89-129 123-154 (157)
211 PF10013 DUF2256: Uncharacteri 29.5 30 0.00066 17.2 0.8 11 92-102 11-21 (42)
212 PF08792 A2L_zn_ribbon: A2L zi 29.5 25 0.00054 16.4 0.5 12 118-129 21-32 (33)
213 smart00731 SprT SprT homologue 29.4 26 0.00056 22.6 0.7 33 89-129 112-144 (146)
214 PF04423 Rad50_zn_hook: Rad50 28.8 21 0.00045 18.6 0.2 12 120-131 22-33 (54)
215 PTZ00448 hypothetical protein; 28.6 35 0.00076 25.8 1.4 22 119-140 315-336 (373)
216 PRK04351 hypothetical protein; 28.3 28 0.00061 22.7 0.7 33 89-130 112-144 (149)
217 PF01286 XPA_N: XPA protein N- 28.1 27 0.00059 16.5 0.5 14 91-104 5-18 (34)
218 TIGR03830 CxxCG_CxxCG_HTH puta 28.0 30 0.00065 21.3 0.8 12 119-130 32-43 (127)
219 PRK00762 hypA hydrogenase nick 27.8 31 0.00067 21.7 0.9 13 89-102 70-82 (124)
220 KOG3507|consensus 27.8 16 0.00035 19.6 -0.3 12 119-130 38-49 (62)
221 PF11781 RRN7: RNA polymerase 27.5 36 0.00078 16.2 0.9 15 3-17 3-17 (36)
222 PF14787 zf-CCHC_5: GAG-polypr 27.2 30 0.00066 16.6 0.6 15 120-134 4-18 (36)
223 PF12773 DZR: Double zinc ribb 26.9 50 0.0011 16.6 1.4 9 119-127 30-38 (50)
224 TIGR00686 phnA alkylphosphonat 26.8 27 0.00059 21.4 0.4 13 89-101 19-31 (109)
225 PF06220 zf-U1: U1 zinc finger 26.7 48 0.001 16.0 1.2 12 119-130 4-15 (38)
226 COG1773 Rubredoxin [Energy pro 26.2 27 0.00057 18.6 0.3 13 119-131 4-16 (55)
227 PRK10220 hypothetical protein; 24.9 36 0.00079 20.9 0.7 14 89-102 20-33 (111)
228 COG4640 Predicted membrane pro 24.8 44 0.00096 25.6 1.3 18 119-136 16-33 (465)
229 KOG0978|consensus 24.8 23 0.0005 29.2 -0.2 21 113-134 674-694 (698)
230 COG5216 Uncharacterized conser 24.7 20 0.00044 19.2 -0.3 8 62-69 44-51 (67)
231 TIGR00244 transcriptional regu 24.6 32 0.00069 22.4 0.5 14 119-132 29-42 (147)
232 PF08394 Arc_trans_TRASH: Arch 24.0 12 0.00026 18.1 -1.2 33 92-129 1-34 (37)
233 KOG3002|consensus 23.1 1.5E+02 0.0033 21.9 3.8 57 63-123 81-141 (299)
234 PRK00420 hypothetical protein; 23.1 42 0.00092 20.7 0.8 8 90-97 41-48 (112)
235 KOG1842|consensus 23.1 26 0.00057 27.2 -0.1 23 61-83 14-36 (505)
236 KOG0717|consensus 22.7 55 0.0012 25.7 1.5 21 33-53 293-313 (508)
237 COG3364 Zn-ribbon containing p 22.6 43 0.00093 20.3 0.7 14 89-102 2-15 (112)
238 PF04780 DUF629: Protein of un 22.1 40 0.00086 26.5 0.7 24 61-84 56-79 (466)
239 PF07800 DUF1644: Protein of u 21.8 2.5E+02 0.0055 18.6 6.0 59 89-150 80-141 (162)
240 TIGR03655 anti_R_Lar restricti 21.7 66 0.0014 16.6 1.3 35 10-44 3-38 (53)
241 KOG1842|consensus 21.3 48 0.001 25.8 0.9 29 89-117 15-43 (505)
242 PF06397 Desulfoferrod_N: Desu 21.1 35 0.00075 16.4 0.1 11 118-128 6-16 (36)
243 PF14122 YokU: YokU-like prote 21.1 53 0.0012 19.2 0.9 22 114-135 31-52 (87)
244 KOG3362|consensus 21.1 59 0.0013 21.1 1.2 18 33-50 130-147 (156)
245 COG5236 Uncharacterized conser 21.1 82 0.0018 23.8 2.0 20 92-111 223-242 (493)
246 KOG2807|consensus 20.9 99 0.0021 23.1 2.4 24 119-142 346-369 (378)
247 PRK11823 DNA repair protein Ra 20.8 46 0.001 25.9 0.8 7 90-96 22-28 (446)
248 KOG0782|consensus 20.8 49 0.0011 26.8 0.9 35 91-131 255-289 (1004)
249 KOG2071|consensus 20.6 49 0.0011 26.7 0.9 27 115-142 416-442 (579)
No 1
>KOG2462|consensus
Probab=99.95 E-value=2.9e-28 Score=165.97 Aligned_cols=119 Identities=22% Similarity=0.352 Sum_probs=107.3
Q ss_pred CCCccccccccccccChHHHHHHHhhhhcCC--CCccccccccccccChhhHHHHHhhhCCCcccCccccccccCccchh
Q psy16646 29 LPPQFHCYVCKKKYRHKRQLVRHFQVNHTNN--YDRVICEICNKEFTHKSSLAEHRVLHFPAQHKCSLCQQAFKRDKHSK 106 (159)
Q Consensus 29 ~~~~~~C~~c~~~f~~~~~l~~h~~~~~~~~--~~~~~c~~c~~~f~~~~~l~~h~~~h~~k~~~C~~C~~~f~~~~~l~ 106 (159)
....|.|.+||+.+.+.++|.+|..+ |..- .+.+.|..|++.+.+..+|..|+++|+ .+++|.+||+.|.+..-|+
T Consensus 127 ~~~r~~c~eCgk~ysT~snLsrHkQ~-H~~~~s~ka~~C~~C~K~YvSmpALkMHirTH~-l~c~C~iCGKaFSRPWLLQ 204 (279)
T KOG2462|consen 127 KHPRYKCPECGKSYSTSSNLSRHKQT-HRSLDSKKAFSCKYCGKVYVSMPALKMHIRTHT-LPCECGICGKAFSRPWLLQ 204 (279)
T ss_pred cCCceeccccccccccccccchhhcc-cccccccccccCCCCCceeeehHHHhhHhhccC-CCcccccccccccchHHhh
Confidence 34568999999999999999999998 5542 156889999999999999999999994 5899999999999999999
Q ss_pred hhhhhhhhhhccccccccCccccchhhHHHhhccCCCccccccC
Q psy16646 107 GDDIREEIEREMKTRNSIGITVRQNQTNKNHRSGDQKKKTAKQL 150 (159)
Q Consensus 107 ~h~~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~k~~~~~ 150 (159)
.|+|+|+|||| |.|+.|++.|+.+++|+.|+++|.+.|.|+|.
T Consensus 205 GHiRTHTGEKP-F~C~hC~kAFADRSNLRAHmQTHS~~K~~qC~ 247 (279)
T KOG2462|consen 205 GHIRTHTGEKP-FSCPHCGKAFADRSNLRAHMQTHSDVKKHQCP 247 (279)
T ss_pred cccccccCCCC-ccCCcccchhcchHHHHHHHHhhcCCccccCc
Confidence 99999999999 99999999999999999999999999999985
No 2
>KOG2462|consensus
Probab=99.93 E-value=1.6e-26 Score=157.54 Aligned_cols=131 Identities=21% Similarity=0.310 Sum_probs=117.5
Q ss_pred hhhcccCCCCCCCCCCC----CCcccCC---CCCccccccccccccChHHHHHHHhhhhcCCCCccccccccccccChhh
Q psy16646 5 KKKSVKNPNAKKRYRPY----VPRVDSS---LPPQFHCYVCKKKYRHKRQLVRHFQVNHTNNYDRVICEICNKEFTHKSS 77 (159)
Q Consensus 5 ~~~~~~~~~~~~~~~~~----~~~~~h~---~~~~~~C~~c~~~f~~~~~l~~h~~~~~~~~~~~~~c~~c~~~f~~~~~ 77 (159)
+...++|+.|++.+... .|...|- ..+.+.|.+|++.|.+-..|..|+++ |. -++.|.+||+.|+..=-
T Consensus 127 ~~~r~~c~eCgk~ysT~snLsrHkQ~H~~~~s~ka~~C~~C~K~YvSmpALkMHirT-H~---l~c~C~iCGKaFSRPWL 202 (279)
T KOG2462|consen 127 KHPRYKCPECGKSYSTSSNLSRHKQTHRSLDSKKAFSCKYCGKVYVSMPALKMHIRT-HT---LPCECGICGKAFSRPWL 202 (279)
T ss_pred cCCceeccccccccccccccchhhcccccccccccccCCCCCceeeehHHHhhHhhc-cC---CCcccccccccccchHH
Confidence 34568899999998854 4555553 36779999999999999999999999 54 47899999999999999
Q ss_pred HHHHHhhh-CCCcccCccccccccCccchhhhhhhhhhhhccccccccCccccchhhHHHhhcc
Q psy16646 78 LAEHRVLH-FPAQHKCSLCQQAFKRDKHSKGDDIREEIEREMKTRNSIGITVRQNQTNKNHRSG 140 (159)
Q Consensus 78 l~~h~~~h-~~k~~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~ 140 (159)
|+.|+++| |||||.|..|+++|...++|+.|+++|.+.|. |.|..|++.|+..+-|..|...
T Consensus 203 LQGHiRTHTGEKPF~C~hC~kAFADRSNLRAHmQTHS~~K~-~qC~~C~KsFsl~SyLnKH~ES 265 (279)
T KOG2462|consen 203 LQGHIRTHTGEKPFSCPHCGKAFADRSNLRAHMQTHSDVKK-HQCPRCGKSFALKSYLNKHSES 265 (279)
T ss_pred hhcccccccCCCCccCCcccchhcchHHHHHHHHhhcCCcc-ccCcchhhHHHHHHHHHHhhhh
Confidence 99999999 99999999999999999999999999999998 9999999999999999999754
No 3
>KOG3576|consensus
Probab=99.77 E-value=1.1e-19 Score=119.04 Aligned_cols=122 Identities=25% Similarity=0.377 Sum_probs=106.5
Q ss_pred CcccCCCCCccccccccccccChHHHHHHHhhhhcCCCCccccccccccccChhhHHHHHhhh-CCCcccCccccccccC
Q psy16646 23 PRVDSSLPPQFHCYVCKKKYRHKRQLVRHFQVNHTNNYDRVICEICNKEFTHKSSLAEHRVLH-FPAQHKCSLCQQAFKR 101 (159)
Q Consensus 23 ~~~~h~~~~~~~C~~c~~~f~~~~~l~~h~~~~~~~~~~~~~c~~c~~~f~~~~~l~~h~~~h-~~k~~~C~~C~~~f~~ 101 (159)
.+.+..+...+.|.+|++.|.....|.+|++. |... +.+.|..||+.|.+.-+|..|.++| |.+||+|..|+++|..
T Consensus 108 t~gsssd~d~ftCrvCgK~F~lQRmlnrh~kc-h~~v-kr~lct~cgkgfndtfdlkrh~rthtgvrpykc~~c~kaftq 185 (267)
T KOG3576|consen 108 TIGSSSDQDSFTCRVCGKKFGLQRMLNRHLKC-HSDV-KRHLCTFCGKGFNDTFDLKRHTRTHTGVRPYKCSLCEKAFTQ 185 (267)
T ss_pred cccCCCCCCeeeeehhhhhhhHHHHHHHHhhh-ccHH-HHHHHhhccCcccchhhhhhhhccccCccccchhhhhHHHHh
Confidence 33334455679999999999999999999999 7777 7899999999999999999999999 9999999999999999
Q ss_pred ccchhhhhhhhhhhh----------ccccccccCccccchhhHHHhhccCCCccc
Q psy16646 102 DKHSKGDDIREEIER----------EMKTRNSIGITVRQNQTNKNHRSGDQKKKT 146 (159)
Q Consensus 102 ~~~l~~h~~~~~~~~----------~~~~C~~C~~~f~~~~~l~~H~~~h~~~k~ 146 (159)
.-+|..|++..+|-. ..|.|++||.+-.....+..|+..|+...+
T Consensus 186 rcsleshl~kvhgv~~~yaykerr~kl~vcedcg~t~~~~e~~~~h~~~~hp~Sp 240 (267)
T KOG3576|consen 186 RCSLESHLKKVHGVQHQYAYKERRAKLYVCEDCGYTSERPEVYYLHLKLHHPFSP 240 (267)
T ss_pred hccHHHHHHHHcCchHHHHHHHhhhheeeecccCCCCCChhHHHHHHHhcCCCCH
Confidence 999999998755431 239999999999999999999988886554
No 4
>KOG3608|consensus
Probab=99.71 E-value=1.6e-18 Score=122.15 Aligned_cols=133 Identities=18% Similarity=0.236 Sum_probs=104.1
Q ss_pred CCCCCCCCCCcccCCCCCccccccccccccChHHHHHHHhhhhcCCCCccccccccccccChhhHHHHHhhhCCCcccCc
Q psy16646 14 AKKRYRPYVPRVDSSLPPQFHCYVCKKKYRHKRQLVRHFQVNHTNNYDRVICEICNKEFTHKSSLAEHRVLHFPAQHKCS 93 (159)
Q Consensus 14 ~~~~~~~~~~~~~h~~~~~~~C~~c~~~f~~~~~l~~h~~~~~~~~~~~~~c~~c~~~f~~~~~l~~h~~~h~~k~~~C~ 93 (159)
.+.++++..|+++|++++...|+.||..|.....|..|.+........+|+|..|.+.|.....|..|+..| ..-|.|+
T Consensus 189 ~~~k~~LreH~r~Hs~eKvvACp~Cg~~F~~~tkl~DH~rRqt~l~~n~fqC~~C~KrFaTeklL~~Hv~rH-vn~ykCp 267 (467)
T KOG3608|consen 189 MGNKYRLREHIRTHSNEKVVACPHCGELFRTKTKLFDHLRRQTELNTNSFQCAQCFKRFATEKLLKSHVVRH-VNCYKCP 267 (467)
T ss_pred hccHHHHHHHHHhcCCCeEEecchHHHHhccccHHHHHHHhhhhhcCCchHHHHHHHHHhHHHHHHHHHHHh-hhccccc
Confidence 455666788889999999999999999998888888888764444436788888888888888888888777 2367888
Q ss_pred cccccccCccchhhhhhhhhh-hhccccccccCccccchhhHHHhhccCCCcccccc
Q psy16646 94 LCQQAFKRDKHSKGDDIREEI-EREMKTRNSIGITVRQNQTNKNHRSGDQKKKTAKQ 149 (159)
Q Consensus 94 ~C~~~f~~~~~l~~h~~~~~~-~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~k~~~~ 149 (159)
.|..+....++|..|++.-+. ++| |+|+.|+++|.+.+.|..|..+|. +..|.|
T Consensus 268 lCdmtc~~~ssL~~H~r~rHs~dkp-fKCd~Cd~~c~~esdL~kH~~~HS-~~~y~C 322 (467)
T KOG3608|consen 268 LCDMTCSSASSLTTHIRYRHSKDKP-FKCDECDTRCVRESDLAKHVQVHS-KTVYQC 322 (467)
T ss_pred ccccCCCChHHHHHHHHhhhccCCC-ccccchhhhhccHHHHHHHHHhcc-ccceec
Confidence 888888888888888876544 455 888888888888888888887777 445554
No 5
>KOG1074|consensus
Probab=99.69 E-value=5.8e-18 Score=130.20 Aligned_cols=64 Identities=16% Similarity=0.106 Sum_probs=49.8
Q ss_pred ccCccccccccCccchhhhhhhhhhhhccccccccCccccchhhHHHhhccCCCccccccCccch
Q psy16646 90 HKCSLCQQAFKRDKHSKGDDIREEIEREMKTRNSIGITVRQNQTNKNHRSGDQKKKTAKQLSMLN 154 (159)
Q Consensus 90 ~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~k~~~~~~~~~ 154 (159)
-.|-+|.+...-.+.|+.|.++|+||+| |+|..||+.|.++.+|..|..+|.-..++.-.-.+|
T Consensus 606 NqCiiC~rVlSC~saLqmHyrtHtGERP-FkCKiCgRAFtTkGNLkaH~~vHka~p~~R~q~ScP 669 (958)
T KOG1074|consen 606 NQCIICLRVLSCPSALQMHYRTHTGERP-FKCKICGRAFTTKGNLKAHMSVHKAKPPARVQFSCP 669 (958)
T ss_pred cceeeeeecccchhhhhhhhhcccCcCc-cccccccchhccccchhhcccccccCccccccccCC
Confidence 4677888888888888888888888888 888888888888888888888887766665555555
No 6
>KOG3623|consensus
Probab=99.68 E-value=1e-17 Score=127.33 Aligned_cols=108 Identities=23% Similarity=0.382 Sum_probs=97.0
Q ss_pred ccccccccccccChHHHHHHHhhhhcCCCCccccccccccccChhhHHHHHhhh--C------------CCcccCccccc
Q psy16646 32 QFHCYVCKKKYRHKRQLVRHFQVNHTNNYDRVICEICNKEFTHKSSLAEHRVLH--F------------PAQHKCSLCQQ 97 (159)
Q Consensus 32 ~~~C~~c~~~f~~~~~l~~h~~~~~~~~~~~~~c~~c~~~f~~~~~l~~h~~~h--~------------~k~~~C~~C~~ 97 (159)
...|++|.+.+.....|+.|+...|...+..|.|..|.++|.+..-|..|+.+| + .+.|+|.+||+
T Consensus 210 lltcpycdrgykrltslkeHikyrhekne~nfsC~lCsytFAyRtQLErhm~~hkpg~dqa~sltqsa~lRKFKCtECgK 289 (1007)
T KOG3623|consen 210 LLTCPYCDRGYKRLTSLKEHIKYRHEKNEPNFSCMLCSYTFAYRTQLERHMQLHKPGGDQAISLTQSALLRKFKCTECGK 289 (1007)
T ss_pred hhcchhHHHHHHHHHHHHHHHHHHHhhCCCCCcchhhhhhhhhHHHHHHHHHhhcCCCcccccccchhhhccccccccch
Confidence 367999999999999999999865655546799999999999999999999988 2 24699999999
Q ss_pred cccCccchhhhhhhhhhhhccccccccCccccchhhHHHhhcc
Q psy16646 98 AFKRDKHSKGDDIREEIEREMKTRNSIGITVRQNQTNKNHRSG 140 (159)
Q Consensus 98 ~f~~~~~l~~h~~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~ 140 (159)
+|.++-.|+.|+|+|.||+| |.|+.|+++|.+..++..|+..
T Consensus 290 AFKfKHHLKEHlRIHSGEKP-feCpnCkKRFSHSGSySSHmSS 331 (1007)
T KOG3623|consen 290 AFKFKHHLKEHLRIHSGEKP-FECPNCKKRFSHSGSYSSHMSS 331 (1007)
T ss_pred hhhhHHHHHhhheeecCCCC-cCCcccccccccCCcccccccc
Confidence 99999999999999999999 9999999999999999999743
No 7
>KOG1074|consensus
Probab=99.64 E-value=3.4e-17 Score=126.04 Aligned_cols=57 Identities=11% Similarity=0.046 Sum_probs=53.2
Q ss_pred ccCccccccccCccchhhhhhhhhhhhccccccccCccccchhhHHHhhccCCCcccc
Q psy16646 90 HKCSLCQQAFKRDKHSKGDDIREEIEREMKTRNSIGITVRQNQTNKNHRSGDQKKKTA 147 (159)
Q Consensus 90 ~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~k~~ 147 (159)
..|..||+.|...+.|..|+++|+++++ |.|..|++.|..+..|..|+.+|..-.+.
T Consensus 880 h~C~vCgk~FsSSsALqiH~rTHtg~KP-F~C~fC~~aFttrgnLKvHMgtH~w~q~~ 936 (958)
T KOG1074|consen 880 HVCNVCGKQFSSSAALEIHMRTHTGPKP-FFCHFCEEAFTTRGNLKVHMGTHMWVQPP 936 (958)
T ss_pred hhhccchhcccchHHHHHhhhcCCCCCC-ccchhhhhhhhhhhhhhhhhccccccCCC
Confidence 6799999999999999999999999999 99999999999999999999999865543
No 8
>KOG3608|consensus
Probab=99.59 E-value=3e-16 Score=110.81 Aligned_cols=139 Identities=19% Similarity=0.282 Sum_probs=105.1
Q ss_pred hhhcccCCCCCCCCCCCC----CcccCC--CCCccccccccccccChHHHHHHHhhhhcCCCCccccccccccccChhhH
Q psy16646 5 KKKSVKNPNAKKRYRPYV----PRVDSS--LPPQFHCYVCKKKYRHKRQLVRHFQVNHTNNYDRVICEICNKEFTHKSSL 78 (159)
Q Consensus 5 ~~~~~~~~~~~~~~~~~~----~~~~h~--~~~~~~C~~c~~~f~~~~~l~~h~~~~~~~~~~~~~c~~c~~~f~~~~~l 78 (159)
.+|.+.||.|+.-|+... |++..+ ...+|.|..|.+.|.+...|..|+.. |-. -|.|+.|..+....++|
T Consensus 204 ~eKvvACp~Cg~~F~~~tkl~DH~rRqt~l~~n~fqC~~C~KrFaTeklL~~Hv~r-Hvn---~ykCplCdmtc~~~ssL 279 (467)
T KOG3608|consen 204 NEKVVACPHCGELFRTKTKLFDHLRRQTELNTNSFQCAQCFKRFATEKLLKSHVVR-HVN---CYKCPLCDMTCSSASSL 279 (467)
T ss_pred CCeEEecchHHHHhccccHHHHHHHhhhhhcCCchHHHHHHHHHhHHHHHHHHHHH-hhh---cccccccccCCCChHHH
Confidence 457889999888777543 333322 34689999999999999999999887 543 47899999988889999
Q ss_pred HHHHhh-h-CCCcccCccccccccCccchhhhhhhhhhhhccccccc--cCccccchhhHHHhhc-cCCCcc--cccc
Q psy16646 79 AEHRVL-H-FPAQHKCSLCQQAFKRDKHSKGDDIREEIEREMKTRNS--IGITVRQNQTNKNHRS-GDQKKK--TAKQ 149 (159)
Q Consensus 79 ~~h~~~-h-~~k~~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~~C~~--C~~~f~~~~~l~~H~~-~h~~~k--~~~~ 149 (159)
..|++. | .++||+|..|.+.|.+.+.|..|+.+|. ++.|.|+. |-.+|.+...++.|.+ +|.|.. +|.|
T Consensus 280 ~~H~r~rHs~dkpfKCd~Cd~~c~~esdL~kH~~~HS--~~~y~C~h~~C~~s~r~~~q~~~H~~evhEg~np~~Y~C 355 (467)
T KOG3608|consen 280 TTHIRYRHSKDKPFKCDECDTRCVRESDLAKHVQVHS--KTVYQCEHPDCHYSVRTYTQMRRHFLEVHEGNNPILYAC 355 (467)
T ss_pred HHHHHhhhccCCCccccchhhhhccHHHHHHHHHhcc--ccceecCCCCCcHHHHHHHHHHHHHHHhccCCCCCceee
Confidence 999775 5 7789999999999999999999988665 55588854 8888888888888844 443443 3544
No 9
>KOG3576|consensus
Probab=99.57 E-value=1.7e-16 Score=104.24 Aligned_cols=81 Identities=20% Similarity=0.285 Sum_probs=75.7
Q ss_pred CccccccccccccChhhHHHHHhhh-CCCcccCccccccccCccchhhhhhhhhhhhccccccccCccccchhhHHHhhc
Q psy16646 61 DRVICEICNKEFTHKSSLAEHRVLH-FPAQHKCSLCQQAFKRDKHSKGDDIREEIEREMKTRNSIGITVRQNQTNKNHRS 139 (159)
Q Consensus 61 ~~~~c~~c~~~f~~~~~l~~h~~~h-~~k~~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~ 139 (159)
..+.|..|++.|....-|+.|++.| ..+.+.|..||+.|...-.|++|.++|+|-+| |+|+.|++.|.++.+|-.|++
T Consensus 116 d~ftCrvCgK~F~lQRmlnrh~kch~~vkr~lct~cgkgfndtfdlkrh~rthtgvrp-ykc~~c~kaftqrcsleshl~ 194 (267)
T KOG3576|consen 116 DSFTCRVCGKKFGLQRMLNRHLKCHSDVKRHLCTFCGKGFNDTFDLKRHTRTHTGVRP-YKCSLCEKAFTQRCSLESHLK 194 (267)
T ss_pred CeeeeehhhhhhhHHHHHHHHhhhccHHHHHHHhhccCcccchhhhhhhhccccCccc-cchhhhhHHHHhhccHHHHHH
Confidence 5689999999999999999999999 77899999999999999999999999999999 999999999999999999954
Q ss_pred -cCC
Q psy16646 140 -GDQ 142 (159)
Q Consensus 140 -~h~ 142 (159)
+|.
T Consensus 195 kvhg 198 (267)
T KOG3576|consen 195 KVHG 198 (267)
T ss_pred HHcC
Confidence 454
No 10
>KOG3623|consensus
Probab=99.56 E-value=6.1e-16 Score=117.89 Aligned_cols=77 Identities=23% Similarity=0.381 Sum_probs=73.9
Q ss_pred CccccccccccccChhhHHHHHhhh-CCCcccCccccccccCccchhhhhhhhhhhhccccccccCccccchhhHHHhh
Q psy16646 61 DRVICEICNKEFTHKSSLAEHRVLH-FPAQHKCSLCQQAFKRDKHSKGDDIREEIEREMKTRNSIGITVRQNQTNKNHR 138 (159)
Q Consensus 61 ~~~~c~~c~~~f~~~~~l~~h~~~h-~~k~~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~~C~~C~~~f~~~~~l~~H~ 138 (159)
.+|.|+.|++.|.-.++|..|.--| |.+||+|.+|.++|..+-.|..|.|.|.||+| |.|+.|+++|.+..++..|+
T Consensus 893 gmyaCDqCDK~FqKqSSLaRHKYEHsGqRPyqC~iCkKAFKHKHHLtEHkRLHSGEKP-fQCdKClKRFSHSGSYSQHM 970 (1007)
T KOG3623|consen 893 GMYACDQCDKAFQKQSSLARHKYEHSGQRPYQCIICKKAFKHKHHLTEHKRLHSGEKP-FQCDKCLKRFSHSGSYSQHM 970 (1007)
T ss_pred ccchHHHHHHHHHhhHHHHHhhhhhcCCCCcccchhhHhhhhhhhhhhhhhhccCCCc-chhhhhhhhcccccchHhhh
Confidence 6899999999999999999999999 88999999999999999999999999999999 99999999999999999997
No 11
>PLN03086 PRLI-interacting factor K; Provisional
Probab=99.35 E-value=1.8e-12 Score=98.57 Aligned_cols=119 Identities=17% Similarity=0.306 Sum_probs=90.2
Q ss_pred cccCCC--CCCCCCCCCCcccCCCCCccccccccccccChHHHHHHHhhhhcCCCCccccccccccccChhhHHHHHhhh
Q psy16646 8 SVKNPN--AKKRYRPYVPRVDSSLPPQFHCYVCKKKYRHKRQLVRHFQVNHTNNYDRVICEICNKEFTHKSSLAEHRVLH 85 (159)
Q Consensus 8 ~~~~~~--~~~~~~~~~~~~~h~~~~~~~C~~c~~~f~~~~~l~~h~~~~~~~~~~~~~c~~c~~~f~~~~~l~~h~~~h 85 (159)
.+.||+ |+..+. ....++++.|+.|+..|. ...|..|+.. +. .++.|. |+..+ ....|..|+..|
T Consensus 433 ~V~Cp~~~Cg~v~~------r~el~~H~~C~~Cgk~f~-~s~LekH~~~-~H---kpv~Cp-Cg~~~-~R~~L~~H~~th 499 (567)
T PLN03086 433 NVVCPHDGCGIVLR------VEEAKNHVHCEKCGQAFQ-QGEMEKHMKV-FH---EPLQCP-CGVVL-EKEQMVQHQAST 499 (567)
T ss_pred ceeCCcccccceee------ccccccCccCCCCCCccc-hHHHHHHHHh-cC---CCccCC-CCCCc-chhHHHhhhhcc
Confidence 445664 555552 333345578999999986 6789999988 42 578999 99755 568899999888
Q ss_pred -CCCcccCccccccccC----------ccchhhhhhhhhhhhccccccccCccccchhhHHHhh-ccCC
Q psy16646 86 -FPAQHKCSLCQQAFKR----------DKHSKGDDIREEIEREMKTRNSIGITVRQNQTNKNHR-SGDQ 142 (159)
Q Consensus 86 -~~k~~~C~~C~~~f~~----------~~~l~~h~~~~~~~~~~~~C~~C~~~f~~~~~l~~H~-~~h~ 142 (159)
..+++.|..|++.|.. .+.|..|... .|.++ +.|..||+.|..+ .+..|+ ..|.
T Consensus 500 Cp~Kpi~C~fC~~~v~~g~~~~d~~d~~s~Lt~HE~~-CG~rt-~~C~~Cgk~Vrlr-dm~~H~~~~h~ 565 (567)
T PLN03086 500 CPLRLITCRFCGDMVQAGGSAMDVRDRLRGMSEHESI-CGSRT-APCDSCGRSVMLK-EMDIHQIAVHQ 565 (567)
T ss_pred CCCCceeCCCCCCccccCccccchhhhhhhHHHHHHh-cCCcc-eEccccCCeeeeh-hHHHHHHHhhc
Confidence 8899999999999853 3478889877 48888 9999999998887 567774 3443
No 12
>PHA00733 hypothetical protein
Probab=99.19 E-value=1.2e-11 Score=77.82 Aligned_cols=79 Identities=18% Similarity=0.203 Sum_probs=64.1
Q ss_pred CccccccccccccChhhHHHH------HhhhCCCcccCccccccccCccchhhhhhhhhhhhccccccccCccccchhhH
Q psy16646 61 DRVICEICNKEFTHKSSLAEH------RVLHFPAQHKCSLCQQAFKRDKHSKGDDIREEIEREMKTRNSIGITVRQNQTN 134 (159)
Q Consensus 61 ~~~~c~~c~~~f~~~~~l~~h------~~~h~~k~~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~~C~~C~~~f~~~~~l 134 (159)
+++.|.+|...|.....|..+ +..++++||.|..||+.|...+.|..|++.+ +.+ +.|+.|++.|.....|
T Consensus 39 ~~~~~~~~~~~~~~~~~l~~~~~l~~~~~~~~~kPy~C~~Cgk~Fss~s~L~~H~r~h--~~~-~~C~~CgK~F~~~~sL 115 (128)
T PHA00733 39 KRLIRAVVKTLIYNPQLLDESSYLYKLLTSKAVSPYVCPLCLMPFSSSVSLKQHIRYT--EHS-KVCPVCGKEFRNTDST 115 (128)
T ss_pred hhHHHHHHhhhccChhhhcchHHHHhhcccCCCCCccCCCCCCcCCCHHHHHHHHhcC--CcC-ccCCCCCCccCCHHHH
Confidence 678899998877776666554 2233678999999999999999999999875 345 8999999999999999
Q ss_pred HHhhccCC
Q psy16646 135 KNHRSGDQ 142 (159)
Q Consensus 135 ~~H~~~h~ 142 (159)
..|++..+
T Consensus 116 ~~H~~~~h 123 (128)
T PHA00733 116 LDHVCKKH 123 (128)
T ss_pred HHHHHHhc
Confidence 99976544
No 13
>PHA02768 hypothetical protein; Provisional
Probab=99.08 E-value=2.7e-11 Score=63.79 Aligned_cols=43 Identities=7% Similarity=0.112 Sum_probs=27.5
Q ss_pred ccCccccccccCccchhhhhhhhhhhhccccccccCccccchhhHH
Q psy16646 90 HKCSLCQQAFKRDKHSKGDDIREEIEREMKTRNSIGITVRQNQTNK 135 (159)
Q Consensus 90 ~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~~C~~C~~~f~~~~~l~ 135 (159)
|+|+.||+.|...+.|..|+++|+ ++ ++|..|++.|.+.+.|.
T Consensus 6 y~C~~CGK~Fs~~~~L~~H~r~H~--k~-~kc~~C~k~f~~~s~l~ 48 (55)
T PHA02768 6 YECPICGEIYIKRKSMITHLRKHN--TN-LKLSNCKRISLRTGEYI 48 (55)
T ss_pred cCcchhCCeeccHHHHHHHHHhcC--Cc-ccCCcccceecccceeE
Confidence 566666666666666666666666 34 66666666666665553
No 14
>PHA00733 hypothetical protein
Probab=99.04 E-value=1.2e-10 Score=73.35 Aligned_cols=83 Identities=14% Similarity=0.280 Sum_probs=67.1
Q ss_pred CCccccccccccccChHHHHHH--Hh--hhhcCCCCccccccccccccChhhHHHHHhhhCCCcccCccccccccCccch
Q psy16646 30 PPQFHCYVCKKKYRHKRQLVRH--FQ--VNHTNNYDRVICEICNKEFTHKSSLAEHRVLHFPAQHKCSLCQQAFKRDKHS 105 (159)
Q Consensus 30 ~~~~~C~~c~~~f~~~~~l~~h--~~--~~~~~~~~~~~c~~c~~~f~~~~~l~~h~~~h~~k~~~C~~C~~~f~~~~~l 105 (159)
.+++.|..|...|.....|..+ +. ..+... .||.|..|++.|.+...|..|++.+ +.++.|..|++.|.....|
T Consensus 38 ~~~~~~~~~~~~~~~~~~l~~~~~l~~~~~~~~~-kPy~C~~Cgk~Fss~s~L~~H~r~h-~~~~~C~~CgK~F~~~~sL 115 (128)
T PHA00733 38 QKRLIRAVVKTLIYNPQLLDESSYLYKLLTSKAV-SPYVCPLCLMPFSSSVSLKQHIRYT-EHSKVCPVCGKEFRNTDST 115 (128)
T ss_pred hhhHHHHHHhhhccChhhhcchHHHHhhcccCCC-CCccCCCCCCcCCCHHHHHHHHhcC-CcCccCCCCCCccCCHHHH
Confidence 5678999999888776666554 11 112234 7999999999999999999998876 4579999999999999999
Q ss_pred hhhhhhhhh
Q psy16646 106 KGDDIREEI 114 (159)
Q Consensus 106 ~~h~~~~~~ 114 (159)
..|+...|+
T Consensus 116 ~~H~~~~h~ 124 (128)
T PHA00733 116 LDHVCKKHN 124 (128)
T ss_pred HHHHHHhcC
Confidence 999987775
No 15
>PLN03086 PRLI-interacting factor K; Provisional
Probab=99.02 E-value=2.6e-10 Score=87.05 Aligned_cols=83 Identities=19% Similarity=0.260 Sum_probs=70.4
Q ss_pred CccccccccccccChhhHHHHHhhhCCCcccCccccccccCccchhhhhhhhhhhhccccccccCccccc----------
Q psy16646 61 DRVICEICNKEFTHKSSLAEHRVLHFPAQHKCSLCQQAFKRDKHSKGDDIREEIEREMKTRNSIGITVRQ---------- 130 (159)
Q Consensus 61 ~~~~c~~c~~~f~~~~~l~~h~~~h~~k~~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~~C~~C~~~f~~---------- 130 (159)
.++.|..|++.|. ...|..|+..+ .+++.|+ ||+.+ ....|..|+.+|...++ +.|+.|++.|..
T Consensus 452 ~H~~C~~Cgk~f~-~s~LekH~~~~-Hkpv~Cp-Cg~~~-~R~~L~~H~~thCp~Kp-i~C~fC~~~v~~g~~~~d~~d~ 526 (567)
T PLN03086 452 NHVHCEKCGQAFQ-QGEMEKHMKVF-HEPLQCP-CGVVL-EKEQMVQHQASTCPLRL-ITCRFCGDMVQAGGSAMDVRDR 526 (567)
T ss_pred cCccCCCCCCccc-hHHHHHHHHhc-CCCccCC-CCCCc-chhHHHhhhhccCCCCc-eeCCCCCCccccCccccchhhh
Confidence 5678999999986 67799998886 3789999 99765 56899999999999999 999999999952
Q ss_pred hhhHHHhhccCCCcccccc
Q psy16646 131 NQTNKNHRSGDQKKKTAKQ 149 (159)
Q Consensus 131 ~~~l~~H~~~h~~~k~~~~ 149 (159)
.+.|..|..++ +.++++|
T Consensus 527 ~s~Lt~HE~~C-G~rt~~C 544 (567)
T PLN03086 527 LRGMSEHESIC-GSRTAPC 544 (567)
T ss_pred hhhHHHHHHhc-CCcceEc
Confidence 45899998875 8888888
No 16
>PHA02768 hypothetical protein; Provisional
Probab=98.93 E-value=7.2e-10 Score=58.43 Aligned_cols=44 Identities=23% Similarity=0.337 Sum_probs=36.4
Q ss_pred ccccccccccccChhhHHHHHhhhCCCcccCccccccccCccchh
Q psy16646 62 RVICEICNKEFTHKSSLAEHRVLHFPAQHKCSLCQQAFKRDKHSK 106 (159)
Q Consensus 62 ~~~c~~c~~~f~~~~~l~~h~~~h~~k~~~C~~C~~~f~~~~~l~ 106 (159)
.|.|+.||+.|...++|..|+++|. ++++|..|++.|.+.+.|.
T Consensus 5 ~y~C~~CGK~Fs~~~~L~~H~r~H~-k~~kc~~C~k~f~~~s~l~ 48 (55)
T PHA02768 5 GYECPICGEIYIKRKSMITHLRKHN-TNLKLSNCKRISLRTGEYI 48 (55)
T ss_pred ccCcchhCCeeccHHHHHHHHHhcC-CcccCCcccceecccceeE
Confidence 4688888888888888888888885 6888888888888877765
No 17
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=98.69 E-value=4.6e-09 Score=47.46 Aligned_cols=24 Identities=8% Similarity=-0.083 Sum_probs=15.5
Q ss_pred hhhhhhhhhhhhccccccccCcccc
Q psy16646 105 SKGDDIREEIEREMKTRNSIGITVR 129 (159)
Q Consensus 105 l~~h~~~~~~~~~~~~C~~C~~~f~ 129 (159)
|.+|+++|+|+++ |.|+.|++.|.
T Consensus 2 l~~H~~~H~~~k~-~~C~~C~k~F~ 25 (26)
T PF13465_consen 2 LRRHMRTHTGEKP-YKCPYCGKSFS 25 (26)
T ss_dssp HHHHHHHHSSSSS-EEESSSSEEES
T ss_pred HHHHhhhcCCCCC-CCCCCCcCeeC
Confidence 5566666666666 66666666664
No 18
>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=98.57 E-value=3.7e-08 Score=44.44 Aligned_cols=23 Identities=30% Similarity=0.545 Sum_probs=16.2
Q ss_pred HHHHHhhh-CCCcccCcccccccc
Q psy16646 78 LAEHRVLH-FPAQHKCSLCQQAFK 100 (159)
Q Consensus 78 l~~h~~~h-~~k~~~C~~C~~~f~ 100 (159)
|..|+++| +++||.|+.|++.|.
T Consensus 2 l~~H~~~H~~~k~~~C~~C~k~F~ 25 (26)
T PF13465_consen 2 LRRHMRTHTGEKPYKCPYCGKSFS 25 (26)
T ss_dssp HHHHHHHHSSSSSEEESSSSEEES
T ss_pred HHHHhhhcCCCCCCCCCCCcCeeC
Confidence 56677777 777777777777664
No 19
>PHA00616 hypothetical protein
Probab=98.55 E-value=1.3e-08 Score=51.13 Aligned_cols=28 Identities=14% Similarity=0.316 Sum_probs=13.8
Q ss_pred ccCccccccccCccchhhhhhhhhhhhc
Q psy16646 90 HKCSLCQQAFKRDKHSKGDDIREEIERE 117 (159)
Q Consensus 90 ~~C~~C~~~f~~~~~l~~h~~~~~~~~~ 117 (159)
|.|..||+.|...+.|..|++.|||+++
T Consensus 2 YqC~~CG~~F~~~s~l~~H~r~~hg~~~ 29 (44)
T PHA00616 2 YQCLRCGGIFRKKKEVIEHLLSVHKQNK 29 (44)
T ss_pred CccchhhHHHhhHHHHHHHHHHhcCCCc
Confidence 4444455555555555555544554444
No 20
>PHA00616 hypothetical protein
Probab=98.54 E-value=2.8e-08 Score=49.96 Aligned_cols=32 Identities=13% Similarity=-0.013 Sum_probs=29.8
Q ss_pred ccccccCccccchhhHHHhhccCCCccccccC
Q psy16646 119 KTRNSIGITVRQNQTNKNHRSGDQKKKTAKQL 150 (159)
Q Consensus 119 ~~C~~C~~~f~~~~~l~~H~~~h~~~k~~~~~ 150 (159)
|.|+.||+.|.+.+.|..|++.|++++++.+-
T Consensus 2 YqC~~CG~~F~~~s~l~~H~r~~hg~~~~~~~ 33 (44)
T PHA00616 2 YQCLRCGGIFRKKKEVIEHLLSVHKQNKLTLE 33 (44)
T ss_pred CccchhhHHHhhHHHHHHHHHHhcCCCcccee
Confidence 89999999999999999999999999988653
No 21
>PHA00732 hypothetical protein
Probab=98.45 E-value=7.7e-08 Score=55.33 Aligned_cols=44 Identities=20% Similarity=0.428 Sum_probs=22.0
Q ss_pred cccccccccccChhhHHHHHhh-hCCCcccCccccccccCccchhhhhhh
Q psy16646 63 VICEICNKEFTHKSSLAEHRVL-HFPAQHKCSLCQQAFKRDKHSKGDDIR 111 (159)
Q Consensus 63 ~~c~~c~~~f~~~~~l~~h~~~-h~~k~~~C~~C~~~f~~~~~l~~h~~~ 111 (159)
|.|..|++.|.....|..|++. |. ++.|+.||+.|. .+..|.++
T Consensus 2 y~C~~Cgk~F~s~s~Lk~H~r~~H~--~~~C~~CgKsF~---~l~~H~~~ 46 (79)
T PHA00732 2 FKCPICGFTTVTLFALKQHARRNHT--LTKCPVCNKSYR---RLNQHFYS 46 (79)
T ss_pred ccCCCCCCccCCHHHHHHHhhcccC--CCccCCCCCEeC---Chhhhhcc
Confidence 4555555555555555555542 32 234555555554 24445443
No 22
>KOG3993|consensus
Probab=98.33 E-value=2.7e-07 Score=67.55 Aligned_cols=130 Identities=18% Similarity=0.202 Sum_probs=82.5
Q ss_pred CCCCCCCCC----CCCCcccCCCCCccccccccccccChHHHHHHHhhhhcCC---------------------------
Q psy16646 11 NPNAKKRYR----PYVPRVDSSLPPQFHCYVCKKKYRHKRQLVRHFQVNHTNN--------------------------- 59 (159)
Q Consensus 11 ~~~~~~~~~----~~~~~~~h~~~~~~~C~~c~~~f~~~~~l~~h~~~~~~~~--------------------------- 59 (159)
|.-|+..+. +..|.-..+.-..|+|++|++.|....+|..|.++ |...
T Consensus 270 CqLCK~kYeD~F~LAQHrC~RIV~vEYrCPEC~KVFsCPANLASHRRW-HKPR~eaa~a~~~P~k~~~~~rae~~ea~rs 348 (500)
T KOG3993|consen 270 CQLCKEKYEDAFALAQHRCPRIVHVEYRCPECDKVFSCPANLASHRRW-HKPRPEAAKAGSPPPKQAVETRAEVQEAERS 348 (500)
T ss_pred HHHHHHhhhhHHHHhhccCCeeEEeeecCCcccccccCchhhhhhhcc-cCCchhhhhcCCCChhhhhhhhhhhhhcccc
Confidence 334555444 44555444555668899999999999999999888 4321
Q ss_pred -----CCccccccccccccChhhHHHHHhhh--CCCc-------------------------------------------
Q psy16646 60 -----YDRVICEICNKEFTHKSSLAEHRVLH--FPAQ------------------------------------------- 89 (159)
Q Consensus 60 -----~~~~~c~~c~~~f~~~~~l~~h~~~h--~~k~------------------------------------------- 89 (159)
+.-|.|..|++.|.....|..|+.+| .+..
T Consensus 349 g~dss~gi~~C~~C~KkFrRqAYLrKHqlthq~~~~~k~~a~~f~~s~~~~l~~~~~~~a~h~~a~~~~g~~vl~~a~sa 428 (500)
T KOG3993|consen 349 GDDSSSGIFSCHTCGKKFRRQAYLRKHQLTHQRAPLAKEKAPKFLLSRVIPLMHFNQAVATHSSASDSHGDEVLYVAGSA 428 (500)
T ss_pred CCcccCceeecHHhhhhhHHHHHHHHhHHhhhccccchhcccCcchhhcccccccccccccccccccccccceeeeeccc
Confidence 01256777888887777777776665 1110
Q ss_pred --ccCccccccccCccchhhhhhhhhhhhccccccccCccccchhhHHHhhccCC
Q psy16646 90 --HKCSLCQQAFKRDKHSKGDDIREEIEREMKTRNSIGITVRQNQTNKNHRSGDQ 142 (159)
Q Consensus 90 --~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~h~ 142 (159)
..|..||..+..+..--.+.+..+.+.. |.|..|-..|.....|.+|+...+
T Consensus 429 el~~pp~~~~ppsss~~sgg~~rlg~~~q~-f~~ky~~atfyss~~ltrhin~~H 482 (500)
T KOG3993|consen 429 ELELPPYDGSPPSSSGSSGGYGRLGIAEQG-FTCKYCPATFYSSPGLTRHINKCH 482 (500)
T ss_pred cccCCCCCCCCcccCCCCCccccccchhhc-cccccchHhhhcCcchHhHhhhcC
Confidence 2334455444444443444444444444 889999999999999999965543
No 23
>KOG3993|consensus
Probab=98.23 E-value=1.7e-07 Score=68.54 Aligned_cols=83 Identities=17% Similarity=0.385 Sum_probs=50.3
Q ss_pred cccccccccccChhhHHHHHhhh-CCCcccCccccccccCccchhhhhhhhh----------------------------
Q psy16646 63 VICEICNKEFTHKSSLAEHRVLH-FPAQHKCSLCQQAFKRDKHSKGDDIREE---------------------------- 113 (159)
Q Consensus 63 ~~c~~c~~~f~~~~~l~~h~~~h-~~k~~~C~~C~~~f~~~~~l~~h~~~~~---------------------------- 113 (159)
|.|..|...+.+.-.|.+|+-.. -.--|+|++|++.|.-..+|..|.+-|-
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 45555555555555555553222 1123555555555555555555544220
Q ss_pred ----hhhccccccccCccccchhhHHHhhccCCCcc
Q psy16646 114 ----IEREMKTRNSIGITVRQNQTNKNHRSGDQKKK 145 (159)
Q Consensus 114 ----~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~k 145 (159)
.+...|.|..|++.|.+..-|+.|+-+|+..-
T Consensus 348 sg~dss~gi~~C~~C~KkFrRqAYLrKHqlthq~~~ 383 (500)
T KOG3993|consen 348 SGDDSSSGIFSCHTCGKKFRRQAYLRKHQLTHQRAP 383 (500)
T ss_pred cCCcccCceeecHHhhhhhHHHHHHHHhHHhhhccc
Confidence 11123999999999999999999988887543
No 24
>PHA00732 hypothetical protein
Probab=98.11 E-value=2.1e-06 Score=49.35 Aligned_cols=47 Identities=30% Similarity=0.528 Sum_probs=26.1
Q ss_pred ccccccccccccChHHHHHHHhhhhcCCCCccccccccccccChhhHHHHHhhh
Q psy16646 32 QFHCYVCKKKYRHKRQLVRHFQVNHTNNYDRVICEICNKEFTHKSSLAEHRVLH 85 (159)
Q Consensus 32 ~~~C~~c~~~f~~~~~l~~h~~~~~~~~~~~~~c~~c~~~f~~~~~l~~h~~~h 85 (159)
||.|..|++.|.....|..|++.+|. ++.|+.|++.|. .+..|..+.
T Consensus 1 py~C~~Cgk~F~s~s~Lk~H~r~~H~----~~~C~~CgKsF~---~l~~H~~~~ 47 (79)
T PHA00732 1 MFKCPICGFTTVTLFALKQHARRNHT----LTKCPVCNKSYR---RLNQHFYSQ 47 (79)
T ss_pred CccCCCCCCccCCHHHHHHHhhcccC----CCccCCCCCEeC---Chhhhhccc
Confidence 35566666666666666666653122 235666666665 255555443
No 25
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=98.09 E-value=1.1e-06 Score=38.36 Aligned_cols=22 Identities=14% Similarity=0.051 Sum_probs=16.4
Q ss_pred ccccccCccccchhhHHHhhcc
Q psy16646 119 KTRNSIGITVRQNQTNKNHRSG 140 (159)
Q Consensus 119 ~~C~~C~~~f~~~~~l~~H~~~ 140 (159)
|.|+.|++.|.+.+.|..|++.
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 4677777777777777777665
No 26
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=97.88 E-value=9.2e-06 Score=36.81 Aligned_cols=25 Identities=12% Similarity=0.112 Sum_probs=21.7
Q ss_pred ccccccCccccchhhHHHhhccCCC
Q psy16646 119 KTRNSIGITVRQNQTNKNHRSGDQK 143 (159)
Q Consensus 119 ~~C~~C~~~f~~~~~l~~H~~~h~~ 143 (159)
|.|+.|++.|.+...|..|++.|..
T Consensus 2 ~~C~~C~~~F~~~~~l~~H~~~h~~ 26 (27)
T PF13912_consen 2 FECDECGKTFSSLSALREHKRSHCS 26 (27)
T ss_dssp EEETTTTEEESSHHHHHHHHCTTTT
T ss_pred CCCCccCCccCChhHHHHHhHHhcC
Confidence 7899999999999999999887754
No 27
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=97.75 E-value=3.3e-05 Score=41.22 Aligned_cols=8 Identities=0% Similarity=-0.375 Sum_probs=3.2
Q ss_pred ccccccCc
Q psy16646 119 KTRNSIGI 126 (159)
Q Consensus 119 ~~C~~C~~ 126 (159)
+.|+.|..
T Consensus 32 v~CPiC~~ 39 (54)
T PF05605_consen 32 VVCPICSS 39 (54)
T ss_pred ccCCCchh
Confidence 33444443
No 28
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=97.75 E-value=6.8e-06 Score=35.75 Aligned_cols=22 Identities=27% Similarity=0.566 Sum_probs=14.4
Q ss_pred ccCccccccccCccchhhhhhh
Q psy16646 90 HKCSLCQQAFKRDKHSKGDDIR 111 (159)
Q Consensus 90 ~~C~~C~~~f~~~~~l~~h~~~ 111 (159)
|.|+.|++.|...+.|..|++.
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 4566666666666666666654
No 29
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=97.74 E-value=8.8e-05 Score=39.54 Aligned_cols=48 Identities=23% Similarity=0.319 Sum_probs=22.4
Q ss_pred cccccccccccChhhHHHHHhh-h--CCCcccCccccccccCccchhhhhhhhh
Q psy16646 63 VICEICNKEFTHKSSLAEHRVL-H--FPAQHKCSLCQQAFKRDKHSKGDDIREE 113 (159)
Q Consensus 63 ~~c~~c~~~f~~~~~l~~h~~~-h--~~k~~~C~~C~~~f~~~~~l~~h~~~~~ 113 (159)
|.|+.|++ ..+...|..|... | ..+.+.|++|...+. ..|..|+..+|
T Consensus 3 f~CP~C~~-~~~~~~L~~H~~~~H~~~~~~v~CPiC~~~~~--~~l~~Hl~~~H 53 (54)
T PF05605_consen 3 FTCPYCGK-GFSESSLVEHCEDEHRSESKNVVCPICSSRVT--DNLIRHLNSQH 53 (54)
T ss_pred cCCCCCCC-ccCHHHHHHHHHhHCcCCCCCccCCCchhhhh--hHHHHHHHHhc
Confidence 44555555 2334455555332 3 223455555555433 25555555443
No 30
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=97.70 E-value=1.4e-05 Score=34.88 Aligned_cols=23 Identities=13% Similarity=0.095 Sum_probs=15.0
Q ss_pred ccccccCccccchhhHHHhhccC
Q psy16646 119 KTRNSIGITVRQNQTNKNHRSGD 141 (159)
Q Consensus 119 ~~C~~C~~~f~~~~~l~~H~~~h 141 (159)
|.|+.|++.|.+...|..|++.|
T Consensus 1 ~~C~~C~~~~~~~~~l~~H~~~~ 23 (24)
T PF13894_consen 1 FQCPICGKSFRSKSELRQHMRTH 23 (24)
T ss_dssp EE-SSTS-EESSHHHHHHHHHHH
T ss_pred CCCcCCCCcCCcHHHHHHHHHhh
Confidence 45777777777777777776654
No 31
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=97.44 E-value=3.7e-05 Score=33.46 Aligned_cols=23 Identities=13% Similarity=0.501 Sum_probs=13.2
Q ss_pred ccCccccccccCccchhhhhhhh
Q psy16646 90 HKCSLCQQAFKRDKHSKGDDIRE 112 (159)
Q Consensus 90 ~~C~~C~~~f~~~~~l~~h~~~~ 112 (159)
|.|+.|++.|.....|..|+.++
T Consensus 1 ~~C~~C~~~~~~~~~l~~H~~~~ 23 (24)
T PF13894_consen 1 FQCPICGKSFRSKSELRQHMRTH 23 (24)
T ss_dssp EE-SSTS-EESSHHHHHHHHHHH
T ss_pred CCCcCCCCcCCcHHHHHHHHHhh
Confidence 45666666666666666666554
No 32
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=97.42 E-value=7.9e-05 Score=44.70 Aligned_cols=74 Identities=14% Similarity=0.099 Sum_probs=22.0
Q ss_pred ccccccccccChhhHHHHHhh-hCCCcccCccccccccCccchhhhhhhhhhhhccccccccCccccchhhHHHhhccCC
Q psy16646 64 ICEICNKEFTHKSSLAEHRVL-HFPAQHKCSLCQQAFKRDKHSKGDDIREEIEREMKTRNSIGITVRQNQTNKNHRSGDQ 142 (159)
Q Consensus 64 ~c~~c~~~f~~~~~l~~h~~~-h~~k~~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~h~ 142 (159)
+|..|+..|.+...|..|+.. |+-. .. ....+.....+..+++.... .. +.|..|++.|.+...|..|++.+.
T Consensus 1 ~C~~C~~~f~~~~~l~~H~~~~H~~~-~~---~~~~l~~~~~~~~~~~~~~~-~~-~~C~~C~~~f~s~~~l~~Hm~~~~ 74 (100)
T PF12756_consen 1 QCLFCDESFSSVDDLLQHMKKKHGFD-IP---DQKYLVDPNRLLNYLRKKVK-ES-FRCPYCNKTFRSREALQEHMRSKH 74 (100)
T ss_dssp -----------------------------------------------------SS-EEBSSSS-EESSHHHHHHHHHHTT
T ss_pred Cccccccccccccccccccccccccc-cc---cccccccccccccccccccC-CC-CCCCccCCCCcCHHHHHHHHcCcc
Confidence 488999999999999999754 4321 11 11122233344444433222 24 889999999999999999988654
Q ss_pred C
Q psy16646 143 K 143 (159)
Q Consensus 143 ~ 143 (159)
.
T Consensus 75 H 75 (100)
T PF12756_consen 75 H 75 (100)
T ss_dssp T
T ss_pred C
Confidence 3
No 33
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=97.41 E-value=3.9e-05 Score=34.67 Aligned_cols=25 Identities=12% Similarity=0.274 Sum_probs=13.8
Q ss_pred cccCccccccccCccchhhhhhhhh
Q psy16646 89 QHKCSLCQQAFKRDKHSKGDDIREE 113 (159)
Q Consensus 89 ~~~C~~C~~~f~~~~~l~~h~~~~~ 113 (159)
||.|..|++.|.....|..|++.|.
T Consensus 1 ~~~C~~C~~~F~~~~~l~~H~~~h~ 25 (27)
T PF13912_consen 1 PFECDECGKTFSSLSALREHKRSHC 25 (27)
T ss_dssp SEEETTTTEEESSHHHHHHHHCTTT
T ss_pred CCCCCccCCccCChhHHHHHhHHhc
Confidence 3455555555555555555555443
No 34
>smart00355 ZnF_C2H2 zinc finger.
Probab=97.36 E-value=0.00012 Score=32.31 Aligned_cols=24 Identities=13% Similarity=0.104 Sum_probs=17.4
Q ss_pred ccccccCccccchhhHHHhhccCC
Q psy16646 119 KTRNSIGITVRQNQTNKNHRSGDQ 142 (159)
Q Consensus 119 ~~C~~C~~~f~~~~~l~~H~~~h~ 142 (159)
|.|+.|++.|.....|..|++.|.
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~~H~ 24 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMRTHX 24 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHHHhc
Confidence 457778888877777777776553
No 35
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=97.29 E-value=8.4e-05 Score=44.59 Aligned_cols=73 Identities=14% Similarity=0.337 Sum_probs=21.0
Q ss_pred ccccccccccChHHHHHHHhhhhcCCCCccccccccccccChhhHHHHHhhhCCCcccCccccccccCccchhhhhhhh
Q psy16646 34 HCYVCKKKYRHKRQLVRHFQVNHTNNYDRVICEICNKEFTHKSSLAEHRVLHFPAQHKCSLCQQAFKRDKHSKGDDIRE 112 (159)
Q Consensus 34 ~C~~c~~~f~~~~~l~~h~~~~~~~~~~~~~c~~c~~~f~~~~~l~~h~~~h~~k~~~C~~C~~~f~~~~~l~~h~~~~ 112 (159)
.|..|+..|.+...|..|+...|.-. .+ ....+.....+..+....-...+.|..|++.|.....|..|++.+
T Consensus 1 ~C~~C~~~f~~~~~l~~H~~~~H~~~-~~-----~~~~l~~~~~~~~~~~~~~~~~~~C~~C~~~f~s~~~l~~Hm~~~ 73 (100)
T PF12756_consen 1 QCLFCDESFSSVDDLLQHMKKKHGFD-IP-----DQKYLVDPNRLLNYLRKKVKESFRCPYCNKTFRSREALQEHMRSK 73 (100)
T ss_dssp ------------------------------------------------------SSEEBSSSS-EESSHHHHHHHHHHT
T ss_pred Cccccccccccccccccccccccccc-cc-----cccccccccccccccccccCCCCCCCccCCCCcCHHHHHHHHcCc
Confidence 47889999999999999987644332 21 111122333333333222223689999999999999999999864
No 36
>PF09237 GAGA: GAGA factor; InterPro: IPR015318 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Members of this entry bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognises the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognises the A in the fourth position of the consensus sequence []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1YUI_A 1YUJ_A.
Probab=97.23 E-value=0.00014 Score=37.45 Aligned_cols=28 Identities=25% Similarity=0.227 Sum_probs=15.9
Q ss_pred ccccccCccccchhhHHHhhccCCCccc
Q psy16646 119 KTRNSIGITVRQNQTNKNHRSGDQKKKT 146 (159)
Q Consensus 119 ~~C~~C~~~f~~~~~l~~H~~~h~~~k~ 146 (159)
-.|+.|+..+.+..+|+.|+.+.++.||
T Consensus 25 atCP~C~a~~~~srnLrRHle~~H~~k~ 52 (54)
T PF09237_consen 25 ATCPICGAVIRQSRNLRRHLEIRHFKKP 52 (54)
T ss_dssp EE-TTT--EESSHHHHHHHHHHHTTTS-
T ss_pred CCCCcchhhccchhhHHHHHHHHhcccC
Confidence 6677777777777777777666555554
No 37
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=96.95 E-value=0.00039 Score=30.63 Aligned_cols=23 Identities=4% Similarity=-0.000 Sum_probs=19.1
Q ss_pred ccccccCccccchhhHHHhhccC
Q psy16646 119 KTRNSIGITVRQNQTNKNHRSGD 141 (159)
Q Consensus 119 ~~C~~C~~~f~~~~~l~~H~~~h 141 (159)
|.|+.|+..|.+...|..|.+.+
T Consensus 1 ~~C~~C~~~f~s~~~~~~H~~s~ 23 (25)
T PF12874_consen 1 FYCDICNKSFSSENSLRQHLRSK 23 (25)
T ss_dssp EEETTTTEEESSHHHHHHHHTTH
T ss_pred CCCCCCCCCcCCHHHHHHHHCcC
Confidence 56889999999999999988654
No 38
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=96.92 E-value=0.00035 Score=49.93 Aligned_cols=52 Identities=15% Similarity=0.198 Sum_probs=37.7
Q ss_pred CCCcccCcc--ccccccCccchhhhhhhh-------------------hhhhccccccccCccccchhhHHHhh
Q psy16646 86 FPAQHKCSL--CQQAFKRDKHSKGDDIRE-------------------EIEREMKTRNSIGITVRQNQTNKNHR 138 (159)
Q Consensus 86 ~~k~~~C~~--C~~~f~~~~~l~~h~~~~-------------------~~~~~~~~C~~C~~~f~~~~~l~~H~ 138 (159)
+++||+|++ |.+++.....|+=|+.-. ..++| |+|+.|++++.....|.=|+
T Consensus 346 d~KpykCpV~gC~K~YknqnGLKYH~lhGH~~~~~~~~p~p~~~~~F~~~~KP-YrCevC~KRYKNlNGLKYHr 418 (423)
T COG5189 346 DGKPYKCPVEGCNKKYKNQNGLKYHMLHGHQNQKLHENPSPEKMNIFSAKDKP-YRCEVCDKRYKNLNGLKYHR 418 (423)
T ss_pred cCceecCCCCCchhhhccccchhhhhhccccCcccCCCCCccccccccccCCc-eeccccchhhccCccceecc
Confidence 356777765 777777666666665322 33477 99999999999999887776
No 39
>PRK04860 hypothetical protein; Provisional
Probab=96.79 E-value=0.00044 Score=45.29 Aligned_cols=39 Identities=15% Similarity=0.163 Sum_probs=31.5
Q ss_pred cccCccccccccCccchhhhhhhhhhhhccccccccCccccchh
Q psy16646 89 QHKCSLCQQAFKRDKHSKGDDIREEIEREMKTRNSIGITVRQNQ 132 (159)
Q Consensus 89 ~~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~~C~~C~~~f~~~~ 132 (159)
+|.|. |+. ....+.+|.+++.++++ |.|..|+..|....
T Consensus 119 ~Y~C~-C~~---~~~~~rrH~ri~~g~~~-YrC~~C~~~l~~~~ 157 (160)
T PRK04860 119 PYRCK-CQE---HQLTVRRHNRVVRGEAV-YRCRRCGETLVFKG 157 (160)
T ss_pred EEEcC-CCC---eeCHHHHHHHHhcCCcc-EECCCCCceeEEec
Confidence 58887 886 66778888888998888 88999988876543
No 40
>smart00355 ZnF_C2H2 zinc finger.
Probab=96.70 E-value=0.0006 Score=29.93 Aligned_cols=23 Identities=22% Similarity=0.392 Sum_probs=14.0
Q ss_pred ccCccccccccCccchhhhhhhh
Q psy16646 90 HKCSLCQQAFKRDKHSKGDDIRE 112 (159)
Q Consensus 90 ~~C~~C~~~f~~~~~l~~h~~~~ 112 (159)
|.|..|++.|...+.|..|++.|
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~~H 23 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMRTH 23 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHHHh
Confidence 35666666666666666666533
No 41
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=96.62 E-value=0.00058 Score=29.80 Aligned_cols=22 Identities=9% Similarity=0.001 Sum_probs=12.6
Q ss_pred ccccccCccccchhhHHHhhccC
Q psy16646 119 KTRNSIGITVRQNQTNKNHRSGD 141 (159)
Q Consensus 119 ~~C~~C~~~f~~~~~l~~H~~~h 141 (159)
|.|+.|++... ...|..|++.+
T Consensus 1 y~C~~C~y~t~-~~~l~~H~~~~ 22 (24)
T PF13909_consen 1 YKCPHCSYSTS-KSNLKRHLKRH 22 (24)
T ss_dssp EE-SSSS-EES-HHHHHHHHHHH
T ss_pred CCCCCCCCcCC-HHHHHHHHHhh
Confidence 45666776666 66666666554
No 42
>PF09237 GAGA: GAGA factor; InterPro: IPR015318 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Members of this entry bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognises the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognises the A in the fourth position of the consensus sequence []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1YUI_A 1YUJ_A.
Probab=96.57 E-value=0.00068 Score=35.00 Aligned_cols=32 Identities=6% Similarity=0.277 Sum_probs=19.5
Q ss_pred CCCcccCccccccccCccchhhhhhhhhhhhc
Q psy16646 86 FPAQHKCSLCQQAFKRDKHSKGDDIREEIERE 117 (159)
Q Consensus 86 ~~k~~~C~~C~~~f~~~~~l~~h~~~~~~~~~ 117 (159)
.+.|-.|++|+..+...-+|.+|+...|+.+|
T Consensus 21 S~~PatCP~C~a~~~~srnLrRHle~~H~~k~ 52 (54)
T PF09237_consen 21 SEQPATCPICGAVIRQSRNLRRHLEIRHFKKP 52 (54)
T ss_dssp TS--EE-TTT--EESSHHHHHHHHHHHTTTS-
T ss_pred cCCCCCCCcchhhccchhhHHHHHHHHhcccC
Confidence 45677788888888887788888777776655
No 43
>PF12171 zf-C2H2_jaz: Zinc-finger double-stranded RNA-binding; InterPro: IPR022755 This zinc finger is found in archaea and eukaryotes, and is approximately 30 amino acids in length. The mammalian members of this group occur multiple times along the protein, joined by flexible linkers, and are referred to as JAZ - dsRNA-binding ZF protein - zinc-fingers. The JAZ proteins are expressed in all tissues tested and localise in the nucleus, particularly the nucleolus []. JAZ preferentially binds to double-stranded (ds) RNA or RNA/DNA hybrids rather than DNA. In addition to binding double-stranded RNA, these zinc-fingers are required for nucleolar localisation. This entry represents the multiple-adjacent-C2H2 zinc finger, JAZ. ; PDB: 4DGW_A 1ZR9_A.
Probab=96.52 E-value=0.0014 Score=29.48 Aligned_cols=22 Identities=9% Similarity=-0.023 Sum_probs=18.6
Q ss_pred ccccccCccccchhhHHHhhcc
Q psy16646 119 KTRNSIGITVRQNQTNKNHRSG 140 (159)
Q Consensus 119 ~~C~~C~~~f~~~~~l~~H~~~ 140 (159)
|.|..|++.|.+...|..|++.
T Consensus 2 ~~C~~C~k~f~~~~~~~~H~~s 23 (27)
T PF12171_consen 2 FYCDACDKYFSSENQLKQHMKS 23 (27)
T ss_dssp CBBTTTTBBBSSHHHHHCCTTS
T ss_pred CCcccCCCCcCCHHHHHHHHcc
Confidence 6789999999999999888765
No 44
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=96.21 E-value=0.0026 Score=45.66 Aligned_cols=71 Identities=21% Similarity=0.345 Sum_probs=45.4
Q ss_pred CCCCcccccc--ccccccChHHHHHHHhhhhcCCCCccccccccccccChhhHHHHHh-hhCCCcccCccccccccCccc
Q psy16646 28 SLPPQFHCYV--CKKKYRHKRQLVRHFQVNHTNNYDRVICEICNKEFTHKSSLAEHRV-LHFPAQHKCSLCQQAFKRDKH 104 (159)
Q Consensus 28 ~~~~~~~C~~--c~~~f~~~~~l~~h~~~~~~~~~~~~~c~~c~~~f~~~~~l~~h~~-~h~~k~~~C~~C~~~f~~~~~ 104 (159)
.+++||.|++ |++.+.....|+-|+.-=|... +...-+ +...+.. .-..|||.|+.|++.+.....
T Consensus 345 ~d~KpykCpV~gC~K~YknqnGLKYH~lhGH~~~-~~~~~p----------~p~~~~~F~~~~KPYrCevC~KRYKNlNG 413 (423)
T COG5189 345 KDGKPYKCPVEGCNKKYKNQNGLKYHMLHGHQNQ-KLHENP----------SPEKMNIFSAKDKPYRCEVCDKRYKNLNG 413 (423)
T ss_pred ecCceecCCCCCchhhhccccchhhhhhccccCc-ccCCCC----------CccccccccccCCceeccccchhhccCcc
Confidence 3458999987 9999999999998875311111 111100 0011111 115689999999999999888
Q ss_pred hhhhh
Q psy16646 105 SKGDD 109 (159)
Q Consensus 105 l~~h~ 109 (159)
|+=|+
T Consensus 414 LKYHr 418 (423)
T COG5189 414 LKYHR 418 (423)
T ss_pred ceecc
Confidence 88775
No 45
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=96.14 E-value=0.0016 Score=28.32 Aligned_cols=23 Identities=22% Similarity=0.316 Sum_probs=13.7
Q ss_pred ccCccccccccCccchhhhhhhhh
Q psy16646 90 HKCSLCQQAFKRDKHSKGDDIREE 113 (159)
Q Consensus 90 ~~C~~C~~~f~~~~~l~~h~~~~~ 113 (159)
|.|+.|+.... ...|..|++.++
T Consensus 1 y~C~~C~y~t~-~~~l~~H~~~~H 23 (24)
T PF13909_consen 1 YKCPHCSYSTS-KSNLKRHLKRHH 23 (24)
T ss_dssp EE-SSSS-EES-HHHHHHHHHHHH
T ss_pred CCCCCCCCcCC-HHHHHHHHHhhC
Confidence 45677776666 666777766654
No 46
>PRK04860 hypothetical protein; Provisional
Probab=96.00 E-value=0.004 Score=40.83 Aligned_cols=37 Identities=19% Similarity=0.447 Sum_probs=29.3
Q ss_pred ccccccccccccChhhHHHHHhhh-CCCcccCccccccccCc
Q psy16646 62 RVICEICNKEFTHKSSLAEHRVLH-FPAQHKCSLCQQAFKRD 102 (159)
Q Consensus 62 ~~~c~~c~~~f~~~~~l~~h~~~h-~~k~~~C~~C~~~f~~~ 102 (159)
+|.|. |+. ....+..|.++| ++++|.|..|+..|...
T Consensus 119 ~Y~C~-C~~---~~~~~rrH~ri~~g~~~YrC~~C~~~l~~~ 156 (160)
T PRK04860 119 PYRCK-CQE---HQLTVRRHNRVVRGEAVYRCRRCGETLVFK 156 (160)
T ss_pred EEEcC-CCC---eeCHHHHHHHHhcCCccEECCCCCceeEEe
Confidence 57887 876 566778888888 88889999998887654
No 47
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=95.51 E-value=0.0075 Score=26.35 Aligned_cols=17 Identities=29% Similarity=0.849 Sum_probs=6.3
Q ss_pred cccccccccChHHHHHH
Q psy16646 35 CYVCKKKYRHKRQLVRH 51 (159)
Q Consensus 35 C~~c~~~f~~~~~l~~h 51 (159)
|..|+..|.+...|..|
T Consensus 3 C~~C~~~f~s~~~~~~H 19 (25)
T PF12874_consen 3 CDICNKSFSSENSLRQH 19 (25)
T ss_dssp ETTTTEEESSHHHHHHH
T ss_pred CCCCCCCcCCHHHHHHH
Confidence 33333333333333333
No 48
>KOG2231|consensus
Probab=95.21 E-value=0.039 Score=43.94 Aligned_cols=97 Identities=15% Similarity=0.330 Sum_probs=46.9
Q ss_pred cccccccccChHHHHHHHhhhhcCCCCcccccccccc---cc------ChhhHHHHHhhh--CCC----cccCccccccc
Q psy16646 35 CYVCKKKYRHKRQLVRHFQVNHTNNYDRVICEICNKE---FT------HKSSLAEHRVLH--FPA----QHKCSLCQQAF 99 (159)
Q Consensus 35 C~~c~~~f~~~~~l~~h~~~~~~~~~~~~~c~~c~~~---f~------~~~~l~~h~~~h--~~k----~~~C~~C~~~f 99 (159)
|..| ..|.+...|+.|+...| +.+.|..|-.. |. ....|+.|+... +++ .-.|..|...|
T Consensus 118 ~~~c-~~~~s~~~Lk~H~~~~H----~~~~c~lC~~~~kif~~e~k~Yt~~el~~h~~~gd~d~~s~rGhp~C~~C~~~f 192 (669)
T KOG2231|consen 118 CLHC-TEFKSVENLKNHMRDQH----KLHLCSLCLQNLKIFINERKLYTRAELNLHLMFGDPDDESCRGHPLCKFCHERF 192 (669)
T ss_pred Cccc-cchhHHHHHHHHHHHhh----hhhccccccccceeeeeeeehehHHHHHHHHhcCCCccccccCCccchhhhhhh
Confidence 4444 34456666777765423 23344444321 21 224444454332 111 13466666666
Q ss_pred cCccchhhhhhhhhhhhcccccccc------CccccchhhHHHhhccC
Q psy16646 100 KRDKHSKGDDIREEIEREMKTRNSI------GITVRQNQTNKNHRSGD 141 (159)
Q Consensus 100 ~~~~~l~~h~~~~~~~~~~~~C~~C------~~~f~~~~~l~~H~~~h 141 (159)
.....|.+|++.+| |.|..| +.-|.....|.+|.+-+
T Consensus 193 ld~~el~rH~~~~h-----~~chfC~~~~~~neyy~~~~dLe~HfR~~ 235 (669)
T KOG2231|consen 193 LDDDELYRHLRFDH-----EFCHFCDYKTGQNEYYNDYDDLEEHFRKG 235 (669)
T ss_pred ccHHHHHHhhccce-----eheeecCcccccchhcccchHHHHHhhhc
Confidence 66666666666555 333333 22355555666664443
No 49
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=95.01 E-value=0.017 Score=25.43 Aligned_cols=20 Identities=10% Similarity=0.049 Sum_probs=13.5
Q ss_pred ccccccCccccchhhHHHhhc
Q psy16646 119 KTRNSIGITVRQNQTNKNHRS 139 (159)
Q Consensus 119 ~~C~~C~~~f~~~~~l~~H~~ 139 (159)
..|+.||+.| ....|..|..
T Consensus 3 ~~C~~CgR~F-~~~~l~~H~~ 22 (25)
T PF13913_consen 3 VPCPICGRKF-NPDRLEKHEK 22 (25)
T ss_pred CcCCCCCCEE-CHHHHHHHHH
Confidence 4577788888 4556677754
No 50
>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=94.88 E-value=0.0091 Score=26.74 Aligned_cols=22 Identities=18% Similarity=0.412 Sum_probs=14.3
Q ss_pred ccCccccccccCccchhhhhhh
Q psy16646 90 HKCSLCQQAFKRDKHSKGDDIR 111 (159)
Q Consensus 90 ~~C~~C~~~f~~~~~l~~h~~~ 111 (159)
|.|..|++.|.....|..|++.
T Consensus 2 ~~C~~C~k~f~~~~~~~~H~~s 23 (27)
T PF12171_consen 2 FYCDACDKYFSSENQLKQHMKS 23 (27)
T ss_dssp CBBTTTTBBBSSHHHHHCCTTS
T ss_pred CCcccCCCCcCCHHHHHHHHcc
Confidence 4566777777776666666543
No 51
>KOG2893|consensus
Probab=94.87 E-value=0.0052 Score=42.38 Aligned_cols=47 Identities=21% Similarity=0.459 Sum_probs=27.5
Q ss_pred CccccccccccccChhhHHHHHhhhCCCcccCccccccccCccchhhhhhh
Q psy16646 61 DRVICEICNKEFTHKSSLAEHRVLHFPAQHKCSLCQQAFKRDKHSKGDDIR 111 (159)
Q Consensus 61 ~~~~c~~c~~~f~~~~~l~~h~~~h~~k~~~C~~C~~~f~~~~~l~~h~~~ 111 (159)
++| |=.|...|.+...|.+|++. +.|+|.+|-+.+.....|..|...
T Consensus 10 kpw-cwycnrefddekiliqhqka---khfkchichkkl~sgpglsihcmq 56 (341)
T KOG2893|consen 10 KPW-CWYCNREFDDEKILIQHQKA---KHFKCHICHKKLFSGPGLSIHCMQ 56 (341)
T ss_pred Cce-eeecccccchhhhhhhhhhh---ccceeeeehhhhccCCCceeehhh
Confidence 455 44566666666666666542 356666666666665566655543
No 52
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=94.37 E-value=0.019 Score=43.12 Aligned_cols=63 Identities=17% Similarity=0.104 Sum_probs=52.3
Q ss_pred cccCccccccccCccchhhhhh--hhhhh--hcccccc--ccCccccchhhHHHhhccCCCccccccCcc
Q psy16646 89 QHKCSLCQQAFKRDKHSKGDDI--REEIE--REMKTRN--SIGITVRQNQTNKNHRSGDQKKKTAKQLSM 152 (159)
Q Consensus 89 ~~~C~~C~~~f~~~~~l~~h~~--~~~~~--~~~~~C~--~C~~~f~~~~~l~~H~~~h~~~k~~~~~~~ 152 (159)
++.|..|...|.....|..|.+ .|.++ ++ +.|+ .|++.|.....+..|..+|.+.+++.+...
T Consensus 289 ~~~~~~~~~~~s~~~~l~~~~~~~~h~~~~~~~-~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 357 (467)
T COG5048 289 PIKSKQCNISFSRSSPLTRHLRSVNHSGESLKP-FSCPYSLCGKLFSRNDALKRHILLHTSISPAKEKLL 357 (467)
T ss_pred CCCCccccCCccccccccccccccccccccCCc-eeeeccCCCccccccccccCCcccccCCCccccccc
Confidence 6788889999999999999988 78888 77 8888 799999999888899888888776665543
No 53
>smart00451 ZnF_U1 U1-like zinc finger. Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins.
Probab=93.82 E-value=0.042 Score=26.00 Aligned_cols=23 Identities=13% Similarity=0.107 Sum_probs=19.6
Q ss_pred ccccccCccccchhhHHHhhccC
Q psy16646 119 KTRNSIGITVRQNQTNKNHRSGD 141 (159)
Q Consensus 119 ~~C~~C~~~f~~~~~l~~H~~~h 141 (159)
|.|+.|+..|.....+..|+...
T Consensus 4 ~~C~~C~~~~~~~~~~~~H~~gk 26 (35)
T smart00451 4 FYCKLCNVTFTDEISVEAHLKGK 26 (35)
T ss_pred eEccccCCccCCHHHHHHHHChH
Confidence 77999999999988999997653
No 54
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=92.94 E-value=0.035 Score=38.35 Aligned_cols=44 Identities=16% Similarity=0.205 Sum_probs=25.0
Q ss_pred CcccCccccccccCccchhhhhhhh----------hhhhc----cccccccCccccch
Q psy16646 88 AQHKCSLCQQAFKRDKHSKGDDIRE----------EIERE----MKTRNSIGITVRQN 131 (159)
Q Consensus 88 k~~~C~~C~~~f~~~~~l~~h~~~~----------~~~~~----~~~C~~C~~~f~~~ 131 (159)
+...|+.|++.|.....+....+.- .+..| +..|+.||..|...
T Consensus 4 k~~~CPvC~~~F~~~~vrs~~~r~~~~d~D~~~~Y~~vnP~~Y~V~vCP~CgyA~~~~ 61 (214)
T PF09986_consen 4 KKITCPVCGKEFKTKKVRSGKIRVIRRDSDFCPRYKGVNPLFYEVWVCPHCGYAAFEE 61 (214)
T ss_pred CceECCCCCCeeeeeEEEcCCceEeeecCCCccccCCCCCeeeeEEECCCCCCccccc
Confidence 4566777777776654444444321 11111 16789999887644
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=92.93 E-value=0.067 Score=25.21 Aligned_cols=8 Identities=13% Similarity=-0.118 Sum_probs=4.6
Q ss_pred ccccccCc
Q psy16646 119 KTRNSIGI 126 (159)
Q Consensus 119 ~~C~~C~~ 126 (159)
+.|+.||.
T Consensus 18 ~~CP~Cg~ 25 (33)
T cd00350 18 WVCPVCGA 25 (33)
T ss_pred CcCcCCCC
Confidence 55666654
No 56
>KOG2893|consensus
Probab=92.81 E-value=0.047 Score=37.83 Aligned_cols=46 Identities=24% Similarity=0.689 Sum_probs=38.1
Q ss_pred ccccccccccChHHHHHHHhhhhcCCCCccccccccccccChhhHHHH-Hhhh
Q psy16646 34 HCYVCKKKYRHKRQLVRHFQVNHTNNYDRVICEICNKEFTHKSSLAEH-RVLH 85 (159)
Q Consensus 34 ~C~~c~~~f~~~~~l~~h~~~~~~~~~~~~~c~~c~~~f~~~~~l~~h-~~~h 85 (159)
+|=+|++-|.....|.+|++. +.|.|.+|.+.+.+-..|..| +..|
T Consensus 12 wcwycnrefddekiliqhqka------khfkchichkkl~sgpglsihcmqvh 58 (341)
T KOG2893|consen 12 WCWYCNREFDDEKILIQHQKA------KHFKCHICHKKLFSGPGLSIHCMQVH 58 (341)
T ss_pred eeeecccccchhhhhhhhhhh------ccceeeeehhhhccCCCceeehhhhh
Confidence 677899999999999999877 789999999987777777777 3444
No 57
>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=92.58 E-value=0.12 Score=24.40 Aligned_cols=23 Identities=17% Similarity=0.515 Sum_probs=14.5
Q ss_pred ccccccccccccChHHHHHHHhh
Q psy16646 32 QFHCYVCKKKYRHKRQLVRHFQV 54 (159)
Q Consensus 32 ~~~C~~c~~~f~~~~~l~~h~~~ 54 (159)
+|.|..|+..|.....+..|+..
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~g 25 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLKG 25 (35)
T ss_pred CeEccccCCccCCHHHHHHHHCh
Confidence 45666677766666666666543
No 58
>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=92.22 E-value=0.11 Score=31.77 Aligned_cols=25 Identities=16% Similarity=0.209 Sum_probs=22.6
Q ss_pred ccc----cccCccccchhhHHHhhccCCC
Q psy16646 119 KTR----NSIGITVRQNQTNKNHRSGDQK 143 (159)
Q Consensus 119 ~~C----~~C~~~f~~~~~l~~H~~~h~~ 143 (159)
|.| ..|++.+.+...++.|++.++|
T Consensus 81 ~~C~~~~~~C~y~~~~~~~m~~H~~~~Hg 109 (109)
T PF12013_consen 81 YRCQCDPPHCGYITRSKKTMRKHWRKEHG 109 (109)
T ss_pred eeeecCCCCCCcEeccHHHHHHHHHHhcC
Confidence 999 9999999999999999887654
No 59
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=91.40 E-value=0.36 Score=29.67 Aligned_cols=49 Identities=18% Similarity=0.012 Sum_probs=31.4
Q ss_pred cCccccccccCccchhhhhhhhhhhhccccccccCccccchhhHHHhhccCC
Q psy16646 91 KCSLCQQAFKRDKHSKGDDIREEIEREMKTRNSIGITVRQNQTNKNHRSGDQ 142 (159)
Q Consensus 91 ~C~~C~~~f~~~~~l~~h~~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~h~ 142 (159)
.|..|...|........- ...+...|.|+.|..-|--.-..-.|...|.
T Consensus 57 ~C~~C~~~f~~~~~~~~~---~~~~~~~y~C~~C~~~FC~dCD~fiHe~Lh~ 105 (112)
T TIGR00622 57 FCFGCQGPFPKPPVSPFD---ELKDSHRYVCAVCKNVFCVDCDVFVHESLHC 105 (112)
T ss_pred cccCcCCCCCCccccccc---ccccccceeCCCCCCccccccchhhhhhccC
Confidence 388888888764321100 0112223889999999888877778877776
No 60
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=91.34 E-value=0.077 Score=25.73 Aligned_cols=34 Identities=21% Similarity=0.461 Sum_probs=22.6
Q ss_pred ccCCCCCCCCCCCCCcccCCCCCcccccccccccc
Q psy16646 9 VKNPNAKKRYRPYVPRVDSSLPPQFHCYVCKKKYR 43 (159)
Q Consensus 9 ~~~~~~~~~~~~~~~~~~h~~~~~~~C~~c~~~f~ 43 (159)
..||+|...|.....+.. .+.....|+.|+..|.
T Consensus 3 i~CP~C~~~f~v~~~~l~-~~~~~vrC~~C~~~f~ 36 (37)
T PF13719_consen 3 ITCPNCQTRFRVPDDKLP-AGGRKVRCPKCGHVFR 36 (37)
T ss_pred EECCCCCceEEcCHHHcc-cCCcEEECCCCCcEee
Confidence 468888888886665422 4444678888877663
No 61
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=91.08 E-value=0.068 Score=28.18 Aligned_cols=20 Identities=15% Similarity=0.190 Sum_probs=11.2
Q ss_pred ccccccCccccchhhHHHhh
Q psy16646 119 KTRNSIGITVRQNQTNKNHR 138 (159)
Q Consensus 119 ~~C~~C~~~f~~~~~l~~H~ 138 (159)
+.|+.||..|....++..|.
T Consensus 18 lrCPRC~~~FR~~K~Y~RHV 37 (65)
T COG4049 18 LRCPRCGMVFRRRKDYIRHV 37 (65)
T ss_pred eeCCchhHHHHHhHHHHHHh
Confidence 55555555555555555553
No 62
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=90.50 E-value=0.11 Score=39.09 Aligned_cols=59 Identities=22% Similarity=0.347 Sum_probs=51.8
Q ss_pred ccccccccccccChhhHHHHHh--hh-CC--CcccCc--cccccccCccchhhhhhhhhhhhccccc
Q psy16646 62 RVICEICNKEFTHKSSLAEHRV--LH-FP--AQHKCS--LCQQAFKRDKHSKGDDIREEIEREMKTR 121 (159)
Q Consensus 62 ~~~c~~c~~~f~~~~~l~~h~~--~h-~~--k~~~C~--~C~~~f~~~~~l~~h~~~~~~~~~~~~C 121 (159)
++.|..|...|.....+..|.+ .| ++ +++.|. .|++.|.+...+..|...+++..+ +.+
T Consensus 289 ~~~~~~~~~~~s~~~~l~~~~~~~~h~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~ 354 (467)
T COG5048 289 PIKSKQCNISFSRSSPLTRHLRSVNHSGESLKPFSCPYSLCGKLFSRNDALKRHILLHTSISP-AKE 354 (467)
T ss_pred CCCCccccCCccccccccccccccccccccCCceeeeccCCCccccccccccCCcccccCCCc-ccc
Confidence 5778889999999999999988 78 77 899999 799999999999999999988876 555
No 63
>PF12907 zf-met2: Zinc-binding
Probab=90.42 E-value=0.097 Score=25.85 Aligned_cols=35 Identities=17% Similarity=0.051 Sum_probs=24.1
Q ss_pred ccccccCccccc---hhhHHHhhc-cCCCccccccCccc
Q psy16646 119 KTRNSIGITVRQ---NQTNKNHRS-GDQKKKTAKQLSML 153 (159)
Q Consensus 119 ~~C~~C~~~f~~---~~~l~~H~~-~h~~~k~~~~~~~~ 153 (159)
+.|..|-..|.. ...|..|.. -|.+....+|++.|
T Consensus 2 i~C~iC~qtF~~t~~~~~L~eH~enKHpK~~~~~CFP~l 40 (40)
T PF12907_consen 2 IICKICRQTFMQTTNEPQLKEHAENKHPKNTFEECFPNL 40 (40)
T ss_pred cCcHHhhHHHHhcCCHHHHHHHHHccCCCCCHHHcCCCC
Confidence 568888866644 456888844 57776677777764
No 64
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=90.40 E-value=0.084 Score=27.83 Aligned_cols=29 Identities=17% Similarity=0.206 Sum_probs=23.4
Q ss_pred CCCcccCccccccccCccchhhhhhhhhh
Q psy16646 86 FPAQHKCSLCQQAFKRDKHSKGDDIREEI 114 (159)
Q Consensus 86 ~~k~~~C~~C~~~f~~~~~l~~h~~~~~~ 114 (159)
||.-+.|+.||..|....+..+|+...|+
T Consensus 14 GE~~lrCPRC~~~FR~~K~Y~RHVNKaH~ 42 (65)
T COG4049 14 GEEFLRCPRCGMVFRRRKDYIRHVNKAHG 42 (65)
T ss_pred CceeeeCCchhHHHHHhHHHHHHhhHHhh
Confidence 56667899999999888888888876665
No 65
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=90.33 E-value=0.12 Score=24.85 Aligned_cols=33 Identities=15% Similarity=0.424 Sum_probs=21.7
Q ss_pred ccCCCCCCCCCCCCCcccCCCCCccccccccccc
Q psy16646 9 VKNPNAKKRYRPYVPRVDSSLPPQFHCYVCKKKY 42 (159)
Q Consensus 9 ~~~~~~~~~~~~~~~~~~h~~~~~~~C~~c~~~f 42 (159)
..||+|..+|...+.+.. .......|+.|+..|
T Consensus 3 i~Cp~C~~~y~i~d~~ip-~~g~~v~C~~C~~~f 35 (36)
T PF13717_consen 3 ITCPNCQAKYEIDDEKIP-PKGRKVRCSKCGHVF 35 (36)
T ss_pred EECCCCCCEEeCCHHHCC-CCCcEEECCCCCCEe
Confidence 457888888887666533 333457787777665
No 66
>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain. This domain contains a CXXCX(19)CXXC motif suggestive of both zinc fingers and thioredoxin, usually found at the N-terminus of prokaryotic proteins. One partially characterized gene, agmX, is among a large set in Myxococcus whose interruption affects adventurous gliding motility.
Probab=89.58 E-value=0.099 Score=25.37 Aligned_cols=33 Identities=18% Similarity=0.435 Sum_probs=17.9
Q ss_pred ccCCCCCCCCCCCCCcccCCCCCccccccccccc
Q psy16646 9 VKNPNAKKRYRPYVPRVDSSLPPQFHCYVCKKKY 42 (159)
Q Consensus 9 ~~~~~~~~~~~~~~~~~~h~~~~~~~C~~c~~~f 42 (159)
+.||+|...+........-.+ ....|+.|+..|
T Consensus 3 ~~CP~C~~~~~v~~~~~~~~~-~~v~C~~C~~~~ 35 (38)
T TIGR02098 3 IQCPNCKTSFRVVDSQLGANG-GKVRCGKCGHVW 35 (38)
T ss_pred EECCCCCCEEEeCHHHcCCCC-CEEECCCCCCEE
Confidence 457777777665443322222 245677776655
No 67
>PF03811 Zn_Tnp_IS1: InsA N-terminal domain; InterPro: IPR003220 Insertion elements are mobile elements in DNA, usually encoding proteins required for transposition, for example transposases. Protein InsA is absolutely required for transposition of insertion element 1. This entry represents a short zinc binding domain found in IS1 InsA family protein. It is found at the N terminus of the protein and may be a DNA-binding domain.; GO: 0006313 transposition, DNA-mediated
Probab=89.00 E-value=0.37 Score=23.21 Aligned_cols=35 Identities=20% Similarity=0.261 Sum_probs=27.5
Q ss_pred hhhhcccCCCCCCCCCCCCCcccCCCCCccccccc
Q psy16646 4 MKKKSVKNPNAKKRYRPYVPRVDSSLPPQFHCYVC 38 (159)
Q Consensus 4 ~~~~~~~~~~~~~~~~~~~~~~~h~~~~~~~C~~c 38 (159)
|-+..+.||.|........+=....|...|.|..|
T Consensus 1 Ma~i~v~CP~C~s~~~v~k~G~~~~G~qryrC~~C 35 (36)
T PF03811_consen 1 MAKIDVHCPRCQSTEGVKKNGKSPSGHQRYRCKDC 35 (36)
T ss_pred CCcEeeeCCCCCCCCcceeCCCCCCCCEeEecCcC
Confidence 45667889999888877777777777778888776
No 68
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=88.68 E-value=0.16 Score=33.19 Aligned_cols=12 Identities=25% Similarity=0.786 Sum_probs=5.8
Q ss_pred ccCccccccccC
Q psy16646 90 HKCSLCQQAFKR 101 (159)
Q Consensus 90 ~~C~~C~~~f~~ 101 (159)
+.|+.||..|..
T Consensus 29 ~~c~~c~~~f~~ 40 (154)
T PRK00464 29 RECLACGKRFTT 40 (154)
T ss_pred eeccccCCcceE
Confidence 445555555444
No 69
>KOG1146|consensus
Probab=87.71 E-value=0.21 Score=42.75 Aligned_cols=90 Identities=13% Similarity=0.126 Sum_probs=55.3
Q ss_pred cccccccccccChHHHHHHHhhhhcCCCCccccccccccccChhhHHHHHhhhCCCcccCccccccccCccchhhhhhhh
Q psy16646 33 FHCYVCKKKYRHKRQLVRHFQVNHTNNYDRVICEICNKEFTHKSSLAEHRVLHFPAQHKCSLCQQAFKRDKHSKGDDIRE 112 (159)
Q Consensus 33 ~~C~~c~~~f~~~~~l~~h~~~~~~~~~~~~~c~~c~~~f~~~~~l~~h~~~h~~k~~~C~~C~~~f~~~~~l~~h~~~~ 112 (159)
+.|..|+..+.....+. ++-. . .+|.|..|...|.....|..|++. |-+.+.......-+.-.+
T Consensus 1261 ~~c~~~~~~~~~~~~~~-~l~~----~-~~~~~~~~~~~~~~~~~l~~~~~k----------~~~~~~~~~~~~~~~l~~ 1324 (1406)
T KOG1146|consen 1261 GECGAVDELLTPSFGIS-TLDV----T-HRYLCRQCKMAFDGEAPLTAHQRK----------FCFAGRGSGGSMPPPLRV 1324 (1406)
T ss_pred chhhhccccccCcccee-eccc----c-hhHHHHHHHhhhcchhHHHHHHHH----------HHhccCccccCCCCcccC
Confidence 66777777776655555 4332 2 567888888888888888777622 222333333333333333
Q ss_pred hhhhccccccccCccccchhhHHHhhcc
Q psy16646 113 EIEREMKTRNSIGITVRQNQTNKNHRSG 140 (159)
Q Consensus 113 ~~~~~~~~C~~C~~~f~~~~~l~~H~~~ 140 (159)
-.... | |..|...|.....|..|.++
T Consensus 1325 ~d~~~-~-c~~c~~~~~~~~alqihm~~ 1350 (1406)
T KOG1146|consen 1325 PDCTY-H-CLACEVLLSGREALQIHMRS 1350 (1406)
T ss_pred ccccc-c-chHHHhhcchhHHHHHHHHH
Confidence 33333 5 88888888888888888665
No 70
>KOG2186|consensus
Probab=86.36 E-value=0.32 Score=34.09 Aligned_cols=52 Identities=17% Similarity=0.336 Sum_probs=32.8
Q ss_pred cccccccccccChhhHHHHHhhhCCCcccCccccccccCccchhhhhhhhhhhh
Q psy16646 63 VICEICNKEFTHKSSLAEHRVLHFPAQHKCSLCQQAFKRDKHSKGDDIREEIER 116 (159)
Q Consensus 63 ~~c~~c~~~f~~~~~l~~h~~~h~~k~~~C~~C~~~f~~~~~l~~h~~~~~~~~ 116 (159)
|.|..||.+..- ..+..|+..-....|.|-.||+.|.+ .+...|..--+...
T Consensus 4 FtCnvCgEsvKK-p~vekH~srCrn~~fSCIDC~k~F~~-~sYknH~kCITEaQ 55 (276)
T KOG2186|consen 4 FTCNVCGESVKK-PQVEKHMSRCRNAYFSCIDCGKTFER-VSYKNHTKCITEAQ 55 (276)
T ss_pred Eehhhhhhhccc-cchHHHHHhccCCeeEEeeccccccc-chhhhhhhhcchHH
Confidence 678888876654 33555654432367788888888887 55566766444333
No 71
>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=86.14 E-value=0.33 Score=23.04 Aligned_cols=8 Identities=13% Similarity=0.048 Sum_probs=4.3
Q ss_pred ccccccCc
Q psy16646 119 KTRNSIGI 126 (159)
Q Consensus 119 ~~C~~C~~ 126 (159)
..|+.||.
T Consensus 19 ~~CP~Cg~ 26 (34)
T cd00729 19 EKCPICGA 26 (34)
T ss_pred CcCcCCCC
Confidence 45555554
No 72
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=84.86 E-value=0.5 Score=23.86 Aligned_cols=11 Identities=18% Similarity=0.452 Sum_probs=6.3
Q ss_pred ccCcccccccc
Q psy16646 90 HKCSLCQQAFK 100 (159)
Q Consensus 90 ~~C~~C~~~f~ 100 (159)
|.|..||..|.
T Consensus 3 Y~C~~Cg~~~~ 13 (44)
T smart00659 3 YICGECGRENE 13 (44)
T ss_pred EECCCCCCEee
Confidence 55666665544
No 73
>KOG4173|consensus
Probab=84.52 E-value=0.4 Score=32.63 Aligned_cols=77 Identities=17% Similarity=0.324 Sum_probs=52.0
Q ss_pred ccccc--ccccccChhhHHHHHhh-hCCCcccCccccccccCccchhhhhhhhhh---------hhccccc--cccCccc
Q psy16646 63 VICEI--CNKEFTHKSSLAEHRVL-HFPAQHKCSLCQQAFKRDKHSKGDDIREEI---------EREMKTR--NSIGITV 128 (159)
Q Consensus 63 ~~c~~--c~~~f~~~~~l~~h~~~-h~~k~~~C~~C~~~f~~~~~l~~h~~~~~~---------~~~~~~C--~~C~~~f 128 (159)
+.|.. |...|.+...+..|..+ |+ -.|..|.+.|.+.--|..|+.-+|. ..+.|.| ..|+..|
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 FACQVAGCCQVFDALDDYEHHYHTLHG---NSCSFCKRAFPTGHLLDAHILEWHDSLFQALVERGQDMYQCLVEGCTEKF 156 (253)
T ss_pred ccccccchHHHHhhhhhHHHhhhhccc---chhHHHHHhCCchhhhhHHHHHHHHHHHHHHHHcCccHHHHHHHhhhhhh
Confidence 45665 66677776666666433 32 3688898999888888888754332 2456888 7899999
Q ss_pred cchhhHHHh-hccCC
Q psy16646 129 RQNQTNKNH-RSGDQ 142 (159)
Q Consensus 129 ~~~~~l~~H-~~~h~ 142 (159)
.+...-..| +++|.
T Consensus 157 kT~r~RkdH~I~~Hk 171 (253)
T KOG4173|consen 157 KTSRDRKDHMIRMHK 171 (253)
T ss_pred hhhhhhhhHHHHhcc
Confidence 888777777 44443
No 74
>smart00834 CxxC_CXXC_SSSS Putative regulatory protein. CxxC_CXXC_SSSS represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=84.21 E-value=0.36 Score=23.63 Aligned_cols=30 Identities=13% Similarity=0.256 Sum_probs=15.8
Q ss_pred cccCCCCCCCCCCCCCcccCCCCCccccccccc
Q psy16646 8 SVKNPNAKKRYRPYVPRVDSSLPPQFHCYVCKK 40 (159)
Q Consensus 8 ~~~~~~~~~~~~~~~~~~~h~~~~~~~C~~c~~ 40 (159)
.+.|+.|+..|........ .....|+.||.
T Consensus 5 ~y~C~~Cg~~fe~~~~~~~---~~~~~CP~Cg~ 34 (41)
T smart00834 5 EYRCEDCGHTFEVLQKISD---DPLATCPECGG 34 (41)
T ss_pred EEEcCCCCCEEEEEEecCC---CCCCCCCCCCC
Confidence 3566666666664433322 33445666664
No 75
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=84.12 E-value=0.45 Score=26.81 Aligned_cols=42 Identities=21% Similarity=0.267 Sum_probs=21.5
Q ss_pred ccCccccccccCccchhhhhhhhhhhhcccccc--ccCccccchhhH
Q psy16646 90 HKCSLCQQAFKRDKHSKGDDIREEIEREMKTRN--SIGITVRQNQTN 134 (159)
Q Consensus 90 ~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~~C~--~C~~~f~~~~~l 134 (159)
+.|+.||....-..+-.... ...++ ++.|. +||.+|....++
T Consensus 2 m~CP~Cg~~a~irtSr~~s~--~~~~~-Y~qC~N~eCg~tF~t~es~ 45 (72)
T PRK09678 2 FHCPLCQHAAHARTSRYITD--TTKER-YHQCQNVNCSATFITYESV 45 (72)
T ss_pred ccCCCCCCccEEEEChhcCh--hhhee-eeecCCCCCCCEEEEEEEE
Confidence 35777775543222222111 13333 37776 788888766554
No 76
>PF14353 CpXC: CpXC protein
Probab=83.75 E-value=0.43 Score=30.06 Aligned_cols=21 Identities=10% Similarity=0.018 Sum_probs=11.8
Q ss_pred ccCCCCCCCCCCCCCcccCCC
Q psy16646 9 VKNPNAKKRYRPYVPRVDSSL 29 (159)
Q Consensus 9 ~~~~~~~~~~~~~~~~~~h~~ 29 (159)
..||+|+..|.......+...
T Consensus 2 itCP~C~~~~~~~v~~~I~~~ 22 (128)
T PF14353_consen 2 ITCPHCGHEFEFEVWTSINAD 22 (128)
T ss_pred cCCCCCCCeeEEEEEeEEcCc
Confidence 357777777665444444433
No 77
>PF01096 TFIIS_C: Transcription factor S-II (TFIIS); InterPro: IPR001222 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIs (TFIIS). In eukaryotes the initiation of transcription of protein encoding genes by polymerase II (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least eight different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, -IIH and -IIS []. During mRNA elongation, Pol II can encounter DNA sequences that cause reverse movement of the enzyme. Such backtracking involves extrusion of the RNA 3'-end into the pore, and can lead to transcriptional arrest. Escape from arrest requires cleavage of the extruded RNA with the help of TFIIS, which induces mRNA cleavage by enhancing the intrinsic nuclease activity of RNA polymerase (Pol) II, past template-encoded pause sites []. TFIIS extends from the polymerase surface via a pore to the internal active site. Two essential and invariant acidic residues in a TFIIS loop complement the Pol II active site and could position a metal ion and a water molecule for hydrolytic RNA cleavage. TFIIS also induces extensive structural changes in Pol II that would realign nucleic acids in the active centre. TFIIS is a protein of about 300 amino acids. It contains three regions: a variable N-terminal domain not required for TFIIS activity; a conserved central domain required for Pol II binding; and a conserved C-terminal C4-type zinc finger essential for RNA cleavage. The zinc finger folds in a conformation termed a zinc ribbon [] characterised by a three-stranded antiparallel beta-sheet and two beta-hairpins. A backbone model for Pol II-TFIIS complex was obtained from X-ray analysis. It shows that a beta hairpin protrudes from the zinc finger and complements the pol II active site []. Some viral proteins also contain the TFIIS zinc ribbon C-terminal domain. The Vaccinia virus protein, unlike its eukaryotic homologue, is an integral RNA polymerase subunit rather than a readily separable transcription factor []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding, 0006351 transcription, DNA-dependent; PDB: 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I 3I4M_I ....
Probab=83.70 E-value=0.22 Score=24.42 Aligned_cols=33 Identities=15% Similarity=0.357 Sum_probs=17.1
Q ss_pred cCCCCCCCCCCCCCcccCCCCCc----cccccccccc
Q psy16646 10 KNPNAKKRYRPYVPRVDSSLPPQ----FHCYVCKKKY 42 (159)
Q Consensus 10 ~~~~~~~~~~~~~~~~~h~~~~~----~~C~~c~~~f 42 (159)
+||+|+.+-.......+..++.+ |.|..|+..|
T Consensus 2 ~Cp~Cg~~~a~~~~~Q~rsaDE~~T~fy~C~~C~~~w 38 (39)
T PF01096_consen 2 KCPKCGHNEAVFFQIQTRSADEPMTLFYVCCNCGHRW 38 (39)
T ss_dssp --SSS-SSEEEEEEESSSSSSSSSEEEEEESSSTEEE
T ss_pred CCcCCCCCeEEEEEeeccCCCCCCeEEEEeCCCCCee
Confidence 57777776654444444444444 6677777654
No 78
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=83.58 E-value=0.33 Score=31.42 Aligned_cols=14 Identities=29% Similarity=0.816 Sum_probs=8.3
Q ss_pred CccccccccccccC
Q psy16646 31 PQFHCYVCKKKYRH 44 (159)
Q Consensus 31 ~~~~C~~c~~~f~~ 44 (159)
.-|.|+.|+..|..
T Consensus 98 ~~Y~Cp~C~~~y~~ 111 (147)
T smart00531 98 AYYKCPNCQSKYTF 111 (147)
T ss_pred cEEECcCCCCEeeH
Confidence 34666666666653
No 79
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=83.52 E-value=0.97 Score=33.36 Aligned_cols=12 Identities=8% Similarity=-0.047 Sum_probs=7.3
Q ss_pred cccchhhHHHhh
Q psy16646 127 TVRQNQTNKNHR 138 (159)
Q Consensus 127 ~f~~~~~l~~H~ 138 (159)
.|.....|..|+
T Consensus 290 vf~~~~el~~h~ 301 (493)
T COG5236 290 VFPYHTELLEHL 301 (493)
T ss_pred EeccHHHHHHHH
Confidence 366666666663
No 80
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=82.32 E-value=0.64 Score=22.92 Aligned_cols=33 Identities=15% Similarity=0.377 Sum_probs=16.4
Q ss_pred cCCCCCCCCCCCCCcccCCCCCc----cccccccccc
Q psy16646 10 KNPNAKKRYRPYVPRVDSSLPPQ----FHCYVCKKKY 42 (159)
Q Consensus 10 ~~~~~~~~~~~~~~~~~h~~~~~----~~C~~c~~~f 42 (159)
+||+|+.+-.....+.+...+.+ |.|..|+..|
T Consensus 2 ~Cp~C~~~~a~~~q~Q~RsaDE~mT~fy~C~~C~~~w 38 (40)
T smart00440 2 PCPKCGNREATFFQLQTRSADEPMTVFYVCTKCGHRW 38 (40)
T ss_pred cCCCCCCCeEEEEEEcccCCCCCCeEEEEeCCCCCEe
Confidence 57777655443333333333333 5666666544
No 81
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=82.22 E-value=0.71 Score=23.42 Aligned_cols=29 Identities=10% Similarity=0.107 Sum_probs=16.2
Q ss_pred cccCCCCCCCCCCCCCcccCCCCCccccccccccc
Q psy16646 8 SVKNPNAKKRYRPYVPRVDSSLPPQFHCYVCKKKY 42 (159)
Q Consensus 8 ~~~~~~~~~~~~~~~~~~~h~~~~~~~C~~c~~~f 42 (159)
.+.||+|+..+....... ...|+.||..+
T Consensus 3 ~y~C~~CG~~~~~~~~~~------~~~Cp~CG~~~ 31 (46)
T PRK00398 3 EYKCARCGREVELDEYGT------GVRCPYCGYRI 31 (46)
T ss_pred EEECCCCCCEEEECCCCC------ceECCCCCCeE
Confidence 466777776665432221 46677776543
No 82
>KOG1146|consensus
Probab=82.11 E-value=0.37 Score=41.40 Aligned_cols=25 Identities=8% Similarity=0.062 Sum_probs=19.4
Q ss_pred CCcccCccccccccCccchhhhhhh
Q psy16646 87 PAQHKCSLCQQAFKRDKHSKGDDIR 111 (159)
Q Consensus 87 ~k~~~C~~C~~~f~~~~~l~~h~~~ 111 (159)
.++|.|..|...+.....|.+|++.
T Consensus 516 ~~p~~C~~C~~stttng~LsihlqS 540 (1406)
T KOG1146|consen 516 GKPYPCRACNYSTTTNGNLSIHLQS 540 (1406)
T ss_pred CCcccceeeeeeeecchHHHHHHHH
Confidence 3578888888888888888888753
No 83
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=81.90 E-value=0.85 Score=24.51 Aligned_cols=10 Identities=20% Similarity=0.624 Sum_probs=5.4
Q ss_pred CCcccCcccc
Q psy16646 87 PAQHKCSLCQ 96 (159)
Q Consensus 87 ~k~~~C~~C~ 96 (159)
..+|.|+.||
T Consensus 48 g~~Y~Cp~CG 57 (61)
T COG2888 48 GNPYRCPKCG 57 (61)
T ss_pred CCceECCCcC
Confidence 3455555555
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=80.88 E-value=0.59 Score=24.30 Aligned_cols=29 Identities=17% Similarity=0.305 Sum_probs=15.7
Q ss_pred ccCCCCCCCCCCCCCcccCCCCCccccccccc
Q psy16646 9 VKNPNAKKRYRPYVPRVDSSLPPQFHCYVCKK 40 (159)
Q Consensus 9 ~~~~~~~~~~~~~~~~~~h~~~~~~~C~~c~~ 40 (159)
|.|+.|+..|..+..... +....|+.||.
T Consensus 6 y~C~~Cg~~fe~~~~~~~---~~~~~CP~Cg~ 34 (52)
T TIGR02605 6 YRCTACGHRFEVLQKMSD---DPLATCPECGG 34 (52)
T ss_pred EEeCCCCCEeEEEEecCC---CCCCCCCCCCC
Confidence 566666666665433322 34445666664
No 85
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=80.88 E-value=0.67 Score=23.95 Aligned_cols=11 Identities=27% Similarity=0.763 Sum_probs=6.2
Q ss_pred cccCccccccc
Q psy16646 89 QHKCSLCQQAF 99 (159)
Q Consensus 89 ~~~C~~C~~~f 99 (159)
.|.|..||+.|
T Consensus 6 ~Y~C~~Cg~~~ 16 (49)
T COG1996 6 EYKCARCGREV 16 (49)
T ss_pred EEEhhhcCCee
Confidence 35566666555
No 86
>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=80.72 E-value=1.2 Score=27.34 Aligned_cols=29 Identities=21% Similarity=0.565 Sum_probs=16.3
Q ss_pred ccccccccccChhhHHHHHhhhCCCcccCccccccccCc
Q psy16646 64 ICEICNKEFTHKSSLAEHRVLHFPAQHKCSLCQQAFKRD 102 (159)
Q Consensus 64 ~c~~c~~~f~~~~~l~~h~~~h~~k~~~C~~C~~~f~~~ 102 (159)
.|..||..|-... -.|..|++||..|...
T Consensus 11 ~Cp~CG~kFYDLn----------k~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 11 TCPSCGAKFYDLN----------KDPIVCPKCGTEFPPE 39 (108)
T ss_pred cCCCCcchhccCC----------CCCccCCCCCCccCcc
Confidence 5666666553311 1366677777666655
No 87
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=79.86 E-value=1 Score=29.75 Aligned_cols=8 Identities=25% Similarity=0.841 Sum_probs=4.9
Q ss_pred cccCcccc
Q psy16646 89 QHKCSLCQ 96 (159)
Q Consensus 89 ~~~C~~C~ 96 (159)
.|.|++||
T Consensus 134 ~~vC~vCG 141 (166)
T COG1592 134 VWVCPVCG 141 (166)
T ss_pred EEEcCCCC
Confidence 46666665
No 88
>KOG3408|consensus
Probab=79.76 E-value=0.48 Score=29.36 Aligned_cols=36 Identities=14% Similarity=0.012 Sum_probs=19.9
Q ss_pred ccccccCccccchhhHHHhhccCCCccccccCccch
Q psy16646 119 KTRNSIGITVRQNQTNKNHRSGDQKKKTAKQLSMLN 154 (159)
Q Consensus 119 ~~C~~C~~~f~~~~~l~~H~~~h~~~k~~~~~~~~~ 154 (159)
|.|-.|.+-|.+...|..|.++-..++..+.+.-.|
T Consensus 58 fyCi~CaRyFi~~~~l~~H~ktK~HKrRvK~l~~~P 93 (129)
T KOG3408|consen 58 FYCIECARYFIDAKALKTHFKTKVHKRRVKELREVP 93 (129)
T ss_pred eehhhhhhhhcchHHHHHHHhccHHHHHHHhcccCC
Confidence 556666666666666666665544444444444333
No 89
>PHA02998 RNA polymerase subunit; Provisional
Probab=79.23 E-value=1.1 Score=29.90 Aligned_cols=37 Identities=19% Similarity=0.321 Sum_probs=23.3
Q ss_pred hcccCCCCCCCCCCCCCcccCCCCCc----ccccccccccc
Q psy16646 7 KSVKNPNAKKRYRPYVPRVDSSLPPQ----FHCYVCKKKYR 43 (159)
Q Consensus 7 ~~~~~~~~~~~~~~~~~~~~h~~~~~----~~C~~c~~~f~ 43 (159)
...+||.|+..-.....+.+...+.| |.|..||..|.
T Consensus 142 t~v~CPkCg~~~A~f~qlQTRSADEPmT~FYkC~~CG~~wk 182 (195)
T PHA02998 142 YNTPCPNCKSKNTTPMMIQTRAADEPPLVRHACRDCKKHFK 182 (195)
T ss_pred cCCCCCCCCCCceEEEEEeeccCCCCceEEEEcCCCCCccC
Confidence 45677777766665555555555544 56777776654
No 90
>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=78.77 E-value=0.65 Score=30.50 Aligned_cols=31 Identities=13% Similarity=0.054 Sum_probs=20.6
Q ss_pred CcccCccccccccCccchhhhhhhhhhhhccccccccCccc
Q psy16646 88 AQHKCSLCQQAFKRDKHSKGDDIREEIEREMKTRNSIGITV 128 (159)
Q Consensus 88 k~~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~~C~~C~~~f 128 (159)
.-|.|+.|+..|+....+. -. |.|+.||...
T Consensus 108 ~~Y~Cp~c~~r~tf~eA~~---------~~-F~Cp~Cg~~L 138 (158)
T TIGR00373 108 MFFICPNMCVRFTFNEAME---------LN-FTCPRCGAML 138 (158)
T ss_pred CeEECCCCCcEeeHHHHHH---------cC-CcCCCCCCEe
Confidence 3577888887777665543 13 8888888764
No 91
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=78.48 E-value=0.66 Score=31.12 Aligned_cols=32 Identities=16% Similarity=0.200 Sum_probs=21.2
Q ss_pred cccCccccccccCccchhhhhhhhhhhhccccccccCccccc
Q psy16646 89 QHKCSLCQQAFKRDKHSKGDDIREEIEREMKTRNSIGITVRQ 130 (159)
Q Consensus 89 ~~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~~C~~C~~~f~~ 130 (159)
-|.|+.|+..|+....+. -. |.|+.||-....
T Consensus 117 ~Y~Cp~C~~rytf~eA~~---------~~-F~Cp~Cg~~L~~ 148 (178)
T PRK06266 117 FFFCPNCHIRFTFDEAME---------YG-FRCPQCGEMLEE 148 (178)
T ss_pred EEECCCCCcEEeHHHHhh---------cC-CcCCCCCCCCee
Confidence 577888887777664432 23 888888876433
No 92
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=78.27 E-value=0.98 Score=26.31 Aligned_cols=12 Identities=33% Similarity=0.728 Sum_probs=5.7
Q ss_pred cccCcccccccc
Q psy16646 89 QHKCSLCQQAFK 100 (159)
Q Consensus 89 ~~~C~~C~~~f~ 100 (159)
-|.|..||..|.
T Consensus 53 IW~C~kCg~~fA 64 (89)
T COG1997 53 IWKCRKCGAKFA 64 (89)
T ss_pred eEEcCCCCCeec
Confidence 344555544443
No 93
>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=78.06 E-value=0.65 Score=23.13 Aligned_cols=12 Identities=0% Similarity=0.122 Sum_probs=5.6
Q ss_pred ccCCCCCCCCCC
Q psy16646 9 VKNPNAKKRYRP 20 (159)
Q Consensus 9 ~~~~~~~~~~~~ 20 (159)
|.|+.|+..|..
T Consensus 6 y~C~~Cg~~fe~ 17 (42)
T PF09723_consen 6 YRCEECGHEFEV 17 (42)
T ss_pred EEeCCCCCEEEE
Confidence 344444444443
No 94
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=74.73 E-value=1.6 Score=23.49 Aligned_cols=8 Identities=25% Similarity=0.165 Sum_probs=4.3
Q ss_pred ccccccCc
Q psy16646 119 KTRNSIGI 126 (159)
Q Consensus 119 ~~C~~C~~ 126 (159)
|.|+.||.
T Consensus 49 Y~CP~CGF 56 (59)
T PRK14890 49 YTCPKCGF 56 (59)
T ss_pred eECCCCCC
Confidence 55555554
No 95
>KOG2186|consensus
Probab=74.27 E-value=2.3 Score=30.04 Aligned_cols=46 Identities=30% Similarity=0.571 Sum_probs=31.8
Q ss_pred cccccccccccChHHHHHHHhhhhcCCCCccccccccccccChhhHHHHHh
Q psy16646 33 FHCYVCKKKYRHKRQLVRHFQVNHTNNYDRVICEICNKEFTHKSSLAEHRV 83 (159)
Q Consensus 33 ~~C~~c~~~f~~~~~l~~h~~~~~~~~~~~~~c~~c~~~f~~~~~l~~h~~ 83 (159)
|.|..||.+.. ...+..|+.. -++ .-|.|--|+..|.. .++..|..
T Consensus 4 FtCnvCgEsvK-Kp~vekH~sr-Crn--~~fSCIDC~k~F~~-~sYknH~k 49 (276)
T KOG2186|consen 4 FTCNVCGESVK-KPQVEKHMSR-CRN--AYFSCIDCGKTFER-VSYKNHTK 49 (276)
T ss_pred Eehhhhhhhcc-ccchHHHHHh-ccC--CeeEEeeccccccc-chhhhhhh
Confidence 67888887654 4567778765 344 45788888888887 55666644
No 96
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=73.70 E-value=1.6 Score=26.93 Aligned_cols=11 Identities=18% Similarity=0.588 Sum_probs=6.2
Q ss_pred ccccccccccc
Q psy16646 63 VICEICNKEFT 73 (159)
Q Consensus 63 ~~c~~c~~~f~ 73 (159)
|.|..||..|.
T Consensus 101 y~C~~Cg~~wr 111 (113)
T COG1594 101 YKCTRCGYRWR 111 (113)
T ss_pred EEecccCCEee
Confidence 55666665543
No 97
>smart00614 ZnF_BED BED zinc finger. DNA-binding domain in chromatin-boundary-element-binding proteins and transposases
Probab=73.69 E-value=2.5 Score=21.80 Aligned_cols=21 Identities=10% Similarity=0.132 Sum_probs=12.7
Q ss_pred ccccccCccccch-----hhHHHhhc
Q psy16646 119 KTRNSIGITVRQN-----QTNKNHRS 139 (159)
Q Consensus 119 ~~C~~C~~~f~~~-----~~l~~H~~ 139 (159)
-.|..|++.+... +.|..|++
T Consensus 19 a~C~~C~~~l~~~~~~gTs~L~rHl~ 44 (50)
T smart00614 19 AKCKYCGKKLSRSSKGGTSNLRRHLR 44 (50)
T ss_pred EEecCCCCEeeeCCCCCcHHHHHHHH
Confidence 4566666666443 46666665
No 98
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=73.57 E-value=2.5 Score=26.78 Aligned_cols=39 Identities=13% Similarity=0.171 Sum_probs=23.9
Q ss_pred hhhcccCCCCCCCCCCCCCcccCCCCCccccccccccccC
Q psy16646 5 KKKSVKNPNAKKRYRPYVPRVDSSLPPQFHCYVCKKKYRH 44 (159)
Q Consensus 5 ~~~~~~~~~~~~~~~~~~~~~~h~~~~~~~C~~c~~~f~~ 44 (159)
-+....||.|..-. ....-....+...|.|..|+++|..
T Consensus 27 ~~~~~~cP~C~s~~-~~k~g~~~~~~qRyrC~~C~~tf~~ 65 (129)
T COG3677 27 QITKVNCPRCKSSN-VVKIGGIRRGHQRYKCKSCGSTFTV 65 (129)
T ss_pred hcccCcCCCCCccc-eeeECCccccccccccCCcCcceee
Confidence 33456777777666 3333334444666888888877753
No 99
>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=73.52 E-value=2.7 Score=18.52 Aligned_cols=19 Identities=11% Similarity=-0.106 Sum_probs=13.2
Q ss_pred cccccCccccchhhHHHhhc
Q psy16646 120 TRNSIGITVRQNQTNKNHRS 139 (159)
Q Consensus 120 ~C~~C~~~f~~~~~l~~H~~ 139 (159)
.|+.|++.+ ....+..|+.
T Consensus 3 ~CPiC~~~v-~~~~in~HLD 21 (26)
T smart00734 3 QCPVCFREV-PENLINSHLD 21 (26)
T ss_pred cCCCCcCcc-cHHHHHHHHH
Confidence 578888877 5556777764
No 100
>PHA00626 hypothetical protein
Probab=71.93 E-value=1.7 Score=23.09 Aligned_cols=14 Identities=7% Similarity=-0.062 Sum_probs=11.9
Q ss_pred cccccccCccccch
Q psy16646 118 MKTRNSIGITVRQN 131 (159)
Q Consensus 118 ~~~C~~C~~~f~~~ 131 (159)
.|+|+.||+.|+..
T Consensus 23 rYkCkdCGY~ft~~ 36 (59)
T PHA00626 23 DYVCCDCGYNDSKD 36 (59)
T ss_pred ceEcCCCCCeechh
Confidence 39999999999764
No 101
>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=71.51 E-value=1.9 Score=19.04 Aligned_cols=10 Identities=10% Similarity=-0.004 Sum_probs=6.5
Q ss_pred cccccCcccc
Q psy16646 120 TRNSIGITVR 129 (159)
Q Consensus 120 ~C~~C~~~f~ 129 (159)
.|+.||..|.
T Consensus 16 ~Cp~CG~~F~ 25 (26)
T PF10571_consen 16 FCPHCGYDFE 25 (26)
T ss_pred cCCCCCCCCc
Confidence 3777777664
No 102
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=71.48 E-value=3.4 Score=34.03 Aligned_cols=25 Identities=20% Similarity=0.348 Sum_probs=13.2
Q ss_pred ccCCCCCCCCCCCCCcccCCCCCcccccccc
Q psy16646 9 VKNPNAKKRYRPYVPRVDSSLPPQFHCYVCK 39 (159)
Q Consensus 9 ~~~~~~~~~~~~~~~~~~h~~~~~~~C~~c~ 39 (159)
.+||+|+.. +..|...+...|..||
T Consensus 445 ~~Cp~Cd~~------lt~H~~~~~L~CH~Cg 469 (730)
T COG1198 445 AECPNCDSP------LTLHKATGQLRCHYCG 469 (730)
T ss_pred ccCCCCCcc------eEEecCCCeeEeCCCC
Confidence 455655543 3444444555666665
No 103
>PF02176 zf-TRAF: TRAF-type zinc finger; PDB: 2EOD_A 2YUC_A 3HCU_A 3HCS_B 3HCT_A.
Probab=70.96 E-value=2.4 Score=22.57 Aligned_cols=42 Identities=14% Similarity=0.057 Sum_probs=17.3
Q ss_pred cccCcc-ccccccCccchhhhhhhhhhhhccccccc----cCccccch
Q psy16646 89 QHKCSL-CQQAFKRDKHSKGDDIREEIEREMKTRNS----IGITVRQN 131 (159)
Q Consensus 89 ~~~C~~-C~~~f~~~~~l~~h~~~~~~~~~~~~C~~----C~~~f~~~ 131 (159)
+..|+. |+..-.....|..|+...-..++ ..|+. |+..+...
T Consensus 9 ~v~C~~~cc~~~i~r~~l~~H~~~~C~~~~-v~C~~~~~GC~~~~~~~ 55 (60)
T PF02176_consen 9 PVPCPNGCCNEMIPRKELDDHLENECPKRP-VPCPYSPYGCKERVPRE 55 (60)
T ss_dssp EEE-TT--S-BEEECCCHHHHHHTTSTTSE-EE-SS----S--EEEHH
T ss_pred EeeCCCCCcccceeHHHHHHHHHccCCCCc-EECCCCCCCCCCccchh
Confidence 445555 33222223456666654444444 55665 66655443
No 104
>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=70.14 E-value=3 Score=20.74 Aligned_cols=20 Identities=15% Similarity=0.165 Sum_probs=9.6
Q ss_pred ccccccCccccch----hhHHHhh
Q psy16646 119 KTRNSIGITVRQN----QTNKNHR 138 (159)
Q Consensus 119 ~~C~~C~~~f~~~----~~l~~H~ 138 (159)
..|..|++.+... +.|..|+
T Consensus 17 a~C~~C~~~~~~~~~~ts~l~~HL 40 (45)
T PF02892_consen 17 AKCKYCGKVIKYSSGGTSNLKRHL 40 (45)
T ss_dssp EEETTTTEE-----SSTHHHHHHH
T ss_pred EEeCCCCeEEeeCCCcHHHHHHhh
Confidence 5566666665442 4566665
No 105
>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=69.90 E-value=1.9 Score=27.44 Aligned_cols=28 Identities=21% Similarity=0.195 Sum_probs=17.0
Q ss_pred CCcccCccccccccCccchhhhhhhhhhhhc
Q psy16646 87 PAQHKCSLCQQAFKRDKHSKGDDIREEIERE 117 (159)
Q Consensus 87 ~k~~~C~~C~~~f~~~~~l~~h~~~~~~~~~ 117 (159)
+.-..|-+||+.|.. |.+|++.|+|-.+
T Consensus 70 ~d~i~clecGk~~k~---LkrHL~~~~gltp 97 (132)
T PF05443_consen 70 PDYIICLECGKKFKT---LKRHLRTHHGLTP 97 (132)
T ss_dssp SS-EE-TBT--EESB---HHHHHHHTT-S-H
T ss_pred cCeeEEccCCcccch---HHHHHHHccCCCH
Confidence 345789999998865 5999999977543
No 106
>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=69.02 E-value=3 Score=19.48 Aligned_cols=10 Identities=10% Similarity=0.036 Sum_probs=5.3
Q ss_pred ccccccCccc
Q psy16646 119 KTRNSIGITV 128 (159)
Q Consensus 119 ~~C~~C~~~f 128 (159)
..|+.||.+.
T Consensus 18 irC~~CG~RI 27 (32)
T PF03604_consen 18 IRCPECGHRI 27 (32)
T ss_dssp SSBSSSS-SE
T ss_pred EECCcCCCeE
Confidence 4566666553
No 107
>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=68.85 E-value=2 Score=26.23 Aligned_cols=25 Identities=16% Similarity=0.234 Sum_probs=22.9
Q ss_pred ccC----ccccccccCccchhhhhhhhhh
Q psy16646 90 HKC----SLCQQAFKRDKHSKGDDIREEI 114 (159)
Q Consensus 90 ~~C----~~C~~~f~~~~~l~~h~~~~~~ 114 (159)
|.| ..|+..+.....+..|++.+||
T Consensus 81 ~~C~~~~~~C~y~~~~~~~m~~H~~~~Hg 109 (109)
T PF12013_consen 81 YRCQCDPPHCGYITRSKKTMRKHWRKEHG 109 (109)
T ss_pred eeeecCCCCCCcEeccHHHHHHHHHHhcC
Confidence 889 9999999999999999998775
No 108
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=68.68 E-value=3.1 Score=26.33 Aligned_cols=15 Identities=27% Similarity=0.569 Sum_probs=9.2
Q ss_pred ccccccccccccChh
Q psy16646 62 RVICEICNKEFTHKS 76 (159)
Q Consensus 62 ~~~c~~c~~~f~~~~ 76 (159)
|+.|..||..|.+.+
T Consensus 1 PH~Ct~Cg~~f~dgs 15 (131)
T PF09845_consen 1 PHQCTKCGRVFEDGS 15 (131)
T ss_pred CcccCcCCCCcCCCc
Confidence 456777777766543
No 109
>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=68.30 E-value=1.8 Score=19.53 Aligned_cols=17 Identities=12% Similarity=0.134 Sum_probs=7.4
Q ss_pred cccccCccccchhhHHHh
Q psy16646 120 TRNSIGITVRQNQTNKNH 137 (159)
Q Consensus 120 ~C~~C~~~f~~~~~l~~H 137 (159)
.|-.|++.| ....+..|
T Consensus 2 sCiDC~~~F-~~~~y~~H 18 (28)
T PF08790_consen 2 SCIDCSKDF-DGDSYKSH 18 (28)
T ss_dssp EETTTTEEE-EGGGTTT-
T ss_pred eeecCCCCc-CcCCcCCC
Confidence 345555555 33334444
No 110
>PF04959 ARS2: Arsenite-resistance protein 2; InterPro: IPR007042 This entry represents Arsenite-resistance protein 2 (also known as Serrate RNA effector molecule homolog) which is thought to play a role in arsenite resistance [], although does not directly confer arsenite resistance but rather modulates arsenic sensitivity []. Arsenite is a carcinogenic compound which can act as a comutagen by inhibiting DNA repair. It is also involved in cell cycle progression at S phase. ; PDB: 3AX1_A.
Probab=68.17 E-value=1.8 Score=29.94 Aligned_cols=30 Identities=20% Similarity=0.475 Sum_probs=23.2
Q ss_pred CCcccCccccccccCccchhhhhhhhhhhh
Q psy16646 87 PAQHKCSLCQQAFKRDKHSKGDDIREEIER 116 (159)
Q Consensus 87 ~k~~~C~~C~~~f~~~~~l~~h~~~~~~~~ 116 (159)
+..|.|..|+|.|........|+..-|.++
T Consensus 75 ~~K~~C~lc~KlFkg~eFV~KHI~nKH~e~ 104 (214)
T PF04959_consen 75 EDKWRCPLCGKLFKGPEFVRKHIFNKHPEK 104 (214)
T ss_dssp SEEEEE-SSS-EESSHHHHHHHHHHH-HHH
T ss_pred CCEECCCCCCcccCChHHHHHHHhhcCHHH
Confidence 447999999999999999999998877764
No 111
>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=67.52 E-value=4 Score=25.71 Aligned_cols=30 Identities=13% Similarity=0.182 Sum_probs=16.7
Q ss_pred cccccccccccChhhHHHHHhhhCCCcccCccccccccCc
Q psy16646 63 VICEICNKEFTHKSSLAEHRVLHFPAQHKCSLCQQAFKRD 102 (159)
Q Consensus 63 ~~c~~c~~~f~~~~~l~~h~~~h~~k~~~C~~C~~~f~~~ 102 (159)
..|..||..|-.. +..|..|++||..|...
T Consensus 10 r~Cp~cg~kFYDL----------nk~p~vcP~cg~~~~~~ 39 (129)
T TIGR02300 10 RICPNTGSKFYDL----------NRRPAVSPYTGEQFPPE 39 (129)
T ss_pred ccCCCcCcccccc----------CCCCccCCCcCCccCcc
Confidence 3566666655331 12366677777666544
No 112
>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=66.11 E-value=4.1 Score=21.17 Aligned_cols=8 Identities=13% Similarity=-0.118 Sum_probs=4.1
Q ss_pred ccccccCc
Q psy16646 119 KTRNSIGI 126 (159)
Q Consensus 119 ~~C~~C~~ 126 (159)
|.|+.|+.
T Consensus 35 w~CP~C~a 42 (50)
T cd00730 35 WVCPVCGA 42 (50)
T ss_pred CCCCCCCC
Confidence 45555543
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=65.55 E-value=3.5 Score=17.88 Aligned_cols=10 Identities=20% Similarity=0.132 Sum_probs=7.6
Q ss_pred hcccCCCCCC
Q psy16646 7 KSVKNPNAKK 16 (159)
Q Consensus 7 ~~~~~~~~~~ 16 (159)
..|.||+|+.
T Consensus 15 v~f~CPnCG~ 24 (24)
T PF07754_consen 15 VPFPCPNCGF 24 (24)
T ss_pred ceEeCCCCCC
Confidence 5788888863
No 114
>PF14205 Cys_rich_KTR: Cysteine-rich KTR
Probab=65.45 E-value=4.2 Score=21.46 Aligned_cols=32 Identities=16% Similarity=0.185 Sum_probs=22.5
Q ss_pred ccCCCCCCCCCCCCCcccCCCCCccccccccc
Q psy16646 9 VKNPNAKKRYRPYVPRVDSSLPPQFHCYVCKK 40 (159)
Q Consensus 9 ~~~~~~~~~~~~~~~~~~h~~~~~~~C~~c~~ 40 (159)
..||.|+.+.+...-..+-...-|.-|+.|-.
T Consensus 5 i~CP~CgnKTR~kir~DT~LkNfPlyCpKCK~ 36 (55)
T PF14205_consen 5 ILCPICGNKTRLKIREDTVLKNFPLYCPKCKQ 36 (55)
T ss_pred EECCCCCCccceeeecCceeccccccCCCCCc
Confidence 46888888888766655555566777777764
No 115
>PF07975 C1_4: TFIIH C1-like domain; InterPro: IPR004595 All proteins in this domain for which functions are known are components of the TFIIH complex which is involved in the initiation of transcription and nucleotide excision repair. It includes the yeast transcription factor Ssl1 (Suppressor of stem-loop protein 1) that is essential for translation initiation and affects UV resistance. The C-terminal region is essential for transcription activity. This regions binds three zinc atoms through two independent domain. The first contains a C4 zinc finger motif, whereas the second is characterised by a CX(2)CX(2-4)FCADCD motif. The solution structure of the second C-terminal domain revealed homology with the regulatory domain of protein kinase C [].; GO: 0006281 DNA repair, 0005634 nucleus; PDB: 1Z60_A.
Probab=65.04 E-value=2.9 Score=21.83 Aligned_cols=25 Identities=4% Similarity=-0.266 Sum_probs=13.4
Q ss_pred cccccccCccccchhhHHHhhccCC
Q psy16646 118 MKTRNSIGITVRQNQTNKNHRSGDQ 142 (159)
Q Consensus 118 ~~~C~~C~~~f~~~~~l~~H~~~h~ 142 (159)
.|.|+.|+..|--.-.+-.|...|.
T Consensus 21 ~y~C~~C~~~FC~dCD~fiHE~LH~ 45 (51)
T PF07975_consen 21 RYRCPKCKNHFCIDCDVFIHETLHN 45 (51)
T ss_dssp EE--TTTT--B-HHHHHTTTTTS-S
T ss_pred eEECCCCCCccccCcChhhhccccC
Confidence 3888888888877766667766664
No 116
>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=63.30 E-value=8 Score=19.81 Aligned_cols=8 Identities=13% Similarity=-0.118 Sum_probs=3.4
Q ss_pred ccccccCc
Q psy16646 119 KTRNSIGI 126 (159)
Q Consensus 119 ~~C~~C~~ 126 (159)
|.|+.|+.
T Consensus 35 w~CP~C~a 42 (47)
T PF00301_consen 35 WVCPVCGA 42 (47)
T ss_dssp -B-TTTSS
T ss_pred CcCcCCCC
Confidence 55666654
No 117
>PF06524 NOA36: NOA36 protein; InterPro: IPR010531 This family consists of several NOA36 proteins which contain 29 highly conserved cysteine residues. The function of this protein is unknown.; GO: 0008270 zinc ion binding, 0005634 nucleus
Probab=62.12 E-value=7.3 Score=27.79 Aligned_cols=19 Identities=16% Similarity=0.291 Sum_probs=8.4
Q ss_pred CcccCccccccccCccchh
Q psy16646 88 AQHKCSLCQQAFKRDKHSK 106 (159)
Q Consensus 88 k~~~C~~C~~~f~~~~~l~ 106 (159)
+++.|+.||........|.
T Consensus 208 k~~PCPKCg~et~eTkdLS 226 (314)
T PF06524_consen 208 KPIPCPKCGYETQETKDLS 226 (314)
T ss_pred CCCCCCCCCCcccccccce
Confidence 3445555554444333333
No 118
>KOG2482|consensus
Probab=61.27 E-value=9.2 Score=28.45 Aligned_cols=22 Identities=32% Similarity=0.766 Sum_probs=15.6
Q ss_pred cccccccccccChHHHHHHHhh
Q psy16646 33 FHCYVCKKKYRHKRQLVRHFQV 54 (159)
Q Consensus 33 ~~C~~c~~~f~~~~~l~~h~~~ 54 (159)
+.|-.|.+.|.....|..||+.
T Consensus 196 ~~CLyCekifrdkntLkeHMrk 217 (423)
T KOG2482|consen 196 LRCLYCEKIFRDKNTLKEHMRK 217 (423)
T ss_pred heeeeeccccCCcHHHHHHHHh
Confidence 5677777777777777777764
No 119
>PF13451 zf-trcl: Probable zinc-binding domain
Probab=60.02 E-value=3.2 Score=21.47 Aligned_cols=13 Identities=23% Similarity=0.468 Sum_probs=5.7
Q ss_pred cccCccccccccC
Q psy16646 89 QHKCSLCQQAFKR 101 (159)
Q Consensus 89 ~~~C~~C~~~f~~ 101 (159)
.+.|..||..|..
T Consensus 4 ~l~C~dCg~~Fvf 16 (49)
T PF13451_consen 4 TLTCKDCGAEFVF 16 (49)
T ss_pred eEEcccCCCeEEE
Confidence 3444444444433
No 120
>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=59.86 E-value=2.9 Score=19.20 Aligned_cols=8 Identities=13% Similarity=-0.068 Sum_probs=3.9
Q ss_pred ccccccCc
Q psy16646 119 KTRNSIGI 126 (159)
Q Consensus 119 ~~C~~C~~ 126 (159)
+.|+.|+.
T Consensus 20 ~vCp~C~~ 27 (30)
T PF08274_consen 20 LVCPECGH 27 (30)
T ss_dssp EEETTTTE
T ss_pred EeCCcccc
Confidence 44555543
No 121
>KOG2482|consensus
Probab=58.80 E-value=18 Score=27.05 Aligned_cols=50 Identities=24% Similarity=0.462 Sum_probs=33.1
Q ss_pred ccccccccccccC-hhhHHHHHh-hhC---CC-------------------cccCccccccccCccchhhhhhh
Q psy16646 62 RVICEICNKEFTH-KSSLAEHRV-LHF---PA-------------------QHKCSLCQQAFKRDKHSKGDDIR 111 (159)
Q Consensus 62 ~~~c~~c~~~f~~-~~~l~~h~~-~h~---~k-------------------~~~C~~C~~~f~~~~~l~~h~~~ 111 (159)
..+|-.|...+.. .+.+..|.. .|+ +. .+.|.+|.+.|.....|+.|++.
T Consensus 144 slqClFCn~e~lgnRs~~l~Hlf~~H~lniGlpDniVyvnelLehLkekL~r~~CLyCekifrdkntLkeHMrk 217 (423)
T KOG2482|consen 144 SLQCLFCNNEGLGNRSEILEHLFHVHGLNIGLPDNIVYVNELLEHLKEKLERLRCLYCEKIFRDKNTLKEHMRK 217 (423)
T ss_pred eeEEEEecchhcccHHHHHHHHHHHhhhccCCCcceeeHHHHHHHHHHHHhhheeeeeccccCCcHHHHHHHHh
Confidence 4568888876543 455555643 342 12 26888888888888888888864
No 122
>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=57.83 E-value=9.4 Score=30.13 Aligned_cols=26 Identities=19% Similarity=0.318 Sum_probs=16.0
Q ss_pred ccCCCCCCCCCCCCCcccCCCCCccccccccc
Q psy16646 9 VKNPNAKKRYRPYVPRVDSSLPPQFHCYVCKK 40 (159)
Q Consensus 9 ~~~~~~~~~~~~~~~~~~h~~~~~~~C~~c~~ 40 (159)
..||+|+ ..+..|.......|..||.
T Consensus 223 ~~C~~C~------~~l~~h~~~~~l~Ch~Cg~ 248 (505)
T TIGR00595 223 LCCPNCD------VSLTYHKKEGKLRCHYCGY 248 (505)
T ss_pred cCCCCCC------CceEEecCCCeEEcCCCcC
Confidence 3455553 4566666666677777774
No 123
>COG5112 UFD2 U1-like Zn-finger-containing protein [General function prediction only]
Probab=57.80 E-value=1.9 Score=26.12 Aligned_cols=33 Identities=18% Similarity=0.184 Sum_probs=19.2
Q ss_pred ccccccCccccchhhHHHhhccCCCccccccCc
Q psy16646 119 KTRNSIGITVRQNQTNKNHRSGDQKKKTAKQLS 151 (159)
Q Consensus 119 ~~C~~C~~~f~~~~~l~~H~~~h~~~k~~~~~~ 151 (159)
+.|-.|.+-|.+...|..|.+........+.+.
T Consensus 56 hYCieCaryf~t~~aL~~HkkgkvHkRR~KelR 88 (126)
T COG5112 56 HYCIECARYFITEKALMEHKKGKVHKRRAKELR 88 (126)
T ss_pred eeeehhHHHHHHHHHHHHHhccchhHHHHHHHh
Confidence 446667777777777777765544333333333
No 124
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=57.38 E-value=5.3 Score=25.51 Aligned_cols=14 Identities=21% Similarity=0.508 Sum_probs=10.0
Q ss_pred cccCccccccccCc
Q psy16646 89 QHKCSLCQQAFKRD 102 (159)
Q Consensus 89 ~~~C~~C~~~f~~~ 102 (159)
.+.|..||..|...
T Consensus 70 ~~~C~~CG~~~~~~ 83 (135)
T PRK03824 70 VLKCRNCGNEWSLK 83 (135)
T ss_pred EEECCCCCCEEecc
Confidence 47788888777654
No 125
>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=56.88 E-value=5.6 Score=24.09 Aligned_cols=8 Identities=38% Similarity=1.173 Sum_probs=3.7
Q ss_pred cccccccc
Q psy16646 63 VICEICNK 70 (159)
Q Consensus 63 ~~c~~c~~ 70 (159)
..|+.||.
T Consensus 3 ~~CpYCg~ 10 (102)
T PF11672_consen 3 IICPYCGG 10 (102)
T ss_pred cccCCCCC
Confidence 34555543
No 126
>smart00778 Prim_Zn_Ribbon Zinc-binding domain of primase-helicase. This region represents the zinc binding domain. It is found in the N-terminal region of the bacteriophage P4 alpha protein, which is a multifunctional protein with origin recognition, helicase and primase activities.
Probab=56.76 E-value=16 Score=17.68 Aligned_cols=31 Identities=23% Similarity=0.203 Sum_probs=18.0
Q ss_pred cccCCCCCCCCCCCCCcccCCCCCccccccccc
Q psy16646 8 SVKNPNAKKRYRPYVPRVDSSLPPQFHCYVCKK 40 (159)
Q Consensus 8 ~~~~~~~~~~~~~~~~~~~h~~~~~~~C~~c~~ 40 (159)
..+||.|..+=+.. .....+...+.|..|+.
T Consensus 3 ~~pCP~CGG~DrFr--~~d~~g~G~~~C~~Cg~ 33 (37)
T smart00778 3 HGPCPNCGGSDRFR--FDDKDGRGTWFCSVCGA 33 (37)
T ss_pred ccCCCCCCCccccc--cccCCCCcCEEeCCCCC
Confidence 56788887744433 23333445677777753
No 127
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=56.40 E-value=11 Score=18.49 Aligned_cols=37 Identities=16% Similarity=0.145 Sum_probs=19.0
Q ss_pred cCCCCCCCCCCCCCcccCCCCCccccccccccccChHHHHH
Q psy16646 10 KNPNAKKRYRPYVPRVDSSLPPQFHCYVCKKKYRHKRQLVR 50 (159)
Q Consensus 10 ~~~~~~~~~~~~~~~~~h~~~~~~~C~~c~~~f~~~~~l~~ 50 (159)
+||.|...-. .... .+-.-..|+.|+..+.....|..
T Consensus 1 ~CP~C~~~l~---~~~~-~~~~id~C~~C~G~W~d~~el~~ 37 (41)
T PF13453_consen 1 KCPRCGTELE---PVRL-GDVEIDVCPSCGGIWFDAGELEK 37 (41)
T ss_pred CcCCCCcccc---eEEE-CCEEEEECCCCCeEEccHHHHHH
Confidence 4677755222 1111 22344667777776665555543
No 128
>PF11494 Ta0938: Ta0938; InterPro: IPR021585 Ta0938 is a protein of unknown function however the structure has been determined. The protein has a novel fold and a putative Zn-binding motif. The structure has two different parts, one region contains a beta sheet flanked by two alpha helices and the other contains a bundle of loops which contain all cysteines in the protein. ; PDB: 2FQH_A.
Probab=56.39 E-value=7.5 Score=23.16 Aligned_cols=39 Identities=13% Similarity=0.168 Sum_probs=13.4
Q ss_pred CCcccCccccccccCccchhhhhhhhhhhhccccccccCccccch
Q psy16646 87 PAQHKCSLCQQAFKRDKHSKGDDIREEIEREMKTRNSIGITVRQN 131 (159)
Q Consensus 87 ~k~~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~~C~~C~~~f~~~ 131 (159)
.+.-.|..||.++..- -.--.|++-.|.|+.|.+.|.+.
T Consensus 12 ~ke~~CalCG~tWg~~------y~Ev~G~rLfFCCd~ca~EF~nm 50 (105)
T PF11494_consen 12 TKEMGCALCGATWGDY------YEEVDGERLFFCCDDCAKEFKNM 50 (105)
T ss_dssp SGGGS-SS---S---S------S-B-TT--BSSS--SSSS-TTS-
T ss_pred cccccccccCCcHHHH------HHhhcCCEEEEEcHHHHHHHHHH
Confidence 3445566666655422 12245666656667777766654
No 129
>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=55.53 E-value=6 Score=19.94 Aligned_cols=8 Identities=0% Similarity=-0.280 Sum_probs=4.4
Q ss_pred ccccccCc
Q psy16646 119 KTRNSIGI 126 (159)
Q Consensus 119 ~~C~~C~~ 126 (159)
|+|..|++
T Consensus 38 ~~C~~C~~ 45 (46)
T PF12760_consen 38 YRCKACRK 45 (46)
T ss_pred EECCCCCC
Confidence 55655553
No 130
>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=55.34 E-value=3.3 Score=24.44 Aligned_cols=11 Identities=36% Similarity=0.912 Sum_probs=5.1
Q ss_pred ccCcccccccc
Q psy16646 90 HKCSLCQQAFK 100 (159)
Q Consensus 90 ~~C~~C~~~f~ 100 (159)
|.|..|++.|.
T Consensus 54 W~C~~C~~~~A 64 (90)
T PF01780_consen 54 WKCKKCGKKFA 64 (90)
T ss_dssp EEETTTTEEEE
T ss_pred eecCCCCCEEe
Confidence 44444444443
No 131
>COG1655 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=54.84 E-value=3.3 Score=28.91 Aligned_cols=41 Identities=12% Similarity=0.187 Sum_probs=23.7
Q ss_pred CCcccCccccccccCccchhhhhhhhhhhhc--------------cccccccCcc
Q psy16646 87 PAQHKCSLCQQAFKRDKHSKGDDIREEIERE--------------MKTRNSIGIT 127 (159)
Q Consensus 87 ~k~~~C~~C~~~f~~~~~l~~h~~~~~~~~~--------------~~~C~~C~~~ 127 (159)
.+.+.|+.|+..|.....+..-+++-.|+-. +..|+.|+..
T Consensus 17 kk~ieCPvC~tkFkkeev~tgsiRiiagDld~~lkygninP~fY~VvvCP~C~yA 71 (267)
T COG1655 17 KKTIECPVCNTKFKKEEVKTGSIRIIAGDLDFFLKYGNINPYFYDVVVCPICYYA 71 (267)
T ss_pred hceeccCcccchhhhhheeccceeEecccccceeeccccCCceeEEEEcchhhHH
Confidence 4456677777777665554444444443321 1678888775
No 132
>PF13878 zf-C2H2_3: zinc-finger of acetyl-transferase ESCO
Probab=54.50 E-value=7.3 Score=19.23 Aligned_cols=12 Identities=17% Similarity=0.174 Sum_probs=6.8
Q ss_pred ccccccCccccc
Q psy16646 119 KTRNSIGITVRQ 130 (159)
Q Consensus 119 ~~C~~C~~~f~~ 130 (159)
-.|+.||..|..
T Consensus 14 ~~C~~CgM~Y~~ 25 (41)
T PF13878_consen 14 TTCPTCGMLYSP 25 (41)
T ss_pred cCCCCCCCEECC
Confidence 346666666544
No 133
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=54.09 E-value=7.3 Score=22.96 Aligned_cols=13 Identities=23% Similarity=0.731 Sum_probs=8.5
Q ss_pred cccCccccccccC
Q psy16646 89 QHKCSLCQQAFKR 101 (159)
Q Consensus 89 ~~~C~~C~~~f~~ 101 (159)
|-.|..||..|..
T Consensus 58 Pa~CkkCGfef~~ 70 (97)
T COG3357 58 PARCKKCGFEFRD 70 (97)
T ss_pred ChhhcccCccccc
Confidence 5667777766655
No 134
>COG3091 SprT Zn-dependent metalloprotease, SprT family [General function prediction only]
Probab=53.32 E-value=5.1 Score=26.06 Aligned_cols=34 Identities=21% Similarity=0.302 Sum_probs=22.4
Q ss_pred cccCccccccccCccchhhhhhhhhhhhccccccccCccc
Q psy16646 89 QHKCSLCQQAFKRDKHSKGDDIREEIEREMKTRNSIGITV 128 (159)
Q Consensus 89 ~~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~~C~~C~~~f 128 (159)
+|.|. |+..+.+. .+|-..-.|+ . |.|..|+-..
T Consensus 117 ~Y~C~-C~q~~l~~---RRhn~~~~g~-~-YrC~~C~gkL 150 (156)
T COG3091 117 PYRCQ-CQQHYLRI---RRHNTVRRGE-V-YRCGKCGGKL 150 (156)
T ss_pred eEEee-cCCccchh---hhcccccccc-e-EEeccCCceE
Confidence 68888 88776554 4455545555 4 8888887643
No 135
>COG4306 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=53.16 E-value=6.1 Score=24.78 Aligned_cols=14 Identities=21% Similarity=0.465 Sum_probs=7.5
Q ss_pred cccCccccccccCc
Q psy16646 89 QHKCSLCQQAFKRD 102 (159)
Q Consensus 89 ~~~C~~C~~~f~~~ 102 (159)
|--|..||..|++.
T Consensus 68 psfchncgs~fpwt 81 (160)
T COG4306 68 PSFCHNCGSRFPWT 81 (160)
T ss_pred cchhhcCCCCCCcH
Confidence 44455566555543
No 136
>PF05129 Elf1: Transcription elongation factor Elf1 like; InterPro: IPR007808 This family of uncharacterised, mostly short, proteins contain a putative zinc binding domain with four conserved cysteines.; PDB: 1WII_A.
Probab=52.85 E-value=2.7 Score=24.31 Aligned_cols=10 Identities=40% Similarity=1.122 Sum_probs=2.7
Q ss_pred CCcccccccc
Q psy16646 30 PPQFHCYVCK 39 (159)
Q Consensus 30 ~~~~~C~~c~ 39 (159)
+..|.|+.|+
T Consensus 20 ~~~F~CPfC~ 29 (81)
T PF05129_consen 20 PKVFDCPFCN 29 (81)
T ss_dssp SS----TTT-
T ss_pred CceEcCCcCC
Confidence 3446666665
No 137
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=52.57 E-value=7.6 Score=23.96 Aligned_cols=25 Identities=16% Similarity=0.066 Sum_probs=15.4
Q ss_pred cccCccccccccCccchhhhhhhhhhhhccccccccCc
Q psy16646 89 QHKCSLCQQAFKRDKHSKGDDIREEIEREMKTRNSIGI 126 (159)
Q Consensus 89 ~~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~~C~~C~~ 126 (159)
...|..||..|.... . .+.|+.||.
T Consensus 70 ~~~C~~Cg~~~~~~~------------~-~~~CP~Cgs 94 (113)
T PRK12380 70 QAWCWDCSQVVEIHQ------------H-DAQCPHCHG 94 (113)
T ss_pred EEEcccCCCEEecCC------------c-CccCcCCCC
Confidence 367888886665432 1 155888874
No 138
>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=52.48 E-value=4.9 Score=20.46 Aligned_cols=38 Identities=13% Similarity=0.097 Sum_probs=19.3
Q ss_pred CccccccccCccchhhhhhhhhhhhcccccc--ccCccccchh
Q psy16646 92 CSLCQQAFKRDKHSKGDDIREEIEREMKTRN--SIGITVRQNQ 132 (159)
Q Consensus 92 C~~C~~~f~~~~~l~~h~~~~~~~~~~~~C~--~C~~~f~~~~ 132 (159)
|+.||....-..+...+ ....+.++.|. +||..|....
T Consensus 2 CP~Cg~~a~ir~S~~~s---~~~~~~Y~qC~N~~Cg~tfv~~~ 41 (47)
T PF04606_consen 2 CPHCGSKARIRTSRQLS---PLTRELYCQCTNPECGHTFVANL 41 (47)
T ss_pred cCCCCCeeEEEEchhhC---cceEEEEEEECCCcCCCEEEEEE
Confidence 67777544333322211 12223447774 4888886543
No 139
>KOG4173|consensus
Probab=51.89 E-value=8.2 Score=26.53 Aligned_cols=75 Identities=25% Similarity=0.515 Sum_probs=49.1
Q ss_pred cccccc--ccccccChHHHHHHHhhhhcCCCCccccccccccccChhhHHHHHhh-h----------CCCcccCc--ccc
Q psy16646 32 QFHCYV--CKKKYRHKRQLVRHFQVNHTNNYDRVICEICNKEFTHKSSLAEHRVL-H----------FPAQHKCS--LCQ 96 (159)
Q Consensus 32 ~~~C~~--c~~~f~~~~~l~~h~~~~~~~~~~~~~c~~c~~~f~~~~~l~~h~~~-h----------~~k~~~C~--~C~ 96 (159)
.+.|+. |-..|.....+..|....|. ..|..|.+.|....-|..|+.- | |.--|+|. .|+
T Consensus 79 ~~~cqvagc~~~~d~lD~~E~hY~~~h~-----~sCs~C~r~~Pt~hLLd~HI~E~HDs~Fqa~veRG~dMy~ClvEgCt 153 (253)
T KOG4173|consen 79 AFACQVAGCCQVFDALDDYEHHYHTLHG-----NSCSFCKRAFPTGHLLDAHILEWHDSLFQALVERGQDMYQCLVEGCT 153 (253)
T ss_pred cccccccchHHHHhhhhhHHHhhhhccc-----chhHHHHHhCCchhhhhHHHHHHHHHHHHHHHHcCccHHHHHHHhhh
Confidence 356765 66667766667777654222 2588899988888877777542 2 11136775 488
Q ss_pred ccccCccchhhhhhh
Q psy16646 97 QAFKRDKHSKGDDIR 111 (159)
Q Consensus 97 ~~f~~~~~l~~h~~~ 111 (159)
-.|.+......|+..
T Consensus 154 ~KFkT~r~RkdH~I~ 168 (253)
T KOG4173|consen 154 EKFKTSRDRKDHMIR 168 (253)
T ss_pred hhhhhhhhhhhHHHH
Confidence 888887777777654
No 140
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=51.82 E-value=12 Score=27.53 Aligned_cols=48 Identities=17% Similarity=0.095 Sum_probs=30.7
Q ss_pred CccccccccCccchhhhhhhhhhhhccccccccCccccchhhHHHhhccCC
Q psy16646 92 CSLCQQAFKRDKHSKGDDIREEIEREMKTRNSIGITVRQNQTNKNHRSGDQ 142 (159)
Q Consensus 92 C~~C~~~f~~~~~l~~h~~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~h~ 142 (159)
|-.|.-.|.....-..-.. +..-+ |.|+.|...|-.....-.|...|-
T Consensus 365 Cf~CQ~~fp~~~~~~~~~~--~ss~r-Y~Ce~CK~~FC~dCdvfiHe~Lh~ 412 (421)
T COG5151 365 CFVCQGPFPKPPVSPFDES--TSSGR-YQCELCKSTFCSDCDVFIHETLHF 412 (421)
T ss_pred ceeccCCCCCCCCCccccc--ccccc-eechhhhhhhhhhhHHHHHHHHhh
Confidence 6677766765543222211 22223 999999999988887778866654
No 141
>PF09332 Mcm10: Mcm10 replication factor; InterPro: IPR015411 Mcm10 is a eukaryotic DNA replication factor that regulates the stability and chromatin association of DNA polymerase alpha []. ; PDB: 2KWQ_A.
Probab=51.34 E-value=3.1 Score=30.98 Aligned_cols=45 Identities=9% Similarity=0.130 Sum_probs=22.5
Q ss_pred ccCccccccccCccch---hhhh-hhhhhhhccccccccCccccchhhH
Q psy16646 90 HKCSLCQQAFKRDKHS---KGDD-IREEIEREMKTRNSIGITVRQNQTN 134 (159)
Q Consensus 90 ~~C~~C~~~f~~~~~l---~~h~-~~~~~~~~~~~C~~C~~~f~~~~~l 134 (159)
+.|..|.+.....+.. ..|. ..+.+.++.|+|..|+.+......|
T Consensus 253 v~C~~C~yt~~~~~~~C~~~~H~l~~~~a~KRFFkC~~C~~Rt~sl~r~ 301 (344)
T PF09332_consen 253 VTCKQCKYTAFKPSDRCKEEGHPLKWHDAVKRFFKCKDCGNRTISLERL 301 (344)
T ss_dssp EEETTT--EESS--HHHHHTT--EEEEEEE-EEEE-T-TS-EEEESSSS
T ss_pred EEcCCCCCcccCcchhHHhcCCceEEeeeeeeeEECCCCCCeeeecccC
Confidence 6788887766554432 2232 2356677779999999987665444
No 142
>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=51.17 E-value=8.4 Score=23.83 Aligned_cols=26 Identities=8% Similarity=0.096 Sum_probs=16.7
Q ss_pred cccCccccccccCccchhhhhhhhhhhhccccccccCcc
Q psy16646 89 QHKCSLCQQAFKRDKHSKGDDIREEIEREMKTRNSIGIT 127 (159)
Q Consensus 89 ~~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~~C~~C~~~ 127 (159)
...|..||..|..... . +.||.||..
T Consensus 70 ~~~C~~Cg~~~~~~~~------------~-~~CP~Cgs~ 95 (115)
T TIGR00100 70 ECECEDCSEEVSPEID------------L-YRCPKCHGI 95 (115)
T ss_pred EEEcccCCCEEecCCc------------C-ccCcCCcCC
Confidence 3678888866665422 2 668888854
No 143
>COG1326 Uncharacterized archaeal Zn-finger protein [General function prediction only]
Probab=49.56 E-value=5.8 Score=26.91 Aligned_cols=38 Identities=13% Similarity=0.176 Sum_probs=24.4
Q ss_pred hhhhcccCCCCCCCCCCCCCcccCC--CCCcccccccccccc
Q psy16646 4 MKKKSVKNPNAKKRYRPYVPRVDSS--LPPQFHCYVCKKKYR 43 (159)
Q Consensus 4 ~~~~~~~~~~~~~~~~~~~~~~~h~--~~~~~~C~~c~~~f~ 43 (159)
+.+.-..||+|+ +....|...-. .+-.+.|..||..++
T Consensus 2 ~~~iy~~Cp~Cg--~eev~hEVik~~g~~~lvrC~eCG~V~~ 41 (201)
T COG1326 2 TEEIYIECPSCG--SEEVSHEVIKERGREPLVRCEECGTVHP 41 (201)
T ss_pred cceEEEECCCCC--cchhhHHHHHhcCCceEEEccCCCcEee
Confidence 344567899998 55454443333 334688999998764
No 144
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=49.02 E-value=6 Score=18.73 Aligned_cols=10 Identities=10% Similarity=0.006 Sum_probs=6.0
Q ss_pred cccccccCcc
Q psy16646 118 MKTRNSIGIT 127 (159)
Q Consensus 118 ~~~C~~C~~~ 127 (159)
.+.|+.||..
T Consensus 22 R~vC~~Cg~I 31 (34)
T PF14803_consen 22 RLVCPACGFI 31 (34)
T ss_dssp EEEETTTTEE
T ss_pred ceECCCCCCE
Confidence 3667777653
No 145
>PF04810 zf-Sec23_Sec24: Sec23/Sec24 zinc finger; InterPro: IPR006895 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. COPII (coat protein complex II)-coated vesicles carry proteins from the endoplasmic reticulum (ER) to the Golgi complex []. COPII-coated vesicles form on the ER by the stepwise recruitment of three cytosolic components: Sar1-GTP to initiate coat formation, Sec23/24 heterodimer to select SNARE and cargo molecules, and Sec13/31 to induce coat polymerisation and membrane deformation []. Sec23 p and Sec24p are structurally related, folding into five distinct domains: a beta-barrel, a zinc-finger, an alpha/beta trunk domain (IPR006896 from INTERPRO), an all-helical region (IPR006900 from INTERPRO), and a C-terminal gelsolin-like domain (IPR007123 from INTERPRO). This entry describes an approximately 55-residue Sec23/24 zinc-binding domain, which lies against the beta-barrel at the periphery of the complex. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006886 intracellular protein transport, 0006888 ER to Golgi vesicle-mediated transport, 0030127 COPII vesicle coat; PDB: 3EFO_B 3EG9_B 3EGD_A 2YRC_A 2NUP_A 2YRD_A 3EGX_A 2NUT_A 3EH1_A 1PD0_A ....
Probab=48.81 E-value=8.9 Score=18.72 Aligned_cols=9 Identities=22% Similarity=-0.008 Sum_probs=4.1
Q ss_pred ccccccCcc
Q psy16646 119 KTRNSIGIT 127 (159)
Q Consensus 119 ~~C~~C~~~ 127 (159)
+.|+.|+..
T Consensus 25 w~C~~C~~~ 33 (40)
T PF04810_consen 25 WICNFCGTK 33 (40)
T ss_dssp EEETTT--E
T ss_pred EECcCCCCc
Confidence 556666554
No 146
>PF11023 DUF2614: Protein of unknown function (DUF2614); InterPro: IPR020912 This entry describes proteins of unknown function, which are thought to be membrane proteins.; GO: 0005887 integral to plasma membrane
Probab=47.98 E-value=7.9 Score=23.80 Aligned_cols=31 Identities=23% Similarity=0.302 Sum_probs=16.6
Q ss_pred hhcccCCCCCCCCCCCCCcccCCCCCccccccccccccC
Q psy16646 6 KKSVKNPNAKKRYRPYVPRVDSSLPPQFHCYVCKKKYRH 44 (159)
Q Consensus 6 ~~~~~~~~~~~~~~~~~~~~~h~~~~~~~C~~c~~~f~~ 44 (159)
-+.+.||+|.+.++.. .+...|..|+....-
T Consensus 67 av~V~CP~C~K~TKmL--------Gr~D~CM~C~~pLTL 97 (114)
T PF11023_consen 67 AVQVECPNCGKQTKML--------GRVDACMHCKEPLTL 97 (114)
T ss_pred ceeeECCCCCChHhhh--------chhhccCcCCCcCcc
Confidence 3556677777665421 122466666655433
No 147
>KOG3408|consensus
Probab=47.96 E-value=12 Score=23.32 Aligned_cols=26 Identities=27% Similarity=0.543 Sum_probs=19.9
Q ss_pred CCCccccccccccccChHHHHHHHhh
Q psy16646 29 LPPQFHCYVCKKKYRHKRQLVRHFQV 54 (159)
Q Consensus 29 ~~~~~~C~~c~~~f~~~~~l~~h~~~ 54 (159)
|-..|.|-+|.+-|.....|..|.++
T Consensus 54 G~GqfyCi~CaRyFi~~~~l~~H~kt 79 (129)
T KOG3408|consen 54 GGGQFYCIECARYFIDAKALKTHFKT 79 (129)
T ss_pred CCceeehhhhhhhhcchHHHHHHHhc
Confidence 44557888888888888888888764
No 148
>COG1327 Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains [Transcription]
Probab=47.91 E-value=9.8 Score=24.78 Aligned_cols=13 Identities=23% Similarity=0.575 Sum_probs=7.2
Q ss_pred ccCccccccccCc
Q psy16646 90 HKCSLCQQAFKRD 102 (159)
Q Consensus 90 ~~C~~C~~~f~~~ 102 (159)
-.|..||..|++.
T Consensus 29 ReC~~C~~RFTTf 41 (156)
T COG1327 29 RECLECGERFTTF 41 (156)
T ss_pred hcccccccccchh
Confidence 3466666655553
No 149
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=47.41 E-value=13 Score=22.39 Aligned_cols=9 Identities=33% Similarity=0.803 Sum_probs=4.5
Q ss_pred Ccccccccc
Q psy16646 31 PQFHCYVCK 39 (159)
Q Consensus 31 ~~~~C~~c~ 39 (159)
..+.|+.|+
T Consensus 20 t~f~CP~Cg 28 (99)
T PRK14892 20 KIFECPRCG 28 (99)
T ss_pred cEeECCCCC
Confidence 345555555
No 150
>KOG3214|consensus
Probab=47.16 E-value=13 Score=22.40 Aligned_cols=42 Identities=26% Similarity=0.633 Sum_probs=21.6
Q ss_pred CCCCccccccccccccChHHHHHHHhhhhcCCCCccccccccccccCh
Q psy16646 28 SLPPQFHCYVCKKKYRHKRQLVRHFQVNHTNNYDRVICEICNKEFTHK 75 (159)
Q Consensus 28 ~~~~~~~C~~c~~~f~~~~~l~~h~~~~~~~~~~~~~c~~c~~~f~~~ 75 (159)
..+..|.|..|+---...-.|..- +.- ....|.+|+.+|+..
T Consensus 19 ~ldt~FnClfcnHek~v~~~~Dk~----~~i--G~~sC~iC~esFqt~ 60 (109)
T KOG3214|consen 19 PLDTQFNCLFCNHEKSVSCTLDKK----HNI--GKASCRICEESFQTT 60 (109)
T ss_pred chheeeccCccccccceeeeehhh----cCc--ceeeeeehhhhhccc
Confidence 344557777776433222222211 111 235688888888754
No 151
>TIGR00240 ATCase_reg aspartate carbamoyltransferase, regulatory subunit. The presence of this regulatory subunit allows feedback inhibition by CTP on aspartate carbamoyltransferase, the first step in the synthesis of CTP from aspartate. In many species, this regulatory subunit is not present. In Thermotoga maritima, the catalytic and regulatory subunits are encoded by a fused gene and the regulatory region has enough sequence differences to score below the trusted cutoff.
Probab=46.78 E-value=15 Score=24.00 Aligned_cols=35 Identities=23% Similarity=0.483 Sum_probs=20.9
Q ss_pred ccCCC--CCCCCCCCCCcccCCCCC---cccccccccccc
Q psy16646 9 VKNPN--AKKRYRPYVPRVDSSLPP---QFHCYVCKKKYR 43 (159)
Q Consensus 9 ~~~~~--~~~~~~~~~~~~~h~~~~---~~~C~~c~~~f~ 43 (159)
.+||| |.-+..+..+.-.-.... .|+|.+|++.|.
T Consensus 104 ~kC~Np~CIT~~E~v~~~F~v~~~~~~~~lrC~YCe~~~~ 143 (150)
T TIGR00240 104 LKCPNPNCISNAEPVSSKFYVRSEEPDIALRCYYCEKEIE 143 (150)
T ss_pred EECCCCCCccCCCCCCcEEEEecCCCceEEEEECCCCEEe
Confidence 44544 776666555443322333 489999988764
No 152
>KOG2593|consensus
Probab=46.35 E-value=7.5 Score=29.77 Aligned_cols=34 Identities=24% Similarity=0.379 Sum_probs=17.4
Q ss_pred hcccCCCCCCCCCCCCCcccC-CCCCccccccccc
Q psy16646 7 KSVKNPNAKKRYRPYVPRVDS-SLPPQFHCYVCKK 40 (159)
Q Consensus 7 ~~~~~~~~~~~~~~~~~~~~h-~~~~~~~C~~c~~ 40 (159)
..|.||+|.+.|....-.+.- .....|.|..|+.
T Consensus 127 ~~Y~Cp~C~kkyt~Lea~~L~~~~~~~F~C~~C~g 161 (436)
T KOG2593|consen 127 AGYVCPNCQKKYTSLEALQLLDNETGEFHCENCGG 161 (436)
T ss_pred ccccCCccccchhhhHHHHhhcccCceEEEecCCC
Confidence 356666666666643333222 2234566666654
No 153
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=46.20 E-value=11 Score=23.41 Aligned_cols=14 Identities=29% Similarity=0.788 Sum_probs=9.1
Q ss_pred cccCccccccccCc
Q psy16646 89 QHKCSLCQQAFKRD 102 (159)
Q Consensus 89 ~~~C~~C~~~f~~~ 102 (159)
.+.|..||..|...
T Consensus 71 ~~~C~~Cg~~~~~~ 84 (117)
T PRK00564 71 ELECKDCSHVFKPN 84 (117)
T ss_pred EEEhhhCCCccccC
Confidence 36788888666543
No 154
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=46.06 E-value=20 Score=18.23 Aligned_cols=11 Identities=27% Similarity=0.646 Sum_probs=6.3
Q ss_pred ccccccccccc
Q psy16646 32 QFHCYVCKKKY 42 (159)
Q Consensus 32 ~~~C~~c~~~f 42 (159)
.+.|+.||..+
T Consensus 20 ~~vC~~Cg~~~ 30 (52)
T smart00661 20 RFVCRKCGYEE 30 (52)
T ss_pred EEECCcCCCeE
Confidence 45666666544
No 155
>PF15135 UPF0515: Uncharacterised protein UPF0515
Probab=45.47 E-value=15 Score=26.02 Aligned_cols=38 Identities=26% Similarity=0.491 Sum_probs=25.3
Q ss_pred hhcccCCCCCCCCCCCCCcccCCCCCccccccccccccC
Q psy16646 6 KKSVKNPNAKKRYRPYVPRVDSSLPPQFHCYVCKKKYRH 44 (159)
Q Consensus 6 ~~~~~~~~~~~~~~~~~~~~~h~~~~~~~C~~c~~~f~~ 44 (159)
|+.-.|-.|.+++++.- -..-.|-..|.|+.|+..|..
T Consensus 130 KeVSRCr~C~~rYDPVP-~dkmwG~aef~C~~C~h~F~G 167 (278)
T PF15135_consen 130 KEVSRCRKCRKRYDPVP-CDKMWGIAEFHCPKCRHNFRG 167 (278)
T ss_pred cccccccccccccCCCc-cccccceeeeecccccccchh
Confidence 34566777777777644 334456666888888887764
No 156
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=45.27 E-value=17 Score=19.26 Aligned_cols=29 Identities=21% Similarity=0.352 Sum_probs=17.8
Q ss_pred hhcccCCCCCCCCCCCCCcccCCCCCccccccccccc
Q psy16646 6 KKSVKNPNAKKRYRPYVPRVDSSLPPQFHCYVCKKKY 42 (159)
Q Consensus 6 ~~~~~~~~~~~~~~~~~~~~~h~~~~~~~C~~c~~~f 42 (159)
....+|+.|++.+.+...+ ..|+.|+..+
T Consensus 3 ~~~~~C~~Cg~~~~~~dDi--------VvCp~Cgapy 31 (54)
T PF14446_consen 3 YEGCKCPVCGKKFKDGDDI--------VVCPECGAPY 31 (54)
T ss_pred ccCccChhhCCcccCCCCE--------EECCCCCCcc
Confidence 3445777888777644333 5677777543
No 157
>PF04216 FdhE: Protein involved in formate dehydrogenase formation; InterPro: IPR006452 This family of sequences describe an accessory protein required for the assembly of formate dehydrogenase of certain proteobacteria although not present in the final complex []. The exact nature of the function of FdhE in the assembly of the complex is unknown, but considering the presence of selenocysteine, molybdopterin, iron-sulphur clusters and cytochrome b556, it is likely to be involved in the insertion of cofactors. ; GO: 0005737 cytoplasm; PDB: 2FIY_B.
Probab=45.24 E-value=1.9 Score=31.30 Aligned_cols=8 Identities=38% Similarity=0.621 Sum_probs=3.0
Q ss_pred cccccccc
Q psy16646 33 FHCYVCKK 40 (159)
Q Consensus 33 ~~C~~c~~ 40 (159)
-.|++||.
T Consensus 173 g~CPvCGs 180 (290)
T PF04216_consen 173 GYCPVCGS 180 (290)
T ss_dssp SS-TTT--
T ss_pred CcCCCCCC
Confidence 45666664
No 158
>KOG4167|consensus
Probab=45.01 E-value=4.3 Score=33.21 Aligned_cols=27 Identities=15% Similarity=0.253 Sum_probs=22.6
Q ss_pred cccCccccccccCccchhhhhhhhhhh
Q psy16646 89 QHKCSLCQQAFKRDKHSKGDDIREEIE 115 (159)
Q Consensus 89 ~~~C~~C~~~f~~~~~l~~h~~~~~~~ 115 (159)
-|.|.+|++.|..-.++..|+++|.-.
T Consensus 792 iFpCreC~kvF~KiKSrNAHMK~Hr~q 818 (907)
T KOG4167|consen 792 IFPCRECGKVFFKIKSRNAHMKTHRQQ 818 (907)
T ss_pred eeehHHHHHHHHHHhhhhHHHHHHHHH
Confidence 489999999999888888888887543
No 159
>PF02748 PyrI_C: Aspartate carbamoyltransferase regulatory chain, metal binding domain; InterPro: IPR020542 Aspartate carbamoyltransferase (aspartate transcarbamylase, ATCase) 2.1.3.2 from EC is an allosteric enzyme that plays a central role in the regulation of the pyrimidine pathway in bacteria. The holoenzyme is a dodecamer composed of six catalytic chains, each with an active site, and six regulatory chains lacking catalytic activity []. The catalytic subunits exist as a dimer of catalytic trimers, (c3)2, while the regulatory subunits exist as a trimer of regulatory dimers, (r2)3, therefore the complete holoenzyme can be represented as (c3)2(r2)3. The association of the catalytic subunits c3 with the regulatory subunits r2 is responsible for the establishment of positive co-operativity between catalytic sites for the binding of aspartate and it dictates the pattern of allosteric response toward nucleotide effectors. ATCase from Escherichia coli is the most extensively studied allosteric enzyme []. The crystal structure of the T-state, the T-state with CTP bound, the R-state with N-phosphonacetyl-L-aspartate (PALA) bound, and the R-state with phosphonoacetamide plus malonate bound have been used in interpreting kinetic and mutational studies. A high-resolution structure of E. coli ATCase in the presence of PALA (a bisubstrate analog) allows a detailed description of the binding at the active site of the enzyme and allows a detailed model of the tetrahedral intermediate to be constructed. The entire regulatory chain has been traced showing that the N-terminal regions of the regulatory chains R1 and R6 are located in close proximity to each other and to the regulatory site. This portion of the molecule may be involved in the observed asymmetry between the regulatory binding sites as well as in the heterotropic response of the enzyme []. The C-terminal domain of the regulatory chains have a rubredoxin-like zinc-bound fold. ATCase from Enterobacter agglomerans (Erwinia herbicola) (Pantoea agglomerans) differs from the other investigated enterobacterial ATCases by its absence of homotropic co-operativity toward the substrate aspartate and its lack of response to ATP which is an allosteric effector (activator) of this family of enzymes. Nevertheless, the E. herbicola ATCase has the same quaternary structure, two trimers of catalytic chains with three dimers of regulatory chains, (c3)2(r2)3, as other enterobacterial ATCases and shows extensive primary structure conservation []. This entry represents the C-terminal domain.; PDB: 2YWW_B 1SKU_D 1Q95_L 8ATC_B 3AT1_D 1RAI_D 4E2F_D 1NBE_B 6AT1_B 2FZC_D ....
Probab=44.90 E-value=15 Score=19.28 Aligned_cols=33 Identities=21% Similarity=0.436 Sum_probs=17.9
Q ss_pred CCCCCC-CCCCCCcc--cCCCCCccccccccccccC
Q psy16646 12 PNAKKR-YRPYVPRV--DSSLPPQFHCYVCKKKYRH 44 (159)
Q Consensus 12 ~~~~~~-~~~~~~~~--~h~~~~~~~C~~c~~~f~~ 44 (159)
|+|.-+ ..+..+.- ...+...++|.+|++.+..
T Consensus 12 p~CITn~~E~v~~~F~v~~~~~~~~rC~YCe~~~~~ 47 (52)
T PF02748_consen 12 PNCITNSNEPVESRFYVIDKEPIKLRCHYCERIITE 47 (52)
T ss_dssp TTBTTT-TSSS--EEEEEETTTCEEEETTT--EEEH
T ss_pred CCcccCCCCCCCceEEEEeCCCCEEEeeCCCCEecc
Confidence 446666 33433333 3456677999999987653
No 160
>COG2331 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=44.16 E-value=7.3 Score=22.11 Aligned_cols=10 Identities=30% Similarity=0.833 Sum_probs=5.3
Q ss_pred cccccccccc
Q psy16646 63 VICEICNKEF 72 (159)
Q Consensus 63 ~~c~~c~~~f 72 (159)
|.|..|+..|
T Consensus 13 Y~c~~cg~~~ 22 (82)
T COG2331 13 YECTECGNRF 22 (82)
T ss_pred EeecccchHH
Confidence 4556665543
No 161
>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=44.03 E-value=16 Score=19.30 Aligned_cols=30 Identities=13% Similarity=0.228 Sum_probs=17.6
Q ss_pred ccCCCCCCCCCCCCCcccCCCCCccccccccccc
Q psy16646 9 VKNPNAKKRYRPYVPRVDSSLPPQFHCYVCKKKY 42 (159)
Q Consensus 9 ~~~~~~~~~~~~~~~~~~h~~~~~~~C~~c~~~f 42 (159)
+.||.|+.......... |+ ...|+.||..+
T Consensus 3 ~~CP~CG~~iev~~~~~---Ge-iV~Cp~CGael 32 (54)
T TIGR01206 3 FECPDCGAEIELENPEL---GE-LVICDECGAEL 32 (54)
T ss_pred cCCCCCCCEEecCCCcc---CC-EEeCCCCCCEE
Confidence 46777777665543332 33 45777777654
No 162
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=43.95 E-value=16 Score=18.88 Aligned_cols=8 Identities=25% Similarity=0.567 Sum_probs=3.6
Q ss_pred cccccccc
Q psy16646 63 VICEICNK 70 (159)
Q Consensus 63 ~~c~~c~~ 70 (159)
+.|..||.
T Consensus 38 ~~C~~Cgy 45 (50)
T PRK00432 38 WHCGKCGY 45 (50)
T ss_pred EECCCcCC
Confidence 34444443
No 163
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=42.98 E-value=23 Score=18.85 Aligned_cols=13 Identities=23% Similarity=0.442 Sum_probs=8.4
Q ss_pred CCCcccccccccc
Q psy16646 29 LPPQFHCYVCKKK 41 (159)
Q Consensus 29 ~~~~~~C~~c~~~ 41 (159)
+...|.|+.||..
T Consensus 11 ~~v~~~Cp~cGip 23 (55)
T PF13824_consen 11 AHVNFECPDCGIP 23 (55)
T ss_pred cccCCcCCCCCCc
Confidence 3445777777764
No 164
>TIGR01384 TFS_arch transcription factor S, archaeal. There has been an apparent duplication event in the Halobacteriaceae lineage (Haloarcula, Haloferax, Haloquadratum, Halobacterium and Natromonas). There appears to be a separate duplication in Methanosphaera stadtmanae.
Probab=42.25 E-value=13 Score=22.30 Aligned_cols=40 Identities=15% Similarity=0.201 Sum_probs=18.9
Q ss_pred ccccccccccccChHHHHHHHhhhhcCCCCcccccccccccc
Q psy16646 32 QFHCYVCKKKYRHKRQLVRHFQVNHTNNYDRVICEICNKEFT 73 (159)
Q Consensus 32 ~~~C~~c~~~f~~~~~l~~h~~~~~~~~~~~~~c~~c~~~f~ 73 (159)
...|+.||..-.....++ ++.--.+...-|.|..|+..+.
T Consensus 62 ~~~Cp~Cg~~~a~f~~~Q--~RsadE~~T~fy~C~~C~~~w~ 101 (104)
T TIGR01384 62 RVECPKCGHKEAYYWLLQ--TRRADEPETRFYKCTKCGYVWR 101 (104)
T ss_pred cCCCCCCCCCeeEEEEec--cCCCCCCcEEEEEeCCCCCeeE
Confidence 367888876432222111 1110011113477888887664
No 165
>KOG1280|consensus
Probab=42.08 E-value=29 Score=25.97 Aligned_cols=39 Identities=28% Similarity=0.528 Sum_probs=20.9
Q ss_pred CccccccccccccChHHHHHHHhhhhcCCCCcccccccc
Q psy16646 31 PQFHCYVCKKKYRHKRQLVRHFQVNHTNNYDRVICEICN 69 (159)
Q Consensus 31 ~~~~C~~c~~~f~~~~~l~~h~~~~~~~~~~~~~c~~c~ 69 (159)
..|.|++|+.+--+...|..|....|........|..|+
T Consensus 78 qSftCPyC~~~Gfte~~f~~Hv~s~Hpda~~~~icp~c~ 116 (381)
T KOG1280|consen 78 QSFTCPYCGIMGFTERQFGTHVLSQHPEASTSVICPLCA 116 (381)
T ss_pred ccccCCcccccccchhHHHHHhhhcCcccCcceeeeccc
Confidence 346667776665566666666655444432223344443
No 166
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=41.98 E-value=11 Score=22.20 Aligned_cols=13 Identities=15% Similarity=0.539 Sum_probs=7.4
Q ss_pred cccCccccccccC
Q psy16646 89 QHKCSLCQQAFKR 101 (159)
Q Consensus 89 ~~~C~~C~~~f~~ 101 (159)
.|.|..|++.|.-
T Consensus 54 IW~C~~C~~~~AG 66 (90)
T PTZ00255 54 IWRCKGCKKTVAG 66 (90)
T ss_pred EEEcCCCCCEEeC
Confidence 4566666655544
No 167
>PRK05580 primosome assembly protein PriA; Validated
Probab=41.55 E-value=23 Score=29.14 Aligned_cols=27 Identities=11% Similarity=0.277 Sum_probs=13.3
Q ss_pred cccCCCCCCCCCCCCCcccCCCCCccccccccc
Q psy16646 8 SVKNPNAKKRYRPYVPRVDSSLPPQFHCYVCKK 40 (159)
Q Consensus 8 ~~~~~~~~~~~~~~~~~~~h~~~~~~~C~~c~~ 40 (159)
...||+|.- .+..|...+...|..||.
T Consensus 390 ~~~C~~C~~------~l~~h~~~~~l~Ch~Cg~ 416 (679)
T PRK05580 390 VAECPHCDA------SLTLHRFQRRLRCHHCGY 416 (679)
T ss_pred ccCCCCCCC------ceeEECCCCeEECCCCcC
Confidence 345555554 333444444455555553
No 168
>PF01927 Mut7-C: Mut7-C RNAse domain; InterPro: IPR002782 This prokaryotic family of proteins have no known function. The proteins contain four conserved cysteines that may be involved in metal binding or disulphide bridges.
Probab=41.43 E-value=15 Score=23.70 Aligned_cols=46 Identities=15% Similarity=0.303 Sum_probs=27.4
Q ss_pred cccccccccccChhhHHHHHhh------hCCCcccCccccccccCccchhhh
Q psy16646 63 VICEICNKEFTHKSSLAEHRVL------HFPAQHKCSLCQQAFKRDKHSKGD 108 (159)
Q Consensus 63 ~~c~~c~~~f~~~~~l~~h~~~------h~~k~~~C~~C~~~f~~~~~l~~h 108 (159)
..|..|+..+...+.-..-... ..+.=+.|+.||+.|...+++.+-
T Consensus 92 sRC~~CN~~L~~v~~~~v~~~vp~~v~~~~~~f~~C~~C~kiyW~GsH~~~~ 143 (147)
T PF01927_consen 92 SRCPKCNGPLRPVSKEEVKDRVPPYVYETYDEFWRCPGCGKIYWEGSHWRRM 143 (147)
T ss_pred CccCCCCcEeeechhhccccccCccccccCCeEEECCCCCCEecccccHHHH
Confidence 4688888755433221110001 123357899999999998876644
No 169
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=41.40 E-value=14 Score=22.84 Aligned_cols=13 Identities=31% Similarity=0.514 Sum_probs=8.2
Q ss_pred cccCccccccccC
Q psy16646 89 QHKCSLCQQAFKR 101 (159)
Q Consensus 89 ~~~C~~C~~~f~~ 101 (159)
...|..||..|..
T Consensus 70 ~~~C~~Cg~~~~~ 82 (114)
T PRK03681 70 ECWCETCQQYVTL 82 (114)
T ss_pred EEEcccCCCeeec
Confidence 3677888765543
No 170
>PF05191 ADK_lid: Adenylate kinase, active site lid; InterPro: IPR007862 Adenylate kinases (ADK; 2.7.4.3 from EC) are phosphotransferases that catalyse the Mg-dependent reversible conversion of ATP and AMP to two molecules of ADP, an essential reaction for many processes in living cells. In large variants of adenylate kinase, the AMP and ATP substrates are buried in a domain that undergoes conformational changes from an open to a closed state when bound to substrate; the ligand is then contained within a highly specific environment required for catalysis. Adenylate kinase is a 3-domain protein consisting of a large central CORE domain flanked by a LID domain on one side and the AMP-binding NMPbind domain on the other []. The LID domain binds ATP and covers the phosphates at the active site. The substrates first bind the CORE domain, followed by closure of the active site by the LID and NMPbind domains. Comparisons of adenylate kinases have revealed a particular divergence in the active site lid. In some organisms, particularly the Gram-positive bacteria, residues in the lid domain have been mutated to cysteines and these cysteine residues (two CX(n)C motifs) are responsible for the binding of a zinc ion. The bound zinc ion in the lid domain is clearly structurally homologous to Zinc-finger domains. However, it is unclear whether the adenylate kinase lid is a novel zinc-finger DNA/RNA binding domain, or that the lid bound zinc serves a purely structural function [].; GO: 0004017 adenylate kinase activity; PDB: 3BE4_A 2OSB_B 2ORI_A 2EU8_A 3DL0_A 1P3J_A 2QAJ_A 2OO7_A 2P3S_A 3DKV_A ....
Probab=41.35 E-value=15 Score=17.57 Aligned_cols=11 Identities=9% Similarity=0.018 Sum_probs=5.2
Q ss_pred ccccccCcccc
Q psy16646 119 KTRNSIGITVR 129 (159)
Q Consensus 119 ~~C~~C~~~f~ 129 (159)
-.|+.||-.+.
T Consensus 22 ~~Cd~cg~~L~ 32 (36)
T PF05191_consen 22 GVCDNCGGELV 32 (36)
T ss_dssp TBCTTTTEBEB
T ss_pred CccCCCCCeeE
Confidence 33555554443
No 171
>PRK14873 primosome assembly protein PriA; Provisional
Probab=40.80 E-value=21 Score=29.33 Aligned_cols=17 Identities=24% Similarity=0.210 Sum_probs=9.7
Q ss_pred CcccCCCCCcccccccc
Q psy16646 23 PRVDSSLPPQFHCYVCK 39 (159)
Q Consensus 23 ~~~~h~~~~~~~C~~c~ 39 (159)
.+..|...+...|..||
T Consensus 401 ~L~~h~~~~~l~Ch~CG 417 (665)
T PRK14873 401 PLGLPSAGGTPRCRWCG 417 (665)
T ss_pred ceeEecCCCeeECCCCc
Confidence 44445555556666666
No 172
>KOG2907|consensus
Probab=40.67 E-value=11 Score=23.22 Aligned_cols=13 Identities=8% Similarity=-0.054 Sum_probs=9.8
Q ss_pred cccccccCccccc
Q psy16646 118 MKTRNSIGITVRQ 130 (159)
Q Consensus 118 ~~~C~~C~~~f~~ 130 (159)
.|.|+.|++.|..
T Consensus 102 FYTC~kC~~k~~e 114 (116)
T KOG2907|consen 102 FYTCPKCKYKFTE 114 (116)
T ss_pred EEEcCccceeeec
Confidence 3888888887764
No 173
>KOG4377|consensus
Probab=39.94 E-value=33 Score=26.31 Aligned_cols=111 Identities=21% Similarity=0.337 Sum_probs=62.8
Q ss_pred CCCccccc--cccccccChHHHHHHHhhhhcCCCC-----------ccccc--cccccccChhhHHHHHhhhCCC-----
Q psy16646 29 LPPQFHCY--VCKKKYRHKRQLVRHFQVNHTNNYD-----------RVICE--ICNKEFTHKSSLAEHRVLHFPA----- 88 (159)
Q Consensus 29 ~~~~~~C~--~c~~~f~~~~~l~~h~~~~~~~~~~-----------~~~c~--~c~~~f~~~~~l~~h~~~h~~k----- 88 (159)
+...|.|. .|+.-+.....+.+|..+ |...+. -|.|. .|.+ +-++...|...|.++
T Consensus 268 ~rEhyhcl~e~C~ykr~~k~DvirH~~~-hkkrdnsL~dgf~rfs~syhC~~~~C~k---sTsdV~~h~nFht~~~n~Gf 343 (480)
T KOG4377|consen 268 GREHYHCLNEYCFYKRGQKNDVIRHVEI-HKKRDNSLIDGFHRFSNSYHCTGQICEK---STSDVLLHDNFHTDKRNNGF 343 (480)
T ss_pred cchhhcccCccccccccchhhhHHHHHH-HhhcccccccchhhcCccchhhhcccCc---ccccccccCccccccccCce
Confidence 34557774 488887778889999888 433211 12332 3655 333444554444222
Q ss_pred ---cccCcccc--ccccCccchhhhhhhhhhhhcc-----------------------ccc--cccCccccchhhHHHhh
Q psy16646 89 ---QHKCSLCQ--QAFKRDKHSKGDDIREEIEREM-----------------------KTR--NSIGITVRQNQTNKNHR 138 (159)
Q Consensus 89 ---~~~C~~C~--~~f~~~~~l~~h~~~~~~~~~~-----------------------~~C--~~C~~~f~~~~~l~~H~ 138 (159)
-|.|..|| ..|.....-.-|.+-+.++... +-| ..|+..+...+....|.
T Consensus 344 rrthfhC~r~gCTdtfK~~khk~yh~kdda~~~dGfkkf~k~e~cay~gCkys~~cnhfhc~r~Gc~~tl~s~sqm~shk 423 (480)
T KOG4377|consen 344 RRTHFHCQRIGCTDTFKDSKHKPYHYKDDAGEIDGFKKFFKDENCAYTGCKYSGICNHFHCDRLGCEATLYSVSQMASHK 423 (480)
T ss_pred ecceeEEeccCCccccccccccccccCcchhhhhhhhhhhccccCCccCcccccceeeeeecccCCceEEEehhhhhhhh
Confidence 36787777 4554333323333333332211 333 56888899999999998
Q ss_pred ccCCC
Q psy16646 139 SGDQK 143 (159)
Q Consensus 139 ~~h~~ 143 (159)
+.|.+
T Consensus 424 rkheR 428 (480)
T KOG4377|consen 424 RKHER 428 (480)
T ss_pred hhhhh
Confidence 87764
No 174
>COG1779 C4-type Zn-finger protein [General function prediction only]
Probab=39.80 E-value=8.6 Score=26.24 Aligned_cols=11 Identities=9% Similarity=0.027 Sum_probs=4.9
Q ss_pred ccccccCcccc
Q psy16646 119 KTRNSIGITVR 129 (159)
Q Consensus 119 ~~C~~C~~~f~ 129 (159)
+.|..||++++
T Consensus 44 ~~C~~CgYR~~ 54 (201)
T COG1779 44 GVCERCGYRST 54 (201)
T ss_pred EEccccCCccc
Confidence 33444444443
No 175
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=39.76 E-value=18 Score=18.71 Aligned_cols=10 Identities=20% Similarity=0.125 Sum_probs=4.5
Q ss_pred hcccCCCCCC
Q psy16646 7 KSVKNPNAKK 16 (159)
Q Consensus 7 ~~~~~~~~~~ 16 (159)
+.-.||.|+.
T Consensus 18 k~~~CPrCG~ 27 (51)
T COG1998 18 KNRFCPRCGP 27 (51)
T ss_pred ccccCCCCCC
Confidence 3344555444
No 176
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=39.02 E-value=16 Score=17.80 Aligned_cols=11 Identities=9% Similarity=-0.179 Sum_probs=5.3
Q ss_pred ccccccCcccc
Q psy16646 119 KTRNSIGITVR 129 (159)
Q Consensus 119 ~~C~~C~~~f~ 129 (159)
+.|..|+..|-
T Consensus 13 f~C~~C~~~FC 23 (39)
T smart00154 13 FKCRHCGNLFC 23 (39)
T ss_pred eECCccCCccc
Confidence 44555554443
No 177
>KOG4727|consensus
Probab=37.59 E-value=18 Score=24.09 Aligned_cols=27 Identities=7% Similarity=-0.002 Sum_probs=22.0
Q ss_pred hhhhccccccccCccccchhhHHHhhc
Q psy16646 113 EIEREMKTRNSIGITVRQNQTNKNHRS 139 (159)
Q Consensus 113 ~~~~~~~~C~~C~~~f~~~~~l~~H~~ 139 (159)
.++...|.|..|+-.|.....+..|+.
T Consensus 70 ~sq~~GyyCdVCdcvvKDSinflDHiN 96 (193)
T KOG4727|consen 70 RSQKGGYYCDVCDCVVKDSINFLDHIN 96 (193)
T ss_pred ccccCceeeeecceeehhhHHHHHHhc
Confidence 445555899999999999999988874
No 178
>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=37.22 E-value=16 Score=19.98 Aligned_cols=10 Identities=50% Similarity=1.182 Sum_probs=3.6
Q ss_pred cccccccccc
Q psy16646 64 ICEICNKEFT 73 (159)
Q Consensus 64 ~c~~c~~~f~ 73 (159)
.|..|+..|.
T Consensus 11 ~C~~C~~~F~ 20 (69)
T PF01363_consen 11 NCMICGKKFS 20 (69)
T ss_dssp B-TTT--B-B
T ss_pred cCcCcCCcCC
Confidence 4666766663
No 179
>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=36.94 E-value=12 Score=23.02 Aligned_cols=13 Identities=31% Similarity=0.843 Sum_probs=8.0
Q ss_pred ccCccccccccCc
Q psy16646 90 HKCSLCQQAFKRD 102 (159)
Q Consensus 90 ~~C~~C~~~f~~~ 102 (159)
..|..||..|...
T Consensus 71 ~~C~~Cg~~~~~~ 83 (113)
T PF01155_consen 71 ARCRDCGHEFEPD 83 (113)
T ss_dssp EEETTTS-EEECH
T ss_pred EECCCCCCEEecC
Confidence 5677777766554
No 180
>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=36.69 E-value=14 Score=18.17 Aligned_cols=22 Identities=23% Similarity=0.312 Sum_probs=12.7
Q ss_pred CCCcccCCCCCccccccccccc
Q psy16646 21 YVPRVDSSLPPQFHCYVCKKKY 42 (159)
Q Consensus 21 ~~~~~~h~~~~~~~C~~c~~~f 42 (159)
.+-+.+-...++..|+.|+..|
T Consensus 18 rVyl~l~~~~~~~~CpYCg~~y 39 (40)
T PF10276_consen 18 RVYLNLDDEPGPVVCPYCGTRY 39 (40)
T ss_dssp CEEEE-TTTTCEEEETTTTEEE
T ss_pred eEEEecCCCCCeEECCCCCCEE
Confidence 3334444433567888888765
No 181
>PF15269 zf-C2H2_7: Zinc-finger
Probab=36.20 E-value=23 Score=17.84 Aligned_cols=22 Identities=14% Similarity=-0.084 Sum_probs=15.2
Q ss_pred ccccccCccccchhhHHHhhcc
Q psy16646 119 KTRNSIGITVRQNQTNKNHRSG 140 (159)
Q Consensus 119 ~~C~~C~~~f~~~~~l~~H~~~ 140 (159)
|+|=+|..+....+.|..|+.-
T Consensus 21 ykcfqcpftc~~kshl~nhmky 42 (54)
T PF15269_consen 21 YKCFQCPFTCNEKSHLFNHMKY 42 (54)
T ss_pred ceeecCCcccchHHHHHHHHHH
Confidence 6677777777777777777643
No 182
>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=36.13 E-value=16 Score=21.95 Aligned_cols=18 Identities=11% Similarity=0.176 Sum_probs=11.8
Q ss_pred ccCCCCCcccccccccccc
Q psy16646 25 VDSSLPPQFHCYVCKKKYR 43 (159)
Q Consensus 25 ~~h~~~~~~~C~~c~~~f~ 43 (159)
..+.+ ++.+|.+||..|.
T Consensus 73 ~l~~g-~~~rC~eCG~~fk 90 (97)
T cd00924 73 WLEKG-KPKRCPECGHVFK 90 (97)
T ss_pred EEeCC-CceeCCCCCcEEE
Confidence 34445 5778887887764
No 183
>PF10537 WAC_Acf1_DNA_bd: ATP-utilising chromatin assembly and remodelling N-terminal; InterPro: IPR013136 ACF (for ATP-utilising chromatin assembly and remodeling factor) is a chromatin-remodeling complex that catalyzes the ATP-dependent assembly of periodic nucleosome arrays. This reaction utilises the energy of ATP hydrolysis by ISWI, the smaller of the two subunits of ACF. Acf1, the large subunit of ACF, is essential for the full activity of the complex. The WAC (WSTF/Acf1/cbp146) domain is an ~110-residue module present at the N-termini of Acf1-related proteins in a variety of organisms. It is found in association with other domains such as the bromodomain, the PHD-type zinc finger, DDT or WAKS. The DNA-binding region of Acf1 includes the WAC domain, which is necessary for the efficient binding of ACF complex to DNA. It seems probable that the WAC domain will be involved in DNA binding in other related factors [, ]. Some proteins known to contain a WAC domain are the Drosophila melanogaster (Fruit fly) ATP-dependent chromatin assembly factor large subunit Acf1, human WSTF (Williams syndrome transcription factor), mouse cbp146, yeast imitation switch two complex protein 1 (ITC1 or YGL133w), and yeast protein YPL216w.
Probab=36.11 E-value=34 Score=20.73 Aligned_cols=37 Identities=16% Similarity=0.266 Sum_probs=22.2
Q ss_pred ccccccccccccChHHHHHHHhhhhcCCCCcccccccccc
Q psy16646 32 QFHCYVCKKKYRHKRQLVRHFQVNHTNNYDRVICEICNKE 71 (159)
Q Consensus 32 ~~~C~~c~~~f~~~~~l~~h~~~~~~~~~~~~~c~~c~~~ 71 (159)
.+.|+.-|..|.....+...+.. ... ..|.|...|++
T Consensus 3 Vf~i~~T~EiF~dYe~Y~~R~~~-y~~--~vwtC~~TGk~ 39 (102)
T PF10537_consen 3 VFYIPFTGEIFRDYEEYLKRMIL-YNQ--RVWTCEITGKS 39 (102)
T ss_pred eEEeCCCCcccCCHHHHHHHHHH-HhC--CeeEEecCCCC
Confidence 45566667777776666655544 332 45777766653
No 184
>PF14311 DUF4379: Domain of unknown function (DUF4379)
Probab=35.95 E-value=19 Score=18.81 Aligned_cols=12 Identities=33% Similarity=0.836 Sum_probs=5.8
Q ss_pred ccCccccccccC
Q psy16646 90 HKCSLCQQAFKR 101 (159)
Q Consensus 90 ~~C~~C~~~f~~ 101 (159)
++|..||..|..
T Consensus 29 W~C~~Cgh~w~~ 40 (55)
T PF14311_consen 29 WKCPKCGHEWKA 40 (55)
T ss_pred EECCCCCCeeEc
Confidence 455555544443
No 185
>smart00132 LIM Zinc-binding domain present in Lin-11, Isl-1, Mec-3. Zinc-binding domain family. Some LIM domains bind protein partners via tyrosine-containing motifs. LIM domains are found in many key regulators of developmental pathways.
Probab=35.15 E-value=20 Score=16.46 Aligned_cols=10 Identities=10% Similarity=0.032 Sum_probs=5.7
Q ss_pred ccccccCccc
Q psy16646 119 KTRNSIGITV 128 (159)
Q Consensus 119 ~~C~~C~~~f 128 (159)
|.|..|+..+
T Consensus 28 f~C~~C~~~L 37 (39)
T smart00132 28 FKCSKCGKPL 37 (39)
T ss_pred CCCcccCCcC
Confidence 5566666544
No 186
>KOG4317|consensus
Probab=35.13 E-value=12 Score=27.47 Aligned_cols=19 Identities=16% Similarity=0.071 Sum_probs=8.2
Q ss_pred ccccccCccccchhhHHHh
Q psy16646 119 KTRNSIGITVRQNQTNKNH 137 (159)
Q Consensus 119 ~~C~~C~~~f~~~~~l~~H 137 (159)
|.|+.|+..|-+..-++.|
T Consensus 20 YtCPRCn~~YCsl~CYr~h 38 (383)
T KOG4317|consen 20 YTCPRCNLLYCSLKCYRNH 38 (383)
T ss_pred ccCCCCCccceeeeeecCC
Confidence 4444444444444333333
No 187
>KOG4167|consensus
Probab=35.10 E-value=9.9 Score=31.27 Aligned_cols=25 Identities=28% Similarity=0.375 Sum_probs=22.7
Q ss_pred CccccccccccccChhhHHHHHhhh
Q psy16646 61 DRVICEICNKEFTHKSSLAEHRVLH 85 (159)
Q Consensus 61 ~~~~c~~c~~~f~~~~~l~~h~~~h 85 (159)
.-|.|..|++.|.-..+++.|+++|
T Consensus 791 giFpCreC~kvF~KiKSrNAHMK~H 815 (907)
T KOG4167|consen 791 GIFPCRECGKVFFKIKSRNAHMKTH 815 (907)
T ss_pred ceeehHHHHHHHHHHhhhhHHHHHH
Confidence 3478999999999999999999999
No 188
>PRK05978 hypothetical protein; Provisional
Probab=35.01 E-value=22 Score=23.22 Aligned_cols=8 Identities=38% Similarity=1.261 Sum_probs=3.6
Q ss_pred Cccccccc
Q psy16646 92 CSLCQQAF 99 (159)
Q Consensus 92 C~~C~~~f 99 (159)
|+.||..|
T Consensus 55 C~~CG~~~ 62 (148)
T PRK05978 55 CAACGEDF 62 (148)
T ss_pred ccccCCcc
Confidence 44444433
No 189
>COG4391 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=34.74 E-value=11 Score=20.39 Aligned_cols=44 Identities=5% Similarity=-0.129 Sum_probs=23.5
Q ss_pred Hhhh-CCCcccCccccccccCccchhhhhhhhhhhhccccccccCccccc
Q psy16646 82 RVLH-FPAQHKCSLCQQAFKRDKHSKGDDIREEIEREMKTRNSIGITVRQ 130 (159)
Q Consensus 82 ~~~h-~~k~~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~~C~~C~~~f~~ 130 (159)
..++ +..++.|..-+-.|...-.+. --|++..-.|+.|+..|..
T Consensus 16 ~~I~~~~~~l~C~g~~~p~~HPrV~L-----~mg~~gev~CPYC~t~y~l 60 (62)
T COG4391 16 ETIEIGDLPLMCPGPEPPNDHPRVFL-----DMGDEGEVVCPYCSTRYRL 60 (62)
T ss_pred eEEEeCCeeEEcCCCCCCCCCCEEEE-----EcCCCCcEecCccccEEEe
Confidence 3344 566777776554544432222 1133333668888887753
No 190
>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=34.70 E-value=30 Score=16.23 Aligned_cols=21 Identities=14% Similarity=0.022 Sum_probs=12.3
Q ss_pred cccccccCccccchhhHHHhhc
Q psy16646 118 MKTRNSIGITVRQNQTNKNHRS 139 (159)
Q Consensus 118 ~~~C~~C~~~f~~~~~l~~H~~ 139 (159)
.+.|+.|++.+.. +-+..|+.
T Consensus 4 ~~~C~nC~R~v~a-~RfA~HLe 24 (33)
T PF08209_consen 4 YVECPNCGRPVAA-SRFAPHLE 24 (33)
T ss_dssp EEE-TTTSSEEEG-GGHHHHHH
T ss_pred eEECCCCcCCcch-hhhHHHHH
Confidence 3678888886543 34566653
No 191
>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=34.69 E-value=39 Score=18.39 Aligned_cols=12 Identities=25% Similarity=0.534 Sum_probs=6.5
Q ss_pred Cccccccccccc
Q psy16646 61 DRVICEICNKEF 72 (159)
Q Consensus 61 ~~~~c~~c~~~f 72 (159)
..+.|+.||...
T Consensus 45 r~~~C~~Cg~~~ 56 (69)
T PF07282_consen 45 RVFTCPNCGFEM 56 (69)
T ss_pred ceEEcCCCCCEE
Confidence 345566666543
No 192
>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=34.45 E-value=24 Score=17.44 Aligned_cols=11 Identities=9% Similarity=-0.058 Sum_probs=4.4
Q ss_pred ccccccCcccc
Q psy16646 119 KTRNSIGITVR 129 (159)
Q Consensus 119 ~~C~~C~~~f~ 129 (159)
+.|+.|+..|-
T Consensus 14 ~~C~~C~~~FC 24 (43)
T PF01428_consen 14 FKCKHCGKSFC 24 (43)
T ss_dssp EE-TTTS-EE-
T ss_pred eECCCCCcccC
Confidence 55555555554
No 193
>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=34.26 E-value=16 Score=30.01 Aligned_cols=9 Identities=22% Similarity=0.641 Sum_probs=4.7
Q ss_pred cccCccccc
Q psy16646 89 QHKCSLCQQ 97 (159)
Q Consensus 89 ~~~C~~C~~ 97 (159)
|..|+.||-
T Consensus 173 p~aCp~CGP 181 (750)
T COG0068 173 PIACPKCGP 181 (750)
T ss_pred cccCcccCC
Confidence 455555553
No 194
>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=34.21 E-value=16 Score=21.61 Aligned_cols=14 Identities=21% Similarity=0.529 Sum_probs=8.2
Q ss_pred cccCccccccccCc
Q psy16646 89 QHKCSLCQQAFKRD 102 (159)
Q Consensus 89 ~~~C~~C~~~f~~~ 102 (159)
.|.|..|++.|.-.
T Consensus 53 IW~C~~C~~~~AGG 66 (91)
T TIGR00280 53 IWTCRKCGAKFAGG 66 (91)
T ss_pred EEEcCCCCCEEeCC
Confidence 56666666665543
No 195
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=33.85 E-value=14 Score=22.25 Aligned_cols=40 Identities=23% Similarity=0.503 Sum_probs=22.3
Q ss_pred CCCCccccccccccccChHHHHHHHhhhhcCCCCcccccccccccc
Q psy16646 28 SLPPQFHCYVCKKKYRHKRQLVRHFQVNHTNNYDRVICEICNKEFT 73 (159)
Q Consensus 28 ~~~~~~~C~~c~~~f~~~~~l~~h~~~~~~~~~~~~~c~~c~~~f~ 73 (159)
.-++.|.|+.||..-.+...++.- ... ....|..||..|.
T Consensus 18 ~L~k~FtCp~Cghe~vs~ctvkk~-----~~~-g~~~Cg~CGls~e 57 (104)
T COG4888 18 VLPKTFTCPRCGHEKVSSCTVKKT-----VNI-GTAVCGNCGLSFE 57 (104)
T ss_pred cCCceEecCccCCeeeeEEEEEec-----Cce-eEEEcccCcceEE
Confidence 356778898888654332222211 111 2356888887665
No 196
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=33.22 E-value=23 Score=27.32 Aligned_cols=30 Identities=17% Similarity=0.218 Sum_probs=19.2
Q ss_pred cCccccccccCccchhhhhhhhhhhhccccccccCccccchh
Q psy16646 91 KCSLCQQAFKRDKHSKGDDIREEIEREMKTRNSIGITVRQNQ 132 (159)
Q Consensus 91 ~C~~C~~~f~~~~~l~~h~~~~~~~~~~~~C~~C~~~f~~~~ 132 (159)
.|+.||..... .|.. .|+|+.||..+....
T Consensus 352 ~Cp~Cg~~m~S-----------~G~~-g~rC~kCg~~~~~~~ 381 (421)
T COG1571 352 VCPRCGGRMKS-----------AGRN-GFRCKKCGTRARETL 381 (421)
T ss_pred CCCccCCchhh-----------cCCC-CcccccccccCCccc
Confidence 68888743322 2333 388888888887654
No 197
>COG4957 Predicted transcriptional regulator [Transcription]
Probab=33.11 E-value=1e+02 Score=19.80 Aligned_cols=35 Identities=31% Similarity=0.525 Sum_probs=25.4
Q ss_pred CCCCCCCcccCCCCCccccccccccccChHHHHHHHhh
Q psy16646 17 RYRPYVPRVDSSLPPQFHCYVCKKKYRHKRQLVRHFQV 54 (159)
Q Consensus 17 ~~~~~~~~~~h~~~~~~~C~~c~~~f~~~~~l~~h~~~ 54 (159)
...+.+..+......-..|-++|+.|. +|++|..+
T Consensus 61 ~~~PAV~~kKSVtpD~IicLEDGkkfK---SLKRHL~t 95 (148)
T COG4957 61 KQKPAVPIKKSVTPDYIICLEDGKKFK---SLKRHLTT 95 (148)
T ss_pred ccCCCCCcccccCCCeEEEeccCcchH---HHHHHHhc
Confidence 344556666666666678999999885 58888887
No 198
>PLN02294 cytochrome c oxidase subunit Vb
Probab=33.06 E-value=21 Score=23.81 Aligned_cols=20 Identities=25% Similarity=0.537 Sum_probs=14.9
Q ss_pred hhhCCCcccCccccccccCc
Q psy16646 83 VLHFPAQHKCSLCQQAFKRD 102 (159)
Q Consensus 83 ~~h~~k~~~C~~C~~~f~~~ 102 (159)
..+.++|..|++||..|.-.
T Consensus 135 ~L~kGkp~RCpeCG~~fkL~ 154 (174)
T PLN02294 135 WLEKGKSFECPVCTQYFELE 154 (174)
T ss_pred EecCCCceeCCCCCCEEEEE
Confidence 34445799999999888643
No 199
>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=32.86 E-value=16 Score=23.68 Aligned_cols=30 Identities=13% Similarity=0.097 Sum_probs=17.3
Q ss_pred cccCccccccccCccchhhhhhhhhhhhccccccccCcccc
Q psy16646 89 QHKCSLCQQAFKRDKHSKGDDIREEIEREMKTRNSIGITVR 129 (159)
Q Consensus 89 ~~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~~C~~C~~~f~ 129 (159)
.|.|..||...... +.+.- -.|+.||..--
T Consensus 112 ~l~C~~Cg~~~~~~---------~~~~l--~~Cp~C~~~~F 141 (146)
T PF07295_consen 112 TLVCENCGHEVELT---------HPERL--PPCPKCGHTEF 141 (146)
T ss_pred eEecccCCCEEEec---------CCCcC--CCCCCCCCCee
Confidence 48888888544332 22222 34888887643
No 200
>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 PRK04023 DNA polymerase II large subunit; Validated
Probab=32.67 E-value=63 Score=28.09 Aligned_cols=8 Identities=38% Similarity=0.766 Sum_probs=3.8
Q ss_pred cccccccc
Q psy16646 33 FHCYVCKK 40 (159)
Q Consensus 33 ~~C~~c~~ 40 (159)
..|+.||.
T Consensus 627 RfCpsCG~ 634 (1121)
T PRK04023 627 RKCPSCGK 634 (1121)
T ss_pred ccCCCCCC
Confidence 34555553
No 202
>KOG2785|consensus
Probab=32.62 E-value=37 Score=25.77 Aligned_cols=25 Identities=16% Similarity=0.194 Sum_probs=19.3
Q ss_pred CccccccccccccChhhHHHHHhhh
Q psy16646 61 DRVICEICNKEFTHKSSLAEHRVLH 85 (159)
Q Consensus 61 ~~~~c~~c~~~f~~~~~l~~h~~~h 85 (159)
.|..|..|+..+.+......|+..+
T Consensus 165 ~Pt~CLfC~~~~k~~e~~~~HM~~~ 189 (390)
T KOG2785|consen 165 IPTDCLFCDKKSKSLEENLKHMFKE 189 (390)
T ss_pred CCcceeecCCCcccHHHHHHHHhhc
Confidence 4567888988888888888887654
No 203
>KOG2231|consensus
Probab=32.04 E-value=45 Score=27.46 Aligned_cols=98 Identities=13% Similarity=0.186 Sum_probs=61.6
Q ss_pred ChHHHHHHHhhhhcC-CC---CccccccccccccChhhHHHHHhhhCCCcccCccc------cccccCccchhhhhhhhh
Q psy16646 44 HKRQLVRHFQVNHTN-NY---DRVICEICNKEFTHKSSLAEHRVLHFPAQHKCSLC------QQAFKRDKHSKGDDIREE 113 (159)
Q Consensus 44 ~~~~l~~h~~~~~~~-~~---~~~~c~~c~~~f~~~~~l~~h~~~h~~k~~~C~~C------~~~f~~~~~l~~h~~~~~ 113 (159)
+...|..|+.. .-. ++ ..-.|..|...|.....|..|++.+ -|.|..| +.-|..-..|..|-+.+|
T Consensus 161 t~~el~~h~~~-gd~d~~s~rGhp~C~~C~~~fld~~el~rH~~~~---h~~chfC~~~~~~neyy~~~~dLe~HfR~~H 236 (669)
T KOG2231|consen 161 TRAELNLHLMF-GDPDDESCRGHPLCKFCHERFLDDDELYRHLRFD---HEFCHFCDYKTGQNEYYNDYDDLEEHFRKGH 236 (669)
T ss_pred hHHHHHHHHhc-CCCccccccCCccchhhhhhhccHHHHHHhhccc---eeheeecCcccccchhcccchHHHHHhhhcC
Confidence 34667777654 221 10 1236889999999999999998754 3344444 455666777888877766
Q ss_pred hhhcccccc--ccCc-----cccchhhHHHhhccCCCccccccC
Q psy16646 114 IEREMKTRN--SIGI-----TVRQNQTNKNHRSGDQKKKTAKQL 150 (159)
Q Consensus 114 ~~~~~~~C~--~C~~-----~f~~~~~l~~H~~~h~~~k~~~~~ 150 (159)
|.|. .|.- .|.....|..|.+.++.++.|-+.
T Consensus 237 -----flCE~~~C~~~~f~~~~~~ei~lk~~~~~~~~e~~~~~~ 275 (669)
T KOG2231|consen 237 -----FLCEEEFCRTKKFYVAFELEIELKAHNRFIQHEKCYICR 275 (669)
T ss_pred -----ccccccccccceeeehhHHHHHHHhhccccchheeccCC
Confidence 5564 3432 234455666666666667777665
No 204
>KOG2785|consensus
Probab=31.06 E-value=29 Score=26.28 Aligned_cols=52 Identities=10% Similarity=-0.012 Sum_probs=41.0
Q ss_pred cccCccccccccCccchhhhhhhhhhhhcc----------------------ccccccC---ccccchhhHHHhhcc
Q psy16646 89 QHKCSLCQQAFKRDKHSKGDDIREEIEREM----------------------KTRNSIG---ITVRQNQTNKNHRSG 140 (159)
Q Consensus 89 ~~~C~~C~~~f~~~~~l~~h~~~~~~~~~~----------------------~~C~~C~---~~f~~~~~l~~H~~~ 140 (159)
|-.|..|++.+........|+-.+||---+ +.|-.|+ +.|.+..+.+.|+..
T Consensus 166 Pt~CLfC~~~~k~~e~~~~HM~~~HgffIPdreYL~D~~GLl~YLgeKV~~~~~CL~CN~~~~~f~sleavr~HM~~ 242 (390)
T KOG2785|consen 166 PTDCLFCDKKSKSLEENLKHMFKEHGFFIPDREYLTDEKGLLKYLGEKVGIGFICLFCNELGRPFSSLEAVRAHMRD 242 (390)
T ss_pred CcceeecCCCcccHHHHHHHHhhccCCcCCchHhhhchhHHHHHHHHHhccCceEEEeccccCcccccHHHHHHHhh
Confidence 577999999999888888888777663211 7777788 889999999999654
No 205
>PF10083 DUF2321: Uncharacterized protein conserved in bacteria (DUF2321); InterPro: IPR016891 This entry is represented by Bacteriophage 'Lactobacillus prophage Lj928', Orf-Ljo1454. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=30.85 E-value=17 Score=23.78 Aligned_cols=13 Identities=8% Similarity=-0.064 Sum_probs=7.9
Q ss_pred ccccccCccccch
Q psy16646 119 KTRNSIGITVRQN 131 (159)
Q Consensus 119 ~~C~~C~~~f~~~ 131 (159)
..|..||+.|+..
T Consensus 69 sYC~~CGkpyPWt 81 (158)
T PF10083_consen 69 SYCHNCGKPYPWT 81 (158)
T ss_pred hhHHhCCCCCchH
Confidence 5566666666553
No 206
>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=30.40 E-value=27 Score=27.34 Aligned_cols=21 Identities=14% Similarity=0.322 Sum_probs=10.1
Q ss_pred ccCccccccccCccchhhhhh
Q psy16646 90 HKCSLCQQAFKRDKHSKGDDI 110 (159)
Q Consensus 90 ~~C~~C~~~f~~~~~l~~h~~ 110 (159)
|.|+.|.+.|.....+..|+.
T Consensus 58 WiCp~CskkF~d~~~~~~H~~ 78 (466)
T PF04780_consen 58 WICPRCSKKFSDAESCLSHME 78 (466)
T ss_pred eeCCcccceeCCHHHHHHHHH
Confidence 344445555555545554443
No 207
>PF00412 LIM: LIM domain; InterPro: IPR001781 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents LIM-type zinc finger (Znf) domains. LIM domains coordinate one or more zinc atoms, and are named after the three proteins (LIN-11, Isl1 and MEC-3) in which they were first found. They consist of two zinc-binding motifs that resemble GATA-like Znf's, however the residues holding the zinc atom(s) are variable, involving Cys, His, Asp or Glu residues. LIM domains are involved in proteins with differing functions, including gene expression, and cytoskeleton organisation and development [, ]. Protein containing LIM Znf domains include: Caenorhabditis elegans mec-3; a protein required for the differentiation of the set of six touch receptor neurons in this nematode. C. elegans. lin-11; a protein required for the asymmetric division of vulval blast cells. Vertebrate insulin gene enhancer binding protein isl-1. Isl-1 binds to one of the two cis-acting protein-binding domains of the insulin gene. Vertebrate homeobox proteins lim-1, lim-2 (lim-5) and lim3. Vertebrate lmx-1, which acts as a transcriptional activator by binding to the FLAT element; a beta-cell-specific transcriptional enhancer found in the insulin gene. Mammalian LH-2, a transcriptional regulatory protein involved in the control of cell differentiation in developing lymphoid and neural cell types. Drosophila melanogaster (Fruit fly) protein apterous, required for the normal development of the wing and halter imaginal discs. Vertebrate protein kinases LIMK-1 and LIMK-2. Mammalian rhombotins. Rhombotin 1 (RBTN1 or TTG-1) and rhombotin-2 (RBTN2 or TTG-2) are proteins of about 160 amino acids whose genes are disrupted by chromosomal translocations in T-cell leukemia. Mammalian and avian cysteine-rich protein (CRP), a 192 amino-acid protein of unknown function. Seems to interact with zyxin. Mammalian cysteine-rich intestinal protein (CRIP), a small protein which seems to have a role in zinc absorption and may function as an intracellular zinc transport protein. Vertebrate paxillin, a cytoskeletal focal adhesion protein. Mus musculus (Mouse) testin which should not be confused with rat testin which is a thiol protease homologue (see IPR000169 from INTERPRO). Helianthus annuus (Common sunflower) pollen specific protein SF3. Chicken zyxin. Zyxin is a low-abundance adhesion plaque protein which has been shown to interact with CRP. Yeast protein LRG1 which is involved in sporulation []. Saccharomyces cerevisiae (Baker's yeast) rho-type GTPase activating protein RGA1/DBM1. C. elegans homeobox protein ceh-14. C. elegans homeobox protein unc-97. S. cerevisiae hypothetical protein YKR090w. C. elegans hypothetical proteins C28H8.6. These proteins generally contain two tandem copies of the LIM domain in their N-terminal section. Zyxin and paxillin are exceptions in that they contain respectively three and four LIM domains at their C-terminal extremity. In apterous, isl-1, LH-2, lin-11, lim-1 to lim-3, lmx-1 and ceh-14 and mec-3 there is a homeobox domain some 50 to 95 amino acids after the LIM domains. LIM domains contain seven conserved cysteine residues and a histidine. The arrangement followed by these conserved residues is: C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] LIM domains bind two zinc ions []. LIM does not bind DNA, rather it seems to act as an interface for protein-protein interaction. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CO8_A 2EGQ_A 2CUR_A 3IXE_B 1CTL_A 1B8T_A 1X62_A 2DFY_C 1IML_A 2CUQ_A ....
Probab=30.08 E-value=24 Score=18.22 Aligned_cols=12 Identities=8% Similarity=0.061 Sum_probs=6.0
Q ss_pred ccccccCccccc
Q psy16646 119 KTRNSIGITVRQ 130 (159)
Q Consensus 119 ~~C~~C~~~f~~ 130 (159)
|.|..|+..+..
T Consensus 27 f~C~~C~~~l~~ 38 (58)
T PF00412_consen 27 FKCSKCGKPLND 38 (58)
T ss_dssp SBETTTTCBTTT
T ss_pred cccCCCCCccCC
Confidence 455555554433
No 208
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=29.82 E-value=21 Score=21.14 Aligned_cols=13 Identities=23% Similarity=0.595 Sum_probs=7.4
Q ss_pred cccCccccccccC
Q psy16646 89 QHKCSLCQQAFKR 101 (159)
Q Consensus 89 ~~~C~~C~~~f~~ 101 (159)
.|.|..|++.|.-
T Consensus 54 IW~C~~C~~~~AG 66 (90)
T PRK03976 54 IWECRKCGAKFAG 66 (90)
T ss_pred EEEcCCCCCEEeC
Confidence 4566666655543
No 209
>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=29.77 E-value=25 Score=17.18 Aligned_cols=14 Identities=7% Similarity=-0.137 Sum_probs=8.6
Q ss_pred ccccccccCccccc
Q psy16646 117 EMKTRNSIGITVRQ 130 (159)
Q Consensus 117 ~~~~C~~C~~~f~~ 130 (159)
|.+.|+.||..+.+
T Consensus 31 p~~~C~~CGE~~~~ 44 (46)
T TIGR03831 31 PALVCPQCGEEYLD 44 (46)
T ss_pred CccccccCCCEeeC
Confidence 44667777766543
No 210
>PF10263 SprT-like: SprT-like family; InterPro: IPR006640 This is a family of uncharacterised bacterial proteins which includes Escherichia coli SprT (P39902 from SWISSPROT). SprT is described as a regulator of bolA gene in stationary phase []. The majority of members contain the metallopeptidase zinc binding signature which has a HExxH motif, however there is no evidence for them being metallopeptidases.
Probab=29.58 E-value=22 Score=22.95 Aligned_cols=32 Identities=16% Similarity=0.307 Sum_probs=17.0
Q ss_pred cccCccccccccCccchhhhhhhhhhhhccccccccCcccc
Q psy16646 89 QHKCSLCQQAFKRDKHSKGDDIREEIEREMKTRNSIGITVR 129 (159)
Q Consensus 89 ~~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~~C~~C~~~f~ 129 (159)
.|.|..|+..+... .+. .... |.|..|+..+.
T Consensus 123 ~~~C~~C~~~~~r~------~~~--~~~~-~~C~~C~~~l~ 154 (157)
T PF10263_consen 123 VYRCPSCGREYKRH------RRS--KRKR-YRCGRCGGPLV 154 (157)
T ss_pred EEEcCCCCCEeeee------ccc--chhh-EECCCCCCEEE
Confidence 46677777655332 222 2222 67777775543
No 211
>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=29.48 E-value=30 Score=17.22 Aligned_cols=11 Identities=27% Similarity=0.945 Sum_probs=6.3
Q ss_pred CccccccccCc
Q psy16646 92 CSLCQQAFKRD 102 (159)
Q Consensus 92 C~~C~~~f~~~ 102 (159)
|..||..|...
T Consensus 11 C~~C~rpf~WR 21 (42)
T PF10013_consen 11 CPVCGRPFTWR 21 (42)
T ss_pred CcccCCcchHH
Confidence 55566555554
No 212
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=29.45 E-value=25 Score=16.43 Aligned_cols=12 Identities=8% Similarity=-0.064 Sum_probs=7.9
Q ss_pred cccccccCcccc
Q psy16646 118 MKTRNSIGITVR 129 (159)
Q Consensus 118 ~~~C~~C~~~f~ 129 (159)
.+.|..||..|.
T Consensus 21 ~~~C~~Cg~~~~ 32 (33)
T PF08792_consen 21 YEVCIFCGSSFP 32 (33)
T ss_pred eEEcccCCcEee
Confidence 366777777664
No 213
>smart00731 SprT SprT homologues. Predicted to have roles in transcription elongation. Contains a conserved HExxH motif, indicating a metalloprotease function.
Probab=29.38 E-value=26 Score=22.55 Aligned_cols=33 Identities=18% Similarity=0.272 Sum_probs=17.7
Q ss_pred cccCccccccccCccchhhhhhhhhhhhccccccccCcccc
Q psy16646 89 QHKCSLCQQAFKRDKHSKGDDIREEIEREMKTRNSIGITVR 129 (159)
Q Consensus 89 ~~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~~C~~C~~~f~ 129 (159)
.|.|..|+..+.+. . ++..... |.|..|+-.+.
T Consensus 112 ~y~C~~C~~~~~~~---r----r~~~~~~-y~C~~C~g~l~ 144 (146)
T smart00731 112 PYRCTGCGQRYLRV---R----RSNNVSR-YRCGKCGGKLI 144 (146)
T ss_pred EEECCCCCCCCceE---c----cccCcce-EEcCCCCCEEE
Confidence 57777777655321 1 1111133 77777776553
No 214
>PF04423 Rad50_zn_hook: Rad50 zinc hook motif; InterPro: IPR007517 The Mre11 complex (Mre11 Rad50 Nbs1) is central to chromosomal maintenance and functions in homologous recombination, telomere maintenance and sister chromatid association. The Rad50 coiled-coil region contains a dimer interface at the apex of the coiled coils in which pairs of conserved Cys-X-X-Cys motifs form interlocking hooks that bind one Zn ion. This alignment includes the zinc hook motif and a short stretch of coiled-coil on either side.; GO: 0004518 nuclease activity, 0005524 ATP binding, 0008270 zinc ion binding, 0006281 DNA repair; PDB: 1L8D_B.
Probab=28.81 E-value=21 Score=18.60 Aligned_cols=12 Identities=8% Similarity=0.047 Sum_probs=6.0
Q ss_pred cccccCccccch
Q psy16646 120 TRNSIGITVRQN 131 (159)
Q Consensus 120 ~C~~C~~~f~~~ 131 (159)
.|+.|++.|...
T Consensus 22 ~CPlC~r~l~~e 33 (54)
T PF04423_consen 22 CCPLCGRPLDEE 33 (54)
T ss_dssp E-TTT--EE-HH
T ss_pred cCCCCCCCCCHH
Confidence 689999988653
No 215
>PTZ00448 hypothetical protein; Provisional
Probab=28.62 E-value=35 Score=25.81 Aligned_cols=22 Identities=14% Similarity=0.105 Sum_probs=19.6
Q ss_pred ccccccCccccchhhHHHhhcc
Q psy16646 119 KTRNSIGITVRQNQTNKNHRSG 140 (159)
Q Consensus 119 ~~C~~C~~~f~~~~~l~~H~~~ 140 (159)
|.|..|+..|.+....+.|.++
T Consensus 315 ~tC~~C~v~F~~~~~qR~H~KS 336 (373)
T PTZ00448 315 LLCRKCNIQLMDHNAFKQHYRS 336 (373)
T ss_pred ccccccccccCCHHHHHHHhhh
Confidence 7899999999998999999665
No 216
>PRK04351 hypothetical protein; Provisional
Probab=28.31 E-value=28 Score=22.69 Aligned_cols=33 Identities=15% Similarity=0.208 Sum_probs=17.9
Q ss_pred cccCccccccccCccchhhhhhhhhhhhccccccccCccccc
Q psy16646 89 QHKCSLCQQAFKRDKHSKGDDIREEIEREMKTRNSIGITVRQ 130 (159)
Q Consensus 89 ~~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~~C~~C~~~f~~ 130 (159)
.|.|..||..+.+. +. +.... |.|..|+-.+..
T Consensus 112 ~Y~C~~Cg~~~~r~-------Rr-~n~~~-yrCg~C~g~L~~ 144 (149)
T PRK04351 112 LYECQSCGQQYLRK-------RR-INTKR-YRCGKCRGKLKL 144 (149)
T ss_pred EEECCCCCCEeeee-------ee-cCCCc-EEeCCCCcEeee
Confidence 46777777554332 11 12344 777777766543
No 217
>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=28.08 E-value=27 Score=16.52 Aligned_cols=14 Identities=29% Similarity=0.631 Sum_probs=6.7
Q ss_pred cCccccccccCccc
Q psy16646 91 KCSLCQQAFKRDKH 104 (159)
Q Consensus 91 ~C~~C~~~f~~~~~ 104 (159)
.|..|++.|..+.-
T Consensus 5 ~C~eC~~~f~dSyL 18 (34)
T PF01286_consen 5 KCDECGKPFMDSYL 18 (34)
T ss_dssp E-TTT--EES-SSC
T ss_pred hHhHhCCHHHHHHH
Confidence 57788888876643
No 218
>TIGR03830 CxxCG_CxxCG_HTH putative zinc finger/helix-turn-helix protein, YgiT family. This model describes a family of predicted regulatory proteins with a conserved zinc finger/HTH architecture. The amino-terminal region contains a novel domain, featuring two CXXC motifs and occuring in a number of small bacterial proteins as well as in the present family. The carboxyl-terminal region consists of a helix-turn-helix domain, modeled by pfam01381. The predicted function is DNA binding and transcriptional regulation.
Probab=27.97 E-value=30 Score=21.34 Aligned_cols=12 Identities=8% Similarity=-0.113 Sum_probs=5.7
Q ss_pred ccccccCccccc
Q psy16646 119 KTRNSIGITVRQ 130 (159)
Q Consensus 119 ~~C~~C~~~f~~ 130 (159)
+.|+.||..+..
T Consensus 32 ~~C~~CGe~~~~ 43 (127)
T TIGR03830 32 WYCPACGEELLD 43 (127)
T ss_pred eECCCCCCEEEc
Confidence 445555554433
No 219
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=27.82 E-value=31 Score=21.65 Aligned_cols=13 Identities=23% Similarity=0.360 Sum_probs=8.6
Q ss_pred cccCccccccccCc
Q psy16646 89 QHKCSLCQQAFKRD 102 (159)
Q Consensus 89 ~~~C~~C~~~f~~~ 102 (159)
...| .||..|...
T Consensus 70 ~~~C-~Cg~~~~~~ 82 (124)
T PRK00762 70 EIEC-ECGYEGVVD 82 (124)
T ss_pred eEEe-eCcCccccc
Confidence 3678 888766544
No 220
>KOG3507|consensus
Probab=27.80 E-value=16 Score=19.59 Aligned_cols=12 Identities=8% Similarity=-0.003 Sum_probs=6.1
Q ss_pred ccccccCccccc
Q psy16646 119 KTRNSIGITVRQ 130 (159)
Q Consensus 119 ~~C~~C~~~f~~ 130 (159)
+.|.+||.+...
T Consensus 38 irCReCG~RIly 49 (62)
T KOG3507|consen 38 IRCRECGYRILY 49 (62)
T ss_pred EehhhcchHHHH
Confidence 455555555433
No 221
>PF11781 RRN7: RNA polymerase I-specific transcription initiation factor Rrn7; InterPro: IPR021752 Rrn7 is a transcription binding factor that associates strongly with both Rrn6 and Rrn11 to form a complex which itself binds the TATA-binding protein and is required for transcription by the core domain of the RNA PolI promoter [],[].
Probab=27.52 E-value=36 Score=16.23 Aligned_cols=15 Identities=20% Similarity=0.162 Sum_probs=7.4
Q ss_pred chhhhcccCCCCCCC
Q psy16646 3 EMKKKSVKNPNAKKR 17 (159)
Q Consensus 3 ~~~~~~~~~~~~~~~ 17 (159)
.++.....|++|..+
T Consensus 3 ~~~~~~~~C~~C~~~ 17 (36)
T PF11781_consen 3 WMRGPNEPCPVCGSR 17 (36)
T ss_pred ccccCCCcCCCCCCe
Confidence 333444456665554
No 222
>PF14787 zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB: 1CL4_A 1DSV_A.
Probab=27.21 E-value=30 Score=16.58 Aligned_cols=15 Identities=7% Similarity=-0.137 Sum_probs=8.8
Q ss_pred cccccCccccchhhH
Q psy16646 120 TRNSIGITVRQNQTN 134 (159)
Q Consensus 120 ~C~~C~~~f~~~~~l 134 (159)
.|+.|++.|...+.=
T Consensus 4 ~CprC~kg~Hwa~~C 18 (36)
T PF14787_consen 4 LCPRCGKGFHWASEC 18 (36)
T ss_dssp C-TTTSSSCS-TTT-
T ss_pred cCcccCCCcchhhhh
Confidence 478888888766553
No 223
>PF12773 DZR: Double zinc ribbon
Probab=26.94 E-value=50 Score=16.61 Aligned_cols=9 Identities=22% Similarity=0.187 Sum_probs=5.7
Q ss_pred ccccccCcc
Q psy16646 119 KTRNSIGIT 127 (159)
Q Consensus 119 ~~C~~C~~~ 127 (159)
..|+.||..
T Consensus 30 ~~C~~Cg~~ 38 (50)
T PF12773_consen 30 KICPNCGAE 38 (50)
T ss_pred CCCcCCcCC
Confidence 456777665
No 224
>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=26.83 E-value=27 Score=21.38 Aligned_cols=13 Identities=23% Similarity=0.552 Sum_probs=7.0
Q ss_pred cccCccccccccC
Q psy16646 89 QHKCSLCQQAFKR 101 (159)
Q Consensus 89 ~~~C~~C~~~f~~ 101 (159)
-|.|++|+..+..
T Consensus 19 ~~iCpeC~~EW~~ 31 (109)
T TIGR00686 19 QLICPSCLYEWNE 31 (109)
T ss_pred eeECccccccccc
Confidence 3556666555543
No 225
>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=26.66 E-value=48 Score=16.00 Aligned_cols=12 Identities=0% Similarity=-0.255 Sum_probs=4.3
Q ss_pred ccccccCccccc
Q psy16646 119 KTRNSIGITVRQ 130 (159)
Q Consensus 119 ~~C~~C~~~f~~ 130 (159)
|.|+.|+.-|..
T Consensus 4 yyCdyC~~~~~~ 15 (38)
T PF06220_consen 4 YYCDYCKKYLTH 15 (38)
T ss_dssp -B-TTT--B-S-
T ss_pred eecccccceecC
Confidence 668888877743
No 226
>COG1773 Rubredoxin [Energy production and conversion]
Probab=26.17 E-value=27 Score=18.60 Aligned_cols=13 Identities=8% Similarity=-0.046 Sum_probs=10.2
Q ss_pred ccccccCccccch
Q psy16646 119 KTRNSIGITVRQN 131 (159)
Q Consensus 119 ~~C~~C~~~f~~~ 131 (159)
|+|..||..|.-.
T Consensus 4 ~~C~~CG~vYd~e 16 (55)
T COG1773 4 WRCSVCGYVYDPE 16 (55)
T ss_pred eEecCCceEeccc
Confidence 7888898887654
No 227
>PRK10220 hypothetical protein; Provisional
Probab=24.91 E-value=36 Score=20.87 Aligned_cols=14 Identities=14% Similarity=0.479 Sum_probs=7.9
Q ss_pred cccCccccccccCc
Q psy16646 89 QHKCSLCQQAFKRD 102 (159)
Q Consensus 89 ~~~C~~C~~~f~~~ 102 (159)
-|.|++|+..+...
T Consensus 20 ~~vCpeC~hEW~~~ 33 (111)
T PRK10220 20 MYICPECAHEWNDA 33 (111)
T ss_pred eEECCcccCcCCcc
Confidence 46666666555543
No 228
>COG4640 Predicted membrane protein [Function unknown]
Probab=24.79 E-value=44 Score=25.60 Aligned_cols=18 Identities=17% Similarity=0.167 Sum_probs=10.2
Q ss_pred ccccccCccccchhhHHH
Q psy16646 119 KTRNSIGITVRQNQTNKN 136 (159)
Q Consensus 119 ~~C~~C~~~f~~~~~l~~ 136 (159)
+.|++||..|....++..
T Consensus 16 ~qC~qCG~~~t~~~sqan 33 (465)
T COG4640 16 VQCTQCGHKFTSRQSQAN 33 (465)
T ss_pred ccccccCCcCCchhhhhh
Confidence 346666666665554433
No 229
>KOG0978|consensus
Probab=24.76 E-value=23 Score=29.18 Aligned_cols=21 Identities=10% Similarity=0.075 Sum_probs=11.6
Q ss_pred hhhhccccccccCccccchhhH
Q psy16646 113 EIEREMKTRNSIGITVRQNQTN 134 (159)
Q Consensus 113 ~~~~~~~~C~~C~~~f~~~~~l 134 (159)
.+.+. .+||.|+..|....-+
T Consensus 674 ~etRq-RKCP~Cn~aFganDv~ 694 (698)
T KOG0978|consen 674 YETRQ-RKCPKCNAAFGANDVH 694 (698)
T ss_pred HHHhc-CCCCCCCCCCCccccc
Confidence 34444 5567777666554433
No 230
>COG5216 Uncharacterized conserved protein [Function unknown]
Probab=24.66 E-value=20 Score=19.24 Aligned_cols=8 Identities=25% Similarity=0.721 Sum_probs=3.5
Q ss_pred cccccccc
Q psy16646 62 RVICEICN 69 (159)
Q Consensus 62 ~~~c~~c~ 69 (159)
...|+.|.
T Consensus 44 VArCPSCS 51 (67)
T COG5216 44 VARCPSCS 51 (67)
T ss_pred EEEcCCce
Confidence 33444443
No 231
>TIGR00244 transcriptional regulator NrdR. Members of this almost entirely bacterial family contain an ATP cone domain (PFAM:PF03477). There is never more than one member per genome. Common gene symbols given include nrdR, ybaD, ribX and ytcG. The member from Streptomyces coelicolor is found upstream in the operon of the class II oxygen-independent ribonucleotide reductase gene nrdJ and was shown to repress nrdJ expression. Many members of this family are found near genes for riboflavin biosynthesis in Gram-negative bacteria, suggesting a role in that pathway. However, a phylogenetic profiling study associates members of this family with the presence of a palindromic signal with consensus acaCwAtATaTwGtgt, termed the NrdR-box, an upstream element for most operons for ribonucleotide reductase of all three classes in bacterial genomes.
Probab=24.63 E-value=32 Score=22.38 Aligned_cols=14 Identities=0% Similarity=-0.218 Sum_probs=12.0
Q ss_pred ccccccCccccchh
Q psy16646 119 KTRNSIGITVRQNQ 132 (159)
Q Consensus 119 ~~C~~C~~~f~~~~ 132 (159)
-.|..||++|++.-
T Consensus 29 ReC~~C~~RFTTyE 42 (147)
T TIGR00244 29 RECLECHERFTTFE 42 (147)
T ss_pred ccCCccCCccceee
Confidence 67999999998864
No 232
>PF08394 Arc_trans_TRASH: Archaeal TRASH domain; InterPro: IPR013603 This region is found in the C terminus of a number of archaeal transcriptional regulators. It is thought to function as a metal-sensing regulatory module [].
Probab=24.01 E-value=12 Score=18.13 Aligned_cols=33 Identities=6% Similarity=0.059 Sum_probs=15.7
Q ss_pred CccccccccCccchhhhhhhhhhhhccc-cccccCcccc
Q psy16646 92 CSLCQQAFKRDKHSKGDDIREEIEREMK-TRNSIGITVR 129 (159)
Q Consensus 92 C~~C~~~f~~~~~l~~h~~~~~~~~~~~-~C~~C~~~f~ 129 (159)
|.+||.......... ..+.+.+| -|+.|-..|.
T Consensus 1 Cd~CG~~I~~eP~~~-----k~~~~~y~fCC~tC~~~fk 34 (37)
T PF08394_consen 1 CDYCGGEITGEPIVV-----KIGNKVYYFCCPTCLSQFK 34 (37)
T ss_pred CCccCCcccCCEEEE-----EECCeEEEEECHHHHHHHH
Confidence 556665555443321 22333333 3366666654
No 233
>KOG3002|consensus
Probab=23.11 E-value=1.5e+02 Score=21.86 Aligned_cols=57 Identities=16% Similarity=0.213 Sum_probs=25.1
Q ss_pred cccccccccccChhhHHHHHhhhCCCcccCc----cccccccCccchhhhhhhhhhhhccccccc
Q psy16646 63 VICEICNKEFTHKSSLAEHRVLHFPAQHKCS----LCQQAFKRDKHSKGDDIREEIEREMKTRNS 123 (159)
Q Consensus 63 ~~c~~c~~~f~~~~~l~~h~~~h~~k~~~C~----~C~~~f~~~~~l~~h~~~~~~~~~~~~C~~ 123 (159)
..|+.|...+.....+....-. ......|+ .|.+.|.+... ..|.+.... ++ +.|+.
T Consensus 81 ~~CP~Cr~~~g~~R~~amEkV~-e~~~vpC~~~~~GC~~~~~Y~~~-~~HE~~C~f-~~-~~CP~ 141 (299)
T KOG3002|consen 81 NKCPTCRLPIGNIRCRAMEKVA-EAVLVPCKNAKLGCTKSFPYGEK-SKHEKVCEF-RP-CSCPV 141 (299)
T ss_pred ccCCccccccccHHHHHHHHHH-HhceecccccccCCceeeccccc-ccccccccc-CC-cCCCC
Confidence 3455555555544443332211 11123333 35566666555 335444443 34 55543
No 234
>PRK00420 hypothetical protein; Validated
Probab=23.10 E-value=42 Score=20.75 Aligned_cols=8 Identities=13% Similarity=0.384 Sum_probs=3.6
Q ss_pred ccCccccc
Q psy16646 90 HKCSLCQQ 97 (159)
Q Consensus 90 ~~C~~C~~ 97 (159)
..|+.||.
T Consensus 41 ~~Cp~Cg~ 48 (112)
T PRK00420 41 VVCPVHGK 48 (112)
T ss_pred eECCCCCC
Confidence 33444444
No 235
>KOG1842|consensus
Probab=23.06 E-value=26 Score=27.16 Aligned_cols=23 Identities=26% Similarity=0.587 Sum_probs=17.1
Q ss_pred CccccccccccccChhhHHHHHh
Q psy16646 61 DRVICEICNKEFTHKSSLAEHRV 83 (159)
Q Consensus 61 ~~~~c~~c~~~f~~~~~l~~h~~ 83 (159)
..|.|++|...|.+...|..|..
T Consensus 14 egflCPiC~~dl~~~~~L~~H~d 36 (505)
T KOG1842|consen 14 EGFLCPICLLDLPNLSALNDHLD 36 (505)
T ss_pred hcccCchHhhhhhhHHHHHHHHh
Confidence 45778888888888888777754
No 236
>KOG0717|consensus
Probab=22.71 E-value=55 Score=25.68 Aligned_cols=21 Identities=33% Similarity=0.774 Sum_probs=19.0
Q ss_pred cccccccccccChHHHHHHHh
Q psy16646 33 FHCYVCKKKYRHKRQLVRHFQ 53 (159)
Q Consensus 33 ~~C~~c~~~f~~~~~l~~h~~ 53 (159)
+.|.+|+++|.+...|..|..
T Consensus 293 lyC~vCnKsFKseKq~kNHEn 313 (508)
T KOG0717|consen 293 LYCVVCNKSFKSEKQLKNHEN 313 (508)
T ss_pred eEEeeccccccchHHHHhhHH
Confidence 889999999999999988875
No 237
>COG3364 Zn-ribbon containing protein [General function prediction only]
Probab=22.57 E-value=43 Score=20.30 Aligned_cols=14 Identities=29% Similarity=0.897 Sum_probs=6.9
Q ss_pred cccCccccccccCc
Q psy16646 89 QHKCSLCQQAFKRD 102 (159)
Q Consensus 89 ~~~C~~C~~~f~~~ 102 (159)
|+.|..||..|...
T Consensus 2 pH~CtrCG~vf~~g 15 (112)
T COG3364 2 PHQCTRCGEVFDDG 15 (112)
T ss_pred Cceecccccccccc
Confidence 34455555555443
No 238
>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=22.09 E-value=40 Score=26.46 Aligned_cols=24 Identities=29% Similarity=0.452 Sum_probs=19.9
Q ss_pred CccccccccccccChhhHHHHHhh
Q psy16646 61 DRVICEICNKEFTHKSSLAEHRVL 84 (159)
Q Consensus 61 ~~~~c~~c~~~f~~~~~l~~h~~~ 84 (159)
+-|.|..|.+.|.+...+..|+..
T Consensus 56 rFWiCp~CskkF~d~~~~~~H~~~ 79 (466)
T PF04780_consen 56 RFWICPRCSKKFSDAESCLSHMEQ 79 (466)
T ss_pred eEeeCCcccceeCCHHHHHHHHHH
Confidence 567899999999999999888753
No 239
>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=21.78 E-value=2.5e+02 Score=18.64 Aligned_cols=59 Identities=15% Similarity=0.175 Sum_probs=35.1
Q ss_pred cccCccccccccCccchhhhhhhhhhhhccccc--cccCccccchhhHHHh-hccCCCccccccC
Q psy16646 89 QHKCSLCQQAFKRDKHSKGDDIREEIEREMKTR--NSIGITVRQNQTNKNH-RSGDQKKKTAKQL 150 (159)
Q Consensus 89 ~~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~~C--~~C~~~f~~~~~l~~H-~~~h~~~k~~~~~ 150 (159)
...|+.|.-........ ...+.+-..|+ ..| +.|++.=+ ...|+.| +..|...+|-+--
T Consensus 80 ~L~CPLCRG~V~GWtvv-e~AR~~LN~K~-RsC~~e~C~F~Gt-Y~eLrKHar~~HP~~rP~~vD 141 (162)
T PF07800_consen 80 ELACPLCRGEVKGWTVV-EPARRFLNAKK-RSCSQESCSFSGT-YSELRKHARSEHPSARPSEVD 141 (162)
T ss_pred cccCccccCceeceEEc-hHHHHHhccCC-ccCcccccccccC-HHHHHHHHHhhCCCCCCccCC
Confidence 56788885433333222 23555666666 667 45665543 4589999 4457777775543
No 240
>TIGR03655 anti_R_Lar restriction alleviation protein, Lar family. Restriction alleviation proteins provide a countermeasure to host cell restriction enzyme defense against foreign DNA such as phage or plasmids. This family consists of homologs to the phage antirestriction protein Lar, and most members belong to phage genomes or prophage regions of bacterial genomes.
Probab=21.66 E-value=66 Score=16.62 Aligned_cols=35 Identities=14% Similarity=0.025 Sum_probs=16.0
Q ss_pred cCCCCCCCCCCCCC-cccCCCCCccccccccccccC
Q psy16646 10 KNPNAKKRYRPYVP-RVDSSLPPQFHCYVCKKKYRH 44 (159)
Q Consensus 10 ~~~~~~~~~~~~~~-~~~h~~~~~~~C~~c~~~f~~ 44 (159)
+||.|+..-....- ...-.+..-+.|..|+.....
T Consensus 3 PCPfCGg~~~~~~~~~~~~~~~~~~~C~~Cga~~~~ 38 (53)
T TIGR03655 3 PCPFCGGADVYLRRGFDPLDLSHYFECSTCGASGPV 38 (53)
T ss_pred CCCCCCCcceeeEeccCCCCCEEEEECCCCCCCccc
Confidence 57777775552211 011111122357777665443
No 241
>KOG1842|consensus
Probab=21.33 E-value=48 Score=25.81 Aligned_cols=29 Identities=14% Similarity=0.204 Sum_probs=15.3
Q ss_pred cccCccccccccCccchhhhhhhhhhhhc
Q psy16646 89 QHKCSLCQQAFKRDKHSKGDDIREEIERE 117 (159)
Q Consensus 89 ~~~C~~C~~~f~~~~~l~~h~~~~~~~~~ 117 (159)
.|.|++|+..|.....|..|.-..|++..
T Consensus 15 gflCPiC~~dl~~~~~L~~H~d~eH~~ed 43 (505)
T KOG1842|consen 15 GFLCPICLLDLPNLSALNDHLDVEHFEED 43 (505)
T ss_pred cccCchHhhhhhhHHHHHHHHhhhccccc
Confidence 35555555555555555555555554444
No 242
>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=21.11 E-value=35 Score=16.39 Aligned_cols=11 Identities=18% Similarity=0.111 Sum_probs=5.6
Q ss_pred cccccccCccc
Q psy16646 118 MKTRNSIGITV 128 (159)
Q Consensus 118 ~~~C~~C~~~f 128 (159)
.|+|..||-..
T Consensus 6 ~YkC~~CGniV 16 (36)
T PF06397_consen 6 FYKCEHCGNIV 16 (36)
T ss_dssp EEE-TTT--EE
T ss_pred EEEccCCCCEE
Confidence 38888888653
No 243
>PF14122 YokU: YokU-like protein
Probab=21.09 E-value=53 Score=19.21 Aligned_cols=22 Identities=9% Similarity=0.172 Sum_probs=15.5
Q ss_pred hhhccccccccCccccchhhHH
Q psy16646 114 IEREMKTRNSIGITVRQNQTNK 135 (159)
Q Consensus 114 ~~~~~~~C~~C~~~f~~~~~l~ 135 (159)
.+-|...|..||..+.....+.
T Consensus 31 ~~tP~i~C~~CgmvYq~d~vi~ 52 (87)
T PF14122_consen 31 TDTPAIICSNCGMVYQDDEVIK 52 (87)
T ss_pred cCCceeeecCCCcEEehhHHHH
Confidence 3445588999999887775543
No 244
>KOG3362|consensus
Probab=21.06 E-value=59 Score=21.09 Aligned_cols=18 Identities=33% Similarity=0.647 Sum_probs=7.2
Q ss_pred cccccccccccChHHHHH
Q psy16646 33 FHCYVCKKKYRHKRQLVR 50 (159)
Q Consensus 33 ~~C~~c~~~f~~~~~l~~ 50 (159)
|.|..||..+.+..-+..
T Consensus 130 ysC~~CG~kyCsv~C~~~ 147 (156)
T KOG3362|consen 130 YSCVNCGTKYCSVRCLKT 147 (156)
T ss_pred hHHHhcCCceeechhhhh
Confidence 334444444444333333
No 245
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=21.05 E-value=82 Score=23.76 Aligned_cols=20 Identities=20% Similarity=0.384 Sum_probs=10.2
Q ss_pred CccccccccCccchhhhhhh
Q psy16646 92 CSLCQQAFKRDKHSKGDDIR 111 (159)
Q Consensus 92 C~~C~~~f~~~~~l~~h~~~ 111 (159)
|..|...|.....|..|.+.
T Consensus 223 C~FC~~~FYdDDEL~~HcR~ 242 (493)
T COG5236 223 CIFCKIYFYDDDELRRHCRL 242 (493)
T ss_pred hhhccceecChHHHHHHHHh
Confidence 55555555555555555443
No 246
>KOG2807|consensus
Probab=20.89 E-value=99 Score=23.14 Aligned_cols=24 Identities=13% Similarity=-0.182 Sum_probs=18.7
Q ss_pred ccccccCccccchhhHHHhhccCC
Q psy16646 119 KTRNSIGITVRQNQTNKNHRSGDQ 142 (159)
Q Consensus 119 ~~C~~C~~~f~~~~~l~~H~~~h~ 142 (159)
|.|..|...|--.-..-.|...|.
T Consensus 346 y~C~~Ck~~FCldCDv~iHesLh~ 369 (378)
T KOG2807|consen 346 YRCESCKNVFCLDCDVFIHESLHN 369 (378)
T ss_pred EEchhccceeeccchHHHHhhhhc
Confidence 888888888887777777766664
No 247
>PRK11823 DNA repair protein RadA; Provisional
Probab=20.83 E-value=46 Score=25.93 Aligned_cols=7 Identities=29% Similarity=0.994 Sum_probs=3.8
Q ss_pred ccCcccc
Q psy16646 90 HKCSLCQ 96 (159)
Q Consensus 90 ~~C~~C~ 96 (159)
+.|+.|+
T Consensus 22 g~Cp~C~ 28 (446)
T PRK11823 22 GRCPECG 28 (446)
T ss_pred eeCcCCC
Confidence 4555554
No 248
>KOG0782|consensus
Probab=20.81 E-value=49 Score=26.77 Aligned_cols=35 Identities=14% Similarity=0.177 Sum_probs=16.0
Q ss_pred cCccccccccCccchhhhhhhhhhhhccccccccCccccch
Q psy16646 91 KCSLCQQAFKRDKHSKGDDIREEIEREMKTRNSIGITVRQN 131 (159)
Q Consensus 91 ~C~~C~~~f~~~~~l~~h~~~~~~~~~~~~C~~C~~~f~~~ 131 (159)
+|..||+.|.+...+. ..|--...|++|...|...
T Consensus 255 kC~~CgKgFQQKf~Fh------sKEivAisCSWCKqayH~K 289 (1004)
T KOG0782|consen 255 KCNTCGKGFQQKFFFH------SKEIVAISCSWCKQAYHLK 289 (1004)
T ss_pred ccchhhhhhhhheeec------cccEEEEEehHHHHHhhcc
Confidence 4555666655543321 1111114456665555444
No 249
>KOG2071|consensus
Probab=20.56 E-value=49 Score=26.66 Aligned_cols=27 Identities=11% Similarity=0.220 Sum_probs=22.5
Q ss_pred hhccccccccCccccchhhHHHhhccCC
Q psy16646 115 EREMKTRNSIGITVRQNQTNKNHRSGDQ 142 (159)
Q Consensus 115 ~~~~~~C~~C~~~f~~~~~l~~H~~~h~ 142 (159)
..+ ..|..||.+|-.......|+..|.
T Consensus 416 ~~p-nqC~~CG~R~~~~ee~sk~md~H~ 442 (579)
T KOG2071|consen 416 DSP-NQCKSCGLRFDDSEERSKHMDIHD 442 (579)
T ss_pred CCc-chhcccccccccchhhhhHhhhhh
Confidence 445 889999999999988888877776
Done!