Query psy4421
Match_columns 167
No_of_seqs 123 out of 1105
Neff 10.5
Searched_HMMs 46136
Date Fri Aug 16 16:41:04 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy4421.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/4421hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2462|consensus 100.0 6.1E-31 1.3E-35 181.9 5.7 134 6-165 129-265 (279)
2 KOG2462|consensus 99.9 7.5E-24 1.6E-28 146.9 5.0 109 41-167 128-239 (279)
3 KOG1074|consensus 99.8 6E-20 1.3E-24 143.3 1.7 56 7-70 353-408 (958)
4 KOG1074|consensus 99.7 4.9E-19 1.1E-23 138.2 3.3 52 116-167 880-931 (958)
5 KOG3608|consensus 99.7 8.3E-18 1.8E-22 120.5 4.9 134 7-167 237-376 (467)
6 KOG3608|consensus 99.7 1E-17 2.3E-22 120.0 4.1 106 43-166 237-344 (467)
7 KOG3576|consensus 99.7 1.2E-17 2.6E-22 111.3 2.9 110 42-167 116-236 (267)
8 KOG3576|consensus 99.6 9.2E-17 2E-21 107.1 1.8 122 4-142 114-239 (267)
9 KOG3623|consensus 99.6 1.5E-16 3.2E-21 123.2 3.1 113 44-165 211-331 (1007)
10 KOG3623|consensus 99.4 2.9E-14 6.3E-19 110.7 1.2 84 2-102 889-972 (1007)
11 PLN03086 PRLI-interacting fact 99.3 1.4E-11 3E-16 95.5 7.6 104 41-167 451-564 (567)
12 PHA00733 hypothetical protein 99.2 9.9E-12 2.1E-16 79.5 3.6 98 57-167 26-123 (128)
13 PHA02768 hypothetical protein; 99.1 3.1E-11 6.8E-16 64.5 1.9 44 115-160 5-48 (55)
14 PF13465 zf-H2C2_2: Zinc-finge 99.0 5E-10 1.1E-14 51.4 2.6 26 130-155 1-26 (26)
15 PLN03086 PRLI-interacting fact 99.0 1.8E-09 3.9E-14 83.9 6.7 102 4-136 450-561 (567)
16 PHA00733 hypothetical protein 98.9 2.1E-09 4.6E-14 68.8 5.3 87 2-102 35-121 (128)
17 KOG3993|consensus 98.9 5E-10 1.1E-14 82.7 1.5 157 2-167 262-482 (500)
18 PHA02768 hypothetical protein; 98.7 3.1E-09 6.8E-14 56.8 0.4 42 44-96 6-47 (55)
19 PHA00732 hypothetical protein 98.5 9.5E-08 2.1E-12 55.8 2.9 45 115-165 1-46 (79)
20 PHA00616 hypothetical protein 98.5 5.4E-08 1.2E-12 49.6 1.1 34 115-148 1-34 (44)
21 PF05605 zf-Di19: Drought indu 98.4 5.8E-07 1.3E-11 48.8 3.6 50 115-167 2-53 (54)
22 PHA00616 hypothetical protein 98.3 4E-07 8.7E-12 46.4 1.7 31 43-73 1-31 (44)
23 KOG3993|consensus 98.3 2E-07 4.3E-12 69.3 0.3 78 82-167 270-380 (500)
24 PF00096 zf-C2H2: Zinc finger, 98.2 6.2E-07 1.4E-11 39.7 1.5 22 144-165 1-22 (23)
25 PF13465 zf-H2C2_2: Zinc-finge 98.2 8.8E-07 1.9E-11 40.5 1.6 15 59-73 2-16 (26)
26 PF13894 zf-C2H2_4: C2H2-type 98.2 1.2E-06 2.5E-11 39.1 1.8 24 144-167 1-24 (24)
27 PHA00732 hypothetical protein 98.1 1.7E-06 3.6E-11 50.6 2.1 47 7-67 1-48 (79)
28 PF13912 zf-C2H2_6: C2H2-type 98.1 2.8E-06 6.1E-11 39.1 2.0 25 143-167 1-25 (27)
29 PF00096 zf-C2H2: Zinc finger, 98.0 5.6E-06 1.2E-10 36.6 2.4 23 44-66 1-23 (23)
30 PF12756 zf-C2H2_2: C2H2 type 97.8 1.5E-05 3.2E-10 48.7 2.5 72 82-166 2-73 (100)
31 PF05605 zf-Di19: Drought indu 97.7 3.8E-05 8.3E-10 41.6 2.6 47 8-65 3-51 (54)
32 PF13894 zf-C2H2_4: C2H2-type 97.6 8.2E-05 1.8E-09 32.8 2.6 23 44-66 1-23 (24)
33 PF13912 zf-C2H2_6: C2H2-type 97.5 4.9E-05 1.1E-09 34.9 1.1 25 115-139 1-25 (27)
34 COG5189 SFP1 Putative transcri 97.5 5.6E-05 1.2E-09 54.7 1.7 52 113-164 347-419 (423)
35 smart00355 ZnF_C2H2 zinc finge 97.4 8.4E-05 1.8E-09 33.3 1.4 23 144-166 1-23 (26)
36 PRK04860 hypothetical protein; 97.4 0.00013 2.7E-09 48.6 2.4 40 114-157 118-157 (160)
37 PF12756 zf-C2H2_2: C2H2 type 97.3 0.00018 3.9E-09 43.8 2.0 72 45-138 1-73 (100)
38 PF09237 GAGA: GAGA factor; I 97.2 0.00041 9E-09 36.3 2.8 34 110-143 19-52 (54)
39 PF12874 zf-met: Zinc-finger o 97.1 0.00028 6.1E-09 31.6 1.5 22 144-165 1-22 (25)
40 PF09237 GAGA: GAGA factor; I 97.1 0.00095 2.1E-08 35.0 3.1 33 39-71 20-52 (54)
41 COG5189 SFP1 Putative transcri 97.1 0.00036 7.8E-09 50.6 2.0 70 41-136 347-419 (423)
42 smart00355 ZnF_C2H2 zinc finge 97.0 0.00084 1.8E-08 29.9 2.4 24 44-67 1-24 (26)
43 PF13909 zf-H2C2_5: C2H2-type 96.9 0.0013 2.7E-08 29.1 2.7 23 44-67 1-23 (24)
44 PF13909 zf-H2C2_5: C2H2-type 96.9 0.00045 9.7E-09 30.6 1.0 23 144-167 1-23 (24)
45 PF12171 zf-C2H2_jaz: Zinc-fin 96.6 0.00089 1.9E-08 30.6 0.9 22 144-165 2-23 (27)
46 PF12874 zf-met: Zinc-finger o 96.5 0.0021 4.5E-08 28.6 1.6 22 44-65 1-22 (25)
47 PF13913 zf-C2HC_2: zinc-finge 95.6 0.0096 2.1E-07 26.6 1.6 21 144-165 3-23 (25)
48 COG5048 FOG: Zn-finger [Genera 95.5 0.0031 6.7E-08 48.2 -0.3 60 6-73 288-353 (467)
49 PF12171 zf-C2H2_jaz: Zinc-fin 95.5 0.016 3.4E-07 26.3 2.2 17 8-24 2-18 (27)
50 smart00451 ZnF_U1 U1-like zinc 95.1 0.02 4.3E-07 27.6 1.9 23 143-165 3-25 (35)
51 PRK04860 hypothetical protein; 94.9 0.023 4.9E-07 37.9 2.4 35 42-88 118-152 (160)
52 KOG2231|consensus 94.6 0.12 2.5E-06 42.1 5.9 48 116-167 183-236 (669)
53 KOG2893|consensus 93.8 0.027 5.9E-07 39.6 0.9 32 46-89 13-44 (341)
54 cd00350 rubredoxin_like Rubred 93.5 0.047 1E-06 26.1 1.3 24 116-151 2-25 (33)
55 COG4049 Uncharacterized protei 92.9 0.045 9.8E-07 29.2 0.7 24 140-163 14-37 (65)
56 smart00451 ZnF_U1 U1-like zinc 92.9 0.11 2.5E-06 24.8 2.2 23 43-65 3-25 (35)
57 PHA00626 hypothetical protein 92.3 0.069 1.5E-06 28.6 0.9 13 142-154 22-34 (59)
58 COG5048 FOG: Zn-finger [Genera 92.0 0.052 1.1E-06 41.5 0.4 53 114-166 288-346 (467)
59 KOG2231|consensus 91.8 0.65 1.4E-05 37.9 6.2 93 52-164 158-260 (669)
60 KOG2482|consensus 91.3 0.63 1.4E-05 34.7 5.2 55 82-136 147-216 (423)
61 KOG1146|consensus 91.0 0.13 2.9E-06 44.5 1.8 55 111-165 461-540 (1406)
62 COG2888 Predicted Zn-ribbon RN 91.0 0.24 5.3E-06 26.9 2.2 36 111-151 23-58 (61)
63 PF02892 zf-BED: BED zinc fing 90.9 0.25 5.4E-06 25.2 2.2 27 140-166 13-43 (45)
64 PF12013 DUF3505: Protein of u 90.2 0.71 1.5E-05 28.6 4.1 25 143-167 80-108 (109)
65 PF09538 FYDLN_acid: Protein o 90.2 0.22 4.7E-06 31.0 1.7 14 142-155 25-38 (108)
66 COG1592 Rubrerythrin [Energy p 89.7 0.21 4.5E-06 33.5 1.5 23 115-150 134-156 (166)
67 PF13719 zinc_ribbon_5: zinc-r 89.7 0.33 7.3E-06 23.8 1.9 33 117-154 4-36 (37)
68 cd00729 rubredoxin_SM Rubredox 89.2 0.25 5.5E-06 23.8 1.2 25 115-151 2-26 (34)
69 PRK00464 nrdR transcriptional 89.0 0.13 2.7E-06 34.2 0.1 12 144-155 29-40 (154)
70 TIGR02098 MJ0042_CXXC MJ0042 f 88.9 0.4 8.6E-06 23.5 1.9 35 7-54 2-36 (38)
71 PF13717 zinc_ribbon_4: zinc-r 88.3 0.49 1.1E-05 23.1 1.9 33 116-153 3-35 (36)
72 KOG1146|consensus 87.9 0.088 1.9E-06 45.6 -1.4 111 9-141 1230-1354(1406)
73 TIGR00622 ssl1 transcription f 86.7 2 4.2E-05 26.9 4.3 48 117-166 57-104 (112)
74 PF09986 DUF2225: Uncharacteri 86.7 0.21 4.5E-06 35.1 0.1 43 114-156 4-61 (214)
75 PRK09678 DNA-binding transcrip 86.0 0.37 8E-06 27.6 0.8 40 116-157 2-43 (72)
76 PRK00398 rpoP DNA-directed RNA 86.0 0.58 1.3E-05 24.1 1.5 30 115-154 3-32 (46)
77 PRK00464 nrdR transcriptional 85.8 0.37 8E-06 32.0 0.9 43 8-59 1-44 (154)
78 smart00531 TFIIE Transcription 85.3 0.87 1.9E-05 30.0 2.5 17 41-57 97-113 (147)
79 COG5236 Uncharacterized conser 85.3 0.49 1.1E-05 35.3 1.4 48 117-165 222-273 (493)
80 smart00659 RPOLCX RNA polymera 85.1 0.81 1.8E-05 23.4 1.8 28 115-153 2-29 (44)
81 PF09986 DUF2225: Uncharacteri 85.0 0.41 9E-06 33.6 0.9 44 5-56 3-61 (214)
82 KOG2893|consensus 84.5 0.29 6.4E-06 34.5 -0.0 45 82-138 13-58 (341)
83 PF09845 DUF2072: Zn-ribbon co 84.1 0.68 1.5E-05 29.7 1.5 15 7-21 1-15 (131)
84 PRK14890 putative Zn-ribbon RN 83.4 2.2 4.8E-05 23.3 3.1 34 113-151 23-56 (59)
85 smart00614 ZnF_BED BED zinc fi 82.7 1 2.2E-05 23.6 1.6 22 143-164 18-44 (50)
86 TIGR02300 FYDLN_acid conserved 82.5 1 2.2E-05 28.7 1.8 14 114-127 25-38 (129)
87 COG1592 Rubrerythrin [Energy p 82.3 0.96 2.1E-05 30.4 1.7 21 82-123 137-157 (166)
88 COG4049 Uncharacterized protei 82.0 0.43 9.3E-06 25.6 -0.0 20 5-24 15-34 (65)
89 PF02176 zf-TRAF: TRAF-type zi 81.7 1.3 2.9E-05 23.9 2.0 43 114-156 8-55 (60)
90 PF08790 zf-LYAR: LYAR-type C2 80.9 0.51 1.1E-05 21.6 0.0 18 144-162 1-18 (28)
91 KOG2482|consensus 80.3 2.3 5.1E-05 31.9 3.2 49 116-164 280-355 (423)
92 KOG2186|consensus 79.9 0.81 1.8E-05 32.7 0.8 46 8-64 4-49 (276)
93 smart00531 TFIIE Transcription 79.7 5.1 0.00011 26.3 4.5 41 110-154 94-134 (147)
94 COG3364 Zn-ribbon containing p 79.5 1.5 3.2E-05 26.8 1.6 19 6-24 1-19 (112)
95 PF04959 ARS2: Arsenite-resist 79.2 1.3 2.8E-05 31.1 1.6 29 39-67 73-101 (214)
96 COG4888 Uncharacterized Zn rib 79.2 0.92 2E-05 27.5 0.8 42 110-155 17-58 (104)
97 PF08274 PhnA_Zn_Ribbon: PhnA 79.1 0.99 2.1E-05 21.1 0.7 24 117-151 4-27 (30)
98 COG5236 Uncharacterized conser 78.9 2.3 5E-05 31.9 2.8 131 8-165 152-303 (493)
99 TIGR02605 CxxC_CxxC_SSSS putat 78.2 0.57 1.2E-05 24.8 -0.3 13 44-56 6-18 (52)
100 KOG2785|consensus 77.7 2.7 5.9E-05 31.9 3.0 52 114-165 165-242 (390)
101 TIGR00373 conserved hypothetic 77.2 2.6 5.6E-05 28.2 2.5 36 110-154 104-139 (158)
102 smart00834 CxxC_CXXC_SSSS Puta 77.1 0.75 1.6E-05 22.8 -0.0 29 116-151 6-34 (41)
103 PF04959 ARS2: Arsenite-resist 76.2 1.4 3.1E-05 30.9 1.1 23 143-165 77-99 (214)
104 PF09723 Zn-ribbon_8: Zinc rib 75.9 0.6 1.3E-05 23.6 -0.6 12 8-19 6-17 (42)
105 smart00734 ZnF_Rad18 Rad18-lik 75.7 2.4 5.2E-05 18.9 1.4 18 145-163 3-20 (26)
106 PF03604 DNA_RNApol_7kD: DNA d 74.5 2.3 5.1E-05 20.1 1.3 9 144-152 18-26 (32)
107 TIGR00244 transcriptional regu 74.2 0.9 1.9E-05 29.8 -0.2 12 144-155 29-40 (147)
108 COG1996 RPC10 DNA-directed RNA 74.2 2 4.4E-05 22.5 1.1 30 114-153 5-34 (49)
109 PF12013 DUF3505: Protein of u 73.5 3.7 8E-05 25.4 2.4 25 44-68 81-109 (109)
110 PRK06266 transcription initiat 73.3 3.2 7E-05 28.3 2.2 35 112-155 114-148 (178)
111 PF10571 UPF0547: Uncharacteri 71.7 2 4.4E-05 19.3 0.7 9 117-125 16-24 (26)
112 PF06524 NOA36: NOA36 protein; 71.2 3.3 7.2E-05 29.9 2.0 15 41-55 140-154 (314)
113 COG1327 Predicted transcriptio 70.2 1.3 2.8E-05 29.1 -0.2 12 144-155 29-40 (156)
114 PF14353 CpXC: CpXC protein 70.1 0.8 1.7E-05 29.3 -1.2 15 43-57 38-52 (128)
115 KOG3408|consensus 69.9 3 6.6E-05 26.3 1.4 26 140-165 54-79 (129)
116 TIGR00373 conserved hypothetic 69.8 3.1 6.7E-05 27.8 1.5 35 38-89 104-138 (158)
117 PF05443 ROS_MUCR: ROS/MUCR tr 69.7 3.6 7.7E-05 26.6 1.7 22 143-167 72-93 (132)
118 smart00440 ZnF_C2C2 C2C2 Zinc 69.4 1.1 2.3E-05 22.4 -0.6 11 144-154 29-39 (40)
119 PRK00432 30S ribosomal protein 69.0 4.2 9.2E-05 21.4 1.6 12 142-153 36-47 (50)
120 PF15269 zf-C2H2_7: Zinc-finge 68.1 6.1 0.00013 20.2 2.0 23 43-65 20-42 (54)
121 KOG2593|consensus 67.3 7.3 0.00016 30.2 3.2 40 111-153 124-163 (436)
122 KOG2593|consensus 67.2 4.2 9.2E-05 31.5 1.9 36 5-51 126-161 (436)
123 COG1997 RPL43A Ribosomal prote 66.3 5.2 0.00011 23.7 1.8 30 115-154 35-64 (89)
124 PF07754 DUF1610: Domain of un 65.7 6.2 0.00013 17.3 1.6 9 114-122 15-23 (24)
125 COG4530 Uncharacterized protei 63.9 5.8 0.00013 24.6 1.7 12 114-125 25-36 (129)
126 PF12760 Zn_Tnp_IS1595: Transp 63.4 11 0.00024 19.3 2.5 28 115-151 18-45 (46)
127 PF01096 TFIIS_C: Transcriptio 62.3 0.38 8.3E-06 23.9 -3.0 10 144-153 29-38 (39)
128 COG3357 Predicted transcriptio 61.9 4.2 9.2E-05 24.3 0.9 14 42-55 57-70 (97)
129 KOG2186|consensus 61.3 5.7 0.00012 28.6 1.6 45 44-100 4-48 (276)
130 KOG2907|consensus 60.6 4.8 0.0001 25.1 1.0 39 115-156 74-115 (116)
131 PF13824 zf-Mss51: Zinc-finger 60.4 9.1 0.0002 20.6 1.9 18 111-128 10-27 (55)
132 PF04606 Ogr_Delta: Ogr/Delta- 59.9 2.9 6.3E-05 21.6 -0.0 37 118-156 2-40 (47)
133 PF13451 zf-trcl: Probable zin 58.7 5.1 0.00011 21.1 0.7 16 141-156 2-17 (49)
134 COG1594 RPB9 DNA-directed RNA 58.3 3.9 8.4E-05 25.7 0.3 38 115-155 72-112 (113)
135 smart00661 RPOL9 RNA polymeras 58.1 11 0.00024 19.5 2.1 11 115-125 20-30 (52)
136 PF07975 C1_4: TFIIH C1-like d 58.0 3.4 7.4E-05 21.9 0.0 16 115-130 21-36 (51)
137 PF08271 TF_Zn_Ribbon: TFIIB z 57.4 6.1 0.00013 19.9 0.9 29 116-153 1-29 (43)
138 KOG4173|consensus 56.7 2.9 6.3E-05 29.0 -0.5 70 85-165 87-168 (253)
139 TIGR01206 lysW lysine biosynth 56.4 8.2 0.00018 20.7 1.3 30 116-153 3-32 (54)
140 PF01363 FYVE: FYVE zinc finge 56.2 8.3 0.00018 21.5 1.5 27 116-154 10-36 (69)
141 smart00154 ZnF_AN1 AN1-like Zi 56.2 6.9 0.00015 19.4 1.0 12 143-154 12-23 (39)
142 COG1571 Predicted DNA-binding 55.7 8.5 0.00018 30.0 1.8 28 117-155 352-379 (421)
143 KOG2785|consensus 55.3 19 0.0004 27.6 3.5 55 82-137 169-242 (390)
144 PRK03824 hypA hydrogenase nick 55.0 4.7 0.0001 26.1 0.3 12 44-55 71-82 (135)
145 PRK04023 DNA polymerase II lar 54.9 16 0.00034 31.9 3.3 8 144-151 664-671 (1121)
146 PF14311 DUF4379: Domain of un 54.2 8.3 0.00018 20.5 1.2 29 114-149 27-55 (55)
147 KOG2807|consensus 53.3 37 0.0008 25.6 4.6 13 9-21 246-258 (378)
148 PHA02998 RNA polymerase subuni 53.0 4.5 9.7E-05 27.4 -0.0 39 115-156 143-184 (195)
149 PF01428 zf-AN1: AN1-like Zinc 52.8 6.2 0.00013 19.9 0.5 13 142-154 12-24 (43)
150 PRK14714 DNA polymerase II lar 51.2 20 0.00043 32.1 3.4 11 115-125 692-702 (1337)
151 PF13878 zf-C2H2_3: zinc-finge 51.1 25 0.00055 17.5 2.6 23 116-138 14-38 (41)
152 PF10276 zf-CHCC: Zinc-finger 49.8 8.7 0.00019 19.2 0.7 12 142-153 28-39 (40)
153 COG4957 Predicted transcriptio 49.2 11 0.00025 24.3 1.3 21 144-167 77-97 (148)
154 PF07282 OrfB_Zn_ribbon: Putat 49.0 15 0.00033 20.4 1.8 13 141-153 44-56 (69)
155 KOG4167|consensus 49.0 3.7 8.1E-05 34.0 -1.0 24 143-166 792-815 (907)
156 KOG4167|consensus 48.1 2.8 6E-05 34.7 -1.8 26 42-67 791-816 (907)
157 PTZ00255 60S ribosomal protein 48.1 12 0.00025 22.5 1.2 30 115-154 36-65 (90)
158 PF13453 zf-TFIIB: Transcripti 47.9 17 0.00037 18.0 1.7 17 144-160 20-36 (41)
159 COG5151 SSL1 RNA polymerase II 47.6 19 0.00042 26.8 2.5 26 42-67 387-412 (421)
160 PF01780 Ribosomal_L37ae: Ribo 46.8 9 0.00019 23.0 0.6 30 115-154 35-64 (90)
161 COG1198 PriA Primosomal protei 46.2 13 0.00029 31.2 1.7 14 139-152 471-484 (730)
162 PF05290 Baculo_IE-1: Baculovi 45.2 17 0.00036 23.5 1.7 17 41-57 78-94 (140)
163 TIGR00100 hypA hydrogenase nic 44.0 12 0.00025 23.6 0.8 25 115-151 70-94 (115)
164 TIGR01562 FdhE formate dehydro 43.7 25 0.00055 26.3 2.6 8 81-88 186-193 (305)
165 COG5151 SSL1 RNA polymerase II 43.7 23 0.0005 26.5 2.4 23 142-164 387-409 (421)
166 COG3677 Transposase and inacti 43.6 12 0.00025 24.2 0.8 16 140-155 50-65 (129)
167 PRK12380 hydrogenase nickel in 42.9 13 0.00027 23.3 0.9 25 115-151 70-94 (113)
168 COG3091 SprT Zn-dependent meta 42.9 12 0.00027 24.7 0.8 36 113-153 115-150 (156)
169 KOG0320|consensus 42.4 3.8 8.1E-05 27.8 -1.6 17 5-21 129-145 (187)
170 PF11672 DUF3268: Protein of u 42.2 17 0.00037 22.4 1.3 8 144-151 32-39 (102)
171 TIGR00280 L37a ribosomal prote 41.9 14 0.0003 22.2 0.9 12 143-154 53-64 (91)
172 PF03811 Zn_Tnp_IS1: InsA N-te 41.3 8.4 0.00018 18.8 -0.1 30 116-149 6-35 (36)
173 cd00065 FYVE FYVE domain; Zinc 40.9 21 0.00046 18.8 1.5 14 114-127 17-30 (57)
174 PF07503 zf-HYPF: HypF finger; 40.6 1.9 4.2E-05 20.9 -2.4 12 143-154 21-32 (35)
175 COG1773 Rubredoxin [Energy pro 40.1 15 0.00033 19.8 0.8 12 143-154 3-14 (55)
176 COG1655 Uncharacterized protei 39.7 6.7 0.00014 27.9 -0.8 38 114-151 18-70 (267)
177 PF14803 Nudix_N_2: Nudix N-te 39.7 5.6 0.00012 19.1 -0.8 8 144-151 23-30 (34)
178 smart00064 FYVE Protein presen 39.3 20 0.00044 19.8 1.3 13 115-127 26-38 (68)
179 TIGR00686 phnA alkylphosphonat 39.1 23 0.00051 22.0 1.6 14 115-128 19-32 (109)
180 COG4896 Uncharacterized protei 38.9 18 0.00039 19.9 0.9 40 82-128 5-44 (68)
181 PF05129 Elf1: Transcription e 38.1 6.6 0.00014 23.0 -0.9 43 110-156 17-59 (81)
182 PF14787 zf-CCHC_5: GAG-polypr 37.7 16 0.00035 17.7 0.6 15 145-159 4-18 (36)
183 PRK00564 hypA hydrogenase nick 37.6 16 0.00034 23.1 0.7 25 115-151 71-96 (117)
184 COG1675 TFA1 Transcription ini 37.4 26 0.00056 23.9 1.7 14 7-20 113-126 (176)
185 PRK10220 hypothetical protein; 37.1 29 0.00062 21.6 1.7 15 115-129 20-34 (111)
186 PF10263 SprT-like: SprT-like 36.7 11 0.00023 24.8 -0.1 33 114-154 122-154 (157)
187 KOG1280|consensus 36.6 48 0.001 25.2 3.1 27 42-68 78-105 (381)
188 PRK14892 putative transcriptio 36.5 20 0.00044 21.9 1.0 37 112-155 18-54 (99)
189 PF15135 UPF0515: Uncharacteri 36.4 53 0.0012 23.8 3.2 14 115-128 155-168 (278)
190 PRK14873 primosome assembly pr 36.3 18 0.00039 30.2 1.0 10 143-152 422-431 (665)
191 PF04780 DUF629: Protein of un 35.8 26 0.00055 27.9 1.7 21 144-164 58-78 (466)
192 KOG3214|consensus 35.3 25 0.00053 21.5 1.2 43 110-156 18-60 (109)
193 PF10013 DUF2256: Uncharacteri 35.3 22 0.00048 17.9 0.9 13 145-157 10-22 (42)
194 PRK03976 rpl37ae 50S ribosomal 35.3 19 0.00042 21.6 0.8 12 143-154 54-65 (90)
195 KOG2071|consensus 34.9 24 0.00052 28.7 1.5 27 140-166 415-441 (579)
196 PRK03681 hypA hydrogenase nick 34.9 12 0.00025 23.5 -0.2 15 42-56 69-83 (114)
197 KOG1280|consensus 34.6 53 0.0011 25.0 3.1 38 113-150 77-116 (381)
198 COG0068 HypF Hydrogenase matur 33.8 8.1 0.00018 32.1 -1.2 58 82-153 126-183 (750)
199 PF08792 A2L_zn_ribbon: A2L zi 33.4 25 0.00055 16.7 0.9 13 142-154 20-32 (33)
200 PF14446 Prok-RING_1: Prokaryo 33.2 39 0.00085 18.2 1.7 15 112-126 18-32 (54)
201 smart00249 PHD PHD zinc finger 32.9 32 0.0007 16.7 1.4 16 112-127 11-26 (47)
202 PTZ00448 hypothetical protein; 32.6 28 0.00061 26.7 1.4 23 143-165 314-336 (373)
203 PF07295 DUF1451: Protein of u 32.3 32 0.00069 22.7 1.5 32 42-91 111-142 (146)
204 PF12907 zf-met2: Zinc-binding 32.3 23 0.00051 17.7 0.7 6 117-122 3-8 (40)
205 KOG2906|consensus 32.2 3.5 7.6E-05 25.0 -2.6 17 42-58 20-36 (105)
206 PF03833 PolC_DP2: DNA polymer 31.1 16 0.00035 31.1 0.0 10 115-124 680-689 (900)
207 PF01155 HypA: Hydrogenase exp 30.8 17 0.00038 22.7 0.1 26 115-152 70-95 (113)
208 PF07649 C1_3: C1-like domain; 30.3 25 0.00055 15.9 0.6 10 114-123 14-23 (30)
209 TIGR00595 priA primosomal prot 30.3 44 0.00095 26.9 2.3 10 142-151 252-261 (505)
210 PF04423 Rad50_zn_hook: Rad50 30.2 23 0.0005 18.7 0.5 11 145-155 22-32 (54)
211 PRK00420 hypothetical protein; 30.0 45 0.00097 20.9 1.8 13 115-127 40-52 (112)
212 PF11781 RRN7: RNA polymerase 29.9 34 0.00074 16.6 1.0 25 116-151 9-33 (36)
213 PRK05978 hypothetical protein; 29.4 20 0.00043 23.7 0.2 31 116-155 34-64 (148)
214 COG4391 Uncharacterized protei 29.3 36 0.00077 18.8 1.1 42 110-155 19-60 (62)
215 cd00924 Cyt_c_Oxidase_Vb Cytoc 29.0 30 0.00066 21.1 0.9 20 135-155 72-91 (97)
216 PF06397 Desulfoferrod_N: Desu 28.8 30 0.00065 16.9 0.7 11 143-153 6-16 (36)
217 TIGR00627 tfb4 transcription f 27.3 50 0.0011 24.4 2.0 25 115-153 255-279 (279)
218 PF00301 Rubredoxin: Rubredoxi 27.0 33 0.0007 17.8 0.7 11 144-154 2-12 (47)
219 PF00628 PHD: PHD-finger; Int 26.6 54 0.0012 16.7 1.6 19 110-128 9-27 (51)
220 TIGR01384 TFS_arch transcripti 26.5 16 0.00034 22.3 -0.6 38 115-155 62-102 (104)
221 KOG2636|consensus 26.3 51 0.0011 26.0 1.9 25 138-162 396-421 (497)
222 COG1779 C4-type Zn-finger prot 26.0 15 0.00032 25.5 -0.9 12 144-155 44-55 (201)
223 PF04810 zf-Sec23_Sec24: Sec23 25.8 15 0.00033 18.1 -0.6 15 139-153 20-34 (40)
224 cd00730 rubredoxin Rubredoxin; 25.5 32 0.00068 18.1 0.5 11 144-154 2-12 (50)
225 PF09963 DUF2197: Uncharacteri 25.0 33 0.00071 18.6 0.5 7 82-88 5-11 (56)
226 smart00132 LIM Zinc-binding do 24.8 24 0.00053 16.4 -0.0 10 44-53 28-37 (39)
227 PF01927 Mut7-C: Mut7-C RNAse 24.6 63 0.0014 21.2 1.9 18 142-159 123-140 (147)
228 PF02591 DUF164: Putative zinc 24.5 98 0.0021 16.4 2.4 31 117-151 24-54 (56)
229 KOG2071|consensus 24.2 58 0.0013 26.7 1.9 28 40-67 415-442 (579)
230 PRK00762 hypA hydrogenase nick 23.9 31 0.00066 22.0 0.3 13 115-128 70-82 (124)
231 PF01286 XPA_N: XPA protein N- 23.5 30 0.00065 16.6 0.2 13 9-21 5-17 (34)
232 smart00731 SprT SprT homologue 23.5 28 0.0006 22.8 0.1 34 114-154 111-144 (146)
233 PRK04351 hypothetical protein; 23.3 51 0.0011 21.8 1.3 35 114-156 111-145 (149)
234 PF02748 PyrI_C: Aspartate car 23.2 42 0.00091 17.8 0.7 17 139-155 31-47 (52)
235 PRK12496 hypothetical protein; 22.8 59 0.0013 21.9 1.5 28 115-154 127-154 (164)
236 PF08209 Sgf11: Sgf11 (transcr 22.5 1E+02 0.0022 14.6 1.9 11 44-54 5-15 (33)
237 PF11494 Ta0938: Ta0938; Inte 22.4 68 0.0015 19.5 1.6 40 4-56 11-50 (105)
238 PLN03238 probable histone acet 22.4 69 0.0015 23.8 1.9 24 113-136 46-69 (290)
239 PLN02294 cytochrome c oxidase 22.2 56 0.0012 22.2 1.3 20 135-155 134-153 (174)
240 COG4640 Predicted membrane pro 22.2 65 0.0014 25.1 1.7 18 115-132 15-32 (465)
241 KOG2636|consensus 22.0 61 0.0013 25.6 1.6 28 37-64 395-423 (497)
242 PLN02748 tRNA dimethylallyltra 22.0 59 0.0013 26.0 1.6 24 142-165 417-441 (468)
243 PF09332 Mcm10: Mcm10 replicat 21.6 31 0.00067 26.3 0.0 16 8-23 253-268 (344)
244 COG5112 UFD2 U1-like Zn-finger 21.5 46 0.001 20.6 0.7 20 144-163 56-75 (126)
245 COG0068 HypF Hydrogenase matur 21.2 19 0.0004 30.1 -1.3 41 10-58 126-166 (750)
246 KOG2857|consensus 21.2 52 0.0011 21.6 1.0 22 115-136 17-38 (157)
247 KOG0717|consensus 20.9 60 0.0013 25.8 1.4 21 44-64 293-313 (508)
248 PF13821 DUF4187: Domain of un 20.8 53 0.0011 17.6 0.8 17 82-99 30-46 (55)
249 COG4338 Uncharacterized protei 20.8 32 0.0007 17.9 -0.0 14 145-158 14-27 (54)
250 PF05191 ADK_lid: Adenylate ki 20.7 45 0.00097 16.1 0.5 12 144-155 2-13 (36)
251 KOG4377|consensus 20.6 95 0.0021 24.4 2.3 26 44-69 272-299 (480)
252 KOG0717|consensus 20.4 55 0.0012 26.0 1.1 22 144-165 293-314 (508)
253 KOG1994|consensus 20.2 49 0.0011 23.6 0.8 22 141-162 237-258 (268)
254 TIGR00319 desulf_FeS4 desulfof 20.2 61 0.0013 15.1 0.9 12 142-153 6-17 (34)
No 1
>KOG2462|consensus
Probab=99.97 E-value=6.1e-31 Score=181.89 Aligned_cols=134 Identities=23% Similarity=0.346 Sum_probs=125.5
Q ss_pred CcccccccccccCchHHHHHHhhhhhccccCCCC---CccceecCccCccccChHHHHHHHHHhhCCCCCCcccccCccc
Q psy4421 6 NINQCVHCHLTLTKSTEVIVKHAQTCISMVRPDS---FKYKYGCYRCSYFTYESNNLKKHILKHTGEKPFSYMYENQQYC 82 (167)
Q Consensus 6 ~~~~C~~C~~~f~~~~~l~~~~~~~~~~h~~~~~---~~~~~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~~~~~~~~~c 82 (167)
.-|.|.+|++.+...++|. +|.++|- .++.+.|.+|++.+.+...|..|+++|+ .+.+ |
T Consensus 129 ~r~~c~eCgk~ysT~snLs--------rHkQ~H~~~~s~ka~~C~~C~K~YvSmpALkMHirTH~--l~c~--------C 190 (279)
T KOG2462|consen 129 PRYKCPECGKSYSTSSNLS--------RHKQTHRSLDSKKAFSCKYCGKVYVSMPALKMHIRTHT--LPCE--------C 190 (279)
T ss_pred Cceeccccccccccccccc--------hhhcccccccccccccCCCCCceeeehHHHhhHhhccC--CCcc--------c
Confidence 4589999999999999999 8888773 3677999999999999999999999998 4777 9
Q ss_pred ccccccccCChHHHHHHHhhcCCCCCCCCCCCcccCCCCCccccCchhHHHHHhhhCCCCceeCCCCcccccCchhHHHH
Q psy4421 83 IHCNSYISSDIKDLIEHCKSCSHMTRPDAFHFKFVCYACEYNTYMSGNIKTHLRLHLDDKPYKCSLCNYECRQNVHLKSH 162 (167)
Q Consensus 83 ~~c~~~~~~~~~~l~~h~~~~~~~~~~~~~~~~~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H 162 (167)
.+||+. |+....|.-|+++ ++||+||.|+.|++.|..+++|+.|+++|.+.|+|.|..|+|+|...+.|.+|
T Consensus 191 ~iCGKa-FSRPWLLQGHiRT-------HTGEKPF~C~hC~kAFADRSNLRAHmQTHS~~K~~qC~~C~KsFsl~SyLnKH 262 (279)
T KOG2462|consen 191 GICGKA-FSRPWLLQGHIRT-------HTGEKPFSCPHCGKAFADRSNLRAHMQTHSDVKKHQCPRCGKSFALKSYLNKH 262 (279)
T ss_pred cccccc-ccchHHhhccccc-------ccCCCCccCCcccchhcchHHHHHHHHhhcCCccccCcchhhHHHHHHHHHHh
Confidence 999999 9999999999999 99999999999999999999999999999999999999999999999999999
Q ss_pred hhh
Q psy4421 163 MKS 165 (167)
Q Consensus 163 ~~~ 165 (167)
..+
T Consensus 263 ~ES 265 (279)
T KOG2462|consen 263 SES 265 (279)
T ss_pred hhh
Confidence 864
No 2
>KOG2462|consensus
Probab=99.89 E-value=7.5e-24 Score=146.88 Aligned_cols=109 Identities=25% Similarity=0.503 Sum_probs=99.5
Q ss_pred ccceecCccCccccChHHHHHHHHHhhC---CCCCCcccccCcccccccccccCChHHHHHHHhhcCCCCCCCCCCCccc
Q psy4421 41 KYKYGCYRCSYFTYESNNLKKHILKHTG---EKPFSYMYENQQYCIHCNSYISSDIKDLIEHCKSCSHMTRPDAFHFKFV 117 (167)
Q Consensus 41 ~~~~~C~~C~~~~~~~~~l~~H~~~h~~---~~~~~~~~~~~~~c~~c~~~~~~~~~~l~~h~~~~~~~~~~~~~~~~~~ 117 (167)
...|.|+.||+.+.+.++|.+|+++|-. .+.+. |..|++. +.....|..|+.+ +. -+++
T Consensus 128 ~~r~~c~eCgk~ysT~snLsrHkQ~H~~~~s~ka~~--------C~~C~K~-YvSmpALkMHirT-------H~--l~c~ 189 (279)
T KOG2462|consen 128 HPRYKCPECGKSYSTSSNLSRHKQTHRSLDSKKAFS--------CKYCGKV-YVSMPALKMHIRT-------HT--LPCE 189 (279)
T ss_pred CCceeccccccccccccccchhhccccccccccccc--------CCCCCce-eeehHHHhhHhhc-------cC--CCcc
Confidence 3459999999999999999999999853 44566 9999999 8899999999988 66 5789
Q ss_pred CCCCCccccCchhHHHHHhhhCCCCceeCCCCcccccCchhHHHHhhhcC
Q psy4421 118 CYACEYNTYMSGNIKTHLRLHLDDKPYKCSLCNYECRQNVHLKSHMKSNH 167 (167)
Q Consensus 118 C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~hh 167 (167)
|.+||+.|...+-|+.|+|+|+|||||.|..|++.|..+++|+.|++||.
T Consensus 190 C~iCGKaFSRPWLLQGHiRTHTGEKPF~C~hC~kAFADRSNLRAHmQTHS 239 (279)
T KOG2462|consen 190 CGICGKAFSRPWLLQGHIRTHTGEKPFSCPHCGKAFADRSNLRAHMQTHS 239 (279)
T ss_pred cccccccccchHHhhcccccccCCCCccCCcccchhcchHHHHHHHHhhc
Confidence 99999999999999999999999999999999999999999999999973
No 3
>KOG1074|consensus
Probab=99.77 E-value=6e-20 Score=143.25 Aligned_cols=56 Identities=18% Similarity=0.347 Sum_probs=51.2
Q ss_pred cccccccccccCchHHHHHHhhhhhccccCCCCCccceecCccCccccChHHHHHHHHHhhCCC
Q psy4421 7 INQCVHCHLTLTKSTEVIVKHAQTCISMVRPDSFKYKYGCYRCSYFTYESNNLKKHILKHTGEK 70 (167)
Q Consensus 7 ~~~C~~C~~~f~~~~~l~~~~~~~~~~h~~~~~~~~~~~C~~C~~~~~~~~~l~~H~~~h~~~~ 70 (167)
+.+|..|.+.|...+.|+ .|.+.|++++||+|++||..|..+.+|+.|...|...-
T Consensus 353 khkCr~CakvfgS~SaLq--------iHlRSHTGERPfqCnvCG~~FSTkGNLKvH~~rH~e~~ 408 (958)
T KOG1074|consen 353 KHKCRFCAKVFGSDSALQ--------IHLRSHTGERPFQCNVCGNRFSTKGNLKVHFQRHREKY 408 (958)
T ss_pred cchhhhhHhhcCchhhhh--------hhhhccCCCCCeeecccccccccccceeeeeeeccccC
Confidence 467999999999999999 99999999999999999999999999999987776543
No 4
>KOG1074|consensus
Probab=99.75 E-value=4.9e-19 Score=138.23 Aligned_cols=52 Identities=29% Similarity=0.571 Sum_probs=50.3
Q ss_pred ccCCCCCccccCchhHHHHHhhhCCCCceeCCCCcccccCchhHHHHhhhcC
Q psy4421 116 FVCYACEYNTYMSGNIKTHLRLHLDDKPYKCSLCNYECRQNVHLKSHMKSNH 167 (167)
Q Consensus 116 ~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~hh 167 (167)
..|.+|++.|...+.|..|+++|+|+|||.|..|++.|..+.+|..|+.+|+
T Consensus 880 h~C~vCgk~FsSSsALqiH~rTHtg~KPF~C~fC~~aFttrgnLKvHMgtH~ 931 (958)
T KOG1074|consen 880 HVCNVCGKQFSSSAALEIHMRTHTGPKPFFCHFCEEAFTTRGNLKVHMGTHM 931 (958)
T ss_pred hhhccchhcccchHHHHHhhhcCCCCCCccchhhhhhhhhhhhhhhhhcccc
Confidence 6899999999999999999999999999999999999999999999999875
No 5
>KOG3608|consensus
Probab=99.71 E-value=8.3e-18 Score=120.46 Aligned_cols=134 Identities=23% Similarity=0.473 Sum_probs=102.2
Q ss_pred cccccccccccCchHHHHHHhhhhhccccCCCCCccceecCccCccccChHHHHHHHHH-hhCCCCCCcccccCcccccc
Q psy4421 7 INQCVHCHLTLTKSTEVIVKHAQTCISMVRPDSFKYKYGCYRCSYFTYESNNLKKHILK-HTGEKPFSYMYENQQYCIHC 85 (167)
Q Consensus 7 ~~~C~~C~~~f~~~~~l~~~~~~~~~~h~~~~~~~~~~~C~~C~~~~~~~~~l~~H~~~-h~~~~~~~~~~~~~~~c~~c 85 (167)
+|.|..|.+.|..+..|. .|+..|- ..|+|+.|+.+....+.|..|++. |...+|++ |..|
T Consensus 237 ~fqC~~C~KrFaTeklL~--------~Hv~rHv--n~ykCplCdmtc~~~ssL~~H~r~rHs~dkpfK--------Cd~C 298 (467)
T KOG3608|consen 237 SFQCAQCFKRFATEKLLK--------SHVVRHV--NCYKCPLCDMTCSSASSLTTHIRYRHSKDKPFK--------CDEC 298 (467)
T ss_pred chHHHHHHHHHhHHHHHH--------HHHHHhh--hcccccccccCCCChHHHHHHHHhhhccCCCcc--------ccch
Confidence 455555555555555555 5555442 247888888888888888888875 77788888 8889
Q ss_pred cccccCChHHHHHHHhhcCCCCCCCCCCCcccCCC--CCccccCchhHHHHHhh-hCCCC--ceeCCCCcccccCchhHH
Q psy4421 86 NSYISSDIKDLIEHCKSCSHMTRPDAFHFKFVCYA--CEYNTYMSGNIKTHLRL-HLDDK--PYKCSLCNYECRQNVHLK 160 (167)
Q Consensus 86 ~~~~~~~~~~l~~h~~~~~~~~~~~~~~~~~~C~~--C~~~~~~~~~l~~H~~~-h~~~~--~~~C~~C~~~f~~~~~l~ 160 (167)
+.. +.+..+|.+|..+ +. +..|.|.. |...+.....++.|++. |.|.. +|.|-.|++.|.+..+|.
T Consensus 299 d~~-c~~esdL~kH~~~-------HS-~~~y~C~h~~C~~s~r~~~q~~~H~~evhEg~np~~Y~CH~Cdr~ft~G~~L~ 369 (467)
T KOG3608|consen 299 DTR-CVRESDLAKHVQV-------HS-KTVYQCEHPDCHYSVRTYTQMRRHFLEVHEGNNPILYACHCCDRFFTSGKSLS 369 (467)
T ss_pred hhh-hccHHHHHHHHHh-------cc-ccceecCCCCCcHHHHHHHHHHHHHHHhccCCCCCceeeecchhhhccchhHH
Confidence 888 8888899999887 66 67788877 88888888999999664 44544 499999999999999999
Q ss_pred HHhhhcC
Q psy4421 161 SHMKSNH 167 (167)
Q Consensus 161 ~H~~~hh 167 (167)
+|++..|
T Consensus 370 ~HL~kkH 376 (467)
T KOG3608|consen 370 AHLMKKH 376 (467)
T ss_pred HHHHHhh
Confidence 9987654
No 6
>KOG3608|consensus
Probab=99.70 E-value=1e-17 Score=119.96 Aligned_cols=106 Identities=21% Similarity=0.499 Sum_probs=58.4
Q ss_pred ceecCccCccccChHHHHHHHHHhhCCCCCCcccccCcccccccccccCChHHHHHHHhhcCCCCCCCCCCCcccCCCCC
Q psy4421 43 KYGCYRCSYFTYESNNLKKHILKHTGEKPFSYMYENQQYCIHCNSYISSDIKDLIEHCKSCSHMTRPDAFHFKFVCYACE 122 (167)
Q Consensus 43 ~~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~~~~~~~~~c~~c~~~~~~~~~~l~~h~~~~~~~~~~~~~~~~~~C~~C~ 122 (167)
+|.|..|.+.|..+..|..|+..|.. .|+ |+.|+.. ....+.|..|+... +..++||+|+.|.
T Consensus 237 ~fqC~~C~KrFaTeklL~~Hv~rHvn--~yk--------CplCdmt-c~~~ssL~~H~r~r------Hs~dkpfKCd~Cd 299 (467)
T KOG3608|consen 237 SFQCAQCFKRFATEKLLKSHVVRHVN--CYK--------CPLCDMT-CSSASSLTTHIRYR------HSKDKPFKCDECD 299 (467)
T ss_pred chHHHHHHHHHhHHHHHHHHHHHhhh--ccc--------ccccccC-CCChHHHHHHHHhh------hccCCCccccchh
Confidence 44444444444444444444444432 334 6666655 55556666665552 3445566666666
Q ss_pred ccccCchhHHHHHhhhCCCCceeCCC--CcccccCchhHHHHhhhc
Q psy4421 123 YNTYMSGNIKTHLRLHLDDKPYKCSL--CNYECRQNVHLKSHMKSN 166 (167)
Q Consensus 123 ~~~~~~~~l~~H~~~h~~~~~~~C~~--C~~~f~~~~~l~~H~~~h 166 (167)
+.+...+.|..|..+|. +-.|.|.. |-++|++..+|.+|.+.+
T Consensus 300 ~~c~~esdL~kH~~~HS-~~~y~C~h~~C~~s~r~~~q~~~H~~ev 344 (467)
T KOG3608|consen 300 TRCVRESDLAKHVQVHS-KTVYQCEHPDCHYSVRTYTQMRRHFLEV 344 (467)
T ss_pred hhhccHHHHHHHHHhcc-ccceecCCCCCcHHHHHHHHHHHHHHHh
Confidence 66666666666666555 44466655 666666666666665544
No 7
>KOG3576|consensus
Probab=99.69 E-value=1.2e-17 Score=111.32 Aligned_cols=110 Identities=23% Similarity=0.368 Sum_probs=91.9
Q ss_pred cceecCccCccccChHHHHHHHHHhhCCCCCCcccccCcccccccccccCChHHHHHHHhhcCCCCCCCCCCCcccCCCC
Q psy4421 42 YKYGCYRCSYFTYESNNLKKHILKHTGEKPFSYMYENQQYCIHCNSYISSDIKDLIEHCKSCSHMTRPDAFHFKFVCYAC 121 (167)
Q Consensus 42 ~~~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~~~~~~~~~c~~c~~~~~~~~~~l~~h~~~~~~~~~~~~~~~~~~C~~C 121 (167)
..|.|..|++.|.....|.+|++-|...+.+- |..||+. |.+.-+|.+|.++ ++|-+||+|..|
T Consensus 116 d~ftCrvCgK~F~lQRmlnrh~kch~~vkr~l--------ct~cgkg-fndtfdlkrh~rt-------htgvrpykc~~c 179 (267)
T KOG3576|consen 116 DSFTCRVCGKKFGLQRMLNRHLKCHSDVKRHL--------CTFCGKG-FNDTFDLKRHTRT-------HTGVRPYKCSLC 179 (267)
T ss_pred CeeeeehhhhhhhHHHHHHHHhhhccHHHHHH--------HhhccCc-ccchhhhhhhhcc-------ccCccccchhhh
Confidence 34889999999988888888988888888887 8889888 8888888888888 888889999999
Q ss_pred CccccCchhHHHHHhhhCC-----------CCceeCCCCcccccCchhHHHHhhhcC
Q psy4421 122 EYNTYMSGNIKTHLRLHLD-----------DKPYKCSLCNYECRQNVHLKSHMKSNH 167 (167)
Q Consensus 122 ~~~~~~~~~l~~H~~~h~~-----------~~~~~C~~C~~~f~~~~~l~~H~~~hh 167 (167)
++.|.++.+|..|.+.-+| ++.|+|+.||.+-.....+..|++.+|
T Consensus 180 ~kaftqrcsleshl~kvhgv~~~yaykerr~kl~vcedcg~t~~~~e~~~~h~~~~h 236 (267)
T KOG3576|consen 180 EKAFTQRCSLESHLKKVHGVQHQYAYKERRAKLYVCEDCGYTSERPEVYYLHLKLHH 236 (267)
T ss_pred hHHHHhhccHHHHHHHHcCchHHHHHHHhhhheeeecccCCCCCChhHHHHHHHhcC
Confidence 9999999888888663332 566899999988888888888887765
No 8
>KOG3576|consensus
Probab=99.63 E-value=9.2e-17 Score=107.14 Aligned_cols=122 Identities=20% Similarity=0.297 Sum_probs=104.9
Q ss_pred cCCcccccccccccCchHHHHHHhhhhhccccCCCCCccceecCccCccccChHHHHHHHHHhhCCCCCCcccccCcccc
Q psy4421 4 SLNINQCVHCHLTLTKSTEVIVKHAQTCISMVRPDSFKYKYGCYRCSYFTYESNNLKKHILKHTGEKPFSYMYENQQYCI 83 (167)
Q Consensus 4 ~~~~~~C~~C~~~f~~~~~l~~~~~~~~~~h~~~~~~~~~~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~~~~~~~~~c~ 83 (167)
+...|.|.+|++.|.....|. +|++.|+..+.+.|.-||+.|.....|++|.++|+|.+||+ |.
T Consensus 114 d~d~ftCrvCgK~F~lQRmln--------rh~kch~~vkr~lct~cgkgfndtfdlkrh~rthtgvrpyk--------c~ 177 (267)
T KOG3576|consen 114 DQDSFTCRVCGKKFGLQRMLN--------RHLKCHSDVKRHLCTFCGKGFNDTFDLKRHTRTHTGVRPYK--------CS 177 (267)
T ss_pred CCCeeeeehhhhhhhHHHHHH--------HHhhhccHHHHHHHhhccCcccchhhhhhhhccccCccccc--------hh
Confidence 355699999999999999999 99999999999999999999999999999999999999999 99
Q ss_pred cccccccCChHHHHHHHhhcCCCCCC----CCCCCcccCCCCCccccCchhHHHHHhhhCCCC
Q psy4421 84 HCNSYISSDIKDLIEHCKSCSHMTRP----DAFHFKFVCYACEYNTYMSGNIKTHLRLHLDDK 142 (167)
Q Consensus 84 ~c~~~~~~~~~~l~~h~~~~~~~~~~----~~~~~~~~C~~C~~~~~~~~~l~~H~~~h~~~~ 142 (167)
.|++. |...-.|..|+..-+..... ...++.|.|+.||.+-.....+..|+..++-..
T Consensus 178 ~c~ka-ftqrcsleshl~kvhgv~~~yaykerr~kl~vcedcg~t~~~~e~~~~h~~~~hp~S 239 (267)
T KOG3576|consen 178 LCEKA-FTQRCSLESHLKKVHGVQHQYAYKERRAKLYVCEDCGYTSERPEVYYLHLKLHHPFS 239 (267)
T ss_pred hhhHH-HHhhccHHHHHHHHcCchHHHHHHHhhhheeeecccCCCCCChhHHHHHHHhcCCCC
Confidence 99999 99888899998763322211 123578999999999999988999988776433
No 9
>KOG3623|consensus
Probab=99.63 E-value=1.5e-16 Score=123.16 Aligned_cols=113 Identities=27% Similarity=0.439 Sum_probs=91.3
Q ss_pred eecCccCccccChHHHHHHHHHhh--CCCCCCcccccCcccccccccccCChHHHHHHHhhcCCCCCC------CCCCCc
Q psy4421 44 YGCYRCSYFTYESNNLKKHILKHT--GEKPFSYMYENQQYCIHCNSYISSDIKDLIEHCKSCSHMTRP------DAFHFK 115 (167)
Q Consensus 44 ~~C~~C~~~~~~~~~l~~H~~~h~--~~~~~~~~~~~~~~c~~c~~~~~~~~~~l~~h~~~~~~~~~~------~~~~~~ 115 (167)
..|++|++.+.....|..|+.-.+ .+..|. |..|... |.....|.+|+......... ....+.
T Consensus 211 ltcpycdrgykrltslkeHikyrhekne~nfs--------C~lCsyt-FAyRtQLErhm~~hkpg~dqa~sltqsa~lRK 281 (1007)
T KOG3623|consen 211 LTCPYCDRGYKRLTSLKEHIKYRHEKNEPNFS--------CMLCSYT-FAYRTQLERHMQLHKPGGDQAISLTQSALLRK 281 (1007)
T ss_pred hcchhHHHHHHHHHHHHHHHHHHHhhCCCCCc--------chhhhhh-hhhHHHHHHHHHhhcCCCcccccccchhhhcc
Confidence 568888888888888888885432 334466 8888888 88888888888775433322 233567
Q ss_pred ccCCCCCccccCchhHHHHHhhhCCCCceeCCCCcccccCchhHHHHhhh
Q psy4421 116 FVCYACEYNTYMSGNIKTHLRLHLDDKPYKCSLCNYECRQNVHLKSHMKS 165 (167)
Q Consensus 116 ~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~ 165 (167)
|+|..|++.|..+..|+.|+|+|.|||||.|..|+|+|+...++..|+.+
T Consensus 282 FKCtECgKAFKfKHHLKEHlRIHSGEKPfeCpnCkKRFSHSGSySSHmSS 331 (1007)
T KOG3623|consen 282 FKCTECGKAFKFKHHLKEHLRIHSGEKPFECPNCKKRFSHSGSYSSHMSS 331 (1007)
T ss_pred ccccccchhhhhHHHHHhhheeecCCCCcCCcccccccccCCcccccccc
Confidence 99999999999999999999999999999999999999999999999854
No 10
>KOG3623|consensus
Probab=99.43 E-value=2.9e-14 Score=110.68 Aligned_cols=84 Identities=23% Similarity=0.390 Sum_probs=78.3
Q ss_pred CCcCCcccccccccccCchHHHHHHhhhhhccccCCCCCccceecCccCccccChHHHHHHHHHhhCCCCCCcccccCcc
Q psy4421 2 QESLNINQCVHCHLTLTKSTEVIVKHAQTCISMVRPDSFKYKYGCYRCSYFTYESNNLKKHILKHTGEKPFSYMYENQQY 81 (167)
Q Consensus 2 ~~~~~~~~C~~C~~~f~~~~~l~~~~~~~~~~h~~~~~~~~~~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~~~~~~~~~ 81 (167)
.+.+.+|.|..|++.|...+.|. +|.-.|+|.+||+|.+|.+.|+.+-.|..|+|.|.|||||+
T Consensus 889 kte~gmyaCDqCDK~FqKqSSLa--------RHKYEHsGqRPyqC~iCkKAFKHKHHLtEHkRLHSGEKPfQ-------- 952 (1007)
T KOG3623|consen 889 KTEDGMYACDQCDKAFQKQSSLA--------RHKYEHSGQRPYQCIICKKAFKHKHHLTEHKRLHSGEKPFQ-------- 952 (1007)
T ss_pred cCccccchHHHHHHHHHhhHHHH--------HhhhhhcCCCCcccchhhHhhhhhhhhhhhhhhccCCCcch--------
Confidence 35677899999999999999999 99889999999999999999999999999999999999999
Q ss_pred cccccccccCChHHHHHHHhh
Q psy4421 82 CIHCNSYISSDIKDLIEHCKS 102 (167)
Q Consensus 82 c~~c~~~~~~~~~~l~~h~~~ 102 (167)
|..|++. |+..-.+.+||.-
T Consensus 953 CdKClKR-FSHSGSYSQHMNH 972 (1007)
T KOG3623|consen 953 CDKCLKR-FSHSGSYSQHMNH 972 (1007)
T ss_pred hhhhhhh-cccccchHhhhcc
Confidence 9999999 9988888888754
No 11
>PLN03086 PRLI-interacting factor K; Provisional
Probab=99.27 E-value=1.4e-11 Score=95.48 Aligned_cols=104 Identities=16% Similarity=0.339 Sum_probs=85.5
Q ss_pred ccceecCccCccccChHHHHHHHHHhhCCCCCCcccccCcccccccccccCChHHHHHHHhhcCCCCCCCCCCCcccCCC
Q psy4421 41 KYKYGCYRCSYFTYESNNLKKHILKHTGEKPFSYMYENQQYCIHCNSYISSDIKDLIEHCKSCSHMTRPDAFHFKFVCYA 120 (167)
Q Consensus 41 ~~~~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~~~~~~~~~c~~c~~~~~~~~~~l~~h~~~~~~~~~~~~~~~~~~C~~ 120 (167)
++.+.|+.|++.|. ...|..|+.+++ +++. |+ |+.. + ....|..|+.. +...+++.|+.
T Consensus 451 ~~H~~C~~Cgk~f~-~s~LekH~~~~H--kpv~--------Cp-Cg~~-~-~R~~L~~H~~t-------hCp~Kpi~C~f 509 (567)
T PLN03086 451 KNHVHCEKCGQAFQ-QGEMEKHMKVFH--EPLQ--------CP-CGVV-L-EKEQMVQHQAS-------TCPLRLITCRF 509 (567)
T ss_pred ccCccCCCCCCccc-hHHHHHHHHhcC--CCcc--------CC-CCCC-c-chhHHHhhhhc-------cCCCCceeCCC
Confidence 34578999999995 678999999874 6888 99 9965 4 66899999988 88999999999
Q ss_pred CCccccC----------chhHHHHHhhhCCCCceeCCCCcccccCchhHHHHhhhcC
Q psy4421 121 CEYNTYM----------SGNIKTHLRLHLDDKPYKCSLCNYECRQNVHLKSHMKSNH 167 (167)
Q Consensus 121 C~~~~~~----------~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~hh 167 (167)
|+..+.. ...|..|.... |.+++.|..||+.|..+ +|..|+...|
T Consensus 510 C~~~v~~g~~~~d~~d~~s~Lt~HE~~C-G~rt~~C~~Cgk~Vrlr-dm~~H~~~~h 564 (567)
T PLN03086 510 CGDMVQAGGSAMDVRDRLRGMSEHESIC-GSRTAPCDSCGRSVMLK-EMDIHQIAVH 564 (567)
T ss_pred CCCccccCccccchhhhhhhHHHHHHhc-CCcceEccccCCeeeeh-hHHHHHHHhh
Confidence 9999852 34789998875 89999999999988876 6667776543
No 12
>PHA00733 hypothetical protein
Probab=99.22 E-value=9.9e-12 Score=79.50 Aligned_cols=98 Identities=18% Similarity=0.220 Sum_probs=66.1
Q ss_pred HHHHHHHHHhhCCCCCCcccccCcccccccccccCChHHHHHHHhhcCCCCCCCCCCCcccCCCCCccccCchhHHHHHh
Q psy4421 57 NNLKKHILKHTGEKPFSYMYENQQYCIHCNSYISSDIKDLIEHCKSCSHMTRPDAFHFKFVCYACEYNTYMSGNIKTHLR 136 (167)
Q Consensus 57 ~~l~~H~~~h~~~~~~~~~~~~~~~c~~c~~~~~~~~~~l~~h~~~~~~~~~~~~~~~~~~C~~C~~~~~~~~~l~~H~~ 136 (167)
..|.++-..-...+++. |.+|... +.+...|..+......+ ...+.++|.|+.|++.|.....|..|++
T Consensus 26 ~~~~~~~~~~~~~~~~~--------~~~~~~~-~~~~~~l~~~~~l~~~~--~~~~~kPy~C~~Cgk~Fss~s~L~~H~r 94 (128)
T PHA00733 26 EELKRYHSLTPEQKRLI--------RAVVKTL-IYNPQLLDESSYLYKLL--TSKAVSPYVCPLCLMPFSSSVSLKQHIR 94 (128)
T ss_pred HHhhhhhcCChhhhhHH--------HHHHhhh-ccChhhhcchHHHHhhc--ccCCCCCccCCCCCCcCCCHHHHHHHHh
Confidence 34444333333345566 7777666 55544444331111111 1334678999999999999999999998
Q ss_pred hhCCCCceeCCCCcccccCchhHHHHhhhcC
Q psy4421 137 LHLDDKPYKCSLCNYECRQNVHLKSHMKSNH 167 (167)
Q Consensus 137 ~h~~~~~~~C~~C~~~f~~~~~l~~H~~~hh 167 (167)
.+ +.+|.|..|++.|.....|..|+...|
T Consensus 95 ~h--~~~~~C~~CgK~F~~~~sL~~H~~~~h 123 (128)
T PHA00733 95 YT--EHSKVCPVCGKEFRNTDSTLDHVCKKH 123 (128)
T ss_pred cC--CcCccCCCCCCccCCHHHHHHHHHHhc
Confidence 76 457999999999999999999998765
No 13
>PHA02768 hypothetical protein; Provisional
Probab=99.12 E-value=3.1e-11 Score=64.49 Aligned_cols=44 Identities=23% Similarity=0.242 Sum_probs=40.9
Q ss_pred cccCCCCCccccCchhHHHHHhhhCCCCceeCCCCcccccCchhHH
Q psy4421 115 KFVCYACEYNTYMSGNIKTHLRLHLDDKPYKCSLCNYECRQNVHLK 160 (167)
Q Consensus 115 ~~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~ 160 (167)
.|.|+.||+.|...++|..|+++|. ++|+|..|++.|...+.|.
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 4899999999999999999999998 7999999999999888774
No 14
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=98.98 E-value=5e-10 Score=51.39 Aligned_cols=26 Identities=38% Similarity=0.925 Sum_probs=23.9
Q ss_pred hHHHHHhhhCCCCceeCCCCcccccC
Q psy4421 130 NIKTHLRLHLDDKPYKCSLCNYECRQ 155 (167)
Q Consensus 130 ~l~~H~~~h~~~~~~~C~~C~~~f~~ 155 (167)
+|..|+++|.|++||.|+.|+++|.+
T Consensus 1 ~l~~H~~~H~~~k~~~C~~C~k~F~~ 26 (26)
T PF13465_consen 1 NLRRHMRTHTGEKPYKCPYCGKSFSN 26 (26)
T ss_dssp HHHHHHHHHSSSSSEEESSSSEEESS
T ss_pred CHHHHhhhcCCCCCCCCCCCcCeeCc
Confidence 58899999999999999999999974
No 15
>PLN03086 PRLI-interacting factor K; Provisional
Probab=98.96 E-value=1.8e-09 Score=83.92 Aligned_cols=102 Identities=15% Similarity=0.273 Sum_probs=82.9
Q ss_pred cCCcccccccccccCchHHHHHHhhhhhccccCCCCCccceecCccCccccChHHHHHHHHHhhCCCCCCcccccCcccc
Q psy4421 4 SLNINQCVHCHLTLTKSTEVIVKHAQTCISMVRPDSFKYKYGCYRCSYFTYESNNLKKHILKHTGEKPFSYMYENQQYCI 83 (167)
Q Consensus 4 ~~~~~~C~~C~~~f~~~~~l~~~~~~~~~~h~~~~~~~~~~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~~~~~~~~~c~ 83 (167)
.++.+.|+.|+..|. ..+|. .|+..++ +++.|+ |++.+ ....|..|+.+|-+++++. |.
T Consensus 450 l~~H~~C~~Cgk~f~-~s~Le--------kH~~~~H--kpv~Cp-Cg~~~-~R~~L~~H~~thCp~Kpi~--------C~ 508 (567)
T PLN03086 450 AKNHVHCEKCGQAFQ-QGEME--------KHMKVFH--EPLQCP-CGVVL-EKEQMVQHQASTCPLRLIT--------CR 508 (567)
T ss_pred cccCccCCCCCCccc-hHHHH--------HHHHhcC--CCccCC-CCCCc-chhHHHhhhhccCCCCcee--------CC
Confidence 456789999999996 57788 7877664 679999 99765 6689999999999999999 99
Q ss_pred cccccccC----------ChHHHHHHHhhcCCCCCCCCCCCcccCCCCCccccCchhHHHHHh
Q psy4421 84 HCNSYISS----------DIKDLIEHCKSCSHMTRPDAFHFKFVCYACEYNTYMSGNIKTHLR 136 (167)
Q Consensus 84 ~c~~~~~~----------~~~~l~~h~~~~~~~~~~~~~~~~~~C~~C~~~~~~~~~l~~H~~ 136 (167)
.|+.. +. ....|..|..+ . +.+++.|..|++.+..+. +..|+.
T Consensus 509 fC~~~-v~~g~~~~d~~d~~s~Lt~HE~~-------C-G~rt~~C~~Cgk~Vrlrd-m~~H~~ 561 (567)
T PLN03086 509 FCGDM-VQAGGSAMDVRDRLRGMSEHESI-------C-GSRTAPCDSCGRSVMLKE-MDIHQI 561 (567)
T ss_pred CCCCc-cccCccccchhhhhhhHHHHHHh-------c-CCcceEccccCCeeeehh-HHHHHH
Confidence 99988 42 24578888876 4 778999999999988874 677754
No 16
>PHA00733 hypothetical protein
Probab=98.94 E-value=2.1e-09 Score=68.78 Aligned_cols=87 Identities=14% Similarity=0.107 Sum_probs=60.2
Q ss_pred CCcCCcccccccccccCchHHHHHHhhhhhccccCCCCCccceecCccCccccChHHHHHHHHHhhCCCCCCcccccCcc
Q psy4421 2 QESLNINQCVHCHLTLTKSTEVIVKHAQTCISMVRPDSFKYKYGCYRCSYFTYESNNLKKHILKHTGEKPFSYMYENQQY 81 (167)
Q Consensus 2 ~~~~~~~~C~~C~~~f~~~~~l~~~~~~~~~~h~~~~~~~~~~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~~~~~~~~~ 81 (167)
+...+++.|..|...|.....|.. .+.+..++.. .+.++|.|+.|++.|.....|..|++.+ +.++.
T Consensus 35 ~~~~~~~~~~~~~~~~~~~~~l~~--~~~l~~~~~~-~~~kPy~C~~Cgk~Fss~s~L~~H~r~h--~~~~~-------- 101 (128)
T PHA00733 35 TPEQKRLIRAVVKTLIYNPQLLDE--SSYLYKLLTS-KAVSPYVCPLCLMPFSSSVSLKQHIRYT--EHSKV-------- 101 (128)
T ss_pred ChhhhhHHHHHHhhhccChhhhcc--hHHHHhhccc-CCCCCccCCCCCCcCCCHHHHHHHHhcC--CcCcc--------
Confidence 345677888888888777665551 1112233333 3467788888888888888888888765 34677
Q ss_pred cccccccccCChHHHHHHHhh
Q psy4421 82 CIHCNSYISSDIKDLIEHCKS 102 (167)
Q Consensus 82 c~~c~~~~~~~~~~l~~h~~~ 102 (167)
|..|++. |.....|..|+..
T Consensus 102 C~~CgK~-F~~~~sL~~H~~~ 121 (128)
T PHA00733 102 CPVCGKE-FRNTDSTLDHVCK 121 (128)
T ss_pred CCCCCCc-cCCHHHHHHHHHH
Confidence 8888888 7877788877665
No 17
>KOG3993|consensus
Probab=98.90 E-value=5e-10 Score=82.67 Aligned_cols=157 Identities=15% Similarity=0.155 Sum_probs=105.8
Q ss_pred CCcCCcccccccccccCchHHHHHHhhhhhccccCCCCCccceecCccCccccChHHHHHHHHHhhCCC--------CCC
Q psy4421 2 QESLNINQCVHCHLTLTKSTEVIVKHAQTCISMVRPDSFKYKYGCYRCSYFTYESNNLKKHILKHTGEK--------PFS 73 (167)
Q Consensus 2 ~~~~~~~~C~~C~~~f~~~~~l~~~~~~~~~~h~~~~~~~~~~~C~~C~~~~~~~~~l~~H~~~h~~~~--------~~~ 73 (167)
.+...-|.|..|...|.+.+.|. +|.-.-+-...|+|++|++.|....||..|.|+|.... |-+
T Consensus 262 ~n~iGdyiCqLCK~kYeD~F~LA--------QHrC~RIV~vEYrCPEC~KVFsCPANLASHRRWHKPR~eaa~a~~~P~k 333 (500)
T KOG3993|consen 262 PNVIGDYICQLCKEKYEDAFALA--------QHRCPRIVHVEYRCPECDKVFSCPANLASHRRWHKPRPEAAKAGSPPPK 333 (500)
T ss_pred cccHHHHHHHHHHHhhhhHHHHh--------hccCCeeEEeeecCCcccccccCchhhhhhhcccCCchhhhhcCCCChh
Confidence 44555689999999999999999 77654444455999999999999999999999986322 111
Q ss_pred -c----------------ccccCcccccccccccCChHHHHHHHhhcCCCCCCCC-------------------------
Q psy4421 74 -Y----------------MYENQQYCIHCNSYISSDIKDLIEHCKSCSHMTRPDA------------------------- 111 (167)
Q Consensus 74 -~----------------~~~~~~~c~~c~~~~~~~~~~l~~h~~~~~~~~~~~~------------------------- 111 (167)
- +.+.-..|..|++. |.....|.+|+.++........
T Consensus 334 ~~~~~rae~~ea~rsg~dss~gi~~C~~C~Kk-FrRqAYLrKHqlthq~~~~~k~~a~~f~~s~~~~l~~~~~~~a~h~~ 412 (500)
T KOG3993|consen 334 QAVETRAEVQEAERSGDDSSSGIFSCHTCGKK-FRRQAYLRKHQLTHQRAPLAKEKAPKFLLSRVIPLMHFNQAVATHSS 412 (500)
T ss_pred hhhhhhhhhhhccccCCcccCceeecHHhhhh-hHHHHHHHHhHHhhhccccchhcccCcchhhcccccccccccccccc
Confidence 0 11223357788888 7777788888666542221110
Q ss_pred ------CCC--------cccCCCCCccccCchhHHHHHhhhCCCCceeCCCCcccccCchhHHHHhhhcC
Q psy4421 112 ------FHF--------KFVCYACEYNTYMSGNIKTHLRLHLDDKPYKCSLCNYECRQNVHLKSHMKSNH 167 (167)
Q Consensus 112 ------~~~--------~~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~hh 167 (167)
.+. ...++.++..+..++.--.+.+.-..+..|.|.+|--.|.+...|.+|+...|
T Consensus 413 a~~~~g~~vl~~a~sael~~pp~~~~ppsss~~sgg~~rlg~~~q~f~~ky~~atfyss~~ltrhin~~H 482 (500)
T KOG3993|consen 413 ASDSHGDEVLYVAGSAELELPPYDGSPPSSSGSSGGYGRLGIAEQGFTCKYCPATFYSSPGLTRHINKCH 482 (500)
T ss_pred cccccccceeeeeccccccCCCCCCCCcccCCCCCccccccchhhccccccchHhhhcCcchHhHhhhcC
Confidence 000 12445555555555443344443444667889999999999999999987765
No 18
>PHA02768 hypothetical protein; Provisional
Probab=98.71 E-value=3.1e-09 Score=56.83 Aligned_cols=42 Identities=19% Similarity=0.412 Sum_probs=24.8
Q ss_pred eecCccCccccChHHHHHHHHHhhCCCCCCcccccCcccccccccccCChHHH
Q psy4421 44 YGCYRCSYFTYESNNLKKHILKHTGEKPFSYMYENQQYCIHCNSYISSDIKDL 96 (167)
Q Consensus 44 ~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~~~~~~~~~c~~c~~~~~~~~~~l 96 (167)
|.|+.||+.|...+.|..|+++|+ ++++ |..|++. |...+.|
T Consensus 6 y~C~~CGK~Fs~~~~L~~H~r~H~--k~~k--------c~~C~k~-f~~~s~l 47 (55)
T PHA02768 6 YECPICGEIYIKRKSMITHLRKHN--TNLK--------LSNCKRI-SLRTGEY 47 (55)
T ss_pred cCcchhCCeeccHHHHHHHHHhcC--Cccc--------CCcccce-eccccee
Confidence 556666666666666666666666 3555 6666665 4444433
No 19
>PHA00732 hypothetical protein
Probab=98.51 E-value=9.5e-08 Score=55.80 Aligned_cols=45 Identities=36% Similarity=0.612 Sum_probs=32.8
Q ss_pred cccCCCCCccccCchhHHHHHhh-hCCCCceeCCCCcccccCchhHHHHhhh
Q psy4421 115 KFVCYACEYNTYMSGNIKTHLRL-HLDDKPYKCSLCNYECRQNVHLKSHMKS 165 (167)
Q Consensus 115 ~~~C~~C~~~~~~~~~l~~H~~~-h~~~~~~~C~~C~~~f~~~~~l~~H~~~ 165 (167)
||.|..|++.|....+|..|++. |. ++.|+.||+.|. .|..|.++
T Consensus 1 py~C~~Cgk~F~s~s~Lk~H~r~~H~---~~~C~~CgKsF~---~l~~H~~~ 46 (79)
T PHA00732 1 MFKCPICGFTTVTLFALKQHARRNHT---LTKCPVCNKSYR---RLNQHFYS 46 (79)
T ss_pred CccCCCCCCccCCHHHHHHHhhcccC---CCccCCCCCEeC---Chhhhhcc
Confidence 46788888888888888888774 54 347888888887 46666654
No 20
>PHA00616 hypothetical protein
Probab=98.47 E-value=5.4e-08 Score=49.62 Aligned_cols=34 Identities=12% Similarity=0.145 Sum_probs=31.6
Q ss_pred cccCCCCCccccCchhHHHHHhhhCCCCceeCCC
Q psy4421 115 KFVCYACEYNTYMSGNIKTHLRLHLDDKPYKCSL 148 (167)
Q Consensus 115 ~~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~ 148 (167)
||+|+.||+.|....+|..|++.|+|++++.|+.
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~~hg~~~~~~~~ 34 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLSVHKQNKLTLEY 34 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHHhcCCCccceeE
Confidence 6899999999999999999999999999998875
No 21
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=98.37 E-value=5.8e-07 Score=48.77 Aligned_cols=50 Identities=24% Similarity=0.531 Sum_probs=37.8
Q ss_pred cccCCCCCccccCchhHHHHHh-hhCCC-CceeCCCCcccccCchhHHHHhhhcC
Q psy4421 115 KFVCYACEYNTYMSGNIKTHLR-LHLDD-KPYKCSLCNYECRQNVHLKSHMKSNH 167 (167)
Q Consensus 115 ~~~C~~C~~~~~~~~~l~~H~~-~h~~~-~~~~C~~C~~~f~~~~~l~~H~~~hh 167 (167)
.|.||.|++ ..+...|..|.. .|.++ +.+.|++|...+. .+|..|+..+|
T Consensus 2 ~f~CP~C~~-~~~~~~L~~H~~~~H~~~~~~v~CPiC~~~~~--~~l~~Hl~~~H 53 (54)
T PF05605_consen 2 SFTCPYCGK-GFSESSLVEHCEDEHRSESKNVVCPICSSRVT--DNLIRHLNSQH 53 (54)
T ss_pred CcCCCCCCC-ccCHHHHHHHHHhHCcCCCCCccCCCchhhhh--hHHHHHHHHhc
Confidence 478999999 566678999955 45544 4689999998655 48999998776
No 22
>PHA00616 hypothetical protein
Probab=98.29 E-value=4e-07 Score=46.43 Aligned_cols=31 Identities=19% Similarity=0.488 Sum_probs=25.1
Q ss_pred ceecCccCccccChHHHHHHHHHhhCCCCCC
Q psy4421 43 KYGCYRCSYFTYESNNLKKHILKHTGEKPFS 73 (167)
Q Consensus 43 ~~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~ 73 (167)
||+|..||+.|...+.|.+|++.|++++++.
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~~hg~~~~~ 31 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLSVHKQNKLT 31 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHHhcCCCccc
Confidence 4778888888888888888888888888776
No 23
>KOG3993|consensus
Probab=98.26 E-value=2e-07 Score=69.25 Aligned_cols=78 Identities=22% Similarity=0.457 Sum_probs=57.7
Q ss_pred cccccccccCChHHHHHHHhhcCCCCCCCCCCCcccCCCCCccccCchhHHHHHhhhC--------C-------------
Q psy4421 82 CIHCNSYISSDIKDLIEHCKSCSHMTRPDAFHFKFVCYACEYNTYMSGNIKTHLRLHL--------D------------- 140 (167)
Q Consensus 82 c~~c~~~~~~~~~~l~~h~~~~~~~~~~~~~~~~~~C~~C~~~~~~~~~l~~H~~~h~--------~------------- 140 (167)
|..|... +.+.=.|.+|.-. .....-|+|+.|++.|.-..+|-.|+|=|- |
T Consensus 270 CqLCK~k-YeD~F~LAQHrC~-------RIV~vEYrCPEC~KVFsCPANLASHRRWHKPR~eaa~a~~~P~k~~~~~rae 341 (500)
T KOG3993|consen 270 CQLCKEK-YEDAFALAQHRCP-------RIVHVEYRCPECDKVFSCPANLASHRRWHKPRPEAAKAGSPPPKQAVETRAE 341 (500)
T ss_pred HHHHHHh-hhhHHHHhhccCC-------eeEEeeecCCcccccccCchhhhhhhcccCCchhhhhcCCCChhhhhhhhhh
Confidence 6677666 5555566666544 444456888888888888888888877442 1
Q ss_pred ------------CCceeCCCCcccccCchhHHHHhhhcC
Q psy4421 141 ------------DKPYKCSLCNYECRQNVHLKSHMKSNH 167 (167)
Q Consensus 141 ------------~~~~~C~~C~~~f~~~~~l~~H~~~hh 167 (167)
+.-|.|.+|++.|+...+|+.|+-+||
T Consensus 342 ~~ea~rsg~dss~gi~~C~~C~KkFrRqAYLrKHqlthq 380 (500)
T KOG3993|consen 342 VQEAERSGDDSSSGIFSCHTCGKKFRRQAYLRKHQLTHQ 380 (500)
T ss_pred hhhccccCCcccCceeecHHhhhhhHHHHHHHHhHHhhh
Confidence 224899999999999999999998875
No 24
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=98.23 E-value=6.2e-07 Score=39.71 Aligned_cols=22 Identities=36% Similarity=0.844 Sum_probs=18.2
Q ss_pred eeCCCCcccccCchhHHHHhhh
Q psy4421 144 YKCSLCNYECRQNVHLKSHMKS 165 (167)
Q Consensus 144 ~~C~~C~~~f~~~~~l~~H~~~ 165 (167)
|.|+.|++.|...++|..|+++
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 6788888888888888888876
No 25
>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=98.19 E-value=8.8e-07 Score=40.46 Aligned_cols=15 Identities=53% Similarity=1.121 Sum_probs=7.8
Q ss_pred HHHHHHHhhCCCCCC
Q psy4421 59 LKKHILKHTGEKPFS 73 (167)
Q Consensus 59 l~~H~~~h~~~~~~~ 73 (167)
|.+|+++|++++||+
T Consensus 2 l~~H~~~H~~~k~~~ 16 (26)
T PF13465_consen 2 LRRHMRTHTGEKPYK 16 (26)
T ss_dssp HHHHHHHHSSSSSEE
T ss_pred HHHHhhhcCCCCCCC
Confidence 445555555555555
No 26
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=98.18 E-value=1.2e-06 Score=39.08 Aligned_cols=24 Identities=29% Similarity=0.891 Sum_probs=18.4
Q ss_pred eeCCCCcccccCchhHHHHhhhcC
Q psy4421 144 YKCSLCNYECRQNVHLKSHMKSNH 167 (167)
Q Consensus 144 ~~C~~C~~~f~~~~~l~~H~~~hh 167 (167)
|.|+.|++.|.+..+|..|++++|
T Consensus 1 ~~C~~C~~~~~~~~~l~~H~~~~H 24 (24)
T PF13894_consen 1 FQCPICGKSFRSKSELRQHMRTHH 24 (24)
T ss_dssp EE-SSTS-EESSHHHHHHHHHHHS
T ss_pred CCCcCCCCcCCcHHHHHHHHHhhC
Confidence 678888888888888888888776
No 27
>PHA00732 hypothetical protein
Probab=98.12 E-value=1.7e-06 Score=50.58 Aligned_cols=47 Identities=17% Similarity=0.314 Sum_probs=35.1
Q ss_pred cccccccccccCchHHHHHHhhhhhccccCC-CCCccceecCccCccccChHHHHHHHHHhh
Q psy4421 7 INQCVHCHLTLTKSTEVIVKHAQTCISMVRP-DSFKYKYGCYRCSYFTYESNNLKKHILKHT 67 (167)
Q Consensus 7 ~~~C~~C~~~f~~~~~l~~~~~~~~~~h~~~-~~~~~~~~C~~C~~~~~~~~~l~~H~~~h~ 67 (167)
||.|..|++.|....+|. .|++. |.+ +.|+.|++.|. .+..|..+..
T Consensus 1 py~C~~Cgk~F~s~s~Lk--------~H~r~~H~~---~~C~~CgKsF~---~l~~H~~~~~ 48 (79)
T PHA00732 1 MFKCPICGFTTVTLFALK--------QHARRNHTL---TKCPVCNKSYR---RLNQHFYSQY 48 (79)
T ss_pred CccCCCCCCccCCHHHHH--------HHhhcccCC---CccCCCCCEeC---ChhhhhcccC
Confidence 688999999999888888 78763 543 57999999887 4666765443
No 28
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=98.07 E-value=2.8e-06 Score=39.14 Aligned_cols=25 Identities=24% Similarity=0.580 Sum_probs=20.5
Q ss_pred ceeCCCCcccccCchhHHHHhhhcC
Q psy4421 143 PYKCSLCNYECRQNVHLKSHMKSNH 167 (167)
Q Consensus 143 ~~~C~~C~~~f~~~~~l~~H~~~hh 167 (167)
||.|..|++.|.+..+|..|++.|+
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 5788888888888888888887764
No 29
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=98.02 E-value=5.6e-06 Score=36.55 Aligned_cols=23 Identities=35% Similarity=0.660 Sum_probs=18.4
Q ss_pred eecCccCccccChHHHHHHHHHh
Q psy4421 44 YGCYRCSYFTYESNNLKKHILKH 66 (167)
Q Consensus 44 ~~C~~C~~~~~~~~~l~~H~~~h 66 (167)
|.|++|++.|..+..|.+|++.|
T Consensus 1 y~C~~C~~~f~~~~~l~~H~~~H 23 (23)
T PF00096_consen 1 YKCPICGKSFSSKSNLKRHMRRH 23 (23)
T ss_dssp EEETTTTEEESSHHHHHHHHHHH
T ss_pred CCCCCCCCccCCHHHHHHHHhHC
Confidence 57888888888888888888764
No 30
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=97.81 E-value=1.5e-05 Score=48.73 Aligned_cols=72 Identities=25% Similarity=0.513 Sum_probs=19.9
Q ss_pred cccccccccCChHHHHHHHhhcCCCCCCCCCCCcccCCCCCccccCchhHHHHHhhhCCCCceeCCCCcccccCchhHHH
Q psy4421 82 CIHCNSYISSDIKDLIEHCKSCSHMTRPDAFHFKFVCYACEYNTYMSGNIKTHLRLHLDDKPYKCSLCNYECRQNVHLKS 161 (167)
Q Consensus 82 c~~c~~~~~~~~~~l~~h~~~~~~~~~~~~~~~~~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~ 161 (167)
|..|+.. +.+...+..|+...+..... ....+.....+....+... ...+.|..|++.|.+...|..
T Consensus 2 C~~C~~~-f~~~~~l~~H~~~~H~~~~~-----------~~~~l~~~~~~~~~~~~~~-~~~~~C~~C~~~f~s~~~l~~ 68 (100)
T PF12756_consen 2 CLFCDES-FSSVDDLLQHMKKKHGFDIP-----------DQKYLVDPNRLLNYLRKKV-KESFRCPYCNKTFRSREALQE 68 (100)
T ss_dssp ------------------------------------------------------------SSEEBSSSS-EESSHHHHHH
T ss_pred ccccccc-cccccccccccccccccccc-----------ccccccccccccccccccc-CCCCCCCccCCCCcCHHHHHH
Confidence 7889999 88899999998763322211 0111112233333333221 236889999999999999999
Q ss_pred Hhhhc
Q psy4421 162 HMKSN 166 (167)
Q Consensus 162 H~~~h 166 (167)
|++.+
T Consensus 69 Hm~~~ 73 (100)
T PF12756_consen 69 HMRSK 73 (100)
T ss_dssp HHHHT
T ss_pred HHcCc
Confidence 98754
No 31
>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=97.69 E-value=3.8e-05 Score=41.58 Aligned_cols=47 Identities=17% Similarity=0.255 Sum_probs=23.8
Q ss_pred ccccccccccCchHHHHHHhhhhhccccC-CCCC-ccceecCccCccccChHHHHHHHHH
Q psy4421 8 NQCVHCHLTLTKSTEVIVKHAQTCISMVR-PDSF-KYKYGCYRCSYFTYESNNLKKHILK 65 (167)
Q Consensus 8 ~~C~~C~~~f~~~~~l~~~~~~~~~~h~~-~~~~-~~~~~C~~C~~~~~~~~~l~~H~~~ 65 (167)
|.|+.|++. .+..+|. .|.. .|.. .+.+.|++|...+. .+|.+|+..
T Consensus 3 f~CP~C~~~-~~~~~L~--------~H~~~~H~~~~~~v~CPiC~~~~~--~~l~~Hl~~ 51 (54)
T PF05605_consen 3 FTCPYCGKG-FSESSLV--------EHCEDEHRSESKNVVCPICSSRVT--DNLIRHLNS 51 (54)
T ss_pred cCCCCCCCc-cCHHHHH--------HHHHhHCcCCCCCccCCCchhhhh--hHHHHHHHH
Confidence 566666663 3345566 4443 2322 23456666665432 356666554
No 32
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=97.60 E-value=8.2e-05 Score=32.80 Aligned_cols=23 Identities=22% Similarity=0.519 Sum_probs=16.6
Q ss_pred eecCccCccccChHHHHHHHHHh
Q psy4421 44 YGCYRCSYFTYESNNLKKHILKH 66 (167)
Q Consensus 44 ~~C~~C~~~~~~~~~l~~H~~~h 66 (167)
|.|+.|++.|.+...|.+|++++
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 56888888888888888888764
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=97.50 E-value=4.9e-05 Score=34.86 Aligned_cols=25 Identities=24% Similarity=0.417 Sum_probs=22.6
Q ss_pred cccCCCCCccccCchhHHHHHhhhC
Q psy4421 115 KFVCYACEYNTYMSGNIKTHLRLHL 139 (167)
Q Consensus 115 ~~~C~~C~~~~~~~~~l~~H~~~h~ 139 (167)
||.|..|+..|.+...|..|++.|.
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 5889999999999999999998775
No 34
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=97.47 E-value=5.6e-05 Score=54.66 Aligned_cols=52 Identities=27% Similarity=0.508 Sum_probs=44.0
Q ss_pred CCcccCCC--CCccccCchhHHHHHhhhC-------------------CCCceeCCCCcccccCchhHHHHhh
Q psy4421 113 HFKFVCYA--CEYNTYMSGNIKTHLRLHL-------------------DDKPYKCSLCNYECRQNVHLKSHMK 164 (167)
Q Consensus 113 ~~~~~C~~--C~~~~~~~~~l~~H~~~h~-------------------~~~~~~C~~C~~~f~~~~~l~~H~~ 164 (167)
++||+|++ |.+.+.....|+.|+..-+ .+|||.|+.|+|++....-|.-|..
T Consensus 347 ~KpykCpV~gC~K~YknqnGLKYH~lhGH~~~~~~~~p~p~~~~~F~~~~KPYrCevC~KRYKNlNGLKYHr~ 419 (423)
T COG5189 347 GKPYKCPVEGCNKKYKNQNGLKYHMLHGHQNQKLHENPSPEKMNIFSAKDKPYRCEVCDKRYKNLNGLKYHRK 419 (423)
T ss_pred CceecCCCCCchhhhccccchhhhhhccccCcccCCCCCccccccccccCCceeccccchhhccCccceeccc
Confidence 48999986 8999999999999977322 2589999999999999988887764
No 35
>smart00355 ZnF_C2H2 zinc finger.
Probab=97.41 E-value=8.4e-05 Score=33.33 Aligned_cols=23 Identities=30% Similarity=0.749 Sum_probs=16.7
Q ss_pred eeCCCCcccccCchhHHHHhhhc
Q psy4421 144 YKCSLCNYECRQNVHLKSHMKSN 166 (167)
Q Consensus 144 ~~C~~C~~~f~~~~~l~~H~~~h 166 (167)
|.|..|++.|...++|..|++.|
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~~H 23 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMRTH 23 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHHHh
Confidence 46777777777777777777644
No 36
>PRK04860 hypothetical protein; Provisional
Probab=97.38 E-value=0.00013 Score=48.57 Aligned_cols=40 Identities=20% Similarity=0.468 Sum_probs=35.1
Q ss_pred CcccCCCCCccccCchhHHHHHhhhCCCCceeCCCCcccccCch
Q psy4421 114 FKFVCYACEYNTYMSGNIKTHLRLHLDDKPYKCSLCNYECRQNV 157 (167)
Q Consensus 114 ~~~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~ 157 (167)
-+|.|. |+. ....++.|.+++.|+++|.|..|+..|....
T Consensus 118 ~~Y~C~-C~~---~~~~~rrH~ri~~g~~~YrC~~C~~~l~~~~ 157 (160)
T PRK04860 118 FPYRCK-CQE---HQLTVRRHNRVVRGEAVYRCRRCGETLVFKG 157 (160)
T ss_pred EEEEcC-CCC---eeCHHHHHHHHhcCCccEECCCCCceeEEec
Confidence 479998 987 6778899999999999999999999987654
No 37
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=97.27 E-value=0.00018 Score=43.81 Aligned_cols=72 Identities=21% Similarity=0.370 Sum_probs=20.6
Q ss_pred ecCccCccccChHHHHHHHHHhhC-CCCCCcccccCcccccccccccCChHHHHHHHhhcCCCCCCCCCCCcccCCCCCc
Q psy4421 45 GCYRCSYFTYESNNLKKHILKHTG-EKPFSYMYENQQYCIHCNSYISSDIKDLIEHCKSCSHMTRPDAFHFKFVCYACEY 123 (167)
Q Consensus 45 ~C~~C~~~~~~~~~l~~H~~~h~~-~~~~~~~~~~~~~c~~c~~~~~~~~~~l~~h~~~~~~~~~~~~~~~~~~C~~C~~ 123 (167)
+|..|+..|.....|..|+...++ ..+-. .. ......+..... ......+.|..|+.
T Consensus 1 ~C~~C~~~f~~~~~l~~H~~~~H~~~~~~~-------------~~-l~~~~~~~~~~~--------~~~~~~~~C~~C~~ 58 (100)
T PF12756_consen 1 QCLFCDESFSSVDDLLQHMKKKHGFDIPDQ-------------KY-LVDPNRLLNYLR--------KKVKESFRCPYCNK 58 (100)
T ss_dssp ----------------------------------------------------------------------SSEEBSSSS-
T ss_pred Cccccccccccccccccccccccccccccc-------------cc-cccccccccccc--------cccCCCCCCCccCC
Confidence 478888888888888888854332 21100 00 111122222211 12223688999999
Q ss_pred cccCchhHHHHHhhh
Q psy4421 124 NTYMSGNIKTHLRLH 138 (167)
Q Consensus 124 ~~~~~~~l~~H~~~h 138 (167)
.|.+...|..|++.+
T Consensus 59 ~f~s~~~l~~Hm~~~ 73 (100)
T PF12756_consen 59 TFRSREALQEHMRSK 73 (100)
T ss_dssp EESSHHHHHHHHHHT
T ss_pred CCcCHHHHHHHHcCc
Confidence 999999999998864
No 38
>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=0.00041 Score=36.29 Aligned_cols=34 Identities=24% Similarity=0.314 Sum_probs=21.1
Q ss_pred CCCCCcccCCCCCccccCchhHHHHHhhhCCCCc
Q psy4421 110 DAFHFKFVCYACEYNTYMSGNIKTHLRLHLDDKP 143 (167)
Q Consensus 110 ~~~~~~~~C~~C~~~~~~~~~l~~H~~~h~~~~~ 143 (167)
...+.|..|++|+..+.+.-+|++|+.+.++.+|
T Consensus 19 ~~S~~PatCP~C~a~~~~srnLrRHle~~H~~k~ 52 (54)
T PF09237_consen 19 SQSEQPATCPICGAVIRQSRNLRRHLEIRHFKKP 52 (54)
T ss_dssp CTTS--EE-TTT--EESSHHHHHHHHHHHTTTS-
T ss_pred hccCCCCCCCcchhhccchhhHHHHHHHHhcccC
Confidence 4455677888888888888888888877776654
No 39
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=97.15 E-value=0.00028 Score=31.58 Aligned_cols=22 Identities=27% Similarity=0.750 Sum_probs=16.8
Q ss_pred eeCCCCcccccCchhHHHHhhh
Q psy4421 144 YKCSLCNYECRQNVHLKSHMKS 165 (167)
Q Consensus 144 ~~C~~C~~~f~~~~~l~~H~~~ 165 (167)
|.|..|++.|.+..+|..|++.
T Consensus 1 ~~C~~C~~~f~s~~~~~~H~~s 22 (25)
T PF12874_consen 1 FYCDICNKSFSSENSLRQHLRS 22 (25)
T ss_dssp EEETTTTEEESSHHHHHHHHTT
T ss_pred CCCCCCCCCcCCHHHHHHHHCc
Confidence 5677788888888888887765
No 40
>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=97.06 E-value=0.00095 Score=34.96 Aligned_cols=33 Identities=24% Similarity=0.353 Sum_probs=23.5
Q ss_pred CCccceecCccCccccChHHHHHHHHHhhCCCC
Q psy4421 39 SFKYKYGCYRCSYFTYESNNLKKHILKHTGEKP 71 (167)
Q Consensus 39 ~~~~~~~C~~C~~~~~~~~~l~~H~~~h~~~~~ 71 (167)
..+.|-.|++|+..+....+|.+|++++++.+|
T Consensus 20 ~S~~PatCP~C~a~~~~srnLrRHle~~H~~k~ 52 (54)
T PF09237_consen 20 QSEQPATCPICGAVIRQSRNLRRHLEIRHFKKP 52 (54)
T ss_dssp TTS--EE-TTT--EESSHHHHHHHHHHHTTTS-
T ss_pred ccCCCCCCCcchhhccchhhHHHHHHHHhcccC
Confidence 345678999999999999999999988887765
No 41
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=97.05 E-value=0.00036 Score=50.63 Aligned_cols=70 Identities=21% Similarity=0.263 Sum_probs=45.2
Q ss_pred ccceecCc--cCccccChHHHHHHHHH-hhCCCCCCcccccCcccccccccccCChHHHHHHHhhcCCCCCCCCCCCccc
Q psy4421 41 KYKYGCYR--CSYFTYESNNLKKHILK-HTGEKPFSYMYENQQYCIHCNSYISSDIKDLIEHCKSCSHMTRPDAFHFKFV 117 (167)
Q Consensus 41 ~~~~~C~~--C~~~~~~~~~l~~H~~~-h~~~~~~~~~~~~~~~c~~c~~~~~~~~~~l~~h~~~~~~~~~~~~~~~~~~ 117 (167)
++||+|+. |++.+++...|+-|+.. |...+..+ -+.-. .+... -...+||+
T Consensus 347 ~KpykCpV~gC~K~YknqnGLKYH~lhGH~~~~~~~--------~p~p~-----------~~~~F-------~~~~KPYr 400 (423)
T COG5189 347 GKPYKCPVEGCNKKYKNQNGLKYHMLHGHQNQKLHE--------NPSPE-----------KMNIF-------SAKDKPYR 400 (423)
T ss_pred CceecCCCCCchhhhccccchhhhhhccccCcccCC--------CCCcc-----------ccccc-------cccCCcee
Confidence 37788875 88888888888877753 43333222 11000 00000 34468999
Q ss_pred CCCCCccccCchhHHHHHh
Q psy4421 118 CYACEYNTYMSGNIKTHLR 136 (167)
Q Consensus 118 C~~C~~~~~~~~~l~~H~~ 136 (167)
|++|++.+.....|+.|+.
T Consensus 401 CevC~KRYKNlNGLKYHr~ 419 (423)
T COG5189 401 CEVCDKRYKNLNGLKYHRK 419 (423)
T ss_pred ccccchhhccCccceeccc
Confidence 9999999999999999865
No 42
>smart00355 ZnF_C2H2 zinc finger.
Probab=96.99 E-value=0.00084 Score=29.87 Aligned_cols=24 Identities=29% Similarity=0.546 Sum_probs=16.6
Q ss_pred eecCccCccccChHHHHHHHHHhh
Q psy4421 44 YGCYRCSYFTYESNNLKKHILKHT 67 (167)
Q Consensus 44 ~~C~~C~~~~~~~~~l~~H~~~h~ 67 (167)
|.|..|++.|.....|..|++.|.
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~~H~ 24 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMRTHX 24 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHHHhc
Confidence 357777777777777777776543
No 43
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=96.95 E-value=0.0013 Score=29.12 Aligned_cols=23 Identities=48% Similarity=0.938 Sum_probs=17.5
Q ss_pred eecCccCccccChHHHHHHHHHhh
Q psy4421 44 YGCYRCSYFTYESNNLKKHILKHT 67 (167)
Q Consensus 44 ~~C~~C~~~~~~~~~l~~H~~~h~ 67 (167)
|.|+.|++... +..|.+|++.+.
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 67999999887 889999988754
No 44
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=96.91 E-value=0.00045 Score=30.63 Aligned_cols=23 Identities=43% Similarity=0.980 Sum_probs=14.3
Q ss_pred eeCCCCcccccCchhHHHHhhhcC
Q psy4421 144 YKCSLCNYECRQNVHLKSHMKSNH 167 (167)
Q Consensus 144 ~~C~~C~~~f~~~~~l~~H~~~hh 167 (167)
|.|+.|++... ...|..|++++|
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 56777777666 667777776654
No 45
>PF12171 zf-C2H2_jaz: Zinc-finger double-stranded RNA-binding; InterPro: IPR022755 This zinc finger is found in archaea and eukaryotes, and is approximately 30 amino acids in length. The mammalian members of this group occur multiple times along the protein, joined by flexible linkers, and are referred to as JAZ - dsRNA-binding ZF protein - zinc-fingers. The JAZ proteins are expressed in all tissues tested and localise in the nucleus, particularly the nucleolus []. JAZ preferentially binds to double-stranded (ds) RNA or RNA/DNA hybrids rather than DNA. In addition to binding double-stranded RNA, these zinc-fingers are required for nucleolar localisation. This entry represents the multiple-adjacent-C2H2 zinc finger, JAZ. ; PDB: 4DGW_A 1ZR9_A.
Probab=96.62 E-value=0.00089 Score=30.60 Aligned_cols=22 Identities=36% Similarity=0.680 Sum_probs=18.6
Q ss_pred eeCCCCcccccCchhHHHHhhh
Q psy4421 144 YKCSLCNYECRQNVHLKSHMKS 165 (167)
Q Consensus 144 ~~C~~C~~~f~~~~~l~~H~~~ 165 (167)
|.|..|++.|.+...|..|+++
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 6788899999988888888865
No 46
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=96.47 E-value=0.0021 Score=28.65 Aligned_cols=22 Identities=23% Similarity=0.467 Sum_probs=14.7
Q ss_pred eecCccCccccChHHHHHHHHH
Q psy4421 44 YGCYRCSYFTYESNNLKKHILK 65 (167)
Q Consensus 44 ~~C~~C~~~~~~~~~l~~H~~~ 65 (167)
|.|..|++.|.++..|..|++.
T Consensus 1 ~~C~~C~~~f~s~~~~~~H~~s 22 (25)
T PF12874_consen 1 FYCDICNKSFSSENSLRQHLRS 22 (25)
T ss_dssp EEETTTTEEESSHHHHHHHHTT
T ss_pred CCCCCCCCCcCCHHHHHHHHCc
Confidence 4567777777777777776643
No 47
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=95.59 E-value=0.0096 Score=26.64 Aligned_cols=21 Identities=24% Similarity=0.504 Sum_probs=12.8
Q ss_pred eeCCCCcccccCchhHHHHhhh
Q psy4421 144 YKCSLCNYECRQNVHLKSHMKS 165 (167)
Q Consensus 144 ~~C~~C~~~f~~~~~l~~H~~~ 165 (167)
..|+.||+.| ..+.|.+|+.+
T Consensus 3 ~~C~~CgR~F-~~~~l~~H~~~ 23 (25)
T PF13913_consen 3 VPCPICGRKF-NPDRLEKHEKI 23 (25)
T ss_pred CcCCCCCCEE-CHHHHHHHHHh
Confidence 3566777777 44566666643
No 48
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=95.54 E-value=0.0031 Score=48.23 Aligned_cols=60 Identities=23% Similarity=0.425 Sum_probs=54.4
Q ss_pred CcccccccccccCchHHHHHHhhhhhccccC--CCCCc--cceecC--ccCccccChHHHHHHHHHhhCCCCCC
Q psy4421 6 NINQCVHCHLTLTKSTEVIVKHAQTCISMVR--PDSFK--YKYGCY--RCSYFTYESNNLKKHILKHTGEKPFS 73 (167)
Q Consensus 6 ~~~~C~~C~~~f~~~~~l~~~~~~~~~~h~~--~~~~~--~~~~C~--~C~~~~~~~~~l~~H~~~h~~~~~~~ 73 (167)
.++.|..|...|.....+. .|.. .|.++ +++.|+ .|++.|.....+..|...|.+..+..
T Consensus 288 ~~~~~~~~~~~~s~~~~l~--------~~~~~~~h~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 (467)
T COG5048 288 LPIKSKQCNISFSRSSPLT--------RHLRSVNHSGESLKPFSCPYSLCGKLFSRNDALKRHILLHTSISPAK 353 (467)
T ss_pred cCCCCccccCCcccccccc--------ccccccccccccCCceeeeccCCCccccccccccCCcccccCCCccc
Confidence 4788999999999999999 8988 79999 999999 89999999999999999998877665
No 49
>PF12171 zf-C2H2_jaz: Zinc-finger double-stranded RNA-binding; InterPro: IPR022755 This zinc finger is found in archaea and eukaryotes, and is approximately 30 amino acids in length. The mammalian members of this group occur multiple times along the protein, joined by flexible linkers, and are referred to as JAZ - dsRNA-binding ZF protein - zinc-fingers. The JAZ proteins are expressed in all tissues tested and localise in the nucleus, particularly the nucleolus []. JAZ preferentially binds to double-stranded (ds) RNA or RNA/DNA hybrids rather than DNA. In addition to binding double-stranded RNA, these zinc-fingers are required for nucleolar localisation. This entry represents the multiple-adjacent-C2H2 zinc finger, JAZ. ; PDB: 4DGW_A 1ZR9_A.
Probab=95.52 E-value=0.016 Score=26.32 Aligned_cols=17 Identities=12% Similarity=0.327 Sum_probs=12.7
Q ss_pred ccccccccccCchHHHH
Q psy4421 8 NQCVHCHLTLTKSTEVI 24 (167)
Q Consensus 8 ~~C~~C~~~f~~~~~l~ 24 (167)
|.|..|++.|.+...+.
T Consensus 2 ~~C~~C~k~f~~~~~~~ 18 (27)
T PF12171_consen 2 FYCDACDKYFSSENQLK 18 (27)
T ss_dssp CBBTTTTBBBSSHHHHH
T ss_pred CCcccCCCCcCCHHHHH
Confidence 56777777777777777
No 50
>smart00451 ZnF_U1 U1-like zinc finger. Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins.
Probab=95.09 E-value=0.02 Score=27.60 Aligned_cols=23 Identities=26% Similarity=0.743 Sum_probs=16.6
Q ss_pred ceeCCCCcccccCchhHHHHhhh
Q psy4421 143 PYKCSLCNYECRQNVHLKSHMKS 165 (167)
Q Consensus 143 ~~~C~~C~~~f~~~~~l~~H~~~ 165 (167)
+|.|..|++.|.....+..|++.
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~g 25 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLKG 25 (35)
T ss_pred CeEccccCCccCCHHHHHHHHCh
Confidence 46777888877777777777653
No 51
>PRK04860 hypothetical protein; Provisional
Probab=94.91 E-value=0.023 Score=37.94 Aligned_cols=35 Identities=23% Similarity=0.618 Sum_probs=31.5
Q ss_pred cceecCccCccccChHHHHHHHHHhhCCCCCCcccccCccccccccc
Q psy4421 42 YKYGCYRCSYFTYESNNLKKHILKHTGEKPFSYMYENQQYCIHCNSY 88 (167)
Q Consensus 42 ~~~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~~~~~~~~~c~~c~~~ 88 (167)
.+|.|. |+. ....+.+|.+++.++++|. |..|+..
T Consensus 118 ~~Y~C~-C~~---~~~~~rrH~ri~~g~~~Yr--------C~~C~~~ 152 (160)
T PRK04860 118 FPYRCK-CQE---HQLTVRRHNRVVRGEAVYR--------CRRCGET 152 (160)
T ss_pred EEEEcC-CCC---eeCHHHHHHHHhcCCccEE--------CCCCCce
Confidence 469998 998 6788999999999999999 9999987
No 52
>KOG2231|consensus
Probab=94.58 E-value=0.12 Score=42.06 Aligned_cols=48 Identities=23% Similarity=0.437 Sum_probs=32.9
Q ss_pred ccCCCCCccccCchhHHHHHhhhCCCCceeCCCC------cccccCchhHHHHhhhcC
Q psy4421 116 FVCYACEYNTYMSGNIKTHLRLHLDDKPYKCSLC------NYECRQNVHLKSHMKSNH 167 (167)
Q Consensus 116 ~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C------~~~f~~~~~l~~H~~~hh 167 (167)
-.|..|...|.....|..|++.++ |.|..| +.-|....+|..|.+.+|
T Consensus 183 p~C~~C~~~fld~~el~rH~~~~h----~~chfC~~~~~~neyy~~~~dLe~HfR~~H 236 (669)
T KOG2231|consen 183 PLCKFCHERFLDDDELYRHLRFDH----EFCHFCDYKTGQNEYYNDYDDLEEHFRKGH 236 (669)
T ss_pred ccchhhhhhhccHHHHHHhhccce----eheeecCcccccchhcccchHHHHHhhhcC
Confidence 467788888888888888877543 344444 344566778888877765
No 53
>KOG2893|consensus
Probab=93.77 E-value=0.027 Score=39.55 Aligned_cols=32 Identities=25% Similarity=0.538 Sum_probs=18.0
Q ss_pred cCccCccccChHHHHHHHHHhhCCCCCCcccccCcccccccccc
Q psy4421 46 CYRCSYFTYESNNLKKHILKHTGEKPFSYMYENQQYCIHCNSYI 89 (167)
Q Consensus 46 C~~C~~~~~~~~~l~~H~~~h~~~~~~~~~~~~~~~c~~c~~~~ 89 (167)
|.+|++.|..+..|.+|++ .|.|+ |-+|.+.+
T Consensus 13 cwycnrefddekiliqhqk----akhfk--------chichkkl 44 (341)
T KOG2893|consen 13 CWYCNREFDDEKILIQHQK----AKHFK--------CHICHKKL 44 (341)
T ss_pred eeecccccchhhhhhhhhh----hccce--------eeeehhhh
Confidence 5566666666555555554 45555 55555553
No 54
>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=93.53 E-value=0.047 Score=26.14 Aligned_cols=24 Identities=29% Similarity=0.790 Sum_probs=14.1
Q ss_pred ccCCCCCccccCchhHHHHHhhhCCCCceeCCCCcc
Q psy4421 116 FVCYACEYNTYMSGNIKTHLRLHLDDKPYKCSLCNY 151 (167)
Q Consensus 116 ~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~ 151 (167)
|.|.+||..+.... .++.|+.||.
T Consensus 2 ~~C~~CGy~y~~~~------------~~~~CP~Cg~ 25 (33)
T cd00350 2 YVCPVCGYIYDGEE------------APWVCPVCGA 25 (33)
T ss_pred EECCCCCCEECCCc------------CCCcCcCCCC
Confidence 56667766554332 4566777764
No 55
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=92.93 E-value=0.045 Score=29.23 Aligned_cols=24 Identities=17% Similarity=0.447 Sum_probs=11.9
Q ss_pred CCCceeCCCCcccccCchhHHHHh
Q psy4421 140 DDKPYKCSLCNYECRQNVHLKSHM 163 (167)
Q Consensus 140 ~~~~~~C~~C~~~f~~~~~l~~H~ 163 (167)
||--+.|+.||..|+..-++.+|.
T Consensus 14 GE~~lrCPRC~~~FR~~K~Y~RHV 37 (65)
T COG4049 14 GEEFLRCPRCGMVFRRRKDYIRHV 37 (65)
T ss_pred CceeeeCCchhHHHHHhHHHHHHh
Confidence 344445555555555554554444
No 56
>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=92.92 E-value=0.11 Score=24.83 Aligned_cols=23 Identities=13% Similarity=0.312 Sum_probs=18.4
Q ss_pred ceecCccCccccChHHHHHHHHH
Q psy4421 43 KYGCYRCSYFTYESNNLKKHILK 65 (167)
Q Consensus 43 ~~~C~~C~~~~~~~~~l~~H~~~ 65 (167)
+|.|.+|+..|.+...+..|...
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~g 25 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLKG 25 (35)
T ss_pred CeEccccCCccCCHHHHHHHHCh
Confidence 47789999988888888888743
No 57
>PHA00626 hypothetical protein
Probab=92.27 E-value=0.069 Score=28.58 Aligned_cols=13 Identities=31% Similarity=0.787 Sum_probs=7.8
Q ss_pred CceeCCCCccccc
Q psy4421 142 KPYKCSLCNYECR 154 (167)
Q Consensus 142 ~~~~C~~C~~~f~ 154 (167)
..|+|+.||+.|+
T Consensus 22 nrYkCkdCGY~ft 34 (59)
T PHA00626 22 DDYVCCDCGYNDS 34 (59)
T ss_pred cceEcCCCCCeec
Confidence 4566666666554
No 58
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=92.02 E-value=0.052 Score=41.47 Aligned_cols=53 Identities=28% Similarity=0.505 Sum_probs=48.3
Q ss_pred CcccCCCCCccccCchhHHHHHh--hhCCC--CceeCC--CCcccccCchhHHHHhhhc
Q psy4421 114 FKFVCYACEYNTYMSGNIKTHLR--LHLDD--KPYKCS--LCNYECRQNVHLKSHMKSN 166 (167)
Q Consensus 114 ~~~~C~~C~~~~~~~~~l~~H~~--~h~~~--~~~~C~--~C~~~f~~~~~l~~H~~~h 166 (167)
.++.|..|...|.....|..|.+ .|.++ +++.|+ .|++.|.+...+..|..+|
T Consensus 288 ~~~~~~~~~~~~s~~~~l~~~~~~~~h~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~ 346 (467)
T COG5048 288 LPIKSKQCNISFSRSSPLTRHLRSVNHSGESLKPFSCPYSLCGKLFSRNDALKRHILLH 346 (467)
T ss_pred cCCCCccccCCccccccccccccccccccccCCceeeeccCCCccccccccccCCcccc
Confidence 36889999999999999999999 89999 999999 7999999999998887765
No 59
>KOG2231|consensus
Probab=91.80 E-value=0.65 Score=37.95 Aligned_cols=93 Identities=17% Similarity=0.341 Sum_probs=55.2
Q ss_pred cccChHHHHHHHHH-hhCCCCCCcccccCcccccccccccCChHHHHHHHhhcCCCCCCCCCCCcccCCCC------Ccc
Q psy4421 52 FTYESNNLKKHILK-HTGEKPFSYMYENQQYCIHCNSYISSDIKDLIEHCKSCSHMTRPDAFHFKFVCYAC------EYN 124 (167)
Q Consensus 52 ~~~~~~~l~~H~~~-h~~~~~~~~~~~~~~~c~~c~~~~~~~~~~l~~h~~~~~~~~~~~~~~~~~~C~~C------~~~ 124 (167)
..+....|..|+.. -.++..+. +-..|..|... |.....+.+|+.. .-|.|..| +.-
T Consensus 158 k~Yt~~el~~h~~~gd~d~~s~r----Ghp~C~~C~~~-fld~~el~rH~~~-----------~h~~chfC~~~~~~ney 221 (669)
T KOG2231|consen 158 KLYTRAELNLHLMFGDPDDESCR----GHPLCKFCHER-FLDDDELYRHLRF-----------DHEFCHFCDYKTGQNEY 221 (669)
T ss_pred ehehHHHHHHHHhcCCCcccccc----CCccchhhhhh-hccHHHHHHhhcc-----------ceeheeecCcccccchh
Confidence 34456677777754 22222221 12339999999 8888889998775 22445554 455
Q ss_pred ccCchhHHHHHhhhCCCCceeCC--CCc-ccccCchhHHHHhh
Q psy4421 125 TYMSGNIKTHLRLHLDDKPYKCS--LCN-YECRQNVHLKSHMK 164 (167)
Q Consensus 125 ~~~~~~l~~H~~~h~~~~~~~C~--~C~-~~f~~~~~l~~H~~ 164 (167)
|.....|..|-+.+ -|.|. .|. +.|.....+..+++
T Consensus 222 y~~~~dLe~HfR~~----HflCE~~~C~~~~f~~~~~~ei~lk 260 (669)
T KOG2231|consen 222 YNDYDDLEEHFRKG----HFLCEEEFCRTKKFYVAFELEIELK 260 (669)
T ss_pred cccchHHHHHhhhc----CccccccccccceeeehhHHHHHHH
Confidence 66677888887744 36777 454 34554445545544
No 60
>KOG2482|consensus
Probab=91.33 E-value=0.63 Score=34.73 Aligned_cols=55 Identities=20% Similarity=0.348 Sum_probs=35.0
Q ss_pred cccccccccCChHHHHHHHhhcCCCCCCCCCCCc---------------ccCCCCCccccCchhHHHHHh
Q psy4421 82 CIHCNSYISSDIKDLIEHCKSCSHMTRPDAFHFK---------------FVCYACEYNTYMSGNIKTHLR 136 (167)
Q Consensus 82 c~~c~~~~~~~~~~l~~h~~~~~~~~~~~~~~~~---------------~~C~~C~~~~~~~~~l~~H~~ 136 (167)
|..|......+.+.+..|+-..+.+..+.+..-+ +.|-.|.+.|..+..|+.||+
T Consensus 147 ClFCn~e~lgnRs~~l~Hlf~~H~lniGlpDniVyvnelLehLkekL~r~~CLyCekifrdkntLkeHMr 216 (423)
T KOG2482|consen 147 CLFCNNEGLGNRSEILEHLFHVHGLNIGLPDNIVYVNELLEHLKEKLERLRCLYCEKIFRDKNTLKEHMR 216 (423)
T ss_pred EEEecchhcccHHHHHHHHHHHhhhccCCCcceeeHHHHHHHHHHHHhhheeeeeccccCCcHHHHHHHH
Confidence 8888887677888888887765555544444322 455555555555555555555
No 61
>KOG1146|consensus
Probab=91.02 E-value=0.13 Score=44.55 Aligned_cols=55 Identities=31% Similarity=0.689 Sum_probs=46.6
Q ss_pred CCCCcccCCCCCccccCchhHHHHHhh-hC------------------------CCCceeCCCCcccccCchhHHHHhhh
Q psy4421 111 AFHFKFVCYACEYNTYMSGNIKTHLRL-HL------------------------DDKPYKCSLCNYECRQNVHLKSHMKS 165 (167)
Q Consensus 111 ~~~~~~~C~~C~~~~~~~~~l~~H~~~-h~------------------------~~~~~~C~~C~~~f~~~~~l~~H~~~ 165 (167)
...+.++|+.|+..|.....|-.|+|. |. +-++|.|..|...+....+|.+|+.+
T Consensus 461 S~~kt~~cpkc~~~yk~a~~L~vhmRskhp~~~~~~c~~gq~~~~~arg~~~~~~~~p~~C~~C~~stttng~LsihlqS 540 (1406)
T KOG1146|consen 461 SFFKTLKCPKCNWHYKLAQTLGVHMRSKHPESQSAYCKAGQNHPRLARGEVYRCPGKPYPCRACNYSTTTNGNLSIHLQS 540 (1406)
T ss_pred cccccccCCccchhhhhHHHhhhcccccccccchhHhHhccccccccccccccCCCCcccceeeeeeeecchHHHHHHHH
Confidence 345789999999999999999999997 11 24678999999999999999999864
No 62
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=91.01 E-value=0.24 Score=26.92 Aligned_cols=36 Identities=25% Similarity=0.545 Sum_probs=23.6
Q ss_pred CCCCcccCCCCCccccCchhHHHHHhhhCCCCceeCCCCcc
Q psy4421 111 AFHFKFVCYACEYNTYMSGNIKTHLRLHLDDKPYKCSLCNY 151 (167)
Q Consensus 111 ~~~~~~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~ 151 (167)
.....|.|+.||...-.+..- -|.+ ..+|.|+.||.
T Consensus 23 e~~v~F~CPnCGe~~I~Rc~~---CRk~--g~~Y~Cp~CGF 58 (61)
T COG2888 23 ETAVKFPCPNCGEVEIYRCAK---CRKL--GNPYRCPKCGF 58 (61)
T ss_pred CceeEeeCCCCCceeeehhhh---HHHc--CCceECCCcCc
Confidence 344579999999665554321 1222 46899999984
No 63
>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=90.92 E-value=0.25 Score=25.22 Aligned_cols=27 Identities=33% Similarity=0.603 Sum_probs=16.0
Q ss_pred CCCceeCCCCcccccC----chhHHHHhhhc
Q psy4421 140 DDKPYKCSLCNYECRQ----NVHLKSHMKSN 166 (167)
Q Consensus 140 ~~~~~~C~~C~~~f~~----~~~l~~H~~~h 166 (167)
++....|..|++.+.. .+.|.+|++..
T Consensus 13 ~~~~a~C~~C~~~~~~~~~~ts~l~~HL~~~ 43 (45)
T PF02892_consen 13 DKKKAKCKYCGKVIKYSSGGTSNLKRHLKKK 43 (45)
T ss_dssp CSS-EEETTTTEE-----SSTHHHHHHHHHT
T ss_pred CcCeEEeCCCCeEEeeCCCcHHHHHHhhhhh
Confidence 3455778888887765 36788888543
No 64
>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=90.20 E-value=0.71 Score=28.64 Aligned_cols=25 Identities=28% Similarity=0.792 Sum_probs=22.3
Q ss_pred ceeC----CCCcccccCchhHHHHhhhcC
Q psy4421 143 PYKC----SLCNYECRQNVHLKSHMKSNH 167 (167)
Q Consensus 143 ~~~C----~~C~~~f~~~~~l~~H~~~hh 167 (167)
.|.| ..|++.+.+...+..|++.+|
T Consensus 80 G~~C~~~~~~C~y~~~~~~~m~~H~~~~H 108 (109)
T PF12013_consen 80 GYRCQCDPPHCGYITRSKKTMRKHWRKEH 108 (109)
T ss_pred CeeeecCCCCCCcEeccHHHHHHHHHHhc
Confidence 4889 899999999999999998876
No 65
>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=90.16 E-value=0.22 Score=30.99 Aligned_cols=14 Identities=29% Similarity=0.648 Sum_probs=7.1
Q ss_pred CceeCCCCcccccC
Q psy4421 142 KPYKCSLCNYECRQ 155 (167)
Q Consensus 142 ~~~~C~~C~~~f~~ 155 (167)
.|..|+.||..|..
T Consensus 25 ~PivCP~CG~~~~~ 38 (108)
T PF09538_consen 25 DPIVCPKCGTEFPP 38 (108)
T ss_pred CCccCCCCCCccCc
Confidence 44555555555543
No 66
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=89.71 E-value=0.21 Score=33.48 Aligned_cols=23 Identities=35% Similarity=0.987 Sum_probs=19.3
Q ss_pred cccCCCCCccccCchhHHHHHhhhCCCCceeCCCCc
Q psy4421 115 KFVCYACEYNTYMSGNIKTHLRLHLDDKPYKCSLCN 150 (167)
Q Consensus 115 ~~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~ 150 (167)
.|.|++||.+ +.|+.|-+|+.||
T Consensus 134 ~~vC~vCGy~-------------~~ge~P~~CPiCg 156 (166)
T COG1592 134 VWVCPVCGYT-------------HEGEAPEVCPICG 156 (166)
T ss_pred EEEcCCCCCc-------------ccCCCCCcCCCCC
Confidence 7999999876 4567889999998
No 67
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=89.68 E-value=0.33 Score=23.81 Aligned_cols=33 Identities=18% Similarity=0.455 Sum_probs=20.8
Q ss_pred cCCCCCccccCchhHHHHHhhhCCCCceeCCCCccccc
Q psy4421 117 VCYACEYNTYMSGNIKTHLRLHLDDKPYKCSLCNYECR 154 (167)
Q Consensus 117 ~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~~f~ 154 (167)
.|+.|+..|.....- +..+.+...|+.|+..|.
T Consensus 4 ~CP~C~~~f~v~~~~-----l~~~~~~vrC~~C~~~f~ 36 (37)
T PF13719_consen 4 TCPNCQTRFRVPDDK-----LPAGGRKVRCPKCGHVFR 36 (37)
T ss_pred ECCCCCceEEcCHHH-----cccCCcEEECCCCCcEee
Confidence 577777777766532 223345677888877664
No 68
>cd00729 rubredoxin_SM Rubredoxin, Small Modular nonheme iron binding domain containing a [Fe(SCys)4] center, present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=89.18 E-value=0.25 Score=23.77 Aligned_cols=25 Identities=32% Similarity=0.773 Sum_probs=15.3
Q ss_pred cccCCCCCccccCchhHHHHHhhhCCCCceeCCCCcc
Q psy4421 115 KFVCYACEYNTYMSGNIKTHLRLHLDDKPYKCSLCNY 151 (167)
Q Consensus 115 ~~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~ 151 (167)
.|+|.+||..+... +.|..|+.||.
T Consensus 2 ~~~C~~CG~i~~g~------------~~p~~CP~Cg~ 26 (34)
T cd00729 2 VWVCPVCGYIHEGE------------EAPEKCPICGA 26 (34)
T ss_pred eEECCCCCCEeECC------------cCCCcCcCCCC
Confidence 36777777664432 24567777774
No 69
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=88.99 E-value=0.13 Score=34.16 Aligned_cols=12 Identities=17% Similarity=0.468 Sum_probs=7.6
Q ss_pred eeCCCCcccccC
Q psy4421 144 YKCSLCNYECRQ 155 (167)
Q Consensus 144 ~~C~~C~~~f~~ 155 (167)
+.|+.||++|..
T Consensus 29 ~~c~~c~~~f~~ 40 (154)
T PRK00464 29 RECLACGKRFTT 40 (154)
T ss_pred eeccccCCcceE
Confidence 666666666654
No 70
>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=88.92 E-value=0.4 Score=23.53 Aligned_cols=35 Identities=20% Similarity=0.369 Sum_probs=23.1
Q ss_pred cccccccccccCchHHHHHHhhhhhccccCCCCCccceecCccCcccc
Q psy4421 7 INQCVHCHLTLTKSTEVIVKHAQTCISMVRPDSFKYKYGCYRCSYFTY 54 (167)
Q Consensus 7 ~~~C~~C~~~f~~~~~l~~~~~~~~~~h~~~~~~~~~~~C~~C~~~~~ 54 (167)
.+.|+.|+..|....+.. . . ......|+.|+..|.
T Consensus 2 ~~~CP~C~~~~~v~~~~~--------~----~-~~~~v~C~~C~~~~~ 36 (38)
T TIGR02098 2 RIQCPNCKTSFRVVDSQL--------G----A-NGGKVRCGKCGHVWY 36 (38)
T ss_pred EEECCCCCCEEEeCHHHc--------C----C-CCCEEECCCCCCEEE
Confidence 367888998887766544 1 1 112477999988764
No 71
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=88.33 E-value=0.49 Score=23.07 Aligned_cols=33 Identities=15% Similarity=0.410 Sum_probs=19.7
Q ss_pred ccCCCCCccccCchhHHHHHhhhCCCCceeCCCCcccc
Q psy4421 116 FVCYACEYNTYMSGNIKTHLRLHLDDKPYKCSLCNYEC 153 (167)
Q Consensus 116 ~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~~f 153 (167)
..|+.|+..|.-.... +-.+.....|+.|+..|
T Consensus 3 i~Cp~C~~~y~i~d~~-----ip~~g~~v~C~~C~~~f 35 (36)
T PF13717_consen 3 ITCPNCQAKYEIDDEK-----IPPKGRKVRCSKCGHVF 35 (36)
T ss_pred EECCCCCCEEeCCHHH-----CCCCCcEEECCCCCCEe
Confidence 3577777777666542 22333456777777666
No 72
>KOG1146|consensus
Probab=87.91 E-value=0.088 Score=45.58 Aligned_cols=111 Identities=14% Similarity=0.135 Sum_probs=68.0
Q ss_pred cccccccccCchHHHHHHhhhhhccccCC--C--CCccceecCccCccccChHHHHHHHHHhhCCCCCCcccccCccccc
Q psy4421 9 QCVHCHLTLTKSTEVIVKHAQTCISMVRP--D--SFKYKYGCYRCSYFTYESNNLKKHILKHTGEKPFSYMYENQQYCIH 84 (167)
Q Consensus 9 ~C~~C~~~f~~~~~l~~~~~~~~~~h~~~--~--~~~~~~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~~~~~~~~~c~~ 84 (167)
.|..|...|....... .+..- + .....+.|..|++.+.....+. ++ ....+|. |..
T Consensus 1230 ~~~~~e~~f~~~~~~~--------~~a~~~~~~~~~sGe~~c~~~~~~~~~~~~~~-~l---~~~~~~~--------~~~ 1289 (1406)
T KOG1146|consen 1230 LPNALEQPFPQEPEPT--------ATAPPKPPELPASGEGECGAVDELLTPSFGIS-TL---DVTHRYL--------CRQ 1289 (1406)
T ss_pred cHHhhhcCccCccccc--------ccCCCCCCcCcCCCcchhhhccccccCcccee-ec---ccchhHH--------HHH
Confidence 4556666666665555 33221 1 1122367888888877766554 33 2344566 888
Q ss_pred ccccccCChHHHHHHHhhcCCCCCCCCCC----------CcccCCCCCccccCchhHHHHHhhhCCC
Q psy4421 85 CNSYISSDIKDLIEHCKSCSHMTRPDAFH----------FKFVCYACEYNTYMSGNIKTHLRLHLDD 141 (167)
Q Consensus 85 c~~~~~~~~~~l~~h~~~~~~~~~~~~~~----------~~~~C~~C~~~~~~~~~l~~H~~~h~~~ 141 (167)
|... |.....+..|...+..+.+...+. ..| |..|...|.....|..|+++-+++
T Consensus 1290 ~~~~-~~~~~~l~~~~~k~~~~~~~~~~~~~~~l~~~d~~~~-c~~c~~~~~~~~alqihm~~~~~~ 1354 (1406)
T KOG1146|consen 1290 CKMA-FDGEAPLTAHQRKFCFAGRGSGGSMPPPLRVPDCTYH-CLACEVLLSGREALQIHMRSSAHR 1354 (1406)
T ss_pred HHhh-hcchhHHHHHHHHHHhccCccccCCCCcccCcccccc-chHHHhhcchhHHHHHHHHHhhhc
Confidence 8777 888888888876655444332221 124 888888888888888887754443
No 73
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=86.68 E-value=2 Score=26.89 Aligned_cols=48 Identities=15% Similarity=0.258 Sum_probs=32.1
Q ss_pred cCCCCCccccCchhHHHHHhhhCCCCceeCCCCcccccCchhHHHHhhhc
Q psy4421 117 VCYACEYNTYMSGNIKTHLRLHLDDKPYKCSLCNYECRQNVHLKSHMKSN 166 (167)
Q Consensus 117 ~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~h 166 (167)
.|-.|+..|........ ..-.....|.|+.|...|-..-++..|...|
T Consensus 57 ~C~~C~~~f~~~~~~~~--~~~~~~~~y~C~~C~~~FC~dCD~fiHe~Lh 104 (112)
T TIGR00622 57 FCFGCQGPFPKPPVSPF--DELKDSHRYVCAVCKNVFCVDCDVFVHESLH 104 (112)
T ss_pred cccCcCCCCCCcccccc--cccccccceeCCCCCCccccccchhhhhhcc
Confidence 48888888876532110 0012245799999999998888888887655
No 74
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=86.68 E-value=0.21 Score=35.11 Aligned_cols=43 Identities=19% Similarity=0.393 Sum_probs=25.0
Q ss_pred CcccCCCCCccccCchhHHHHHhh----------hCCCCc-----eeCCCCcccccCc
Q psy4421 114 FKFVCYACEYNTYMSGNIKTHLRL----------HLDDKP-----YKCSLCNYECRQN 156 (167)
Q Consensus 114 ~~~~C~~C~~~~~~~~~l~~H~~~----------h~~~~~-----~~C~~C~~~f~~~ 156 (167)
+.+.||+|+..|....-.....++ -.|..| ..|+.||.+|...
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 456778888777765433322221 122344 3799999887653
No 75
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=85.99 E-value=0.37 Score=27.57 Aligned_cols=40 Identities=13% Similarity=0.199 Sum_probs=22.9
Q ss_pred ccCCCCCccccCchhHHHHHhhhCCCCceeCC--CCcccccCch
Q psy4421 116 FVCYACEYNTYMSGNIKTHLRLHLDDKPYKCS--LCNYECRQNV 157 (167)
Q Consensus 116 ~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~--~C~~~f~~~~ 157 (167)
+.|+.|+.......+-..... ..+..+.|. .||.+|....
T Consensus 2 m~CP~Cg~~a~irtSr~~s~~--~~~~Y~qC~N~eCg~tF~t~e 43 (72)
T PRK09678 2 FHCPLCQHAAHARTSRYITDT--TKERYHQCQNVNCSATFITYE 43 (72)
T ss_pred ccCCCCCCccEEEEChhcChh--hheeeeecCCCCCCCEEEEEE
Confidence 457777765544433222222 346667887 7888886543
No 76
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=85.99 E-value=0.58 Score=24.10 Aligned_cols=30 Identities=17% Similarity=0.561 Sum_probs=17.6
Q ss_pred cccCCCCCccccCchhHHHHHhhhCCCCceeCCCCccccc
Q psy4421 115 KFVCYACEYNTYMSGNIKTHLRLHLDDKPYKCSLCNYECR 154 (167)
Q Consensus 115 ~~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~~f~ 154 (167)
.|.|+.||..+..... .....|+.||..+.
T Consensus 3 ~y~C~~CG~~~~~~~~----------~~~~~Cp~CG~~~~ 32 (46)
T PRK00398 3 EYKCARCGREVELDEY----------GTGVRCPYCGYRIL 32 (46)
T ss_pred EEECCCCCCEEEECCC----------CCceECCCCCCeEE
Confidence 4677777766554321 11567777776543
No 77
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=85.83 E-value=0.37 Score=31.97 Aligned_cols=43 Identities=12% Similarity=0.252 Sum_probs=24.4
Q ss_pred ccccccccccCchHHHHHHhhhhhccccCC-CCCccceecCccCccccChHHH
Q psy4421 8 NQCVHCHLTLTKSTEVIVKHAQTCISMVRP-DSFKYKYGCYRCSYFTYESNNL 59 (167)
Q Consensus 8 ~~C~~C~~~f~~~~~l~~~~~~~~~~h~~~-~~~~~~~~C~~C~~~~~~~~~l 59 (167)
+.|+.|+..+....+-+ -+.. ..-++.++|+.||++|.....+
T Consensus 1 m~cp~c~~~~~~~~~s~---------~~~~~~~~~~~~~c~~c~~~f~~~e~~ 44 (154)
T PRK00464 1 MRCPFCGHPDTRVIDSR---------PAEDGNAIRRRRECLACGKRFTTFERV 44 (154)
T ss_pred CcCCCCCCCCCEeEecc---------ccCCCCceeeeeeccccCCcceEeEec
Confidence 47999998763221111 0111 1122348999999999866543
No 78
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=85.35 E-value=0.87 Score=29.97 Aligned_cols=17 Identities=18% Similarity=0.188 Sum_probs=9.8
Q ss_pred ccceecCccCccccChH
Q psy4421 41 KYKYGCYRCSYFTYESN 57 (167)
Q Consensus 41 ~~~~~C~~C~~~~~~~~ 57 (167)
..-|.|+.|+..|....
T Consensus 97 ~~~Y~Cp~C~~~y~~~e 113 (147)
T smart00531 97 NAYYKCPNCQSKYTFLE 113 (147)
T ss_pred CcEEECcCCCCEeeHHH
Confidence 33466666666665443
No 79
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=85.35 E-value=0.49 Score=35.35 Aligned_cols=48 Identities=19% Similarity=0.449 Sum_probs=25.7
Q ss_pred cCCCCCccccCchhHHHHHhhhCCCCceeCCCCc----ccccCchhHHHHhhh
Q psy4421 117 VCYACEYNTYMSGNIKTHLRLHLDDKPYKCSLCN----YECRQNVHLKSHMKS 165 (167)
Q Consensus 117 ~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~----~~f~~~~~l~~H~~~ 165 (167)
.|..|...|.....|..|+|..+ |+-|.|..=+ .-|....+|.+|.+.
T Consensus 222 ~C~FC~~~FYdDDEL~~HcR~~H-E~ChICD~v~p~~~QYFK~Y~~Le~HF~~ 273 (493)
T COG5236 222 LCIFCKIYFYDDDELRRHCRLRH-EACHICDMVGPIRYQYFKSYEDLEAHFRN 273 (493)
T ss_pred hhhhccceecChHHHHHHHHhhh-hhhhhhhccCccchhhhhCHHHHHHHhhc
Confidence 56666666666677777766433 3333333222 224455566666653
No 80
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=85.06 E-value=0.81 Score=23.45 Aligned_cols=28 Identities=18% Similarity=0.627 Sum_probs=17.6
Q ss_pred cccCCCCCccccCchhHHHHHhhhCCCCceeCCCCcccc
Q psy4421 115 KFVCYACEYNTYMSGNIKTHLRLHLDDKPYKCSLCNYEC 153 (167)
Q Consensus 115 ~~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~~f 153 (167)
.|.|..||..|... ...+..|+.||.+-
T Consensus 2 ~Y~C~~Cg~~~~~~-----------~~~~irC~~CG~rI 29 (44)
T smart00659 2 IYICGECGRENEIK-----------SKDVVRCRECGYRI 29 (44)
T ss_pred EEECCCCCCEeecC-----------CCCceECCCCCceE
Confidence 36777777766543 13457788887643
No 81
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=85.00 E-value=0.41 Score=33.61 Aligned_cols=44 Identities=20% Similarity=0.341 Sum_probs=28.0
Q ss_pred CCcccccccccccCchHHHHHHhhhhhccccC---CCC-------Cccc-----eecCccCccccCh
Q psy4421 5 LNINQCVHCHLTLTKSTEVIVKHAQTCISMVR---PDS-------FKYK-----YGCYRCSYFTYES 56 (167)
Q Consensus 5 ~~~~~C~~C~~~f~~~~~l~~~~~~~~~~h~~---~~~-------~~~~-----~~C~~C~~~~~~~ 56 (167)
++.++|++|+..|....-.. ...+ .++ +..| ..|+.||+.+...
T Consensus 3 ~k~~~CPvC~~~F~~~~vrs--------~~~r~~~~d~D~~~~Y~~vnP~~Y~V~vCP~CgyA~~~~ 61 (214)
T PF09986_consen 3 DKKITCPVCGKEFKTKKVRS--------GKIRVIRRDSDFCPRYKGVNPLFYEVWVCPHCGYAAFEE 61 (214)
T ss_pred CCceECCCCCCeeeeeEEEc--------CCceEeeecCCCccccCCCCCeeeeEEECCCCCCccccc
Confidence 57789999999998864322 2221 122 2222 5799999977644
No 82
>KOG2893|consensus
Probab=84.53 E-value=0.29 Score=34.54 Aligned_cols=45 Identities=31% Similarity=0.595 Sum_probs=35.3
Q ss_pred cccccccccCChHHHHHHHhhcCCCCCCCCCCCcccCCCCCccccCchhHHHH-Hhhh
Q psy4421 82 CIHCNSYISSDIKDLIEHCKSCSHMTRPDAFHFKFVCYACEYNTYMSGNIKTH-LRLH 138 (167)
Q Consensus 82 c~~c~~~~~~~~~~l~~h~~~~~~~~~~~~~~~~~~C~~C~~~~~~~~~l~~H-~~~h 138 (167)
|=.|++. |....-|++|++. +-|+|.+|-+...+...|..| +++|
T Consensus 13 cwycnre-fddekiliqhqka-----------khfkchichkkl~sgpglsihcmqvh 58 (341)
T KOG2893|consen 13 CWYCNRE-FDDEKILIQHQKA-----------KHFKCHICHKKLFSGPGLSIHCMQVH 58 (341)
T ss_pred eeecccc-cchhhhhhhhhhh-----------ccceeeeehhhhccCCCceeehhhhh
Confidence 8889988 8888888887766 678899998877777777777 5555
No 83
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=84.11 E-value=0.68 Score=29.65 Aligned_cols=15 Identities=20% Similarity=0.569 Sum_probs=13.1
Q ss_pred cccccccccccCchH
Q psy4421 7 INQCVHCHLTLTKST 21 (167)
Q Consensus 7 ~~~C~~C~~~f~~~~ 21 (167)
|+.|..|+..|.+.+
T Consensus 1 PH~Ct~Cg~~f~dgs 15 (131)
T PF09845_consen 1 PHQCTKCGRVFEDGS 15 (131)
T ss_pred CcccCcCCCCcCCCc
Confidence 678999999998876
No 84
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=83.45 E-value=2.2 Score=23.29 Aligned_cols=34 Identities=26% Similarity=0.676 Sum_probs=21.9
Q ss_pred CCcccCCCCCccccCchhHHHHHhhhCCCCceeCCCCcc
Q psy4421 113 HFKFVCYACEYNTYMSGNIKTHLRLHLDDKPYKCSLCNY 151 (167)
Q Consensus 113 ~~~~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~ 151 (167)
...|.|+.||.....+.. .-|.. ..+|.|+.||.
T Consensus 23 ~~~F~CPnCG~~~I~RC~---~CRk~--~~~Y~CP~CGF 56 (59)
T PRK14890 23 AVKFLCPNCGEVIIYRCE---KCRKQ--SNPYTCPKCGF 56 (59)
T ss_pred cCEeeCCCCCCeeEeech---hHHhc--CCceECCCCCC
Confidence 356999999987444322 11112 36899999985
No 85
>smart00614 ZnF_BED BED zinc finger. DNA-binding domain in chromatin-boundary-element-binding proteins and transposases
Probab=82.74 E-value=1 Score=23.63 Aligned_cols=22 Identities=23% Similarity=0.631 Sum_probs=14.8
Q ss_pred ceeCCCCcccccCc-----hhHHHHhh
Q psy4421 143 PYKCSLCNYECRQN-----VHLKSHMK 164 (167)
Q Consensus 143 ~~~C~~C~~~f~~~-----~~l~~H~~ 164 (167)
.-.|..|++.+... +.|.+|++
T Consensus 18 ~a~C~~C~~~l~~~~~~gTs~L~rHl~ 44 (50)
T smart00614 18 RAKCKYCGKKLSRSSKGGTSNLRRHLR 44 (50)
T ss_pred EEEecCCCCEeeeCCCCCcHHHHHHHH
Confidence 35677777766554 57777776
No 86
>TIGR02300 FYDLN_acid conserved hypothetical protein TIGR02300. Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=82.54 E-value=1 Score=28.68 Aligned_cols=14 Identities=7% Similarity=-0.446 Sum_probs=6.8
Q ss_pred CcccCCCCCccccC
Q psy4421 114 FKFVCYACEYNTYM 127 (167)
Q Consensus 114 ~~~~C~~C~~~~~~ 127 (167)
.|..|+.||..|..
T Consensus 25 ~p~vcP~cg~~~~~ 38 (129)
T TIGR02300 25 RPAVSPYTGEQFPP 38 (129)
T ss_pred CCccCCCcCCccCc
Confidence 34455555554433
No 87
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=82.33 E-value=0.96 Score=30.39 Aligned_cols=21 Identities=24% Similarity=0.371 Sum_probs=18.2
Q ss_pred cccccccccCChHHHHHHHhhcCCCCCCCCCCCcccCCCCCc
Q psy4421 82 CIHCNSYISSDIKDLIEHCKSCSHMTRPDAFHFKFVCYACEY 123 (167)
Q Consensus 82 c~~c~~~~~~~~~~l~~h~~~~~~~~~~~~~~~~~~C~~C~~ 123 (167)
|++||.. ..++.|.+||+|+-
T Consensus 137 C~vCGy~---------------------~~ge~P~~CPiCga 157 (166)
T COG1592 137 CPVCGYT---------------------HEGEAPEVCPICGA 157 (166)
T ss_pred cCCCCCc---------------------ccCCCCCcCCCCCC
Confidence 9999987 66688999999994
No 88
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=82.03 E-value=0.43 Score=25.58 Aligned_cols=20 Identities=15% Similarity=0.514 Sum_probs=10.4
Q ss_pred CCcccccccccccCchHHHH
Q psy4421 5 LNINQCVHCHLTLTKSTEVI 24 (167)
Q Consensus 5 ~~~~~C~~C~~~f~~~~~l~ 24 (167)
+.-+.|+-|+..|....++.
T Consensus 15 E~~lrCPRC~~~FR~~K~Y~ 34 (65)
T COG4049 15 EEFLRCPRCGMVFRRRKDYI 34 (65)
T ss_pred ceeeeCCchhHHHHHhHHHH
Confidence 33445555555555555555
No 89
>PF02176 zf-TRAF: TRAF-type zinc finger; PDB: 2EOD_A 2YUC_A 3HCU_A 3HCS_B 3HCT_A.
Probab=81.72 E-value=1.3 Score=23.91 Aligned_cols=43 Identities=16% Similarity=0.372 Sum_probs=25.9
Q ss_pred CcccCCC-CCccccCchhHHHHHhhhCCCCceeCCC----CcccccCc
Q psy4421 114 FKFVCYA-CEYNTYMSGNIKTHLRLHLDDKPYKCSL----CNYECRQN 156 (167)
Q Consensus 114 ~~~~C~~-C~~~~~~~~~l~~H~~~h~~~~~~~C~~----C~~~f~~~ 156 (167)
.+..|+. |+..-..+..|..|....-..++..|.+ |+..+...
T Consensus 8 ~~v~C~~~cc~~~i~r~~l~~H~~~~C~~~~v~C~~~~~GC~~~~~~~ 55 (60)
T PF02176_consen 8 RPVPCPNGCCNEMIPRKELDDHLENECPKRPVPCPYSPYGCKERVPRE 55 (60)
T ss_dssp SEEE-TT--S-BEEECCCHHHHHHTTSTTSEEE-SS----S--EEEHH
T ss_pred CEeeCCCCCcccceeHHHHHHHHHccCCCCcEECCCCCCCCCCccchh
Confidence 4567877 3333334668899998777778889999 88776543
No 90
>PF08790 zf-LYAR: LYAR-type C2HC zinc finger ; InterPro: IPR014898 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This C2HC zinc finger domain is found in LYAR proteins such as Q08288 from SWISSPROT, which are involved in cell growth regulation. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1WJV_A.
Probab=80.90 E-value=0.51 Score=21.61 Aligned_cols=18 Identities=28% Similarity=0.606 Sum_probs=11.5
Q ss_pred eeCCCCcccccCchhHHHH
Q psy4421 144 YKCSLCNYECRQNVHLKSH 162 (167)
Q Consensus 144 ~~C~~C~~~f~~~~~l~~H 162 (167)
|.|..|++.| ...++..|
T Consensus 1 ~sCiDC~~~F-~~~~y~~H 18 (28)
T PF08790_consen 1 FSCIDCSKDF-DGDSYKSH 18 (28)
T ss_dssp EEETTTTEEE-EGGGTTT-
T ss_pred CeeecCCCCc-CcCCcCCC
Confidence 5688899888 44444444
No 91
>KOG2482|consensus
Probab=80.31 E-value=2.3 Score=31.86 Aligned_cols=49 Identities=20% Similarity=0.358 Sum_probs=37.0
Q ss_pred ccCCCCCccccCchhHHHHHhhhCC---------------------------CCceeCCCCcccccCchhHHHHhh
Q psy4421 116 FVCYACEYNTYMSGNIKTHLRLHLD---------------------------DKPYKCSLCNYECRQNVHLKSHMK 164 (167)
Q Consensus 116 ~~C~~C~~~~~~~~~l~~H~~~h~~---------------------------~~~~~C~~C~~~f~~~~~l~~H~~ 164 (167)
.+|-.|.....+...|..||..-+. ...-.|-.|...|-....|..|+-
T Consensus 280 v~CLfC~~~~en~~~l~eHmk~vHe~Dl~Ki~sd~~Ln~YqrvrviNyiRkq~~~~~c~~cd~~F~~e~~l~~hm~ 355 (423)
T KOG2482|consen 280 VVCLFCTNFYENPVFLFEHMKIVHEFDLLKIQSDYSLNFYQRVRVINYIRKQKKKSRCAECDLSFWKEPGLLIHMV 355 (423)
T ss_pred eEEEeeccchhhHHHHHHHHHHHHHhhHHhhccccccchhhhhhHHHHHHHHhhccccccccccccCcchhhhhcc
Confidence 6888888888888888888774332 112357789889999999999874
No 92
>KOG2186|consensus
Probab=79.93 E-value=0.81 Score=32.66 Aligned_cols=46 Identities=17% Similarity=0.249 Sum_probs=32.8
Q ss_pred ccccccccccCchHHHHHHhhhhhccccCCCCCccceecCccCccccChHHHHHHHH
Q psy4421 8 NQCVHCHLTLTKSTEVIVKHAQTCISMVRPDSFKYKYGCYRCSYFTYESNNLKKHIL 64 (167)
Q Consensus 8 ~~C~~C~~~f~~~~~l~~~~~~~~~~h~~~~~~~~~~~C~~C~~~~~~~~~l~~H~~ 64 (167)
|.|..||.+... ..+. +|+..-.+ .-|.|-+|+..|.. .....|..
T Consensus 4 FtCnvCgEsvKK-p~ve--------kH~srCrn-~~fSCIDC~k~F~~-~sYknH~k 49 (276)
T KOG2186|consen 4 FTCNVCGESVKK-PQVE--------KHMSRCRN-AYFSCIDCGKTFER-VSYKNHTK 49 (276)
T ss_pred Eehhhhhhhccc-cchH--------HHHHhccC-CeeEEeeccccccc-chhhhhhh
Confidence 689999998654 4566 67665445 44999999999987 44555643
No 93
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=79.70 E-value=5.1 Score=26.34 Aligned_cols=41 Identities=15% Similarity=0.361 Sum_probs=27.1
Q ss_pred CCCCCcccCCCCCccccCchhHHHHHhhhCCCCceeCCCCccccc
Q psy4421 110 DAFHFKFVCYACEYNTYMSGNIKTHLRLHLDDKPYKCSLCNYECR 154 (167)
Q Consensus 110 ~~~~~~~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~~f~ 154 (167)
......|.|+.|+..|.....+..- .. ...|.|+.||....
T Consensus 94 e~~~~~Y~Cp~C~~~y~~~ea~~~~---d~-~~~f~Cp~Cg~~l~ 134 (147)
T smart00531 94 ETNNAYYKCPNCQSKYTFLEANQLL---DM-DGTFTCPRCGEELE 134 (147)
T ss_pred ccCCcEEECcCCCCEeeHHHHHHhc---CC-CCcEECCCCCCEEE
Confidence 3445579999999888865443220 12 34499999998664
No 94
>COG3364 Zn-ribbon containing protein [General function prediction only]
Probab=79.51 E-value=1.5 Score=26.76 Aligned_cols=19 Identities=26% Similarity=0.503 Sum_probs=14.9
Q ss_pred CcccccccccccCchHHHH
Q psy4421 6 NINQCVHCHLTLTKSTEVI 24 (167)
Q Consensus 6 ~~~~C~~C~~~f~~~~~l~ 24 (167)
+|+.|..||..|.+-+...
T Consensus 1 MpH~CtrCG~vf~~g~~~i 19 (112)
T COG3364 1 MPHQCTRCGEVFDDGSEEI 19 (112)
T ss_pred CCceecccccccccccHHH
Confidence 5788999999998865544
No 95
>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=79.23 E-value=1.3 Score=31.14 Aligned_cols=29 Identities=21% Similarity=0.372 Sum_probs=22.0
Q ss_pred CCccceecCccCccccChHHHHHHHHHhh
Q psy4421 39 SFKYKYGCYRCSYFTYESNNLKKHILKHT 67 (167)
Q Consensus 39 ~~~~~~~C~~C~~~~~~~~~l~~H~~~h~ 67 (167)
..+..|.|..|+|.|.....+.+|+...+
T Consensus 73 ~~~~K~~C~lc~KlFkg~eFV~KHI~nKH 101 (214)
T PF04959_consen 73 EDEDKWRCPLCGKLFKGPEFVRKHIFNKH 101 (214)
T ss_dssp SSSEEEEE-SSS-EESSHHHHHHHHHHH-
T ss_pred HcCCEECCCCCCcccCChHHHHHHHhhcC
Confidence 34556999999999999999999997643
No 96
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=79.22 E-value=0.92 Score=27.53 Aligned_cols=42 Identities=17% Similarity=0.308 Sum_probs=27.9
Q ss_pred CCCCCcccCCCCCccccCchhHHHHHhhhCCCCceeCCCCcccccC
Q psy4421 110 DAFHFKFVCYACEYNTYMSGNIKTHLRLHLDDKPYKCSLCNYECRQ 155 (167)
Q Consensus 110 ~~~~~~~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~ 155 (167)
+..++.|.|+.|+..-.+...+. .........|..||.+|..
T Consensus 17 ~~L~k~FtCp~Cghe~vs~ctvk----k~~~~g~~~Cg~CGls~e~ 58 (104)
T COG4888 17 QVLPKTFTCPRCGHEKVSSCTVK----KTVNIGTAVCGNCGLSFEC 58 (104)
T ss_pred ccCCceEecCccCCeeeeEEEEE----ecCceeEEEcccCcceEEE
Confidence 44678899999997665544321 1222345789999998853
No 97
>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=79.12 E-value=0.99 Score=21.06 Aligned_cols=24 Identities=21% Similarity=0.407 Sum_probs=9.9
Q ss_pred cCCCCCccccCchhHHHHHhhhCCCCceeCCCCcc
Q psy4421 117 VCYACEYNTYMSGNIKTHLRLHLDDKPYKCSLCNY 151 (167)
Q Consensus 117 ~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~ 151 (167)
+|+.|+..+.. .+...+.|+.|+.
T Consensus 4 ~Cp~C~se~~y-----------~D~~~~vCp~C~~ 27 (30)
T PF08274_consen 4 KCPLCGSEYTY-----------EDGELLVCPECGH 27 (30)
T ss_dssp --TTT-----E-----------E-SSSEEETTTTE
T ss_pred CCCCCCCccee-----------ccCCEEeCCcccc
Confidence 46666665555 2344577777764
No 98
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=78.90 E-value=2.3 Score=31.95 Aligned_cols=131 Identities=21% Similarity=0.402 Sum_probs=72.6
Q ss_pred cccc--ccccccCchHHHHHHhhhhhccccCCCCCccceecCccCc---cccC------hHHHHHHHHHhhCCCCCCccc
Q psy4421 8 NQCV--HCHLTLTKSTEVIVKHAQTCISMVRPDSFKYKYGCYRCSY---FTYE------SNNLKKHILKHTGEKPFSYMY 76 (167)
Q Consensus 8 ~~C~--~C~~~f~~~~~l~~~~~~~~~~h~~~~~~~~~~~C~~C~~---~~~~------~~~l~~H~~~h~~~~~~~~~~ 76 (167)
|.|+ .|..+......|. .|.+..++ .+.|.+|-. .|.. ...|..|+..-..+.-|
T Consensus 152 F~CP~skc~~~C~~~k~lk--------~H~K~~H~--~~~C~~C~~nKk~F~~E~~lF~~~~Lr~H~~~G~~e~GF---- 217 (493)
T COG5236 152 FKCPKSKCHRRCGSLKELK--------KHYKAQHG--FVLCSECIGNKKDFWNEIRLFRSSTLRDHKNGGLEEEGF---- 217 (493)
T ss_pred hcCCchhhhhhhhhHHHHH--------HHHHhhcC--cEEhHhhhcCcccCccceeeeecccccccccCCccccCc----
Confidence 4555 3555555566777 66654332 256777743 3332 33444444321111122
Q ss_pred ccCcccccccccccCChHHHHHHHhhcCCCCCCCCCCCcccCCCCC----ccccCchhHHHHHhhhCCCCceeCCC--Cc
Q psy4421 77 ENQQYCIHCNSYISSDIKDLIEHCKSCSHMTRPDAFHFKFVCYACE----YNTYMSGNIKTHLRLHLDDKPYKCSL--CN 150 (167)
Q Consensus 77 ~~~~~c~~c~~~~~~~~~~l~~h~~~~~~~~~~~~~~~~~~C~~C~----~~~~~~~~l~~H~~~h~~~~~~~C~~--C~ 150 (167)
-+-..|..|... |-+...|..|+.. . -++-+.|..-+ .-|.+-..|-.|-+ ..-|.|.. |-
T Consensus 218 KGHP~C~FC~~~-FYdDDEL~~HcR~-------~-HE~ChICD~v~p~~~QYFK~Y~~Le~HF~----~~hy~ct~qtc~ 284 (493)
T COG5236 218 KGHPLCIFCKIY-FYDDDELRRHCRL-------R-HEACHICDMVGPIRYQYFKSYEDLEAHFR----NAHYCCTFQTCR 284 (493)
T ss_pred CCCchhhhccce-ecChHHHHHHHHh-------h-hhhhhhhhccCccchhhhhCHHHHHHHhh----cCceEEEEEEEe
Confidence 233458999977 8888889999886 2 23333333322 23555566767655 23466654 32
Q ss_pred ----ccccCchhHHHHhhh
Q psy4421 151 ----YECRQNVHLKSHMKS 165 (167)
Q Consensus 151 ----~~f~~~~~l~~H~~~ 165 (167)
..|.....|..|+..
T Consensus 285 ~~k~~vf~~~~el~~h~~~ 303 (493)
T COG5236 285 VGKCYVFPYHTELLEHLTR 303 (493)
T ss_pred cCcEEEeccHHHHHHHHHH
Confidence 468888888888754
No 99
>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=78.18 E-value=0.57 Score=24.75 Aligned_cols=13 Identities=23% Similarity=0.345 Sum_probs=6.6
Q ss_pred eecCccCccccCh
Q psy4421 44 YGCYRCSYFTYES 56 (167)
Q Consensus 44 ~~C~~C~~~~~~~ 56 (167)
|.|..|+..|...
T Consensus 6 y~C~~Cg~~fe~~ 18 (52)
T TIGR02605 6 YRCTACGHRFEVL 18 (52)
T ss_pred EEeCCCCCEeEEE
Confidence 4555555554443
No 100
>KOG2785|consensus
Probab=77.69 E-value=2.7 Score=31.92 Aligned_cols=52 Identities=15% Similarity=0.303 Sum_probs=44.3
Q ss_pred CcccCCCCCccccCchhHHHHHhhhCC-----------------------CCceeCCCCc---ccccCchhHHHHhhh
Q psy4421 114 FKFVCYACEYNTYMSGNIKTHLRLHLD-----------------------DKPYKCSLCN---YECRQNVHLKSHMKS 165 (167)
Q Consensus 114 ~~~~C~~C~~~~~~~~~l~~H~~~h~~-----------------------~~~~~C~~C~---~~f~~~~~l~~H~~~ 165 (167)
.|-.|..|+..+.+...-..||..++| ...+.|-.|+ +.|++..+.+.|+..
T Consensus 165 ~Pt~CLfC~~~~k~~e~~~~HM~~~HgffIPdreYL~D~~GLl~YLgeKV~~~~~CL~CN~~~~~f~sleavr~HM~~ 242 (390)
T KOG2785|consen 165 IPTDCLFCDKKSKSLEENLKHMFKEHGFFIPDREYLTDEKGLLKYLGEKVGIGFICLFCNELGRPFSSLEAVRAHMRD 242 (390)
T ss_pred CCcceeecCCCcccHHHHHHHHhhccCCcCCchHhhhchhHHHHHHHHHhccCceEEEeccccCcccccHHHHHHHhh
Confidence 457899999999999988999998886 3357888898 999999999999964
No 101
>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=77.17 E-value=2.6 Score=28.16 Aligned_cols=36 Identities=11% Similarity=0.298 Sum_probs=26.9
Q ss_pred CCCCCcccCCCCCccccCchhHHHHHhhhCCCCceeCCCCccccc
Q psy4421 110 DAFHFKFVCYACEYNTYMSGNIKTHLRLHLDDKPYKCSLCNYECR 154 (167)
Q Consensus 110 ~~~~~~~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~~f~ 154 (167)
.....-|.|+.|+..|+....+. ..|.|+.||....
T Consensus 104 e~~~~~Y~Cp~c~~r~tf~eA~~---------~~F~Cp~Cg~~L~ 139 (158)
T TIGR00373 104 ETNNMFFICPNMCVRFTFNEAME---------LNFTCPRCGAMLD 139 (158)
T ss_pred ccCCCeEECCCCCcEeeHHHHHH---------cCCcCCCCCCEee
Confidence 34445689999998888877763 3699999997654
No 102
>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=77.10 E-value=0.75 Score=22.79 Aligned_cols=29 Identities=24% Similarity=0.441 Sum_probs=15.8
Q ss_pred ccCCCCCccccCchhHHHHHhhhCCCCceeCCCCcc
Q psy4421 116 FVCYACEYNTYMSGNIKTHLRLHLDDKPYKCSLCNY 151 (167)
Q Consensus 116 ~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~ 151 (167)
|+|+.|+..|...... .....-.|+.||.
T Consensus 6 y~C~~Cg~~fe~~~~~-------~~~~~~~CP~Cg~ 34 (41)
T smart00834 6 YRCEDCGHTFEVLQKI-------SDDPLATCPECGG 34 (41)
T ss_pred EEcCCCCCEEEEEEec-------CCCCCCCCCCCCC
Confidence 5677777766544322 1123456777775
No 103
>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=76.16 E-value=1.4 Score=30.90 Aligned_cols=23 Identities=17% Similarity=0.548 Sum_probs=10.4
Q ss_pred ceeCCCCcccccCchhHHHHhhh
Q psy4421 143 PYKCSLCNYECRQNVHLKSHMKS 165 (167)
Q Consensus 143 ~~~C~~C~~~f~~~~~l~~H~~~ 165 (167)
.|.|..|+|.|.-..-+.+|+..
T Consensus 77 K~~C~lc~KlFkg~eFV~KHI~n 99 (214)
T PF04959_consen 77 KWRCPLCGKLFKGPEFVRKHIFN 99 (214)
T ss_dssp EEEE-SSS-EESSHHHHHHHHHH
T ss_pred EECCCCCCcccCChHHHHHHHhh
Confidence 35555555555555555555443
No 104
>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=75.86 E-value=0.6 Score=23.60 Aligned_cols=12 Identities=17% Similarity=0.512 Sum_probs=6.7
Q ss_pred ccccccccccCc
Q psy4421 8 NQCVHCHLTLTK 19 (167)
Q Consensus 8 ~~C~~C~~~f~~ 19 (167)
|.|..||..|..
T Consensus 6 y~C~~Cg~~fe~ 17 (42)
T PF09723_consen 6 YRCEECGHEFEV 17 (42)
T ss_pred EEeCCCCCEEEE
Confidence 556666655543
No 105
>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=75.71 E-value=2.4 Score=18.95 Aligned_cols=18 Identities=28% Similarity=0.678 Sum_probs=10.0
Q ss_pred eCCCCcccccCchhHHHHh
Q psy4421 145 KCSLCNYECRQNVHLKSHM 163 (167)
Q Consensus 145 ~C~~C~~~f~~~~~l~~H~ 163 (167)
.|+.|++.+ ....+.+|+
T Consensus 3 ~CPiC~~~v-~~~~in~HL 20 (26)
T smart00734 3 QCPVCFREV-PENLINSHL 20 (26)
T ss_pred cCCCCcCcc-cHHHHHHHH
Confidence 466666665 334555554
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=74.51 E-value=2.3 Score=20.11 Aligned_cols=9 Identities=22% Similarity=0.785 Sum_probs=3.9
Q ss_pred eeCCCCccc
Q psy4421 144 YKCSLCNYE 152 (167)
Q Consensus 144 ~~C~~C~~~ 152 (167)
..|+.||.+
T Consensus 18 irC~~CG~R 26 (32)
T PF03604_consen 18 IRCPECGHR 26 (32)
T ss_dssp SSBSSSS-S
T ss_pred EECCcCCCe
Confidence 445555543
No 107
>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=74.20 E-value=0.9 Score=29.76 Aligned_cols=12 Identities=17% Similarity=0.429 Sum_probs=6.4
Q ss_pred eeCCCCcccccC
Q psy4421 144 YKCSLCNYECRQ 155 (167)
Q Consensus 144 ~~C~~C~~~f~~ 155 (167)
-.|..||++|++
T Consensus 29 ReC~~C~~RFTT 40 (147)
T TIGR00244 29 RECLECHERFTT 40 (147)
T ss_pred ccCCccCCccce
Confidence 345555555554
No 108
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=74.20 E-value=2 Score=22.54 Aligned_cols=30 Identities=13% Similarity=0.564 Sum_probs=18.8
Q ss_pred CcccCCCCCccccCchhHHHHHhhhCCCCceeCCCCcccc
Q psy4421 114 FKFVCYACEYNTYMSGNIKTHLRLHLDDKPYKCSLCNYEC 153 (167)
Q Consensus 114 ~~~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~~f 153 (167)
..|.|..|+..|... .......|+.||.+-
T Consensus 5 ~~Y~C~~Cg~~~~~~----------~~~~~irCp~Cg~rI 34 (49)
T COG1996 5 MEYKCARCGREVELD----------QETRGIRCPYCGSRI 34 (49)
T ss_pred EEEEhhhcCCeeehh----------hccCceeCCCCCcEE
Confidence 357888888877211 123457888888643
No 109
>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=73.51 E-value=3.7 Score=25.40 Aligned_cols=25 Identities=36% Similarity=0.792 Sum_probs=22.4
Q ss_pred eec----CccCccccChHHHHHHHHHhhC
Q psy4421 44 YGC----YRCSYFTYESNNLKKHILKHTG 68 (167)
Q Consensus 44 ~~C----~~C~~~~~~~~~l~~H~~~h~~ 68 (167)
|.| ..|++.+.+...|.+|.+.++|
T Consensus 81 ~~C~~~~~~C~y~~~~~~~m~~H~~~~Hg 109 (109)
T PF12013_consen 81 YRCQCDPPHCGYITRSKKTMRKHWRKEHG 109 (109)
T ss_pred eeeecCCCCCCcEeccHHHHHHHHHHhcC
Confidence 899 9999999999999999987653
No 110
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=73.31 E-value=3.2 Score=28.30 Aligned_cols=35 Identities=14% Similarity=0.452 Sum_probs=25.3
Q ss_pred CCCcccCCCCCccccCchhHHHHHhhhCCCCceeCCCCcccccC
Q psy4421 112 FHFKFVCYACEYNTYMSGNIKTHLRLHLDDKPYKCSLCNYECRQ 155 (167)
Q Consensus 112 ~~~~~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~ 155 (167)
...-|.|+.|+..|.....+ +..|.|+.||.....
T Consensus 114 ~~~~Y~Cp~C~~rytf~eA~---------~~~F~Cp~Cg~~L~~ 148 (178)
T PRK06266 114 NNMFFFCPNCHIRFTFDEAM---------EYGFRCPQCGEMLEE 148 (178)
T ss_pred CCCEEECCCCCcEEeHHHHh---------hcCCcCCCCCCCCee
Confidence 34568999999888777654 236899999975543
No 111
>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=71.67 E-value=2 Score=19.26 Aligned_cols=9 Identities=33% Similarity=0.969 Sum_probs=4.1
Q ss_pred cCCCCCccc
Q psy4421 117 VCYACEYNT 125 (167)
Q Consensus 117 ~C~~C~~~~ 125 (167)
.|+.||..|
T Consensus 16 ~Cp~CG~~F 24 (26)
T PF10571_consen 16 FCPHCGYDF 24 (26)
T ss_pred cCCCCCCCC
Confidence 344444444
No 112
>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=71.19 E-value=3.3 Score=29.85 Aligned_cols=15 Identities=27% Similarity=0.552 Sum_probs=8.6
Q ss_pred ccceecCccCccccC
Q psy4421 41 KYKYGCYRCSYFTYE 55 (167)
Q Consensus 41 ~~~~~C~~C~~~~~~ 55 (167)
-+.|.|..|....-.
T Consensus 140 Grif~CsfC~~flCE 154 (314)
T PF06524_consen 140 GRIFKCSFCDNFLCE 154 (314)
T ss_pred CeEEEeecCCCeeec
Confidence 344777777664433
No 113
>COG1327 Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains [Transcription]
Probab=70.19 E-value=1.3 Score=29.13 Aligned_cols=12 Identities=17% Similarity=0.407 Sum_probs=5.9
Q ss_pred eeCCCCcccccC
Q psy4421 144 YKCSLCNYECRQ 155 (167)
Q Consensus 144 ~~C~~C~~~f~~ 155 (167)
-.|..||.+|++
T Consensus 29 ReC~~C~~RFTT 40 (156)
T COG1327 29 RECLECGERFTT 40 (156)
T ss_pred hcccccccccch
Confidence 345555555543
No 114
>PF14353 CpXC: CpXC protein
Probab=70.08 E-value=0.8 Score=29.27 Aligned_cols=15 Identities=13% Similarity=0.239 Sum_probs=11.1
Q ss_pred ceecCccCccccChH
Q psy4421 43 KYGCYRCSYFTYESN 57 (167)
Q Consensus 43 ~~~C~~C~~~~~~~~ 57 (167)
.+.|+.||..|.-..
T Consensus 38 ~~~CP~Cg~~~~~~~ 52 (128)
T PF14353_consen 38 SFTCPSCGHKFRLEY 52 (128)
T ss_pred EEECCCCCCceecCC
Confidence 488999988776544
No 115
>KOG3408|consensus
Probab=69.87 E-value=3 Score=26.30 Aligned_cols=26 Identities=23% Similarity=0.404 Sum_probs=16.2
Q ss_pred CCCceeCCCCcccccCchhHHHHhhh
Q psy4421 140 DDKPYKCSLCNYECRQNVHLKSHMKS 165 (167)
Q Consensus 140 ~~~~~~C~~C~~~f~~~~~l~~H~~~ 165 (167)
|...|.|-.|.+-|.....|..|.++
T Consensus 54 G~GqfyCi~CaRyFi~~~~l~~H~kt 79 (129)
T KOG3408|consen 54 GGGQFYCIECARYFIDAKALKTHFKT 79 (129)
T ss_pred CCceeehhhhhhhhcchHHHHHHHhc
Confidence 34456666666666666666666654
No 116
>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=69.77 E-value=3.1 Score=27.77 Aligned_cols=35 Identities=11% Similarity=0.294 Sum_probs=23.8
Q ss_pred CCCccceecCccCccccChHHHHHHHHHhhCCCCCCcccccCcccccccccc
Q psy4421 38 DSFKYKYGCYRCSYFTYESNNLKKHILKHTGEKPFSYMYENQQYCIHCNSYI 89 (167)
Q Consensus 38 ~~~~~~~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~~~~~~~~~c~~c~~~~ 89 (167)
..+..-|.|+.|+..|.....+.. .|. |+.||..+
T Consensus 104 e~~~~~Y~Cp~c~~r~tf~eA~~~---------~F~--------Cp~Cg~~L 138 (158)
T TIGR00373 104 ETNNMFFICPNMCVRFTFNEAMEL---------NFT--------CPRCGAML 138 (158)
T ss_pred ccCCCeEECCCCCcEeeHHHHHHc---------CCc--------CCCCCCEe
Confidence 334455788888887777776651 566 88888774
No 117
>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=69.67 E-value=3.6 Score=26.61 Aligned_cols=22 Identities=23% Similarity=0.513 Sum_probs=10.2
Q ss_pred ceeCCCCcccccCchhHHHHhhhcC
Q psy4421 143 PYKCSLCNYECRQNVHLKSHMKSNH 167 (167)
Q Consensus 143 ~~~C~~C~~~f~~~~~l~~H~~~hh 167 (167)
...|-+||+.|... .+|+++||
T Consensus 72 ~i~clecGk~~k~L---krHL~~~~ 93 (132)
T PF05443_consen 72 YIICLECGKKFKTL---KRHLRTHH 93 (132)
T ss_dssp -EE-TBT--EESBH---HHHHHHTT
T ss_pred eeEEccCCcccchH---HHHHHHcc
Confidence 35566666666543 56666553
No 118
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=69.40 E-value=1.1 Score=22.45 Aligned_cols=11 Identities=36% Similarity=0.932 Sum_probs=7.8
Q ss_pred eeCCCCccccc
Q psy4421 144 YKCSLCNYECR 154 (167)
Q Consensus 144 ~~C~~C~~~f~ 154 (167)
|.|..|+..+.
T Consensus 29 y~C~~C~~~w~ 39 (40)
T smart00440 29 YVCTKCGHRWR 39 (40)
T ss_pred EEeCCCCCEeC
Confidence 77877877654
No 119
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=68.97 E-value=4.2 Score=21.42 Aligned_cols=12 Identities=25% Similarity=0.852 Sum_probs=8.9
Q ss_pred CceeCCCCcccc
Q psy4421 142 KPYKCSLCNYEC 153 (167)
Q Consensus 142 ~~~~C~~C~~~f 153 (167)
..+.|..||..+
T Consensus 36 ~r~~C~~Cgyt~ 47 (50)
T PRK00432 36 DRWHCGKCGYTE 47 (50)
T ss_pred CcEECCCcCCEE
Confidence 567888888754
No 120
>PF15269 zf-C2H2_7: Zinc-finger
Probab=68.14 E-value=6.1 Score=20.19 Aligned_cols=23 Identities=30% Similarity=0.761 Sum_probs=19.1
Q ss_pred ceecCccCccccChHHHHHHHHH
Q psy4421 43 KYGCYRCSYFTYESNNLKKHILK 65 (167)
Q Consensus 43 ~~~C~~C~~~~~~~~~l~~H~~~ 65 (167)
.|+|-+|..+...++.|..|++-
T Consensus 20 ~ykcfqcpftc~~kshl~nhmky 42 (54)
T PF15269_consen 20 KYKCFQCPFTCNEKSHLFNHMKY 42 (54)
T ss_pred cceeecCCcccchHHHHHHHHHH
Confidence 37899999988888888888864
No 121
>KOG2593|consensus
Probab=67.34 E-value=7.3 Score=30.25 Aligned_cols=40 Identities=18% Similarity=0.352 Sum_probs=28.6
Q ss_pred CCCCcccCCCCCccccCchhHHHHHhhhCCCCceeCCCCcccc
Q psy4421 111 AFHFKFVCYACEYNTYMSGNIKTHLRLHLDDKPYKCSLCNYEC 153 (167)
Q Consensus 111 ~~~~~~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~~f 153 (167)
.....|.|+.|.+.|.....++- +-.....|.|..|+--.
T Consensus 124 t~~~~Y~Cp~C~kkyt~Lea~~L---~~~~~~~F~C~~C~gel 163 (436)
T KOG2593|consen 124 TNVAGYVCPNCQKKYTSLEALQL---LDNETGEFHCENCGGEL 163 (436)
T ss_pred cccccccCCccccchhhhHHHHh---hcccCceEEEecCCCch
Confidence 44457999999999988766542 33335679999998533
No 122
>KOG2593|consensus
Probab=67.21 E-value=4.2 Score=31.48 Aligned_cols=36 Identities=17% Similarity=0.290 Sum_probs=21.8
Q ss_pred CCcccccccccccCchHHHHHHhhhhhccccCCCCCccceecCccCc
Q psy4421 5 LNINQCVHCHLTLTKSTEVIVKHAQTCISMVRPDSFKYKYGCYRCSY 51 (167)
Q Consensus 5 ~~~~~C~~C~~~f~~~~~l~~~~~~~~~~h~~~~~~~~~~~C~~C~~ 51 (167)
...|.|+.|.+.|...-.+. ........|.|..|+-
T Consensus 126 ~~~Y~Cp~C~kkyt~Lea~~-----------L~~~~~~~F~C~~C~g 161 (436)
T KOG2593|consen 126 VAGYVCPNCQKKYTSLEALQ-----------LLDNETGEFHCENCGG 161 (436)
T ss_pred cccccCCccccchhhhHHHH-----------hhcccCceEEEecCCC
Confidence 45577888888776554444 2223344577877764
No 123
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=66.27 E-value=5.2 Score=23.73 Aligned_cols=30 Identities=30% Similarity=0.549 Sum_probs=19.6
Q ss_pred cccCCCCCccccCchhHHHHHhhhCCCCceeCCCCccccc
Q psy4421 115 KFVCYACEYNTYMSGNIKTHLRLHLDDKPYKCSLCNYECR 154 (167)
Q Consensus 115 ~~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~~f~ 154 (167)
.|.|+.|++.- +.++. -.-+.|..||..|.
T Consensus 35 ~~~Cp~C~~~~--------VkR~a--~GIW~C~kCg~~fA 64 (89)
T COG1997 35 KHVCPFCGRTT--------VKRIA--TGIWKCRKCGAKFA 64 (89)
T ss_pred CCcCCCCCCcc--------eeeec--cCeEEcCCCCCeec
Confidence 57888888652 22323 24578888888875
No 124
>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=65.72 E-value=6.2 Score=17.34 Aligned_cols=9 Identities=33% Similarity=0.870 Sum_probs=5.2
Q ss_pred CcccCCCCC
Q psy4421 114 FKFVCYACE 122 (167)
Q Consensus 114 ~~~~C~~C~ 122 (167)
..|.|+.||
T Consensus 15 v~f~CPnCG 23 (24)
T PF07754_consen 15 VPFPCPNCG 23 (24)
T ss_pred ceEeCCCCC
Confidence 456666665
No 125
>COG4530 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=63.91 E-value=5.8 Score=24.58 Aligned_cols=12 Identities=8% Similarity=-0.283 Sum_probs=5.8
Q ss_pred CcccCCCCCccc
Q psy4421 114 FKFVCYACEYNT 125 (167)
Q Consensus 114 ~~~~C~~C~~~~ 125 (167)
.|..|++||++|
T Consensus 25 dPiVsPytG~s~ 36 (129)
T COG4530 25 DPIVSPYTGKSY 36 (129)
T ss_pred CccccCcccccc
Confidence 344455555444
No 126
>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=63.42 E-value=11 Score=19.27 Aligned_cols=28 Identities=25% Similarity=0.634 Sum_probs=17.5
Q ss_pred cccCCCCCccccCchhHHHHHhhhCCCCceeCCCCcc
Q psy4421 115 KFVCYACEYNTYMSGNIKTHLRLHLDDKPYKCSLCNY 151 (167)
Q Consensus 115 ~~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~ 151 (167)
.+.|+.|+..-.. .+ .+...|.|..|++
T Consensus 18 g~~CP~Cg~~~~~--~~-------~~~~~~~C~~C~~ 45 (46)
T PF12760_consen 18 GFVCPHCGSTKHY--RL-------KTRGRYRCKACRK 45 (46)
T ss_pred CCCCCCCCCeeeE--Ee-------CCCCeEECCCCCC
Confidence 3779999865111 11 1156799998875
No 127
>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=62.32 E-value=0.38 Score=23.92 Aligned_cols=10 Identities=30% Similarity=0.793 Sum_probs=7.5
Q ss_pred eeCCCCcccc
Q psy4421 144 YKCSLCNYEC 153 (167)
Q Consensus 144 ~~C~~C~~~f 153 (167)
|.|..||..|
T Consensus 29 y~C~~C~~~w 38 (39)
T PF01096_consen 29 YVCCNCGHRW 38 (39)
T ss_dssp EEESSSTEEE
T ss_pred EEeCCCCCee
Confidence 7787887765
No 128
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=61.87 E-value=4.2 Score=24.25 Aligned_cols=14 Identities=14% Similarity=0.437 Sum_probs=11.3
Q ss_pred cceecCccCccccC
Q psy4421 42 YKYGCYRCSYFTYE 55 (167)
Q Consensus 42 ~~~~C~~C~~~~~~ 55 (167)
.|-.|..||+.|..
T Consensus 57 ~Pa~CkkCGfef~~ 70 (97)
T COG3357 57 RPARCKKCGFEFRD 70 (97)
T ss_pred cChhhcccCccccc
Confidence 46789999998877
No 129
>KOG2186|consensus
Probab=61.30 E-value=5.7 Score=28.57 Aligned_cols=45 Identities=22% Similarity=0.481 Sum_probs=32.9
Q ss_pred eecCccCccccChHHHHHHHHHhhCCCCCCcccccCcccccccccccCChHHHHHHH
Q psy4421 44 YGCYRCSYFTYESNNLKKHILKHTGEKPFSYMYENQQYCIHCNSYISSDIKDLIEHC 100 (167)
Q Consensus 44 ~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~~~~~~~~~c~~c~~~~~~~~~~l~~h~ 100 (167)
|.|+.||....-+ .+.+|+..=++ .-|. |+.|+.. |.. ..+..|.
T Consensus 4 FtCnvCgEsvKKp-~vekH~srCrn-~~fS--------CIDC~k~-F~~-~sYknH~ 48 (276)
T KOG2186|consen 4 FTCNVCGESVKKP-QVEKHMSRCRN-AYFS--------CIDCGKT-FER-VSYKNHT 48 (276)
T ss_pred Eehhhhhhhcccc-chHHHHHhccC-CeeE--------Eeecccc-ccc-chhhhhh
Confidence 8899999876544 57778877666 4566 9999999 665 4455553
No 130
>KOG2907|consensus
Probab=60.61 E-value=4.8 Score=25.08 Aligned_cols=39 Identities=28% Similarity=0.646 Sum_probs=25.4
Q ss_pred cccCCCCCccccCchhHHHHHhhhCCCCc---eeCCCCcccccCc
Q psy4421 115 KFVCYACEYNTYMSGNIKTHLRLHLDDKP---YKCSLCNYECRQN 156 (167)
Q Consensus 115 ~~~C~~C~~~~~~~~~l~~H~~~h~~~~~---~~C~~C~~~f~~~ 156 (167)
..+|+.||-.-+.-..|+ +| .++|.. |.|+.|++.|...
T Consensus 74 ~~kCpkCghe~m~Y~T~Q--lR-SADEGQTVFYTC~kC~~k~~e~ 115 (116)
T KOG2907|consen 74 KHKCPKCGHEEMSYHTLQ--LR-SADEGQTVFYTCPKCKYKFTEN 115 (116)
T ss_pred hccCcccCCchhhhhhhh--cc-cccCCceEEEEcCccceeeecc
Confidence 368999997654444332 22 344443 8999999998753
No 131
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=60.43 E-value=9.1 Score=20.64 Aligned_cols=18 Identities=33% Similarity=0.534 Sum_probs=11.4
Q ss_pred CCCCcccCCCCCccccCc
Q psy4421 111 AFHFKFVCYACEYNTYMS 128 (167)
Q Consensus 111 ~~~~~~~C~~C~~~~~~~ 128 (167)
.+...|.|+.||..+.-+
T Consensus 10 ~~~v~~~Cp~cGipthcS 27 (55)
T PF13824_consen 10 PAHVNFECPDCGIPTHCS 27 (55)
T ss_pred ccccCCcCCCCCCcCccC
Confidence 444567888888655443
No 132
>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=59.92 E-value=2.9 Score=21.63 Aligned_cols=37 Identities=14% Similarity=0.261 Sum_probs=20.0
Q ss_pred CCCCCccccCchhHHHHHhhhCCCCceeCCC--CcccccCc
Q psy4421 118 CYACEYNTYMSGNIKTHLRLHLDDKPYKCSL--CNYECRQN 156 (167)
Q Consensus 118 C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~--C~~~f~~~ 156 (167)
||.||....-..+...+. -..+.-+.|.. ||.+|...
T Consensus 2 CP~Cg~~a~ir~S~~~s~--~~~~~Y~qC~N~~Cg~tfv~~ 40 (47)
T PF04606_consen 2 CPHCGSKARIRTSRQLSP--LTRELYCQCTNPECGHTFVAN 40 (47)
T ss_pred cCCCCCeeEEEEchhhCc--ceEEEEEEECCCcCCCEEEEE
Confidence 667775544444332221 12245577866 88877654
No 133
>PF13451 zf-trcl: Probable zinc-binding domain
Probab=58.68 E-value=5.1 Score=21.06 Aligned_cols=16 Identities=31% Similarity=0.503 Sum_probs=13.1
Q ss_pred CCceeCCCCcccccCc
Q psy4421 141 DKPYKCSLCNYECRQN 156 (167)
Q Consensus 141 ~~~~~C~~C~~~f~~~ 156 (167)
++.+.|..||..|...
T Consensus 2 Dk~l~C~dCg~~FvfT 17 (49)
T PF13451_consen 2 DKTLTCKDCGAEFVFT 17 (49)
T ss_pred CeeEEcccCCCeEEEe
Confidence 5678999999988764
No 134
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=58.32 E-value=3.9 Score=25.67 Aligned_cols=38 Identities=29% Similarity=0.564 Sum_probs=23.1
Q ss_pred cccCCCCCccccCchhHHHHHhhhCCCC---ceeCCCCcccccC
Q psy4421 115 KFVCYACEYNTYMSGNIKTHLRLHLDDK---PYKCSLCNYECRQ 155 (167)
Q Consensus 115 ~~~C~~C~~~~~~~~~l~~H~~~h~~~~---~~~C~~C~~~f~~ 155 (167)
-+.|+.|+..-.....|+.- -+++. -|.|..||.+|+.
T Consensus 72 ~~~CpkCg~~ea~y~~~QtR---saDEp~T~Fy~C~~Cg~~wre 112 (113)
T COG1594 72 KEKCPKCGNKEAYYWQLQTR---SADEPETRFYKCTRCGYRWRE 112 (113)
T ss_pred cccCCCCCCceeEEEeeehh---ccCCCceEEEEecccCCEeec
Confidence 36788888654444443322 22232 3899999987753
No 135
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=58.09 E-value=11 Score=19.55 Aligned_cols=11 Identities=45% Similarity=1.262 Sum_probs=5.6
Q ss_pred cccCCCCCccc
Q psy4421 115 KFVCYACEYNT 125 (167)
Q Consensus 115 ~~~C~~C~~~~ 125 (167)
.+.|+.|+..+
T Consensus 20 ~~vC~~Cg~~~ 30 (52)
T smart00661 20 RFVCRKCGYEE 30 (52)
T ss_pred EEECCcCCCeE
Confidence 45555555443
No 136
>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=57.98 E-value=3.4 Score=21.91 Aligned_cols=16 Identities=13% Similarity=0.559 Sum_probs=5.3
Q ss_pred cccCCCCCccccCchh
Q psy4421 115 KFVCYACEYNTYMSGN 130 (167)
Q Consensus 115 ~~~C~~C~~~~~~~~~ 130 (167)
.|+|+.|...|-..-.
T Consensus 21 ~y~C~~C~~~FC~dCD 36 (51)
T PF07975_consen 21 RYRCPKCKNHFCIDCD 36 (51)
T ss_dssp EE--TTTT--B-HHHH
T ss_pred eEECCCCCCccccCcC
Confidence 4555555555544433
No 137
>PF08271 TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013137 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIB (TFIIB). In eukaryotes the initiation of transcription of protein encoding genes by the polymerase II complexe (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least seven different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, and -IIH []. TFIIB and TFIID are responsible for promoter recognition and interaction with pol II; together with Pol II, they form a minimal initiation complex capable of transcription under certain conditions. The TATA box of a Pol II promoter is bound in the initiation complex by the TBP subunit of TFIID, which bends the DNA around the C-terminal domain of TFIIB whereas the N-terminal zinc finger of TFIIB interacts with Pol II [, ]. The TFIIB zinc finger adopts a zinc ribbon fold characterised by two beta-hairpins forming two structurally similar zinc-binding sub-sites []. The zinc finger contacts the rbp1 subunit of Pol II through its dock domain, a conserved region of about 70 amino acids located close to the polymerase active site []. In the Pol II complex this surface is located near the RNA exit groove. Interestingly this sequence is best conserved in the three polymerases that utilise a TFIIB-like general transcription factor (Pol II, Pol III, and archaeal RNA polymerase) but not in Pol I []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1VD4_A 1PFT_A 3K1F_M 3K7A_M 1RO4_A 1RLY_A 1DL6_A.
Probab=57.39 E-value=6.1 Score=19.86 Aligned_cols=29 Identities=14% Similarity=0.348 Sum_probs=14.9
Q ss_pred ccCCCCCccccCchhHHHHHhhhCCCCceeCCCCcccc
Q psy4421 116 FVCYACEYNTYMSGNIKTHLRLHLDDKPYKCSLCNYEC 153 (167)
Q Consensus 116 ~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~~f 153 (167)
|.|+.|+...... -....-+.|+.||...
T Consensus 1 m~Cp~Cg~~~~~~---------D~~~g~~vC~~CG~Vl 29 (43)
T PF08271_consen 1 MKCPNCGSKEIVF---------DPERGELVCPNCGLVL 29 (43)
T ss_dssp ESBTTTSSSEEEE---------ETTTTEEEETTT-BBE
T ss_pred CCCcCCcCCceEE---------cCCCCeEECCCCCCEe
Confidence 4577777643211 1223456788887644
No 138
>KOG4173|consensus
Probab=56.66 E-value=2.9 Score=29.03 Aligned_cols=70 Identities=17% Similarity=0.254 Sum_probs=44.8
Q ss_pred ccccccCChHHHHHHHhhcCCCCCCCCCCCcccCCCCCccccCchhHHHHHhhhC----------CCCceeCC--CCccc
Q psy4421 85 CNSYISSDIKDLIEHCKSCSHMTRPDAFHFKFVCYACEYNTYMSGNIKTHLRLHL----------DDKPYKCS--LCNYE 152 (167)
Q Consensus 85 c~~~~~~~~~~l~~h~~~~~~~~~~~~~~~~~~C~~C~~~~~~~~~l~~H~~~h~----------~~~~~~C~--~C~~~ 152 (167)
|... +.....+..|..+ ..+ -.|..|.+.|.+...|..|+.-.+ |.-.|.|- .|+..
T Consensus 87 c~~~-~d~lD~~E~hY~~-------~h~---~sCs~C~r~~Pt~hLLd~HI~E~HDs~Fqa~veRG~dMy~ClvEgCt~K 155 (253)
T KOG4173|consen 87 CCQV-FDALDDYEHHYHT-------LHG---NSCSFCKRAFPTGHLLDAHILEWHDSLFQALVERGQDMYQCLVEGCTEK 155 (253)
T ss_pred hHHH-HhhhhhHHHhhhh-------ccc---chhHHHHHhCCchhhhhHHHHHHHHHHHHHHHHcCccHHHHHHHhhhhh
Confidence 4444 5555555555443 222 268888888888888887765332 44458884 48888
Q ss_pred ccCchhHHHHhhh
Q psy4421 153 CRQNVHLKSHMKS 165 (167)
Q Consensus 153 f~~~~~l~~H~~~ 165 (167)
|.+.-+-..|+..
T Consensus 156 FkT~r~RkdH~I~ 168 (253)
T KOG4173|consen 156 FKTSRDRKDHMIR 168 (253)
T ss_pred hhhhhhhhhHHHH
Confidence 8887777777643
No 139
>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=56.39 E-value=8.2 Score=20.72 Aligned_cols=30 Identities=23% Similarity=0.461 Sum_probs=14.9
Q ss_pred ccCCCCCccccCchhHHHHHhhhCCCCceeCCCCcccc
Q psy4421 116 FVCYACEYNTYMSGNIKTHLRLHLDDKPYKCSLCNYEC 153 (167)
Q Consensus 116 ~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~~f 153 (167)
|+|+.|+..+...... .|+ ...|+.||..|
T Consensus 3 ~~CP~CG~~iev~~~~-------~Ge-iV~Cp~CGael 32 (54)
T TIGR01206 3 FECPDCGAEIELENPE-------LGE-LVICDECGAEL 32 (54)
T ss_pred cCCCCCCCEEecCCCc-------cCC-EEeCCCCCCEE
Confidence 4666666654433221 122 34666666544
No 140
>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=56.21 E-value=8.3 Score=21.46 Aligned_cols=27 Identities=15% Similarity=0.310 Sum_probs=11.0
Q ss_pred ccCCCCCccccCchhHHHHHhhhCCCCceeCCCCccccc
Q psy4421 116 FVCYACEYNTYMSGNIKTHLRLHLDDKPYKCSLCNYECR 154 (167)
Q Consensus 116 ~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~~f~ 154 (167)
-.|..|++.|... .+.+.|..||..|=
T Consensus 10 ~~C~~C~~~F~~~------------~rrhhCr~CG~~vC 36 (69)
T PF01363_consen 10 SNCMICGKKFSLF------------RRRHHCRNCGRVVC 36 (69)
T ss_dssp SB-TTT--B-BSS------------S-EEE-TTT--EEE
T ss_pred CcCcCcCCcCCCc------------eeeEccCCCCCEEC
Confidence 3577788777431 34566777776653
No 141
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=56.16 E-value=6.9 Score=19.38 Aligned_cols=12 Identities=25% Similarity=0.578 Sum_probs=9.3
Q ss_pred ceeCCCCccccc
Q psy4421 143 PYKCSLCNYECR 154 (167)
Q Consensus 143 ~~~C~~C~~~f~ 154 (167)
|+.|..|++.|=
T Consensus 12 ~f~C~~C~~~FC 23 (39)
T smart00154 12 GFKCRHCGNLFC 23 (39)
T ss_pred CeECCccCCccc
Confidence 788888887774
No 142
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=55.70 E-value=8.5 Score=29.96 Aligned_cols=28 Identities=21% Similarity=0.554 Sum_probs=15.9
Q ss_pred cCCCCCccccCchhHHHHHhhhCCCCceeCCCCcccccC
Q psy4421 117 VCYACEYNTYMSGNIKTHLRLHLDDKPYKCSLCNYECRQ 155 (167)
Q Consensus 117 ~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~ 155 (167)
.|+.||....+ .|.+-|.|+.||.+++.
T Consensus 352 ~Cp~Cg~~m~S-----------~G~~g~rC~kCg~~~~~ 379 (421)
T COG1571 352 VCPRCGGRMKS-----------AGRNGFRCKKCGTRARE 379 (421)
T ss_pred CCCccCCchhh-----------cCCCCcccccccccCCc
Confidence 56666654333 23336777777766654
No 143
>KOG2785|consensus
Probab=55.32 E-value=19 Score=27.65 Aligned_cols=55 Identities=20% Similarity=0.445 Sum_probs=38.1
Q ss_pred cccccccccCChHHHHHHHhhcCCCCCCCCC----------------CCcccCCCCC---ccccCchhHHHHHhh
Q psy4421 82 CIHCNSYISSDIKDLIEHCKSCSHMTRPDAF----------------HFKFVCYACE---YNTYMSGNIKTHLRL 137 (167)
Q Consensus 82 c~~c~~~~~~~~~~l~~h~~~~~~~~~~~~~----------------~~~~~C~~C~---~~~~~~~~l~~H~~~ 137 (167)
|..|+.. +.+...-..||..-+...++... ...+.|..|+ +.|.+....+.||..
T Consensus 169 CLfC~~~-~k~~e~~~~HM~~~HgffIPdreYL~D~~GLl~YLgeKV~~~~~CL~CN~~~~~f~sleavr~HM~~ 242 (390)
T KOG2785|consen 169 CLFCDKK-SKSLEENLKHMFKEHGFFIPDREYLTDEKGLLKYLGEKVGIGFICLFCNELGRPFSSLEAVRAHMRD 242 (390)
T ss_pred eeecCCC-cccHHHHHHHHhhccCCcCCchHhhhchhHHHHHHHHHhccCceEEEeccccCcccccHHHHHHHhh
Confidence 7888888 77777777777763322222111 1237888898 899999999999884
No 144
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=55.03 E-value=4.7 Score=26.15 Aligned_cols=12 Identities=17% Similarity=0.205 Sum_probs=6.1
Q ss_pred eecCccCccccC
Q psy4421 44 YGCYRCSYFTYE 55 (167)
Q Consensus 44 ~~C~~C~~~~~~ 55 (167)
+.|..||..|..
T Consensus 71 ~~C~~CG~~~~~ 82 (135)
T PRK03824 71 LKCRNCGNEWSL 82 (135)
T ss_pred EECCCCCCEEec
Confidence 455555554443
No 145
>PRK04023 DNA polymerase II large subunit; Validated
Probab=54.91 E-value=16 Score=31.86 Aligned_cols=8 Identities=25% Similarity=0.754 Sum_probs=4.7
Q ss_pred eeCCCCcc
Q psy4421 144 YKCSLCNY 151 (167)
Q Consensus 144 ~~C~~C~~ 151 (167)
+.|+.||.
T Consensus 664 y~CPKCG~ 671 (1121)
T PRK04023 664 DECEKCGR 671 (1121)
T ss_pred CcCCCCCC
Confidence 45666664
No 146
>PF14311 DUF4379: Domain of unknown function (DUF4379)
Probab=54.21 E-value=8.3 Score=20.52 Aligned_cols=29 Identities=24% Similarity=0.400 Sum_probs=18.5
Q ss_pred CcccCCCCCccccCchhHHHHHhhhCCCCceeCCCC
Q psy4421 114 FKFVCYACEYNTYMSGNIKTHLRLHLDDKPYKCSLC 149 (167)
Q Consensus 114 ~~~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C 149 (167)
..++|+.|+..|...-..+. .....|+.|
T Consensus 27 v~W~C~~Cgh~w~~~v~~R~-------~~~~~CP~C 55 (55)
T PF14311_consen 27 VWWKCPKCGHEWKASVNDRT-------RRGKGCPYC 55 (55)
T ss_pred EEEECCCCCCeeEccHhhhc-------cCCCCCCCC
Confidence 35899999888877654433 233456665
No 147
>KOG2807|consensus
Probab=53.33 E-value=37 Score=25.62 Aligned_cols=13 Identities=8% Similarity=0.414 Sum_probs=7.6
Q ss_pred cccccccccCchH
Q psy4421 9 QCVHCHLTLTKST 21 (167)
Q Consensus 9 ~C~~C~~~f~~~~ 21 (167)
.|..=..+|+.++
T Consensus 246 ~~sLvkmGFP~~~ 258 (378)
T KOG2807|consen 246 ECSLVKMGFPSRS 258 (378)
T ss_pred CCceEEecCCCcc
Confidence 4555566676554
No 148
>PHA02998 RNA polymerase subunit; Provisional
Probab=53.00 E-value=4.5 Score=27.45 Aligned_cols=39 Identities=23% Similarity=0.432 Sum_probs=24.2
Q ss_pred cccCCCCCccccCchhHHHHHhhhCCCCc---eeCCCCcccccCc
Q psy4421 115 KFVCYACEYNTYMSGNIKTHLRLHLDDKP---YKCSLCNYECRQN 156 (167)
Q Consensus 115 ~~~C~~C~~~~~~~~~l~~H~~~h~~~~~---~~C~~C~~~f~~~ 156 (167)
...|+.|+..-.....++. | .++|.+ |.|..||..|..+
T Consensus 143 ~v~CPkCg~~~A~f~qlQT--R-SADEPmT~FYkC~~CG~~wkpp 184 (195)
T PHA02998 143 NTPCPNCKSKNTTPMMIQT--R-AADEPPLVRHACRDCKKHFKPP 184 (195)
T ss_pred CCCCCCCCCCceEEEEEee--c-cCCCCceEEEEcCCCCCccCCc
Confidence 4689999865444433322 2 233433 8999999988754
No 149
>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=52.85 E-value=6.2 Score=19.91 Aligned_cols=13 Identities=31% Similarity=0.782 Sum_probs=7.6
Q ss_pred CceeCCCCccccc
Q psy4421 142 KPYKCSLCNYECR 154 (167)
Q Consensus 142 ~~~~C~~C~~~f~ 154 (167)
-|+.|..|+..|=
T Consensus 12 ~~~~C~~C~~~FC 24 (43)
T PF01428_consen 12 LPFKCKHCGKSFC 24 (43)
T ss_dssp SHEE-TTTS-EE-
T ss_pred CCeECCCCCcccC
Confidence 4678888888774
No 150
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=51.19 E-value=20 Score=32.10 Aligned_cols=11 Identities=27% Similarity=0.736 Sum_probs=7.0
Q ss_pred cccCCCCCccc
Q psy4421 115 KFVCYACEYNT 125 (167)
Q Consensus 115 ~~~C~~C~~~~ 125 (167)
+|.|+.|+...
T Consensus 692 vy~CPsCGaev 702 (1337)
T PRK14714 692 VYVCPDCGAEV 702 (1337)
T ss_pred ceeCccCCCcc
Confidence 46677777653
No 151
>PF13878 zf-C2H2_3: zinc-finger of acetyl-transferase ESCO
Probab=51.08 E-value=25 Score=17.52 Aligned_cols=23 Identities=22% Similarity=0.316 Sum_probs=12.0
Q ss_pred ccCCCCCccccCc--hhHHHHHhhh
Q psy4421 116 FVCYACEYNTYMS--GNIKTHLRLH 138 (167)
Q Consensus 116 ~~C~~C~~~~~~~--~~l~~H~~~h 138 (167)
-.|+.|+..|... ..-..|.+.|
T Consensus 14 ~~C~~CgM~Y~~~~~eD~~~H~~yH 38 (41)
T PF13878_consen 14 TTCPTCGMLYSPGSPEDEKLHKKYH 38 (41)
T ss_pred cCCCCCCCEECCCCHHHHHHHHHHH
Confidence 4677777655443 3334454444
No 152
>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=49.80 E-value=8.7 Score=19.21 Aligned_cols=12 Identities=25% Similarity=0.708 Sum_probs=8.4
Q ss_pred CceeCCCCcccc
Q psy4421 142 KPYKCSLCNYEC 153 (167)
Q Consensus 142 ~~~~C~~C~~~f 153 (167)
++-.|++||..|
T Consensus 28 ~~~~CpYCg~~y 39 (40)
T PF10276_consen 28 GPVVCPYCGTRY 39 (40)
T ss_dssp CEEEETTTTEEE
T ss_pred CeEECCCCCCEE
Confidence 356777777766
No 153
>COG4957 Predicted transcriptional regulator [Transcription]
Probab=49.19 E-value=11 Score=24.31 Aligned_cols=21 Identities=19% Similarity=0.290 Sum_probs=13.3
Q ss_pred eeCCCCcccccCchhHHHHhhhcC
Q psy4421 144 YKCSLCNYECRQNVHLKSHMKSNH 167 (167)
Q Consensus 144 ~~C~~C~~~f~~~~~l~~H~~~hh 167 (167)
..|-++|+.|. +|.+|+.+|+
T Consensus 77 IicLEDGkkfK---SLKRHL~t~~ 97 (148)
T COG4957 77 IICLEDGKKFK---SLKRHLTTHY 97 (148)
T ss_pred EEEeccCcchH---HHHHHHhccc
Confidence 56777777765 3566666653
No 154
>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=48.98 E-value=15 Score=20.40 Aligned_cols=13 Identities=23% Similarity=0.892 Sum_probs=7.4
Q ss_pred CCceeCCCCcccc
Q psy4421 141 DKPYKCSLCNYEC 153 (167)
Q Consensus 141 ~~~~~C~~C~~~f 153 (167)
.+.|.|+.||..+
T Consensus 44 ~r~~~C~~Cg~~~ 56 (69)
T PF07282_consen 44 GRVFTCPNCGFEM 56 (69)
T ss_pred cceEEcCCCCCEE
Confidence 3456666666543
No 155
>KOG4167|consensus
Probab=48.97 E-value=3.7 Score=34.03 Aligned_cols=24 Identities=21% Similarity=0.376 Sum_probs=21.8
Q ss_pred ceeCCCCcccccCchhHHHHhhhc
Q psy4421 143 PYKCSLCNYECRQNVHLKSHMKSN 166 (167)
Q Consensus 143 ~~~C~~C~~~f~~~~~l~~H~~~h 166 (167)
-|.|.+|++.|--.-++..|+++|
T Consensus 792 iFpCreC~kvF~KiKSrNAHMK~H 815 (907)
T KOG4167|consen 792 IFPCRECGKVFFKIKSRNAHMKTH 815 (907)
T ss_pred eeehHHHHHHHHHHhhhhHHHHHH
Confidence 489999999999999999999887
No 156
>KOG4167|consensus
Probab=48.11 E-value=2.8 Score=34.73 Aligned_cols=26 Identities=15% Similarity=0.410 Sum_probs=16.9
Q ss_pred cceecCccCccccChHHHHHHHHHhh
Q psy4421 42 YKYGCYRCSYFTYESNNLKKHILKHT 67 (167)
Q Consensus 42 ~~~~C~~C~~~~~~~~~l~~H~~~h~ 67 (167)
.-|.|..|++.|.-...+..|+++|.
T Consensus 791 giFpCreC~kvF~KiKSrNAHMK~Hr 816 (907)
T KOG4167|consen 791 GIFPCRECGKVFFKIKSRNAHMKTHR 816 (907)
T ss_pred ceeehHHHHHHHHHHhhhhHHHHHHH
Confidence 34677777777766666666666554
No 157
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=48.11 E-value=12 Score=22.50 Aligned_cols=30 Identities=17% Similarity=0.421 Sum_probs=16.3
Q ss_pred cccCCCCCccccCchhHHHHHhhhCCCCceeCCCCccccc
Q psy4421 115 KFVCYACEYNTYMSGNIKTHLRLHLDDKPYKCSLCNYECR 154 (167)
Q Consensus 115 ~~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~~f~ 154 (167)
.|.|+.|++.-..+. +...+.|..|++.|.
T Consensus 36 ~y~CpfCgk~~vkR~----------a~GIW~C~~C~~~~A 65 (90)
T PTZ00255 36 KYFCPFCGKHAVKRQ----------AVGIWRCKGCKKTVA 65 (90)
T ss_pred CccCCCCCCCceeee----------eeEEEEcCCCCCEEe
Confidence 467777764422211 124567777777664
No 158
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=47.89 E-value=17 Score=17.99 Aligned_cols=17 Identities=18% Similarity=0.182 Sum_probs=9.2
Q ss_pred eeCCCCcccccCchhHH
Q psy4421 144 YKCSLCNYECRQNVHLK 160 (167)
Q Consensus 144 ~~C~~C~~~f~~~~~l~ 160 (167)
+.|+.|+-.+-...+|.
T Consensus 20 d~C~~C~G~W~d~~el~ 36 (41)
T PF13453_consen 20 DVCPSCGGIWFDAGELE 36 (41)
T ss_pred EECCCCCeEEccHHHHH
Confidence 45666665555555443
No 159
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=47.63 E-value=19 Score=26.82 Aligned_cols=26 Identities=19% Similarity=0.234 Sum_probs=17.6
Q ss_pred cceecCccCccccChHHHHHHHHHhh
Q psy4421 42 YKYGCYRCSYFTYESNNLKKHILKHT 67 (167)
Q Consensus 42 ~~~~C~~C~~~~~~~~~l~~H~~~h~ 67 (167)
..|.|..|...|...-....|...|.
T Consensus 387 ~rY~Ce~CK~~FC~dCdvfiHe~Lh~ 412 (421)
T COG5151 387 GRYQCELCKSTFCSDCDVFIHETLHF 412 (421)
T ss_pred cceechhhhhhhhhhhHHHHHHHHhh
Confidence 34778888877777766666665543
No 160
>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=46.78 E-value=9 Score=22.97 Aligned_cols=30 Identities=20% Similarity=0.455 Sum_probs=16.7
Q ss_pred cccCCCCCccccCchhHHHHHhhhCCCCceeCCCCccccc
Q psy4421 115 KFVCYACEYNTYMSGNIKTHLRLHLDDKPYKCSLCNYECR 154 (167)
Q Consensus 115 ~~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~~f~ 154 (167)
.|.|+.|++.-..+. . -.-+.|..|++.|.
T Consensus 35 ky~Cp~Cgk~~vkR~--------a--~GIW~C~~C~~~~A 64 (90)
T PF01780_consen 35 KYTCPFCGKTSVKRV--------A--TGIWKCKKCGKKFA 64 (90)
T ss_dssp -BEESSSSSSEEEEE--------E--TTEEEETTTTEEEE
T ss_pred CCcCCCCCCceeEEe--------e--eEEeecCCCCCEEe
Confidence 467777776533221 1 23467777777764
No 161
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=46.23 E-value=13 Score=31.21 Aligned_cols=14 Identities=29% Similarity=0.643 Sum_probs=9.7
Q ss_pred CCCCceeCCCCccc
Q psy4421 139 LDDKPYKCSLCNYE 152 (167)
Q Consensus 139 ~~~~~~~C~~C~~~ 152 (167)
....|..|+.||..
T Consensus 471 ~~~~p~~Cp~Cgs~ 484 (730)
T COG1198 471 QEPIPQSCPECGSE 484 (730)
T ss_pred CCCCCCCCCCCCCC
Confidence 34567888888864
No 162
>PF05290 Baculo_IE-1: Baculovirus immediate-early protein (IE-0); InterPro: IPR007954 This entry contains the Baculovirus immediate-early protein IE-0.
Probab=45.19 E-value=17 Score=23.53 Aligned_cols=17 Identities=24% Similarity=0.393 Sum_probs=10.5
Q ss_pred ccceecCccCccccChH
Q psy4421 41 KYKYGCYRCSYFTYESN 57 (167)
Q Consensus 41 ~~~~~C~~C~~~~~~~~ 57 (167)
.+-|+|++|..+...+.
T Consensus 78 ~~lYeCnIC~etS~ee~ 94 (140)
T PF05290_consen 78 PKLYECNICKETSAEER 94 (140)
T ss_pred CCceeccCcccccchhh
Confidence 35577777777654443
No 163
>TIGR00100 hypA hydrogenase nickel insertion protein HypA. In Hpylori, hypA mutant abolished hydrogenase activity and decrease in urease activity. Nickel supplementation in media restored urease activity and partial hydrogenase activity. HypA probably involved in inserting Ni in enzymes.
Probab=44.04 E-value=12 Score=23.56 Aligned_cols=25 Identities=20% Similarity=0.497 Sum_probs=16.5
Q ss_pred cccCCCCCccccCchhHHHHHhhhCCCCceeCCCCcc
Q psy4421 115 KFVCYACEYNTYMSGNIKTHLRLHLDDKPYKCSLCNY 151 (167)
Q Consensus 115 ~~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~ 151 (167)
.+.|..|+..|..... .+.|+.||.
T Consensus 70 ~~~C~~Cg~~~~~~~~------------~~~CP~Cgs 94 (115)
T TIGR00100 70 ECECEDCSEEVSPEID------------LYRCPKCHG 94 (115)
T ss_pred EEEcccCCCEEecCCc------------CccCcCCcC
Confidence 4778888876665421 356888875
No 164
>TIGR01562 FdhE formate dehydrogenase accessory protein FdhE. The only sequence scoring between trusted and noise is that from Aquifex aeolicus, which shows certain structural differences from the proteobacterial forms in the alignment. However it is notable that A. aeolicus also has a sequence scoring above trusted to the alpha subunit of formate dehydrogenase (TIGR01553).
Probab=43.73 E-value=25 Score=26.28 Aligned_cols=8 Identities=38% Similarity=0.795 Sum_probs=6.5
Q ss_pred cccccccc
Q psy4421 81 YCIHCNSY 88 (167)
Q Consensus 81 ~c~~c~~~ 88 (167)
+|+.||..
T Consensus 186 ~CPvCGs~ 193 (305)
T TIGR01562 186 LCPACGSP 193 (305)
T ss_pred cCCCCCCh
Confidence 59999876
No 165
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=43.68 E-value=23 Score=26.45 Aligned_cols=23 Identities=22% Similarity=0.492 Sum_probs=13.5
Q ss_pred CceeCCCCcccccCchhHHHHhh
Q psy4421 142 KPYKCSLCNYECRQNVHLKSHMK 164 (167)
Q Consensus 142 ~~~~C~~C~~~f~~~~~l~~H~~ 164 (167)
..|.|+.|...|-...+.-.|..
T Consensus 387 ~rY~Ce~CK~~FC~dCdvfiHe~ 409 (421)
T COG5151 387 GRYQCELCKSTFCSDCDVFIHET 409 (421)
T ss_pred cceechhhhhhhhhhhHHHHHHH
Confidence 44666666666666555555544
No 166
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=43.58 E-value=12 Score=24.16 Aligned_cols=16 Identities=25% Similarity=0.605 Sum_probs=12.8
Q ss_pred CCCceeCCCCcccccC
Q psy4421 140 DDKPYKCSLCNYECRQ 155 (167)
Q Consensus 140 ~~~~~~C~~C~~~f~~ 155 (167)
|...|.|..|++.|..
T Consensus 50 ~~qRyrC~~C~~tf~~ 65 (129)
T COG3677 50 GHQRYKCKSCGSTFTV 65 (129)
T ss_pred cccccccCCcCcceee
Confidence 3677999999998864
No 167
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=42.93 E-value=13 Score=23.35 Aligned_cols=25 Identities=16% Similarity=0.483 Sum_probs=16.4
Q ss_pred cccCCCCCccccCchhHHHHHhhhCCCCceeCCCCcc
Q psy4421 115 KFVCYACEYNTYMSGNIKTHLRLHLDDKPYKCSLCNY 151 (167)
Q Consensus 115 ~~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~ 151 (167)
.+.|..|+..|.... ..+.|+.||.
T Consensus 70 ~~~C~~Cg~~~~~~~------------~~~~CP~Cgs 94 (113)
T PRK12380 70 QAWCWDCSQVVEIHQ------------HDAQCPHCHG 94 (113)
T ss_pred EEEcccCCCEEecCC------------cCccCcCCCC
Confidence 478888886665532 3356888884
No 168
>COG3091 SprT Zn-dependent metalloprotease, SprT family [General function prediction only]
Probab=42.92 E-value=12 Score=24.72 Aligned_cols=36 Identities=17% Similarity=0.545 Sum_probs=26.0
Q ss_pred CCcccCCCCCccccCchhHHHHHhhhCCCCceeCCCCcccc
Q psy4421 113 HFKFVCYACEYNTYMSGNIKTHLRLHLDDKPYKCSLCNYEC 153 (167)
Q Consensus 113 ~~~~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~~f 153 (167)
-.+|.|. |+..+... ++|-.+-.|+ .|.|..|+-..
T Consensus 115 ~~~Y~C~-C~q~~l~~---RRhn~~~~g~-~YrC~~C~gkL 150 (156)
T COG3091 115 TYPYRCQ-CQQHYLRI---RRHNTVRRGE-VYRCGKCGGKL 150 (156)
T ss_pred ceeEEee-cCCccchh---hhcccccccc-eEEeccCCceE
Confidence 3479999 99886654 5565555666 89999998644
No 169
>KOG0320|consensus
Probab=42.40 E-value=3.8 Score=27.83 Aligned_cols=17 Identities=12% Similarity=0.321 Sum_probs=10.3
Q ss_pred CCcccccccccccCchH
Q psy4421 5 LNINQCVHCHLTLTKST 21 (167)
Q Consensus 5 ~~~~~C~~C~~~f~~~~ 21 (167)
+.-|.|+.|...|..+.
T Consensus 129 ~~~~~CPiCl~~~sek~ 145 (187)
T KOG0320|consen 129 EGTYKCPICLDSVSEKV 145 (187)
T ss_pred ccccCCCceecchhhcc
Confidence 33467777777665544
No 170
>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=42.15 E-value=17 Score=22.36 Aligned_cols=8 Identities=38% Similarity=1.177 Sum_probs=4.9
Q ss_pred eeCCCCcc
Q psy4421 144 YKCSLCNY 151 (167)
Q Consensus 144 ~~C~~C~~ 151 (167)
|.|..|+-
T Consensus 32 y~C~~C~A 39 (102)
T PF11672_consen 32 YVCTPCDA 39 (102)
T ss_pred EECCCCCc
Confidence 66666653
No 171
>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=41.92 E-value=14 Score=22.23 Aligned_cols=12 Identities=17% Similarity=0.564 Sum_probs=7.3
Q ss_pred ceeCCCCccccc
Q psy4421 143 PYKCSLCNYECR 154 (167)
Q Consensus 143 ~~~C~~C~~~f~ 154 (167)
.+.|..|++.|.
T Consensus 53 IW~C~~C~~~~A 64 (91)
T TIGR00280 53 IWTCRKCGAKFA 64 (91)
T ss_pred EEEcCCCCCEEe
Confidence 456666666664
No 172
>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=41.32 E-value=8.4 Score=18.75 Aligned_cols=30 Identities=20% Similarity=0.548 Sum_probs=16.3
Q ss_pred ccCCCCCccccCchhHHHHHhhhCCCCceeCCCC
Q psy4421 116 FVCYACEYNTYMSGNIKTHLRLHLDDKPYKCSLC 149 (167)
Q Consensus 116 ~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C 149 (167)
..|+.|+..- .+..|=....|...|.|..|
T Consensus 6 v~CP~C~s~~----~v~k~G~~~~G~qryrC~~C 35 (36)
T PF03811_consen 6 VHCPRCQSTE----GVKKNGKSPSGHQRYRCKDC 35 (36)
T ss_pred eeCCCCCCCC----cceeCCCCCCCCEeEecCcC
Confidence 3566665432 12334344556667777776
No 173
>cd00065 FYVE FYVE domain; Zinc-binding domain; targets proteins to membrane lipids via interaction with phosphatidylinositol-3-phosphate, PI3P; present in Fab1, YOTB, Vac1, and EEA1;
Probab=40.91 E-value=21 Score=18.79 Aligned_cols=14 Identities=14% Similarity=0.211 Sum_probs=7.0
Q ss_pred CcccCCCCCccccC
Q psy4421 114 FKFVCYACEYNTYM 127 (167)
Q Consensus 114 ~~~~C~~C~~~~~~ 127 (167)
+.+.|..||..|-.
T Consensus 17 rk~~Cr~Cg~~~C~ 30 (57)
T cd00065 17 RRHHCRNCGRIFCS 30 (57)
T ss_pred cccccCcCcCCcCh
Confidence 34455555555443
No 174
>PF07503 zf-HYPF: HypF finger; InterPro: IPR011125 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Proteins of the HypF family are involved in the maturation and regulation of hydrogenase []. In the N terminus they appear to have two zinc finger domains that are similar to those found in the DnaJ chaperone []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3TTD_A 3TSQ_A 3TTC_A 3TSP_A 3TTF_A 3TSU_A.
Probab=40.64 E-value=1.9 Score=20.86 Aligned_cols=12 Identities=17% Similarity=0.393 Sum_probs=5.4
Q ss_pred ceeCCCCccccc
Q psy4421 143 PYKCSLCNYECR 154 (167)
Q Consensus 143 ~~~C~~C~~~f~ 154 (167)
+..|..||-.++
T Consensus 21 ~isC~~CGPr~~ 32 (35)
T PF07503_consen 21 FISCTNCGPRYS 32 (35)
T ss_dssp T--BTTCC-SCC
T ss_pred CccCCCCCCCEE
Confidence 456777765543
No 175
>COG1773 Rubredoxin [Energy production and conversion]
Probab=40.15 E-value=15 Score=19.77 Aligned_cols=12 Identities=33% Similarity=1.065 Sum_probs=8.5
Q ss_pred ceeCCCCccccc
Q psy4421 143 PYKCSLCNYECR 154 (167)
Q Consensus 143 ~~~C~~C~~~f~ 154 (167)
.|+|..||..|.
T Consensus 3 ~~~C~~CG~vYd 14 (55)
T COG1773 3 RWRCSVCGYVYD 14 (55)
T ss_pred ceEecCCceEec
Confidence 577777877664
No 176
>COG1655 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=39.69 E-value=6.7 Score=27.85 Aligned_cols=38 Identities=21% Similarity=0.473 Sum_probs=23.9
Q ss_pred CcccCCCCCccccCchhHHHHHhhhCCC----------Cc-----eeCCCCcc
Q psy4421 114 FKFVCYACEYNTYMSGNIKTHLRLHLDD----------KP-----YKCSLCNY 151 (167)
Q Consensus 114 ~~~~C~~C~~~~~~~~~l~~H~~~h~~~----------~~-----~~C~~C~~ 151 (167)
+.+.||+|+..|....-+..-.|+-+|+ .| ..|+.|..
T Consensus 18 k~ieCPvC~tkFkkeev~tgsiRiiagDld~~lkygninP~fY~VvvCP~C~y 70 (267)
T COG1655 18 KTIECPVCNTKFKKEEVKTGSIRIIAGDLDFFLKYGNINPYFYDVVVCPICYY 70 (267)
T ss_pred ceeccCcccchhhhhheeccceeEecccccceeeccccCCceeEEEEcchhhH
Confidence 4578999988887765444444444442 12 26999986
No 177
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=39.67 E-value=5.6 Score=19.09 Aligned_cols=8 Identities=25% Similarity=1.082 Sum_probs=4.1
Q ss_pred eeCCCCcc
Q psy4421 144 YKCSLCNY 151 (167)
Q Consensus 144 ~~C~~C~~ 151 (167)
+.|+.||.
T Consensus 23 ~vC~~Cg~ 30 (34)
T PF14803_consen 23 LVCPACGF 30 (34)
T ss_dssp EEETTTTE
T ss_pred eECCCCCC
Confidence 45555554
No 178
>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 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=39.11 E-value=23 Score=21.96 Aligned_cols=14 Identities=21% Similarity=0.655 Sum_probs=9.2
Q ss_pred cccCCCCCccccCc
Q psy4421 115 KFVCYACEYNTYMS 128 (167)
Q Consensus 115 ~~~C~~C~~~~~~~ 128 (167)
.|.|+.|+..|...
T Consensus 19 ~~iCpeC~~EW~~~ 32 (109)
T TIGR00686 19 QLICPSCLYEWNEN 32 (109)
T ss_pred eeECcccccccccc
Confidence 47777777666554
No 180
>COG4896 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=38.85 E-value=18 Score=19.91 Aligned_cols=40 Identities=18% Similarity=0.353 Sum_probs=22.2
Q ss_pred cccccccccCChHHHHHHHhhcCCCCCCCCCCCcccCCCCCccccCc
Q psy4421 82 CIHCNSYISSDIKDLIEHCKSCSHMTRPDAFHFKFVCYACEYNTYMS 128 (167)
Q Consensus 82 c~~c~~~~~~~~~~l~~h~~~~~~~~~~~~~~~~~~C~~C~~~~~~~ 128 (167)
|++|++.-+.....+..-... ...-+.|.|+.|.-....+
T Consensus 5 CiiCd~v~~iD~rt~~tKrLr-------N~PIrtymC~eC~~Rva~k 44 (68)
T COG4896 5 CIICDRVDEIDNRTFKTKRLR-------NKPIRTYMCPECEHRVAIK 44 (68)
T ss_pred EEEecceeeecchhHHHHHhh-------CCCceeEechhhHhhhchh
Confidence 888877644444444433222 2333568888887554443
No 181
>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=38.09 E-value=6.6 Score=23.04 Aligned_cols=43 Identities=16% Similarity=0.247 Sum_probs=17.1
Q ss_pred CCCCCcccCCCCCccccCchhHHHHHhhhCCCCceeCCCCcccccCc
Q psy4421 110 DAFHFKFVCYACEYNTYMSGNIKTHLRLHLDDKPYKCSLCNYECRQN 156 (167)
Q Consensus 110 ~~~~~~~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~ 156 (167)
...++.|.|+.|+..-...-.+ ....+.....|..||..|...
T Consensus 17 ~~l~~~F~CPfC~~~~sV~v~i----dkk~~~~~~~C~~Cg~~~~~~ 59 (81)
T PF05129_consen 17 PKLPKVFDCPFCNHEKSVSVKI----DKKEGIGILSCRVCGESFQTK 59 (81)
T ss_dssp ---SS----TTT--SS-EEEEE----ETTTTEEEEEESSS--EEEEE
T ss_pred CCCCceEcCCcCCCCCeEEEEE----EccCCEEEEEecCCCCeEEEc
Confidence 4456789999999332222111 111333457899999988654
No 182
>PF14787 zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB: 1CL4_A 1DSV_A.
Probab=37.70 E-value=16 Score=17.74 Aligned_cols=15 Identities=13% Similarity=0.253 Sum_probs=8.7
Q ss_pred eCCCCcccccCchhH
Q psy4421 145 KCSLCNYECRQNVHL 159 (167)
Q Consensus 145 ~C~~C~~~f~~~~~l 159 (167)
.|..|++.|-+.++-
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 577888888776543
No 183
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=37.64 E-value=16 Score=23.07 Aligned_cols=25 Identities=20% Similarity=0.470 Sum_probs=15.9
Q ss_pred cccCCCCCccccCchhHHHHHhhhCCCCce-eCCCCcc
Q psy4421 115 KFVCYACEYNTYMSGNIKTHLRLHLDDKPY-KCSLCNY 151 (167)
Q Consensus 115 ~~~C~~C~~~~~~~~~l~~H~~~h~~~~~~-~C~~C~~ 151 (167)
.+.|..|+..|..... .| .|+.||.
T Consensus 71 ~~~C~~Cg~~~~~~~~------------~~~~CP~Cgs 96 (117)
T PRK00564 71 ELECKDCSHVFKPNAL------------DYGVCEKCHS 96 (117)
T ss_pred EEEhhhCCCccccCCc------------cCCcCcCCCC
Confidence 4788888866655421 23 4888885
No 184
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=37.42 E-value=26 Score=23.94 Aligned_cols=14 Identities=21% Similarity=0.605 Sum_probs=6.2
Q ss_pred cccccccccccCch
Q psy4421 7 INQCVHCHLTLTKS 20 (167)
Q Consensus 7 ~~~C~~C~~~f~~~ 20 (167)
-|.|+.|...|+..
T Consensus 113 ~y~C~~~~~r~sfd 126 (176)
T COG1675 113 YYVCPNCHVKYSFD 126 (176)
T ss_pred ceeCCCCCCcccHH
Confidence 34444444444333
No 185
>PRK10220 hypothetical protein; Provisional
Probab=37.09 E-value=29 Score=21.62 Aligned_cols=15 Identities=13% Similarity=0.397 Sum_probs=10.5
Q ss_pred cccCCCCCccccCch
Q psy4421 115 KFVCYACEYNTYMSG 129 (167)
Q Consensus 115 ~~~C~~C~~~~~~~~ 129 (167)
.|.|+.|+..|....
T Consensus 20 ~~vCpeC~hEW~~~~ 34 (111)
T PRK10220 20 MYICPECAHEWNDAE 34 (111)
T ss_pred eEECCcccCcCCccc
Confidence 578888887776543
No 186
>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=36.74 E-value=11 Score=24.79 Aligned_cols=33 Identities=21% Similarity=0.487 Sum_probs=22.2
Q ss_pred CcccCCCCCccccCchhHHHHHhhhCCCCceeCCCCccccc
Q psy4421 114 FKFVCYACEYNTYMSGNIKTHLRLHLDDKPYKCSLCNYECR 154 (167)
Q Consensus 114 ~~~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~~f~ 154 (167)
-.|.|..|+..+.... ++ ....|.|..|+..|.
T Consensus 122 ~~~~C~~C~~~~~r~~------~~--~~~~~~C~~C~~~l~ 154 (157)
T PF10263_consen 122 YVYRCPSCGREYKRHR------RS--KRKRYRCGRCGGPLV 154 (157)
T ss_pred eEEEcCCCCCEeeeec------cc--chhhEECCCCCCEEE
Confidence 3689999997764432 22 234499999997664
No 187
>KOG1280|consensus
Probab=36.61 E-value=48 Score=25.24 Aligned_cols=27 Identities=19% Similarity=0.573 Sum_probs=22.1
Q ss_pred cceecCccCccccChHHHHHHHHH-hhC
Q psy4421 42 YKYGCYRCSYFTYESNNLKKHILK-HTG 68 (167)
Q Consensus 42 ~~~~C~~C~~~~~~~~~l~~H~~~-h~~ 68 (167)
..|.|++|+....+...|.-|... |..
T Consensus 78 qSftCPyC~~~Gfte~~f~~Hv~s~Hpd 105 (381)
T KOG1280|consen 78 QSFTCPYCGIMGFTERQFGTHVLSQHPE 105 (381)
T ss_pred ccccCCcccccccchhHHHHHhhhcCcc
Confidence 359999999999999999999855 554
No 188
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=36.46 E-value=20 Score=21.90 Aligned_cols=37 Identities=22% Similarity=0.275 Sum_probs=22.4
Q ss_pred CCCcccCCCCCccccCchhHHHHHhhhCCCCceeCCCCcccccC
Q psy4421 112 FHFKFVCYACEYNTYMSGNIKTHLRLHLDDKPYKCSLCNYECRQ 155 (167)
Q Consensus 112 ~~~~~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~ 155 (167)
....|.|+.|+.. .....+. .+..-..|..||..+..
T Consensus 18 lpt~f~CP~Cge~-~v~v~~~------k~~~h~~C~~CG~y~~~ 54 (99)
T PRK14892 18 LPKIFECPRCGKV-SISVKIK------KNIAIITCGNCGLYTEF 54 (99)
T ss_pred CCcEeECCCCCCe-EeeeecC------CCcceEECCCCCCccCE
Confidence 3467999999942 2211111 13444789999987754
No 189
>PF15135 UPF0515: Uncharacterised protein UPF0515
Probab=36.39 E-value=53 Score=23.77 Aligned_cols=14 Identities=29% Similarity=0.415 Sum_probs=9.1
Q ss_pred cccCCCCCccccCc
Q psy4421 115 KFVCYACEYNTYMS 128 (167)
Q Consensus 115 ~~~C~~C~~~~~~~ 128 (167)
-|.|+.|+..|...
T Consensus 155 ef~C~~C~h~F~G~ 168 (278)
T PF15135_consen 155 EFHCPKCRHNFRGF 168 (278)
T ss_pred eeecccccccchhh
Confidence 36777777766644
No 190
>PRK14873 primosome assembly protein PriA; Provisional
Probab=36.31 E-value=18 Score=30.18 Aligned_cols=10 Identities=20% Similarity=0.949 Sum_probs=6.4
Q ss_pred ceeCCCCccc
Q psy4421 143 PYKCSLCNYE 152 (167)
Q Consensus 143 ~~~C~~C~~~ 152 (167)
+..|+.||..
T Consensus 422 p~~Cp~Cgs~ 431 (665)
T PRK14873 422 DWRCPRCGSD 431 (665)
T ss_pred CccCCCCcCC
Confidence 5667777753
No 191
>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=35.82 E-value=26 Score=27.88 Aligned_cols=21 Identities=24% Similarity=0.490 Sum_probs=10.9
Q ss_pred eeCCCCcccccCchhHHHHhh
Q psy4421 144 YKCSLCNYECRQNVHLKSHMK 164 (167)
Q Consensus 144 ~~C~~C~~~f~~~~~l~~H~~ 164 (167)
..|+.|++.|....++..|+.
T Consensus 58 WiCp~CskkF~d~~~~~~H~~ 78 (466)
T PF04780_consen 58 WICPRCSKKFSDAESCLSHME 78 (466)
T ss_pred eeCCcccceeCCHHHHHHHHH
Confidence 345555555555555555543
No 192
>KOG3214|consensus
Probab=35.35 E-value=25 Score=21.50 Aligned_cols=43 Identities=14% Similarity=0.383 Sum_probs=26.5
Q ss_pred CCCCCcccCCCCCccccCchhHHHHHhhhCCCCceeCCCCcccccCc
Q psy4421 110 DAFHFKFVCYACEYNTYMSGNIKTHLRLHLDDKPYKCSLCNYECRQN 156 (167)
Q Consensus 110 ~~~~~~~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~ 156 (167)
...+..|.|+.|+-.-.....| .....-....|.+|+.+|...
T Consensus 18 ~~ldt~FnClfcnHek~v~~~~----Dk~~~iG~~sC~iC~esFqt~ 60 (109)
T KOG3214|consen 18 EPLDTQFNCLFCNHEKSVSCTL----DKKHNIGKASCRICEESFQTT 60 (109)
T ss_pred cchheeeccCccccccceeeee----hhhcCcceeeeeehhhhhccc
Confidence 4456679999998543222222 122234457899999999764
No 193
>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=35.30 E-value=22 Score=17.95 Aligned_cols=13 Identities=15% Similarity=0.414 Sum_probs=8.4
Q ss_pred eCCCCcccccCch
Q psy4421 145 KCSLCNYECRQNV 157 (167)
Q Consensus 145 ~C~~C~~~f~~~~ 157 (167)
.|..||+.|++.-
T Consensus 10 ~C~~C~rpf~WRK 22 (42)
T PF10013_consen 10 ICPVCGRPFTWRK 22 (42)
T ss_pred cCcccCCcchHHH
Confidence 5777777776543
No 194
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=35.25 E-value=19 Score=21.56 Aligned_cols=12 Identities=17% Similarity=0.595 Sum_probs=6.8
Q ss_pred ceeCCCCccccc
Q psy4421 143 PYKCSLCNYECR 154 (167)
Q Consensus 143 ~~~C~~C~~~f~ 154 (167)
.+.|..|++.|.
T Consensus 54 IW~C~~C~~~~A 65 (90)
T PRK03976 54 IWECRKCGAKFA 65 (90)
T ss_pred EEEcCCCCCEEe
Confidence 356666666553
No 195
>KOG2071|consensus
Probab=34.92 E-value=24 Score=28.71 Aligned_cols=27 Identities=22% Similarity=0.522 Sum_probs=21.5
Q ss_pred CCCceeCCCCcccccCchhHHHHhhhc
Q psy4421 140 DDKPYKCSLCNYECRQNVHLKSHMKSN 166 (167)
Q Consensus 140 ~~~~~~C~~C~~~f~~~~~l~~H~~~h 166 (167)
...+..|..||.+|........|+-.|
T Consensus 415 ~~~pnqC~~CG~R~~~~ee~sk~md~H 441 (579)
T KOG2071|consen 415 KDSPNQCKSCGLRFDDSEERSKHMDIH 441 (579)
T ss_pred cCCcchhcccccccccchhhhhHhhhh
Confidence 356789999999999888777777554
No 196
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=34.86 E-value=12 Score=23.53 Aligned_cols=15 Identities=13% Similarity=0.255 Sum_probs=10.6
Q ss_pred cceecCccCccccCh
Q psy4421 42 YKYGCYRCSYFTYES 56 (167)
Q Consensus 42 ~~~~C~~C~~~~~~~ 56 (167)
..+.|..|+..|...
T Consensus 69 ~~~~C~~Cg~~~~~~ 83 (114)
T PRK03681 69 AECWCETCQQYVTLL 83 (114)
T ss_pred cEEEcccCCCeeecC
Confidence 347788888877654
No 197
>KOG1280|consensus
Probab=34.62 E-value=53 Score=25.03 Aligned_cols=38 Identities=21% Similarity=0.455 Sum_probs=26.2
Q ss_pred CCcccCCCCCccccCchhHHHHHhhhCCCCc--eeCCCCc
Q psy4421 113 HFKFVCYACEYNTYMSGNIKTHLRLHLDDKP--YKCSLCN 150 (167)
Q Consensus 113 ~~~~~C~~C~~~~~~~~~l~~H~~~h~~~~~--~~C~~C~ 150 (167)
+..|.|++|+..-.....|..|...-+-+.+ -.|+.|+
T Consensus 77 ~qSftCPyC~~~Gfte~~f~~Hv~s~Hpda~~~~icp~c~ 116 (381)
T KOG1280|consen 77 PQSFTCPYCGIMGFTERQFGTHVLSQHPEASTSVICPLCA 116 (381)
T ss_pred cccccCCcccccccchhHHHHHhhhcCcccCcceeeeccc
Confidence 3468999999888888888999654332332 4566665
No 198
>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=33.81 E-value=8.1 Score=32.10 Aligned_cols=58 Identities=19% Similarity=0.311 Sum_probs=34.7
Q ss_pred cccccccccCChHHHHHHHhhcCCCCCCCCCCCcccCCCCCccccCchhHHHHHhhhCCCCceeCCCCcccc
Q psy4421 82 CIHCNSYISSDIKDLIEHCKSCSHMTRPDAFHFKFVCYACEYNTYMSGNIKTHLRLHLDDKPYKCSLCNYEC 153 (167)
Q Consensus 82 c~~c~~~~~~~~~~l~~h~~~~~~~~~~~~~~~~~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~~f 153 (167)
|..||-. |+-...|.-.... .+-..---|+.|.+.+....+-+- |+ +|..|+.||-..
T Consensus 126 CT~CGPR-fTIi~alPYDR~n-------TsM~~F~lC~~C~~EY~dP~nRRf----HA--Qp~aCp~CGP~~ 183 (750)
T COG0068 126 CTNCGPR-FTIIEALPYDREN-------TSMADFPLCPFCDKEYKDPLNRRF----HA--QPIACPKCGPHL 183 (750)
T ss_pred cCCCCcc-eeeeccCCCCccc-------CccccCcCCHHHHHHhcCcccccc----cc--ccccCcccCCCe
Confidence 8888877 6554444333222 111122368888888888766443 43 578899999633
No 199
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=33.44 E-value=25 Score=16.66 Aligned_cols=13 Identities=15% Similarity=0.340 Sum_probs=8.1
Q ss_pred CceeCCCCccccc
Q psy4421 142 KPYKCSLCNYECR 154 (167)
Q Consensus 142 ~~~~C~~C~~~f~ 154 (167)
.-+.|..||..|.
T Consensus 20 ~~~~C~~Cg~~~~ 32 (33)
T PF08792_consen 20 DYEVCIFCGSSFP 32 (33)
T ss_pred CeEEcccCCcEee
Confidence 3466777776654
No 200
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=33.21 E-value=39 Score=18.16 Aligned_cols=15 Identities=20% Similarity=0.091 Sum_probs=9.6
Q ss_pred CCCcccCCCCCcccc
Q psy4421 112 FHFKFVCYACEYNTY 126 (167)
Q Consensus 112 ~~~~~~C~~C~~~~~ 126 (167)
++....|+.|+..+.
T Consensus 18 ~dDiVvCp~CgapyH 32 (54)
T PF14446_consen 18 GDDIVVCPECGAPYH 32 (54)
T ss_pred CCCEEECCCCCCccc
Confidence 444567888876643
No 201
>smart00249 PHD PHD zinc finger. The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the PTZ00448 hypothetical protein; Provisional
Probab=32.57 E-value=28 Score=26.69 Aligned_cols=23 Identities=26% Similarity=0.479 Sum_probs=18.9
Q ss_pred ceeCCCCcccccCchhHHHHhhh
Q psy4421 143 PYKCSLCNYECRQNVHLKSHMKS 165 (167)
Q Consensus 143 ~~~C~~C~~~f~~~~~l~~H~~~ 165 (167)
.|.|..|+..|......+.|.++
T Consensus 314 ~~tC~~C~v~F~~~~~qR~H~KS 336 (373)
T PTZ00448 314 MLLCRKCNIQLMDHNAFKQHYRS 336 (373)
T ss_pred CccccccccccCCHHHHHHHhhh
Confidence 57899999999887888888765
No 203
>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=32.32 E-value=32 Score=22.72 Aligned_cols=32 Identities=16% Similarity=0.270 Sum_probs=20.4
Q ss_pred cceecCccCccccChHHHHHHHHHhhCCCCCCcccccCcccccccccccC
Q psy4421 42 YKYGCYRCSYFTYESNNLKKHILKHTGEKPFSYMYENQQYCIHCNSYISS 91 (167)
Q Consensus 42 ~~~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~~~~~~~~~c~~c~~~~~~ 91 (167)
..|.|..||....... ++..| . |+.|+...|.
T Consensus 111 G~l~C~~Cg~~~~~~~---------~~~l~-~--------Cp~C~~~~F~ 142 (146)
T PF07295_consen 111 GTLVCENCGHEVELTH---------PERLP-P--------CPKCGHTEFT 142 (146)
T ss_pred ceEecccCCCEEEecC---------CCcCC-C--------CCCCCCCeee
Confidence 4499999998654322 33333 3 9999887443
No 204
>PF12907 zf-met2: Zinc-binding
Probab=32.30 E-value=23 Score=17.69 Aligned_cols=6 Identities=33% Similarity=1.309 Sum_probs=2.9
Q ss_pred cCCCCC
Q psy4421 117 VCYACE 122 (167)
Q Consensus 117 ~C~~C~ 122 (167)
.|.+|.
T Consensus 3 ~C~iC~ 8 (40)
T PF12907_consen 3 ICKICR 8 (40)
T ss_pred CcHHhh
Confidence 444454
No 205
>KOG2906|consensus
Probab=32.24 E-value=3.5 Score=24.97 Aligned_cols=17 Identities=24% Similarity=0.618 Sum_probs=13.1
Q ss_pred cceecCccCccccChHH
Q psy4421 42 YKYGCYRCSYFTYESNN 58 (167)
Q Consensus 42 ~~~~C~~C~~~~~~~~~ 58 (167)
..|.|+.|++.|.-...
T Consensus 20 ~rf~C~tCpY~~~I~~e 36 (105)
T KOG2906|consen 20 NRFSCRTCPYVFPISRE 36 (105)
T ss_pred eeEEcCCCCceeeEeee
Confidence 46899999998876543
No 206
>PF03833 PolC_DP2: DNA polymerase II large subunit DP2; InterPro: IPR016033 DP2 is the large subunit of a two-subunit novel archaebacterial replicative DNA polymerase first characterised for Pyrococcus furiosus. The structure of DP2 appears to be organised as a ~950 residue component separated from a ~300 residue component by a ~150 residue intein. The other subunit, DP1, has sequence similarity to the eukaryotic DNA polymerase delta small subunit. This entry represents the N-terminal ~950 residue component of DP2.; GO: 0003887 DNA-directed DNA polymerase activity; PDB: 3O59_X.
Probab=31.15 E-value=16 Score=31.14 Aligned_cols=10 Identities=30% Similarity=0.859 Sum_probs=0.0
Q ss_pred cccCCCCCcc
Q psy4421 115 KFVCYACEYN 124 (167)
Q Consensus 115 ~~~C~~C~~~ 124 (167)
.|.|+.|+..
T Consensus 680 ~~~Cp~C~~~ 689 (900)
T PF03833_consen 680 VYVCPDCGIE 689 (900)
T ss_dssp ----------
T ss_pred ceeccccccc
Confidence 3555555543
No 207
>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=30.85 E-value=17 Score=22.66 Aligned_cols=26 Identities=15% Similarity=0.388 Sum_probs=15.4
Q ss_pred cccCCCCCccccCchhHHHHHhhhCCCCceeCCCCccc
Q psy4421 115 KFVCYACEYNTYMSGNIKTHLRLHLDDKPYKCSLCNYE 152 (167)
Q Consensus 115 ~~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~~ 152 (167)
.+.|..|+..|..... .+.|+.||..
T Consensus 70 ~~~C~~Cg~~~~~~~~------------~~~CP~Cgs~ 95 (113)
T PF01155_consen 70 RARCRDCGHEFEPDEF------------DFSCPRCGSP 95 (113)
T ss_dssp EEEETTTS-EEECHHC------------CHH-SSSSSS
T ss_pred cEECCCCCCEEecCCC------------CCCCcCCcCC
Confidence 3678888887766432 1448888764
No 208
>PF07649 C1_3: C1-like domain; InterPro: IPR011424 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in IPR002219 from INTERPRO. C1 domains are protein kinase C-like zinc finger structures. Diacylglycerol (DAG) kinases (DGKs) have a two or three commonly conserved cysteine-rich C1 domains []. DGKs modulate the balance between the two signaling lipids, DAG and phosphatidic acid (PA), by phosphorylating DAG to yield PA []. The PKD (protein kinase D) family are novel DAG receptors. They have twin C1 domains, designated C1a and C1b, which bind DAG or phorbol esters. Individual C1 domains differ in ligand-binding activity and selectivity []. ; GO: 0047134 protein-disulfide reductase activity, 0055114 oxidation-reduction process; PDB: 1V5N_A.
Probab=30.35 E-value=25 Score=15.94 Aligned_cols=10 Identities=20% Similarity=1.075 Sum_probs=3.4
Q ss_pred CcccCCCCCc
Q psy4421 114 FKFVCYACEY 123 (167)
Q Consensus 114 ~~~~C~~C~~ 123 (167)
..|.|.+|..
T Consensus 14 ~~Y~C~~Cdf 23 (30)
T PF07649_consen 14 WFYRCSECDF 23 (30)
T ss_dssp -EEE-TTT--
T ss_pred ceEECccCCC
Confidence 3455555544
No 209
>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=30.32 E-value=44 Score=26.93 Aligned_cols=10 Identities=30% Similarity=0.793 Sum_probs=6.2
Q ss_pred CceeCCCCcc
Q psy4421 142 KPYKCSLCNY 151 (167)
Q Consensus 142 ~~~~C~~C~~ 151 (167)
.|..|+.||.
T Consensus 252 ~~~~Cp~C~s 261 (505)
T TIGR00595 252 IPKTCPQCGS 261 (505)
T ss_pred CCCCCCCCCC
Confidence 3556777764
No 210
>PF04423 Rad50_zn_hook: Rad50 zinc hook motif; InterPro: IPR007517 The Mre11 complex (Mre11 Rad50 Nbs1) is central to chromosomal maintenance and functions in homologous recombination, telomere maintenance and sister chromatid association. The Rad50 coiled-coil region contains a dimer interface at the apex of the coiled coils in which pairs of conserved Cys-X-X-Cys motifs form interlocking hooks that bind one Zn ion. This alignment includes the zinc hook motif and a short stretch of coiled-coil on either side.; GO: 0004518 nuclease activity, 0005524 ATP binding, 0008270 zinc ion binding, 0006281 DNA repair; PDB: 1L8D_B.
Probab=30.19 E-value=23 Score=18.71 Aligned_cols=11 Identities=27% Similarity=0.685 Sum_probs=5.8
Q ss_pred eCCCCcccccC
Q psy4421 145 KCSLCNYECRQ 155 (167)
Q Consensus 145 ~C~~C~~~f~~ 155 (167)
.|+.|++.|..
T Consensus 22 ~CPlC~r~l~~ 32 (54)
T PF04423_consen 22 CCPLCGRPLDE 32 (54)
T ss_dssp E-TTT--EE-H
T ss_pred cCCCCCCCCCH
Confidence 89999988875
No 211
>PRK00420 hypothetical protein; Validated
Probab=30.04 E-value=45 Score=20.95 Aligned_cols=13 Identities=15% Similarity=0.151 Sum_probs=8.3
Q ss_pred cccCCCCCccccC
Q psy4421 115 KFVCYACEYNTYM 127 (167)
Q Consensus 115 ~~~C~~C~~~~~~ 127 (167)
...|+.|+....-
T Consensus 40 ~~~Cp~Cg~~~~v 52 (112)
T PRK00420 40 EVVCPVHGKVYIV 52 (112)
T ss_pred ceECCCCCCeeee
Confidence 4568888875443
No 212
>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=29.89 E-value=34 Score=16.55 Aligned_cols=25 Identities=28% Similarity=0.546 Sum_probs=13.7
Q ss_pred ccCCCCCccccCchhHHHHHhhhCCCCceeCCCCcc
Q psy4421 116 FVCYACEYNTYMSGNIKTHLRLHLDDKPYKCSLCNY 151 (167)
Q Consensus 116 ~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~ 151 (167)
..|++|+..+.. ..+..|.|..||-
T Consensus 9 ~~C~~C~~~~~~-----------~~dG~~yC~~cG~ 33 (36)
T PF11781_consen 9 EPCPVCGSRWFY-----------SDDGFYYCDRCGH 33 (36)
T ss_pred CcCCCCCCeEeE-----------ccCCEEEhhhCce
Confidence 347777755222 2245666766663
No 213
>PRK05978 hypothetical protein; Provisional
Probab=29.45 E-value=20 Score=23.74 Aligned_cols=31 Identities=19% Similarity=0.386 Sum_probs=17.7
Q ss_pred ccCCCCCccccCchhHHHHHhhhCCCCceeCCCCcccccC
Q psy4421 116 FVCYACEYNTYMSGNIKTHLRLHLDDKPYKCSLCNYECRQ 155 (167)
Q Consensus 116 ~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~ 155 (167)
-+|+.|++.-...+-|. -.-.|+.||..|..
T Consensus 34 grCP~CG~G~LF~g~Lk---------v~~~C~~CG~~~~~ 64 (148)
T PRK05978 34 GRCPACGEGKLFRAFLK---------PVDHCAACGEDFTH 64 (148)
T ss_pred CcCCCCCCCcccccccc---------cCCCccccCCcccc
Confidence 37888876544333222 12358888877754
No 214
>COG4391 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=29.34 E-value=36 Score=18.79 Aligned_cols=42 Identities=17% Similarity=0.260 Sum_probs=20.9
Q ss_pred CCCCCcccCCCCCccccCchhHHHHHhhhCCCCceeCCCCcccccC
Q psy4421 110 DAFHFKFVCYACEYNTYMSGNIKTHLRLHLDDKPYKCSLCNYECRQ 155 (167)
Q Consensus 110 ~~~~~~~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~ 155 (167)
..+..++.|+.-+..+...--+ +.+ ..+.--.|++|+..|+.
T Consensus 19 ~~~~~~l~C~g~~~p~~HPrV~---L~m-g~~gev~CPYC~t~y~l 60 (62)
T COG4391 19 EIGDLPLMCPGPEPPNDHPRVF---LDM-GDEGEVVCPYCSTRYRL 60 (62)
T ss_pred EeCCeeEEcCCCCCCCCCCEEE---EEc-CCCCcEecCccccEEEe
Confidence 3445566666554442222110 111 22344678888888764
No 215
>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=28.95 E-value=30 Score=21.07 Aligned_cols=20 Identities=25% Similarity=0.537 Sum_probs=15.0
Q ss_pred HhhhCCCCceeCCCCcccccC
Q psy4421 135 LRLHLDDKPYKCSLCNYECRQ 155 (167)
Q Consensus 135 ~~~h~~~~~~~C~~C~~~f~~ 155 (167)
+..+.| +++.|..||.-|.-
T Consensus 72 ~~l~~g-~~~rC~eCG~~fkL 91 (97)
T cd00924 72 MWLEKG-KPKRCPECGHVFKL 91 (97)
T ss_pred EEEeCC-CceeCCCCCcEEEE
Confidence 445565 78999999988853
No 216
>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=28.76 E-value=30 Score=16.86 Aligned_cols=11 Identities=36% Similarity=0.751 Sum_probs=5.3
Q ss_pred ceeCCCCcccc
Q psy4421 143 PYKCSLCNYEC 153 (167)
Q Consensus 143 ~~~C~~C~~~f 153 (167)
-|+|..||...
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 47788887644
No 217
>TIGR00627 tfb4 transcription factor tfb4. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=27.29 E-value=50 Score=24.41 Aligned_cols=25 Identities=24% Similarity=0.450 Sum_probs=15.2
Q ss_pred cccCCCCCccccCchhHHHHHhhhCCCCceeCCCCcccc
Q psy4421 115 KFVCYACEYNTYMSGNIKTHLRLHLDDKPYKCSLCNYEC 153 (167)
Q Consensus 115 ~~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~~f 153 (167)
.|.|+.|...|-.. |-.|+.||-.|
T Consensus 255 GyvCs~Clsi~C~~--------------p~~C~~Cgt~f 279 (279)
T TIGR00627 255 GFVCSVCLSVLCQY--------------TPICKTCKTAF 279 (279)
T ss_pred eEECCCccCCcCCC--------------CCCCCCCCCCC
Confidence 37777776665532 23677777655
No 218
>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=27.02 E-value=33 Score=17.81 Aligned_cols=11 Identities=36% Similarity=1.210 Sum_probs=7.8
Q ss_pred eeCCCCccccc
Q psy4421 144 YKCSLCNYECR 154 (167)
Q Consensus 144 ~~C~~C~~~f~ 154 (167)
|.|..||..+.
T Consensus 2 y~C~~CgyvYd 12 (47)
T PF00301_consen 2 YQCPVCGYVYD 12 (47)
T ss_dssp EEETTTSBEEE
T ss_pred cCCCCCCEEEc
Confidence 67888886654
No 219
>PF00628 PHD: PHD-finger; InterPro: IPR019787 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the PHD (homeodomain) zinc finger domain [,], which is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in chromatin-mediated transcriptional regulation. The PHD finger motif is reminiscent of, but distinct from the C3HC4 type RING finger. The function of this domain is not yet known but in analogy with the LIM domain it could be involved in protein-protein interaction and be important for the assembly or activity of multicomponent complexes involved in transcriptional activation or repression. Alternatively, the interactions could be intra-molecular and be important in maintaining the structural integrity of the protein. In similarity to the RING finger and the LIM domain, the PHD finger is thought to bind two zinc ions. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0005515 protein binding; PDB: 3ZVY_A 2LGG_A 3SOW_A 3SOU_B 3ASL_A 3ASK_A 3ZVZ_B 3T6R_A 2LGK_A 3SOX_B ....
Probab=26.64 E-value=54 Score=16.70 Aligned_cols=19 Identities=16% Similarity=0.072 Sum_probs=12.9
Q ss_pred CCCCCcccCCCCCccccCc
Q psy4421 110 DAFHFKFVCYACEYNTYMS 128 (167)
Q Consensus 110 ~~~~~~~~C~~C~~~~~~~ 128 (167)
........|..|+..|...
T Consensus 9 ~~~~~~i~C~~C~~~~H~~ 27 (51)
T PF00628_consen 9 DDDGDMIQCDSCNRWYHQE 27 (51)
T ss_dssp CTTSSEEEBSTTSCEEETT
T ss_pred CCCCCeEEcCCCChhhCcc
Confidence 4455667888888776654
No 220
>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=26.49 E-value=16 Score=22.30 Aligned_cols=38 Identities=26% Similarity=0.520 Sum_probs=22.4
Q ss_pred cccCCCCCccccCchhHHHHHhhhCCCC---ceeCCCCcccccC
Q psy4421 115 KFVCYACEYNTYMSGNIKTHLRLHLDDK---PYKCSLCNYECRQ 155 (167)
Q Consensus 115 ~~~C~~C~~~~~~~~~l~~H~~~h~~~~---~~~C~~C~~~f~~ 155 (167)
...|+.|+..-.....++ .|. ++|. -|.|..|+..++.
T Consensus 62 ~~~Cp~Cg~~~a~f~~~Q--~Rs-adE~~T~fy~C~~C~~~w~~ 102 (104)
T TIGR01384 62 RVECPKCGHKEAYYWLLQ--TRR-ADEPETRFYKCTKCGYVWRE 102 (104)
T ss_pred cCCCCCCCCCeeEEEEec--cCC-CCCCcEEEEEeCCCCCeeEe
Confidence 368999986554443332 121 3332 2899999977653
No 221
>KOG2636|consensus
Probab=26.32 E-value=51 Score=26.04 Aligned_cols=25 Identities=28% Similarity=0.639 Sum_probs=11.1
Q ss_pred hCCCCceeCCCCc-ccccCchhHHHH
Q psy4421 138 HLDDKPYKCSLCN-YECRQNVHLKSH 162 (167)
Q Consensus 138 h~~~~~~~C~~C~-~~f~~~~~l~~H 162 (167)
|.-..-|.|.+|| +++.=+-.+.+|
T Consensus 396 HGL~~ey~CEICGNy~Y~GrkaF~RH 421 (497)
T KOG2636|consen 396 HGLDIEYNCEICGNYVYKGRKAFDRH 421 (497)
T ss_pred cCCCcccceeeccCccccCcHHHHHH
Confidence 4444455555555 333333344444
No 222
>COG1779 C4-type Zn-finger protein [General function prediction only]
Probab=26.00 E-value=15 Score=25.51 Aligned_cols=12 Identities=25% Similarity=0.686 Sum_probs=7.6
Q ss_pred eeCCCCcccccC
Q psy4421 144 YKCSLCNYECRQ 155 (167)
Q Consensus 144 ~~C~~C~~~f~~ 155 (167)
+.|..||+++..
T Consensus 44 ~~C~~CgYR~~D 55 (201)
T COG1779 44 GVCERCGYRSTD 55 (201)
T ss_pred EEccccCCcccc
Confidence 467777766653
No 223
>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=25.80 E-value=15 Score=18.13 Aligned_cols=15 Identities=20% Similarity=0.563 Sum_probs=8.6
Q ss_pred CCCCceeCCCCcccc
Q psy4421 139 LDDKPYKCSLCNYEC 153 (167)
Q Consensus 139 ~~~~~~~C~~C~~~f 153 (167)
.+.+.+.|..|+..-
T Consensus 20 ~~~~~w~C~~C~~~N 34 (40)
T PF04810_consen 20 DGGKTWICNFCGTKN 34 (40)
T ss_dssp TTTTEEEETTT--EE
T ss_pred CCCCEEECcCCCCcC
Confidence 345678888887644
No 224
>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=25.54 E-value=32 Score=18.12 Aligned_cols=11 Identities=36% Similarity=1.189 Sum_probs=8.0
Q ss_pred eeCCCCccccc
Q psy4421 144 YKCSLCNYECR 154 (167)
Q Consensus 144 ~~C~~C~~~f~ 154 (167)
|+|..||+.+.
T Consensus 2 y~C~~CgyiYd 12 (50)
T cd00730 2 YECRICGYIYD 12 (50)
T ss_pred cCCCCCCeEEC
Confidence 67888887665
No 225
>PF09963 DUF2197: Uncharacterized protein conserved in bacteria (DUF2197); InterPro: IPR019241 This family represents various hypothetical bacterial proteins with no known function.
Probab=25.01 E-value=33 Score=18.59 Aligned_cols=7 Identities=43% Similarity=1.203 Sum_probs=4.2
Q ss_pred ccccccc
Q psy4421 82 CIHCNSY 88 (167)
Q Consensus 82 c~~c~~~ 88 (167)
|..|++.
T Consensus 5 C~lCdk~ 11 (56)
T PF09963_consen 5 CILCDKK 11 (56)
T ss_pred EEecCCE
Confidence 5666655
No 226
>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=24.79 E-value=24 Score=16.44 Aligned_cols=10 Identities=20% Similarity=0.700 Sum_probs=6.8
Q ss_pred eecCccCccc
Q psy4421 44 YGCYRCSYFT 53 (167)
Q Consensus 44 ~~C~~C~~~~ 53 (167)
|.|..|+..+
T Consensus 28 f~C~~C~~~L 37 (39)
T smart00132 28 FKCSKCGKPL 37 (39)
T ss_pred CCCcccCCcC
Confidence 6777777654
No 227
>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=24.58 E-value=63 Score=21.17 Aligned_cols=18 Identities=17% Similarity=0.429 Sum_probs=11.2
Q ss_pred CceeCCCCcccccCchhH
Q psy4421 142 KPYKCSLCNYECRQNVHL 159 (167)
Q Consensus 142 ~~~~C~~C~~~f~~~~~l 159 (167)
.-+.|+.||+.|=..+-+
T Consensus 123 ~f~~C~~C~kiyW~GsH~ 140 (147)
T PF01927_consen 123 EFWRCPGCGKIYWEGSHW 140 (147)
T ss_pred eEEECCCCCCEecccccH
Confidence 346788888766444443
No 228
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=24.54 E-value=98 Score=16.36 Aligned_cols=31 Identities=16% Similarity=0.323 Sum_probs=15.7
Q ss_pred cCCCCCccccCchhHHHHHhhhCCCCceeCCCCcc
Q psy4421 117 VCYACEYNTYMSGNIKTHLRLHLDDKPYKCSLCNY 151 (167)
Q Consensus 117 ~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~ 151 (167)
.|..|+....... . .++..++....|+.||+
T Consensus 24 ~C~gC~~~l~~~~--~--~~i~~~~~i~~Cp~CgR 54 (56)
T PF02591_consen 24 TCSGCHMELPPQE--L--NEIRKGDEIVFCPNCGR 54 (56)
T ss_pred ccCCCCEEcCHHH--H--HHHHcCCCeEECcCCCc
Confidence 5666655433321 1 22233355677777775
No 229
>KOG2071|consensus
Probab=24.21 E-value=58 Score=26.65 Aligned_cols=28 Identities=21% Similarity=0.256 Sum_probs=23.0
Q ss_pred CccceecCccCccccChHHHHHHHHHhh
Q psy4421 40 FKYKYGCYRCSYFTYESNNLKKHILKHT 67 (167)
Q Consensus 40 ~~~~~~C~~C~~~~~~~~~l~~H~~~h~ 67 (167)
...+..|..||..|.......+|+..|.
T Consensus 415 ~~~pnqC~~CG~R~~~~ee~sk~md~H~ 442 (579)
T KOG2071|consen 415 KDSPNQCKSCGLRFDDSEERSKHMDIHD 442 (579)
T ss_pred cCCcchhcccccccccchhhhhHhhhhh
Confidence 4567899999999999988888877664
No 230
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=23.88 E-value=31 Score=22.01 Aligned_cols=13 Identities=23% Similarity=0.797 Sum_probs=9.0
Q ss_pred cccCCCCCccccCc
Q psy4421 115 KFVCYACEYNTYMS 128 (167)
Q Consensus 115 ~~~C~~C~~~~~~~ 128 (167)
.+.| .|+..|...
T Consensus 70 ~~~C-~Cg~~~~~~ 82 (124)
T PRK00762 70 EIEC-ECGYEGVVD 82 (124)
T ss_pred eEEe-eCcCccccc
Confidence 4788 888776654
No 231
>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=23.48 E-value=30 Score=16.61 Aligned_cols=13 Identities=23% Similarity=0.534 Sum_probs=6.2
Q ss_pred cccccccccCchH
Q psy4421 9 QCVHCHLTLTKST 21 (167)
Q Consensus 9 ~C~~C~~~f~~~~ 21 (167)
.|.+|++.|....
T Consensus 5 ~C~eC~~~f~dSy 17 (34)
T PF01286_consen 5 KCDECGKPFMDSY 17 (34)
T ss_dssp E-TTT--EES-SS
T ss_pred hHhHhCCHHHHHH
Confidence 5788888886644
No 232
>smart00731 SprT SprT homologues. Predicted to have roles in transcription elongation. Contains a conserved HExxH motif, indicating a metalloprotease function.
Probab=23.46 E-value=28 Score=22.75 Aligned_cols=34 Identities=18% Similarity=0.439 Sum_probs=22.2
Q ss_pred CcccCCCCCccccCchhHHHHHhhhCCCCceeCCCCccccc
Q psy4421 114 FKFVCYACEYNTYMSGNIKTHLRLHLDDKPYKCSLCNYECR 154 (167)
Q Consensus 114 ~~~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~~f~ 154 (167)
-.|.|..|+..+.. +.+ +..-..|.|..|+-.+.
T Consensus 111 ~~y~C~~C~~~~~~------~rr-~~~~~~y~C~~C~g~l~ 144 (146)
T smart00731 111 YPYRCTGCGQRYLR------VRR-SNNVSRYRCGKCGGKLI 144 (146)
T ss_pred EEEECCCCCCCCce------Ecc-ccCcceEEcCCCCCEEE
Confidence 37899989977642 222 22226699999987664
No 233
>PRK04351 hypothetical protein; Provisional
Probab=23.26 E-value=51 Score=21.83 Aligned_cols=35 Identities=20% Similarity=0.517 Sum_probs=23.9
Q ss_pred CcccCCCCCccccCchhHHHHHhhhCCCCceeCCCCcccccCc
Q psy4421 114 FKFVCYACEYNTYMSGNIKTHLRLHLDDKPYKCSLCNYECRQN 156 (167)
Q Consensus 114 ~~~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~ 156 (167)
-.|.|..|+..+... ++ + +...|.|..|+-.+...
T Consensus 111 y~Y~C~~Cg~~~~r~------Rr-~-n~~~yrCg~C~g~L~~~ 145 (149)
T PRK04351 111 YLYECQSCGQQYLRK------RR-I-NTKRYRCGKCRGKLKLI 145 (149)
T ss_pred EEEECCCCCCEeeee------ee-c-CCCcEEeCCCCcEeeec
Confidence 369999999765432 22 2 24679999999776544
No 234
>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=23.21 E-value=42 Score=17.80 Aligned_cols=17 Identities=12% Similarity=0.384 Sum_probs=10.6
Q ss_pred CCCCceeCCCCcccccC
Q psy4421 139 LDDKPYKCSLCNYECRQ 155 (167)
Q Consensus 139 ~~~~~~~C~~C~~~f~~ 155 (167)
.+...|.|.+|++.|..
T Consensus 31 ~~~~~~rC~YCe~~~~~ 47 (52)
T PF02748_consen 31 KEPIKLRCHYCERIITE 47 (52)
T ss_dssp TTTCEEEETTT--EEEH
T ss_pred CCCCEEEeeCCCCEecc
Confidence 44566889999887754
No 235
>PRK12496 hypothetical protein; Provisional
Probab=22.84 E-value=59 Score=21.87 Aligned_cols=28 Identities=18% Similarity=0.412 Sum_probs=18.3
Q ss_pred cccCCCCCccccCchhHHHHHhhhCCCCceeCCCCccccc
Q psy4421 115 KFVCYACEYNTYMSGNIKTHLRLHLDDKPYKCSLCNYECR 154 (167)
Q Consensus 115 ~~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~~f~ 154 (167)
.|.|..|++.|.... ..-.|+.||....
T Consensus 127 ~~~C~gC~~~~~~~~------------~~~~C~~CG~~~~ 154 (164)
T PRK12496 127 RKVCKGCKKKYPEDY------------PDDVCEICGSPVK 154 (164)
T ss_pred eEECCCCCccccCCC------------CCCcCCCCCChhh
Confidence 378999998875421 1135999986543
No 236
>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=22.53 E-value=1e+02 Score=14.63 Aligned_cols=11 Identities=18% Similarity=0.331 Sum_probs=5.5
Q ss_pred eecCccCcccc
Q psy4421 44 YGCYRCSYFTY 54 (167)
Q Consensus 44 ~~C~~C~~~~~ 54 (167)
+.|+.|++.+.
T Consensus 5 ~~C~nC~R~v~ 15 (33)
T PF08209_consen 5 VECPNCGRPVA 15 (33)
T ss_dssp EE-TTTSSEEE
T ss_pred EECCCCcCCcc
Confidence 55666666543
No 237
>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=22.44 E-value=68 Score=19.50 Aligned_cols=40 Identities=15% Similarity=0.188 Sum_probs=16.6
Q ss_pred cCCcccccccccccCchHHHHHHhhhhhccccCCCCCccceecCccCccccCh
Q psy4421 4 SLNINQCVHCHLTLTKSTEVIVKHAQTCISMVRPDSFKYKYGCYRCSYFTYES 56 (167)
Q Consensus 4 ~~~~~~C~~C~~~f~~~~~l~~~~~~~~~~h~~~~~~~~~~~C~~C~~~~~~~ 56 (167)
+.|.-.|..|+.+.... ...+...+--|-|..|.+-|.+.
T Consensus 11 g~ke~~CalCG~tWg~~-------------y~Ev~G~rLfFCCd~ca~EF~nm 50 (105)
T PF11494_consen 11 GTKEMGCALCGATWGDY-------------YEEVDGERLFFCCDDCAKEFKNM 50 (105)
T ss_dssp -SGGGS-SS---S---S-------------S-B-TT--BSSS--SSSS-TTS-
T ss_pred ccccccccccCCcHHHH-------------HHhhcCCEEEEEcHHHHHHHHHH
Confidence 56777888888886532 23444444557789999888776
No 238
>PLN03238 probable histone acetyltransferase MYST; Provisional
Probab=22.37 E-value=69 Score=23.79 Aligned_cols=24 Identities=17% Similarity=0.283 Sum_probs=14.7
Q ss_pred CCcccCCCCCccccCchhHHHHHh
Q psy4421 113 HFKFVCYACEYNTYMSGNIKTHLR 136 (167)
Q Consensus 113 ~~~~~C~~C~~~~~~~~~l~~H~~ 136 (167)
...|.|+.|-+-|.....|.+|+.
T Consensus 46 ~~lyiCe~Clky~~~~~~l~~H~~ 69 (290)
T PLN03238 46 TKLYICEYCLKYMRKKKSLLRHLA 69 (290)
T ss_pred CeEEEcCCCcchhCCHHHHHHHHH
Confidence 345666666666666666666643
No 239
>PLN02294 cytochrome c oxidase subunit Vb
Probab=22.16 E-value=56 Score=22.18 Aligned_cols=20 Identities=20% Similarity=0.534 Sum_probs=14.8
Q ss_pred HhhhCCCCceeCCCCcccccC
Q psy4421 135 LRLHLDDKPYKCSLCNYECRQ 155 (167)
Q Consensus 135 ~~~h~~~~~~~C~~C~~~f~~ 155 (167)
+..+.| +++.|..||..|.-
T Consensus 134 f~L~kG-kp~RCpeCG~~fkL 153 (174)
T PLN02294 134 FWLEKG-KSFECPVCTQYFEL 153 (174)
T ss_pred EEecCC-CceeCCCCCCEEEE
Confidence 344554 68999999998864
No 240
>COG4640 Predicted membrane protein [Function unknown]
Probab=22.16 E-value=65 Score=25.12 Aligned_cols=18 Identities=11% Similarity=0.182 Sum_probs=13.4
Q ss_pred cccCCCCCccccCchhHH
Q psy4421 115 KFVCYACEYNTYMSGNIK 132 (167)
Q Consensus 115 ~~~C~~C~~~~~~~~~l~ 132 (167)
.+.|++||..|..+..+-
T Consensus 15 ~~qC~qCG~~~t~~~sqa 32 (465)
T COG4640 15 DVQCTQCGHKFTSRQSQA 32 (465)
T ss_pred cccccccCCcCCchhhhh
Confidence 345999999888876543
No 241
>KOG2636|consensus
Probab=22.04 E-value=61 Score=25.65 Aligned_cols=28 Identities=18% Similarity=0.484 Sum_probs=20.9
Q ss_pred CCCCccceecCccC-ccccChHHHHHHHH
Q psy4421 37 PDSFKYKYGCYRCS-YFTYESNNLKKHIL 64 (167)
Q Consensus 37 ~~~~~~~~~C~~C~-~~~~~~~~l~~H~~ 64 (167)
.|.-...|.|.+|| +++.....+.+|-.
T Consensus 395 LHGL~~ey~CEICGNy~Y~GrkaF~RHF~ 423 (497)
T KOG2636|consen 395 LHGLDIEYNCEICGNYVYKGRKAFDRHFN 423 (497)
T ss_pred hcCCCcccceeeccCccccCcHHHHHHhH
Confidence 34444559999999 67778888888864
No 242
>PLN02748 tRNA dimethylallyltransferase
Probab=22.02 E-value=59 Score=25.99 Aligned_cols=24 Identities=21% Similarity=0.454 Sum_probs=20.2
Q ss_pred CceeCCCCcc-cccCchhHHHHhhh
Q psy4421 142 KPYKCSLCNY-ECRQNVHLKSHMKS 165 (167)
Q Consensus 142 ~~~~C~~C~~-~f~~~~~l~~H~~~ 165 (167)
+.|.|..|++ .+.-..++..|+++
T Consensus 417 ~~~~Ce~C~~~~~~G~~eW~~Hlks 441 (468)
T PLN02748 417 TQYVCEACGNKVLRGAHEWEQHKQG 441 (468)
T ss_pred ccccccCCCCcccCCHHHHHHHhcc
Confidence 5688999997 78888899999864
No 243
>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=21.63 E-value=31 Score=26.29 Aligned_cols=16 Identities=25% Similarity=0.538 Sum_probs=6.7
Q ss_pred ccccccccccCchHHH
Q psy4421 8 NQCVHCHLTLTKSTEV 23 (167)
Q Consensus 8 ~~C~~C~~~f~~~~~l 23 (167)
+.|..|..+....+..
T Consensus 253 v~C~~C~yt~~~~~~~ 268 (344)
T PF09332_consen 253 VTCKQCKYTAFKPSDR 268 (344)
T ss_dssp EEETTT--EESS--HH
T ss_pred EEcCCCCCcccCcchh
Confidence 5566666665554443
No 244
>COG5112 UFD2 U1-like Zn-finger-containing protein [General function prediction only]
Probab=21.47 E-value=46 Score=20.58 Aligned_cols=20 Identities=20% Similarity=0.200 Sum_probs=9.7
Q ss_pred eeCCCCcccccCchhHHHHh
Q psy4421 144 YKCSLCNYECRQNVHLKSHM 163 (167)
Q Consensus 144 ~~C~~C~~~f~~~~~l~~H~ 163 (167)
+-|..|.+-|.+.-.|..|.
T Consensus 56 hYCieCaryf~t~~aL~~Hk 75 (126)
T COG5112 56 HYCIECARYFITEKALMEHK 75 (126)
T ss_pred eeeehhHHHHHHHHHHHHHh
Confidence 44444555555444444444
No 245
>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=21.23 E-value=19 Score=30.13 Aligned_cols=41 Identities=17% Similarity=0.112 Sum_probs=20.2
Q ss_pred ccccccccCchHHHHHHhhhhhccccCCCCCccceecCccCccccChHH
Q psy4421 10 CVHCHLTLTKSTEVIVKHAQTCISMVRPDSFKYKYGCYRCSYFTYESNN 58 (167)
Q Consensus 10 C~~C~~~f~~~~~l~~~~~~~~~~h~~~~~~~~~~~C~~C~~~~~~~~~ 58 (167)
|..||..|.-..+|- --...-+...--.|+.|.+-+....+
T Consensus 126 CT~CGPRfTIi~alP--------YDR~nTsM~~F~lC~~C~~EY~dP~n 166 (750)
T COG0068 126 CTNCGPRFTIIEALP--------YDRENTSMADFPLCPFCDKEYKDPLN 166 (750)
T ss_pred cCCCCcceeeeccCC--------CCcccCccccCcCCHHHHHHhcCccc
Confidence 666776666555443 22221122221237777766655554
No 246
>KOG2857|consensus
Probab=21.17 E-value=52 Score=21.56 Aligned_cols=22 Identities=23% Similarity=0.339 Sum_probs=19.9
Q ss_pred cccCCCCCccccCchhHHHHHh
Q psy4421 115 KFVCYACEYNTYMSGNIKTHLR 136 (167)
Q Consensus 115 ~~~C~~C~~~~~~~~~l~~H~~ 136 (167)
.|+|+.|...+-+..-++.|+.
T Consensus 17 KYKCpkC~vPYCSl~CfKiHk~ 38 (157)
T KOG2857|consen 17 KYKCPKCSVPYCSLPCFKIHKS 38 (157)
T ss_pred hccCCCCCCccccchhhhhccC
Confidence 5899999999999999999876
No 247
>KOG0717|consensus
Probab=20.93 E-value=60 Score=25.84 Aligned_cols=21 Identities=24% Similarity=0.284 Sum_probs=18.1
Q ss_pred eecCccCccccChHHHHHHHH
Q psy4421 44 YGCYRCSYFTYESNNLKKHIL 64 (167)
Q Consensus 44 ~~C~~C~~~~~~~~~l~~H~~ 64 (167)
+-|..|+++|.+...|..|..
T Consensus 293 lyC~vCnKsFKseKq~kNHEn 313 (508)
T KOG0717|consen 293 LYCVVCNKSFKSEKQLKNHEN 313 (508)
T ss_pred eEEeeccccccchHHHHhhHH
Confidence 669999999999998888864
No 248
>PF13821 DUF4187: Domain of unknown function (DUF4187)
Probab=20.83 E-value=53 Score=17.64 Aligned_cols=17 Identities=29% Similarity=0.636 Sum_probs=12.2
Q ss_pred cccccccccCChHHHHHH
Q psy4421 82 CIHCNSYISSDIKDLIEH 99 (167)
Q Consensus 82 c~~c~~~~~~~~~~l~~h 99 (167)
|..|+.. +.+...|..+
T Consensus 30 C~~Cg~~-Y~d~~dL~~~ 46 (55)
T PF13821_consen 30 CFWCGTK-YDDEEDLERN 46 (55)
T ss_pred eeeeCCc-cCCHHHHHhC
Confidence 8888877 7777666654
No 249
>COG4338 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=20.80 E-value=32 Score=17.90 Aligned_cols=14 Identities=14% Similarity=0.406 Sum_probs=9.0
Q ss_pred eCCCCcccccCchh
Q psy4421 145 KCSLCNYECRQNVH 158 (167)
Q Consensus 145 ~C~~C~~~f~~~~~ 158 (167)
.|+.|++-|++.-.
T Consensus 14 ICpvCqRPFsWRkK 27 (54)
T COG4338 14 ICPVCQRPFSWRKK 27 (54)
T ss_pred hhhhhcCchHHHHH
Confidence 57777777766543
No 250
>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=20.72 E-value=45 Score=16.14 Aligned_cols=12 Identities=17% Similarity=0.321 Sum_probs=7.3
Q ss_pred eeCCCCcccccC
Q psy4421 144 YKCSLCNYECRQ 155 (167)
Q Consensus 144 ~~C~~C~~~f~~ 155 (167)
..|+.||..|.-
T Consensus 2 r~C~~Cg~~Yh~ 13 (36)
T PF05191_consen 2 RICPKCGRIYHI 13 (36)
T ss_dssp EEETTTTEEEET
T ss_pred cCcCCCCCcccc
Confidence 356777766643
No 251
>KOG4377|consensus
Probab=20.62 E-value=95 Score=24.36 Aligned_cols=26 Identities=27% Similarity=0.542 Sum_probs=20.4
Q ss_pred eec--CccCccccChHHHHHHHHHhhCC
Q psy4421 44 YGC--YRCSYFTYESNNLKKHILKHTGE 69 (167)
Q Consensus 44 ~~C--~~C~~~~~~~~~l~~H~~~h~~~ 69 (167)
|.| ..|.+.+..+..+.+|..+|...
T Consensus 272 yhcl~e~C~ykr~~k~DvirH~~~hkkr 299 (480)
T KOG4377|consen 272 YHCLNEYCFYKRGQKNDVIRHVEIHKKR 299 (480)
T ss_pred hcccCccccccccchhhhHHHHHHHhhc
Confidence 556 57888888889999999887644
No 252
>KOG0717|consensus
Probab=20.40 E-value=55 Score=26.02 Aligned_cols=22 Identities=32% Similarity=0.625 Sum_probs=17.6
Q ss_pred eeCCCCcccccCchhHHHHhhh
Q psy4421 144 YKCSLCNYECRQNVHLKSHMKS 165 (167)
Q Consensus 144 ~~C~~C~~~f~~~~~l~~H~~~ 165 (167)
+.|..|.++|.+.-+|.-|..+
T Consensus 293 lyC~vCnKsFKseKq~kNHEnS 314 (508)
T KOG0717|consen 293 LYCVVCNKSFKSEKQLKNHENS 314 (508)
T ss_pred eEEeeccccccchHHHHhhHHH
Confidence 6788888888888888777653
No 253
>KOG1994|consensus
Probab=20.21 E-value=49 Score=23.57 Aligned_cols=22 Identities=23% Similarity=0.607 Sum_probs=19.0
Q ss_pred CCceeCCCCcccccCchhHHHH
Q psy4421 141 DKPYKCSLCNYECRQNVHLKSH 162 (167)
Q Consensus 141 ~~~~~C~~C~~~f~~~~~l~~H 162 (167)
..-|-|-.||..|....+|..|
T Consensus 237 ~eh~YC~fCG~~y~~~edl~eh 258 (268)
T KOG1994|consen 237 SEHYYCFFCGIKYKDEEDLYEH 258 (268)
T ss_pred ccceEEEEeccccCCHHHHHHh
Confidence 3458899999999999999877
No 254
>TIGR00319 desulf_FeS4 desulfoferrodoxin FeS4 iron-binding domain. Neelaredoxin, a monomeric blue non-heme iron protein, lacks this domain.
Probab=20.15 E-value=61 Score=15.15 Aligned_cols=12 Identities=33% Similarity=0.888 Sum_probs=8.1
Q ss_pred CceeCCCCcccc
Q psy4421 142 KPYKCSLCNYEC 153 (167)
Q Consensus 142 ~~~~C~~C~~~f 153 (167)
+-|+|..||..+
T Consensus 6 ~~ykC~~Cgniv 17 (34)
T TIGR00319 6 QVYKCEVCGNIV 17 (34)
T ss_pred cEEEcCCCCcEE
Confidence 357788887654
Done!