Query psy3483
Match_columns 99
No_of_seqs 102 out of 1785
Neff 11.2
Searched_HMMs 46136
Date Fri Aug 16 17:53:00 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy3483.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/3483hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2462|consensus 99.9 6.4E-24 1.4E-28 122.2 3.9 82 8-99 162-243 (279)
2 KOG2462|consensus 99.8 7.6E-22 1.6E-26 113.8 3.4 83 3-93 183-265 (279)
3 KOG3623|consensus 99.7 1.2E-17 2.6E-22 107.0 0.7 82 3-92 890-971 (1007)
4 KOG3576|consensus 99.6 5.6E-17 1.2E-21 90.6 0.7 85 4-96 114-198 (267)
5 KOG3623|consensus 99.5 1E-14 2.3E-19 93.9 0.5 85 6-92 239-330 (1007)
6 PHA00733 hypothetical protein 99.2 8.3E-12 1.8E-16 66.5 3.6 87 5-96 38-124 (128)
7 KOG3576|consensus 99.2 2.9E-12 6.3E-17 72.0 1.7 88 2-97 140-238 (267)
8 KOG1074|consensus 99.2 2.7E-12 5.9E-17 83.9 -0.3 83 6-96 604-693 (958)
9 KOG3608|consensus 99.2 7.6E-12 1.6E-16 75.3 1.3 90 2-95 202-316 (467)
10 PHA02768 hypothetical protein; 99.1 5.5E-11 1.2E-15 53.8 1.5 43 43-88 6-48 (55)
11 KOG1074|consensus 99.0 2.2E-10 4.9E-15 75.2 2.0 56 43-99 880-935 (958)
12 PF13465 zf-H2C2_2: Zinc-finge 99.0 8.2E-10 1.8E-14 43.0 2.6 26 58-83 1-26 (26)
13 PHA00616 hypothetical protein 98.9 8.7E-10 1.9E-14 47.6 1.5 29 71-99 1-29 (44)
14 KOG3608|consensus 98.8 4.9E-09 1.1E-13 63.6 3.3 86 2-96 287-377 (467)
15 PLN03086 PRLI-interacting fact 98.8 1.1E-08 2.3E-13 65.9 4.5 77 5-94 451-537 (567)
16 PHA02768 hypothetical protein; 98.7 2.3E-09 4.9E-14 48.5 -0.1 40 7-55 5-44 (55)
17 PHA00733 hypothetical protein 98.5 1.5E-07 3.4E-12 50.2 3.0 54 3-66 69-122 (128)
18 PLN03086 PRLI-interacting fact 98.4 5E-07 1.1E-11 58.5 5.0 77 6-93 477-562 (567)
19 PF13465 zf-H2C2_2: Zinc-finge 98.4 6.1E-08 1.3E-12 37.6 -0.0 18 1-18 8-25 (26)
20 PHA00616 hypothetical protein 98.4 1.7E-07 3.7E-12 40.6 1.1 32 43-75 2-33 (44)
21 PHA00732 hypothetical protein 98.4 4.1E-07 8.9E-12 44.6 2.4 44 7-64 1-45 (79)
22 PF00096 zf-C2H2: Zinc finger, 98.3 9E-07 1.9E-11 33.2 2.1 23 72-94 1-23 (23)
23 KOG3993|consensus 98.1 8.3E-07 1.8E-11 55.2 0.5 25 71-95 356-380 (500)
24 PF13912 zf-C2H2_6: C2H2-type 98.1 2.6E-06 5.6E-11 33.2 1.6 26 71-96 1-26 (27)
25 PF13894 zf-C2H2_4: C2H2-type 98.0 8.3E-06 1.8E-10 30.5 2.4 24 72-95 1-24 (24)
26 PF09237 GAGA: GAGA factor; I 98.0 1.2E-05 2.7E-10 35.7 2.8 33 67-99 20-52 (54)
27 PF05605 zf-Di19: Drought indu 97.9 3.6E-05 7.8E-10 35.0 4.1 49 43-95 3-53 (54)
28 PHA00732 hypothetical protein 97.8 1.2E-05 2.6E-10 39.5 1.4 47 42-95 1-48 (79)
29 KOG3993|consensus 97.6 2.7E-05 5.8E-10 48.8 1.3 60 6-67 294-380 (500)
30 smart00355 ZnF_C2H2 zinc finge 97.6 8.6E-05 1.9E-09 28.0 2.3 24 72-95 1-24 (26)
31 PF00096 zf-C2H2: Zinc finger, 97.6 6E-05 1.3E-09 28.0 1.6 20 44-64 2-21 (23)
32 PF05605 zf-Di19: Drought indu 97.6 7.3E-05 1.6E-09 34.0 2.1 50 7-66 2-52 (54)
33 PF12756 zf-C2H2_2: C2H2 type 97.4 0.00017 3.7E-09 36.5 2.6 73 9-94 1-73 (100)
34 COG5189 SFP1 Putative transcri 97.3 0.00014 3.1E-09 44.2 1.8 70 5-92 347-419 (423)
35 PRK04860 hypothetical protein; 97.3 0.00033 7.1E-09 39.0 2.7 40 41-85 118-157 (160)
36 PF13912 zf-C2H2_6: C2H2-type 97.2 0.0001 2.2E-09 28.5 0.4 20 7-27 1-20 (27)
37 PF13909 zf-H2C2_5: C2H2-type 97.1 0.00065 1.4E-08 25.4 2.2 23 72-95 1-23 (24)
38 PF12874 zf-met: Zinc-finger o 97.1 0.0004 8.7E-09 26.2 1.6 23 72-94 1-23 (25)
39 PF13894 zf-C2H2_4: C2H2-type 97.0 0.00061 1.3E-08 25.1 1.8 22 43-65 1-22 (24)
40 PF12171 zf-C2H2_jaz: Zinc-fin 96.6 0.00044 9.5E-09 26.8 -0.2 22 72-93 2-23 (27)
41 PF09237 GAGA: GAGA factor; I 96.3 0.0083 1.8E-07 26.8 2.9 34 37-71 19-52 (54)
42 PRK04860 hypothetical protein; 96.0 0.0034 7.3E-08 35.0 1.1 36 7-53 119-154 (160)
43 PF13913 zf-C2HC_2: zinc-finge 95.6 0.015 3.3E-07 22.0 1.9 18 73-91 4-21 (25)
44 smart00451 ZnF_U1 U1-like zinc 95.1 0.024 5.3E-07 22.9 1.9 23 71-93 3-25 (35)
45 COG4049 Uncharacterized protei 94.2 0.027 5.8E-07 25.6 1.0 27 66-92 12-38 (65)
46 cd00350 rubredoxin_like Rubred 94.0 0.062 1.3E-06 21.7 1.8 24 43-79 2-25 (33)
47 PF09986 DUF2225: Uncharacteri 93.8 0.052 1.1E-06 31.8 2.0 17 5-21 3-19 (214)
48 PF09538 FYDLN_acid: Protein o 93.5 0.055 1.2E-06 28.3 1.5 28 9-54 11-38 (108)
49 KOG1146|consensus 93.4 0.036 7.8E-07 40.0 0.9 26 68-93 515-540 (1406)
50 COG2888 Predicted Zn-ribbon RN 93.0 0.054 1.2E-06 25.0 0.9 31 43-79 28-58 (61)
51 COG5048 FOG: Zn-finger [Genera 91.9 0.035 7.5E-07 34.9 -0.6 55 42-97 289-349 (467)
52 cd00729 rubredoxin_SM Rubredox 91.8 0.18 4E-06 20.5 1.8 10 70-79 17-26 (34)
53 TIGR02098 MJ0042_CXXC MJ0042 f 90.5 0.25 5.3E-06 20.5 1.6 13 8-20 3-15 (38)
54 TIGR00373 conserved hypothetic 90.5 0.2 4.3E-06 28.0 1.6 13 8-20 110-122 (158)
55 PF13717 zinc_ribbon_4: zinc-r 90.5 0.29 6.3E-06 20.2 1.7 12 9-20 4-15 (36)
56 PF13719 zinc_ribbon_5: zinc-r 90.4 0.25 5.3E-06 20.5 1.5 11 9-19 4-14 (37)
57 PHA00626 hypothetical protein 90.1 0.092 2E-06 23.9 0.1 12 71-82 23-34 (59)
58 PRK14890 putative Zn-ribbon RN 90.1 0.19 4.1E-06 23.2 1.0 32 42-79 25-56 (59)
59 PRK06266 transcription initiat 90.0 0.22 4.9E-06 28.4 1.6 15 7-21 117-131 (178)
60 PF09723 Zn-ribbon_8: Zinc rib 89.0 0.17 3.7E-06 21.7 0.5 11 8-18 6-16 (42)
61 COG5048 FOG: Zn-finger [Genera 89.0 0.21 4.5E-06 31.4 1.1 61 7-75 289-355 (467)
62 COG1592 Rubrerythrin [Energy p 88.9 0.37 8E-06 27.2 1.9 23 42-78 134-156 (166)
63 KOG2186|consensus 88.6 0.47 1E-05 28.5 2.2 56 7-73 3-58 (276)
64 PF10571 UPF0547: Uncharacteri 87.5 0.53 1.1E-05 18.0 1.4 11 72-82 15-25 (26)
65 PRK00398 rpoP DNA-directed RNA 86.4 1.2 2.6E-05 19.3 2.4 8 43-50 22-29 (46)
66 COG1997 RPL43A Ribosomal prote 86.3 0.69 1.5E-05 23.2 1.7 32 41-83 34-65 (89)
67 PF03811 Zn_Tnp_IS1: InsA N-te 85.3 1 2.2E-05 18.6 1.8 15 34-48 21-35 (36)
68 KOG4167|consensus 84.8 0.17 3.7E-06 34.8 -1.0 25 71-95 792-816 (907)
69 smart00531 TFIIE Transcription 84.5 1.3 2.8E-05 24.4 2.5 39 38-81 95-133 (147)
70 PF09845 DUF2072: Zn-ribbon co 84.3 0.65 1.4E-05 25.1 1.2 15 7-21 1-15 (131)
71 PF12013 DUF3505: Protein of u 83.9 1.3 2.7E-05 23.0 2.2 25 72-96 81-109 (109)
72 PF14353 CpXC: CpXC protein 83.6 0.73 1.6E-05 24.6 1.2 13 8-20 2-14 (128)
73 TIGR02605 CxxC_CxxC_SSSS putat 83.6 0.56 1.2E-05 20.8 0.7 12 7-18 5-16 (52)
74 smart00659 RPOLCX RNA polymera 83.5 1.8 3.8E-05 18.8 2.2 10 70-79 18-27 (44)
75 TIGR02300 FYDLN_acid conserved 83.4 0.75 1.6E-05 24.8 1.2 28 9-54 11-38 (129)
76 KOG3408|consensus 82.3 0.76 1.6E-05 24.5 0.9 26 68-93 54-79 (129)
77 COG1198 PriA Primosomal protei 82.2 1.4 3E-05 30.8 2.4 12 9-20 437-448 (730)
78 PF05443 ROS_MUCR: ROS/MUCR tr 81.7 1.1 2.3E-05 24.4 1.4 23 71-96 72-94 (132)
79 KOG2893|consensus 81.6 0.26 5.5E-06 29.5 -1.0 44 6-62 10-53 (341)
80 PF07754 DUF1610: Domain of un 81.5 0.89 1.9E-05 17.1 0.8 10 6-15 15-24 (24)
81 smart00614 ZnF_BED BED zinc fi 80.6 2.3 5E-05 18.7 2.1 21 72-92 19-44 (50)
82 PF15269 zf-C2H2_7: Zinc-finge 80.4 1.5 3.2E-05 19.1 1.4 21 72-92 21-41 (54)
83 PF02892 zf-BED: BED zinc fing 80.4 2.3 5.1E-05 18.0 2.1 23 69-91 14-40 (45)
84 PF06524 NOA36: NOA36 protein; 79.7 0.54 1.2E-05 28.5 -0.1 28 67-94 205-232 (314)
85 PF04959 ARS2: Arsenite-resist 79.1 0.73 1.6E-05 27.1 0.3 23 71-93 77-99 (214)
86 PRK09678 DNA-binding transcrip 78.8 0.74 1.6E-05 22.3 0.2 18 38-55 23-42 (72)
87 KOG4173|consensus 78.6 0.53 1.1E-05 27.5 -0.4 74 8-92 80-167 (253)
88 PF09963 DUF2197: Uncharacteri 78.4 1.8 4E-05 19.8 1.4 7 71-77 31-37 (56)
89 PF15135 UPF0515: Uncharacteri 78.3 4.1 8.9E-05 24.7 3.1 17 4-20 109-125 (278)
90 PRK00464 nrdR transcriptional 78.2 0.46 9.9E-06 26.5 -0.7 13 43-55 29-41 (154)
91 PF03604 DNA_RNApol_7kD: DNA d 77.7 2.8 6E-05 16.9 1.7 9 71-79 17-25 (32)
92 PTZ00255 60S ribosomal protein 77.3 1.6 3.4E-05 22.1 1.1 31 41-82 35-65 (90)
93 COG3364 Zn-ribbon containing p 76.6 1.4 3E-05 22.8 0.8 16 6-21 1-16 (112)
94 COG4888 Uncharacterized Zn rib 75.9 2.2 4.8E-05 22.0 1.4 12 6-17 21-32 (104)
95 PF01780 Ribosomal_L37ae: Ribo 75.5 1.1 2.5E-05 22.6 0.4 31 41-82 34-64 (90)
96 KOG2186|consensus 75.3 1.2 2.7E-05 26.9 0.5 44 43-90 4-47 (276)
97 PF05495 zf-CHY: CHY zinc fing 75.1 2.6 5.5E-05 20.2 1.5 60 7-81 10-71 (71)
98 KOG2593|consensus 74.9 2 4.4E-05 27.9 1.4 10 41-50 127-136 (436)
99 PF05129 Elf1: Transcription e 74.0 1.4 3.1E-05 21.8 0.5 12 42-53 46-57 (81)
100 PRK14873 primosome assembly pr 73.8 2.6 5.7E-05 29.2 1.8 10 9-18 385-394 (665)
101 PF07975 C1_4: TFIIH C1-like d 73.7 0.48 1E-05 21.3 -1.1 24 71-94 21-44 (51)
102 TIGR00280 L37a ribosomal prote 73.4 1.8 3.8E-05 22.0 0.7 30 42-82 35-64 (91)
103 smart00734 ZnF_Rad18 Rad18-lik 73.2 4.3 9.4E-05 15.3 1.7 19 73-92 3-21 (26)
104 PF10276 zf-CHCC: Zinc-finger 72.9 2.6 5.7E-05 17.9 1.1 12 6-17 28-39 (40)
105 COG1996 RPC10 DNA-directed RNA 71.9 3.9 8.4E-05 18.2 1.6 8 43-50 7-14 (49)
106 COG0068 HypF Hydrogenase matur 71.7 1.4 3E-05 30.6 0.2 56 10-80 126-182 (750)
107 PF08790 zf-LYAR: LYAR-type C2 71.5 3 6.6E-05 16.2 1.0 18 8-27 1-18 (28)
108 smart00154 ZnF_AN1 AN1-like Zi 71.4 2.2 4.8E-05 17.9 0.7 15 7-21 12-26 (39)
109 TIGR00622 ssl1 transcription f 71.3 4.2 9.2E-05 21.5 1.9 27 69-95 79-105 (112)
110 smart00834 CxxC_CXXC_SSSS Puta 71.2 2.2 4.8E-05 17.6 0.7 14 7-20 5-18 (41)
111 PLN02294 cytochrome c oxidase 70.6 2.6 5.5E-05 24.0 1.0 16 5-20 139-154 (174)
112 PF01363 FYVE: FYVE zinc finge 70.5 3.5 7.6E-05 19.3 1.4 11 71-81 25-35 (69)
113 KOG1280|consensus 69.8 3.4 7.5E-05 26.2 1.5 22 5-27 77-98 (381)
114 PRK03976 rpl37ae 50S ribosomal 69.4 2.3 5.1E-05 21.5 0.7 31 41-82 35-65 (90)
115 TIGR01206 lysW lysine biosynth 69.0 6.3 0.00014 17.9 2.0 11 8-18 3-13 (54)
116 TIGR00595 priA primosomal prot 68.7 4.3 9.4E-05 27.1 1.9 10 9-18 215-224 (505)
117 COG3091 SprT Zn-dependent meta 67.0 3.9 8.5E-05 22.8 1.3 33 41-79 116-148 (156)
118 PF01096 TFIIS_C: Transcriptio 65.3 3.9 8.5E-05 17.1 0.9 8 43-50 29-36 (39)
119 smart00440 ZnF_C2C2 C2C2 Zinc 65.1 6.7 0.00015 16.5 1.6 8 43-50 29-36 (40)
120 PF01428 zf-AN1: AN1-like Zinc 64.3 2.9 6.4E-05 17.8 0.4 16 6-21 12-27 (43)
121 COG4896 Uncharacterized protei 63.9 5.7 0.00012 18.6 1.3 9 42-50 31-39 (68)
122 PF13451 zf-trcl: Probable zin 63.4 4.2 9.1E-05 18.1 0.8 15 5-19 2-16 (49)
123 smart00661 RPOL9 RNA polymeras 62.9 10 0.00022 16.5 2.0 10 71-80 20-29 (52)
124 COG3357 Predicted transcriptio 62.6 6.4 0.00014 20.0 1.4 27 41-78 57-83 (97)
125 KOG3507|consensus 62.5 7 0.00015 18.1 1.4 31 41-83 19-49 (62)
126 PF08271 TF_Zn_Ribbon: TFIIB z 61.5 7.4 0.00016 16.5 1.4 10 8-17 1-10 (43)
127 PF05191 ADK_lid: Adenylate ki 60.9 8.4 0.00018 15.9 1.5 10 9-18 3-12 (36)
128 KOG2482|consensus 59.3 5.3 0.00012 25.5 1.0 33 7-40 195-227 (423)
129 PRK12380 hydrogenase nickel in 58.0 8.9 0.00019 20.2 1.6 24 43-79 71-94 (113)
130 PF04423 Rad50_zn_hook: Rad50 55.7 4.5 9.8E-05 18.1 0.2 12 9-20 22-33 (54)
131 TIGR00100 hypA hydrogenase nic 55.4 11 0.00023 20.0 1.6 24 43-79 71-94 (115)
132 PRK03824 hypA hydrogenase nick 55.3 11 0.00023 20.6 1.7 13 7-19 70-82 (135)
133 COG4391 Uncharacterized protei 55.1 7.9 0.00017 18.1 1.0 12 7-18 48-59 (62)
134 KOG2482|consensus 54.9 8.5 0.00018 24.6 1.3 23 72-94 196-218 (423)
135 PF11672 DUF3268: Protein of u 54.6 17 0.00036 19.0 2.2 13 6-18 1-13 (102)
136 COG1998 RPS31 Ribosomal protei 54.5 7.4 0.00016 17.4 0.8 25 44-79 21-45 (51)
137 COG4530 Uncharacterized protei 53.9 7.6 0.00016 20.5 0.9 14 69-82 24-37 (129)
138 smart00064 FYVE Protein presen 53.9 12 0.00025 17.4 1.5 6 45-50 29-34 (68)
139 PRK00564 hypA hydrogenase nick 53.8 11 0.00023 20.0 1.5 11 43-53 72-82 (117)
140 KOG1146|consensus 53.1 7.9 0.00017 29.2 1.1 53 41-95 1283-1352(1406)
141 KOG4167|consensus 52.7 2.9 6.3E-05 29.3 -0.9 25 42-67 792-816 (907)
142 cd00065 FYVE FYVE domain; Zinc 52.5 14 0.0003 16.4 1.6 8 44-51 20-27 (57)
143 PF14446 Prok-RING_1: Prokaryo 52.1 15 0.00032 16.8 1.6 7 72-78 22-28 (54)
144 TIGR00416 sms DNA repair prote 51.2 15 0.00032 24.4 2.1 8 43-50 8-15 (454)
145 PRK12496 hypothetical protein; 50.8 13 0.00027 21.1 1.5 11 8-18 128-138 (164)
146 PF13878 zf-C2H2_3: zinc-finge 50.3 22 0.00047 15.0 2.1 7 44-50 15-21 (41)
147 PRK11823 DNA repair protein Ra 50.0 16 0.00035 24.1 2.1 8 43-50 8-15 (446)
148 PRK14714 DNA polymerase II lar 49.7 27 0.0006 26.5 3.3 34 8-51 668-701 (1337)
149 PF07295 DUF1451: Protein of u 49.3 9.7 0.00021 21.2 0.9 8 43-50 113-120 (146)
150 COG5112 UFD2 U1-like Zn-finger 49.1 5.8 0.00012 20.8 0.0 23 71-93 55-77 (126)
151 PF10013 DUF2256: Uncharacteri 48.7 8.2 0.00018 16.6 0.5 12 9-20 10-21 (42)
152 PRK05580 primosome assembly pr 48.7 14 0.00031 25.8 1.8 8 10-17 384-391 (679)
153 cd00924 Cyt_c_Oxidase_Vb Cytoc 48.6 12 0.00027 19.2 1.2 17 66-83 75-91 (97)
154 PRK03681 hypA hydrogenase nick 48.1 15 0.00033 19.4 1.5 25 43-79 71-95 (114)
155 PTZ00043 cytochrome c oxidase 47.1 10 0.00022 22.8 0.8 17 5-21 179-195 (268)
156 COG5152 Uncharacterized conser 46.8 9.3 0.0002 22.5 0.6 12 7-18 196-207 (259)
157 PRK04023 DNA polymerase II lar 46.5 27 0.00057 26.0 2.8 9 8-16 627-635 (1121)
158 COG2879 Uncharacterized small 45.3 27 0.00059 16.5 1.9 16 84-99 25-40 (65)
159 PF14369 zf-RING_3: zinc-finge 45.2 10 0.00022 15.5 0.5 11 9-19 23-33 (35)
160 PF01155 HypA: Hydrogenase exp 44.2 6.4 0.00014 20.7 -0.3 25 43-80 71-95 (113)
161 COG1773 Rubredoxin [Energy pro 44.1 13 0.00027 17.1 0.7 12 71-82 3-14 (55)
162 PF04780 DUF629: Protein of un 42.2 23 0.00049 23.8 1.9 23 71-93 57-79 (466)
163 PRK00432 30S ribosomal protein 41.3 33 0.0007 15.3 1.8 11 70-80 36-46 (50)
164 cd01121 Sms Sms (bacterial rad 40.9 25 0.00053 22.8 1.9 7 44-50 16-22 (372)
165 COG4957 Predicted transcriptio 40.4 25 0.00055 19.4 1.6 22 72-96 77-98 (148)
166 PF07282 OrfB_Zn_ribbon: Putat 40.2 34 0.00075 15.9 2.0 16 67-82 42-57 (69)
167 COG5216 Uncharacterized conser 40.0 17 0.00038 16.8 0.8 13 67-79 40-52 (67)
168 PRK14892 putative transcriptio 39.7 35 0.00075 17.7 2.0 7 8-14 22-28 (99)
169 PF01286 XPA_N: XPA protein N- 39.7 15 0.00033 15.0 0.6 12 73-84 5-16 (34)
170 COG1675 TFA1 Transcription ini 39.1 22 0.00048 20.5 1.3 8 72-79 133-140 (176)
171 KOG2231|consensus 38.4 32 0.0007 24.2 2.2 18 9-27 184-201 (669)
172 COG5432 RAD18 RING-finger-cont 37.5 7.7 0.00017 24.2 -0.6 16 34-50 52-67 (391)
173 PHA02998 RNA polymerase subuni 37.4 30 0.00065 20.1 1.7 12 72-83 172-183 (195)
174 COG3677 Transposase and inacti 37.1 19 0.00042 19.5 0.9 18 67-84 49-66 (129)
175 PF14255 Cys_rich_CPXG: Cystei 37.1 15 0.00033 16.6 0.4 10 9-18 2-11 (52)
176 KOG2785|consensus 37.0 60 0.0013 21.3 3.1 23 71-93 217-242 (390)
177 PF14803 Nudix_N_2: Nudix N-te 37.0 32 0.00069 14.0 1.3 7 43-49 23-29 (34)
178 COG1571 Predicted DNA-binding 36.5 30 0.00066 22.9 1.8 14 71-84 367-380 (421)
179 PF04216 FdhE: Protein involve 36.3 14 0.0003 22.9 0.3 13 68-80 235-247 (290)
180 PF12773 DZR: Double zinc ribb 36.3 42 0.00092 14.4 1.9 8 72-79 30-37 (50)
181 PF12647 RNHCP: RNHCP domain; 36.1 38 0.00083 17.3 1.8 26 6-31 3-30 (92)
182 COG1326 Uncharacterized archae 35.2 67 0.0015 19.0 2.8 10 72-81 31-40 (201)
183 PRK06260 threonine synthase; V 33.8 40 0.00087 21.9 2.1 9 42-50 19-27 (397)
184 PLN03238 probable histone acet 33.6 62 0.0013 20.4 2.7 25 69-93 46-70 (290)
185 KOG3362|consensus 33.5 14 0.0003 20.6 -0.0 20 72-91 130-149 (156)
186 PF00301 Rubredoxin: Rubredoxi 33.3 23 0.0005 15.6 0.7 11 72-82 2-12 (47)
187 KOG0717|consensus 33.0 31 0.00067 23.2 1.4 21 72-92 293-313 (508)
188 PF02748 PyrI_C: Aspartate car 32.9 28 0.0006 15.7 0.9 16 4-19 32-47 (52)
189 PF09416 UPF1_Zn_bind: RNA hel 32.7 47 0.001 18.7 1.9 50 2-51 9-69 (152)
190 PRK05978 hypothetical protein; 32.7 28 0.00062 19.5 1.1 8 9-16 35-42 (148)
191 PF01927 Mut7-C: Mut7-C RNAse 32.5 25 0.00055 19.3 0.9 21 69-89 122-142 (147)
192 cd00730 rubredoxin Rubredoxin; 32.4 22 0.00048 15.8 0.5 11 72-82 2-12 (50)
193 PF02148 zf-UBP: Zn-finger in 31.5 20 0.00044 16.5 0.4 16 69-84 9-24 (63)
194 PF02591 DUF164: Putative zinc 31.4 59 0.0013 14.5 2.6 16 65-80 40-55 (56)
195 PRK03564 formate dehydrogenase 31.4 84 0.0018 20.0 3.0 10 7-16 187-196 (309)
196 PRK05654 acetyl-CoA carboxylas 30.9 74 0.0016 20.0 2.8 12 43-54 47-58 (292)
197 KOG4727|consensus 30.9 31 0.00068 19.9 1.1 22 71-92 75-96 (193)
198 COG4338 Uncharacterized protei 30.8 16 0.00035 16.2 -0.0 13 9-21 14-26 (54)
199 TIGR00515 accD acetyl-CoA carb 30.2 30 0.00066 21.6 1.0 12 9-20 28-39 (285)
200 PF11494 Ta0938: Ta0938; Inte 29.8 42 0.00091 17.4 1.3 39 4-55 11-50 (105)
201 PF06397 Desulfoferrod_N: Desu 29.5 28 0.00061 14.4 0.6 10 71-80 6-15 (36)
202 PF08209 Sgf11: Sgf11 (transcr 29.5 51 0.0011 13.3 1.5 20 43-64 5-24 (33)
203 COG1594 RPB9 DNA-directed RNA 28.9 53 0.0011 17.4 1.7 12 71-82 100-111 (113)
204 PF02176 zf-TRAF: TRAF-type zi 28.8 66 0.0014 14.3 2.3 20 57-76 24-43 (60)
205 PF02891 zf-MIZ: MIZ/SP-RING z 28.6 31 0.00067 15.2 0.7 8 72-79 42-49 (50)
206 PF12230 PRP21_like_P: Pre-mRN 28.4 19 0.00041 21.4 0.0 30 42-73 168-197 (229)
207 PTZ00303 phosphatidylinositol 28.4 47 0.001 24.3 1.8 6 45-50 484-489 (1374)
208 PF14787 zf-CCHC_5: GAG-polypr 28.4 33 0.00072 14.2 0.7 14 73-86 4-17 (36)
209 CHL00174 accD acetyl-CoA carbo 28.2 89 0.0019 19.8 2.8 11 43-53 58-68 (296)
210 COG1655 Uncharacterized protei 28.1 27 0.00059 21.2 0.6 17 5-21 17-33 (267)
211 KOG1842|consensus 27.6 34 0.00073 22.9 1.0 21 72-92 16-36 (505)
212 KOG2071|consensus 26.9 75 0.0016 22.1 2.4 29 67-95 414-442 (579)
213 KOG0227|consensus 26.6 39 0.00084 19.9 1.0 20 72-91 54-73 (222)
214 PTZ00448 hypothetical protein; 26.3 55 0.0012 21.4 1.7 24 71-94 314-337 (373)
215 PF08792 A2L_zn_ribbon: A2L zi 26.2 39 0.00085 13.6 0.7 10 72-81 22-31 (33)
216 PF08274 PhnA_Zn_Ribbon: PhnA 26.1 32 0.0007 13.5 0.5 7 43-49 20-26 (30)
217 PF04810 zf-Sec23_Sec24: Sec23 25.9 41 0.00088 14.0 0.8 12 5-16 22-33 (40)
218 PRK04351 hypothetical protein; 25.9 65 0.0014 18.0 1.8 33 42-83 112-144 (149)
219 TIGR01384 TFS_arch transcripti 25.7 61 0.0013 16.5 1.6 36 43-81 63-100 (104)
220 KOG2907|consensus 25.6 41 0.00088 18.0 0.9 37 43-83 75-114 (116)
221 TIGR00627 tfb4 transcription f 25.2 69 0.0015 20.0 1.9 10 72-81 256-265 (279)
222 PF14690 zf-ISL3: zinc-finger 24.8 33 0.00072 14.4 0.4 10 7-16 2-11 (47)
223 smart00731 SprT SprT homologue 24.3 68 0.0015 17.6 1.7 32 42-81 112-143 (146)
224 KOG1088|consensus 24.1 50 0.0011 17.8 1.0 12 43-54 99-110 (124)
225 COG0675 Transposase and inacti 24.1 1E+02 0.0023 19.0 2.7 16 69-84 320-335 (364)
226 COG5236 Uncharacterized conser 24.1 70 0.0015 20.8 1.8 75 9-95 222-305 (493)
227 PRK12722 transcriptional activ 24.1 71 0.0015 18.7 1.7 28 43-79 135-162 (187)
228 PF13824 zf-Mss51: Zinc-finger 24.0 50 0.0011 15.2 0.9 15 67-81 10-24 (55)
229 COG1656 Uncharacterized conser 23.8 47 0.001 19.0 1.0 9 43-51 131-139 (165)
230 KOG1813|consensus 23.7 78 0.0017 20.1 1.9 14 6-19 240-253 (313)
231 PLN00104 MYST -like histone ac 23.6 69 0.0015 21.6 1.8 25 69-93 196-220 (450)
232 PF01215 COX5B: Cytochrome c o 23.5 31 0.00068 19.0 0.2 16 69-84 110-125 (136)
233 TIGR00143 hypF [NiFe] hydrogen 23.4 24 0.00052 25.0 -0.2 12 10-21 93-104 (711)
234 KOG1994|consensus 22.8 45 0.00098 20.2 0.8 24 67-90 235-258 (268)
235 PF05741 zf-nanos: Nanos RNA b 22.7 34 0.00074 15.7 0.3 10 7-16 33-42 (55)
236 KOG0320|consensus 22.5 13 0.00029 21.5 -1.3 10 72-81 168-177 (187)
237 PRK00420 hypothetical protein; 22.4 76 0.0017 16.9 1.5 7 44-50 42-48 (112)
238 PTZ00064 histone acetyltransfe 22.3 89 0.0019 21.5 2.1 25 69-93 278-302 (552)
239 COG1579 Zn-ribbon protein, pos 22.3 1E+02 0.0022 18.9 2.2 13 68-80 218-230 (239)
240 PF09082 DUF1922: Domain of un 22.0 54 0.0012 15.8 0.8 10 8-18 4-13 (68)
241 KOG2272|consensus 22.0 1.4E+02 0.0031 18.6 2.8 19 65-83 215-233 (332)
242 PF14354 Lar_restr_allev: Rest 21.9 47 0.001 15.0 0.6 10 7-16 3-12 (61)
243 PRK01343 zinc-binding protein; 21.9 43 0.00094 15.5 0.5 12 7-18 9-20 (57)
244 PF10071 DUF2310: Zn-ribbon-co 21.8 52 0.0011 20.3 1.0 7 72-78 242-248 (258)
245 PF14311 DUF4379: Domain of un 21.8 53 0.0012 14.6 0.8 12 8-19 29-40 (55)
246 PF11023 DUF2614: Protein of u 21.8 52 0.0011 17.5 0.9 13 6-18 68-80 (114)
247 PF13248 zf-ribbon_3: zinc-rib 21.7 32 0.0007 12.7 0.1 6 10-15 19-24 (26)
248 PRK07591 threonine synthase; V 21.5 86 0.0019 20.7 2.0 8 43-50 34-41 (421)
249 PRK12860 transcriptional activ 21.3 80 0.0017 18.5 1.6 27 43-78 135-161 (189)
250 PF01844 HNH: HNH endonuclease 21.2 44 0.00096 13.9 0.5 11 10-20 1-11 (47)
251 COG5151 SSL1 RNA polymerase II 21.1 73 0.0016 20.4 1.5 27 69-95 386-412 (421)
252 PF14447 Prok-RING_4: Prokaryo 21.1 48 0.001 15.2 0.6 6 45-50 42-47 (55)
253 PF03884 DUF329: Domain of unk 20.8 53 0.0011 15.2 0.7 12 8-19 3-14 (57)
254 PF11789 zf-Nse: Zinc-finger o 20.8 1.1E+02 0.0023 14.0 1.8 31 41-76 23-53 (57)
255 PF04606 Ogr_Delta: Ogr/Delta- 20.7 59 0.0013 14.0 0.8 7 10-16 2-8 (47)
256 PF10263 SprT-like: SprT-like 20.7 79 0.0017 17.3 1.5 31 42-81 123-153 (157)
257 PF06220 zf-U1: U1 zinc finger 20.6 88 0.0019 12.9 1.3 12 71-82 3-14 (38)
258 TIGR03831 YgiT_finger YgiT-typ 20.6 44 0.00095 13.8 0.4 11 8-18 33-43 (46)
259 PRK05452 anaerobic nitric oxid 20.2 1.3E+02 0.0028 20.4 2.6 9 71-79 458-466 (479)
260 PF09297 zf-NADH-PPase: NADH p 20.1 80 0.0017 12.2 1.3 10 69-78 19-28 (32)
No 1
>KOG2462|consensus
Probab=99.89 E-value=6.4e-24 Score=122.23 Aligned_cols=82 Identities=32% Similarity=0.604 Sum_probs=63.8
Q ss_pred eeCccccccccccchhhhccchhhccCCCCCCCcceeccCCCcccccChhHHHHHHHhhCCCCceecCCCCccccCchHH
Q psy3483 8 VTCMYCSKILTYETETIMNHCKFCKAVSRPTKYQRYVCCLCSKYRHSDASKMRSHIRTHTKDRPYKCFYCDYRSNERSNV 87 (99)
Q Consensus 8 ~~c~~c~~~f~~~~~~~~~h~~~~~~~~~~~~~~~~~c~~c~~~~~~~~~~~~~h~~~~~~~~~~~C~~c~~~f~~~~~l 87 (99)
+.|.+|++.+..-- .|.+| +++|+ -+.+|++||+.|... ..|+.|+++||||+||.|..|+++|..++||
T Consensus 162 ~~C~~C~K~YvSmp-ALkMH------irTH~--l~c~C~iCGKaFSRP-WLLQGHiRTHTGEKPF~C~hC~kAFADRSNL 231 (279)
T KOG2462|consen 162 FSCKYCGKVYVSMP-ALKMH------IRTHT--LPCECGICGKAFSRP-WLLQGHIRTHTGEKPFSCPHCGKAFADRSNL 231 (279)
T ss_pred ccCCCCCceeeehH-HHhhH------hhccC--CCcccccccccccch-HHhhcccccccCCCCccCCcccchhcchHHH
Confidence 44444444444333 44444 55554 567899999987776 9999999999999999999999999999999
Q ss_pred HHHHHHhcCCCC
Q psy3483 88 KAHMIRRHSVKP 99 (99)
Q Consensus 88 ~~H~~~~~~~kp 99 (99)
..|++||.+.|+
T Consensus 232 RAHmQTHS~~K~ 243 (279)
T KOG2462|consen 232 RAHMQTHSDVKK 243 (279)
T ss_pred HHHHHhhcCCcc
Confidence 999999998774
No 2
>KOG2462|consensus
Probab=99.85 E-value=7.6e-22 Score=113.76 Aligned_cols=83 Identities=22% Similarity=0.389 Sum_probs=77.0
Q ss_pred CCCceeeCccccccccccchhhhccchhhccCCCCCCCcceeccCCCcccccChhHHHHHHHhhCCCCceecCCCCcccc
Q psy3483 3 STELIVTCMYCSKILTYETETIMNHCKFCKAVSRPTKYQRYVCCLCSKYRHSDASKMRSHIRTHTKDRPYKCFYCDYRSN 82 (99)
Q Consensus 3 ~~~~~~~c~~c~~~f~~~~~~~~~h~~~~~~~~~~~~~~~~~c~~c~~~~~~~~~~~~~h~~~~~~~~~~~C~~c~~~f~ 82 (99)
+...++.|.+|||.|...= .|+-| +++|+||+||.|..|++.|... ++|+.|+.+|.+.++|+|..|++.|.
T Consensus 183 TH~l~c~C~iCGKaFSRPW-LLQGH------iRTHTGEKPF~C~hC~kAFADR-SNLRAHmQTHS~~K~~qC~~C~KsFs 254 (279)
T KOG2462|consen 183 THTLPCECGICGKAFSRPW-LLQGH------IRTHTGEKPFSCPHCGKAFADR-SNLRAHMQTHSDVKKHQCPRCGKSFA 254 (279)
T ss_pred ccCCCcccccccccccchH-Hhhcc------cccccCCCCccCCcccchhcch-HHHHHHHHhhcCCccccCcchhhHHH
Confidence 4457899999999999887 89999 9999999999999999988888 99999999999999999999999999
Q ss_pred CchHHHHHHHH
Q psy3483 83 ERSNVKAHMIR 93 (99)
Q Consensus 83 ~~~~l~~H~~~ 93 (99)
..+.|..|...
T Consensus 255 l~SyLnKH~ES 265 (279)
T KOG2462|consen 255 LKSYLNKHSES 265 (279)
T ss_pred HHHHHHHhhhh
Confidence 99999999753
No 3
>KOG3623|consensus
Probab=99.66 E-value=1.2e-17 Score=107.04 Aligned_cols=82 Identities=21% Similarity=0.481 Sum_probs=75.2
Q ss_pred CCCceeeCccccccccccchhhhccchhhccCCCCCCCcceeccCCCcccccChhHHHHHHHhhCCCCceecCCCCcccc
Q psy3483 3 STELIVTCMYCSKILTYETETIMNHCKFCKAVSRPTKYQRYVCCLCSKYRHSDASKMRSHIRTHTKDRPYKCFYCDYRSN 82 (99)
Q Consensus 3 ~~~~~~~c~~c~~~f~~~~~~~~~h~~~~~~~~~~~~~~~~~c~~c~~~~~~~~~~~~~h~~~~~~~~~~~C~~c~~~f~ 82 (99)
+++..|-|+.|+|.|...+ .|-+| --.|+|.+||+|.+|.+.|..+ ..|..|.+.|.|++||+|..|++.|.
T Consensus 890 te~gmyaCDqCDK~FqKqS-SLaRH------KYEHsGqRPyqC~iCkKAFKHK-HHLtEHkRLHSGEKPfQCdKClKRFS 961 (1007)
T KOG3623|consen 890 TEDGMYACDQCDKAFQKQS-SLARH------KYEHSGQRPYQCIICKKAFKHK-HHLTEHKRLHSGEKPFQCDKCLKRFS 961 (1007)
T ss_pred CccccchHHHHHHHHHhhH-HHHHh------hhhhcCCCCcccchhhHhhhhh-hhhhhhhhhccCCCcchhhhhhhhcc
Confidence 4466799999999998777 77788 6789999999999999999988 99999999999999999999999999
Q ss_pred CchHHHHHHH
Q psy3483 83 ERSNVKAHMI 92 (99)
Q Consensus 83 ~~~~l~~H~~ 92 (99)
.+..+..||-
T Consensus 962 HSGSYSQHMN 971 (1007)
T KOG3623|consen 962 HSGSYSQHMN 971 (1007)
T ss_pred cccchHhhhc
Confidence 9999999975
No 4
>KOG3576|consensus
Probab=99.63 E-value=5.6e-17 Score=90.56 Aligned_cols=85 Identities=27% Similarity=0.563 Sum_probs=76.5
Q ss_pred CCceeeCccccccccccchhhhccchhhccCCCCCCCcceeccCCCcccccChhHHHHHHHhhCCCCceecCCCCccccC
Q psy3483 4 TELIVTCMYCSKILTYETETIMNHCKFCKAVSRPTKYQRYVCCLCSKYRHSDASKMRSHIRTHTKDRPYKCFYCDYRSNE 83 (99)
Q Consensus 4 ~~~~~~c~~c~~~f~~~~~~~~~h~~~~~~~~~~~~~~~~~c~~c~~~~~~~~~~~~~h~~~~~~~~~~~C~~c~~~f~~ 83 (99)
+...|.|..|+|.|.... +|..| ++.|..-+.+.|..||+.|-.. -.|..|+++|+|.+||+|..|+++|.+
T Consensus 114 d~d~ftCrvCgK~F~lQR-mlnrh------~kch~~vkr~lct~cgkgfndt-fdlkrh~rthtgvrpykc~~c~kaftq 185 (267)
T KOG3576|consen 114 DQDSFTCRVCGKKFGLQR-MLNRH------LKCHSDVKRHLCTFCGKGFNDT-FDLKRHTRTHTGVRPYKCSLCEKAFTQ 185 (267)
T ss_pred CCCeeeeehhhhhhhHHH-HHHHH------hhhccHHHHHHHhhccCcccch-hhhhhhhccccCccccchhhhhHHHHh
Confidence 455699999999999888 99999 9999998999999999987766 789999999999999999999999999
Q ss_pred chHHHHHHHHhcC
Q psy3483 84 RSNVKAHMIRRHS 96 (99)
Q Consensus 84 ~~~l~~H~~~~~~ 96 (99)
+-.|..|++.-+|
T Consensus 186 rcsleshl~kvhg 198 (267)
T KOG3576|consen 186 RCSLESHLKKVHG 198 (267)
T ss_pred hccHHHHHHHHcC
Confidence 9999999875444
No 5
>KOG3623|consensus
Probab=99.46 E-value=1e-14 Score=93.88 Aligned_cols=85 Identities=22% Similarity=0.536 Sum_probs=70.8
Q ss_pred ceeeCccccccccccchhhhccchhh---ccC-CC---CCCCcceeccCCCcccccChhHHHHHHHhhCCCCceecCCCC
Q psy3483 6 LIVTCMYCSKILTYETETIMNHCKFC---KAV-SR---PTKYQRYVCCLCSKYRHSDASKMRSHIRTHTKDRPYKCFYCD 78 (99)
Q Consensus 6 ~~~~c~~c~~~f~~~~~~~~~h~~~~---~~~-~~---~~~~~~~~c~~c~~~~~~~~~~~~~h~~~~~~~~~~~C~~c~ 78 (99)
..|.|..|..+|.++. .|..|+.+. +.. .. -...+.|+|.+||+.|..+ ..|..|+++|.|++||.|+.|+
T Consensus 239 ~nfsC~lCsytFAyRt-QLErhm~~hkpg~dqa~sltqsa~lRKFKCtECgKAFKfK-HHLKEHlRIHSGEKPfeCpnCk 316 (1007)
T KOG3623|consen 239 PNFSCMLCSYTFAYRT-QLERHMQLHKPGGDQAISLTQSALLRKFKCTECGKAFKFK-HHLKEHLRIHSGEKPFECPNCK 316 (1007)
T ss_pred CCCcchhhhhhhhhHH-HHHHHHHhhcCCCcccccccchhhhccccccccchhhhhH-HHHHhhheeecCCCCcCCcccc
Confidence 3488999999999998 899995443 111 11 1234669999999999988 9999999999999999999999
Q ss_pred ccccCchHHHHHHH
Q psy3483 79 YRSNERSNVKAHMI 92 (99)
Q Consensus 79 ~~f~~~~~l~~H~~ 92 (99)
+.|..+..+..|+.
T Consensus 317 KRFSHSGSySSHmS 330 (1007)
T KOG3623|consen 317 KRFSHSGSYSSHMS 330 (1007)
T ss_pred cccccCCccccccc
Confidence 99999999999875
No 6
>PHA00733 hypothetical protein
Probab=99.25 E-value=8.3e-12 Score=66.47 Aligned_cols=87 Identities=16% Similarity=0.291 Sum_probs=66.7
Q ss_pred CceeeCccccccccccchhhhccchhhccCCCCCCCcceeccCCCcccccChhHHHHHHHhhCCCCceecCCCCccccCc
Q psy3483 5 ELIVTCMYCSKILTYETETIMNHCKFCKAVSRPTKYQRYVCCLCSKYRHSDASKMRSHIRTHTKDRPYKCFYCDYRSNER 84 (99)
Q Consensus 5 ~~~~~c~~c~~~f~~~~~~~~~h~~~~~~~~~~~~~~~~~c~~c~~~~~~~~~~~~~h~~~~~~~~~~~C~~c~~~f~~~ 84 (99)
.+++.|..|.+.|.... .|..+..+...+.. .+.++|.|+.|++.|... ..+..|++.+ +.+|.|..|++.|...
T Consensus 38 ~~~~~~~~~~~~~~~~~-~l~~~~~l~~~~~~-~~~kPy~C~~Cgk~Fss~-s~L~~H~r~h--~~~~~C~~CgK~F~~~ 112 (128)
T PHA00733 38 QKRLIRAVVKTLIYNPQ-LLDESSYLYKLLTS-KAVSPYVCPLCLMPFSSS-VSLKQHIRYT--EHSKVCPVCGKEFRNT 112 (128)
T ss_pred hhhHHHHHHhhhccChh-hhcchHHHHhhccc-CCCCCccCCCCCCcCCCH-HHHHHHHhcC--CcCccCCCCCCccCCH
Confidence 56678999998887665 55554222222333 347889999999988877 8899998876 4579999999999999
Q ss_pred hHHHHHHHHhcC
Q psy3483 85 SNVKAHMIRRHS 96 (99)
Q Consensus 85 ~~l~~H~~~~~~ 96 (99)
..|..|+...++
T Consensus 113 ~sL~~H~~~~h~ 124 (128)
T PHA00733 113 DSTLDHVCKKHN 124 (128)
T ss_pred HHHHHHHHHhcC
Confidence 999999887664
No 7
>KOG3576|consensus
Probab=99.24 E-value=2.9e-12 Score=71.96 Aligned_cols=88 Identities=24% Similarity=0.451 Sum_probs=73.5
Q ss_pred CCCCceeeCccccccccccchhhhccchhhccCCCCCCCcceeccCCCcccccChhHHHHHHHh-h----------CCCC
Q psy3483 2 KSTELIVTCMYCSKILTYETETIMNHCKFCKAVSRPTKYQRYVCCLCSKYRHSDASKMRSHIRT-H----------TKDR 70 (99)
Q Consensus 2 h~~~~~~~c~~c~~~f~~~~~~~~~h~~~~~~~~~~~~~~~~~c~~c~~~~~~~~~~~~~h~~~-~----------~~~~ 70 (99)
|++.+.+.|..||++|-.-. .|..| ++.|+|-+||.|..|++.|... -+|..|.+. | ..++
T Consensus 140 h~~vkr~lct~cgkgfndtf-dlkrh------~rthtgvrpykc~~c~kaftqr-csleshl~kvhgv~~~yaykerr~k 211 (267)
T KOG3576|consen 140 HSDVKRHLCTFCGKGFNDTF-DLKRH------TRTHTGVRPYKCSLCEKAFTQR-CSLESHLKKVHGVQHQYAYKERRAK 211 (267)
T ss_pred ccHHHHHHHhhccCcccchh-hhhhh------hccccCccccchhhhhHHHHhh-ccHHHHHHHHcCchHHHHHHHhhhh
Confidence 56677889999999999888 99999 9999999999999999977655 788888653 2 2356
Q ss_pred ceecCCCCccccCchHHHHHHHHhcCC
Q psy3483 71 PYKCFYCDYRSNERSNVKAHMIRRHSV 97 (99)
Q Consensus 71 ~~~C~~c~~~f~~~~~l~~H~~~~~~~ 97 (99)
.|.|..||..-.....+..|+..++..
T Consensus 212 l~vcedcg~t~~~~e~~~~h~~~~hp~ 238 (267)
T KOG3576|consen 212 LYVCEDCGYTSERPEVYYLHLKLHHPF 238 (267)
T ss_pred eeeecccCCCCCChhHHHHHHHhcCCC
Confidence 799999999888888888898877654
No 8
>KOG1074|consensus
Probab=99.18 E-value=2.7e-12 Score=83.87 Aligned_cols=83 Identities=14% Similarity=0.407 Sum_probs=74.2
Q ss_pred ceeeCccccccccccchhhhccchhhccCCCCCCCcceeccCCCcccccChhHHHHHHHhhCCC----CceecC---CCC
Q psy3483 6 LIVTCMYCSKILTYETETIMNHCKFCKAVSRPTKYQRYVCCLCSKYRHSDASKMRSHIRTHTKD----RPYKCF---YCD 78 (99)
Q Consensus 6 ~~~~c~~c~~~f~~~~~~~~~h~~~~~~~~~~~~~~~~~c~~c~~~~~~~~~~~~~h~~~~~~~----~~~~C~---~c~ 78 (99)
.|.+|-.|.+.....+ .|++| ++.|+|++||+|.+||+.|.++ .+|..|+.+|... ..+.|+ .|-
T Consensus 604 dPNqCiiC~rVlSC~s-aLqmH------yrtHtGERPFkCKiCgRAFtTk-GNLkaH~~vHka~p~~R~q~ScP~~~ic~ 675 (958)
T KOG1074|consen 604 DPNQCIICLRVLSCPS-ALQMH------YRTHTGERPFKCKICGRAFTTK-GNLKAHMSVHKAKPPARVQFSCPSTFICQ 675 (958)
T ss_pred Cccceeeeeecccchh-hhhhh------hhcccCcCccccccccchhccc-cchhhcccccccCccccccccCCchhhhc
Confidence 3678999999999999 99999 9999999999999999999888 9999999988554 357898 899
Q ss_pred ccccCchHHHHHHHHhcC
Q psy3483 79 YRSNERSNVKAHMIRRHS 96 (99)
Q Consensus 79 ~~f~~~~~l~~H~~~~~~ 96 (99)
+.|.+.-.+..|.+.|.+
T Consensus 676 ~kftn~V~lpQhIriH~~ 693 (958)
T KOG1074|consen 676 KKFTNAVTLPQHIRIHLG 693 (958)
T ss_pred ccccccccccceEEeecC
Confidence 999999999999999884
No 9
>KOG3608|consensus
Probab=99.17 E-value=7.6e-12 Score=75.34 Aligned_cols=90 Identities=33% Similarity=0.651 Sum_probs=63.5
Q ss_pred CCCCceeeCccccccccccchhhhccchh-------------h-----------ccCCCCCCCcceeccCCCcccccChh
Q psy3483 2 KSTELIVTCMYCSKILTYETETIMNHCKF-------------C-----------KAVSRPTKYQRYVCCLCSKYRHSDAS 57 (99)
Q Consensus 2 h~~~~~~~c~~c~~~f~~~~~~~~~h~~~-------------~-----------~~~~~~~~~~~~~c~~c~~~~~~~~~ 57 (99)
|+++|..-|+.||.-|..+. .|-.|++- | +++..|. ..|.|+.|.-+.... +
T Consensus 202 Hs~eKvvACp~Cg~~F~~~t-kl~DH~rRqt~l~~n~fqC~~C~KrFaTeklL~~Hv~rHv--n~ykCplCdmtc~~~-s 277 (467)
T KOG3608|consen 202 HSNEKVVACPHCGELFRTKT-KLFDHLRRQTELNTNSFQCAQCFKRFATEKLLKSHVVRHV--NCYKCPLCDMTCSSA-S 277 (467)
T ss_pred cCCCeEEecchHHHHhcccc-HHHHHHHhhhhhcCCchHHHHHHHHHhHHHHHHHHHHHhh--hcccccccccCCCCh-H
Confidence 56666666666666666555 45455111 0 0033332 347899998865555 8
Q ss_pred HHHHHHHh-hCCCCceecCCCCccccCchHHHHHHHHhc
Q psy3483 58 KMRSHIRT-HTKDRPYKCFYCDYRSNERSNVKAHMIRRH 95 (99)
Q Consensus 58 ~~~~h~~~-~~~~~~~~C~~c~~~f~~~~~l~~H~~~~~ 95 (99)
+|..|++. |..++||+|..|+..|...++|..|..+|.
T Consensus 278 sL~~H~r~rHs~dkpfKCd~Cd~~c~~esdL~kH~~~HS 316 (467)
T KOG3608|consen 278 SLTTHIRYRHSKDKPFKCDECDTRCVRESDLAKHVQVHS 316 (467)
T ss_pred HHHHHHHhhhccCCCccccchhhhhccHHHHHHHHHhcc
Confidence 89999876 788999999999999999999999998886
No 10
>PHA02768 hypothetical protein; Provisional
Probab=99.07 E-value=5.5e-11 Score=53.75 Aligned_cols=43 Identities=23% Similarity=0.394 Sum_probs=35.7
Q ss_pred eeccCCCcccccChhHHHHHHHhhCCCCceecCCCCccccCchHHH
Q psy3483 43 YVCCLCSKYRHSDASKMRSHIRTHTKDRPYKCFYCDYRSNERSNVK 88 (99)
Q Consensus 43 ~~c~~c~~~~~~~~~~~~~h~~~~~~~~~~~C~~c~~~f~~~~~l~ 88 (99)
|.|++||+.|... +.|..|++.|+ ++++|..|++.|...+.|+
T Consensus 6 y~C~~CGK~Fs~~-~~L~~H~r~H~--k~~kc~~C~k~f~~~s~l~ 48 (55)
T PHA02768 6 YECPICGEIYIKR-KSMITHLRKHN--TNLKLSNCKRISLRTGEYI 48 (55)
T ss_pred cCcchhCCeeccH-HHHHHHHHhcC--CcccCCcccceecccceeE
Confidence 6799999977766 88999999988 6889999999888777654
No 11
>KOG1074|consensus
Probab=98.98 E-value=2.2e-10 Score=75.23 Aligned_cols=56 Identities=36% Similarity=0.685 Sum_probs=51.5
Q ss_pred eeccCCCcccccChhHHHHHHHhhCCCCceecCCCCccccCchHHHHHHHHhcCCCC
Q psy3483 43 YVCCLCSKYRHSDASKMRSHIRTHTKDRPYKCFYCDYRSNERSNVKAHMIRRHSVKP 99 (99)
Q Consensus 43 ~~c~~c~~~~~~~~~~~~~h~~~~~~~~~~~C~~c~~~f~~~~~l~~H~~~~~~~kp 99 (99)
..|.+||+.|.++ +.|..|+++|++++||.|..|++.|..+.+|..||.+|....|
T Consensus 880 h~C~vCgk~FsSS-sALqiH~rTHtg~KPF~C~fC~~aFttrgnLKvHMgtH~w~q~ 935 (958)
T KOG1074|consen 880 HVCNVCGKQFSSS-AALEIHMRTHTGPKPFFCHFCEEAFTTRGNLKVHMGTHMWVQP 935 (958)
T ss_pred hhhccchhcccch-HHHHHhhhcCCCCCCccchhhhhhhhhhhhhhhhhccccccCC
Confidence 4699999988888 9999999999999999999999999999999999999976543
No 12
>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=98.96 E-value=8.2e-10 Score=43.03 Aligned_cols=26 Identities=46% Similarity=1.012 Sum_probs=22.9
Q ss_pred HHHHHHHhhCCCCceecCCCCccccC
Q psy3483 58 KMRSHIRTHTKDRPYKCFYCDYRSNE 83 (99)
Q Consensus 58 ~~~~h~~~~~~~~~~~C~~c~~~f~~ 83 (99)
+|..|++.|++++||.|..|++.|.+
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 47789999999999999999998863
No 13
>PHA00616 hypothetical protein
Probab=98.88 E-value=8.7e-10 Score=47.65 Aligned_cols=29 Identities=21% Similarity=0.480 Sum_probs=17.4
Q ss_pred ceecCCCCccccCchHHHHHHHHhcCCCC
Q psy3483 71 PYKCFYCDYRSNERSNVKAHMIRRHSVKP 99 (99)
Q Consensus 71 ~~~C~~c~~~f~~~~~l~~H~~~~~~~kp 99 (99)
||+|..||+.|...++|..|++.++|++|
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~~hg~~~ 29 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLSVHKQNK 29 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHHhcCCCc
Confidence 45566666666666666666666665543
No 14
>KOG3608|consensus
Probab=98.80 E-value=4.9e-09 Score=63.56 Aligned_cols=86 Identities=23% Similarity=0.441 Sum_probs=64.4
Q ss_pred CCCCceeeCccccccccccchhhhccchhhccCCCCCCCcceeccC--CCcccccChhHHHHHHHh-hCC--CCceecCC
Q psy3483 2 KSTELIVTCMYCSKILTYETETIMNHCKFCKAVSRPTKYQRYVCCL--CSKYRHSDASKMRSHIRT-HTK--DRPYKCFY 76 (99)
Q Consensus 2 h~~~~~~~c~~c~~~f~~~~~~~~~h~~~~~~~~~~~~~~~~~c~~--c~~~~~~~~~~~~~h~~~-~~~--~~~~~C~~ 76 (99)
|+.++||+|..|++.+..++ .|..| ...|. +.-|.|.- |...+... ..+..|.+- |.| ..+|.|-.
T Consensus 287 Hs~dkpfKCd~Cd~~c~~es-dL~kH------~~~HS-~~~y~C~h~~C~~s~r~~-~q~~~H~~evhEg~np~~Y~CH~ 357 (467)
T KOG3608|consen 287 HSKDKPFKCDECDTRCVRES-DLAKH------VQVHS-KTVYQCEHPDCHYSVRTY-TQMRRHFLEVHEGNNPILYACHC 357 (467)
T ss_pred hccCCCccccchhhhhccHH-HHHHH------HHhcc-ccceecCCCCCcHHHHHH-HHHHHHHHHhccCCCCCceeeec
Confidence 67788888888888888887 88888 66665 45577766 76655554 677777654 434 45699999
Q ss_pred CCccccCchHHHHHHHHhcC
Q psy3483 77 CDYRSNERSNVKAHMIRRHS 96 (99)
Q Consensus 77 c~~~f~~~~~l~~H~~~~~~ 96 (99)
|++.|..-.+|.+|+...++
T Consensus 358 Cdr~ft~G~~L~~HL~kkH~ 377 (467)
T KOG3608|consen 358 CDRFFTSGKSLSAHLMKKHG 377 (467)
T ss_pred chhhhccchhHHHHHHHhhc
Confidence 99999999999999776554
No 15
>PLN03086 PRLI-interacting factor K; Provisional
Probab=98.78 E-value=1.1e-08 Score=65.89 Aligned_cols=77 Identities=16% Similarity=0.271 Sum_probs=56.3
Q ss_pred CceeeCccccccccccchhhhccchhhccCCCCCCCcceeccCCCcccccChhHHHHHHHhhCCCCceecCCCCccccC-
Q psy3483 5 ELIVTCMYCSKILTYETETIMNHCKFCKAVSRPTKYQRYVCCLCSKYRHSDASKMRSHIRTHTKDRPYKCFYCDYRSNE- 83 (99)
Q Consensus 5 ~~~~~c~~c~~~f~~~~~~~~~h~~~~~~~~~~~~~~~~~c~~c~~~~~~~~~~~~~h~~~~~~~~~~~C~~c~~~f~~- 83 (99)
++.+.|+.|++.|. .. .+..| ...+. .++.|+ ||. +... ..+..|+..+...+++.|..|+..|..
T Consensus 451 ~~H~~C~~Cgk~f~-~s-~LekH------~~~~H--kpv~Cp-Cg~-~~~R-~~L~~H~~thCp~Kpi~C~fC~~~v~~g 517 (567)
T PLN03086 451 KNHVHCEKCGQAFQ-QG-EMEKH------MKVFH--EPLQCP-CGV-VLEK-EQMVQHQASTCPLRLITCRFCGDMVQAG 517 (567)
T ss_pred ccCccCCCCCCccc-hH-HHHHH------HHhcC--CCccCC-CCC-Ccch-hHHHhhhhccCCCCceeCCCCCCccccC
Confidence 45678889988885 34 67788 44442 667888 886 4444 788888888888889999999888742
Q ss_pred ---------chHHHHHHHHh
Q psy3483 84 ---------RSNVKAHMIRR 94 (99)
Q Consensus 84 ---------~~~l~~H~~~~ 94 (99)
...|..|+...
T Consensus 518 ~~~~d~~d~~s~Lt~HE~~C 537 (567)
T PLN03086 518 GSAMDVRDRLRGMSEHESIC 537 (567)
T ss_pred ccccchhhhhhhHHHHHHhc
Confidence 24677887764
No 16
>PHA02768 hypothetical protein; Provisional
Probab=98.71 E-value=2.3e-09 Score=48.55 Aligned_cols=40 Identities=13% Similarity=0.333 Sum_probs=34.6
Q ss_pred eeeCccccccccccchhhhccchhhccCCCCCCCcceeccCCCcccccC
Q psy3483 7 IVTCMYCSKILTYETETIMNHCKFCKAVSRPTKYQRYVCCLCSKYRHSD 55 (99)
Q Consensus 7 ~~~c~~c~~~f~~~~~~~~~h~~~~~~~~~~~~~~~~~c~~c~~~~~~~ 55 (99)
.|.|+.||+.|...+ .|..| ++.|+ +++.|..|++.|...
T Consensus 5 ~y~C~~CGK~Fs~~~-~L~~H------~r~H~--k~~kc~~C~k~f~~~ 44 (55)
T PHA02768 5 GYECPICGEIYIKRK-SMITH------LRKHN--TNLKLSNCKRISLRT 44 (55)
T ss_pred ccCcchhCCeeccHH-HHHHH------HHhcC--CcccCCcccceeccc
Confidence 489999999999999 99999 88888 678899999966543
No 17
>PHA00733 hypothetical protein
Probab=98.48 E-value=1.5e-07 Score=50.23 Aligned_cols=54 Identities=15% Similarity=0.288 Sum_probs=43.5
Q ss_pred CCCceeeCccccccccccchhhhccchhhccCCCCCCCcceeccCCCcccccChhHHHHHHHhh
Q psy3483 3 STELIVTCMYCSKILTYETETIMNHCKFCKAVSRPTKYQRYVCCLCSKYRHSDASKMRSHIRTH 66 (99)
Q Consensus 3 ~~~~~~~c~~c~~~f~~~~~~~~~h~~~~~~~~~~~~~~~~~c~~c~~~~~~~~~~~~~h~~~~ 66 (99)
.+++||.|+.|++.|.... .|..| +..+ ..++.|.+|++.|... ..|..|+.-.
T Consensus 69 ~~~kPy~C~~Cgk~Fss~s-~L~~H------~r~h--~~~~~C~~CgK~F~~~-~sL~~H~~~~ 122 (128)
T PHA00733 69 KAVSPYVCPLCLMPFSSSV-SLKQH------IRYT--EHSKVCPVCGKEFRNT-DSTLDHVCKK 122 (128)
T ss_pred CCCCCccCCCCCCcCCCHH-HHHHH------HhcC--CcCccCCCCCCccCCH-HHHHHHHHHh
Confidence 3578999999999999998 88888 5544 3468999999987776 8888887654
No 18
>PLN03086 PRLI-interacting factor K; Provisional
Probab=98.44 E-value=5e-07 Score=58.47 Aligned_cols=77 Identities=17% Similarity=0.343 Sum_probs=60.8
Q ss_pred ceeeCccccccccccchhhhccchhhccCCCCCCCcceeccCCCccccc---------ChhHHHHHHHhhCCCCceecCC
Q psy3483 6 LIVTCMYCSKILTYETETIMNHCKFCKAVSRPTKYQRYVCCLCSKYRHS---------DASKMRSHIRTHTKDRPYKCFY 76 (99)
Q Consensus 6 ~~~~c~~c~~~f~~~~~~~~~h~~~~~~~~~~~~~~~~~c~~c~~~~~~---------~~~~~~~h~~~~~~~~~~~C~~ 76 (99)
+++.|+ |++.+ .+. .|..| ...+...+++.|..|+..+.. ....+..|.... +.+++.|..
T Consensus 477 kpv~Cp-Cg~~~-~R~-~L~~H------~~thCp~Kpi~C~fC~~~v~~g~~~~d~~d~~s~Lt~HE~~C-G~rt~~C~~ 546 (567)
T PLN03086 477 EPLQCP-CGVVL-EKE-QMVQH------QASTCPLRLITCRFCGDMVQAGGSAMDVRDRLRGMSEHESIC-GSRTAPCDS 546 (567)
T ss_pred CCccCC-CCCCc-chh-HHHhh------hhccCCCCceeCCCCCCccccCccccchhhhhhhHHHHHHhc-CCcceEccc
Confidence 678999 99765 445 88889 888999999999999986531 124788888885 999999999
Q ss_pred CCccccCchHHHHHHHH
Q psy3483 77 CDYRSNERSNVKAHMIR 93 (99)
Q Consensus 77 c~~~f~~~~~l~~H~~~ 93 (99)
|++.+..+ .+..|+..
T Consensus 547 Cgk~Vrlr-dm~~H~~~ 562 (567)
T PLN03086 547 CGRSVMLK-EMDIHQIA 562 (567)
T ss_pred cCCeeeeh-hHHHHHHH
Confidence 99987665 67777654
No 19
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=98.38 E-value=6.1e-08 Score=37.65 Aligned_cols=18 Identities=28% Similarity=0.593 Sum_probs=15.2
Q ss_pred CCCCCceeeCcccccccc
Q psy3483 1 MKSTELIVTCMYCSKILT 18 (99)
Q Consensus 1 ~h~~~~~~~c~~c~~~f~ 18 (99)
+|+|++||+|+.|++.|.
T Consensus 8 ~H~~~k~~~C~~C~k~F~ 25 (26)
T PF13465_consen 8 THTGEKPYKCPYCGKSFS 25 (26)
T ss_dssp HHSSSSSEEESSSSEEES
T ss_pred hcCCCCCCCCCCCcCeeC
Confidence 478899999999998885
No 20
>PHA00616 hypothetical protein
Probab=98.36 E-value=1.7e-07 Score=40.55 Aligned_cols=32 Identities=16% Similarity=0.285 Sum_probs=18.1
Q ss_pred eeccCCCcccccChhHHHHHHHhhCCCCceecC
Q psy3483 43 YVCCLCSKYRHSDASKMRSHIRTHTKDRPYKCF 75 (99)
Q Consensus 43 ~~c~~c~~~~~~~~~~~~~h~~~~~~~~~~~C~ 75 (99)
|+|+.||+.|... +.+..|++.+++++++.|.
T Consensus 2 YqC~~CG~~F~~~-s~l~~H~r~~hg~~~~~~~ 33 (44)
T PHA00616 2 YQCLRCGGIFRKK-KEVIEHLLSVHKQNKLTLE 33 (44)
T ss_pred CccchhhHHHhhH-HHHHHHHHHhcCCCcccee
Confidence 4556666555544 5566666666666555544
No 21
>PHA00732 hypothetical protein
Probab=98.35 E-value=4.1e-07 Score=44.61 Aligned_cols=44 Identities=20% Similarity=0.409 Sum_probs=30.6
Q ss_pred eeeCccccccccccchhhhccchhhccCCC-CCCCcceeccCCCcccccChhHHHHHHH
Q psy3483 7 IVTCMYCSKILTYETETIMNHCKFCKAVSR-PTKYQRYVCCLCSKYRHSDASKMRSHIR 64 (99)
Q Consensus 7 ~~~c~~c~~~f~~~~~~~~~h~~~~~~~~~-~~~~~~~~c~~c~~~~~~~~~~~~~h~~ 64 (99)
||.|..|++.|.... .|..| ++. |.+ +.|+.|++.|. .+..|..
T Consensus 1 py~C~~Cgk~F~s~s-~Lk~H------~r~~H~~---~~C~~CgKsF~----~l~~H~~ 45 (79)
T PHA00732 1 MFKCPICGFTTVTLF-ALKQH------ARRNHTL---TKCPVCNKSYR----RLNQHFY 45 (79)
T ss_pred CccCCCCCCccCCHH-HHHHH------hhcccCC---CccCCCCCEeC----Chhhhhc
Confidence 578888888888887 88888 653 443 46888888654 2455553
No 22
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=98.27 E-value=9e-07 Score=33.20 Aligned_cols=23 Identities=43% Similarity=0.752 Sum_probs=19.4
Q ss_pred eecCCCCccccCchHHHHHHHHh
Q psy3483 72 YKCFYCDYRSNERSNVKAHMIRR 94 (99)
Q Consensus 72 ~~C~~c~~~f~~~~~l~~H~~~~ 94 (99)
|.|..|++.|.....|..|++.|
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 67888999999999998888764
No 23
>KOG3993|consensus
Probab=98.09 E-value=8.3e-07 Score=55.19 Aligned_cols=25 Identities=12% Similarity=0.493 Sum_probs=23.0
Q ss_pred ceecCCCCccccCchHHHHHHHHhc
Q psy3483 71 PYKCFYCDYRSNERSNVKAHMIRRH 95 (99)
Q Consensus 71 ~~~C~~c~~~f~~~~~l~~H~~~~~ 95 (99)
.|.|..|++.|.....|..|+.+|.
T Consensus 356 i~~C~~C~KkFrRqAYLrKHqlthq 380 (500)
T KOG3993|consen 356 IFSCHTCGKKFRRQAYLRKHQLTHQ 380 (500)
T ss_pred eeecHHhhhhhHHHHHHHHhHHhhh
Confidence 6999999999999999999988875
No 24
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=98.08 E-value=2.6e-06 Score=33.18 Aligned_cols=26 Identities=23% Similarity=0.430 Sum_probs=21.8
Q ss_pred ceecCCCCccccCchHHHHHHHHhcC
Q psy3483 71 PYKCFYCDYRSNERSNVKAHMIRRHS 96 (99)
Q Consensus 71 ~~~C~~c~~~f~~~~~l~~H~~~~~~ 96 (99)
||.|..|++.|.....|..|++.|.+
T Consensus 1 ~~~C~~C~~~F~~~~~l~~H~~~h~~ 26 (27)
T PF13912_consen 1 PFECDECGKTFSSLSALREHKRSHCS 26 (27)
T ss_dssp SEEETTTTEEESSHHHHHHHHCTTTT
T ss_pred CCCCCccCCccCChhHHHHHhHHhcC
Confidence 58899999999999999999887753
No 25
>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=98.00 E-value=8.3e-06 Score=30.53 Aligned_cols=24 Identities=25% Similarity=0.625 Sum_probs=18.2
Q ss_pred eecCCCCccccCchHHHHHHHHhc
Q psy3483 72 YKCFYCDYRSNERSNVKAHMIRRH 95 (99)
Q Consensus 72 ~~C~~c~~~f~~~~~l~~H~~~~~ 95 (99)
|.|..|+..|.....|..|+.+++
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 678888888888888888888763
No 26
>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=97.97 E-value=1.2e-05 Score=35.65 Aligned_cols=33 Identities=27% Similarity=0.530 Sum_probs=22.3
Q ss_pred CCCCceecCCCCccccCchHHHHHHHHhcCCCC
Q psy3483 67 TKDRPYKCFYCDYRSNERSNVKAHMIRRHSVKP 99 (99)
Q Consensus 67 ~~~~~~~C~~c~~~f~~~~~l~~H~~~~~~~kp 99 (99)
.++.|-.|++|+..+.+..+|.+|+...++.||
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 456788888888888888888888888877776
No 27
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=97.93 E-value=3.6e-05 Score=35.03 Aligned_cols=49 Identities=27% Similarity=0.575 Sum_probs=27.4
Q ss_pred eeccCCCcccccChhHHHHHHHh-hCC-CCceecCCCCccccCchHHHHHHHHhc
Q psy3483 43 YVCCLCSKYRHSDASKMRSHIRT-HTK-DRPYKCFYCDYRSNERSNVKAHMIRRH 95 (99)
Q Consensus 43 ~~c~~c~~~~~~~~~~~~~h~~~-~~~-~~~~~C~~c~~~f~~~~~l~~H~~~~~ 95 (99)
|.|+.|++ .+.. ..|..|... |.. .+.+.|+.|...+. .+|..|+..++
T Consensus 3 f~CP~C~~-~~~~-~~L~~H~~~~H~~~~~~v~CPiC~~~~~--~~l~~Hl~~~H 53 (54)
T PF05605_consen 3 FTCPYCGK-GFSE-SSLVEHCEDEHRSESKNVVCPICSSRVT--DNLIRHLNSQH 53 (54)
T ss_pred cCCCCCCC-ccCH-HHHHHHHHhHCcCCCCCccCCCchhhhh--hHHHHHHHHhc
Confidence 55666666 4444 556666443 333 23566777765433 36666766544
No 28
>PHA00732 hypothetical protein
Probab=97.80 E-value=1.2e-05 Score=39.49 Aligned_cols=47 Identities=21% Similarity=0.424 Sum_probs=37.5
Q ss_pred ceeccCCCcccccChhHHHHHHHh-hCCCCceecCCCCccccCchHHHHHHHHhc
Q psy3483 42 RYVCCLCSKYRHSDASKMRSHIRT-HTKDRPYKCFYCDYRSNERSNVKAHMIRRH 95 (99)
Q Consensus 42 ~~~c~~c~~~~~~~~~~~~~h~~~-~~~~~~~~C~~c~~~f~~~~~l~~H~~~~~ 95 (99)
||.|..|++.|... ..+..|++. |. ++.|..|++.|. .+..|.++..
T Consensus 1 py~C~~Cgk~F~s~-s~Lk~H~r~~H~---~~~C~~CgKsF~---~l~~H~~~~~ 48 (79)
T PHA00732 1 MFKCPICGFTTVTL-FALKQHARRNHT---LTKCPVCNKSYR---RLNQHFYSQY 48 (79)
T ss_pred CccCCCCCCccCCH-HHHHHHhhcccC---CCccCCCCCEeC---ChhhhhcccC
Confidence 47899999988777 999999984 65 368999999997 4777776543
No 29
>KOG3993|consensus
Probab=97.60 E-value=2.7e-05 Score=48.76 Aligned_cols=60 Identities=22% Similarity=0.471 Sum_probs=44.7
Q ss_pred ceeeCccccccccccchhhhccchhhccC------CCC---------------------CCCcceeccCCCcccccChhH
Q psy3483 6 LIVTCMYCSKILTYETETIMNHCKFCKAV------SRP---------------------TKYQRYVCCLCSKYRHSDASK 58 (99)
Q Consensus 6 ~~~~c~~c~~~f~~~~~~~~~h~~~~~~~------~~~---------------------~~~~~~~c~~c~~~~~~~~~~ 58 (99)
..|.|++|+|.|.... +|-.|.+|.... ... ..+..|.|.+|++.|..+ .-
T Consensus 294 vEYrCPEC~KVFsCPA-NLASHRRWHKPR~eaa~a~~~P~k~~~~~rae~~ea~rsg~dss~gi~~C~~C~KkFrRq-AY 371 (500)
T KOG3993|consen 294 VEYRCPECDKVFSCPA-NLASHRRWHKPRPEAAKAGSPPPKQAVETRAEVQEAERSGDDSSSGIFSCHTCGKKFRRQ-AY 371 (500)
T ss_pred eeecCCcccccccCch-hhhhhhcccCCchhhhhcCCCChhhhhhhhhhhhhccccCCcccCceeecHHhhhhhHHH-HH
Confidence 3589999999999998 999998875110 000 112358999999999888 78
Q ss_pred HHHHHHhhC
Q psy3483 59 MRSHIRTHT 67 (99)
Q Consensus 59 ~~~h~~~~~ 67 (99)
|..|+.+|.
T Consensus 372 LrKHqlthq 380 (500)
T KOG3993|consen 372 LRKHQLTHQ 380 (500)
T ss_pred HHHhHHhhh
Confidence 889987763
No 30
>smart00355 ZnF_C2H2 zinc finger.
Probab=97.59 E-value=8.6e-05 Score=28.02 Aligned_cols=24 Identities=29% Similarity=0.533 Sum_probs=19.0
Q ss_pred eecCCCCccccCchHHHHHHHHhc
Q psy3483 72 YKCFYCDYRSNERSNVKAHMIRRH 95 (99)
Q Consensus 72 ~~C~~c~~~f~~~~~l~~H~~~~~ 95 (99)
|.|..|++.|.....|..|++.|.
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~~H~ 24 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMRTHX 24 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHHHhc
Confidence 468888888888888888887654
No 31
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=97.57 E-value=6e-05 Score=28.02 Aligned_cols=20 Identities=35% Similarity=0.725 Sum_probs=9.9
Q ss_pred eccCCCcccccChhHHHHHHH
Q psy3483 44 VCCLCSKYRHSDASKMRSHIR 64 (99)
Q Consensus 44 ~c~~c~~~~~~~~~~~~~h~~ 64 (99)
.|+.|++.|... ..|..|++
T Consensus 2 ~C~~C~~~f~~~-~~l~~H~~ 21 (23)
T PF00096_consen 2 KCPICGKSFSSK-SNLKRHMR 21 (23)
T ss_dssp EETTTTEEESSH-HHHHHHHH
T ss_pred CCCCCCCccCCH-HHHHHHHh
Confidence 455555544444 55555544
No 32
>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=97.55 E-value=7.3e-05 Score=34.03 Aligned_cols=50 Identities=26% Similarity=0.640 Sum_probs=33.9
Q ss_pred eeeCccccccccccchhhhccchhhccCCCCCCC-cceeccCCCcccccChhHHHHHHHhh
Q psy3483 7 IVTCMYCSKILTYETETIMNHCKFCKAVSRPTKY-QRYVCCLCSKYRHSDASKMRSHIRTH 66 (99)
Q Consensus 7 ~~~c~~c~~~f~~~~~~~~~h~~~~~~~~~~~~~-~~~~c~~c~~~~~~~~~~~~~h~~~~ 66 (99)
.|.|++|++.|. .. .|..|+ ...|..+ +.+.|++|... .. ..+..|+..+
T Consensus 2 ~f~CP~C~~~~~-~~-~L~~H~-----~~~H~~~~~~v~CPiC~~~--~~-~~l~~Hl~~~ 52 (54)
T PF05605_consen 2 SFTCPYCGKGFS-ES-SLVEHC-----EDEHRSESKNVVCPICSSR--VT-DNLIRHLNSQ 52 (54)
T ss_pred CcCCCCCCCccC-HH-HHHHHH-----HhHCcCCCCCccCCCchhh--hh-hHHHHHHHHh
Confidence 589999999655 34 677774 3344433 45889999873 23 5778887654
No 33
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=97.41 E-value=0.00017 Score=36.50 Aligned_cols=73 Identities=14% Similarity=0.429 Sum_probs=21.2
Q ss_pred eCccccccccccchhhhccchhhccCCCCCCCcceeccCCCcccccChhHHHHHHHhhCCCCceecCCCCccccCchHHH
Q psy3483 9 TCMYCSKILTYETETIMNHCKFCKAVSRPTKYQRYVCCLCSKYRHSDASKMRSHIRTHTKDRPYKCFYCDYRSNERSNVK 88 (99)
Q Consensus 9 ~c~~c~~~f~~~~~~~~~h~~~~~~~~~~~~~~~~~c~~c~~~~~~~~~~~~~h~~~~~~~~~~~C~~c~~~f~~~~~l~ 88 (99)
+|..|+..|.... .+..| +....+-.. ..... .... ..+..+... .....+.|..|+..|.....|.
T Consensus 1 ~C~~C~~~f~~~~-~l~~H------~~~~H~~~~---~~~~~-l~~~-~~~~~~~~~-~~~~~~~C~~C~~~f~s~~~l~ 67 (100)
T PF12756_consen 1 QCLFCDESFSSVD-DLLQH------MKKKHGFDI---PDQKY-LVDP-NRLLNYLRK-KVKESFRCPYCNKTFRSREALQ 67 (100)
T ss_dssp -------------------------------------------------------------SSEEBSSSS-EESSHHHHH
T ss_pred Ccccccccccccc-ccccc------ccccccccc---ccccc-cccc-ccccccccc-ccCCCCCCCccCCCCcCHHHHH
Confidence 5889999998877 78888 533222110 00000 1111 222222221 1223699999999999999999
Q ss_pred HHHHHh
Q psy3483 89 AHMIRR 94 (99)
Q Consensus 89 ~H~~~~ 94 (99)
.|++.+
T Consensus 68 ~Hm~~~ 73 (100)
T PF12756_consen 68 EHMRSK 73 (100)
T ss_dssp HHHHHT
T ss_pred HHHcCc
Confidence 999865
No 34
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=97.32 E-value=0.00014 Score=44.20 Aligned_cols=70 Identities=20% Similarity=0.243 Sum_probs=40.4
Q ss_pred CceeeCc--cccccccccchhhhccchhhc-cCCCCCCCcceeccCCCcccccChhHHHHHHHhhCCCCceecCCCCccc
Q psy3483 5 ELIVTCM--YCSKILTYETETIMNHCKFCK-AVSRPTKYQRYVCCLCSKYRHSDASKMRSHIRTHTKDRPYKCFYCDYRS 81 (99)
Q Consensus 5 ~~~~~c~--~c~~~f~~~~~~~~~h~~~~~-~~~~~~~~~~~~c~~c~~~~~~~~~~~~~h~~~~~~~~~~~C~~c~~~f 81 (99)
++||+|+ .|.|.++..- .|..|+..+. ....| +.| -++--..| -...+||.|.+|++.+
T Consensus 347 ~KpykCpV~gC~K~Yknqn-GLKYH~lhGH~~~~~~--~~p--~p~~~~~F-------------~~~~KPYrCevC~KRY 408 (423)
T COG5189 347 GKPYKCPVEGCNKKYKNQN-GLKYHMLHGHQNQKLH--ENP--SPEKMNIF-------------SAKDKPYRCEVCDKRY 408 (423)
T ss_pred CceecCCCCCchhhhcccc-chhhhhhccccCcccC--CCC--Cccccccc-------------cccCCceeccccchhh
Confidence 4788884 4777777666 6777732211 01111 111 11111112 2347899999999999
Q ss_pred cCchHHHHHHH
Q psy3483 82 NERSNVKAHMI 92 (99)
Q Consensus 82 ~~~~~l~~H~~ 92 (99)
.+..-|.-|+.
T Consensus 409 KNlNGLKYHr~ 419 (423)
T COG5189 409 KNLNGLKYHRK 419 (423)
T ss_pred ccCccceeccc
Confidence 88888877654
No 35
>PRK04860 hypothetical protein; Provisional
Probab=97.25 E-value=0.00033 Score=38.96 Aligned_cols=40 Identities=23% Similarity=0.453 Sum_probs=33.1
Q ss_pred cceeccCCCcccccChhHHHHHHHhhCCCCceecCCCCccccCch
Q psy3483 41 QRYVCCLCSKYRHSDASKMRSHIRTHTKDRPYKCFYCDYRSNERS 85 (99)
Q Consensus 41 ~~~~c~~c~~~~~~~~~~~~~h~~~~~~~~~~~C~~c~~~f~~~~ 85 (99)
-+|.|. |+. .. ..+..|.++++++++|.|..|+..|....
T Consensus 118 ~~Y~C~-C~~---~~-~~~rrH~ri~~g~~~YrC~~C~~~l~~~~ 157 (160)
T PRK04860 118 FPYRCK-CQE---HQ-LTVRRHNRVVRGEAVYRCRRCGETLVFKG 157 (160)
T ss_pred EEEEcC-CCC---ee-CHHHHHHHHhcCCccEECCCCCceeEEec
Confidence 368997 986 33 67899999999999999999999876543
No 36
>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=97.22 E-value=0.0001 Score=28.50 Aligned_cols=20 Identities=20% Similarity=0.444 Sum_probs=10.7
Q ss_pred eeeCccccccccccchhhhcc
Q psy3483 7 IVTCMYCSKILTYETETIMNH 27 (99)
Q Consensus 7 ~~~c~~c~~~f~~~~~~~~~h 27 (99)
||+|..|++.|.... .|..|
T Consensus 1 ~~~C~~C~~~F~~~~-~l~~H 20 (27)
T PF13912_consen 1 PFECDECGKTFSSLS-ALREH 20 (27)
T ss_dssp SEEETTTTEEESSHH-HHHHH
T ss_pred CCCCCccCCccCChh-HHHHH
Confidence 345555555555555 55555
No 37
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=97.12 E-value=0.00065 Score=25.44 Aligned_cols=23 Identities=48% Similarity=1.008 Sum_probs=16.0
Q ss_pred eecCCCCccccCchHHHHHHHHhc
Q psy3483 72 YKCFYCDYRSNERSNVKAHMIRRH 95 (99)
Q Consensus 72 ~~C~~c~~~f~~~~~l~~H~~~~~ 95 (99)
|.|..|+.... ...|..|++.++
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 67888887776 778888887764
No 38
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=97.12 E-value=0.0004 Score=26.24 Aligned_cols=23 Identities=13% Similarity=0.499 Sum_probs=18.8
Q ss_pred eecCCCCccccCchHHHHHHHHh
Q psy3483 72 YKCFYCDYRSNERSNVKAHMIRR 94 (99)
Q Consensus 72 ~~C~~c~~~f~~~~~l~~H~~~~ 94 (99)
|.|..|+..|.....+..|++.+
T Consensus 1 ~~C~~C~~~f~s~~~~~~H~~s~ 23 (25)
T PF12874_consen 1 FYCDICNKSFSSENSLRQHLRSK 23 (25)
T ss_dssp EEETTTTEEESSHHHHHHHHTTH
T ss_pred CCCCCCCCCcCCHHHHHHHHCcC
Confidence 57888888888888888887654
No 39
>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=97.03 E-value=0.00061 Score=25.14 Aligned_cols=22 Identities=41% Similarity=0.831 Sum_probs=11.0
Q ss_pred eeccCCCcccccChhHHHHHHHh
Q psy3483 43 YVCCLCSKYRHSDASKMRSHIRT 65 (99)
Q Consensus 43 ~~c~~c~~~~~~~~~~~~~h~~~ 65 (99)
|.|+.|+..|... ..+..|+..
T Consensus 1 ~~C~~C~~~~~~~-~~l~~H~~~ 22 (24)
T PF13894_consen 1 FQCPICGKSFRSK-SELRQHMRT 22 (24)
T ss_dssp EE-SSTS-EESSH-HHHHHHHHH
T ss_pred CCCcCCCCcCCcH-HHHHHHHHh
Confidence 3466666655544 556666554
No 40
>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=96.61 E-value=0.00044 Score=26.77 Aligned_cols=22 Identities=27% Similarity=0.504 Sum_probs=17.6
Q ss_pred eecCCCCccccCchHHHHHHHH
Q psy3483 72 YKCFYCDYRSNERSNVKAHMIR 93 (99)
Q Consensus 72 ~~C~~c~~~f~~~~~l~~H~~~ 93 (99)
|.|..|++.|.....+..|+++
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 6788888888888888877654
No 41
>PF09237 GAGA: GAGA factor; InterPro: IPR015318 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Members of this entry bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognises the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognises the A in the fourth position of the consensus sequence []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1YUI_A 1YUJ_A.
Probab=96.32 E-value=0.0083 Score=26.81 Aligned_cols=34 Identities=18% Similarity=0.415 Sum_probs=21.5
Q ss_pred CCCCcceeccCCCcccccChhHHHHHHHhhCCCCc
Q psy3483 37 PTKYQRYVCCLCSKYRHSDASKMRSHIRTHTKDRP 71 (99)
Q Consensus 37 ~~~~~~~~c~~c~~~~~~~~~~~~~h~~~~~~~~~ 71 (99)
...++|..|++|+...... .+|..|+....+.+|
T Consensus 19 ~~S~~PatCP~C~a~~~~s-rnLrRHle~~H~~k~ 52 (54)
T PF09237_consen 19 SQSEQPATCPICGAVIRQS-RNLRRHLEIRHFKKP 52 (54)
T ss_dssp CTTS--EE-TTT--EESSH-HHHHHHHHHHTTTS-
T ss_pred hccCCCCCCCcchhhccch-hhHHHHHHHHhcccC
Confidence 3456788999999976665 899999987766655
No 42
>PRK04860 hypothetical protein; Provisional
Probab=95.99 E-value=0.0034 Score=35.00 Aligned_cols=36 Identities=19% Similarity=0.325 Sum_probs=29.0
Q ss_pred eeeCccccccccccchhhhccchhhccCCCCCCCcceeccCCCcccc
Q psy3483 7 IVTCMYCSKILTYETETIMNHCKFCKAVSRPTKYQRYVCCLCSKYRH 53 (99)
Q Consensus 7 ~~~c~~c~~~f~~~~~~~~~h~~~~~~~~~~~~~~~~~c~~c~~~~~ 53 (99)
+|.|. |+. ... .+..| .+.++++++|.|..|+..+.
T Consensus 119 ~Y~C~-C~~---~~~-~~rrH------~ri~~g~~~YrC~~C~~~l~ 154 (160)
T PRK04860 119 PYRCK-CQE---HQL-TVRRH------NRVVRGEAVYRCRRCGETLV 154 (160)
T ss_pred EEEcC-CCC---eeC-HHHHH------HHHhcCCccEECCCCCceeE
Confidence 68897 988 333 66788 88899999999999998654
No 43
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=95.61 E-value=0.015 Score=22.04 Aligned_cols=18 Identities=17% Similarity=0.436 Sum_probs=9.1
Q ss_pred ecCCCCccccCchHHHHHH
Q psy3483 73 KCFYCDYRSNERSNVKAHM 91 (99)
Q Consensus 73 ~C~~c~~~f~~~~~l~~H~ 91 (99)
.|+.||+.| ....|..|+
T Consensus 4 ~C~~CgR~F-~~~~l~~H~ 21 (25)
T PF13913_consen 4 PCPICGRKF-NPDRLEKHE 21 (25)
T ss_pred cCCCCCCEE-CHHHHHHHH
Confidence 455555555 333444554
No 44
>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=0.024 Score=22.95 Aligned_cols=23 Identities=22% Similarity=0.502 Sum_probs=17.4
Q ss_pred ceecCCCCccccCchHHHHHHHH
Q psy3483 71 PYKCFYCDYRSNERSNVKAHMIR 93 (99)
Q Consensus 71 ~~~C~~c~~~f~~~~~l~~H~~~ 93 (99)
+|.|..|+..|.....+..|+..
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~g 25 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLKG 25 (35)
T ss_pred CeEccccCCccCCHHHHHHHHCh
Confidence 47788888888877777777653
No 45
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=94.22 E-value=0.027 Score=25.63 Aligned_cols=27 Identities=15% Similarity=0.282 Sum_probs=18.6
Q ss_pred hCCCCceecCCCCccccCchHHHHHHH
Q psy3483 66 HTKDRPYKCFYCDYRSNERSNVKAHMI 92 (99)
Q Consensus 66 ~~~~~~~~C~~c~~~f~~~~~l~~H~~ 92 (99)
..|+.-+.|+.|+..|....++.+|.-
T Consensus 12 RDGE~~lrCPRC~~~FR~~K~Y~RHVN 38 (65)
T COG4049 12 RDGEEFLRCPRCGMVFRRRKDYIRHVN 38 (65)
T ss_pred cCCceeeeCCchhHHHHHhHHHHHHhh
Confidence 345666777777777777777777754
No 46
>cd00350 rubredoxin_like Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center. The family includes rubredoxins, a small electron transfer protein, and a slightly smaller modular rubredoxin domain present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=94.00 E-value=0.062 Score=21.75 Aligned_cols=24 Identities=29% Similarity=0.837 Sum_probs=14.8
Q ss_pred eeccCCCcccccChhHHHHHHHhhCCCCceecCCCCc
Q psy3483 43 YVCCLCSKYRHSDASKMRSHIRTHTKDRPYKCFYCDY 79 (99)
Q Consensus 43 ~~c~~c~~~~~~~~~~~~~h~~~~~~~~~~~C~~c~~ 79 (99)
|.|.+||..+... ..++.|+.|+.
T Consensus 2 ~~C~~CGy~y~~~-------------~~~~~CP~Cg~ 25 (33)
T cd00350 2 YVCPVCGYIYDGE-------------EAPWVCPVCGA 25 (33)
T ss_pred EECCCCCCEECCC-------------cCCCcCcCCCC
Confidence 5677777643322 25778888764
No 47
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=93.84 E-value=0.052 Score=31.76 Aligned_cols=17 Identities=24% Similarity=0.510 Sum_probs=14.2
Q ss_pred CceeeCccccccccccc
Q psy3483 5 ELIVTCMYCSKILTYET 21 (99)
Q Consensus 5 ~~~~~c~~c~~~f~~~~ 21 (99)
++...||+|++.|..+.
T Consensus 3 ~k~~~CPvC~~~F~~~~ 19 (214)
T PF09986_consen 3 DKKITCPVCGKEFKTKK 19 (214)
T ss_pred CCceECCCCCCeeeeeE
Confidence 46679999999998775
No 48
>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=93.46 E-value=0.055 Score=28.26 Aligned_cols=28 Identities=21% Similarity=0.418 Sum_probs=18.5
Q ss_pred eCccccccccccchhhhccchhhccCCCCCCCcceeccCCCccccc
Q psy3483 9 TCMYCSKILTYETETIMNHCKFCKAVSRPTKYQRYVCCLCSKYRHS 54 (99)
Q Consensus 9 ~c~~c~~~f~~~~~~~~~h~~~~~~~~~~~~~~~~~c~~c~~~~~~ 54 (99)
.|+.||+.|. .|.. .|..|+.||..|..
T Consensus 11 ~Cp~CG~kFY----DLnk--------------~PivCP~CG~~~~~ 38 (108)
T PF09538_consen 11 TCPSCGAKFY----DLNK--------------DPIVCPKCGTEFPP 38 (108)
T ss_pred cCCCCcchhc----cCCC--------------CCccCCCCCCccCc
Confidence 6888888877 2222 35678888875543
No 49
>KOG1146|consensus
Probab=93.36 E-value=0.036 Score=40.03 Aligned_cols=26 Identities=27% Similarity=0.751 Sum_probs=22.1
Q ss_pred CCCceecCCCCccccCchHHHHHHHH
Q psy3483 68 KDRPYKCFYCDYRSNERSNVKAHMIR 93 (99)
Q Consensus 68 ~~~~~~C~~c~~~f~~~~~l~~H~~~ 93 (99)
+.++|.|..|...+....+|.+|+..
T Consensus 515 ~~~p~~C~~C~~stttng~LsihlqS 540 (1406)
T KOG1146|consen 515 PGKPYPCRACNYSTTTNGNLSIHLQS 540 (1406)
T ss_pred CCCcccceeeeeeeecchHHHHHHHH
Confidence 45689999999999999999999764
No 50
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=92.95 E-value=0.054 Score=25.00 Aligned_cols=31 Identities=19% Similarity=0.620 Sum_probs=16.2
Q ss_pred eeccCCCcccccChhHHHHHHHhhCCCCceecCCCCc
Q psy3483 43 YVCCLCSKYRHSDASKMRSHIRTHTKDRPYKCFYCDY 79 (99)
Q Consensus 43 ~~c~~c~~~~~~~~~~~~~h~~~~~~~~~~~C~~c~~ 79 (99)
|.|+.||...... . .+...-..+|.|+.||.
T Consensus 28 F~CPnCGe~~I~R-c-----~~CRk~g~~Y~Cp~CGF 58 (61)
T COG2888 28 FPCPNCGEVEIYR-C-----AKCRKLGNPYRCPKCGF 58 (61)
T ss_pred eeCCCCCceeeeh-h-----hhHHHcCCceECCCcCc
Confidence 6778887532222 1 11122245788888873
No 51
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=91.90 E-value=0.035 Score=34.89 Aligned_cols=55 Identities=20% Similarity=0.446 Sum_probs=40.5
Q ss_pred ceeccCCCcccccChhHHHHHHH--hhCCC--CceecC--CCCccccCchHHHHHHHHhcCC
Q psy3483 42 RYVCCLCSKYRHSDASKMRSHIR--THTKD--RPYKCF--YCDYRSNERSNVKAHMIRRHSV 97 (99)
Q Consensus 42 ~~~c~~c~~~~~~~~~~~~~h~~--~~~~~--~~~~C~--~c~~~f~~~~~l~~H~~~~~~~ 97 (99)
++.|..|...+... ..+..|.. .|+++ +++.|+ .|++.|.....+..|...|++.
T Consensus 289 ~~~~~~~~~~~s~~-~~l~~~~~~~~h~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~ 349 (467)
T COG5048 289 PIKSKQCNISFSRS-SPLTRHLRSVNHSGESLKPFSCPYSLCGKLFSRNDALKRHILLHTSI 349 (467)
T ss_pred CCCCccccCCcccc-ccccccccccccccccCCceeeeccCCCccccccccccCCcccccCC
Confidence 45667777766665 77777777 68888 788888 6888888888877777777654
No 52
>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=91.83 E-value=0.18 Score=20.54 Aligned_cols=10 Identities=40% Similarity=0.796 Sum_probs=5.8
Q ss_pred CceecCCCCc
Q psy3483 70 RPYKCFYCDY 79 (99)
Q Consensus 70 ~~~~C~~c~~ 79 (99)
.|..|+.|+.
T Consensus 17 ~p~~CP~Cg~ 26 (34)
T cd00729 17 APEKCPICGA 26 (34)
T ss_pred CCCcCcCCCC
Confidence 3556666653
No 53
>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=90.54 E-value=0.25 Score=20.46 Aligned_cols=13 Identities=15% Similarity=0.501 Sum_probs=7.4
Q ss_pred eeCcccccccccc
Q psy3483 8 VTCMYCSKILTYE 20 (99)
Q Consensus 8 ~~c~~c~~~f~~~ 20 (99)
..|+.|+..|.-.
T Consensus 3 ~~CP~C~~~~~v~ 15 (38)
T TIGR02098 3 IQCPNCKTSFRVV 15 (38)
T ss_pred EECCCCCCEEEeC
Confidence 4566666665533
No 54
>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=90.52 E-value=0.2 Score=27.99 Aligned_cols=13 Identities=15% Similarity=0.329 Sum_probs=6.5
Q ss_pred eeCcccccccccc
Q psy3483 8 VTCMYCSKILTYE 20 (99)
Q Consensus 8 ~~c~~c~~~f~~~ 20 (99)
|.|+.|+..|...
T Consensus 110 Y~Cp~c~~r~tf~ 122 (158)
T TIGR00373 110 FICPNMCVRFTFN 122 (158)
T ss_pred EECCCCCcEeeHH
Confidence 4555555554443
No 55
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=90.50 E-value=0.29 Score=20.21 Aligned_cols=12 Identities=25% Similarity=0.592 Sum_probs=6.7
Q ss_pred eCcccccccccc
Q psy3483 9 TCMYCSKILTYE 20 (99)
Q Consensus 9 ~c~~c~~~f~~~ 20 (99)
.|+.|+..|.-.
T Consensus 4 ~Cp~C~~~y~i~ 15 (36)
T PF13717_consen 4 TCPNCQAKYEID 15 (36)
T ss_pred ECCCCCCEEeCC
Confidence 466666665433
No 56
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=90.41 E-value=0.25 Score=20.53 Aligned_cols=11 Identities=27% Similarity=0.615 Sum_probs=5.6
Q ss_pred eCccccccccc
Q psy3483 9 TCMYCSKILTY 19 (99)
Q Consensus 9 ~c~~c~~~f~~ 19 (99)
.|+.|+..|.-
T Consensus 4 ~CP~C~~~f~v 14 (37)
T PF13719_consen 4 TCPNCQTRFRV 14 (37)
T ss_pred ECCCCCceEEc
Confidence 45555555543
No 57
>PHA00626 hypothetical protein
Probab=90.15 E-value=0.092 Score=23.94 Aligned_cols=12 Identities=33% Similarity=0.955 Sum_probs=6.1
Q ss_pred ceecCCCCcccc
Q psy3483 71 PYKCFYCDYRSN 82 (99)
Q Consensus 71 ~~~C~~c~~~f~ 82 (99)
.|.|..|+..|+
T Consensus 23 rYkCkdCGY~ft 34 (59)
T PHA00626 23 DYVCCDCGYNDS 34 (59)
T ss_pred ceEcCCCCCeec
Confidence 455555555443
No 58
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=90.08 E-value=0.19 Score=23.25 Aligned_cols=32 Identities=19% Similarity=0.672 Sum_probs=16.6
Q ss_pred ceeccCCCcccccChhHHHHHHHhhCCCCceecCCCCc
Q psy3483 42 RYVCCLCSKYRHSDASKMRSHIRTHTKDRPYKCFYCDY 79 (99)
Q Consensus 42 ~~~c~~c~~~~~~~~~~~~~h~~~~~~~~~~~C~~c~~ 79 (99)
.|.|+.||...... -. +-..-..+|.|+.||.
T Consensus 25 ~F~CPnCG~~~I~R-C~-----~CRk~~~~Y~CP~CGF 56 (59)
T PRK14890 25 KFLCPNCGEVIIYR-CE-----KCRKQSNPYTCPKCGF 56 (59)
T ss_pred EeeCCCCCCeeEee-ch-----hHHhcCCceECCCCCC
Confidence 36777777641111 10 1112245788888874
No 59
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=90.04 E-value=0.22 Score=28.35 Aligned_cols=15 Identities=20% Similarity=0.569 Sum_probs=8.6
Q ss_pred eeeCccccccccccc
Q psy3483 7 IVTCMYCSKILTYET 21 (99)
Q Consensus 7 ~~~c~~c~~~f~~~~ 21 (99)
-|.|+.|+..|....
T Consensus 117 ~Y~Cp~C~~rytf~e 131 (178)
T PRK06266 117 FFFCPNCHIRFTFDE 131 (178)
T ss_pred EEECCCCCcEEeHHH
Confidence 456666666655443
No 60
>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=89.04 E-value=0.17 Score=21.66 Aligned_cols=11 Identities=18% Similarity=0.522 Sum_probs=6.8
Q ss_pred eeCcccccccc
Q psy3483 8 VTCMYCSKILT 18 (99)
Q Consensus 8 ~~c~~c~~~f~ 18 (99)
|.|..||..|.
T Consensus 6 y~C~~Cg~~fe 16 (42)
T PF09723_consen 6 YRCEECGHEFE 16 (42)
T ss_pred EEeCCCCCEEE
Confidence 56666666654
No 61
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=88.98 E-value=0.21 Score=31.43 Aligned_cols=61 Identities=20% Similarity=0.363 Sum_probs=47.8
Q ss_pred eeeCccccccccccchhhhccchhhccCC--CCCCC--cceecc--CCCcccccChhHHHHHHHhhCCCCceecC
Q psy3483 7 IVTCMYCSKILTYETETIMNHCKFCKAVS--RPTKY--QRYVCC--LCSKYRHSDASKMRSHIRTHTKDRPYKCF 75 (99)
Q Consensus 7 ~~~c~~c~~~f~~~~~~~~~h~~~~~~~~--~~~~~--~~~~c~--~c~~~~~~~~~~~~~h~~~~~~~~~~~C~ 75 (99)
++.|..|...|.... .+..| .. .|.++ +++.|+ .|++.+... ..+..|...+++..++.+.
T Consensus 289 ~~~~~~~~~~~s~~~-~l~~~------~~~~~h~~~~~~~~~~p~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~ 355 (467)
T COG5048 289 PIKSKQCNISFSRSS-PLTRH------LRSVNHSGESLKPFSCPYSLCGKLFSRN-DALKRHILLHTSISPAKEK 355 (467)
T ss_pred CCCCccccCCccccc-ccccc------ccccccccccCCceeeeccCCCcccccc-ccccCCcccccCCCccccc
Confidence 567888888888887 88888 77 68888 888888 788876666 7778888888877766654
No 62
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=88.92 E-value=0.37 Score=27.19 Aligned_cols=23 Identities=30% Similarity=0.758 Sum_probs=18.6
Q ss_pred ceeccCCCcccccChhHHHHHHHhhCCCCceecCCCC
Q psy3483 42 RYVCCLCSKYRHSDASKMRSHIRTHTKDRPYKCFYCD 78 (99)
Q Consensus 42 ~~~c~~c~~~~~~~~~~~~~h~~~~~~~~~~~C~~c~ 78 (99)
.|.|++||.. +.++-|..|+.||
T Consensus 134 ~~vC~vCGy~--------------~~ge~P~~CPiCg 156 (166)
T COG1592 134 VWVCPVCGYT--------------HEGEAPEVCPICG 156 (166)
T ss_pred EEEcCCCCCc--------------ccCCCCCcCCCCC
Confidence 6899999873 3457799999998
No 63
>KOG2186|consensus
Probab=88.56 E-value=0.47 Score=28.54 Aligned_cols=56 Identities=20% Similarity=0.453 Sum_probs=35.4
Q ss_pred eeeCccccccccccchhhhccchhhccCCCCCCCcceeccCCCcccccChhHHHHHHHhhCCCCcee
Q psy3483 7 IVTCMYCSKILTYETETIMNHCKFCKAVSRPTKYQRYVCCLCSKYRHSDASKMRSHIRTHTKDRPYK 73 (99)
Q Consensus 7 ~~~c~~c~~~f~~~~~~~~~h~~~~~~~~~~~~~~~~~c~~c~~~~~~~~~~~~~h~~~~~~~~~~~ 73 (99)
-|.|..||-...-. .+..|+.-| ++ ..|.|..|++.|.. ....+|...-+....|.
T Consensus 3 ~FtCnvCgEsvKKp--~vekH~srC------rn-~~fSCIDC~k~F~~--~sYknH~kCITEaQKYg 58 (276)
T KOG2186|consen 3 FFTCNVCGESVKKP--QVEKHMSRC------RN-AYFSCIDCGKTFER--VSYKNHTKCITEAQKYG 58 (276)
T ss_pred EEehhhhhhhcccc--chHHHHHhc------cC-CeeEEeeccccccc--chhhhhhhhcchHHHhh
Confidence 37789999886644 456673222 22 45889999986553 56777776655544443
No 64
>PF10571 UPF0547: Uncharacterised protein family UPF0547; InterPro: IPR018886 This domain may well be a type of zinc-finger as it carries two pairs of highly conserved cysteine residues though with no accompanying histidines. Several members are annotated as putative helicases.
Probab=87.47 E-value=0.53 Score=17.98 Aligned_cols=11 Identities=27% Similarity=0.525 Sum_probs=6.2
Q ss_pred eecCCCCcccc
Q psy3483 72 YKCFYCDYRSN 82 (99)
Q Consensus 72 ~~C~~c~~~f~ 82 (99)
-.|+.||..|.
T Consensus 15 ~~Cp~CG~~F~ 25 (26)
T PF10571_consen 15 KFCPHCGYDFE 25 (26)
T ss_pred CcCCCCCCCCc
Confidence 35666666553
No 65
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=86.39 E-value=1.2 Score=19.28 Aligned_cols=8 Identities=25% Similarity=0.629 Sum_probs=3.6
Q ss_pred eeccCCCc
Q psy3483 43 YVCCLCSK 50 (99)
Q Consensus 43 ~~c~~c~~ 50 (99)
..|+.||.
T Consensus 22 ~~Cp~CG~ 29 (46)
T PRK00398 22 VRCPYCGY 29 (46)
T ss_pred eECCCCCC
Confidence 34444443
No 66
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=86.27 E-value=0.69 Score=23.18 Aligned_cols=32 Identities=19% Similarity=0.456 Sum_probs=20.9
Q ss_pred cceeccCCCcccccChhHHHHHHHhhCCCCceecCCCCccccC
Q psy3483 41 QRYVCCLCSKYRHSDASKMRSHIRTHTKDRPYKCFYCDYRSNE 83 (99)
Q Consensus 41 ~~~~c~~c~~~~~~~~~~~~~h~~~~~~~~~~~C~~c~~~f~~ 83 (99)
..|.|+.|++. ... ..+.-.|.|..|+..|.-
T Consensus 34 ~~~~Cp~C~~~-~Vk----------R~a~GIW~C~kCg~~fAG 65 (89)
T COG1997 34 AKHVCPFCGRT-TVK----------RIATGIWKCRKCGAKFAG 65 (89)
T ss_pred cCCcCCCCCCc-cee----------eeccCeEEcCCCCCeecc
Confidence 34789999874 211 133456999999887753
No 67
>PF03811 Zn_Tnp_IS1: InsA N-terminal domain; InterPro: IPR003220 Insertion elements are mobile elements in DNA, usually encoding proteins required for transposition, for example transposases. Protein InsA is absolutely required for transposition of insertion element 1. This entry represents a short zinc binding domain found in IS1 InsA family protein. It is found at the N terminus of the protein and may be a DNA-binding domain.; GO: 0006313 transposition, DNA-mediated
Probab=85.31 E-value=1 Score=18.63 Aligned_cols=15 Identities=40% Similarity=0.707 Sum_probs=8.1
Q ss_pred CCCCCCCcceeccCC
Q psy3483 34 VSRPTKYQRYVCCLC 48 (99)
Q Consensus 34 ~~~~~~~~~~~c~~c 48 (99)
-....|.+.|.|..|
T Consensus 21 G~~~~G~qryrC~~C 35 (36)
T PF03811_consen 21 GKSPSGHQRYRCKDC 35 (36)
T ss_pred CCCCCCCEeEecCcC
Confidence 444455555666554
No 68
>KOG4167|consensus
Probab=84.80 E-value=0.17 Score=34.75 Aligned_cols=25 Identities=20% Similarity=0.259 Sum_probs=22.9
Q ss_pred ceecCCCCccccCchHHHHHHHHhc
Q psy3483 71 PYKCFYCDYRSNERSNVKAHMIRRH 95 (99)
Q Consensus 71 ~~~C~~c~~~f~~~~~l~~H~~~~~ 95 (99)
.|.|.+|++.|.-...+.+|+++|.
T Consensus 792 iFpCreC~kvF~KiKSrNAHMK~Hr 816 (907)
T KOG4167|consen 792 IFPCRECGKVFFKIKSRNAHMKTHR 816 (907)
T ss_pred eeehHHHHHHHHHHhhhhHHHHHHH
Confidence 4999999999999999999999884
No 69
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=84.45 E-value=1.3 Score=24.41 Aligned_cols=39 Identities=18% Similarity=0.255 Sum_probs=21.7
Q ss_pred CCCcceeccCCCcccccChhHHHHHHHhhCCCCceecCCCCccc
Q psy3483 38 TKYQRYVCCLCSKYRHSDASKMRSHIRTHTKDRPYKCFYCDYRS 81 (99)
Q Consensus 38 ~~~~~~~c~~c~~~~~~~~~~~~~h~~~~~~~~~~~C~~c~~~f 81 (99)
.....|.|+.|+..+... ..+. .... ...|.|+.||...
T Consensus 95 ~~~~~Y~Cp~C~~~y~~~-ea~~---~~d~-~~~f~Cp~Cg~~l 133 (147)
T smart00531 95 TNNAYYKCPNCQSKYTFL-EANQ---LLDM-DGTFTCPRCGEEL 133 (147)
T ss_pred cCCcEEECcCCCCEeeHH-HHHH---hcCC-CCcEECCCCCCEE
Confidence 444568888888754433 2221 1112 3348888887654
No 70
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=84.32 E-value=0.65 Score=25.12 Aligned_cols=15 Identities=13% Similarity=0.483 Sum_probs=12.0
Q ss_pred eeeCccccccccccc
Q psy3483 7 IVTCMYCSKILTYET 21 (99)
Q Consensus 7 ~~~c~~c~~~f~~~~ 21 (99)
|++|..||+.|...+
T Consensus 1 PH~Ct~Cg~~f~dgs 15 (131)
T PF09845_consen 1 PHQCTKCGRVFEDGS 15 (131)
T ss_pred CcccCcCCCCcCCCc
Confidence 568889999988665
No 71
>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=83.94 E-value=1.3 Score=23.02 Aligned_cols=25 Identities=24% Similarity=0.724 Sum_probs=22.6
Q ss_pred eec----CCCCccccCchHHHHHHHHhcC
Q psy3483 72 YKC----FYCDYRSNERSNVKAHMIRRHS 96 (99)
Q Consensus 72 ~~C----~~c~~~f~~~~~l~~H~~~~~~ 96 (99)
|.| ..|+........+..|++..+|
T Consensus 81 ~~C~~~~~~C~y~~~~~~~m~~H~~~~Hg 109 (109)
T PF12013_consen 81 YRCQCDPPHCGYITRSKKTMRKHWRKEHG 109 (109)
T ss_pred eeeecCCCCCCcEeccHHHHHHHHHHhcC
Confidence 899 8999999999999999988765
No 72
>PF14353 CpXC: CpXC protein
Probab=83.58 E-value=0.73 Score=24.63 Aligned_cols=13 Identities=31% Similarity=0.843 Sum_probs=9.8
Q ss_pred eeCcccccccccc
Q psy3483 8 VTCMYCSKILTYE 20 (99)
Q Consensus 8 ~~c~~c~~~f~~~ 20 (99)
.+|+.|+..|...
T Consensus 2 itCP~C~~~~~~~ 14 (128)
T PF14353_consen 2 ITCPHCGHEFEFE 14 (128)
T ss_pred cCCCCCCCeeEEE
Confidence 3689999887654
No 73
>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=83.57 E-value=0.56 Score=20.81 Aligned_cols=12 Identities=17% Similarity=0.465 Sum_probs=7.9
Q ss_pred eeeCcccccccc
Q psy3483 7 IVTCMYCSKILT 18 (99)
Q Consensus 7 ~~~c~~c~~~f~ 18 (99)
.|.|..|+..|.
T Consensus 5 ey~C~~Cg~~fe 16 (52)
T TIGR02605 5 EYRCTACGHRFE 16 (52)
T ss_pred EEEeCCCCCEeE
Confidence 366777777665
No 74
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=83.53 E-value=1.8 Score=18.78 Aligned_cols=10 Identities=30% Similarity=0.816 Sum_probs=5.5
Q ss_pred CceecCCCCc
Q psy3483 70 RPYKCFYCDY 79 (99)
Q Consensus 70 ~~~~C~~c~~ 79 (99)
.+..|+.||.
T Consensus 18 ~~irC~~CG~ 27 (44)
T smart00659 18 DVVRCRECGY 27 (44)
T ss_pred CceECCCCCc
Confidence 3456666654
No 75
>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=83.44 E-value=0.75 Score=24.75 Aligned_cols=28 Identities=7% Similarity=0.006 Sum_probs=18.3
Q ss_pred eCccccccccccchhhhccchhhccCCCCCCCcceeccCCCccccc
Q psy3483 9 TCMYCSKILTYETETIMNHCKFCKAVSRPTKYQRYVCCLCSKYRHS 54 (99)
Q Consensus 9 ~c~~c~~~f~~~~~~~~~h~~~~~~~~~~~~~~~~~c~~c~~~~~~ 54 (99)
.|+.||+.|. .|.+ .|..|+.||..+..
T Consensus 11 ~Cp~cg~kFY----DLnk--------------~p~vcP~cg~~~~~ 38 (129)
T TIGR02300 11 ICPNTGSKFY----DLNR--------------RPAVSPYTGEQFPP 38 (129)
T ss_pred cCCCcCcccc----ccCC--------------CCccCCCcCCccCc
Confidence 6888888876 2222 35678888875443
No 76
>KOG3408|consensus
Probab=82.28 E-value=0.76 Score=24.51 Aligned_cols=26 Identities=15% Similarity=0.327 Sum_probs=22.1
Q ss_pred CCCceecCCCCccccCchHHHHHHHH
Q psy3483 68 KDRPYKCFYCDYRSNERSNVKAHMIR 93 (99)
Q Consensus 68 ~~~~~~C~~c~~~f~~~~~l~~H~~~ 93 (99)
|--.|.|.+|.+-|.....|..|.++
T Consensus 54 G~GqfyCi~CaRyFi~~~~l~~H~kt 79 (129)
T KOG3408|consen 54 GGGQFYCIECARYFIDAKALKTHFKT 79 (129)
T ss_pred CCceeehhhhhhhhcchHHHHHHHhc
Confidence 34459999999999999999999775
No 77
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=82.22 E-value=1.4 Score=30.76 Aligned_cols=12 Identities=25% Similarity=0.479 Sum_probs=7.2
Q ss_pred eCcccccccccc
Q psy3483 9 TCMYCSKILTYE 20 (99)
Q Consensus 9 ~c~~c~~~f~~~ 20 (99)
.|..||..+...
T Consensus 437 ~C~~Cg~v~~Cp 448 (730)
T COG1198 437 LCRDCGYIAECP 448 (730)
T ss_pred ecccCCCcccCC
Confidence 467777665443
No 78
>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=81.71 E-value=1.1 Score=24.42 Aligned_cols=23 Identities=22% Similarity=0.473 Sum_probs=14.0
Q ss_pred ceecCCCCccccCchHHHHHHHHhcC
Q psy3483 71 PYKCFYCDYRSNERSNVKAHMIRRHS 96 (99)
Q Consensus 71 ~~~C~~c~~~f~~~~~l~~H~~~~~~ 96 (99)
-..|.+||+.|.. |.+|+++|+|
T Consensus 72 ~i~clecGk~~k~---LkrHL~~~~g 94 (132)
T PF05443_consen 72 YIICLECGKKFKT---LKRHLRTHHG 94 (132)
T ss_dssp -EE-TBT--EESB---HHHHHHHTT-
T ss_pred eeEEccCCcccch---HHHHHHHccC
Confidence 4689999997754 4889988865
No 79
>KOG2893|consensus
Probab=81.61 E-value=0.26 Score=29.46 Aligned_cols=44 Identities=25% Similarity=0.574 Sum_probs=28.2
Q ss_pred ceeeCccccccccccchhhhccchhhccCCCCCCCcceeccCCCcccccChhHHHHH
Q psy3483 6 LIVTCMYCSKILTYETETIMNHCKFCKAVSRPTKYQRYVCCLCSKYRHSDASKMRSH 62 (99)
Q Consensus 6 ~~~~c~~c~~~f~~~~~~~~~h~~~~~~~~~~~~~~~~~c~~c~~~~~~~~~~~~~h 62 (99)
++| |.+|.+.|..+. -|..| ...+.|.|-+|.+-.++- -.|..|
T Consensus 10 kpw-cwycnrefddek-iliqh----------qkakhfkchichkkl~sg-pglsih 53 (341)
T KOG2893|consen 10 KPW-CWYCNREFDDEK-ILIQH----------QKAKHFKCHICHKKLFSG-PGLSIH 53 (341)
T ss_pred Cce-eeecccccchhh-hhhhh----------hhhccceeeeehhhhccC-CCceee
Confidence 443 779999998877 55555 233458899988755544 344433
No 80
>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=81.51 E-value=0.89 Score=17.05 Aligned_cols=10 Identities=20% Similarity=0.524 Sum_probs=7.5
Q ss_pred ceeeCccccc
Q psy3483 6 LIVTCMYCSK 15 (99)
Q Consensus 6 ~~~~c~~c~~ 15 (99)
.+|.|+.||+
T Consensus 15 v~f~CPnCG~ 24 (24)
T PF07754_consen 15 VPFPCPNCGF 24 (24)
T ss_pred ceEeCCCCCC
Confidence 3688888874
No 81
>smart00614 ZnF_BED BED zinc finger. DNA-binding domain in chromatin-boundary-element-binding proteins and transposases
Probab=80.63 E-value=2.3 Score=18.74 Aligned_cols=21 Identities=33% Similarity=0.706 Sum_probs=10.8
Q ss_pred eecCCCCccccCc-----hHHHHHHH
Q psy3483 72 YKCFYCDYRSNER-----SNVKAHMI 92 (99)
Q Consensus 72 ~~C~~c~~~f~~~-----~~l~~H~~ 92 (99)
..|..|++.+... ++|..|+.
T Consensus 19 a~C~~C~~~l~~~~~~gTs~L~rHl~ 44 (50)
T smart00614 19 AKCKYCGKKLSRSSKGGTSNLRRHLR 44 (50)
T ss_pred EEecCCCCEeeeCCCCCcHHHHHHHH
Confidence 3455555544433 46666655
No 82
>PF15269 zf-C2H2_7: Zinc-finger
Probab=80.40 E-value=1.5 Score=19.09 Aligned_cols=21 Identities=48% Similarity=1.007 Sum_probs=15.7
Q ss_pred eecCCCCccccCchHHHHHHH
Q psy3483 72 YKCFYCDYRSNERSNVKAHMI 92 (99)
Q Consensus 72 ~~C~~c~~~f~~~~~l~~H~~ 92 (99)
|+|..|......++.|..|++
T Consensus 21 ykcfqcpftc~~kshl~nhmk 41 (54)
T PF15269_consen 21 YKCFQCPFTCNEKSHLFNHMK 41 (54)
T ss_pred ceeecCCcccchHHHHHHHHH
Confidence 677777777777777777765
No 83
>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=80.39 E-value=2.3 Score=18.04 Aligned_cols=23 Identities=35% Similarity=0.615 Sum_probs=10.4
Q ss_pred CCceecCCCCccccCc----hHHHHHH
Q psy3483 69 DRPYKCFYCDYRSNER----SNVKAHM 91 (99)
Q Consensus 69 ~~~~~C~~c~~~f~~~----~~l~~H~ 91 (99)
.....|..|++.+... ++|..|+
T Consensus 14 ~~~a~C~~C~~~~~~~~~~ts~l~~HL 40 (45)
T PF02892_consen 14 KKKAKCKYCGKVIKYSSGGTSNLKRHL 40 (45)
T ss_dssp SS-EEETTTTEE-----SSTHHHHHHH
T ss_pred cCeEEeCCCCeEEeeCCCcHHHHHHhh
Confidence 3345566666555443 4666665
No 84
>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=79.68 E-value=0.54 Score=28.50 Aligned_cols=28 Identities=21% Similarity=0.523 Sum_probs=21.6
Q ss_pred CCCCceecCCCCccccCchHHHHHHHHh
Q psy3483 67 TKDRPYKCFYCDYRSNERSNVKAHMIRR 94 (99)
Q Consensus 67 ~~~~~~~C~~c~~~f~~~~~l~~H~~~~ 94 (99)
...+++.|+.|+.-.....+|.+..++|
T Consensus 205 ~k~k~~PCPKCg~et~eTkdLSmStR~h 232 (314)
T PF06524_consen 205 EKGKPIPCPKCGYETQETKDLSMSTRSH 232 (314)
T ss_pred ccCCCCCCCCCCCcccccccceeeeecc
Confidence 4567899999998877777777766655
No 85
>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=79.12 E-value=0.73 Score=27.15 Aligned_cols=23 Identities=17% Similarity=0.437 Sum_probs=11.2
Q ss_pred ceecCCCCccccCchHHHHHHHH
Q psy3483 71 PYKCFYCDYRSNERSNVKAHMIR 93 (99)
Q Consensus 71 ~~~C~~c~~~f~~~~~l~~H~~~ 93 (99)
.|.|..|++.|.....+..|+..
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 86
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=78.77 E-value=0.74 Score=22.28 Aligned_cols=18 Identities=28% Similarity=0.183 Sum_probs=9.9
Q ss_pred CCCcceecc--CCCcccccC
Q psy3483 38 TKYQRYVCC--LCSKYRHSD 55 (99)
Q Consensus 38 ~~~~~~~c~--~c~~~~~~~ 55 (99)
..+..++|. .||..|...
T Consensus 23 ~~~~Y~qC~N~eCg~tF~t~ 42 (72)
T PRK09678 23 TKERYHQCQNVNCSATFITY 42 (72)
T ss_pred hheeeeecCCCCCCCEEEEE
Confidence 334456666 677655443
No 87
>KOG4173|consensus
Probab=78.61 E-value=0.53 Score=27.52 Aligned_cols=74 Identities=19% Similarity=0.430 Sum_probs=49.3
Q ss_pred eeC--ccccccccccchhhhccchhhccCCCCCCCcceeccCCCcccccChhHHHHHHH----------hhCCCCceecC
Q psy3483 8 VTC--MYCSKILTYETETIMNHCKFCKAVSRPTKYQRYVCCLCSKYRHSDASKMRSHIR----------THTKDRPYKCF 75 (99)
Q Consensus 8 ~~c--~~c~~~f~~~~~~~~~h~~~~~~~~~~~~~~~~~c~~c~~~~~~~~~~~~~h~~----------~~~~~~~~~C~ 75 (99)
+-| ..|-+.|.... .+..| ...-. ...|.+|.+.|.+. ..|..|+. +-.|..-|+|.
T Consensus 80 ~~cqvagc~~~~d~lD-~~E~h------Y~~~h---~~sCs~C~r~~Pt~-hLLd~HI~E~HDs~Fqa~veRG~dMy~Cl 148 (253)
T KOG4173|consen 80 FACQVAGCCQVFDALD-DYEHH------YHTLH---GNSCSFCKRAFPTG-HLLDAHILEWHDSLFQALVERGQDMYQCL 148 (253)
T ss_pred ccccccchHHHHhhhh-hHHHh------hhhcc---cchhHHHHHhCCch-hhhhHHHHHHHHHHHHHHHHcCccHHHHH
Confidence 445 34666776665 66666 32211 13699999988877 77887754 23456668886
Q ss_pred C--CCccccCchHHHHHHH
Q psy3483 76 Y--CDYRSNERSNVKAHMI 92 (99)
Q Consensus 76 ~--c~~~f~~~~~l~~H~~ 92 (99)
+ |+..|........|+.
T Consensus 149 vEgCt~KFkT~r~RkdH~I 167 (253)
T KOG4173|consen 149 VEGCTEKFKTSRDRKDHMI 167 (253)
T ss_pred HHhhhhhhhhhhhhhhHHH
Confidence 5 9888988887777754
No 88
>PF09963 DUF2197: Uncharacterized protein conserved in bacteria (DUF2197); InterPro: IPR019241 This family represents various hypothetical bacterial proteins with no known function.
Probab=78.36 E-value=1.8 Score=19.83 Aligned_cols=7 Identities=43% Similarity=1.060 Sum_probs=3.4
Q ss_pred ceecCCC
Q psy3483 71 PYKCFYC 77 (99)
Q Consensus 71 ~~~C~~c 77 (99)
.|.|.+|
T Consensus 31 tYmC~eC 37 (56)
T PF09963_consen 31 TYMCDEC 37 (56)
T ss_pred ceeChhH
Confidence 3555554
No 89
>PF15135 UPF0515: Uncharacterised protein UPF0515
Probab=78.34 E-value=4.1 Score=24.71 Aligned_cols=17 Identities=12% Similarity=0.335 Sum_probs=12.6
Q ss_pred CCceeeCcccccccccc
Q psy3483 4 TELIVTCMYCSKILTYE 20 (99)
Q Consensus 4 ~~~~~~c~~c~~~f~~~ 20 (99)
.++.|.|..|+..++.+
T Consensus 109 ~drqFaC~~Cd~~WwRr 125 (278)
T PF15135_consen 109 VDRQFACSSCDHMWWRR 125 (278)
T ss_pred cceeeeccccchHHHhc
Confidence 45778999998776654
No 90
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=78.17 E-value=0.46 Score=26.50 Aligned_cols=13 Identities=23% Similarity=0.306 Sum_probs=9.8
Q ss_pred eeccCCCcccccC
Q psy3483 43 YVCCLCSKYRHSD 55 (99)
Q Consensus 43 ~~c~~c~~~~~~~ 55 (99)
++|+.||..|...
T Consensus 29 ~~c~~c~~~f~~~ 41 (154)
T PRK00464 29 RECLACGKRFTTF 41 (154)
T ss_pred eeccccCCcceEe
Confidence 7888888876554
No 91
>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=77.75 E-value=2.8 Score=16.87 Aligned_cols=9 Identities=33% Similarity=0.888 Sum_probs=4.3
Q ss_pred ceecCCCCc
Q psy3483 71 PYKCFYCDY 79 (99)
Q Consensus 71 ~~~C~~c~~ 79 (99)
+..|+.||.
T Consensus 17 ~irC~~CG~ 25 (32)
T PF03604_consen 17 PIRCPECGH 25 (32)
T ss_dssp TSSBSSSS-
T ss_pred cEECCcCCC
Confidence 445555554
No 92
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=77.30 E-value=1.6 Score=22.13 Aligned_cols=31 Identities=19% Similarity=0.467 Sum_probs=19.8
Q ss_pred cceeccCCCcccccChhHHHHHHHhhCCCCceecCCCCcccc
Q psy3483 41 QRYVCCLCSKYRHSDASKMRSHIRTHTKDRPYKCFYCDYRSN 82 (99)
Q Consensus 41 ~~~~c~~c~~~~~~~~~~~~~h~~~~~~~~~~~C~~c~~~f~ 82 (99)
..|.|+.|++..... .+.-.|.|..|++.|.
T Consensus 35 a~y~CpfCgk~~vkR-----------~a~GIW~C~~C~~~~A 65 (90)
T PTZ00255 35 AKYFCPFCGKHAVKR-----------QAVGIWRCKGCKKTVA 65 (90)
T ss_pred CCccCCCCCCCceee-----------eeeEEEEcCCCCCEEe
Confidence 347899998632211 2334689999987765
No 93
>COG3364 Zn-ribbon containing protein [General function prediction only]
Probab=76.59 E-value=1.4 Score=22.80 Aligned_cols=16 Identities=13% Similarity=0.488 Sum_probs=12.5
Q ss_pred ceeeCccccccccccc
Q psy3483 6 LIVTCMYCSKILTYET 21 (99)
Q Consensus 6 ~~~~c~~c~~~f~~~~ 21 (99)
.|++|..||..|..-+
T Consensus 1 MpH~CtrCG~vf~~g~ 16 (112)
T COG3364 1 MPHQCTRCGEVFDDGS 16 (112)
T ss_pred CCceeccccccccccc
Confidence 3678999999988755
No 94
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=75.92 E-value=2.2 Score=22.02 Aligned_cols=12 Identities=25% Similarity=0.415 Sum_probs=8.0
Q ss_pred ceeeCccccccc
Q psy3483 6 LIVTCMYCSKIL 17 (99)
Q Consensus 6 ~~~~c~~c~~~f 17 (99)
+.|.|+.|+.--
T Consensus 21 k~FtCp~Cghe~ 32 (104)
T COG4888 21 KTFTCPRCGHEK 32 (104)
T ss_pred ceEecCccCCee
Confidence 457788777653
No 95
>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=75.46 E-value=1.1 Score=22.62 Aligned_cols=31 Identities=23% Similarity=0.534 Sum_probs=19.1
Q ss_pred cceeccCCCcccccChhHHHHHHHhhCCCCceecCCCCcccc
Q psy3483 41 QRYVCCLCSKYRHSDASKMRSHIRTHTKDRPYKCFYCDYRSN 82 (99)
Q Consensus 41 ~~~~c~~c~~~~~~~~~~~~~h~~~~~~~~~~~C~~c~~~f~ 82 (99)
..|.|+.|++..... .. .-.|.|..|++.|.
T Consensus 34 ~ky~Cp~Cgk~~vkR---------~a--~GIW~C~~C~~~~A 64 (90)
T PF01780_consen 34 AKYTCPFCGKTSVKR---------VA--TGIWKCKKCGKKFA 64 (90)
T ss_dssp S-BEESSSSSSEEEE---------EE--TTEEEETTTTEEEE
T ss_pred CCCcCCCCCCceeEE---------ee--eEEeecCCCCCEEe
Confidence 347899998743211 12 23589999987664
No 96
>KOG2186|consensus
Probab=75.31 E-value=1.2 Score=26.86 Aligned_cols=44 Identities=16% Similarity=0.489 Sum_probs=23.1
Q ss_pred eeccCCCcccccChhHHHHHHHhhCCCCceecCCCCccccCchHHHHH
Q psy3483 43 YVCCLCSKYRHSDASKMRSHIRTHTKDRPYKCFYCDYRSNERSNVKAH 90 (99)
Q Consensus 43 ~~c~~c~~~~~~~~~~~~~h~~~~~~~~~~~C~~c~~~f~~~~~l~~H 90 (99)
|.|.+||-. .-. ..+..|+..-.+ .-|.|.-|+..|-. .++..|
T Consensus 4 FtCnvCgEs-vKK-p~vekH~srCrn-~~fSCIDC~k~F~~-~sYknH 47 (276)
T KOG2186|consen 4 FTCNVCGES-VKK-PQVEKHMSRCRN-AYFSCIDCGKTFER-VSYKNH 47 (276)
T ss_pred Eehhhhhhh-ccc-cchHHHHHhccC-CeeEEeeccccccc-chhhhh
Confidence 456666653 222 445556555444 45666666666655 334444
No 97
>PF05495 zf-CHY: CHY zinc finger; InterPro: IPR008913 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Pirh2 is an eukaryotic ubiquitin protein ligase, which has been shown to promote p53 degradation in mammals. Pirh2 physically interacts with p53 and promotes ubiquitination of p53 independently of MDM2. Like MDM2, Pirh2 is thought to participate in an autoregulatory feedback loop that controls p53 function. Pirh2 proteins contain three distinct zinc fingers, the CHY-type, the CTCHY-type which is C-terminal to the CHY-type zinc finger and a RING finger. The CHY-type zinc finger has no currently known function []. As well as Pirh2, the CHY-type zinc finger is also found in the following proteins: Yeast helper of Tim protein 13. Hot13 may have a role in the assembly and recycling of the small Tims, a complex of the mitochondrial intermembrane space that participates in the TIM22 import pathway for assembly of the inner membrane [] Several plant hypothetical proteins that also contain haemerythrin cation binding domains Several protozoan hypothetical proteins that also contain a Myb domain The solution structure of this zinc finger has been solved and binds 3 zinc atoms as shown in the following schematic representation: ++---------+-----+ || | | CXHYxxxxxxxxxCCxxxxxCxxCHxxxxxHxxxxxxxxxxxCxxCxxxxxxxxxCxxC | | | | | | | | +-+-----------------+--+ +--+---------+--+ 'C': conserved cysteine involved in the binding of one zinc atom. 'H': conserved histidine involved in the binding of one zinc atom. More information about these proteins can be found at Protein of the Month: Zinc Fingers []; GO: 0008270 zinc ion binding; PDB: 2DKT_A 2K2C_A.
Probab=75.07 E-value=2.6 Score=20.24 Aligned_cols=60 Identities=17% Similarity=0.292 Sum_probs=29.0
Q ss_pred eeeCccccccccccc--hhhhccchhhccCCCCCCCcceeccCCCcccccChhHHHHHHHhhCCCCceecCCCCccc
Q psy3483 7 IVTCMYCSKILTYET--ETIMNHCKFCKAVSRPTKYQRYVCCLCSKYRHSDASKMRSHIRTHTKDRPYKCFYCDYRS 81 (99)
Q Consensus 7 ~~~c~~c~~~f~~~~--~~~~~h~~~~~~~~~~~~~~~~~c~~c~~~~~~~~~~~~~h~~~~~~~~~~~C~~c~~~f 81 (99)
-..++-|++.|.-.. ..+.+| .......+...|..|+..+... .. ..+ ..+.|+.|+..|
T Consensus 10 ~~~~~cC~~~y~C~~CHde~~~H------~~~~~~~~~v~Cg~C~~~~~~~-~~-------~c~-~~~~C~~C~~~~ 71 (71)
T PF05495_consen 10 AIRFPCCGKYYPCRFCHDELEDH------PFDRWPVKRVICGKCRTEQPID-EY-------SCG-ADYFCPICGLYF 71 (71)
T ss_dssp EEEETTTTEEESSHHHHHHCSSS---------TTT--EEEETTT--EEES--SB-------TT---SEEETTTTEEE
T ss_pred EEECCcccCeecHHHHHHHhccC------ccccccccCeECCCCCCccChh-hh-------hcC-CCccCcCcCCCC
Confidence 356777888876442 123344 2222333467899998754433 11 111 468888887543
No 98
>KOG2593|consensus
Probab=74.90 E-value=2 Score=27.94 Aligned_cols=10 Identities=50% Similarity=1.009 Sum_probs=5.0
Q ss_pred cceeccCCCc
Q psy3483 41 QRYVCCLCSK 50 (99)
Q Consensus 41 ~~~~c~~c~~ 50 (99)
+.|.|+.|.+
T Consensus 127 ~~Y~Cp~C~k 136 (436)
T KOG2593|consen 127 AGYVCPNCQK 136 (436)
T ss_pred ccccCCcccc
Confidence 3455555554
No 99
>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=74.02 E-value=1.4 Score=21.78 Aligned_cols=12 Identities=17% Similarity=0.470 Sum_probs=5.7
Q ss_pred ceeccCCCcccc
Q psy3483 42 RYVCCLCSKYRH 53 (99)
Q Consensus 42 ~~~c~~c~~~~~ 53 (99)
...|..|+..|.
T Consensus 46 ~~~C~~Cg~~~~ 57 (81)
T PF05129_consen 46 ILSCRVCGESFQ 57 (81)
T ss_dssp EEEESSS--EEE
T ss_pred EEEecCCCCeEE
Confidence 356777766443
No 100
>PRK14873 primosome assembly protein PriA; Provisional
Probab=73.76 E-value=2.6 Score=29.15 Aligned_cols=10 Identities=20% Similarity=0.567 Sum_probs=6.0
Q ss_pred eCcccccccc
Q psy3483 9 TCMYCSKILT 18 (99)
Q Consensus 9 ~c~~c~~~f~ 18 (99)
.|..||..+.
T Consensus 385 ~C~~Cg~~~~ 394 (665)
T PRK14873 385 ACARCRTPAR 394 (665)
T ss_pred EhhhCcCeeE
Confidence 4666666654
No 101
>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=73.66 E-value=0.48 Score=21.31 Aligned_cols=24 Identities=21% Similarity=0.310 Sum_probs=8.6
Q ss_pred ceecCCCCccccCchHHHHHHHHh
Q psy3483 71 PYKCFYCDYRSNERSNVKAHMIRR 94 (99)
Q Consensus 71 ~~~C~~c~~~f~~~~~l~~H~~~~ 94 (99)
.|.|+.|...|-..=++-+|...|
T Consensus 21 ~y~C~~C~~~FC~dCD~fiHE~LH 44 (51)
T PF07975_consen 21 RYRCPKCKNHFCIDCDVFIHETLH 44 (51)
T ss_dssp EE--TTTT--B-HHHHHTTTTTS-
T ss_pred eEECCCCCCccccCcChhhhcccc
Confidence 355555555555444444444433
No 102
>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=73.42 E-value=1.8 Score=21.99 Aligned_cols=30 Identities=23% Similarity=0.553 Sum_probs=19.0
Q ss_pred ceeccCCCcccccChhHHHHHHHhhCCCCceecCCCCcccc
Q psy3483 42 RYVCCLCSKYRHSDASKMRSHIRTHTKDRPYKCFYCDYRSN 82 (99)
Q Consensus 42 ~~~c~~c~~~~~~~~~~~~~h~~~~~~~~~~~C~~c~~~f~ 82 (99)
.|.|+.|++..... .+.-.|.|..|++.|.
T Consensus 35 ~y~CpfCgk~~vkR-----------~a~GIW~C~~C~~~~A 64 (91)
T TIGR00280 35 KYVCPFCGKKTVKR-----------GSTGIWTCRKCGAKFA 64 (91)
T ss_pred CccCCCCCCCceEE-----------EeeEEEEcCCCCCEEe
Confidence 47799888632211 2334689999987764
No 103
>smart00734 ZnF_Rad18 Rad18-like CCHC zinc finger. Yeast Rad18p functions with Rad5p in error-free post-replicative DNA repair. This zinc finger is likely to bind nucleic-acids.
Probab=73.22 E-value=4.3 Score=15.34 Aligned_cols=19 Identities=16% Similarity=0.361 Sum_probs=10.0
Q ss_pred ecCCCCccccCchHHHHHHH
Q psy3483 73 KCFYCDYRSNERSNVKAHMI 92 (99)
Q Consensus 73 ~C~~c~~~f~~~~~l~~H~~ 92 (99)
.|+.|++.+ ....+..|+.
T Consensus 3 ~CPiC~~~v-~~~~in~HLD 21 (26)
T smart00734 3 QCPVCFREV-PENLINSHLD 21 (26)
T ss_pred cCCCCcCcc-cHHHHHHHHH
Confidence 466666655 3345555543
No 104
>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=72.86 E-value=2.6 Score=17.89 Aligned_cols=12 Identities=33% Similarity=0.636 Sum_probs=8.7
Q ss_pred ceeeCccccccc
Q psy3483 6 LIVTCMYCSKIL 17 (99)
Q Consensus 6 ~~~~c~~c~~~f 17 (99)
++..|++|+..|
T Consensus 28 ~~~~CpYCg~~y 39 (40)
T PF10276_consen 28 GPVVCPYCGTRY 39 (40)
T ss_dssp CEEEETTTTEEE
T ss_pred CeEECCCCCCEE
Confidence 456788888766
No 105
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=71.91 E-value=3.9 Score=18.24 Aligned_cols=8 Identities=38% Similarity=1.269 Sum_probs=4.2
Q ss_pred eeccCCCc
Q psy3483 43 YVCCLCSK 50 (99)
Q Consensus 43 ~~c~~c~~ 50 (99)
|.|..||+
T Consensus 7 Y~C~~Cg~ 14 (49)
T COG1996 7 YKCARCGR 14 (49)
T ss_pred EEhhhcCC
Confidence 45555555
No 106
>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=71.70 E-value=1.4 Score=30.60 Aligned_cols=56 Identities=21% Similarity=0.459 Sum_probs=28.3
Q ss_pred CccccccccccchhhhccchhhccCCCCCCCcce-eccCCCcccccChhHHHHHHHhhCCCCceecCCCCcc
Q psy3483 10 CMYCSKILTYETETIMNHCKFCKAVSRPTKYQRY-VCCLCSKYRHSDASKMRSHIRTHTKDRPYKCFYCDYR 80 (99)
Q Consensus 10 c~~c~~~f~~~~~~~~~h~~~~~~~~~~~~~~~~-~c~~c~~~~~~~~~~~~~h~~~~~~~~~~~C~~c~~~ 80 (99)
|..||-+|.-.. .|..- +.++.-+.| .|+.|.+.+... ... +.| ..|..|+.||..
T Consensus 126 CT~CGPRfTIi~-alPYD-------R~nTsM~~F~lC~~C~~EY~dP-~nR----RfH--AQp~aCp~CGP~ 182 (750)
T COG0068 126 CTNCGPRFTIIE-ALPYD-------RENTSMADFPLCPFCDKEYKDP-LNR----RFH--AQPIACPKCGPH 182 (750)
T ss_pred cCCCCcceeeec-cCCCC-------cccCccccCcCCHHHHHHhcCc-ccc----ccc--cccccCcccCCC
Confidence 677777776544 33332 223322221 366676543333 222 222 447888888863
No 107
>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=71.51 E-value=3 Score=16.25 Aligned_cols=18 Identities=28% Similarity=0.610 Sum_probs=10.4
Q ss_pred eeCccccccccccchhhhcc
Q psy3483 8 VTCMYCSKILTYETETIMNH 27 (99)
Q Consensus 8 ~~c~~c~~~f~~~~~~~~~h 27 (99)
|.|-.|++.|... .+..|
T Consensus 1 ~sCiDC~~~F~~~--~y~~H 18 (28)
T PF08790_consen 1 FSCIDCSKDFDGD--SYKSH 18 (28)
T ss_dssp EEETTTTEEEEGG--GTTT-
T ss_pred CeeecCCCCcCcC--CcCCC
Confidence 4577788888433 34444
No 108
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=71.37 E-value=2.2 Score=17.89 Aligned_cols=15 Identities=20% Similarity=0.436 Sum_probs=12.1
Q ss_pred eeeCccccccccccc
Q psy3483 7 IVTCMYCSKILTYET 21 (99)
Q Consensus 7 ~~~c~~c~~~f~~~~ 21 (99)
|+.|..|++.|-.+-
T Consensus 12 ~f~C~~C~~~FC~~H 26 (39)
T smart00154 12 GFKCRHCGNLFCGEH 26 (39)
T ss_pred CeECCccCCcccccc
Confidence 788999999987543
No 109
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=71.26 E-value=4.2 Score=21.50 Aligned_cols=27 Identities=19% Similarity=0.224 Sum_probs=23.5
Q ss_pred CCceecCCCCccccCchHHHHHHHHhc
Q psy3483 69 DRPYKCFYCDYRSNERSNVKAHMIRRH 95 (99)
Q Consensus 69 ~~~~~C~~c~~~f~~~~~l~~H~~~~~ 95 (99)
...|.|..|...|...-++.+|...|+
T Consensus 79 ~~~y~C~~C~~~FC~dCD~fiHe~Lh~ 105 (112)
T TIGR00622 79 SHRYVCAVCKNVFCVDCDVFVHESLHC 105 (112)
T ss_pred ccceeCCCCCCccccccchhhhhhccC
Confidence 447999999999999999999988775
No 110
>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=71.19 E-value=2.2 Score=17.65 Aligned_cols=14 Identities=14% Similarity=0.301 Sum_probs=10.4
Q ss_pred eeeCcccccccccc
Q psy3483 7 IVTCMYCSKILTYE 20 (99)
Q Consensus 7 ~~~c~~c~~~f~~~ 20 (99)
.|.|..||..|...
T Consensus 5 ~y~C~~Cg~~fe~~ 18 (41)
T smart00834 5 EYRCEDCGHTFEVL 18 (41)
T ss_pred EEEcCCCCCEEEEE
Confidence 47888999887633
No 111
>PLN02294 cytochrome c oxidase subunit Vb
Probab=70.59 E-value=2.6 Score=24.00 Aligned_cols=16 Identities=19% Similarity=0.472 Sum_probs=11.9
Q ss_pred CceeeCcccccccccc
Q psy3483 5 ELIVTCMYCSKILTYE 20 (99)
Q Consensus 5 ~~~~~c~~c~~~f~~~ 20 (99)
.+|..|+.||..|..+
T Consensus 139 Gkp~RCpeCG~~fkL~ 154 (174)
T PLN02294 139 GKSFECPVCTQYFELE 154 (174)
T ss_pred CCceeCCCCCCEEEEE
Confidence 3577888888887755
No 112
>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=70.46 E-value=3.5 Score=19.31 Aligned_cols=11 Identities=18% Similarity=0.341 Sum_probs=3.7
Q ss_pred ceecCCCCccc
Q psy3483 71 PYKCFYCDYRS 81 (99)
Q Consensus 71 ~~~C~~c~~~f 81 (99)
.+.|..||..|
T Consensus 25 rhhCr~CG~~v 35 (69)
T PF01363_consen 25 RHHCRNCGRVV 35 (69)
T ss_dssp EEE-TTT--EE
T ss_pred eEccCCCCCEE
Confidence 34455544443
No 113
>KOG1280|consensus
Probab=69.83 E-value=3.4 Score=26.23 Aligned_cols=22 Identities=27% Similarity=0.407 Sum_probs=10.7
Q ss_pred CceeeCccccccccccchhhhcc
Q psy3483 5 ELIVTCMYCSKILTYETETIMNH 27 (99)
Q Consensus 5 ~~~~~c~~c~~~f~~~~~~~~~h 27 (99)
+..|+|++|+..-..+. .|.-|
T Consensus 77 ~qSftCPyC~~~Gfte~-~f~~H 98 (381)
T KOG1280|consen 77 PQSFTCPYCGIMGFTER-QFGTH 98 (381)
T ss_pred cccccCCcccccccchh-HHHHH
Confidence 34566666665433333 34444
No 114
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=69.43 E-value=2.3 Score=21.52 Aligned_cols=31 Identities=16% Similarity=0.449 Sum_probs=19.4
Q ss_pred cceeccCCCcccccChhHHHHHHHhhCCCCceecCCCCcccc
Q psy3483 41 QRYVCCLCSKYRHSDASKMRSHIRTHTKDRPYKCFYCDYRSN 82 (99)
Q Consensus 41 ~~~~c~~c~~~~~~~~~~~~~h~~~~~~~~~~~C~~c~~~f~ 82 (99)
..|.|+.|++..... .+.-.|.|..|++.|.
T Consensus 35 a~y~CpfCgk~~vkR-----------~a~GIW~C~~C~~~~A 65 (90)
T PRK03976 35 AKHVCPVCGRPKVKR-----------VGTGIWECRKCGAKFA 65 (90)
T ss_pred cCccCCCCCCCceEE-----------EEEEEEEcCCCCCEEe
Confidence 347899887632211 2234689999987764
No 115
>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=68.97 E-value=6.3 Score=17.93 Aligned_cols=11 Identities=18% Similarity=0.540 Sum_probs=7.6
Q ss_pred eeCcccccccc
Q psy3483 8 VTCMYCSKILT 18 (99)
Q Consensus 8 ~~c~~c~~~f~ 18 (99)
+.|+.||..+.
T Consensus 3 ~~CP~CG~~ie 13 (54)
T TIGR01206 3 FECPDCGAEIE 13 (54)
T ss_pred cCCCCCCCEEe
Confidence 56778887654
No 116
>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=68.66 E-value=4.3 Score=27.13 Aligned_cols=10 Identities=40% Similarity=0.796 Sum_probs=5.7
Q ss_pred eCcccccccc
Q psy3483 9 TCMYCSKILT 18 (99)
Q Consensus 9 ~c~~c~~~f~ 18 (99)
.|..||....
T Consensus 215 ~C~~Cg~~~~ 224 (505)
T TIGR00595 215 LCRSCGYILC 224 (505)
T ss_pred EhhhCcCccC
Confidence 4666666544
No 117
>COG3091 SprT Zn-dependent metalloprotease, SprT family [General function prediction only]
Probab=66.96 E-value=3.9 Score=22.84 Aligned_cols=33 Identities=24% Similarity=0.525 Sum_probs=23.2
Q ss_pred cceeccCCCcccccChhHHHHHHHhhCCCCceecCCCCc
Q psy3483 41 QRYVCCLCSKYRHSDASKMRSHIRTHTKDRPYKCFYCDY 79 (99)
Q Consensus 41 ~~~~c~~c~~~~~~~~~~~~~h~~~~~~~~~~~C~~c~~ 79 (99)
-+|.|. |+..+.+ ...|..+-.|+ .|.|..|+-
T Consensus 116 ~~Y~C~-C~q~~l~----~RRhn~~~~g~-~YrC~~C~g 148 (156)
T COG3091 116 YPYRCQ-CQQHYLR----IRRHNTVRRGE-VYRCGKCGG 148 (156)
T ss_pred eeEEee-cCCccch----hhhcccccccc-eEEeccCCc
Confidence 468898 9885443 35566666677 899999964
No 118
>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=65.30 E-value=3.9 Score=17.10 Aligned_cols=8 Identities=63% Similarity=1.817 Sum_probs=5.3
Q ss_pred eeccCCCc
Q psy3483 43 YVCCLCSK 50 (99)
Q Consensus 43 ~~c~~c~~ 50 (99)
|.|..|+.
T Consensus 29 y~C~~C~~ 36 (39)
T PF01096_consen 29 YVCCNCGH 36 (39)
T ss_dssp EEESSSTE
T ss_pred EEeCCCCC
Confidence 66777765
No 119
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=65.12 E-value=6.7 Score=16.48 Aligned_cols=8 Identities=50% Similarity=1.356 Sum_probs=4.6
Q ss_pred eeccCCCc
Q psy3483 43 YVCCLCSK 50 (99)
Q Consensus 43 ~~c~~c~~ 50 (99)
|.|..|+.
T Consensus 29 y~C~~C~~ 36 (40)
T smart00440 29 YVCTKCGH 36 (40)
T ss_pred EEeCCCCC
Confidence 55666654
No 120
>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=64.28 E-value=2.9 Score=17.82 Aligned_cols=16 Identities=25% Similarity=0.526 Sum_probs=10.1
Q ss_pred ceeeCccccccccccc
Q psy3483 6 LIVTCMYCSKILTYET 21 (99)
Q Consensus 6 ~~~~c~~c~~~f~~~~ 21 (99)
.|+.|..|++.|-.+-
T Consensus 12 ~~~~C~~C~~~FC~~H 27 (43)
T PF01428_consen 12 LPFKCKHCGKSFCLKH 27 (43)
T ss_dssp SHEE-TTTS-EE-TTT
T ss_pred CCeECCCCCcccCccc
Confidence 5789999999987553
No 121
>COG4896 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=63.91 E-value=5.7 Score=18.56 Aligned_cols=9 Identities=33% Similarity=1.003 Sum_probs=4.8
Q ss_pred ceeccCCCc
Q psy3483 42 RYVCCLCSK 50 (99)
Q Consensus 42 ~~~c~~c~~ 50 (99)
.|.|++|..
T Consensus 31 tymC~eC~~ 39 (68)
T COG4896 31 TYMCPECEH 39 (68)
T ss_pred eEechhhHh
Confidence 355666543
No 122
>PF13451 zf-trcl: Probable zinc-binding domain
Probab=63.37 E-value=4.2 Score=18.13 Aligned_cols=15 Identities=20% Similarity=0.611 Sum_probs=9.5
Q ss_pred CceeeCccccccccc
Q psy3483 5 ELIVTCMYCSKILTY 19 (99)
Q Consensus 5 ~~~~~c~~c~~~f~~ 19 (99)
++.+.|..||..|..
T Consensus 2 Dk~l~C~dCg~~Fvf 16 (49)
T PF13451_consen 2 DKTLTCKDCGAEFVF 16 (49)
T ss_pred CeeEEcccCCCeEEE
Confidence 456677777776643
No 123
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=62.86 E-value=10 Score=16.55 Aligned_cols=10 Identities=30% Similarity=0.949 Sum_probs=5.1
Q ss_pred ceecCCCCcc
Q psy3483 71 PYKCFYCDYR 80 (99)
Q Consensus 71 ~~~C~~c~~~ 80 (99)
.+.|+.|+..
T Consensus 20 ~~vC~~Cg~~ 29 (52)
T smart00661 20 RFVCRKCGYE 29 (52)
T ss_pred EEECCcCCCe
Confidence 3555555544
No 124
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=62.64 E-value=6.4 Score=20.00 Aligned_cols=27 Identities=22% Similarity=0.479 Sum_probs=16.2
Q ss_pred cceeccCCCcccccChhHHHHHHHhhCCCCceecCCCC
Q psy3483 41 QRYVCCLCSKYRHSDASKMRSHIRTHTKDRPYKCFYCD 78 (99)
Q Consensus 41 ~~~~c~~c~~~~~~~~~~~~~h~~~~~~~~~~~C~~c~ 78 (99)
+|-.|..||..|... .-.+|-.|+.|.
T Consensus 57 ~Pa~CkkCGfef~~~-----------~ik~pSRCP~CK 83 (97)
T COG3357 57 RPARCKKCGFEFRDD-----------KIKKPSRCPKCK 83 (97)
T ss_pred cChhhcccCcccccc-----------ccCCcccCCcch
Confidence 355677787655432 224567777775
No 125
>KOG3507|consensus
Probab=62.49 E-value=7 Score=18.11 Aligned_cols=31 Identities=23% Similarity=0.502 Sum_probs=19.7
Q ss_pred cceeccCCCcccccChhHHHHHHHhhCCCCceecCCCCccccC
Q psy3483 41 QRYVCCLCSKYRHSDASKMRSHIRTHTKDRPYKCFYCDYRSNE 83 (99)
Q Consensus 41 ~~~~c~~c~~~~~~~~~~~~~h~~~~~~~~~~~C~~c~~~f~~ 83 (99)
..|.|..|+..... .....+.|.+||....+
T Consensus 19 miYiCgdC~~en~l------------k~~D~irCReCG~RIly 49 (62)
T KOG3507|consen 19 MIYICGDCGQENTL------------KRGDVIRCRECGYRILY 49 (62)
T ss_pred EEEEeccccccccc------------cCCCcEehhhcchHHHH
Confidence 34888888863221 22457889999875443
No 126
>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=61.54 E-value=7.4 Score=16.48 Aligned_cols=10 Identities=20% Similarity=0.550 Sum_probs=6.8
Q ss_pred eeCccccccc
Q psy3483 8 VTCMYCSKIL 17 (99)
Q Consensus 8 ~~c~~c~~~f 17 (99)
+.|+.|+...
T Consensus 1 m~Cp~Cg~~~ 10 (43)
T PF08271_consen 1 MKCPNCGSKE 10 (43)
T ss_dssp ESBTTTSSSE
T ss_pred CCCcCCcCCc
Confidence 4678888753
No 127
>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=60.91 E-value=8.4 Score=15.85 Aligned_cols=10 Identities=30% Similarity=0.823 Sum_probs=5.8
Q ss_pred eCcccccccc
Q psy3483 9 TCMYCSKILT 18 (99)
Q Consensus 9 ~c~~c~~~f~ 18 (99)
.|+.||+.|-
T Consensus 3 ~C~~Cg~~Yh 12 (36)
T PF05191_consen 3 ICPKCGRIYH 12 (36)
T ss_dssp EETTTTEEEE
T ss_pred CcCCCCCccc
Confidence 4666666644
No 128
>KOG2482|consensus
Probab=59.27 E-value=5.3 Score=25.47 Aligned_cols=33 Identities=24% Similarity=0.462 Sum_probs=23.9
Q ss_pred eeeCccccccccccchhhhccchhhccCCCCCCC
Q psy3483 7 IVTCMYCSKILTYETETIMNHCKFCKAVSRPTKY 40 (99)
Q Consensus 7 ~~~c~~c~~~f~~~~~~~~~h~~~~~~~~~~~~~ 40 (99)
.+.|-+|.+.|..+- .|+.|++-.++.+.++..
T Consensus 195 r~~CLyCekifrdkn-tLkeHMrkK~HrrinPkn 227 (423)
T KOG2482|consen 195 RLRCLYCEKIFRDKN-TLKEHMRKKRHRRINPKN 227 (423)
T ss_pred hheeeeeccccCCcH-HHHHHHHhccCcccCCCc
Confidence 478999999999998 899995544444444433
No 129
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=57.97 E-value=8.9 Score=20.21 Aligned_cols=24 Identities=21% Similarity=0.366 Sum_probs=15.1
Q ss_pred eeccCCCcccccChhHHHHHHHhhCCCCceecCCCCc
Q psy3483 43 YVCCLCSKYRHSDASKMRSHIRTHTKDRPYKCFYCDY 79 (99)
Q Consensus 43 ~~c~~c~~~~~~~~~~~~~h~~~~~~~~~~~C~~c~~ 79 (99)
..|..|+..|... ...+.|+.||.
T Consensus 71 ~~C~~Cg~~~~~~-------------~~~~~CP~Cgs 94 (113)
T PRK12380 71 AWCWDCSQVVEIH-------------QHDAQCPHCHG 94 (113)
T ss_pred EEcccCCCEEecC-------------CcCccCcCCCC
Confidence 5688888654432 23456888874
No 130
>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=55.74 E-value=4.5 Score=18.10 Aligned_cols=12 Identities=33% Similarity=0.708 Sum_probs=6.3
Q ss_pred eCcccccccccc
Q psy3483 9 TCMYCSKILTYE 20 (99)
Q Consensus 9 ~c~~c~~~f~~~ 20 (99)
.||.|++.|...
T Consensus 22 ~CPlC~r~l~~e 33 (54)
T PF04423_consen 22 CCPLCGRPLDEE 33 (54)
T ss_dssp E-TTT--EE-HH
T ss_pred cCCCCCCCCCHH
Confidence 799999988654
No 131
>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=55.36 E-value=11 Score=19.96 Aligned_cols=24 Identities=25% Similarity=0.456 Sum_probs=15.5
Q ss_pred eeccCCCcccccChhHHHHHHHhhCCCCceecCCCCc
Q psy3483 43 YVCCLCSKYRHSDASKMRSHIRTHTKDRPYKCFYCDY 79 (99)
Q Consensus 43 ~~c~~c~~~~~~~~~~~~~h~~~~~~~~~~~C~~c~~ 79 (99)
..|..|+..+... +..+.|+.|+.
T Consensus 71 ~~C~~Cg~~~~~~-------------~~~~~CP~Cgs 94 (115)
T TIGR00100 71 CECEDCSEEVSPE-------------IDLYRCPKCHG 94 (115)
T ss_pred EEcccCCCEEecC-------------CcCccCcCCcC
Confidence 5688888754432 12467888874
No 132
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=55.27 E-value=11 Score=20.60 Aligned_cols=13 Identities=15% Similarity=0.621 Sum_probs=8.7
Q ss_pred eeeCccccccccc
Q psy3483 7 IVTCMYCSKILTY 19 (99)
Q Consensus 7 ~~~c~~c~~~f~~ 19 (99)
.+.|..||..|..
T Consensus 70 ~~~C~~CG~~~~~ 82 (135)
T PRK03824 70 VLKCRNCGNEWSL 82 (135)
T ss_pred EEECCCCCCEEec
Confidence 4677777776654
No 133
>COG4391 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=55.10 E-value=7.9 Score=18.13 Aligned_cols=12 Identities=42% Similarity=0.800 Sum_probs=8.7
Q ss_pred eeeCcccccccc
Q psy3483 7 IVTCMYCSKILT 18 (99)
Q Consensus 7 ~~~c~~c~~~f~ 18 (99)
.-.|++|+..|.
T Consensus 48 ev~CPYC~t~y~ 59 (62)
T COG4391 48 EVVCPYCSTRYR 59 (62)
T ss_pred cEecCccccEEE
Confidence 346888888775
No 134
>KOG2482|consensus
Probab=54.85 E-value=8.5 Score=24.63 Aligned_cols=23 Identities=26% Similarity=0.816 Sum_probs=20.9
Q ss_pred eecCCCCccccCchHHHHHHHHh
Q psy3483 72 YKCFYCDYRSNERSNVKAHMIRR 94 (99)
Q Consensus 72 ~~C~~c~~~f~~~~~l~~H~~~~ 94 (99)
+.|..|.+.|..+..|..||+.-
T Consensus 196 ~~CLyCekifrdkntLkeHMrkK 218 (423)
T KOG2482|consen 196 LRCLYCEKIFRDKNTLKEHMRKK 218 (423)
T ss_pred heeeeeccccCCcHHHHHHHHhc
Confidence 78999999999999999999853
No 135
>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=54.56 E-value=17 Score=18.97 Aligned_cols=13 Identities=23% Similarity=0.554 Sum_probs=9.3
Q ss_pred ceeeCcccccccc
Q psy3483 6 LIVTCMYCSKILT 18 (99)
Q Consensus 6 ~~~~c~~c~~~f~ 18 (99)
+|-.|++||..-.
T Consensus 1 ~p~~CpYCg~~~~ 13 (102)
T PF11672_consen 1 KPIICPYCGGPAE 13 (102)
T ss_pred CCcccCCCCCeeE
Confidence 4667999997643
No 136
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=54.51 E-value=7.4 Score=17.40 Aligned_cols=25 Identities=28% Similarity=0.580 Sum_probs=14.4
Q ss_pred eccCCCcccccChhHHHHHHHhhCCCCceecCCCCc
Q psy3483 44 VCCLCSKYRHSDASKMRSHIRTHTKDRPYKCFYCDY 79 (99)
Q Consensus 44 ~c~~c~~~~~~~~~~~~~h~~~~~~~~~~~C~~c~~ 79 (99)
.|+.||.. ..+..|. ..|.|..|+.
T Consensus 21 ~CPrCG~g-----vfmA~H~------dR~~CGkCgy 45 (51)
T COG1998 21 FCPRCGPG-----VFMADHK------DRWACGKCGY 45 (51)
T ss_pred cCCCCCCc-----chhhhcC------ceeEeccccc
Confidence 47888763 2233331 2578888875
No 137
>COG4530 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=53.91 E-value=7.6 Score=20.49 Aligned_cols=14 Identities=14% Similarity=0.078 Sum_probs=9.7
Q ss_pred CCceecCCCCcccc
Q psy3483 69 DRPYKCFYCDYRSN 82 (99)
Q Consensus 69 ~~~~~C~~c~~~f~ 82 (99)
..|..|+.||++|+
T Consensus 24 rdPiVsPytG~s~P 37 (129)
T COG4530 24 RDPIVSPYTGKSYP 37 (129)
T ss_pred CCccccCcccccch
Confidence 55777777777763
No 138
>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 PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=53.83 E-value=11 Score=20.04 Aligned_cols=11 Identities=27% Similarity=0.407 Sum_probs=7.5
Q ss_pred eeccCCCcccc
Q psy3483 43 YVCCLCSKYRH 53 (99)
Q Consensus 43 ~~c~~c~~~~~ 53 (99)
..|..||..+.
T Consensus 72 ~~C~~Cg~~~~ 82 (117)
T PRK00564 72 LECKDCSHVFK 82 (117)
T ss_pred EEhhhCCCccc
Confidence 56888886443
No 140
>KOG1146|consensus
Probab=53.10 E-value=7.9 Score=29.16 Aligned_cols=53 Identities=21% Similarity=0.432 Sum_probs=36.0
Q ss_pred cceeccCCCcccccChhHHHHHHHh-----------------hCCCCceecCCCCccccCchHHHHHHHHhc
Q psy3483 41 QRYVCCLCSKYRHSDASKMRSHIRT-----------------HTKDRPYKCFYCDYRSNERSNVKAHMIRRH 95 (99)
Q Consensus 41 ~~~~c~~c~~~~~~~~~~~~~h~~~-----------------~~~~~~~~C~~c~~~f~~~~~l~~H~~~~~ 95 (99)
..|.|..|...|... .-+..|.+. +....+| |..|...|.....|.+|++.-.
T Consensus 1283 ~~~~~~~~~~~~~~~-~~l~~~~~k~~~~~~~~~~~~~~~l~~~d~~~~-c~~c~~~~~~~~alqihm~~~~ 1352 (1406)
T KOG1146|consen 1283 HRYLCRQCKMAFDGE-APLTAHQRKFCFAGRGSGGSMPPPLRVPDCTYH-CLACEVLLSGREALQIHMRSSA 1352 (1406)
T ss_pred hhHHHHHHHhhhcch-hHHHHHHHHHHhccCccccCCCCcccCcccccc-chHHHhhcchhHHHHHHHHHhh
Confidence 457788887655555 556666531 1122345 9999999999999999988543
No 141
>KOG4167|consensus
Probab=52.67 E-value=2.9 Score=29.29 Aligned_cols=25 Identities=24% Similarity=0.452 Sum_probs=21.0
Q ss_pred ceeccCCCcccccChhHHHHHHHhhC
Q psy3483 42 RYVCCLCSKYRHSDASKMRSHIRTHT 67 (99)
Q Consensus 42 ~~~c~~c~~~~~~~~~~~~~h~~~~~ 67 (99)
.|.|.+|++.|+-. .++..|+++|.
T Consensus 792 iFpCreC~kvF~Ki-KSrNAHMK~Hr 816 (907)
T KOG4167|consen 792 IFPCRECGKVFFKI-KSRNAHMKTHR 816 (907)
T ss_pred eeehHHHHHHHHHH-hhhhHHHHHHH
Confidence 48899999988776 88999998874
No 142
>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=52.52 E-value=14 Score=16.40 Aligned_cols=8 Identities=25% Similarity=0.758 Sum_probs=4.0
Q ss_pred eccCCCcc
Q psy3483 44 VCCLCSKY 51 (99)
Q Consensus 44 ~c~~c~~~ 51 (99)
.|..||..
T Consensus 20 ~Cr~Cg~~ 27 (57)
T cd00065 20 HCRNCGRI 27 (57)
T ss_pred ccCcCcCC
Confidence 35555543
No 143
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=52.14 E-value=15 Score=16.79 Aligned_cols=7 Identities=29% Similarity=0.657 Sum_probs=3.0
Q ss_pred eecCCCC
Q psy3483 72 YKCFYCD 78 (99)
Q Consensus 72 ~~C~~c~ 78 (99)
..|+.|+
T Consensus 22 VvCp~Cg 28 (54)
T PF14446_consen 22 VVCPECG 28 (54)
T ss_pred EECCCCC
Confidence 4444443
No 144
>TIGR00416 sms DNA repair protein RadA. The gene protuct codes for a probable ATP-dependent protease involved in both DNA repair and degradation of proteins, peptides, glycopeptides. Also known as sms. Residues 11-28 of the SEED alignment contain a putative Zn binding domain. Residues 110-117 of the seed contain a putative ATP binding site both documented in Haemophilus and in Listeria monocytogenes. for E.coli see ( J. BACTERIOL. 178:5045-5048(1996)).
Probab=51.22 E-value=15 Score=24.41 Aligned_cols=8 Identities=38% Similarity=1.132 Sum_probs=3.8
Q ss_pred eeccCCCc
Q psy3483 43 YVCCLCSK 50 (99)
Q Consensus 43 ~~c~~c~~ 50 (99)
|.|..||.
T Consensus 8 y~C~~Cg~ 15 (454)
T TIGR00416 8 FVCQHCGA 15 (454)
T ss_pred EECCcCCC
Confidence 44544543
No 145
>PRK12496 hypothetical protein; Provisional
Probab=50.77 E-value=13 Score=21.07 Aligned_cols=11 Identities=27% Similarity=0.522 Sum_probs=7.5
Q ss_pred eeCcccccccc
Q psy3483 8 VTCMYCSKILT 18 (99)
Q Consensus 8 ~~c~~c~~~f~ 18 (99)
+.|..|++.|.
T Consensus 128 ~~C~gC~~~~~ 138 (164)
T PRK12496 128 KVCKGCKKKYP 138 (164)
T ss_pred EECCCCCcccc
Confidence 55777777765
No 146
>PF13878 zf-C2H2_3: zinc-finger of acetyl-transferase ESCO
Probab=50.25 E-value=22 Score=15.03 Aligned_cols=7 Identities=29% Similarity=0.837 Sum_probs=4.0
Q ss_pred eccCCCc
Q psy3483 44 VCCLCSK 50 (99)
Q Consensus 44 ~c~~c~~ 50 (99)
.|.+||-
T Consensus 15 ~C~~CgM 21 (41)
T PF13878_consen 15 TCPTCGM 21 (41)
T ss_pred CCCCCCC
Confidence 4666654
No 147
>PRK11823 DNA repair protein RadA; Provisional
Probab=49.98 E-value=16 Score=24.14 Aligned_cols=8 Identities=50% Similarity=1.207 Sum_probs=4.3
Q ss_pred eeccCCCc
Q psy3483 43 YVCCLCSK 50 (99)
Q Consensus 43 ~~c~~c~~ 50 (99)
|.|..||.
T Consensus 8 y~C~~Cg~ 15 (446)
T PRK11823 8 YVCQECGA 15 (446)
T ss_pred EECCcCCC
Confidence 55555554
No 148
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=49.72 E-value=27 Score=26.55 Aligned_cols=34 Identities=26% Similarity=0.483 Sum_probs=19.3
Q ss_pred eeCccccccccccchhhhccchhhccCCCCCCCcceeccCCCcc
Q psy3483 8 VTCMYCSKILTYETETIMNHCKFCKAVSRPTKYQRYVCCLCSKY 51 (99)
Q Consensus 8 ~~c~~c~~~f~~~~~~~~~h~~~~~~~~~~~~~~~~~c~~c~~~ 51 (99)
+.|+.||..... .-|..|++.. ...+.|+.||..
T Consensus 668 rkCPkCG~~t~~------~fCP~CGs~t----e~vy~CPsCGae 701 (1337)
T PRK14714 668 RRCPSCGTETYE------NRCPDCGTHT----EPVYVCPDCGAE 701 (1337)
T ss_pred EECCCCCCcccc------ccCcccCCcC----CCceeCccCCCc
Confidence 679999975321 1244443332 124678888863
No 149
>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=49.32 E-value=9.7 Score=21.17 Aligned_cols=8 Identities=38% Similarity=0.891 Sum_probs=5.1
Q ss_pred eeccCCCc
Q psy3483 43 YVCCLCSK 50 (99)
Q Consensus 43 ~~c~~c~~ 50 (99)
+.|..||.
T Consensus 113 l~C~~Cg~ 120 (146)
T PF07295_consen 113 LVCENCGH 120 (146)
T ss_pred EecccCCC
Confidence 56666665
No 150
>COG5112 UFD2 U1-like Zn-finger-containing protein [General function prediction only]
Probab=49.05 E-value=5.8 Score=20.76 Aligned_cols=23 Identities=13% Similarity=0.137 Sum_probs=19.3
Q ss_pred ceecCCCCccccCchHHHHHHHH
Q psy3483 71 PYKCFYCDYRSNERSNVKAHMIR 93 (99)
Q Consensus 71 ~~~C~~c~~~f~~~~~l~~H~~~ 93 (99)
.+.|.+|.+-|.....|..|.+.
T Consensus 55 qhYCieCaryf~t~~aL~~Hkkg 77 (126)
T COG5112 55 QHYCIECARYFITEKALMEHKKG 77 (126)
T ss_pred eeeeehhHHHHHHHHHHHHHhcc
Confidence 37899999999999899888763
No 151
>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=48.72 E-value=8.2 Score=16.60 Aligned_cols=12 Identities=25% Similarity=0.789 Sum_probs=9.3
Q ss_pred eCcccccccccc
Q psy3483 9 TCMYCSKILTYE 20 (99)
Q Consensus 9 ~c~~c~~~f~~~ 20 (99)
.|+.|++.|.-.
T Consensus 10 ~C~~C~rpf~WR 21 (42)
T PF10013_consen 10 ICPVCGRPFTWR 21 (42)
T ss_pred cCcccCCcchHH
Confidence 489999988654
No 152
>PRK05580 primosome assembly protein PriA; Validated
Probab=48.69 E-value=14 Score=25.81 Aligned_cols=8 Identities=25% Similarity=0.721 Sum_probs=4.1
Q ss_pred Cccccccc
Q psy3483 10 CMYCSKIL 17 (99)
Q Consensus 10 c~~c~~~f 17 (99)
|..||...
T Consensus 384 C~~Cg~~~ 391 (679)
T PRK05580 384 CRDCGWVA 391 (679)
T ss_pred hhhCcCcc
Confidence 55555543
No 153
>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=48.62 E-value=12 Score=19.23 Aligned_cols=17 Identities=18% Similarity=0.352 Sum_probs=13.1
Q ss_pred hCCCCceecCCCCccccC
Q psy3483 66 HTKDRPYKCFYCDYRSNE 83 (99)
Q Consensus 66 ~~~~~~~~C~~c~~~f~~ 83 (99)
+.+ +|..|.+||..|..
T Consensus 75 ~~g-~~~rC~eCG~~fkL 91 (97)
T cd00924 75 EKG-KPKRCPECGHVFKL 91 (97)
T ss_pred eCC-CceeCCCCCcEEEE
Confidence 344 79999999988864
No 154
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=48.10 E-value=15 Score=19.36 Aligned_cols=25 Identities=24% Similarity=0.491 Sum_probs=14.4
Q ss_pred eeccCCCcccccChhHHHHHHHhhCCCCceecCCCCc
Q psy3483 43 YVCCLCSKYRHSDASKMRSHIRTHTKDRPYKCFYCDY 79 (99)
Q Consensus 43 ~~c~~c~~~~~~~~~~~~~h~~~~~~~~~~~C~~c~~ 79 (99)
..|..|+..+... . ...+.|+.||.
T Consensus 71 ~~C~~Cg~~~~~~-~-----------~~~~~CP~Cgs 95 (114)
T PRK03681 71 CWCETCQQYVTLL-T-----------QRVRRCPQCHG 95 (114)
T ss_pred EEcccCCCeeecC-C-----------ccCCcCcCcCC
Confidence 5688888744322 0 11256888874
No 155
>PTZ00043 cytochrome c oxidase subunit; Provisional
Probab=47.10 E-value=10 Score=22.78 Aligned_cols=17 Identities=18% Similarity=0.487 Sum_probs=13.4
Q ss_pred CceeeCccccccccccc
Q psy3483 5 ELIVTCMYCSKILTYET 21 (99)
Q Consensus 5 ~~~~~c~~c~~~f~~~~ 21 (99)
.++..|+.||..|....
T Consensus 179 GkpqRCpECGqVFKLVr 195 (268)
T PTZ00043 179 GFLYRCGECDQIFMLVR 195 (268)
T ss_pred CCCccCCCCCcEEEEEE
Confidence 45789999999988543
No 156
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=46.82 E-value=9.3 Score=22.48 Aligned_cols=12 Identities=25% Similarity=0.401 Sum_probs=6.3
Q ss_pred eeeCcccccccc
Q psy3483 7 IVTCMYCSKILT 18 (99)
Q Consensus 7 ~~~c~~c~~~f~ 18 (99)
||.|..|.+.|.
T Consensus 196 PF~C~iCKkdy~ 207 (259)
T COG5152 196 PFLCGICKKDYE 207 (259)
T ss_pred ceeehhchhhcc
Confidence 455555555544
No 157
>PRK04023 DNA polymerase II large subunit; Validated
Probab=46.46 E-value=27 Score=25.99 Aligned_cols=9 Identities=33% Similarity=0.656 Sum_probs=5.9
Q ss_pred eeCcccccc
Q psy3483 8 VTCMYCSKI 16 (99)
Q Consensus 8 ~~c~~c~~~ 16 (99)
..|+.||..
T Consensus 627 RfCpsCG~~ 635 (1121)
T PRK04023 627 RKCPSCGKE 635 (1121)
T ss_pred ccCCCCCCc
Confidence 457777765
No 158
>COG2879 Uncharacterized small protein [Function unknown]
Probab=45.31 E-value=27 Score=16.48 Aligned_cols=16 Identities=38% Similarity=0.569 Sum_probs=11.1
Q ss_pred chHHHHHHHHhcCCCC
Q psy3483 84 RSNVKAHMIRRHSVKP 99 (99)
Q Consensus 84 ~~~l~~H~~~~~~~kp 99 (99)
=.++..|++.++.++|
T Consensus 25 YdnYVehmr~~hPd~p 40 (65)
T COG2879 25 YDNYVEHMRKKHPDKP 40 (65)
T ss_pred HHHHHHHHHHhCcCCC
Confidence 3467778887777665
No 159
>PF14369 zf-RING_3: zinc-finger
Probab=45.17 E-value=10 Score=15.45 Aligned_cols=11 Identities=18% Similarity=0.392 Sum_probs=8.8
Q ss_pred eCccccccccc
Q psy3483 9 TCMYCSKILTY 19 (99)
Q Consensus 9 ~c~~c~~~f~~ 19 (99)
.|+.|+.+|..
T Consensus 23 ~CP~C~~gFvE 33 (35)
T PF14369_consen 23 ACPRCHGGFVE 33 (35)
T ss_pred CCcCCCCcEeE
Confidence 49999988864
No 160
>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=44.19 E-value=6.4 Score=20.70 Aligned_cols=25 Identities=20% Similarity=0.393 Sum_probs=14.2
Q ss_pred eeccCCCcccccChhHHHHHHHhhCCCCceecCCCCcc
Q psy3483 43 YVCCLCSKYRHSDASKMRSHIRTHTKDRPYKCFYCDYR 80 (99)
Q Consensus 43 ~~c~~c~~~~~~~~~~~~~h~~~~~~~~~~~C~~c~~~ 80 (99)
..|..||..|... . ..+.|+.|+..
T Consensus 71 ~~C~~Cg~~~~~~-~------------~~~~CP~Cgs~ 95 (113)
T PF01155_consen 71 ARCRDCGHEFEPD-E------------FDFSCPRCGSP 95 (113)
T ss_dssp EEETTTS-EEECH-H------------CCHH-SSSSSS
T ss_pred EECCCCCCEEecC-C------------CCCCCcCCcCC
Confidence 5788898865433 1 12558888754
No 161
>COG1773 Rubredoxin [Energy production and conversion]
Probab=44.06 E-value=13 Score=17.08 Aligned_cols=12 Identities=25% Similarity=0.866 Sum_probs=6.8
Q ss_pred ceecCCCCcccc
Q psy3483 71 PYKCFYCDYRSN 82 (99)
Q Consensus 71 ~~~C~~c~~~f~ 82 (99)
.|+|..||..|.
T Consensus 3 ~~~C~~CG~vYd 14 (55)
T COG1773 3 RWRCSVCGYVYD 14 (55)
T ss_pred ceEecCCceEec
Confidence 356666665543
No 162
>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=42.25 E-value=23 Score=23.79 Aligned_cols=23 Identities=17% Similarity=0.379 Sum_probs=20.3
Q ss_pred ceecCCCCccccCchHHHHHHHH
Q psy3483 71 PYKCFYCDYRSNERSNVKAHMIR 93 (99)
Q Consensus 71 ~~~C~~c~~~f~~~~~l~~H~~~ 93 (99)
-|.|+.|.+.|.....+..|+..
T Consensus 57 FWiCp~CskkF~d~~~~~~H~~~ 79 (466)
T PF04780_consen 57 FWICPRCSKKFSDAESCLSHMEQ 79 (466)
T ss_pred EeeCCcccceeCCHHHHHHHHHH
Confidence 47899999999999999999764
No 163
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=41.28 E-value=33 Score=15.26 Aligned_cols=11 Identities=27% Similarity=0.815 Sum_probs=8.2
Q ss_pred CceecCCCCcc
Q psy3483 70 RPYKCFYCDYR 80 (99)
Q Consensus 70 ~~~~C~~c~~~ 80 (99)
..+.|..|+..
T Consensus 36 ~r~~C~~Cgyt 46 (50)
T PRK00432 36 DRWHCGKCGYT 46 (50)
T ss_pred CcEECCCcCCE
Confidence 46888888864
No 164
>cd01121 Sms Sms (bacterial radA) DNA repair protein. This protein is not related to archael radA any more than is to other RecA-like NTPases. Sms has a role in recombination and recombinational repair and is responsible for the stabilization or processing of branched DNA molecules.
Probab=40.86 E-value=25 Score=22.77 Aligned_cols=7 Identities=29% Similarity=0.809 Sum_probs=3.8
Q ss_pred eccCCCc
Q psy3483 44 VCCLCSK 50 (99)
Q Consensus 44 ~c~~c~~ 50 (99)
.|+.|+.
T Consensus 16 ~cp~c~~ 22 (372)
T cd01121 16 KCPECGE 22 (372)
T ss_pred ECcCCCC
Confidence 4666653
No 165
>COG4957 Predicted transcriptional regulator [Transcription]
Probab=40.36 E-value=25 Score=19.37 Aligned_cols=22 Identities=14% Similarity=0.227 Sum_probs=15.0
Q ss_pred eecCCCCccccCchHHHHHHHHhcC
Q psy3483 72 YKCFYCDYRSNERSNVKAHMIRRHS 96 (99)
Q Consensus 72 ~~C~~c~~~f~~~~~l~~H~~~~~~ 96 (99)
..|.++|+.| ..|.+|+.+|.|
T Consensus 77 IicLEDGkkf---KSLKRHL~t~~g 98 (148)
T COG4957 77 IICLEDGKKF---KSLKRHLTTHYG 98 (148)
T ss_pred EEEeccCcch---HHHHHHHhcccC
Confidence 4577777765 467778777765
No 166
>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=40.21 E-value=34 Score=15.88 Aligned_cols=16 Identities=19% Similarity=0.673 Sum_probs=11.5
Q ss_pred CCCCceecCCCCcccc
Q psy3483 67 TKDRPYKCFYCDYRSN 82 (99)
Q Consensus 67 ~~~~~~~C~~c~~~f~ 82 (99)
...+.|.|+.||....
T Consensus 42 ~~~r~~~C~~Cg~~~~ 57 (69)
T PF07282_consen 42 RSGRVFTCPNCGFEMD 57 (69)
T ss_pred cccceEEcCCCCCEEC
Confidence 4466789999987644
No 167
>COG5216 Uncharacterized conserved protein [Function unknown]
Probab=39.98 E-value=17 Score=16.85 Aligned_cols=13 Identities=15% Similarity=0.427 Sum_probs=8.0
Q ss_pred CCCCceecCCCCc
Q psy3483 67 TKDRPYKCFYCDY 79 (99)
Q Consensus 67 ~~~~~~~C~~c~~ 79 (99)
.|++...|+.|..
T Consensus 40 ~GE~VArCPSCSL 52 (67)
T COG5216 40 NGEVVARCPSCSL 52 (67)
T ss_pred CCceEEEcCCceE
Confidence 4566666666654
No 168
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=39.67 E-value=35 Score=17.71 Aligned_cols=7 Identities=29% Similarity=0.913 Sum_probs=4.6
Q ss_pred eeCcccc
Q psy3483 8 VTCMYCS 14 (99)
Q Consensus 8 ~~c~~c~ 14 (99)
|.|+.|+
T Consensus 22 f~CP~Cg 28 (99)
T PRK14892 22 FECPRCG 28 (99)
T ss_pred eECCCCC
Confidence 5666666
No 169
>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=39.65 E-value=15 Score=15.00 Aligned_cols=12 Identities=25% Similarity=0.379 Sum_probs=4.8
Q ss_pred ecCCCCccccCc
Q psy3483 73 KCFYCDYRSNER 84 (99)
Q Consensus 73 ~C~~c~~~f~~~ 84 (99)
.|.+|++.|..+
T Consensus 5 ~C~eC~~~f~dS 16 (34)
T PF01286_consen 5 KCDECGKPFMDS 16 (34)
T ss_dssp E-TTT--EES-S
T ss_pred hHhHhCCHHHHH
Confidence 566676666544
No 170
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=39.06 E-value=22 Score=20.49 Aligned_cols=8 Identities=25% Similarity=0.820 Sum_probs=4.1
Q ss_pred eecCCCCc
Q psy3483 72 YKCFYCDY 79 (99)
Q Consensus 72 ~~C~~c~~ 79 (99)
|.|+.||.
T Consensus 133 F~Cp~Cg~ 140 (176)
T COG1675 133 FTCPKCGE 140 (176)
T ss_pred CCCCCCCc
Confidence 55555543
No 171
>KOG2231|consensus
Probab=38.39 E-value=32 Score=24.24 Aligned_cols=18 Identities=17% Similarity=0.619 Sum_probs=11.6
Q ss_pred eCccccccccccchhhhcc
Q psy3483 9 TCMYCSKILTYETETIMNH 27 (99)
Q Consensus 9 ~c~~c~~~f~~~~~~~~~h 27 (99)
.|..|...|.... .|..|
T Consensus 184 ~C~~C~~~fld~~-el~rH 201 (669)
T KOG2231|consen 184 LCKFCHERFLDDD-ELYRH 201 (669)
T ss_pred cchhhhhhhccHH-HHHHh
Confidence 4666777666665 66666
No 172
>COG5432 RAD18 RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms]
Probab=37.45 E-value=7.7 Score=24.24 Aligned_cols=16 Identities=25% Similarity=0.663 Sum_probs=9.5
Q ss_pred CCCCCCCcceeccCCCc
Q psy3483 34 VSRPTKYQRYVCCLCSK 50 (99)
Q Consensus 34 ~~~~~~~~~~~c~~c~~ 50 (99)
++.|.+.+|+ |++|..
T Consensus 52 IR~hL~~qp~-CP~Cr~ 67 (391)
T COG5432 52 IRRHLGTQPF-CPVCRE 67 (391)
T ss_pred HHHHhcCCCC-Cccccc
Confidence 3445666665 777753
No 173
>PHA02998 RNA polymerase subunit; Provisional
Probab=37.43 E-value=30 Score=20.08 Aligned_cols=12 Identities=17% Similarity=0.304 Sum_probs=7.1
Q ss_pred eecCCCCccccC
Q psy3483 72 YKCFYCDYRSNE 83 (99)
Q Consensus 72 ~~C~~c~~~f~~ 83 (99)
|.|..|+..|..
T Consensus 172 YkC~~CG~~wkp 183 (195)
T PHA02998 172 HACRDCKKHFKP 183 (195)
T ss_pred EEcCCCCCccCC
Confidence 566666665543
No 174
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=37.14 E-value=19 Score=19.50 Aligned_cols=18 Identities=22% Similarity=0.421 Sum_probs=13.6
Q ss_pred CCCCceecCCCCccccCc
Q psy3483 67 TKDRPYKCFYCDYRSNER 84 (99)
Q Consensus 67 ~~~~~~~C~~c~~~f~~~ 84 (99)
.+...|.|..|++.|...
T Consensus 49 ~~~qRyrC~~C~~tf~~~ 66 (129)
T COG3677 49 RGHQRYKCKSCGSTFTVE 66 (129)
T ss_pred ccccccccCCcCcceeee
Confidence 346679999999888754
No 175
>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG
Probab=37.10 E-value=15 Score=16.57 Aligned_cols=10 Identities=30% Similarity=1.002 Sum_probs=7.7
Q ss_pred eCcccccccc
Q psy3483 9 TCMYCSKILT 18 (99)
Q Consensus 9 ~c~~c~~~f~ 18 (99)
.|++||..+.
T Consensus 2 ~CPyCge~~~ 11 (52)
T PF14255_consen 2 QCPYCGEPIE 11 (52)
T ss_pred CCCCCCCeeE
Confidence 5888888765
No 176
>KOG2785|consensus
Probab=36.99 E-value=60 Score=21.27 Aligned_cols=23 Identities=26% Similarity=0.625 Sum_probs=18.2
Q ss_pred ceecCCCC---ccccCchHHHHHHHH
Q psy3483 71 PYKCFYCD---YRSNERSNVKAHMIR 93 (99)
Q Consensus 71 ~~~C~~c~---~~f~~~~~l~~H~~~ 93 (99)
.+.|..|. +.|........||..
T Consensus 217 ~~~CL~CN~~~~~f~sleavr~HM~~ 242 (390)
T KOG2785|consen 217 GFICLFCNELGRPFSSLEAVRAHMRD 242 (390)
T ss_pred CceEEEeccccCcccccHHHHHHHhh
Confidence 36777787 888888889999874
No 177
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=36.98 E-value=32 Score=13.96 Aligned_cols=7 Identities=43% Similarity=1.070 Sum_probs=3.4
Q ss_pred eeccCCC
Q psy3483 43 YVCCLCS 49 (99)
Q Consensus 43 ~~c~~c~ 49 (99)
+.|+.||
T Consensus 23 ~vC~~Cg 29 (34)
T PF14803_consen 23 LVCPACG 29 (34)
T ss_dssp EEETTTT
T ss_pred eECCCCC
Confidence 3455554
No 178
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=36.54 E-value=30 Score=22.89 Aligned_cols=14 Identities=29% Similarity=0.750 Sum_probs=9.2
Q ss_pred ceecCCCCccccCc
Q psy3483 71 PYKCFYCDYRSNER 84 (99)
Q Consensus 71 ~~~C~~c~~~f~~~ 84 (99)
-|.|..|+..+...
T Consensus 367 g~rC~kCg~~~~~~ 380 (421)
T COG1571 367 GFRCKKCGTRARET 380 (421)
T ss_pred CcccccccccCCcc
Confidence 67777777665443
No 179
>PF04216 FdhE: Protein involved in formate dehydrogenase formation; InterPro: IPR006452 This family of sequences describe an accessory protein required for the assembly of formate dehydrogenase of certain proteobacteria although not present in the final complex []. The exact nature of the function of FdhE in the assembly of the complex is unknown, but considering the presence of selenocysteine, molybdopterin, iron-sulphur clusters and cytochrome b556, it is likely to be involved in the insertion of cofactors. ; GO: 0005737 cytoplasm; PDB: 2FIY_B.
Probab=36.29 E-value=14 Score=22.86 Aligned_cols=13 Identities=23% Similarity=0.230 Sum_probs=7.8
Q ss_pred CCCceecCCCCcc
Q psy3483 68 KDRPYKCFYCDYR 80 (99)
Q Consensus 68 ~~~~~~C~~c~~~ 80 (99)
+.+.+.|..|+.-
T Consensus 235 ~~rve~C~~C~~Y 247 (290)
T PF04216_consen 235 AYRVEVCESCGSY 247 (290)
T ss_dssp SEEEEEETTTTEE
T ss_pred cEEEEECCcccch
Confidence 3445677777643
No 180
>PF12773 DZR: Double zinc ribbon
Probab=36.27 E-value=42 Score=14.40 Aligned_cols=8 Identities=25% Similarity=0.480 Sum_probs=3.3
Q ss_pred eecCCCCc
Q psy3483 72 YKCFYCDY 79 (99)
Q Consensus 72 ~~C~~c~~ 79 (99)
..|..|+.
T Consensus 30 ~~C~~Cg~ 37 (50)
T PF12773_consen 30 KICPNCGA 37 (50)
T ss_pred CCCcCCcC
Confidence 33444443
No 181
>PF12647 RNHCP: RNHCP domain; InterPro: IPR024439 This domain is found in uncharacterised bacterial proteins. It is typically between 94 and 143 amino acids in length and has a conserved RNHCP sequence motif.
Probab=36.13 E-value=38 Score=17.33 Aligned_cols=26 Identities=27% Similarity=0.522 Sum_probs=17.2
Q ss_pred ceeeCcccccccccc--chhhhccchhh
Q psy3483 6 LIVTCMYCSKILTYE--TETIMNHCKFC 31 (99)
Q Consensus 6 ~~~~c~~c~~~f~~~--~~~~~~h~~~~ 31 (99)
..|.|..||....-. -+...+||..|
T Consensus 3 ~~F~C~~CG~~V~p~~~g~~~RNHCP~C 30 (92)
T PF12647_consen 3 ESFTCVHCGLTVSPLAAGSAHRNHCPSC 30 (92)
T ss_pred cccCccccCCCcccCCCCCCccCcCccc
Confidence 578999999875332 11466776666
No 182
>COG1326 Uncharacterized archaeal Zn-finger protein [General function prediction only]
Probab=35.25 E-value=67 Score=18.97 Aligned_cols=10 Identities=20% Similarity=0.468 Sum_probs=4.7
Q ss_pred eecCCCCccc
Q psy3483 72 YKCFYCDYRS 81 (99)
Q Consensus 72 ~~C~~c~~~f 81 (99)
+.|..||..+
T Consensus 31 vrC~eCG~V~ 40 (201)
T COG1326 31 VRCEECGTVH 40 (201)
T ss_pred EEccCCCcEe
Confidence 4455554433
No 183
>PRK06260 threonine synthase; Validated
Probab=33.81 E-value=40 Score=21.88 Aligned_cols=9 Identities=33% Similarity=0.807 Sum_probs=5.9
Q ss_pred ceeccCCCc
Q psy3483 42 RYVCCLCSK 50 (99)
Q Consensus 42 ~~~c~~c~~ 50 (99)
.+.|+.|+.
T Consensus 19 ~~~Cp~cg~ 27 (397)
T PRK06260 19 IYTCPECGG 27 (397)
T ss_pred cccCCCCCC
Confidence 356777765
No 184
>PLN03238 probable histone acetyltransferase MYST; Provisional
Probab=33.64 E-value=62 Score=20.37 Aligned_cols=25 Identities=20% Similarity=0.517 Sum_probs=18.6
Q ss_pred CCceecCCCCccccCchHHHHHHHH
Q psy3483 69 DRPYKCFYCDYRSNERSNVKAHMIR 93 (99)
Q Consensus 69 ~~~~~C~~c~~~f~~~~~l~~H~~~ 93 (99)
..-|.|..|.+-|.....+.+|+..
T Consensus 46 ~~lyiCe~Clky~~~~~~l~~H~~~ 70 (290)
T PLN03238 46 TKLYICEYCLKYMRKKKSLLRHLAK 70 (290)
T ss_pred CeEEEcCCCcchhCCHHHHHHHHHh
Confidence 4567888888888888888887663
No 185
>KOG3362|consensus
Probab=33.45 E-value=14 Score=20.56 Aligned_cols=20 Identities=25% Similarity=0.541 Sum_probs=14.1
Q ss_pred eecCCCCccccCchHHHHHH
Q psy3483 72 YKCFYCDYRSNERSNVKAHM 91 (99)
Q Consensus 72 ~~C~~c~~~f~~~~~l~~H~ 91 (99)
|.|..||-.+....-+..|.
T Consensus 130 ysC~~CG~kyCsv~C~~~Hn 149 (156)
T KOG3362|consen 130 YSCVNCGTKYCSVRCLKTHN 149 (156)
T ss_pred hHHHhcCCceeechhhhhcc
Confidence 77778887777766666654
No 186
>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=33.29 E-value=23 Score=15.57 Aligned_cols=11 Identities=36% Similarity=1.017 Sum_probs=6.4
Q ss_pred eecCCCCcccc
Q psy3483 72 YKCFYCDYRSN 82 (99)
Q Consensus 72 ~~C~~c~~~f~ 82 (99)
|+|..|+..+.
T Consensus 2 y~C~~CgyvYd 12 (47)
T PF00301_consen 2 YQCPVCGYVYD 12 (47)
T ss_dssp EEETTTSBEEE
T ss_pred cCCCCCCEEEc
Confidence 56666665543
No 187
>KOG0717|consensus
Probab=32.98 E-value=31 Score=23.21 Aligned_cols=21 Identities=19% Similarity=0.400 Sum_probs=17.4
Q ss_pred eecCCCCccccCchHHHHHHH
Q psy3483 72 YKCFYCDYRSNERSNVKAHMI 92 (99)
Q Consensus 72 ~~C~~c~~~f~~~~~l~~H~~ 92 (99)
+.|..|++.|.....+..|..
T Consensus 293 lyC~vCnKsFKseKq~kNHEn 313 (508)
T KOG0717|consen 293 LYCVVCNKSFKSEKQLKNHEN 313 (508)
T ss_pred eEEeeccccccchHHHHhhHH
Confidence 788889999988888888764
No 188
>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=32.95 E-value=28 Score=15.67 Aligned_cols=16 Identities=31% Similarity=0.847 Sum_probs=9.6
Q ss_pred CCceeeCccccccccc
Q psy3483 4 TELIVTCMYCSKILTY 19 (99)
Q Consensus 4 ~~~~~~c~~c~~~f~~ 19 (99)
+...+.|.+|++.+..
T Consensus 32 ~~~~~rC~YCe~~~~~ 47 (52)
T PF02748_consen 32 EPIKLRCHYCERIITE 47 (52)
T ss_dssp TTCEEEETTT--EEEH
T ss_pred CCCEEEeeCCCCEecc
Confidence 3445788999887754
No 189
>PF09416 UPF1_Zn_bind: RNA helicase (UPF2 interacting domain); InterPro: IPR018999 UPF1 (or regulator of nonsense transcripts 1 homologue) is an essential RNA helicase that detects mRNAs containing premature stop codons and triggers their degradation. This domain contains 3 zinc binding motifs and forms interactions with another protein (UPF2) that is also involved nonsense-mediated mRNA decay (NMD) []. ; GO: 0003677 DNA binding, 0004386 helicase activity, 0005524 ATP binding, 0008270 zinc ion binding, 0000184 nuclear-transcribed mRNA catabolic process, nonsense-mediated decay, 0005737 cytoplasm; PDB: 2IYK_B 2WJY_A 2WJV_A 2XZL_A.
Probab=32.73 E-value=47 Score=18.73 Aligned_cols=50 Identities=22% Similarity=0.363 Sum_probs=19.5
Q ss_pred CCCCceeeCccccccccccc-----hhhhccchhh--cc----CCCCCCCcceeccCCCcc
Q psy3483 2 KSTELIVTCMYCSKILTYET-----ETIMNHCKFC--KA----VSRPTKYQRYVCCLCSKY 51 (99)
Q Consensus 2 h~~~~~~~c~~c~~~f~~~~-----~~~~~h~~~~--~~----~~~~~~~~~~~c~~c~~~ 51 (99)
|.++--.+|..|++.|-... +++..|...- .. -....++...+|-.||..
T Consensus 9 ~~p~~vv~C~~c~kWFCNg~~~~s~SHIv~HLv~srh~ev~LH~~s~lgdt~leCy~Cg~~ 69 (152)
T PF09416_consen 9 HDPSCVVKCNTCNKWFCNGRGNTSGSHIVNHLVRSRHKEVSLHPDSPLGDTVLECYNCGSR 69 (152)
T ss_dssp --CCCEEEETTTTEEEES--TTSSS-HHHHHHHHHT---EEE-TTSTT-S-B---TTT---
T ss_pred CCcccEeEcCCCCcEeecCCCCCcccHHHHHHHHccCCceeeCCCCCCCCcEEEEEecCCC
Confidence 44455577889999884432 1344442111 11 122334556788888853
No 190
>PRK05978 hypothetical protein; Provisional
Probab=32.66 E-value=28 Score=19.45 Aligned_cols=8 Identities=25% Similarity=0.638 Sum_probs=5.1
Q ss_pred eCcccccc
Q psy3483 9 TCMYCSKI 16 (99)
Q Consensus 9 ~c~~c~~~ 16 (99)
+|+.||+.
T Consensus 35 rCP~CG~G 42 (148)
T PRK05978 35 RCPACGEG 42 (148)
T ss_pred cCCCCCCC
Confidence 56777765
No 191
>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=32.45 E-value=25 Score=19.34 Aligned_cols=21 Identities=24% Similarity=0.302 Sum_probs=14.8
Q ss_pred CCceecCCCCccccCchHHHH
Q psy3483 69 DRPYKCFYCDYRSNERSNVKA 89 (99)
Q Consensus 69 ~~~~~C~~c~~~f~~~~~l~~ 89 (99)
+.-+.|+.|++.|=.-+.+..
T Consensus 122 ~~f~~C~~C~kiyW~GsH~~~ 142 (147)
T PF01927_consen 122 DEFWRCPGCGKIYWEGSHWRR 142 (147)
T ss_pred CeEEECCCCCCEecccccHHH
Confidence 446899999998865554443
No 192
>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=32.36 E-value=22 Score=15.85 Aligned_cols=11 Identities=36% Similarity=1.026 Sum_probs=7.2
Q ss_pred eecCCCCcccc
Q psy3483 72 YKCFYCDYRSN 82 (99)
Q Consensus 72 ~~C~~c~~~f~ 82 (99)
|+|..||..+.
T Consensus 2 y~C~~CgyiYd 12 (50)
T cd00730 2 YECRICGYIYD 12 (50)
T ss_pred cCCCCCCeEEC
Confidence 56777776654
No 193
>PF02148 zf-UBP: Zn-finger in ubiquitin-hydrolases and other protein; InterPro: IPR001607 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 UBP-type zinc finger domains, which display some similarity with the Zn-binding domain of the insulinase family. The UBP-type zinc finger domain is found only in a small subfamily of ubiquitin C-terminal hydrolases (deubiquitinases or UBP) [, ], All members of this subfamily are isopeptidase-T, which are known to cleave isopeptide bonds between ubiquitin moieties. Some of the proteins containing an UBP zinc finger include: Homo sapiens (Human) deubiquitinating enzyme 13 (UBPD) Human deubiquitinating enzyme 5 (UBP5) Dictyostelium discoideum (Slime mold) deubiquitinating enzyme A (UBPA) Saccharomyces cerevisiae (Baker's yeast) deubiquitinating enzyme 8 (UBP8) Yeast deubiquitinating enzyme 14 (UBP14) More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3GV4_A 3PHD_B 3C5K_A 2UZG_A 3IHP_B 2G43_B 2G45_D 2I50_A 3MHH_A 3MHS_A ....
Probab=31.50 E-value=20 Score=16.51 Aligned_cols=16 Identities=25% Similarity=0.667 Sum_probs=9.3
Q ss_pred CCceecCCCCccccCc
Q psy3483 69 DRPYKCFYCDYRSNER 84 (99)
Q Consensus 69 ~~~~~C~~c~~~f~~~ 84 (99)
...|.|..|+..+.-+
T Consensus 9 ~~lw~CL~Cg~~~C~~ 24 (63)
T PF02148_consen 9 SNLWLCLTCGYVGCGR 24 (63)
T ss_dssp SSEEEETTTS-EEETT
T ss_pred CceEEeCCCCcccccC
Confidence 4467777777665543
No 194
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=31.38 E-value=59 Score=14.54 Aligned_cols=16 Identities=19% Similarity=0.227 Sum_probs=11.8
Q ss_pred hhCCCCceecCCCCcc
Q psy3483 65 THTKDRPYKCFYCDYR 80 (99)
Q Consensus 65 ~~~~~~~~~C~~c~~~ 80 (99)
...++....|+.|++.
T Consensus 40 i~~~~~i~~Cp~CgRi 55 (56)
T PF02591_consen 40 IRKGDEIVFCPNCGRI 55 (56)
T ss_pred HHcCCCeEECcCCCcc
Confidence 3445778899999874
No 195
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=31.36 E-value=84 Score=20.01 Aligned_cols=10 Identities=20% Similarity=0.547 Sum_probs=7.3
Q ss_pred eeeCcccccc
Q psy3483 7 IVTCMYCSKI 16 (99)
Q Consensus 7 ~~~c~~c~~~ 16 (99)
.-.|+.||..
T Consensus 187 ~~~CPvCGs~ 196 (309)
T PRK03564 187 RQFCPVCGSM 196 (309)
T ss_pred CCCCCCCCCc
Confidence 3568888875
No 196
>PRK05654 acetyl-CoA carboxylase subunit beta; Validated
Probab=30.92 E-value=74 Score=20.01 Aligned_cols=12 Identities=25% Similarity=0.437 Sum_probs=7.3
Q ss_pred eeccCCCccccc
Q psy3483 43 YVCCLCSKYRHS 54 (99)
Q Consensus 43 ~~c~~c~~~~~~ 54 (99)
+.|+.|+..+.-
T Consensus 47 ~vc~~c~~h~rl 58 (292)
T PRK05654 47 NVCPKCGHHMRI 58 (292)
T ss_pred CCCCCCCCCeeC
Confidence 457777765443
No 197
>KOG4727|consensus
Probab=30.90 E-value=31 Score=19.86 Aligned_cols=22 Identities=27% Similarity=0.477 Sum_probs=18.1
Q ss_pred ceecCCCCccccCchHHHHHHH
Q psy3483 71 PYKCFYCDYRSNERSNVKAHMI 92 (99)
Q Consensus 71 ~~~C~~c~~~f~~~~~l~~H~~ 92 (99)
-|.|.+|+-.+...-++..|+-
T Consensus 75 GyyCdVCdcvvKDSinflDHiN 96 (193)
T KOG4727|consen 75 GYYCDVCDCVVKDSINFLDHIN 96 (193)
T ss_pred ceeeeecceeehhhHHHHHHhc
Confidence 3899999998888888887753
No 198
>COG4338 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=30.83 E-value=16 Score=16.22 Aligned_cols=13 Identities=15% Similarity=0.700 Sum_probs=9.8
Q ss_pred eCccccccccccc
Q psy3483 9 TCMYCSKILTYET 21 (99)
Q Consensus 9 ~c~~c~~~f~~~~ 21 (99)
.|+.|++.|....
T Consensus 14 ICpvCqRPFsWRk 26 (54)
T COG4338 14 ICPVCQRPFSWRK 26 (54)
T ss_pred hhhhhcCchHHHH
Confidence 4899999886553
No 199
>TIGR00515 accD acetyl-CoA carboxylase, carboxyl transferase, beta subunit. The enzyme acetyl-CoA carboxylase contains a biotin carboxyl carrier protein or domain, a biotin carboxylase, and a carboxyl transferase. This model represents the beta chain of the carboxyl transferase for cases in which the architecture of the protein is as in E. coli, in which the carboxyltransferase portion consists of two non-identical subnits, alpha and beta.
Probab=30.18 E-value=30 Score=21.55 Aligned_cols=12 Identities=25% Similarity=0.694 Sum_probs=7.8
Q ss_pred eCcccccccccc
Q psy3483 9 TCMYCSKILTYE 20 (99)
Q Consensus 9 ~c~~c~~~f~~~ 20 (99)
+|+.|+.....+
T Consensus 28 ~c~~c~~~~~~~ 39 (285)
T TIGR00515 28 KCPKCGQVLYTK 39 (285)
T ss_pred ECCCCcchhhHH
Confidence 477777765544
No 200
>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=29.81 E-value=42 Score=17.36 Aligned_cols=39 Identities=13% Similarity=0.159 Sum_probs=13.7
Q ss_pred CCceeeCccccccccccchhhhccchhhccCCCCCCCc-ceeccCCCcccccC
Q psy3483 4 TELIVTCMYCSKILTYETETIMNHCKFCKAVSRPTKYQ-RYVCCLCSKYRHSD 55 (99)
Q Consensus 4 ~~~~~~c~~c~~~f~~~~~~~~~h~~~~~~~~~~~~~~-~~~c~~c~~~~~~~ 55 (99)
|.+.-.|..||+++-... . .. .+++ .|-|+.|.+.|...
T Consensus 11 g~ke~~CalCG~tWg~~y----~--------Ev-~G~rLfFCCd~ca~EF~nm 50 (105)
T PF11494_consen 11 GTKEMGCALCGATWGDYY----E--------EV-DGERLFFCCDDCAKEFKNM 50 (105)
T ss_dssp -SGGGS-SS---S---SS-------------B--TT--BSSS--SSSS-TTS-
T ss_pred ccccccccccCCcHHHHH----H--------hh-cCCEEEEEcHHHHHHHHHH
Confidence 455667999998875222 1 12 2333 35678888766554
No 201
>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=29.55 E-value=28 Score=14.40 Aligned_cols=10 Identities=40% Similarity=0.680 Sum_probs=3.8
Q ss_pred ceecCCCCcc
Q psy3483 71 PYKCFYCDYR 80 (99)
Q Consensus 71 ~~~C~~c~~~ 80 (99)
.|.|..||..
T Consensus 6 ~YkC~~CGni 15 (36)
T PF06397_consen 6 FYKCEHCGNI 15 (36)
T ss_dssp EEE-TTT--E
T ss_pred EEEccCCCCE
Confidence 3566666543
No 202
>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=29.52 E-value=51 Score=13.30 Aligned_cols=20 Identities=20% Similarity=0.439 Sum_probs=9.1
Q ss_pred eeccCCCcccccChhHHHHHHH
Q psy3483 43 YVCCLCSKYRHSDASKMRSHIR 64 (99)
Q Consensus 43 ~~c~~c~~~~~~~~~~~~~h~~ 64 (99)
+.|+.|++... . .-+..|..
T Consensus 5 ~~C~nC~R~v~-a-~RfA~HLe 24 (33)
T PF08209_consen 5 VECPNCGRPVA-A-SRFAPHLE 24 (33)
T ss_dssp EE-TTTSSEEE-G-GGHHHHHH
T ss_pred EECCCCcCCcc-h-hhhHHHHH
Confidence 45666666322 2 44454543
No 203
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=28.87 E-value=53 Score=17.40 Aligned_cols=12 Identities=50% Similarity=0.993 Sum_probs=8.5
Q ss_pred ceecCCCCcccc
Q psy3483 71 PYKCFYCDYRSN 82 (99)
Q Consensus 71 ~~~C~~c~~~f~ 82 (99)
-|.|..||..+.
T Consensus 100 Fy~C~~Cg~~wr 111 (113)
T COG1594 100 FYKCTRCGYRWR 111 (113)
T ss_pred EEEecccCCEee
Confidence 378888887653
No 204
>PF02176 zf-TRAF: TRAF-type zinc finger; PDB: 2EOD_A 2YUC_A 3HCU_A 3HCS_B 3HCT_A.
Probab=28.76 E-value=66 Score=14.27 Aligned_cols=20 Identities=25% Similarity=0.665 Sum_probs=10.3
Q ss_pred hHHHHHHHhhCCCCceecCC
Q psy3483 57 SKMRSHIRTHTKDRPYKCFY 76 (99)
Q Consensus 57 ~~~~~h~~~~~~~~~~~C~~ 76 (99)
..+..|....-..++..|..
T Consensus 24 ~~l~~H~~~~C~~~~v~C~~ 43 (60)
T PF02176_consen 24 KELDDHLENECPKRPVPCPY 43 (60)
T ss_dssp CCHHHHHHTTSTTSEEE-SS
T ss_pred HHHHHHHHccCCCCcEECCC
Confidence 45566655444445555655
No 205
>PF02891 zf-MIZ: MIZ/SP-RING zinc finger; InterPro: IPR004181 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents MIZ-type zinc finger domains. Miz1 (Msx-interacting-zinc finger) is a zinc finger-containing protein with homology to the yeast protein, Nfi-1. Miz1 is a sequence specific DNA binding protein that can function as a positive-acting transcription factor. Miz1 binds to the homeobox protein Msx2, enhancing the specific DNA-binding ability of Msx2 []. Other proteins containing this domain include the human pias family (protein inhibitor of activated STAT protein). More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3I2D_A.
Probab=28.62 E-value=31 Score=15.22 Aligned_cols=8 Identities=38% Similarity=1.078 Sum_probs=3.6
Q ss_pred eecCCCCc
Q psy3483 72 YKCFYCDY 79 (99)
Q Consensus 72 ~~C~~c~~ 79 (99)
|.|+.|++
T Consensus 42 W~CPiC~~ 49 (50)
T PF02891_consen 42 WKCPICNK 49 (50)
T ss_dssp -B-TTT--
T ss_pred eECcCCcC
Confidence 99998874
No 206
>PF12230 PRP21_like_P: Pre-mRNA splicing factor PRP21 like protein; InterPro: IPR022030 This domain family is found in eukaryotes, and is typically between 212 and 238 amino acids in length. The family is found in association with PF01805 from PFAM. There are two completely conserved residues (W and H) that may be functionally important. PRP21 is required for assembly of the prespliceosome and it interacts with U2 snRNP and/or pre-mRNA in the prespliceosome. This family also contains proteins similar to PRP21, such as the mammalian SF3a. SF3a also interacts with U2 snRNP from the prespliceosome, converting it to its active form. ; PDB: 4DGW_B.
Probab=28.42 E-value=19 Score=21.38 Aligned_cols=30 Identities=20% Similarity=0.387 Sum_probs=0.0
Q ss_pred ceeccCCCcccccChhHHHHHHHhhCCCCcee
Q psy3483 42 RYVCCLCSKYRHSDASKMRSHIRTHTKDRPYK 73 (99)
Q Consensus 42 ~~~c~~c~~~~~~~~~~~~~h~~~~~~~~~~~ 73 (99)
...|++||.... . ..+..|+++...+..|+
T Consensus 168 ~~~cPitGe~IP-~-~e~~eHmRi~LlDP~wk 197 (229)
T PF12230_consen 168 MIICPITGEMIP-A-DEMDEHMRIELLDPRWK 197 (229)
T ss_dssp --------------------------------
T ss_pred cccccccccccc-c-ccccccccccccccccc
Confidence 367888887433 3 67888888776665553
No 207
>PTZ00303 phosphatidylinositol kinase; Provisional
Probab=28.40 E-value=47 Score=24.28 Aligned_cols=6 Identities=33% Similarity=0.944 Sum_probs=2.5
Q ss_pred ccCCCc
Q psy3483 45 CCLCSK 50 (99)
Q Consensus 45 c~~c~~ 50 (99)
|..||.
T Consensus 484 CRkCGr 489 (1374)
T PTZ00303 484 CRSCGI 489 (1374)
T ss_pred ccCCcc
Confidence 444443
No 208
>PF14787 zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB: 1CL4_A 1DSV_A.
Probab=28.39 E-value=33 Score=14.21 Aligned_cols=14 Identities=21% Similarity=0.214 Sum_probs=7.8
Q ss_pred ecCCCCccccCchH
Q psy3483 73 KCFYCDYRSNERSN 86 (99)
Q Consensus 73 ~C~~c~~~f~~~~~ 86 (99)
.|+.|++.|.-.++
T Consensus 4 ~CprC~kg~Hwa~~ 17 (36)
T PF14787_consen 4 LCPRCGKGFHWASE 17 (36)
T ss_dssp C-TTTSSSCS-TTT
T ss_pred cCcccCCCcchhhh
Confidence 57788887654443
No 209
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=28.25 E-value=89 Score=19.77 Aligned_cols=11 Identities=18% Similarity=0.443 Sum_probs=6.9
Q ss_pred eeccCCCcccc
Q psy3483 43 YVCCLCSKYRH 53 (99)
Q Consensus 43 ~~c~~c~~~~~ 53 (99)
+.|+.|+.-+.
T Consensus 58 ~vcp~c~~h~r 68 (296)
T CHL00174 58 NICEQCGYHLK 68 (296)
T ss_pred CCCCCCCCCcC
Confidence 45777776444
No 210
>COG1655 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=28.11 E-value=27 Score=21.19 Aligned_cols=17 Identities=18% Similarity=0.460 Sum_probs=14.1
Q ss_pred CceeeCccccccccccc
Q psy3483 5 ELIVTCMYCSKILTYET 21 (99)
Q Consensus 5 ~~~~~c~~c~~~f~~~~ 21 (99)
++...||+|+..|..+.
T Consensus 17 kk~ieCPvC~tkFkkee 33 (267)
T COG1655 17 KKTIECPVCNTKFKKEE 33 (267)
T ss_pred hceeccCcccchhhhhh
Confidence 45688999999998775
No 211
>KOG1842|consensus
Probab=27.58 E-value=34 Score=22.92 Aligned_cols=21 Identities=19% Similarity=0.352 Sum_probs=11.9
Q ss_pred eecCCCCccccCchHHHHHHH
Q psy3483 72 YKCFYCDYRSNERSNVKAHMI 92 (99)
Q Consensus 72 ~~C~~c~~~f~~~~~l~~H~~ 92 (99)
|.|+.|...|.+...|..|..
T Consensus 16 flCPiC~~dl~~~~~L~~H~d 36 (505)
T KOG1842|consen 16 FLCPICLLDLPNLSALNDHLD 36 (505)
T ss_pred ccCchHhhhhhhHHHHHHHHh
Confidence 555555555555555555543
No 212
>KOG2071|consensus
Probab=26.89 E-value=75 Score=22.13 Aligned_cols=29 Identities=28% Similarity=0.483 Sum_probs=22.4
Q ss_pred CCCCceecCCCCccccCchHHHHHHHHhc
Q psy3483 67 TKDRPYKCFYCDYRSNERSNVKAHMIRRH 95 (99)
Q Consensus 67 ~~~~~~~C~~c~~~f~~~~~l~~H~~~~~ 95 (99)
....|-+|..||..|-.......|+..|-
T Consensus 414 y~~~pnqC~~CG~R~~~~ee~sk~md~H~ 442 (579)
T KOG2071|consen 414 YKDSPNQCKSCGLRFDDSEERSKHMDIHD 442 (579)
T ss_pred ccCCcchhcccccccccchhhhhHhhhhh
Confidence 45667899999999988877777766653
No 213
>KOG0227|consensus
Probab=26.56 E-value=39 Score=19.90 Aligned_cols=20 Identities=30% Similarity=0.524 Sum_probs=13.8
Q ss_pred eecCCCCccccCchHHHHHH
Q psy3483 72 YKCFYCDYRSNERSNVKAHM 91 (99)
Q Consensus 72 ~~C~~c~~~f~~~~~l~~H~ 91 (99)
|.|..|.-...+..++..|.
T Consensus 54 yeCkLClT~H~ne~Syl~Ht 73 (222)
T KOG0227|consen 54 YECKLCLTLHNNEGSYLAHT 73 (222)
T ss_pred eeehhhhhhhcchhhhhhhh
Confidence 77777777666666666664
No 214
>PTZ00448 hypothetical protein; Provisional
Probab=26.26 E-value=55 Score=21.38 Aligned_cols=24 Identities=17% Similarity=0.314 Sum_probs=19.4
Q ss_pred ceecCCCCccccCchHHHHHHHHh
Q psy3483 71 PYKCFYCDYRSNERSNVKAHMIRR 94 (99)
Q Consensus 71 ~~~C~~c~~~f~~~~~l~~H~~~~ 94 (99)
.|.|..|+..|........|.++.
T Consensus 314 ~~tC~~C~v~F~~~~~qR~H~KSD 337 (373)
T PTZ00448 314 MLLCRKCNIQLMDHNAFKQHYRSE 337 (373)
T ss_pred CccccccccccCCHHHHHHHhhhh
Confidence 578999999998777888887653
No 215
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=26.18 E-value=39 Score=13.55 Aligned_cols=10 Identities=20% Similarity=0.663 Sum_probs=5.0
Q ss_pred eecCCCCccc
Q psy3483 72 YKCFYCDYRS 81 (99)
Q Consensus 72 ~~C~~c~~~f 81 (99)
+.|..|+..|
T Consensus 22 ~~C~~Cg~~~ 31 (33)
T PF08792_consen 22 EVCIFCGSSF 31 (33)
T ss_pred EEcccCCcEe
Confidence 4455555443
No 216
>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=26.08 E-value=32 Score=13.54 Aligned_cols=7 Identities=43% Similarity=0.994 Sum_probs=2.9
Q ss_pred eeccCCC
Q psy3483 43 YVCCLCS 49 (99)
Q Consensus 43 ~~c~~c~ 49 (99)
+.|++|+
T Consensus 20 ~vCp~C~ 26 (30)
T PF08274_consen 20 LVCPECG 26 (30)
T ss_dssp EEETTTT
T ss_pred EeCCccc
Confidence 3344443
No 217
>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=25.91 E-value=41 Score=14.00 Aligned_cols=12 Identities=17% Similarity=0.490 Sum_probs=6.0
Q ss_pred CceeeCcccccc
Q psy3483 5 ELIVTCMYCSKI 16 (99)
Q Consensus 5 ~~~~~c~~c~~~ 16 (99)
.+.|.|+.|+..
T Consensus 22 ~~~w~C~~C~~~ 33 (40)
T PF04810_consen 22 GKTWICNFCGTK 33 (40)
T ss_dssp TTEEEETTT--E
T ss_pred CCEEECcCCCCc
Confidence 345667776654
No 218
>PRK04351 hypothetical protein; Provisional
Probab=25.87 E-value=65 Score=18.02 Aligned_cols=33 Identities=21% Similarity=0.465 Sum_probs=20.8
Q ss_pred ceeccCCCcccccChhHHHHHHHhhCCCCceecCCCCccccC
Q psy3483 42 RYVCCLCSKYRHSDASKMRSHIRTHTKDRPYKCFYCDYRSNE 83 (99)
Q Consensus 42 ~~~c~~c~~~~~~~~~~~~~h~~~~~~~~~~~C~~c~~~f~~ 83 (99)
.|.|..|+..+... . +. ....|.|..|+..+..
T Consensus 112 ~Y~C~~Cg~~~~r~-R------r~--n~~~yrCg~C~g~L~~ 144 (149)
T PRK04351 112 LYECQSCGQQYLRK-R------RI--NTKRYRCGKCRGKLKL 144 (149)
T ss_pred EEECCCCCCEeeee-e------ec--CCCcEEeCCCCcEeee
Confidence 48898899754432 1 11 2356999999865543
No 219
>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=25.67 E-value=61 Score=16.52 Aligned_cols=36 Identities=25% Similarity=0.416 Sum_probs=18.1
Q ss_pred eeccCCCcccccChhHHHHHHHhh--CCCCceecCCCCccc
Q psy3483 43 YVCCLCSKYRHSDASKMRSHIRTH--TKDRPYKCFYCDYRS 81 (99)
Q Consensus 43 ~~c~~c~~~~~~~~~~~~~h~~~~--~~~~~~~C~~c~~~f 81 (99)
..|+.||..-... ..+ ..++. .-..-|.|..|+..+
T Consensus 63 ~~Cp~Cg~~~a~f-~~~--Q~RsadE~~T~fy~C~~C~~~w 100 (104)
T TIGR01384 63 VECPKCGHKEAYY-WLL--QTRRADEPETRFYKCTKCGYVW 100 (104)
T ss_pred CCCCCCCCCeeEE-EEe--ccCCCCCCcEEEEEeCCCCCee
Confidence 5788888632111 111 12221 122348888888654
No 220
>KOG2907|consensus
Probab=25.61 E-value=41 Score=17.95 Aligned_cols=37 Identities=19% Similarity=0.364 Sum_probs=19.9
Q ss_pred eeccCCCcccccChhHHHHHHH-h-hCCC-CceecCCCCccccC
Q psy3483 43 YVCCLCSKYRHSDASKMRSHIR-T-HTKD-RPYKCFYCDYRSNE 83 (99)
Q Consensus 43 ~~c~~c~~~~~~~~~~~~~h~~-~-~~~~-~~~~C~~c~~~f~~ 83 (99)
..|+.||.. . ......|. + ..|+ .-|-|+.|+..|..
T Consensus 75 ~kCpkCghe-~---m~Y~T~QlRSADEGQTVFYTC~kC~~k~~e 114 (116)
T KOG2907|consen 75 HKCPKCGHE-E---MSYHTLQLRSADEGQTVFYTCPKCKYKFTE 114 (116)
T ss_pred ccCcccCCc-h---hhhhhhhcccccCCceEEEEcCccceeeec
Confidence 568888863 1 11222222 1 2222 23889999987754
No 221
>TIGR00627 tfb4 transcription factor tfb4. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=25.21 E-value=69 Score=20.02 Aligned_cols=10 Identities=20% Similarity=0.418 Sum_probs=4.6
Q ss_pred eecCCCCccc
Q psy3483 72 YKCFYCDYRS 81 (99)
Q Consensus 72 ~~C~~c~~~f 81 (99)
|.|+.|.-.|
T Consensus 256 yvCs~Clsi~ 265 (279)
T TIGR00627 256 FVCSVCLSVL 265 (279)
T ss_pred EECCCccCCc
Confidence 4444444433
No 222
>PF14690 zf-ISL3: zinc-finger of transposase IS204/IS1001/IS1096/IS1165
Probab=24.78 E-value=33 Score=14.45 Aligned_cols=10 Identities=20% Similarity=0.391 Sum_probs=6.7
Q ss_pred eeeCcccccc
Q psy3483 7 IVTCMYCSKI 16 (99)
Q Consensus 7 ~~~c~~c~~~ 16 (99)
|..|+.||..
T Consensus 2 ~~~Cp~Cg~~ 11 (47)
T PF14690_consen 2 PPRCPHCGSP 11 (47)
T ss_pred CccCCCcCCC
Confidence 4567888854
No 223
>smart00731 SprT SprT homologues. Predicted to have roles in transcription elongation. Contains a conserved HExxH motif, indicating a metalloprotease function.
Probab=24.27 E-value=68 Score=17.58 Aligned_cols=32 Identities=22% Similarity=0.403 Sum_probs=17.8
Q ss_pred ceeccCCCcccccChhHHHHHHHhhCCCCceecCCCCccc
Q psy3483 42 RYVCCLCSKYRHSDASKMRSHIRTHTKDRPYKCFYCDYRS 81 (99)
Q Consensus 42 ~~~c~~c~~~~~~~~~~~~~h~~~~~~~~~~~C~~c~~~f 81 (99)
.|.|..|+..+... .+ +.....|.|..|+..+
T Consensus 112 ~y~C~~C~~~~~~~-------rr-~~~~~~y~C~~C~g~l 143 (146)
T smart00731 112 PYRCTGCGQRYLRV-------RR-SNNVSRYRCGKCGGKL 143 (146)
T ss_pred EEECCCCCCCCceE-------cc-ccCcceEEcCCCCCEE
Confidence 57887787643322 11 1112458888887654
No 224
>KOG1088|consensus
Probab=24.11 E-value=50 Score=17.77 Aligned_cols=12 Identities=17% Similarity=0.124 Sum_probs=5.4
Q ss_pred eeccCCCccccc
Q psy3483 43 YVCCLCSKYRHS 54 (99)
Q Consensus 43 ~~c~~c~~~~~~ 54 (99)
..|+.||..|..
T Consensus 99 l~CpetG~vfpI 110 (124)
T KOG1088|consen 99 LVCPETGRVFPI 110 (124)
T ss_pred EecCCCCcEeec
Confidence 345555544433
No 225
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=24.07 E-value=1e+02 Score=18.98 Aligned_cols=16 Identities=25% Similarity=0.698 Sum_probs=10.7
Q ss_pred CCceecCCCCccccCc
Q psy3483 69 DRPYKCFYCDYRSNER 84 (99)
Q Consensus 69 ~~~~~C~~c~~~f~~~ 84 (99)
.+.|.|+.||..+...
T Consensus 320 ~r~~~C~~cg~~~~rD 335 (364)
T COG0675 320 GRLFKCPRCGFVHDRD 335 (364)
T ss_pred ceeEECCCCCCeehhh
Confidence 4568888888655443
No 226
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=24.06 E-value=70 Score=20.85 Aligned_cols=75 Identities=19% Similarity=0.514 Sum_probs=35.7
Q ss_pred eCccccccccccchhhhccchhhccCCCCCCCcceeccCCCc---ccccChhHHHHHHHhhCCCCceecCC--C--C--c
Q psy3483 9 TCMYCSKILTYETETIMNHCKFCKAVSRPTKYQRYVCCLCSK---YRHSDASKMRSHIRTHTKDRPYKCFY--C--D--Y 79 (99)
Q Consensus 9 ~c~~c~~~f~~~~~~~~~h~~~~~~~~~~~~~~~~~c~~c~~---~~~~~~~~~~~h~~~~~~~~~~~C~~--c--~--~ 79 (99)
.|..|...|..-. .|..||+. .| ++-+.|+.-+. .++-.+..|- .|.....|.|.. | + .
T Consensus 222 ~C~FC~~~FYdDD-EL~~HcR~-----~H--E~ChICD~v~p~~~QYFK~Y~~Le----~HF~~~hy~ct~qtc~~~k~~ 289 (493)
T COG5236 222 LCIFCKIYFYDDD-ELRRHCRL-----RH--EACHICDMVGPIRYQYFKSYEDLE----AHFRNAHYCCTFQTCRVGKCY 289 (493)
T ss_pred hhhhccceecChH-HHHHHHHh-----hh--hhhhhhhccCccchhhhhCHHHHH----HHhhcCceEEEEEEEecCcEE
Confidence 3667776666665 66666322 12 22233433321 0111112222 333344466643 2 1 2
Q ss_pred cccCchHHHHHHHHhc
Q psy3483 80 RSNERSNVKAHMIRRH 95 (99)
Q Consensus 80 ~f~~~~~l~~H~~~~~ 95 (99)
.|.....|..|+-.-+
T Consensus 290 vf~~~~el~~h~~~~h 305 (493)
T COG5236 290 VFPYHTELLEHLTRFH 305 (493)
T ss_pred EeccHHHHHHHHHHHh
Confidence 5777778888865444
No 227
>PRK12722 transcriptional activator FlhC; Provisional
Probab=24.05 E-value=71 Score=18.72 Aligned_cols=28 Identities=18% Similarity=0.383 Sum_probs=16.5
Q ss_pred eeccCCCcccccChhHHHHHHHhhCCCCceecCCCCc
Q psy3483 43 YVCCLCSKYRHSDASKMRSHIRTHTKDRPYKCFYCDY 79 (99)
Q Consensus 43 ~~c~~c~~~~~~~~~~~~~h~~~~~~~~~~~C~~c~~ 79 (99)
..|..||..|... .+.....|.|+.|..
T Consensus 135 ~~C~~Cgg~fv~~---------~~e~~~~f~CplC~~ 162 (187)
T PRK12722 135 SSCNCCGGHFVTH---------AHDPVGSFVCGLCQP 162 (187)
T ss_pred ccCCCCCCCeecc---------ccccCCCCcCCCCCC
Confidence 3577777655433 123344688888864
No 228
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=24.02 E-value=50 Score=15.15 Aligned_cols=15 Identities=13% Similarity=0.443 Sum_probs=10.9
Q ss_pred CCCCceecCCCCccc
Q psy3483 67 TKDRPYKCFYCDYRS 81 (99)
Q Consensus 67 ~~~~~~~C~~c~~~f 81 (99)
.+...|.|+.||-.+
T Consensus 10 ~~~v~~~Cp~cGipt 24 (55)
T PF13824_consen 10 PAHVNFECPDCGIPT 24 (55)
T ss_pred ccccCCcCCCCCCcC
Confidence 446679999998643
No 229
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=23.81 E-value=47 Score=19.00 Aligned_cols=9 Identities=44% Similarity=0.980 Sum_probs=4.7
Q ss_pred eeccCCCcc
Q psy3483 43 YVCCLCSKY 51 (99)
Q Consensus 43 ~~c~~c~~~ 51 (99)
+.|+.||+.
T Consensus 131 ~~C~~Cgki 139 (165)
T COG1656 131 YRCPKCGKI 139 (165)
T ss_pred eECCCCccc
Confidence 345566553
No 230
>KOG1813|consensus
Probab=23.72 E-value=78 Score=20.08 Aligned_cols=14 Identities=29% Similarity=0.622 Sum_probs=9.1
Q ss_pred ceeeCccccccccc
Q psy3483 6 LIVTCMYCSKILTY 19 (99)
Q Consensus 6 ~~~~c~~c~~~f~~ 19 (99)
-||.|..|.+.|..
T Consensus 240 ~Pf~c~icr~~f~~ 253 (313)
T KOG1813|consen 240 LPFKCFICRKYFYR 253 (313)
T ss_pred CCcccccccccccc
Confidence 46677777776653
No 231
>PLN00104 MYST -like histone acetyltransferase; Provisional
Probab=23.59 E-value=69 Score=21.56 Aligned_cols=25 Identities=20% Similarity=0.498 Sum_probs=21.3
Q ss_pred CCceecCCCCccccCchHHHHHHHH
Q psy3483 69 DRPYKCFYCDYRSNERSNVKAHMIR 93 (99)
Q Consensus 69 ~~~~~C~~c~~~f~~~~~l~~H~~~ 93 (99)
..-|.|..|.+-|.....|..|+..
T Consensus 196 ~~lyiCe~Cl~y~~~~~~~~~H~~~ 220 (450)
T PLN00104 196 SKLYFCEFCLKFMKRKEQLQRHMKK 220 (450)
T ss_pred CeEEEchhhhhhhcCHHHHHHHHhc
Confidence 4468999999999999999999874
No 232
>PF01215 COX5B: Cytochrome c oxidase subunit Vb This family consists of chains F and S ; InterPro: IPR002124 Cytochrome c oxidase (1.9.3.1 from EC) is an oligomeric enzymatic complex which is a component of the respiratory chain complex and is involved in the transfer of electrons from cytochrome c to oxygen []. In eukaryotes this enzyme complex is located in the mitochondrial inner membrane; in aerobic prokaryotes it is found in the plasma membrane. In eukaryotes, in addition to the three large subunits, I, II and III, that form the catalytic centre of the enzyme complex, there are a variable number of small polypeptidic subunits. One of these subunits, which is known as Vb in mammals, V in Dictyostelium discoideum (Slime mold) and IV in yeast, binds a zinc atom. The sequence of subunit Vb is well conserved and includes three conserved cysteines that coordinate the zinc ion [, ]. Two of these cysteines are clustered in the C-terminal section of the subunit.; GO: 0004129 cytochrome-c oxidase activity, 0005740 mitochondrial envelope; PDB: 2EIL_S 2ZXW_S 3ASN_S 1OCO_S 3AG4_S 3ABK_S 1OCZ_S 1OCC_F 3ASO_S 3ABL_S ....
Probab=23.46 E-value=31 Score=19.02 Aligned_cols=16 Identities=19% Similarity=0.463 Sum_probs=12.4
Q ss_pred CCceecCCCCccccCc
Q psy3483 69 DRPYKCFYCDYRSNER 84 (99)
Q Consensus 69 ~~~~~C~~c~~~f~~~ 84 (99)
.++..|.+||..|...
T Consensus 110 g~~~RCpeCG~~fkL~ 125 (136)
T PF01215_consen 110 GKPQRCPECGQVFKLK 125 (136)
T ss_dssp TSEEEETTTEEEEEEE
T ss_pred CCccCCCCCCeEEEEE
Confidence 4589999999887643
No 233
>TIGR00143 hypF [NiFe] hydrogenase maturation protein HypF. A previously described regulatory effect of HypF mutatation is attributable to loss of activity of a regulatory hydrogenase. A zinc finger-like region CXXCX(18)CXXCX(24)CXXCX(18)CXXC region further supported the regulatory hypothesis. However, more recent work (PUBMED:11375153) shows the direct effect is on the activity of expressed hydrogenases with nickel/iron centers, rather than on expression.
Probab=23.44 E-value=24 Score=25.00 Aligned_cols=12 Identities=25% Similarity=0.517 Sum_probs=7.8
Q ss_pred Cccccccccccc
Q psy3483 10 CMYCSKILTYET 21 (99)
Q Consensus 10 c~~c~~~f~~~~ 21 (99)
|..||-.|.-..
T Consensus 93 Ct~CGPr~~i~~ 104 (711)
T TIGR00143 93 CTHCGPRFTIIE 104 (711)
T ss_pred ccCCCCCeEEee
Confidence 677777765444
No 234
>KOG1994|consensus
Probab=22.83 E-value=45 Score=20.22 Aligned_cols=24 Identities=21% Similarity=0.753 Sum_probs=19.9
Q ss_pred CCCCceecCCCCccccCchHHHHH
Q psy3483 67 TKDRPYKCFYCDYRSNERSNVKAH 90 (99)
Q Consensus 67 ~~~~~~~C~~c~~~f~~~~~l~~H 90 (99)
...-.|.|..||-.|.....|..|
T Consensus 235 LR~eh~YC~fCG~~y~~~edl~eh 258 (268)
T KOG1994|consen 235 LRSEHYYCFFCGIKYKDEEDLYEH 258 (268)
T ss_pred HhccceEEEEeccccCCHHHHHHh
Confidence 345569999999999999888876
No 235
>PF05741 zf-nanos: Nanos RNA binding domain; InterPro: IPR024161 Nanos is a highly conserved RNA-binding protein in higher eukaryotes and functions as a key regulatory protein in translational control using a 3' untranslated region during the development and maintenance of germ cells. Nanos comprises a non-conserved amino-terminus and highly conserved carboxy- terminal regions. The C-terminal region has two conserved Cys-Cys-His-Cys (CCHC)-type zinc-finger motifs that are indispensable for nanos function [, , ]. The structure of the nanos-type zinc finger is composed of two independent zinc-finger (ZF) lobes, the N-terminal ZF1 and the C-terminal ZF2, which are connected by a linker helix []. These lobes create a large cleft. Zinc ions in ZF1 and ZF2 are bound to the CCHC motif by tetrahedral coordination.; PDB: 3ALR_B.
Probab=22.72 E-value=34 Score=15.68 Aligned_cols=10 Identities=20% Similarity=0.537 Sum_probs=2.6
Q ss_pred eeeCcccccc
Q psy3483 7 IVTCMYCSKI 16 (99)
Q Consensus 7 ~~~c~~c~~~ 16 (99)
.+.|+.||.+
T Consensus 33 ~y~Cp~CgAt 42 (55)
T PF05741_consen 33 KYVCPICGAT 42 (55)
T ss_dssp G---TTT---
T ss_pred cCcCCCCcCc
Confidence 3667777765
No 236
>KOG0320|consensus
Probab=22.54 E-value=13 Score=21.46 Aligned_cols=10 Identities=30% Similarity=0.587 Sum_probs=5.6
Q ss_pred eecCCCCccc
Q psy3483 72 YKCFYCDYRS 81 (99)
Q Consensus 72 ~~C~~c~~~f 81 (99)
..|+.|.+..
T Consensus 168 ~~CP~C~kkI 177 (187)
T KOG0320|consen 168 NKCPTCRKKI 177 (187)
T ss_pred CCCCCccccc
Confidence 5566666533
No 237
>PRK00420 hypothetical protein; Validated
Probab=22.36 E-value=76 Score=16.90 Aligned_cols=7 Identities=43% Similarity=0.757 Sum_probs=4.0
Q ss_pred eccCCCc
Q psy3483 44 VCCLCSK 50 (99)
Q Consensus 44 ~c~~c~~ 50 (99)
.|+.||.
T Consensus 42 ~Cp~Cg~ 48 (112)
T PRK00420 42 VCPVHGK 48 (112)
T ss_pred ECCCCCC
Confidence 3666665
No 238
>PTZ00064 histone acetyltransferase; Provisional
Probab=22.34 E-value=89 Score=21.51 Aligned_cols=25 Identities=24% Similarity=0.238 Sum_probs=21.4
Q ss_pred CCceecCCCCccccCchHHHHHHHH
Q psy3483 69 DRPYKCFYCDYRSNERSNVKAHMIR 93 (99)
Q Consensus 69 ~~~~~C~~c~~~f~~~~~l~~H~~~ 93 (99)
..-|.|..|.+-|.....|.+|+..
T Consensus 278 d~LYICEfCLkY~~s~~~l~rH~~~ 302 (552)
T PTZ00064 278 DTLHFCEYCLDFFCFEDELIRHLSR 302 (552)
T ss_pred CeEEEccchhhhhCCHHHHHHHHhc
Confidence 4458999999999999999999874
No 239
>COG1579 Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only]
Probab=22.31 E-value=1e+02 Score=18.89 Aligned_cols=13 Identities=38% Similarity=0.621 Sum_probs=10.9
Q ss_pred CCCceecCCCCcc
Q psy3483 68 KDRPYKCFYCDYR 80 (99)
Q Consensus 68 ~~~~~~C~~c~~~ 80 (99)
+.....|+.||+.
T Consensus 218 ~d~iv~CP~CgRI 230 (239)
T COG1579 218 KDEIVFCPYCGRI 230 (239)
T ss_pred CCCCccCCccchH
Confidence 6778889999975
No 240
>PF09082 DUF1922: Domain of unknown function (DUF1922); InterPro: IPR015166 Members of this family consist of a beta-sheet region followed by an alpha-helix and an unstructured C terminus. The beta-sheet region contains a CXCX...XCXC sequence with Cys residues located in two proximal loops and pointing towards each other. This precise function of this set of bacterial proteins is, as yet, unknown []. ; PDB: 1GH9_A.
Probab=21.99 E-value=54 Score=15.79 Aligned_cols=10 Identities=30% Similarity=0.820 Sum_probs=4.0
Q ss_pred eeCcccccccc
Q psy3483 8 VTCMYCSKILT 18 (99)
Q Consensus 8 ~~c~~c~~~f~ 18 (99)
|.| .||+...
T Consensus 4 frC-~Cgr~ly 13 (68)
T PF09082_consen 4 FRC-DCGRYLY 13 (68)
T ss_dssp EEE-TTS--EE
T ss_pred EEe-cCCCEEE
Confidence 455 4665533
No 241
>KOG2272|consensus
Probab=21.98 E-value=1.4e+02 Score=18.57 Aligned_cols=19 Identities=16% Similarity=0.260 Sum_probs=11.4
Q ss_pred hhCCCCceecCCCCccccC
Q psy3483 65 THTKDRPYKCFYCDYRSNE 83 (99)
Q Consensus 65 ~~~~~~~~~C~~c~~~f~~ 83 (99)
.|.-...|.|..|.+-|.-
T Consensus 215 KhWHveHFvCa~CekPFlG 233 (332)
T KOG2272|consen 215 KHWHVEHFVCAKCEKPFLG 233 (332)
T ss_pred cccchhheeehhcCCcccc
Confidence 3444456777777766643
No 242
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=21.90 E-value=47 Score=14.99 Aligned_cols=10 Identities=20% Similarity=0.886 Sum_probs=6.5
Q ss_pred eeeCcccccc
Q psy3483 7 IVTCMYCSKI 16 (99)
Q Consensus 7 ~~~c~~c~~~ 16 (99)
..+|+.||..
T Consensus 3 LkPCPFCG~~ 12 (61)
T PF14354_consen 3 LKPCPFCGSA 12 (61)
T ss_pred CcCCCCCCCc
Confidence 3468888755
No 243
>PRK01343 zinc-binding protein; Provisional
Probab=21.87 E-value=43 Score=15.47 Aligned_cols=12 Identities=33% Similarity=0.467 Sum_probs=8.8
Q ss_pred eeeCcccccccc
Q psy3483 7 IVTCMYCSKILT 18 (99)
Q Consensus 7 ~~~c~~c~~~f~ 18 (99)
...|+.|++.+.
T Consensus 9 ~~~CP~C~k~~~ 20 (57)
T PRK01343 9 TRPCPECGKPST 20 (57)
T ss_pred CCcCCCCCCcCc
Confidence 356999998754
No 244
>PF10071 DUF2310: Zn-ribbon-containing, possibly nucleic-acid-binding protein (DUF2310); InterPro: IPR016908 This group represents uncharacterised conserved proteins.
Probab=21.83 E-value=52 Score=20.32 Aligned_cols=7 Identities=43% Similarity=1.113 Sum_probs=3.6
Q ss_pred eecCCCC
Q psy3483 72 YKCFYCD 78 (99)
Q Consensus 72 ~~C~~c~ 78 (99)
|+|..|-
T Consensus 242 FKCD~CR 248 (258)
T PF10071_consen 242 FKCDPCR 248 (258)
T ss_pred ccCCcce
Confidence 5555553
No 245
>PF14311 DUF4379: Domain of unknown function (DUF4379)
Probab=21.82 E-value=53 Score=14.59 Aligned_cols=12 Identities=17% Similarity=0.321 Sum_probs=8.7
Q ss_pred eeCccccccccc
Q psy3483 8 VTCMYCSKILTY 19 (99)
Q Consensus 8 ~~c~~c~~~f~~ 19 (99)
+.|+.||..|..
T Consensus 29 W~C~~Cgh~w~~ 40 (55)
T PF14311_consen 29 WKCPKCGHEWKA 40 (55)
T ss_pred EECCCCCCeeEc
Confidence 778888776654
No 246
>PF11023 DUF2614: Protein of unknown function (DUF2614); InterPro: IPR020912 This entry describes proteins of unknown function, which are thought to be membrane proteins.; GO: 0005887 integral to plasma membrane
Probab=21.77 E-value=52 Score=17.54 Aligned_cols=13 Identities=31% Similarity=0.588 Sum_probs=8.9
Q ss_pred ceeeCcccccccc
Q psy3483 6 LIVTCMYCSKILT 18 (99)
Q Consensus 6 ~~~~c~~c~~~f~ 18 (99)
....||.|++..+
T Consensus 68 v~V~CP~C~K~TK 80 (114)
T PF11023_consen 68 VQVECPNCGKQTK 80 (114)
T ss_pred eeeECCCCCChHh
Confidence 4566888887754
No 247
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=21.68 E-value=32 Score=12.73 Aligned_cols=6 Identities=33% Similarity=1.065 Sum_probs=3.0
Q ss_pred Cccccc
Q psy3483 10 CMYCSK 15 (99)
Q Consensus 10 c~~c~~ 15 (99)
|+.||.
T Consensus 19 C~~CG~ 24 (26)
T PF13248_consen 19 CPNCGA 24 (26)
T ss_pred ChhhCC
Confidence 555554
No 248
>PRK07591 threonine synthase; Validated
Probab=21.45 E-value=86 Score=20.69 Aligned_cols=8 Identities=38% Similarity=0.604 Sum_probs=4.1
Q ss_pred eeccCCCc
Q psy3483 43 YVCCLCSK 50 (99)
Q Consensus 43 ~~c~~c~~ 50 (99)
+.|+.|+.
T Consensus 34 ~~C~~cg~ 41 (421)
T PRK07591 34 HVCEECFG 41 (421)
T ss_pred ccCCCCCC
Confidence 44555553
No 249
>PRK12860 transcriptional activator FlhC; Provisional
Probab=21.28 E-value=80 Score=18.54 Aligned_cols=27 Identities=22% Similarity=0.593 Sum_probs=16.0
Q ss_pred eeccCCCcccccChhHHHHHHHhhCCCCceecCCCC
Q psy3483 43 YVCCLCSKYRHSDASKMRSHIRTHTKDRPYKCFYCD 78 (99)
Q Consensus 43 ~~c~~c~~~~~~~~~~~~~h~~~~~~~~~~~C~~c~ 78 (99)
..|..||..|... .+.....|.|+.|.
T Consensus 135 ~~C~~Cgg~fv~~---------~~e~~~~f~CplC~ 161 (189)
T PRK12860 135 ARCCRCGGKFVTH---------AHDLRHNFVCGLCQ 161 (189)
T ss_pred ccCCCCCCCeecc---------ccccCCCCcCCCCC
Confidence 4577777654432 22334468888885
No 250
>PF01844 HNH: HNH endonuclease; InterPro: IPR002711 HNH endonuclease is found in bacteria and viruses [, , ]. This family includes pyocins, colicins and anaredoxins.; GO: 0003676 nucleic acid binding, 0004519 endonuclease activity; PDB: 2QGP_C.
Probab=21.16 E-value=44 Score=13.86 Aligned_cols=11 Identities=36% Similarity=0.788 Sum_probs=4.3
Q ss_pred Ccccccccccc
Q psy3483 10 CMYCSKILTYE 20 (99)
Q Consensus 10 c~~c~~~f~~~ 20 (99)
|..|++.+...
T Consensus 1 C~~C~~~~~~~ 11 (47)
T PF01844_consen 1 CQYCGKPGSDN 11 (47)
T ss_dssp -TTT--B--GG
T ss_pred CCCCCCcCccC
Confidence 67888887655
No 251
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=21.13 E-value=73 Score=20.43 Aligned_cols=27 Identities=19% Similarity=0.298 Sum_probs=22.4
Q ss_pred CCceecCCCCccccCchHHHHHHHHhc
Q psy3483 69 DRPYKCFYCDYRSNERSNVKAHMIRRH 95 (99)
Q Consensus 69 ~~~~~C~~c~~~f~~~~~l~~H~~~~~ 95 (99)
...|.|..|...|...-+..+|...|.
T Consensus 386 s~rY~Ce~CK~~FC~dCdvfiHe~Lh~ 412 (421)
T COG5151 386 SGRYQCELCKSTFCSDCDVFIHETLHF 412 (421)
T ss_pred ccceechhhhhhhhhhhHHHHHHHHhh
Confidence 446999999999999989989987763
No 252
>PF14447 Prok-RING_4: Prokaryotic RING finger family 4
Probab=21.13 E-value=48 Score=15.22 Aligned_cols=6 Identities=33% Similarity=1.242 Sum_probs=3.1
Q ss_pred ccCCCc
Q psy3483 45 CCLCSK 50 (99)
Q Consensus 45 c~~c~~ 50 (99)
|+.|+.
T Consensus 42 CPfC~~ 47 (55)
T PF14447_consen 42 CPFCGT 47 (55)
T ss_pred CCCCCC
Confidence 555554
No 253
>PF03884 DUF329: Domain of unknown function (DUF329); InterPro: IPR005584 The biological function of these short proteins is unknown, but they contain four conserved cysteines, suggesting that they all bind zinc. YacG (Q5X8H6 from SWISSPROT) from Escherichia coli has been shown to bind zinc and contains the structural motifs typical of zinc-binding proteins []. The conserved four cysteine motif in these proteins (-C-X(2)-C-X(15)-C-X(3)-C-) is not found in other zinc-binding proteins with known structures.; GO: 0008270 zinc ion binding; PDB: 1LV3_A.
Probab=20.83 E-value=53 Score=15.16 Aligned_cols=12 Identities=33% Similarity=0.838 Sum_probs=5.1
Q ss_pred eeCccccccccc
Q psy3483 8 VTCMYCSKILTY 19 (99)
Q Consensus 8 ~~c~~c~~~f~~ 19 (99)
..|+.|++.+..
T Consensus 3 v~CP~C~k~~~~ 14 (57)
T PF03884_consen 3 VKCPICGKPVEW 14 (57)
T ss_dssp EE-TTT--EEE-
T ss_pred ccCCCCCCeecc
Confidence 467777776543
No 254
>PF11789 zf-Nse: Zinc-finger of the MIZ type in Nse subunit; PDB: 2YU4_A 3HTK_C.
Probab=20.79 E-value=1.1e+02 Score=13.96 Aligned_cols=31 Identities=10% Similarity=0.156 Sum_probs=13.3
Q ss_pred cceeccCCCcccccChhHHHHHHHhhCCCCceecCC
Q psy3483 41 QRYVCCLCSKYRHSDASKMRSHIRTHTKDRPYKCFY 76 (99)
Q Consensus 41 ~~~~c~~c~~~~~~~~~~~~~h~~~~~~~~~~~C~~ 76 (99)
.|.....|+..|. . ..+..+. .......|+.
T Consensus 23 ~PV~s~~C~H~fe-k-~aI~~~i---~~~~~~~CPv 53 (57)
T PF11789_consen 23 DPVKSKKCGHTFE-K-EAILQYI---QRNGSKRCPV 53 (57)
T ss_dssp SEEEESSS--EEE-H-HHHHHHC---TTTS-EE-SC
T ss_pred CCcCcCCCCCeec-H-HHHHHHH---HhcCCCCCCC
Confidence 4455566776443 2 4444443 2344566665
No 255
>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=20.72 E-value=59 Score=14.03 Aligned_cols=7 Identities=29% Similarity=0.799 Sum_probs=3.8
Q ss_pred Ccccccc
Q psy3483 10 CMYCSKI 16 (99)
Q Consensus 10 c~~c~~~ 16 (99)
|+.||..
T Consensus 2 CP~Cg~~ 8 (47)
T PF04606_consen 2 CPHCGSK 8 (47)
T ss_pred cCCCCCe
Confidence 5556554
No 256
>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=20.68 E-value=79 Score=17.28 Aligned_cols=31 Identities=26% Similarity=0.552 Sum_probs=17.7
Q ss_pred ceeccCCCcccccChhHHHHHHHhhCCCCceecCCCCccc
Q psy3483 42 RYVCCLCSKYRHSDASKMRSHIRTHTKDRPYKCFYCDYRS 81 (99)
Q Consensus 42 ~~~c~~c~~~~~~~~~~~~~h~~~~~~~~~~~C~~c~~~f 81 (99)
.|.|..|+..+... . ++ ....|.|..|+..+
T Consensus 123 ~~~C~~C~~~~~r~-~------~~--~~~~~~C~~C~~~l 153 (157)
T PF10263_consen 123 VYRCPSCGREYKRH-R------RS--KRKRYRCGRCGGPL 153 (157)
T ss_pred EEEcCCCCCEeeee-c------cc--chhhEECCCCCCEE
Confidence 47788888643322 1 11 22348888887554
No 257
>PF06220 zf-U1: U1 zinc finger; InterPro: IPR013085 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. C2H2-type (classical) zinc fingers (Znf) were the first class to be characterised. They contain a short beta hairpin and an alpha helix (beta/beta/alpha structure), where a single zinc atom is held in place by Cys(2)His(2) (C2H2) residues in a tetrahedral array. C2H2 Znf's can be divided into three groups based on the number and pattern of fingers: triple-C2H2 (binds single ligand), multiple-adjacent-C2H2 (binds multiple ligands), and separated paired-C2H2 []. C2H2 Znf's are the most common DNA-binding motifs found in eukaryotic transcription factors, and have also been identified in prokaryotes []. Transcription factors usually contain several Znf's (each with a conserved beta/beta/alpha structure) capable of making multiple contacts along the DNA, where the C2H2 Znf motifs recognise DNA sequences by binding to the major groove of DNA via a short alpha-helix in the Znf, the Znf spanning 3-4 bases of the DNA []. C2H2 Znf's can also bind to RNA and protein targets []. This entry represents a C2H2-type zinc finger motif found in several U1 small nuclear ribonucleoprotein C (U1-C) proteins. Some proteins contain multiple copies of this motif. The U1 small nuclear ribonucleoprotein (U1 snRNP) binds to the pre-mRNA 5' splice site at early stages of spliceosome assembly. Recruitment of U1 to a class of weak 5' splice site is promoted by binding of the protein TIA-1 to uridine-rich sequences immediately downstream from the 5' splice site. Binding of TIA-1 in the vicinity of a 5' splice site helps to stabilise U1 snRNP recruitment, at least in part, via a direct interaction with U1-C, thus providing one molecular mechanism for the function of this splicing regulator []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2VRD_A.
Probab=20.58 E-value=88 Score=12.93 Aligned_cols=12 Identities=33% Similarity=0.725 Sum_probs=4.4
Q ss_pred ceecCCCCcccc
Q psy3483 71 PYKCFYCDYRSN 82 (99)
Q Consensus 71 ~~~C~~c~~~f~ 82 (99)
.|-|..|+..|.
T Consensus 3 ryyCdyC~~~~~ 14 (38)
T PF06220_consen 3 RYYCDYCKKYLT 14 (38)
T ss_dssp S-B-TTT--B-S
T ss_pred Ceecccccceec
Confidence 366777777663
No 258
>TIGR03831 YgiT_finger YgiT-type zinc finger domain. This domain model describes a small domain with two copies of a putative zinc-binding motif CXXC (usually CXXCG). Most member proteins consist largely of this domain or else carry an additional C-terminal helix-turn-helix domain, resembling that of the phage protein Cro and modeled by pfam01381.
Probab=20.57 E-value=44 Score=13.83 Aligned_cols=11 Identities=18% Similarity=0.555 Sum_probs=7.1
Q ss_pred eeCcccccccc
Q psy3483 8 VTCMYCSKILT 18 (99)
Q Consensus 8 ~~c~~c~~~f~ 18 (99)
+.|+.||..+.
T Consensus 33 ~~C~~CGE~~~ 43 (46)
T TIGR03831 33 LVCPQCGEEYL 43 (46)
T ss_pred cccccCCCEee
Confidence 45777776543
No 259
>PRK05452 anaerobic nitric oxide reductase flavorubredoxin; Provisional
Probab=20.18 E-value=1.3e+02 Score=20.36 Aligned_cols=9 Identities=22% Similarity=0.707 Sum_probs=5.5
Q ss_pred ceecCCCCc
Q psy3483 71 PYKCFYCDY 79 (99)
Q Consensus 71 ~~~C~~c~~ 79 (99)
.|.|+.|+-
T Consensus 458 ~~~cp~c~~ 466 (479)
T PRK05452 458 NFLCPECSL 466 (479)
T ss_pred CCcCcCCCC
Confidence 366777663
No 260
>PF09297 zf-NADH-PPase: NADH pyrophosphatase zinc ribbon domain; InterPro: IPR015376 This domain has a zinc ribbon structure and is often found between two NUDIX domains.; GO: 0016787 hydrolase activity, 0046872 metal ion binding; PDB: 1VK6_A 2GB5_A.
Probab=20.07 E-value=80 Score=12.21 Aligned_cols=10 Identities=20% Similarity=0.571 Sum_probs=4.3
Q ss_pred CCceecCCCC
Q psy3483 69 DRPYKCFYCD 78 (99)
Q Consensus 69 ~~~~~C~~c~ 78 (99)
+..-.|+.|+
T Consensus 19 g~~r~C~~Cg 28 (32)
T PF09297_consen 19 GWARRCPSCG 28 (32)
T ss_dssp SS-EEESSSS
T ss_pred cCEeECCCCc
Confidence 3344555554
Done!